Sat, 14 Dec 2019

Package comperes updated to version 0.2.3 with previous version 0.2.2 dated 2019-01-12

Title: Manage Competition Results
Description: Tools for storing and managing competition results. Competition is understood as a set of games in which players gain some abstract scores. There are two ways for storing results: in long (one row per game-player) and wide (one row per game with fixed amount of players) formats. This package provides functions for creation and conversion between them. Also there are functions for computing their summary and Head-to-Head values for players. They leverage grammar of data manipulation from 'dplyr'.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>

Diff between comperes versions 0.2.2 dated 2019-01-12 and 0.2.3 dated 2019-12-14

 DESCRIPTION                         |   30 -
 MD5                                 |   34 -
 NAMESPACE                           |   52 --
 NEWS.md                             |    5 
 R/data.R                            |    6 
 R/outer-methods.R                   |   55 --
 R/pairgames.R                       |    2 
 R/zzz.R                             |only
 build/vignette.rds                  |binary
 inst/doc/formats.R                  |   18 
 inst/doc/formats.html               |  496 +++++++++++++++++-------
 inst/doc/manipulation.R             |   28 -
 inst/doc/manipulation.html          |  739 +++++++++++++++++++++++-------------
 man/convert-pair-value.Rd           |    3 
 man/hp_survey.Rd                    |    6 
 man/reexports.Rd                    |    5 
 tests/testthat/test-head-to-head.R  |   14 
 tests/testthat/test-outer-methods.R |   11 
 tests/testthat/test-zzz.R           |only
 19 files changed, 915 insertions(+), 589 deletions(-)

More information about comperes at CRAN
Permanent link

Package rcheology updated to version 3.6.2.0 with previous version 3.6.1.0 dated 2019-07-07

Title: Data on Base Packages for Current and Previous Versions of R
Description: Provides a dataset of functions in all base packages of R versions 1.0.1 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

Diff between rcheology versions 3.6.1.0 dated 2019-07-07 and 3.6.2.0 dated 2019-12-14

 DESCRIPTION                              |    6 +++---
 MD5                                      |   14 +++++++-------
 NEWS.md                                  |    4 ++++
 README.md                                |    2 +-
 data/Rversions.rda                       |binary
 data/rcheology.rda                       |binary
 man/figures/README-unnamed-chunk-5-1.png |binary
 man/figures/README-unnamed-chunk-6-1.png |binary
 8 files changed, 15 insertions(+), 11 deletions(-)

More information about rcheology at CRAN
Permanent link

Package tidytree updated to version 0.3.1 with previous version 0.3.0 dated 2019-11-21

Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Bradley Jones [ctb], Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between tidytree versions 0.3.0 dated 2019-11-21 and 0.3.1 dated 2019-12-14

 DESCRIPTION            |    6 +++---
 MD5                    |   12 ++++++------
 NEWS.md                |    7 ++++++-
 R/groupOTU.R           |    5 +++++
 build/vignette.rds     |binary
 inst/doc/tidytree.R    |    2 +-
 inst/doc/tidytree.html |    4 ++--
 7 files changed, 23 insertions(+), 13 deletions(-)

More information about tidytree at CRAN
Permanent link

Package SPOT updated to version 2.0.5 with previous version 2.0.4 dated 2019-05-17

Title: Sequential Parameter Optimization Toolbox
Description: A set of tools for model based optimization and tuning of algorithms. It includes surrogate models, optimizers and design of experiment approaches. The main interface is spot, which uses sequentially updated surrogate models for the purpose of efficient optimization. The main goal is to ease the burden of objective function evaluations, when a single evaluation requires a significant amount of resources.
Author: Thomas Bartz-Beielstein [aut], Joerg Stork [aut], Martin Zaefferer [aut, cre], Margarita Rebolledo [ctb], Christian Lasarczyk [ctb], Joerg Ziegenhirt [ctb], Wolfgang Konen [ctb], Oliver Flasch [ctb], Patrick Koch [ctb], Martina Friese [ctb], Lorenzo Gentile [ctb], Frederik Rehbach [aut]
Maintainer: Martin Zaefferer <martin.zaefferer@gmx.de>

Diff between SPOT versions 2.0.4 dated 2019-05-17 and 2.0.5 dated 2019-12-14

 DESCRIPTION                                     |   20 
 MD5                                             |  256 +-
 NAMESPACE                                       |   21 
 R/buildCVModel.R                                |only
 R/buildKrigingDACE.R                            | 2902 ++++++++++++------------
 R/buildKrigingForrester.R                       |   24 
 R/buildRandomForest.R                           |    4 
 R/buildRanger.R                                 |only
 R/cyclone.R                                     |    2 
 R/evaluate.R                                    |   43 
 R/funOptimLecture.R                             |only
 R/infillExpectedImprovement.R                   |only
 R/infillGetFullPrediction.R                     |only
 R/package.R                                     |    4 
 R/plotFunction.R                                |    6 
 R/plotModel.R                                   |  114 
 R/plotSingleDimFunction.R                       |only
 R/satter.R                                      |   78 
 R/spot.R                                        |  660 ++---
 R/wrapper.R                                     |  116 
 README.md                                       |only
 data/dataGasSensor.RData                        |binary
 inst/consoleCallTrialScript.R                   |only
 man/OCBA.Rd                                     |   84 
 man/SPOT-package.Rd                             |  126 -
 man/buildCVModel.Rd                             |only
 man/buildEnsembleStack.Rd                       |  108 
 man/buildKriging.Rd                             |  236 -
 man/buildKrigingDACE.Rd                         |  134 -
 man/buildLM.Rd                                  |  104 
 man/buildLOESS.Rd                               |  100 
 man/buildRSM.Rd                                 |  100 
 man/buildRandomForest.Rd                        |   90 
 man/buildRanger.Rd                              |only
 man/calculationBarthMuschelknautz.Rd            |   48 
 man/calculationMothes.Rd                        |   44 
 man/checkForNAs.Rd                              |   38 
 man/checkFunEvalsDesignSize.Rd                  |   46 
 man/checkInputDimensionsionalityCorrect.Rd      |   38 
 man/checkInputTypesInControl.Rd                 |   30 
 man/checkLowerNotEqualsUpper.Rd                 |   36 
 man/checkLowerSmallerThanUpper.Rd               |   34 
 man/checkTypesOfInput.Rd                        |   42 
 man/corrcubic.Rd                                |   72 
 man/correxp.Rd                                  |   72 
 man/correxpg.Rd                                 |   72 
 man/corrgauss.Rd                                |   72 
 man/corrkriging.Rd                              |   70 
 man/corrlin.Rd                                  |   72 
 man/corrnoisygauss.Rd                           |   70 
 man/corrnoisykriging.Rd                         |   70 
 man/corrspherical.Rd                            |   72 
 man/corrspline.Rd                               |   72 
 man/daceEvalFit.Rd                              |   46 
 man/daceFixTheta.Rd                             |   64 
 man/daceGetFit.Rd                               |   84 
 man/daceLikelihood.Rd                           |   50 
 man/daceObjfunc.Rd                              |   78 
 man/dacePrepareFit.Rd                           |   68 
 man/daceStartParameters.Rd                      |   62 
 man/dataGasSensor.Rd                            |   94 
 man/descentSpotRSM.Rd                           |   52 
 man/designLHD.Rd                                |  106 
 man/designLHDNorm.Rd                            |   79 
 man/designUniformRandom.Rd                      |   84 
 man/duplicateAndReplicateHandling.Rd            |   64 
 man/evaluateModel.Rd                            |   46 
 man/expectedImprovement.Rd                      |   64 
 man/funCyclone.Rd                               |  121 -
 man/funOptimLecture.Rd                          |only
 man/funSphere.Rd                                |   40 
 man/infillExpectedImprovement.Rd                |only
 man/infillGetFullPrediction.Rd                  |only
 man/initialInputCheck.Rd                        |   56 
 man/krigingLikelihood.Rd                        |   70 
 man/linearAdaptedSE.Rd                          |only
 man/maxNearestNeighbourDistance.Rd              |only
 man/normalizeMatrix.Rd                          |   50 
 man/normalizeMatrix2.Rd                         |   58 
 man/objectiveFunctionEvaluation.Rd              |   72 
 man/optimDE.Rd                                  |   88 
 man/optimES.Rd                                  |  124 -
 man/optimGenoud.Rd                              |   88 
 man/optimLBFGSB.Rd                              |   92 
 man/optimLHD.Rd                                 |   92 
 man/optimNLOPTR.Rd                              |  120 
 man/plot.spotRSM.Rd                             |   34 
 man/plotData.Rd                                 |  131 -
 man/plotFunction.Rd                             |  172 -
 man/plotModel.Rd                                |  111 
 man/plotSingleDimFunction.Rd                    |only
 man/predict.cvModel.Rd                          |only
 man/predict.dace.Rd                             |  122 -
 man/predict.ensembleStack.Rd                    |   50 
 man/predict.kriging.Rd                          |   86 
 man/predict.spotLOESS.Rd                        |   54 
 man/predict.spotLinearModel.Rd                  |   38 
 man/predict.spotRSM.Rd                          |   50 
 man/predict.spotRandomForest.Rd                 |   38 
 man/predict.spotRanger.Rd                       |only
 man/predictKrigingReinterpolation.Rd            |  114 
 man/print.Rd                                    |   48 
 man/print.spotLOESS.Rd                          |   41 
 man/print.spotLinearModel.Rd                    |   34 
 man/print.spotRSM.Rd                            |   40 
 man/print.spotRandomForest.Rd                   |   34 
 man/print.spotRanger.Rd                         |only
 man/regpoly0.Rd                                 |   60 
 man/regpoly1.Rd                                 |   64 
 man/regpoly2.Rd                                 |   62 
 man/repairNonNumeric.Rd                         |   44 
 man/repeatsOCBA.Rd                              |   64 
 man/repmat.Rd                                   |   44 
 man/satter.Rd                                   |   68 
 man/spot.Rd                                     |  228 -
 man/spotAlgEs.Rd                                |  163 -
 man/spotAlgEsDominantReco.Rd                    |   53 
 man/spotAlgEsGetSuccessRate.Rd                  |   48 
 man/spotAlgEsHps.Rd                             |   44 
 man/spotAlgEsIndividualInitial.Rd               |   92 
 man/spotAlgEsInitParentPop.Rd                   |   92 
 man/spotAlgEsInterReco.Rd                       |   52 
 man/spotAlgEsInterRecoBeSw02.Rd                 |   48 
 man/spotAlgEsMarriage.Rd                        |   48 
 man/spotAlgEsMarriageWithReplace.Rd             |   48 
 man/spotAlgEsObjMutation.Rd                     |   34 
 man/spotAlgEsSelection.Rd                       |   50 
 man/spotAlgEsStratMutation.Rd                   |   54 
 man/spotAlgEsTermination.Rd                     |   66 
 man/spotControl.Rd                              |  125 -
 man/spotFillControlList.Rd                      |only
 man/spotHelpBslash.Rd                           |   40 
 man/spotLoop.Rd                                 |  104 
 man/wrapBatchTools.Rd                           |only
 man/wrapFunction.Rd                             |   76 
 man/wrapFunctionParallel.Rd                     |only
 man/wrapSystemCommand.Rd                        |only
 man/wrapSystem_parseMatrixToString.Rd           |only
 tests/testthat.R                                |    4 
 tests/testthat/test.000TestSetup.R              |only
 tests/testthat/test.buildCVModel.R              |only
 tests/testthat/test.infillExpectedImprovement.R |only
 tests/testthat/test.plots.R                     |only
 143 files changed, 5974 insertions(+), 5612 deletions(-)

More information about SPOT at CRAN
Permanent link

Package robustHD updated to version 0.6.1 with previous version 0.6.0 dated 2019-12-09

Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear model selection techniques based on least angle regression and sparse regression.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>

Diff between robustHD versions 0.6.0 dated 2019-12-09 and 0.6.1 dated 2019-12-14

 DESCRIPTION         |    8 ++++----
 MD5                 |   14 +++++++-------
 NEWS                |    5 +++++
 R/fastLasso.R       |    4 ++--
 R/test.R            |   15 ++++++++-------
 build/partial.rdb   |binary
 src/fastSparseLTS.h |    4 ++--
 src/robustHD_init.c |    8 ++++----
 8 files changed, 32 insertions(+), 26 deletions(-)

More information about robustHD at CRAN
Permanent link

Package RMySQL updated to version 0.10.18 with previous version 0.10.17 dated 2019-03-04

Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), David James [aut], Saikat DebRoy [aut], Hadley Wickham [aut], Jeffrey Horner [aut], RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between RMySQL versions 0.10.17 dated 2019-03-04 and 0.10.18 dated 2019-12-14

 DESCRIPTION |    6 +++---
 MD5         |    6 +++---
 NEWS.md     |    4 ++++
 configure   |    3 ---
 4 files changed, 10 insertions(+), 9 deletions(-)

More information about RMySQL at CRAN
Permanent link

Package RDS updated to version 0.9-2 with previous version 0.9-0 dated 2019-05-31

Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation with data collected using Respondent-Driven Sampling. This includes Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential Sampling estimator. The package is part of the "RDS Analyst" suite of packages for the analysis of respondent-driven sampling data. See Gile and Handcock (2010) <doi:10.1111/j.1467-9531.2010.01223.x> and Gile and Handcock (2015) <doi:10.1111/rssa.12091>.
Author: Mark S. Handcock [aut, cre], Krista J. Gile [aut], Ian E. Fellows [aut], W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>

Diff between RDS versions 0.9-0 dated 2019-05-31 and 0.9-2 dated 2019-12-14

 DESCRIPTION                            |   10 +--
 MD5                                    |   94 ++++++++++++++++-----------------
 NAMESPACE                              |    3 +
 R/MA.sampling-c.R                      |   61 ++++++++++-----------
 R/MA.util.R                            |    6 +-
 R/bootstrap-intervals.R                |    1 
 R/bootstrap.contingency.test.R         |    2 
 R/control.rds.estimates.R              |   21 +++++++
 R/control.utilities.R                  |   46 ++++++++++------
 R/hcg-bootstrap.R                      |   16 +++--
 R/hcg-util.R                           |   22 ++++---
 R/rds.interval.estimate.R              |   41 ++++++++++++--
 R/weights.R                            |   12 +++-
 man/LRT.trend.test.Rd                  |   13 +++-
 man/MA.estimates.Rd                    |   31 ++++++++--
 man/RDS.HCG.estimates.Rd               |   13 +++-
 man/RDS.I.estimates.Rd                 |   13 +++-
 man/RDS.II.estimates.Rd                |   10 ++-
 man/RDS.Rd                             |    1 
 man/RDS.SS.estimates.Rd                |   16 ++++-
 man/RDS.bootstrap.intervals.Rd         |   23 +++++---
 man/RDS.compare.two.proportions.Rd     |   10 ++-
 man/as.rds.data.frame.Rd               |   26 +++++----
 man/bootstrap.contingency.test.Rd      |   13 +++-
 man/bootstrap.incidence.Rd             |   23 +++++---
 man/bottleneck.plot.Rd                 |   10 ++-
 man/compute.weights.Rd                 |   12 +++-
 man/control.rds.estimates.Rd           |   25 +++++++-
 man/convergence.plot.Rd                |   10 ++-
 man/cumulative.estimate.Rd             |    9 ++-
 man/differential.activity.estimates.Rd |   10 ++-
 man/get.h.hat.Rd                       |    7 +-
 man/get.recruitment.time.Rd            |    8 ++
 man/gile.ss.weights.Rd                 |   13 +++-
 man/hcg.weights.Rd                     |   20 ++++++-
 man/homophily.estimates.Rd             |   18 ++++--
 man/impute.degree.Rd                   |   12 +++-
 man/impute.visibility_mle.Rd           |   18 ++++--
 man/plot.rds.data.frame.Rd             |   10 ++-
 man/print.rds.interval.estimate.Rd     |    7 ++
 man/print.summary.svyglm.RDS.Rd        |   10 ++-
 man/rds.I.weights.Rd                   |    3 -
 man/rds.interval.estimate.Rd           |   12 +++-
 man/rdssampleC.Rd                      |only
 man/reingold.tilford.plot.Rd           |   19 ++++--
 man/rid.from.coupons.Rd                |    9 ++-
 man/set.control.class.Rd               |   10 +--
 man/summary.svyglm.RDS.Rd              |    3 -
 man/ult.Rd                             |only
 49 files changed, 544 insertions(+), 238 deletions(-)

More information about RDS at CRAN
Permanent link

Package osmdata updated to version 0.1.2 with previous version 0.1.1 dated 2019-05-22

Title: Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server and processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre], Bob Rudis [aut], Robin Lovelace [aut], Maëlle Salmon [aut], Andrew Smith [ctb], James Smith [ctb], Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Finkelstein Noam [ctb, cph] (Author of included stub.R code), Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>

Diff between osmdata versions 0.1.1 dated 2019-05-22 and 0.1.2 dated 2019-12-14

 DESCRIPTION                      |   11 +-
 MD5                              |   88 +++++++++--------
 NAMESPACE                        |    1 
 NEWS.md                          |   18 +++
 R/features.R                     |   20 ++-
 R/get-osmdata.R                  |   56 ++++++++---
 R/getbb.R                        |   36 +++----
 R/opq.R                          |   89 ++++++++++-------
 R/overpass-query.R               |   14 +-
 R/poly2line.R                    |   12 +-
 R/trim-osmdata.R                 |   91 +++++++++++++++++-
 R/utils.R                        |only
 R/zzz.R                          |   20 +--
 build/vignette.rds               |binary
 inst/doc/osm-sf-translation.R    |   16 +--
 inst/doc/osm-sf-translation.Rmd  |    8 -
 inst/doc/osm-sf-translation.html |  135 ++++++++++++++------------
 inst/doc/osmdata-sc.R            |   20 +--
 inst/doc/osmdata-sc.Rmd          |   10 -
 inst/doc/osmdata-sc.html         |  117 ++++++++++++-----------
 inst/doc/osmdata.R               |  128 ++++++++++++-------------
 inst/doc/osmdata.Rmd             |  107 ++++++++++-----------
 inst/doc/osmdata.html            |  197 ++++++++++++++++++++-------------------
 inst/figures                     |only
 man/add_osm_feature.Rd           |   38 +++++--
 man/available_features.Rd        |    2 
 man/available_tags.Rd            |    2 
 man/figures/osmhex.png           |only
 man/get_overpass_url.Rd          |    2 
 man/getbb.Rd                     |   21 ++--
 man/opq.Rd                       |   36 +++----
 man/osm_poly2line.Rd             |   12 +-
 man/osmdata.Rd                   |   14 +-
 man/set_overpass_url.Rd          |   12 +-
 man/unique_osmdata.Rd            |    6 -
 man/unname_osmdata_sf.Rd         |only
 src/convert-osm-rcpp.cpp         |    3 
 tests/testthat/test-elevation.R  |only
 tests/testthat/test-extract.R    |    8 -
 tests/testthat/test-features.R   |    2 
 tests/testthat/test-getbb.R      |   22 ++++
 tests/testthat/test-osmdata.R    |  103 ++++++++++----------
 tests/testthat/test-trim.R       |    9 +
 tests/valgrind-test.R            |only
 vignettes/osm-sf-translation.Rmd |    8 -
 vignettes/osmdata-refs.bib       |    4 
 vignettes/osmdata-sc.Rmd         |   10 -
 vignettes/osmdata.Rmd            |  107 ++++++++++-----------
 48 files changed, 928 insertions(+), 687 deletions(-)

More information about osmdata at CRAN
Permanent link

Package multinets updated to version 0.2.2 with previous version 0.2.1 dated 2018-07-07

Title: Multilevel Networks Analysis
Description: Analyze multilevel networks as described in Lazega et al (2008) <doi:10.1016/j.socnet.2008.02.001> and in Lazega and Snijders (2016, ISBN:978-3-319-24520-1). The package was developed essentially as an extension to 'igraph'.
Author: Neylson Crepalde [aut, cre]
Maintainer: Neylson Crepalde <neylsoncrepalde@gmail.com>

Diff between multinets versions 0.2.1 dated 2018-07-07 and 0.2.2 dated 2019-12-14

 DESCRIPTION                               |   12 +-
 MD5                                       |   68 ++++++------
 NAMESPACE                                 |   26 ++--
 NEWS.md                                   |   59 ++++++-----
 R/RcppExports.R                           |   38 +++----
 R/extract_highlevel.R                     |   78 +++++++-------
 R/extract_lowlevel.R                      |   78 +++++++-------
 R/extract_mesolevel.R                     |  104 +++++++++----------
 R/is_multilevel.R                         |  126 ++++++++++++------------
 R/layout_multilevel.R                     |  154 ++++++++++++++---------------
 R/linked_sim.R                            |   72 ++++++-------
 R/mode_transformation.R                   |  116 +++++++++++-----------
 R/rcpp_roxy.R                             |    6 -
 R/set_color_multilevel.R                  |  139 +++++++++++++-------------
 R/set_shape_multilevel.R                  |   84 ++++++++--------
 R/zzz.R                                   |   14 +-
 README.md                                 |  157 ++++++++++++++----------------
 man/extract_highlevel.Rd                  |   78 +++++++-------
 man/extract_lowlevel.Rd                   |   78 +++++++-------
 man/extract_mesolevel.Rd                  |   78 +++++++-------
 man/figures/README-example-1.png          |binary
 man/is_multilevel.Rd                      |   94 ++++++++---------
 man/layout_multilevel.Rd                  |  100 +++++++++----------
 man/linked_sim.Rd                         |   86 ++++++++--------
 man/mode_transformation.Rd                |   96 +++++++++---------
 man/set_color_multilevel.Rd               |   88 ++++++++--------
 man/set_shape_multilevel.Rd               |   76 +++++++-------
 src/RcppExports.cpp                       |    4 
 src/get_edge_color.cpp                    |   10 -
 src/open_plot.cpp                         |    4 
 tests/testthat.R                          |    8 -
 tests/testthat/test-extraction.R          |   26 ++--
 tests/testthat/test-is_multilevel.R       |   28 ++---
 tests/testthat/test-layout_conditions.R   |   22 ++--
 tests/testthat/test-mode_transformation.R |   44 ++++----
 35 files changed, 1129 insertions(+), 1122 deletions(-)

More information about multinets at CRAN
Permanent link

Package MPTinR updated to version 1.12.0 with previous version 1.11.0 dated 2018-06-23

Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre], David Kellen [aut], Quentin Gronau [aut], Christian Mueller [ctb], Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>

Diff between MPTinR versions 1.11.0 dated 2018-06-23 and 1.12.0 dated 2019-12-14

 DESCRIPTION                       |   10 ++---
 MD5                               |   38 +++++++++++-----------
 NAMESPACE                         |   21 +++++++++++-
 NEWS                              |   22 +++++++++++++
 R/RcppExports.R                   |    8 ++--
 R/bmpt.fia.R                      |    4 +-
 R/prediction.plot.R               |    2 -
 R/select.mpt.R                    |    3 +
 build/partial.rdb                 |binary
 build/vignette.rds                |binary
 inst/doc/mptinr_introduction.R    |   64 +++++++++++++++++++-------------------
 inst/doc/mptinr_introduction.Rnw  |    2 -
 inst/doc/mptinr_introduction.pdf  |binary
 man/check.mpt.Rd                  |    1 
 man/fit.mpt.Rd                    |    4 --
 man/fit.mpt.old.Rd                |    4 --
 man/make.eqn.Rd                   |    2 -
 man/make.mpt.cf.Rd                |    2 -
 src/RcppExports.cpp               |   20 +++++------
 vignettes/mptinr_introduction.Rnw |    2 -
 20 files changed, 122 insertions(+), 87 deletions(-)

More information about MPTinR at CRAN
Permanent link

Package caseMatch updated to version 1.0.8 with previous version 1.0.7 dated 2017-01-06

Title: Identify Similar Cases for Qualitative Case Studies
Description: Allows users to identify similar cases for qualitative case studies using statistical matching methods.
Author: Rich Nielsen
Maintainer: Rich Nielsen <rnielsen@mit.edu>

Diff between caseMatch versions 1.0.7 dated 2017-01-06 and 1.0.8 dated 2019-12-14

 DESCRIPTION    |    8 ++++----
 MD5            |    4 ++--
 R/case.match.R |    2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

More information about caseMatch at CRAN
Permanent link

Package broom updated to version 0.5.3 with previous version 0.5.2 dated 2019-04-07

Title: Convert Statistical Analysis Objects into Tidy Tibbles
Description: Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.
Author: David Robinson [aut], Alex Hayes [aut, cre] (<https://orcid.org/0000-0002-4985-5160>), Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb]
Maintainer: Alex Hayes <alexpghayes@gmail.com>

