Title: Diverse Basic Statistical and Graphical Functions
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Herv
Maintainer: Maxime Herv <mx.herve@gmail.com>
Diff between RVAideMemoire versions 0.9-60 dated 2016-08-20 and 0.9-61 dated 2016-10-31
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS | 3 +++ R/MVA.cmv.R | 22 ++++++++++++++++++++++ R/MVA.cv.R | 6 ++++++ R/zzz.R | 2 +- man/MVA.cor.Rd | 6 ------ man/MVA.corplot.Rd | 5 ----- man/MVA.load.Rd | 6 ------ man/MVA.loadplot.Rd | 6 ------ man/MVA.scoreplot.Rd | 6 ------ man/MVA.scores.Rd | 6 ------ man/PLSDA.VIP.Rd | 2 +- man/RVAideMemoire-package.Rd | 4 ++-- 14 files changed, 52 insertions(+), 56 deletions(-)
Title: R Object-Oriented Programming with or without References
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.oo versions 1.20.0 dated 2016-02-17 and 1.21.0 dated 2016-10-31
DESCRIPTION | 10 +-- MD5 | 30 +++++------ NAMESPACE | 7 ++ NEWS | 8 +++ R/050.Object.R | 36 ++++++++++--- R/060.Class.R | 20 ++++--- R/BasicObject.R | 122 ++++++++++++++++++++++++---------------------- R/ll.default.R | 2 inst/CITATION | 4 - man/BasicObject.Rd | 2 man/Class.Rd | 2 man/DOLLAR.BasicObject.Rd | 2 man/DOLLAR.Class.Rd | 2 man/DOLLAR.Object.Rd | 2 man/Object.Rd | 4 + man/R.oo-package.Rd | 2 16 files changed, 153 insertions(+), 102 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb],
Adam Obeng [ctb],
Pablo Barberá [ctb],
Will Lowe [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.9.8.3 dated 2016-10-16 and 0.9.8.5 dated 2016-10-31
DESCRIPTION | 8 +++--- MD5 | 21 +++++++++-------- NEWS.md | 4 +++ R/dfm-main.R | 4 +-- R/selectFeatures.R | 6 ----- README.md | 16 ++++++++++--- inst/CITATION |only inst/doc/LitVignette.html | 12 +++++----- inst/doc/quickstart.html | 48 ++++++++++++++++++++-------------------- man/stopwords.Rd | 4 --- src/sequences.cpp | 12 +++++----- tests/testthat/testSimilarity.R | 22 +++++++++++++----- 12 files changed, 87 insertions(+), 70 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/MH sampler. Also serves as a drop-in replacement for package BayesTree.
Author: Vincent Dorie Developer [aut, cre],
Hugh Chipman Developer [aut],
Robert McCulloch Developer [aut]
Maintainer: Vincent Dorie Developer <vdorie@gmail.com>
Diff between dbarts versions 0.8-5 dated 2014-11-13 and 0.8-6 dated 2016-10-31
dbarts-0.8-5/dbarts/tests/test-all.R |only dbarts-0.8-5/dbarts/tools/m4/m4_ax_pthread.m4 |only dbarts-0.8-6/dbarts/DESCRIPTION | 21 dbarts-0.8-6/dbarts/MD5 | 176 dbarts-0.8-6/dbarts/NAMESPACE | 16 dbarts-0.8-6/dbarts/R/A_class.R | 19 dbarts-0.8-6/dbarts/R/bart.R | 20 dbarts-0.8-6/dbarts/R/data.R | 311 dbarts-0.8-6/dbarts/R/dbarts.R | 288 dbarts-0.8-6/dbarts/R/guessNumCores.R |only dbarts-0.8-6/dbarts/R/hooks.R | 2 dbarts-0.8-6/dbarts/R/multipleAssignment.R |only dbarts-0.8-6/dbarts/R/plotTree.R |only dbarts-0.8-6/dbarts/R/utility.R | 90 dbarts-0.8-6/dbarts/R/xbart.R |only dbarts-0.8-6/dbarts/README.md | 4 dbarts-0.8-6/dbarts/TODO | 7 dbarts-0.8-6/dbarts/cleanup | 2 dbarts-0.8-6/dbarts/configure | 9233 +++++----- dbarts-0.8-6/dbarts/configure.ac | 34 dbarts-0.8-6/dbarts/inst/NEWS.Rd | 32 dbarts-0.8-6/dbarts/inst/common/hillData.R | 2 dbarts-0.8-6/dbarts/inst/include/dbarts/bartFit.hpp | 13 dbarts-0.8-6/dbarts/inst/include/dbarts/data.hpp | 12 dbarts-0.8-6/dbarts/inst/include/dbarts/results.hpp | 20 dbarts-0.8-6/dbarts/inst/include/dbarts/scratch.hpp | 5 dbarts-0.8-6/dbarts/inst/include/dbarts/state.hpp | 4 dbarts-0.8-6/dbarts/man/bart.Rd | 19 dbarts-0.8-6/dbarts/man/dbarts.Rd | 2 dbarts-0.8-6/dbarts/man/dbartsControl.Rd | 2 dbarts-0.8-6/dbarts/man/dbartsData.Rd |only dbarts-0.8-6/dbarts/man/dbartsSampler-class.Rd | 56 dbarts-0.8-6/dbarts/man/guessNumCores.Rd |only dbarts-0.8-6/dbarts/man/makeind.Rd | 43 dbarts-0.8-6/dbarts/man/pdbart.Rd | 2 dbarts-0.8-6/dbarts/man/xbart.Rd |only dbarts-0.8-6/dbarts/src/Makevars.in | 16 dbarts-0.8-6/dbarts/src/Makevars.win | 15 dbarts-0.8-6/dbarts/src/R_interface.cpp | 1114 - dbarts-0.8-6/dbarts/src/R_interface.hpp |only dbarts-0.8-6/dbarts/src/R_interface_common.cpp |only dbarts-0.8-6/dbarts/src/R_interface_common.hpp |only dbarts-0.8-6/dbarts/src/R_interface_crossvalidate.cpp |only dbarts-0.8-6/dbarts/src/R_interface_crossvalidate.hpp |only dbarts-0.8-6/dbarts/src/R_interface_sampler.cpp |only dbarts-0.8-6/dbarts/src/R_interface_sampler.hpp |only dbarts-0.8-6/dbarts/src/config.hpp.in | 3 dbarts-0.8-6/dbarts/src/config.hpp.win | 6 dbarts-0.8-6/dbarts/src/crossvalidate.cpp |only dbarts-0.8-6/dbarts/src/crossvalidate.hpp |only dbarts-0.8-6/dbarts/src/dbarts/Makefile | 10 dbarts-0.8-6/dbarts/src/dbarts/bartFit.cpp | 510 dbarts-0.8-6/dbarts/src/dbarts/binaryIO.cpp |only dbarts-0.8-6/dbarts/src/dbarts/binaryIO.hpp |only dbarts-0.8-6/dbarts/src/dbarts/config.hpp.in | 4 dbarts-0.8-6/dbarts/src/dbarts/config.hpp.win | 6 dbarts-0.8-6/dbarts/src/dbarts/functions.cpp | 4 dbarts-0.8-6/dbarts/src/dbarts/node.cpp | 63 dbarts-0.8-6/dbarts/src/dbarts/node.hpp | 3 dbarts-0.8-6/dbarts/src/dbarts/state.cpp | 18 dbarts-0.8-6/dbarts/src/dbarts/tree.cpp | 189 dbarts-0.8-6/dbarts/src/dbarts/tree.hpp | 3 dbarts-0.8-6/dbarts/src/external/Makefile | 16 dbarts-0.8-6/dbarts/src/external/adaptiveRadixTree.c |only dbarts-0.8-6/dbarts/src/external/binaryIO.c |only dbarts-0.8-6/dbarts/src/external/config.h.in | 15 dbarts-0.8-6/dbarts/src/external/config.h.win | 20 dbarts-0.8-6/dbarts/src/external/io.c | 8 dbarts-0.8-6/dbarts/src/external/linearAlgebra.c | 48 dbarts-0.8-6/dbarts/src/external/moments.c | 22 dbarts-0.8-6/dbarts/src/external/random.c | 26 dbarts-0.8-6/dbarts/src/external/randomBase.c | 134 dbarts-0.8-6/dbarts/src/external/randomNorm.c | 6 dbarts-0.8-6/dbarts/src/external/string.c |only dbarts-0.8-6/dbarts/src/guessNumCores.cpp |only dbarts-0.8-6/dbarts/src/guessNumCores.hpp |only dbarts-0.8-6/dbarts/src/include/external/R.h |only dbarts-0.8-6/dbarts/src/include/external/Rinternals.h |only dbarts-0.8-6/dbarts/src/include/external/adaptiveRadixTree.h |only dbarts-0.8-6/dbarts/src/include/external/alloca.h | 1 dbarts-0.8-6/dbarts/src/include/external/binaryIO.h |only dbarts-0.8-6/dbarts/src/include/external/io.h | 6 dbarts-0.8-6/dbarts/src/include/external/linearAlgebra.h | 6 dbarts-0.8-6/dbarts/src/include/external/random.h | 3 dbarts-0.8-6/dbarts/src/include/external/stats.h | 15 dbarts-0.8-6/dbarts/src/include/external/stats_mt.h | 1 dbarts-0.8-6/dbarts/src/include/external/stddef.h | 9 dbarts-0.8-6/dbarts/src/include/external/string.h |only dbarts-0.8-6/dbarts/src/include/rc |only dbarts-0.8-6/dbarts/src/makeModelMatrixFromDataFrame.c |only dbarts-0.8-6/dbarts/src/makeModelMatrixFromDataFrame.h |only dbarts-0.8-6/dbarts/src/rc |only dbarts-0.8-6/dbarts/tests/testthat.R |only dbarts-0.8-6/dbarts/tests/testthat/test-01-dbartsDataArgs.R | 175 dbarts-0.8-6/dbarts/tests/testthat/test-03-dbartsControl.R | 30 dbarts-0.8-6/dbarts/tests/testthat/test-04-continuousResponse.R | 10 dbarts-0.8-6/dbarts/tests/testthat/test-05-binaryResponse.R | 3 dbarts-0.8-6/dbarts/tests/testthat/test-06-dbartsSampler.R | 45 dbarts-0.8-6/dbarts/tests/testthat/test-08-xbart.R |only dbarts-0.8-6/dbarts/tests/testthat/test-10-makeModelMatrix.R |only dbarts-0.8-6/dbarts/tests/testthat/test-11-multipleAssignment.R |only dbarts-0.8-6/dbarts/tools/build-aux/config.guess | 232 dbarts-0.8-6/dbarts/tools/build-aux/config.sub | 64 dbarts-0.8-6/dbarts/tools/m4/ax_check_compile_flag.m4 |only dbarts-0.8-6/dbarts/tools/m4/ax_cxx_namespace_std.m4 |only dbarts-0.8-6/dbarts/tools/m4/ax_ext.m4 |only dbarts-0.8-6/dbarts/tools/m4/ax_gcc_x86_avx_xgetbv.m4 |only dbarts-0.8-6/dbarts/tools/m4/ax_gcc_x86_cpuid.m4 |only dbarts-0.8-6/dbarts/tools/m4/ax_pthread.m4 |only dbarts-0.8-6/dbarts/tools/m4/ax_snprintf_in_namespace_std.m4 |only 110 files changed, 7162 insertions(+), 6132 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models and mixed effects models. However, some of the functions
also deal with other statistical measures, like Cronbach's Alpha,
Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.5.0 dated 2016-09-26 and 0.6.0 dated 2016-10-31
sjstats-0.5.0/sjstats/R/cronb.R |only sjstats-0.5.0/sjstats/R/mic.R |only sjstats-0.5.0/sjstats/R/reliab_test.R |only sjstats-0.5.0/sjstats/man/cronb.Rd |only sjstats-0.5.0/sjstats/man/mic.Rd |only sjstats-0.6.0/sjstats/DESCRIPTION | 8 sjstats-0.6.0/sjstats/MD5 | 32 +-- sjstats-0.6.0/sjstats/NAMESPACE | 6 sjstats-0.6.0/sjstats/NEWS | 111 ++++++----- sjstats-0.6.0/sjstats/NEWS.md | 63 +++--- sjstats-0.6.0/sjstats/R/S3-methods.R | 6 sjstats-0.6.0/sjstats/R/bootstrap.R | 14 + sjstats-0.6.0/sjstats/R/internal_consistency.R |only sjstats-0.6.0/sjstats/R/se.R | 19 + sjstats-0.6.0/sjstats/R/var_pop.R |only sjstats-0.6.0/sjstats/build/partial.rdb |binary sjstats-0.6.0/sjstats/man/bootstrap.Rd | 132 +++++++------ sjstats-0.6.0/sjstats/man/reliab_test.Rd | 239 +++++++++++++++++-------- sjstats-0.6.0/sjstats/man/se.Rd | 14 + sjstats-0.6.0/sjstats/man/sjstats-package.Rd | 4 sjstats-0.6.0/sjstats/man/var_pop.Rd |only 21 files changed, 410 insertions(+), 238 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, PCA and correlation matrices, cluster analyses, scatter
plots, Likert scales, effects plots of regression models (including interaction
terms) and much more. This package supports labelled data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.1.0 dated 2016-09-27 and 2.1.1 dated 2016-10-31
sjPlot-2.1.0/sjPlot/man/adjust_plot_range.Rd |only sjPlot-2.1.1/sjPlot/DESCRIPTION | 8 sjPlot-2.1.1/sjPlot/MD5 | 49 sjPlot-2.1.1/sjPlot/NAMESPACE | 425 +++--- sjPlot-2.1.1/sjPlot/NEWS | 9 sjPlot-2.1.1/sjPlot/NEWS.md | 13 sjPlot-2.1.1/sjPlot/R/helpfunctions.R | 1708 ++++++++++++------------- sjPlot-2.1.1/sjPlot/R/sjPlotAnova.R | 10 sjPlot-2.1.1/sjPlot/R/sjPlotCorr.R | 98 - sjPlot-2.1.1/sjPlot/R/sjPlotGLME.R | 12 sjPlot-2.1.1/sjPlot/R/sjPlotGroupFrequencies.R | 1582 +++++++++++------------ sjPlot-2.1.1/sjPlot/R/sjPlotLinreg.R | 28 sjPlot-2.1.1/sjPlot/R/sjPlotOdds.R | 172 -- sjPlot-2.1.1/sjPlot/R/sjPlotPCA.R | 16 sjPlot-2.1.1/sjPlot/R/sjPlotPropTable.R | 10 sjPlot-2.1.1/sjPlot/R/sjPlotScatter.R | 21 sjPlot-2.1.1/sjPlot/R/sjTabItemAnalysis.R | 4 sjPlot-2.1.1/sjPlot/R/sjTabPCA.R | 2 sjPlot-2.1.1/sjPlot/R/sjplot.R |only sjPlot-2.1.1/sjPlot/build/partial.rdb |binary sjPlot-2.1.1/sjPlot/man/save_plot.Rd | 106 - sjPlot-2.1.1/sjPlot/man/set_theme.Rd | 94 - sjPlot-2.1.1/sjPlot/man/sjPlot-package.Rd | 4 sjPlot-2.1.1/sjPlot/man/sjc.kgap.Rd | 134 - sjPlot-2.1.1/sjPlot/man/sjp.corr.Rd | 259 +-- sjPlot-2.1.1/sjPlot/man/sjp.setTheme.Rd | 510 +++---- sjPlot-2.1.1/sjPlot/man/sjplot.Rd |only 27 files changed, 2589 insertions(+), 2685 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks when working with
data : 1) Reading and writing data between R and other statistical software
packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this
includes easy ways to get and set label attributes, to convert labelled
vectors into factors (and vice versa), or to deal with multiple declared
missing values etc. 2) Data transformation tasks like recoding,
dichotomizing or grouping variables, setting and replacing missing values.
The data transformation functions also support labelled data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.0.0 dated 2016-09-25 and 2.0.1 dated 2016-10-31
DESCRIPTION | 15 -- MD5 | 28 ++- NAMESPACE | 5 NEWS | 13 + NEWS.md | 16 ++ R/count_na.R |only R/drop_labels.R | 152 ++++++++++----------- R/frq.R | 284 +++++++++++++++++++-------------------- R/prop_table.R | 4 R/set_na.R | 336 +++++++++++++++++++++++++---------------------- build/partial.rdb |binary man/count_na.Rd |only man/frq.Rd | 2 man/merge_imputations.Rd | 132 +++++++++--------- man/set_na.Rd | 13 + man/sjmisc-package.Rd | 66 ++++----- 16 files changed, 572 insertions(+), 494 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial data, in R.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Michael Sumner [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.2-1 dated 2016-10-27 and 0.2-2 dated 2016-10-31
DESCRIPTION | 12 +- MD5 | 81 +++++++++++++------- NAMESPACE | 2 R/RcppExports.R |only R/grid.R | 2 R/init.R | 1 R/read.R | 21 ++++- R/sf.R | 2 R/sfc.R | 2 R/wkb.R | 12 ++ cleanup | 2 configure | 182 ++++++++++++++++++++++++++++++++++++++------- configure.in | 109 ++++++++++++++++++++------ demo/nc.R | 11 ++ inst/doc/sfr.R | 13 +-- inst/doc/sfr.Rmd | 78 ++++++++++++------- inst/doc/sfr.html | 58 +++++++------- man |only src/RcppExports.cpp |only src/gdal_read.cpp | 16 +++ src/wkb.cpp | 129 +++++++++++++++++++++---------- tests/gdal_geom.R | 8 + tests/gdal_geom.Rout.save | 23 +++++ tests/sfc.R | 2 tests/sfc.Rout.save | 4 tests/testthat/test_crs.R | 6 - tests/testthat/test_read.R | 2 tests/testthat/test_tm.R | 16 ++- tests/testthat/test_wkb.R | 11 +- tools/winlibs.R | 5 - vignettes/sfr.Rmd | 78 ++++++++++++------- 31 files changed, 636 insertions(+), 252 deletions(-)
Title: Real-Time Adaptive Penalization for Streaming Lasso Models
Description: An implementation of the Real-time Adaptive Penalization (RAP) algorithm through which to iteratively update a regularization parameter in a streaming context.
Author: Ricardo Pio Monti
Maintainer: Ricardo Pio Monti <ricardo.monti08@gmail.com>
Diff between rRAP versions 1.0 dated 2016-10-09 and 1.1 dated 2016-10-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- man/RAP.Rd | 2 +- man/rRAP-package.Rd | 2 +- man/update.RAP.Rd | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Fast and Easy Quality Control of EWAS Results Files
Description: Tools for (automated and manual) quality control of
the results of Epigenome-Wide Association Studies.
Author: Peter J. van der Most,
Leanne K. Kupers,
Ilja Nolte
Maintainer: Peter J. van der Most <p.j.van.der.most@umcg.nl>
Diff between QCEWAS versions 1.0-8 dated 2016-10-18 and 1.0-9 dated 2016-10-31
QCEWAS-1.0-8/QCEWAS/R/script_v10-8_package.R |only QCEWAS-1.0-8/QCEWAS/inst/doc/QCEWAS_Quick_Start_Guide_v108.docx |only QCEWAS-1.0-9/QCEWAS/DESCRIPTION | 8 ++++---- QCEWAS-1.0-9/QCEWAS/MD5 | 8 ++++---- QCEWAS-1.0-9/QCEWAS/R/script_v10-9_package.R |only QCEWAS-1.0-9/QCEWAS/inst/doc/QCEWAS_Quick_Start_Guide_v109.docx |only QCEWAS-1.0-9/QCEWAS/man/QCEWAS-package.Rd | 4 ++-- 7 files changed, 10 insertions(+), 10 deletions(-)
Title: Multiple Testing Procedures of Cox (2011) and Wong and Cox
(2007)
Description: Performs the multiple testing procedures of Cox (2011) <doi:10.5170/CERN-2011-006> and Wong and Cox (2007) <doi:10.1080/02664760701240014>.
Author: Christiana Kartsonaki
Maintainer: Christiana Kartsonaki <christiana.kartsonaki@gmail.com>
Diff between ManyTests versions 1.1 dated 2014-07-24 and 1.2 dated 2016-10-31
DESCRIPTION | 14 ++--- MD5 | 16 +++--- NAMESPACE | 3 + man/FDR.Rd | 94 ++++++++++++++++++++-------------------- man/ManyTests-package.Rd | 86 ++++++++++++++++++------------------ man/local_slope.Rd | 110 +++++++++++++++++++++++------------------------ man/ordered_values.Rd | 96 ++++++++++++++++++++--------------------- man/plot_pvalues.Rd | 100 +++++++++++++++++++++--------------------- man/t_0.Rd | 92 +++++++++++++++++++-------------------- 9 files changed, 307 insertions(+), 304 deletions(-)
Title: Collect and Retrieve Annotation Data for Various Genomic Data
Using Different Webservices
Description: Cross-species identification of novel gene candidates using the NCBI web service is provided. Further, sets of miRNA target genes can be identified by using the targetscan.org API.
Author: Daniel Fischer [aut, cre], Anu Sironen [aut]
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between hoardeR versions 0.9.1 dated 2016-10-10 and 0.9.2 dated 2016-10-31
hoardeR-0.9.1/hoardeR/vignettes/coverageExample.jpg |only hoardeR-0.9.1/hoardeR/vignettes/pigFlanking.jpg |only hoardeR-0.9.2/hoardeR/DESCRIPTION | 8 +++--- hoardeR-0.9.2/hoardeR/MD5 | 24 +++++++++---------- hoardeR-0.9.2/hoardeR/R/getFastaFromBed.R | 1 hoardeR-0.9.2/hoardeR/R/plotHit.R | 2 + hoardeR-0.9.2/hoardeR/build/vignette.rds |binary hoardeR-0.9.2/hoardeR/inst/ChangeLog | 3 ++ hoardeR-0.9.2/hoardeR/inst/doc/hoardeR-vignette.R | 8 ++++-- hoardeR-0.9.2/hoardeR/inst/doc/hoardeR-vignette.Rmd | 18 +++++++++++--- hoardeR-0.9.2/hoardeR/inst/doc/hoardeR-vignette.pdf |binary hoardeR-0.9.2/hoardeR/man/hoardeR-package.Rd | 4 +-- hoardeR-0.9.2/hoardeR/vignettes/coverageExample.png |only hoardeR-0.9.2/hoardeR/vignettes/hoardeR-vignette.Rmd | 18 +++++++++++--- hoardeR-0.9.2/hoardeR/vignettes/pigFlanking.png |only 15 files changed, 58 insertions(+), 28 deletions(-)
Title: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Description: The goal of checkpoint is to solve the problem of package
reproducibility in R. Specifically, checkpoint allows you to install packages
as they existed on CRAN on a specific snapshot date as if you had a CRAN time
machine. To achieve reproducibility, the checkpoint() function installs the
packages required or called by your project and scripts to a local library
exactly as they existed at the specified point in time. Only those packages
are available to your project, thereby avoiding any package updates that came
later and may have altered your results. In this way, anyone using checkpoint's
checkpoint() can ensure the reproducibility of your scripts or projects at any
time. To create the snapshot archives, once a day (at midnight UTC) Microsoft
refreshes the Austria CRAN mirror, on the "Microsoft R Archived Network"
server (<https://mran.microsoft.com/>). Immediately after completion
of the rsync mirror process, the process takes a snapshot, thus creating the
archive. Snapshot archives exist starting from 2014-09-17.
Author: Microsoft Corporation
Maintainer: Andrie de Vries <adevries@microsoft.com>
Diff between checkpoint versions 0.3.16 dated 2016-04-14 and 0.3.18 dated 2016-10-31
DESCRIPTION | 10 ++-- MD5 | 37 +++++++++----- NAMESPACE | 2 R/checkpoint.R | 82 +++++++++++++++++++++++++++++---- R/checkpoint_log.R |only R/checkpoint_paths.R | 3 - R/checkpoint_remove.R |only R/mranUrl.R | 49 ++++++++++++++----- build/vignette.rds |binary inst/doc/checkpoint.Rmd | 4 - inst/doc/checkpoint.html | 50 +++++++++++--------- inst/examples/example_remove.R |only man/checkpoint.Rd | 21 +++++++- man/checkpointArchives.Rd |only man/checkpointRemove.Rd |only man/getValidSnapshots.Rd | 2 tests/localMRAN |only tests/testthat/framed.sty |only tests/testthat/test-0-is-404.R | 12 ++++ tests/testthat/test-2-snapshot-dates.R | 10 ++++ tests/testthat/test-3-checkpoint.R | 29 +++++++---- vignettes/checkpoint.Rmd | 4 - 22 files changed, 236 insertions(+), 79 deletions(-)
Title: Tools for Detecting Influential Data in Mixed Effects Models
Description: Provides a collection of tools for
detecting influential cases in generalized mixed effects
models. It analyses models that were estimated using 'lme4'. The
basic rationale behind identifying influential data is that
when iteratively single units are omitted from the data, models
based on these data should not produce substantially different
estimates. To standardize the assessment of how influential a
(single group of) observation(s) is, several measures of
influence are common practice, such as DFBETAS and Cook's Distance.
In addition, we provide a measure of percentage change of the fixed point
estimates and a simple procedure to detect changing levels of significance.
Author: Rense Nieuwenhuis, Ben Pelzer, Manfred te Grotenhuis
Maintainer: Rense Nieuwenhuis <rense.nieuwenhuis@sofi.su.se>
Diff between influence.ME versions 0.9-7 dated 2016-08-17 and 0.9-8 dated 2016-10-31
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- inst/CITATION | 44 ++++++++++++++++++++++---------------------- 3 files changed, 29 insertions(+), 29 deletions(-)
Title: Weighted Effect Coding
Description: Provides functions to create factor variables with contrasts based on weighted effect coding. In weighted effect coding the estimates from a first order regression model show the deviations per group from the sample mean. This is especially useful when a researcher has no directional hypotheses and uses a sample from a population in which the number of observation per group is different The package also provides functionality for interactions between two factor variables based on weighted effect coding. Please note that this is a beta version: while functional, it does not follow all R conventions.
Author: Rense Nieuwenhuis, Manfred te Grotenhuis, Ben Pelzer, Alexanter Schmidt, Ruben Konig, Rob Eisinga
Maintainer: Rense Nieuwenhuis <rense.nieuwenhuis@sofi.su.se>
Diff between wec versions 0.1 dated 2015-08-28 and 0.2 dated 2016-10-31
DESCRIPTION | 9 +++--- MD5 | 13 ++++---- NAMESPACE | 1 R/interact.wec.int.R |only data/BMI.RData |binary man/BMI.Rd | 7 ++-- man/contr.wec.Rd | 34 +++++++---------------- man/contr.wec.interact.Rd | 68 ++++++++++++++++++++++------------------------ 8 files changed, 61 insertions(+), 71 deletions(-)
Title: Capture the Genes and Variants Related to a Genetic Disease from
Public Databases and PubMed
Description: Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature based on the public databases including HPO (Human Phenotype Ontology, <http://human-phenotype-ontology.github.io/about.html>), Orphanet <http://www.orpha.net/consor/cgi-bin/index.php>, OMIM (Online Mendelian Inheritance in Man, <http://www.omim.org>), ClinVar <http://www.ncbi.nlm.nih.gov/clinvar>, and UniProt (Universal Protein Resource, <http://www.uniprot.org>) and PubMed abstracts. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. UniProt focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the UniProt are manually curated from UniProtKB/Swiss-Prot. Additionally, PubMed provides the primary and latest source of the information. Text mining was employed to capture the information from PubMed abstracts.
Author: Zongfu Cao
Maintainer: Zongfu Cao <caozongfu@gmail.com>
Diff between VarfromPDB versions 2.1.10 dated 2016-10-25 and 2.1.11 dated 2016-10-31
DESCRIPTION | 6 +- MD5 | 8 +-- R/extract_clinvar.R | 121 ++------------------------------------------------- R/extract_omim.R | 2 R/variants_compile.R | 25 ++++++++-- 5 files changed, 32 insertions(+), 130 deletions(-)
Title: Calculating Proportionality Between Vectors of Compositional
Data
Description: The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, this approach lacks statistical validity
when applied to relative data, including those biological count data produced by
microarray assays or high-throughput RNA-sequencing. Two metrics of proportionality,
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and rho [Erb and
Notredame (2016) <DOI:10.1007/s12064-015-0220-8>], both derived from compositional
data analysis, a branch of math dealing specifically with relative data,
represent novel alternatives to correlation. This package introduces a programmatic
framework for the calculation of feature dependence through proportionality, as
discussed in the cited publications.
Author: Thomas Quinn [aut, cre],
David Lovell [aut]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between propr versions 2.0.1 dated 2016-09-30 and 2.0.4 dated 2016-10-31
propr-2.0.1/propr/inst/doc/propr-vignette.R |only propr-2.0.1/propr/inst/doc/propr-vignette.Rmd |only propr-2.0.1/propr/inst/doc/propr-vignette.html |only propr-2.0.1/propr/vignettes/propr-vignette.Rmd |only propr-2.0.4/propr/DESCRIPTION | 12 +- propr-2.0.4/propr/MD5 | 63 +++++++++---- propr-2.0.4/propr/NAMESPACE | 15 ++- propr-2.0.4/propr/NEWS.md | 42 ++++++++- propr-2.0.4/propr/R/RcppExports.R | 4 propr-2.0.4/propr/R/classes.R | 19 ++++ propr-2.0.4/propr/R/methods.R | 110 ++---------------------- propr-2.0.4/propr/R/perb.R | 35 +++++++ propr-2.0.4/propr/R/plot.R |only propr-2.0.4/propr/R/simplify.R | 8 - propr-2.0.4/propr/README.md | 6 - propr-2.0.4/propr/build/vignette.rds |binary propr-2.0.4/propr/data |only propr-2.0.4/propr/inst/doc/introduction.R |only propr-2.0.4/propr/inst/doc/introduction.Rmd |only propr-2.0.4/propr/inst/doc/introduction.html |only propr-2.0.4/propr/inst/doc/visualize.R |only propr-2.0.4/propr/inst/doc/visualize.Rmd |only propr-2.0.4/propr/inst/doc/visualize.html |only propr-2.0.4/propr/man/bokeh.Rd |only propr-2.0.4/propr/man/bucket.Rd |only propr-2.0.4/propr/man/caneToad.counts.Rd |only propr-2.0.4/propr/man/caneToad.groups.Rd |only propr-2.0.4/propr/man/mds.Rd |only propr-2.0.4/propr/man/perb.Rd | 10 +- propr-2.0.4/propr/man/plotCheck.Rd |only propr-2.0.4/propr/man/prism.Rd |only propr-2.0.4/propr/man/propr.Rd | 11 -- propr-2.0.4/propr/man/proprPerb.Rd | 4 propr-2.0.4/propr/man/simplify.Rd | 8 - propr-2.0.4/propr/man/slate.Rd |only propr-2.0.4/propr/man/snapshot.Rd |only propr-2.0.4/propr/man/top.Rd |only propr-2.0.4/propr/src/RcppExports.cpp | 7 - propr-2.0.4/propr/src/backend.cpp | 18 --- propr-2.0.4/propr/tests/testthat/test-Rcpp.R | 4 propr-2.0.4/propr/tests/testthat/test-perb.R | 113 +++++++++++++++++++++++++ propr-2.0.4/propr/vignettes/introduction.Rmd |only propr-2.0.4/propr/vignettes/visualize.Rmd |only 43 files changed, 308 insertions(+), 181 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions where showing the progress is
useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time)
can be set through options.
Functions can exploit parallel processing resources.
Author: Peter Solymos [aut, cre], Zygmunt Zawadzki [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between pbapply versions 1.3-0 dated 2016-09-26 and 1.3-1 dated 2016-10-31
pbapply-1.3-0/pbapply/tests |only pbapply-1.3-1/pbapply/DESCRIPTION | 8 pbapply-1.3-1/pbapply/MD5 | 19 - pbapply-1.3-1/pbapply/R/closepb.R | 1 pbapply-1.3-1/pbapply/R/splitpb.R | 2 pbapply-1.3-1/pbapply/R/timerProgressBar.R | 304 +++++++++++++++++--------- pbapply-1.3-1/pbapply/R/unix/startpb.R | 3 pbapply-1.3-1/pbapply/R/windows/startpb.R | 3 pbapply-1.3-1/pbapply/R/zzz.R | 3 pbapply-1.3-1/pbapply/man/pboptions.Rd | 4 pbapply-1.3-1/pbapply/man/timerProgressBar.Rd | 51 +++- 11 files changed, 267 insertions(+), 131 deletions(-)
Title: Simple Tools for Examining and Cleaning Dirty Data
Description: The main janitor functions can: perfectly format data.frame column
names; isolate duplicate records; and provide quick one- and two-variable
tabulations (i.e., frequency tables and crosstabs). Other janitor functions
nicely format the results of these tabulations. These tabulate-and-report
functions approximate popular features of SPSS and Microsoft Excel. This package
follows the principles of the "tidyverse" and works well with the pipe function
%>%. janitor was built with beginning-to-intermediate R users in mind and is
optimized for user-friendliness. Advanced R users can already do everything
covered here, but with janitor they can do it faster and save their thinking for
the fun stuff.
Author: Sam Firke [aut, cre],
Chris Haid [ctb]
Maintainer: Sam Firke <samuel.firke@gmail.com>
Diff between janitor versions 0.2.0 dated 2016-10-03 and 0.2.1 dated 2016-10-31
DESCRIPTION | 18 ++++----- MD5 | 24 ++++++------- NEWS.md | 9 ++++ R/add_totals.R | 4 +- R/crosstab.R | 37 +++++++++----------- R/tabyl.R | 43 +++++++++++------------ R/use_first_valid_of.R | 28 +++++++++------ README.md | 56 ++++++++++++++++++++----------- inst/doc/introduction.html | 2 - man/crosstab.Rd | 8 ---- man/tabyl.Rd | 10 ----- tests/testthat/test-add-totals.R | 23 ++++++++---- tests/testthat/test-use-first-valid-of.R | 17 +++++++++ 13 files changed, 158 insertions(+), 121 deletions(-)
Title: Financial Data from U.S. Securities and Exchange Commission
Description: Download and display company financial data from the U.S. Securities
and Exchange Commission's EDGAR database. It contains a suite of functions with
web scraping and XBRL parsing capabilities that allows users to extract data from EDGAR
in an automated and scalable manner. See <https://www.sec.gov/edgar/searchedgar/companysearch.html>
for more information.
Author: Seward Lee
Maintainer: Seward Lee <sewardlee337@gmail.com>
Diff between finreportr versions 1.0.0 dated 2016-03-29 and 1.0.1 dated 2016-10-31
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + R/backend_utilities.R | 2 +- R/get_balance_sheet.R | 4 ++-- R/get_cash_flow.R | 4 ++-- R/get_financial.R | 13 +++++++++---- R/get_income.R | 4 ++-- README.md | 18 +++++++++++++++--- build/vignette.rds |binary inst/doc/finreportr.html | 11 +++++------ man/GetBalanceSheet.Rd | 4 ++-- man/GetCashFlow.Rd | 4 ++-- man/GetIncome.Rd | 4 ++-- 14 files changed, 61 insertions(+), 44 deletions(-)
Title: Simultaneous Edit-Imputation for Continuous Microdata
Description: An integrated editing and imputation method for continuous microdata under linear constraints is implemented. It relies on a Bayesian nonparametric hierarchical modeling approach as described in Kim et al. (2015) <DOI:10.1080/01621459.2015.1040881>. In this approach, the joint distribution of the data is estimated by a flexible joint probability model. The generated edit-imputed data are guaranteed to satisfy all imposed edit rules, whose types include ratio edits, balance edits and range restrictions.
Author: Quanli Wang, Hang J. Kim, Jerome P. Reiter, Lawrence H. Cox and Alan F. Karr
Maintainer: Quanli Wang <quanli@stat.duke.edu>
Diff between EditImputeCont versions 1.0.1 dated 2016-02-19 and 1.0.2 dated 2016-10-31
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- man/EditImputeCont-package.Rd | 2 +- man/Rcpp_bei-class.Rd | 2 +- man/readData.Rd | 2 +- src/newmat6.cpp | 2 +- 6 files changed, 15 insertions(+), 14 deletions(-)
More information about EditImputeCont at CRAN
Permanent link
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 2.39-5 dated 2016-06-26 and 2.40-1 dated 2016-10-30
survival-2.39-5/survival/noweb/yates.Rnw |only survival-2.40-1/survival/DESCRIPTION | 7 survival-2.40-1/survival/MD5 | 164 +++-- survival-2.40-1/survival/NAMESPACE | 6 survival-2.40-1/survival/R/Surv.S | 4 survival-2.40-1/survival/R/coxph.R | 9 survival-2.40-1/survival/R/is.ratetable.S | 5 survival-2.40-1/survival/R/model.matrix.coxph.R | 5 survival-2.40-1/survival/R/normalizetime.R |only survival-2.40-1/survival/R/plot.survfit.R | 44 + survival-2.40-1/survival/R/predict.coxph.R | 2 survival-2.40-1/survival/R/predict.survreg.S | 2 survival-2.40-1/survival/R/print.summary.survfit.S | 5 survival-2.40-1/survival/R/print.summary.survfitms.S | 6 survival-2.40-1/survival/R/print.survfit.S | 15 survival-2.40-1/survival/R/residuals.coxph.S | 7 survival-2.40-1/survival/R/statefig.R |only survival-2.40-1/survival/R/survSplit.R | 57 + survival-2.40-1/survival/R/survfit.R | 15 survival-2.40-1/survival/R/survfit.coxph.R | 59 +- survival-2.40-1/survival/R/survfit.matrix.R | 12 survival-2.40-1/survival/R/survfitCI.R | 234 ++++---- survival-2.40-1/survival/R/survfitKM.S | 9 survival-2.40-1/survival/R/survfitms.R | 68 +- survival-2.40-1/survival/R/survreg.S | 9 survival-2.40-1/survival/ToDo | 14 survival-2.40-1/survival/build/vignette.rds |binary survival-2.40-1/survival/data/datalist | 2 survival-2.40-1/survival/data/myeloid.rda |only survival-2.40-1/survival/data/rhDNase.rda |only survival-2.40-1/survival/inst/CITATION | 2 survival-2.40-1/survival/inst/NEWS.Rd | 62 ++ survival-2.40-1/survival/inst/doc/adjcurve.R | 22 survival-2.40-1/survival/inst/doc/adjcurve.Rnw | 28 survival-2.40-1/survival/inst/doc/adjcurve.pdf |binary survival-2.40-1/survival/inst/doc/compete.R | 6 survival-2.40-1/survival/inst/doc/compete.Rnw | 20 survival-2.40-1/survival/inst/doc/compete.pdf |binary survival-2.40-1/survival/inst/doc/multi.R |only survival-2.40-1/survival/inst/doc/multi.Rnw |only survival-2.40-1/survival/inst/doc/multi.pdf |only survival-2.40-1/survival/inst/doc/splines.pdf |binary survival-2.40-1/survival/inst/doc/tests.pdf |binary survival-2.40-1/survival/inst/doc/timedep.pdf |binary survival-2.40-1/survival/inst/doc/validate.pdf |binary survival-2.40-1/survival/man/Surv.Rd | 2 survival-2.40-1/survival/man/lines.survfit.Rd | 19 survival-2.40-1/survival/man/myeloid.Rd |only survival-2.40-1/survival/man/nwtco.Rd | 2 survival-2.40-1/survival/man/ratetable.Rd | 2 survival-2.40-1/survival/man/rhDNase.Rd |only survival-2.40-1/survival/man/statefig.Rd |only survival-2.40-1/survival/man/survSplit.Rd | 27 survival-2.40-1/survival/man/survfit.coxph.Rd | 5 survival-2.40-1/survival/man/survfit.formula.Rd | 24 survival-2.40-1/survival/man/survfit.object.Rd | 19 survival-2.40-1/survival/man/survival-internal.Rd | 3 survival-2.40-1/survival/man/tmerge.Rd | 17 survival-2.40-1/survival/noweb/Makefile | 2 survival-2.40-1/survival/noweb/Readme | 6 survival-2.40-1/survival/noweb/coxph.Rnw | 15 survival-2.40-1/survival/noweb/coxsurv.Rnw | 62 +- survival-2.40-1/survival/noweb/msurv.nw | 268 ++++----- survival-2.40-1/survival/noweb/plot.Rnw | 40 + survival-2.40-1/survival/noweb/plot.Rnw.orig |only survival-2.40-1/survival/noweb/statefig.Rnw |only survival-2.40-1/survival/noweb/survfit.Rnw | 39 - survival-2.40-1/survival/noweb/survfitCI.Rnw | 430 +++++++-------- survival-2.40-1/survival/noweb/survfitms.Rnw | 75 +- survival-2.40-1/survival/noweb/zzz |only survival-2.40-1/survival/src/dmatrix.c | 32 - survival-2.40-1/survival/src/init.c | 4 survival-2.40-1/survival/src/survfitci.c | 214 +++---- survival-2.40-1/survival/src/survproto.h | 7 survival-2.40-1/survival/tests/coxsurv.R | 9 survival-2.40-1/survival/tests/coxsurv.Rout.save | 18 survival-2.40-1/survival/tests/finegray.R | 4 survival-2.40-1/survival/tests/finegray.Rout.save | 12 survival-2.40-1/survival/tests/mstate.R | 201 ++++++- survival-2.40-1/survival/tests/mstate.Rout.save | 231 +++++++- survival-2.40-1/survival/tests/summary_survfit.R | 4 survival-2.40-1/survival/tests/summary_survfit.Rout.save | 12 survival-2.40-1/survival/tests/survSplit.R |only survival-2.40-1/survival/tests/survSplit.Rout.save |only survival-2.40-1/survival/tests/testci.R | 14 survival-2.40-1/survival/tests/testci.Rout.save | 22 survival-2.40-1/survival/tests/testci2.R | 30 - survival-2.40-1/survival/tests/testci2.Rout.save | 39 - survival-2.40-1/survival/vignettes/.install_extras |only survival-2.40-1/survival/vignettes/adjcurve.Rnw | 28 survival-2.40-1/survival/vignettes/compete.Rnw | 20 survival-2.40-1/survival/vignettes/mstate.rda |only survival-2.40-1/survival/vignettes/multi.Rnw |only 93 files changed, 1854 insertions(+), 1004 deletions(-)
Title: GNU Privacy Guard for R
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods.
Includes utilities for public key encryption, creating and verifying digital signatures,
and managing your local keyring. Note that some functionality depends on the version of
GnuPG that is installed on the system. On Windows this package can be used together with
'GPG4Win' which provides a GUI for managing keys and entering passphrases.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between gpg versions 0.3 dated 2016-10-21 and 0.4 dated 2016-10-30
DESCRIPTION | 12 - MD5 | 29 ++-- NAMESPACE | 2 NEWS | 5 R/keys.R | 18 ++ R/password.R | 13 + R/signing.R | 8 - inst/doc/intro.R | 31 ++-- inst/doc/intro.Rmd | 84 +++++++---- inst/doc/intro.html | 373 +++++++++++++++++++++++++++++----------------------- man/gpg_keys.Rd | 3 src/engine.c | 15 +- src/keys.c | 17 +- src/keysig.c |only src/sign.c | 72 ++++++---- vignettes/intro.Rmd | 84 +++++++---- 16 files changed, 474 insertions(+), 292 deletions(-)
Title: Penalized Likelihood Estimation and Dynamic Prediction under the
Joint Frailty-Copula Models Between Tumour Progression and
Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction under the joint frailty-copula model between tumour progression and death for meta-analysis.
The method is applicable for meta-analytic data combining several studies. The data should have information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.9 dated 2016-10-22 and 2.10 dated 2016-10-30
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++++---- R/jointCox.indep.reg.R | 8 ++++---- R/jointCox.reg.R | 8 ++++---- data/dataOvarian1.rda |only data/dataOvarian2.rda |only data/datalist |only man/dataOvarian1.Rd |only man/dataOvarian2.Rd |only man/joint.Cox-package.Rd | 4 ++-- 10 files changed, 23 insertions(+), 18 deletions(-)
Title: Holonomic Gradient Method and Gradient Descent
Description: The holonomic gradient method (HGM, hgm) gives a way to evaluate normalization
constants of unnormalized probability distributions by utilizing holonomic
systems of differential or difference equations. The holonomic gradient descent (HGD, hgd) gives a method
to find maximal likelihood estimates by utilizing the HGM.
Author: Nobuki Takayama, Tamio Koyama, Tomonari Sei, Hiromasa Nakayama, Kenta Nishiyama
Maintainer: Nobuki Takayama <takayama@math.kobe-u.ac.jp>
Diff between hgm versions 1.11 dated 2015-04-03 and 1.16 dated 2016-10-30
DESCRIPTION | 8 MD5 | 37 +-- NAMESPACE | 1 R/hgm.c2wishart.R |only R/hgm.cwishart.R | 19 + R/zhgm_names.R | 1 man/hgm-package.Rd | 4 man/hgm.c2wishart.Rd |only man/hgm.cwishart.Rd | 37 ++- src/code-n-2f1.c |only src/code-n.c | 14 - src/jack-n.c | 603 +++++++++++++++++++++++++++++++++++++++++++++------ src/mh-r.c | 43 +++ src/mh.c | 161 +++++++++++++ src/mh.h | 18 + src/oxprint.h | 1 src/rk.c | 19 - src/sfile.c | 6 src/sfile.h | 8 src/usage-jack-n.h |only src/usage-w-n.h |only src/wmain.c | 392 ++++++++++++++++++++++++++++----- 22 files changed, 1205 insertions(+), 167 deletions(-)
Title: Access to the LinkedIn API via R
Description: A series of functions that allow users
to access the 'LinkedIn' API to get information about connections,
search for people and jobs, share updates with their network,
and create group discussions. For more information about using
the API please visit <https://developer.linkedin.com/>.
Author: Michael Piccirilli <michael.r.piccirilli@gmail.com>
Maintainer: Michael Piccirilli <michael.r.piccirilli@gmail.com>
Diff between Rlinkedin versions 0.1 dated 2015-05-04 and 0.2 dated 2016-10-30
Rlinkedin-0.1/Rlinkedin/README.md |only Rlinkedin-0.2/Rlinkedin/DESCRIPTION | 17 ++++--- Rlinkedin-0.2/Rlinkedin/MD5 | 55 +++++++++++------------ Rlinkedin-0.2/Rlinkedin/NAMESPACE | 4 + Rlinkedin-0.2/Rlinkedin/R/Rlinkedin-package.R | 11 ++-- Rlinkedin-0.2/Rlinkedin/R/getCompany.R | 24 +++++++--- Rlinkedin-0.2/Rlinkedin/R/getGroupPosts.R | 16 +++++- Rlinkedin-0.2/Rlinkedin/R/getGroups.R | 28 ++++++++--- Rlinkedin-0.2/Rlinkedin/R/getJobs.R | 17 ++++++- Rlinkedin-0.2/Rlinkedin/R/getMyConnections.R | 13 +++++ Rlinkedin-0.2/Rlinkedin/R/getProfile.R | 30 ++++++++++-- Rlinkedin-0.2/Rlinkedin/R/inOAuth.R | 9 ++- Rlinkedin-0.2/Rlinkedin/R/searchCompanies.R | 19 +++---- Rlinkedin-0.2/Rlinkedin/R/searchJobs.R | 19 +++++-- Rlinkedin-0.2/Rlinkedin/R/searchPeople.R | 20 ++++++-- Rlinkedin-0.2/Rlinkedin/R/submitGroupPost.R | 9 +++ Rlinkedin-0.2/Rlinkedin/man/Rlinkedin-package.Rd | 8 +-- Rlinkedin-0.2/Rlinkedin/man/getCompany.Rd | 6 +- Rlinkedin-0.2/Rlinkedin/man/getGroupPosts.Rd | 6 +- Rlinkedin-0.2/Rlinkedin/man/getGroups.Rd | 6 +- Rlinkedin-0.2/Rlinkedin/man/getJobs.Rd | 12 ++--- Rlinkedin-0.2/Rlinkedin/man/getMyConnections.Rd | 10 ++-- Rlinkedin-0.2/Rlinkedin/man/getProfile.Rd | 14 +++-- Rlinkedin-0.2/Rlinkedin/man/inOAuth.Rd | 6 +- Rlinkedin-0.2/Rlinkedin/man/searchCompanies.Rd | 2 Rlinkedin-0.2/Rlinkedin/man/searchJobs.Rd | 6 +- Rlinkedin-0.2/Rlinkedin/man/searchPeople.Rd | 6 +- Rlinkedin-0.2/Rlinkedin/man/submitGroupPost.Rd | 16 +++--- Rlinkedin-0.2/Rlinkedin/man/submitShare.Rd | 2 29 files changed, 261 insertions(+), 130 deletions(-)
Title: Performance Analysis and Companion Functions for Binary
Classification Models
Description: Provides companion function for analysing the performance of
classification models. Also, provides function to optimise probability cut-
off score based on used specified objectives, Plot 'ROC' Curve in 'ggplot2',
'AUROC', 'IV', 'WOE' Calculation, 'KS Statistic' etc to aid accuracy improvement
in binary classification models.
Author: Selva Prabhakaran
Maintainer: Selva Prabhakaran <selva86@gmail.com>
Diff between InformationValue versions 1.2.1 dated 2015-12-06 and 1.2.3 dated 2016-10-30
DESCRIPTION | 17 +++++-- MD5 | 56 ++++++++++++------------- NAMESPACE | 6 +- R/Main.R | 6 -- R/playground.R | 28 +++++++++++- README.md | 89 +++++++++++++++++++++++------------------ data/ActualsAndScores.RData |binary data/SimData.RData |binary inst/doc/InformationValue.html | 28 ++++-------- man/AUROC.Rd | 2 man/ActualsAndScores.Rd | 2 man/Concordance.Rd | 2 man/IV.Rd | 2 man/SimData.Rd | 2 man/WOE.Rd | 2 man/WOETable.Rd | 2 man/confusionMatrix.Rd | 2 man/kappaCohen.Rd | 2 man/ks_plot.Rd | 2 man/ks_stat.Rd | 4 - man/misClassError.Rd | 2 man/npv.Rd | 2 man/optimalCutoff.Rd | 2 man/plotROC.Rd | 2 man/precision.Rd | 2 man/sensitivity.Rd | 2 man/somersD.Rd | 2 man/specificity.Rd | 2 man/youdensIndex.Rd | 2 29 files changed, 153 insertions(+), 119 deletions(-)
More information about InformationValue at CRAN
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Title: Companion to Applied Linear Statistical Models
Description: Functions and Data set to Accompany Applied Linear Statistical
Models Fifth Edition, Michael H. Kutner; Christopher J. Nachtsheim; John Neter;
William Li, 2005.(ISBN-10: 0071122214, ISBN-13: 978-0071122214, <https://www.amazon.co.uk/Applied-Linear-Statistical-Models-Intl/dp/0071122214>) Present the function on the package that does not exist in
the R. In this version of the package Chapters 1 to 9 and 16 to 18, have been investigated. In
future versions more chapters to be checked.
Author: Ali Ghanbari <a.ghanbari541@gmail.com>
Maintainer: Ali Ghanbari <a.ghanbari541@gmail.com>
Diff between ALSM versions 0.1.0 dated 2016-09-09 and 0.1.1 dated 2016-10-30
DESCRIPTION | 12 +++++------ MD5 | 38 +++++++++++++++++++++++++++++-------- NAMESPACE | 19 ++++++++++++++++++ R/16_17_18_oneway.R |only R/3_bftest.R | 2 - R/6_ci.reg.R | 4 +-- R/9_model.s.R | 2 - data/ABTElectronicsCorporation.rda |only data/CashOffers.rda |only data/FillingMachines.rda |only data/HayFeverRelief.rda |only data/KentonFoodCompany.rda |only data/ProductivityImprovement.rda |only data/ProgrammerRequirements.rda |only data/RustInhibitor.rda |only data/ServoData.rda |only data/WindingSpeeds.rda |only man/9_AICp.Rd | 2 - man/9_SBCp.Rd | 2 - man/9_boxcox.sse.Rd | 2 + man/ABTElectronicsCorporation.Rd |only man/CashOffers.Rd |only man/FillingMachines.Rd |only man/HayFeverRelief.Rd |only man/KentonFoodCompany.Rd |only man/ProductivityImprovement.Rd |only man/ProgrammerRequirements.Rd |only man/RustInhibitor.Rd |only man/ServoData.Rd |only man/WindingSpeeds.Rd |only man/oneway.Rd |only 31 files changed, 63 insertions(+), 20 deletions(-)
Title: Markov-Switching GARCH Models
Description: The MSGARCH package offers methods to fit (by Maximum Likelihood or Bayesian), simulate, and forecast various Markov-Switching GARCH processes.
Author: Keven Bluteau [aut, cre],
David Ardia [aut],
Denis-Alexandre Trottier [aut],
Kris Boudt [ctb],
Brian Peterson [ctb]
Maintainer: Keven Bluteau <Keven.Bluteau@unine.ch>
Diff between MSGARCH versions 0.16 dated 2016-08-25 and 0.17 dated 2016-10-29
MSGARCH-0.16/MSGARCH/R/sim.ahead.R |only MSGARCH-0.16/MSGARCH/src/Gas.cpp |only MSGARCH-0.16/MSGARCH/vignettes |only MSGARCH-0.17/MSGARCH/DESCRIPTION | 17 ++--- MSGARCH-0.17/MSGARCH/MD5 | 91 +++++++++++++-------------- MSGARCH-0.17/MSGARCH/NAMESPACE | 1 MSGARCH-0.17/MSGARCH/NEWS | 26 ++----- MSGARCH-0.17/MSGARCH/R/AIC.R | 5 - MSGARCH-0.17/MSGARCH/R/BIC.R | 5 - MSGARCH-0.17/MSGARCH/R/DIC.R | 11 +-- MSGARCH-0.17/MSGARCH/R/MSGARCH.R | 19 ++--- MSGARCH-0.17/MSGARCH/R/Pstate.R | 5 - MSGARCH-0.17/MSGARCH/R/bayes.R | 12 ++- MSGARCH-0.17/MSGARCH/R/cdf.R | 5 - MSGARCH-0.17/MSGARCH/R/f.theta.mixture.R | 22 +----- MSGARCH-0.17/MSGARCH/R/findParameters.R | 60 +++++------------ MSGARCH-0.17/MSGARCH/R/ht.R | 12 +-- MSGARCH-0.17/MSGARCH/R/kernel.R | 5 - MSGARCH-0.17/MSGARCH/R/mle.R | 23 +++--- MSGARCH-0.17/MSGARCH/R/pdf.R | 5 - MSGARCH-0.17/MSGARCH/R/pit.R | 13 +-- MSGARCH-0.17/MSGARCH/R/pred.R | 7 -- MSGARCH-0.17/MSGARCH/R/print.R | 21 +++--- MSGARCH-0.17/MSGARCH/R/risk.R | 13 ++- MSGARCH-0.17/MSGARCH/R/sim.R | 2 MSGARCH-0.17/MSGARCH/R/simahead.R | 7 -- MSGARCH-0.17/MSGARCH/R/spec.R | 1 MSGARCH-0.17/MSGARCH/R/transmat.R | 21 +++--- MSGARCH-0.17/MSGARCH/R/unc.vol.R | 21 +++++- MSGARCH-0.17/MSGARCH/R/utils.R | 94 ++++++++++++++++------------ MSGARCH-0.17/MSGARCH/inst/doc |only MSGARCH-0.17/MSGARCH/man/AIC.Rd | 5 - MSGARCH-0.17/MSGARCH/man/BIC.Rd | 5 - MSGARCH-0.17/MSGARCH/man/DIC.Rd | 11 +-- MSGARCH-0.17/MSGARCH/man/MSGARCH-package.Rd | 21 +++--- MSGARCH-0.17/MSGARCH/man/Pstate.Rd | 5 - MSGARCH-0.17/MSGARCH/man/cdf.Rd | 5 - MSGARCH-0.17/MSGARCH/man/fit.bayes.Rd | 11 ++- MSGARCH-0.17/MSGARCH/man/fit.mle.Rd | 14 +--- MSGARCH-0.17/MSGARCH/man/ht.Rd | 11 +-- MSGARCH-0.17/MSGARCH/man/kernel.Rd | 5 - MSGARCH-0.17/MSGARCH/man/pdf.Rd | 5 - MSGARCH-0.17/MSGARCH/man/pit.Rd | 9 +- MSGARCH-0.17/MSGARCH/man/pred.Rd | 5 - MSGARCH-0.17/MSGARCH/man/risk.Rd | 9 +- MSGARCH-0.17/MSGARCH/man/sim.Rd | 2 MSGARCH-0.17/MSGARCH/man/simahead.Rd | 7 -- MSGARCH-0.17/MSGARCH/man/transmat.Rd | 5 - MSGARCH-0.17/MSGARCH/src/GAS.cpp |only 49 files changed, 318 insertions(+), 341 deletions(-)
Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our paper
in the Journal of Statistical Software (2016, v71i02). Either version 2 or 3
of the 'Protocol Buffers' 'API' is supported.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.6 dated 2016-09-09 and 0.4.7 dated 2016-10-29
ChangeLog | 11 +++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- README.md | 10 ++++++---- inst/NEWS.Rd | 7 +++++++ inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-paper.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary inst/doc/RProtoBuf-unitTests.pdf |binary src/lookup.cpp | 2 +- vignettes/RProtoBuf-paper.bib | 2 +- vignettes/figures/fig-SER.pdf |binary 12 files changed, 43 insertions(+), 23 deletions(-)
Title: Finding Files in Project Subdirectories
Description: Robust, reliable and flexible paths to files below a
project root. The 'root' of a project is defined as a directory
that matches a certain criterion, e.g., it contains a certain
regular file.
Author: Kirill Müller [aut, cre]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between rprojroot versions 1.0-2 dated 2016-03-28 and 1.1 dated 2016-10-29
DESCRIPTION | 15 +- MD5 | 42 +++-- NAMESPACE | 8 + NEWS.md | 27 +++ R/criterion.R | 56 +++++++ R/file.R | 15 -- R/has-file.R | 57 +++++++ R/root.R | 16 +- R/rprojroot-package.R |only R/shortcut.R | 8 + build/vignette.rds |binary inst/doc/rprojroot.R | 49 ++++-- inst/doc/rprojroot.Rmd | 158 ++++++++++++++++----- inst/doc/rprojroot.html | 300 +++++++++++++++++++++++++--------------- man/criteria.Rd | 18 ++ man/find_root_file.Rd | 21 +- man/root_criterion.Rd | 42 +++++ man/rprojroot-package.Rd |only tests/testthat/package |only tests/testthat/test-criterion.R | 13 + tests/testthat/test-root.R | 34 ++++ tests/testthat/test-testthat.R |only vignettes/rprojroot.Rmd | 46 +++++- 23 files changed, 705 insertions(+), 220 deletions(-)
Title: Build Panel Data Sets from PSID Raw Data
Description: Makes it easy to build panel data in wide format from Panel Survey
of Income Dynamics (PSID) delivered raw data. Deals with data downloaded and
pre-processed by 'Stata' or 'SAS', or can optionally download directly from
the PSID server using the 'SAScii' package. 'psidR' takes care of merging
data from each wave onto a cross-period index file, so that individuals can be
followed over time. The user must specify which years they are interested in,
and the PSID variable names (e.g. ER21003) for each year (they differ in each
year). There are different panel data designs and sample subsetting criteria
implemented ("SRC", "SEO", "immigrant" and "latino" samples).
Author: Florian Oswald
Maintainer: Florian Oswald <florian.oswald@gmail.com>
Diff between psidR versions 1.3 dated 2015-05-15 and 1.4 dated 2016-10-29
psidR-1.3/psidR/inst/example-calls.r |only psidR-1.3/psidR/tests/testthat/test_psidR.R |only psidR-1.4/psidR/DESCRIPTION | 27 +- psidR-1.4/psidR/MD5 | 32 +- psidR-1.4/psidR/NAMESPACE | 5 psidR-1.4/psidR/NEWS | 14 - psidR-1.4/psidR/R/build.panel.r | 301 +++++++++++++++-------- psidR-1.4/psidR/R/makeids.r | 34 +- psidR-1.4/psidR/inst/examples |only psidR-1.4/psidR/inst/psid-lists |only psidR-1.4/psidR/man/build.panel.Rd | 99 +++---- psidR-1.4/psidR/man/build.psid.Rd |only psidR-1.4/psidR/man/get.psid.Rd | 2 psidR-1.4/psidR/man/make.char.Rd | 2 psidR-1.4/psidR/man/makeids.Rd | 2 psidR-1.4/psidR/man/psidR.Rd | 4 psidR-1.4/psidR/man/testPSID.Rd | 2 psidR-1.4/psidR/tests/testthat/test_buildpanel.R |only psidR-1.4/psidR/tests/testthat/test_testPSID.R |only 19 files changed, 324 insertions(+), 200 deletions(-)
Title: Quantitative Fatty Acid Signature Analysis
Description: Accurate estimates of the diets of predators are required
in many areas of ecology, but for many species current methods are
imprecise, limited to the last meal, and often biased. The diversity
of fatty acids and their patterns in organisms, coupled with the
narrow limitations on their biosynthesis, properties of digestion in
monogastric animals, and the prevalence of large storage reservoirs of
lipid in many predators, led us to propose the use of quantitative
fatty acid signature analysis (QFASA) to study predator diets.
Author: Sara Iverson [aut],
Chris Field [aut],
Don Bowen [aut],
Wade Blanchard [aut],
Connie Stewart [aut, cph],
Shelley Lang [aut],
Justin Kamerman [cre, cph]
Maintainer: Justin Kamerman <justin.kamerman@unb.ca>
Diff between QFASA versions 1.0.1 dated 2016-06-15 and 1.0.2 dated 2016-10-29
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++----- NEWS.md | 4 ++++ R/qfasa.R | 5 +++++ README.md | 12 ++++++++---- inst/doc/ModelingWorkflow.html | 4 ++-- tests/testthat/testMatrixDimensions.R |only 7 files changed, 31 insertions(+), 17 deletions(-)
Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre],
Joel Gombin [ctb],
Sebastian Jeworutzki [ctb],
Kent Russell [ctb],
Richard Zijdeman [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap versions 1.6 dated 2016-10-21 and 1.6-1 dated 2016-10-29
DESCRIPTION | 12 +- MD5 | 93 ++++++++++++-------- NEWS | 6 + R/append_data.R | 18 --- R/bb.R | 82 ++++++++--------- R/end_of_the_world.R | 37 +++----- R/geocode_OSM.R | 51 ++++++----- R/get_proj4_code.R | 91 ++++++++++++------- R/gridplot.R | 4 R/lines_midpoints.R | 2 R/map_coloring.R | 6 - R/plot_all.R | 5 - R/plot_map.R | 6 - R/plot_misc_functions.R | 6 - R/preprocess_shapes.R | 46 +++++---- R/print_tmap.R | 12 +- R/process_meta.R | 2 R/process_shapes.R | 10 +- R/qtm.R | 2 R/read_osm.R | 2 R/set_projection.R | 88 ++++++++++--------- R/tm_shape.R | 2 inst/doc/tmap-modes.Rmd | 6 - inst/doc/tmap-modes.html | 151 +++++++------------------------- inst/doc/tmap-nutshell.Rmd | 6 - inst/doc/tmap-nutshell.html | 194 ++++++++++++------------------------------ man/append_data.Rd | 13 ++ man/bb.Rd | 8 + man/geocode_OSM.Rd | 4 man/get_proj4.Rd | 10 +- man/map_coloring.Rd | 5 - man/qtm.Rd | 2 man/rev_geocode_OSM.Rd | 4 man/set_projection.Rd | 21 +--- man/tm_facets.Rd | 1 man/tm_shape.Rd | 2 vignettes/tmap-modes.Rmd | 6 - vignettes/tmap-modes_files |only vignettes/tmap-nutshell.Rmd | 6 - vignettes/tmap-nutshell_files |only 40 files changed, 445 insertions(+), 577 deletions(-)
Title: Fit Mixtures of Archetype Species
Description: Fitting Mixtures to Species distributions using BFGS and analytical derivatives.
Author: Piers K Dunstan, Scott D Foster and Ross Darnell
Maintainer: Piers Dunstan <Piers.Dunstan@csiro.au>
Diff between SpeciesMix versions 0.3.1 dated 2013-10-02 and 0.3.4 dated 2016-10-29
DESCRIPTION | 11 +- MD5 | 6 - R/SpeciesMix.R | 248 +-------------------------------------------------------- src/Tweedie.h | 11 +- 4 files changed, 21 insertions(+), 255 deletions(-)
Title: Parser Combinator for R
Description: Parser generator for R using combinatory parsers. It
is inspired by combinatory parsers developed in Haskell.
Author: Chapman Siu
Maintainer: Chapman Siu <chpmn.siu@gmail.com>
Diff between Ramble versions 0.1.0 dated 2016-05-21 and 0.1.1 dated 2016-10-29
DESCRIPTION | 10 MD5 | 63 +-- NAMESPACE | 3 R/parser.R | 337 ++++++++++++++---- R/utils.R | 26 - build/vignette.rds |binary inst/doc/Higher-Order_Functions_for_Parsing_in_R.Rmd | 2 inst/doc/Higher-Order_Functions_for_Parsing_in_R.html | 146 ++++--- man/Alpha.Rd | 7 man/AlphaNum.Rd | 7 man/Digit.Rd | 7 man/Lower.Rd | 7 man/SpaceCheck.Rd | 7 man/String.Rd | 11 man/Unlist.Rd | 8 man/Upper.Rd | 7 man/alt.Rd | 13 man/grapes-thentree-grapes.Rd |only man/ident.Rd | 7 man/identifier.Rd | 7 man/many.Rd | 5 man/maybe.Rd |only man/nat.Rd | 7 man/natural.Rd | 7 man/some.Rd | 5 man/space.Rd | 7 man/symbol.Rd | 7 man/then.Rd | 14 man/thentree.Rd |only man/token.Rd | 7 man/using.Rd | 13 tests/testthat/test_functions.R | 98 ++++- tests/testthat/test_functions2.R |only tests/testthat/test_repetition.R |only vignettes/Higher-Order_Functions_for_Parsing_in_R.Rmd | 2 35 files changed, 629 insertions(+), 218 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: The qgraph package can be used to visualize data as networks as well as provides an interface for visualizing weighted graphical models.
Author: Sacha Epskamp, Giulio Costantini, Jonas Haslbeck, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.3.5 dated 2016-08-31 and 1.4.0 dated 2016-10-29
DESCRIPTION | 8 - MD5 | 17 +-- NAMESPACE | 2 NEWS | 11 ++ R/PLOT.R | 46 +++++++-- R/drawNode.R | 148 ++++++++++++++++++++++++++++- R/pathways.R |only R/pie2.R |only R/qgraph.R | 283 +++++++++++++++++++++++++++++++++++++++++++++++--------- man/pathways.Rd |only man/qgraph.Rd | 25 ++++ 11 files changed, 475 insertions(+), 65 deletions(-)
Title: Offers Various Swiss Maps as Data Frames and 'ggplot2' Objects
Description: Offers various swiss maps as data frames and 'ggplot2' objects and gives the
possibility to add layers of data on the maps. Data are publicly available
from the swiss federal statistical office.
Author: Sandro Petrillo Burri [aut, cre],
Eric Stephani [aut],
Lisa Bottinelli [ctb]
Maintainer: Sandro Petrillo Burri <gibo.gaf@gmail.com>
Diff between ggswissmaps versions 0.0.9 dated 2016-09-19 and 0.1.1 dated 2016-10-29
ggswissmaps-0.0.9/ggswissmaps/man/theme_white.Rd |only ggswissmaps-0.1.1/ggswissmaps/DESCRIPTION | 12 + ggswissmaps-0.1.1/ggswissmaps/MD5 | 32 ++-- ggswissmaps-0.1.1/ggswissmaps/NEWS | 69 +++++++--- ggswissmaps-0.1.1/ggswissmaps/R/ggswissmaps_00funs.R | 20 -- ggswissmaps-0.1.1/ggswissmaps/R/ggswissmaps_data.R | 62 +++----- ggswissmaps-0.1.1/ggswissmaps/R/zzz.R |only ggswissmaps-0.1.1/ggswissmaps/README.md | 3 ggswissmaps-0.1.1/ggswissmaps/data/shp_df.rda |binary ggswissmaps-0.1.1/ggswissmaps/inst/doc/ggswissmaps_intro.R | 15 -- ggswissmaps-0.1.1/ggswissmaps/inst/doc/ggswissmaps_intro.Rmd | 43 ------ ggswissmaps-0.1.1/ggswissmaps/inst/doc/ggswissmaps_intro.html | 47 +----- ggswissmaps-0.1.1/ggswissmaps/man/ggswissmaps.Rd | 15 +- ggswissmaps-0.1.1/ggswissmaps/man/maps2.Rd | 13 + ggswissmaps-0.1.1/ggswissmaps/man/maps2_.Rd | 6 ggswissmaps-0.1.1/ggswissmaps/man/shp_df.Rd | 9 - ggswissmaps-0.1.1/ggswissmaps/man/theme_white_f.Rd | 8 - ggswissmaps-0.1.1/ggswissmaps/vignettes/ggswissmaps_intro.Rmd | 43 ------ 18 files changed, 163 insertions(+), 234 deletions(-)
Title: Estimation of the Conditional Survival Function for Ordered
Multivariate Failure Time Data
Description: Method to implement some newly developed methods for the
estimation of the conditional survival function.
Author: Luis Meira-Machado and Marta Sestelo
Maintainer: Luis Meira-Machado <lmachado@math.uminho.pt>
Diff between condSURV versions 0.1.0 dated 2016-05-25 and 1.0.0 dated 2016-10-29
condSURV-0.1.0/condSURV/man/survKMW.Rd |only condSURV-0.1.0/condSURV/man/survLDM.Rd |only condSURV-0.1.0/condSURV/man/survPLDM.Rd |only condSURV-1.0.0/condSURV/DESCRIPTION | 12 condSURV-1.0.0/condSURV/MD5 | 41 - condSURV-1.0.0/condSURV/NAMESPACE | 5 condSURV-1.0.0/condSURV/NEWS |only condSURV-1.0.0/condSURV/R/Beran.R | 5 condSURV-1.0.0/condSURV/R/survCOND.R |only condSURV-1.0.0/condSURV/R/survCS.R | 61 +- condSURV-1.0.0/condSURV/R/survIPCW.R | 638 +++++++++++++++++------- condSURV-1.0.0/condSURV/R/survKMW.R | 220 ++++++-- condSURV-1.0.0/condSURV/R/survLDM.R | 58 +- condSURV-1.0.0/condSURV/R/survPLDM.R | 67 +- condSURV-1.0.0/condSURV/R/whichCS.R |only condSURV-1.0.0/condSURV/build/partial.rdb |binary condSURV-1.0.0/condSURV/data/bladderCS.rda |only condSURV-1.0.0/condSURV/man/KM.Rd | 5 condSURV-1.0.0/condSURV/man/KMW.Rd | 14 condSURV-1.0.0/condSURV/man/bladderCS.Rd |only condSURV-1.0.0/condSURV/man/condSURV-package.Rd | 15 condSURV-1.0.0/condSURV/man/gbcsCS.Rd | 2 condSURV-1.0.0/condSURV/man/plot.surv.Rd | 2 condSURV-1.0.0/condSURV/man/survCOND.Rd |only condSURV-1.0.0/condSURV/man/survCS.Rd | 56 +- condSURV-1.0.0/condSURV/man/survIPCW.Rd | 20 26 files changed, 879 insertions(+), 342 deletions(-)
Title: R Interface to a 'PostGIS' Database
Description: Provides additional functions to the
'RPostgreSQL' package to interface R with a 'PostGIS'-enabled
database, as well as convenient wrappers to common 'PostgreSQL'
queries.
Author: Mathieu Basille [aut],
David Bucklin [aut, cre]
Maintainer: David Bucklin <dbucklin@ufl.edu>
Diff between rpostgis versions 1.0.2 dated 2016-09-26 and 1.0.3 dated 2016-10-28
DESCRIPTION | 8 ++-- MD5 | 55 +++++++++++++++++--------------- NAMESPACE | 1 NEWS | 8 ++++ R/dbAddKey.R | 4 +- R/dbAsDate.R | 1 R/dbColumn.R | 4 +- R/dbComment.R | 8 ++-- R/dbDrop.R | 8 ++-- R/dbIndex.R | 4 +- R/dbSchema.R | 1 R/dbTableInfo.R | 1 R/dbUtils.R | 79 +++++++++++++++++++++++++++++++++++++++++++++-- R/dbVacuum.R | 4 +- R/pgGetBoundary.R | 1 R/pgGetGeom.R | 1 R/pgGetRast.R | 1 R/pgInsert.R | 3 + R/pgInsertize.R | 6 +-- R/pgListGeom.R | 1 R/pgMakePts.R | 2 + R/pgPostGIS.R | 1 R/pgSRID.R | 1 README.md | 2 - man/dbBuildTableQuery.Rd |only man/dbComment.Rd | 4 +- man/dbConnCheck.Rd |only man/dbDrop.Rd | 4 +- man/dbExistsTable.Rd |only man/dbTableNameFix.Rd | 4 +- 30 files changed, 162 insertions(+), 55 deletions(-)
Title: R API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export, Engage and JQL API. The R functions allow for event and profile data export as well as for segmentation, retention, funnel and addiction analysis. Results are always parsed into convenient R objects. Furthermore it is possible to load and update profiles.
Author: Meinhard Ploner [aut, cre, cph],
ProSiebenSat.1 Digital GmbH [cph]
Maintainer: Meinhard Ploner <meinhard.ploner@gmail.com>
Diff between RMixpanel versions 0.4-1 dated 2016-09-21 and 0.5-0 dated 2016-10-28
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++++----- NAMESPACE | 2 ++ R/mixpanelGetFunnel.R |only R/mixpanelGetFunnelList.R |only R/mixpanelGetRetention.R | 2 +- README.md | 10 ++++++---- build/partial.rdb |binary man/mixpanelGetFunnel.Rd |only man/mixpanelGetFunnelList.Rd |only 10 files changed, 25 insertions(+), 17 deletions(-)
Title: Prototype Object-Based Programming
Description: An object oriented system using object-based, also
called prototype-based, rather than class-based object oriented ideas.
Author: Hadley Wickham [cre],
Gabor Grothendieck [aut],
Louis Kates [aut],
Thomas Petzoldt [aut]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between proto versions 0.3-10 dated 2012-12-22 and 1.0.0 dated 2016-10-28
proto-0.3-10/proto/COPYRIGHTS |only proto-0.3-10/proto/README.debian |only proto-0.3-10/proto/demo/proto.R |only proto-0.3-10/proto/inst/NEWS |only proto-0.3-10/proto/inst/README |only proto-0.3-10/proto/man/graph.proto.Rd |only proto-0.3-10/proto/vignettes/README |only proto-0.3-10/proto/vignettes/Z.cls |only proto-0.3-10/proto/vignettes/cloning3.dot |only proto-0.3-10/proto/vignettes/proto-raw |only proto-0.3-10/proto/vignettes/proto-raw.tex |only proto-1.0.0/proto/DESCRIPTION | 33 proto-1.0.0/proto/MD5 | 62 proto-1.0.0/proto/NAMESPACE | 14 proto-1.0.0/proto/NEWS.md |only proto-1.0.0/proto/R/graph.proto.R | 76 - proto-1.0.0/proto/R/proto.R | 467 +++++-- proto-1.0.0/proto/README.md |only proto-1.0.0/proto/build |only proto-1.0.0/proto/demo/00Index | 4 proto-1.0.0/proto/demo/proto-gWidgets.R |only proto-1.0.0/proto/demo/proto-vignette.R | 396 +++--- proto-1.0.0/proto/inst/ReleaseNotes.txt |only proto-1.0.0/proto/inst/THANKS | 2 proto-1.0.0/proto/inst/doc/proto.Rnw | 1380 +++++++++++++++++++++- proto-1.0.0/proto/inst/doc/proto.pdf |binary proto-1.0.0/proto/inst/doc/protoref.Rnw | 53 proto-1.0.0/proto/inst/doc/protoref.pdf |binary proto-1.0.0/proto/man/proto-package.Rd | 88 - proto-1.0.0/proto/man/proto.Rd | 542 ++++---- proto-1.0.0/proto/tests |only proto-1.0.0/proto/vignettes/proto-concordance.tex |only proto-1.0.0/proto/vignettes/proto-dot.pdf |binary proto-1.0.0/proto/vignettes/proto-smoothing03.pdf |binary proto-1.0.0/proto/vignettes/proto-smoothing04.pdf |binary proto-1.0.0/proto/vignettes/proto-smoothing06.pdf |binary proto-1.0.0/proto/vignettes/proto-smoothing10.pdf |binary proto-1.0.0/proto/vignettes/proto.Rnw | 1380 +++++++++++++++++++++- proto-1.0.0/proto/vignettes/proto.tex | 1380 +++++++++++++++++++++- proto-1.0.0/proto/vignettes/protoref.Rnw | 53 40 files changed, 5094 insertions(+), 836 deletions(-)
Title: Statistical Comparison of Two Networks Based on Three Invariance
Measures
Description: This permutation based hypothesis test, suited for Gaussian and
binary data, assesses the difference between two networks based on several
invariance measures (network structure invariance, global strength invariance,
edge invariance). Network structures are estimated with l1-regularized partial
correlations (Gaussian data) or with l1-regularized logistic regression (eLasso,
binary data). Suited for comparison of independent and dependent samples
(currently, only for one group measured twice).
Author: Claudia D. van Borkulo, with contributions from Sacha Epskamp and Alex Millner
Maintainer: Claudia van Borkulo <cvborkulo@gmail.com>
Diff between NetworkComparisonTest versions 2.0.0 dated 2016-09-06 and 2.0.1 dated 2016-10-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/NCT.R | 5 ++++- man/networkcomparisontest-package.Rd | 4 ++-- man/networkcomparisontest.rd | 8 ++++---- 5 files changed, 18 insertions(+), 15 deletions(-)
More information about NetworkComparisonTest at CRAN
Permanent link
Title: Tools for Units of Measurement
Description: Collection of tools to make working with physical measurements
easier. Convert between metric and imperial units, or calculate a dimension's
unknown value from other dimensions' measurements.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between measurements versions 1.0.0 dated 2016-07-26 and 1.1.0 dated 2016-10-28
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- NAMESPACE | 1 + NEWS | 4 ++++ R/conv_multiunit.R |only man/conv_multiunit.Rd |only 6 files changed, 14 insertions(+), 7 deletions(-)
Title: Simulation-Based Bayesian Inference for Latent Traits of Item
Response Models
Description: Functions for simulating realizations from the posterior distribution of
a latent trait of an item response model. Distributions are conditional on one or
a subset of response patterns (e.g., sum scores). Functions for computing likelihoods,
Fisher and observed information, posterior modes, and profile likelihood confidence
intervals are also included. These functions are designed to be easily amenable to
user-specified models.
Author: Timothy R. Johnson
Maintainer: Timothy R. Johnson <trjohns@uidaho.edu>
Diff between ltbayes versions 0.3 dated 2014-07-28 and 0.4 dated 2016-10-28
DESCRIPTION | 12 MD5 | 22 - NAMESPACE | 15 build/vignette.rds |binary inst/doc/custom-models.R | 6 inst/doc/custom-models.Rmd | 4 inst/doc/custom-models.html | 78 ++- inst/doc/example-plots.R | 4 inst/doc/example-plots.Rmd | 884 ++++++++++++++++++++++---------------------- inst/doc/example-plots.html | 83 ++-- vignettes/custom-models.Rmd | 4 vignettes/example-plots.Rmd | 884 ++++++++++++++++++++++---------------------- 12 files changed, 1013 insertions(+), 983 deletions(-)
Title: Item Response Models for Multiple Ratings
Description:
Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program.
Author:
Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between immer versions 0.5-0 dated 2016-05-31 and 0.6-0 dated 2016-10-28
DESCRIPTION | 11 - MD5 | 122 ++++++++-------- R/IRT.likelihood.immer_HRM.R | 20 +- R/MHprop_hrm.R | 25 +-- R/MHprop_refresh.R | 68 ++++----- R/agree_aicken.R | 14 - R/anova_immer.R | 35 ++-- R/immer_HRM.R | 148 +++++++++---------- R/immer_agree2.R | 75 ++++------ R/immer_cml.R | 88 +++++------ R/immer_collect_traces.R | 92 ++++++------ R/immer_ic_calc.R | 10 - R/immer_ic_hrm.R | 17 +- R/immer_identifiers_relabel.R | 54 +++---- R/immer_mcmc_draw_variance.R | 4 R/immer_opcat.R | 28 +-- R/immer_reshape_wideformat.R | 50 +++--- R/immer_unique_patterns.R | 33 ++-- R/inits_item_parameters.R | 26 +-- R/inits_raterpars_hrm.R | 12 - R/inits_theta_1dim.R | 18 +- R/lc2_agreement.R | 208 +++++++++++++-------------- R/logLik.lc2_agreement.R | 8 - R/logLik_immer.R | 16 +- R/loglik_HRM.R | 52 +++--- R/lpcm_data_prep.R | 94 ++++++------ R/lpcm_generate_design.R | 125 ++++++++-------- R/lpcm_inits.R | 26 +-- R/plot.immer_HRM.R | 4 R/prior_hrm.R | 45 ++---- R/probs2logits.R | 30 ++-- R/probs_gpcm.R | 43 ++--- R/probs_hrm.R | 35 ++-- R/rtrnorm.R | 2 R/sampling_hrm_a.R | 34 ++-- R/sampling_hrm_b.R | 28 +-- R/sampling_hrm_mu_theta_1dim.R | 8 - R/sampling_hrm_phi.R | 104 +++++++------ R/sampling_hrm_psi.R | 32 ++-- R/sampling_hrm_theta_1dim.R | 21 +- R/sampling_hrm_xi.R | 58 +++---- R/simulate_hrm.R | 56 +++---- R/zzz.R | 8 - data/data.immer01a.rda |binary data/data.immer01b.rda |binary data/data.immer02.rda |binary data/data.immer03.rda |binary data/data.immer04a.rda |binary data/data.immer04b.rda |binary data/data.immer05.rda |binary data/data.immer06.rda |binary data/data.immer07.rda |binary data/data.immer08.rda |binary data/data.immer09.rda |binary data/data.immer10.rda |binary inst/NEWS | 17 ++ man/data.immer.Rd | 19 ++ man/immer-package.Rd | 2 man/immer_agree2.Rd | 14 + man/lc2_agreement.Rd | 2 src/HRM_aux_rcpp_functions.cpp | 306 ++++++++++++++++------------------------- src/subimmer.h | 244 ++++++++++++++------------------ 62 files changed, 1266 insertions(+), 1325 deletions(-)
Title: R Interface for International Monetary Fund(IMF) Data API
Description: Search, extract and formulate IMF's datasets.
Author: Ming-Jer Lee [aut, cre]
Maintainer: Ming-Jer Lee <mingjerli@gmail.com>
Diff between IMFData versions 0.1.0 dated 2016-08-16 and 0.2.0 dated 2016-10-28
DESCRIPTION | 10 - MD5 | 8 R/IMFData.R | 34 +++ README.md | 442 +++++++++++++++++++++++++++++++++++++++++++++-- man/CompactDataMethod.Rd | 14 + 5 files changed, 479 insertions(+), 29 deletions(-)
Title: Models for Health Economic Evaluation
Description: Health Economic Evaluation Modelling.
Markov models (decision trees, homogeneous and non-homogeneous)
for health economic evaluation. Model comparison,
sensitivity and probabilistic analysis.
Author: Antoine Filipovic-Pierucci [aut, cre],
Kevin Zarca [aut],
Matthew Wiener [ctb],
Zdenek Kabat [ctb],
Vojtech Filipec [ctb]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>
Diff between heemod versions 0.5.0 dated 2016-10-17 and 0.5.1 dated 2016-10-28
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS.md | 6 + inst/doc/a-introduction.html | 4 - inst/doc/b-time-dependency.html | 4 - inst/doc/c-homogeneous.html | 4 - inst/doc/d-non-homogeneous.html | 4 - inst/doc/e-probabilistic.html | 10 +- inst/doc/f-sensitivity.html | 4 - inst/doc/g-heterogeneity.html | 140 ++++++++++++++++++++-------------------- inst/doc/h-tabular.html | 6 - inst/doc/i-reproduction.html | 4 - 12 files changed, 111 insertions(+), 105 deletions(-)
Title: Drat R Archive Template
Description: Creation and use of R Repositories via helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel with contributions by Carl Boettiger, Sebastian
Gibb, Colin Gillespie, Jan Górecki, Matt Jones, Thomas Leeper, Steven Pav
and Jan Schulz.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between drat versions 0.1.1 dated 2016-08-07 and 0.1.2 dated 2016-10-28
ChangeLog | 27 ++++++++++++++++++++++++ DESCRIPTION | 10 ++++----- MD5 | 22 ++++++++++---------- R/pruneRepo.R | 26 ++++++++++++++---------- README.md | 39 +++++++++++++++++++++--------------- inst/NEWS.Rd | 11 ++++++++++ inst/doc/DratFAQ.Rmd | 25 +++++++++++++++++++---- inst/doc/DratFAQ.html | 15 +++++++++---- inst/doc/DratForPackageAuthors.Rmd | 2 - inst/doc/DratForPackageAuthors.html | 2 - vignettes/DratFAQ.Rmd | 25 +++++++++++++++++++---- vignettes/DratForPackageAuthors.Rmd | 2 - 12 files changed, 148 insertions(+), 58 deletions(-)
Title: ACE and AVAS for Selecting Multiple Regression Transformations
Description: Two nonparametric methods for multiple regression transform selection are provided.
The first, Alternative Conditional Expectations (ACE),
is an algorithm to find the fixed point of maximal
correlation, i.e. it finds a set of transformed response variables that maximizes R^2
using smoothing functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal Transformations
for Multiple Regression and Correlation". Journal of the American Statistical Association.
80:580-598. <doi:10.1080/01621459.1985.10478157>].
Also included is the Additivity Variance Stabilization (AVAS) method which works better than ACE when
correlation is low [see Tibshirani, R.. 1986. "Estimating Transformations for Regression via Additivity
and Variance Stabilization". Journal of the American Statistical Association. 83:394-405.
<doi:10.1080/01621459.1988.10478610>]. A good introduction to these two methods is in chapter 16 of
Frank Harrel's "Regression Modeling Strategies" in the Springer Series in Statistics.
Author: Phil Spector, Jerome Friedman, Robert Tibshirani, Thomas Lumley, Shawn Garbett, Jonathan Baron
Maintainer: Shawn Garbett <shawn.garbett@vanderbilt.edu>
Diff between acepack versions 1.4.0 dated 2016-10-20 and 1.4.1 dated 2016-10-28
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NEWS | 4 ++++ src/ace.f | 24 +++++++++++++++++------- src/avas.f | 52 +++++++++++++++++++++++++++++++++++++++++----------- src/rlsmo.f | 6 ++++++ 6 files changed, 78 insertions(+), 27 deletions(-)
Title: Shape Selection for Landsat Time Series of Forest Dynamics
Description: Landsat satellites collect important data about global forest conditions. Documentation about Landsat's role in forest disturbance estimation is available at the site <http://landsat.gsfc.nasa.gov/?p=9513>. By constrained quadratic B-splines, this package delivers an optimal shape-restricted trajectory to a time series of Landsat imagery for the purpose of modeling annual forest disturbance dynamics to behave in an ecologically sensible manner assuming one of seven possible "shapes", namely, flat, decreasing, one-jump (decreasing, jump up, decreasing), inverted vee (increasing then decreasing), vee (decreasing then increasing), linear increasing, and double-jump (decreasing, jump up, decreasing, jump up, decreasing). The main routine selects the best shape according to the minimum Bayes information criterion (BIC) or the cone information criterion (CIC), which is defined as the log of the estimated predictive squared error. The package also provides parameters summarizing the temporal pattern including year(s) of inflection, magnitude of change, pre- and post-inflection rates of growth or recovery. In addition, it contains routines for converting a flat map of disturbance agents to time-series disturbance maps and a graphical routine displaying the fitted trajectory of Landsat imagery.
Author: Mary C. Meyer, Xiyue Liao, Elizabeth Freeman, Gretchen G. Moisen
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between ShapeSelectForest versions 1.2 dated 2015-12-25 and 1.3 dated 2016-10-28
ChangeLog |only DESCRIPTION | 12 +++++--- MD5 | 10 ++++--- R/shape.R | 80 +++++++++++++++++++++++++++++++++++++++++++++++++-------- inst/CITATION |only man/getedf0.Rd | 4 +- man/shape.Rd | 5 ++- 7 files changed, 88 insertions(+), 23 deletions(-)
More information about ShapeSelectForest at CRAN
Permanent link
Title: Compare Detrital Zircon Suites
Description: Compare detrital zircon suites by uploading univariate,
U-Pb age, or bivariate, U-Pb age and Lu-Hf data, in a 'shiny'-based
user-interface. Outputs publication quality figures using 'ggplot2', and
tables of statistics currently in use in the detrital zircon geochronology
community.
Author: Magnus Kristoffersen [aut, cre]
Maintainer: Magnus Kristoffersen <magnus.kristoffersen@geo.uio.no>
Diff between detzrcr versions 0.1.1 dated 2016-08-23 and 0.1.2 dated 2016-10-28
DESCRIPTION | 10 MD5 | 36 ++- NAMESPACE | 7 NEWS.md | 10 R/calculations.R | 228 ++++++++++++++++------ R/plotting.R | 104 ++++++++-- README.md | 2 inst/CITATION |only inst/shiny-apps/detzrcr_app/app.R | 392 +++++++++++++++++++++++++++++--------- man/calc_o_param.Rd | 2 man/check_conc.Rd | 6 man/combine_matrices.Rd |only man/make_tiling.Rd |only man/o_param_matrix_age.Rd | 2 man/o_param_matrix_tdm.Rd | 2 man/plot_axis_lim.Rd | 4 man/plot_dens.Rd | 4 man/plot_dens_hist.Rd | 4 man/plot_point_scale.Rd |only man/plot_text_options.Rd |only man/plot_tile.Rd |only man/tile_func.Rd |only man/tiling.Rd |only 23 files changed, 625 insertions(+), 188 deletions(-)
Title: Beyond the Border
Description: Kernel density estimation dedicated to urban geography.
Author: Psar Analyse Urbaine Insee - Thierry Cornely, Laure Genebes, Arlindo Dos
Santos, Cynthia Faivre, Auriane Renaud and Francois Semecurbe
Maintainer: Arlindo Dos Santos <Arlindo.Dos-Santos@insee.fr>
Diff between btb versions 0.1.2 dated 2016-10-26 and 0.1.3 dated 2016-10-28
DESCRIPTION | 8 +- MD5 | 6 - src/rcppLissage.cpp | 20 +++-- src/rcppLissageMedian.cpp | 154 +++------------------------------------------- 4 files changed, 32 insertions(+), 156 deletions(-)
Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random
Forest. The Weighted Subspace Random Forest algorithm was
proposed in the International Journal of Data Warehousing and
Mining by Baoxun Xu, Joshua Zhexue Huang, Graham Williams, Qiang
Wang, and Yunming Ye (2012) <DOI:10.4018/jdwm.2012040103>. The
algorithm can classify very high-dimensional data with random
forests built using small subspaces. A novel variable weighting
method is used for variable subspace selection in place of the
traditional random variable sampling.This new approach is
particularly useful in building models from high-dimensional data.
Author: Qinghan Meng [aut],
He Zhao [aut, cre],
Graham Williams [aut],
Junchao Lv [ctb],
Baoxun Xu [aut]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wsrf versions 1.6.25 dated 2016-09-10 and 1.7.0 dated 2016-10-28
DESCRIPTION | 8 +- MD5 | 48 ++++++------ R/predict.wsrf.R | 94 +++++++++++++++--------- R/print.wsrf.R | 6 - R/wsrf.default.R | 24 +++--- README.md | 14 +-- inst/NEWS.Rd | 35 ++++++++- inst/doc/wsrf-guide.R | 6 - inst/doc/wsrf-guide.Rmd | 10 +- inst/doc/wsrf-guide.html | 34 ++++---- man/combine.wsrf.Rd | 4 - man/predict.wsrf.Rd | 20 +++-- man/subset.wsrf.Rd | 4 - man/wsrf.Rd | 13 ++- src/dataset.cpp | 6 + src/meta_data.cpp | 2 src/rforest.cpp | 180 +++++++++++++++++++++++++++++++++-------------- src/rforest.h | 56 -------------- src/utility.h | 19 ++++ src/wsrf.cpp | 20 +---- src/wsrf.h | 2 tests/wsrftest.R | 8 +- tests/wsrftest.Rout.save | 8 +- vignettes/wsrf-guide.Rmd | 10 +- vignettes/wsrf-guide.bib | 2 25 files changed, 367 insertions(+), 266 deletions(-)
Title: Class-Focused Pattern Metric Comparisons using Simulation
Description: Provides tools for estimating composition and configuration parameters from a categorical (binary) landscape map (grid) and then simulates a selected number of statistically similar landscapes. Class-focused pattern metrics are computed for each simulated map to produce empirical distributions against which statistical comparisons can be made. The code permits the analysis of single maps or pairs of maps.
Author: Tarmo K. Remmel, (Marie-Josee Fortin, Ferenc Csillag, Sandor Kabos)
Maintainer: Tarmo K. Remmel <remmelt@yorku.ca>
Diff between PatternClass versions 1.5 dated 2013-07-23 and 1.7.1 dated 2016-10-28
PatternClass-1.5/PatternClass/data/ClassPatternData.rda |only PatternClass-1.5/PatternClass/man/ClassPatternData.Rd |only PatternClass-1.7.1/PatternClass/DESCRIPTION | 12 +- PatternClass-1.7.1/PatternClass/MD5 | 52 ++++++------ PatternClass-1.7.1/PatternClass/NAMESPACE | 7 + PatternClass-1.7.1/PatternClass/R/build.lut.R | 16 +-- PatternClass-1.7.1/PatternClass/R/buildsurfs.R | 2 PatternClass-1.7.1/PatternClass/R/doubleplotter.R | 2 PatternClass-1.7.1/PatternClass/R/findcol.R | 21 ++-- PatternClass-1.7.1/PatternClass/R/findrow.R | 20 ++-- PatternClass-1.7.1/PatternClass/R/imaks.R | 18 ++-- PatternClass-1.7.1/PatternClass/R/singlemap.R | 32 +++---- PatternClass-1.7.1/PatternClass/R/singleplotter.R | 49 ++++++----- PatternClass-1.7.1/PatternClass/R/surfplot.R | 21 ++-- PatternClass-1.7.1/PatternClass/R/wi.R | 26 +----- PatternClass-1.7.1/PatternClass/R/wtest.run.R | 30 +++--- PatternClass-1.7.1/PatternClass/data/WhittleData.rda |only PatternClass-1.7.1/PatternClass/data/data.rda |only PatternClass-1.7.1/PatternClass/man/PatternClass-package.Rd | 8 - PatternClass-1.7.1/PatternClass/man/WhittleData.Rd |only PatternClass-1.7.1/PatternClass/man/build.lut.Rd | 12 +- PatternClass-1.7.1/PatternClass/man/buildsurfs.Rd | 4 PatternClass-1.7.1/PatternClass/man/data.Rd |only PatternClass-1.7.1/PatternClass/man/doubleplotter.Rd | 14 +-- PatternClass-1.7.1/PatternClass/man/findcol.Rd |only PatternClass-1.7.1/PatternClass/man/findrow.Rd |only PatternClass-1.7.1/PatternClass/man/imaks.Rd | 4 PatternClass-1.7.1/PatternClass/man/singlemap.Rd | 14 ++- PatternClass-1.7.1/PatternClass/man/singleplotter.Rd | 12 +- PatternClass-1.7.1/PatternClass/man/surfplot.Rd | 6 - PatternClass-1.7.1/PatternClass/man/wi.Rd |only PatternClass-1.7.1/PatternClass/man/wtest.run.Rd |only 32 files changed, 203 insertions(+), 179 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers.
Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures
can either be created and verified manually or via x509 certificates. AES can be
used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public
key) encryption or EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.9.4 dated 2016-05-25 and 0.9.5 dated 2016-10-28
openssl-0.9.4/openssl/inst/testkey.pem |only openssl-0.9.4/openssl/src/read.c |only openssl-0.9.5/openssl/DESCRIPTION | 12 openssl-0.9.5/openssl/MD5 | 138 +++++----- openssl-0.9.5/openssl/NAMESPACE | 38 ++ openssl-0.9.5/openssl/NEWS | 12 openssl-0.9.5/openssl/R/aes.R | 2 openssl-0.9.5/openssl/R/base.R |only openssl-0.9.5/openssl/R/cert.R | 4 openssl-0.9.5/openssl/R/envelope.R | 2 openssl-0.9.5/openssl/R/hash.R | 18 - openssl-0.9.5/openssl/R/mykey.R | 2 openssl-0.9.5/openssl/R/pkcs12.R |only openssl-0.9.5/openssl/R/rand.R | 20 - openssl-0.9.5/openssl/R/read.R | 58 ++-- openssl-0.9.5/openssl/R/rsa.R | 2 openssl-0.9.5/openssl/R/signing.R | 2 openssl-0.9.5/openssl/R/write.R | 2 openssl-0.9.5/openssl/R/writessh.R | 2 openssl-0.9.5/openssl/build/vignette.rds |binary openssl-0.9.5/openssl/configure | 2 openssl-0.9.5/openssl/inst/doc/bignum.R | 13 openssl-0.9.5/openssl/inst/doc/bignum.Rmd | 17 - openssl-0.9.5/openssl/inst/doc/bignum.html | 49 +-- openssl-0.9.5/openssl/inst/doc/crypto_hashing.Rmd | 2 openssl-0.9.5/openssl/inst/doc/crypto_hashing.html | 23 - openssl-0.9.5/openssl/inst/doc/keys.R | 34 -- openssl-0.9.5/openssl/inst/doc/keys.Rmd | 46 --- openssl-0.9.5/openssl/inst/doc/keys.html | 71 ++--- openssl-0.9.5/openssl/inst/doc/secure_rng.Rmd | 2 openssl-0.9.5/openssl/inst/doc/secure_rng.html | 24 - openssl-0.9.5/openssl/man/aes_cbc.Rd | 8 openssl-0.9.5/openssl/man/base64_encode.Rd | 2 openssl-0.9.5/openssl/man/certificates.Rd | 2 openssl-0.9.5/openssl/man/encrypt_envelope.Rd | 4 openssl-0.9.5/openssl/man/hash.Rd | 17 - openssl-0.9.5/openssl/man/keygen.Rd | 4 openssl-0.9.5/openssl/man/openssl.Rd | 1 openssl-0.9.5/openssl/man/pkcs12.Rd |only openssl-0.9.5/openssl/man/rand_bytes.Rd | 11 openssl-0.9.5/openssl/man/read_key.Rd | 16 - openssl-0.9.5/openssl/man/rsa_encrypt.Rd | 6 openssl-0.9.5/openssl/man/signatures.Rd | 2 openssl-0.9.5/openssl/man/write_pem.Rd | 6 openssl-0.9.5/openssl/src/Makevars.win | 6 openssl-0.9.5/openssl/src/aes.c | 12 openssl-0.9.5/openssl/src/base64.c | 4 openssl-0.9.5/openssl/src/cert.c | 14 - openssl-0.9.5/openssl/src/compatibility.c |only openssl-0.9.5/openssl/src/compatibility.h |only openssl-0.9.5/openssl/src/error.c | 1 openssl-0.9.5/openssl/src/keys.c |only openssl-0.9.5/openssl/src/openssh.c | 75 ++--- openssl-0.9.5/openssl/src/password.c |only openssl-0.9.5/openssl/src/pem.c |only openssl-0.9.5/openssl/src/pkcs12.c |only openssl-0.9.5/openssl/src/rand.c | 14 - openssl-0.9.5/openssl/src/ssl.c | 7 openssl-0.9.5/openssl/src/stream.c | 13 openssl-0.9.5/openssl/src/utils.h | 1 openssl-0.9.5/openssl/tests/certigo |only openssl-0.9.5/openssl/tests/google.dk |only openssl-0.9.5/openssl/tests/testthat/test_hash_output_length.R | 28 +- openssl-0.9.5/openssl/tests/testthat/test_pkcs12.R |only openssl-0.9.5/openssl/tests/testthat/test_rand_error.R | 6 openssl-0.9.5/openssl/tools/winlibs.R | 4 openssl-0.9.5/openssl/vignettes/bignum.Rmd | 17 - openssl-0.9.5/openssl/vignettes/crypto_hashing.Rmd | 2 openssl-0.9.5/openssl/vignettes/keys.Rmd | 46 --- openssl-0.9.5/openssl/vignettes/secure_rng.Rmd | 2 70 files changed, 493 insertions(+), 435 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.8-6 dated 2016-06-15 and 1.9-0 dated 2016-10-28
openair-1.8-6/openair/R/GoogleMapsPlot.R |only openair-1.8-6/openair/inst/staticdocs |only openair-1.8-6/openair/man/GoogleMapsPlot.Rd |only openair-1.9-0/openair/DESCRIPTION | 16 openair-1.9-0/openair/MD5 | 51 +- openair-1.9-0/openair/NAMESPACE | 3 openair-1.9-0/openair/R/RcppExports.R | 2 openair-1.9-0/openair/R/getMeta.R | 5 openair-1.9-0/openair/R/importAURN.R | 597 ++++++++++++---------------- openair-1.9-0/openair/R/importKCL.R | 2 openair-1.9-0/openair/R/polarPlot.R | 4 openair-1.9-0/openair/R/scatterPlot.R | 31 - openair-1.9-0/openair/R/summaryPlot.R | 241 +++++------ openair-1.9-0/openair/R/timeAverage.R | 41 - openair-1.9-0/openair/R/timePlot.R | 465 +++++++++++---------- openair-1.9-0/openair/R/timeProp.R | 4 openair-1.9-0/openair/R/timeVariation.R | 4 openair-1.9-0/openair/R/trajLevel.R | 5 openair-1.9-0/openair/R/trendLevel.R | 2 openair-1.9-0/openair/R/utilities.R | 6 openair-1.9-0/openair/R/windRose.R | 37 - openair-1.9-0/openair/README.md | 209 +++------ openair-1.9-0/openair/inst/CITATION | 10 openair-1.9-0/openair/man/importAURN.Rd | 506 +++++++++-------------- openair-1.9-0/openair/man/importMeta.Rd | 5 openair-1.9-0/openair/man/summaryPlot.Rd | 163 ++++--- openair-1.9-0/openair/man/timePlot.Rd | 413 ++++++++++--------- openair-1.9-0/openair/src/RcppExports.cpp | 10 28 files changed, 1334 insertions(+), 1498 deletions(-)
Title: Functions for Reading Ontologies into R
Description: Functions for reading ontologies into R as lists and manipulating sets of ontological terms.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologyIndex versions 2.0 dated 2016-08-03 and 2.2 dated 2016-10-28
ontologyIndex-2.0/ontologyIndex/data/mpo_to_hpo.RData |only ontologyIndex-2.0/ontologyIndex/inst/doc/ontologyIndex-guide.R |only ontologyIndex-2.0/ontologyIndex/inst/doc/ontologyIndex-guide.Rmd |only ontologyIndex-2.0/ontologyIndex/inst/doc/ontologyIndex-guide.html |only ontologyIndex-2.0/ontologyIndex/man/exclude_branches.Rd |only ontologyIndex-2.0/ontologyIndex/man/force_compatibility.Rd |only ontologyIndex-2.0/ontologyIndex/man/get_mpo_to_hpo.Rd |only ontologyIndex-2.0/ontologyIndex/man/get_terms_by_set_matrix.Rd |only ontologyIndex-2.0/ontologyIndex/man/intersection_with_branches.Rd |only ontologyIndex-2.0/ontologyIndex/man/mpo_to_hpo.Rd |only ontologyIndex-2.0/ontologyIndex/man/prune_branches.Rd |only ontologyIndex-2.0/ontologyIndex/vignettes/ontologyIndex-guide.Rmd |only ontologyIndex-2.2/ontologyIndex/DESCRIPTION | 14 ontologyIndex-2.2/ontologyIndex/MD5 | 64 + ontologyIndex-2.2/ontologyIndex/NAMESPACE | 25 ontologyIndex-2.2/ontologyIndex/NEWS.md | 11 ontologyIndex-2.2/ontologyIndex/R/data.R | 340 +++++----- ontologyIndex-2.2/ontologyIndex/R/descendants.R |only ontologyIndex-2.2/ontologyIndex/R/generic.R |only ontologyIndex-2.2/ontologyIndex/R/sets.R | 212 ------ ontologyIndex-2.2/ontologyIndex/build/vignette.rds |binary ontologyIndex-2.2/ontologyIndex/data/datalist | 1 ontologyIndex-2.2/ontologyIndex/data/go.RData |binary ontologyIndex-2.2/ontologyIndex/data/hpo.RData |binary ontologyIndex-2.2/ontologyIndex/data/mpo.RData |binary ontologyIndex-2.2/ontologyIndex/inst/doc/intro-to-ontologyX.R |only ontologyIndex-2.2/ontologyIndex/inst/doc/intro-to-ontologyX.Rmd |only ontologyIndex-2.2/ontologyIndex/inst/doc/intro-to-ontologyX.html |only ontologyIndex-2.2/ontologyIndex/inst/doc/reading-ontologies.R |only ontologyIndex-2.2/ontologyIndex/inst/doc/reading-ontologies.Rmd |only ontologyIndex-2.2/ontologyIndex/inst/doc/reading-ontologies.html |only ontologyIndex-2.2/ontologyIndex/man/check.Rd |only ontologyIndex-2.2/ontologyIndex/man/exclude_descendants.Rd |only ontologyIndex-2.2/ontologyIndex/man/get_OBO.Rd |only ontologyIndex-2.2/ontologyIndex/man/get_OWL.Rd |only ontologyIndex-2.2/ontologyIndex/man/get_ancestors.Rd | 4 ontologyIndex-2.2/ontologyIndex/man/get_descendants.Rd | 14 ontologyIndex-2.2/ontologyIndex/man/get_ontology.Rd | 11 ontologyIndex-2.2/ontologyIndex/man/get_term_descendancy_matrix.Rd | 4 ontologyIndex-2.2/ontologyIndex/man/get_term_property.Rd | 18 ontologyIndex-2.2/ontologyIndex/man/intersection_with_descendants.Rd |only ontologyIndex-2.2/ontologyIndex/man/minimal_set.Rd | 4 ontologyIndex-2.2/ontologyIndex/man/ontology_index.Rd |only ontologyIndex-2.2/ontologyIndex/man/owl_list_attributes.Rd |only ontologyIndex-2.2/ontologyIndex/man/owl_properties.Rd |only ontologyIndex-2.2/ontologyIndex/man/print.ontology_index.Rd |only ontologyIndex-2.2/ontologyIndex/man/prune_descendants.Rd |only ontologyIndex-2.2/ontologyIndex/vignettes/intro-to-ontologyX.Rmd |only ontologyIndex-2.2/ontologyIndex/vignettes/reading-ontologies.Rmd |only 49 files changed, 303 insertions(+), 419 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data
analysis by a unified model specification, along with some data manipulation
functions. This package covers fitting of variety models including Cox
regression models, linear regression models, Poisson regression models, logistic
models and others whose likelihood is expressed in negative binomial, gamma and
Weibull distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.1.0 dated 2016-05-05 and 0.1.1 dated 2016-10-28
epifit-0.1.0/epifit/src/mumul.h |only epifit-0.1.0/epifit/src/select.h |only epifit-0.1.1/epifit/DESCRIPTION | 8 epifit-0.1.1/epifit/MD5 | 87 - epifit-0.1.1/epifit/NAMESPACE | 75 epifit-0.1.1/epifit/NEWS | 130 - epifit-0.1.1/epifit/R/AIC.epifit.R | 44 epifit-0.1.1/epifit/R/calcAge.R | 64 epifit-0.1.1/epifit/R/convertFromFactor.R | 162 + epifit-0.1.1/epifit/R/convertNA.R | 109 - epifit-0.1.1/epifit/R/countNA.R | 60 epifit-0.1.1/epifit/R/epifit-package.R | 66 epifit-0.1.1/epifit/R/epifit.R | 1471 +++++++++--------- epifit-0.1.1/epifit/R/extractVariable.R | 68 epifit-0.1.1/epifit/R/getIndex.R | 110 - epifit-0.1.1/epifit/R/listNumericIncompatibility.R | 104 - epifit-0.1.1/epifit/R/modes.R | 28 epifit-0.1.1/epifit/R/modules.R | 96 + epifit-0.1.1/epifit/R/print.epifit.R | 78 epifit-0.1.1/epifit/R/pullOneValue.R | 182 +- epifit-0.1.1/epifit/R/pytable.R | 138 - epifit-0.1.1/epifit/R/removeVariable.R | 66 epifit-0.1.1/epifit/R/selectByIndex.R | 56 epifit-0.1.1/epifit/R/selectVariable.R | 8 epifit-0.1.1/epifit/R/showContents.R | 250 +-- epifit-0.1.1/epifit/man/AIC.epifit.Rd | 72 epifit-0.1.1/epifit/man/calcAge.Rd | 50 epifit-0.1.1/epifit/man/convertFromFactor.Rd | 10 epifit-0.1.1/epifit/man/convertNA.Rd | 18 epifit-0.1.1/epifit/man/countNA.Rd | 54 epifit-0.1.1/epifit/man/epifit-package.Rd | 72 epifit-0.1.1/epifit/man/epifit.Rd | 2 epifit-0.1.1/epifit/man/extractVariable.Rd | 52 epifit-0.1.1/epifit/man/getIndex.Rd | 68 epifit-0.1.1/epifit/man/listNumericIncompatibility.Rd | 64 epifit-0.1.1/epifit/man/modes.Rd | 42 epifit-0.1.1/epifit/man/print.epifit.Rd | 38 epifit-0.1.1/epifit/man/pullOneValue.Rd | 60 epifit-0.1.1/epifit/man/pytable.Rd | 62 epifit-0.1.1/epifit/man/selectByIndex.Rd | 68 epifit-0.1.1/epifit/man/selectVariable.Rd | 54 epifit-0.1.1/epifit/man/showContents.Rd | 80 epifit-0.1.1/epifit/src/Makevars | 2 epifit-0.1.1/epifit/src/mumul.cpp | 49 epifit-0.1.1/epifit/src/scanvarname.cpp |only epifit-0.1.1/epifit/src/select.cpp | 63 46 files changed, 2305 insertions(+), 2135 deletions(-)
Title: Foreach Parallel Adaptor using the Future API of the 'future'
Package
Description: Provides a '%dopar%' adaptor such that any type of futures can
be used as backends for the 'foreach' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 0.2.1 dated 2016-09-08 and 0.3.0 dated 2016-10-28
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NEWS | 11 +++++++++++ R/doFuture.R | 18 +++++++++++++++++- tests/foreach,nested.R | 37 ++++++++++++++++++++++++++++++------- tests/foreach,nested_dopar.R |only 6 files changed, 67 insertions(+), 16 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with Rscript to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L Davis. Ports examples from the argparse Python module by the
Python Software Foundation. Ports examples from the getopt package by Allen
Day.
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 1.0.1 dated 2014-04-05 and 1.0.4 dated 2016-10-28
DESCRIPTION | 11 ++++---- MD5 | 18 ++++++------- NAMESPACE | 2 + NEWS | 21 +++++++++++++++ R/argparse.R | 51 +++++++++++++++++++++++++++++++------- build/vignette.rds |binary inst/doc/argparse.R | 14 ---------- inst/doc/argparse.pdf |binary man/ArgumentParser.Rd | 40 +++++++++++++++--------------- tests/testthat/test-argparse.R | 54 ++++++++++++++++++++++++++++++++++++----- 10 files changed, 147 insertions(+), 64 deletions(-)
Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Text mining for word processing and sentiment analysis using
'dplyr', 'ggplot2', and other tidy tools.
Author: Gabriela De Queiroz [ctb],
David Robinson [aut],
Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between tidytext versions 0.1.1 dated 2016-06-25 and 0.1.2 dated 2016-10-27
DESCRIPTION | 14 +-- MD5 | 72 ++++++++------- NAMESPACE | 1 NEWS.md | 9 + R/globals.R | 2 R/pair_count.R | 6 - R/sentiments.R | 44 +++++++++ R/sparse_casters.R | 4 R/tidytext.R |only R/unnest_tokens.R | 41 +++++++- README.md | 73 +++++++-------- build/vignette.rds |binary inst/CITATION |only inst/doc/tf_idf.R | 2 inst/doc/tf_idf.Rmd | 4 inst/doc/tf_idf.html | 26 ++--- inst/doc/tidying_casting.R | 11 -- inst/doc/tidying_casting.Rmd | 11 -- inst/doc/tidying_casting.html | 162 +++++++++++++---------------------- inst/doc/tidytext.R | 25 +++-- inst/doc/tidytext.Rmd | 29 +++--- inst/doc/tidytext.html | 131 +++++++++++++--------------- inst/doc/topic_modeling.R | 23 +++- inst/doc/topic_modeling.Rmd | 18 +++ inst/doc/topic_modeling.html | 99 +++++++++------------ inst/extdata |only man/cast_sparse.Rd | 3 man/document_term_casters.Rd | 1 man/get_sentiments.Rd |only man/pair_count.Rd | 2 man/tidytext.Rd |only man/unnest_tokens.Rd | 17 +++ tests/testthat/test-pair-count.R | 69 -------------- tests/testthat/test-sentiments.R |only tests/testthat/test-sparse-casters.R | 7 + tests/testthat/test-unnest-tokens.R | 78 ++++++++++++++++ vignettes/tf_idf.Rmd | 4 vignettes/tidying_casting.Rmd | 11 -- vignettes/tidytext.Rmd | 29 +++--- vignettes/topic_modeling.Rmd | 18 +++ 40 files changed, 580 insertions(+), 466 deletions(-)
Title: Functions for Calculating Ontological Similarities
Description: Functions for calculating semantic similarities between ontological terms or sets of ontological terms based on term information content and assessing statistical significance of similarity in the context of a collection of sets of ontological terms.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologySimilarity versions 2.1 dated 2016-09-09 and 2.2 dated 2016-10-27
ontologySimilarity-2.1/ontologySimilarity/src/Makevars |only ontologySimilarity-2.2/ontologySimilarity/DESCRIPTION | 10 - ontologySimilarity-2.2/ontologySimilarity/MD5 | 27 +-- ontologySimilarity-2.2/ontologySimilarity/R/data.R | 4 ontologySimilarity-2.2/ontologySimilarity/data/GO_IC.RData |binary ontologySimilarity-2.2/ontologySimilarity/data/gene_GO_terms.RData |binary ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-GO-example.R | 7 ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-GO-example.Rmd | 11 - ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-GO-example.html | 29 +-- ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-examples.html | 84 +++++----- ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-introduction.Rmd | 2 ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-introduction.html | 40 ++-- ontologySimilarity-2.2/ontologySimilarity/man/gene_GO_terms.Rd | 4 ontologySimilarity-2.2/ontologySimilarity/vignettes/ontologySimilarity-GO-example.Rmd | 11 - ontologySimilarity-2.2/ontologySimilarity/vignettes/ontologySimilarity-introduction.Rmd | 2 15 files changed, 121 insertions(+), 110 deletions(-)
More information about ontologySimilarity at CRAN
Permanent link
Title: Multiple Hypotheses Testing for Discrete Data
Description: A Comprehensive tool for almost all existing multiple testing
methods for discrete data. The package also provides some novel multiple testing
procedures controlling FWER/FDR for discrete data. Given discrete p-values
and their domains, the [method].p.adjust function returns adjusted p-values,
which can be used to compare with the nominal significant level alpha and make
decisions.
Author: Yalin Zhu, Wenge Guo
Maintainer: Yalin Zhu <yalin.zhu@outlook.com>
Diff between MHTdiscrete versions 0.1.0 dated 2016-10-20 and 0.1.1 dated 2016-10-27
DESCRIPTION | 16 +++-- MD5 | 43 ++++++++------- NAMESPACE | 4 + R/FDRSD.R |only R/FDRSU.R | 140 ++++++++++++++++++++++++++++++++++++++++--------- R/FWERSD.R | 19 +++++- R/FWERSS.R | 30 +++++++++- R/FWERSU.R | 20 +++++-- R/MHTdiscrete.R | 15 ++++- R/Pval.R | 1 man/GTBH.p.adjust.Rd |only man/GTBY.p.adjust.Rd |only man/MBH.p.adjust.Rd | 8 ++ man/MBL.p.adjust.Rd |only man/MBY.p.adjust.Rd | 8 ++ man/MBonf.p.adjust.Rd | 3 + man/MHTdiscrete.Rd | 23 +++++++- man/MHoch.p.adjust.Rd | 8 ++ man/MHolm.p.adjust.Rd | 8 ++ man/Roth.p.adjust.Rd | 3 + man/Roth.rej.Rd | 7 ++ man/Sidak.p.adjust.Rd |only man/TH.p.adjust.Rd | 7 ++ man/Tarone.p.adjust.Rd | 5 + man/getPval.Rd | 3 + 25 files changed, 305 insertions(+), 66 deletions(-)
Title: Detecting Differentially Expressed Genes in Time Course RNA-Seq
Data
Description: Uses a negative binomial mixed-effects (NBME) model to detect
nonparallel differential expression(NPDE) genes and parallel differential
expression(PDE) genes in the time course RNA-seq data.
Author: Fan Gao, Xiaoxiao Sun
Maintainer: Fan Gao <fangaohz@gmail.com>
Diff between timeSeq versions 1.0.1 dated 2015-09-25 and 1.0.2 dated 2016-10-27
timeSeq-1.0.1/timeSeq/R/timeSeq.geneset.R |only timeSeq-1.0.1/timeSeq/R/timeSeq.genesetscreeplot.R |only timeSeq-1.0.1/timeSeq/R/timeSeq.plot.R |only timeSeq-1.0.1/timeSeq/data/Idgf2.RData |only timeSeq-1.0.1/timeSeq/data/object_by_timeSeq.RData |only timeSeq-1.0.1/timeSeq/data/object_by_timeSeq.geneset.RData |only timeSeq-1.0.1/timeSeq/man/Idgf2.Rd |only timeSeq-1.0.1/timeSeq/man/object_by_timeSeq.Rd |only timeSeq-1.0.1/timeSeq/man/object_by_timeSeq.geneset.Rd |only timeSeq-1.0.1/timeSeq/man/timeSeq.geneset.Rd |only timeSeq-1.0.1/timeSeq/man/timeSeq.genesetscreeplot.Rd |only timeSeq-1.0.1/timeSeq/man/timeSeq.plot.Rd |only timeSeq-1.0.1/timeSeq/man/timeSeq_1.0.1-package.Rd |only timeSeq-1.0.1/timeSeq/vignettes/Idgf2.png |only timeSeq-1.0.2/timeSeq/DESCRIPTION | 17 timeSeq-1.0.2/timeSeq/MD5 | 57 +-- timeSeq-1.0.2/timeSeq/NAMESPACE | 7 timeSeq-1.0.2/timeSeq/R/timeSeq.R | 226 +++++------- timeSeq-1.0.2/timeSeq/R/timeSeq.heatmap.R | 4 timeSeq-1.0.2/timeSeq/R/timeSeq.permutate.R | 229 ++++--------- timeSeq-1.0.2/timeSeq/R/timeSeq.screeplot.R | 6 timeSeq-1.0.2/timeSeq/R/timeSeq.sort.R | 4 timeSeq-1.0.2/timeSeq/build/vignette.rds |binary timeSeq-1.0.2/timeSeq/data/pAbp.RData |only timeSeq-1.0.2/timeSeq/data/simulate.dt.RData |only timeSeq-1.0.2/timeSeq/inst/doc/my-vignette.R | 23 - timeSeq-1.0.2/timeSeq/inst/doc/my-vignette.Rmd | 209 +++++------ timeSeq-1.0.2/timeSeq/inst/doc/my-vignette.html | 122 ++++-- timeSeq-1.0.2/timeSeq/man/pAbp.Rd |only timeSeq-1.0.2/timeSeq/man/simulate.dt.Rd |only timeSeq-1.0.2/timeSeq/man/timeSeq.Rd | 202 ++++------- timeSeq-1.0.2/timeSeq/man/timeSeq.heatmap.Rd | 117 ++---- timeSeq-1.0.2/timeSeq/man/timeSeq.permutate.Rd | 89 ++--- timeSeq-1.0.2/timeSeq/man/timeSeq.screeplot.Rd | 119 ++---- timeSeq-1.0.2/timeSeq/man/timeSeq.sort.Rd | 72 ++-- timeSeq-1.0.2/timeSeq/man/timeSeq_1.0.2-package.Rd |only timeSeq-1.0.2/timeSeq/vignettes/heatmap.png |binary timeSeq-1.0.2/timeSeq/vignettes/my-vignette.Rmd | 209 +++++------ timeSeq-1.0.2/timeSeq/vignettes/scree.png |binary 39 files changed, 742 insertions(+), 970 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7-th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-77 dated 2016-10-01 and 0.1-79 dated 2016-10-27
DESCRIPTION | 8 MD5 | 37 NAMESPACE | 9 NEWS | 5 R/CausalDiagramContCont.R | 1 R/ICA.BinBin.Grid.Sample.Uncert.R | 1524 +++++++++++++++++++------------------- R/MaxEntContCont.R |only R/MaxEntICABinBin.R | 695 ++++++++--------- R/Pred.TrialT.ContCont.R | 248 +++--- R/plot.MaxEntContCont.R |only R/plot.MetaAnalyticMTS.R | 16 R/plot.SurvSurv.R | 80 - R/plot.TrialLevelMA.R | 38 R/summary_MaxEntContCont.R |only man/ARMD.Rd | 40 man/ICA.BinBin.Grid.Sample.Rd | 2 man/ICAContCont.Rd | 178 ++-- man/MICAContCont.Rd | 208 ++--- man/MaxEntICAContCont.Rd |only man/Pred.TrialT.ContCont.Rd | 198 ++-- man/plot.MaxEntContCont.Rd |only man/summary.gen.Rd | 2 22 files changed, 1653 insertions(+), 1636 deletions(-)
Title: Tools to Create Gene Sets
Description: A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example for use with the RSNPset package, or to export to a PLINK set.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>
Diff between snplist versions 0.15 dated 2015-11-20 and 0.16 dated 2016-10-27
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 5 +++++ R/makeGeneSet.R | 4 ++-- build/vignette.rds |binary inst/doc/snplist.R | 18 +++++++----------- inst/doc/snplist.Rnw | 20 ++++++++------------ inst/doc/snplist.pdf |binary man/snplist-package.Rd | 4 ++-- vignettes/snplist.Rnw | 20 ++++++++------------ 10 files changed, 45 insertions(+), 52 deletions(-)
Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals and other
information on the model.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.2.0 dated 2016-09-07 and 3.2.1 dated 2016-10-27
DESCRIPTION | 8 MD5 | 61 + NEWS | 8 R/as.char.R | 4 R/call.dots.R | 2 R/dotlib.R | 14 R/gbm.R | 43 - R/gbm.backcompat.R |only R/lib.R | 83 +- R/plot_gbm.R | 81 +- R/plotmo.R | 7 R/plotres.R | 2 R/printcall.R | 6 R/w1.R | 6 R/xgboost.R |only R/xy.R | 21 inst/doc/modguide.pdf |binary inst/doc/plotmo-notes.pdf | 982 +++++++++++++++---------------- inst/doc/plotres-notes.pdf |binary inst/slowtests/linmod.R | 139 ++-- inst/slowtests/linmod.milbo.tutorial.R | 1 inst/slowtests/make.bat | 2 inst/slowtests/test.gbm.R | 206 +++++- inst/slowtests/test.gbm.Rout.save | 218 +++++- inst/slowtests/test.linmod.R |only inst/slowtests/test.linmod.Rout.save |only inst/slowtests/test.linmod.bat |only inst/slowtests/test.ltut.R | 475 +-------------- inst/slowtests/test.ltut.Rout.save | 1009 +------------------------------- inst/slowtests/test.non.earth.Rout.save | 6 inst/slowtests/test.plotmo.Rout.save | 4 inst/slowtests/test.plotmo3.R | 5 inst/slowtests/test.plotmo3.Rout.save | 5 inst/slowtests/test.plotres.Rout.save | 2 34 files changed, 1248 insertions(+), 2152 deletions(-)
Title: Functions for Visualising Sets of Ontological Terms
Description: Functions for visualising sets of ontological terms using the 'graphviz' layout system.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologyPlot versions 1.3 dated 2016-09-09 and 1.4 dated 2016-10-27
ontologyPlot-1.3/ontologyPlot/man/only_phenotype_abnormalities.Rd |only ontologyPlot-1.4/ontologyPlot/DESCRIPTION | 10 - ontologyPlot-1.4/ontologyPlot/MD5 | 29 ++--- ontologyPlot-1.4/ontologyPlot/NAMESPACE | 2 ontologyPlot-1.4/ontologyPlot/R/attributes.R | 2 ontologyPlot-1.4/ontologyPlot/R/graphs.R | 30 +---- ontologyPlot-1.4/ontologyPlot/R/sets.R | 8 - ontologyPlot-1.4/ontologyPlot/inst/doc/plotting-ontological-terms.R | 3 ontologyPlot-1.4/ontologyPlot/inst/doc/plotting-ontological-terms.Rmd | 42 ++++++-- ontologyPlot-1.4/ontologyPlot/inst/doc/plotting-ontological-terms.html | 52 +++++++--- ontologyPlot-1.4/ontologyPlot/inst/doc/plotting-term-grids.html | 6 - ontologyPlot-1.4/ontologyPlot/man/n_most_frequent_terms.Rd | 2 ontologyPlot-1.4/ontologyPlot/man/ontologyPlot-package.Rd | 2 ontologyPlot-1.4/ontologyPlot/man/remove_links.Rd | 8 - ontologyPlot-1.4/ontologyPlot/man/remove_uninformative_terms.Rd | 6 - ontologyPlot-1.4/ontologyPlot/vignettes/plotting-ontological-terms.Rmd | 42 ++++++-- 16 files changed, 144 insertions(+), 100 deletions(-)
Title: Odds Ratio Calculation for GAM(M)s & GLM(M)s
Description: Simplified odds ratio calculation of GAM(M)s & GLM(M)s.
Provides structured output (data frame) of all predictors and their corresponding odds ratios and confident intervals
for further analyses. It helps to avoid false references of predictors and increments by
specifying these parameters in a list instead of using 'exp(coef(model))'
(standard approach of odds ratio calculation for GLMs) which just returns a plain numeric output.
For GAM(M)s, odds ratio calculation is highly simplified with this package since it takes care of
the multiple 'predict()' calls of the chosen predictor while holding other predictors constant.
Also, this package allows odds ratio calculation of percentage steps across the whole
predictor distribution range for GAM(M)s. In both cases, confident intervals are returned additionally.
Calculated odds ratio of GAM(M)s can be inserted into the smooth function plot.
Author: Patrick Schratz
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between oddsratio versions 0.2 dated 2016-10-11 and 0.3.0 dated 2016-10-27
oddsratio-0.2/oddsratio/R/odds.ratio.gam.R |only oddsratio-0.2/oddsratio/R/odds.ratio.glm.R |only oddsratio-0.2/oddsratio/inst/doc/exemplary-function-usage.R |only oddsratio-0.2/oddsratio/inst/doc/exemplary-function-usage.Rmd |only oddsratio-0.2/oddsratio/inst/doc/exemplary-function-usage.html |only oddsratio-0.2/oddsratio/vignettes/exemplary-function-usage.Rmd |only oddsratio-0.3.0/oddsratio/DESCRIPTION | 20 ++-- oddsratio-0.3.0/oddsratio/MD5 | 41 ++++++---- oddsratio-0.3.0/oddsratio/NAMESPACE | 12 ++ oddsratio-0.3.0/oddsratio/NEWS | 12 ++ oddsratio-0.3.0/oddsratio/NEWS.md | 15 +++ oddsratio-0.3.0/oddsratio/R/add.oddsratio.into.plot.R |only oddsratio-0.3.0/oddsratio/R/calc.oddsratio.gam.R |only oddsratio-0.3.0/oddsratio/R/calc.oddsratio.glm.R |only oddsratio-0.3.0/oddsratio/R/helper.funs.R |only oddsratio-0.3.0/oddsratio/R/pl.smooth.gam.R |only oddsratio-0.3.0/oddsratio/build/vignette.rds |binary oddsratio-0.3.0/oddsratio/inst/Plots |only oddsratio-0.3.0/oddsratio/inst/doc/function.tutorial.R |only oddsratio-0.3.0/oddsratio/inst/doc/function.tutorial.Rmd |only oddsratio-0.3.0/oddsratio/inst/doc/function.tutorial.html |only oddsratio-0.3.0/oddsratio/inst/wordpress.Rmd |only oddsratio-0.3.0/oddsratio/inst/wordpress.md |only oddsratio-0.3.0/oddsratio/inst/wordpress_files |only oddsratio-0.3.0/oddsratio/man/add.oddsratio.into.plot.Rd |only oddsratio-0.3.0/oddsratio/man/calc.oddsratio.gam.Rd | 31 +++++-- oddsratio-0.3.0/oddsratio/man/calc.oddsratio.glm.Rd | 24 ++++- oddsratio-0.3.0/oddsratio/man/gam.to.df.Rd |only oddsratio-0.3.0/oddsratio/man/no.plot.Rd |only oddsratio-0.3.0/oddsratio/man/pl.smooth.gam.Rd |only oddsratio-0.3.0/oddsratio/vignettes/function.tutorial.Rmd |only 31 files changed, 119 insertions(+), 36 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise de cluster hierarquico e nao hierarquico, regressao linear, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.9.4 dated 2016-08-16 and 1.9.5 dated 2016-10-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/CA.R | 8 ++++---- man/MVar.pt-package.Rd | 4 ++-- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Calibrates and Reweights Units in Samples
Description: Provides user-friendly tools for calibration in survey sampling.
The package is production-oriented, and its interface is inspired by the famous
popular macro 'Calmar' for SAS, so that 'Calmar' users can quickly get used to
'icarus'. In addition to calibration (with linear, raking and logit methods),
'icarus' features functions for calibration on tight bounds and penalized
calibration.
Author: Antoine Rebecq [aut, cre]
Maintainer: Antoine Rebecq <antoine.rebecq@m4x.org>
Diff between icarus versions 0.2.1 dated 2016-04-18 and 0.2.2 dated 2016-10-27
DESCRIPTION | 14 ++++-- MD5 | 50 ++++++++++++------------ NAMESPACE | 2 R/calib.R | 7 +-- R/calibration.R | 4 + README.md | 4 - man/HTmean.Rd | 4 - man/HTtotal.Rd | 2 man/addMargin.Rd | 2 man/calWeights_ex2.Rd | 2 man/calibration.Rd | 15 +++---- man/calibrationMarginStats.Rd | 4 - man/colToDummies.Rd | 2 man/dataPop.Rd | 8 +-- man/data_ex2.Rd | 4 - man/marginStats.Rd | 6 +- man/poptest_calmar.Rd | 8 +-- man/poptest_calmar_nr.Rd | 8 +-- man/regroupCalibrationModalities.Rd | 15 +++---- man/regroupModalities.Rd | 2 man/table_margins_1.Rd | 2 man/table_margins_2.Rd | 2 man/weightedMean.Rd | 4 - man/weightedTotal.Rd | 2 tests/testthat/test_calibration.R | 37 ++++++++++++++++- tests/testthat/test_calibration_small_dataset.R | 36 +++++++++++++---- 26 files changed, 156 insertions(+), 90 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers.
Author: Jordan Read [aut, cre],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut]
Maintainer: Jordan Read <jread@usgs.gov>
Diff between geoknife versions 1.3.0 dated 2016-04-06 and 1.4.0 dated 2016-10-27
DESCRIPTION | 15 +++++---- MD5 | 54 +++++++++++++++++----------------- R/01-webdata-obj.R | 12 ++----- R/02-webgeom-obj.R | 34 +++++++++++++++++++-- R/04-webprocess-obj.R | 2 - R/06-simplegeom-obj.R | 3 + R/geoknife-generic.R | 4 ++ R/parseTimeseries.R | 1 R/query-webdata.R | 2 - R/query-webgeom.R | 4 +- R/result.R | 2 - R/values-webgeom.R | 35 +++++++++++++++++----- README.md | 6 +-- build/vignette.rds |binary inst/doc/geoknife.R | 2 - inst/doc/geoknife.Rmd | 13 +++----- inst/doc/geoknife.html | 39 +++++++++++------------- inst/doc/plot_geotiff.html | 20 +++++------- inst/extdata/get_attribute_values.xml | 2 - inst/extdata/multi_poly_post.xml | 2 - man/geoknife-methods.Rd | 5 +++ man/query.Rd | 2 - man/simplegeom-methods.Rd | 1 man/webgeom-methods.Rd | 28 +++++++++++++++++ man/webprocess-methods.Rd | 4 +- tests/testthat/test-query_webgeom.R | 8 +++++ tests/testthat/test-webdata_object.R | 2 - vignettes/geoknife.Rmd | 13 +++----- 28 files changed, 201 insertions(+), 114 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
package. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot package.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.6.3 dated 2016-09-30 and 0.7.0 dated 2016-10-27
cowplot-0.6.3/cowplot/man/plot_theme.Rd |only cowplot-0.6.3/cowplot/man/switch_axis_position.Rd |only cowplot-0.7.0/cowplot/DESCRIPTION | 8 - cowplot-0.7.0/cowplot/MD5 | 42 ++++----- cowplot-0.7.0/cowplot/NAMESPACE | 2 cowplot-0.7.0/cowplot/NEWS | 5 + cowplot-0.7.0/cowplot/R/draw.R | 2 cowplot-0.7.0/cowplot/R/switch_axis.R | 36 ++++---- cowplot-0.7.0/cowplot/R/themes.R | 38 ++------ cowplot-0.7.0/cowplot/inst/doc/axis_position.R | 50 +++++------ cowplot-0.7.0/cowplot/inst/doc/axis_position.Rmd | 57 +++++-------- cowplot-0.7.0/cowplot/inst/doc/axis_position.html | 82 ++++++++----------- cowplot-0.7.0/cowplot/inst/doc/introduction.html | 52 ++++++------ cowplot-0.7.0/cowplot/inst/doc/plot_annotations.Rmd | 2 cowplot-0.7.0/cowplot/inst/doc/plot_annotations.html | 38 ++++---- cowplot-0.7.0/cowplot/inst/doc/plot_grid.R | 8 - cowplot-0.7.0/cowplot/inst/doc/plot_grid.Rmd | 8 - cowplot-0.7.0/cowplot/inst/doc/plot_grid.html | 52 ++++-------- cowplot-0.7.0/cowplot/inst/doc/shared_legends.html | 28 +++--- cowplot-0.7.0/cowplot/man/theme_nothing.Rd | 11 -- cowplot-0.7.0/cowplot/vignettes/axis_position.Rmd | 57 +++++-------- cowplot-0.7.0/cowplot/vignettes/plot_annotations.Rmd | 2 cowplot-0.7.0/cowplot/vignettes/plot_grid.Rmd | 8 - 23 files changed, 251 insertions(+), 337 deletions(-)
Title: A Bit of Glue Between R and Stata
Description: A simple R -> Stata interface allowing the user to
execute Stata commands (both inline and from a .do file)
from R.
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Diff between RStata versions 1.1.0 dated 2016-09-15 and 1.1.1 dated 2016-10-27
RStata-1.1.0/RStata/NEWS |only RStata-1.1.1/RStata/DESCRIPTION | 6 +++--- RStata-1.1.1/RStata/MD5 | 7 +++---- RStata-1.1.1/RStata/R/stata.R | 22 +++++++++++++--------- RStata-1.1.1/RStata/README.md | 19 +++++++++++++------ 5 files changed, 32 insertions(+), 22 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation.
Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 2.2-0 dated 2016-07-25 and 2.3-0 dated 2016-10-27
DESCRIPTION | 8 +-- MD5 | 86 +++++++++++++++++++++-------------------- NAMESPACE | 2 R/jomo.MCMCchain.R | 6 +- R/jomo.R | 6 +- R/jomo.lm.MCMCchain.R |only R/jomo.lm.R |only R/jomo1ran.MCMCchain.R | 8 +-- R/jomo1ran.R | 8 +-- R/jomo1rancathr.MCMCchain.R | 9 ++-- R/jomo1rancathr.R | 9 ++-- R/jomo1ranconhr.MCMCchain.R | 5 +- R/jomo1ranconhr.R | 7 +-- R/jomo1ranmixhr.MCMCchain.R | 7 +-- R/jomo1ranmixhr.R | 9 ++-- R/jomo2.MCMCchain.R | 4 - R/jomo2.R | 4 - R/jomo2hr.MCMCchain.R | 7 +-- R/jomo2hr.R | 9 ++-- inst/CITATION | 2 man/cldata.Rd | 2 man/jomo.MCMCchain.Rd | 13 +++--- man/jomo.Rd | 15 ++++--- man/jomo.lm.MCMCchain.Rd |only man/jomo.lm.Rd |only man/jomo1.MCMCchain.Rd | 2 man/jomo1.Rd | 2 man/jomo1ran.MCMCchain.Rd | 12 +++-- man/jomo1ran.Rd | 11 +++-- man/jomo1rancathr.MCMCchain.Rd | 10 ++-- man/jomo1rancathr.Rd | 9 ++-- man/jomo1ranconhr.MCMCchain.Rd | 13 +++--- man/jomo1ranconhr.Rd | 11 +++-- man/jomo1ranmixhr.MCMCchain.Rd | 9 ++-- man/jomo1ranmixhr.Rd | 9 ++-- man/jomo2.MCMCchain.Rd | 13 +++--- man/jomo2.Rd | 13 +++--- man/jomo2hr.MCMCchain.Rd | 9 ++-- man/jomo2hr.Rd | 9 ++-- src/MCMCjomo1ranconhr.c | 7 +-- src/MCMCjomo1ranmixhr.c | 7 +-- src/MCMCjomo2hr.c | 7 +-- src/MCMCjomolm.c |only src/Makevars | 2 src/jomo1ranconhr.c | 7 +-- src/jomo1ranmixhr.c | 7 +-- src/jomolm.c |only 47 files changed, 229 insertions(+), 166 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial data, in R.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Michael Sumner [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.2-0 dated 2016-10-26 and 0.2-1 dated 2016-10-27
DESCRIPTION | 6 ++--- MD5 | 41 ++++++++++++++++++++---------------- R/geom.R | 11 +++++++-- R/read.R | 3 +- inst/doc/sfr.R | 10 ++++---- inst/doc/sfr.Rmd | 42 ++++++++++++++++++------------------- inst/doc/sfr.html | 52 +++++++++++++++++++++++----------------------- inst/shape |only src/gdal_geom.cpp | 17 ++++++++------- src/gdal_read.cpp | 4 +-- src/gdal_write.cpp | 2 - tests/gdal_geom.R | 5 ++-- tests/gdal_geom.Rout.save | 10 +++++--- tests/geos.R | 3 +- tests/geos.Rout.save | 8 ++++--- tests/grid.R | 5 ++-- tests/grid.Rout.save | 29 ++++++------------------- tests/roundtrip.R | 3 +- tests/roundtrip.Rout.save | 8 ++++--- vignettes/nc.gpkg |only vignettes/sfr.Rmd | 42 ++++++++++++++++++------------------- 21 files changed, 156 insertions(+), 145 deletions(-)
Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return coda mcmc objects that can then be summarized
using the coda package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between MCMCpack versions 1.3-7 dated 2016-08-21 and 1.3-8 dated 2016-10-27
DESCRIPTION | 8 +++---- MD5 | 52 +++++++++++++++++++++++------------------------ man/MCMCSVDreg.Rd | 2 - man/MCMCdynamicEI.Rd | 2 - man/MCMCfactanal.Rd | 2 - man/MCMChierEI.Rd | 2 - man/MCMChlogit.Rd | 2 - man/MCMChpoisson.Rd | 2 - man/MCMChregress.Rd | 2 - man/MCMCirt1d.Rd | 2 - man/MCMCirtHier1d.Rd | 2 - man/MCMCirtKd.Rd | 2 - man/MCMCirtKdRob.Rd | 2 - man/MCMClogit.Rd | 2 - man/MCMCmetrop1R.Rd | 2 - man/MCMCmixfactanal.Rd | 2 - man/MCMCmnl.Rd | 2 - man/MCMCoprobit.Rd | 2 - man/MCMCordfactanal.Rd | 2 - man/MCMCpoisson.Rd | 2 - man/MCMCprobit.Rd | 2 - man/MCMCquantreg.Rd | 2 - man/MCMCregress.Rd | 2 - man/MCMCregressChange.Rd | 6 +++-- man/MCMCtobit.Rd | 2 - man/SSVSquantreg.Rd | 2 - src/MCMCpoissonChange.cc | 2 - 27 files changed, 58 insertions(+), 56 deletions(-)
Title: Hierarchical Models for Parametric and Semi-Parametric Analyses
of Semi-Competing Risks Data
Description: Parametric and semi-parametric analyses of semi-competing risks/univariate survival data.
Author: Kyu Ha Lee, Catherine Lee, and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between SemiCompRisks versions 2.4 dated 2016-03-09 and 2.5 dated 2016-10-27
SemiCompRisks-2.4/SemiCompRisks/R/BayesID.R |only SemiCompRisks-2.4/SemiCompRisks/R/BayesSurv.R |only SemiCompRisks-2.4/SemiCompRisks/R/FreqID.R |only SemiCompRisks-2.4/SemiCompRisks/R/FreqSurv.R |only SemiCompRisks-2.4/SemiCompRisks/R/initiate.startValues.R |only SemiCompRisks-2.4/SemiCompRisks/man/BayesID.Rd |only SemiCompRisks-2.4/SemiCompRisks/man/BayesSurv.Rd |only SemiCompRisks-2.4/SemiCompRisks/man/FreqID.Rd |only SemiCompRisks-2.4/SemiCompRisks/man/FreqSurv.Rd |only SemiCompRisks-2.4/SemiCompRisks/man/initiate.startValues.Rd |only SemiCompRisks-2.5/SemiCompRisks/DESCRIPTION | 14 SemiCompRisks-2.5/SemiCompRisks/MD5 | 64 SemiCompRisks-2.5/SemiCompRisks/NAMESPACE | 39 SemiCompRisks-2.5/SemiCompRisks/R/BayesID_AFT.R |only SemiCompRisks-2.5/SemiCompRisks/R/BayesID_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/BayesSurv_AFT.R |only SemiCompRisks-2.5/SemiCompRisks/R/BayesSurv_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/FreqID_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/FreqSurv_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/initiate.startValues_AFT.R |only SemiCompRisks-2.5/SemiCompRisks/R/initiate.startValues_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/internalFunc.R | 358 - SemiCompRisks-2.5/SemiCompRisks/R/methods.R | 3393 +++++++--- SemiCompRisks-2.5/SemiCompRisks/R/old.functions.R |only SemiCompRisks-2.5/SemiCompRisks/R/simID.R | 5 SemiCompRisks-2.5/SemiCompRisks/R/simSurv.R | 2 SemiCompRisks-2.5/SemiCompRisks/build |only SemiCompRisks-2.5/SemiCompRisks/inst |only SemiCompRisks-2.5/SemiCompRisks/man/BayesID_AFT.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/BayesID_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/BayesSurv_AFT.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/BayesSurv_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/FreqID_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/FreqSurv_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/SemiCompRisks-package.Rd | 25 SemiCompRisks-2.5/SemiCompRisks/man/initiate.startValues_AFT.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/initiate.startValues_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/methods.Rd | 58 SemiCompRisks-2.5/SemiCompRisks/man/old.functions.Rd |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPscr.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPscr.h |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPscr_Updates.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPsurv.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPsurv.h |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPsurv_Updates.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNscr.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNscr.h |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNscr_Updates.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNsurv.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNsurv.h |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNsurv_Updates.c |only SemiCompRisks-2.5/SemiCompRisks/src/BpeDpCorScrSM.h | 8 SemiCompRisks-2.5/SemiCompRisks/src/Utilities.c | 1192 +++ SemiCompRisks-2.5/SemiCompRisks/vignettes |only 54 files changed, 4068 insertions(+), 1090 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-
implied instrumental variables.
Author: Zachary Fisher, Ken Bollen, Kathleen Gates, and Mikko Rönkkö.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.7 dated 2016-03-22 and 0.4.8 dated 2016-10-27
DESCRIPTION | 9 MD5 | 10 R/miive.R | 612 ++++++++++++++++++++----------------------- R/miivs.R | 806 ++++++++++++++++++++++++++++++--------------------------- R/miivvarcov.R |only R/optimMIIV.R |only man/miive.Rd | 22 + 7 files changed, 751 insertions(+), 708 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 1.1.1 dated 2016-05-03 and 1.2.0 dated 2016-10-27
lamW-1.1.1/lamW/inst/NEWS.Rd |only lamW-1.2.0/lamW/DESCRIPTION | 13 +- lamW-1.2.0/lamW/MD5 | 24 ++- lamW-1.2.0/lamW/NAMESPACE | 3 lamW-1.2.0/lamW/R/RcppExports.R | 2 lamW-1.2.0/lamW/build/partial.rdb |binary lamW-1.2.0/lamW/inst/News.Rd |only lamW-1.2.0/lamW/inst/include/lamW.h | 8 - lamW-1.2.0/lamW/inst/include/lamW_RcppExports.h | 36 ++--- lamW-1.2.0/lamW/man/lamW-package.Rd | 4 lamW-1.2.0/lamW/man/lamW.Rd | 2 lamW-1.2.0/lamW/src/Makevars |only lamW-1.2.0/lamW/src/Makevars.win |only lamW-1.2.0/lamW/src/RcppExports.cpp | 54 ++++---- lamW-1.2.0/lamW/src/lambertW.cpp | 155 ++++++++++++++++-------- 15 files changed, 179 insertions(+), 122 deletions(-)
Title: Decrypt Passwords from Gnome Keyring and Windows Data Protection
API
Description: Currently this package decrypts passwords stored in the Gnome
Keyring using secret tool, and strings encrypted with the Windows Data
Protection API. OSX Keychain coming soon.
Author: Josh Gilfillan
Maintainer: Josh Gilfillan <joshua.i.gilfillan+keyringr@gmail.com>
Diff between keyringr versions 0.1.0 dated 2016-10-23 and 0.2.0 dated 2016-10-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/decrypt_dpapi_pw.R | 22 +++++++++++++++++++++- R/decrypt_gk_pw.R | 17 +++++++++++++---- man/decrypt_dpapi_pw.Rd | 20 ++++++++++++++++++++ man/decrypt_gk_pw.Rd | 12 ++++++++++-- 6 files changed, 73 insertions(+), 16 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; the Daymet gridded estimates of daily weather parameters
for North America, version 3, available from the Oak Ridge National Laboratory's
Distributed Active Archive Center (DAAC); and the International Tree Ring Data Bank.
Additional data sources are in the works, global soils (HWSD),
MODIS satellite data products, the National Atlas (US), Natural Earth, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.3.1 dated 2016-10-12 and 2.3.2 dated 2016-10-27
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/NED_FUNCTIONS.R | 4 ++-- R/NHD_FUNCTIONS.R | 2 +- README.md | 2 +- inst/CITATION | 4 ++-- man/FedData-package.Rd | 4 ++-- tests/testthat/test.NED.R | 6 +++--- tests/testthat/test.NHD.R | 4 ++-- 9 files changed, 25 insertions(+), 25 deletions(-)
Title: Set of Installed Fonts
Description: Provides a set of fonts with permissive licences. This is
useful when you want to avoid system fonts to make sure your
outputs are reproducible.
Author: Lionel Henry [cre, aut],
RStudio [cph],
George Douros [cph] (Symbola font)
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between fontquiver versions 0.1.0 dated 2016-09-04 and 0.2.0 dated 2016-10-26
fontquiver-0.1.0/fontquiver/R/font-bitstream-vera.R |only fontquiver-0.1.0/fontquiver/R/font-dejavu.R |only fontquiver-0.1.0/fontquiver/man/font_bitstream_vera.Rd |only fontquiver-0.1.0/fontquiver/man/font_dejavu.Rd |only fontquiver-0.2.0/fontquiver/DESCRIPTION | 24 - fontquiver-0.2.0/fontquiver/LICENSE |only fontquiver-0.2.0/fontquiver/MD5 | 39 + fontquiver-0.2.0/fontquiver/NAMESPACE | 17 fontquiver-0.2.0/fontquiver/NEWS.md | 29 + fontquiver-0.2.0/fontquiver/R/font-getters.R |only fontquiver-0.2.0/fontquiver/R/fontset-bitstream-vera.R |only fontquiver-0.2.0/fontquiver/R/fontset-dejavu.R |only fontquiver-0.2.0/fontquiver/R/fontset-liberation.R |only fontquiver-0.2.0/fontquiver/R/fontset-symbola.R |only fontquiver-0.2.0/fontquiver/R/fontset.R |only fontquiver-0.2.0/fontquiver/R/html-dependency.R | 88 ++- fontquiver-0.2.0/fontquiver/R/utils.R | 230 +++++++++- fontquiver-0.2.0/fontquiver/README.md | 125 ++++- fontquiver-0.2.0/fontquiver/inst |only fontquiver-0.2.0/fontquiver/man/font_families.Rd |only fontquiver-0.2.0/fontquiver/man/font_variants.Rd |only fontquiver-0.2.0/fontquiver/man/fonts.Rd |only fontquiver-0.2.0/fontquiver/man/fontset_info.Rd |only fontquiver-0.2.0/fontquiver/man/fontset_list.Rd |only fontquiver-0.2.0/fontquiver/man/fontset_register.Rd |only fontquiver-0.2.0/fontquiver/man/fontset_variants.Rd |only fontquiver-0.2.0/fontquiver/man/htmlFontDependency.Rd | 22 fontquiver-0.2.0/fontquiver/man/splice_fonts.Rd |only fontquiver-0.2.0/fontquiver/tests/testthat/test-fonts.R | 18 fontquiver-0.2.0/fontquiver/tests/testthat/test-html-dependency.R |only 30 files changed, 481 insertions(+), 111 deletions(-)
Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation
(DES) package for R. Designed to be a generic framework, it leverages the
power of 'Rcpp' to boost the performance, turning DES in R feasible. As a
noteworthy characteristic, 'simmer' exploits the concept of trajectory: a
common path in the simulation model for entities of the same type.
