Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R
without printing the content of graphics windows to an embosser of some kind. This
is not as immediate as is required for efficient access to statistical output.
The functions here are created so that blind people can make even better use
of R. This includes the text descriptions of graphs, convenience functions
to replace the functionality offered in many GUI front ends, and experimental
functionality for optimising graphical content to prepare it for embossing as
tactile images.
Author: A. Jonathan R. Godfrey [aut, cre], Duncan Murdoch [ctb], Greg Snow
[ctb], Henrik Bengtsson [ctb], James Curtis [ctb], Paul Murrell [ctb], Timothy Bilton [ctb], Yihui Xie
[ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Diff between BrailleR versions 0.24.1 dated 2016-03-19 and 0.24.2 dated 2016-03-29
DESCRIPTION | 10 ++-- MD5 | 10 ++-- inst/NEWS | 3 + inst/doc/BrailleRHistory.html | 36 ++++++++--------- inst/doc/Ex1histograms.html | 87 +++++++++++++++++++++--------------------- man/BrailleR-package.Rd | 4 - 6 files changed, 77 insertions(+), 73 deletions(-)
Title: Deployment Interface for R Markdown Documents and Shiny
Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and
'RStudio Connect'. Supported content types include R Markdown documents,
Shiny applications, plots, and static web content.
Author: JJ Allaire
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rsconnect versions 0.4.2 dated 2016-03-20 and 0.4.2.1 dated 2016-03-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/proxies.Rd | 8 +------- 3 files changed, 7 insertions(+), 13 deletions(-)
Title: An Individual-Based Population Genetic Simulation Environment
Description: An interface between R and the metasim simulation engine.
The simulation environment is documented in: "A
Strand. Metasim 1.0: an individual-based environment for
simulating population genetics of complex population
dynamics. Mol. Ecol. Notes, 2:373-376, 2002".
The current version has eliminated the backend encoded output routines.
These routines were accessed using "landscape.write.foreign". Now only
output to GenePop files remains.
R based routines for population genetic data analysis have improved dramatically
and many can use the 'genind' format defined by the adegenet package.
There is now a new function called "landscape.make.genind" which converts
a landscape to a genind object. Please contact the maintainer if other
output formats are needed.
Author: Allan Strand <stranda@cofc.edu>,
James Niehaus
Maintainer: Allan Strand <stranda@cofc.edu>
Diff between rmetasim versions 2.0.4.1 dated 2016-02-26 and 3.0.2 dated 2016-03-29
rmetasim-2.0.4.1/rmetasim/R/ape_interface.R |only rmetasim-2.0.4.1/rmetasim/R/output_formats.R |only rmetasim-2.0.4.1/rmetasim/R/simcoal.R |only rmetasim-3.0.2/rmetasim/CHANGELOG | 24 rmetasim-3.0.2/rmetasim/DESCRIPTION | 37 rmetasim-3.0.2/rmetasim/MD5 | 135 +- rmetasim-3.0.2/rmetasim/NAMESPACE | 39 rmetasim-3.0.2/rmetasim/R/amova.R | 14 rmetasim-3.0.2/rmetasim/R/assign.R | 4 rmetasim-3.0.2/rmetasim/R/create_landscape.R | 113 - rmetasim-3.0.2/rmetasim/R/diversity.R | 10 rmetasim-3.0.2/rmetasim/R/dnadiversity.R | 63 - rmetasim-3.0.2/rmetasim/R/landscape.allelefreq.R | 2 rmetasim-3.0.2/rmetasim/R/landscape.coalinput.R |only rmetasim-3.0.2/rmetasim/R/landscape.freq.locnames.R |only rmetasim-3.0.2/rmetasim/R/landscape.ind.freq.R |only rmetasim-3.0.2/rmetasim/R/landscape.make.genind.R |only rmetasim-3.0.2/rmetasim/R/landscape.make.genpop.R |only rmetasim-3.0.2/rmetasim/R/landscape.mig.matrix.R | 3 rmetasim-3.0.2/rmetasim/R/landscape.sample.R | 148 +- rmetasim-3.0.2/rmetasim/R/landscape.write.foreign.R |only rmetasim-3.0.2/rmetasim/R/landscape.write.genepop.R |only rmetasim-3.0.2/rmetasim/R/landscapeIO.R | 19 rmetasim-3.0.2/rmetasim/R/loci.R | 25 rmetasim-3.0.2/rmetasim/R/pegas_interface.R |only rmetasim-3.0.2/rmetasim/README.md |only rmetasim-3.0.2/rmetasim/inst/doc/CreatingLandscapes.R |only rmetasim-3.0.2/rmetasim/inst/doc/Simulating.R |only rmetasim-3.0.2/rmetasim/man/SimulationComponents.Rd | 12 rmetasim-3.0.2/rmetasim/man/landscape.Fst.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.allelecount.Rd | 16 rmetasim-3.0.2/rmetasim/man/landscape.allelefreq.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.amova.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.amova.locus.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.clean.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.coalinput.Rd | 8 rmetasim-3.0.2/rmetasim/man/landscape.compress.Rd | 7 rmetasim-3.0.2/rmetasim/man/landscape.demography.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.exp.het.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.freq.locnames.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.ind.freq.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.locus.Rd | 4 rmetasim-3.0.2/rmetasim/man/landscape.locus.states.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.make.genind.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.make.genpop.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.mismatchdist.Rd | 4 rmetasim-3.0.2/rmetasim/man/landscape.modify.epoch.Rd | 5 rmetasim-3.0.2/rmetasim/man/landscape.new.empty.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.new.epoch.Rd | 5 rmetasim-3.0.2/rmetasim/man/landscape.new.example.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.new.floatparam.