Title: Spatial Forecast Verification
Description: Contains functions to perform spatial forecast verification.
Author: Eric Gilleland <EricG@ucar.edu>
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.2-2 dated 2014-12-23 and 0.2-3 dated 2015-05-19
DESCRIPTION | 10 ++-- MD5 | 37 +++++++++------ NAMESPACE | 112 ++++++++++++++++++++++++++++++++++++++++++++++ R/DataObjects.R | 62 ++++++++++++++++++++----- R/Features.R | 64 +++++++++++++++++++++----- R/Fint2d.R |only R/Geom.R | 49 +++++++++++++++----- R/LocMeasures.R | 31 ++++++------ R/QlossRigid.R |only R/craer.R |only R/minboundmatch.R |only R/rigider.R |only man/Fint2d.Rd |only man/SpatialVx-internal.Rd | 2 man/SpatialVx-package.Rd | 16 ++++-- man/craer.Rd |only man/datasets.Rd | 2 man/deltamm.Rd | 14 ++++- man/fss2dfun.Rd | 2 man/hoods2d.Rd | 2 man/minboundmatch.Rd |only man/pphindcast2d.Rd | 4 - man/rigider.Rd |only man/upscale2d.Rd | 2 24 files changed, 326 insertions(+), 83 deletions(-)
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Title: Functions for Generating Restricted Permutations of Data
Description: A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.
Author: Gavin L. Simpson [aut, cph, cre],
R Core Team [cph],
Douglas M. Bates [ctb],
Jari Oksanen [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between permute versions 0.8-3 dated 2014-01-29 and 0.8-4 dated 2015-05-19
permute-0.8-3/permute/R/Blocks.R |only permute-0.8-3/permute/inst/tests |only permute-0.8-3/permute/vignettes/Z.cls |only permute-0.8-4/permute/DESCRIPTION | 20 +- permute-0.8-4/permute/MD5 | 34 ++-- permute-0.8-4/permute/R/blocks.R |only permute-0.8-4/permute/README.md |only permute-0.8-4/permute/build/vignette.rds |binary permute-0.8-4/permute/data/jackal.rda |binary permute-0.8-4/permute/inst/ChangeLog | 17 +- permute-0.8-4/permute/inst/doc/permutations.R | 10 - permute-0.8-4/permute/inst/doc/permutations.Rnw | 12 - permute-0.8-4/permute/inst/doc/permutations.pdf |binary permute-0.8-4/permute/man/check.Rd | 102 ++++++------ permute-0.8-4/permute/tests/Examples/permute-Ex.Rout.save | 118 ++++++-------- permute-0.8-4/permute/tests/test-all.R | 6 permute-0.8-4/permute/tests/testthat |only permute-0.8-4/permute/vignettes/permutations.Rnw | 12 - 18 files changed, 165 insertions(+), 166 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph],
Thibaut Jombart [aut, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 0.7 dated 2015-03-05 and 0.8 dated 2015-05-19
DESCRIPTION | 12 +- MD5 | 67 +++++++------ NAMESPACE | 23 +++- NEWS | 45 +++++++++ R/IO.R | 117 ++++++++++++++++------- R/VCFloci.R |only R/amova.R | 27 ++--- R/conversion.R | 40 +++++++- R/haplotype.R | 31 +++++- R/hw.test.R | 46 ++++++++- R/summary.loci.R | 17 ++- R/zzz.R | 4 build/vignette.rds |binary data |only inst/doc/ReadingFiles.R | 58 ++--------- inst/doc/ReadingFiles.Rnw | 220 ++++++++++++++++++++++++++++++++++++--------- inst/doc/ReadingFiles.pdf |binary man/Fst.Rd | 6 - man/LD.Rd | 9 - man/VCFloci.Rd |only man/alleles2loci.Rd |only man/conversion.Rd | 6 - man/haplotype.Rd | 3 man/heterozygosity.Rd | 5 - man/hw.test.Rd | 31 +++++- man/jaguar.Rd |only man/read.vcf.Rd | 83 ++++++++++------ man/subset.haplotype.Rd |only man/summary.loci.Rd | 12 +- man/theta.h.Rd | 5 - man/theta.k.Rd | 5 - man/theta.msat.Rd | 6 - man/utilities.Rd | 11 +- man/write.loci.Rd | 5 - src/pegas.c | 16 ++- src/readVCFbin.c |only vignettes/ReadingFiles.Rnw | 220 ++++++++++++++++++++++++++++++++++++--------- vignettes/pegas.bib | 7 + 38 files changed, 816 insertions(+), 321 deletions(-)
Title: Statistical Methods for the Item Count Technique and List
Experiment
Description: Allows researchers to conduct multivariate statistical analyses of survey data with list experiments. This survey methodology is also known as the item count technique or the unmatched count technique and is an alternative to the commonly used randomized response method. The package implements the methods developed by Imai (2011), Blair and Imai (2012), Blair, Imai, and Lyall (2013), Imai, Park, and Greene (2014), and Aronow, Coppock, Crawford, and Green (2015). This includes a Bayesian MCMC implementation of regression for the standard and multiple sensitive item list experiment designs and a random effects setup, a Bayesian MCMC hierarchical regression model with up to three hierarchical groups, the combined list experiment and endorsement experiment regression model, a joint model of the list experiment that enables the analysis of the list experiment as a predictor in outcome regression models, and a method for combining list experiments with direct questions. In addition, the package implements the statistical test that is designed to detect certain failures of list experiments, and a placebo test for the list experiment using data from direct questions.
Author: Graeme Blair [aut, cre], Kosuke Imai [aut, cre], Bethany Park [ctb],
Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@columbia.edu>
Diff between list versions 7.1 dated 2014-11-29 and 8.0 dated 2015-05-19
list-7.1/list/R/onAttach.R |only list-8.0/list/ChangeLog | 16 - list-8.0/list/DESCRIPTION | 43 +--- list-8.0/list/MD5 | 44 +++- list-8.0/list/NAMESPACE | 10 - list-8.0/list/R/bayesglm.R |only list-8.0/list/R/combinedListDirect.R |only list-8.0/list/R/ictreg.R | 262 ++++++++++++++++----------- list-8.0/list/R/ictregBayes.R | 32 +-- list-8.0/list/R/ictregBayesHier.R | 13 - list-8.0/list/README.md |only list-8.0/list/build |only list-8.0/list/data/combinedListExps.rdata |only list-8.0/list/inst/doc |only list-8.0/list/man/combinedListDirect.Rd |only list-8.0/list/man/combinedListExps.Rd |only list-8.0/list/man/comp.listEndorse.Rd | 4 list-8.0/list/man/ictreg.Rd | 5 list-8.0/list/man/ictreg.joint.Rd | 5 list-8.0/list/man/ictregBayes.Rd | 16 - list-8.0/list/man/mexico.Rd | 2 list-8.0/list/man/predict.ictregBayesHier.Rd | 1 list-8.0/list/tests |only list-8.0/list/vignettes |only 24 files changed, 254 insertions(+), 199 deletions(-)
Title: Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging
Description: Bayesian Model Averaging to create probabilistic forecasts
from ensemble forecasts and weather observations.
