Title: STRUctural Modeling of Latent Variables for General Pedigree
Description: Implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre],
Yeunjoo Song [aut],
Stephen Cahn [ctb]
Maintainer: Nathan Morris <nathan.morris@cwru.edu>
Diff between strum versions 0.6 dated 2015-03-02 and 0.6.1 dated 2015-05-11
ChangeLog | 11 ++++++++++- DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/strum.R | 22 ++++++++++++++++++---- inst/doc/strum-example.Rnw | 6 +++++- inst/doc/strum-example.pdf |binary inst/doc/strum-intro.Rnw | 6 +++++- inst/doc/strum-intro.pdf |binary man/strum-package.Rd | 8 +++++--- vignettes/strum-example.Rnw | 6 +++++- vignettes/strum-intro.Rnw | 6 +++++- 11 files changed, 67 insertions(+), 26 deletions(-)
Title: Sampling Surface Simulation for Areal Sampling Methods
Description: Sampling surface simulation is useful in the comparison of different areal sampling methods
in forestry, ecology and natural resources. The sampSurf package allows the simulation
of numerous sampling methods for standing trees and downed woody debris in a spatial context.
It also provides an S4 class and method structure that facilitates the addition of new sampling
methods.
Author: Jeffrey H. Gove
Maintainer: Jeffrey H. Gove <jgove@fs.fed.us>
Diff between sampSurf versions 0.7-2 dated 2014-02-03 and 0.7-3 dated 2015-05-11
DESCRIPTION | 21 +++++++++++---------- MD5 | 30 +++++++++++++++--------------- R/TractClass.R | 3 ++- R/chainsawSliver.R | 9 ++++++--- build/vignette.rds |binary inst/doc/ArealSamplingClass.pdf |binary inst/doc/GettingStarted.Rnw | 4 ++-- inst/doc/GettingStarted.pdf |binary inst/doc/InclusionZoneClass.pdf |binary inst/doc/InclusionZoneGridClass.pdf |binary inst/doc/Overview.pdf |binary inst/doc/StemClass.pdf |binary inst/doc/TractClass.pdf |binary inst/doc/sampSurfClass.pdf |binary man/chainSawIZ.Rd | 2 ++ vignettes/GettingStarted.Rnw | 4 ++-- 16 files changed, 40 insertions(+), 33 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.7-1 dated 2015-03-24 and 0.7-2 dated 2015-05-11
DESCRIPTION | 15 +- MD5 | 149 ++++++++++++++-------------- R/LRT.trend.R | 4 R/RDS.compare.proportions.R | 6 - R/bgk_kde.R | 1 R/errorbar.R |only R/gf.R |only R/llmeC.R | 6 - R/me.impute.R | 29 +++-- R/rds-doc.R | 1 R/robust.inverse.R | 13 +- R/utils.R | 15 ++ data/faux.RData |binary inst/CITATION | 2 man/LRT.trend.test.Rd | 2 man/LRT.value.trend.Rd | 2 man/RDS.I.estimates.Rd | 2 man/RDS.II.estimates.Rd | 2 man/RDS.Rd | 2 man/RDS.SS.estimates.Rd | 2 man/RDS.bootstrap.intervals.Rd | 2 man/RDS.compare.proportions.Rd | 2 man/RDS.compare.two.proportions.Rd | 2 man/as.char.Rd | 2 man/as.rds.data.frame.Rd | 2 man/assert.valid.rds.data.frame.Rd | 2 man/bottleneck.plot.Rd | 2 man/compute.weights.Rd | 2 man/control.rds.estimates.Rd | 2 man/convergence.plot.Rd | 2 man/count.transitions.Rd | 2 man/cumulative.estimate.Rd | 2 man/differential.activity.estimates.Rd | 2 man/extract-methods.Rd | 2 man/faux.Rd | 3 man/fauxmadrona.Rd | 2 man/fauxsycamore.Rd | 2 man/get.h.hat.Rd | 2 man/get.id.Rd | 2 man/get.net.size.Rd | 2 man/get.number.of.recruits.Rd | 2 man/get.population.size.Rd | 2 man/get.rid.Rd | 2 man/get.seed.id.Rd | 2 man/get.seed.rid.Rd | 2 man/get.stationary.distribution.Rd | 2 man/get.wave.Rd | 2 man/gf.weights.Rd |only man/gile.ss.weights.Rd | 2 man/homophily.estimates.Rd | 2 man/impute.degree.Rd | 17 +-- man/indexing-methods.Rd | 2 man/is.rds.data.frame.Rd | 2 man/is.rds.interval.estimate.Rd | 2 man/is.rds.interval.estimate.list.Rd | 2 man/plot.rds.data.frame.Rd | 2 man/print.differential.activity.estimate.Rd | 2 man/print.pvalue.table.Rd | 2 man/print.rds.data.frame.Rd | 2 man/print.rds.interval.estimate.Rd | 2 man/print.summary.svyglm.RDS.Rd | 2 man/rds.I.weights.Rd | 2 man/rds.interval.estimate.Rd | 2 man/read.rdsat.Rd | 2 man/read.rdsobj.Rd | 2 man/reingold.tilford.plot.Rd | 2 man/rid.from.coupons.Rd | 2 man/set.control.class.Rd | 2 man/show.rds.data.frame.Rd | 2 man/summary.svyglm.Rd | 2 man/transition.counts.to.Markov.mle.Rd | 2 man/vh.weights.Rd | 2 man/write.graphviz.Rd | 2 man/write.netdraw.Rd | 2 man/write.rdsat.Rd | 2 man/write.rdsobj.Rd | 2 src/llmeC.c | 6 - 77 files changed, 209 insertions(+), 176 deletions(-)
Title: Probabilistic Fisher Discriminant Analysis
Description: Probabilistic Fisher discriminant analysis (pFDA) is a probabilistic version of the popular and powerful Fisher linear discriminant analysis for dimensionality reduction and classification.
Author: Charles Bouveyron & Camille Brunet
Maintainer: Charles Bouveyron <charles.bouveyron@parisdescartes.fr>
Diff between probFDA versions 1.0 dated 2015-01-27 and 1.0.1 dated 2015-05-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pFDA-internal.R | 3 ++- man/pfda.Rd | 5 +++-- man/predict.pfda.Rd | 5 +++-- man/probFDA-package.Rd | 7 ++++--- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Generalized Beta Distribution of the Second Kind: Properties,
Likelihood, Estimation
Description: Package GB2 explores the Generalized Beta distribution of the second kind. Density, cumulative distribution function, quantiles and moments of the distributions are given. Functions for the full log-likelihood, the profile log-likelihood and the scores are provided. Formulas for various indicators of inequality and poverty under the GB2 are implemented. The GB2 is fitted by the methods of maximum pseudo-likelihood estimation using the full and profile log-likelihood, and non-linear least squares estimation of the model parameters. Various plots for the visualization and analysis of the results are provided. Variance estimation of the parameters is provided for the method of maximum pseudo-likelihood estimation. A mixture distribution based on the compounding property of the GB2 is presented (denoted as "compound" in the documentation). This mixture distribution is based on the discretization of the distribution of the underlying random scale parameter. The discretization can be left or right tail. Density, cumulative distribution function, moments and quantiles for the mixture distribution are provided. The compound mixture distribution is fitted using the method of maximum pseudo-likelihood estimation. The fit can also incorporate the use of auxiliary information. In this new version of the package, the mixture case is complemented with new functions for variance estimation by linearization and comparative density plots.
Author: Monique Graf <monique.p.n.graf@bluewin.ch>, Desislava Nedyalkova <desislava.nedyalkova@gmail.com>.
