Title: Diagnostics for Pharmacometric Models
Description: Diagnostics for non-linear mixed-effects (population)
models from 'NONMEM' <http://www.iconplc.com/innovation/nonmem/>.
'xpose' facilitates data import, creation of numerical run summary
and provide 'ggplot2'-based graphics for data exploration and model
diagnostics.
Author: Benjamin Guiastrennec [aut, cre, cph],
Andrew C. Hooker [aut, cph],
Anna Olofsson [aut, cph],
Sebastian Ueckert [aut, cph],
Ron Keizer [aut],
Nick Solomon [ctb] (Wrote the geom_qq_line function),
Kajsa Harling [ctb],
Mike K. Smith [ctb],
Elodie Plan [ctb],
Mats O. Karlsson [aut, cph],
Pharmetheus [ctb],
Pfizer [ctb]
Maintainer: Benjamin Guiastrennec <guiastrennec@gmail.com>
Diff between xpose versions 0.4.1 dated 2018-01-09 and 0.4.2 dated 2018-01-30
DESCRIPTION | 6 +-- MD5 | 42 +++++++++++------------ NEWS.md | 6 +++ R/vpc_data.R | 9 +++-- README.md | 2 - inst/doc/access_xpdb_data.html | 53 +++++++++++++++--------------- inst/doc/customize_plots.html | 2 - inst/doc/import_model_outputs.html | 2 - inst/doc/introduction.html | 2 - inst/doc/multiple_pages.html | 2 - inst/doc/vpc.html | 2 - man/figures/readme_example_figure_2-1.png |binary man/figures/readme_example_figure_3-1.png |binary man/figures/readme_example_figure_4-1.png |binary man/figures/readme_example_figure_5-1.png |binary tests/testthat/data/ctrl_psn_vpc.RData |binary tests/testthat/data/ctrl_special.RData |binary tests/testthat/test-model-summary.R | 10 +++++ tests/testthat/test-read_nm_files.R | 2 + tests/testthat/test-read_nm_tables.R | 7 ++- tests/testthat/test-vpc.R | 5 +- tests/testthat/test-xpose_data.R | 4 +- 22 files changed, 90 insertions(+), 66 deletions(-)
Title: Transcription Factor Binding Site Identification Tool
Description: Identifies and scores possible Transcription Factor
Binding Sites and allows for FDR analysis and pruning. It supports
splitting of sequences based on size or a specified GFF, grouping
by G+C content, and specification of Markov model order. The heavy
lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam
Siepel
Maintainer: Ritika Ramani<rramani@cshl.edu>
Diff between rtfbs versions 0.3.5 dated 2016-08-16 and 0.3.9 dated 2018-01-30
ChangeLog | 5 ++++- DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + R/tfbs.R | 2 +- inst/doc/vignette.pdf |binary man/rtfbs-package.Rd | 10 +++++----- src/Makevars.in | 2 +- src/Makevars.win | 2 +- src/external_libs.h | 2 +- src/rph_init.c | 1 + src/rph_tfbs.c | 22 ++++++++++++++-------- src/sufficient_stats.c | 2 +- src/version | 2 +- 14 files changed, 50 insertions(+), 39 deletions(-)
Title: Maximum Likelihood Estimates of Gaussian Processes
Description: Maximum likelihood Gaussian process modeling for univariate and multi-dimensional outputs with diagnostic plots following Santner et al (2003) <doi:10.1007/978-1-4757-3799-8>. Contact the maintainer for a package version that includes sensitivity analysis.
Author: Garrett M. Dancik
Maintainer: Garrett M. Dancik <dancikg@easternct.edu>
Diff between mlegp versions 3.1.5 dated 2018-01-30 and 3.1.6 dated 2018-01-30
mlegp-3.1.5/mlegp/build |only mlegp-3.1.5/mlegp/inst/doc/mlegp.R |only mlegp-3.1.5/mlegp/inst/doc/mlegp.Rnw |only mlegp-3.1.6/mlegp/DESCRIPTION | 11 ++++------- mlegp-3.1.6/mlegp/MD5 | 8 +++----- mlegp-3.1.6/mlegp/inst/CITATION |only mlegp-3.1.6/mlegp/inst/doc/mlegp.pdf |binary 7 files changed, 7 insertions(+), 12 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 as a number of
epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.19 dated 2017-08-09 and 2.24 dated 2018-01-30
Epi-2.19/Epi/inst/doc/Follow-up.R |only Epi-2.19/Epi/inst/doc/Follow-up.pdf |only Epi-2.19/Epi/inst/doc/Follow-up.rnw |only Epi-2.19/Epi/man/merge.data.frame.Rd |only Epi-2.19/Epi/vignettes/Follow-up.rnw |only Epi-2.19/Epi/vignettes/index.html |only Epi-2.24/Epi/CHANGES | 37 ++++++++++++++ Epi-2.24/Epi/DESCRIPTION | 10 ++-- Epi-2.24/Epi/MD5 | 70 ++++++++++++++-------------- Epi-2.24/Epi/NAMESPACE | 2 Epi-2.24/Epi/R/LCa.fit.R | 46 +++++++++--------- Epi-2.24/Epi/R/ROC.R | 4 - Epi-2.24/Epi/R/Relevel.R | 63 +++++++++++++++++++++++-- Epi-2.24/Epi/R/addCov.Lexis.R | 32 +++++++++--- Epi-2.24/Epi/R/ci.cum.R | 12 ++-- Epi-2.24/Epi/R/ci.lin.R | 65 +++++++++++++------------- Epi-2.24/Epi/R/cutLexis.R | 2 Epi-2.24/Epi/R/lexis.R | 19 ------- Epi-2.24/Epi/R/mcutLexis.R | 25 ++++++---- Epi-2.24/Epi/build/vignette.rds |binary Epi-2.24/Epi/inst/doc/flup.R |only Epi-2.24/Epi/inst/doc/flup.pdf |only Epi-2.24/Epi/inst/doc/flup.rnw |only Epi-2.24/Epi/inst/doc/index.html | 8 +-- Epi-2.24/Epi/inst/doc/simLexis.R | 40 +++++++++++----- Epi-2.24/Epi/inst/doc/simLexis.pdf |binary Epi-2.24/Epi/inst/doc/simLexis.rnw | 65 ++++++++++++++++---------- Epi-2.24/Epi/inst/doc/yll.R | 24 ++++++--- Epi-2.24/Epi/inst/doc/yll.pdf |binary Epi-2.24/Epi/inst/doc/yll.rnw | 20 ++++++-- Epi-2.24/Epi/man/LCa.fit.Rd | 87 ++++++++++++++++++++--------------- Epi-2.24/Epi/man/Relevel.Rd | 73 ++++++++++++++++++++++++----- Epi-2.24/Epi/man/addCov.Lexis.Rd | 48 ++++++++++++------- Epi-2.24/Epi/man/ci.lin.Rd | 25 +++++----- Epi-2.24/Epi/man/cutLexis.Rd | 1 Epi-2.24/Epi/man/mcutLexis.Rd | 19 ++++++- Epi-2.24/Epi/man/transform.Lexis.Rd | 22 +++++--- Epi-2.24/Epi/vignettes/flup.rnw |only Epi-2.24/Epi/vignettes/sL.pdf |only Epi-2.24/Epi/vignettes/simLexis.rnw | 65 ++++++++++++++++---------- Epi-2.24/Epi/vignettes/yl.pdf |only Epi-2.24/Epi/vignettes/yll.rnw | 20 ++++++-- 42 files changed, 589 insertions(+), 315 deletions(-)
Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the
JavaScript library 'DataTables' (typically via R Markdown or Shiny). The
'DataTables' library has been included in this R package. The package name
'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre],
Joe Cheng [ctb],
JJ Allaire [ctb],
Xianying Tan [ctb],
Maximilian Girlich [ctb],
jQuery contributors [ctb, cph] (jQuery in htmlwidgets/lib),
SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib),
Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib),
Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib),
Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib),
RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between DT versions 0.3 dated 2018-01-23 and 0.4 dated 2018-01-30
DESCRIPTION | 10 ++++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ inst/doc/DT.html | 10 +++++----- inst/htmlwidgets/datatables.js | 22 ++++++++++++++-------- 5 files changed, 37 insertions(+), 21 deletions(-)
Title: Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Description: Provides functions for fitting and validation of subgroup
identification and personalized medicine models under the general subgroup
identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>.
This package is intended for use for both randomized controlled trials and
observational studies.
Author: Jared Huling [aut, cre],
Aaron Potvien [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized versions 0.1.2 dated 2017-11-28 and 0.1.3 dated 2018-01-30
DESCRIPTION | 8 - MD5 | 13 + NAMESPACE | 8 + R/data.R |only R/weighted_svm.R | 1 README.md | 188 ++++++++++-------------- data |only inst/doc/usage_of_the_personalized_package.html | 4 man/LaLonde.Rd |only 9 files changed, 109 insertions(+), 113 deletions(-)
Title: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Description: Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML) .