Author: Iñaki Ucar [aut, cph, cre],
Bart Smeets [aut, cph]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer versions 3.4.4 dated 2016-10-06 and 3.5.0 dated 2016-10-26
simmer-3.4.4/simmer/man/resource.Rd |only simmer-3.4.4/simmer/src/activity.cpp |only simmer-3.5.0/simmer/DESCRIPTION | 14 simmer-3.5.0/simmer/MD5 | 181 +-- simmer-3.5.0/simmer/NAMESPACE | 11 simmer-3.5.0/simmer/NEWS.md | 16 simmer-3.5.0/simmer/R/RcppExports.R | 144 ++ simmer-3.5.0/simmer/R/activity.R | 12 simmer-3.5.0/simmer/R/plot.R | 8 simmer-3.5.0/simmer/R/simulator.R | 108 -- simmer-3.5.0/simmer/R/trajectory.R | 319 +++++- simmer-3.5.0/simmer/R/utils.R | 13 simmer-3.5.0/simmer/R/wrap.R | 2 simmer-3.5.0/simmer/TODO | 1 simmer-3.5.0/simmer/inst/doc/A-introduction.html | 62 - simmer-3.5.0/simmer/inst/doc/B-terminology.Rmd | 2 simmer-3.5.0/simmer/inst/doc/B-terminology.html | 8 simmer-3.5.0/simmer/inst/doc/C-trajectories.R | 236 +++- simmer-3.5.0/simmer/inst/doc/C-trajectories.Rmd | 354 +++++- simmer-3.5.0/simmer/inst/doc/C-trajectories.html | 530 +++++++--- simmer-3.5.0/simmer/inst/doc/D-bank-1.html | 4 simmer-3.5.0/simmer/inst/doc/E-queueing-systems.html | 4 simmer-3.5.0/simmer/inst/doc/F-ctmc.html | 4 simmer-3.5.0/simmer/man/activate.Rd |only simmer-3.5.0/simmer/man/add_generator.Rd | 10 simmer-3.5.0/simmer/man/add_resource.Rd | 4 simmer-3.5.0/simmer/man/batch.Rd | 8 simmer-3.5.0/simmer/man/branch.Rd | 6 simmer-3.5.0/simmer/man/clone.Rd | 8 simmer-3.5.0/simmer/man/create_trajectory.Rd | 11 simmer-3.5.0/simmer/man/get_capacity.Rd |only simmer-3.5.0/simmer/man/get_head.Rd | 8 simmer-3.5.0/simmer/man/get_mon.Rd | 10 simmer-3.5.0/simmer/man/get_n_activities.Rd | 6 simmer-3.5.0/simmer/man/get_n_generated.Rd | 6 simmer-3.5.0/simmer/man/get_next_activity.Rd | 2 simmer-3.5.0/simmer/man/join.Rd | 2 simmer-3.5.0/simmer/man/leave.Rd | 6 simmer-3.5.0/simmer/man/log_.Rd |only simmer-3.5.0/simmer/man/now.Rd | 4 simmer-3.5.0/simmer/man/peek.Rd | 4 simmer-3.5.0/simmer/man/plot_attributes.Rd | 2 simmer-3.5.0/simmer/man/plot_evolution_arrival_times.Rd | 2 simmer-3.5.0/simmer/man/plot_resource_usage.Rd | 2 simmer-3.5.0/simmer/man/plot_resource_utilization.Rd | 2 simmer-3.5.0/simmer/man/print_activity.Rd | 2 simmer-3.5.0/simmer/man/renege_in.Rd | 8 simmer-3.5.0/simmer/man/reset.Rd | 4 simmer-3.5.0/simmer/man/rollback.Rd | 6 simmer-3.5.0/simmer/man/run.Rd | 6 simmer-3.5.0/simmer/man/seize.Rd | 15 simmer-3.5.0/simmer/man/select.Rd | 9 simmer-3.5.0/simmer/man/send.Rd |only simmer-3.5.0/simmer/man/set_attribute.Rd | 6 simmer-3.5.0/simmer/man/set_capacity.Rd |only simmer-3.5.0/simmer/man/set_prioritization.Rd | 6 simmer-3.5.0/simmer/man/set_trajectory.Rd |only simmer-3.5.0/simmer/man/simmer.Rd | 4 simmer-3.5.0/simmer/man/timeout.Rd | 6 simmer-3.5.0/simmer/man/wrap.Rd | 4 simmer-3.5.0/simmer/src/RcppExports.cpp | 463 +++++++- simmer-3.5.0/simmer/src/activity.h | 511 ++++++++- simmer-3.5.0/simmer/src/entity.h | 4 simmer-3.5.0/simmer/src/process.cpp | 172 +-- simmer-3.5.0/simmer/src/process.h | 175 ++- simmer-3.5.0/simmer/src/resource.cpp | 24 simmer-3.5.0/simmer/src/resource.h | 20 simmer-3.5.0/simmer/src/simmer.h | 17 simmer-3.5.0/simmer/src/simmer_rcpp.cpp | 204 +++ simmer-3.5.0/simmer/src/simulator.h | 72 - simmer-3.5.0/simmer/tests/testthat/test-chaining.R | 2 simmer-3.5.0/simmer/tests/testthat/test-plot.R | 6 simmer-3.5.0/simmer/tests/testthat/test-simmer-generator.R | 14 simmer-3.5.0/simmer/tests/testthat/test-simmer-resource-preemption.R | 16 simmer-3.5.0/simmer/tests/testthat/test-simmer-resource-priorities.R | 6 simmer-3.5.0/simmer/tests/testthat/test-simmer-resource-schedule.R | 18 simmer-3.5.0/simmer/tests/testthat/test-simmer-resource.R | 29 simmer-3.5.0/simmer/tests/testthat/test-simmer.R | 18 simmer-3.5.0/simmer/tests/testthat/test-simulation-1.R | 8 simmer-3.5.0/simmer/tests/testthat/test-simulation-2.R | 2 simmer-3.5.0/simmer/tests/testthat/test-trajectory-activate-deactivate.R |only simmer-3.5.0/simmer/tests/testthat/test-trajectory-batch-separate.R | 36 simmer-3.5.0/simmer/tests/testthat/test-trajectory-branch.R | 4 simmer-3.5.0/simmer/tests/testthat/test-trajectory-log.R |only simmer-3.5.0/simmer/tests/testthat/test-trajectory-renege.R | 56 - simmer-3.5.0/simmer/tests/testthat/test-trajectory-rollback.R | 2 simmer-3.5.0/simmer/tests/testthat/test-trajectory-seize-release.R | 44 simmer-3.5.0/simmer/tests/testthat/test-trajectory-select.R | 38 simmer-3.5.0/simmer/tests/testthat/test-trajectory-send-trap.R |only simmer-3.5.0/simmer/tests/testthat/test-trajectory-set-capacity-queue.R |only simmer-3.5.0/simmer/tests/testthat/test-trajectory-set-trajectory-distribution.R |only simmer-3.5.0/simmer/tests/testthat/test-trajectory-setattribute.R | 6 simmer-3.5.0/simmer/tests/testthat/test-trajectory-setprioritization.R | 3 simmer-3.5.0/simmer/tests/testthat/test-trajectory-timeout.R | 2 simmer-3.5.0/simmer/tests/testthat/test-trajectory.R | 30 simmer-3.5.0/simmer/tests/testthat/test-wrap.R | 2 simmer-3.5.0/simmer/vignettes/B-terminology.Rmd | 2 simmer-3.5.0/simmer/vignettes/C-trajectories.Rmd | 354 +++++- 98 files changed, 3418 insertions(+), 1154 deletions(-)
Title: Interface to the iDigBio Data API
Description: An interface to iDigBio's search API that allows downloading
specimen records. Searches are returned as a data.frame. Other functions
such as the metadata end points return lists of information. iDigBio is a US
project focused on digitizing and serving museum specimen collections on the
web. See <https://www.idigbio.org> for information on iDigBio.
Author: Francois Michonneau [aut, cph],
Matthew Collins [aut, cre],
Scott Chamberlain [ctb],
Kevin Love [ctb],
Hem Nalini Morzaria-Luna [ctb]
Maintainer: Matthew Collins <mcollins@acis.ufl.edu>
Diff between ridigbio versions 0.3.3 dated 2016-01-12 and 0.3.4 dated 2016-10-26
DESCRIPTION | 28 ++++++++++++++---------- MD5 | 21 ++++++++++-------- NAMESPACE | 1 R/base.R | 6 ++--- R/idig_build_attrib.R |only R/idig_search.R | 27 ++++++++++++++++++----- R/idig_search_records.R | 35 ++++++++++++++++++++++++++++-- README.md | 2 - man/idig_build_attrib.Rd |only man/idig_search.Rd | 4 +-- man/idig_search_records.Rd | 32 ++++++++++++++++++++++++++- tests/testthat/test-idig_build_attrib.R |only tests/testthat/test-idig_search_records.R | 20 +++++++++++++++-- 13 files changed, 140 insertions(+), 36 deletions(-)
Title: Fits Psychometric Functions for Multiple Groups
Description: Quickly fits and plots psychometric functions (normal, logistic,
Weibull or any or any function defined by the user) for multiple groups.
Author: Linares Daniel [aut, cre],
López-Moliner Joan [aut]
Maintainer: Linares Daniel <danilinares@gmail.com>
Diff between quickpsy versions 0.1.3 dated 2016-06-13 and 0.1.4 dated 2016-10-26
DESCRIPTION | 6 +++--- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + R/plotcurves_.R | 11 +++++++---- R/plotthresholds_.R | 2 +- R/quickpsy.R | 5 ++--- R/quickpsy_.R | 3 ++- R/quickreadfiles.R | 3 ++- R/thresholds.R | 13 +++---------- README.md |only man/quickpsy.Rd | 5 ++--- man/thresholds.Rd | 15 ++++++--------- 12 files changed, 40 insertions(+), 45 deletions(-)
Title: Heller-Heller-Gorfine Tests of Independence and Equality of
Distributions
Description: Heller-Heller-Gorfine ('HHG') tests are a set of powerful statistical
tests of multivariate k-sample homogeneity and independence. For the univariate
case, the package also offers implementations of the 'MinP DDP' and 'MinP ADP'
tests, which are consistent against all continuous alternatives but are
distribution-free, and are thus much faster to apply.
Author: Barak Brill & Shachar Kaufman, based in part on an earlier
implementation by Ruth Heller and Yair Heller.
Maintainer: Barak Brill <barakbri@mail.tau.ac.il>
Diff between HHG versions 1.5.1 dated 2015-07-14 and 2.0 dated 2016-10-26
DESCRIPTION | 18 MD5 | 60 +- NAMESPACE | 2 R/HHG_additional_univariate.R |only R/HHG_extras.R | 3 R/HHG_univariate.R | 792 +++++++++++++++++++++++----- R/HHG_utils.R | 56 + build/vignette.rds |binary inst/doc/HHG.R | 310 ++++++++++ inst/doc/HHG.Rmd | 347 +++++++++++- inst/doc/HHG.html | 322 ++++++++++- man/Fast.independence.test.Rd |only man/Fast.independence.test.nulltable.Rd |only man/HHG-package.Rd | 56 + man/hhg.example.datagen.Rd | 6 man/hhg.univariate.ind.combined.test.Rd | 80 ++ man/hhg.univariate.ind.nulltable.Rd | 53 + man/hhg.univariate.ind.pvalue.Rd | 45 + man/hhg.univariate.ind.stat.Rd | 66 ++ man/hhg.univariate.ks.combined.test.Rd | 82 ++ man/hhg.univariate.ks.nulltable.Rd | 41 + man/hhg.univariate.ks.pvalue.Rd | 34 + man/hhg.univariate.ks.stat.Rd | 45 + man/hhg.univariate.nulltable.from.mstats.Rd | 49 + man/nr_bins_equipartition.Rd |only src/HHG.cpp | 134 +++- src/HHG.h | 19 src/Makevars.win | 4 src/SequentialTest.cpp | 1 src/StatsComputer.cpp | 650 +++++++++++++++++++--- src/StatsComputer.h | 15 vignettes/HHG.Rmd | 457 ++++++++++++---- vignettes/style.css | 8 33 files changed, 3193 insertions(+), 562 deletions(-)
Title: Sustainable Transport Planning
Description: Functionality and data access tools for transport planning,
including origin-destination analysis, route allocation and modelling travel
patterns.
Author: Robin Lovelace [aut, cre],
Richard Ellison [aut],
Barry Rowlingson [aut] (Author of overline),
Nick Bearman [aut] (Co-author of gclip),
Malcolm Morgan [aut] (Co-author of angle_diff)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.1.4 dated 2016-08-29 and 0.1.5 dated 2016-10-26
stplanr-0.1.4/stplanr/inst/osm_routenet.R |only stplanr-0.1.4/stplanr/man/cyclestreet_pat.Rd |only stplanr-0.1.4/stplanr/man/graphhopper_pat.Rd |only stplanr-0.1.5/stplanr/DESCRIPTION | 12 stplanr-0.1.5/stplanr/MD5 | 103 +-- stplanr-0.1.5/stplanr/NAMESPACE | 5 stplanr-0.1.5/stplanr/NEWS | 15 stplanr-0.1.5/stplanr/R/RcppExports.R | 2 stplanr-0.1.5/stplanr/R/crs-funs.R | 30 - stplanr-0.1.5/stplanr/R/cyclestreets.R | 2 stplanr-0.1.5/stplanr/R/data.r | 56 + stplanr-0.1.5/stplanr/R/linefuns.R | 71 ++ stplanr-0.1.5/stplanr/R/load-stats19.R | 10 stplanr-0.1.5/stplanr/R/od-funs.R | 167 ++++- stplanr-0.1.5/stplanr/R/osrmfunctions.R | 73 +- stplanr-0.1.5/stplanr/R/overline.R | 4 stplanr-0.1.5/stplanr/R/radiate.R | 8 stplanr-0.1.5/stplanr/R/route-transport-api.R | 47 + stplanr-0.1.5/stplanr/R/routes.R | 284 +++++----- stplanr-0.1.5/stplanr/R/toptail.R | 21 stplanr-0.1.5/stplanr/README.md | 41 - stplanr-0.1.5/stplanr/data/destination_zones.rda |only stplanr-0.1.5/stplanr/data/destinations.rda |only stplanr-0.1.5/stplanr/data/flow_dests.rda |only stplanr-0.1.5/stplanr/inst/doc/introducing-stplanr.html | 41 - stplanr-0.1.5/stplanr/man/angle_diff.Rd | 3 stplanr-0.1.5/stplanr/man/api_pat.Rd |only stplanr-0.1.5/stplanr/man/buff_geo.Rd | 8 stplanr-0.1.5/stplanr/man/destination_zones.Rd |only stplanr-0.1.5/stplanr/man/flow.Rd | 1 stplanr-0.1.5/stplanr/man/flow_dests.Rd |only stplanr-0.1.5/stplanr/man/gprojected.Rd | 1 stplanr-0.1.5/stplanr/man/is_linepoint.Rd | 1 stplanr-0.1.5/stplanr/man/line2df.Rd | 1 stplanr-0.1.5/stplanr/man/line2route.Rd | 15 stplanr-0.1.5/stplanr/man/line_bearing.Rd | 1 stplanr-0.1.5/stplanr/man/line_length.Rd |only stplanr-0.1.5/stplanr/man/line_midpoint.Rd | 3 stplanr-0.1.5/stplanr/man/line_segment.Rd |only stplanr-0.1.5/stplanr/man/n_vertices.Rd | 1 stplanr-0.1.5/stplanr/man/nearest_cyclestreets.Rd | 6 stplanr-0.1.5/stplanr/man/od2line.Rd | 21 stplanr-0.1.5/stplanr/man/od2odf.Rd | 4 stplanr-0.1.5/stplanr/man/od_dist.Rd | 3 stplanr-0.1.5/stplanr/man/onewaygeo.Rd | 2 stplanr-0.1.5/stplanr/man/onewayid.Rd | 2 stplanr-0.1.5/stplanr/man/points2flow.Rd | 1 stplanr-0.1.5/stplanr/man/points2odf.Rd | 1 stplanr-0.1.5/stplanr/man/reproject.Rd | 1 stplanr-0.1.5/stplanr/man/route_cyclestreet.Rd | 51 + stplanr-0.1.5/stplanr/man/route_graphhopper.Rd | 24 stplanr-0.1.5/stplanr/man/route_transportapi_public.Rd | 12 stplanr-0.1.5/stplanr/man/update_line_geometry.Rd | 1 stplanr-0.1.5/stplanr/man/viaroute.Rd | 9 stplanr-0.1.5/stplanr/src/RcppExports.cpp | 18 stplanr-0.1.5/stplanr/tests/testthat/test-calc_catchment.R | 2 stplanr-0.1.5/stplanr/tests/testthat/test-route_cyclestreet.R | 6 stplanr-0.1.5/stplanr/tests/testthat/test-route_graphhopper.R | 8 58 files changed, 793 insertions(+), 406 deletions(-)
Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre],
Kent Russell [aut, ctb],
Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Susie Lu [aut, cph] (d3-legend library, http://d3-legend.susielu.com/),
Speros Kokenes [aut, cph] (d3-lasso-plugin library,
https://github.com/skokenes/D3-Lasso-Plugin)
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.6.2 dated 2016-03-24 and 0.7 dated 2016-10-26
scatterD3-0.6.2/scatterD3/inst/htmlwidgets/lib/d3-3.5.6.min.js |only scatterD3-0.6.2/scatterD3/inst/htmlwidgets/lib/d3-legend.min.js |only scatterD3-0.6.2/scatterD3/inst/htmlwidgets/lib/scatterD3.css |only scatterD3-0.7/scatterD3/DESCRIPTION | 8 scatterD3-0.7/scatterD3/MD5 | 59 scatterD3-0.7/scatterD3/NEWS | 23 scatterD3-0.7/scatterD3/R/scatterD3.R | 454 +- scatterD3-0.7/scatterD3/README.md | 74 scatterD3-0.7/scatterD3/build/vignette.rds |binary scatterD3-0.7/scatterD3/inst/doc/introduction.R | 128 scatterD3-0.7/scatterD3/inst/doc/introduction.Rmd | 253 + scatterD3-0.7/scatterD3/inst/doc/introduction.html | 363 +- scatterD3-0.7/scatterD3/inst/htmlwidgets/lib/d3 |only scatterD3-0.7/scatterD3/inst/htmlwidgets/lib/d3-lasso-plugin/lasso.js | 92 scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-arrows.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-axes.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-dots.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-ellipses.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-exports.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-labels.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-lasso.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-legend.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-lines.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-setup.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3-utils.js |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3.css |only scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3.js | 1628 +++------- scatterD3-0.7/scatterD3/inst/htmlwidgets/scatterD3.yaml | 44 scatterD3-0.7/scatterD3/man/scatterD3.Rd | 131 scatterD3-0.7/scatterD3/vignettes/introduction.Rmd | 253 + 30 files changed, 2019 insertions(+), 1491 deletions(-)
Title: Methods for the Indirect Estimation of Bilateral Migration
Description: Indirect methods for estimating bilateral migration flows in the presence of partial or missing data. Methods might be relevant to other categorical data situations on non-migration data, where for example, marginal totals are known and only auxiliary bilateral data is available.
Author: Guy J. Abel
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between migest versions 1.7.2 dated 2016-05-15 and 1.7.3 dated 2016-10-26
migest-1.7.2/migest/R/fn_migest.R |only migest-1.7.3/migest/DESCRIPTION | 6 ++-- migest-1.7.3/migest/MD5 | 43 +++++++++++++++++++----------- migest-1.7.3/migest/R/block.matrix.R.R |only migest-1.7.3/migest/R/block.sum.R.R |only migest-1.7.3/migest/R/cm2.R |only migest-1.7.3/migest/R/cm3.R |only migest-1.7.3/migest/R/ffs.R |only migest-1.7.3/migest/R/fm.R |only migest-1.7.3/migest/R/ipf2.R |only migest-1.7.3/migest/R/ipf2.b.R.R |only migest-1.7.3/migest/R/ipf3.R |only migest-1.7.3/migest/R/ipf3.qi.R.R |only migest-1.7.3/migest/R/rc9.R |only migest-1.7.3/migest/demo/cfplot_nat.R | 7 ++-- migest-1.7.3/migest/demo/cfplot_reg.R | 8 +++-- migest-1.7.3/migest/demo/cfplot_reg2.R | 24 ++++++++-------- migest-1.7.3/migest/man/block.matrix.Rd |only migest-1.7.3/migest/man/block.sum.Rd |only migest-1.7.3/migest/man/cm2.Rd | 10 +++--- migest-1.7.3/migest/man/cm3.Rd | 8 ++--- migest-1.7.3/migest/man/ffs.Rd | 4 +- migest-1.7.3/migest/man/fm.Rd | 2 - migest-1.7.3/migest/man/ipf2.Rd | 8 ++--- migest-1.7.3/migest/man/ipf2.b.Rd |only migest-1.7.3/migest/man/ipf3.Rd | 6 ++-- migest-1.7.3/migest/man/ipf3.qi.Rd | 8 ++--- migest-1.7.3/migest/man/migest-package.Rd | 4 +- migest-1.7.3/migest/man/rc9.Rd | 10 +++--- migest-1.7.3/migest/man/rc9.fund.Rd | 9 +++--- 30 files changed, 87 insertions(+), 70 deletions(-)
Title: Incremental Decomposition Methods
Description: Incremental Multiple Correspondence Analysis and Principal
Component Analysis.
Author: Alfonso Iodice D' Enza [aut], Angelos Markos [aut, cre], Davide
Buttarazzi [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between idm versions 1.3.1 dated 2016-03-10 and 1.7.1 dated 2016-10-26
DESCRIPTION | 13 - MD5 | 52 +++-- NAMESPACE | 22 +- R/add_es.R | 41 ++-- R/add_svd.R | 3 R/ani_plot.R | 26 ++ R/do_es.r | 5 R/h_exact_mca.r | 46 ++--- R/i_mca.r | 11 - R/i_pca.r | 463 +++++++++++++++++++++++++--------------------------- R/mat_split.r | 5 R/plot.i_mca.R | 23 +- R/plot.i_pca.r | 29 ++- R/plot_fun.R | 20 +- R/r_live_mca.r | 32 +-- R/static_plot.r | 49 +++-- R/update.i_mca.R | 230 ++++++++++++------------- R/update.i_pca.R | 122 ++++++------- data/enron.rda |only man/add_es.Rd | 200 +++++++++++----------- man/enron.Rd |only man/i_mca.Rd | 186 ++++++++++---------- man/i_pca.Rd | 164 +++++++++--------- man/idm.Rd | 62 +++--- man/plot.i_mca.Rd | 40 ++-- man/plot.i_pca.Rd | 101 +++++------ man/update.i_mca.Rd | 119 ++++++------- man/update.i_pca.Rd | 107 ++++++------ 28 files changed, 1127 insertions(+), 1044 deletions(-)
Title: A Few GPU Enabled Functions
Description: Provides R interfaces to a handful of common
functions implemented using the Nvidia CUDA toolkit. Some of the
functions require at least GPU Compute Capability 1.3.
Thanks to Craig Stark at UC Irvine for donating time on his lab's Mac.
Author: Josh Buckner [aut, cre],
Mark Seligman [aut],
Fan Meng [aut],
Justin Wilson [ctb]
Maintainer: Josh Buckner <nullsatz@gmail.com>
Diff between gputools versions 1.0 dated 2015-11-11 and 1.1 dated 2016-10-26
DESCRIPTION | 14 MD5 | 23 NEWS | 5 R/gpuCor.R | 9 configure | 2567 +++++++++++++++++++++++++++--------------------------- configure.ac | 134 +- inst |only src/Makefile.in | 28 src/correlation.h | 3 src/kendall.cu | 154 +-- src/kendall.h | 5 src/rinterface.cu | 5 src/rinterface.h | 3 13 files changed, 1512 insertions(+), 1438 deletions(-)
Title: Dynamic Web-Based Analytics for the Energy Industry
Description: A 'Shiny' web application for energy industry analytics.
Take an overview of the industry, measure Key Performance Indicators,
identify changes in the industry over time, and discover new relationships in the data.
Author: Paul Govan [aut, cre]
Maintainer: Paul Govan <pgovan1@aggienetwork.com>
Diff between eAnalytics versions 0.1.0 dated 2016-07-29 and 0.1.1 dated 2016-10-26
eAnalytics-0.1.0/eAnalytics/inst/images/Dashboard2.png |only eAnalytics-0.1.1/eAnalytics/DESCRIPTION | 12 eAnalytics-0.1.1/eAnalytics/MD5 | 19 eAnalytics-0.1.1/eAnalytics/NEWS.md |only eAnalytics-0.1.1/eAnalytics/R/eAnalytics.R | 2 eAnalytics-0.1.1/eAnalytics/README.md | 58 - eAnalytics-0.1.1/eAnalytics/build |only eAnalytics-0.1.1/eAnalytics/inst/app/rsconnect |only eAnalytics-0.1.1/eAnalytics/inst/app/server.r | 403 +++++++--- eAnalytics-0.1.1/eAnalytics/inst/app/ui.r | 629 ++++++++++------- eAnalytics-0.1.1/eAnalytics/inst/doc |only eAnalytics-0.1.1/eAnalytics/inst/images/Dashboard.png |binary eAnalytics-0.1.1/eAnalytics/vignettes |only 13 files changed, 733 insertions(+), 390 deletions(-)
Title: Beyond the Border
Description: Kernel density estimation dedicated to urban geography.
Author: Psar Analyse Urbaine Insee - Thierry Cornely, Laure Genebes, Arlindo Dos
Santos, Cynthia Faivre, Auriane Renaud and Francois Semecurbe
Maintainer: Arlindo Dos Santos <Arlindo.Dos-Santos@insee.fr>
Diff between btb versions 0.0.7 dated 2016-08-10 and 0.1.2 dated 2016-10-26
btb-0.0.7/btb/R/Class_carroyage.R |only btb-0.0.7/btb/man/Carroyage.Rd |only btb-0.0.7/btb/man/kernel_smoothing.Rd |only btb-0.0.7/btb/man/smoothing_to_grid.Rd |only btb-0.0.7/btb/src/rcpp_lissage.cpp |only btb-0.1.2/btb/DESCRIPTION | 14 +++--- btb-0.1.2/btb/MD5 | 21 +++++----- btb-0.1.2/btb/NAMESPACE | 15 ++++--- btb-0.1.2/btb/R/Grid.R |only btb-0.1.2/btb/R/RcppExports.R | 19 +++++++-- btb-0.1.2/btb/man/Grid-class.Rd |only btb-0.1.2/btb/man/kernelSmoothing.Rd |only btb-0.1.2/btb/man/reunion.Rd | 12 ++--- btb-0.1.2/btb/man/smoothingToGrid.Rd |only btb-0.1.2/btb/src/RcppExports.cpp | 67 +++++++++++++++++++++++--------- btb-0.1.2/btb/src/rcppLissage.cpp |only btb-0.1.2/btb/src/rcppLissageMedian.cpp |only 17 files changed, 99 insertions(+), 49 deletions(-)
More information about tigreBrowserWriter at CRAN
Permanent link
Title: Functions to Support the Multicriteria Decision Aiding Process
Description: Functions which can be useful to support the analyst in the Multicriteria Decision Aiding (MCDA) process involving multiple, conflicting criteria.
Author: Patrick Meyer, Sébastien Bigaret, Richard Hodgett, Alexandru-Liviu Olteanu
Maintainer: Patrick Meyer <patrick.meyer@telecom-bretagne.eu>
Diff between MCDA versions 0.0.12 dated 2015-11-05 and 0.0.13 dated 2016-10-26
DESCRIPTION | 8 +++--- MD5 | 19 ++++++++++---- NAMESPACE | 1 R/pairwiseConsistencyMeasures.R |only R/plotPiecewiseLinearValueFunctions.R | 2 - R/plotRadarPerformanceTable.R | 44 +++++++++++++++++++++++++++------- inst/datasets |only man/pairwiseConsistencyMeasures.Rd |only man/plotRadarPerformanceTable.Rd | 8 ++++-- tests/example.R |only tests/example2.R |only tests/pairwiseConsistencyMeasures.R |only tests/plotRadarPerformanceTable.R | 2 - 13 files changed, 61 insertions(+), 23 deletions(-)
Title: Jane Austen's Complete Novels
Description: Full texts for Jane Austen's 6 completed novels, ready for text
analysis. These novels are "Sense and Sensibility", "Pride and Prejudice",
"Mansfield Park", "Emma", "Northanger Abbey", and "Persuasion".
Author: Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between janeaustenr versions 0.1.3 dated 2016-10-23 and 0.1.4 dated 2016-10-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 11 ++++++++++- R/austen_books.R | 2 +- tests/testthat/test_austen_books.R | 9 +++++++++ 5 files changed, 28 insertions(+), 10 deletions(-)
Title: Genome-Wide Association Study with SLOPE
Description: Genome-wide association study (GWAS) performed with SLOPE,
short for Sorted L-One Penalized Estimation, a
method for estimating the vector of coefficients in linear model.
In the first step of GWAS, SNPs are clumped according to their correlations and
distances. Then, SLOPE is performed on data where each clump has
one representative.
Author: Damian Brzyski [aut],
Christine Peterson [aut],
Emmanuel J. Candes [aut],
Malgorzata Bogdan [aut],
Chiara Sabatti [aut],
Piotr Sobczyk [cre, aut]
Maintainer: Piotr Sobczyk <piotr.sobczyk@pwr.edu.pl>
Diff between geneSLOPE versions 0.36.6 dated 2016-02-02 and 0.37.0 dated 2016-10-26
geneSLOPE-0.36.6/geneSLOPE/README.md |only geneSLOPE-0.37.0/geneSLOPE/DESCRIPTION | 10 +- geneSLOPE-0.37.0/geneSLOPE/MD5 | 21 ++--- geneSLOPE-0.37.0/geneSLOPE/NAMESPACE | 4 - geneSLOPE-0.37.0/geneSLOPE/R/clump_snps.R | 15 ++- geneSLOPE-0.37.0/geneSLOPE/R/geneSLOPE.R | 6 - geneSLOPE-0.37.0/geneSLOPE/R/identify_clump.R | 32 ++------ geneSLOPE-0.37.0/geneSLOPE/R/select_snps.R | 65 ++++++++++------- geneSLOPE-0.37.0/geneSLOPE/inst/doc/GWASwithSLOPE.html | 39 ++++------ geneSLOPE-0.37.0/geneSLOPE/man/clump_snps.Rd | 5 + geneSLOPE-0.37.0/geneSLOPE/man/geneSLOPE.Rd | 4 - geneSLOPE-0.37.0/geneSLOPE/man/select_snps.Rd | 8 +- 12 files changed, 113 insertions(+), 96 deletions(-)
Title: Fast Utility Function for Time Parsing and Conversion
Description: Fast functions for timestamp
manipulation that avoid system calls and take shortcuts
to facilitate operations on very large data.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between fasttime versions 1.0-1 dated 2015-07-28 and 1.0-2 dated 2016-10-26
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS |only man/fastPOSIXct.Rd | 6 +++--- src/tparse.c | 19 +++++++++++++++---- 5 files changed, 25 insertions(+), 13 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.3.1 dated 2016-10-18 and 1.3.2 dated 2016-10-26
DESCRIPTION | 6 - MD5 | 12 +-- NEWS | 6 + R/wrappers.R | 4 - inst/doc/article.pdf |binary inst/doc/heavytails.pdf |binary src/sampler.cpp | 156 ++++++++++++++++++++---------------------------- 7 files changed, 84 insertions(+), 100 deletions(-)
Title: Integrate R with 'RDocumentation.org'
Description: Wraps around the default help functionality in R. Instead of plain documentation files, documentation will now show up as it does on 'RDocumentation.org', a platform that shows R documentation from CRAN, GitHub and Bioconductor, together with informative stats to assess the package quality and possibilities to discuss packages.
Author: Ludovic Vannoorenberghe [cre],
Jonathan Cornelissen [aut],
Hannes Buseyne [ctb],
Filip Schouwenaars [ctb]
Maintainer: Ludovic Vannoorenberghe <ludovic@datacamp.com>
Diff between RDocumentation versions 0.7.0 dated 2016-10-03 and 0.7.1 dated 2016-10-26
RDocumentation-0.7.0/RDocumentation/tests/testthat/test-check-package.R |only RDocumentation-0.7.1/RDocumentation/DESCRIPTION | 19 - RDocumentation-0.7.1/RDocumentation/MD5 | 33 +- RDocumentation-0.7.1/RDocumentation/NAMESPACE | 2 RDocumentation-0.7.1/RDocumentation/NEWS.md | 8 RDocumentation-0.7.1/RDocumentation/R/defaults.R | 12 RDocumentation-0.7.1/RDocumentation/R/install.R | 12 RDocumentation-0.7.1/RDocumentation/R/overrides.R | 161 ++++------ RDocumentation-0.7.1/RDocumentation/R/utils.R | 19 - RDocumentation-0.7.1/RDocumentation/R/view_help.R | 89 ++--- RDocumentation-0.7.1/RDocumentation/R/zzz.R | 1 RDocumentation-0.7.1/RDocumentation/README.md | 10 RDocumentation-0.7.1/RDocumentation/man/check_package.Rd | 2 RDocumentation-0.7.1/RDocumentation/man/documentation.Rd | 4 RDocumentation-0.7.1/RDocumentation/man/install_package.Rd | 4 RDocumentation-0.7.1/RDocumentation/man/view_help.Rd | 6 RDocumentation-0.7.1/RDocumentation/tests/testthat/test-help.R | 89 ++++- RDocumentation-0.7.1/RDocumentation/tests/testthat/test-utils.R |only RDocumentation-0.7.1/RDocumentation/tests/testthat/test-view-help.R |only 19 files changed, 266 insertions(+), 205 deletions(-)
More information about RDocumentation at CRAN
Permanent link
Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Description: The primary aim of MasterBayes is to use MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled C++ for efficiency.
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield <j.hadfield@ed.ac.uk>
Diff between MasterBayes versions 2.53.1 dated 2016-09-07 and 2.54 dated 2016-10-26
DESCRIPTION | 8 +- MD5 | 8 +- R/MCMCped.R | 3 R/getXlist.R | 207 ++++++++++++++++++++++++++++++++++++++++++++++++++++++--- src/MCMCped.cc | 2 5 files changed, 210 insertions(+), 18 deletions(-)
Title: Latent Variable Models
Description: Estimation and simulation of latent variable models.
Author: Klaus K. Holst
Maintainer: Klaus K. Holst <kkho@biostat.ku.dk>
Diff between lava versions 1.4.4 dated 2016-08-13 and 1.4.5 dated 2016-10-26
lava-1.4.4/lava/R/zconfband.R |only lava-1.4.4/lava/R/zimages.R |only lava-1.4.4/lava/R/zksmooth.R |only lava-1.4.4/lava/R/zoperators.R |only lava-1.4.4/lava/R/ztoformula.R |only lava-1.4.4/lava/R/ztr.R |only lava-1.4.5/lava/DESCRIPTION | 16 - lava-1.4.5/lava/INDEX | 31 +- lava-1.4.5/lava/MD5 | 170 ++++++----- lava-1.4.5/lava/NAMESPACE | 36 ++ lava-1.4.5/lava/NEWS | 38 ++ lava-1.4.5/lava/R/Objective.R | 25 - lava-1.4.5/lava/R/addhook.R | 24 + lava-1.4.5/lava/R/assoc.R | 174 +++++++++++ lava-1.4.5/lava/R/backdoor.R |only lava-1.4.5/lava/R/baptize.R | 2 lava-1.4.5/lava/R/bootstrap.R | 3 lava-1.4.5/lava/R/categorical.R | 12 lava-1.4.5/lava/R/children.R | 106 ++++++- lava-1.4.5/lava/R/coef.R | 16 - lava-1.4.5/lava/R/complik.R |only lava-1.4.5/lava/R/confband.R |only lava-1.4.5/lava/R/contr.R |only lava-1.4.5/lava/R/covariance.R | 8 lava-1.4.5/lava/R/describecoef.R | 4 lava-1.4.5/lava/R/diagtest.R | 9 lava-1.4.5/lava/R/distribution.R | 5 lava-1.4.5/lava/R/dsep.R |only lava-1.4.5/lava/R/dsort.R | 13 lava-1.4.5/lava/R/estimate.default.R | 176 ++++++++++- lava-1.4.5/lava/R/estimate.lvm.R | 32 +- lava-1.4.5/lava/R/exogenous.R | 2 lava-1.4.5/lava/R/finalize.R | 5 lava-1.4.5/lava/R/fix.R | 56 ++- lava-1.4.5/lava/R/fixsome.R | 11 lava-1.4.5/lava/R/glmest.R | 25 + lava-1.4.5/lava/R/gof.R | 6 lava-1.4.5/lava/R/img.R |only lava-1.4.5/lava/R/index.sem.R | 6 lava-1.4.5/lava/R/information.R | 15 - lava-1.4.5/lava/R/kappa.R |only lava-1.4.5/lava/R/ksmooth.R |only lava-1.4.5/lava/R/latent.R | 60 +--- lava-1.4.5/lava/R/lava-package.R | 5 lava-1.4.5/lava/R/lmers.R | 8 lava-1.4.5/lava/R/matrices.R | 29 + lava-1.4.5/lava/R/merge.R | 26 + lava-1.4.5/lava/R/modelsearch.R | 48 ++- lava-1.4.5/lava/R/multinomial.R | 157 ---------- lava-1.4.5/lava/R/normal.R | 49 ++- lava-1.4.5/lava/R/operators.R |only lava-1.4.5/lava/R/optims.R | 21 + lava-1.4.5/lava/R/ordinal.R | 6 lava-1.4.5/lava/R/partialcor.R | 29 + lava-1.4.5/lava/R/path.R | 42 ++ lava-1.4.5/lava/R/plot.R | 152 ++++++++-- lava-1.4.5/lava/R/plot.estimate.R | 4 lava-1.4.5/lava/R/print.R | 32 +- lava-1.4.5/lava/R/regression.R | 3 lava-1.4.5/lava/R/sim.R | 342 +++++++++++++---------- lava-1.4.5/lava/R/sim.default.R | 176 +++++++++-- lava-1.4.5/lava/R/summary.R | 22 - lava-1.4.5/lava/R/toformula.R |only lava-1.4.5/lava/R/tr.R |only lava-1.4.5/lava/R/transform.R | 19 + lava-1.4.5/lava/R/utils.R | 58 --- lava-1.4.5/lava/inst/doc/reference.pdf |binary lava-1.4.5/lava/man/backdoor.Rd |only lava-1.4.5/lava/man/children.Rd | 8 lava-1.4.5/lava/man/complik.Rd |only lava-1.4.5/lava/man/confband.Rd | 24 + lava-1.4.5/lava/man/contr.Rd |only lava-1.4.5/lava/man/density.sim.Rd | 10 lava-1.4.5/lava/man/diagtest.Rd | 5 lava-1.4.5/lava/man/dsep.lvm.Rd |only lava-1.4.5/lava/man/dsort.Rd | 5 lava-1.4.5/lava/man/estimate.default.Rd | 31 ++ lava-1.4.5/lava/man/estimate.lvm.Rd | 4 lava-1.4.5/lava/man/images.Rd | 2 lava-1.4.5/lava/man/internal.Rd | 1 lava-1.4.5/lava/man/ksmooth2.Rd | 2 lava-1.4.5/lava/man/lava.options.Rd | 12 lava-1.4.5/lava/man/modelsearch.Rd | 8 lava-1.4.5/lava/man/multinomial.Rd | 1 lava-1.4.5/lava/man/op_concat.Rd | 2 lava-1.4.5/lava/man/op_match.Rd | 2 lava-1.4.5/lava/man/partialcor.Rd | 4 lava-1.4.5/lava/man/path.Rd | 6 lava-1.4.5/lava/man/plot.lvm.Rd | 41 +- lava-1.4.5/lava/man/sim.Rd | 43 +- lava-1.4.5/lava/man/sim.default.Rd | 5 lava-1.4.5/lava/man/toformula.Rd | 2 lava-1.4.5/lava/man/tr.Rd | 9 lava-1.4.5/lava/tests/testthat/test-constrain.R | 8 lava-1.4.5/lava/tests/testthat/test-graph.R |only lava-1.4.5/lava/tests/testthat/test-inference.R | 17 - lava-1.4.5/lava/tests/testthat/test-multigroup.R | 8 97 files changed, 1728 insertions(+), 846 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.3.3 dated 2016-09-12 and 2.3.4 dated 2016-10-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/evenn.R | 24 ++++++++++++------------ man/eVenn-package.Rd | 4 ++-- 4 files changed, 21 insertions(+), 21 deletions(-)
Title: A Novel Topology-Based Pathway Enrichment Analysis Approach
Description: We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database.
We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.
Author: Wei Jiang
Maintainer: Wei Jiang <jiangwei@hrbmu.edu.cn>
Diff between TPEA versions 1.0 dated 2016-08-29 and 2.0 dated 2016-10-26
DESCRIPTION | 14 ++++--- INDEX | 34 ++++++++++++++++- MD5 | 84 +++++++++++++++++++++++++++++++++++++++---- NAMESPACE | 6 ++- R/DownloadKGML.R |only R/NodeGene.R |only R/NodeGeneData.R |only R/PathNetwork.R |only R/UPDATE.R |only R/ViewLatestTime.R |only R/filterNode.R |only R/getEntry.R |only R/getGeneFromEnzyme.R |only R/getGeneFromKGene.R |only R/getGeneFromKO.R |only R/getGraphics.R |only R/getKGeneFromEnzyme.R |only R/getKGeneFromKO.R |only R/getNonMetabolicGraph.R |only R/getOrgAndIdType.R |only R/getPathway.R |only R/getProduct.R |only R/getReaction.R |only R/getRelation.R |only R/getSimpleGraph.R |only R/getSubstrate.R |only R/getSubtype.R |only R/getUGraph.R |only R/getUnknowProduct.R |only R/getUnknowReaction.R |only R/getUnknowRelation.R |only R/getUnknowSubstrate.R |only R/getUnknowSubtype.R |only R/importLatesData.R |only R/mapNode.R |only R/simplifyGraph.R |only data/gene2ec.rda |only data/gene2ko.rda |only data/keggGene2gene.rda |only data/node_gene.rda |binary data/num_node_gene_score.rda |binary man/DownloadKGML.Rd |only man/NodeGene.Rd |only man/NodeGeneData.Rd |only man/PathNetwork.Rd |only man/TPEA-package.Rd | 12 ++++-- man/TPEA.Rd | 2 + man/UPDATE.Rd |only man/ViewLatestTime.Rd |only man/filterNode.Rd |only man/gene2ec.Rd |only man/gene2ko.Rd |only man/getEntry.Rd |only man/getGeneFromEnzyme.Rd |only man/getGeneFromKGene.Rd |only man/getGeneFromKO.Rd |only man/getGraphics.Rd |only man/getKGeneFromEnzyme.Rd |only man/getKGeneFromKO.Rd |only man/getNonMetabolicGraph.Rd |only man/getOrgAndIdType.Rd |only man/getPathway.Rd |only man/getProduct.Rd |only man/getReaction.Rd |only man/getRelation.Rd |only man/getSimpleGraph.Rd |only man/getSubstrate.Rd |only man/getSubtype.Rd |only man/getUGraph.Rd |only man/getUnknowProduct.Rd |only man/getUnknowReaction.Rd |only man/getUnknowRelation.Rd |only man/getUnknowSubstrate.Rd |only man/getUnknowSubtype.Rd |only man/importLatesData.Rd |only man/keggGene2gene.Rd |only man/mapNode.Rd |only man/simplifyGraph.Rd |only 78 files changed, 134 insertions(+), 18 deletions(-)
Title: Tools for Analyzing Planar Shape and Associated Patterns
Description: An evolving and growing collection of tools for the quantification, assessment, and comparison of planar shape and pattern. The current flagship functionality is in the spatial decomposition of planar shapes using 'ShrinkShape' to incrementally shrink shapes to extinction while computing area, perimeter, and number of parts at each iteration of shrinking. The spectra of results are returned in graphic and tabular formats. Additional utility tools for handling data are provided and this package will be added to as more tools are created, cleaned-up, and documented.
Author: Tarmo K. Remmel
Maintainer: Tarmo K. Remmel <remmelt@yorku.ca>
Diff between ShapePattern versions 1.0 dated 2016-04-27 and 1.0.1 dated 2016-10-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/batchssr.R | 11 +++-------- R/shpsplitter.R | 12 +++--------- R/ssr.R | 15 +++++++-------- build/partial.rdb |binary 6 files changed, 22 insertions(+), 34 deletions(-)
Title: OCI Based Oracle Database Interface for R
Description: Oracle Database interface (DBI) driver for R.
This is a DBI-compliant Oracle driver based on the OCI.
Author: Denis Mukhin, David A. James and Jake Luciani
Maintainer: Rajendra S. Pingte <rajendra.pingte@oracle.com>
Diff between ROracle versions 1.2-2 dated 2016-02-17 and 1.3-1 dated 2016-10-26
ROracle-1.2-2/ROracle/inst/doc/man/de/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/de/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/en/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/en/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/es/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/es/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/fr/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/fr/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/it/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/it/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/ja/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/ja/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/ko/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/ko/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/pt_BR/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/pt_BR/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/zh_CN/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/zh_CN/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/zh_TW/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/inst/doc/man/zh_TW/dbSetDataMappings-methods.Rd |only ROracle-1.2-2/ROracle/man/dbCallProc-methods.Rd |only ROracle-1.2-2/ROracle/man/dbSetDataMappings-methods.Rd |only ROracle-1.3-1/ROracle/DESCRIPTION | 8 ROracle-1.3-1/ROracle/INSTALL | 62 ROracle-1.3-1/ROracle/MD5 | 47 ROracle-1.3-1/ROracle/NAMESPACE | 8 ROracle-1.3-1/ROracle/NEWS | 22 ROracle-1.3-1/ROracle/R/dbi.R | 33 ROracle-1.3-1/ROracle/R/oci.R | 232 ++ ROracle-1.3-1/ROracle/configure | 18 ROracle-1.3-1/ROracle/configure.ac | 10 ROracle-1.3-1/ROracle/inst/doc/man/en/oracleProc-methods.Rd |only ROracle-1.3-1/ROracle/src/rodbi.c | 1032 +++++++++- ROracle-1.3-1/ROracle/src/rodbi.h | 7 ROracle-1.3-1/ROracle/src/rooci.c | 287 ++ ROracle-1.3-1/ROracle/src/rooci.h | 25 36 files changed, 1623 insertions(+), 168 deletions(-)
Title: Entrez in R
Description: Provides an R interface to the NCBI's EUtils API
allowing users to search databases like GenBank and PubMed, process the
results of those searches and pull data into their R sessions.
Author: David Winter [aut, cre],
Scott Chamberlain [ctb],
Han Guangchun [ctb]
Maintainer: David Winter <david.winter@gmail.com>
Diff between rentrez versions 1.0.2 dated 2016-04-21 and 1.0.4 dated 2016-10-26
DESCRIPTION | 10 - MD5 | 16 +- NEWS | 9 + R/base.r | 5 R/entrez_fetch.r | 17 +- build/vignette.rds |binary inst/doc/rentrez_tutorial.html | 312 +++++++++++++++++++++-------------------- man/entrez_fetch.Rd | 18 +- tests/testthat/test_fetch.r | 4 9 files changed, 218 insertions(+), 173 deletions(-)
Title: Orthogonalizing EM
Description: Solves penalized least squares problems using the orthogonalizing EM algorithm of Xiong et al. (2016) <doi:10.1080/00401706.2015.1054436>. The main fitting function is oem() and the functions cv.oem() and xval.oem() are for cross validation, the latter being an accelerated cross validation function for linear models. The big.oem() function allows for out of memory fitting.
Author: Bin Dai [aut],
Jared Huling [aut, cre],
Yixuan Qiu [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between oem versions 2.0.2 dated 2016-10-25 and 2.0.3 dated 2016-10-26
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- inst/doc/oem_vignette.html | 42 +++++++++++++++++++++--------------------- src/oem_big.h | 6 +++--- src/oem_dense.h | 6 +++--- src/oem_logistic_dense.h | 6 +++--- src/oem_logistic_sparse.h | 6 +++--- src/oem_sparse.h | 10 +++++----- src/oem_xtx.h | 6 +++--- src/oem_xval_dense.h | 6 +++--- src/utils.cpp | 10 +++++----- 11 files changed, 62 insertions(+), 62 deletions(-)
Title: Integrative Random Forest for Gene Regulatory Network Inference
Description: Provides a flexible integrative algorithm that allows information from prior data, such as protein protein interactions and gene knock-down, to be jointly considered for gene regulatory network inference.
Author: Francesca Petralia [aut, cre],
Pei Wang [aut],
Zhidong Tu [aut],
Jialiang Yang [aut],
Adele Cutler [ctb],
Leo Breiman [ctb],
Andy Liaw [ctb],
Matthew Wiener [ctb]
Maintainer: Francesca Petralia <francesca.petralia@mssm.edu>
Diff between iRafNet versions 0.1-1 dated 2016-01-27 and 1.1-1 dated 2016-10-26
DESCRIPTION | 43 ++++++++++++++++++++++--------------------- MD5 | 20 ++++++++++++++------ NAMESPACE | 9 +++++++-- R/IRafNet_network.R |only R/Run_permutation.R |only R/iRafNet.R | 18 ++++++++++++------ R/iRafNet_permutation.R |only R/roc_curve.R |only man/Run_permutation.Rd |only man/iRafNet.Rd | 27 ++++++++++----------------- man/iRafNet_network.Rd |only man/iRafNet_permutation.Rd |only man/roc_curve.Rd |only src/regTree.c | 12 ++++-------- src/regrf.c | 3 +++ 15 files changed, 72 insertions(+), 60 deletions(-)
Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 2.2 dated 2016-08-01 and 2.3 dated 2016-10-26
DESCRIPTION | 8 +- MD5 | 158 ++++++++++++++++++++++----------------------- NAMESPACE | 4 - R/Arotation.R | 2 R/acg.R | 16 +--- R/bic.mixvmf.R | 8 +- R/circ.cor1.R | 6 - R/circ.summary.R | 12 +-- R/circlin.cor.R | 2 R/conc.test.R | 12 +-- R/dirknn.R | 24 +++--- R/dirknn.tune.R | 22 +++--- R/embed.aov.R | 14 +-- R/euclid.R | 12 ++- R/euclid.inv.R | 10 +- R/eul2rot.R | 16 ++-- R/fb.saddle.R | 8 +- R/fishkent.R | 22 +++--- R/ggvm.R | 4 - R/group.gof.R | 2 R/group.vm.R | 14 +-- R/hcf.aov.R | 14 +-- R/hcf.circaov.R | 6 - R/het.aov.R | 10 +- R/het.circaov.R | 6 - R/kent.datacontour.R | 13 +-- R/kent.mle.R | 6 - R/knn.reg.R | 26 +++---- R/knnreg.tune.R | 25 +++---- R/kuiper.R | 6 - R/lambert.R | 2 R/lambert.inv.R | 10 +- R/lr.aov.R | 18 ++--- R/lr.circaov.R | 40 +++++------ R/meandir.test.R | 34 +++------ R/mediandir.R | 16 ++-- R/mediandir_2.R | 5 - R/mix.vmf.R | 38 +++++----- R/mixvmf.contour.R | 4 - R/pvm.R | 18 ++--- R/rayleigh.R | 14 +-- R/rmatrixfisher.R | 8 +- R/rot.matrix.R | 12 +-- R/rsop.R | 4 - R/rvmf.R | 50 +++++++------- R/rvnomises.R | 4 - R/spher.cor.R | 14 +-- R/spher.reg.R | 6 - R/spherconc.test.R | 18 ++--- R/spml.reg.R | 17 +--- R/tang.conc.R | 6 - R/vec.R | 5 + R/visual.check.R | 34 +++------ R/vm.kde.R | 14 +-- R/vmf.R | 12 +-- R/vmf.da.R | 41 +++++------ R/vmf.kde.R | 16 ++-- R/vmf.kerncontour.R | 17 ++-- R/vmfda.pred.R | 11 +-- R/vmfkde.tune.R | 10 +- R/vmkde.tune.R | 4 - R/watson.R | 6 - R/wood.mle.R | 10 +- man/Directional-package.Rd | 6 - man/acg.Rd | 2 man/circ.cor1.Rd | 4 - man/euclid.inv.Rd | 2 man/eul2rot.Rd | 2 man/f.rbing.Rd | 2 man/fb.saddle.Rd | 1 man/kuiper.Rd | 4 - man/meandir.test.Rd | 2 man/rayleigh.Rd | 3 man/rmatrixfisher.Rd | 4 - man/rmixvmf.Rd | 2 man/rot2eul.Rd | 2 man/rvmf.Rd | 4 - man/visual.check.Rd | 38 +++------- man/vmf.kde.Rd | 2 man/wood.mle.Rd | 4 - 80 files changed, 529 insertions(+), 561 deletions(-)
More information about clust.bin.pair at CRAN
Permanent link
Title: Programming with Big Data -- Demonstrations and Examples Using
'pbdR' Packages
Description: A set of demos of 'pbdR' packages, together with a useful,
unifying vignette.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut]
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdDEMO versions 0.3-0 dated 2016-01-24 and 0.3-1 dated 2016-10-25
pbdDEMO-0.3-0/pbdDEMO/COPYING |only pbdDEMO-0.3-0/pbdDEMO/INSTALL |only pbdDEMO-0.3-0/pbdDEMO/build |only pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_cov.r |only pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_lmfit.r |only pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_pca.r |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/pics/Phylogeny_of_Retroviruses.jpg |only pbdDEMO-0.3-1/pbdDEMO/ChangeLog | 5 pbdDEMO-0.3-1/pbdDEMO/DESCRIPTION | 21 +- pbdDEMO-0.3-1/pbdDEMO/MD5 | 70 ++++----- pbdDEMO-0.3-1/pbdDEMO/R/load_balance.r | 2 pbdDEMO-0.3-1/pbdDEMO/README.md | 47 ++++-- pbdDEMO-0.3-1/pbdDEMO/data/TREFHT.rda |binary pbdDEMO-0.3-1/pbdDEMO/demo/00Index | 1 pbdDEMO-0.3-1/pbdDEMO/demo/balance.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/binning.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/gbd_dmat.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/mcmc_rjags.r |only pbdDEMO-0.3-1/pbdDEMO/demo/monte_carlo.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/nc4_serial.r | 4 pbdDEMO-0.3-1/pbdDEMO/demo/ols.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/ols_dmat.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/phyclust_bootstrap.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/quantile.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/randmat_global.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/randmat_local.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/read_csv.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/read_ncdf.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/sample_stat.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/sample_stat_dmat.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/trefht.r | 2 pbdDEMO-0.3-1/pbdDEMO/inst/CITATION | 25 ++- pbdDEMO-0.3-1/pbdDEMO/inst/doc/pbdDEMO-guide.Rnw | 2 pbdDEMO-0.3-1/pbdDEMO/inst/doc/pbdDEMO-guide.pdf |binary pbdDEMO-0.3-1/pbdDEMO/man/load_balance.Rd | 2 pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-guide.Rnw | 2 pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/01-introduction.tex | 3 pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/applications/a4-Bayes.tex | 74 ++++++++-- pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/pbdDEMO.bib | 8 + pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/pics/Phylogeny_of_Retroviruses.png |only pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/pics/galaxy_rjags.pdf |only 41 files changed, 196 insertions(+), 100 deletions(-)
Title: Mean-Variance Regularization
Description: This is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data. It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm). Among those are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. Key features include:
(i) Normalization and/or variance stabilization of the data,
(ii) Computation of mean-variance-regularized t-statistics (F-statistics to follow),
(iii) Generation of diverse diagnostic plots,
(iv) Computationally efficient implementation using C/C++ interfacing and an option for parallel computing to enjoy a faster and easier experience in the R environment.
Author: Jean-Eudes Dazard [aut, cre], Hua Xu [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>
Diff between MVR versions 1.30.3 dated 2016-01-28 and 1.31.0 dated 2016-10-25
MVR-1.30.3/MVR/inst/doc/MVR_1.30.3.pdf |only MVR-1.31.0/MVR/DESCRIPTION | 12 MVR-1.31.0/MVR/MD5 | 34 MVR-1.31.0/MVR/NAMESPACE | 28 MVR-1.31.0/MVR/R/MVRr.internal.r | 763 +++++++++++------- MVR-1.31.0/MVR/R/MVRr.r | 1034 ++++++++++++++----------- MVR-1.31.0/MVR/inst/NEWS | 11 MVR-1.31.0/MVR/inst/doc/MVR_1.31.0.pdf |only MVR-1.31.0/MVR/man/MVR-package.Rd | 40 MVR-1.31.0/MVR/man/MVR.news.Rd | 12 MVR-1.31.0/MVR/man/Real-data.Rd | 12 MVR-1.31.0/MVR/man/Synthetic-data.Rd | 12 MVR-1.31.0/MVR/man/cluster.diagnostic.Rd | 53 - MVR-1.31.0/MVR/man/mvr.Rd | 71 - MVR-1.31.0/MVR/man/mvrt.test.Rd | 112 +- MVR-1.31.0/MVR/man/normalization.diagnostic.Rd | 51 - MVR-1.31.0/MVR/man/stabilization.diagnostic.Rd | 54 - MVR-1.31.0/MVR/man/target.diagnostic.Rd | 51 - MVR-1.31.0/MVR/src/MVRc.cpp | 1 19 files changed, 1285 insertions(+), 1066 deletions(-)
Title: Morphometrics using R
Description: A complete toolkit for morphometrics, from data extraction to
multivariate analyses. Most common 2D morphometrics approaches are
included: outlines, open outlines, configurations of landmarks,
traditional morphometrics, and facilities for data preparation,
manipulation and visualization with a consistent grammar throughout.
Momocs allows reproducible, complex morphometric analyses, paves the
way for a pure open-source workflow in R, and other morphometrics
approaches should be easy to plug in, or develop from, on top of this
canvas.
Author: Vincent Bonhomme [aut, cre],
Julien Claude [aut]
Maintainer: Vincent Bonhomme <bonhomme.vincent@gmail.com>
Diff between Momocs versions 1.0.0 dated 2016-03-18 and 1.1.0 dated 2016-10-25
DESCRIPTION | 26 ++-- MD5 | 189 +++++++++++++++--------------- NAMESPACE | 16 ++ R/Momocs-package.R | 8 - R/babel-import.R | 49 +++++--- R/cl-def-Ldk.R | 2 R/cl-def-Opn.R | 2 R/cl-def-Out.R | 10 - R/cl-handling.R | 42 +++++- R/cl-utilities.R | 45 +++++++ R/coo-shapedescriptors.R | 33 ++++- R/coo-utilities.R | 63 +++++++++- R/core-premodern.R | 2 R/gr-Coo.R | 10 - R/gr-LDA.R | 91 +++++++------- R/gr-PCA.R | 6 R/gr-PCA2.R | 16 +- R/gr-domesticplotters.R | 15 +- R/gr-layers.R | 11 + R/mult-Manova.R | 12 + R/mult-PCA.R | 12 + R/mult-mshapes.R | 3 build/vignette.rds |binary inst/NEWS.Rd | 7 + inst/doc/Momocs_speed_dating.R | 6 inst/doc/Momocs_speed_dating.Rmd | 26 ++-- inst/doc/Momocs_speed_dating.html | 232 ++++++++++++++++++++------------------ man/MANOVA.Rd | 12 + man/Momocs.Rd | 6 man/Out.Rd | 6 man/OutCoe.Rd | 2 man/add_ldk.Rd |only man/boxplot.PCA.Rd | 2 man/coo_align.Rd | 1 man/coo_aligncalliper.Rd | 1 man/coo_alignminradius.Rd | 1 man/coo_alignxax.Rd | 1 man/coo_baseline.Rd | 1 man/coo_bookstein.Rd | 1 man/coo_calliper.Rd | 1 man/coo_centdist.Rd | 1 man/coo_center.Rd | 1 man/coo_centpos.Rd | 1 man/coo_centsize.Rd | 1 man/coo_close.Rd | 2 man/coo_down.Rd | 1 man/coo_dxy.Rd | 1 man/coo_elongation.Rd | 2 man/coo_extract.Rd | 1 man/coo_flip.Rd | 1 man/coo_force2close.Rd | 1 man/coo_interpolate.Rd | 1 man/coo_jitter.Rd | 1 man/coo_left.Rd | 1 man/coo_listpanel.Rd | 4 man/coo_lw.Rd | 2 man/coo_nb.Rd | 1 man/coo_perim.Rd | 1 man/coo_perimcum.Rd | 1 man/coo_perimpts.Rd | 1 man/coo_rev.Rd | 1 man/coo_right.Rd | 1 man/coo_rotate.Rd | 1 man/coo_rotatecenter.Rd | 1 man/coo_sample.Rd | 1 man/coo_samplerr.Rd | 1 man/coo_scale.Rd | 1 man/coo_scalexy.Rd | 1 man/coo_shear.Rd | 1 man/coo_slice.Rd | 1 man/coo_slide.Rd | 1 man/coo_slidedirection.Rd | 3 man/coo_slidegap.Rd | 3 man/coo_smooth.Rd | 1 man/coo_smoothcurve.Rd | 3 man/coo_solidity.Rd | 2 man/coo_template.Rd | 3 man/coo_trans.Rd | 3 man/coo_trim.Rd | 6 man/coo_trimbottom.Rd |only man/coo_trimtop.Rd |only man/coo_up.Rd | 1 man/coo_width.Rd | 2 man/def_ldk.Rd | 8 - man/def_slidings.Rd | 6 man/get_ldk.Rd | 6 man/get_slidings.Rd | 6 man/import_txt.Rd | 4 man/is_closed.Rd | 1 man/lf_structure.Rd | 2 man/nef2Coe.Rd | 7 - man/panel.Coo.Rd | 2 man/plot.LDA.Rd | 6 man/plot.PCA.Rd | 6 man/plot2.PCA.Rd | 10 - man/slidings_scheme.Rd | 6 vignettes/Momocs_speed_dating.Rmd | 26 ++-- 97 files changed, 731 insertions(+), 398 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a
Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <mdramins@ipipan.waw.pl>
Diff between rmcfs versions 1.1.1 dated 2016-03-29 and 1.1.2 dated 2016-10-25
rmcfs-1.1.1/rmcfs/LICENSE |only rmcfs-1.1.1/rmcfs/java/src/dmLab/mcfs/tree/parser/J48NodeParser.java |only rmcfs-1.1.1/rmcfs/java/src/dmLab/utils/cmatrix/AccuracyMeasure.java |only rmcfs-1.1.2/rmcfs/DESCRIPTION | 10 rmcfs-1.1.2/rmcfs/LICENSE.note |only rmcfs-1.1.2/rmcfs/MD5 | 127 - rmcfs-1.1.2/rmcfs/NEWS | 62 rmcfs-1.1.2/rmcfs/R/rmcfs.R | 196 +- rmcfs-1.1.2/rmcfs/R/rmcfs.plot.R | 46 rmcfs-1.1.2/rmcfs/inst/java/dmLab.jar |binary rmcfs-1.1.2/rmcfs/inst/java/weka12.jar |binary rmcfs-1.1.2/rmcfs/java/src/dmLab/DMLabInfo.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/Array.java | 13 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/FArray.java | 40 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/functions/SelectFunctions.java | 5 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/loader/fileLoader/FileLoaderADX.java | 15 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/loader/fileLoader/FileLoaderArff.java | 2 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/saver/Array2ADX.java | 31 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/Classifier.java | 175 + rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/Prediction.java | 121 - rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/PredictionResult.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/WekaClassifier.java | 77 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/WekaTree.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/adx/ADXClassifier.java | 31 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/attributeIndicators/SliqNodeIndicators.java | 7 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/bayesNet/BayesNetClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/ensemble/EnsembleClassifier.java | 18 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/hyperPipes/HyperPipesClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/j48/J48Classifier.java | 299 --- rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/j48/J48Params.java | 18 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/knn/KNNClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/logistic/LogisticClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/m5 |only rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/nb/NBClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/randomForest/RandomForestClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/ripper/RipperClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/rnd/RNDClassifier.java | 19 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/sliq/SliqClassifier.java | 19 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/svm/SVMClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/experiment/classification/ClassificationBody.java | 913 ++++------ rmcfs-1.1.2/rmcfs/java/src/dmLab/experiment/classification/ClassificationParams.java | 23 rmcfs-1.1.2/rmcfs/java/src/dmLab/experiment/ensembleOptimization/EnsembleExperiment.java | 15 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/MCFSFinalCV.java | 41 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/MCFSParams.java | 93 - rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/attributesID/AttributesID.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/attributesID/DependencyFactors.java | 7 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/attributesRI/AttributesRI.java | 6 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/MCFSExperiment.java | 30 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/framework/GlobalStats.java | 37 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/framework/MCFSFramework.java | 52 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/framework/MCFSJob.java | 38 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/modules/Projection.java | 47 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/modules/Split.java | 22 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/Tree.java | 62 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/parser/J48Parser.java | 53 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/parser/M5Parser.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/parser/TreeNodeParser.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/parser/TreeParser.java | 60 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/ArrayUtils.java | 11 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/MathUtils.java | 343 +-- rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/StringUtils.java | 3 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/cmatrix/ConfusionMatrix.java | 16 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/cmatrix/QualityMeasure.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/dataframe/DataFrame.java | 5 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/statFunctions/StatFunctions.java | 48 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/statList/StatsList.java | 37 rmcfs-1.1.2/rmcfs/man/build.idgraph.Rd | 2 rmcfs-1.1.2/rmcfs/man/mcfs.Rd | 7 rmcfs-1.1.2/rmcfs/man/plot.mcfs.Rd | 4 69 files changed, 1767 insertions(+), 1579 deletions(-)
Title: Read and Combine Multiple Data Files
Description: Combine multiple data files from a common directory.
The data files will be read into R and bound together, creating a
single large data.frame. A general function is provided along with
a specific function for data that was collected using the open-source
experiment builder 'OpenSesame' <http://osdoc.cogsci.nl/>.
Author: Pascal J. Kieslich [aut, cre],
Felix Henninger [aut]
Maintainer: Pascal J. Kieslich <kieslich@psychologie.uni-mannheim.de>
Diff between readbulk versions 1.0.0 dated 2016-02-14 and 1.1.0 dated 2016-10-25
DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- NAMESPACE | 8 ++++---- NEWS.md |only R/read_bulk.R | 12 +++++++++--- R/read_opensesame.R | 4 +++- README.md | 7 ++++++- man/read_bulk.Rd | 7 +++++-- man/read_opensesame.Rd | 5 ++++- 9 files changed, 45 insertions(+), 25 deletions(-)
Title: Process and Analyze Mouse-Tracking Data
Description: Mouse-tracking, the analysis of mouse movements in computerized
experiments, is a method that is becoming increasingly popular in the
cognitive sciences. The mousetrap package offers functions for importing,
preprocessing, analyzing, aggregating, and visualizing mouse-tracking data.
Author: Pascal J. Kieslich [aut, cre],
Felix Henninger [aut],
Dirk U. Wulff [ctb],
Sarah Brockhaus [ctb]
Maintainer: Pascal J. Kieslich <kieslich@psychologie.uni-mannheim.de>
Diff between mousetrap versions 1.2.0 dated 2016-07-09 and 2.0.0 dated 2016-10-25
mousetrap-1.2.0/mousetrap/R/variables.R |only mousetrap-1.2.0/mousetrap/man/mt_calculate_derivatives.Rd |only mousetrap-1.2.0/mousetrap/man/mt_calculate_deviations.Rd |only mousetrap-1.2.0/mousetrap/man/mt_calculate_measures.Rd |only mousetrap-1.2.0/mousetrap/man/mt_id.Rd |only mousetrap-1.2.0/mousetrap/man/mt_variable_labels.Rd |only mousetrap-2.0.0/mousetrap/DESCRIPTION | 23 mousetrap-2.0.0/mousetrap/MD5 | 105 - mousetrap-2.0.0/mousetrap/NAMESPACE | 9 mousetrap-2.0.0/mousetrap/NEWS.md | 37 mousetrap-2.0.0/mousetrap/R/aggregate.R |only mousetrap-2.0.0/mousetrap/R/bimodality.R | 6 mousetrap-2.0.0/mousetrap/R/check.R | 8 mousetrap-2.0.0/mousetrap/R/data.R | 32 mousetrap-2.0.0/mousetrap/R/derivatives.R | 250 +-- mousetrap-2.0.0/mousetrap/R/deviations.R | 150 - mousetrap-2.0.0/mousetrap/R/export.R |only mousetrap-2.0.0/mousetrap/R/import.R | 722 +++++--- mousetrap-2.0.0/mousetrap/R/measures.R | 276 +-- mousetrap-2.0.0/mousetrap/R/mousetrap.R | 25 mousetrap-2.0.0/mousetrap/R/movement_angle.R | 51 mousetrap-2.0.0/mousetrap/R/preprocess.R | 1139 +++++++------- mousetrap-2.0.0/mousetrap/R/reshape.R | 645 ++----- mousetrap-2.0.0/mousetrap/R/riverbed.R | 6 mousetrap-2.0.0/mousetrap/R/sample_entropy.R | 45 mousetrap-2.0.0/mousetrap/R/standardize.R | 16 mousetrap-2.0.0/mousetrap/R/startupmessage.R |only mousetrap-2.0.0/mousetrap/R/utils.R | 147 + mousetrap-2.0.0/mousetrap/R/visualize.R | 134 + mousetrap-2.0.0/mousetrap/README.md | 4 mousetrap-2.0.0/mousetrap/man/mousetrap.Rd | 25 mousetrap-2.0.0/mousetrap/man/mt_add_variables.Rd |only mousetrap-2.0.0/mousetrap/man/mt_aggregate.Rd | 101 - mousetrap-2.0.0/mousetrap/man/mt_aggregate_per_subject.Rd | 67 mousetrap-2.0.0/mousetrap/man/mt_align_start.Rd | 31 mousetrap-2.0.0/mousetrap/man/mt_average.Rd | 82 - mousetrap-2.0.0/mousetrap/man/mt_check_bimodality.Rd | 4 mousetrap-2.0.0/mousetrap/man/mt_check_resolution.Rd | 12 mousetrap-2.0.0/mousetrap/man/mt_derivatives.Rd |only mousetrap-2.0.0/mousetrap/man/mt_deviations.Rd |only mousetrap-2.0.0/mousetrap/man/mt_example.Rd | 32 mousetrap-2.0.0/mousetrap/man/mt_exclude_initiation.Rd | 41 mousetrap-2.0.0/mousetrap/man/mt_export_long.Rd |only mousetrap-2.0.0/mousetrap/man/mt_import_long.Rd | 88 - mousetrap-2.0.0/mousetrap/man/mt_import_mousetrap.Rd | 71 mousetrap-2.0.0/mousetrap/man/mt_import_wide.Rd | 98 - mousetrap-2.0.0/mousetrap/man/mt_measures.Rd |only mousetrap-2.0.0/mousetrap/man/mt_movement_angle.Rd | 27 mousetrap-2.0.0/mousetrap/man/mt_plot.Rd | 31 mousetrap-2.0.0/mousetrap/man/mt_plot_per_trajectory.Rd | 37 mousetrap-2.0.0/mousetrap/man/mt_plot_riverbed.Rd | 2 mousetrap-2.0.0/mousetrap/man/mt_remap_symmetric.Rd | 42 mousetrap-2.0.0/mousetrap/man/mt_resample.Rd | 47 mousetrap-2.0.0/mousetrap/man/mt_reshape.Rd | 152 + mousetrap-2.0.0/mousetrap/man/mt_sample_entropy.Rd | 26 mousetrap-2.0.0/mousetrap/man/mt_space_normalize.Rd | 57 mousetrap-2.0.0/mousetrap/man/mt_standardize.Rd | 4 mousetrap-2.0.0/mousetrap/man/mt_subset.Rd | 30 mousetrap-2.0.0/mousetrap/man/mt_time_normalize.Rd | 53 mousetrap-2.0.0/mousetrap/man/reexports.Rd |only mousetrap-2.0.0/mousetrap/man/scale_within.Rd | 8 61 files changed, 2786 insertions(+), 2212 deletions(-)
Title: Multivariate Bias Correction of Climate Model Outputs
Description: Calibrate and apply multivariate bias correction algorithms
for climate model simulations of multiple climate variables. Three methods
by Cannon (2016, submitted) are supported: MBCp, MBCr, and MBCn.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between MBC versions 0.1 dated 2016-10-13 and 0.10-1 dated 2016-10-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/MBC-QDM.R | 45 +++++++++++++++++++++++++++++++-------------- man/MBCn.Rd | 6 +++++- man/MBCp.Rd | 6 +++++- man/MBCr.Rd | 6 +++++- man/QDM.Rd | 7 ++++++- 7 files changed, 61 insertions(+), 27 deletions(-)
Title: Extractive Summarization of Text with the LexRank Algorithm
Description: An R implementation of the LexRank algorithm described by G. Erkan and D. R. Radev (2004) <DOI:10.1613/jair.1523>.
Author: Adam Spannbauer <spannbaueradam@gmail.com>
Maintainer: Adam Spannbauer <spannbaueradam@gmail.com>
Diff between lexRankr versions 0.2.0 dated 2016-09-21 and 0.3.0 dated 2016-10-25
DESCRIPTION | 12 +++++++----- MD5 | 13 ++++++++----- NAMESPACE | 2 ++ NEWS.md | 5 +++++ R/RcppExports.R |only R/sentenceSimil.R | 30 ++++++++++++++++++------------ README.md | 4 +++- src |only 8 files changed, 43 insertions(+), 23 deletions(-)
Title: Identify Favorable Subsets of Germplasm Collections
Description: Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.
Author: Ryan C. Graebner and Alfonso Cuesta-Marcos
Maintainer: Ryan C. Graebner <ryan.graebner@gmail.com>
Diff between GeneticSubsetter versions 0.7 dated 2016-03-29 and 0.8 dated 2016-10-25
DESCRIPTION | 11 +++---- MD5 | 48 ++++++++++++++++++------------- NAMESPACE | 2 - R/CoreSetOptimizer.R | 25 +++++++++------- R/CoreSetter.R | 71 ++++++++++++++++++++++++++++------------------ R/CoreSetterCombined.R | 71 +++++++++++++++++++++++++++++++++------------- R/CoreSetterPoly.R |only R/MTK.R | 2 - R/Mat.R |only R/MtkCalc.R | 2 - R/SubsetterMTK.R | 2 - build |only data/genotypes.rda |binary inst |only man/CoreSetOptimizer.Rd | 6 +-- man/CoreSetter.Rd | 8 ++--- man/CoreSetterCombined.Rd | 12 +++---- man/CoreSetterPoly.Rd |only man/GeneticSubsetter.Rd | 5 +-- man/MTK.Rd | 2 - man/Mat.Rd |only man/MtkCalc.Rd | 2 - man/PicCalc.Rd | 2 - man/SubsetterMTK.Rd | 2 - man/SubsetterPIC.Rd | 2 - man/genotypes.Rd | 5 +-- man/genotypes.poly.Rd |only vignettes |only 28 files changed, 171 insertions(+), 109 deletions(-)
More information about GeneticSubsetter at CRAN
Permanent link
Title: Bayesian Network Modeling and Analysis
Description: A 'Shiny' web application for creating interactive Bayesian Network models,
learning the structure and parameters of Bayesian networks, and utilities for classical
network analysis.
Author: Paul Govan [aut, cre]
Maintainer: Paul Govan <pgovan1@aggienetwork.com>
Diff between BayesianNetwork versions 0.1.0 dated 2016-07-20 and 0.1.1 dated 2016-10-25
DESCRIPTION | 10 MD5 | 16 - NEWS.md |only R/BayesianNetwork.R | 2 README.md | 42 +-- build |only inst/bn/rsconnect |only inst/bn/server.R | 212 +++++++++-------- inst/bn/ui.R | 629 ++++++++++++++++++++++++++++++++-------------------- inst/doc |only vignettes |only 11 files changed, 544 insertions(+), 367 deletions(-)
More information about BayesianNetwork at CRAN
Permanent link
Title: Forecasting Using Smoothing Functions
Description: The set of smoothing functions used for time series analysis and in forecasting.
Currently the package includes exponential smoothing models and SARIMA in state-space
form + several simulation functions.
Author: Ivan Svetunkov [aut, cre] (Research Associate at Lancaster Centre for
Forecasting, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 1.4.5 dated 2016-10-17 and 1.4.6 dated 2016-10-25
DESCRIPTION | 8 - MD5 | 70 ++++----- NAMESPACE | 11 + NEWS | 23 +++ R/RcppExports.R | 8 - R/es.R | 70 ++++++++- R/methods.R | 284 ++++++++++++++++++++++++++++++++++---- R/simces.R |only R/simes.R | 21 ++ R/simssarima.R |only R/ssarima.R | 1 R/ssfunctions.R | 148 ++++++++++++++----- README.md | 2 build/vignette.rds |binary inst/doc/ces.html | 53 +++---- inst/doc/es.html | 93 +++++++----- inst/doc/ges.html | 28 ++- inst/doc/simulate.R | 48 +++++- inst/doc/simulate.Rmd | 82 +++++++++- inst/doc/simulate.html | 105 +++++++++++--- inst/doc/sma.html | 8 - inst/doc/smooth-Documentation.pdf |binary inst/doc/smooth.html | 4 inst/doc/ssarima.html | 35 ++-- man/AICc.Rd | 4 man/ces.Rd | 2 man/es.Rd | 11 - man/ges.Rd | 2 man/orders-lags-modelType.Rd |only man/simes.Rd | 3 man/simssarima.Rd |only man/sma.Rd | 2 man/ssarima.Rd | 4 src/RcppExports.cpp | 20 ++ src/ssgeneralfun.cpp | 48 +++--- tests/testthat/test_es.R | 6 tests/testthat/test_simulate.R | 10 + vignettes/simulate.Rmd | 82 +++++++++- 38 files changed, 993 insertions(+), 303 deletions(-)
Title: Searching for Footprints of Selection using Haplotype
Homozygosity Based Tests
Description: Functions for the detection of footprints of selection on
dense SNP data using Extended Homozygosity Haplotype (EHH)
based tests. The package includes computation of EHH, iHS
(within population) and Rsb or XP-EHH (across pairs of populations)
statistics. Various plotting functions are also included to
facilitate visualization and interpretation of the results.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Mathieu Gautier <mathieu.gautier@supagro.inra.fr>
Diff between rehh versions 2.0.0 dated 2016-08-01 and 2.0.1 dated 2016-10-25
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 36 ++++++++++++++++++------------------ R/calc_ehh.R | 6 +++++- R/calc_ehhs.R | 16 +++++++++------- R/scan_hh.R | 6 +++++- inst/doc/rehh.R | 6 +++--- inst/doc/rehh.Rmd | 14 +++++++------- inst/doc/rehh.pdf |binary man/calc_ehh.Rd | 3 ++- man/calc_ehhs.Rd | 3 ++- man/scan_hh.Rd | 3 ++- src/CALL_EHH.c | 5 +++-- src/CALL_EHHS.c | 3 ++- src/CALL_SCAN_HH.c | 7 ++++--- src/hh_utils.c | 32 ++++++++++++++++++++++++++++++++ src/hh_utils.h | 5 ++--- vignettes/rehh.Rmd | 14 +++++++------- vignettes/rehh.html | 12 ++++++------ 19 files changed, 116 insertions(+), 65 deletions(-)
Title: R Commander
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.3-0 dated 2016-08-24 and 2.3-1 dated 2016-10-25
DESCRIPTION | 10 MD5 | 22 +- NEWS | 8 R/startup.R | 4 inst/CITATION | 28 ++ inst/po/ca/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/de/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/eu/LC_MESSAGES/R-Rcmdr.mo |binary man/Rcmdr-package.Rd | 12 - po/R-ca.po | 4 po/R-de.po | 337 +++++++++++++++++++++++++------ po/R-eu.po | 406 ++++++++++++++++++++++++++++++-------- 12 files changed, 657 insertions(+), 174 deletions(-)
Title: R Interface to 'Bloomberg'
Description: An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Author: Whit Armstrong, Dirk Eddelbuettel and John Laing
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.4 dated 2016-05-08 and 0.3.5 dated 2016-10-25
ChangeLog | 64 ++++++++++++++++++ DESCRIPTION | 16 ++-- MD5 | 44 ++++++------ NAMESPACE | 1 R/RcppExports.R | 10 ++ R/bsrch.R | 8 +- R/getBars.R | 9 +- R/getTicks.R | 77 +++++++++++----------- R/portfolio.R |only README.md | 15 +++- build/vignette.rds |binary inst/NEWS.Rd | 17 ++++- inst/doc/rblpapi-intro.Rmd | 8 +- inst/doc/rblpapi-intro.html | 66 ++++++++++++------- inst/unitTests/runit.getTicks.R | 30 +++++++- man/bsrch.Rd | 2 man/getBars.Rd | 7 +- man/getMultipleTicks.Rd | 9 +- man/getPortfolio.Rd |only man/getTicks.Rd | 24 +++++-- src/RcppExports.cpp | 136 ++++++++++++++++++++++------------------ src/bds.cpp | 59 +++++++++++++++-- src/getTicks.cpp | 43 +++++------- vignettes/rblpapi-intro.Rmd | 8 +- 24 files changed, 427 insertions(+), 226 deletions(-)
Title: Orthogonalizing EM
Description: Solves penalized least squares problems using the orthogonalizing EM algorithm of Xiong et al. (2016) <doi:10.1080/00401706.2015.1054436>. The main fitting function is oem() and the functions cv.oem() and xval.oem() are for cross validation, the latter being an accelerated cross validation function for linear models. The big.oem() function allows for out of memory fitting.
Author: Bin Dai [aut],
Jared Huling [aut, cre],
Yixuan Qiu [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between oem versions 2.0.1 dated 2016-10-19 and 2.0.2 dated 2016-10-25
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------ README.md | 1 inst/doc/oem_vignette.html | 48 ++++++++++++++++++++++---------------------- src/oem_dense.h | 8 +++---- src/oem_logistic_dense.h | 8 +++---- src/oem_logistic_sparse.cpp | 2 - src/oem_logistic_sparse.h | 9 +++----- 8 files changed, 49 insertions(+), 49 deletions(-)
Title: Loading NONMEM Output Files and Simulate with Parameter
Uncertainty
Description: Loading NONMEM (NONlinear Mixed-Effect Modeling, <http://www.iconplc.com/innovation/solutions/nonmem/> ) output files and simulate with parameter uncertainty.
Author: Magnus Astrand
Maintainer: Magnus Astrand <magnus.astrand@astrazeneca.com>
Diff between nonmem2R versions 0.1.4 dated 2016-05-10 and 0.1.5 dated 2016-10-25
DESCRIPTION | 8 - MD5 | 19 +- NAMESPACE | 5 R/LoadNonmemOutput.R | 20 ++ R/Simulation.R | 291 ++++++++++++++++++++++++++++++++----------- R/VPCs.R |only inst/extdata/vpc_results.csv |only inst/extdata/vpctab004.dat |only man/extload.Rd | 5 man/grid.sim.Rd | 29 ++-- man/grid.sim.internal1.Rd |only man/grid.sim.internal2.Rd |only man/grid.sim.internal3.Rd |only man/vpcfig.Rd |only 14 files changed, 286 insertions(+), 91 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Diff between mvMORPH versions 1.0.7 dated 2016-06-18 and 1.0.8 dated 2016-10-25
mvMORPH-1.0.7/mvMORPH/vignettes/How_to_use_mvMORPH.html |only mvMORPH-1.0.8/mvMORPH/DESCRIPTION | 8 +- mvMORPH-1.0.8/mvMORPH/MD5 | 33 ++++---- mvMORPH-1.0.8/mvMORPH/R/mvBM.r | 3 mvMORPH-1.0.8/mvMORPH/R/mvBMTS.r | 4 - mvMORPH-1.0.8/mvMORPH/R/mvEB.r | 21 +++-- mvMORPH-1.0.8/mvMORPH/R/mvOU.r | 3 mvMORPH-1.0.8/mvMORPH/R/mvOUTS.r | 3 mvMORPH-1.0.8/mvMORPH/R/mvSHIFT.r | 26 ++++--- mvMORPH-1.0.8/mvMORPH/R/zzz.r | 2 mvMORPH-1.0.8/mvMORPH/README.md | 16 ++-- mvMORPH-1.0.8/mvMORPH/inst/doc/How_to_use_mvMORPH.R | 48 ++++++++++++- mvMORPH-1.0.8/mvMORPH/inst/doc/How_to_use_mvMORPH.Rmd | 59 ++++++++++++++-- mvMORPH-1.0.8/mvMORPH/inst/doc/How_to_use_mvMORPH.pdf |binary mvMORPH-1.0.8/mvMORPH/inst/doc/tutorial_mvMORPH.Rmd | 2 mvMORPH-1.0.8/mvMORPH/inst/doc/tutorial_mvMORPH.pdf |binary mvMORPH-1.0.8/mvMORPH/vignettes/How_to_use_mvMORPH.Rmd | 59 ++++++++++++++-- mvMORPH-1.0.8/mvMORPH/vignettes/tutorial_mvMORPH.Rmd | 2 18 files changed, 222 insertions(+), 67 deletions(-)
Title: Multiscale Clustering of Geometrical Network
Description: Co-Expression Network Analysis by adopting network embedding technique.
Author: Won-Min Song, Bin Zhang
Maintainer: Won-Min Song <wonmin1984@gmail.com>
Diff between MEGENA versions 1.3.4-6 dated 2016-10-06 and 1.3.5-2 dated 2016-10-25
MEGENA-1.3.4-6/MEGENA/inst/doc/MEGENA_pipeline_10052016.R |only MEGENA-1.3.4-6/MEGENA/inst/doc/MEGENA_pipeline_10052016.Rmd |only MEGENA-1.3.4-6/MEGENA/inst/doc/MEGENA_pipeline_10052016.html |only MEGENA-1.3.4-6/MEGENA/vignettes/MEGENA_pipeline_10052016.Rmd |only MEGENA-1.3.5-2/MEGENA/DESCRIPTION | 6 MEGENA-1.3.5-2/MEGENA/MD5 | 31 ++-- MEGENA-1.3.5-2/MEGENA/NAMESPACE | 4 MEGENA-1.3.5-2/MEGENA/R/ClusteringPackage.R | 79 +++++++---- MEGENA-1.3.5-2/MEGENA/R/Combined_functions.R | 44 ++++-- MEGENA-1.3.5-2/MEGENA/R/ModuleHierarchyPlot.R |only MEGENA-1.3.5-2/MEGENA/R/ModulePlot.R | 16 +- MEGENA-1.3.5-2/MEGENA/R/NetworkSummary.R | 24 ++- MEGENA-1.3.5-2/MEGENA/R/PFN_Computation.R | 4 MEGENA-1.3.5-2/MEGENA/build/vignette.rds |binary MEGENA-1.3.5-2/MEGENA/inst/doc/MEGENA_pipeline_10062016.R |only MEGENA-1.3.5-2/MEGENA/inst/doc/MEGENA_pipeline_10062016.Rmd |only MEGENA-1.3.5-2/MEGENA/inst/doc/MEGENA_pipeline_10062016.html |only MEGENA-1.3.5-2/MEGENA/man/calculate.PFN.Rd | 5 MEGENA-1.3.5-2/MEGENA/man/do.MEGENA.Rd | 3 MEGENA-1.3.5-2/MEGENA/man/get.DegreeHubStatistic.Rd |only MEGENA-1.3.5-2/MEGENA/man/plot_module_hierarchy.Rd |only MEGENA-1.3.5-2/MEGENA/vignettes/MEGENA_pipeline_10062016.Rmd |only 22 files changed, 137 insertions(+), 79 deletions(-)
Title: Joint Random Forest (JRF) for the Simultaneous Estimation of
Multiple Related Networks
Description: Simultaneous estimation of multiple related networks.
Author: Francesca Petralia Developer [aut, cre],
Pei Wang Developer [aut],
Zhidong Tu Developer [aut],
Won-min Song Developer [aut],
Adele Cutler Developer [ctb],
Leo Breiman Developer [ctb],
Andy Liaw Developer [ctb],
Matthew Wiener Developer [ctb]
Maintainer: Francesca Petralia Developer <francesca.petralia@mssm.edu>
Diff between JRF versions 0.1-3 dated 2016-01-20 and 0.1-4 dated 2016-10-25
DESCRIPTION | 8 ++-- MD5 | 20 ++++++----- NAMESPACE | 2 + R/JRF.R | 19 +++++----- R/JRF_network.R |only R/JRF_permutation.R | 4 +- R/Run_permutation.R |only man/JRF.Rd | 4 +- man/JRF_network.Rd |only man/JRF_permutation.Rd | 6 +-- man/Run_permutation.Rd |only src/regTree.c | 8 ++++ src/regrf.c | 86 ------------------------------------------------- 13 files changed, 44 insertions(+), 113 deletions(-)
Title: Imputation for Proteomics
Description: Functions to analyse missing value mechanisms and to impute data sets in the context of bottom-up MS-based proteomics.
Author: Quentin Giai Gianetto
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Diff between imp4p versions 0.1 dated 2016-08-18 and 0.2 dated 2016-10-25
imp4p-0.1/imp4p/R/delete_na_rows.R |only imp4p-0.1/imp4p/man/delete_na_rows.Rd |only imp4p-0.2/imp4p/DESCRIPTION | 6 +-- imp4p-0.2/imp4p/MD5 | 54 +++++++++++++++--------------- imp4p-0.2/imp4p/NAMESPACE | 2 - imp4p-0.2/imp4p/R/estim_bound.R | 2 + imp4p-0.2/imp4p/R/estim_mix.R | 6 +-- imp4p-0.2/imp4p/R/impute_igcda.R | 6 +-- imp4p-0.2/imp4p/R/impute_mi.R |only imp4p-0.2/imp4p/R/impute_mix.R | 7 ++- imp4p-0.2/imp4p/R/impute_pa.R | 27 +++++++++++---- imp4p-0.2/imp4p/R/impute_rand.R |only imp4p-0.2/imp4p/R/impute_slsa.R | 13 ++++++- imp4p-0.2/imp4p/R/mi_mix.R | 34 +++++++++++++++--- imp4p-0.2/imp4p/R/prob_mcar.R | 9 ++++- imp4p-0.2/imp4p/R/prob_mcar_tab.R | 6 ++- imp4p-0.2/imp4p/man/estim_mix.Rd | 53 +++++++++++++---------------- imp4p-0.2/imp4p/man/imp4p-package.Rd | 4 +- imp4p-0.2/imp4p/man/impute_igcda.Rd | 9 +---- imp4p-0.2/imp4p/man/impute_mi.Rd |only imp4p-0.2/imp4p/man/impute_mix.Rd | 29 ++++++---------- imp4p-0.2/imp4p/man/impute_pa.Rd | 13 ++++--- imp4p-0.2/imp4p/man/impute_rand.Rd |only imp4p-0.2/imp4p/man/impute_slsa.Rd | 19 +++------- imp4p-0.2/imp4p/man/mi_mix.Rd | 29 ++++++---------- imp4p-0.2/imp4p/man/miss_mcar_process.Rd | 9 +---- imp4p-0.2/imp4p/man/miss_mnar_process.Rd | 9 +---- imp4p-0.2/imp4p/man/miss_total_process.Rd | 9 +---- imp4p-0.2/imp4p/man/prob_mcar.Rd | 13 ++----- imp4p-0.2/imp4p/man/proba_mcar_tab.Rd | 11 +----- imp4p-0.2/imp4p/man/sim_data.Rd | 6 +-- 31 files changed, 203 insertions(+), 182 deletions(-)
Title: Useful Functions for Building Physics
Description: A collection of functions useful for the analysis of
building physics experiments.
Author: Neurobat AG
Maintainer: David Lindelöf <david.lindelof@neurobat.net>
Diff between homeR versions 0.2 dated 2016-06-06 and 0.3.0 dated 2016-10-25
homeR-0.2/homeR/tests/testthat/oilConsumption.RData |only homeR-0.3.0/homeR/DESCRIPTION | 12 +- homeR-0.3.0/homeR/MD5 | 17 ++- homeR-0.3.0/homeR/NAMESPACE | 5 - homeR-0.3.0/homeR/NEWS.md |only homeR-0.3.0/homeR/R/bhm.R | 69 ++++++++++----- homeR-0.3.0/homeR/man/bhm.Rd | 15 ++- homeR-0.3.0/homeR/man/logposterior.Rd |only homeR-0.3.0/homeR/man/pmv.Rd | 6 - homeR-0.3.0/homeR/tests/testthat/alv.RData |only homeR-0.3.0/homeR/tests/testthat/fakeMonthlyEnergy.RData |only homeR-0.3.0/homeR/tests/testthat/test_bhm.R | 52 +++++++++-- 12 files changed, 124 insertions(+), 52 deletions(-)
Title: Read Data from Files Readable by 'gnumeric'
Description: Read data files readable by 'gnumeric' into 'R'. Can read
whole sheet or a range, from several file formats, including
the native format of 'gnumeric'. Reading is done by using
'ssconvert' (a file converter utility included in the 'gnumeric'
distribution <http://projects.gnome.org/gnumeric/>) to convert
the requested part to CSV. From 'gnumeric' files (but not other
formats) can list sheet names and sheet sizes or read all
sheets.
Author: Karoly Antal <antalk2@gmail.com>.
Maintainer: Karoly Antal <antalk2@gmail.com>
Diff between gnumeric versions 0.7-4 dated 2015-07-03 and 0.7-6 dated 2016-10-25
DESCRIPTION | 20 ++++++------ MD5 | 6 +-- R/read.gnumeric.R | 52 ++++++++++++++++---------------- man/read.gnumeric.sheet.Rd | 72 +++++++++++++++++++++++---------------------- 4 files changed, 76 insertions(+), 74 deletions(-)
Title: A View Generator for Multidimensional Data
Description: A tool to explore wide data sets, by detecting, ranking
and plotting groups of statistically dependent columns.
Author: Thibault Sellam
Maintainer: Thibault Sellam <thibault.sellam@cwi.nl>
Diff between findviews versions 0.1.1 dated 2016-10-10 and 0.1.2 dated 2016-10-25
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 8 +++++++- R/findviews.R | 2 -- R/findviews_to_compare.R | 5 ++--- R/findviews_to_predict.R | 5 ++--- README.md | 2 ++ man/findviews_core.Rd | 2 -- man/findviews_to_compare_core.Rd | 2 -- man/findviews_to_predict_core.Rd | 2 -- 10 files changed, 25 insertions(+), 27 deletions(-)
Title: Read RSS/Atom Feeds from R
Description: Retrieve data from RSS/Atom feeds.
Author: Andrew Collier [aut, cre]
Maintainer: Andrew Collier <andrew@exegetic.biz>
Diff between feedeR versions 0.0.4 dated 2016-08-14 and 0.0.7 dated 2016-10-25
DESCRIPTION | 10 ++++--- MD5 | 13 +++++---- NAMESPACE | 1 R/read.R | 63 +++++++++++++++++++++++++++++++++++++-------- README.md | 7 +++++ man/feed.extract.Rd | 11 ++++++- man/parse.rdf.Rd |only tests/testthat/test_util.R | 11 +++++-- 8 files changed, 91 insertions(+), 25 deletions(-)
Title: Ensemble Partial Least Squares Regression
Description: An algorithmic framework for measuring feature importance, outlier detection, model applicability domain evaluation, and ensemble predictive modeling with (sparse) partial least squares regressions.
Author: Nan Xiao <me@nanx.me>, Dong-Sheng Cao,
Miao-Zhu Li <miaozhu.li@duke.edu>, Qing-Song Xu <qsxu@csu.edu.cn>
Maintainer: Nan Xiao <me@nanx.me>
Diff between enpls versions 4.5 dated 2016-09-15 and 5.0 dated 2016-10-25
DESCRIPTION | 12 +-- MD5 | 67 ++++++++++++-------- NAMESPACE | 11 +++ NEWS.md | 60 ++++++++++-------- R/enpls.ad.R |only R/enpls.od.R | 2 R/enspls.ad.R |only R/enspls.fit.R | 3 R/enspls.od.R | 5 - R/plot.enpls.R | 147 +++++++++++++++++++++++++++++++++++++++++---- R/plot.enspls.R | 132 +++++++++++++++++++++++++++++++++++++--- R/print.enpls.R | 60 ++++++++++++++++++ R/print.enspls.R | 69 ++++++++++++++++++++- README.md | 2 inst/doc/enpls.R | 22 ++++++ inst/doc/enpls.Rmd | 80 +++++++++++++++++++----- inst/doc/enpls.html | 63 +++++++++++++++---- man/enpls.ad.Rd |only man/enpls.ad.core.fit.Rd |only man/enpls.ad.core.pred.Rd |only man/enpls.od.Rd | 2 man/enspls.ad.Rd |only man/enspls.ad.core.fit.Rd |only man/enspls.ad.core.pred.Rd |only man/enspls.fit.Rd | 3 man/enspls.od.Rd | 3 man/plot.cv.enpls.Rd | 5 + man/plot.cv.enspls.Rd | 5 + man/plot.enpls.ad.Rd |only man/plot.enpls.od.Rd | 4 - man/plot.enspls.ad.Rd |only man/plot.enspls.od.Rd | 4 - man/print.enpls.ad.Rd |only man/print.enpls.od.Rd | 2 man/print.enspls.ad.Rd |only man/print.enspls.fit.Rd | 3 man/print.enspls.fs.Rd | 3 man/print.enspls.od.Rd | 3 man/rgb2alpha.Rd |only vignettes/enpls.Rmd | 80 +++++++++++++++++++----- vignettes/enpls.bib | 13 +++ 41 files changed, 721 insertions(+), 144 deletions(-)
Title: scrypt key derivation functions for R
Description: scrypt is an R package for working with scrypt. Scrypt is a
password-based key derivation function created by Colin Percival. The
algorithm was specifically designed to make it costly to perform
large-scale custom hardware attacks by requiring large amounts of memory.
Author: RStudio, Inc.; Colin Percival
Maintainer: ORPHANED
Diff between scrypt versions 0.1.0 dated 2014-02-25 and 0.1.1 dated 2016-10-25
DESCRIPTION | 11 +++++++---- MD5 | 6 +++--- src/Makevars.win | 2 +- src/util.cpp | 2 +- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Capture the Genes and Variants Related to a Genetic Disease from
Public Databases and PubMed
Description: Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature based on the public databases including HPO (Human Phenotype Ontology, <http://human-phenotype-ontology.github.io/about.html>), Orphanet <http://www.orpha.net/consor/cgi-bin/index.php>, OMIM (Online Mendelian Inheritance in Man, <http://www.omim.org>), ClinVar <http://www.ncbi.nlm.nih.gov/clinvar>, and UniProt (Universal Protein Resource, <http://www.uniprot.org>) and PubMed abstracts. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. UniProt focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the UniProt are manually curated from UniProtKB/Swiss-Prot. Additionally, PubMed provides the primary and latest source of the information. Text mining was employed to capture the information from PubMed abstracts.
Author: Zongfu Cao
Maintainer: Zongfu Cao <caozongfu@gmail.com>
Diff between VarfromPDB versions 2.1.9 dated 2016-08-20 and 2.1.10 dated 2016-10-25
DESCRIPTION | 8 ++-- MD5 | 6 +-- R/extract_clinvar.R | 95 +++++++++++++++++++++++++++------------------------- R/extract_omim.R | 15 +++++++- 4 files changed, 71 insertions(+), 53 deletions(-)
Title: Stochastic Newton Sampler (SNS)
Description: Stochastic Newton Sampler (SNS) is a Metropolis-Hastings-based, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability density functions (PDFs) where the proposal density function is a multivariate Gaussian resulting from a second-order Taylor-series expansion of log-density around the current point. The mean of the Gaussian proposal is the full Newton-Raphson step from the current point. A Boolean flag allows for switching from SNS to Newton-Raphson optimization (by choosing the mean of proposal function as next point). This can be used during burn-in to get close to the mode of the PDF (which is unique due to concavity). For high-dimensional densities, mixing can be improved via 'state space partitioning' strategy, in which SNS is applied to disjoint subsets of state space, wrapped in a Gibbs cycle. Numerical differentiation is available when analytical expressions for gradient and Hessian are not available. Facilities for validation and numerical differentiation of log-density are provided.
Author: Alireza S. Mahani, Asad Hasan, Marshall Jiang, Mansour T.A. Sharabiani
Maintainer: Alireza Mahani <alireza.s.mahani@gmail.com>
Diff between sns versions 1.1.1 dated 2016-09-08 and 1.1.2 dated 2016-10-25
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- inst/CITATION |only inst/doc/SNS.pdf |binary man/plot.sns.Rd | 4 ++++ man/predict.sns.Rd | 4 ++++ man/sns.Rd | 3 +++ man/sns.check.logdensity.Rd | 6 +++--- man/sns.fghEval.numaug.Rd | 6 +++--- man/sns.part.Rd | 4 ++++ man/sns.run.Rd | 6 +++--- man/summary.sns.Rd | 4 ++++ 13 files changed, 48 insertions(+), 24 deletions(-)
Title: Quantitative Fatty Acid Signature Analysis in R
Description: An implementation of Quantitative Fatty Acid Signature
Analysis (QFASA) in R. QFASA is a method of estimating the diet
composition of predators. The fundamental unit of information in
QFASA is a fatty acid signature (signature), which is a vector of
proportions describing the composition of fatty acids within lipids.
Signature data from at least one predator and from samples of all
potential prey types are required. Calibration coefficients, which
adjust for the differential metabolism of individual fatty acids by
predators, are also required. Given those data inputs, a predator
signature is modeled as a mixture of prey signatures and its diet
estimate is obtained as the mixture that minimizes a measure of
distance between the observed and modeled signatures. A variety of
estimation options and simulation capabilities are implemented.
Please refer to the vignette for additional details and references.
Author: Jeffrey F. Bromaghin [aut, cre]
Maintainer: Jeffrey F. Bromaghin <jbromaghin@usgs.gov>
Diff between qfasar versions 1.0.0 dated 2016-08-25 and 1.1.0 dated 2016-10-25
DESCRIPTION | 12 ++-- MD5 | 60 +++++++++++++-------- R/adj_diet_fat.R | 8 +- R/cc_aug.R | 2 R/comp_chi_gamma.R | 54 ++++++++----------- R/est_diet.R | 137 ++++++++++++++++++++++++-------------------------- R/find_boot_ss.R | 24 ++++---- R/gof.R | 24 +------- R/make_diet_rand.R | 2 R/make_pred_sigs.R | 4 - R/make_prey_part.R | 8 +- build/vignette.rds |binary inst/doc/qfasar.Rmd | 56 +++++++++++--------- inst/doc/qfasar.html | 73 ++++++++++++++++++-------- man/cc_aug.Rd | 2 man/comp_chi_gamma.Rd | 12 ---- man/est_diet.Rd | 15 ++--- man/find_boot_ss.Rd | 24 ++++---- man/gof.Rd | 24 +------- man/make_diet_rand.Rd | 2 man/make_pred_sigs.Rd | 4 - man/make_prey_part.Rd | 8 +- tests |only vignettes/qfasar.Rmd | 56 +++++++++++--------- 24 files changed, 306 insertions(+), 305 deletions(-)
Title: Client for 'Turfjs' for 'Geospatial' Analysis
Description: Client for 'Turfjs' (<http://turfjs.org>) for
'geospatial' analysis. The package revolves around using 'GeoJSON'
data. Functions are included for creating 'GeoJSON' data objects,
measuring aspects of 'GeoJSON', and combining, transforming,
and creating random 'GeoJSON' data objects.
Author: Scott Chamberlain [aut, cre],
Jeff Hollister [aut],
Morgan Herlocker [cph]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between lawn versions 0.1.7 dated 2016-05-03 and 0.3.0 dated 2016-10-25
lawn-0.1.7/lawn/NEWS |only lawn-0.1.7/lawn/R/aggregate.R |only lawn-0.1.7/lawn/R/jenks.R |only lawn-0.1.7/lawn/R/quantile.R |only lawn-0.1.7/lawn/R/reclass.R |only lawn-0.1.7/lawn/R/size.R |only lawn-0.1.7/lawn/inst/js/turf.js |only lawn-0.1.7/lawn/man/lawn_erase.Rd |only lawn-0.1.7/lawn/tests/testthat/test-aggregate.R |only lawn-0.1.7/lawn/tests/testthat/test-jenks.R |only lawn-0.1.7/lawn/tests/testthat/test-quantile.R |only lawn-0.1.7/lawn/tests/testthat/test-reclass.R |only lawn-0.1.7/lawn/tests/testthat/test-size.R |only lawn-0.3.0/lawn/DESCRIPTION | 16 lawn-0.3.0/lawn/MD5 | 283 ++++--- lawn-0.3.0/lawn/NAMESPACE | 27 lawn-0.3.0/lawn/NEWS.md |only lawn-0.3.0/lawn/R/as.turf.R | 22 lawn-0.3.0/lawn/R/average.R | 14 lawn-0.3.0/lawn/R/bbox_polygon.R | 6 lawn-0.3.0/lawn/R/buffer.R | 14 lawn-0.3.0/lawn/R/circle.R |only lawn-0.3.0/lawn/R/collect.R |only lawn-0.3.0/lawn/R/count.R | 21 lawn-0.3.0/lawn/R/data-types.R | 10 lawn-0.3.0/lawn/R/defunct-deprecated.R |only lawn-0.3.0/lawn/R/deviation.R | 37 lawn-0.3.0/lawn/R/erase.R | 15 lawn-0.3.0/lawn/R/extent.R | 2 lawn-0.3.0/lawn/R/featurecollection.R | 29 lawn-0.3.0/lawn/R/filter.R | 15 lawn-0.3.0/lawn/R/geometrycollection.R |only lawn-0.3.0/lawn/R/kinks.R | 14 lawn-0.3.0/lawn/R/lawn-package.R | 2 lawn-0.3.0/lawn/R/lawn_bbox.R |only lawn-0.3.0/lawn/R/lawn_feature.R |only lawn-0.3.0/lawn/R/linestring.R | 4 lawn-0.3.0/lawn/R/max.R | 13 lawn-0.3.0/lawn/R/median.R | 17 lawn-0.3.0/lawn/R/merge.R | 12 lawn-0.3.0/lawn/R/min.R | 13 lawn-0.3.0/lawn/R/multilinestring.R |only lawn-0.3.0/lawn/R/multipoint.R |only lawn-0.3.0/lawn/R/multipolygon.R |only lawn-0.3.0/lawn/R/onLoad.R | 15 lawn-0.3.0/lawn/R/point.R | 7 lawn-0.3.0/lawn/R/polygon.R | 10 lawn-0.3.0/lawn/R/print_methods.R | 35 lawn-0.3.0/lawn/R/random.R | 2 lawn-0.3.0/lawn/R/remove.R | 13 lawn-0.3.0/lawn/R/sum.R | 13 lawn-0.3.0/lawn/R/tag.R | 25 lawn-0.3.0/lawn/R/tesselate.R |only lawn-0.3.0/lawn/R/variance.R | 13 lawn-0.3.0/lawn/R/view.R | 2 lawn-0.3.0/lawn/R/zzz.R | 16 lawn-0.3.0/lawn/README.md | 49 - 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Title: Hierarchical Optimal Matching and Machine Learning Toolbox
Description: Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.
Author: Teemu Daniel Laajala <teelaa@utu.fi>
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between hamlet versions 0.9.4-2 dated 2015-10-15 and 0.9.5 dated 2016-10-25
DESCRIPTION | 11 ++++++----- MD5 | 31 +++++++++++++++++++++---------- R/simurun.R |only build/vignette.rds |binary inst/CITATION |only inst/doc/introduction.pdf |binary man/hamlet-package.Rd | 11 ++++------- man/match.allocate.Rd | 7 ++++--- man/match.bb.Rd | 7 ++++--- man/orxlong.Rd | 2 +- man/orxwide.Rd | 2 +- man/vcaplong.Rd | 4 +++- man/vcapwide.Rd | 4 +++- vignettes/introduction-007.pdf |only vignettes/introduction-013.pdf |only vignettes/introduction-014.pdf |only vignettes/introduction-016.pdf |only vignettes/introduction-017.pdf |only vignettes/introduction-019.pdf |only vignettes/introduction-020.pdf |only vignettes/introduction-022.pdf |only vignettes/introduction-023.pdf |only 22 files changed, 47 insertions(+), 32 deletions(-)
Title: A Companion to the e-Book "YaRrr!: The Pirate's Guide to R"
Description: Contains a mixture of functions and data sets referred to in the introductory e-book "YaRrr!: The Pirate's Guide to R". The latest version of the e-book is available for free at <https://www.thepiratesguidetor.com>.
Author: Nathaniel Phillips [aut, cre]
Maintainer: Nathaniel Phillips <yarrr.book@gmail.com>
Diff between yarrr versions 0.1.1 dated 2016-10-16 and 0.1.2 dated 2016-10-25
DESCRIPTION | 8 MD5 | 22 - NEWS.md | 6 R/pirateplot_function.R | 520 +++++++++++++++++++++++++++++++++++------------ R/zzz.R | 12 - README.md | 21 - inst/doc/guide.html | 6 inst/doc/pirateplot.R | 107 +++++---- inst/doc/pirateplot.Rmd | 147 ++++++++----- inst/doc/pirateplot.html | 163 +++++++++----- man/pirateplot.Rd | 33 +- vignettes/pirateplot.Rmd | 147 ++++++++----- 12 files changed, 790 insertions(+), 402 deletions(-)
Title: A Statistically Sound data.frame Processor/Conditioner
Description: A data.frame processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
Prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: Inf, NA, too many categorical levels, rare categorical levels, new
categorical levels (levels seen during application, but not during training).
'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.27 dated 2016-08-17 and 0.5.28 dated 2016-10-24
vtreat-0.5.27/vtreat/man/makekWayCrossValidationOrderedByColumn.Rd |only vtreat-0.5.28/vtreat/DESCRIPTION | 10 vtreat-0.5.28/vtreat/MD5 | 86 ++--- vtreat-0.5.28/vtreat/NAMESPACE | 1 vtreat-0.5.28/vtreat/R/deviationFact.R | 16 vtreat-0.5.28/vtreat/R/effectTreatmentC.R | 8 vtreat-0.5.28/vtreat/R/effectTreatmentN.R | 8 vtreat-0.5.28/vtreat/R/outOfSample.R | 144 ++++---- vtreat-0.5.28/vtreat/R/prevalenceFact.R | 8 vtreat-0.5.28/vtreat/R/utils.R | 7 vtreat-0.5.28/vtreat/R/vtreat.R | 49 +- vtreat-0.5.28/vtreat/R/vtreatImpl.R | 55 +-- vtreat-0.5.28/vtreat/README.md | 82 ++-- vtreat-0.5.28/vtreat/build/vignette.rds |binary vtreat-0.5.28/vtreat/inst/doc/vtreat.Rmd | 4 vtreat-0.5.28/vtreat/inst/doc/vtreat.html | 172 ++++------ vtreat-0.5.28/vtreat/inst/doc/vtreatCrossFrames.Rmd | 2 vtreat-0.5.28/vtreat/inst/doc/vtreatCrossFrames.html | 120 +++--- vtreat-0.5.28/vtreat/inst/doc/vtreatGrouping.html | 10 vtreat-0.5.28/vtreat/inst/doc/vtreatOverfit.html | 74 +--- vtreat-0.5.28/vtreat/inst/doc/vtreatRareLevels.R |only vtreat-0.5.28/vtreat/inst/doc/vtreatRareLevels.Rmd |only vtreat-0.5.28/vtreat/inst/doc/vtreatRareLevels.html |only vtreat-0.5.28/vtreat/inst/doc/vtreatScaleMode.html | 66 +-- vtreat-0.5.28/vtreat/inst/doc/vtreatSignificance.html | 28 - vtreat-0.5.28/vtreat/inst/doc/vtreatSplitting.html | 10 vtreat-0.5.28/vtreat/inst/doc/vtreatVariableTypes.Rmd | 19 - vtreat-0.5.28/vtreat/inst/doc/vtreatVariableTypes.html | 108 +++--- vtreat-0.5.28/vtreat/man/buildEvalSets.Rd | 18 - vtreat-0.5.28/vtreat/man/designTreatmentsC.Rd | 8 vtreat-0.5.28/vtreat/man/designTreatmentsN.Rd | 8 vtreat-0.5.28/vtreat/man/designTreatmentsZ.Rd | 10 vtreat-0.5.28/vtreat/man/getSplitPlanAppLabels.Rd | 10 vtreat-0.5.28/vtreat/man/mkCrossFrameCExperiment.Rd | 8 vtreat-0.5.28/vtreat/man/mkCrossFrameNExperiment.Rd | 8 vtreat-0.5.28/vtreat/man/prepare.Rd | 2 vtreat-0.5.28/vtreat/man/problemAppPlan.Rd | 17 vtreat-0.5.28/vtreat/man/vtreat-package.Rd | 4 vtreat-0.5.28/vtreat/tests/testthat/testExpmtDesign.R | 27 - vtreat-0.5.28/vtreat/tests/testthat/testPC.R |only vtreat-0.5.28/vtreat/tests/testthat/testParallel.R | 8 vtreat-0.5.28/vtreat/tests/testthat/testStability.R | 2 vtreat-0.5.28/vtreat/tests/testthat/testZW.R | 3 vtreat-0.5.28/vtreat/vignettes/vtreat.Rmd | 4 vtreat-0.5.28/vtreat/vignettes/vtreatCrossFrames.Rmd | 2 vtreat-0.5.28/vtreat/vignettes/vtreatRareLevels.Rmd |only vtreat-0.5.28/vtreat/vignettes/vtreatVariableTypes.Rmd | 19 - 47 files changed, 619 insertions(+), 626 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data.
Author: Beata Nowok, Gillian M Raab, Joshua Snoke and Chris Dibben
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.2-1 dated 2016-03-15 and 1.3-0 dated 2016-10-24
DESCRIPTION | 8 MD5 | 60 +-- NAMESPACE | 32 - NEWS | 62 ++- R/IO.r | 267 ++++++------- R/compare.syn.r | 10 R/functions.syn.r | 147 +++++-- R/methods.syn.r | 46 ++ R/multi.compare.syn.r |only R/padModel.syn.r | 10 R/sampler.syn.r | 120 +++--- R/syn.r | 355 +++++++++++------ R/syn.strata.r |only R/utility.syn.r | 913 +++++++++++++++++++++++++++------------------- build/vignette.rds |binary data/SD2011.rda |binary inst/CITATION |only inst/doc/synthpop.pdf |binary man/compare.fit.synds.Rd | 4 man/compare.synds.Rd | 9 man/glm.synds.Rd | 15 man/multi.compare.Rd |only man/replicated.uniques.Rd | 5 man/sdc.Rd | 7 man/summary.fit.synds.Rd | 11 man/summary.synds.Rd | 5 man/syn.Rd | 86 +++- man/syn.nested.Rd |only man/syn.polr.Rd | 2 man/syn.polyreg.Rd | 2 man/synthpop-package.Rd | 4 man/tab.utility.Rd |only man/utility.synds.Rd | 5 man/write.syn.Rd | 7 34 files changed, 1344 insertions(+), 848 deletions(-)
Title: Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Description: Provides an abstraction for managing, installing,
and switching between sets of installed R packages. This allows users to
maintain multiple package libraries simultaneously, e.g. to maintain
strict, package-version-specific reproducibility of many analyses, or
work within a development/production release paradigm. Introduces a
generalized package installation process which supports multiple repository
and non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between switchr versions 0.10.14 dated 2016-05-22 and 0.11.0 dated 2016-10-24
switchr-0.10.14/switchr/inst/cranarchivetest.R |only switchr-0.10.14/switchr/inst/examples/localcheckout.R |only switchr-0.10.14/switchr/inst/gamvsmgcvtest.R |only switchr-0.10.14/switchr/inst/oldlib.R |only switchr-0.10.14/switchr/inst/sinfo3.0.2.txt |only switchr-0.10.14/switchr/inst/switchr.Rmd |only switchr-0.10.14/switchr/inst/talk2015.html |only switchr-0.10.14/switchr/inst/talks/BarugLightning.html |only switchr-0.10.14/switchr/inst/talks/BarugLightning.pdf |only switchr-0.10.14/switchr/inst/talks/BarugLightning.tex |only switchr-0.10.14/switchr/inst/talks/BarugLightning2.html |only switchr-0.10.14/switchr/inst/talks/BarugLightningOld.html |only switchr-0.10.14/switchr/inst/talks/BarugTalk.pdf |only switchr-0.10.14/switchr/inst/winbug.R |only switchr-0.10.14/switchr/inst/windowsbugdat.txt |only switchr-0.10.14/switchr/inst/windowsbugdat2.txt |only switchr-0.11.0/switchr/DESCRIPTION | 12 +-- switchr-0.11.0/switchr/MD5 | 44 +++-------- switchr-0.11.0/switchr/R/accessors.R | 16 ++-- switchr-0.11.0/switchr/R/biocManifest.R | 5 - switchr-0.11.0/switchr/R/cmethods.R | 2 switchr-0.11.0/switchr/build/vignette.rds |binary switchr-0.11.0/switchr/inst/doc/switchrvign.R | 49 ++++-------- switchr-0.11.0/switchr/inst/doc/switchrvign.Rnw | 30 ------- switchr-0.11.0/switchr/inst/doc/switchrvign.pdf |binary switchr-0.11.0/switchr/man/BiocSVNManifest.Rd | 5 - switchr-0.11.0/switchr/man/archive_retries.Rd | 3 switchr-0.11.0/switchr/man/cmethods.Rd | 5 - switchr-0.11.0/switchr/man/manifest_methods.Rd | 2 switchr-0.11.0/switchr/tests/winpath.R | 55 ++++++-------- switchr-0.11.0/switchr/vignettes/switchrvign.Rnw | 30 ------- 31 files changed, 83 insertions(+), 175 deletions(-)
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial trading strategies.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, ctb],
Wouter Thielen [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between quantmod versions 0.4-6 dated 2016-08-28 and 0.4-7 dated 2016-10-24
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- R/getOptionChain.R | 6 ++---- man/getSymbols.MySQL.Rd | 2 +- man/quantmod-package.Rd | 6 +++--- 5 files changed, 16 insertions(+), 17 deletions(-)
Title: One Rule Machine Learning Classification Algorithm with
Enhancements
Description: Implements the One Rule (OneR) Machine Learning classification algorithm with enhancements for sophisticated handling of numeric data and missing values together with extensive diagnostic functions. It is useful as a baseline for machine learning models and the rules are often helpful heuristics.
Author: Holger von Jouanne-Diedrich
Maintainer: Holger von Jouanne-Diedrich <holger.jouanne-diedrich@h-ab.de>
Diff between OneR versions 2.0 dated 2016-08-12 and 2.1 dated 2016-10-24
DESCRIPTION | 10 ++++---- MD5 | 20 ++++++++-------- NAMESPACE | 1 NEWS | 11 +++++++++ R/OneR.R | 64 ++++++++++++++++++++++++++++++++++++++++------------- R/OneR_main.R | 4 +-- build/vignette.rds |binary inst/doc/OneR.Rmd | 12 ++++----- inst/doc/OneR.html | 40 +++++++++++++++++++-------------- man/eval_model.Rd | 18 +++++++++++++- vignettes/OneR.Rmd | 12 ++++----- 11 files changed, 129 insertions(+), 63 deletions(-)
Title: Printing Floating Point Numbers in a Human-Friendly Format
Description: Print vectors (and data frames) of floating point numbers
using a non-scientific format optimized for human readers. Vectors
of numbers are rounded using significant digits, aligned at the
decimal point, and all zeros trailing the decimal point are dropped.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between lucid versions 1.3 dated 2015-07-02 and 1.4 dated 2016-10-24
lucid-1.3/lucid/NEWS |only lucid-1.3/lucid/README.md |only lucid-1.3/lucid/data/antibiotic.txt.gz |only lucid-1.3/lucid/inst/doc/lucid_printing.Rnw |only lucid-1.3/lucid/inst/doc/lucid_printing.pdf |only lucid-1.3/lucid/vignettes/lucid_printing-concordance.tex |only lucid-1.3/lucid/vignettes/lucid_printing.Rnw |only lucid-1.4/lucid/DESCRIPTION | 19 - lucid-1.4/lucid/MD5 | 35 +-- lucid-1.4/lucid/NAMESPACE | 36 +-- lucid-1.4/lucid/R/antibiotic.R |only lucid-1.4/lucid/R/lucid.r | 86 ++++++- lucid-1.4/lucid/R/vc.r | 117 ++++++++-- lucid-1.4/lucid/build/vignette.rds |binary lucid-1.4/lucid/data/antibiotic.txt |only lucid-1.4/lucid/inst/doc/lucid_printing.R | 39 ++- lucid-1.4/lucid/inst/doc/lucid_printing.Rmd |only lucid-1.4/lucid/inst/doc/lucid_printing.html |only lucid-1.4/lucid/man/antibiotic.Rd | 75 ++---- lucid-1.4/lucid/man/lucid.Rd | 48 +--- lucid-1.4/lucid/man/vc.Rd | 57 ++-- lucid-1.4/lucid/tests |only lucid-1.4/lucid/vignettes/lucid.bib | 173 ++++++++------- lucid-1.4/lucid/vignettes/lucid_printing.Rmd |only 24 files changed, 428 insertions(+), 257 deletions(-)
Title: Tools to Evaluate DNA Profile Evidence
Description: Tools to determine DNA profile Weight of Evidence.
For further information see the 'likeLTD' guide provided,
or Balding, D.J. (2013) <DOI:10.1073/pnas.1219739110>.
Author: David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Maintainer: Christopher Steele <c.steele.11@ucl.ac.uk>
Diff between likeLTD versions 6.1.0 dated 2016-05-30 and 6.1.1 dated 2016-10-24
DESCRIPTION | 10 MD5 | 56 R/hypothesis-peaks.R | 1298 +++++++++--------- R/maximize-peaks.R | 1694 +++++++++++------------ R/reports-peaks.R | 2082 ++++++++++++++--------------- R/reports.R | 4 build/vignette.rds |binary inst/doc/likeLTDguide.pdf |binary inst/doc/usage.pdf |binary inst/extdata/hammer/hammer-CSP.csv | 10 inst/extdata/hammer/hammer-reference.csv | 8 inst/extdata/hammer/space-CSP.csv | 10 inst/extdata/hammer/space-reference.csv | 8 inst/extdata/nodropin/hammer-CSP.csv | 10 inst/extdata/nodropin/hammer-reference.csv | 8 inst/extdata/nodropout/CSP.csv | 10 inst/extdata/nodropout/reference.csv | 4 inst/extdata/novictim/hammer-CSP.csv | 10 inst/extdata/novictim/hammer-reference.csv | 4 man/CSP.heights.plot.Rd | 16 man/allele.report.peaks.Rd | 16 man/get.likely.genotypes.peaks.Rd | 44 man/locus.likes.peaks.Rd | 44 man/optimisation.params.peaks.Rd | 38 man/output.report.peaks.Rd | 44 man/peaks.results.plot.Rd | 44 man/read.known.profiles.Rd | 16 man/read.peaks.profile.Rd | 16 src/maximizePeaks.cpp | 5 29 files changed, 2757 insertions(+), 2752 deletions(-)
Title: Miscellaneous Functions for the USGS INL Project Office
Description: A collection of functions for creating high-level graphics,
performing raster-based analysis, processing MODFLOW-based models, and
overlaying multi-polygon objects. Used to support packages and scripts written
by researchers at the United States Geological Survey (USGS)
Idaho National Laboratory (INL) Project Office.
Author: Jason Fisher [aut, cre]
Maintainer: Jason Fisher <jfisher@usgs.gov>
Diff between inlmisc versions 0.2.1 dated 2016-10-15 and 0.2.2 dated 2016-10-24
inlmisc-0.2.1/inlmisc/NEWS |only inlmisc-0.2.2/inlmisc/DESCRIPTION | 8 ++++---- inlmisc-0.2.2/inlmisc/LICENSE.note |only inlmisc-0.2.2/inlmisc/MD5 | 23 ++++++++++++++--------- inlmisc-0.2.2/inlmisc/NAMESPACE | 1 + inlmisc-0.2.2/inlmisc/NEWS.md |only inlmisc-0.2.2/inlmisc/R/ReadCodeChunks.R |only inlmisc-0.2.2/inlmisc/R/ReadModflowBinary.R | 16 ++++++++-------- inlmisc-0.2.2/inlmisc/R/ReplaceInTemplate.R | 4 ++-- inlmisc-0.2.2/inlmisc/R/zzz.R | 2 +- inlmisc-0.2.2/inlmisc/README.md | 10 +++++----- inlmisc-0.2.2/inlmisc/inst/CITATION |only inlmisc-0.2.2/inlmisc/inst/misc |only inlmisc-0.2.2/inlmisc/man/ReadCodeChunks.Rd |only inlmisc-0.2.2/inlmisc/man/ReadModflowBinary.Rd | 6 +++--- inlmisc-0.2.2/inlmisc/man/ReplaceInTemplate.Rd | 4 ++-- 16 files changed, 40 insertions(+), 34 deletions(-)
Title: Quality Control for Graphics in R
Description: Functions to generate
graphics files, compare them with "model" files,
and report the results, including visual and textual
diffs of any differences.
Author: Stephen Gardiner and Paul Murrell
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between graphicsQC versions 1.0-7 dated 2016-03-03 and 1.0-8 dated 2016-10-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/graphicsqc.bib | 2 +- inst/doc/graphicsqc.pdf |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Creating Continuously Integrated Package Repositories from
Manifests
Description: Repository based tools for department and analysis level
reproducibility. 'GRANBase' allows creation of custom branched, continuous
integration-ready R repositories, including incremental testing of only packages
which have changed versions since the last repository build.
Author: Gabriel Becker[aut,cre], Cory Barr [cre,ctb]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between GRANBase versions 1.1.14 dated 2016-05-22 and 1.2.0 dated 2016-10-24
GRANBase-1.1.14/GRANBase/inst/GRAN/session.rda |only GRANBase-1.1.14/GRANBase/inst/GRAN/testBioc.R |only GRANBase-1.1.14/GRANBase/inst/manualTests/startup.Rs |only GRANBase-1.1.14/GRANBase/inst/todo.txt |only GRANBase-1.2.0/GRANBase/DESCRIPTION | 6 GRANBase-1.2.0/GRANBase/MD5 | 28 - GRANBase-1.2.0/GRANBase/NAMESPACE | 2 GRANBase-1.2.0/GRANBase/R/Utilities.R | 38 + GRANBase-1.2.0/GRANBase/R/accessors.R | 20 GRANBase-1.2.0/GRANBase/R/buildBranchesInRepo.R | 391 +++++++++---------- GRANBase-1.2.0/GRANBase/R/clear.R | 2 GRANBase-1.2.0/GRANBase/R/makeSrcDirs.R | 2 GRANBase-1.2.0/GRANBase/R/migrateToFinalRepo.R | 50 ++ GRANBase-1.2.0/GRANBase/R/testPackages.R | 150 ++++--- GRANBase-1.2.0/GRANBase/build/vignette.rds |binary GRANBase-1.2.0/GRANBase/inst/doc/GRAN-Overview.pdf |binary GRANBase-1.2.0/GRANBase/man/staging-methods.Rd | 12 17 files changed, 426 insertions(+), 275 deletions(-)
Title: Variance Stabilization by Data-Driven Haar-Fisz (for
Microarrays)
Description: Contains the normalizing and variance stabilizing
Data-Driven Haar-Fisz algorithm. Also contains related algorithms
for simulating from certain microarray gene intensity models and
evaluation of certain transformations. Contains cDNA and shipping
credit flow data.
Author: Efthimios Motakis [aut],
Guy Nason [aut, cre],
Piotr Fryzlewicz [aut]
Maintainer: Guy Nason <g.p.nason@bristol.ac.uk>
Diff between DDHFm versions 1.1.1 dated 2013-10-31 and 1.1.2 dated 2016-10-24
DESCRIPTION | 17 +++++++++-------- MD5 | 22 ++++++++++++---------- NAMESPACE | 4 ++++ build/vignette.rds |binary data/ShipCreditFlow.rda |only data/cdna.rda |binary data/datalist | 1 + inst/CHANGES | 2 ++ inst/doc/DDHFm.pdf |binary man/DDHFm.Rd | 13 +++++++++++-- man/ShipCreditFlow.Rd |only vignettes/DDHFm-cdna-ddhfm.pdf |binary vignettes/DDHFm-cdna-vsn.pdf |binary 13 files changed, 39 insertions(+), 20 deletions(-)
Title: Linear Regression Based on Linear Structure Between Covariates
Description: Linear regression based on a recursive structural equation model
(explicit multiples correlations) found by a MCMC algorithm. It permits to face
highly correlated covariates. Variable selection is included (by lasso,
elastic net, etc.). It also provides some graphical tools for basic
statistics (Boxplot with confidence intervals, etc) and regression trees.
Author: Clement THERY [aut, cre],
Christophe BIERNACKI [ctb],
Gaetan LORIDANT [ctb],
Florian WATRIN [ctb],
Quentin GRIMONPREZ [ctb],
Vincent KUBICKI [ctb],
Samuel BLANCK [ctb],
Jeremie KELLNER [ctb]
Maintainer: Clement THERY <corregeous@correg.org>
Diff between CorReg versions 1.1.1 dated 2015-12-09 and 1.1.9 dated 2016-10-24
DESCRIPTION | 8 ++--- MD5 | 30 ++++++++++-------- NAMESPACE | 4 ++ NEWS | 1 R/BoxPlot.R | 83 +++++++++++++++++++++++++++++++--------------------- R/Hist.R |only R/MSE_loc.R | 2 - R/R2Z.R | 2 - R/cleanZ.R | 18 +++++------ R/cleanZtest.R | 11 +++++- R/correg.R | 2 - R/structureFinder.R | 33 ++++++++++++-------- man/BoxPlot.Rd | 8 ++--- man/Hist.Rd |only man/MSE_loc.Rd | 2 - man/cleanZ.Rd |only man/cleanZtest.Rd |only src/rechercheZ.cpp | 38 +++++++++++++++++++++++ 18 files changed, 159 insertions(+), 83 deletions(-)
Title: Tau-Leaping Stochastic Simulation
Description: Implements adaptive tau leaping to approximate the
trajectory of a continuous-time stochastic process as
described by Cao et al. (2007) The Journal of Chemical Physics
<doi:10.1063/1.2745299>. This package is based upon work
supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip
Johnson and NIH R01-AI049334 to Rustom
Antia.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between adaptivetau versions 2.2 dated 2014-11-19 and 2.2-1 dated 2016-10-24
DESCRIPTION | 21 ++++++++++--------- MD5 | 12 +++++------ NEWS | 9 +++++++- build/vignette.rds |binary inst/doc/adaptivetau.pdf |binary src/Rwrappers.h | 7 +++++- src/adaptivetau.cpp | 50 ++++++++++++++++++++++++----------------------- 7 files changed, 57 insertions(+), 42 deletions(-)
Title: Bayesian Spatial Survival Analysis with Parametric Proportional
Hazards Models
Description: Bayesian inference for parametric proportional hazards spatial
survival models; flexible spatial survival models.
Author: Benjamin M. Taylor and Barry S. Rowlingson
Additional contributions
Ziyu Zheng
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between spatsurv versions 0.9-12 dated 2016-06-29 and 0.9-14 dated 2016-10-24
DESCRIPTION | 8 MD5 | 50 +-- NAMESPACE | 5 R/BsplineHaz.R | 106 +++---- R/calibratemcmc.R | 384 +++++++++++++------------- R/circulant.R | 14 R/multiWayHaz.R |only R/nonspatial_log_likelihood_and_derivatives.R | 139 ++++----- R/spatgrid.R | 90 +++--- R/spatsurvMisc.R | 126 ++++---- R/survspat.R | 282 +++++++++---------- README.md | 4 inst/CITATION | 5 man/BsplineHaz.Rd | 30 +- man/QuadApprox.Rd | 2 man/blockDiag.Rd |only man/circulant.matrix.Rd | 2 man/fixParHaz.Rd |only man/gencens.Rd | 2 man/getOptCellwidth.Rd | 2 man/inference.control.Rd | 2 man/insert.Rd |only man/invtransformweibull.Rd | 2 man/multiWayHaz.Rd |only man/plot.FFTgrid.Rd |only man/setupHazard.Rd | 2 man/survspat.Rd | 2 man/transformweibull.Rd | 2 tests/test_survspat.R | 16 - 29 files changed, 652 insertions(+), 625 deletions(-)
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood [aut, cre], Adam Maidman [ctb]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>
Diff between rqPen versions 1.4 dated 2016-04-21 and 1.5 dated 2016-10-24
DESCRIPTION | 10 - LICENSE | 4 MD5 | 14 +- NEWS | 4 R/Adamsfunc.R | 143 +++++++++++++++++++++ R/mainFunctions.R | 19 ++ man/rq.group.fit.Rd | 4 src/QCD.cpp | 340 +++++++++++++++++++++++++++++++++++++++++++++++++++- 8 files changed, 516 insertions(+), 22 deletions(-)
Title: Tuning of the Latent Dirichlet Allocation Models Parameters
Description: For this first version only metrics to estimate the best fitting
number of topics are implemented.
Author: Murzintcev Nikita [aut, cre]
Maintainer: Murzintcev Nikita <nikita@lreis.ac.cn>
Diff between ldatuning versions 0.1.0 dated 2015-09-16 and 0.2.0 dated 2016-10-24
DESCRIPTION | 13 ++-- LICENSE | 2 MD5 | 28 ++++---- NAMESPACE | 2 R/ldatuning.R | 3 R/main.R | 40 +++++++----- build/vignette.rds |binary inst/doc/topics.R | 4 + inst/doc/topics.Rmd | 16 +++-- inst/doc/topics.html | 136 +++++++++++++++++++++++++++++++------------ man/Deveaud2014.Rd | 2 man/FindTopicsNumber.Rd | 12 ++- man/FindTopicsNumber_plot.Rd | 8 +- man/ldatuning.Rd | 5 - vignettes/topics.Rmd | 19 +++--- 15 files changed, 189 insertions(+), 101 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Implementations of functions which have been introduced in
R since version 3.0.0. The backports are conditionally exported which
results in R resolving the function names to the version shipped with R (if
available) and uses the implemented backports as fallback. This way package
developers can make use of the new functions without worrying about the
minimum required R version.
Author: Michel Lang <michellang@gmail.com>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.0.3 dated 2016-06-28 and 1.0.4 dated 2016-10-24
backports-1.0.3/backports/R/anyNA.r |only backports-1.0.3/backports/R/dir.exists.r |only backports-1.0.3/backports/R/endsWith.r |only backports-1.0.3/backports/R/file.x.r |only backports-1.0.3/backports/R/lengths.r |only backports-1.0.3/backports/R/startsWith.r |only backports-1.0.3/backports/R/strrep.r |only backports-1.0.3/backports/R/trimws.r |only backports-1.0.3/backports/tests/testthat |only backports-1.0.3/backports/tests/testthat.R |only backports-1.0.4/backports/DESCRIPTION | 12 ++-- backports-1.0.4/backports/MD5 | 65 ++++++++++++---------- backports-1.0.4/backports/NAMESPACE | 2 backports-1.0.4/backports/NEWS.md | 7 ++ backports-1.0.4/backports/R/anyNA.R |only backports-1.0.4/backports/R/dir.exists.R |only backports-1.0.4/backports/R/endsWith.R |only backports-1.0.4/backports/R/file.info.R |only backports-1.0.4/backports/R/file.mode.R |only backports-1.0.4/backports/R/file.mtime.R |only backports-1.0.4/backports/R/file.size.R |only backports-1.0.4/backports/R/hasName.R |only backports-1.0.4/backports/R/lengths.R |only backports-1.0.4/backports/R/startsWith.R |only backports-1.0.4/backports/R/strrep.R |only backports-1.0.4/backports/R/trimws.R |only backports-1.0.4/backports/man/anyNA.Rd | 2 backports-1.0.4/backports/man/dir.exists.Rd | 4 - backports-1.0.4/backports/man/endsWith.Rd | 2 backports-1.0.4/backports/man/file.info.Rd |only backports-1.0.4/backports/man/file.size.Rd | 8 +- backports-1.0.4/backports/man/hasName.Rd |only backports-1.0.4/backports/man/lengths.Rd | 4 - backports-1.0.4/backports/man/startsWith.Rd | 2 backports-1.0.4/backports/man/strrep.Rd | 2 backports-1.0.4/backports/man/trimws.Rd | 2 backports-1.0.4/backports/tests/helper |only backports-1.0.4/backports/tests/test_anyNA.R |only backports-1.0.4/backports/tests/test_dir.exists.R |only backports-1.0.4/backports/tests/test_file.info.R |only backports-1.0.4/backports/tests/test_file.mode.R |only backports-1.0.4/backports/tests/test_file.mtime.R |only backports-1.0.4/backports/tests/test_file.size.R |only backports-1.0.4/backports/tests/test_hasName.R |only backports-1.0.4/backports/tests/test_lengths.R |only backports-1.0.4/backports/tests/test_startsWith.R |only backports-1.0.4/backports/tests/test_strrep.R |only backports-1.0.4/backports/tests/test_trimws.R |only 48 files changed, 65 insertions(+), 47 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>
Diff between surveyplanning versions 2.2 dated 2016-10-19 and 2.4 dated 2016-10-24
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- R/dom_optimal_allocation.R | 75 +++++++++++++++++++-------------------- R/expsize.R | 55 ++++++++++++---------------- R/expvar.R | 10 ++--- R/optsize.R | 36 +++++++++--------- R/ratio_dom_optimal_allocation.R | 28 +++++++------- inst/CITATION | 4 +- inst/NEWS | 4 ++ man/surveyplanning-package.Rd | 4 +- 10 files changed, 119 insertions(+), 123 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between dynRB versions 0.8 dated 2016-08-01 and 0.9 dated 2016-10-24
DESCRIPTION | 6 - MD5 | 12 +-- R/dynRB-internal.R | 131 +++++++++++++++++++++++++-------- R/dynRB_Pn.R | 122 +++++++++++++++++++----------- R/dynRB_VPa.R | 201 ++++++++++++++++++++++++++++++++------------------- R/dynRB_Vn.R | 110 +++++++++++++++++---------- man/dynRB-package.Rd | 4 - 7 files changed, 382 insertions(+), 204 deletions(-)
Title: Aligned Rank Transform
Description: The Aligned Rank Transform for nonparametric
factorial ANOVAs as described by J. O. Wobbrock,
L. Findlater, D. Gergle, & J. J. Higgins, "The Aligned
Rank Transform for nonparametric factorial analyses
using only ANOVA procedures", CHI 2011 <DOI:10.1145/1978942.1978963>.
Author: Matthew Kay [aut, cre],
Jacob O. Wobbrock [aut]
Maintainer: Matthew Kay <mjskay@umich.edu>
Diff between ARTool versions 0.10.2 dated 2016-03-29 and 0.10.4 dated 2016-10-24
DESCRIPTION | 15 - MD5 | 22 - NEWS | 16 + R/release.questions.R | 20 - build/vignette.rds |binary inst/doc/art-contrasts.R | 4 inst/doc/art-contrasts.Rmd | 591 +++++++++++++++++++++--------------------- inst/doc/art-contrasts.html | 146 ++++++---- inst/doc/art-effect-size.Rmd | 355 ++++++++++++------------- inst/doc/art-effect-size.html | 120 ++++---- vignettes/art-contrasts.Rmd | 591 +++++++++++++++++++++--------------------- vignettes/art-effect-size.Rmd | 355 ++++++++++++------------- 12 files changed, 1172 insertions(+), 1063 deletions(-)
Title: Tools for Designing and Weighting Survey Samples
Description: Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example datasets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <rvallian@umd.edu>
Diff between PracTools versions 0.3 dated 2015-11-16 and 0.4 dated 2016-10-23
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- R/clusOpt2.R | 2 +- R/clusOpt3.R | 4 ++-- data/Domainy1y2.RData |binary data/MDarea.pop.RData |binary data/hospital.RData |binary data/labor.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary man/BW2stagePPS.Rd | 2 +- man/BW3stagePPS.Rd | 2 +- man/CVcalc2.Rd | 2 +- man/CVcalc3.Rd | 6 +++--- man/NRFUopt.Rd | 2 +- man/nhis.Rd | 14 +++++++------- man/nhis.large.Rd | 2 +- man/nhispart.Rd | 2 +- 21 files changed, 43 insertions(+), 43 deletions(-)
Title: Structural Time Series Models
Description: Fit the basic structural time series model by maximum likelihood.
Author: Javier López-de-Lacalle <javlacalle@yahoo.es>
Maintainer: Javier López-de-Lacalle <javlacalle@yahoo.es>
Diff between stsm versions 1.7 dated 2015-01-26 and 1.9 dated 2016-10-23
DESCRIPTION | 12 +- MD5 | 44 ++++---- NAMESPACE | 9 + NEWS | 19 +++ R/mloglik-td.R | 74 ++++++++++--- R/stsm-class.R | 73 ++++++++++++- R/stsm-methods.R | 117 ++++++++++++++++++++- R/transPars.R | 230 +++++++++++++++++++++++++++++++++++------- build/vignette.rds |binary inst/doc/index.html | 6 - inst/doc/stsm-intro.Rnw | 6 - inst/doc/stsm-intro.pdf |binary man/maxlik-fd.Rd | 6 - man/mloglik-fd.Rd | 4 man/mloglik-td.Rd | 4 man/stsm-class.Rd | 2 man/stsm-methods-get.Rd | 12 +- man/stsm-methods-set.Rd | 4 man/stsm-methods-transPars.Rd | 8 - man/stsm-model.Rd | 2 src/KFKSDS-steady-v2.h | 8 - src/KFKSDS-steady.h | 2 vignettes/stsm-intro.Rnw | 6 - 23 files changed, 519 insertions(+), 129 deletions(-)
Title: A Simple Data Science Challenge System
Description: A simple data science challenge system using R Markdown and Dropbox <https://www.dropbox.com/>.
It requires no network configuration, does not depend on external platforms
like e.g. Kaggle <https://www.kaggle.com/> and can be easily installed on a personal computer.
Author: Adrien Todeschini [aut, cre],
Robin Genuer [ctb]
Maintainer: Adrien Todeschini <adrien.todeschini@gmail.com>
Diff between rchallenge versions 1.2.0 dated 2016-10-05 and 1.3.0 dated 2016-10-23
rchallenge-1.2.0/rchallenge/inst/glyphicons |only rchallenge-1.2.0/rchallenge/man/glyphicon.Rd |only rchallenge-1.3.0/rchallenge/DESCRIPTION | 6 rchallenge-1.3.0/rchallenge/MD5 | 59 ++----- rchallenge-1.3.0/rchallenge/NAMESPACE | 1 rchallenge-1.3.0/rchallenge/NEWS.md | 7 rchallenge-1.3.0/rchallenge/R/display.r | 95 ++++++----- rchallenge-1.3.0/rchallenge/R/new.r | 4 rchallenge-1.3.0/rchallenge/R/plots.r | 2 rchallenge-1.3.0/rchallenge/R/rchallenge.r | 31 +++ rchallenge-1.3.0/rchallenge/R/update.r | 108 ++++++------- rchallenge-1.3.0/rchallenge/README.md | 39 ++-- rchallenge-1.3.0/rchallenge/inst/template/challenge_en.rmd | 94 +++++------ rchallenge-1.3.0/rchallenge/inst/template/challenge_fr.rmd | 100 ++++++------ rchallenge-1.3.0/rchallenge/man/get_best.Rd | 18 +- rchallenge-1.3.0/rchallenge/man/html_img.Rd | 4 rchallenge-1.3.0/rchallenge/man/icon.Rd |only rchallenge-1.3.0/rchallenge/man/plot_activity.Rd | 2 rchallenge-1.3.0/rchallenge/man/print_leaderboard.Rd | 9 - rchallenge-1.3.0/rchallenge/man/print_readerr.Rd | 11 - rchallenge-1.3.0/rchallenge/man/publish.Rd | 4 rchallenge-1.3.0/rchallenge/man/rchallenge-defunct.Rd |only rchallenge-1.3.0/rchallenge/man/rchallenge-package.Rd | 10 - rchallenge-1.3.0/rchallenge/man/str_rank.Rd | 5 rchallenge-1.3.0/rchallenge/man/update_rank_diff.Rd | 8 25 files changed, 334 insertions(+), 283 deletions(-)
Title: Models Multivariate Cases Using Random Forests
Description: Models and predicts Multiple Features in single random forest considering the linear relation among the features.
Author: Raziur Rahman
Maintainer: Raziur Rahman <razeeebuet@gmail.com>
Diff between MultivariateRandomForest versions 1.1 dated 2016-03-24 and 1.1.1 dated 2016-10-23
MultivariateRandomForest-1.1.1/MultivariateRandomForest/DESCRIPTION | 31 +--- MultivariateRandomForest-1.1.1/MultivariateRandomForest/MD5 | 41 ++--- MultivariateRandomForest-1.1.1/MultivariateRandomForest/NAMESPACE | 12 + MultivariateRandomForest-1.1.1/MultivariateRandomForest/R/CrossValidation.R | 26 +-- MultivariateRandomForest-1.1.1/MultivariateRandomForest/R/Imputation.R | 71 +++++----- MultivariateRandomForest-1.1.1/MultivariateRandomForest/R/RcppExports.R |only MultivariateRandomForest-1.1.1/MultivariateRandomForest/R/build_forest_predict.R |only MultivariateRandomForest-1.1.1/MultivariateRandomForest/R/build_single_tree.R | 48 ++++-- MultivariateRandomForest-1.1.1/MultivariateRandomForest/R/single_tree_prediction.R | 15 +- MultivariateRandomForest-1.1.1/MultivariateRandomForest/R/variable_importance_measure.R |only MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/CrossValidation.Rd | 26 +-- MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/Imputation.Rd | 12 - MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/Node_cost.Rd |only MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/build_forest_predict.Rd |only MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/build_single_tree.Rd | 33 ++-- MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/predicting.Rd | 18 +- MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/single_tree_prediction.Rd | 10 - MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/split_node.Rd | 30 ++-- MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/splitt.Rd |only MultivariateRandomForest-1.1.1/MultivariateRandomForest/man/variable_importance_measure.Rd |only MultivariateRandomForest-1.1.1/MultivariateRandomForest/src |only MultivariateRandomForest-1.1/MultivariateRandomForest/R/Multi_D_mod.R |only MultivariateRandomForest-1.1/MultivariateRandomForest/R/MultivariateRandomForest.R |only MultivariateRandomForest-1.1/MultivariateRandomForest/R/predicting.R |only MultivariateRandomForest-1.1/MultivariateRandomForest/R/split_node.R |only MultivariateRandomForest-1.1/MultivariateRandomForest/R/spliting.R |only MultivariateRandomForest-1.1/MultivariateRandomForest/man/Multi_D_mod.Rd |only MultivariateRandomForest-1.1/MultivariateRandomForest/man/MultivariateRandomForest.Rd |only MultivariateRandomForest-1.1/MultivariateRandomForest/man/spliting.Rd |only 29 files changed, 199 insertions(+), 174 deletions(-)
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Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <sen-zhao@sen-zhao.com>
Diff between Grace versions 0.5 dated 2016-10-22 and 0.5.1 dated 2016-10-23
DESCRIPTION | 8 +-- MD5 | 14 ++--- NAMESPACE | 2 R/cvGrace.R | 30 +++++------- R/grace.R | 41 ++++++++++------- R/grace.test.R | 129 ++++++++++++++++++++++++++++++++++++------------------ man/grace.Rd | 8 +-- man/grace.test.Rd | 24 ++++++---- 8 files changed, 156 insertions(+), 100 deletions(-)
Title: Bayesian Adjustment for Confounding
Description: Estimating the average causal effect based on the Bayesian Adjustment for Confounding (BAC) algorithm.
Author: Chi Wang <chi.wang@uky.edu>
Maintainer: Chi Wang <chi.wang@uky.edu>
Diff between bacr versions 1.0 dated 2015-08-07 and 1.0.1 dated 2016-10-23
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- R/bac.R | 51 ++++++++++++++++++++++++++------------------------- inst |only man/bac.Rd | 6 +++--- man/bacr-package.Rd | 10 +++++----- 6 files changed, 44 insertions(+), 41 deletions(-)
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Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups
preprocessed through matching, weighting or subclassification, for example,
using propensity scores. Includes integration with 'MatchIt', 'twang', 'Matching', and
'CBPS' for assessing balance on the output of their preprocessing functions. Users
can also specify data for balance assessment not generated through the above packages.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah@unc.edu>
Diff between cobalt versions 1.2.0 dated 2016-09-01 and 1.3.0 dated 2016-10-23
DESCRIPTION | 10 MD5 | 43 - NAMESPACE | 8 R/Under_construction/int.poly.R |only R/Under_construction/under_construction.R | 33 + R/bal.tab.R | 735 ++++++++++-------------------- R/f.build.R | 4 R/get.C.R |only R/love.plot.R | 465 ++++++++++-------- R/print.bal.tab.R | 229 ++++++++- R/x2base.R | 15 inst/doc/cobalt.R | 22 inst/doc/cobalt.Rmd | 70 +- inst/doc/cobalt.html | 138 ++--- man/bal.tab.CBPS.Rd | 265 +++++----- man/bal.tab.Match.Rd | 281 +++++------ man/bal.tab.Rd | 152 +++--- man/bal.tab.df.formula.Rd | 397 ++++++++-------- man/bal.tab.matchit.Rd | 9 man/bal.tab.ps.Rd | 251 +++++----- man/f.build.Rd | 7 man/love.plot.Rd | 27 - man/print.bal.tab.Rd |only vignettes/cobalt.Rmd | 70 +- 24 files changed, 1684 insertions(+), 1547 deletions(-)
Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.3 dated 2015-12-20 and 0.6.4 dated 2016-10-23
DESCRIPTION | 8 - MD5 | 37 +++---- NAMESPACE | 2 NEWS | 22 +++- R/crossv.R | 218 ++++++++++++++++++++++-------------------- R/gui.stylo.R | 36 +++++- R/make.table.of.frequencies.R | 6 - R/oppose.R | 18 ++- R/perform.delta.R | 34 +++++- R/perform.impostors.R |only R/perform.knn.R | 52 +++++++++- R/perform.naivebayes.R | 46 +++++++- R/perform.nsc.R | 33 +++++- R/perform.svm.R | 46 +++++++- inst/CITATION | 33 +++--- man/crossv.Rd |only man/perform.delta.Rd | 10 + man/perform.impostors.Rd |only man/perform.knn.Rd | 29 +++++ man/perform.naivebayes.Rd | 29 +++++ man/perform.svm.Rd | 10 + 21 files changed, 488 insertions(+), 181 deletions(-)
Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>
Diff between texreg versions 1.36.7 dated 2016-06-21 and 1.36.18 dated 2016-10-23
DESCRIPTION | 20 +- MD5 | 26 +- NAMESPACE | 184 ++++++++++----------- R/classDefinition.R | 40 ++-- R/extract.R | 444 +++++++++++++++++++++++++++++++++++++++++++-------- R/internal.R | 47 ++++- R/plotreg.R | 2 R/texreg.R | 26 +- build/vignette.rds |binary inst/doc/texreg.R | 46 ++--- inst/doc/texreg.Rnw | 156 +++++++++-------- inst/doc/texreg.pdf |binary man/extract.Rd | 59 +++++- vignettes/texreg.Rnw | 156 +++++++++-------- 14 files changed, 807 insertions(+), 399 deletions(-)
Title: Jane Austen's Complete Novels
Description: Full texts for Jane Austen's 6 completed novels, ready for text
analysis. These novels are "Sense and Sensibility", "Pride and Prejudice",
"Mansfield Park", "Emma", "Northanger Abbey", and "Persuasion".
Author: Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between janeaustenr versions 0.1.2 dated 2016-09-17 and 0.1.3 dated 2016-10-23
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- R/austen_books.R | 1 + tests |only 4 files changed, 10 insertions(+), 7 deletions(-)
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate
'API' at <http://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for
each of the 'API' 'endpoints': data, data categories, data sets, data types,
locations, location categories, and stations. In addition, we have an interface
for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical
Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS',
tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut, cre],
Brooke Anderson [ctb],
Maëlle Salmon [ctb],
Adam Erickson [ctb],
Nicholas Potter [ctb],
Joseph Stachelek [ctb],
Alex Simmons [ctb],
Karthik Ram [ctb],
Hart Edmund [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 0.6.4 dated 2016-10-07 and 0.6.5 dated 2016-10-22
rnoaa-0.6.4/rnoaa/R/aaa.r |only rnoaa-0.6.5/rnoaa/DESCRIPTION | 8 +- rnoaa-0.6.5/rnoaa/MD5 | 59 ++++++++-------- rnoaa-0.6.5/rnoaa/NEWS.md | 88 +++++++++++++++---------- rnoaa-0.6.5/rnoaa/R/argo.R | 2 rnoaa-0.6.5/rnoaa/R/caching.R | 2 rnoaa-0.6.5/rnoaa/R/coops.R | 74 +++++++++------------ rnoaa-0.6.5/rnoaa/R/ersst.R | 5 - rnoaa-0.6.5/rnoaa/R/ghcnd.R | 18 +++-- rnoaa-0.6.5/rnoaa/R/isd.R | 4 - rnoaa-0.6.5/rnoaa/R/isd_stations.R | 8 +- rnoaa-0.6.5/rnoaa/R/meteo_cache.r | 8 +- rnoaa-0.6.5/rnoaa/R/meteo_distance.R | 28 +++---- rnoaa-0.6.5/rnoaa/R/seaice.r | 12 +-- rnoaa-0.6.5/rnoaa/R/storm_shp.R | 2 rnoaa-0.6.5/rnoaa/R/storms.R | 4 - rnoaa-0.6.5/rnoaa/R/tornadoes.R | 7 + rnoaa-0.6.5/rnoaa/R/zzz.r | 2 rnoaa-0.6.5/rnoaa/man/argo.Rd | 4 - rnoaa-0.6.5/rnoaa/man/coops.Rd | 28 ++----- rnoaa-0.6.5/rnoaa/man/ersst.Rd | 3 rnoaa-0.6.5/rnoaa/man/ghcnd.Rd | 13 ++- rnoaa-0.6.5/rnoaa/man/ghcnd_search.Rd | 3 rnoaa-0.6.5/rnoaa/man/isd.Rd | 2 rnoaa-0.6.5/rnoaa/man/isd_stations.Rd | 7 + rnoaa-0.6.5/rnoaa/man/meteo_clear_cache.Rd | 5 + rnoaa-0.6.5/rnoaa/man/meteo_nearby_stations.Rd | 23 +++--- rnoaa-0.6.5/rnoaa/man/meteo_pull_monitors.Rd | 3 rnoaa-0.6.5/rnoaa/man/meteo_tidy_ghcnd.Rd | 3 rnoaa-0.6.5/rnoaa/man/storms.Rd | 2 rnoaa-0.6.5/rnoaa/man/tornadoes.Rd | 5 - 31 files changed, 234 insertions(+), 198 deletions(-)
Title: Model-Based Clustering of Categorical Sequences
Description: Clustering categorical sequences by means of finite mixtures with Markov model components is the main utility of ClickClust. The package also allows detecting blocks of equivalent states by forward and backward state selection procedures.