Diff between broom versions 0.5.2 dated 2019-04-07 and 0.5.3 dated 2019-12-14

 DESCRIPTION                     |    9 
 MD5                             |  410 ++++++++++++++++++++--------------------
 NAMESPACE                       |    2 
 NEWS.md                         |    4 
 R/caret-tidiers.R               |    2 
 R/lmodel2-tidiers.R             |   19 -
 R/stats-loess-tidiers.R         |    4 
 README.md                       |  125 +++++++-----
 build/vignette.rds              |binary
 inst/doc/adding-tidiers.R       |    8 
 inst/doc/adding-tidiers.html    |   95 ++++-----
 inst/doc/available-methods.R    |    4 
 inst/doc/available-methods.html |   11 -
 inst/doc/bootstrapping.R        |   22 +-
 inst/doc/bootstrapping.html     |  271 +++++++++++++-------------
 inst/doc/broom.R                |   22 +-
 inst/doc/broom.html             |  197 +++++++++----------
 inst/doc/broom_and_dplyr.R      |   30 +-
 inst/doc/broom_and_dplyr.html   |  337 ++++++++++++++++----------------
 inst/doc/glossary.R             |    6 
 inst/doc/glossary.html          |   11 -
 inst/doc/kmeans.R               |   22 +-
 inst/doc/kmeans.html            |  228 +++++++++++-----------
 man/argument_glossary.Rd        |   44 ++--
 man/augment.Mclust.Rd           |  163 ++++++++-------
 man/augment.betareg.Rd          |  194 +++++++++---------
 man/augment.coxph.Rd            |  260 +++++++++++++------------
 man/augment.decomposed.ts.Rd    |  255 ++++++++++++------------
 man/augment.factanal.Rd         |  171 ++++++++--------
 man/augment.felm.Rd             |  165 ++++++++--------
 man/augment.glm.Rd              |  139 ++++++-------
 man/augment.glmRob.Rd           |  147 +++++++-------
 man/augment.htest.Rd            |  171 ++++++++--------
 man/augment.ivreg.Rd            |  221 ++++++++++-----------
 man/augment.kmeans.Rd           |  161 +++++++--------
 man/augment.lm.Rd               |  257 ++++++++++++-------------
 man/augment.lmRob.Rd            |  147 +++++++-------
 man/augment.loess.Rd            |  163 +++++++--------
 man/augment.mjoint.Rd           |  178 ++++++++---------
 man/augment.nlrq.Rd             |  108 +++++-----
 man/augment.nls.Rd              |  177 ++++++++---------
 man/augment.plm.Rd              |  167 ++++++++--------
 man/augment.poLCA.Rd            |  177 ++++++++---------
 man/augment.prcomp.Rd           |  172 ++++++++--------
 man/augment.rlm.Rd              |  143 +++++++------
 man/augment.rq.Rd               |  231 +++++++++++-----------
 man/augment.rqs.Rd              |  233 +++++++++++-----------
 man/augment.smooth.spline.Rd    |  129 ++++++------
 man/augment.speedlm.Rd          |  170 ++++++++--------
 man/augment.stl.Rd              |  163 ++++++++-------
 man/augment.survreg.Rd          |  260 +++++++++++++------------
 man/augment_columns.Rd          |   84 ++++----
 man/bootstrap.Rd                |   70 +++---
 man/brms_tidiers.Rd             |  186 +++++++++---------
 man/broom.Rd                    |   32 +--
 man/column_glossary.Rd          |   48 ++--
 man/confint_tidy.Rd             |   68 +++---
 man/data.frame_tidiers.Rd       |  170 ++++++++--------
 man/durbinWatsonTest_tidiers.Rd |  100 ++++-----
 man/emmeans_tidiers.Rd          |  190 +++++++++---------
 man/finish_glance.Rd            |   72 +++----
 man/fix_data_frame.Rd           |   44 ++--
 man/geeglm_tidiers.Rd           |  184 +++++++++--------
 man/glance.Arima.Rd             |  101 ++++-----
 man/glance.Gam.Rd               |  111 +++++-----
 man/glance.Mclust.Rd            |   96 ++++-----
 man/glance.aareg.Rd             |  132 ++++++------
 man/glance.betareg.Rd           |  132 ++++++------
 man/glance.biglm.Rd             |  101 ++++-----
 man/glance.binDesign.Rd         |  133 ++++++------
 man/glance.cch.Rd               |  141 +++++++------
 man/glance.coxph.Rd             |  127 ++++++------
 man/glance.cv.glmnet.Rd         |  104 +++++-----
 man/glance.ergm.Rd              |  115 +++++------
 man/glance.factanal.Rd          |  117 +++++------
 man/glance.felm.Rd              |   94 ++++-----
 man/glance.fitdistr.Rd          |   99 ++++-----
 man/glance.garch.Rd             |  104 +++++-----
 man/glance.glm.Rd               |  125 ++++++------
 man/glance.glmRob.Rd            |  105 +++++-----
 man/glance.glmnet.Rd            |   98 ++++-----
 man/glance.gmm.Rd               |   99 ++++-----
 man/glance.ivreg.Rd             |  175 ++++++++---------
 man/glance.kmeans.Rd            |  103 +++++-----
 man/glance.lavaan.Rd            |  165 ++++++++--------
 man/glance.lm.Rd                |  129 ++++++------
 man/glance.lmRob.Rd             |  107 +++++-----
 man/glance.lmodel2.Rd           |  101 +++++----
 man/glance.mjoint.Rd            |  101 ++++-----
 man/glance.muhaz.Rd             |  103 +++++-----
 man/glance.multinom.Rd          |   99 ++++-----
 man/glance.nlrq.Rd              |  112 +++++-----
 man/glance.nls.Rd               |  111 +++++-----
 man/glance.orcutt.Rd            |  109 +++++-----
 man/glance.plm.Rd               |  109 +++++-----
 man/glance.poLCA.Rd             |  161 +++++++--------
 man/glance.pyears.Rd            |  131 ++++++------
 man/glance.ridgelm.Rd           |  105 +++++-----
 man/glance.rlm.Rd               |  137 ++++++-------
 man/glance.rq.Rd                |  126 ++++++------
 man/glance.smooth.spline.Rd     |   91 ++++----
 man/glance.speedlm.Rd           |  117 +++++------
 man/glance.survdiff.Rd          |  132 ++++++------
 man/glance.survexp.Rd           |  132 ++++++------
 man/glance.survfit.Rd           |  146 +++++++-------
 man/glance.survreg.Rd           |  144 +++++++-------
 man/glance_optim.Rd             |  105 +++++-----
 man/insert_NAs.Rd               |   30 +-
 man/list_tidiers.Rd             |   77 +++----
 man/lme4_tidiers.Rd             |  257 ++++++++++++-------------
 man/matrix_tidiers.Rd           |   98 ++++-----
 man/mcmc_tidiers.Rd             |  205 +++++++++++---------
 man/mgcv_glance_gam.Rd          |  111 +++++-----
 man/mgcv_tidy_gam.Rd            |  111 +++++-----
 man/nlme_tidiers.Rd             |  220 ++++++++++-----------
 man/null_tidiers.Rd             |   64 +++---
 man/ordinal_tidiers.Rd          |  300 ++++++++++++++++-------------
 man/reexports.Rd                |   50 ++--
 man/rowwise_df_tidiers.Rd       |  182 ++++++++---------
 man/rstanarm_tidiers.Rd         |  223 ++++++++++-----------
 man/sp_tidiers.Rd               |   96 ++++-----
 man/sparse_tidiers.Rd           |   60 ++---
 man/summary_tidiers.Rd          |  116 +++++------
 man/tidy.Arima.Rd               |  123 ++++++------
 man/tidy.Gam.Rd                 |  107 +++++-----
 man/tidy.Kendall.Rd             |  122 +++++------
 man/tidy.Mclust.Rd              |  155 +++++++--------
 man/tidy.TukeyHSD.Rd            |  118 +++++------
 man/tidy.aareg.Rd               |  156 ++++++++-------
 man/tidy.acf.Rd                 |  102 +++++----
 man/tidy.anova.Rd               |  118 +++++------
 man/tidy.aov.Rd                 |  116 +++++------
 man/tidy.aovlist.Rd             |  118 +++++------
 man/tidy.betareg.Rd             |  162 +++++++--------
 man/tidy.biglm.Rd               |  189 +++++++++---------
 man/tidy.binDesign.Rd           |  117 +++++------
 man/tidy.binWidth.Rd            |  135 ++++++-------
 man/tidy.boot.Rd                |  159 +++++++--------
 man/tidy.btergm.Rd              |  181 ++++++++---------
 man/tidy.cch.Rd                 |  200 ++++++++++---------
 man/tidy.cld.Rd                 |   78 +++----
 man/tidy.coeftest.Rd            |  106 +++++-----
 man/tidy.confint.glht.Rd        |   78 +++----
 man/tidy.confusionMatrix.Rd     |  160 +++++++--------
 man/tidy.coxph.Rd               |  237 +++++++++++------------
 man/tidy.cv.glmnet.Rd           |  202 +++++++++----------
 man/tidy.density.Rd             |   81 ++++---
 man/tidy.dist.Rd                |  134 ++++++-------
 man/tidy.ergm.Rd                |  172 ++++++++--------
 man/tidy.factanal.Rd            |  113 +++++------
 man/tidy.felm.Rd                |  196 +++++++++----------
 man/tidy.fitdistr.Rd            |  113 +++++------
 man/tidy.ftable.Rd              |   93 ++++-----
 man/tidy.gamlss.Rd              |  120 +++++------
 man/tidy.garch.Rd               |  117 +++++------
 man/tidy.glht.Rd                |  135 ++++++-------
 man/tidy.glm.Rd                 |  129 ++++++------
 man/tidy.glmRob.Rd              |  163 ++++++++-------
 man/tidy.glmnet.Rd              |  188 +++++++++---------
 man/tidy.gmm.Rd                 |  283 ++++++++++++++-------------
 man/tidy.htest.Rd               |  157 +++++++--------
 man/tidy.ivreg.Rd               |  178 ++++++++---------
 man/tidy.kappa.Rd               |  128 ++++++------
 man/tidy.kde.Rd                 |  132 ++++++------
 man/tidy.kmeans.Rd              |   99 ++++-----
 man/tidy.lavaan.Rd              |  149 +++++++-------
 man/tidy.lm.Rd                  |  277 +++++++++++++--------------
 man/tidy.lmRob.Rd               |  165 ++++++++--------
 man/tidy.lmodel2.Rd             |  150 +++++++-------
 man/tidy.manova.Rd              |  129 ++++++------
 man/tidy.map.Rd                 |  102 ++++-----
 man/tidy.mjoint.Rd              |  237 +++++++++++------------
 man/tidy.mle2.Rd                |  110 +++++-----
 man/tidy.muhaz.Rd               |  103 +++++-----
 man/tidy.multinom.Rd            |  160 +++++++--------
 man/tidy.nlrq.Rd                |  128 ++++++------
 man/tidy.nls.Rd                 |  166 ++++++++--------
 man/tidy.orcutt.Rd              |  117 +++++------
 man/tidy.pairwise.htest.Rd      |  142 +++++++------
 man/tidy.plm.Rd                 |  168 ++++++++--------
 man/tidy.poLCA.Rd               |  217 ++++++++++-----------
 man/tidy.power.htest.Rd         |  107 +++++-----
 man/tidy.prcomp.Rd              |  238 +++++++++++------------
 man/tidy.pyears.Rd              |  170 ++++++++--------
 man/tidy.rcorr.Rd               |  162 +++++++--------
 man/tidy.ridgelm.Rd             |  141 ++++++-------
 man/tidy.rlm.Rd                 |  133 ++++++------
 man/tidy.roc.Rd                 |  146 +++++++-------
 man/tidy.rq.Rd                  |  135 ++++++-------
 man/tidy.rqs.Rd                 |  139 ++++++-------
 man/tidy.spec.Rd                |  100 ++++-----
 man/tidy.speedlm.Rd             |  147 +++++++-------
 man/tidy.summary.glht.Rd        |   78 +++----
 man/tidy.survdiff.Rd            |  150 +++++++-------
 man/tidy.survexp.Rd             |  158 ++++++++-------
 man/tidy.survfit.Rd             |  179 +++++++++--------
 man/tidy.survreg.Rd             |  188 +++++++++---------
 man/tidy.table.Rd               |   96 ++++-----
 man/tidy.ts.Rd                  |  110 +++++-----
 man/tidy.zoo.Rd                 |  146 +++++++-------
 man/tidy_irlba.Rd               |  177 ++++++++---------
 man/tidy_optim.Rd               |  131 ++++++------
 man/tidy_svd.Rd                 |  249 ++++++++++++------------
 man/tidy_xyz.Rd                 |  125 ++++++------
 man/vector_tidiers.Rd           |   74 +++----
 tests/testthat/test-lfe.R       |    2 
 206 files changed, 13953 insertions(+), 13456 deletions(-)

More information about broom at CRAN
Permanent link

Package QuantumOps updated to version 3.0.0 with previous version 2.5.3 dated 2019-08-30

Title: Performs Common Linear Algebra Operations Used in Quantum Computing and Implements Quantum Algorithms
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help learn quantum mechanics and algorithms. Can create arbitrarily sized kets and bras and implements quantum gates, inner products, and tensor products. Creates arbitrarily controlled versions of all gates and can simulate complete or partial measurements of kets. Has functionality to convert functions into equivalent quantum gates and model quantum noise. Includes larger applications, such as Steane error correction <DOI:10.1103/physrevlett.77.793>, Quantum Fourier Transform and Shor's algorithm (Shor 1999), Grover's algorithm (1996), Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018) <arXiv:1804.00633>.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>

Diff between QuantumOps versions 2.5.3 dated 2019-08-30 and 3.0.0 dated 2019-12-14

 DESCRIPTION              |   10 +-
 MD5                      |   50 ++++++++++----
 NAMESPACE                |   12 +++
 NEWS.md                  |   18 +++++
 R/AmplitudeDamping.R     |only
 R/CoherentNoise.R        |only
 R/DecomposeGate.R        |only
 R/FullAdder.R            |only
 R/PauliNoise.R           |only
 R/PauliOperators.R       |only
 R/QAOA.R                 |   48 ++++++++++---
 R/QFT.R                  |   57 ++++++++++++++--
 R/QuantumClassifier.R    |  162 +++++++++++++++++++++++++++++++++--------------
 R/RandomizeCompile.R     |only
 R/SynthesizeCircuit.R    |only
 R/TOFFOLI.R              |   59 +++++++++++++----
 R/convert_ket2DM.R       |only
 R/many.R                 |    5 -
 R/nBitAddition.R         |only
 R/opDM.R                 |only
 R/ranket.R               |only
 R/single.R               |    6 +
 man/AmplitudeDamping.Rd  |only
 man/CoherentNoise.Rd     |only
 man/DecomposeGate.Rd     |only
 man/FullAdder.Rd         |only
 man/PauliNoise.Rd        |only
 man/PauliOperators.Rd    |only
 man/QAOA.Rd              |    4 -
 man/QFT.Rd               |   10 ++
 man/QuantumClassifier.Rd |   18 +++--
 man/RandomizeCompile.Rd  |only
 man/SynthesizeCircuit.Rd |only
 man/TOFFOLI.Rd           |   10 ++
 man/convert_ket2DM.Rd    |only
 man/nBitAddition.Rd      |only
 man/opDM.Rd              |only
 man/ranket.Rd            |only
 38 files changed, 355 insertions(+), 114 deletions(-)

More information about QuantumOps at CRAN
Permanent link

Package pca3d updated to version 0.10.1 with previous version 0.10 dated 2017-02-17

Title: Three Dimensional PCA Plots
Description: Functions simplifying presentation of PCA models in a 3D interactive representation using 'rgl'.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>

Diff between pca3d versions 0.10 dated 2017-02-17 and 0.10.1 dated 2019-12-14

 DESCRIPTION        |    7 ++++---
 MD5                |   16 ++++++++--------
 R/helpers.R        |   19 +++++++++++--------
 R/pca2d.R          |    2 +-
 R/pca3d.R          |    2 +-
 build/vignette.rds |binary
 data/metabo.rda    |binary
 inst/doc/pca3d.R   |   20 ++++++++++----------
 inst/doc/pca3d.pdf |binary
 9 files changed, 35 insertions(+), 31 deletions(-)

More information about pca3d at CRAN
Permanent link

Package Numero updated to version 1.4.0 with previous version 1.3.3 dated 2019-10-31

Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut], Stefan Mutter [aut], Aaron E. Casey [aut], Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>

Diff between Numero versions 1.3.3 dated 2019-10-31 and 1.4.0 dated 2019-12-14

 Numero-1.3.3/Numero/inst/extcode/circus.js              |only
 Numero-1.3.3/Numero/inst/extcode/examples.R             |only
 Numero-1.4.0/Numero/DESCRIPTION                         |    8 
 Numero-1.4.0/Numero/MD5                                 |   71 ++-
 Numero-1.4.0/Numero/NAMESPACE                           |    5 
 Numero-1.4.0/Numero/R/nroAggregate.R                    |    4 
 Numero-1.4.0/Numero/R/nroDestratify.R                   |   15 
 Numero-1.4.0/Numero/R/nroImpute.R                       |    6 
 Numero-1.4.0/Numero/R/nroKmeans.R                       |    4 
 Numero-1.4.0/Numero/R/nroKohonen.R                      |    2 
 Numero-1.4.0/Numero/R/nroLabel.R                        |    2 
 Numero-1.4.0/Numero/R/nroMatch.R                        |    2 
 Numero-1.4.0/Numero/R/nroPair.R                         |   23 -
 Numero-1.4.0/Numero/R/nroPermute.R                      |    2 
 Numero-1.4.0/Numero/R/nroPlot.save.R                    |   10 
 Numero-1.4.0/Numero/R/nroStatistic.R                    |only
 Numero-1.4.0/Numero/R/nroTrain.R                        |    7 
 Numero-1.4.0/Numero/R/numero.clean.R                    |   46 +-
 Numero-1.4.0/Numero/inst/doc/intro.html                 |  351 +++++++++-------
 Numero-1.4.0/Numero/inst/extcode/a_globals.js           |only
 Numero-1.4.0/Numero/inst/extcode/createhoverdistrict.js |only
 Numero-1.4.0/Numero/inst/extcode/createsymbol.js        |only
 Numero-1.4.0/Numero/inst/extcode/downloadregions.js     |only
 Numero-1.4.0/Numero/inst/extcode/getdistrictdata.js     |only
 Numero-1.4.0/Numero/inst/extcode/initmenu.js            |only
 Numero-1.4.0/Numero/inst/extcode/initpage.js            |only
 Numero-1.4.0/Numero/inst/extcode/initregions.js         |only
 Numero-1.4.0/Numero/inst/extcode/locatesubplot.js       |only
 Numero-1.4.0/Numero/inst/extcode/pointerdowndistrict.js |only
 Numero-1.4.0/Numero/inst/extcode/pointerdownsymbol.js   |only
 Numero-1.4.0/Numero/inst/extcode/pointeroverdistrict.js |only
 Numero-1.4.0/Numero/inst/extcode/pointeroversymbol.js   |only
 Numero-1.4.0/Numero/inst/extcode/refreshmenu.js         |only
 Numero-1.4.0/Numero/inst/extcode/removehovers.js        |only
 Numero-1.4.0/Numero/inst/extcode/updatehighlights.js    |only
 Numero-1.4.0/Numero/man/nroPair.Rd                      |   15 
 Numero-1.4.0/Numero/man/nroStatistic.Rd                 |only
 Numero-1.4.0/Numero/man/numero.clean.Rd                 |   46 +-
 Numero-1.4.0/Numero/src/Numero_init.c                   |    2 
 Numero-1.4.0/Numero/src/abacus.h                        |   10 
 Numero-1.4.0/Numero/src/abacus.matrix.add.cpp           |   25 +
 Numero-1.4.0/Numero/src/abacus.matrix.insert.cpp        |   23 +
 Numero-1.4.0/Numero/src/abacus.statistic.cpp            |   71 ++-
 Numero-1.4.0/Numero/src/abacus.version.cpp              |    2 
 Numero-1.4.0/Numero/src/nro_diffuse.cpp                 |   14 
 Numero-1.4.0/Numero/src/nro_statistic.cpp               |only
 Numero-1.4.0/Numero/src/nro_train.cpp                   |    4 
 47 files changed, 512 insertions(+), 258 deletions(-)

More information about Numero at CRAN
Permanent link

Package MetStaT (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-11-18 1.0

Permanent link
Package highlight updated to version 0.4.7.4 with previous version 0.4.7.3 dated 2019-12-01

Title: Syntax Highlighter
Description: Syntax highlighter for R code based on the results of the R parser. Rendering in HTML and latex markup. Custom Sweave driver performing syntax highlighting of R code chunks.
Author: Romain Francois [aut, cre], Andre Simon [ctb]
Maintainer: ORPHANED

Diff between highlight versions 0.4.7.3 dated 2019-12-01 and 0.4.7.4 dated 2019-12-14

 DESCRIPTION      |    6 +++---
 MD5              |    6 +++---
 src/Makevars     |    1 +
 src/Makevars.win |    1 +
 4 files changed, 8 insertions(+), 6 deletions(-)

More information about highlight at CRAN
Permanent link

Fri, 13 Dec 2019

Package SSLASSO updated to version 1.2-2 with previous version 1.2-1 dated 2018-08-28

Title: The Spike-and-Slab LASSO
Description: Efficient coordinate ascent algorithm for fitting regularization paths for linear models penalized by Spike-and-Slab LASSO of Rockova and George (2018) <doi:10.1080/01621459.2016.1260469>.
Author: Veronika Rockova [aut,cre], Gemma Moran [aut]
Maintainer: Gemma Moran <gm2918@columbia.edu>

Diff between SSLASSO versions 1.2-1 dated 2018-08-28 and 1.2-2 dated 2019-12-13

 DESCRIPTION        |   11 ++++++-----
 MD5                |   13 +++++++------
 NAMESPACE          |    3 ++-
 NEWS.md            |only
 R/SSLASSO.R        |   24 +++++++++++++++---------
 R/standard.R       |    4 ++--
 man/SSLASSO.Rd     |    2 +-
 src/SSL_gaussian.c |    2 +-
 8 files changed, 34 insertions(+), 25 deletions(-)

More information about SSLASSO at CRAN
Permanent link

Package retistruct updated to version 0.6.2 with previous version 0.6.1 dated 2019-12-09

Title: Retinal Reconstruction Program
Description: Reconstructs retinae by morphing a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates.
Author: David C. Sterratt [aut, cre, cph], Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>

Diff between retistruct versions 0.6.1 dated 2019-12-09 and 0.6.2 dated 2019-12-13

 DESCRIPTION                                   |   14 
 MD5                                           |  132 +++----
 NAMESPACE                                     |    1 
 NEWS                                          |   15 
 R/AnnotatedOutline.R                          |  117 +++---
 R/CountSet.R                                  |   24 -
 R/FeatureSet.R                                |   67 +--
 R/FeatureSetCommon.R                          |only
 R/Fragment.R                                  |   23 -
 R/LandmarkSet.R                               |   23 -
 R/Outline.R                                   |   79 +++-
 R/OutlineCommon.R                             |   18 
 R/PathOutline.R                               |   26 +
 R/PointSet.R                                  |   22 -
 R/ReconstructedCountSet.R                     |   34 +
 R/ReconstructedFeatureSet.R                   |   50 +-
 R/ReconstructedLandmarkSet.R                  |   16 
 R/ReconstructedOutline.R                      |  426 ++++++++++++-----------
 R/ReconstructedPointSet.R                     |   44 +-
 R/RetinalOutline.R                            |   22 -
 R/RetinalReconstructedOutline.R               |   36 +
 R/StitchedOutline.R                           |   42 --
 R/TriangulatedFragment.R                      |   57 +--
 R/TriangulatedOutline.R                       |   32 +
 R/misc.R                                      |    2 
 R/r6-serialize.R                              |    2 
 R/retistruct-gui.R                            |    2 
 R/retistruct.R                                |    4 
 inst/WORDLIST                                 |   15 
 man/AnnotatedOutline.Rd                       |  319 +++++++++++++++++
 man/CountSet.Rd                               |  100 ++++-
 man/E.Rd                                      |   22 +
 man/FeatureSet.Rd                             |   87 +++-
 man/FeatureSetCommon.Rd                       |only
 man/Fragment.Rd                               |   78 +++-
 man/LandmarkSet.Rd                            |   99 ++++-
 man/Outline.Rd                                |  287 ++++++++++++++-
 man/OutlineCommon.Rd                          |only
 man/PathOutline.Rd                            |  154 ++++++++
 man/PointSet.Rd                               |   98 ++++-
 man/R6_to_list.Rd                             |    2 
 man/ReconstructedCountSet.Rd                  |  103 ++++-
 man/ReconstructedFeatureSet.Rd                |   82 +++-
 man/ReconstructedLandmarkSet.Rd               |   59 ++-
 man/ReconstructedOutline.Rd                   |  470 +++++++++++++++++++++++++-
 man/ReconstructedPointSet.Rd                  |  109 +++++-
 man/RetinalOutline.Rd                         |  120 +++++-
 man/RetinalReconstructedOutline.Rd            |  140 ++++++-
 man/StitchedOutline.Rd                        |  135 ++++++-
 man/TriangulatedFragment.Rd                   |  123 ++++--
 man/TriangulatedOutline.Rd                    |  140 +++++++
 man/dE.Rd                                     |   22 +
 man/fire.Rd                                   |   23 +
 man/flatplot.AnnotatedOutline.Rd              |    3 
 man/flatplot.Outline.Rd                       |   17 
 man/flatplot.ReconstructedOutline.Rd          |   11 
 man/flatplot.StitchedOutline.Rd               |    3 
 man/flatplot.TriangulatedOutline.Rd           |    3 
 man/projection.ReconstructedOutline.Rd        |   30 +
 man/projection.RetinalReconstructedOutline.Rd |   26 +
 man/report.Rd                                 |    2 
 man/retistruct.batch.Rd                       |   12 
 man/retistruct.cli.Rd                         |    9 
 man/retistruct.cli.figure.Rd                  |   10 
 man/retistruct.reconstruct.Rd                 |   11 
 man/sinusoidal.Rd                             |    9 
 man/sphericalplot.ReconstructedOutline.Rd     |    3 
 tests/spelling.R                              |only
 tests/testthat/test-reconstruct.R             |   18 
 69 files changed, 3351 insertions(+), 933 deletions(-)

