Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. Concorde
itself is not included in the package and has to be obtained separately
from http://www.math.uwaterloo.ca/tsp/concorde.html.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between TSP versions 1.1-1 dated 2015-05-15 and 1.1-2 dated 2015-06-30
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 6 ++++-- build/vignette.rds |binary data/USCA312.rda |binary data/USCA312_map.rda |binary data/USCA50.rda |binary inst/NEWS | 3 +++ inst/doc/TSP.pdf |binary 9 files changed, 20 insertions(+), 15 deletions(-)
Title: Infrastructure for Seriation
Description: Infrastructure for seriation with an implementation of several
seriation/sequencing techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT).
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph],
Fionn Murtagh [ctb, cph],
Michael Brusco [ctb, cph],
Stephanie Stahl [ctb, cph],
Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.1-0 dated 2015-06-09 and 1.1-1 dated 2015-06-30
DESCRIPTION | 11 +-- MD5 | 48 +++++++-------- NAMESPACE | 7 +- R/dissimilartiy.R | 140 ++++++++++++++++++++++++++++++++++------------ R/permutation_vector.R | 18 +++-- R/permute.R | 2 R/pimage.R | 12 +-- build/vignette.rds |binary data/Chameleon.rda |binary data/Irish.rda |binary data/Munsingen.rda |binary data/Psych24.rda |binary data/Townships.rda |binary data/Wood.rda |binary data/Zoo.rda |binary inst/NEWS | 11 +++ inst/doc/seriation.pdf |binary man/col.Rd | 2 man/criterion.Rd | 1 man/dissimilarity.Rd | 66 +++++++++++++-------- man/get_order.Rd | 40 ++++++++----- man/hmap.Rd | 12 ++- man/permutation.Rd | 2 man/permutation_vector.Rd | 5 - man/pimage.Rd | 16 ++--- 25 files changed, 257 insertions(+), 136 deletions(-)
Title: Survey Sampling
Diff between sampling versions 2.6 dated 2013-11-08 and 2.7 dated 2015-06-30
Description: Functions for drawing and calibrating samples.
Author: Yves Tillé
Maintainer: Alina Matei <alina.matei@unine.ch>
sampling-2.6/sampling/R/gencalib.r |only
sampling-2.6/sampling/inst/doc/vignettes |only
sampling-2.7/sampling/DESCRIPTION | 8 -
sampling-2.7/sampling/MD5 | 53 +++++----
sampling-2.7/sampling/NAMESPACE | 2
sampling-2.7/sampling/R/HTstrata.r | 2
sampling-2.7/sampling/R/Hajekstrata.r | 17 +-
sampling-2.7/sampling/R/gencalib.R |only
sampling-2.7/sampling/R/getdata.r | 1
sampling-2.7/sampling/R/mstage.r | 98 +++++++++--------
sampling-2.7/sampling/R/varHT.r |only
sampling-2.7/sampling/build |only
sampling-2.7/sampling/data/MU284.rda |binary
sampling-2.7/sampling/inst/doc/HT_Hajek_estimators.R |only
sampling-2.7/sampling/inst/doc/HT_Hajek_estimators.Snw |only
sampling-2.7/sampling/inst/doc/HT_Hajek_estimators.pdf |only
sampling-2.7/sampling/inst/doc/UPexamples.R |only
sampling-2.7/sampling/inst/doc/UPexamples.Snw |only
sampling-2.7/sampling/inst/doc/UPexamples.pdf |only
sampling-2.7/sampling/inst/doc/calibration.R |only
sampling-2.7/sampling/inst/doc/calibration.Snw |only
sampling-2.7/sampling/inst/doc/calibration.pdf |only
sampling-2.7/sampling/man/Hajekstrata.Rd | 2
sampling-2.7/sampling/man/calibev.Rd | 10 -
sampling-2.7/sampling/man/gencalib.Rd | 2
sampling-2.7/sampling/man/mstage.Rd | 57 +++++++--
sampling-2.7/sampling/man/samplecube.Rd | 2
sampling-2.7/sampling/man/varHT.Rd |only
sampling-2.7/sampling/man/varest.Rd | 2
sampling-2.7/sampling/man/vartaylor_ratio.Rd | 8 -
sampling-2.7/sampling/vignettes |only
31 files changed, 156 insertions(+), 108 deletions(-)
Title: True Random Numbers using RANDOM.ORG
Description: The true random number service provided by the RANDOM.ORG
website created by Mads Haahr samples atmospheric noise via radio tuned to
an unused broadcasting frequency together with a skew correction algorithm
due to John von Neumann. More background is available in the included
vignette based on an essay by Mads Haahr. In its current form, the package
offers functions to retrieve random integers, randomized sequences and
random strings.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between random versions 0.2.4 dated 2015-05-17 and 0.2.5 dated 2015-06-30
ChangeLog | 10 ++++++++++ DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 1 + R/random.R | 8 ++++---- README.md | 3 ++- inst/doc/random-essay.pdf |binary inst/doc/random-intro.pdf |binary 8 files changed, 29 insertions(+), 17 deletions(-)
Title: An R Package for Text Analysis
Description: A set of tools to analyze texts. Includes, amongst others,
functions for automatic language detection, hyphenation, several indices of
lexical diversity (e.g., type token ratio, HD-D/vocd-D, MTLD) and readability
(e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for language
corpora are also provided, to enable frequency analyses (supports Celex and
Leipzig Corpora Collection file formats) and measures like tf-idf. Note: For
full functionality a local installation of TreeTagger is recommended. 'koRpus'
also includes a plugin for the R GUI and IDE RKWard, providing graphical dialogs
for its basic features. The respective R package 'rkward' cannot be installed
directly from a repository, as it is a part of RKWard. To make full use of this
feature, please install RKWard from https://rkward.kde.org (plugins are detected
automatically). Due to some restrictions on CRAN, the full package sources are
only available from the project homepage.