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.new.individuals.Rd | 10 rmetasim-3.0.2/rmetasim/man/landscape.new.intparam.Rd | 4 rmetasim-3.0.2/rmetasim/man/landscape.new.local.demo.Rd | 5 rmetasim-3.0.2/rmetasim/man/landscape.new.locus.Rd | 16 rmetasim-3.0.2/rmetasim/man/landscape.new.switchparam.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.sample.Rd | 19 rmetasim-3.0.2/rmetasim/man/landscape.simulate.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.states.Rd | 4 rmetasim-3.0.2/rmetasim/man/landscape.theta.h.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.theta.k.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.theta.s.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.write.foreign.Rd | 32 rmetasim-3.0.2/rmetasim/src/AlleleObj.cc | 21 rmetasim-3.0.2/rmetasim/src/AlleleTbl.cc | 4 rmetasim-3.0.2/rmetasim/src/Democlass.cc | 5 rmetasim-3.0.2/rmetasim/src/Eigen.h | 5 rmetasim-3.0.2/rmetasim/src/FastAllele.cc | 21 rmetasim-3.0.2/rmetasim/src/FastSeqAllele.cc | 10 rmetasim-3.0.2/rmetasim/src/Landscape.cc | 852 --------------- rmetasim-3.0.2/rmetasim/src/Landscape.h | 56 rmetasim-3.0.2/rmetasim/src/Makevars | 6 rmetasim-3.0.2/rmetasim/src/PackedIndividual.h | 8 rmetasim-3.0.2/rmetasim/src/RandLib.h | 8 rmetasim-3.0.2/rmetasim/src/TransMat.cc | 12 rmetasim-3.0.2/rmetasim/src/metasim.h | 4 rmetasim-3.0.2/rmetasim/src/rmetasim.cc | 211 --- rmetasim-3.0.2/rmetasim/src/rmetasim.h | 13 rmetasim-3.0.2/rmetasim/vignettes |only 79 files changed, 493 insertions(+), 1556 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a
Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <mdramins@ipipan.waw.pl>
Diff between rmcfs versions 1.1.0 dated 2016-03-28 and 1.1.1 dated 2016-03-29
rmcfs-1.1.0/rmcfs/man/info.Rd |only rmcfs-1.1.1/rmcfs/DESCRIPTION | 14 - rmcfs-1.1.1/rmcfs/MD5 | 44 ++-- rmcfs-1.1.1/rmcfs/NAMESPACE | 10 - rmcfs-1.1.1/rmcfs/R/onLoad.R | 16 - rmcfs-1.1.1/rmcfs/R/rmcfs.R | 38 +++- rmcfs-1.1.1/rmcfs/R/rmcfs.plot.R | 10 - rmcfs-1.1.1/rmcfs/R/utils.R | 16 - rmcfs-1.1.1/rmcfs/inst/java/dmLab.jar |binary rmcfs-1.1.1/rmcfs/java/src/dmLab/DMLabInfo.java | 4 rmcfs-1.1.1/rmcfs/java/src/dmLab/array/loader/fileLoader/FileLoader.java | 14 - rmcfs-1.1.1/rmcfs/java/src/dmLab/mcfs/MCFSParams.java | 93 +++++----- rmcfs-1.1.1/rmcfs/java/src/dmLab/mcfs/mcfsEngine/MCFSExperiment.java | 21 +- rmcfs-1.1.1/rmcfs/java/src/dmLab/mcfs/mcfsEngine/framework/MCFSFramework.java | 7 rmcfs-1.1.1/rmcfs/man/artificial.data.Rd | 2 rmcfs-1.1.1/rmcfs/man/build.idgraph.Rd | 6 rmcfs-1.1.1/rmcfs/man/export.result.Rd | 6 rmcfs-1.1.1/rmcfs/man/filter.data.Rd | 8 rmcfs-1.1.1/rmcfs/man/import.result.Rd | 6 rmcfs-1.1.1/rmcfs/man/mcfs.Rd | 37 ++- rmcfs-1.1.1/rmcfs/man/plot.idgraph.Rd | 6 rmcfs-1.1.1/rmcfs/man/plot.mcfs.Rd | 8 rmcfs-1.1.1/rmcfs/man/print.mcfs.Rd | 6 rmcfs-1.1.1/rmcfs/man/showme.Rd |only 24 files changed, 209 insertions(+), 163 deletions(-)
Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture
Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau <anders.ellern.bilgrau@gmail.com>
Diff between GMCM versions 1.2.2 dated 2015-08-05 and 1.2.3 dated 2016-03-29
GMCM-1.2.2/GMCM/inst/tests |only GMCM-1.2.3/GMCM/DESCRIPTION | 8 - GMCM-1.2.3/GMCM/MD5 | 140 +++++++++++++-------------- GMCM-1.2.3/GMCM/R/EMAlgortihm.R | 2 GMCM-1.2.3/GMCM/R/EStep.R | 2 GMCM-1.2.3/GMCM/R/GMCM-package.R | 12 +- GMCM-1.2.3/GMCM/R/PseudoEMAlgorithm.R | 2 GMCM-1.2.3/GMCM/R/SimulateGMCMData.R | 30 ++++- GMCM-1.2.3/GMCM/R/Uhat.R | 2 GMCM-1.2.3/GMCM/R/choose.theta.R | 2 GMCM-1.2.3/GMCM/R/colSds.R | 2 GMCM-1.2.3/GMCM/R/cummean.R | 2 GMCM-1.2.3/GMCM/R/dgmcm.loglik.R | 2 GMCM-1.2.3/GMCM/R/fit.full.GMCM.R | 2 GMCM-1.2.3/GMCM/R/fit.meta.GMCM.R | 2 GMCM-1.2.3/GMCM/R/full2meta.R | 2 GMCM-1.2.3/GMCM/R/get.IDR2.R | 2 GMCM-1.2.3/GMCM/R/is.theta.R | 2 GMCM-1.2.3/GMCM/R/logit.R | 2 GMCM-1.2.3/GMCM/R/rho.transform.R | 2 GMCM-1.2.3/GMCM/R/rtheta.R | 2 GMCM-1.2.3/GMCM/R/tt.R | 4 GMCM-1.2.3/GMCM/README.md | 14 +- GMCM-1.2.3/GMCM/build/vignette.rds |binary GMCM-1.2.3/GMCM/inst/CITATION | 63 +++++++----- GMCM-1.2.3/GMCM/inst/NEWS.Rd | 15 ++ GMCM-1.2.3/GMCM/inst/doc/GMCM-JStatSoft.Rnw | 13 +- GMCM-1.2.3/GMCM/inst/doc/GMCM-JStatSoft.pdf |binary GMCM-1.2.3/GMCM/man/EMAlgorithm.Rd | 2 GMCM-1.2.3/GMCM/man/EStep.Rd | 2 GMCM-1.2.3/GMCM/man/GMCM-package.Rd | 10 + GMCM-1.2.3/GMCM/man/PseudoEMAlgorithm.Rd | 2 GMCM-1.2.3/GMCM/man/SimulateGMCMData.Rd | 30 ++++- GMCM-1.2.3/GMCM/man/Uhat.Rd | 2 GMCM-1.2.3/GMCM/man/choose.theta.Rd | 2 GMCM-1.2.3/GMCM/man/colSds.Rd | 2 GMCM-1.2.3/GMCM/man/cummean.Rd | 2 GMCM-1.2.3/GMCM/man/dgmcm.loglik.Rd | 2 GMCM-1.2.3/GMCM/man/fit.full.GMCM.Rd | 2 GMCM-1.2.3/GMCM/man/fit.meta.GMCM.Rd | 2 GMCM-1.2.3/GMCM/man/freshVsFrozen.Rd | 2 GMCM-1.2.3/GMCM/man/full2meta.Rd | 2 GMCM-1.2.3/GMCM/man/get.IDR.Rd | 2 GMCM-1.2.3/GMCM/man/is.theta.Rd | 2 GMCM-1.2.3/GMCM/man/logit.Rd | 2 GMCM-1.2.3/GMCM/man/rho.transform.Rd | 2 GMCM-1.2.3/GMCM/man/rtheta.Rd | 2 GMCM-1.2.3/GMCM/man/tt.Rd | 4 GMCM-1.2.3/GMCM/man/u133VsExon.Rd | 2 GMCM-1.2.3/GMCM/tests/test-all.R | 8 - GMCM-1.2.3/GMCM/tests/testthat |only GMCM-1.2.3/GMCM/vignettes/GMCM-JStatSoft.Rnw | 13 +- 52 files changed, 250 insertions(+), 182 deletions(-)
Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium for
diallelic genetic marker data. All classical tests (chi-square, exact,
likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium
are included in the package, as well as functions for power computation and
for the simulation of marker data under equilibrium and disequilibrium.