Author: Hervé Perdry [cre, cph],
Claire Dandine-Roulland [aut, cph],
Deepak Bandyopadhyay [cph] (C++ gzstream class),
Lutz Kettner [cph] (C++ gzstream class)
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.5.2 dated 2018-01-24 and 1.5.3 dated 2018-01-30
gaston-1.5.2/gaston/R/pvalues.thinning.r |only gaston-1.5.3/gaston/DESCRIPTION | 19 +++- gaston-1.5.3/gaston/MD5 | 78 +++++++++++-------- gaston-1.5.3/gaston/NAMESPACE | 2 gaston-1.5.3/gaston/NEWS | 4 gaston-1.5.3/gaston/R/getNumThreads.r |only gaston-1.5.3/gaston/R/manhattan.r | 4 gaston-1.5.3/gaston/R/qqplot.pvalues.r | 6 - gaston-1.5.3/gaston/R/setThreadOptions.r | 13 --- gaston-1.5.3/gaston/R/zzz.r | 4 gaston-1.5.3/gaston/inst/doc/gaston.pdf |binary gaston-1.5.3/gaston/inst/include/gaston |only gaston-1.5.3/gaston/inst/include/gaston.h | 40 ++++----- gaston-1.5.3/gaston/man/DM.Rd | 7 + gaston-1.5.3/gaston/man/GRM.Rd | 7 + gaston-1.5.3/gaston/man/LD.plot.Rd | 3 gaston-1.5.3/gaston/man/association.test.Rd | 7 + gaston-1.5.3/gaston/man/bed.loadings.Rd | 7 + gaston-1.5.3/gaston/man/lik.contour.Rd | 7 + gaston-1.5.3/gaston/man/lmm.aireml.Rd | 7 + gaston-1.5.3/gaston/man/lmm.diago.Rd | 7 + gaston-1.5.3/gaston/man/lmm.diago.likelihood.Rd | 7 + gaston-1.5.3/gaston/man/lmm.restricted.likelihood.Rd | 7 + gaston-1.5.3/gaston/man/logistic.mm.aireml.Rd | 7 + gaston-1.5.3/gaston/man/qqplot.pvalues.Rd | 7 - gaston-1.5.3/gaston/man/reshape.GRM.Rd | 7 + gaston-1.5.3/gaston/man/score.fixed.Rd | 7 + gaston-1.5.3/gaston/man/score.variance.Rd | 7 + gaston-1.5.3/gaston/man/setThreadOptions.Rd | 24 +++-- gaston-1.5.3/gaston/src/gaston_init.c | 2 gaston-1.5.3/gaston/src/logp_thinning.cpp | 2 gaston-1.5.3/gaston/src/pre_likelihood.cpp | 4 32 files changed, 212 insertions(+), 91 deletions(-)
Title: Covariance Matrix Tests
Description: Testing functions for Covariance Matrices. These tests include high-dimension homogeneity of covariance
matrix testing described by Schott (2007) <doi:10.1016/j.csda.2007.03.004> and high-dimensional one-sample tests of
covariance matrix structure described by Fisher, et al. (2010) <doi:10.1016/j.jmva.2010.07.004>. Covariance matrix
tests use C++ to speed performance and allow larger data sets.
Author: Ben Barnard [aut, cre],
Dean Young [aut]
Maintainer: Ben Barnard <ben_barnard@outlook.com>
Diff between covTestR versions 0.1.2 dated 2017-12-23 and 0.1.3 dated 2018-01-30
covTestR-0.1.2/covTestR/man/Ahmad2015.Rd |only covTestR-0.1.2/covTestR/man/Ahmad2017.Rd |only covTestR-0.1.2/covTestR/man/BoxesM.Rd |only covTestR-0.1.2/covTestR/man/Chaipitak2013.Rd |only covTestR-0.1.2/covTestR/man/Chen2010.Rd |only covTestR-0.1.2/covTestR/man/Fisher2012.Rd |only covTestR-0.1.2/covTestR/man/Ishii2016.Rd |only covTestR-0.1.2/covTestR/man/LedoitWolf2002.Rd |only covTestR-0.1.2/covTestR/man/Nagao1973.Rd |only covTestR-0.1.2/covTestR/man/Schott2001.Rd |only covTestR-0.1.2/covTestR/man/Schott2007.Rd |only covTestR-0.1.2/covTestR/man/Srivastava2005.Rd |only covTestR-0.1.2/covTestR/man/Srivastava2007.Rd |only covTestR-0.1.2/covTestR/man/Srivastava2011.Rd |only covTestR-0.1.2/covTestR/man/Srivastava2014.Rd |only covTestR-0.1.2/covTestR/man/SrivastavaYanagihara2010.Rd |only covTestR-0.1.3/covTestR/DESCRIPTION | 8 covTestR-0.1.3/covTestR/MD5 | 81 +--- covTestR-0.1.3/covTestR/NAMESPACE | 102 ++--- covTestR-0.1.3/covTestR/R/Ahmad2015.R | 218 +++++------ covTestR-0.1.3/covTestR/R/Ahmad2017.R | 106 ++--- covTestR-0.1.3/covTestR/R/BoxesM.R | 90 ++-- covTestR-0.1.3/covTestR/R/Chaipitak2013.R | 103 ++--- covTestR-0.1.3/covTestR/R/Chen2010.R | 214 +++++------ covTestR-0.1.3/covTestR/R/DocumentHomogeneityStatistics.R |only covTestR-0.1.3/covTestR/R/DocumentStructureStatistics.R |only covTestR-0.1.3/covTestR/R/Fisher2012.R | 257 ++++++-------- covTestR-0.1.3/covTestR/R/Ishii2016.R | 103 ++--- covTestR-0.1.3/covTestR/R/LedoitWolf2002.R | 214 +++++------ covTestR-0.1.3/covTestR/R/Nagao1973.R | 226 +++++------- covTestR-0.1.3/covTestR/R/RcppExports.R | 122 +++--- covTestR-0.1.3/covTestR/R/Schott2001.R | 101 ++--- covTestR-0.1.3/covTestR/R/Schott2007.R | 104 ++--- covTestR-0.1.3/covTestR/R/Srivastava2005.R | 225 +++++------- covTestR-0.1.3/covTestR/R/Srivastava2007.R | 106 ++--- covTestR-0.1.3/covTestR/R/Srivastava2011.R | 236 ++++++------ covTestR-0.1.3/covTestR/R/Srivastava2014.R | 100 ++--- covTestR-0.1.3/covTestR/R/SrivastavaYanagihara2010.R | 101 ++--- covTestR-0.1.3/covTestR/R/covTestR-package.R | 24 - covTestR-0.1.3/covTestR/R/helpers.R | 42 +- covTestR-0.1.3/covTestR/R/homogeneityCovariances.R | 216 +++++------ covTestR-0.1.3/covTestR/R/structureCovariances.R | 201 +++++----- covTestR-0.1.3/covTestR/man/covTestR-package.Rd | 28 - covTestR-0.1.3/covTestR/man/homogeneityCovariances.Rd | 97 ++--- covTestR-0.1.3/covTestR/man/homogeneityStatistics.Rd |only covTestR-0.1.3/covTestR/man/past.Rd | 24 - covTestR-0.1.3/covTestR/man/structureCovariances.Rd | 93 ++--- covTestR-0.1.3/covTestR/man/structureStatistics.Rd |only covTestR-0.1.3/covTestR/man/tr.Rd | 24 - covTestR-0.1.3/covTestR/src/Makevars | 2 covTestR-0.1.3/covTestR/src/RcppExports.cpp | 12 covTestR-0.1.3/covTestR/src/Srivastava2005.cpp |only 52 files changed, 1714 insertions(+), 1866 deletions(-)
Title: Multi-Model Inference
Description: Tools for performing model selection and model averaging. Automated
model selection through subsetting the maximum model, with optional
constraints for model inclusion. Model parameter and prediction
averaging based on model weights derived from information criteria
(AICc and alike) or custom model weighting schemes.
Author: Kamil Bartoń
Maintainer: Kamil Bartoń <kamil.barton@go2.pl>
Diff between MuMIn versions 1.40.0 dated 2017-10-02 and 1.40.4 dated 2018-01-30
MuMIn-1.40.0/MuMIn/R/ext-gamm.R |only MuMIn-1.40.0/MuMIn/R/ext-mark.R |only MuMIn-1.40.0/MuMIn/R/methods-unmarkedFit.R |only MuMIn-1.40.0/MuMIn/R/xtable-methods.R |only MuMIn-1.40.4/MuMIn/DESCRIPTION | 23 +++++++++------- MuMIn-1.40.4/MuMIn/MD5 | 39 ++++++++++++++-------------- MuMIn-1.40.4/MuMIn/NAMESPACE | 13 +++++---- MuMIn-1.40.4/MuMIn/NEWS | 15 ++++++++++ MuMIn-1.40.4/MuMIn/R/class-gamm.R |only MuMIn-1.40.4/MuMIn/R/class-glmmTMB.R |only MuMIn-1.40.4/MuMIn/R/class-mark.R |only MuMIn-1.40.4/MuMIn/R/class-unmarkedFit.R |only MuMIn-1.40.4/MuMIn/R/getAllTerms.R | 13 ++++----- MuMIn-1.40.4/MuMIn/R/makeArgs.R | 24 ----------------- MuMIn-1.40.4/MuMIn/R/methods-logLik.R | 25 ----------------- MuMIn-1.40.4/MuMIn/R/methods-nobs.R | 5 ++- MuMIn-1.40.4/MuMIn/R/methods-predict.R | 1 MuMIn-1.40.4/MuMIn/R/methods-xtable.R |only MuMIn-1.40.4/MuMIn/R/utils-models.R | 23 +++++++++++----- MuMIn-1.40.4/MuMIn/data/Beetle.rda |binary MuMIn-1.40.4/MuMIn/data/Cement.rda |binary MuMIn-1.40.4/MuMIn/data/GPA.rda |binary MuMIn-1.40.4/MuMIn/man/QAIC.Rd | 2 - MuMIn-1.40.4/MuMIn/man/supported-classes.Rd | 1 MuMIn-1.40.4/MuMIn/tests/classes.R | 17 ++++++++++++ 25 files changed, 102 insertions(+), 99 deletions(-)
Title: Interactive Viewing of Spatial Data in R
Description: Quickly and conveniently create interactive visualisations of spatial data with or without background maps. Attributes of displayed features are fully queryable via pop-up windows. Additional functionality includes methods to visualise true- and false-color raster images, bounding boxes, small multiples and 3D raster data cubes.
