Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-8 dated 2014-09-21 and 0.3-11 dated 2015-05-29
rgeos-0.3-11/rgeos/ChangeLog | 2165 +++++------- rgeos-0.3-11/rgeos/DESCRIPTION | 14 rgeos-0.3-11/rgeos/MD5 | 62 rgeos-0.3-11/rgeos/NAMESPACE | 1 rgeos-0.3-11/rgeos/R/AAA.R | 5 rgeos-0.3-11/rgeos/R/labelpt.R | 42 rgeos-0.3-11/rgeos/R/over.R | 10 rgeos-0.3-11/rgeos/configure | 94 rgeos-0.3-11/rgeos/configure.ac | 29 rgeos-0.3-11/rgeos/inst/ChangeLog | 2165 +++++------- rgeos-0.3-11/rgeos/inst/README |only rgeos-0.3-11/rgeos/inst/SVN_VERSION | 2 rgeos-0.3-11/rgeos/man/class-SpatialCollections.Rd | 4 rgeos-0.3-11/rgeos/man/comment-functions.Rd | 3 rgeos-0.3-11/rgeos/man/experimental-functions.Rd | 3 rgeos-0.3-11/rgeos/man/labelpt.Rd | 5 rgeos-0.3-11/rgeos/man/pred-binary-gIntersects.Rd | 2 rgeos-0.3-11/rgeos/man/pred-unary-gIsSimple.Rd | 2 rgeos-0.3-11/rgeos/man/pred-unary-gIsValid.Rd | 2 rgeos-0.3-11/rgeos/man/topo-bin-gIntersection.Rd | 5 rgeos-0.3-11/rgeos/man/topo-bin-gUnion.Rd | 4 rgeos-0.3-11/rgeos/man/topo-unary-gDelaunayTriangulation.Rd | 3 rgeos-0.3-11/rgeos/src/init.c | 2 rgeos-0.3-11/rgeos/src/rgeos.c | 4 rgeos-0.3-11/rgeos/src/rgeos.h | 1 rgeos-0.3-11/rgeos/src/rgeos_coord.c | 2 rgeos-0.3-11/rgeos/src/rgeos_geos2R.c | 4 rgeos-0.3-11/rgeos/src/rgeos_poly2nb.c | 2 rgeos-0.3-11/rgeos/src/rgeos_predicate_binary.c | 8 rgeos-0.3-11/rgeos/src/rgeos_topology.c | 6 rgeos-0.3-11/rgeos/src/rgeos_topology_binary.c | 3 rgeos-0.3-11/rgeos/src/rgeos_validate.c | 6 rgeos-0.3-8/rgeos/inst/README.windows |only 33 files changed, 2177 insertions(+), 2483 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol <v.plagnol@ucl.ac.uk>
Diff between ExomeDepth versions 1.1.4 dated 2015-01-23 and 1.1.5 dated 2015-05-29
ExomeDepth-1.1.4/ExomeDepth/inst/doc/ExomeDepth-vignette.R |only ExomeDepth-1.1.4/ExomeDepth/inst/doc/ExomeDepth-vignette.Rnw |only ExomeDepth-1.1.4/ExomeDepth/vignettes/ExomeDepth-vignette.Rnw |only ExomeDepth-1.1.5/ExomeDepth/DESCRIPTION | 8 +-- ExomeDepth-1.1.5/ExomeDepth/MD5 | 23 ++++------ ExomeDepth-1.1.5/ExomeDepth/R/class_definition.R | 22 +++------ ExomeDepth-1.1.5/ExomeDepth/build/vignette.rds |binary ExomeDepth-1.1.5/ExomeDepth/data/Conrad.hg19.RData |binary ExomeDepth-1.1.5/ExomeDepth/data/ExomeCount.RData |binary ExomeDepth-1.1.5/ExomeDepth/data/exons.hg19.RData |binary ExomeDepth-1.1.5/ExomeDepth/data/exons.hg19.X.RData |binary ExomeDepth-1.1.5/ExomeDepth/data/genes.hg19.RData |binary ExomeDepth-1.1.5/ExomeDepth/inst/doc/ExomeDepth-vignette.pdf |binary ExomeDepth-1.1.5/ExomeDepth/vignettes/.install_extras |only ExomeDepth-1.1.5/ExomeDepth/vignettes/ExomeDepth-vignette.R |only ExomeDepth-1.1.5/ExomeDepth/vignettes/ExomeDepth-vignette.pdf |only 16 files changed, 23 insertions(+), 30 deletions(-)
Title: Goodness-of-Fit Tests for the Exponential and Two-Parameter
Weibull Distributions
Description: An implementation of a large number of the goodness-of-fit tests for the exponential and Weibull distributions classified into families: the tests based on the empirical distribution function, the tests based on the probability plot, the tests based on the normalized spacings, the tests based on the Laplace transform and the likelihood-based tests.