Author: m.eik michalke [aut, cre],
Earl Brown [ctb],
Alberto Mirisola [ctb],
Alexandre Brulet [ctb],
Laura Hauser [ctb]
Maintainer: m.eik michalke <meik.michalke@hhu.de>
Diff between koRpus versions 0.05-5 dated 2014-03-19 and 0.05-6 dated 2015-06-30
koRpus-0.05-5/koRpus/inst/rkward/plugins/koRpus.js |only koRpus-0.05-5/koRpus/inst/rkward/plugins/koRpus.xml |only koRpus-0.05-5/koRpus/inst/rkward/rkwarddev_koRpus_plugin_script_NG.R |only koRpus-0.05-5/koRpus/inst/tests |only koRpus-0.05-5/koRpus/tests/test_koRpus_package.R |only koRpus-0.05-6/koRpus/ChangeLog | 25 koRpus-0.05-6/koRpus/DESCRIPTION | 40 koRpus-0.05-6/koRpus/MD5 | 267 +- koRpus-0.05-6/koRpus/NAMESPACE | 6 koRpus-0.05-6/koRpus/R/00_class_10_kRp.readability.R | 3 koRpus-0.05-6/koRpus/R/01_method_plot.kRp.tagged.R | 5 koRpus-0.05-6/koRpus/R/01_method_show.kRp.readability.R | 17 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.TTR.R | 1 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.lang.R | 5 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.readability.R | 13 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.tagged.R | 1 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.txt.freq.R | 1 koRpus-0.05-6/koRpus/R/freq.analysis.R | 4 koRpus-0.05-6/koRpus/R/guess.lang.R | 6 koRpus-0.05-6/koRpus/R/kRp.POS.tags.R | 8 koRpus-0.05-6/koRpus/R/kRp.text.transform.R | 64 koRpus-0.05-6/koRpus/R/koRpus-internal.R | 20 koRpus-0.05-6/koRpus/R/koRpus-internal.lexdiv.formulae.R | 2 koRpus-0.05-6/koRpus/R/koRpus-internal.rdb.formulae.R | 269 +- koRpus-0.05-6/koRpus/R/koRpus-internal.rdb.params.grades.R | 1 koRpus-0.05-6/koRpus/R/koRpus-internal.roxy.all.R | 62 koRpus-0.05-6/koRpus/R/koRpus-package.R | 14 koRpus-0.05-6/koRpus/R/readability.R | 21 koRpus-0.05-6/koRpus/R/readability.num.R | 34 koRpus-0.05-6/koRpus/R/set.kRp.env.R | 3 koRpus-0.05-6/koRpus/R/treetag.R | 13 koRpus-0.05-6/koRpus/R/tuldava.R |only koRpus-0.05-6/koRpus/inst/CITATION | 8 koRpus-0.05-6/koRpus/inst/NEWS.Rd | 31 koRpus-0.05-6/koRpus/inst/doc/koRpus_vignette.pdf |binary koRpus-0.05-6/koRpus/inst/rkward/koRpus.pluginmap | 173 - koRpus-0.05-6/koRpus/inst/rkward/plugins/FrequencyAnalysis.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/FrequencyAnalysis.xml |only koRpus-0.05-6/koRpus/inst/rkward/plugins/Hyphenation.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/Hyphenation.xml |only koRpus-0.05-6/koRpus/inst/rkward/plugins/LexicalDiversity.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/LexicalDiversity.xml |only koRpus-0.05-6/koRpus/inst/rkward/plugins/Readability.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/Readability.xml |only koRpus-0.05-6/koRpus/inst/rkward/plugins/TokenizingPOStagging.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/TokenizingPOStagging.xml |only koRpus-0.05-6/koRpus/inst/rkward/rkwarddev_koRpus_plugin_script.R | 1319 ++++++---- koRpus-0.05-6/koRpus/inst/shiny/demo/server.R | 98 koRpus-0.05-6/koRpus/inst/shiny/demo/ui.R | 223 - koRpus-0.05-6/koRpus/man/ARI.Rd | 56 koRpus-0.05-6/koRpus/man/C.ld.Rd | 31 koRpus-0.05-6/koRpus/man/CTTR.Rd | 31 koRpus-0.05-6/koRpus/man/DRP.Rd | 39 koRpus-0.05-6/koRpus/man/ELF.Rd | 47 koRpus-0.05-6/koRpus/man/FOG.Rd | 72 koRpus-0.05-6/koRpus/man/FORCAST.Rd | 48 koRpus-0.05-6/koRpus/man/HDD.Rd | 44 koRpus-0.05-6/koRpus/man/K.ld.Rd | 31 koRpus-0.05-6/koRpus/man/LIX.Rd | 48 koRpus-0.05-6/koRpus/man/MATTR.Rd | 42 koRpus-0.05-6/koRpus/man/MSTTR.Rd | 31 koRpus-0.05-6/koRpus/man/MTLD.Rd | 74 koRpus-0.05-6/koRpus/man/R.ld.Rd | 31 koRpus-0.05-6/koRpus/man/RIX.Rd | 51 