Routines for dealing with markers on the X-chromosome are included.
Functions for testing equilibrium in the presence of missing data by
using multiple imputation are also provided. Implements several graphics
for exploring the equilibrium status of a large set of diallelic markers:
ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman <jan.graffelman@upc.edu>
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between HardyWeinberg versions 1.5.5 dated 2015-02-26 and 1.5.6 dated 2016-03-29
DESCRIPTION | 11 +- MD5 | 118 +++++++++++++++++------------ NAMESPACE | 4 - R/AFtest.R |only R/Chisquare.R | 5 - R/Chisquare.x.R |only R/Chisquarex.R |only R/CombineExact.R | 2 R/HW.chi.mat.R |only R/HWAlltests.R | 52 +++++++------ R/HWChisq.R | 119 +++++++++++++++++++++--------- R/HWChisqStats.R |only R/HWClo.R |only R/HWData.R | 156 ++++++++++++++++++++++++++------------- R/HWExact.R | 170 ++++++++++++++++++++++++++++++------------- R/HWExactPrevious.R |only R/HWExactStats.R |only R/HWGenotypePlot.R | 4 - R/HWLratio.R | 92 ++++++++++++++++++----- R/HWPerm.R | 62 ++++++++++++++- R/HWTernaryPlot.R | 35 +++----- R/MakeCounts.R | 9 +- R/UniqueGenotypeCounts.R | 9 +- R/agcounts.R |only R/auxiliartable.R |only R/generate.outcomes.R |only R/mac.R | 3 R/make.outcomes.R |only R/n.outcomes.R |only R/recode.R | 90 +++++++++++++++++----- R/sample.prob.R |only R/sample.prob.last.R |only R/subsamples.prob.R |only R/vaf.R | 22 +---- build/vignette.rds |binary inst/CITATION | 2 inst/doc/HardyWeinberg.R | 105 ++++++++++++++++++++------ inst/doc/HardyWeinberg.Rnw | 122 ++++++++++++++++++++++++++---- inst/doc/HardyWeinberg.pdf |binary man/AFtest.Rd |only man/HWAlltests.Rd | 8 +- man/HWAlr.Rd | 2 man/HWAlrPlot.Rd | 2 man/HWChisq.Rd | 49 ++++++++++-- man/HWChisqMat.Rd | 2 man/HWChisqStats.Rd |only man/HWClo.Rd |only man/HWClr.Rd | 2 man/HWClrPlot.Rd | 2 man/HWData.Rd | 43 ++++++++-- man/HWExact.Rd | 19 +++- man/HWExactMat.Rd | 2 man/HWExactPrevious.Rd |only man/HWExactStats.Rd |only man/HWGenotypePlot.Rd | 3 man/HWIlr.Rd | 2 man/HWIlrPlot.Rd | 2 man/HWLratio.Rd | 16 +++- man/HWMissing.Rd | 4 - man/HWPerm.Rd | 16 +++- man/HWPower.Rd | 2 man/HWTernaryPlot.Rd | 8 -- man/HardyWeinberg-package.Rd | 13 +-- man/MakeCounts.Rd | 9 +- man/Markers.Rd | 2 man/UniqueGenotypeCounts.Rd | 5 - man/agcounts.Rd |only man/recode.Rd | 20 +++-- man/vaf.Rd | 11 +- vignettes/HardyWeinberg.Rnw | 122 ++++++++++++++++++++++++++---- vignettes/HardyWeinberg.bib | 18 ++++ 71 files changed, 1137 insertions(+), 439 deletions(-)
Title: Aligned Rank Transform
Description: The Aligned Rank Transform for nonparametric
factorial ANOVAs as described by J. O. Wobbrock,
L. Findlater, D. Gergle, & J. J. Higgins, "The Aligned
Rank Transform for nonparametric factorial analyses
using only ANOVA procedures", CHI 2011 <DOI:10.1145/1978942.1978963>.
Author: Matthew Kay [aut, cre],
Jacob O. Wobbrock [aut]
Maintainer: Matthew Kay <mjskay@uw.edu>
Diff between ARTool versions 0.10.0 dated 2016-01-11 and 0.10.2 dated 2016-03-29
DESCRIPTION | 15 - MD5 | 19 - NEWS | 69 ++-- R/release.questions.R |only build/vignette.rds |binary inst/doc/art-contrasts.R | 27 - inst/doc/art-contrasts.Rmd | 580 ++++++++++++++++++++---------------------- inst/doc/art-contrasts.html | 99 +++---- inst/doc/art-effect-size.R |only inst/doc/art-effect-size.Rmd |only inst/doc/art-effect-size.html |only vignettes/art-contrasts.Rmd | 580 ++++++++++++++++++++---------------------- vignettes/art-effect-size.Rmd |only 13 files changed, 696 insertions(+), 693 deletions(-)
Title: Time to Target Plot
Description: Implementation of Time to Target plot based on the work
of Ribeiro and Rosseti (2015) <DOI:10.1007/s11590-014-0760-8>,
that describe a numerical method that gives the probability of
an algorithm A finds a solution at least as good as a given
target value in smaller computation time than algorithm B.
Author: Carlos A. Martinez [aut, cre] based on the work of Ribeiro and Rosseti (2015).
Maintainer: Carlos A. Martinez <amartin@unal.edu.co>
Diff between tttplot versions 1.0 dated 2016-03-20 and 1.1.1 dated 2016-03-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/RCode.R | 42 ++++++++++++++++-------------------------- man/tttPlot.Rd | 10 +++++----- man/tttPlotCompare.Rd | 21 ++++++++++++--------- 6 files changed, 43 insertions(+), 50 deletions(-)
Title: Partition-Assisted Clustering
Description: Implements Partition-Assisted Clustering, which utilizes a collection of partition based nonparametric density estimation techniques to improve the robustness and accuracy of downstream clustering.
The package also provides functions for effectively visualizing the clustering results.
It is particularly useful for finding and visualizing subpopulations in single-cell data analysis.