Maintainer: Desislava Nedyalkova <desislava.nedyalkova@gmail.com>
Diff between GB2 versions 1.2 dated 2014-06-25 and 2.1 dated 2015-05-11
GB2-1.2/GB2/R/CompoundFitAux.R |only GB2-1.2/GB2/man/CompoundFitAux.Rd |only GB2-2.1/GB2/DESCRIPTION | 18 ++--- GB2-2.1/GB2/MD5 | 74 ++++++++++++---------- GB2-2.1/GB2/NAMESPACE | 22 ++++++ GB2-2.1/GB2/R/Compound.R | 16 ++-- GB2-2.1/GB2/R/CompoundAuxDensPlot.r |only GB2-2.1/GB2/R/CompoundAuxFit.R |only GB2-2.1/GB2/R/CompoundAuxVarest.r |only GB2-2.1/GB2/R/CompoundDensPlot.r |only GB2-2.1/GB2/R/CompoundFit.R | 58 ++++++++--------- GB2-2.1/GB2/R/CompoundIndicators.R | 36 +++++++---- GB2-2.1/GB2/R/CompoundMoments.R | 10 +-- GB2-2.1/GB2/R/CompoundQuantiles.R | 26 +++---- GB2-2.1/GB2/R/CompoundVarest.R |only GB2-2.1/GB2/R/Contindic.R | 14 ++-- GB2-2.1/GB2/man/Compound.Rd | 11 +-- GB2-2.1/GB2/man/CompoundAuxDensPlot.Rd |only GB2-2.1/GB2/man/CompoundAuxFit.Rd |only GB2-2.1/GB2/man/CompoundAuxVarest.Rd |only GB2-2.1/GB2/man/CompoundDensPlot.Rd |only GB2-2.1/GB2/man/CompoundFit.Rd | 41 +++++++----- GB2-2.1/GB2/man/CompoundIndicators.Rd | 33 +++++----- GB2-2.1/GB2/man/CompoundMoments.Rd | 8 +- GB2-2.1/GB2/man/CompoundQuantiles.Rd | 8 +- GB2-2.1/GB2/man/CompoundVarest.Rd |only GB2-2.1/GB2/man/Contindic.Rd | 38 +++++------ GB2-2.1/GB2/man/Contprof.Rd | 2 GB2-2.1/GB2/man/Fisk.Rd | 2 GB2-2.1/GB2/man/Gini.Rd | 2 GB2-2.1/GB2/man/Indicators.Rd | 2 GB2-2.1/GB2/man/LogDensity.Rd | 2 GB2-2.1/GB2/man/LogLikelihood.Rd | 2 GB2-2.1/GB2/man/MLfitGB2.Rd | 2 GB2-2.1/GB2/man/MLfullGB2.Rd | 8 +- GB2-2.1/GB2/man/MLprofGB2.Rd | 2 GB2-2.1/GB2/man/Moments.Rd | 2 GB2-2.1/GB2/man/NonlinearFit.Rd | 2 GB2-2.1/GB2/man/PlotsML.Rd | 4 - GB2-2.1/GB2/man/ProfLogLikelihood.Rd | 2 GB2-2.1/GB2/man/RobustWeights.Rd | 2 GB2-2.1/GB2/man/Thomae.Rd | 2 GB2-2.1/GB2/man/Varest.Rd | 108 +++++++++++++-------------------- GB2-2.1/GB2/man/gb2.Rd | 2 44 files changed, 293 insertions(+), 268 deletions(-)
Title: Analysis of Phenotypic, Genotypic and Environmental Data
Description: Easy integration of phenotypic, genotypic and environmental information with "ecogen" objects. Geostatistical tools for analyzing spatial patterns in population biology and extra functions.
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser <leandroroser@ege.fcen.uba.ar>
Diff between EcoGenetics versions 1.1.0 dated 2015-02-19 and 1.2.0 dated 2015-05-11
EcoGenetics-1.1.0/EcoGenetics/R/eco.autocor.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.boothet.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.char2num.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.geary.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.getisord.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.joincount.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.laglistw.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.localmoran.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.moran.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.rarefact.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.rescale.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.sort.R |only EcoGenetics-1.1.0/EcoGenetics/R/ecogen.definition.R |only EcoGenetics-1.1.0/EcoGenetics/R/latlon2distm.R |only EcoGenetics-1.1.0/EcoGenetics/R/other.classes.R |only EcoGenetics-1.1.0/EcoGenetics/data/eco.test.rda |only EcoGenetics-1.1.0/EcoGenetics/man/RelDist-class.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/RelDist-methods.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.autocor.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.boothet.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.char2num.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.geary.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.getisord.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.joincount.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.laglistw.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.localmoran.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.moran.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.rarefact.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.rescale.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.sort.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/latlon2distm.Rd |only EcoGenetics-1.2.0/EcoGenetics/DESCRIPTION | 47 EcoGenetics-1.2.0/EcoGenetics/MD5 | 251 +- EcoGenetics-1.2.0/EcoGenetics/NAMESPACE | 145 - EcoGenetics-1.2.0/EcoGenetics/NEWS | 51 EcoGenetics-1.2.0/EcoGenetics/R/ZZZ.R | 2 EcoGenetics-1.2.0/EcoGenetics/R/auxiliar.R |only EcoGenetics-1.2.0/EcoGenetics/R/classes.R |only EcoGenetics-1.2.0/EcoGenetics/R/control.R |only EcoGenetics-1.2.0/EcoGenetics/R/deprecated.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.2columns.R | 102 EcoGenetics-1.2.0/EcoGenetics/R/eco.2geneland.R | 88 EcoGenetics-1.2.0/EcoGenetics/R/eco.2genepop.R | 183 - EcoGenetics-1.2.0/EcoGenetics/R/eco.2gstudio.R | 47 EcoGenetics-1.2.0/EcoGenetics/R/eco.2hierfstat.R | 95 EcoGenetics-1.2.0/EcoGenetics/R/eco.2spagedi.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.NDVI.R | 324 +-- EcoGenetics-1.2.0/EcoGenetics/R/eco.NDVI.post.R | 242 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.alfreq.R | 103 EcoGenetics-1.2.0/EcoGenetics/R/eco.append.R | 45 EcoGenetics-1.2.0/EcoGenetics/R/eco.association.R | 301 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.cbind.R | 226 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.clear.R | 29 EcoGenetics-1.2.0/EcoGenetics/R/eco.cormantel.R | 339 +-- EcoGenetics-1.2.0/EcoGenetics/R/eco.correlog.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.detrend.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.forestplot.R | 264 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.gsa.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.lagweight.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.lmtree.R | 192 - EcoGenetics-1.2.0/EcoGenetics/R/eco.lsa.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.mantel.R | 118 - EcoGenetics-1.2.0/EcoGenetics/R/eco.merge.R | 239 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.order.R | 172 - EcoGenetics-1.2.0/EcoGenetics/R/eco.pairtest.R | 205 + EcoGenetics-1.2.0/EcoGenetics/R/eco.post.geneland.R | 69 EcoGenetics-1.2.0/EcoGenetics/R/eco.rankplot.R | 382 ++- EcoGenetics-1.2.0/EcoGenetics/R/eco.rbind.R | 94 EcoGenetics-1.2.0/EcoGenetics/R/eco.remove.R | 30 EcoGenetics-1.2.0/EcoGenetics/R/eco.subset.R | 85 EcoGenetics-1.2.0/EcoGenetics/R/eco.theilsen.R | 156 - EcoGenetics-1.2.0/EcoGenetics/R/eco.variogram.R | 151 - EcoGenetics-1.2.0/EcoGenetics/R/eco.weight.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.break.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.crosscor.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.ecogen.definition.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.geary.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.jackknife.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.joincount.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.mantel.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.moran.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.multitable.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.random.test.R |only EcoGenetics-1.2.0/EcoGenetics/R/plot.methods.R |only EcoGenetics-1.2.0/EcoGenetics/R/show_summary.methods.R |only EcoGenetics-1.2.0/EcoGenetics/data/eco.test.RData |only EcoGenetics-1.2.0/EcoGenetics/data/eco2.RData |only EcoGenetics-1.2.0/EcoGenetics/data/eco3.RData |only EcoGenetics-1.2.0/EcoGenetics/data/tab.RData |only EcoGenetics-1.2.0/EcoGenetics/man/EcoGenetics-package.Rd | 1057 +++++----- EcoGenetics-1.2.0/EcoGenetics/man/aue.char2num.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.circle.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.circle.w.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.diamond.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.filter.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.image2df.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.point.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.rescale.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.sort.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.square.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/coordinates.Rd | 38 EcoGenetics-1.2.0/EcoGenetics/man/eco.2columns.Rd | 64 EcoGenetics-1.2.0/EcoGenetics/man/eco.2geneland.Rd | 76 EcoGenetics-1.2.0/EcoGenetics/man/eco.2genepop.Rd | 74 EcoGenetics-1.2.0/EcoGenetics/man/eco.2gstudio.Rd | 66 EcoGenetics-1.2.0/EcoGenetics/man/eco.2hierfstat.Rd | 64 EcoGenetics-1.2.0/EcoGenetics/man/eco.2spagedi.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.NDVI.Rd | 161 - EcoGenetics-1.2.0/EcoGenetics/man/eco.NDVI.post.Rd | 194 + EcoGenetics-1.2.0/EcoGenetics/man/eco.Rd | 36 EcoGenetics-1.2.0/EcoGenetics/man/eco.alfreq.Rd | 68 EcoGenetics-1.2.0/EcoGenetics/man/eco.append.Rd | 66 EcoGenetics-1.2.0/EcoGenetics/man/eco.association.Rd | 113 - EcoGenetics-1.2.0/EcoGenetics/man/eco.autol-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.cbind.Rd | 81 EcoGenetics-1.2.0/EcoGenetics/man/eco.clear.Rd | 60 EcoGenetics-1.2.0/EcoGenetics/man/eco.cormantel.Rd | 201 + EcoGenetics-1.2.0/EcoGenetics/man/eco.correlog-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.correlog-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.correlog.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.detrend-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.detrend-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.detrend.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.gsa-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.gsa-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.gsa.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lagweight-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lagweight-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lagweight.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lmtree-methods.Rd | 38 EcoGenetics-1.2.0/EcoGenetics/man/eco.lmtree.Rd | 185 - 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Title: Import Stata 13 and 14 Data Files
Description: Function to read and write the Stata 13 (and newer) file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre],
R Core Team [cph]
Maintainer: Sebastian Jeworutzki <Sebastian.Jeworutzki@ruhr-uni-bochum.de>
Diff between readstata13 versions 0.6.1 dated 2015-03-24 and 0.7 dated 2015-05-11
DESCRIPTION | 14 +- MD5 | 43 ++++--- NAMESPACE | 2 NEWS |only R/read.R | 28 +++-- R/readstata13.R | 2 R/save.R | 82 +++++++++++---- R/tools.R | 9 - README.md | 10 - man/as.caldays.Rd | 2 man/get.label.Rd | 2 man/get.label.name.Rd | 2 man/get.lang.Rd | 2 man/get.origin.codes.Rd | 2 man/get.varlabel.Rd | 2 man/read.dta13.Rd | 11 +- man/readstata13.Rd | 4 man/save.dta13.Rd | 8 - man/set.label.Rd | 2 man/set.lang.Rd | 2 man/stbcal.Rd | 2 src/rcpp_readstata.cpp | 262 +++++++++++++++++++++++++++--------------------- src/rcpp_savestata.cpp | 61 ++++++++--- 23 files changed, 342 insertions(+), 212 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with
quantitative discourse analysis of transcripts containing
discourse including frequency counts of sentence types, words,
sentences, turns of talk, syllables and other assorted analysis
tasks. The package provides parsing tools for preparing
transcript data. Many functions enable the user to aggregate
data by any number of grouping variables, providing analysis
and seamless integration with other R packages that undertake
higher level analysis and visualization of text. This affords
the user a more efficient and targeted analysis. 'qdap' is
designed for transcript analysis, however, many functions are
applicable to other areas of Text Mining/Natural Language
Processing.
