Tue, 13 Dec 2016

Package XGR updated to version 1.0.6 with previous version 1.0.5 dated 2016-11-23

Title: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

Diff between XGR versions 1.0.5 dated 2016-11-23 and 1.0.6 dated 2016-12-13

 DESCRIPTION                    |    8 
 MD5                            |   86 ++++----
 R/xCircos.r                    |    2 
 R/xEnrichBarplot.r             |   18 +
 R/xEnrichCompare.r             |    2 
 R/xGR2GeneScores.r             |    3 
 R/xGRscores.r                  |   22 ++
 R/xGRviaGeneAnno.r             |    2 
 R/xGRviaGenomicAnno.r          |    9 
 R/xGRviaGenomicAnnoAdv.r       |    9 
 R/xSNP2GeneScores.r            |    5 
 R/xSNPscores.r                 |   23 ++
 R/xSubneterGR.r                |    3 
 R/xSubneterGenes.r             |    6 
 R/xSubneterSNPs.r              |    3 
 R/xVisNet.r                    |    8 
 data/ImmunoBase.RData          |binary
 data/JKscience_TS2A.RData      |binary
 inst/CITATION                  |   22 +-
 inst/NEWS                      |   12 +
 inst/xCircos.html              |    6 
 inst/xEnrichBarplot.html       |    6 
 inst/xEnrichCompare.html       |    6 
 inst/xGR2GeneScores.html       |    7 
 inst/xGRscores.html            |    9 
 inst/xGRviaGenomicAnno.html    |  410 ++++++++++++++++++++++++++++++++++++++++-
 inst/xGRviaGenomicAnnoAdv.html |  410 ++++++++++++++++++++++++++++++++++++++++-
 inst/xSNP2GeneScores.html      |    7 
 inst/xSNPscores.html           |    7 
 inst/xSubneterGR.html          |   17 +
 inst/xSubneterSNPs.html        |    7 
 inst/xVisNet.html              |   14 +
 man/xCircos.Rd                 |    6 
 man/xEnrichBarplot.Rd          |    6 
 man/xEnrichCompare.Rd          |    6 
 man/xGR2GeneScores.Rd          |    5 
 man/xGRscores.Rd               |    7 
 man/xGRviaGenomicAnno.Rd       |  266 ++++++++++++++++++++++++++
 man/xGRviaGenomicAnnoAdv.Rd    |  266 ++++++++++++++++++++++++++
 man/xSNP2GeneScores.Rd         |    5 
 man/xSNPscores.Rd              |    5 
 man/xSubneterGR.Rd             |   15 -
 man/xSubneterSNPs.Rd           |    5 
 man/xVisNet.Rd                 |   12 -
 44 files changed, 1606 insertions(+), 147 deletions(-)

More information about XGR at CRAN
Permanent link

Package wec updated to version 0.4 with previous version 0.3 dated 2016-11-15

Title: Weighted Effect Coding
Description: Provides functions to create factor variables with contrasts based on weighted effect coding, and their interactions. In weighted effect coding the estimates from a first order regression model show the deviations per group from the sample mean. This is especially useful when a researcher has no directional hypotheses and uses a sample from a population in which the number of observation per group is different.
Author: Rense Nieuwenhuis, Manfred te Grotenhuis, Ben Pelzer, Alexander Schmidt, Ruben Konig, Rob Eisinga
Maintainer: Rense Nieuwenhuis <rense.nieuwenhuis@sofi.su.se>

Diff between wec versions 0.3 dated 2016-11-15 and 0.4 dated 2016-12-13

 DESCRIPTION         |   11 ++++----
 MD5                 |   14 +++++-----
 NAMESPACE           |    1 
 R/wec.interact.R    |   71 +++++++++++++++++++++++++++++++++++-----------------
 data/PUMS.rdata     |binary
 inst/CITATION       |    8 ++---
 man/PUMS.Rd         |    4 +-
 man/wec.interact.Rd |   14 +++++-----
 8 files changed, 75 insertions(+), 48 deletions(-)

More information about wec at CRAN
Permanent link

Package VizOR updated to version 0.8-5 with previous version 0.7-9 dated 2013-11-14

Title: Graphical Visualization Tools for Complex Observational Data with Focus on Health Sciences
Description: Provides individual- and aggregate-level graphical depictions of patterns of treatment and response in patient registries, and a graphical tool for examining potential for confounding in analyses of observational data.
Author: Drew Griffin Levy [aut], David C. Norris [aut, cre]
Maintainer: David C. Norris <david@dnc-llc.com>

Diff between VizOR versions 0.7-9 dated 2013-11-14 and 0.8-5 dated 2016-12-13

 DESCRIPTION                        |   27 ++--
 MD5                                |  106 ++++++++++---------
 NAMESPACE                          |   24 +++-
 R/Extract.colored.R                |    2 
 R/VizOR-package.R                  |    6 -
 R/color.colored.R                  |    3 
 R/droplevels.colored.R             |    2 
 R/key.colored.R                    |    3 
 R/panel.marginal.density.R         |only
 R/panel.plotbraids.R               |   16 +-
 R/plotbraids.R                     |   15 ++
 R/predReg.R                        |   19 +--
 R/radarplot.R                      |    9 +
 R/relevel.colored.R                |    1 
 R/timeline.R                       |   12 +-
 build/vignette.rds                 |binary
 inst/doc/ConfoundingPotential.Rnw  |    4 
 inst/doc/ConfoundingPotential.pdf  |binary
 inst/doc/Radar.R                   |    9 +
 inst/doc/Radar.Rnw                 |   11 +
 inst/doc/Radar.pdf                 |binary
 inst/doc/TreatmentPatterns.R       |only
 inst/doc/TreatmentPatterns.Rnw     |only
 inst/doc/TreatmentPatterns.pdf     |only
 inst/extdata                       |only
 man/Extract.colored.Rd             |   16 +-
 man/VizOR-package.Rd               |   34 +++---
 man/alphatize.Rd                   |   15 +-
 man/beNiceToLaTeX.Rd               |   22 +--
 man/color.Rd                       |   14 +-
 man/color.colored.Rd               |   18 +--
 man/colored.Rd                     |   43 +++----
 man/controller.Rd                  |   30 ++---
 man/droplevels.colored.Rd          |   20 +--
 man/fastback.Rd                    |   23 +---
 man/key.Rd                         |   15 +-
 man/key.colored.Rd                 |   21 +--
 man/panel.marginal.density.Rd      |only
 man/panel.plotbraids.Rd            |   40 +++----
 man/panel.prevalence.Rd            |   62 +++++------
 man/panel.radarplot.Rd             |   66 +++--------
 man/plotbraids.Rd                  |   87 +++++++--------
 man/predReg.Rd                     |   93 ++++++++--------
 man/prepanel.prevalence.Rd         |   23 +---
 man/radarplot.Rd                   |  205 ++++++++++++++++---------------------
 man/relevel.colored.Rd             |   18 +--
 man/remvar.Rd                      |   18 +--
 man/representNA.Rd                 |   29 ++---
 man/representNA.data.frame.Rd      |   15 +-
 man/timeline.Rd                    |  126 ++++++++++------------
 man/vlbw.Rd                        |   22 +--
 vignettes/ConfoundingPotential.Rnw |    4 
 vignettes/Radar.Rnw                |   11 +
 vignettes/TreatmentPatterns.Rnw    |only
 54 files changed, 672 insertions(+), 687 deletions(-)

More information about VizOR at CRAN
Permanent link

Package snplist updated to version 0.17 with previous version 0.16 dated 2016-10-27

Title: Tools to Create Gene Sets
Description: A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example for use with the RSNPset package, or to export to a PLINK set.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>

Diff between snplist versions 0.16 dated 2016-10-27 and 0.17 dated 2016-12-13

 DESCRIPTION            |    8 ++++----
 MD5                    |   18 +++++++++---------
 NEWS                   |    4 ++++
 R/setGeneTable.R       |    5 ++++-
 R/setSNPTable.R        |    9 +++++----
 build/vignette.rds     |binary
 inst/doc/snplist.Rnw   |    2 +-
 inst/doc/snplist.pdf   |binary
 man/snplist-package.Rd |    4 ++--
 vignettes/snplist.Rnw  |    2 +-
 10 files changed, 30 insertions(+), 22 deletions(-)

More information about snplist at CRAN
Permanent link

Package MALDIquant updated to version 1.16 with previous version 1.15 dated 2016-06-25

Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Author: Sebastian Gibb [aut, cre], Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>

Diff between MALDIquant versions 1.15 dated 2016-06-25 and 1.16 dated 2016-12-13

 MALDIquant-1.15/MALDIquant/R/which.closest-functions.R                   |only
 MALDIquant-1.15/MALDIquant/tests/testthat/test_which.closest-functions.R |only
 MALDIquant-1.16/MALDIquant/DESCRIPTION                                   |    9 
 MALDIquant-1.16/MALDIquant/MD5                                           |  165 +++++-----
 MALDIquant-1.16/MALDIquant/NAMESPACE                                     |    1 
 MALDIquant-1.16/MALDIquant/NEWS                                          |   16 
 MALDIquant-1.16/MALDIquant/R/AllClasses.R                                |   18 -
 MALDIquant-1.16/MALDIquant/R/AllGenerics.R                               |   18 -
 MALDIquant-1.16/MALDIquant/R/Deprecated.R                                |    7 
 MALDIquant-1.16/MALDIquant/R/alignSpectra-functions.R                    |   18 -
 MALDIquant-1.16/MALDIquant/R/approxfun-methods.R                         |   18 -
 MALDIquant-1.16/MALDIquant/R/as-methods.R                                |   18 -
 MALDIquant-1.16/MALDIquant/R/as.matrix-functions.R                       |   18 -
 MALDIquant-1.16/MALDIquant/R/as.matrix-methods.R                         |   18 -
 MALDIquant-1.16/MALDIquant/R/averageMassSpectra-functions.R              |   18 -
 MALDIquant-1.16/MALDIquant/R/binPeaks-functions.R                        |   18 -
 MALDIquant-1.16/MALDIquant/R/calculateLabelPositions-functions.R         |   18 -
 MALDIquant-1.16/MALDIquant/R/calibrateIntensity-functions.R              |   18 -
 MALDIquant-1.16/MALDIquant/R/calibrateIntensity-methods.R                |   18 -
 MALDIquant-1.16/MALDIquant/R/colMedians-functions.R                      |   18 -
 MALDIquant-1.16/MALDIquant/R/constructor-functions.R                     |   18 -
 MALDIquant-1.16/MALDIquant/R/coordinates-methods.R                       |   18 -
 MALDIquant-1.16/MALDIquant/R/deprecated-functions.R                      |   18 -
 MALDIquant-1.16/MALDIquant/R/detectPeaks-methods.R                       |   18 -
 MALDIquant-1.16/MALDIquant/R/determineWarpingFunctions-functions.R       |   18 -
 MALDIquant-1.16/MALDIquant/R/doByLabels-functions.R                      |   18 -
 MALDIquant-1.16/MALDIquant/R/estimateBaseline-functions.R                |   18 -
 MALDIquant-1.16/MALDIquant/R/estimateBaseline-methods.R                  |   18 -
 MALDIquant-1.16/MALDIquant/R/estimateNoise-functions.R                   |   18 -
 MALDIquant-1.16/MALDIquant/R/estimateNoise-methods.R                     |   18 -
 MALDIquant-1.16/MALDIquant/R/filterPeaks-functions.R                     |   18 -
 MALDIquant-1.16/MALDIquant/R/findEmptyMassObjects-functions.R            |   18 -
 MALDIquant-1.16/MALDIquant/R/findLocalMaxima-methods.R                   |   18 -
 MALDIquant-1.16/MALDIquant/R/grouper-functions.R                         |   18 -
 MALDIquant-1.16/MALDIquant/R/intensity-methods.R                         |   18 -
 MALDIquant-1.16/MALDIquant/R/intensityMatrix-functions.R                 |   18 -
 MALDIquant-1.16/MALDIquant/R/irregular-functions.R                       |   18 -
 MALDIquant-1.16/MALDIquant/R/isEmpty-methods.R                           |   18 -
 MALDIquant-1.16/MALDIquant/R/isFunctionList-functions.R                  |   18 -
 MALDIquant-1.16/MALDIquant/R/isMassObject-functions.R                    |   18 -
 MALDIquant-1.16/MALDIquant/R/isMassObjectList-functions.R                |   18 -
 MALDIquant-1.16/MALDIquant/R/isRegular-methods.R                         |   18 -
 MALDIquant-1.16/MALDIquant/R/isValidHalfWindowSize-functions.R           |   18 -
 MALDIquant-1.16/MALDIquant/R/labelPeaks-methods.R                        |   20 -
 MALDIquant-1.16/MALDIquant/R/lapply-functions.R                          |   18 -
 MALDIquant-1.16/MALDIquant/R/length-methods.R                            |   18 -
 MALDIquant-1.16/MALDIquant/R/lines-methods.R                             |   18 -
 MALDIquant-1.16/MALDIquant/R/localMaxima-functions.R                     |   18 -
 MALDIquant-1.16/MALDIquant/R/mapply-functions.R                          |   18 -
 MALDIquant-1.16/MALDIquant/R/mass-methods.R                              |   18 -
 MALDIquant-1.16/MALDIquant/R/match.closest-functions.R                   |only
 MALDIquant-1.16/MALDIquant/R/memoryUsage-functions.R                     |   18 -
 MALDIquant-1.16/MALDIquant/R/merge-functions.R                           |   18 -
 MALDIquant-1.16/MALDIquant/R/metaData-methods.R                          |   18 -
 MALDIquant-1.16/MALDIquant/R/monoisotopic-functions.R                    |   29 -
 MALDIquant-1.16/MALDIquant/R/monoisotopicPeaks-methods.R                 |   18 -
 MALDIquant-1.16/MALDIquant/R/morphologicalFilter-functions.R             |   18 -
 MALDIquant-1.16/MALDIquant/R/msiSlices-functions.R                       |   18 -
 MALDIquant-1.16/MALDIquant/R/mz-methods.R                                |   18 -
 MALDIquant-1.16/MALDIquant/R/onAttach.R                                  |   18 -
 MALDIquant-1.16/MALDIquant/R/plot-methods.R                              |   18 -
 MALDIquant-1.16/MALDIquant/R/plotMsiSlice-functions.R                    |   18 -
 MALDIquant-1.16/MALDIquant/R/plotMsiSlice-methods.R                      |   18 -
 MALDIquant-1.16/MALDIquant/R/points-methods.R                            |   18 -
 MALDIquant-1.16/MALDIquant/R/range-functions.R                           |   18 -
 MALDIquant-1.16/MALDIquant/R/referencePeaks-functions.R                  |   18 -
 MALDIquant-1.16/MALDIquant/R/removeBaseline-methods.R                    |   18 -
 MALDIquant-1.16/MALDIquant/R/removeEmptyMassObjects-functions.R          |   18 -
 MALDIquant-1.16/MALDIquant/R/replaceNegativeIntensityValues-functions.R  |   18 -
 MALDIquant-1.16/MALDIquant/R/show-functions.R                            |   18 -
 MALDIquant-1.16/MALDIquant/R/show-methods.R                              |   18 -
 MALDIquant-1.16/MALDIquant/R/smoothIntensity-methods.R                   |   18 -
 MALDIquant-1.16/MALDIquant/R/smoothingFilters-functions.R                |   18 -
 MALDIquant-1.16/MALDIquant/R/snr-methods.R                               |   18 -
 MALDIquant-1.16/MALDIquant/R/subset-methods.R                            |   18 -
 MALDIquant-1.16/MALDIquant/R/totalIonCurrent-methods.R                   |   18 -
 MALDIquant-1.16/MALDIquant/R/transformIntensity-methods.R                |   18 -
 MALDIquant-1.16/MALDIquant/R/trim-methods.R                              |   18 -
 MALDIquant-1.16/MALDIquant/R/unlist-functions.R                          |   18 -
 MALDIquant-1.16/MALDIquant/R/valid-methods.R                             |   18 -
 MALDIquant-1.16/MALDIquant/R/warp-functions.R                            |   18 -
 MALDIquant-1.16/MALDIquant/R/warpingFunction-functions.R                 |   18 -
 MALDIquant-1.16/MALDIquant/build/vignette.rds                            |binary
 MALDIquant-1.16/MALDIquant/inst/doc/MALDIquant-intro.pdf                 |binary
 MALDIquant-1.16/MALDIquant/man/match.closest.Rd                          |only
 MALDIquant-1.16/MALDIquant/tests/testthat/test_match.closest-functions.R |only
 86 files changed, 117 insertions(+), 1426 deletions(-)

More information about MALDIquant at CRAN
Permanent link

Package wru updated to version 0.1-1 with previous version 0.0-2 dated 2016-03-11

Title: Who Are You? Bayesian Prediction of Racial Category Using Surname and Geolocation
Description: This open-source software package enables researchers to predict individual ethnicity using his/her surname, geolocation, and other attributes such as gender and age. The method utilizes the Bayes' rule to compute the posterior probability of each racial category for any given individual voter. The package implements methods described in Imai and Khanna (2015) "Improving Ecological Inference by Predicting Individual Ethnicity from Voter Registration Records" <DOI:10.1093/pan/mpw001>.
Author: Kabir Khanna [aut, cre], Kosuke Imai [aut, cre]
Maintainer: Kabir Khanna <kkhanna@princeton.edu>

Diff between wru versions 0.0-2 dated 2016-03-11 and 0.1-1 dated 2016-12-13

 DESCRIPTION                     |   16 +
 MD5                             |   23 +-
 NAMESPACE                       |    4 
 R/census.helper.api.R           |  374 +++++++++++++++++++++++++++++++++++++++-
 R/getCensusApi.R                |    4 
 R/getCensusApi2.R               |   22 +-
 R/getCensusData.R               |only
 R/race.pred.R                   |  138 +++++++++++---
 README.md                       |   37 +++
 man/census.helper.api.Rd        |    9 
 man/census.helper.api.local.Rd  |only
 man/census.helper.api.online.Rd |only
 man/censusData.Rd               |only
 man/getCensusData.Rd            |only
 man/race.pred.Rd                |   52 +++--
 15 files changed, 592 insertions(+), 87 deletions(-)

More information about wru at CRAN
Permanent link

Package sparkTable updated to version 1.3.0 with previous version 1.2.0 dated 2016-03-07

Title: Sparklines and Graphical Tables for TeX and HTML
Description: Create sparklines and graphical tables for documents and websites.
Author: Alexander Kowarik, Bernhard Meindl, Matthias Templ
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>

Diff between sparkTable versions 1.2.0 dated 2016-03-07 and 1.3.0 dated 2016-12-13

 sparkTable-1.2.0/sparkTable/inst/shinystuff/shinypara_global.R |only
 sparkTable-1.2.0/sparkTable/inst/shinystuff/shinypara_server.R |only
 sparkTable-1.2.0/sparkTable/inst/shinystuff/shinypara_ui.R     |only
 sparkTable-1.2.0/sparkTable/inst/shinystuff/www                |only
 sparkTable-1.3.0/sparkTable/DESCRIPTION                        |   12 -
 sparkTable-1.3.0/sparkTable/MD5                                |   41 ++++--
 sparkTable-1.3.0/sparkTable/R/classes.r                        |   16 +-
 sparkTable-1.3.0/sparkTable/R/customizeSparkTable.R            |   64 +++-------
 sparkTable-1.3.0/sparkTable/R/methods.r                        |   20 +--
 sparkTable-1.3.0/sparkTable/inst/shinystuff/customize          |only
 sparkTable-1.3.0/sparkTable/man/customizeSparkTable.Rd         |   23 ---
 sparkTable-1.3.0/sparkTable/man/export.Rd                      |    2 
 sparkTable-1.3.0/sparkTable/man/newSparkTable.Rd               |    2 
 sparkTable-1.3.0/sparkTable/man/reshapeExt.Rd                  |    2 
 sparkTable-1.3.0/sparkTable/man/showSparkTable.Rd              |    4 
 15 files changed, 82 insertions(+), 104 deletions(-)

More information about sparkTable at CRAN
Permanent link

Package SocialMediaMineR updated to version 0.4 with previous version 0.3 dated 2016-03-20

Title: A Social Media Search and Analytic Tool
Description: Social media search and analytic tool that takes one or multiple URL(s) and returns the information about the popularity and reach of the URL(s) on social media. The function get_socialmedia() retrieves the number of shares, likes, pins, and hits on Facebook (<http://www.facebook.com>), Pinterest (<http://www.pinterest.com>), StumbleUpon (<http://www.stumbleupon.com>), LinkedIn (<http://www.linkedin.com>), and Reddit (<http://www.reddit.com>). The package also includes dedicated functions for each social network platform and a function to resolve shortened URLs.
Author: Marco Bastos
Maintainer: Marco Bastos <marco@toledobastos.com>

