Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and exploration of data from
environmental monitoring programs. The package name stands for "water quality"
and reflects the original focus on time series data for physical and
chemical properties of water, as well as the plankton. Intended for programs
that sample approximately monthly at discrete stations, a feature of many
legacy data sets. Most of the functions should be useful for analysis of
similar-frequency time series regardless of the subject matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby <wq@fastmail.net>
Diff between wq versions 0.4.4 dated 2015-07-30 and 0.4.5 dated 2015-12-21
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 4 ++++ R/eofPlot.R | 2 +- build/vignette.rds |binary inst/doc/wq-package.pdf |binary man/wq-package.Rd | 6 +++--- 7 files changed, 19 insertions(+), 15 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>
Diff between visNetwork versions 0.1.2 dated 2015-10-30 and 0.2.0 dated 2015-12-21
DESCRIPTION | 8 MD5 | 106 +++++---- NAMESPACE | 4 NEWS | 11 R/visClustering.R | 40 +++ R/visConfigure.R | 17 + R/visDocumentation.R | 3 R/visEdges.R | 17 + R/visFit.R |only R/visFocus.R |only R/visGroups.R | 34 +- R/visHierarchicalLayout.R | 19 + R/visInteraction.R | 17 + R/visLayout.R | 22 + R/visLegend.R | 12 - R/visNetwork.R | 31 ++ R/visNetworkEvents.R | 12 - R/visNetworkProxy.R |only R/visNodes.R | 17 + R/visOptions.R | 264 +++++++++++++++++----- R/visPhysics.R | 17 + R/visRedraw.R |only README.md | 21 + inst/doc/Introduction-to-visNetwork.R | 2 inst/doc/Introduction-to-visNetwork.Rmd | 2 inst/doc/Introduction-to-visNetwork.html | 100 ++++---- inst/doc/network/index.html | 22 + inst/examples/all_examples.R | 29 ++ inst/htmlwidgets/lib/vis/vis.map | 2 inst/htmlwidgets/lib/vis/vis.min.css | 2 inst/htmlwidgets/lib/vis/vis.min.js | 42 +-- inst/htmlwidgets/visNetwork.js | 364 +++++++++++++++++++++++-------- inst/shiny/server.R | 69 ----- inst/shiny/src |only inst/shiny/ui.R | 23 - man/visConfigure.Rd | 3 man/visDocumentation.Rd | 3 man/visEdges.Rd | 3 man/visEvents.Rd | 3 man/visFit.Rd |only man/visFocus.Rd |only man/visGroups.Rd | 10 man/visHierarchicalLayout.Rd | 3 man/visInteraction.Rd | 3 man/visLayout.Rd | 3 man/visLegend.Rd | 3 man/visNetwork-shiny.Rd | 8 man/visNetwork.Rd | 3 man/visNetworkProxy.Rd |only man/visNodes.Rd | 3 man/visOptions.Rd | 84 ++++++- man/visPhysics.Rd | 3 man/visRedraw.Rd |only vignettes/Introduction-to-visNetwork.Rmd | 2 54 files changed, 1037 insertions(+), 429 deletions(-)
Title: A Toolbox for Systemic Risk
Description: A toolbox for systemic risk based on liabilities matrices. Contains
a Gibbs sampler for liabilities matrices where only row and column sums of the
liabilities matrix as well as some other fixed entries are observed. Includes models
for power law distribution on the degree distribution.
Author: Axel Gandy and Luitgard A.M. Veraart
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between systemicrisk versions 0.2 dated 2015-03-19 and 0.3 dated 2015-12-21
DESCRIPTION | 18 MD5 | 77 +- NAMESPACE | 22 R/ExponentialFitnessLinkFun.R |only R/HierarchicalModels.R |only R/RcppExports.R | 201 +++--- R/lib_ErdosRenyExponential_MCMC.R | 194 +++-- R/lib_FindFeasibleMatrix.R | 164 +++-- R/lib_Network_Evaluations.R | 408 ++++++------ build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/HierarchicalModels.R |only inst/doc/HierarchicalModels.Rmd |only inst/doc/HierarchicalModels.html |only inst/doc/Introduction.R | 72 +- inst/doc/Introduction.Rmd | 144 ++-- inst/doc/Introduction.html | 654 ++++++++++---------- man/ERE_step_cycle.Rd | 74 +- man/GibbsSteps_kcycle.Rd | 88 +- man/Model.Indep.p.lambda.Rd |only man/Model.additivelink.exponential.fitness.Rd |only man/Model.fitness.conditionalmeandegree.Rd |only man/Model.fitness.genlambdaparprior.Rd |only man/Model.fitness.meandegree.Rd |only man/Model.lambda.GammaPrior.Rd |only man/Model.lambda.Gammaprior_mult.Rd |only man/Model.lambda.constant.Rd |only man/Model.p.BetaPrior.Rd |only man/Model.p.Betaprior_mult.Rd |only man/Model.p.Fitness.Servedio.Rd |only man/Model.p.constant.Rd |only man/choosethin.Rd |only man/cloneMatrix.Rd | 66 +- man/default.Rd | 3 man/default_cascade.Rd | 2 man/default_clearing.Rd | 104 +-- man/diagnose.Rd |only man/findFeasibleMatrix.Rd |only man/findFeasibleMatrix_targetmean.Rd |only man/genL.Rd |only man/getfeasibleMatr.Rd | 58 - man/sample_ERE.Rd | 83 +- man/sample_HierarchicalModel.Rd |only man/steps_ERE.Rd | 81 +- src/RcppExports.cpp | 68 +- src/lib_FeasibleMatrix.cpp |only src/lib_sample_kcycle.cpp | 92 ++ tests/testthat.R | 1 tests/testthat/test-gibbs_kcycle.R | 50 - tests/testthat/test_FeasibleMatrix.R |only tests/testthat/test_HierarchicalModels.R |only tests/testthat/test_HierarchicalModels_choosethin.R |only vignettes/HierarchicalModels.Rmd |only vignettes/Introduction.Rmd | 144 ++-- 54 files changed, 1518 insertions(+), 1350 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between rms versions 4.4-0 dated 2015-09-28 and 4.4-1 dated 2015-12-21
DESCRIPTION | 8 - MD5 | 55 +++++----- NEWS | 13 ++ R/Glm.s | 34 +++--- R/Gls.s | 54 +++++----- R/bj.s | 226 ++++++++++++++++++++---------------------- R/contrast.s | 2 R/cph.s | 9 + R/ggplot.Predict.s | 21 ++- R/lrm.s | 79 +++++++------- R/npsurv.s | 39 +++++-- R/ols.s | 20 ++- R/orm.s | 8 + R/plot.nomogram.s | 2 R/residuals.lrm.s | 2 R/rms.s | 24 ++-- R/rms.trans.s | 148 +++++++++++++++------------ R/rmsMisc.s | 11 -- R/survplot.npsurv.s | 187 ++++++++++++++++++++-------------- R/survreg.distributions.s | 12 +- R/val.prob.s | 2 R/validate.ols.s | 2 README.md | 3 man/cph.Rd | 3 man/ggplot.Predict.Rd | 7 - man/npsurv.Rd | 37 ++++-- man/survplot.Rd | 64 +++++++++-- tests/anova-ols-mult-impute.r |only tests/latex.r |only tests/rms.r |only 30 files changed, 619 insertions(+), 453 deletions(-)
Title: Calculate Accurate Precision-Recall and ROC Curves
Description: Accurate calculations and visualization of Precision-Recall and ROC
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.1.1 dated 2015-12-04 and 0.2.0 dated 2015-12-21
DESCRIPTION | 8 +- MD5 | 54 +++++++++--------- R/etc_utils_autoplot.R | 134 +++++++++++++++++++-------------------------- R/etc_utils_fortify.R | 55 +++++++++--------- R/etc_utils_plot.R | 93 ++++++++++++++++--------------- R/g_auc.R | 34 ++++++----- R/main_evalmod.R | 77 ++++++++++++------------- R/mm2_join_data.R | 6 +- R/precrec.R | 90 +++++++++++++++--------------- README.md | 6 -- build/vignette.rds |binary inst/doc/introduction.R | 4 - inst/doc/introduction.Rmd | 9 +-- inst/doc/introduction.html | 26 ++++---- man/B1000.Rd | 12 ++-- man/B500.Rd | 12 ++-- man/IB1000.Rd | 12 ++-- man/IB500.Rd | 12 ++-- man/P10N10.Rd | 2 man/auc.Rd | 36 ++++++------ man/autoplot.Rd | 130 +++++++++++++++++++------------------------ man/evalmod.Rd | 77 ++++++++++++------------- man/fortify.Rd | 57 +++++++++---------- man/join_labels.Rd | 2 man/join_scores.Rd | 4 - man/plot.Rd | 95 +++++++++++++++++-------------- man/precrec.Rd | 36 ++++++------ vignettes/introduction.Rmd | 9 +-- 28 files changed, 532 insertions(+), 560 deletions(-)
Title: Cause-Specific Framework for Competing-Risk Analysis
Description: Numerical integration of cause-specific survival curves to arrive at cause-specific cumulative incidence functions,
with three usage modes: 1) Convenient API for parametric survival regression followed by competing-risk analysis, 2) API for
CFC, accepting user-specified survival functions in R, and 3) Same as 2, but accepting survival functions in C++.