Author: Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.2.0 dated 2014-10-04 and 2.2.1 dated 2015-05-11
DESCRIPTION | 48 MD5 | 947 +++++------ NAMESPACE | 48 NEWS | 127 + R/Animate.character.R |only R/add_incomplete.R |only R/as.tdm.R | 16 R/automated_readability_index.R | 2 R/build_qdap_vignette.R | 25 R/check_text.R | 2 R/dispersion_plot.R | 25 R/end_mark.R | 2 R/formality.R | 165 + R/incomplete_replace.R | 4 R/lexical_classification.R |only R/multigsub.R | 45 R/name2sex.R | 41 R/phrase_net.R | 6 R/polarity.R | 156 + R/pos.R | 21 R/qdap-package.R | 2 R/qdap_df.R | 2 R/scrubber.R | 3 R/sentSplit.R | 28 R/strip.R | 84 R/termco.R | 34 R/termco.h.R | 5 R/trans_context.R | 5 R/type_token_ratio.R |only R/word_length.R |only R/word_position.R |only R/word_stats.R | 2 README.md | 21 build/vignette.rds |binary data/DATA.SPLIT.rda |binary data/DATA.rda |binary data/DATA2.rda |binary data/env.syl.rda |binary data/hamlet.rda |binary data/mraja1.rda |binary data/mraja1spl.rda |binary data/pres_debate_raw2012.rda |binary data/pres_debates2012.rda |binary data/raj.act.1.rda |binary data/raj.act.1POS.rda |binary data/raj.act.2.rda |binary data/raj.act.3.rda |binary data/raj.act.4.rda |binary data/raj.act.5.rda |binary data/raj.demographics.rda |binary data/raj.rda |binary data/rajPOS.rda |binary data/rajSPLIT.rda |binary data/raw.time.span.rda |binary data/sample.time.span.rda |binary inst/CITATION | 4 inst/Rmd_vignette/funs/extra_functions.txt | 20 inst/Rmd_vignette/qdap_vignette.Rmd | 1356 +++++++++++++++- inst/doc/cleaning_and_debugging.pdf |binary inst/doc/tm_package_compatibility.pdf |binary man/Animate.Rd | 3 man/Animate.character.Rd |only man/Animate.discourse_map.Rd | 3 man/Animate.formality.Rd | 21 man/Animate.gantt.Rd | 3 man/Animate.gantt_plot.Rd | 3 man/Animate.lexical_classification.Rd |only man/Animate.polarity.Rd | 25 man/DATA.Rd | 3 man/DATA.SPLIT.Rd | 3 man/DATA2.Rd | 3 man/Dissimilarity.Rd | 3 man/Filter.Rd | 3 man/NAer.Rd | 3 man/Network.Rd | 3 man/Network.formality.Rd | 3 man/Network.lexical_classification.Rd |only man/Network.polarity.Rd | 3 man/Readability.Rd | 5 man/Search.Rd | 3 man/Title.Rd | 3 man/Trim.Rd | 3 man/Word_Frequency_Matrix.Rd | 3 man/addNetwork.Rd | 3 man/add_incomplete.Rd |only man/adjacency_matrix.Rd | 3 man/all_words.Rd | 3 man/as.tdm.Rd | 17 man/bag_o_words.Rd | 3 man/beg2char.Rd | 3 man/blank2NA.Rd | 3 man/bracketX.Rd | 3 man/build_qdap_vignette.Rd | 3 man/capitalizer.Rd | 3 man/chain.Rd | 3 man/check_spelling.Rd | 3 man/check_spelling_interactive.character.Rd | 3 man/check_spelling_interactive.check_spelling.Rd | 3 man/check_spelling_interactive.factor.Rd | 3 man/check_text.Rd | 3 man/chunker.Rd | 3 man/clean.Rd | 3 man/cm_2long.Rd | 3 man/cm_code.blank.Rd | 3 man/cm_code.combine.Rd | 3 man/cm_code.exclude.Rd | 3 man/cm_code.overlap.Rd | 3 man/cm_code.transform.Rd | 3 man/cm_combine.dummy.Rd | 3 man/cm_df.fill.Rd | 3 man/cm_df.temp.Rd | 3 man/cm_df.transcript.Rd | 3 man/cm_df2long.Rd | 3 man/cm_distance.Rd | 3 man/cm_dummy2long.Rd | 3 man/cm_long2dummy.Rd | 3 man/cm_range.temp.Rd | 3 man/cm_range2long.Rd | 3 man/cm_time.temp.Rd | 3 man/cm_time2long.Rd | 3 man/colSplit.Rd | 3 man/colcomb2class.Rd | 3 man/colsplit2df.Rd | 3 man/comma_spacer.Rd | 3 man/common.Rd | 3 man/common.list.Rd | 3 man/condense.Rd | 3 man/counts.Rd | 3 man/counts.SMOG.Rd | 3 man/counts.automated_readability_index.Rd | 3 man/counts.character_table.Rd | 3 man/counts.coleman_liau.Rd | 3 man/counts.end_mark_by.Rd | 3 man/counts.flesch_kincaid.Rd | 3 man/counts.formality.Rd | 3 man/counts.fry.Rd | 3 man/counts.linsear_write.Rd | 3 man/counts.object_pronoun_type.Rd | 3 man/counts.polarity.Rd | 3 man/counts.pos.Rd | 3 man/counts.pos_by.Rd | 3 man/counts.pronoun_type.Rd | 3 man/counts.question_type.Rd | 3 man/counts.subject_pronoun_type.Rd | 3 man/counts.termco.Rd | 3 man/counts.word_length.Rd |only man/counts.word_position.Rd |only man/counts.word_stats.Rd | 3 man/cumulative.Rd | 15 man/data_viewing.Rd | 3 man/deprecated.Rd | 3 man/dir_map.Rd | 3 man/discourse_map.Rd | 3 man/dispersion_plot.Rd | 28 man/dist_tab.Rd | 3 man/diversity.Rd | 3 man/duplicates.Rd | 3 man/end_inc.Rd | 3 man/end_mark.Rd | 3 man/env.syl.Rd | 3 man/exclude.Rd | 3 man/formality.Rd | 3 man/freq_terms.Rd | 3 man/gantt.Rd | 3 man/gantt_plot.Rd | 3 man/gantt_rep.Rd | 3 man/gantt_wrap.Rd | 3 man/gradient_cloud.Rd | 3 man/hamlet.Rd | 5 man/igraph_params.Rd | 3 man/imperative.Rd | 3 man/incomplete_replace.Rd | 3 man/is.global.Rd | 3 man/justification.Rd | 3 man/key_merge.Rd | 3 man/kullback_leibler.Rd | 3 man/lexical_classification.Rd |only man/mraja1.Rd | 3 man/mraja1spl.Rd | 3 man/multicsv.Rd | 3 man/multigsub.Rd | 12 man/multiscale.Rd | 3 man/name2sex.Rd | 3 man/new_project.Rd | 3 man/ngrams.Rd | 3 man/object_pronoun_type.Rd | 3 man/outlier_detect.Rd | 3 man/outlier_labeler.Rd | 3 man/paste2.Rd | 3 man/phrase_net.Rd | 9 man/plot.Network.Rd | 3 man/plot.SMOG.Rd | 3 man/plot.animated_character.Rd |only man/plot.animated_discourse_map.Rd | 3 man/plot.animated_formality.Rd | 3 man/plot.animated_lexical_classification.Rd |only man/plot.animated_polarity.Rd | 7 man/plot.automated_readability_index.Rd | 3 man/plot.character_table.Rd | 3 man/plot.cm_distance.Rd | 3 man/plot.cmspans.Rd | 3 man/plot.coleman_liau.Rd | 3 man/plot.combo_syllable_sum.Rd | 3 man/plot.cumulative_animated_formality.Rd | 3 man/plot.cumulative_animated_lexical_classification.Rd |only man/plot.cumulative_animated_polarity.Rd | 3 man/plot.cumulative_combo_syllable_sum.Rd | 3 man/plot.cumulative_end_mark.Rd | 3 man/plot.cumulative_formality.Rd | 3 man/plot.cumulative_lexical_classification.Rd |only man/plot.cumulative_polarity.Rd | 3 man/plot.cumulative_syllable_freq.Rd | 3 man/plot.discourse_map.Rd | 3 man/plot.diversity.Rd | 3 man/plot.end_mark.Rd | 3 man/plot.end_mark_by.Rd | 3 man/plot.end_mark_by_count.Rd | 3 man/plot.end_mark_by_preprocessed.Rd | 3 man/plot.end_mark_by_proportion.Rd | 3 man/plot.end_mark_by_score.Rd | 3 man/plot.flesch_kincaid.Rd | 3 man/plot.formality.Rd | 3 man/plot.formality_scores.Rd | 3 man/plot.freq_terms.Rd | 3 man/plot.gantt.Rd | 3 man/plot.kullback_leibler.Rd | 3 man/plot.lexical.Rd |only man/plot.lexical_classification.Rd |only man/plot.lexical_classification_preprocessed.Rd |only man/plot.lexical_classification_score.Rd |only man/plot.linsear_write.Rd | 3 man/plot.linsear_write_count.Rd | 3 man/plot.linsear_write_scores.Rd | 3 man/plot.object_pronoun_type.Rd | 3 man/plot.polarity.Rd | 3 man/plot.polarity_count.Rd | 3 man/plot.polarity_score.Rd | 3 man/plot.pos.Rd | 3 man/plot.pos_by.Rd | 3 man/plot.pos_preprocessed.Rd | 3 man/plot.pronoun_type.Rd | 3 man/plot.question_type.Rd | 3 man/plot.question_type_preprocessed.Rd | 3 man/plot.readability_count.Rd | 3 man/plot.readability_score.Rd | 3 man/plot.rmgantt.Rd | 3 man/plot.sent_split.Rd | 3 man/plot.subject_pronoun_type.Rd | 3 man/plot.sum_cmspans.Rd | 3 man/plot.sums_gantt.Rd | 3 man/plot.syllable_freq.Rd | 3 man/plot.table_count.Rd | 3 man/plot.table_proportion.Rd | 3 man/plot.table_score.Rd | 3 man/plot.termco.Rd | 3 man/plot.type_token_ratio.Rd |only man/plot.weighted_wfm.Rd | 3 man/plot.wfdf.Rd | 3 man/plot.wfm.Rd | 3 man/plot.word_cor.Rd | 3 man/plot.word_length.Rd |only man/plot.word_position.Rd |only man/plot.word_proximity.Rd | 3 man/plot.word_stats.Rd | 3 man/plot.word_stats_counts.Rd | 3 man/polarity.Rd | 7 man/pos.Rd | 10 man/potential_NA.Rd | 3 man/power.Rd | 3 man/preprocessed.Rd | 3 man/preprocessed.check_spelling_interactive.Rd | 3 man/preprocessed.end_mark_by.Rd | 3 man/preprocessed.formality.Rd | 3 man/preprocessed.lexical_classification.Rd |only man/preprocessed.object_pronoun_type.Rd | 3 man/preprocessed.pos.Rd | 3 man/preprocessed.pos_by.Rd | 3 man/preprocessed.pronoun_type.Rd | 3 man/preprocessed.question_type.Rd | 3 man/preprocessed.subject_pronoun_type.Rd | 3 man/preprocessed.word_position.Rd |only man/pres_debate_raw2012.Rd | 3 man/pres_debates2012.Rd | 3 man/print.Dissimilarity.Rd | 3 man/print.Network.Rd | 3 man/print.SMOG.Rd | 3 man/print.adjacency_matrix.Rd | 3 man/print.all_words.Rd | 3 man/print.animated_character.Rd |only man/print.animated_discourse_map.Rd | 3 man/print.animated_formality.Rd | 3 man/print.animated_lexical_classification.Rd |only man/print.animated_polarity.Rd | 7 man/print.automated_readability_index.Rd | 3 man/print.boolean_qdap.Rd | 3 man/print.character_table.Rd | 3 man/print.check_spelling.Rd | 3 man/print.check_spelling_interactive.Rd | 3 man/print.check_text.Rd | 3 man/print.cm_distance.Rd | 3 man/print.coleman_liau.Rd | 3 man/print.colsplit2df.Rd | 3 man/print.combo_syllable_sum.Rd | 3 man/print.cumulative_animated_formality.Rd | 3 man/print.cumulative_animated_lexical_classification.Rd |only man/print.cumulative_animated_polarity.Rd | 3 man/print.cumulative_combo_syllable_sum.Rd | 3 man/print.cumulative_end_mark.Rd | 3 man/print.cumulative_formality.Rd | 3 man/print.cumulative_lexical_classification.Rd |only man/print.cumulative_polarity.Rd | 3 man/print.cumulative_syllable_freq.Rd | 3 man/print.discourse_map.Rd | 3 man/print.diversity.Rd | 3 man/print.end_mark.Rd | 3 man/print.end_mark_by.Rd | 3 man/print.end_mark_by_preprocessed.Rd | 3 man/print.flesch_kincaid.Rd | 3 man/print.formality.Rd | 3 man/print.formality_scores.Rd | 3 man/print.fry.Rd | 3 man/print.kullback_leibler.Rd | 3 man/print.lexical_classification.Rd |only man/print.lexical_classification_by.Rd |only man/print.lexical_classification_preprocessed.Rd |only man/print.lexical_classification_score.Rd |only man/print.linsear_write.Rd | 3 man/print.linsear_write_count.Rd | 3 man/print.linsear_write_scores.Rd | 3 man/print.ngrams.Rd | 3 man/print.object_pronoun_type.Rd | 3 man/print.phrase_net.Rd | 3 man/print.polarity.Rd | 3 man/print.polarity_count.Rd | 3 man/print.polarity_score.Rd | 3 man/print.polysyllable_sum.Rd | 3 man/print.pos.Rd | 3 man/print.pos_by.Rd | 3 man/print.pos_preprocessed.Rd | 3 man/print.pronoun_type.Rd | 3 man/print.qdapProj.Rd | 3 man/print.qdap_context.Rd | 3 man/print.question_type.Rd | 3 man/print.question_type_preprocessed.Rd | 3 man/print.readability_count.Rd | 3 man/print.readability_score.Rd | 3 man/print.sent_split.Rd | 3 man/print.sub_holder.Rd | 3 man/print.subject_pronoun_type.Rd | 3 man/print.sum_cmspans.Rd | 3 man/print.sums_gantt.Rd | 3 man/print.syllable_sum.Rd | 3 man/print.table_count.Rd | 3 man/print.table_proportion.Rd | 3 man/print.table_score.Rd | 3 man/print.termco.Rd | 3 man/print.trunc.Rd | 3 man/print.type_token_ratio.Rd |only man/print.wfm.Rd | 3 man/print.wfm_summary.Rd | 3 man/print.which_misspelled.Rd | 3 man/print.word_associate.Rd | 3 man/print.word_cor.Rd | 3 man/print.word_length.Rd |only man/print.word_list.Rd | 3 man/print.word_position.Rd |only man/print.word_proximity.Rd | 3 man/print.word_stats.Rd | 3 man/print.word_stats_counts.Rd | 3 man/pronoun_type.Rd | 3 man/prop.Rd | 3 man/proportions.Rd | 3 