More information about retistruct at CRAN
Permanent link

Package highfrequency updated to version 0.6.2 with previous version 0.6.1 dated 2019-08-29

Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency trades and quotes data, calculate various liquidity measures, estimate and forecast volatility, detect price jumps and investigate microstructure noise and intraday periodicity.
Author: Kris Boudt [aut, cre] (<https://orcid.org/0000-0002-1000-5142>), Jonathan Cornelissen [aut], Scott Payseur [aut], Giang Nguyen [ctb], Onno Kleen [aut] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Kris Boudt <kris.boudt@ugent.be>

Diff between highfrequency versions 0.6.1 dated 2019-08-29 and 0.6.2 dated 2019-12-13

 highfrequency-0.6.1/highfrequency/tests/testthat/Rplots.pdf                |only
 highfrequency-0.6.2/highfrequency/DESCRIPTION                              |   43 +++-
 highfrequency-0.6.2/highfrequency/MD5                                      |   87 ++++------
 highfrequency-0.6.2/highfrequency/NEWS.md                                  |   33 ++-
 highfrequency-0.6.2/highfrequency/R/data_handling.R                        |    8 
 highfrequency-0.6.2/highfrequency/R/internal_preavering_estimators.R       |   10 -
 highfrequency-0.6.2/highfrequency/R/realized_measures.R                    |   22 +-
 highfrequency-0.6.2/highfrequency/R/spot_vol_and_drift.R                   |   12 +
 highfrequency-0.6.2/highfrequency/inst/doc/data_handing.R                  |   16 -
 highfrequency-0.6.2/highfrequency/inst/doc/data_handing.html               |   39 +---
 highfrequency-0.6.2/highfrequency/man/AJjumptest.Rd                        |   13 +
 highfrequency-0.6.2/highfrequency/man/BNSjumptest.Rd                       |   14 +
 highfrequency-0.6.2/highfrequency/man/aggregatePrice.Rd                    |   11 +
 highfrequency-0.6.2/highfrequency/man/aggregateQuotes.Rd                   |   10 -
 highfrequency-0.6.2/highfrequency/man/aggregateTrades.Rd                   |   10 -
 highfrequency-0.6.2/highfrequency/man/aggregatets.Rd                       |   10 -
 highfrequency-0.6.2/highfrequency/man/harModel.Rd                          |   20 +-
 highfrequency-0.6.2/highfrequency/man/heavyModel.Rd                        |   13 +
 highfrequency-0.6.2/highfrequency/man/ivInference.Rd                       |   13 +
 highfrequency-0.6.2/highfrequency/man/medRQ.Rd                             |    3 
 highfrequency-0.6.2/highfrequency/man/medRV.Rd                             |    3 
 highfrequency-0.6.2/highfrequency/man/minRQ.Rd                             |    3 
 highfrequency-0.6.2/highfrequency/man/minRV.Rd                             |    3 
 highfrequency-0.6.2/highfrequency/man/quotesCleanup.Rd                     |   21 +-
 highfrequency-0.6.2/highfrequency/man/rAVGCov.Rd                           |    9 -
 highfrequency-0.6.2/highfrequency/man/rBPCov.Rd                            |   10 -
 highfrequency-0.6.2/highfrequency/man/rBeta.Rd                             |    9 -
 highfrequency-0.6.2/highfrequency/man/rCov.Rd                              |    9 -
 highfrequency-0.6.2/highfrequency/man/rHYCov.Rd                            |   11 +
 highfrequency-0.6.2/highfrequency/man/rKernelCov.Rd                        |   13 +
 highfrequency-0.6.2/highfrequency/man/rKurt.Rd                             |    3 
 highfrequency-0.6.2/highfrequency/man/rMPV.Rd                              |   10 -
 highfrequency-0.6.2/highfrequency/man/rOWCov.Rd                            |   14 +
 highfrequency-0.6.2/highfrequency/man/rQPVar.Rd                            |    5 
 highfrequency-0.6.2/highfrequency/man/rQuar.Rd                             |    3 
 highfrequency-0.6.2/highfrequency/man/rRTSCov.Rd                           |   17 +
 highfrequency-0.6.2/highfrequency/man/rSkew.Rd                             |    3 
 highfrequency-0.6.2/highfrequency/man/rTPVar.Rd                            |    7 
 highfrequency-0.6.2/highfrequency/man/rTSCov.Rd                            |   13 +
 highfrequency-0.6.2/highfrequency/man/rThresholdCov.Rd                     |    9 -
 highfrequency-0.6.2/highfrequency/man/spotDrift.Rd                         |   12 +
 highfrequency-0.6.2/highfrequency/man/spotvol.Rd                           |   12 +
 highfrequency-0.6.2/highfrequency/man/tradesCleanup.Rd                     |   16 +
 highfrequency-0.6.2/highfrequency/man/tradesCleanupUsingQuotes.Rd          |    8 
 highfrequency-0.6.2/highfrequency/tests/testthat/tests_realized_measures.R |    4 
 45 files changed, 399 insertions(+), 215 deletions(-)

More information about highfrequency at CRAN
Permanent link

Package EMVS updated to version 1.1 with previous version 1.0 dated 2018-04-24

Title: The Expectation-Maximization Approach to Bayesian Variable Selection
Description: An efficient expectation-maximization algorithm for fitting Bayesian spike-and-slab regularization paths for linear regression. Rockova and George (2014) <doi:10.1080/01621459.2013.869223>.
Author: Veronika Rockova [aut,cre], Gemma Moran [aut]
Maintainer: Gemma Moran <gm2918@columbia.edu>

Diff between EMVS versions 1.0 dated 2018-04-24 and 1.1 dated 2019-12-13

 DESCRIPTION                |   12 ++++++------
 MD5                        |   11 ++++++-----
 NAMESPACE                  |    3 ++-
 NEWS.md                    |only
 R/EMVS.R                   |   16 +++++++++-------
 build/vignette.rds         |binary
 inst/doc/EMVS_vignette.pdf |binary
 7 files changed, 23 insertions(+), 19 deletions(-)

More information about EMVS at CRAN
Permanent link

Package dslabs updated to version 0.7.3 with previous version 0.7.2 dated 2019-12-11

Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Author: Rafael A. Irizarry, Amy Gill
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>

Diff between dslabs versions 0.7.2 dated 2019-12-11 and 0.7.3 dated 2019-12-13

 DESCRIPTION                                      |    6 -
 MD5                                              |   68 ++++++++--------
 NAMESPACE                                        |   16 +--
 R/us_contagious_disease.R                        |    3 
 data/us_contagious_diseases.rda                  |binary
 inst/script/make-weekly_us_contagious_diseases.R |   77 +++++++-----------
 man/admissions.Rd                                |   58 +++++++-------
 man/brca.Rd                                      |   94 +++++++++++------------
 man/brexit_polls.Rd                              |   68 ++++++++--------
 man/death_prob.Rd                                |   56 ++++++-------
 man/divorce_margarine.Rd                         |   56 ++++++-------
 man/ds_theme_set.Rd                              |   68 ++++++++--------
 man/gapminder.Rd                                 |   72 ++++++++---------
 man/greenhouse_gases.Rd                          |   56 ++++++-------
 man/heights.Rd                                   |   48 +++++------
 man/historic_co2.Rd                              |   56 ++++++-------
 man/mnist_27.Rd                                  |   70 ++++++++---------
 man/movielens.Rd                                 |   70 ++++++++---------
 man/murders.Rd                                   |   60 +++++++-------
 man/na_example.Rd                                |   36 ++++----
 man/nyc_regents_scores.Rd                        |   64 +++++++--------
 man/olive.Rd                                     |   70 ++++++++---------
 man/outlier_example.Rd                           |   38 ++++-----
 man/polls_2008.Rd                                |   58 +++++++-------
 man/polls_us_election_2016.Rd                    |   84 ++++++++++----------
 man/read_mnist.Rd                                |   78 +++++++++----------
 man/reported_heights.Rd                          |   52 ++++++------
 man/research_funding_rates.Rd                    |   78 +++++++++----------
 man/rfalling_object.Rd                           |   82 ++++++++++----------
 man/stars.Rd                                     |   58 +++++++-------
 man/take_poll.Rd                                 |   46 +++++------
 man/temp_carbon.Rd                               |   60 +++++++-------
 man/tissue_gene_expression.Rd                    |   68 ++++++++--------
 man/trump_tweets.Rd                              |   68 ++++++++--------
 man/us_contagious_diseases.Rd                    |   65 ++++++++-------
 35 files changed, 999 insertions(+), 1008 deletions(-)

More information about dslabs at CRAN
Permanent link

Package bayes4psy updated to version 1.2.0 with previous version 1.1.1 dated 2019-06-28

Title: User Friendly Bayesian Data Analysis for Psychology
Description: Contains several Bayesian models for data analysis of psychological tests. A user friendly interface for these models should enable students and researchers to perform professional level Bayesian data analysis without advanced knowledge in programming and Bayesian statistics.
Author: Jure Demšar [cre, aut], Grega Repovš [aut], Erik Štrumbelj [aut], Trustees of Columbia University [cph], John Kruschke [cph] (R/shared_functions.R - mcmc_hdi, src/stan_files/ttest.stan), Rasmus Baath [cph] (R/b_bootstrap.R)
Maintainer: Jure Demšar <jure.demsar@fri.uni-lj.si>

Diff between bayes4psy versions 1.1.1 dated 2019-06-28 and 1.2.0 dated 2019-12-13

 bayes4psy-1.1.1/bayes4psy/man/rstanarm-datasets.Rd                                 |only
 bayes4psy-1.2.0/bayes4psy/DESCRIPTION                                              |   13 
 bayes4psy-1.2.0/bayes4psy/MD5                                                      |  140 +-
 bayes4psy-1.2.0/bayes4psy/NAMESPACE                                                |    2 
 bayes4psy-1.2.0/bayes4psy/NEWS.md                                                  |   10 
 bayes4psy-1.2.0/bayes4psy/R/b_color.R                                              |    5 
 bayes4psy-1.2.0/bayes4psy/R/b_linear.R                                             |    5 
 bayes4psy-1.2.0/bayes4psy/R/b_reaction_time.R                                      |    5 
 bayes4psy-1.2.0/bayes4psy/R/b_success_rate.R                                       |    5 
 bayes4psy-1.2.0/bayes4psy/R/b_ttest.R                                              |   17 
 bayes4psy-1.2.0/bayes4psy/R/color_class.R                                          |  526 +++++-----
 bayes4psy-1.2.0/bayes4psy/R/data.R                                                 |  139 ++
 bayes4psy-1.2.0/bayes4psy/R/linear_class.R                                         |  299 +++--
 bayes4psy-1.2.0/bayes4psy/R/reaction_time_class.R                                  |  312 +++--
 bayes4psy-1.2.0/bayes4psy/R/success_rate_class.R                                   |  272 ++---
 bayes4psy-1.2.0/bayes4psy/R/ttest_class.R                                          |  291 +++--
 bayes4psy-1.2.0/bayes4psy/README.md                                                |    2 
 bayes4psy-1.2.0/bayes4psy/build                                                    |only
 bayes4psy-1.2.0/bayes4psy/data/adaptation_level.rda                                |only
 bayes4psy-1.2.0/bayes4psy/data/after_images.rda                                    |only
 bayes4psy-1.2.0/bayes4psy/data/after_images_opponent_process.rda                   |only
 bayes4psy-1.2.0/bayes4psy/data/after_images_stimuli.rda                            |only
 bayes4psy-1.2.0/bayes4psy/data/after_images_trichromatic.rda                       |only
 bayes4psy-1.2.0/bayes4psy/data/flanker.rda                                         |only
 bayes4psy-1.2.0/bayes4psy/data/stroop_extended.rda                                 |only
 bayes4psy-1.2.0/bayes4psy/data/stroop_simple.rda                                   |only
 bayes4psy-1.2.0/bayes4psy/inst/doc                                                 |only
 bayes4psy-1.2.0/bayes4psy/man/b_ttest.Rd                                           |    4 
 bayes4psy-1.2.0/bayes4psy/man/bayes4psy-datasets.Rd                                |only
 bayes4psy-1.2.0/bayes4psy/man/color_class-class.Rd                                 |   33 
 bayes4psy-1.2.0/bayes4psy/man/color_class-compare_distributions.Rd                 |    2 
 bayes4psy-1.2.0/bayes4psy/man/color_class-compare_means.Rd                         |    2 
 bayes4psy-1.2.0/bayes4psy/man/color_class-plot_distributions.Rd                    |    2 
 bayes4psy-1.2.0/bayes4psy/man/color_class-plot_distributions_difference.Rd         |    2 
 bayes4psy-1.2.0/bayes4psy/man/color_class-plot_hsv.Rd                              |only
 bayes4psy-1.2.0/bayes4psy/man/color_class-plot_means.Rd                            |    2 
 bayes4psy-1.2.0/bayes4psy/man/color_class-plot_means_difference.Rd                 |    2 
 bayes4psy-1.2.0/bayes4psy/man/linear_class-class.Rd                                |   37 
 bayes4psy-1.2.0/bayes4psy/man/linear_class-compare_distributions.Rd                |    2 
 bayes4psy-1.2.0/bayes4psy/man/linear_class-compare_means.Rd                        |    2 
 bayes4psy-1.2.0/bayes4psy/man/linear_class-plot_distributions.Rd                   |    2 
 bayes4psy-1.2.0/bayes4psy/man/linear_class-plot_distributions_difference.Rd        |    2 
 bayes4psy-1.2.0/bayes4psy/man/linear_class-plot_means.Rd                           |    2 
 bayes4psy-1.2.0/bayes4psy/man/linear_class-plot_means_difference.Rd                |    2 
 bayes4psy-1.2.0/bayes4psy/man/plot-color_class-missing-method.Rd                   |only
 bayes4psy-1.2.0/bayes4psy/man/plot-linear_class-missing-method.Rd                  |only
 bayes4psy-1.2.0/bayes4psy/man/plot-reaction_time_class-missing-method.Rd           |only
 bayes4psy-1.2.0/bayes4psy/man/plot-success_rate_class-missing-method.Rd            |only
 bayes4psy-1.2.0/bayes4psy/man/plot-ttest_class-missing-method.Rd                   |only
 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-class.Rd                         |   38 
 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-compare_distributions.Rd         |    2 
 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-compare_means.Rd                 |    2 
 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-plot_distributions.Rd            |    2 
 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-plot_distributions_difference.Rd |    2 
 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-plot_means.Rd                    |    2 
 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-plot_means_difference.Rd         |    2 
 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-class.Rd                          |   36 
 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-compare_distributions.Rd          |    2 
 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-compare_means.Rd                  |    2 
 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-plot_distributions.Rd             |    2 
 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-plot_distributions_difference.Rd  |    2 
 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-plot_means.Rd                     |    2 
 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-plot_means_difference.Rd          |    2 
 bayes4psy-1.2.0/bayes4psy/man/ttest_class-class.Rd                                 |   47 
 bayes4psy-1.2.0/bayes4psy/man/ttest_class-compare_distributions.Rd                 |    2 
 bayes4psy-1.2.0/bayes4psy/man/ttest_class-compare_means.Rd                         |    4 
 bayes4psy-1.2.0/bayes4psy/man/ttest_class-plot_distributions.Rd                    |    2 
 bayes4psy-1.2.0/bayes4psy/man/ttest_class-plot_distributions_difference.Rd         |    2 
 bayes4psy-1.2.0/bayes4psy/man/ttest_class-plot_means.Rd                            |    4 
 bayes4psy-1.2.0/bayes4psy/man/ttest_class-plot_means_difference.Rd                 |    4 
 bayes4psy-1.2.0/bayes4psy/src/stan_files/reaction_time.stan                        |    4 
 bayes4psy-1.2.0/bayes4psy/src/stan_files/ttest.stan                                |   34 
 bayes4psy-1.2.0/bayes4psy/tests/testthat/test_bootstrap.R                          |only
 bayes4psy-1.2.0/bayes4psy/vignettes                                                |only
 74 files changed, 1354 insertions(+), 988 deletions(-)

More information about bayes4psy at CRAN
Permanent link

Package MatchThem updated to version 0.9.1 with previous version 0.9.0 dated 2019-11-01

Title: Matching and Weighting Multiply Imputed Datasets
Description: Provides the necessary tools for the pre-processing techniques of matching and weighting multiply imputed datasets to control for effects of confounders and to reduce the degree of dependence on certain modeling assumptions in studying the causal associations between an exposure and an outcome. This package includes functions to perform matching within and across the multiply imputed datasets using several matching methods, to estimate weights of units in the imputed datasets using several weighting methods, to calculate the causal effect estimate in each matched or weighted dataset using parametric or non-parametric statistical models, and to pool the obtained estimates from these models according to Rubin's rules (please see <https://github.com/FarhadPishgar/MatchThem> for details).
Author: Farhad Pishgar [aut, cre], Noah Greifer [aut], Clémence Leyrat [ctb], Elizabeth Stuart [ctb]
Maintainer: Farhad Pishgar <Farhad.Pishgar@Gmail.com>

Diff between MatchThem versions 0.9.0 dated 2019-11-01 and 0.9.1 dated 2019-12-13

 DESCRIPTION             |   14 -
 MD5                     |   46 ++---
 NAMESPACE               |   18 +
 NEWS.md                 |   16 +
 R/class.functions.R     |  437 +++++++++++++++++++++++++++++++++++++++++++++---
 R/complete.R            |   23 --
 R/internal.functions.R  |  195 +++++++--------------
 R/is.R                  |  107 +++++++++++
 R/matchthem.R           |   27 +-
 R/mimids.R              |    2 
 R/mimipo.R              |only
 R/mimira.R              |only
 R/pool.R                |   65 +++++--
 R/weightthem.R          |   27 +-
 R/wimids.R              |    2 
 R/with.R                |   35 +--
 README.md               |  116 ++++++------
 inst/doc/cheatsheet.pdf |binary
 man/complete.Rd         |    2 
 man/is.mimipo.Rd        |only
 man/is.mimira.Rd        |only
 man/mimids.Rd           |    2 
 man/mimipo.Rd           |only
 man/mimira.Rd           |only
 man/pool.Rd             |    8 
 man/wimids.Rd           |    2 
 man/with.Rd             |   22 --
 27 files changed, 838 insertions(+), 328 deletions(-)

More information about MatchThem at CRAN
Permanent link

Package mixlm updated to version 1.2.4 with previous version 1.2.3 dated 2018-01-03

Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm() and glm(). A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm(), glm() and associated summaries from the package 'stats'.
Author: Kristian Hovde Liland [aut, cre], Solve S<e6>b<f8> [ctb], R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between mixlm versions 1.2.3 dated 2018-01-03 and 1.2.4 dated 2019-12-13

 DESCRIPTION        |    8 ++++----
 MD5                |   12 ++++++------
 NEWS               |   11 ++++++++++-
 R/mixlm.R          |    6 ++++--
 R/statistics.R     |   35 +++++++++++++++++++++++------------
 R/utilities.R      |   15 ++++++++++-----
 man/CIgrandMean.Rd |    1 +
 7 files changed, 58 insertions(+), 30 deletions(-)

More information about mixlm at CRAN
Permanent link

Package Rcssplot updated to version 1.0.0 with previous version 0.3.0 dated 2018-02-25

Title: Styling of Graphics using Cascading Style Sheets
Description: Provides a means to style plots through cascading style sheets. This separates the aesthetics from the data crunching in plots and charts.
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>

Diff between Rcssplot versions 0.3.0 dated 2018-02-25 and 1.0.0 dated 2019-12-13

 Rcssplot-0.3.0/Rcssplot/man/Rcssabline.Rd                    |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssarrows.Rd                    |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssaxis.Rd                      |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssbarplot.Rd                   |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssbox.Rd                       |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssboxplot.Rd                   |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsscontour.Rd                   |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssgrid.Rd                      |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsshist.Rd                      |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssjpeg.Rd                      |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsslegend.Rd                    |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsslines.Rd                     |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssmatplot.Rd                   |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssmtext.Rd                     |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsspar.Rd                       |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsspdf.Rd                       |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssplot.Rd                      |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsspng.Rd                       |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsspoints.Rd                    |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsspolygon.Rd                   |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssrect.Rd                      |only
 Rcssplot-0.3.0/Rcssplot/man/Rcssstripchart.Rd                |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsstext.Rd                      |only
 Rcssplot-0.3.0/Rcssplot/man/Rcsstitle.Rd                     |only
 Rcssplot-1.0.0/Rcssplot/DESCRIPTION                          |   13 
 Rcssplot-1.0.0/Rcssplot/MD5                                  |  105 
 Rcssplot-1.0.0/Rcssplot/NAMESPACE                            |   53 
 Rcssplot-1.0.0/Rcssplot/R/Rcss.R                             |  434 ++--
 Rcssplot-1.0.0/Rcssplot/R/RcssGet.R                          |  307 +-
 Rcssplot-1.0.0/Rcssplot/R/RcssHelpers.R                      |   54 
 Rcssplot-1.0.0/Rcssplot/R/RcssLexer.R                        |  497 ++--
 Rcssplot-1.0.0/Rcssplot/R/RcssMisc.R                         |only
 Rcssplot-1.0.0/Rcssplot/R/RcssParser.R                       |  224 +-
 Rcssplot-1.0.0/Rcssplot/R/RcssUpdate.R                       |  224 --
 Rcssplot-1.0.0/Rcssplot/R/RcssWatch.R                        |only
 Rcssplot-1.0.0/Rcssplot/R/RcssWrappers.R                     | 1189 ++++++-----
 Rcssplot-1.0.0/Rcssplot/build/vignette.rds                   |binary
 Rcssplot-1.0.0/Rcssplot/inst/doc/Rcssplot.R                  |  144 -
 Rcssplot-1.0.0/Rcssplot/inst/doc/Rcssplot.Rnw                |  274 +-
 Rcssplot-1.0.0/Rcssplot/inst/doc/Rcssplot.pdf                |binary
 Rcssplot-1.0.0/Rcssplot/man/Rcss.Rd                          |   18 
 Rcssplot-1.0.0/Rcssplot/man/RcssChange.Rd                    |   18 
 Rcssplot-1.0.0/Rcssplot/man/RcssChangePropertyValue.Rd       |   15 
 Rcssplot-1.0.0/Rcssplot/man/RcssGetCompulsoryClass.Rd        |   17 
 Rcssplot-1.0.0/Rcssplot/man/RcssGetDefaultStyle.Rd           |    6 
 Rcssplot-1.0.0/Rcssplot/man/RcssGetPropertyValue.Rd          |    9 
 Rcssplot-1.0.0/Rcssplot/man/RcssGetPropertyValueOrDefault.Rd |   16 
 Rcssplot-1.0.0/Rcssplot/man/RcssOverload.Rd                  |    6 
 Rcssplot-1.0.0/Rcssplot/man/RcssProperty.Rd                  |   17 
 Rcssplot-1.0.0/Rcssplot/man/RcssValue.Rd                     |   19 
 Rcssplot-1.0.0/Rcssplot/man/RcssWatch.Rd                     |only
 Rcssplot-1.0.0/Rcssplot/man/abline.Rd                        |only
 Rcssplot-1.0.0/Rcssplot/man/arrows.Rd                        |only
 Rcssplot-1.0.0/Rcssplot/man/axis.Rd                          |only
 Rcssplot-1.0.0/Rcssplot/man/barplot.Rd                       |only
 Rcssplot-1.0.0/Rcssplot/man/box.Rd                           |only
 Rcssplot-1.0.0/Rcssplot/man/boxplot.Rd                       |only
 Rcssplot-1.0.0/Rcssplot/man/contour.Rd                       |only
 Rcssplot-1.0.0/Rcssplot/man/ctext.Rd                         |only
 Rcssplot-1.0.0/Rcssplot/man/grid.Rd                          |only
 Rcssplot-1.0.0/Rcssplot/man/hist.Rd                          |only
 Rcssplot-1.0.0/Rcssplot/man/jpeg.Rd                          |only
 Rcssplot-1.0.0/Rcssplot/man/legend.Rd                        |only
 Rcssplot-1.0.0/Rcssplot/man/lines.Rd                         |only
 Rcssplot-1.0.0/Rcssplot/man/matplot.Rd                       |only
 Rcssplot-1.0.0/Rcssplot/man/mtext.Rd                         |only
 Rcssplot-1.0.0/Rcssplot/man/par.Rd                           |only
 Rcssplot-1.0.0/Rcssplot/man/parplot.Rd                       |only
 Rcssplot-1.0.0/Rcssplot/man/pdf.Rd                           |only
 Rcssplot-1.0.0/Rcssplot/man/plot.Rd                          |only
 Rcssplot-1.0.0/Rcssplot/man/png.Rd                           |only
 Rcssplot-1.0.0/Rcssplot/man/points.Rd                        |only
 Rcssplot-1.0.0/Rcssplot/man/polygon.Rd                       |only
 Rcssplot-1.0.0/Rcssplot/man/print.Rcss.Rd                    |    7 
 Rcssplot-1.0.0/Rcssplot/man/printRcss.Rd                     |   10 
 Rcssplot-1.0.0/Rcssplot/man/rect.Rd                          |only
 Rcssplot-1.0.0/Rcssplot/man/stripchart.Rd                    |only
 Rcssplot-1.0.0/Rcssplot/man/text.Rd                          |only
 Rcssplot-1.0.0/Rcssplot/man/title.Rd                         |only
 Rcssplot-1.0.0/Rcssplot/vignettes/Rcssplot.Rnw               |  274 +-
 80 files changed, 2162 insertions(+), 1788 deletions(-)

