Title: Multi-States Semi-Markov Models
Diff between SemiMarkov versions 1.3.1 dated 2014-06-16 and 1.4 dated 2014-10-05
Description: Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model.
Author: Agnieszka Listwon-Krol, Philippe Saint-Pierre
Maintainer: Agnieszka Listwon-Krol
DESCRIPTION | 14 +++++------
MD5 | 10 ++++----
R/SemiMarkov.r | 63 ++++++++++++++++++++++++++++++++---------------------
man/hazard.Rd | 45 ++++++++++++++++++++-----------------
man/plot.hazard.Rd | 31 ++++++++++++++------------
man/semiMarkov.Rd | 57 ++++++++++++++++++++++++++---------------------
6 files changed, 122 insertions(+), 98 deletions(-)
Title: Automates the creation of new statistical analysis projects.
Diff between ProjectTemplate versions 0.5-1 dated 2014-03-17 and 0.6 dated 2014-10-05
More information about ProjectTemplate at CRAN
Description: ProjectTemplate provides functions to
automatically build a directory structure for a new R
project. Using this structure, ProjectTemplate
automates data loading, preprocessing, library
importing and unit testing.
Author: Aleksandar Blagotic [ctb],
Diego Valle-Jones [ctb],
Jeffrey Breen [ctb],
Joakim Lundborg [ctb],
John Myles White [aut, cph],
Josh Bode [ctb],
Kenton White [ctb],
Kirill Mueller [ctb, cre],
Matteo Redaelli [ctb],
Noah Lorang [ctb],
Patrick Schalk [ctb]
Maintainer: Kirill Mueller
ProjectTemplate-0.5-1/ProjectTemplate/R/extensions.dispatch.table.R |only
ProjectTemplate-0.5-1/ProjectTemplate/man/extensions.dispatch.table.Rd |only
ProjectTemplate-0.5-1/ProjectTemplate/tests/1.R |only
ProjectTemplate-0.5-1/ProjectTemplate/tests/2.R |only
ProjectTemplate-0.5-1/ProjectTemplate/tests/3.R |only
ProjectTemplate-0.5-1/ProjectTemplate/tests/4.R |only
ProjectTemplate-0.5-1/ProjectTemplate/tests/5.R |only
ProjectTemplate-0.6/ProjectTemplate/DESCRIPTION | 52 -
ProjectTemplate-0.6/ProjectTemplate/MD5 | 183 ++--
ProjectTemplate-0.6/ProjectTemplate/NAMESPACE | 4
ProjectTemplate-0.6/ProjectTemplate/R/add.extension.R |only
ProjectTemplate-0.6/ProjectTemplate/R/arff.reader.R | 4
ProjectTemplate-0.6/ProjectTemplate/R/cache.R | 2
ProjectTemplate-0.6/ProjectTemplate/R/clean.variable.name.R | 2
ProjectTemplate-0.6/ProjectTemplate/R/create.project.R | 17
ProjectTemplate-0.6/ProjectTemplate/R/csv.reader.R | 2
ProjectTemplate-0.6/ProjectTemplate/R/csv2.reader.R | 2
ProjectTemplate-0.6/ProjectTemplate/R/db.reader.R | 18
ProjectTemplate-0.6/ProjectTemplate/R/dbf.reader.R | 6
ProjectTemplate-0.6/ProjectTemplate/R/default.config.R |only
ProjectTemplate-0.6/ProjectTemplate/R/epiinfo.reader.R | 6
ProjectTemplate-0.6/ProjectTemplate/R/get.project.R | 9
ProjectTemplate-0.6/ProjectTemplate/R/load.project.R | 457 ++++------
ProjectTemplate-0.6/ProjectTemplate/R/migrate.project.R |only
ProjectTemplate-0.6/ProjectTemplate/R/mp3.reader.R | 6
ProjectTemplate-0.6/ProjectTemplate/R/mtp.reader.R | 4
ProjectTemplate-0.6/ProjectTemplate/R/new.config.R |only
ProjectTemplate-0.6/ProjectTemplate/R/octave.reader.R | 4
ProjectTemplate-0.6/ProjectTemplate/R/ppm.reader.R | 4
ProjectTemplate-0.6/ProjectTemplate/R/preinstalled.readers.R |only
ProjectTemplate-0.6/ProjectTemplate/R/reload.project.R | 7
ProjectTemplate-0.6/ProjectTemplate/R/require.package.R | 45
ProjectTemplate-0.6/ProjectTemplate/R/spss.reader.R | 4
ProjectTemplate-0.6/ProjectTemplate/R/sql.reader.R | 127 +-
ProjectTemplate-0.6/ProjectTemplate/R/stata.reader.R | 4
ProjectTemplate-0.6/ProjectTemplate/R/stub.tests.R | 8
ProjectTemplate-0.6/ProjectTemplate/R/systat.reader.R | 4
ProjectTemplate-0.6/ProjectTemplate/R/test.project.R | 10
ProjectTemplate-0.6/ProjectTemplate/R/translate.dcf.R | 10
ProjectTemplate-0.6/ProjectTemplate/R/tsv.reader.R | 2
ProjectTemplate-0.6/ProjectTemplate/R/url.reader.R | 10
ProjectTemplate-0.6/ProjectTemplate/R/wsv.reader.R | 7
ProjectTemplate-0.6/ProjectTemplate/R/xls.reader.R | 8
ProjectTemplate-0.6/ProjectTemplate/R/xlsx.reader.R | 10
ProjectTemplate-0.6/ProjectTemplate/R/xport.reader.R | 4
ProjectTemplate-0.6/ProjectTemplate/inst/NEWS.Rd | 57 +
ProjectTemplate-0.6/ProjectTemplate/inst/defaults/config |only
ProjectTemplate-0.6/ProjectTemplate/inst/defaults/full.tar |binary
ProjectTemplate-0.6/ProjectTemplate/inst/defaults/minimal.tar |binary
ProjectTemplate-0.6/ProjectTemplate/inst/example_data/example.foo |only
ProjectTemplate-0.6/ProjectTemplate/inst/example_data/example_09.wsv | 8
ProjectTemplate-0.6/ProjectTemplate/inst/example_data/foo.reader.R |only
ProjectTemplate-0.6/ProjectTemplate/man/ProjectTemplate.Rd | 2
ProjectTemplate-0.6/ProjectTemplate/man/add.extension.Rd |only