koRpus-0.05-6/koRpus/man/S.ld.Rd | 31 koRpus-0.05-6/koRpus/man/SMOG.Rd | 68 koRpus-0.05-6/koRpus/man/TRI.Rd | 41 koRpus-0.05-6/koRpus/man/TTR.Rd | 34 koRpus-0.05-6/koRpus/man/U.ld.Rd | 31 koRpus-0.05-6/koRpus/man/bormuth.Rd | 63 koRpus-0.05-6/koRpus/man/cTest-methods.Rd | 63 koRpus-0.05-6/koRpus/man/clozeDelete-methods.Rd | 62 koRpus-0.05-6/koRpus/man/coleman.Rd | 67 koRpus-0.05-6/koRpus/man/coleman.liau.Rd | 46 koRpus-0.05-6/koRpus/man/correct-methods.Rd | 122 koRpus-0.05-6/koRpus/man/dale.chall.Rd | 47 koRpus-0.05-6/koRpus/man/danielson.bryan.Rd | 40 koRpus-0.05-6/koRpus/man/dickes.steiwer.Rd | 40 koRpus-0.05-6/koRpus/man/farr.jenkins.paterson.Rd | 55 koRpus-0.05-6/koRpus/man/flesch.Rd | 62 koRpus-0.05-6/koRpus/man/flesch.kincaid.Rd | 39 koRpus-0.05-6/koRpus/man/freq.analysis.Rd | 114 koRpus-0.05-6/koRpus/man/fucks.Rd | 38 koRpus-0.05-6/koRpus/man/get.kRp.env.Rd | 41 koRpus-0.05-6/koRpus/man/guess.lang.Rd | 75 koRpus-0.05-6/koRpus/man/harris.jacobson.Rd | 84 koRpus-0.05-6/koRpus/man/hyph.XX.Rd | 72 koRpus-0.05-6/koRpus/man/hyphen.Rd | 132 - koRpus-0.05-6/koRpus/man/jumbleWords.Rd | 32 koRpus-0.05-6/koRpus/man/kRp.POS.tags.Rd | 129 koRpus-0.05-6/koRpus/man/kRp.TTR-class.Rd | 28 koRpus-0.05-6/koRpus/man/kRp.analysis-class.Rd | 7 koRpus-0.05-6/koRpus/man/kRp.cluster.Rd | 36 koRpus-0.05-6/koRpus/man/kRp.corp.freq-class.Rd | 69 koRpus-0.05-6/koRpus/man/kRp.filter.wclass.Rd | 31 koRpus-0.05-6/koRpus/man/kRp.hyph.pat-class.Rd | 15 koRpus-0.05-6/koRpus/man/kRp.hyphen-class.Rd | 5 koRpus-0.05-6/koRpus/man/kRp.lang-class.Rd | 5 koRpus-0.05-6/koRpus/man/kRp.readability-class.Rd | 74 koRpus-0.05-6/koRpus/man/kRp.tagged-class.Rd | 29 koRpus-0.05-6/koRpus/man/kRp.taggedText-methods.Rd | 23 koRpus-0.05-6/koRpus/man/kRp.text.analysis.Rd | 107 koRpus-0.05-6/koRpus/man/kRp.text.paste.Rd | 20 koRpus-0.05-6/koRpus/man/kRp.text.transform.Rd | 58 koRpus-0.05-6/koRpus/man/kRp.txt.freq-class.Rd | 5 koRpus-0.05-6/koRpus/man/kRp.txt.trans-class.Rd | 19 koRpus-0.05-6/koRpus/man/koRpus-package.Rd | 56 koRpus-0.05-6/koRpus/man/lex.div.Rd | 342 +- koRpus-0.05-6/koRpus/man/lex.div.num.Rd | 55 koRpus-0.05-6/koRpus/man/linsear.write.Rd | 39 koRpus-0.05-6/koRpus/man/maas.Rd | 34 koRpus-0.05-6/koRpus/man/manage.hyph.pat.Rd | 83 koRpus-0.05-6/koRpus/man/nWS.Rd | 72 koRpus-0.05-6/koRpus/man/plot-methods.Rd | 48 koRpus-0.05-6/koRpus/man/query-methods.Rd | 117 koRpus-0.05-6/koRpus/man/read.BAWL.Rd | 41 koRpus-0.05-6/koRpus/man/read.corp.LCC.Rd | 77 koRpus-0.05-6/koRpus/man/read.corp.celex.Rd | 19 koRpus-0.05-6/koRpus/man/read.corp.custom.Rd | 65 koRpus-0.05-6/koRpus/man/read.hyph.pat.Rd | 42 koRpus-0.05-6/koRpus/man/read.tagged.Rd | 115 koRpus-0.05-6/koRpus/man/readability.Rd | 897 +++--- koRpus-0.05-6/koRpus/man/readability.num.Rd | 135 - koRpus-0.05-6/koRpus/man/segment.optimizer.Rd | 64 koRpus-0.05-6/koRpus/man/set.kRp.env.Rd | 42 koRpus-0.05-6/koRpus/man/show-methods.Rd | 33 koRpus-0.05-6/koRpus/man/spache.Rd | 46 koRpus-0.05-6/koRpus/man/strain.Rd | 39 koRpus-0.05-6/koRpus/man/summary-methods.Rd | 47 koRpus-0.05-6/koRpus/man/textFeatures.Rd | 67 koRpus-0.05-6/koRpus/man/tokenize.Rd | 195 - koRpus-0.05-6/koRpus/man/traenkle.bailer.Rd | 41 koRpus-0.05-6/koRpus/man/treetag.Rd | 268 -- koRpus-0.05-6/koRpus/man/tuldava.Rd |only koRpus-0.05-6/koRpus/man/wheeler.smith.Rd | 66 koRpus-0.05-6/koRpus/tests/testthat |only koRpus-0.05-6/koRpus/tests/testthat.R |only 137 files changed, 4388 insertions(+), 4349 deletions(-)
Title: Coercion Routines for Network Data Objects
Description: Functions implemented in this package allow to coerce (i.e.