Author: Meryam Krit
Maintainer: Meryam Krit <meryam.krit@imag.fr>
Diff between EWGoF versions 2.0 dated 2014-04-08 and 2.1 dated 2015-05-29
EWGoF-2.0/EWGoF/src/Makevars |only EWGoF-2.0/EWGoF/src/Makevars.win |only EWGoF-2.1/EWGoF/DESCRIPTION | 20 ++++++------- EWGoF-2.1/EWGoF/MD5 | 20 ++++++------- EWGoF-2.1/EWGoF/NAMESPACE | 2 - EWGoF-2.1/EWGoF/R/LK.test.R | 30 +++++--------------- EWGoF-2.1/EWGoF/R/MLEst.R | 25 ++++++++++++++++ EWGoF-2.1/EWGoF/R/WLK.test.R | 52 ++++++++++++++++++++++++++--------- EWGoF-2.1/EWGoF/R/WNS.test.R | 2 - EWGoF-2.1/EWGoF/man/EWGoF-package.Rd | 12 ++++---- EWGoF-2.1/EWGoF/man/WLK.test.Rd | 9 +++++- EWGoF-2.1/EWGoF/man/WNS.test.Rd | 2 - 12 files changed, 108 insertions(+), 66 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-20 0.1.0
Title: Read Tabular Data
Description: Read flat/tabular text files from disk.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph]
Maintainer: ORPHANED
Diff between readr versions 0.1.0 dated 2015-04-08 and 0.1.1 dated 2015-05-29
DESCRIPTION | 12 ++++++++---- MD5 | 4 ++-- src/Iconv.h | 16 ++++++---------- 3 files changed, 16 insertions(+), 16 deletions(-)
Title: Easier 'NetCDF' File Handling
Description: Set of tools to simplify the handling of 'NetCDF' files with the 'RNetCDF' package.
Most functions are wrappers of basic functions from the 'RNetCDF' package to easily run combinations of these
functions for frequently encountered tasks.
Author: Jannis v. Buttlar
Maintainer: Jannis v. Buttlar <jbuttlar@bgc-jena.mpg.de>
Diff between ncdf.tools versions 0.7.1.291 dated 2014-04-07 and 0.7.1.295 dated 2015-05-29
DESCRIPTION | 19 +++++---- MD5 | 80 +++++++++++++++++++++-------------------- R/createLatLongTime.R | 2 - R/infoNcdfVars.R | 2 - R/modifyNcdfCopyAtts.R | 4 ++ R/modifyNcdfSetMissing.R | 2 - R/modifyNcdfStdFile.R |only R/transNcdfRotate.R | 47 +++++++++++++++++------- R/transNcdfSubset.R | 73 +++++++++++++++++++------------------ man/aggregateNcdf.Rd | 3 + man/checkNcdfFile.Rd | 3 + man/classR2Ncdf.Rd | 3 + man/closeAllNcfiles.Rd | 1 man/convertBinary2Ncdf.Rd | 3 + man/convertDateNcdf2R.Rd | 3 + man/convertDateR2Ncdf.Rd | 3 + man/convertFilename2Date.Rd | 3 + man/createLatLongTime.Rd | 3 + man/createStdNcdfFile.Rd | 3 + man/indexDatacube.Rd | 4 +- man/infoNcdfAtts.Rd | 3 + man/infoNcdfDims.Rd | 3 + man/infoNcdfVars.Rd | 3 + man/modifyNcdfAddDim.Rd | 3 + man/modifyNcdfAppendHistory.Rd | 3 + man/modifyNcdfCopyAtts.Rd | 4 +- man/modifyNcdfCopyMetadata.Rd | 3 + man/modifyNcdfCopyVar.Rd | 3 + man/modifyNcdfDefAtts.Rd | 3 + man/modifyNcdfSetMissing.Rd | 5 +- man/modifyNcdfStdFile.Rd |only man/modifyNcdfStdNames.Rd | 3 + man/ncdf.tools-package.Rd | 12 +++--- man/plotDatacube.Rd | 3 + man/readFLUXNETNcdf.Rd | 3 + man/readNcdf.Rd | 3 + man/readNcdfCoordinates.Rd | 3 + man/readNcdfVarName.Rd | 3 + man/transNcdfCutFiles.Rd | 3 + man/transNcdfMerge.Rd | 3 + man/transNcdfRotate.Rd | 9 +++- man/transNcdfSubset.Rd | 15 ++++--- 42 files changed, 212 insertions(+), 142 deletions(-)
Title: A Parallel-Voting Version of the Support-Vector-Machine
Algorithm
Description: By sampling your data, running the Support-Vector-Machine algorithm on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular Support-Vector-Machine and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>
Diff between parallelSVM versions 0.1-5 dated 2015-05-29 and 0.1-6 dated 2015-05-29
DESCRIPTION | 11 ++++++----- MD5 | 8 +++++--- data |only man/parallelSVM-package.Rd | 8 ++++---- man/parallelSVM.Rd | 6 +++--- 5 files changed, 18 insertions(+), 15 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.3.0 dated 2015-04-30 and 4.4.0 dated 2015-05-29