ProjectTemplate-0.6/ProjectTemplate/man/arff.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/cache.Rd | 6
ProjectTemplate-0.6/ProjectTemplate/man/cache.name.Rd | 5
ProjectTemplate-0.6/ProjectTemplate/man/cache.project.Rd | 2
ProjectTemplate-0.6/ProjectTemplate/man/clean.variable.name.Rd | 6
ProjectTemplate-0.6/ProjectTemplate/man/create.project.Rd | 34
ProjectTemplate-0.6/ProjectTemplate/man/csv.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/csv2.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/db.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/dbf.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/default.config.Rd |only
ProjectTemplate-0.6/ProjectTemplate/man/epiinfo.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/file.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/get.project.Rd | 2
ProjectTemplate-0.6/ProjectTemplate/man/load.project.Rd | 8
ProjectTemplate-0.6/ProjectTemplate/man/migrate.project.Rd |only
ProjectTemplate-0.6/ProjectTemplate/man/mp3.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/mtp.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/new.config.Rd |only
ProjectTemplate-0.6/ProjectTemplate/man/octave.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/ppm.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/preinstalled.readers.Rd |only
ProjectTemplate-0.6/ProjectTemplate/man/r.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/rdata.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/reload.project.Rd | 8
ProjectTemplate-0.6/ProjectTemplate/man/require.package.Rd | 30
ProjectTemplate-0.6/ProjectTemplate/man/run.project.Rd | 2
ProjectTemplate-0.6/ProjectTemplate/man/show.project.Rd | 2
ProjectTemplate-0.6/ProjectTemplate/man/spss.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/sql.reader.Rd | 17
ProjectTemplate-0.6/ProjectTemplate/man/stata.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/stub.tests.Rd | 2
ProjectTemplate-0.6/ProjectTemplate/man/systat.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/test.project.Rd | 2
ProjectTemplate-0.6/ProjectTemplate/man/translate.dcf.Rd | 6
ProjectTemplate-0.6/ProjectTemplate/man/tsv.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/url.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/wsv.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/xls.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/xlsx.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/man/xport.reader.Rd | 9
ProjectTemplate-0.6/ProjectTemplate/tests/run-all.R |only
ProjectTemplate-0.6/ProjectTemplate/tests/testthat |only
97 files changed, 776 insertions(+), 663 deletions(-)
Permanent link
Title: Computation of power and level tables for hypothesis tests.
Diff between PoweR versions 1.0.1 dated 2013-11-06 and 1.0.2 dated 2014-10-05
Description: Functions for the computation of power and level tables for hypothesis tests, in LaTeX format, functions to build explanatory graphs for studying power of test statistics.
Author: Pierre Lafaye de Micheaux
Maintainer: P. Lafaye de Micheaux
DESCRIPTION | 11 +-
MD5 | 68 ++++++------
NAMESPACE | 2
R/compquant.R | 30 ++++-
R/create.alter.R | 2
R/gensample.R | 46 ++++----
R/getindex.R | 2
R/getnbparlaws.R | 2
R/getnbparstats.R | 2
R/law.cstr.R | 2
R/many.crit.R | 24 +++-
R/many.pval.R | 101 ++++++++++++++----
R/powcomp-easy.R | 56 +++++++++-
R/powcomp-fast.R | 161 ++++++++++++++++++++++--------
R/pvalueMC.R | 3
R/stat.cstr.R | 2
R/statcompute.R | 25 ++--
inst/HISTORY | 9 +
inst/printTemplates/print.power1.R | 9 +
man/compquant.Rd | 23 +++-
man/gensample.Rd | 3
man/many.crit.Rd | 12 ++
man/many.pval.Rd | 21 +++
man/powcomp-easy.Rd | 27 ++++-
man/powcomp-fast.Rd | 19 ++-
man/statcompute.Rd | 9 +
src/Makevars |only
src/calcpuiss.cpp | 33 +++---
src/calcpuissRcpp.cpp |only
src/laws-stats/stats/pvalues/pvalue24.cpp | 19 +++
src/laws-stats/stats/pvalues/pvalue27.cpp | 18 +++
src/laws-stats/stats/pvalues/pvalue28.cpp | 16 ++
src/laws-stats/stats/pvalues/pvalue34.cpp | 17 ++-
src/laws-stats/stats/pvalues/pvalue83.cpp | 3
src/laws-stats/stats/pvalues/pvaluej.cpp |only
src/laws-stats/stats/stat28.cpp | 2
src/laws-stats/stats/statj.cpp |only
37 files changed, 574 insertions(+), 205 deletions(-)
Title: Tools to manage a parametric function that describes phenology
Diff between phenology versions 3.72 dated 2014-08-25 and 4.0 dated 2014-10-05
Description: Functions to fit and test the phenology of species based on counts. The package includes also several useful more general functions.