Diff between SocialMediaMineR versions 0.3 dated 2016-03-20 and 0.4 dated 2016-12-13

 ChangeLog                       |    4 ++++
 DESCRIPTION                     |   14 +++++++-------
 MD5                             |   26 +++++++++++++-------------
 R/get_facebook.R                |    2 +-
 R/get_reddit.R                  |    1 +
 R/get_socialmedia.R             |   23 ++++++++++++-----------
 man/SocialMediaMineR-package.Rd |    8 ++++----
 man/get_facebook.Rd             |    8 ++++----
 man/get_linkedin.Rd             |    4 ++--
 man/get_pinterest.Rd            |    4 ++--
 man/get_reddit.Rd               |    4 ++--
 man/get_socialmedia.Rd          |    2 +-
 man/get_stumbleupon.Rd          |    2 +-
 man/get_url.Rd                  |    2 +-
 14 files changed, 55 insertions(+), 49 deletions(-)

More information about SocialMediaMineR at CRAN
Permanent link

Package scatterD3 updated to version 0.8.1 with previous version 0.8 dated 2016-11-18

Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre], Kent Russell [aut, ctb], Mike Bostock [aut, cph] (d3.js library, http://d3js.org), Susie Lu [aut, cph] (d3-legend library, http://d3-legend.susielu.com/), Speros Kokenes [aut, cph] (d3-lasso-plugin library, https://github.com/skokenes/D3-Lasso-Plugin)
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

Diff between scatterD3 versions 0.8 dated 2016-11-18 and 0.8.1 dated 2016-12-13

 DESCRIPTION                         |    8 -
 MD5                                 |   18 ++--
 NEWS                                |   11 ++
 inst/doc/introduction.R             |   15 ++-
 inst/doc/introduction.Rmd           |   22 ++++-
 inst/doc/introduction.html          |  151 ++++++++++++++++++------------------
 inst/htmlwidgets/scatterD3-axes.js  |   14 +--
 inst/htmlwidgets/scatterD3-setup.js |   97 ++++++++++++++++-------
 inst/htmlwidgets/scatterD3.js       |   44 +++++-----
 vignettes/introduction.Rmd          |   22 ++++-
 10 files changed, 251 insertions(+), 151 deletions(-)

More information about scatterD3 at CRAN
Permanent link

Package rdrobust updated to version 0.95 with previous version 0.94 dated 2016-09-20

Title: Robust Data-Driven Statistical Inference in Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell, <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>

Diff between rdrobust versions 0.94 dated 2016-09-20 and 0.95 dated 2016-12-13

 DESCRIPTION             |    8 ++++----
 MD5                     |   18 +++++++++---------
 R/functions.R           |   11 ++++++++++-
 R/rdbwselect.R          |   36 ++++++++++++++++++++----------------
 R/rdplot.R              |    9 ++++++++-
 R/rdrobust.R            |   12 ++++++++++--
 man/rdbwselect.Rd       |    6 +++---
 man/rdplot.Rd           |    6 +++---
 man/rdrobust-package.Rd |    4 ++--
 man/rdrobust.Rd         |    7 +++----
 10 files changed, 72 insertions(+), 45 deletions(-)

More information about rdrobust at CRAN
Permanent link

New package poptrend with initial version 0.1.0
Package: poptrend
Title: Estimate Smooth and Linear Trends from Population Count Survey Data
Version: 0.1.0
Authors@R: person("Jonas", "Knape", email = "jonas.knape@slu.se", role = c("aut", "cre"))
Description: Functions to estimate and plot smooth or linear population trends, or population indices, from animal or plant count survey data.
Depends: R (>= 3.1.2)
License: GPL-3
LazyData: true
Imports: mgcv (>= 1.7.0), stats, graphics
RoxygenNote: 5.0.1
URL: https://github.com/jknape/poptrend
NeedsCompilation: no
Packaged: 2016-12-13 14:40:49 UTC; jonas
Author: Jonas Knape [aut, cre]
Maintainer: Jonas Knape <jonas.knape@slu.se>
Repository: CRAN
Date/Publication: 2016-12-13 19:54:47

More information about poptrend at CRAN
Permanent link

Package ncvreg updated to version 3.7-0 with previous version 3.6-0 dated 2016-06-13

Title: Regularization Paths for SCAD and MCP Penalized Regression Models
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>

Diff between ncvreg versions 3.6-0 dated 2016-06-13 and 3.7-0 dated 2016-12-13

 ncvreg-3.6-0/ncvreg/R/summary.cv.ncvreg.R    |only
 ncvreg-3.6-0/ncvreg/R/summary.cv.ncvsurv.R   |only
 ncvreg-3.6-0/ncvreg/tests                    |only
 ncvreg-3.7-0/ncvreg/DESCRIPTION              |    9 
 ncvreg-3.7-0/ncvreg/MD5                      |   74 +++---
 ncvreg-3.7-0/ncvreg/NAMESPACE                |    3 
 ncvreg-3.7-0/ncvreg/NEWS                     |  325 +++++++++++++--------------
 ncvreg-3.7-0/ncvreg/R/fir.R                  |   35 ++
 ncvreg-3.7-0/ncvreg/R/lamNames.R             |only
 ncvreg-3.7-0/ncvreg/R/ncvreg.R               |   55 +---
 ncvreg-3.7-0/ncvreg/R/ncvsurv.R              |    7 
 ncvreg-3.7-0/ncvreg/R/perm.ncvreg.R          |    2 
 ncvreg-3.7-0/ncvreg/R/plot.fir.R             |   21 +
 ncvreg-3.7-0/ncvreg/R/predict.R              |    2 
 ncvreg-3.7-0/ncvreg/R/predict.surv.R         |    2 
 ncvreg-3.7-0/ncvreg/R/summary-cv-ncvreg.R    |only
 ncvreg-3.7-0/ncvreg/R/summary-cv-ncvsurv.R   |only
 ncvreg-3.7-0/ncvreg/R/summary-ncvreg.R       |only
 ncvreg-3.7-0/ncvreg/R/summary-ncvsurv.R      |only
 ncvreg-3.7-0/ncvreg/inst/doc/quick-start.pdf |binary
 ncvreg-3.7-0/ncvreg/inst/interactive-tests   |only
 ncvreg-3.7-0/ncvreg/inst/tests/coerce.R      |   13 -
 ncvreg-3.7-0/ncvreg/inst/tests/fir.R         |   47 +++
 ncvreg-3.7-0/ncvreg/inst/tests/ncvreg.R      |    8 
 ncvreg-3.7-0/ncvreg/inst/tests/ncvsurv.R     |    3 
 ncvreg-3.7-0/ncvreg/inst/tests/parallel.R    |   28 +-
 ncvreg-3.7-0/ncvreg/man/Lung.Rd              |    2 
 ncvreg-3.7-0/ncvreg/man/fir.Rd               |   51 +++-
 ncvreg-3.7-0/ncvreg/man/ncvreg.Rd            |    6 
 ncvreg-3.7-0/ncvreg/man/ncvsurv.Rd           |    6 
 ncvreg-3.7-0/ncvreg/man/plot.fir.Rd          |   22 +
 ncvreg-3.7-0/ncvreg/src/binomial.c           |   36 +-
 ncvreg-3.7-0/ncvreg/src/cox-dh.c             |  215 ++++++++---------
 ncvreg-3.7-0/ncvreg/src/gaussian.c           |   18 -
 ncvreg-3.7-0/ncvreg/src/ncvreg.c             |   12 
 ncvreg-3.7-0/ncvreg/src/poisson.c            |   10 
 ncvreg-3.7-0/ncvreg/src/raw.c                |   14 -
 37 files changed, 567 insertions(+), 459 deletions(-)

More information about ncvreg at CRAN
Permanent link

New package MODISSnow with initial version 0.1.0.0
Package: MODISSnow
Type: Package
Title: Provides a Function to Download MODIS Snow Cover
Version: 0.1.0.0
Authors@R: c( person("Johannes", "Signer", email = "jmsigner@gmail.com", role = c("aut", "cre")), person("Joel", "Trubilowicz", role = "aut"))
Description: Package for downloading Moderate-resolution Imaging Spectroradiometer (MODIS) snow cover data. Global daily snow cover at 500 m resolution derived from MODIS is made available by the National Snow and Ice Center Data Center <http://nsidc.org/>.
Imports: raster, RCurl, lubridate, gdalUtils
URL: https://github.com/jmsigner/MODISSnow
BugReports: https://github.com/jmsigner/MODISSnow/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-12-13 14:23:45 UTC; jsigner
Author: Johannes Signer [aut, cre], Joel Trubilowicz [aut]
Maintainer: Johannes Signer <jmsigner@gmail.com>
Repository: CRAN
Date/Publication: 2016-12-13 19:52:48

More information about MODISSnow at CRAN
Permanent link

Package landscapeR updated to version 1.1.3 with previous version 1.1.2 dated 2016-09-07

Title: Categorical Landscape Simulation Facility
Description: Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion) and von Neumann neighbourhood (four cells, aka Rook case). Outputs are raster dataset exportable to any common GIS format.
Author: Dario Masante [aut, cre]
Maintainer: Dario Masante <dario.masante@gmail.com>

Diff between landscapeR versions 1.1.2 dated 2016-09-07 and 1.1.3 dated 2016-12-13

 DESCRIPTION              |   12 ++++++------
 MD5                      |   32 ++++++++++++++++----------------
 NEWS.md                  |    9 +++++++++
 R/expandClass.R          |    2 +-
 R/makeClass.R            |    7 ++++---
 R/makeLine.R             |    9 +++++----
 R/makePatch.R            |    8 ++++----
 R/rmSingle.R             |   18 ++++++++++--------
 inst/doc/landscapeR.R    |   10 +++++++++-
 inst/doc/landscapeR.Rmd  |   16 ++++++++++++----
 inst/doc/landscapeR.html |   46 ++++++++++++++++++++++++++++------------------
 man/expandClass.Rd       |    2 +-
 man/makeClass.Rd         |    9 +++++----
 man/makeLine.Rd          |    7 ++++---
 man/makePatch.Rd         |    6 +++---
 man/rmSingle.Rd          |   11 +++++++----
 vignettes/landscapeR.Rmd |   16 ++++++++++++----
 17 files changed, 136 insertions(+), 84 deletions(-)

More information about landscapeR at CRAN
Permanent link

Package incidence updated to version 1.1.0 with previous version 1.0.1 dated 2016-11-22

Title: Compute, Handle, Plot and Model Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Thibaut Jombart [aut, cre], Rich FitzJohn [aut], Jun Cai [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>

Diff between incidence versions 1.0.1 dated 2016-11-22 and 1.1.0 dated 2016-12-13

 DESCRIPTION                           |   13 +--
 MD5                                   |  128 ++++++++++++++++----------------
 NAMESPACE                             |    2 
 NEWS.md                               |   13 ++-
 R/conversion.R                        |   17 ++--
 R/fit.R                               |    1 
 R/incidence.R                         |   63 +++++++++++----
 R/plot.R                              |   30 +++++--
 R/subset.R                            |   11 +-
 README.md                             |   79 +++++++++++--------
 inst/doc/customize_plot.R             |   24 +++---
 inst/doc/customize_plot.Rmd           |   34 ++++----
 inst/doc/customize_plot.html          |   96 +++++++++++++++---------
 inst/doc/incidence_class.Rmd          |    4 -
 inst/doc/incidence_class.html         |   17 ++--
 inst/doc/overview.Rmd                 |    6 -
 inst/doc/overview.html                |   95 ++++++++++++++---------
 man/incidence.Rd                      |   23 +++--
 man/plot.incidence.Rd                 |   11 ++
 tests/testthat/rds/df.rds             |binary
 tests/testthat/rds/df2.rds            |binary
 tests/testthat/rds/df3.rds            |only
 tests/testthat/rds/dfl.rds            |binary
 tests/testthat/rds/fit.i.rds          |binary
 tests/testthat/rds/fit.i.sex.rds      |binary
 tests/testthat/rds/incidence.res1.rds |binary
 tests/testthat/rds/incidence.res2.rds |binary
 tests/testthat/rds/incidence.res3.rds |binary
 tests/testthat/rds/incidence.res4.rds |binary
 tests/testthat/rds/incidence.res5.rds |binary
 tests/testthat/rds/incidence.res6.rds |binary
 tests/testthat/rds/incidence.res7.rds |binary
 tests/testthat/rds/incidence.res8.rds |binary
 tests/testthat/rds/o.fit.i.rds        |binary
 tests/testthat/rds/o.fit.i.sex.rds    |binary
 tests/testthat/rds/p.fit.i.2.rds      |binary
 tests/testthat/rds/p.fit.i.rds        |binary
 tests/testthat/rds/p.fit.sex.rds      |binary
 tests/testthat/rds/p.i.14.rds         |binary
 tests/testthat/rds/p.i.2.rds          |binary
 tests/testthat/rds/p.i.3.rds          |binary
 tests/testthat/rds/p.i.rds            |binary
 tests/testthat/rds/p.sex.2.rds        |binary
 tests/testthat/rds/p.sex.3.rds        |binary
 tests/testthat/rds/p.sex.4.rds        |binary
 tests/testthat/rds/p.sex.rds          |binary
 tests/testthat/rds/print.fit.i.rds    |binary
 tests/testthat/rds/print.fit.sex.rds  |binary
 tests/testthat/rds/print1.rds         |binary
 tests/testthat/rds/print2.rds         |binary
 tests/testthat/rds/res.g.1.rds        |binary
 tests/testthat/rds/res.g.2.rds        |binary
 tests/testthat/rds/res.g.3.rds        |binary
 tests/testthat/rds/x.sub1.rds         |binary
 tests/testthat/rds/x.sub2.rds         |binary
 tests/testthat/rds/x.sub3.rds         |binary
 tests/testthat/rds/x.sub4.rds         |binary
 tests/testthat/rds/x.sub5.rds         |binary
 tests/testthat/rds/y.sub1.rds         |only
 tests/testthat/test-conversions.R     |    7 +
 tests/testthat/test-incidence.R       |  136 ++++++++++++++++++----------------
 tests/testthat/test-plot.R            |   22 ++---
 tests/testthat/test-subset.R          |    6 +
 vignettes/customize_plot.Rmd          |   34 ++++----
 vignettes/incidence_class.Rmd         |    4 -
 vignettes/overview.Rmd                |    6 -
 66 files changed, 518 insertions(+), 364 deletions(-)

More information about incidence at CRAN
Permanent link

Package hansard updated to version 0.3.4 with previous version 0.2.5 dated 2016-11-12

Title: Provides Easy Downloading Capabilities for the UK Parliament API
Description: Provides functions to download data from the <http://www.data.parliament.uk/> APIs. Because of the structure of the API, there is a named function for each type of available data for ease of use. Functions for each new API will be added as and when they become available on the API.
Author: Evan Odell [aut, cre]
Maintainer: Evan Odell <evanodell91@gmail.com>

Diff between hansard versions 0.2.5 dated 2016-11-12 and 0.3.4 dated 2016-12-13

 hansard-0.2.5/hansard/R/election.R                       |only
 hansard-0.2.5/hansard/R/lords_ammendments.R              |only
 hansard-0.2.5/hansard/inst/doc/hansard-example.R         |only
 hansard-0.2.5/hansard/inst/doc/hansard-example.Rmd       |only
 hansard-0.2.5/hansard/inst/doc/hansard-example.html      |only
 hansard-0.2.5/hansard/man/lords_ammendments.Rd           |only
 hansard-0.2.5/hansard/vignettes/hansard-example.Rmd      |only
 hansard-0.3.4/hansard/DESCRIPTION                        |   11 
 hansard-0.3.4/hansard/MD5                                |  132 +++---
 hansard-0.3.4/hansard/NAMESPACE                          |    9 
 hansard-0.3.4/hansard/NEWS.md                            |   37 +
 hansard-0.3.4/hansard/R/all_answered_questions.R         |   40 +
 hansard-0.3.4/hansard/R/bills.R                          |   74 ++-
 hansard-0.3.4/hansard/R/commons_answered_questions.R     |   91 ++--
 hansard-0.3.4/hansard/R/commons_divisions.R              |  307 +++++++++++----
 hansard-0.3.4/hansard/R/commons_oral_question_times.R    |  102 ++++
 hansard-0.3.4/hansard/R/commons_oral_questions.R         |  175 +++++++-
 hansard-0.3.4/hansard/R/commons_terms.R                  |   20 
 hansard-0.3.4/hansard/R/commons_written_questions.R      |   99 +++-
 hansard-0.3.4/hansard/R/constituencies.R                 |   38 -
 hansard-0.3.4/hansard/R/early_day_motions.R              |  168 ++++++--
 hansard-0.3.4/hansard/R/election_results.R               |   74 ++-
 hansard-0.3.4/hansard/R/elections.R                      |only
 hansard-0.3.4/hansard/R/epetition.R                      |   98 ++--
 hansard-0.3.4/hansard/R/hansard.r                        |   12 
 hansard-0.3.4/hansard/R/hansard_basic.R                  |only
 hansard-0.3.4/hansard/R/hansard_generic.R                |only
 hansard-0.3.4/hansard/R/lords_amendments.R               |only
 hansard-0.3.4/hansard/R/lords_attendance.R               |   58 +-
 hansard-0.3.4/hansard/R/lords_divisions.R                |  244 ++++++++---
 hansard-0.3.4/hansard/R/lords_vote_record.R              |only
 hansard-0.3.4/hansard/R/lords_written_questions.R        |    6 
 hansard-0.3.4/hansard/R/members.R                        |  262 ++++++------
 hansard-0.3.4/hansard/R/members_search.R                 |only
 hansard-0.3.4/hansard/R/mp_edms.R                        |only
 hansard-0.3.4/hansard/R/mp_questions.R                   |only
 hansard-0.3.4/hansard/R/mp_vote_record.R                 |only
 hansard-0.3.4/hansard/R/papers_laid.R                    |   18 
 hansard-0.3.4/hansard/R/publication_logs.R               |   16 
 hansard-0.3.4/hansard/R/research_briefings.R             |  149 +++----
 hansard-0.3.4/hansard/R/sessions_info.R                  |   39 +
 hansard-0.3.4/hansard/R/tv_programmes.R                  |    6 
 hansard-0.3.4/hansard/README.md                          |   26 -
 hansard-0.3.4/hansard/build/vignette.rds                 |binary
 hansard-0.3.4/hansard/inst/CITATION                      |    4 
 hansard-0.3.4/hansard/inst/doc/introduction.R            |only
 hansard-0.3.4/hansard/inst/doc/introduction.Rmd          |only
 hansard-0.3.4/hansard/inst/doc/introduction.html         |only
 hansard-0.3.4/hansard/man/all_answered_questions.Rd      |    2 
 hansard-0.3.4/hansard/man/bills.Rd                       |    6 
 hansard-0.3.4/hansard/man/commons_answered_questions.Rd  |    2 
 hansard-0.3.4/hansard/man/commons_division_date.Rd       |only
 hansard-0.3.4/hansard/man/commons_divisions.Rd           |   40 +
 hansard-0.3.4/hansard/man/commons_oral_question_times.Rd |   19 
 hansard-0.3.4/hansard/man/commons_oral_questions.Rd      |   28 +
 hansard-0.3.4/hansard/man/commons_terms.Rd               |    2 
 hansard-0.3.4/hansard/man/commons_written_questions.Rd   |   13 
 hansard-0.3.4/hansard/man/constituencies.Rd              |    2 
 hansard-0.3.4/hansard/man/early_day_motions.Rd           |   25 +
 hansard-0.3.4/hansard/man/election_results.Rd            |   14 
 hansard-0.3.4/hansard/man/elections.Rd                   |   16 
 hansard-0.3.4/hansard/man/epetition.Rd                   |    7 
 hansard-0.3.4/hansard/man/hansard.Rd                     |   12 
 hansard-0.3.4/hansard/man/hansard_basic.Rd               |only
 hansard-0.3.4/hansard/man/hansard_generic.Rd             |only
 hansard-0.3.4/hansard/man/lords_amendments.Rd            |only
 hansard-0.3.4/hansard/man/lords_attendance.Rd            |    4 
 hansard-0.3.4/hansard/man/lords_divisions.Rd             |   11 
 hansard-0.3.4/hansard/man/lords_vote_record.Rd           |only
 hansard-0.3.4/hansard/man/lords_written_questions.Rd     |    2 
 hansard-0.3.4/hansard/man/members.Rd                     |    2 
 hansard-0.3.4/hansard/man/members_search.Rd              |   25 -
 hansard-0.3.4/hansard/man/mp_edms.Rd                     |only
 hansard-0.3.4/hansard/man/mp_questions.Rd                |only
 hansard-0.3.4/hansard/man/mp_vote_record.Rd              |only
 hansard-0.3.4/hansard/man/papers_laid.Rd                 |    2 
 hansard-0.3.4/hansard/man/publication_logs.Rd            |    2 
 hansard-0.3.4/hansard/man/research_briefings.Rd          |    2 
 hansard-0.3.4/hansard/man/sessions_info.Rd               |    5 
 hansard-0.3.4/hansard/man/tv_programmes.Rd               |    2 
 hansard-0.3.4/hansard/vignettes/introduction.Rmd         |only
 81 files changed, 1724 insertions(+), 836 deletions(-)