DESCRIPTION | 8 MD5 | 94 NAMESPACE | 1 NEWS | 45 R/check.index.R | 12 R/earth.R | 879 +++-- R/earth.cv.R | 195 - R/earth.methods.R | 3 R/elegend.R | 4 R/evimp.R | 7 R/lib.R | 8 R/mars.to.earth.R | 5 R/model.matrix.earth.R | 18 R/plot.earth.R | 232 + R/plotd.R | 3 R/print.earth.R | 151 inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/make.bat | 4 inst/slowtests/test.big.R | 130 inst/slowtests/test.big.Rout.save | 413 +- inst/slowtests/test.cv.R | 8 inst/slowtests/test.cv.Rout.save | 2358 ++++++-------- inst/slowtests/test.earthc.bat | 32 inst/slowtests/test.earthc.c | 9 inst/slowtests/test.earthc.mak | 8 inst/slowtests/test.earthc.out.save | 2852 +++++++++-------- inst/slowtests/test.earthmain.out.save | 12 inst/slowtests/test.full.R | 22 inst/slowtests/test.full.Rout.save | 3485 ++++++++++----------- inst/slowtests/test.glm.Rout.save | 4958 +++++++++++++++--------------- inst/slowtests/test.incorrect.R |only inst/slowtests/test.incorrect.Rout.save |only inst/slowtests/test.incorrect.bat |only inst/slowtests/test.mods.R | 683 +++- inst/slowtests/test.mods.Rout.save | 945 +++-- inst/slowtests/test.mods.bat | 8 inst/slowtests/test.pmethod.cv.R |only inst/slowtests/test.pmethod.cv.Rout.save |only inst/slowtests/test.pmethod.cv.bat |only inst/slowtests/test.varmod.Rout.save | 1665 +++++----- inst/slowtests/test.varmod.mgcv.Rout.save | 160 inst/slowtests/test.weights.R | 174 + inst/slowtests/test.weights.Rout.save | 300 + man/earth.Rd | 232 - man/plot.earth.Rd | 16 man/plot.earth.models.Rd | 2 man/update.earth.Rd | 3 src/earth.c | 1440 ++++---- src/earth.h | 105 src/leaps.f | 8 51 files changed, 11758 insertions(+), 9939 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-29 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-16 2.0.7
2012-03-29 2.0.5
2012-03-22 2.0.1
2009-07-18 1.9.4
2009-03-22 1.9.3
2009-02-28 1.9.2
2008-09-05 1.8.1
2008-04-24 1.7.7
2008-04-14 1.7.6
2006-12-12 1.6.5
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph],
Simon Blomberg [aut, cph],
Ben Bolker [aut, cph],
Julien Claude [aut, cph],
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph],
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph],
Olivier Gascuel [aut, cph],
Christoph Heibl [aut, cph],
Anthony Ives [aut, cph],
Daniel Lawson [aut, cph],
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph],
Jim Lemon [aut, cph],
Rosemary McCloskey [aut, cph],
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph],
Korbinian Strimmer [aut, cph],
Damien de Vienne [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 3.2 dated 2014-12-05 and 3.3 dated 2015-05-29
DESCRIPTION | 14 ++- MD5 | 98 ++++++++++++------------ NAMESPACE | 5 + R/CDF.birth.death.R | 174 ++++++++++++++++++++++++++++++++++++++++++-- R/DNA.R | 29 ++++--- R/PGLS.R | 7 - R/ace.R | 14 ++- R/as.bitsplits.R | 10 ++ R/as.phylo.R | 7 - R/binaryPGLMM.R |only R/compar.gee.R | 7 + R/corphylo.R |only R/dbd.R | 9 +- R/dist.topo.R | 72 +++++++++++------- R/parafit.R | 6 - R/plot.phylo.R | 38 ++++----- R/read.tree.R | 8 +- R/root.R | 8 +- R/write.nexus.R | 15 +-- R/write.nexus.data.R | 6 - build/vignette.rds |binary data/hivtree.newick.rda |binary data/landplants.newick.rda |binary data/opsin.newick.rda |binary inst/doc/MoranI.pdf |binary man/DNAbin.Rd | 2 man/LTT.Rd | 6 + man/MoranI.Rd | 4 - man/ace.Rd | 14 ++- man/as.bitsplits.Rd | 8 +- man/binaryPGLMM.Rd |only man/boot.phylo.Rd | 3 man/coalescent.intervals.Rd | 7 - man/collapsed.intervals.Rd | 13 --- man/corphylo.Rd |only man/def.Rd | 2 man/del.gaps.Rd | 32 ++++---- man/dist.topo.Rd | 18 ++-- man/is.binary.tree.Rd | 2 man/landplants.Rd | 3 man/node.depth.Rd | 10 -- man/read.dna.Rd | 6 - man/read.tree.Rd | 2 man/rlineage.Rd | 53 ++++++++++--- man/root.Rd | 11 ++ man/seg.sites.Rd | 5 - man/skyline.Rd | 42 ++-------- man/skylineplot.Rd | 34 ++------ man/where.Rd | 3 man/woodmouse.Rd | 3 man/write.dna.Rd | 6 - src/dist_dna.c | 24 ++---- 52 files changed, 513 insertions(+), 327 deletions(-)
Title: Tools for ABC Analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage.