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>
Diff between CFC versions 1.0.0 dated 2015-12-18 and 1.0.1 dated 2015-12-21
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/cfc_survreg.R | 2 +- inst/doc/cfc.pdf |binary vignettes/weib.cpp | 6 +++--- 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in
the Global Charcoal Database. Main functionalities includes data extraction
and sites selection, transformation and interpolation of the charcoal
records as well as compositing.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between paleofire versions 1.1.7 dated 2015-11-12 and 1.1.8 dated 2015-12-21
DESCRIPTION | 11 ++-- MD5 | 101 +++++++++++++++++++++---------------------- NAMESPACE | 8 ++- NEWS | 14 +++++ R/paleofire-package.R | 6 +- R/pfAddData.R | 71 +++++++++++++++++++++++++++--- R/pfGridding.R | 3 - R/pfTransform.R | 34 +++++++------- README.md | 2 build/vignette.rds |binary demo/example-1.R | 4 - inst/COPYING | 31 +++++++------ inst/THANKS | 2 inst/doc/paleofire-paper.pdf |binary man/checkGCDversion.Rd | 4 + man/contiguous.Rd | 4 + man/kdffreq.Rd | 9 ++- man/paleofire-internal.Rd | 3 - man/paleofire-package.Rd | 10 ++-- man/pfAddData.Rd | 15 +++--- man/pfBoxCox.Rd | 5 +- man/pfCircular.Rd | 4 + man/pfComposite.Rd | 4 + man/pfCompositeLF.Rd | 5 +- man/pfDiagnostic.Rd | 7 ++ man/pfDotMap.Rd | 16 +++--- man/pfExtract.Rd | 4 + man/pfGridding.Rd | 14 +++-- man/pfInteractive.Rd | 7 ++ man/pfKruskal.Rd | 4 + man/pfMinMax.Rd | 4 + man/pfPublication.Rd | 2 man/pfResolution.Rd | 4 + man/pfSimpleGrid.Rd | 50 +++++++++++---------- man/pfSiteSel.Rd | 9 ++- man/pfToKml.Rd | 4 + man/pfTransform.Rd | 5 +- man/plot.CHAR.Rd | 7 ++ man/plot.contiguous.Rd | 4 + man/plot.kdffreq.Rd | 12 ++--- man/plot.pfCircular.Rd | 4 + man/plot.pfComposite.Rd | 4 + man/plot.pfCompositeLF.Rd | 5 +- man/plot.pfGridding.Rd | 4 + man/plot.pfKruskal.Rd | 4 + man/plot.pfSiteSel.Rd | 5 +- man/plot.potveg.Rd | 10 ++-- man/potveg.Rd | 7 ++ man/pretreatment.Rd | 12 ++--- man/rbind.pfAddData.Rd |only man/summary.pfSiteSel.Rd | 4 + man/triCube.Rd | 4 + 52 files changed, 365 insertions(+), 201 deletions(-)
Title: Functions for Simple Fisheries Stock Assessment Methods
Description: Functions to perform a variety of simple fish stock assessment
methods. Detailed vignettes are available on the fishR website listed below.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.3 dated 2015-10-22 and 0.8.4 dated 2015-12-21
DESCRIPTION | 21 +-- MD5 | 205 ++++++++++++++++++------------------- NAMESPACE | 4 R/CIDists.R | 31 ++--- R/FSAUtils.R | 118 +++++++++++++++------ R/alkSummaries.R | 1 R/fitPlot.R | 14 +- R/lencat.R | 4 R/residPlot.R | 41 +++---- man/BluegillJL.Rd | 3 man/BrookTroutTH.Rd | 5 man/ChinookArg.Rd | 7 - man/CodNorwegian.Rd | 3 man/CutthroatAL.Rd | 5 man/Ecoli.Rd | 4 man/FSA-internals.Rd | 2 man/FSA.Rd | 2 man/FSAUtils.Rd | 3 man/Mirex.Rd | 10 - man/PSDlit.Rd | 3 man/PikeNY.Rd | 3 man/PikeNYPartial1.Rd | 13 +- man/SMBassLS.Rd | 9 - man/SMBassWB.Rd | 3 man/Schnute.Rd | 3 man/SpotVA1.Rd | 3 man/Subset.Rd | 3 man/Summarize.Rd | 7 - man/WR79.Rd | 3 man/WSlit.Rd | 3 man/WhitefishLC.Rd | 9 - man/addRadCap.Rd | 3 man/addZeroCatch.Rd | 5 man/ageBias.Rd | 11 + man/agePrecision.Rd | 3 man/alkAgeDist.Rd | 3 man/alkIndivAge.Rd | 3 man/alkMeanVar.Rd | 5 man/alkPlot.Rd | 7 - man/bcFuns.Rd | 3 man/binCI.Rd | 3 man/bootCase.Rd | 5 man/capHistConvert.Rd | 9 - man/capHistSum.Rd | 3 man/catchCurve.Rd | 3 man/chapmanRobson.Rd | 3 man/chooseColors.Rd | 3 man/col2rgbt.Rd | 3 man/compIntercepts.Rd | 11 + man/compSlopes.Rd | 11 + man/depletion.Rd | 3 man/dunnTest.Rd | 3 man/expandCounts.Rd | 9 - man/expandLenFreq.Rd | 5 man/extraTests.Rd | 5 man/fact2num.Rd | 3 man/fishR.Rd | 3 man/fitPlot.Rd | 3 man/fsaNews.Rd | 3 man/gConvert.Rd | 3 man/geomean.Rd |only man/growthModels.Rd | 5 man/headtail.Rd | 2 man/hist.formula.Rd | 3 man/hoCoef.Rd | 5 man/hyperCI.Rd | 3 man/knitUtil.Rd | 9 - man/ksTest.Rd | 3 man/lagratio.Rd | 3 man/lencat.Rd | 7 - man/logbtcf.Rd | 3 man/lwCompPreds.Rd | 5 man/mapvalues.Rd | 2 man/metaM.Rd | 7 - man/mrClosed.Rd | 5 man/mrOpen.Rd | 3 man/nlsBoot.Rd | 3 man/oddeven.Rd | 2 man/perc.Rd | 3 man/plotBinResp.Rd | 3 man/poiCI.Rd | 3 man/psdAdd.Rd | 3 man/psdCI.Rd | 3 man/psdCalc.Rd | 3 man/psdPlot.Rd | 3 man/psdVal.Rd | 3 man/rcumsum.Rd | 4 man/removal.Rd | 5 man/residPlot.Rd | 3 man/se.Rd | 3 man/srStarts.Rd | 3 man/stockRecruitment.Rd | 5 man/sumTable.Rd | 3 man/tictactoe.Rd | 5 man/validn.Rd | 3 man/vbStarts.Rd | 5 man/wrAdd.Rd | 5 man/wsVal.Rd | 3 tests/testthat/Rplots.pdf |binary tests/testthat/test_FSAUtils.R | 47 ++++++++ tests/testthat/test_Internals.R | 6 - tests/testthat/test_addZeroCatch.R | 2 tests/testthat/test_lencat.R | 4 tests/testthat/test_sumTable.R | 8 - 104 files changed, 536 insertions(+), 354 deletions(-)
Title: U.S. State Cartogram Heatmaps in R; an Alternative to Choropleth
Maps for USA States
Description: Cartogram heatmaps are an alternative to choropleth maps for USA States
and are based on work by the Washington Post graphics department in their report
on "The states most threatened by trade". "State bins" preserve as much of the
geographic placement of the states as possible but has the look and feel of a
traditional heatmap. Functions are provided that allow for use of a binned,
discrete scale, a continuous scale or manually specified colors depending on
what is needed for the underlying data.