Author: Marc Girondot
Maintainer: Marc Girondot
phenology-3.72/phenology/R/convert.ts.R |only
phenology-3.72/phenology/R/phenology-swot.R |only
phenology-3.72/phenology/man/convert.ts.Rd |only
phenology-3.72/phenology/man/phenology_swot.Rd |only
phenology-4.0/phenology/DESCRIPTION | 8 -
phenology-4.0/phenology/MD5 | 146 +++++++++----------
phenology-4.0/phenology/NAMESPACE | 5
phenology-4.0/phenology/NEWS | 10 +
phenology-4.0/phenology/R/MHalgoGen.R | 24 ++-
phenology-4.0/phenology/R/adapt_parameters.R | 3
phenology-4.0/phenology/R/add_phenology.R | 61 ++-----
phenology-4.0/phenology/R/convert.tz.R |only
phenology-4.0/phenology/R/ind_long_lat.R | 15 -
phenology-4.0/phenology/R/local.search.R | 11 -
phenology-4.0/phenology/R/par_init.R | 12 +
phenology-4.0/phenology/R/phenology-package.R | 7
phenology-4.0/phenology/R/read_phenology.R | 5
phenology-4.0/phenology/man/BE_to_LBLE.Rd | 2
phenology-4.0/phenology/man/ChangeCoordinate.Rd | 2
phenology-4.0/phenology/man/Gratiot.Rd | 2
phenology-4.0/phenology/man/LBLE_to_BE.Rd | 2
phenology-4.0/phenology/man/LBLE_to_L.Rd | 2
phenology-4.0/phenology/man/L_to_LBLE.Rd | 2
phenology-4.0/phenology/man/MinBMinE_to_Min.Rd | 2
phenology-4.0/phenology/man/ScalePreviousPlot.Rd | 2
phenology-4.0/phenology/man/adapt_parameters.Rd | 9 -
phenology-4.0/phenology/man/add_SD.Rd | 2
phenology-4.0/phenology/man/add_phenology.Rd | 17 +-
phenology-4.0/phenology/man/as.mcmc.mcmcComposite.Rd | 2
phenology-4.0/phenology/man/as.par.mcmcComposite.Rd | 2
phenology-4.0/phenology/man/asc.Rd | 2
phenology-4.0/phenology/man/barplot_errbar.Rd | 2
phenology-4.0/phenology/man/chr.Rd | 2
phenology-4.0/phenology/man/clean.knitr.Rd | 2
phenology-4.0/phenology/man/compare_AIC.Rd | 2
phenology-4.0/phenology/man/compassRose2.Rd | 2
phenology-4.0/phenology/man/convert.tz.Rd |only
phenology-4.0/phenology/man/extract_result.Rd | 2
phenology-4.0/phenology/man/fit_phenology.Rd | 6
phenology-4.0/phenology/man/getTide.Rd | 6
phenology-4.0/phenology/man/growlnotify.Rd | 2
phenology-4.0/phenology/man/ind_long_lat.Rd | 2
phenology-4.0/phenology/man/likelihood_phenology.Rd | 10 -
phenology-4.0/phenology/man/local.search.Rd | 13 +
phenology-4.0/phenology/man/logLik.phenology.Rd | 2
phenology-4.0/phenology/man/map.scale2.Rd | 2
phenology-4.0/phenology/man/map_Gratiot.Rd | 2
phenology-4.0/phenology/man/map_phenology.Rd | 6
phenology-4.0/phenology/man/moon_phase.Rd | 2
phenology-4.0/phenology/man/par_init.Rd | 14 +
phenology-4.0/phenology/man/phenology-package.Rd | 10 -
phenology-4.0/phenology/man/phenology.Rd | 2
phenology-4.0/phenology/man/phenology_MHmcmc.Rd | 6
phenology-4.0/phenology/man/phenology_MHmcmc_p.Rd | 2
phenology-4.0/phenology/man/plot.mcmcComposite.Rd | 8 -
phenology-4.0/phenology/man/plot.phenology.Rd | 6
phenology-4.0/phenology/man/plot.phenologymap.Rd | 2
phenology-4.0/phenology/man/plot_add.Rd | 2
phenology-4.0/phenology/man/plot_delta.Rd | 2
phenology-4.0/phenology/man/plot_errbar.Rd | 6
phenology-4.0/phenology/man/plot_phi.Rd | 2
phenology-4.0/phenology/man/print.phenology.Rd | 2
phenology-4.0/phenology/man/print.phenologymap.Rd | 2
phenology-4.0/phenology/man/print.phenologyout.Rd | 2
phenology-4.0/phenology/man/read_folder.Rd | 2
phenology-4.0/phenology/man/remove_site.Rd | 2
phenology-4.0/phenology/man/result_Gratiot.Rd | 2