Author: Volodymyr Melnykov [aut, cre],
Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Volodymyr Melnykov <vmelnykov@cba.ua.edu>
Diff between ClickClust versions 1.1.4 dated 2015-04-08 and 1.1.5 dated 2016-10-22
DESCRIPTION | 17 ++++++++++------- MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 4 ++++ NEWS | 5 +++++ inst/CITATION | 28 +++++++++++++++++----------- man/B3.Rd | 5 ++--- man/BackwardSearch.Rd | 5 +++-- man/C.Rd | 4 ++-- man/ClickClust-package.Rd | 4 +++- man/ClickClust.Rd | 6 ++++-- man/ClickPlot.Rd | 4 +++- man/ForwardSearch.Rd | 4 +++- man/Predict.Rd | 4 +++- man/ReadData.Rd | 4 +++- man/SimData.Rd | 4 +++- man/VarEst.Rd | 4 +++- man/msnbc323.Rd | 4 +++- man/print.summary.Rd | 5 ++++- man/synth.Rd | 4 ++-- 19 files changed, 95 insertions(+), 56 deletions(-)
Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading and writing foreign files containing
spectral data from spectrometers and their associated software, and output
from simulation models in common use. As well as functions for exchange
of spectral data with other R packages.
Author: Pedro J. Aphalo [aut, cre],
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.11 dated 2016-09-25 and 0.4.12 dated 2016-10-22
photobiologyInOut-0.4.11/photobiologyInOut/R/read-libradtran-vesa.r |only photobiologyInOut-0.4.11/photobiologyInOut/man/read_libradtran_vesa.Rd |only photobiologyInOut-0.4.11/photobiologyInOut/vignettes/data-vignettes/libradtran-multi.dat |only photobiologyInOut-0.4.11/photobiologyInOut/vignettes/data-vignettes/libradtran-plain-2col.dat |only photobiologyInOut-0.4.11/photobiologyInOut/vignettes/data-vignettes/libradtran-plain.dat |only photobiologyInOut-0.4.12/photobiologyInOut/DESCRIPTION | 14 photobiologyInOut-0.4.12/photobiologyInOut/MD5 | 36 photobiologyInOut-0.4.12/photobiologyInOut/NAMESPACE | 3 photobiologyInOut-0.4.12/photobiologyInOut/NEWS | 7 photobiologyInOut-0.4.12/photobiologyInOut/R/read-csi-dat.r | 6 photobiologyInOut-0.4.12/photobiologyInOut/R/read-libradtran.r |only photobiologyInOut-0.4.12/photobiologyInOut/inst/CITATION | 4 photobiologyInOut-0.4.12/photobiologyInOut/inst/doc/user-guide.R | 35 photobiologyInOut-0.4.12/photobiologyInOut/inst/doc/user-guide.Rnw | 95 photobiologyInOut-0.4.12/photobiologyInOut/inst/doc/user-guide.pdf | 3536 +++++----- photobiologyInOut-0.4.12/photobiologyInOut/inst/staticdocs/index.r | 3 photobiologyInOut-0.4.12/photobiologyInOut/man/read_csi_dat.Rd | 6 photobiologyInOut-0.4.12/photobiologyInOut/man/read_uvspec_disort.Rd |only photobiologyInOut-0.4.12/photobiologyInOut/man/read_uvspec_disort_vesa.Rd |only photobiologyInOut-0.4.12/photobiologyInOut/vignettes/data-vignettes/uvspec-disort.dat |only photobiologyInOut-0.4.12/photobiologyInOut/vignettes/data-vignettes/uvspec-disort.inp |only photobiologyInOut-0.4.12/photobiologyInOut/vignettes/data-vignettes/uvspec-multi.dat |only photobiologyInOut-0.4.12/photobiologyInOut/vignettes/data-vignettes/uvspec-plain-2col.dat |only photobiologyInOut-0.4.12/photobiologyInOut/vignettes/user-guide-concordance.tex | 18 photobiologyInOut-0.4.12/photobiologyInOut/vignettes/user-guide.Rnw | 95 25 files changed, 2213 insertions(+), 1645 deletions(-)
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Title: Useful Tools for Structural Equation Modeling
Description: Provides useful tools for structural equation modeling packages.
Author: Terrence D. Jorgensen [aut, cre],
Sunthud Pornprasertmanit [aut],
Patrick Miller [aut],
Alexander Schoemann [aut],
Yves Rosseel [aut],
Corbin Quick [ctb],
Mauricio Garnier-Villarreal [ctb],
James Selig [ctb],
Aaron Boulton [ctb],
Kristopher Preacher [ctb],
Donna Coffman [ctb],
Mijke Rhemtulla [ctb],
Alexander Robitzsch [ctb],
Craig Enders [ctb],
Ruber Arslan [ctb],
Bell Clinton [ctb],
Pavel Panko [ctb],
Edgar Merkle [ctb],
Steven Chesnut [ctb],
Jarrett Byrnes [ctb],
Jason Rights [ctb],
Ylenio Longo [ctb]
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>
Diff between semTools versions 0.4-13 dated 2016-09-06 and 0.4-14 dated 2016-10-22
semTools-0.4-13/semTools/R/ci.reliability.R |only semTools-0.4-13/semTools/R/impliedStat.R |only semTools-0.4-13/semTools/man/ci.reliability.Rd |only semTools-0.4-13/semTools/man/impliedFactorStat.Rd |only semTools-0.4-13/semTools/man/nullRMSEA.Rd |only semTools-0.4-14/semTools/DESCRIPTION | 18 semTools-0.4-14/semTools/MD5 | 231 semTools-0.4-14/semTools/NAMESPACE | 97 semTools-0.4-14/semTools/R/NET.R | 354 - semTools-0.4-14/semTools/R/PAVranking.R | 1892 ++++---- semTools-0.4-14/semTools/R/TSML.R | 758 +-- semTools-0.4-14/semTools/R/auxiliary.R | 1055 ++-- semTools-0.4-14/semTools/R/clipboard.R | 443 - semTools-0.4-14/semTools/R/compareFit.R | 322 - semTools-0.4-14/semTools/R/dataDiagnosis.R | 264 - semTools-0.4-14/semTools/R/efa.R | 744 +-- semTools-0.4-14/semTools/R/fitIndices.R | 319 - semTools-0.4-14/semTools/R/fitOpenMx.R | 2314 ++++----- semTools-0.4-14/semTools/R/fmi.R | 287 - semTools-0.4-14/semTools/R/imposeStart.R | 46 semTools-0.4-14/semTools/R/indProd.R | 334 - semTools-0.4-14/semTools/R/kd.R | 124 semTools-0.4-14/semTools/R/lisrel2lavaan.R | 3246 +++++++------- semTools-0.4-14/semTools/R/loadingFromAlpha.R | 16 semTools-0.4-14/semTools/R/longInvariance.R | 904 +-- semTools-0.4-14/semTools/R/measurementInvariance.R | 316 - semTools-0.4-14/semTools/R/measurementInvarianceCat.R | 448 - semTools-0.4-14/semTools/R/miPowerFit.R | 370 - semTools-0.4-14/semTools/R/missingBootstrap.R | 1242 ++--- semTools-0.4-14/semTools/R/monteCarloMed.R | 126 semTools-0.4-14/semTools/R/mvrnonnorm.R | 246 - semTools-0.4-14/semTools/R/parcelAllocation.R | 662 +- semTools-0.4-14/semTools/R/partialInvariance.R | 1452 +++--- semTools-0.4-14/semTools/R/partialInvarianceCat.R | 1478 +++--- semTools-0.4-14/semTools/R/permuteMeasEq.R | 1806 +++---- semTools-0.4-14/semTools/R/poolMAlloc.R | 2128 ++++----- semTools-0.4-14/semTools/R/powerAnalysis.R | 298 - semTools-0.4-14/semTools/R/powerAnalysisNested.R | 264 - semTools-0.4-14/semTools/R/powerAnalysisSS.R | 202 semTools-0.4-14/semTools/R/probeInteraction.R | 1344 ++--- semTools-0.4-14/semTools/R/quark.R | 768 +-- semTools-0.4-14/semTools/R/reliability.R | 736 +-- semTools-0.4-14/semTools/R/residualCovariate.R | 28 semTools-0.4-14/semTools/R/runMI.R | 1148 ++-- semTools-0.4-14/semTools/R/singleParamTest.R | 276 - semTools-0.4-14/semTools/R/splitSample.R | 144 semTools-0.4-14/semTools/R/tukeySEM.R | 56 semTools-0.4-14/semTools/R/wald.R | 154 semTools-0.4-14/semTools/R/zzz.R | 18 semTools-0.4-14/semTools/build/vignette.rds |binary semTools-0.4-14/semTools/inst/CITATION | 4 semTools-0.4-14/semTools/man/BootMiss-class.Rd | 82 semTools-0.4-14/semTools/man/Net-class.Rd | 68 semTools-0.4-14/semTools/man/PAVranking.Rd | 288 - semTools-0.4-14/semTools/man/SSpower.Rd | 174 semTools-0.4-14/semTools/man/auxiliary.Rd | 240 - semTools-0.4-14/semTools/man/bsBootMiss.Rd | 242 - semTools-0.4-14/semTools/man/chisqSmallN.Rd |only semTools-0.4-14/semTools/man/clipboard.Rd | 166 semTools-0.4-14/semTools/man/combinequark.Rd | 70 semTools-0.4-14/semTools/man/compareFit.Rd | 94 semTools-0.4-14/semTools/man/dat2way.Rd | 60 semTools-0.4-14/semTools/man/dat3way.Rd | 68 semTools-0.4-14/semTools/man/datCat.Rd | 60 semTools-0.4-14/semTools/man/efaUnrotate.Rd | 96 semTools-0.4-14/semTools/man/exLong.Rd | 62 semTools-0.4-14/semTools/man/findRMSEApower.Rd | 74 semTools-0.4-14/semTools/man/findRMSEApowernested.Rd | 76 semTools-0.4-14/semTools/man/findRMSEAsamplesize.Rd | 74 semTools-0.4-14/semTools/man/findRMSEAsamplesizenested.Rd | 74 semTools-0.4-14/semTools/man/fitMeasuresMx.Rd | 104 semTools-0.4-14/semTools/man/fmi.Rd | 172 semTools-0.4-14/semTools/man/htmt.Rd | 78 semTools-0.4-14/semTools/man/imposeStart.Rd | 290 - semTools-0.4-14/semTools/man/indProd.Rd | 178 semTools-0.4-14/semTools/man/kd.Rd | 150 semTools-0.4-14/semTools/man/kurtosis.Rd | 114 semTools-0.4-14/semTools/man/lavaanStar-class.Rd | 1 semTools-0.4-14/semTools/man/lisrel2lavaan.Rd | 166 semTools-0.4-14/semTools/man/loadingFromAlpha.Rd | 44 semTools-0.4-14/semTools/man/longInvariance.Rd | 200 semTools-0.4-14/semTools/man/mardiaKurtosis.Rd | 92 semTools-0.4-14/semTools/man/mardiaSkew.Rd | 92 semTools-0.4-14/semTools/man/maximalRelia.Rd | 132 semTools-0.4-14/semTools/man/measurementInvariance.Rd | 164 semTools-0.4-14/semTools/man/measurementInvarianceCat.Rd | 144 semTools-0.4-14/semTools/man/miPowerFit.Rd | 194 semTools-0.4-14/semTools/man/monteCarloMed.Rd | 162 semTools-0.4-14/semTools/man/moreFitIndices.Rd | 206 semTools-0.4-14/semTools/man/mvrnonnorm.Rd | 64 semTools-0.4-14/semTools/man/net.Rd | 112 semTools-0.4-14/semTools/man/nullMx.Rd | 70 semTools-0.4-14/semTools/man/nullRmsea.Rd |only semTools-0.4-14/semTools/man/parcelAllocation.Rd | 114 semTools-0.4-14/semTools/man/partialInvariance.Rd | 340 - semTools-0.4-14/semTools/man/permuteMeasEq-class.Rd | 102 semTools-0.4-14/semTools/man/permuteMeasEq.Rd | 598 +- semTools-0.4-14/semTools/man/plotProbe.Rd | 236 - semTools-0.4-14/semTools/man/plotRMSEAdist.Rd | 94 semTools-0.4-14/semTools/man/plotRMSEApower.Rd | 116 semTools-0.4-14/semTools/man/plotRMSEApowernested.Rd | 80 semTools-0.4-14/semTools/man/poolMAlloc.Rd | 270 - semTools-0.4-14/semTools/man/probe2WayMC.Rd | 216 semTools-0.4-14/semTools/man/probe2WayRC.Rd | 166 semTools-0.4-14/semTools/man/probe3WayMC.Rd | 256 - semTools-0.4-14/semTools/man/probe3WayRC.Rd | 216 semTools-0.4-14/semTools/man/reliability.Rd | 170 semTools-0.4-14/semTools/man/reliabilityL2.Rd | 122 semTools-0.4-14/semTools/man/residualCovariate.Rd | 74 semTools-0.4-14/semTools/man/rotate.Rd | 136 semTools-0.4-14/semTools/man/runMI.Rd | 322 - semTools-0.4-14/semTools/man/saturateMx.Rd | 70 semTools-0.4-14/semTools/man/simParcel.Rd | 78 semTools-0.4-14/semTools/man/singleParamTest.Rd | 140 semTools-0.4-14/semTools/man/skew.Rd | 114 semTools-0.4-14/semTools/man/splitSample.rd | 102 semTools-0.4-14/semTools/man/standardizeMx.Rd | 176 semTools-0.4-14/semTools/man/tukeySEM.rd | 108 semTools-0.4-14/semTools/man/twostage-class.Rd | 104 semTools-0.4-14/semTools/man/twostage.Rd | 187 120 files changed, 19630 insertions(+), 19556 deletions(-)
Title: Applications of Empirical Dynamic Modeling from Time Series
Description: A new implementation of EDM algorithms and is based on research software previously developed for internal use in the Sugihara Lab (UCSD/SIO). Contains C++ compiled objects that use time delay embedding to perform state-space reconstruction and nonlinear forecasting and an R interface to those objects using 'Rcpp'. It supports both the simplex projection method from Sugihara & May (1990) <DOI:10.1038/344734a0> and the S-map algorithm in Sugihara (1994) <DOI:10.1098/rsta.1994.0106>. In addition, this package implements convergent cross mapping as described in Sugihara et al. (2012) <DOI:10.1126/science.1227079> and multiview embedding as described in Ye & Sugihara (2016) <DOI:10.1126/science.aag0863>.
Author: Hao Ye [aut, cre],
Adam Clark [aut],
Ethan Deyle [aut],
Oliver Keyes [ctb],
George Sugihara [ctb, ccp]
Maintainer: Hao Ye <hye@ucsd.edu>
Diff between rEDM versions 0.4.7 dated 2016-03-10 and 0.5.3 dated 2016-10-22
rEDM-0.4.7/rEDM/inst/include |only rEDM-0.4.7/rEDM/man/BlockLNLP.Rd |only rEDM-0.4.7/rEDM/man/LNLP.Rd |only rEDM-0.4.7/rEDM/man/Rcpp_BlockLNLP-class.Rd |only rEDM-0.4.7/rEDM/man/Rcpp_LNLP-class.Rd |only rEDM-0.4.7/rEDM/man/Rcpp_Xmap-class.Rd |only rEDM-0.4.7/rEDM/man/Xmap.Rd |only rEDM-0.4.7/rEDM/man/rEDM-package.Rd |only rEDM-0.5.3/rEDM/DESCRIPTION | 19 - rEDM-0.5.3/rEDM/MD5 | 392 ++------------------------- rEDM-0.5.3/rEDM/NAMESPACE | 13 rEDM-0.5.3/rEDM/R/RcppExports.R | 6 rEDM-0.5.3/rEDM/R/block_lnlp_interface.R | 58 ++-- rEDM-0.5.3/rEDM/R/lnlp_interface.R | 2 rEDM-0.5.3/rEDM/R/multiview_interface.R |only rEDM-0.5.3/rEDM/R/rEDM_package.R | 53 +-- rEDM-0.5.3/rEDM/build/vignette.rds |binary rEDM-0.5.3/rEDM/inst/doc/rEDM_tutorial.html | 401 ++++++++++++---------------- rEDM-0.5.3/rEDM/man/block_3sp.Rd | 4 rEDM-0.5.3/rEDM/man/block_lnlp.Rd | 77 ++--- rEDM-0.5.3/rEDM/man/ccm.Rd | 42 +- rEDM-0.5.3/rEDM/man/ccm_means.Rd | 8 rEDM-0.5.3/rEDM/man/compute_stats.Rd |only rEDM-0.5.3/rEDM/man/e054_succession.Rd | 4 rEDM-0.5.3/rEDM/man/e120_biodiversity.Rd | 6 rEDM-0.5.3/rEDM/man/make_block.Rd |only rEDM-0.5.3/rEDM/man/make_surrogate_data.Rd | 10 rEDM-0.5.3/rEDM/man/multiview.Rd |only rEDM-0.5.3/rEDM/man/paramecium_didinium.Rd | 4 rEDM-0.5.3/rEDM/man/rEDM.Rd |only rEDM-0.5.3/rEDM/man/sardine_anchovy_sst.Rd | 4 rEDM-0.5.3/rEDM/man/simplex.Rd | 80 ++--- rEDM-0.5.3/rEDM/man/sockeye_returns.Rd | 4 rEDM-0.5.3/rEDM/man/tentmap_del.Rd | 2 rEDM-0.5.3/rEDM/man/test_nonlinearity.Rd | 6 rEDM-0.5.3/rEDM/man/thrips_block.Rd | 2 rEDM-0.5.3/rEDM/man/two_species_model.Rd | 4 rEDM-0.5.3/rEDM/src/RcppExports.cpp | 15 - rEDM-0.5.3/rEDM/src/block_lnlp.cpp | 11 rEDM-0.5.3/rEDM/src/block_lnlp.h | 1 rEDM-0.5.3/rEDM/src/forecast_machine.cpp | 110 ++++--- rEDM-0.5.3/rEDM/src/forecast_machine.h | 10 42 files changed, 520 insertions(+), 828 deletions(-)
Title: Penalized Likelihood Estimation and Dynamic Prediction under the
Joint Frailty-Copula Models Between Tumour Progression and
Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction under the joint frailty-copula model between tumour progression and death for meta-analysis.
The method is applicable for meta-analytic data combining several studies. The data should have information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.8 dated 2016-09-30 and 2.9 dated 2016-10-22
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/jointCox.indep.reg.R | 8 ++++---- R/jointCox.reg.R | 8 ++++---- man/F.prediction.Rd | 14 +++++--------- man/F.window.Rd | 14 +++++--------- man/F.windows.Rd | 14 +++++--------- man/joint.Cox-package.Rd | 6 +++--- man/jointCox.indep.reg.Rd | 6 +++--- man/jointCox.reg.Rd | 6 +++--- 10 files changed, 46 insertions(+), 58 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Provides new statistics to locate and tag peaks and valleys in 2D
plots, a statistics to add a label with the equation of a polynomial fitted
with lm(), or R^2 or adjusted R^2 or information criteria for any model
fitted with function lm(). Additional statistics give access to functions
in package 'broom'. Provides a function for flexibly converting time
series to data frames suitable for plotting with ggplot(). In addition
provides two statistics and two geometries useful for diagnosing what data
are passed to compute_group() and compute_panel() functions and to
geometries.
Author: Pedro J. Aphalo [aut, cre],
Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.2.10 dated 2016-07-30 and 0.2.12 dated 2016-10-22
ggpmisc-0.2.10/ggpmisc/inst/doc/examples.R |only ggpmisc-0.2.10/ggpmisc/inst/doc/examples.Rmd |only ggpmisc-0.2.10/ggpmisc/inst/doc/examples.html |only ggpmisc-0.2.10/ggpmisc/vignettes/examples.Rmd |only ggpmisc-0.2.12/ggpmisc/DESCRIPTION | 30 ++++--- ggpmisc-0.2.12/ggpmisc/MD5 | 74 +++++++++++-------- ggpmisc-0.2.12/ggpmisc/NAMESPACE | 8 ++ ggpmisc-0.2.12/ggpmisc/NEWS | 25 ++++++ ggpmisc-0.2.12/ggpmisc/R/geom-debug.R | 3 ggpmisc-0.2.12/ggpmisc/R/ggpmisc.R | 12 ++- ggpmisc-0.2.12/ggpmisc/R/stat-debug-group.R | 3 ggpmisc-0.2.12/ggpmisc/R/stat-debug-panel.R | 3 ggpmisc-0.2.12/ggpmisc/R/stat-dens2d-filter.r |only ggpmisc-0.2.12/ggpmisc/R/stat-dens2d-labels.r |only ggpmisc-0.2.12/ggpmisc/R/stat-fit-broom.R | 6 - ggpmisc-0.2.12/ggpmisc/R/stat-fit-deviations.R | 3 ggpmisc-0.2.12/ggpmisc/R/stat-fit-residuals.R | 1 ggpmisc-0.2.12/ggpmisc/R/stat-peaks.R | 11 +- ggpmisc-0.2.12/ggpmisc/R/stat-poly-eq.R | 10 +- ggpmisc-0.2.12/ggpmisc/R/try-data-frame.R | 10 +- ggpmisc-0.2.12/ggpmisc/README.md | 23 +++-- ggpmisc-0.2.12/ggpmisc/build/vignette.rds |binary ggpmisc-0.2.12/ggpmisc/inst/doc/debug.R |only ggpmisc-0.2.12/ggpmisc/inst/doc/debug.Rmd |only ggpmisc-0.2.12/ggpmisc/inst/doc/debug.html |only ggpmisc-0.2.12/ggpmisc/inst/doc/examples-dens2d.R |only ggpmisc-0.2.12/ggpmisc/inst/doc/examples-dens2d.Rmd |only ggpmisc-0.2.12/ggpmisc/inst/doc/examples-dens2d.html |only ggpmisc-0.2.12/ggpmisc/inst/doc/user-guide.R |only ggpmisc-0.2.12/ggpmisc/inst/doc/user-guide.Rmd |only ggpmisc-0.2.12/ggpmisc/inst/doc/user-guide.html |only ggpmisc-0.2.12/ggpmisc/inst/staticdocs/index.r | 2 ggpmisc-0.2.12/ggpmisc/man/find_peaks.Rd | 2 ggpmisc-0.2.12/ggpmisc/man/geom_debug.Rd | 2 ggpmisc-0.2.12/ggpmisc/man/ggpmisc-ggproto.Rd | 5 + ggpmisc-0.2.12/ggpmisc/man/ggpmisc-package.Rd | 10 ++ ggpmisc-0.2.12/ggpmisc/man/stat_debug_group.Rd | 2 ggpmisc-0.2.12/ggpmisc/man/stat_debug_panel.Rd | 2 ggpmisc-0.2.12/ggpmisc/man/stat_dens2d_filter.Rd |only ggpmisc-0.2.12/ggpmisc/man/stat_dens2d_labels.Rd |only ggpmisc-0.2.12/ggpmisc/man/stat_fit_deviations.Rd | 2 ggpmisc-0.2.12/ggpmisc/man/stat_fit_glance.Rd | 2 ggpmisc-0.2.12/ggpmisc/man/stat_peaks.Rd | 4 - ggpmisc-0.2.12/ggpmisc/man/stat_poly_eq.Rd | 8 +- ggpmisc-0.2.12/ggpmisc/man/try_data_frame.Rd | 8 +- ggpmisc-0.2.12/ggpmisc/vignettes/debug.Rmd |only ggpmisc-0.2.12/ggpmisc/vignettes/examples-dens2d.Rmd |only ggpmisc-0.2.12/ggpmisc/vignettes/user-guide.Rmd |only 48 files changed, 174 insertions(+), 97 deletions(-)
Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while
controlling false discovery rate for RNA-seq experimental design. Our
procedure depends on the Voom method proposed for RNA-seq data analysis
by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size
calculation method proposed for microarray experiments by Liu and Hwang
(2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions
that calculates appropriate sample sizes for two-sample t-test for RNA-seq
experiments with fixed or varied set of parameters. The outputs also contain a
plot of power versus sample size, a table of power at different sample sizes,
and a table of critical test values at different sample sizes.
To install this package, please use
'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.
Author: Ran Bi [aut, cre],
Peng Liu [aut],
Tim Triche [ctb]
Maintainer: Ran Bi <biran@iastate.edu>
Diff between ssizeRNA versions 1.2.6 dated 2016-07-15 and 1.2.8 dated 2016-10-22
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/check.power.R | 18 +++++++++--------- R/sim.counts.R | 30 ++++++++++++++++-------------- R/ssizeRNA_single.R | 16 ++++++++-------- R/ssizeRNA_vary.R | 24 ++++++++++++------------ inst/NEWS.txt | 6 ++++++ inst/doc/ssizeRNA.R | 12 ++++++------ inst/doc/ssizeRNA.Rnw | 30 +++++++++++++++--------------- inst/doc/ssizeRNA.pdf |binary man/check.power.Rd | 12 ++++++------ man/sim.counts.Rd | 18 +++++++++--------- man/ssizeRNA_single.Rd | 12 ++++++------ man/ssizeRNA_vary.Rd | 20 ++++++++++---------- vignettes/ssizeRNA.Rnw | 30 +++++++++++++++--------------- 15 files changed, 136 insertions(+), 128 deletions(-)
Title: Continuous-Lag Spatial Markov Chains
Description: A set of functions is provided for 1) the stratum lengths analysis along a chosen direction, 2) fast estimation of continuous lag spatial Markov chains model parameters and probability computing (also for large data sets), 3) transition probability maps and transiograms drawing, 4) simulation methods for categorical random fields.
Author: Luca Sartore
Maintainer: Luca Sartore <drwolf85@gmail.com>
Diff between spMC versions 0.3.6 dated 2014-12-30 and 0.3.8 dated 2016-10-22
DESCRIPTION | 10 ++++------ MD5 | 31 ++++++++++++++++--------------- NAMESPACE | 2 ++ NEWS | 17 +++++++++++++++++ R/embed_MC.R | 11 ++++++++--- R/image.pemt.R | 6 +++--- R/sim_ck.R | 1 + R/sim_ik.R | 1 + R/sim_mcs.R | 6 +++++- R/sim_path.R | 3 ++- inst |only man/embed_MC.Rd | 2 +- man/image.pemt.Rd | 7 ++++--- man/multi_tpfit.Rd | 2 +- man/spMC-package.Rd | 6 ++++-- man/tpfit.Rd | 2 +- src/mcs.h | 15 ++++++++++----- 17 files changed, 80 insertions(+), 42 deletions(-)
Title: Flexibly Reshape Data: A Reboot of the Reshape Package
Description: Flexibly restructure and aggregate data using just two
functions: melt and 'dcast' (or 'acast').
Author: Hadley Wickham <h.wickham@gmail.com>
Maintainer: Hadley Wickham <h.wickham@gmail.com>
Diff between reshape2 versions 1.4.1 dated 2014-12-06 and 1.4.2 dated 2016-10-22
DESCRIPTION | 11 ++++++----- LICENSE | 2 +- MD5 | 46 +++++++++++++++++++++++----------------------- NAMESPACE | 4 +++- R/RcppExports.R | 2 +- R/reshape.r | 4 +++- inst/CITATION | 2 +- man/add_margins.Rd | 3 ++- man/cast.Rd | 5 +++-- man/colsplit.Rd | 3 ++- man/french_fries.Rd | 3 ++- man/guess_value.Rd | 3 ++- man/margins.Rd | 3 ++- man/melt.Rd | 3 ++- man/melt.array.Rd | 9 +++++---- man/melt.data.frame.Rd | 8 ++++---- man/melt.default.Rd | 8 ++++---- man/melt.list.Rd | 8 ++++---- man/melt_check.Rd | 3 ++- man/parse_formula.Rd | 3 ++- man/recast.Rd | 3 ++- man/smiths.Rd | 3 ++- man/tips.Rd | 3 ++- src/RcppExports.cpp | 30 +++++++++++++----------------- 24 files changed, 93 insertions(+), 79 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that Armadillo
requires a fairly recent compiler; for the g++ family at least version 4.6.*
is required.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.7.400.2.0 dated 2016-08-25 and 0.7.500.0.0 dated 2016-10-22
ChangeLog | 19 + DESCRIPTION | 12 MD5 | 38 +- README.md | 4 inst/NEWS.Rd | 10 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/armadillo_bits/Mat_meat.hpp | 2 inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/arrayops_meat.hpp | 9 inst/include/armadillo_bits/auxlib_bones.hpp | 22 + inst/include/armadillo_bits/auxlib_meat.hpp | 260 +++++++++++++++- inst/include/armadillo_bits/diskio_meat.hpp | 23 - inst/include/armadillo_bits/fn_elem.hpp | 6 inst/include/armadillo_bits/fn_qz.hpp | 11 inst/include/armadillo_bits/operator_cube_times.hpp | 34 ++ inst/include/armadillo_bits/subview_cube_each_bones.hpp | 11 inst/include/armadillo_bits/subview_cube_each_meat.hpp | 79 ++++ inst/include/armadillo_bits/subview_elem1_meat.hpp | 2 vignettes/RcppArmadillo.bib | 41 +- 20 files changed, 508 insertions(+), 81 deletions(-)
Title: A Fast, Easy-to-Use Tool for Manipulating Tables in Databases
and a Wrapper of MADlib
Description: Provides an R interface for the Pivotal Data stack
running on 'PostgreSQL', 'Greenplum' or 'Apache HAWQ (incubating)'
databases with parallel and distributed computation ability for big data
processing. 'PivotalR' provides an R interface to various database
operations on tables or views. These operations are almost the same as
the corresponding native R operations. Thus users of R do not need
to learn 'SQL' when they operate on objects in the database. It also
provides a wrapper for 'Apache MADlib (incubating)', which is an open-
source library for parallel and scalable in-database analytics.
Author: Predictive Analytics Team at Pivotal Inc.
<user@madlb.incubator.apache.org>, with contributions from Data Science Team
at Pivotal Inc.
Maintainer: Rahul Iyer <riyer@pivotal.io>
Diff between PivotalR versions 0.1.17.45 dated 2015-01-03 and 0.1.18.2 dated 2016-10-22
PivotalR-0.1.17.45/PivotalR/tests/test-examples.r |only PivotalR-0.1.17.45/PivotalR/tests/test-madlib_glm.r |only PivotalR-0.1.18.2/PivotalR/DESCRIPTION | 46 +- PivotalR-0.1.18.2/PivotalR/MD5 | 234 +++++++------ PivotalR-0.1.18.2/PivotalR/NAMESPACE | 149 ++++++-- PivotalR-0.1.18.2/PivotalR/R/PivotalR.R | 7 PivotalR-0.1.18.2/PivotalR/R/db_conn-rpostgresql.R | 5 PivotalR-0.1.18.2/PivotalR/R/generic.cv.R | 1 PivotalR-0.1.18.2/PivotalR/R/madlib-glm.R | 20 - PivotalR-0.1.18.2/PivotalR/R/madlib-kmeans.R |only PivotalR-0.1.18.2/PivotalR/R/madlib-lda.R |only PivotalR-0.1.18.2/PivotalR/R/madlib-lm.R | 8 PivotalR-0.1.18.2/PivotalR/R/madlib-randomForest.R |only PivotalR-0.1.18.2/PivotalR/R/madlib-rpart.R | 17 PivotalR-0.1.18.2/PivotalR/R/madlib-svm.R |only PivotalR-0.1.18.2/PivotalR/R/method-delete_.R | 9 PivotalR-0.1.18.2/PivotalR/R/testing.R | 15 PivotalR-0.1.18.2/PivotalR/R/utilities.R | 6 PivotalR-0.1.18.2/PivotalR/R/utility-conn_attr.R | 12 PivotalR-0.1.18.2/PivotalR/R/utility-generic.R | 2 PivotalR-0.1.18.2/PivotalR/R/utility-madlib.R | 42 +- PivotalR-0.1.18.2/PivotalR/README.md | 7 PivotalR-0.1.18.2/PivotalR/build/vignette.rds |binary PivotalR-0.1.18.2/PivotalR/data/abalone.RData |binary PivotalR-0.1.18.2/PivotalR/data/null.data.RData |binary PivotalR-0.1.18.2/PivotalR/inst/doc/pivotalr.pdf |binary PivotalR-0.1.18.2/PivotalR/man/aggregate-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/aic.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/arith-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/array.len.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/arraydb.to.arrayr.Rd | 12 PivotalR-0.1.18.2/PivotalR/man/as.db.data.frame-methods.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/as.environment.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/as.factor-methods.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/by-methods.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/cbind2.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/clean.madlib.temp.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/coef.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/compare-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/conn.eql.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/conn.id.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/connection-info.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/content.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/crossprod.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.Rcrossprod-class.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.Rquery-class.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/db.connect.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.data.frame-class.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/db.data.frame.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.disconnect.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/db.existsObject.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.list.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.obj-class.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/db.objects.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.q.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.search.path.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.table-class.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/db.view-class.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/delete-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/dim-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/eql-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/extract-replace-methods.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/func-methods.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/generic.bagging.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/generic.cv.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/getTree.rf.madlib.Rd |only PivotalR-0.1.18.2/PivotalR/man/groups.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/ifelse.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/is.db.data.frame.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/is.factor-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/is.na-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/key.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/logical-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/madlib.arima.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/madlib.elnet.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/madlib.glm.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/madlib.kmeans.Rd |only 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PivotalR-0.1.18.2/PivotalR/man/predict.elnet.madlib.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/predict.lda.madlib.Rd |only PivotalR-0.1.18.2/PivotalR/man/predict.rf.madlib.Rd |only PivotalR-0.1.18.2/PivotalR/man/preview.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/print-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/print.arima.madlib.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/print.dt.madlib.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/print.elnet.madlib.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/print.lm.madlib.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/print.logregr.madlib.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/print.none.obj.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/print.rf.madlib.Rd |only PivotalR-0.1.18.2/PivotalR/man/print.summary.madlib.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/residuals.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/row_actions.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/sample-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/scale-methods.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/sort-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/subset-methods.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/summary.arima.madlib.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/summary.elnet.madlib.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/summary.lm.madlib.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/summary.logregr.madlib.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/text.dt.madlib.Rd | 2 PivotalR-0.1.18.2/PivotalR/man/type-cast.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/unique-methods.Rd | 4 PivotalR-0.1.18.2/PivotalR/man/vcov.Rd | 2 PivotalR-0.1.18.2/PivotalR/tests/testthat |only 123 files changed, 508 insertions(+), 377 deletions(-)
Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for
reproducible model validation, calibration, and comparison.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <me@nanx.me>
Maintainer: Nan Xiao <me@nanx.me>
Diff between hdnom versions 4.1 dated 2016-08-05 and 4.2 dated 2016-10-22
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- README.md | 25 +++++++++++++++++++++++-- inst/CITATION |only inst/doc/hdnom.Rmd | 9 +++++---- inst/doc/hdnom.html | 19 +++++++++++-------- vignettes/hdnom.Rmd | 9 +++++---- vignettes/hdnom.bib | 11 +++++++++++ vignettes/hdnom.css | 2 +- vignettes/header.html | 2 +- 10 files changed, 69 insertions(+), 31 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <sen-zhao@sen-zhao.com>
Diff between Grace versions 0.4.3 dated 2016-10-15 and 0.5 dated 2016-10-22
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 2 +- R/cvGrace.R | 14 ++++++++++++++ R/grace.R | 20 +++++++++++++++++++- R/grace.test.R | 47 +++++++++++++++++++++++++++++++++++++++++++---- R/make.L.R | 8 ++++++++ man/grace.test.Rd | 16 ++++++++++++---- 8 files changed, 109 insertions(+), 22 deletions(-)
Title: Rstudio Addin for Version Control and Assignment Management
using Git
Description: An Rstudio addin for version control that allows users to clone
repositories, create and delete branches, and sync forks on GitHub, GitLab, etc.
Furthermore, the addin uses the GitLab API to allow instructors to create
forks and merge requests for all students/teams with one click of a button.
Author: Vincent Nijs [aut, cre],
Sanjiv Erat [aut]
Maintainer: Vincent Nijs <vnijs@ucsd.edu>
Diff between gitgadget versions 0.2.0 dated 2016-09-14 and 0.2.1 dated 2016-10-22
DESCRIPTION | 19 ++++++++----- MD5 | 26 +++++++++++++---- NAMESPACE | 6 ++++ NEWS.md |only R/gadget.R | 24 ++++++++++++++-- R/git.R | 76 ++++++++++++++++++++++++++++++++++++++++++++++------ README.md | 2 - build |only inst/doc |only man/assign_work.Rd |only man/collect_work.Rd |only man/create_group.Rd |only man/create_repo.Rd |only man/fetch_work.Rd |only man/gitgadget.Rd | 5 ++- vignettes |only 16 files changed, 132 insertions(+), 26 deletions(-)
Title: Unconditional Exact Test
Description: Performs unconditional exact tests and power calculations for 2x2 contingency tables. Unconditional exact tests are often more powerful than conditional exact tests and asymptotic tests.
Author: Peter Calhoun [aut, cre]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>
Diff between Exact versions 1.6 dated 2015-05-25 and 1.7 dated 2016-10-22
DESCRIPTION | 16 +- MD5 | 30 +++-- NAMESPACE | 3 R/binom.CI.R |only R/binomialCode.R | 271 ++++++++---------------------------------------- R/boschloo_TX.R |only R/csmApprox_TX.R |only R/csmMod_Tbls.R |only R/csm_Tbls.R |only R/exact.test.R | 183 +++++++++++++++----------------- R/fisher.2x2.R | 7 - R/maxPvalue.R |only R/multinomialCode.R | 124 ++++++++------------- R/power.exact.test.R | 81 +++++++------- R/santner_TX.R |only R/zpooled_TX.R |only R/zunpooled_TX.R |only build |only man/Exact-package.Rd | 74 +++++-------- man/exact.test.Rd | 156 ++++++++++----------------- man/power.exact.test.Rd | 111 +++++-------------- 21 files changed, 386 insertions(+), 670 deletions(-)
Title: R Package for Analyzing Endorsement Experiments
Description: This R package implements the statistical model proposed by Bullock, Imai, and Shapiro (2011; Political Analysis) to analyze endorsement experiments. Endorsement experiments are a survey methodology for eliciting truthful responses to sensitive questions. This methodology is helpful when measuring support for socially sensitive political actors such as militant groups. The model is fitted with the Markov chain Monte Carlo algorithm and produces the output containing draws from the posterior distribution.
Author: Yuki Shiraito [aut, cre], Kosuke Imai [aut], Bryn Rosenfeld [ctb]
Maintainer: Yuki Shiraito <shiraito@princeton.edu>
Diff between endorse versions 1.4.1 dated 2014-05-04 and 1.5.0 dated 2016-10-22
ChangeLog | 1 DESCRIPTION | 13 MD5 | 12 NAMESPACE | 6 R/endorse.R | 1599 ++++++++++++++++++++++++++++---------------------------- man/endorse.Rd | 1605 +++++++++++++++++++++++++++++---------------------------- src/endorse.c | 30 + 7 files changed, 1688 insertions(+), 1578 deletions(-)
Title: Convert from UTC to Local Time for United States Counties
Description: Inputs date-times in Coordinated Universal Time (UTC)
and converts to a local date-time and local date for US counties, based on
each county's Federal Information Processing Standard (FIPS) code.
This work was supported in part by grants from the National Institute of
Environmental Health Sciences (R00ES022631) and the National Science
Foundation (1331399).
Author: Brooke Anderson [aut, cre],
Zhiming Guo [ctb]
Maintainer: Brooke Anderson <brooke.anderson@colostate.edu>
Diff between countytimezones versions 0.1.0 dated 2016-06-13 and 1.0.0 dated 2016-10-22
DESCRIPTION | 18 ++++++++++------ MD5 | 25 ++++++++++++----------- NEWS.md |only R/add_local_time.R | 17 ++++++++++++++- R/data.R | 8 ------- README.md | 45 ++++++++++++++++++++++++++---------------- build/vignette.rds |binary data/county_tzs.rda |binary data/floyd.rda |binary inst/doc/countytimezones.R | 12 ++++++++--- inst/doc/countytimezones.Rmd | 19 ++++++++++++++--- inst/doc/countytimezones.html | 41 ++++++++++++++++++++------------------ man/county_tzs.Rd | 8 ------- vignettes/countytimezones.Rmd | 19 ++++++++++++++--- 14 files changed, 131 insertions(+), 81 deletions(-)
More information about countytimezones at CRAN
Permanent link
Title: Optimal and Fast Univariate k-Means Clustering
Description: A dynamic programming algorithm for optimal univariate k-means
clustering. Minimizing the sum of squares of within-cluster distances, the
algorithm guarantees optimality and reproducibility. Its advantage over
heuristic k-means algorithms in efficiency and accuracy is increasingly
pronounced as the number of clusters k increases. It provides an alternative
to heuristic k-means algorithms for univariate clustering.
Author: Joe Song [aut, cre], Haizhou Wang [aut]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between Ckmeans.1d.dp versions 3.4.6-3 dated 2016-10-05 and 3.4.6-4 dated 2016-10-22
DESCRIPTION | 8 +++--- MD5 | 19 +++++++------- NEWS | 27 +++++++++++++++++++++ R/ahist.R |only R/visualize.R | 47 ++---------------------------------- man/Ckmeans.1d.dp-package.Rd | 2 - man/Ckmeans.1d.dp.Rd | 5 +++ man/ahist.Rd | 55 +++++++++++++++++++++++++++++++++++-------- man/plot.Ckmeans.1d.dp.Rd | 14 +++------- man/print.Ckmeans.1d.dp.Rd | 7 +++-- src/Ckmeans.1d.dp.h | 1 11 files changed, 105 insertions(+), 80 deletions(-)
Title: Flexibly Reshape Data
Description: Flexibly restructure and aggregate data using
just two functions: melt and cast.
Author: Hadley Wickham [aut, cre]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between reshape versions 0.8.5 dated 2014-04-22 and 0.8.6 dated 2016-10-21
DESCRIPTION | 20 +++++++++++--------- LICENSE | 2 +- MD5 | 10 +++++----- NAMESPACE | 26 ++++++++++++++++++++++++++ NEWS | 4 ++++ inst/CITATION | 2 +- 6 files changed, 48 insertions(+), 16 deletions(-)
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in
photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse
ratios and other derived quantities from spectral data. Local maxima and
minima. Conversion between energy- and photon-based units. Wavelength
interpolation. Astronomical calculations related solar angles and day
length. Colours and vision.
Author: Pedro J. Aphalo [aut, cre],
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.9.11 dated 2016-09-11 and 0.9.12 dated 2016-10-21
photobiology-0.9.11/photobiology/inst/doc/userguide.R |only photobiology-0.9.11/photobiology/inst/doc/userguide.Rmd |only photobiology-0.9.11/photobiology/inst/doc/userguide.html |only photobiology-0.9.11/photobiology/man/altitude.Rd |only photobiology-0.9.11/photobiology/man/date2seconds.Rd |only photobiology-0.9.11/photobiology/man/date2tod.Rd |only photobiology-0.9.11/photobiology/man/time2seconds.Rd |only photobiology-0.9.11/photobiology/vignettes/userguide.Rmd |only photobiology-0.9.12/photobiology/DESCRIPTION | 16 photobiology-0.9.12/photobiology/MD5 | 126 - photobiology-0.9.12/photobiology/NAMESPACE | 9 photobiology-0.9.12/photobiology/NEWS | 36 photobiology-0.9.12/photobiology/R/meeus.r |only photobiology-0.9.12/photobiology/R/photobiology.r | 4 photobiology-0.9.12/photobiology/R/rbindspct.r | 1 photobiology-0.9.12/photobiology/R/spct.absorbance.R | 7 photobiology-0.9.12/photobiology/R/spct.absorptance.R | 9 photobiology-0.9.12/photobiology/R/spct.fscale.r | 60 photobiology-0.9.12/photobiology/R/spct.irrad.r | 7 photobiology-0.9.12/photobiology/R/spct.normalize.r | 12 photobiology-0.9.12/photobiology/R/spct.operators.r | 101 photobiology-0.9.12/photobiology/R/spct.response.R | 10 photobiology-0.9.12/photobiology/R/spct.summaries.r | 8 photobiology-0.9.12/photobiology/R/spct.transmittance.r | 9 photobiology-0.9.12/photobiology/R/sun.calc.r | 1048 ++++++---- photobiology-0.9.12/photobiology/R/zmspct.classes.R | 5 photobiology-0.9.12/photobiology/README.md | 4 photobiology-0.9.12/photobiology/build/vignette.rds |binary photobiology-0.9.12/photobiology/data/A.illuminant.spct.rda |binary photobiology-0.9.12/photobiology/data/D65.illuminant.spct.rda |binary photobiology-0.9.12/photobiology/data/beesxyz.spct.rda |binary photobiology-0.9.12/photobiology/data/black_body.spct.rda |binary photobiology-0.9.12/photobiology/data/ccd.spct.rda |binary photobiology-0.9.12/photobiology/data/ciev10.spct.rda |binary photobiology-0.9.12/photobiology/data/ciev2.spct.rda |binary photobiology-0.9.12/photobiology/data/ciexyzCC10.spct.rda |binary photobiology-0.9.12/photobiology/data/ciexyzCC2.spct.rda |binary photobiology-0.9.12/photobiology/data/ciexyzCMF10.spct.rda |binary photobiology-0.9.12/photobiology/data/ciexyzCMF2.spct.rda |binary photobiology-0.9.12/photobiology/data/clear.spct.rda |binary photobiology-0.9.12/photobiology/data/clear_body.spct.rda |binary photobiology-0.9.12/photobiology/data/filter-cps-mspct.rda |binary photobiology-0.9.12/photobiology/data/opaque.spct.rda |binary photobiology-0.9.12/photobiology/data/photodiode.spct.rda |binary photobiology-0.9.12/photobiology/data/polyester.spct.rda |binary photobiology-0.9.12/photobiology/data/sun.daily.data.rda |binary photobiology-0.9.12/photobiology/data/sun.daily.spct.rda |binary photobiology-0.9.12/photobiology/data/sun.data.rda |binary photobiology-0.9.12/photobiology/data/sun.spct.rda |binary photobiology-0.9.12/photobiology/data/white_body.spct.rda |binary photobiology-0.9.12/photobiology/data/yellow.gel.rda |binary photobiology-0.9.12/photobiology/inst/doc/userguide-astronomy.R |only photobiology-0.9.12/photobiology/inst/doc/userguide-astronomy.Rmd |only photobiology-0.9.12/photobiology/inst/doc/userguide-astronomy.html |only photobiology-0.9.12/photobiology/inst/doc/userguide-intro.Rmd |only photobiology-0.9.12/photobiology/inst/doc/userguide-intro.html |only photobiology-0.9.12/photobiology/inst/doc/userguide-radiation.R |only photobiology-0.9.12/photobiology/inst/doc/userguide-radiation.Rmd |only photobiology-0.9.12/photobiology/inst/doc/userguide-radiation.html |only photobiology-0.9.12/photobiology/inst/staticdocs/README.md | 12 photobiology-0.9.12/photobiology/inst/staticdocs/index.r | 17 photobiology-0.9.12/photobiology/man/as.solar_date.Rd |only photobiology-0.9.12/photobiology/man/as_tod.Rd |only photobiology-0.9.12/photobiology/man/day_night.Rd | 85 photobiology-0.9.12/photobiology/man/format.solar_time.Rd |only photobiology-0.9.12/photobiology/man/fscale.Rd | 32 photobiology-0.9.12/photobiology/man/fscale_spct.Rd | 2 photobiology-0.9.12/photobiology/man/is.solar_time.Rd |only photobiology-0.9.12/photobiology/man/julian_day.Rd |only photobiology-0.9.12/photobiology/man/photobiology-package.Rd | 4 photobiology-0.9.12/photobiology/man/print.solar_time.Rd |only photobiology-0.9.12/photobiology/man/solar_time.Rd |only photobiology-0.9.12/photobiology/man/subset2mspct.Rd | 2 photobiology-0.9.12/photobiology/man/sun_angles.Rd | 49 photobiology-0.9.12/photobiology/man/tz_time_diff.Rd |only photobiology-0.9.12/photobiology/vignettes/userguide-astronomy.Rmd |only photobiology-0.9.12/photobiology/vignettes/userguide-intro.Rmd |only photobiology-0.9.12/photobiology/vignettes/userguide-radiation.Rmd |only 78 files changed, 1035 insertions(+), 640 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis
tests in multivariate linear models. HE plots represent sums-of-squares-and-
products matrices for linear hypotheses and for error using ellipses (in two
dimensions) and ellipsoids (in three dimensions). The related 'candisc' package
provides visualizations in a reduced-rank canonical discriminant space when
there are more than a few response variables.
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.3-1 dated 2016-06-14 and 1.3-3 dated 2016-10-21
DESCRIPTION | 13 +- MD5 | 156 ++++++++++++++++---------------- NEWS | 5 + R/Mahalanobis.R | 15 ++- R/bartlettTests.R | 7 - build/vignette.rds |binary data/AddHealth.RData |binary data/Adopted.RData |binary data/Bees.rda |binary data/FootHead.rda |binary data/Headache.RData |binary data/Hernior.RData |binary data/MockJury.RData |binary data/NLSY.RData |binary data/NeuroCog.RData |binary data/Oslo.RData |binary data/Parenting.RData |only data/Plastic.rda |binary data/Pottery2.RData |binary data/Probe1.RData |binary data/Probe2.RData |binary data/RatWeight.RData |binary data/ReactTime.RData |binary data/Rohwer.rda |binary data/RootStock.rda |binary data/Sake.RData |binary data/Skulls.RData |binary data/SocGrades.RData |binary data/SocialCog.RData |binary data/VocabGrowth.rda |binary data/WeightLoss.RData |binary data/schooldata.RData |binary inst/CITATION | 4 inst/doc/HE-examples.pdf |binary inst/doc/repeated.pdf |binary man/Parenting.Rd |only man/ReactTime.Rd | 2 man/Rohwer.Rd | 5 - man/heplot-package.Rd | 10 +- vignettes/fig/plot-Ortho-fm1.pdf |binary vignettes/fig/plot-Ortho-fm3.pdf |binary vignettes/fig/plot-grades-can-class.pdf |binary vignettes/fig/plot-grades-can-gpa.pdf |binary vignettes/fig/plot-grades-can-sex.pdf |binary vignettes/fig/plot-grades-pairs.pdf |binary vignettes/fig/plot-hern-can-age.pdf |binary vignettes/fig/plot-hern-can-build.pdf |binary vignettes/fig/plot-hern-can-cardiac.pdf |binary vignettes/fig/plot-hern-can-pstat.pdf |binary vignettes/fig/plot-hern-pairs.pdf |binary vignettes/fig/plot-jury-can1.pdf |binary vignettes/fig/plot-jury-mod1-HE.pdf |binary vignettes/fig/plot-jury-mod1-pairs.pdf |binary vignettes/fig/plot-jury-mod2-HE.pdf |binary vignettes/fig/plot-jury-mod3-eff.pdf |binary vignettes/fig/plot-obk-HE1.pdf |binary vignettes/fig/plot-obk-HE2.pdf |binary vignettes/fig/plot-obk-HE3.pdf |binary vignettes/fig/plot-obk2-HE1.pdf |binary vignettes/fig/plot-obk2-HE2.pdf |binary vignettes/fig/plot-ortho-HE.pdf |binary vignettes/fig/plot-ortho-nonlin-HE.pdf |binary vignettes/fig/plot-ortho-xyplot1.pdf |binary vignettes/fig/plot-ortho-xyplot2.pdf |binary vignettes/fig/plot-plastic2.pdf |binary vignettes/fig/plot-rohwer-HE1.pdf |binary vignettes/fig/plot-rohwer-HE2.pdf |binary vignettes/fig/plot-rohwer-HE3.pdf |binary vignettes/fig/plot-rohwer-HE4.pdf |binary vignettes/fig/plot-skulls-HE-pairs.pdf |binary vignettes/fig/plot-skulls-bwplot.pdf |binary vignettes/fig/plot-skulls-can2.pdf |binary vignettes/fig/plot-skulls4.pdf |binary vignettes/fig/plot-voc1.pdf |binary vignettes/fig/plot-voc4.pdf |binary vignettes/fig/plot-voc8.pdf |binary vignettes/fig/plot-wl-HE1.pdf |binary vignettes/fig/plot-wl-HE2.pdf |binary vignettes/fig/plot-wl-HE3.pdf |binary vignettes/fig/plot-wl-means.pdf |binary 80 files changed, 116 insertions(+), 101 deletions(-)
Title: GNU Privacy Guard for R
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods.
Includes utilities for public key encryption, creating and verifying digital signatures,
and managing your local keyring. Note that some functionality depends on the version of
GnuPG that is installed on the system. On Windows this package can be used together with
'GPG4Win' which provides graphics utilities for managing keys and entering passphrases.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between gpg versions 0.2 dated 2016-10-15 and 0.3 dated 2016-10-21
gpg-0.2/gpg/R/server.R |only gpg-0.2/gpg/man/gpg_keyserver.Rd |only gpg-0.3/gpg/DESCRIPTION | 13 + gpg-0.3/gpg/MD5 | 49 +++---- gpg-0.3/gpg/NAMESPACE | 2 gpg-0.3/gpg/NEWS |only gpg-0.3/gpg/R/encrypt.R | 21 +-- gpg-0.3/gpg/R/keygen.R | 26 +++ gpg-0.3/gpg/R/keys.R | 51 +++++-- gpg-0.3/gpg/R/password.R |only gpg-0.3/gpg/R/restart.R | 12 - gpg-0.3/gpg/R/signing.R | 59 +++++--- gpg-0.3/gpg/build/vignette.rds |binary gpg-0.3/gpg/configure | 12 + gpg-0.3/gpg/inst/doc/intro.R | 28 ++-- gpg-0.3/gpg/inst/doc/intro.Rmd | 47 ++++-- gpg-0.3/gpg/inst/doc/intro.html | 269 ++++++++++++++++++++------------------- gpg-0.3/gpg/man/gpg_encrypt.Rd | 21 +-- gpg-0.3/gpg/man/gpg_info.Rd | 4 gpg-0.3/gpg/man/gpg_keygen.Rd | 14 +- gpg-0.3/gpg/man/gpg_keys.Rd | 25 ++- gpg-0.3/gpg/man/gpg_sign.Rd | 31 ++-- gpg-0.3/gpg/man/pinentry.Rd |only gpg-0.3/gpg/src/encrypt.c | 29 ++-- gpg-0.3/gpg/src/engine.c | 5 gpg-0.3/gpg/src/keys.c | 8 - gpg-0.3/gpg/src/sign.c | 39 ++++- gpg-0.3/gpg/vignettes/intro.Rmd | 47 ++++-- 28 files changed, 499 insertions(+), 313 deletions(-)
Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre],
Joel Gombin [ctb],
Sebastian Jeworutzki [ctb],
Kent Russell [ctb],
Richard Zijdeman [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap versions 1.4-1 dated 2016-05-06 and 1.6 dated 2016-10-21
tmap-1.4-1/tmap/R/process_bubbles.R |only tmap-1.4-1/tmap/R/process_col_vector.R |only tmap-1.4-1/tmap/man/tm_bubbles.Rd |only tmap-1.6/tmap/DESCRIPTION | 14 - tmap-1.6/tmap/MD5 | 190 +++++++++++--------- tmap-1.6/tmap/NAMESPACE | 15 + tmap-1.6/tmap/NEWS | 20 ++ tmap-1.6/tmap/R/append_data.R | 140 ++++++++++----- tmap-1.6/tmap/R/cartogram.R |only tmap-1.6/tmap/R/cat2shape.R |only tmap-1.6/tmap/R/crop_shape.R | 51 ++++- tmap-1.6/tmap/R/geocode_OSM.R | 269 +++++++++++++++++++++++++--- tmap-1.6/tmap/R/get_asp_ratio.R | 18 + tmap-1.6/tmap/R/get_raster_data.R | 44 +++- tmap-1.6/tmap/R/get_sp_coordinates.R | 2 tmap-1.6/tmap/R/gridplot.R | 8 tmap-1.6/tmap/R/grob_mod.R |only tmap-1.6/tmap/R/legend_prepare.R | 63 +++++- tmap-1.6/tmap/R/meta_plot.R | 263 +++++++++++++++++++++++----- tmap-1.6/tmap/R/meta_plot_items.R | 244 ++++++++++++++++++++++---- tmap-1.6/tmap/R/num2pal.R | 107 ++++++----- tmap-1.6/tmap/R/num2shape.R |only tmap-1.6/tmap/R/onLoad.R | 4 tmap-1.6/tmap/R/pkg.R | 29 ++- tmap-1.6/tmap/R/plot_all.R | 8 tmap-1.6/tmap/R/plot_map.R | 4 tmap-1.6/tmap/R/plot_misc_functions.R | 115 +++++++++--- tmap-1.6/tmap/R/preprocess_gt.R | 4 tmap-1.6/tmap/R/preprocess_shapes.R | 4 tmap-1.6/tmap/R/print_tmap.R | 200 +++++++++++++-------- tmap-1.6/tmap/R/process_color.R | 2 tmap-1.6/tmap/R/process_color_aes.R |only tmap-1.6/tmap/R/process_fill.R | 30 +-- tmap-1.6/tmap/R/process_layers.R | 44 +++- tmap-1.6/tmap/R/process_legend_format.R |only tmap-1.6/tmap/R/process_lines.R | 55 +---- tmap-1.6/tmap/R/process_meta.R | 80 ++++++-- tmap-1.6/tmap/R/process_other_aes.R |only tmap-1.6/tmap/R/process_raster.R | 23 +- tmap-1.6/tmap/R/process_shapes.R | 8 tmap-1.6/tmap/R/process_symbols.R |only tmap-1.6/tmap/R/process_text.R | 89 +-------- tmap-1.6/tmap/R/process_tm.R | 105 +++++++++-- tmap-1.6/tmap/R/process_varnames.R | 2 tmap-1.6/tmap/R/qtm.R | 180 ++++++++++++------- tmap-1.6/tmap/R/save_tmap.R | 34 ++- tmap-1.6/tmap/R/smooth_map.R | 82 ++++++-- tmap-1.6/tmap/R/smooth_raster_cover.R | 27 +- tmap-1.6/tmap/R/split_g.R | 23 ++ tmap-1.6/tmap/R/split_tm.R | 2 tmap-1.6/tmap/R/style_catalogue.R | 4 tmap-1.6/tmap/R/symbol_functions.R |only tmap-1.6/tmap/R/theme_ps.R |only tmap-1.6/tmap/R/tm_add_legend.R |only tmap-1.6/tmap/R/tm_layers.R | 279 ++++++++++++++++++++++-------- tmap-1.6/tmap/R/tm_layout.R | 44 ++-- tmap-1.6/tmap/R/tm_misc_elements.R | 96 +++++++++- tmap-1.6/tmap/R/tm_shape.R | 8 tmap-1.6/tmap/R/tm_view.R | 10 - tmap-1.6/tmap/R/tmap_icons.R |only tmap-1.6/tmap/R/tmap_mode.R | 6 tmap-1.6/tmap/R/view_tmap.R | 146 ++++++++++----- tmap-1.6/tmap/data/NLD_muni.rda |binary tmap-1.6/tmap/data/NLD_prov.rda |binary tmap-1.6/tmap/inst/doc/tmap-modes.R | 4 tmap-1.6/tmap/inst/doc/tmap-modes.Rmd | 8 tmap-1.6/tmap/inst/doc/tmap-modes.html | 5 tmap-1.6/tmap/inst/doc/tmap-nutshell.R | 25 +- tmap-1.6/tmap/inst/doc/tmap-nutshell.Rmd | 114 ++++++++---- tmap-1.6/tmap/inst/doc/tmap-nutshell.html | 180 ++++++++++++------- tmap-1.6/tmap/inst/img |only tmap-1.6/tmap/man/animation_tmap.Rd | 5 tmap-1.6/tmap/man/append_data.Rd | 10 - tmap-1.6/tmap/man/bb.Rd | 20 -- tmap-1.6/tmap/man/calc_densities.Rd | 1 tmap-1.6/tmap/man/cartogram.Rd |only tmap-1.6/tmap/man/crop_shape.Rd | 15 + tmap-1.6/tmap/man/geocode_OSM.Rd | 43 +++- tmap-1.6/tmap/man/get_asp_ratio.Rd | 4 tmap-1.6/tmap/man/last_map.Rd |only tmap-1.6/tmap/man/map_coloring.Rd | 3 tmap-1.6/tmap/man/poly_to_raster.Rd | 2 tmap-1.6/tmap/man/polygons.Rd | 29 ++- tmap-1.6/tmap/man/qtm.Rd | 50 +++-- tmap-1.6/tmap/man/rev_geocode_OSM.Rd |only tmap-1.6/tmap/man/save_tmap.Rd | 13 - tmap-1.6/tmap/man/smooth_map.Rd | 20 +- tmap-1.6/tmap/man/smooth_raster_cover.Rd | 2 tmap-1.6/tmap/man/theme_ps.Rd |only tmap-1.6/tmap/man/tm_add_legend.Rd |only tmap-1.6/tmap/man/tm_compass.Rd | 6 tmap-1.6/tmap/man/tm_credits.Rd | 4 tmap-1.6/tmap/man/tm_facets.Rd | 40 ++-- tmap-1.6/tmap/man/tm_layout.Rd | 77 ++++---- tmap-1.6/tmap/man/tm_lines.Rd | 24 +- tmap-1.6/tmap/man/tm_logo.Rd |only tmap-1.6/tmap/man/tm_raster.Rd | 20 +- tmap-1.6/tmap/man/tm_scale_bar.Rd | 7 tmap-1.6/tmap/man/tm_shape.Rd | 8 tmap-1.6/tmap/man/tm_symbols.Rd |only tmap-1.6/tmap/man/tm_text.Rd | 24 +- tmap-1.6/tmap/man/tm_view.Rd | 21 +- tmap-1.6/tmap/man/tmap-package.Rd | 29 ++- tmap-1.6/tmap/man/tmap_icons.Rd |only tmap-1.6/tmap/man/tmap_leaflet.Rd | 9 tmap-1.6/tmap/man/tmap_mode.Rd | 9 tmap-1.6/tmap/vignettes/tmap-modes.Rmd | 8 tmap-1.6/tmap/vignettes/tmap-nutshell.Rmd | 114 ++++++++---- 108 files changed, 2876 insertions(+), 1272 deletions(-)
Title: Robust Variance Meta-Regression
Description: Functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
Author: Zachary Fisher, Elizabeth Tipton, and Zhipeng Hou.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between robumeta versions 1.6 dated 2015-03-18 and 1.7 dated 2016-10-21
robumeta-1.6/robumeta/R/robumeta.R |only robumeta-1.7/robumeta/DESCRIPTION | 10 +++++----- robumeta-1.7/robumeta/MD5 | 13 +++++++++---- robumeta-1.7/robumeta/NAMESPACE | 1 + robumeta-1.7/robumeta/R/forest.robu.R |only robumeta-1.7/robumeta/R/group.center.R |only robumeta-1.7/robumeta/R/group.mean.R |only robumeta-1.7/robumeta/R/print.robu.R |only robumeta-1.7/robumeta/R/robu.R |only robumeta-1.7/robumeta/R/sensitivity.R |only robumeta-1.7/robumeta/data/oswald2013.RData |binary 11 files changed, 15 insertions(+), 9 deletions(-)
Title: 'pbdR' Distributed Matrix Methods
Description: A set of classes for managing distributed matrices, and
a collection of methods for computing linear algebra and
statistics. Computation is handled mostly by routines from the
'pbdBASE' package, which itself relies on the 'ScaLAPACK' and
'PBLAS' numerical libraries for distributed computing.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
ZhaoKang Wang [ctb],
Michael Lawrence [ctb],
R Core team [ctb] (some wrappers taken from the base and stats
packages)
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdDMAT versions 0.4-0 dated 2016-01-24 and 0.4-2 dated 2016-10-21
pbdDMAT-0.4-0/pbdDMAT/build |only pbdDMAT-0.4-0/pbdDMAT/inst/tests |only pbdDMAT-0.4-0/pbdDMAT/tests |only pbdDMAT-0.4-0/pbdDMAT/vignettes/workingwith-include |only pbdDMAT-0.4-2/pbdDMAT/ChangeLog | 13 ++ pbdDMAT-0.4-2/pbdDMAT/DESCRIPTION | 38 ++--- pbdDMAT-0.4-2/pbdDMAT/MD5 | 108 +++++++---------- pbdDMAT-0.4-2/pbdDMAT/NAMESPACE | 4 pbdDMAT-0.4-2/pbdDMAT/R/accessors.r | 14 +- pbdDMAT-0.4-2/pbdDMAT/R/as.ddmatrix.r | 39 +++++- pbdDMAT-0.4-2/pbdDMAT/R/constructors.r | 4 pbdDMAT-0.4-2/pbdDMAT/R/ddmatrix_bind.r | 58 ++------- pbdDMAT-0.4-2/pbdDMAT/R/ddmatrix_cond.r | 34 +++-- pbdDMAT-0.4-2/pbdDMAT/R/ddmatrix_eigen.r | 16 +- pbdDMAT-0.4-2/pbdDMAT/R/ddmatrix_isdot.r | 4 pbdDMAT-0.4-2/pbdDMAT/R/ddmatrix_prcomp.R | 3 pbdDMAT-0.4-2/pbdDMAT/R/ddmatrix_reductions.R | 102 +++++++++------- pbdDMAT-0.4-2/pbdDMAT/R/ddvector_misc.R | 4 pbdDMAT-0.4-2/pbdDMAT/R/getLocal.r | 5 pbdDMAT-0.4-2/pbdDMAT/README.md | 82 ++++++------ pbdDMAT-0.4-2/pbdDMAT/demo/basic1.r | 2 pbdDMAT-0.4-2/pbdDMAT/demo/basic2.r | 2 pbdDMAT-0.4-2/pbdDMAT/demo/basic3.r | 2 pbdDMAT-0.4-2/pbdDMAT/demo/cholesky.r | 2 pbdDMAT-0.4-2/pbdDMAT/demo/matprod.r | 2 pbdDMAT-0.4-2/pbdDMAT/demo/reductions.r | 2 pbdDMAT-0.4-2/pbdDMAT/demo/solve.r | 2 pbdDMAT-0.4-2/pbdDMAT/demo/svd.r | 2 pbdDMAT-0.4-2/pbdDMAT/inst/CITATION | 27 ++-- pbdDMAT-0.4-2/pbdDMAT/inst/RNACI/RNACI.h | 127 +++++++++----------- pbdDMAT-0.4-2/pbdDMAT/inst/doc/pbdDMAT-guide.Rnw | 2 pbdDMAT-0.4-2/pbdDMAT/inst/doc/pbdDMAT-guide.pdf |binary pbdDMAT-0.4-2/pbdDMAT/inst/tests_batch |only pbdDMAT-0.4-2/pbdDMAT/man/accessors.Rd | 3 pbdDMAT-0.4-2/pbdDMAT/man/binds.Rd | 9 - pbdDMAT-0.4-2/pbdDMAT/man/ddmatrix-constructors.Rd | 3 pbdDMAT-0.4-2/pbdDMAT/man/getLocal.Rd | 5 pbdDMAT-0.4-2/pbdDMAT/src/Makevars | 1 pbdDMAT-0.4-2/pbdDMAT/vignettes/pbdDMAT-guide.Rnw | 2 39 files changed, 382 insertions(+), 341 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>
Diff between NNS versions 0.2.2 dated 2016-09-29 and 0.2.3 dated 2016-10-21
NNS-0.2.2/NNS/R/Classifier.R |only NNS-0.2.2/NNS/man/VN.class.Rd |only NNS-0.2.3/NNS/DESCRIPTION | 8 NNS-0.2.3/NNS/MD5 | 102 +++++----- NNS-0.2.3/NNS/NAMESPACE | 4 NNS-0.2.3/NNS/R/ANOVA.R | 1 NNS-0.2.3/NNS/R/ARMA.R | 16 + NNS-0.2.3/NNS/R/Binary_ANOVA.R | 20 -- NNS-0.2.3/NNS/R/Causation.R | 1 NNS-0.2.3/NNS/R/Co_PM_cor.R | 1 NNS-0.2.3/NNS/R/Correlation.R | 14 + NNS-0.2.3/NNS/R/Dependence.R | 31 ++- NNS-0.2.3/NNS/R/FSD.R | 1 NNS-0.2.3/NNS/R/Feature_probability.R | 13 - NNS-0.2.3/NNS/R/Find_Interval.R | 1 NNS-0.2.3/NNS/R/Multivariate_Regression.R | 38 ++-- NNS-0.2.3/NNS/R/NNS_term_matrix.R |only NNS-0.2.3/NNS/R/Normalization.R | 1 NNS-0.2.3/NNS/R/Numerical_Differentiation.R | 1 NNS-0.2.3/NNS/R/Partial_Moments.R | 4 NNS-0.2.3/NNS/R/Partition_Map.R | 89 ++------- NNS-0.2.3/NNS/R/Regression.R | 264 ++++++++++------------------ NNS-0.2.3/NNS/R/SD_Efficient_Set.R | 1 NNS-0.2.3/NNS/R/SSD.R | 1 NNS-0.2.3/NNS/R/Seasonality_Test.R | 8 NNS-0.2.3/NNS/R/TSD.R | 1 NNS-0.2.3/NNS/R/Uni_SD_Routines.R | 3 NNS-0.2.3/NNS/R/dy_d_wrt.R | 10 - NNS-0.2.3/NNS/R/dy_dx.R | 21 +- NNS-0.2.3/NNS/man/Co.PM.cor.Rd | 3 NNS-0.2.3/NNS/man/FSD.Rd | 3 NNS-0.2.3/NNS/man/Feature.probability.Rd | 10 - NNS-0.2.3/NNS/man/NNS.diff.Rd | 3 NNS-0.2.3/NNS/man/NNS.term.matrix.Rd |only NNS-0.2.3/NNS/man/TSD.Rd | 3 NNS-0.2.3/NNS/man/VN.ANOVA.Rd | 3 NNS-0.2.3/NNS/man/VN.ANOVA.bin.Rd | 3 NNS-0.2.3/NNS/man/VN.ARMA.Rd | 9 NNS-0.2.3/NNS/man/VN.FSD.Rd | 3 NNS-0.2.3/NNS/man/VN.M.reg.Rd | 20 +- NNS-0.2.3/NNS/man/VN.SD.Efficient.Set.Rd | 3 NNS-0.2.3/NNS/man/VN.SSD.Rd | 3 NNS-0.2.3/NNS/man/VN.SSD.uni.Rd | 3 NNS-0.2.3/NNS/man/VN.TSD.Rd | 3 NNS-0.2.3/NNS/man/VN.caus.Rd | 3 NNS-0.2.3/NNS/man/VN.cor.Rd | 10 + NNS-0.2.3/NNS/man/VN.dep.Rd | 5 NNS-0.2.3/NNS/man/VN.norm.Rd | 3 NNS-0.2.3/NNS/man/VN.reg.Rd | 28 +- NNS-0.2.3/NNS/man/VN.seas.Rd | 6 NNS-0.2.3/NNS/man/dy.d_.Rd | 11 - NNS-0.2.3/NNS/man/dy.dx.Rd | 9 NNS-0.2.3/NNS/man/findInterval2.Rd | 3 NNS-0.2.3/NNS/man/partition.map.Rd | 2 54 files changed, 405 insertions(+), 402 deletions(-)
Title: Topological Analysis of Knotted Proteins, Biopolymers and 3D
Structures
Description: Contains functions for the topological analysis of polymers, with a focus on protein structures.
Author: Federico Comoglio and Maurizio Rinaldi
Maintainer: Federico Comoglio <federico.comoglio@gmail.com>
Diff between Rknots versions 1.3.1 dated 2015-12-23 and 1.3.2 dated 2016-10-21
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/AlexanderBriggs.R | 2 - build/vignette.rds |binary inst/doc/Rknots_vignette.html | 78 +++++++++++++++++++++++------------------- 5 files changed, 52 insertions(+), 44 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly
configurable drop-in replacements for base url() and download.file() with
better performance, support for encryption (https, ftps), gzip compression,
authentication, and other 'libcurl' goodies. The core of the package implements a
framework for performing fully customized requests where data can be processed
either in memory, on disk, or streaming via the callback or connection
interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly
web client see the 'httr' package which builds on this package with http
specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 2.1 dated 2016-09-22 and 2.2 dated 2016-10-21
DESCRIPTION | 8 ++--- MD5 | 30 ++++++++++---------- NEWS | 5 +++ inst/doc/intro.Rmd | 8 ++++- inst/doc/intro.html | 54 ++++++++++++++++++++----------------- src/curl.c | 5 +++ src/multi.c | 8 +++-- tests/testthat/helper-version.R | 12 ++++++++ tests/testthat/test-auth.R | 18 ++++++------ tests/testthat/test-certificates.R | 2 - tests/testthat/test-cookies.R | 6 ++-- tests/testthat/test-gc.R | 2 - tests/testthat/test-handle.R | 54 ++++++++++++++++++------------------- tests/testthat/test-multi.R | 18 ++++++------ tests/testthat/test-post.R | 12 ++++---- vignettes/intro.Rmd | 8 ++++- 16 files changed, 146 insertions(+), 104 deletions(-)
Title: Regression Estimation Based on the Compound Covariate Method
Under the Cox Proportional Hazard Model
Description: Calculate regression coefficients and their standard deviations under the Cox proportional hazard model with a large number of covariates. A shrinkage type estimation based on the compound covariate method (Emura, Chen & Chen, 2012 PLoS ONE) and a univariate gene selection method under dependent censoring (Emura & Chen, 2014 Statistical Methods in Medical Research) are implemented. Algorithms for simulating gene expressions in these references are also given.
Author: Takeshi Emura & Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 2.0 dated 2015-10-31 and 2.1 dated 2016-10-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/dependCox.reg.CV.R | 6 +++--- R/dependCox.reg.R | 6 +++--- man/compound.Cox-package.Rd | 4 ++-- man/dependCox.reg.CV.Rd | 33 ++++++++++++++++++++++++++++++--- man/dependCox.reg.Rd | 34 +++++++++++++++++++++++++++++++--- 7 files changed, 79 insertions(+), 24 deletions(-)
Title: Statistical Comparison of Multiple Algorithms in Multiple
Problems
Description: Given a matrix with results of different algorithms for different
problems, the package uses statistical tests and corrections to assess the
differences between algorithms.
Author: Borja Calvo [aut, cre],
Guzman Santafe [aut]
Maintainer: Borja Calvo <borja.calvo@ehu.eus>
Diff between scmamp versions 0.2.5 dated 2015-12-21 and 0.2.55 dated 2016-10-21
DESCRIPTION | 12 MD5 | 37 NAMESPACE | 2 R/plotting.R | 29 R/sysdata.rda |binary R/tests.R | 6 README.md | 2 build/vignette.rds |binary data/data_blum_2015.RData |binary data/data_gh_2008.RData |binary data/data_gh_2010.RData |binary inst/doc/Data_loading_and_manipulation.R | 12 inst/doc/Data_loading_and_manipulation.Rmd | 4 inst/doc/Data_loading_and_manipulation.html | 431 +++----- inst/doc/Statistical_assessment_of_the_differences.Rmd | 2 inst/doc/Statistical_assessment_of_the_differences.html | 788 ++++++---------- man/drawAlgorithmGraph.Rd | 3 vignettes/Data_loading_and_manipulation.Rmd | 4 vignettes/Statistical_assessment_of_the_differences.Rmd | 2 vignettes/refs.bib |only 20 files changed, 572 insertions(+), 762 deletions(-)
Title: Numerical Integration over Spheres and Balls in n-Dimensions;
Multivariate Polar Coordinates
Description: Provides several methods to integrate functions over the unit
sphere and ball in n-dimensional Euclidean space. Routines for converting to/from
multivariate polar/spherical coordinates are also provided.
Author: John P. Nolan, American University
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between SphericalCubature versions 1.2 dated 2016-07-23 and 1.3 dated 2016-10-21
DESCRIPTION | 10 +-- MD5 | 14 ++-- NAMESPACE | 3 R/SphericalCubature.R | 118 +++++++++++++++++++++++++++++---------- demo/SphericalCubature.R | 20 ++---- man/SphericalCubature-package.Rd | 3 man/SphericalMisc.Rd | 13 +++- man/adaptIntegrateSphereTri.Rd | 9 +- 8 files changed, 128 insertions(+), 62 deletions(-)
More information about SphericalCubature at CRAN
Permanent link
Title: Randomization Inference for Treatment Effects on a Binary
Outcome
Description: Computes attributable effects based confidence interval, permutation
test confidence interval, or asymptotic confidence interval for the
the average treatment effect on a binary outcome.
Author: Joseph Rigdon, Wen Wei Loh, Michael G. Hudgens
Maintainer: Wen Wei Loh <wwloh@email.unc.edu>
Diff between RI2by2 versions 1.2 dated 2014-06-16 and 1.3 dated 2016-10-21
RI2by2-1.2/RI2by2/man/Perm.CI2.Rd |only RI2by2-1.2/RI2by2/man/RI2by2-package.Rd |only RI2by2-1.2/RI2by2/man/comb.Rd |only RI2by2-1.2/RI2by2/man/nchoosem.Rd |only RI2by2-1.2/RI2by2/man/pval.Rd |only RI2by2-1.2/RI2by2/man/pval2.Rd |only RI2by2-1.3/RI2by2/DESCRIPTION | 26 ++++++++++++---------- RI2by2-1.3/RI2by2/MD5 | 24 ++++++++++---------- RI2by2-1.3/RI2by2/NAMESPACE | 9 ++++++- RI2by2-1.3/RI2by2/R/RI2by2.R | 37 +++++++++++++++++++++++++++++--- RI2by2-1.3/RI2by2/R/RcppExports.R |only RI2by2-1.3/RI2by2/man/AE.CI.Rd | 26 ++++++++++++---------- RI2by2-1.3/RI2by2/man/Perm.CI.RLH.Rd |only RI2by2-1.3/RI2by2/man/Perm.CI.Rd | 31 +++++++++++++++----------- RI2by2-1.3/RI2by2/man/Robins.CI.Rd | 23 ++++++++++--------- RI2by2-1.3/RI2by2/src |only RI2by2-1.3/RI2by2/tests |only 17 files changed, 113 insertions(+), 63 deletions(-)
Title: Multivariate Meshes and Histograms in Arbitrary Dimensions
Description: Define, manipulate and plot meshes on simplices, spheres, balls, rectangles and tubes.
Directional and other multivariate histograms are provided.
Author: John P. Nolan
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between mvmesh versions 1.3 dated 2016-05-16 and 1.4 dated 2016-10-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/mvmesh.R | 45 +++++++++++++++++++++++++++------------------ man/UnitSphere.Rd | 3 ++- man/mvmesh-geom.Rd | 4 ++-- man/mvmesh-package.Rd | 1 + 6 files changed, 41 insertions(+), 30 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.23-5 dated 2016-07-18 and 2.24 dated 2016-10-21
DESCRIPTION | 10 MD5 | 53 +- NAMESPACE | 2 R/S4-classes.R | 6 R/helpers.R | 26 - R/lsmeans.R | 131 +---- R/lstrends.R |only R/ref.grid.R | 72 +- R/summary.R | 3 R/transformations.R | 19 build/vignette.rds |binary inst/NEWS | 37 + inst/doc/extending.R | 100 +++ inst/doc/extending.pdf |binary inst/doc/extending.rnw | 145 ++++- inst/doc/using-lsmeans.R | 103 ++-- inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 38 - man/lsmeans-package.Rd | 2 man/lsmeans.Rd | 14 man/models.Rd | 8 man/ref.grid.Rd | 3 man/update.Rd | 4 tests/tests1.R | 8 tests/tests1.Rout.save | 1112 ++++++++++++++++++++++---------------------- vignettes/extending.rnw | 145 ++++- vignettes/lsmeans.bib | 8 vignettes/using-lsmeans.rnw | 38 - 28 files changed, 1230 insertions(+), 857 deletions(-)
Title: A Future for BatchJobs
Description: Simple parallel and distributed processing using futures
that utilizes the 'BatchJobs' framework,
e.g. 'fit %<-% { lm(y ~ x) }'.
This package implements the Future API of the 'future' package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.BatchJobs versions 0.13.0 dated 2016-08-03 and 0.13.1 dated 2016-10-21
DESCRIPTION | 10 +-- MD5 | 43 +++++++------ NEWS | 10 +++ R/BatchJobsFuture-class.R | 125 +++++++++++++++++++++++++------------- R/batchjobs_custom.R | 15 ++-- R/batchjobs_interactive.R | 9 ++ R/batchjobs_local.R | 13 +-- R/batchjobs_multicore.R | 19 ++--- R/batchjobs_template.R | 36 +++++----- R/tempRegistry.R | 93 ++++++++++++++++++++++++++-- inst/doc/future.BatchJobs.html | 20 +++--- inst/doc/future.BatchJobs.md.rsp | 14 ++-- man/BatchJobsFuture.Rd | 13 +++ man/batchjobs_custom.Rd | 17 +++-- man/batchjobs_local.Rd | 15 +++- man/batchjobs_multicore.Rd | 20 ++++-- man/batchjobs_template.Rd | 29 ++++++-- tests/batchjobs_job.delay.R |only tests/batchjobs_multicore.R | 24 +++++-- tests/future,labels.R |only tests/globals,formulas.R |only tests/globals,manual.R |only tests/globals,subassignment.R |only tests/incl/start,load-only.R | 5 + vignettes/future.BatchJobs.md.rsp | 14 ++-- 25 files changed, 370 insertions(+), 174 deletions(-)
More information about future.BatchJobs at CRAN
Permanent link
Title: Furniture for Health, Behavioral, and Social Scientists
Description: Package contains two main functions (i.e., two pieces of furniture):
table1() which produces a well-formatted table of descriptives common as Table 1
in research articles; and washer() which is helpful in cleaning up your data.
Should be useful for quantitative research in applied fields (e.g., health,
behavioral, and social sciences). It also contains a simple operator to
help with data exploration.
Author: Tyson Barrett [aut, cre],
Emily Brignone [aut]
Maintainer: Tyson Barrett <t.barrett@aggiemail.usu.edu>
Diff between furniture versions 1.0.1 dated 2016-09-20 and 1.2.0 dated 2016-10-21
DESCRIPTION | 24 ++++-- MD5 | 27 ++++++- NAMESPACE | 3 R/Table1.R | 165 ++++++++++++++++++++++-------------------------- R/furniture.R |only R/nhanes_data.R |only R/operators.R |only R/zzz.R |only build |only data |only inst |only man/furniture.Rd |only man/grapes-xt-grapes.Rd |only man/nhanes10.Rd |only man/table1.Rd | 63 +++++++++--------- man/table1_.Rd | 15 +--- tests |only vignettes |only 18 files changed, 156 insertions(+), 141 deletions(-)
Title: Observed-Score Linking and Equating
Description: Contains methods for observed-score linking
and equating under the single-group, equivalent-groups,
and nonequivalent-groups with anchor test(s) designs.
Equating types include identity, mean, linear, general
linear, equipercentile, circle-arc, and composites of
these. Equating methods include synthetic, nominal
weights, Tucker, Levine observed score, Levine true
score, Braun/Holland, frequency estimation, and chained
equating. Plotting and summary methods, and methods for
multivariate presmoothing and bootstrap error estimation
are also provided.
Author: Anthony Albano <tony.d.albano@gmail.com>
Maintainer: Anthony Albano <tony.d.albano@gmail.com>
Diff between equate versions 2.0-4 dated 2016-04-26 and 2.0-5 dated 2016-10-21
equate-2.0-4/equate/R/smoothing.R |only equate-2.0-5/equate/DESCRIPTION | 6 equate-2.0-5/equate/MD5 | 38 - equate-2.0-5/equate/NEWS | 20 equate-2.0-5/equate/NEWS.md |only equate-2.0-5/equate/R/KBneat.R | 2 equate-2.0-5/equate/R/equate-package.R | 7 equate-2.0-5/equate/R/equate.R | 76 ++- equate-2.0-5/equate/R/equipercentile.R | 94 ++-- equate-2.0-5/equate/R/linear.R | 247 ++++++++++- equate-2.0-5/equate/R/presmoothing.R |only equate-2.0-5/equate/R/synthetic.R | 106 ++-- equate-2.0-5/equate/inst/CITATION |only equate-2.0-5/equate/inst/doc/equatevignette.R | 176 +++---- equate-2.0-5/equate/inst/doc/equatevignette.Rnw | 188 ++++---- equate-2.0-5/equate/inst/doc/equatevignette.pdf |binary equate-2.0-5/equate/man/KBneat.Rd | 2 equate-2.0-5/equate/man/equate-package.Rd | 7 equate-2.0-5/equate/man/equate.Rd | 67 ++- equate-2.0-5/equate/man/presmoothing.Rd | 2 equate-2.0-5/equate/vignettes/equatebibfile.bib | 513 +++++++++++------------ equate-2.0-5/equate/vignettes/equatevignette.Rnw | 188 ++++---- 22 files changed, 1017 insertions(+), 722 deletions(-)
Title: Convolution-Based Nonstationary Spatial Modeling
Description: Fits convolution-based nonstationary
Gaussian process models to point-referenced spatial data. The nonstationary
covariance function allows the user to specify the underlying correlation
structure and which spatial dependence parameters should be allowed to
vary over space: the anisotropy, nugget variance, and process variance.
The parameters are estimated via maximum likelihood, using a local
likelihood approach. Also provided are functions to fit stationary spatial
models for comparison, calculate the Kriging predictor and standard errors,
and create various plots to visualize nonstationarity.
Author: Mark D. Risser [aut, cre]
Maintainer: Mark D. Risser <markdrisser@gmail.com>
Diff between convoSPAT versions 1.1 dated 2016-04-29 and 1.1.1 dated 2016-10-21
convoSPAT-1.1.1/convoSPAT/DESCRIPTION | 11 - convoSPAT-1.1.1/convoSPAT/MD5 | 59 ++--- convoSPAT-1.1.1/convoSPAT/NAMESPACE | 2 convoSPAT-1.1.1/convoSPAT/R/convoSPAT_fitpred.R | 129 +++++++++++-- convoSPAT-1.1.1/convoSPAT/man/Aniso_fit.Rd | 6 convoSPAT-1.1.1/convoSPAT/man/NSconvo_fit.Rd | 7 convoSPAT-1.1.1/convoSPAT/man/NSconvo_sim.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/US.mc.grids.Rd | 2 convoSPAT-1.1.1/convoSPAT/man/US.prediction.locs.Rd | 2 convoSPAT-1.1.1/convoSPAT/man/USprecip97.Rd | 2 convoSPAT-1.1.1/convoSPAT/man/evaluate_CV.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/f_mc_kernels.Rd | 4 convoSPAT-1.1.1/convoSPAT/man/kernel_cov.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/make_aniso_loglik.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/make_aniso_loglik_kappa.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/make_global_loglik1.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/make_global_loglik1_kappa.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/make_global_loglik2.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/make_global_loglik2_kappa.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/make_global_loglik3.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/make_global_loglik3_kappa.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/make_global_loglik4_kappa.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/mc_N.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/plot.Aniso.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/plot.NSconvo.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/predict.Aniso.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/predict.NSconvo.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/simdata.Rd | 2 convoSPAT-1.1.1/convoSPAT/man/summary.Aniso.Rd | 3 convoSPAT-1.1.1/convoSPAT/man/summary.NSconvo.Rd | 3 convoSPAT-1.1/convoSPAT/vignettes |only 31 files changed, 203 insertions(+), 80 deletions(-)
Title: Statistical Methods and Models for Claims Reserving in General
Insurance
Description: Various statistical methods and models which are
typically used for the estimation of outstanding claims reserves
in general insurance, including those to estimate the claims
development result as required under Solvency II.
Author: Markus Gesmann [aut, cre],
Daniel Murphy [aut],
Yanwei (Wayne) Zhang [aut],
Alessandro Carrato [aut],
Giuseppe Crupi [aut],
Christophe Dutang [ctb],
Arnaud Lacoume [ctb],
Arthur Charpentier [ctb],
Mario Wuthrich [aut],
Fabio Concina [aut]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between ChainLadder versions 0.2.2 dated 2015-08-31 and 0.2.3 dated 2016-10-21
ChainLadder-0.2.2/ChainLadder/vignettes/Log-incremental |only ChainLadder-0.2.3/ChainLadder/DESCRIPTION | 14 ChainLadder-0.2.3/ChainLadder/MD5 | 67 - ChainLadder-0.2.3/ChainLadder/NAMESPACE | 6 ChainLadder-0.2.3/ChainLadder/NEWS | 670 ---------- ChainLadder-0.2.3/ChainLadder/R/ChainLadder.R | 6 ChainLadder-0.2.3/ChainLadder/R/MackChainLadderFunctions.R | 43 ChainLadder-0.2.3/ChainLadder/R/PIC.R | 38 ChainLadder-0.2.3/ChainLadder/R/Triangles.R | 71 - ChainLadder-0.2.3/ChainLadder/R/glmReserve.R | 103 + ChainLadder-0.2.3/ChainLadder/R/tweedieReserve.R | 11 ChainLadder-0.2.3/ChainLadder/README.md | 22 ChainLadder-0.2.3/ChainLadder/THANKS | 3 ChainLadder-0.2.3/ChainLadder/build/vignette.rds |binary ChainLadder-0.2.3/ChainLadder/inst/doc/ChainLadder.R | 2 ChainLadder-0.2.3/ChainLadder/inst/doc/ChainLadder.Rnw | 128 - ChainLadder-0.2.3/ChainLadder/inst/doc/ChainLadder.pdf |binary ChainLadder-0.2.3/ChainLadder/inst/doc/NEWS.R |only ChainLadder-0.2.3/ChainLadder/inst/doc/NEWS.Rmd |only ChainLadder-0.2.3/ChainLadder/inst/doc/NEWS.html |only ChainLadder-0.2.3/ChainLadder/inst/unitTests/runit.MackChainLadder.R | 30 ChainLadder-0.2.3/ChainLadder/inst/unitTests/runit.Triangles.r |only ChainLadder-0.2.3/ChainLadder/inst/unitTests/runit.glmReserving.r |only ChainLadder-0.2.3/ChainLadder/man/ChainLadder-package.Rd | 2 ChainLadder-0.2.3/ChainLadder/man/as.LongTriangle.Rd |only ChainLadder-0.2.3/ChainLadder/man/chainladder.Rd | 3 ChainLadder-0.2.3/ChainLadder/man/glmReserve.Rd | 56 ChainLadder-0.2.3/ChainLadder/vignettes/ChainLadder.Rnw | 128 - ChainLadder-0.2.3/ChainLadder/vignettes/ChainLadder.bib | 8 ChainLadder-0.2.3/ChainLadder/vignettes/NEWS.Rmd |only 30 files changed, 451 insertions(+), 960 deletions(-)
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in
part to support an MS level course in nonparametric statistical methods. Methods
include adjustments for multiple comparisons, implementation of multivariate
Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence
region, some permutation tests for linear models, and some algorithms for
calculating exact probabilities associated with one- and two- stage testing
involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.2.3 dated 2016-08-28 and 1.2.5 dated 2016-10-20
DESCRIPTION | 17 ++++++++++---- MD5 | 18 ++++++++------- NAMESPACE | 4 +-- R/aov.P.R | 14 ++++++++++- R/page.test.unbalanced.R |only R/probest.R | 8 ++++-- man/MultNonParam-package.Rd | 46 -------------------------------------- man/page.test.unbalanced.Rd |only man/probest.Rd | 5 ++-- src/aovp.f90 | 13 ++++++----- src/probest.f90 | 52 ++++++++++++++++++++++++++++++++++++++------ 11 files changed, 97 insertions(+), 80 deletions(-)
Title: Analysis of Music and Speech
Description: Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ...
Also contains functions ported from the 'rastamat' 'Matlab' package.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de> with contributions
from Sebastian Krey, Olaf Mersmann, Sarah Schnackenberg, Guillaume Guenard,
Andrea Preusser, Anita Thieler, Johanna Mielke and Claus Weihs, as well as code fragments
and ideas from the former package 'sound' by Matthias Heymann
and functions from 'rastamat' by Daniel P. W. Ellis.
The included parts of the libmad MPEG audio decoder library are
authored by Underbit Technologies.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between tuneR versions 1.3.0 dated 2016-09-15 and 1.3.1 dated 2016-10-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/readMidi.R | 47 +++++++++++++++++++++++++---------------------- R/readWave.R | 16 +++++++++++++--- 4 files changed, 45 insertions(+), 32 deletions(-)
Title: Tree Ring Analysis of Disturbance Events in R
Description: Tree Ring Analysis of Disturbance Events in R (TRADER) package provides only one way for disturbance reconstruction from tree-ring data.
Author: Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>
Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>
Diff between TRADER versions 1.2-1 dated 2016-02-10 and 1.2-2 dated 2016-10-20
DESCRIPTION | 8 +- MD5 | 30 +++---- NAMESPACE | 2 R/trader.R | 172 +++++++++++++++++++++++---------------------- man/TRADER-package.Rd | 4 - man/abrams.Rd | 2 man/absoluteIncreaseALL.Rd | 2 man/boundaryLineALL.Rd | 2 man/doAll.Rd | 38 ++++++++- man/growthAveragingALL.Rd | 2 man/plotBoundary.Rd | 2 man/plotFirstYears.Rd | 2 man/plotGrowth.Rd | 2 man/plotNORelease.Rd | 2 man/splechtna.Rd | 2 man/splechtnaALL.Rd | 2 16 files changed, 151 insertions(+), 123 deletions(-)
Title: Infrastructure for Running and Cycling Data from GPS-Enabled
Tracking Devices
Description: The aim of this package is to provide infrastructure for handling running and cycling
data from GPS-enabled tracking devices. After extraction and appropriate
manipulation of the training or competition attributes, the data are placed
into session-based and unit-aware data objects of class trackeRdata (S3 class). The
information in the resulting data objects can then be visualised, summarised,
and analysed through corresponding flexible and extensible methods.
Author: Hannah Frick [aut, cre],
Ioannis Kosmidis [aut]
Maintainer: Hannah Frick <h.frick@ucl.ac.uk>
Diff between trackeR versions 0.0.3 dated 2016-06-23 and 0.0.4 dated 2016-10-20
DESCRIPTION | 12 MD5 | 47 - NAMESPACE | 1 NEWS | 9 R/Wprime.R | 5 R/read.R | 20 R/trackeRdata.R | 39 R/trackeRdata_summary.R | 16 R/trackeRdata_zones.R | 4 build/vignette.rds |binary data/run.rda |binary data/runs.rda |binary inst/doc/TourDetrackeR.Rmd | 50 - inst/doc/TourDetrackeR.html | 46 - inst/doc/trackeR.R | 176 ---- inst/doc/trackeR.Rnw | 1725 ++++++++++++++++++++++++++------------------ inst/doc/trackeR.pdf |binary man/GC2trackeRdata.Rd | 4 man/readContainer.Rd | 4 man/readDirectory.Rd | 4 man/sanityChecks.Rd |only man/trackeRdata.Rd | 4 vignettes/TourDetrackeR.Rmd | 50 - vignettes/trackeR.Rnw | 1725 ++++++++++++++++++++++++++------------------ vignettes/trackeR.bib | 52 - 25 files changed, 2293 insertions(+), 1700 deletions(-)
Title: Thermal Image Analysis
Description: A collection of functions and routines for inputting thermal
image video files, plotting and converting binary raw data into estimates of
temperature. First published 2015-03-26. Written primarily for research purposes
in biological applications of thermal images. v1 included the base calculations
for converting thermal image binary values to temperatures. v2 included additional
equations for providing heat transfer calculations and an import function for thermal
image files (v2.2.3 fixed error importing jpg to windows OS).
Author: Glenn J. Tattersall
Maintainer: Glenn J. Tattersall <gtatters@brocku.ca>
Diff between Thermimage versions 2.2.1 dated 2016-08-04 and 2.2.3 dated 2016-10-20
DESCRIPTION | 10 +++--- MD5 | 10 +++--- R/freeparameters.R | 2 - R/hconv.R | 3 + R/readflirJPG.R | 84 +++++++++++++++++++++++++++++------------------------ man/readflirJPG.Rd | 3 + 6 files changed, 63 insertions(+), 49 deletions(-)
Title: Perceptual Analysis, Visualization and Organization of Spectral
Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color
from spectral data.
Author: Rafael Maia [aut, cre],
Chad Eliason [aut],
Pierre-Paul Bitton [aut]
Maintainer: Rafael Maia <rm72@zips.uakron.edu>
Diff between pavo versions 0.5-5 dated 2016-03-08 and 0.5-6 dated 2016-10-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 5 +++++ R/internal.R | 4 ++-- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the book
"Numerical Methods and Optimization in Finance" by M.
'Gilli', D. 'Maringer' and E. Schumann (2011), ISBN
978-0123756626. The package provides implementations of
several optimisation heuristics, such as Differential
Evolution, Genetic Algorithms and Threshold Accepting.
There are also functions for the valuation of financial
instruments, such as bonds and options, and functions that
help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between NMOF versions 0.36-2 dated 2015-10-20 and 0.40-0 dated 2016-10-20
NMOF-0.36-2/NMOF/R/randomp.R |only NMOF-0.36-2/NMOF/inst/unitTests/report.txt |only NMOF-0.40-0/NMOF/DESCRIPTION | 25 NMOF-0.40-0/NMOF/MD5 | 103 +-- NMOF-0.40-0/NMOF/NAMESPACE | 10 NMOF-0.40-0/NMOF/NEWS | 98 +++ NMOF-0.40-0/NMOF/R/DEopt.R | 21 NMOF-0.40-0/NMOF/R/GAopt.R | 6 NMOF-0.40-0/NMOF/R/LSopt.R | 6 NMOF-0.40-0/NMOF/R/TAopt.R | 101 ++- NMOF-0.40-0/NMOF/R/bracket.R | 6 NMOF-0.40-0/NMOF/R/gridSearch.R | 2 NMOF-0.40-0/NMOF/R/integrate.R | 2 NMOF-0.40-0/NMOF/R/internals.R | 4 NMOF-0.40-0/NMOF/R/mc.R | 12 NMOF-0.40-0/NMOF/R/pm.R | 13 NMOF-0.40-0/NMOF/R/portfolio.R |only NMOF-0.40-0/NMOF/R/repairMatrix.R | 9 NMOF-0.40-0/NMOF/R/restartOpt.R | 12 NMOF-0.40-0/NMOF/R/testFun.R | 73 +- NMOF-0.40-0/NMOF/R/xtContractValue.R |only NMOF-0.40-0/NMOF/build/vignette.rds |binary NMOF-0.40-0/NMOF/inst/CITATION | 30 - NMOF-0.40-0/NMOF/inst/NMOFex/NMOFman.R | 661 ++++++++++++----------- NMOF-0.40-0/NMOF/inst/doc/An_overview.R | 16 NMOF-0.40-0/NMOF/inst/doc/An_overview.Rnw | 45 + NMOF-0.40-0/NMOF/inst/doc/An_overview.pdf |binary NMOF-0.40-0/NMOF/inst/doc/DEnss.pdf |binary NMOF-0.40-0/NMOF/inst/doc/LSselect.pdf |binary NMOF-0.40-0/NMOF/inst/doc/PSlms.pdf |binary NMOF-0.40-0/NMOF/inst/doc/TAportfolio.pdf |binary NMOF-0.40-0/NMOF/inst/doc/qTableEx.pdf |binary NMOF-0.40-0/NMOF/inst/doc/repair.pdf |binary NMOF-0.40-0/NMOF/inst/doc/vectorise.pdf |binary NMOF-0.40-0/NMOF/inst/unitTests/runTests.R | 28 NMOF-0.40-0/NMOF/inst/unitTests/test_results.txt |only NMOF-0.40-0/NMOF/inst/unitTests/unitTests2.R | 413 +++++++------- NMOF-0.40-0/NMOF/inst/unitTests/unitTestsDEopt.R | 19 NMOF-0.40-0/NMOF/inst/unitTests/unitTests_mc.R |only NMOF-0.40-0/NMOF/man/DEopt.Rd | 459 ++++++++------- NMOF-0.40-0/NMOF/man/GAopt.Rd | 1 NMOF-0.40-0/NMOF/man/LSopt.Rd | 7 NMOF-0.40-0/NMOF/man/PSopt.Rd | 1 NMOF-0.40-0/NMOF/man/TA.info.Rd | 1 NMOF-0.40-0/NMOF/man/TAopt.Rd | 23 NMOF-0.40-0/NMOF/man/bracketing.Rd | 8 NMOF-0.40-0/NMOF/man/callHestoncf.Rd | 1 NMOF-0.40-0/NMOF/man/gridSearch.Rd | 1 NMOF-0.40-0/NMOF/man/mc.Rd | 30 + NMOF-0.40-0/NMOF/man/options.Rd | 12 NMOF-0.40-0/NMOF/man/pm.Rd | 5 NMOF-0.40-0/NMOF/man/repairMatrix.Rd | 8 NMOF-0.40-0/NMOF/man/testFunctions.Rd | 19 NMOF-0.40-0/NMOF/man/xtContractValue.Rd |only NMOF-0.40-0/NMOF/tests/README | 2 NMOF-0.40-0/NMOF/vignettes/An_overview.Rnw | 45 + 56 files changed, 1335 insertions(+), 1003 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, also handling experimental and random panels. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.4.8 dated 2016-09-21 and 1.5.0 dated 2016-10-20
DESCRIPTION | 8 ++-- MD5 | 33 +++++++++-------- R/RcppExports.R | 4 ++ R/gmm.R | 27 ++++++-------- inst/CITATION | 2 - inst/add/cvNAM.R | 13 ++++--- inst/add/sparseGMM.R | 79 +++++++++++++++++++++---------------------- inst/doc/gwa_description.pdf |binary inst/doc/vignette1.Rmd | 12 ++++-- inst/doc/vignette1.html | 16 +++++--- inst/doc/vignette2.Rmd | 4 +- inst/doc/vignette2.html | 8 ++-- man/Internals.Rd | 3 + man/NAM-package.Rd | 4 +- src/RcppExports.cpp | 15 ++++++++ src/emBL.cpp |only vignettes/vignette1.Rmd | 12 ++++-- vignettes/vignette2.Rmd | 4 +- 18 files changed, 138 insertions(+), 106 deletions(-)
Title: Reproducible Data Retrieval from the ICPSR Archive
Description: Reproducible, programmatic retrieval of datasets from the
Inter-university Consortium for Political and Social Research archive.
Author: Frederick Solt [aut, cre],
Kellen Gracey [aut],
Eric Persson [ctb]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Diff between icpsrdata versions 0.1.1 dated 2016-07-24 and 0.2.0 dated 2016-10-20
DESCRIPTION | 10 +- MD5 | 20 ++--- NAMESPACE | 9 ++ NEWS.md | 9 ++ R/icpsrdownload.R | 142 ++++++++++++++++++--------------------- README.md | 3 build/vignette.rds |binary inst/doc/icpsrdata-vignette.Rmd | 13 ++- inst/doc/icpsrdata-vignette.html | 15 ++-- man/icpsr_download.Rd | 14 ++- vignettes/icpsrdata-vignette.Rmd | 13 ++- 11 files changed, 135 insertions(+), 113 deletions(-)
Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between Barnard versions 1.7 dated 2016-10-19 and 1.8 dated 2016-10-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/barnard.test.R | 5 +++-- man/barnard.test.Rd | 2 +- src/Barnard.c | 21 ++++++++++++++++----- 5 files changed, 28 insertions(+), 16 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.0.3 dated 2016-10-14 and 0.0.4 dated 2016-10-20
ChangeLog | 39 +++++++++++++++++++++++++++ DESCRIPTION | 8 ++--- MD5 | 23 ++++++++------- R/anytime.R | 20 +++++++++++-- R/init.R | 4 +- README.md | 75 +++++++++++++++++++++++++--------------------------- build/partial.rdb |binary cleanup |only inst/NEWS.Rd | 24 +++++++++++++--- man/anytime.Rd | 22 ++++++++++++--- src/RcppExports.cpp | 4 +- src/anytime.cpp | 72 ++++++++++++++++++++++++++++++++++--------------- tests/allFormats.R | 14 ++++++++- 13 files changed, 211 insertions(+), 94 deletions(-)
Title: ACE and AVAS for Selecting Multiple Regression Transformations
Description: Two nonparametric methods for multiple regression transform selection are provided.
The first, Alternative Conditional Expectations (ACE),
is an algorithm to find the fixed point of maximal
correlation, i.e. it finds a set of transformed response variables that maximizes R^2
using smoothing functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal Transformations
for Multiple Regression and Correlation". Journal of the American Statistical Association.
80:580-598. <doi:10.1080/01621459.1985.10478157>].
Also included is the Additivity Variance Stabilization (AVAS) method which works better than ACE when
correlation is low [see Tibshirani, R.. 1986. "Estimating Transformations for Regression via Additivity
and Variance Stabilization". Journal of the American Statistical Association. 83:394-405.
<doi:10.1080/01621459.1988.10478610>].
Author: Phil Spector, Jerome Friedman, Robert Tibshirani, Thomas Lumley, Shawn Garbett, Jonathan Baron
Maintainer: Shawn Garbett <shawn.garbett@vanderbilt.edu>
Diff between acepack versions 1.3-3.3 dated 2013-05-03 and 1.4.0 dated 2016-10-20
acepack-1.3-3.3/acepack/CHANGES |only acepack-1.3-3.3/acepack/README |only acepack-1.3-3.3/acepack/README.ace |only acepack-1.3-3.3/acepack/README.avas |only acepack-1.3-3.3/acepack/ace.doc |only acepack-1.4.0/acepack/DESCRIPTION | 26 + acepack-1.4.0/acepack/LICENSE | 153 --------- acepack-1.4.0/acepack/LICENSE.note |only acepack-1.4.0/acepack/MD5 | 25 - acepack-1.4.0/acepack/NEWS |only acepack-1.4.0/acepack/inst |only acepack-1.4.0/acepack/man/ace.Rd | 16 - acepack-1.4.0/acepack/src/ace.f | 210 ++++++------- acepack-1.4.0/acepack/src/avas.f | 499 ++++++++++++++++--------------- acepack-1.4.0/acepack/src/rlsmo.f | 573 ++++++++++++++++++------------------ acepack-1.4.0/acepack/tests |only 16 files changed, 703 insertions(+), 799 deletions(-)
Title: Generalized and Safe-Bayesian Ridge and Lasso Regression
Description: Functions for Generalized and Safe-Bayesian Ridge and Lasso Regression models with both fixed and varying variance.
Author: Rianne de Heide [aut, cre],
Gustavo de los Campos [ctb],
Paulino Perez Rodriguez [ctb],
Bob Wheeler [ctb]
Maintainer: Rianne de Heide <r.de.heide@cwi.nl>
Diff between SafeBayes versions 1.0 dated 2016-05-23 and 1.1 dated 2016-10-20
DESCRIPTION | 8 ++++---- MD5 | 37 +++++++++++++++++++++---------------- NEWS |only R/GBRidgeFV.R |only R/GBlassoFV.R |only R/SBLassoISq.R | 7 +++++++ R/SBLassoRSq.R | 7 +++++++ R/SBRidgeISq.R | 7 +++++++ R/SBRidgeRSq.R | 7 +++++++ man/GBLasso.Rd | 4 ++-- man/GBLassoFV.Rd |only man/GBRidge.Rd | 4 ++-- man/GBRidgeFV.Rd |only man/SBLassoISq.Rd | 7 ++++--- man/SBLassoIlog.Rd | 8 ++++---- man/SBLassoRSq.Rd | 7 ++++--- man/SBLassoRlog.Rd | 7 ++++--- man/SBRidgeISq.Rd | 7 ++++--- man/SBRidgeIlog.Rd | 7 ++++--- man/SBRidgeRSq.Rd | 7 ++++--- man/SBRidgeRlog.Rd | 7 ++++--- src/dists.cc | 11 +++++------ 22 files changed, 94 insertions(+), 55 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.1.6 dated 2016-09-10 and 1.2.3 dated 2016-10-20
yuima-1.1.6/yuima/man/info.Output.Rd |only yuima-1.1.6/yuima/man/param.Output.Rd |only yuima-1.1.6/yuima/man/yuima.Output-class.Rd |only yuima-1.2.3/yuima/DESCRIPTION | 6 yuima-1.2.3/yuima/MD5 | 43 - yuima-1.2.3/yuima/NAMESPACE | 23 yuima-1.2.3/yuima/NEWS | 2 yuima-1.2.3/yuima/R/FunctionAndOperators.R | 21 yuima-1.2.3/yuima/R/MethodForLaw.R |only yuima-1.2.3/yuima/R/NewClasses.R | 26 yuima-1.2.3/yuima/R/PointProcessClasses.R | 4 yuima-1.2.3/yuima/R/qmle.R | 584 +++++++-------- yuima-1.2.3/yuima/R/setMultiModel.R | 2 yuima-1.2.3/yuima/R/sim.euler.R | 5 yuima-1.2.3/yuima/R/simulate.R | 59 - yuima-1.2.3/yuima/R/simulateForMapsIntegralAndOperator.R | 10 yuima-1.2.3/yuima/R/yuima.data.R | 10 yuima-1.2.3/yuima/R/yuima.law.r |only yuima-1.2.3/yuima/R/yuima.model.R | 3 yuima-1.2.3/yuima/man/LawMethods.Rd |only yuima-1.2.3/yuima/man/info.Map.Rd |only yuima-1.2.3/yuima/man/param.Map.Rd |only yuima-1.2.3/yuima/man/setLaw.Rd |only yuima-1.2.3/yuima/man/setMap.Rd | 8 yuima-1.2.3/yuima/man/yuima.Map-class.Rd |only yuima-1.2.3/yuima/man/yuima.law-class.rd |only yuima-1.2.3/yuima/src/RcppExports.cpp | 6 yuima-1.2.3/yuima/src/qmlecpp.cpp | 134 +-- 28 files changed, 510 insertions(+), 436 deletions(-)
Title: Wavelets Statistics and Transforms
Description: Performs 1, 2 and 3D real and complex-valued wavelet transforms,
nondecimated transforms, wavelet packet transforms, nondecimated
wavelet packet transforms, multiple wavelet transforms,
complex-valued wavelet transforms, wavelet shrinkage for
various kinds of data, locally stationary wavelet time series,
nonstationary multiscale transfer function modeling, density
estimation.
Author: Guy Nason [aut, cre]
Maintainer: Guy Nason <G.P.Nason@bristol.ac.uk>
Diff between wavethresh versions 4.6.6 dated 2013-10-21 and 4.6.8 dated 2016-10-20
DESCRIPTION | 12 +-- MD5 | 12 +-- NAMESPACE | 13 +++ R/function.r | 170 ++++++++++++++++++++++++++++++++++++++++----------- R/wavde.r | 20 ------ inst/CHANGES | 22 ++++++ man/filter.select.rd | 8 ++ 7 files changed, 190 insertions(+), 67 deletions(-)
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear and Logistic Mixed Models (AIREML
Algorithm), Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.4.6 dated 2016-07-11 and 1.4.7 dated 2016-10-20
gaston-1.4.6/gaston/TODO |only gaston-1.4.6/gaston/vignettes/gaston-015.pdf |only gaston-1.4.6/gaston/vignettes/gaston-026.pdf |only gaston-1.4.6/gaston/vignettes/gaston-028.pdf |only gaston-1.4.6/gaston/vignettes/gaston-030.pdf |only gaston-1.4.6/gaston/vignettes/gaston-032.pdf |only gaston-1.4.6/gaston/vignettes/gaston-037.pdf |only gaston-1.4.6/gaston/vignettes/gaston-039.pdf |only gaston-1.4.6/gaston/vignettes/gaston-041.pdf |only gaston-1.4.6/gaston/vignettes/gaston-043.pdf |only gaston-1.4.6/gaston/vignettes/gaston-045.pdf |only gaston-1.4.6/gaston/vignettes/gaston-047.pdf |only gaston-1.4.6/gaston/vignettes/gaston-051.pdf |only gaston-1.4.6/gaston/vignettes/gaston-052.pdf |only gaston-1.4.6/gaston/vignettes/gaston-053.pdf |only gaston-1.4.7/gaston/DESCRIPTION | 12 - gaston-1.4.7/gaston/MD5 | 95 +++----- gaston-1.4.7/gaston/NAMESPACE | 11 gaston-1.4.7/gaston/NEWS | 15 + gaston-1.4.7/gaston/R/bm.r | 8 gaston-1.4.7/gaston/R/bm_as_bm.r | 1 gaston-1.4.7/gaston/R/bm_bind.r | 127 ++++++++-- gaston-1.4.7/gaston/R/bm_genomic_sex.r | 48 ++-- gaston-1.4.7/gaston/R/bm_grm.r | 14 - gaston-1.4.7/gaston/R/bm_ld_thinner.r | 11 gaston-1.4.7/gaston/R/bm_select.r | 11 gaston-1.4.7/gaston/R/bm_stats.r | 211 ++++++++++++----- gaston-1.4.7/gaston/R/bm_subsetting.r | 8 gaston-1.4.7/gaston/R/ld_plot.r |only gaston-1.4.7/gaston/R/ld_plot_exemple.r |only gaston-1.4.7/gaston/R/score.r | 79 ++++-- gaston-1.4.7/gaston/R/zzz.r |only gaston-1.4.7/gaston/inst/doc/gaston.R | 159 ++++++++----- gaston-1.4.7/gaston/inst/doc/gaston.Rnw | 173 +++++++++++--- gaston-1.4.7/gaston/inst/doc/gaston.pdf |binary gaston-1.4.7/gaston/man/GRM.Rd | 4 gaston-1.4.7/gaston/man/LD.Rd | 7 gaston-1.4.7/gaston/man/LD.plot.Rd |only gaston-1.4.7/gaston/man/LD.thin.Rd | 2 gaston-1.4.7/gaston/man/score.variance.Rd | 29 +- gaston-1.4.7/gaston/man/select.inds.Rd | 4 gaston-1.4.7/gaston/man/select.snps.Rd | 5 gaston-1.4.7/gaston/man/set.genomic.sex.Rd | 9 gaston-1.4.7/gaston/man/set.stats.Rd | 39 ++- gaston-1.4.7/gaston/src/Makevars |only gaston-1.4.7/gaston/src/Makevars.win |only gaston-1.4.7/gaston/src/ai-reml-1k-covar.h | 1 gaston-1.4.7/gaston/src/ai-reml-logit-1k-covar.h | 1 gaston-1.4.7/gaston/src/davies.c |only gaston-1.4.7/gaston/src/gwas_lmm_diago_wald.cpp | 63 ++--- gaston-1.4.7/gaston/src/gwas_lmm_diago_wald_mt.cpp | 43 ++- gaston-1.4.7/gaston/src/m4_bind_inds.cpp | 146 ++++++++++++ gaston-1.4.7/gaston/src/m4_kinship.cpp | 71 +++++- gaston-1.4.7/gaston/src/m4_kinship_p.cpp | 65 ++++- gaston-1.4.7/gaston/src/m4_ldthin_left.cpp | 59 ++-- gaston-1.4.7/gaston/src/m4_ldthin_random.cpp | 60 ++--- gaston-1.4.7/gaston/src/m4_ldthin_right.cpp | 59 ++-- gaston-1.4.7/gaston/src/m4_recode.cpp |only gaston-1.4.7/gaston/src/m4_stats.cpp | 248 +++++++++++++++------ gaston-1.4.7/gaston/vignettes/gaston.Rnw | 130 ++++++++--- 60 files changed, 1428 insertions(+), 600 deletions(-)
Title: Robust Estimation of the Proportion of Treatment Effect
Explained by Surrogate Marker Information
Description: Provides functions to estimate the proportion of treatment effect on the primary outcome that is explained by the treatment effect on the surrogate marker.
Author: Layla Parast
Maintainer: Layla Parast <parast@rand.org>
Diff between Rsurrogate versions 1.0 dated 2015-10-23 and 2.0 dated 2016-10-20
DESCRIPTION | 10 MD5 | 30 ++ NAMESPACE | 3 R/Functions_Rsurrogate.R | 431 +++++++++++++++++++++++++++++++++++++++++-- man/Aug.R.s.surv.estimate.Rd |only man/R.s.estimate.Rd | 103 +++++----- man/R.s.surv.estimate.Rd |only man/R.t.surv.estimate.Rd |only man/augment.est.vector.Rd |only man/censor.weight.Rd |only man/cumsum2.Rd |only man/d_example_surv.Rd | 8 man/delta.estimate.Rd | 24 +- man/delta.s.estimate.Rd | 41 ++-- man/delta.s.surv.estimate.Rd |only man/delta.surv.estimate.Rd |only man/delta.t.surv.estimate.Rd |only man/fieller.ci.Rd | 6 man/helper.si.Rd |only man/perturb.nu.vector.Rd |only man/pred.smooth.Rd | 3 man/pred.smooth.surv.Rd |only 22 files changed, 550 insertions(+), 109 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-20 dated 2016-09-07 and 0.3-21 dated 2016-10-20
ChangeLog | 30 +++++++++++++++++++++++++++++ DESCRIPTION | 16 +++++++-------- MD5 | 28 ++++++++++++++------------- NAMESPACE | 2 - R/rgeos_misc.R | 41 ++++++++++++++++++++++++++++++++++++++++ R/rgeos_spExtensions_Methods.R | 2 - R/rgeos_topology.R | 6 ++--- configure | 18 ++++++++--------- inst/ChangeLog | 30 +++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 - man/misc-gNearestPoints.Rd |only src/init.c | 3 +- src/rgeos.h | 4 ++- src/rgeos_misc.c | 26 +++++++++++++++++++++++++ tests/testthat/test-linearref.R | 21 ++++++++++++-------- tests/testthat/test-misc.R |only 16 files changed, 183 insertions(+), 46 deletions(-)
Title: Estimating Time-Varying Mixed Graphical Models
Description: Estimation of time-varying Mixed Graphical models and mixed VAR models using L1-regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between mgm versions 1.1-6 dated 2016-06-16 and 1.1-7 dated 2016-10-20
DESCRIPTION | 10 - MD5 | 46 +++-- NAMESPACE | 7 NEWS |only R/RcppExports.R | 2 R/estimation_msg.R |only R/mgmfit.R | 12 - R/mgmfit_core.R | 419 +++++++++++++++++++++++++++++++++++++++------------- R/plot.mgm.R |only R/plot.rs.R |only R/predict.mgm.R | 62 +++++-- R/print.mgm.R | 55 ++++-- R/print.rs.R |only R/rs.mgm.R |only R/startup_msg.R |only R/summary.mgm.R | 154 +++++++++---------- R/summary.rs.R |only R/tv.mgmfit.R | 3 R/tv_var.mgm.R | 4 R/var.mgm.R | 9 - README.md | 30 +-- man/mgmfit.Rd | 4 man/plot.rs.Rd |only man/predict.mgm.Rd | 15 + man/print.rs.Rd |only man/rs.mgm.Rd |only man/summary.mgm.Rd | 3 man/summary.rs.Rd |only man/var.mgm.Rd | 6 src/RcppExports.cpp | 10 - 30 files changed, 581 insertions(+), 270 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is available, as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of R markdown instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.5.0 dated 2016-08-29 and 3.5.1 dated 2016-10-20
lessR-3.5.0/lessR/R/print.outall.R |only lessR-3.5.0/lessR/R/print.outpiece.R |only lessR-3.5.1/lessR/DESCRIPTION | 8 lessR-3.5.1/lessR/MD5 | 72 ++-- lessR-3.5.1/lessR/NAMESPACE | 4 lessR-3.5.1/lessR/NEWS | 32 + lessR-3.5.1/lessR/R/ANOVAz1.R | 8 lessR-3.5.1/lessR/R/Help.R | 2 lessR-3.5.1/lessR/R/LineChart.R | 19 - lessR-3.5.1/lessR/R/Plot.R | 507 ++++++++++++++++------------- lessR-3.5.1/lessR/R/Regression.R | 2 lessR-3.5.1/lessR/R/bx.zmain.R | 7 lessR-3.5.1/lessR/R/corScree.R | 18 - lessR-3.5.1/lessR/R/cr.data.frame.R | 4 lessR-3.5.1/lessR/R/details.R | 2 lessR-3.5.1/lessR/R/dp.zmain.R | 117 ++++-- lessR-3.5.1/lessR/R/dpmat.zmain.R | 2 lessR-3.5.1/lessR/R/hst.zmain.R | 14 lessR-3.5.1/lessR/R/lc.zmain.R | 48 +- lessR-3.5.1/lessR/R/logit.z4Pred.R | 10 lessR-3.5.1/lessR/R/plt.zmain.R | 451 ++++++++++++++----------- lessR-3.5.1/lessR/R/print.outall.r |only lessR-3.5.1/lessR/R/print.outpiece.r |only lessR-3.5.1/lessR/R/reg.z1anvBasic.R | 2 lessR-3.5.1/lessR/R/reg.z1modelBasic.R | 2 lessR-3.5.1/lessR/R/reg.z2Relations.R | 2 lessR-3.5.1/lessR/R/reg.z3dnResidual.R | 6 lessR-3.5.1/lessR/R/reg.z3resfitResidual.R | 14 lessR-3.5.1/lessR/R/reg.z3txtResidual.R | 4 lessR-3.5.1/lessR/R/reg.z4Pred.R | 2 lessR-3.5.1/lessR/R/reg.z5Plot.R | 16 lessR-3.5.1/lessR/R/tt.z1group.R | 8 lessR-3.5.1/lessR/R/tt.z2group.R | 16 lessR-3.5.1/lessR/R/ttp2zgraph.R | 8 lessR-3.5.1/lessR/R/zzz.R | 89 ++--- lessR-3.5.1/lessR/inst/CITATION | 4 lessR-3.5.1/lessR/man/Plot.Rd | 200 +++++++---- lessR-3.5.1/lessR/man/Read.Rd | 2 lessR-3.5.1/lessR/man/ttest.Rd | 2 39 files changed, 984 insertions(+), 720 deletions(-)
Title: Group Sorted L1 Penalized Estimation
Description: Group SLOPE is a penalized linear regression method that is used
for adaptive selection of groups of significant predictors in a
high-dimensional linear model.
The Group SLOPE method can control the (group) false discovery rate at a
user-specified level (i.e., control the expected proportion of irrelevant
among all selected groups of predictors).
Author: Alexej Gossmann [aut, cre],
Damian Brzyski [aut],
Weijie Su [aut],
Malgorzata Bogdan [aut],
Ewout van den Berg [ctb] (A part of the optimization code was obtained
from http://statweb.stanford.edu/~candes/SortedL1/software.html
under GNU GPL-3),
Emmanuel Candes [ctb] (A part of the optimization code was obtained
from http://statweb.stanford.edu/~candes/SortedL1/software.html
under GNU GPL-3)
Maintainer: Alexej Gossmann <alexej.go@googlemail.com>
Diff between grpSLOPE versions 0.1.0 dated 2016-04-24 and 0.2.0 dated 2016-10-20
grpSLOPE-0.1.0/grpSLOPE/R/RcppExports.R |only grpSLOPE-0.1.0/grpSLOPE/man/lambdaChiMCAdjustment.Rd |only grpSLOPE-0.1.0/grpSLOPE/man/lambdaMC.Rd |only grpSLOPE-0.1.0/grpSLOPE/man/proxSortedL1.Rd |only grpSLOPE-0.1.0/grpSLOPE/src |only grpSLOPE-0.2.0/grpSLOPE/DESCRIPTION | 13 grpSLOPE-0.2.0/grpSLOPE/MD5 | 46 grpSLOPE-0.2.0/grpSLOPE/NAMESPACE | 11 grpSLOPE-0.2.0/grpSLOPE/R/generics.R |only grpSLOPE-0.2.0/grpSLOPE/R/grpslope.R | 460 ++++----- grpSLOPE-0.2.0/grpSLOPE/R/lambda_seq.R | 136 -- grpSLOPE-0.2.0/grpSLOPE/README.md | 36 grpSLOPE-0.2.0/grpSLOPE/build/vignette.rds |binary grpSLOPE-0.2.0/grpSLOPE/inst/doc/basic-usage.R | 51 - grpSLOPE-0.2.0/grpSLOPE/inst/doc/basic-usage.Rmd | 138 +- grpSLOPE-0.2.0/grpSLOPE/inst/doc/basic-usage.html | 370 ++++--- grpSLOPE-0.2.0/grpSLOPE/man/coef.grpSLOPE.Rd |only grpSLOPE-0.2.0/grpSLOPE/man/grpSLOPE.Rd | 74 - grpSLOPE-0.2.0/grpSLOPE/man/lambdaGroupSLOPE.Rd | 90 - grpSLOPE-0.2.0/grpSLOPE/man/predict.grpSLOPE.Rd |only grpSLOPE-0.2.0/grpSLOPE/man/proxGroupSortedL1.Rd | 19 grpSLOPE-0.2.0/grpSLOPE/man/proximalGradientSolverGroupSLOPE.Rd | 9 grpSLOPE-0.2.0/grpSLOPE/man/sigma.grpSLOPE.Rd |only grpSLOPE-0.2.0/grpSLOPE/tests/testthat/test_generics.R |only grpSLOPE-0.2.0/grpSLOPE/tests/testthat/test_grpSLOPE.R | 485 +++++++++- grpSLOPE-0.2.0/grpSLOPE/tests/testthat/test_lambda.R | 50 - grpSLOPE-0.2.0/grpSLOPE/tests/testthat/test_proximal_gradient_method.R | 35 grpSLOPE-0.2.0/grpSLOPE/vignettes/basic-usage.Rmd | 138 +- 28 files changed, 1253 insertions(+), 908 deletions(-)
Title: Repulsive Text and Label Geoms for 'ggplot2'
Description:
Provides text and label geoms for 'ggplot2' that help to avoid overlapping
text labels. Labels repel away from each other and away from the data
points.
Author: Kamil Slowikowski [aut, cre]
Maintainer: Kamil Slowikowski <kslowikowski@fas.harvard.edu>
Diff between ggrepel versions 0.5 dated 2016-02-08 and 0.6.3 dated 2016-10-20
DESCRIPTION | 8 MD5 | 44 - NEWS | 51 + R/RcppExports.R | 31 R/geom-label-repel.R | 127 ++- R/geom-text-repel.R | 192 ++++- README.md | 8 inst/doc/ggrepel.Rmd | 112 ++- inst/doc/ggrepel.html | 216 ++++-- man/geom_text_repel.Rd | 62 + src/RcppExports.cpp | 56 - src/repel_boxes.cpp | 336 +++++----- vignettes/Makefile | 2 vignettes/figures/ggrepel/animated.gif |binary vignettes/figures/ggrepel/geom_label_repel-1.png |binary vignettes/figures/ggrepel/geom_text-1.png |binary vignettes/figures/ggrepel/geom_text_repel-1.png |binary vignettes/figures/ggrepel/geom_text_repel_empty_string-1.png |only vignettes/figures/ggrepel/geom_text_repel_options-1.png |binary vignettes/figures/ggrepel/geom_text_repel_point_padding_na-1.png |only vignettes/figures/ggrepel/line_plot-1.png |binary vignettes/figures/ggrepel/volcano-1.png |binary vignettes/ggrepel.Rmd | 112 ++- vignettes/ggrepel.md | 122 ++- 24 files changed, 991 insertions(+), 488 deletions(-)
Title: Datasets from Hosmer, Lemeshow and Sturdivant, "Applied Logistic
Regression" (3rd Ed., 2013)
Description: An unofficial companion to "Applied
Logistic Regression" by D.W. Hosmer, S. Lemeshow and
R.X. Sturdivant (3rd ed., 2013) containing the dataset used in the book.
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Diff between aplore3 versions 0.7 dated 2014-12-21 and 0.9 dated 2016-10-20
DESCRIPTION | 19 ++++++++------- MD5 | 52 +++++++++++++++++++++--------------------- R/aplore3.R | 12 ++++----- R/icu.R | 2 - README.md | 22 ++++++++--------- build/vignette.rds |binary data/icu.rda |binary inst/doc/aplore3-examples.pdf |binary man/aplore3.Rd | 15 ++++++------ man/aps.Rd | 8 ++++-- man/burn1000.Rd | 3 +- man/burn13m.Rd | 3 +- man/burn_eval_1.Rd | 3 +- man/burn_eval_2.Rd | 3 +- man/chdage.Rd | 5 ++-- man/glow11m.Rd | 3 +- man/glow500.Rd | 3 +- man/glow_bonemed.Rd | 3 +- man/glow_mis_comp.Rd | 3 +- man/glow_mis_wmissing.Rd | 3 +- man/glow_rand.Rd | 3 +- man/icu.Rd | 5 ++-- man/lowbwt.Rd | 5 ++-- man/myopia.Rd | 3 +- man/nhanes.Rd | 3 +- man/polypharm.Rd | 3 +- man/scale_example.Rd | 3 +- 27 files changed, 103 insertions(+), 84 deletions(-)
Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files, sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.matlab versions 3.6.0 dated 2016-07-05 and 3.6.1 dated 2016-10-19
DESCRIPTION | 8 ++++---- MD5 | 15 +++++++++------ NEWS | 8 ++++++++ R/readMat.R | 26 ++++++++++++++++++-------- R/writeMat.R | 2 +- inst/mat-files/Matrix-v6.mat |only inst/mat-files/Matrix-v7.3.mat |only inst/mat-files/Matrix-v7.mat |only man/R.matlab-package.Rd | 2 +- tests/readMat.R | 13 +++++++++++++ 10 files changed, 54 insertions(+), 20 deletions(-)
Title: Draws Diagrams Useful for Checking Latent Scales
Description: A graph
proposed by Rosenbaum is useful
for checking some properties of various
sorts of latent scale, this program generates commands
to obtain the graph using 'dot' from 'graphviz'.
Author: Michael Dewey
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between latdiag versions 0.2-2 dated 2016-03-14 and 0.2-3 dated 2016-10-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ inst/CITATION | 6 +++--- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Knowledge Discovery by Accuracy Maximization
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction from noisy and high-dimensional data.
Author: Stefano Cacciatore, Leonardo Tenori, Claudio Luchinat, Phillip R. Bennett, and David A. MacIntyre
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Diff between KODAMA versions 1.0 dated 2016-10-12 and 1.1 dated 2016-10-19
DESCRIPTION | 8 MD5 | 30 +-- R/KOD.R | 38 +-- build/vignette.rds |binary inst/doc/KODAMA.Rmd | 4 inst/doc/KODAMA.pdf | 498 +++++++++++++++++++++++++-------------------------- man/core_cpp.Rd | 3 man/k.test.Rd | 2 man/knn.kodama.Rd | 1 man/loads.Rd | 2 man/mcplot.Rd | 6 man/pls.kodama.Rd | 1 src/RcppExports.cpp | 4 src/kd_split.cpp | 6 src/prova.cpp | 355 ++++++++++++------------------------ vignettes/KODAMA.Rmd | 4 16 files changed, 429 insertions(+), 533 deletions(-)
Title: Joint Mean-Covariance Models using 'Armadillo' and S4
Description: Fit joint mean-covariance models for longitudinal data. The models
and their components are represented using S4 classes and methods. The core
computational algorithms are implemented using the 'Armadillo' C++ library
for numerical linear algebra and 'RcppArmadillo' glue.
Author: Jianxin Pan [aut, cre],
Yi Pan [aut]
Maintainer: Jianxin Pan <Jianxin.Pan@manchester.ac.uk>
Diff between jmcm versions 0.1.6.0 dated 2016-08-29 and 0.1.7.0 dated 2016-10-19
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/RcppExports.R | 20 +++++++++++++------- R/jmcm.R | 6 +++--- man/acd_estimation.Rd | 8 ++++++-- man/hpc_estimation.Rd | 8 ++++++-- man/mcd_estimation.Rd | 8 ++++++-- src/RcppExports.cpp | 44 +++++++++++++++++++++++++------------------- src/acd.cpp | 9 +++++++-- src/acd.h | 8 ++++++++ src/external.cpp | 46 ++++++++++++++++++++++++++++++++++++++-------- src/hpc.cpp | 9 +++++++-- src/hpc.h | 8 ++++++++ src/mcd.cpp | 9 +++++++-- src/mcd.h | 8 ++++++++ 15 files changed, 159 insertions(+), 66 deletions(-)
Title: Boosting Methods for 'GAMLSS'
Description: Boosting models for fitting generalized additive models for
location, shape and scale ('GAMLSS') to potentially high dimensional
data.
Author: Benjamin Hofner, Andreas Mayr, Nora Fenske, Matthias Schmid
Maintainer: Benjamin Hofner <benjamin.hofner@fau.de>
Diff between gamboostLSS versions 1.2-1 dated 2016-03-11 and 1.2-2 dated 2016-10-19
gamboostLSS-1.2-1/gamboostLSS/vignettes/cvrisk |only gamboostLSS-1.2-2/gamboostLSS/DESCRIPTION | 10 - gamboostLSS-1.2-2/gamboostLSS/MD5 | 38 ++--- gamboostLSS-1.2-2/gamboostLSS/build/vignette.rds |binary gamboostLSS-1.2-2/gamboostLSS/data/india.RData |binary gamboostLSS-1.2-2/gamboostLSS/data/india.bnd.RData |binary gamboostLSS-1.2-2/gamboostLSS/inst/CITATION | 32 ++-- gamboostLSS-1.2-2/gamboostLSS/inst/NEWS.Rd | 10 + gamboostLSS-1.2-2/gamboostLSS/inst/doc/gamboostLSS_Tutorial.R | 71 +++------- gamboostLSS-1.2-2/gamboostLSS/inst/doc/gamboostLSS_Tutorial.Rnw | 39 +++-- gamboostLSS-1.2-2/gamboostLSS/inst/doc/gamboostLSS_Tutorial.pdf |binary gamboostLSS-1.2-2/gamboostLSS/man/as.families.Rd | 6 gamboostLSS-1.2-2/gamboostLSS/man/cvrisk.Rd | 6 gamboostLSS-1.2-2/gamboostLSS/man/families.Rd | 2 gamboostLSS-1.2-2/gamboostLSS/man/gamboostLSS-package.Rd | 8 - gamboostLSS-1.2-2/gamboostLSS/man/mboostLSS.Rd | 6 gamboostLSS-1.2-2/gamboostLSS/man/methods.Rd | 6 gamboostLSS-1.2-2/gamboostLSS/man/weighted_median.Rd | 7 gamboostLSS-1.2-2/gamboostLSS/vignettes/bib.bib | 8 - gamboostLSS-1.2-2/gamboostLSS/vignettes/fig-crossvalidation.pdf |only gamboostLSS-1.2-2/gamboostLSS/vignettes/gamboostLSS_Tutorial.Rnw | 39 +++-- 21 files changed, 153 insertions(+), 135 deletions(-)
Title: Logistic Regression
Description: The BayesLogit package does posterior simulation for binomial and
multinomial logistic regression using the Polya-Gamma latent variable
technique. This method is fully automatic, exact, and fast. A routine to
efficiently sample from the Polya-Gamma class of distributions is included.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle <jesse.windle@gmail.com>
Diff between BayesLogit versions 0.5.1 dated 2014-07-21 and 0.6 dated 2016-10-19
DESCRIPTION | 8 +++--- MD5 | 36 ++++++++++++++--------------- NAMESPACE | 5 +++- R/LogitWrapper.R | 3 +- man/logit.combine.Rd | 3 +- src/CUBS_update.cpp | 6 ++++ src/DynExpFamMH.cpp | 6 ++++ src/FSF_nmix.cpp | 6 ++++ src/InvertY.cpp | 7 +++++ src/LogitWrapper.cpp | 6 ++++ src/Matrix.h | 27 +++++++++++++++++++++ src/MatrixFrame.cpp | 3 ++ src/MatrixFrame.h | 62 ++++++++++++++++++++++++++++++++++++++++++++++++-- src/PolyaGamma.cpp | 24 +++++++++++++++++++ src/PolyaGamma.h | 2 - src/PolyaGammaAlt.cpp | 6 ++++ src/PolyaGammaSP.cpp | 6 ++++ src/RNG.cpp | 7 +++++ src/RRNG.cpp | 7 +++++ 19 files changed, 202 insertions(+), 28 deletions(-)
Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between Barnard versions 1.6 dated 2015-10-20 and 1.7 dated 2016-10-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Barnard.c | 5 +++-- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>
Diff between surveyplanning versions 2.0 dated 2016-08-01 and 2.2 dated 2016-10-19
DESCRIPTION | 8 - MD5 | 14 +- R/dom_optimal_allocation.R | 226 ++++++++++++++++++------------------------ R/expvar.R | 87 ++++++++-------- inst/CITATION | 4 inst/NEWS | 4 man/expvar.Rd | 2 man/surveyplanning-package.Rd | 4 8 files changed, 169 insertions(+), 180 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: Hierarchical Latent Space Network Model (HLSM)
Description: R-package to implement Hierarchical Latent Space Network Model (HLSM) for ensemble of networks as described in Sweet et. al. (2012).<DOI:10.3102/1076998612458702>.
Author: Samrachana Adhikari, Brian Junker, Tracy Sweet, Andrew C. Thomas
Maintainer: Samrachana Adhikari <asam.cmu@gmail.com>
Diff between HLSM versions 0.5 dated 2015-11-15 and 0.6 dated 2016-10-19
DESCRIPTION | 12 +++---- MD5 | 16 ++++----- NAMESPACE | 17 +++------- R/HLSM_run.R | 68 +++++++++++++++++++++++++++-------------- R/HLSM_run_fixedEF.R | 76 ++++++++++++++++++++++++++++++---------------- R/covFunction.R | 7 +--- demo/HLSM.school.advice.R | 4 -- man/plots.Rd | 23 ------------- src/HLSM.cpp | 46 +++++++++++++++------------ 9 files changed, 141 insertions(+), 128 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-01 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-06-13 1.1.6
2016-05-17 1.1.5
2016-01-08 1.1.4
2015-11-15 1.1.2
2015-07-24 1.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-20 1.2.2
2016-07-18 1.2.0
Title: A Package for Sparse VAR/VECM Estimation
Description: A wrapper for sparse VAR/VECM time series models estimation
using penalties like ENET, SCAD and MCP.
Author: Simone Vazzoler [aut, cre],
Lorenzo Frattarolo [aut],
Monica Billio [aut]
Maintainer: Simone Vazzoler <svazzole@gmail.com>
Diff between sparsevar versions 0.0.7 dated 2016-07-06 and 0.0.9 dated 2016-10-19
sparsevar-0.0.7/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_7ce18901aee92ab7c7661d60f1ba4e1b.RData |only sparsevar-0.0.7/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_7ce18901aee92ab7c7661d60f1ba4e1b.rdb |only sparsevar-0.0.7/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_7ce18901aee92ab7c7661d60f1ba4e1b.rdx |only sparsevar-0.0.9/sparsevar/DESCRIPTION | 12 sparsevar-0.0.9/sparsevar/MD5 | 52 - sparsevar-0.0.9/sparsevar/NAMESPACE | 2 sparsevar-0.0.9/sparsevar/NEWS.md | 7 sparsevar-0.0.9/sparsevar/R/createSparseMatrix.R | 75 -- sparsevar-0.0.9/sparsevar/R/fitVAR.R | 172 +++-- sparsevar-0.0.9/sparsevar/R/fitVECM.R | 15 sparsevar-0.0.9/sparsevar/R/simulateVAR.R | 86 +- sparsevar-0.0.9/sparsevar/R/timeSlice.R | 218 ++++--- sparsevar-0.0.9/sparsevar/R/utilsVAR.R | 311 ++++++---- sparsevar-0.0.9/sparsevar/README.md | 27 sparsevar-0.0.9/sparsevar/inst/doc/using.R | 10 sparsevar-0.0.9/sparsevar/inst/doc/using.Rmd | 31 sparsevar-0.0.9/sparsevar/inst/doc/using.pdf |binary sparsevar-0.0.9/sparsevar/man/computeForecasts.Rd |only sparsevar-0.0.9/sparsevar/man/createSparseMatrix.Rd | 9 sparsevar-0.0.9/sparsevar/man/fitVAR.Rd | 12 sparsevar-0.0.9/sparsevar/man/informCrit.Rd |only sparsevar-0.0.9/sparsevar/man/simulateVAR.Rd | 6 sparsevar-0.0.9/sparsevar/man/testGranger.Rd | 2 sparsevar-0.0.9/sparsevar/vignettes/using.Rmd | 31 sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_3875fca48dd018157a6c4a96b6a44b9a.RData |only sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_3875fca48dd018157a6c4a96b6a44b9a.rdb |only sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_3875fca48dd018157a6c4a96b6a44b9a.rdx |only sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-4_3897a5d4efc534c41ac499bc2c9439b6.rdb |binary sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-4_3897a5d4efc534c41ac499bc2c9439b6.rdx |binary sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-5_18789e32a330a381ec44593f5f2f6b41.rdb |binary sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-5_18789e32a330a381ec44593f5f2f6b41.rdx |binary 31 files changed, 646 insertions(+), 432 deletions(-)
Title: Empirical Bayes Estimation and Inference in R
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models
and some other density estimation and regression methods based on convex
optimization.
Author: Roger Koenker [aut, cre],
Jiaying Gu [ctb],
Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between REBayes versions 0.63 dated 2016-07-21 and 0.68 dated 2016-10-19
REBayes-0.63/REBayes/R/predict.R |only REBayes-0.68/REBayes/DESCRIPTION | 8 +- REBayes-0.68/REBayes/MD5 | 90 ++++++++++++++++-------------- REBayes-0.68/REBayes/NAMESPACE | 6 +- REBayes-0.68/REBayes/R/Bmix.R | 4 + REBayes-0.68/REBayes/R/GLmix.R | 2 REBayes-0.68/REBayes/R/KWDual.R | 2 REBayes-0.68/REBayes/R/Pmix.R | 6 +- REBayes-0.68/REBayes/R/medde.R | 44 +++++++++----- REBayes-0.68/REBayes/R/predict.Bmix.R |only REBayes-0.68/REBayes/R/predict.GLmix.R |only REBayes-0.68/REBayes/R/predict.Pmix.R |only REBayes-0.68/REBayes/build |only REBayes-0.68/REBayes/demo/00Index | 1 REBayes-0.68/REBayes/demo/Silverman.R |only REBayes-0.68/REBayes/inst/ChangeLog | 17 +++++ REBayes-0.68/REBayes/inst/Readme | 9 +-- REBayes-0.68/REBayes/inst/doc/rebayes.R |only REBayes-0.68/REBayes/inst/doc/rebayes.Rnw |only REBayes-0.68/REBayes/inst/doc/rebayes.pdf |binary REBayes-0.68/REBayes/man/Bmix.Rd | 15 +++-- REBayes-0.68/REBayes/man/Cosslett.Rd | 10 +-- REBayes-0.68/REBayes/man/GLmix.Rd | 18 +++--- REBayes-0.68/REBayes/man/GVmix.Rd | 14 ++-- REBayes-0.68/REBayes/man/Gammamix.Rd | 14 ++-- REBayes-0.68/REBayes/man/Gompertzmix.Rd | 16 ++--- REBayes-0.68/REBayes/man/KWDual.Rd | 8 +- REBayes-0.68/REBayes/man/L1norm.Rd | 4 - REBayes-0.68/REBayes/man/Norberg.Rd | 4 - REBayes-0.68/REBayes/man/Pmix.Rd | 22 ++++--- REBayes-0.68/REBayes/man/Rxiv.Rd | 2 REBayes-0.68/REBayes/man/TLmix.Rd | 12 ++-- REBayes-0.68/REBayes/man/Tncpmix.Rd | 18 +++--- REBayes-0.68/REBayes/man/WGLVmix.Rd | 16 ++--- REBayes-0.68/REBayes/man/WGVmix.Rd | 2 REBayes-0.68/REBayes/man/WLVmix.Rd | 18 +++--- REBayes-0.68/REBayes/man/WTLVmix.Rd | 18 +++--- REBayes-0.68/REBayes/man/Weibullmix.Rd | 14 ++-- REBayes-0.68/REBayes/man/bball.Rd | 16 ++--- REBayes-0.68/REBayes/man/flies.Rd | 10 +-- REBayes-0.68/REBayes/man/medde.Rd | 30 ++++++---- REBayes-0.68/REBayes/man/plot.medde.Rd | 2 REBayes-0.68/REBayes/man/predict.Bmix.Rd |only REBayes-0.68/REBayes/man/predict.GLmix.Rd | 14 +++- REBayes-0.68/REBayes/man/predict.Pmix.Rd |only REBayes-0.68/REBayes/man/qmedde.Rd | 2 REBayes-0.68/REBayes/man/rmedde.Rd | 2 REBayes-0.68/REBayes/man/tacks.Rd | 12 ++-- REBayes-0.68/REBayes/man/tannenbaum.Rd | 2 REBayes-0.68/REBayes/man/traprule.Rd | 2 REBayes-0.68/REBayes/vignettes |only 51 files changed, 286 insertions(+), 220 deletions(-)
Title: Population (and Individual) Optimal Experimental Design
Description: Optimal experimental designs for both population and individual
studies based on nonlinear mixed-effect models. Often this is based on a
computation of the Fisher Information Matrix. This package was developed
for pharmacometric problems, and examples and predefined models are available
for these types of systems.