More information about hansard at CRAN
Permanent link

Package FLSSS updated to version 5.1 with previous version 5.0.1 dated 2016-04-20

Title: Multi-Threaded Multidimensional Fixed Size Subset Sum Solver and Extension to General-Purpose Knapsack Problem
Description: A novel algorithm for solving the subset sum problem with bounded error in multidimensional real domain and its application to the general-purpose knapsack problem.
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>

Diff between FLSSS versions 5.0.1 dated 2016-04-20 and 5.1 dated 2016-12-13

 FLSSS-5.0.1/FLSSS/man/FLSSS-package.Rd      |only
 FLSSS-5.0.1/FLSSS/src/RcppExports.cpp       |only
 FLSSS-5.1/FLSSS/DESCRIPTION                 |   16 
 FLSSS-5.1/FLSSS/MD5                         |   20 
 FLSSS-5.1/FLSSS/R/FLSSS_20160323.r          |  312 +++-
 FLSSS-5.1/FLSSS/build                       |only
 FLSSS-5.1/FLSSS/inst                        |only
 FLSSS-5.1/FLSSS/man/FLSSS.Rd                |only
 FLSSS-5.1/FLSSS/man/mFLSSSpar.Rd            |  106 +
 FLSSS-5.1/FLSSS/man/mmFLknapsack.Rd         |only
 FLSSS-5.1/FLSSS/src/FLSSS_20160322.cpp      | 1219 ++++++++++++++-----
 FLSSS-5.1/FLSSS/src/FLSSSmulti_20160323.cpp | 1754 ++++++++++++++++------------
 FLSSS-5.1/FLSSS/src/Makevars.win            |    2 
 FLSSS-5.1/FLSSS/vignettes                   |only
 14 files changed, 2249 insertions(+), 1180 deletions(-)

More information about FLSSS at CRAN
Permanent link

Package DIFtree updated to version 2.1.4 with previous version 2.0.4 dated 2016-07-21

Title: Item Focused Trees for the Identification of Items in Differential Item Functioning
Description: Item focused recursive partitioning for simultaneous selection of items and variables that induce Differential Item Functioning (DIF) based on the Rasch Model or the Logistic Regression Approach for DIF detection.
Author: Moritz Berger
Maintainer: Moritz Berger <moritz.berger@stat.uni-muenchen.de>

Diff between DIFtree versions 2.0.4 dated 2016-07-21 and 2.1.4 dated 2016-12-13

 DESCRIPTION         |   10 +++++-----
 MD5                 |   18 +++++++++---------
 NAMESPACE           |    1 +
 R/DIFtree.R         |    6 +++---
 R/DIFtree.default.R |    2 ++
 R/plot.DIFtree.R    |    8 ++++++--
 R/predict.DIFtree.R |   11 +++++++++--
 R/ptree.R           |    2 +-
 R/summary.DIFtree.R |   10 ++++++----
 R/tree_Rasch.R      |    4 ++--
 10 files changed, 44 insertions(+), 28 deletions(-)

More information about DIFtree at CRAN
Permanent link

New package BUCSS with initial version 0.0.1
Package: BUCSS
Type: Package
Title: Bias and Uncertainty Corrected Sample Size
Version: 0.0.1
Author: Samantha F. Anderson <sander10@nd.edu, Ken Kelley <kkelley@nd.edu>, Scott E. Maxwell <smaxwell@nd.edu>
Maintainer: Ken Kelley <kkelley@nd.edu>
Description: Implements a method of correcting for publication bias and uncertainty when planning sample sizes in a future study from an original study.
License: GPL (>= 3)
Imports: stats
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-12-13 16:20:18 UTC; kkelley
Repository: CRAN
Date/Publication: 2016-12-13 19:52:17

More information about BUCSS at CRAN
Permanent link

Package anytime updated to version 0.1.2 with previous version 0.1.1 dated 2016-11-27

Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor, or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between anytime versions 0.1.1 dated 2016-11-27 and 0.1.2 dated 2016-12-13

 ChangeLog           |   31 +++++++++++++++++++++++++++++++
 DESCRIPTION         |    8 ++++----
 MD5                 |   19 ++++++++++---------
 R/RcppExports.R     |    4 ++++
 build/partial.rdb   |binary
 inst/NEWS.Rd        |    8 ++++++++
 src/RcppExports.cpp |   11 +++++++++++
 src/anytime.cpp     |   49 +++++++++++++++++++++++++++----------------------
 tests/allFormats.R  |    4 ++++
 tests/gh_issue_33.R |only
 tests/utilities.R   |    3 +++
 11 files changed, 102 insertions(+), 35 deletions(-)

More information about anytime at CRAN
Permanent link

Package adespatial updated to version 0.0-7 with previous version 0.0-6 dated 2016-11-27

Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Author: Stéphane Dray, Guillaume Blanchet, Daniel Borcard, Guillaume Guenard, Thibaut Jombart, Guillaume Larocque, Pierre Legendre, Naima Madi, Helene H Wagner
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>

Diff between adespatial versions 0.0-6 dated 2016-11-27 and 0.0-7 dated 2016-12-13

 DESCRIPTION             |   15 ++++++++-------
 MD5                     |   30 +++++++++++++++++++-----------
 R/dist.ldc.R            |    6 +++---
 R/moran.randtest.R      |    2 +-
 R/moranNP.randtest.R    |    4 ++--
 R/multispati.R          |    6 +++---
 R/scalogram.R           |    2 +-
 build                   |only
 inst/doc                |only
 man/dist.ldc.Rd         |    6 +++---
 man/moran.randtest.Rd   |    2 +-
 man/moranNP.randtest.Rd |    4 ++--
 man/multispati.Rd       |    6 +++---
 man/scalogram.Rd        |    2 +-
 vignettes               |only
 15 files changed, 47 insertions(+), 38 deletions(-)

More information about adespatial at CRAN
Permanent link

Package adegraphics updated to version 1.0-6 with previous version 1.0-5 dated 2016-03-02

Title: An S4 Lattice-Based Package for the Representation of Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

Diff between adegraphics versions 1.0-5 dated 2016-03-02 and 1.0-6 dated 2016-12-13

 adegraphics-1.0-5/adegraphics/R/add.R                            |only
 adegraphics-1.0-6/adegraphics/DESCRIPTION                        |   30 
 adegraphics-1.0-6/adegraphics/MD5                                |   72 -
 adegraphics-1.0-6/adegraphics/NAMESPACE                          |    6 
 adegraphics-1.0-6/adegraphics/R/ADEg.C1.R                        |   23 
 adegraphics-1.0-6/adegraphics/R/ADEg.S2.R                        |    5 
 adegraphics-1.0-6/adegraphics/R/C1.curves.R                      |only
 adegraphics-1.0-6/adegraphics/R/addtext.R                        |only
 adegraphics-1.0-6/adegraphics/R/ade4-plot.R                      |  512 ++++++----
 adegraphics-1.0-6/adegraphics/R/genericMethod.R                  |    2 
 adegraphics-1.0-6/adegraphics/R/panelfunctions.R                 |    5 
 adegraphics-1.0-6/adegraphics/R/s.Spatial.R                      |  189 ++-
 adegraphics-1.0-6/adegraphics/R/utilsclass.R                     |    9 
 adegraphics-1.0-6/adegraphics/build/vignette.rds                 |binary
 adegraphics-1.0-6/adegraphics/inst/doc/adegraphics.Rmd           |    3 
 adegraphics-1.0-6/adegraphics/inst/doc/adegraphics.html          |  169 +--
 adegraphics-1.0-6/adegraphics/man/ADEg-class.Rd                  |    2 
 adegraphics-1.0-6/adegraphics/man/ADEgS.Rd                       |    4 
 adegraphics-1.0-6/adegraphics/man/C1.curve-class.Rd              |   15 
 adegraphics-1.0-6/adegraphics/man/addtext.Rd                     |   15 
 adegraphics-1.0-6/adegraphics/man/adeg.panel.nb.Rd               |    4 
 adegraphics-1.0-6/adegraphics/man/panel-methods.Rd               |    2 
 adegraphics-1.0-6/adegraphics/man/s.Spatial.Rd                   |    5 
 adegraphics-1.0-6/adegraphics/man/s.class.Rd                     |    3 
 adegraphics-1.0-6/adegraphics/man/s.image.Rd                     |    4 
 adegraphics-1.0-6/adegraphics/man/s.traject.Rd                   |    8 
 adegraphics-1.0-6/adegraphics/man/s.value.Rd                     |    1 
 adegraphics-1.0-6/adegraphics/man/s1d.class.Rd                   |    3 
 adegraphics-1.0-6/adegraphics/man/s1d.curves.Rd                  |only
 adegraphics-1.0-6/adegraphics/man/table.image.Rd                 |    4 
 adegraphics-1.0-6/adegraphics/man/table.value.Rd                 |    5 
 adegraphics-1.0-6/adegraphics/man/triangle.class.Rd              |    9 
 adegraphics-1.0-6/adegraphics/tests/add.R                        |    2 
 adegraphics-1.0-6/adegraphics/tests/panelSpatial.R               |    5 
 adegraphics-1.0-6/adegraphics/tests/slogo.R                      |    2 
 adegraphics-1.0-6/adegraphics/tests/straject.R                   |    8 
 adegraphics-1.0-6/adegraphics/vignettes/adegraphics.Rmd          |    3 
 adegraphics-1.0-6/adegraphics/vignettes/gargsVSclass.csv         |   84 -
 adegraphics-1.0-6/adegraphics/vignettes/tableparamVSfunction.csv |    1 
 39 files changed, 739 insertions(+), 475 deletions(-)

More information about adegraphics at CRAN
Permanent link

New package structree with initial version 1.1.3
Package: structree
Type: Package
Title: Tree-Structured Clustering
Version: 1.1.3
Date: 2016-12-13
Author: Moritz Berger
Depends: mgcv, penalized
Maintainer: Moritz Berger <moritz.berger@stat.uni-muenchen.de>
Description: Tree-structured modelling of categorical predictors or measurement units.
License: GPL-2
LazyLoad: yes
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-12-13 13:02:51 UTC; bergerm
Repository: CRAN
Date/Publication: 2016-12-13 15:49:49

More information about structree at CRAN
Permanent link

Package progress updated to version 1.1.1 with previous version 1.0.2 dated 2015-06-04

Title: Terminal Progress Bars
Description: Configurable Progress bars, they may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. The package also provides a 'C++' 'API', that works with or without 'Rcpp'.
Author: Gábor Csárdi [aut, cre], Rich FitzJohn [aut]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between progress versions 1.0.2 dated 2015-06-04 and 1.1.1 dated 2016-12-13

 progress-1.0.2/progress/R/progress.r                   |only
 progress-1.0.2/progress/R/utils.r                      |only
 progress-1.0.2/progress/inst/README.md                 |only
 progress-1.1.1/progress/DESCRIPTION                    |   26 +++--
 progress-1.1.1/progress/LICENSE                        |    4 
 progress-1.1.1/progress/MD5                            |   25 +++--
 progress-1.1.1/progress/NAMESPACE                      |    2 
 progress-1.1.1/progress/R/progress.R                   |only
 progress-1.1.1/progress/R/utils.R                      |only
 progress-1.1.1/progress/inst/NEWS.md                   |   10 ++
 progress-1.1.1/progress/inst/README.metacran           |only
 progress-1.1.1/progress/inst/include/RProgress.h       |   14 ++-
 progress-1.1.1/progress/inst/logo.png                  |only
 progress-1.1.1/progress/inst/logo.svg                  |only
 progress-1.1.1/progress/man/progress_bar.Rd            |   24 +++++
 progress-1.1.1/progress/tests/testthat/test-cpp.R      |    2 
 progress-1.1.1/progress/tests/testthat/test-overhead.R |only
 progress-1.1.1/progress/tests/testthat/test-progress.R |   74 +++++++++++++++--
 18 files changed, 145 insertions(+), 36 deletions(-)

More information about progress at CRAN
Permanent link

Package NormPsy updated to version 1.0.4 with previous version 1.0.3 dated 2015-02-27

Title: Normalisation of Psychometric Tests
Description: Functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). Functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores are also provided.
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>

Diff between NormPsy versions 1.0.3 dated 2015-02-27 and 1.0.4 dated 2016-12-13

 DESCRIPTION                |    8 +--
 MD5                        |   12 ++---
 NAMESPACE                  |    3 +
 R/predictMMSE.R            |   21 ++-------
 man/NormPsy-package.Rd     |   51 ++++++++++-------------
 man/normMMSE.Rd            |   99 +++++++++++++++++++++------------------------
 src/backtransformation.f90 |    2 
 7 files changed, 92 insertions(+), 104 deletions(-)

More information about NormPsy at CRAN
Permanent link

Package nhanesA updated to version 0.6.4.3.3 with previous version 0.6.4.2 dated 2016-08-02

Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>

Diff between nhanesA versions 0.6.4.2 dated 2016-08-02 and 0.6.4.3.3 dated 2016-12-13

 DESCRIPTION                       |   11 +++++-----
 MD5                               |   20 +++++++++----------
 R/nhanes.R                        |   21 +++++++++++--------
 README.md                         |    6 ++---
 build/vignette.rds                |binary
 inst/doc/Introducing_nhanesA.R    |   28 +++++++++++++-------------
 inst/doc/Introducing_nhanesA.Rmd  |   37 ++++++++++++++++++-----------------
 inst/doc/Introducing_nhanesA.html |   40 +++++++++++++++++++-------------------
 man/nhanesSearch.Rd               |    2 -
 man/nhanesSearchTableNames.Rd     |    2 -
 vignettes/Introducing_nhanesA.Rmd |   37 ++++++++++++++++++-----------------
 11 files changed, 105 insertions(+), 99 deletions(-)

More information about nhanesA at CRAN
Permanent link

Package matrixpls updated to version 1.0.4 with previous version 1.0.3 dated 2016-12-06

Title: Matrix-Based Partial Least Squares Estimation
Description: Partial Least Squares Path Modeling algorithm and related algorithms. The algorithm implementations aim for computational efficiency using matrix algebra and covariance data. The package is designed toward Monte Carlo simulations and includes functions to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö <mikko.ronkko@aalto.fi>

Diff between matrixpls versions 1.0.3 dated 2016-12-06 and 1.0.4 dated 2016-12-13

 DESCRIPTION   |    8 ++++----
 MD5           |    4 ++--
 R/estimator.R |    3 +--
 3 files changed, 7 insertions(+), 8 deletions(-)

More information about matrixpls at CRAN
Permanent link

Package lcmm updated to version 1.7.6 with previous version 1.7.5 dated 2016-03-16

Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>

Diff between lcmm versions 1.7.5 dated 2016-03-16 and 1.7.6 dated 2016-12-13

 DESCRIPTION            |    8 ++++----
 MD5                    |   36 ++++++++++++++++++------------------
 NEWS                   |    9 +++++++--
 R/VarExpl.Jointlcmm.R  |    2 +-
 R/VarExpl.hlme.R       |    2 +-
 R/VarExpl.lcmm.R       |    2 +-
 R/VarExpl.multlcmm.R   |    2 +-
 R/multlcmm.R           |    9 +++++++++
 R/plot.predictY.R      |    2 +-
 inst/CITATION          |    2 +-
 man/gridsearch.Rd      |    2 +-
 man/lcmm.Rd            |    2 +-
 src/Jointhet.f90       |    4 ++--
 src/cvpl.f90           |    2 +-
 src/hetmixCont.f90     |   11 +++++++++--
 src/hetmixContMult.f90 |    4 ++--
 src/hetmixOrd.f90      |    4 ++--
 src/predictCont.f90    |    2 +-
 src/predictMult.f90    |    2 +-
 19 files changed, 64 insertions(+), 43 deletions(-)

More information about lcmm at CRAN
Permanent link

Package furniture updated to version 1.4.1 with previous version 1.2.2 dated 2016-11-15

Title: Furniture for Applied Quantitative Researchers
Description: Contains two main functions (i.e., two pieces of furniture): table1() which produces a well-formatted table of descriptives common as Table 1 in research articles and washer() which is helpful in cleaning up your data. In addition, tableM() provides a descriptive table to understand patterns of missing values in the stratifying variable. These furniture functions are designed to simplify common tasks in quantitative analysis.
Author: Tyson Barrett [aut, cre], Emily Brignone [aut]
Maintainer: Tyson Barrett <t.barrett@aggiemail.usu.edu>

Diff between furniture versions 1.2.2 dated 2016-11-15 and 1.4.1 dated 2016-12-13

 furniture-1.2.2/furniture/R/Simple_Table1.R                   |only
 furniture-1.2.2/furniture/man/simple_table1.Rd                |only
 furniture-1.2.2/furniture/tests/testthat/test_simple_table1.R |only
 furniture-1.4.1/furniture/DESCRIPTION                         |   14 
 furniture-1.4.1/furniture/MD5                                 |   38 
 furniture-1.4.1/furniture/NAMESPACE                           |    3 
 furniture-1.4.1/furniture/R/Table1.R                          |  655 +++++++---
 furniture-1.4.1/furniture/R/zzz.R                             |    2 
 furniture-1.4.1/furniture/build/vignette.rds                  |binary
 furniture-1.4.1/furniture/inst/doc/Furniture.R                |   41 
 furniture-1.4.1/furniture/inst/doc/Furniture.Rmd              |   55 
 furniture-1.4.1/furniture/inst/doc/Furniture.html             |  197 +--
 furniture-1.4.1/furniture/inst/doc/Table1.R                   |   40 
 furniture-1.4.1/furniture/inst/doc/Table1.Rmd                 |   67 -
 furniture-1.4.1/furniture/inst/doc/Table1.html                |  371 +++--
 furniture-1.4.1/furniture/man/table1.Rd                       |   29 
 furniture-1.4.1/furniture/man/tableM.Rd                       |only
 furniture-1.4.1/furniture/tests/testthat/test_table1.R        |  112 +
 furniture-1.4.1/furniture/tests/testthat/test_tableM.R        |only
 furniture-1.4.1/furniture/tests/testthat/test_washer.R        |    1 
 furniture-1.4.1/furniture/vignettes/Furniture.Rmd             |   55 
 furniture-1.4.1/furniture/vignettes/Table1                    |only
 furniture-1.4.1/furniture/vignettes/Table1.Rmd                |   67 -
 23 files changed, 1234 insertions(+), 513 deletions(-)

More information about furniture at CRAN
Permanent link

Package FSAdata updated to version 0.3.5 with previous version 0.3.4 dated 2016-08-24

Title: Data to Support Fish Stock Assessment ('FSA') Package
Description: The datasets to support the Fish Stock Assessment ('FSA') package.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>

Diff between FSAdata versions 0.3.4 dated 2016-08-24 and 0.3.5 dated 2016-12-13

 DESCRIPTION           |    8 ++++----
 MD5                   |    8 ++++----
 R/FSAdata-internals.R |   13 +------------
 R/Mosquitofish.R      |    6 +++---
 man/Mosquitofish.Rd   |    6 +++---
 5 files changed, 15 insertions(+), 26 deletions(-)

More information about FSAdata at CRAN
Permanent link

Package FSA updated to version 0.8.11 with previous version 0.8.10 dated 2016-09-24

Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>

Diff between FSA versions 0.8.10 dated 2016-09-24 and 0.8.11 dated 2016-12-13

 FSA-0.8.10/FSA/tests/testthat/test_AgeComparisons.R             |only
 FSA-0.8.10/FSA/tests/testthat/test_AgeLengthKey.R               |only
 FSA-0.8.10/FSA/tests/testthat/test_CatchCurve_ChapmanRobson.R   |only
 FSA-0.8.10/FSA/tests/testthat/test_FSAUtils.R                   |only
 FSA-0.8.10/FSA/tests/testthat/test_LWCompPreds.R                |only
 FSA-0.8.10/FSA/tests/testthat/test_PSD.R                        |only
 FSA-0.8.10/FSA/tests/testthat/test_StockRecruit.R               |only
 FSA-0.8.10/FSA/tests/testthat/test_Summarize.R                  |only
 FSA-0.8.10/FSA/tests/testthat/test_VonBertalanffy.R             |only
 FSA-0.8.10/FSA/tests/testthat/test_WSWR.R                       |only
 FSA-0.8.10/FSA/tests/testthat/test_addZeroCatch.R               |only
 FSA-0.8.10/FSA/tests/testthat/test_bcFuns.R                     |only
 FSA-0.8.10/FSA/tests/testthat/test_bootstrap.R                  |only
 FSA-0.8.10/FSA/tests/testthat/test_capHist.R                    |only
 FSA-0.8.10/FSA/tests/testthat/test_comparisonsDVR.R             |only
 FSA-0.8.10/FSA/tests/testthat/test_depletion.R                  |only
 FSA-0.8.10/FSA/tests/testthat/test_dunnTest.R                   |only
 FSA-0.8.10/FSA/tests/testthat/test_expandCounts.R               |only
 FSA-0.8.10/FSA/tests/testthat/test_expandLenFreq.R              |only
 FSA-0.8.10/FSA/tests/testthat/test_extraTests.R                 |only
 FSA-0.8.10/FSA/tests/testthat/test_fitResidPlots.R              |only
 FSA-0.8.10/FSA/tests/testthat/test_growthFuns.R                 |only
 FSA-0.8.10/FSA/tests/testthat/test_growthUtils.R                |only
 FSA-0.8.10/FSA/tests/testthat/test_histFormula.R                |only
 FSA-0.8.10/FSA/tests/testthat/test_histFromSum.R                |only
 FSA-0.8.10/FSA/tests/testthat/test_ksTest.R                     |only
 FSA-0.8.10/FSA/tests/testthat/test_lencat.R                     |only
 FSA-0.8.10/FSA/tests/testthat/test_metaM.R                      |only
 FSA-0.8.10/FSA/tests/testthat/test_mrClosed.R                   |only
 FSA-0.8.10/FSA/tests/testthat/test_mrOpen.R                     |only
 FSA-0.8.10/FSA/tests/testthat/test_removal.R                    |only
 FSA-0.8.10/FSA/tests/testthat/test_sumTable.R                   |only
 FSA-0.8.11/FSA/DESCRIPTION                                      |   12 
 FSA-0.8.11/FSA/MD5                                              |  280 ++++++----
 FSA-0.8.11/FSA/NAMESPACE                                        |    1 
 FSA-0.8.11/FSA/NEWS.md                                          |   43 +
 FSA-0.8.11/FSA/R/CIDists.R                                      |  202 +++++--
 FSA-0.8.11/FSA/R/FSA-internals.R                                |  207 ++++---
 FSA-0.8.11/FSA/R/FSAUtils.R                                     |   91 +--
 FSA-0.8.11/FSA/R/Summarize.R                                    |   12 
 FSA-0.8.11/FSA/R/addZeroCatch.R                                 |   16 
 FSA-0.8.11/FSA/R/ageComparisons.R                               |   59 +-
 FSA-0.8.11/FSA/R/alkIndivAge.R                                  |   29 -
 FSA-0.8.11/FSA/R/alkPlot.R                                      |   34 -
 FSA-0.8.11/FSA/R/alkSummaries.R                                 |   12 
 FSA-0.8.11/FSA/R/bcFuns.R                                       |   10 
 FSA-0.8.11/FSA/R/bootstrap.R                                    |   40 -
 FSA-0.8.11/FSA/R/capHistConvert.R                               |   34 -
 FSA-0.8.11/FSA/R/capHistSum.R                                   |    2 
 FSA-0.8.11/FSA/R/catchCurve.R                                   |   50 -
 FSA-0.8.11/FSA/R/chapmanRobson.R                                |   41 -
 FSA-0.8.11/FSA/R/comparisonsDVR.R                               |   16 
 FSA-0.8.11/FSA/R/depletion.R                                    |  105 +--
 FSA-0.8.11/FSA/R/dunnTest.R                                     |   20 
 FSA-0.8.11/FSA/R/expandCounts.R                                 |   16 
 FSA-0.8.11/FSA/R/expandLenFreq.R                                |   32 -
 FSA-0.8.11/FSA/R/extraTests.R                                   |   18 
 FSA-0.8.11/FSA/R/fitPlot.R                                      |   65 +-
 FSA-0.8.11/FSA/R/growthDataUtils.R                              |   15 
 FSA-0.8.11/FSA/R/growthModels.R                                 |  105 ++-
 FSA-0.8.11/FSA/R/hist.formula.R                                 |   24 
 FSA-0.8.11/FSA/R/histFromSum.R                                  |   28 -
 FSA-0.8.11/FSA/R/knitUtil.R                                     |   82 +-
 FSA-0.8.11/FSA/R/ksTest.R                                       |   12 
 FSA-0.8.11/FSA/R/lencat.R                                       |   22 
 FSA-0.8.11/FSA/R/lwCompPreds.R                                  |   19 
 FSA-0.8.11/FSA/R/metaM.R                                        |   55 +
 FSA-0.8.11/FSA/R/mrClosed.R                                     |  117 ++--
 FSA-0.8.11/FSA/R/mrOpen.R                                       |   38 -
 FSA-0.8.11/FSA/R/nlsTracePlot.R                                 |only
 FSA-0.8.11/FSA/R/plotBinResp.R                                  |    9 
 FSA-0.8.11/FSA/R/psdAdd.R                                       |   16 
 FSA-0.8.11/FSA/R/psdCI.R                                        |   18 
 FSA-0.8.11/FSA/R/psdCalc.R                                      |   35 -
 FSA-0.8.11/FSA/R/psdPlot.R                                      |    6 
 FSA-0.8.11/FSA/R/psdVal.R                                       |    8 
 FSA-0.8.11/FSA/R/removal.R                                      |   46 -
 FSA-0.8.11/FSA/R/residPlot.R                                    |   58 +-
 FSA-0.8.11/FSA/R/srStarts.R                                     |   20 
 FSA-0.8.11/FSA/R/stockRecruitment.R                             |   19 
 FSA-0.8.11/FSA/R/sumTable.R                                     |   10 
 FSA-0.8.11/FSA/R/tictactoe.R                                    |   16 
 FSA-0.8.11/FSA/R/vbStarts.R                                     |  227 +++++---
 FSA-0.8.11/FSA/R/wrAdd.R                                        |   18 
 FSA-0.8.11/FSA/R/wsVal.R                                        |    4 
 FSA-0.8.11/FSA/man/FSA-internals.Rd                             |    6 
 FSA-0.8.11/FSA/man/addZeroCatch.Rd                              |    2 
 FSA-0.8.11/FSA/man/ageBias.Rd                                   |    4 
 FSA-0.8.11/FSA/man/binCI.Rd                                     |   29 -
 FSA-0.8.11/FSA/man/bootCase.Rd                                  |    4 
 FSA-0.8.11/FSA/man/catchCurve.Rd                                |    8 
 FSA-0.8.11/FSA/man/chapmanRobson.Rd                             |    4 
 FSA-0.8.11/FSA/man/chooseColors.Rd                              |    6 
 FSA-0.8.11/FSA/man/col2rgbt.Rd                                  |    2 
 FSA-0.8.11/FSA/man/depletion.Rd                                 |   38 -
 FSA-0.8.11/FSA/man/expandLenFreq.Rd                             |    2 
 FSA-0.8.11/FSA/man/growthModels.Rd                              |    6 
 FSA-0.8.11/FSA/man/mrClosed.Rd                                  |   12 
 FSA-0.8.11/FSA/man/nlsTracePlot.Rd                              |only
 FSA-0.8.11/FSA/man/plotBinResp.Rd                               |    3 
 FSA-0.8.11/FSA/man/poiCI.Rd                                     |   41 -
 FSA-0.8.11/FSA/man/psdCI.Rd                                     |    6 
 FSA-0.8.11/FSA/man/psdCalc.Rd                                   |   21 
 FSA-0.8.11/FSA/man/residPlot.Rd                                 |   31 -
 FSA-0.8.11/FSA/man/vbStarts.Rd                                  |   43 +
 FSA-0.8.11/FSA/tests/testthat/EXS_AgeLengthKey.R                |only
 FSA-0.8.11/FSA/tests/testthat/EXS_CatchCurve.R                  |only
 FSA-0.8.11/FSA/tests/testthat/EXS_PSD.R                         |only
 FSA-0.8.11/FSA/tests/testthat/EXS_Summarize.R                   |only
 FSA-0.8.11/FSA/tests/testthat/EXS_addZeroCatch.R                |only
 FSA-0.8.11/FSA/tests/testthat/EXS_bootstrap.R                   |only
 FSA-0.8.11/FSA/tests/testthat/EXS_capHist.R                     |only
 FSA-0.8.11/FSA/tests/testthat/EXS_comparisonsDVR.R              |only
 FSA-0.8.11/FSA/tests/testthat/EXS_dunnTest.R                    |only
 FSA-0.8.11/FSA/tests/testthat/EXS_extraTests.R                  |only
 FSA-0.8.11/FSA/tests/testthat/EXS_fitResidPlots.R               |only
 FSA-0.8.11/FSA/tests/testthat/EXS_growthFuns.R                  |only
 FSA-0.8.11/FSA/tests/testthat/EXS_growthUtils.R                 |only
 FSA-0.8.11/FSA/tests/testthat/EXS_lencat.R                      |only
 FSA-0.8.11/FSA/tests/testthat/EXS_mrOpen.R                      |only
 FSA-0.8.11/FSA/tests/testthat/EXS_sumTable.R                    |only
 FSA-0.8.11/FSA/tests/testthat/Rplots.pdf                        |binary
 FSA-0.8.11/FSA/tests/testthat/test_AgeComparisons_MSG.R         |only
 FSA-0.8.11/FSA/tests/testthat/test_AgeComparisons_OUT.R         |only
 FSA-0.8.11/FSA/tests/testthat/test_AgeComparisons_VALIDATE.R    |only
 FSA-0.8.11/FSA/tests/testthat/test_AgeLengthKey_MSG.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_AgeLengthKey_OUT.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_AgeLengthKey_VALIDATE.R      |only
 FSA-0.8.11/FSA/tests/testthat/test_CatchCurve_MSG.R             |only
 FSA-0.8.11/FSA/tests/testthat/test_CatchCurve_OUT.R             |only
 FSA-0.8.11/FSA/tests/testthat/test_CatchCurve_VALIDATE.R        |only
 FSA-0.8.11/FSA/tests/testthat/test_FSAUtils_MSG.R               |only
 FSA-0.8.11/FSA/tests/testthat/test_FSAUtils_OUT.R               |only
 FSA-0.8.11/FSA/tests/testthat/test_Internals.R                  |  178 +++---
 FSA-0.8.11/FSA/tests/testthat/test_LWCompPreds_MSG.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_LWCompPreds_OUT.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_PSD_MSG.R                    |only
 FSA-0.8.11/FSA/tests/testthat/test_PSD_OUT.R                    |only
 FSA-0.8.11/FSA/tests/testthat/test_PSD_VALIDATE.R               |only
 FSA-0.8.11/FSA/tests/testthat/test_StockRecruit_MSG.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_StockRecruit_OUT.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_Summarize_MSG.R              |only
 FSA-0.8.11/FSA/tests/testthat/test_Summarize_OUT_VALIDATE.R     |only
 FSA-0.8.11/FSA/tests/testthat/test_VonBertalanffy_MSG.R         |only
 FSA-0.8.11/FSA/tests/testthat/test_VonBertalanffy_OUT.R         |only
 FSA-0.8.11/FSA/tests/testthat/test_VonBertalanffy_VALIDATE.R    |only
 FSA-0.8.11/FSA/tests/testthat/test_WSWR_MSG.R                   |only
 FSA-0.8.11/FSA/tests/testthat/test_WSWR_OUT.R                   |only
 FSA-0.8.11/FSA/tests/testthat/test_WSWR_VALIDATE.R              |only
 FSA-0.8.11/FSA/tests/testthat/test_addZeroCatch_MSG.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_addZeroCatch_OUT.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_addZeroCatch_VALIDATE.R      |only
 FSA-0.8.11/FSA/tests/testthat/test_bcFuns_MSG.R                 |only
 FSA-0.8.11/FSA/tests/testthat/test_bcFuns_OUT.R                 |only
 FSA-0.8.11/FSA/tests/testthat/test_bootstrap_MSG.R              |only
 FSA-0.8.11/FSA/tests/testthat/test_bootstrap_OUT.R              |only
 FSA-0.8.11/FSA/tests/testthat/test_capHist_MSG.R                |only
 FSA-0.8.11/FSA/tests/testthat/test_capHist_OUT.R                |only
 FSA-0.8.11/FSA/tests/testthat/test_capHist_VALIDATE.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_ciDists_MSG.R                |only
 FSA-0.8.11/FSA/tests/testthat/test_ciDists_OUT.R                |only
 FSA-0.8.11/FSA/tests/testthat/test_ciDists_VALIDATE.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_comparisonsDVR_MSG.R         |only
 FSA-0.8.11/FSA/tests/testthat/test_comparisonsDVR_OUT.R         |only
 FSA-0.8.11/FSA/tests/testthat/test_depletion_MSG.R              |only
 FSA-0.8.11/FSA/tests/testthat/test_depletion_OUT.R              |only
 FSA-0.8.11/FSA/tests/testthat/test_depletion_VALIDATE.R         |only
 FSA-0.8.11/FSA/tests/testthat/test_dunnTest_MSG.R               |only
 FSA-0.8.11/FSA/tests/testthat/test_dunnTest_OUT.R               |only
 FSA-0.8.11/FSA/tests/testthat/test_dunnTest_VALIDATE.R          |only
 FSA-0.8.11/FSA/tests/testthat/test_expandCounts_MSG.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_expandCounts_OUT_VALIDATE.R  |only
 FSA-0.8.11/FSA/tests/testthat/test_expandLenFreq_MSG.R          |only
 FSA-0.8.11/FSA/tests/testthat/test_expandLenFreq_OUT_VALIDATE.R |only
 FSA-0.8.11/FSA/tests/testthat/test_extraTests_MSG.R             |only
 FSA-0.8.11/FSA/tests/testthat/test_extraTests_OUT.R             |only
 FSA-0.8.11/FSA/tests/testthat/test_extraTests_VALIDATE.R        |only
 FSA-0.8.11/FSA/tests/testthat/test_fitResidPlots_MSG.R          |only
 FSA-0.8.11/FSA/tests/testthat/test_fitResidPlots_OUT.R          |only
 FSA-0.8.11/FSA/tests/testthat/test_growthFuns_MSG.R             |only
 FSA-0.8.11/FSA/tests/testthat/test_growthFuns_OUT.R             |only
 FSA-0.8.11/FSA/tests/testthat/test_growthUtils_MSG.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_growthUtils_OUT.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_histFormula_MSG.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_histFormula_OUT.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_histFromSum_MSG.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_knitUtil_OUT.R               |only
 FSA-0.8.11/FSA/tests/testthat/test_ksTest_MSG.R                 |only
 FSA-0.8.11/FSA/tests/testthat/test_ksTest_OUT.R                 |only
 FSA-0.8.11/FSA/tests/testthat/test_ksTest_VALIDATE.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_lencat_MSG.R                 |only
 FSA-0.8.11/FSA/tests/testthat/test_lencat_OUT.R                 |only
 FSA-0.8.11/FSA/tests/testthat/test_lencat_VALIDATE.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_metaM_MSG.R                  |only
 FSA-0.8.11/FSA/tests/testthat/test_metaM_OUT.R                  |only
 FSA-0.8.11/FSA/tests/testthat/test_metaM_VALIDATE.R             |only
 FSA-0.8.11/FSA/tests/testthat/test_mrClosed_MSG.R               |only
 FSA-0.8.11/FSA/tests/testthat/test_mrClosed_OUT.R               |only
 FSA-0.8.11/FSA/tests/testthat/test_mrClosed_VALIDATE.R          |only
 FSA-0.8.11/FSA/tests/testthat/test_mrOpen_MSG.R                 |only
 FSA-0.8.11/FSA/tests/testthat/test_mrOpen_OUT.R                 |only
 FSA-0.8.11/FSA/tests/testthat/test_mrOpen_VALIDATE.R            |only
 FSA-0.8.11/FSA/tests/testthat/test_nlsTracePlot_MSG.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_nlsTracePlot_OUT.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_removal_MSG.R                |only
 FSA-0.8.11/FSA/tests/testthat/test_removal_OUT.R                |only
 FSA-0.8.11/FSA/tests/testthat/test_removal_VALIDATE.R           |only
 FSA-0.8.11/FSA/tests/testthat/test_sumTable_MSG.R               |only
 FSA-0.8.11/FSA/tests/testthat/test_sumTable_OUT_VALIDATE.R      |only
 209 files changed, 1689 insertions(+), 1231 deletions(-)

More information about FSA at CRAN
Permanent link

Package extremeStat updated to version 0.6.0 with previous version 0.5.16 dated 2016-05-12

Title: Extreme Value Statistics and Quantile Estimation
Description: Code to fit, plot and compare several (extreme value) distribution functions. Can also compute (truncated) distribution quantile estimates and draw a plot with return periods on a linear scale.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>

Diff between extremeStat versions 0.5.16 dated 2016-05-12 and 0.6.0 dated 2016-12-13

 DESCRIPTION                    |   12 +--
 MD5                            |   51 +++++++-------
 NAMESPACE                      |    2 
 NEWS                           |   25 +++++--
 R/distLextreme.R               |   30 ++++++++
 R/distLextremePlot.R           |    4 -
 R/distLfit.R                   |   15 +---
 R/distLgof.R                   |   43 ++++++++----
 R/distLgofPlot.R               |   40 ++++++-----
 R/distLplot.R                  |   18 ++---
 R/distLprint.R                 |    8 --
 R/distLquantile.R              |  146 +++++++++++++++++++++++++++--------------
 R/extremeStat-package.R        |    9 +-
 R/q_gpd.R                      |   87 ++++++++++++++++--------
 README.md                      |only
 build/vignette.rds             |binary
 inst/doc/extremeStat.Rmd       |    6 +
 inst/doc/extremeStat.html      |   31 ++++----
 man/distLextreme.Rd            |   20 +++++
 man/distLgof.Rd                |   22 ++++--
 man/distLgofPlot.Rd            |    7 +
 man/distLplot.Rd               |    2 
 man/distLquantile.Rd           |   85 ++++++++++++++++-------
 man/extremeStat.Rd             |    9 +-
 man/q_gpd.Rd                   |   39 +++++++---
 tests/testthat/test-quantile.R |   10 +-
 vignettes/extremeStat.Rmd      |    6 +
 27 files changed, 476 insertions(+), 251 deletions(-)

More information about extremeStat at CRAN
Permanent link

Package Directional updated to version 2.4 with previous version 2.3 dated 2016-10-26

Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Directional versions 2.3 dated 2016-10-26 and 2.4 dated 2016-12-13

 DESCRIPTION                |    8 +-
 MD5                        |  140 ++++++++++++++++++++++-----------------------
 NAMESPACE                  |    3 
 R/acg.R                    |    9 --
 R/bic.mixvmf.R             |    2 
 R/circ.cor1.R              |    2 
 R/circ.cor2.R              |    2 
 R/circ.summary.R           |    6 -
 R/circlin.cor.R            |    3 
 R/conc.test.R              |    5 -
 R/dirknn.R                 |   13 +---
 R/dirknn.tune.R            |   18 ++---
 R/embed.aov.R              |    6 -
 R/embed.circaov.R          |   10 +--
 R/ggvm.R                   |    5 -
 R/group.gof.R              |    4 -
 R/group.vm.R               |    2 
 R/hcf.aov.R                |    6 -
 R/hcf.circaov.R            |    6 -
 R/het.aov.R                |    9 --
 R/het.circaov.R            |    5 -
 R/kent.datacontour.R       |    8 +-
 R/knn.reg.R                |   39 ++----------
 R/knnreg.tune.R            |   31 ++++-----
 R/kuiper.R                 |    2 
 R/lambert.inv.R            |    1 
 R/lr.aov.R                 |   12 +--
 R/lr.circaov.R             |    4 -
 R/meandir.test.R           |   32 +++-------
 R/mediandir.R              |   11 ---
 R/mediandir_2.R            |   20 ++----
 R/mix.vmf.R                |    7 --
 R/mixvmf.contour.R         |   17 +----
 R/pvm.R                    |   21 ++----
 R/rayleigh.R               |   10 +--
 R/rmixvmf.R                |   12 ---
 R/rot.matrix.R             |    2 
 R/rvmf.R                   |   11 +--
 R/rvnomises.R              |    4 -
 R/spher.cor.R              |   17 +----
 R/spher.reg.R              |    4 -
 R/spherconc.test.R         |   10 +--
 R/spml.reg.R               |   53 ++++++-----------
 R/tang.conc.R              |    5 -
 R/vec.R                    |    3 
 R/visual.check.R           |    9 --
 R/vm.kde.R                 |    2 
 R/vmf.R                    |    6 -
 R/vmf.da.R                 |   14 +---
 R/vmf.kde.R                |    3 
 R/vmf.kerncontour.R        |    9 +-
 R/vmfda.pred.R             |    6 -
 R/vmfkde.tune.R            |    9 +-
 R/vmkde.tune.R             |    5 -
 R/watson.R                 |    2 
 R/wood.mle.R               |   49 +++++++--------
 man/Directional-package.Rd |    4 -
 man/acg.Rd                 |    2 
 man/circ.summary.Rd        |    2 
 man/circlin.cor.Rd         |    2 
 man/fishkent.Rd            |    2 
 man/hcf.aov.Rd             |    2 
 man/kent.mle.Rd            |    2 
 man/knn.reg.Rd             |    2 
 man/lambert.inv.Rd         |    2 
 man/meandir.test.Rd        |   11 +--
 man/quat2rot.Rd            |    2 
 man/rotation.Rd            |   17 ++++-
 man/spher.cor.Rd           |    4 -
 man/spml.reg.Rd            |    7 +-
 man/vec.Rd                 |    3 
 71 files changed, 326 insertions(+), 452 deletions(-)