phenology-4.0/phenology/man/result_Gratiot1.Rd | 2
phenology-4.0/phenology/man/result_Gratiot2.Rd | 2
phenology-4.0/phenology/man/result_Gratiot_Flat.Rd | 2
phenology-4.0/phenology/man/result_Gratiot_mcmc.Rd | 2
phenology-4.0/phenology/man/shift_sinusoid.Rd | 2
phenology-4.0/phenology/man/summary.mcmcComposite.Rd | 2
phenology-4.0/phenology/man/summary.phenology.Rd | 2
phenology-4.0/phenology/man/summary.phenologymap.Rd | 2
phenology-4.0/phenology/man/summary.phenologyout.Rd | 2
phenology-4.0/phenology/man/toggle_Min_PMin.Rd | 2
77 files changed, 276 insertions(+), 240 deletions(-)
Title: Phylogenetic analysis in R
Diff between phangorn versions 1.99-7 dated 2014-02-02 and 1.99-8 dated 2014-10-05
Description: Phylogenetic analysis in R (Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
Distance methods & Hadamard conjugation)
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep
DESCRIPTION | 15
MD5 | 166
NAMESPACE | 140
NEWS | 1564 +++---
R/Coalescent.R | 230
R/Densi.R | 377 -
R/SOWH.R |only
R/cladePar.R | 38
R/clanistic.R | 824 +--
R/dist.p.R | 158
R/distSeq.R | 388 -
R/fitch.R | 992 ++--
R/networx.R | 2145 ++++----
R/parsimony.R | 1621 +++---
R/phyDat.R | 1566 +++---
R/phylo.R | 9758 +++++++++++++++++++---------------------
R/sankoff.R | 202
R/simSeq.R |only
R/treeManipulation.R | 2090 ++++----
R/treedist.R | 578 +-
R/zzz.R | 20
README.md |only
build/vignette.rds |binary
inst/CITATION | 34
inst/README | 44
inst/doc/Ancestral.R | 220
inst/doc/Ancestral.Rnw | 340 -
inst/doc/Ancestral.pdf |binary
inst/doc/Trees.R | 442 -
inst/doc/Trees.Rnw | 510 +-
inst/doc/Trees.pdf |binary
inst/doc/phangorn-specials.R | 218
inst/doc/phangorn-specials.Rnw | 514 +-
inst/doc/phangorn-specials.pdf |binary
inst/extdata/Blosum62.dat | 44
inst/extdata/Dayhoff.dat | 44
inst/extdata/HIVb.dat | 44
inst/extdata/HIVw.dat | 44
inst/extdata/JTT.dat | 44
inst/extdata/MtZoa.dat | 60
inst/extdata/RtREV.dat | 44
inst/extdata/VT.dat | 44
inst/extdata/mtREV24.dat | 78
inst/extdata/mtmam.dat | 154
man/Ancestors.Rd | 98
man/NJ.Rd | 84
man/SH.test.Rd | 96
man/SOWH.test.Rd |only
man/ancestral.pml.Rd | 142
man/as.splits.Rd | 143
man/bab.Rd | 124
man/bootstrap.pml.Rd | 195
man/cladePar.Rd | 125
man/consensusNet.Rd | 119
man/densiTree.Rd | 170
man/dist.hamming.Rd | 98
man/dist.p.Rd | 142
man/getClans.Rd | 244 -
man/hadamard.Rd | 162
man/lento.Rd | 94
man/midpoint.Rd | 100
man/modelTest.Rd | 134
man/nni.Rd | 72
man/parsimony.Rd | 161
man/plot.networx.Rd | 184
man/pml.Rd | 304 -
man/pml.fit.Rd | 158
man/pmlCluster.Rd | 132
man/pmlMix.Rd | 206
man/pmlPart.Rd | 133
man/simSeq.Rd | 39
man/splitsNetwork.Rd | 10
man/superTree.Rd | 140
man/treedist.Rd | 92
src/Makevars | 4
src/dist.c | 4
src/fitch.c | 113
src/init.c | 46
src/ml.c | 234
src/phangorn.c | 305 +
src/sankoff.c | 4
vignettes/Ancestral.Rnw | 340 -
vignettes/Trees.Rnw | 510 +-
vignettes/phangorn-specials.Rnw | 514 +-
vignettes/phangorn.bib | 588 +-
vignettes/primates.dna | 122
86 files changed, 16692 insertions(+), 15787 deletions(-)
Title: Local Log-linear Models for Capture-Recapture
Diff between lllcrc versions 1.1 dated 2014-03-12 and 1.2 dated 2014-10-05
Description: Applies local log-linear capture-recapture models (LLLMs) for
closed populations, as described in the doctoral thesis of Zachary Kurtz.