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann
Gneiting, University of Washington.
Maintainer: Chris Fraley <fraley@u.washington.edu>
Diff between ensembleBMA versions 5.1.1 dated 2015-03-19 and 5.1.2 dated 2015-05-19
CHANGELOG | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/fitBMAgamma.R | 9 ++++----- R/fitBMAgamma0.R | 19 +++++++++---------- 5 files changed, 23 insertions(+), 23 deletions(-)
Title: Chemical Thermodynamics and Activity Diagrams
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
and low-temperature geochemistry. The features include calculation of the standard molal
thermodynamic properties and chemical affinities of reactions involving minerals and/or
biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous
species; amino acid group additivity for the standard molal thermodynamic properties of
neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state
for aqueous species; construction of equilibrium activity diagrams as a function of
temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.0.3.1 dated 2014-02-12 and 1.0.5 dated 2015-05-19
CHNOSZ-1.0.3.1/CHNOSZ/demo/TPX.R |only CHNOSZ-1.0.5/CHNOSZ/DESCRIPTION | 29 CHNOSZ-1.0.5/CHNOSZ/MD5 | 229 - CHNOSZ-1.0.5/CHNOSZ/R/affinity.R | 9 CHNOSZ-1.0.5/CHNOSZ/R/diagram.R | 58 CHNOSZ-1.0.5/CHNOSZ/R/equilibrate.R | 16 CHNOSZ-1.0.5/CHNOSZ/R/examples.R | 7 CHNOSZ-1.0.5/CHNOSZ/R/findit.R | 2 CHNOSZ-1.0.5/CHNOSZ/R/iprotein.R | 3 CHNOSZ-1.0.5/CHNOSZ/R/mosaic.R |only CHNOSZ-1.0.5/CHNOSZ/R/species.R | 3 CHNOSZ-1.0.5/CHNOSZ/R/subcrt.R | 6 CHNOSZ-1.0.5/CHNOSZ/R/transfer.R | 5 CHNOSZ-1.0.5/CHNOSZ/R/util.affinity.R | 16 CHNOSZ-1.0.5/CHNOSZ/R/util.data.R | 8 CHNOSZ-1.0.5/CHNOSZ/R/util.expression.R | 2 CHNOSZ-1.0.5/CHNOSZ/R/util.misc.R | 6 CHNOSZ-1.0.5/CHNOSZ/R/util.plot.R | 29 CHNOSZ-1.0.5/CHNOSZ/R/util.program.R | 8 CHNOSZ-1.0.5/CHNOSZ/R/wjd.R | 3 CHNOSZ-1.0.5/CHNOSZ/build/vignette.rds |binary CHNOSZ-1.0.5/CHNOSZ/data/OBIGT.csv | 2 CHNOSZ-1.0.5/CHNOSZ/data/opt.csv | 4 CHNOSZ-1.0.5/CHNOSZ/data/protein.csv | 105 CHNOSZ-1.0.5/CHNOSZ/data/refs.csv | 1 CHNOSZ-1.0.5/CHNOSZ/demo/00Index | 11 CHNOSZ-1.0.5/CHNOSZ/demo/buffer.R |only CHNOSZ-1.0.5/CHNOSZ/demo/diagram.R |only CHNOSZ-1.0.5/CHNOSZ/demo/findit.R | 68 CHNOSZ-1.0.5/CHNOSZ/demo/ionize.R |only CHNOSZ-1.0.5/CHNOSZ/demo/mosaic.R |only CHNOSZ-1.0.5/CHNOSZ/demo/revisit.R |only CHNOSZ-1.0.5/CHNOSZ/demo/solubility.R |only CHNOSZ-1.0.5/CHNOSZ/demo/wjd.R |only CHNOSZ-1.0.5/CHNOSZ/demo/yeastgfp.R |only CHNOSZ-1.0.5/CHNOSZ/inst/CHECKLIST | 45 CHNOSZ-1.0.5/CHNOSZ/inst/NEWS | 81 CHNOSZ-1.0.5/CHNOSZ/inst/doc/anintro.R | 45 CHNOSZ-1.0.5/CHNOSZ/inst/doc/anintro.Rnw | 193 - CHNOSZ-1.0.5/CHNOSZ/inst/doc/anintro.pdf |binary CHNOSZ-1.0.5/CHNOSZ/inst/doc/equilibrium.R | 14 CHNOSZ-1.0.5/CHNOSZ/inst/doc/equilibrium.Rnw | 18 CHNOSZ-1.0.5/CHNOSZ/inst/doc/equilibrium.pdf |binary CHNOSZ-1.0.5/CHNOSZ/inst/doc/hotspring.R | 469 +- CHNOSZ-1.0.5/CHNOSZ/inst/doc/hotspring.Rnw | 923 +++-- CHNOSZ-1.0.5/CHNOSZ/inst/doc/hotspring.pdf |binary CHNOSZ-1.0.5/CHNOSZ/inst/doc/wjd.R | 88 CHNOSZ-1.0.5/CHNOSZ/inst/doc/wjd.Rnw | 52 CHNOSZ-1.0.5/CHNOSZ/inst/doc/wjd.pdf |binary CHNOSZ-1.0.5/CHNOSZ/inst/extdata/protein/DS11.csv |only CHNOSZ-1.0.5/CHNOSZ/inst/extdata/protein/DS13.csv |only CHNOSZ-1.0.5/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv | 2 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-IAPWS95.R | 18 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-affinity.R | 29 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-diagram.R | 32 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-equilibrate.R | 2 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-findit.R | 6 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-ionize.aa.R | 16 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-ionize.aa_pK.R | 18 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-revisit.R | 8 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-subcrt.R | 10 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-water.R | 4 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-wjd.R | 4 CHNOSZ-1.0.5/CHNOSZ/man/CHNOSZ-package.Rd | 55 CHNOSZ-1.0.5/CHNOSZ/man/EOSregress.Rd | 5 CHNOSZ-1.0.5/CHNOSZ/man/IAPWS95.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/affinity.Rd | 116 CHNOSZ-1.0.5/CHNOSZ/man/anim.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/basis.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/buffer.Rd | 7 CHNOSZ-1.0.5/CHNOSZ/man/data.Rd | 13 CHNOSZ-1.0.5/CHNOSZ/man/diagram.Rd | 65 CHNOSZ-1.0.5/CHNOSZ/man/eos.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/eqdata.