Author: Dangna Li, Henry Li
Maintainer: Dangna Li <ldangna@gmail.com>
Diff between PAC versions 1.0.2 dated 2016-03-29 and 1.0.3 dated 2016-03-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 1 + R/PAC.R | 1 + src/bsp.cc | 4 ++-- 5 files changed, 11 insertions(+), 9 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InSilicoVA versions 1.1.1 dated 2016-03-27 and 1.1.2 dated 2016-03-29
DESCRIPTION | 8 +++--- MD5 | 6 ++-- R/diag.r | 68 +++++++++++++++++++++++++++++++++---------------------- man/csmf.diag.Rd | 29 ++++++----------------- 4 files changed, 56 insertions(+), 55 deletions(-)
Title: Visualise Twitter Interactions
Description: Allows building an edge table from data frame of tweets,
also provides function to build nodes and another create a temporal graph.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between graphTweets versions 0.3 dated 2016-03-11 and 0.3.1 dated 2016-03-29
DESCRIPTION | 17 +++++++++-------- MD5 | 15 ++++++++------- NAMESPACE | 2 +- NEWS.md |only R/dynamize.R | 2 ++ README.md | 4 ++++ tests/testthat/test_dynamise.R | 6 ++++++ tests/testthat/test_edges.R | 12 ++++++++++++ tests/testthat/test_nodes.R | 4 ++++ 9 files changed, 46 insertions(+), 16 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.2.3 dated 2016-01-21 and 2.3 dated 2016-03-29
DESCRIPTION | 8 +- MD5 | 8 +- R/evenn.R | 169 ++++++++++++++++++++++++++++----------------------- man/eVenn-package.Rd | 4 - man/evenn.Rd | 12 ++- 5 files changed, 110 insertions(+), 91 deletions(-)
Title: Combined Analysis of Pleiotropy and Epistasis
Description: Combines complementary information across multiple related
phenotypes to infer directed epistatic interactions between genetic markers.
This analysis can be applied to a variety of engineered and natural populations.
Author: Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and Greg W.
Carter
Maintainer: Anna L. Tyler <Anna.Tyler@jax.org>
Diff between cape versions 1.3 dated 2014-09-26 and 2.0 dated 2016-03-29
cape-1.3/cape/R/create.covar.R |only cape-1.3/cape/R/linkage.blocks.stepwise.R |only cape-1.3/cape/R/one.pairscan.R |only cape-1.3/cape/R/remove.ind.with.missing.pheno.R |only cape-1.3/cape/R/set.covar.R |only cape-1.3/cape/R/set.pairscan.thresh.R |only cape-1.3/cape/man/create.covar.Rd |only cape-1.3/cape/man/linkage.blocks.stepwise.Rd |only cape-1.3/cape/man/one.pairscan.Rd |only cape-1.3/cape/man/remove.ind.with.missing.pheno.Rd |only cape-1.3/cape/man/set.covar.Rd |only cape-1.3/cape/man/set.pairscan.thresh.Rd |only cape-1.3/cape/vignettes/Network_Collapsed.pdf |only cape-1.3/cape/vignettes/Network_Full.pdf |only cape-1.3/cape/vignettes/pair_regression.pdf |only cape-1.3/cape/vignettes/svd.pdf |only cape-1.3/cape/vignettes/variant_influences.pdf |only cape-2.0/cape/DESCRIPTION | 23 cape-2.0/cape/MD5 | 209 +++-- cape-2.0/cape/NAMESPACE | 9 cape-2.0/cape/R/bin.vector.R |only cape-2.0/cape/R/calc.p.R | 45 - cape-2.0/cape/R/direct.influence.R | 79 -- cape-2.0/cape/R/error.prop.R | 74 +- cape-2.0/cape/R/filter.hwe.R |only cape-2.0/cape/R/filter.maf.R |only cape-2.0/cape/R/genome.wide.threshold.1D.R | 35 cape-2.0/cape/R/genome.wide.threshold.1D.parallel.R |only cape-2.0/cape/R/get.chr.markers.R |only cape-2.0/cape/R/get.col.R |only cape-2.0/cape/R/get.covar.R | 88 +- cape-2.0/cape/R/get.eigentraits.R | 31 cape-2.0/cape/R/get.geno.R |only cape-2.0/cape/R/get.geno.with.covar.R |only cape-2.0/cape/R/get.linearly.independent.R | 40 - cape-2.0/cape/R/get.marker.chr.R |only cape-2.0/cape/R/get.marker.idx.R |only cape-2.0/cape/R/get.marker.location.R |only cape-2.0/cape/R/get.marker.name.R |only cape-2.0/cape/R/get.marker.num.R |only cape-2.0/cape/R/get.marker.val.R |only cape-2.0/cape/R/get.network.R | 50 + cape-2.0/cape/R/get.pairs.for.pairscan.R | 19 cape-2.0/cape/R/get.pheno.R |only cape-2.0/cape/R/histPheno.R |only cape-2.0/cape/R/impute.missing.geno.R |only cape-2.0/cape/R/kinship.R |only cape-2.0/cape/R/kinship.on.the.fly.R |only cape-2.0/cape/R/linkage.blocks.network.R |only cape-2.0/cape/R/make.data.obj.R |only cape-2.0/cape/R/marker2covar.R |only cape-2.0/cape/R/myImagePlot.R | 89 -- cape-2.0/cape/R/one.pairscan.parallel.R |only cape-2.0/cape/R/one.singlescan.R | 14 cape-2.0/cape/R/pairscan.R | 128 +-- cape-2.0/cape/R/pairscan.kin.R |only cape-2.0/cape/R/pairscan.noKin.R |only cape-2.0/cape/R/pairscan.null.R | 154 ++-- cape-2.0/cape/R/pheno2covar.R |only cape-2.0/cape/R/plotCollapsedVarInf.R | 2 cape-2.0/cape/R/plotNetwork.R | 125 ++- cape-2.0/cape/R/plotPairscan.R | 52 - cape-2.0/cape/R/plotPheno.R |only cape-2.0/cape/R/plotPhenoCor.R |only cape-2.0/cape/R/plotSVD.R | 29 cape-2.0/cape/R/plotSinglescan.R | 323 ++++++--- cape-2.0/cape/R/plotSinglescan.heat.R | 10 cape-2.0/cape/R/plotVariantInfluences.R | 133 +-- cape-2.0/cape/R/qqPheno.R |only cape-2.0/cape/R/read.geno.R |only cape-2.0/cape/R/read.pheno.R |only cape-2.0/cape/R/read.population.R | 424 ++++++----- cape-2.0/cape/R/remove.ind.R |only cape-2.0/cape/R/remove.markers.R |only cape-2.0/cape/R/select.by.chr.R | 6 cape-2.0/cape/R/select.markers.for.pairscan.R | 162 +--- cape-2.0/cape/R/singlescan.R | 392 ++++++---- cape-2.0/cape/R/sortByThenBy.R |only cape-2.0/cape/R/sortCross.R |only cape-2.0/cape/R/writeVariantInfluences.R | 29 cape-2.0/cape/build/vignette.rds |binary cape-2.0/cape/data/obesity.cross.rda |binary cape-2.0/cape/inst/doc/cape.R | 194 +++-- cape-2.0/cape/inst/doc/cape.Rnw | 607 +++++++---------- cape-2.0/cape/inst/doc/cape.pdf |binary cape-2.0/cape/man/bin.vector.Rd |only cape-2.0/cape/man/calc.p.Rd | 9 cape-2.0/cape/man/direct.influence.Rd | 5 cape-2.0/cape/man/error.prop.Rd | 8 cape-2.0/cape/man/filter.hwe.Rd |only cape-2.0/cape/man/filter.maf.Rd |only cape-2.0/cape/man/genome.wide.threshold.1D.Rd | 10 