man/proportions.character_table.Rd | 3 man/proportions.end_mark_by.Rd | 3 man/proportions.formality.Rd | 3 man/proportions.object_pronoun_type.Rd | 3 man/proportions.pos.Rd | 3 man/proportions.pos_by.Rd | 3 man/proportions.pronoun_type.Rd | 3 man/proportions.question_type.Rd | 3 man/proportions.subject_pronoun_type.Rd | 3 man/proportions.termco.Rd | 3 man/proportions.word_length.Rd |only man/proportions.word_position.Rd |only man/qcombine.Rd | 3 man/qcv.Rd | 3 man/qdap.Rd | 3 man/qdap_df.Rd | 3 man/qheat.Rd | 3 man/qprep.Rd | 3 man/qtheme.Rd | 3 man/question_type.Rd | 3 man/raj.Rd | 3 man/raj.act.1.Rd | 3 man/raj.act.1POS.Rd | 3 man/raj.act.2.Rd | 3 man/raj.act.3.Rd | 3 man/raj.act.4.Rd | 3 man/raj.act.5.Rd | 3 man/raj.demographics.Rd | 3 man/rajPOS.Rd | 3 man/rajSPLIT.Rd | 3 man/random_data.Rd | 3 man/rank_freq_plot.Rd | 3 man/raw.time.span.Rd | 3 man/read.transcript.Rd | 3 man/replace_abbreviation.Rd | 3 man/replace_contraction.Rd | 3 man/replace_number.Rd | 3 man/replace_ordinal.Rd | 3 man/replace_symbol.Rd | 3 man/replacer.Rd | 3 man/rm_row.Rd | 3 man/rm_stopwords.Rd | 3 man/sample.time.span.Rd | 3 man/scores.Rd | 3 man/scores.SMOG.Rd | 3 man/scores.automated_readability_index.Rd | 3 man/scores.character_table.Rd | 3 man/scores.coleman_liau.Rd | 3 man/scores.end_mark_by.Rd | 3 man/scores.flesch_kincaid.Rd | 3 man/scores.formality.Rd | 3 man/scores.fry.Rd | 3 man/scores.lexical_classification.Rd |only man/scores.linsear_write.Rd | 3 man/scores.object_pronoun_type.Rd | 3 man/scores.polarity.Rd | 3 man/scores.pos_by.Rd | 3 man/scores.pronoun_type.Rd | 3 man/scores.question_type.Rd | 3 man/scores.subject_pronoun_type.Rd | 3 man/scores.termco.Rd | 3 man/scores.word_length.Rd |only man/scores.word_position.Rd |only man/scores.word_stats.Rd | 3 man/scrubber.Rd | 3 man/sentSplit.Rd | 16 man/space_fill.Rd | 3 man/spaste.Rd | 3 man/speakerSplit.Rd | 3 man/stemmer.Rd | 3 man/strWrap.Rd | 3 man/strip.Rd | 27 man/subject_pronoun_type.Rd | 3 man/summary.cmspans.Rd | 3 man/summary.wfdf.Rd | 3 man/summary.wfm.Rd | 3 man/syllabication.Rd | 3 man/synonyms.Rd | 3 man/t.DocumentTermMatrix.Rd | 3 man/t.TermDocumentMatrix.Rd | 3 man/termco.Rd | 28 man/termco_c.Rd | 3 man/tot_plot.Rd | 3 man/trans_cloud.Rd | 3 man/trans_context.Rd | 6 man/trans_venn.Rd | 3 man/type_text_ratio.Rd |only man/unique_by.Rd | 3 man/visual.Rd | 3 man/visual.discourse_map.Rd | 3 man/weight.Rd | 3 man/word_associate.Rd | 3 man/word_cor.Rd | 3 man/word_count.Rd | 3 man/word_diff_list.Rd | 3 man/word_length.Rd |only man/word_list.Rd | 3 man/word_network_plot.Rd | 3 man/word_position.Rd |only man/word_proximity.Rd | 3 man/word_stats.Rd | 3 tests/testthat/test-add_incomplete.R |only tests/testthat/test-adjacency_matrix.R | 5 tests/testthat/test-all_words.R | 1 tests/testthat/test-as.tdm.R | 6 tests/testthat/test-bag_o_words.R | 4 tests/testthat/test-beg2char.R | 1 tests/testthat/test-blank2NA.R | 1 tests/testthat/test-bracketX.R | 30 tests/testthat/test-capitalizer.R | 8 tests/testthat/test-chunker.R | 3 tests/testthat/test-cm_2long.R | 8 tests/testthat/test-cm_code.blank.R | 10 tests/testthat/test-cmspans.R | 5 tests/testthat/test-colSplit.R | 5 tests/testthat/test-colcomb2class.R | 3 tests/testthat/test-common.R | 2 tests/testthat/test-dispersion_plot.R | 1 tests/testthat/test-end_mark.R | 3 tests/testthat/test-formality.R |only tests/testthat/test-phrase_net.R | 1 tests/testthat/test-polarity.R |only tests/testthat/test-pos.R |only tests/testthat/test-replace_number.R | 8 tests/testthat/test-strip.R |only tests/testthat/test-syllable_sum.R | 8 tests/testthat/test-wfm.R | 30 tests/testthat/test-word_length.R |only 500 files changed, 3477 insertions(+), 1228 deletions(-)
Title: Phylogenetic Comparative Methods for Function-Valued and Other
High-Dimensional Traits
Description: Tools for studying the evolution of function-valued traits (as well as other high-dimensional traits) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 1.0.0 dated 2015-03-19 and 1.1.0 dated 2015-05-11
DESCRIPTION | 11 - MD5 | 15 + NAMESPACE | 8 R/phylocurve.R | 366 +++++++++++++++++++++++++++++++++++++++++- man/GP.fit.Rd |only man/nonlinear.fit.Rd |only man/phylocurve-package.Rd | 4 man/phylocurve.Rd | 4 man/phylocurve.generalized.Rd |only man/phylocurve.trim.Rd |only man/polynomial.fit.Rd |only 11 files changed, 390 insertions(+), 18 deletions(-)
Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut],
Bas Kempen [ctb],
Gerard Heuvelink [ctb],
Brendan Malone [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>
Diff between GSIF versions 0.4-5 dated 2015-04-22 and 0.4-6 dated 2015-05-11
DESCRIPTION | 14 +++++++------- MD5 | 18 ++++++++++-------- NAMESPACE | 2 +- R/AAAA.R | 12 ++++++++---- R/autopredict.R |only R/fkmeans.R | 4 ++-- R/spmultinom.R | 4 ++-- demo/cookfarm_3DT_RF.R | 9 +++++---- man/FAO.SoilProfileCollection.Rd | 2 +- man/autopredict.Rd |only man/cookfarm.Rd | 2 +- 11 files changed, 37 insertions(+), 30 deletions(-)
Title: Aster Models
Description: Aster models are exponential family regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the exponential family canonical
parameterization (aster transform of usual parameterization).
Unlike the aster package, this package does dependence groups (nodes of
the graph need not be conditionally independent given their predecessor
node), including multinomial and two-parameter normal as families. Thus
this package also generalizes mark-capture-recapture analysis.