convert) network data between classes provided by other R packages.
Currently supported classes are those defined in packages: network and
igraph.
Author: Michal Bojanowski
Maintainer: Michal Bojanowski <m.bojanowski@icm.edu.pl>
Diff between intergraph versions 2.0-1 dated 2015-01-17 and 2.0-2 dated 2015-06-30
DESCRIPTION | 10 ++++----- MD5 | 42 ++++++++++++++++++------------------- NAMESPACE | 2 - R/attrmap.R | 4 +-- R/netcompare.R | 4 +-- README.md | 1 build/vignette.rds |binary data/exIgraph.rda |binary data/exIgraph2.rda |binary inst/doc/howto.R | 5 ++-- inst/doc/howto.Rmd | 9 ++++---- inst/doc/howto.html | 50 ++++++++++++--------------------------------- inst/tests/test-asIgraph.R | 4 +-- man/as.matrix.igraph.Rd | 2 - man/asDF.Rd | 2 - man/asIgraph.Rd | 2 - man/asNetwork.Rd | 2 - man/attrmap.Rd | 2 - man/dumpAttr.Rd | 2 - man/exNetwork.Rd | 2 - man/intergraph-package.Rd | 2 - man/netcompare.Rd | 2 - 22 files changed, 65 insertions(+), 84 deletions(-)
Title: Information Retrieval for Genetic Datasets
Description: Information retrieval from National Center for Biotechnology Information (NCBI) databases, with main focus on identifying genes in unannotated organisms via Blast similarity search in annotated organisms.
Author: Daniel Fischer [aut, cre],
Anu Sironen [aut]
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between hoardeR versions 0.0-2 dated 2014-06-06 and 0.1 dated 2015-06-30
DESCRIPTION | 26 +++++++---- MD5 | 69 +++++++++++++++++++++++-------- NAMESPACE | 20 +++++++-- R/blastSeq.R | 106 +++++++++++++++++++++++++++++++++++++++++------- R/getAssemblies.R |only R/getBlastResult.R | 6 +- R/getEnsgInfo.R | 5 +- R/helpFunctions.R |only R/importBlastTab.R |only R/importFA.R | 1 R/importGTF.R | 15 +++--- R/importPedMap.R |only R/importVCF.R |only R/importXML.R | 24 +++++----- R/plot.xmlImport.R |only R/print.ensgInfo.R |only R/print.fa.R |only R/print.pedMap.R |only R/print.xmlImport.R |only R/speciesFigure.R |only R/subDose.R |only R/subGProbs.R |only R/subPhased.R |only R/summary.ensgInfo.R |only R/summary.fa.R |only R/summary.pedMap.R |only R/summary.xmlImport.R |only ToDo | 2 data |only inst/ChangeLog | 16 +++++++ inst/extdata |only man/blastSeq.Rd | 23 +++++++--- man/getAssemblies.Rd |only man/getEnsgInfo.Rd | 2 man/getGeneLocation.Rd | 2 man/hoardeR-package.Rd | 16 +++---- man/importBlastTab.Rd |only man/importFA.Rd | 82 +++++++++++++++++++------------------ man/importGTF.Rd | 6 +- man/importPedMap.Rd |only man/importXML.Rd | 7 +-- man/print.ensgInfo.Rd |only man/print.fa.Rd |only man/print.pedMap.Rd |only man/print.xmlImport.Rd |only man/species.Rd |only man/speciesFigure.Rd |only man/subDose.Rd |only man/subGprobs.Rd |only man/subPhased.Rd |only man/summary.ensgInfo.Rd |only man/summary.fa.Rd |only man/summary.pedMap.Rd |only 53 files changed, 297 insertions(+), 131 deletions(-)
Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. The spatial autocorrelation is modelled by a set of random effects, which are assigned a conditional autoregressive (CAR) prior distribution. A number of different CAR priors are available for the random effects, and full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development is supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayes versions 4.1 dated 2015-04-01 and 4.2 dated 2015-06-30