More information about Directional at CRAN
Permanent link

Package Compositional updated to version 2.2 with previous version 2.0 dated 2016-10-11

Title: Compositional Data Analysis
Description: A collection of functions for compositional data analysis.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Compositional versions 2.0 dated 2016-10-11 and 2.2 dated 2016-12-13

 Compositional-2.0/Compositional/R/rmvnorm.R                  |only
 Compositional-2.0/Compositional/R/rmvt.R                     |only
 Compositional-2.0/Compositional/man/rmvnorm.Rd               |only
 Compositional-2.0/Compositional/man/rmvt.Rd                  |only
 Compositional-2.2/Compositional/DESCRIPTION                  |   10 
 Compositional-2.2/Compositional/MD5                          |  272 +++++------
 Compositional-2.2/Compositional/NAMESPACE                    |    3 
 Compositional-2.2/Compositional/R/alfa.R                     |   12 
 Compositional-2.2/Compositional/R/alfa.knn.R                 |   13 
 Compositional-2.2/Compositional/R/alfa.profile.R             |    6 
 Compositional-2.2/Compositional/R/alfa.rda.R                 |    2 
 Compositional-2.2/Compositional/R/alfa.reg.R                 |   79 +--
 Compositional-2.2/Compositional/R/alfa.ridge.R               |    5 
 Compositional-2.2/Compositional/R/alfa.tune.R                |    6 
 Compositional-2.2/Compositional/R/alfadist.R                 |    3 
 Compositional-2.2/Compositional/R/alfainv.R                  |   10 
 Compositional-2.2/Compositional/R/alfaknn.tune.R             |   30 -
 Compositional-2.2/Compositional/R/alfapcr.tune.R             |    6 
 Compositional-2.2/Compositional/R/alfarda.tune.R             |    8 
 Compositional-2.2/Compositional/R/alfareg.tune.R             |   22 
 Compositional-2.2/Compositional/R/alfaridge.plot.R           |    4 
 Compositional-2.2/Compositional/R/alfaridge.tune.R           |   12 
 Compositional-2.2/Compositional/R/bic.mixcompnorm.R          |   11 
 Compositional-2.2/Compositional/R/bivt.contour.R             |    8 
 Compositional-2.2/Compositional/R/comp.den.R                 |    5 
 Compositional-2.2/Compositional/R/comp.kerncontour.R         |    5 
 Compositional-2.2/Compositional/R/comp.knn.R                 |   18 
 Compositional-2.2/Compositional/R/comp.reg.R                 |   17 
 Compositional-2.2/Compositional/R/comp.test.R                |   30 -
 Compositional-2.2/Compositional/R/compknn.tune.R             |   49 -
 Compositional-2.2/Compositional/R/ddiri.R                    |   17 
 Compositional-2.2/Compositional/R/diri.contour.R             |    8 
 Compositional-2.2/Compositional/R/diri.est.R                 |   30 -
 Compositional-2.2/Compositional/R/diri.nr.R                  |   12 
 Compositional-2.2/Compositional/R/diri.reg.R                 |   73 +-
 Compositional-2.2/Compositional/R/diri.reg2.R                |   68 --
 Compositional-2.2/Compositional/R/dirimean.test.R            |   14 
 Compositional-2.2/Compositional/R/eel.test1.R                |   14 
 Compositional-2.2/Compositional/R/eel.test2.R                |   48 -
 Compositional-2.2/Compositional/R/el.test1.R                 |    1 
 Compositional-2.2/Compositional/R/el.test2.R                 |   11 
 Compositional-2.2/Compositional/R/frechet.R                  |    9 
 Compositional-2.2/Compositional/R/glm.pcr.R                  |   22 
 Compositional-2.2/Compositional/R/glmpcr.tune.R              |   43 -
 Compositional-2.2/Compositional/R/hotel1T2.R                 |   15 
 Compositional-2.2/Compositional/R/hotel2T2.R                 |    4 
 Compositional-2.2/Compositional/R/james.R                    |   13 
 Compositional-2.2/Compositional/R/js.compreg.R               |   60 --
 Compositional-2.2/Compositional/R/kl.compreg.R               |   63 --
 Compositional-2.2/Compositional/R/kl.diri.R                  |    2 
 Compositional-2.2/Compositional/R/maov.R                     |    6 
 Compositional-2.2/Compositional/R/maovjames.R                |    9 
 Compositional-2.2/Compositional/R/mix.compnorm.R             |    8 
 Compositional-2.2/Compositional/R/mixnorm.contour.R          |    8 
 Compositional-2.2/Compositional/R/mkde.R                     |    9 
 Compositional-2.2/Compositional/R/mkde.tune.R                |    6 
 Compositional-2.2/Compositional/R/multivreg.R                |   14 
 Compositional-2.2/Compositional/R/multivt.R                  |   17 
 Compositional-2.2/Compositional/R/norm.contour.R             |    8 
 Compositional-2.2/Compositional/R/ols.compreg.R              |   46 -
 Compositional-2.2/Compositional/R/pcr.R                      |   16 
 Compositional-2.2/Compositional/R/pcr.tune.R                 |   28 -
 Compositional-2.2/Compositional/R/rcompnorm.R                |    4 
 Compositional-2.2/Compositional/R/rcompsn.R                  |    4 
 Compositional-2.2/Compositional/R/rcompt.R                   |    2 
 Compositional-2.2/Compositional/R/rda.R                      |    8 
 Compositional-2.2/Compositional/R/rda.tune.R                 |   25 -
 Compositional-2.2/Compositional/R/rdiri.R                    |    2 
 Compositional-2.2/Compositional/R/ridge.plot.R               |   16 
 Compositional-2.2/Compositional/R/ridge.reg.R                |   27 -
 Compositional-2.2/Compositional/R/ridge.tune.R               |   52 --
 Compositional-2.2/Compositional/R/rmixcomp.R                 |   18 
 Compositional-2.2/Compositional/R/skewnorm.contour.R         |    5 
 Compositional-2.2/Compositional/R/spat.med.R                 |    5 
 Compositional-2.2/Compositional/R/spatmed.reg.R              |   54 --
 Compositional-2.2/Compositional/R/sscov.R                    |   10 
 Compositional-2.2/Compositional/R/sym.test.R                 |    4 
 Compositional-2.2/Compositional/R/ternary.R                  |   10 
 Compositional-2.2/Compositional/man/Compositional-package.Rd |    4 
 Compositional-2.2/Compositional/man/alfa.Rd                  |    3 
 Compositional-2.2/Compositional/man/alfa.pcr.Rd              |    7 
 Compositional-2.2/Compositional/man/alfa.profile.Rd          |    3 
 Compositional-2.2/Compositional/man/alfa.rda.Rd              |    3 
 Compositional-2.2/Compositional/man/alfa.reg.Rd              |   15 
 Compositional-2.2/Compositional/man/alfa.ridge.Rd            |    7 
 Compositional-2.2/Compositional/man/alfa.tune.Rd             |    3 
 Compositional-2.2/Compositional/man/alfadist.Rd              |    3 
 Compositional-2.2/Compositional/man/alfainv.Rd               |    3 
 Compositional-2.2/Compositional/man/alfapcr.tune.Rd          |   10 
 Compositional-2.2/Compositional/man/alfarda.tune.Rd          |    5 
 Compositional-2.2/Compositional/man/alfareg.tune.Rd          |    7 
 Compositional-2.2/Compositional/man/alfaridge.plot.Rd        |    7 
 Compositional-2.2/Compositional/man/alfaridge.tune.Rd        |    9 
 Compositional-2.2/Compositional/man/bic.mixcompnorm.Rd       |    7 
 Compositional-2.2/Compositional/man/bivt.contour.Rd          |    4 
 Compositional-2.2/Compositional/man/comp.den.Rd              |    4 
 Compositional-2.2/Compositional/man/comp.kerncontour.Rd      |    2 
 Compositional-2.2/Compositional/man/comp.knn.Rd              |    3 
 Compositional-2.2/Compositional/man/comp.reg.Rd              |   11 
 Compositional-2.2/Compositional/man/comp.test.Rd             |   18 
 Compositional-2.2/Compositional/man/compknn.tune.Rd          |    3 
 Compositional-2.2/Compositional/man/ddiri.Rd                 |    2 
 Compositional-2.2/Compositional/man/diri.contour.Rd          |    2 
 Compositional-2.2/Compositional/man/diri.est.Rd              |    4 
 Compositional-2.2/Compositional/man/diri.nr.Rd               |    2 
 Compositional-2.2/Compositional/man/diri.reg.Rd              |    7 
 Compositional-2.2/Compositional/man/eel.test1.Rd             |    4 
 Compositional-2.2/Compositional/man/eel.test2.Rd             |    8 
 Compositional-2.2/Compositional/man/el.test1.Rd              |    4 
 Compositional-2.2/Compositional/man/el.test2.Rd              |    6 
 Compositional-2.2/Compositional/man/frechet.Rd               |    3 
 Compositional-2.2/Compositional/man/glm.pcr.Rd               |    4 
 Compositional-2.2/Compositional/man/glmpcr.tune.Rd           |    4 
 Compositional-2.2/Compositional/man/hotel1T2.Rd              |   10 
 Compositional-2.2/Compositional/man/hotel2T2.Rd              |   14 
 Compositional-2.2/Compositional/man/james.Rd                 |    8 
 Compositional-2.2/Compositional/man/kl.compreg.Rd            |    7 
 Compositional-2.2/Compositional/man/maov.Rd                  |    6 
 Compositional-2.2/Compositional/man/maovjames.Rd             |    6 
 Compositional-2.2/Compositional/man/mix.compnorm.Rd          |    2 
 Compositional-2.2/Compositional/man/mixnorm.contour.Rd       |    2 
 Compositional-2.2/Compositional/man/mkde.Rd                  |    4 
 Compositional-2.2/Compositional/man/mkde.tune.Rd             |    2 
 Compositional-2.2/Compositional/man/multivreg.Rd             |    6 
 Compositional-2.2/Compositional/man/multivt.Rd               |    2 
 Compositional-2.2/Compositional/man/norm.contour.Rd          |    2 
 Compositional-2.2/Compositional/man/ols.compreg.Rd           |    5 
 Compositional-2.2/Compositional/man/pcr.Rd                   |    6 
 Compositional-2.2/Compositional/man/pcr.tune.Rd              |    6 
 Compositional-2.2/Compositional/man/rcompt.Rd                |    2 
 Compositional-2.2/Compositional/man/rda.Rd                   |    2 
 Compositional-2.2/Compositional/man/rda.tune.Rd              |    2 
 Compositional-2.2/Compositional/man/ridge.plot.Rd            |    4 
 Compositional-2.2/Compositional/man/ridge.reg.Rd             |    8 
 Compositional-2.2/Compositional/man/ridge.tune.Rd            |    6 
 Compositional-2.2/Compositional/man/skewnorm.contour.Rd      |    2 
 Compositional-2.2/Compositional/man/spatmed.reg.Rd           |   12 
 Compositional-2.2/Compositional/man/sscov.Rd                 |    2 
 Compositional-2.2/Compositional/man/ternary.Rd               |    4 
 139 files changed, 734 insertions(+), 1183 deletions(-)

More information about Compositional at CRAN
Permanent link

Package commonmark updated to version 1.1 with previous version 1.0 dated 2016-12-01

Title: High Performance CommonMark and Github Markdown Rendering in R
Description: The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. The latest version of this package also adds support for Github extensions including tables, autolinks and strikethrough text.
Author: Jeroen Ooms [aut, cre], John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between commonmark versions 1.0 dated 2016-12-01 and 1.1 dated 2016-12-13

 commonmark-1.0/commonmark/src/cmark/scanners.re           |only
 commonmark-1.0/commonmark/src/extensions/ext_scanners.re  |only
 commonmark-1.1/commonmark/DESCRIPTION                     |    6 
 commonmark-1.1/commonmark/MD5                             |   44 
 commonmark-1.1/commonmark/NEWS                            |    3 
 commonmark-1.1/commonmark/R/markdown.R                    |   12 
 commonmark-1.1/commonmark/man/commonmark.Rd               |   11 
 commonmark-1.1/commonmark/src/Makevars                    |    3 
 commonmark-1.1/commonmark/src/cmark/arena.c               |    2 
 commonmark-1.1/commonmark/src/cmark/blocks.c              |   16 
 commonmark-1.1/commonmark/src/cmark/buffer.c              |    4 
 commonmark-1.1/commonmark/src/cmark/case_fold_switch.inc  | 1972 +
 commonmark-1.1/commonmark/src/cmark/chunk.h               |   18 
 commonmark-1.1/commonmark/src/cmark/cmark.c               |    6 
 commonmark-1.1/commonmark/src/cmark/cmark_extension_api.h |    8 
 commonmark-1.1/commonmark/src/cmark/commonmark.c          |    6 
 commonmark-1.1/commonmark/src/cmark/html.c                |    4 
 commonmark-1.1/commonmark/src/cmark/inlines.c             |   24 
 commonmark-1.1/commonmark/src/cmark/node.c                |   16 
 commonmark-1.1/commonmark/src/cmark/parser.h              |    1 
 commonmark-1.1/commonmark/src/cmark/render.c              |    6 
 commonmark-1.1/commonmark/src/cmark/scanners.c            |19912 +++++---------
 commonmark-1.1/commonmark/src/extensions/autolink.c       |   33 
 commonmark-1.1/commonmark/src/extensions/table.c          |  262 
 24 files changed, 9706 insertions(+), 12663 deletions(-)

More information about commonmark at CRAN
Permanent link

New package chi2x3way with initial version 1.0
Package: chi2x3way
Type: Package
Title: Chi-Squared and Tau Index Partitions for Three-Way Contingency Tables
Version: 1.0
Date: 2016-12-12
Author: Rosaria Lombardo, Yoshio Takane and Eric J Beh
Maintainer: Rosaria Lombardo <rosaria.lombardo@unina2.it>
Description: Provides two index partitions for three-way contingency tables: partition of the association measure chi-squared and of the predictability index tau under several representative hypotheses about the expected frequencies (hypothesized probabilities).
Depends: R (> 3.3.0), methods, tools
LazyData: true
License: GPL (> 2)
URL: https://www.R-project.org
NeedsCompilation: no
Packaged: 2016-12-13 08:05:07 UTC; Amministratore
Repository: CRAN
Date/Publication: 2016-12-13 15:33:41

More information about chi2x3way at CRAN
Permanent link

New package bpp with initial version 1.0.0
Package: bpp
Type: Package
Title: Computations Around Bayesian Predictive Power
Version: 1.0.0
Date: 2016-12-13
Author: Kaspar Rufibach, Paul Jordan, Markus Abt
Maintainer: Kaspar Rufibach <kaspar.rufibach@roche.com>
Depends: mvtnorm, R (>= 2.10)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Description: Implements functions to update Bayesian Predictive Power Computations after not stopping a clinical trial at an interim analysis. Such an interim analysis can either be blinded or unblinded. Code is provided for Normally distributed endpoints with known variance, with a prominent example being the hazard ratio.
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-12-13 07:39:28 UTC; rufiback
Repository: CRAN
Date/Publication: 2016-12-13 15:33:39

More information about bpp at CRAN
Permanent link

Package bnstruct updated to version 1.0.2 with previous version 1.0.1 dated 2016-11-10

Title: Bayesian Network Structure Learning from Data with Missing Values
Description: Bayesian Network Structure Learning from Data with Missing Values. The package implements the Silander-Myllymaki complete search, the Max-Min Parents-and-Children, the Hill-Climbing, the Max-Min Hill-climbing heuristic searches, and the Structural Expectation-Maximization algorithm. Available scoring functions are BDeu, AIC, BIC. The package also implements methods for generating and using bootstrap samples, imputed data, inference.
Author: Francesco Sambo [aut, cre], Alberto Franzin [aut]
Maintainer: Francesco Sambo <francesco.sambo@unipd.it>

Diff between bnstruct versions 1.0.1 dated 2016-11-10 and 1.0.2 dated 2016-12-13

 bnstruct-1.0.1/bnstruct/man/write.xgmml.Rd                |only
 bnstruct-1.0.2/bnstruct/DESCRIPTION                       |    8 
 bnstruct-1.0.2/bnstruct/MD5                               |   54 ++-
 bnstruct-1.0.2/bnstruct/NAMESPACE                         |    5 
 bnstruct-1.0.2/bnstruct/R/AllClasses.R                    |   61 ++-
 bnstruct-1.0.2/bnstruct/R/AllGenerics.R                   |  121 +++++++
 bnstruct-1.0.2/bnstruct/R/BN-methods.R                    |   39 ++
 bnstruct-1.0.2/bnstruct/R/BNDataset-methods.R             |   69 ++++
 bnstruct-1.0.2/bnstruct/R/io-methods.R                    |   79 +++--
 bnstruct-1.0.2/bnstruct/R/learn-methods.R                 |  178 +++++++++++
 bnstruct-1.0.2/bnstruct/build/vignette.rds                |binary
 bnstruct-1.0.2/bnstruct/data/asia_10000.rda               |binary
 bnstruct-1.0.2/bnstruct/data/child_NA_5000.rda            |binary
 bnstruct-1.0.2/bnstruct/inst/doc/bnstruct.R               |  114 +++----
 bnstruct-1.0.2/bnstruct/inst/doc/bnstruct.Rnw             |  217 ++++++--------
 bnstruct-1.0.2/bnstruct/inst/doc/bnstruct.pdf             |binary
 bnstruct-1.0.2/bnstruct/inst/examples/dbn.R               |only
 bnstruct-1.0.2/bnstruct/inst/examples/test_bp_asia.R      |   60 ---
 bnstruct-1.0.2/bnstruct/inst/examples/test_bp_child.R     |   37 --
 bnstruct-1.0.2/bnstruct/inst/extdata/asia_2_layers.data   |only
 bnstruct-1.0.2/bnstruct/inst/extdata/asia_2_layers.header |only
 bnstruct-1.0.2/bnstruct/inst/scripts                      |only
 bnstruct-1.0.2/bnstruct/man/BN-class.Rd                   |    1 
 bnstruct-1.0.2/bnstruct/man/BNDataset-class.Rd            |   11 
 bnstruct-1.0.2/bnstruct/man/learn.dynamic.network.Rd      |only
 bnstruct-1.0.2/bnstruct/man/learn.network.Rd              |    5 
 bnstruct-1.0.2/bnstruct/man/learn.structure.Rd            |    2 
 bnstruct-1.0.2/bnstruct/man/num.time.steps-set.Rd         |only
 bnstruct-1.0.2/bnstruct/man/num.time.steps.Rd             |only
 bnstruct-1.0.2/bnstruct/man/read.dataset.Rd               |    7 
 bnstruct-1.0.2/bnstruct/man/write_xgmml.Rd                |only
 bnstruct-1.0.2/bnstruct/vignettes/andes_crosses.eps       |only
 bnstruct-1.0.2/bnstruct/vignettes/bnstruct.Rnw            |  217 ++++++--------
 33 files changed, 788 insertions(+), 497 deletions(-)

More information about bnstruct at CRAN
Permanent link

Package Bchron updated to version 4.2.6 with previous version 4.2.5 dated 2016-08-02

Title: Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling
Description: Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); Age-depth modelling as per the algorithm of Haslett and Parnell (2008) <DOI:10.1111/j.1467-9876.2008.00623.x>; Relative sea level rate estimation incorporating time uncertainty in polynomial regression models; and non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM). The package includes a vignette which explains most of the basic functionality.
Author: Andrew Parnell
Maintainer: Andrew Parnell <Andrew.Parnell@ucd.ie>