Author: Andrew C. Hooker [aut, cre, trl, cph],
Sebastian Ueckert [aut] (MATLAB version),
Marco Foracchia [aut] (O-Matrix version),
Joakim Nyberg [aut] (MATLAB version),
Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker <andrew.hooker@farmbio.uu.se>
Diff between PopED versions 0.3.0 dated 2015-12-29 and 0.3.1 dated 2016-10-19
PopED-0.3.0/PopED/inst/examples/PopED_output_summary_D_cont_opt_1.txt |only PopED-0.3.0/PopED/inst/examples/ex.1.c.PK.1.comp.oral.md.ODE.R |only PopED-0.3.0/PopED/inst/examples/ex.2.c.warfarin.discrete.optimization.R |only PopED-0.3.0/PopED/inst/examples/ex.2.d.warfarin.ODE.compiled.R |only PopED-0.3.0/PopED/inst/examples/ex.2.e.warfarin.ED.R |only PopED-0.3.0/PopED/inst/examples/ex.2.f.warfarin.Ds.R |only PopED-0.3.0/PopED/inst/examples/ex.8.a.tmdd_qss_one_target.R |only PopED-0.3.0/PopED/inst/examples/ex.8.b.tmdd_qss_one_target_compiled.R |only PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_ED_Laplace_opt.txt |only PopED-0.3.0/PopED/tests/testthat/Rplots.pdf |only PopED-0.3.1/PopED/DESCRIPTION | 18 PopED-0.3.1/PopED/MD5 | 319 ++-- PopED-0.3.1/PopED/NAMESPACE | 5 PopED-0.3.1/PopED/NEWS | 28 PopED-0.3.1/PopED/R/PopED.R | 4 PopED-0.3.1/PopED/R/a_line_search.R | 6 PopED-0.3.1/PopED/R/blockfinal.R | 62 PopED-0.3.1/PopED/R/blockheader.R | 3 PopED-0.3.1/PopED/R/build_sfg.R | 20 PopED-0.3.1/PopED/R/calc_ofv_and_fim.R | 75 PopED-0.3.1/PopED/R/cell.R | 2 PopED-0.3.1/PopED/R/create.poped.database.R | 431 +++-- PopED-0.3.1/PopED/R/create_design.R | 16 PopED-0.3.1/PopED/R/create_design_space.R | 179 ++ PopED-0.3.1/PopED/R/downsizing_general_design.R | 6 PopED-0.3.1/PopED/R/ed_laplace_ofv.R | 181 +- PopED-0.3.1/PopED/R/ed_mftot.R | 33 PopED-0.3.1/PopED/R/evaluate.e.ofv.fim.R | 3 PopED-0.3.1/PopED/R/evaluate_design.R |only PopED-0.3.1/PopED/R/fileparts.R | 2 PopED-0.3.1/PopED/R/fprintf.R | 5 PopED-0.3.1/PopED/R/inv.R | 16 PopED-0.3.1/PopED/R/m1.R | 3 PopED-0.3.1/PopED/R/m3.R | 149 + PopED-0.3.1/PopED/R/mc_mean.R |only PopED-0.3.1/PopED/R/median_hilow_poped.R |only PopED-0.3.1/PopED/R/mf.R | 2 PopED-0.3.1/PopED/R/mf3.R | 8 PopED-0.3.1/PopED/R/mf6.R | 110 - PopED-0.3.1/PopED/R/model_prediction.R | 19 PopED-0.3.1/PopED/R/ofv_criterion.R | 10 PopED-0.3.1/PopED/R/optim_ARS.R | 8 PopED-0.3.1/PopED/R/optim_LS.R | 2 PopED-0.3.1/PopED/R/plot_efficiency_of_windows.R | 184 +- PopED-0.3.1/PopED/R/plot_model_prediction.R | 34 PopED-0.3.1/PopED/R/poped_gui.R |only PopED-0.3.1/PopED/R/poped_optim.R | 479 +++++- PopED-0.3.1/PopED/R/summary.poped_optim.R |only PopED-0.3.1/PopED/R/test_for_zeros.R | 4 PopED-0.3.1/PopED/R/tic.R | 2 PopED-0.3.1/PopED/R/toc.R | 2 PopED-0.3.1/PopED/R/update_designinlist.R | 30 PopED-0.3.1/PopED/R/v.R | 17 PopED-0.3.1/PopED/README.md | 5 PopED-0.3.1/PopED/build |only PopED-0.3.1/PopED/inst/doc |only PopED-0.3.1/PopED/inst/examples/ex.1.a.PK.1.comp.oral.md.intro.R | 82 - PopED-0.3.1/PopED/inst/examples/ex.1.b.PK.1.comp.oral.md.re-parameterize.R | 97 - PopED-0.3.1/PopED/inst/examples/ex.1.c.PK.1.comp.oral.md.ODE.compiled.R |only PopED-0.3.1/PopED/inst/examples/ex.10.PKPD.HCV.compiled.R | 11 PopED-0.3.1/PopED/inst/examples/ex.2.a.warfarin.evaluate.R | 27 PopED-0.3.1/PopED/inst/examples/ex.2.b.warfarin.optimize.R | 100 - PopED-0.3.1/PopED/inst/examples/ex.2.c.warfarin.ODE.compiled.R |only PopED-0.3.1/PopED/inst/examples/ex.2.d.warfarin.ED.R |only PopED-0.3.1/PopED/inst/examples/ex.2.e.warfarin.Ds.R |only PopED-0.3.1/PopED/inst/examples/ex.3.a.PKPD.1.comp.oral.md.imax.D-opt.R | 59 PopED-0.3.1/PopED/inst/examples/ex.3.b.PKPD.1.comp.oral.md.imax.ED-opt.R | 58 PopED-0.3.1/PopED/inst/examples/ex.4.PKPD.1.comp.emax.R | 58 PopED-0.3.1/PopED/inst/examples/ex.5.PD.emax.hill.R | 55 PopED-0.3.1/PopED/inst/examples/ex.6.PK.1.comp.oral.sd.R | 210 -- PopED-0.3.1/PopED/inst/examples/ex.7.PK.1.comp.maturation.R | 151 +- PopED-0.3.1/PopED/inst/examples/ex.8.tmdd_qss_one_target_compiled.R |only PopED-0.3.1/PopED/inst/examples/ex.9.PK.2.comp.oral.md.ode.compiled.R | 96 - PopED-0.3.1/PopED/inst/examples/one_comp_oral_CL.c | 6 PopED-0.3.1/PopED/inst/shinyapp/server.R | 754 +++++++++- PopED-0.3.1/PopED/inst/shinyapp/ui.R | 347 +++- PopED-0.3.1/PopED/man/Doptim.Rd | 4 PopED-0.3.1/PopED/man/Dtrace.Rd | 4 PopED-0.3.1/PopED/man/LEDoptim.Rd | 2 PopED-0.3.1/PopED/man/LinMatrixH.Rd | 5 PopED-0.3.1/PopED/man/LinMatrixL.Rd | 4 PopED-0.3.1/PopED/man/LinMatrixLH.Rd | 5 PopED-0.3.1/PopED/man/LinMatrixL_occ.Rd | 5 PopED-0.3.1/PopED/man/PopED.Rd | 81 - PopED-0.3.1/PopED/man/RS_opt.Rd | 6 PopED-0.3.1/PopED/man/RS_opt_gen.Rd | 5 PopED-0.3.1/PopED/man/a_line_search.Rd | 9 PopED-0.3.1/PopED/man/bfgsb_min.Rd | 4 PopED-0.3.1/PopED/man/blockexp.Rd | 4 PopED-0.3.1/PopED/man/blockfinal.Rd | 6 PopED-0.3.1/PopED/man/blockheader.Rd | 4 PopED-0.3.1/PopED/man/blockopt.Rd | 4 PopED-0.3.1/PopED/man/calc_autofocus.Rd | 4 PopED-0.3.1/PopED/man/calc_ofv_and_fim.Rd | 9 PopED-0.3.1/PopED/man/calc_ofv_and_grad.Rd | 4 PopED-0.3.1/PopED/man/cell.Rd | 2 PopED-0.3.1/PopED/man/create.poped.database.Rd | 313 ++-- PopED-0.3.1/PopED/man/create_design_space.Rd | 31 PopED-0.3.1/PopED/man/downsizing_general_design.Rd | 4 PopED-0.3.1/PopED/man/ed_laplace_ofv.Rd | 53 PopED-0.3.1/PopED/man/ed_mftot.Rd | 6 PopED-0.3.1/PopED/man/efficiency.Rd |only PopED-0.3.1/PopED/man/evaluate.e.ofv.fim.Rd | 19 PopED-0.3.1/PopED/man/evaluate.fim.Rd | 5 PopED-0.3.1/PopED/man/evaluate_design.Rd |only PopED-0.3.1/PopED/man/fileparts.Rd | 2 PopED-0.3.1/PopED/man/get_rse.Rd | 1 PopED-0.3.1/PopED/man/gradf_eps.Rd | 5 PopED-0.3.1/PopED/man/inv.Rd | 6 PopED-0.3.1/PopED/man/log_prior_pdf.Rd | 4 PopED-0.3.1/PopED/man/mc_mean.Rd |only PopED-0.3.1/PopED/man/median_hilow_poped.Rd |only PopED-0.3.1/PopED/man/mf.Rd | 1 PopED-0.3.1/PopED/man/mf3.Rd | 1 PopED-0.3.1/PopED/man/mf5.Rd | 1 PopED-0.3.1/PopED/man/mf6.Rd | 1 PopED-0.3.1/PopED/man/mf7.Rd | 1 PopED-0.3.1/PopED/man/mf8.Rd | 1 PopED-0.3.1/PopED/man/mfea.Rd | 25 PopED-0.3.1/PopED/man/mftot.Rd | 5 PopED-0.3.1/PopED/man/mftot0.Rd | 5 PopED-0.3.1/PopED/man/mftot1.Rd | 5 PopED-0.3.1/PopED/man/mftot2.Rd | 1 PopED-0.3.1/PopED/man/mftot3.Rd | 1 PopED-0.3.1/PopED/man/mftot4.Rd | 5 PopED-0.3.1/PopED/man/mftot5.Rd | 5 PopED-0.3.1/PopED/man/mftot6.Rd | 5 PopED-0.3.1/PopED/man/mftot7.Rd | 5 PopED-0.3.1/PopED/man/model_prediction.Rd | 2 PopED-0.3.1/PopED/man/ofv_criterion.Rd | 5 PopED-0.3.1/PopED/man/ofv_fim.Rd | 7 PopED-0.3.1/PopED/man/optim_ARS.Rd | 2 PopED-0.3.1/PopED/man/optim_LS.Rd | 2 PopED-0.3.1/PopED/man/plot_efficiency_of_windows.Rd | 58 PopED-0.3.1/PopED/man/plot_model_prediction.Rd | 28 PopED-0.3.1/PopED/man/poped_gui.Rd |only PopED-0.3.1/PopED/man/poped_optim.Rd | 127 + PopED-0.3.1/PopED/man/poped_optimize.Rd | 30 PopED-0.3.1/PopED/man/test_for_zeros.Rd | 1 PopED-0.3.1/PopED/man/tic.Rd | 2 PopED-0.3.1/PopED/man/toc.Rd | 2 PopED-0.3.1/PopED/tests/testthat/PopED_output_summary_D_cont_opt_1.txt | 298 +-- PopED-0.3.1/PopED/tests/testthat/PopED_output_summary_RS.txt |only PopED-0.3.1/PopED/tests/testthat/PopED_output_summary_RS_1.txt | 112 - PopED-0.3.1/PopED/tests/testthat/PopED_output_summary_mfea_opt_1.txt | 174 -- PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_LEDoptim.R | 2 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_RS_opt.R | 2 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_RS_opt_gen.R | 5 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_a_line_search.R | 5 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_create_design_space.R | 15 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_ed_laplace_ofv.R | 50 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_evaluate_design.R |only PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_mfea.R | 21 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_ofv_fim.R | 2 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_poped-package.R | 75 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_poped_optim.R | 93 - PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_poped_optimize.R | 26 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_test_for_zeros.R | 1 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/warfarin_optimize.R | 4 PopED-0.3.1/PopED/tests/testthat/helper_options.R | 2 PopED-0.3.1/PopED/tests/testthat/test_E_family.R |only PopED-0.3.1/PopED/tests/testthat/test_create_databases.R | 2 PopED-0.3.1/PopED/tests/testthat/test_evaluate_design.R |only PopED-0.3.1/PopED/tests/testthat/test_examples.R | 52 PopED-0.3.1/PopED/tests/testthat/test_optimization.R | 70 PopED-0.3.1/PopED/vignettes |only 166 files changed, 4134 insertions(+), 2424 deletions(-)
Title: Organic Mass Spectrometry
Description: Organic/biological mass spectrometry data analysis.
Author: Nathan Dodder [cre, aut, cph],
Katharine Mullen [ctb]
Maintainer: Nathan Dodder <ndodder@mail.sdsu.edu>
Diff between OrgMassSpecR versions 0.4-4 dated 2014-05-23 and 0.4-6 dated 2016-10-19
DESCRIPTION | 20 - LICENSE | 4 MD5 | 122 +++++------ NAMESPACE | 47 ++-- R/ConvertConcentration.R | 128 ++++++------ R/ConvertPeptide.R | 156 +++++++-------- R/DeadVolume.R | 14 - R/Digest.R | 262 ++++++++++++------------- R/DrawChromatogram.R | 80 +++---- R/ExchangeableAmides.R | 18 - R/FlowTime.R | 18 - R/FragmentPeptide.R | 312 +++++++++++++++--------------- R/IsotopicDistribution.R | 170 ++++++++-------- R/IsotopicDistributionHDX.R | 228 ++++++++++----------- R/IsotopicDistributionN.R | 236 +++++++++++----------- R/ListFormula.R | 88 ++++---- R/MolecularWeight.R | 72 +++--- R/MonoisotopicMass.R | 78 +++---- R/PeptideSpectrum.R | 206 +++++++++---------- R/ReadMspDirectory.R | 100 ++++----- R/ReadMspFile.R | 58 ++--- R/RetentionIndex.R | 14 - R/SpectrumSimilarity.R | 116 +++++------ R/WriteMspFile.R | 66 +++--- build/vignette.rds |binary data/example.chromatogram.multiple.txt.gz |binary data/example.chromatogram.single.txt.gz |binary data/example.sequence.rda |binary data/example.spectrum.authentic.txt.gz |binary data/example.spectrum.labeled.txt.gz |binary data/example.spectrum.peptide.txt.gz |binary data/example.spectrum.unknown.txt.gz |binary inst/NEWS.Rd | 202 ++++++++++--------- inst/doc/OrgMassSpecR-examples.R | 167 +++++++--------- inst/doc/OrgMassSpecR-examples.Rmd | 308 ++++++++++++++--------------- man/ConvertConcentration.Rd | 94 ++++----- man/ConvertPeptide.Rd | 56 ++--- man/DeadVolume.Rd | 26 +- man/Digest.Rd | 146 +++++++------- man/DrawChromatogram.Rd | 106 +++++----- man/ExchangeableAmides.Rd | 46 ++-- man/FlowTime.Rd | 34 +-- man/FragmentPeptide.Rd | 124 +++++------ man/IsotopicDistribution.Rd | 90 ++++---- man/IsotopicDistributionHDX.Rd | 90 ++++---- man/IsotopicDistributionN.Rd | 164 +++++++-------- man/ListFormula.Rd | 64 +++--- man/MolecularWeight.Rd | 56 ++--- man/MonoisotopicMass.Rd | 122 +++++------ man/OrgMassSpecR-package.Rd | 26 +- man/PeptideSpectrum.Rd | 66 +++--- man/ReadMspDirectory.Rd | 68 +++--- man/ReadMspFile.Rd | 54 ++--- man/RetentionIndex.Rd | 32 +-- man/SpectrumSimilarity.Rd | 84 ++++---- man/WriteMspFile.Rd | 104 +++++----- man/example.chromatogram.single.Rd | 26 +- man/example.sequence.Rd | 18 - man/example.spectrum.labeled.Rd | 24 +- man/example.spectrum.peptide.Rd | 22 +- man/example.spectrum.unknown.Rd | 28 +- vignettes/OrgMassSpecR-examples.Rmd | 308 ++++++++++++++--------------- 62 files changed, 2691 insertions(+), 2677 deletions(-)
Title: Orthogonalizing EM
Description: Solves penalized least squares problems using the orthogonalizing EM algorithm of Xiong et al. (2016) <doi:10.1080/00401706.2015.1054436>. The main fitting function is oem() and the functions cv.oem() and xval.oem() are for cross validation, the latter being an accelerated cross validation function for linear models. The big.oem() function allows for out of memory fitting.
Author: Bin Dai [aut],
Jared Huling [aut, cre],
Yixuan Qiu [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between oem versions 1.02.1 dated 2014-01-06 and 2.0.1 dated 2016-10-19
oem-1.02.1/oem/R/coef.oemfit.R |only oem-1.02.1/oem/R/cv.oemfit.R |only oem-1.02.1/oem/R/getmin.R |only oem-1.02.1/oem/R/lambda.interp.R |only oem-1.02.1/oem/R/plot.oemfit.R |only oem-1.02.1/oem/R/predict.oemfit.R |only oem-1.02.1/oem/R/print.oemfit.R |only oem-1.02.1/oem/data |only oem-1.02.1/oem/man/calHousing.Rd |only oem-1.02.1/oem/man/example9.Rd |only oem-1.02.1/oem/man/oem-package.Rd |only oem-1.02.1/oem/man/oemfit.Rd |only oem-1.02.1/oem/man/plot.oemfit.Rd |only oem-1.02.1/oem/man/predict.oemfit.Rd |only oem-1.02.1/oem/man/print.oemfit.Rd |only oem-1.02.1/oem/src/Makevars00 |only oem-2.0.1/oem/DESCRIPTION | 36 + oem-2.0.1/oem/MD5 | 91 +++- oem-2.0.1/oem/NAMESPACE | 65 ++- oem-2.0.1/oem/R/big_oem.R |only oem-2.0.1/oem/R/cv_oem.R |only oem-2.0.1/oem/R/deprecated_functions.R |only oem-2.0.1/oem/R/methods.R |only oem-2.0.1/oem/R/oem.R | 603 ++++++++++++++++++++++++++---- oem-2.0.1/oem/R/oem_xtx.R |only oem-2.0.1/oem/R/oem_xval.R |only oem-2.0.1/oem/R/utils.R |only oem-2.0.1/oem/README.md |only oem-2.0.1/oem/build |only oem-2.0.1/oem/inst |only oem-2.0.1/oem/man/big.oem.Rd |only oem-2.0.1/oem/man/cv.oem.Rd |only oem-2.0.1/oem/man/deprecated.Rd |only oem-2.0.1/oem/man/logLik.Rd |only oem-2.0.1/oem/man/oem.Rd |only oem-2.0.1/oem/man/oem.xtx.Rd |only oem-2.0.1/oem/man/plot.Rd |only oem-2.0.1/oem/man/predict.cv.oem.Rd |only oem-2.0.1/oem/man/predict.oem.Rd |only oem-2.0.1/oem/man/predict.xval.oem.Rd |only oem-2.0.1/oem/man/print.Rd |only oem-2.0.1/oem/man/summary.Rd |only oem-2.0.1/oem/man/xval.oem.Rd |only oem-2.0.1/oem/src/DataStd.h |only oem-2.0.1/oem/src/Makevars | 9 oem-2.0.1/oem/src/Makevars.win | 14 oem-2.0.1/oem/src/Rutils.cpp |only oem-2.0.1/oem/src/Rutils.h |only oem-2.0.1/oem/src/Spectra |only oem-2.0.1/oem/src/lanczos.cpp |only oem-2.0.1/oem/src/lanczos.h |only oem-2.0.1/oem/src/oem_base.h |only oem-2.0.1/oem/src/oem_big.cpp |only oem-2.0.1/oem/src/oem_big.h |only oem-2.0.1/oem/src/oem_dense.cpp |only oem-2.0.1/oem/src/oem_dense.h |only oem-2.0.1/oem/src/oem_logistic_dense.cpp |only oem-2.0.1/oem/src/oem_logistic_dense.h |only oem-2.0.1/oem/src/oem_logistic_sparse.cpp |only oem-2.0.1/oem/src/oem_logistic_sparse.h |only oem-2.0.1/oem/src/oem_sparse.cpp |only oem-2.0.1/oem/src/oem_sparse.h |only oem-2.0.1/oem/src/oem_xtx.cpp |only oem-2.0.1/oem/src/oem_xtx.h |only oem-2.0.1/oem/src/oem_xval_dense.cpp |only oem-2.0.1/oem/src/oem_xval_dense.h |only oem-2.0.1/oem/src/utils.cpp |only oem-2.0.1/oem/src/utils.h |only oem-2.0.1/oem/vignettes |only 69 files changed, 689 insertions(+), 129 deletions(-)
Title: Omics Data Integration Project
Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: horizontal integration with regularised Generalised Canonical Correlation Analysis and vertical integration with multi-group Partial Least Squares.
Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>
Diff between mixOmics versions 6.1.0 dated 2016-09-04 and 6.1.1 dated 2016-10-19
DESCRIPTION | 8 MD5 | 161 +++--- NAMESPACE | 4 NEWS | 23 R/AUC_ROC.R | 2 R/MCVfold.R | 144 +++++- R/block.pls.R | 5 R/block.plsda.R | 7 R/block.spls.R | 6 R/block.splsda.R | 6 R/check_entry.R | 14 R/circosPlot.R | 3 R/internal_graphic.perf.R | 31 - R/internal_graphicModule.R | 23 R/internal_mint.block.R | 6 R/internal_mint.block_helpers.R | 33 + R/internal_predict.DA.R | 59 +- R/internal_wrapper.mint.R | 2 R/internal_wrapper.mint.block.R | 2 R/mint.pca.R |only R/perf.R | 35 + R/perf.diablo.R | 931 ++++++++++++++++++++++++---------------- R/plot.perf.R | 65 ++ R/plot.tune.R | 21 R/plotIndiv.R | 101 +++- R/plotIndiv.mint.R | 17 R/plotIndiv.pca.R | 3 R/plotIndiv.pls.R | 5 R/plotIndiv.sgcca.R | 5 R/plotLoadings.R | 2 R/plotLoadings.mint.splsda.R | 2 R/plotLoadings.pca.R |only R/plotLoadings.spls.R | 1 R/plotVar.R | 23 R/plsda.R | 2 R/predict.mint.block.pls.R | 73 ++- R/roc_utils.R | 3 R/selectVar.R | 8 R/splsda.R | 2 R/tune.diablo.R | 209 ++++++-- R/tune.splsda.R | 26 - R/wrapper.rgcca.R | 2 R/wrapper.sgcca.R | 4 data/breast.TCGA.rda |binary data/breast.tumors.rda |binary data/linnerud.rda |binary data/liver.toxicity.rda |binary data/multidrug.rda |binary data/nutrimouse.rda |binary data/srbct.rda |binary data/stemcells.rda |binary data/vac18.rda |binary data/vac18.simulated.rda |binary data/yeast.rda |binary man/auroc.Rd | 6 man/block.pls.Rd | 4 man/block.plsda.Rd | 4 man/block.spls.Rd | 4 man/block.splsda.Rd | 8 man/cim.Rd | 2 man/circosPlot.Rd | 2 man/mint.block.pls.Rd | 4 man/mint.block.plsda.Rd | 4 man/mint.block.spls.Rd | 4 man/mint.block.splsda.Rd | 4 man/mint.pca.Rd |only man/mint.pls.Rd | 2 man/mint.plsda.Rd | 2 man/mint.spls.Rd | 2 man/mint.splsda.Rd | 2 man/perf.Rd | 38 + man/plot.perf.Rd | 23 man/plot.tune.Rd | 6 man/plotContrib.Rd | 31 - man/plotIndiv.Rd | 8 man/plotLoadings.Rd | 10 man/plotVar.Rd | 2 man/predict.Rd | 26 - man/selectVar.Rd | 14 man/tune.block.splsda.Rd | 11 man/tune.splsda.Rd | 6 man/wrapper.rgcca.Rd | 6 man/wrapper.sgcca.Rd | 8 83 files changed, 1541 insertions(+), 781 deletions(-)
Title: A Lending Club API Wrapper
Description: Functions to access Lending Club's API and assist the investor manage
their account. Lending Club is a peer-to-peer lending service where loans are
broken up into $25 notes that investors buy with the expectation of earning a
return on the interest. You can learn more about the API here:
<http://www.lendingclub.com/developers/lc-api.action>.
Author: Ryan Kuhn
Maintainer: Ryan Kuhn <kuhnrl30@gmail.com>
Diff between LendingClub versions 0.1.2 dated 2016-09-26 and 1.0.0 dated 2016-10-19
LendingClub-0.1.2/LendingClub/R/BuySecondary.R |only LendingClub-0.1.2/LendingClub/man/BuySecondary.Rd |only LendingClub-0.1.2/LendingClub/man/DetailedNotesOwned.Rd |only LendingClub-0.1.2/LendingClub/man/FolioBuy.Rd |only LendingClub-1.0.0/LendingClub/DESCRIPTION | 19 +-- LendingClub-1.0.0/LendingClub/MD5 | 82 ++++++------- LendingClub-1.0.0/LendingClub/NAMESPACE | 2 LendingClub-1.0.0/LendingClub/R/AccountSummary.R | 5 LendingClub-1.0.0/LendingClub/R/AddFunds.R | 10 - LendingClub-1.0.0/LendingClub/R/AvailableCash.R | 5 LendingClub-1.0.0/LendingClub/R/CancelTransfer.R | 4 LendingClub-1.0.0/LendingClub/R/CleanData.R | 23 ++- LendingClub-1.0.0/LendingClub/R/CreatePortfolio.R | 4 LendingClub-1.0.0/LendingClub/R/DetailedNotesOwned.R | 8 - LendingClub-1.0.0/LendingClub/R/FolioBuy.R | 25 +-- LendingClub-1.0.0/LendingClub/R/FolioSell.R | 17 +- LendingClub-1.0.0/LendingClub/R/LC_GET.R | 3 LendingClub-1.0.0/LendingClub/R/LC_POST.R | 1 LendingClub-1.0.0/LendingClub/R/ListedLoans.R | 15 +- LendingClub-1.0.0/LendingClub/R/MakeCredential.R | 13 +- LendingClub-1.0.0/LendingClub/R/MakeURL.R | 1 LendingClub-1.0.0/LendingClub/R/NotesOwned.R | 18 ++ LendingClub-1.0.0/LendingClub/R/Print.R | 2 LendingClub-1.0.0/LendingClub/R/SubmitOrder.R | 13 +- LendingClub-1.0.0/LendingClub/R/WithdrawFunds.R | 2 LendingClub-1.0.0/LendingClub/README.md | 48 +++++-- LendingClub-1.0.0/LendingClub/build/vignette.rds |binary LendingClub-1.0.0/LendingClub/man/AccountSummary.Rd | 4 LendingClub-1.0.0/LendingClub/man/AddFunds.Rd | 10 - LendingClub-1.0.0/LendingClub/man/AvailableCash.Rd | 4 LendingClub-1.0.0/LendingClub/man/CancelTransfer.Rd | 4 LendingClub-1.0.0/LendingClub/man/CleanData.Rd | 1 LendingClub-1.0.0/LendingClub/man/CreatePortfolio.Rd | 4 LendingClub-1.0.0/LendingClub/man/FolioSell.Rd | 24 ++- LendingClub-1.0.0/LendingClub/man/LC_GET.Rd | 1 LendingClub-1.0.0/LendingClub/man/LC_POST.Rd | 1 LendingClub-1.0.0/LendingClub/man/ListedLoans.Rd | 8 + LendingClub-1.0.0/LendingClub/man/MakeCredential.Rd | 15 ++ LendingClub-1.0.0/LendingClub/man/MakeURL.Rd | 1 LendingClub-1.0.0/LendingClub/man/NotesOwned.Rd | 19 ++- LendingClub-1.0.0/LendingClub/man/SubmitOrder.Rd | 12 + LendingClub-1.0.0/LendingClub/man/WithdrawFunds.Rd | 2 LendingClub-1.0.0/LendingClub/man/print.LendingClub_api.Rd | 1 LendingClub-1.0.0/LendingClub/vignettes/LendingClub.Rmd | 2 44 files changed, 263 insertions(+), 170 deletions(-)
Title: Advanced Tables for Markdown/HTML
Description: Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While allowing
advanced layout, the underlying css-structure is simple in order to maximize
compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package
also contains a few text formatting functions that help outputting text
compatible with HTML/'LaTeX'.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between htmlTable versions 1.6 dated 2016-07-24 and 1.7 dated 2016-10-19
DESCRIPTION | 8 MD5 | 140 NAMESPACE | 73 NEWS | 155 R/data-SCB.R | 28 R/deprecated.R | 78 R/htmlTable.R | 2168 +- R/htmlTable_helpers.R | 1958 +- R/htmlTable_render.R | 512 R/interactiveTable.R | 474 R/txtFrmt.R | 590 README.md | 2358 +- build/vignette.rds |binary inst/doc/general.R | 342 inst/doc/general.Rmd | 634 inst/doc/general.html | 8356 ++++----- inst/doc/tables.R | 450 inst/doc/tables.Rmd | 830 inst/doc/tables.html |20466 ++++++++++++------------ inst/examples/data-SCB_example.R | 60 inst/examples/htmlTable_example.R | 106 inst/examples/interactiveTable_example.R | 38 inst/html_components/button.html | 4 inst/javascript/button.js | 48 inst/javascript/toggler.js | 80 man/SCB.Rd | 104 man/htmlTable.Rd | 772 man/interactiveTable.Rd | 152 man/outputInt.Rd | 40 man/prAddCells.Rd | 104 man/prAddSemicolon2StrEnd.Rd | 56 man/prAttr4RgroupAdd.Rd | 46 man/prConvertDfFactors.Rd | 38 man/prGetAlign.Rd | 46 man/prGetCgroupHeader.Rd | 148 man/prGetRgroupLine.Rd | 108 man/prGetRowlabelPos.Rd | 76 man/prGetScriptString.Rd | 40 man/prGetStyle.Rd | 68 man/prGetThead.Rd | 188 man/prMergeClr.Rd | 46 man/prPrepareAlign.Rd | 86 man/prPrepareCgroup.Rd | 90 man/prPrepareColors.Rd | 50 man/prPrepareCss.Rd | 68 man/prSkipRownames.Rd | 40 man/prTblNo.Rd | 64 man/pvalueFormatter.Rd | 38 man/splitLines4Table.Rd | 38 man/tblNoLast.Rd | 52 man/tblNoNext.Rd | 52 man/txtInt.Rd | 72 man/txtMergeLines.Rd | 78 man/txtPval.Rd | 98 man/txtRound.Rd | 114 tests/testInteractive.R | 54 tests/testthat.R | 6 tests/testthat/test-htmlTable.R | 690 tests/testthat/test-htmlTable_cgroup.R | 228 tests/testthat/test-htmlTable_dates.R |only tests/testthat/test-htmlTable_rgroup_tspanner.R | 462 tests/testthat/test-htmlTable_total.R | 118 tests/testthat/test-interactiveTable.R | 632 tests/testthat/test-txtFrmt.R | 292 tests/testthat/test-txtMergeLines.R | 48 tests/visual_tests/htmlTable_vtests.R | 230 tests/visual_tests/pandoc_test.Rmd | 58 tests/visual_tests/word_test.Rmd | 84 tests/visual_tests/word_test.html |only vignettes/custom.css | 324 vignettes/general.Rmd | 634 vignettes/tables.Rmd | 830 72 files changed, 23884 insertions(+), 23734 deletions(-)
Title: Extra Additive Terms for GAMLSS Models
Description: Interface for extra smooth functions including tensor products, neural networks and decision trees.
Author: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>, Bob Rigby, Vlasios Voudouris, Daniil Kiose
Maintainer: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>
Diff between gamlss.add versions 4.3-4 dated 2015-07-17 and 5.0-1 dated 2016-10-19
gamlss.add-4.3-4/gamlss.add/R/gam_gamlss.R |only gamlss.add-5.0-1/gamlss.add/DESCRIPTION | 14 +- gamlss.add-5.0-1/gamlss.add/MD5 | 33 +++--- gamlss.add-5.0-1/gamlss.add/NAMESPACE | 104 ++++++++++----------- gamlss.add-5.0-1/gamlss.add/R/ba.R |only gamlss.add-5.0-1/gamlss.add/R/freeKnots-18-06-13.R | 6 - gamlss.add-5.0-1/gamlss.add/R/ga_new.R |only gamlss.add-5.0-1/gamlss.add/man/blag.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/fitFixedKnots.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/fk.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/ga.Rd | 85 +++++++++-------- gamlss.add-5.0-1/gamlss.add/man/gamlss.fk.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/gamlss.ga.Rd | 12 +- gamlss.add-5.0-1/gamlss.add/man/gamlss.nn.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/la.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/nn.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/penLags.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/plotNN.Rd | 4 gamlss.add-5.0-1/gamlss.add/man/tr.Rd | 9 + 19 files changed, 150 insertions(+), 133 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.9.4 dated 2016-07-25 and 2.10.3 dated 2016-10-19
frailtypack-2.10.3/frailtypack/DESCRIPTION | 10 frailtypack-2.10.3/frailtypack/MD5 | 171 frailtypack-2.10.3/frailtypack/NAMESPACE | 3 frailtypack-2.10.3/frailtypack/NEWS | 14 frailtypack-2.10.3/frailtypack/R/additivePenal.R | 21 frailtypack-2.10.3/frailtypack/R/frailtyPenal.R | 20 frailtypack-2.10.3/frailtypack/R/longiPenal.R | 97 frailtypack-2.10.3/frailtypack/R/plot.frailtyPenal.R | 90 frailtypack-2.10.3/frailtypack/R/plot.predJoint.R | 94 frailtypack-2.10.3/frailtypack/R/prediction.R | 2181 +-- frailtypack-2.10.3/frailtypack/R/print.predJoint.R | 42 frailtypack-2.10.3/frailtypack/R/waldtest.R | 84 frailtypack-2.10.3/frailtypack/inst/doc/Package_summary.Rmd | 54 frailtypack-2.10.3/frailtypack/inst/doc/Package_summary.html | 29 frailtypack-2.10.3/frailtypack/man/frailtyPenal.Rd | 7 frailtypack-2.10.3/frailtypack/man/plot.predJoint.Rd | 6 frailtypack-2.10.3/frailtypack/man/plotFrailtyPenal.Rd | 3 frailtypack-2.10.3/frailtypack/man/prediction.Rd | 43 frailtypack-2.10.3/frailtypack/src/AparamMultive.f90 | 284 frailtypack-2.10.3/frailtypack/src/aGhermite.f90 | 518 frailtypack-2.10.3/frailtypack/src/aaOptim.f90 | 3205 ++-- frailtypack-2.10.3/frailtypack/src/aaOptimres.f90 | 1676 +- frailtypack-2.10.3/frailtypack/src/aaUseFunction.f90 | 14 frailtypack-2.10.3/frailtypack/src/aaUseFunctionG.f90 | 36 frailtypack-2.10.3/frailtypack/src/aamarq98o.f90 | 928 - frailtypack-2.10.3/frailtypack/src/additive.f90 | 4867 +++---- frailtypack-2.10.3/frailtypack/src/afuncpasres.f90 | 3 frailtypack-2.10.3/frailtypack/src/aresidusMartingale.f90 | 50 frailtypack-2.10.3/frailtypack/src/atestWald.f90 | 13 frailtypack-2.10.3/frailtypack/src/distance.f90 | 93 frailtypack-2.10.3/frailtypack/src/epoce.f90 | 16 frailtypack-2.10.3/frailtypack/src/epoce_log.f90 | 1535 +- frailtypack-2.10.3/frailtypack/src/epoce_long.f90 | 220 frailtypack-2.10.3/frailtypack/src/frailtypack.f90 | 95 frailtypack-2.10.3/frailtypack/src/funcpaG_tps.f90 | 705 - frailtypack-2.10.3/frailtypack/src/funcpaGcpm.f90 | 907 - frailtypack-2.10.3/frailtypack/src/funcpaGcpm_intcens.f90 | 995 - frailtypack-2.10.3/frailtypack/src/funcpaGcpm_log.f90 | 855 - frailtypack-2.10.3/frailtypack/src/funcpaGsplines.f90 | 859 - frailtypack-2.10.3/frailtypack/src/funcpaGsplines_intcens.f90 | 853 - frailtypack-2.10.3/frailtypack/src/funcpaGsplines_log.f90 | 873 - frailtypack-2.10.3/frailtypack/src/funcpaGweib.f90 | 661 frailtypack-2.10.3/frailtypack/src/funcpaGweib_intcens.f90 | 669 - frailtypack-2.10.3/frailtypack/src/funcpaGweib_log.f90 | 666 - frailtypack-2.10.3/frailtypack/src/funcpaMultivCpm.f90 | 689 - frailtypack-2.10.3/frailtypack/src/funcpaMultivSplines.f90 | 1150 - frailtypack-2.10.3/frailtypack/src/funcpaMultivWeib.f90 | 498 frailtypack-2.10.3/frailtypack/src/funcpaacpm.f90 | 1370 +- frailtypack-2.10.3/frailtypack/src/funcpaasplines.f90 | 1346 +- frailtypack-2.10.3/frailtypack/src/funcpaaweib.f90 | 1119 - frailtypack-2.10.3/frailtypack/src/funcpaj_tps.f90 | 881 - frailtypack-2.10.3/frailtypack/src/funcpajcpm.f90 | 545 frailtypack-2.10.3/frailtypack/src/funcpajcpm_log.f90 | 546 frailtypack-2.10.3/frailtypack/src/funcpajgeneral.f90 | 675 - frailtypack-2.10.3/frailtypack/src/funcpajsplines.f90 | 736 - frailtypack-2.10.3/frailtypack/src/funcpajsplines_fam.f90 | 745 - frailtypack-2.10.3/frailtypack/src/funcpajsplines_intcens.f90 | 661 frailtypack-2.10.3/frailtypack/src/funcpajsplines_log.f90 | 730 - frailtypack-2.10.3/frailtypack/src/funcpajweib.f90 | 459 frailtypack-2.10.3/frailtypack/src/funcpajweib_fam.f90 | 410 frailtypack-2.10.3/frailtypack/src/funcpajweib_intcens.f90 | 457 frailtypack-2.10.3/frailtypack/src/funcpajweib_log.f90 | 465 frailtypack-2.10.3/frailtypack/src/funcpancpm.f90 | 1163 - frailtypack-2.10.3/frailtypack/src/funcpansplines.f90 | 1238 - frailtypack-2.10.3/frailtypack/src/funcpanweib.f90 | 814 - frailtypack-2.10.3/frailtypack/src/funcpas_tps.f90 | 847 - frailtypack-2.10.3/frailtypack/src/funcpascpm.f90 | 660 frailtypack-2.10.3/frailtypack/src/funcpascpm_intcens.f90 | 653 frailtypack-2.10.3/frailtypack/src/funcpascpm_log.f90 | 616 frailtypack-2.10.3/frailtypack/src/funcpassplines.f90 | 621 frailtypack-2.10.3/frailtypack/src/funcpassplines_intcens.f90 | 743 - frailtypack-2.10.3/frailtypack/src/funcpassplines_log.f90 | 635 frailtypack-2.10.3/frailtypack/src/funcpasweib.f90 | 467 frailtypack-2.10.3/frailtypack/src/funcpasweib_intcens.f90 | 561 frailtypack-2.10.3/frailtypack/src/funcpasweib_log.f90 | 507 frailtypack-2.10.3/frailtypack/src/joint.f90 | 6634 +++++----- frailtypack-2.10.3/frailtypack/src/joint_longi.f90 | 51 frailtypack-2.10.3/frailtypack/src/multiveJoint.f90 | 4 frailtypack-2.10.3/frailtypack/src/nested.f90 | 5325 ++++---- frailtypack-2.10.3/frailtypack/src/prediction.f90 | 831 + frailtypack-2.10.3/frailtypack/src/prediction_biv.f90 | 65 frailtypack-2.10.3/frailtypack/src/prediction_sha_logn.f90 | 448 frailtypack-2.10.3/frailtypack/src/prediction_tri.f90 | 64 frailtypack-2.10.3/frailtypack/src/risque.f90 | 260 frailtypack-2.10.3/frailtypack/src/survival.f90 | 1070 - frailtypack-2.10.3/frailtypack/vignettes/Package_summary.Rmd | 54 frailtypack-2.9.4/frailtypack/src/prediction_log.f90 |only 87 files changed, 31540 insertions(+), 30838 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.4.6 dated 2016-09-05 and 4.4.7 dated 2016-10-19
DESCRIPTION | 17 - MD5 | 53 ++-- NEWS | 5 R/as.char.R | 4 R/call.dots.R | 45 ++- R/do.par.R | 20 - R/dot.R | 74 ++++- R/dotlib.R | 14 - R/earth.R | 4 R/evimp.R | 2 R/lib.R | 120 ++++++--- R/plot.earth.R | 24 - R/printcall.R | 4 R/stop.if.dots.R | 9 R/varmod.R | 2 inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/doc/index.html | 8 inst/slowtests/test.full.R | 2 inst/slowtests/test.full.Rout.save | 6 inst/slowtests/test.varmod.Rout.save | 2 inst/slowtests/test.varmod.mgcv.Rout.save | 2 inst/slowtests/test.weights.Rout.save | 2 man/earth.Rd | 371 ------------------------------ man/earth.object.Rd |only man/format.earth.Rd | 4 man/plot.evimp.Rd | 2 man/plot.varmod.Rd | 2 28 files changed, 275 insertions(+), 523 deletions(-)
Title: Functions, Data and Code for Count Data
Description: Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).
Author: Joseph M Hilbe <hilbe@asu.edu>
Maintainer: Andrew Robinson <apro@unimelb.edu.au>
Diff between COUNT versions 1.3.2 dated 2014-08-15 and 1.3.4 dated 2016-10-19
DESCRIPTION | 12 ++++++------ MD5 | 48 ++++++++++++++++++++++++------------------------ NAMESPACE | 5 +++++ data/affairs.rda |binary data/azcabgptca.rda |binary data/azdrg112.rda |binary data/azpro.rda |binary data/azprocedure.rda |binary data/badhealth.rda |binary data/fasttrakg.rda |binary data/fishing.rda |binary data/lbw.rda |binary data/lbwgrp.rda |binary data/loomis.rda |binary data/mdvis.rda |binary data/medpar.rda |binary data/nuts.rda |binary data/rwm.rda |binary data/rwm1984.rda |binary data/rwm5yr.rda |binary data/ships.rda |binary data/smoking.rda |binary data/titanic.rda |binary data/titanicgrp.rda |binary man/nuts.Rd | 25 ++++++++++++++----------- 25 files changed, 49 insertions(+), 41 deletions(-)
Title: General Utility Functions for the 'Agricultural Production
Systems Simulator'
Description: Contains functions designed to facilitate the loading
and transformation of 'Agricultural Production Systems Simulator'
output files <https://www.apsim.info>. Input meteorological data
(also known as "weather" or "met") files can also be generated
from user supplied data.
Author: Justin Fainges
Maintainer: Justin Fainges <Justin.Fainges@csiro.au>
Diff between APSIM versions 0.9.0 dated 2016-06-06 and 0.9.1 dated 2016-10-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/MetFunctions.R | 11 +++++++++-- README.md | 5 +++++ man/loadMet.Rd | 1 + 5 files changed, 23 insertions(+), 10 deletions(-)
Title: Visualization and Imputation of Missing Values - Graphical User
Interface
Description: A graphical user interface for the methods implemented in the
package VIM. It allows an easy handling of the
implemented plot and imputation methods.
Author: Daniel Schopfhauser, Matthias Templ, Andreas Alfons, Alexander Kowarik,
Bernd Prantner
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between VIMGUI versions 0.9.0 dated 2013-10-11 and 0.10.0 dated 2016-10-18
VIMGUI-0.10.0/VIMGUI/DESCRIPTION | 29 VIMGUI-0.10.0/VIMGUI/MD5 | 199 VIMGUI-0.10.0/VIMGUI/NAMESPACE | 54 VIMGUI-0.10.0/VIMGUI/R/TKRaggr.R | 3 VIMGUI-0.10.0/VIMGUI/R/TKRmarginmatrix.R | 7 VIMGUI-0.10.0/VIMGUI/R/TKRmatrixplot.R | 3 VIMGUI-0.10.0/VIMGUI/R/TKRparcoordMiss.R | 8 VIMGUI-0.10.0/VIMGUI/R/TKRpbox.R | 3 VIMGUI-0.10.0/VIMGUI/R/TKRscattmatrixMiss.R | 7 VIMGUI-0.10.0/VIMGUI/R/VIMGUI.R | 6 VIMGUI-0.10.0/VIMGUI/R/vmGUImenu.R | 3 VIMGUI-0.10.0/VIMGUI/R/zzz.R | 5 VIMGUI-0.10.0/VIMGUI/README | 8 VIMGUI-0.10.0/VIMGUI/build |only VIMGUI-0.10.0/VIMGUI/inst/CITATION |only VIMGUI-0.10.0/VIMGUI/inst/doc/VIM-Imputation.pdf | 7903 ++++++------- VIMGUI-0.10.0/VIMGUI/man/TKRaggr.Rd | 193 VIMGUI-0.10.0/VIMGUI/man/TKRmarginmatrix.Rd | 137 VIMGUI-0.10.0/VIMGUI/man/TKRmatrixplot.Rd | 146 VIMGUI-0.10.0/VIMGUI/man/TKRparcoordMiss.Rd | 247 VIMGUI-0.10.0/VIMGUI/man/TKRpbox.Rd | 149 VIMGUI-0.10.0/VIMGUI/man/TKRscattmatrixMiss.Rd | 193 VIMGUI-0.10.0/VIMGUI/man/VIMGUI.Rd | 23 VIMGUI-0.10.0/VIMGUI/man/vmGUImenu.Rd | 107 VIMGUI-0.10.0/VIMGUI/vignettes/fig-growdot-chorizon_Ca.pdf |binary VIMGUI-0.10.0/VIMGUI/vignettes/fig-marginmatrix-tao.pdf |binary VIMGUI-0.10.0/VIMGUI/vignettes/fig-scattmatrix-tao.pdf |binary VIMGUI-0.9.0/VIMGUI/inst/doc/VIM-EU-SILC.R |only VIMGUI-0.9.0/VIMGUI/inst/doc/VIM-EU-SILC.Rnw |only VIMGUI-0.9.0/VIMGUI/inst/doc/VIM-EU-SILC.pdf |only VIMGUI-0.9.0/VIMGUI/inst/tklibs |only VIMGUI-0.9.0/VIMGUI/vignettes/Thumbs.db |only VIMGUI-0.9.0/VIMGUI/vignettes/VIM-EU-SILC.Rnw |only VIMGUI-0.9.0/VIMGUI/vignettes/VIM-EU-SILC.bib |only VIMGUI-0.9.0/VIMGUI/vignettes/fig-aggr.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/fig-margin.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/fig-matrix.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/fig-parallel.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/fig-spine.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/screenshot1.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/screenshot2.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/screenshot3.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/screenshot4.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/screenshot5.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/screenshot6.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/screenshot7.pdf |only VIMGUI-0.9.0/VIMGUI/vignettes/screenshot8.pdf |only 47 files changed, 4876 insertions(+), 4557 deletions(-)
Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix
design, along with visualizations of several common set, element and attribute
related tasks.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>
Diff between UpSetR versions 1.2.4 dated 2016-09-02 and 1.3.0 dated 2016-10-18
DESCRIPTION | 8 +++--- MD5 | 48 +++++++++++++++++++-------------------- NEWS | 8 ++++++ R/MainBar.R | 19 ++++++++++++--- R/Matrix.R | 11 +++++++- R/SizeBar.R | 16 ++++++++++--- R/upset.R | 14 ++++++----- README.md | 8 +++--- inst/doc/attribute.plots.R | 10 ++++---- inst/doc/attribute.plots.Rmd | 10 ++++---- inst/doc/attribute.plots.html | 10 ++++---- inst/doc/basic.usage.R | 20 ++++++++-------- inst/doc/basic.usage.Rmd | 22 ++++++++--------- inst/doc/basic.usage.html | 25 ++++++++++---------- inst/doc/queries.R | 10 ++++---- inst/doc/queries.Rmd | 10 ++++---- inst/doc/queries.html | 10 ++++---- inst/doc/set.metadata.plots.R | 18 +++++++------- inst/doc/set.metadata.plots.Rmd | 18 +++++++------- inst/doc/set.metadata.plots.html | 38 +++++++++++++++--------------- man/upset.Rd | 18 ++++++++------ vignettes/attribute.plots.Rmd | 10 ++++---- vignettes/basic.usage.Rmd | 22 ++++++++--------- vignettes/queries.Rmd | 10 ++++---- vignettes/set.metadata.plots.Rmd | 18 +++++++------- 25 files changed, 227 insertions(+), 184 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.3.0 dated 2016-08-24 and 1.3.1 dated 2016-10-18
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS | 14 +++++++++++++- R/wrappers.R | 12 +++++++++--- inst/CITATION | 8 ++++---- inst/doc/article.pdf |binary inst/doc/heavytails.pdf |binary src/progutils.cpp | 9 ++++----- src/progutils.h | 2 +- src/sampler.cpp | 40 ++++++++++++++++++++++++++++++++-------- 10 files changed, 75 insertions(+), 34 deletions(-)
Title: Wrapper for the 'Intro.js' Library
Description: A wrapper for the 'Intro.js' library (For more info: <http://www.introjs.com>).
This package makes it easy to include step-by-step introductions, and clickable hints in a 'Shiny'
application. It supports both static introductions in the UI, and programmatic introductions from
the server-side.
Author: Carl Ganz [aut, cre],
Afshin Mehrabani [ctb, cph] (intro.js in javascript/introjs)
Maintainer: Carl Ganz <carlganz@gmail.com>
Diff between rintrojs versions 0.1.0 dated 2016-09-01 and 0.1.1 dated 2016-10-18
DESCRIPTION | 12 +++---- MD5 | 14 ++++---- NEWS.md |only R/introjs.R | 21 ++++++++++-- README.md | 53 ++++++++++++++++++++++++++++---- inst/CITATION |only inst/javascript/introjs/introjs.min.css | 2 - inst/javascript/rintro.js | 33 +++++++++++++------ man/introjs.Rd | 2 - 9 files changed, 102 insertions(+), 35 deletions(-)
Title: Distributions to be Used for GAMLSS Modelling
Description: The different distributions used for the response variables in GAMLSS
modelling.
Author: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>, Bob
Rigby with contributions from
Calliope Akantziliotou, Gillian Heller, Raydonal Ospina
<rospina@ime.usp.br>, Nicoletta Motpan, Fiona McElduff, Vlasios
Voudouris, Majid Djennad, Marco Enea and Alexios Ghalanos.
Maintainer: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>
Diff between gamlss.dist versions 4.3-6 dated 2016-05-18 and 5.0-0 dated 2016-10-18
DESCRIPTION | 14 - MD5 | 92 +++++------ NAMESPACE | 3 R/DELAPORT.R | 2 R/EGB2.R | 350 +++++++++++++++++++++---------------------- R/GB2.R | 366 ++++++++++++++++++++++----------------------- R/NBF.R |only R/PIG.R | 2 R/SI.R | 2 R/SICHEL-10-09-12.R | 2 man/BB.Rd | 2 man/BCCG.Rd | 2 man/EGB2.Rd | 4 man/EXP.Rd | 4 man/GA.Rd | 2 man/GB1.Rd | 2 man/GB2.Rd | 4 man/GE.Rd | 2 man/GG.Rd | 2 man/GIG.Rd | 4 man/GT.Rd | 2 man/GU.rd | 2 man/JSUoriginal.Rd | 2 man/LG.Rd | 2 man/LOGISTIC.Rd | 156 +++++++++---------- man/NBF.Rd |only man/NBI.Rd | 162 +++++++++---------- man/NBII.Rd | 2 man/PE.Rd | 2 man/PO.Rd | 2 man/RG.Rd | 2 man/RGE.Rd | 2 man/SEP.Rd | 2 man/SEP1.Rd | 2 man/SHASH.Rd | 2 man/TF.Rd | 2 man/WEI.Rd | 2 man/WEI2.Rd | 2 man/WEI3.Rd | 2 man/ZABB.Rd | 2 man/ZANBI.Rd | 3 man/ZAP.Rd | 3 man/ZIP.Rd | 2 man/ZIPIG.Rd | 2 man/gamlss.dist.package.Rd | 4 man/gamlss.family.Rd | 2 man/gen.Family.Rd | 2 man/hazardFun.Rd | 2 48 files changed, 617 insertions(+), 616 deletions(-)
Title: GAMLSS Data
Description: Data for GAMLSS models.
Author: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>, Bob
Rigby
Maintainer: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>
Diff between gamlss.data versions 4.3-4 dated 2016-05-18 and 5.0-0 dated 2016-10-18
gamlss.data-4.3-4/gamlss.data/data/film90.rda |only gamlss.data-4.3-4/gamlss.data/data/leukemia.RData |only gamlss.data-5.0-0/gamlss.data/DESCRIPTION | 14 +- gamlss.data-5.0-0/gamlss.data/MD5 | 88 +++++++++--------- gamlss.data-5.0-0/gamlss.data/data/CD4.rda |binary gamlss.data-5.0-0/gamlss.data/data/LGAclaims.rda |binary gamlss.data-5.0-0/gamlss.data/data/Leukemia.RData |only gamlss.data-5.0-0/gamlss.data/data/Mums.rda |binary gamlss.data-5.0-0/gamlss.data/data/VictimsOfCrime.rda |binary gamlss.data-5.0-0/gamlss.data/data/acidity.rda |binary gamlss.data-5.0-0/gamlss.data/data/aep.rda |binary gamlss.data-5.0-0/gamlss.data/data/aids.rda |binary gamlss.data-5.0-0/gamlss.data/data/alveolar.rda |binary gamlss.data-5.0-0/gamlss.data/data/computer.rda |binary gamlss.data-5.0-0/gamlss.data/data/datalist | 3 gamlss.data-5.0-0/gamlss.data/data/db.rda |binary gamlss.data-5.0-0/gamlss.data/data/dbbmi.rda |binary gamlss.data-5.0-0/gamlss.data/data/eu15.RData |only gamlss.data-5.0-0/gamlss.data/data/fabric.rda |binary gamlss.data-5.0-0/gamlss.data/data/film30.rda |binary gamlss.data-5.0-0/gamlss.data/data/film90.RData |only gamlss.data-5.0-0/gamlss.data/data/glass.rda |binary gamlss.data-5.0-0/gamlss.data/data/glasses.RData |binary gamlss.data-5.0-0/gamlss.data/data/grip.RData |binary gamlss.data-5.0-0/gamlss.data/data/hodges.rda |binary gamlss.data-5.0-0/gamlss.data/data/hodges1.rda |binary gamlss.data-5.0-0/gamlss.data/data/lice.rda |binary gamlss.data-5.0-0/gamlss.data/data/margolin.rda |binary gamlss.data-5.0-0/gamlss.data/data/meta.rda |binary gamlss.data-5.0-0/gamlss.data/data/mvi.rda |binary gamlss.data-5.0-0/gamlss.data/data/mviBig.rda |binary gamlss.data-5.0-0/gamlss.data/data/oil.RData |binary gamlss.data-5.0-0/gamlss.data/data/parzen.rda |binary gamlss.data-5.0-0/gamlss.data/data/polio.rda |binary gamlss.data-5.0-0/gamlss.data/data/rent.rda |binary gamlss.data-5.0-0/gamlss.data/data/rent99.polys.rda |binary gamlss.data-5.0-0/gamlss.data/data/rent99.rda |binary gamlss.data-5.0-0/gamlss.data/data/respInf.rda |binary gamlss.data-5.0-0/gamlss.data/data/species.rda |binary gamlss.data-5.0-0/gamlss.data/data/stylo.rda |binary gamlss.data-5.0-0/gamlss.data/data/tensile.rda |binary gamlss.data-5.0-0/gamlss.data/data/trd.RData |binary gamlss.data-5.0-0/gamlss.data/data/tse.rda |binary gamlss.data-5.0-0/gamlss.data/data/usair.rda |binary gamlss.data-5.0-0/gamlss.data/data/vas5.rda |binary gamlss.data-5.0-0/gamlss.data/man/eu15.Rd |only gamlss.data-5.0-0/gamlss.data/man/film90.Rd | 24 ++-- gamlss.data-5.0-0/gamlss.data/man/leukemia.Rd | 8 - 48 files changed, 70 insertions(+), 67 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting, displaying and checking GAMLSS Models.
Author: Mikis Stasinopoulos [aut, cre, cph],
Bob Rigby [aut],
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb],
Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>
Diff between gamlss versions 4.4-0 dated 2016-05-18 and 5.0-0 dated 2016-10-18
gamlss-4.4-0/gamlss/R/gen-Likelihood-12-06-13.R |only gamlss-5.0-0/gamlss/DESCRIPTION | 20 - gamlss-5.0-0/gamlss/MD5 | 143 ++++---- gamlss-5.0-0/gamlss/NAMESPACE | 3 gamlss-5.0-0/gamlss/R/HistDist-03-10-13.R | 34 +- gamlss-5.0-0/gamlss/R/PROFILE_new_19-08-12.R | 8 gamlss-5.0-0/gamlss/R/SUMMARY.R | 329 ++++++++++---------- gamlss-5.0-0/gamlss/R/dtop.R | 127 +++++-- gamlss-5.0-0/gamlss/R/fitted-plot.R | 390 ++++++++++++------------ gamlss-5.0-0/gamlss/R/gamlss.R | 9 gamlss-5.0-0/gamlss/R/gamlssVGD.R | 4 gamlss-5.0-0/gamlss/R/gen-Likelihood.R |only gamlss-5.0-0/gamlss/R/getPEF.R |only gamlss-5.0-0/gamlss/R/lms.R | 64 +-- gamlss-5.0-0/gamlss/R/pb_03-02-2014.R | 1 gamlss-5.0-0/gamlss/R/pb_goingtozero.R | 6 gamlss-5.0-0/gamlss/R/pb_new.R | 27 + gamlss-5.0-0/gamlss/R/plot.R | 246 +++++++-------- gamlss-5.0-0/gamlss/R/predict.gamlss.R | 95 ++--- gamlss-5.0-0/gamlss/R/predictAll.R |only gamlss-5.0-0/gamlss/R/print.R | 84 ++--- gamlss-5.0-0/gamlss/R/profterm_18_05_13.R | 8 gamlss-5.0-0/gamlss/R/term.plot-new.R | 20 - gamlss-5.0-0/gamlss/R/vcov-gamlss.R | 66 ++-- gamlss-5.0-0/gamlss/inst/doc/NEWS.txt | 38 ++ gamlss-5.0-0/gamlss/man/IC.Rd | 2 gamlss-5.0-0/gamlss/man/LR.test.Rd | 2 gamlss-5.0-0/gamlss/man/Q.stats.Rd | 2 gamlss-5.0-0/gamlss/man/Rsq.Rd | 2 gamlss-5.0-0/gamlss/man/bfp.Rd | 2 gamlss-5.0-0/gamlss/man/calibration.Rd | 2 gamlss-5.0-0/gamlss/man/centiles.Rd | 2 gamlss-5.0-0/gamlss/man/centiles.com.Rd | 2 gamlss-5.0-0/gamlss/man/centiles.pred.Rd | 2 gamlss-5.0-0/gamlss/man/centiles.split.Rd | 2 gamlss-5.0-0/gamlss/man/coef.gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/deviance.gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/dtop.Rd | 9 gamlss-5.0-0/gamlss/man/edf.Rd | 2 gamlss-5.0-0/gamlss/man/fitDist.Rd | 2 gamlss-5.0-0/gamlss/man/fitted.gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/fittedPlot.Rd | 2 gamlss-5.0-0/gamlss/man/formula.gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/gamlss.control.Rd | 140 ++++---- gamlss-5.0-0/gamlss/man/gamlss.cs.Rd | 2 gamlss-5.0-0/gamlss/man/gamlss.fp.Rd | 2 gamlss-5.0-0/gamlss/man/gamlss.package.Rd | 4 gamlss-5.0-0/gamlss/man/gamlss.ps.Rd | 2 gamlss-5.0-0/gamlss/man/gamlssML.Rd | 2 gamlss-5.0-0/gamlss/man/gen.likelihood.Rd | 3 gamlss-5.0-0/gamlss/man/getPEF.Rd |only gamlss-5.0-0/gamlss/man/glim.control.Rd | 2 gamlss-5.0-0/gamlss/man/histDist.Rd | 8 gamlss-5.0-0/gamlss/man/lms.Rd | 2 gamlss-5.0-0/gamlss/man/lo.Rd | 2 gamlss-5.0-0/gamlss/man/loglogSurv.Rd | 2 gamlss-5.0-0/gamlss/man/par.plot.Rd | 2 gamlss-5.0-0/gamlss/man/pcat.Rd | 4 gamlss-5.0-0/gamlss/man/pdf.plot.Rd | 2 gamlss-5.0-0/gamlss/man/plot.gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/polyS.Rd | 2 gamlss-5.0-0/gamlss/man/predict.gamlss.Rd | 11 gamlss-5.0-0/gamlss/man/print.gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/prof.dev.Rd | 2 gamlss-5.0-0/gamlss/man/prof.term.Rd | 2 gamlss-5.0-0/gamlss/man/ps.Rd | 2 gamlss-5.0-0/gamlss/man/refit.Rd | 2 gamlss-5.0-0/gamlss/man/residuals.gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/ri.Rd | 2 gamlss-5.0-0/gamlss/man/rqres.plot.Rd | 2 gamlss-5.0-0/gamlss/man/rvcov.Rd | 2 gamlss-5.0-0/gamlss/man/summary.gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/update.gamlss.Rd | 2 gamlss-5.0-0/gamlss/man/z.scores.Rd | 2 75 files changed, 1052 insertions(+), 933 deletions(-)
Title: Some Useful Functions from Spreadsheets and 'SPSS' Statistics
Description: Package implements several popular functions from Excel ('COUNTIF', 'VLOOKUP', etc.) and 'SPSS' Statistics ('RECODE', 'COUNT', etc.). Also there are functions for basic tables with value labels/variable labels support. Package aimed to help people to move data processing from Excel/'SPSS' to R.
Author: Gregory Demin
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between expss versions 0.5.1 dated 2016-07-07 and 0.5.5 dated 2016-10-18
expss-0.5.1/expss/R/methods.R |only expss-0.5.5/expss/DESCRIPTION | 9 expss-0.5.5/expss/MD5 | 164 +++++-- expss-0.5.5/expss/NAMESPACE | 92 ++++ expss-0.5.5/expss/NEWS | 12 expss-0.5.5/expss/R/S3_methods.R |only expss-0.5.5/expss/R/add_rows.R |only expss-0.5.5/expss/R/count_if.R | 24 - expss-0.5.5/expss/R/criteria_functions.R | 106 ++++- expss-0.5.5/expss/R/dichotomy.R | 2 expss-0.5.5/expss/R/dtfrm.R | 33 + expss-0.5.5/expss/R/f.R | 2 expss-0.5.5/expss/R/fre.R | 104 +---- expss-0.5.5/expss/R/if_na.R | 14 expss-0.5.5/expss/R/if_val.R | 254 ++++++++---- expss-0.5.5/expss/R/info.R | 10 expss-0.5.5/expss/R/keep.R |only expss-0.5.5/expss/R/labels.R | 134 ++++-- expss-0.5.5/expss/R/merge.R |only expss-0.5.5/expss/R/modify.R | 37 + expss-0.5.5/expss/R/na_if.R | 15 expss-0.5.5/expss/R/prop.R |only expss-0.5.5/expss/R/read_spss.R | 52 +- expss-0.5.5/expss/R/sort.R |only expss-0.5.5/expss/R/sum.R | 9 expss-0.5.5/expss/R/utils.R | 28 + expss-0.5.5/expss/R/values2labels.R | 20 expss-0.5.5/expss/R/vec_ops.R | 85 +++- expss-0.5.5/expss/R/vlookup.R | 89 +--- expss-0.5.5/expss/R/where.R |only expss-0.5.5/expss/R/write_labels.R | 27 - expss-0.5.5/expss/R/zzz_experimental.R | 97 ++-- expss-0.5.5/expss/inst/doc/UsageExamples.R | 14 expss-0.5.5/expss/inst/doc/UsageExamples.Rmd | 14 expss-0.5.5/expss/inst/doc/UsageExamples.html | 20 expss-0.5.5/expss/man/add_rows.Rd |only expss-0.5.5/expss/man/as.labelled.Rd |only expss-0.5.5/expss/man/compute.Rd | 11 expss-0.5.5/expss/man/criteria.Rd | 65 ++- expss-0.5.5/expss/man/dtfrm.Rd | 17 expss-0.5.5/expss/man/if_na.Rd | 9 expss-0.5.5/expss/man/if_val.Rd | 88 ++-- expss-0.5.5/expss/man/keep.Rd |only expss-0.5.5/expss/man/merge.simple_table.Rd |only expss-0.5.5/expss/man/modify.Rd | 3 expss-0.5.5/expss/man/na_if.Rd | 7 expss-0.5.5/expss/man/prop.Rd |only expss-0.5.5/expss/man/sort_asc.Rd |only expss-0.5.5/expss/man/val_lab.Rd | 13 expss-0.5.5/expss/man/vectors.Rd | 42 +- expss-0.5.5/expss/man/where.Rd |only expss-0.5.5/expss/tests/testthat/rds/add_rows1.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows10.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows2.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows3.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows4.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows5.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows6.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows6a.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows6b.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows7.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows8.rds |only expss-0.5.5/expss/tests/testthat/rds/add_rows9.rds |only expss-0.5.5/expss/tests/testthat/rds/cro_mean_out.txt |only expss-0.5.5/expss/tests/testthat/rds/fre2.6.rds |only expss-0.5.5/expss/tests/testthat/rds/fre2.7.rds |only expss-0.5.5/expss/tests/testthat/rds/fre_ex3.1.rds |only expss-0.5.5/expss/tests/testthat/rds/fre_ex3.2.rds |only expss-0.5.5/expss/tests/testthat/rds/fre_ex3.3.rds |only expss-0.5.5/expss/tests/testthat/rds/fre_out.txt |only expss-0.5.5/expss/tests/testthat/rds/fre_out_unrounded.txt |only expss-0.5.5/expss/tests/testthat/rds/info13.rds |only expss-0.5.5/expss/tests/testthat/rds/merge10.rds |only expss-0.5.5/expss/tests/testthat/rds/merge11.rds |only expss-0.5.5/expss/tests/testthat/rds/merge12.rds |only expss-0.5.5/expss/tests/testthat/rds/merge7.rds |only expss-0.5.5/expss/tests/testthat/rds/merge8.rds |only expss-0.5.5/expss/tests/testthat/rds/merge9.rds |only expss-0.5.5/expss/tests/testthat/rds/nsk.rds |only expss-0.5.5/expss/tests/testthat/test_add_rows.R |only expss-0.5.5/expss/tests/testthat/test_count_if.R | 10 expss-0.5.5/expss/tests/testthat/test_criteria_functions.R |only expss-0.5.5/expss/tests/testthat/test_default_dataset.R | 9 expss-0.5.5/expss/tests/testthat/test_dichotomy.R | 10 expss-0.5.5/expss/tests/testthat/test_dtfrm.R | 11 expss-0.5.5/expss/tests/testthat/test_experimental.R | 50 ++ expss-0.5.5/expss/tests/testthat/test_fre.R | 110 +++++ expss-0.5.5/expss/tests/testthat/test_if_na.R | 23 - expss-0.5.5/expss/tests/testthat/test_if_val.R | 270 +++++++++++-- expss-0.5.5/expss/tests/testthat/test_if_val_with_na.R | 102 ++-- expss-0.5.5/expss/tests/testthat/test_info.R | 9 expss-0.5.5/expss/tests/testthat/test_keep.R |only expss-0.5.5/expss/tests/testthat/test_labels.R | 106 +++++ expss-0.5.5/expss/tests/testthat/test_mean_if.R | 24 + expss-0.5.5/expss/tests/testthat/test_merge.R |only expss-0.5.5/expss/tests/testthat/test_methods.R | 70 +++ expss-0.5.5/expss/tests/testthat/test_modify.R | 73 +++ expss-0.5.5/expss/tests/testthat/test_na_if.R | 4 expss-0.5.5/expss/tests/testthat/test_prop.R |only expss-0.5.5/expss/tests/testthat/test_selectors.R | 22 - expss-0.5.5/expss/tests/testthat/test_sort.R |only expss-0.5.5/expss/tests/testthat/test_sum.R | 6 expss-0.5.5/expss/tests/testthat/test_values2labels.R | 14 expss-0.5.5/expss/tests/testthat/test_vec_ops.R | 77 +++ expss-0.5.5/expss/tests/testthat/test_vlookup.R | 35 + expss-0.5.5/expss/tests/testthat/test_where.R |only expss-0.5.5/expss/tests/testthat/test_write_labels.R | 46 ++ expss-0.5.5/expss/vignettes/UsageExamples.Rmd | 14 108 files changed, 2167 insertions(+), 650 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero-or-One Inflated
Beta Regression
Description: Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu <fang.liu.131@nd.edu> with contributions from Yunchuan Kong
Maintainer: Fang Liu <fang.liu.131@nd.edu>
Diff between zoib versions 1.4.1 dated 2016-07-26 and 1.4.2 dated 2016-10-18
DESCRIPTION | 8 +-- MD5 | 16 +++---- R/check.psrf.R | 68 ++++-------------------------- R/paraplot.R | 9 +--- R/zoib.R | 117 ++++++++++++++-------------------------------------- man/paraplot.Rd | 11 ---- man/zoib-package.Rd | 9 ++-- man/zoib.Rd | 3 + tests/test1.R | 2 9 files changed, 70 insertions(+), 173 deletions(-)
Title: Nonparametric Methods for Cognitive Diagnosis
Description: An array of nonparametric and parametric estimation methods for cognitive diagnostic models, including nonparametric classification of examinee attribute profiles, joint maximum likelihood estimation (JMLE) of examinee attribute profiles and item parameters, and nonparametric refinement of the Q-matrix, as well as conditional maximum likelihood estimation (CMLE) of examinee attribute profiles given item parameters and CMLE of item parameters given examinee attribute profiles. Currently the nonparametric methods in the package support both conjunctive and disjunctive models, and the parametric methods in the package support the DINA model, the DINO model, the NIDA model, the G-NIDA model, and the R-RUM model.
Author: Yi Zheng [aut, cre],
Chia-Yi Chiu [aut],
Jeffrey A. Douglas [ctb]
Maintainer: Yi Zheng <yi.isabel.zheng@asu.edu>
Diff between NPCD versions 1.0-9 dated 2015-10-03 and 1.0-10 dated 2016-10-18
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NAMESPACE | 2 +- R/JMLE.R | 16 ++++++++++++++-- R/ModelFit.R |only R/print.NPCD.R | 1 + man/JMLE.Rd | 1 + man/ModelFit.Rd |only man/NPCD.Rd | 6 ++++-- man/ParMLE.Rd | 1 + 10 files changed, 35 insertions(+), 16 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it makes possible to create and manipulate multivariate
network data with different formats, and there are effective ways available to treat multiple
networks with routines that combine algebraic systems like the partially ordered semigroup or
the semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. It also provides an algebraic approach for two-mode networks
through Galois derivations between families of the pairs of subsets in the two domains.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 2.3 dated 2016-10-17 and 2.4.1 dated 2016-10-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/bnd.R | 7 ++----- inst/CHANGELOG | 5 ++++- man/multiplex-package.Rd | 4 ++-- 5 files changed, 16 insertions(+), 16 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Leslie Pérez Cáceres,
Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 2.0 dated 2016-10-07 and 2.1 dated 2016-10-18
DESCRIPTION | 8 +- MD5 | 32 +++++------ NEWS | 7 ++ R/irace.R | 40 +++++++++---- R/main.R | 6 +- R/race-wrapper.R | 4 + R/version.R | 2 README.md | 126 +++++++++----------------------------------- build/vignette.rds |binary inst/CITATION | 4 + inst/doc/irace-package.Rnw | 61 +++++++++------------ inst/doc/irace-package.pdf |binary man/irace-package.Rd | 4 - tests/testthat.R | 3 - vignettes/NEWS.txt | 7 ++ vignettes/irace-package.Rnw | 61 +++++++++------------ vignettes/irace-package.bib | 20 ++++++ 17 files changed, 173 insertions(+), 212 deletions(-)
Title: The Guardian API Wrapper
Description: Provides an interface to the Open Platform's Content API of the Guardian Media Group. It retrieves content from news outlets The Observer, The Guardian, and guardian.co.uk from 1999 to current day.
Author: Marco Bastos [aut, cre],
Cornelius Puschmann [aut],
Mark Johnman [ctb]
Maintainer: Marco Bastos <marco@toledobastos.com>
Diff between GuardianR versions 0.7 dated 2016-09-16 and 0.8 dated 2016-10-18
ChangeLog | 9 ++++--- DESCRIPTION | 8 +++--- MD5 | 12 ++++----- R/guardianr.R | 21 ++++++++-------- man/GuardianR-package.Rd | 4 +-- man/get_guardian.Rd | 59 ++++++++++++++++++++++++++++++++++++++++++++--- man/get_json.Rd | 2 - 7 files changed, 86 insertions(+), 29 deletions(-)
Title: Automated Feature Selection from 'caret'
Description: Automated feature selection using variety of models
provided by 'caret' package.
This work was funded by Poland-Singapore bilateral cooperation
project no 2/3/POL-SIN/2012.
Author: Jakub Szlek [aut, cre],
Aleksander Mendyk [ctb]
Maintainer: Jakub Szlek <j.szlek@uj.edu.pl>
Diff between fscaret versions 0.9.4 dated 2015-04-20 and 0.9.4.1 dated 2016-10-18
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 3 +++ R/fscaret.R | 6 +++--- R/impCalc.R | 34 ++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/NEWS.Rd | 13 +++++++++++++ inst/doc/fscaret.pdf |binary man/fscaret-package.Rd | 4 ++-- man/fscaret.Rd | 5 ++++- man/impCalc.Rd | 10 +++++++--- 11 files changed, 74 insertions(+), 29 deletions(-)
Title: Species Identification using DNA Barcodes
Description: To perform species identification using DNA barcodes.
Author: Ai-bing ZHANG [aut, cre],
Meng-di HAO [aut],
Cai-qing YANG [aut],
Zhi-yong SHI [aut]
Maintainer: Ai-bing ZHANG <Zhangab2008@mail.cnu.edu.cn>
Diff between BarcodingR versions 1.0-1 dated 2016-07-19 and 1.0-2 dated 2016-10-18
BarcodingR-1.0-1/BarcodingR/R/concensus.identify.R |only BarcodingR-1.0-2/BarcodingR/DESCRIPTION | 6 - BarcodingR-1.0-2/BarcodingR/MD5 | 50 ++++++------- BarcodingR-1.0-2/BarcodingR/R/DNAbin2kmerFreqMatrix.R | 8 +- BarcodingR-1.0-2/BarcodingR/R/FMF.R | 4 - BarcodingR-1.0-2/BarcodingR/R/FMFtheta12.R | 2 BarcodingR-1.0-2/BarcodingR/R/TDR2.R | 6 - BarcodingR-1.0-2/BarcodingR/R/barcodes.eval.R | 6 - BarcodingR-1.0-2/BarcodingR/R/barcoding.spe.identify.R | 7 + BarcodingR-1.0-2/BarcodingR/R/barcoding.spe.identify2.R | 9 +- BarcodingR-1.0-2/BarcodingR/R/bbsik.R | 4 - BarcodingR-1.0-2/BarcodingR/R/char2NumVector.R | 4 - BarcodingR-1.0-2/BarcodingR/R/consensus.identify.R |only BarcodingR-1.0-2/BarcodingR/R/optimize.kmer.R | 4 - BarcodingR-1.0-2/BarcodingR/man/DNAbin2kmerFreqMatrix.Rd | 6 - BarcodingR-1.0-2/BarcodingR/man/FMF.Rd | 4 - BarcodingR-1.0-2/BarcodingR/man/FMFtheta12.Rd | 2 BarcodingR-1.0-2/BarcodingR/man/TDR2.Rd | 6 - BarcodingR-1.0-2/BarcodingR/man/barcodes.eval.Rd | 6 - BarcodingR-1.0-2/BarcodingR/man/barcoding.spe.identify.Rd | 6 + BarcodingR-1.0-2/BarcodingR/man/barcoding.spe.identify2.Rd | 6 + BarcodingR-1.0-2/BarcodingR/man/bbsik.Rd | 2 BarcodingR-1.0-2/BarcodingR/man/char2NumVector.Rd | 4 - BarcodingR-1.0-2/BarcodingR/man/consensus.identify.Rd | 4 - BarcodingR-1.0-2/BarcodingR/man/optimize.kmer.Rd | 4 - BarcodingR-1.0-2/BarcodingR/man/pineMothITS1.Rd | 6 - BarcodingR-1.0-2/BarcodingR/man/pineMothITS2.Rd | 10 +- 27 files changed, 93 insertions(+), 83 deletions(-)
Title: Fast and Easy Quality Control of EWAS Results Files
Description: Tools for (automated and manual) quality control of
the results of Epigenome-Wide Association Studies.
Author: Peter J. van der Most,
Leanne K. Kupers,
Ilja Nolte
Maintainer: Peter J. van der Most <p.j.van.der.most@umcg.nl>
Diff between QCEWAS versions 1.0-7 dated 2016-06-13 and 1.0-8 dated 2016-10-18
QCEWAS-1.0-7/QCEWAS/R/script_v10-7_package.R |only QCEWAS-1.0-8/QCEWAS/DESCRIPTION | 14 +- QCEWAS-1.0-8/QCEWAS/MD5 | 25 ++--- QCEWAS-1.0-8/QCEWAS/NAMESPACE | 2 QCEWAS-1.0-8/QCEWAS/R/script_v10-8_package.R |only QCEWAS-1.0-8/QCEWAS/inst/CITATION |only QCEWAS-1.0-8/QCEWAS/inst/doc |only QCEWAS-1.0-8/QCEWAS/inst/extdata/sample_markers_to_exclude.txt |only QCEWAS-1.0-8/QCEWAS/inst/extdata/translation_table.txt | 2 QCEWAS-1.0-8/QCEWAS/man/EWAS_QC.Rd | 47 +++++++--- QCEWAS-1.0-8/QCEWAS/man/EWAS_plots.Rd | 14 ++ QCEWAS-1.0-8/QCEWAS/man/EWAS_series.Rd | 24 ++--- QCEWAS-1.0-8/QCEWAS/man/P_correlation.Rd | 9 + QCEWAS-1.0-8/QCEWAS/man/P_lambda.Rd | 41 +++++--- QCEWAS-1.0-8/QCEWAS/man/QCEWAS-package.Rd | 7 + QCEWAS-1.0-8/QCEWAS/man/translate_header.Rd | 12 -- 16 files changed, 126 insertions(+), 71 deletions(-)
Title: Person Fit
Description: Several person-fit statistics (PFSs) are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro
Maintainer: Jorge N. Tendeiro <j.n.tendeiro@rug.nl>
Diff between PerFit versions 1.4 dated 2015-07-20 and 1.4.1 dated 2016-10-18
DESCRIPTION | 15 +++++++++------ MD5 | 11 ++++++----- data/InadequacyData.RData |binary data/IntelligenceData.RData |binary data/PhysFuncData.RData |binary inst |only man/PerFit-package.Rd | 2 ++ 7 files changed, 17 insertions(+), 11 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author:
BIFIE
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between BIFIEsurvey versions 1.9.4-0 dated 2016-06-01 and 1.11-0 dated 2016-10-18
DESCRIPTION | 8 +-- MD5 | 38 +++++++++--------- R/BIFIE.by.R | 50 ++++++++++++------------ R/BIFIE.waldtest.R | 42 ++++++++++---------- R/bifietable.R | 12 ++--- R/zzz.R | 4 - data/data.bifie01.rda |binary data/data.pisaNLD.rda |binary data/data.test1.rda |binary data/data.timss1.ind.rda |binary data/data.timss1.rda |binary data/data.timss2.rda |binary data/data.timss3.rda |binary data/data.timss4.rda |binary data/data.timssrep.rda |binary inst/NEWS | 15 ++++++- man/BIFIE.ecdf.Rd | 4 + man/BIFIE.linreg.Rd | 82 ++++++++++++++++++++++++++++++++++++++++ man/BIFIEsurvey-package.Rd | 2 src/univar_helpers.h | 92 ++++++++++++++++++++++----------------------- 20 files changed, 222 insertions(+), 127 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-
of-design-space plots and similar graphics for exploring the properties of
experimental designs. The design region is explored via random sampling, which
allows for more flexibility than traditional variance dispersion graphs. A
formula interface is leveraged to provide access to complex model formulae.
Graphics can be constructed simultaneously for multiple experimental designs
and/or multiple model formulae. Instead of using pointwise optimization to
find the minimum and maximum scaled prediction variance curves, which can be
inaccurate and time consuming, this package uses quantile regression as an
alternative.
Author: Pieter Schoonees [aut, cre, cph], Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between vdg versions 1.1.3 dated 2016-01-05 and 1.2.0 dated 2016-10-18
DESCRIPTION | 10 +++++----- MD5 | 47 ++++++++++++++++++++++++----------------------- R/LHS.R | 4 ++++ R/meanspv.R | 5 +++++ R/plot.spv.R | 4 ++++ R/print.spv.R | 4 ++++ R/runif_sphere.R | 4 ++++ R/sampler.R | 4 ++++ R/spv.R | 4 ++++ R/vdg-package.R | 6 +++++- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 32 +++++++++++++++++++++++--------- inst/doc/vdg.Rnw | 16 ++++++++-------- inst/doc/vdg.pdf |binary man/LHS.Rd | 5 +++++ man/meanspv.Rd | 8 ++++++++ man/plot.spv.Rd | 5 +++++ man/print.spv.Rd | 5 +++++ man/runif_sphere.Rd | 5 +++++ man/sampler.Rd | 5 +++++ man/spv.Rd | 5 +++++ man/vdg-package.Rd | 5 +++++ vignettes/vdg.Rnw | 16 ++++++++-------- vignettes/vdg.bib | 19 +++++++++++++++---- 25 files changed, 160 insertions(+), 58 deletions(-)
Title: Tools for the Analysis of Animal Track Data
Description: Functions for accessing and manipulating spatial data for animal
tracking, with straightforward coercion from and to other formats. Filter
for speed and create time spent maps from animal track data. There are
coercion methods to convert between 'trip' and 'ltraj' from 'adehabitatLT',
and between 'trip' and 'psp' and 'ppp' from 'spatstat'.
Author: Michael D. Sumner [aut, cre],
Sebastian Luque [ctb],
Anthony Fischbach [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between trip versions 1.1-21 dated 2015-05-21 and 1.5.0 dated 2016-10-18
ChangeLog | 1966 ++++++++++++++++++++-------------------- DESCRIPTION | 26 MD5 | 103 +- NAMESPACE | 138 +- NEWS | 530 +++++----- R/AllClass.R | 314 +++--- R/AllMethod.R | 1104 +++++++++++----------- R/as.trip.R | 122 +- R/coerce.R | 308 +++--- R/colours.R | 198 ++-- R/distance.R | 70 - R/filter.R | 574 +++++------ R/grid.R | 819 ++++++++-------- R/interpequal.R | 72 - R/speedDistanceAngle.R | 150 +-- R/trip-deprecated.R | 120 +- R/trip-package.r |only R/trip.R | 1934 +++++++++++++++++++-------------------- README.md | 96 - build/vignette.rds |binary data |only inst/doc/trip.R | 142 +- inst/doc/trip.Rmd | 217 ++-- inst/doc/trip.html | 553 ++++------- inst/triptopology.r |only man/TimeOrderedRecords-class.Rd | 60 - man/TimeOrderedRecords.Rd | 44 man/adjust.duplicateTimes.Rd | 98 + man/argos.sigma.Rd | 84 - man/as.Other.Rd | 128 +- man/as.trip-methods.Rd | 90 - man/cut.trip.Rd | 208 ++-- man/filter.penSS.Rd | 204 ++-- man/forceCompliance.Rd | 62 - man/homedist.Rd | 50 - man/makeGridTopology.Rd | 72 - man/oc.theme.Rd | 86 - man/rasterize.Rd | 93 - man/readArgos.Rd | 194 +-- man/sda.Rd | 74 - man/sepIdGaps.Rd | 96 + man/speedfilter.Rd | 132 +- man/trackAngle.Rd | 64 - man/trackDistance.Rd | 146 +- man/trip-accessors.Rd | 91 - man/trip-class.Rd | 124 +- man/trip-internal.Rd | 91 - man/trip-methods.Rd | 285 ++--- man/trip-package.Rd |only man/trip.split.exact.Rd | 82 - man/tripGrid.Rd | 83 - man/tripGrid.interp.Rd | 132 +- man/walrus818.Rd |only tests |only vignettes/trip.Rmd | 217 ++-- 55 files changed, 6355 insertions(+), 6291 deletions(-)
Title: Nonparametric Estimation of Preferential Attachment and Node
Fitness in Temporal Complex Networks
Description: A statistically sound method for estimating jointly the attachment function and node fitness in a temporal complex network by maximizing a suitable penalized log-likelihood function is implemented in this package. Tutorial can be found in the accompanying vignette. For a list of references, please run the command: citation("PAFit").
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>
Diff between PAFit versions 0.8.6 dated 2016-09-07 and 0.8.7 dated 2016-10-18
DESCRIPTION | 10 - MD5 | 34 +++--- R/CreateDataCV.R | 4 R/GetStatistics.R | 64 ++++++++---- R/PAFit.R | 39 ++++--- R/RcppExports.R | 4 R/calculate_error_PA.R |only R/calculate_error_fitness.R |only R/performCV.R | 14 ++ R/plot.pafit.r | 6 - build/vignette.rds |binary inst/doc/Tutorial.pdf.asis | 2 man/CreateDataCV.Rd | 4 man/GetStatistics.Rd | 20 ++- man/PAFit-package.Rd | 6 - man/performCV.Rd | 24 +++- man/plot.PAFit.Rd | 22 ++-- src/Cpp_code.cpp | 229 +++++++++++++++++++++++++------------------- src/RcppExports.cpp | 7 - 19 files changed, 289 insertions(+), 200 deletions(-)
Title: Get the Timezone Information
Description: A function to retrieve the system timezone on Unix systems
which has been found to find an answer when 'Sys.timezone()' has failed.
It is based on an answer by Duane McCully posted on 'StackOverflow', and
adapted to be callable from R. The package also builds on Windows, but
just returns NULL.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between gettz versions 0.0.1 dated 2016-09-10 and 0.0.2 dated 2016-10-18
ChangeLog | 11 +++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ README.md | 14 +++++++++++++- build/partial.rdb |binary man/gettz-package.Rd | 5 +++-- src/gettz.cpp | 2 ++ 7 files changed, 42 insertions(+), 15 deletions(-)
Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with
conditional heteroscedasticity are provided. First, continuous
distributions can be used for the (right and/or left censored or truncated)
response with separate linear predictors for the mean and variance.
Second, cumulative link models for ordinal data
(obtained by interval-censoring continuous data) can be employed for
heteroscedastic extended logistic regression (HXLR). In the latter type of
models, the intercepts depend on the thresholds that define the intervals.
Author: Jakob Messner [aut, cre],
Achim Zeileis [aut]
Maintainer: Jakob Messner <jwmm@elektro.dtu.dk>
Diff between crch versions 0.9-2 dated 2016-02-29 and 1.0-0 dated 2016-10-18
DESCRIPTION | 14 ++++---- MD5 | 40 ++++++++++++------------ NAMESPACE | 3 + NEWS | 8 ++++ R/crch.R | 86 ++++++++++++++++++++++++++++++++++++++++++++-------- R/crch.boost.R | 9 ++--- R/mtable.R |only build/partial.rdb |only build/vignette.rds |binary data/RainIbk.rda |binary inst/CITATION | 44 +++++++++++++------------- inst/doc/crch.pdf |binary man/coef.crch.Rd | 1 man/crch.Rd | 7 +++- man/crch.control.Rd | 7 +++- man/hxlr.Rd | 6 +-- src/clogis.c | 4 -- src/cnorm.c | 4 -- src/tlogis.c | 10 +++--- src/tnorm.c | 10 +++--- src/tt.c | 10 +++--- vignettes/crch.bib | 27 +++++++++++++++- 22 files changed, 195 insertions(+), 95 deletions(-)
Title: Bibliometric and Co-Citation Analysis Tool
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from SCOPUS and
Thomson Reuters' ISI Web of Knowledge databases, performing bibliometric analysis
and building data matrices for co-citation, coupling and scientific collaboration analysis.
Author: Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 1.1 dated 2016-09-07 and 1.2 dated 2016-10-18
bibliometrix-1.1/bibliometrix/R/keywordsAssoc.R |only bibliometrix-1.1/bibliometrix/man/keywordsAssoc.Rd |only bibliometrix-1.2/bibliometrix/DESCRIPTION | 8 bibliometrix-1.2/bibliometrix/MD5 | 33 +- bibliometrix-1.2/bibliometrix/NAMESPACE | 4 bibliometrix-1.2/bibliometrix/NEWS | 14 + bibliometrix-1.2/bibliometrix/R/citations.R | 31 ++ bibliometrix-1.2/bibliometrix/R/keywordAssoc.R |only bibliometrix-1.2/bibliometrix/R/keywordGrowth.R |only bibliometrix-1.2/bibliometrix/R/stopwords.R |only bibliometrix-1.2/bibliometrix/R/summary.bibliometrix.R | 25 + bibliometrix-1.2/bibliometrix/R/termExtraction.R |only bibliometrix-1.2/bibliometrix/R/zzz.R |only bibliometrix-1.2/bibliometrix/data/stopwords.rda |only bibliometrix-1.2/bibliometrix/inst/CITATION |only bibliometrix-1.2/bibliometrix/inst/doc/bibliometrix-vignette.R | 66 ++++ bibliometrix-1.2/bibliometrix/inst/doc/bibliometrix-vignette.Rmd | 78 +++++ bibliometrix-1.2/bibliometrix/inst/doc/bibliometrix-vignette.html | 133 ++++++++-- bibliometrix-1.2/bibliometrix/man/KeywordGrowth.Rd |only bibliometrix-1.2/bibliometrix/man/citations.Rd | 13 bibliometrix-1.2/bibliometrix/man/keywordAssoc.Rd |only bibliometrix-1.2/bibliometrix/man/stopwords.Rd |only bibliometrix-1.2/bibliometrix/man/termExtraction.Rd |only bibliometrix-1.2/bibliometrix/vignettes/bibliometrix-vignette.Rmd | 78 +++++ 24 files changed, 413 insertions(+), 70 deletions(-)
Title: Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MS-Based Untargeted Metabolomics
Description: Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample.
Author: Xavier Domingo-Almenara, Sara Samino, Maria Vinaixa, Alexandre Perera, Oscar Yanes
Maintainer: Xavier Domingo-Almenara <xavier.domingo@urv.cat>
Diff between erah versions 1.0.3 dated 2016-10-13 and 1.0.4 dated 2016-10-18
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- NAMESPACE | 2 +- NEWS | 5 +++++ R/MSimport.R |only man/importMSP.Rd |only 6 files changed, 15 insertions(+), 8 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super Imposition by
Translation And Rotation) growth curve models. SITAR is a shape-invariant model
with a regression B-spline mean curve and subject-specific random effects on
both the measurement and age scales.
Author: Tim Cole
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.0.7 dated 2016-07-31 and 1.0.8 dated 2016-10-17
DESCRIPTION | 8 ++--- MD5 | 18 ++++++----- NAMESPACE | 4 ++ NEWS | 11 +++++++ R/BICadj.R | 4 +- R/plot.sitar.R | 57 ++++++++++++++++++++----------------- R/sitar.R | 11 +------ R/sitarlib.R | 82 +++++++++++++++++++++++++++--------------------------- R/timegap.R |only man/plot.sitar.Rd | 7 +++- man/timegap.Rd |only 11 files changed, 111 insertions(+), 91 deletions(-)
Title: Functions for Calculating Daily Solar Radiation and
Evapotranspiration
Description: Calculating daily global solar radiation at horizontal surface using several well-known models (i.e. Angstrom-Prescott, Supit-Van Kappel, Hargreaves, Bristow and Campbell, and Mahmood-Hubbard), and model calibration based on ground-truth data, and (3) model auto-calibration. The FAO Penmann-Monteith equation to calculate evapotranspiration is also included.
Author: Jedrzej S. Bojanowski
Maintainer: Jedrzej S. Bojanowski <jedrzej.bojanowski@gmail.com>
Diff between sirad versions 2.3-1 dated 2015-12-12 and 2.3-3 dated 2016-10-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/bcauto.R | 27 ++++++++++++++++----------- R/et0.r | 2 +- R/exd.R | 8 +++++++- R/exh.R | 19 +++++++++++++------ man/extrat.Rd | 4 ++-- man/sirad-package.Rd | 6 +++--- 8 files changed, 53 insertions(+), 35 deletions(-)
Title: Models for Health Economic Evaluation
Description: Health Economic Evaluation Modelling.
Markov models (decision trees, homogeneous and non-homogeneous)
for health economic evaluation. Model comparison,
sensitivity and probabilistic analysis.
Author: Antoine Filipovic-Pierucci [aut, cre],
Kevin Zarca [aut],
Matthew Wiener [ctb],
Zdenek Kabat [ctb],
Vojtech Filipec [ctb]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>
Diff between heemod versions 0.4.0 dated 2016-09-16 and 0.5.0 dated 2016-10-17
heemod-0.4.0/heemod/inst/doc/b-homogeneous.R |only heemod-0.4.0/heemod/inst/doc/b-homogeneous.Rmd |only heemod-0.4.0/heemod/inst/doc/b-homogeneous.html |only heemod-0.4.0/heemod/inst/doc/c-non-homogeneous.R |only heemod-0.4.0/heemod/inst/doc/c-non-homogeneous.Rmd |only heemod-0.4.0/heemod/inst/doc/c-non-homogeneous.html |only heemod-0.4.0/heemod/inst/doc/d-probabilistic.R |only heemod-0.4.0/heemod/inst/doc/d-probabilistic.Rmd |only heemod-0.4.0/heemod/inst/doc/d-probabilistic.html |only heemod-0.4.0/heemod/inst/doc/e-sensitivity.R |only heemod-0.4.0/heemod/inst/doc/e-sensitivity.Rmd |only heemod-0.4.0/heemod/inst/doc/e-sensitivity.html |only heemod-0.4.0/heemod/inst/examples/example_define_matrix.R |only heemod-0.4.0/heemod/inst/examples/example_define_model.R |only heemod-0.4.0/heemod/inst/examples/example_plot.run_models.R |only heemod-0.4.0/heemod/inst/examples/example_run_models.R |only heemod-0.4.0/heemod/inst/examples/example_run_probabilistic.R |only heemod-0.4.0/heemod/inst/examples/example_run_sensitivity.R |only heemod-0.4.0/heemod/man/define_distrib.Rd |only heemod-0.4.0/heemod/man/define_matrix.Rd |only heemod-0.4.0/heemod/man/define_model.Rd |only heemod-0.4.0/heemod/man/define_sensitivity.Rd |only heemod-0.4.0/heemod/man/get_model.Rd |only heemod-0.4.0/heemod/man/plot.run_models.Rd |only heemod-0.4.0/heemod/man/run_models.Rd |only heemod-0.4.0/heemod/man/run_models_tabular.Rd |only heemod-0.4.0/heemod/man/run_probabilistic.Rd |only heemod-0.4.0/heemod/man/run_sensitivity.Rd |only heemod-0.4.0/heemod/man/summary.run_models.Rd |only heemod-0.4.0/heemod/vignettes/b-homogeneous.Rmd |only heemod-0.4.0/heemod/vignettes/c-non-homogeneous.Rmd |only heemod-0.4.0/heemod/vignettes/d-probabilistic.Rmd |only heemod-0.4.0/heemod/vignettes/e-sensitivity.Rmd |only heemod-0.5.0/heemod/DESCRIPTION | 8 heemod-0.5.0/heemod/MD5 | 313 +++++----- heemod-0.5.0/heemod/NAMESPACE | 49 + heemod-0.5.0/heemod/NEWS.md |only heemod-0.5.0/heemod/R/acceptability_curve.R | 2 heemod-0.5.0/heemod/R/combine.R | 39 - 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heemod-0.5.0/heemod/tests/testthat/test_model.R | 187 ++++- heemod-0.5.0/heemod/tests/testthat/test_probabilistic.R | 32 - heemod-0.5.0/heemod/tests/testthat/test_run_model.R | 172 ++++- heemod-0.5.0/heemod/tests/testthat/test_sensitivity.R | 139 +++- heemod-0.5.0/heemod/tests/testthat/test_states.R | 10 heemod-0.5.0/heemod/tests/testthat/test_tabular_input.R | 290 ++++++++- heemod-0.5.0/heemod/vignettes/a-introduction.Rmd | 82 +- heemod-0.5.0/heemod/vignettes/b-time-dependency.Rmd |only heemod-0.5.0/heemod/vignettes/c-homogeneous.Rmd |only heemod-0.5.0/heemod/vignettes/d-non-homogeneous.Rmd |only heemod-0.5.0/heemod/vignettes/e-probabilistic.Rmd |only heemod-0.5.0/heemod/vignettes/f-sensitivity.Rmd |only heemod-0.5.0/heemod/vignettes/g-heterogeneity.Rmd | 32 - heemod-0.5.0/heemod/vignettes/h-tabular.Rmd | 26 heemod-0.5.0/heemod/vignettes/i-reproduction.Rmd | 22 196 files changed, 2325 insertions(+), 1389 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Simulation testing and implementation of data-limited fishery stock
assessment methods.
Author: Tom Carruthers and Adrian Hordyk
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 3.2.1 dated 2016-08-11 and 3.2.2 dated 2016-10-17
DESCRIPTION | 8 MD5 | 51 - NAMESPACE | 32 - R/ClassMeths.r | 2 R/DLM_input.R | 75 ++ R/DLM_output.R | 21 R/DataObj.r | 61 + R/MSEObj.r | 1515 ++++++++++++++++++++++++++++++++++++++++-------- R/MiscFuns.r | 77 +- R/MiscInt.r | 4 R/RcppExports.R | 14 R/runMSE.r | 45 - build/vignette.rds |binary inst/doc/DLMtool.R | 7 inst/doc/DLMtool.Rmd | 62 + inst/doc/DLMtool.html | 376 ++++++----- man/Cplot.Rd |only man/EtargetLopt.Rd |only man/Jplot.Rd |only man/Kplot.Rd | 16 man/L95target.Rd |only man/MPStats.Rd |only man/Pplot.Rd | 72 ++ man/Splot.Rd |only man/VOIplot.Rd | 8 man/barplot.MSE.Rd |only man/boxplot.DLM_data.Rd |only man/boxplot.MSE.Rd |only man/minlenLopt1.Rd |only man/plotFun.Rd |only src/RcppExports.cpp | 10 vignettes/DLMtool.Rmd | 62 + 32 files changed, 1961 insertions(+), 557 deletions(-)
Title: Conditional Visualization for Statistical Models
Description: Exploring fitted models by interactively taking 2-D and 3-D
sections in data space.
Author: Mark O'Connell [aut, cre],
Catherine Hurley [ths],
Katarina Domijan [ths],
Achim Zeileis [ctb] (spineplot, see copied.R),
R Core Team [ctb] (barplot, see copied.R)
Maintainer: Mark O'Connell <mark.oconnell@maths.nuim.ie>
Diff between condvis versions 0.3-3 dated 2016-07-04 and 0.4-1 dated 2016-10-17
DESCRIPTION | 12 +- MD5 | 49 +++++------ NEWS | 29 ++++++ R/ceplot.R | 13 +-- R/ceplot.interactive.R | 68 ++++++++++----- R/ceplot.shiny.R | 32 +++++-- R/ceplot.static.R | 17 ++- R/condtour.R | 143 ++++++++++++++++++++++++--------- R/diagnosticplots.R | 8 - R/makepath.R | 3 R/plotxc.R | 114 ++++++++++++++++++-------- R/plotxs.R | 85 +++++++++++-------- R/similarityweight.R | 11 -- R/update.R | 31 ++++--- R/weightcolor.R |only README.md | 9 +- demo/condvis-classification.R | 3 demo/condvis-regression.R | 2 man/ceplot.Rd | 4 man/condtour.Rd | 14 ++- man/condvis-package.Rd | 6 - man/plotxc.Rd | 37 ++++++-- man/plotxs.Rd | 10 ++ man/similarityweight.Rd | 2 tests/testthat/test.makepath.R | 2 tests/testthat/test.similarityweight.R | 6 + 26 files changed, 482 insertions(+), 228 deletions(-)
Title: Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions
induced by stochastic covariates. Miscellaneous functions for data preparation
and simulation are also provided. For more information, see: (i) "Life tables
with covariates: Dynamic model for nonlinear analysis of longitudinal data"
by Akushevich, I. et al. (2005), Mathematical Population Studies 12(2), 51(80),
<DOI:10.1080/08898480590932296>; (ii) "Stochastic model for analysis of
longitudinal data on aging and mortality" by Yashin A. et al. (2007),
Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>;
(iii) "Health decline, aging and mortality: how are they related?"
by Yashin A. et al. (2007),
Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.3.8 dated 2016-10-05 and 1.4.2 dated 2016-10-17
DESCRIPTION | 8 MD5 | 40 ++- NAMESPACE | 1 R/simdata_cont.R | 2 R/spm.impute.R |only R/spm_discrete.R | 2 R/spm_pobs.R | 6 README.md | 73 +++++++ inst/doc/stpm-vignette.R | 40 +-- inst/doc/stpm-vignette.Rmd | 40 +-- inst/doc/stpm-vignette.html | 446 ++++++++++++++++++++++---------------------- man/func1.Rd |only man/getNextY.Rd |only man/getNextY.cont.Rd |only man/getNextY.discr.Rd |only man/getNextY.discr.m.Rd |only man/getPrevY.discr.Rd |only man/getPrevY.discr.m.Rd |only man/m.Rd |only man/mu.Rd |only man/sigma_sq.Rd |only man/simdata_cont.Rd | 2 man/spm.impute.Rd |only man/spm_pobs.Rd | 5 src/simdataND.cpp | 1 src/spm_integral_MD.cpp | 50 +--- vignettes/stpm-vignette.Rmd | 40 +-- 27 files changed, 421 insertions(+), 335 deletions(-)
Title: Fitting Step-Functions
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Timo Aspelmeier [cre, aut],
Thomas Hotz [aut],
Hannes Sieling [aut],
Pein Florian [ctb]
Maintainer: Timo Aspelmeier <timo.aspelmeier@mathematik.uni-goettingen.de>
Diff between stepR versions 1.0-5.1 dated 2016-10-11 and 1.0-6 dated 2016-10-17
ChangeLog | 11 +++++++++++ DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- src/BinTree.h | 50 ++++++++++++++++++++++++++++---------------------- src/Bounds.cpp | 22 ++++++++++++++-------- src/Jump.h | 19 ++++++++++++------- src/Step.cpp | 1 + src/Step.h | 24 +++++++++++++++--------- src/StepBinom.cpp | 1 + src/StepGaussVar.cpp | 1 + src/StepPoisson.cpp | 1 + 11 files changed, 97 insertions(+), 59 deletions(-)
Title: Discrete Choice (Binary, Poisson and Ordered) Models with Random
Parameters
Description: An implementation of simulated maximum likelihood method for the
estimation of Binary (Probit and Logit), Ordered (Probit and Logit) and
Poisson models with random parameters for cross-sectional and longitudinal
data.
Author: Mauricio Sarrias <msarrias86@gmail.com>
Maintainer: Mauricio Sarrias <msarrias86@gmail.com>
Diff between Rchoice versions 0.3 dated 2015-04-29 and 0.3-1 dated 2016-10-17
DESCRIPTION | 16 ++++-- MD5 | 38 ++++++++------- NAMESPACE | 6 +- R/Rchoice.MakeDraws.R | 68 ++++++++++++++------------- R/Rchoice.R | 4 - R/Rchoice.logLiks.R | 11 +++- R/Rchoice.methods.R | 112 ++++++++++++++++++++++++++-------------------- R/Rchoice.modelform.R | 15 ++++-- README.md |only inst/CITATION |only inst/NEWS.Rd | 8 +++ man/AIC.Rchoice.Rd | 4 - man/Rchoice.Rd | 52 +++++++++++---------- man/bread.Rchoice.Rd | 17 ++++-- man/cov.Rchoice.Rd | 20 ++++---- man/effect.Rchoice.Rd | 4 - man/estfun.Rchoice.Rd | 13 +++-- man/getSummary.Rchoice.Rd | 13 ++--- man/plot.Rchoice.Rd | 7 ++ man/rFormula.Rd | 2 man/vcov.Rchoice.Rd | 2 21 files changed, 233 insertions(+), 179 deletions(-)
Title: Phylogenetic Linear Regression
Description: Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.
Author: Lam Si Tung Ho [aut, cre],
Cecile Ane [aut],
Robert Lachlan [ctb],
Kelsey Tarpinian [ctb],
Rachel Feldman [ctb],
Qing Yu [ctb]
Maintainer: Lam Si Tung Ho <lamho86@gmail.com>
Diff between phylolm versions 2.4 dated 2016-01-09 and 2.5 dated 2016-10-17
DESCRIPTION | 17 - MD5 | 22 + R/OU1d.R |only R/phyloglm.R | 11 R/phylolm.R | 357 ++++++++++++++++++++++++----- R/testingTreeWithQuartetCF.r | 15 + R/tools.R | 528 +++++++++++++++++++++---------------------- README.md | 8 man/OU1d.loglik.Rd |only man/phylolm-package.Rd | 6 man/phylolm.Rd | 35 ++ man/transf.branch.lengths.Rd | 180 +++++++------- tests |only 13 files changed, 740 insertions(+), 439 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it makes possible to create and manipulate multivariate
network data with different formats, and there are effective ways available to treat multiple
networks with routines that combine algebraic systems like the partially ordered semigroup or
the semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. It also provides an algebraic approach for two-mode networks
through Galois derivations between families of the pairs of subsets in the two domains.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 2.2 dated 2016-10-12 and 2.3 dated 2016-10-17
DESCRIPTION | 8 +-- MD5 | 16 +++---- R/bnd.R | 7 ++- R/rel.sys.R | 90 +++++++++++++++++++++++------------------- inst/CHANGELOG | 5 +- inst/doc/TwoModeNetworks.Rnw | 2 inst/doc/TwoModeNetworks.r | 2 man/multiplex-package.Rd | 18 ++++---- vignettes/TwoModeNetworks.Rnw | 2 9 files changed, 83 insertions(+), 67 deletions(-)
Title: Implementation of 2D Correlation Analysis in R
Description: Implementation of two-dimensional (2D) correlation analysis based
on the Fourier-transformation approach described by Isao Noda (I. Noda
(1993) <DOI:10.1366/0003702934067694>). Additionally there are two plot
functions for the resulting correlation matrix: The first one creates
colored 2D plots, while the second one generates 3D plots.
Author: Robert Geitner [cre, aut],
Robby Fritzsch [aut],
Thomas Bocklitz [aut],
Juergen Popp [ctb, cph]
Maintainer: Robert Geitner <robert.geitner@uni-jena.de>
Diff between corr2D versions 0.1.10 dated 2016-07-26 and 0.1.11 dated 2016-10-17
DESCRIPTION | 10 ++-- MD5 | 18 ++++---- R/corr2d.R | 73 +++++++++++++++++++++++++++-------- R/corr2d_plot.R | 100 ++++++++++++++++++++++++++++++++++++++++++------- R/sim2ddata.R | 80 ++++++++++++++++++++++++++++++++++----- inst/doc/corr2D.html | 10 ++-- man/corr2d.Rd | 2 man/plot_corr2d.Rd | 3 - man/plot_corr2din3d.Rd | 2 man/sim2ddata.Rd | 21 +++++----- 10 files changed, 247 insertions(+), 72 deletions(-)
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan <seshanv@mskcc.org>
Diff between clinfun versions 1.0.11 dated 2015-08-11 and 1.0.12 dated 2016-10-17
CHANGES | 4 ++++ DESCRIPTION | 6 +++--- INDEX | 1 + MD5 | 12 +++++++----- NAMESPACE | 2 +- R/aucVardiTest.R |only man/aucVardiTest.Rd |only man/calogrank.Rd | 1 + 8 files changed, 17 insertions(+), 9 deletions(-)
Title: Some Tools for Imaging
Description: Some tools for (bio)imaging.
Author: Volker Schmid
Maintainer: Volker Schmid <stats@volkerschmid.de>
Diff between bioimagetools versions 0.3.0 dated 2016-10-14 and 0.3.1 dated 2016-10-17
DESCRIPTION | 9 +++++---- MD5 | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values
are introduced, which can be used for exploring the data and the structure of
the missing and/or imputed values. Depending on this structure of the missing
values, the corresponding methods may help to identify the mechanism generating
the missing values and allows to explore the data including missing values.
In addition, the quality of imputation can be visually explored using various
univariate, bivariate, multiple and multivariate plot methods. A graphical user
interface available in the separate package VIMGUI allows an easy handling of
the implemented plot methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik, Bernd Prantner
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 4.5.0 dated 2016-06-29 and 4.6.0 dated 2016-10-17
VIM-4.5.0/VIM/src/Makevars |only VIM-4.5.0/VIM/src/Makevars.win |only VIM-4.6.0/VIM/DESCRIPTION | 31 +- VIM-4.6.0/VIM/MD5 | 100 +++---- VIM-4.6.0/VIM/NAMESPACE | 266 ++++++++++--------- VIM-4.6.0/VIM/NEWS | 2 VIM-4.6.0/VIM/R/VIM-package.R | 6 VIM-4.6.0/VIM/R/aggr.R | 20 - VIM-4.6.0/VIM/R/hotdeck.R | 149 ---------- VIM-4.6.0/VIM/R/irmi.R | 3 VIM-4.6.0/VIM/R/kNNFaster.R | 95 +++--- VIM-4.6.0/VIM/R/regressionImp.R | 140 +++++----- VIM-4.6.0/VIM/inst |only VIM-4.6.0/VIM/man/SBS5242.Rd | 60 ++-- VIM-4.6.0/VIM/man/VIM-package.Rd | 104 +++---- VIM-4.6.0/VIM/man/aggr.Rd | 436 ++++++++++++++++---------------- VIM-4.6.0/VIM/man/alphablend.Rd | 64 ++-- VIM-4.6.0/VIM/man/barMiss.Rd | 271 ++++++++++--------- VIM-4.6.0/VIM/man/bgmap.Rd | 84 +++--- VIM-4.6.0/VIM/man/chorizonDL.Rd | 186 ++++++------- VIM-4.6.0/VIM/man/colSequence.Rd | 152 +++++------ VIM-4.6.0/VIM/man/colormapMiss.Rd | 318 +++++++++++------------ VIM-4.6.0/VIM/man/countInf.Rd | 58 ++-- VIM-4.6.0/VIM/man/growdotMiss.Rd | 274 ++++++++++---------- VIM-4.6.0/VIM/man/histMiss.Rd | 280 ++++++++++---------- VIM-4.6.0/VIM/man/hotdeck.Rd | 136 +++++---- VIM-4.6.0/VIM/man/initialise.Rd | 84 +++--- VIM-4.6.0/VIM/man/irmi.Rd | 244 +++++++++-------- VIM-4.6.0/VIM/man/kNN.Rd | 195 +++++++------- VIM-4.6.0/VIM/man/kola.background.Rd | 48 +-- VIM-4.6.0/VIM/man/mapMiss.Rd | 176 ++++++------ VIM-4.6.0/VIM/man/marginmatrix.Rd | 154 +++++------ VIM-4.6.0/VIM/man/marginplot.Rd | 264 +++++++++---------- VIM-4.6.0/VIM/man/matrixplot.Rd | 246 +++++++++--------- VIM-4.6.0/VIM/man/mosaicMiss.Rd | 186 ++++++------- VIM-4.6.0/VIM/man/pairsVIM.Rd | 186 ++++++------- VIM-4.6.0/VIM/man/parcoordMiss.Rd | 296 ++++++++++----------- VIM-4.6.0/VIM/man/pbox.Rd | 252 +++++++++--------- VIM-4.6.0/VIM/man/prepare.Rd | 154 +++++------ VIM-4.6.0/VIM/man/print.summary.aggr.Rd | 60 ++-- VIM-4.6.0/VIM/man/regressionImp.Rd | 111 ++++---- VIM-4.6.0/VIM/man/rugNA.Rd | 132 ++++----- VIM-4.6.0/VIM/man/scattJitt.Rd | 208 +++++++-------- VIM-4.6.0/VIM/man/scattMiss.Rd | 236 ++++++++--------- VIM-4.6.0/VIM/man/scattmatrixMiss.Rd | 244 +++++++++-------- VIM-4.6.0/VIM/man/sleep.Rd | 60 ++-- VIM-4.6.0/VIM/man/spineMiss.Rd | 296 ++++++++++----------- VIM-4.6.0/VIM/man/tao.Rd | 62 ++-- VIM-4.6.0/VIM/man/testdata.Rd | 62 ++-- VIM-4.6.0/VIM/man/vmGUIenvir.Rd | 101 +++---- VIM-4.6.0/VIM/tests/test_data_frame.R |only VIM-4.6.0/VIM/tests/test_gowerDind.R | 2 VIM-4.6.0/VIM/tests/test_kNN.R | 2 53 files changed, 3639 insertions(+), 3657 deletions(-)
Title: Forecasting Using Smoothing Functions
Description: The set of smoothing functions used for time series analysis and in forecasting.
Currently the package includes exponential smoothing models and SARIMA in state-space
form + several simulation functions.
Author: Ivan Svetunkov [aut, cre] (Research Associate at Lancaster Centre for
Forecasting, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 1.4.4 dated 2016-09-20 and 1.4.5 dated 2016-10-17
DESCRIPTION | 10 MD5 | 86 +++---- NAMESPACE | 1 NEWS | 13 + R/RcppExports.R | 4 R/autoces.R | 32 +- R/autossarima.R | 50 ++-- R/ces.R | 6 R/es.R | 23 + R/ges.R | 8 R/methods.R | 25 +- R/simes.R | 78 +++--- R/sma.R | 6 R/ssarima.R | 223 +++++------------- R/ssfunctions.R | 127 ++++++++-- README.md | 4 inst/doc/ces.R | 8 inst/doc/ces.Rmd | 8 inst/doc/ces.html | 66 ++--- inst/doc/es.R | 2 inst/doc/es.Rmd | 2 inst/doc/es.html | 59 ++-- inst/doc/ges.html | 10 inst/doc/simulate.html | 14 - inst/doc/sma.html | 6 inst/doc/smooth-Documentation.pdf |binary inst/doc/smooth.html | 4 inst/doc/ssarima.html | 64 +++-- man/autoces.Rd | 29 +- man/autossarima.Rd | 27 +- man/ces.Rd | 43 +-- man/es.Rd | 40 +-- man/forecastSmooth.Rd | 7 man/ges.Rd | 35 +- man/sma.Rd | 31 +- man/ssarima.Rd | 34 +- src/RcppExports.cpp | 36 +++ src/ssgeneralfun.cpp | 455 +++++++++++++++++++++++++++++++++++--- tests/testthat/test_ces.R | 2 tests/testthat/test_es.R | 2 tests/testthat/test_ges.R | 2 tests/testthat/test_ssarima.R | 2 vignettes/ces.Rmd | 8 vignettes/es.Rmd | 2 44 files changed, 1082 insertions(+), 612 deletions(-)
Title: A Tool to Associate FASTA Sequences and Features
Description: Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.
Author: Bettina Budeus
Maintainer: Bettina Budeus <bettina.budeus@stud.uni-due.de>
Diff between SeqFeatR versions 0.2.3 dated 2016-05-25 and 0.2.4 dated 2016-10-17
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS | 5 +++++ inst/CITATION |only inst/doc/SeqFeatR_tutorial.pdf |binary 5 files changed, 13 insertions(+), 7 deletions(-)
Title: Non-Negative Matrix Factorization (NMF) using CUDA
Description: Wrapper package for the nmfgpu library, which implements several
Non-negative Matrix Factorization (NMF) algorithms for CUDA platforms.
By using the acceleration of GPGPU computing, the NMF can be used for
real-world problems inside the R environment. All CUDA devices starting with
Kepler architecture are supported by the library.
Author: Sven Koitka [aut, cre, cph],
Christoph M. Friedrich [ctb]
Maintainer: Sven Koitka <sven.koitka@fh-dortmund.de>
Diff between nmfgpu4R versions 0.2.5.1 dated 2016-07-10 and 0.2.5.2 dated 2016-10-17
DESCRIPTION | 10 ++++++---- MD5 | 20 ++++++++++---------- R/helper.R | 2 +- R/nmfgpu.R | 2 +- R/nmfgpu4R.R | 2 +- src/Helper.cpp | 2 +- src/Helper.h | 4 ++-- src/WrapperNMFGPU.cpp | 2 +- src/WrapperNMFGPU.h | 2 +- src/nmfgpu.h | 2 +- src/nmfgpu4R.cpp | 2 +- 11 files changed, 26 insertions(+), 24 deletions(-)
Title: Genome Structure Rearrangement Calling in Genomes with High
Synteny
Description: Pipeline to read and analyze raw SNP array data.
The data is preprocessed and normalized.
Genotypes and CNVs are called.
Synteny blocks are calculated and translocations detected.
The results can be plotted with special functions.
Author: Fabian Grandke [cre, aut],
Birgit Samans [aut]
Maintainer: Fabian Grandke <grafabian@gmail.com>
Diff between gsrc versions 1.0.1 dated 2016-06-05 and 1.1 dated 2016-10-17
gsrc-1.0.1/gsrc/inst/doc/synteny_blocks.R |only gsrc-1.0.1/gsrc/inst/doc/synteny_blocks.Rmd |only gsrc-1.0.1/gsrc/inst/doc/synteny_blocks.html |only gsrc-1.0.1/gsrc/inst/extdata |only gsrc-1.0.1/gsrc/vignettes/synteny_blocks.Rmd |only gsrc-1.1/gsrc/DESCRIPTION | 14 gsrc-1.1/gsrc/MD5 | 77 - gsrc-1.1/gsrc/NAMESPACE | 4 gsrc-1.1/gsrc/NEWS |only gsrc-1.1/gsrc/R/filter.R | 151 +- gsrc-1.1/gsrc/R/plot.R | 588 ++++++---- gsrc-1.1/gsrc/R/preprocess.R | 77 - gsrc-1.1/gsrc/R/process.R | 301 +++-- gsrc-1.1/gsrc/R/raw.R | 157 +- gsrc-1.1/gsrc/R/synteny.R | 270 ++-- gsrc-1.1/gsrc/R/tools.R | 155 +- gsrc-1.1/gsrc/build/vignette.rds |binary gsrc-1.1/gsrc/inst/CITATION |only gsrc-1.1/gsrc/inst/doc/introduction.R | 80 - gsrc-1.1/gsrc/inst/doc/introduction.Rmd | 281 ++-- gsrc-1.1/gsrc/inst/doc/introduction.html | 419 ++++--- gsrc-1.1/gsrc/inst/doc/synteny.R |only gsrc-1.1/gsrc/inst/doc/synteny.Rmd |only gsrc-1.1/gsrc/inst/doc/synteny.html |only gsrc-1.1/gsrc/man/filter_cnv.Rd |only gsrc-1.1/gsrc/man/intens_theta.Rd | 2 gsrc-1.1/gsrc/man/plot_cnv.Rd |only gsrc-1.1/gsrc/man/plot_trans_locations.Rd | 2 gsrc-1.1/gsrc/man/read_intensities.Rd | 3 gsrc-1.1/gsrc/man/read_sample_sheets.Rd | 7 gsrc-1.1/gsrc/man/trans_location.Rd | 11 gsrc-1.1/gsrc/tests |only gsrc-1.1/gsrc/vignettes/brassica_synteny_filtered.rda |only gsrc-1.1/gsrc/vignettes/cotton_synteny_filtered.rda |only gsrc-1.1/gsrc/vignettes/introduction.Rmd | 281 ++-- gsrc-1.1/gsrc/vignettes/introduction_files/figure-html/unnamed-chunk-18-1.png |only gsrc-1.1/gsrc/vignettes/introduction_files/figure-html/unnamed-chunk-21-1.png |only gsrc-1.1/gsrc/vignettes/introduction_files/figure-html/unnamed-chunk-22-1.png |only gsrc-1.1/gsrc/vignettes/introduction_files/figure-html/unnamed-chunk-23-1.png |only gsrc-1.1/gsrc/vignettes/introduction_files/figure-html/unnamed-chunk-25-1.png |binary gsrc-1.1/gsrc/vignettes/introduction_files/figure-html/unnamed-chunk-28-1.png |binary gsrc-1.1/gsrc/vignettes/introduction_files/figure-html/unnamed-chunk-31-1.png |only gsrc-1.1/gsrc/vignettes/introduction_files/figure-html/unnamed-chunk-32-1.png |only gsrc-1.1/gsrc/vignettes/introduction_files/figure-html/unnamed-chunk-33-1.png |only gsrc-1.1/gsrc/vignettes/synteny.Rmd |only 45 files changed, 1743 insertions(+), 1137 deletions(-)
Title: Hierarchical Modelling of Faecal Egg Counts
Description: An implementation of hierarchical models
for faecal egg count data to assess anthelmintic
efficacy. Bayesian inference is done via MCMC sampling using Stan.
Author: Craig Wang [cre, aut],
Michaela Paul [aut],
Reinhard Furrer [ctb],
Trustees of Columbia University [cph] (rstanarm)
Maintainer: Craig Wang <craig.wang@uzh.ch>
Diff between eggCounts versions 1.1-1 dated 2016-07-29 and 1.1-2 dated 2016-10-17
DESCRIPTION | 15 +++--- MD5 | 17 +++---- NAMESPACE | 2 inst/NEWS | 8 ++- man/eggCounts-package.Rd | 6 +- man/fec_stan.Rd | 6 +- man/fecr_stan.Rd | 4 - src/Makevars.win |only src/include/models.hpp | 114 ++++++++++++++++++++++++++++++++++++++++++++--- tests/test.R | 4 - 10 files changed, 142 insertions(+), 34 deletions(-)
Title: Bayesian Analysis of Heterogeneous Treatment Effect
Description: It is vital to assess the heterogeneity of treatment effects
(HTE) when making health care decisions for an individual patient or a group
of patients. Nevertheless, it remains challenging to evaluate HTE based
on information collected from clinical studies that are often designed and
conducted to evaluate the efficacy of a treatment for the overall population.
The Bayesian framework offers a principled and flexible approach to estimate
and compare treatment effects across subgroups of patients defined by their
characteristics. This package allows users to explore a wide range of Bayesian
HTE analysis models, and produce posterior inferences about HTE.
Author: Chenguang Wang [aut, cre],
Ravi Varadhan [aut],
Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>
Diff between beanz versions 1.6 dated 2016-07-29 and 1.7 dated 2016-10-17
DESCRIPTION | 6 - MD5 | 31 ++--- NAMESPACE | 1 R/beanz_present.R | 60 ++++++++++ R/beanz_stan.R | 1 exec/bs.stan | 29 +++-- exec/ds.stan | 19 ++- exec/eds.stan | 22 ++- exec/srs.stan | 21 ++- inst/doc/beanz_vignettes.R | 7 + inst/doc/beanz_vignettes.Rmd | 13 ++ inst/doc/beanz_vignettes.html | 179 +++++++++++++++++-------------- inst/shiny/beanz_ui.R | 85 ++++++++++++-- inst/shiny/server.R | 10 + man/r.pred.subgrp.effect.Rd |only src/include/models.hpp | 240 +++++++++++++++++++++++++++++++++--------- vignettes/beanz_vignettes.Rmd | 13 ++ 17 files changed, 551 insertions(+), 186 deletions(-)
Title: R Interface to the Vowpal Wabbit
Description: The 'Vowpal Wabbit' project is a fast out-of-core learning
system sponsored by Microsoft Research (having started at Yahoo! Research)
and written by John Langford along with a number of contributors. This R
package does not include the distributed computing implementation of the
cluster/ directory of the upstream sources. Use of the software as a network
service is also not directly supported as the aim is a simpler direct call
from R for validation and comparison.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RVowpalWabbit versions 0.0.7 dated 2016-07-17 and 0.0.8 dated 2016-10-17
ChangeLog | 8 ++++++++ DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ README.md | 2 +- tests/test2.r | 2 +- tests/test6.r | 2 +- tests/test8.r | 2 +- 7 files changed, 23 insertions(+), 14 deletions(-)
Title: An API Client for Wikimedia Traffic Data
Description: Pageview data from the 'Wikimedia' sites, such as
'Wikipedia' <https://www.wikipedia.org/>, from entire projects to per-article
levels of granularity, through the new RESTful API and data source <https://
wikimedia.org/api/rest_v1/?doc>.
Author: Oliver Keyes [aut, cre], Jeremiah Lewis [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between pageviews versions 0.2.0 dated 2016-01-14 and 0.3.0 dated 2016-10-17
DESCRIPTION | 18 +-- MD5 | 36 +++---- NAMESPACE | 2 NEWS | 12 ++ R/pageviews.R | 1 R/query.R | 134 ++++++++++------------------ R/timestamps.R | 45 ++++----- R/utils.R | 90 ++++++++++++++++-- README.md | 8 + build/vignette.rds |binary inst/doc/Accessing_Wikimedia_pageviews.R | 39 +------- inst/doc/Accessing_Wikimedia_pageviews.Rmd | 48 ++-------- inst/doc/Accessing_Wikimedia_pageviews.html | 126 +++++++++++++++----------- man/article_pageviews.Rd | 4 man/pageview_timestamps.Rd | 7 + man/project_pageviews.Rd | 4 man/top_articles.Rd | 16 +-- tests/testthat/test.R | 88 +++++++++++++++++- vignettes/Accessing_Wikimedia_pageviews.Rmd | 48 ++-------- 19 files changed, 405 insertions(+), 321 deletions(-)
Title: Irucka Embry's Miscellaneous Functions
Description: A collection of Irucka Embry's miscellaneous functions
(Engineering Economics, Civil & Environmental/Water Resources Engineering,
Geometry, Statistics, GNU Octave length functions, Trigonometric functions
in degrees, etc.).
Author: Irucka Embry [aut, cre], Felix Andrews [aut, ctb] (zoo), Hans Werner
Borchers [aut, ctb] (pracma), Samit Basu [aut, ctb] (FreeMat)
Maintainer: Irucka Embry <iembry@ecoccs.com>
Diff between iemisc versions 0.9.5 dated 2016-08-04 and 0.9.6 dated 2016-10-17
iemisc-0.9.5/iemisc/inst/doc/Open-Channel-Flow_Examples.R |only iemisc-0.9.5/iemisc/inst/doc/Open-Channel-Flow_Examples.Rmd |only iemisc-0.9.5/iemisc/inst/doc/Open-Channel-Flow_Examples.html |only iemisc-0.9.5/iemisc/vignettes/Open-Channel-Flow_Examples.Rmd |only iemisc-0.9.6/iemisc/DESCRIPTION | 18 ++--- iemisc-0.9.6/iemisc/MD5 | 36 +++++----- iemisc-0.9.6/iemisc/NAMESPACE | 6 + iemisc-0.9.6/iemisc/NEWS.md | 11 ++- iemisc-0.9.6/iemisc/R/Manningcirc.R | 2 iemisc-0.9.6/iemisc/R/Manningrect.R | 4 - iemisc-0.9.6/iemisc/R/Manningtrap.R | 4 - iemisc-0.9.6/iemisc/R/Manningtri.R | 2 iemisc-0.9.6/iemisc/R/concr_mix_normal_strength.R |only iemisc-0.9.6/iemisc/R/iemisc.R | 13 +-- iemisc-0.9.6/iemisc/R/size.R | 8 +- iemisc-0.9.6/iemisc/README.md | 2 iemisc-0.9.6/iemisc/build/vignette.rds |binary iemisc-0.9.6/iemisc/inst/doc/Open-Channel-Flow_Examples_Geometric_Shapes.R |only iemisc-0.9.6/iemisc/inst/doc/Open-Channel-Flow_Examples_Geometric_Shapes.Rmd |only iemisc-0.9.6/iemisc/inst/doc/Open-Channel-Flow_Examples_Geometric_Shapes.html |only iemisc-0.9.6/iemisc/man/concr_mix_normal_strength.Rd |only iemisc-0.9.6/iemisc/man/iemisc.Rd | 9 +- iemisc-0.9.6/iemisc/man/size.Rd | 1 iemisc-0.9.6/iemisc/vignettes/Open-Channel-Flow_Examples_Geometric_Shapes.Rmd |only 24 files changed, 71 insertions(+), 45 deletions(-)
Title: Graphical Independence Networks
Description: Probability propagation in graphical independence networks, also
known as Bayesian networks or probabilistic expert systems.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRain versions 1.2-5 dated 2015-12-30 and 1.3-0 dated 2016-10-17
gRain-1.2-5/gRain/R/cptable.R |only gRain-1.2-5/gRain/man/andtable.Rd |only gRain-1.2-5/gRain/man/compile.grain.Rd |only gRain-1.2-5/gRain/man/compileCPT.Rd |only gRain-1.2-5/gRain/man/extractCPT.Rd |only gRain-1.2-5/gRain/man/gRain-package.Rd |only gRain-1.2-5/gRain/man/grain.Rd |only gRain-1.2-5/gRain/man/loadSaveHuginNet.Rd |only gRain-1.2-5/gRain/man/predict.Rd |only gRain-1.2-5/gRain/man/propagate.grain.Rd |only gRain-1.2-5/gRain/man/simulate.Rd |only gRain-1.3-0/gRain/ChangeLog | 656 +++++++++---------- gRain-1.3-0/gRain/DESCRIPTION | 20 gRain-1.3-0/gRain/MD5 | 94 +- gRain-1.3-0/gRain/NAMESPACE | 138 ++-- gRain-1.3-0/gRain/R/CPT-POT-compile.R | 391 ++++++----- gRain-1.3-0/gRain/R/CPT-POT-extract.R | 300 +++++--- gRain-1.3-0/gRain/R/Generics.R | 51 + gRain-1.3-0/gRain/R/cptable-create.R |only gRain-1.3-0/gRain/R/cptable-special.R |only gRain-1.3-0/gRain/R/display.R | 140 ++-- gRain-1.3-0/gRain/R/evi.R |only gRain-1.3-0/gRain/R/evidence-func.R |only gRain-1.3-0/gRain/R/evidence-joint.R |only gRain-1.3-0/gRain/R/evidence.R | 969 ++++++++++++----------------- gRain-1.3-0/gRain/R/finding.R | 713 +++++++++++---------- gRain-1.3-0/gRain/R/gRain-package.R |only gRain-1.3-0/gRain/R/grain-compile.R | 284 ++++---- gRain-1.3-0/gRain/R/grain-main.R | 374 +++++++---- gRain-1.3-0/gRain/R/grain-simulate.R | 225 +++--- gRain-1.3-0/gRain/R/grain-utilities.R | 287 ++++---- gRain-1.3-0/gRain/R/loadSaveHuginNet.R | 912 ++++++++++++++------------- gRain-1.3-0/gRain/R/potentialList.R | 132 +-- gRain-1.3-0/gRain/R/predict.R | 169 ++--- gRain-1.3-0/gRain/R/propagate.R | 312 +++++---- gRain-1.3-0/gRain/R/querygrain.R | 405 +++++++----- gRain-1.3-0/gRain/R/repeatPattern.R | 129 ++- gRain-1.3-0/gRain/R/summary.R | 96 +- gRain-1.3-0/gRain/R/update.R | 127 ++- gRain-1.3-0/gRain/R/zzz.R | 32 gRain-1.3-0/gRain/build/vignette.rds |binary gRain-1.3-0/gRain/inst/CITATION | 38 - gRain-1.3-0/gRain/inst/doc/gRain-intro.pdf |binary gRain-1.3-0/gRain/man/compile-cpt.Rd |only gRain-1.3-0/gRain/man/cptable.Rd | 188 ++--- gRain-1.3-0/gRain/man/evidence-object.Rd |only gRain-1.3-0/gRain/man/extract-cpt.Rd |only gRain-1.3-0/gRain/man/finding.Rd | 204 ++---- gRain-1.3-0/gRain/man/grain-compile.Rd |only gRain-1.3-0/gRain/man/grain-evi.Rd |only gRain-1.3-0/gRain/man/grain-evidence.Rd |only gRain-1.3-0/gRain/man/grain-generics.Rd |only gRain-1.3-0/gRain/man/grain-main.Rd |only gRain-1.3-0/gRain/man/grain-predict.Rd |only gRain-1.3-0/gRain/man/grain-propagate.Rd |only gRain-1.3-0/gRain/man/grain-simulate.Rd |only gRain-1.3-0/gRain/man/internal-gRain.Rd | 95 +- gRain-1.3-0/gRain/man/load-save-hugin.Rd |only gRain-1.3-0/gRain/man/logical.Rd |only gRain-1.3-0/gRain/man/mendel.Rd |only gRain-1.3-0/gRain/man/querygrain.Rd | 255 +++---- gRain-1.3-0/gRain/man/repeatPattern.Rd | 149 +--- gRain-1.3-0/gRain/man/set-jevidence.Rd |only gRain-1.3-0/gRain/man/update.CPTgrain.Rd | 141 +--- 64 files changed, 4303 insertions(+), 3723 deletions(-)
Title: Fine-Scale Population Analysis
Description: Statistical tool set for population genetics. The package provides empirical Bayes estimator of Fst, Nei's Gst, and Weir & Cockerham's theta adapted for pairwise comparison. It also provides interfaces to read and manipulate 'GENEPOP' format data files.
Author: Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada
Maintainer: Reiichiro Nakamichi <nakamichi@affrc.go.jp>
Diff between FinePop versions 1.0.1 dated 2016-09-08 and 1.1.1 dated 2016-10-17
FinePop-1.0.1/FinePop/R/clip.genepop.maf.R |only FinePop-1.0.1/FinePop/R/clip.genepop.name.R |only FinePop-1.0.1/FinePop/man/clip.genepop.maf.Rd |only FinePop-1.0.1/FinePop/man/clip.genepop.name.Rd |only FinePop-1.1.1/FinePop/DESCRIPTION | 10 +++---- FinePop-1.1.1/FinePop/MD5 | 28 +++++++++++---------- FinePop-1.1.1/FinePop/NAMESPACE | 2 - FinePop-1.1.1/FinePop/R/EBFST.R | 2 - FinePop-1.1.1/FinePop/R/GstN.R |only FinePop-1.1.1/FinePop/R/clip.genepop.R |only FinePop-1.1.1/FinePop/R/read.genepop.R | 9 ++++++- FinePop-1.1.1/FinePop/R/thetaWC.pair.R |only FinePop-1.1.1/FinePop/build/partial.rdb |binary FinePop-1.1.1/FinePop/man/EBFST.Rd | 32 +++++++++++-------------- FinePop-1.1.1/FinePop/man/FinePop-package.Rd | 6 +++- FinePop-1.1.1/FinePop/man/GstN.Rd |only FinePop-1.1.1/FinePop/man/clip.genepop.Rd |only FinePop-1.1.1/FinePop/man/data.JSM.Rd | 8 +++--- FinePop-1.1.1/FinePop/man/read.genepop.Rd | 19 ++++++++++---- FinePop-1.1.1/FinePop/man/thetaWC.pair.Rd |only 20 files changed, 68 insertions(+), 48 deletions(-)
Title: A Tool to Downsize Large Workflows for Testing
Description: Toggles the test and production versions of a large workflow.
Author: William Landau [aut, cre]
Maintainer: William Landau <will.landau@gmail.com>
Diff between downsize versions 0.2.0 dated 2016-10-14 and 0.2.1 dated 2016-10-17
downsize-0.2.0/downsize/man/check_downsized.Rd |only downsize-0.2.0/downsize/tests/testthat/test-check_downsized.R |only downsize-0.2.1/downsize/DESCRIPTION | 8 +- downsize-0.2.1/downsize/MD5 | 34 ++++------ downsize-0.2.1/downsize/NAMESPACE | 2 downsize-0.2.1/downsize/R/namespace.R | 2 downsize-0.2.1/downsize/R/ui.R | 31 +++++---- downsize-0.2.1/downsize/R/utils.R | 15 ---- downsize-0.2.1/downsize/inst/doc/downsize.Rmd | 4 - downsize-0.2.1/downsize/inst/doc/downsize.html | 7 -- downsize-0.2.1/downsize/man/downsize.Rd | 13 ++- downsize-0.2.1/downsize/man/my_mode.Rd | 2 downsize-0.2.1/downsize/man/production_mode.Rd | 3 downsize-0.2.1/downsize/man/test_mode.Rd | 3 downsize-0.2.1/downsize/tests/testthat/test-check_args.R | 5 - downsize-0.2.1/downsize/tests/testthat/test-downsize.R | 16 +++- downsize-0.2.1/downsize/tests/testthat/test-ds.R | 1 downsize-0.2.1/downsize/tests/testthat/test-make_small.R | 3 downsize-0.2.1/downsize/vignettes/downsize.Rmd | 4 - 19 files changed, 72 insertions(+), 81 deletions(-)
Title: Censored Spatial Models
Description: It fits linear regression models for censored spatial data. It provides different estimation methods as the SAEM (Stochastic Approximation of Expectation Maximization) algorithm and seminaive that uses Kriging prediction to estimate the response at censored locations and predict new values at unknown locations. It also offers graphical tools for assessing the fitted model.
Author: Alejandro Ordonez, Christian E. Galarza, Victor H. Lachos
Maintainer: Alejandro Ordonez <ordonezjosealejandro@gmail.com>
Diff between CensSpatial versions 1.0 dated 2016-10-08 and 1.1 dated 2016-10-17
DESCRIPTION | 8 ++-- MD5 | 26 +++++++------- NAMESPACE | 2 + R/Seminaivefin.R | 12 +++--- R/predgraphicsfin.R | 26 ++++++++------ R/predgraphicsprin.R | 48 +++++++++------------------ data/depth.rda |only man/algnaive12.Rd | 4 +- man/depth.Rd |only man/derivQfun.Rd | 14 ++++--- man/localinfmeas.Rd | 18 ++++++---- man/predSCL.Rd | 9 ++--- man/predgraphics.Rd | 90 +++++++++++++++++++-------------------------------- man/rspacens.Rd | 2 - man/seminaive_1.Rd | 8 ++-- 15 files changed, 123 insertions(+), 144 deletions(-)
Title: Deployment Interface for R Markdown Documents and Shiny
Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and
'RStudio Connect'. Supported content types include R Markdown documents,
Shiny applications, plots, and static web content.
Author: JJ Allaire
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rsconnect versions 0.4.3 dated 2016-05-03 and 0.5 dated 2016-10-16
DESCRIPTION | 12 ++-- MD5 | 35 ++++++----- NAMESPACE | 2 R/applications.R | 2 R/bundle.R | 123 ++++++++++++++++++++++++++++++++++++------ R/configureApp.R | 6 +- R/connect.R | 9 ++- R/deployApp.R | 52 +++++++++++------ R/deployDoc.R | 29 ++++++--- R/deployments.R | 35 +++++++++-- R/lucid.R | 7 +- R/onLoad.R |only R/rpubs.R | 4 - R/title.R |only man/deployApp.Rd | 13 +++- man/generateAppName.Rd |only man/listBundleFiles.Rd |only man/options.Rd | 2 tests/testthat/test-bundle.R | 9 +++ tests/testthat/test-connect.R | 1 tests/testthat/test-title.R |only 21 files changed, 256 insertions(+), 85 deletions(-)
Title: Hyperparameter Search for Gradient Boosted Trees
Description: An implementation of hyperparameter optimization for Gradient
Boosted Trees on binary classification and regression problems. The current
version provides two optimization methods: Bayesian optimization and random
search.
Author: Waley W. J. Liang
Maintainer: Waley W. J. Liang <wliang10@gmail.com>
Diff between gbts versions 1.0.0 dated 2016-10-08 and 1.0.1 dated 2016-10-16
DESCRIPTION | 13 +++++----- MD5 | 11 ++++---- NEWS.md |only R/gbt.R | 14 ++++++++++- R/gbts.R | 76 +++++++++++++++++++++++++++++++++--------------------------- README.md | 2 - man/gbts.Rd | 66 +++++++++++++++++++++++++++++----------------------- 7 files changed, 106 insertions(+), 76 deletions(-)
Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for all URL-handling needs, including encoding and decoding,
parsing, parameter extraction and modification. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes [aut, cre], Jay Jacobs [aut, cre], Drew Schmidt [aut],
Mark Greenaway [ctb], Bob Rudis [ctb], Alex Pinto [ctb], Maryam Khezrzadeh [ctb],
Adam M. Costello [cph], Jeff Bezanson [cph]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between urltools versions 1.5.1 dated 2016-08-31 and 1.6.0 dated 2016-10-16
DESCRIPTION | 17 ++-- MD5 | 62 +++++++++-------- NAMESPACE | 2 NEWS | 16 ++++ R/RcppExports.R | 45 +++++++++++- R/accessors.R | 3 R/suffix.R | 13 ++- R/urltools.R | 2 R/zzz.R | 15 ++-- inst/doc/urltools.Rmd | 3 inst/doc/urltools.html | 7 + man/encoder.Rd | 4 - man/param_remove.Rd | 2 man/param_set.Rd | 4 - man/puny.Rd |only man/scheme.Rd | 3 man/urltools.Rd | 2 src/RcppExports.cpp | 142 ++++++++++++++++++++++----------------- src/compose.cpp | 14 +-- src/param.cpp | 10 +- src/parameter.cpp | 100 ++++++++++++++++++--------- src/parameter.h | 13 +-- src/parsing.cpp | 39 ++++++++-- src/puny.cpp |only src/punycode.c |only src/punycode.h |only src/urltools.cpp | 4 - src/utf8.c |only src/utf8.h |only tests/testthat/test_get_set.R | 22 ++++++ tests/testthat/test_memory.R |only tests/testthat/test_parameters.R | 14 +++ tests/testthat/test_parsing.R | 2 tests/testthat/test_puny.R |only tests/testthat/test_suffixes.R | 25 ++++++ vignettes/urltools.Rmd | 3 36 files changed, 411 insertions(+), 177 deletions(-)
Title: Species Distribution Modelling
Description: An extensible R framework for developing species distribution
models using individual and community-based approaches, generate ensembles of
models, evaluate the models, and predict species potential distributions in
space and time.
Author: Babak Naimi, Miguel B. Araujo
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between sdm versions 1.0-25 dated 2016-07-15 and 1.0-28 dated 2016-10-16
DESCRIPTION | 16 +++++++------- MD5 | 19 ++++++++++------ NAMESPACE | 2 - R/ensemble.R |only R/evaluates.R | 40 ++++++++++++++++++++++------------- R/sdm.R | 6 ++--- R/sdmFormula.R | 38 ++++++++++++++++++++++++++++++++- R/show.R | 30 +++++++++++++++++++------- inst/CITATION |only inst/doc/quick_sdm.html | 54 ++++++++++++++++++++++++------------------------ inst/test |only man/ensemble.Rd |only 12 files changed, 134 insertions(+), 71 deletions(-)
Title: 3D Reconstruction of Archaeological Excavations
Description: A toolset for 3D reconstruction and analysis of excavations. It provides methods to reconstruct natural and artificial surfaces based on field measurements. This allows to spatially contextualize documented subunits and features. Intended to be part of a 3D visualization workflow.
Author: Clemens Schmid [cre, cph, aut]
Maintainer: Clemens Schmid <clemens@nevrome.de>
Diff between recexcavAAR versions 0.2.1 dated 2016-09-19 and 0.2.2 dated 2016-10-16
DESCRIPTION | 17 +- MD5 | 28 ++-- NEWS.md | 7 + README.md | 13 -- inst/doc/recexcavAAR-vignette-1.R | 146 ++++++++++++---------- inst/doc/recexcavAAR-vignette-1.Rmd | 158 +++++++++++++----------- inst/doc/recexcavAAR-vignette-1.html | 188 ++++++++++++++++------------- inst/doc/recexcavAAR-vignette-2.R | 191 +++++++++++++---------------- inst/doc/recexcavAAR-vignette-2.Rmd | 199 +++++++++++++------------------ inst/doc/recexcavAAR-vignette-2.html | 223 +++++++++++++++-------------------- src/fillhexa.cpp | 4 src/spitcenter.cpp | 2 tests/testthat/test_fillhexa.R | 4 vignettes/recexcavAAR-vignette-1.Rmd | 158 +++++++++++++----------- vignettes/recexcavAAR-vignette-2.Rmd | 199 +++++++++++++------------------ 15 files changed, 744 insertions(+), 793 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data, and is
also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Diff between PrevMap versions 1.3.2 dated 2015-12-05 and 1.4 dated 2016-10-16
DESCRIPTION | 17 MD5 | 74 NAMESPACE | 56 R/foo.R | 9119 +++++++++++++++++++++++++------------ R/galicia.R |only R/galicia.boundary.R |only build |only data/galicia.boundary.rdata |only data/galicia.rdata |only inst |only man/Laplace.sampling.Rd | 10 man/Laplace.sampling.SPDE.Rd |only man/Laplace.sampling.lr.Rd | 4 man/adjust.sigma2.Rd | 2 man/binary.probit.Bayes.Rd | 6 man/binomial.logistic.Bayes.Rd | 22 man/binomial.logistic.MCML.Rd | 51 man/coef.PrevMap.ps.Rd |only man/continuous.sample.Rd | 4 man/control.mcmc.Bayes.SPDE.Rd |only man/control.mcmc.MCML.Rd | 5 man/discrete.sample.Rd | 8 man/galicia.Rd |only man/galicia.boundary.Rd |only man/linear.model.Bayes.Rd | 8 man/linear.model.MLE.Rd | 21 man/lm.ps.MCML.Rd |only man/matern.kernel.Rd | 4 man/plot.pred.PrevMap.ps.Rd |only man/poisson.log.MCML.Rd | 12 man/set.par.ps.Rd |only man/spatial.pred.binomial.Bayes.Rd | 2 man/spatial.pred.binomial.MCML.Rd | 2 man/spatial.pred.linear.Bayes.Rd | 2 man/spatial.pred.linear.MLE.Rd | 2 man/spatial.pred.lm.ps.Rd |only man/spatial.pred.poisson.MCML.Rd | 2 man/summary.PrevMap.Rd | 4 man/summary.PrevMap.ps.Rd |only vignettes |only 40 files changed, 6519 insertions(+), 2918 deletions(-)
Title: Parametric Linkage Analysis in R
Description: Parametric linkage analysis and other likelihood-based pedigree analyses based on the Elston-Stewart algorithm, including singlepoint LOD scores, power analysis and computation of marker genotype distributions. Multipoint analysis is provided through a convenient MERLIN wrapper. Includes many utility functions for creating, manipulating and plotting pedigrees, markers and linkage results.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <magnusdv@studmed.uio.no>
Diff between paramlink versions 0.9-8 dated 2016-04-27 and 0.9-9 dated 2016-10-16
DESCRIPTION | 13 +- MD5 | 26 ++--- NAMESPACE | 1 NEWS | 18 +++ R/as.matrix.linkdat.R | 4 R/createPedigree.R | 216 ++++++++++++++++++++++++++++++++++++++++------- R/linkdat.R | 6 - R/utils.R | 28 +++++- man/as.matrix.linkdat.Rd | 5 - man/createPedigree.Rd | 97 +++++++++++++++------ man/inbreeding.Rd | 18 ++- man/linkdat.Rd | 5 - man/linkdat.utils.Rd | 28 ++---- man/mergePed.Rd | 5 - 14 files changed, 362 insertions(+), 108 deletions(-)
Title: Fused Lasso Approach in Regression Coefficient Clustering
Description: Fused lasso method to cluster and estimate regression coefficients
of the same covariate across different data sets when a large number of
independent data sets are combined. Package supports Gaussian, binomial,
Poisson and Cox PH models.
Author: Lu Tang, Ling Zhou, Peter X.K. Song
Maintainer: Lu Tang <lutang@umich.edu>
Diff between metafuse versions 1.0-1 dated 2015-11-07 and 2.0-1 dated 2016-10-16
metafuse-1.0-1/metafuse/R/metafuse.R |only metafuse-2.0-1/metafuse/DESCRIPTION | 18 +++-- metafuse-2.0-1/metafuse/MD5 | 16 ++--- metafuse-2.0-1/metafuse/NAMESPACE | 8 +- metafuse-2.0-1/metafuse/R/metafuse_functions.R |only metafuse-2.0-1/metafuse/build/partial.rdb |binary metafuse-2.0-1/metafuse/man/datagenerator.Rd | 45 ++++++++------ metafuse-2.0-1/metafuse/man/metafuse-package.Rd | 50 +++++++--------- metafuse-2.0-1/metafuse/man/metafuse.Rd | 74 ++++++++++++------------ metafuse-2.0-1/metafuse/man/metafuse.l.Rd | 62 ++++++++++---------- 10 files changed, 143 insertions(+), 130 deletions(-)
Title: Currency Formatting and Conversion
Description: Reformat currency-based data as numeric values (or numeric values
as currency-based data) and convert between currencies.
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between lucr versions 0.1.1 dated 2015-10-28 and 0.2.0 dated 2016-10-16
DESCRIPTION | 12 ++++++---- MD5 | 34 +++++++++++++++--------------- NAMESPACE | 2 - NEWS.md | 2 - R/RcppExports.R | 2 - R/api.R | 3 ++ README.md | 5 ++-- man/conversion_rates.Rd | 2 - man/currency_convert.Rd | 2 - man/from_currency.Rd | 2 - man/historic_currency.Rd | 5 ++-- man/list_currencies.Rd | 2 - man/lucr.Rd | 2 - man/to_currency.Rd | 3 +- src/RcppExports.cpp | 36 +++++++++++++++---------------- src/format.h | 44 +++++++++++++++++++++++++++++++-------- src/rrency.cpp | 6 ++--- tests/testthat/test_conversion.R | 7 ++++++ 18 files changed, 106 insertions(+), 65 deletions(-)
Title: IBM in-Database Analytics for R
Description: Functionality required to efficiently use R with
IBM DB2(C) for Linux, Unix and Windows, IBM dashDB(C) as well as
DB2 for z/OS (C) in conjunction with IBM DB2 Analytics Accelerator (C).
Many basic and complex R operations are pushed down into the database,
which removes the main memory boundary of R and allows to make full
use of parallel processing in the underlying database.
Author: IBM Corporation
Maintainer: Alexander Eckert <inza@de.ibm.com>
Diff between ibmdbR versions 1.47.1 dated 2015-12-10 and 1.48.0 dated 2016-10-16
DESCRIPTION | 19 MD5 | 122 ++-- NAMESPACE | 21 NEWS.md |only R/AllClass.R | 52 +- R/aggregate.R | 182 +++---- R/close.R | 45 - R/coldef.R | 730 ++++++++++++++-------------- R/connect.R | 62 +- R/connection.R | 369 +++++++++----- R/data.frame.R | 690 +++++++++++++-------------- R/data.frame.methods.R | 274 +++++----- R/divClust.R |only R/glm.R |only R/idadf.R | 38 - R/kMeans.R | 445 +++++++++-------- R/list.R | 458 +++++++++--------- R/lm.R | 1058 ++++++++++++++++++++++------------------- R/merge.R | 302 +++++------ R/model.management.R | 214 +++++--- R/nb.R | 454 ++++++++++------- R/parse.formula.R | 270 ++++++---- R/plot.idaLm.R | 1002 +++++++++++++++++++-------------------- R/rules.R | 520 ++++++++++++-------- R/sample.R | 214 ++++---- R/save.R | 170 +++++- R/sql.R | 1068 +++++++++++++++++++++++++++--------------- R/statistics.R | 898 +++++++++++++++++------------------ R/tree.R | 864 +++++++++++++++++---------------- R/twoStep.R |only R/update.R | 52 +- build/vignette.rds |binary inst/doc/ibmdbR.Rnw | 4 inst/doc/ibmdbR.pdf |binary man/as.ida.data.frame.Rd | 125 ++-- man/createview.Rd | 105 ++-- man/ida.col.def.methods.Rd | 74 +- man/ida.data.frame.Rd | 220 ++++---- man/ida.data.frame.methods.Rd | 112 ++-- man/ida.list.Rd | 180 +++---- man/ida.list.methods.Rd | 72 +- man/idaArule.Rd | 180 +++---- man/idaConnect.Rd | 106 ++-- man/idaDivCluster.Rd |only man/idaDropModel.Rd | 84 +-- man/idaGetModelName.Rd | 86 +-- man/idaGlm.Rd |only man/idaKMeans.Rd | 222 ++++---- man/idaListAccelerators.Rd |only man/idaListModels.Rd | 102 ++-- man/idaLm.Rd | 311 ++++++------ man/idaMerge.Rd | 228 ++++---- man/idaNb.Rd | 173 +++--- man/idaQuery.Rd | 126 ++-- man/idaRetrieveModel.Rd | 96 +-- man/idaSample.Rd | 162 +++--- man/idaTable.Rd | 110 ++-- man/idaTree.Rd | 254 ++++----- man/idaTwoStep.Rd |only man/idadf.Rd | 148 ++--- man/idatools.Rd | 164 +++--- man/init.Rd | 104 ++-- man/overview.Rd | 82 +-- man/showtables.Rd | 91 +-- tests/main.R | 66 +- vignettes/ibmdbR.Rnw | 4 66 files changed, 7770 insertions(+), 6614 deletions(-)
Title: A Package for Graphical Modelling in R
Description: The 'gRbase' package provides general features
which are used by other graphical modelling packages, in particular
by the packages 'gRain', 'gRim' and 'gRc'.
'gRbase' contains several data sets relevant for use in connection with
graphical models. Almost all data sets used in the book Graphical
Models with R (2012) are contained in 'gRbase'.
'gRbase' implements several graph algorithms (based mainly on
representing graphs as adjacency matrices - either in the form
of a standard matrix or a sparse matrix). Some graph
algorithms are:
(i) maximum cardinality search (for marked and unmarked graphs).
(ii) moralize.
(iii) triangulate.
(iv) junction tree.
'gRbase' facilitates array operations,
'gRbase' implements functions for testing for conditional independence.
'gRbase' illustrates how hierarchical log-linear models may be
implemented and describes concept of graphical meta
data. These features, however, are not maintained anymore and
remains in 'gRbase' only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The 'gRbase' Package, Journal of Statistical Software, Vol 14,
No 17, 2005.