More information about Rcssplot at CRAN
Permanent link

Package emIRT updated to version 0.0.9 with previous version 0.0.8 dated 2017-02-14

Title: EM Algorithms for Estimating Item Response Theory Models
Description: Various Expectation-Maximization (EM) algorithms are implemented for item response theory (IRT) models. The current implementation includes IRT models for binary and ordinal responses, along with dynamic and hierarchical IRT models with binary responses. The latter two models are derived and implemented using variational EM. Subsequent edits also include variational network and text scaling models.
Author: Kosuke Imai <kimai@princeton.edu>, James Lo <lojames@usc.edu>, Jonathan Olmsted <jpolmsted@gmail.com>
Maintainer: James Lo <lojames@usc.edu>

Diff between emIRT versions 0.0.8 dated 2017-02-14 and 0.0.9 dated 2019-12-13

 ChangeLog        |    7 ++++++-
 DESCRIPTION      |    8 ++++----
 MD5              |   17 +++++++++--------
 NAMESPACE        |    3 ++-
 man/dwnom.Rd     |    6 +++---
 man/dynIRT.Rd    |    7 +++----
 man/mq_data.Rd   |    7 +++----
 man/ordIRT.Rd    |   26 +++++++++++++-------------
 src/calcLB.cpp   |    6 +++---
 src/emIRT_init.c |only
 10 files changed, 46 insertions(+), 41 deletions(-)

More information about emIRT at CRAN
Permanent link

Package rsconnect updated to version 0.8.16 with previous version 0.8.15 dated 2019-07-22

Title: Deployment Interface for R Markdown Documents and Shiny Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'RStudio Connect'. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.
Author: JJ Allaire
Maintainer: Jonathan McPherson <jonathan@rstudio.com>

Diff between rsconnect versions 0.8.15 dated 2019-07-22 and 0.8.16 dated 2019-12-13

 DESCRIPTION                          |   12 +--
 MD5                                  |   66 ++++++++++--------
 NAMESPACE                            |    1 
 NEWS.md                              |only
 R/accounts.R                         |  124 +++++++++++++++++++++++++++++++----
 R/applications.R                     |  102 ++++++++++++++++++++--------
 R/bundle.R                           |   56 +++++++++++++--
 R/connect.R                          |   13 +++
 R/dependencies.R                     |    6 -
 R/deployAPI.R                        |    4 -
 R/deployApp.R                        |   50 +++++++++++---
 R/deploySite.R                       |    9 +-
 R/deployments.R                      |   11 ++-
 R/http.R                             |   41 ++++++-----
 R/lint-framework.R                   |   14 +++
 R/lint-utils.R                       |   12 +++
 R/linters.R                          |   36 +++++++++-
 R/rsa.R                              |   40 +++++++++--
 R/utils.R                            |   33 +++++++--
 README.md                            |   45 ++++++++----
 inst/resources/environment.py        |   12 ++-
 man/accounts.Rd                      |    4 -
 man/applications.Rd                  |   16 ++--
 man/connectApiUser.Rd                |only
 man/connectUser.Rd                   |    1 
 man/deployApp.Rd                     |   16 +++-
 man/deploySite.Rd                    |   14 ++-
 man/figures                          |only
 man/setAccountInfo.Rd                |    2 
 man/writeManifest.Rd                 |    4 -
 tests/testthat/multibyte-characters  |only
 tests/testthat/shinyapp-with-browser |only
 tests/testthat/test-bundle.R         |  105 +++++++++++++++++++++++++++++
 tests/testthat/test-hashes.R         |only
 tests/testthat/test-http.R           |   42 +++++++++++
 tests/testthat/test-lint.R           |   18 ++++-
 36 files changed, 732 insertions(+), 177 deletions(-)

More information about rsconnect at CRAN
Permanent link

Package fulltext updated to version 1.4.0 with previous version 1.3.0 dated 2019-06-27

Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text 'scholarly' data, including 'Biomed Central', Public Library of Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ', 'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality included for searching for articles, downloading full or partial text, downloading supplementary materials, converting to various data formats.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between fulltext versions 1.3.0 dated 2019-06-27 and 1.4.0 dated 2019-12-13

 fulltext-1.3.0/fulltext/inst/doc/fulltext_vignette.Rmd     |only
 fulltext-1.3.0/fulltext/inst/doc/fulltext_vignette.html    |only
 fulltext-1.3.0/fulltext/inst/vign/fulltext_vignette.Rmd    |only
 fulltext-1.3.0/fulltext/inst/vign/fulltext_vignette.md     |only
 fulltext-1.3.0/fulltext/vignettes/fulltext_vignette.Rmd    |only
 fulltext-1.4.0/fulltext/DESCRIPTION                        |   15 
 fulltext-1.4.0/fulltext/MD5                                |   89 +-
 fulltext-1.4.0/fulltext/NEWS.md                            |   24 
 fulltext-1.4.0/fulltext/R/ft_browse.R                      |   15 
 fulltext-1.4.0/fulltext/R/ft_get.R                         |  428 +++++++------
 fulltext-1.4.0/fulltext/R/ft_links.R                       |   77 +-
 fulltext-1.4.0/fulltext/R/ft_table.R                       |   16 
 fulltext-1.4.0/fulltext/R/fulltext-package.R               |    2 
 fulltext-1.4.0/fulltext/R/plos_code.R                      |   25 
 fulltext-1.4.0/fulltext/R/plugins_get.R                    |   90 +-
 fulltext-1.4.0/fulltext/R/plugins_get_links.R              |    2 
 fulltext-1.4.0/fulltext/R/plugins_links.R                  |   58 +
 fulltext-1.4.0/fulltext/README.md                          |   49 -
 fulltext-1.4.0/fulltext/build/vignette.rds                 |binary
 fulltext-1.4.0/fulltext/inst/doc/formats.Rmd               |    3 
 fulltext-1.4.0/fulltext/inst/doc/formats.html              |    2 
 fulltext-1.4.0/fulltext/inst/doc/fulltext.Rmd              |only
 fulltext-1.4.0/fulltext/inst/doc/fulltext.html             |only
 fulltext-1.4.0/fulltext/inst/doc/getting_fulltext.Rmd      |   28 
 fulltext-1.4.0/fulltext/inst/doc/getting_fulltext.html     |   28 
 fulltext-1.4.0/fulltext/inst/vign/fulltext.Rmd             |only
 fulltext-1.4.0/fulltext/inst/vign/fulltext.md              |only
 fulltext-1.4.0/fulltext/inst/vign/getting_fulltext.md      |   28 
 fulltext-1.4.0/fulltext/man/biorxiv_search.Rd              |    3 
 fulltext-1.4.0/fulltext/man/cache.Rd                       |   13 
 fulltext-1.4.0/fulltext/man/cache_file_info.Rd             |    5 
 fulltext-1.4.0/fulltext/man/eupmc.Rd                       |   10 
 fulltext-1.4.0/fulltext/man/ft_abstract.Rd                 |   13 
 fulltext-1.4.0/fulltext/man/ft_browse.Rd                   |    7 
 fulltext-1.4.0/fulltext/man/ft_get.Rd                      |  123 ++-
 fulltext-1.4.0/fulltext/man/ft_links.Rd                    |   11 
 fulltext-1.4.0/fulltext/man/ft_search.Rd                   |   22 
 fulltext-1.4.0/fulltext/man/ft_table.Rd                    |    3 
 fulltext-1.4.0/fulltext/man/ftxt_cache.Rd                  |    5 
 fulltext-1.4.0/fulltext/man/fulltext-package.Rd            |    2 
 fulltext-1.4.0/fulltext/man/microsoft-internals.Rd         |   24 
 fulltext-1.4.0/fulltext/man/scopus_search.Rd               |   37 -
 fulltext-1.4.0/fulltext/tests/testthat/test-ft_abstract.R  |    8 
 fulltext-1.4.0/fulltext/tests/testthat/test-ft_browse.R    |   10 
 fulltext-1.4.0/fulltext/tests/testthat/test-ft_get.r       |   38 +
 fulltext-1.4.0/fulltext/tests/testthat/test-ft_get_utils.R |only
 fulltext-1.4.0/fulltext/tests/testthat/test-ft_links.R     |    2 
 fulltext-1.4.0/fulltext/tests/testthat/test-ft_search.R    |   18 
 fulltext-1.4.0/fulltext/vignettes/formats.Rmd              |    3 
 fulltext-1.4.0/fulltext/vignettes/fulltext.Rmd             |only
 fulltext-1.4.0/fulltext/vignettes/getting_fulltext.Rmd     |   28 
 51 files changed, 817 insertions(+), 547 deletions(-)

More information about fulltext at CRAN
Permanent link

Package rasterVis updated to version 0.47 with previous version 0.46 dated 2019-07-02

Title: Visualization Methods for Raster Data
Description: Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
Author: Oscar Perpinan Lamigueiro [cre, aut] (<https://orcid.org/0000-0002-4134-7196>), Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>

Diff between rasterVis versions 0.46 dated 2019-07-02 and 0.47 dated 2019-12-13

 DESCRIPTION                |    8 ++++----
 MD5                        |   12 ++++++------
 build/partial.rdb          |binary
 man/horizonplot-methods.Rd |    3 ++-
 man/levelplot-methods.Rd   |   11 +++++++----
 man/plot3d.Rd              |    6 +++---
 man/vectorplot.Rd          |    8 ++++----
 7 files changed, 26 insertions(+), 22 deletions(-)

More information about rasterVis at CRAN
Permanent link

Package Qtools updated to version 1.5.1 with previous version 1.4.1 dated 2019-07-13

Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These include methods for transformation-based quantile regression, quantile-based measures of location, scale and shape, methods for quantiles of discrete variables, quantile-based multiple imputation, and restricted quantile regression. A vignette is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>), Alessio Farcomeni [ctb] (Contributions to midrq code)
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>

Diff between Qtools versions 1.4.1 dated 2019-07-13 and 1.5.1 dated 2019-12-13

 DESCRIPTION           |    8 -
 MD5                   |   26 +++---
 NEWS                  |    8 +
 R/Qtools.R            |  214 +++++++++++++++++++++++++++-----------------------
 build/vignette.rds    |binary
 inst/doc/Qtools.R     |    2 
 inst/doc/Qtools.html  |    8 +
 man/Qtools-package.Rd |    4 
 man/cmidecdf.Rd       |    5 -
 man/midrq.Rd          |    6 -
 man/midrqControl.Rd   |    3 
 man/summary.midrq.Rd  |    8 +
 man/vcov.midrq.Rd     |    8 +
 src/Qtools.cpp        |    9 +-
 14 files changed, 179 insertions(+), 130 deletions(-)

More information about Qtools at CRAN
Permanent link

Package jiebaR updated to version 0.11 with previous version 0.10.99 dated 2019-03-12

Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging For R.
Author: Qin Wenfeng, Wu Yanyi
Maintainer: Qin Wenfeng <mail@qinwenfeng.com>

Diff between jiebaR versions 0.10.99 dated 2019-03-12 and 0.11 dated 2019-12-13

 jiebaR-0.10.99/jiebaR/README.md                           |only
 jiebaR-0.11/jiebaR/DESCRIPTION                            |    8 
 jiebaR-0.11/jiebaR/MD5                                    |   13 -
 jiebaR-0.11/jiebaR/build/vignette.rds                     |binary
 jiebaR-0.11/jiebaR/inst/doc/Quick_Start_Guide.Rmd         |   18 +-
 jiebaR-0.11/jiebaR/inst/doc/Quick_Start_Guide.html        |  119 +++++++-------
 jiebaR-0.11/jiebaR/inst/include/lib/limonp/StringUtil.hpp |   37 ++--
 jiebaR-0.11/jiebaR/vignettes/Quick_Start_Guide.Rmd        |   18 +-
 8 files changed, 112 insertions(+), 101 deletions(-)

More information about jiebaR at CRAN
Permanent link

Package fishmethods updated to version 1.11-1 with previous version 1.11-0 dated 2018-11-20

Title: Fishery Science Methods and Models
Description: Functions for applying a wide range of fisheries stock assessment methods.
Author: Gary A. Nelson <gary.nelson@mass.gov>
Maintainer: Gary A. Nelson <gary.nelson@mass.gov>

Diff between fishmethods versions 1.11-0 dated 2018-11-20 and 1.11-1 dated 2019-12-13

 fishmethods-1.11-0/fishmethods/R/astrocalc4r.R      |only
 fishmethods-1.11-1/fishmethods/DESCRIPTION          |   12 -
 fishmethods-1.11-1/fishmethods/MD5                  |   58 ++---
 fishmethods-1.11-1/fishmethods/NAMESPACE            |    5 
 fishmethods-1.11-1/fishmethods/R/M.empirical.R      |   10 -
 fishmethods-1.11-1/fishmethods/R/agesurv.R          |   67 ++++--
 fishmethods-1.11-1/fishmethods/R/alk.R              |  146 ++++++++------
 fishmethods-1.11-1/fishmethods/R/astrocalc4r.r      |only
 fishmethods-1.11-1/fishmethods/R/clus.vb.fit.R      |   34 +--
 fishmethods-1.11-1/fishmethods/R/dbsra.R            |    1 
 fishmethods-1.11-1/fishmethods/R/deplet.R           |   12 -
 fishmethods-1.11-1/fishmethods/R/dlproj.R           |    1 
 fishmethods-1.11-1/fishmethods/R/fm_telemetry.R     |    9 
 fishmethods-1.11-1/fishmethods/R/grotag.R           |    4 
 fishmethods-1.11-1/fishmethods/R/growth.R           |   10 -
 fishmethods-1.11-1/fishmethods/R/growthlrt.R        |   10 -
 fishmethods-1.11-1/fishmethods/R/growthmultifit.R   |    2 
 fishmethods-1.11-1/fishmethods/R/irm_cr.R           |    4 
 fishmethods-1.11-1/fishmethods/R/irm_h.R            |    2 
 fishmethods-1.11-1/fishmethods/R/pwpop.R            |    4 
 fishmethods-1.11-1/fishmethods/R/sr.R               |  195 +++++++++-----------
 fishmethods-1.11-1/fishmethods/man/M.empirical.Rd   |   13 -
 fishmethods-1.11-1/fishmethods/man/agesurv.Rd       |   22 +-
 fishmethods-1.11-1/fishmethods/man/astrocalc4r.Rd   |    2 
 fishmethods-1.11-1/fishmethods/man/clus.vb.fit.Rd   |   15 -
 fishmethods-1.11-1/fishmethods/man/dbsra.Rd         |    2 
 fishmethods-1.11-1/fishmethods/man/dlproj.Rd        |    5 
 fishmethods-1.11-1/fishmethods/man/growth.Rd        |    4 
 fishmethods-1.11-1/fishmethods/man/growthResid.Rd   |    5 
 fishmethods-1.11-1/fishmethods/man/growthTraject.Rd |    5 
 fishmethods-1.11-1/fishmethods/man/growthlrt.Rd     |    2 
 31 files changed, 357 insertions(+), 304 deletions(-)

More information about fishmethods at CRAN
Permanent link

Package DynTxRegime updated to version 4.3 with previous version 4.2 dated 2019-10-17

Title: Methods for Estimating Optimal Dynamic Treatment Regimes
Description: Methods to estimate dynamic treatment regimes using Interactive Q-Learning, Q-Learning, weighted learning, and value-search methods based on Augmented Inverse Probability Weighted Estimators and Inverse Probability Weighted Estimators.
Author: S. T. Holloway, E. B. Laber, K. A. Linn, B. Zhang, M. Davidian, and A. A. Tsiatis
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>

Diff between DynTxRegime versions 4.2 dated 2019-10-17 and 4.3 dated 2019-12-13

 DESCRIPTION                     |    8 ++---
 MD5                             |   12 ++++----
 NAMESPACE                       |    1 
 NEWS                            |    7 +++++
 R/C_TypedFit_fSet.R             |    1 
 R/F_PropensityFit_fSet.R        |   56 ++++++++++++++++++++--------------------
 R/H_class_OptimalSeqCoarsened.R |    1 
 7 files changed, 47 insertions(+), 39 deletions(-)

More information about DynTxRegime at CRAN
Permanent link

New package WorldFlora with initial version 1.0
Package: WorldFlora
Type: Package
Title: Standardize Plant Names According to World Flora Online Taxonomic Backbone
Version: 1.0
Date: 2019-12-02
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Description: World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website.
License: GPL-2
Depends: R (>= 3.5.0)
Suggests: data.table, utils
Packaged: 2019-12-06 14:10:47 UTC; RKINDT
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2019-12-13 15:40:11 UTC

More information about WorldFlora at CRAN
Permanent link

Package siland updated to version 1.4.5 with previous version 1.2 dated 2019-03-20

Title: Spatial Influence of Landscape
Description: Method to estimate the spatial influence scales of landscape variables on a response variable. The method is based on Chandler and Hepinstall-Cymerman (2016) Estimating the spatial scales of landscape effects on abundance, Landscape ecology, 31: 1383-1394, <doi:10.1007/s10980-016-0380-z>.
Author: Carpentier F. and Martin O.
Maintainer: Martin Olivier <olivier.martin@inra.fr>

Diff between siland versions 1.2 dated 2019-03-20 and 1.4.5 dated 2019-12-13

 siland-1.2/siland/R/AIC.siland.R               |only
 siland-1.2/siland/R/BIC.siland.R               |only
 siland-1.2/siland/R/data.gis.R                 |only
 siland-1.2/siland/R/fitted.siland.R            |only
 siland-1.2/siland/R/land.gis.R                 |only
 siland-1.2/siland/R/plotsif.R                  |only
 siland-1.2/siland/R/plotsiland.R               |only
 siland-1.2/siland/R/plotsiland.land.R          |only
 siland-1.2/siland/R/plotsiland.sif.R           |only
 siland-1.2/siland/R/residuals.siland.R         |only
 siland-1.2/siland/R/siland.R                   |only
 siland-1.2/siland/R/siland.quantile.R          |only
 siland-1.2/siland/man/AIC.siland.Rd            |only
 siland-1.2/siland/man/BIC.siland.Rd            |only
 siland-1.2/siland/man/data.gis.Rd              |only
 siland-1.2/siland/man/fitted.siland.Rd         |only
 siland-1.2/siland/man/land.gis.Rd              |only
 siland-1.2/siland/man/plotcontri.Rd            |only
 siland-1.2/siland/man/plotsif.Rd               |only
 siland-1.2/siland/man/plotsiland.Rd            |only
 siland-1.2/siland/man/plotsiland.land.Rd       |only
 siland-1.2/siland/man/plotsiland.sif.Rd        |only
 siland-1.2/siland/man/print.siland.Rd          |only
 siland-1.2/siland/man/residuals.siland.Rd      |only
 siland-1.2/siland/man/siland.Rd                |only
 siland-1.2/siland/man/siland.quantile.Rd       |only
 siland-1.2/siland/man/summary.siland.Rd        |only
 siland-1.4.5/siland/DESCRIPTION                |   14 
 siland-1.4.5/siland/MD5                        |  105 +++--
 siland-1.4.5/siland/NAMESPACE                  |   64 ++-
 siland-1.4.5/siland/R/AIC.Bsiland.R            |only
 siland-1.4.5/siland/R/AIC.Fsiland.R            |only
 siland-1.4.5/siland/R/BIC.Bsiland.R            |only
 siland-1.4.5/siland/R/BIC.Fsiland.R            |only
 siland-1.4.5/siland/R/Bsiland.R                |only
 siland-1.4.5/siland/R/Bsiland.lik.R            |only
 siland-1.4.5/siland/R/BsilandMinusLoglik.R     |only
 siland-1.4.5/siland/R/BsilandMinusLoglikGLMM.R |only
 siland-1.4.5/siland/R/BsilandMinusLoglikLMM.R  |only
 siland-1.4.5/siland/R/Fsiland.R                |only
 siland-1.4.5/siland/R/Fsiland.lik.R            |only
 siland-1.4.5/siland/R/Fsiland.quantile.R       |only
 siland-1.4.5/siland/R/bufferforsiland.R        |only
 siland-1.4.5/siland/R/fitted.Bsiland.R         |only
 siland-1.4.5/siland/R/fitted.Fsiland.R         |only
 siland-1.4.5/siland/R/landtoraster.R           |only
 siland-1.4.5/siland/R/landtorasterold.R        |only
 siland-1.4.5/siland/R/miscsiland.R             |  463 +++----------------------
 siland-1.4.5/siland/R/plotBsiland.land.R       |only
 siland-1.4.5/siland/R/plotFsiland.R            |only
 siland-1.4.5/siland/R/plotFsiland.land.R       |only
 siland-1.4.5/siland/R/plotFsiland.sif.R        |only
 siland-1.4.5/siland/R/print.Bsiland.R          |only
 siland-1.4.5/siland/R/residuals.Bsiland.R      |only
 siland-1.4.5/siland/R/residuals.Fsiland.R      |only
 siland-1.4.5/siland/R/summary.Bsiland.R        |only
 siland-1.4.5/siland/build/partial.rdb          |binary
 siland-1.4.5/siland/build/vignette.rds         |only
 siland-1.4.5/siland/data/dataCmoth.RData       |binary
 siland-1.4.5/siland/data/dataSiland.RData      |binary
 siland-1.4.5/siland/data/datalist              |only
 siland-1.4.5/siland/data/landCmoth.RData       |binary
 siland-1.4.5/siland/data/landSiland.RData      |binary
 siland-1.4.5/siland/inst                       |only
 siland-1.4.5/siland/man/AIC.Bsiland.Rd         |only
 siland-1.4.5/siland/man/AIC.Fsiland.Rd         |only
 siland-1.4.5/siland/man/BIC.Bsiland.Rd         |only
 siland-1.4.5/siland/man/BIC.Fsiland.Rd         |only
 siland-1.4.5/siland/man/Bsiland.Rd             |only
 siland-1.4.5/siland/man/Bsiland.lik.Rd         |only
 siland-1.4.5/siland/man/Fsiland.Rd             |only
 siland-1.4.5/siland/man/Fsiland.lik.Rd         |only
 siland-1.4.5/siland/man/Fsiland.quantile.Rd    |only
 siland-1.4.5/siland/man/bufferforsiland.Rd     |only
 siland-1.4.5/siland/man/dataCmoth.Rd           |   17 
 siland-1.4.5/siland/man/dataSiland.Rd          |   38 --
 siland-1.4.5/siland/man/fitted.Bsiland.Rd      |only
 siland-1.4.5/siland/man/fitted.Fsiland.Rd      |only
 siland-1.4.5/siland/man/landCmoth.Rd           |   48 --
 siland-1.4.5/siland/man/landSiland.Rd          |   32 -
 siland-1.4.5/siland/man/landtoraster.Rd        |only
 siland-1.4.5/siland/man/plotBsiland.land.Rd    |only
 siland-1.4.5/siland/man/plotFsiland.Rd         |only
 siland-1.4.5/siland/man/plotFsiland.land.Rd    |only
 siland-1.4.5/siland/man/plotFsiland.sif.Rd     |only
 siland-1.4.5/siland/man/print.Bsiland.Rd       |only
 siland-1.4.5/siland/man/print.Fsiland.Rd       |only
 siland-1.4.5/siland/man/residuals.Bsiland.Rd   |only
 siland-1.4.5/siland/man/residuals.Fsiland.Rd   |only
 siland-1.4.5/siland/man/summary.Bsiland.Rd     |only
 siland-1.4.5/siland/man/summary.Fsiland.Rd     |only
 siland-1.4.5/siland/vignettes                  |only
 92 files changed, 214 insertions(+), 567 deletions(-)