Author: Tim Appelhans [cre, aut],
Florian Detsch [aut],
Christoph Reudenbach [aut],
Stefan Woellauer [aut],
Spaska Forteva [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb],
Kenton Russell [ctb],
Michael Sumner [ctb],
Environmental Informatics Marburg [ctb]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between mapview versions 2.2.0 dated 2017-11-02 and 2.3.0 dated 2018-01-30
mapview-2.2.0/mapview/R/addFeatures.R |only mapview-2.2.0/mapview/R/addHomeButton.R |only mapview-2.2.0/mapview/R/addLogo.R |only mapview-2.2.0/mapview/R/addMouseCoordinates.R |only mapview-2.2.0/mapview/R/leafletView.R |only mapview-2.3.0/mapview/DESCRIPTION | 18 - mapview-2.3.0/mapview/MD5 | 64 ++--- mapview-2.3.0/mapview/NAMESPACE | 2 mapview-2.3.0/mapview/NEWS | 24 + mapview-2.3.0/mapview/NEWS.md | 24 + mapview-2.3.0/mapview/R/RcppExports.R | 16 - mapview-2.3.0/mapview/R/extensions.R |only mapview-2.3.0/mapview/R/extent.R | 1 mapview-2.3.0/mapview/R/legend.R | 26 +- mapview-2.3.0/mapview/R/mapView.R | 146 +++++++++++- mapview-2.3.0/mapview/R/mapshot.R | 9 mapview-2.3.0/mapview/R/missing.R |only mapview-2.3.0/mapview/R/popup.R | 73 ++++-- mapview-2.3.0/mapview/R/projection.R | 30 ++ mapview-2.3.0/mapview/R/raster.R |only mapview-2.3.0/mapview/R/sf.R | 5 mapview-2.3.0/mapview/R/stars.R |only mapview-2.3.0/mapview/data/breweries.rda |binary mapview-2.3.0/mapview/data/franconia.rda |binary mapview-2.3.0/mapview/data/poppendorf.rda |binary mapview-2.3.0/mapview/data/trails.rda |binary mapview-2.3.0/mapview/inst/htmlwidgets/lib/joda |only mapview-2.3.0/mapview/man/addFeatures.Rd | 2 mapview-2.3.0/mapview/man/addHomeButton.Rd | 2 mapview-2.3.0/mapview/man/addImageQuery.Rd |only mapview-2.3.0/mapview/man/addLogo.Rd | 2 mapview-2.3.0/mapview/man/addMouseCoordinates.Rd | 2 mapview-2.3.0/mapview/man/addStarsImage.Rd |only mapview-2.3.0/mapview/man/mapView.Rd | 39 ++- mapview-2.3.0/mapview/man/popup.Rd | 8 mapview-2.3.0/mapview/man/viewExtent.Rd | 1 mapview-2.3.0/mapview/src/RcppExports.cpp | 36 +- mapview-2.3.0/mapview/src/brewCppFun.cpp | 31 +- mapview-2.3.0/mapview/tests/testthat/test-mapviewControls.R | 6 39 files changed, 442 insertions(+), 125 deletions(-)
Title: Affinity Propagation Clustering
Description: Implements Affinity Propagation clustering introduced by Frey and
Dueck (2007) <DOI:10.1126/science.1136800>. The algorithms are largely
analogous to the 'Matlab' code published by Frey and Dueck.
The package further provides leveraged affinity propagation and an
algorithm for exemplar-based agglomerative clustering that can also be
used to join clusters obtained from affinity propagation. Various
plotting functions are available for analyzing clustering results.
Author: Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Diff between apcluster versions 1.4.4 dated 2017-07-04 and 1.4.5 dated 2018-01-30
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/NEWS | 5 +++++ inst/doc/apcluster.R | 7 ++++++- inst/doc/apcluster.Rnw | 13 ++++++++++++- inst/doc/apcluster.pdf |binary man/ch22Promoters.Rd | 19 ++++++++++--------- vignettes/apcluster.Rnw | 13 ++++++++++++- 9 files changed, 57 insertions(+), 24 deletions(-)
Title: Using Tip Dates with Phylogenetic Trees in BEAST (Software for
Phylogenetic Analysis)
Description: Assist performing tip-dating of phylogenetic trees with BEAST.
Author: Adrien Rieux, Camilo Khatchikian
Maintainer: Camilo Khatchikian <ckhatchikian@gmail.com>
Diff between TipDatingBeast versions 1.0-6 dated 2017-11-21 and 1.0-7 dated 2018-01-30
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/RandomCluster.R | 23 ++--------------------- R/RandomDates.R | 23 +++-------------------- inst/example/Tutorial_TipDatingBEAST.pdf |binary man/PlotDRT.Rd | 2 +- man/RandomCluster.Rd | 11 +++++------ man/RandomDates.Rd | 5 ++--- man/TaxaOut.Rd | 3 +-- man/TaxonOut.Rd | 5 ++--- man/TipDatingBeast-package.Rd | 4 ++-- 11 files changed, 32 insertions(+), 72 deletions(-)
More information about TipDatingBeast at CRAN
Permanent link
Title: Build Powerful Pivot Tables and Dynamically Slice & Dice your
Data
Description: Build powerful pivot tables (aka Pivot Grid, Pivot Chart, Cross-Tab)
and dynamically slice & dice / drag 'n' drop your data. 'rpivotTable' is a
wrapper of 'pivottable', a powerful open-source Pivot Table library implemented
in 'JavaScript' by Nicolas Kruchten. Aligned to 'pivottable' v2.19.0.
Author: Enzo Martoglio [aut, cre],
Nicolas Kruchten [ctb, cph],
Nagarajan Chinnasamy [ctb, cph],
Kenton Russell [ctb]
Maintainer: Enzo Martoglio <enzo@smartinsightsfromdata.com>
Diff between rpivotTable versions 0.2.0 dated 2017-04-16 and 0.3.0 dated 2018-01-30
rpivotTable-0.2.0/rpivotTable/inst/doc/NEWS.pdf |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/c3_renderers.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/d3_renderers.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/export_renderers.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/gchart_renderers.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.css |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.da.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.de.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.es.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.fr.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.it.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.nl.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.pt.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.ru.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.tr.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.zh.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot_spec.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot_spec.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/tips_data.min.js |only rpivotTable-0.3.0/rpivotTable/DESCRIPTION | 22 rpivotTable-0.3.0/rpivotTable/MD5 | 100 rpivotTable-0.3.0/rpivotTable/R/locale.R | 29 rpivotTable-0.3.0/rpivotTable/R/rpivotTable.R | 94 rpivotTable-0.3.0/rpivotTable/README.md | 5 rpivotTable-0.3.0/rpivotTable/build/vignette.rds |binary rpivotTable-0.3.0/rpivotTable/inst/doc/NEWS.Rmd | 14 rpivotTable-0.3.0/rpivotTable/inst/doc/NEWS.html |only rpivotTable-0.3.0/rpivotTable/inst/doc/rpivotTableIntroduction.R | 9 rpivotTable-0.3.0/rpivotTable/inst/doc/rpivotTableIntroduction.Rmd | 25 rpivotTable-0.3.0/rpivotTable/inst/doc/rpivotTableIntroduction.html | 1387 +++++++++- rpivotTable-0.3.0/rpivotTable/inst/examples/onRefresh-shiny.R | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/c3_renderers.min.js | 4 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/d3_renderers.min.js | 4 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/export_renderers.min.js | 4 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/gchart_renderers.min.js | 4 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.cs.min.js |only rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.da.min.js | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.de.min.js | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.es.min.js | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.fr.min.js | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.it.min.js | 4 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.min.css | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.min.js | 4 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.nl.min.js | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.pl.min.js |only rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.pt.min.js | 4 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.ru.min.js | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.sq.min.js |only rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.tr.min.js | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.zh.min.js | 2 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/rpivotTable.css | 35 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/lib/subtotal |only rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/rpivotTable.js | 69 rpivotTable-0.3.0/rpivotTable/inst/htmlwidgets/rpivotTable.yaml | 33 rpivotTable-0.3.0/rpivotTable/man/change_locale.Rd | 8 rpivotTable-0.3.0/rpivotTable/man/renderRpivotTable.Rd | 2 rpivotTable-0.3.0/rpivotTable/man/rpivotTable.Rd | 40 rpivotTable-0.3.0/rpivotTable/man/rpivotTableOutput.Rd | 2 rpivotTable-0.3.0/rpivotTable/tests/testthat/test_locale.R | 5 rpivotTable-0.3.0/rpivotTable/tests/testthat/test_params.R | 4 rpivotTable-0.3.0/rpivotTable/vignettes/NEWS.Rmd | 14 rpivotTable-0.3.0/rpivotTable/vignettes/rpivotTableIntroduction.Rmd | 25 63 files changed, 1625 insertions(+), 345 deletions(-)
Title: Simple Memory Profiling for R
Description: A simple and light-weight API for memory profiling of R expressions. The profiling is built on top of R's built-in memory profiler ('utils::Rprofmem()'), which records every memory allocation done by R (also native code).