Author: Matt Nunes [aut, cre],
Dennis Prangle [aut]
Maintainer: Matt Nunes <m.nunes@lancaster.ac.uk>
Diff between abctools versions 1.0 dated 2014-12-16 and 1.0.2 dated 2015-05-29
DESCRIPTION | 18 ++++++++++-------- MD5 | 14 +++++++------- R/semiauto.abc.R | 4 ++-- data/coal.rda |binary data/coalobs.rda |binary man/abctools-package.Rd | 11 ++++++----- man/cov.pi.Rd | 5 +++-- man/mc.ci.Rd | 5 +++-- 8 files changed, 31 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-22 1.1.1
2014-11-07 0.2.0
Title: Various R Programming Tools
Description: Functions to assist in R programming, including:
- assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
'getDependencies', 'keywords', 'scat'),
- calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
- test if a value is missing, empty or contains only NA and NULL values ('invalid'),
- manipulate R's .Last function ('addLast'),
- define macros ('defmacro'),
- detect odd and even integers ('odd', 'even'),
- convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
- perform a binary search ('binsearch'),
- sort strings containing both numeric and character components ('mixedsort'),
- create a factor variable from the quantiles of a continuous variable ('quantcut'),
- enumerate permutations and combinations ('combinations', 'permutation'),
- calculate and convert between fold-change and log-ratio ('foldchange',
'logratio2foldchange', 'foldchange2logratio'),
- calculate probabilities and generate random numbers from Dirichlet distributions
('rdirichlet', 'ddirichlet'),
- apply a function over adjacent subsets of a vector ('running'),
- modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
- efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
- generate significance stars from p-values ('stars.pval'),
- convert characters to/from ASCII codes.
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gtools versions 3.4.2 dated 2015-04-10 and 3.5.0 dated 2015-05-29
ChangeLog | 796 ++++++++++++++++++++----------------------- DESCRIPTION | 35 + MD5 | 42 +- NAMESPACE | 10 NEWS | 47 ++ R/asc.R |only R/checkReverseDependencies.R |only R/dirichlet.R | 6 R/keywords.R | 11 R/mixedsort.R | 98 +++-- R/quantcut.R | 7 R/roman2int.R |only R/smartbind.R | 1 R/strmacro.R | 23 - R/trimws.R |only R/unByteCode.R |only data/ELISA.rda |binary inst/ChangeLog | 796 ++++++++++++++++++++----------------------- inst/NEWS | 47 ++ man/ASCIIfy.Rd | 3 man/asc.Rd |only man/mixedsort.Rd | 91 +++- man/quantcut.Rd | 26 - man/roman2int.Rd |only man/unByteCode.Rd |only src/roman2int.c |only tests/test_ddirichlet.R |only 27 files changed, 1082 insertions(+), 957 deletions(-)
Title: Modified Variance Estimators for Generalized Estimating
Equations
Description: Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.
Author: Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Diff between geesmv versions 1.0 dated 2014-11-04 and 1.1 dated 2015-05-29
DESCRIPTION | 6 - MD5 | 22 ++-- R/GEE.var.fg.R | 288 ++++++++++++++++++++++++++++---------------------------- R/GEE.var.gst.R | 22 ++-- R/GEE.var.kc.R | 18 +-- R/GEE.var.lz.R | 14 +- R/GEE.var.mbn.R | 39 ++++--- R/GEE.var.md.R | 18 +-- R/GEE.var.mk.R | 14 +- R/GEE.var.pan.R | 21 ++-- R/GEE.var.wl.R | 39 ++++--- man/geesmv.Rd | 2 12 files changed, 268 insertions(+), 235 deletions(-)
Title: Functional Data Analysis: K-Mean Alignment
Description: It performs simultaneously clustering and alignment of a multidimensional or unidimensional functional dataset by means of k-mean alignment.
Author: Alice Parodi, Mirco Patriarca, Laura Sangalli, Piercesare Secchi, Simone Vantini, Valeria Vitelli
Maintainer: Alice Parodi <alicecarla.parodi@polimi.it>
Diff between fdakma versions 1.2 dated 2015-03-12 and 1.2.1 dated 2015-05-29
DESCRIPTION | 10 MD5 | 6 R/kma.R | 1202 ++++++++++++++++++++++++----------------------------- R/kma.similarity.R | 57 +- 4 files changed, 591 insertions(+), 684 deletions(-)
Title: Explorer of World Population Prospects
Description: A shiny interface for exploring data in the 'wpp2012' (or 2010, 2008) package.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wppExplorer versions 1.6-1 dated 2015-04-11 and 1.6-2 dated 2015-05-29