More information about siland at CRAN
Permanent link

New package rfishnet2 with initial version 0.1.0
Package: rfishnet2
Type: Package
Title: Exploratory Data Analysis for FishNet2 Data
Version: 0.1.0
Authors@R: c(person( "Margaux Armfield", "email = margaux.armfield@gmail.com", role = "aut"), person("Kennedy Dorsey", email = "kadorsey97@gmail.com", role = c("aut", "cre")))
Maintainer: Kennedy Dorsey <kadorsey97@gmail.com>
Description: Provides data processing and summarization of data from FishNet2.net in text and graphical outputs. Allows efficient filtering of information and data cleaning.
License: MIT + file LICENSE
URL: https://github.com/kdors/rfishnet2
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6)
Imports: pracma (>= 2.2.5), ggplot2 (>= 3.2.1), sf (>= 0.8-0)
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-12-06 10:19:31 UTC; kennedy
Author: Margaux Armfield email = margaux.armfield@gmail.com [aut], Kennedy Dorsey [aut, cre]
Repository: CRAN
Date/Publication: 2019-12-13 15:40:05 UTC

More information about rfishnet2 at CRAN
Permanent link

New package qmix with initial version 0.1.2.0
Package: qmix
Title: Finite Quantile Mixture Models
Version: 0.1.2.0
Author: Xiao Lu
Maintainer: Xiao Lu <xiao.lu.research@gmail.com>
Description: Estimates finite quantile mixture models using Markov chain Monte Carlo methods. The finite quantile mixture models include both fixed- and random-quantile specifications that are applicable to both continuous and binary dependent variables. Tools are available to assess convergence and summarize the estimation results.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Biarch: true
Depends: R (>= 3.4.0)
Imports: methods, Formula, Rcpp (>= 0.12.0), rstan (>= 2.18.1),
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-12-04 13:23:20 UTC; xiaolu
Repository: CRAN
Date/Publication: 2019-12-13 15:10:02 UTC

More information about qmix at CRAN
Permanent link

Package ehelp updated to version 1.1.1 with previous version 1.1 dated 2019-11-12

Title: Enhanced Help to Enable "Docstring"-Comments in Users Functions
Description: By overloading the R help() function, this package allows users to use "docstring" style comments within their own defined functions.
Author: Marcelo Ponce [aut, cre]
Maintainer: Marcelo Ponce <mponce@scinet.utoronto.ca>

Diff between ehelp versions 1.1 dated 2019-11-12 and 1.1.1 dated 2019-12-13

 DESCRIPTION         |    6 
 MD5                 |   18 +-
 NEWS                |    1 
 R/ehelp-utils.R     |    6 
 R/ehelp.R           |    3 
 README.md           |   43 +++--
 build/vignette.rds  |binary
 inst/doc/eHelp.html |  443 ++++++++++++++++++++++++++++++++++++++--------------
 man/ehelp.Rd        |    1 
 man/print.ehelp.Rd  |    4 
 10 files changed, 381 insertions(+), 144 deletions(-)

More information about ehelp at CRAN
Permanent link

New package fastpos with initial version 0.1.0
Package: fastpos
Type: Package
Title: Finds the Critical Sequential Point of Stability for a Pearson Correlation
Version: 0.1.0
Date: 2019-12-06
Authors@R: person("Johannes", "Titz", email = "johannes.titz@gmail.com", role = c("aut", "cre", "cph"))
Description: Finds the critical sample size ("point of stability") for a correlation to stabilize in Schoenbrodt and Perugini's definition of sequential stability (see <doi:10.1016/j.jrp.2013.05.009>).
License: GPL-3
Imports: Rcpp (>= 1.0.1), plyr, MASS, pbapply
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
BugReports: https://github.com/johannes-titz/fastpos
Encoding: UTF-8
RoxygenNote: 7.0.2
Suggests: knitr, rmarkdown, testthat (>= 2.1.0), covr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-12-06 12:43:09 UTC; jt
Author: Johannes Titz [aut, cre, cph]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Repository: CRAN
Date/Publication: 2019-12-13 15:40:08 UTC

More information about fastpos at CRAN
Permanent link

New package ClusBoot with initial version 1.0
Package: ClusBoot
Type: Package
Title: Bootstrap Clustering
Version: 1.0
Date: 2019-11-11
Author: Sugnet Lubbe
Maintainer: Sugnet Lubbe <slubbe@sun.ac.za>
Description: Clustering algorithms are designed to cluster objects into a number of clusters. Any clustering algorithm provides the 'best' grouping of objects according to some criterion. This does not guarantee a 'good' clustering solution in the sense that some allocations were not simply the result of chance. This package allows the user to apply any clustering algorithm to a data set. The cluster allocations are subjected to a bootstrap analysis to determine the extent to which the clustering structure is stable and fundamental to the data set. For more information see <https://slubbe.wixsite.com/academic-cv/conference-presentations>.
License: AGPL-3
NeedsCompilation: no
Packaged: 2019-12-05 14:52:51 UTC; filz
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2019-12-13 15:20:02 UTC

More information about ClusBoot at CRAN
Permanent link

Package tfdatasets updated to version 2.0.0 with previous version 1.13.1 dated 2019-04-09

Title: Interface to 'TensorFlow' Datasets
Description: Interface to 'TensorFlow' Datasets, a high-level library for building complex input pipelines from simple, re-usable pieces. See <https://www.tensorflow.org/programmers_guide/datasets> for additional details.
Author: Daniel Falbel [ctb, cph, cre], JJ Allaire [aut, cph], Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>), Kevin Ushey [aut], RStudio [cph, fnd], Google Inc. [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>

Diff between tfdatasets versions 1.13.1 dated 2019-04-09 and 2.0.0 dated 2019-12-13

 DESCRIPTION                                         |   14 -
 MD5                                                 |  163 ++++++++++-----
 NAMESPACE                                           |   42 +++-
 NEWS.md                                             |only
 R/data.R                                            |only
 R/dataset_methods.R                                 |  119 +++++++++--
 R/dataset_properties.R                              |   24 +-
 R/feature_spec.R                                    |only
 R/input_fn.R                                        |   18 -
 R/reexports.R                                       |    3 
 R/symbols.R                                         |   14 -
 R/tensors_dataset.R                                 |   20 +
 R/utils.R                                           |   30 ++
 README.md                                           |    7 
 build/vignette.rds                                  |binary
 data                                                |only
 inst/doc/feature_columns.R                          |only
 inst/doc/feature_columns.Rmd                        |only
 inst/doc/feature_columns.html                       |only
 inst/doc/feature_spec.R                             |only
 inst/doc/feature_spec.Rmd                           |only
 inst/doc/feature_spec.html                          |only
 inst/doc/introduction.R                             |   33 ---
 inst/doc/introduction.Rmd                           |   58 -----
 inst/doc/introduction.html                          |  209 ++++++++------------
 man/all_nominal.Rd                                  |only
 man/all_numeric.Rd                                  |only
 man/dataset_batch.Rd                                |   32 +--
 man/dataset_cache.Rd                                |   32 +--
 man/dataset_collect.Rd                              |only
 man/dataset_concatenate.Rd                          |   32 +--
 man/dataset_decode_delim.Rd                         |   32 +--
 man/dataset_filter.Rd                               |   32 +--
 man/dataset_interleave.Rd                           |   32 +--
 man/dataset_map.Rd                                  |   35 +--
 man/dataset_map_and_batch.Rd                        |   46 ++--
 man/dataset_padded_batch.Rd                         |   41 ++-
 man/dataset_prefetch.Rd                             |   32 +--
 man/dataset_prefetch_to_device.Rd                   |   32 +--
 man/dataset_prepare.Rd                              |   16 +
 man/dataset_repeat.Rd                               |   32 +--
 man/dataset_shuffle.Rd                              |   43 ++--
 man/dataset_shuffle_and_repeat.Rd                   |   35 +--
 man/dataset_skip.Rd                                 |   32 +--
 man/dataset_take.Rd                                 |   32 +--
 man/dataset_use_spec.Rd                             |only
 man/dataset_window.Rd                               |only
 man/delim_record_spec.Rd                            |   38 ++-
 man/dense_features.Rd                               |only
 man/feature_spec.Rd                                 |only
 man/file_list_dataset.Rd                            |    2 
 man/fit.FeatureSpec.Rd                              |only
 man/fixed_length_record_dataset.Rd                  |    9 
 man/has_type.Rd                                     |only
 man/hearts.Rd                                       |only
 man/input_fn.Rd                                     |    2 
 man/iterator_get_next.Rd                            |    9 
 man/iterator_initializer.Rd                         |    9 
 man/iterator_make_initializer.Rd                    |    9 
 man/iterator_string_handle.Rd                       |    9 
 man/layer_input_from_dataset.Rd                     |only
 man/make-iterator.Rd                                |   25 +-
 man/make_csv_dataset.Rd                             |   29 ++
 man/read_files.Rd                                   |   11 -
 man/reexports.Rd                                    |   16 +
 man/scaler.Rd                                       |only
 man/scaler_min_max.Rd                               |only
 man/scaler_standard.Rd                              |only
 man/selectors.Rd                                    |only
 man/sparse_tensor_slices_dataset.Rd                 |    5 
 man/step_bucketized_column.Rd                       |only
 man/step_categorical_column_with_hash_bucket.Rd     |only
 man/step_categorical_column_with_identity.Rd        |only
 man/step_categorical_column_with_vocabulary_file.Rd |only
 man/step_categorical_column_with_vocabulary_list.Rd |only
 man/step_crossed_column.Rd                          |only
 man/step_embedding_column.Rd                        |only
 man/step_indicator_column.Rd                        |only
 man/step_numeric_column.Rd                          |only
 man/step_remove_column.Rd                           |only
 man/step_shared_embeddings_column.Rd                |only
 man/steps.Rd                                        |only
 man/tensor_slices_dataset.Rd                        |    5 
 man/tensors_dataset.Rd                              |    5 
 man/text_line_dataset.Rd                            |    8 
 man/tfrecord_dataset.Rd                             |    8 
 tests/testthat.R                                    |    9 
 tests/testthat/test-dataset-fitting.R               |    9 
 tests/testthat/test-dataset-methods.R               |   45 ++++
 tests/testthat/test-dataset-prepare.R               |   24 ++
 tests/testthat/test-dataset-properties.R            |   15 +
 tests/testthat/test-decode-csv.R                    |    7 
 tests/testthat/test-feature_spec.R                  |only
 tests/testthat/test-iterators.R                     |   13 -
 tests/testthat/test-tensor-datasets.R               |   12 +
 tests/testthat/utils.R                              |   21 +-
 vignettes/feature_columns.Rmd                       |only
 vignettes/feature_spec.Rmd                          |only
 vignettes/images                                    |only
 vignettes/introduction.Rmd                          |   58 -----
 100 files changed, 1038 insertions(+), 696 deletions(-)

More information about tfdatasets at CRAN
Permanent link

New package statcanR with initial version 0.1.0
Package: statcanR
Type: Package
Title: Client for Statistics Canada's Open Economic Data
Version: 0.1.0
Authors@R: c( person("Thierry", "Warin", email = "thierry.warin@skema.edu", role =c("aut", "cre")), person("Romain", "Le Duc", role = "aut"))
Description: An easy connection with R to Statistics Canada's Web Data Service. Open economic data (formerly known as CANSIM tables, now identified by Product IDs (PID)) are accessible as a data frame, directly in the user's R environment. Warin, Le Duc (2019) <doi:10.6084/m9.figshare.10544735>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: data.table, curl
URL: http://github.com/warint/statcanR
BugReports: https://github.com/warint/statcanR/issues
NeedsCompilation: no
Packaged: 2019-12-04 21:58:53 UTC; paquettem
Author: Thierry Warin [aut, cre], Romain Le Duc [aut]
Maintainer: Thierry Warin <thierry.warin@skema.edu>
Repository: CRAN
Date/Publication: 2019-12-13 14:20:02 UTC

More information about statcanR at CRAN
Permanent link

New package SequenceSpikeSlab with initial version 0.1
Package: SequenceSpikeSlab
Type: Package
Title: Exact Bayesian Model Selection Methods for the Sparse Normal Sequence Model
Version: 0.1
Authors@R: c( person("Steven", "de Rooij", email = "steven.de.rooij@gmail.com", role = c("cre", "aut")), person("Tim", "van Erven", email = "tim@timvanerven.nl", role = "aut"), person("Botond", "Szabo", email = "b.t.szabo@math.leidenuniv.nl", role = "aut"))
Author: Steven de Rooij [cre, aut], Tim van Erven [aut], Botond Szabo [aut]
Maintainer: Steven de Rooij <steven.de.rooij@gmail.com>
Description: Contains fast functions to calculate the exact Bayes posterior for the Sparse Normal Sequence Model, which implement the algorithms described in Van Erven and Szabo (2018) <arXiv:1810.10883>. For general hierarchical priors, sample sizes up to 10,000 are feasible within half an hour on a standard laptop. For beta-binomial spike-and-slab priors, a faster algorithm is provided, which can handle sample sizes of 100,000 in half an hour. In the implementation, special care has been taken to assure numerical stability of the methods even for such large sample sizes.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.18), RcppProgress (>= 0.4.1), selectiveInference (>= 1.2.5)
LinkingTo: Rcpp, RcppProgress
RoxygenNote: 7.0.2
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-12-04 21:14:26 UTC; tve
Repository: CRAN
Date/Publication: 2019-12-13 14:20:12 UTC

More information about SequenceSpikeSlab at CRAN
Permanent link

New package sail with initial version 0.1.0
Package: sail
Title: Sparse Additive Interaction Learning
Version: 0.1.0
Authors@R: c( person("Sahir", "Bhatnagar", email = "sahir.bhatnagar@gmail.com", role = c("aut", "cre"), comment = "http://sahirbhatnagar.com/"), person("Yi", "Yang", email = "yi.yang6@mcgill.ca", role = c("aut"), comment = "http://www.math.mcgill.ca/yyang/"), person("Celia", "Greenwood", email = "celia.greenwood@mcgill.ca", role = c("aut"), comment = "https://www.mcgill.ca/statisticalgenetics/") )
Description: Sparse additive interaction learning with the strong heredity property, i.e., an interaction is selected only if its corresponding main effects are also included. Fits a linear model with non-linear interactions via penalized maximum likelihood. Interactions are limited to a single exposure or environment variable. For more information, see the website below and the accompanying paper: Bhatnagar et al., "A sparse additive model for high-dimensional interactions with an exposure variable", 2019, <DOI:10.1101/445304>.
Depends: R (>= 3.4.0)
Imports: glmnet, gglasso, methods
Suggests: grpreg, truncnorm, foreach, doParallel, testthat, covr, vdiffr, knitr, rmarkdown
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/sahirbhatnagar/sail/issues
URL: https://sahirbhatnagar.com/sail
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-12-05 04:59:48 UTC; sahir
Author: Sahir Bhatnagar [aut, cre] (http://sahirbhatnagar.com/), Yi Yang [aut] (http://www.math.mcgill.ca/yyang/), Celia Greenwood [aut] (https://www.mcgill.ca/statisticalgenetics/)
Maintainer: Sahir Bhatnagar <sahir.bhatnagar@gmail.com>
Repository: CRAN
Date/Publication: 2019-12-13 15:00:02 UTC

More information about sail at CRAN
Permanent link

New package NLPclient with initial version 1.0
Package: NLPclient
Version: 1.0
Title: Stanford 'CoreNLP' Annotation Client
Description: Stanford 'CoreNLP' annotation client. Stanford 'CoreNLP' <https://stanfordnlp.github.io/CoreNLP/index.html> integrates all NLP tools from the Stanford Natural Language Processing Group, including a part-of-speech (POS) tagger, a named entity recognizer (NER), a parser, and a coreference resolution system, and provides model files for the analysis of English. More information can be found in the README.
Authors@R: c(person("Florian", "Schwendinger", role = c("aut", "cre"), email = "FlorianSchwendinger@gmx.at"), person("Kurt", "Hornik", role = c("aut")))
Imports: NLP (>= 0.1-10), utils, xml2, curl
Depends: R (>= 3.2.0)
License: GPL-2
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-12-04 21:29:21 UTC; florian
Author: Florian Schwendinger [aut, cre], Kurt Hornik [aut]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Repository: CRAN
Date/Publication: 2019-12-13 14:20:15 UTC

More information about NLPclient at CRAN
Permanent link

Package mice updated to version 3.7.0 with previous version 3.6.0 dated 2019-07-10

Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.
Author: Stef van Buuren [aut, cre], Karin Groothuis-Oudshoorn [aut], Alexander Robitzsch [ctb], Gerko Vink [ctb], Lisa Doove [ctb], Shahab Jolani [ctb], Rianne Schouten [ctb], Philipp Gaffert [ctb], Florian Meinfelder [ctb], Bernie Gray [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>

Diff between mice versions 3.6.0 dated 2019-07-10 and 3.7.0 dated 2019-12-13

 DESCRIPTION                                   |   22 
 MD5                                           |  139 +--
 NAMESPACE                                     |    1 
 NEWS.md                                       |  978 +++++++++++++-------------
 R/check.R                                     |   86 +-
 R/edit.setup.R                                |    3 
 R/imports.R                                   |    2 
 R/method.R                                    |    6 
 R/mice.impute.2l.pan.R                        |    4 
 R/mice.impute.2lonly.mean.R                   |   83 +-
 R/mice.impute.2lonly.norm.R                   |  106 ++
 R/mice.impute.2lonly.pmm.R                    |  184 ++--
 R/mice.impute.polr.R                          |  194 ++---
 R/mice.impute.rf.R                            |  158 ++--
 R/mira.R                                      |  105 +-
 R/predictorMatrix.R                           |    2 
 man/ampute.Rd                                 |   37 
 man/appendbreak.Rd                            |    3 
 man/bwplot.mads.Rd                            |   11 
 man/bwplot.mids.Rd                            |   18 
 man/cbind.Rd                                  |    2 
 man/densityplot.mids.Rd                       |   19 
 man/extend.formula.Rd                         |    9 
 man/extend.formulas.Rd                        |   11 
 man/fluxplot.Rd                               |   21 
 man/make.blocks.Rd                            |    7 
 man/make.method.Rd                            |    8 
 man/mdc.Rd                                    |   15 
 man/mice.Rd                                   |   27 
 man/mice.impute.2l.bin.Rd                     |    7 
 man/mice.impute.2l.lmer.Rd                    |    7 
 man/mice.impute.2l.norm.Rd                    |    7 
 man/mice.impute.2l.pan.Rd                     |   23 
 man/mice.impute.2lonly.mean.Rd                |   46 -
 man/mice.impute.2lonly.norm.Rd                |   61 +
 man/mice.impute.2lonly.pmm.Rd                 |   31 
 man/mice.impute.cart.Rd                       |   31 
 man/mice.impute.jomoImpute.Rd                 |   14 
 man/mice.impute.lda.Rd                        |   31 
 man/mice.impute.logreg.Rd                     |   31 
 man/mice.impute.logreg.boot.Rd                |   31 
 man/mice.impute.mean.Rd                       |   31 
 man/mice.impute.midastouch.Rd                 |   46 -
 man/mice.impute.norm.Rd                       |   31 
 man/mice.impute.norm.boot.Rd                  |   31 
 man/mice.impute.norm.nob.Rd                   |   31 
 man/mice.impute.norm.predict.Rd               |   31 
 man/mice.impute.panImpute.Rd                  |   14 
 man/mice.impute.pmm.Rd                        |   43 -
 man/mice.impute.polr.Rd                       |   60 +
 man/mice.impute.polyreg.Rd                    |   43 -
 man/mice.impute.quadratic.Rd                  |   31 
 man/mice.impute.rf.Rd                         |   41 -
 man/mice.impute.ri.Rd                         |   31 
 man/mids2mplus.Rd                             |   10 
 man/mids2spss.Rd                              |   11 
 man/mipo.Rd                                   |   13 
 man/mira-class.Rd                             |   28 
 man/parlmice.Rd                               |   16 
 man/plot.mids.Rd                              |   12 
 man/pool.Rd                                   |    2 
 man/pool.compare.Rd                           |    2 
 man/quickpred.Rd                              |   10 
 man/squeeze.Rd                                |    3 
 man/stripplot.mids.Rd                         |   18 
 man/summary.Rd                                |    3 
 man/xyplot.mads.Rd                            |   11 
 man/xyplot.mids.Rd                            |   15 
 tests/testthat/test-mice.impute.2lonly.mean.R |   34 
 tests/testthat/test-mice.impute.2lonly.norm.R |only
 tests/testthat/test-rbind.R                   |    4 
 71 files changed, 1880 insertions(+), 1357 deletions(-)

More information about mice at CRAN
Permanent link

Package lbreg updated to version 1.3 with previous version 1.2 dated 2018-01-19

Title: Log-Binomial Regression with Constrained Optimization
Description: Maximum likelihood estimation of log-binomial regression with special functionality when the MLE is on the boundary of the parameter space.
Author: Bernardo B. Andrade
Maintainer: Bernardo Andrade <bbandrade@unb.br>

Diff between lbreg versions 1.2 dated 2018-01-19 and 1.3 dated 2019-12-13

 DESCRIPTION          |    8 ++++----
 MD5                  |   17 +++++++++--------
 NEWS                 |only
 R/lbreg.fit.R        |   39 ++++++++++++++++++---------------------
 R/predict.lbreg.R    |   35 ++++++++++++++---------------------
 build/partial.rdb    |binary
 man/lbreg-package.Rd |    4 ++--
 man/lbreg.Rd         |    2 +-
 man/predict.lbreg.Rd |    2 +-
 man/relrisk.Rd       |    2 +-
 10 files changed, 50 insertions(+), 59 deletions(-)

More information about lbreg at CRAN
Permanent link

New package imputeFin with initial version 0.1.0
Package: imputeFin
Title: Imputation of Financial Time Series with Missing Values
Version: 0.1.0
Date: 2019-12-05
Description: Missing values often occur in financial data due to a variety of reasons (errors in the collection process or in the processing stage, lack of asset liquidity, lack of reporting of funds, etc.). However, most data analysis methods expect complete data and cannot be employed with missing values. One convenient way to deal with this issue without having to redesign the data analysis method is to impute the missing values. This package provides an efficient way to impute the missing values based on modeling the time series with a random walk or an autoregressive (AR) model, convenient to model log-prices and log-volumes in financial data. In the current version, the imputation is univariate-based (so no asset correlation is used). The package is based on the paper: J. Liu, S. Kumar, and D. P. Palomar (2019). Parameter Estimation of Heavy-Tailed AR Model With Missing Data Via Stochastic EM. IEEE Trans. on Signal Processing, vol. 67, no. 8, pp. 2159-2172. <doi:10.1109/TSP.2019.2899816>.
Authors@R: c( person("Junyan", "Liu", role = "aut", email = "jliubl@connect.ust.hk"), person(c("Daniel", "P."), "Palomar", role = c("cre", "aut"), email = "daniel.p.palomar@gmail.com") )
Maintainer: Daniel P. Palomar <daniel.p.palomar@gmail.com>
URL: https://CRAN.R-project.org/package=imputeFin, https://github.com/dppalomar/imputeFin
BugReports: https://github.com/dppalomar/imputeFin/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.0
Imports: MASS, zoo
Suggests: bookdown, knitr, ggplot2, prettydoc, rmarkdown, R.rsp, testthat, xts
VignetteBuilder: knitr, rmarkdown, R.rsp
NeedsCompilation: no
Packaged: 2019-12-05 02:45:30 UTC; palomar
Author: Junyan Liu [aut], Daniel P. Palomar [cre, aut]
Repository: CRAN
Date/Publication: 2019-12-13 15:00:06 UTC