CARBayes-4.1/CARBayes/R/S.CARcluster.R |only CARBayes-4.1/CARBayes/R/binomial.clusterCAR.R |only CARBayes-4.1/CARBayes/R/gaussian.bymCAR.R |only CARBayes-4.1/CARBayes/R/gaussian.clusterCAR.R |only CARBayes-4.1/CARBayes/R/gaussian.independent.R |only CARBayes-4.1/CARBayes/R/poisson.clusterCAR.R |only CARBayes-4.1/CARBayes/R/poisson.clusterCARagg.R |only CARBayes-4.1/CARBayes/man/S.CARcluster.Rd |only CARBayes-4.2/CARBayes/DESCRIPTION | 16 - CARBayes-4.2/CARBayes/MD5 | 85 +++--- CARBayes-4.2/CARBayes/NAMESPACE | 7 CARBayes-4.2/CARBayes/R/S.CARbym.R | 9 CARBayes-4.2/CARBayes/R/S.CARlocalised.R |only CARBayes-4.2/CARBayes/R/S.independent.R | 9 CARBayes-4.2/CARBayes/R/binomial.bymCAR.R | 26 + CARBayes-4.2/CARBayes/R/binomial.dissimilarityCAR.R | 38 +- CARBayes-4.2/CARBayes/R/binomial.iarCAR.R | 33 +- CARBayes-4.2/CARBayes/R/binomial.independent.R | 15 - CARBayes-4.2/CARBayes/R/binomial.lerouxCAR.R | 29 +- CARBayes-4.2/CARBayes/R/binomial.localisedCAR.R |only CARBayes-4.2/CARBayes/R/combine.data.shapefile.R | 8 CARBayes-4.2/CARBayes/R/gaussian.dissimilarityCAR.R | 67 +++- CARBayes-4.2/CARBayes/R/gaussian.iarCAR.R | 50 ++- CARBayes-4.2/CARBayes/R/gaussian.lerouxCAR.R | 41 +-- CARBayes-4.2/CARBayes/R/poisson.bymCAR.R | 26 + CARBayes-4.2/CARBayes/R/poisson.dissimilarityCAR.R | 38 +- CARBayes-4.2/CARBayes/R/poisson.iarCAR.R | 33 +- CARBayes-4.2/CARBayes/R/poisson.independent.R | 17 - CARBayes-4.2/CARBayes/R/poisson.lerouxCAR.R | 28 +- CARBayes-4.2/CARBayes/R/poisson.localisedCAR.R |only CARBayes-4.2/CARBayes/R/poisson.localisedCARagg.R |only CARBayes-4.2/CARBayes/R/print.carbayes.R | 83 ++++-- CARBayes-4.2/CARBayes/R/summarise.lincomb.R | 3 CARBayes-4.2/CARBayes/build/vignette.rds |binary CARBayes-4.2/CARBayes/inst/doc/CARBayesvignette.R | 53 +-- CARBayes-4.2/CARBayes/inst/doc/CARBayesvignette.Rnw | 152 +++++------ CARBayes-4.2/CARBayes/inst/doc/CARBayesvignette.pdf |binary CARBayes-4.2/CARBayes/man/CARBayes-package.Rd | 51 --- CARBayes-4.2/CARBayes/man/S.CARbym.Rd | 58 ++-- CARBayes-4.2/CARBayes/man/S.CARdissimilarity.Rd | 31 +- CARBayes-4.2/CARBayes/man/S.CARiar.Rd | 29 +- CARBayes-4.2/CARBayes/man/S.CARleroux.Rd | 29 +- CARBayes-4.2/CARBayes/man/S.CARlocalised.Rd |only CARBayes-4.2/CARBayes/man/S.independent.Rd | 33 +- CARBayes-4.2/CARBayes/man/combine.data.shapefile.Rd | 6 CARBayes-4.2/CARBayes/man/highlight.borders.Rd | 2 CARBayes-4.2/CARBayes/man/print.carbayes.Rd | 10 CARBayes-4.2/CARBayes/src/RcppExports.cpp | 256 ++++++++----------- CARBayes-4.2/CARBayes/vignettes/CARBayesvignette.Rnw | 152 +++++------ CARBayes-4.2/CARBayes/vignettes/jss996.bib | 46 ++- 50 files changed, 831 insertions(+), 738 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between XML versions 3.98-1.2 dated 2015-05-31 and 3.98-1.3 dated 2015-06-30
DESCRIPTION | 11 ++++------- MD5 | 6 +++--- NAMESPACE | 1 + man/readHTMLTable.Rd | 34 +++++++++++++++++++++------------- 4 files changed, 29 insertions(+), 23 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.8-0 dated 2015-06-26 and 1.9-0 dated 2015-06-30
DESCRIPTION | 14 ++--- MD5 | 41 ++++++++------- NAMESPACE | 71 +++++++++++++++++++-------- R/acceleration_algorithm.R |only R/calc_exp_TK.R | 1 R/calc_posterior.v2.R | 9 +-- R/calc_prob.v5.R | 2 R/stud_prior.R | 28 ++++------ R/tam.fa.R | 4 - R/tam.latreg.R | 2 R/tam.mml.2pl.R | 76 ++++++++++++++++++++++++++-- R/tam.mml.3pl.R | 118 ++++++++++++++++++++++++++++++++++++++++++--- R/tam.mml.3pl.preproc.R | 4 + R/tam.mml.R | 59 ++++++++++++++++++++-- R/tam.mml.mfr.R | 64 +++++++++++++++++++----- R/tam.pv.R | 2 R/tam.se.R | 6 +- inst/NEWS | 24 +++++++++ man/TAM-internal.Rd | 2 man/TAM-package.Rd | 2 man/tam.mml.Rd | 55 ++++++++++++++++++++ man/tamaanify.Rd | 2 22 files changed, 471 insertions(+), 115 deletions(-)
Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/>
Provides functions to allow one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: Duncan Temple Lang and the CRAN team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between RCurl versions 1.95-4.6 dated 2015-04-24 and 1.95-4.7 dated 2015-06-30