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between profmem versions 0.4.0 dated 2016-09-15 and 0.5.0 dated 2018-01-30
DESCRIPTION | 8 - MD5 | 33 ++-- NAMESPACE | 7 + NEWS | 83 +++++++++++- R/Rprofmem-class.R | 75 ++++++++++- R/profmem.R | 313 ++++++++++++++++++++++++++++++++++++++++++----- R/readRprofmem.R | 55 +++++--- build/vignette.rds |binary inst/doc/profmem.html | 136 ++++++++------------ inst/doc/profmem.md.rsp | 102 +++++++-------- inst/extdata |only man/profmem.Rd | 98 ++++++++++++-- man/readRprofmem.Rd | 7 - man/total.Rd | 3 tests/exceptions.R |only tests/profmem,nested.R |only tests/profmem.R | 30 ++++ tests/readRprofmem.R | 79 ++++++++++- vignettes/profmem.md.rsp | 102 +++++++-------- 19 files changed, 828 insertions(+), 303 deletions(-)
Title: Simulate Temporally Autocorrelated Population Time Series
Description: Temporally autocorrelated populations are correlated in their vital rates (growth, death, etc.) from year to year. It is very common for populations, whether they be bacteria, plants, or humans, to be temporally autocorrelated. This poses a challenge for stochastic population modeling, because a temporally correlated population will behave differently from an uncorrelated one.
This package provides tools for simulating populations with white noise (no temporal autocorrelation), red noise (positive temporal autocorrelation), and blue noise (negative temporal autocorrelation). The algebraic formulation for autocorrelated noise comes from Ruokolainen et al. (2009) <doi:10.1016/j.tree.2009.04.009>. The simulations are based on an assumption of an asexually reproducing population, but it can also be used to simulate females of a sexually reproducing species.
Author: Julia Pilowsky [aut, cre],
Elizabeth Crone [ctb]
Maintainer: Julia Pilowsky <jap2178@caa.columbia.edu>
Diff between colorednoise versions 0.0.1 dated 2017-10-10 and 0.0.2 dated 2018-01-30
DESCRIPTION | 14 - MD5 | 43 ++- NAMESPACE | 2 R/RcppExports.R |only R/raw_noise.R | 31 -- R/simulate_populations.R | 104 --------- R/utils.R | 7 README.md | 5 build/vignette.rds |binary inst/doc/noise.R | 34 +-- inst/doc/noise.Rmd | 38 +-- inst/doc/noise.html | 421 +++++++++++++++++++++++++++++---------- man/autocorr_sim.Rd | 18 - man/autocorrelation.Rd | 8 man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/raw_estim.Rd | 2 man/raw_noise.Rd | 2 man/timeseries.Rd | 48 ++-- src |only tests/testthat/test_timeseries.R | 16 - vignettes/noise.Rmd | 38 +-- 22 files changed, 459 insertions(+), 372 deletions(-)
Title: Insertion Deletion Analysis While Accounting for Possible
Missing Data
Description: Genome-wide gene insertion and deletion rates can be modelled in a maximum
likelihood framework with the additional flexibility of modelling potential missing
data using the models included within. These models simultaneously estimate insertion
and deletion (indel) rates of gene families and proportions of "missing" data for
(multiple) taxa of interest. The likelihood framework is utilized for parameter
estimation. A phylogenetic tree of the taxa and gene presence/absence patterns
(with data ordered by the tips of the tree) are required. See Dang et al.
(2016) <doi:10.1534/genetics.116.191973> for more details.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@binghamton.edu>
Diff between indelmiss versions 1.0.7 dated 2016-08-21 and 1.0.8 dated 2018-01-30
DESCRIPTION | 14 ++---- MD5 | 28 ++++++------ NEWS | 7 +++ R/RcppExports.R | 6 +- R/indel-functions.R | 8 ++- inst/CITATION | 12 +++-- man/indelmiss-package.Rd | 2 man/indelrates.Rd | 105 ++++++++++++++++++++++----------------------- man/plot.indelmiss.Rd | 18 +++---- man/plotp.Rd | 18 +++---- man/plotrates.Rd | 18 +++---- man/plottree.Rd | 20 ++++---- man/print.indelmiss.Rd | 14 +++--- src/RcppExports.cpp | 33 +++++++++----- tests/testthat/test_main.R | 2 15 files changed, 165 insertions(+), 140 deletions(-)
Title: Factor Adjusted Robust Model Selection
Description: Implements a consistent model selection strategy for high dimensional sparse regression when the covariate dependence can be reduced through factor models. By separating the latent factors from idiosyncratic components, the problem is transformed from model selection with highly correlated covariates to that with weakly correlated variables. It is appropriate for cases where we have many variables compared to the number of samples. Moreover, it implements a robust procedure to estimate distribution parameters wherever possible, hence being suitable for cases when the underlying distribution deviates from Gaussianity. See the paper on the 'FarmSelect' method, Fan et al.(2017) <arXiv:1612.08490>, for detailed description of methods and further references.
Author: Koushiki Bose [aut, cre],
Yuan Ke [aut],
Kaizheng Wang [aut]
Maintainer: Koushiki Bose <bose@princeton.edu>
Diff between FarmSelect versions 1.0.0 dated 2018-01-17 and 1.0.1 dated 2018-01-30
FarmSelect-1.0.0/FarmSelect/man/farm.adjust.Rd |only FarmSelect-1.0.0/FarmSelect/man/farm.cov.Rd |only FarmSelect-1.0.0/FarmSelect/man/farm.mean.Rd |only FarmSelect-1.0.1/FarmSelect/DESCRIPTION | 6 FarmSelect-1.0.1/FarmSelect/MD5 | 26 FarmSelect-1.0.1/FarmSelect/NAMESPACE | 4 FarmSelect-1.0.1/FarmSelect/R/RcppExports.R | 20 FarmSelect-1.0.1/FarmSelect/R/main_funcs.R | 359 ++++--- FarmSelect-1.0.1/FarmSelect/inst/doc/FarmSelect-vignette.R | 13 FarmSelect-1.0.1/FarmSelect/inst/doc/FarmSelect-vignette.Rmd | 39 FarmSelect-1.0.1/FarmSelect/inst/doc/FarmSelect-vignette.html | 468 ++++++---- FarmSelect-1.0.1/FarmSelect/man/farm.res.Rd |only FarmSelect-1.0.1/FarmSelect/man/farm.select.Rd | 34 FarmSelect-1.0.1/FarmSelect/src/Cppfunctions.cpp | 80 + FarmSelect-1.0.1/FarmSelect/src/RcppExports.cpp | 73 + FarmSelect-1.0.1/FarmSelect/vignettes/FarmSelect-vignette.Rmd | 39 16 files changed, 773 insertions(+), 388 deletions(-)
Title: Dimension Reduction and Estimation Methods
Description: We provide 111 linear and nonlinear dimension reduction techniques.
Intrinsic dimension estimation methods for exploratory analysis are also provided.
