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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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
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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(-)
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(-)
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(-)
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(-)
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 Hervé
Maintainer: Maxime Hervé <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(-)
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(-)
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(-)
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(-)
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 Hervé
Maintainer: Maxime Hervé <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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)