RCurl-1.95-4.6/RCurl/FAQ.html |only RCurl-1.95-4.6/RCurl/cacert.pem |only RCurl-1.95-4.7/RCurl/DESCRIPTION | 16 ++++++----- RCurl-1.95-4.7/RCurl/MD5 | 36 +++++++++++++------------ RCurl-1.95-4.7/RCurl/R/zzz.R |only RCurl-1.95-4.7/RCurl/inst/doc/FAQ.html |only RCurl-1.95-4.7/RCurl/inst/doc/philosophy.html | 24 +++++++++------- RCurl-1.95-4.7/RCurl/inst/etc |only RCurl-1.95-4.7/RCurl/man/basicTextGatherer.Rd | 9 ++++-- RCurl-1.95-4.7/RCurl/man/curlPerform.Rd | 3 +- RCurl-1.95-4.7/RCurl/man/dynCurlReader.Rd | 6 ++-- RCurl-1.95-4.7/RCurl/man/ftpUpload.Rd | 3 +- RCurl-1.95-4.7/RCurl/man/getBinaryURL.Rd | 3 +- RCurl-1.95-4.7/RCurl/man/getCurlHandle.Rd | 3 +- RCurl-1.95-4.7/RCurl/man/getURIAsynchronous.Rd | 7 ++-- RCurl-1.95-4.7/RCurl/man/getURL.Rd | 8 +++-- RCurl-1.95-4.7/RCurl/man/guessMIMEType.Rd | 5 +-- RCurl-1.95-4.7/RCurl/man/mimeTypeExtensions.Rd | 4 +- RCurl-1.95-4.7/RCurl/man/postForm.Rd | 11 ++++--- RCurl-1.95-4.7/RCurl/man/scp.Rd | 6 ++-- RCurl-1.95-4.7/RCurl/tests/dynSetReader.R | 4 +- 21 files changed, 85 insertions(+), 63 deletions(-)
Title: Function to Create a Random List for Crossover Studies
Description: Contains a function to randomize subjects, patients in groups of
sequences (treatment sequences).
If a blocksize is given, the randomization will be done within blocks.
The randomization may be controlled by a Wald-Wolfowitz runs test.
Functions to obtain the p-value of that test are included.
The package is mainly intended for randomization of bioequivalence studies
but may be used also for other clinical crossover studies.
Contains two helper functions sequences() and williams() to get the sequences
of commonly used designs in BE studies.
Author: D. Labes
Maintainer: D. Labes <detlewlabes@gmx.de>
Diff between randomizeBE versions 0.3-1 dated 2012-12-27 and 0.3-2 dated 2015-06-30
DESCRIPTION | 31 ++++++++++++++++--------------- MD5 | 12 ++++++------ NAMESPACE | 3 +++ NEWS | 4 ++++ man/pruns.exact.Rd | 3 --- man/runs.pvalue.Rd | 6 ++---- man/sequences.Rd | 2 +- 7 files changed, 32 insertions(+), 29 deletions(-)
Title: Tools to Manage a Parametric Function that Describes Phenology
Description: Functions used to fit and test the phenology of species based on counts.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between phenology versions 4.2 dated 2015-05-09 and 4.2.4 dated 2015-06-30
phenology-4.2.4/phenology/DESCRIPTION | 11 phenology-4.2.4/phenology/MD5 | 49 - phenology-4.2.4/phenology/NAMESPACE | 8 phenology-4.2.4/phenology/NEWS | 12 phenology-4.2.4/phenology/R/LikelihoodRMU.R |only phenology-4.2.4/phenology/R/Likelihood_phenology.R | 28 phenology-4.2.4/phenology/R/Lnegbin.R | 12 phenology-4.2.4/phenology/R/add_phenology.R | 24 phenology-4.2.4/phenology/R/fitRMU.R | 546 +++++++++++++----- phenology-4.2.4/phenology/R/fitRMU_MHmcmc.R |only phenology-4.2.4/phenology/R/fitRMU_MHmcmc_p.R |only phenology-4.2.4/phenology/R/fit_phenology.R | 8 phenology-4.2.4/phenology/R/format_par.R | 2 phenology-4.2.4/phenology/R/logLik.fitRMU.R |only phenology-4.2.4/phenology/R/phenology-package.R | 32 - phenology-4.2.4/phenology/R/phenology_MHmcmc.R |only phenology-4.2.4/phenology/R/phenology_MHmcmc_p.R | 29 phenology-4.2.4/phenology/R/plot.fitRMU.R |only phenology-4.2.4/phenology/R/plot.phenology.R | 51 - phenology-4.2.4/phenology/man/add_phenology.Rd | 7 phenology-4.2.4/phenology/man/fitRMU.Rd | 132 +++- phenology-4.2.4/phenology/man/fitRMU_MHmcmc.Rd |only phenology-4.2.4/phenology/man/fitRMU_MHmcmc_p.Rd |only phenology-4.2.4/phenology/man/likelihood_phenology.Rd | 2 phenology-4.2.4/phenology/man/logLik.fitRMU.Rd |only phenology-4.2.4/phenology/man/phenology-package.Rd | 34 - phenology-4.2.4/phenology/man/phenology_MHmcmc.Rd | 8 phenology-4.2.4/phenology/man/plot.fitRMU.Rd |only phenology-4.2.4/phenology/man/plot.phenology.Rd | 2 phenology-4.2/phenology/R/Script_MCMC.r |only phenology-4.2/phenology/R/fonctionfit.R |only phenology-4.2/phenology/R/phenology_fonctionMCMC.R |only 32 files changed, 717 insertions(+), 280 deletions(-)
Title: Wrapper Functions for MAESTRA/MAESPA
Description: A bundle of functions for modifying MAESTRA/MAESPA input files,reading output files, and visualizing the stand in 3D. Handy for running sensitivity analyses, scenario analyses, etc.