Diff between Bchron versions 4.2.5 dated 2016-08-02 and 4.2.6 dated 2016-12-13

 Bchron-4.2.5/Bchron/data/Glendalough.txt.gz              |only
 Bchron-4.2.5/Bchron/data/Sluggan.txt.gz                  |only
 Bchron-4.2.5/Bchron/data/TestChronData.txt.gz            |only
 Bchron-4.2.5/Bchron/data/TestRSLData.txt.gz              |only
 Bchron-4.2.5/Bchron/data/intcal13.txt.gz                 |only
 Bchron-4.2.5/Bchron/data/marine13.txt.gz                 |only
 Bchron-4.2.5/Bchron/data/normal.txt.gz                   |only
 Bchron-4.2.5/Bchron/data/shcal13.txt.gz                  |only
 Bchron-4.2.5/Bchron/man/Bchron-package.Rd                |only
 Bchron-4.2.6/Bchron/DESCRIPTION                          |   22 
 Bchron-4.2.6/Bchron/MD5                                  |  124 +-
 Bchron-4.2.6/Bchron/NAMESPACE                            |   43 
 Bchron-4.2.6/Bchron/R/Bchron.R                           |only
 Bchron-4.2.6/Bchron/R/BchronCalibrate.R                  |   65 +
 Bchron-4.2.6/Bchron/R/BchronDensity.R                    |   48 
 Bchron-4.2.6/Bchron/R/BchronDensityFast.R                |   35 
 Bchron-4.2.6/Bchron/R/BchronRSL.R                        |   49 
 Bchron-4.2.6/Bchron/R/Bchronology.R                      |  772 +++++++++++----
 Bchron-4.2.6/Bchron/R/CreateCalCurve.R                   |   41 
 Bchron-4.2.6/Bchron/R/SampleAges.R                       |   38 
 Bchron-4.2.6/Bchron/R/data.R                             |only
 Bchron-4.2.6/Bchron/R/hdr.R                              |   23 
 Bchron-4.2.6/Bchron/R/plot.BchronCalibratedDates.R       |   21 
 Bchron-4.2.6/Bchron/R/plot.BchronDensityRun.R            |   14 
 Bchron-4.2.6/Bchron/R/plot.BchronDensityRunFast.R        |   14 
 Bchron-4.2.6/Bchron/R/plot.BchronRSLRun.R                |   11 
 Bchron-4.2.6/Bchron/R/plot.BchronologyRun.R              |   20 
 Bchron-4.2.6/Bchron/R/predict.BchronologyRun.R           |  263 +++--
 Bchron-4.2.6/Bchron/R/summary.BchronCalibratedDates.R    |   20 
 Bchron-4.2.6/Bchron/R/summary.BchronDensityRun.R         |   11 
 Bchron-4.2.6/Bchron/R/summary.BchronRSLRun.R             |   38 
 Bchron-4.2.6/Bchron/R/summary.BchronologyRun.R           |   20 
 Bchron-4.2.6/Bchron/build/vignette.rds                   |binary
 Bchron-4.2.6/Bchron/data/Glendalough.rda                 |only
 Bchron-4.2.6/Bchron/data/Sluggan.rda                     |only
 Bchron-4.2.6/Bchron/data/TestChronData.rda               |only
 Bchron-4.2.6/Bchron/data/TestRSLData.rda                 |only
 Bchron-4.2.6/Bchron/data/intcal13.rda                    |only
 Bchron-4.2.6/Bchron/data/marine13.rda                    |only
 Bchron-4.2.6/Bchron/data/normal.rda                      |only
 Bchron-4.2.6/Bchron/data/shcal13.rda                     |only
 Bchron-4.2.6/Bchron/inst/doc/Bchron.R                    |   28 
 Bchron-4.2.6/Bchron/inst/doc/Bchron.Rmd                  |   41 
 Bchron-4.2.6/Bchron/inst/doc/Bchron.html                 |  110 +-
 Bchron-4.2.6/Bchron/man/Bchron.Rd                        |only
 Bchron-4.2.6/Bchron/man/BchronCalibrate.Rd               |   85 -
 Bchron-4.2.6/Bchron/man/BchronDensity.Rd                 |  102 -
 Bchron-4.2.6/Bchron/man/BchronDensityFast.Rd             |   72 -
 Bchron-4.2.6/Bchron/man/BchronRSL.Rd                     |   81 -
 Bchron-4.2.6/Bchron/man/Bchronology.Rd                   |  170 +--
 Bchron-4.2.6/Bchron/man/CreateCalCurve.Rd                |   51 
 Bchron-4.2.6/Bchron/man/Glendalough.Rd                   |   38 
 Bchron-4.2.6/Bchron/man/SampleAges.Rd                    |   37 
 Bchron-4.2.6/Bchron/man/Sluggan.Rd                       |   37 
 Bchron-4.2.6/Bchron/man/TestChronData.Rd                 |   41 
 Bchron-4.2.6/Bchron/man/TestRSLData.Rd                   |   35 
 Bchron-4.2.6/Bchron/man/hdr.Rd                           |   32 
 Bchron-4.2.6/Bchron/man/intcal13.Rd                      |   17 
 Bchron-4.2.6/Bchron/man/marine13.Rd                      |   17 
 Bchron-4.2.6/Bchron/man/normal.Rd                        |   15 
 Bchron-4.2.6/Bchron/man/plot.BchronCalibratedDates.Rd    |   78 -
 Bchron-4.2.6/Bchron/man/plot.BchronDensityRun.Rd         |   56 -
 Bchron-4.2.6/Bchron/man/plot.BchronDensityRunFast.Rd     |   41 
 Bchron-4.2.6/Bchron/man/plot.BchronRSLRun.Rd             |   34 
 Bchron-4.2.6/Bchron/man/plot.BchronologyRun.Rd           |   56 -
 Bchron-4.2.6/Bchron/man/predict.BchronologyRun.Rd        |   47 
 Bchron-4.2.6/Bchron/man/shcal13.Rd                       |   17 
 Bchron-4.2.6/Bchron/man/summary.BchronCalibratedDates.Rd |   42 
 Bchron-4.2.6/Bchron/man/summary.BchronDensityRun.Rd      |   39 
 Bchron-4.2.6/Bchron/man/summary.BchronRSLRun.Rd          |   40 
 Bchron-4.2.6/Bchron/man/summary.BchronologyRun.Rd        |   52 -
 Bchron-4.2.6/Bchron/src/Bchron.c                         |    1 
 Bchron-4.2.6/Bchron/vignettes/Bchron.Rmd                 |   41 
 73 files changed, 1981 insertions(+), 1264 deletions(-)

More information about Bchron at CRAN
Permanent link

Package admixturegraph updated to version 1.0.2 with previous version 1.0.1 dated 2016-08-16

Title: Admixture Graph Manipulation and Fitting
Description: Implements tools for building and visualising admixture graphs and for extracting equations from them. These equations can be compared to f- statistics obtained from data to test the consistency of a graph against data -- for example by comparing the sign of f_4-statistics with the signs predicted by the graph -- and graph parameters (edge lengths and admixture proportions) can be fitted to observed statistics.
Author: Thomas Mailund [cre, aut], Kalle Leppala [aut], Svend Nielsen [aut]
Maintainer: Thomas Mailund <mailund@birc.au.dk>

Diff between admixturegraph versions 1.0.1 dated 2016-08-16 and 1.0.2 dated 2016-12-13

 DESCRIPTION                                                       |   10 
 MD5                                                               |  163 
 NAMESPACE                                                         |   10 
 R/admixture_graph.R                                               |    4 
 R/agraph.R                                                        |   72 
 R/data.R                                                          |  137 
 R/fitting.R                                                       |    2 
 R/mcmc.R                                                          |  159 
 R/plot.R                                                          |   14 
 R/propose.R                                                       |11460 ++++++++--
 README.md                                                         |   76 
 build/vignette.rds                                                |binary
 data/datalist                                                     |only
 data/graphs_2_0.RData                                             |only
 data/graphs_3_0.RData                                             |only
 data/graphs_3_1.RData                                             |only
 data/graphs_4_0.RData                                             |only
 data/graphs_4_1.RData                                             |only
 data/graphs_4_2.RData                                             |only
 data/graphs_5_0.RData                                             |only
 data/graphs_5_1.RData                                             |only
 data/graphs_5_2.RData                                             |only
 data/graphs_6_0.RData                                             |only
 data/graphs_6_1.RData                                             |only
 data/graphs_6_2.RData                                             |only
 data/graphs_7_0.RData                                             |only
 data/graphs_7_1.RData                                             |only
 data/graphs_8_0.RData                                             |only
 inst/doc/admixturegraph.R                                         |  371 
 inst/doc/admixturegraph.Rmd                                       |  199 
 inst/doc/admixturegraph.html                                      |  856 
 man/add_a_leaf.Rd                                                 |   14 
 man/add_an_admixture.Rd                                           |   16 
 man/add_an_admixture2.Rd                                          |   14 
 man/admixturegraph-package.Rd                                     |    4 
 man/agraph.Rd                                                     |    8 
 man/all_graphs.Rd                                                 |only
 man/canonise_graph.Rd                                             |only
 man/eight_leaves_trees.Rd                                         |    9 
 man/fit_graph_list.Rd                                             |only
 man/fit_permutations_and_graphs.Rd                                |    4 
 man/five_leaves_graphs.Rd                                         |   19 
 man/four_leaves_graphs.Rd                                         |   17 
 man/graph_to_vector.Rd                                            |only
 man/graphs_2_0.Rd                                                 |only
 man/graphs_3_0.Rd                                                 |only
 man/graphs_3_1.Rd                                                 |only
 man/graphs_4_0.Rd                                                 |only
 man/graphs_4_1.Rd                                                 |only
 man/graphs_4_2.Rd                                                 |only
 man/graphs_5_0.Rd                                                 |only
 man/graphs_5_1.Rd                                                 |only
 man/graphs_5_2.Rd                                                 |only
 man/graphs_6_0.Rd                                                 |only
 man/graphs_6_1.Rd                                                 |only
 man/graphs_6_2.Rd                                                 |only
 man/graphs_7_0.Rd                                                 |only
 man/graphs_7_1.Rd                                                 |only
 man/graphs_8_0.Rd                                                 |only
 man/is_descendant_of.Rd                                           |only
 man/log_sum_of_logs.Rd                                            |   10 
 man/make_an_outgroup.Rd                                           |   10 
 man/make_mcmc_model.Rd                                            |    4 
 man/model_bayes_factor_n.Rd                                       |    4 
 man/model_likelihood_n.Rd                                         |    2 
 man/remove_duplicates.Rd                                          |only
 man/rename_nodes.Rd                                               |only
 man/run_metropolis_hasting.Rd                                     |   12 
 man/seven_leaves_graphs.Rd                                        |only
 man/seven_leaves_trees.Rd                                         |   38 
 man/six_leaves_graphs.Rd                                          |   15 
 man/vector_to_graph.Rd                                            |only
 vignettes/admixturegraph.Rmd                                      |  199 
 vignettes/admixturegraph_files/figure-html/bears_graph-1.png      |binary
 vignettes/admixturegraph_files/figure-html/new_admixtures-1.png   |binary
 vignettes/admixturegraph_files/figure-html/new_leaves-1.png       |binary
 vignettes/admixturegraph_files/figure-html/new_root-1.png         |binary
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-1-1.png  |binary
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-11-1.png |binary
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-12-1.png |binary
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-13-1.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-14-1.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-1.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-2.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-1.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-2.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-1.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-2.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-3.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-4.png |only
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-3-1.png  |binary
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-4-1.png  |binary
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-5-1.png  |binary
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-6-1.png  |binary
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-7-1.png  |binary
 vignettes/admixturegraph_files/figure-html/unnamed-chunk-9-1.png  |binary
 vignettes/admixturegraph_files/figure-latex                       |only
 97 files changed, 11609 insertions(+), 2323 deletions(-)

More information about admixturegraph at CRAN
Permanent link

Package ade4 updated to version 1.7-5 with previous version 1.7-4 dated 2016-03-01

Title: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences
Description: Multivariate data analysis and graphical display.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

Diff between ade4 versions 1.7-4 dated 2016-03-01 and 1.7-5 dated 2016-12-13

 ChangeLog                  |  139 +++++++++++++++++
 DESCRIPTION                |    8 -
 MD5                        |  354 ++++++++++++++++++++++-----------------------
 NAMESPACE                  |    8 -
 R/dudi.hillsmith.R         |   24 ++-
 R/dudi.pco.R               |    2 
 R/inertia.dudi.R           |  189 +++++++++++++++++-------
 R/nipals.R                 |    3 
 R/orthobasis.R             |    4 
 R/randtest.amova.R         |    4 
 R/scatterutil.R            |    9 -
 R/suprow.R                 |   87 ++++++++++-
 data/mafragh.rda           |binary
 man/PI2newick.Rd           |    3 
 man/ade4.package.Rd        |    3 
 man/adegraphicsLoaded.Rd   |    2 
 man/aminoacyl.Rd           |    3 
 man/apqe.Rd                |   93 +++++------
 man/ardeche.Rd             |    5 
 man/as.taxo.Rd             |    3 
 man/atlas.Rd               |    1 
 man/atya.Rd                |    3 
 man/avijons.Rd             |    5 
 man/aviurba.Rd             |    3 
 man/banque.Rd              |   14 -
 man/baran95.Rd             |    5 
 man/bca.rlq.Rd             |    2 
 man/between.Rd             |    5 
 man/betweencoinertia.Rd    |    2 
 man/buech.Rd               |    5 
 man/bwca.dpcoa.Rd          |    2 
 man/cailliez.Rd            |    3 
 man/carni70.Rd             |    3 
 man/carniherbi49.Rd        |    2 
 man/casitas.Rd             |    9 -
 man/cca.Rd                 |    5 
 man/chatcat.Rd             |    5 
 man/chats.Rd               |    3 
 man/clementines.Rd         |    7 
 man/coinertia.Rd           |    9 -
 man/combine.4thcorner.Rd   |    2 
 man/corkdist.Rd            |    3 
 man/costatis.Rd            |    1 
 man/costatis.randtest.Rd   |    1 
 man/discrimin.Rd           |    2 
 man/discrimin.coa.Rd       |    2 
 man/dist.binary.Rd         |    3 
 man/dist.dudi.Rd           |    3 
 man/dist.genet.Rd          |    9 -
 man/dist.ktab.Rd           |  311 +++++++++++++++++++--------------------
 man/dist.neig.Rd           |    3 
 man/dist.prop.Rd           |    3 
 man/dist.quant.Rd          |    3 
 man/divcmax.Rd             |    3 
 man/dotchart.phylog.Rd     |    3 
 man/doubs.Rd               |   11 -
 man/dpcoa.Rd               |    2 
 man/dudi.Rd                |    4 
 man/dudi.acm.Rd            |    2 
 man/dudi.coa.Rd            |    5 
 man/dudi.dec.Rd            |    9 -
 man/dudi.fca.Rd            |    7 
 man/dudi.hillsmith.Rd      |    4 
 man/dudi.mix.Rd            |    2 
 man/dudi.nsc.Rd            |    2 
 man/dudi.pca.Rd            |    2 
 man/dudi.pco.Rd            |    2 
 man/elec88.Rd              |    5 
 man/escopage.Rd            |    7 
 man/euro123.Rd             |    1 
 man/foucart.Rd             |    4 
 man/fourthcorner.Rd        |    2 
 man/fruits.Rd              |   11 -
 man/gearymoran.Rd          |    5 
 man/granulo.Rd             |    7 
 man/gridrowcol.Rd          |    9 -
 man/ichtyo.Rd              |    9 -
 man/inertia.dudi.Rd        |   54 ++++--
 man/is.euclid.Rd           |    9 -
 man/julliot.Rd             |    3 
 man/jv73.Rd                |    7 
 man/kdist.Rd               |    2 
 man/kdist2ktab.Rd          |    2 
 man/kdisteuclid.Rd         |    3 
 man/krandtest.Rd           |    2 
 man/ktab.Rd                |    4 
 man/ktab.data.frame.Rd     |    2 
 man/ktab.list.df.Rd        |    2 
 man/ktab.list.dudi.Rd      |    2 
 man/ktab.match2ktabs.Rd    |    5 
 man/ktab.within.Rd         |    2 
 man/lascaux.Rd             |    5 
 man/lingoes.Rd             |    5 
 man/macon.Rd               |    3 
 man/macroloire.Rd          |  161 ++++++++++----------
 man/mafragh.Rd             |   30 ++-
 man/mantel.rtest.Rd        |    3 
 man/mariages.Rd            |    5 
 man/mbpcaiv.Rd             |    2 
 man/mbpls.Rd               |    2 
 man/mcoa.Rd                |    5 
 man/mdpcoa.Rd              |    1 
 man/meau.Rd                |    5 
 man/meaudret.Rd            |    5 
 man/mfa.Rd                 |    5 
 man/microsatt.Rd           |   17 +-
 man/mjrochet.Rd            |    3 
 man/mld.Rd                 |    3 
 man/mollusc.Rd             |    3 
 man/monde84.Rd             |    3 
 man/morphosport.Rd         |    5 
 man/multiblock.Rd          |    2 
 man/multispati.Rd          |    2 
 man/multispati.randtest.Rd |    5 
 man/multispati.rtest.Rd    |    5 
 man/newick.eg.Rd           |    3 
 man/newick2phylog.Rd       |    3 
 man/niche.Rd               |    7 
 man/nipals.Rd              |    2 
 man/njplot.Rd              |    5 
 man/originality.Rd         |    1 
 man/orthobasis.Rd          |    5 
 man/orthogram.Rd           |    3 
 man/ours.Rd                |    9 -
 man/palm.Rd                |    3 
 man/pcaiv.Rd               |    5 
 man/pcaivortho.Rd          |    9 -
 man/pcw.Rd                 |    2 
 man/phylog.Rd              |    3 
 man/plot.between.Rd        |    7 
 man/plot.phylog.Rd         |    3 
 man/plot.within.Rd         |    9 -
 man/procuste.Rd            |    7 
 man/procuste.rtest.Rd      |    2 
 man/pta.Rd                 |    9 -
 man/quasieuclid.Rd         |    3 
 man/randboot.multiblock.Rd |    2 
 man/randtest.coinertia.Rd  |    3 
 man/randtest.pcaiv.Rd      |    4 
 man/reconst.Rd             |    2 
 man/rhone.Rd               |    3 
 man/rlq.Rd                 |    2 
 man/rpjdl.Rd               |    7 
 man/s.match.class.Rd       |    2 
 man/sarcelles.Rd           |    7 
 man/scalewt.Rd             |    2 
 man/scatter.Rd             |    2 
 man/scatter.fca.Rd         |    3 
 man/scatterutil.Rd         |    2 
 man/sco.class.Rd           |    2 
 man/sco.gauss.Rd           |    2 
 man/sco.label.Rd           |    2 
 man/sco.match.Rd           |    2 
 man/statico.Rd             |    5 
 man/statico.krandtest.Rd   |    1 
 man/steppe.Rd              |    5 
 man/supcol.Rd              |    2 
 man/suprow.Rd              |   18 +-
 man/symbols.phylog.Rd      |    3 
 man/syndicats.Rd           |    4 
 man/t3012.Rd               |    3 
 man/table.phylog.Rd        |    3 
 man/tarentaise.Rd          |    3 
 man/testdim.Rd             |    2 
 man/testdim.multiblock.Rd  |    2 
 man/trichometeo.Rd         |    5 
 man/ungulates.Rd           |    5 
 man/variance.phylog.Rd     |    3 
 man/veuvage.Rd             |    1 
 man/wca.rlq.Rd             |    2 
 man/westafrica.Rd          |   13 -
 man/within.Rd              |    7 
 man/withincoinertia.Rd     |    2 
 man/withinpca.Rd           |    7 
 man/witwit.coa.Rd          |    9 -
 man/woangers.Rd            |  197 ++++++++++++-------------
 man/worksurv.Rd            |    5 
 src/adesub.c               |    2 
 178 files changed, 1298 insertions(+), 1044 deletions(-)

More information about ade4 at CRAN
Permanent link

Package SoyNAM updated to version 1.3 with previous version 1.2 dated 2015-11-18

Title: Soybean Nested Association Mapping Dataset
Description: Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB), pre-formatted for general analysis and genome-wide association analysis using the NAM package.
Author: Alencar Xavier, William Beavis, James Specht, Brian Diers, Reka Howard, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>

Diff between SoyNAM versions 1.2 dated 2015-11-18 and 1.3 dated 2016-12-13

 DESCRIPTION           |   18 +++++++++++-------
 MD5                   |   12 ++++++------
 R/BLUP.R              |   22 ++++++++++++++++++++++
 data/soybase.RData    |binary
 data/soynam.RData     |binary
 man/BLUP.Rd           |    1 +
 man/SoyNAM-package.Rd |    4 ++--
 7 files changed, 42 insertions(+), 15 deletions(-)