cape-2.0/cape/man/genome.wide.threshold.1D.parallel.Rd |only cape-2.0/cape/man/get.chr.markers.Rd |only cape-2.0/cape/man/get.col.Rd |only cape-2.0/cape/man/get.col.num.Rd | 3 cape-2.0/cape/man/get.covar.Rd | 24 cape-2.0/cape/man/get.geno.Rd |only cape-2.0/cape/man/get.geno.with.covar.Rd |only cape-2.0/cape/man/get.linearly.independent.Rd | 6 cape-2.0/cape/man/get.marker.chr.Rd |only cape-2.0/cape/man/get.marker.idx.Rd |only cape-2.0/cape/man/get.marker.location.Rd |only cape-2.0/cape/man/get.marker.name.Rd |only cape-2.0/cape/man/get.marker.num.Rd |only cape-2.0/cape/man/get.marker.val.Rd |only cape-2.0/cape/man/get.network.Rd | 21 cape-2.0/cape/man/get.pairs.for.pairscan.Rd | 19 cape-2.0/cape/man/get.pheno.Rd |only cape-2.0/cape/man/histPheno.Rd |only cape-2.0/cape/man/impute.missing.geno.Rd |only cape-2.0/cape/man/kinship.Rd |only cape-2.0/cape/man/kinship.on.the.fly.Rd |only cape-2.0/cape/man/linkage.blocks.network.Rd |only cape-2.0/cape/man/make.data.obj.Rd |only cape-2.0/cape/man/marker2covar.Rd |only cape-2.0/cape/man/norm.pheno.Rd | 11 cape-2.0/cape/man/one.pairscan.parallel.Rd |only cape-2.0/cape/man/one.singlescan.Rd | 5 cape-2.0/cape/man/pairscan.Rd | 63 + cape-2.0/cape/man/pairscan.kin.Rd |only cape-2.0/cape/man/pairscan.noKin.Rd |only cape-2.0/cape/man/pairscan.null.Rd | 22 cape-2.0/cape/man/pheno2covar.Rd |only cape-2.0/cape/man/plotCollapsedVarInf.Rd | 2 cape-2.0/cape/man/plotNetwork.Rd | 15 cape-2.0/cape/man/plotPairscan.Rd | 18 cape-2.0/cape/man/plotPheno.Rd |only cape-2.0/cape/man/plotPhenoCor.Rd |only cape-2.0/cape/man/plotSVD.Rd | 14 cape-2.0/cape/man/plotSinglescan.Rd | 58 + cape-2.0/cape/man/plotSinglescan.heat.Rd | 15 cape-2.0/cape/man/plotVariantInfluences.Rd | 26 cape-2.0/cape/man/qqPheno.Rd |only cape-2.0/cape/man/read.geno.Rd |only cape-2.0/cape/man/read.pheno.Rd |only cape-2.0/cape/man/read.population.Rd | 8 cape-2.0/cape/man/remove.ind.Rd |only cape-2.0/cape/man/remove.markers.Rd |only cape-2.0/cape/man/select.by.chr.Rd | 16 cape-2.0/cape/man/select.markers.for.pairscan.Rd | 37 - cape-2.0/cape/man/singlescan.Rd | 55 + cape-2.0/cape/man/sortByThenBy.Rd |only cape-2.0/cape/man/sortCross.Rd |only cape-2.0/cape/vignettes/cape-017.pdf |only cape-2.0/cape/vignettes/cape-019.pdf |only cape-2.0/cape/vignettes/cape.Rnw | 607 +++++++---------- cape-2.0/cape/vignettes/cape.bib | 47 + cape-2.0/cape/vignettes/interaction_fig.pdf |binary cape-2.0/cape/vignettes/reparam.pdf |binary 150 files changed, 2583 insertions(+), 2116 deletions(-)
Title: Binary Logic
Description: Convert to binary numbers (Base2). Shift, rotate, summary. Based on logical vector.
Author: Daniel Dörrhöfer <ddo@openmailbox.org>
Maintainer: Daniel Dörrhöfer <ddo@openmailbox.org>
Diff between binaryLogic versions 0.3.2 dated 2016-01-19 and 0.3.4 dated 2016-03-29
DESCRIPTION | 6 +- LICENSE | 2 MD5 | 20 ++++---- NAMESPACE | 2 R/BinaryS3.R | 27 ++++++++--- R/binHelper.R | 51 ++++++++++++++++++++ README.md | 42 +++++++++++++++-- man/as.binary.Rd | 6 ++ man/bin2gray.Rd |only man/gray2bin.Rd |only tests/testthat/test-BinaryS3.R | 28 +++++++++++ tests/testthat/test-binHelper.R | 98 ++++++++++++++++++++++++++++++++++++++++ 12 files changed, 259 insertions(+), 23 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.9.2 dated 2016-02-02 and 0.9.3 dated 2016-03-29
DESCRIPTION | 11 MD5 | 66 +-- NAMESPACE | 3 R/check_wkt.r | 19 - R/gbifmap.r | 8 R/geometry_utils.R |only R/name_usage.r | 12 R/occ_data.R | 22 - R/occ_download.R | 10 R/occ_search.r | 48 +- R/rgbif-package.r | 1 R/wkt_parse.R |only R/zzz.r | 8 README.md | 119 +++--- build/vignette.rds |binary inst/assets/img/unnamed-chunk-8-1.png |binary inst/doc/issues_vignette.Rmd | 206 +++++----- inst/doc/issues_vignette.html | 206 +++++----- inst/doc/rgbif_vignette.html | 641 +++++++++++++++++----------------- inst/vign/figure/gbifmap1-1.png |binary inst/vign/issues_vignette.md | 206 +++++----- inst/vign/rgbif_vignette.md | 641 +++++++++++++++++----------------- man/check_wkt.Rd | 3 man/occ_data.Rd | 128 ++++++ man/occ_search.Rd | 124 ++++++ man/wkt_parse.Rd |only tests/testthat/test-count_facet.r | 11 tests/testthat/test-elevation.R | 5 tests/testthat/test-name_suggest.r | 1 tests/testthat/test-nodes.r | 10 tests/testthat/test-occ_data.R | 80 ++++ tests/testthat/test-occ_issues.R | 2 tests/testthat/test-occ_search.r | 81 ++++ tests/testthat/test-wkt_large.R |only vignettes/issues_vignette.Rmd | 206 +++++----- vignettes/rgbif_vignette.Rmd | 641 +++++++++++++++++----------------- 36 files changed, 2012 insertions(+), 1507 deletions(-)
Title: R/Weka Interface
Description: An R interface to Weka (Version 3.7.13).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package 'RWeka' contains the interface code, the
Weka jar is in a separate package 'RWekajars'. For more information
on Weka see <http://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre],
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWeka versions 0.4-25 dated 2016-03-15 and 0.4-26 dated 2016-03-29
CHANGELOG | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/attributes.R | 3 ++- R/classifiers.R | 6 ++++-- R/filters.R | 3 ++- build/vignette.rds |binary inst/doc/RWeka.pdf |binary 8 files changed, 22 insertions(+), 14 deletions(-)
Title: Build Regression Models Quickly and Display the Results Using
'ggplot2'
Description: A set of functions to extract results from regression models and
plot the effect size using 'ggplot2' seamlessly. While 'broom' is useful to
convert statistical analysis objects into tidy data frames, 'coefplot' is adept at showing
multivariate regression results. With specific outcome, this package could build regression models
automatically, extract results into a data frame and provide a quicker way to summarize
models' statistical findings using 'ggplot2'.