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/equilibrate.Rd | 14 CHNOSZ-1.0.5/CHNOSZ/man/examples.Rd | 29 CHNOSZ-1.0.5/CHNOSZ/man/extdata.Rd | 12 CHNOSZ-1.0.5/CHNOSZ/man/findit.Rd | 40 CHNOSZ-1.0.5/CHNOSZ/man/info.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/ionize.aa.Rd | 24 CHNOSZ-1.0.5/CHNOSZ/man/iprotein.Rd | 5 CHNOSZ-1.0.5/CHNOSZ/man/makeup.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/more.aa.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/mosaic.Rd |only CHNOSZ-1.0.5/CHNOSZ/man/objective.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/protein.Rd | 88 CHNOSZ-1.0.5/CHNOSZ/man/protein.info.Rd | 19 CHNOSZ-1.0.5/CHNOSZ/man/read.expr.Rd | 62 CHNOSZ-1.0.5/CHNOSZ/man/revisit.Rd | 50 CHNOSZ-1.0.5/CHNOSZ/man/sideeffects.Rd | 4 CHNOSZ-1.0.5/CHNOSZ/man/species.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/subcrt.Rd | 14 CHNOSZ-1.0.5/CHNOSZ/man/swap.basis.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/taxonomy.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/transfer.Rd | 17 CHNOSZ-1.0.5/CHNOSZ/man/util.affinity.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.args.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.array.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.blast.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.character.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.data.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.expression.Rd | 9 CHNOSZ-1.0.5/CHNOSZ/man/util.fasta.Rd | 3 CHNOSZ-1.0.5/CHNOSZ/man/util.formula.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.list.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.matrix.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.misc.Rd | 9 CHNOSZ-1.0.5/CHNOSZ/man/util.plot.Rd | 14 CHNOSZ-1.0.5/CHNOSZ/man/util.program.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.seq.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.units.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/water.Rd | 6 CHNOSZ-1.0.5/CHNOSZ/man/wjd.Rd | 44 CHNOSZ-1.0.5/CHNOSZ/vignettes/anintro.Rnw | 193 - CHNOSZ-1.0.5/CHNOSZ/vignettes/anintro.lyx | 1607 +++++++-- CHNOSZ-1.0.5/CHNOSZ/vignettes/equilibrium.Rnw | 18 CHNOSZ-1.0.5/CHNOSZ/vignettes/equilibrium.lyx | 33 CHNOSZ-1.0.5/CHNOSZ/vignettes/hotspring.Rnw | 923 +++-- CHNOSZ-1.0.5/CHNOSZ/vignettes/hotspring.lyx | 3218 ++++++++++++-------- CHNOSZ-1.0.5/CHNOSZ/vignettes/vig.bib | 2443 +++------------ CHNOSZ-1.0.5/CHNOSZ/vignettes/wjd.Rnw | 52 CHNOSZ-1.0.5/CHNOSZ/vignettes/wjd.lyx | 986 ++++-- 122 files changed, 6911 insertions(+), 6041 deletions(-)
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Title: Estimating Regional Trends of a Prevalence from a DHS
Description: Spatial estimation of a prevalence surface
or a relative risks surface, using data from a Demographic and Health
Survey (DHS) or an analog survey.
Author: Joseph Larmarange - IRD CEPED
Maintainer: Joseph Larmarange <joseph.larmarange@ird.fr>
Diff between prevR versions 2.9 dated 2013-12-28 and 3.1 dated 2015-05-19
prevR-2.9/prevR/R/idw.prevR.r |only prevR-2.9/prevR/build |only prevR-2.9/prevR/inst/doc |only prevR-2.9/prevR/man/as.SpatialGrid-prevR-method.Rd |only prevR-2.9/prevR/man/fdhs.prevR.rd |only prevR-2.9/prevR/man/krige-prevR-method.Rd |only prevR-2.9/prevR/man/plot-prevR-method.Rd |only prevR-2.9/prevR/vignettes |only prevR-3.1/prevR/DESCRIPTION | 30 +- prevR-3.1/prevR/MD5 | 118 ++++----- prevR-3.1/prevR/NAMESPACE | 77 ++++-- prevR-3.1/prevR/R/NA.outside.SpatialPolygons.prevR.r | 17 + prevR-3.1/prevR/R/Noptim.r |only prevR-3.1/prevR/R/as.SpatialGrid.prevR.r | 31 ++ prevR-3.1/prevR/R/as.data.frame.prevR.r | 37 ++ prevR-3.1/prevR/R/as.prevR.r | 66 +++++ prevR-3.1/prevR/R/changeproj.prevR.r | 34 ++ prevR-3.1/prevR/R/colors.prevR.r | 87 ++++++- prevR-3.1/prevR/R/create.boundary.prevR.r | 44 +++ prevR-3.1/prevR/R/direct.label_prevR.r |only prevR-3.1/prevR/R/export.prevR.r | 76 +++++- prevR-3.1/prevR/R/eyefit.prevR.r | 208 ++++++++-------- prevR-3.1/prevR/R/import.dhs.prevR.r | 35 ++ prevR-3.1/prevR/R/is.prevR.r | 42 +++ prevR-3.1/prevR/R/kde.prevR.r | 156 +++++++++++- prevR-3.1/prevR/R/krige.prevR.r | 235 ++++++++++++++++++- prevR-3.1/prevR/R/plot.prevR.r | 44 +++ prevR-3.1/prevR/R/point.in.SpatialPolygons.prevR.r | 16 + prevR-3.1/prevR/R/prevR-package.r |only prevR-3.1/prevR/R/print.prevR.r | 18 + prevR-3.1/prevR/R/quick.prevR.r |only prevR-3.1/prevR/R/rings.prevR.r | 77 +++++- prevR-3.1/prevR/R/setClass.prevR.r | 90 +++++++ prevR-3.1/prevR/R/show.prevR.r | 18 + prevR-3.1/prevR/R/summary.prevR.r | 84 ++++-- prevR-3.1/prevR/R/theme_prevR.r |only prevR-3.1/prevR/R/xyz2dataframe.prevR.r | 34 ++ prevR-3.1/prevR/data/TMWorldBorders.rda |binary prevR-3.1/prevR/data/fdhs.rda |binary prevR-3.1/prevR/demo/prevR.r | 4 prevR-3.1/prevR/inst/po/fr/LC_MESSAGES/R-prevR.mo |binary prevR-3.1/prevR/man/NA.outside.SpatialPolygons.Rd | 35 +- prevR-3.1/prevR/man/Noptim.Rd |only prevR-3.1/prevR/man/TMWorldBorders.Rd | 57 ++-- prevR-3.1/prevR/man/as.SpatialGrid.Rd |only prevR-3.1/prevR/man/as.data.frame.prevR.Rd | 46 ++- prevR-3.1/prevR/man/as.prevR.Rd | 100 ++++---- prevR-3.1/prevR/man/changeproj-prevR-method.Rd | 44 ++- prevR-3.1/prevR/man/create.boundary.Rd | 59 ++-- prevR-3.1/prevR/man/direct.label_prevR.Rd |only prevR-3.1/prevR/man/export-prevR-method.Rd | 118 +++++---- prevR-3.1/prevR/man/fdhs.Rd |only prevR-3.1/prevR/man/import.dhs.Rd | 43 ++- prevR-3.1/prevR/man/is.prevR.Rd | 67 +++-- prevR-3.1/prevR/man/kde-prevR-method.Rd | 168 ++++++++----- prevR-3.1/prevR/man/krige-ANY-prevR-method.Rd |only prevR-3.1/prevR/man/plot-prevR-missing-method.Rd |only prevR-3.1/prevR/man/point.in.SpatialPolygons.Rd | 26 +- prevR-3.1/prevR/man/prevR-class.Rd | 116 +++++---- prevR-3.1/prevR/man/prevR-package.Rd | 203 ++++++++++------ prevR-3.1/prevR/man/prevR.colors.Rd | 87 ++++--- prevR-3.1/prevR/man/print-prevR-method.Rd | 42 +-- prevR-3.1/prevR/man/quick.prevR.Rd |only prevR-3.1/prevR/man/rings-prevR-method.Rd | 115 +++++---- prevR-3.1/prevR/man/show-prevR-method.Rd | 33 +- prevR-3.1/prevR/man/summary-prevR-method.Rd | 46 +-- prevR-3.1/prevR/man/theme_prevR.Rd |only prevR-3.1/prevR/man/xyz2dataframe.Rd | 55 ++-- prevR-3.1/prevR/po/R-fr.po | 58 ++-- prevR-3.1/prevR/po/R-prevR.pot | 40 ++- 70 files changed, 2337 insertions(+), 899 deletions(-)
Title: Analysis of Multiple Social Networks with Algebra
Description: Algebraic procedures for the analysis of multiple social networks
are delivered with this package. Among other things, it is possible to
create and manipulate multivariate network data with different formats,
and there are effective ways available to treat multiple networks with
routines that combine algebraic systems like the partially ordered
semigroup or the semiring structure together with the relational bundles
occurring in different types of multivariate network data sets. As well an
algebraic approach for two-mode networks is made through Galois
derivations between families of the pair of subsets.
Author: J. Antonio Rivero Ostoic
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 1.5 dated 2015-05-01 and 1.6 dated 2015-05-19
DESCRIPTION | 8 MD5 | 32 +- R/dhc.R | 18 - R/diagram.levels.R | 95 +++--- R/fltr.R |only R/galois.R | 686 ++++++++++++++++++++++++++++------------------- R/print.reduced.R | 7 R/redl.R | 9 inst/CHANGELOG | 12 inst/doc/TwoMode.R | 22 - inst/doc/TwoMode.Rnw | 53 +-- inst/doc/TwoMode.pdf |binary man/diagram.Rd | 4 man/diagram.levels.Rd | 2 man/fltr.Rd |only man/galois.Rd | 3 man/multiplex-package.Rd | 4 vignettes/TwoMode.Rnw | 53 +-- 18 files changed, 581 insertions(+), 427 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.4.3 dated 2015-04-18 and 0.4.4 dated 2015-05-19
DESCRIPTION | 23 MD5 | 275 - NAMESPACE | 39 NEWS | 194 R/Analyse_SAR.OSLdata.R | 993 ++-- R/CW2pHMi.R | 458 +- R/CW2pLM.R | 169 R/CW2pLMi.R | 357 - R/CW2pPMi.R | 322 - R/Luminescence-package.R |only R/RLum.Results-class.R | 25 R/Risoe.BINfileData2RLum.Analysis.R | 274 - R/Risoe.BINfileData2RLum.Data.Curve.R | 242 - R/RisoeBINfileData-class.R | 24 R/Second2Gray.R | 268 - R/analyse_IRSAR.RF.R | 1717 ++++---- R/analyse_SAR.CWOSL.R | 330 - R/analyse_SAR.TL.R | 898 ++-- R/analyse_pIRIRSequence.R | 1458 +++---- R/apply_CosmicRayRemoval.R | 232 - R/apply_EfficiencyCorrection.R | 159 R/calc_AliquotSize.R | 838 ++-- R/calc_CentralDose.R | 498 +- R/calc_CommonDose.R | 346 - R/calc_CosmicDoseRate.R | 1148 ++--- R/calc_FadingCorr.R | 367 + R/calc_FiniteMixture.R | 1155 ++--- R/calc_FuchsLang2001.R | 470 +- R/calc_HomogeneityTest.R | 261 - R/calc_IEU.R | 872 ++-- R/calc_MaxDose.R | 225 - R/calc_MinDose.R | 1598 +++---- R/calc_OSLLxTxRatio.R | 360 - R/calc_SourceDoseRate.R | 313 - R/calc_Statistics.R | 100 R/calc_TLLxTxRatio.R | 292 - R/extract_IrradiationTimes.R | 285 - R/fit_CWCurve.R | 1089 ++--- R/fit_LMCurve.R | 1460 +++---- R/get_Layout.R | 142 R/get_RLum.R | 176 R/merge_RLum.Analysis.R | 256 - R/merge_RLum.Data.Curve.R | 435 +- R/merge_RLum.R | 205 R/merge_Risoe.BINfileData.R | 507 +- R/plot_AbanicoPlot.R | 6357 +++++++++++++++---------------- R/plot_DRTResults.R | 1458 +++---- R/plot_GrowthCurve.R | 1828 ++++---- R/plot_Histogram.R | 362 - R/plot_KDE.R | 1775 ++++---- R/plot_RLum.Analysis.R | 403 - R/plot_RLum.Data.Curve.R | 253 - R/plot_RLum.Data.Image.R | 334 - R/plot_RLum.Data.Spectrum.R | 674 +-- R/plot_RLum.R | 171 R/plot_RLum.Results.R | 1948 ++++----- R/plot_RadialPlot.R | 3062 +++++++------- R/plot_Risoe.BINfileData.R | 413 -- R/readBIN2R.R | 1392 +++--- R/readSPE2R.R | 862 ++-- R/readXSYG2R.R | 263 - R/writeR2BIN.R | 1727 ++++---- R/zzz.R | 24 inst/NEWS.Rd | 157 man/Analyse_SAR.OSLdata.Rd | 271 - man/BaseDataSet.CosmicDoseRate.Rd | 93 man/CW2pHMi.Rd | 340 - man/CW2pLM.Rd | 155 man/CW2pLMi.Rd | 252 - man/CW2pPMi.Rd | 267 - man/ExampleData.BINfileData.Rd | 81 man/ExampleData.CW_OSL_Curve.Rd | 69 man/ExampleData.DeValues.Rd | 156 man/ExampleData.FittingLM.Rd | 50 man/ExampleData.LxTxData.Rd | 40 man/ExampleData.LxTxOSLData.Rd | 31 man/ExampleData.RLum.Analysis.Rd | 58 man/ExampleData.RLum.Data.Image.Rd | 46 man/ExampleData.XSYG.Rd | 124 man/Luminescence-package.Rd | 76 man/RLum-class.Rd | 39 man/RLum.Analysis-class.Rd | 114 man/RLum.Data-class.Rd | 44 man/RLum.Data.Curve-class.Rd | 99 man/RLum.Data.Image-class.Rd | 101 man/RLum.Data.Spectrum-class.Rd | 105 man/RLum.Results-class.Rd | 86 man/Risoe.BINfileData-class.Rd | 316 - man/Risoe.BINfileData2RLum.Analysis.Rd | 121 man/Risoe.BINfileData2RLum.Data.Curve.Rd | 119 man/Second2Gray.Rd | 140 man/analyse_IRSAR.RF.Rd | 450 +- man/analyse_SAR.CWOSL.Rd | 301 - man/analyse_SAR.TL.Rd | 194 man/analyse_pIRIRSequence.Rd | 298 - man/apply_CosmicRayRemoval.Rd | 172 man/apply_EfficiencyCorrection.Rd | 98 man/calc_AliquotSize.Rd | 252 - man/calc_CentralDose.Rd | 166 man/calc_CommonDose.Rd | 168 man/calc_CosmicDoseRate.Rd | 443 +- man/calc_FadingCorr.Rd | 164 man/calc_FiniteMixture.Rd | 321 - man/calc_FuchsLang2001.Rd | 159 man/calc_HomogeneityTest.Rd | 98 man/calc_IEU.Rd | 131 man/calc_MaxDose.Rd | 207 - man/calc_MinDose.Rd | 514 +- man/calc_OSLLxTxRatio.Rd | 202 man/calc_SourceDoseRate.Rd | 185 man/calc_Statistics.Rd | 97 man/calc_TLLxTxRatio.Rd | 146 man/extract_IrradiationTimes.Rd | 224 - man/fit_CWCurve.Rd | 305 - man/fit_LMCurve.Rd | 433 +- man/get_Layout.Rd | 108 man/get_RLum.Rd | 124 man/merge_RLum.Analysis.Rd | 112 man/merge_RLum.Data.Curve.Rd | 168 man/merge_RLum.Rd | 112 man/merge_Risoe.BINfileData.Rd | 160 man/plot_AbanicoPlot.Rd | 703 +-- man/plot_DRTResults.Rd | 309 - man/plot_GrowthCurve.Rd | 271 - man/plot_Histogram.Rd | 207 - man/plot_KDE.Rd | 331 - man/plot_RLum.Analysis.Rd | 179 man/plot_RLum.Data.Curve.Rd | 108 man/plot_RLum.Data.Image.Rd | 177 man/plot_RLum.Data.Spectrum.Rd | 359 - man/plot_RLum.Rd | 121 man/plot_RLum.Results.Rd | 109 man/plot_RadialPlot.Rd | 480 +- man/plot_Risoe.BINfileData.Rd | 199 man/readBIN2R.Rd | 136 man/readSPE2R.Rd | 207 - man/readXSYG2R.Rd | 269 - man/sTeve.Rd | 59 man/writeR2BIN.Rd | 143 139 files changed, 30124 insertions(+), 29466 deletions(-)
Title: Longitudinal Data
Description: Tools for longitudinal data and joint longitudinal data (used by packages kml and kml3d).
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Dai Fang [ctb],
Luke Tierney [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between longitudinalData versions 2.2 dated 2014-03-20 and 2.3 dated 2015-05-19
longitudinalData-2.2/longitudinalData/data/constants.rda |only longitudinalData-2.3/longitudinalData/DESCRIPTION | 29 longitudinalData-2.3/longitudinalData/MD5 | 33 longitudinalData-2.3/longitudinalData/NAMESPACE | 10 longitudinalData-2.3/longitudinalData/R/constants.r |only longitudinalData-2.3/longitudinalData/R/function.r | 46 longitudinalData-2.3/longitudinalData/R/imputCopyMean.R | 602 +++++----- longitudinalData-2.3/longitudinalData/R/imputLinearInterpol.R | 420 +++--- longitudinalData-2.3/longitudinalData/R/imputation.r | 2 longitudinalData-2.3/longitudinalData/R/longDataPlot.r | 15 longitudinalData-2.3/longitudinalData/R/myMisc3d.r |only longitudinalData-2.3/longitudinalData/man/ListPartition-class.Rd | 5 longitudinalData-2.3/longitudinalData/man/LongData-class.Rd | 2 longitudinalData-2.3/longitudinalData/man/LongData3d-class.Rd | 3 longitudinalData-2.3/longitudinalData/man/longData-internal.Rd | 10 longitudinalData-2.3/longitudinalData/man/longData.Rd | 2 longitudinalData-2.3/longitudinalData/man/longitudinalData-package.Rd | 4 longitudinalData-2.3/longitudinalData/man/reshapeLong.Rd | 13 longitudinalData-2.3/longitudinalData/man/reshapeWide.Rd | 12 19 files changed, 659 insertions(+), 549 deletions(-)
More information about longitudinalData at CRAN
Permanent link
Title: Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction
Data
Description: To facilitate retrieving and processing biochemical reaction data such as Rhea, MetaCyc, KEGG and Unipathway, the package provides the functions to download and parse data, instantiate generic reaction and check mass-balance. The package aims to construct an integrated metabolic network and genome-scale metabolic model.