ChangeLog | 6 +++++- DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/explore/server.R | 13 ++++++------- man/wppExplorer-package.Rd | 4 ++-- 5 files changed, 21 insertions(+), 18 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of several plotting and table output functions for visualizing data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.8 dated 2015-04-22 and 1.8.1 dated 2015-05-29
sjPlot-1.8.1/sjPlot/DESCRIPTION | 13 sjPlot-1.8.1/sjPlot/MD5 | 159 - sjPlot-1.8.1/sjPlot/NAMESPACE | 3 sjPlot-1.8.1/sjPlot/NEWS | 29 sjPlot-1.8.1/sjPlot/R/helpfunctions.R | 113 sjPlot-1.8.1/sjPlot/R/sjPlotAncovaLSMeans.R | 1255 ++++---- sjPlot-1.8.1/sjPlot/R/sjPlotAnova.R | 201 - sjPlot-1.8.1/sjPlot/R/sjPlotClusterAnalysis.R | 200 - sjPlot-1.8.1/sjPlot/R/sjPlotCorr.R | 725 ++-- sjPlot-1.8.1/sjPlot/R/sjPlotDist.R | 8 sjPlot-1.8.1/sjPlot/R/sjPlotFrequencies.R | 1794 ++++++------ sjPlot-1.8.1/sjPlot/R/sjPlotGLME.R | 3683 ++++++++++++------------- sjPlot-1.8.1/sjPlot/R/sjPlotGroupFrequencies.R | 13 sjPlot-1.8.1/sjPlot/R/sjPlotInteractions.R | 2718 +++++++++--------- sjPlot-1.8.1/sjPlot/R/sjPlotLikert.R | 65 sjPlot-1.8.1/sjPlot/R/sjPlotLinreg.R | 454 +-- sjPlot-1.8.1/sjPlot/R/sjPlotLinregMultiple.R | 26 sjPlot-1.8.1/sjPlot/R/sjPlotOdds.R | 1655 +++++------ sjPlot-1.8.1/sjPlot/R/sjPlotOddsMultiple.R | 848 ++--- sjPlot-1.8.1/sjPlot/R/sjPlotPCA.R | 934 +++--- sjPlot-1.8.1/sjPlot/R/sjPlotPropTable.R | 1388 ++++----- sjPlot-1.8.1/sjPlot/R/sjPlotScatter.R | 38 sjPlot-1.8.1/sjPlot/R/sjPlotSetTheme.R | 1675 +++++------ sjPlot-1.8.1/sjPlot/R/sjPlotStackFrequencies.R | 37 sjPlot-1.8.1/sjPlot/R/sjTabCorr.R | 1058 +++---- sjPlot-1.8.1/sjPlot/R/sjTabDataFrame.R | 786 ++--- sjPlot-1.8.1/sjPlot/R/sjTabFrequencies.R | 341 +- sjPlot-1.8.1/sjPlot/R/sjTabGrpmean.R | 408 +- sjPlot-1.8.1/sjPlot/R/sjTabItemAnalysis.R | 867 ++--- sjPlot-1.8.1/sjPlot/R/sjTabLinReg.R | 669 +++- sjPlot-1.8.1/sjPlot/R/sjTabMannWhitney.R | 214 - sjPlot-1.8.1/sjPlot/R/sjTabOdds.R | 957 ++++-- sjPlot-1.8.1/sjPlot/R/sjTabPCA.R | 1224 ++++---- sjPlot-1.8.1/sjPlot/R/sjTabPropTable.R | 35 sjPlot-1.8.1/sjPlot/R/sjTabSPSS.R | 655 ++-- sjPlot-1.8.1/sjPlot/R/sjTabStackFrq.R | 1097 +++---- sjPlot-1.8.1/sjPlot/R/zzz.R | 4 sjPlot-1.8.1/sjPlot/README.md | 65 sjPlot-1.8.1/sjPlot/man/adjust_plot_range.Rd | 2 sjPlot-1.8.1/sjPlot/man/dist_chisq.Rd | 4 sjPlot-1.8.1/sjPlot/man/dist_f.Rd | 4 sjPlot-1.8.1/sjPlot/man/dist_norm.Rd | 4 sjPlot-1.8.1/sjPlot/man/dist_t.Rd | 4 sjPlot-1.8.1/sjPlot/man/sjPlot-package.Rd | 103 sjPlot-1.8.1/sjPlot/man/sjc.qclus.Rd | 21 sjPlot-1.8.1/sjPlot/man/sjp.aov1.Rd | 6 sjPlot-1.8.1/sjPlot/man/sjp.chi2.Rd | 122 sjPlot-1.8.1/sjPlot/man/sjp.corr.Rd | 57 sjPlot-1.8.1/sjPlot/man/sjp.frq.Rd | 607 ++-- sjPlot-1.8.1/sjPlot/man/sjp.glm.Rd | 122 sjPlot-1.8.1/sjPlot/man/sjp.glmer.Rd | 437 +- sjPlot-1.8.1/sjPlot/man/sjp.glmm.Rd | 24 sjPlot-1.8.1/sjPlot/man/sjp.grpfrq.Rd | 15 sjPlot-1.8.1/sjPlot/man/sjp.int.Rd | 766 ++--- sjPlot-1.8.1/sjPlot/man/sjp.likert.Rd | 48 sjPlot-1.8.1/sjPlot/man/sjp.lm.Rd | 63 sjPlot-1.8.1/sjPlot/man/sjp.lmer.Rd | 410 +- sjPlot-1.8.1/sjPlot/man/sjp.lmm.Rd | 20 sjPlot-1.8.1/sjPlot/man/sjp.pca.Rd | 5 sjPlot-1.8.1/sjPlot/man/sjp.scatter.Rd | 38 sjPlot-1.8.1/sjPlot/man/sjp.setTheme.Rd | 22 sjPlot-1.8.1/sjPlot/man/sjp.stackfrq.Rd | 19 sjPlot-1.8.1/sjPlot/man/sjp.xtab.Rd | 21 sjPlot-1.8.1/sjPlot/man/sjt.corr.Rd | 368 +- sjPlot-1.8.1/sjPlot/man/sjt.df.Rd | 310 +- sjPlot-1.8.1/sjPlot/man/sjt.frq.Rd | 476 +-- sjPlot-1.8.1/sjPlot/man/sjt.glm.Rd | 658 ++-- sjPlot-1.8.1/sjPlot/man/sjt.glmer.Rd |only sjPlot-1.8.1/sjPlot/man/sjt.grpmean.Rd | 30 sjPlot-1.8.1/sjPlot/man/sjt.itemanalysis.Rd | 380 +- sjPlot-1.8.1/sjPlot/man/sjt.lm.Rd | 812 ++--- sjPlot-1.8.1/sjPlot/man/sjt.lmer.Rd |only sjPlot-1.8.1/sjPlot/man/sjt.mwu.Rd | 22 sjPlot-1.8.1/sjPlot/man/sjt.pca.Rd | 381 +- sjPlot-1.8.1/sjPlot/man/sjt.stackfrq.Rd | 425 +- sjPlot-1.8.1/sjPlot/man/sjt.xtab.Rd | 444 +-- sjPlot-1.8.1/sjPlot/man/view_spss.Rd | 247 - sjPlot-1.8/sjPlot/man/sj.setGeomColors.Rd |only sjPlot-1.8/sjPlot/man/sjp.emm.int.Rd |only sjPlot-1.8/sjPlot/tests |only 80 files changed, 17485 insertions(+), 16426 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny
applications without having to know any JavaScript. Examples include hiding an
element, disabling an input, resetting an input back to its original value,
and many more useful functions. Even if you do know JavaScript,