Author: Xikun Han [aut, cre]
Maintainer: Xikun Han <hanxikun2014@163.com>
Diff between quickReg versions 0.0.1 dated 2016-03-03 and 0.0.2 dated 2016-03-29
DESCRIPTION | 12 ++-- MD5 | 45 ++++++++--------- NAMESPACE | 1 NEWS |only R/data.R | 2 R/dataframe.R | 2 R/dataframe.reg.R | 12 +++- R/detail.R | 2 R/detail.reg.R | 2 R/display.data.frame.R | 50 +++++++++++-------- R/display.reg.R | 66 +++++++++++++------------ R/plot.reg.R | 108 +++++++++++++++++++++-------------------- R/reg.R | 56 +++++++++++++-------- build/vignette.rds |binary inst/doc/quickReg.R | 28 ++++++++-- inst/doc/quickReg.Rmd | 26 ++++++++-- inst/doc/quickReg.html | 119 +++++++++++++++++++--------------------------- man/dataframe.reg.Rd | 4 + man/diabetes.Rd | 2 man/display.data.frame.Rd | 14 +++-- man/display.reg.Rd | 3 - man/plot.reg.Rd | 9 +-- man/reg.Rd | 2 vignettes/quickReg.Rmd | 26 ++++++++-- 24 files changed, 336 insertions(+), 255 deletions(-)
Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods 'kernlab'
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut]
Maintainer: Alexandros Karatzoglou <alexis@ci.tuwien.ac.at>
Diff between kernlab versions 0.9-23 dated 2016-01-26 and 0.9-24 dated 2016-03-29
DESCRIPTION | 6 +++--- MD5 | 42 +++++++++++++++++++++--------------------- R/gausspr.R | 2 +- R/kfa.R | 2 +- R/kha.R | 2 +- R/kkmeans.R | 2 +- R/kpca.R | 2 +- R/kqr.R | 2 +- R/ksvm.R | 2 +- R/lssvm.R | 2 +- R/rvm.R | 2 +- R/sigest.R | 2 +- R/specc.R | 2 +- build/vignette.rds |binary data/income.rda |binary data/musk.rda |binary data/promotergene.rda |binary data/reuters.rda |binary data/spam.rda |binary data/spirals.rda |binary data/ticdata.rda |binary inst/CITATION | 8 ++++---- 22 files changed, 39 insertions(+), 39 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [ctb],
David R. Hunter [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm.count versions 3.2.0 dated 2015-06-19 and 3.2.2 dated 2016-03-29
DESCRIPTION | 8 ++-- LICENSE | 2 - MD5 | 38 +++++++++++------------ R/InitReference.R | 9 +++++ R/InitWtErgmTerm.R | 9 +++++ R/InitWtMHP.R | 9 +++++ R/zzz.R | 13 +++++++ inst/CITATION | 11 ++++-- inst/NEWS.Rd | 75 +++++++++++++++++++++++++++++++--------------- man/ergm-references.Rd | 9 +++++ man/ergm-terms.Rd | 9 +++++ man/ergm.count-package.Rd | 11 ++++++ man/zach.Rd | 9 +++++ src/include_stubs.c | 18 +++++++++++ src/wtMHproposals.c | 18 +++++++++++ src/wtMHproposals.h | 18 +++++++++++ src/wtchangestats.c | 18 +++++++++++ src/wtchangestats.h | 18 +++++++++++ tests/valued_fit.R | 11 ++++++ tests/valued_sim.R | 9 +++++ 20 files changed, 267 insertions(+), 55 deletions(-)
More information about CrossClustering at CRAN
Permanent link
Title: Readable Check Functions to Ensure Code Integrity
Description: Lots of predicates (is_* functions) to check the state of your
variables, and assertions (assert_* functions) to throw errors if they
aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive versions 0.3-2 dated 2016-03-08 and 0.3-3 dated 2016-03-29
DESCRIPTION | 10 MD5 | 10 NAMESPACE | 2 NEWS | 1 R/exports-reflection.R | 508 ++++++++++++++++++++++++------------------------- man/is_r.Rd | 2 6 files changed, 271 insertions(+), 262 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, PCA and correlation matrices, cluster analyses, scatter
plots, Likert scales, effects plots of regression models (including interaction
terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.9.3 dated 2016-03-24 and 1.9.4 dated 2016-03-29
DESCRIPTION | 12 MD5 | 20 NEWS | 9 NEWS.md | 19 R/sjPlotFrequencies.R | 1568 ++++++------- R/sjPlotGLME.R | 5116 ++++++++++++++++++++++----------------------- R/sjPlotStackFrequencies.R | 908 +++---- build/partial.rdb |binary man/sjPlot-package.Rd | 4 man/sjp.frq.Rd | 602 ++--- man/sjp.stackfrq.Rd | 2 11 files changed, 4146 insertions(+), 4114 deletions(-)
Title: An Imgur.com API Client Package
Description: A complete API client for the image hosting service Imgur.com, including the an imgur graphics device, enabling the easy upload and sharing of plots.