Author: Byoungnam Min, Byeonghyeok Park, Kyoung Heon Kim and In-Geol Choi
Maintainer: Byoungnam Min <mbnmbn00@gmail.com>
Diff between RbioRXN versions 1.5 dated 2015-01-14 and 1.5.1 dated 2015-05-19
DESCRIPTION | 16 ++++++++-------- MD5 | 16 ++++++++-------- NAMESPACE | 3 ++- R/RbioRXN-internal.R | 34 ++++++++++++++++++++++------------ R/get.chebi.all.R | 18 +++++++++--------- R/get.metacyc.all.R | 2 +- R/get.rhea.all.R | 2 +- data/example.rda |binary man/RbioRXN-package.Rd | 10 +++++----- 9 files changed, 56 insertions(+), 45 deletions(-)
Title: Network Generator for Combinatorial Graph Problems
Description: Methods for the generation of a wide range of network geographies, e.g., grid networks or clustered networks. Useful for the generation of benchmarking instances for the investigation of, e.g., Vehicle-Routing-Problems or Travelling Salesperson Problems.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between netgen versions 1.0 dated 2015-02-03 and 1.1 dated 2015-05-19
netgen-1.0/netgen/R/getOptimalPointMatching.R |only netgen-1.0/netgen/man/makeClusteredNetwork.Rd |only netgen-1.1/netgen/DESCRIPTION | 17 netgen-1.1/netgen/MD5 | 140 +++-- netgen-1.1/netgen/NAMESPACE | 10 netgen-1.1/netgen/NEWS |only netgen-1.1/netgen/R/asCharacterNetwork.R | 20 netgen-1.1/netgen/R/asDataFrameNetwork.R | 63 +- netgen-1.1/netgen/R/asMatrixNetwork.R | 13 netgen-1.1/netgen/R/autoplotNetwork.R | 104 ++-- netgen-1.1/netgen/R/buildDepots.R | 18 netgen-1.1/netgen/R/computeDistancesToNearestClusterCenter.R | 48 - netgen-1.1/netgen/R/decorateGGPlot.R | 20 netgen-1.1/netgen/R/determineNumberOfPointsPerCluster.r | 66 +- netgen-1.1/netgen/R/dynamise.R | 78 +-- netgen-1.1/netgen/R/exportToFile.R |only netgen-1.1/netgen/R/exportToTSPlibFormat.R |only netgen-1.1/netgen/R/forceToBounds.R | 22 netgen-1.1/netgen/R/generateClusterCenters.R | 16 netgen-1.1/netgen/R/generateClusteredNetwork.R | 247 +++++----- netgen-1.1/netgen/R/generateGridNetwork.R | 55 +- netgen-1.1/netgen/R/generateRandomNetwork.R | 67 +- netgen-1.1/netgen/R/getDepotCoordinates.R | 11 netgen-1.1/netgen/R/getNumberOfClusters.R | 21 netgen-1.1/netgen/R/getNumberOfDepots.R | 13 netgen-1.1/netgen/R/getNumberOfNodes.R | 9 netgen-1.1/netgen/R/hasDepots.R | 6 netgen-1.1/netgen/R/helpers.R | 30 + netgen-1.1/netgen/R/importFromFile.R |only netgen-1.1/netgen/R/importFromTSPlibFormat.R |only netgen-1.1/netgen/R/makeNetwork.R | 82 +-- netgen-1.1/netgen/R/morphInstances.R | 122 ++-- netgen-1.1/netgen/R/pointMatching.R |only netgen-1.1/netgen/R/printNetwork.R | 32 - netgen-1.1/netgen/R/rescaleNetwork.R |only netgen-1.1/netgen/R/visualizeMorphing.R | 138 ++--- netgen-1.1/netgen/R/visualizePointMatching.R | 105 ++-- netgen-1.1/netgen/R/zzz.R | 2 netgen-1.1/netgen/inst |only netgen-1.1/netgen/man/as.character.Network.Rd | 2 netgen-1.1/netgen/man/as.data.frame.Network.Rd | 6 netgen-1.1/netgen/man/as.matrix.Network.Rd | 8 netgen-1.1/netgen/man/autoplot.Network.Rd | 18 netgen-1.1/netgen/man/dynamise.Rd | 13 netgen-1.1/netgen/man/exportToFile.Rd |only netgen-1.1/netgen/man/exportToTSPlibFormat.Rd |only netgen-1.1/netgen/man/generateClusteredNetwork.Rd | 26 - netgen-1.1/netgen/man/generateGridNetwork.Rd | 12 netgen-1.1/netgen/man/generateRandomNetwork.Rd | 8 netgen-1.1/netgen/man/getDepotCoordinates.Rd | 2 netgen-1.1/netgen/man/getNumberOfClusters.Rd | 2 netgen-1.1/netgen/man/getNumberOfDepots.Rd | 2 netgen-1.1/netgen/man/getNumberOfNodes.Rd | 6 netgen-1.1/netgen/man/getOptimalPointMatching.Rd | 18 netgen-1.1/netgen/man/getPointDistributionStrategies.Rd | 2 netgen-1.1/netgen/man/hasDepots.Rd | 2 netgen-1.1/netgen/man/importFromFile.Rd |only netgen-1.1/netgen/man/importFromTSPlibFormat.Rd |only netgen-1.1/netgen/man/makeNetwork.Rd | 20 netgen-1.1/netgen/man/morphInstances.Rd | 34 - netgen-1.1/netgen/man/rescaleNetwork.Rd |only netgen-1.1/netgen/man/visualizeMorphing.Rd | 6 netgen-1.1/netgen/man/visualizePointMatching.Rd | 16 netgen-1.1/netgen/tests/testthat/test_export_and_import.R |only netgen-1.1/netgen/tests/testthat/test_generateGridNetwork.R | 2 netgen-1.1/netgen/tests/testthat/test_getOptimalPointMatching.R |only netgen-1.1/netgen/tests/testthat/test_import.R |only netgen-1.1/netgen/tests/testthat/test_morphInstances.R | 25 + netgen-1.1/netgen/tests/testthat/test_rescaleNetwork.R |only 69 files changed, 997 insertions(+), 808 deletions(-)
Title: Hierarchical Generalized Linear Models
Description: Implemented here are procedures for fitting hierarchical generalized linear models (HGLM). It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model.