Author: Bob Rudis (@hrbrmstr)
Maintainer: Bob Rudis <bob@rudis.net>
Diff between statebins versions 1.0 dated 2014-08-27 and 1.2.2 dated 2015-12-21
DESCRIPTION | 29 ++--- LICENSE | 2 MD5 | 17 +-- NAMESPACE | 40 ++++++- R/statebins-package.R | 12 ++ R/statebins.R | 235 +++++++++++++++++++++++++++++++++++++------- man/statebins-package.Rd | 3 man/statebins.Rd | 26 ++-- man/statebins_continuous.Rd | 25 ++-- man/statebins_manual.Rd |only 10 files changed, 304 insertions(+), 85 deletions(-)
Title: Statistical Comparison of Multiple Algorithms in Multiple
Problems
Description: Given a matrix with results of different algorithms for different
problems, the package uses statistical tests and corrections to assess the
differences between algorithms.
Author: Borja Calvo [aut, cre],
Guzman Santafe [aut]
Maintainer: Borja Calvo <borja.calvo@ehu.eus>
Diff between scmamp versions 0.2.4 dated 2015-12-01 and 0.2.5 dated 2015-12-21
DESCRIPTION | 15 +++--- MD5 | 93 ++++++++++++++++++++-------------------- R/loading_functions.R | 4 - R/plotting.R | 4 - R/scmamp.R | 2 README.md |only man/adjustBergmannHommel.Rd | 3 - man/adjustFinner.Rd | 3 - man/adjustHolland.Rd | 3 - man/adjustLi.Rd | 2 man/adjustRom.Rd | 2 man/adjustShaffer.Rd | 2 man/anovaTest.Rd | 3 - man/booleanMatrix.Rd | 3 - man/contrastEstimationMatrix.Rd | 4 - man/customPost.Rd | 2 man/data.blum.2015.Rd | 4 - man/data.gh.2008.Rd | 8 +-- man/data.gh.2010.Rd | 10 ++-- man/drawAlgorithmGraph.Rd | 3 - man/exhaustiveSets.Rd | 3 - man/filterData.Rd | 5 +- man/friedmanAlignedRanksPost.Rd | 2 man/friedmanAlignedRanksTest.Rd | 3 - man/friedmanPost.Rd | 2 man/friedmanTest.Rd | 3 - man/imanDavenportTest.Rd | 2 man/multipleComparisonTest.Rd | 34 ++++++-------- man/nemenyiTest.Rd | 2 man/plotCD.Rd | 3 - man/plotDensities.Rd | 5 +- man/plotPvalues.Rd | 3 - man/plotRanking.Rd | 3 - man/postHocTest.Rd | 35 +++++++-------- man/qqplotGaussian.Rd | 4 - man/quadePost.Rd | 3 - man/quadeTest.Rd | 3 - man/rankMatrix.Rd | 3 - man/readComparisonDir.Rd | 8 +-- man/readComparisonFile.Rd | 3 - man/readExperimentDir.Rd | 10 ++-- man/readExperimentFile.Rd | 2 man/scmamp.Rd | 6 +- man/summarizeData.Rd | 14 ++---- man/tukeyPost.Rd | 2 man/tukeyTest.Rd | 2 man/wilcoxonSignedTest.Rd | 2 man/writeTabular.Rd | 6 +- 48 files changed, 181 insertions(+), 162 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.1-1 dated 2015-11-02 and 1.1-3 dated 2015-12-21
ChangeLog | 1522 +++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 MD5 | 42 - R/ogr_write.R | 10 build/vignette.rds |binary configure | 18 data/GridsDatums.rda |binary inst/ChangeLog | 1522 +++++++++++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary inst/etc/obj_with_comments.RData |binary man/GridsDatums.Rd | 10 man/project.Rd | 25 man/spTransform-methods.Rd | 30 man/writeOGR.Rd | 5 src/Makevars.in | 1 src/Makevars.win | 10 src/OGR_write.cpp | 42 - src/ogrsource.cpp | 12 src/projectit.cpp | 2 tests/tripup.R | 65 - tests/tripup.Rout.save | 181 +++- 22 files changed, 3391 insertions(+), 116 deletions(-)
Title: Solve Nonlinear Optimization with Nonlinear Constraints
Description: Optimization for nonlinear objective and constraint functions. Linear or nonlinear equality and inequality constraints are allowed. It accepts the input parameters as a constrained matrix.