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between aster2 versions 0.1 dated 2010-11-03 and 0.2-1 dated 2015-05-11
DESCRIPTION | 31 +++++++++++++++++++++++-------- MD5 |only NEWS |only R/asterdata.R | 3 +++ R/onAttach.R | 11 ++++++----- data/hornworm.rda |only inst/makedata/sim.Rout |only inst/makedata/toy.Rout |only man/aster2-package.Rd | 2 ++ man/echinacea.Rd | 2 +- man/hornworm.Rd |only src/families.c | 4 ++-- 12 files changed, 37 insertions(+), 16 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.1-4 dated 2014-11-06 and 1.1-5 dated 2015-05-11
GGIR-1.1-4/GGIR/R/g.convert.day.names.R |only GGIR-1.1-5/GGIR/DESCRIPTION | 20 GGIR-1.1-5/GGIR/MD5 | 71 +- GGIR-1.1-5/GGIR/R/g.abr.day.names.R |only GGIR-1.1-5/GGIR/R/g.analyse.R | 290 ++-------- GGIR-1.1-5/GGIR/R/g.binread.R | 865 ++++++++++++++------------------ GGIR-1.1-5/GGIR/R/g.calibrate.R | 223 ++++---- GGIR-1.1-5/GGIR/R/g.createcoordinates.R | 43 - GGIR-1.1-5/GGIR/R/g.detecmidnight.R | 13 GGIR-1.1-5/GGIR/R/g.dotorcomma.R | 6 GGIR-1.1-5/GGIR/R/g.downsample.R | 3 GGIR-1.1-5/GGIR/R/g.extractheadervars.R | 5 GGIR-1.1-5/GGIR/R/g.getM5L5.R | 12 GGIR-1.1-5/GGIR/R/g.getmeta.R | 211 +++---- GGIR-1.1-5/GGIR/R/g.impute.R | 40 - GGIR-1.1-5/GGIR/R/g.inspectfile.R | 328 +++++------- GGIR-1.1-5/GGIR/R/g.metric.R | 37 - GGIR-1.1-5/GGIR/R/g.part1.R | 142 +++-- GGIR-1.1-5/GGIR/R/g.part2.R | 232 +++----- GGIR-1.1-5/GGIR/R/g.plot.R | 28 - GGIR-1.1-5/GGIR/R/g.report.part2.R |only GGIR-1.1-5/GGIR/R/g.shell.GGIR.R | 113 +++- GGIR-1.1-5/GGIR/R/g.weardec.R | 9 GGIR-1.1-5/GGIR/inst/NEWS.Rd | 16 GGIR-1.1-5/GGIR/man/GGIR-package.Rd | 45 - GGIR-1.1-5/GGIR/man/data.calibrate.Rd | 3 GGIR-1.1-5/GGIR/man/data.getmeta.Rd | 3 GGIR-1.1-5/GGIR/man/data.inspectfile.Rd | 3 GGIR-1.1-5/GGIR/man/g.analyse.Rd | 40 - GGIR-1.1-5/GGIR/man/g.binread.Rd | 2 GGIR-1.1-5/GGIR/man/g.calibrate.Rd | 14 GGIR-1.1-5/GGIR/man/g.getmeta.Rd | 20 GGIR-1.1-5/GGIR/man/g.impute.Rd | 6 GGIR-1.1-5/GGIR/man/g.inspectfile.Rd | 6 GGIR-1.1-5/GGIR/man/g.part1.Rd | 36 - GGIR-1.1-5/GGIR/man/g.part2.Rd | 38 + GGIR-1.1-5/GGIR/man/g.plot.Rd | 2 GGIR-1.1-5/GGIR/man/g.shell.GGIR.Rd | 208 ------- 38 files changed, 1384 insertions(+), 1749 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.0.36 dated 2014-09-29 and 1.0.69 dated 2015-05-11
DESCRIPTION | 11 MD5 | 70 NAMESPACE | 32 NEWS | 9 R/CarmaNoise.R | 10 R/ClassCogarch.R |only R/DiagnosticCogarch.R |only R/MM.COGARCH.R |only R/WoodChanfGn.R | 2 R/adaBayes.R | 2 R/asymptotic_term_second.R | 2 R/asymptotic_term_third.R | 2 R/asymptotic_term_third_function.R | 2 R/cce.R | 5372 ++++++++++++++++++------------------- R/cogarchNoise.R |only R/hyavar.R |only R/llag.R | 31 R/lse.R | 2 R/qgv.R | 2 R/qmle.R | 450 ++- R/rng.R | 6 R/setCarma.R | 37 R/setCogarch.R |only R/sim.euler.R | 20 R/simFunctional.R | 2 R/simulate.R | 978 +++++- R/toLatex.R | 248 + R/yuima.R | 44 R/yuima.model.R | 2 man/Diagnostic.Cogarch.Rd |only man/cce.Rd | 828 +++-- man/cogarch.gmm.incr.rd |only man/cogarch.gmm.rd |only man/cogarch.info-class.Rd |only man/cogarchNoise.Rd |only man/gmm.rd |only man/hyavar.Rd |only man/setCarma.Rd | 3 man/setCogarch.Rd |only man/simulate.Rd | 5 man/toLatex.Rd | 13 man/yuima.cogarch-class.Rd |only src/carmafilter.c |only src/cce_functions.c | 228 + 44 files changed, 4854 insertions(+), 3559 deletions(-)
Title: Probability of Sharing Rare Variants among Relatives
Description: Computes estimates of the probability of related individuals sharing a rare variant.
Author: Alexandre Bureau, Ingo Ruczinski, Samuel G. Younkin
Maintainer: Alexandre Bureau <alexandre.bureau@msp.ulaval.ca>
Diff between RVsharing versions 1.1.0 dated 2013-10-30 and 1.3.4 dated 2015-05-11
DESCRIPTION | 14 - MD5 | 42 +-- NAMESPACE | 7 R/AllClasses.R | 12 - R/AllGenerics.R | 4 R/PFU.R | 84 +++---- R/functions.R | 316 +++++++++++++-------------- R/methods-RVsharingProb.R | 138 ++++++------ R/methods-pedigree.R | 63 +++-- R/methods-trio.R | 50 ++-- R/ped2trio.R | 358 +++++++++++++++---------------- R/rare_variant_sharing_v3.R | 424 +++++++++++++++++++++++++++++-------- R/zzz.R | 20 - man/GeneDrop.Rd | 50 ++-- man/GeneDropSim.fn.Rd | 86 +++---- man/GeneDropSimExcessSharing.fn.Rd | 97 ++++---- man/RVsharing.Rd | 96 ++++---- man/RVsharingProb.rd | 48 ++-- man/Trio.Rd | 26 +- man/compute.kinship.prop.coef.Rd | 70 +++--- man/ped.list.Rd | 12 - man/ped2trio.Rd | 60 ++--- 22 files changed, 1175 insertions(+), 902 deletions(-)
Title: PLS Analyses for Genomics
Description: Routines for PLS-based genomic analyses,
implementing PLS methods for classification with
microarray data and prediction of transcription factor
activities from combined ChIP-chip analysis. The >=1.2-1
versions include two new classification methods for microarray
data: GSIM and Ridge PLS. The >=1.3 versions includes a
new classification method combining variable selection and
compression in logistic regression context: RIRLS-SPLS; and
an adaptive version of the sparse PLS.
Author: Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>,
Ghislain Durif <ghislain.durif@univ-lyon1.fr>,
Sophie Lambert-Lacroix <Sophie.Lambert@imag.fr>, Julie Peyre
<Julie.Peyre@imag.fr>, and Korbinian Strimmer
<strimmer@uni-leipzig.de>.
Maintainer: Ghislain Durif <ghislain.durif@univ-lyon1.fr>
Diff between plsgenomics versions 1.3 dated 2015-05-07 and 1.3-1 dated 2015-05-11
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").