Author: Moudud Alam, Lars Ronnegard, Xia Shen
Maintainer: Xia Shen <xia.shen@ki.se>
Diff between hglm versions 2.0-11 dated 2014-10-30 and 2.1-0 dated 2015-05-19
ChangeLog | 28 DESCRIPTION | 12 MD5 | 44 - NAMESPACE | 21 R/GLM.MME.R | 237 ++--- R/hglm.default.R | 1271 +++++++++++++++--------------- R/hglm.formula.R | 10 R/hglm2.R | 2 R/hglm2.formula.R | 31 R/likelihood.R | 128 ++- R/logLik.hglm.R |only R/lrt.R | 7 R/print.hglm.R | 4 R/print.summary.hglm.R | 4 R/summary.hglm.R | 2 build/vignette.rds |binary inst/doc/hglm.Rnw | 2 inst/doc/hglm.pdf |binary man/hglm-package.Rd | 88 +- man/hglm.Rd | 438 +++++----- man/hglm2.Rd | 4 man/logLik.hglm.Rd |only vignettes/hglm-knitr-knitr-compressed.pdf |binary vignettes/hglm.Rnw | 2 24 files changed, 1248 insertions(+), 1087 deletions(-)
Title: Doubly Robust Generalized Estimating Equations
Description: Fit restricted mean models for the conditional association
between an exposure and an outcome, given covariates. Three methods
are implemented: O-estimation, where a nuisance model for the
association between the covariates and the outcome is used;
E-estimation where a nuisance model for the association
between the covariates and the exposure is used, and doubly robust (DR)
estimation where both nuisance models are used. In DR-estimation,
the estimates will be consistent when at least one of the nuisance
models is correctly specified, not necessarily both.
Author: Johan Zetterqvist <johan.zetterqvist@ki.se> , Arvid Sjölander <arvid.sjolander@ki.se> with contributions from Alexander Ploner.
Maintainer: Johan Zetterqvist <johan.zetterqvist@ki.se>
Diff between drgee versions 1.1.1 dated 2015-05-09 and 1.1.2 dated 2015-05-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 7 ++++++- R/drgeeData.R | 16 ++++++++-------- R/gee.R | 1 + 5 files changed, 23 insertions(+), 17 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely nonparametric, in particular the DDalpha-procedure. The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.1.0 dated 2014-12-20 and 1.1.1 dated 2015-05-19
ddalpha-1.1.0/ddalpha/src/Makevars.win |only ddalpha-1.1.1/ddalpha/DESCRIPTION | 10 +- ddalpha-1.1.1/ddalpha/MD5 | 75 +++++++++---------- ddalpha-1.1.1/ddalpha/NAMESPACE | 1 ddalpha-1.1.1/ddalpha/R/ddalpha-internal.r | 41 +++++----- ddalpha-1.1.1/ddalpha/R/ddalpha.classify.r | 35 ++++++-- ddalpha-1.1.1/ddalpha/R/ddalpha.test.r |only ddalpha-1.1.1/ddalpha/R/ddalpha.train.r | 44 +++++++---- ddalpha-1.1.1/ddalpha/R/ddalphaf.r | 11 +- ddalpha-1.1.1/ddalpha/R/depth.graph.r | 12 ++- ddalpha-1.1.1/ddalpha/R/depth.projection.r | 8 +- ddalpha-1.1.1/ddalpha/R/depth.randomTukey.r | 3 ddalpha-1.1.1/ddalpha/R/depth.space.randomTukey.r | 4 - ddalpha-1.1.1/ddalpha/R/depth.space.zonoid.r | 4 - ddalpha-1.1.1/ddalpha/R/depth.zonoid.r | 4 - ddalpha-1.1.1/ddalpha/R/is.in.convex.r | 4 - ddalpha-1.1.1/ddalpha/R/separator.polynomial.r | 8 +- ddalpha-1.1.1/ddalpha/man/ddalpha-package.Rd | 6 - ddalpha-1.1.1/ddalpha/man/ddalpha.getErrorRateCV.Rd |only ddalpha-1.1.1/ddalpha/man/ddalpha.getErrorRateJK.Rd |only ddalpha-1.1.1/ddalpha/man/ddalpha.test.Rd |only ddalpha-1.1.1/ddalpha/man/ddalpha.train.Rd | 7 + ddalpha-1.1.1/ddalpha/man/ddalphaf.train.Rd | 4 + ddalpha-1.1.1/ddalpha/man/depth.graph.Rd | 8 ++ ddalpha-1.1.1/ddalpha/man/depth.projection.Rd | 5 + ddalpha-1.1.1/ddalpha/man/depth.randomTukey.Rd | 5 + ddalpha-1.1.1/ddalpha/man/depth.space.projection.Rd | 6 + ddalpha-1.1.1/ddalpha/man/depth.space.randomTukey.Rd | 5 + ddalpha-1.1.1/ddalpha/man/depth.space.zonoid.Rd | 5 + ddalpha-1.1.1/ddalpha/man/depth.zonoid.Rd | 5 + ddalpha-1.1.1/ddalpha/man/is.in.convex.Rd | 5 + ddalpha-1.1.1/ddalpha/src/Common.cpp | 3 ddalpha-1.1.1/ddalpha/src/Common.h | 2 ddalpha-1.1.1/ddalpha/src/DataStructures.h | 1 ddalpha-1.1.1/ddalpha/src/Knn.cpp | 21 +++-- ddalpha-1.1.1/ddalpha/src/Polynomial.cpp | 25 +++--- ddalpha-1.1.1/ddalpha/src/ProjectionDepth.cpp | 12 ++- ddalpha-1.1.1/ddalpha/src/ZonoidDepth.cpp | 10 +- ddalpha-1.1.1/ddalpha/src/ZonoidDepth.h | 2 ddalpha-1.1.1/ddalpha/src/ddalpha.cpp | 33 ++++++-- ddalpha-1.1.1/ddalpha/src/stdafx.h | 40 +++++++--- 41 files changed, 310 insertions(+), 164 deletions(-)
Title: Markov Chain Monte Carlo Methods for Redistricting Simulation
Description: Enables researchers to sample redistricting plans from a pre-specified target distribution using a Markov Chain Monte Carlo algorithm. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. The algorithm also can be used in combination with efficient simulation methods such as simulated and parallel tempering algorithms. Tools for analysis such as inverse probability reweighting and plotting functionality are included. The package implements methods described in Fifield, Higgins, Imai and Tarr (2015) ``A New Automated Redistricting Simulator Using Markov Chain Monte Carlo,'' working paper available at <http://http://imai.princeton.edu/research/files/redist.pdf>.