shinyjs can be used as convenience functions to avoid dealing with message
passing and writing JavaScript code. shinyjs can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.0.6.0 dated 2015-05-26 and 0.0.6.2 dated 2015-05-29
DESCRIPTION | 6 +- MD5 | 23 +++++----- R/extendShinyjs.R | 80 ++++++++++++++++++++++++++++++------ R/useShinyjs.R | 2 R/utils.R | 28 ++++++++++-- README.md | 65 ++++++++++++++++++++--------- inst/doc/overview.Rmd | 64 +++++++++++++++++++++------- inst/doc/overview.html | 47 ++++++++++++++------- man/extendShinyjs.Rd | 41 +++++++++++++++++- man/js.Rd | 2 tests/test-empty.js |only tests/testthat/test-extendShinyjs.R | 37 ++++++++++++++-- vignettes/overview.Rmd | 64 +++++++++++++++++++++------- 13 files changed, 352 insertions(+), 107 deletions(-)
Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological
Database using the published API (http://api.neotomadb.org/). The functions
in this package access various pre-built API functions and attempt to return
the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb],
Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>
Diff between neotoma versions 1.2-0 dated 2015-05-03 and 1.3.0 dated 2015-05-29
DESCRIPTION | 6 - MD5 | 21 +++--- NAMESPACE | 3 NEWS | 4 + R/get_chroncontrol.R | 116 ++++++++++++++++++++++++++-------- R/write_agefile.R | 2 README.md | 22 ++++-- inst/img/histogramplot.png |binary man/get_chroncontrol.Rd | 10 ++ man/get_chroncontrol.default.Rd |only man/get_chroncontrol.download.Rd |only man/get_chroncontrol.download_list.Rd |only tests/testthat/test_neotoma.R | 15 ++++ 13 files changed, 152 insertions(+), 47 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data. Including multivariate cumulative incidence models, and
bivariate random effects probit models (Liability models). Also contains
two-stage binomial modelling that can do pairwise odds-ratio dependence
modelling based marginal logistic regression models. This is an alternative
to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.1.0 dated 2015-02-16 and 1.1.1 dated 2015-05-29
mets-1.1.0/mets/man/survpois.Rd |only mets-1.1.1/mets/DESCRIPTION | 10 mets-1.1.1/mets/MD5 | 88 +++--- mets-1.1.1/mets/NAMESPACE | 8 mets-1.1.1/mets/NEWS | 14 - mets-1.1.1/mets/R/bicomprisk.R | 80 ++++- mets-1.1.1/mets/R/bicomprisksim.R | 153 +++++------ mets-1.1.1/mets/R/binomial.twostage.R | 2 mets-1.1.1/mets/R/biprobit.R | 8 mets-1.1.1/mets/R/biprobit.time.R | 140 +++++++++- mets-1.1.1/mets/R/casewise.R | 4 mets-1.1.1/mets/R/clusterindex-reshape.R | 4 mets-1.1.1/mets/R/cor.R | 361 +++++++++++++++----------- mets-1.1.1/mets/R/divide.conquer.R | 10 mets-1.1.1/mets/R/exmarg.R |only mets-1.1.1/mets/R/ipw.R | 297 +++++++++++++++++++-- mets-1.1.1/mets/R/lifetable.R | 254 ++++++++++++++---- mets-1.1.1/mets/R/methodstwinlm.R | 2 mets-1.1.1/mets/R/mets-package.R | 4 mets-1.1.1/mets/R/plot.bptwin.R | 19 + mets-1.1.1/mets/R/procformula.R | 1 mets-1.1.1/mets/R/sim-nordic-twin.R | 305 +++++++++++++++++++-- mets-1.1.1/mets/R/twinlm.R | 10 mets-1.1.1/mets/R/twostage.R | 2 mets-1.1.1/mets/R/utils.R | 136 --------- mets-1.1.1/mets/man/Grandom.cif.Rd | 98 +++---- mets-1.1.1/mets/man/bicomprisk.Rd | 54 +++ mets-1.1.1/mets/man/biprobit.Rd | 6 mets-1.1.1/mets/man/casewise.Rd | 2 mets-1.1.1/mets/man/casewise.test.Rd | 2 mets-1.1.1/mets/man/concordance.Rd | 2 mets-1.1.1/mets/man/cor.cif.Rd | 10 mets-1.1.1/mets/man/divide.conquer.Rd | 2 mets-1.1.1/mets/man/divide.conquer.timereg.Rd | 7 mets-1.1.1/mets/man/easy.binomial.twostage.Rd | 2 mets-1.1.1/mets/man/eventpois.Rd |only mets-1.1.1/mets/man/internal.Rd | 2 mets-1.1.1/mets/man/ipw.Rd | 5 mets-1.1.1/mets/man/ipw2.Rd |only mets-1.1.1/mets/man/random.cif.Rd | 55 +-- mets-1.1.1/mets/man/summary.cor.Rd | 12 mets-1.1.1/mets/man/twinlm.Rd | 2 mets-1.1.1/mets/man/twostage.Rd | 2 mets-1.1.1/mets/src/cor.cpp | 49 ++- mets-1.1.1/mets/src/mvn.cpp | 49 +++ mets-1.1.1/mets/src/plackettMLE.cpp | 2 mets-1.1.1/mets/src/tools.cpp | 66 +++- 47 files changed, 1623 insertions(+), 718 deletions(-)
Title: Longitudinal Targeted Maximum Likelihood Estimation
Description: Targeted Maximum Likelihood Estimation (TMLE) of
treatment/censoring specific mean outcome or marginal structural model for
point-treatment and longitudinal data.