The method is relevant when there are 3-5 capture occasions, with auxiliary
covariates available for all capture occasions. As part of estimating the
number of missing population units, the method estimates the "rate of
missingness" as it varies over the covariate space. In addition,
user-friendly functions are provided to recreate (approximately) the method
of Zwane and van der Heijden (2004), which applied the VGAM package
in a way that is closely related to LLLMs.
Author: Zach Kurtz
Maintainer: Zach Kurtz
DESCRIPTION | 25 +++---
MD5 | 108 ++++++++++++++---------------
NAMESPACE | 2
R/graph.R | 4 -
R/llsimulate.R | 2
R/regression.R | 2
R/user.R | 4 -
man/AICc.vgam.Rd | 20 ++---
man/age.sex.zip.Rd | 24 ++----
man/apply.ic.fit.Rd | 61 +++++++---------
man/apply.local.ml.Rd | 30 +++-----
man/as.num.Rd | 6 -
man/captures.Rd | 25 ++----
man/construct.vgam.Rd | 26 +++----
man/extract.CI.Rd | 35 ++++-----
man/flat.IC.Rd | 45 +++++-------
man/flat.log.linear.Rd | 26 +++----
man/formatdata.Rd | 33 ++++----
man/french.1.Rd | 38 ++++------
man/get.IC.Rd | 39 ++++------
man/ic.all.Rd | 32 ++++----
man/ic.fit.Rd | 57 +++++++--------
man/ic.wghts.Rd | 23 ++----
man/init.pop.Rd | 22 ++---
man/initialize.u.vec.Rd | 11 +-
man/llcrc.flat.boots.Rd | 22 ++---
man/lllcrc-package.Rd | 33 ++++----
man/lllcrc.Rd | 136 ++++++++++++++++---------------------
man/lllcrc.boots.Rd | 42 +++++------
man/llm.sim.Rd | 102 +++++++++++----------------
man/local.ml.Rd | 33 ++++----
man/make.design.matrix.Rd | 10 +-
man/make.hierarchical.term.sets.Rd | 11 +-
man/make.patterns.template.Rd | 13 +--
man/micro.post.stratify.Rd | 48 +++++--------
man/odd.evens.Rd | 11 +-
man/patterns.Rd | 16 ++--
man/patterns.possible.Rd | 7 +
man/pirls.Rd | 58 +++++++--------
man/plot.Rd | 72 ++++++++-----------
man/plot.llsim.Rd | 12 +--
man/pop.to.counts.Rd | 10 +-
man/poptop.Rd | 30 +++-----
man/rates.by.category.Rd | 23 ++----
man/resample.captures.Rd | 15 +---
man/saturated.local.Rd | 21 ++---
man/smooth.patterns.Rd | 35 ++++-----
man/stackydens.Rd | 7 +
man/string.to.array.Rd | 15 +---
man/summarize.by.factors.Rd | 15 +---
man/summary.Rd | 10 +-
man/vgam.crc.Rd | 103 ++++++++++++----------------
man/vgam.crc.boots.Rd | 42 +++++------
man/y.string.to.y.glm.Rd | 13 +--
man/zglm.Rd | 31 +++-----
55 files changed, 789 insertions(+), 907 deletions(-)
Title: Tools for processing COPAS large-particle flow cytometer data
Diff between COPASutils versions 0.1 dated 2014-07-04 and 0.1.4 dated 2014-10-05
Description: A logical workflow for the reading, processing, and visualization
of data obtained from the Union Biometrica Complex Object Parametric
Analyzer and Sorter (COPAS) platform large-particle flow cytometers and a
powerful suite of functions for the rapid processing and analysis of large
high-throughput screening data sets. It combines the speed of dplyr with
the elegance of ggplot2 to make analysis of COPAS data fast and painless.