Author: Ben Fifield <bfifield@princeton.edu>, Alexander Tarr <atarr@princeton.edu>, Michael Higgins <mjh5@princeton.edu>, and Kosuke Imai <kimai@princeton.edu>
Maintainer: Ben Fifield <bfifield@princeton.edu>
Diff between redist versions 1.0 dated 2015-05-18 and 1.1 dated 2015-05-19
ChangeLog |only DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- R/redist.R | 29 +++++++++++++++++++++++------ man/redist.mcmc.Rd | 3 ++- src/check_contiguity.h | 2 -- src/constraint_calc_helper.cpp | 20 ++++++++++++++++---- src/constraint_calc_helper.h | 4 ++-- src/make_swaps_helper.h | 4 ++-- src/redist_analysis.h | 4 ++-- src/sw_mh_helper.h | 4 ++-- 11 files changed, 63 insertions(+), 34 deletions(-)
Title: Robust Algorithm for Principal Component Analysis
Description: The FastHCS algorithm of Schmitt and Vakili (2014) for high-dimensional, robust PCA modelling and associated outlier detection and diagnostic tools.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili <vakili.kaveh.email@gmail.com>
Diff between FastHCS versions 0.0.4 dated 2015-01-08 and 0.0.5 dated 2015-05-19
FastHCS-0.0.4/FastHCS/data/Ionosphere.txt.gz |only FastHCS-0.0.4/FastHCS/man/Ionosphere.Rd |only FastHCS-0.0.5/FastHCS/DESCRIPTION | 10 - FastHCS-0.0.5/FastHCS/MD5 | 26 +-- FastHCS-0.0.5/FastHCS/NAMESPACE | 7 FastHCS-0.0.5/FastHCS/R/FastHCS.R | 187 ++++++++++++++++++------ FastHCS-0.0.5/FastHCS/data/datalist | 1 FastHCS-0.0.5/FastHCS/man/DnaAlteration.Rd | 2 FastHCS-0.0.5/FastHCS/man/FHCSkernelEVD.Rd |only FastHCS-0.0.5/FastHCS/man/FHCSpsdo.Rd |only FastHCS-0.0.5/FastHCS/man/FastHCS-package.Rd | 25 +-- FastHCS-0.0.5/FastHCS/man/FastHCS.Rd | 10 - FastHCS-0.0.5/FastHCS/man/compPcaParams.Rd | 17 -- FastHCS-0.0.5/FastHCS/man/plot.FastHCS.Rd | 17 +- FastHCS-0.0.5/FastHCS/src/FastHCS.cpp | 205 +++------------------------ FastHCS-0.0.5/FastHCS/src/mystruc.h |only FastHCS-0.0.5/FastHCS/src/psdo.cpp |only 17 files changed, 224 insertions(+), 283 deletions(-)
Title: Tests for Type I Error in Qualitative Comparative Analysis (QCA)
Description: Implements tests for Type I error in Qualitative Comparative Analysis (QCA) that take into account the multiple hypothesis tests inherent in the procedure. Tests can be carried out on three variants of QCA: crisp-set QCA (csQCA), multi-value QCA (mvQCA) and fuzzy-set QCA (fsQCA). For fsQCA, the fsQCApermTest() command implements a permutation test that provides 95% confidence intervals for the number of counterexamples and degree of consistency, respectively. The distributions of permuted values can be plotted against the observed values. For csQCA and mvQCA, simple binomial tests are implemented in csQCAbinTest() and mvQCAbinTest(), respectively.
Author: Bear Braumoeller <braumoeller.1@osu.edu>
Maintainer: Bear Braumoeller <braumoeller.1@osu.edu>
Diff between QCAfalsePositive versions 1.0 dated 2015-05-06 and 1.1.1 dated 2015-05-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/fsQCApermTest.R | 29 +++++++++++++++++++---------- R/summary.fsQCApt.R | 6 +++--- 4 files changed, 28 insertions(+), 19 deletions(-)
More information about QCAfalsePositive at CRAN
Permanent link
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for HTTP 2.0, SSL (https://, ftps://), gzip, and other 'libcurl' goodies.
The core of the package implements a framework for performing fully customizable
requests where data can be processed either in memory, on disk, or streaming via
the callback or connection interfaces. Some knowledge of 'libcurl' is recommended;
for a more-user-friendly web client see the 'httr' package which builds on this
package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.5 dated 2015-02-01 and 0.6 dated 2015-05-19
curl-0.5/curl/R/curl_download.R |only curl-0.5/curl/R/curl_escape.R |only curl-0.5/curl/R/curl_version.R |only curl-0.5/curl/man/utilities.Rd |only curl-0.5/curl/src/utils.h |only curl-0.6/curl/DESCRIPTION | 38 +++++---- curl-0.6/curl/LICENSE | 2 curl-0.6/curl/MD5 | 80 ++++++++++++++----- curl-0.6/curl/NAMESPACE | 30 ++++++- curl-0.6/curl/NEWS | 6 + curl-0.6/curl/R/curl.R | 12 +- curl-0.6/curl/R/download.R |only curl-0.6/curl/R/escape.R |only curl-0.6/curl/R/fetch.R |only curl-0.6/curl/R/form.R |only curl-0.6/curl/R/handle.R |only curl-0.6/curl/R/onload.R |only curl-0.6/curl/R/parse_headers.R |only curl-0.6/curl/R/proxy.R |only curl-0.6/curl/R/utilities.R |only curl-0.6/curl/build |only curl-0.6/curl/configure | 17 ++-- curl-0.6/curl/data |only curl-0.6/curl/inst |only curl-0.6/curl/man/curl.Rd | 13 +-- curl-0.6/curl/man/curl_download.Rd | 39 ++++++--- curl-0.6/curl/man/curl_escape.Rd |only curl-0.6/curl/man/curl_fetch.Rd |only curl-0.6/curl/man/curl_options.Rd |only curl-0.6/curl/man/form_file.Rd |only curl-0.6/curl/man/handle.Rd |only curl-0.6/curl/man/handle_cookies.Rd |only curl-0.6/curl/man/ie_proxy_info.Rd |only curl-0.6/curl/man/parse_date.Rd |only curl-0.6/curl/man/parse_headers.Rd |only curl-0.6/curl/src/Makevars | 5 + curl-0.6/curl/src/Makevars.win | 25 +++-- curl-0.6/curl/src/apple.h |only curl-0.6/curl/src/callbacks.c |only curl-0.6/curl/src/callbacks.h |only curl-0.6/curl/src/curl-common.h |only curl-0.6/curl/src/curl-symbols.h | 21 +++++ curl-0.6/curl/src/curl.c | 56 +++++++------ curl-0.6/curl/src/download.c | 62 +++++--------- curl-0.6/curl/src/escape.c | 36 +++++--- curl-0.6/curl/src/fetch.c |only curl-0.6/curl/src/form.c |only curl-0.6/curl/src/getdate.c |only curl-0.6/curl/src/handle.c |only curl-0.6/curl/src/ieproxy.c |only curl-0.6/curl/src/init.c |only curl-0.6/curl/src/utils.c | 134 ++++++++++++++++++++++---------- curl-0.6/curl/src/winhttp32.def |only curl-0.6/curl/src/winhttp64.def |only curl-0.6/curl/tests |only curl-0.6/curl/tools/symbols-in-versions |only curl-0.6/curl/tools/symbols.R |only curl-0.6/curl/tools/winlibs.R | 4 curl-0.6/curl/vignettes |only 59 files changed, 385 insertions(+), 195 deletions(-)