More information about SoyNAM at CRAN
Permanent link

New package xaringan with initial version 0.1
Package: xaringan
Type: Package
Title: Presentation Ninja
Version: 0.1
Date: 2016-12-12
Authors@R: c( person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name"), person("Ole Petter", "Bang", role = "ctb", comment = "CSS in rmarkdown/templates/xaringan/resources/example.css") )
Description: Create HTML5 slides with R Markdown and the JavaScript library 'remark.js' (<https://remarkjs.com>).
Imports: htmltools, knitr, servr (>= 0.5), rmarkdown
Suggests: rstudioapi, testit
License: MIT + file LICENSE
URL: https://github.com/yihui/xaringan
BugReports: https://github.com/yihui/xaringan/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-12-13 07:00:26 UTC; yihui
Author: Yihui Xie [aut, cre], Ole Petter Bang [ctb] (CSS in rmarkdown/templates/xaringan/resources/example.css)
Maintainer: Yihui Xie <xie@yihui.name>
Repository: CRAN
Date/Publication: 2016-12-13 08:25:56

More information about xaringan at CRAN
Permanent link

Package timedelay updated to version 1.0.5 with previous version 1.0.4 dated 2016-11-29

Title: Time Delay Estimation for Stochastic Time Series of Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>

Diff between timedelay versions 1.0.4 dated 2016-11-29 and 1.0.5 dated 2016-12-13

 DESCRIPTION              |    8 +-
 MD5                      |    8 +-
 R/bayesian.R             |  172 ++++++++++++++++++++++++++++++++++++++++-------
 man/bayesian.Rd          |   31 +++++---
 man/timedelay-package.Rd |   18 ++++
 5 files changed, 194 insertions(+), 43 deletions(-)

More information about timedelay at CRAN
Permanent link

New package shinyFeedback with initial version 0.0.1
Package: shinyFeedback
Type: Package
Title: Displays User Feedback Next to Shiny Inputs
Version: 0.0.1
Date: 2016-12-12
Authors@R: person("Andy", "Merlino", email = "merlinoa88@gmail.com", role = c("aut", "cre"))
Description: Easily display user feedback next to Shiny inputs. The feedback message is displayed when the feedback condition evaluates to TRUE.
License: GPL-3
LazyData: true
Depends: R (>= 3.1.2)
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: shiny, digest
NeedsCompilation: no
Packaged: 2016-12-13 05:07:41 UTC; andy
Author: Andy Merlino [aut, cre]
Maintainer: Andy Merlino <merlinoa88@gmail.com>
Repository: CRAN
Date/Publication: 2016-12-13 07:57:21

More information about shinyFeedback at CRAN
Permanent link

Package sensitivity updated to version 1.13.0 with previous version 1.12.2 dated 2016-06-28

Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Gilles Pujol, Bertrand Iooss, Alexandre Janon with contributions from Khalid Boumhaout, Sebastien Da Veiga, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Bernardo Ramos, Olivier Roustant, Taieb Touati, Frank Weber, Roelof Oomen, Thibault Delage
Maintainer: Bertrand Iooss <biooss@yahoo.fr>

Diff between sensitivity versions 1.12.2 dated 2016-06-28 and 1.13.0 dated 2016-12-13

 DESCRIPTION                |   10 
 MD5                        |   69 ++--
 NAMESPACE                  |   19 +
 R/PLI.R                    |    5 
 R/PLIquantile.r            |only
 R/PoincareConstant.R       |   56 ++-
 R/PoincareOptimal.R        |only
 R/base.R                   |   65 ++++
 R/morris_sfd.R             |   30 +-
 R/sobolEff.R               |   46 ++-
 R/sobolSalt.R              |only
 R/sobolmartinez.R          |    4 
 R/sobolroa_subroutines.R   |only
 R/sobolroalhs.R            |  671 ++++++++++++++++++++-------------------------
 R/sobolroauc.R             |only
 man/PLI.Rd                 |   15 -
 man/PLIquantile.Rd         |only
 man/PoincareConstant.Rd    |  115 +++++--
 man/PoincareOptimal.Rd     |only
 man/morris.Rd              |    8 
 man/sensiFdiv.Rd           |    7 
 man/sensiHSIC.Rd           |    7 
 man/sensitivity-package.Rd |   16 -
 man/sobol.Rd               |    2 
 man/sobol2002.Rd           |    2 
 man/sobol2007.Rd           |    2 
 man/sobolCert.Rd           |    6 
 man/sobolEff.Rd            |   17 -
 man/sobolMultOut.Rd        |    2 
 man/sobolSalt.Rd           |only
 man/soboljansen.Rd         |    2 
 man/sobolmara.Rd           |    2 
 man/sobolmartinez.Rd       |    4 
 man/sobolowen.Rd           |    3 
 man/sobolroalhs.Rd         |   99 +++---
 man/sobolroauc.Rd          |only
 man/soboltouati.Rd         |    6 
 src/LG_Rowsort.cpp         |only
 src/LG_estimator.cpp       |only
 src/Makevars               |    2 
 src/as.cpp                 |    6 
 41 files changed, 743 insertions(+), 555 deletions(-)

More information about sensitivity at CRAN
Permanent link

Package RVAideMemoire updated to version 0.9-62 with previous version 0.9-61 dated 2016-10-31

Title: Diverse Basic Statistical and Graphical Functions
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Herv
Maintainer: Maxime Herv <mx.herve@gmail.com>

Diff between RVAideMemoire versions 0.9-61 dated 2016-10-31 and 0.9-62 dated 2016-12-13

 DESCRIPTION                  |    8 ++++----
 MD5                          |   12 ++++++------
 NEWS                         |    3 +++
 R/se.R                       |    2 +-
 R/zzz.R                      |    2 +-
 man/RVAideMemoire-package.Rd |    4 ++--
 man/se.Rd                    |    2 --
 7 files changed, 17 insertions(+), 16 deletions(-)

More information about RVAideMemoire at CRAN
Permanent link

Package RDML updated to version 0.9-5 with previous version 0.9-1 dated 2015-07-22

Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) format files and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization for the structure of RDML object and GUI for RDML editing.
Author: Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh <k.blag@yandex.ru>

Diff between RDML versions 0.9-1 dated 2015-07-22 and 0.9-5 dated 2016-12-13

 RDML-0.9-1/RDML/R/RDML.asserts.R                    |only
 RDML-0.9-5/RDML/CHANGELOG                           |   15 
 RDML-0.9-5/RDML/DESCRIPTION                         |   27 
 RDML-0.9-5/RDML/MD5                                 |  160 -
 RDML-0.9-5/RDML/NAMESPACE                           |   23 
 RDML-0.9-5/RDML/R/RDML.AsDendrogram.R               |   59 
 RDML-0.9-5/RDML/R/RDML.AsTable.R                    |  128 -
 RDML-0.9-5/RDML/R/RDML.GetFData.R                   |   53 
 RDML-0.9-5/RDML/R/RDML.Merge.R                      |   41 
 RDML-0.9-5/RDML/R/RDML.R                            |  183 -
 RDML-0.9-5/RDML/R/RDML.SetFData.R                   |  160 -
 RDML-0.9-5/RDML/R/RDML.init.R                       | 2041 ++++++++++------
 RDML-0.9-5/RDML/R/RDML.types.R                      | 2475 ++++++++++----------
 RDML-0.9-5/RDML/R/functional_wrappers.R             |    8 
 RDML-0.9-5/RDML/R/rdmlEdit.R                        |only
 RDML-0.9-5/RDML/README.md                           |   12 
 RDML-0.9-5/RDML/build/vignette.rds                  |binary
 RDML-0.9-5/RDML/inst/RDMLedit                       |only
 RDML-0.9-5/RDML/inst/doc/CreateRDML.R               |only
 RDML-0.9-5/RDML/inst/doc/CreateRDML.Rmd             |only
 RDML-0.9-5/RDML/inst/doc/CreateRDML.html            |only
 RDML-0.9-5/RDML/inst/doc/RDML.R                     |  299 ++
 RDML-0.9-5/RDML/inst/doc/RDML.Rmd                   |  144 -
 RDML-0.9-5/RDML/inst/doc/RDML.html                  |  870 ++++++-
 RDML-0.9-5/RDML/inst/extdata/from_abi7500           |only
 RDML-0.9-5/RDML/inst/extdata/from_tables            |only
 RDML-0.9-5/RDML/man/AsDendrogram-function.Rd        |    2 
 RDML-0.9-5/RDML/man/GetFData-function.Rd            |    2 
 RDML-0.9-5/RDML/man/MergeRDMLs.Rd                   |    4 
 RDML-0.9-5/RDML/man/RDML.Rd                         |  118 
 RDML-0.9-5/RDML/man/adpsType.Rd                     |   47 
 RDML-0.9-5/RDML/man/annotationType.Rd               |   14 
 RDML-0.9-5/RDML/man/asdendrogram-method.Rd          |   12 
 RDML-0.9-5/RDML/man/astable-function.Rd             |    2 
 RDML-0.9-5/RDML/man/astable-method.Rd               |   26 
 RDML-0.9-5/RDML/man/baseTemperatureType.Rd          |   28 
 RDML-0.9-5/RDML/man/cdnaSynthesisMethodType.Rd      |   17 
 RDML-0.9-5/RDML/man/commercialAssayType.Rd          |   14 
 RDML-0.9-5/RDML/man/cqDetectionMethodType.Rd        |   18 
 RDML-0.9-5/RDML/man/dataCollectionSoftwareType.Rd   |   18 
 RDML-0.9-5/RDML/man/dataType.Rd                     |   52 
 RDML-0.9-5/RDML/man/documentationType.Rd            |   12 
 RDML-0.9-5/RDML/man/dyeType.Rd                      |   12 
 RDML-0.9-5/RDML/man/enumType.Rd                     |   13 
 RDML-0.9-5/RDML/man/experimentType.Rd               |   12 
 RDML-0.9-5/RDML/man/experimenterType.Rd             |   20 
 RDML-0.9-5/RDML/man/getfdata-method.Rd              |   20 
 RDML-0.9-5/RDML/man/gradientType.Rd                 |   12 
 RDML-0.9-5/RDML/man/idReferencesType.Rd             |    8 
 RDML-0.9-5/RDML/man/idType.Rd                       |   12 
 RDML-0.9-5/RDML/man/labelFormatType.Rd              |   10 
 RDML-0.9-5/RDML/man/lidOpenType.Rd                  |    6 
 RDML-0.9-5/RDML/man/loopType.Rd                     |   14 
 RDML-0.9-5/RDML/man/mdpsType.Rd                     |   27 
 RDML-0.9-5/RDML/man/measureType.Rd                  |   10 
 RDML-0.9-5/RDML/man/new-method.Rd                   |   29 
 RDML-0.9-5/RDML/man/nucleotideType.Rd               |   14 
 RDML-0.9-5/RDML/man/oligoType.Rd                    |   14 
 RDML-0.9-5/RDML/man/pauseType.Rd                    |   10 
 RDML-0.9-5/RDML/man/pcrFormatType.Rd                |   25 
 RDML-0.9-5/RDML/man/primingMethodType.Rd            |   12 
 RDML-0.9-5/RDML/man/quantityType.Rd                 |   12 
 RDML-0.9-5/RDML/man/quantityUnitType.Rd             |   10 
 RDML-0.9-5/RDML/man/rdmlBaseType.Rd                 |   14 
 RDML-0.9-5/RDML/man/rdmlEdit.Rd                     |only
 RDML-0.9-5/RDML/man/rdmlIdType.Rd                   |   10 
 RDML-0.9-5/RDML/man/reactIdType.Rd                  |   12 
 RDML-0.9-5/RDML/man/reactType.Rd                    |   20 
 RDML-0.9-5/RDML/man/runType.Rd                      |   39 
 RDML-0.9-5/RDML/man/sampleType.Rd                   |   38 
 RDML-0.9-5/RDML/man/sampleTypeType.Rd               |   10 
 RDML-0.9-5/RDML/man/sequencesType.Rd                |    9 
 RDML-0.9-5/RDML/man/setfdata-function.Rd            |    2 
 RDML-0.9-5/RDML/man/setfdata-method.Rd              |   16 
 RDML-0.9-5/RDML/man/stepType.Rd                     |   12 
 RDML-0.9-5/RDML/man/targetType.Rd                   |   19 
 RDML-0.9-5/RDML/man/targetTypeType.Rd               |   10 
 RDML-0.9-5/RDML/man/temperatureType.Rd              |    6 
 RDML-0.9-5/RDML/man/templateQuantityType.Rd         |   10 
 RDML-0.9-5/RDML/man/thermalCyclingConditionsType.Rd |    8 
 RDML-0.9-5/RDML/man/xRefType.Rd                     |   12 
 RDML-0.9-5/RDML/vignettes/CreateRDML.Rmd            |only
 RDML-0.9-5/RDML/vignettes/RDML.Rmd                  |  144 -
 RDML-0.9-5/RDML/vignettes/RDML.bib                  |only
 RDML-0.9-5/RDML/vignettes/bench_df.csv              |only
 85 files changed, 4807 insertions(+), 2970 deletions(-)

More information about RDML at CRAN
Permanent link

Package prclust updated to version 1.3 with previous version 1.2 dated 2016-07-19

Title: Penalized Regression-Based Clustering Method
Description: Clustering is unsupervised and exploratory in nature. Yet, it can be performed through penalized regression with grouping pursuit. In this package, we provide two algorithms for fitting the penalized regression-based clustering (PRclust) with non-convex grouping penalties, such as group truncated lasso, MCP and SCAD. One algorithm is based on quadratic penalty and difference convex method. Another algorithm is based on difference convex and ADMM, called DC-ADD, which is more efficient. Generalized cross validation and stability based method were provided to select the tuning parameters. Rand index, adjusted Rand index and Jaccard index were provided to estimate the agreement between estimated cluster memberships and the truth.
Author: Chong Wu, Wei Pan
Maintainer: Chong Wu <wuxx0845@umn.edu>

Diff between prclust versions 1.2 dated 2016-07-19 and 1.3 dated 2016-12-13

 prclust-1.2/prclust/man/clustStat.Rd              |only
 prclust-1.3/prclust/DESCRIPTION                   |   10 
 prclust-1.3/prclust/MD5                           |   24 
 prclust-1.3/prclust/NAMESPACE                     |    7 
 prclust-1.3/prclust/R/GCVOrignial.R               |   45 -
 prclust-1.3/prclust/R/RcppExports.R               |  103 ++
 prclust-1.3/prclust/R/stability.R                 |   14 
 prclust-1.3/prclust/man/GCV.Rd                    |   49 -
 prclust-1.3/prclust/man/PRclust.Rd                |   60 -
 prclust-1.3/prclust/man/clusterStat.Rd            |only
 prclust-1.3/prclust/man/prclust-package.Rd        |   15 
 prclust-1.3/prclust/man/stability.Rd              |   13 
 prclust-1.3/prclust/src/ADMM_OrignialPRclust2.cpp |  817 ++++++++--------------
 prclust-1.3/prclust/src/RcppExports.cpp           |  144 ---
 14 files changed, 510 insertions(+), 791 deletions(-)

More information about prclust at CRAN
Permanent link

New package nricens with initial version 1.3
Package: nricens
Type: Package
Title: NRI for Risk Prediction Models with Time to Event and Binary Response Data
Version: 1.3
Date: 2016-12-12
Author: Eisuke Inoue
Depends: survival
Maintainer: Eisuke Inoue <inoue-ei@ncchd.go.jp>
Description: Calculating the net reclassification improvement (NRI) for risk prediction models with time to event and binary data.
License: GPL-2
NeedsCompilation: no
Packaged: 2016-12-12 04:33:59 UTC; inoue
Repository: CRAN
Date/Publication: 2016-12-13 08:04:31

More information about nricens at CRAN
Permanent link

New package LBSPR with initial version 0.1.0
Package: LBSPR
Title: Length-Based Spawning Potential Ratio
Version: 0.1.0
Authors@R: person("Adrian", "Hordyk", email = "ar.hordyk@gmail.com", role = c("aut", "cre"))
Description: Simulate expected equilibrium length composition, YPR, and SPR using the LBSPR model. Fit the LBSPR model to length data to estimate selectivity, relative fishing mortality, and spawning potential ratio for data-limited fisheries.
URL: https://github.com/AdrianHordyk/LBSPR
BugReports: https://github.com/AdrianHordyk/LBSPR/issues
Depends: R (>= 3.2.4)
License: GPL-3
LazyData: true
Imports: ggplot2, gridExtra, tidyr, RColorBrewer, plotrix, dplyr, graphics, methods, Rcpp
RoxygenNote: 5.0.1
LinkingTo: Rcpp
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-12-13 06:02:55 UTC; arhor
Author: Adrian Hordyk [aut, cre]
Maintainer: Adrian Hordyk <ar.hordyk@gmail.com>
Repository: CRAN
Date/Publication: 2016-12-13 08:25:51

More information about LBSPR at CRAN
Permanent link

Package KODAMA updated to version 1.2 with previous version 1.1 dated 2016-10-19

Title: Knowledge Discovery by Accuracy Maximization
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction from noisy and high-dimensional data.
Author: Stefano Cacciatore, Leonardo Tenori, Claudio Luchinat, Phillip R. Bennett, and David A. MacIntyre
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>

Diff between KODAMA versions 1.1 dated 2016-10-19 and 1.2 dated 2016-12-13

 DESCRIPTION          |    8 
 MD5                  |   60 +--
 NAMESPACE            |    2 
 R/KOD.R              |  275 ++++++++++----
 R/RcppExports.R      |  123 +++++-
 inst/doc/KODAMA.Rmd  |    2 
 inst/doc/KODAMA.pdf  |  950 ++++++++++++++++++++++++---------------------------
 man/KODAMA.Rd        |   19 -
 man/MetRef.Rd        |    7 
 man/USA.Rd           |    7 
 man/core_cpp.Rd      |    7 
 man/dinisurface.Rd   |    5 
 man/helicoid.Rd      |    5 
 man/k.test.Rd        |    6 
 man/knn.double.cv.Rd |   22 -
 man/knn.kodama.Rd    |   21 -
 man/loads.Rd         |    6 
 man/lymphoma.Rd      |    7 
 man/mcplot.Rd        |   12 
 man/normalization.Rd |    7 
 man/pls.double.cv.Rd |   19 -
 man/pls.kodama.Rd    |   23 -
 man/scaling.Rd       |    7 
 man/swissroll.Rd     |   12 
 man/transformy.Rd    |    7 
 src/RcppExports.cpp  |   74 +--
 src/Rsvm.c           |only
 src/cmeans.c         |only
 src/cshell.c         |only
 src/floyd.c          |only
 src/prova.cpp        |  371 +++++++++----------
 src/svm.cpp          |only
 src/svm.h            |only
 vignettes/KODAMA.Rmd |    2 
 34 files changed, 1146 insertions(+), 920 deletions(-)

More information about KODAMA at CRAN
Permanent link

Package GrapheR updated to version 1.9-86 with previous version 1.9-85 dated 2015-10-18

Title: A Multi-Platform GUI for Drawing Customizable Graphs in R
Description: A multi-platform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
Author: Maxime Herv
Maintainer: Maxime Herv <mx.herve@gmail.com>

Diff between GrapheR versions 1.9-85 dated 2015-10-18 and 1.9-86 dated 2016-12-13

 GrapheR-1.9-85/GrapheR/build                  |only
 GrapheR-1.9-85/GrapheR/inst/doc/manual_de.Rnw |only
 GrapheR-1.9-85/GrapheR/inst/doc/manual_en.Rnw |only
 GrapheR-1.9-85/GrapheR/inst/doc/manual_fr.Rnw |only
 GrapheR-1.9-86/GrapheR/DESCRIPTION            |    8 ++++----
 GrapheR-1.9-86/GrapheR/MD5                    |   14 +++++---------
 GrapheR-1.9-86/GrapheR/NEWS                   |    3 +++
 GrapheR-1.9-86/GrapheR/R/Sources.R            |   18 +++++++++---------
 GrapheR-1.9-86/GrapheR/R/zzzz.R               |    2 +-
 GrapheR-1.9-86/GrapheR/man/GrapheR-package.Rd |    4 ++--
 10 files changed, 24 insertions(+), 25 deletions(-)

More information about GrapheR at CRAN
Permanent link

New package FinancialMath with initial version 0.1.0
Package: FinancialMath
Type: Package
Title: Financial Mathematics for Actuaries
Version: 0.1.0
Authors@R: c(person("Kameron", "Penn", email = "rfinancialmathpkg@gmail.com",role = c("aut", "cre")),person("Jack", "Schmidt", email = "rfinancialmathpkg@gmail.com",role = "aut"))
Author: Kameron Penn [aut, cre], Jack Schmidt [aut]
Maintainer: Kameron Penn <rfinancialmathpkg@gmail.com>
Description: Contains financial math functions and introductory derivative functions included in the Society of Actuaries and Casualty Actuarial Society 'Financial Mathematics' exam, and some topics in the 'Models for Financial Economics' exam.
License: GPL-2
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2016-12-13 00:32:02 UTC; Kameron
Repository: CRAN
Date/Publication: 2016-12-13 07:56:47