Author: John Wambaugh and Robert Pearce, Schmitt method implementation by Jimena Davis, dynamic model adapted from code by R. Woodrow Setzer, Rabbit parameters from Nisha Sipes
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.1 dated 2015-03-06 and 1.2 dated 2015-05-11
httk-1.1/httk/R/Calc_elimination_rate.r |only httk-1.1/httk/R/Parameterize_SteadyState.r |only httk-1.2/httk/DESCRIPTION | 10 httk-1.2/httk/MD5 | 126 ++++++------ httk-1.2/httk/NAMESPACE | 2 httk-1.2/httk/R/3compPBPKmodel_inits.R | 14 - httk-1.2/httk/R/Calc_Hepatic_Clearance.r | 46 ++-- httk-1.2/httk/R/Calc_elimination_rate.R |only httk-1.2/httk/R/Calc_ratioblood2plasma.R | 40 --- httk-1.2/httk/R/Calc_total_clearance.R | 11 - httk-1.2/httk/R/Calc_volume_of_distribution.R | 72 +++---- httk-1.2/httk/R/Export_PBTK_Jarnac.R | 18 - httk-1.2/httk/R/Export_PBTK_SBML.R | 18 - httk-1.2/httk/R/Get_invitroPK_param.r | 2 httk-1.2/httk/R/Parameterize_3comp.r | 7 httk-1.2/httk/R/Parameterize_PBTK.r | 51 ++--- httk-1.2/httk/R/Parameterize_SteadyState.R |only httk-1.2/httk/R/Predict_partitioning_Schmitt.R | 55 ++--- httk-1.2/httk/R/add_chemtable.R | 31 ++- httk-1.2/httk/R/calc_analytic_css.R | 60 ++--- httk-1.2/httk/R/calc_chem_stats.R | 18 - httk-1.2/httk/R/calc_css.R | 30 +- httk-1.2/httk/R/calc_mc_css.R | 9 httk-1.2/httk/R/calc_stats.R | 6 httk-1.2/httk/R/get_cheminfo.R | 26 +- httk-1.2/httk/R/parameterize_1comp.R | 33 ++- httk-1.2/httk/R/parameterize_schmitt.R |only httk-1.2/httk/R/pbtk1comp_inits.R |only httk-1.2/httk/R/solve_1comp.R | 201 ++++++++++++-------- httk-1.2/httk/R/solve_3comp.R | 142 +++++++++----- httk-1.2/httk/R/solve_pbtk.R | 124 ++++++++---- httk-1.2/httk/data/Tables.RData |binary httk-1.2/httk/man/Calc_elimination_rate.Rd | 11 - httk-1.2/httk/man/Calc_ratioblood2plasma.Rd | 13 - httk-1.2/httk/man/Calc_volume_of_distriution.Rd | 20 - httk-1.2/httk/man/PK_physiology_data.Rd | 2 httk-1.2/httk/man/Parameterize_PBTK.Rd | 15 - httk-1.2/httk/man/Parameterize_SteadyState.Rd | 19 - httk-1.2/httk/man/Wetmore_Css.Rd | 4 httk-1.2/httk/man/Wetmore_Oral_Equiv.Rd | 4 httk-1.2/httk/man/add_chemtable.Rd | 6 httk-1.2/httk/man/calc_analytic_css.Rd | 14 - httk-1.2/httk/man/calc_css.Rd | 150 -------------- httk-1.2/httk/man/calc_hepatic_clearance.Rd | 9 httk-1.2/httk/man/calc_mc_css.Rd | 13 - httk-1.2/httk/man/calc_mc_oral_equiv.Rd | 4 httk-1.2/httk/man/calc_stats.Rd | 13 - httk-1.2/httk/man/calc_total_clearance.Rd | 11 - httk-1.2/httk/man/chem_invivo_PK_data.Rd | 2 httk-1.2/httk/man/chem_invivo_PK_summary_data.Rd | 2 httk-1.2/httk/man/chem_physical_and_invitro_data.Rd | 2 httk-1.2/httk/man/export_pbtk_jarnac.Rd | 2 httk-1.2/httk/man/export_pbtk_sbml.Rd | 2 httk-1.2/httk/man/get_cheminfo.Rd | 7 httk-1.2/httk/man/get_wetmore_cheminfo.Rd | 4 httk-1.2/httk/man/monte_carlo.Rd | 18 - httk-1.2/httk/man/parameterize_1comp.Rd | 15 - httk-1.2/httk/man/parameterize_3comp.Rd | 16 - httk-1.2/httk/man/parameterize_schmitt.Rd |only httk-1.2/httk/man/predict_partitioning_schmitt.Rd | 54 ++--- httk-1.2/httk/man/solve_1comp_pk.Rd | 25 +- httk-1.2/httk/man/solve_3comp_pbpk.Rd | 25 +- httk-1.2/httk/man/solve_pbtk.Rd | 25 +- httk-1.2/httk/man/tissue_data.Rd | 2 httk-1.2/httk/src/3compPBPKmodel.c | 50 ++-- httk-1.2/httk/src/pbtk1comp.c |only httk-1.2/httk/tests |only 67 files changed, 880 insertions(+), 831 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes. Currently only fixed-effects models are implemented,
i.e., no random-effects models. Many (150+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE, using Fisher scoring. VGLMs can be
loosely thought of as multivariate GLMs. VGAMs are data-driven
VGLMs (i.e., with smoothing). The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Note that these functions are subject to change,
especially before version 1.0.0 is released; see the NEWS
file for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 0.9-7 dated 2015-03-06 and 0.9-8 dated 2015-05-11
VGAM-0.9-7/VGAM/R/family.quantal.R |only VGAM-0.9-8/VGAM/DESCRIPTION | 34 VGAM-0.9-8/VGAM/MD5 | 249 - VGAM-0.9-8/VGAM/NAMESPACE | 13 VGAM-0.9-8/VGAM/NEWS | 38 VGAM-0.9-8/VGAM/R/family.actuary.R | 4323 ++++++++++++++++++---------- VGAM-0.9-8/VGAM/R/family.basics.R | 16 VGAM-0.9-8/VGAM/R/family.binomial.R | 178 - VGAM-0.9-8/VGAM/R/family.categorical.R | 470 --- VGAM-0.9-8/VGAM/R/family.censored.R | 6 VGAM-0.9-8/VGAM/R/family.extremes.R | 266 - VGAM-0.9-8/VGAM/R/family.genetic.R | 326 -- VGAM-0.9-8/VGAM/R/family.glmgam.R | 325 -- VGAM-0.9-8/VGAM/R/family.nonlinear.R | 4 VGAM-0.9-8/VGAM/R/family.normal.R | 543 --- VGAM-0.9-8/VGAM/R/family.positive.R | 12 VGAM-0.9-8/VGAM/R/family.rcim.R | 2 VGAM-0.9-8/VGAM/R/family.rcqo.R | 46 VGAM-0.9-8/VGAM/R/family.ts.R | 497 +++ VGAM-0.9-8/VGAM/R/family.univariate.R | 326 +- VGAM-0.9-8/VGAM/R/family.zeroinf.R | 38 VGAM-0.9-8/VGAM/R/vgam.R | 51 VGAM-0.9-8/VGAM/build |only VGAM-0.9-8/VGAM/data/Huggins89.t1.rda |binary VGAM-0.9-8/VGAM/data/Huggins89table1.rda |binary VGAM-0.9-8/VGAM/data/alclevels.rda |binary VGAM-0.9-8/VGAM/data/alcoff.rda |binary VGAM-0.9-8/VGAM/data/auuc.rda |binary VGAM-0.9-8/VGAM/data/backPain.rda |binary VGAM-0.9-8/VGAM/data/beggs.rda |binary VGAM-0.9-8/VGAM/data/car.all.rda |binary VGAM-0.9-8/VGAM/data/cfibrosis.rda |binary VGAM-0.9-8/VGAM/data/corbet.rda |binary VGAM-0.9-8/VGAM/data/crashbc.rda |binary VGAM-0.9-8/VGAM/data/crashf.rda |binary VGAM-0.9-8/VGAM/data/crashi.rda |binary VGAM-0.9-8/VGAM/data/crashmc.rda |binary VGAM-0.9-8/VGAM/data/crashp.rda |binary VGAM-0.9-8/VGAM/data/crashtr.rda |binary VGAM-0.9-8/VGAM/data/deermice.rda |binary VGAM-0.9-8/VGAM/data/ducklings.rda |binary VGAM-0.9-8/VGAM/data/finney44.rda |binary VGAM-0.9-8/VGAM/data/flourbeetle.rda |binary VGAM-0.9-8/VGAM/data/hspider.rda |binary VGAM-0.9-8/VGAM/data/lakeO.rda |binary VGAM-0.9-8/VGAM/data/leukemia.rda |binary VGAM-0.9-8/VGAM/data/marital.nz.rda |binary VGAM-0.9-8/VGAM/data/melbmaxtemp.rda |binary VGAM-0.9-8/VGAM/data/pneumo.rda |binary VGAM-0.9-8/VGAM/data/prinia.rda |binary VGAM-0.9-8/VGAM/data/ruge.rda |binary VGAM-0.9-8/VGAM/data/toxop.rda |binary VGAM-0.9-8/VGAM/data/venice.rda |binary VGAM-0.9-8/VGAM/data/venice90.rda |binary VGAM-0.9-8/VGAM/data/wine.rda |binary VGAM-0.9-8/VGAM/inst/CITATION | 23 VGAM-0.9-8/VGAM/inst/doc |only VGAM-0.9-8/VGAM/man/AR1.Rd |only