Author: Remko Duursma
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between Maeswrap versions 1.4.11 dated 2012-05-25 and 1.7 dated 2015-06-30
Maeswrap-1.4.11/Maeswrap/R/Maeswrap-internal.R |only Maeswrap-1.4.11/Maeswrap/R/replacePAR.R |only Maeswrap-1.4.11/Maeswrap/R/trim.R |only Maeswrap-1.4.11/Maeswrap/man/BatchUtilities.Rd |only Maeswrap-1.4.11/Maeswrap/man/addarrow.Rd |only Maeswrap-1.4.11/Maeswrap/man/readPAR.Rd |only Maeswrap-1.4.11/Maeswrap/man/replaceNAMELIST.Rd |only Maeswrap-1.4.11/Maeswrap/man/utilities.Rd |only Maeswrap-1.7/Maeswrap/DESCRIPTION | 16 - Maeswrap-1.7/Maeswrap/MD5 | 100 +++++----- Maeswrap-1.7/Maeswrap/NAMESPACE | 44 ++++ Maeswrap-1.7/Maeswrap/R/Maeswrap-package.R |only Maeswrap-1.7/Maeswrap/R/Openstand.R | 23 +- Maeswrap-1.7/Maeswrap/R/Plotstand.R | 215 ++++++++++++++++++----- Maeswrap-1.7/Maeswrap/R/addarrow.R | 16 - Maeswrap-1.7/Maeswrap/R/checkwatbal.R | 14 + Maeswrap-1.7/Maeswrap/R/coord3dshape.R | 5 Maeswrap-1.7/Maeswrap/R/crownsurface.R |only Maeswrap-1.7/Maeswrap/R/delempty.R | 3 Maeswrap-1.7/Maeswrap/R/maesparunall.R | 104 +++++++++++ Maeswrap-1.7/Maeswrap/R/maestrarunall.R | 2 Maeswrap-1.7/Maeswrap/R/maybeQuote.R | 5 Maeswrap-1.7/Maeswrap/R/parseFile.R |only Maeswrap-1.7/Maeswrap/R/parsePARline.R |only Maeswrap-1.7/Maeswrap/R/plot3dtriangles.R | 7 Maeswrap-1.7/Maeswrap/R/plottree.R | 2 Maeswrap-1.7/Maeswrap/R/plotuspar.R | 119 ++++++++---- Maeswrap-1.7/Maeswrap/R/printme.R | 3 Maeswrap-1.7/Maeswrap/R/randomstand.R |only Maeswrap-1.7/Maeswrap/R/readNameList.R |only Maeswrap-1.7/Maeswrap/R/readPAR.R | 128 ++++++------- Maeswrap-1.7/Maeswrap/R/readdayflux.R | 24 ++ Maeswrap-1.7/Maeswrap/R/readhrflux.R | 28 ++ Maeswrap-1.7/Maeswrap/R/readmet.R | 32 ++- Maeswrap-1.7/Maeswrap/R/readuspar.R | 22 +- Maeswrap-1.7/Maeswrap/R/readwatbal.R | 29 ++- Maeswrap-1.7/Maeswrap/R/replaceNAMELIST.R | 164 ++++++++++++----- Maeswrap-1.7/Maeswrap/R/replacemetdata.R | 72 ++++--- Maeswrap-1.7/Maeswrap/R/replacemetvar.R | 71 ++++++- Maeswrap-1.7/Maeswrap/R/revchar.R | 39 ++++ Maeswrap-1.7/Maeswrap/R/runmaespa.R | 148 ++++++++------- Maeswrap-1.7/Maeswrap/R/runmaestra.R | 2 Maeswrap-1.7/Maeswrap/R/trynumeric.R |only Maeswrap-1.7/Maeswrap/R/writeListToFile.R |only Maeswrap-1.7/Maeswrap/man/Maeswrap-package.Rd | 41 ++-- Maeswrap-1.7/Maeswrap/man/Plotstand.Rd | 169 ++++++++++-------- Maeswrap-1.7/Maeswrap/man/batchutil.Rd |only Maeswrap-1.7/Maeswrap/man/checkwatbal.Rd | 28 +- Maeswrap-1.7/Maeswrap/man/maeswrapdefinitions.Rd | 20 +- Maeswrap-1.7/Maeswrap/man/parseFile.Rd |only Maeswrap-1.7/Maeswrap/man/plotuspar.Rd | 70 ++++--- Maeswrap-1.7/Maeswrap/man/randomstand.Rd |only Maeswrap-1.7/Maeswrap/man/readNameList.Rd |only Maeswrap-1.7/Maeswrap/man/readdayflux.Rd | 28 +- Maeswrap-1.7/Maeswrap/man/readhrflux.Rd | 23 +- Maeswrap-1.7/Maeswrap/man/readmet.Rd | 28 +- Maeswrap-1.7/Maeswrap/man/readwatbal.Rd | 23 +- Maeswrap-1.7/Maeswrap/man/replacePAR.Rd | 68 ++++--- Maeswrap-1.7/Maeswrap/man/replacemetvar.Rd | 59 +++--- Maeswrap-1.7/Maeswrap/man/revchar.Rd | 42 ++-- Maeswrap-1.7/Maeswrap/man/runfiletest.Rd | 21 +- 61 files changed, 1370 insertions(+), 687 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions in
Causal Models
Description: An implementation of a conditional causal effect identification algorithm constructed by Ilya Shpitser and Judea Pearl (2006) for deriving expressions of joint interventional distributions in causal models, which contain unobserved variables and induce directed acyclic graphs.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.1.1 dated 2015-04-28 and 1.1.3 dated 2015-06-30