Author: Joshua Schwab [aut, cre],
Samuel Lendle [aut],
Maya Petersen [aut],
Mark van der Laan [aut],
Susan Gruber [ctb]
Maintainer: Joshua Schwab <joshuaschwab@yahoo.com>
Diff between ltmle versions 0.9-5 dated 2015-05-07 and 0.9-6 dated 2015-05-29
DESCRIPTION | 10 ++-- MD5 | 34 +++++++------ NAMESPACE | 2 NEWS | 9 +++ R/GeneralUtilities.R | 14 +++++ R/ltmle.R | 87 ++++++++++++++++++++--------------- R/zzz.R | 6 -- data/PreviousReleaseTests.RData |binary data/datalist |only man/ltmle.rd | 4 - tests/testthat/test-(init).R |only tests/testthat/test-BaselineCovMSM.R | 14 ++--- tests/testthat/test-CheckInputs.R | 37 ++++++-------- tests/testthat/test-CleanData.R | 2 tests/testthat/test-GetDefaultForm.R | 2 tests/testthat/test-Weights.R | 5 -- tests/testthat/test-prevRelease.R | 6 ++ tests/testthat/test-random.R | 2 tests/testthat/test-summary.ltmle.R | 24 ++++++++- 19 files changed, 157 insertions(+), 101 deletions(-)
Title: Estimate Number of Latent Factors and Factor Matrix for Factor
Analysis
Description: These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (http://arxiv.org/abs/1503.03515).
Author: Art B. Owen [aut],
Jingshu Wang [aut, cre]
Maintainer: Jingshu Wang <wangjingshususan@gmail.com>
Diff between esaBcv versions 1.1.1 dated 2015-04-11 and 1.2.1 dated 2015-05-29
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/ESA_BCV.R | 4 ++-- man/ESA.Rd | 2 +- man/EsaBcv.Rd | 2 +- man/esaBcv_package.Rd | 2 +- man/plot.esabcv.Rd | 2 +- man/simdat.Rd | 2 +- 9 files changed, 19 insertions(+), 19 deletions(-)
Title: Compute Statistics Helper Functions
Description: A small package containing helper utilities for creating function
for computing statistics.
Author: Andrew Redd <Andrew.Redd@hsc.utah.edu>
Maintainer: Andrew Redd <Andrew.Redd@hsc.utah.edu>
Diff between dostats versions 1.3.1 dated 2014-05-28 and 1.3.2 dated 2015-05-29
dostats-1.3.1/dostats/R/formula.R |only dostats-1.3.1/dostats/R/hdf.R |only dostats-1.3.1/dostats/inst/tests |only dostats-1.3.1/dostats/man/Table1.Rd |only dostats-1.3.1/dostats/man/hdf.Rd |only dostats-1.3.1/dostats/man/internal.Rd |only dostats-1.3.2/dostats/DESCRIPTION | 13 - dostats-1.3.2/dostats/MD5 | 79 ++++---- dostats-1.3.2/dostats/NAMESPACE | 82 +++----- dostats-1.3.2/dostats/NEWS | 68 +++---- dostats-1.3.2/dostats/R/T.R | 8 dostats-1.3.2/dostats/R/capply.R | 28 +-- dostats-1.3.2/dostats/R/collect.R | 108 +++++------ dostats-1.3.2/dostats/R/onarg.R | 128 ++++++------- dostats-1.3.2/dostats/R/pval.R | 166 ++++++++--------- dostats-1.3.2/dostats/R/utils.R | 222 +++++++++++++----------- dostats-1.3.2/dostats/R/wargs.R | 164 ++++++++--------- dostats-1.3.2/dostats/README.md | 34 +-- dostats-1.3.2/dostats/inst/ex_dostats.R | 8 dostats-1.3.2/dostats/man/T.Rd | 35 +-- dostats-1.3.2/dostats/man/capply.Rd | 41 ++-- dostats-1.3.2/dostats/man/class.stats.Rd | 69 +++---- dostats-1.3.2/dostats/man/collect.Rd | 59 +++--- dostats-1.3.2/dostats/man/compose.Rd | 105 +++++------ dostats-1.3.2/dostats/man/contains.Rd | 55 +++-- dostats-1.3.2/dostats/man/dostats.Rd | 71 +++---- dostats-1.3.2/dostats/man/fill_v.Rd | 41 ++-- dostats-1.3.2/dostats/man/head-tail-utils.Rd.Rd |only dostats-1.3.2/dostats/man/listrows.Rd | 29 +-- dostats-1.3.2/dostats/man/make_call.Rd | 51 ++--- dostats-1.3.2/dostats/man/make_new_id.Rd | 29 +-- dostats-1.3.2/dostats/man/me.Rd | 29 +-- dostats-1.3.2/dostats/man/onarg.Rd | 59 +++--- dostats-1.3.2/dostats/man/pval.Rd | 57 +++--- dostats-1.3.2/dostats/man/redirf.Rd | 35 +-- dostats-1.3.2/dostats/man/seq_consecutive.Rd | 41 ++-- dostats-1.3.2/dostats/man/wargs.Rd | 59 +++--- dostats-1.3.2/dostats/tests/test_package.R | 6 dostats-1.3.2/dostats/tests/testthat |only 39 files changed, 997 insertions(+), 982 deletions(-)