Author: Tyler Shimko
Maintainer: Erik Andersen
DESCRIPTION | 6 -
MD5 | 66 ++++++++++----------
NAMESPACE | 2
R/COPASutils_functions.R | 112 ++++++++++++++++++++++++-----------
build/vignette.rds |binary
data/BioSorter.RData |binary
data/PresentationStyle.RData |binary
data/bubbleSVMmodel_noProfiler.RData |binary
data/doseData.RData |binary
data/plateData1.RData |binary
data/plateData2.RData |binary
inst/doc/Overview.R | 2
inst/doc/Overview.Rmd | 18 ++++-
inst/doc/Overview.html | 41 +++++++++---
man/BioSorter.Rd | 2
man/COPASutils.Rd | 2
man/bubbleSVMmodel_noProfiler.Rd | 2
man/doseData.Rd | 2
man/edgeEffect.Rd | 6 -
man/extractTime.Rd | 2
man/fillWells.Rd | 2
man/plateData1.Rd | 2
man/plateData2.Rd | 2
man/plotCompare.Rd | 12 +++
man/plotCorMatrix.Rd | 18 ++++-
man/plotDR.Rd | 14 +++-
man/plotDR_allTraits.Rd | 6 -
man/plotTrait.Rd | 14 ++++
man/presentation.Rd | 2
man/readPlate.Rd | 2
man/readSorter.Rd | 2
man/removeWells.Rd | 6 +
man/summarizePlate.Rd | 7 +-
vignettes/Overview.Rmd | 18 ++++-
34 files changed, 251 insertions(+), 119 deletions(-)
Title: Automated runs and evaluations of ecological niche models
Diff between ENMeval versions 0.1.0 dated 2014-08-26 and 0.1.1 dated 2014-10-05
Description: Automatically partitions data into evaluation bins, executes ecological niche models across a range of settings, and calculates a variety of evaluation statistics. Current version only implements ENMs with Maxent (Phillips et al. 2006).
Author: Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A. Boria, Jamie M. Kass, Maria Uriarte and Robert P. Anderson
Maintainer: Robert Muscarella
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 8 ++++++--
R/calc.aicc.R | 5 ++++-
data/enmeval_results.rda |binary
man/calc.aicc.Rd | 6 +++---
6 files changed, 22 insertions(+), 15 deletions(-)
More information about ropensecretsapi at CRAN
Permanent link
Title: Rainfall Frequency (Design Storm) Estimates from the US National
Weather Service
Diff between rainfreq versions 0.1 dated 2014-05-23 and 0.2 dated 2014-10-05
Description: Estimates of rainfall at desired frequency (e.g., 1% annual
chance or 100-year return period) and desired duration (e.g.,
24-hour duration) are often required in the design of dams and other
hydraulic structures, catastrophe risk modeling, environmental
planning and management. One major source of such estimates for the
USA is the NOAA National Weather Service's (NWS) division of
Hydrometeorological Design Studies Center (HDSC). Raw data from
NWS-HDSC is available at 1-km resolution and comes as a huge number
of GIS files. This package provides functionality to easily access
and analyze the 1-km GIS files provided by NWS' PF Data Server for
the entire USA. This package also comes with datasets on record point
rainfall measurements provided by NWS-HDSC.
Author: Gopi Goteti
Maintainer: Gopi Goteti
rainfreq-0.1/rainfreq/inst/doc/rainfreq_demo.Rnw |only
rainfreq-0.1/rainfreq/inst/doc/rainfreq_demo.pdf |only
rainfreq-0.1/rainfreq/vignettes/rainfreq_demo.Rnw |only
rainfreq-0.2/rainfreq/DESCRIPTION | 12 +--
rainfreq-0.2/rainfreq/LICENSE |only
rainfreq-0.2/rainfreq/MD5 | 27 ++++---
rainfreq-0.2/rainfreq/NAMESPACE | 2
rainfreq-0.2/rainfreq/NEWS | 11 +++
rainfreq-0.2/rainfreq/R/extract_freq.r | 9 ++
rainfreq-0.2/rainfreq/build/vignette.rds |binary
rainfreq-0.2/rainfreq/inst/doc/rainfreq_demo.R | 76 ++++------------------
rainfreq-0.2/rainfreq/inst/doc/rainfreq_demo.Rmd |only
rainfreq-0.2/rainfreq/inst/doc/rainfreq_demo.html |only
rainfreq-0.2/rainfreq/man/extract_freq.Rd | 68 ++++++++-----------
rainfreq-0.2/rainfreq/man/rain_max_usa.Rd | 37 +++++-----
rainfreq-0.2/rainfreq/man/rain_max_world.Rd | 37 +++++-----
rainfreq-0.2/rainfreq/man/rainfreq.Rd | 29 +++-----
rainfreq-0.2/rainfreq/vignettes/rainfreq_demo.Rmd |only
18 files changed, 142 insertions(+), 166 deletions(-)
Title: Programming with Big Data -- Interface to MPI
Diff between pbdMPI versions 0.2-4 dated 2014-05-31 and 0.2-5 dated 2014-10-05
Description: pbdMPI provides an efficient interface to MPI by utilizing S4
classes and methods with a focus on Single Program/Multiple Data (SPMD)
parallel programming style, which is intended for batch parallel
execution.