Author: Xianyan Chen <xychen@uga.edu>, Xiangrong Yin <yinxiangrong@uky.edu>
Maintainer: Xianyan Chen <xychen@uga.edu>
Diff between NlcOptim versions 0.2 dated 2015-10-26 and 0.3 dated 2015-12-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/NlcOptim.R | 17 ++++++++++------- man/NlcOptim.Rd | 6 +++--- 4 files changed, 19 insertions(+), 16 deletions(-)
Title: MOdelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the
mathematical and statistical modelling of bioassay data. They use advanced and
innovative methods for a valuable quantitative environmental risk assessment.
Author: Marie Laure Delignette-Muller [aut], Philippe Ruiz [aut], Sandrine
Charles [aut], Wandrille Duchemin [ctb], Christelle Lopes [ctb], Guillaume Kon-
Kam-king [ctb], Philippe Veber [aut]
Maintainer: Philippe Ruiz <philippe.ruiz@univ-lyon1.fr>
Diff between morse versions 2.1.0 dated 2015-12-14 and 2.1.1 dated 2015-12-21
DESCRIPTION | 8 ++--- MD5 | 28 ++++++++--------- NEWS | 6 +++ R/morse.R | 2 - R/plot.reproData.R | 2 - R/plot.reproFitTT.R | 2 - R/plot.survData.R | 2 - R/plot.survFitTT.R | 2 - inst/doc/modelling.pdf |binary inst/doc/tutorial.html | 78 ++++++++++++++++++++++++------------------------- man/morse-package.Rd | 2 - man/plot.reproData.Rd | 2 - man/plot.reproFitTT.Rd | 2 - man/plot.survData.Rd | 2 - man/plot.survFitTT.Rd | 2 - 15 files changed, 73 insertions(+), 67 deletions(-)
Title: Create Interactive Charts with the JavaScript 'MetricsGraphics'
Library
Description: Provides an 'htmlwidgets' interface to the
'MetricsGraphics.js' ('D3'-based) charting library which is geared towards
displaying time-series data. Chart types include line charts, scatterplots,
histograms and rudimentary bar charts. Support for laying out multiple charts
into a grid layout is also provided. All charts are interactive and many
have an option for line, label and region annotations.
Author: Bob Rudis [aut, cre],
Ali Almossawi [ctb, cph] (MetricsGraphics library),
Hamilton Ulmer [ctb, cph] (MetricsGraphics library),
Mozilla [cph] (MetricsGraphics library),
jQuery Foundation and contributors [ctb, cph] (jQuery library)
Maintainer: Bob Rudis <bob@rudis.net>
Diff between metricsgraphics versions 0.8.5 dated 2015-06-14 and 0.9.0 dated 2015-12-21
metricsgraphics-0.8.5/metricsgraphics/R/metricsgraphics-package.R |only metricsgraphics-0.8.5/metricsgraphics/R/metricsgraphics.R |only metricsgraphics-0.8.5/metricsgraphics/R/mjs_grid.R |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/addons |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/highlightjs-default.css |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/metricsgraphics-demo-dark.css |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/metricsgraphics-demo.css |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/railscasts.css |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metricsgraphics.yaml |only metricsgraphics-0.9.0/metricsgraphics/DESCRIPTION | 22 metricsgraphics-0.9.0/metricsgraphics/MD5 | 110 metricsgraphics-0.9.0/metricsgraphics/NAMESPACE | 5 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More information about metricsgraphics at CRAN
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Title: Interface to Dygraphs Interactive Time Series Charting Library
Description: An R interface to the 'dygraphs' JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between dygraphs versions 0.5 dated 2015-10-20 and 0.6 dated 2015-12-21
DESCRIPTION | 8 ++-- MD5 | 38 ++++++++++---------- R/annotation.R | 10 +++-- R/axis.R | 20 +++++++++- R/dygraph.R | 81 ++++++++++++++++++++++++++++--------------- R/event.R | 20 +++++++--- R/options.R | 6 +++ R/range-selector.R | 5 ++ R/series.R | 45 ++++++++++++++++++++++- R/shading.R | 14 ++++--- inst/NEWS | 11 +++++ inst/htmlwidgets/dygraphs.js | 71 ++++++++++++++++++++++--------------- man/dyAnnotation.Rd | 5 +- man/dyAxis.Rd | 10 ++++- man/dyEvent.Rd | 16 +++++--- man/dyOptions.Rd | 31 +++++++++------- man/dySeries.Rd | 5 ++ man/dyShading.Rd | 8 ++-- man/dygraph.Rd | 14 +++++-- tests/testthat/test-event.R | 4 +- 20 files changed, 286 insertions(+), 136 deletions(-)
Title: Comparative Phylogenetic Analyses of Diversification
Description: Contains a number of comparative phylogenetic methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of 'BiSSE' (Binary State
Speciation and Extinction) and its unresolved tree extensions,
'MuSSE' (Multiple State Speciation and Extinction), 'QuaSSE',
'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
models of discrete and continuous trait evolution and constant rate
speciation and extinction.