For more details on dimensionality techniques, see the paper by
Ma and Zhu (2013) <doi:10.1111/j.1751-5823.2012.00182.x> if you are interested in
statistical approach, or Engel, Huttenberger, and Hamann (2012)
<doi:10.4230/OASIcs.VLUDS.2011.135> for a broader multi-disciplinary overview.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>
Diff between Rdimtools versions 0.2.0 dated 2018-01-02 and 0.3.0 dated 2018-01-30
DESCRIPTION | 12 MD5 | 232 ++++++++-- NAMESPACE | 62 ++ R/RcppExports.R | 39 + R/auxiliary.R | 153 ++++++- R/estimate_boxcount.R | 3 R/linear_ADR.R |only R/linear_AMMC.R |only R/linear_ANMM.R | 6 R/linear_ASI.R |only R/linear_CNPE.R |only R/linear_CRP.R |only R/linear_DAGDNE.R |only R/linear_DNE.R |only R/linear_DSPP.R | 6 R/linear_ELDE.R |only R/linear_ELPP2.R |only R/linear_ESLPP.R | 4 R/linear_EXTLPP.R | 2 R/linear_FA.R | 2 R/linear_FSCORE.R |only R/linear_ICA.R | 2 R/linear_ISOPROJ.R | 52 +- R/linear_KMVP.R | 7 R/linear_KUDP.R | 12 R/linear_LASSO.R |only R/linear_LDA.R | 10 R/linear_LDAKM.R |only R/linear_LDE.R | 6 R/linear_LDP.R |only R/linear_LEA.R | 5 R/linear_LFDA.R | 7 R/linear_LLTSA.R |only R/linear_LMDS.R | 2 R/linear_LPCA.R |only R/linear_LPE.R |only R/linear_LPFDA.R |only R/linear_LPMIP.R |only R/linear_LPP.R | 139 ++---- R/linear_LQMI.R |only R/linear_LSCORE.R |only R/linear_LSDA.R |only R/linear_LSDF.R |only R/linear_LSIR.R |only R/linear_LSPP.R | 10 R/linear_MCFS.R |only R/linear_MFA.R |only R/linear_MLIE.R |only R/linear_MMC.R | 11 R/linear_MMP.R |only R/linear_MMSD.R |only R/linear_MODP.R |only R/linear_MSD.R |only R/linear_MVP.R | 10 R/linear_NOLPP.R |only R/linear_NONPP.R |only R/linear_NPCA.R |only R/linear_NPE.R | 11 R/linear_ODP.R |only R/linear_OLDA.R |only R/linear_OLPP.R | 7 R/linear_ONPP.R |only R/linear_OPLS.R | 2 R/linear_PFLPP.R |only R/linear_RLDA.R |only R/linear_RSIR.R |only R/linear_SAMMC.R |only R/linear_SAVE.R |only R/linear_SDA.R |only R/linear_SIR.R |only R/linear_SLPE.R |only R/linear_SLPP.R | 4 R/linear_SPP.R | 4 R/linear_SSLDP.R |only R/linear_ULDA.R |only R/nonlinear_CRDA.R | 3 R/nonlinear_DVE.R |only R/nonlinear_ILTSA.R |only R/nonlinear_KLDE.R | 2 R/nonlinear_KLFDA.R | 9 R/nonlinear_KLSDA.R |only R/nonlinear_KMFA.R |only R/nonlinear_KMMC.R | 4 R/nonlinear_KQMI.R |only R/nonlinear_KSDA.R |only R/nonlinear_LAPEIG.R | 34 - R/nonlinear_LLE.R | 50 +- R/nonlinear_LTSA.R | 59 +- R/nonlinear_MVE.R | 38 - R/nonlinear_MVU.R | 7 R/nonlinear_PLP.R | 2 R/nonlinear_SPLAPEIG.R |only R/nonlinear_TSNE.R | 22 - R/oos_LINEAR.R | 2 R/package-Rdimtools.R | 63 ++ build/partial.rdb |binary inst/REFERENCES.bib | 929 +++++++++++++++++++++++++++++++++++++++++++- man/Rdimtools.Rd | 55 ++ man/estimate_boxcount.Rd | 2 man/linear_ADR.Rd |only man/linear_AMMC.Rd |only man/linear_ASI.Rd |only man/linear_CNPE.Rd |only man/linear_CRP.Rd |only man/linear_DAGDNE.Rd |only man/linear_DNE.Rd |only man/linear_ELDE.Rd |only man/linear_ELPP2.Rd |only man/linear_FSCORE.Rd |only man/linear_ISOPROJ.Rd | 5 man/linear_LASSO.Rd |only man/linear_LDA.Rd | 2 man/linear_LDAKM.Rd |only man/linear_LDP.Rd |only man/linear_LLTSA.Rd |only man/linear_LPCA.Rd |only man/linear_LPE.Rd |only man/linear_LPFDA.Rd |only man/linear_LPMIP.Rd |only man/linear_LPP.Rd | 35 - man/linear_LQMI.Rd |only man/linear_LSCORE.Rd |only man/linear_LSDA.Rd |only man/linear_LSDF.Rd |only man/linear_LSIR.Rd |only man/linear_MCFS.Rd |only man/linear_MFA.Rd |only man/linear_MLIE.Rd |only man/linear_MMP.Rd |only man/linear_MMSD.Rd |only man/linear_MODP.Rd |only man/linear_MSD.Rd |only man/linear_NOLPP.Rd |only man/linear_NONPP.Rd |only man/linear_NPCA.Rd |only man/linear_NPE.Rd | 3 man/linear_ODP.Rd |only man/linear_OLDA.Rd |only man/linear_ONPP.Rd |only man/linear_PFLPP.Rd |only man/linear_RSIR.Rd |only man/linear_SAMMC.Rd |only man/linear_SAVE.Rd |only man/linear_SDA.Rd |only man/linear_SIR.Rd |only man/linear_SLPE.Rd |only man/linear_SSLDP.Rd |only man/linear_ULDA.Rd |only man/linear_rlda.Rd |only man/nonlinear_CRDA.Rd | 3 man/nonlinear_DVE.Rd |only man/nonlinear_ILTSA.Rd |only man/nonlinear_KLSDA.Rd |only man/nonlinear_KMFA.Rd |only man/nonlinear_KQMI.Rd |only man/nonlinear_KSDA.Rd |only man/nonlinear_LAPEIG.Rd | 9 man/nonlinear_LLE.Rd | 10 man/nonlinear_LTSA.Rd | 9 man/nonlinear_MVE.Rd | 3 man/nonlinear_MVU.Rd | 7 man/nonlinear_PLP.Rd | 2 man/nonlinear_SPLAPEIG.Rd |only man/nonlinear_TSNE.Rd | 22 - man/oos_LINEAR.Rd | 2 src/RcppExports.cpp | 123 +++++ src/Rdimtools_auxiliary.cpp | 52 ++ src/methods_handytools.cpp |only src/methods_handytools.h |only src/methods_linear.cpp | 195 +++++++-- src/methods_linear.h | 72 ++- 171 files changed, 2138 insertions(+), 519 deletions(-)
Title: Markov Chain Models for Phylogenetic Trees
Description: Allows for fitting of maximum likelihood models using Markov chains
on phylogenetic trees for analysis of discrete character data. Examples of such
discrete character data include restriction sites, gene family presence/absence,
intron presence/absence, and gene family size data. Hypothesis-driven user-
specified substitution rate matrices can be estimated. Allows for biologically
realistic models combining constrained substitution rate matrices, site rate
variation, site partitioning, branch-specific rates, allowing for non-stationary
prior root probabilities, correcting for sampling bias, etc. See Dang and Golding
(2016) <doi:10.1093/bioinformatics/btv541> for more details.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@binghamton.edu>
Diff between markophylo versions 1.0.4 dated 2015-12-31 and 1.0.6 dated 2018-01-30
DESCRIPTION | 13 - MD5 | 34 ++-- NAMESPACE | 1 NEWS | 13 + R/RcppExports.R | 12 - R/custom-general14.R | 14 + R/estimatesrates_f.R |only build/vignette.rds |binary inst/CITATION | 16 - inst/doc/estimaterates.R | 6 inst/doc/estimaterates.Rmd | 14 - inst/doc/estimaterates.html | 366 +++++++++++++++++++++++--------------------- man/estimaterates.Rd | 93 +++++------ man/estimaterates_f.Rd |only man/markophylo-package.Rd | 4 man/patterns.Rd | 6 man/plottree.Rd | 16 - src/RcppExports.cpp | 66 ++++--- vignettes/estimaterates.Rmd | 14 - 19 files changed, 375 insertions(+), 313 deletions(-)
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi, Winston Chang
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 2.0.0 dated 2018-01-28 and 2.0.1 dated 2018-01-30
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NEWS.md | 6 ++++++ src/Makevars | 5 +++-- src/tools/px.dSYM |only tests/testthat/test-utils.R | 5 ++++- 6 files changed, 22 insertions(+), 10 deletions(-)
Title: BMRB Data Access and Visualization
Description: The Biological Magnetic Resonance Data Bank (BMRB,<http://
www.bmrb.wisc.edu/>) collects, annotates, archives, and disseminates (worldwide
in the public domain) the important spectral and quantitative data derived
from NMR(Nuclear Magnetic Resonance) spectroscopic investigations of biological
macromolecules and metabolites. This package provides an interface to BMRB
database for easy data access and includes a minimal set of data visualization
functions. Users are encouraged to make their own data visualizations using BMRB
data.
Author: Kumaran Baskaran
Maintainer: Kumaran Baskaran<kbaskaran@bmrb.wisc.edu>
Diff between RBMRB versions 2.1.0 dated 2017-09-22 and 2.1.2 dated 2018-01-30
DESCRIPTION | 8 ++-- MD5 | 9 ++-- NAMESPACE | 1 R/RBMRB.R | 93 ++++++++++++++++++++++++++++++++++---------------- man/filter_outlier.Rd |only man/filter_residue.Rd | 2 - 6 files changed, 76 insertions(+), 37 deletions(-)
Title: Interface to the 'g:Profiler' Toolkit
Description: Functional enrichment analysis, gene identifier conversion and
mapping homologous genes across related organisms via the 'g:Profiler' toolkit
(<https://biit.cs.ut.ee/gprofiler/>).
Author: Juri Reimand <juri.reimand@ut.ee>, Raivo Kolde
<rkolde@gmail.com>, Tambet Arak <tambet.arak@gmail.com>
Maintainer: Ivan Kuzmin <ivan.kuzmin@ut.ee>
Diff between gProfileR versions 0.6.2 dated 2017-12-19 and 0.6.3 dated 2018-01-30
ChangeLog | 7 DESCRIPTION | 6 MD5 | 12 NAMESPACE | 2 R/gProfileR.R | 1055 +++++++++++++++++++++++++------------------------ man/get_tls_version.Rd |only man/gprofiler.Rd | 10 man/set_tls_version.Rd |only 8 files changed, 579 insertions(+), 513 deletions(-)
Title: Cryptocurrency Market Data
Description: Retrieves all the daily open, high, low and close values for all crypto currencies. This retrieves the historical market data by web scraping tables provided by 'Cryptocurrency Market Capitalizations' <https://coinmarketcap.com>.