Author: Wei-Chen Chen [aut, cre],
George Ostrouchov [aut],
Drew Schmidt [aut],
Pragneshkumar Patel [aut],
Hao Yu [aut],
Christian Heckendorf [ctb] (FreeBSD),
Brian Ripley [ctb] (Windows HPC Pack 2012),
R Core team [ctb] (some functions are modified from the base packages)
Maintainer: Wei-Chen Chen
pbdMPI-0.2-4/pbdMPI/vignettes/pbdMPI-include/jss.bst |only
pbdMPI-0.2-4/pbdMPI/vignettes/pbdMPI-include/jss.cls |only
pbdMPI-0.2-5/pbdMPI/ChangeLog | 26 +
pbdMPI-0.2-5/pbdMPI/DESCRIPTION | 8
pbdMPI-0.2-5/pbdMPI/MD5 | 150 +++++-----
pbdMPI-0.2-5/pbdMPI/NAMESPACE | 1
pbdMPI-0.2-5/pbdMPI/R/000_globalVariables.r |only
pbdMPI-0.2-5/pbdMPI/R/api_split.r |only
pbdMPI-0.2-5/pbdMPI/R/api_tool.r | 123 +++++---
pbdMPI-0.2-5/pbdMPI/R/spmd_utility.r | 6
pbdMPI-0.2-5/pbdMPI/R/zzz.r.in | 75 +++--
pbdMPI-0.2-5/pbdMPI/cleanup | 1
pbdMPI-0.2-5/pbdMPI/configure | 13
pbdMPI-0.2-5/pbdMPI/configure.ac | 10
pbdMPI-0.2-5/pbdMPI/data/control.r | 52 +--
pbdMPI-0.2-5/pbdMPI/demo/00Index | 3
pbdMPI-0.2-5/pbdMPI/demo/allgather.r | 2
pbdMPI-0.2-5/pbdMPI/demo/allreduce.r | 2
pbdMPI-0.2-5/pbdMPI/demo/any_all.r | 2
pbdMPI-0.2-5/pbdMPI/demo/bcast.r | 2
pbdMPI-0.2-5/pbdMPI/demo/divide.r | 11
pbdMPI-0.2-5/pbdMPI/demo/gather.r | 2
pbdMPI-0.2-5/pbdMPI/demo/new_allgather.r |only
pbdMPI-0.2-5/pbdMPI/demo/new_allreduce.r |only
pbdMPI-0.2-5/pbdMPI/demo/pbdApply.r | 2
pbdMPI-0.2-5/pbdMPI/demo/pbdLapply.r | 2
pbdMPI-0.2-5/pbdMPI/demo/reduce.r | 2
pbdMPI-0.2-5/pbdMPI/demo/scatter.r | 2
pbdMPI-0.2-5/pbdMPI/demo/seed.r | 2
pbdMPI-0.2-5/pbdMPI/demo/simple_balance.r | 2
pbdMPI-0.2-5/pbdMPI/demo/simple_io.r | 2
pbdMPI-0.2-5/pbdMPI/demo/simple_pairs.r | 2
pbdMPI-0.2-5/pbdMPI/demo/sort.r | 2
pbdMPI-0.2-5/pbdMPI/demo/task_pull.r | 2
pbdMPI-0.2-5/pbdMPI/inst/doc/pbdMPI-guide.Rnw | 11
pbdMPI-0.2-5/pbdMPI/inst/doc/pbdMPI-guide.pdf |binary
pbdMPI-0.2-5/pbdMPI/man/aa_allgather-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/aa_allreduce-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/aa_bcast-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/aa_gather-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/aa_reduce-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/aa_scatter-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ab_recv-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ab_send-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ac_irecv-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ac_isend-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ad_sendrecv-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ad_sendrecv.replace-method.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/cc_comm.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/dd_info.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/dd_is.comm.null.Rd |only
pbdMPI-0.2-5/pbdMPI/man/dd_sourcetag.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/dd_wait.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/vv_get_jid.Rd | 5
pbdMPI-0.2-5/pbdMPI/man/vv_print_cat.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/vv_seed.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ww_comm_as_gbd.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ww_comm_balance.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ww_comm_read.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/ww_comm_write.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/xx_comm_allpairs.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/xx_comm_any_all.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/xx_comm_base.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/xx_comm_dist.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/xx_comm_pairwise.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/xx_comm_range.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/xx_comm_sort.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/xx_comm_stop_warning.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/xx_comm_which.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/yy_api_apply.Rd | 2
pbdMPI-0.2-5/pbdMPI/man/zz_spmd_internal.Rd | 1
pbdMPI-0.2-5/pbdMPI/src/Makevars.in | 1
pbdMPI-0.2-5/pbdMPI/src/spmd_communicator.c | 8
pbdMPI-0.2-5/pbdMPI/src/spmd_utility.c | 17 +
pbdMPI-0.2-5/pbdMPI/vignettes/build_pdf.sh | 11
pbdMPI-0.2-5/pbdMPI/vignettes/pbdMPI-guide.Rnw | 11
pbdMPI-0.2-5/pbdMPI/vignettes/pbdMPI-include/01-acknowledgement.tex | 14
pbdMPI-0.2-5/pbdMPI/vignettes/pbdMPI-include/01-introduction.tex | 9
pbdMPI-0.2-5/pbdMPI/vignettes/pbdMPI-include/03-faq.tex | 48 +++
pbdMPI-0.2-5/pbdMPI/vignettes/pbdMPI-include/my_jss.cls |only
80 files changed, 468 insertions(+), 241 deletions(-)
Title: Ordinal Regression for High-dimensional Data
Diff between ordinalgmifs versions 1.0.0 dated 2014-09-24 and 1.0.1 dated 2014-10-05
Description: This package provides a function for fitting cumulative link, adjacent category, forward and backward continuation ratio, and stereotype ordinal response models when the number of parameters exceeds the sample size, using the the generalized monotone incremental forward stagewise method.