NOTICE Proper functionality of 'gRbase' requires that the packages graph,
'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for
installation instructions please refer to the web page given below.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRbase versions 1.7-5 dated 2016-02-20 and 1.8-1 dated 2016-10-16
gRbase-1.7-5/gRbase/R/array-addon.R |only gRbase-1.7-5/gRbase/R/array-parray.R |only gRbase-1.7-5/gRbase/R/array-simulateArray.R |only gRbase-1.7-5/gRbase/R/array-table-operations.R |only gRbase-1.7-5/gRbase/R/arrayCombine.R |only gRbase-1.7-5/gRbase/R/c-arrayops.R |only gRbase-1.7-5/gRbase/R/c-combnPrimR.R |only gRbase-1.7-5/gRbase/R/c-setops.R |only gRbase-1.7-5/gRbase/R/c-utilities.R |only gRbase-1.7-5/gRbase/R/graph-algo-JunctionTree.R |only gRbase-1.7-5/gRbase/R/graph-algo-MPD.R |only gRbase-1.7-5/gRbase/R/graph-algo-mcs.R |only gRbase-1.7-5/gRbase/R/graph-algo-minimalTriang.R |only gRbase-1.7-5/gRbase/R/graph-algo-moralize.R |only gRbase-1.7-5/gRbase/R/graph-algo-rip.R |only gRbase-1.7-5/gRbase/R/graph-algo-topoSort.R |only gRbase-1.7-5/gRbase/R/graph-algo-triangulate.R |only gRbase-1.7-5/gRbase/R/tableInterface.R |only gRbase-1.7-5/gRbase/data/BodyFat.txt.gz |only gRbase-1.7-5/gRbase/data/cad1.txt.gz |only gRbase-1.7-5/gRbase/data/cad2.txt.gz |only gRbase-1.7-5/gRbase/data/carcass.txt.gz |only gRbase-1.7-5/gRbase/data/carcassall.txt.gz |only gRbase-1.7-5/gRbase/data/dietox.txt.gz |only gRbase-1.7-5/gRbase/data/math.txt.gz |only gRbase-1.7-5/gRbase/data/mathmark.txt.gz |only gRbase-1.7-5/gRbase/data/milkcomp.txt.gz |only gRbase-1.7-5/gRbase/data/milkcomp1.txt.gz |only gRbase-1.7-5/gRbase/data/rats.txt.gz |only gRbase-1.7-5/gRbase/data/wine.txt.gz |only gRbase-1.7-5/gRbase/inst/doc/gRbase-arrayops.R |only gRbase-1.7-5/gRbase/inst/doc/gRbase-arrayops.Rnw |only gRbase-1.7-5/gRbase/inst/doc/gRbase-arrayops.pdf |only gRbase-1.7-5/gRbase/man/DATA-BodyFat.Rd |only gRbase-1.7-5/gRbase/man/DATA-Nutrimouse.Rd |only gRbase-1.7-5/gRbase/man/DATA-ashtrees.Rd |only gRbase-1.7-5/gRbase/man/DATA-breastcancer.Rd |only gRbase-1.7-5/gRbase/man/DATA-cad.Rd |only gRbase-1.7-5/gRbase/man/DATA-carcass.Rd |only gRbase-1.7-5/gRbase/man/DATA-chestSim.Rd |only gRbase-1.7-5/gRbase/man/DATA-dietox.Rd |only gRbase-1.7-5/gRbase/man/DATA-dumping.Rd |only gRbase-1.7-5/gRbase/man/DATA-lizard.Rd |only gRbase-1.7-5/gRbase/man/DATA-mathmark.Rd |only gRbase-1.7-5/gRbase/man/DATA-mildew.Rd |only gRbase-1.7-5/gRbase/man/DATA-milkcomp.Rd |only gRbase-1.7-5/gRbase/man/DATA-rats.Rd |only gRbase-1.7-5/gRbase/man/DATA-reinis.Rd |only gRbase-1.7-5/gRbase/man/DATA-wine.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-coerce.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-edgeList.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-getClique.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-glist2adjMAT.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-is-graph.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-isGraphical.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-mcs.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-minimalTriang.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-moralize.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-mpd.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-operations1.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-querygraph.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-randomDag.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-rip.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-topoSort.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-triangulate.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-ugdag.Rd |only gRbase-1.7-5/gRbase/man/GraphAlgo-vpar.Rd |only gRbase-1.7-5/gRbase/man/array-parray.Rd |only gRbase-1.7-5/gRbase/man/array-simulateArray.Rd |only gRbase-1.7-5/gRbase/man/array-tabMult.Rd |only gRbase-1.7-5/gRbase/man/array-table-operations.Rd |only gRbase-1.7-5/gRbase/man/arrayCombine.Rd |only gRbase-1.7-5/gRbase/man/compile-propagate.Rd |only gRbase-1.7-5/gRbase/man/iplot.Rd |only gRbase-1.7-5/gRbase/src/MakevarsOLD |only gRbase-1.7-5/gRbase/src/c-arrayops.c |only gRbase-1.7-5/gRbase/src/c-combnPrimC.c |only gRbase-1.7-5/gRbase/src/c-setops.c |only gRbase-1.7-5/gRbase/src/c-utilities.c |only gRbase-1.7-5/gRbase/vignettes/gRbase-arrayops.Rnw |only gRbase-1.8-1/gRbase/ChangeLog | 1120 ++++++------ gRbase-1.8-1/gRbase/DESCRIPTION | 71 gRbase-1.8-1/gRbase/MD5 | 264 +- gRbase-1.8-1/gRbase/NAMESPACE | 364 ++-- gRbase-1.8-1/gRbase/R/Generics.R | 105 - gRbase-1.8-1/gRbase/R/RcppExports.R | 70 gRbase-1.8-1/gRbase/R/combnC-c.R |only gRbase-1.8-1/gRbase/R/cov2pcor.R |only gRbase-1.8-1/gRbase/R/data-ashtrees.R |only gRbase-1.8-1/gRbase/R/data-bodyfat.R |only gRbase-1.8-1/gRbase/R/data-breastcancer.R |only gRbase-1.8-1/gRbase/R/data-cad.R |only gRbase-1.8-1/gRbase/R/data-carcass.R |only gRbase-1.8-1/gRbase/R/data-chestsim.R |only gRbase-1.8-1/gRbase/R/data-dietox.R |only gRbase-1.8-1/gRbase/R/data-dumping.R |only gRbase-1.8-1/gRbase/R/data-lizard.R |only gRbase-1.8-1/gRbase/R/data-mathmark.R |only gRbase-1.8-1/gRbase/R/data-mildew.R |only gRbase-1.8-1/gRbase/R/data-milkcomp.R |only gRbase-1.8-1/gRbase/R/data-nutrimouse.R |only gRbase-1.8-1/gRbase/R/data-rats.R |only gRbase-1.8-1/gRbase/R/data-reinis.R |only gRbase-1.8-1/gRbase/R/data-winecomp.R |only gRbase-1.8-1/gRbase/R/gRbase-internal.R |only gRbase-1.8-1/gRbase/R/gRbase-package.R |only gRbase-1.8-1/gRbase/R/gRbase-utilities-FIXME-cleanup.R | 345 +-- gRbase-1.8-1/gRbase/R/graph-coerce.R | 562 +----- gRbase-1.8-1/gRbase/R/graph-create-ugdag.R | 194 +- gRbase-1.8-1/gRbase/R/graph-iplot.R |only gRbase-1.8-1/gRbase/R/graph-mcs.R |only gRbase-1.8-1/gRbase/R/graph-mintriang.R |only gRbase-1.8-1/gRbase/R/graph-moralize.R |only gRbase-1.8-1/gRbase/R/graph-mpd.R |only gRbase-1.8-1/gRbase/R/graph-properties.R | 781 +++++--- gRbase-1.8-1/gRbase/R/graph-querygraph.R | 418 ++-- gRbase-1.8-1/gRbase/R/graph-rip.R |only gRbase-1.8-1/gRbase/R/graph-topoSort.R |only gRbase-1.8-1/gRbase/R/graph-triangulate.R |only gRbase-1.8-1/gRbase/R/graph-utilities.R | 598 ++++-- gRbase-1.8-1/gRbase/R/graph-xxx2yyy.R |only gRbase-1.8-1/gRbase/R/processFormula.R | 1106 ++++++------ gRbase-1.8-1/gRbase/R/t_arDist.R |only gRbase-1.8-1/gRbase/R/t_array-algebra-cR.R |only gRbase-1.8-1/gRbase/R/t_array-algebra.R |only gRbase-1.8-1/gRbase/R/t_array-create.R |only gRbase-1.8-1/gRbase/R/t_array-lowlevel-ops.R |only gRbase-1.8-1/gRbase/R/t_array-operations-bristol.R |only gRbase-1.8-1/gRbase/R/t_array-operations.R |only gRbase-1.8-1/gRbase/R/t_array-parray.R |only gRbase-1.8-1/gRbase/R/t_array-properties.R |only gRbase-1.8-1/gRbase/R/t_array-simulate-R.R |only gRbase-1.8-1/gRbase/R/t_array-slice.R |only gRbase-1.8-1/gRbase/R/u_setops-c.R |only gRbase-1.8-1/gRbase/R/u_utilities-c.R |only gRbase-1.8-1/gRbase/R/yyOLD-gRbase.R | 1525 ++++++++-------- gRbase-1.8-1/gRbase/R/yyyPrim.R | 68 gRbase-1.8-1/gRbase/TODO | 12 gRbase-1.8-1/gRbase/build/vignette.rds |binary gRbase-1.8-1/gRbase/data/BodyFat.RData |only gRbase-1.8-1/gRbase/data/cad1.RData |only gRbase-1.8-1/gRbase/data/cad2.RData |only gRbase-1.8-1/gRbase/data/carcass.RData |only gRbase-1.8-1/gRbase/data/carcassall.RData |only gRbase-1.8-1/gRbase/data/dietox.RData |only gRbase-1.8-1/gRbase/data/math.RData |only gRbase-1.8-1/gRbase/data/mathmark.RData |only gRbase-1.8-1/gRbase/data/milkcomp.RData |only gRbase-1.8-1/gRbase/data/milkcomp1.RData |only gRbase-1.8-1/gRbase/data/rats.RData |only gRbase-1.8-1/gRbase/data/wine.RData |only gRbase-1.8-1/gRbase/inst/CITATION | 40 gRbase-1.8-1/gRbase/inst/doc/gRbase-arrays.R |only gRbase-1.8-1/gRbase/inst/doc/gRbase-arrays.Rnw |only gRbase-1.8-1/gRbase/inst/doc/gRbase-arrays.pdf |only gRbase-1.8-1/gRbase/inst/doc/gRbase-graphs.pdf |binary gRbase-1.8-1/gRbase/inst/include/gRbase_RcppExports.h | 695 +++---- gRbase-1.8-1/gRbase/man/BodyFat.Rd |only gRbase-1.8-1/gRbase/man/Nutrimouse.Rd |only gRbase-1.8-1/gRbase/man/ZOLD-gModel.Rd | 122 - gRbase-1.8-1/gRbase/man/ZOLD-gRfit.Rd | 110 - gRbase-1.8-1/gRbase/man/ZOLD-gmData.Rd | 314 +-- gRbase-1.8-1/gRbase/man/ZOLD-hllm.Rd | 122 - gRbase-1.8-1/gRbase/man/ZOLD-validVarTypes.Rd | 86 gRbase-1.8-1/gRbase/man/array-algebra.Rd |only gRbase-1.8-1/gRbase/man/array-create.Rd |only gRbase-1.8-1/gRbase/man/array-dimnames.Rd |only gRbase-1.8-1/gRbase/man/array-distribution.Rd |only gRbase-1.8-1/gRbase/man/array-normalize.Rd |only gRbase-1.8-1/gRbase/man/array-operations.Rd |only gRbase-1.8-1/gRbase/man/array-properties.Rd |only gRbase-1.8-1/gRbase/man/array-slice.Rd |only gRbase-1.8-1/gRbase/man/arraypack-internal.Rd | 136 - gRbase-1.8-1/gRbase/man/ashtrees.Rd |only gRbase-1.8-1/gRbase/man/breastcancer.Rd |only gRbase-1.8-1/gRbase/man/cad.Rd |only gRbase-1.8-1/gRbase/man/carcass.Rd |only gRbase-1.8-1/gRbase/man/chestSim.Rd |only gRbase-1.8-1/gRbase/man/combnPrim.Rd | 136 - gRbase-1.8-1/gRbase/man/compareModels.Rd | 62 gRbase-1.8-1/gRbase/man/cov2pcor.Rd | 79 gRbase-1.8-1/gRbase/man/dietox.Rd |only gRbase-1.8-1/gRbase/man/dumping.Rd |only gRbase-1.8-1/gRbase/man/gRbase-generics.Rd |only gRbase-1.8-1/gRbase/man/gRbase-internal.Rd | 495 ++--- gRbase-1.8-1/gRbase/man/gRbase-utilities.Rd | 122 - gRbase-1.8-1/gRbase/man/gRbase.Rd | 108 - gRbase-1.8-1/gRbase/man/graph-cliques.Rd |only gRbase-1.8-1/gRbase/man/graph-coerce.Rd |only gRbase-1.8-1/gRbase/man/graph-create.Rd |only gRbase-1.8-1/gRbase/man/graph-edgeList.Rd |only gRbase-1.8-1/gRbase/man/graph-gcproperties.Rd |only gRbase-1.8-1/gRbase/man/graph-iplot.Rd |only gRbase-1.8-1/gRbase/man/graph-is.Rd |only gRbase-1.8-1/gRbase/man/graph-mcs.Rd |only gRbase-1.8-1/gRbase/man/graph-minimaltriang.Rd |only gRbase-1.8-1/gRbase/man/graph-moralize.Rd |only gRbase-1.8-1/gRbase/man/graph-mpd.Rd |only gRbase-1.8-1/gRbase/man/graph-query.Rd |only gRbase-1.8-1/gRbase/man/graph-randomdag.Rd |only gRbase-1.8-1/gRbase/man/graph-rip.Rd |only gRbase-1.8-1/gRbase/man/graph-toposort.Rd |only gRbase-1.8-1/gRbase/man/graph-triangulate.Rd |only gRbase-1.8-1/gRbase/man/graph-vpar.Rd |only gRbase-1.8-1/gRbase/man/graph-xxx2yyy.Rd |only gRbase-1.8-1/gRbase/man/lizard.Rd |only gRbase-1.8-1/gRbase/man/mathmark.Rd |only gRbase-1.8-1/gRbase/man/mildew.Rd |only gRbase-1.8-1/gRbase/man/milkcomp.Rd |only gRbase-1.8-1/gRbase/man/old-array-operations.Rd |only gRbase-1.8-1/gRbase/man/old-parray.Rd |only gRbase-1.8-1/gRbase/man/rats.Rd |only gRbase-1.8-1/gRbase/man/reinis.Rd |only gRbase-1.8-1/gRbase/man/removeRedundant.Rd | 158 - gRbase-1.8-1/gRbase/man/simulateArray.Rd |only gRbase-1.8-1/gRbase/man/wine.Rd |only gRbase-1.8-1/gRbase/src/RcppExports.cpp | 1533 ++++++++--------- gRbase-1.8-1/gRbase/src/_t_array_properties.cpp |only gRbase-1.8-1/gRbase/src/_t_array_properties.h |only gRbase-1.8-1/gRbase/src/_t_arrayops.c |only gRbase-1.8-1/gRbase/src/_t_tableCore.cpp | 287 ++- gRbase-1.8-1/gRbase/src/_u_setops.c |only gRbase-1.8-1/gRbase/src/_u_utilities.c |only gRbase-1.8-1/gRbase/src/combnC.c | 26 gRbase-1.8-1/gRbase/src/combnPrimC.c |only gRbase-1.8-1/gRbase/src/concatenate.h | 53 gRbase-1.8-1/gRbase/vignettes/gRbase-arrays.Rnw |only gRbase-1.8-1/gRbase/vignettes/gRbase.bib | 326 +-- 228 files changed, 6592 insertions(+), 6021 deletions(-)
More information about DirectStandardisation at CRAN
Permanent link
Title: Plotting D3 Hierarchical Plots in R and Shiny
Description: Plotting hierarchical plots in R such as Sunburst, Treemap, Circle Treemap, Partition Chart, collapsible indented tree and collapsible tree.
Author: Antoine GUILLOT [cre],
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org. The partitionChart, sunburst, the treemap, the
zoomable circlePacking, the collapsible indented tree and the
collapsible tree are all derived from his works.)
Maintainer: Antoine GUILLOT <antoine.guil@outlook.fr>
Diff between D3partitionR versions 0.1 dated 2016-10-01 and 0.2.0 dated 2016-10-16
DESCRIPTION | 15 MD5 | 14 R/AdditionalFunctions.R | 24 R/D3partitionR.R | 64 +- inst/htmlwidgets/D3partitionR.js | 936 +++++++++++++++++++++++++++------- inst/htmlwidgets/lib/style/circle.css | 30 + man/D3partitionR-shiny.Rd | 2 man/D3partitionR.Rd | 45 + 8 files changed, 886 insertions(+), 244 deletions(-)
Title: A Companion to the e-Book "YaRrr!: The Pirate's Guide to R"
Description: Contains a mixture of functions and data sets referred to in the introductory e-book "YaRrr!: The Pirate's Guide to R". The latest version of the e-book is available for free at <https://www.thepiratesguidetor.com>.
Author: Nathaniel Phillips [aut, cre]
Maintainer: Nathaniel Phillips <yarrr.book@gmail.com>
Diff between yarrr versions 0.0.9 dated 2016-10-08 and 0.1.1 dated 2016-10-16
DESCRIPTION | 12 MD5 | 31 - NAMESPACE | 1 NEWS.md |only R/pirateplot_function.R | 1018 ++++++++++++++++++++++------------------------- README.md | 52 -- build/vignette.rds |binary inst/doc/guide.html | 6 inst/doc/piratepal.R | 11 inst/doc/piratepal.Rmd | 13 inst/doc/piratepal.html | 17 inst/doc/pirateplot.R | 229 +++++++--- inst/doc/pirateplot.Rmd | 297 +++++++++---- inst/doc/pirateplot.html | 343 ++++++++++++--- man/pirateplot.Rd | 153 +++++-- vignettes/piratepal.Rmd | 13 vignettes/pirateplot.Rmd | 297 +++++++++---- 17 files changed, 1481 insertions(+), 1012 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
Eli Grey [ctb, cph] (FileSaver library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 1.0 dated 2016-07-08 and 1.1 dated 2016-10-16
DESCRIPTION | 16 +- MD5 | 104 ++++++++++--------- NAMESPACE | 3 R/beamer_presentation.R | 101 +++++++++++++++--- R/github_document.R | 3 R/html_dependencies.R | 11 ++ R/html_document.R | 42 +++++++ R/html_document_base.R | 2 R/html_fragment.R | 8 - R/html_notebook.R | 42 +++++++ R/html_notebook_output.R | 28 ++--- R/html_paged.R |only R/html_resources.R | 3 R/html_vignette.R | 2 R/ioslides_presentation.R | 11 ++ R/knit_print.R |only R/md_document.R | 2 R/output_format.R | 37 ++++++ R/pandoc.R | 24 ++++ R/params.R | 20 ++- R/pdf_document.R | 2 R/render.R | 167 +++++++++++++++++++++++++------ R/render_site.R | 3 R/shiny.R | 5 R/slidy_presentation.R | 11 ++ R/util.R | 54 ++++++++-- R/word_document.R | 4 R/zzz.R | 28 +++++ inst/NEWS | 49 +++++++++ inst/rmd/h/default.html | 50 +++++++++ inst/rmd/h/navigation-1.1/codefolding.js | 5 inst/rmd/h/pagedtable-0.0.1 |only inst/rmd/ioslides/default.html | 6 - inst/rmd/latex/default-1.14.tex | 8 - inst/rmd/latex/default-1.15.2.tex | 8 - inst/rmd/latex/default-1.17.0.2.tex | 7 - inst/rmd/latex/default.tex | 1 inst/rmd/slidy/default.html | 9 + man/beamer_presentation.Rd | 15 ++ man/github_document.Rd | 14 ++ man/html_document.Rd | 11 +- man/html_fragment.Rd | 13 ++ man/html_notebook_output.Rd | 6 - man/html_vignette.Rd | 14 ++ man/ioslides_presentation.Rd | 17 ++- man/md_document.Rd | 13 ++ man/navbar_html.Rd |only man/output_format.Rd | 15 ++ man/pdf_document.Rd | 18 ++- man/render.Rd | 2 man/slidy_presentation.Rd | 17 ++- man/word_document.Rd | 14 ++ man/yaml_front_matter.Rd |only tests/testthat/test-formats.R | 21 ++- tests/testthat/test-formats.Rmd | 10 + 55 files changed, 872 insertions(+), 204 deletions(-)
More information about ebimetagenomics at CRAN
Permanent link
Title: Simulation, Estimation and Forecasting of Beta-Skew-t-EGARCH
Models
Description: Simulation, estimation and forecasting of first-order Beta-Skew-t-EGARCH models with leverage (one-component, two-component, skewed versions).
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between betategarch versions 3.2 dated 2014-09-18 and 3.3 dated 2016-10-16
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 1 + NEWS | 6 ++++++ man/betategarch-package.Rd | 12 ++++++++---- man/coef.tegarch.Rd | 5 ++++- man/nasdaq.Rd | 5 +++-- man/predict.tegarch.Rd | 4 +++- man/tegarch.Rd | 5 ++++- man/tegarchLogl.Rd | 4 +++- man/tegarchSim.Rd | 4 +++- src/betategarch.cpp | 8 ++++---- 12 files changed, 56 insertions(+), 32 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-18 0.1.3
2016-08-13 0.1.2
2016-08-06 0.1.0
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito
<mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 0.5.1 dated 2015-10-20 and 1.0.0 dated 2016-10-16
MAINT.Data-0.5.1/MAINT.Data/man/IdtClMANOVA-class.Rd |only MAINT.Data-0.5.1/MAINT.Data/man/IdtHetNMANOVA-class.Rd |only MAINT.Data-0.5.1/MAINT.Data/man/IdtSngDE-class.Rd |only MAINT.Data-0.5.1/MAINT.Data/man/lda-methods.Rd |only MAINT.Data-0.5.1/MAINT.Data/man/qda-methods.Rd |only MAINT.Data-0.5.1/MAINT.Data/man/stdEr.Rd |only MAINT.Data-1.0.0/MAINT.Data/CHANGELOG | 20 MAINT.Data-1.0.0/MAINT.Data/DESCRIPTION | 27 MAINT.Data-1.0.0/MAINT.Data/MD5 | 124 +- MAINT.Data-1.0.0/MAINT.Data/NAMESPACE | 31 MAINT.Data-1.0.0/MAINT.Data/R/Azzalini_sn_code.R |only MAINT.Data-1.0.0/MAINT.Data/R/CPLogLik.grads.R |only MAINT.Data-1.0.0/MAINT.Data/R/CPMaxLik.R |only MAINT.Data-1.0.0/MAINT.Data/R/CholeskiGradients.R | 23 MAINT.Data-1.0.0/MAINT.Data/R/ClasGenMetDef.R | 160 ++ MAINT.Data-1.0.0/MAINT.Data/R/Conversions.R |only MAINT.Data-1.0.0/MAINT.Data/R/DACrossVal.R | 88 + MAINT.Data-1.0.0/MAINT.Data/R/IData.R | 191 +-- MAINT.Data-1.0.0/MAINT.Data/R/IdtMaxLikN.R |only MAINT.Data-1.0.0/MAINT.Data/R/IdtMaxLikNC2.R | 67 - MAINT.Data-1.0.0/MAINT.Data/R/IdtMaxLikSN.R |only MAINT.Data-1.0.0/MAINT.Data/R/MxtDist.fit.R |only MAINT.Data-1.0.0/MAINT.Data/R/RepLOptim.R | 239 ++-- MAINT.Data-1.0.0/MAINT.Data/R/RestCPMaxLik.R |only MAINT.Data-1.0.0/MAINT.Data/R/Rfasttle.R |only MAINT.Data-1.0.0/MAINT.Data/R/Rfulltle.R |only MAINT.Data-1.0.0/MAINT.Data/R/RobMxtDEst.R |only MAINT.Data-1.0.0/MAINT.Data/R/Robldaqda.R |only MAINT.Data-1.0.0/MAINT.Data/R/SNmle.R |only MAINT.Data-1.0.0/MAINT.Data/R/SkNObsLikGradients.R |only MAINT.Data-1.0.0/MAINT.Data/R/fasttle.R |only MAINT.Data-1.0.0/MAINT.Data/R/feasmu0.R |only MAINT.Data-1.0.0/MAINT.Data/R/fulltle.R |only MAINT.Data-1.0.0/MAINT.Data/R/lqda.R | 497 ++++++-- MAINT.Data-1.0.0/MAINT.Data/R/mle.R | 893 ++++++++-------- MAINT.Data-1.0.0/MAINT.Data/R/mleVCOV.R |only MAINT.Data-1.0.0/MAINT.Data/R/msnCP.dev.R |only MAINT.Data-1.0.0/MAINT.Data/R/msnCP.dev.grad.R |only MAINT.Data-1.0.0/MAINT.Data/R/pdwt.solve.R |only MAINT.Data-1.0.0/MAINT.Data/R/sknda.R |only MAINT.Data-1.0.0/MAINT.Data/R/sysdata.rda |only MAINT.Data-1.0.0/MAINT.Data/data/CarsData.RData |only MAINT.Data-1.0.0/MAINT.Data/man/BestModel-methods.Rd | 29 MAINT.Data-1.0.0/MAINT.Data/man/CarsData.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/ConfTests-class.Rd | 33 MAINT.Data-1.0.0/MAINT.Data/man/DACrossVal.Rd | 40 MAINT.Data-1.0.0/MAINT.Data/man/IData-class.Rd | 37 MAINT.Data-1.0.0/MAINT.Data/man/IData.Rd | 15 MAINT.Data-1.0.0/MAINT.Data/man/IdtE-class.Rd | 30 MAINT.Data-1.0.0/MAINT.Data/man/IdtMANOVA-class.Rd | 68 - MAINT.Data-1.0.0/MAINT.Data/man/IdtMxE-class.Rd | 31 MAINT.Data-1.0.0/MAINT.Data/man/IdtMxNDE-class.Rd | 44 MAINT.Data-1.0.0/MAINT.Data/man/IdtMxNDRE-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/IdtMxNandSNDE-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/IdtMxSNDE-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/IdtNDE-class.Rd | 15 MAINT.Data-1.0.0/MAINT.Data/man/IdtNandSNDE-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/IdtSNDE-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/IdtSNgenda-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/IdtSNlocda-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/IdtSngNDE-class.Rd | 37 MAINT.Data-1.0.0/MAINT.Data/man/IdtSngNDRE-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/IdtSngNandSNDE-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/IdtSngSNDE-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/Idtlda-class.Rd | 20 MAINT.Data-1.0.0/MAINT.Data/man/Idtqda-class.Rd | 88 - MAINT.Data-1.0.0/MAINT.Data/man/MAINT.Data-internal.Rd | 168 ++- MAINT.Data-1.0.0/MAINT.Data/man/MAINT.Data-package.Rd | 286 +++-- MAINT.Data-1.0.0/MAINT.Data/man/MANOVA-methods.Rd | 158 +- MAINT.Data-1.0.0/MAINT.Data/man/RepLOptim.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/RobEstControl-class.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/RobEstControl.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/RobMxtDEst-methods.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/coef-methods.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/da-methods.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/extmatrix.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/fasttle-methods.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/fulltle-methods.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/mle-methods.Rd | 73 - MAINT.Data-1.0.0/MAINT.Data/man/stdEr-methods.Rd |only MAINT.Data-1.0.0/MAINT.Data/man/testMod-methods.Rd | 109 - MAINT.Data-1.0.0/MAINT.Data/man/vcov-methods.Rd |only MAINT.Data-1.0.0/MAINT.Data/src |only 83 files changed, 2277 insertions(+), 1364 deletions(-)
Title: Tidy Up and Test XPath Queries on HTML and XML Content
Description: HTML documents can be beautiful and pristine. They can also be
wretched, evil, malformed demon-spawn. Now, you can tidy up that HTML and XHTML
before processing it with your favorite angle-bracket crunching tools, going beyond
the limited tidying that 'libxml2' affords in the 'XML' and 'xml2' packages and
taming even the ugliest HTML code generated by the likes of Google Docs and Microsoft
Word. It's also possible to use the functions provided to format or "pretty print"
HTML content as it is being tidied. Utilities are also included that make it
possible to view formatted and "pretty printed" HTML/XML
content from HTML/XML document objects, nodes, node sets and plain character HTML/XML
using 'vkbeautify' (by Vadim Kiryukhin) and 'highlight.js' (by Ivan Sagalaev).
Also (optionally) enables filtering of nodes via XPath or viewing an HTML/XML document
in "tree" view using 'xml-viewer' (by Julian Gruber). See
<https://github.com/vkiryukhin/vkBeautify> and
<https://github.com/juliangruber/xml-viewer> for more information about 'vkbeautify'
and 'xml-viewer', respectively.
Author: Bob Rudis [aut, cre],
Dave Raggett [ctb, aut] (Original HTML Tidy library),
Charles Reitzel [ctb, aut] (Modern HTML Tidy library),
Björn Höhrmann [ctb, aut] (HTML5 Support),
Kenton Russell [aut, ctb] (xml-viewer integration),
Vadim Kiryukhin [ctb, cph] (vkbeautify library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Julian Gruber [ctb, cph] (xml-viewer library)
Maintainer: Bob Rudis <bob@rud.is>
Diff between htmltidy versions 0.2.0 dated 2016-09-10 and 0.3.0 dated 2016-10-16
DESCRIPTION | 47 +++++++++--- MD5 | 158 +++++++++++++++++++++++++++++++++++++---- NAMESPACE | 12 +++ NEWS.md | 14 ++- R/RcppExports.R | 6 - R/htmltidy-package.r | 14 ++- R/response.r |only R/shiny-tree-view.R |only R/shiny.R |only R/tidy.r | 44 +++++++---- R/xmltreeview.R |only R/xmlview.R |only README.md | 59 +++++++++++++-- inst/COPYRIGHTS | 10 ++ inst/extdata |only inst/htmlwidgets |only man/highlight_styles.Rd |only man/htmltidy.Rd | 12 ++- man/renderXmlview.Rd |only man/tidy_html.Rd | 41 +++++++--- man/xml_tree_view.Rd |only man/xml_view.Rd |only man/xmltreeview-shiny.Rd |only man/xmlviewOutput.Rd |only src/RcppExports.cpp | 15 ++- src/htmltidy.cpp | 40 ++++++++-- tests/testthat/test-htmltidy.R | 6 + 27 files changed, 394 insertions(+), 84 deletions(-)
Title: Construction of Regular and Irregular Histograms with Different
Options for Automatic Choice of Bins
Description: Automatic construction of regular and irregular histograms as described in Rozenholc/Mildenberger/Gather (2010).
Author: Thoralf Mildenberger [aut, cre],
Yves Rozenholc [aut],
David Zasada [aut]
Maintainer: Thoralf Mildenberger <mild@zhaw.ch>
Diff between histogram versions 0.0-23 dated 2009-12-24 and 0.0-24 dated 2016-10-16
DESCRIPTION | 27 +- MD5 |only NAMESPACE | 2 NEWS |only R/histogram.R | 162 ++++++------ R/histogram.irregular.R | 632 ++++++++++++++++++++++++------------------------ man/histogram.Rd | 4 7 files changed, 425 insertions(+), 402 deletions(-)
More information about KnapsackSampling at CRAN
Permanent link
Title: Fitting Semi-Parametric log-Symmetric Regression Models
Description: Set of tools to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, asymmetric and possibly, censored. Under this setup, both the median and the skewness of the response variable distribution are explicitly modeled by using semi-parametric functions, whose non-parametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.
Author: Luis Hernando Vanegas <hvanegasp@gmail.com> and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas <hvanegasp@gmail.com>
Diff between ssym versions 1.5.6 dated 2016-07-21 and 1.5.7 dated 2016-10-16
ssym-1.5.6/ssym/R/itpEC.R |only ssym-1.5.6/ssym/man/itpEC.Rd |only ssym-1.5.7/ssym/DESCRIPTION | 8 ++++---- ssym-1.5.7/ssym/MD5 | 12 +++++------- ssym-1.5.7/ssym/R/ssym.l2.R | 4 ++-- ssym-1.5.7/ssym/R/summary.ssym.R | 5 +++-- ssym-1.5.7/ssym/man/ssym-package.Rd | 4 ++-- ssym-1.5.7/ssym/man/ssym.l2.Rd | 4 +--- 8 files changed, 17 insertions(+), 20 deletions(-)
Title: Response-Surface Analysis
Description: Provides functions to generate response-surface designs,
fit first- and second-order response-surface models,
make surface plots, obtain the path of steepest ascent,
and do canonical analysis.
Author: Russell V Lenth [aut, cre]
Maintainer: Russell V Lenth <russell-lenth@uiowa.edu>
Diff between rsm versions 2.7-4 dated 2015-10-07 and 2.8 dated 2016-10-16
DESCRIPTION | 20 ++++++++---- MD5 | 19 ++++++------ NAMESPACE | 77 ++++++++++++++++++++++++++++++++++++++++++++++--- R/lsmeans-support.R |only R/rsm.R | 11 ++++++- build/vignette.rds |binary inst/NEWS | 4 ++ inst/doc/rs-illus.pdf |binary inst/doc/rsm-plots.pdf |binary inst/doc/rsm.pdf |binary man/rsm.Rd | 23 ++++++++++++++ 11 files changed, 132 insertions(+), 22 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb],
Adam Obeng [ctb],
Pablo Barberá [ctb],
Will Lowe [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.9.8 dated 2016-07-28 and 0.9.8.3 dated 2016-10-16
quanteda-0.9.8.3/quanteda/DESCRIPTION | 27 +- quanteda-0.9.8.3/quanteda/MD5 | 54 ++-- quanteda-0.9.8.3/quanteda/NEWS.md | 4 quanteda-0.9.8.3/quanteda/R/RcppExports.R | 6 quanteda-0.9.8.3/quanteda/R/dfm-weighting.R | 60 ++--- quanteda-0.9.8.3/quanteda/R/findSequences.R | 5 quanteda-0.9.8.3/quanteda/R/joinTokens.R | 2 quanteda-0.9.8.3/quanteda/R/quanteda.R |only quanteda-0.9.8.3/quanteda/R/readability.R | 186 ++++++++-------- quanteda-0.9.8.3/quanteda/R/stopwords.R | 4 quanteda-0.9.8.3/quanteda/R/textfile.R | 21 + quanteda-0.9.8.3/quanteda/README.md | 23 + quanteda-0.9.8.3/quanteda/inst/doc/LitVignette.html | 10 quanteda-0.9.8.3/quanteda/inst/doc/quickstart.R | 10 quanteda-0.9.8.3/quanteda/inst/doc/quickstart.Rmd | 27 -- quanteda-0.9.8.3/quanteda/inst/doc/quickstart.html | 54 +--- quanteda-0.9.8.3/quanteda/man/docfreq.Rd | 12 - quanteda-0.9.8.3/quanteda/man/findSequences.Rd | 5 quanteda-0.9.8.3/quanteda/man/joinTokens.Rd | 2 quanteda-0.9.8.3/quanteda/man/quanteda-package.Rd | 10 quanteda-0.9.8.3/quanteda/man/readability.Rd | 10 quanteda-0.9.8.3/quanteda/man/scrabble.Rd | 10 quanteda-0.9.8.3/quanteda/man/tf.Rd | 39 ++- quanteda-0.9.8.3/quanteda/src/RcppExports.cpp | 60 ++--- quanteda-0.9.8.3/quanteda/src/sequences.cpp | 45 +-- quanteda-0.9.8.3/quanteda/src/tokens_join.cpp | 9 quanteda-0.9.8.3/quanteda/tests/testthat/testTextfile.R | 16 - quanteda-0.9.8.3/quanteda/vignettes/quickstart.Rmd | 27 -- quanteda-0.9.8/quanteda/R/quanteda-package.R |only 29 files changed, 333 insertions(+), 405 deletions(-)
Title: Tint is not Tufte
Description: A 'tufte'-alike style for 'rmarkdown'.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tint versions 0.0.2 dated 2016-10-07 and 0.0.3 dated 2016-10-15
ChangeLog | 41 +++++++ DESCRIPTION | 8 - MD5 | 20 ++- README.md | 36 +++++- inst/NEWS.Rd |only inst/examples |only inst/rmarkdown/templates/html/skeleton/skeleton.Rmd | 30 ++--- inst/rmarkdown/templates/html/template.yaml | 2 inst/rmarkdown/templates/pdf/resources/tintPdf-template.tex | 63 ++++++++++++ inst/rmarkdown/templates/pdf/skeleton/skeleton.Rmd | 31 +++-- inst/rmarkdown/templates/pdf/template.yaml | 2 tests |only 12 files changed, 182 insertions(+), 51 deletions(-)
Title: 'Htmlwidget' for 'Kerry Rodden' 'd3.js' Sequence Sunburst
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the
convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Kerry Rodden [aut, cph] (sequences library in htmlwidgets/lib,
https://gist.github.com/kerryrodden/7090426),
Kent Russell [aut, cre] (R interface),
Florian Breitwieser [ctb] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between sunburstR versions 0.6.2 dated 2016-09-19 and 0.6.3 dated 2016-10-15
sunburstR-0.6.2/sunburstR/inst/htmlwidgets/lib/d3 |only sunburstR-0.6.3/sunburstR/DESCRIPTION | 19 ++++---- sunburstR-0.6.3/sunburstR/MD5 | 11 +---- sunburstR-0.6.3/sunburstR/NEWS.md | 6 ++ sunburstR-0.6.3/sunburstR/R/sunburst.R | 33 ++++++++------- sunburstR-0.6.3/sunburstR/inst/htmlwidgets/sunburst.yaml | 4 - 6 files changed, 38 insertions(+), 35 deletions(-)
Title: Spatial Modeling on Stream Networks
Description: Geostatistical modeling for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including covariates, can be fit with ML or REML. Mapping and other graphical functions are included.
Author: Jay Ver Hoef and Erin Peterson
Maintainer: Jay Ver Hoef <ver.hoef@SpatialStreamNetworks.com>
Diff between SSN versions 1.1.7 dated 2016-03-17 and 1.1.8 dated 2016-10-15
SSN-1.1.7/SSN/R/Torgegram.r |only SSN-1.1.7/SSN/inst/doc/SSN.R |only SSN-1.1.7/SSN/src/additiveFunctionValues.cpp |only SSN-1.1.8/SSN/DESCRIPTION | 11 +++++---- SSN-1.1.8/SSN/MD5 | 32 ++++++++++++++++----------- SSN-1.1.8/SSN/NAMESPACE | 9 ++++--- SSN-1.1.8/SSN/R/FCSD.R |only SSN-1.1.8/SSN/R/FCSD01.R |only SSN-1.1.8/SSN/R/FUDJ.R |only SSN-1.1.8/SSN/R/FUSD.R |only SSN-1.1.8/SSN/R/Torgegram.R |only SSN-1.1.8/SSN/R/reachNeiSSN.R |only SSN-1.1.8/SSN/build/vignette.rds |binary SSN-1.1.8/SSN/data/mf04.rda |binary SSN-1.1.8/SSN/data/mf04p.rda |binary SSN-1.1.8/SSN/data/modelFits.rda |binary SSN-1.1.8/SSN/inst/doc/SSN.pdf |binary SSN-1.1.8/SSN/inst/doc/STARS.pdf |binary SSN-1.1.8/SSN/man/FCSD.Rd |only SSN-1.1.8/SSN/man/FCSD01.Rd |only SSN-1.1.8/SSN/man/FUDJ.Rd |only SSN-1.1.8/SSN/man/FUSD.Rd |only SSN-1.1.8/SSN/man/reachNeiSSN.Rd |only SSN-1.1.8/SSN/src/init.c | 4 +-- 24 files changed, 33 insertions(+), 23 deletions(-)
Title: Similarity Regression
Description: Functions for performing Bayesian similarity regression,
and evaluating the probability of association between sets of ontological terms
and binary response vector. A random model is compared with one in which
the log odds of a true response is linked to the semantic similarity
between terms and a latent characteristic ontological profile.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between SimReg versions 2.1 dated 2016-08-16 and 3.0 dated 2016-10-15
SimReg-2.1/SimReg/R/functions.R |only SimReg-2.1/SimReg/R/generics.R |only SimReg-2.1/SimReg/R/multiSimReg.R |only SimReg-2.1/SimReg/R/plots.R |only SimReg-2.1/SimReg/R/simReg.R |only SimReg-2.1/SimReg/man/P-open-paren-gamma-equals-1-close-paren.Rd |only SimReg-2.1/SimReg/man/P_y_given_x.Rd |only SimReg-2.1/SimReg/man/acceptance_traces.Rd |only SimReg-2.1/SimReg/man/as.data.frame.sim_reg_summary.Rd |only SimReg-2.1/SimReg/man/as_row_leaves.Rd |only SimReg-2.1/SimReg/man/final_sample.Rd |only SimReg-2.1/SimReg/man/full_names.Rd |only SimReg-2.1/SimReg/man/log_odds_trace.Rd |only SimReg-2.1/SimReg/man/multi_sim_reg.Rd |only SimReg-2.1/SimReg/man/phi_plot.Rd |only SimReg-2.1/SimReg/man/plot.sim_reg_samples.Rd |only SimReg-2.1/SimReg/man/print.sim_reg_samples.Rd |only SimReg-2.1/SimReg/man/prune_sim_mat.Rd |only SimReg-2.1/SimReg/man/s.Rd |only SimReg-2.1/SimReg/man/s_phi.Rd |only SimReg-2.1/SimReg/man/s_x.Rd |only SimReg-2.1/SimReg/man/sim_reg_mc.Rd |only SimReg-2.1/SimReg/man/sim_reg_summary.Rd |only SimReg-2.1/SimReg/man/subset_sim_reg_samples.Rd |only SimReg-2.1/SimReg/man/summary.sim_reg_samples.Rd |only SimReg-2.1/SimReg/man/term_marginals_from_phi_vec.Rd |only SimReg-2.1/SimReg/man/term_pair_marginals.Rd |only SimReg-2.1/SimReg/src/Chain.cpp |only SimReg-2.1/SimReg/src/Chain.h |only SimReg-2.1/SimReg/src/DeltaLikelihood.cpp |only SimReg-2.1/SimReg/src/DeltaLikelihood.h |only SimReg-2.1/SimReg/src/HPO.cpp |only SimReg-2.1/SimReg/src/HPO.h |only SimReg-2.1/SimReg/src/Interface.cpp |only SimReg-2.1/SimReg/src/Interface.h |only SimReg-2.1/SimReg/src/Likelihood.cpp |only SimReg-2.1/SimReg/src/Likelihood.h |only SimReg-2.1/SimReg/src/Similarity.cpp |only SimReg-2.1/SimReg/src/Similarity.h |only SimReg-2.1/SimReg/src/State.cpp |only SimReg-2.1/SimReg/src/State.h |only SimReg-2.1/SimReg/src/TermList.cpp |only SimReg-2.1/SimReg/src/TermList.h |only SimReg-2.1/SimReg/src/Update.cpp |only SimReg-2.1/SimReg/src/Update.h |only SimReg-2.1/SimReg/src/Utils.cpp |only SimReg-2.1/SimReg/src/Utils.h |only SimReg-3.0/SimReg/DESCRIPTION | 22 - SimReg-3.0/SimReg/MD5 | 97 ++--- SimReg-3.0/SimReg/NAMESPACE | 55 +-- SimReg-3.0/SimReg/R/RcppExports.R |only SimReg-3.0/SimReg/R/generic.R |only SimReg-3.0/SimReg/R/inference.R |only SimReg-3.0/SimReg/R/ml.R |only SimReg-3.0/SimReg/R/phi-priors.R |only SimReg-3.0/SimReg/R/pick.R |only SimReg-3.0/SimReg/R/plot.R |only SimReg-3.0/SimReg/inst/doc/SimReg-Introduction.R | 9 SimReg-3.0/SimReg/inst/doc/SimReg-Introduction.Rmd | 24 - SimReg-3.0/SimReg/inst/doc/SimReg-Introduction.html | 66 +-- SimReg-3.0/SimReg/inst/doc/SimReg-Priors.R | 19 - SimReg-3.0/SimReg/inst/doc/SimReg-Priors.Rmd | 42 +- SimReg-3.0/SimReg/inst/doc/SimReg-Priors.html | 97 ++--- SimReg-3.0/SimReg/man/SimReg-package.Rd | 26 - SimReg-3.0/SimReg/man/get_term_marginals.Rd |only SimReg-3.0/SimReg/man/get_terms.Rd |only SimReg-3.0/SimReg/man/log_BF.Rd |only SimReg-3.0/SimReg/man/plot.sim_reg_summary.Rd | 20 - SimReg-3.0/SimReg/man/plot_term_marginals.Rd |only SimReg-3.0/SimReg/man/print.sim_reg_output.Rd |only SimReg-3.0/SimReg/man/print.sim_reg_summary.Rd | 9 SimReg-3.0/SimReg/man/prob_association.Rd |only SimReg-3.0/SimReg/man/sim_reg.Rd | 168 +--------- SimReg-3.0/SimReg/man/sum_log_probs.Rd |only SimReg-3.0/SimReg/man/summary.sim_reg_output.Rd |only SimReg-3.0/SimReg/man/term_marginals.Rd | 12 SimReg-3.0/SimReg/src/RcppExports.cpp |only SimReg-3.0/SimReg/src/bgml.cpp |only SimReg-3.0/SimReg/src/fml.cpp |only SimReg-3.0/SimReg/src/ml.cpp |only SimReg-3.0/SimReg/src/utils.h |only SimReg-3.0/SimReg/vignettes/SimReg-Introduction.Rmd | 24 - SimReg-3.0/SimReg/vignettes/SimReg-Priors.Rmd | 42 +- 83 files changed, 255 insertions(+), 477 deletions(-)
Title: 'IUCN' Red List Client
Description: 'IUCN' Red List (<http://apiv3.iucnredlist.org/api/v3/docs>) client.
The 'IUCN' Red List is a global list of threatened and endangered species.
Functions cover all of the Red List 'API' routes. An 'API' key is required.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rredlist versions 0.1.0 dated 2016-01-26 and 0.2.0 dated 2016-10-15
DESCRIPTION | 10 ++++----- MD5 | 52 ++++++++++++++++++++++++------------------------ NAMESPACE | 2 + NEWS.md | 24 +++++++++++++++++++++- R/rl_common_names.R | 4 +-- R/rl_habitats.R | 6 ++--- R/rl_history.R |only R/rl_measures.R | 6 ++--- R/rl_narrative.R | 6 ++--- R/rl_search.R | 6 ++--- R/rl_sp_citation.R | 6 ++--- R/rl_sp_count.R | 2 - R/rl_synonyms.R | 4 +-- R/rl_threats.R | 6 ++--- R/rredlist-package.R | 30 ++++++++++++++------------- R/zzz.R | 6 +++-- README.md | 25 +++++++++-------------- man/rl_common_names.Rd | 4 +-- man/rl_habitats.Rd | 9 +++++--- man/rl_history.Rd |only man/rl_measures.Rd | 4 +-- man/rl_narrative.Rd | 4 +-- man/rl_search.Rd | 4 +-- man/rl_sp_citation.Rd | 4 +-- man/rl_sp_count.Rd | 4 +-- man/rl_synonyms.Rd | 4 +-- man/rl_threats.Rd | 4 +-- man/rredlist-package.Rd | 30 ++++++++++++++------------- 28 files changed, 148 insertions(+), 118 deletions(-)
Title: Nonparametric Boundary Regression
Description: A variety of functions for the best known and most innovative approaches to nonparametric boundary estimation. The selected methods are concerned with empirical, smoothed, unrestricted as well as constrained fits under both separate and multiple shape constraints. They cover robust approaches to outliers as well as data envelopment techniques based on piecewise polynomials, splines, local linear fitting, extreme values and kernel smoothing. The package also seamlessly allows for Monte Carlo comparisons among these different estimation methods. Its use is illustrated via a number of empirical applications and simulated examples.
Author: Abdelaati Daouia <Abdelaati.Daouia@tse-fr.eu>, Thibault Laurent <thibault.laurent@univ-tlse1.fr>, Hohsuk Noh <word5810@gmail.com>
Maintainer: Thibault Laurent <thibault.laurent@univ-tlse1.fr>
Diff between npbr versions 1.3 dated 2016-06-20 and 1.4 dated 2016-10-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/kern_smooth.R | 2 +- inst/doc/ex-npbr.pdf |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Estimation of Multivariate Long-Memory Models Parameters
Description: Computation of an estimation of the long-memory parameters and
the long-run covariance matrix using a multivariate model
(Lobato (1999) <10.1016/S0304-4076(98)00038-4>; Shimotsu (2007) <10.1016/j.jeconom.2006.01.003>). Two semi-parametric methods are
implemented: a Fourier based approach (Shimotsu (2007) <10.1016/j.jeconom.2006.01.003>) and a wavelet based
approach (Achard and Gannaz (2016) <10.1111/jtsa.12170>).
Author: Sophie Achard [aut, cre],
Irene Gannaz [aut]
Maintainer: Sophie Achard <sophie.achard@gipsa-lab.fr>
Diff between multiwave versions 1.0 dated 2015-10-28 and 1.1 dated 2016-10-15
multiwave-1.0/multiwave/R/varfima.R |only multiwave-1.0/multiwave/man/varfima.Rd |only multiwave-1.1/multiwave/DESCRIPTION | 14 +++--- multiwave-1.1/multiwave/MD5 | 52 +++++++++++------------ multiwave-1.1/multiwave/NAMESPACE | 2 multiwave-1.1/multiwave/R/fivarma.R |only multiwave-1.1/multiwave/R/mfw.R | 18 +++---- multiwave-1.1/multiwave/R/mww.R | 21 ++++----- multiwave-1.1/multiwave/R/mww_wav.R | 20 ++++---- multiwave-1.1/multiwave/man/DWTexact.Rd | 4 - multiwave-1.1/multiwave/man/K_eval.Rd | 5 +- multiwave-1.1/multiwave/man/compute_nj.Rd | 5 +- multiwave-1.1/multiwave/man/fivarma.Rd |only multiwave-1.1/multiwave/man/mfw.Rd | 7 +-- multiwave-1.1/multiwave/man/mfw_cov_eval.Rd | 6 +- multiwave-1.1/multiwave/man/mfw_eval.Rd | 7 +-- multiwave-1.1/multiwave/man/multiwave-package.Rd | 7 +-- multiwave-1.1/multiwave/man/mww.Rd | 7 +-- multiwave-1.1/multiwave/man/mww_cov_eval.Rd | 7 +-- multiwave-1.1/multiwave/man/mww_eval.Rd | 6 +- multiwave-1.1/multiwave/man/mww_wav.Rd | 7 +-- multiwave-1.1/multiwave/man/mww_wav_cov_eval.Rd | 6 +- multiwave-1.1/multiwave/man/mww_wav_eval.Rd | 6 +- multiwave-1.1/multiwave/man/psi_hat_exact.Rd | 5 +- multiwave-1.1/multiwave/man/scaling_filter.Rd | 5 +- multiwave-1.1/multiwave/man/scaling_function.Rd | 5 +- multiwave-1.1/multiwave/man/toeplitz_nonsym.Rd | 5 +- multiwave-1.1/multiwave/man/varma.Rd | 6 +- multiwave-1.1/multiwave/man/vfracdiff.Rd | 6 +- 29 files changed, 126 insertions(+), 113 deletions(-)
Title: Advanced Statistical Methods to Model and Adjust for Bias in
Meta-Analysis
Description: The following methods are implemented to evaluate how sensitive the results of a meta-analysis are to potential bias in meta-analysis and to support Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 5 "Small-Study Effects in Meta-Analysis":
- Copas selection model described in Copas & Shi (2001) <DOI:10.1177/096228020101000402>;
- limit meta-analysis by Rücker et al. (2011) <DOI:10.1093/biostatistics/kxq046>;
- upper bound for outcome reporting bias by Copas & Jackson (2004) <DOI:10.1111/j.0006-341X.2004.00161.x>.
Author: Guido Schwarzer [aut, cre],
James Carpenter [aut],
Gerta Rücker [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between metasens versions 0.3-0 dated 2016-02-17 and 0.3-1 dated 2016-10-15
DESCRIPTION | 18 ++++++++++-------- MD5 | 15 ++++++++------- NEWS | 9 +++++++++ R/plot.copas.R | 8 ++++---- man/copas.Rd | 8 ++++---- man/limitmeta.Rd | 4 ++-- man/metasens-package.Rd |only man/orbbound.Rd | 2 +- man/plot.copas.Rd | 4 ++-- 9 files changed, 40 insertions(+), 28 deletions(-)
Title: Miscellaneous Functions for the USGS INL Project Office
Description: A collection of functions for creating high-level graphics,
performing raster-based analysis, processing MODFLOW-based models, and
overlaying multi-polygon objects. Used to support packages and scripts written
by researchers at the United States Geological Survey (USGS)
Idaho National Laboratory (INL) Project Office.
Author: Jason Fisher [aut, cre]
Maintainer: Jason Fisher <jfisher@usgs.gov>
Diff between inlmisc versions 0.1.2 dated 2016-09-16 and 0.2.1 dated 2016-10-15
DESCRIPTION | 6 +-- MD5 | 46 ++++++++++++------------- NEWS | 11 ++++++ R/AddInsetMap.R | 14 +++---- R/BumpDisconnectCells.R | 14 +++---- R/ExportRasterStack.R | 2 - R/PlotCrossSection.R | 80 ++++++++++++++++++++------------------------- R/PlotGraph.R | 12 ++---- R/PlotMap.R | 75 +++++++++++++++++++++++++++++++----------- R/ReplaceInTemplate.R | 4 +- R/RmSmallCellChunks.R | 14 +++---- R/SetPolygons.R | 16 ++++----- R/SummariseBudget.R | 3 - README.md | 9 +++-- man/AddInsetMap.Rd | 14 +++---- man/BumpDisconnectCells.Rd | 14 +++---- man/ExportRasterStack.Rd | 2 - man/PlotCrossSection.Rd | 66 ++++++++++++++++++++++--------------- man/PlotGraph.Rd | 11 ++---- man/PlotMap.Rd | 56 +++++++++++++++++++++++-------- man/ReplaceInTemplate.Rd | 4 +- man/RmSmallCellChunks.Rd | 14 +++---- man/SetPolygons.Rd | 16 ++++----- man/SummariseBudget.Rd | 3 - 24 files changed, 287 insertions(+), 219 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <sen-zhao@sen-zhao.com>
Diff between Grace versions 0.4.2 dated 2016-10-04 and 0.4.3 dated 2016-10-15
DESCRIPTION | 9 ++++----- MD5 | 6 +++--- R/grace.test.R | 9 ++++++--- man/grace.test.Rd | 8 ++++---- 4 files changed, 17 insertions(+), 15 deletions(-)
Title: Dynamic Models for Survival Data
Description: Functions to fit time-varying coefficient models for interval
censored and right censored survival data. Three major approaches are
implemented: 1) Bayesian Cox model with time-independent, time-varying or
dynamic coefficients for right censored and interval censored data; 2)
Spline based time-varying coefficient Cox model for right censored data; 3)
Transformation model with time-varying coefficients for right censored data
using estimating equations.
Author: Wenjie Wang [cre, aut],
Ming-Hui Chen [aut],
Xiaojing Wang [aut],
Jun Yan [aut]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>
Diff between dynsurv versions 0.3-2 dated 2016-08-30 and 0.3-3 dated 2016-10-15
ChangeLog | 11 DESCRIPTION | 21 - MD5 | 26 - R/data.R | 6 inst/CITATION | 12 man/bcos.Rd | 2 man/tooth.Rd | 4 src/CoxModel.h | 330 +++++++++-------- src/DynamicCoxModel.h | 17 src/DynamicGORHModel.h | 19 - src/DynamicModel.h | 905 ++++++++++++++++++++++++------------------------- src/IntRegModel.h | 2 src/TimeIndepModel.h | 4 src/TimeVaryingModel.h | 12 14 files changed, 700 insertions(+), 671 deletions(-)
Title: Collocation Inference for Dynamic Systems
Description: These functions implement collocation-inference
for continuous-time and discrete-time stochastic processes.
They provide model-based smoothing, gradient-matching,
generalized profiling and forwards prediction error methods.
Author: Giles Hooker <gjh27@cornell.edu>,
Luo Xiao <lx42@cornell.edu>,
James Ramsay <ramsay@psych.mcgill.ca>
Maintainer: Giles Hooker <gjh27@cornell.edu>
Diff between CollocInfer versions 1.0.2 dated 2015-08-20 and 1.0.3 dated 2016-10-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/CollocInferPlots.R | 11 ++++++----- man/CollocInferPlots.rd | 4 +++- 4 files changed, 16 insertions(+), 13 deletions(-)
Title: The Multivariate Normal and t Distributions
Description: Functions are provided for computing the density and the
distribution function of multivariate normal and "t" random variables,
and for generating random vectors sampled from these distributions.
Probabilities are computed via non-Monte Carlo methods; different routines
are used in the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz, R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between mnormt versions 1.5-4 dated 2016-03-08 and 1.5-5 dated 2016-10-15
mnormt-1.5-4/mnormt/INDEX |only mnormt-1.5-5/mnormt/DESCRIPTION | 8 ++++---- mnormt-1.5-5/mnormt/MD5 | 13 ++++++------- mnormt-1.5-5/mnormt/NEWS | 7 ++++--- mnormt-1.5-5/mnormt/R/mnormt.R | 4 +--- mnormt-1.5-5/mnormt/inst/CITATION | 2 +- mnormt-1.5-5/mnormt/man/dmnorm.Rd | 35 +++++++++++++++++++++-------------- mnormt-1.5-5/mnormt/man/dmt.Rd | 35 +++++++++++++++-------------------- 8 files changed, 52 insertions(+), 52 deletions(-)
More information about fontLiberation at CRAN
Permanent link
Title: Biometric Exploratory Analysis Creation House
Description: A platform is provided for interactive analyses with a goal of totally easy to develop, deploy, interact, and explore (TEDDIE). Using this package, users can create customized analyses and make them available to end users who can perform interactive analyses and save analyses to RTF or HTML files. It allows developers to focus on R code for analysis, instead of dealing with html or shiny code.
Author: Danni Yu [aut, cre],
Michael Man [aut],
ChenChen Yu [com]
Maintainer: Danni Yu <danni.yu@gmail.com>
Diff between BEACH versions 1.1.1 dated 2016-10-05 and 1.1.2 dated 2016-10-15
DESCRIPTION | 18 +- MD5 | 15 +- NAMESPACE | 2 build/partial.rdb |binary inst/app/README.md | 2 inst/app/data |only inst/app/functions/BridgingAnalysis_configuration.csv | 1 inst/app/server.r | 127 ++++++++++++------ inst/app/ui.r | 7 9 files changed, 111 insertions(+), 61 deletions(-)
Title: Fast Clustering Using Adaptive Density Peak Detection
Description: An implementation of ADPclust clustering procedures (Fast
Clustering Using Adaptive Density Peak Detection). The work is built and
improved upon the idea of Rodriguez and Laio (2014)<DOI:10.1126/science.1242072>.
ADPclust clusters data by finding density peaks in a density-distance plot
generated from local multivariate Gaussian density estimation. It includes
an automatic centroids selection and parameter optimization algorithm, which
finds the number of clusters and cluster centroids by comparing average
silhouettes on a grid of testing clustering results; It also includes a user
interactive algorithm that allows the user to manually selects cluster
centroids from a two dimensional "density-distance plot". Here is the
research article associated with this package: "Wang, Xiao-Feng, and
Yifan Xu (2015)<DOI:10.1177/0962280215609948> Fast clustering using adaptive
density peak detection." Statistical methods in medical research". url:
http://smm.sagepub.com/content/early/2015/10/15/0962280215609948.abstract.
Author: Yifan (Ethan) Xu [aut, cre],
Xiao-Feng Wang [aut]
Maintainer: Yifan (Ethan) Xu <ethan.yifanxu@gmail.com>
Diff between ADPclust versions 0.6.5 dated 2015-12-03 and 0.7 dated 2016-10-15
ADPclust-0.6.5/ADPclust/R/ADPclust-package.r |only ADPclust-0.6.5/ADPclust/R/belongsTo.R |only ADPclust-0.6.5/ADPclust/R/checkh.R |only ADPclust-0.6.5/ADPclust/R/findCluster.R |only ADPclust-0.6.5/ADPclust/R/findClusterAuto.R |only ADPclust-0.6.5/ADPclust/R/findFd.R |only ADPclust-0.6.5/ADPclust/R/pickCenter.R |only ADPclust-0.6.5/ADPclust/R/pickOutlier.R |only ADPclust-0.6.5/ADPclust/R/plotClust.R |only ADPclust-0.6.5/ADPclust/man/ADPclust.Rd |only ADPclust-0.6.5/ADPclust/man/findCluster.Rd |only ADPclust-0.6.5/ADPclust/man/findClusterAuto.Rd |only ADPclust-0.6.5/ADPclust/man/findFd.Rd |only ADPclust-0.7/ADPclust/DESCRIPTION | 34 +- ADPclust-0.7/ADPclust/MD5 | 106 +++--- ADPclust-0.7/ADPclust/NAMESPACE | 22 - ADPclust-0.7/ADPclust/R/ADPclust.R | 304 ++++++++++-------- ADPclust-0.7/ADPclust/R/AMISE.R | 12 ADPclust-0.7/ADPclust/R/FindCentersAutoD.R |only ADPclust-0.7/ADPclust/R/FindCentersAutoV.R |only ADPclust-0.7/ADPclust/R/FindClustersAuto.R |only ADPclust-0.7/ADPclust/R/FindClustersGivenCenters.R |only ADPclust-0.7/ADPclust/R/FindClustersManual.R |only ADPclust-0.7/ADPclust/R/FindDistm.R |only ADPclust-0.7/ADPclust/R/FindFD.R |only ADPclust-0.7/ADPclust/R/FindH.R |only ADPclust-0.7/ADPclust/R/FindSilhouette.R |only ADPclust-0.7/ADPclust/R/IsDup.R |only ADPclust-0.7/ADPclust/R/PickCenters.R |only ADPclust-0.7/ADPclust/R/ROT.R | 8 ADPclust-0.7/ADPclust/R/clust10.R | 4 ADPclust-0.7/ADPclust/R/clust3.R | 4 ADPclust-0.7/ADPclust/R/clust5.1.R | 4 ADPclust-0.7/ADPclust/R/clust5.R | 2 ADPclust-0.7/ADPclust/R/dat_gene.R | 4 ADPclust-0.7/ADPclust/R/defCol.R | 4 ADPclust-0.7/ADPclust/R/plot.adpclust.R | 123 +++---- ADPclust-0.7/ADPclust/R/summary.adpclust.R | 25 - ADPclust-0.7/ADPclust/build/vignette.rds |binary ADPclust-0.7/ADPclust/inst/doc/ADPclust.R | 23 - ADPclust-0.7/ADPclust/inst/doc/ADPclust.Rmd | 40 +- ADPclust-0.7/ADPclust/inst/doc/ADPclust.html | 172 +++++----- ADPclust-0.7/ADPclust/man/AMISE.Rd | 10 ADPclust-0.7/ADPclust/man/FindCentersAutoD.Rd |only ADPclust-0.7/ADPclust/man/FindCentersAutoV.Rd |only ADPclust-0.7/ADPclust/man/FindClustersAuto.Rd |only ADPclust-0.7/ADPclust/man/FindClustersGivenCenters.Rd |only ADPclust-0.7/ADPclust/man/FindClustersManual.Rd |only ADPclust-0.7/ADPclust/man/FindDistm.Rd |only ADPclust-0.7/ADPclust/man/FindFD.Rd |only ADPclust-0.7/ADPclust/man/FindH.Rd |only ADPclust-0.7/ADPclust/man/ROT.Rd | 8 ADPclust-0.7/ADPclust/man/adpclust.Rd |only ADPclust-0.7/ADPclust/man/clust10.Rd | 4 ADPclust-0.7/ADPclust/man/clust3.Rd | 4 ADPclust-0.7/ADPclust/man/clust5.1.Rd | 4 ADPclust-0.7/ADPclust/man/clust5.Rd | 2 ADPclust-0.7/ADPclust/man/dat_gene.Rd | 4 ADPclust-0.7/ADPclust/man/defCol.Rd |only ADPclust-0.7/ADPclust/man/plot.adpclust.Rd | 10 ADPclust-0.7/ADPclust/man/summary.adpclust.Rd | 9 ADPclust-0.7/ADPclust/tests |only ADPclust-0.7/ADPclust/vignettes/ADPclust.Rmd | 40 +- 63 files changed, 547 insertions(+), 439 deletions(-)
Title: Partially Balanced Incomplete Block Designs
Description: Assists in calculating the efficiencies of Partially Balanced Incomplete Block Designs with any number of associate classes. This will help the researchers in calculating the efficiencies of their PBIB designs very quickly and efficiently.
Author: Parneet Kaur <parneet.nonu93@gmail.com>, Kush Sharma <kush.vashishtha@gmail.com>, Davinder Kumar Garg <dkgarg_stat@yahoo.co.in>
Maintainer: Kush Sharma <kush.vashishtha@gmail.com>
Diff between PBIBD versions 1.0 dated 2016-08-25 and 1.1 dated 2016-10-14
DESCRIPTION | 12 ++++++------ MD5 | 19 +++++++++++-------- NAMESPACE | 1 + R/apbibd.R |only R/apbibd3.R | 2 +- build |only man/PBIBD-package.Rd | 18 +++++++++--------- man/apbibd.Rd |only man/apbibd2.Rd | 6 +++--- man/apbibd3.Rd | 6 +++--- man/apbibd4.Rd | 8 ++++---- man/apbibd5.Rd | 12 ++++++------ 12 files changed, 44 insertions(+), 40 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>.
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 0.9-0 dated 2016-04-26 and 0.9-1 dated 2016-10-14
DESCRIPTION | 18 +++++--- MD5 | 50 ++++++++++++----------- NAMESPACE | 7 +-- NEWS | 72 ++++++++++++++++++++++++++++++++++ R/decomp.design.R | 3 + R/decomp.tau.R | 2 R/forest.netmeta.R | 94 +++++++++++++++++++++++++++++++++------------ R/netconnection.R | 13 +++++- R/netdistance.R | 5 ++ R/netgraph.R | 50 ++++++++++++++++++++--- R/netheat.R | 6 ++ R/netmeasures.R | 17 ++++++-- R/nma.krahn.R | 4 + R/nma.ruecker.R | 5 +- R/print.netmeta.R | 4 - R/shadowtext.R |only R/stress.R | 7 --- R/tau.within.R | 4 + man/decomp.design.Rd | 2 man/forest.netmeta.Rd | 61 ++++++++++++++++++++++++++--- man/netgraph.Rd | 25 ++++++++++- man/netheat.Rd | 2 man/netmeasures.Rd | 2 man/netmeta-package.Rd |only man/netmeta.Rd | 6 +- man/pairwise.Rd | 6 +- man/print.decomp.design.Rd | 2 27 files changed, 368 insertions(+), 99 deletions(-)
Title: Plot and Manipulate Multigraphs
Description: Functions to plot and manipulate multigraphs and bipartite graphs with different layout options.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <jaro@econ.au.dk>
Diff between multigraph versions 0.30 dated 2016-08-16 and 0.40 dated 2016-10-14
multigraph-0.30/multigraph/R/area.R |only multigraph-0.30/multigraph/R/stss.R |only multigraph-0.30/multigraph/man/area.Rd |only multigraph-0.30/multigraph/man/stss.Rd |only multigraph-0.40/multigraph/DESCRIPTION | 12 multigraph-0.40/multigraph/MD5 | 22 - multigraph-0.40/multigraph/R/bmgraph.R | 173 +++++----- multigraph-0.40/multigraph/R/frcd.R |only multigraph-0.40/multigraph/R/mbnd.R | 7 multigraph-0.40/multigraph/R/multigraph.R | 316 +++++++++---------- multigraph-0.40/multigraph/R/popl.R | 4 multigraph-0.40/multigraph/man/bmgraph.Rd | 8 multigraph-0.40/multigraph/man/frcd.Rd |only multigraph-0.40/multigraph/man/multigraph-package.Rd | 8 multigraph-0.40/multigraph/man/multigraph.Rd | 10 15 files changed, 292 insertions(+), 268 deletions(-)
Title: Cluster Detection with Hypothesis Free Scan Statistic
Description: Multiple scan statistic with variable window for one dimension data and scan statistic based on connected components in 2D or 3D.
Author: Robin Loche, Benoit Giron, David Abrial, Lionel Cucala, Myriam Charras-Garrido, Jocelyn De-Goer
Maintainer: David Abrial <graphscan@clermont.inra.fr>
Diff between graphscan versions 1.1 dated 2015-09-21 and 1.1.1 dated 2016-10-14
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/graphscan_1d_array_function.R | 11 +++++++---- man/cluster.Rd | 6 ++++-- man/events_series.Rd | 3 ++- man/france_two_clusters.Rd | 6 ++++-- man/graphscan-class.Rd | 7 ++++--- man/graphscan-plot.Rd | 4 ++-- man/graphscan.Rd | 35 ++++++++++++++--------------------- man/graphscan_1d.Rd | 17 ++++++++++------- src/2D_detection_cluster.c | 14 ++++++++++---- src/unif_aleat.c | 13 ++++++------- 12 files changed, 78 insertions(+), 68 deletions(-)
Title: Download and Aggregate High Frequency Trading Data from Bovespa
Description: Downloads and aggregates high frequency trading data for Brazilian instruments directly from Bovespa ftp site <ftp://ftp.bmf.com.br/MarketData/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetHFData versions 1.1.0 dated 2016-08-15 and 1.2.0 dated 2016-10-14
DESCRIPTION | 6 ++-- MD5 | 20 +++++++------- NEWS.md | 9 +++++- R/ghfd_get_HF_data.R | 19 +++++++------ R/ghfd_get_available_tickers_from_ftp.R | 1 R/ghfd_read_file.R | 24 ++++++++++++---- inst/doc/ghfd-vignette.html | 41 +++++++++++++++-------------- man/ghfd_get_HF_data.Rd | 8 ++--- man/ghfd_get_available_tickers_from_ftp.Rd | 2 - man/ghfd_get_ftp_contents.Rd | 2 - man/ghfd_read_file.Rd | 2 - 11 files changed, 79 insertions(+), 55 deletions(-)
Title: Evolutionary Learning of Globally Optimal Trees
Description: Commonly used classification and regression tree methods like the CART algorithm
are recursive partitioning methods that build the model in a forward stepwise search.
Although this approach is known to be an efficient heuristic, the results of recursive
tree methods are only locally optimal, as splits are chosen to maximize homogeneity at
the next step only. An alternative way to search over the parameter space of trees is
to use global optimization methods like evolutionary algorithms. The 'evtree' package
implements an evolutionary algorithm for learning globally optimal classification and
regression trees in R. CPU and memory-intensive tasks are fully computed in C++ while
the 'partykit' package is leveraged to represent the resulting trees in R, providing
unified infrastructure for summaries, visualizations, and predictions.
Author: Thomas Grubinger [aut, cre],
Achim Zeileis [aut],
Karl-Peter Pfeiffer [aut]
Maintainer: Thomas Grubinger <Thomas.Grubinger@scch.at>
Diff between evtree versions 1.0-0 dated 2014-10-15 and 1.0-1 dated 2016-10-14
DESCRIPTION | 17 MD5 | 40 - NAMESPACE | 1 NEWS | 7 build/vignette.rds |binary data/BBBClub.rda |binary data/ContraceptiveChoice.RData |binary data/GermanCredit.RData |binary data/MAGICGammaTelescope.RData |binary data/StatlogHeart.RData |binary inst/doc/evtree.R | 1100 ++++++++++++++++++------------------- inst/doc/evtree.Rnw | 2 inst/doc/evtree.pdf |binary man/MAGICGammaTelescope.Rd | 2 src/container.cpp | 12 src/container.h | 2 src/node.cpp | 26 src/tree.cpp | 70 +- src/tree.h | 1 tests/Examples/evtree-Ex.Rout.save | 36 - vignettes/evtree.Rnw | 2 21 files changed, 666 insertions(+), 652 deletions(-)
Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences
on websites (i.e., clickstream). A click can be represented by a number,
character or string. Clickstreams can be modeled as zero- (only computes
occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>
Diff between clickstream versions 1.1.8 dated 2016-04-26 and 1.1.9 dated 2016-10-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ R/clickstream-package.R | 8 ++++---- inst/CITATION | 29 +++++++++++++++++++---------- man/clickstream-package.Rd | 11 +++++++---- 6 files changed, 44 insertions(+), 27 deletions(-)
Title: Cognitive Diagnosis Modeling
Description:
Functions for cognitive diagnosis modeling
and multidimensional item response modeling for
dichotomous and polytomous data. This package
enables the estimation of the DINA and DINO model,
the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic
model (GDM), the multidimensional linear compensatory
item response model and the structured latent class
model (SLCA).
Author:
Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 5.1-0 dated 2016-08-29 and 5.2-1 dated 2016-10-14
DESCRIPTION | 8 - MD5 | 77 ++++++++++-------- R/din.R | 4 R/gdina.R | 2 R/gdina_proc_noninvariance_multiple_groups.R.R |only R/gdina_reduced_skillspace.R.R |only R/gdina_se_itemwise.R.R |only R/item_by_group.R | 31 +++++++ data/data.Students.rda |binary data/data.cdm01.rda |binary data/data.cdm02.rda |binary data/data.cdm03.rda |binary data/data.cdm04.rda |binary data/data.dcm.rda |binary data/data.dtmr.rda |binary data/data.ecpe.rda |binary data/data.fraction1.rda |binary data/data.fraction2.rda |binary data/data.hr.rda |binary data/data.jang.rda |binary data/data.melab.rda |binary data/data.mg.rda |binary data/data.pgdina.rda |binary data/data.sda6.rda |binary data/data.timss03.G8.su.rda |binary data/data.timss07.G4.lee.rda |binary data/data.timss11.G4.AUT.part.rda |binary data/data.timss11.G4.AUT.rda |binary data/fraction.subtraction.data.rda |binary data/fraction.subtraction.qmatrix.rda |binary data/sim.dina.rda |binary data/sim.dino.rda |binary data/sim.qmatrix.rda |binary inst/CITATION |only inst/NEWS | 20 ++++ inst/NEWS.txt |only man/CDM-package.Rd | 102 +++++++++++++------------ man/data.cdm.Rd | 9 +- man/gdina.Rd | 15 ++- man/gdina.wald.Rd | 2 man/item_by_group.Rd | 18 +++- man/sequential.items.Rd | 4 42 files changed, 187 insertions(+), 105 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.0.2 dated 2016-09-15 and 0.0.3 dated 2016-10-14
ChangeLog | 24 +++++++++++++++ DESCRIPTION | 10 +++--- MD5 | 21 ++++++------- R/RcppExports.R | 4 ++ R/anytime.R | 10 +++++- README.md | 2 - build/partial.rdb |binary inst/NEWS.Rd | 8 +++++ man/anytime.Rd | 10 +++++- src/RcppExports.cpp | 13 ++++++++ src/anytime.cpp | 83 ++++++++++++++++++++++++++++++++++++---------------- tests/gh_issue_12.R |only 12 files changed, 142 insertions(+), 43 deletions(-)
Title: Convert R Markdown Files to DataCamp Light HTML Files
Description: DataCamp Light (<https://github.com/datacamp/datacamp-light>) is a light-weight implementation of the DataCamp UI,
that allows you to embed interactive exercises inside HTML documents. The tutorial package makes it easy to create these
HTML files from R Markdown files. An extension to knitr, tutorial detects appropriately formatted code chunks and replaces them
with DataCamp Light readable chunks in the resulting HTML file.
Author: Filip Schouwenaars
Maintainer: Filip Schouwenaars <filip@datacamp.com>
Diff between tutorial versions 0.4.2 dated 2016-09-12 and 0.4.3 dated 2016-10-14
tutorial-0.4.2/tutorial/inst/example.html |only tutorial-0.4.3/tutorial/DESCRIPTION | 8 +++---- tutorial-0.4.3/tutorial/MD5 | 19 ++++++++---------- tutorial-0.4.3/tutorial/R/example.R | 13 +++++++++++- tutorial-0.4.3/tutorial/README.md | 15 +++++++++----- tutorial-0.4.3/tutorial/inst/doc/tutorial-basics.Rmd | 8 +++++-- tutorial-0.4.3/tutorial/inst/doc/tutorial-basics.html | 14 ++++++++----- tutorial-0.4.3/tutorial/inst/example.Rmd | 4 ++- tutorial-0.4.3/tutorial/man/build_example.Rd | 5 +++- tutorial-0.4.3/tutorial/tests/testthat/test-example.R | 2 - tutorial-0.4.3/tutorial/vignettes/tutorial-basics.Rmd | 8 +++++-- 11 files changed, 64 insertions(+), 32 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-13 0.1
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType',
'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output
formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted
into polygons or raster images, hence after the plot has been created, it no
longer relies on the font files. No external software such as 'Ghostscript' is
needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.4-4 dated 2015-10-29 and 0.4-5 dated 2016-10-14
DESCRIPTION | 14 ++++++++------ MD5 | 12 +++++++++--- build |only inst/NEWS.Rd | 8 ++++++++ inst/doc |only src/devfuns.c | 12 +++++++++--- vignettes |only 7 files changed, 34 insertions(+), 12 deletions(-)
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal .
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.6.2.1 dated 2016-09-19 and 1.7.1 dated 2016-10-14
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- configure | 2 +- data/rgbs.txt.gz |binary src/Makefile.in | 25 ++++++++++++------------- src/Makefile.root.in | 2 +- src/configure | 18 +++++++++--------- src/denseCpuKernels.cpp | 1 - src/sparseCpuKernels.cpp | 1 - src/training.cpp | 6 +++--- 10 files changed, 39 insertions(+), 42 deletions(-)
Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Description: An S4 update of the 'mefa' package
using sparse matrices for enhanced efficiency.
Sparse array-like objects are supported via
lists of sparse matrices.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between mefa4 versions 0.3-3 dated 2016-03-01 and 0.3-4 dated 2016-10-14
mefa4-0.3-3/mefa4/inst/ChangeLog |only mefa4-0.3-4/mefa4/DESCRIPTION | 8 +- mefa4-0.3-4/mefa4/MD5 | 13 ++-- mefa4-0.3-4/mefa4/NAMESPACE | 8 +- mefa4-0.3-4/mefa4/R/mefa4utilities.R | 113 +++++++++++++++++++++++++++++------ mefa4-0.3-4/mefa4/inst/CITATION | 2 mefa4-0.3-4/mefa4/man/findMax.Rd |only mefa4-0.3-4/mefa4/man/nameAlnum.Rd | 53 ++++++++-------- mefa4-0.3-4/mefa4/man/notin.Rd |only 9 files changed, 137 insertions(+), 60 deletions(-)
Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Spencer Aiello, Tom Kraljevic and Petr Maj, with contributions from the
H2O.ai team
Maintainer: Tom Kraljevic <tomk@0xdata.com>
Diff between h2o versions 3.10.0.6 dated 2016-09-03 and 3.10.0.8 dated 2016-10-14
h2o-3.10.0.6/h2o/man/na.omit.Rd |only h2o-3.10.0.8/h2o/DESCRIPTION | 8 h2o-3.10.0.8/h2o/MD5 | 95 +++++---- h2o-3.10.0.8/h2o/NAMESPACE | 23 ++ h2o-3.10.0.8/h2o/R/classes.R | 17 + h2o-3.10.0.8/h2o/R/communication.R | 9 h2o-3.10.0.8/h2o/R/connection.R | 39 +-- h2o-3.10.0.8/h2o/R/deeplearning.R | 10 h2o-3.10.0.8/h2o/R/export.R | 2 h2o-3.10.0.8/h2o/R/frame.R | 292 +++++++++++++++++++++++++--- h2o-3.10.0.8/h2o/R/gbm.R | 106 +++++----- h2o-3.10.0.8/h2o/R/glm.R | 25 +- h2o-3.10.0.8/h2o/R/import.R | 3 h2o-3.10.0.8/h2o/R/kmeans.R | 23 +- h2o-3.10.0.8/h2o/R/kvstore.R | 84 +++++++- h2o-3.10.0.8/h2o/R/models.R | 109 ++++++++-- h2o-3.10.0.8/h2o/R/naivebayes.R | 9 h2o-3.10.0.8/h2o/R/parse.R | 2 h2o-3.10.0.8/h2o/R/randomforest.R | 88 ++++---- h2o-3.10.0.8/h2o/inst/buildnum.txt | 2 h2o-3.10.0.8/h2o/man/H2OConnection-class.Rd | 4 h2o-3.10.0.8/h2o/man/h2o-package.Rd | 4 h2o-3.10.0.8/h2o/man/h2o.as_date.Rd |only h2o-3.10.0.8/h2o/man/h2o.ascharacter.Rd |only h2o-3.10.0.8/h2o/man/h2o.asfactor.Rd |only h2o-3.10.0.8/h2o/man/h2o.asnumeric.Rd |only h2o-3.10.0.8/h2o/man/h2o.colnames.Rd |only h2o-3.10.0.8/h2o/man/h2o.columns_by_type.Rd |only h2o-3.10.0.8/h2o/man/h2o.deeplearning.Rd | 3 h2o-3.10.0.8/h2o/man/h2o.diff.Rd |only h2o-3.10.0.8/h2o/man/h2o.dim.Rd |only h2o-3.10.0.8/h2o/man/h2o.dimnames.Rd |only h2o-3.10.0.8/h2o/man/h2o.download_mojo.Rd |only h2o-3.10.0.8/h2o/man/h2o.download_pojo.Rd | 8 h2o-3.10.0.8/h2o/man/h2o.exportFile.Rd | 2 h2o-3.10.0.8/h2o/man/h2o.gbm.Rd | 94 ++++----- h2o-3.10.0.8/h2o/man/h2o.glm.Rd | 23 +- h2o-3.10.0.8/h2o/man/h2o.head.Rd | 12 - h2o-3.10.0.8/h2o/man/h2o.importFile.Rd | 5 h2o-3.10.0.8/h2o/man/h2o.init.Rd | 6 h2o-3.10.0.8/h2o/man/h2o.ischaracter.Rd |only h2o-3.10.0.8/h2o/man/h2o.isfactor.Rd |only h2o-3.10.0.8/h2o/man/h2o.isnumeric.Rd |only h2o-3.10.0.8/h2o/man/h2o.kmeans.Rd | 28 +- h2o-3.10.0.8/h2o/man/h2o.log10.Rd |only h2o-3.10.0.8/h2o/man/h2o.log1p.Rd |only h2o-3.10.0.8/h2o/man/h2o.log2.Rd |only h2o-3.10.0.8/h2o/man/h2o.median.Rd | 1 h2o-3.10.0.8/h2o/man/h2o.na_omit.Rd |only h2o-3.10.0.8/h2o/man/h2o.naiveBayes.Rd | 3 h2o-3.10.0.8/h2o/man/h2o.names.Rd |only h2o-3.10.0.8/h2o/man/h2o.parseRaw.Rd | 3 h2o-3.10.0.8/h2o/man/h2o.parseSetup.Rd | 3 h2o-3.10.0.8/h2o/man/h2o.partialPlot.Rd |only h2o-3.10.0.8/h2o/man/h2o.print.Rd |only h2o-3.10.0.8/h2o/man/h2o.randomForest.Rd | 74 +++---- h2o-3.10.0.8/h2o/man/h2o.str.Rd |only h2o-3.10.0.8/h2o/man/h2o.trunc.Rd |only h2o-3.10.0.8/h2o/man/plot.H2OModel.Rd | 33 +-- h2o-3.10.0.8/h2o/man/print.H2OFrame.Rd | 5 60 files changed, 900 insertions(+), 357 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown") objects in R expressions by code
inspection using various strategies, e.g. conservative or liberal. The objective
of this package is to make it as simple as possible to identify global objects
for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.7.0 dated 2016-09-08 and 0.7.1 dated 2016-10-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 8 ++++++++ R/Globals-class.R | 17 +++++++++++------ R/walkAST.R | 6 +++++- tests/Globals.R | 9 +++++++++ tests/walkAST.R | 1 + 7 files changed, 43 insertions(+), 16 deletions(-)
Title: A Tool to Downsize Large Workflows for Testing
Description: Toggles the test and production versions of a large workflow.
Author: William Landau [aut, cre]
Maintainer: William Landau <will.landau@gmail.com>
Diff between downsize versions 0.1.0 dated 2016-09-21 and 0.2.0 dated 2016-10-14
DESCRIPTION | 18 +++---- MD5 | 68 ++++++++++++++++------------ NAMESPACE | 16 ++++++ R/deprecated.R | 49 +++++++++++++++++++- R/help.R |only R/subset.R | 15 ++++-- R/ui.R | 85 +++++++++++++++++++----------------- R/utils.R | 21 +++++--- inst/doc/downsize.R | 26 +++++------ inst/doc/downsize.Rmd | 42 ++++++++--------- inst/doc/downsize.html | 50 ++++++++++----------- man/arg_small.Rd | 2 man/check_args.Rd | 2 man/check_downsized.Rd | 2 man/downsize.Rd | 11 ++-- man/downsize_error.Rd | 2 man/ds.Rd | 4 + man/help_downsize.Rd |only man/make_small.Rd | 2 man/my_mode.Rd |only man/production_mode.Rd |only man/scale_down.Rd | 11 +++- man/scale_up.Rd | 14 +++-- man/scaling.Rd | 14 +++-- man/should_downsize.Rd | 2 man/subset_dim.Rd | 2 man/subset_length.Rd | 2 man/subset_ncol.Rd | 2 man/subset_nrow.Rd | 2 man/subset_single_dim.Rd | 2 man/test_mode.Rd |only man/use_arg_small.Rd | 2 tests/testthat/test-deprecated.R |only tests/testthat/test-downsize.R | 12 ++--- tests/testthat/test-ds.R | 16 ++---- tests/testthat/test-help_downsize.R |only tests/testthat/test-my_mode.R |only tests/testthat/test-scaling.R | 6 +- vignettes/downsize.Rmd | 42 ++++++++--------- 39 files changed, 324 insertions(+), 220 deletions(-)
Title: Clustering Method Based on Local
Description: We developed the clues R package to provide functions
for automatically estimating the number of clusters and
getting the final cluster partition without any input
parameter except the stopping rule for convergence.
The package also provides functions to
evaluate and compare the performances of partitions of a data
set both numerically and graphically.
Author: Fang Chang [aut, ctb],
Weiliang Qiu [aut, cre],
Vincent Carey [aut, ctb],
Ruben H. Zamar [aut, ctb],
Ross Lazarus [aut, ctb],
Xiaogang Wang [aut, ctb]
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>
Diff between clues versions 0.5.6 dated 2015-02-18 and 0.5.9 dated 2016-10-14
DESCRIPTION | 37 +++++++++++++++++++++++++------------ MD5 | 10 +++++----- NAMESPACE | 1 + NEWS | 16 ++++++++++++++-- R/view.R | 7 +++++-- src/clustering2.f95 | 16 +++++++++++++--- 6 files changed, 63 insertions(+), 24 deletions(-)
Title: Analyze System Scalability with the Universal Scalability Law
Description: The Universal Scalability Law is a model to predict hardware and
software scalability. It uses system capacity as a function of load to
forecast the scalability for the system.
Author: Neil J. Gunther [aut],
Stefan Moeding [aut, cre]
Maintainer: Stefan Moeding <stm@moeding.net>
Diff between usl versions 1.6.0 dated 2016-06-18 and 1.7.0 dated 2016-10-13
usl-1.6.0/usl/vignettes/usl-orausl2-1.pdf |only usl-1.7.0/usl/DESCRIPTION | 8 ++++---- usl-1.7.0/usl/MD5 | 25 ++++++++++++------------- usl-1.7.0/usl/NEWS | 6 ++++++ usl-1.7.0/usl/R/print.R | 4 +--- usl-1.7.0/usl/README.md | 10 ++++++---- usl-1.7.0/usl/inst/doc/usl.R | 2 +- usl-1.7.0/usl/inst/doc/usl.Rnw | 2 +- usl-1.7.0/usl/inst/doc/usl.pdf |binary usl-1.7.0/usl/tests/t03.Rout.save | 6 +++--- usl-1.7.0/usl/tests/t04.Rout.save | 14 ++++++++------ usl-1.7.0/usl/tests/t06.Rout.save | 14 ++++++++------ usl-1.7.0/usl/tests/t08.Rout.save | 14 ++++++++------ usl-1.7.0/usl/vignettes/usl.Rnw | 2 +- 14 files changed, 59 insertions(+), 48 deletions(-)
Title: Simple Network of Workstations
Description: Support for simple parallel computing in R.
Author: Luke Tierney, A. J. Rossini, Na Li, H. Sevcikova
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between snow versions 0.4-1 dated 2015-10-31 and 0.4-2 dated 2016-10-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/snow.R | 2 ++ 3 files changed, 7 insertions(+), 5 deletions(-)
Title: Fast Rolling Functions for Seismology using Rcpp
Description: Fast versions of seismic analysis functions that 'roll' over a
vector of values. See the RcppRoll package for alternative
versions of basic statistical functions such as rolling mean,
median, etc.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Mary Templeton [aut],
Gillian Sharer [aut, cre]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>
Diff between seismicRoll versions 1.0.1 dated 2015-03-11 and 1.1.2 dated 2016-10-13
DESCRIPTION | 27 +++++++------- MD5 | 30 +++++++-------- NAMESPACE | 2 - R/RcppExports.R | 2 - R/findOutliers.R | 71 +++++++++++++++++++++++------------- R/seismicRoll.R | 17 ++++++++ man/findOutliers.Rd | 48 +++++++++++------------- man/roll_hampel.Rd | 6 +-- man/roll_mean.Rd | 6 +-- man/roll_median.Rd | 4 +- man/roll_sd.Rd | 6 +-- man/roll_stalta.Rd | 24 ++++++------ man/seismicRoll.Rd | 19 +++++++++ src/Makevars.win | 2 - src/RcppExports.cpp | 98 ++++++++++++++++++++------------------------------- src/source_files.cpp | 2 - 16 files changed, 200 insertions(+), 164 deletions(-)
Title: Quality Report Generation for MaxQuant Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (see <http://www.maxquant.org>).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow <chris.bielow@mdc-berlin.de>
Maintainer: Chris Bielow <chris.bielow@mdc-berlin.de>
Diff between PTXQC versions 0.80.13 dated 2016-10-11 and 0.80.14 dated 2016-10-13
DESCRIPTION | 10 +-- MD5 | 24 +++---- NAMESPACE | 1 NEWS | 3 R/fcn_computeQC.R | 85 +++++----------------------- README.md | 2 inst/doc/PTXQC-Basic_Guide_for_R_users.html | 54 ++++++++--------- inst/doc/PTXQC-CustomizeReport.html | 4 - inst/doc/PTXQC-DragNDrop.html | 4 - inst/doc/PTXQC-FAQ.html | 4 - inst/doc/PTXQC-Input_And_Output_Data.html | 4 - inst/dragNdrop/README.md | 2 tests/testthat/test_computeQC.R | 4 - 13 files changed, 78 insertions(+), 123 deletions(-)
Title: Into the extRemes Package
Description: Graphical User Interface (GUI) to some of the functions in the package extRemes version >= 2.0 are included.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between in2extRemes versions 1.0-2 dated 2015-07-24 and 1.0-3 dated 2016-10-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/evdfit.gui.R | 2 +- inst/CITATION | 27 ++++++++++++--------------- 4 files changed, 20 insertions(+), 23 deletions(-)
Title: Two-Sample Tests for High-Dimensional Mean Vectors
Description: Provides various tests for comparing high-dimensional mean vectors in two sample populations.
Author: Lifeng Lin and Wei Pan
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between highmean versions 2.0 dated 2016-02-27 and 3.0 dated 2016-10-13
DESCRIPTION | 8 ++++---- MD5 | 44 +++++++++++++++++++++++--------------------- NAMESPACE | 4 ++-- R/cpval_aSPU.R |only R/epval_Bai1996.R | 11 +++++++---- R/epval_Cai2014.R | 11 +++++++---- R/epval_Chen2010.R | 11 +++++++---- R/epval_Chen2014.R | 11 +++++++---- R/epval_Sri2008.R | 11 +++++++---- R/epval_aSPU.R | 11 +++++++---- man/apval_Bai1996.Rd | 5 ++++- man/apval_Cai2014.Rd | 5 ++++- man/apval_Chen2010.Rd | 5 ++++- man/apval_Chen2014.Rd | 3 +++ man/apval_Sri2008.Rd | 5 ++++- man/apval_aSPU.Rd | 13 ++++++++----- man/cpval_aSPU.Rd |only man/epval_Bai1996.Rd | 5 ++++- man/epval_Cai2014.Rd | 7 +++++-- man/epval_Chen2010.Rd | 7 +++++-- man/epval_Chen2014.Rd | 5 ++++- man/epval_Sri2008.Rd | 5 ++++- man/epval_aSPU.Rd | 9 ++++++--- man/highmean-package.Rd | 14 +++++++------- 24 files changed, 133 insertions(+), 77 deletions(-)
Title: Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MS-Based Untargeted Metabolomics
Description: Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample.
Author: Xavier Domingo-Almenara, Sara Samino, Maria Vinaixa, Alexandre Perera, Oscar Yanes
Maintainer: Xavier Domingo-Almenara <xavier.domingo@urv.cat>
Diff between erah versions 1.0.2 dated 2016-09-02 and 1.0.3 dated 2016-10-13
DESCRIPTION | 10 ++++---- MD5 | 12 +++++----- NEWS | 11 +++++++-- R/erah.R | 2 - R/file.R | 55 +++++++++++++++++++++++++++++++----------------- R/missingCompRecovery.R | 7 +++--- inst/doc/eRahManual.pdf |binary 7 files changed, 61 insertions(+), 36 deletions(-)
Title: Conditioned Latin Hypercube Sampling
Description: Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006) <DOI:10.1016/j.cageo.2005.12.009>. This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012, <DOI:10.1201/b12728-46>).
Author: Pierre Roudier
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between clhs versions 0.5-5 dated 2015-12-18 and 0.5-6 dated 2016-10-13
DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- NEWS | 4 ++++ R/clhs-raster.R | 12 +++++------- README.md |only inst/doc/vignette.pdf |binary 6 files changed, 19 insertions(+), 16 deletions(-)
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Includes also
utilities for sequence data management under the ACNUC system.
Author: Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>
Diff between seqinr versions 3.3-2 dated 2016-10-07 and 3.3-3 dated 2016-10-13
DESCRIPTION | 15 ++++++++------- MD5 | 8 ++++++-- data/gcO2.rda |only data/gcT.rda |only inst/CITATION | 2 +- man/gcO2.Rd |only man/gcT.Rd |only 7 files changed, 15 insertions(+), 10 deletions(-)
Title: A Collection of Methods for Singular Spectrum Analysis
Description: Methods and tools for Singular Spectrum Analysis including decomposition, forecasting and gap-filling for univariate and multivariate time series.
Author: Anton Korobeynikov, Alex Shlemov, Konstantin Usevich, Nina Golyandina
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between Rssa versions 0.13-1 dated 2015-09-28 and 0.14 dated 2016-10-13
DESCRIPTION | 12 MD5 | 93 +++---- NAMESPACE | 44 --- R/autossa.R | 7 R/cadzow.R | 2 R/capabilities.R |only R/chankel.R | 201 ++++----------- R/common.R | 14 - R/forecast.R | 21 - R/gapfill.R | 31 +- R/hankel.R | 233 +++++++----------- R/hbhankel.R | 237 +++++++----------- R/igapfill.R | 8 R/init.R.in | 1 R/mhankel.R | 163 ++++-------- R/ossa.R | 206 ++++++++++++---- R/plot.R | 8 R/plotn.R | 9 R/pssa.R | 296 +++++++++------------- R/ssa.R | 324 +++++++------------------ R/toeplitz.R | 212 ++++------------ R/wossa.R |only man/Barbara.rd | 2 man/Rssa-package.Rd | 17 - man/cadzow.Rd | 35 ++ man/calcv.Rd | 18 - man/clplot.Rd | 1 man/decompose.Rd | 13 - man/fossa.Rd | 81 +++++- man/gapfill.Rd | 17 - man/hankel.Rd | 6 man/igapfill.Rd | 4 man/iossa.Rd | 12 man/iossa.result.Rd | 5 man/lrr.Rd | 6 man/owcor.Rd | 5 man/parest.Rd | 6 man/plot.Rd | 11 man/plot.reconstruct.Rd | 7 man/rforecast.Rd | 11 man/ssa.Rd | 56 +++- man/ssa.capabilities.Rd |only man/summarize.gaps.Rd | 7 man/toeplitz.Rd | 5 man/vforecast.Rd | 12 man/wcor.Rd | 19 - src/hankel.c | 205 --------------- src/hbhankel.c | 618 +++++++++++++++++++++++++++++++----------------- src/toeplitz.c | 84 ------ 49 files changed, 1542 insertions(+), 1843 deletions(-)
Title: IP Address Geolocation
Description: Connectors to online and offline sources for taking IP addresses
and geolocating them to country, city, timezone and other geographic ranges. For
individual connectors, see the package index.
Author: Oliver Keyes [aut, cre], Drew Schmidt [aut], David Robinson [ctb],
Chris Davis [ctb], Maxmind, Inc. [cph], Pascal Gloor [cph]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between rgeolocate versions 0.7.0 dated 2016-04-22 and 0.8.0 dated 2016-10-13
DESCRIPTION | 10 ++-- MD5 | 24 +++++------ NEWS | 6 ++ R/RcppExports.R | 2 R/ip_api.R | 8 +-- README.md | 6 +- build/vignette.rds |binary inst/doc/Introduction_to_rgeolocate.html | 11 ++--- man/ip_api.Rd | 4 - src/RcppExports.cpp | 34 +++++++-------- src/maxmind.cpp | 6 +- src/maxminddb.c | 66 +++++++++++++++---------------- src/maxminddb.h | 2 13 files changed, 92 insertions(+), 87 deletions(-)
Title: Build Dependency Graphs using Projection
Description: Implements a general framework for creating dependency graphs using projection. Both lasso and sparse additive model projections are implemented. Both Pearson correlation and distance covariance are used to generate the graph.
Author: Jianqing Fan, Yang Feng and Lucy Xia
Maintainer: Yang Feng <yang.feng@columbia.edu>
Diff between pgraph versions 0.6 dated 2016-06-14 and 0.8 dated 2016-10-13
DESCRIPTION | 10 +++--- MD5 | 26 ++++++++--------- NAMESPACE | 6 ++++ R/funs.R | 1 R/greg.R | 28 +++++++++++++++--- R/pgraph.R | 43 ++++++++++++++++++++++------ R/projcore.R | 84 +++++++++++++++++++++++++++++--------------------------- R/projcov.R | 57 ++++++++++++++++++++++---------------- R/roc.R | 30 -------------------- man/greg.Rd | 26 +++++++++++++++-- man/pgraph.Rd | 42 ++++++++++++++++++++++------ man/projcore.Rd | 34 +++++++++------------- man/projcov.Rd | 35 ++++++++++++++++++----- man/roc.Rd | 31 -------------------- 14 files changed, 259 insertions(+), 194 deletions(-)
Title: An Infra-Structure for Performance Estimation of Predictive
Models
Description: An infra-structure for estimating the predictive performance of
predictive models. In this context, it can also be used to compare and/or select
among different alternative ways of solving one or more predictive tasks. The
main goal of the package is to provide a generic infra-structure to estimate
the values of different metrics of predictive performance using different
estimation procedures. These estimation tasks can be applied to any solutions
(workflows) to the predictive tasks. The package provides easy to use standard
workflows that allow the usage of any available R modeling algorithm together
with some pre-defined data pre-processing steps and also prediction post-
processing methods. It also provides means for addressing issues related with
the statistical significance of the observed differences.
Author: Luis Torgo [aut, cre]
Maintainer: Luis Torgo <ltorgo@dcc.fc.up.pt>
Diff between performanceEstimation versions 1.0.2 dated 2015-09-07 and 1.1.0 dated 2016-10-13
CHANGES | 23 ++ DESCRIPTION | 32 +- MD5 | 44 ++- NAMESPACE | 1 R/classDefs.R | 16 - R/evaluationMetrics.R | 70 +++--- R/experiments.R | 399 ++++++++++++++++++------------------ R/methods.R | 11 R/resultsAnalysis.R | 17 - R/resultsManipulation.R | 30 ++ R/smote.R | 16 - R/workflows.R | 60 +++-- inst/doc/performanceEstimation.R |only inst/doc/performanceEstimation.Rmd |only inst/doc/performanceEstimation.html |only man/EstimationTask-class.Rd | 51 ++-- man/classificationMetrics.Rd | 57 +++-- man/mcEstimates.Rd | 4 man/rankWorkflows.Rd | 13 - man/regressionMetrics.Rd | 8 man/results2table.Rd |only man/standardPRE.Rd | 4 man/standardWF.Rd | 24 ++ man/topPerformer.Rd | 10 man/topPerformers.Rd | 10 25 files changed, 536 insertions(+), 364 deletions(-)
More information about performanceEstimation at CRAN
Permanent link
Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time
series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between imputeTS versions 1.6 dated 2016-06-03 and 1.7 dated 2016-10-13
imputeTS-1.6/imputeTS/R/int.preCheck.R |only imputeTS-1.7/imputeTS/DESCRIPTION | 11 imputeTS-1.7/imputeTS/MD5 | 119 +++-- imputeTS-1.7/imputeTS/NAMESPACE | 54 +- imputeTS-1.7/imputeTS/NEWS | 235 ++++++----- imputeTS-1.7/imputeTS/R/imputeTS-package.R | 56 +- imputeTS-1.7/imputeTS/R/int.algoInterface.R | 85 ++-- imputeTS-1.7/imputeTS/R/na.interpolation.R | 201 +++++---- imputeTS-1.7/imputeTS/R/na.kalman.R | 315 ++++++++------ imputeTS-1.7/imputeTS/R/na.locf.R | 267 ++++++------ imputeTS-1.7/imputeTS/R/na.ma.R | 304 +++++++------- imputeTS-1.7/imputeTS/R/na.mean.R | 184 ++++---- imputeTS-1.7/imputeTS/R/na.random.R | 161 ++++--- imputeTS-1.7/imputeTS/R/na.remove.R | 130 +++--- imputeTS-1.7/imputeTS/R/na.replace.R | 129 +++--- imputeTS-1.7/imputeTS/R/na.seadec.R | 189 ++++---- imputeTS-1.7/imputeTS/R/na.seasplit.R | 185 ++++---- imputeTS-1.7/imputeTS/R/plotNA.distribution.R | 141 +++--- imputeTS-1.7/imputeTS/R/plotNA.distributionBar.R | 301 +++++++------- imputeTS-1.7/imputeTS/R/plotNA.gapsize.R | 270 ++++++------ imputeTS-1.7/imputeTS/R/plotNA.imputations.R | 240 ++++++----- imputeTS-1.7/imputeTS/R/statsNA.R | 421 ++++++++++---------- imputeTS-1.7/imputeTS/R/tsAirgap.R | 64 +-- imputeTS-1.7/imputeTS/R/tsAirgapComplete.R | 62 +- imputeTS-1.7/imputeTS/README.md | 281 ++++++------- imputeTS-1.7/imputeTS/data/tsHeating.rda |binary imputeTS-1.7/imputeTS/data/tsHeatingComplete.rda |binary imputeTS-1.7/imputeTS/data/tsNH4.rda |binary imputeTS-1.7/imputeTS/data/tsNH4Complete.rda |binary imputeTS-1.7/imputeTS/inst/CITATION | 23 - imputeTS-1.7/imputeTS/man/imputeTS-package.Rd | 64 +-- imputeTS-1.7/imputeTS/man/na.interpolation.Rd | 112 ++--- imputeTS-1.7/imputeTS/man/na.kalman.Rd | 163 +++---- imputeTS-1.7/imputeTS/man/na.locf.Rd | 134 +++--- imputeTS-1.7/imputeTS/man/na.ma.Rd | 151 +++---- imputeTS-1.7/imputeTS/man/na.mean.Rd | 103 ++-- imputeTS-1.7/imputeTS/man/na.random.Rd | 98 ++-- imputeTS-1.7/imputeTS/man/na.remove.Rd | 93 ++-- imputeTS-1.7/imputeTS/man/na.replace.Rd | 82 +-- imputeTS-1.7/imputeTS/man/na.seadec.Rd | 101 ++-- imputeTS-1.7/imputeTS/man/na.seasplit.Rd | 105 ++-- imputeTS-1.7/imputeTS/man/plotNA.distribution.Rd | 113 ++--- imputeTS-1.7/imputeTS/man/plotNA.distributionBar.Rd | 133 +++--- imputeTS-1.7/imputeTS/man/plotNA.gapsize.Rd | 136 +++--- imputeTS-1.7/imputeTS/man/plotNA.imputations.Rd | 151 +++---- imputeTS-1.7/imputeTS/man/statsNA.Rd | 118 ++--- imputeTS-1.7/imputeTS/man/tsAirgap.Rd | 86 ++-- imputeTS-1.7/imputeTS/man/tsAirgapComplete.Rd | 86 ++-- imputeTS-1.7/imputeTS/man/tsHeating.Rd | 84 +-- imputeTS-1.7/imputeTS/man/tsHeatingComplete.Rd | 84 +-- imputeTS-1.7/imputeTS/man/tsNH4.Rd | 78 +-- imputeTS-1.7/imputeTS/man/tsNH4Complete.Rd | 78 +-- imputeTS-1.7/imputeTS/tests |only 53 files changed, 3558 insertions(+), 3223 deletions(-)
Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Model Averaging in linear models and
generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from Liang et al (2008)
<DOI:10.1198/016214507000001337>
for linear models or mixtures of g-priors in GLMs of Li and Clyde (2015)
<http://arxiv.org/abs/1503.06913>. Other model
selection criteria include AIC, BIC and Empirical Bayes estimates of g.
Sampling probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an efficient MCMC algorithm
samples models using the BAS tree structure as an efficient hash table.
Uniform priors over all models or beta-binomial prior distributions on
model size are allowed, and for large p truncated priors on the model
space may be used. The user may force variables to always be included.
Details behind the sampling algorithm are provided in
Clyde, Ghosh and Littman (2010) <DOI:10.1198/jcgs.2010.09049>.
This material is based upon work supported by the National Science
Foundation under Grant DMS-1106891. Any opinions, findings, and
conclusions or recommendations expressed in this material are those of
the author(s) and do not necessarily reflect the views of the
National Science Foundation.
Author: Merlise Clyde [aut, cre, cph],
Michael Littman [ctb],
Quanli Wang [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@stat.duke.edu>
Diff between BAS versions 1.4.1 dated 2016-09-20 and 1.4.2 dated 2016-10-13
BAS-1.4.1/BAS/src/igam.c |only BAS-1.4.1/BAS/src/incompleteGamma.c |only BAS-1.4.2/BAS/DESCRIPTION | 11 +-- BAS-1.4.2/BAS/MD5 | 40 ++++++-------- BAS-1.4.2/BAS/NEWS.md | 9 +++ BAS-1.4.2/BAS/R/bas.gglm.R | 25 ++++++-- BAS-1.4.2/BAS/demo/BAS.hald.R | 4 + BAS-1.4.2/BAS/inst/doc/BAS-vignette.R | 4 + BAS-1.4.2/BAS/inst/doc/BAS-vignette.Rmd | 8 ++ BAS-1.4.2/BAS/inst/doc/BAS-vignette.html | 52 +++++++++--------- BAS-1.4.2/BAS/man/bas.glm.Rd | 12 +++- BAS-1.4.2/BAS/man/bayesglm.Rd | 2 BAS-1.4.2/BAS/src/ZS.approx.full.np.c | 4 - BAS-1.4.2/BAS/src/ZS.approx.null.np.c | 4 - BAS-1.4.2/BAS/src/betapriorfamily.c | 88 ++++++++++++++++++++++++++----- BAS-1.4.2/BAS/src/betapriorfamily.h | 1 BAS-1.4.2/BAS/src/cch.c | 4 - BAS-1.4.2/BAS/src/gamma.c | 6 +- BAS-1.4.2/BAS/src/hyp2f1.c | 44 ++++++++++----- BAS-1.4.2/BAS/src/hyperg.c | 14 ++-- BAS-1.4.2/BAS/src/hypergeometric1F1.c | 7 +- BAS-1.4.2/BAS/vignettes/BAS-vignette.Rmd | 8 ++ 22 files changed, 238 insertions(+), 109 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed);
- generalised linear mixed models (if R packages 'metafor', 'lme4', 'numDeriv', and 'BiasedUrn' are installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.5-0 dated 2016-08-17 and 4.6-0 dated 2016-10-13
DESCRIPTION | 9 +- MD5 | 93 ++++++++++++----------- NAMESPACE | 4 - NEWS | 98 +++++++++++++++++++++++++ R/asin2ir.R |only R/asin2p.R | 10 +- R/backtransf.R | 26 +++++- R/catmeth.R | 29 +++++-- R/forest.meta.R | 187 +++++++++++++++++++++++++++++++++++++++--------- R/funnel.default.R | 4 - R/funnel.meta.R | 5 - R/is.relative.effect.R | 2 R/meta-internal.R | 7 + R/metabias.meta.R | 14 +++ R/metacont.R | 51 ++++++++----- R/metacum.R | 58 +++++++++++--- R/metagen.R | 9 ++ R/metainf.R | 58 +++++++++++--- R/metaprop.R | 16 ++-- R/metarate.R |only R/metareg.R | 7 + R/print.meta.R | 63 +++++++++++++--- R/print.summary.meta.R | 114 ++++++++++++++++++----------- R/setchar.R | 2 R/settings.meta.R | 14 +++ R/subgroup.R | 56 ++++++++++---- R/summary.meta.R | 46 ++++++++++- R/trimfill.default.R | 10 ++ R/trimfill.meta.R | 12 ++- R/update.meta.R | 59 +++++++++++++-- R/xlab.R | 42 +++++++++- data/woodyplants.txt.gz |only inst/CITATION |only man/forest.Rd | 18 ++++ man/funnel.Rd | 16 ++-- man/meta-package.Rd |only man/metabias.Rd | 20 +++-- man/metabin.Rd | 15 +-- man/metacont.Rd | 70 ++++++++++++++--- man/metacor.Rd | 9 +- man/metacr.Rd | 4 - man/metagen.Rd | 26 ++++-- man/metainc.Rd | 9 +- man/metainf.Rd | 4 - man/metaprop.Rd | 21 ++--- man/metarate.Rd |only man/print.meta.Rd | 16 +++- man/settings.meta.Rd | 3 man/trimfill.Rd | 15 ++- man/update.meta.Rd | 7 + man/woodyplants.Rd |only 51 files changed, 1036 insertions(+), 322 deletions(-)
Title: Two-Level Normal Independent Sampling Estimation
Description: Functions for two level normal models as described in Everson and Morris (2000). J. R. Statist. Soc. B, 62 prt 2, pp.399--412.
Author: S-PLUS original by Phil Everson; R port by Roger D. Peng <rpeng@jhsph.edu>
Maintainer: Roger D. Peng <rpeng@jhsph.edu>
Diff between tlnise versions 2.0 dated 2013-05-24 and 2.0-2 dated 2016-10-12
DESCRIPTION | 20 ++++++++------------ MD5 | 8 ++++---- NAMESPACE | 4 +++- R/internal.R | 6 ++---- inst/CITATION | 2 +- 5 files changed, 18 insertions(+), 22 deletions(-)
Title: Exploring Genomic Relations for Precision Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes or SNPs, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks and TF binding sites) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.0.3 dated 2016-08-26 and 1.0.4 dated 2016-10-12
XGR-1.0.3/XGR/data/datalist |only XGR-1.0.4/XGR/DESCRIPTION | 12 - XGR-1.0.4/XGR/MD5 | 163 ++++++++++++------------ XGR-1.0.4/XGR/NAMESPACE | 4 XGR-1.0.4/XGR/R/xCircos.r | 96 +++++++++----- XGR-1.0.4/XGR/R/xConverter.r | 7 - XGR-1.0.4/XGR/R/xEnrichConciser.r | 2 XGR-1.0.4/XGR/R/xEnricher.r | 4 XGR-1.0.4/XGR/R/xEnricherGenes.r | 10 - XGR-1.0.4/XGR/R/xEnricherYours.r | 12 + XGR-1.0.4/XGR/R/xGRviaGeneAnno.r | 4 XGR-1.0.4/XGR/R/xGRviaGenomicAnno.r | 139 +++++++++++++++------ XGR-1.0.4/XGR/R/xGRviaGenomicAnnoAdv.r | 141 +++++++++++++++------ XGR-1.0.4/XGR/R/xRDataLoader.r | 13 + XGR-1.0.4/XGR/R/xSM2DF.r |only XGR-1.0.4/XGR/R/xSNP2GeneScores.r | 6 XGR-1.0.4/XGR/R/xSNP2nGenes.r | 82 ++---------- XGR-1.0.4/XGR/R/xSNPlocations.r |only XGR-1.0.4/XGR/R/xSNPscores.r | 20 +-- XGR-1.0.4/XGR/R/xSocialiser.r | 6 XGR-1.0.4/XGR/R/xSocialiserGenes.r | 6 XGR-1.0.4/XGR/R/xSocialiserSNPs.r | 8 + XGR-1.0.4/XGR/R/xSparseMatrix.r | 2 XGR-1.0.4/XGR/R/xSubneterSNPs.r | 7 - XGR-1.0.4/XGR/data/ImmunoBase.RData |binary XGR-1.0.4/XGR/data/JKscience_TS2A.RData |binary XGR-1.0.4/XGR/inst/NEWS | 10 + XGR-1.0.4/XGR/inst/xCircos.html | 39 ++++- XGR-1.0.4/XGR/inst/xDAGanno.html | 2 XGR-1.0.4/XGR/inst/xDAGsim.html | 6 XGR-1.0.4/XGR/inst/xEnrichCompare.html | 2 XGR-1.0.4/XGR/inst/xEnrichConciser.html | 2 XGR-1.0.4/XGR/inst/xEnrichDAGplotAdv.html | 2 XGR-1.0.4/XGR/inst/xEnricher.html | 2 XGR-1.0.4/XGR/inst/xEnricherGenes.html | 48 +++---- XGR-1.0.4/XGR/inst/xEnricherYours.html | 2 XGR-1.0.4/XGR/inst/xGRviaGeneAnno.html | 49 +++---- XGR-1.0.4/XGR/inst/xGRviaGenomicAnno.html | 173 +++++++++++++++++++++++++- XGR-1.0.4/XGR/inst/xGRviaGenomicAnnoAdv.html | 177 ++++++++++++++++++++++++++- XGR-1.0.4/XGR/inst/xRDataLoader.html | 8 - XGR-1.0.4/XGR/inst/xSM2DF.html |only XGR-1.0.4/XGR/inst/xSNP2GeneScores.html | 8 - XGR-1.0.4/XGR/inst/xSNP2nGenes.html | 12 + XGR-1.0.4/XGR/inst/xSNPlocations.html |only XGR-1.0.4/XGR/inst/xSNPscores.html | 4 XGR-1.0.4/XGR/inst/xSubneterSNPs.html | 30 ++-- XGR-1.0.4/XGR/man/xCircos.Rd | 41 ++++-- XGR-1.0.4/XGR/man/xConverter.Rd | 2 XGR-1.0.4/XGR/man/xDAGanno.Rd | 4 XGR-1.0.4/XGR/man/xDAGsim.Rd | 8 - XGR-1.0.4/XGR/man/xEnrichBarplot.Rd | 2 XGR-1.0.4/XGR/man/xEnrichCompare.Rd | 4 XGR-1.0.4/XGR/man/xEnrichConciser.Rd | 6 XGR-1.0.4/XGR/man/xEnrichDAGplot.Rd | 2 XGR-1.0.4/XGR/man/xEnrichDAGplotAdv.Rd | 4 XGR-1.0.4/XGR/man/xEnrichNetplot.Rd | 2 XGR-1.0.4/XGR/man/xEnrichViewer.Rd | 2 XGR-1.0.4/XGR/man/xEnricher.Rd | 4 XGR-1.0.4/XGR/man/xEnricherGenes.Rd | 50 +++---- XGR-1.0.4/XGR/man/xEnricherSNPs.Rd | 2 XGR-1.0.4/XGR/man/xEnricherYours.Rd | 4 XGR-1.0.4/XGR/man/xFunArgs.Rd | 2 XGR-1.0.4/XGR/man/xGRsampling.Rd | 2 XGR-1.0.4/XGR/man/xGRviaGeneAnno.Rd | 51 +++---- XGR-1.0.4/XGR/man/xGRviaGenomicAnno.Rd | 125 ++++++++++++++++++- XGR-1.0.4/XGR/man/xGRviaGenomicAnnoAdv.Rd | 129 ++++++++++++++++++- XGR-1.0.4/XGR/man/xLiftOver.Rd | 2 XGR-1.0.4/XGR/man/xRDataLoader.Rd | 10 - XGR-1.0.4/XGR/man/xRd2HTML.Rd | 2 XGR-1.0.4/XGR/man/xRdWrap.Rd | 2 XGR-1.0.4/XGR/man/xSM2DF.Rd |only XGR-1.0.4/XGR/man/xSNP2GeneScores.Rd | 10 - XGR-1.0.4/XGR/man/xSNP2nGenes.Rd | 14 +- XGR-1.0.4/XGR/man/xSNPlocations.Rd |only XGR-1.0.4/XGR/man/xSNPscores.Rd | 4 XGR-1.0.4/XGR/man/xSocialiser.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserDAGplot.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserDAGplotAdv.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserGenes.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserNetplot.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserSNPs.Rd | 2 XGR-1.0.4/XGR/man/xSparseMatrix.Rd | 2 XGR-1.0.4/XGR/man/xSubneterGenes.Rd | 2 XGR-1.0.4/XGR/man/xSubneterSNPs.Rd | 32 ++-- XGR-1.0.4/XGR/man/xVisKernels.Rd | 2 XGR-1.0.4/XGR/man/xVisNet.Rd | 2 86 files changed, 1329 insertions(+), 533 deletions(-)
Title: Structural Equation Modelling in R with 'OpenMx'
Description: Create, run, and report structural equation and twin models quickly.
If you're just starting out, try typing '?umx'.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.3.0 dated 2016-08-18 and 1.4.0 dated 2016-10-12
umx-1.3.0/umx/man/getOpenMx.Rd |only umx-1.4.0/umx/DESCRIPTION | 8 umx-1.4.0/umx/MD5 | 141 +++---- umx-1.4.0/umx/NAMESPACE | 5 umx-1.4.0/umx/NEWS | 14 umx-1.4.0/umx/R/build_run_modify.r | 524 ++++++++++++++++----------- umx-1.4.0/umx/R/deprecated.r | 5 umx-1.4.0/umx/R/fit_and_reporting.r | 275 ++++++++------ umx-1.4.0/umx/R/misc_and_utility.r | 67 ++- umx-1.4.0/umx/R/xmu.r | 30 + umx-1.4.0/umx/man/RMSEA.MxModel.Rd | 2 umx-1.4.0/umx/man/RMSEA.Rd | 2 umx-1.4.0/umx/man/RMSEA.summary.mxmodel.Rd | 2 umx-1.4.0/umx/man/confint.MxModel.Rd | 2 umx-1.4.0/umx/man/extractAIC.MxModel.Rd | 2 umx-1.4.0/umx/man/install.OpenMx.Rd |only umx-1.4.0/umx/man/loadings.Rd | 2 umx-1.4.0/umx/man/logLik.Rd | 2 umx-1.4.0/umx/man/plot.MxModel.Rd | 30 + umx-1.4.0/umx/man/residuals.MxModel.Rd | 2 umx-1.4.0/umx/man/umx-deprecated.Rd | 4 umx-1.4.0/umx/man/umx.Rd | 21 - umx-1.4.0/umx/man/umxACE.Rd | 70 ++- umx-1.4.0/umx/man/umxACESexLim.Rd | 11 umx-1.4.0/umx/man/umxACEcov.Rd | 17 umx-1.4.0/umx/man/umxCF_SexLim.Rd | 11 umx-1.4.0/umx/man/umxCI.Rd | 3 umx-1.4.0/umx/man/umxCI_boot.Rd | 2 umx-1.4.0/umx/man/umxCP.Rd | 11 umx-1.4.0/umx/man/umxCompare.Rd | 3 umx-1.4.0/umx/man/umxDiagnose.Rd | 8 umx-1.4.0/umx/man/umxEquate.Rd | 6 umx-1.4.0/umx/man/umxExpCov.Rd | 10 umx-1.4.0/umx/man/umxExpMeans.Rd | 3 umx-1.4.0/umx/man/umxFactor.Rd | 2 umx-1.4.0/umx/man/umxFitIndices.Rd | 40 +- umx-1.4.0/umx/man/umxGxE.Rd | 11 umx-1.4.0/umx/man/umxGxE_window.Rd | 11 umx-1.4.0/umx/man/umxIP.Rd | 11 umx-1.4.0/umx/man/umxJiggle.Rd | 2 umx-1.4.0/umx/man/umxLabel.Rd | 8 umx-1.4.0/umx/man/umxLatent.Rd | 8 umx-1.4.0/umx/man/umxMatrix.Rd |only umx-1.4.0/umx/man/umxModify.Rd | 6 umx-1.4.0/umx/man/umxPath.Rd | 12 umx-1.4.0/umx/man/umxPlotACE.Rd | 16 umx-1.4.0/umx/man/umxPlotACEcov.Rd | 20 - umx-1.4.0/umx/man/umxPlotCP.Rd | 32 + umx-1.4.0/umx/man/umxPlotGxE.Rd | 32 + umx-1.4.0/umx/man/umxPlotIP.Rd | 30 + umx-1.4.0/umx/man/umxRAM.Rd | 6 umx-1.4.0/umx/man/umxRAM2Ordinal.Rd | 6 umx-1.4.0/umx/man/umxRun.Rd | 6 umx-1.4.0/umx/man/umxSummary.MxModel.Rd | 4 umx-1.4.0/umx/man/umxSummaryACE.Rd | 16 umx-1.4.0/umx/man/umxSummaryACEcov.Rd | 17 umx-1.4.0/umx/man/umxSummaryCP.Rd | 14 umx-1.4.0/umx/man/umxSummaryGxE.Rd | 14 umx-1.4.0/umx/man/umxSummaryIP.Rd | 14 umx-1.4.0/umx/man/umxThresholdMatrix.Rd | 7 umx-1.4.0/umx/man/umxValues.Rd | 7 umx-1.4.0/umx/man/umx_drop_ok.Rd | 2 umx-1.4.0/umx/man/umx_fix_first_loadings.Rd | 7 umx-1.4.0/umx/man/umx_fix_latents.Rd | 7 umx-1.4.0/umx/man/umx_get_options.Rd | 2 umx-1.4.0/umx/man/umx_make_TwinData.Rd | 14 umx-1.4.0/umx/man/umx_make_sql_from_excel.Rd | 1 umx-1.4.0/umx/man/umx_pad.Rd | 2 umx-1.4.0/umx/man/umx_rename.Rd | 2 umx-1.4.0/umx/man/umx_standardize_RAM.Rd | 2 umx-1.4.0/umx/man/umx_time.Rd | 11 umx-1.4.0/umx/man/xmu_dot_make_paths.Rd | 4 umx-1.4.0/umx/man/xmu_dot_make_residuals.Rd | 6 73 files changed, 1068 insertions(+), 639 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (<http://www.synbreed.tum.de>). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Hans-Juergen Auinger <auinger@tum.de>
Diff between synbreed versions 0.11-29 dated 2016-01-18 and 0.11-41 dated 2016-10-12
synbreed-0.11-29/synbreed/vignettes/IntroSyn.pdf |only synbreed-0.11-41/synbreed/DESCRIPTION | 16 synbreed-0.11-41/synbreed/MD5 | 52 synbreed-0.11-41/synbreed/R/LD.r | 101 synbreed-0.11-41/synbreed/R/LDDist.r | 43 synbreed-0.11-41/synbreed/R/codeGeno.r | 1490 +++++------ synbreed-0.11-41/synbreed/R/discard.markers.r | 4 synbreed-0.11-41/synbreed/R/kinship.r | 15 synbreed-0.11-41/synbreed/R/manhattanPlot.r | 23 synbreed-0.11-41/synbreed/R/plot.relationshipMatrix.r | 187 + synbreed-0.11-41/synbreed/R/read.write.vcf.r | 4 synbreed-0.11-41/synbreed/build |only synbreed-0.11-41/synbreed/inst/doc |only synbreed-0.11-41/synbreed/java/COPYRIGHTS | 4 synbreed-0.11-41/synbreed/man/LDDist.Rd | 3 synbreed-0.11-41/synbreed/man/codeGeno.Rd | 15 synbreed-0.11-41/synbreed/man/discard.individuals.Rd | 2 synbreed-0.11-41/synbreed/man/discard.markers.Rd | 2 synbreed-0.11-41/synbreed/man/manhattanPlot.Rd | 7 synbreed-0.11-41/synbreed/man/plot.relationshipMatrix.Rd | 18 synbreed-0.11-41/synbreed/vignettes/IntroSyn.Rnw |only synbreed-0.11-41/synbreed/vignettes/IntroSyn.tex | 1766 +++++++------- synbreed-0.11-41/synbreed/vignettes/figs/cattleHist.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/genMapCattle.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/genMapMaize.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/genMapMice.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/maizeHist.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/miceHist.pdf |binary 28 files changed, 1957 insertions(+), 1795 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
T. Davies;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
P. Hewson;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.46-1 dated 2016-07-08 and 1.47-0 dated 2016-10-12
spatstat-1.46-1/spatstat/man/circumradius.Rd |only spatstat-1.46-1/spatstat/tests/testsAtoN.R |only spatstat-1.46-1/spatstat/tests/testsPtoZ.R |only spatstat-1.47-0/spatstat/DESCRIPTION | 19 spatstat-1.47-0/spatstat/MD5 | 339 +++++++------ spatstat-1.47-0/spatstat/NAMESPACE | 86 +++ spatstat-1.47-0/spatstat/NEWS | 267 ++++++++++ spatstat-1.47-0/spatstat/R/Fest.R | 5 spatstat-1.47-0/spatstat/R/First.R | 3 spatstat-1.47-0/spatstat/R/Hest.R | 1 spatstat-1.47-0/spatstat/R/Jest.R | 24 spatstat-1.47-0/spatstat/R/Kest.R | 4 spatstat-1.47-0/spatstat/R/Kmeasure.R | 22 spatstat-1.47-0/spatstat/R/addvar.R | 2 spatstat-1.47-0/spatstat/R/bc.R |only spatstat-1.47-0/spatstat/R/boundingcircle.R |only spatstat-1.47-0/spatstat/R/breakpts.R | 5 spatstat-1.47-0/spatstat/R/bw.ppl.R | 17 spatstat-1.47-0/spatstat/R/clusterinfo.R | 24 spatstat-1.47-0/spatstat/R/density.lpp.R | 4 spatstat-1.47-0/spatstat/R/density.ppp.R | 121 +++- spatstat-1.47-0/spatstat/R/disc.R | 8 spatstat-1.47-0/spatstat/R/dummy.R | 9 spatstat-1.47-0/spatstat/R/edgeRipley.R | 8 spatstat-1.47-0/spatstat/R/eval.fv.R | 6 spatstat-1.47-0/spatstat/R/fardist.R | 12 spatstat-1.47-0/spatstat/R/fitted.ppm.R | 3 spatstat-1.47-0/spatstat/R/fv.R | 29 - spatstat-1.47-0/spatstat/R/geyer.R | 14 spatstat-1.47-0/spatstat/R/hierpair.family.R | 2 spatstat-1.47-0/spatstat/R/images.R | 6 spatstat-1.47-0/spatstat/R/intensity.R | 6 spatstat-1.47-0/spatstat/R/kernel2d.R |only spatstat-1.47-0/spatstat/R/kppm.R | 6 spatstat-1.47-0/spatstat/R/leverage.R | 6 spatstat-1.47-0/spatstat/R/linalg.R | 106 ++-- spatstat-1.47-0/spatstat/R/linearK.R | 35 - spatstat-1.47-0/spatstat/R/linearKmulti.R | 32 - spatstat-1.47-0/spatstat/R/lineardisc.R | 49 + spatstat-1.47-0/spatstat/R/linearpcf.R | 36 - spatstat-1.47-0/spatstat/R/linearpcfmulti.R | 36 - spatstat-1.47-0/spatstat/R/linequad.R | 142 +++-- spatstat-1.47-0/spatstat/R/linfun.R | 23 spatstat-1.47-0/spatstat/R/linim.R | 65 ++ spatstat-1.47-0/spatstat/R/linnet.R | 72 ++ spatstat-1.47-0/spatstat/R/lintess.R | 10 spatstat-1.47-0/spatstat/R/lpp.R | 8 spatstat-1.47-0/spatstat/R/lppm.R | 4 spatstat-1.47-0/spatstat/R/mincontrast.R | 6 spatstat-1.47-0/spatstat/R/minkowski.R | 61 +- spatstat-1.47-0/spatstat/R/morphology.R | 15 spatstat-1.47-0/spatstat/R/nnfunlpp.R | 18 spatstat-1.47-0/spatstat/R/options.R | 24 spatstat-1.47-0/spatstat/R/otherpackages.R |only spatstat-1.47-0/spatstat/R/pairwise.family.R | 2 spatstat-1.47-0/spatstat/R/parres.R | 4 spatstat-1.47-0/spatstat/R/pcfinhom.R | 10 spatstat-1.47-0/spatstat/R/pcfmulti.R | 13 spatstat-1.47-0/spatstat/R/pcfmulti.inhom.R | 13 spatstat-1.47-0/spatstat/R/persp.im.R | 42 - spatstat-1.47-0/spatstat/R/pixellate.R | 16 spatstat-1.47-0/spatstat/R/plot.fv.R | 5 spatstat-1.47-0/spatstat/R/plot.im.R | 35 + spatstat-1.47-0/spatstat/R/plot.owin.R | 5 spatstat-1.47-0/spatstat/R/plot.ppp.R | 33 - spatstat-1.47-0/spatstat/R/plot3d.R | 48 + spatstat-1.47-0/spatstat/R/pool.R | 26 - spatstat-1.47-0/spatstat/R/pp3.R | 22 spatstat-1.47-0/spatstat/R/psp.R | 7 spatstat-1.47-0/spatstat/R/quadratcount.R | 14 spatstat-1.47-0/spatstat/R/rLGCP.R | 13 spatstat-1.47-0/spatstat/R/random.R | 55 +- spatstat-1.47-0/spatstat/R/relrisk.R | 4 spatstat-1.47-0/spatstat/R/relrisk.ppm.R | 2 spatstat-1.47-0/spatstat/R/resid4plot.R | 2 spatstat-1.47-0/spatstat/R/resolve.defaults.R | 21 spatstat-1.47-0/spatstat/R/rho2hat.R | 2 spatstat-1.47-0/spatstat/R/rhohat.R | 8 spatstat-1.47-0/spatstat/R/rmh.default.R | 39 + spatstat-1.47-0/spatstat/R/rmh.ppm.R | 7 spatstat-1.47-0/spatstat/R/smooth.ppp.R | 102 +++- spatstat-1.47-0/spatstat/R/sparse3Darray.R | 52 +- spatstat-1.47-0/spatstat/R/sparselinalg.R | 2 spatstat-1.47-0/spatstat/R/summary.im.R | 11 spatstat-1.47-0/spatstat/R/summary.quad.R | 103 ++-- spatstat-1.47-0/spatstat/R/superimpose.R | 17 spatstat-1.47-0/spatstat/R/symbolmap.R | 85 ++- spatstat-1.47-0/spatstat/R/tapplysum.R |only spatstat-1.47-0/spatstat/R/terse.R | 92 ++- spatstat-1.47-0/spatstat/R/treebranches.R | 12 spatstat-1.47-0/spatstat/R/units.R | 38 + spatstat-1.47-0/spatstat/R/util.R | 120 +--- spatstat-1.47-0/spatstat/R/vcov.ppm.R | 4 spatstat-1.47-0/spatstat/R/weightedStats.R |only spatstat-1.47-0/spatstat/R/window.R | 5 spatstat-1.47-0/spatstat/R/wingeom.R | 66 +- spatstat-1.47-0/spatstat/data/chicago.rda |binary spatstat-1.47-0/spatstat/data/dendrite.rda |binary spatstat-1.47-0/spatstat/data/simplenet.rda |binary spatstat-1.47-0/spatstat/data/spiders.rda |binary spatstat-1.47-0/spatstat/demo/spatstat.R | 2 spatstat-1.47-0/spatstat/inst/doc/BEGINNER.txt | 15 spatstat-1.47-0/spatstat/inst/doc/datasets.R | 131 ++--- spatstat-1.47-0/spatstat/inst/doc/datasets.Rnw | 1 spatstat-1.47-0/spatstat/inst/doc/datasets.pdf |binary spatstat-1.47-0/spatstat/inst/doc/getstart.pdf |binary spatstat-1.47-0/spatstat/inst/doc/replicated.pdf |binary spatstat-1.47-0/spatstat/inst/doc/shapefiles.pdf |binary spatstat-1.47-0/spatstat/inst/doc/updates.R | 13 spatstat-1.47-0/spatstat/inst/doc/updates.Rnw | 245 ++++++++- spatstat-1.47-0/spatstat/inst/doc/updates.pdf |binary spatstat-1.47-0/spatstat/man/Extract.linim.Rd |only spatstat-1.47-0/spatstat/man/Kinhom.Rd | 17 spatstat-1.47-0/spatstat/man/MinkowskiSum.Rd | 18 spatstat-1.47-0/spatstat/man/Smooth.ppp.Rd | 3 spatstat-1.47-0/spatstat/man/anyNA.im.Rd |only spatstat-1.47-0/spatstat/man/applynbd.Rd | 11 spatstat-1.47-0/spatstat/man/as.linnet.linim.Rd | 15 spatstat-1.47-0/spatstat/man/as.linnet.psp.Rd | 4 spatstat-1.47-0/spatstat/man/bc.ppm.Rd |only spatstat-1.47-0/spatstat/man/boundingcircle.Rd |only spatstat-1.47-0/spatstat/man/bw.ppl.Rd | 6 spatstat-1.47-0/spatstat/man/density.ppp.Rd | 73 ++ spatstat-1.47-0/spatstat/man/diameter.linnet.Rd | 23 spatstat-1.47-0/spatstat/man/dilation.Rd | 3 spatstat-1.47-0/spatstat/man/discs.Rd | 26 - spatstat-1.47-0/spatstat/man/eval.fv.Rd | 18 spatstat-1.47-0/spatstat/man/grow.rectangle.Rd | 21 spatstat-1.47-0/spatstat/man/improve.kppm.Rd | 7 spatstat-1.47-0/spatstat/man/invoke.symbolmap.Rd | 2 spatstat-1.47-0/spatstat/man/kppm.Rd | 23 spatstat-1.47-0/spatstat/man/laslett.Rd | 3 spatstat-1.47-0/spatstat/man/lengths.psp.Rd | 12 spatstat-1.47-0/spatstat/man/lgcp.estK.Rd | 20 spatstat-1.47-0/spatstat/man/lgcp.estpcf.Rd | 13 spatstat-1.47-0/spatstat/man/linearKinhom.Rd | 51 +- spatstat-1.47-0/spatstat/man/linearpcfinhom.Rd | 7 spatstat-1.47-0/spatstat/man/linequad.Rd |only spatstat-1.47-0/spatstat/man/linfun.Rd | 3 spatstat-1.47-0/spatstat/man/linim.Rd | 4 spatstat-1.47-0/spatstat/man/lintess.Rd | 2 spatstat-1.47-0/spatstat/man/lppm.Rd | 13 spatstat-1.47-0/spatstat/man/mean.im.Rd | 1 spatstat-1.47-0/spatstat/man/mean.linim.Rd |only spatstat-1.47-0/spatstat/man/methods.linfun.Rd | 13 spatstat-1.47-0/spatstat/man/nnfun.lpp.Rd | 8 spatstat-1.47-0/spatstat/man/plot.im.Rd | 35 + spatstat-1.47-0/spatstat/man/plot.pp3.Rd | 26 - spatstat-1.47-0/spatstat/man/plot.ppp.Rd | 11 spatstat-1.47-0/spatstat/man/ppm.Rd | 5 spatstat-1.47-0/spatstat/man/ppm.ppp.Rd | 53 ++ spatstat-1.47-0/spatstat/man/rLGCP.Rd | 34 - spatstat-1.47-0/spatstat/man/rSSI.Rd | 23 spatstat-1.47-0/spatstat/man/rcellnumber.Rd | 25 spatstat-1.47-0/spatstat/man/rescale.Rd | 18 spatstat-1.47-0/spatstat/man/rex.Rd |only spatstat-1.47-0/spatstat/man/rhohat.Rd | 15 spatstat-1.47-0/spatstat/man/rmh.default.Rd | 25 spatstat-1.47-0/spatstat/man/rmh.ppm.Rd | 20 spatstat-1.47-0/spatstat/man/simulate.kppm.Rd | 7 spatstat-1.47-0/spatstat/man/spatstat-deprecated.Rd | 11 spatstat-1.47-0/spatstat/man/spatstat-internal.Rd | 64 ++ spatstat-1.47-0/spatstat/man/spatstat-package.Rd | 8 spatstat-1.47-0/spatstat/man/summary.im.Rd | 6 spatstat-1.47-0/spatstat/man/summary.kppm.Rd | 20 spatstat-1.47-0/spatstat/man/sumouter.Rd | 20 spatstat-1.47-0/spatstat/man/symbolmap.Rd | 15 spatstat-1.47-0/spatstat/man/weighted.median.Rd |only spatstat-1.47-0/spatstat/src/linalg.c | 79 +++ spatstat-1.47-0/spatstat/src/lineardisc.c | 26 - spatstat-1.47-0/spatstat/src/linearradius.c |only spatstat-1.47-0/spatstat/src/linequad.c | 510 -------------------- spatstat-1.47-0/spatstat/src/linequad.h |only spatstat-1.47-0/spatstat/src/ply.c |only spatstat-1.47-0/spatstat/src/ply.h |only spatstat-1.47-0/spatstat/tests/testsAtoF.R |only spatstat-1.47-0/spatstat/tests/testsGtoK.R |only spatstat-1.47-0/spatstat/tests/testsLtoM.R |only spatstat-1.47-0/spatstat/tests/testsNtoP.R |only spatstat-1.47-0/spatstat/tests/testsQtoR.R |only spatstat-1.47-0/spatstat/tests/testsStoZ.R |only spatstat-1.47-0/spatstat/vignettes/datasets.Rnw | 1 spatstat-1.47-0/spatstat/vignettes/packagesizes.txt | 1 spatstat-1.47-0/spatstat/vignettes/updates.Rnw | 245 ++++++++- 184 files changed, 3300 insertions(+), 1787 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification arose from verifying high-resolution forecasts, where coarser-resolution models generally are favored even when a human forecaster finds the higher-resolution model to be considerably better. Most newly proposed methods, which largely come from image analysis, computer vision, and similar, are available, with more on the way.
Author: Eric Gilleland <EricG@ucar.edu>
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.4 dated 2016-02-22 and 0.5 dated 2016-10-12
DESCRIPTION | 9 MD5 | 35 +- R/FeatureFinder.R | 64 ++--- R/Features.R | 619 ++++++++++++++++++++++++++------------------------- R/Fint2d.R | 135 +++++++---- R/LocMeasures.R | 184 ++++++++++----- R/MergeForce.R | 1 R/craer.R | 40 ++- R/deltamm.R | 118 +++++---- R/minboundmatch.R | 24 - R/plot.matched.R |only R/rigider.R | 43 ++- man/craer.Rd | 3 man/deltamm.Rd | 19 + man/locmeasures2d.Rd | 22 - man/locperf.Rd | 14 - man/minboundmatch.Rd | 28 ++ man/rigider.Rd | 13 - man/saller.Rd | 2 19 files changed, 795 insertions(+), 578 deletions(-)
Title: Software for Project AERO
Description: Implements methods for anticipating the emergence and eradication
of infectious diseases from surveillance time series. Also provides support
for computational experiments testing the performance of such methods.
Author: Eamon O'Dea [aut, cre]
Maintainer: Eamon O'Dea <odea35@gmail.com>
Diff between spaero versions 0.1.1 dated 2016-05-22 and 0.2.0 dated 2016-10-12
DESCRIPTION | 11 - MD5 | 26 ++-- NEWS.md | 30 ++++- R/analysis.R | 163 +++++++++++++++------------- R/simulation.R | 103 ++++++++++------- build/vignette.rds |binary inst/doc/spaero-introduction.Rmd | 11 + inst/doc/spaero-introduction.pdf |binary man/create_simulator.Rd | 21 ++- man/get_stats.Rd | 38 +++--- src/transition_rates.c | 33 +++++ tests/testthat/test-simulator.R | 136 +++++++++++------------ tests/testthat/test-stats.R | 221 +++++++++++++++++++------------------- vignettes/spaero-introduction.Rmd | 9 + 14 files changed, 455 insertions(+), 347 deletions(-)
Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.
Author: Jerome Sueur <sueur@mnhn.fr> [cre, au], Thierry Aubin [au],
Caroline Simonis [au], Laurent Lellouch [main ctrb],
Ethan C. Brown [ctrb], Marion Depraetere [ctrb],
Camille Desjonqueres [ctrb], Francois Fabianek [ctrb],
Amandine Gasc [ctrb], Stefanie LaZerte [ctrb], Jonathan Lees [ctrb],
Jean Marchal [ctrb], Sandrine Pavoine [ctrb], Alicia Stotz [ctrb],
Luis J. Villanueva-Rivera [ctrb], Zev Ross [ctrb],
Carl G. Witthoft [ctrb], Hristo Zhivomirov [ctrb].
Maintainer: Jerome Sueur <sueur@mnhn.fr>
Diff between seewave versions 2.0.4 dated 2016-07-11 and 2.0.5 dated 2016-10-12
DESCRIPTION | 8 - MD5 | 32 +++--- NEWS | 17 +++ R/seewave.r | 198 +++++++++++++++++++++--------------------- inst/doc/seewave_IO.pdf |binary inst/doc/seewave_analysis.pdf |binary man/ACI.Rd | 2 man/AR.Rd | 2 man/NDSI.Rd | 16 +-- man/bwfilter.Rd | 2 man/dBscale.Rd | 2 man/ffilter.Rd | 2 man/fma.Rd | 6 - man/fund.Rd | 2 man/seewave.package.Rd | 4 man/smoothw.Rd | 2 man/zc.Rd | 2 17 files changed, 159 insertions(+), 138 deletions(-)
Title: Integrated Taxonomic Information System Client
Description: An interface to the Integrated Taxonomic Information System ('ITIS')
(<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST
'API' methods (<https://www.itis.gov/ws_description.html>), as well as the
'Solr' web service (<https://www.itis.gov/solr_documentation.html>).
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between ritis versions 0.5.0 dated 2016-06-22 and 0.5.4 dated 2016-10-12
DESCRIPTION | 15 +++++------ MD5 | 24 +++++++++--------- NEWS.md | 9 ++++++ R/search_common.R | 2 - R/zzz.R | 4 +-- README.md | 52 ++++++++++++++++++--------------------- inst/doc/ritis_vignette.Rmd | 51 ++++++++++++++++++-------------------- inst/doc/ritis_vignette.html | 49 +++++++++++++++++------------------- inst/vign/ritis_vignette.Rmd | 4 +-- inst/vign/ritis_vignette.md | 51 ++++++++++++++++++-------------------- man/search_common.Rd | 2 - tests/testthat/test-itis_facet.R | 2 - vignettes/ritis_vignette.Rmd | 51 ++++++++++++++++++-------------------- 13 files changed, 155 insertions(+), 161 deletions(-)
Title: R Commander Plug-in for University Level Applied Statistics
Description: An R Commander "plug-in" extending functionality of linear models
and providing an interface to Partial Least Squares Regression and Linear and
Quadratic Discriminant analysis. Several statistical summaries are extended,
predictions are offered for additional types of analyses, and extra plots, tests
and mixed models are available.
Author: Kristian Hovde Liland [aut, cre],
Solve Sb [aut]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between RcmdrPlugin.NMBU versions 1.8.6 dated 2016-08-27 and 1.8.7 dated 2016-10-12
DESCRIPTION | 17 +++++++++---- MD5 | 14 +++++------ NAMESPACE | 3 +- R/NMBU.GUI.Data.R | 56 +++++++++++++++++++++++----------------------- R/NMBU.GUI.Models.R | 37 +++++++++++++++++++++++------- R/NMBU.RcmdrPlugin.NMBU.R | 3 ++ R/NMBU.Utilities.R | 7 +++++ inst/etc/menus.txt | 5 ---- 8 files changed, 87 insertions(+), 55 deletions(-)
More information about RcmdrPlugin.NMBU at CRAN
Permanent link
Title: Ridge Estimation of Vector Auto-Regressive (VAR) Processes
Description: Ridge maximum likelihood estimation of vector auto-regressive processes and supporting functions for their exploitation.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between ragt2ridges versions 0.2.2 dated 2016-09-24 and 0.2.3 dated 2016-10-12
DESCRIPTION | 10 MD5 | 25 + R/RcppExports.R | 56 ++- R/momentS.r |only R/ridgeVAR1.r | 12 inst/NEWS.Rd | 9 inst/include |only man/momentS.Rd |only man/ragt2ridges-package.Rd | 2 man/ridgeVAR1.Rd | 2 man/sparsifyVAR1.Rd | 2 src/RcppExports.cpp | 665 ++++++++++++++++++++++++++++++++++----------- src/defaultTarget.h |only src/rags2ridges.h |only src/ragt2ridges.cpp | 437 ----------------------------- src/ridgePchordal.h |only 16 files changed, 586 insertions(+), 634 deletions(-)
Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least
Squares. The methods include filter methods, wrapper methods and embedded
methods. Both regression and classification is supported.
Author: Kristian Hovde Liland, Tahir Mehmood, Solve Sæbø
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between plsVarSel versions 0.9 dated 2016-07-27 and 0.9.1 dated 2016-10-12
DESCRIPTION | 8 ++-- MD5 | 12 +++---- R/lda_from_pls.R | 10 ++++- R/shaving.R | 84 ++++++++++++++++++++++++++++++++++++++----------- inst/CITATION | 2 - man/lda_from_pls_cv.Rd | 4 +- man/shaving.Rd | 12 +++++-- 7 files changed, 98 insertions(+), 34 deletions(-)
Title: Programming with Big Data -- Base Wrappers for Distributed
Matrices
Description: An interface to and extensions for the 'PBLAS' and
'ScaLAPACK' numerical libraries. This enables R to utilize
distributed linear algebra for codes written in the 'SPMD' fashion.
This interface is deliberately low-level and mimics the style of
the native libraries it wraps. For a much higher level way of
managing distributed matrices, see the 'pbdDMAT' package.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Ewan Higgs [ctb]
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdBASE versions 0.4-3 dated 2016-01-24 and 0.4-5 dated 2016-10-12
pbdBASE-0.4-3/pbdBASE/build |only pbdBASE-0.4-3/pbdBASE/man/base.rpdsyev.Rd |only pbdBASE-0.4-3/pbdBASE/src/base/linalg/auxil.f90 |only pbdBASE-0.4-3/pbdBASE/src/base/utils/scale.f90 |only pbdBASE-0.4-3/pbdBASE/src/utils/test.c |only pbdBASE-0.4-5/pbdBASE/ChangeLog | 14 ++ pbdBASE-0.4-5/pbdBASE/DESCRIPTION | 31 ++--- pbdBASE-0.4-5/pbdBASE/MD5 | 70 +++++------ pbdBASE-0.4-5/pbdBASE/NAMESPACE | 5 pbdBASE-0.4-5/pbdBASE/R/base_mpi_blacs.r | 5 pbdBASE-0.4-5/pbdBASE/R/base_scalapack.r | 31 ++--- pbdBASE-0.4-5/pbdBASE/R/get_conf.r | 2 pbdBASE-0.4-5/pbdBASE/R/pbdBASE-package.r | 3 pbdBASE-0.4-5/pbdBASE/R/redist.r |only pbdBASE-0.4-5/pbdBASE/README.md | 31 ++--- pbdBASE-0.4-5/pbdBASE/inst/CITATION | 28 ++-- pbdBASE-0.4-5/pbdBASE/inst/RNACI/RNACI.h | 127 +++++++++------------ pbdBASE-0.4-5/pbdBASE/inst/doc/pbdBASE-guide.Rnw | 2 pbdBASE-0.4-5/pbdBASE/inst/doc/pbdBASE-guide.pdf |binary pbdBASE-0.4-5/pbdBASE/man/base.redist.Rd |only pbdBASE-0.4-5/pbdBASE/man/base.rpdsyevr.Rd |only pbdBASE-0.4-5/pbdBASE/man/gridexit.Rd | 3 pbdBASE-0.4-5/pbdBASE/src/Makevars.in | 10 - pbdBASE-0.4-5/pbdBASE/src/Makevars.win | 6 pbdBASE-0.4-5/pbdBASE/src/base/expm/matexp.c | 13 -- pbdBASE-0.4-5/pbdBASE/src/base/linalg/linalg.h | 9 + pbdBASE-0.4-5/pbdBASE/src/base/linalg/norms.f90 |only pbdBASE-0.4-5/pbdBASE/src/base/stats/stats.h | 7 + pbdBASE-0.4-5/pbdBASE/src/base/utils/redist.c |only pbdBASE-0.4-5/pbdBASE/src/base/utils/scale.c |only pbdBASE-0.4-5/pbdBASE/src/base/utils/utils.h | 12 + pbdBASE-0.4-5/pbdBASE/src/base_lm.c | 1 pbdBASE-0.4-5/pbdBASE/src/base_p_matexp.c | 7 - pbdBASE-0.4-5/pbdBASE/src/base_putil.c | 7 - pbdBASE-0.4-5/pbdBASE/src/base_scalapack.c | 125 ++++++++++++-------- pbdBASE-0.4-5/pbdBASE/src/comm_utils.c | 19 +-- pbdBASE-0.4-5/pbdBASE/src/export_blacs/pkg_Bdef.h | 13 +- pbdBASE-0.4-5/pbdBASE/src/export_blacs/pkg_tools.c | 1 pbdBASE-0.4-5/pbdBASE/src/pbdBASE.h | 2 pbdBASE-0.4-5/pbdBASE/src/redist.c |only pbdBASE-0.4-5/pbdBASE/src/scalapack.h | 20 +++ pbdBASE-0.4-5/pbdBASE/vignettes/pbdBASE-guide.Rnw | 2 42 files changed, 344 insertions(+), 262 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it makes possible to create and manipulate multivariate
network data with different formats, and there are effective ways available to treat multiple
networks with routines that combine algebraic systems like the partially ordered semigroup or
the semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. It also provides an algebraic approach for two-mode networks
through Galois derivations between families of the pairs of subsets in the two domains.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 2.1 dated 2016-09-14 and 2.2 dated 2016-10-12
DESCRIPTION | 8 +- MD5 | 26 +++---- R/bnd.R | 9 +- R/jnt.R | 20 +++-- R/read.srt.R | 148 +++++++++++++++++++++--------------------- R/rel.sys.R | 36 +++++++--- R/zbind.R | 42 +++++++---- inst/CHANGELOG | 16 ++++ inst/doc/TwoModeNetworks.Rnw | 66 ++++++++---------- inst/doc/TwoModeNetworks.pdf |binary inst/doc/TwoModeNetworks.r | 43 +++++++----- man/multiplex-package.Rd | 4 - man/read.srt.Rd | 30 +++----- vignettes/TwoModeNetworks.Rnw | 66 ++++++++---------- 14 files changed, 278 insertions(+), 236 deletions(-)
Title: An Interactive Visualisation of Meta-Analysis as a Physical
Weighing Machine
Description: An interactive application to visualise meta-analysis data as a
physical weighing machine. The interface is based on the Shiny web application
framework, though can be run locally and with the user's own data.
Author: Jack Bowden <j.bowden@bristol.ac.uk> (conception), Christopher Jackson
<chris.jackson@mrc-bsu.cam.ac.uk> (programming)
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between MetaAnalyser versions 0.2 dated 2016-08-10 and 0.2.1 dated 2016-10-12
DESCRIPTION | 16 ++++++++++------ MD5 | 13 +++++++------ NAMESPACE | 2 +- inst/CITATION | 2 +- inst/NEWS |only man/MetaAnalyser.Rd | 3 ++- man/metasumm.Rd | 2 +- man/resd_dsl.Rd | 3 ++- 8 files changed, 24 insertions(+), 17 deletions(-)
Title: Tools for Two-Dimensional Monte-Carlo Simulations
Description: A complete framework to build and study Two-Dimensional Monte-Carlo simulations, aka Second-Order Monte-Carlo simulations. Also includes various distributions (pert, triangular, Bernoulli, empirical discrete and continuous).
Author: Regis Pouillot [aut, cre],
Marie-Laure Delignette-Muller [ctb],
Jean-Baptiste Denis [ctb]
Maintainer: Regis Pouillot <rpouillot@yahoo.fr>
Diff between mc2d versions 0.1-16 dated 2016-02-15 and 0.1-17 dated 2016-10-12
DESCRIPTION | 12 ++--- MD5 | 18 ++++---- R/betagen.R | 39 +++++++++---------- R/pert.R | 92 ++++++++++++++++++++++++--------------------- R/triang.R | 74 ++++++++++++++++++++++-------------- build/vignette.rds |binary data/ec.rda |binary inst/NEWS | 7 +++ inst/doc/docmcEnglish.pdf |binary inst/doc/mc2dLmEnglish.pdf |binary 10 files changed, 137 insertions(+), 105 deletions(-)
Title: Matrix Correlation Coefficients
Description: Computation and visualization of matrix correlation coefficients.
The main method is the Similarity of Matrices Index, while various related
measures like r1, r2, r3, r4, Yanai's GCD, RV, RV2 and adjusted RV are included
for comparison.
Author: Kristian Hovde Liland [aut, cre],
Tormod Ns [ctb],
Ulf Geir Indahl [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nofima.no>
Diff between MatrixCorrelation versions 0.8.1 dated 2016-04-25 and 0.9 dated 2016-10-12
DESCRIPTION | 12 ++++++------ MD5 | 19 +++++++++++-------- NAMESPACE | 2 ++ R/PMI.R |only R/RV.R | 17 +++++++++-------- R/RcppExports.R | 6 +++++- R/allCorrelations.R | 5 +++-- man/PSI.Rd |only man/RV.Rd | 2 +- man/allCorrelations.Rd | 4 ++-- src/RV2cpp.cpp |only src/RcppExports.cpp | 30 +++++++++++++++++++++--------- 12 files changed, 60 insertions(+), 37 deletions(-)
More information about MatrixCorrelation at CRAN
Permanent link
Title: Knowledge Discovery by Accuracy Maximization
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction from noisy and high-dimensional data.