Author: Thomas J. Leeper [aut, cre],
Aaron Statham [ctb],
Yihui Xie [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between imguR versions 1.0.1 dated 2016-02-19 and 1.0.3 dated 2016-03-29
DESCRIPTION | 10 +++---- MD5 | 10 +++---- NAMESPACE | 65 +++++++++++++++++++++++++++++++++++++++++++++ NEWS | 4 ++ R/http.r | 85 ++++++++++++++++++++++++++++++++++-------------------------- README.md | 2 - 6 files changed, 128 insertions(+), 48 deletions(-)
Title: Simple Metrics to Summarize Growth Curves
Description: This is a simple package that fits the logistic equation to
microbial growth curve data (e.g., repeated absorbance measurements
taken from a plate reader over time). From this fit, a variety of
metrics are provided, including the maximum growth rate,
the doubling time, the carrying capacity, the area under the logistic
curve, and the time to the inflection point.
Author: Kathleen sprouffske [aut, cre]
Maintainer: Kathleen sprouffske <sprouffske@gmail.com>
Diff between growthcurver versions 0.2.0 dated 2016-03-09 and 0.2.1 dated 2016-03-29
DESCRIPTION | 8 - MD5 | 30 +++--- R/fit-logistic.R | 33 ++++--- R/helpers.R | 26 +++-- R/summarize-growth-by-plate.R | 27 +++-- R/summarize-growth.R | 84 ++++++++++++------ R/utils.R | 2 build/vignette.rds |binary inst/doc/Growthcurver-vignette.R | 12 ++ inst/doc/Growthcurver-vignette.Rmd | 85 ++++++++++++------ inst/doc/Growthcurver-vignette.html | 155 ++++++++++++++++++++++------------ man/SummarizeGrowth.Rd | 12 +- man/SummarizeGrowthByPlate.Rd | 21 ++-- man/gcvals.Rd | 5 - tests/testthat/test_SummarizeGrowth.R | 12 ++ vignettes/Growthcurver-vignette.Rmd | 85 ++++++++++++------ 16 files changed, 404 insertions(+), 193 deletions(-)
Title: Interpolate Data for Smooth Animations
Description: In order to create smooth animation between states of data,
tweening is necessary. This package provides a range of functions for
creating tweened data that plugs right into functions such as gg_animate()
from the 'gganimate' package. Furthermore it adds a number of vectorized
interpolaters for common R data types such as numeric, date and colour.
Author: Thomas Lin Pedersen [aut, cre]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between tweenr versions 0.1.2 dated 2016-02-11 and 0.1.3 dated 2016-03-29
DESCRIPTION | 9 ++-- MD5 | 4 - README.md | 125 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++--- 3 files changed, 127 insertions(+), 11 deletions(-)
Title: Linear/Nonlinear SVM Classification Solver Based on ADMM and
IADMM Algorithms
Description:
Solve large-scale regularised linear/kernel classification by using ADMM and IADMM algorithms. This package provides linear L2-regularised primal classification (both ADMM and IADMM are available), kernel L2-regularised dual classification (IADMM) as well as L1-regularised primal classification (both ADMM and IADMM are available).
Author: Ben DAI <bendai2-c@my.cityu.edu.hk>; Junhui Wang <j.h.wang@cityu.edu.hk>
Maintainer: Ben DAI <bendai2-c@my.cityu.edu.hk>
Diff between svmadmm versions 0.2 dated 2016-03-17 and 0.3 dated 2016-03-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/kerneliadmm.c | 3 +-- src/linear_math.c | 44 ++++++++++++++++++++++---------------------- src/linearadmm.c | 5 ++--- 5 files changed, 32 insertions(+), 34 deletions(-)
Title: Tools for Analyzing Content Homogeneity and News Diffusion using
Computational Text Analysis
Description: A collection of tools for measuring the similarity of news content and tracing the flow of (news) messages over
time and across media.
Author: Kasper Welbers & Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between RNewsflow versions 1.0 dated 2016-02-21 and 1.0.1 dated 2016-03-29
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Generate Random Strings
Description: Generate random strings of a dictated size of symbol set and
distribution of the lengths of strings.
Author: Alan Gu
Maintainer: Alan Gu <alan.on.ca@gmail.com>
Diff between randstr versions 0.1.1 dated 2016-03-28 and 0.2.0 dated 2016-03-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/generatelens.r | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Partition-Assisted Clustering
Description: Implements Partition-Assisted Clustering, which utilizes a collection of partition based nonparametric density estimation techniques to improve the robustness and accuracy of downstream clustering.
The package also provides functions for effectively visualizing the clustering results.
It is particularly useful for finding and visualizing subpopulations in single-cell data analysis.
Author: Dangna Li, Henry Li
Maintainer: Dangna Li <ldangna@gmail.com>
Diff between PAC versions 1.0.1 dated 2016-03-27 and 1.0.2 dated 2016-03-29
PAC-1.0.1/PAC/configure.ac |only PAC-1.0.2/PAC/DESCRIPTION | 6 +++--- PAC-1.0.2/PAC/MD5 | 8 ++++---- PAC-1.0.2/PAC/R/PAC.R | 1 - PAC-1.0.2/PAC/cleanup.win |only PAC-1.0.2/PAC/src/Makevars | 4 +++- 6 files changed, 10 insertions(+), 9 deletions(-)
Title: Probabilistic Models to Analyze and Gaussianize Heavy-Tailed,
Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze
skewed, heavy-tailed data. It is based on an input/output system, where the
output random variable (RV) Y is a non-linearly transformed version of an input
RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed).
The transformed RV Y has a Lambert W x F distribution. This package contains
functions to model and analyze skewed, heavy-tailed data the Lambert Way:
simulate random samples, estimate parameters, compute quantiles, and plot/
print results nicely. Probably the most important function is 'Gaussianize',
which works similarly to 'scale', but actually makes the data Gaussian.
A do-it-yourself toolkit allows users to define their own Lambert W x
'MyFavoriteDistribution' and use it in their analysis right away.
Author: Georg M. Goerg <im@gmge.org>
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between LambertW versions 0.6.2 dated 2016-02-05 and 0.6.4 dated 2016-03-29
DESCRIPTION | 12 +- MD5 | 38 ++++----- NEWS | 8 + R/RcppExports.R | 2 R/dU.R | 4 R/pU.R | 4 R/qU.R | 8 + man/estimate-moments.Rd | 2 src/skewness.cpp | 3 tests/testthat/test_H_gamma.R | 3 tests/testthat/test_IGMM.R | 34 ++++---- tests/testthat/test_LambertW_fit_methods.R | 7 - tests/testthat/test_MLE_LambertW.R | 20 ++-- tests/testthat/test_W.R | 17 ---- tests/testthat/test_W_gamma.R | 13 +-- tests/testthat/test_dpqr_LambertW.R | 12 +- tests/testthat/test_dpqr_U.R | 122 +++++++++++++++++++++++++++++ tests/testthat/test_get_support.R | 8 + tests/testthat/test_lp_norm.R | 8 - tests/testthat/test_theta_tau.R | 11 ++ 20 files changed, 239 insertions(+), 97 deletions(-)
Title: Group Sequential Bayes Design
Description: Group Sequential Operating Characteristics for Clinical,
Bayesian two-arm Trials with known Sigma and Normal Endpoints.