Author: Jesse Vent [aut, cre]
Maintainer: Jesse Vent <jesse@solutiondesign.io>
Diff between crypto versions 0.1.0 dated 2018-01-14 and 0.1.1 dated 2018-01-30
DESCRIPTION | 13 ++++++------- MD5 | 12 ++++++------ R/getCoins.R | 25 ++++++++++++++++++------- R/listCoins.R | 17 +++++++++++++---- README.md | 36 +++++++++++++++++++----------------- man/getCoins.Rd | 18 +++++++++++++++--- man/listCoins.Rd | 6 +++++- 7 files changed, 82 insertions(+), 45 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-30 0.6
2015-01-28 0.3
2014-07-24 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-17 1.0
Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension
that allows for the creation of time aware tibbles. Some immediate
advantages of this include: the ability to perform time-based subsetting
on tibbles, quickly summarising and aggregating results by time periods,
and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut]
Maintainer: Davis Vaughan <dvaughan@business-science.io>
Diff between tibbletime versions 0.1.0 dated 2018-01-02 and 0.1.1 dated 2018-01-30
tibbletime-0.1.0/tibbletime/R/ceiling_index.R |only tibbletime-0.1.0/tibbletime/R/floor_index.R |only tibbletime-0.1.1/tibbletime/DESCRIPTION | 11 tibbletime-0.1.1/tibbletime/MD5 | 76 ++-- tibbletime-0.1.1/tibbletime/NAMESPACE | 1 tibbletime-0.1.1/tibbletime/NEWS.md | 33 + tibbletime-0.1.1/tibbletime/R/aaa.R | 2 tibbletime-0.1.1/tibbletime/R/as_period.R | 21 + tibbletime-0.1.1/tibbletime/R/collapse_index.R | 182 ++++++++-- tibbletime-0.1.1/tibbletime/R/compat-dplyr.R | 84 +++- tibbletime-0.1.1/tibbletime/R/compat-tidyr.R | 62 +-- tibbletime-0.1.1/tibbletime/R/create_series.R | 23 + tibbletime-0.1.1/tibbletime/R/filter_time.R | 15 tibbletime-0.1.1/tibbletime/R/getters.R | 8 tibbletime-0.1.1/tibbletime/R/index-based-generics.R | 12 tibbletime-0.1.1/tibbletime/R/parse_period.R | 70 ++- tibbletime-0.1.1/tibbletime/R/parse_time_formula.R | 5 tibbletime-0.1.1/tibbletime/R/partition_index.R | 99 +++-- tibbletime-0.1.1/tibbletime/R/rollify.R | 9 tibbletime-0.1.1/tibbletime/R/round-index.R |only tibbletime-0.1.1/tibbletime/README.md | 10 tibbletime-0.1.1/tibbletime/inst/doc/TT-01-time-based-filtering.html | 6 tibbletime-0.1.1/tibbletime/inst/doc/TT-02-changing-time-periods.html | 72 ++- tibbletime-0.1.1/tibbletime/inst/doc/TT-03-rollify-for-rolling-analysis.html | 36 - tibbletime-0.1.1/tibbletime/inst/doc/TT-04-use-with-dplyr.R | 6 tibbletime-0.1.1/tibbletime/inst/doc/TT-04-use-with-dplyr.Rmd | 17 tibbletime-0.1.1/tibbletime/inst/doc/TT-04-use-with-dplyr.html | 102 ++--- tibbletime-0.1.1/tibbletime/man/as_period.Rd | 30 + tibbletime-0.1.1/tibbletime/man/ceiling_index.Rd | 2 tibbletime-0.1.1/tibbletime/man/collapse_by.Rd |only tibbletime-0.1.1/tibbletime/man/collapse_index.Rd | 23 + tibbletime-0.1.1/tibbletime/man/create_series.Rd | 15 tibbletime-0.1.1/tibbletime/man/filter_time.Rd | 15 tibbletime-0.1.1/tibbletime/man/floor_index.Rd | 2 tibbletime-0.1.1/tibbletime/man/parse_period.Rd | 6 tibbletime-0.1.1/tibbletime/man/partition_index.Rd | 9 tibbletime-0.1.1/tibbletime/man/rollify.Rd | 9 tibbletime-0.1.1/tibbletime/tests/testthat/test_collapse_index.R | 7 tibbletime-0.1.1/tibbletime/tests/testthat/test_parse_period.R | 11 tibbletime-0.1.1/tibbletime/tests/testthat/test_print.R | 2 tibbletime-0.1.1/tibbletime/vignettes/TT-04-use-with-dplyr.Rmd | 17 41 files changed, 760 insertions(+), 350 deletions(-)
Title: The Abnormal Blood Profile Score to Detect Blood Doping
Description: An implementation of the Abnormal Blood Profile Score (ABPS,
part of the Athlete Biological Passport program of the World Anti-Doping
Agency), which combines several blood parameters into a single score in
order to detect blood doping (Sottas et al. (2006)
<doi:10.2202/1557-4679.1011>). The package also contains functions to
calculate other scores used in anti-doping programs, such as the
OFF-score (Gore et al. (2003) <http://www.haematologica.org/content/88/3/333>),
as well as example data.
Author: Frédéric Schütz [aut, cre],
Alix Zollinger [aut]
Maintainer: Frédéric Schütz <schutz@mathgen.ch>
Diff between ABPS versions 0.1 dated 2017-12-19 and 0.2 dated 2018-01-30
DESCRIPTION | 8 +-- MD5 | 19 ++++---- NEWS |only R/ABPS.R | 41 +++++++++-------- R/OFFscore.R | 95 ++++++++++++++++++++++++++++------------- R/data.R | 63 +++++++++++++-------------- man/ABPS.Rd | 28 ++++++------ man/OFFscore.Rd | 59 ++++++++++++++----------- man/bloodcontrol.Rd | 36 +++++++-------- man/blooddoping.Rd | 27 ++++++----- tests/testthat/test_OFFscore.R | 54 ++++++++++++----------- 11 files changed, 240 insertions(+), 190 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 1.9.1 dated 2017-05-21 and 1.9.2 dated 2018-01-30
DESCRIPTION | 23 MD5 | 38 - NAMESPACE | 14 R/Gprop-odds.r | 7 R/cox-aalen.r | 2 R/event.split.r | 2 R/new.aalen.r | 4 R/recurrent.r |only R/sim-pc-hazard.r | 1035 +++++++++++++++++++++++++++++++++++--- R/two-stage-reg.r | 7 man/Gprop.odds.Rd | 7 man/cause.pchazard.sim.Rd |only man/invsubdist.Rd |only man/pc.hazard.Rd | 8 man/recurrent.marginal.coxmean.Rd |only man/recurrent.marginal.mean.Rd |only man/sim.cause.cox.Rd |only man/sim.cif.Rd |only man/sim.cox.Rd | 30 - man/simsubdist.Rd |only src/comprisk.c | 26 src/cox-aalen.c | 55 +- src/mgresid.c | 4 src/timeregister.c | 10 24 files changed, 1107 insertions(+), 165 deletions(-)
Title: Practical Numerical Math Functions
Description: Provides a large number of functions from numerical analysis and
linear algebra, numerical optimization, differential equations,
time series, plus some well-known special mathematical functions.
Uses 'MATLAB' function names where appropriate to simplify porting.
Author: Hans W. Borchers [aut, cre]
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between pracma versions 2.1.1 dated 2017-11-21 and 2.1.4 dated 2018-01-30
pracma-2.1.1/pracma/R/direct1d.R |only pracma-2.1.1/pracma/man/direct1d.Rd |only pracma-2.1.4/pracma/DESCRIPTION | 12 ++++++------ pracma-2.1.4/pracma/MD5 | 22 ++++++++++++---------- pracma-2.1.4/pracma/NEWS | 17 ++++++++++++++++- pracma-2.1.4/pracma/NEWS.md | 15 ++++++++++++++- pracma-2.1.4/pracma/R/anms.R | 2 +- pracma-2.1.4/pracma/R/bsxfun.R | 6 +++++- pracma-2.1.4/pracma/R/findpeaks.R | 2 +- pracma-2.1.4/pracma/R/fminsearch.R | 2 ++ pracma-2.1.4/pracma/R/poisson2disk.R |only pracma-2.1.4/pracma/R/shubert.R |only pracma-2.1.4/pracma/man/bsxfun.Rd | 6 ++++-- pracma-2.1.4/pracma/man/poisson2disk.Rd |only pracma-2.1.4/pracma/man/shubert.Rd |only 15 files changed, 61 insertions(+), 23 deletions(-)
Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs, pairwise comparisons, graphical approaches, assesses variance homogeneity and normality of data in each group via tests and plots.
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between onewaytests versions 1.5 dated 2017-10-11 and 1.6 dated 2018-01-30
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- inst |only man/ag.test.Rd | 2 ++ man/aov.test.Rd | 2 ++ man/bf.test.Rd | 2 ++ man/james.test.Rd | 2 ++ man/kw.test.Rd | 2 ++ man/onewaytests.Rd | 2 +- man/welch.test.Rd | 2 ++ 10 files changed, 27 insertions(+), 14 deletions(-)
Title: Modelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the
mathematical and statistical modelling of toxicity test data. They use advanced and
innovative methods for a valuable quantitative environmental risk assessment.