Author: Kellie J. Archer, Jiayi Hou, Qing Zhou, Kyle Ferber, John G. Layne, Amanda Gentry
Maintainer: Kellie J. Archer
DESCRIPTION | 8 +++---
MD5 | 12 ++++-----
R/ordinal.gmifs.R | 13 +++++++--
R/plot.ordinalgmifs.R | 62 +++++++++++++++++++++++++++++++++--------------
R/predict.ordinalgmifs.R | 32 +++++++++++++++++-------
man/ordinal.gmifs.Rd | 4 +--
man/plot.ordinalgmifs.Rd | 11 +++++++-
7 files changed, 99 insertions(+), 43 deletions(-)
Title: An R Package for Simulating IRT-Based Computerized Adaptive
Tests
Diff between catIrt versions 0.4-2 dated 2014-06-21 and 0.5-0 dated 2014-10-05
Description: Functions designed to simulate data that conform to basic
unidimensional IRT models (for now 3-parameter binary response models
and graded response models) along with Post-Hoc CAT simulations of
those models with various item selection methods, ability estimation
methods, and termination criteria.
Author: Steven W. Nydick
Maintainer: Steven W. Nydick
catIrt-0.4-2/catIrt/R/q.brm.R |only
catIrt-0.4-2/catIrt/R/q.grm.R |only
catIrt-0.4-2/catIrt/src/simIrt.c |only
catIrt-0.5-0/catIrt/DESCRIPTION | 10 +-
catIrt-0.5-0/catIrt/MD5 | 84 ++++++++---------
catIrt-0.5-0/catIrt/NAMESPACE | 1
catIrt-0.5-0/catIrt/R/ExtractOperators.R | 25 +++++
catIrt-0.5-0/catIrt/R/FI.brm.R | 63 +++----------
catIrt-0.5-0/catIrt/R/FI.default.R | 107 ----------------------
catIrt-0.5-0/catIrt/R/FI.grm.R | 144 +++++-------------------------
catIrt-0.5-0/catIrt/R/IKL.R | 5 -
catIrt-0.5-0/catIrt/R/KL.brm.R | 24 ++---
catIrt-0.5-0/catIrt/R/KL.default.R | 49 ----------
catIrt-0.5-0/catIrt/R/KL.grm.R | 101 +++------------------
catIrt-0.5-0/catIrt/R/WFI.R | 19 ++-
catIrt-0.5-0/catIrt/R/bmeEst.R | 27 ++---
catIrt-0.5-0/catIrt/R/catIrt.R | 9 +
catIrt-0.5-0/catIrt/R/eapEst.R | 42 ++++----
catIrt-0.5-0/catIrt/R/integrate.q.R |only
catIrt-0.5-0/catIrt/R/integrate.s.R |only
catIrt-0.5-0/catIrt/R/lder1.brm.R | 47 ++++++---
catIrt-0.5-0/catIrt/R/lder1.grm.R | 113 +++++++++--------------
catIrt-0.5-0/catIrt/R/lder2.brm.R | 35 +++----
catIrt-0.5-0/catIrt/R/lder2.grm.R | 74 +++------------
catIrt-0.5-0/catIrt/R/logLik.brm.R | 47 +++------
catIrt-0.5-0/catIrt/R/logLik.grm.R | 95 +++----------------
catIrt-0.5-0/catIrt/R/mleEst.R | 23 ++--
catIrt-0.5-0/catIrt/R/p.brm.R | 16 +--
catIrt-0.5-0/catIrt/R/p.grm.R | 18 +--
catIrt-0.5-0/catIrt/R/pder1.brm.R | 24 ++---
catIrt-0.5-0/catIrt/R/pder1.grm.R | 20 +---
catIrt-0.5-0/catIrt/R/pder2.brm.R | 25 ++---
catIrt-0.5-0/catIrt/R/pder2.grm.R | 21 +---
catIrt-0.5-0/catIrt/R/print.catIrt.R | 18 +++
catIrt-0.5-0/catIrt/R/simIrt.R | 13 ++
catIrt-0.5-0/catIrt/R/termGLR.R | 2
catIrt-0.5-0/catIrt/R/termSPRT.R | 4
catIrt-0.5-0/catIrt/R/wleEst.R | 37 +++----
catIrt-0.5-0/catIrt/inst/NEWS.Rd | 35 +++++++
catIrt-0.5-0/catIrt/man/FI.Rd | 2
catIrt-0.5-0/catIrt/man/KL.Rd | 2
catIrt-0.5-0/catIrt/man/catIrt-package.Rd | 4
catIrt-0.5-0/catIrt/man/itChoose.Rd | 2
catIrt-0.5-0/catIrt/man/mleEst.Rd | 13 --
catIrt-0.5-0/catIrt/src/brm.c |only
catIrt-0.5-0/catIrt/src/grm.c |only
catIrt-0.5-0/catIrt/src/sim.c |only
47 files changed, 494 insertions(+), 906 deletions(-)