Author: Stefano Cacciatore, Leonardo Tenori, Claudio Luchinat, Phillip R. Bennett, and David A. MacIntyre
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Diff between KODAMA versions 0.0.1 dated 2014-11-25 and 1.0 dated 2016-10-12
KODAMA-0.0.1/KODAMA/R/KODAMA.R |only KODAMA-0.0.1/KODAMA/R/simulated.R |only KODAMA-0.0.1/KODAMA/man/KNN.CV.Rd |only KODAMA-0.0.1/KODAMA/man/PCA.CA.KNN.CV.Rd |only KODAMA-0.0.1/KODAMA/man/PLS.SVM.CV.Rd |only KODAMA-0.0.1/KODAMA/man/classprob.Rd |only KODAMA-0.0.1/KODAMA/man/core.Rd |only KODAMA-0.0.1/KODAMA/man/kfold.Rd |only KODAMA-0.0.1/KODAMA/man/knn.dist.Rd |only KODAMA-0.0.1/KODAMA/man/knn.predict.Rd |only KODAMA-0.0.1/KODAMA/man/knn.probability.Rd |only KODAMA-0.0.1/KODAMA/man/majority.Rd |only KODAMA-1.0/KODAMA/DESCRIPTION | 21 +- KODAMA-1.0/KODAMA/MD5 | 102 ++++++++--- KODAMA-1.0/KODAMA/NAMESPACE | 28 ++- KODAMA-1.0/KODAMA/R/KOD.R |only KODAMA-1.0/KODAMA/R/RcppExports.R |only KODAMA-1.0/KODAMA/R/datasets.R |only KODAMA-1.0/KODAMA/R/preprocessing.R | 260 +++++++++++++++-------------- KODAMA-1.0/KODAMA/build |only KODAMA-1.0/KODAMA/data/lymphoma.RData |binary KODAMA-1.0/KODAMA/inst |only KODAMA-1.0/KODAMA/man/KODAMA.Rd | 222 ++++++++++++------------ KODAMA-1.0/KODAMA/man/MetRef.Rd | 90 +++++----- KODAMA-1.0/KODAMA/man/USA.Rd | 94 +++++----- KODAMA-1.0/KODAMA/man/core_cpp.Rd |only KODAMA-1.0/KODAMA/man/dinisurface.Rd | 81 ++++----- KODAMA-1.0/KODAMA/man/floyd.Rd |only KODAMA-1.0/KODAMA/man/helicoid.Rd | 81 ++++----- KODAMA-1.0/KODAMA/man/k.test.Rd |only KODAMA-1.0/KODAMA/man/knn.double.cv.Rd |only KODAMA-1.0/KODAMA/man/knn.kodama.Rd |only KODAMA-1.0/KODAMA/man/loads.Rd |only KODAMA-1.0/KODAMA/man/lymphoma.Rd | 103 ++++++----- KODAMA-1.0/KODAMA/man/mcplot.Rd |only KODAMA-1.0/KODAMA/man/normalization.Rd | 123 +++++++------ KODAMA-1.0/KODAMA/man/pls.double.cv.Rd |only KODAMA-1.0/KODAMA/man/pls.kodama.Rd |only KODAMA-1.0/KODAMA/man/scaling.Rd | 114 +++++++----- KODAMA-1.0/KODAMA/man/spirals.Rd | 100 +++++------ KODAMA-1.0/KODAMA/man/swissroll.Rd | 106 ++++++----- KODAMA-1.0/KODAMA/man/transformy.Rd | 83 +++++---- KODAMA-1.0/KODAMA/src |only KODAMA-1.0/KODAMA/vignettes |only 44 files changed, 891 insertions(+), 717 deletions(-)
Title: A Very Basic Templating Engine
Description: Replace parameters in strings and/or text files with specified
values.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between infuser versions 0.2.4 dated 2016-08-30 and 0.2.5 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/helpers.R | 9 ++++----- build/vignette.rds |binary inst/doc/getting_started.Rmd | 2 +- inst/doc/getting_started.html | 6 +++--- vignettes/getting_started.Rmd | 2 +- 7 files changed, 19 insertions(+), 20 deletions(-)
Title: Collection of Tools for Genomic Data Analysis
Description: A loose collection of tools for the analysis of expression and genotype data, currently with the main focus on (e)QTL and MDR analysis.
Author: Daniel Fischer
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between GenomicTools versions 0.2.1 dated 2016-10-07 and 0.2.2 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/importGFF3.R | 15 +++++++++++++-- build/vignette.rds |binary data/annotTrack.rda |binary data/geneEXP.rda |binary data/genotData.rda |binary data/mdrExample.rda |binary data/phenoData.rda |binary inst/doc/GenomicTools-Vignette.pdf |binary man/GenomicTools-package.Rd | 4 ++-- 12 files changed, 31 insertions(+), 20 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 7.2 dated 2016-09-09 and 7.3 dated 2016-10-12
ChangeLog | 5 DESCRIPTION | 6 MD5 | 40 +- NAMESPACE | 3 R/arfima.R | 62 +-- R/etsforecast.R | 1 R/fitBATS.R | 808 ++++++++++++++++++++---------------------- R/fitTBATS.R | 800 ++++++++++++++++++++--------------------- R/forecastBATS.R | 30 - R/forecastTBATS.R | 36 - R/getResponse.R | 50 +- R/ggplot.R | 10 R/naive.R | 3 R/nnetar.R | 51 ++ R/simulate.R | 191 +++++++-- README.md | 1 man/forecast.nnetar.Rd |only man/nnetar.Rd | 16 man/simulate.Rd | 12 tests/testthat/Rplots.pdf |only tests/testthat/test-bats.R | 2 tests/testthat/test-hfitted.R | 25 - 22 files changed, 1148 insertions(+), 1004 deletions(-)
Title: Ecological Niche in R and GRASS
Description: A set of tools for the analysis of ecological niche of species and calculation of habitat suitability maps.
Author: Fernando Canovas, Chiara Magliozzi, Jose Antonio Palazon-Ferrando, Frederico Mestre, Mercedes Gonzalez-Wanguemert
Maintainer: Fernando Garcia Canovas <fcgarcia@ualg.pt>
Diff between ENiRG versions 1.0 dated 2016-05-05 and 1.0.1 dated 2016-10-12
ChangeLog | 16 +++++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/enirg.R | 2 +- inst/CITATION | 11 +++++------ man/ENiRG-package.Rd | 8 ++++---- man/apis.enirg.Rd | 4 ++-- man/enirg.Rd | 6 +++++- 8 files changed, 43 insertions(+), 26 deletions(-)
Title: Functions and Data for the Second Edition of "Data Mining with
R"
Description: Functions and data accompanying the second edition of the book "Data Mining with R, learning with case studies" by Luis Torgo, published by CRC Press.
Author: Luis Torgo [aut, cre]
Maintainer: Luis Torgo <ltorgo@dcc.fc.up.pt>
Diff between DMwR2 versions 0.0.1 dated 2016-09-09 and 0.0.2 dated 2016-10-12
CHANGES | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/CITATION | 2 +- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Design and Analysis of Experiments with R
Description: Contains Data frames and functions used in the book "Design and Analysis of Experiments with R".
Author: John Lawson
Maintainer: John Lawson <lawson@byu.edu>
Diff between daewr versions 1.1-6 dated 2015-07-22 and 1.1-7 dated 2016-10-12
DESCRIPTION | 13 +++-- MD5 | 128 ++++++++++++++++++++++++++-------------------------- R/colormap.R | 45 +++++++++--------- data/Apo.rda |binary data/BPmonitor.rda |binary data/Bdish.rda |binary data/Bff.rda |binary data/BoxM.rda |binary data/COdata.rda |binary data/MPV.rda |binary data/Naph.rda |binary data/SPMPV.rda |binary data/Smotor.rda |binary data/Tet.rda |binary data/Treb.rda |binary data/antifungal.rda |binary data/apple.rda |binary data/arso.rda |binary data/augm.rda |binary data/bha.rda |binary data/bioequiv.rda |binary data/bioeqv.rda |binary data/blood.rda |binary data/bread.rda |binary data/cake.rda |binary data/cement.rda |binary data/chem.rda |binary data/chipman.rda |binary data/cont.rda |binary data/cpipe.rda |binary data/culture.rda |binary data/dairy.rda |binary data/drug.rda |binary data/eptaxr.rda |binary data/eptaxs2.rda |binary data/eptaxyb.rda |binary data/gagerr.rda |binary data/gear.rda |binary data/hardwood.rda |binary data/inject.rda |binary data/pastry.rda |binary data/pest.rda |binary data/pesticide.rda |binary data/plasma.rda |binary data/polvdat.rda |binary data/polymer.rda |binary data/prodstd.rda |binary data/qsar.rda |binary data/rcb.rda |binary data/residue.rda |binary data/rubber.rda |binary data/sausage.rda |binary data/soup.rda |binary data/soupmx.rda |binary data/splitPdes.rda |binary data/strung.rda |binary data/strungtile.rda |binary data/sugarbeet.rda |binary data/taste.rda |binary data/teach.rda |binary data/tile.rda |binary data/virus.rda |binary data/volt.rda |binary data/web.rda |binary man/colormap.Rd | 8 +-- 65 files changed, 99 insertions(+), 95 deletions(-)
Title: Tools for CM SAF Netcdf Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing Essential Climate Variables related to the energy and water
cycle of the atmosphere (www.cmsaf.eu). It is a joint cooperation of seven
National Meteorological and Hydrological Services, including the Deutscher
Wetterdienst (DWD).
The cmsaf R-package provides a small collection of R-functions, which are
inspired by the Climate Data Operators (cdo). This gives the opportunity to
analyse and manipulate CM SAF data without the need of installing cdo.
The cmsaf R-package is tested for CM SAF netcdf data, which are structured
in three-dimensional arrays (longitude, latitude, time) on a rectangular grid.
Layered CM SAF data have to be converted with the provided `levbox_mergetime`
function. The cmsaf R-package functions have only minor checks for deviations
from the recommended data structure, and give only few specific error messages.
Thus, there is no warranty of accurate results.
Scripts for an easy application of the functions are provided at the CM SAF homepage
(http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.6.1 dated 2016-01-28 and 1.7.0 dated 2016-10-12
DESCRIPTION | 12 ++--- MD5 | 116 ++++++++++++++++++++++++++++++--------------------- NAMESPACE | 14 +++++- R/box_mergetime.R | 8 +++ R/cmsaf.add.R | 2 R/cmsaf.addc.R | 2 R/cmsaf.div.R | 2 R/cmsaf.divc.R | 2 R/cmsaf.mul.R | 2 R/cmsaf.mulc.R | 2 R/cmsaf.sub.R | 2 R/cmsaf.subc.R | 2 R/dayrange.R | 2 R/divdpm.R | 2 R/extract.period.R | 8 +++ R/fldmax.R | 11 +++- R/fldmean.R | 6 +- R/fldmin.R | 8 +++ R/levbox_mergetime.R | 14 ++++-- R/mon.anomaly.R | 29 ++++++++++-- R/monmax.R |only R/monmean.R | 2 R/monmin.R |only R/monsd.R |only R/monsum.R | 54 +++++++++++------------ R/muldpm.R | 2 R/multimonmean.R | 4 - R/multimonsum.R | 4 - R/ncinfo.R | 5 +- R/remapbil.R | 24 ++++++---- R/seas.anomaly.R | 25 ++++++++++ R/seasmean.R | 4 - R/sellonlatbox.R | 8 +++ R/selmon.R | 8 +++ R/selperiod.R | 8 +++ R/selpoint.R | 14 ++++-- R/seltime.R | 8 +++ R/selyear.R | 8 +++ R/timmax.R |only R/timmean.R | 2 R/timmin.R |only R/timsd.R |only R/trend.R | 2 R/wfldmean.R | 2 R/year.anomaly.R | 25 ++++++++++ R/yearmean.R | 2 R/yearsum.R | 2 R/ymonmax.R |only R/ymonmean.R | 4 - R/ymonmin.R |only R/ymonsd.R |only R/ymonsum.R | 2 R/yseasmax.R |only R/yseasmean.R | 4 - R/yseasmin.R |only R/yseassd.R |only man/cmsaf-package.Rd | 4 - man/monmax.Rd |only man/monmin.Rd |only man/monsd.Rd |only man/ncinfo.Rd | 3 - man/selperiod.Rd | 2 man/timmax.Rd |only man/timmin.Rd |only man/timsd.Rd |only man/ymonmax.Rd |only man/ymonmin.Rd |only man/ymonsd.Rd |only man/yseasmax.Rd |only man/yseasmin.Rd |only man/yseassd.Rd |only 71 files changed, 323 insertions(+), 155 deletions(-)
Title: Exact Binary Sequential Designs and Analysis
Description: For a series of binary responses, create stopping boundary with exact results after stopping, allowing updating for missing assessments.
Author: Jenn Kirk, Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between binseqtest versions 1.0.1 dated 2015-07-02 and 1.0.2 dated 2016-10-12
CHANGELOG | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary inst/CITATION | 2 +- inst/doc/ExactBinarySequentialDesigns.pdf |binary man/binseqtest-package.Rd | 2 +- 7 files changed, 16 insertions(+), 12 deletions(-)
Title: Multi-Parameter Regression (MPR)
Description: Package for fitting Multi-Parameter Regression (MPR) models to right-censored survival data. These are flexible parametric regression models which extend standard models, for example, proportional hazards.
Author: Kevin Burke
Maintainer: Kevin Burke <kevin.burke@ul.ie>
Diff between mpr versions 1.0.3 dated 2016-09-21 and 1.0.4 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/mpr-internal.R | 4 ++++ R/mpr.R | 16 ++++++++-------- R/stepmpr.R | 4 ++-- R/update.mpr.R | 2 +- 6 files changed, 24 insertions(+), 20 deletions(-)
Title: a Bunch of Structure and Sequence Analysis
Description: Reads and plots placements obtained using pplacer/guppy (see http://matsen.fhcrc.org/pplacer/ for details). Read PDB file (protein 3D structure file).
Author: pierre lefeuvre
Maintainer: pierre lefeuvre <pierre.lefeuvre@cirad.fr>
Diff between BoSSA versions 1.2 dated 2010-01-26 and 2.0 dated 2016-10-12
BoSSA-1.2/BoSSA/R/AccNumb.R |only BoSSA-1.2/BoSSA/R/FastaSorter.R |only BoSSA-1.2/BoSSA/R/InfoFasta.R |only BoSSA-1.2/BoSSA/R/InfoGB.R |only BoSSA-1.2/BoSSA/R/InfoGenBank.R |only BoSSA-1.2/BoSSA/R/InfoSeq.R |only BoSSA-1.2/BoSSA/R/TaxoGB.r |only BoSSA-1.2/BoSSA/R/blast.R |only BoSSA-1.2/BoSSA/R/distGPS.R |only BoSSA-1.2/BoSSA/R/getGB.R |only BoSSA-1.2/BoSSA/R/grpPhylogeo.R |only BoSSA-1.2/BoSSA/R/outBLAST.R |only BoSSA-1.2/BoSSA/R/read.PDB.R |only BoSSA-1.2/BoSSA/R/rename.R |only BoSSA-1.2/BoSSA/R/sortBLAST.R |only BoSSA-1.2/BoSSA/R/submitBLAST.R |only BoSSA-1.2/BoSSA/man/FastaSorter.Rd |only BoSSA-1.2/BoSSA/man/InfoGenBank.Rd |only BoSSA-1.2/BoSSA/man/TaxoGB.Rd |only BoSSA-1.2/BoSSA/man/blast.Rd |only BoSSA-1.2/BoSSA/man/distGPS.Rd |only BoSSA-1.2/BoSSA/man/grpPhylogeo.Rd |only BoSSA-1.2/BoSSA/man/read.PDB.Rd |only BoSSA-2.0/BoSSA/DESCRIPTION | 24 ++++++++++-------------- BoSSA-2.0/BoSSA/MD5 |only BoSSA-2.0/BoSSA/NAMESPACE | 25 ++++++++++++++----------- BoSSA-2.0/BoSSA/R/get_edge.R |only BoSSA-2.0/BoSSA/R/pplace_to_matrix.R |only BoSSA-2.0/BoSSA/R/pplace_to_table.R |only BoSSA-2.0/BoSSA/R/pplace_tree.R |only BoSSA-2.0/BoSSA/R/read_jplace.R |only BoSSA-2.0/BoSSA/R/read_pdb.R |only BoSSA-2.0/BoSSA/R/read_sqlite.R |only BoSSA-2.0/BoSSA/R/sub_pplace.R |only BoSSA-2.0/BoSSA/build |only BoSSA-2.0/BoSSA/data |only BoSSA-2.0/BoSSA/inst |only BoSSA-2.0/BoSSA/man/BoSSA-package.Rd |only BoSSA-2.0/BoSSA/man/pplace.Rd |only BoSSA-2.0/BoSSA/man/pplace_to_matrix.Rd |only BoSSA-2.0/BoSSA/man/pplace_to_table.Rd |only BoSSA-2.0/BoSSA/man/pplace_tree.Rd |only BoSSA-2.0/BoSSA/man/read_pdb.Rd |only BoSSA-2.0/BoSSA/man/read_sqlite.Rd |only BoSSA-2.0/BoSSA/man/sub_pplace.Rd |only 45 files changed, 24 insertions(+), 25 deletions(-)
Title: Sure Independence Screening
Description: Variable selection techniques are essential tools for model
selection and estimation in high-dimensional statistical models. Through this
publicly available package, we provide a unified environment to carry out
variable selection using iterative sure independence screening (SIS) and all
of its variants in generalized linear models and the Cox proportional hazards
model.
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao
Wu
Maintainer: Yang Feng <yang.feng@columbia.edu>
Diff between SIS versions 0.8-1 dated 2016-08-13 and 0.8-3 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/standardize.R | 3 ++- inst |only man/standardize.Rd | 3 ++- 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Themes for Shiny
Description: Themes for use with Shiny. Includes several Bootstrap themes
from <http://bootswatch.com/>, which are packaged for use with Shiny
applications.
Author: Winston Chang [aut, cre],
RStudio [cph],
Thomas Park [ctb, cph] (Bootswatch themes),
Lukasz Dziedzic [ctb, cph] (Lato font),
Nathan Willis [ctb, cph] (News Cycle font),
Google Corporation [ctb, cph] (Open Sans and Roboto fonts),
Matt McInerney [ctb, cph] (Raleway font),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font),
Canonical Ltd [ctb, cph] (Ubuntu font)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinythemes versions 1.1 dated 2016-09-19 and 1.1.1 dated 2016-10-12
DESCRIPTION | 12 ++-- MD5 | 13 ++--- NAMESPACE | 4 + NEWS.md | 5 + R/shinytheme.R | 132 +++++++++++++++++++++++++++++++++++++++++++++++---- README.md | 63 ++++++++++++++++-------- man/shinytheme.Rd | 2 man/themeSelector.Rd |only 8 files changed, 187 insertions(+), 44 deletions(-)
Title: IUCN Redlisting Tools
Description: Includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see <http://www.iucn.org> for more information) red list criteria.
Author: Pedro Cardoso
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between red versions 0.1.1 dated 2016-09-28 and 0.1.2 dated 2016-10-12
DESCRIPTION | 8 +-- MD5 | 8 +-- R/red.R | 146 ++++++++++++++++++++++++++++---------------------------- man/map.easy.Rd | 4 - man/map.sdm.Rd | 10 ++- 5 files changed, 90 insertions(+), 86 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; the Daymet gridded estimates of daily weather parameters
for North America, version 3, available from the Oak Ridge National Laboratory's
Distributed Active Archive Center (DAAC); and the International Tree Ring Data Bank.
Additional data sources are in the works, global soils (HWSD),
MODIS satellite data products, the National Atlas (US), Natural Earth, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.3.0 dated 2016-10-03 and 2.3.1 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/SSURGO_FUNCTIONS.R | 1 + inst/CITATION | 4 ++-- man/FedData-package.Rd | 4 ++-- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Group Sequential Design Class for Clinical Trials
Description: S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.
Author: David A Schoenfeld, PhD and Hui Zheng, PhD
Maintainer: "Hui Zheng, PhD" <hzheng1@mgh.harvard.edu>
Diff between seqmon versions 0.2 dated 2007-10-22 and 2.1 dated 2016-10-12
seqmon-0.2/seqmon/INDEX |only seqmon-0.2/seqmon/R/seqmon.R |only seqmon-0.2/seqmon/gen.R |only seqmon-0.2/seqmon/seqmon.R |only seqmon-2.1/seqmon/DESCRIPTION | 27 ++-- seqmon-2.1/seqmon/LICENSE |only seqmon-2.1/seqmon/MD5 |only seqmon-2.1/seqmon/NAMESPACE |only seqmon-2.1/seqmon/R/sequential_design_class.R |only seqmon-2.1/seqmon/man/alphaspend.Rd |only seqmon-2.1/seqmon/man/alphaspendf.Rd |only seqmon-2.1/seqmon/man/betaspend.Rd |only seqmon-2.1/seqmon/man/betaspendf.Rd |only seqmon-2.1/seqmon/man/calcBoundaries-methods.Rd |only seqmon-2.1/seqmon/man/calcBoundaries.Rd |only seqmon-2.1/seqmon/man/curtail.Rd |only seqmon-2.1/seqmon/man/curtailDesign-methods.Rd |only seqmon-2.1/seqmon/man/curtailDesign.Rd |only seqmon-2.1/seqmon/man/getProbabilities-methods.Rd |only seqmon-2.1/seqmon/man/getProbabilities.Rd |only seqmon-2.1/seqmon/man/plotBoundaries-methods.Rd |only seqmon-2.1/seqmon/man/plotBoundaries.Rd |only seqmon-2.1/seqmon/man/printSummary-methods.Rd |only seqmon-2.1/seqmon/man/printSummary.Rd |only seqmon-2.1/seqmon/man/seqmon-package.Rd |only seqmon-2.1/seqmon/man/seqmon.Rd | 100 +++++++----------- seqmon-2.1/seqmon/man/sequential.design-class.Rd |only seqmon-2.1/seqmon/man/sequential.design.Rd |only seqmon-2.1/seqmon/man/setAlphaspendfString-methods.Rd |only seqmon-2.1/seqmon/man/setAlphaspendfString.Rd |only seqmon-2.1/seqmon/man/setBaseAlphaspendf-methods.Rd |only seqmon-2.1/seqmon/man/setBaseAlphaspendf.Rd |only seqmon-2.1/seqmon/man/setBaseBetaspendf-methods.Rd |only seqmon-2.1/seqmon/man/setBaseBetaspendf.Rd |only seqmon-2.1/seqmon/man/setBetaspendfString-methods.Rd |only seqmon-2.1/seqmon/man/setBetaspendfString.Rd |only seqmon-2.1/seqmon/man/setCurrentLook-methods.Rd |only seqmon-2.1/seqmon/man/setCurrentLook.Rd |only seqmon-2.1/seqmon/man/setDatestamp-methods.Rd |only seqmon-2.1/seqmon/man/setDatestamp.Rd |only seqmon-2.1/seqmon/man/setNoncentrality-methods.Rd |only seqmon-2.1/seqmon/man/setNoncentrality.Rd |only seqmon-2.1/seqmon/man/setTimes-methods.Rd |only seqmon-2.1/seqmon/man/setTimes.Rd |only seqmon-2.1/seqmon/man/updateDesign-methods.Rd |only seqmon-2.1/seqmon/man/updateDesign.Rd |only 46 files changed, 55 insertions(+), 72 deletions(-)
Title: R Interface for Bokeh
Description: A native R plotting library that provides a flexible declarative interface for creating interactive web-based graphics, backed by the Bokeh visualization library <http://bokeh.pydata.org/>.
Author: Ryan Hafen [aut, cre],
Kenton Russell [ctb],
Jonathan Owen [ctb],
Barret Schloerke [ctb],
Saptasrhi Guha [ctb],
Continuum Analytics, Inc. [aut, cph] (Bokeh library in htmlwidgets/lib,
http://bokeh.pydata.org)
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between rbokeh versions 0.4.2 dated 2016-03-08 and 0.5.0 dated 2016-10-11
rbokeh-0.4.2/rbokeh/data/flightFreq.rda |only rbokeh-0.5.0/rbokeh/DESCRIPTION | 21 rbokeh-0.5.0/rbokeh/MD5 | 194 +- rbokeh-0.5.0/rbokeh/NAMESPACE | 6 rbokeh-0.5.0/rbokeh/NEWS.md | 69 + rbokeh-0.5.0/rbokeh/R/attr_mapping.R | 60 rbokeh-0.5.0/rbokeh/R/bokeh_render_json.R | 6 rbokeh-0.5.0/rbokeh/R/constants.R | 74 - rbokeh-0.5.0/rbokeh/R/fig_axis.R | 43 rbokeh-0.5.0/rbokeh/R/fig_callback.R | 8 rbokeh-0.5.0/rbokeh/R/fig_gmap.R | 34 rbokeh-0.5.0/rbokeh/R/fig_grid.R | 365 +++-- rbokeh-0.5.0/rbokeh/R/fig_hover.R | 40 rbokeh-0.5.0/rbokeh/R/fig_layer.R | 51 rbokeh-0.5.0/rbokeh/R/fig_legend.R | 2 rbokeh-0.5.0/rbokeh/R/fig_range.R | 22 rbokeh-0.5.0/rbokeh/R/fig_tap.R | 24 rbokeh-0.5.0/rbokeh/R/fig_title.R |only rbokeh-0.5.0/rbokeh/R/fig_tool.R | 37 rbokeh-0.5.0/rbokeh/R/figure.R | 130 - rbokeh-0.5.0/rbokeh/R/helpers.R | 379 +---- rbokeh-0.5.0/rbokeh/R/helpers_extra_pars.R | 52 rbokeh-0.5.0/rbokeh/R/json_helpers.R | 6 rbokeh-0.5.0/rbokeh/R/layer__utils.R | 94 - rbokeh-0.5.0/rbokeh/R/layer_bar.R | 97 + rbokeh-0.5.0/rbokeh/R/layer_glyphs.R | 64 rbokeh-0.5.0/rbokeh/R/layer_hexbin.R | 39 rbokeh-0.5.0/rbokeh/R/layer_image.R | 90 - rbokeh-0.5.0/rbokeh/R/layer_lines.R | 134 + rbokeh-0.5.0/rbokeh/R/layer_map.R | 3 rbokeh-0.5.0/rbokeh/R/layer_points.R | 25 rbokeh-0.5.0/rbokeh/R/layer_shapes.R | 67 rbokeh-0.5.0/rbokeh/R/layer_stats.R | 147 +- rbokeh-0.5.0/rbokeh/R/layer_text.R | 17 rbokeh-0.5.0/rbokeh/R/make_glyph.R | 110 - rbokeh-0.5.0/rbokeh/R/misc.R | 7 rbokeh-0.5.0/rbokeh/R/output_gist.R | 21 rbokeh-0.5.0/rbokeh/R/output_html.R | 60 rbokeh-0.5.0/rbokeh/R/output_json.R | 8 rbokeh-0.5.0/rbokeh/R/output_prerender.R | 11 rbokeh-0.5.0/rbokeh/R/output_save.R | 25 rbokeh-0.5.0/rbokeh/R/point_types.R | 10 rbokeh-0.5.0/rbokeh/R/prepare_figure.R | 236 ++- rbokeh-0.5.0/rbokeh/R/rbokeh-package.R | 11 rbokeh-0.5.0/rbokeh/R/shiny.R | 12 rbokeh-0.5.0/rbokeh/R/theme_axis.R | 57 rbokeh-0.5.0/rbokeh/R/theme_grid.R | 44 rbokeh-0.5.0/rbokeh/R/theme_legend.R | 21 rbokeh-0.5.0/rbokeh/R/theme_palettes.R | 152 ++ rbokeh-0.5.0/rbokeh/R/theme_plot.R | 41 rbokeh-0.5.0/rbokeh/R/theme_title.R |only rbokeh-0.5.0/rbokeh/R/themes.R | 36 rbokeh-0.5.0/rbokeh/README.md | 19 rbokeh-0.5.0/rbokeh/build |only rbokeh-0.5.0/rbokeh/data/flightfreq.rda |only rbokeh-0.5.0/rbokeh/inst/doc |only rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh-compiler.min.js | 36 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.css | 38 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js | 98 - rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh.min.css | 2 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh.min.js | 140 +- rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/loader.css |only rbokeh-0.5.0/rbokeh/inst/htmlwidgets/rbokeh.js | 73 - rbokeh-0.5.0/rbokeh/inst/htmlwidgets/rbokeh.yaml | 3 rbokeh-0.5.0/rbokeh/man/catjitter.Rd | 7 rbokeh-0.5.0/rbokeh/man/elements.Rd | 2 rbokeh-0.5.0/rbokeh/man/figure.Rd | 10 rbokeh-0.5.0/rbokeh/man/gmap.Rd | 19 rbokeh-0.5.0/rbokeh/man/gmap_style.Rd | 15 rbokeh-0.5.0/rbokeh/man/grid_plot.Rd | 45 rbokeh-0.5.0/rbokeh/man/ly_abline.Rd | 16 rbokeh-0.5.0/rbokeh/man/ly_annular_wedge.Rd | 25 rbokeh-0.5.0/rbokeh/man/ly_annulus.Rd | 23 rbokeh-0.5.0/rbokeh/man/ly_arc.Rd | 26 rbokeh-0.5.0/rbokeh/man/ly_bar.Rd | 39 rbokeh-0.5.0/rbokeh/man/ly_boxplot.Rd | 15 rbokeh-0.5.0/rbokeh/man/ly_crect.Rd | 2 rbokeh-0.5.0/rbokeh/man/ly_density.Rd | 6 rbokeh-0.5.0/rbokeh/man/ly_hist.Rd | 6 rbokeh-0.5.0/rbokeh/man/ly_image.Rd | 4 rbokeh-0.5.0/rbokeh/man/ly_image_url.Rd | 2 rbokeh-0.5.0/rbokeh/man/ly_quantile.Rd | 4 rbokeh-0.5.0/rbokeh/man/ly_text.Rd | 2 rbokeh-0.5.0/rbokeh/man/ly_wedge.Rd | 25 rbokeh-0.5.0/rbokeh/man/nyctaxihex.Rd | 11 rbokeh-0.5.0/rbokeh/man/palettes.Rd | 16 rbokeh-0.5.0/rbokeh/man/point_types.Rd | 3 rbokeh-0.5.0/rbokeh/man/print_model_json.Rd | 2 rbokeh-0.5.0/rbokeh/man/set_palette.Rd |only rbokeh-0.5.0/rbokeh/man/set_theme.Rd | 31 rbokeh-0.5.0/rbokeh/man/sub_names.Rd | 2 rbokeh-0.5.0/rbokeh/man/theme_axis.Rd | 10 rbokeh-0.5.0/rbokeh/man/theme_grid.Rd | 10 rbokeh-0.5.0/rbokeh/man/theme_legend.Rd | 25 rbokeh-0.5.0/rbokeh/man/theme_plot.Rd | 43 rbokeh-0.5.0/rbokeh/man/theme_title.Rd |only rbokeh-0.5.0/rbokeh/man/x_axis.Rd | 12 rbokeh-0.5.0/rbokeh/man/y_axis.Rd | 12 rbokeh-0.5.0/rbokeh/tests/testthat/test-css-svg.R | 7 rbokeh-0.5.0/rbokeh/tests/testthat/test-figures.R | 672 ++++++++-- rbokeh-0.5.0/rbokeh/vignettes |only 101 files changed, 2970 insertions(+), 1850 deletions(-)
More information about PRISMAstatement at CRAN
Permanent link
Title: Tools to Convert ODM Files
Description: Transformation of 'ODM' (see <http://www.cdisc.org/odm>) files into R format, Microsoft Office format, 'CDA' format and vice versa. 'ODM' format is commonly used in clinical trials. Semantic annotation (such as 'UMLS', 'SNOMED' or 'LOINC' codes) are transformed accordingly.
Author: Martin Dugas
Maintainer: Martin Dugas <dugas@uni-muenster.de>
Diff between ODMconverter versions 2.1 dated 2015-04-02 and 2.2 dated 2016-10-11
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + R/ODM2R.R | 38 +++++++++++++++++++++++--------------- man/ODM2R.Rd | 8 +++++++- 5 files changed, 40 insertions(+), 25 deletions(-)
Title: Calculate the NLTT Statistic
Description: Provides functions to calculate the normalised Lineage-Through-
Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures
the difference between two Lineage-Through-Time curves, where each curve is
normalised both in time and in number of lineages.
Author: Thijs Janzen [aut, cre],
Richel Bilderbeek [aut]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between nLTT versions 1.3 dated 2016-10-05 and 1.3.1 dated 2016-10-11
nLTT-1.3.1/nLTT/DESCRIPTION | 6 nLTT-1.3.1/nLTT/MD5 | 44 +- nLTT-1.3.1/nLTT/NAMESPACE | 2 nLTT-1.3.1/nLTT/R/get_average_nltt_matrix.R | 27 - nLTT-1.3.1/nLTT/README.md |only nLTT-1.3.1/nLTT/build/vignette.rds |binary nLTT-1.3.1/nLTT/inst/doc/trees_with_root_edge.R | 4 nLTT-1.3.1/nLTT/inst/doc/trees_with_root_edge.Rmd | 4 nLTT-1.3.1/nLTT/inst/doc/trees_with_root_edge.html | 18 - nLTT-1.3.1/nLTT/inst/doc/vignette_get_nltt_values.R | 112 +++---- nLTT-1.3.1/nLTT/inst/doc/vignette_get_nltt_values.Rmd | 127 ++++---- nLTT-1.3.1/nLTT/inst/doc/vignette_get_nltt_values.html | 155 +++++----- nLTT-1.3.1/nLTT/inst/doc/vignette_nltts_plot.R | 25 - nLTT-1.3.1/nLTT/inst/doc/vignette_nltts_plot.html | 32 +- nLTT-1.3.1/nLTT/inst/doc/vignette_stretch_nltt_matrix.html | 36 +- nLTT-1.3.1/nLTT/inst/doc/walkthrough.R |only nLTT-1.3.1/nLTT/inst/doc/walkthrough.Rmd |only nLTT-1.3.1/nLTT/inst/doc/walkthrough.html |only nLTT-1.3.1/nLTT/man/nLTT-package.Rd | 64 ++-- nLTT-1.3.1/nLTT/tests/testthat/test_get_average_nltt_matrix.R | 41 -- nLTT-1.3.1/nLTT/vignettes/trees_with_root_edge.Rmd | 4 nLTT-1.3.1/nLTT/vignettes/vignette_get_nltt_values.Rmd | 102 +++--- nLTT-1.3.1/nLTT/vignettes/walkthrough.Rmd |only nLTT-1.3/nLTT/inst/doc/vignette_get_average_nltt.R |only nLTT-1.3/nLTT/inst/doc/vignette_get_average_nltt.Rmd |only nLTT-1.3/nLTT/inst/doc/vignette_get_average_nltt.html |only nLTT-1.3/nLTT/man/get_average_nltt_matrix_impl_1.Rd |only nLTT-1.3/nLTT/man/get_average_nltt_matrix_impl_2.Rd |only 28 files changed, 397 insertions(+), 406 deletions(-)
Title: 'stats' for Seasonal Adjustment on the Fly with 'ggplot2'
Description: Provides 'ggplot2' 'stats' that estimate seasonally adjusted series
and rolling summaries such as rolling average on the fly for time series.
Author: Peter Ellis [aut, cre],
Christophe Sax [ctb]
Maintainer: Peter Ellis <peter.ellis2013nz@gmail.com>
Diff between ggseas versions 0.5.0 dated 2016-10-10 and 0.5.1 dated 2016-10-11
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ R/ggseas.R |only R/misc_doc.R | 2 -- build/vignette.rds |binary inst/doc/ggsdc.Rmd | 2 +- inst/doc/ggsdc.html | 4 ++-- man/ggseas-package.Rd |only vignettes/ggsdc.Rmd | 2 +- 9 files changed, 15 insertions(+), 15 deletions(-)
Title: Fragility Index
Description: Implements and extends the fragility index calculation for
dichotomous results as described in Walsh, Srinathan, McAuley,
Mrkobrada, Levine, Ribic, Molnar, Dattani, Burke, Guyatt,
Thabane, Walter, Pogue, and Devereaux (2014)
<DOI:10.1016/j.jclinepi.2013.10.019>.
Author: Kipp Johnson [aut, cre]
Maintainer: Kipp Johnson <kipp.william.johnson@gmail.com>
Diff between fragilityindex versions 0.0.4 dated 2016-10-06 and 0.0.7 dated 2016-10-11
DESCRIPTION | 16 ++++++++-------- MD5 | 17 +++++++++++++---- NAMESPACE | 12 ++++++++++++ R/fragility.index.R | 9 ++++++--- R/glmfit2table.R |only R/logisticfragility.R |only R/logisticfragilityinternal.R |only R/revfragility.index.R |only README.md |only man/fragility.index.Rd | 6 ++++-- man/glmfit2table.Rd |only man/logisticfragility.Rd |only man/logisticfragilityinternal.Rd |only man/revfragility.index.Rd |only 14 files changed, 43 insertions(+), 17 deletions(-)
More information about fragilityindex at CRAN
Permanent link
Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data
manipulation and the creation of new data, structured from basic forest
inventory data. The purpose of this package is provide functions to support
these activities.
Author: Clayton Vieira Fraga Filho,
Ana Paula Simiqueli,
Gilson Fernandes da Silva,
Miqueias Fernandes,
Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>
Diff between Fgmutils versions 0.9.3 dated 2016-09-26 and 0.9.4 dated 2016-10-11
DESCRIPTION | 8 +-- MD5 | 22 +++++---- NAMESPACE | 3 + NEWS | 3 + R/avaliaEstimativas.R | 104 +++++++++++++++++++------------------------- R/avaliaVolumeAgeBased.R |only R/avaliaVolumeAvancado.R | 1 R/evalAgeBased.R |only R/projectBaseOriented.R |only R/roundAge.R | 12 +++-- R/separaDados.R | 6 +- man/avaliaVolumeAgeBased.Rd |only man/evalAgeBased.Rd |only man/projectBaseOriented.Rd |only man/roundAge.Rd | 4 + 15 files changed, 85 insertions(+), 78 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multilevel models
using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 1.0.1 dated 2016-09-16 and 1.1.0 dated 2016-10-11
brms-1.0.1/brms/inst/doc/brms_families.R |only brms-1.0.1/brms/inst/doc/brms_families.html |only brms-1.1.0/brms/DESCRIPTION | 10 brms-1.1.0/brms/MD5 | 73 +- brms-1.1.0/brms/R/brm.R | 3 brms-1.1.0/brms/R/brmsfit-helpers.R | 155 ++-- brms-1.1.0/brms/R/brmsfit-methods.R | 104 +-- brms-1.1.0/brms/R/brmsformula.R | 32 brms-1.1.0/brms/R/data-helpers.R | 125 ++- brms-1.1.0/brms/R/extract_draws.R | 177 +++-- brms-1.1.0/brms/R/linear_predictor.R | 96 ++ brms-1.1.0/brms/R/loglik.R | 3 brms-1.1.0/brms/R/make_stancode.R | 75 +- brms-1.1.0/brms/R/make_standata.R | 124 +-- brms-1.1.0/brms/R/misc.R | 73 +- brms-1.1.0/brms/R/plots.R | 13 brms-1.1.0/brms/R/rename.R | 125 ++- brms-1.1.0/brms/R/stan-helpers.R | 166 +++-- brms-1.1.0/brms/R/stan-predictor.R | 242 ++++--- brms-1.1.0/brms/R/sysdata.rda |binary brms-1.1.0/brms/R/validate.R | 564 +++++++++++------ brms-1.1.0/brms/build/vignette.rds |binary brms-1.1.0/brms/inst/NEWS.Rd | 48 + brms-1.1.0/brms/inst/chunks/fun_inv_gaussian.stan | 4 brms-1.1.0/brms/inst/chunks/tdataC_inv_gaussian.stan |only brms-1.1.0/brms/inst/chunks/tdataD_inv_gaussian.stan |only brms-1.1.0/brms/inst/doc/brms.pdf |binary brms-1.1.0/brms/inst/doc/brms_families.Rmd | 12 brms-1.1.0/brms/inst/doc/brms_families.pdf |only brms-1.1.0/brms/man/brmsformula.Rd | 32 brms-1.1.0/brms/man/residuals.brmsfit.Rd | 15 brms-1.1.0/brms/tests/testthat/tests.brmsfit-helpers.R | 10 brms-1.1.0/brms/tests/testthat/tests.brmsfit-methods.R | 24 brms-1.1.0/brms/tests/testthat/tests.make_stancode.R | 107 ++- brms-1.1.0/brms/tests/testthat/tests.make_standata.R | 89 +- brms-1.1.0/brms/tests/testthat/tests.plots.R | 2 brms-1.1.0/brms/tests/testthat/tests.rename.R | 45 + brms-1.1.0/brms/tests/testthat/tests.stan-helpers.R | 35 - brms-1.1.0/brms/tests/testthat/tests.validate.R | 36 - brms-1.1.0/brms/vignettes/brms_families.Rmd | 12 40 files changed, 1677 insertions(+), 954 deletions(-)
Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre]
Maintainer: Matti Vuorre <mv2521@columbia.edu>
Diff between bmlm versions 1.0.0 dated 2016-07-19 and 1.2.1 dated 2016-10-11
bmlm-1.0.0/bmlm/R/bmlm.R |only bmlm-1.0.0/bmlm/inst/stan |only bmlm-1.0.0/bmlm/man/getpps.Rd |only bmlm-1.2.1/bmlm/DESCRIPTION | 16 ++- bmlm-1.2.1/bmlm/MD5 | 48 +++++++---- bmlm-1.2.1/bmlm/NAMESPACE | 3 bmlm-1.2.1/bmlm/NEWS.md | 28 ++++++ bmlm-1.2.1/bmlm/R/bmlm-package.R |only bmlm-1.2.1/bmlm/R/mlm.R | 85 ++++++++++++-------- bmlm-1.2.1/bmlm/R/mlm_plot.R | 148 +++++++++++++++++++++++------------ bmlm-1.2.1/bmlm/R/stanmodels.R |only bmlm-1.2.1/bmlm/R/utils.R | 53 ++---------- bmlm-1.2.1/bmlm/R/zzz.R |only bmlm-1.2.1/bmlm/README.md | 18 ++-- bmlm-1.2.1/bmlm/cleanup |only bmlm-1.2.1/bmlm/cleanup.win |only bmlm-1.2.1/bmlm/exec |only bmlm-1.2.1/bmlm/inst/chunks |only bmlm-1.2.1/bmlm/man/bmlm.Rd | 2 bmlm-1.2.1/bmlm/man/mlm.Rd | 38 ++++---- bmlm-1.2.1/bmlm/man/mlm_pars_plot.Rd | 6 - bmlm-1.2.1/bmlm/man/mlm_path_plot.Rd | 18 +--- bmlm-1.2.1/bmlm/man/mlm_summary.Rd | 10 -- bmlm-1.2.1/bmlm/src |only bmlm-1.2.1/bmlm/tools |only 25 files changed, 276 insertions(+), 197 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU')
tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests
and gene-based and some pathway based association tests (Pathway based Sum of
Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU'
test for multiple traits - single 'SNP' (single-nucleotide-polymorphism)
association in generalized estimation equations, 'MTaSPUs' test for multiple
traits - single 'SNP' association with Genome Wide Association Studies ('GWAS')
summary statistics, Gene-based Association Test that uses an extended Simes
procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version
of 'GATES' test for pathway-based association testing ('GATES-Simes'). ).
The tests can be used with genetic and other data sets with covariates. The
response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set
association with individual-level data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP'
set association with summary statistics ('aSPUs'), (3) Single trait-pathway
association with individual-level data ('aSPUpath'), (4) Single trait-pathway
association with summary statistics ('aSPUsPath'), (5) Multiple traits-single
'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-
single SNP association with summary statistics ('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics('MTaSPUsSetPath').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.44 dated 2016-09-22 and 1.45 dated 2016-10-11
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- R/MTaSPUs.R | 4 +++- R/MTaSPUsSet.R | 2 +- R/MTaSPUsSetScore.R | 2 +- R/aSPUboot.R | 2 +- R/aSPUboot2.R | 2 +- R/aSPUperm.R | 2 +- R/aSPUperm2.R | 2 +- R/aSPUpermC2.R | 2 +- R/aSPUr.R | 1 + R/aSPUs.R | 3 +-- R/aSPUsim1.R | 2 +- R/aSPUsim2.R | 2 +- R/aSPUsimC2.R | 2 +- R/aSPUwboot.R | 4 ++-- R/aSPUwperm.R | 2 +- R/aSPUwsim.R | 2 +- inst/doc/MTaSPUsSet.Rmd | 4 ++-- inst/doc/MTaSPUsSet.html | 4 ++-- vignettes/MTaSPUsSet.Rmd | 4 ++-- 21 files changed, 49 insertions(+), 47 deletions(-)
Title: Fitting Step-Functions
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Timo Aspelmeier [cre, aut],
Thomas Hotz [aut],
Hannes Sieling [aut],
Pein Florian [ctb]
Maintainer: Timo Aspelmeier <timo.aspelmeier@mathematik.uni-goettingen.de>
Diff between stepR versions 1.0-5 dated 2016-10-05 and 1.0-5.1 dated 2016-10-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/BinTree.h | 1 + src/Bounds.cpp | 1 + src/Jump.h | 2 ++ src/Step.h | 1 + 6 files changed, 13 insertions(+), 8 deletions(-)
Title: An Enhanced Chart for Simple and Truthful Representation of
Single Observations over Multiple Classes
Description: The sinaplot is a data visualization chart suitable for plotting
any single variable in a multiclass data set. It is an enhanced jitter strip
chart, where the width of the jitter is controlled by the density
distribution of the data within each class.
Author: Nikos Sidiropoulos [aut, cre],
Sina Hadi Sohi [aut],
Nicolas Rapin [aut],
Frederik Otzen Bagger [aut]
Maintainer: Nikos Sidiropoulos <nikos.sidiro@gmail.com>
Diff between sinaplot versions 0.1.5 dated 2016-05-17 and 1.0.0 dated 2016-10-11
DESCRIPTION | 15 +- MD5 | 22 +- NAMESPACE | 9 - NEWS | 58 ++++++- R/sinaplot.R | 367 ++++++++++++++++++++++--------------------------- README.md | 1 inst/doc/SinaPlot.R | 19 +- inst/doc/SinaPlot.Rmd | 27 ++- inst/doc/SinaPlot.html | 123 ++++++---------- man/blood.Rd | 2 man/sinaplot.Rd | 88 +++++------ vignettes/SinaPlot.Rmd | 27 ++- 12 files changed, 381 insertions(+), 377 deletions(-)
Title: Non-Parametric Bayesian Spectrum Estimation for Multirate Data
Description: Computes linear Bayesian spectral estimates from multirate
data for second-order stationary time series. Provides credible
intervals and methods for plotting various spectral estimates.
Author: Ben Powell [aut, cre],
Guy Nason [aut]
Maintainer: Ben Powell <ben.powell@bristol.ac.uk>
Diff between regspec versions 2.3 dated 2016-08-26 and 2.4 dated 2016-10-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/regspec17.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.3.3 dated 2016-09-12 and 0.3.3.1 dated 2016-10-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/zzz.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Christoph Berreth [ctr], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.1.24 dated 2016-09-12 and 3.1.24.1 dated 2016-10-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/zzz.R | 2 -- data/weather.rda |binary 4 files changed, 6 insertions(+), 8 deletions(-)
Title: Piecewise Structural Equation Modeling
Description: Implements piecewise structural equation models.
Author: Jon Lefcheck
Maintainer: Jon Lefcheck <jslefche@vims.edu>
Diff between piecewiseSEM versions 1.1.3 dated 2016-07-11 and 1.2.0 dated 2016-10-11
DESCRIPTION | 8 +- MD5 | 50 ++++++------ NAMESPACE | 1 NEWS.md | 13 +++ R/endogenous.reverse.R | 44 ++++++++--- R/filter.exogenous.R | 51 ++++++++----- R/get.basis.set.R | 21 +++++ R/get.dag.R | 31 +++++-- R/get.formula.list.R | 4 - R/get.random.formula.R | 30 ++----- R/get.scaled.data.R | 7 + R/get.scaled.model.R | 2 R/get.sort.dag.R | 44 +++-------- R/rsquared.R |only R/sem.basis.set.R | 171 ++++++++++++++++++++++++++------------------ R/sem.coefs.R | 69 ++++++++++------- R/sem.missing.paths.R | 51 ++++++++----- R/sem.model.fits.R | 34 +++++--- R/sem.plot.R | 3 README.md | 4 - inst/doc/piecewiseSEM.Rmd | 6 - inst/doc/piecewiseSEM.html | 14 +-- man/endogenous.reverse.Rd | 6 + man/filter.exogenous.Rd | 49 +----------- man/piecewiseSEM-package.Rd | 6 - man/rsquared.Rd |only vignettes/piecewiseSEM.Rmd | 6 - 27 files changed, 418 insertions(+), 307 deletions(-)
Title: Flexible BUGS-Compatible System for Hierarchical Statistical
Modeling and Algorithm Development
Description: Flexible application of algorithms to models specified in the BUGS
language. Algorithms can be written in the NIMBLE language and made available to
any model.
Author: Perry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson-
Bergman, Duncan Temple Lang
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.6 dated 2016-09-02 and 0.6-1 dated 2016-10-11
DESCRIPTION | 6 INSTALL | 6 MD5 | 289 ++--- NAMESPACE | 3 NEWS | 16 R/BUGS_model.R | 5 R/BUGS_modelDef.R | 30 R/BUGS_testBUGS.R | 4 R/MCMC_conjugacy.R | 5 R/MCMC_run.R | 2 R/RCfunction_compile.R | 2 R/cppDefs_RCfunction.R | 30 R/cppDefs_core.R | 2 R/cppDefs_cppProject.R | 77 + R/cppInterfaces_modelValues.R | 46 R/cppInterfaces_models.R | 58 - R/cppInterfaces_nimbleFunctions.R | 351 ++++-- R/cppInterfaces_otherTypes.R | 256 ++-- R/cppInterfaces_utils.R | 140 +- R/genCpp_processSpecificCalls.R | 12 R/genCpp_sizeProcessing.R | 93 + R/nimbleFunction_core.R | 4 R/nimbleFunction_keywordProcessing.R | 44 R/nimbleFunction_nodeFunction.R | 3 R/nimbleFunction_nodeFunctionNew.R | 3 R/nimbleProject.R | 127 ++ R/options.R | 4 R/setNimbleInternalFunctions.R | 2 R/types_nimbleFunctionList.R | 9 R/types_nodeFxnVector.R | 40 R/types_numericLists.R | 252 ++-- R/types_util.R | 23 README.md | 8 configure | 12 configure.ac | 12 configure.win | 5 inst/CppCode/GNUmakefile | 4 inst/CppCode/ModelClassUtils.cpp | 13 inst/CppCode/NamedObjects.cpp | 20 inst/CppCode/RcppNimbleUtils.cpp |only inst/CppCode/RcppUtils.cpp | 1456 +++------------------------- inst/CppCode/accessorClasses.cpp | 304 ++--- inst/CppCode/dists.cpp | 1 inst/CppCode/dllFinalizer.cpp |only inst/CppCode/nimDists.cpp | 13 inst/include/nimble/ModelClassUtils.h | 6 inst/include/nimble/NamedObjects.h | 8 inst/include/nimble/NimArr.h | 7 inst/include/nimble/NimArrBase.h | 4 inst/include/nimble/RcppNimbleUtils.h |only inst/include/nimble/RcppUtils.h | 357 ------ inst/include/nimble/accessorClasses.h | 26 inst/include/nimble/dllFinalizer.h |only inst/include/nimble/dynamicRegistrations.h |only inst/include/nimble/nodeFun.h | 1 inst/tests/test_utils.R | 62 - man/BUGSdeclClass-class.Rd | 2 man/Categorical.Rd | 2 man/CmodelBaseClass-class.Rd | 2 man/CnimbleFunctionBase-class.Rd | 2 man/Constraint.Rd | 2 man/Dirichlet.Rd | 2 man/Exponential.Rd | 2 man/Interval.Rd | 2 man/MCMCconf-class.Rd | 2 man/MCMCsuite.Rd | 2 man/MCMCsuiteClass-class.Rd | 2 man/Multinomial.Rd | 2 man/Multivariate-t.Rd | 2 man/MultivariateNormal.Rd | 2 man/Rmatrix2mvOneVar.Rd |only man/RmodelBaseClass-class.Rd | 2 man/Wishart.Rd | 2 man/asRow.Rd | 2 man/autoBlock.Rd | 2 man/buildAuxiliaryFilter.Rd | 2 man/buildBootstrapFilter.Rd | 2 man/buildEnsembleKF.Rd | 2 man/buildLiuWestFilter.Rd | 2 man/buildMCEM.Rd | 2 man/buildMCMC.Rd | 2 man/checkInterrupt.Rd | 2 man/codeBlockClass-class.Rd | 2 man/combine_MCMC_comparison_results.Rd | 2 man/compareMCMCs.Rd | 2 man/compileNimble.Rd | 2 man/configureMCMC.Rd | 2 man/decide.Rd | 2 man/decideAndJump.Rd | 2 man/declare.Rd | 2 man/deregisterDistributions.Rd | 2 man/getBUGSexampleDir.Rd | 2 man/getDefinition.Rd | 2 man/getLoadingNamespace.Rd | 2 man/getNimbleOption.Rd | 2 man/getParam.Rd | 2 man/getsize.Rd | 2 man/identityMatrix.Rd | 2 man/initializeModel.Rd | 2 man/is.nf.Rd | 2 man/makeParamInfo.Rd | 2 man/make_MCMC_comparison_pages.Rd | 2 man/modelBaseClass-class.Rd | 2 man/modelDefClass-class.Rd | 2 man/modelValues.Rd | 2 man/modelValuesBaseClass-class.Rd | 2 man/modelValuesConf.Rd | 2 man/nfMethod.Rd | 2 man/nfVar.Rd | 2 man/nimArray.Rd | 2 man/nimCat.Rd | 2 man/nimCopy.Rd | 2 man/nimDim.Rd | 2 man/nimInteger.Rd | 2 man/nimMatrix.Rd | 2 man/nimNumeric.Rd | 2 man/nimPrint.Rd | 2 man/nimStop.Rd | 2 man/nimble-internal.Rd | 1 man/nimbleCode.Rd | 2 man/nimbleFunction.Rd | 2 man/nimbleFunctionBase-class.Rd | 2 man/nimbleFunctionList-class.Rd |only man/nimbleFunctionVirtual.Rd | 2 man/nimbleModel.Rd | 2 man/nimbleOptions.Rd | 2 man/nodeFunctions.Rd | 2 man/rankSample.Rd | 2 man/readBUGSmodel.Rd | 2 man/registerDistributions.Rd | 2 man/rename_MCMC_comparison_method.Rd | 2 man/reshape_comparison_results.Rd | 2 man/resize.Rd | 2 man/run.time.Rd | 2 man/runMCMC.Rd | 2 man/samplers.Rd | 2 man/setAndCalculate.Rd | 2 man/setAndCalculateOne.Rd | 2 man/setSize.Rd | 2 man/setupOutputs.Rd | 2 man/simNodes.Rd | 2 man/simNodesMV.Rd | 2 man/singleVarAccessClass-class.Rd | 2 man/t.Rd | 2 man/testBUGSmodel.Rd | 2 man/updateMCMCcomparisonWithHighOrderESS.Rd | 2 man/valueInCompiledNimbleFunction.Rd | 2 man/values.Rd | 2 src/nimble.cpp | 56 - 149 files changed, 1788 insertions(+), 2710 deletions(-)
Title: Color Space Manipulation
Description: Carries out mapping between assorted color spaces including
RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV),
CIELAB and polar CIELAB. Qualitative, sequential, and
diverging color palettes based on HCL colors are provided.
Author: Ross Ihaka [aut],
Paul Murrell [aut],
Kurt Hornik [aut],
Jason C. Fisher [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between colorspace versions 1.2-6 dated 2015-03-10 and 1.2-7 dated 2016-10-11
DESCRIPTION | 15 ++++++++------- LICENSE | 2 +- MD5 | 31 ++++++++++++++++--------------- NAMESPACE | 5 ++++- NEWS | 10 ++++++++++ R/choose_palette.R | 26 ++++++++++++++------------ R/colorspace.R | 2 +- build/partial.rdb |only build/vignette.rds |binary data/USSouthPolygon.rda |binary inst/CITATION | 28 +++++++++++++++++++++++++--- inst/doc/hcl-colors.pdf |binary man/USSouthPolygon.Rd | 2 +- man/choose_palette.Rd | 16 +++++++++++----- man/desaturate.Rd | 2 +- man/rainbow_hcl.Rd | 18 +++++++++++------- vignettes/hcl-colors.Rout.save | 4 +--- 17 files changed, 104 insertions(+), 57 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with both continuous and discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.28 dated 2016-10-03 and 2.29 dated 2016-10-11
BDgraph-2.28/BDgraph/src/Ig.cpp |only BDgraph-2.28/BDgraph/src/gcgm_bd_multi_update.cpp |only BDgraph-2.28/BDgraph/src/gcgm_rj.cpp |only BDgraph-2.28/BDgraph/src/ggm_bd_multi_update.cpp |only BDgraph-2.28/BDgraph/src/ggm_rj.cpp |only BDgraph-2.28/BDgraph/src/rgcwish.cpp |only BDgraph-2.28/BDgraph/src/rgcwish.h |only BDgraph-2.28/BDgraph/src/scaleFree.cpp |only BDgraph-2.29/BDgraph/DESCRIPTION | 8 BDgraph-2.29/BDgraph/MD5 | 49 -- BDgraph-2.29/BDgraph/R/bdgraph.sim.R | 4 BDgraph-2.29/BDgraph/man/bdgraph.Rd | 4 BDgraph-2.29/BDgraph/man/bdgraph.sim.Rd | 4 BDgraph-2.29/BDgraph/man/bdgraph.ts.Rd | 2 BDgraph-2.29/BDgraph/man/compare.Rd | 6 BDgraph-2.29/BDgraph/man/gnorm.Rd | 4 BDgraph-2.29/BDgraph/man/plotroc.Rd | 6 BDgraph-2.29/BDgraph/man/rgwish.Rd | 2 BDgraph-2.29/BDgraph/man/rwish.Rd | 2 BDgraph-2.29/BDgraph/man/summary.bdgraph.Rd | 4 BDgraph-2.29/BDgraph/src/MyLapack.cpp | 123 ++--- BDgraph-2.29/BDgraph/src/MyLapack.h | 34 - BDgraph-2.29/BDgraph/src/bd_for_ts.cpp | 513 +++++++++++++++++++++- BDgraph-2.29/BDgraph/src/gcgm_bd.cpp | 479 ++++++++++++++++++++ BDgraph-2.29/BDgraph/src/ggm_bd.cpp | 458 +++++++++++++++++++ BDgraph-2.29/BDgraph/src/gm_rj.cpp |only BDgraph-2.29/BDgraph/src/matrix.cpp | 40 + BDgraph-2.29/BDgraph/src/matrix.h | 2 BDgraph-2.29/BDgraph/src/rgwish.cpp | 102 ++++ BDgraph-2.29/BDgraph/src/rgwish.h | 4 30 files changed, 1693 insertions(+), 157 deletions(-)
Title: Segregation Measures for Multitype Spatial Point Patterns
Description: Summaries for measuring segregation/mingling in multitype spatial
point patterns with graph based neighbourhood description. Included indices:
Mingling, Shannon, Simpson (also the non-spatial) Included functionals:
Mingling, Shannon, Simpson, ISAR, MCI. Included neighbourhoods: Geometric, k-
nearest neighbours, Gabriel, Delaunay. Dixon's test.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>
Diff between spatialsegregation versions 2.42 dated 2016-10-10 and 2.43 dated 2016-10-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Pp.cpp | 12 ++++++------ 3 files changed, 12 insertions(+), 12 deletions(-)
More information about spatialsegregation at CRAN
Permanent link
Title: Testing Workbench for Precision-Recall Curves
Description: A testing workbench for evaluating precision-recall curves under various conditions.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between prcbench versions 0.5.0 dated 2016-09-09 and 0.5.2 dated 2016-10-11
DESCRIPTION | 22 +++++++++++----------- MD5 | 10 +++++----- R/tool_zzz.R | 22 +++++++++++++++++++++- README.md | 30 ++++++++++++++++-------------- inst/doc/introduction.html | 28 ++++++++++++++-------------- tests/testthat/test_tool_pm.R | 4 ++++ 6 files changed, 71 insertions(+), 45 deletions(-)
Title: Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between mixAK versions 4.2 dated 2015-08-02 and 4.4 dated 2016-10-11
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 6 ++++++ R/cbplot.R | 23 +++++++++++++---------- data/Acidity.rda |binary data/Enzyme.rda |binary data/Galaxy.rda |binary man/cbplot.Rd | 10 ++++++---- src/AK_LAPACK.h | 1 + src/Dist_MVT.cpp | 5 +++-- src/NMix_Utils.cpp | 3 ++- 11 files changed, 45 insertions(+), 31 deletions(-)
Title: Spatial Graph Based Clustering Summaries for Spatial Point
Patterns
Description: Graph based clustering summaries for spatial point patterns.
Includes Connectivity function, Cumulative connectivity function and clustering
function, plus the triangle/triplet intensity function T.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>
Diff between SGCS versions 2.4 dated 2016-10-10 and 2.5 dated 2016-10-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Pp.cpp | 20 ++++++++++---------- 3 files changed, 16 insertions(+), 16 deletions(-)
Title: Calculate Accurate Precision-Recall and ROC (Receiver Operator
Characteristics) Curves
Description: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics)
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.5.0 dated 2016-09-09 and 0.5.2 dated 2016-10-11
DESCRIPTION | 14 ++-- MD5 | 6 - README.md | 20 +++--- inst/doc/introduction.html | 136 ++++++++++++++++++++++----------------------- 4 files changed, 89 insertions(+), 87 deletions(-)
Title: Title: Learn Data Science Through the "Data Science Live Book"
Description: Around 10% of almost any predictive modeling project
is spent in predictive modeling, 'funModeling' and the book <http://
livebook.datascienceheroes.com/> are intended to cover remaining 90%: data
preparation, profiling, selecting best variables 'dataViz', assessing model
performance and other functions.
Author: Pablo Casas
Maintainer: Pablo Casas <pabloc@datascienceheroes.com>
Diff between funModeling versions 1.3 dated 2016-10-05 and 1.4 dated 2016-10-11
DESCRIPTION | 8 ++--- MD5 | 8 ++--- R/models_lib.R | 6 --- R/numbers.R | 88 +++++++++++++++++++++++++++++---------------------------- man/freq.Rd | 4 +- 5 files changed, 58 insertions(+), 56 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [cre, ctb],
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.9 dated 2016-04-29 and 0.10 dated 2016-10-11
DESCRIPTION | 14 ++++++---- MD5 | 16 ++++++------ NAMESPACE | 2 + NEWS | 14 ++++++++++ R/eval.r | 66 ++++++++++++++++++++++++++++++++++++++++++++++----- R/replay.r | 34 +++++++++++++++++++++++++- R/watcher.r | 27 +++++++++++++++++--- man/evaluate.Rd | 7 ++++- man/flush_console.Rd |only man/inject_funs.Rd |only 10 files changed, 155 insertions(+), 25 deletions(-)
Title: Compositional Data Analysis
Description: A collection of functions for compositional data analysis.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Compositional versions 1.8 dated 2016-08-05 and 2.0 dated 2016-10-11
DESCRIPTION | 8 +- MD5 | 152 +++++++++++++++++++++---------------------- NAMESPACE | 8 +- R/alfa.R | 16 ++-- R/alfa.knn.R | 25 +++---- R/alfa.pcr.R | 2 R/alfa.profile.R | 8 +- R/alfa.reg.R | 23 +++--- R/alfa.tune.R | 8 +- R/alfainv.R | 10 +- R/alfaknn.tune.R | 148 ++++++++++++++++++++--------------------- R/alfapcr.tune.R | 8 +- R/alfarda.tune.R | 8 +- R/alfareg.tune.R | 48 +++++++------ R/alfaridge.tune.R | 6 - R/bic.mixcompnorm.R | 6 - R/bivt.contour.R | 28 +++---- R/comp.den.R | 6 - R/comp.kerncontour.R | 18 ++--- R/comp.knn.R | 79 +++++++++++----------- R/comp.reg.R | 10 +- R/compknn.tune.R | 85 ++++++++++++------------ R/ddiri.R | 4 - R/diri.contour.R | 28 +++---- R/diri.est.R | 18 ++--- R/diri.nr.R | 61 ++++------------- R/diri.reg.R | 28 +++---- R/diri.reg2.R | 30 ++++---- R/dirimean.test.R | 12 +-- R/eel.test1.R | 14 +-- R/eel.test2.R | 26 +++---- R/el.test1.R | 6 - R/el.test2.R | 12 +-- R/frechet.R | 12 +-- R/glm.pcr.R | 7 - R/glmpcr.tune.R | 18 ++--- R/helm.R | 2 R/hotel1T2.R | 12 +-- R/hotel2T2.R | 18 ++--- R/james.R | 25 +++---- R/js.compreg.R | 20 ++--- R/kl.compreg.R | 20 ++--- R/kl.diri.R | 2 R/maov.R | 8 +- R/maovjames.R | 14 +-- R/mix.compnorm.R | 16 ++-- R/mixnorm.contour.R | 12 +-- R/mkde.R | 6 - R/mkde.tune.R | 14 +-- R/multivreg.R | 13 +-- R/multivt.R | 6 - R/norm.contour.R | 19 ++--- R/ols.compreg.R | 25 +++---- R/pcr.R | 9 +- R/pcr.tune.R | 12 +-- R/rcompnorm.R | 4 - R/rcompsn.R | 4 - R/rcompt.R | 4 - R/rda.R | 18 ++--- R/rda.tune.R | 25 +++---- R/rdiri.R | 2 R/ridge.plot.R | 6 - R/ridge.reg.R | 5 - R/ridge.tune.R | 12 +-- R/rmixcomp.R | 4 - R/rmvnorm.R | 5 - R/skewnorm.contour.R | 20 ++--- R/spat.med.R | 16 ++-- R/spatmed.reg.R | 22 +++--- R/sscov.R | 6 - R/sym.test.R | 15 ++-- R/ternary.R | 18 ++--- man/Compositional-package.Rd | 4 - man/comp.knn.Rd | 2 man/diri.nr.Rd | 4 - man/rda.Rd | 2 man/spat.med.Rd | 4 - 77 files changed, 706 insertions(+), 735 deletions(-)
Title: Bootstrapped Robustness Assessment for Qualitative Comparative
Analysis
Description: Test the robustness of a user's Qualitative Comparative Analysis
solutions to randomness, using the bootstrapped assessment: baQCA(). This
package also includes a function that provides recommendations for improving
solutions to reach typical significance levels: brQCA().
Author: C. Ben Gibson [aut, cre],
Burrel Vann Jr [aut]
Maintainer: C. Ben Gibson <cbgibson@uci.edu>
Diff between braQCA versions 0.9.9.3 dated 2016-09-30 and 0.9.9.4 dated 2016-10-11
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Estimating Dynamic Heritability and Twin Model Comparison
Description: Twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.
Author: Liang He
Maintainer: Liang He <liang.he@duke.edu>
Diff between ACEt versions 1.6.9 dated 2016-09-10 and 1.7.0 dated 2016-10-11
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/AtCtEtp.R | 40 +++++++++++++++++++++++++++++++++------- R/mcmc_epsp.R | 9 +++++++++ man/ACEt-package.Rd | 6 +++--- man/AtCtEtp.Rd | 1 + src/AtCtEtp.cpp | 6 +++++- src/RInterface.cc | 8 ++++---- src/mcmc.cc | 33 +++++++++++++++++++++++++++++---- src/mcmc.h | 2 +- 10 files changed, 100 insertions(+), 35 deletions(-)
Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), Mahalanobis distance are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis and John Burkardt
Maintainer: Manos Papadakis <papadakm95@gmail.com>
Diff between Rfast versions 1.4 dated 2016-10-08 and 1.5 dated 2016-10-10
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- man/colrange.Rd | 3 ++- man/mahala.Rd | 5 ++--- man/transpose.Rd | 2 +- man/ttests.Rd | 10 +++++----- 6 files changed, 20 insertions(+), 20 deletions(-)
Title: Robust PCA by Projection Pursuit
Description: Provides functions for robust PCA by projection pursuit.
Author: Peter Filzmoser, Heinrich Fritz, Klaudius Kalcher
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between pcaPP versions 1.9-60 dated 2014-10-21 and 1.9-61 dated 2016-10-10
ChangeLog | 22 +++++++++- DESCRIPTION | 10 ++-- MD5 | 18 ++++---- NAMESPACE | 8 +++ R/PCdiagplot.R | 40 +++++++++--------- build/vignette.rds |binary inst/doc/matlab.R | 110 ++++++++++++++++++++++++++-------------------------- inst/doc/matlab.pdf |binary src/R_meal.h | 6 ++ src/pcaPP.cpp | 4 + 10 files changed, 128 insertions(+), 90 deletions(-)
Title: Platform for EDGAR Filing Management
Description: In the USA, firms file different forms with the U.S. Securities and
Exchange Commission (SEC) through EDGAR (Electronic Data Gathering, Analysis,
and Retrieval system). EDGAR automated system collects all the different
necessary filings and make it publicly available. Secondly, it validates
collected filings, then perform indexing and accepting of these submitted
forms. Investors, regulators, and researchers often require these forms for
various purposes. This package helps in data gathering, management, and
visualization in this regard. It downloads SEC EDGAR quarterly master
indexes, daily master indexes, and filings from SEC.org site and perform
sentiment analysis of these filing.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil
<bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 1.0.5 dated 2016-08-17 and 1.0.6 dated 2016-10-10
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- R/getMasterIndex.R | 2 +- R/getWordfrquency.R | 2 +- R/mergeCompustat.R | 36 +++++++++++++++++++----------------- man/getMasterIndex.Rd | 2 +- man/getWordfrquency.Rd | 2 +- man/mergeCompustat.Rd | 30 ++++++++++++++++-------------- 8 files changed, 54 insertions(+), 50 deletions(-)
Title: Access WHO Global Health Observatory Data from R
Description: Access WHO Global Health Observatory
data from R via the Athena web service,
an application program interface providing
a simple query interface to the World
Health Organization's data and statistics content.
Author: Antoine Filipovic-Pierucci [aut,cre]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>
Diff between rgho versions 0.2.2 dated 2016-09-26 and 0.2.3 dated 2016-10-10
rgho-0.2.2/rgho/tests |only rgho-0.2.3/rgho/DESCRIPTION | 6 rgho-0.2.3/rgho/MD5 | 22 rgho-0.2.3/rgho/NEWS.md | 6 rgho-0.2.3/rgho/inst/doc/a-intro.html | 104 +- rgho-0.2.3/rgho/inst/doc/b-dimensions.html | 4 rgho-0.2.3/rgho/inst/doc/c-codes-gho.html | 1280 +++++++++++++------------- rgho-0.2.3/rgho/inst/doc/d-codes-country.html | 20 rgho-0.2.3/rgho/inst/doc/e-details.html | 4 9 files changed, 725 insertions(+), 721 deletions(-)
Title: Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken - Nonparametric Statistical Methods, Third Edition
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider, Eric Chicken, Rachel Becvarik
Maintainer: Grant Schneider <schneider.393@osu.edu>
Diff between NSM3 versions 1.8 dated 2016-10-10 and 1.9 dated 2016-10-10
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/theil.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Kernel Regression Smoothing with Local or Global Plug-in
Bandwidth
Description: Kernel regression smoothing with adaptive local or global plug-in
bandwidth selection.
Author: Eva Herrmann <eherrmann@mathematik.tu-darmstadt.de> (F77 & S original);
Packaged for R and enhanced by Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between lokern versions 1.1-6 dated 2014-11-18 and 1.1-8 dated 2016-10-10
lokern-1.1-6/lokern/tests/glk1.Rout_Win64_Uwe |only lokern-1.1-8/lokern/ChangeLog | 13 + lokern-1.1-8/lokern/DESCRIPTION | 10 lokern-1.1-8/lokern/MD5 | 37 +-- lokern-1.1-8/lokern/NAMESPACE | 12 + lokern-1.1-8/lokern/R/glkerns.R | 74 ++++--- lokern-1.1-8/lokern/R/lokerns.R | 95 ++++++--- lokern-1.1-8/lokern/R/varNPreg.R | 4 lokern-1.1-8/lokern/demo/glk-derivs.R | 3 lokern-1.1-8/lokern/man/KernS-methods.Rd | 5 lokern-1.1-8/lokern/man/glkerns.Rd | 57 ++++- lokern-1.1-8/lokern/man/lokerns.Rd | 44 +++- lokern-1.1-8/lokern/man/xSim.Rd | 2 lokern-1.1-8/lokern/src/auxkerns.f | 236 +++++++++++++--------- lokern-1.1-8/lokern/src/glkerns.f | 78 ++++--- lokern-1.1-8/lokern/src/lokerns.f | 70 +++--- lokern-1.1-8/lokern/src/monitor.c | 40 +++ lokern-1.1-8/lokern/tests/glk1.R | 30 ++ lokern-1.1-8/lokern/tests/glk1.Rout.save | 272 +++++--------------------- lokern-1.1-8/lokern/tests/lok1.Rout.save | 106 +++++----- 20 files changed, 641 insertions(+), 547 deletions(-)
Title: Individual Tree Growth Modeling
Description: Individual tree model is an instrument to support the decision with
regard to forest management. This package provides functions that let you work
with data for this model. Also other support functions and extension related to
this model are available.
Author: Clayton Vieira Fraga Filho, Miqueias Fernandes
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>
Diff between ITGM versions 0.3 dated 2016-09-26 and 0.4 dated 2016-10-10
ITGM-0.3/ITGM/R/primeirasMedicoes.R |only ITGM-0.3/ITGM/man/primeirasMedicoes.Rd |only ITGM-0.4/ITGM/DESCRIPTION | 6 +++--- ITGM-0.4/ITGM/MD5 | 14 +++++++++----- ITGM-0.4/ITGM/NAMESPACE | 4 +++- ITGM-0.4/ITGM/R/firstsMeasurements.R |only ITGM-0.4/ITGM/R/getModelsExclusiveOfLiterature.R |only ITGM-0.4/ITGM/R/getModelsGenericOfLiterature.R |only ITGM-0.4/ITGM/man/firstsMeasurements.Rd |only ITGM-0.4/ITGM/man/getModelsExclusiveOfLiterature.Rd |only ITGM-0.4/ITGM/man/getModelsGenericOfLiterature.Rd |only ITGM-0.4/ITGM/tests/testthat/testPrimeirasMedicoes.R | 4 ++-- 12 files changed, 17 insertions(+), 11 deletions(-)
Title: Collect and Retrieve Annotation Data for Various Genomic Data
Using Different Webservices
Description: Cross-species identification of novel gene candidates using the NCBI web service is provided. Further, sets of miRNA target genes can be identified by using the targetscan.org API.
Author: Daniel Fischer [aut, cre], Anu Sironen [aut]
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between hoardeR versions 0.9 dated 2016-09-01 and 0.9.1 dated 2016-10-10
hoardeR-0.9.1/hoardeR/DESCRIPTION | 13 hoardeR-0.9.1/hoardeR/MD5 | 80 +- hoardeR-0.9.1/hoardeR/NAMESPACE | 26 hoardeR-0.9.1/hoardeR/R/aaa.R | 35 hoardeR-0.9.1/hoardeR/R/blastSeq.R | 76 +- hoardeR-0.9.1/hoardeR/R/createSpecies.R |only hoardeR-0.9.1/hoardeR/R/exportBed.R | 8 hoardeR-0.9.1/hoardeR/R/exportFA.R | 7 hoardeR-0.9.1/hoardeR/R/findSpecies.R |only hoardeR-0.9.1/hoardeR/R/getAnnotation.R | 111 ++- hoardeR-0.9.1/hoardeR/R/getBlastResult.R | 2 hoardeR-0.9.1/hoardeR/R/getFastaFromBed.R | 66 + hoardeR-0.9.1/hoardeR/R/importBed.R |only hoardeR-0.9.1/hoardeR/R/importXML.R | 5 hoardeR-0.9.1/hoardeR/R/intersectXMLAnnot.R | 11 hoardeR-0.9.1/hoardeR/R/plotHit.R | 203 +++-- hoardeR-0.9.1/hoardeR/R/print.fa.R | 3 hoardeR-0.9.1/hoardeR/R/sendFA.R | 4 hoardeR-0.9.1/hoardeR/R/summary.fa.R | 2 hoardeR-0.9.1/hoardeR/R/tableSpecies.R | 36 - hoardeR-0.9.1/hoardeR/build/vignette.rds |binary hoardeR-0.9.1/hoardeR/data/species.rda |binary hoardeR-0.9.1/hoardeR/inst/ChangeLog | 23 hoardeR-0.9.1/hoardeR/inst/doc/hoardeR-vignette.R | 568 +++++++++++---- hoardeR-0.9.1/hoardeR/inst/doc/hoardeR-vignette.Rmd | 683 ++++++++++++------- hoardeR-0.9.1/hoardeR/inst/doc/hoardeR-vignette.pdf |only hoardeR-0.9.1/hoardeR/man/blastSeq.Rd | 7 hoardeR-0.9.1/hoardeR/man/exportBed.Rd | 4 hoardeR-0.9.1/hoardeR/man/exportFA.Rd | 4 hoardeR-0.9.1/hoardeR/man/findSpecies.Rd |only hoardeR-0.9.1/hoardeR/man/getAnnotation.Rd | 18 hoardeR-0.9.1/hoardeR/man/getFastaFromBed.Rd | 13 hoardeR-0.9.1/hoardeR/man/hoardeR-package.Rd | 6 hoardeR-0.9.1/hoardeR/man/importBed.Rd |only hoardeR-0.9.1/hoardeR/man/plotHit.Rd | 23 hoardeR-0.9.1/hoardeR/man/species.Rd | 10 hoardeR-0.9.1/hoardeR/man/tableSpecies.Rd | 3 hoardeR-0.9.1/hoardeR/vignettes/coverageExample.jpg |only hoardeR-0.9.1/hoardeR/vignettes/hoardeR-vignette.Rmd | 683 ++++++++++++------- hoardeR-0.9.1/hoardeR/vignettes/pigFlanking.jpg |only hoardeR-0.9/hoardeR/R/importPedMap.R |only hoardeR-0.9/hoardeR/R/print.pedMap.R |only hoardeR-0.9/hoardeR/R/summary.pedMap.R |only hoardeR-0.9/hoardeR/R/updateSpecies.R |only hoardeR-0.9/hoardeR/inst/doc/hoardeR-vignette.html |only hoardeR-0.9/hoardeR/man/importPedMap.Rd |only hoardeR-0.9/hoardeR/man/print.pedMap.Rd |only hoardeR-0.9/hoardeR/man/summary.pedMap.Rd |only hoardeR-0.9/hoardeR/vignettes/coverageExample.png |only hoardeR-0.9/hoardeR/vignettes/pigFlanking.png |only 50 files changed, 1870 insertions(+), 863 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an
abstraction for a value that may be available at some point in the future.
The state of a future can either be unresolved or resolved. As soon as it
is resolved, the value is available. Futures are useful constructs in for
instance concurrent evaluation, e.g. parallel processing and distributed
processing on compute clusters. The purpose of this package is to provide
a lightweight interface for using futures in R. Functions 'future()' and
'value()' exist for creating futures and requesting their values, e.g.
'f <- future({ mandelbrot(-0.75, 0, side=3) })' and 'v <- value(f)'. The
'resolved()' function can be used to check if a future is resolved or
not. An infix assignment operator '%<-%' exists for creating futures whose
values are accessible by the assigned variables (as promises), e.g. 'v %<-%
{ mandelbrot(-0.75, 0, side=3) }'. This package implements synchronous "lazy"
and "eager" futures, and asynchronous "multicore", "multisession" and ad hoc
"cluster" futures. Globals variables and functions are automatically identified
and exported. Required packages are attached in external R sessions whenever
needed. All types of futures are designed to behave the same such that the
exact same code work regardless of futures used or number of cores, background
sessions or cluster nodes available. Additional types of futures are provided by
other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.1.0 dated 2016-10-10 and 1.1.1 dated 2016-10-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 11 ++++++++++- R/remote.R | 44 ++++++++++++++++++++++++-------------------- 4 files changed, 40 insertions(+), 27 deletions(-)
Title: A View Generator for Multidimensional Data
Description: A tool to explore wide data sets, by detecting, ranking
and plotting groups of statistically dependent columns.
Author: Thibault Sellam
Maintainer: Thibault Sellam <thibault.sellam@cwi.nl>
Diff between findviews versions 0.1.0 dated 2016-10-09 and 0.1.1 dated 2016-10-10
DESCRIPTION | 10 ++++++---- MD5 | 9 +++++---- NEWS.md |only R/web_app_plots.R | 2 +- README.md | 17 +++++++++++++++-- tests/testthat/test-findviews-trunk.R | 3 ++- 6 files changed, 29 insertions(+), 12 deletions(-)
Title: Spatial Graph Based Clustering Summaries for Spatial Point
Patterns
Description: Graph based clustering summaries for spatial point patterns.
Includes Connectivity function, Cumulative connectivity function and clustering
function, plus the triangle/triplet intensity function T.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>
Diff between SGCS versions 2.3 dated 2015-03-09 and 2.4 dated 2016-10-10
SGCS-2.3/SGCS/README.md |only SGCS-2.4/SGCS/DESCRIPTION | 14 +++--- SGCS-2.4/SGCS/MD5 | 65 ++++++++++++++++------------- SGCS-2.4/SGCS/NAMESPACE | 4 + SGCS-2.4/SGCS/R/K-function.R | 3 - SGCS-2.4/SGCS/R/R-function.R | 4 - SGCS-2.4/SGCS/R/arcs.R |only SGCS-2.4/SGCS/R/clustering-function.R | 10 ++-- SGCS-2.4/SGCS/R/denominator-of-clustfun.R |only SGCS-2.4/SGCS/R/internalise_pp.R | 6 +- SGCS-2.4/SGCS/R/morpho-Area.R | 20 ++++---- SGCS-2.4/SGCS/R/morpho-Euler.R | 6 +- SGCS-2.4/SGCS/man/Kfun.Rd | 5 +- SGCS-2.4/SGCS/man/Rfun.Rd | 5 +- SGCS-2.4/SGCS/man/SGCS.Rd | 11 ++-- SGCS-2.4/SGCS/man/Tfun.Rd | 5 +- SGCS-2.4/SGCS/man/arcs.Rd |only SGCS-2.4/SGCS/man/bounding_box_xy.Rd | 3 - SGCS-2.4/SGCS/man/clustfun.Rd | 4 + SGCS-2.4/SGCS/man/clustfun_denominator.Rd |only SGCS-2.4/SGCS/man/confun.Rd | 20 ++++---- SGCS-2.4/SGCS/man/default_r.Rd | 3 - SGCS-2.4/SGCS/man/edge_distance.Rd | 3 - SGCS-2.4/SGCS/man/internal_to_ppp.Rd | 3 - SGCS-2.4/SGCS/man/internalise_pp.Rd | 7 +-- SGCS-2.4/SGCS/man/morphoArea.Rd | 5 +- SGCS-2.4/SGCS/man/morphoEuler.Rd | 3 - SGCS-2.4/SGCS/man/morphoLength.Rd | 3 - SGCS-2.4/SGCS/man/pairwise_distances.Rd | 3 - SGCS-2.4/SGCS/man/translation_weights.Rd | 3 - SGCS-2.4/SGCS/src/Components.cpp |only SGCS-2.4/SGCS/src/Components.h |only SGCS-2.4/SGCS/src/Pp.cpp | 21 ++++----- SGCS-2.4/SGCS/src/arcs.cpp | 2 SGCS-2.4/SGCS/src/clustfun-denominator.cpp |only SGCS-2.4/SGCS/src/confun.cpp |only SGCS-2.4/SGCS/src/getArcs.cpp |only SGCS-2.4/SGCS/src/morphoArea.cpp |only SGCS-2.4/SGCS/src/morphoEuler.cpp |only SGCS-2.4/SGCS/src/morphoLength.cpp |only 40 files changed, 138 insertions(+), 103 deletions(-)
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: marginal Bayesian Nonparametric models, marginal Bayesian proportional hazards models, generalized accelerated failure time frailty models, and standard semiparametric frailty models within the context of proportional hazards, proportional odds and accelerated failure time.
Author: Haiming Zhou <zhouh@niu.edu> and Tim Hanson <hansont@stat.sc.edu>
Maintainer: Haiming Zhou <zhouh@niu.edu>
Diff between spBayesSurv versions 1.0.4 dated 2016-08-16 and 1.0.5 dated 2016-10-10
spBayesSurv-1.0.4/spBayesSurv/R/SuperSurvRegBayes2.R |only spBayesSurv-1.0.4/spBayesSurv/man/SuperSurvRegBayes2.Rd |only spBayesSurv-1.0.5/spBayesSurv/DESCRIPTION | 10 spBayesSurv-1.0.5/spBayesSurv/MD5 | 44 spBayesSurv-1.0.5/spBayesSurv/NAMESPACE | 10 spBayesSurv-1.0.5/spBayesSurv/R/SuperSurvRegBayes.R |only spBayesSurv-1.0.5/spBayesSurv/R/frailtyGAFT.R | 1075 +++--- spBayesSurv-1.0.5/spBayesSurv/R/survregbayes.R | 1557 +++++----- spBayesSurv-1.0.5/spBayesSurv/R/survregbayes2.R | 1438 ++++----- spBayesSurv-1.0.5/spBayesSurv/R/wrappers.R | 72 spBayesSurv-1.0.5/spBayesSurv/man/SuperSurvRegBayes.Rd |only spBayesSurv-1.0.5/spBayesSurv/man/frailtyGAFT.Rd | 410 +- spBayesSurv-1.0.5/spBayesSurv/man/spBayesSurv-package.Rd | 2 spBayesSurv-1.0.5/spBayesSurv/man/survregbayes.Rd | 396 +- spBayesSurv-1.0.5/spBayesSurv/man/survregbayes2.Rd | 379 +- spBayesSurv-1.0.5/spBayesSurv/src/spSurv_AFT_BP.cpp | 327 +- spBayesSurv-1.0.5/spBayesSurv/src/spSurv_AFT_MPT.cpp | 12 spBayesSurv-1.0.5/spBayesSurv/src/spSurv_PHPOAFT_BP.cpp | 14 spBayesSurv-1.0.5/spBayesSurv/src/spSurv_PH_BP.cpp | 317 +- spBayesSurv-1.0.5/spBayesSurv/src/spSurv_PH_MPT.cpp | 29 spBayesSurv-1.0.5/spBayesSurv/src/spSurv_PO_BP.cpp | 317 +- spBayesSurv-1.0.5/spBayesSurv/src/spSurv_PO_MPT.cpp | 25 spBayesSurv-1.0.5/spBayesSurv/src/spSurv_common.cpp | 48 spBayesSurv-1.0.5/spBayesSurv/src/spSurv_common.h | 12 spBayesSurv-1.0.5/spBayesSurv/src/spSurv_frailty_GRF_LDTFP.cpp | 137 25 files changed, 3708 insertions(+), 2923 deletions(-)
Title: Segregation Measures for Multitype Spatial Point Patterns
Description: Summaries for measuring segregation/mingling in multitype spatial
point patterns with graph based neighbourhood description. Included indices:
Mingling, Shannon, Simpson (also the non-spatial) Included functionals:
Mingling, Shannon, Simpson, ISAR, MCI. Included neighbourhoods: Geometric, k-
nearest neighbours, Gabriel, Delaunay. Dixon's test.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>
Diff between spatialsegregation versions 2.40 dated 2014-03-09 and 2.42 dated 2016-10-10
spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-ISAR.Rd |only spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-MCI.Rd |only spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-biomass.Rd |only spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-mingling.Rd |only spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-segregationFun.Rd |only spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-shannon.Rd |only spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-simpson.Rd |only spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-tests.Rd |only spatialsegregation-2.42/spatialsegregation/DESCRIPTION | 25 +-- spatialsegregation-2.42/spatialsegregation/MD5 | 48 +++--- spatialsegregation-2.42/spatialsegregation/NAMESPACE | 38 +++-- spatialsegregation-2.42/spatialsegregation/R/biomass.R | 32 +++- spatialsegregation-2.42/spatialsegregation/R/bivariate_tests.R | 26 +++ spatialsegregation-2.42/spatialsegregation/R/fun.R | 70 +++++++--- spatialsegregation-2.42/spatialsegregation/R/isar.R | 55 +++++-- spatialsegregation-2.42/spatialsegregation/R/mci.R | 25 ++- spatialsegregation-2.42/spatialsegregation/R/mingling.R | 50 +++++-- spatialsegregation-2.42/spatialsegregation/R/modifiers.R | 20 -- spatialsegregation-2.42/spatialsegregation/R/shannon.R | 37 ++++- spatialsegregation-2.42/spatialsegregation/R/simpson.R | 41 ++++- spatialsegregation-2.42/spatialsegregation/man/biomassF.Rd |only spatialsegregation-2.42/spatialsegregation/man/dixon.Rd |only spatialsegregation-2.42/spatialsegregation/man/isarF.Rd |only spatialsegregation-2.42/spatialsegregation/man/mciF.Rd |only spatialsegregation-2.42/spatialsegregation/man/minglingF.Rd |only spatialsegregation-2.42/spatialsegregation/man/print.segtest.Rd |only spatialsegregation-2.42/spatialsegregation/man/segregationFun.Rd |only spatialsegregation-2.42/spatialsegregation/man/sg.modify.pp.Rd |only spatialsegregation-2.42/spatialsegregation/man/shannonF.Rd |only spatialsegregation-2.42/spatialsegregation/man/simpsonF.Rd |only spatialsegregation-2.42/spatialsegregation/src/Fun.cpp | 4 spatialsegregation-2.42/spatialsegregation/src/Graph.cpp | 15 +- spatialsegregation-2.42/spatialsegregation/src/Pp.cpp | 9 - spatialsegregation-2.42/spatialsegregation/src/biomass.cpp | 12 + 34 files changed, 339 insertions(+), 168 deletions(-)
More information about spatialsegregation at CRAN
Permanent link
Title: MCMC Generalised Linear Mixed Models
Description: MCMC Generalised Linear Mixed Models.
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield <j.hadfield@ed.ac.uk>
Diff between MCMCglmm versions 2.22.1 dated 2016-01-30 and 2.23 dated 2016-10-10
MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-Lsurface.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-MsurfaceMCMC.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-Pmarg.NI.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-Psurface.NI.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-Psurface.flat.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-Psurface.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-Psurface.persp.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-Psurface.persp2.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-PsurfaceMCMC.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-dinvgamma.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-dnorm.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-dnorm1.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-muvar.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-talk.BPMsurface.pdf |only MCMCglmm-2.22.1/MCMCglmm/vignettes/Lecture1-talk.Lsurface.pdf |only 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More information about haploReconstruct at CRAN
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Title: A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations
Description: A fold change rank based method is presented to search for
differentially expressed genes and to detect recurrent chromosomal copy number aberrations.
This method may be useful for high-throughput biological data (microarray, sequencing, ...).
Probabilities are associated with genes/probes in the dataset and there is no problem of
multiple tests when using this method. For aCGH data, segmentation results are obtained by
merging the significant probes detected.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele <doulaye@igbmc.fr>
Diff between fcros versions 1.5 dated 2016-07-01 and 1.5.1 dated 2016-10-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/fcros-package.Rd | 4 ++-- src/fcros.cpp | 12 ++++++------ 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It is best suited to data from a Freesurfer analysis (cortical
thickness, volumes, local gyrification index, surface area), but also works
with e.g., tractography data from FSL. It contains a graphical user
interface for graph visualization and data exploration.
Author: Christopher G. Watson <cgwatson@bu.edu>
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 0.62.0 dated 2016-04-23 and 0.72.0 dated 2016-10-10
DESCRIPTION | 8 MD5 | 212 +++++++++++--------- NAMESPACE | 9 R/NBS.R | 147 ++++++-------- R/SPM.R | 51 ++-- R/analysis_random_graphs.R | 4 R/assign_lobes.R | 48 +++- R/auc_diff.R |only R/boot_global.R | 2 R/brainGraph_init.R | 39 ++- R/centr_lev.R | 13 - R/check_resid.R | 13 - R/cor_diff_test.R |only R/corr_matrix.R | 25 +- R/count_homologous.R | 14 - R/count_interlobar.R | 14 - R/dti_create_mats.R | 77 ++++--- R/edge_asymmetry.R | 18 - R/graph_attr_dt.R | 14 - R/graph_contract_brain.R | 12 - R/graph_efficiency.R | 10 R/individ_contrib.R | 4 R/make_empty_brainGraph.R | 9 R/part_coeff.R | 34 ++- R/permute_group.R | 4 R/permute_group_auc.R |only R/plot_boot.R | 16 - R/plot_brainGraph.R | 309 ++++++++++++++++++++++++++++-- R/plot_brainGraph_gui.R | 52 ++++- R/plot_brainGraph_list.R | 85 -------- R/plot_brainGraph_mni.R | 19 - R/plot_corr_mat.R | 26 +- R/plot_global.R | 35 ++- R/plot_perm_diffs.R | 44 ++-- R/plot_rich_norm.R | 43 ++-- R/plot_vertex_measures.R | 35 +-- R/rich_club_attrs.R |only R/rich_club_coeff.R | 4 R/rich_club_norm.R | 24 +- R/rich_core.R | 14 - R/robustness.R | 4 R/set_brainGraph_attributes.R | 103 ++++------ R/sim_rand_graph_clust.R | 16 - R/sim_rand_graph_par.R | 11 - R/small_world.R | 4 R/spatial_dist.R | 21 -- R/update_brainGraph_gui.R | 398 ++++++++++++--------------------------- R/vec_transform.R | 6 R/vertex_attr_dt.R | 20 + R/vulnerability.R | 12 - R/within_module_degree_z_score.R | 19 + R/write_brainnet.R | 37 ++- data/aal116.rda |binary data/aal2.120.rda |only data/aal2.94.rda |only data/aal90.rda |binary data/brainsuite.rda |binary data/destrieux.rda |binary data/destrieux.scgm.rda |binary data/dk.rda |binary data/dk.scgm.rda |binary data/dkt.rda |binary data/dkt.scgm.rda |binary data/dosenbach160.rda |only data/hoa112.rda |binary data/lpba40.rda |binary man/NBS.Rd | 15 - man/SPM.Rd | 9 man/aal116.Rd | 5 man/aal2.120.Rd |only man/aal2.94.Rd |only man/aal90.Rd | 5 man/assign_lobes.Rd | 2 man/auc_diff.Rd |only man/boot_global.Rd | 2 man/brainGraph_init.Rd | 22 +- man/brainsuite.Rd | 5 man/centr_lev.Rd | 4 man/cor.diff.test.Rd |only man/corr.matrix.Rd | 28 +- man/destrieux.Rd | 5 man/destrieux.scgm.Rd | 5 man/dk.Rd | 6 man/dk.scgm.Rd | 6 man/dkt.Rd | 6 man/dkt.scgm.Rd | 6 man/dosenbach160.Rd |only man/dti_create_mats.Rd | 6 man/edge_asymmetry.Rd | 4 man/graph.contract.brain.Rd | 4 man/graph.efficiency.Rd | 4 man/hoa112.Rd | 5 man/lpba40.Rd | 5 man/part.coeff.Rd | 5 man/permute.group.auc.Rd |only man/plot_boot.Rd | 1 man/plot_brainGraph.Rd | 56 ++++- man/plot_brainGraph_list.Rd | 24 -- man/plot_brainGraph_mni.Rd | 10 man/plot_corr_mat.Rd | 6 man/plot_global.Rd | 8 man/plot_perm_diffs.Rd | 7 man/plot_rich_norm.Rd | 9 man/plot_vertex_measures.Rd | 21 +- man/rich.club.attrs.Rd |only man/rich.club.norm.Rd | 16 - man/rich.core.Rd | 4 man/set.brainGraph.attributes.Rd | 5 man/sim.rand.graph.clust.Rd | 5 man/update_brainGraph_gui.Rd | 4 man/vertex_attr_dt.Rd | 7 man/vulnerability.Rd | 4 man/within_module_deg_z_score.Rd | 5 man/write.brainnet.Rd | 24 +- 114 files changed, 1379 insertions(+), 1139 deletions(-)
Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Description: Scrapes various data from the Bureau of Labor Statistics, which is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>
Diff between blscrapeR versions 1.0.1 dated 2016-10-03 and 1.0.2 dated 2016-10-10
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 8 ++++++++ R/get_bls_state.R | 4 ++-- R/qcew_api.R | 2 +- inst/doc/Employment_and_Unemployment.html | 4 ++-- inst/doc/Inflation_and_Prices.html | 4 ++-- inst/doc/Mapping_BLS_Data.html | 4 ++-- inst/doc/Pay_and_Benefits.html | 4 ++-- inst/doc/QCEW_API.html | 4 ++-- inst/doc/qcew.html | 4 ++-- tests/testthat/test_bls_csv.R | 2 +- 12 files changed, 38 insertions(+), 30 deletions(-)
Title: Fast Multivariate Normal and Student's t Methods
Description: Provides computationally efficient tools related to
the multivariate normal and Student's t distributions. The main functionalities are:
simulating multivariate random vectors, evaluating multivariate
normal or Student's t densities and Mahalanobis distances. These tools are very efficient
thanks to the use of C++ code and of the OpenMP API.
Author: Matteo Fasiolo, using the C++ parallel RNG of Thijs van den Berg and
Ziggurat algorithm of Jens Maurer and Steven Watanabe (boost)
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between mvnfast versions 0.1.6 dated 2016-10-09 and 0.1.7 dated 2016-10-10
DESCRIPTION | 8 ++-- MD5 | 16 ++++----- R/dmvt.R | 12 ++++++- R/rmvt.R | 4 +- inst/CITATION | 2 - inst/doc/mvnfast.html | 82 ++++++++++++++++++++++++------------------------- inst/tests/test-dmvt.R | 3 - man/dmvt.Rd | 4 +- man/rmvt.Rd | 4 +- 9 files changed, 72 insertions(+), 63 deletions(-)
Title: A Collection of Functions Related to Item Response Theory (IRT)
Description: A collection of functions useful in learning and practicing IRT,
which can be combined into larger programs. Provides basic CTT analysis,
a simple common interface to the estimation of item
parameters in IRT models for binary responses with three different programs
(ICL, BILOG-MG, and ltm), ability estimation (MLE, BME, EAP, WLE, plausible
values), item and person fit statistics, scaling methods (MM, MS, Stocking-Lord,
and the complete Hebaera method), and a rich array of parametric and
non-parametric (kernel) plots. Estimates and plots Haberman's interaction model
when all items are dichotomously scored.
Author: Ivailo Partchev
Maintainer: Ivailo Partchev <partchev@gmail.com>
Diff between irtoys versions 0.1.7 dated 2014-01-22 and 0.2.0 dated 2016-10-10
irtoys-0.1.7/irtoys/README |only irtoys-0.1.7/irtoys/man/tgp.Rd |only irtoys-0.2.0/irtoys/DESCRIPTION | 27 irtoys-0.2.0/irtoys/MD5 | 119 ++- irtoys-0.2.0/irtoys/NAMESPACE | 41 - irtoys-0.2.0/irtoys/NEWS | 14 irtoys-0.2.0/irtoys/R/ability.R | 74 +- irtoys-0.2.0/irtoys/R/estimate.R | 551 +++++++++--------- irtoys-0.2.0/irtoys/R/interaction.R |only irtoys-0.2.0/irtoys/R/irtoys-package.R | 278 +++++---- irtoys-0.2.0/irtoys/R/itemfit.R | 395 ++++++------- irtoys-0.2.0/irtoys/R/nonpar.R | 389 +++++++----- irtoys-0.2.0/irtoys/R/readin.R | 240 ++++--- irtoys-0.2.0/irtoys/R/scale.R | 328 +++++----- irtoys-0.2.0/irtoys/R/tracelines.R | 850 ++++++++++++++-------------- irtoys-0.2.0/irtoys/R/utils.R | 13 irtoys-0.2.0/irtoys/build |only irtoys-0.2.0/irtoys/data/b1.RData |only irtoys-0.2.0/irtoys/data/b2.RData |only irtoys-0.2.0/irtoys/data/b3.RData |only irtoys-0.2.0/irtoys/inst |only irtoys-0.2.0/irtoys/man/Scored.Rd | 6 irtoys-0.2.0/irtoys/man/Scored2pl.Rd | 12 irtoys-0.2.0/irtoys/man/Unscored.Rd | 11 irtoys-0.2.0/irtoys/man/ability.Rd |only irtoys-0.2.0/irtoys/man/api.Rd | 41 - irtoys-0.2.0/irtoys/man/b1.Rd |only irtoys-0.2.0/irtoys/man/b2.Rd |only irtoys-0.2.0/irtoys/man/b3.Rd |only irtoys-0.2.0/irtoys/man/dpv.Rd | 44 - irtoys-0.2.0/irtoys/man/eap.Rd | 38 - irtoys-0.2.0/irtoys/man/erf.Rd |only irtoys-0.2.0/irtoys/man/est.Rd | 264 ++++---- irtoys-0.2.0/irtoys/man/iif.Rd | 52 - irtoys-0.2.0/irtoys/man/interactionModel.Rd |only irtoys-0.2.0/irtoys/man/irf.Rd | 65 +- irtoys-0.2.0/irtoys/man/irfPlot.Rd |only irtoys-0.2.0/irtoys/man/irtoys-package.Rd | 139 ++-- irtoys-0.2.0/irtoys/man/itf.Rd | 190 ++---- irtoys-0.2.0/irtoys/man/mlebme.Rd | 53 - irtoys-0.2.0/irtoys/man/normal.qu.Rd | 43 - irtoys-0.2.0/irtoys/man/npp.Rd | 76 +- irtoys-0.2.0/irtoys/man/plot.iif.Rd | 42 - irtoys-0.2.0/irtoys/man/plot.imp.Rd |only irtoys-0.2.0/irtoys/man/plot.irf.Rd | 42 - irtoys-0.2.0/irtoys/man/plot.tif.Rd | 35 - irtoys-0.2.0/irtoys/man/plot.trf.Rd | 35 - irtoys-0.2.0/irtoys/man/qrs.Rd | 30 irtoys-0.2.0/irtoys/man/read.ip.bilog.Rd | 31 - irtoys-0.2.0/irtoys/man/read.ip.icl.Rd | 35 - irtoys-0.2.0/irtoys/man/read.qu.icl.Rd | 26 irtoys-0.2.0/irtoys/man/read.resp.Rd | 57 - irtoys-0.2.0/irtoys/man/rim.Rd |only irtoys-0.2.0/irtoys/man/sca.Rd | 85 +- irtoys-0.2.0/irtoys/man/sco.Rd | 30 irtoys-0.2.0/irtoys/man/scoreMetric.Rd |only irtoys-0.2.0/irtoys/man/scp.Rd | 40 - irtoys-0.2.0/irtoys/man/sim.Rd | 24 irtoys-0.2.0/irtoys/man/tet.Rd | 30 irtoys-0.2.0/irtoys/man/tgf.Rd |only irtoys-0.2.0/irtoys/man/tia.Rd | 48 - irtoys-0.2.0/irtoys/man/tif.Rd | 42 - irtoys-0.2.0/irtoys/man/trf.Rd | 40 - irtoys-0.2.0/irtoys/man/tsc.Rd | 36 - irtoys-0.2.0/irtoys/man/wle.Rd | 40 - irtoys-0.2.0/irtoys/src |only irtoys-0.2.0/irtoys/vignettes |only 67 files changed, 2708 insertions(+), 2393 deletions(-)
Title: Analysis of Diffusion Weighted Imaging (DWI) Data
Description: Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging
modality, that measures diffusion of water in tissues like the human
brain. The package contains R-functions to process diffusion-weighted
data. The functionality includes diffusion tensor imaging (DTI),
diffusion kurtosis imaging (DKI), modeling for high angular resolution
diffusion weighted imaging (HARDI) using Q-ball-reconstruction and
tensor mixture models, several methods for structural adaptive
smoothing including POAS and msPOAS, and a streamline fiber tracking
for tensor and tensor mixture models.
The package provides functionality to manipulate and visualize results
in 2D and 3D.
Author: Karsten Tabelow [aut, cre],
Joerg Polzehl [aut],
Felix Anker [ctb]
Maintainer: Karsten Tabelow <karsten.tabelow@wias-berlin.de>
Diff between dti versions 1.2-6 dated 2016-09-14 and 1.2-6.1 dated 2016-10-10
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- src/Converter.cpp | 77 ++++++++++++++++++++++++------------------- src/Converter.h | 50 ++++++++++++++++++++++++++-- src/Fiber.cpp | 22 +++--------- src/Fiber.h | 68 ++++++++++++++++++++++++++++++++------ src/Fibertracking.cpp | 38 ++++++--------------- src/Vector.h | 1 src/Voxel.cpp | 20 ----------- src/Voxel.h | 89 +++++++++++++++++++++++++++++++++++++++++--------- 10 files changed, 256 insertions(+), 135 deletions(-)
Title: Correlations in R
Description: A tool for exploring correlations.
It makes it possible to easily perform routine tasks when
exploring correlation matrices such as ignoring the diagonal,
focusing on the correlations of certain variables against others,
or rearranging and visualising the matrix in terms of the
strength of the correlations.
Author: Simon Jackson [aut, cre]
Maintainer: Simon Jackson <drsimonjackson@gmail.com>
Diff between corrr versions 0.2.0 dated 2016-08-11 and 0.2.1 dated 2016-10-10
DESCRIPTION | 6 +- MD5 | 26 +++++----- R/cor_df.R | 100 +++++++++++++++++++++++++----------------- R/correlate.R | 2 R/dataframe.R | 7 ++ R/matrix.R | 4 - R/output.R | 55 ++++++++++++++++++----- README.md | 10 +--- inst/doc/using-corrr.html | 18 +++---- man/correlate.Rd | 2 man/fashion.Rd | 17 ++++++- man/network_plot.Rd | 10 +++- man/rplot.Rd | 14 ++++- tests/testthat/test-fashion.R | 27 ++++++++++- 14 files changed, 200 insertions(+), 98 deletions(-)
Title: Analysis and Visualisation of Ecological Communities
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson <quicklizard@googlemail.com>
Diff between cheddar versions 0.1-630 dated 2015-08-24 and 0.1-631 dated 2016-10-10
DESCRIPTION | 8 +- LICENSE | 2 MD5 | 22 +++---- inst/doc/CheddarQuickstart.pdf |binary inst/doc/Collections.pdf |binary inst/doc/Community.pdf |binary inst/doc/ImportExport.pdf |binary inst/doc/PlotsAndStats.pdf |binary man/cheddar.Rd | 20 +++--- src/anneal.cpp | 123 ++++++++++++++++++++--------------------- src/shortest_paths.cpp | 61 ++++---------------- src/trophic_chains.cpp | 115 +------------------------------------- 12 files changed, 105 insertions(+), 246 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 1.1 dated 2016-09-26 and 1.1.1 dated 2016-10-10
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/auxilaryfunctions.R | 44 ++++++++++++++++++++++++++------------------ R/boral.jags.R | 18 +++++++++++------- R/unseenfunctions.R | 8 ++++---- man/coefsplot.Rd | 7 +------ man/create.life.Rd | 2 +- man/get.more.measures.Rd | 4 ++-- 8 files changed, 56 insertions(+), 49 deletions(-)
Title: Interpolate Data for Smooth Animations
Description: In order to create smooth animation between states of data,
tweening is necessary. This package provides a range of functions for
creating tweened data that plugs right into functions such as gg_animate()
from the 'gganimate' package. Furthermore it adds a number of vectorized
interpolaters for common R data types such as numeric, date and colour.
Author: Thomas Lin Pedersen [aut, cre]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between tweenr versions 0.1.4 dated 2016-08-30 and 0.1.5 dated 2016-10-10
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------- R/RcppExports.R | 2 - R/interpolate.R | 12 ++++++++--- R/tween.R | 8 +++++-- README.md | 4 +-- src/RcppExports.cpp | 50 +++++++++++++++++++++++------------------------ src/stateInterpolate.cpp | 6 ++++- 8 files changed, 59 insertions(+), 45 deletions(-)
Title: 'stats' for Seasonal Adjustment on the Fly with 'ggplot2'
Description: Provides 'ggplot2' 'stats' that estimate seasonally adjusted series
and rolling summaries such as rolling average on the fly for time series.
Author: Peter Ellis [aut, cre],
Christophe Sax [ctb]
Maintainer: Peter Ellis <peter.ellis2013nz@gmail.com>
Diff between ggseas versions 0.4.0 dated 2016-03-27 and 0.5.0 dated 2016-10-10
DESCRIPTION | 9 +++++---- MD5 | 11 ++++++++--- R/ggsdc.R | 34 +++++++++++++++++++++------------- build |only inst |only man/ggsdc.Rd | 6 +++++- vignettes |only 7 files changed, 39 insertions(+), 21 deletions(-)
Title: Tools for Interacting with 'PostgreSQL' / 'PostGIS' Databases
Description: Functions to convert geometry and 'hstore' data types from
'PostgreSQL' into standard R objects, as well as to simplify
the import of R data frames (including spatial data frames) into 'PostgreSQL'.
Author: Philippe Marchand [aut, cre],
Richard Ellison [aut]
Maintainer: Philippe Marchand <pmarchand@sesync.org>
Diff between postGIStools versions 0.2.0 dated 2016-08-29 and 0.2.1 dated 2016-10-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/postgis_insert_update.R | 2 +- tests/testthat/test_insert_update.R | 29 ++++++++++++++++++++++++++++- 5 files changed, 43 insertions(+), 9 deletions(-)
Title: Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken - Nonparametric Statistical Methods, Third Edition
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider, Eric Chicken, Rachel Becvarik
Maintainer: Grant Schneider <schneider.393@osu.edu>
Diff between NSM3 versions 1.7 dated 2016-09-07 and 1.8 dated 2016-10-10
DESCRIPTION | 8 - MD5 | 4 R/theil.R | 272 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 142 insertions(+), 142 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an
abstraction for a value that may be available at some point in the future.
The state of a future can either be unresolved or resolved. As soon as it
is resolved, the value is available. Futures are useful constructs in for
instance concurrent evaluation, e.g. parallel processing and distributed
processing on compute clusters. The purpose of this package is to provide
a lightweight interface for using futures in R. Functions 'future()' and
'value()' exist for creating futures and requesting their values, e.g.
'f <- future({ mandelbrot(-0.75, 0, side=3) })' and 'v <- value(f)'. The
'resolved()' function can be used to check if a future is resolved or
not. An infix assignment operator '%<-%' exists for creating futures whose
values are accessible by the assigned variables (as promises), e.g. 'v %<-%
{ mandelbrot(-0.75, 0, side=3) }'. This package implements synchronous "lazy"
and "eager" futures, and asynchronous "multicore", "multisession" and ad hoc
"cluster" futures. Globals variables and functions are automatically identified
and exported. Required packages are attached in external R sessions whenever
needed. All types of futures are designed to behave the same such that the
exact same code work regardless of futures used or number of cores, background
sessions or cluster nodes available. Additional types of futures are provided by
other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.0.1 dated 2016-07-04 and 1.1.0 dated 2016-10-10
future-1.0.1/future/man/futureAssign.Rd |only future-1.1.0/future/DESCRIPTION | 46 +- future-1.1.0/future/MD5 | 180 +++++---- future-1.1.0/future/NAMESPACE | 12 future-1.1.0/future/NEWS | 39 ++ future-1.1.0/future/R/ClusterFuture-class.R | 70 ++- future-1.1.0/future/R/ClusterRegistry.R | 34 + future-1.1.0/future/R/ConstantFuture-class.R | 10 future-1.1.0/future/R/EagerFuture-class.R | 32 + future-1.1.0/future/R/Future-class.R | 200 ++++++---- future-1.1.0/future/R/LazyFuture-class.R | 44 +- future-1.1.0/future/R/MulticoreFuture-class.R | 36 + future-1.1.0/future/R/MultiprocessFuture-class.R | 12 future-1.1.0/future/R/MultisessionFuture-class.R | 6 future-1.1.0/future/R/UniprocessFuture-class.R | 20 - future-1.1.0/future/R/availableCores.R | 13 future-1.1.0/future/R/cluster.R | 26 - future-1.1.0/future/R/constant.R | 3 future-1.1.0/future/R/eager.R | 33 - future-1.1.0/future/R/flapply.R | 45 +- future-1.1.0/future/R/future.R | 180 ++++++++- future-1.1.0/future/R/futureAssign.R | 51 -- future-1.1.0/future/R/futureAssign_OP.R | 36 + future-1.1.0/future/R/futureCall.R | 8 future-1.1.0/future/R/futures.R | 4 future-1.1.0/future/R/globals.R | 137 ++++--- future-1.1.0/future/R/globals_OP.R |only future-1.1.0/future/R/label_OP.R |only future-1.1.0/future/R/lazy.R | 34 - future-1.1.0/future/R/multicore.R | 29 - future-1.1.0/future/R/multiprocess.R | 28 - future-1.1.0/future/R/multisession.R | 22 - future-1.1.0/future/R/nbrOfWorkers.R | 4 future-1.1.0/future/R/plan_OP.R | 2 future-1.1.0/future/R/remote.R | 30 - future-1.1.0/future/R/resolve.R | 2 future-1.1.0/future/R/tweak.R | 2 future-1.1.0/future/R/tweakExpression.R | 141 ++++++- future-1.1.0/future/R/tweak_OP.R | 2 future-1.1.0/future/R/tweak_parallel_PSOCK.R |only future-1.1.0/future/R/utils.R | 4 future-1.1.0/future/R/values.R | 2 future-1.1.0/future/build/vignette.rds |binary future-1.1.0/future/demo/mandelbrot.R | 3 future-1.1.0/future/inst/doc/future-1-overview.html | 92 ++--- future-1.1.0/future/inst/doc/future-2-issues.html | 116 ++---- future-1.1.0/future/inst/doc/future-2-issues.md.rsp | 190 ++-------- future-1.1.0/future/inst/doc/future-3-topologies.html | 10 future-1.1.0/future/inst/doc/future-3-topologies.md.rsp | 14 future-1.1.0/future/inst/doc/future-4-startup.html |only future-1.1.0/future/inst/doc/future-4-startup.md.rsp |only future-1.1.0/future/man/ClusterFuture-class.Rd | 39 +- future-1.1.0/future/man/ConstantFuture-class.Rd | 18 future-1.1.0/future/man/EagerFuture-class.Rd | 18 future-1.1.0/future/man/Future-class.Rd | 12 future-1.1.0/future/man/LazyFuture-class.Rd | 18 future-1.1.0/future/man/MulticoreFuture-class.Rd | 12 future-1.1.0/future/man/MultiprocessFuture-class.Rd | 9 future-1.1.0/future/man/UniprocessFuture-class.Rd | 4 future-1.1.0/future/man/availableCores.Rd | 15 future-1.1.0/future/man/cluster.Rd | 44 +- future-1.1.0/future/man/eager.Rd | 29 - future-1.1.0/future/man/flapply.Rd |only future-1.1.0/future/man/future.Rd | 274 +++++++++++++-- future-1.1.0/future/man/futures.Rd | 4 future-1.1.0/future/man/getExpression.Rd | 2 future-1.1.0/future/man/getGlobalsAndPackages.Rd |only future-1.1.0/future/man/grapes-globals-grapes.Rd |only future-1.1.0/future/man/grapes-label-grapes.Rd |only future-1.1.0/future/man/grapes-plan-grapes.Rd | 2 future-1.1.0/future/man/grapes-tweak-grapes.Rd | 2 future-1.1.0/future/man/lazy.Rd | 21 - future-1.1.0/future/man/multicore.Rd | 31 - future-1.1.0/future/man/multiprocess.Rd | 29 - future-1.1.0/future/man/multisession.Rd | 31 + future-1.1.0/future/man/nbrOfWorkers.Rd | 14 future-1.1.0/future/man/remote.Rd | 42 +- future-1.1.0/future/man/resolve.Rd | 2 future-1.1.0/future/man/run.Rd |only future-1.1.0/future/man/tweak.Rd | 6 future-1.1.0/future/man/tweak_parallel_PSOCK.Rd |only future-1.1.0/future/man/values.Rd | 2 future-1.1.0/future/tests/ClusterRegistry.R | 12 future-1.1.0/future/tests/Future-class.R | 25 + future-1.1.0/future/tests/early-signaling.R | 10 future-1.1.0/future/tests/future,labels.R |only future-1.1.0/future/tests/globals,formulas.R |only future-1.1.0/future/tests/globals,manual.R |only future-1.1.0/future/tests/globals,subassignment.R |only future-1.1.0/future/tests/incl/end.R | 3 future-1.1.0/future/tests/incl/start,load-only.R | 5 future-1.1.0/future/tests/multicore.R | 2 future-1.1.0/future/tests/multisession.R | 25 + future-1.1.0/future/tests/nested_futures.R |only future-1.1.0/future/tests/rng.R | 5 future-1.1.0/future/tests/tweak.R | 16 future-1.1.0/future/tests/utils.R | 10 future-1.1.0/future/vignettes/future-2-issues.md.rsp | 190 ++-------- future-1.1.0/future/vignettes/future-3-topologies.md.rsp | 14 future-1.1.0/future/vignettes/future-4-startup.md.rsp |only 100 files changed, 1783 insertions(+), 1218 deletions(-)
Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function
and random generation for a number of univariate
and multivariate distributions. This package implements the
following distributions: Bernoulli, beta-binomial, beta-negative
binomial, beta prime, Bhattacharjee, Birnbaum-Saunders,
bivariate normal, bivariate Poisson, categorical, Dirichlet,
Dirichlet-multinomial, discrete Laplace, discrete normal,
discrete uniform, discrete Weibull, Frechet, gamma-Poisson,
generalized extreme value, Gompertz, generalized Pareto,
Gumbel, half-Cauchy, half-normal, half-t, Huber density,
inverse chi-squared, inverse-gamma, Kumaraswamy, Laplace,
logarithmic, Lomax, multivariate hypergeometric, multinomial,
non-standard t, non-standard beta, normal mixture,
Poisson mixture, Pareto, power, reparametrized beta,
Rayleigh, Skellam, slash, triangular, truncated normal,
truncated Poisson, Tukey lambda, Wald, zero-inflated binomial,
zero-inflated negative binomial, zero-inflated Poisson.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>
Diff between extraDistr versions 1.8.1 dated 2016-07-29 and 1.8.2 dated 2016-10-10
extraDistr-1.8.1/extraDistr/man/DiscrWeibull.Rd |only extraDistr-1.8.2/extraDistr/DESCRIPTION | 25 extraDistr-1.8.2/extraDistr/MD5 | 228 - extraDistr-1.8.2/extraDistr/NAMESPACE | 2 extraDistr-1.8.2/extraDistr/NEWS.md | 13 extraDistr-1.8.2/extraDistr/R/RcppExports.R | 10 extraDistr-1.8.2/extraDistr/R/bernoulli-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/beta-binomial-distribution.R | 6 extraDistr-1.8.2/extraDistr/R/beta-negative-binomial-distribution.R | 6 extraDistr-1.8.2/extraDistr/R/beta-prime-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/bhattacharjee-distribution.R | 6 extraDistr-1.8.2/extraDistr/R/birnbaum-saunders-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/bivariate-normal-distribution.R | 4 extraDistr-1.8.2/extraDistr/R/bivariate-poisson-distribution.R | 4 extraDistr-1.8.2/extraDistr/R/categorical-distribution.R | 18 extraDistr-1.8.2/extraDistr/R/dirichlet-distribution.R | 4 extraDistr-1.8.2/extraDistr/R/dirichlet-multinomial-distribution.R | 4 extraDistr-1.8.2/extraDistr/R/discrete-laplace-distribution.R | 6 extraDistr-1.8.2/extraDistr/R/discrete-normal-distribution.R | 2 extraDistr-1.8.2/extraDistr/R/discrete-uniform-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/discrete-weibull-distribution.R | 18 extraDistr-1.8.2/extraDistr/R/frechet-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/gamma-poisson-distribution.R | 6 extraDistr-1.8.2/extraDistr/R/gev-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/gompertz-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/gpd-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/gumbel-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/half-cauchy-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/half-normal-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/half-t-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/huber-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/inverse-gamma-distribution.R | 2 extraDistr-1.8.2/extraDistr/R/kumaraswamy-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/laplace-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/logarithmic-series-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/lomax-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/mixture-of-normal-distributions.R | 6 extraDistr-1.8.2/extraDistr/R/mixture-of-poisson-distributions.R | 6 extraDistr-1.8.2/extraDistr/R/multinomial-distribution.R | 4 extraDistr-1.8.2/extraDistr/R/multivariate-hypergeometric-distribution.R | 16 extraDistr-1.8.2/extraDistr/R/non-standard-beta-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/non-standard-t-distribution.R | 28 extraDistr-1.8.2/extraDistr/R/pareto-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/power-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/proportion-distribution.R | 54 extraDistr-1.8.2/extraDistr/R/rayleigh-distribution.R | 8 extraDistr-1.8.2/extraDistr/R/skellam-distribution.R | 4 extraDistr-1.8.2/extraDistr/R/slash-distribution.R | 6 extraDistr-1.8.2/extraDistr/R/triangular-distribution.R | 10 extraDistr-1.8.2/extraDistr/R/truncated-normal-distribution.R | 47 extraDistr-1.8.2/extraDistr/R/truncated-poisson-distributtion.R | 8 extraDistr-1.8.2/extraDistr/R/tuckey-lambda-distribution.R |only extraDistr-1.8.2/extraDistr/R/wald-distribution.R | 6 extraDistr-1.8.2/extraDistr/R/zero-inflated-binomial-distribution.R | 9 extraDistr-1.8.2/extraDistr/R/zero-inflated-negative-binomial-distribution.R | 9 extraDistr-1.8.2/extraDistr/R/zero-inflated-poisson-distribution.R | 10 extraDistr-1.8.2/extraDistr/man/DiscreteWeibull.Rd |only extraDistr-1.8.2/extraDistr/man/PropBeta.Rd | 46 extraDistr-1.8.2/extraDistr/man/Triangular.Rd | 2 extraDistr-1.8.2/extraDistr/man/TruncNormal.Rd | 39 extraDistr-1.8.2/extraDistr/man/TuckeyLambda.Rd |only extraDistr-1.8.2/extraDistr/src/RcppExports.cpp | 1364 +++++----- extraDistr-1.8.2/extraDistr/src/bernoulli-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/beta-binomial-distribution.cpp | 19 extraDistr-1.8.2/extraDistr/src/beta-negative-binomial-distribution.cpp | 21 extraDistr-1.8.2/extraDistr/src/beta-prime-distribution.cpp | 10 extraDistr-1.8.2/extraDistr/src/bhattacharjee-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/birnbaum-saunders-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/bivariate-normal-distribution.cpp | 11 extraDistr-1.8.2/extraDistr/src/bivariate-poisson-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/categorical-distribution.cpp | 133 extraDistr-1.8.2/extraDistr/src/dirichlet-distribution.cpp | 37 extraDistr-1.8.2/extraDistr/src/dirichlet-multinomial-distribution.cpp | 61 extraDistr-1.8.2/extraDistr/src/discrete-laplace-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/discrete-normal-distribution.cpp | 2 extraDistr-1.8.2/extraDistr/src/discrete-uniform-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/discrete-weibull-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/frechet-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/gamma-poisson-distribution.cpp | 17 extraDistr-1.8.2/extraDistr/src/gev-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/gompertz-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/gpd-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/gumbel-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/half-cauchy-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/half-normal-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/half-t-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/huber-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/inverse-gamma-distribution.cpp | 2 extraDistr-1.8.2/extraDistr/src/kumaraswamy-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/laplace-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/logarithmic-series-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/lomax-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/mixture-of-normal-distributions.cpp | 100 extraDistr-1.8.2/extraDistr/src/mixture-of-poisson-distributions.cpp | 96 extraDistr-1.8.2/extraDistr/src/multinomial-distribution.cpp | 86 extraDistr-1.8.2/extraDistr/src/multivariate-hypergeometric-distribution.cpp | 40 extraDistr-1.8.2/extraDistr/src/non-standard-t-distribution.cpp | 16 extraDistr-1.8.2/extraDistr/src/non-standart-beta-distribution.cpp | 23 extraDistr-1.8.2/extraDistr/src/pareto-distribution.cpp | 10 extraDistr-1.8.2/extraDistr/src/power-distribution.cpp | 10 extraDistr-1.8.2/extraDistr/src/proportion-distribution.cpp | 23 extraDistr-1.8.2/extraDistr/src/rayleigh-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/shared.cpp | 50 extraDistr-1.8.2/extraDistr/src/shared.h | 7 extraDistr-1.8.2/extraDistr/src/skellam-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/slash-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/triangular-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/truncated-normal-distribution.cpp | 62 extraDistr-1.8.2/extraDistr/src/truncated-poisson-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/tuckey-lambda-distribution.cpp |only extraDistr-1.8.2/extraDistr/src/wald-distribution.cpp | 6 extraDistr-1.8.2/extraDistr/src/zero-inflated-binomial-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/zero-inflated-negative-binomial-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/src/zero-inflated-poisson-distribution.cpp | 8 extraDistr-1.8.2/extraDistr/tests/testthat/test-NAs.R |only extraDistr-1.8.2/extraDistr/tests/testthat/test-discrete.R | 2 extraDistr-1.8.2/extraDistr/tests/testthat/test-inappropriate-parameters.R | 195 - extraDistr-1.8.2/extraDistr/tests/testthat/test-quantile-functions.R | 31 118 files changed, 2040 insertions(+), 1436 deletions(-)
Title: Testing Generalized Linear Hypotheses for Generalized Linear
Model Parameters by Profile Deviance
Description: Calculation of signed root deviance profiles for linear combinations of parameters in a generalized linear model. Multiple tests and simultaneous confidence intervals are provided.
Author: Daniel Gerhard
Maintainer: Daniel Gerhard <00gerhard@gmail.com>
Diff between mcprofile versions 0.2-1 dated 2014-11-16 and 0.2-3 dated 2016-10-09
DESCRIPTION | 11 ++++---- MD5 | 12 ++++---- NAMESPACE | 6 +++- R/methods.R | 2 - build/vignette.rds |binary inst/doc/mcprofile.R | 2 - inst/doc/mcprofile.html | 66 ++++++++++++++++++++++++------------------------ 7 files changed, 52 insertions(+), 47 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.2.0.1 dated 2016-07-27 and 1.2.1 dated 2016-10-09
ddalpha-1.2.0.1/ddalpha/man/plotf.Rd |only ddalpha-1.2.1/ddalpha/DESCRIPTION | 10 ddalpha-1.2.1/ddalpha/MD5 | 123 ++++----- ddalpha-1.2.1/ddalpha/NAMESPACE | 18 + ddalpha-1.2.1/ddalpha/R/compclassf.r | 20 - ddalpha-1.2.1/ddalpha/R/dataf.geneexp.r | 2 ddalpha-1.2.1/ddalpha/R/dataf.growth.r | 2 ddalpha-1.2.1/ddalpha/R/dataf.medflies.r | 2 ddalpha-1.2.1/ddalpha/R/dataf.sim.r | 32 +- ddalpha-1.2.1/ddalpha/R/dataf.tecator.r | 3 ddalpha-1.2.1/ddalpha/R/ddalpha-internal.r | 190 +++++++++++++- ddalpha-1.2.1/ddalpha/R/ddalpha.classify.r | 18 + ddalpha-1.2.1/ddalpha/R/ddalpha.test.r | 2 ddalpha-1.2.1/ddalpha/R/ddalpha.train.r | 33 +- ddalpha-1.2.1/ddalpha/R/ddalphaf.r | 41 +-- ddalpha-1.2.1/ddalpha/R/depth.contours.r | 56 ++-- ddalpha-1.2.1/ddalpha/R/depth.r |only ddalpha-1.2.1/ddalpha/R/draw.ddplot.r | 25 + ddalpha-1.2.1/ddalpha/R/routines.r | 31 ++ ddalpha-1.2.1/ddalpha/inst/CITATION | 35 -- ddalpha-1.2.1/ddalpha/man/CustomMethods.Rd | 2 ddalpha-1.2.1/ddalpha/man/compclassf.classify.Rd | 15 - ddalpha-1.2.1/ddalpha/man/compclassf.train.Rd | 4 ddalpha-1.2.1/ddalpha/man/dataf..Rd | 4 ddalpha-1.2.1/ddalpha/man/dataf.geneexp.Rd | 4 ddalpha-1.2.1/ddalpha/man/dataf.growth.Rd | 4 ddalpha-1.2.1/ddalpha/man/dataf.medflies.Rd | 4 ddalpha-1.2.1/ddalpha/man/dataf.sim.1.CFF07.Rd | 6 ddalpha-1.2.1/ddalpha/man/dataf.sim.2.CFF07.Rd | 6 ddalpha-1.2.1/ddalpha/man/dataf.tecator.Rd | 6 ddalpha-1.2.1/ddalpha/man/ddalpha-package.Rd | 29 +- ddalpha-1.2.1/ddalpha/man/ddalpha.classify.Rd | 26 + ddalpha-1.2.1/ddalpha/man/ddalpha.train.Rd | 48 ++- ddalpha-1.2.1/ddalpha/man/ddalphaf.classify.Rd | 17 - ddalpha-1.2.1/ddalpha/man/ddalphaf.train.Rd | 4 ddalpha-1.2.1/ddalpha/man/depth..Rd | 14 - ddalpha-1.2.1/ddalpha/man/depth.Mahalanobis.Rd | 12 ddalpha-1.2.1/ddalpha/man/depth.contours.Rd | 6 ddalpha-1.2.1/ddalpha/man/depth.contours.ddalpha.Rd | 10 ddalpha-1.2.1/ddalpha/man/depth.graph.Rd | 4 ddalpha-1.2.1/ddalpha/man/depth.halfspace.Rd | 8 ddalpha-1.2.1/ddalpha/man/depth.potential.Rd | 4 ddalpha-1.2.1/ddalpha/man/depth.projection.Rd | 15 - ddalpha-1.2.1/ddalpha/man/depth.simplicial.Rd | 5 ddalpha-1.2.1/ddalpha/man/depth.simplicialVolume.Rd | 4 ddalpha-1.2.1/ddalpha/man/depth.space..Rd | 14 - ddalpha-1.2.1/ddalpha/man/depth.space.Mahalanobis.Rd | 11 ddalpha-1.2.1/ddalpha/man/depth.space.halfspace.Rd | 8 ddalpha-1.2.1/ddalpha/man/depth.space.potential.Rd | 4 ddalpha-1.2.1/ddalpha/man/depth.space.projection.Rd | 15 - ddalpha-1.2.1/ddalpha/man/depth.space.simplicial.Rd | 5 ddalpha-1.2.1/ddalpha/man/depth.space.simplicialVolume.Rd | 4 ddalpha-1.2.1/ddalpha/man/depth.space.spatial.Rd | 9 ddalpha-1.2.1/ddalpha/man/depth.space.zonoid.Rd | 8 ddalpha-1.2.1/ddalpha/man/depth.spatial.Rd | 9 ddalpha-1.2.1/ddalpha/man/depth.zonoid.Rd | 6 ddalpha-1.2.1/ddalpha/man/dknn.classify.Rd | 2 ddalpha-1.2.1/ddalpha/man/dknn.classify.trained.Rd | 2 ddalpha-1.2.1/ddalpha/man/dknn.train.Rd | 2 ddalpha-1.2.1/ddalpha/man/draw.ddplot.Rd | 8 ddalpha-1.2.1/ddalpha/man/getdata.Rd | 16 - ddalpha-1.2.1/ddalpha/man/is.in.convex.Rd | 2 ddalpha-1.2.1/ddalpha/man/plot.ddalpha.Rd |only ddalpha-1.2.1/ddalpha/man/plot.ddalphaf.Rd |only ddalpha-1.2.1/ddalpha/man/plot.functional.Rd |only 65 files changed, 671 insertions(+), 358 deletions(-)
Title: Velocity and Accuracy of the LOg-RAnk TEst
Description: The algorithm implemented in this package was
designed to quickly estimates the distribution of the
log-rank especially for heavy unbalanced groups. VALORATE
estimates the null distribution and the p-value of the
log-rank test based on a recent formulation. For a given
number of alterations that define the size of survival
groups, the estimation involves a weighted sum of
distributions that are conditional on a co-occurrence term
where mutations and events are both present. The estimation
of conditional distributions is quite fast allowing the
analysis of large datasets in few minutes
<http://bioinformatica.mty.itesm.mx/valorate>.
Author: Victor Trevino [aut, cre]
Maintainer: Victor Trevino <vtrevino@itesm.mx>
Diff between valorate versions 1.0-0 dated 2016-10-02 and 1.0-1 dated 2016-10-09
DESCRIPTION | 8 ++-- MD5 | 24 ++++++------- R/valorate.R | 55 +++++++++++++++++++++----------- man/New_Valorate.Rd | 11 ++++-- man/prepare.n1.Rd | 2 - man/valorate.p.value.Rd | 2 - man/valorate.plot.empirical.Rd | 2 - man/valorate.plot.kaplan.Rd | 2 - man/valorate.plot.sampling.densities.Rd | 7 ++-- man/valorate.plot.subpop.Rd | 2 - man/valorate.risk.Rd | 2 - man/valorate.survdiff.Rd | 2 - src/valorate_samplings.c | 27 ++++++++++++--- 13 files changed, 93 insertions(+), 53 deletions(-)
Title: Fast Bayesian Methods for AB Testing
Description: A suite of functions that allow the user to analyze A/B test
data in a Bayesian framework. Intended to be a drop-in replacement for
common frequentist hypothesis test such as the t-test and chi-sq test.
Author: Frank Portman [aut, cre]
Maintainer: Frank Portman <frank1214@gmail.com>
Diff between bayesAB versions 0.6.0 dated 2016-09-13 and 0.7.0 dated 2016-10-09
bayesAB-0.6.0/bayesAB/src/bayesCountTest.cpp |only bayesAB-0.6.0/bayesAB/src/bayesPropTestClosed.cpp |only bayesAB-0.7.0/bayesAB/DESCRIPTION | 11 - bayesAB-0.7.0/bayesAB/MD5 | 61 ++++---- bayesAB-0.7.0/bayesAB/NAMESPACE | 8 - bayesAB-0.7.0/bayesAB/NEWS.md |only bayesAB-0.7.0/bayesAB/R/bandit.R |only bayesAB-0.7.0/bayesAB/R/bayesAB.R | 10 + bayesAB-0.7.0/bayesAB/R/bayesTest.R | 2 bayesAB-0.7.0/bayesAB/R/combine.R | 9 - bayesAB-0.7.0/bayesAB/R/generics.R | 88 +++++++++-- bayesAB-0.7.0/bayesAB/R/makePlots.R | 36 +++- bayesAB-0.7.0/bayesAB/R/plotDists.R | 18 ++ bayesAB-0.7.0/bayesAB/R/util.R | 25 ++- bayesAB-0.7.0/bayesAB/README.md | 30 ++- bayesAB-0.7.0/bayesAB/inst/doc/introduction.html | 143 ++++++++++++++----- bayesAB-0.7.0/bayesAB/man/banditize.Rd |only bayesAB-0.7.0/bayesAB/man/bayesAB.Rd | 9 + bayesAB-0.7.0/bayesAB/man/bayesTest.Rd | 2 bayesAB-0.7.0/bayesAB/man/combine.Rd | 2 bayesAB-0.7.0/bayesAB/man/deployBandit.Rd |only bayesAB-0.7.0/bayesAB/man/installPlumber.Rd |only bayesAB-0.7.0/bayesAB/man/plot.bayesTest.Rd | 11 + bayesAB-0.7.0/bayesAB/man/plotBeta.Rd | 4 bayesAB-0.7.0/bayesAB/man/plotGamma.Rd | 4 bayesAB-0.7.0/bayesAB/man/plotInvGamma.Rd | 4 bayesAB-0.7.0/bayesAB/man/plotLogNormal.Rd | 4 bayesAB-0.7.0/bayesAB/man/plotNormal.Rd | 4 bayesAB-0.7.0/bayesAB/man/plotPareto.Rd | 4 bayesAB-0.7.0/bayesAB/man/plotPoisson.Rd | 4 bayesAB-0.7.0/bayesAB/man/summary.bayesTest.Rd | 8 + bayesAB-0.7.0/bayesAB/src/closedTests.cpp |only bayesAB-0.7.0/bayesAB/tests/testthat/Rplots.pdf |binary bayesAB-0.7.0/bayesAB/tests/testthat/test-bandit.R |only bayesAB-0.7.0/bayesAB/tests/testthat/test-dists.R | 14 - bayesAB-0.7.0/bayesAB/tests/testthat/test-generics.R | 3 36 files changed, 391 insertions(+), 127 deletions(-)
Title: Relative Distribution Methods
Description: Tools for the comparison of distributions. This includes nonparametric estimation of the relative distribution PDF and CDF and numerical summaries as described in "Relative Distribution Methods in the Social Sciences" by Mark S. Handcock and Martina Morris, Springer-Verlag, 1999, Springer-Verlag, ISBN 0387987789.
Author: Mark S. Handcock <handcock@stat.ucla.edu>
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between reldist versions 1.6-4 dated 2015-01-27 and 1.6-6 dated 2016-10-09
DESCRIPTION | 17 ++++++----------- MD5 | 12 ++++++------ NAMESPACE | 6 ++++++ R/bgk_kde.R | 4 +++- R/wtd.quantile.R | 39 +++------------------------------------ inst/CITATION | 4 ++-- tests/FigSM.R | 16 ++++++++-------- 7 files changed, 34 insertions(+), 64 deletions(-)
Title: Fast Multivariate Normal and Student's t Methods
Description: Provides computationally efficient tools related to
the multivariate normal and Student's t distributions. The main functionalities are:
simulating multivariate random vectors, evaluating multivariate
normal or Student's t densities and Mahalanobis distances. These tools are very efficient
thanks to the use of C++ code and of the OpenMP API.
Author: Matteo Fasiolo, using the C++ parallel RNG of Thijs van den Berg and
Ziggurat algorithm of Jens Maurer and Steven Watanabe (boost)
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between mvnfast versions 0.1.5 dated 2016-08-30 and 0.1.6 dated 2016-10-09
mvnfast-0.1.5/mvnfast/src/dmvnCpp.cpp |only mvnfast-0.1.6/mvnfast/DESCRIPTION | 16 +-- mvnfast-0.1.6/mvnfast/MD5 | 41 ++++--- mvnfast-0.1.6/mvnfast/R/dmvn.R | 14 +- mvnfast-0.1.6/mvnfast/R/dmvt.R |only mvnfast-0.1.6/mvnfast/R/rmvn.R | 42 +++++++ mvnfast-0.1.6/mvnfast/R/rmvt.R |only mvnfast-0.1.6/mvnfast/build/vignette.rds |binary mvnfast-0.1.6/mvnfast/inst/CITATION | 13 +- mvnfast-0.1.6/mvnfast/inst/doc/mvnfast.R | 35 +++++- mvnfast-0.1.6/mvnfast/inst/doc/mvnfast.Rmd | 62 +++++++++-- mvnfast-0.1.6/mvnfast/inst/doc/mvnfast.html | 142 ++++++++++++++++++++------- mvnfast-0.1.6/mvnfast/inst/tests/test-dmvn.R | 2 mvnfast-0.1.6/mvnfast/inst/tests/test-dmvt.R |only mvnfast-0.1.6/mvnfast/inst/tests/test-rmvn.R | 72 +++++++++++-- mvnfast-0.1.6/mvnfast/inst/tests/test-rmvt.R |only mvnfast-0.1.6/mvnfast/man/dmvn.Rd | 11 +- mvnfast-0.1.6/mvnfast/man/dmvt.Rd |only mvnfast-0.1.6/mvnfast/man/rmvn.Rd | 24 +++- mvnfast-0.1.6/mvnfast/man/rmvt.Rd |only mvnfast-0.1.6/mvnfast/src/dmvtCpp.cpp |only mvnfast-0.1.6/mvnfast/src/msCpp.cpp | 2 mvnfast-0.1.6/mvnfast/src/mvnfast.h | 5 mvnfast-0.1.6/mvnfast/src/rmvnCpp.cpp | 17 +-- mvnfast-0.1.6/mvnfast/src/rmvtCpp.cpp |only mvnfast-0.1.6/mvnfast/vignettes/mvnfast.Rmd | 62 +++++++++-- 26 files changed, 428 insertions(+), 132 deletions(-)
Title: A Tool for Calculation and Optimization of the Expected Gain
from Multi-Stage Selection
Description: Multi-stage selection is practiced in numerous fields of life and social sciences and particularly in breeding. A special characteristic of multi-stage selection is that candidates are evaluated in successive stages with increasing intensity and effort, and only a fraction of the superior candidates is selected and promoted to the next stage. For the optimum design of such selection programs, the selection gain plays a crucial role. It can be calculated by integration of a truncated multivariate normal (MVN) distribution. While mathematical formulas for calculating the selection gain and the variance among selected candidates were developed long time ago, solutions for numerical calculation were not available. This package can also be used for optimizing multi-stage selection programs for a given total budget and different costs of evaluating the candidates in each stage.
Author: Xuefei Mi, Jose Marulanda, H. Friedrich Utz, Albrecht E. Melchinger (Project contact person: Melchinger@uni-hohenheim.de )
Maintainer: Xuefei Mi <mi_xue_fei@hotmail.com>
Diff between selectiongain versions 2.0.50.1 dated 2016-03-14 and 2.0.591 dated 2016-10-09
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- R/multistagegain.R | 5 +++-- R/multistageoptimum.search.R | 19 ++++++++++++++----- R/multistageoptimum.searchThreeS.R |only R/multistagevariance.R | 5 ++++- man/multistagegain.Rd | 27 +++++++++++++++------------ man/multistageoptimum.searchThreeS.Rd |only 8 files changed, 47 insertions(+), 29 deletions(-)
Title: Automatic Generation of Qualitative Color Palettes
Description: Automatic generation of distinct qualitative color palettes,
optionally adapted to color blindness. It takes a subspace of the HSL color
space as input and projects it to the DIN99d color space where it selects
and return colors that are maximally distinct.
Author: Johan Larsson [aut, cre]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between qualpalr versions 0.1.0 dated 2016-08-31 and 0.2.1 dated 2016-10-09
qualpalr-0.1.0/qualpalr/R/wrappers.R |only qualpalr-0.1.0/qualpalr/tests/testthat/ciede2000testdata.RData |only qualpalr-0.1.0/qualpalr/tests/testthat/hsl_rgb_hex.RData |only qualpalr-0.2.1/qualpalr/DESCRIPTION | 18 qualpalr-0.2.1/qualpalr/MD5 | 33 - qualpalr-0.2.1/qualpalr/NEWS.md | 32 + qualpalr-0.2.1/qualpalr/R/color_formulas.R | 300 +++++++--- qualpalr-0.2.1/qualpalr/R/main.R | 214 ++++--- qualpalr-0.2.1/qualpalr/README.md | 35 - qualpalr-0.2.1/qualpalr/inst/doc/introduction.R | 65 ++ qualpalr-0.2.1/qualpalr/inst/doc/introduction.Rmd | 106 +++ qualpalr-0.2.1/qualpalr/inst/doc/introduction.html | 139 ++-- qualpalr-0.2.1/qualpalr/man/pairs.qualpal.Rd | 13 qualpalr-0.2.1/qualpalr/man/plot.qualpal.Rd | 2 qualpalr-0.2.1/qualpalr/man/qualpal.Rd | 82 +- qualpalr-0.2.1/qualpalr/tests/testthat/rgb_hsl.RData |only qualpalr-0.2.1/qualpalr/tests/testthat/test_color.R | 89 ++ qualpalr-0.2.1/qualpalr/tests/testthat/test_qualpal.R | 9 qualpalr-0.2.1/qualpalr/vignettes/introduction.Rmd | 106 +++ qualpalr-0.2.1/qualpalr/vignettes/qualpal.bib |only 20 files changed, 902 insertions(+), 341 deletions(-)
Title: Case Influence in Structural Equation Models
Description: A set of tools for evaluating several measures of case influence for structural equation models. Functions are based on the approach of J Pek and RC MacCallum (Sensitivity analysis in structural equation models: cases and their influence, Multivariate Behavioral Research, 2011).
Author: Massimiliano Pastore & Gianmarco Altoe'
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between influence.SEM versions 1.5 dated 2015-05-30 and 2.0 dated 2016-10-09
DESCRIPTION | 10 +++++----- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 2 ++ NEWS | 8 +++++++- R/Deltachi.R | 6 +++--- R/Likedist.R | 24 ++++++++++++++++++++---- R/bollen.loglik.R |only R/explore.influence.R | 5 +++-- R/fitinfluence.R | 32 ++++++++++++++++++++------------ R/genCookDist.R | 4 ++-- R/parinfluence.R | 4 ++-- man/Likedist.Rd | 19 ++++++++++++------- man/PDII.Rd | 2 +- man/Q.Rd | 10 ---------- man/bollen.loglik.Rd |only man/explore.influence.Rd | 6 +++++- man/fitinfluence.Rd | 25 ++++++++++++++----------- 17 files changed, 112 insertions(+), 75 deletions(-)
Title: Robust and Sparse Regression via Gamma-Divergence
Description: Robust regression via gamma-divergence with L1, elastic net and ridge.
Author: Takayuki Kawashima
Maintainer: Takayuki Kawashima <t-kawa@ism.ac.jp>
Diff between gamreg versions 0.1 dated 2016-10-07 and 0.2 dated 2016-10-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/sparse_gamreg.cpp | 3 +++ 3 files changed, 9 insertions(+), 6 deletions(-)
Title: Data Correction and Imputation Using Deductive Methods
Description: Attempt to repair inconsistencies and missing values in data
records by using information from valid values and validation rules
restricting the data.
Author: Mark van der Loo [cre, aut],
Edwin de Jonge [aut]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between deductive versions 0.1.0 dated 2016-03-11 and 0.1.1 dated 2016-10-09
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS |only R/linimpute.R | 3 ++- R/typocorr.R | 4 ++-- man/correct_typos.Rd | 4 ++-- src/imputezero.c | 7 ++++--- tests/testthat/test_correct_typos.R | 9 +++++++++ 8 files changed, 30 insertions(+), 18 deletions(-)
Title: Generalized Survival Models
Description: R implementation of generalized survival models, where g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth. For fully parametric models, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects.
Author: Mark Clements [aut, cre], Xing-Rong Liu [aut], Paul Lambert [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.3.2 dated 2016-04-13 and 1.3.4 dated 2016-10-09
DESCRIPTION | 10 MD5 | 46 + NAMESPACE | 6 R/pm2-3.R | 622 ++++++++++++++------ R/tvc.coxph.R |only inst/Rcpp-tests.R |only inst/doc/Introduction.R | 41 - inst/doc/Introduction.Rnw | 35 - inst/doc/Introduction.pdf |binary inst/ihe-expect-utilities-males.png |only inst/ihe-expected-utilites.png |only inst/test.do |only inst/tvc-cox.R |only inst/working_code.R | 407 +++++++++++++ man/cox.tvc.Rd |only man/predict-methods.Rd | 5 man/pstpm2-class.Rd | 1 man/pstpm2.Rd | 32 - man/stpm2.Rd | 24 man/tvcCoxph-class.Rd |only src/RuniqueCombs.c |only src/RuniqueCombs.h |only src/bspline.c |only src/c_optim.cpp | 109 +++ src/c_optim.h | 10 src/cox_ph.cpp |only src/gsl_bspline.c |only src/gsl_bspline.h |only src/test-nmmin.cpp | 1068 ++++++++++++++++++++++-------------- vignettes/Introduction.Rnw | 35 - vignettes/auto/Introduction.el | 27 31 files changed, 1751 insertions(+), 727 deletions(-)
Title: Permutation Based QQ Plot and Inflation Factor Estimation
Description: Provides users the necessary utility functions to generate permutation-based QQ plots and also estimate inflation factor based on the empirical NULL distribution. While it has general utility, it is particularly helpful when the skewness of the Fisher's Exact test in sparse data situations with imbalanced case-control sample sizes renders the reliance on the uniform chi-square expected distribution inappropriate.
Author: Slave Petrovski and Quanli Wang
Maintainer: Quanli Wang <quanli@stat.duke.edu>
Diff between QQperm versions 1.0 dated 2016-09-26 and 1.0.1 dated 2016-10-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/IGM.R | 4 ++++ R/QQ.R | 4 ++-- demo/example.R | 2 +- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.50.2 dated 2016-04-24 and 0.51.0 dated 2016-10-09
matrixStats-0.50.2/matrixStats/R/rowMedians.S4.R |only matrixStats-0.51.0/matrixStats/DESCRIPTION | 12 matrixStats-0.51.0/matrixStats/MD5 | 84 - matrixStats-0.51.0/matrixStats/NAMESPACE | 7 matrixStats-0.51.0/matrixStats/NEWS | 8 matrixStats-0.51.0/matrixStats/R/allocMatrix.R | 6 matrixStats-0.51.0/matrixStats/R/anyMissing.R | 6 matrixStats-0.51.0/matrixStats/R/binCounts.R | 2 matrixStats-0.51.0/matrixStats/R/binMeans.R | 2 matrixStats-0.51.0/matrixStats/R/diff2.R | 2 matrixStats-0.51.0/matrixStats/R/indexByRow.R | 2 matrixStats-0.51.0/matrixStats/R/logSumExp.R | 3 matrixStats-0.51.0/matrixStats/R/meanOver.R | 2 matrixStats-0.51.0/matrixStats/R/product.R | 2 matrixStats-0.51.0/matrixStats/R/psortKM.R | 2 matrixStats-0.51.0/matrixStats/R/rowCounts.R | 18 matrixStats-0.51.0/matrixStats/R/rowCumsums.R | 16 matrixStats-0.51.0/matrixStats/R/rowDiffs.R | 4 matrixStats-0.51.0/matrixStats/R/rowLogSumExps.R | 10 matrixStats-0.51.0/matrixStats/R/rowMads.R | 4 matrixStats-0.51.0/matrixStats/R/rowMedians.R |only matrixStats-0.51.0/matrixStats/R/rowOrderStats.R | 4 matrixStats-0.51.0/matrixStats/R/rowRanges.R | 12 matrixStats-0.51.0/matrixStats/R/rowRanks.R | 4 matrixStats-0.51.0/matrixStats/R/rowVars.R | 4 matrixStats-0.51.0/matrixStats/R/signTabulate.R | 2 matrixStats-0.51.0/matrixStats/R/sumOver.R | 2 matrixStats-0.51.0/matrixStats/R/validateIndices.R | 4 matrixStats-0.51.0/matrixStats/R/weightedMean.R | 2 matrixStats-0.51.0/matrixStats/R/weightedMedian.R | 2 matrixStats-0.51.0/matrixStats/R/x_OP_y.R | 4 matrixStats-0.51.0/matrixStats/build/vignette.rds |binary matrixStats-0.51.0/matrixStats/inst/benchmarking/binMeans.md.rsp | 2 matrixStats-0.51.0/matrixStats/inst/doc/matrixStats-methods.html | 774 +++++----- matrixStats-0.51.0/matrixStats/inst/doc/matrixStats-methods.md.rsp | 2 matrixStats-0.51.0/matrixStats/man/anyMissing.Rd | 2 matrixStats-0.51.0/matrixStats/man/binMeans.Rd | 2 matrixStats-0.51.0/matrixStats/man/indexByRow.Rd | 2 matrixStats-0.51.0/matrixStats/man/matrixStats-package.Rd | 4 matrixStats-0.51.0/matrixStats/man/rowMedians.Rd | 4 matrixStats-0.51.0/matrixStats/src/allocMatrix2.c | 6 matrixStats-0.51.0/matrixStats/src/api.h |only matrixStats-0.51.0/matrixStats/src/init.c |only matrixStats-0.51.0/matrixStats/src/rowOrderStats.c | 2 matrixStats-0.51.0/matrixStats/vignettes/matrixStats-methods.md.rsp | 2 45 files changed, 516 insertions(+), 518 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares
or REML by adding the function r() to formulas of lm and glm. A collection of
text-book statistics for higher education is also included, e.g. modifications
of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sb [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.1.4 dated 2016-08-26 and 1.1.5 dated 2016-10-08
DESCRIPTION | 14 +++++++++----- MD5 | 4 ++-- R/statistics.R | 26 +++++++++++++++++--------- 3 files changed, 28 insertions(+), 16 deletions(-)
Title: Generate, Visualise, and Compare Fast and Frugal Decision Trees
Description: Contains several functions that allow you
to create, visualise, and test Fast and Frugal Trees (FFTrees). FFTrees are very simple decision trees for
classifying cases (i.e.; breast cancer patients) into one of two classes (e.g.;
no cancer vs. true cancer) based on a small number of cues (e.g.; test results). FFTrees can be preferable to more complex algorithms (such as
logistic regression) because they are easy to communicate and implement, and are
robust against noisy data.