More information about FinancialMath at CRAN
Permanent link

Package fields updated to version 8.7 with previous version 8.4-1 dated 2016-05-05

Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging and compact covariances for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range). A major feature is that any covariance function implemented in R and following a simple fields format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details in addition to the manual pages. The commented source code can be viewed by expanding the source code file (ending in tar.gz) and looking in the R subdirectory. Please cite fields along with its DOI in your publications!
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>

Diff between fields versions 8.4-1 dated 2016-05-05 and 8.7 dated 2016-12-13

 fields-8.4-1/fields/README                   |only
 fields-8.4-1/fields/src/dcopy.f              |only
 fields-8.4-1/fields/src/ddot.f               |only
 fields-8.4-1/fields/src/multeb.f             |only
 fields-8.4-1/fields/src/radfn2.f             |only
 fields-8.7/fields/DESCRIPTION                |    8 
 fields-8.7/fields/MD5                        |  125 +++++-----
 fields-8.7/fields/NAMESPACE                  |    1 
 fields-8.7/fields/R/Krig.family.R            |    2 
 fields-8.7/fields/R/MLESpatialProcess.R      |  327 ++++++---------------------
 fields-8.7/fields/R/MLESpatialProcess.fast.R |  102 --------
 fields-8.7/fields/R/fastTps.MLE.R            |  113 ---------
 fields-8.7/fields/R/fastTpsMLE.R             |only
 fields-8.7/fields/R/fields.mkpoly.R          |    8 
 fields-8.7/fields/R/mKrig.MLE.joint.R        |    5 
 fields-8.7/fields/R/mKrig.R                  |  163 ++++++++-----
 fields-8.7/fields/R/mKrig.family.R           |   39 ++-
 fields-8.7/fields/R/mKrigCheckXY.R           |only
 fields-8.7/fields/R/mKrigMLEGrid.R           |only
 fields-8.7/fields/R/mKrigMLEJoint.R          |only
 fields-8.7/fields/R/plot.spatialProcess.R    |   49 +---
 fields-8.7/fields/R/predictSurface.Krig.R    |    2 
 fields-8.7/fields/R/print.spatialProcess.R   |only
 fields-8.7/fields/R/sim.mKrig.approx.R       |    4 
 fields-8.7/fields/R/sim.spatialProcess.R     |only
 fields-8.7/fields/R/spatialProcess.R         |   77 ++++--
 fields-8.7/fields/R/splint.R                 |   16 -
 fields-8.7/fields/R/stationary.image.cov.R   |    5 
 fields-8.7/fields/R/summary.spatialProcess.R |   24 -
 fields-8.7/fields/man/MLESpatialProcess.Rd   |  277 ++++++++--------------
 fields-8.7/fields/man/REML.test.Rd           |    2 
 fields-8.7/fields/man/Tps.Rd                 |    2 
 fields-8.7/fields/man/bplot.Rd               |   19 -
 fields-8.7/fields/man/exp.cov.Rd             |   12 
 fields-8.7/fields/man/fields-internal.Rd     |   10 
 fields-8.7/fields/man/fields.Rd              |    2 
 fields-8.7/fields/man/mKrig.MLE.Rd           |  154 +++++-------
 fields-8.7/fields/man/mKrig.Rd               |  179 +++++++-------
 fields-8.7/fields/man/mKrigMLE.Rd            |only
 fields-8.7/fields/man/plot.Krig.Rd           |   17 -
 fields-8.7/fields/man/sim.Krig.Rd            |  105 ++++----
 fields-8.7/fields/man/spatialProcess.Rd      |  238 ++++++++++++++-----
 fields-8.7/fields/man/splint.Rd              |    5 
 fields-8.7/fields/src/css.f                  |   18 -
 fields-8.7/fields/src/csstr.f                |    6 
 fields-8.7/fields/src/cvrf.f                 |    8 
 fields-8.7/fields/src/dchold.f               |   16 -
 fields-8.7/fields/src/ddfind.f               |    2 
 fields-8.7/fields/src/dlv.f                  |    6 
 fields-8.7/fields/src/dmaket.f               |   15 -
 fields-8.7/fields/src/drdfun.f               |    3 
 fields-8.7/fields/src/dsetup.f               |   18 -
 fields-8.7/fields/src/expfn.f                |    2 
 fields-8.7/fields/src/ifind.f                |    7 
 fields-8.7/fields/src/igpoly.f               |   25 +-
 fields-8.7/fields/src/inpoly.f               |   30 +-
 fields-8.7/fields/src/mltdrb.f               |   27 +-
 fields-8.7/fields/src/multrb.f               |   15 -
 fields-8.7/fields/src/rcss.f                 |   10 
 fields-8.7/fields/src/rcssr.f                |    4 
 fields-8.7/fields/src/rcsswt.f               |    4 
 fields-8.7/fields/src/rdist.f                |    4 
 fields-8.7/fields/src/sortm.f                |   79 +++++-
 fields-8.7/fields/tests/Tps.test.R           |   42 ++-
 fields-8.7/fields/tests/cov.test.R           |   21 +
 fields-8.7/fields/tests/cov.test.Rout.save   |    9 
 fields-8.7/fields/tests/mKrig.MLE.test.R     |    3 
 fields-8.7/fields/tests/mKrig.Z.Rout.save    |    7 
 fields-8.7/fields/tests/mKrig.test.Rout.save |    8 
 fields-8.7/fields/tests/mKrigMLETest.R       |only
 70 files changed, 1201 insertions(+), 1280 deletions(-)

More information about fields at CRAN
Permanent link

Package fanc updated to version 2.2 with previous version 2.1 dated 2016-11-08

Title: Penalized Likelihood Factor Analysis via Nonconvex Penalty
Description: Computes the penalized maximum likelihood estimates of factor loadings and unique variances for various tuning parameters. The pathwise coordinate descent along with EM algorithm is used. This package also includes a new graphical tool which outputs path diagram, goodness-of-fit indices and model selection criteria for each regularization parameter. The user can change the regularization parameter by manipulating scrollbars, which is helpful to find a suitable value of regularization parameter.
Author: Kei Hirose, Michio Yamamoto, Haruhisa Nagata
Maintainer: Kei Hirose <mail@keihirose.com>

Diff between fanc versions 2.1 dated 2016-11-08 and 2.2 dated 2016-12-13

 DESCRIPTION   |    8 ++++----
 MD5           |    4 ++--
 R/plot.fanc.R |   26 ++++++++++----------------
 3 files changed, 16 insertions(+), 22 deletions(-)

More information about fanc at CRAN
Permanent link

Package electionsBR updated to version 0.2.0 with previous version 0.1.1 dated 2016-08-18

Title: R Functions to Download and Clean Brazilian Electoral Data
Description: Offers a set of functions that automatically downloads and aggregates election data from Brazil, directly from the Superior Electoral Court website. Among others, there are data available on local and federal elections for all positions (city councillor, mayor, state deputy, federal deputy, governor, and president) disaggregated by state of the Federation, city, zone, and polling stations. In addition, data on the verification (blank votes, null votes, abstention), candidates' and voters' backgrounds are also available.
Author: Denisson Silva [aut, cre], Fernando Meireles [aut], Beatriz Costa [ctb]
Maintainer: Denisson Silva <denissonsilva@ufmg.br>

Diff between electionsBR versions 0.1.1 dated 2016-08-18 and 0.2.0 dated 2016-12-13

 electionsBR-0.1.1/electionsBR/man/Moda.Rd                   |only
 electionsBR-0.1.1/electionsBR/man/juntaDados.Rd             |only
 electionsBR-0.1.1/electionsBR/man/test_fed_year.Rd          |only
 electionsBR-0.1.1/electionsBR/man/test_local_year.Rd        |only
 electionsBR-0.2.0/electionsBR/DESCRIPTION                   |   14 +-
 electionsBR-0.2.0/electionsBR/MD5                           |   58 ++++++------
 electionsBR-0.2.0/electionsBR/NAMESPACE                     |    7 -
 electionsBR-0.2.0/electionsBR/NEWS.md                       |only
 electionsBR-0.2.0/electionsBR/R/candidate_fed.R             |   19 ++-
 electionsBR-0.2.0/electionsBR/R/candidate_local.R           |   41 ++++++--
 electionsBR-0.2.0/electionsBR/R/details_mun_zone_fed.R      |   17 ++-
 electionsBR-0.2.0/electionsBR/R/details_mun_zone_local.R    |   41 +++++++-
 electionsBR-0.2.0/electionsBR/R/legend_fed.R                |   17 ++-
 electionsBR-0.2.0/electionsBR/R/legend_local.R              |   20 ++--
 electionsBR-0.2.0/electionsBR/R/party_mun_zone_fed.R        |   24 +++-
 electionsBR-0.2.0/electionsBR/R/party_mun_zone_local.R      |   31 +++++-
 electionsBR-0.2.0/electionsBR/R/utils.R                     |   46 ++++-----
 electionsBR-0.2.0/electionsBR/R/vote_mun_zone_fed.R         |   18 ++-
 electionsBR-0.2.0/electionsBR/R/vote_mun_zone_local.R       |   33 +++++-
 electionsBR-0.2.0/electionsBR/R/voter_affiliation.R         |only
 electionsBR-0.2.0/electionsBR/R/voter_profile.R             |only
 electionsBR-0.2.0/electionsBR/README.md                     |   23 +++-
 electionsBR-0.2.0/electionsBR/inst                          |only
 electionsBR-0.2.0/electionsBR/man/candidate_fed.Rd          |    7 +
 electionsBR-0.2.0/electionsBR/man/candidate_local.Rd        |   13 +-
 electionsBR-0.2.0/electionsBR/man/details_mun_zone_fed.Rd   |    7 +
 electionsBR-0.2.0/electionsBR/man/details_mun_zone_local.Rd |   11 +-
 electionsBR-0.2.0/electionsBR/man/legend_fed.Rd             |    7 +
 electionsBR-0.2.0/electionsBR/man/legend_local.Rd           |    9 +
 electionsBR-0.2.0/electionsBR/man/party_mun_zone_fed.Rd     |    7 +
 electionsBR-0.2.0/electionsBR/man/party_mun_zone_local.Rd   |   10 +-
 electionsBR-0.2.0/electionsBR/man/vote_mun_zone_fed.Rd      |    7 +
 electionsBR-0.2.0/electionsBR/man/vote_mun_zone_local.Rd    |   10 +-
 electionsBR-0.2.0/electionsBR/man/voter_affiliation.Rd      |only
 electionsBR-0.2.0/electionsBR/man/voter_profile.Rd          |only
 35 files changed, 356 insertions(+), 141 deletions(-)

More information about electionsBR at CRAN
Permanent link

Package ECctmc updated to version 0.2.3 with previous version 0.2.2 dated 2016-08-12

Title: Simulation from Endpoint-Conditioned Continuous Time Markov Chains
Description: Draw sample paths for endpoint-conditioned continuous time Markov chains via modified rejection sampling or uniformization.
Author: Jon Fintzi [aut, cre]
Maintainer: Jon Fintzi <fintzij@uw.edu>

Diff between ECctmc versions 0.2.2 dated 2016-08-12 and 0.2.3 dated 2016-12-13

 DESCRIPTION                       |    8 -
 MD5                               |   26 +++--
 NAMESPACE                         |    5 -
 R/RcppExports.R                   |   29 +++++-
 R/sample_path.R                   |  161 ++++++++++++++++++++++------------
 build/vignette.rds                |binary
 inst/doc/ECctmc_vignette.html     |    6 -
 inst/include/ECctmc.h             |    8 -
 inst/include/ECctmc_RcppExports.h |  100 ++++++++++++++-------
 man/comp_expmat.Rd                |only
 man/sample_path.Rd                |    7 +
 man/sample_path_unif2.Rd          |    4 
 man/sample_path_unif3.Rd          |only
 src/RcppExports.cpp               |  173 +++++++++++++++++++++++++------------
 src/simulation_functions.cpp      |  177 ++++++++++++++++++++++++++++++++++++--
 15 files changed, 527 insertions(+), 177 deletions(-)

More information about ECctmc at CRAN
Permanent link

Package dyn updated to version 0.2-9.1 with previous version 0.2-9 dated 2012-12-22

Title: Time Series Regression
Description: Time series regression. The dyn class interfaces ts, irts(), its, zoo() and zooreg() time series classes to lm(), glm(), loess(), quantreg::rq(), MASS::rlm(), MCMCpack::MCMCregress(), quantreg::rq(), randomForest::randomForest() and other regression functions allowing those functions to be used with time series including specifications that may contain lags, diffs and missing values.
Author: G. Grothendieck
Maintainer: M. Leeds <markleeds2@gmail.com>

Diff between dyn versions 0.2-9 dated 2012-12-22 and 0.2-9.1 dated 2016-12-13

 dyn-0.2-9.1/dyn/DESCRIPTION         |   17 +++++++++--------
 dyn-0.2-9.1/dyn/MD5                 |   16 ++++++++--------
 dyn-0.2-9.1/dyn/NAMESPACE           |   35 +++++++++++++++++++++++++++++++++++
 dyn-0.2-9.1/dyn/NEWS                |   13 +++++++++++++
 dyn-0.2-9.1/dyn/R/dyn.R             |   17 +++++++++++++----
 dyn-0.2-9.1/dyn/R/model.frame.dyn.R |    4 ++++
 dyn-0.2-9.1/dyn/demo/dyn-rq.R       |    6 +++---
 dyn-0.2-9.1/dyn/inst/COPYRIGHTS     |only
 dyn-0.2-9.1/dyn/man/baltimore.Rd    |    8 +++-----
 dyn-0.2-9/dyn/COPYRIGHTS            |only
 10 files changed, 88 insertions(+), 28 deletions(-)

More information about dyn at CRAN
Permanent link

Package d3r updated to version 0.6.0 with previous version 0.5.0 dated 2016-11-23

Title: 'd3.js' Utilities for R
Description: Helper functions for using 'd3.js' in R.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Kent Russell [aut, cre] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between d3r versions 0.5.0 dated 2016-11-23 and 0.6.0 dated 2016-12-13

 d3r-0.5.0/d3r/man/change_to_id.Rd           |only
 d3r-0.6.0/d3r/DESCRIPTION                   |    8 ++--
 d3r-0.6.0/d3r/MD5                           |   12 ++++---
 d3r-0.6.0/d3r/NEWS.md                       |   12 +++++++
 d3r-0.6.0/d3r/R/hierarchy.R                 |   39 ++++++++++++-----------
 d3r-0.6.0/d3r/inst/examples/fromd3jsonWIP.R |only
 d3r-0.6.0/d3r/inst/examples/jqr_d3r.R       |only
 d3r-0.6.0/d3r/man/change_to_name.Rd         |only
 d3r-0.6.0/d3r/tests/testthat/test_hier.R    |   46 +++++++++++++++-------------
 9 files changed, 69 insertions(+), 48 deletions(-)

More information about d3r at CRAN
Permanent link

Package adephylo updated to version 1.1-10 with previous version 1.1-6 dated 2013-11-30

Title: Adephylo: Exploratory Analyses for the Phylogenetic Comparative Method
Description: Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
Author: Thibaut Jombart <t.jombart@imperial.ac.uk>, Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anders Ellern Bilgrau <abilgrau@math.aau.dk>
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>

Diff between adephylo versions 1.1-6 dated 2013-11-30 and 1.1-10 dated 2016-12-13

 adephylo-1.1-10/adephylo/ChangeLog                              |   15 
 adephylo-1.1-10/adephylo/DESCRIPTION                            |   31 -
 adephylo-1.1-10/adephylo/MD5                                    |  132 ++---
 adephylo-1.1-10/adephylo/NAMESPACE                              |   79 ++-
 adephylo-1.1-10/adephylo/R/abouheif.R                           |   98 +++
 adephylo-1.1-10/adephylo/R/adephylo-package.R                   |only
 adephylo-1.1-10/adephylo/R/bullseye.R                           |   70 ++
 adephylo-1.1-10/adephylo/R/dibas.R                              |  131 +++++
 adephylo-1.1-10/adephylo/R/distances.R                          |  136 +++++
 adephylo-1.1-10/adephylo/R/moran.R                              |   62 ++
 adephylo-1.1-10/adephylo/R/orthobasis.R                         |  115 ++++
 adephylo-1.1-10/adephylo/R/orthogram.R                          |  124 +++++
 adephylo-1.1-10/adephylo/R/partition.R                          |   80 +++
 adephylo-1.1-10/adephylo/R/ppca.R                               |  247 +++++++++-
 adephylo-1.1-10/adephylo/R/proximities.R                        |  130 +++++
 adephylo-1.1-10/adephylo/R/table.phylo4d.R                      |  120 ++++
 adephylo-1.1-10/adephylo/R/utils.R                              |  141 ++++-
 adephylo-1.1-10/adephylo/build/vignette.rds                     |binary
 adephylo-1.1-10/adephylo/data/carni19.RData                     |binary
 adephylo-1.1-10/adephylo/data/carni70.RData                     |binary
 adephylo-1.1-10/adephylo/data/lizards.RData                     |binary
 adephylo-1.1-10/adephylo/data/maples.RData                      |binary
 adephylo-1.1-10/adephylo/data/mjrochet.RData                    |binary
 adephylo-1.1-10/adephylo/data/palm.RData                        |binary
 adephylo-1.1-10/adephylo/data/procella.RData                    |binary
 adephylo-1.1-10/adephylo/data/tithonia.RData                    |binary
 adephylo-1.1-10/adephylo/data/ungulates.RData                   |binary
 adephylo-1.1-10/adephylo/inst/doc/adephylo.pdf                  |binary
 adephylo-1.1-10/adephylo/man/abouheif.Rd                        |  130 ++---
 adephylo-1.1-10/adephylo/man/adephylo-package.Rd                |only
 adephylo-1.1-10/adephylo/man/bullseye.Rd                        |  113 ++--
 adephylo-1.1-10/adephylo/man/carni19.Rd                         |   33 -
 adephylo-1.1-10/adephylo/man/carni70.Rd                         |   39 -
 adephylo-1.1-10/adephylo/man/dibas.Rd                           |   85 +--
 adephylo-1.1-10/adephylo/man/distRoot.Rd                        |   86 +--
 adephylo-1.1-10/adephylo/man/distTips.Rd                        |  112 ++--
 adephylo-1.1-10/adephylo/man/listDD.Rd                          |   46 +
 adephylo-1.1-10/adephylo/man/listTips.Rd                        |   37 -
 adephylo-1.1-10/adephylo/man/lizards.Rd                         |   59 +-
 adephylo-1.1-10/adephylo/man/maples.Rd                          |   39 -
 adephylo-1.1-10/adephylo/man/miscUtils.Rd                       |   51 +-
 adephylo-1.1-10/adephylo/man/mjrochet.Rd                        |   53 --
 adephylo-1.1-10/adephylo/man/moranIdx.Rd                        |   65 +-
 adephylo-1.1-10/adephylo/man/orthobasis.Rd                      |  136 ++---
 adephylo-1.1-10/adephylo/man/orthogram.Rd                       |  196 ++++---
 adephylo-1.1-10/adephylo/man/palm.Rd                            |   51 +-
 adephylo-1.1-10/adephylo/man/ppca.Rd                            |  229 ++++-----
 adephylo-1.1-10/adephylo/man/procella.Rd                        |   54 +-
 adephylo-1.1-10/adephylo/man/proxTips.Rd                        |  237 ++++-----
 adephylo-1.1-10/adephylo/man/sp.tips.Rd                         |   74 +-
 adephylo-1.1-10/adephylo/man/table.phylo4d.Rd                   |  181 ++++---
 adephylo-1.1-10/adephylo/man/tithonia.Rd                        |   69 +-
 adephylo-1.1-10/adephylo/man/treePart.Rd                        |   71 +-
 adephylo-1.1-10/adephylo/man/ungulates.Rd                       |   47 -
 adephylo-1.1-10/adephylo/src/adesub.c                           |   88 ---
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-012.pdf        |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-016.pdf        |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-018.pdf        |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-aboutest.pdf   |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-figFourBas.pdf |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-lm1.pdf        |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-loadings.pdf   |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-orthobas1.pdf  |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-pca1.pdf       |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-pca2.pdf       |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-phylo4d.pdf    |binary
 adephylo-1.1-10/adephylo/vignettes/figs/adephylo-resid.pdf      |binary
 adephylo-1.1-6/adephylo/TODO                                    |only
 adephylo-1.1-6/adephylo/man/adephylo.package.Rd                 |only
 69 files changed, 2799 insertions(+), 1293 deletions(-)

More information about adephylo at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.