Title: Community Assembly by Traits: Individuals and Beyond
Description: Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models.
Author: Adrien Taudiere, Cyrille Violle with contribution by Francois Munoz
Maintainer: Adrien Taudiere <adrien.taudiere@cefe.cnrs.fr>
Diff between cati versions 0.96 dated 2015-02-13 and 0.99 dated 2015-05-29
DESCRIPTION | 14 - MD5 | 66 ++--- NAMESPACE | 66 ++--- R/allfunctions_cati.r | 3 inst/CITATION | 24 + man/AbToInd.Rd | 88 +++---- man/Auxiliary.functions.rd | 68 ++--- man/CVNND.Rd | 196 ++++++++-------- man/ComIndex.Rd | 474 +++++++++++++++++++-------------------- man/ComIndexMulti.Rd | 432 +++++++++++++++++------------------ man/Fred.Rd | 114 ++++----- man/IndexByGroups.Rd | 74 +++--- man/MinMaxMST.Rd | 136 +++++------ man/Pval.Rd | 96 +++---- man/RandCom.Rd | 172 +++++++------- man/RaoRel.Rd | 360 ++++++++++++++--------------- man/SumBL.Rd | 132 +++++----- man/Tstats.Rd | 546 +++++++++++++++++++++++---------------------- man/as.listofindex.Rd | 154 ++++++------ man/cati-package.Rd | 65 ++--- man/decompCTRE.Rd | 176 +++++++------- man/finch.ind.Rd | 74 +++--- man/partvar.Rd | 186 +++++++-------- man/plot.listofindex.Rd | 292 ++++++++++++------------ man/plotCorTstats.Rd | 158 ++++++------- man/plotDistri.Rd | 274 +++++++++++----------- man/plotRandtest.Rd | 126 +++++----- man/plotSESvar.Rd | 162 ++++++------- man/plotSpPop.Rd | 256 ++++++++++----------- man/plotSpVar.Rd | 268 +++++++++++----------- man/samplingSubsetData.Rd | 118 ++++----- man/ses.Rd | 126 +++++----- man/ses.listofindex.Rd | 80 +++--- man/traitflex.anova.Rd | 186 +++++++-------- 34 files changed, 2890 insertions(+), 2872 deletions(-)
Title: Analogue and Weighted Averaging Methods for Palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer
function models for prediction of environmental data from species
data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre],
Jari Oksanen [aut]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between analogue versions 0.16-0 dated 2014-11-18 and 0.16-3 dated 2015-05-29
analogue-0.16-0/analogue/inst/tests |only analogue-0.16-3/analogue/DESCRIPTION | 10 - analogue-0.16-3/analogue/MD5 | 31 ++-- analogue-0.16-3/analogue/NAMESPACE | 1 analogue-0.16-3/analogue/R/Stratiplot.matrix.R |only analogue-0.16-3/analogue/R/join.R | 71 +--------- analogue-0.16-3/analogue/R/predict.logitreg.R | 4 analogue-0.16-3/analogue/R/tran.R | 7 analogue-0.16-3/analogue/README.md | 10 - analogue-0.16-3/analogue/build/vignette.rds |binary analogue-0.16-3/analogue/inst/ChangeLog | 12 + analogue-0.16-3/analogue/inst/NEWS.Rd | 26 +++ analogue-0.16-3/analogue/inst/doc/analogue_methods.pdf |binary analogue-0.16-3/analogue/man/Stratiplot.Rd | 5 analogue-0.16-3/analogue/man/tran.Rd | 1 analogue-0.16-3/analogue/tests/Examples/analogue-Ex.Rout.save | 19 +- analogue-0.16-3/analogue/tests/test-all.R | 7 analogue-0.16-3/analogue/tests/testthat |only 18 files changed, 105 insertions(+), 99 deletions(-)