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 Hervé
Maintainer: Maxime Hervé <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
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