VGAM-0.9-8/VGAM/man/AR1UC.Rd |only VGAM-0.9-8/VGAM/man/VGAM-package.Rd | 21 VGAM-0.9-8/VGAM/man/acat.Rd | 9 VGAM-0.9-8/VGAM/man/betaII.Rd | 28 VGAM-0.9-8/VGAM/man/betaR.Rd | 8 VGAM-0.9-8/VGAM/man/betaff.Rd | 6 VGAM-0.9-8/VGAM/man/betaprime.Rd | 6 VGAM-0.9-8/VGAM/man/binom2.or.Rd | 6 VGAM-0.9-8/VGAM/man/brat.Rd | 4 VGAM-0.9-8/VGAM/man/bratt.Rd | 4 VGAM-0.9-8/VGAM/man/cao.Rd | 10 VGAM-0.9-8/VGAM/man/cdf.lmscreg.Rd | 8 VGAM-0.9-8/VGAM/man/constraints.Rd | 4 VGAM-0.9-8/VGAM/man/cqo.Rd | 7 VGAM-0.9-8/VGAM/man/cumulative.Rd | 6 VGAM-0.9-8/VGAM/man/dagum.Rd | 36 VGAM-0.9-8/VGAM/man/deermice.Rd | 3 VGAM-0.9-8/VGAM/man/dirmul.old.Rd | 11 VGAM-0.9-8/VGAM/man/exponential.Rd | 2 VGAM-0.9-8/VGAM/man/fill.Rd | 31 VGAM-0.9-8/VGAM/man/fisk.Rd | 40 VGAM-0.9-8/VGAM/man/genbetaII.Rd | 73 VGAM-0.9-8/VGAM/man/genbetaIIUC.Rd |only VGAM-0.9-8/VGAM/man/genpoisUC.Rd |only VGAM-0.9-8/VGAM/man/genpoisson.Rd | 76 VGAM-0.9-8/VGAM/man/iam.Rd | 12 VGAM-0.9-8/VGAM/man/inv.lomax.Rd | 45 VGAM-0.9-8/VGAM/man/inv.paralogistic.Rd | 41 VGAM-0.9-8/VGAM/man/is.buggy.Rd |only VGAM-0.9-8/VGAM/man/lms.bcg.Rd | 8 VGAM-0.9-8/VGAM/man/lms.bcn.Rd | 19 VGAM-0.9-8/VGAM/man/lms.yjn.Rd | 8 VGAM-0.9-8/VGAM/man/loglinb3.Rd | 6 VGAM-0.9-8/VGAM/man/lomax.Rd | 19 VGAM-0.9-8/VGAM/man/micmen.Rd | 6 VGAM-0.9-8/VGAM/man/multinomial.Rd | 6 VGAM-0.9-8/VGAM/man/negbinomial.Rd | 4 VGAM-0.9-8/VGAM/man/notdocumentedyet.Rd | 10 VGAM-0.9-8/VGAM/man/paralogistic.Rd | 42 VGAM-0.9-8/VGAM/man/plotdeplot.lmscreg.Rd | 6 VGAM-0.9-8/VGAM/man/plotqtplot.lmscreg.Rd | 6 VGAM-0.9-8/VGAM/man/posbernoulli.t.Rd | 11 VGAM-0.9-8/VGAM/man/posbernoulli.tb.Rd | 1 VGAM-0.9-8/VGAM/man/posnormal.Rd | 16 VGAM-0.9-8/VGAM/man/pospoisson.Rd | 6 VGAM-0.9-8/VGAM/man/propodds.Rd | 6 VGAM-0.9-8/VGAM/man/qtplot.lmscreg.Rd | 6 VGAM-0.9-8/VGAM/man/rhobit.Rd | 14 VGAM-0.9-8/VGAM/man/rrvglm-class.Rd | 2 VGAM-0.9-8/VGAM/man/rrvglm.Rd | 9 VGAM-0.9-8/VGAM/man/s.Rd | 1 VGAM-0.9-8/VGAM/man/sinmad.Rd | 35 VGAM-0.9-8/VGAM/man/sinmadUC.Rd | 5 VGAM-0.9-8/VGAM/man/smartpred.Rd | 6 VGAM-0.9-8/VGAM/man/sratio.Rd | 9 VGAM-0.9-8/VGAM/man/tobit.Rd | 23 VGAM-0.9-8/VGAM/man/undocumented-methods.Rd | 13 VGAM-0.9-8/VGAM/man/uninormal.Rd | 1 VGAM-0.9-8/VGAM/man/vgam-class.Rd | 2 VGAM-0.9-8/VGAM/man/vgam.Rd | 10 VGAM-0.9-8/VGAM/man/vglm-class.Rd | 2 VGAM-0.9-8/VGAM/man/vglm.Rd | 6 VGAM-0.9-8/VGAM/man/vglm.control.Rd | 2 VGAM-0.9-8/VGAM/man/vglmff-class.Rd | 6 VGAM-0.9-8/VGAM/man/wrapup.smart.Rd | 14 VGAM-0.9-8/VGAM/man/zapoisson.Rd | 6 VGAM-0.9-8/VGAM/man/zero.Rd | 2 VGAM-0.9-8/VGAM/vignettes |only 126 files changed, 4654 insertions(+), 3983 deletions(-)
Title: Implementation of the Panel Data Approach Method for Program
Evaluation
Description: Implements the Panel Data Approach Method for program evaluation as developed in Hsiao, Ching and Ki Wan (2012). pampe estimates the effect of an intervention by comparing the evolution of the outcome for a unit affected by an intervention or treatment to the evolution of the unit had it not been affected by the intervention.
Author: Ainhoa Vega-Bayo
Maintainer: Ainhoa Vega-Bayo <ainhoa.vega@gmail.com>
Diff between pampe versions 1.0 dated 2015-02-13 and 1.1.1 dated 2015-05-11
DESCRIPTION | 9 +- MD5 | 18 +++-- R/pampe.R | 152 ++++++++++++++++++++++++++++++++++++-------------- R/pampeData.R |only R/plot.robustness.R | 12 ++- R/robustness.R | 23 +++++-- R/summary.pampe.R | 44 ++++++++++++++ R/xtable.pampe.R |only R/xtable.robustness.R |only man/pampe.Rd | 15 +++- man/pampeData.Rd |only man/robustness.Rd | 18 +---- 12 files changed, 210 insertions(+), 81 deletions(-)
Title: Bindings to OpenSSL
Description: Interfaces to the OpenSSL libraries libssl and libcrypto.
Currently implements bindings to the OpenSSL secure random number
generator, base64 encoder and hashing functions.
Author: Jeroen Ooms, Oliver Keyes
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.3 dated 2015-01-07 and 0.4 dated 2015-05-11
DESCRIPTION | 10 +- MD5 | 43 +++++----- NAMESPACE | 6 + NEWS |only R/base64.R |only R/hash.R | 2 build/vignette.rds |binary configure | 7 - inst/doc/crypto_hashing.R | 2 inst/doc/crypto_hashing.Rmd | 9 -- inst/doc/crypto_hashing.html | 131 ++++++++++++++---------------- inst/doc/secure_rng.R | 2 inst/doc/secure_rng.Rmd | 9 -- inst/doc/secure_rng.html | 136 ++++++++++++++------------------ man/base64.Rd |only man/hash.Rd | 2 man/openssl.Rd | 2 man/rand_bytes.Rd | 2 src/Makevars.win | 6 - src/base64.c |only src/digest.c | 2 tests/testthat/test_hash_output_value.R | 2 tests/testthat/test_salting.R |only vignettes/crypto_hashing.Rmd | 9 -- vignettes/secure_rng.Rmd | 9 -- 25 files changed, 177 insertions(+), 214 deletions(-)
Title: Interface to NetCDF Datasets
Description: An interface to the NetCDF file format designed by Unidata
for efficient storage of array-oriented scientific data and descriptions.
The R interface is closely based on the C API of the NetCDF library,
and it includes calendar conversions from the Unidata UDUNITS library.
The current implementation supports all operations on NetCDF datasets
in classic and 64-bit offset file formats, and NetCDF4-classic format
is supported for reading and modification of existing files.
Author: Pavel Michna, with contributions from Milton Woods
Maintainer: Milton Woods <mwoods@users.r-forge.r-project.org>
Diff between RNetCDF versions 1.6.3-1 dated 2014-08-31 and 1.7-3 dated 2015-05-11
RNetCDF-1.6.3-1/RNetCDF/LICENSE.note |only RNetCDF-1.6.3-1/RNetCDF/inst/HDF5_COPYING |only RNetCDF-1.7-3/RNetCDF/DESCRIPTION | 39 - RNetCDF-1.7-3/RNetCDF/INSTALL | 16 RNetCDF-1.7-3/RNetCDF/LICENSE |only RNetCDF-1.7-3/RNetCDF/MD5 | 38 - RNetCDF-1.7-3/RNetCDF/R/RNetCDF.R | 412 +++++++--------- RNetCDF-1.7-3/RNetCDF/R/load.R.in | 24 RNetCDF-1.7-3/RNetCDF/R/windows/load.R | 24 RNetCDF-1.7-3/RNetCDF/configure | 731 ++++++++++++++++++----------- RNetCDF-1.7-3/RNetCDF/configure.ac | 143 ++--- RNetCDF-1.7-3/RNetCDF/configure.win | 2 RNetCDF-1.7-3/RNetCDF/inst/udunits |only RNetCDF-1.7-3/RNetCDF/man/var.get.nc.Rd | 18 RNetCDF-1.7-3/RNetCDF/man/var.put.nc.Rd | 8 RNetCDF-1.7-3/RNetCDF/src/Makevars.in | 4 RNetCDF-1.7-3/RNetCDF/src/Makevars.win | 16 RNetCDF-1.7-3/RNetCDF/src/RNetCDF.c | 352 ++++++------- RNetCDF-1.7-3/RNetCDF/tests/RNetCDF-test.R | 256 +++++----- 19 files changed, 1139 insertions(+), 944 deletions(-)