Author: Virgile Baudrot [aut],
Sandrine Charles [aut],
Marie Laure Delignette-Muller [aut],
Wandrille Duchemin [ctb],
Guillaume Kon-Kam-King [ctb],
Christelle Lopes [ctb],
Philippe Ruiz [aut],
Philippe Veber [aut]
Maintainer: Philippe Veber <philippe.veber@univ-lyon1.fr>
Diff between morse versions 2.2.0 dated 2016-06-13 and 3.0.0 dated 2018-01-30
morse-2.2.0/morse/R/as.survData.R |only morse-2.2.0/morse/R/errorTable.R |only morse-2.2.0/morse/R/plot.survData.R |only morse-2.2.0/morse/R/plotDoseResponse.survData.R |only morse-2.2.0/morse/R/summary.survData.R |only morse-2.2.0/morse/man/as.survData.Rd |only morse-2.2.0/morse/man/plot.survData.Rd |only morse-2.2.0/morse/man/summary.survData.Rd |only morse-2.2.0/morse/vignettes/biblio.bib |only morse-2.2.0/morse/vignettes/clean.sh |only morse-3.0.0/morse/DESCRIPTION | 32 morse-3.0.0/morse/MD5 | 227 +++-- morse-3.0.0/morse/NAMESPACE | 45 - morse-3.0.0/morse/NEWS | 14 morse-3.0.0/morse/R/JAGS_models.R |only morse-3.0.0/morse/R/LCx.R |only morse-3.0.0/morse/R/LCx.survFit.R |only morse-3.0.0/morse/R/modelData.R |only morse-3.0.0/morse/R/modelData.survDataCstExp.R |only morse-3.0.0/morse/R/modelData.survDataVarExp.R |only morse-3.0.0/morse/R/morse-internal.R | 20 morse-3.0.0/morse/R/morse.R | 248 +++-- morse-3.0.0/morse/R/msgTable.R |only morse-3.0.0/morse/R/plot.LCx.R |only morse-3.0.0/morse/R/plot.reproData.R | 37 morse-3.0.0/morse/R/plot.reproFitTT.R | 85 +- morse-3.0.0/morse/R/plot.survDataCstExp.R |only morse-3.0.0/morse/R/plot.survDataVarExp.R |only morse-3.0.0/morse/R/plot.survFitCstExp.R |only morse-3.0.0/morse/R/plot.survFitPredict.R |only morse-3.0.0/morse/R/plot.survFitTKTD.R | 84 - morse-3.0.0/morse/R/plot.survFitTT.R | 61 - morse-3.0.0/morse/R/plot.survFitVarExp.R |only morse-3.0.0/morse/R/plot.survLCxCstExp.R |only morse-3.0.0/morse/R/plotDoseResponse.R | 8 morse-3.0.0/morse/R/plotDoseResponse.reproData.R | 50 - morse-3.0.0/morse/R/plotDoseResponse.survDataCstExp.R |only morse-3.0.0/morse/R/ppc.R | 6 morse-3.0.0/morse/R/ppc.reproFitTT.R | 32 morse-3.0.0/morse/R/ppc.survFitCstExp.R |only morse-3.0.0/morse/R/ppc.survFitTKTD.R | 11 morse-3.0.0/morse/R/ppc.survFitTT.R | 32 morse-3.0.0/morse/R/ppc.survFitVarExp.R |only morse-3.0.0/morse/R/predict.survFit.R |only morse-3.0.0/morse/R/print.reproFitTT.R | 4 morse-3.0.0/morse/R/print.survFitCstExp.R |only morse-3.0.0/morse/R/print.survFitTKTD.R | 6 morse-3.0.0/morse/R/print.survFitTT.R | 4 morse-3.0.0/morse/R/print.survFitVarExp.R |only morse-3.0.0/morse/R/reproData.R | 35 morse-3.0.0/morse/R/reproDataCheck.R | 22 morse-3.0.0/morse/R/reproFitTT.R | 57 - morse-3.0.0/morse/R/summary.reproData.R | 12 morse-3.0.0/morse/R/summary.reproFitTT.R | 18 morse-3.0.0/morse/R/summary.survDataCstExp.R |only morse-3.0.0/morse/R/summary.survDataVarExp.R |only morse-3.0.0/morse/R/summary.survFit.R |only morse-3.0.0/morse/R/summary.survFitTKTD.R | 16 morse-3.0.0/morse/R/summary.survFitTT.R | 18 morse-3.0.0/morse/R/survData.R | 209 ++++ morse-3.0.0/morse/R/survDataCheck.R | 153 ++- morse-3.0.0/morse/R/survFit.R |only morse-3.0.0/morse/R/survFit.survDataCstExp.R |only morse-3.0.0/morse/R/survFit.survDataVarExp.R |only morse-3.0.0/morse/R/survFitTKTD.R | 192 ++-- morse-3.0.0/morse/R/survFitTT.R | 285 ------ morse-3.0.0/morse/R/survFitTT.survDataCstExp.R |only morse-3.0.0/morse/R/survFit_utils.R |only morse-3.0.0/morse/README.md | 5 morse-3.0.0/morse/build/vignette.rds |binary morse-3.0.0/morse/data/cadmium1.rda |binary morse-3.0.0/morse/data/cadmium2.rda |binary morse-3.0.0/morse/data/chlordan.rda |binary morse-3.0.0/morse/data/copper.rda |binary morse-3.0.0/morse/data/dichromate.rda |binary morse-3.0.0/morse/data/propiconazole.rda |binary morse-3.0.0/morse/data/propiconazole_pulse_exposure.rda |only morse-3.0.0/morse/data/zinc.rda |binary morse-3.0.0/morse/inst/doc/modelling.Snw | 427 ++++++---- morse-3.0.0/morse/inst/doc/modelling.pdf |binary morse-3.0.0/morse/inst/doc/tutorial.R | 124 -- morse-3.0.0/morse/inst/doc/tutorial.Rmd | 402 ++++++--- morse-3.0.0/morse/inst/doc/tutorial.html | 679 ++++++++++------ morse-3.0.0/morse/man/LCx.Rd |only morse-3.0.0/morse/man/LCx.survFit.Rd |only morse-3.0.0/morse/man/cadmium1.Rd | 15 morse-3.0.0/morse/man/cadmium2.Rd | 24 morse-3.0.0/morse/man/chlordan.Rd | 11 morse-3.0.0/morse/man/copper.Rd | 11 morse-3.0.0/morse/man/dichromate.Rd | 11 morse-3.0.0/morse/man/is_exposure_constant.Rd |only morse-3.0.0/morse/man/morse-package.Rd | 64 - morse-3.0.0/morse/man/plot.LCx.Rd |only morse-3.0.0/morse/man/plot.reproData.Rd | 27 morse-3.0.0/morse/man/plot.reproFitTT.Rd | 62 - morse-3.0.0/morse/man/plot.survDataCstExp.Rd |only morse-3.0.0/morse/man/plot.survDataVarExp.Rd |only morse-3.0.0/morse/man/plot.survFitCstExp.Rd |only morse-3.0.0/morse/man/plot.survFitPredict.Rd |only morse-3.0.0/morse/man/plot.survFitTKTD.Rd | 36 morse-3.0.0/morse/man/plot.survFitTT.Rd | 36 morse-3.0.0/morse/man/plot.survFitVarExp.Rd |only morse-3.0.0/morse/man/plotDoseResponse.Rd | 9 morse-3.0.0/morse/man/plotDoseResponse.reproData.Rd | 47 - morse-3.0.0/morse/man/plotDoseResponse.survData.Rd | 38 morse-3.0.0/morse/man/ppc.Rd | 7 morse-3.0.0/morse/man/ppc.reproFitTT.Rd | 29 morse-3.0.0/morse/man/ppc.survFitCstExp.Rd |only morse-3.0.0/morse/man/ppc.survFitTKTD.Rd | 7 morse-3.0.0/morse/man/ppc.survFitTT.Rd | 15 morse-3.0.0/morse/man/ppc.survFitVarExp.Rd |only morse-3.0.0/morse/man/predict.survFit.Rd |only morse-3.0.0/morse/man/print.reproFitTT.Rd | 5 morse-3.0.0/morse/man/print.survFitCstExp.Rd |only morse-3.0.0/morse/man/print.survFitTKTD.Rd | 7 morse-3.0.0/morse/man/print.survFitTT.Rd | 5 morse-3.0.0/morse/man/print.survFitVarExp.Rd |only morse-3.0.0/morse/man/priors_survData.Rd |only morse-3.0.0/morse/man/propiconazole.Rd | 21 morse-3.0.0/morse/man/propiconazole_pulse_exposure.Rd |only morse-3.0.0/morse/man/reproData.Rd | 7 morse-3.0.0/morse/man/reproDataCheck.Rd | 9 morse-3.0.0/morse/man/reproFitTT.Rd | 38 morse-3.0.0/morse/man/summary.reproData.Rd | 9 morse-3.0.0/morse/man/summary.reproFitTT.Rd | 15 morse-3.0.0/morse/man/summary.survDataCstExp.Rd |only morse-3.0.0/morse/man/summary.survDataVarExp.Rd |only morse-3.0.0/morse/man/summary.survFit.Rd |only morse-3.0.0/morse/man/summary.survFitTKTD.Rd | 11 morse-3.0.0/morse/man/summary.survFitTT.Rd | 15 morse-3.0.0/morse/man/survData.Rd | 34 morse-3.0.0/morse/man/survDataCheck.Rd | 18 morse-3.0.0/morse/man/survData_join.Rd |only morse-3.0.0/morse/man/survFit.Rd |only morse-3.0.0/morse/man/survFit.survDataCstExp.Rd |only morse-3.0.0/morse/man/survFit.survDataVarExp.Rd |only morse-3.0.0/morse/man/survFitTKTD.Rd | 36 morse-3.0.0/morse/man/survFitTT.Rd | 73 - morse-3.0.0/morse/man/survFitTT.survDataCstExp.Rd |only morse-3.0.0/morse/man/zinc.Rd | 11 morse-3.0.0/morse/tests/testthat/helper-utils.R |only morse-3.0.0/morse/tests/testthat/test-ggplot.R |only morse-3.0.0/morse/tests/testthat/test-modelData.R |only morse-3.0.0/morse/tests/testthat/test-repro.R | 92 -- morse-3.0.0/morse/tests/testthat/test-surv.R | 206 ++-- morse-3.0.0/morse/tests/testthat/test-survFit.R |only morse-3.0.0/morse/vignettes/modelling.Snw | 427 ++++++---- morse-3.0.0/morse/vignettes/tutorial.Rmd | 402 ++++++--- 148 files changed, 3126 insertions(+), 2424 deletions(-)
Title: Maximum Likelihood Estimates of Gaussian Processes
Description: Maximum likelihood Gaussian process modeling for
univariate and multi-dimensional outputs with diagnostic plots.
Contact the maintainer for a package version that implements
sensitivity analysis functionality.