Author: Richard G. FitzJohn <fitzjohn@zoology.ubc.ca>, with 'GeoSSE' and
'ClaSSE' by Emma E. Goldberg <eeg@uic.edu>, and 'BiSSE-ness' by Karen
Magnuson-Ford.
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>
Diff between diversitree versions 0.9-7 dated 2014-02-20 and 0.9-8 dated 2015-12-21
DESCRIPTION | 37 ++++++++----------- MD5 | 74 ++++++++++++++++++++------------------ NAMESPACE | 13 ++++++ R/asr-bisse.R | 15 +++++++ R/asr.R | 12 ++++-- R/check.R | 2 - R/mcmc.R | 14 +++---- R/mle-methods.R | 4 +- R/mle.R | 10 ++--- R/model-bd.R | 4 +- R/model-pgls.R | 8 ++-- R/model-quasse-common.R | 2 - R/model-quasse.R | 6 +-- R/plot-alt-util.R | 4 +- R/plot-alt.R | 8 ++-- R/profiles-plot.R | 10 ++--- R/split.R | 8 +++- R/t.R | 8 ++-- R/time-machine.R | 13 +++--- build |only configure | 2 - configure.ac | 2 - inst/CONTRIBUTORS.md |only inst/tests/run-tests.R | 1 inst/tests/test-asr.R | 4 +- inst/tests/test-expm.R | 2 - inst/tests/test-mcmc.R | 2 - inst/tests/test-ode.R | 12 +++--- inst/tests/test-pgls.R | 2 - inst/tests/test-quasse-internal.R | 4 ++ inst/tests/test-quasse-split.R | 2 + inst/tests/test-quasse.R | 2 + inst/tests/test-time-machine.R | 2 - inst/tests/test-unresolved.R | 2 - inst/update-gh-pages.sh |only man/diversitree-package.Rd |only man/make.bisse.td.Rd | 2 - man/make.quasse.Rd | 2 - src/TimeMachine.cpp | 9 ++++ src/TimeMachine.h | 15 ++++--- 40 files changed, 188 insertions(+), 131 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.25 dated 2015-11-19 and 2.26 dated 2015-12-21
BDgraph-2.25/BDgraph/data/CellSignal.RData |only BDgraph-2.25/BDgraph/man/CellSignal.Rd |only BDgraph-2.26/BDgraph/DESCRIPTION | 8 ++++---- BDgraph-2.26/BDgraph/MD5 | 10 ++++------ BDgraph-2.26/BDgraph/inst/doc/BDgraph.pdf |binary BDgraph-2.26/BDgraph/inst/doc/vignette.pdf |binary BDgraph-2.26/BDgraph/vignettes/BDgraph.pdf |binary 7 files changed, 8 insertions(+), 10 deletions(-)
More information about surveyoutliers at CRAN
Permanent link
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.6.5 dated 2015-11-03 and 1.6.7 dated 2015-12-21
DESCRIPTION | 10 - MD5 | 16 - R/checkPrep.R | 24 +- R/linearRelation.R | 458 ++++++++++++++++++++++++++------------------------ R/timeAverage.R | 7 R/trendLevel.R | 21 ++ R/windRose.R | 2 man/linearRelation.Rd | 198 +++++++++++---------- man/trendLevel.Rd | 9 9 files changed, 405 insertions(+), 340 deletions(-)
Title: A Framework for Coalescent Simulation
Description: Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results.
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Author: Paul Staab [aut, cre],
Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between coala versions 0.2.1 dated 2015-11-17 and 0.3.0 dated 2015-12-21
coala-0.2.1/coala/R/tempfile.R |only coala-0.3.0/coala/DESCRIPTION | 34 - coala-0.3.0/coala/MD5 | 115 +++--- coala-0.3.0/coala/NAMESPACE | 10 coala-0.3.0/coala/NEWS.md | 27 + coala-0.3.0/coala/R/RcppExports.R | 53 +- coala-0.3.0/coala/R/feature_ignore_singletons.R |only coala-0.3.0/coala/R/feature_selection.R | 182 ++++++++-- coala-0.3.0/coala/R/import_popgenome.R |only coala-0.3.0/coala/R/segsites.R | 29 + coala-0.3.0/coala/R/simulator_class.R | 4 coala-0.3.0/coala/R/simulator_ms.R | 43 -- coala-0.3.0/coala/R/simulator_msms.R | 2 coala-0.3.0/coala/R/sumstat.R | 16 coala-0.3.0/coala/R/sumstat_four_gamete.R | 6 coala-0.3.0/coala/R/sumstat_jsfs.R | 19 - coala-0.3.0/coala/R/sumstat_nucleotide_div.R | 5 coala-0.3.0/coala/R/sumstat_seg_sites.R | 5 coala-0.3.0/coala/R/sumstat_sfs.R | 7 coala-0.3.0/coala/R/sumstat_tajimas_d.R | 5 coala-0.3.0/coala/R/sumstat_trees.R | 5 coala-0.3.0/coala/R/tools.R |only coala-0.3.0/coala/README.md | 32 + coala-0.3.0/coala/build/vignette.rds |binary coala-0.3.0/coala/inst/doc/coala-abc.html | 4 coala-0.3.0/coala/inst/doc/coala-data-import.R |only coala-0.3.0/coala/inst/doc/coala-data-import.Rmd |only coala-0.3.0/coala/inst/doc/coala-data-import.html |only coala-0.3.0/coala/inst/doc/coala-extend.html | 2 coala-0.3.0/coala/inst/doc/coala-install.Rmd | 6 coala-0.3.0/coala/inst/doc/coala-install.html | 9 coala-0.3.0/coala/inst/doc/coala-intro.html | 10 coala-0.3.0/coala/inst/example_fasta_files |only coala-0.3.0/coala/inst/include/coala.h | 8 coala-0.3.0/coala/man/activate_ms.Rd | 15 coala-0.3.0/coala/man/as.segsites.GENOME.Rd |only coala-0.3.0/coala/man/as.segsites.Rd |only coala-0.3.0/coala/man/calc_jsfs.Rd | 17 coala-0.3.0/coala/man/calc_sumstats_from_data.Rd | 10 coala-0.3.0/coala/man/conv_to_ms_arg.Rd | 22 + coala-0.3.0/coala/man/create_segsites.Rd | 38 +- coala-0.3.0/coala/man/feat_ignore_singletons.Rd |only coala-0.3.0/coala/man/feat_selection.Rd | 55 ++- coala-0.3.0/coala/man/sumstat_four_gamete.Rd | 7 coala-0.3.0/coala/man/sumstat_jsfs.Rd | 11 coala-0.3.0/coala/man/sumstat_nucleotide_div.Rd | 6 coala-0.3.0/coala/man/sumstat_seg_sites.Rd | 6 coala-0.3.0/coala/man/sumstat_sfs.Rd | 6 coala-0.3.0/coala/man/sumstat_tajimas_d.Rd | 6 coala-0.3.0/coala/man/sumstat_trees.Rd | 6 coala-0.3.0/coala/src/RcppExports.cpp | 19 - coala-0.3.0/coala/src/seg_sites.cpp | 35 + coala-0.3.0/coala/src/stat_jsfs.cpp | 82 ++-- coala-0.3.0/coala/src/stat_nucleotide_div.cpp | 7 coala-0.3.0/coala/tests/testthat/test-feature-ign-singletons.R |only coala-0.3.0/coala/tests/testthat/test-feature-mutation.R | 2 coala-0.3.0/coala/tests/testthat/test-feature-selection.R | 47 ++ coala-0.3.0/coala/tests/testthat/test-import-popgenome.R |only coala-0.3.0/coala/tests/testthat/test-simulator-ms.R | 9 coala-0.3.0/coala/tests/testthat/test-simulator-msms.R | 2 coala-0.3.0/coala/tests/testthat/test-sumstat-jsfs.R | 103 +++-- coala-0.3.0/coala/tests/testthat/test-sumstat-pi.R | 24 - coala-0.3.0/coala/tests/testthat/test-sumstat-tajimas-d.R | 24 - coala-0.3.0/coala/tests/testthat/test-tools.R |only coala-0.3.0/coala/vignettes/coala-data-import.Rmd |only coala-0.3.0/coala/vignettes/coala-install.Rmd | 6 66 files changed, 854 insertions(+), 349 deletions(-)
Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Description: Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non-Exclusive clades that includes a defined portion of non-target taxa.
Author: Timothy Stephens [aut, cre, trl] (R port),
Debashish Bhattacharya [aut],
Mark Ragan [aut],
Cheong Xin Chan [aut, cph] (Original Perl implementation)
Maintainer: Timothy Stephens <timothy.stephens1@uqconnect.edu.au>
Diff between PhySortR versions 1.0.2 dated 2015-12-16 and 1.0.3 dated 2015-12-21
DESCRIPTION | 16 MD5 | 12 NAMESPACE | 12 R/sortTrees.R | 1148 ++++++++++++++++++++++++------------------------- man/PhySortR.Rd | 4 man/convert.eNewick.Rd | 52 +- man/sortTrees.Rd | 228 ++++----- 7 files changed, 738 insertions(+), 734 deletions(-)
Title: Linear Time Series Analysis
Description: Methods of developing linear time series modelling.
Methods are given for loglikelihood computation, forecasting
and simulation.
Author: A.I. McLeod, Hao Yu, Zinovi Krougly
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Diff between ltsa versions 1.4.5 dated 2015-08-22 and 1.4.6 dated 2015-12-21
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NAMESPACE | 2 ++ NEWS | 3 +++ R/innovationVariance.R |only man/PredictionVariance.Rd | 7 ++++--- man/exactLoglikelihood.Rd | 20 +++++++++++++++----- man/innovationVariance.Rd |only 8 files changed, 35 insertions(+), 17 deletions(-)
Title: Redraw Base Graphics Using 'grid' Graphics
Description: Functions to convert a page of plots drawn with the
graphics package into identical output drawn with the grid package.