More information about imputeFin at CRAN
Permanent link

Package heritability updated to version 1.3 with previous version 1.2 dated 2016-12-22

Title: Marker-Based Estimation of Heritability Using Individual Plant or Plot Data
Description: Implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants or plot-level data in a field trial. Heritability can then be estimated using a mixed model for the individual plant or plot data. For comparison, also mixed-model based estimation using genotypic means and estimation of repeatability with ANOVA are implemented. For illustration the package contains several datasets for the model species Arabidopsis thaliana.
Author: Willem Kruijer, with a contribution from Ian White (the internal function pin). Contains data collected by Padraic Flood and Rik Kooke.
Maintainer: Willem Kruijer <willem.kruijer@wur.nl>

Diff between heritability versions 1.2 dated 2016-12-22 and 1.3 dated 2019-12-13

 DESCRIPTION              |    8 
 MD5                      |    6 
 R/AI_algorithm.R         |  498 +++++++++++++++++++++++------------------------
 R/AI_algorithm_weights.r |  434 ++++++++++++++++++++--------------------
 4 files changed, 473 insertions(+), 473 deletions(-)

More information about heritability at CRAN
Permanent link

New package gorica with initial version 0.1.0
Package: gorica
Type: Package
Date: 2019-11-24
Title: Evaluation of Inequality Constrained Hypotheses Using GORICA
Version: 0.1.0
Authors@R: c( person(c("Rebecca M."), "Kuiper", role = "aut"), person(c("Altinisik"), "Yasin", role = "aut"), person(c("Caspar", "J."), "van Lissa", role = c("aut", "cre"), email = "c.j.vanlissa@uu.nl") )
Description: Implements the generalized order-restricted information criterion approximation (GORICA) by Kuiper, Hoijtink, & Silvapulle (2012) <doi:10.1016/j.jspi.2012.03.007>. The GORICA is an AIC-like information criterion that can be utilized to evaluate informative hypotheses specifying directional relationships between model parameters in terms of (in)equality constraints. The GORICA is applicable not only to normal linear models, but also to generalized linear models (GLMs), generalized linear mixed models (GLMMs), and structural equation models (SEMs). In addition, the GORICA can be utilized in the context of contingency tables for which (in)equality constrained hypotheses do not necessarily contain linear restrictions on cell probabilities, but instead often contain non-linear restrictions on cell probabilities.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://informative-hypotheses.sites.uu.nl/software/goric/
NeedsCompilation: no
RoxygenNote: 6.1.1
Depends: R (>= 3.0.0), bain (>= 0.2.2), stats
Imports: MASS, mvtnorm, quadprog, lme4, lavaan
Suggests: testthat
Packaged: 2019-12-04 18:05:48 UTC; Lissa102
Author: Rebecca M. Kuiper [aut], Altinisik Yasin [aut], Caspar J. van Lissa [aut, cre]
Maintainer: Caspar J. van Lissa <c.j.vanlissa@uu.nl>
Repository: CRAN
Date/Publication: 2019-12-13 14:20:09 UTC

More information about gorica at CRAN
Permanent link

New package christmas with initial version 1.0.0
Package: christmas
Type: Package
Title: Generation of Christmas Cards
Version: 1.0.0
Depends: R (>= 3.4)
Imports: animation (>= 2.6), grDevices, graphics, stats, methods
Author: Jose Barrera-Gomez
Maintainer: Jose Barrera-Gomez <jose.barrera@isglobal.org>
Description: Generates a number of Christmas cards, most of them being animated. The name of each card includes the year in which it was created.
License: GPL-2
URL: https://sites.google.com/view/josebarrera/
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-12-04 22:56:10 UTC; jose
Repository: CRAN
Date/Publication: 2019-12-13 14:30:02 UTC

More information about christmas at CRAN
Permanent link

New package ttbary with initial version 0.1-1
Package: ttbary
Version: 0.1-1
Date: 2019-11-30
Title: Barycenter Methods for Spatial Point Patterns
Authors@R: c(person("Raoul", "Müller", email = "raoul.mueller@uni-goettingen.de", role = "aut"), person("Dominic", "Schuhmacher", email = "dominic.schuhmacher@mathematik.uni-goettingen.de", role = c("aut","cre"), comment = c(ORCID = "0000-0001-7079-6313")))
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Depends: R (>= 3.0.0), spatstat (>= 1.50-0)
LinkingTo: Rcpp
Imports: grDevices, graphics, stats, Rcpp
Description: Computes a point pattern in R^2 or on a graph that is representative of a collection of many data patterns. The result is an approximate barycenter (also known as Fréchet mean or prototype) based on a transport-transform metric. Possible choices include Optimal SubPattern Assignment (OSPA) and Spike Time metrics. Details can be found in Müller, Schuhmacher and Mateu (2019) <arXiv:1909.07266>.
LazyData: yes
Encoding: UTF-8
License: GPL (>= 2)
RoxygenNote: 7.0.0
NeedsCompilation: yes
Packaged: 2019-11-30 13:00:17 UTC; schumi
Author: Raoul Müller [aut], Dominic Schuhmacher [aut, cre] (<https://orcid.org/0000-0001-7079-6313>)
Repository: CRAN
Date/Publication: 2019-12-13 13:20:02 UTC

More information about ttbary at CRAN
Permanent link

New package qgg with initial version 1.0.0
Package: qgg
Type: Package
Title: Statistical Tools for Quantitative Genetic Analyses
Version: 1.0.0
Date: 2019-11-29
Authors@R: c(person("Peter", "Soerensen", email = "peter.sorensen@r-qgg.org", role = c("aut", "cre")), person("Palle", "Duun Rohde", email = "palle.d.rohde@mbg.au.dk", role = "aut"), person("Izel", "Fourie Soerensen", email = "izel.sorensen@gmail.com", role = "aut"))
Maintainer: Peter Soerensen <peter.sorensen@r-qgg.org>
Description: Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses. Rohde et al. (2019) <doi:10.1101/503631>.
License: GPL-3
Encoding: UTF-8
Imports: data.table, parallel, statmod, stats, MCMCpack, MASS
RoxygenNote: 6.1.1
URL: https://github.com/psoerensen/qgg
BugReports: https://github.com/psoerensen/qgg/issues
NeedsCompilation: yes
Packaged: 2019-11-30 18:00:15 UTC; Peter
Author: Peter Soerensen [aut, cre], Palle Duun Rohde [aut], Izel Fourie Soerensen [aut]
Repository: CRAN
Date/Publication: 2019-12-13 13:10:03 UTC

More information about qgg at CRAN
Permanent link

New package hackeRnews with initial version 0.1.0
Package: hackeRnews
Title: Wrapper for the 'Official Hacker News' API
Version: 0.1.0
Authors@R: c( person(given = "Ryszard", family = "Szymanski", role = c("aut", "cre"), email = "ryszard.szymanski@outlook.com"), person(given = "Piotr", family = "Janus", role = c("aut")), person(given = "Zuzanna", family = "Magierska", role = c("aut")), person(given = "Rafal", family = "Muszynski", role = c("aut")), person(given = "Andrzej", family = "Nowikowski", role = c("aut")) )
Maintainer: Ryszard Szymanski <ryszard.szymanski@outlook.com>
Description: Use the <https://hacker-news.firebaseio.com/v0/> API through R. Retrieve posts, articles and other items in form of convenient R objects.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: covr, testthat (>= 2.1.0), httptest, knitr, rmarkdown, spelling
RoxygenNote: 6.1.1
Imports: utils, httr, jsonlite, tibble, future.apply
VignetteBuilder: knitr
URL: https://github.com/szymanskir/hackeRnews
BugReports: https://github.com/szymanskir/hackeRnews/issues
Language: en-US
NeedsCompilation: no
Packaged: 2019-11-30 17:02:26 UTC; szymanskir
Author: Ryszard Szymanski [aut, cre], Piotr Janus [aut], Zuzanna Magierska [aut], Rafal Muszynski [aut], Andrzej Nowikowski [aut]
Repository: CRAN
Date/Publication: 2019-12-13 13:20:05 UTC

More information about hackeRnews at CRAN
Permanent link

New package dhReg with initial version 0.1.0
Package: dhReg
Type: Package
Title: Dynamic Harmonic Regression
Version: 0.1.0
Author: Pranay Gaikwad
Maintainer: Pranay Gaikwad <pranay3113@gmail.com>
Description: Building and forecasting time series data with multiple seasonality using Dynamic Harmonic Regression.
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 6.1.1
Depends: forecast, future.apply, stats, future, testthat
URL: https://otexts.com/fpp2/dhr.html
NeedsCompilation: no
Packaged: 2019-12-03 08:25:18 UTC; Priyanka Gaikwad
Repository: CRAN
Date/Publication: 2019-12-13 14:00:02 UTC

More information about dhReg at CRAN
Permanent link

New package climate with initial version 0.3.0
Package: climate
Title: Interface to Download Meteorological (and Hydrological) Datasets
Version: 0.3.0
Authors@R: c(person(given = "Bartosz", family = "Czernecki", role = c("aut", "cre"), email = "nwp@amu.edu.pl", comment = c(ORCID = "0000-0001-6496-1386")), person(given = "Arkadiusz", family = "Głogowski", role = "aut", email = "arkadiusz.glogowski@upwr.edu.pl", comment = c(ORCID = "0000-0002-7587-8892")), person(given = "Jakub", family = "Nowosad", role = "aut", email = "nowosad.jakub@gmail.com", comment = c(ORCID = "0000-0002-1057-3721")), person("IMGW-PIB", role = "ctb", comment = "source of the data"))
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories: OGIMET (<http://ogimet.com/index.phtml.en>), University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair>), and Polish Institute of Meterology and Water Management - National Research Institute (<https://dane.imgw.pl>). This package also allows for adding geographical coordinates for each observation.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.1
Depends: R (>= 3.1)
Imports: RCurl, XML, imgw
Suggests: testthat, knitr, rmarkdown, dplyr, tidyr, maps
URL: https://github.com/bczernecki/climate
BugReports: https://github.com/bczernecki/climate/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-12-04 13:48:17 UTC; bartosz
Author: Bartosz Czernecki [aut, cre] (<https://orcid.org/0000-0001-6496-1386>), Arkadiusz Głogowski [aut] (<https://orcid.org/0000-0002-7587-8892>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), IMGW-PIB [ctb] (source of the data)
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Repository: CRAN
Date/Publication: 2019-12-13 13:50:02 UTC

More information about climate at CRAN
Permanent link

New package bestSDP with initial version 0.1.2
Package: bestSDP
Type: Package
Title: Burden Estimate of Common Communicable Diseases in Settlements of Displaced Populations
Version: 0.1.2
Authors@R: person("You", "Li", email = "You.Li2@ed.ac.uk", role = c("aut", "cre"))
Maintainer: You Li <You.Li2@ed.ac.uk>
Description: Provides a practical tool for estimating the burden of common communicable diseases in settlements of displaced populations. An online version of the tool can be found at <http://who-refugee-bod.ecdf.ed.ac.uk/shiny/app/>. Estimates of burden of disease aim to synthesize data about cause-specific morbidity and mortality through a systematic approach that enables evidence-based decisions and comparisons across settings. The focus of this tool is on four acute communicable diseases and syndromes, including Acute respiratory infections, Acute diarrheal diseases, Acute jaundice syndrome and Acute febrile illnesses.
License: GPL (>= 2)
Imports: shiny, shinythemes, shinydashboard, shinyWidgets, shinyBS, shinyjs, tidyr, dplyr, readxl, ggplot2, rlist, DT, stringr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-11-30 21:44:12 UTC; youli
Author: You Li [aut, cre]
Repository: CRAN
Date/Publication: 2019-12-13 13:10:06 UTC

More information about bestSDP at CRAN
Permanent link

Package UCSCXenaTools updated to version 1.2.10 with previous version 1.2.9 dated 2019-11-25

Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Xue-Song Liu [aut] (<https://orcid.org/0000-0002-7736-0077>), Martin Morgan [ctb], Christine Stawitz [rev] (Christine reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/315>), Carl Ganz [rev] (Carl reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/315>)
Maintainer: Shixiang Wang <w_shixiang@163.com>

Diff between UCSCXenaTools versions 1.2.9 dated 2019-11-25 and 1.2.10 dated 2019-12-13

 DESCRIPTION                 |    9 +++++----
 MD5                         |   12 ++++++------
 NEWS.md                     |    5 +++++
 data/XenaData.rda           |binary
 inst/doc/USCSXenaTools.Rmd  |    5 ++++-
 inst/doc/USCSXenaTools.html |   29 +++++++++++++++--------------
 vignettes/USCSXenaTools.Rmd |    5 ++++-
 7 files changed, 39 insertions(+), 26 deletions(-)

More information about UCSCXenaTools at CRAN
Permanent link

New package poibin with initial version 1.4
Package: poibin
Type: Package
Title: The Poisson Binomial Distribution
Version: 1.4
Date: 2019-12-12
Author: Yili Hong
Maintainer: Yili Hong <yilihong@vt.edu>
Description: Implementation of both the exact and approximation methods for computing the cdf of the Poisson binomial distribution. It also provides the pmf, quantile function, and random number generation for the Poisson binomial distribution. We would like to acknowledge that the C code for FFT is adopted from R distribution (fft.c, by Ross Ihaka from University of Auckland, dated February 1997).
License: GPL-2
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2019-12-12 22:22:10 UTC; yilihong
Repository: CRAN
Date/Publication: 2019-12-13 05:40:02 UTC

More information about poibin at CRAN
Permanent link

New package asciicast with initial version 1.0.0
Package: asciicast
Title: Create 'Ascii' Screen Casts from R Scripts
Version: 1.0.0
Authors@R: c( person(given = "Gábor", family = "Csárdi", role = c("aut", "cre"), email = "csardi.gabor@gmail.com"), person(given = "Romain", family = "Francois", role = "aut"), person(given = "Mario", family = "Nebl", role = "aut", comment = "https://github.com/marionebl/svg-term author"), person(given = "Marcin", family = "Kulik", role = "aut", comment = "https://github.com/asciinema/asciinema-player author"))
Description: Record 'asciicast' screen casts from R scripts. Convert them to animated SVG images, to be used in 'README' files, or blog posts. Includes 'asciinema-player' as an 'HTML' widget, and an 'asciicast' 'knitr' engine, to embed 'ascii' screen casts in 'Rmarkdown' documents.
License: MIT + file LICENSE
Imports: curl, jsonlite, processx (>= 3.4.0), tibble, utils, uuid, V8
Suggests: cli, htmlwidgets, knitr, rmarkdown
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.1.9000
VignetteBuilder: asciicast
NeedsCompilation: no
Packaged: 2019-12-01 14:49:00 UTC; gaborcsardi
Author: Gábor Csárdi [aut, cre], Romain Francois [aut], Mario Nebl [aut] (https://github.com/marionebl/svg-term author), Marcin Kulik [aut] (https://github.com/asciinema/asciinema-player author)
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Repository: CRAN
Date/Publication: 2019-12-13 13:00:02 UTC

More information about asciicast at CRAN
Permanent link

Package quantreg updated to version 5.54 with previous version 5.52 dated 2019-11-09

Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included.
Author: Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>

Diff between quantreg versions 5.52 dated 2019-11-09 and 5.54 dated 2019-12-13

 DESCRIPTION        |    6 +++---
 MD5                |   12 ++++++------
 R/boot.R           |    4 ++--
 R/crq.R            |    2 +-
 build/vignette.rds |binary
 inst/ChangeLog     |   12 ++++++++++++
 man/crq.Rd         |    2 +-
 7 files changed, 25 insertions(+), 13 deletions(-)

More information about quantreg at CRAN
Permanent link

Package magclass updated to version 5.7.0 with previous version 5.5.0 dated 2019-12-06

Title: Data Class and Tools for Handling Spatial-Temporal Data
Description: Data class for increased interoperability working with spatial- temporal data together with corresponding functions and methods (conversions, basic calculations and basic data manipulation). The class distinguishes between spatial, temporal and other dimensions to facilitate the development and interoperability of tools build for it. Additional features are name-based addressing of data and internal consistency checks (e.g. checking for the right data order in calculations).
Author: Jan Philipp Dietrich [aut, cre], Benjamin Leon Bodirsky [aut], Markus Bonsch [aut], Florian Humpenoeder [aut], Stephen Bi [aut], Kristine Karstens [aut], Lavinia Baumstark [ctb], Christoph Bertram [ctb], Anastasis Giannousakis [ctb], David Klein [ctb], Ina Neher [ctb], Michaja Pehl [ctb], Anselm Schultes [ctb], Miodrag Stevanovic [ctb], Xiaoxi Wang [ctb]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>

Diff between magclass versions 5.5.0 dated 2019-12-06 and 5.7.0 dated 2019-12-13

 magclass-5.5.0/magclass/vignettes/magclass-concept.md    |only
 magclass-5.5.0/magclass/vignettes/magclass.md            |only
 magclass-5.7.0/magclass/DESCRIPTION                      |    8 +-
 magclass-5.7.0/magclass/MD5                              |   33 +++++-----
 magclass-5.7.0/magclass/NAMESPACE                        |    1 
 magclass-5.7.0/magclass/R/getDim.R                       |   46 +++++++++++----
 magclass-5.7.0/magclass/R/getItems.R                     |   15 ++++
 magclass-5.7.0/magclass/R/getSets.R                      |   13 +++-
 magclass-5.7.0/magclass/R/mcalc.R                        |    4 -
 magclass-5.7.0/magclass/build/vignette.rds               |binary
 magclass-5.7.0/magclass/inst/doc/magclass-concept.html   |    4 -
 magclass-5.7.0/magclass/inst/doc/magclass-expansion.html |    4 -
 magclass-5.7.0/magclass/inst/doc/magclass.html           |    7 +-
 magclass-5.7.0/magclass/man/getDim.Rd                    |   17 ++++-
 magclass-5.7.0/magclass/man/getItems.Rd                  |    2 
 magclass-5.7.0/magclass/man/getSets.Rd                   |    4 -
 magclass-5.7.0/magclass/tests/testthat/test-getDim.R     |only
 magclass-5.7.0/magclass/tests/testthat/test-getItems.R   |    8 ++
 magclass-5.7.0/magclass/tests/testthat/test-getSets.R    |    6 +
 19 files changed, 120 insertions(+), 52 deletions(-)

More information about magclass at CRAN
Permanent link

Package lmerTest updated to version 3.1-1 with previous version 3.1-0 dated 2019-02-11

Title: Tests in Linear Mixed Effects Models
Description: Provides p-values in type I, II or III anova and summary tables for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via the pbkrtest package. Model selection methods include step, drop1 and anova-like tables for random effects (ranova). Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed effects are also available.
Author: Alexandra Kuznetsova [aut], Per Bruun Brockhoff [aut, ths], Rune Haubo Bojesen Christensen [aut], Sofie Pødenphant Jensen [ctb, cre]
Maintainer: Sofie Pødenphant Jensen <sofp@dtu.dk>

Diff between lmerTest versions 3.1-0 dated 2019-02-11 and 3.1-1 dated 2019-12-13

 DESCRIPTION       |   18 ++++++++++--------
 MD5               |    6 +++---
 NEWS.md           |    6 ++++++
 tests/test_lmer.R |   14 --------------
 4 files changed, 19 insertions(+), 25 deletions(-)

More information about lmerTest at CRAN
Permanent link

Package ERP updated to version 2.2 with previous version 2.1 dated 2018-10-05

Title: Significance Analysis of Event-Related Potentials Data
Description: Functions for signal detection and identification designed for Event-Related Potentials (ERP) data in a linear model framework. The functional F-test proposed in Causeur, Sheu, Perthame, Rufini (2018, submitted) for analysis of variance issues in ERP designs is implemented for signal detection (tests for mean difference among groups of curves in One-way ANOVA designs for example). Once an experimental effect is declared significant, identification of significant intervals is achieved by the multiple testing procedures reviewed and compared in Sheu, Perthame, Lee and Causeur (2016, <DOI:10.1214/15-AOAS888>). Some of the methods gathered in the package are the classical FDR- and FWER-controlling procedures, also available using function p.adjust. The package also implements the Guthrie-Buchwald procedure (Guthrie and Buchwald, 1991 <DOI:10.1111/j.1469-8986.1991.tb00417.x>), which accounts for the auto-correlation among t-tests to control erroneous detection of short intervals. The Adaptive Factor-Adjustment method is an extension of the method described in Causeur, Chu, Hsieh and Sheu (2012, <DOI:10.3758/s13428-012-0230-0>). It assumes a factor model for the correlation among tests and combines adaptively the estimation of the signal and the updating of the dependence modelling (see Sheu et al., 2016, <DOI:10.1214/15-AOAS888> for further details).
Author: David Causeur, Ching-Fan Sheu, Mei-Chen Chu, Flavia Rufini
Maintainer: David Causeur <david.causeur@agrocampus-ouest.fr>

Diff between ERP versions 2.1 dated 2018-10-05 and 2.2 dated 2019-12-13

 ERP-2.1/ERP/R/ERP-internal.R  |only
 ERP-2.2/ERP/DESCRIPTION       |    8 ++--
 ERP-2.2/ERP/MD5               |   15 +++----
 ERP-2.2/ERP/R/emfa.R          |    5 +-
 ERP-2.2/ERP/R/erpFtest.R      |   17 ++++----
 ERP-2.2/ERP/R/erpfatest.R     |   83 +++++++++++++++++++++---------------------
 ERP-2.2/ERP/R/ifa.R           |    2 -
 ERP-2.2/ERP/build/partial.rdb |binary
 ERP-2.2/ERP/inst/doc/ERP.html |   16 ++++----
 9 files changed, 71 insertions(+), 75 deletions(-)

More information about ERP at CRAN
Permanent link

Package clusterSim updated to version 0.48-3 with previous version 0.48-2 dated 2019-11-21

Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data). (MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>, HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>, RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>, JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>, MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>, JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>, DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>, CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>, HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>, TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>, BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>, WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>

Diff between clusterSim versions 0.48-2 dated 2019-11-21 and 0.48-3 dated 2019-12-13

 DESCRIPTION             |    8 ++++----
 MD5                     |   19 ++++++++++---------
 R/cluster.Gen.r         |    6 +++---
 R/data.Normalization2.r |only
 R/speccl.r              |   42 +++++++++++++++++++++---------------------
 data/data_binary.rda    |binary
 data/data_interval.rda  |binary
 data/data_mixed.rda     |binary
 data/data_nominal.rda   |binary
 data/data_ordinal.rda   |binary
 data/data_ratio.rda     |binary
 11 files changed, 38 insertions(+), 37 deletions(-)

More information about clusterSim at CRAN
Permanent link

Package bayest updated to version 1.1 with previous version 1.0 dated 2019-08-02

Title: Bayesian t-Test
Description: Provides an Markov-Chain-Monte-Carlo algorithm for Bayesian t-tests on the effect size. The underlying Gibbs sampler is based on a two-component Gaussian mixture and approximates the posterior distributions of the effect size, the difference of means and difference of standard deviations. A posterior analysis of the effect size via the region of practical equivalence is provided, too. For more details about the Gibbs sampler see Kelter (2019) <arXiv:1906.07524>.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>

Diff between bayest versions 1.0 dated 2019-08-02 and 1.1 dated 2019-12-13

 DESCRIPTION         |    8 ++---
 MD5                 |    8 ++---
 R/bayest.R          |   74 ++++++++++++++++++++++++++++++++++++++++++++--------
 build/partial.rdb   |binary
 man/bayes.t.test.Rd |    4 +-
 5 files changed, 74 insertions(+), 20 deletions(-)

More information about bayest at CRAN
Permanent link

New package yamlet with initial version 0.2.1
Package: yamlet
Type: Package
Title: Store Data Specification as YAML
Version: 0.2.1
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Description: A data specification is useful both for developing and documenting data. The 'yamlet' package reads YAML-formatted metadata and applies it as data item attributes. Data and metadata are stored independently and optionally associated by naming conventions. For compact representation, keys label and guide are assigned by default to the first two anonymous values for each named item. Defaults can be over-ridden by stored metadata or by function arguments. See package?yamlet and ?decorate.data.frame.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: yaml, csv, encode, ggplot2
RoxygenNote: 7.0.2
NeedsCompilation: no
Packaged: 2019-12-04 13:13:26 UTC; tim.bergsma
Repository: CRAN
Date/Publication: 2019-12-13 10:50:03 UTC

More information about yamlet at CRAN
Permanent link

Package mrbsizeR updated to version 1.2.1 with previous version 1.2 dated 2019-12-06