Author: Nathaniel Phillips [aut, cre]
Maintainer: Nathaniel Phillips <Nathaniel.D.Phillips.is@gmail.com>
Diff between FFTrees versions 1.1.6 dated 2016-09-10 and 1.1.8 dated 2016-10-08
FFTrees-1.1.6/FFTrees/inst/doc/FFTrees_overview.R |only FFTrees-1.1.6/FFTrees/inst/doc/FFTrees_overview.Rmd |only FFTrees-1.1.6/FFTrees/inst/doc/FFTrees_overview.html |only FFTrees-1.1.6/FFTrees/vignettes/FFTrees_overview.Rmd |only FFTrees-1.1.8/FFTrees/DESCRIPTION | 8 FFTrees-1.1.8/FFTrees/MD5 | 75 +++--- FFTrees-1.1.8/FFTrees/NAMESPACE | 1 FFTrees-1.1.8/FFTrees/R/FFTrees.R | 215 ++++++------------ FFTrees-1.1.8/FFTrees/R/FFTreesguide_function.R | 2 FFTrees-1.1.8/FFTrees/R/auc_function.R | 13 - FFTrees-1.1.8/FFTrees/R/cartpred_function.R | 46 ++- FFTrees-1.1.8/FFTrees/R/classtable_function.R | 56 ++-- FFTrees-1.1.8/FFTrees/R/cuerank_function.R | 36 --- FFTrees-1.1.8/FFTrees/R/growFFTrees_function.R | 143 +++++++---- FFTrees-1.1.8/FFTrees/R/helper.R |only FFTrees-1.1.8/FFTrees/R/lrpred_function.R | 23 + FFTrees-1.1.8/FFTrees/R/plotFFTrees_function.R | 10 FFTrees-1.1.8/FFTrees/R/predictFFTrees_function.R | 23 + FFTrees-1.1.8/FFTrees/R/summaryFFTrees_function.R | 2 FFTrees-1.1.8/FFTrees/README.md | 10 FFTrees-1.1.8/FFTrees/build/vignette.rds |binary FFTrees-1.1.8/FFTrees/inst/doc/FFTrees_algorithm.html | 7 FFTrees-1.1.8/FFTrees/inst/doc/FFTrees_examples.R | 21 - FFTrees-1.1.8/FFTrees/inst/doc/FFTrees_examples.Rmd | 21 - FFTrees-1.1.8/FFTrees/inst/doc/FFTrees_examples.html | 31 +- FFTrees-1.1.8/FFTrees/inst/doc/FFTrees_function.Rmd | 4 FFTrees-1.1.8/FFTrees/inst/doc/FFTrees_function.html | 17 - FFTrees-1.1.8/FFTrees/inst/doc/FFTrees_plot.html | 13 - FFTrees-1.1.8/FFTrees/inst/doc/guide.R |only FFTrees-1.1.8/FFTrees/inst/doc/guide.Rmd |only FFTrees-1.1.8/FFTrees/inst/doc/guide.html |only FFTrees-1.1.8/FFTrees/man/FFTrees.Rd | 10 FFTrees-1.1.8/FFTrees/man/auc.Rd | 8 FFTrees-1.1.8/FFTrees/man/cart.pred.Rd | 10 FFTrees-1.1.8/FFTrees/man/classtable.Rd | 14 + FFTrees-1.1.8/FFTrees/man/cuerank.Rd | 19 + FFTrees-1.1.8/FFTrees/man/grow.FFTrees.Rd | 36 ++- FFTrees-1.1.8/FFTrees/man/plot.FFTrees.Rd | 10 FFTrees-1.1.8/FFTrees/man/predict.FFTrees.Rd | 26 ++ FFTrees-1.1.8/FFTrees/man/summary.FFTrees.Rd | 2 FFTrees-1.1.8/FFTrees/vignettes/FFTrees_examples.Rmd | 21 - FFTrees-1.1.8/FFTrees/vignettes/FFTrees_function.Rmd | 4 FFTrees-1.1.8/FFTrees/vignettes/guide.Rmd |only 43 files changed, 525 insertions(+), 412 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans and
K-Medoids Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans and k-medoids
clustering with the option to plot, validate, predict (new data) and estimate the
optimal number of clusters. The package takes advantage of 'RcppArmadillo' to
speed up the computationally intensive parts of the functions.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.0.1 dated 2016-09-09 and 1.0.3 dated 2016-10-08
DESCRIPTION | 10 MD5 | 32 NEWS.md | 17 R/RcppExports.R | 2 R/clustering_functions.R | 7 README.md | 7 inst/doc/the_clusterR_package.Rmd | 2 inst/doc/the_clusterR_package.html | 14 src/Makevars | 1 src/RcppExports.cpp | 376 +-- src/kmeans_miniBatchKmeans_GMM_Medoids.cpp | 1136 ++++++++-- src/utils_rcpp.cpp | 40 src/utils_rcpp.h | 6 tests/testthat/test-dissimilarity_matrices.R | 268 +- tests/testthat/test-gmm.R | 189 + tests/testthat/test-plot2d_silhouette_plot_ext_validation_center_scale_dist_mat.R | 6 vignettes/the_clusterR_package.Rmd | 2 17 files changed, 1656 insertions(+), 459 deletions(-)
Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, poisson), Mahalanobis distance are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis and John Burkardt
Maintainer: Manos Papadakis <papadakm95@gmail.com>
Diff between Rfast versions 1.3 dated 2016-08-09 and 1.4 dated 2016-10-08
Rfast-1.3/Rfast/R/fast_cpp.R |only Rfast-1.3/Rfast/man/Rbeta.Rd |only Rfast-1.3/Rfast/man/Rbinom.Rd |only Rfast-1.3/Rfast/man/Rnorm.Rd |only Rfast-1.3/Rfast/man/Rpois.Rd |only Rfast-1.3/Rfast/man/Runif.Rd |only Rfast-1.3/Rfast/man/generate_key_1.Rd |only Rfast-1.3/Rfast/man/generate_key_2.Rd |only Rfast-1.3/Rfast/src/fast.cpp |only Rfast-1.4/Rfast/DESCRIPTION | 12 - Rfast-1.4/Rfast/MD5 | 218 +++++++++++++----- Rfast-1.4/Rfast/NAMESPACE | 7 Rfast-1.4/Rfast/R/Digamma.R |only Rfast-1.4/Rfast/R/Lgamma.R |only Rfast-1.4/Rfast/R/Match.R |only Rfast-1.4/Rfast/R/Order.R |only Rfast-1.4/Rfast/R/Trigamma.R |only Rfast-1.4/Rfast/R/all_equals.R |only Rfast-1.4/Rfast/R/allbetas.R | 6 Rfast-1.4/Rfast/R/beta.mle.R |only Rfast-1.4/Rfast/R/binary_search.R |only Rfast-1.4/Rfast/R/colMads.R | 6 Rfast-1.4/Rfast/R/colMaxs.R |only Rfast-1.4/Rfast/R/colMedians.R |only Rfast-1.4/Rfast/R/colMins.R |only Rfast-1.4/Rfast/R/colVars.R | 8 Rfast-1.4/Rfast/R/colmeans.R |only Rfast-1.4/Rfast/R/colrange.R | 17 - Rfast-1.4/Rfast/R/colsums.R |only Rfast-1.4/Rfast/R/comb_n.R |only Rfast-1.4/Rfast/R/cora.R | 4 Rfast-1.4/Rfast/R/correls.R | 6 Rfast-1.4/Rfast/R/count_value.R |only Rfast-1.4/Rfast/R/cova.R | 2 Rfast-1.4/Rfast/R/design_matrix.R |only Rfast-1.4/Rfast/R/diri.nr2.R | 26 -- Rfast-1.4/Rfast/R/dista.R | 8 Rfast-1.4/Rfast/R/floyd.R |only Rfast-1.4/Rfast/R/ftests.R | 10 Rfast-1.4/Rfast/R/hash.find.R |only Rfast-1.4/Rfast/R/hash.list.R |only Rfast-1.4/Rfast/R/is_element.R |only Rfast-1.4/Rfast/R/logistic_only.R |only Rfast-1.4/Rfast/R/lower_triangle.R |only Rfast-1.4/Rfast/R/med.R |only Rfast-1.4/Rfast/R/mvbetas.R | 4 Rfast-1.4/Rfast/R/nth.R |only Rfast-1.4/Rfast/R/permutation.R |only Rfast-1.4/Rfast/R/permutation_next.R |only Rfast-1.4/Rfast/R/permutation_prev.R |only Rfast-1.4/Rfast/R/poisson_only.R |only Rfast-1.4/Rfast/R/proptests.R |only Rfast-1.4/Rfast/R/racg.R |only Rfast-1.4/Rfast/R/regression.R |only Rfast-1.4/Rfast/R/rmvlaplace.R |only Rfast-1.4/Rfast/R/rmvnorm.R |only Rfast-1.4/Rfast/R/rmvt.R |only Rfast-1.4/Rfast/R/rowMaxs.R |only Rfast-1.4/Rfast/R/rowMedians.R |only Rfast-1.4/Rfast/R/rowMins.R |only Rfast-1.4/Rfast/R/rowVars.R |only Rfast-1.4/Rfast/R/rowmeans.R |only Rfast-1.4/Rfast/R/rowrange.R |only Rfast-1.4/Rfast/R/rowsums.R |only Rfast-1.4/Rfast/R/sort_cor_vectors.R |only Rfast-1.4/Rfast/R/sort_index.R |only Rfast-1.4/Rfast/R/sort_mat.R |only Rfast-1.4/Rfast/R/sort_unique.R |only Rfast-1.4/Rfast/R/standardise.R | 13 - Rfast-1.4/Rfast/R/transpose.R |only Rfast-1.4/Rfast/R/ttests.R | 8 Rfast-1.4/Rfast/R/univglms.R | 9 Rfast-1.4/Rfast/R/upper_triangle.R |only Rfast-1.4/Rfast/R/which_isFactor.R |only Rfast-1.4/Rfast/R/zip.mle.R |only Rfast-1.4/Rfast/man/Lgamma.Rd |only Rfast-1.4/Rfast/man/Match.Rd | 4 Rfast-1.4/Rfast/man/Order.Rd |only Rfast-1.4/Rfast/man/Rfast-package.Rd | 6 Rfast-1.4/Rfast/man/all_equals.Rd |only Rfast-1.4/Rfast/man/allbetas.Rd | 4 Rfast-1.4/Rfast/man/beta.mle.Rd |only Rfast-1.4/Rfast/man/binary_search.Rd |only Rfast-1.4/Rfast/man/colMads.Rd | 8 Rfast-1.4/Rfast/man/colMedians.Rd | 11 Rfast-1.4/Rfast/man/colMins.Rd | 8 Rfast-1.4/Rfast/man/colVars.Rd | 9 Rfast-1.4/Rfast/man/colmeans.Rd | 12 - Rfast-1.4/Rfast/man/colrange.Rd | 12 - Rfast-1.4/Rfast/man/colsums.Rd | 10 Rfast-1.4/Rfast/man/comb_n.Rd |only Rfast-1.4/Rfast/man/count_value.Rd |only Rfast-1.4/Rfast/man/cova.Rd | 8 Rfast-1.4/Rfast/man/design_matrix.Rd | 2 Rfast-1.4/Rfast/man/diri.nr2.Rd | 15 - Rfast-1.4/Rfast/man/floyd.Rd |only Rfast-1.4/Rfast/man/ftests.Rd | 2 Rfast-1.4/Rfast/man/g2Test.Rd | 2 Rfast-1.4/Rfast/man/g2Test_univariate.Rd | 2 Rfast-1.4/Rfast/man/hash.find.Rd | 2 Rfast-1.4/Rfast/man/hash.list.Rd | 6 Rfast-1.4/Rfast/man/is_element.Rd |only Rfast-1.4/Rfast/man/logistic_only.Rd | 2 Rfast-1.4/Rfast/man/lower_tri.Rd |only Rfast-1.4/Rfast/man/mahala.Rd | 7 Rfast-1.4/Rfast/man/mvbetas.Rd | 1 Rfast-1.4/Rfast/man/permutation.Rd |only Rfast-1.4/Rfast/man/poisson_only.Rd | 2 Rfast-1.4/Rfast/man/proptests.Rd |only Rfast-1.4/Rfast/man/racg.Rd |only Rfast-1.4/Rfast/man/rmvlaplace.Rd |only Rfast-1.4/Rfast/man/rmvnorm.Rd |only Rfast-1.4/Rfast/man/rowMins.Rd | 11 Rfast-1.4/Rfast/man/sort_cor_vectors.Rd |only Rfast-1.4/Rfast/man/sort_mat.Rd | 13 - Rfast-1.4/Rfast/man/sort_unique.Rd |only Rfast-1.4/Rfast/man/standardise.Rd | 3 Rfast-1.4/Rfast/man/transpose.Rd |only Rfast-1.4/Rfast/man/ttests.Rd | 2 Rfast-1.4/Rfast/man/univglms.Rd | 2 Rfast-1.4/Rfast/man/which_isFactor.Rd | 3 Rfast-1.4/Rfast/man/zip.mle.Rd |only Rfast-1.4/Rfast/src/Hash_list.cpp |only Rfast-1.4/Rfast/src/Match.cpp |only Rfast-1.4/Rfast/src/Order.cpp |only Rfast-1.4/Rfast/src/all__functions.cpp | 361 ------------------------------- Rfast-1.4/Rfast/src/binarysearch.cpp |only Rfast-1.4/Rfast/src/colmaxs.cpp |only Rfast-1.4/Rfast/src/colmeans.cpp |only Rfast-1.4/Rfast/src/colmeds.cpp |only Rfast-1.4/Rfast/src/colmins.cpp |only Rfast-1.4/Rfast/src/colrange.cpp |only Rfast-1.4/Rfast/src/colsums.cpp |only Rfast-1.4/Rfast/src/count_value.cpp |only Rfast-1.4/Rfast/src/design_matrix.cpp |only Rfast-1.4/Rfast/src/dg_mat.cpp |only Rfast-1.4/Rfast/src/dg_vec.cpp |only Rfast-1.4/Rfast/src/diri_nr_type2.cpp |only Rfast-1.4/Rfast/src/floyd_john.cpp |only Rfast-1.4/Rfast/src/g2t.cpp | 3 Rfast-1.4/Rfast/src/hash_find.cpp |only Rfast-1.4/Rfast/src/is_element.cpp |only Rfast-1.4/Rfast/src/k_comb_n.cpp |only Rfast-1.4/Rfast/src/l_mat.cpp |only Rfast-1.4/Rfast/src/l_vec.cpp |only Rfast-1.4/Rfast/src/logistic_only.cpp |only Rfast-1.4/Rfast/src/lower_triangle.cpp |only Rfast-1.4/Rfast/src/med.cpp |only Rfast-1.4/Rfast/src/mn.cpp | 58 +++- Rfast-1.4/Rfast/src/mn.h | 15 - Rfast-1.4/Rfast/src/nth.cpp |only Rfast-1.4/Rfast/src/permutation.cpp |only Rfast-1.4/Rfast/src/permutation_next.cpp |only Rfast-1.4/Rfast/src/permutation_prev.cpp |only Rfast-1.4/Rfast/src/poisson_only.cpp |only Rfast-1.4/Rfast/src/regression.cpp |only Rfast-1.4/Rfast/src/rowMaxs.cpp |only Rfast-1.4/Rfast/src/rowMins.cpp |only Rfast-1.4/Rfast/src/rowmeans.cpp |only Rfast-1.4/Rfast/src/rowrange.cpp |only Rfast-1.4/Rfast/src/rowsums.cpp |only Rfast-1.4/Rfast/src/sort_cor_vecs.cpp |only Rfast-1.4/Rfast/src/sort_double.cpp |only Rfast-1.4/Rfast/src/sort_index.cpp |only Rfast-1.4/Rfast/src/sort_int.cpp |only Rfast-1.4/Rfast/src/sort_mat.cpp |only Rfast-1.4/Rfast/src/tr_mat.cpp |only Rfast-1.4/Rfast/src/tr_vec.cpp |only Rfast-1.4/Rfast/src/transpose.cpp |only Rfast-1.4/Rfast/src/upper_triangle.cpp |only Rfast-1.4/Rfast/src/which_isFactor.cpp |only 171 files changed, 370 insertions(+), 600 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including 'GBIF', 'USGS' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics'
Engine, 'eBird', 'AntWeb', and 'iDigBio'. Includes functionality for
retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [ctb],
Ted Hart [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.5.0 dated 2016-04-23 and 0.5.4 dated 2016-10-08
spocc-0.5.0/spocc/man/spocc_colClasses.Rd |only spocc-0.5.4/spocc/DESCRIPTION | 29 - spocc-0.5.4/spocc/MD5 | 77 ++-- spocc-0.5.4/spocc/NAMESPACE | 6 spocc-0.5.4/spocc/NEWS.md | 26 + spocc-0.5.4/spocc/R/as.antweb.R | 8 spocc-0.5.4/spocc/R/as.bison.R | 12 spocc-0.5.4/spocc/R/as.ecoengine.R | 4 spocc-0.5.4/spocc/R/as.gbif.R | 16 spocc-0.5.4/spocc/R/as.idigbio.R | 12 spocc-0.5.4/spocc/R/as.inat.R | 6 spocc-0.5.4/spocc/R/as.vertnet.R | 4 spocc-0.5.4/spocc/R/ecoengine_helpers.R | 4 spocc-0.5.4/spocc/R/inat.R | 19 - spocc-0.5.4/spocc/R/methods.r | 8 spocc-0.5.4/spocc/R/occ.r | 2 spocc-0.5.4/spocc/R/occ2df.R | 14 spocc-0.5.4/spocc/R/occ_options.r | 6 spocc-0.5.4/spocc/R/plugin_helpers.R | 14 spocc-0.5.4/spocc/R/plugins.r | 49 +- spocc-0.5.4/spocc/R/spocc-package.R | 4 spocc-0.5.4/spocc/R/wkt_vis.r | 2 spocc-0.5.4/spocc/R/zzz.r | 23 - spocc-0.5.4/spocc/README.md | 76 +--- spocc-0.5.4/spocc/build/vignette.rds |binary spocc-0.5.4/spocc/inst/doc/spocc_vignette.Rmd | 241 ++++++------- spocc-0.5.4/spocc/inst/doc/spocc_vignette.html | 241 ++++++------- spocc-0.5.4/spocc/man/as.antweb.Rd | 4 spocc-0.5.4/spocc/man/as.bison.Rd | 8 spocc-0.5.4/spocc/man/as.gbif.Rd | 8 spocc-0.5.4/spocc/man/as.idigbio.Rd | 4 spocc-0.5.4/spocc/man/as.inat.Rd | 2 spocc-0.5.4/spocc/man/occ_options.Rd | 2 spocc-0.5.4/spocc/man/spocc_objects.Rd | 4 spocc-0.5.4/spocc/tests/testthat/test-has_coords.R | 6 spocc-0.5.4/spocc/tests/testthat/test-occ.R | 31 + spocc-0.5.4/spocc/tests/testthat/test-occ2df.R | 23 - spocc-0.5.4/spocc/tests/testthat/test-options.R | 12 spocc-0.5.4/spocc/tests/testthat/test-taxize-integration.R | 5 spocc-0.5.4/spocc/vignettes/spocc_vignette.Rmd | 241 ++++++------- 40 files changed, 641 insertions(+), 612 deletions(-)
Title: Simulation of Diffusion Processes
Description: Provides the functions for simulating and modeling of stochastic differential equations (SDE's). Statistical analysis and simulation of the solution of SDE's enabled many searchers in different domains to use these equations to modeling practical problems, in financial and actuarial modeling and other areas of application. For example, modeling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996).
Author: Arsalane Chouaib Guidoum [cre, aut],
Kamal Boukhetala [aut]
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between Sim.DiffProc versions 3.3 dated 2016-09-22 and 3.4 dated 2016-10-08
Sim.DiffProc-3.3/Sim.DiffProc/inst/doc/FitSDE.Rnw |only Sim.DiffProc-3.3/Sim.DiffProc/inst/doc/FitSDE.pdf |only Sim.DiffProc-3.3/Sim.DiffProc/inst/doc/Introduction.R |only Sim.DiffProc-3.3/Sim.DiffProc/inst/doc/Introduction.Rnw |only Sim.DiffProc-3.3/Sim.DiffProc/inst/doc/Introduction.pdf |only Sim.DiffProc-3.3/Sim.DiffProc/inst/doc/SDEs.R |only Sim.DiffProc-3.3/Sim.DiffProc/inst/doc/SDEs.Rnw |only Sim.DiffProc-3.3/Sim.DiffProc/inst/doc/SDEs.pdf |only Sim.DiffProc-3.3/Sim.DiffProc/man/rsde2d.Rd |only Sim.DiffProc-3.3/Sim.DiffProc/man/rsde3d.Rd |only Sim.DiffProc-3.3/Sim.DiffProc/vignettes/Core_FitSDE.tex |only Sim.DiffProc-3.3/Sim.DiffProc/vignettes/FitSDE-022.pdf |only Sim.DiffProc-3.3/Sim.DiffProc/vignettes/FitSDE-026.pdf |only Sim.DiffProc-3.3/Sim.DiffProc/vignettes/FitSDE.Rnw |only Sim.DiffProc-3.3/Sim.DiffProc/vignettes/Introduction.Rnw |only Sim.DiffProc-3.3/Sim.DiffProc/vignettes/SDEs.Rnw |only Sim.DiffProc-3.4/Sim.DiffProc/DESCRIPTION | 10 Sim.DiffProc-3.4/Sim.DiffProc/MD5 | 78 +- Sim.DiffProc-3.4/Sim.DiffProc/NAMESPACE | 72 - Sim.DiffProc-3.4/Sim.DiffProc/NEWS | 5 Sim.DiffProc-3.4/Sim.DiffProc/R/ftpsde.R | 505 +++----------- Sim.DiffProc-3.4/Sim.DiffProc/R/rsde.R | 437 +----------- Sim.DiffProc-3.4/Sim.DiffProc/R/snssde.R | 406 ++++------- Sim.DiffProc-3.4/Sim.DiffProc/R/utils.R | 448 ++++++------ Sim.DiffProc-3.4/Sim.DiffProc/R/zzz.r | 10 Sim.DiffProc-3.4/Sim.DiffProc/build/vignette.rds |binary Sim.DiffProc-3.4/Sim.DiffProc/demo/Sim.DiffProc.R | 131 +-- Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/Sim.DiffProc.R |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/Sim.DiffProc.Rmd |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/Sim.DiffProc.html |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/Thumbs.db |binary Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/fitsde.R |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/fitsde.Rmd |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/fitsde.html |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/fptsde.R |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/fptsde.Rmd |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/fptsde.html |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/sde.R |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/sde.Rmd |only Sim.DiffProc-3.4/Sim.DiffProc/inst/doc/sde.html |only Sim.DiffProc-3.4/Sim.DiffProc/man/Sim.DiffProc-package.Rd | 128 +-- Sim.DiffProc-3.4/Sim.DiffProc/man/bconfint.Rd | 5 Sim.DiffProc-3.4/Sim.DiffProc/man/fptsde1d.Rd | 74 -- Sim.DiffProc-3.4/Sim.DiffProc/man/fptsde2d.Rd | 60 - Sim.DiffProc-3.4/Sim.DiffProc/man/fptsde3d.Rd | 64 - Sim.DiffProc-3.4/Sim.DiffProc/man/rsde1d.Rd | 131 +-- Sim.DiffProc-3.4/Sim.DiffProc/man/snssde1d.Rd | 7 Sim.DiffProc-3.4/Sim.DiffProc/man/snssde2d.Rd | 9 Sim.DiffProc-3.4/Sim.DiffProc/man/snssde3d.Rd | 8 Sim.DiffProc-3.4/Sim.DiffProc/tests/fptsde.R | 55 - Sim.DiffProc-3.4/Sim.DiffProc/tests/rsde.R | 81 +- Sim.DiffProc-3.4/Sim.DiffProc/vignettes/Sim.DiffProc.Rmd |only Sim.DiffProc-3.4/Sim.DiffProc/vignettes/Thumbs.db |binary Sim.DiffProc-3.4/Sim.DiffProc/vignettes/fitsde.Rmd |only Sim.DiffProc-3.4/Sim.DiffProc/vignettes/fptsde.Rmd |only Sim.DiffProc-3.4/Sim.DiffProc/vignettes/sde.Rmd |only 56 files changed, 953 insertions(+), 1771 deletions(-)
Title: Tools for Conducting Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct
respirometry experiments. Strong emphasis is on aquatic respirometry. Tools
focus on helping the researcher setup and conduct experiments. Analysis of the
resulting data is not a focus since analyses are often specific to a particular
setup, and thus are better created by the researcher individually. This
package provides tools for intermittent, flow-through, and closed respirometry
techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between respirometry versions 0.1.0 dated 2016-08-23 and 0.2.0 dated 2016-10-08
DESCRIPTION | 12 +++---- MD5 | 79 ++++++++++++++++++++++++++++---------------------- NAMESPACE | 4 ++ NEWS | 45 ++++++++++++++++++++-------- R/Q10.R | 31 ++++++++++++++++--- R/closed.R |only R/co2_add.R | 7 ++-- R/co2_flush.R | 5 +-- R/co2_rate.R | 4 +- R/conv_NH4.R | 2 - R/conv_o2.R | 10 +++++- R/correct_bubble.R | 2 - R/flush_carb.R | 2 - R/flush_o2.R | 46 +++++++++++++++++++++++------ R/flush_water.R | 14 +++++++- R/goal_flush_pH.R | 2 - R/guess_TA.R | 51 ++++++++++++++++++++++++-------- R/import_presens.R |only R/import_witrox.R |only R/max_MO2.R | 5 ++- R/mean_pH.R | 4 ++ R/predict_NH4.R | 3 - R/predict_pH.R | 21 ++++++++++++- R/scale_MO2.R |only inst |only man/Q10.Rd | 35 ++++++++++++++++++---- man/closed.Rd |only man/co2_add.Rd | 9 +++-- man/co2_flush.Rd | 7 +++- man/co2_rate.Rd | 4 +- man/conv_NH4.Rd | 2 - man/conv_o2.Rd | 4 +- man/correct_bubble.Rd | 2 - man/flush_carb.Rd | 2 - man/flush_o2.Rd | 16 +++++----- man/flush_water.Rd | 14 +++++++- man/goal_flush_pH.Rd | 2 - man/guess_TA.Rd | 11 +++++- man/import_presens.Rd |only man/import_witrox.Rd |only man/max_MO2.Rd | 5 ++- man/predict_NH4.Rd | 2 - man/predict_pH.Rd | 2 - man/scale_MO2.Rd |only 44 files changed, 334 insertions(+), 132 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories, a method for
variable selection based on the SVD, Bézier lines with arrows complementing the
ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.4 dated 2016-10-04 and 1.4.1 dated 2016-10-08
Gmisc-1.4.1/Gmisc/DESCRIPTION | 8 +- Gmisc-1.4.1/Gmisc/MD5 | 89 +++++++++++------------ Gmisc-1.4.1/Gmisc/NAMESPACE | 2 Gmisc-1.4.1/Gmisc/NEWS | 4 + Gmisc-1.4.1/Gmisc/R/bezierArrowGradient.R | 2 Gmisc-1.4.1/Gmisc/R/bezierArrowSmpl.R | 4 - Gmisc-1.4.1/Gmisc/R/bezier_private_functions.R | 4 - Gmisc-1.4.1/Gmisc/R/convertShowMissing.R |only Gmisc-1.4.1/Gmisc/R/deprecated.R | 2 Gmisc-1.4.1/Gmisc/R/descGetMissing.R |only Gmisc-1.4.1/Gmisc/R/descriptionStats.R | 22 ++--- Gmisc-1.4.1/Gmisc/R/docx_document.R | 6 - Gmisc-1.4.1/Gmisc/R/fastDoCall.R | 2 Gmisc-1.4.1/Gmisc/R/figCaptionNo.R | 4 - Gmisc-1.4.1/Gmisc/R/getDescriptionStatsBy.R | 14 +-- Gmisc-1.4.1/Gmisc/R/getPval.R | 2 Gmisc-1.4.1/Gmisc/R/getSvdMostInfluential.R | 4 - Gmisc-1.4.1/Gmisc/R/private_functions.R | 70 ------------------ Gmisc-1.4.1/Gmisc/R/transitionClass.R | 14 +-- Gmisc-1.4.1/Gmisc/R/transitionClass_helpers.R | 2 Gmisc-1.4.1/Gmisc/R/transitionPlot.R | 16 ++-- Gmisc-1.4.1/Gmisc/R/transitionPlot_helpers.R | 8 +- Gmisc-1.4.1/Gmisc/inst/doc/Descriptives.html | 48 ++++++------ Gmisc-1.4.1/Gmisc/inst/doc/Transition-class.html | 4 - Gmisc-1.4.1/Gmisc/inst/doc/transitionPlot.html | 4 - Gmisc-1.4.1/Gmisc/man/Gmisc-deprecated.Rd | 2 Gmisc-1.4.1/Gmisc/man/Transition-class.Rd | 10 +- Gmisc-1.4.1/Gmisc/man/bezierArrowGradient.Rd | 4 - Gmisc-1.4.1/Gmisc/man/bezierArrowSmpl.Rd | 2 Gmisc-1.4.1/Gmisc/man/convertShowMissing.Rd |only Gmisc-1.4.1/Gmisc/man/descGetMissing.Rd |only Gmisc-1.4.1/Gmisc/man/describeFactors.Rd | 4 - Gmisc-1.4.1/Gmisc/man/docx_document.Rd | 4 - Gmisc-1.4.1/Gmisc/man/fastDoCall.Rd | 2 Gmisc-1.4.1/Gmisc/man/getDescriptionStatsBy.Rd | 8 +- Gmisc-1.4.1/Gmisc/man/getPval.Rd | 2 Gmisc-1.4.1/Gmisc/man/getSvdMostInfluential.Rd | 2 Gmisc-1.4.1/Gmisc/man/prCaptionFix.Rd | 4 - Gmisc-1.4.1/Gmisc/man/prGetStatistics.Rd | 2 Gmisc-1.4.1/Gmisc/man/prGridPlotTitle.Rd | 2 Gmisc-1.4.1/Gmisc/man/prTcPlotArrows.Rd | 2 Gmisc-1.4.1/Gmisc/man/prTpGetBoxPropClr.Rd | 4 - Gmisc-1.4.1/Gmisc/man/prTpGetColors.Rd | 4 - Gmisc-1.4.1/Gmisc/man/prTpPlotArrows.Rd | 2 Gmisc-1.4.1/Gmisc/man/prTpPlotBoxes.Rd | 8 +- Gmisc-1.4.1/Gmisc/man/transitionPlot.Rd | 14 +-- Gmisc-1.4.1/Gmisc/tests/testthat/test-boxGrobs.R |only Gmisc-1.4/Gmisc/man/prConvertShowMissing.Rd |only Gmisc-1.4/Gmisc/man/prDescGetMissing.Rd |only 49 files changed, 180 insertions(+), 237 deletions(-)
Title: Estimation of Extreme Value Dependence for Time Series Data
Description: Estimation of the sample univariate, cross and return time extremograms. The package can also adds empirical confidence bands to each of the extremogram plots via a permutation procedure under the assumption that the data are independent. Finally, the stationary bootstrap allows us to construct credible confidence bands for the extremograms.
Author: Nadezda Frolova, Ivor Cribben
Maintainer: Nadezda Frolova <nfrolova@ualberta.ca>
Diff between extremogram versions 1.0.1 dated 2016-03-28 and 1.0.2 dated 2016-10-08
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/bootconf1.R | 19 +++++++------------ R/bootconf2.R | 13 +++++++------ R/bootconfr.R | 11 +++++++---- R/extremogram1.R | 22 +++++++--------------- R/extremogram2.R | 16 +++++++++------- R/extremogramr.R | 24 +++++++----------------- R/permfn1.R | 4 ++-- R/permfn2.R | 8 ++++---- man/bootconf1.Rd | 4 +--- man/bootconf2.Rd | 4 +--- man/bootconfr.Rd | 4 +--- man/extremogram1.Rd | 5 +---- man/extremogram2.Rd | 4 +--- man/extremogramr.Rd | 4 +--- 16 files changed, 75 insertions(+), 105 deletions(-)
Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre],
Peter Rousseeuw [aut] (Fortran original),
Anja Struyf [aut] (S original),
Mia Hubert [aut] (S original),
Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)),
Matthias Studer [ctb],
Pierre Roudier [ctb],
Juan Gonzalez [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.0.4 dated 2016-04-18 and 2.0.5 dated 2016-10-08
DESCRIPTION | 14 +++--- MD5 | 34 ++++++++-------- R/clusGap.R | 46 ++++++++++++++++------ R/daisy.q | 10 ++-- R/diana.q | 10 ++-- R/pam.q | 12 ++++- R/plotpart.q | 15 +++---- README | 2 inst/NEWS.Rd | 45 ++++++++++++++++----- man/clusGap.Rd | 99 +++++++++++++++++++++++++++++++++--------------- man/clusplot.default.Rd | 24 ++++------- man/daisy.Rd | 13 ++++-- man/diana.Rd | 6 ++ man/fanny.Rd | 2 man/pam.Rd | 4 + man/silhouette.Rd | 10 ++-- src/pam.c | 7 ++- src/twins.c | 20 ++++----- 18 files changed, 241 insertions(+), 132 deletions(-)
Title: Regression Spline Functions and Classes Too
Description: A complementary package on splines providing functions
constructing B-splines, monotone splines (M-splines) and its integral
(I-splines), convex splines (C-splines), and integral of B-splines.
Piecewise constant basis is allowed for B-spline and M-spline basis.
Author: Wenjie Wang [aut, cre],
Jun Yan [ctb]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>
Diff between splines2 versions 0.1.0 dated 2016-09-06 and 0.2.1 dated 2016-10-07
splines2-0.1.0/splines2/R/splines-package.R |only splines2-0.2.1/splines2/DESCRIPTION | 16 +++- splines2-0.2.1/splines2/MD5 | 39 ++++++++---- splines2-0.2.1/splines2/NAMESPACE | 11 +++ splines2-0.2.1/splines2/NEWS.md |only splines2-0.2.1/splines2/R/bSpline.R |only splines2-0.2.1/splines2/R/cSpline.R |only splines2-0.2.1/splines2/R/iSpline.R | 87 ++++++++++++++++++--------- splines2-0.2.1/splines2/R/ibs.R | 34 +++++----- splines2-0.2.1/splines2/R/mSpline.R | 39 ++++++------ splines2-0.2.1/splines2/R/predict.R | 65 +++++++++++++++----- splines2-0.2.1/splines2/R/print.R |only splines2-0.2.1/splines2/R/splines2-package.R |only splines2-0.2.1/splines2/README.md |only splines2-0.2.1/splines2/build |only splines2-0.2.1/splines2/inst |only splines2-0.2.1/splines2/man/bSpline.Rd |only splines2-0.2.1/splines2/man/cSpline.Rd |only splines2-0.2.1/splines2/man/iSpline.Rd | 30 +++++---- splines2-0.2.1/splines2/man/ibs.Rd | 23 +++---- splines2-0.2.1/splines2/man/mSpline.Rd | 32 +++++---- splines2-0.2.1/splines2/man/predict.Rd | 36 ++++++++--- splines2-0.2.1/splines2/man/print.Rd |only splines2-0.2.1/splines2/man/splines2.Rd | 8 +- splines2-0.2.1/splines2/vignettes |only 25 files changed, 273 insertions(+), 147 deletions(-)
Title: Render R Markdown Outputs Lazily
Description: An R Markdown html document format that provides the ability to lazily
load plot outputs as the user scrolls over them. This is useful for large R
Markdown documents with many plots, as it allows for a fast initial page load and
defers loading of individual graphics to the time that the user navigates near them.
Author: Ryan Hafen [aut, cre],
Barret Schloerke [aut],
jQuery Foundation [cph] (jQuery.js library),
Sourcey [cph] (recliner.js library)
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between lazyrmd versions 0.1.0 dated 2016-08-01 and 0.2.0 dated 2016-10-07
lazyrmd-0.1.0/lazyrmd/NEWS.md |only lazyrmd-0.1.0/lazyrmd/inst/doc/bc5930df80ffdf606fde3da6ebf158b5.html |only lazyrmd-0.1.0/lazyrmd/inst/doc/d3-3.5.2 |only lazyrmd-0.1.0/lazyrmd/inst/doc/d3.min.js |only lazyrmd-0.1.0/lazyrmd/inst/doc/htmlwidgets-0.6 |only lazyrmd-0.1.0/lazyrmd/inst/doc/htmlwidgets.js |only lazyrmd-0.1.0/lazyrmd/inst/doc/lazy_example.R |only lazyrmd-0.1.0/lazyrmd/inst/doc/lazy_widgets |only lazyrmd-0.1.0/lazyrmd/inst/doc/lib |only lazyrmd-0.1.0/lazyrmd/inst/doc/simpleNetwork-binding-0.2.12 |only lazyrmd-0.1.0/lazyrmd/inst/doc/simpleNetwork.js |only lazyrmd-0.1.0/lazyrmd/man/lazyhtml_document.Rd |only lazyrmd-0.1.0/lazyrmd/vignettes/.install_extras |only lazyrmd-0.1.0/lazyrmd/vignettes/lazy_widgets |only lazyrmd-0.2.0/lazyrmd/DESCRIPTION | 18 - lazyrmd-0.2.0/lazyrmd/MD5 | 41 --- lazyrmd-0.2.0/lazyrmd/NAMESPACE | 5 lazyrmd-0.2.0/lazyrmd/NEWS |only lazyrmd-0.2.0/lazyrmd/R/lazyhtml_document.R | 20 + lazyrmd-0.2.0/lazyrmd/R/print_lazy_widget.R | 7 lazyrmd-0.2.0/lazyrmd/README.md | 6 lazyrmd-0.2.0/lazyrmd/build/vignette.rds |binary lazyrmd-0.2.0/lazyrmd/inst/doc/lazy_example.Rmd | 34 -- lazyrmd-0.2.0/lazyrmd/inst/doc/lazy_example.html | 135 ---------- lazyrmd-0.2.0/lazyrmd/man/lazy_render.Rd |only lazyrmd-0.2.0/lazyrmd/vignettes/lazy_example.Rmd | 34 -- 26 files changed, 67 insertions(+), 233 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Leslie Pérez Cáceres,
Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 1.07 dated 2015-09-11 and 2.0 dated 2016-10-07
irace-1.07/irace/inst/examples/acotsp/hook-run |only irace-1.07/irace/inst/examples/acotsp/tune-conf |only irace-1.07/irace/inst/examples/hook-run-python |only irace-1.07/irace/inst/examples/hypervolume/hook-evaluate |only irace-1.07/irace/inst/examples/hypervolume/hook-run |only irace-1.07/irace/inst/examples/moaco/hook-evaluate |only irace-1.07/irace/inst/examples/moaco/hook-run |only irace-1.07/irace/inst/examples/moaco/tune-conf |only irace-1.07/irace/inst/examples/mpi |only irace-1.07/irace/inst/examples/sge-cluster/hook-evaluate |only irace-1.07/irace/inst/examples/sge-cluster/hook-run |only irace-1.07/irace/inst/examples/sge-cluster/tune-main |only irace-1.07/irace/inst/examples/tune-main-cluster |only irace-1.07/irace/inst/examples/tune-main-tmp |only irace-1.07/irace/inst/templates/candidates.tmpl |only irace-1.07/irace/inst/templates/forbidden.tmpl |only irace-1.07/irace/inst/templates/hook-evaluate.tmpl |only irace-1.07/irace/inst/templates/hook-run.tmpl |only irace-1.07/irace/inst/templates/instances-list.tmpl |only irace-1.07/irace/inst/templates/parameters.tmpl |only irace-1.07/irace/inst/templates/tune-conf.tmpl |only irace-1.07/irace/inst/templates/tune-main.tmpl |only irace-1.07/irace/man/candidates.print.Rd |only irace-1.07/irace/man/candidates.print.command.Rd |only irace-1.07/irace/man/checkConfiguration.Rd |only irace-1.07/irace/man/defaultConfiguration.Rd |only irace-1.07/irace/man/hook.evaluate.default.Rd |only irace-1.07/irace/man/hook.run.default.Rd |only irace-1.07/irace/man/printConfiguration.Rd |only irace-1.07/irace/man/readConfiguration.Rd |only irace-1.07/irace/man/removeCandidatesMetaData.Rd |only irace-2.0/irace/BUGS |only irace-2.0/irace/DESCRIPTION | 24 irace-2.0/irace/MD5 | 154 + irace-2.0/irace/NAMESPACE | 14 irace-2.0/irace/NEWS | 103 + irace-2.0/irace/R/cluster.R | 130 - irace-2.0/irace/R/generation.R | 146 - irace-2.0/irace/R/irace.R | 1033 +++++++----- irace-2.0/irace/R/main.R | 430 ++-- irace-2.0/irace/R/model.R | 131 - irace-2.0/irace/R/parameterAnalysis.R |only irace-2.0/irace/R/race-wrapper.R | 551 +++--- irace-2.0/irace/R/race.R | 839 +++++---- irace-2.0/irace/R/readConfiguration.R | 688 ++++--- irace-2.0/irace/R/readParameters.R | 127 - irace-2.0/irace/R/testing.R | 75 irace-2.0/irace/R/tnorm.R | 18 irace-2.0/irace/R/utils.R | 391 +++- irace-2.0/irace/R/version.R | 2 irace-2.0/irace/README.md | 195 +- irace-2.0/irace/build |only irace-2.0/irace/inst/CITATION | 26 irace-2.0/irace/inst/bin/irace.bat |only irace-2.0/irace/inst/bin/parallel-irace | 57 irace-2.0/irace/inst/bin/parallel-irace-mpi |only irace-2.0/irace/inst/bin/parallel-irace-qsub |only irace-2.0/irace/inst/doc |only irace-2.0/irace/inst/examples/acotsp/README | 3 irace-2.0/irace/inst/examples/acotsp/default.txt | 2 irace-2.0/irace/inst/examples/acotsp/forbidden.txt | 2 irace-2.0/irace/inst/examples/acotsp/parameters-acotsp.txt | 12 irace-2.0/irace/inst/examples/acotsp/scenario.txt |only irace-2.0/irace/inst/examples/acotsp/target-runner |only irace-2.0/irace/inst/examples/hypervolume/README | 10 irace-2.0/irace/inst/examples/hypervolume/target-evaluator |only irace-2.0/irace/inst/examples/hypervolume/target-runner |only irace-2.0/irace/inst/examples/matlab |only irace-2.0/irace/inst/examples/moaco/parameters.txt | 4 irace-2.0/irace/inst/examples/moaco/scenario.txt |only irace-2.0/irace/inst/examples/moaco/target-evaluator |only irace-2.0/irace/inst/examples/moaco/target-runner |only irace-2.0/irace/inst/examples/sge-cluster/README | 16 irace-2.0/irace/inst/examples/sge-cluster/irace-sge-cluster |only irace-2.0/irace/inst/examples/sge-cluster/target-evaluator |only irace-2.0/irace/inst/examples/sge-cluster/target-runner |only irace-2.0/irace/inst/examples/target-runner-python |only irace-2.0/irace/inst/templates/configurations.txt.tmpl |only irace-2.0/irace/inst/templates/forbidden.txt.tmpl |only irace-2.0/irace/inst/templates/instances-list.txt.tmpl |only irace-2.0/irace/inst/templates/parameters.txt.tmpl |only irace-2.0/irace/inst/templates/scenario.txt.tmpl |only irace-2.0/irace/inst/templates/target-evaluator.tmpl |only irace-2.0/irace/inst/templates/target-runner.tmpl |only irace-2.0/irace/man/buildCommandLine.Rd | 4 irace-2.0/irace/man/checkIraceScenario.Rd |only irace-2.0/irace/man/checkScenario.Rd |only irace-2.0/irace/man/configurations.print.Rd |only irace-2.0/irace/man/configurations.print.command.Rd |only irace-2.0/irace/man/defaultScenario.Rd |only irace-2.0/irace/man/getConfigurationById.Rd |only irace-2.0/irace/man/getConfigurationByIteration.Rd |only irace-2.0/irace/man/getFinalElites.Rd |only irace-2.0/irace/man/irace-package.Rd | 31 irace-2.0/irace/man/irace.Rd |only irace-2.0/irace/man/irace.cmdline.Rd | 10 irace-2.0/irace/man/irace.main.Rd | 13 irace-2.0/irace/man/irace.usage.Rd | 5 irace-2.0/irace/man/parallelCoordinatesPlot.Rd |only irace-2.0/irace/man/parameterFrequency.Rd |only irace-2.0/irace/man/printScenario.Rd |only irace-2.0/irace/man/readConfigurationsFile.Rd |only irace-2.0/irace/man/readParameters.Rd | 32 irace-2.0/irace/man/readScenario.Rd |only irace-2.0/irace/man/removeConfigurationsMetaData.Rd |only irace-2.0/irace/man/target.evaluator.default.Rd |only irace-2.0/irace/man/target.runner.default.Rd |only irace-2.0/irace/man/testing.main.Rd |only irace-2.0/irace/tests |only irace-2.0/irace/vignettes |only 110 files changed, 3071 insertions(+), 2207 deletions(-)
Title: Genotype Plus Genotype-by-Environment Biplots
Description: Create biplots for GGE (genotype plus genotype-by-environment) and
GGB (genotype plus genotype-by-block-of-environments) models.
Author: Kevin Wright [aut, cre],
Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between gge versions 1.0 dated 2015-12-14 and 1.1 dated 2016-10-07
gge-1.0/gge/R/gge.r |only gge-1.1/gge/DESCRIPTION | 10 +-- gge-1.1/gge/MD5 | 19 +++--- gge-1.1/gge/R/gge.R |only gge-1.1/gge/build/vignette.rds |binary gge-1.1/gge/inst/doc/gge.R | 17 ++++- gge-1.1/gge/inst/doc/gge.Rmd | 25 ++++++-- gge-1.1/gge/inst/doc/gge.html | 128 +++++++++++++++++++++++++++++++++-------- gge-1.1/gge/man/RedGrayBlue.Rd | 12 --- gge-1.1/gge/man/gge.Rd | 18 ++++- gge-1.1/gge/tests |only gge-1.1/gge/vignettes/gge.Rmd | 25 ++++++-- 12 files changed, 192 insertions(+), 62 deletions(-)
Title: Simulation of Fatigue Lifetimes
Description: Provides methods for simulation and analysis of a very general fatigue
lifetime model for (metal matrix) composite materials.
Author: Markus Baaske [aut, cre], Felix Ballani [aut, ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>
Diff between simLife versions 0.2.3 dated 2016-06-26 and 0.3 dated 2016-10-07
DESCRIPTION | 10 MD5 | 64 ++-- R/densify.R | 240 ++++++++-------- R/rsaSpheroids.r | 99 +++--- R/simLife.R | 611 +++++++++++++++++++++++-------------------- R/times.R | 216 ++++++++------- man/CLF.Rd | 2 man/SF.Rd | 2 man/areaCrit.Rd | 6 man/densifyCluster.Rd | 15 - man/drawDefectProjections.Rd | 6 man/getCrackTime.Rd | 16 - man/getCylinderProjection.Rd | 4 man/getDelamTime.Rd | 16 - man/getSpheroidProjection.Rd | 2 man/plotDefectAcc.Rd | 24 - man/rsa.Rd | 8 man/showDensity.Rd | 29 +- man/simCluster.Rd | 6 man/simCrackTime.Rd | 23 - man/simDefect.Rd | 14 man/simFerrit.Rd | 4 man/simFracture.Rd | 77 +++-- man/simParticle.Rd | 6 man/simTimes.Rd | 25 - man/woehler.Rd | 66 ++-- man/woehlerDiagram.Rd | 22 - src/GeometricPrimitives.cpp | 2 src/GeometricPrimitives.h | 2 src/Vector.h | 2 src/convert.cpp | 2 src/sim2Life.cpp | 88 ++---- src/sim2Life.h | 9 33 files changed, 903 insertions(+), 815 deletions(-)
Title: A Time Input Widget for Shiny
Description: Provides a time input widget for Shiny. This widget allows intuitive time input in the
'[hh]:[mm]:[ss]' or '[hh]:[mm]' (24H) format by using a separate numeric input for each time
component. The interface with R uses 'DateTimeClasses' objects. See the project page for more
information and examples.
Author: Gerhard Burger [aut, cre]
Maintainer: Gerhard Burger <burger.ga@gmail.com>
Diff between shinyTime versions 0.2.0 dated 2016-07-19 and 0.2.1 dated 2016-10-07
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md |only R/input-time.R | 13 +++++-------- inst/www/input_binding_time.js | 32 +++++++++++++++++++++++++++++++- 5 files changed, 43 insertions(+), 15 deletions(-)
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Includes also
utilities for sequence data management under the ACNUC system.
Author: Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>
Diff between seqinr versions 3.3-1 dated 2016-09-06 and 3.3-2 dated 2016-10-07
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- data/SEQINR.UTIL.RData |binary data/sysdata.rda |binary man/SEQINR.UTIL.Rd | 4 ++-- man/translate.Rd | 7 +++++-- 6 files changed, 18 insertions(+), 15 deletions(-)
Title: Robust Rank Correlation Coefficient and Test
Description: The 'rococo' package provides a robust gamma rank correlation
coefficient along with a permutation-based rank correlation test.
The rank correlation coefficient and the test are explicitly
designed for dealing with noisy numerical data.
Author: Martin Krone, Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Diff between rococo versions 1.1.3 dated 2016-04-18 and 1.1.4 dated 2016-10-07
DESCRIPTION | 8 +-- MD5 | 20 ++++---- R/rococo.R | 76 +++++++++++++++++++++++++++--- R/rococo.test-methods.R | 112 ++++++++++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/NEWS | 5 ++ inst/doc/rococo.Rnw | 6 ++ inst/doc/rococo.pdf |binary man/rococo.Rd | 5 +- man/rococo.test-methods.Rd | 7 ++ vignettes/rococo.Rnw | 6 ++ 11 files changed, 211 insertions(+), 34 deletions(-)
Title: Interface Between GRASS 7 Geographical Information System and R
Description: Interpreted interface between GRASS 7 geographical
information system and R, based on starting R from within the GRASS GIS
environment, or running free-standing R in a temporary GRASS location;
the package provides facilities for using all GRASS commands from the
R command line. This package may not be used for GRASS 6, for which
spgrass6 should be used.
Author: Roger Bivand [cre, aut],
Rainer Krug [ctb],
Markus Neteler [ctb],
Sebastian Jeworutzki [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass7 versions 0.1-8 dated 2016-05-09 and 0.1-9 dated 2016-10-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/xml1.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional
data. Ensembles of classification, regression, survival and probability prediction
trees are supported. Data from genome-wide association studies can be analyzed
efficiently. In addition to data frames, datasets of class 'gwaa.data' (R package
'GenABEL') can be directly analyzed.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>
Diff between ranger versions 0.5.0 dated 2016-06-24 and 0.6.0 dated 2016-10-07
DESCRIPTION | 17 ++-- MD5 | 80 ++++++++++----------- NEWS | 8 ++ R/RcppExports.R | 6 - R/csrf.R | 4 - R/getTerminalNodeIDs.R | 49 ++----------- R/importance.R | 32 ++++---- R/predict.R | 115 +++++++++++++++++++------------ R/ranger.R | 61 +++++++++------- man/getTerminalNodeIDs.Rd | 6 + man/importance_pvalues.Rd | 10 +- man/predict.ranger.Rd | 12 ++- man/predict.ranger.forest.Rd | 14 +++ man/ranger.Rd | 35 ++++----- src/Forest.cpp | 17 ++-- src/Forest.h | 9 +- src/ForestClassification.cpp | 13 ++- src/ForestProbability.cpp | 38 +++++++--- src/ForestRegression.cpp | 17 +++- src/ForestSurvival.cpp | 24 ++++-- src/RcppExports.cpp | 15 ++-- src/TreeClassification.h | 6 + src/TreeProbability.h | 18 ++-- src/TreeRegression.h | 4 + src/TreeSurvival.cpp | 20 ++++- src/TreeSurvival.h | 9 +- src/globals.h | 8 ++ src/rangerCpp.cpp | 9 +- src/utility.cpp | 4 + src/utility.h | 7 + src/version.h | 2 tests/testthat/test_classification.R | 24 ++++-- tests/testthat/test_importance.R | 5 + tests/testthat/test_importance_pvalues.R | 12 ++- tests/testthat/test_predict.R | 76 ++++++++++++++++++++ tests/testthat/test_print.R | 2 tests/testthat/test_probability.R | 36 +++++++++ tests/testthat/test_ranger.R | 33 ++++++++ tests/testthat/test_regression.R | 2 tests/testthat/test_survival.R | 4 - tests/testthat/test_unordered.R | 50 +++++++++++++ 41 files changed, 628 insertions(+), 285 deletions(-)
Title: Collection of Tools for Genomic Data Analysis
Description: A loose collection of tools for the analysis of expression and genotype data, currently with the main focus on (e)QTL and MDR analysis.
Author: Daniel Fischer
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between GenomicTools versions 0.2 dated 2016-09-06 and 0.2.1 dated 2016-10-07
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ NAMESPACE | 2 +- R/importGFF3.R | 17 ++++++++++++++++- build/vignette.rds |binary data/annotTrack.rda |binary data/geneEXP.rda |binary data/genotData.rda |binary data/mdrExample.rda |binary data/phenoData.rda |binary inst/ChangeLog | 4 ++++ inst/doc/GenomicTools-Vignette.pdf |binary man/GenomicTools-package.Rd | 4 ++-- man/importGFF3.Rd |only 14 files changed, 40 insertions(+), 20 deletions(-)
Title: Data for "GAMs: An Introduction with R"
Description: Data sets and scripts used in the book "Generalized
Additive Models: An Introduction with R", Wood (2006) CRC.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between gamair versions 0.0-9 dated 2015-07-22 and 1.0-0 dated 2016-10-07
ChangeLog | 7 ++++++ DESCRIPTION | 7 +++--- MD5 | 55 ++++++++++++++++++++++++++++++++++++++++++-------- data/aral.bnd.rda |only data/aral.rda |only data/bone.rda |only data/canWeather.rda |only data/datalist | 14 ++++++++++++ data/gas.rda |only data/german.polys.rda |only data/larynx.rda |only data/med.rda |only data/meh.rda |only data/mpg.rda |only data/prostate.rda |only data/sitka.rda |only data/swer.rda |only data/wesdr.rda |only man/aral.Rd |only man/bird.Rd | 3 +- man/bone.Rd |only man/canWeather.Rd |only man/ch1.Rd |only man/ch1.solutions.Rd |only man/ch2.Rd |only man/ch2.solutions.Rd |only man/ch3.Rd |only man/ch3.solutions.Rd |only man/ch4.Rd |only man/ch4.solutions.Rd |only man/ch5.Rd |only man/ch5.solutions.Rd |only man/ch6.Rd |only man/ch6.solutions.Rd |only man/ch7.Rd |only man/ch7.solutions.Rd |only man/chicago.Rd | 1 man/coast.Rd | 4 +-- man/gamair-package.Rd | 24 ++++++++++++++++----- man/gas.Rd |only man/larynx.Rd |only man/meh.Rd |only man/mpg.Rd |only man/prostate.Rd |only man/sitka.Rd |only man/sole.Rd | 24 ++++++++++++++++++++- man/swer.Rd |only man/wesdr.Rd |only 48 files changed, 116 insertions(+), 23 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Ilya Shpitser and Judea Pearl, an algorithm for transportability from multiple domains with limited experiments by Elias Bareinboim and Judea Pearl and a selection bias recovery algorithm by Elias Bareinboim and Jin Tian. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Jin Tian.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.2.4 dated 2016-02-23 and 1.3.0 dated 2016-10-07
causaleffect-1.2.4/causaleffect/R/getNonIgnorableNodes.R |only causaleffect-1.2.4/causaleffect/R/perm.R |only causaleffect-1.2.4/causaleffect/R/sid.R |only causaleffect-1.2.4/causaleffect/R/simplify.meta.expression.R |only causaleffect-1.2.4/causaleffect/R/trz.R |only causaleffect-1.2.4/causaleffect/R/usid.R |only causaleffect-1.2.4/causaleffect/R/zid.R |only causaleffect-1.2.4/causaleffect/inst/doc/causaleffect.tex.rsp |only causaleffect-1.2.4/causaleffect/vignettes/causaleffect.tex.rsp |only causaleffect-1.3.0/causaleffect/DESCRIPTION | 10 causaleffect-1.3.0/causaleffect/MD5 | 94 +++--- causaleffect-1.3.0/causaleffect/NAMESPACE | 5 causaleffect-1.3.0/causaleffect/NEWS | 8 causaleffect-1.3.0/causaleffect/R/activate.interventions.R | 31 + causaleffect-1.3.0/causaleffect/R/cancel.R |only causaleffect-1.3.0/causaleffect/R/cancel.rc.R |only causaleffect-1.3.0/causaleffect/R/causal.effect.R | 61 +-- causaleffect-1.3.0/causaleffect/R/compute.q.R |only causaleffect-1.3.0/causaleffect/R/deconstruct.R | 156 ++++++++-- causaleffect-1.3.0/causaleffect/R/factorize.R | 21 - causaleffect-1.3.0/causaleffect/R/generalize.R |only causaleffect-1.3.0/causaleffect/R/get.expression.R | 54 ++- causaleffect-1.3.0/causaleffect/R/id.R | 138 +++++--- causaleffect-1.3.0/causaleffect/R/idc.R | 19 + causaleffect-1.3.0/causaleffect/R/identify.R |only causaleffect-1.3.0/causaleffect/R/insert.R |only causaleffect-1.3.0/causaleffect/R/join.R | 51 +-- causaleffect-1.3.0/causaleffect/R/meta.transport.R | 30 - causaleffect-1.3.0/causaleffect/R/organize.terms.R | 26 - causaleffect-1.3.0/causaleffect/R/parse.deconstruct.R | 48 +-- causaleffect-1.3.0/causaleffect/R/parse.expression.R | 72 ++-- causaleffect-1.3.0/causaleffect/R/parse.joint.R | 12 causaleffect-1.3.0/causaleffect/R/parse.layout.R |only causaleffect-1.3.0/causaleffect/R/probability.R | 8 causaleffect-1.3.0/causaleffect/R/rc.R |only causaleffect-1.3.0/causaleffect/R/recover.R |only causaleffect-1.3.0/causaleffect/R/simplify.R | 53 +-- causaleffect-1.3.0/causaleffect/R/simplify.causal.R |only causaleffect-1.3.0/causaleffect/R/simplify.expression.R | 99 +++--- causaleffect-1.3.0/causaleffect/R/simplify.rc.R |only causaleffect-1.3.0/causaleffect/R/simplify.trmz.R |only causaleffect-1.3.0/causaleffect/R/transport.R | 29 - causaleffect-1.3.0/causaleffect/R/trmz.R |only causaleffect-1.3.0/causaleffect/R/zzaux.effect.R | 26 - causaleffect-1.3.0/causaleffect/build/vignette.rds |binary causaleffect-1.3.0/causaleffect/inst/doc/causaleffect.ltx |only causaleffect-1.3.0/causaleffect/inst/doc/causaleffect.pdf |binary causaleffect-1.3.0/causaleffect/inst/doc/simplification.ltx |only causaleffect-1.3.0/causaleffect/inst/doc/simplification.pdf |only causaleffect-1.3.0/causaleffect/man/causal.effect.Rd | 19 - causaleffect-1.3.0/causaleffect/man/causaleffect-package.Rd | 17 - causaleffect-1.3.0/causaleffect/man/generalize.Rd |only causaleffect-1.3.0/causaleffect/man/get.expression.Rd | 4 causaleffect-1.3.0/causaleffect/man/meta.transport.Rd | 38 +- causaleffect-1.3.0/causaleffect/man/parse.graphml.Rd | 12 causaleffect-1.3.0/causaleffect/man/recover.Rd |only causaleffect-1.3.0/causaleffect/man/transport.Rd | 24 - causaleffect-1.3.0/causaleffect/man/zzaux.effect.Rd | 15 causaleffect-1.3.0/causaleffect/vignettes/causaleffect.ltx |only causaleffect-1.3.0/causaleffect/vignettes/giden.pdf |only causaleffect-1.3.0/causaleffect/vignettes/ginsert.pdf |only causaleffect-1.3.0/causaleffect/vignettes/gtian.pdf |only causaleffect-1.3.0/causaleffect/vignettes/jmlr2e.sty |only causaleffect-1.3.0/causaleffect/vignettes/simplification.bib |only causaleffect-1.3.0/causaleffect/vignettes/simplification.ltx |only 65 files changed, 702 insertions(+), 478 deletions(-)
Title: Transcriptome Overlap Measure
Description: A new bioinformatic tool for comparing transcriptomes of two biological samples from the same or different species. The mapping is conducted based on the overlap of the associated genes of different samples. More examples and detailed explanations are available in the vignette.
Author: Jingyi Jessica Li <jli@stat.ucla.edu>, Wei Vivian Li <liw@ucla.edu>
Maintainer: Jingyi Jessica Li <jli@stat.ucla.edu>
Diff between TROM versions 1.1 dated 2015-06-26 and 1.2 dated 2016-10-07
DESCRIPTION | 11 - MD5 | 38 ++--- NAMESPACE | 8 + R/TROM-internal.R | 250 ++++++++++++++++++------------------- R/choose.z.R | 27 ++- R/sp.associated.idx.R | 2 R/sp.ortholog.z.R | 2 R/sp.std.R |only R/ws.trom.two.R | 5 inst/doc/TROM-manual.pdf |only inst/doc/TROM_Vignette.pdf |binary man/TROM-package.Rd | 16 +- man/bs.trom.Rd | 2 man/choose.z.Rd | 18 ++ man/find.top.GO.slim.terms.Rd | 2 man/find.top.GO.terms.Rd | 2 man/heatmap.3.Rd | 2 man/select.associated.genes.Rd | 2 man/select.associated.orthologs.Rd | 2 man/ws.trom.Rd | 2 man/ws.trom.orthologs.Rd | 2 21 files changed, 219 insertions(+), 174 deletions(-)
Title: Borenstein Analysis
Description: An implementation of the analysis about seed components from Borenstein et.al. 2008.
Author: Claus Jonathan Fritzemeier
Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between RSeed versions 0.1.31 dated 2012-05-04 and 0.1.60 dated 2016-10-07
DESCRIPTION | 17 ++++++-------- MD5 | 6 ++--- NAMESPACE | 7 ++++-- R/borenstein.R | 66 +++++++++++++++++++++------------------------------------ 4 files changed, 41 insertions(+), 55 deletions(-)
Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of
Extension Education Program Evaluation in R" and "An R
Companion for the Handbook of Biological Statistics".
Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 1.0.1 dated 2016-09-12 and 1.1.0 dated 2016-10-07
DESCRIPTION | 14 +++++++------- MD5 | 18 ++++++++++++------ NAMESPACE | 3 +++ R/cldList.r |only R/pairwisePermutationMatrix.r | 6 ++---- R/pairwisePermutationSymmetry.r |only R/pairwisePermutationSymmetryMatrix.r |only R/pairwisePermutationTest.r | 8 +++----- man/cldList.Rd |only man/pairwisePermutationMatrix.Rd | 2 +- man/pairwisePermutationSymmetry.Rd |only man/pairwisePermutationSymmetryMatrix.Rd |only man/pairwisePermutationTest.Rd | 2 +- 13 files changed, 29 insertions(+), 24 deletions(-)
Title: Power Estimates for ANOVA Designs
Description: Functions for bootstrapping the power of ANOVA designs
based on estimated means and standard deviations of the conditions.
Please refer to the documentation of the boot.power.anova() function
for further details.
Author: Frank Papenmeier [aut, cre]
Maintainer: Frank Papenmeier <frank.papenmeier@uni-tuebingen.de>
Diff between powerbydesign versions 1.0.2 dated 2016-04-05 and 1.0.3 dated 2016-10-07
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NEWS |only R/boot.power.anova.R | 8 +++++++- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Client for the 'Pangaea' Database
Description: Tools to interact with the 'Pangaea' Database (<https://
www.pangaea.de>), including functions for searching for data, fetching 'datasets'
by 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH' service.
Author: Scott Chamberlain [aut, cre],
Kara Woo [aut],
Andrew MacDonald [aut],
Naupaka Zimmerman [aut],
Gavin Simpson [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between pangaear versions 0.2.0 dated 2016-05-06 and 0.2.4 dated 2016-10-07
DESCRIPTION | 12 +- MD5 | 34 ++--- NAMESPACE | 2 NEWS.md | 19 +++ R/pangaear-package.R | 2 R/pg_data.R | 70 +++++++---- R/pg_list_identifiers.R | 11 - R/pg_list_records.R | 54 ++++----- R/pg_search.R | 112 +++++++++++++----- R/zzz.R | 25 ++-- README.md | 216 +++++++++++++++--------------------- man/pg_data.Rd | 35 +++-- man/pg_list_identifiers.Rd | 40 +++--- man/pg_list_records.Rd | 58 +++++---- man/pg_search.Rd | 41 +++++- tests/testthat/test-oai_functions.R | 38 +++--- tests/testthat/test-pg_data.R | 6 + tests/testthat/test-pg_search.r | 10 + 18 files changed, 447 insertions(+), 338 deletions(-)
Title: Machina Time Series Generation and Backtesting
Description: Connects to <https://machi.na/> and allows the creation
of time series, and running backtests on selected strategy if requested.
Author: Nelson Mark [aut],
Gursky Michael [aut],
Kamal Akram [ctb],
Norton Tim [cre]
Maintainer: Norton Tim <tnorton@machi.na>
Diff between machina versions 0.1.5 dated 2016-08-03 and 0.1.6 dated 2016-10-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/machinaWS.functions.R | 2 +- R/versions.R | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence plots from
various types machine learning models in R.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.0.4 dated 2016-09-17 and 0.1.0 dated 2016-10-06
DESCRIPTION | 15 +- MD5 | 20 +-- NEWS.md | 15 ++ R/partial.R | 104 +++++++++------- R/plotPartial.R | 272 ++++++++++++++++++++++++++++++------------ R/utils.R | 46 +++++++ README.md | 55 ++++++-- man/partial.Rd | 69 ++++++++-- man/plotPartial.Rd | 52 ++++---- tests/testthat/test-partial.R | 2 tests/testthat/test-utils.R | 28 ++++ 11 files changed, 491 insertions(+), 187 deletions(-)
More information about fragilityindex at CRAN
Permanent link
Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in
the estimation of the joint size-shape-orientation distribution of spheroidal
shaped particles based on the same measured quantities of corresponding planar
vertical section profiles. A single trivariate discretized version of the (stereological)
integral equation in the case of prolate and oblate spheroids is solved
numerically by the EM algorithm. The estimation of diameter distribution of
spheres from planar sections (Wicksell's corpuscle problem) is also implemented.
Further, the package provides routines for the simulation of a Poisson germ-
grain process with either spheroids, spherocylinders or spheres as grains together
with functions for planar sections.
For the purpose of exact simulation a bivariate size-shape distribution is implemented.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>
Diff between unfoldr versions 0.5.8 dated 2016-06-24 and 0.6 dated 2016-10-06
DESCRIPTION | 14 +- MD5 | 59 +++++----- R/cylinder.R | 136 ++++++++++++------------- R/sphere.R | 40 +++---- R/spheroid.R | 216 +++++++++++++++++++++++----------------- R/unfolding.R | 38 +++---- man/drawSpheroidIntersection.Rd |only man/planarSection.Rd | 2 man/simCylinderSystem.Rd | 38 +++---- man/simModel3d.Rd | 7 - man/simSphereSystem.Rd | 14 +- man/simSpheroidSystem.Rd | 29 ++--- man/spheroids3d.Rd | 8 + man/trivarHist.Rd | 2 man/unfold.Rd | 10 - man/updateIntersections.Rd | 2 man/verticalSection.Rd | 4 src/GeometricPrimitives.cpp | 5 src/GeometricPrimitives.h | 26 +++- src/Intersector.cpp | 2 src/SimCylinder.cpp | 51 +++++---- src/SimEllipsoid.cpp | 75 +++++++++---- src/SimEllipsoid.h | 3 src/SimSphere.cpp | 53 ++++++--- src/SimSphere.h | 4 src/Utils.cpp | 11 +- src/Utils.h | 15 +- src/Vector.h | 8 + src/directions.cpp | 2 src/ellipt.cpp | 2 src/unfold.cpp | 4 31 files changed, 508 insertions(+), 372 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: "Thomas W. Jones <jones.thos.w@gmail.com>"
Maintainer: Thomas W. Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 2.0.2 dated 2016-06-06 and 2.0.3 dated 2016-10-06
DESCRIPTION | 8 +++---- MD5 | 10 ++++---- R/CreateDtm.R | 8 +++++-- R/CreateTcm.R | 10 ++++++-- R/RcppExports.R | 2 - src/RcppExports.cpp | 58 ++++++++++++++++++++++++++-------------------------- 6 files changed, 52 insertions(+), 44 deletions(-)
Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation
(DES) package for R. Designed to be a generic framework, it leverages the
power of 'Rcpp' to boost the performance, turning DES in R feasible. As a
noteworthy characteristic, 'simmer' exploits the concept of trajectory: a
common path in the simulation model for entities of the same type.
Author: Bart Smeets [aut, cph],
Iñaki Ucar [aut, cph, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer versions 3.4.3 dated 2016-10-02 and 3.4.4 dated 2016-10-06
simmer-3.4.3/simmer/inst/staticdocs |only simmer-3.4.4/simmer/DESCRIPTION | 6 simmer-3.4.4/simmer/MD5 | 23 +- simmer-3.4.4/simmer/NEWS.md | 94 +++++----- simmer-3.4.4/simmer/inst/doc/A-introduction.html | 74 +++---- simmer-3.4.4/simmer/inst/doc/B-terminology.html | 4 simmer-3.4.4/simmer/inst/doc/C-trajectories.html | 38 ++-- simmer-3.4.4/simmer/inst/doc/D-bank-1.html | 4 simmer-3.4.4/simmer/inst/doc/E-queueing-systems.html | 4 simmer-3.4.4/simmer/inst/doc/F-ctmc.html | 4 simmer-3.4.4/simmer/src/process.cpp | 10 - simmer-3.4.4/simmer/tests/testthat/test-trajectory-seize-release.R | 17 + simmer-3.4.4/simmer/tests/testthat/test-trajectory-select.R | 26 +- 13 files changed, 159 insertions(+), 145 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.1.4 dated 2016-01-28 and 0.1.5 dated 2016-10-06
DESCRIPTION | 10 MD5 | 76 ++-- NAMESPACE | 2 NEWS | 18 + R/RStoolbox.R | 4 R/RcppExports.R | 2 R/encodeQA.R | 2 R/ggR.R | 2 R/histMatch.R | 5 R/pifMatch.R | 52 +-- R/radCor.R | 410 ++++++++++++------------ R/rasterPCA.R | 74 ++-- R/readMeta.R | 469 ++++++++++++++------------- R/spectralIndices.R | 32 - R/stackMeta.R | 24 + R/superClass.R | 621 +++++++++++++++++++------------------ R/sysdata.rda |binary R/unsuperClass.R | 6 README.md | 2 data/lsat.rda |binary data/rlogo.rda |binary data/srtm.rda |binary inst/external/trainingPolygons.rds |binary man/encodeQA.Rd | 2 man/ggR.Rd | 2 man/pifMatch.Rd | 46 +- man/rasterPCA.Rd | 13 man/spectralIndices.Rd | 2 man/superClass.Rd | 4 man/unsuperClass.Rd | 6 src/RcppExports.cpp | 82 ++-- src/predictKmeans.cpp | 7 src/spectralIndices.cpp | 3 tests/testdata |only tests/testthat/test-normImage.R |only tests/testthat/test-radCor.R | 13 tests/testthat/test-rasterPCA.R |only tests/testthat/test-readMeta.R |only tests/testthat/test-superClass.R | 158 +++++---- tests/testthat/test-unsuperClass.R |only 40 files changed, 1141 insertions(+), 1008 deletions(-)
Title: Implementations of Semi-Supervised Learning Approaches for
Classification
Description: A collection of implementations of semi-supervised classifiers and methods to evaluate their performance. The package includes implementations of, among others, Implicitly Constrained Learning, Moment Constrained Learning, the Transductive SVM, Manifold regularization, Maximum Contrastive Pessimistic Likelihood estimation, S4VM and WellSVM.
Author: Jesse Krijthe [aut, cre]
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between RSSL versions 0.6 dated 2016-09-14 and 0.6.1 dated 2016-10-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/Plotting.R | 2 +- tests/testthat/test-SVM.R | 8 ++++---- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Pathwise Calibrated Sparse Shooting Algorithm
Description: Computationally efficient tools for fitting generalized linear model with convex or non-convex penalty. Users can enjoy the superior statistical property of non-convex penalty such as SCAD and MCP which has significantly less estimation error and overfitting compared to convex penalty such as lasso and ridge. Computation is handled by multi-stage convex relaxation and the PathwIse CAlibrated Sparse Shooting algOrithm (PICASSO) which exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. The computation is memory-optimized using the sparse matrix output.
Author: Jason Ge, Xingguo Li, Mengdi Wang, Tong Zhang, Han Liu and Tuo Zhao
Maintainer: Jason Ge <jiange@princeton.edu>
Diff between picasso versions 0.5.0 dated 2015-12-18 and 0.5.4 dated 2016-10-06
picasso-0.5.0/picasso/R/lasso.sc.cov.R |only picasso-0.5.0/picasso/R/lasso.sc.naive.R |only picasso-0.5.0/picasso/R/logit.R |only picasso-0.5.0/picasso/R/picasso.lasso.R |only picasso-0.5.0/picasso/R/picasso.scio.R |only picasso-0.5.0/picasso/R/scio.generator.R |only picasso-0.5.0/picasso/R/scio.plot.R |only picasso-0.5.0/picasso/R/scio.sc.R |only picasso-0.5.0/picasso/man/coef.lasso.Rd |only picasso-0.5.0/picasso/man/plot.lasso.Rd |only picasso-0.5.0/picasso/man/plot.scio.Rd |only picasso-0.5.0/picasso/man/plot.sim.Rd |only picasso-0.5.0/picasso/man/predict.lasso.Rd |only picasso-0.5.0/picasso/man/print.lasso.Rd |only picasso-0.5.0/picasso/man/print.scio.Rd |only picasso-0.5.0/picasso/man/print.sim.Rd |only picasso-0.5.0/picasso/man/scio.generator.Rd |only picasso-0.5.0/picasso/man/scio.plot.Rd |only picasso-0.5.0/picasso/src/Makevars.win |only picasso-0.5.0/picasso/src/SFGen.c |only picasso-0.5.0/picasso/src/euc_proj.c |only picasso-0.5.0/picasso/src/lambda_max.c |only picasso-0.5.0/picasso/src/mathlib.h |only picasso-0.5.0/picasso/src/mymath.h |only picasso-0.5.0/picasso/src/mymath1.c |only picasso-0.5.0/picasso/src/picasso_lasso_sc_cov.c |only picasso-0.5.0/picasso/src/picasso_lasso_sc_naive.c |only picasso-0.5.0/picasso/src/picasso_logit_cyclic.c |only picasso-0.5.0/picasso/src/picasso_logit_greedy.c |only picasso-0.5.0/picasso/src/picasso_logit_prox.c |only picasso-0.5.0/picasso/src/picasso_logit_stoc.c |only picasso-0.5.0/picasso/src/picasso_scio_sc.c |only picasso-0.5.0/picasso/src/standardize_design.c |only picasso-0.5.4/picasso/DESCRIPTION | 14 - picasso-0.5.4/picasso/MD5 | 82 +++----- picasso-0.5.4/picasso/NAMESPACE | 34 +-- picasso-0.5.4/picasso/R/gaussian_solver.R |only picasso-0.5.4/picasso/R/logit_solver.R |only picasso-0.5.4/picasso/R/picasso.R | 73 +++---- picasso-0.5.4/picasso/R/picasso.gaussian.R |only picasso-0.5.4/picasso/R/picasso.logit.R | 117 +++++------ picasso-0.5.4/picasso/R/picasso.poisson.R |only picasso-0.5.4/picasso/R/poisson_solver.R |only picasso-0.5.4/picasso/build/vignette.rds |binary picasso-0.5.4/picasso/inst/doc/PICASSO.pdf |binary picasso-0.5.4/picasso/inst/doc/vignette.pdf |binary picasso-0.5.4/picasso/man/coef.gaussian.Rd |only picasso-0.5.4/picasso/man/coef.logit.Rd | 4 picasso-0.5.4/picasso/man/coef.poisson.Rd |only picasso-0.5.4/picasso/man/picasso-package.Rd | 14 - picasso-0.5.4/picasso/man/picasso.Rd | 213 ++++++++++++++------- picasso-0.5.4/picasso/man/plot.gaussian.Rd |only picasso-0.5.4/picasso/man/plot.logit.Rd | 4 picasso-0.5.4/picasso/man/plot.poisson.Rd |only picasso-0.5.4/picasso/man/predict.gaussian.Rd |only picasso-0.5.4/picasso/man/predict.logit.Rd | 29 -- picasso-0.5.4/picasso/man/predict.poisson.Rd |only picasso-0.5.4/picasso/man/print.gaussian.Rd |only picasso-0.5.4/picasso/man/print.logit.Rd | 4 picasso-0.5.4/picasso/man/print.poisson.Rd |only picasso-0.5.4/picasso/src/IRLS_solver.c |only picasso-0.5.4/picasso/src/IRLS_solver.h |only picasso-0.5.4/picasso/src/mathutils.c |only picasso-0.5.4/picasso/src/mathutils.h |only picasso-0.5.4/picasso/src/picasso_gaussian_cov.c |only picasso-0.5.4/picasso/src/picasso_gaussian_naive.c |only picasso-0.5.4/picasso/src/picasso_logit.c |only picasso-0.5.4/picasso/src/picasso_poisson.c |only picasso-0.5.4/picasso/vignettes/PICASSO.pdf |binary 69 files changed, 300 insertions(+), 288 deletions(-)
Title: Aids in Processing and Plotting Data from a Lemna-Tec
Scananalyzer
Description: Extracts traits from imaging data produced using a Lemna-Tec Scananalyzer
(see <http://www.lemnatec.com/products/hardware-solutions/scanalyzer-3d> for more
information). Growth rates between successive imagings are obtained and those for
a nominated set of intervals can also be calculated. Profile or longitudinal plots
of the traits and growth rates can be produced. These allow one to check for
anomalous data and to explore growth patterns in the data.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between imageData versions 0.1-21 dated 2016-05-16 and 0.1-26 dated 2016-10-06
imageData-0.1-21/imageData/R/data.longi.v2.r |only imageData-0.1-26/imageData/DESCRIPTION | 18 - imageData-0.1-26/imageData/MD5 | 23 - imageData-0.1-26/imageData/NAMESPACE | 1 imageData-0.1-26/imageData/R/PVA.r | 182 ++++++++------- imageData-0.1-26/imageData/R/data.longi.v5.r |only imageData-0.1-26/imageData/build/partial.rdb |binary imageData-0.1-26/imageData/inst/NEWS.Rd | 26 ++ imageData-0.1-26/imageData/inst/doc/imageData-manual.pdf |binary imageData-0.1-26/imageData/man/calcTimes.Rd |only imageData-0.1-26/imageData/man/imageData-pkg.Rd | 7 imageData-0.1-26/imageData/man/imagetimesPlot.Rd | 56 +++- imageData-0.1-26/imageData/man/importExcel.Rd | 62 +++-- imageData-0.1-26/imageData/man/longitudinalPrime.Rd | 12 14 files changed, 245 insertions(+), 142 deletions(-)
Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Description: This model fitting tool incorporates cyclic coordinate descent and
majorization-minimization approaches to fit a variety of regression models
found in large-scale observational healthcare data. Implementations focus
on computational optimization and fine-scale parallelization to yield
efficient inference in massive datasets.
Author: Marc A. Suchard [aut, cre],
Martijn J. Schuemie [aut],
Trevor R. Shaddox [aut]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between Cyclops versions 1.2.0 dated 2016-08-01 and 1.2.2 dated 2016-10-06
Cyclops-1.2.0/Cyclops/src/cyclops/SqlModelData.cpp |only Cyclops-1.2.0/Cyclops/src/cyclops/SqlModelData.h |only Cyclops-1.2.2/Cyclops/DESCRIPTION | 6 Cyclops-1.2.2/Cyclops/MD5 | 63 - Cyclops-1.2.2/Cyclops/NAMESPACE | 1 Cyclops-1.2.2/Cyclops/NEWS | 6 Cyclops-1.2.2/Cyclops/R/Abridge.R |only Cyclops-1.2.2/Cyclops/R/DataManagement.R | 2 Cyclops-1.2.2/Cyclops/R/ModelFit.R | 24 Cyclops-1.2.2/Cyclops/R/RcppExports.R | 2 Cyclops-1.2.2/Cyclops/README.md | 6 Cyclops-1.2.2/Cyclops/man/createAbridgePrior.Rd |only Cyclops-1.2.2/Cyclops/man/createCyclopsData.Rd | 6 Cyclops-1.2.2/Cyclops/man/fitCyclopsModel.Rd | 5 Cyclops-1.2.2/Cyclops/src/Makevars | 3 Cyclops-1.2.2/Cyclops/src/RcppExports.cpp | 348 +++++----- Cyclops-1.2.2/Cyclops/src/RcppModelData.cpp | 11 Cyclops-1.2.2/Cyclops/src/RcppModelData.h | 8 Cyclops-1.2.2/Cyclops/src/cyclops/CyclicCoordinateDescent.cpp | 2 Cyclops-1.2.2/Cyclops/src/cyclops/CyclicCoordinateDescent.h | 11 Cyclops-1.2.2/Cyclops/src/cyclops/Iterators.h | 33 Cyclops-1.2.2/Cyclops/src/cyclops/ModelData.cpp | 8 Cyclops-1.2.2/Cyclops/src/cyclops/Types.h | 13 Cyclops-1.2.2/Cyclops/src/cyclops/drivers/AbstractCrossValidationDriver.cpp | 24 Cyclops-1.2.2/Cyclops/src/cyclops/drivers/CrossValidationSelector.cpp | 14 Cyclops-1.2.2/Cyclops/src/cyclops/engine/AbstractModelSpecifics.cpp | 4 Cyclops-1.2.2/Cyclops/src/cyclops/engine/ModelSpecifics.h | 23 Cyclops-1.2.2/Cyclops/src/cyclops/engine/ModelSpecifics.hpp | 23 Cyclops-1.2.2/Cyclops/src/cyclops/engine/ParallelLoops.h | 291 ++++---- Cyclops-1.2.2/Cyclops/src/cyclops/engine/Ranges.h | 16 Cyclops-1.2.2/Cyclops/src/cyclops/engine/Recursions.hpp | 4 Cyclops-1.2.2/Cyclops/src/cyclops/priors/CovariatePrior.cpp | 2 Cyclops-1.2.2/Cyclops/src/utils/HParSearch.cpp | 25 Cyclops-1.2.2/Cyclops/tests/testthat/test-Abridge.R |only Cyclops-1.2.2/Cyclops/tests/testthat/test-smallPoisson.R | 19 35 files changed, 566 insertions(+), 437 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can visualise activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <niedballa@izw-berlin.de>
Diff between camtrapR versions 0.99.4 dated 2016-08-12 and 0.99.5 dated 2016-10-06
DESCRIPTION | 8 MD5 | 60 +++--- NEWS | 21 ++ R/activityDensity.R | 8 R/activityHistogram.R | 1 R/activityOverlap.R | 4 R/appendSpeciesNames.R | 11 - R/checkSpeciesIdentification.R | 10 - R/detectionHistory.R | 1 R/getSpeciesImages.R | 223 +++++++++++++++----------- R/imageRename.R | 61 ++----- R/recordTable.R | 55 +----- R/recordTableIndividual.R | 57 +----- R/spatialDetectionHistory.R | 1 R/variousOtherHelperFunctions.R | 74 ++++++++ data/recordTableSample.rda |binary inst/doc/DataExploration.html | 14 - inst/doc/DataExtraction.html | 152 +++++++++-------- inst/doc/ImageOrganisation.html | 56 +++--- inst/doc/SpeciesIndividualIdentification.R | 23 ++ inst/doc/SpeciesIndividualIdentification.Rmd | 48 +++++ inst/doc/SpeciesIndividualIdentification.html | 136 +++++++++------ man/activityDensity.Rd | 2 man/activityOverlap.Rd | 2 man/activityRadial.Rd | 2 man/addCopyrightTag.Rd | 4 man/camtrapR-package.Rd | 4 man/getSpeciesImages.Rd | 60 +++++- man/recordTable.Rd | 44 ++++- man/recordTableIndividual.Rd | 10 - vignettes/SpeciesIndividualIdentification.Rmd | 48 +++++ 31 files changed, 737 insertions(+), 463 deletions(-)
Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level".
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between reportr versions 1.2.1 dated 2016-04-01 and 1.2.2 dated 2016-10-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 16 ++++++++++++++++ R/reportr.R | 5 ++++- 4 files changed, 27 insertions(+), 8 deletions(-)
Title: Multiscale Clustering of Geometrical Network
Description: Co-Expression Network Analysis by adopting network embedding technique.
Author: Won-Min Song, Bin Zhang
Maintainer: Won-Min Song <wonmin1984@gmail.com>
Diff between MEGENA versions 1.3.4-1 dated 2016-07-11 and 1.3.4-6 dated 2016-10-06
MEGENA-1.3.4-1/MEGENA/man/set.parallel.backend.Rd |only MEGENA-1.3.4-6/MEGENA/DESCRIPTION | 12 +- MEGENA-1.3.4-6/MEGENA/MD5 | 26 +++--- MEGENA-1.3.4-6/MEGENA/NAMESPACE | 6 + MEGENA-1.3.4-6/MEGENA/R/ClusteringPackage.R | 20 ++-- MEGENA-1.3.4-6/MEGENA/R/Combined_functions.R | 7 + MEGENA-1.3.4-6/MEGENA/R/Downstream_TableManip.R | 8 - MEGENA-1.3.4-6/MEGENA/R/ModulePlot.R |only MEGENA-1.3.4-6/MEGENA/R/PFN_Computation.R | 95 +++++++++++----------- MEGENA-1.3.4-6/MEGENA/build |only MEGENA-1.3.4-6/MEGENA/inst |only MEGENA-1.3.4-6/MEGENA/man/calculate.PFN.Rd | 7 + MEGENA-1.3.4-6/MEGENA/man/compute.PFN.par.Rd |only MEGENA-1.3.4-6/MEGENA/man/plot_module.Rd |only MEGENA-1.3.4-6/MEGENA/man/plot_subgraph.Rd |only MEGENA-1.3.4-6/MEGENA/src/RcppExports.cpp | 18 +--- MEGENA-1.3.4-6/MEGENA/vignettes |only 17 files changed, 111 insertions(+), 88 deletions(-)
Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast cumulative
residuals, excess risk models and more. Flexible competing risks regression
including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy Silver
and Klaus Holst
Maintainer: Thomas Scheike <ts@biostat.ku.dk>
Diff between timereg versions 1.8.9 dated 2015-05-28 and 1.9.0 dated 2016-10-06
DESCRIPTION | 27 ++--- MD5 | 74 ++++++++------- NAMESPACE | 31 ++++++ R/aalen.r | 18 ++- R/base.r | 96 +++---------------- R/clusterindex-reshape.r | 2 R/comprisk.r | 34 ++++-- R/cox-aalen.r | 23 +++- R/cox.ipw.r | 5 - R/cox.marg.r |only R/event.r | 4 R/event.split.r |only R/ipcw-residualmean.r | 13 +- R/kmplot.r | 9 + R/mgresid.r | 15 +-- R/new.aalen.r | 15 ++- R/new.cox-aalen.r | 24 +++- R/new.dynreg.r | 4 R/plots.r | 4 R/predict-timereg.r | 19 ++- R/prop-odds-subdist.r | 28 +++-- R/qcut.r |only R/residualsTimereg.r |only R/restricted.residual.mean.r | 5 - R/timecox.r | 8 - R/two-stage-reg.r | 99 +++++++++++--------- man/aalen.Rd | 10 +- man/comp.risk.Rd | 8 - man/cox.aalen.Rd | 9 + man/cox.ipw.Rd |only man/event.split.Rd |only man/internal-addreg.Rd | 15 ++- man/predict.timereg.Rd | 14 ++ man/prep.comp.risk.Rd | 4 man/prop.odds.Rd | 11 ++ man/prop.odds.subdist.Rd | 5 - man/res.mean.Rd | 12 +- man/wald.test.Rd | 3 src/aalen.c | 40 ++++++-- src/cox-aalen.c | 210 +++++++++++++++++++++++++++---------------- src/two-stage-reg.c | 11 +- 41 files changed, 550 insertions(+), 359 deletions(-)
Title: Flexible Univariate Count Models Based on Renewal Processes
Description: Flexible univariate count models based on renewal
processes. The models may include covariates and can be specified
with familiar formula syntax as in glm().
Author: Tarak Kharrat, Georgi N. Boshnakov
Maintainer: Tarak Kharrat <tarak.kharrat@gmail.com>
Diff between Countr versions 3.2.6 dated 2016-09-14 and 3.2.7 dated 2016-10-06
DESCRIPTION | 15 ++++++++------- MD5 | 28 +++++++++++++++++++--------- NAMESPACE | 1 + NEWS | 4 ++++ R/Countr.R | 10 +++++----- R/Renewal_methods.R | 2 +- build |only inst/doc |only src/conv_all.cpp | 10 +++++++--- src/conv_dePril.cpp | 11 ++++++++--- src/conv_naive.cpp | 10 ++++++---- src/modifiedRenewal.cpp | 12 ++++++++---- vignettes |only 13 files changed, 67 insertions(+), 36 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-31 0.6.0
2016-05-05 0.5.6
2016-01-25 0.5.2
2015-12-02 0.5.0
2015-07-07 0.4.2
2015-06-19 0.4.0
2014-12-20 0.3.3
2014-07-21 0.2.0
2014-03-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-31 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-06 1.3.0
2016-06-24 1.2.0
2016-04-20 1.1.4
2016-04-18 1.1.3
2016-04-13 1.1.2
2016-02-16 1.1.1
2016-01-26 1.1.0
2015-08-10 1.0.1
Title: Convert Spatial Data Using Tidy Tables
Description: Tools to convert from specific formats to more general forms of
spatial data. Using tables to store the actual entities present in spatial
data provides far greater flexibility, and the functions here deliberately
minimize the level of interpretation applied, leaving that for specific
applications. Includes round-trip for 'Spatial' classes and long-form
tables, analogous to 'ggplot2::fortify'.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between spbabel versions 0.4.0 dated 2016-08-07 and 0.4.5 dated 2016-10-06
DESCRIPTION | 10 +- MD5 | 43 +++++++---- NAMESPACE | 8 +- NEWS.md | 18 ++++ R/gobbleGeom.r |only R/mtable.r | 74 +++++++++----------- R/raster_geom.r |only R/spFromTable.r | 18 +++- R/sptable.r | 137 ++++++++++++++------------------------ R/trip.r |only R/unique_ids.r | 20 ++--- R/utils.r | 50 +++++-------- README.md | 37 ++++++++++ inst/devignette |only inst/doc/spbabel.Rmd | 2 inst/doc/spbabel.html | 18 ++-- inst/examples |only inst/sf_convert.r |only man/sptable.Rd | 15 ++-- tests/testthat/test-map_table.R | 8 ++ tests/testthat/test-misc.R |only tests/testthat/test-replacement.R |only tests/testthat/test-spFromTable.R | 20 ++++- tests/testthat/test-sptable.R | 5 + tests/testthat/test-trip.R |only tests/testthat/test-utils.R |only vignettes/spbabel.Rmd | 2 27 files changed, 265 insertions(+), 220 deletions(-)
Title: Develop and Run Spatially Explicit Discrete Event Simulation
Models
Description: Implement a variety of event-based models, with a focus on
spatially explicit models. These include raster-based, event-based, and
agent-based models. The core simulation components are built upon a discrete
event simulation (DES) framework that facilitates modularity, and easily
enables the user to include additional functionality by running user-built
simulation modules. Included are numerous tools to visualize raster and
other maps. The suggested package 'fastshp' can be installed with
`install.packages("fastshp", repos = "http://rforge.net", type = "source")`.
Author: Alex M Chubaty [aut, cre],
Eliot J B McIntire [aut],
Yong Luo [ctb],
Steve Cumming [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alexander.chubaty@canada.ca>
Diff between SpaDES versions 1.2.0 dated 2016-06-24 and 1.3.0 dated 2016-10-06
SpaDES-1.2.0/SpaDES/man/nlayers.Rd |only SpaDES-1.2.0/SpaDES/man/simList-accessors-objects.Rd |only SpaDES-1.2.0/SpaDES/man/simList-accessors-params.Rd |only SpaDES-1.3.0/SpaDES/DESCRIPTION | 70 SpaDES-1.3.0/SpaDES/MD5 | 498 SpaDES-1.3.0/SpaDES/NAMESPACE | 1034 - SpaDES-1.3.0/SpaDES/NEWS | 534 SpaDES-1.3.0/SpaDES/R/POM.R |only SpaDES-1.3.0/SpaDES/R/SELES.R | 563 SpaDES-1.3.0/SpaDES/R/agent.R | 176 SpaDES-1.3.0/SpaDES/R/check.R | 545 SpaDES-1.3.0/SpaDES/R/checkpoint.R | 726 - SpaDES-1.3.0/SpaDES/R/copy.R | 78 SpaDES-1.3.0/SpaDES/R/environment.R | 401 SpaDES-1.3.0/SpaDES/R/experiment.R | 1149 - SpaDES-1.3.0/SpaDES/R/helpers.R | 305 SpaDES-1.3.0/SpaDES/R/initialize.R | 710 - SpaDES-1.3.0/SpaDES/R/load.R | 630 - SpaDES-1.3.0/SpaDES/R/mapReduce.R | 167 SpaDES-1.3.0/SpaDES/R/mergeRaster.R | 150 SpaDES-1.3.0/SpaDES/R/misc-methods.R | 1452 +- SpaDES-1.3.0/SpaDES/R/module-dependencies-class.R | 451 SpaDES-1.3.0/SpaDES/R/module-dependencies-methods.R | 541 SpaDES-1.3.0/SpaDES/R/module-repository.R | 957 - SpaDES-1.3.0/SpaDES/R/module-template.R | 1660 +- SpaDES-1.3.0/SpaDES/R/moduleCoverage.R | 300 SpaDES-1.3.0/SpaDES/R/moduleMetadata.R | 213 SpaDES-1.3.0/SpaDES/R/movement.R | 252 SpaDES-1.3.0/SpaDES/R/neighbourhood.R | 1926 +-- SpaDES-1.3.0/SpaDES/R/numerical-comparisons.R | 72 SpaDES-1.3.0/SpaDES/R/plotting-classes.R | 584 SpaDES-1.3.0/SpaDES/R/plotting-colours.R | 1218 + SpaDES-1.3.0/SpaDES/R/plotting-diagrams.R | 719 - SpaDES-1.3.0/SpaDES/R/plotting-helpers.R | 3124 +++-- SpaDES-1.3.0/SpaDES/R/plotting-other.R | 831 - SpaDES-1.3.0/SpaDES/R/plotting.R | 2806 +--- SpaDES-1.3.0/SpaDES/R/priority.R | 86 SpaDES-1.3.0/SpaDES/R/probability.R | 94 SpaDES-1.3.0/SpaDES/R/progress.R | 230 SpaDES-1.3.0/SpaDES/R/rstudio-addins.R |only SpaDES-1.3.0/SpaDES/R/save.R | 326 SpaDES-1.3.0/SpaDES/R/shine.R | 742 - SpaDES-1.3.0/SpaDES/R/simList-accessors.R | 6168 +++++----- SpaDES-1.3.0/SpaDES/R/simList-class.R | 514 SpaDES-1.3.0/SpaDES/R/simulation.R | 2353 ++- SpaDES-1.3.0/SpaDES/R/spades-classes.R | 72 SpaDES-1.3.0/SpaDES/R/spades-package.R | 899 - 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SpaDES-1.3.0/SpaDES/vignettes/ii-modules.Rmd | 1630 +- SpaDES-1.3.0/SpaDES/vignettes/iii-plotting.Rmd | 874 - 264 files changed, 42433 insertions(+), 38828 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Vijay Barve [ctb],
Dan Mcglinn [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.9.4 dated 2016-06-29 and 0.9.5 dated 2016-10-06
DESCRIPTION | 17 MD5 | 94 ++-- NAMESPACE | 2 NEWS.md | 55 ++ R/check_wkt.r | 12 R/dataset_search.r | 5 R/gbif_photos.r | 38 + R/occ_count.r | 111 ++++- R/occ_data.R | 168 ++++---- R/occ_facet.R |only R/occ_search.r | 254 ++++++------- R/occ_spellcheck.R |only R/overload_classes.R |only R/print_gbif.R |only R/zzz.r | 51 ++ README.md | 205 +++++----- inst/assets/img/unnamed-chunk-8-1.png |binary inst/doc/issues_vignette.Rmd | 286 +++++++------- inst/doc/issues_vignette.html | 286 +++++++------- inst/doc/rgbif_vignette.Rmd | 657 ++++++++++++++++++++++++++++++---- inst/doc/rgbif_vignette.html | 437 +++++++++++----------- inst/doc/taxonomic_names.Rmd | 54 +- inst/doc/taxonomic_names.html | 54 +- inst/singlemaplayout.html | 8 inst/vign/figure/gbifmap1-1.png |binary inst/vign/issues_vignette.md | 286 +++++++------- inst/vign/rgbif_vignette.md | 435 +++++++++++----------- inst/vign/taxonomic_names.md | 54 +- man/check_wkt.Rd | 3 man/dataset_search.Rd | 6 man/dataset_suggest.Rd | 3 man/gbif_photos.Rd | 12 man/occ_count.Rd | 79 +++- man/occ_data.Rd | 180 ++++++++- man/occ_facet.Rd |only man/occ_search.Rd | 232 +++++++++++- man/occ_spellcheck.Rd |only tests/testthat/test-dataset_search.r | 25 - tests/testthat/test-gbif_names.R | 1 tests/testthat/test-gbif_photos.R | 26 - tests/testthat/test-name_lookup.r | 5 tests/testthat/test-name_suggest.r | 4 tests/testthat/test-nodes.r | 2 tests/testthat/test-occ_count.r | 17 tests/testthat/test-occ_data.R | 25 + tests/testthat/test-occ_facet.R |only tests/testthat/test-occ_metadata.r | 2 tests/testthat/test-occ_search.r | 38 + tests/testthat/test-occ_spellcheck.R |only vignettes/issues_vignette.Rmd | 286 +++++++------- vignettes/rgbif_vignette.Rmd | 435 +++++++++++----------- vignettes/taxonomic_names.Rmd | 54 +- 52 files changed, 3088 insertions(+), 1916 deletions(-)
Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre],
Mei-Ling Ting Lee [ctb],
Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>
Diff between clusrank versions 0.4-4 dated 2016-09-26 and 0.4-5 dated 2016-10-06
clusrank-0.4-4/clusrank/data/eye.rda |only clusrank-0.4-5/clusrank/DESCRIPTION | 6 - clusrank-0.4-5/clusrank/MD5 | 16 ++-- clusrank-0.4-5/clusrank/R/RcppExports.R | 2 clusrank-0.4-5/clusrank/R/clusWilcox.R | 8 +- clusrank-0.4-5/clusrank/R/clusranksum.R | 7 +- clusrank-0.4-5/clusrank/R/eye.R | 48 +++++++++----- clusrank-0.4-5/clusrank/data/eye.RData |only clusrank-0.4-5/clusrank/man/eye.Rd | 50 +++++++++------ clusrank-0.4-5/clusrank/src/RcppExports.cpp | 90 ++++++++++++++-------------- 10 files changed, 124 insertions(+), 103 deletions(-)
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph],
Nicolas Muller [aut],
Reto Buergin [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 1.8-12 dated 2016-06-24 and 1.8-13 dated 2016-10-05
TraMineR-1.8-12/TraMineR/src/src |only TraMineR-1.8-12/TraMineR/vignettes/Graphiques |only TraMineR-1.8-13/TraMineR/DESCRIPTION | 8 - TraMineR-1.8-13/TraMineR/MD5 | 54 +--------- TraMineR-1.8-13/TraMineR/NEWS | 12 ++ TraMineR-1.8-13/TraMineR/inst/CITATION | 2 TraMineR-1.8-13/TraMineR/inst/doc/TraMineR-state-sequence.pdf |binary TraMineR-1.8-13/TraMineR/man/TraMineR-package.Rd | 8 - TraMineR-1.8-13/TraMineR/src/eventseq.cpp | 2 9 files changed, 27 insertions(+), 59 deletions(-)
Title: General Purpose R Interface to 'Solr'
Description: Provides a set of functions for querying and parsing data
from 'Solr' (<http://lucene.apache.org/solr>) 'endpoints' (local and
remote), including search, 'faceting', 'highlighting', 'stats', and
'more like this'. In addition, some functionality is included for
creating, deleting, and updating documents in a 'Solr' 'database'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between solrium versions 0.3.0 dated 2016-02-10 and 0.4.0 dated 2016-10-05
solrium-0.3.0/solrium/R/parsers.r |only solrium-0.4.0/solrium/DESCRIPTION | 12 - solrium-0.4.0/solrium/MD5 | 101 ++++++++-------- solrium-0.4.0/solrium/NAMESPACE | 27 ++-- solrium-0.4.0/solrium/NEWS.md | 15 ++ solrium-0.4.0/solrium/R/add.R | 9 - solrium-0.4.0/solrium/R/commit.R | 38 +++--- solrium-0.4.0/solrium/R/config_get.R | 66 +++++----- solrium-0.4.0/solrium/R/config_params.R | 2 solrium-0.4.0/solrium/R/connect.R | 2 solrium-0.4.0/solrium/R/core_split.R | 4 solrium-0.4.0/solrium/R/delete.R | 2 solrium-0.4.0/solrium/R/optimize.R | 4 solrium-0.4.0/solrium/R/parsers.R |only solrium-0.4.0/solrium/R/ping.R | 44 +++--- solrium-0.4.0/solrium/R/solr_all.r | 17 +- solrium-0.4.0/solrium/R/solr_facet.r | 60 ++++++--- solrium-0.4.0/solrium/R/solr_get.R | 18 +- solrium-0.4.0/solrium/R/solr_group.r | 67 +++++++--- solrium-0.4.0/solrium/R/solr_highlight.r | 15 +- solrium-0.4.0/solrium/R/solr_mlt.r | 35 +++-- solrium-0.4.0/solrium/R/solr_search.r | 26 ++-- solrium-0.4.0/solrium/R/solr_stats.r | 21 +-- solrium-0.4.0/solrium/R/solrium-package.R | 34 ++--- solrium-0.4.0/solrium/R/update_csv.R | 24 +-- solrium-0.4.0/solrium/R/zzz.r | 10 + solrium-0.4.0/solrium/build/vignette.rds |binary solrium-0.4.0/solrium/man/add.Rd | 9 - solrium-0.4.0/solrium/man/collapse_pivot_names.Rd | 6 solrium-0.4.0/solrium/man/commit.Rd | 12 - solrium-0.4.0/solrium/man/config_get.Rd | 9 - solrium-0.4.0/solrium/man/delete.Rd | 2 solrium-0.4.0/solrium/man/optimize.Rd | 2 solrium-0.4.0/solrium/man/ping.Rd | 21 ++- solrium-0.4.0/solrium/man/pivot_flatten_tabular.Rd | 8 - solrium-0.4.0/solrium/man/solr_all.Rd | 4 solrium-0.4.0/solrium/man/solr_facet.Rd | 22 ++- solrium-0.4.0/solrium/man/solr_get.Rd | 8 - solrium-0.4.0/solrium/man/solr_group.Rd | 53 ++++++-- solrium-0.4.0/solrium/man/solr_mlt.Rd | 20 +-- solrium-0.4.0/solrium/man/solr_parse.Rd | 14 -- solrium-0.4.0/solrium/man/solr_search.Rd | 14 +- solrium-0.4.0/solrium/man/solr_stats.Rd | 4 solrium-0.4.0/solrium/man/solrium-package.Rd | 25 ++- solrium-0.4.0/solrium/man/update_csv.Rd | 6 solrium-0.4.0/solrium/tests/testthat/test-core_create.R | 2 solrium-0.4.0/solrium/tests/testthat/test-errors.R | 2 solrium-0.4.0/solrium/tests/testthat/test-ping.R | 2 solrium-0.4.0/solrium/tests/testthat/test-solr_all.R |only solrium-0.4.0/solrium/tests/testthat/test-solr_facet.r | 32 ++++- solrium-0.4.0/solrium/tests/testthat/test-solr_mlt.r | 20 +-- solrium-0.4.0/solrium/tests/testthat/test-solr_search.r | 68 ++++++++++ solrium-0.4.0/solrium/tests/testthat/test-solr_stats.r | 50 +++++++ 53 files changed, 681 insertions(+), 387 deletions(-)
Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson [aut, cre, cph],
Michael Hahsler [ctb]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>
Diff between arulesCBA versions 1.0.1 dated 2016-09-26 and 1.0.2 dated 2016-10-05
DESCRIPTION | 20 ++++++++++++-------- MD5 | 8 ++++---- R/classifier.R | 22 ++-------------------- inst/doc/arulesCBA.pdf |binary man/classifier.Rd | 3 ++- 5 files changed, 20 insertions(+), 33 deletions(-)
Title: A Simple Data Science Challenge System
Description: A simple data science challenge system using R Markdown and Dropbox <https://www.dropbox.com/>.
It requires no network configuration, does not depend on external platforms
like e.g. Kaggle <https://www.kaggle.com/> and can be easily installed on a personal computer.
Author: Adrien Todeschini [aut, cre],
Robin Genuer [ctb]
Maintainer: Adrien Todeschini <adrien.todeschini@gmail.com>
Diff between rchallenge versions 1.1.1 dated 2015-11-26 and 1.2.0 dated 2016-10-05
rchallenge-1.1.1/rchallenge/R/dev_utils.r |only rchallenge-1.2.0/rchallenge/DESCRIPTION | 6 - rchallenge-1.2.0/rchallenge/MD5 | 14 ++-- rchallenge-1.2.0/rchallenge/NEWS.md |only rchallenge-1.2.0/rchallenge/R/new.r | 19 +++-- rchallenge-1.2.0/rchallenge/R/rchallenge.r | 21 ++++-- rchallenge-1.2.0/rchallenge/README.md | 59 +++++++++--------- rchallenge-1.2.0/rchallenge/man/publish.Rd | 17 +++-- rchallenge-1.2.0/rchallenge/man/rchallenge-package.Rd | 22 ++++-- 9 files changed, 95 insertions(+), 63 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting
library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between visNetwork versions 1.0.1 dated 2016-06-20 and 1.0.2 dated 2016-10-05
visNetwork-1.0.1/visNetwork/inst/htmlwidgets/lib/vis/vis-network.min.js |only visNetwork-1.0.2/visNetwork/DESCRIPTION | 8 visNetwork-1.0.2/visNetwork/MD5 | 174 +++--- visNetwork-1.0.2/visNetwork/NAMESPACE | 2 visNetwork-1.0.2/visNetwork/NEWS | 15 visNetwork-1.0.2/visNetwork/R/visConfigure.R | 2 visNetwork-1.0.2/visNetwork/R/visDocumentation.R | 2 visNetwork-1.0.2/visNetwork/R/visEdges.R | 22 visNetwork-1.0.2/visNetwork/R/visExport.R | 2 visNetwork-1.0.2/visNetwork/R/visFit.R | 9 visNetwork-1.0.2/visNetwork/R/visFocus.R | 2 visNetwork-1.0.2/visNetwork/R/visGetEdges.R |only visNetwork-1.0.2/visNetwork/R/visGetNodes.R |only visNetwork-1.0.2/visNetwork/R/visGetPositions.R | 2 visNetwork-1.0.2/visNetwork/R/visGroups.R | 2 visNetwork-1.0.2/visNetwork/R/visHierarchicalLayout.R | 2 visNetwork-1.0.2/visNetwork/R/visIgraph.R | 2 visNetwork-1.0.2/visNetwork/R/visIgraphLayout.R | 4 visNetwork-1.0.2/visNetwork/R/visInteraction.R | 4 visNetwork-1.0.2/visNetwork/R/visLayout.R | 2 visNetwork-1.0.2/visNetwork/R/visLegend.R | 2 visNetwork-1.0.2/visNetwork/R/visMoveNode.R | 2 visNetwork-1.0.2/visNetwork/R/visNetwork.R | 77 ++ visNetwork-1.0.2/visNetwork/R/visNetworkEvents.R | 11 visNetwork-1.0.2/visNetwork/R/visNetworkProxy.R | 3 visNetwork-1.0.2/visNetwork/R/visNodes.R | 1 visNetwork-1.0.2/visNetwork/R/visOptions.R | 57 +- visNetwork-1.0.2/visNetwork/R/visPhysics.R | 2 visNetwork-1.0.2/visNetwork/R/visRedraw.R | 2 visNetwork-1.0.2/visNetwork/R/visRemoveEdges.R | 10 visNetwork-1.0.2/visNetwork/R/visRemoveNodes.R | 13 visNetwork-1.0.2/visNetwork/R/visSave.R | 1 visNetwork-1.0.2/visNetwork/R/visSelectEdges.R | 8 visNetwork-1.0.2/visNetwork/R/visSelectNodes.R | 8 visNetwork-1.0.2/visNetwork/R/visSetData.R | 2 visNetwork-1.0.2/visNetwork/R/visSetOptions.R | 1 visNetwork-1.0.2/visNetwork/R/visSetSelection.R | 14 visNetwork-1.0.2/visNetwork/R/visStabilize.R | 2 visNetwork-1.0.2/visNetwork/R/visUnselectAll.R | 2 visNetwork-1.0.2/visNetwork/R/visUpdateEdges.R | 2 visNetwork-1.0.2/visNetwork/R/visUpdateNodes.R | 9 visNetwork-1.0.2/visNetwork/README.md | 16 visNetwork-1.0.2/visNetwork/inst/doc/Introduction-to-visNetwork.html | 92 +-- visNetwork-1.0.2/visNetwork/inst/htmlwidgets/lib/export/html2canvas/html2canvas.js | 16 visNetwork-1.0.2/visNetwork/inst/htmlwidgets/lib/vis/vis.min.js |only visNetwork-1.0.2/visNetwork/inst/htmlwidgets/visNetwork.js | 281 +++++++--- visNetwork-1.0.2/visNetwork/inst/htmlwidgets/visNetwork.yaml | 2 visNetwork-1.0.2/visNetwork/inst/shiny/server.R | 1 visNetwork-1.0.2/visNetwork/inst/shiny/src/server/options_server.R | 13 visNetwork-1.0.2/visNetwork/inst/shiny/src/server/proxy_anim_server.R | 2 visNetwork-1.0.2/visNetwork/inst/shiny/src/server/proxy_get_server.R |only visNetwork-1.0.2/visNetwork/inst/shiny/src/server/proxy_options_server.R | 3 visNetwork-1.0.2/visNetwork/inst/shiny/src/server/proxy_select_server.R | 3 visNetwork-1.0.2/visNetwork/inst/shiny/src/ui/options_ui.R | 2 visNetwork-1.0.2/visNetwork/inst/shiny/src/ui/proxy_get_ui.R |only visNetwork-1.0.2/visNetwork/inst/shiny/ui.R | 3 visNetwork-1.0.2/visNetwork/man/visConfigure.Rd | 3 visNetwork-1.0.2/visNetwork/man/visDocumentation.Rd | 3 visNetwork-1.0.2/visNetwork/man/visEdges.Rd | 23 visNetwork-1.0.2/visNetwork/man/visEvents.Rd | 13 visNetwork-1.0.2/visNetwork/man/visExport.Rd | 3 visNetwork-1.0.2/visNetwork/man/visFit.Rd | 3 visNetwork-1.0.2/visNetwork/man/visFocus.Rd | 3 visNetwork-1.0.2/visNetwork/man/visGetEdges.Rd |only visNetwork-1.0.2/visNetwork/man/visGetNodes.Rd |only visNetwork-1.0.2/visNetwork/man/visGetPositions.Rd | 3 visNetwork-1.0.2/visNetwork/man/visGroups.Rd | 3 visNetwork-1.0.2/visNetwork/man/visHierarchicalLayout.Rd | 3 visNetwork-1.0.2/visNetwork/man/visIgraphLayout.Rd | 3 visNetwork-1.0.2/visNetwork/man/visInteraction.Rd | 3 visNetwork-1.0.2/visNetwork/man/visLayout.Rd | 3 visNetwork-1.0.2/visNetwork/man/visLegend.Rd | 3 visNetwork-1.0.2/visNetwork/man/visMoveNode.Rd | 3 visNetwork-1.0.2/visNetwork/man/visNetwork-igraph.Rd | 3 visNetwork-1.0.2/visNetwork/man/visNetwork-shiny.Rd | 5 visNetwork-1.0.2/visNetwork/man/visNetwork.Rd | 22 visNetwork-1.0.2/visNetwork/man/visNodes.Rd | 3 visNetwork-1.0.2/visNetwork/man/visOptions.Rd | 16 visNetwork-1.0.2/visNetwork/man/visPhysics.Rd | 3 visNetwork-1.0.2/visNetwork/man/visRedraw.Rd | 3 visNetwork-1.0.2/visNetwork/man/visRemoveEdges.Rd | 5 visNetwork-1.0.2/visNetwork/man/visRemoveNodes.Rd | 7 visNetwork-1.0.2/visNetwork/man/visSave.Rd | 3 visNetwork-1.0.2/visNetwork/man/visSelectEdges.Rd | 3 visNetwork-1.0.2/visNetwork/man/visSelectNodes.Rd | 3 visNetwork-1.0.2/visNetwork/man/visSetData.Rd | 3 visNetwork-1.0.2/visNetwork/man/visSetOptions.Rd | 3 visNetwork-1.0.2/visNetwork/man/visSetSelection.Rd | 3 visNetwork-1.0.2/visNetwork/man/visStabilize.Rd | 3 visNetwork-1.0.2/visNetwork/man/visUnselectAll.Rd | 3 visNetwork-1.0.2/visNetwork/man/visUpdateEdges.Rd | 3 visNetwork-1.0.2/visNetwork/man/visUpdateNodes.Rd | 7 92 files changed, 798 insertions(+), 297 deletions(-)
Title: Plot Categorical Data Using Quasirandom Noise and Density
Estimates
Description: Generate a violin point plot, a combination of a violin/histogram
plot and a scatter plot by offsetting points within a category based on their
density using quasirandom noise.
Author: Scott Sherrill-Mix, Erik Clarke
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>
Diff between vipor versions 0.4.3 dated 2016-07-27 and 0.4.4 dated 2016-10-05
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/violinPoint.R | 8 ++++---- inst/doc/methodComparison.R | 20 ++++++++++++++------ inst/doc/methodComparison.Rnw | 10 +++++++--- inst/doc/methodComparison.pdf |binary inst/doc/usageExamples.pdf |binary man/digits2number.Rd | 2 +- man/number2digits.Rd | 2 +- tests/testthat/tests.R | 16 +++++++++++++++- vignettes/methodComparison.Rnw | 10 +++++++--- 11 files changed, 63 insertions(+), 33 deletions(-)
Title: Fitting Step-Functions
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Timo Aspelmeier [cre, aut],
Thomas Hotz [aut],
Hannes Sieling [aut],
Pein Florian [ctb]
Maintainer: Timo Aspelmeier <timo.aspelmeier@mathematik.uni-goettingen.de>
Diff between stepR versions 1.0-4 dated 2016-03-24 and 1.0-5 dated 2016-10-05
ChangeLog | 65 ++++++++++++++++++++++++++++++++------------------- DESCRIPTION | 8 +++--- MD5 | 24 +++++++++--------- inst/CITATION | 2 - src/BinTree.h | 14 +++++++--- src/Bounds.cpp | 11 +++++++- src/Jump.cpp | 2 - src/Jump.h | 6 ++++ src/Step.cpp | 2 - src/Step.h | 19 ++++++++++---- src/StepBinom.cpp | 6 ++-- src/StepGaussVar.cpp | 8 +++--- src/StepPoisson.cpp | 6 ++-- 13 files changed, 108 insertions(+), 65 deletions(-)
Title: Structural Equation Modeling Using the Reticular Action Model
(RAM) Notation
Description: We rewrite of RAMpath software developed by John McArdle and Steven Boker as an R package. In addition to performing regular SEM analysis through the R package lavaan, RAMpath has unique features. First, it can generate path diagrams according to a given model. Second, it can display path tracing rules through path diagrams and decompose total effects into their respective direct and indirect effects as well as decompose variance and covariance into individual bridges. Furthermore, RAMpath can fit dynamic system models automatically based on latent change scores and generate vector field plots based upon results obtained from a bivariate dynamic system. Starting version 0.4, RAMpath can conduct power analysis for both univariate and bivariate latent change score models.
Author: Zhiyong Zhang, Jack McArdle, Aki Hamagami, & Kevin Grimm
Maintainer: Zhiyong Zhang <zzhang4@nd.edu>
Diff between RAMpath versions 0.3.8 dated 2014-01-21 and 0.4 dated 2016-10-05
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++++-- NAMESPACE | 8 ++++++-- R/power.R |only man/plot.lcs.power.Rd |only man/powerBLCS.Rd |only man/powerLCS.Rd |only 7 files changed, 19 insertions(+), 11 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modelling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete variable
models are supported.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.19 dated 2016-08-18 and 1.20.1 dated 2016-10-05
DESCRIPTION | 7 - MD5 | 66 ++++++++-------- NAMESPACE | 1 NEWS.md | 30 +++++++ R/03-estimation.R | 5 - R/EMstep.group.R | 24 +++--- R/EMstep.utils.R | 26 ++---- R/LoadPars.R | 7 + R/PLCI.mirt.R | 72 +++++++++++++----- R/PrepData.R | 5 + R/itemfit.R | 141 ++++++++++++++++++++---------------- R/itemplot.internal.R | 24 +++++- R/mdirt.R | 6 + R/mirt-package.R | 8 +- R/mirt.R | 13 +-- R/mirtCluster.R | 1 R/mixedmirt.R | 12 ++- R/personfit.R | 6 + R/poly2dich.R |only R/shinyItemplot.R | 26 +++--- R/utils.R | 9 ++ README.md | 4 - build/vignette.rds |binary man/LSAT6.Rd | 8 +- man/PLCI.mirt.Rd | 9 ++ man/itemfit.Rd | 88 ++++++++++++---------- man/mdirt.Rd | 8 +- man/mirt.Rd | 13 +-- man/mixedmirt.Rd | 1 man/poly2dich.Rd |only tests/tests/test-01-mirtOne.R | 8 +- tests/tests/test-02-mirtTwo.R | 2 tests/tests/test-04-multipleGroup.R | 14 +-- tests/tests/test-09-mirt.model.R | 2 tests/tests/test-11-discrete.R | 20 ++--- 35 files changed, 415 insertions(+), 251 deletions(-)
Title: Code Analysis Tools for R
Description: Code analysis tools for R.
Author: Luke Tierney <luke-tierney@uiowa.edu>
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between codetools versions 0.2-14 dated 2015-07-15 and 0.2-15 dated 2016-10-05
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/codetools.R | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Statistical Analysis of Point Processes
Description: Functions for statistical analysis of point processes.
Author: The Institute of Statistical Mathematics
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>
Diff between SAPP versions 1.0.4 dated 2014-07-31 and 1.0.7 dated 2016-10-05
SAPP-1.0.4/SAPP/inst/doc/SAPP-manual.pdf |only SAPP-1.0.4/SAPP/inst/doc/index.html |only SAPP-1.0.7/SAPP/DESCRIPTION | 11 SAPP-1.0.7/SAPP/MD5 | 88 ++--- SAPP-1.0.7/SAPP/NAMESPACE | 3 SAPP-1.0.7/SAPP/R/SAPP.R | 15 SAPP-1.0.7/SAPP/data/Brastings.rda |binary SAPP-1.0.7/SAPP/data/PProcess.rda |binary SAPP-1.0.7/SAPP/data/PoissonData.rda |binary SAPP-1.0.7/SAPP/data/SelfExcit.rda |binary SAPP-1.0.7/SAPP/data/main2003JUL26.rda |binary SAPP-1.0.7/SAPP/data/res2003JUL26.rda |binary SAPP-1.0.7/SAPP/inst/doc/changes.txt | 29 + SAPP-1.0.7/SAPP/man/Brastings.Rd | 8 SAPP-1.0.7/SAPP/man/PProcess.Rd | 4 SAPP-1.0.7/SAPP/man/PoissonData.Rd | 4 SAPP-1.0.7/SAPP/man/SAPP-package.Rd | 4 SAPP-1.0.7/SAPP/man/SelfExcit.Rd | 6 SAPP-1.0.7/SAPP/man/eptren.Rd | 36 +- SAPP-1.0.7/SAPP/man/etarpp.Rd | 24 - SAPP-1.0.7/SAPP/man/etasap.Rd | 16 SAPP-1.0.7/SAPP/man/etasim.Rd | 16 SAPP-1.0.7/SAPP/man/linlin.Rd | 18 - SAPP-1.0.7/SAPP/man/linsim.Rd | 18 - SAPP-1.0.7/SAPP/man/main2003JUL26.Rd | 4 SAPP-1.0.7/SAPP/man/momori.Rd | 14 SAPP-1.0.7/SAPP/man/pgraph.Rd | 34 +- SAPP-1.0.7/SAPP/man/ptspec.Rd | 16 SAPP-1.0.7/SAPP/man/res2003JUL26.Rd | 4 SAPP-1.0.7/SAPP/man/respoi.Rd | 20 - SAPP-1.0.7/SAPP/man/simbvh.Rd | 24 - SAPP-1.0.7/SAPP/src/aftpoi.f | 520 ++++++++++++++++++++----------- SAPP-1.0.7/SAPP/src/comsub.f | 40 +- SAPP-1.0.7/SAPP/src/eptrenf.f | 387 +++++++++++++++-------- SAPP-1.0.7/SAPP/src/etas.f | 426 ++++++++++++++++--------- SAPP-1.0.7/SAPP/src/etasimf.f | 43 +- SAPP-1.0.7/SAPP/src/linlinf.f | 382 ++++++++++++++-------- SAPP-1.0.7/SAPP/src/linsimf.f | 67 ++- SAPP-1.0.7/SAPP/src/momori.c | 69 ++-- SAPP-1.0.7/SAPP/src/pgraphf.f | 298 ++++++++++------- SAPP-1.0.7/SAPP/src/ptspecf.f | 34 +- SAPP-1.0.7/SAPP/src/raftpoi.f | 91 +++-- SAPP-1.0.7/SAPP/src/retas.f | 86 +++-- SAPP-1.0.7/SAPP/src/sapp.h | 2 SAPP-1.0.7/SAPP/src/sapp_f.h | 2 SAPP-1.0.7/SAPP/src/simbvhf.f | 81 +++- 46 files changed, 1865 insertions(+), 1079 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: R functions for random univariate and multivariate finite mixture model generation, estimation, clustering and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.8.2 dated 2016-06-20 and 2.8.3 dated 2016-10-05
DESCRIPTION | 6 MD5 | 52 +- R/RCLRMIX.R | 2 R/RCLSMIX.R | 4 R/REBMIX.R | 2 R/RNGMIX.R | 2 R/is.error.R | 6 R/legendA.R | 6 R/plot.RCLRMIX.R | 124 +++--- R/plot.RCLSMIX.R | 87 ++-- R/plot.RNGMIX.R | 40 +- inst/NEWS.Rd | 9 inst/doc/rebmix.R | 4 inst/doc/rebmix.Rnw | 8 inst/doc/rebmix.pdf |binary src/Rrebmix.cpp | 14 src/Rrebmvnorm.cpp | 14 src/base.cpp | 23 - src/base.h | 4 src/rebmix.cpp | 1 src/rebmixf.cpp | 953 +++++++++++++++++++++++++++++++++++++-------------- src/rebmixf.h | 13 src/rebmvnormf.cpp | 537 ++++++++++++++++------------ src/rebmvnormf.h | 3 src/rngmixf.cpp | 3 src/rngmixf.h | 1 vignettes/rebmix.Rnw | 8 27 files changed, 1258 insertions(+), 668 deletions(-)
Title: Tools and Plots for Multi-Well Plates
Description: Collection of functions for working with multi-well microtitre
plates, mainly 96, 384 and 1536 well plates.
Author: Scott Warchal [aut, cre]
Maintainer: Scott Warchal <s.warchal@sms.ed.ac.uk>
Diff between platetools versions 0.0.1 dated 2016-06-13 and 0.0.2 dated 2016-10-05
platetools-0.0.1/platetools/R/b_score.R |only platetools-0.0.2/platetools/DESCRIPTION | 11 - platetools-0.0.2/platetools/MD5 | 57 +++++----- platetools-0.0.2/platetools/NAMESPACE | 2 platetools-0.0.2/platetools/R/b_grid.R | 3 platetools-0.0.2/platetools/R/b_map.R | 17 -- platetools-0.0.2/platetools/R/bhit_map.R | 39 ++---- platetools-0.0.2/platetools/R/check_plate_input.R |only platetools-0.0.2/platetools/R/hit_grid.R | 4 platetools-0.0.2/platetools/R/hit_map.R | 7 - platetools-0.0.2/platetools/R/med_smooth.R | 29 +++++ platetools-0.0.2/platetools/R/missing_wells.R | 26 ++-- platetools-0.0.2/platetools/R/pc_grid.R | 2 platetools-0.0.2/platetools/R/pc_map.R | 2 platetools-0.0.2/platetools/R/pchit_grid.R | 2 platetools-0.0.2/platetools/R/pchit_map.R | 2 platetools-0.0.2/platetools/R/plate_map.R | 3 platetools-0.0.2/platetools/R/raw_grid.R | 35 ++---- platetools-0.0.2/platetools/R/raw_map.R | 10 - platetools-0.0.2/platetools/R/z_grid.R | 4 platetools-0.0.2/platetools/R/z_map.R | 8 - platetools-0.0.2/platetools/man/b_score.Rd | 2 platetools-0.0.2/platetools/man/check_plate_input.Rd |only platetools-0.0.2/platetools/man/pc_map.Rd | 2 platetools-0.0.2/platetools/man/raw_grid.Rd | 2 platetools-0.0.2/platetools/tests/testthat/test-basic_plots.R |only platetools-0.0.2/platetools/tests/testthat/test-grid_plots.R |only platetools-0.0.2/platetools/tests/testthat/test-med_smooth.R | 40 ++----- platetools-0.0.2/platetools/tests/testthat/test-missing_wells.R | 12 +- platetools-0.0.2/platetools/tests/testthat/test-plate_effects.R | 24 +++- platetools-0.0.2/platetools/tests/testthat/test-plate_map.R | 32 ++++- platetools-0.0.2/platetools/tests/testthat/test-plot_wrapper.R | 16 ++ 32 files changed, 202 insertions(+), 191 deletions(-)
Title: Hierarchical Nominal Clustering Package
Description: Package for hierarchical clustering of objects characterized by
nominal variables.
Author: Zdenek Sulc [aut, cre],
Hana Rezankova [aut]
Maintainer: Zdenek Sulc <zdenek.sulc@vse.cz>
Diff between nomclust versions 0.91.1010 dated 2015-06-03 and 1.00.1011 dated 2016-10-05
DESCRIPTION | 22 +++++++++++------- MD5 | 66 +++++++++++++++++++++++++++++------------------------- NAMESPACE | 11 ++++++--- R/WCE.R | 1 R/WCM.R | 3 +- R/eskin.R | 9 ++++--- R/good1.R | 11 +++++---- R/good2.R | 9 ++++--- R/good3.R | 9 ++++--- R/good4.R | 9 ++++--- R/iof.R | 9 ++++--- R/lin.R | 10 +++++--- R/lin1.R | 9 ++++--- R/morlini.R | 16 ++++++++----- R/nomclust.R | 7 ++++- R/nomprox.R |only R/of.R | 9 ++++--- R/sm.R | 9 ++++--- R/ve.R |only R/vm.R |only data/data20.RData |binary man/eskin.Rd | 10 ++++---- man/evalclust.Rd | 3 +- man/good1.Rd | 11 +++++---- man/good2.Rd | 13 ++++++---- man/good3.Rd | 11 +++++---- man/good4.Rd | 11 +++++---- man/iof.Rd | 13 ++++++---- man/lin.Rd | 11 +++++---- man/lin1.Rd | 11 +++++---- man/morlini.Rd | 9 ++++--- man/nomclust.Rd | 5 ++-- man/nomprox.Rd |only man/of.Rd | 9 ++++--- man/sm.Rd | 11 +++++---- man/ve.Rd |only man/vm.Rd |only 37 files changed, 219 insertions(+), 128 deletions(-)
Title: Calculate the NLTT Statistic
Description: Provides functions to calculate the normalised Lineage-Through-
Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures
the difference between two Lineage-Through-Time curves, where each curve is
normalised both in time and in number of lineages.
Author: Thijs Janzen [aut, cre],
Richel Bilderbeek [aut]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between nLTT versions 1.2.1 dated 2016-06-06 and 1.3 dated 2016-10-05
nLTT-1.2.1/nLTT/man/mcmc_nltt.Rd |only nLTT-1.3/nLTT/DESCRIPTION | 30 nLTT-1.3/nLTT/MD5 | 74 +- nLTT-1.3/nLTT/NAMESPACE | 24 nLTT-1.3/nLTT/R/ABC_SMC.R | 694 +++++++++++--------- nLTT-1.3/nLTT/R/get_average_nltt_matrix.R |only nLTT-1.3/nLTT/R/get_nltt_values.R |only nLTT-1.3/nLTT/R/get_phylogeny_nltt_matrix.R |only nLTT-1.3/nLTT/R/nLTTDiff.R | 239 ++++-- nLTT-1.3/nLTT/R/nltts_plot.R |only nLTT-1.3/nLTT/R/plot_nLTT.R | 121 ++- nLTT-1.3/nLTT/R/stretch_nltt_matrix.R |only nLTT-1.3/nLTT/build |only nLTT-1.3/nLTT/inst |only nLTT-1.3/nLTT/man/MCMC_nLTT.Rd |only nLTT-1.3/nLTT/man/abc_smc_nltt.Rd | 173 ++-- nLTT-1.3/nLTT/man/exampleTrees.Rd | 2 nLTT-1.3/nLTT/man/get_average_nltt_matrix.Rd |only nLTT-1.3/nLTT/man/get_average_nltt_matrix_impl_1.Rd |only nLTT-1.3/nLTT/man/get_average_nltt_matrix_impl_2.Rd |only nLTT-1.3/nLTT/man/get_nltt_values.Rd |only nLTT-1.3/nLTT/man/get_phylogeny_nltt_matrix.Rd |only nLTT-1.3/nLTT/man/nLTT-internal.Rd | 4 nLTT-1.3/nLTT/man/nLTT-package.Rd | 3 nLTT-1.3/nLTT/man/nLTTstat.Rd | 75 -- nLTT-1.3/nLTT/man/nLTTstat_exact.Rd | 52 - nLTT-1.3/nLTT/man/nltt_diff.Rd |only nLTT-1.3/nLTT/man/nltt_diff_exact.Rd |only nLTT-1.3/nLTT/man/nltt_lines.Rd | 56 - nLTT-1.3/nLTT/man/nltt_plot.Rd | 68 - nLTT-1.3/nLTT/man/nltts_plot.Rd |only nLTT-1.3/nLTT/man/stretch_nltt_matrix.Rd |only nLTT-1.3/nLTT/tests |only nLTT-1.3/nLTT/vignettes |only 34 files changed, 913 insertions(+), 702 deletions(-)
Title: Estimates Pseudotimes for Single Cell Expression Data
Description: Implements the DeLorean model to estimate pseudotimes for
single cell expression data. The DeLorean model uses a Gaussian process
latent variable model to model uncertainty in the capture time of
cross-sectional data.
Author: John Reid <john.reid@mrc-bsu.cam.ac.uk>
Maintainer: John Reid <john.reid@mrc-bsu.cam.ac.uk>
Diff between DeLorean versions 1.2.3 dated 2016-06-29 and 1.2.4 dated 2016-10-05
DESCRIPTION | 8 ++-- MD5 | 35 +++++++++++---------- NAMESPACE | 1 NEWS.md | 5 +++ R/model.r | 37 ++++++++++++++-------- R/package.r | 1 R/plot.r | 49 +++++++++++++++++++++++++++++- inst/Stan/exact-sizes.stan | 2 - inst/Stan/exact.stan | 2 - inst/Stan/lowrank-sizes.stan | 2 - inst/Stan/lowrank.stan | 2 - inst/doc/DeLorean.R | 2 - inst/doc/DeLorean.Rmd | 6 +-- inst/doc/DeLorean.html | 42 +++++++++++-------------- man/calc.inducing.pseudotimes.Rd | 6 +++ man/init.orderings.vs.pseudotimes.plot.Rd |only man/plot.de.lorean.Rd | 2 + man/prepare.for.stan.Rd | 6 +++ vignettes/DeLorean.Rmd | 2 - 19 files changed, 141 insertions(+), 69 deletions(-)
Title: Comparative 'Phylogenetic' Analyses of Diversification
Description: Contains a number of comparative 'phylogenetic' methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of 'BiSSE' (Binary State
'Speciation' and Extinction) and its unresolved tree extensions,
'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE',
'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
models of discrete and continuous trait evolution and constant rate
'speciation' and extinction.
Author: Richard G. FitzJohn <fitzjohn@zoology.ubc.ca>, with 'GeoSSE' and
'ClaSSE' by Emma E. Goldberg <eeg@uic.edu>, and 'BiSSE-ness' by Karen
Magnuson-Ford.
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>
Diff between diversitree versions 0.9-8 dated 2015-12-21 and 0.9-9 dated 2016-10-05
DESCRIPTION | 17 - MD5 | 50 ++--- R/t.R | 4 build/partial.rdb |binary inst/tests/helper-diversitree.R | 12 - inst/tests/test-asr-t.R | 354 ++++++++++++++++++++-------------------- inst/tests/test-asr.R | 165 +++++++++--------- inst/tests/test-bd.R | 1 inst/tests/test-mcmc.R | 9 - inst/tests/test-mle.R | 4 inst/tests/test-pgls.R | 29 ++- man/asr-bisse.Rd | 4 man/diversitree-package.Rd | 2 man/make.bd.t.Rd | 2 man/make.bisse.Rd | 4 man/make.bm.Rd | 2 man/make.mkn.Rd | 2 man/make.musse.Rd | 4 src/continuous.c | 4 src/dnchbv.f | 6 src/expm.f | 21 +- src/hyperg.f | 2 src/quasse-eqs-fftC.c | 2 src/rfftw.c | 2 src/util.c | 11 + src/util.h | 3 26 files changed, 363 insertions(+), 353 deletions(-)
Title: Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions
induced by stochastic covariates. Miscellaneous functions for data preparation
and simulation are also provided. For more information, see: (i) "Life tables
with covariates: Dynamic model for nonlinear analysis of longitudinal data"
by Akushevich, I. et al. (2005), Mathematical Population Studies 12(2), 51(80),
<DOI:10.1080/08898480590932296>; (ii) "Stochastic model for analysis of
longitudinal data on aging and mortality" by Yashin A. et al. (2007),
Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>;
(iii) "Health decline, aging and mortality: how are they related?"
by Yashin A. et al. (2007),
Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.3.4 dated 2016-09-04 and 1.3.8 dated 2016-10-05
DESCRIPTION | 8 MD5 | 36 +- R/prepare_data.R | 80 ++++- R/spm.R | 12 R/spm_continuous.R | 27 +- R/spm_discrete.R | 19 - R/spm_projection.R | 38 ++ R/spm_time-dependent.R | 54 ++-- README.md | 10 inst/doc/stpm-vignette.R | 99 +++++++ inst/doc/stpm-vignette.Rmd | 141 +++++++++- inst/doc/stpm-vignette.html | 589 +++++++++++++++++++++++++++++++++----------- man/prepare_data.Rd | 5 man/prepare_data_cont.Rd | 4 man/prepare_data_discr.Rd | 6 man/spm.Rd | 5 man/spm_continuous.Rd | 20 + man/spm_time_dep.Rd | 20 + vignettes/stpm-vignette.Rmd | 141 +++++++++- 19 files changed, 1041 insertions(+), 273 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
Sami Samhuri [ctb, cph] (Javascript strftime library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 0.14 dated 2016-09-09 and 0.14.1 dated 2016-10-05
shiny-0.14.1/shiny/DESCRIPTION | 10 shiny-0.14.1/shiny/MD5 | 192 shiny-0.14.1/shiny/NEWS.md | 61 shiny-0.14.1/shiny/R/fileupload.R | 2 shiny-0.14.1/shiny/R/input-date.R | 62 shiny-0.14.1/shiny/R/input-select.R | 2 shiny-0.14.1/shiny/R/input-slider.R | 7 shiny-0.14.1/shiny/R/input-utils.R | 13 shiny-0.14.1/shiny/R/jqueryui.R | 2 shiny-0.14.1/shiny/R/render-plot.R | 65 shiny-0.14.1/shiny/R/server-input-handlers.R | 21 shiny-0.14.1/shiny/R/showcase.R | 2 shiny-0.14.1/shiny/R/update-input.R | 32 shiny-0.14.1/shiny/inst/www/shared/datepicker/css/bootstrap-datepicker3.css |only shiny-0.14.1/shiny/inst/www/shared/datepicker/css/bootstrap-datepicker3.min.css |only shiny-0.14.1/shiny/inst/www/shared/datepicker/js/bootstrap-datepicker.js | 2141 shiny-0.14.1/shiny/inst/www/shared/datepicker/js/bootstrap-datepicker.min.js | 5 shiny-0.14.1/shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ar.min.js |only 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shiny-0.14.1/shiny/inst/www/shared/shiny.min.js | 6 shiny-0.14.1/shiny/inst/www/shared/shiny.min.js.map | 2 shiny-0.14.1/shiny/man/dateInput.Rd | 21 shiny-0.14.1/shiny/man/dateRangeInput.Rd | 15 shiny-0.14.1/shiny/man/updateDateInput.Rd | 15 shiny-0.14.1/shiny/man/updateDateRangeInput.Rd | 14 shiny-0.14.1/shiny/tests/testthat/test-bootstrap.r | 19 shiny-0.14.1/shiny/tests/testthat/test-plot-coordmap.R | 118 shiny-0.14/shiny/inst/www/shared/datepicker/css/datepicker.css |only shiny-0.14/shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.bg.js |only shiny-0.14/shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ca.js |only shiny-0.14/shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.cs.js |only shiny-0.14/shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.da.js |only shiny-0.14/shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.de.js |only 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shiny-0.14/shiny/inst/www/shared/datepicker/less |only 152 files changed, 18584 insertions(+), 12665 deletions(-)
Title: Interface to the 'USGS' 'BISON' 'API'
Description: Interface to the 'USGS' 'BISON' 'API', a 'database' for
species occurrence data on the web. Data comes from species in the
United States from participating data providers. You can get
data via 'taxonomic' and location based queries. A simple function
is provided to help visualize data.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rbison versions 0.4.8 dated 2015-07-01 and 0.5.0 dated 2016-10-05
rbison-0.4.8/rbison/R/bison_solr.R |only rbison-0.5.0/rbison/DESCRIPTION | 13 - rbison-0.5.0/rbison/LICENSE | 2 rbison-0.5.0/rbison/MD5 | 59 ++-- rbison-0.5.0/rbison/NAMESPACE | 7 rbison-0.5.0/rbison/NEWS.md |only rbison-0.5.0/rbison/R/bison.R | 34 +- rbison-0.5.0/rbison/R/bison_providers.R | 23 - rbison-0.5.0/rbison/R/bison_solr.r |only rbison-0.5.0/rbison/R/bison_stats.R | 21 - rbison-0.5.0/rbison/R/bison_tax.R | 14 - rbison-0.5.0/rbison/R/bisonmap.R | 23 + rbison-0.5.0/rbison/R/citation_datause.R | 70 ++--- rbison-0.5.0/rbison/R/rbison-package.R | 28 +- rbison-0.5.0/rbison/R/zzz.R | 89 +++---- rbison-0.5.0/rbison/README.md | 226 +++++++++---------- rbison-0.5.0/rbison/build/vignette.rds |binary rbison-0.5.0/rbison/man/all_states.Rd | 2 rbison-0.5.0/rbison/man/bison.Rd | 8 rbison-0.5.0/rbison/man/bison_datause.Rd | 2 rbison-0.5.0/rbison/man/bison_providers.Rd | 2 rbison-0.5.0/rbison/man/bison_solr.Rd | 5 rbison-0.5.0/rbison/man/bison_stats.Rd | 2 rbison-0.5.0/rbison/man/bison_tax.Rd | 2 rbison-0.5.0/rbison/man/bisonmap.Rd | 2 rbison-0.5.0/rbison/man/fips.Rd | 2 rbison-0.5.0/rbison/man/is.bison.Rd | 2 rbison-0.5.0/rbison/man/is.bison_solr.Rd | 2 rbison-0.5.0/rbison/man/rbison-package.Rd | 20 - rbison-0.5.0/rbison/tests/testthat/Rplots.pdf |binary rbison-0.5.0/rbison/tests/testthat/test-bison_solr.R | 6 rbison-0.5.0/rbison/tests/testthat/test-bisonmap.R | 2 32 files changed, 343 insertions(+), 325 deletions(-)
Title: JavaScript Charts API Tool
Description: API for using 'AmCharts' Library. Based on 'htmlwidgets',
it provides a global architecture to generate 'JavaScript' source code
for charts. Most of classes in the library have their equivalent in R with S4
classes; for those classes, not all properties have been referenced but can
easily be added in the constructors. Complex properties (e.g. 'JavaScript'
object) can be passed as named list. See examples at <http:// datastorm-
open.github.io/introduction_ramcharts/>. and <http://www.amcharts.com/> for
more information about the library. The package includes the free version of
'AmCharts' Library. Its only limitation is a small link to the web site
displayed on your charts. If you enjoy this library, do not hesitate
to refer to this page <http://www.amcharts.com/online-store/> to purchase a
licence, and thus support its creators and get a period of Priority Support.
See also <http://www.amcharts.com/about/> for more information about 'AmCharts'
company.
Author: Jeffery Petit [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Benoit Thieurmel [aut, ctb],
Elena Salette [aut, ctb],
Titouan Robert [aut, ctb]
Maintainer: Jeffery Petit <jeffery.petit@datastorm.fr>
Diff between rAmCharts versions 2.0.3 dated 2016-06-15 and 2.1.1 dated 2016-10-05
DESCRIPTION | 34 MD5 | 139 +- NAMESPACE | 7 R/base_data.R | 13 R/base_startupMessage.R | 5 R/chart_amBarplot.R | 192 +-- R/chart_amCandlestick.R | 5 R/chart_amDataset.R |only R/chart_amFloatingBar.R | 5 R/chart_amGauge.R | 15 R/chart_amRadar.R | 29 R/chart_amTimeSeries.R | 4 R/class_AmChart.R | 10 R/class_AmChart_constructors.R | 87 - R/class_AmChart_setters.R | 73 - R/class_AmLegend.R | 3 R/class_AmObject.R | 87 - R/class_AmStockChart_setters.R | 10 R/class_AxisBase_setters.R | 2 R/class_DataSet_setters.R | 18 R/class_GaugeAxis_setters.R | 2 R/class_PeriodSelector.R | 2 R/class_StockPanel.R | 5 R/class_StockPanel_setters.R | 8 R/class_Title.R | 25 R/union_AmCharts.R | 8 R/utils_amOptions.R | 53 data/data_gantt.rda |only inst/conf.yaml | 2 inst/htmlwidgets/lib/amcharts.js | 562 +++++----- inst/htmlwidgets/lib/amstock.js | 100 - inst/htmlwidgets/lib/funnel.js | 28 inst/htmlwidgets/lib/gauge.js | 48 inst/htmlwidgets/lib/lang/cs.js |only inst/htmlwidgets/lib/pie.js | 23 inst/htmlwidgets/lib/plugins/dataloader/dataloader.min.js | 2 inst/htmlwidgets/lib/plugins/dataloader/lang/cs.js |only inst/htmlwidgets/lib/plugins/export/export.min.js | 96 - inst/htmlwidgets/lib/plugins/export/lang/cs.js |only inst/htmlwidgets/lib/plugins/export/lang/de.js | 4 inst/htmlwidgets/lib/plugins/export/lang/en.js | 4 inst/htmlwidgets/lib/plugins/export/lang/fr.js | 4 inst/htmlwidgets/lib/plugins/export/lang/ko.js | 4 inst/htmlwidgets/lib/plugins/export/lang/lt.js | 4 inst/htmlwidgets/lib/plugins/export/lang/pl.js | 4 inst/htmlwidgets/lib/plugins/export/lang/pt.js | 4 inst/htmlwidgets/lib/plugins/export/libs/fabric.js/fabric.min.js | 23 inst/htmlwidgets/lib/serial.js | 144 +- inst/htmlwidgets/lib/xy.js | 38 inst/htmlwidgets/ramcharts_base.js | 212 ++- inst/htmlwidgets/ramcharts_base.yaml | 2 inst/shiny/src/bar/bar_server.R | 40 inst/shiny/src/gauge/gauge_server.R | 20 inst/shiny/src/lines/lines_server.R | 32 inst/shiny/src/pie/pie_server.R | 20 inst/shiny/src/radar/radar_server.R | 14 inst/shiny/src/xy/xy_server.R | 12 man/AmChart-class.Rd | 3 man/AmStockChart.Rd | 2 man/DataSet.Rd | 9 man/Title.Rd | 14 man/amBarplot.Rd | 33 man/amOptions.Rd | 7 man/amRadar.Rd | 7 man/amStockMultiSet.Rd |only man/amTimeSeries.Rd | 2 man/data_gantt.Rd |only man/initialize-AmChart.Rd | 34 man/initialize-AmLegend.Rd | 2 man/initialize-StockPanel.Rd | 12 man/listProperties-AmObject.Rd | 1 man/methods-AmObject.Rd | 16 man/show-AmObject-method.Rd | 10 tests/testthat/test_amchart_setters.R | 2 74 files changed, 1266 insertions(+), 1175 deletions(-)
Title: Classes with Reference Semantics
Description: The R6 package allows the creation of classes with reference
semantics, similar to R's built-in reference classes. Compared to reference
classes, R6 classes are simpler and lighter-weight, and they are not built
on S4 classes so they do not require the methods package. These classes
allow public and private members, and they support inheritance, even when
the classes are defined in different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>
Diff between R6 versions 2.1.3 dated 2016-08-19 and 2.2.0 dated 2016-10-05
R6-2.1.3/R6/NEWS |only R6-2.2.0/R6/DESCRIPTION | 6 - R6-2.2.0/R6/MD5 | 42 ++++---- R6-2.2.0/R6/NAMESPACE | 2 R6-2.2.0/R6/NEWS.md |only R6-2.2.0/R6/R/clone.R | 4 R6-2.2.0/R6/R/is.R |only R6-2.2.0/R6/R/new.R | 14 ++ R6-2.2.0/R6/R/print.R | 10 - R6-2.2.0/R6/README.md | 10 - R6-2.2.0/R6/build/vignette.rds |binary R6-2.2.0/R6/inst/doc/Debugging.Rmd | 4 R6-2.2.0/R6/inst/doc/Introduction.R | 21 +--- R6-2.2.0/R6/inst/doc/Introduction.Rmd | 30 ++--- R6-2.2.0/R6/inst/doc/Introduction.html | 38 ++----- R6-2.2.0/R6/inst/doc/Performance.Rmd | 4 R6-2.2.0/R6/inst/doc/Performance.html | 137 +++++++++++++-------------- R6-2.2.0/R6/inst/doc/Portable.Rmd | 4 R6-2.2.0/R6/man/is.R6.Rd |only R6-2.2.0/R6/tests/testthat/test-finalizer.R |only R6-2.2.0/R6/tests/testthat/test-s3-methods.R |only R6-2.2.0/R6/vignettes/Debugging.Rmd | 4 R6-2.2.0/R6/vignettes/Introduction.Rmd | 30 ++--- R6-2.2.0/R6/vignettes/Performance.Rmd | 4 R6-2.2.0/R6/vignettes/Portable.Rmd | 4 25 files changed, 180 insertions(+), 188 deletions(-)
Title: Title: Learn Data Science Through the "Data Science Live Book"
Description: Around 10% of almost any predictive modeling project
is spent in predictive modeling, 'funModeling' and the book <http://
livebook.datascienceheroes.com/> are intended to cover remaining 90%: data
preparation, profiling, selecting best variables 'dataViz', assessing model
performance and other functions.
Author: Pablo Casas
Maintainer: Pablo Casas <pabloc@datascienceheroes.com>
Diff between funModeling versions 1.2 dated 2016-08-10 and 1.3 dated 2016-10-05
DESCRIPTION | 15 +- MD5 | 12 +- NAMESPACE | 3 R/cross_plot.R | 4 R/models_lib.R | 277 +++++++++++++++++++++++++++++++++---------------------- R/numbers.R | 82 ++++++++++++++++ man/freq.Rd |only man/gain_lift.Rd |only 8 files changed, 274 insertions(+), 119 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description:
Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 3.1-1 dated 2016-03-29 and 3.1-2 dated 2016-10-05
DESCRIPTION | 12 MD5 | 36 - NEWS | 16 R/Effect.R | 16 R/effectsclmm.R | 18 R/effectsmer.R | 3 R/plot-methods.R | 86 ++- R/plot.effpoly.R | 71 +- data/Arrests.rda |binary data/BEPS.rda |binary data/Cowles.rda |binary data/Hartnagel.rda |binary data/Prestige.rda |binary data/TitanicSurvival.rda |binary data/WVS.rda |binary data/Wells.rda |binary man/effect.Rd | 1198 +++++++++++++++++++++++------------------------ man/effects-package.Rd | 4 man/summary.effect.Rd | 14 19 files changed, 784 insertions(+), 690 deletions(-)
Title: Distance Sampling Simulations
Description: Performs distance sampling simulations. It repeatedly generates
instances of a user defined population within a given survey region, generates
realisations of a survey design (currently these must be generated using
Distance software in advance <http://distancesampling.org/>) and simulates
the detection process. The data are then analysed so that the results can
be compared for accuracy and precision across all replications. This will
allow users to select survey designs which will give them the best accuracy
and precision given their expectations about population distribution. Any
uncertainty in population distribution or population parameters can be
included by running the different survey designs for a number of different
population descriptions. An example simulation can be found in the help file for
make.simulation.
Author: Laura Marshall <lhm@st-and.ac.uk>
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Diff between DSsim versions 1.0.6 dated 2016-08-10 and 1.0.7 dated 2016-10-05
DESCRIPTION | 37 ++++++++++++++++++------------------- MD5 | 14 ++++++++------ NEWS | 15 +++++++++++++++ R/Class.Constructors.R | 8 ++++++++ R/LT.SegmentedGrid.Design.R |only R/LT.SegmentedTrack.Design.R |only R/Simulation.R | 9 ++++++--- R/data.for.distance.R | 3 +-- man/data.for.distance.Rd | 3 +-- 9 files changed, 57 insertions(+), 32 deletions(-)
Title: Optimal and Fast Univariate k-Means Clustering
Description: A dynamic programming algorithm for optimal univariate k-means
clustering. Minimizing the sum of squares of within-cluster distances, the
algorithm guarantees optimality and reproducibility. Its advantage over
heuristic k-means algorithms in efficiency and accuracy is increasingly
pronounced as the number of clusters k increases. It provides an alternative
to heuristic k-means algorithms for univariate clustering.