Author: Garrett M. Dancik
Maintainer: Garrett M. Dancik <dancikg@easternct.edu>
Diff between mlegp versions 3.1.4 dated 2013-12-10 and 3.1.5 dated 2018-01-30
mlegp-3.1.4/mlegp/inst/vignettes |only mlegp-3.1.5/mlegp/DESCRIPTION | 8 ++++---- mlegp-3.1.5/mlegp/MD5 | 20 ++++++++++++-------- mlegp-3.1.5/mlegp/NAMESPACE | 13 ++++++++++++- mlegp-3.1.5/mlegp/R/mlegp.R | 12 ++++++++---- mlegp-3.1.5/mlegp/build |only mlegp-3.1.5/mlegp/inst/doc/mlegp.R |only mlegp-3.1.5/mlegp/inst/doc/mlegp.Rnw |only mlegp-3.1.5/mlegp/inst/doc/mlegp.pdf |binary mlegp-3.1.5/mlegp/man/createGP.Rd | 2 +- mlegp-3.1.5/mlegp/man/mlegp.Rd | 11 ++++++----- mlegp-3.1.5/mlegp/src/mlegp_init.c |only mlegp-3.1.5/mlegp/src/nelder_mead_min.c | 4 ++-- mlegp-3.1.5/mlegp/vignettes |only 14 files changed, 45 insertions(+), 25 deletions(-)
Title: Quality Control Charts for 'ggplot'
Description: Plot single and faceted type quality control charts
for 'ggplot'.
Author: Kenith Grey
Maintainer: Kenith Grey <kenithgrey@r-bar.net>
Diff between ggQC versions 0.0.1 dated 2017-03-29 and 0.0.2 dated 2018-01-30
DESCRIPTION | 17 - MD5 | 65 ++++--- NAMESPACE | 3 R/02_QC_FUNs.R | 30 +++ R/02_QC_Violations.R |only R/03_Summay_FUNs.R | 91 +++++++--- R/04_facet_qc_violations.R |only R/04_stat_pareto.r |only R/04_stat_qc.R | 43 ++-- R/04_stat_qc_violations.r |only R/0_QC_Constants.r | 44 +++- build/vignette.rds |binary inst/doc/XbarR_HOTTO.html | 78 ++++---- inst/doc/XmR_HOWTO.html | 62 +++--- man/QC_Violations.Rd |only man/stat_QC.Rd | 26 +- man/stat_QC_labels.Rd | 17 + man/stat_pareto.Rd |only man/stat_qc_violations.Rd |only tests/testthat/Wheeler104_results.csv | 4 tests/testthat/Wheeler105_results.csv | 4 tests/testthat/Wheeler108_results.csv | 10 - tests/testthat/Wheeler49_Result.csv | 4 tests/testthat/Wheeler49_and_WheelerEMP15_Result.csv | 6 tests/testthat/Wheeler91_QC_Result.csv |only tests/testthat/WheelerEMP15_Result.csv | 4 tests/testthat/Wheeler_91_LongForm_QC_Grouping_Violation.csv |only tests/testthat/sxBar_sBar_QC_ylines_results.csv | 4 tests/testthat/testThat_Violation.R |only tests/testthat/test_Indv.r | 18 - tests/testthat/test_Rbar--Rbar_UCL--Rbar_LCL.r | 1 tests/testthat/test_count_and_proportion_data.R | 4 tests/testthat/test_ggplots.R | 4 tests/testthat/test_sBar--sBar_UCL--sBar_LCL.r | 3 tests/testthat/test_xBar_Bar--xBar_rBar_UL_CL--Grouping_FUN.r | 13 + tests/testthat/test_xMedian_rBar_w_limits__xMedian_rMedian_w_limits.R | 2 tests/testthat/wheeler91.csv |only tests/testthat/xMedian_rBar_QC_ylines_results.csv | 6 tests/testthat/xMedian_rMedian_QC_ylines_results.csv | 6 39 files changed, 349 insertions(+), 220 deletions(-)
Title: Produce Descriptive and Comparative Tables Easily
Description: Easily create descriptive and comparative tables.
It makes use and integrates directly with the tidyverse family of packages, and pipes.
Tables are produced as data frames/lists of data frames for easy manipulation after creation,
and ready to be saved as csv, or piped to DT::datatable() or pander::pander() to integrate into reports.
Author: Maxime Wack [aut, cre]
Maintainer: Maxime Wack <maximewack@free.fr>
Diff between desctable versions 0.1.0 dated 2017-05-15 and 0.1.1 dated 2018-01-30
DESCRIPTION | 6 MD5 | 18 R/convenience_functions.R | 3 README.md | 62 - build/vignette.rds |binary inst/doc/desctable.R | 2 inst/doc/desctable.Rmd | 6 inst/doc/desctable.html | 2760 ++++++++++++++++++++++++++++++++++++++++++---- man/fisher.test.Rd | 7 vignettes/desctable.Rmd | 6 10 files changed, 2596 insertions(+), 274 deletions(-)
More information about DataVisualizations at CRAN
Permanent link
Title: White Matter Normalization for Magnetic Resonance Images using
WhiteStripe
Description: Shinohara (2014) <DOI:10.1016/j.nicl.2014.08.008>
introduced 'WhiteStripe', an intensity-based normalization of T1
and T2 images, where normal
appearing white matter performs well, but requires segmentation.
This method performs white matter mean and standard deviation
estimates on data that has been rigidly-registered to the 'MNI'
template and uses histogram-based methods.
Author: R. Taki Shinohara, John Muschelli
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between WhiteStripe versions 2.2.2 dated 2017-03-08 and 2.3.0 dated 2018-01-30
DESCRIPTION | 18 - MD5 | 29 +- NEWS.md |only R/download_img_data.R | 21 +- R/smooth_hist.R | 4 R/t1.voi.R | 6 R/whitestripe_ind.R | 189 ++++++++++-------- build/vignette.rds |binary inst/doc/Running_WhiteStripe.html | 382 +++++++++++++++++++++++++++++--------- man/get.deriv.smooth.hist.Rd | 2 man/smooth_hist.Rd | 2 man/t2.voi.hist.Rd | 6 man/whitestripe.Rd | 25 +- man/whitestripe_hybrid.Rd | 9 man/whitestripe_ind_to_mask.Rd | 12 - man/whitestripe_norm.Rd | 2 16 files changed, 489 insertions(+), 218 deletions(-)
Title: A Bunch of Structure and Sequence Analysis
Description: Reads and plots phylogenetic placements obtained using the 'epa', 'pplacer' and 'guppy' softwares.
Author: Pierre Lefeuvre
Maintainer: Pierre Lefeuvre <pierre.lefeuvre@cirad.fr>
Diff between BoSSA versions 3.0 dated 2017-12-06 and 3.1 dated 2018-01-30
DESCRIPTION | 12 - MD5 | 24 +-- build/partial.rdb |binary inst/doc/bossa-analysis.R | 1 inst/doc/bossa-analysis.Rmd | 22 +- inst/doc/bossa-analysis.html | 269 ++++++++++++++++------------------ inst/doc/bossa-refpkg.R | 1 inst/doc/bossa-refpkg.Rmd | 37 ++-- inst/doc/bossa-refpkg.html | 340 +++++++++++++++++++------------------------ man/read_jplace.Rd | 4 man/read_sqlite.Rd | 2 vignettes/bossa-analysis.Rmd | 22 +- vignettes/bossa-refpkg.Rmd | 37 ++-- 13 files changed, 372 insertions(+), 399 deletions(-)
More information about String2AdjMatrix at CRAN
Permanent link
Title: Extension to 'spatstat' for Local Composite Likelihood
Description: Extension to the 'spatstat' package, enabling the user
to fit point process models to point pattern data
by local composite likelihood ('geographically weighted
regression').
Author: Adrian Baddeley [aut, cre]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.local versions 3.5-6 dated 2017-03-30 and 3.5-7 dated 2018-01-30
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/plot.loccit.Rd | 2 +- man/plot.locmincon.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
More information about spatstat.local at CRAN
Permanent link
Title: Fixed Effects Nonlinear Maximum Likelihood Models
Description: Efficient estimation of multiple fixed-effects maximum likelihood models
with, possibly, non-linear in parameters right hand sides. Standard-errors
can easily be clustered. It also includes tools to seamlessly export (to Latex)
the results of various estimations.
Author: Laurent Berge
Maintainer: Laurent Berge <laurent.berge@uni.lu>
Diff between FENmlm versions 2.0 dated 2018-01-18 and 2.0.1 dated 2018-01-30
FENmlm-2.0.1/FENmlm/DESCRIPTION | 8 - FENmlm-2.0.1/FENmlm/MD5 | 22 ++-- FENmlm-2.0.1/FENmlm/R/ML_Families.R | 110 ++++++++++++++++-------- FENmlm-2.0.1/FENmlm/R/MiscFuns.R | 18 ++- FENmlm-2.0.1/FENmlm/R/femlm.R |only FENmlm-2.0.1/FENmlm/inst/NEWS.Rd | 12 ++ FENmlm-2.0.1/FENmlm/man/FENmlm-package.Rd | 16 ++- FENmlm-2.0.1/FENmlm/man/femlm.Rd | 44 ++++++++- FENmlm-2.0.1/FENmlm/man/res2table.Rd | 4 FENmlm-2.0.1/FENmlm/man/res2tex.Rd | 4 FENmlm-2.0.1/FENmlm/src/RcppExports.cpp | 4 FENmlm-2.0.1/FENmlm/src/Rcpp_get_derivative.cpp | 102 ++++++++++++++-------- FENmlm-2.0/FENmlm/R/feNmlm.R |only 13 files changed, 234 insertions(+), 110 deletions(-)