Title: Scale Space Multiresolution Analysis of Random Signals
Description: A method for the multiresolution analysis of spatial fields and images to capture scale-dependent features. mrbsizeR is based on scale space smoothing and uses differences of smooths at neighbouring scales for finding features on different scales. To infer which of the captured features are credible, Bayesian analysis is used. The scale space multiresolution analysis has three steps: (1) Bayesian signal reconstruction. (2) Using differences of smooths, scale-dependent features of the reconstructed signal can be found. (3) Posterior credibility analysis of the differences of smooths created. The method has first been proposed by Holmstrom, Pasanen, Furrer, Sain (2011) <DOI:10.1016/j.csda.2011.04.011>. Matlab code is available under <http://cc.oulu.fi/~lpasanen/MRBSiZer/>.
Author: Thimo Schuster [aut], Roman Flury [cre, aut], Leena Pasanen [ctb], Reinhard Furrer [ctb]
Maintainer: Roman Flury <roman.flury@math.uzh.ch>

Diff between mrbsizeR versions 1.2 dated 2019-12-06 and 1.2.1 dated 2019-12-13

 DESCRIPTION           |    8 ++---
 MD5                   |   12 +++----
 NEWS.md               |   10 ++++++
 R/eigenQsphere.R      |   76 +++++++++++++++++++++++++-------------------------
 inst/doc/mrbsizeR.pdf |binary
 man/eigenQsphere.Rd   |    8 ++---
 src/rcpp_helper.cpp   |    2 -
 7 files changed, 63 insertions(+), 53 deletions(-)

More information about mrbsizeR at CRAN
Permanent link

Package ICAMS updated to version 2.0.10 with previous version 2.0.8 dated 2019-07-24

Title: In-depth Characterization and Analysis of Mutational Signatures ('ICAMS')
Description: Analysis and visualization of experimentally elucidated mutational signatures -- the kind of analysis and visualization in Boot et al., "In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors", Genome Research 2018, <doi:10.1101/gr.230219.117>. 'ICAMS' stands for In-depth Characterization and Analysis of Mutational Signatures. 'ICAMS' has functions to read in variant call files (VCFs) and to collate the corresponding catalogs of mutational spectra and to analyze and plot catalogs of mutational spectra and signatures. Handles both "counts-based" and "density-based" catalogs of mutational spectra or signatures.
Author: Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu
Maintainer: Steve Rozen <steverozen@gmail.com>

Diff between ICAMS versions 2.0.8 dated 2019-07-24 and 2.0.10 dated 2019-12-13

 ICAMS-2.0.10/ICAMS/DESCRIPTION                                             |    6 
 ICAMS-2.0.10/ICAMS/MD5                                                     |  186 +-
 ICAMS-2.0.10/ICAMS/NAMESPACE                                               |   10 
 ICAMS-2.0.10/ICAMS/R/COMPOSITE.R                                           |only
 ICAMS-2.0.10/ICAMS/R/ICAMS.R                                               |   21 
 ICAMS-2.0.10/ICAMS/R/ID_functions.R                                        |only
 ICAMS-2.0.10/ICAMS/R/VCF_to_catalog_functions.R                            |  844 ++++++----
 ICAMS-2.0.10/ICAMS/R/data.R                                                |   75 
 ICAMS-2.0.10/ICAMS/R/other_catalog_formats.R                               |  227 ++
 ICAMS-2.0.10/ICAMS/R/plot.R                                                |   79 
 ICAMS-2.0.10/ICAMS/R/read_write_catalog.R                                  |   52 
 ICAMS-2.0.10/ICAMS/R/strandbias_functions.R                                |only
 ICAMS-2.0.10/ICAMS/R/sysdata.rda                                           |binary
 ICAMS-2.0.10/ICAMS/R/test_functions.R                                      |    2 
 ICAMS-2.0.10/ICAMS/R/utility_functions.R                                   |  321 +++
 ICAMS-2.0.10/ICAMS/README.md                                               |   27 
 ICAMS-2.0.10/ICAMS/data/all.abundance.rda                                  |binary
 ICAMS-2.0.10/ICAMS/data/catalog.row.order.rda                              |binary
 ICAMS-2.0.10/ICAMS/data/catalog.row.order.sp.rda                           |only
 ICAMS-2.0.10/ICAMS/data/datalist                                           |only
 ICAMS-2.0.10/ICAMS/data/gene.expression.data.HepG2.rda                     |only
 ICAMS-2.0.10/ICAMS/data/gene.expression.data.MCF10A.rda                    |only
 ICAMS-2.0.10/ICAMS/data/trans.ranges.GRCh37.rda                            |binary
 ICAMS-2.0.10/ICAMS/data/trans.ranges.GRCh38.rda                            |binary
 ICAMS-2.0.10/ICAMS/data/trans.ranges.GRCm38.rda                            |binary
 ICAMS-2.0.10/ICAMS/inst/WORDLIST                                           |   53 
 ICAMS-2.0.10/ICAMS/inst/extdata/strelka.regress.cat.dbs.144.csv            |    2 
 ICAMS-2.0.10/ICAMS/man/AnnotateDBSVCF.Rd                                   |only
 ICAMS-2.0.10/ICAMS/man/AnnotateIDVCF.Rd                                    |only
 ICAMS-2.0.10/ICAMS/man/AnnotateSBSVCF.Rd                                   |only
 ICAMS-2.0.10/ICAMS/man/Canonicalize1Del.Rd                                 |only
 ICAMS-2.0.10/ICAMS/man/Canonicalize1ID.Rd                                  |   14 
 ICAMS-2.0.10/ICAMS/man/Canonicalize1INS.Rd                                 |    8 
 ICAMS-2.0.10/ICAMS/man/CanonicalizeID.Rd                                   |    9 
 ICAMS-2.0.10/ICAMS/man/CatalogRowOrder.Rd                                  |   14 
 ICAMS-2.0.10/ICAMS/man/CheckAndFixChrNames.Rd                              |only
 ICAMS-2.0.10/ICAMS/man/CheckAndReorderRownames.Rd                          |only
 ICAMS-2.0.10/ICAMS/man/CreateOneColDBSMatrix.Rd                            |   29 
 ICAMS-2.0.10/ICAMS/man/CreateOneColIDMatrix.Rd                             |   18 
 ICAMS-2.0.10/ICAMS/man/CreateOneColSBSMatrix.Rd                            |   15 
 ICAMS-2.0.10/ICAMS/man/FindDelMH.Rd                                        |   66 
 ICAMS-2.0.10/ICAMS/man/FindMaxRepeatDel.Rd                                 |   50 
 ICAMS-2.0.10/ICAMS/man/FindMaxRepeatIns.Rd                                 |    6 
 ICAMS-2.0.10/ICAMS/man/GeneExpressionData.Rd                               |only
 ICAMS-2.0.10/ICAMS/man/GetExomeKmerCounts.Rd                               |    7 
 ICAMS-2.0.10/ICAMS/man/GetStrandedKmerCounts.Rd                            |    3 
 ICAMS-2.0.10/ICAMS/man/GetVAF.Rd                                           |    9 
 ICAMS-2.0.10/ICAMS/man/ICAMS.Rd                                            |   21 
 ICAMS-2.0.10/ICAMS/man/InferRownames.Rd                                    |only
 ICAMS-2.0.10/ICAMS/man/MutectVCFFilesToCatalog.Rd                          |   24 
 ICAMS-2.0.10/ICAMS/man/MutectVCFFilesToCatalogAndPlotToPdf.Rd              |   31 
 ICAMS-2.0.10/ICAMS/man/Plot96PartOfCompositeToPDF.Rd                       |only
 ICAMS-2.0.10/ICAMS/man/PlotCatalog.Rd                                      |    5 
 ICAMS-2.0.10/ICAMS/man/PlotTransBiasGeneExp.Rd                             |only
 ICAMS-2.0.10/ICAMS/man/PlotTransBiasGeneExpToPdf.Rd                        |only
 ICAMS-2.0.10/ICAMS/man/ReadAndSplitMutectVCFs.Rd                           |   17 
 ICAMS-2.0.10/ICAMS/man/ReadAndSplitStrelkaSBSVCFs.Rd                       |    9 
 ICAMS-2.0.10/ICAMS/man/ReadBedRanges.Rd                                    |    3 
 ICAMS-2.0.10/ICAMS/man/ReadCatalog.Rd                                      |    8 
 ICAMS-2.0.10/ICAMS/man/ReadDukeNUSCat192.Rd                                |    9 
 ICAMS-2.0.10/ICAMS/man/ReadMutectVCF.Rd                                    |   13 
 ICAMS-2.0.10/ICAMS/man/ReadMutectVCFs.Rd                                   |   16 
 ICAMS-2.0.10/ICAMS/man/ReadStapleGT96SBS.Rd                                |    2 
 ICAMS-2.0.10/ICAMS/man/ReadStrelkaIDVCF.Rd                                 |    2 
 ICAMS-2.0.10/ICAMS/man/ReadStrelkaIDVCFs.Rd                                |   15 
 ICAMS-2.0.10/ICAMS/man/ReadStrelkaSBSVCFs.Rd                               |    9 
 ICAMS-2.0.10/ICAMS/man/RenameColumnsWithNameStrand.Rd                      |only
 ICAMS-2.0.10/ICAMS/man/RenameColumnsWithNameVAF.Rd                         |only
 ICAMS-2.0.10/ICAMS/man/Restaple96.Rd                                       |only
 ICAMS-2.0.10/ICAMS/man/StrelkaIDVCFFilesToCatalog.Rd                       |   23 
 ICAMS-2.0.10/ICAMS/man/StrelkaIDVCFFilesToCatalogAndPlotToPdf.Rd           |   35 
 ICAMS-2.0.10/ICAMS/man/StrelkaSBSVCFFilesToCatalog.Rd                      |   15 
 ICAMS-2.0.10/ICAMS/man/StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd          |   23 
 ICAMS-2.0.10/ICAMS/man/TestPlotCatCOMPOSITE.Rd                             |only
 ICAMS-2.0.10/ICAMS/man/TransRownames.ID.PCAWG.SigPro.Rd                    |only
 ICAMS-2.0.10/ICAMS/man/TransRownames.ID.SigPro.PCAWG.Rd                    |only
 ICAMS-2.0.10/ICAMS/man/TranscriptRanges.Rd                                 |   17 
 ICAMS-2.0.10/ICAMS/man/TransformCatalog.Rd                                 |    2 
 ICAMS-2.0.10/ICAMS/man/Unstaple96.Rd                                       |only
 ICAMS-2.0.10/ICAMS/man/VCFsToDBSCatalogs.Rd                                |    6 
 ICAMS-2.0.10/ICAMS/man/VCFsToIDCatalogs.Rd                                 |   21 
 ICAMS-2.0.10/ICAMS/man/VCFsToSBSCatalogs.Rd                                |    6 
 ICAMS-2.0.10/ICAMS/man/WriteCatalog.Rd                                     |    2 
 ICAMS-2.0.10/ICAMS/man/WriteCatalogIndelSigPro.Rd                          |only
 ICAMS-2.0.10/ICAMS/man/as.catalog.Rd                                       |   25 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_1strandbias_functions.R             |only
 ICAMS-2.0.10/ICAMS/tests/testthat/test_AnnotateIDVCF.R                     |only
 ICAMS-2.0.10/ICAMS/tests/testthat/test_COMPOSITE.R                         |only
 ICAMS-2.0.10/ICAMS/tests/testthat/test_CheckAndFixChrNames.R               |only
 ICAMS-2.0.10/ICAMS/tests/testthat/test_ID_fns.R                            |   18 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_MakeCatalogFromMutectGRCh38VCF.R    |    2 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_MakeCatalogFromStrelkaGRCh38VCF.R   |    4 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.DBS136Catalog.R         |    4 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.DBS144Catalog.R         |    8 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.DBS78Catalog.R          |    8 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.IndelCatalog.R          |    4 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.SBS1536Catalog.R        |    8 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.SBS192Catalog.R         |   16 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.SBS96Catalog.R          |    8 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_PyrPenta.R                          |    1 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_ReadVCF.R                           |only
 ICAMS-2.0.10/ICAMS/tests/testthat/test_SigProfiler_formats.R               |only
 ICAMS-2.0.10/ICAMS/tests/testthat/test_TransRownames.ID.PCAWG.SigPro.R     |only
 ICAMS-2.0.10/ICAMS/tests/testthat/test_as.catalog.R                        |only
 ICAMS-2.0.10/ICAMS/tests/testthat/test_extended_seq.context_functions.R    |    3 
 ICAMS-2.0.10/ICAMS/tests/testthat/test_methods_for_subsetting_catalogs.R   |   14 
 ICAMS-2.0.10/ICAMS/tests/testthat/testdata/sigProfiler_ID_signatures.csv   |only
 ICAMS-2.0.10/ICAMS/tests/testthat/testdata/test_AddSeqContext.Rdata        |binary
 ICAMS-2.0.10/ICAMS/tests/testthat/testdata/test_AnnotateIDVCF.Rdata        |only
 ICAMS-2.0.8/ICAMS/R/INDELS_related_functions.R                             |only
 ICAMS-2.0.8/ICAMS/man/AddAndCheckSequenceID.Rd                             |only
 ICAMS-2.0.8/ICAMS/man/Canonicalize1DEL.Rd                                  |only
 ICAMS-2.0.8/ICAMS/tests/testthat/test_AddAndCheckSequenceID.R              |only
 ICAMS-2.0.8/ICAMS/tests/testthat/test_ReadAndSplitVCF.R                    |only
 ICAMS-2.0.8/ICAMS/tests/testthat/testdata/test_AddAndCheckSequenceID.Rdata |only
 115 files changed, 1894 insertions(+), 716 deletions(-)

More information about ICAMS at CRAN
Permanent link

Package HelpersMG updated to version 3.9 with previous version 3.8 dated 2019-10-06

Title: Tools for Environmental Analyses, Ecotoxicology and Various R Functions
Description: Contains many functions useful for managing 'NetCDF' files (see <http://en.wikipedia.org/wiki/NetCDF>), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between HelpersMG versions 3.8 dated 2019-10-06 and 3.9 dated 2019-12-13

 DESCRIPTION                     |   10 +-
 MD5                             |  138 ++++++++++++++++++++--------------------
 NAMESPACE                       |    1 
 NEWS                            |   15 ++++
 R/HelpersMG-package.R           |    4 -
 R/MHalgoGen.R                   |    9 +-
 R/MovingWindow.R                |only
 R/d.R                           |   14 ++--
 R/dSnbinom.R                    |   30 +++++---
 R/plot.mcmcComposite.R          |   50 +++-----------
 man/ChangeCoordinate.Rd         |    7 +-
 man/ExtractAIC.glm.Rd           |    6 +
 man/HelpersMG-package.Rd        |    4 -
 man/IC_clean_data.Rd            |   22 ++++--
 man/IC_correlation_simplify.Rd  |    7 +-
 man/IC_threshold_matrix.Rd      |   23 ++++--
 man/LD50.Rd                     |   33 ++++++---
 man/LD50_MHmcmc.Rd              |   31 ++++++--
 man/LD50_MHmcmc_p.Rd            |   15 ++--
 man/MHalgoGen.Rd                |   37 +++++++---
 man/MovingWindow.Rd             |only
 man/ScalePreviousPlot.Rd        |    6 +
 man/as.mcmc.mcmcComposite.Rd    |   12 ++-
 man/as.parameters.Rd            |   13 ++-
 man/as.quantiles.Rd             |   25 ++++---
 man/asc.Rd                      |    6 +
 man/barplot_errbar.Rd           |   23 ++++--
 man/cArrows.Rd                  |   25 +++++--
 man/chr.Rd                      |    6 +
 man/compare.Rd                  |    5 -
 man/compare_AIC.Rd              |    6 +
 man/compare_AICc.Rd             |    6 +
 man/compare_BIC.Rd              |    6 +
 man/contingencyTable.compare.Rd |   12 ++-
 man/d.Rd                        |   18 +++--
 man/dSnbinom.Rd                 |   23 ++++--
 man/ellipse.Rd                  |   21 ++++--
 man/flexit.Rd                   |   17 ++++
 man/ind_long_lat.Rd             |   12 ++-
 man/index.periodic.Rd           |   11 +--
 man/inside.search.Rd            |   12 ++-
 man/invlogit.Rd                 |    4 -
 man/local.search.Rd             |   10 ++
 man/logLik.LD50.Rd              |    9 +-
 man/logit.Rd                    |    4 -
 man/merge.mcmcComposite.Rd      |   12 ++-
 man/minmax.periodic.Rd          |   22 ++++--
 man/moon.info.Rd                |    8 +-
 man/newcompassRose.Rd           |   11 ++-
 man/newdbeta.Rd                 |    3 
 man/newmap.scale.Rd             |   11 ++-
 man/pSnbinom.Rd                 |   18 +++--
 man/plot.IconoCorel.Rd          |   22 ++++--
 man/plot.LD50.Rd                |   26 +++++--
 man/plot.mcmcComposite.Rd       |   44 +++++++-----
 man/plot_add.Rd                 |    6 +
 man/plot_errbar.Rd              |   33 ++++++---
 man/predict.LD50.Rd             |   20 ++++-
 man/qSnbinom.Rd                 |   18 +++--
 man/qvlmer.Rd                   |    3 
 man/rSnbinom.Rd                 |    6 +
 man/read_folder.Rd              |    9 ++
 man/series.compare.Rd           |    8 +-
 man/summary.mcmcComposite.Rd    |   12 ++-
 man/sun.info.Rd                 |    8 +-
 man/symbol.Female.Rd            |    3 
 man/symbol.Male.Rd              |    3 
 man/symmetricize.Rd             |    7 +-
 man/tide.info.Rd                |   18 +++--
 man/tnirp.Rd                    |    6 +
 man/universalmclapply.Rd        |   15 +++-
 71 files changed, 702 insertions(+), 398 deletions(-)

More information about HelpersMG at CRAN
Permanent link

Package poibin (with last version 1.4) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-12-13 1.4
2018-05-16 1.3
2013-02-14 1.2
2012-10-30 1.01
2011-04-09 1.0

Permanent link
Package GPB (with last version 1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-12-13 1.1
2017-02-07 1.0

Permanent link
Package statsExpressions updated to version 0.1.2 with previous version 0.1.1 dated 2019-08-28

Title: Expressions with Statistical Details
Description: Statistical processing backend for 'ggstatsplot', this package creates expressions with details from statistical tests. Currently, it supports only the most common types of statistical tests: parametric, nonparametric, robust, and bayesian versions of t-test/anova, correlation analyses, contingency table analysis.
Author: Indrajeet Patil [cre, aut, ctb] (<https://orcid.org/0000-0003-1995-6531>), Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

Diff between statsExpressions versions 0.1.1 dated 2019-08-28 and 0.1.2 dated 2019-12-13

 DESCRIPTION                                       |   17 
 MD5                                               |  150 ++---
 NAMESPACE                                         |   11 
 NEWS.md                                           |    4 
 R/helpers_bf_tests.R                              |    7 
 R/helpers_contingency_tabs_expressions.R          |    2 
 R/helpers_corr_test_expressions.R                 |    1 
 R/helpers_effsize_ci.R                            |    4 
 R/helpers_t_onesample_expressions.R               |   67 +-
 R/helpers_t_test_expressions.R                    |   35 -
 R/reexports.R                                     |   12 
 README.md                                         |   11 
 inst/CITATION                                     |    3 
 inst/doc/stats_details.R                          |    2 
 inst/doc/stats_details.html                       |   34 -
 inst/doc/tests_and_coverage.R                     |    2 
 inst/doc/tests_and_coverage.Rmd                   |  214 ++++---
 inst/doc/tests_and_coverage.html                  |  592 ++++++++++++----------
 man/Titanic_full.Rd                               |   72 +-
 man/VR_dilemma.Rd                                 |   84 +--
 man/bf_contingency_tab.Rd                         |  268 +++++----
 man/bf_corr_test.Rd                               |  150 ++---
 man/bf_expr.Rd                                    |  118 ++--
 man/bf_extractor.Rd                               |   58 +-
 man/bf_oneway_anova.Rd                            |  171 +++---
 man/bf_ttest.Rd                                   |  280 +++++-----
 man/bugs_long.Rd                                  |   82 +--
 man/effsize_ci_message.Rd                         |   46 -
 man/effsize_t_parametric.Rd                       |  271 +++++-----
 man/effsize_type_switch.Rd                        |   42 -
 man/expr_anova_bayes.Rd                           |  141 ++---
 man/expr_anova_nonparametric.Rd                   |  192 +++----
 man/expr_anova_parametric.Rd                      |  250 ++++-----
 man/expr_anova_robust.Rd                          |  217 ++++----
 man/expr_contingency_tab.Rd                       |  288 +++++-----
 man/expr_corr_test.Rd                             |  202 +++----
 man/expr_t_bayes.Rd                               |  135 ++---
 man/expr_t_nonparametric.Rd                       |  296 +++++------
 man/expr_t_onesample.Rd                           |  257 +++++----
 man/expr_t_parametric.Rd                          |  240 ++++----
 man/expr_t_robust.Rd                              |  205 ++++---
 man/expr_template.Rd                              |  192 +++----
 man/figures/README-example_anova-1.png            |binary
 man/figures/README-example_anova_parametric-1.png |binary
 man/figures/README-example_contingency-1.png      |binary
 man/figures/README-example_corr-1.png             |binary
 man/figures/README-example_t_one-1.png            |binary
 man/figures/README-example_t_two-1.png            |binary
 man/intent_morality.Rd                            |  106 +--
 man/iris_long.Rd                                  |   84 +--
 man/long_to_wide_converter.Rd                     |   74 +-
 man/movies_long.Rd                                |   96 +--
 man/movies_wide.Rd                                |  100 +--
 man/reexports.Rd                                  |   64 +-
 man/robcor_ci.Rd                                  |  372 ++++++-------
 man/stats_type_switch.Rd                          |   42 -
 man/t1way_ci.Rd                                   |  364 ++++++-------
 man/yuend_ci.Rd                                   |  374 +++++++------
 tests/README.md                                   |  216 ++++----
 tests/testthat/test-effsize_helpers.R             |  271 +++++-----
 tests/testthat/test-expr_anova_bayes.R            |    5 
 tests/testthat/test-expr_anova_nonparametric.R    |    3 
 tests/testthat/test-expr_anova_parametric.R       |  115 ++--
 tests/testthat/test-expr_anova_robust.R           |   19 
 tests/testthat/test-expr_contingency_tab.R        |   20 
 tests/testthat/test-expr_corr_test.R              |    6 
 tests/testthat/test-expr_t_bayes.R                |    8 
 tests/testthat/test-expr_t_nonparametric.R        |    6 
 tests/testthat/test-expr_t_onesample.R            |    5 
 tests/testthat/test-expr_t_parametric.R           |  118 ++--
 tests/testthat/test-expr_t_robust.R               |  160 +++--
 tests/testthat/test-expr_templates.R              |  232 ++++----
 tests/testthat/test-helpers_bf_tests.R            |   18 
 tests/testthat/test-subtitle_misc_helpers.R       |    2 
 tests/testthat/test-switch_statements.R           |    4 
 vignettes/tests_and_coverage.Rmd                  |  214 ++++---
 76 files changed, 4463 insertions(+), 4060 deletions(-)

More information about statsExpressions at CRAN
Permanent link

Package SparseM updated to version 1.78 with previous version 1.77 dated 2017-04-23

Title: Sparse Linear Algebra
Description: Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.
Author: Roger Koenker <rkoenker@uiuc.edu> and Pin Ng <Pin.Ng@NAU.EDU>
Maintainer: Roger Koenker <rkoenker@uiuc.edu>

Diff between SparseM versions 1.77 dated 2017-04-23 and 1.78 dated 2019-12-13

 DESCRIPTION          |    6 +++---
 MD5                  |   10 +++++-----
 R/SparseM.R          |    5 ++---
 build/vignette.rds   |binary
 inst/ChangeLog       |    5 +++++
 inst/doc/SparseM.pdf |binary
 6 files changed, 15 insertions(+), 11 deletions(-)

More information about SparseM at CRAN
Permanent link

Package GPB updated to version 1.1 with previous version 1.0 dated 2017-02-07

Title: Generalized Poisson Binomial Distribution
Description: Functions that compute the distribution functions for the Generalized Poisson Binomial distribution as described in Zhang et al. (2018)<doi: 10.1080/00949655.2018.1440294>, which provides the cdf, pmf, quantile function, and random number generation for the distribution. The C code for fast Fourier transformation (FFT) is written by Ross Ihaka from University of Auckland, which implements the FFT algorithm in Singleton (1969) <doi: 10.1109/TAU.1969.1162042>.
Author: Yili Hong [aut, cre], Man Zhang [aut, ctb], Ross Ihaka [aut, cph]
Maintainer: Yili Hong <yilihong@vt.edu>