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NAMESPACE | 4 +++- NEWS |only R/id.R | 7 +++---- R/idc.R | 5 +++-- R/observed.graph.R | 6 +++--- R/unobserved.graph.R | 2 +- man/causaleffect-package.Rd | 7 +++---- 9 files changed, 28 insertions(+), 26 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.1.2 dated 2015-06-29 and 1.1.3 dated 2015-06-30
stochvol-1.1.2/stochvol/vignettes/heavytails.R |only stochvol-1.1.2/stochvol/vignettes/heavytails.pdf |only stochvol-1.1.2/stochvol/vignettes/heavytails.tex |only stochvol-1.1.3/stochvol/DESCRIPTION | 6 +++--- stochvol-1.1.3/stochvol/MD5 | 17 +++++++++-------- stochvol-1.1.3/stochvol/NEWS | 3 +++ stochvol-1.1.3/stochvol/build/vignette.rds |binary stochvol-1.1.3/stochvol/inst/doc/article.pdf |binary stochvol-1.1.3/stochvol/inst/doc/heavytails.R |only stochvol-1.1.3/stochvol/inst/doc/heavytails.Rnw |only stochvol-1.1.3/stochvol/inst/doc/heavytails.pdf |only stochvol-1.1.3/stochvol/vignettes/Makefile | 2 +- stochvol-1.1.3/stochvol/vignettes/heavytails.Rnw |only 13 files changed, 16 insertions(+), 12 deletions(-)
Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.4 dated 2015-05-28 and 1.5 dated 2015-06-30
DESCRIPTION | 19 ++--- MD5 | 12 +-- NAMESPACE | 20 ++++- R/forestFloor_source.R | 166 +++++++++++++++++++++------------------------ man/forestFloor-package.Rd | 5 - man/plot.forestFloor.Rd | 39 ++-------- tests/stdUsage.R | 12 ++- 7 files changed, 130 insertions(+), 143 deletions(-)
Title: PCIC Implementation of Climdex Routines
Description: PCIC's implementation of Climdex routines for computation of
extreme climate indices.
Author: David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate Impacts
Consortium
Maintainer: James Hiebert <hiebert@uvic.ca>
Diff between climdex.pcic versions 1.1-5.1 dated 2015-03-13 and 1.1-6 dated 2015-06-30
CHANGELOG | 6 + DESCRIPTION | 8 +- MD5 | 102 ++++++++++++++-------------- R/climdex.r | 80 ++++++++++++++------- man/climdex.cdd.Rd | 2 man/climdex.csdi.Rd | 2 man/climdex.cwd.Rd | 2 man/climdex.dtr.Rd | 2 man/climdex.fd.Rd | 2 man/climdex.get.available.indices.Rd | 2 man/climdex.gsl.Rd | 2 man/climdex.id.Rd | 2 man/climdex.pcic.Rd | 2 man/climdex.prcptot.Rd | 2 man/climdex.quantile.Rd | 2 man/climdex.r10mm.Rd | 2 man/climdex.r20mm.Rd | 2 man/climdex.r95ptot.Rd | 2 man/climdex.r99ptot.Rd | 2 man/climdex.rnnmm.Rd | 2 man/climdex.rx1day.Rd | 2 man/climdex.rx5day.Rd | 2 man/climdex.sdii.Rd | 2 man/climdex.su.Rd | 2 man/climdex.tn10p.Rd | 2 man/climdex.tn90p.Rd | 2 man/climdex.tnn.Rd | 2 man/climdex.tnx.Rd | 2 man/climdex.tr.Rd | 2 man/climdex.tx10p.Rd | 2 man/climdex.tx90p.Rd | 2 man/climdex.txn.Rd | 2 man/climdex.txx.Rd | 2 man/climdex.wsdi.Rd | 2 man/climdexInput.Rd | 7 + man/climdexInput.csv.Rd | 4 - man/climdexInput.raw.Rd | 78 +++++++++++++++++++-- man/ec.1018935.Rd | 2 man/get.last.monthday.of.year.Rd | 2 man/get.outofbase.quantiles.Rd | 4 - man/get.series.lengths.at.ends.Rd | 2 man/growing.season.length.Rd | 2 man/nday.consec.prec.max.Rd | 2 man/number.days.op.threshold.Rd | 2 man/percent.days.op.threshold.Rd | 2 man/select.blocks.gt.length.Rd | 2 man/simple.precipitation.intensity.index.Rd | 2 man/spell.length.max.Rd | 2 man/threshold.exceedance.duration.index.Rd | 2 man/total.precip.op.threshold.Rd | 2 src/zhang_running_quantile.cc | 4 - tests/test_primitives.R | 2 52 files changed, 239 insertions(+), 140 deletions(-)