Author: Florian Gerber, Thomas Gsponer
Maintainer: Florian Gerber <florian.gerber@math.uzh.ch>
Diff between gsbDesign versions 0.96-3 dated 2015-07-08 and 1.00 dated 2016-03-29
ChangeLog | 6 +++++ DESCRIPTION | 10 ++++---- MD5 | 29 ++++++++++++++++--------- R/package.r | 21 ++++++++++++++++-- build |only demo |only inst/CITATION | 55 +++++++++++++++++++++++++++++-------------------- inst/doc |only man/gsb-package.Rd | 28 +++++++++++------------- man/gsb.Rd | 23 ++++++++------------ man/gsbBayesUpdate.Rd | 2 - man/gsbCriteria.Rd | 2 - man/plot.gsbMainOut.Rd | 2 - man/tab.Rd | 2 - vignettes |only 15 files changed, 108 insertions(+), 72 deletions(-)
Title: Identify Favorable Subsets of Germplasm Collections
Description: Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.
Author: Ryan C. Graebner and Alfonso Cuesta-Marcos
Maintainer: Ryan C. Graebner <ryan.graebner@gmail.com>
Diff between GeneticSubsetter versions 0.6 dated 2015-10-14 and 0.7 dated 2016-03-29
GeneticSubsetter-0.6/GeneticSubsetter/man/PIC.Rd |only GeneticSubsetter-0.7/GeneticSubsetter/DESCRIPTION | 6 ++-- GeneticSubsetter-0.7/GeneticSubsetter/MD5 | 14 +++++----- GeneticSubsetter-0.7/GeneticSubsetter/R/CoreSetOptimizer.R | 1 GeneticSubsetter-0.7/GeneticSubsetter/man/CoreSetOptimizer.Rd | 2 - GeneticSubsetter-0.7/GeneticSubsetter/man/CoreSetter.Rd | 2 - GeneticSubsetter-0.7/GeneticSubsetter/man/CoreSetterCombined.Rd | 2 - GeneticSubsetter-0.7/GeneticSubsetter/man/GeneticSubsetter.Rd | 4 +- GeneticSubsetter-0.7/GeneticSubsetter/man/HET.Rd |only 9 files changed, 15 insertions(+), 16 deletions(-)
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Title: Visualizes Random Forests with Feature Contributions
Description: Form visualizations of high dimensional mapping structures of random forests and feature contributions.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.9.1 dated 2016-01-03 and 1.9.3 dated 2016-03-29
DESCRIPTION | 10 +-- MD5 | 50 ++++++++-------- NAMESPACE | 7 +- NEWS | 14 ++++ R/RcppExports.R | 8 +- R/Xtestmerger.R |only R/checkPlotTest.R |only R/fcol.R | 29 +++++++++ R/forestFloor_randomForest_multiClass.R | 97 ++++++++++++++++++++++++++++---- R/forestFloor_randomForest_regression.R | 63 +++++++++++++++++--- R/forestFloor_source.R | 35 +++++++---- R/plot.forestFloor_multiClass.R | 21 +++++- R/plot.forestFloor_regression.R | 16 ++++- R/show3d.R | 39 ++++++++++++ man/Xtestmerger.Rd |only man/fcol.Rd | 6 + man/forestFloor.Rd | 23 +++++-- man/plot.forestFloor.Rd | 7 ++ man/plot_simplex3.Rd | 2 man/recTree.Rd | 20 +++++- man/show3d.Rd | 11 +++ src/RcppExports.cpp | 14 ++-- src/testcpp_rec6.cpp | 51 ++++++++++++++-- tests/allExamples.R | 70 +++++++++++------------ tests/stdUsage.R | 68 ++++++++++++++++------ tests/testBinaryClass.R | 17 ++++- tests/testMultiClass.cpp.R | 59 ++++++++++++++----- tests/test_Xtestmerger.R |only 28 files changed, 564 insertions(+), 173 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description:
Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 3.1-0 dated 2016-03-25 and 3.1-1 dated 2016-03-29
DESCRIPTION | 14 ++-- MD5 | 6 +- NEWS | 4 + man/effects-package.Rd | 143 ++++++++++++++++++++++++------------------------- 4 files changed, 86 insertions(+), 81 deletions(-)
Title: Interface to Bold Systems 'API'
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic 'barcode' data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 0.3.4 dated 2016-03-23 and 0.3.5 dated 2016-03-29
DESCRIPTION | 10 +++++----- MD5 | 35 +++++++++++++++++++---------------- NEWS.md | 15 +++++++++++++-- R/bold_identify.R | 7 ++++--- R/bold_tax_id.R | 5 ++--- R/bold_tax_name.R | 4 ++-- R/zzz.R | 2 +- README.md | 20 ++++++++++---------- inst/doc/bold_vignette.Rmd | 2 +- inst/doc/bold_vignette.html | 2 +- man/bold_identify.Rd | 5 +++-- man/bold_tax_id.Rd | 5 ++--- man/bold_tax_name.Rd | 4 ++-- tests/testthat/test-bold_identify.R |only tests/testthat/test-bold_seq.R | 16 +++++++++------- tests/testthat/test-bold_seqspec.R | 18 ++++++++++-------- tests/testthat/test-bold_specimens.R | 18 +++++++++++------- tests/testthat/test-bold_tax_id.R |only tests/testthat/test-bold_tax_name.R |only vignettes/bold_vignette.Rmd | 2 +- 20 files changed, 96 insertions(+), 74 deletions(-)
Title: Assertions for Checking the State of R
Description: A set of predicates and assertions for checking the state and
capabilities of R, the operating system it is running on, and the IDE
being used. This is mainly for use by other package developers who
want to include run-time testing features in their own packages.
End-users will usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.reflection versions 0.0-2 dated 2016-03-06 and 0.0-3 dated 2016-03-29
DESCRIPTION | 10 MD5 | 36 - NAMESPACE | 2 NEWS | 2 R/assert-is-r-version.R | 7 R/assert-r-has-capability.R | 308 +++++++------- R/is-current.R | 26 + R/is-ide.R | 352 ++++++++-------- R/is-r-mode.R | 8 R/is-r-version.R | 12 R/r-has-capability.R | 710 ++++++++++++++++----------------- man/is_package_current.Rd | 2 man/is_r.Rd | 14 man/r_can_find_tools.Rd | 146 +++--- tests/testthat.R | 12 tests/testthat/test-is-32-64-bit.R | 34 - tests/testthat/test-is-decimal-point.R | 176 ++++---- tests/testthat/test-is-ide.R | 244 +++++------ tests/testthat/test-is-r-mode.R | 82 +-- 19 files changed, 1118 insertions(+), 1065 deletions(-)
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