Author: Joe Song [aut, cre], Haizhou Wang [aut]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between Ckmeans.1d.dp versions 3.4.6-2 dated 2016-09-25 and 3.4.6-3 dated 2016-10-05
DESCRIPTION | 20 ++++++++-------- MD5 | 16 +++++++----- NAMESPACE | 2 + NEWS | 21 ++++++++++++++++- R/Ckmeans.1d.dp.R | 24 +++---------------- R/visualize.R |only man/Ckmeans.1d.dp-package.Rd | 2 - man/Ckmeans.1d.dp.Rd | 15 +++++++----- man/ahist.Rd | 53 +++++++++++++++++++++++++++++++++---------- man/plot.Ckmeans.1d.dp.Rd |only 10 files changed, 96 insertions(+), 57 deletions(-)
More information about automultinomial at CRAN
Permanent link
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 1.0 dated 2016-01-04 and 2.0 dated 2016-10-04
gjam-1.0/gjam/data |only gjam-1.0/gjam/man/forestTraits.Rd |only gjam-1.0/gjam/src/byRcppCpp.cpp |only gjam-1.0/gjam/src/conditionalMVNRcppCpp.cpp |only gjam-1.0/gjam/src/tnormMVNmatrixRcppCpp.cpp |only gjam-2.0/gjam/DESCRIPTION | 12 gjam-2.0/gjam/MD5 | 70 gjam-2.0/gjam/NAMESPACE | 11 gjam-2.0/gjam/R/RcppExports.R | 38 gjam-2.0/gjam/R/gjamCensorY.r | 40 gjam-2.0/gjam/R/gjamDeZero.r |only gjam-2.0/gjam/R/gjamGibbs.r | 458 - gjam-2.0/gjam/R/gjamHfunctions.R | 8701 ++++++++++++++++++++++--- gjam-2.0/gjam/R/gjamIIE.r |only gjam-2.0/gjam/R/gjamIIEplot.r |only gjam-2.0/gjam/R/gjamOrdination.R |only gjam-2.0/gjam/R/gjamPlot.r | 1072 --- gjam-2.0/gjam/R/gjamPoints2Grid.R |only gjam-2.0/gjam/R/gjamPredict.r |only gjam-2.0/gjam/R/gjamReZero.r |only gjam-2.0/gjam/R/gjamSimData.r | 201 gjam-2.0/gjam/R/gjamSpec2Trait.r |only gjam-2.0/gjam/R/gjamTrimY.r |only gjam-2.0/gjam/build/vignette.rds |binary gjam-2.0/gjam/inst/doc/gjamDimRedVignette.R |only gjam-2.0/gjam/inst/doc/gjamDimRedVignette.Rmd |only gjam-2.0/gjam/inst/doc/gjamDimRedVignette.html |only gjam-2.0/gjam/inst/doc/gjamTraitsVignette.R |only gjam-2.0/gjam/inst/doc/gjamTraitsVignette.Rmd |only gjam-2.0/gjam/inst/doc/gjamTraitsVignette.html |only gjam-2.0/gjam/inst/doc/gjamVignette.R | 511 + gjam-2.0/gjam/inst/doc/gjamVignette.Rmd | 994 ++ gjam-2.0/gjam/inst/doc/gjamVignette.html | 1261 ++- gjam-2.0/gjam/man/gjam-package.Rd | 61 gjam-2.0/gjam/man/gjamCensorY.Rd | 54 gjam-2.0/gjam/man/gjamDeZero.Rd |only gjam-2.0/gjam/man/gjamGibbs.Rd | 202 gjam-2.0/gjam/man/gjamIIE.Rd |only gjam-2.0/gjam/man/gjamIIEplot.Rd |only gjam-2.0/gjam/man/gjamOrdination.Rd |only gjam-2.0/gjam/man/gjamPlot.Rd | 80 gjam-2.0/gjam/man/gjamPoints2Grid.Rd |only gjam-2.0/gjam/man/gjamPredict.Rd |only gjam-2.0/gjam/man/gjamReZero.Rd |only gjam-2.0/gjam/man/gjamSimData.Rd | 90 gjam-2.0/gjam/man/gjamSpec2Trait.Rd |only gjam-2.0/gjam/man/gjamTrimY.Rd |only gjam-2.0/gjam/src/RcppExports.cpp | 158 gjam-2.0/gjam/src/cppFns.cpp |only gjam-2.0/gjam/vignettes/gjamDimRedVignette.Rmd |only gjam-2.0/gjam/vignettes/gjamTraitsVignette.Rmd |only gjam-2.0/gjam/vignettes/gjamVignette.Rmd | 994 ++ 52 files changed, 11202 insertions(+), 3806 deletions(-)
Title: A Toolbox for Multivariate Meta-Analysis
Description: A toolbox for meta-analysis. This package includes a collection of functions for (1) implementing robust multivariate meta-analysis of continuous or binary outcomes; and (2) a bivariate Egger's test for detecting publication bias.
Author: Yong Chen [aut, cre],
Chuan Hong [aut],
Haitao Chu [ctb],
Yulun Liu [ctb]
Maintainer: Yong Chen <ychen.upenn@gmail.com>
Diff between xmeta versions 1.1-1 dated 2016-06-13 and 1.1-2 dated 2016-10-04
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/xmeta-package.Rd | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Modern Text Mining Framework for R
Description: Fast and memory-friendly tools for text vectorization,
topic modeling (LDA, LSA), word embeddings (GloVe), similarities.
This package provides a source-agnostic streaming API, which allows researchers
to perform analysis of collections of documents which are larger than available RAM.
All core functions are parallelized to benefit from multicore machines.
Author: Dmitriy Selivanov [aut, cre],
Lincoln Mullen [ctb]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between text2vec versions 0.3.0 dated 2016-03-31 and 0.4.0 dated 2016-10-04
text2vec-0.3.0/text2vec/R/glove.R |only text2vec-0.3.0/text2vec/R/matrix.R |only text2vec-0.3.0/text2vec/R/similarity.R |only text2vec-0.3.0/text2vec/inst/doc/advanced.R |only text2vec-0.3.0/text2vec/inst/doc/advanced.Rmd |only text2vec-0.3.0/text2vec/inst/doc/advanced.html |only text2vec-0.3.0/text2vec/man/GloveFitter.Rd |only text2vec-0.3.0/text2vec/man/HashCorpus.Rd |only text2vec-0.3.0/text2vec/man/VocabCorpus.Rd |only text2vec-0.3.0/text2vec/man/VocabularyBuilder.Rd |only text2vec-0.3.0/text2vec/man/ilines.Rd |only text2vec-0.3.0/text2vec/src/sort.cpp |only text2vec-0.3.0/text2vec/tests/testthat/not-test-glove.R |only text2vec-0.3.0/text2vec/tests/testthat/not-test-perf.R |only text2vec-0.3.0/text2vec/vignettes/advanced.Rmd |only text2vec-0.4.0/text2vec/DESCRIPTION | 31 text2vec-0.4.0/text2vec/MD5 | 166 +- text2vec-0.4.0/text2vec/NAMESPACE | 47 text2vec-0.4.0/text2vec/NEWS.md |only text2vec-0.4.0/text2vec/R/RcppExports.R |only text2vec-0.4.0/text2vec/R/analogies.R | 82 - text2vec-0.4.0/text2vec/R/distance.R |only text2vec-0.4.0/text2vec/R/distance_RWMD.R |only text2vec-0.4.0/text2vec/R/dtm.R | 103 - text2vec-0.4.0/text2vec/R/iterators.R | 498 +++++-- text2vec-0.4.0/text2vec/R/model_GloVe.R |only text2vec-0.4.0/text2vec/R/model_LDA.R |only text2vec-0.4.0/text2vec/R/model_LSA.R |only text2vec-0.4.0/text2vec/R/model_tfidf.R |only text2vec-0.4.0/text2vec/R/models_R6.R |only text2vec-0.4.0/text2vec/R/models_S3.R |only text2vec-0.4.0/text2vec/R/tcm.R | 208 +-- text2vec-0.4.0/text2vec/R/text2vec.R | 61 text2vec-0.4.0/text2vec/R/tokenizers.R | 62 text2vec-0.4.0/text2vec/R/transformers.R | 168 +- text2vec-0.4.0/text2vec/R/utils.R | 124 + text2vec-0.4.0/text2vec/R/vectorizers.R | 110 + text2vec-0.4.0/text2vec/R/vocabulary.R | 193 +- text2vec-0.4.0/text2vec/R/zzz.R | 12 text2vec-0.4.0/text2vec/README.md | 60 text2vec-0.4.0/text2vec/build/vignette.rds |binary text2vec-0.4.0/text2vec/inst/doc/files-multicore.R |only text2vec-0.4.0/text2vec/inst/doc/files-multicore.Rmd |only text2vec-0.4.0/text2vec/inst/doc/files-multicore.html |only text2vec-0.4.0/text2vec/inst/doc/glove.R | 92 - text2vec-0.4.0/text2vec/inst/doc/glove.Rmd | 149 +- text2vec-0.4.0/text2vec/inst/doc/glove.html | 365 ++++- text2vec-0.4.0/text2vec/inst/doc/text-vectorization.R | 260 ++- text2vec-0.4.0/text2vec/inst/doc/text-vectorization.Rmd | 376 +++-- text2vec-0.4.0/text2vec/inst/doc/text-vectorization.html | 662 +++++++--- text2vec-0.4.0/text2vec/man/GlobalVectors.Rd |only text2vec-0.4.0/text2vec/man/LatentDirichletAllocation.Rd |only text2vec-0.4.0/text2vec/man/LatentSemanticAnalysis.Rd |only text2vec-0.4.0/text2vec/man/RelaxedWordMoversDistance.Rd |only text2vec-0.4.0/text2vec/man/TfIdf.Rd |only text2vec-0.4.0/text2vec/man/as.lda_c.Rd |only text2vec-0.4.0/text2vec/man/create_dtm.Rd | 53 text2vec-0.4.0/text2vec/man/create_tcm.Rd | 56 text2vec-0.4.0/text2vec/man/create_vocabulary.Rd | 31 text2vec-0.4.0/text2vec/man/distances.Rd |only text2vec-0.4.0/text2vec/man/fit.Rd |only text2vec-0.4.0/text2vec/man/fit_transform.Rd |only text2vec-0.4.0/text2vec/man/get_dtm.Rd | 16 text2vec-0.4.0/text2vec/man/get_idf.Rd | 2 text2vec-0.4.0/text2vec/man/get_tcm.Rd | 14 text2vec-0.4.0/text2vec/man/get_tf.Rd | 2 text2vec-0.4.0/text2vec/man/glove.Rd | 58 text2vec-0.4.0/text2vec/man/ifiles.Rd | 24 text2vec-0.4.0/text2vec/man/itoken.Rd | 42 text2vec-0.4.0/text2vec/man/normalize.Rd |only text2vec-0.4.0/text2vec/man/prepare_analogy_questions.Rd | 4 text2vec-0.4.0/text2vec/man/reexports.Rd | 8 text2vec-0.4.0/text2vec/man/similarities.Rd |only text2vec-0.4.0/text2vec/man/text2vec.Rd | 11 text2vec-0.4.0/text2vec/man/tokenizers.Rd | 34 text2vec-0.4.0/text2vec/man/transform.Rd |only text2vec-0.4.0/text2vec/man/transform_tf.Rd | 23 text2vec-0.4.0/text2vec/man/vectorizers.Rd | 30 text2vec-0.4.0/text2vec/src/Corpus.h | 18 text2vec-0.4.0/text2vec/src/GloveFit.h | 305 +++- text2vec-0.4.0/text2vec/src/GloveFitter.cpp | 147 +- text2vec-0.4.0/text2vec/src/HashCorpus.cpp | 16 text2vec-0.4.0/text2vec/src/HashCorpus.h | 191 +- text2vec-0.4.0/text2vec/src/LDA_gibbs.cpp |only text2vec-0.4.0/text2vec/src/RcppExports.cpp |only text2vec-0.4.0/text2vec/src/SparseTripletMatrix.h | 100 - text2vec-0.4.0/text2vec/src/VocabCorpus.cpp | 18 text2vec-0.4.0/text2vec/src/VocabCorpus.h | 309 ++-- text2vec-0.4.0/text2vec/src/Vocabulary.cpp | 18 text2vec-0.4.0/text2vec/src/Vocabulary.h | 192 +- text2vec-0.4.0/text2vec/src/matrix_utils.cpp |only text2vec-0.4.0/text2vec/src/text2vec.h | 29 text2vec-0.4.0/text2vec/src/uint_hash.cpp | 16 text2vec-0.4.0/text2vec/src/utils.cpp | 112 - text2vec-0.4.0/text2vec/tests/testthat/not-test-doc2vec.R | 104 - text2vec-0.4.0/text2vec/tests/testthat/test-distances.R |only text2vec-0.4.0/text2vec/tests/testthat/test-hash-corpus.R | 37 text2vec-0.4.0/text2vec/tests/testthat/test-iterators.R | 82 - text2vec-0.4.0/text2vec/tests/testthat/test-lsa.R |only text2vec-0.4.0/text2vec/tests/testthat/test-s3-interface.R |only text2vec-0.4.0/text2vec/tests/testthat/test-tcm.R | 24 text2vec-0.4.0/text2vec/tests/testthat/test-utils.R | 52 text2vec-0.4.0/text2vec/tests/testthat/test-vocab-corpus.R | 114 - text2vec-0.4.0/text2vec/tests/testthat/test-vocab-high-level.R | 30 text2vec-0.4.0/text2vec/tests/testthat/utf8.r |only text2vec-0.4.0/text2vec/vignettes/files-multicore.Rmd |only text2vec-0.4.0/text2vec/vignettes/glove.Rmd | 149 +- text2vec-0.4.0/text2vec/vignettes/text-vectorization.Rmd | 376 +++-- 108 files changed, 4250 insertions(+), 2426 deletions(-)
Title: Post-Processing of the Markov Chain Simulated by ChronoModel
Description: Provides a list of functions for the statistical analysis and the post-processing of the Markov Chains simulated by ChronoModel (see <http://www.chronomodel.fr> for more information). ChronoModel is a friendly software to construct a chronological model in a Bayesian framework. Its output is a sampled Markov chain from the posterior distribution of dates component the chronology.
Author: Anne Philippe and Marie-Anne Vibet
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between RChronoModel versions 0.2 dated 2016-06-21 and 0.3 dated 2016-10-04
DESCRIPTION | 13 - MD5 | 15 - NAMESPACE | 13 - R/prog.R | 480 +++++++++++++++++++++++++++++++++++-------- man/DatesHiatus.Rd |only man/MarginalStatistics.Rd | 2 man/MultiCredibleInterval.Rd | 2 man/MultiDatesPlot.Rd |only man/MultiHPD.Rd |only man/TempoActivityPlot.Rd |only man/TempoPlot.Rd |only 11 files changed, 418 insertions(+), 107 deletions(-)
Title: Persist Attributes Across Data Operations
Description: In base R, object attributes are lost when objects are modified by
common data operations such as subset, filter, slice, append, extract
etc. This packages allows objects to be marked as 'sticky' and have
attributes persisted during these operations or when inserted
into or extracted from recursive (i.e. list- or table-like) objects.
Author: Christopher Brown [aut, cre],
Decision Patterns [cph]
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between sticky versions 0.3.3 dated 2016-09-26 and 0.3.6 dated 2016-10-04
sticky-0.3.3/sticky/inst/doc/sticky.R |only sticky-0.3.3/sticky/inst/doc/sticky.Rmd |only sticky-0.3.3/sticky/inst/doc/sticky.html |only sticky-0.3.3/sticky/vignettes/sticky.Rmd |only sticky-0.3.6/sticky/DESCRIPTION | 16 +++++------ sticky-0.3.6/sticky/MD5 | 34 ++++++++++++------------- sticky-0.3.6/sticky/NAMESPACE | 2 - sticky-0.3.6/sticky/NEWS | 31 ++++++++++++++++++---- sticky-0.3.6/sticky/R/append.R | 1 sticky-0.3.6/sticky/R/sticky.R | 10 +------ sticky-0.3.6/sticky/README.md | 12 ++++---- sticky-0.3.6/sticky/build/vignette.rds |binary sticky-0.3.6/sticky/inst/doc/introduction.R |only sticky-0.3.6/sticky/inst/doc/introduction.Rmd |only sticky-0.3.6/sticky/inst/doc/introduction.html |only sticky-0.3.6/sticky/man/append.Rd | 2 - sticky-0.3.6/sticky/man/extract.Rd | 2 - sticky-0.3.6/sticky/man/init.Rd | 5 ++- sticky-0.3.6/sticky/man/print.sticky.Rd | 6 ++-- sticky-0.3.6/sticky/man/sticky.Rd | 12 ++++---- sticky-0.3.6/sticky/man/subset.sticky.Rd | 2 - sticky-0.3.6/sticky/vignettes/introduction.Rmd |only 22 files changed, 75 insertions(+), 60 deletions(-)
Title: A Toolbox for the Analysis of Proteomics Data
Description: Tools for the statistical analysis and visualization of (relative
and absolute) quantitative (LFQ,TMT,HRM) Proteomics data.
Author: Erik Ahrne
Maintainer: Erik Ahrne <erik.ahrne@unibas.ch>
Diff between SafeQuant versions 2.2.2 dated 2016-01-07 and 2.3 dated 2016-10-04
SafeQuant-2.2.2/SafeQuant/exec/mFuzzClustering.R |only SafeQuant-2.2.2/SafeQuant/inst/testData |only SafeQuant-2.2.2/SafeQuant/inst/version |only SafeQuant-2.3/SafeQuant/DESCRIPTION | 12 SafeQuant-2.3/SafeQuant/MD5 | 201 ++-- SafeQuant-2.3/SafeQuant/NAMESPACE | 9 SafeQuant-2.3/SafeQuant/R/ExpressionAnalysis.R | 478 ++++++---- SafeQuant-2.3/SafeQuant/R/Graphics.R | 337 ++++++- SafeQuant-2.3/SafeQuant/R/Parser.R | 55 - SafeQuant-2.3/SafeQuant/R/SafeQuantAnalysis.R | 23 SafeQuant-2.3/SafeQuant/R/TMT.R | 296 ++++++ SafeQuant-2.3/SafeQuant/R/UserOptions.R | 136 +- SafeQuant-2.3/SafeQuant/README.md | 8 SafeQuant-2.3/SafeQuant/exec/installDependencies.R |only SafeQuant-2.3/SafeQuant/exec/safeQuant.R | 362 +++++-- SafeQuant-2.3/SafeQuant/inst/manuals/SafeQuant-man.pdf |binary SafeQuant-2.3/SafeQuant/inst/manuals/tsv_spreadsheet_help.docx |binary SafeQuant-2.3/SafeQuant/inst/manuals/tsv_spreadsheet_help.pdf |binary SafeQuant-2.3/SafeQuant/man/COLORS.Rd | 5 SafeQuant-2.3/SafeQuant/man/addIdQvalues.Rd | 4 SafeQuant-2.3/SafeQuant/man/addScaffoldPTMFAnnotations.Rd | 2 SafeQuant-2.3/SafeQuant/man/barplotMSSignal.Rd | 2 SafeQuant-2.3/SafeQuant/man/calibrationCurve.Rd | 2 SafeQuant-2.3/SafeQuant/man/createExpDesign.Rd | 4 SafeQuant-2.3/SafeQuant/man/createExpressionDataset.Rd | 2 SafeQuant-2.3/SafeQuant/man/createPairedExpDesign.Rd |only SafeQuant-2.3/SafeQuant/man/cvBoxplot.Rd | 2 SafeQuant-2.3/SafeQuant/man/expDesignTagToExpDesign.Rd | 18 SafeQuant-2.3/SafeQuant/man/export.Rd | 2 SafeQuant-2.3/SafeQuant/man/getAAProteinCoordinates.Rd | 2 SafeQuant-2.3/SafeQuant/man/getAllCV.Rd | 2 SafeQuant-2.3/SafeQuant/man/getAllEBayes.Rd | 10 SafeQuant-2.3/SafeQuant/man/getBaselineIntensity.Rd | 2 SafeQuant-2.3/SafeQuant/man/getCV.Rd | 2 SafeQuant-2.3/SafeQuant/man/getExpDesignProgenesisCsv.Rd | 2 SafeQuant-2.3/SafeQuant/man/getGlobalNormFactors.Rd | 4 SafeQuant-2.3/SafeQuant/man/getIBAQEset.Rd | 4 SafeQuant-2.3/SafeQuant/man/getIdLevelQvals.Rd | 2 SafeQuant-2.3/SafeQuant/man/getImpuritiesMatrix.Rd | 2 SafeQuant-2.3/SafeQuant/man/getIntSumPerProtein.Rd | 4 SafeQuant-2.3/SafeQuant/man/getLoocvFoldError.Rd | 2 SafeQuant-2.3/SafeQuant/man/getMaxIndex.Rd | 2 SafeQuant-2.3/SafeQuant/man/getMeanCenteredRange.Rd | 2 SafeQuant-2.3/SafeQuant/man/getModifProteinCoordinates.Rd | 2 SafeQuant-2.3/SafeQuant/man/getMotifX.Rd | 2 SafeQuant-2.3/SafeQuant/man/getNbDetectablePeptides.Rd | 2 SafeQuant-2.3/SafeQuant/man/getNbMisCleavages.Rd | 2 SafeQuant-2.3/SafeQuant/man/getNbPeptidesPerProtein.Rd | 2 SafeQuant-2.3/SafeQuant/man/getNbSpectraPerProtein.Rd | 2 SafeQuant-2.3/SafeQuant/man/getPeptides.Rd | 2 SafeQuant-2.3/SafeQuant/man/getRTNormFactors.Rd | 2 SafeQuant-2.3/SafeQuant/man/getRatios.Rd | 4 SafeQuant-2.3/SafeQuant/man/getScoreCutOff.Rd | 2 SafeQuant-2.3/SafeQuant/man/getSignalPerCondition.Rd | 2 SafeQuant-2.3/SafeQuant/man/getTopX.Rd | 2 SafeQuant-2.3/SafeQuant/man/getUserOptions.Rd | 2 SafeQuant-2.3/SafeQuant/man/globalNormalize.Rd | 2 SafeQuant-2.3/SafeQuant/man/hClustHeatMap.Rd | 2 SafeQuant-2.3/SafeQuant/man/isCon.Rd | 2 SafeQuant-2.3/SafeQuant/man/isDecoy.Rd | 2 SafeQuant-2.3/SafeQuant/man/isStrippedACs.Rd | 2 SafeQuant-2.3/SafeQuant/man/maPlotSQ.Rd |only SafeQuant-2.3/SafeQuant/man/missinValueBarplot.Rd | 2 SafeQuant-2.3/SafeQuant/man/option_list.Rd | 230 ---- SafeQuant-2.3/SafeQuant/man/pairsAnnot.Rd | 2 SafeQuant-2.3/SafeQuant/man/parseMaxQuantProteinGroupTxt.Rd | 2 SafeQuant-2.3/SafeQuant/man/parseProgenesisFeatureCsv.Rd | 2 SafeQuant-2.3/SafeQuant/man/parseProgenesisPeptideMeasurementCsv.Rd | 6 SafeQuant-2.3/SafeQuant/man/parseProgenesisProteinCsv.Rd | 2 SafeQuant-2.3/SafeQuant/man/parseScaffoldPTMReport.Rd | 2 SafeQuant-2.3/SafeQuant/man/parseScaffoldRawFile.Rd | 2 SafeQuant-2.3/SafeQuant/man/perFeatureNormalization.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotAbsEstCalibrationCurve.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotAdjustedVsNonAdjustedRatio.Rd |only SafeQuant-2.3/SafeQuant/man/plotExpDesign.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotIdScoreVsFDR.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotMSSignalDistributions.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotNbIdentificationsVsRT.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotNbValidDeFeaturesPerFDR.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotPrecMassErrorDistrib.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotPrecMassErrorVsScore.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotQValueVsPValue.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotROC.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotRTNorm.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotRTNormSummary.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotScoreDistrib.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotVolcano.Rd | 2 SafeQuant-2.3/SafeQuant/man/plotXYDensity.Rd | 6 SafeQuant-2.3/SafeQuant/man/purityCorrectTMT.Rd | 2 SafeQuant-2.3/SafeQuant/man/removeOutliers.Rd | 2 SafeQuant-2.3/SafeQuant/man/rollUp.Rd | 2 SafeQuant-2.3/SafeQuant/man/rtNormalize.Rd | 2 SafeQuant-2.3/SafeQuant/man/safeQuantAnalysis.Rd | 11 SafeQuant-2.3/SafeQuant/man/setNbPeptidesPerProtein.Rd | 2 SafeQuant-2.3/SafeQuant/man/setNbSpectraPerProtein.Rd | 2 SafeQuant-2.3/SafeQuant/man/sqNormalize.Rd | 2 SafeQuant-2.3/SafeQuant/man/standardise.Rd | 2 SafeQuant-2.3/SafeQuant/man/stripACs.Rd | 2 SafeQuant-2.3/SafeQuant/tests/initTestSession.R | 33 SafeQuant-2.3/SafeQuant/tests/testData/scaffold_tmt10plex_calibMix_raw.xls |only SafeQuant-2.3/SafeQuant/tests/testExpressionAnalysis.R | 116 +- SafeQuant-2.3/SafeQuant/tests/testGraphics.R | 20 SafeQuant-2.3/SafeQuant/tests/testParser.R | 40 SafeQuant-2.3/SafeQuant/tests/testSafeQuantAnalysis.R | 21 SafeQuant-2.3/SafeQuant/tests/testTMT.R | 113 ++ 105 files changed, 1801 insertions(+), 897 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model 'MGHD' is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD', mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' is a 'MSGHD' with convex contour plots. The 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Aisha ElSherbiny, Ryan P. Browne, Brian C. Franczak, and Paul D. McNicholas.
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between MixGHD versions 1.8 dated 2015-09-24 and 2.0 dated 2016-10-04
MixGHD-1.8/MixGHD/R/usedSelection.R |only MixGHD-2.0/MixGHD/DESCRIPTION | 13 - MixGHD-2.0/MixGHD/MD5 | 41 ++-- MixGHD-2.0/MixGHD/NAMESPACE | 10 - MixGHD-2.0/MixGHD/R/DA.R | 12 - MixGHD-2.0/MixGHD/R/GHD.R | 355 +++++++++++++++++------------------- MixGHD-2.0/MixGHD/R/MCGHD.R | 127 ++++++++++++ MixGHD-2.0/MixGHD/R/MGHD.R | 82 ++++++++ MixGHD-2.0/MixGHD/R/MGHFA.R | 90 +++++++++ MixGHD-2.0/MixGHD/R/MSGHD.R | 97 +++++++++ MixGHD-2.0/MixGHD/R/cMSGHD.R | 95 +++++++++ MixGHD-2.0/MixGHD/R/contourpl.R |only MixGHD-2.0/MixGHD/man/ARI.Rd | 2 MixGHD-2.0/MixGHD/man/DA.Rd | 5 MixGHD-2.0/MixGHD/man/MCGHD.Rd | 4 MixGHD-2.0/MixGHD/man/MGHD.Rd | 4 MixGHD-2.0/MixGHD/man/MGHFA.Rd | 6 MixGHD-2.0/MixGHD/man/MSGHD.Rd | 6 MixGHD-2.0/MixGHD/man/cMSGHD.Rd | 4 MixGHD-2.0/MixGHD/man/contourpl.Rd |only MixGHD-2.0/MixGHD/src |only 21 files changed, 725 insertions(+), 228 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <sen-zhao@sen-zhao.com>
Diff between Grace versions 0.4.1 dated 2016-09-21 and 0.4.2 dated 2016-10-04
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/cvGrace.R | 2 +- R/grace.R | 2 +- R/grace.test.R | 2 +- R/make.L.R | 2 +- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories, a method for
variable selection based on the SVD, Bézier lines with arrows complementing the
ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.3.1 dated 2016-02-07 and 1.4 dated 2016-10-04
DESCRIPTION | 11 MD5 | 285 - NAMESPACE | 151 NEWS | 800 +-- R/Gmisc.R | 86 R/RcppExports.R | 2 R/assert.R |only R/bezierArrowGradient.R | 604 +- R/bezierArrowSmpl.R | 348 - R/bezier_private_functions.R | 802 +-- R/boxGrobs.R |only R/copyAllNewAttributes.R | 64 R/deprecated.R | 36 R/descriptionStats.R | 940 +-- R/docx_document.R | 630 +- R/fastDoCall.R | 118 R/figCaptionNo.R | 264 - R/getDescriptionStatsBy.R | 1040 ++-- R/getPval.R | 178 R/getSvdMostInfluential.R | 298 - R/insertRowAndKeepAttr.R | 146 R/mergeDesc.R | 418 - R/mergeLists.R | 196 R/private_functions.R | 578 +- R/transitionClass.R | 2372 +++++----- R/transitionClass_helpers.R | 836 +-- R/transitionPlot.R | 1058 ++-- R/transitionPlot_helpers.R | 1272 ++--- build/vignette.rds |binary inst/doc/Descriptives.R | 274 - inst/doc/Descriptives.Rmd | 390 - inst/doc/Descriptives.html | 1624 +++--- inst/doc/Grid-based_flowcharts.R |only inst/doc/Grid-based_flowcharts.Rmd |only inst/doc/Grid-based_flowcharts.html |only inst/doc/Transition-class.R | 184 inst/doc/Transition-class.Rmd | 274 - inst/doc/Transition-class.html | 394 - inst/doc/transitionPlot.R | 230 inst/doc/transitionPlot.Rmd | 350 - inst/doc/transitionPlot.html | 431 - inst/examples/bezierArrowGradient_example.R | 60 inst/examples/bezierArrowSmpl_example.R | 44 inst/examples/connectGrob_example.R |only inst/examples/data-SCB_example.R | 60 inst/examples/fastDoCall_ex.R | 52 inst/examples/getDescriptionStatsBy_example.R | 160 inst/examples/getSvdMostInfluential_example.R | 186 inst/examples/mergeLists_example.R | 6 inst/examples/transitionClass_example.R | 52 inst/extdata/Full_test_suite.Rmd | 362 - inst/include/Gmisc.h | 64 inst/rmarkdown/docx.css | 410 - inst/rmarkdown/templates/CONSORT_v2010_docx/skeleton/skeleton.Rmd | 240 - inst/rmarkdown/templates/STROBE_v4_docx/skeleton/skeleton.Rmd | 220 man/Gmisc-deprecated.Rd | 38 man/Gmisc-package.Rd | 102 man/Transition-class.Rd | 324 - man/assert.Rd |only man/bezierArrowGradient.Rd | 188 man/bezierArrowSmpl.Rd | 154 man/box.Rd |only man/boxPropGrob.Rd |only man/calculateLinesAndArrow.Rd | 92 man/connect.Rd |only man/copyAllNewAttributes.Rd | 72 man/describeFactors.Rd | 162 man/describeMean.Rd | 136 man/describeMedian.Rd | 130 man/describeProp.Rd | 128 man/docx_document.Rd | 164 man/fastDoCall.Rd | 136 man/figCapNo.Rd | 104 man/figCapNoLast.Rd | 52 man/figCapNoNext.Rd | 52 man/getAbsoluteWidth.Rd | 68 man/getBezierAdj4Arrw.Rd | 50 man/getDescriptionStatsBy.Rd | 450 - man/getGridVal.Rd | 50 man/getPval.Rd | 158 man/getSvdMostInfluential.Rd | 294 - man/getVectorAngle.Rd | 50 man/gnrlBezierPoints.Rd | 76 man/htmlTable_latex.Rd | 56 man/insertRowAndKeepAttr.Rd | 68 man/isHorizontal.Rd | 38 man/mergeDesc.Rd | 262 - man/mergeLists.Rd | 58 man/mergeLists_internal.Rd | 42 man/prCaptionFix.Rd | 38 man/prConvertShowMissing.Rd | 46 man/prDescGetAndValidateDefaultRef.Rd | 46 man/prDescGetMissing.Rd | 82 man/prFtpHeaderStyle.Rd | 54 man/prFtpOtherChanges.Rd | 38 man/prFtpOtherRemoval.Rd | 38 man/prFtpScriptRemoval.Rd | 38 man/prGetStatistics.Rd | 114 man/prGetTextGrobCex.Rd | 38 man/prGridPlotTitle.Rd | 60 man/prPasteVec.Rd | 32 man/prPushMarginViewport.Rd | 60 man/prSetMaxWidth.Rd | 44 man/prTcMatchClr.Rd | 58 man/prTcPlotArrows.Rd | 84 man/prTcPlotBoxColumn.Rd | 58 man/prTcValidateAndPrepClr.Rd | 58 man/prTpGetBoxPositions.Rd | 72 man/prTpGetBoxPropClr.Rd | 50 man/prTpGetBoxSizedTextGrob.Rd | 48 man/prTpGetColors.Rd | 66 man/prTpPlotArrows.Rd | 102 man/prTpPlotBox.Rd | 66 man/prTpPlotBoxes.Rd | 232 man/transitionPlot.Rd | 352 - man/validateAndConvertVectorInputs.Rd | 56 src/RcppExports.cpp | 18 tests/cpp_tests/visual_line_debugging.R | 134 tests/performance/bezierArrowProfiler.R | 46 tests/testthat.R | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test-bezier.R | 204 tests/testthat/test-copyAllAttributes.R | 84 tests/testthat/test-descriptionStats.R | 296 - tests/testthat/test-docx_document.R | 354 - tests/testthat/test-fastDoCall.R | 92 tests/testthat/test-figCapNo.R | 96 tests/testthat/test-fig_caption.R | 54 tests/testthat/test-getDescriptionStats.R | 948 ++- tests/testthat/test-insertRowAndKeepAttr.R | 40 tests/testthat/test-mergeLists.R | 132 tests/testthat/test-transitionClass.R | 310 - tests/visual_tests/FTP_test/FTP_test.Rmd | 296 - tests/visual_tests/FTP_test/Setup_and_munge.R | 124 tests/visual_tests/Full_test_suite.Rmd | 362 - tests/visual_tests/Highlighting_test.Rmd | 48 tests/visual_tests/MathJax_test.Rmd | 44 tests/visual_tests/Max_width_test.Rmd | 28 tests/visual_tests/bezierArrowGradient_vtests.R | 126 tests/visual_tests/bezierArrowRcpp_vtests.R | 170 tests/visual_tests/bezierArrowSmpl_vtests.R | 210 tests/visual_tests/tansitionPlot_vtests.R | 344 - tests/visual_tests/test-bezier-adjustment.R | 262 - tests/visual_tests/transitionClass_vtest.R | 78 vignettes/Descriptives.Rmd | 390 - vignettes/Grid-based_flowcharts.Rmd |only vignettes/Transition-class.Rmd | 274 - vignettes/custom.css | 324 - vignettes/transitionPlot.Rmd | 350 - 149 files changed, 15898 insertions(+), 15730 deletions(-)
Title: Multi-Purpose Core Subset Selection
Description: Core Hunter is a tool to sample diverse, representative subsets from large germplasm
collections, with minimum redundancy. Such so-called core collections have applications in plant
breeding and genetic resource management in general. Core Hunter can construct cores based on
genetic marker data, phenotypic traits or precomputed distance matrices, optimizing one of many
provided evaluation measures depending on the precise purpose of the core (e.g. high diversity,
representativeness, or allelic richness). In addition, multiple measures can be simultaneously
optimized as part of a weighted index to bring the different perspectives closer together.
The Core Hunter library is implemented in Java 8 as an open source project (see
<http://www.corehunter.org>).
Author: Herman De Beukelaer [aut, cre],
Guy Davenport [aut],
Veerle Fack [ths]
Maintainer: Herman De Beukelaer <herman.debeukelaer@gmail.com>
Diff between corehunter versions 3.0.0 dated 2016-10-03 and 3.0.1 dated 2016-10-04
corehunter-3.0.0/corehunter/R/onLoad.R |only corehunter-3.0.1/corehunter/DESCRIPTION | 26 ++++++++++++++------------ corehunter-3.0.1/corehunter/MD5 | 14 +++++++------- corehunter-3.0.1/corehunter/NEWS.md | 10 ++++++++-- corehunter-3.0.1/corehunter/R/corehunter.R | 10 +++++++++- corehunter-3.0.1/corehunter/R/java.R | 22 ++++++++-------------- corehunter-3.0.1/corehunter/R/zzz.R |only corehunter-3.0.1/corehunter/README.md | 7 +++++-- corehunter-3.0.1/corehunter/man/corehunter.Rd | 10 +++++++++- 9 files changed, 60 insertions(+), 39 deletions(-)
Title: Methods for Changepoint Detection
Description: Implements various mainstream and specialised changepoint methods for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included. The cpt.mean(), cpt.var(), cpt.meanvar() functions should be your first point of call.
Author: Rebecca Killick [aut, cre],
Kaylea Haynes [aut],
Idris Eckley [ths, aut],
Paul Fearnhead [ctb, ths],
Jamie Lee [ctr]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between changepoint versions 2.2.1 dated 2016-02-26 and 2.2.2 dated 2016-10-04
DESCRIPTION | 10 MD5 | 43 ++- NAMESPACE | 1 NEWS | 16 + R/PELT_one_func_minseglen.R | 4 R/cpt.R | 5 R/cpt.class.R | 448 ++++++++++++++++++++++++++++++---------- R/exp.R | 10 R/gamma.R | 11 R/multiple.nonparametric.R | 17 + R/multiple.norm.R | 4 R/poisson.R | 10 R/single.nonparametric.R | 2 R/single.norm.R | 14 - R/zzz.R | 2 inst/CITATION | 2 man/BINSEG.Rd |only man/PELT.Rd |only man/changepoint-package.Rd | 4 man/class_input.Rd |only man/decision.Rd |only man/logLik-methods.Rd | 3 man/penalty_decision.Rd |only src/BinSeg_one_func_minseglen.c | 3 tests/testthat/test-examples.R | 11 25 files changed, 455 insertions(+), 165 deletions(-)
Title: Client for the YouTube API
Description: Get comments posted on YouTube videos, information on how many
times a video has been liked, search for videos with particular content, and
much more. You can also scrape captions from a few videos. To learn more about
the YouTube API, see <https://developers.google.com/youtube/v3/>.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 0.3.0 dated 2016-08-04 and 0.4.0 dated 2016-10-04
DESCRIPTION | 6 +- MD5 | 68 +++++++++++++------------- NAMESPACE | 2 NEWS.md | 7 ++ R/get_channel_stats.R | 2 R/get_comment_threads.R |only R/get_comments.R | 27 +++++++--- R/get_playlist_items.R | 24 ++++++--- R/get_playlists.R | 24 ++++++--- R/get_stats.R | 4 - R/get_subscriptions.R | 29 ++++++++--- R/list_abuse_report_reasons.R | 2 R/list_channel_activities.R | 25 +++++++-- R/list_channel_resources.R | 35 +++++++++---- R/list_channel_sections.R | 20 +++++-- R/list_channel_videos.R |only R/list_guidecats.R | 24 +++++++-- R/list_videocats.R | 21 +++++--- R/yt_oauth.R | 4 - inst/doc/tuber-ex.R | 24 +++++++++ inst/doc/tuber-ex.Rmd | 27 ++++++++++ inst/doc/tuber-ex.html | 28 +++++++++- man/get_comment_threads.Rd |only man/get_comments.Rd | 16 +++--- man/get_playlist_items.Rd | 10 ++- man/get_playlists.Rd | 12 +++- man/get_subscriptions.Rd | 14 +++-- man/list_channel_activities.Rd | 15 +++-- man/list_channel_resources.Rd | 17 ++++-- man/list_channel_sections.Rd | 11 +++- man/list_channel_videos.Rd |only man/list_guidecats.Rd | 10 ++- man/list_videocats.Rd | 12 +++- tests/testthat/test-list-channel-activities.R | 2 tests/testthat/test-list-channel-sections.R | 2 vignettes/tuber-ex.Rmd | 27 ++++++++++ vignettes/tuber-ex.md | 29 ++++++++++- 37 files changed, 435 insertions(+), 145 deletions(-)
Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between SIDES versions 1.6 dated 2016-09-27 and 1.7 dated 2016-10-04
DESCRIPTION | 8 +- MD5 | 10 +-- R/IDENTIFICATION.R | 8 +- R/SIDES_MAIN.R | 144 +++++++++++++++++++++++++++++++++++++++++++++------ R/TEST_STAT_PVAL.R | 3 + man/SIDES-package.Rd | 4 - 6 files changed, 146 insertions(+), 31 deletions(-)
Title: Rank Preserving Structural Failure Time Models
Description: Implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.
Author: Simon Bond [aut, cre] (primary author of code, secondary author of
vignette),
Annabel Allison [aut] (primary author of vignette, secondary author of
code)
Maintainer: Simon Bond <simon.bond@addenbrookes.nhs.uk>
Diff between rpsftm versions 1.0.0 dated 2016-09-13 and 1.0.1 dated 2016-10-04
DESCRIPTION | 16 MD5 | 73 +-- NAMESPACE | 34 - NEWS.md |only R/data.R | 42 - R/est_eqn.R | 78 +-- R/extract_z.R | 116 ++--- R/plot.rpsftm.R | 46 +- R/print.rpsftm.R | 50 +- R/rand.R | 46 +- R/rpsftm-package.R | 36 - R/rpsftm.R | 594 +++++++++++++-------------- R/summary.rpsftm.R | 58 +- R/terms.inner.R | 54 +- R/untreated.R | 94 ++-- README.md | 66 +-- build/vignette.rds |binary inst/doc/rpsftm_vignette.R | 138 +++--- inst/doc/rpsftm_vignette.Rmd | 578 +++++++++++++-------------- inst/doc/rpsftm_vignette.html | 724 +++++++++++++++++----------------- man/est_eqn.Rd | 80 +-- man/extract_z.Rd | 88 ++-- man/immdef.Rd | 62 +- man/plot.rpsftm.Rd | 46 +- man/print.rpsftm.Rd | 46 +- man/rand.Rd | 48 +- man/rpsftm-package.Rd | 52 +- man/rpsftm.Rd | 178 ++++---- man/summary.rpsftm.Rd | 46 +- man/terms.inner.Rd | 40 - man/untreated.Rd | 70 +-- tests/testthat.R | 8 tests/testthat/test_errors.R | 360 ++++++++-------- tests/testthat/test_rpsftm.R | 536 ++++++++++++------------- vignettes/dev/adjustedHR.Rmd | 216 +++++----- vignettes/dev/rpsftm_vignette_v1.Rmd | 574 +++++++++++++-------------- vignettes/dev/rpsftm_vignette_v2.Rmd | 744 +++++++++++++++++------------------ vignettes/rpsftm_vignette.Rmd | 578 +++++++++++++-------------- 38 files changed, 3310 insertions(+), 3305 deletions(-)
Title: Goodness of Fit Tests for High-Dimensional Linear Regression
Models
Description: Performs goodness of fits tests for both high and low-dimensional linear models.
It can test for a variety of model misspecifications including nonlinearity and heteroscedasticity.
In addition one can test the significance of potentially large groups of variables, and also
produce p-values for the significance of individual variables in high-dimensional linear
regression.
Author: Rajen Shah [aut, cre],
Peter Buhlmann [aut]
Maintainer: Rajen Shah <r.shah@statslab.cam.ac.uk>
Diff between RPtests versions 0.1.0 dated 2016-06-20 and 0.1.1 dated 2016-10-04
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/RPtest_single.R | 4 ++-- R/RcppExports.R | 2 +- man/RPtest_single.Rd | 2 +- src/RcppExports.cpp | 10 +++++----- 6 files changed, 17 insertions(+), 17 deletions(-)
Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP API
from R functions using the annotations in the R documentation around your
functions.
Author: Trestle Technology, LLC [aut],
Jeff Allen [cre],
Frans van Dunné [ctb]
Maintainer: Jeff Allen <cran@trestletech.com>
Diff between plumber versions 0.2.4 dated 2016-04-14 and 0.3.1 dated 2016-10-04
plumber-0.2.4/plumber/tests/testthat/files/appender.R |only plumber-0.2.4/plumber/tests/testthat/files/filters-example.R |only plumber-0.2.4/plumber/tests/testthat/files/github-plumber.R |only plumber-0.3.1/plumber/DESCRIPTION | 27 ++-- plumber-0.3.1/plumber/MD5 | 53 ++++++--- plumber-0.3.1/plumber/NEWS.md | 17 +++ plumber-0.3.1/plumber/R/globals.R |only plumber-0.3.1/plumber/R/plumber.R | 42 ++++--- plumber-0.3.1/plumber/R/post-body.R | 25 ++++ plumber-0.3.1/plumber/R/query-string.R | 10 - plumber-0.3.1/plumber/R/response.R | 4 plumber-0.3.1/plumber/R/serializer-content-type.R |only plumber-0.3.1/plumber/R/serializer-html.R | 18 +-- plumber-0.3.1/plumber/R/serializer-json.R | 22 ++-- plumber-0.3.1/plumber/R/serializer-xml.R | 14 +- plumber-0.3.1/plumber/R/serializer.R | 18 ++- plumber-0.3.1/plumber/README.md | 18 +++ plumber-0.3.1/plumber/inst/examples/01-append |only plumber-0.3.1/plumber/inst/examples/02-filters |only plumber-0.3.1/plumber/inst/examples/03-github |only plumber-0.3.1/plumber/inst/examples/04-mean-sum |only plumber-0.3.1/plumber/inst/examples/05-static |only plumber-0.3.1/plumber/inst/examples/07-mailgun/mailgun.R | 2 plumber-0.3.1/plumber/inst/examples/08-identity |only plumber-0.3.1/plumber/inst/examples/09-content-type |only plumber-0.3.1/plumber/inst/hosted |only plumber-0.3.1/plumber/tests/testthat/files/content-type.R |only plumber-0.3.1/plumber/tests/testthat/files/serializer.R | 18 ++- plumber-0.3.1/plumber/tests/testthat/test-content-type.R |only plumber-0.3.1/plumber/tests/testthat/test-postbody.R |only plumber-0.3.1/plumber/tests/testthat/test-routing.R | 6 - plumber-0.3.1/plumber/tests/testthat/test-serializer-json.R | 4 plumber-0.3.1/plumber/tests/testthat/test-serializer.R | 60 ++++++++--- 33 files changed, 245 insertions(+), 113 deletions(-)
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.6.1 dated 2016-03-09 and 1.6.4 dated 2016-10-04
msm-1.6.1/msm/src/doc |only msm-1.6.1/msm/vignettes/_region_.tex |only msm-1.6.4/msm/ChangeLog | 22 +++++ msm-1.6.4/msm/DESCRIPTION | 8 - msm-1.6.4/msm/MD5 | 123 +++++++++++++++++++++--------- msm-1.6.4/msm/R/pearson.R | 4 msm-1.6.4/msm/R/utils.R | 13 ++- msm-1.6.4/msm/build/vignette.rds |binary msm-1.6.4/msm/inst/NEWS | 23 +++++ msm-1.6.4/msm/inst/doc/msm-manual.R | 82 ++++++++++---------- msm-1.6.4/msm/inst/doc/msm-manual.pdf |binary msm-1.6.4/msm/man/surface.msm.Rd | 3 msm-1.6.4/msm/tests/testthat/test_utils.r | 1 msm-1.6.4/msm/vignettes/Sweave-local.sty |only msm-1.6.4/msm/vignettes/figures |only msm-1.6.4/msm/vignettes/msm-manual.Rnw |only msm-1.6.4/msm/vignettes/msm.bib |only 17 files changed, 196 insertions(+), 83 deletions(-)
Title: Fast and Simple MongoDB Client for R
Description: High-performance MongoDB client based on 'libmongoc' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, SSL
encryption and SASL authentication. The vignette gives a brief overview
of the available methods in the package.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.9 dated 2016-09-26 and 0.9.1 dated 2016-10-04
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- NAMESPACE | 2 ++ NEWS | 5 ++++- R/mongo.R | 16 ++++++++++++---- R/object.R | 31 +++++++++++++++++++++---------- R/ssl.R |only inst/doc/intro.Rmd | 2 +- inst/doc/intro.html | 6 +++--- man/mongo.Rd | 4 +++- man/ssl_options.Rd |only src/client.c | 36 ++++++++++++++++++++++++++++++++++-- src/collection.c | 5 +++-- vignettes/intro.Rmd | 2 +- 14 files changed, 101 insertions(+), 40 deletions(-)
Title: MINimal VALidation for Stoichiometric Reactions
Description: For a given set of stoichiometric reactions, this package
evaluates the mass and charge balance, extracts all reactants, products, orphan
metabolites, metabolite names and compartments. Also are included some options
to write models in TSV and SBML formats.
Author: Daniel Osorio [aut,cre], Janneth Gonzalez [aut], Andres Pinzon-Velasco [aut].
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Diff between minval versions 0.4 dated 2016-05-18 and 0.5 dated 2016-10-04
minval-0.4/minval/R/chebi.candidates.R |only minval-0.4/minval/R/chebi.formula.R |only minval-0.4/minval/R/chebi.id.R |only minval-0.4/minval/R/is.chebi.R |only minval-0.4/minval/R/is.validsyntax.R |only minval-0.4/minval/R/minval-internal.R |only minval-0.4/minval/R/orphan.products.R |only minval-0.4/minval/R/orphan.reactants.R |only minval-0.4/minval/R/toChEBI.R |only minval-0.4/minval/R/unbalanced.R |only minval-0.4/minval/data |only minval-0.4/minval/inst/tests/runit.chebi.formula.R |only minval-0.4/minval/inst/tests/runit.is.chebi.R |only minval-0.4/minval/inst/tests/runit.is.validsyntax.R |only minval-0.4/minval/inst/tests/runit.orphan.products.R |only minval-0.4/minval/inst/tests/runit.orphan.reactants.R |only minval-0.4/minval/inst/tests/runit.toChEBI.R |only minval-0.4/minval/inst/tests/runit.unbalanced.R |only minval-0.4/minval/man/chebi.Rd |only minval-0.4/minval/man/chebi.candidates.Rd |only minval-0.4/minval/man/chebi.formula.Rd |only minval-0.4/minval/man/chebi.id.Rd |only minval-0.4/minval/man/glugln.Rd |only minval-0.4/minval/man/is.chebi.Rd |only minval-0.4/minval/man/is.validsyntax.Rd |only minval-0.4/minval/man/minval-package.Rd |only minval-0.4/minval/man/orphan.products.Rd |only minval-0.4/minval/man/orphan.reactants.Rd |only minval-0.4/minval/man/toChEBI.Rd |only minval-0.4/minval/man/unbalanced.Rd |only minval-0.5/minval/DESCRIPTION | 18 +- minval-0.5/minval/MD5 | 95 ++++++-------- minval-0.5/minval/NAMESPACE | 26 +++ minval-0.5/minval/NEWS | 5 minval-0.5/minval/R/compartments.R | 49 +++++-- minval-0.5/minval/R/convert2sbml.R |only minval-0.5/minval/R/convert2sbmlR.R |only minval-0.5/minval/R/getChEBI.R |only minval-0.5/minval/R/isBalanced.R |only minval-0.5/minval/R/isValidSyntax.R |only minval-0.5/minval/R/mapReactions.R |only minval-0.5/minval/R/metabolites.R | 71 +++++++--- minval-0.5/minval/R/minvalInternal.R |only minval-0.5/minval/R/orphanProducts.R |only minval-0.5/minval/R/orphanReactants.R |only minval-0.5/minval/R/products.R | 66 +++++++-- minval-0.5/minval/R/reactants.R | 62 ++++++--- minval-0.5/minval/R/stoichiometricMatrix.R |only minval-0.5/minval/R/writeTSVmod.R |only minval-0.5/minval/R/xls2sbml.R |only minval-0.5/minval/README.md | 54 ++++--- minval-0.5/minval/inst/extdata |only minval-0.5/minval/inst/tests/runit.compartments.R | 2 minval-0.5/minval/inst/tests/runit.isBalanced.R |only minval-0.5/minval/inst/tests/runit.isValidSyntax.R |only minval-0.5/minval/inst/tests/runit.metabolites.R | 2 minval-0.5/minval/inst/tests/runit.orphanProducts.R |only minval-0.5/minval/inst/tests/runit.orphanReactants.R |only minval-0.5/minval/inst/tests/runit.products.R | 2 minval-0.5/minval/inst/tests/runit.reactants.R | 3 minval-0.5/minval/inst/tests/runit.stoichiometricMatrix.R |only minval-0.5/minval/man/compartments.Rd | 58 +++++--- minval-0.5/minval/man/convert2sbml.Rd |only minval-0.5/minval/man/convert2sbmlR.Rd |only minval-0.5/minval/man/getChEBI.Rd |only minval-0.5/minval/man/isBalanced.Rd |only minval-0.5/minval/man/isValidSyntax.Rd |only minval-0.5/minval/man/mapReactions.Rd |only minval-0.5/minval/man/metabolites.Rd | 83 +++++++----- minval-0.5/minval/man/orphanProducts.Rd |only minval-0.5/minval/man/orphanReactants.Rd |only minval-0.5/minval/man/products.Rd | 64 +++++---- minval-0.5/minval/man/reactants.Rd | 65 +++++---- minval-0.5/minval/man/stoichiometricMatrix.Rd |only minval-0.5/minval/man/writeTSVmod.Rd |only minval-0.5/minval/man/xls2sbml.Rd |only 76 files changed, 476 insertions(+), 249 deletions(-)
Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation, manipulation and simulation of multistate
data - the Lexis suite of functions, which includes interfaces to
'mstate', 'etm' and 'cmprsk' packages.
Also contains functions for Age-Period-Cohort and Lee-Carter
modeling and a function for interval censored data and some useful
functions for tabulation and plotting, as well some epidemiological
datasets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <bxc@steno.dk>
Diff between Epi versions 2.0 dated 2016-01-06 and 2.7 dated 2016-10-04
Epi-2.0/Epi/inst/doc/sim-Lexis.R |only Epi-2.0/Epi/inst/doc/sim-Lexis.pdf |only Epi-2.7/Epi/CHANGES | 54 ++++++ Epi-2.7/Epi/DESCRIPTION | 20 +- Epi-2.7/Epi/MD5 | 72 ++++---- Epi-2.7/Epi/NAMESPACE | 24 ++ Epi-2.7/Epi/R/Cplot.R | 14 + Epi-2.7/Epi/R/LCa.fit.R |only Epi-2.7/Epi/R/Ns.r | 228 ++++++++++++++++++-------- Epi-2.7/Epi/R/apc.LCa.R |only Epi-2.7/Epi/R/apc.fit.R | 66 ++++--- Epi-2.7/Epi/R/boxes.MS.R | 4 Epi-2.7/Epi/R/cal.yr.R | 8 Epi-2.7/Epi/R/clear.R | 28 +-- Epi-2.7/Epi/R/erl.R |only Epi-2.7/Epi/R/lexis.R | 29 ++- Epi-2.7/Epi/R/rm.tr.R |only Epi-2.7/Epi/R/summary.Lexis.r | 36 ++-- Epi-2.7/Epi/build/vignette.rds |binary Epi-2.7/Epi/inst/CITATION | 4 Epi-2.7/Epi/inst/doc/Follow-up.R | 318 ++++++++++++++++++------------------- Epi-2.7/Epi/inst/doc/Follow-up.pdf |binary Epi-2.7/Epi/inst/doc/index.html | 4 Epi-2.7/Epi/inst/doc/simLexis.R | 24 +- Epi-2.7/Epi/inst/doc/simLexis.pdf |binary Epi-2.7/Epi/inst/doc/simLexis.rnw | 1 Epi-2.7/Epi/man/LCa.fit.Rd |only Epi-2.7/Epi/man/Ns.Rd | 65 ++++++- Epi-2.7/Epi/man/Relevel.Rd | 1 Epi-2.7/Epi/man/apc.LCa.Rd |only Epi-2.7/Epi/man/apc.fit.Rd | 107 ++++++++---- Epi-2.7/Epi/man/boxes.MS.Rd | 3 Epi-2.7/Epi/man/ci.lin.Rd | 1 Epi-2.7/Epi/man/erl.Rd |only Epi-2.7/Epi/man/foreign.Lexis.Rd | 2 Epi-2.7/Epi/man/gen.exp.Rd | 84 +++++---- Epi-2.7/Epi/man/lls.Rd | 5 Epi-2.7/Epi/man/rm.tr.Rd |only Epi-2.7/Epi/man/subset.Lexis.Rd | 2 Epi-2.7/Epi/man/summary.Lexis.rd | 5 Epi-2.7/Epi/vignettes/index.html | 4 Epi-2.7/Epi/vignettes/simLexis.rnw | 1 42 files changed, 763 insertions(+), 451 deletions(-)
Title: Modeling Correlational Magnitude Transformations in
Discretization Contexts
Description: Modeling the correlation transitions under specified distributional assumptions within the realm of discretization in the context of the latency and threshold concepts.
Author: Rawan Allozi, Hakan Demirtas
Maintainer: Rawan Allozi <ralloz2@uic.edu>
Diff between CorrToolBox versions 1.1 dated 2016-07-21 and 1.2 dated 2016-10-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/mps2cps.R | 6 ++++-- man/CorrToolBox-package.Rd | 4 ++-- man/mps2cps.Rd | 2 +- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: A ggplot2 Extension to Visualize Two Variables per Color
Aesthetic Through Color Space Projections
Description: A ggplot2 extension to visualize two
variables through one color aesthetic via mapping to a color space
projection. With this technique for 2-D color mapping, one can create a
dichotomous choropleth in R as well as other visualizations with
bivariate color scales. Includes two new scales and a new guide for ggplot2.
Author: William Murphy [aut, cre],
Hadley Wickham [ctb] (Original author for copied and derived code),
Winston Chang [ctb] (Original author for copied and derived code)
Maintainer: William Murphy <william.murphy.rd@gmail.com>
Diff between colorplaner versions 0.1.1 dated 2016-09-21 and 0.1.2 dated 2016-10-04
DESCRIPTION | 8 - MD5 | 19 +- NEWS.md | 5 build/vignette.rds |binary inst/doc/colorplaner.R | 108 +++++++++++----- inst/doc/colorplaner.Rmd | 269 +++++++++++++++++++++++++++++++--------- inst/doc/colorplaner.html | 92 ++++++++----- inst/doc/other_projections.R |only inst/doc/other_projections.Rmd | 138 ++++++++++++++++++++ inst/doc/other_projections.html | 114 ++++++++++++++++ vignettes/colorplaner.Rmd | 10 - 11 files changed, 620 insertions(+), 143 deletions(-)
Title: Backward Pipe Operator
Description: Provides a backward-pipe operator for 'magrittr' (%<%) or
'pipeR' (%<<%) that allows for a performing operations from right-to-left.
This indispensable for writing clear code where there is natural
right-to-left ordering common with nested structures
and hierarchies such as trees/directories or markup languages such as HTML
and XML.
Author: Christopher Brown [cre, aut],
Decision Patterns [cph]
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between backpipe versions 0.1.5 dated 2015-10-21 and 0.1.8.1 dated 2016-10-04
DESCRIPTION | 19 ++++---- LICENSE | 2 MD5 | 20 ++++---- NAMESPACE | 2 NEWS | 5 ++ README.md | 110 +++++++++++++++++++++++++++++++++++-------------- inst/doc/backpipe.Rmd | 103 ++++++++++++++++++++++++++++++++------------- inst/doc/backpipe.html | 79 ++++++++++++++++++++++++----------- man/backpipe.Rd | 9 ++-- man/backpipes.Rd | 33 +++++++------- vignettes/backpipe.Rmd | 103 ++++++++++++++++++++++++++++++++------------- 11 files changed, 328 insertions(+), 157 deletions(-)
Title: Design and Analysis of Disease Surveillance Activities
Description: A range of functions for the design and
analysis of disease surveillance activities. These functions were
originally developed for animal health surveillance activities but can be
equally applied to aquatic animal, wildlife, plant and human health
surveillance activities. Utilities are included for sample size calculation
and analysis of representative surveys for disease freedom, risk-based
studies for disease freedom and for prevalence estimation.
Author: Evan Sergeant
Maintainer: Evan Sergeant <evan@ausvet.com.au>
Diff between RSurveillance versions 0.1.0 dated 2014-12-08 and 0.2.0 dated 2016-10-03
RSurveillance-0.1.0/RSurveillance/man/sd.tp.Rd |only RSurveillance-0.2.0/RSurveillance/DESCRIPTION | 16 RSurveillance-0.2.0/RSurveillance/MD5 | 131 +++--- RSurveillance-0.2.0/RSurveillance/NAMESPACE | 7 RSurveillance-0.2.0/RSurveillance/R/adj_risk_sim.R |only RSurveillance-0.2.0/RSurveillance/R/freedom_functions_1.R | 205 +++++----- RSurveillance-0.2.0/RSurveillance/R/freedom_functions_2.R | 10 RSurveillance-0.2.0/RSurveillance/R/n_rb2stage.R |only RSurveillance-0.2.0/RSurveillance/R/prevalence_functions.R | 52 -- RSurveillance-0.2.0/RSurveillance/R/risk_based_functions.R | 78 --- RSurveillance-0.2.0/RSurveillance/R/sep_passive.R |only RSurveillance-0.2.0/RSurveillance/R/sse_rb2stage.R |only RSurveillance-0.2.0/RSurveillance/man/adj.risk.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/adj.risk.sim.Rd |only RSurveillance-0.2.0/RSurveillance/man/ap.Rd | 5 RSurveillance-0.2.0/RSurveillance/man/binom.agresti.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/binom.cp.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/binom.jeffreys.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/disc.prior.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/epi.calc.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/n.2stage.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.ap.Rd | 5 RSurveillance-0.2.0/RSurveillance/man/n.binom.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.c.freecalc.Rd | 11 RSurveillance-0.2.0/RSurveillance/man/n.c.hp.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/n.freecalc.Rd | 5 RSurveillance-0.2.0/RSurveillance/man/n.freedom.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.hp.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/n.hypergeo.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.pfree.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/n.pooled.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.rb.2stage.1.Rd |only RSurveillance-0.2.0/RSurveillance/man/n.rb.2stage.2.Rd |only RSurveillance-0.2.0/RSurveillance/man/n.rb.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/n.rb.varse.Rd | 13 RSurveillance-0.2.0/RSurveillance/man/n.tp.Rd | 5 RSurveillance-0.2.0/RSurveillance/man/pfree.1.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/pfree.calc.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/pfree.equ.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/pstar.calc.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/se.parallel.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/se.series.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/sep.binom.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/sep.binom.imperfect.Rd | 11 RSurveillance-0.2.0/RSurveillance/man/sep.exact.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/sep.freecalc.Rd | 10 RSurveillance-0.2.0/RSurveillance/man/sep.hp.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/sep.hypergeo.Rd | 10 RSurveillance-0.2.0/RSurveillance/man/sep.passive.Rd |only RSurveillance-0.2.0/RSurveillance/man/sep.pfree.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.pooled.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.prior.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.rb.bin.Rd | 11 RSurveillance-0.2.0/RSurveillance/man/sep.rb.bin.varse.Rd | 15 RSurveillance-0.2.0/RSurveillance/man/sep.rb.hypergeo.Rd | 15 RSurveillance-0.2.0/RSurveillance/man/sep.rb.hypergeo.varse.Rd | 17 RSurveillance-0.2.0/RSurveillance/man/sep.rb2.binom.Rd | 15 RSurveillance-0.2.0/RSurveillance/man/sep.rb2.hypergeo.Rd | 17 RSurveillance-0.2.0/RSurveillance/man/sep.sys.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.var.se.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sp.parallel.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sp.series.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sph.binom.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/sph.hp.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/spp.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sse.combined.Rd | 27 - RSurveillance-0.2.0/RSurveillance/man/sse.rb.2stage.Rd | 39 - RSurveillance-0.2.0/RSurveillance/man/tp.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/tp.normal.Rd | 5 RSurveillance-0.2.0/RSurveillance/tests/RSurveillance.R | 40 + 71 files changed, 482 insertions(+), 475 deletions(-)
Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in
the Global Charcoal Database. Main functionalities includes data extraction
and sites selection, transformation and interpolation of the charcoal
records as well as compositing.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between paleofire versions 1.1.8 dated 2015-12-21 and 1.1.9 dated 2016-10-03
DESCRIPTION | 8 +++--- MD5 | 55 +++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS | 12 +++++++++ R/kdffreq.R | 39 +++++++++++++++++++++--------- R/paleofire-package.R | 4 +-- R/pfAddData.R | 17 ++++++++++--- R/pfCompositeLF.R | 54 ++++++++++++++++++++++++++++++++---------- R/pfGridding.R | 5 +-- R/pfResolution.R | 10 +++++-- R/pfSiteSel.R | 12 +++++++-- R/potveg.R | 42 +++++++++++++++++--------------- R/zzz.R | 2 - README.md | 6 ++-- build/vignette.rds |binary data/countries.rda |binary data/dem.rda |binary inst/doc/paleofire-paper.pdf |binary man/contrib.pfCompositeLF.Rd |only man/kdffreq.Rd | 28 +++++++++++++++------ man/paleofire-internal.Rd | 1 man/paleofire-package.Rd | 2 - man/pfAddData.Rd | 16 +++++++++++- man/pfCompositeLF.Rd | 2 - man/pfGridding.Rd | 1 man/plot.kdffreq.Rd | 9 ++++++- man/plot.pfCompositeLF.Rd | 2 - man/plot.pfGridding.Rd | 4 +-- man/plot.potveg.Rd | 4 ++- 29 files changed, 226 insertions(+), 110 deletions(-)
Title: An R Toolbox for Psychologists, Neuropsychologists and
Neuroscientists
Description: An R package containing free datasets as well as several statistical functions useful in psychology, neuropsychology and neuroscience.
Author: Dominique Makowski [aut, cre],
Phillip Alday [ctb]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between neuropsychology versions 0.1 dated 2016-09-21 and 0.2.4 dated 2016-10-03
neuropsychology-0.1/neuropsychology/tests/testthat/test-basics.R |only neuropsychology-0.2.4/neuropsychology/DESCRIPTION | 26 +- neuropsychology-0.2.4/neuropsychology/MD5 | 58 ++++-- neuropsychology-0.2.4/neuropsychology/NAMESPACE | 13 - neuropsychology-0.2.4/neuropsychology/R/APAze.R | 95 ++++++++-- neuropsychology-0.2.4/neuropsychology/R/Ncolours.R |only neuropsychology-0.2.4/neuropsychology/R/assess.R |only neuropsychology-0.2.4/neuropsychology/R/braincloud.R |only neuropsychology-0.2.4/neuropsychology/R/cortable.R | 62 ++++-- neuropsychology-0.2.4/neuropsychology/R/describe.R | 37 +-- neuropsychology-0.2.4/neuropsychology/R/extract_text.R |only neuropsychology-0.2.4/neuropsychology/R/format_p.R |only neuropsychology-0.2.4/neuropsychology/R/get_factors.R | 13 - neuropsychology-0.2.4/neuropsychology/R/get_numeric.R | 13 - neuropsychology-0.2.4/neuropsychology/README.md | 95 ++++++++-- neuropsychology-0.2.4/neuropsychology/data/masks.rda |only neuropsychology-0.2.4/neuropsychology/inst/CITATION | 6 neuropsychology-0.2.4/neuropsychology/man/APAze.Rd | 28 +- neuropsychology-0.2.4/neuropsychology/man/Ncolours.Rd |only neuropsychology-0.2.4/neuropsychology/man/assess.Rd |only neuropsychology-0.2.4/neuropsychology/man/braincloud.Rd |only neuropsychology-0.2.4/neuropsychology/man/cortable.Rd | 54 ++--- neuropsychology-0.2.4/neuropsychology/man/describe.Rd | 37 +++ neuropsychology-0.2.4/neuropsychology/man/extract_text.Rd |only neuropsychology-0.2.4/neuropsychology/man/format_p.Rd |only neuropsychology-0.2.4/neuropsychology/man/get_factors.Rd | 8 neuropsychology-0.2.4/neuropsychology/man/get_numeric.Rd | 10 - neuropsychology-0.2.4/neuropsychology/man/masks.Rd |only neuropsychology-0.2.4/neuropsychology/man/personality.Rd | 6 neuropsychology-0.2.4/neuropsychology/man/theme_neuropsychology.Rd | 20 -- neuropsychology-0.2.4/neuropsychology/tests/testthat/Lutz2008.pdf |only neuropsychology-0.2.4/neuropsychology/tests/testthat/Sperduti2016a.pdf |only neuropsychology-0.2.4/neuropsychology/tests/testthat/Sperduti2016b.pdf |only neuropsychology-0.2.4/neuropsychology/tests/testthat/assess_plot.png |only neuropsychology-0.2.4/neuropsychology/tests/testthat/assess_plot2.png |only neuropsychology-0.2.4/neuropsychology/tests/testthat/braincloud.png |only neuropsychology-0.2.4/neuropsychology/tests/testthat/cortable_plot.png |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-APAze.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-assess.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-cortable.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-describe.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-extract_text.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-textcloud.R |only 43 files changed, 386 insertions(+), 195 deletions(-)
More information about neuropsychology at CRAN
Permanent link
Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.5.3 dated 2016-08-01 and 0.5.4 dated 2016-10-03
DESCRIPTION | 8 - MD5 | 24 +-- R/patch_age.R | 12 + R/range_expansion.R | 8 - inst/doc/MetaLandSim.pdf |binary inst/doc/landscape_simulation.Rnw | 280 ++++++++++++++++++------------------- inst/doc/landscape_simulation.pdf |binary inst/doc/parametrization.pdf |binary inst/doc/range_expansion.pdf |binary man/MetaLandSim-package.Rd | 4 man/range_expansion.Rd | 1 man/range_raster.Rd | 10 - vignettes/landscape_simulation.Rnw | 280 ++++++++++++++++++------------------- 13 files changed, 316 insertions(+), 311 deletions(-)
More information about LabourMarketAreas at CRAN
Permanent link
Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyse data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>
Diff between strvalidator versions 1.7.0 dated 2016-07-05 and 1.8.0 dated 2016-10-03
strvalidator-1.7.0/strvalidator/R/calculateBalance.r |only strvalidator-1.7.0/strvalidator/R/calculateBalance_gui.r |only strvalidator-1.7.0/strvalidator/R/calculateHeterozygous.r |only strvalidator-1.7.0/strvalidator/R/calculateHeterozygous_gui.r |only strvalidator-1.7.0/strvalidator/man/calculateBalance.Rd |only strvalidator-1.7.0/strvalidator/man/calculateBalance_gui.Rd |only strvalidator-1.7.0/strvalidator/man/calculateHeterozygous.Rd |only strvalidator-1.7.0/strvalidator/man/calculateHeterozygous_gui.Rd |only strvalidator-1.7.0/strvalidator/tests/testthat/test-calculateBalance.r |only strvalidator-1.8.0/strvalidator/DESCRIPTION | 10 strvalidator-1.8.0/strvalidator/MD5 | 129 strvalidator-1.8.0/strvalidator/NAMESPACE | 13 strvalidator-1.8.0/strvalidator/NEWS | 98 strvalidator-1.8.0/strvalidator/R/addColor.r | 8 strvalidator-1.8.0/strvalidator/R/addData.r | 20 strvalidator-1.8.0/strvalidator/R/calculateAT6.r | 25 strvalidator-1.8.0/strvalidator/R/calculateConcordance.r | 53 strvalidator-1.8.0/strvalidator/R/calculateConcordance_gui.r | 41 strvalidator-1.8.0/strvalidator/R/calculateCopies.r |only strvalidator-1.8.0/strvalidator/R/calculateCopies_gui.r |only strvalidator-1.8.0/strvalidator/R/calculateDropout.r | 105 strvalidator-1.8.0/strvalidator/R/calculateDropout_gui.r | 48 strvalidator-1.8.0/strvalidator/R/calculateHb.r |only strvalidator-1.8.0/strvalidator/R/calculateHb_gui.r |only strvalidator-1.8.0/strvalidator/R/calculateHeight.r | 443 +-- strvalidator-1.8.0/strvalidator/R/calculateHeight_gui.r | 172 + strvalidator-1.8.0/strvalidator/R/calculateLb.r | 92 strvalidator-1.8.0/strvalidator/R/calculateLb_gui.r | 53 strvalidator-1.8.0/strvalidator/R/calculateMixture.r | 12 strvalidator-1.8.0/strvalidator/R/calculatePeaks.r | 207 - strvalidator-1.8.0/strvalidator/R/calculatePeaks_gui.r | 55 strvalidator-1.8.0/strvalidator/R/calculateResultType.r | 18 strvalidator-1.8.0/strvalidator/R/calculateResultType_gui.r | 20 strvalidator-1.8.0/strvalidator/R/calculateSlope.r | 2 strvalidator-1.8.0/strvalidator/R/calculateSlope_gui.r | 7 strvalidator-1.8.0/strvalidator/R/calculateSpike.r | 2 strvalidator-1.8.0/strvalidator/R/cropData_gui.r | 2 strvalidator-1.8.0/strvalidator/R/filterProfile.r | 806 +++-- strvalidator-1.8.0/strvalidator/R/filterProfile_gui.r | 129 strvalidator-1.8.0/strvalidator/R/getKit.r | 2 strvalidator-1.8.0/strvalidator/R/globals.R | 7 strvalidator-1.8.0/strvalidator/R/maskAT.r | 13 strvalidator-1.8.0/strvalidator/R/plotContamination_gui.r |only strvalidator-1.8.0/strvalidator/R/plotDistribution_gui.r | 3 strvalidator-1.8.0/strvalidator/R/plotStutter_gui.r | 2 strvalidator-1.8.0/strvalidator/R/strvalidator-package.r | 65 strvalidator-1.8.0/strvalidator/R/strvalidator.r | 44 strvalidator-1.8.0/strvalidator/R/tableBalance.r | 192 - strvalidator-1.8.0/strvalidator/R/tableBalance_gui.r | 26 strvalidator-1.8.0/strvalidator/data/ref61.RData |only strvalidator-1.8.0/strvalidator/data/ref62.RData |only strvalidator-1.8.0/strvalidator/data/ref7.RData |only strvalidator-1.8.0/strvalidator/data/set6.RData |only strvalidator-1.8.0/strvalidator/data/set7.RData |only strvalidator-1.8.0/strvalidator/inst/CITATION |only strvalidator-1.8.0/strvalidator/inst/extdata/set3.txt | 1362 +++++----- strvalidator-1.8.0/strvalidator/man/calculateConcordance.Rd | 5 strvalidator-1.8.0/strvalidator/man/calculateCopies.Rd |only strvalidator-1.8.0/strvalidator/man/calculateCopies_gui.Rd |only strvalidator-1.8.0/strvalidator/man/calculateHb.Rd |only strvalidator-1.8.0/strvalidator/man/calculateHb_gui.Rd |only strvalidator-1.8.0/strvalidator/man/calculateHeight.Rd | 34 strvalidator-1.8.0/strvalidator/man/calculateLb.Rd | 2 strvalidator-1.8.0/strvalidator/man/calculatePeaks.Rd | 30 strvalidator-1.8.0/strvalidator/man/calculateSlope.Rd | 2 strvalidator-1.8.0/strvalidator/man/calculateSpike.Rd | 2 strvalidator-1.8.0/strvalidator/man/filterProfile.Rd | 21 strvalidator-1.8.0/strvalidator/man/getKit.Rd | 2 strvalidator-1.8.0/strvalidator/man/plotContamination_gui.Rd |only strvalidator-1.8.0/strvalidator/man/ref61.Rd |only strvalidator-1.8.0/strvalidator/man/ref62.Rd |only strvalidator-1.8.0/strvalidator/man/ref7.Rd |only strvalidator-1.8.0/strvalidator/man/set6.Rd |only strvalidator-1.8.0/strvalidator/man/set7.Rd |only strvalidator-1.8.0/strvalidator/man/tableBalance.Rd | 15 strvalidator-1.8.0/strvalidator/tests/testthat/test-calculateConcordance.r | 187 + strvalidator-1.8.0/strvalidator/tests/testthat/test-calculateHb.r |only strvalidator-1.8.0/strvalidator/tests/testthat/test-calculateHeight.r | 409 ++- strvalidator-1.8.0/strvalidator/tests/testthat/test-calculateLb.r | 43 strvalidator-1.8.0/strvalidator/tests/testthat/test-filterProfile.r | 370 ++ strvalidator-1.8.0/strvalidator/tests/testthat/test-tableBalance.r | 339 +- 81 files changed, 3579 insertions(+), 2168 deletions(-)
Title: Tools to Support the Sheffield Elicitation Framework
Description: Implements various methods for eliciting a probability distribution
for a single parameter from an expert or a group of experts. The expert
provides a small number of probability judgements, corresponding
to points on his or her cumulative distribution function. A range of parametric
distributions can then be fitted and displayed, with feedback provided in the
form of fitted probabilities and percentiles. A graphical interface for the roulette elicitation
method is also provided. For multiple experts, a weighted linear pool can be
calculated. Also includes functions for eliciting beliefs about population distributions.
Author: Jeremy Oakley
Maintainer: Jeremy Oakley <j.oakley@sheffield.ac.uk>
Diff between SHELF versions 1.2.0 dated 2016-08-17 and 1.2.1 dated 2016-10-03
SHELF-1.2.0/SHELF/R/SHELF1.2.0-package.R |only SHELF-1.2.0/SHELF/inst/doc/Bivariate-copula.R |only SHELF-1.2.0/SHELF/inst/doc/Bivariate-copula.Rmd |only SHELF-1.2.0/SHELF/inst/doc/Bivariate-copula.pdf |only SHELF-1.2.1/SHELF/DESCRIPTION | 10 - SHELF-1.2.1/SHELF/MD5 | 39 ++-- SHELF-1.2.1/SHELF/R/SHELF-package.R |only SHELF-1.2.1/SHELF/R/elicit.R | 5 SHELF-1.2.1/SHELF/R/expertdensity.R | 3 SHELF-1.2.1/SHELF/R/fitdist.R | 12 + SHELF-1.2.1/SHELF/R/makeLinearPoolPlot.R | 4 SHELF-1.2.1/SHELF/R/plotfit.R | 6 SHELF-1.2.1/SHELF/R/shinyplotgroup.R | 11 - SHELF-1.2.1/SHELF/R/shinyplotsingle.R | 4 SHELF-1.2.1/SHELF/inst/NEWS.md | 21 ++ SHELF-1.2.1/SHELF/inst/doc/Dirichlet-elicitation.pdf |binary SHELF-1.2.1/SHELF/inst/doc/Multivariate-normal-copula.pdf |binary SHELF-1.2.1/SHELF/inst/doc/SHELF-overview.Rmd | 4 SHELF-1.2.1/SHELF/inst/doc/SHELF-overview.pdf |binary SHELF-1.2.1/SHELF/man/SHELF-package.Rd | 10 - SHELF-1.2.1/SHELF/man/fitdist.Rd | 4 SHELF-1.2.1/SHELF/tests/testthat/test-fitting.R | 111 +++++++++++++- SHELF-1.2.1/SHELF/vignettes/SHELF-overview.Rmd | 4 23 files changed, 188 insertions(+), 60 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College Scorecard data
using the public API. It is based on the dplyr model of
piped commands to select and filter data in a single chained function call.
An API key from the U.S. Department of Education is required.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <b.skinner@vanderbilt.edu>
Diff between rscorecard versions 0.2.5 dated 2016-05-18 and 0.2.8 dated 2016-10-03
DESCRIPTION | 6 - MD5 | 18 +-- R/get.R | 4 R/rscorecard.R | 2 build/vignette.rds |binary inst/doc/introduction.R | 37 ++++++ inst/doc/introduction.Rmd | 9 + inst/doc/introduction.html | 250 +++++++++++++++++++++++++++++++-------------- man/rscorecard.Rd | 2 vignettes/introduction.Rmd | 9 + 10 files changed, 240 insertions(+), 97 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed. Provides summary and visualization functions for 'randomForest'
results.
Author: Eric Archer [aut, cre]
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between rfPermute versions 2.1.1 dated 2016-08-04 and 2.1.5 dated 2016-10-03
rfPermute-2.1.1/rfPermute/R/clean.rf.data.R |only rfPermute-2.1.1/rfPermute/R/exptd.err.rate.R |only rfPermute-2.1.1/rfPermute/R/plot.rfPermute.R |only rfPermute-2.1.1/rfPermute/R/proximity.plot.R |only rfPermute-2.1.1/rfPermute/R/rfpNews.R |only rfPermute-2.1.1/rfPermute/man/clean.rf.data.Rd |only rfPermute-2.1.1/rfPermute/man/exptd.err.rate.Rd |only rfPermute-2.1.1/rfPermute/man/plot.rfPermute.Rd |only rfPermute-2.1.1/rfPermute/man/proximity.plot.Rd |only rfPermute-2.1.1/rfPermute/man/rfpNews.Rd |only rfPermute-2.1.5/rfPermute/DESCRIPTION | 9 +- rfPermute-2.1.5/rfPermute/MD5 | 51 +++++++------- rfPermute-2.1.5/rfPermute/NAMESPACE | 22 ++---- rfPermute-2.1.5/rfPermute/R/classConfInt.R | 4 - rfPermute-2.1.5/rfPermute/R/cleanRFdata.R |only rfPermute-2.1.5/rfPermute/R/confusionMatrix.R | 4 - rfPermute-2.1.5/rfPermute/R/dataSets.R |only rfPermute-2.1.5/rfPermute/R/exptdErrRate.R |only rfPermute-2.1.5/rfPermute/R/plot.rp.importance.R | 2 rfPermute-2.1.5/rfPermute/R/plotNull.R |only rfPermute-2.1.5/rfPermute/R/plotVotes.R | 36 ++-------- rfPermute-2.1.5/rfPermute/R/proximityPlot.R |only rfPermute-2.1.5/rfPermute/R/rfPermute.R | 8 +- rfPermute-2.1.5/rfPermute/R/rp.combine.R | 7 +- rfPermute-2.1.5/rfPermute/README.md | 69 ++++++++++++++------ rfPermute-2.1.5/rfPermute/data |only rfPermute-2.1.5/rfPermute/man/classConfInt.Rd | 4 - rfPermute-2.1.5/rfPermute/man/cleanRFdata.Rd |only rfPermute-2.1.5/rfPermute/man/confusionMatrix.Rd | 2 rfPermute-2.1.5/rfPermute/man/exptdErrRate.Rd |only rfPermute-2.1.5/rfPermute/man/plot.rp.importance.Rd | 2 rfPermute-2.1.5/rfPermute/man/plotNull.Rd |only rfPermute-2.1.5/rfPermute/man/plotVotes.Rd | 9 ++ rfPermute-2.1.5/rfPermute/man/proximityPlot.Rd |only rfPermute-2.1.5/rfPermute/man/rfPermute.Rd | 8 +- rfPermute-2.1.5/rfPermute/man/rp.combine.Rd | 5 + rfPermute-2.1.5/rfPermute/man/symb.metab.Rd |only 37 files changed, 130 insertions(+), 112 deletions(-)
Title: Integrate R with 'RDocumentation.org'
Description: Wraps around the default help functionality in R. Instead of plain documentation files, documentation will now show up as it does on 'RDocumentation.org', a platform that shows R documentation from CRAN, GitHub and Bioconductor, together with informative stats to assess the package quality and possibilities to discuss packages.
Author: Jonathan Cornelissen <jonathan@datacamp.com>
Maintainer: Ludovic Vannoorenberghe <ludovic@datacamp.com>
Diff between RDocumentation versions 0.6 dated 2016-09-28 and 0.7.0 dated 2016-10-03
RDocumentation-0.6/RDocumentation/man/makeDefault.Rd |only RDocumentation-0.6/RDocumentation/tests/testthat/test-RProfile.R |only RDocumentation-0.6/RDocumentation/tests/testthat/test-help-search.R |only RDocumentation-0.7.0/RDocumentation/DESCRIPTION | 6 - RDocumentation-0.7.0/RDocumentation/MD5 | 24 ++-- RDocumentation-0.7.0/RDocumentation/NAMESPACE | 4 RDocumentation-0.7.0/RDocumentation/NEWS.md |only RDocumentation-0.7.0/RDocumentation/R/defaults.R |only RDocumentation-0.7.0/RDocumentation/R/overrides.R | 51 +++++----- RDocumentation-0.7.0/RDocumentation/R/utils.R | 13 -- RDocumentation-0.7.0/RDocumentation/R/view_help.R | 5 RDocumentation-0.7.0/RDocumentation/R/zzz.R | 20 ++- RDocumentation-0.7.0/RDocumentation/README.md | 1 RDocumentation-0.7.0/RDocumentation/man/defaults.Rd |only RDocumentation-0.7.0/RDocumentation/tests/testthat/test-defaults.R |only RDocumentation-0.7.0/RDocumentation/tests/testthat/test-help.R | 26 +++-- RDocumentation-0.7.0/RDocumentation/tests/testthat/test-r-profile.R |only 17 files changed, 83 insertions(+), 67 deletions(-)
More information about RDocumentation at CRAN
Permanent link
Title: Occurrence Filtering, Geographic and Taxonomic Standardization
and Generation of Species Range Polygons
Description: Provides tools for filtering occurrence records, generating alpha-hull-derived range polygons and mapping species richness.
Author: Pascal Title
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between rangeBuilder versions 1.2 dated 2016-04-14 and 1.3 dated 2016-10-03
ChangeLog | 13 +++- DESCRIPTION | 11 +-- MD5 | 43 +++++++------ NAMESPACE | 1 R/coordError.R | 140 ++++++++++++++++++++++++++------------------ R/downloadDates.R |only R/getDynamicAlphaHull.R | 12 +-- R/getExtentOfList.R | 9 ++ R/nonSquamates.R | 32 +++++----- R/repDBfunctions.R | 12 +++ R/richnessRaster.R | 11 +-- R/standardizeCountry.R | 77 +++++++++++++++++++----- R/synonymMatch.R | 2 R/sysdata.rda |binary inst |only man/acceptedAndSynonyms.Rd | 8 +- man/downloadDates.Rd |only man/getDynamicAlphaHull.Rd | 16 +++-- man/getExtentOfList.Rd | 2 man/queryGISD.Rd | 7 +- man/rangeBuilder-package.Rd | 8 +- man/richnessRaster.Rd | 20 ++++-- man/standardizeCountry.Rd | 14 +++- man/synonymMatch.Rd | 8 +- 24 files changed, 294 insertions(+), 152 deletions(-)
Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic
matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot
<tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>,
Fernando Cagua <fernando@cagua.co>
Maintainer: Matthew Hutchinson <matthewhutchinson15@gmail.com>
Diff between paco versions 0.2.3 dated 2015-11-10 and 0.3.0 dated 2016-10-03
paco-0.2.3/paco/R/residuals.paco.r |only paco-0.2.3/paco/man/coordpcoa.Rd |only paco-0.2.3/paco/man/residuals.paco.Rd |only paco-0.3.0/paco/DESCRIPTION | 13 +++-- paco-0.3.0/paco/MD5 | 37 +++++++-------- paco-0.3.0/paco/NAMESPACE | 2 paco-0.3.0/paco/R/PACo.r | 72 ++++++++++++++++++++++--------- paco-0.3.0/paco/R/add_pcoord.r | 13 +++-- paco-0.3.0/paco/R/coordpcoa.r | 10 ++-- paco-0.3.0/paco/R/paco_data.r | 8 +++ paco-0.3.0/paco/R/paco_links.r | 48 +++++++++++++++----- paco-0.3.0/paco/R/prepare_data.r | 13 +++-- paco-0.3.0/paco/R/residuals_paco.r |only paco-0.3.0/paco/README.md | 2 paco-0.3.0/paco/man/PACo.Rd | 28 +++++++----- paco-0.3.0/paco/man/add_pcoord.Rd | 12 ++--- paco-0.3.0/paco/man/gl_links.Rd | 4 - paco-0.3.0/paco/man/gophertree.Rd | 2 paco-0.3.0/paco/man/licetree.Rd | 2 paco-0.3.0/paco/man/paco_links.Rd | 22 +++++++-- paco-0.3.0/paco/man/prepare_paco_data.Rd | 14 ++---- paco-0.3.0/paco/man/residuals_paco.Rd |only 22 files changed, 196 insertions(+), 106 deletions(-)
Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers
<dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David
Miller <dave@ninepointeightone.net> and Jon Bishop
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between mrds versions 2.1.16 dated 2016-08-10 and 2.1.17 dated 2016-10-03
DESCRIPTION | 7 MD5 | 44 +-- NEWS | 7 R/create.ddfobj.R | 3 R/ddf.R | 596 ++++++++++++++++++++++++------------------------- R/gof.ds.R | 14 - R/gof.io.R | 180 ++++++++------ R/gof.io.fi.R | 14 - R/gof.trial.R | 175 +++++++------- R/integratepdf.r | 11 R/keyfct.hn.R | 26 +- R/keyfct.hz.R | 24 - R/plot.ds.R | 4 R/predict.ds.R | 2 R/predict.io.fi.R | 4 R/sethazard.R | 38 +-- R/setinitial.ds.R | 11 README.md | 82 +++--- data/book.tee.data.rda |binary man/ddf.Rd | 4 man/integratepdf.Rd | 10 man/plot.ds.Rd | 4 man/setinitial.ds.Rd | 8 23 files changed, 659 insertions(+), 609 deletions(-)
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.8 dated 2016-06-28 and 0.9 dated 2016-10-03
DESCRIPTION | 8 - MD5 | 56 +++++---- NAMESPACE | 10 + NEWS | 40 ++++++ R/arx.R | 14 +- R/gets-internal.R | 147 +++---------------------- R/getsm.R | 14 ++ R/getsv.R | 10 + R/iim.R | 2 R/isat.R | 84 +++++++++++--- R/isattest.R | 28 ++-- R/isatvar.R | 252 +++++++++++++++++++++++++++++-------------- R/isvarcor.R |only R/isvareffcor.R |only R/predict.arx.R | 304 ++++++++++++++++++++++++++++++++++++++++++---------- R/predict.gets.R |only R/predict.isat.R |only R/print.arx.R | 14 +- R/print.gets.R | 25 ++-- R/print.isat.R | 26 ++-- R/sim.R | 4 R/tim.R | 2 man/coef.arx.Rd | 297 ++++++++++++++++++++++++++------------------------ man/coef.gets.Rd | 261 ++++++++++++++++++++++++-------------------- man/coef.isat.Rd | 223 +++++++++++++++++++++----------------- man/gets-package.Rd | 4 man/getsm.Rd | 4 man/isat.Rd | 4 man/isattest.Rd | 12 +- man/isatvar.Rd | 15 +- man/isvarcor.Rd |only man/isvareffcor.Rd |only 32 files changed, 1114 insertions(+), 746 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; the Daymet gridded estimates of daily weather parameters
for North America, version 3, available from the Oak Ridge National Laboratory's
Distributed Active Archive Center (DAAC); and the International Tree Ring Data Bank.
Additional data sources are in the works, global soils (HWSD),
MODIS satellite data products, the National Atlas (US), Natural Earth, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.2.0 dated 2016-09-26 and 2.3.0 dated 2016-10-03
DESCRIPTION | 22 +++++++----- MD5 | 50 ++++++++++++++++------------- NAMESPACE | 34 +++++++++++++++++-- R/DAYMET_FUNCTIONS.R |only R/GHCN_FUNCTIONS.R | 72 +++++++++++++++++++++++++----------------- R/ITRDB_FUNCTIONS.R | 32 +++++++++--------- R/NED_FUNCTIONS.R | 21 +++++------- R/NHD_FUNCTIONS.R | 25 ++++++-------- R/SSURGO_FUNCTIONS.R | 32 +++++++++--------- R/UTILITY_FUNCTIONS.R | 5 +- README.md | 67 +++++++++++++++++++++------------------ data |only inst/CITATION | 4 +- inst/FedDataTester.R | 66 ++++++++++++++++++++++---------------- inst/img/DAYMET.png |only inst/img/NED.png |binary man/FedData-package.Rd | 15 +++++++- man/download_daymet_tile.Rd |only man/get_daymet.Rd |only man/get_daymet_tile.Rd |only man/get_ghcn_daily.Rd | 5 +- man/get_ghcn_daily_station.Rd | 6 ++- man/get_itrdb.Rd | 3 + man/get_ned.Rd | 4 +- man/get_nhd.Rd | 3 + man/get_ssurgo.Rd | 3 + man/tiles.Rd |only tests/testthat/test.DAYMET.R |only tests/testthat/test.NED.R | 8 ++-- tests/testthat/test.NHD.R | 6 +-- 30 files changed, 281 insertions(+), 202 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 2.2.1 dated 2016-09-04 and 2.3.0 dated 2016-10-03
dtwclust-2.2.1/dtwclust/R/all_cent.R |only dtwclust-2.2.1/dtwclust/inst/doc/dtwclust.R |only dtwclust-2.2.1/dtwclust/src/update_lcm.c |only dtwclust-2.2.1/dtwclust/tests/testthat/test_distances.R |only dtwclust-2.2.1/dtwclust/tests/testthat/test_pairwise.R |only dtwclust-2.2.1/dtwclust/tests/testthat/test_repetitions.R |only dtwclust-2.2.1/dtwclust/tests/testthat/test_tadpole.R |only dtwclust-2.3.0/dtwclust/DESCRIPTION | 23 dtwclust-2.3.0/dtwclust/MD5 | 125 dtwclust-2.3.0/dtwclust/NAMESPACE | 6 dtwclust-2.3.0/dtwclust/R/DBA.R | 460 +- dtwclust-2.3.0/dtwclust/R/NCCc.R | 10 dtwclust-2.3.0/dtwclust/R/SBD.R | 435 +- dtwclust-2.3.0/dtwclust/R/TADPole.R | 643 +-- dtwclust-2.3.0/dtwclust/R/all-cent.R |only dtwclust-2.3.0/dtwclust/R/ddist.R | 378 +- dtwclust-2.3.0/dtwclust/R/dtw-basic.R |only dtwclust-2.3.0/dtwclust/R/dtw-lb.R | 69 dtwclust-2.3.0/dtwclust/R/dtw2.R | 54 dtwclust-2.3.0/dtwclust/R/dtwclust-classes.R | 13 dtwclust-2.3.0/dtwclust/R/dtwclust-methods.R | 1587 ++++----- dtwclust-2.3.0/dtwclust/R/dtwclust.R | 1761 ++++------ dtwclust-2.3.0/dtwclust/R/fuzzy.R | 42 dtwclust-2.3.0/dtwclust/R/lb-improved.R | 18 dtwclust-2.3.0/dtwclust/R/lb-keogh.R | 18 dtwclust-2.3.0/dtwclust/R/partitional.R | 41 dtwclust-2.3.0/dtwclust/R/pkg.R | 91 dtwclust-2.3.0/dtwclust/R/reinterpolate.R | 33 dtwclust-2.3.0/dtwclust/R/shape-extraction.R | 294 - dtwclust-2.3.0/dtwclust/R/utils.R | 148 dtwclust-2.3.0/dtwclust/R/zscore.R | 115 dtwclust-2.3.0/dtwclust/README.md | 53 dtwclust-2.3.0/dtwclust/build/vignette.rds |binary dtwclust-2.3.0/dtwclust/inst/NEWS.Rd | 17 dtwclust-2.3.0/dtwclust/inst/doc/dtwclust.Rnw | 116 dtwclust-2.3.0/dtwclust/inst/doc/dtwclust.pdf |binary dtwclust-2.3.0/dtwclust/inst/dtwclust-examples.R | 10 dtwclust-2.3.0/dtwclust/man/DBA.Rd | 25 dtwclust-2.3.0/dtwclust/man/TADPole.Rd | 16 dtwclust-2.3.0/dtwclust/man/dtw2.Rd |only dtwclust-2.3.0/dtwclust/man/dtw_basic.Rd |only dtwclust-2.3.0/dtwclust/man/dtw_lb.Rd | 9 dtwclust-2.3.0/dtwclust/man/dtwclust-class.Rd | 7 dtwclust-2.3.0/dtwclust/man/dtwclust-methods.Rd | 10 dtwclust-2.3.0/dtwclust/man/dtwclust-package.Rd | 51 dtwclust-2.3.0/dtwclust/man/dtwclust.Rd | 66 dtwclust-2.3.0/dtwclust/man/dtwclustControl-class.Rd | 2 dtwclust-2.3.0/dtwclust/man/dtwclustFamily-class.Rd | 2 dtwclust-2.3.0/dtwclust/man/lb_improved.Rd | 4 dtwclust-2.3.0/dtwclust/man/lb_keogh.Rd | 4 dtwclust-2.3.0/dtwclust/man/reinterpolate.Rd | 12 dtwclust-2.3.0/dtwclust/man/shape_extraction.Rd | 8 dtwclust-2.3.0/dtwclust/man/zscore.Rd | 12 dtwclust-2.3.0/dtwclust/src/dtw-basic.c |only dtwclust-2.3.0/dtwclust/src/update-lcm.c |only dtwclust-2.3.0/dtwclust/tests/testthat.R | 14 dtwclust-2.3.0/dtwclust/tests/testthat/helper_all.R | 32 dtwclust-2.3.0/dtwclust/tests/testthat/test_all_distances.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_centroids.R | 468 +- dtwclust-2.3.0/dtwclust/tests/testthat/test_custom_distance.R | 107 dtwclust-2.3.0/dtwclust/tests/testthat/test_cvis.R | 54 dtwclust-2.3.0/dtwclust/tests/testthat/test_dtw_basic.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_fuzzy.R | 97 dtwclust-2.3.0/dtwclust/tests/testthat/test_hierarchical.R | 82 dtwclust-2.3.0/dtwclust/tests/testthat/test_lbs.R | 158 dtwclust-2.3.0/dtwclust/tests/testthat/test_methods.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_partitional.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_types.R | 103 dtwclust-2.3.0/dtwclust/tests/testthat/test_zparallel.R | 26 dtwclust-2.3.0/dtwclust/vignettes/REFERENCES.bib | 73 dtwclust-2.3.0/dtwclust/vignettes/dtwclust-concordance.tex | 4 dtwclust-2.3.0/dtwclust/vignettes/dtwclust.Rnw | 116 72 files changed, 4241 insertions(+), 3881 deletions(-)
Title: Density Surface Modelling of Distance Sampling Data
Description: Density surface modelling of line transect data. A Generalized
Additive Model-based approach is used to calculate spatially-explicit estimates
of animal abundance from distance sampling (also presence/absence and strip
transect) data. Several utility functions are provided for model checking,
plotting and variance estimation.
Author: David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington,
Sharon Hedley.
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between dsm versions 2.2.12 dated 2016-08-11 and 2.2.13 dated 2016-10-03
DESCRIPTION | 9 +++++---- MD5 | 20 ++++++++++---------- NEWS | 4 ++++ R/dsm.R | 38 ++++++++++++++------------------------ R/dsm.var.gam.R | 29 +++++++++++++++++++++++++++-- R/dsm.var.prop.R | 9 +++++++-- R/print.summary.dsm.var.R | 7 +++++-- R/summary.dsm.var.R | 5 ++++- R/zzz.R | 32 +++++++++++++++++++++++--------- man/dsm.Rd | 2 +- man/dsm.var.gam.Rd | 28 +++++++++++++++++++++++++++- 11 files changed, 127 insertions(+), 56 deletions(-)
Title: Distributed-Lag Structural Equation Modelling with Second-Order
Polynomial Lag Shapes
Description: Estimation and path analysis functionalities for structural equation models with second-order polynomial lag shapes.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>
Diff between dlsem versions 1.3.2 dated 2016-09-16 and 1.4 dated 2016-10-03
dlsem-1.3.2/dlsem/vignettes/figures/dagsam.png |only dlsem-1.3.2/dlsem/vignettes/figures/polylag.png |only dlsem-1.4/dlsem/DESCRIPTION | 9 dlsem-1.4/dlsem/MD5 | 37 +- dlsem-1.4/dlsem/NAMESPACE | 1 dlsem-1.4/dlsem/build/vignette.rds |binary dlsem-1.4/dlsem/inst/doc/dlsem_tutorial.R | 24 - dlsem-1.4/dlsem/inst/doc/dlsem_tutorial.Rnw | 372 ++++++------------------ dlsem-1.4/dlsem/inst/doc/dlsem_tutorial.pdf |binary dlsem-1.4/dlsem/man/EM.imputation.Rd | 2 dlsem-1.4/dlsem/man/applyDiff.Rd | 2 dlsem-1.4/dlsem/man/dlsem-package.Rd | 6 dlsem-1.4/dlsem/man/dlsem.Rd | 3 dlsem-1.4/dlsem/man/edgeCoeff.Rd | 2 dlsem-1.4/dlsem/man/fitIndices.Rd | 2 dlsem-1.4/dlsem/man/isIndep.Rd | 2 dlsem-1.4/dlsem/man/lagPlot.Rd | 2 dlsem-1.4/dlsem/man/pathAnal.Rd | 2 dlsem-1.4/dlsem/man/unirootTest.Rd | 2 dlsem-1.4/dlsem/vignettes/dlsem_tutorial.Rnw | 372 ++++++------------------ dlsem-1.4/dlsem/vignettes/figures/sampledag.png |only 21 files changed, 261 insertions(+), 579 deletions(-)
Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Description: Scrapes various data from the Bureau of Labor Statistics, which is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>
Diff between blscrapeR versions 0.4.2 dated 2016-07-29 and 1.0.1 dated 2016-10-03
DESCRIPTION | 6 +- MD5 | 64 +++++++++++++++++++----------- NAMESPACE | 1 NEWS.md | 26 ++++++++++++ R/area_titles.R |only R/get_bls_county.R | 4 - R/maps.R | 2 R/niacs.R |only R/qcew_api.R |only R/size_titles.R |only README.md | 2 build/vignette.rds |binary data/area_titles.rda |only data/niacs.rda |only data/size_titles.rda |only inst/doc/Employment_and_Unemployment.html | 4 - inst/doc/Inflation_and_Prices.Rmd | 2 inst/doc/Inflation_and_Prices.html | 8 +-- inst/doc/Mapping_BLS_Data.R | 2 inst/doc/Mapping_BLS_Data.Rmd | 2 inst/doc/Mapping_BLS_Data.html | 6 +- inst/doc/Pay_and_Benefits.R | 2 inst/doc/Pay_and_Benefits.Rmd | 2 inst/doc/Pay_and_Benefits.html | 6 +- inst/doc/QCEW_API.R |only inst/doc/QCEW_API.Rmd |only inst/doc/QCEW_API.html |only inst/doc/qcew.R |only inst/doc/qcew.Rmd |only inst/doc/qcew.html |only man/area_titles.Rd |only man/bls_map_county.Rd | 2 man/bls_map_state.Rd | 2 man/niacs.Rd |only man/qcew_api.Rd |only man/size_titles.Rd |only tests/testthat/test_bls_csv.R | 2 tests/testthat/test_qcew_api.R |only vignettes/Inflation_and_Prices.Rmd | 2 vignettes/Mapping_BLS_Data.Rmd | 2 vignettes/Pay_and_Benefits.Rmd | 2 vignettes/QCEW_API.Rmd |only vignettes/qcew.Rmd |only 43 files changed, 96 insertions(+), 55 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex
macroevolutionary dynamics on phylogenetic trees. It is a companion
package to the command line program BAMM (Bayesian Analysis of
Macroevolutionary Mixtures) and is entirely oriented towards the analysis,
interpretation, and visualization of evolutionary rates. Functionality
includes visualization of rate shifts on phylogenies, estimating
evolutionary rates through time, comparing posterior distributions of
evolutionary rates across clades, comparing diversification models using
Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi,
Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.1.4 dated 2016-06-13 and 2.1.5 dated 2016-10-03
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NAMESPACE | 2 ++ R/BAMMtools-package.R | 1 + R/getJenksBreaks.R | 9 +++++---- R/stepBF.R |only R/traitDependentBAMM.R | 28 ++++++++++++++++++---------- man/getJenksBreaks.Rd | 9 +++++---- man/stepBF.Rd |only man/traitDependentBAMM.Rd | 11 ++++++----- 10 files changed, 50 insertions(+), 34 deletions(-)
Title: Sparse Principal Component Regression
Description: The sparse principal component regression is computed. The regularization parameters are optimized by cross-validation.
Author: Shuichi Kawano
Maintainer: Shuichi Kawano <skawano@uec.ac.jp>
Diff between spcr versions 1.2.1 dated 2014-12-04 and 2.0 dated 2016-10-03
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++++++------ NAMESPACE | 8 ++++---- R/SPCRLoG.R |only R/SPCRMultiLoG.R |only R/SPCRPoi.R |only R/cv.spcr.R | 6 +++--- R/cv.spcrglm.R |only R/softthresh.R |only R/spcrglm.R |only man/cv.spcr.Rd | 14 +++++++------- man/cv.spcrglm.Rd |only man/spcr.Rd | 12 ++++++------ man/spcrglm.Rd |only src/SPCR.c | 2 +- 15 files changed, 42 insertions(+), 34 deletions(-)
Title: Simulation of the Forensic DNA Process
Description: Simulate the forensic DNA process: generate random or fixed DNA
profiles, create forensic samples including mixtures of diploid and haploid
cells, simulate DNA extraction, normalization, degradation, amplification
including stutters and inter-locus balance, and capillary electrophoresis.
DNA profiles are visualized as electropherograms and saved in tables.
The command pcrsim() opens up a graphical user interface which allow the user
to create projects, to enter, load, and save parameters required for the simulation.
The simulation is transparent and the parameters used in each step of the simulation
can be viewed in the result tables.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>
Diff between pcrsim versions 1.0.0 dated 2016-04-21 and 1.0.1 dated 2016-10-03
DESCRIPTION | 8 +- MD5 | 17 +++--- NEWS | 8 ++ R/calibratePCRsim.r | 65 +++++++---------------- R/calibrateScaling.r | 39 +++++++++---- R/getParameter.r | 6 +- R/pcrsim.r | 38 +++++++++---- README.md |only inst/extdata/tutorial_pcrsim_project.RData |binary inst/extdata/tutorial_strvalidator_project.RData |binary 10 files changed, 102 insertions(+), 79 deletions(-)
Title: Pre-Process of Time Series Data Set in R
Description: Pre-process for discrete time series data set which is not continuous at the column
of 'date'. Refilling records of missing 'date' and other columns to the hollow data set so that
final data set is able to be dealt with time series analysis.
Author: Will Kuan <aiien61will@gmail.com>
Maintainer: Will Kuan <aiien61will@gmail.com>
Diff between tigerhitteR versions 1.0.2 dated 2016-07-07 and 1.1.0 dated 2016-10-03
tigerhitteR-1.0.2/tigerhitteR/man/dateRefill.fromsFile.Rd |only tigerhitteR-1.1.0/tigerhitteR/DESCRIPTION | 11 tigerhitteR-1.1.0/tigerhitteR/MD5 | 10 tigerhitteR-1.1.0/tigerhitteR/NAMESPACE | 20 tigerhitteR-1.1.0/tigerhitteR/R/tigerhitteR.R | 443 ++++------ tigerhitteR-1.1.0/tigerhitteR/man/dateRefill.fromData.Rd | 13 tigerhitteR-1.1.0/tigerhitteR/man/dateRefill.fromFileToExcel.Rd |only 7 files changed, 250 insertions(+), 247 deletions(-)
Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods 'kernlab'
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut]
Maintainer: Alexandros Karatzoglou <alexandros.karatzoglou@gmail.com>
Diff between kernlab versions 0.9-24 dated 2016-03-29 and 0.9-25 dated 2016-10-03
DESCRIPTION | 10 - MD5 | 14 +- inst/doc/kernlab.pdf |binary src/esa.cpp | 322 +++++++++++++++++++++++++-------------------------- src/msufsort.cpp | 2 src/msufsort.h | 2 src/stringkernel.cpp | 38 +++--- src/stringkernel.h | 8 - 8 files changed, 199 insertions(+), 197 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with both continuous and discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.27 dated 2016-04-22 and 2.28 dated 2016-10-03
BDgraph-2.27/BDgraph/src/gcgm_DMH_bd.cpp |only BDgraph-2.27/BDgraph/src/gcgm_DMH_bd_multi_update.cpp |only BDgraph-2.27/BDgraph/src/gcgm_DMH_rj.cpp |only BDgraph-2.27/BDgraph/src/ggm_DMH_bd.cpp |only BDgraph-2.27/BDgraph/src/ggm_DMH_bd_multi_update.cpp |only BDgraph-2.27/BDgraph/src/ggm_DMH_rj.cpp |only BDgraph-2.28/BDgraph/DESCRIPTION | 11 - BDgraph-2.28/BDgraph/MD5 | 97 +++++++------ BDgraph-2.28/BDgraph/NAMESPACE | 15 +- BDgraph-2.28/BDgraph/NEWS | 18 +- BDgraph-2.28/BDgraph/R/bdgraph.R | 56 +++---- BDgraph-2.28/BDgraph/R/bdgraph.sim.R | 50 +++--- BDgraph-2.28/BDgraph/R/bdgraph.ts.R |only BDgraph-2.28/BDgraph/R/rcwish.R |only BDgraph-2.28/BDgraph/R/rgcwish.R |only BDgraph-2.28/BDgraph/R/rgwish.R | 21 +- BDgraph-2.28/BDgraph/man/BDgraph-package.Rd | 2 BDgraph-2.28/BDgraph/man/bdgraph.Rd | 9 - BDgraph-2.28/BDgraph/man/bdgraph.npn.Rd | 6 BDgraph-2.28/BDgraph/man/bdgraph.sim.Rd | 8 - BDgraph-2.28/BDgraph/man/bdgraph.ts.Rd |only BDgraph-2.28/BDgraph/man/compare.Rd | 5 BDgraph-2.28/BDgraph/man/geneExpression.Rd | 4 BDgraph-2.28/BDgraph/man/pgraph.Rd | 2 BDgraph-2.28/BDgraph/man/plinks.Rd | 4 BDgraph-2.28/BDgraph/man/plot.bdgraph.Rd | 4 BDgraph-2.28/BDgraph/man/plot.sim.Rd | 3 BDgraph-2.28/BDgraph/man/plotcoda.Rd | 4 BDgraph-2.28/BDgraph/man/plotroc.Rd | 8 - BDgraph-2.28/BDgraph/man/print.bdgraph.Rd | 4 BDgraph-2.28/BDgraph/man/rcwish.Rd |only BDgraph-2.28/BDgraph/man/rgcwish.Rd |only BDgraph-2.28/BDgraph/man/rgwish.Rd | 4 BDgraph-2.28/BDgraph/man/rwish.Rd | 4 BDgraph-2.28/BDgraph/man/select.Rd | 4 BDgraph-2.28/BDgraph/man/summary.bdgraph.Rd | 4 BDgraph-2.28/BDgraph/man/surveyData.Rd | 4 BDgraph-2.28/BDgraph/man/traceplot.Rd | 4 BDgraph-2.28/BDgraph/src/Ig.cpp | 2 BDgraph-2.28/BDgraph/src/Makevars | 1 BDgraph-2.28/BDgraph/src/Makevars.win | 1 BDgraph-2.28/BDgraph/src/MyLapack.cpp |only BDgraph-2.28/BDgraph/src/MyLapack.h |only BDgraph-2.28/BDgraph/src/bd_for_ts.cpp |only BDgraph-2.28/BDgraph/src/copula.cpp | 4 BDgraph-2.28/BDgraph/src/gcgm_DMH.cpp |only BDgraph-2.28/BDgraph/src/gcgm_bd.cpp | 24 +-- BDgraph-2.28/BDgraph/src/gcgm_bd_multi_update.cpp | 24 +-- BDgraph-2.28/BDgraph/src/gcgm_rj.cpp | 23 +-- BDgraph-2.28/BDgraph/src/ggm_DMH.cpp |only BDgraph-2.28/BDgraph/src/ggm_bd.cpp | 33 ++-- BDgraph-2.28/BDgraph/src/ggm_bd_multi_update.cpp | 33 ++-- BDgraph-2.28/BDgraph/src/ggm_rj.cpp | 22 +- BDgraph-2.28/BDgraph/src/matrix.cpp | 133 +++++++++++++++++- BDgraph-2.28/BDgraph/src/matrix.h | 15 +- BDgraph-2.28/BDgraph/src/rgcwish.cpp |only BDgraph-2.28/BDgraph/src/rgcwish.h |only BDgraph-2.28/BDgraph/src/rgwish.cpp | 21 -- BDgraph-2.28/BDgraph/src/scaleFree.cpp | 2 59 files changed, 418 insertions(+), 275 deletions(-)
Title: Create and Navigate Large Multi-Panel Visual Displays
Description: An extension of Trellis Display that enables creation,
organization, and interactive viewing of multi-panel displays created
against potentially very large data sets. The dynamic viewer tiles
panels of a display across the screen in a web browser and allows the
user to interactively page through the panels and sort and filter them
based on "cognostic" metrics computed for each panel. Panels can be
created using many of R's plotting capabilities, including base R
graphics, 'lattice', 'ggplot2', and many 'htmlwidgets'. Conditioning is
handled through the 'datadr' package, which enables 'Trelliscope' displays
with potentially millions of panels to be created against terabytes of
data on systems like 'Hadoop'. While designed to scale, 'Trelliscope'
displays can also be very useful for small data sets.
Author: Ryan Hafen [aut, cre],
Jeremiah Rounds [ctb],
Barret Schloerke [ctb],
Landon Sego [ctb]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between trelliscope versions 0.9.4 dated 2016-03-25 and 0.9.7 dated 2016-10-03
DESCRIPTION | 14 +++--- MD5 | 44 ++++++++++---------- NAMESPACE | 10 ++++ NEWS.md | 21 ++++++--- R/cognostics.R | 2 R/convert.R |only R/makeDisplay.R | 17 +++++-- R/makeDisplay_internals.R | 11 ++++- R/qtrellis.R | 2 R/state.R | 12 ----- R/trelliscope-package.R | 4 - R/view.R | 6 +- README.md | 16 +++---- inst/trelliscopeViewer/server/_fns.R | 22 ++++++++++ inst/trelliscopeViewer/server/panelTable.R | 11 +++-- inst/trelliscopeViewer/www/assets/custom/custom.css | 3 + inst/trelliscopeViewer/www/assets/custom/main.js | 21 +++++---- inst/trelliscopeViewer/www/index.html | 8 +-- man/cogScagnostics.Rd | 2 man/makeDisplay.Rd | 13 +++-- man/trelliscope-package.Rd | 2 man/vdbConvert.Rd |only man/view.Rd | 5 +- tests/testthat/_init.R | 2 24 files changed, 159 insertions(+), 89 deletions(-)
Title: Streamlined Estimation of Survival for Static, Dynamic and
Stochastic Treatment and Monitoring Regimes
Description: Analysis of longitudinal time-to-event or time-to-failure data.
Estimates the counterfactual discrete survival curve under static, dynamic and
stochastic interventions on treatment (exposure) and monitoring events over time.
Estimators (IPW, MSM-IPW, GCOMP, longitudinal TMLE) adjust for measured time-varying
confounding and informative right-censoring. Model fitting can be performed either
with GLM or H2O-3 machine learning libraries, including the ensemble-based
SuperLearner ('h2oEnsemble').
The exposure, monitoring and censoring variables can be coded as either binary,
categorical or continuous. Each can be multivariate (e.g., can use more than one
column of dummy indicators for different censoring events).
The input data needs to be in long format.
Author: Oleg Sofrygin [aut, cre],
Mark J. van der Laan [aut],
Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
Diff between stremr versions 0.1 dated 2016-10-01 and 0.2 dated 2016-10-03
DESCRIPTION | 10 ++++--- MD5 | 30 ++++++++++----------- R/BinomialGLMsClass.R | 4 ++ R/BinomialMLclass.R | 3 -- R/BinomialModelClass.R | 10 +++---- R/reports.R | 10 +++++++ R/zzz.R | 18 ++++++------ README.md | 6 ++-- man/set_all_stremr_options.Rd | 2 - man/survMSM.Rd | 2 + tests/RUnit/RUnit_tests_04a_sims10K_speedglm.R | 15 ++++++---- tests/RUnit/RUnit_tests_04b_sims10K_h2oGLM.R | 5 ++- tests/RUnit/RUnit_tests_04c_sims10K_h2o_ALL_ML.R | 15 ++++++---- tests/RUnit/RUnit_tests_05_stremr_example_SL.R | 5 ++- tests/RUnit/RUnit_tests_06_direct_regression_def.R | 17 +++++++---- tests/examples/4_survMSM_example.R | 2 + 16 files changed, 92 insertions(+), 62 deletions(-)
Title: 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
Description: 'Rcpp' integration for 'GNU GSL' vectors and matrices
The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs as it
provides a standard C interface to a wide range of mathematical routines
such as special functions, permutations, combinations, fast fourier
transforms, eigensystems, random numbers, quadrature, random distributions,
quasi-random sequences, Monte Carlo integration, N-tuples, differential
equations, simulated annealing, numerical differentiation, interpolation,
series acceleration, Chebyshev approximations, root-finding, discrete
Hankel transforms physical constants, basis splines and wavelets. There
are over 1000 functions in total with an extensive test suite.
The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data
structures and R using concepts from 'Rcpp' which is itself a package that
eases the interfaces between R and C++.
This package also serves as a prime example of how to build a package
that uses 'Rcpp' to connect to another third-party library. The 'autoconf'
script, 'inline' plugin and example package can all be used as a stanza to
write a similar package against another library.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppGSL versions 0.3.0 dated 2015-08-30 and 0.3.1 dated 2016-10-03
RcppGSL-0.3.0/RcppGSL/R/unit.test.R |only RcppGSL-0.3.0/RcppGSL/inst/unitTests/runTests.R |only RcppGSL-0.3.1/RcppGSL/ChangeLog | 17 ++++ RcppGSL-0.3.1/RcppGSL/DESCRIPTION | 8 +- RcppGSL-0.3.1/RcppGSL/MD5 | 32 +++----- RcppGSL-0.3.1/RcppGSL/README.md | 69 +++++++++++++++++ RcppGSL-0.3.1/RcppGSL/build/vignette.rds |binary RcppGSL-0.3.1/RcppGSL/inst/NEWS.Rd | 14 +++ RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-intro.R | 6 - RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-intro.Rnw | 6 - RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-intro.pdf |binary RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-unitTests.R | 12 +-- RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-unitTests.Rnw | 12 +-- RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-unitTests.pdf |binary RcppGSL-0.3.1/RcppGSL/tests/doRUnit.R | 70 ++++++++++-------- RcppGSL-0.3.1/RcppGSL/vignettes/RcppGSL-intro.Rnw | 6 - RcppGSL-0.3.1/RcppGSL/vignettes/RcppGSL-unitTests.Rnw | 12 +-- RcppGSL-0.3.1/RcppGSL/vignettes/buildVignette.R | 2 18 files changed, 182 insertions(+), 84 deletions(-)
Title: High-Performance Stemmer, Tokenizer, and Spell Checker for R
Description: A spell checker and morphological analyzer library designed for
languages with rich morphology and complex word compounding or character
encoding. The package can check and analyze individual words as well as
search for incorrect words within a text, latex, html or xml document. Use
the 'devtools' package to spell check R documentation with 'hunspell'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between hunspell versions 2.0 dated 2016-09-08 and 2.1 dated 2016-10-03
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------- NEWS | 7 ++++- R/hunspell.R | 2 - inst/doc/intro.R | 17 +++++++++--- inst/doc/intro.Rmd | 60 ++++++++++++++++++++++++++++----------------- inst/doc/intro.html | 56 +++++++++++++++++------------------------- man/hunspell.Rd | 2 - src/hunspell/suggestmgr.cc | 4 +-- vignettes/intro.Rmd | 34 ++++++++++++------------- 10 files changed, 112 insertions(+), 94 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.1-1 dated 2016-04-14 and 1.2-0 dated 2016-10-03
DESCRIPTION | 10 +++---- MD5 | 31 +++++++++++++---------- NAMESPACE | 21 +++++++--------- NEWS.md |only R/AAAhelpers.R | 5 +++ R/AAAparameter.R | 8 +++--- R/graph.R | 2 - R/groupedmatrix.R | 64 +++++++++++++++++++------------------------------ R/inspectDT.R |only R/iplot.R | 22 ++++++++-------- R/matrix.R | 2 - R/paracoord.R | 2 - R/plotly.R |only R/scatterplot.R | 20 ++++++++------- README.md | 8 +++--- inst/doc/arulesViz.pdf |binary man/inspectDT.Rd |only man/plot.Rd | 53 ++++++++++++++++++++++++++-------------- man/plotly_arules.Rd |only 19 files changed, 130 insertions(+), 118 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.4-2 dated 2016-08-06 and 1.5-0 dated 2016-10-02
arules-1.4-2/arules/src/listops.c |only arules-1.4-2/arules/src/listops.h |only arules-1.4-2/arules/src/nstats.c |only arules-1.4-2/arules/src/nstats.h |only arules-1.4-2/arules/src/params.c |only arules-1.4-2/arules/src/params.h |only arules-1.4-2/arules/src/scan.c |only arules-1.4-2/arules/src/scan.h |only arules-1.5-0/arules/DESCRIPTION | 8 +- arules-1.5-0/arules/MD5 | 58 +++++++--------- arules-1.5-0/arules/NAMESPACE | 3 arules-1.5-0/arules/NEWS.md |only arules-1.5-0/arules/R/AllClasses.R | 6 + arules-1.5-0/arules/R/apriori.R | 2 arules-1.5-0/arules/R/inspect.R | 19 +++-- arules-1.5-0/arules/R/is.redundant.R | 2 arules-1.5-0/arules/R/itemMatrix.R | 12 ++- arules-1.5-0/arules/R/plot.R |only arules-1.5-0/arules/R/ruleInduction.R | 5 + arules-1.5-0/arules/README.md | 51 ++++++++------ arules-1.5-0/arules/inst/doc/arules.pdf |binary arules-1.5-0/arules/man/ASparameter-class.Rd | 6 + arules-1.5-0/arules/man/apriori.Rd | 30 ++++++-- arules-1.5-0/arules/man/associations-class.Rd | 1 arules-1.5-0/arules/man/eclat.Rd | 4 + arules-1.5-0/arules/man/is.redundant.Rd | 24 ++++-- arules-1.5-0/arules/man/itemMatrix-class.Rd | 1 arules-1.5-0/arules/man/weclat.Rd | 13 ++- arules-1.5-0/arules/src/rapriori.c | 55 ++++++++++++--- arules-1.5-0/arules/src/rapriori.h | 1 arules-1.5-0/arules/src/reclat.c | 2 arules-1.5-0/arules/tests/testthat/test-apriori.R | 22 ++---- arules-1.5-0/arules/tests/testthat/test-associations.R | 13 ++- arules-1.5-0/arules/tests/testthat/test-measures.R | 18 +++- arules-1.5-0/arules/tests/testthat/test-ruleInduction.R | 34 +++------ 35 files changed, 244 insertions(+), 146 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast access to images stored in the NIfTI-1 file
format <http://nifti.nimh.nih.gov/nifti-1>, with seamless synchronisation
between compiled C and interpreted R code. Not to be confused with
'RNiftyReg', which provides tools for image registration.
Author: Jon Clayden [cre, aut],
Bob Cox [aut],
Mark Jenkinson [aut],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 0.2.1 dated 2016-09-20 and 0.2.2 dated 2016-10-02
DESCRIPTION | 25 +++++++++++++++++++------ MD5 | 9 +++++---- NEWS | 9 ++++++++- R/xform.R | 14 ++++++++++---- inst/COPYRIGHTS |only tests/testthat/test-10-xform.R | 3 +++ 6 files changed, 45 insertions(+), 15 deletions(-)
Title: Isotope Pattern, Profile and Centroid Calculation for Mass
Spectrometry
Description: Fast and very memory-efficient calculation of isotope patterns,
subsequent convolution to theoretical envelopes (profiles) plus valley
detection and centroidization or intensoid calculation. Batch processing,
resolution interpolation, wrapper, adduct calculations and molecular
formula parsing.
Author: Martin Loos, Christian Gerber
Maintainer: Martin Loos <mloos@looscomputing.ch>
Diff between enviPat versions 2.1 dated 2016-03-14 and 2.2 dated 2016-10-02
DESCRIPTION | 10 ++++---- MD5 | 16 ++++++------- NEWS | 9 ++++++- R/check_chemform.R | 57 ++++++++++++++++++++++++++++------------------- R/enviPat.R | 2 - data/adducts.rda |binary data/isotopes.rda |binary data/resolution_list.rda |binary man/check_chemform.Rd | 17 +++++++------- 9 files changed, 65 insertions(+), 46 deletions(-)
Title: Divide and Recombine for Large, Complex Data
Description: Methods for dividing data into subsets, applying analytical
methods to the subsets, and recombining the results. Comes with a generic
MapReduce interface as well. Works with key-value pairs stored in memory,
on local disk, or on HDFS, in the latter case using the R and Hadoop
Integrated Programming Environment (RHIPE).
Author: Ryan Hafen [aut, cre],
Landon Sego [ctb]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between datadr versions 0.8.5 dated 2016-03-16 and 0.8.6 dated 2016-10-02
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 5 ++++- R/datadr-package.R | 2 +- R/dataops_read.R | 3 +-- R/ddo_ddf_kvHDFS.R | 4 +++- R/divSpec_condDiv.R | 4 ++-- R/divSpec_rrDiv.R | 2 +- R/divide.R | 2 +- R/divide_df.R | 3 ++- R/recombine.R | 2 +- README.md | 23 +++++++++++------------ man/condDiv.Rd | 2 +- man/datadr-package.Rd | 2 +- man/divide.Rd | 2 +- man/makeExtractable.Rd | 4 +++- man/readHDFStextFile.Rd | 2 +- man/recombine.Rd | 2 +- man/rrDiv.Rd | 2 +- 19 files changed, 59 insertions(+), 53 deletions(-)
Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation
(DES) package for R. Designed to be a generic framework, it leverages the
power of 'Rcpp' to boost the performance, turning DES in R feasible. As a
noteworthy characteristic, 'simmer' exploits the concept of trajectory: a
common path in the simulation model for entities of the same type.
Author: Bart Smeets [aut, cph],
Iñaki Ucar [aut, cph, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer versions 3.4.2 dated 2016-09-03 and 3.4.3 dated 2016-10-02
DESCRIPTION | 15 LICENSE | 2 MD5 | 146 +++---- NEWS.md | 16 R/RcppExports.R | 2 R/convenience_funcs.R | 54 +- R/plot.R | 142 +++---- R/simulator.R | 194 ++++----- R/trajectory.R | 203 ++++------ R/utils.R | 26 - R/wrap.R | 52 +- TODO | 1 inst/doc/A-introduction.html | 74 ++- inst/doc/B-terminology.html | 4 inst/doc/C-trajectories.html | 50 +- inst/doc/D-bank-1.html | 4 inst/doc/E-queueing-systems.html | 4 inst/doc/F-ctmc.html | 4 man/add_generator.Rd | 18 man/add_resource.Rd | 8 man/batch.Rd | 6 man/branch.Rd | 2 man/clone.Rd | 4 man/create_trajectory.Rd | 16 man/from.Rd | 8 man/from_to.Rd | 8 man/plot_resource_utilization.Rd | 2 man/renege_in.Rd | 2 man/reset.Rd | 2 man/seize.Rd | 8 man/set_attribute.Rd | 2 man/simmer.Rd | 10 man/timeout.Rd | 4 man/wrap.Rd | 8 src/RcppExports.cpp | 416 ++++++++++----------- src/activity.cpp | 10 src/activity.h | 249 ++++++------ src/entity.h | 6 src/policy.cpp | 4 src/policy.h | 13 src/process.cpp | 54 +- src/process.h | 81 ++-- src/resource.cpp | 24 - src/resource.h | 92 ++-- src/simmer.h | 2 src/simmer_rcpp.cpp | 18 src/simulator.h | 67 +-- src/stats.h | 12 tests/testthat.R | 2 tests/testthat/test-chaining.R | 8 tests/testthat/test-convenience-funcs.R | 24 - tests/testthat/test-plot.R | 32 - tests/testthat/test-simmer-generator.R | 72 +-- tests/testthat/test-simmer-resource-preemption.R | 112 ++--- tests/testthat/test-simmer-resource-priorities.R | 46 +- tests/testthat/test-simmer-resource-schedule.R | 91 ++-- tests/testthat/test-simmer-resource.R | 100 ++--- tests/testthat/test-simmer.R | 84 ++-- tests/testthat/test-simulation-1.R | 56 +- tests/testthat/test-simulation-2.R | 12 tests/testthat/test-trajectory-batch-separate.R | 210 ++++++---- tests/testthat/test-trajectory-branch.R | 38 - tests/testthat/test-trajectory-clone-synchronize.R | 64 +-- tests/testthat/test-trajectory-leave.R | 24 - tests/testthat/test-trajectory-renege.R | 193 ++++++--- tests/testthat/test-trajectory-rollback.R | 60 +-- tests/testthat/test-trajectory-seize-release.R | 78 ++- tests/testthat/test-trajectory-select.R | 86 ++-- tests/testthat/test-trajectory-setattribute.R | 55 +- tests/testthat/test-trajectory-setprioritization.R | 32 - tests/testthat/test-trajectory-timeout.R | 16 tests/testthat/test-trajectory.R | 154 +++---- tests/testthat/test-util-funcs.R | 2 tests/testthat/test-wrap.R | 60 +-- 74 files changed, 2004 insertions(+), 1856 deletions(-)
Title: Estimate Quantitative Genetics Parameters from Generalised
Linear Mixed Models
Description: Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.
Author: Pierre de Villemereuil <bonamy@horus.ens.fr>
Maintainer: Pierre de Villemereuil <bonamy@horus.ens.fr>
Diff between QGglmm versions 0.5 dated 2016-09-28 and 0.5.1 dated 2016-10-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/QGglmmHowTo.Rnw | 6 +++--- inst/doc/QGglmmHowTo.pdf |binary vignettes/QGglmmHowTo.Rnw | 6 +++--- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for working with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 1.8 dated 2016-08-31 and 1.9 dated 2016-10-02
DESCRIPTION | 8 +++--- MD5 | 60 ++++++++++++++++++++++++++-------------------------- R/mif.R | 2 - R/mif2.R | 17 ++++++++++---- build/partial.rdb |binary inst/NEWS | 20 +++++++++++++++++ inst/NEWS.Rd | 11 +++++++++ man/abc.Rd | 2 - man/basic_probes.Rd | 3 -- man/gompertz.Rd | 2 - man/kalman.Rd | 2 - man/mif2.Rd | 4 +-- man/package.Rd | 14 ++++++------ man/pfilter.Rd | 2 - man/pmcmc.Rd | 2 - man/pomp.Rd | 20 ++++++++--------- man/probe.Rd | 2 - man/ricker.Rd | 2 - man/sir.Rd | 4 +-- src/SSA_simulator.c | 2 - src/dmeasure.c | 2 - src/dprior.c | 2 - src/euler.c | 4 +-- src/initstate.c | 2 - src/partrans.c | 2 - src/pomp_fun.c | 17 ++++++++++++-- src/rmeasure.c | 2 - src/rprior.c | 2 - src/skeleton.c | 2 - src/ssa.c | 10 +++++++- src/trajectory.c | 5 ++-- 31 files changed, 142 insertions(+), 87 deletions(-)
Title: Goodness-of-Fit Tests for Copulae
Description: Several GoF tests for Copulae are provided. A new hybrid test is implemented which supports all of the individual tests. Estimation methods for the margins are provided. All the tests support parameter estimation and predefined values. The parameters are estimated by pseudo maximum likelihood but if it fails the estimation switches automatically to inversion of Kendall's tau. All the tests support automatized parallelization of the bootstrapping tasks.
Author: Ostap Okhrin <ostap.okhrin@tu-dresden.de>,
Simon Trimborn <simon.trimborn@wiwi.hu-berlin.de>,
Shulin Zhang <slzhang@swufe.edu.cn>,
Qian M. Zhou <qmzhou@sfu.ca>
Maintainer: Simon Trimborn <simon.trimborn@wiwi.hu-berlin.de>
Diff between gofCopula versions 0.2-2 dated 2016-09-22 and 0.2-3 dated 2016-10-02
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/Tstats.R | 2 +- R/goftime.R | 2 +- R/tests.R | 12 ++++++------ R/tests_CheckTime.R | 12 ++++++------ R/tests_copula_helper.R | 34 +++++++++++++++------------------- R/tests_copula_new.R | 20 ++++++++++---------- R/tests_vine11.R | 4 ++-- R/tests_vine12.R | 4 ++-- R/tests_vine2.R | 7 ++++--- 12 files changed, 64 insertions(+), 67 deletions(-)
More information about fixedTimeEvents at CRAN
Permanent link
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between embryogrowth versions 6.3 dated 2016-07-18 and 6.4 dated 2016-10-02
DESCRIPTION | 8 MD5 | 67 - NAMESPACE | 1 NEWS | 20 R/GenerateAnchor.R | 3 R/STRN.R | 4 R/STRN_fit.R | 3 R/embryogrowth-package.R | 4 R/info.nests.R | 1526 +++++++++++++++++++------------------- R/plot.NestsResult.R | 9 R/plot.tsd.R | 37 R/plotR.R | 49 - R/plotR_hist.R | 9 R/predict.tsd.R | 2 R/searchR.R | 14 R/tsd.R | 2 R/web.tsd.R |only data/DatabaseTSD.rda |binary data/nest.rda |binary data/resultNest_4p.rda |binary data/resultNest_4p_transition.rda |binary data/resultNest_4p_weight.rda |binary data/resultNest_6p.rda |binary data/resultNest_newp.rda |binary data/tempConst.rda |binary inst |only man/GenerateAnchor.Rd | 3 man/embryogrowth-package.Rd | 4 man/info.nests.Rd | 20 man/plotR.Rd | 28 man/plotR_hist.Rd | 8 man/predict.tsd.Rd | 2 man/searchR.Rd | 14 man/tsd.Rd | 2 man/web.tsd.Rd |only 35 files changed, 967 insertions(+), 872 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Multivariate mixed model solver for multiple random effects allowing the specification of variance covariance structures. ML/REML estimates are obtained using the Average Information (AI), Expectation-Maximization (EM), Newton-Raphson (NR), or Efficient Mixed Model Association (EMMA) algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program. Multivariate models (multiple responses) can be fitted currently with NR, AI and EMMA algorithms allowing multiple random effects as well. Covariance structures for the residual component is currently supported only for balanced univariate Newton Raphson.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between sommer versions 2.1 dated 2016-08-31 and 2.2 dated 2016-10-01
CHANGELOG | 12 ++ DESCRIPTION | 8 - MD5 | 74 ++++++++--------- NAMESPACE | 4 R/AI.R | 6 - R/EM.R | 4 R/LD.decay.R |only R/MAI.R | 6 - R/MAI2.R | 14 +-- R/MMERM.R | 20 +++- R/MNR.R | 23 +++-- R/NR.R | 2 R/NRR.R | 2 R/ai2help.R | 2 R/atcg1234.R | 18 +++- R/manhattan.R | 9 +- R/mmer.R | 38 ++++++-- R/mmer2.R | 5 - R/mmerSNOW.R | 43 +++++++--- R/score.calcMV.R | 13 ++- inst/doc/sommer.R | 3 inst/doc/sommer.Rmd | 9 +- inst/doc/sommer.pdf |binary man/A.mat.Rd | 7 + man/CPdata.Rd | 3 man/FDdata.Rd | 23 +++++ man/LD.decay.Rd |only man/PolyData.Rd | 3 man/RICE.Rd | 3 man/TP.prep.Rd | 3 man/Technow_data.Rd | 3 man/cornHybrid.Rd | 25 +++++ man/manhattan.Rd | 3 man/mmer.Rd | 214 ++++++++++++++++---------------------------------- man/mmer2.Rd | 185 ++++++++++++++++--------------------------- man/sommer-package.Rd | 69 ++++++++++++---- man/wheatLines.Rd | 3 vignettes/sommer.Rmd | 9 +- vignettes/sommer.html | 97 +++++++++++----------- 39 files changed, 528 insertions(+), 437 deletions(-)
Title: R Bindings for Selenium WebDriver
Description: The RSelenium package provides a set of R bindings for the
Selenium 2.0 WebDriver using the JsonWireProtocol. Selenium automates web
browsers (commonly referred to as browsers). Using RSelenium you can
automate browsers locally or remotely.
Author: John Harrison <johndharrison0@gmail.com>
Maintainer: John Harrison <johndharrison0@gmail.com>
Diff between RSelenium versions 1.4.0 dated 2016-07-30 and 1.4.5 dated 2016-10-01
RSelenium-1.4.0/RSelenium/inst/tests |only RSelenium-1.4.0/RSelenium/tests/test-all.R |only RSelenium-1.4.0/RSelenium/tests/testthat/test-open.r |only RSelenium-1.4.5/RSelenium/DESCRIPTION | 14 - RSelenium-1.4.5/RSelenium/MD5 | 67 +++-- RSelenium-1.4.5/RSelenium/NAMESPACE | 2 RSelenium-1.4.5/RSelenium/NEWS | 30 +- RSelenium-1.4.5/RSelenium/R/errorHandler.R | 20 + RSelenium-1.4.5/RSelenium/R/remoteDriver.R | 8 RSelenium-1.4.5/RSelenium/R/util.R | 134 ++++++---- RSelenium-1.4.5/RSelenium/R/webElement.R | 2 RSelenium-1.4.5/RSelenium/README.md | 23 + RSelenium-1.4.5/RSelenium/build/vignette.rds |binary RSelenium-1.4.5/RSelenium/inst/doc/RSelenium-docker.Rmd |only RSelenium-1.4.5/RSelenium/inst/doc/RSelenium-docker.html |only RSelenium-1.4.5/RSelenium/inst/examples |only RSelenium-1.4.5/RSelenium/inst/sauceTests |only RSelenium-1.4.5/RSelenium/man/RSelenium-package.Rd | 2 RSelenium-1.4.5/RSelenium/man/checkForServer.Rd | 6 RSelenium-1.4.5/RSelenium/man/errorHandler-class.Rd | 2 RSelenium-1.4.5/RSelenium/man/makeFirefoxProfile.Rd | 2 RSelenium-1.4.5/RSelenium/man/remoteDriver-class.Rd | 3 RSelenium-1.4.5/RSelenium/man/startServer.Rd | 4 RSelenium-1.4.5/RSelenium/tests/README.md |only RSelenium-1.4.5/RSelenium/tests/testthat.R |only RSelenium-1.4.5/RSelenium/tests/testthat/helper.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-api_example_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-cookie_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-misc_remoteDriver_methods_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-page_loading_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-takes_screenshots_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-util_function_tests.R |only RSelenium-1.4.5/RSelenium/vignettes/RSelenium-docker.Rmd |only RSelenium-1.4.5/RSelenium/vignettes/SeleniumDockerHub.png |only RSelenium-1.4.5/RSelenium/vignettes/SeleniumRunUbuntu.png |only RSelenium-1.4.5/RSelenium/vignettes/SeleniumRunWin10.png |only RSelenium-1.4.5/RSelenium/vignettes/TightVNC.png |only RSelenium-1.4.5/RSelenium/vignettes/VinagreVNC.png |only RSelenium-1.4.5/RSelenium/vignettes/Win10PullFirefox.png |only RSelenium-1.4.5/RSelenium/vignettes/node-firefox.png |only RSelenium-1.4.5/RSelenium/vignettes/ubuntuHelloWorld.png |only RSelenium-1.4.5/RSelenium/vignettes/windowsToolbox.png |only 42 files changed, 219 insertions(+), 100 deletions(-)
Title: Color Science Methods and Data
Description: Methods and data for color science - color conversions by observer,
illuminant and gamma. Color matching functions and chromaticity diagrams.
Color indices, color differences and spectral data conversion/analysis.
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama <rxprtgama@gmail.com>
Diff between colorscience versions 1.0.2 dated 2016-02-28 and 1.0.4 dated 2016-10-01
DESCRIPTION | 10 MD5 | 144 ++++---- NAMESPACE | 5 R/colorscience.R | 176 +++++----- data/CentralsISCCNBS.rda |binary data/ChromaticAdaptation.rda |binary data/DeMarcoPokornySmith2degConeFundamentals1992.rda |binary data/ISObrightnessReflectometerRSD.rda |binary data/MaterialReferenceData.rda |binary data/MaxChromaFromExtrapRenotationData.rda |binary data/MaxChromasForStandardMunsellHuesAndValues.rda |binary data/Munsell100hues55.rda |binary data/Munsell100hues55FM100.rda |binary data/MunsellHues.rda |binary data/MunsellNeutrals2sRGB.rda |binary data/MunsellSpectral.rda |binary data/SmithPokorny2degConeFundamentals1975.rda |binary data/StockmanMacLeodJohnson10degConeFundamentals1993.rda |binary data/StockmanMacLeodJohnson2degCIEadjConeFundamentals1993.rda |binary data/StockmanMacLeodJohnson2degStilesBurchConeFundamentals1993.rda |binary data/StockmanSharpe10degCMFS2000.rda |binary data/StockmanSharpe2degCMFadj2000.rda |binary data/SystemISCCNBS.rda |binary data/TCSdata.rda |binary data/VosEstevezWalraven2degConeFundamentals1990.rda |binary data/VosWalraven2degConeFundamentals1971.rda |binary data/XYZperfectreflectingdiffuser.rda |binary data/cccie31.rda |binary data/cccie64.rda |binary data/ciexyz31.rda |binary data/ciexyz64.rda |binary data/conversionIlluminance.rda |binary data/conversionLuminance.rda |binary data/daylightcomponents.rda |binary data/huedegreemunsell.rda |binary data/illuminantA.rda |binary data/illuminantD65.rda |binary data/illuminants.rda |binary data/tristimulusMunsell.rda |binary data/whitepointsRGB.rda |binary data/whitepointsilluminants.rda |binary man/Berger59.Whiteness.Rd | 2 man/CIE.Whiteness.Rd | 2 man/CIE1960UCS2CIE1964.Rd | 2 man/CIE1976uvSaturation.Rd | 5 man/CheckColorLookup.Rd | 7 man/ColorBlockFromMunsell.Rd | 6 man/DIN6167.YellownessIndex.Rd | 2 man/DominantWavelength.Rd | 2 man/HunterLab2XYZ.Rd | 2 man/Lab2XYZ.Rd | 2 man/Luv2XYZ.Rd | 2 man/Luv2Yuv.Rd | 2 man/Maxwell.triangle.Rd | 2 man/MunsellSpecToHVC.Rd | 2 man/RGB2XYZ.Rd | 10 man/RxRyRz2XYZ.Rd | 2 man/SystemISCCNBS.Rd | 11 man/Taube60.Whiteness.Rd | 2 man/XYZ2HunterLab.Rd | 2 man/XYZ2Lab.Rd | 2 man/XYZ2Luv.Rd | 2 man/XYZ2RGB.Rd | 10 man/XYZ2RxRyRz.Rd | 2 man/XYZ2xyY.Rd | 2 man/Yuv2Luv.Rd | 2 man/chromaticity.diagram.Rd | 2 man/chromaticity.diagram.color.Rd | 2 man/createIsoTempLinesTable.Rd | 4 man/makeChromaticAdaptationMatrix.Rd | 4 man/spectra2CCT.Rd | 3 man/spectra2CRIGAIFSCI.Rd | 3 man/spectra2ISObrightness.Rd | 2 73 files changed, 236 insertions(+), 206 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.7 dated 2015-11-15 and 0.0.8 dated 2016-10-01
ChangeLog | 32 +++++++++++++ DESCRIPTION | 8 +-- MD5 | 13 ++--- README.md | 6 +- inst/NEWS.Rd |only inst/include/annoylib.h | 35 +++++++++----- inst/tests/runit.index.R | 7 ++ src/annoy.cpp | 115 ++++++++++++++++++++++++++++++++++++++++++----- 8 files changed, 181 insertions(+), 35 deletions(-)
Title: 3D Lever and Linkage Mechanism Modeling
Description: Creates kinematic and static force models of 3D levers and linkage mechanisms, with particular application to the fields of engineering and biomechanics.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between linkR versions 1.0.1 dated 2015-06-19 and 1.1.1 dated 2016-10-01
linkR-1.0.1/linkR/R/avectors.R |only linkR-1.0.1/linkR/R/findOptimalPointAlignment.R |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH488595.txt |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH490463.txt |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH492487.txt |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH493661.txt |only linkR-1.0.1/linkR/inst/extdata/owl_landmarks.txt |only linkR-1.0.1/linkR/inst/extdata/owl_link_associations.txt |only linkR-1.0.1/linkR/inst/extdata/salmo_salar_1.txt |only linkR-1.0.1/linkR/inst/extdata/salmo_salar_2.txt |only linkR-1.0.1/linkR/inst/extdata/salmo_salar_3.txt |only linkR-1.0.1/linkR/inst/extdata/salmon_landmarks.txt |only linkR-1.0.1/linkR/inst/extdata/salmon_link_associations.txt |only linkR-1.1.1/linkR/DESCRIPTION | 14 linkR-1.1.1/linkR/MD5 | 100 ++- linkR-1.1.1/linkR/NAMESPACE | 6 linkR-1.1.1/linkR/R/CSToEA.R | 3 linkR-1.1.1/linkR/R/angleOnCircleFromPoint.R | 2 linkR-1.1.1/linkR/R/animateLinkage.R | 132 +++- linkR-1.1.1/linkR/R/applySolveChain.R | 21 linkR-1.1.1/linkR/R/applyTransformationsChain.R | 56 +- linkR-1.1.1/linkR/R/avec.R |only linkR-1.1.1/linkR/R/centroidSize.R |only linkR-1.1.1/linkR/R/combineLinkages.R | 10 linkR-1.1.1/linkR/R/copyTransformation.R | 41 + linkR-1.1.1/linkR/R/defineLinkage.R | 57 +- linkR-1.1.1/linkR/R/drawLinkage.R | 269 ++++++++-- linkR-1.1.1/linkR/R/intersectCircles.R | 2 linkR-1.1.1/linkR/R/linkR_data.R |only linkR-1.1.1/linkR/R/linkR_examples.R | 132 +--- linkR-1.1.1/linkR/R/linkageKinematics.R | 56 +- linkR-1.1.1/linkR/R/minAngle.R |only linkR-1.1.1/linkR/R/proj3DTo2D.R | 9 linkR-1.1.1/linkR/R/solveKinematicChain.R | 21 linkR-1.1.1/linkR/R/sourcePartial_linkR.R |only linkR-1.1.1/linkR/R/tMatrixEP.R | 17 linkR-1.1.1/linkR/R/vectorsToEP.R | 2 linkR-1.1.1/linkR/R/writeLinkageLayers.R |only linkR-1.1.1/linkR/inst/CITATION |only linkR-1.1.1/linkR/inst/extdata/specimens |only linkR-1.1.1/linkR/inst/extdata/test_configs |only linkR-1.1.1/linkR/man/animateLinkage.Rd | 54 -- linkR-1.1.1/linkR/man/cprod.Rd |only linkR-1.1.1/linkR/man/defineLinkage.Rd | 75 -- linkR-1.1.1/linkR/man/drawLinkage.Rd |only linkR-1.1.1/linkR/man/linkR-package.Rd | 20 linkR-1.1.1/linkR/man/rotationMatrixZYX.Rd |only 47 files changed, 680 insertions(+), 419 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.6 dated 2016-07-18 and 1.7 dated 2016-10-01
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++--------- NEWS | 13 +++++++++++-- R/HelpersMG-package.R | 4 ++-- R/MHalgoGen.R | 30 +++++++++++++++++++++++++++++- R/asc.R | 2 +- R/chr.R | 3 ++- R/radioButtons_withHTML.R |only man/HelpersMG-package.Rd | 4 ++-- man/MHalgoGen.Rd | 30 +++++++++++++++++++++++++++++- man/chr.Rd | 2 +- 11 files changed, 92 insertions(+), 25 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7-th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-76 dated 2016-09-24 and 0.1-77 dated 2016-10-01
DESCRIPTION | 8 MD5 | 8 NEWS | 4 R/CausalDiagramBinBin.R | 657 +++++++++++++++++++++++---------------------- man/CausalDiagramBinBin.Rd | 126 ++++---- 5 files changed, 415 insertions(+), 388 deletions(-)
Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers. Among available
features there are: pattern searching (e.g., with ICU Java-like regular
expressions or the Unicode Collation Algorithm), random string generation,
case mapping, string transliteration, concatenation,
Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski [aut, cre] and Bartek Tartanus [ctb] (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 1.1.1 dated 2016-05-27 and 1.1.2 dated 2016-10-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 8 +++++++- configure | 23 ++++++++++++++++++----- src/icu55/common/putil.cpp | 9 ++++++++- src/stri_sub.cpp | 8 ++++---- src/stri_time_calendar.cpp | 3 ++- 7 files changed, 49 insertions(+), 22 deletions(-)
Title: Supervised Classification Learning and Prediction using Patient
Rule Induction Method (PRIM)
Description: The Patient Rule Induction Method (PRIM) is typically
used for "bump hunting" data mining to identify regions with abnormally
high concentrations of data with large or small values. This package
extends this methodology so that it can be applied to binary classification
problems and used for prediction.
Author: David Shaub [aut, cre]
Maintainer: David Shaub <davidshaub@gmx.com>
Diff between supervisedPRIM versions 1.0.1 dated 2016-08-22 and 2.0.0 dated 2016-10-01
DESCRIPTION | 12 +- MD5 | 16 +-- R/supervisedPRIM-package.R | 3 R/supervisedPRIM.R | 166 ++++++++++++++++++++--------------- README.md | 29 ++++++ inst/NEWS.md | 3 man/predict.supervisedPRIM.Rd | 5 - man/supervisedPRIM.Rd | 7 + tests/testthat/test-supervisedPRIM.R | 40 ++++++-- 9 files changed, 183 insertions(+), 98 deletions(-)
More information about supervisedPRIM at CRAN
Permanent link
Title: Statistical Modeling of Animal Movements
Description: Animal movement models including moving-resting process
with embedded Brownian motion, Brownian motion with measurement error.
Author: Jun Yan <jun.yan@uconn.edu> and
Vladimir Pozdnyakov <vladimir.pozdnyakov@uconn.edu>
Maintainer: Jun Yan <jun.yan@uconn.edu>
Diff between smam versions 0.2-2 dated 2013-11-04 and 0.3-0 dated 2016-10-01
ChangeLog | 6 + DESCRIPTION | 19 ++- MD5 | 24 ++-- NAMESPACE | 30 +++-- R/RcppExports.R |only R/bmme.R | 83 +++++++++++++++- R/movres.R | 256 ++++++++++++++++++++++++++++++++++++++++++++------ man/dtm.Rd | 80 +++++++-------- man/fitBmme.Rd | 76 ++++++-------- man/fitMovRes.Rd | 106 ++++++++++---------- man/integr.control.Rd |only man/rMovRes.Rd | 72 ++++++-------- man/rbmme.Rd | 51 ++++----- src/RcppExports.cpp |only src/movres-llk.cpp |only 15 files changed, 533 insertions(+), 270 deletions(-)
Title: Simultaneous Confidence Bands for the Mean of Functional Data
Description: Statistical methods for estimating and inferring the mean of functional data. The methods include simultaneous confidence bands, local polynomial fitting, bandwidth selection by plug-in and cross-validation, goodness-of-fit tests for parametric models, equality tests for two-sample problems, and plotting functions.
Author: David Degras
Maintainer: David Degras <ddegrasv@gmail.com>
Diff between SCBmeanfd versions 1.2 dated 2016-09-24 and 1.2.1 dated 2016-10-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/plot.SCBand.R | 14 +++++++------- R/scb.model.R | 27 +++++++++++++-------------- man/SCBmeanfd-package.Rd | 11 +++++------ 5 files changed, 33 insertions(+), 35 deletions(-)
Title: Tools to Manage a Parametric Function that Describes Phenology
Description: Functions used to fit and test the phenology of species based on counts.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between phenology versions 5.2 dated 2016-07-18 and 5.3 dated 2016-10-01
DESCRIPTION | 8 MD5 | 29 +-- NEWS | 17 + R/add_phenology.R | 2 R/phenology-package.R | 4 R/phenology.R | 3 R/plot.phenology.R | 17 + inst/shiny/babel.Rdata |only inst/shiny/server.R | 394 +++++++++++++++++++++++++++++++++-------- inst/shiny/ui.R | 172 +++++++++++++---- inst/shiny/www/fr.png |only inst/shiny/www/gb.png |only inst/shiny/www/logoRASTOMA.png |only inst/shiny/www/logoSWOT.png |only inst/shiny/www/pt.png |only inst/shiny/www/sp.png |only man/phenology-package.Rd | 4 man/phenology.Rd | 3 man/plot.phenology.Rd | 4 19 files changed, 507 insertions(+), 150 deletions(-)
More information about expandFunctions at CRAN
Permanent link