The result looks like the original graphics-based plot, but consists
of grid grobs and viewports that can then be manipulated with
grid functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridGraphics versions 0.1-3 dated 2015-02-09 and 0.1-5 dated 2015-12-21
DESCRIPTION | 9 +++-- MD5 | 20 ++++++------ NAMESPACE | 6 +++ R/axis.R | 54 ++++++++++++++++++--------------- R/graphics.R | 6 +++ R/plotdiff.R | 57 ++++++++++++++++++++++++----------- R/title.R | 2 - inst/NEWS.Rd | 27 ++++++++++++++++ inst/test-scripts/test-hist.POSIXt.R | 4 +- man/grid.echo.Rd | 9 +++-- man/plotdiff.Rd | 6 --- 11 files changed, 132 insertions(+), 68 deletions(-)
Title: Offers Various Swiss Maps as ggplot2 Objects
Description: Offers various swiss maps as ggplot2 objects and gives the
possibility to add layers of data on the maps. Data are publicly available
from the swiss federal statistical office.
Author: Sandro Petrillo Burri [aut, cre],
Eric Stephani [aut],
Lisa Bottinelli [ctb]
Maintainer: Sandro Petrillo Burri <gibo.gaf@gmail.com>
Diff between ggswissmaps versions 0.0.2 dated 2014-11-07 and 0.0.6 dated 2015-12-21
DESCRIPTION | 23 ++++++++++----- MD5 | 29 +++++++++++++----- NAMESPACE | 12 +------ NEWS | 26 ++++++++++++++++- R/ggswissmaps_data.R | 78 +++++++++++++++++++++++++++++++++++++++++++++++++-- R/ggswissmaps_funs.R |only README.md |only build |only data/datalist |only data/maps.rda |binary data/maps2.rda |only data/shp_df.rda |only inst |only man/ggswissmaps.Rd | 3 + man/maps.Rd | 7 ++-- man/maps2.Rd |only man/shp_df.Rd |only man/theme_white.Rd | 28 +++--------------- man/theme_white_f.Rd |only vignettes |only 20 files changed, 151 insertions(+), 55 deletions(-)
Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre],
Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>
Diff between clusrank versions 0.1-0 dated 2015-12-14 and 0.1-1 dated 2015-12-21
DESCRIPTION | 12 ++++-------- MD5 | 8 ++++---- inst/doc/clsrank.Rnw | 6 +++--- inst/doc/clsrank.pdf |binary vignettes/clsrank.Rnw | 6 +++--- 5 files changed, 14 insertions(+), 18 deletions(-)
Title: Boosting Conditional Logit Model
Description: A set of functions to fit a boosting conditional logit model.
Author: Haolun Shi and Guosheng Yin
Maintainer: Haolun Shi <shl2003@connect.hku.hk>
Diff between clogitboost versions 1.0 dated 2015-11-26 and 1.1 dated 2015-12-21
DESCRIPTION | 17 ++----- MD5 | 20 ++++---- R/clogitboost.R | 2 R/fitclogitboost.R | 102 ++++++++++++++++++++++++--------------------- R/plot.clogitboost.R | 4 - man/clogitboost.Rd | 30 ++++++------- man/marginal.Rd | 10 ++-- man/plot.clogitboost.Rd | 12 ++--- man/predict.clogitboost.Rd | 18 +++---- man/summary.clogitboost.Rd | 12 ++--- man/travel.Rd | 14 +++--- 11 files changed, 121 insertions(+), 120 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.3.0 dated 2015-09-28 and 3.3.1 dated 2015-12-21
DESCRIPTION | 10 ++- MD5 | 90 ++++++++++++++++----------------- NAMESPACE | 2 NEWS | 10 +++ R/choropleth.R | 46 ++++++++-------- README.md | 8 ++ build/vignette.rds |binary inst/doc/a-introduction.html | 2 inst/doc/b-state-choropleth.html | 6 +- inst/doc/c-county-choropleth.html | 8 +- inst/doc/d-country-choropleth.html | 6 +- inst/doc/f-world-bank-data.html | 6 +- inst/doc/h-creating-your-own-maps.html | 2 inst/doc/i-creating-admin1-maps.html | 6 +- man/Admin1Choropleth.Rd | 6 -- man/Choropleth.Rd | 6 -- man/CountryChoropleth.Rd | 6 -- man/CountyChoropleth.Rd | 6 -- man/CountyZoomChoropleth.Rd | 6 -- man/StateChoropleth.Rd | 6 -- man/USAChoropleth.Rd | 10 +-- man/admin1_choropleth.Rd | 24 ++++---- man/choroplethr.Rd | 8 +- man/choroplethr_acs.Rd | 8 +- man/choroplethr_animate.Rd | 2 man/choroplethr_wdi.Rd | 11 ++-- man/continental_us_states.Rd | 2 man/country_choropleth.Rd | 12 ++-- man/county_choropleth.Rd | 32 +++++------ man/county_choropleth_acs.Rd | 14 ++--- man/county_zoom_choropleth.Rd | 6 +- man/df_county_demographics.Rd | 2 man/df_japan_census.Rd | 2 man/df_pop_country.Rd | 2 man/df_pop_county.Rd | 2 man/df_pop_state.Rd | 2 man/df_president.Rd | 2 man/df_president_ts.Rd | 4 - man/df_state_demographics.Rd | 2 man/get_acs_data.Rd | 8 +- man/get_acs_df.Rd | 2 man/get_county_demographics.Rd | 4 - man/get_state_demographics.Rd | 4 - man/state_choropleth.Rd | 26 ++++----- man/state_choropleth_acs.Rd | 10 +-- man/zip_map.Rd | 8 +- 46 files changed, 225 insertions(+), 222 deletions(-)