Diff between GPB versions 1.0 dated 2017-02-07 and 1.1 dated 2019-12-13

 DESCRIPTION        |   16 +++++++++-------
 MD5                |    9 +++++----
 man/GPB-package.Rd |    2 +-
 man/pgpb.Rd        |    3 ++-
 src/GPB_init.c     |only
 src/dftcf.c        |   28 ++++++++++++++--------------
 6 files changed, 31 insertions(+), 27 deletions(-)

More information about GPB at CRAN
Permanent link

New package ctmle with initial version 0.1.2
Package: ctmle
Type: Package
Title: Collaborative Targeted Maximum Likelihood Estimation
Version: 0.1.2
Date: 2019-12-08
Authors@R: c(person("Cheng", "Ju", email = "jucheng1992@gmail.com", role = c("aut", "cre")),person("Susan", "Gruber", role = c("aut")),person("Richard", "Wyss", role = c("ctb")),person("Jenny","Haggstrom", role = c("ctb")),person("Mark", "van der Laan", role = c("aut", "ths")))
Maintainer: Cheng Ju <jucheng1992@gmail.com>
Description: Implements the general template for collaborative targeted maximum likelihood estimation. It also provides several commonly used C-TMLE instantiation, like the vanilla/scalable variable-selection C-TMLE (Ju et al. (2017) <doi:10.1177/0962280217729845>) and the glmnet-C-TMLE algorithm (Ju et al. (2017) <arXiv:1706.10029>).
License: GPL-2
Depends: R (>= 2.14.0), SuperLearner, tmle, glmnet, stats
Imports:
Suggests: testthat, knitr, rmarkdown, dplyr
LazyLoad: yes
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-12-13 05:53:26 UTC; jucheng
Author: Cheng Ju [aut, cre], Susan Gruber [aut], Richard Wyss [ctb], Jenny Haggstrom [ctb], Mark van der Laan [aut, ths]
Repository: CRAN
Date/Publication: 2019-12-13 09:10:02 UTC

More information about ctmle at CRAN
Permanent link

Package censReg updated to version 0.5-30 with previous version 0.5-26 dated 2017-03-21

Title: Censored Regression (Tobit) Models
Description: Maximum Likelihood estimation of censored regression (Tobit) models with cross-sectional and panel data.
Author: Arne Henningsen <arne.henningsen@gmail.com>
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

Diff between censReg versions 0.5-26 dated 2017-03-21 and 0.5-30 dated 2019-12-13

 DESCRIPTION                       |    8 
 MD5                               |   22 
 NAMESPACE                         |    2 
 R/censReg.R                       |   20 
 build/vignette.rds                |binary
 inst/NEWS.Rd                      |    8 
 inst/doc/censReg.pdf              |binary
 tests/censRegPanelTest.R          |   53 +-
 tests/censRegPanelTest.RData.save |binary
 tests/censRegPanelTest.Rout.save  |  199 ++++++-
 tests/censRegTest.R               |  147 ++---
 tests/censRegTest.Rout.save       |  974 ++++++++++++++++++++++++--------------
 12 files changed, 943 insertions(+), 490 deletions(-)

More information about censReg at CRAN
Permanent link

Package daarem updated to version 0.4.1 with previous version 0.4 dated 2019-09-27

Title: Damped Anderson Acceleration with Epsilon Monotonicity for Accelerating EM-Like Monotone Algorithms
Description: Implements the DAAREM method for accelerating the convergence of slow, monotone sequences from smooth, fixed-point iterations such as the EM algorithm. For further details about the DAAREM method. see Henderson, N.C. and Varadhan, R. (2018) <arXiv:1803.06673>.
Author: Nicholas Henderson [cre, aut], Ravi Varadhan [aut]
Maintainer: Nicholas Henderson <nchender@umich.edu>

Diff between daarem versions 0.4 dated 2019-09-27 and 0.4.1 dated 2019-12-13

 DESCRIPTION             |    8 +-
 MD5                     |    8 +-
 NEWS                    |    6 +
 R/daarem_base_noobjfn.R |  131 ++++++++++++++++--------------------
 R/daarem_base_objfn.R   |  171 ++++++++++++++++++++++--------------------------
 5 files changed, 151 insertions(+), 173 deletions(-)

More information about daarem at CRAN
Permanent link

Package poibin updated to version 1.4 with previous version 1.3 dated 2018-05-16

Title: The Poisson Binomial Distribution
Description: Implementation of both the exact and approximation methods for computing the cdf of the Poisson binomial distribution. It also provides the pmf, quantile function, and random number generation for the Poisson binomial distribution. We would like to acknowledge that the C code for FFT is adopted from R distribution (fft.c, by Ross Ihaka from University of Auckland, dated February 1997).
Author: Yili Hong
Maintainer: Yili Hong <yilihong@vt.edu>

Diff between poibin versions 1.3 dated 2018-05-16 and 1.4 dated 2019-12-13

 DESCRIPTION           |   10 +++++-----
 MD5                   |   14 +++++++-------
 NAMESPACE             |    2 +-
 R/funs.R              |    7 +++++++
 build/partial.rdb     |binary
 man/poibin-package.Rd |    1 +
 man/ppoibin.Rd        |    3 ++-
 src/dftcf.c           |   28 ++++++++++++++--------------
 8 files changed, 37 insertions(+), 28 deletions(-)

More information about poibin at CRAN
Permanent link

Package phylocurve updated to version 2.0.10 with previous version 2.0.9 dated 2017-08-09

Title: Phylogenetic Comparative Methods for High-Dimensional Traits
Description: Tools for studying the evolution of high-dimensional traits (morphometric, function-valued, etc.) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit <http://www.phylocurve.org> for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>

Diff between phylocurve versions 2.0.9 dated 2017-08-09 and 2.0.10 dated 2019-12-13

 DESCRIPTION                 |    8 
 MD5                         |   12 
 R/RcppExports.R             |   70 
 R/fast_geomorph_functions.R | 1696 +++++++-------
 R/phylocurve.R              | 5094 ++++++++++++++++++++++----------------------
 man/ultraFastAnc.Rd         |  102 
 src/RcppExports.cpp         |   33 
 7 files changed, 3514 insertions(+), 3501 deletions(-)

More information about phylocurve at CRAN
Permanent link

Package pbdSLAP updated to version 0.2-7 with previous version 0.2-6 dated 2019-06-24

Title: Programming with Big Data -- Scalable Linear Algebra Packages
Description: Utilizing scalable linear algebra packages mainly including 'BLACS', 'PBLAS', and 'ScaLAPACK' in double precision via 'pbdMPI' based on 'ScaLAPACK' version 2.0.2.
Author: Wei-Chen Chen [aut, cre], Drew Schmidt [aut], George Ostrouchov [aut], Pragneshkumar Patel [aut], Brian Ripley [ctb] (Solaris & Mac)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>

Diff between pbdSLAP versions 0.2-6 dated 2019-06-24 and 0.2-7 dated 2019-12-13

 ChangeLog                                     |    5 +++++
 DESCRIPTION                                   |    8 ++++----
 MD5                                           |   22 +++++++++++-----------
 configure                                     |    4 ++--
 configure.ac                                  |    4 ++--
 inst/doc/pbdSLAP-guide.pdf                    |binary
 src/BLACS/dgamn2d_.c                          |    8 ++++++--
 src/BLACS/dgamx2d_.c                          |    8 ++++++--
 src/BLACS/igamn2d_.c                          |    8 ++++++--
 src/BLACS/igamx2d_.c                          |    8 ++++++--
 vignettes/pbdSLAP-include/01-introduction.tex |    6 +++---
 vignettes/pbdSLAP-include/02-extra.tex        |   12 ++++++------
 12 files changed, 57 insertions(+), 36 deletions(-)

More information about pbdSLAP at CRAN
Permanent link

Package lqmm updated to version 1.5.5 with previous version 1.5.4 dated 2018-04-13

Title: Linear Quantile Mixed Models
Description: Functions to fit quantile regression models for hierarchical data (2-level nested designs) as described in Geraci and Bottai (2014, Statistics and Computing) <doi:10.1007/s11222-013-9381-9>. A vignette is given in Geraci (2014, Journal of Statistical Software) <doi:10.18637/jss.v057.i13> and included in the package documents. The packages also provides functions to fit quantile models for independent data and for count responses.
Author: Marco Geraci
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>

Diff between lqmm versions 1.5.4 dated 2018-04-13 and 1.5.5 dated 2019-12-13

 lqmm-1.5.4/lqmm/inst/doc            |only
 lqmm-1.5.5/lqmm/DESCRIPTION         |   11 +-
 lqmm-1.5.5/lqmm/MD5                 |   13 +--
 lqmm-1.5.5/lqmm/NEWS                |    7 +
 lqmm-1.5.5/lqmm/R/auxiliary.R       |    2 
 lqmm-1.5.5/lqmm/R/lqm.R             |  142 +++++++++++++++++-------------------
 lqmm-1.5.5/lqmm/R/lqmm.R            |   13 +--
 lqmm-1.5.5/lqmm/man/lqmm-package.Rd |    4 -
 8 files changed, 94 insertions(+), 98 deletions(-)

More information about lqmm at CRAN
Permanent link

Package geepack updated to version 1.3-1 with previous version 1.3-0 dated 2019-12-12

Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can also handle clustered categorical responses.
Author: Søren Højsgaard [aut, cre, cph], Ulrich Halekoh [aut, cph], Jun Yan [aut, cph], Claus Ekstrøm [ctb]
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>

Diff between geepack versions 1.3-0 dated 2019-12-12 and 1.3-1 dated 2019-12-13

 ChangeLog                   |    5 +++++
 DESCRIPTION                 |    6 +++---
 MD5                         |   10 +++++-----
 inst/doc/geepack-manual.pdf |binary
 src/gee2.cc                 |    1 +
 src/ordgee.cc               |    3 ++-
 6 files changed, 16 insertions(+), 9 deletions(-)

More information about geepack at CRAN
Permanent link

Package DELTD updated to version 2.6.5 with previous version 1.3.1 dated 2019-09-24

Title: Kernel Density Estimation using Lifetime Distributions
Description: A collection of asymmetrical kernels belong to lifetime distributions for kernel density estimation is presented. Mean Squared Errors (MSE) are calculated for estimated curves. For this purpose, R functions allow the distribution to be Gamma, Exponential or Weibull. For details see Chen (2000), Jin and Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>.
Author: Javaria Ahmad Khan, Atif Akbar.
Maintainer: Javaria Ahmad Khan <jakhan0@yahoo.com>

Diff between DELTD versions 1.3.1 dated 2019-09-24 and 2.6.5 dated 2019-12-13

 DELTD-1.3.1/DELTD/man/denBS.Rd         |only
 DELTD-1.3.1/DELTD/man/denEr.Rd         |only
 DELTD-1.3.1/DELTD/man/denGamma.Rd      |only
 DELTD-1.3.1/DELTD/man/denLN.Rd         |only
 DELTD-1.3.1/DELTD/man/suicide.Rd       |only
 DELTD-2.6.5/DELTD/DESCRIPTION          |   15 -
 DELTD-2.6.5/DELTD/MD5                  |   30 +--
 DELTD-2.6.5/DELTD/NAMESPACE            |   12 -
 DELTD-2.6.5/DELTD/R/DELTD.R            |  326 ++++++++++++++++++++++++---------
 DELTD-2.6.5/DELTD/man/BS.Rd            |only
 DELTD-2.6.5/DELTD/man/DELTD-package.Rd |only
 DELTD-2.6.5/DELTD/man/Erlang.Rd        |only
 DELTD-2.6.5/DELTD/man/Gamma.Rd         |only
 DELTD-2.6.5/DELTD/man/LN.Rd            |only
 DELTD-2.6.5/DELTD/man/dencomb.Rd       |   29 ++
 DELTD-2.6.5/DELTD/man/mseBS.Rd         |   19 +
 DELTD-2.6.5/DELTD/man/mseEr.Rd         |   19 +
 DELTD-2.6.5/DELTD/man/mseGamma.Rd      |   20 +-
 DELTD-2.6.5/DELTD/man/mseLN.Rd         |   19 +
 DELTD-2.6.5/DELTD/man/plot.BS.Rd       |only
 DELTD-2.6.5/DELTD/man/plot.Erlang.Rd   |only
 DELTD-2.6.5/DELTD/man/plot.Gamma.Rd    |only
 DELTD-2.6.5/DELTD/man/plot.LN.Rd       |only
 23 files changed, 350 insertions(+), 139 deletions(-)

More information about DELTD at CRAN
Permanent link

Package bgsmtr updated to version 0.7 with previous version 0.6 dated 2019-12-02

Title: Bayesian Group Sparse Multi-Task Regression
Description: Implementation of Bayesian multi-task regression models and was developed within the context of imaging genetics. The package can currently fit two models. The Bayesian group sparse multi-task regression model of Greenlaw et al. (2017)<doi:10.1093/bioinformatics/btx215> can be fit with implementation using Gibbs sampling. An extension of this model developed by Song, Ge et al. to accommodate both spatial correlation as well as correlation across brain hemispheres can also be fit using either mean-field variational Bayes or Gibbs sampling. The model can also be used more generally for multivariate (non-imaging) phenotypes with spatial correlation.
Author: Yin Song, Shufei Ge, Liangliang Wang, Jiguo Cao, Keelin Greenlaw, Mary Lesperance, Farouk S. Nathoo
Maintainer: Yin Song <yinsong@uvic.ca>

Diff between bgsmtr versions 0.6 dated 2019-12-02 and 0.7 dated 2019-12-13

 DESCRIPTION       |    8 ++++----
 MD5               |    6 +++---
 R/all_functions.R |   10 +++++-----
 man/sp_bgsmtr.Rd  |    2 +-
 4 files changed, 13 insertions(+), 13 deletions(-)

More information about bgsmtr at CRAN
Permanent link

Thu, 12 Dec 2019

Package ALTopt updated to version 0.1.2 with previous version 0.1.1 dated 2015-08-27

Title: Optimal Experimental Designs for Accelerated Life Testing
Description: Creates the optimal (D, U and I) designs for the accelerated life testing with right censoring or interval censoring. It uses generalized linear model (GLM) approach to derive the asymptotic variance-covariance matrix of regression coefficients. The failure time distribution is assumed to follow Weibull distribution with a known shape parameter and log-linear link functions are used to model the relationship between failure time parameters and stress variables. The acceleration model may have multiple stress factors, although most ALTs involve only two or less stress factors. ALTopt package also provides several plotting functions including contour plot, Fraction of Use Space (FUS) plot and Variance Dispersion graphs of Use Space (VDUS) plot. For more details, see Seo and Pan (2015) <doi:10.32614/RJ-2015-029>.
Author: Kangwon Seo [aut, cre], Rong Pan [aut]
Maintainer: Kangwon Seo <seoka@missouri.edu>

Diff between ALTopt versions 0.1.1 dated 2015-08-27 and 0.1.2 dated 2019-12-12

 DESCRIPTION                 |   15 +--
 MD5                         |   56 ++++++------
 NAMESPACE                   |    3 
 R/ALTopt.R                  |   23 +++--
 build/partial.rdb           |binary
 man/ALTopt-package.Rd       |   16 ++-
 man/Dobj.ic.Rd              |   25 ++---
 man/Dobj.rc.Rd              |   25 ++---
 man/ExtendedForm.Rd         |   25 ++---
 man/Iobj.ic.Rd              |   25 ++---
 man/Iobj.rc.Rd              |   25 ++---
 man/PreVar.Rd               |   23 ++---
 man/Uobj.ic.Rd              |   25 ++---
 man/Uobj.rc.Rd              |   25 ++---
 man/alteval.ic.Rd           |  148 +++++++++++++++++---------------
 man/alteval.rc.Rd           |  143 ++++++++++++++++---------------
 man/altopt.ic.Rd            |  199 +++++++++++++++++++++++---------------------
 man/altopt.rc.Rd            |  194 ++++++++++++++++++++++--------------------
 man/compare.fus.Rd          |   89 +++++++++----------
 man/compare.vdus.Rd         |   89 +++++++++----------
 man/convert.stress.level.Rd |   93 ++++++++++----------
 man/design.plot.Rd          |   73 +++++++---------
 man/kmeansCls.Rd            |   23 ++---
 man/pv.contour.ic.Rd        |  135 ++++++++++++++++-------------
 man/pv.contour.rc.Rd        |  130 +++++++++++++++-------------
 man/pv.fus.ic.Rd            |  118 +++++++++++++-------------
 man/pv.fus.rc.Rd            |  113 +++++++++++++-----------
 man/pv.vdus.ic.Rd           |  118 +++++++++++++-------------
 man/pv.vdus.rc.Rd           |  113 +++++++++++++-----------
 29 files changed, 1092 insertions(+), 997 deletions(-)

More information about ALTopt at CRAN
Permanent link

Package TDAstats updated to version 0.4.1 with previous version 0.4.0 dated 2018-11-05

Title: Pipeline for Topological Data Analysis
Description: A comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent homology in a Vietoris-Rips complex. The tools this package currently provides can be conveniently split into three main sections: (1) calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing persistent homology and statistical inference. The published form of TDAstats can be found in Wadhwa et al. (2018) <doi:10.21105/joss.00860>. For a general background on computing persistent homology for topological data analysis, see Otter et al. (2017) <doi:10.1140/epjds/s13688-017-0109-5>. To learn more about how the permutation test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner (2017) <doi:10.1007/s41468-017-0008-7>. To learn more about how TDAstats calculates persistent homology, you can visit the GitHub repository for Ripser, the software that works behind the scenes at <https://github.com/Ripser/ripser>. This package has been published as Wadhwa et al. (2018) <doi:10.21105/joss.00860>.
Author: Raoul Wadhwa [aut, cre], Andrew Dhawan [aut], Drew Williamson [aut], Jacob Scott [aut], Jason Cory Brunson [ctb], Shota Ochi [ctb]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>

Diff between TDAstats versions 0.4.0 dated 2018-11-05 and 0.4.1 dated 2019-12-12

 TDAstats-0.4.0/TDAstats/tests/testthat/test_inputformat.R       |only
 TDAstats-0.4.1/TDAstats/DESCRIPTION                             |   14 
 TDAstats-0.4.1/TDAstats/MD5                                     |   87 -
 TDAstats-0.4.1/TDAstats/NAMESPACE                               |   23 
 TDAstats-0.4.1/TDAstats/R/RcppExports.R                         |   14 
 TDAstats-0.4.1/TDAstats/R/TDAstats.R                            |   30 
 TDAstats-0.4.1/TDAstats/R/calculate.R                           |  203 +-
 TDAstats-0.4.1/TDAstats/R/data.R                                |   68 
 TDAstats-0.4.1/TDAstats/R/inference.R                           |  747 +++++----
 TDAstats-0.4.1/TDAstats/R/utility.R                             |   74 
 TDAstats-0.4.1/TDAstats/R/visuals.R                             |  285 +--
 TDAstats-0.4.1/TDAstats/R/zzz.R                                 |   16 
 TDAstats-0.4.1/TDAstats/build/vignette.rds                      |binary
 TDAstats-0.4.1/TDAstats/inst/CITATION                           |   34 
 TDAstats-0.4.1/TDAstats/inst/doc/inference.R                    |  162 +-
 TDAstats-0.4.1/TDAstats/inst/doc/inference.Rmd                  |  444 ++---
 TDAstats-0.4.1/TDAstats/inst/doc/inference.html                 |  801 ++++------
 TDAstats-0.4.1/TDAstats/inst/doc/inputformat.R                  |  124 -
 TDAstats-0.4.1/TDAstats/inst/doc/inputformat.Rmd                |  234 +-
 TDAstats-0.4.1/TDAstats/inst/doc/inputformat.html               |  682 +++-----
 TDAstats-0.4.1/TDAstats/inst/doc/intro.R                        |  102 -
 TDAstats-0.4.1/TDAstats/inst/doc/intro.Rmd                      |  390 ++--
 TDAstats-0.4.1/TDAstats/inst/doc/intro.html                     |  777 ++++-----
 TDAstats-0.4.1/TDAstats/man/TDAstats.Rd                         |   32 
 TDAstats-0.4.1/TDAstats/man/calculate_homology.Rd               |   97 -
 TDAstats-0.4.1/TDAstats/man/circle2d.Rd                         |   36 
 TDAstats-0.4.1/TDAstats/man/figures/HexTDA.png                  |binary
 TDAstats-0.4.1/TDAstats/man/id_significant.Rd                   |only
 TDAstats-0.4.1/TDAstats/man/permutation_test.Rd                 |   84 -
 TDAstats-0.4.1/TDAstats/man/phom.dist.Rd                        |   54 
 TDAstats-0.4.1/TDAstats/man/plot_barcode.Rd                     |   88 -
 TDAstats-0.4.1/TDAstats/man/plot_persist.Rd                     |   92 -
 TDAstats-0.4.1/TDAstats/man/sphere3d.Rd                         |   36 
 TDAstats-0.4.1/TDAstats/man/unif2d.Rd                           |   36 
 TDAstats-0.4.1/TDAstats/man/unif3d.Rd                           |   36 
 TDAstats-0.4.1/TDAstats/tests/testthat.R                        |    8 
 TDAstats-0.4.1/TDAstats/tests/testthat/test_aaaload.R           |   44 
 TDAstats-0.4.1/TDAstats/tests/testthat/test_calculate_errors.R  |   80 
 TDAstats-0.4.1/TDAstats/tests/testthat/test_inference.R         |  309 ++-
 TDAstats-0.4.1/TDAstats/tests/testthat/test_ioformat.R          |only
 TDAstats-0.4.1/TDAstats/tests/testthat/test_plots.R             |  134 -
 TDAstats-0.4.1/TDAstats/tests/testthat/test_ripser_accurate.R   |  138 -
 TDAstats-0.4.1/TDAstats/tests/testthat/test_ripser_consistent.R |  168 +-
 TDAstats-0.4.1/TDAstats/vignettes/inference.Rmd                 |  444 ++---
 TDAstats-0.4.1/TDAstats/vignettes/inputformat.Rmd               |  234 +-
 TDAstats-0.4.1/TDAstats/vignettes/intro.Rmd                     |  390 ++--
 46 files changed, 3932 insertions(+), 3919 deletions(-)

More information about TDAstats at CRAN
Permanent link

Package spsur updated to version 1.0.0.4 with previous version 1.0.0.3 dated 2019-03-23

Title: Spatial Seemingly Unrelated Regression Models
Description: A collection of functions to test and estimate Seemingly Unrelated Regression (usually called SUR) models, with spatial structure, by maximum likelihood and three-stage least squares. The package estimates the most common spatial specifications, that is, SUR with Spatial Lag of X regressors (called SUR-SLX), SUR with Spatial Lag Model (called SUR-SLM), SUR with Spatial Error Model (called SUR-SEM), SUR with Spatial Durbin Model (called SUR-SDM), SUR with Spatial Durbin Error Model (called SUR-SDEM), SUR with Spatial Autoregressive terms and Spatial Autoregressive Disturbances (called SUR-SARAR) and SUR with Spatially Independent Model (called SUR-SIM). The methodology of these models can be found in next references Mur, J., Lopez, F., and Herrera, M. (2010) <doi:10.1080/17421772.2010.516443> Lopez, F.A., Mur, J., and Angulo, A. (2014) <doi:10.1007/s00168-014-0624-2>.
Author: Ana Angulo [aut], Fernando A Lopez [aut], Roman Minguez [aut, cre], Jesus Mur [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>

Diff between spsur versions 1.0.0.3 dated 2019-03-23 and 1.0.0.4 dated 2019-12-12

 DESCRIPTION                  |   10 
 MD5                          |   69 +-
 NAMESPACE                    |   94 +--
 R/aux_functions.R            |   25 
 R/cov_spsur.R                | 1244 +++++++++++++++++++++----------------------
 R/dgp_spSUR.R                |  754 +++++++++++++-------------
 R/fit_spsur.R                |  763 +++++++++++++-------------
 R/fit_spsur_3sls.R           |    7 
 R/impacts.R                  |  686 +++++++++++------------
 R/lmtestspsur.R              |  436 +++++++--------
 R/lrtestspsur.R              |  632 ++++++++++-----------
 R/spsur3sls.R                |  610 ++++++++++-----------
 R/spsurml.R                  | 1032 +++++++++++++++++------------------
 R/spsurtime.R                |  500 ++++++++---------
 R/summary.spsur.R            |    2 
 build/vignette.rds           |binary
 inst/doc/spsur-vignette.R    |   84 +-
 inst/doc/spsur-vignette.html |  611 ++++++++++-----------
 man/NCOVR.Rd                 |  134 ++--
 man/W.Rd                     |   54 -
 man/Wspc.Rd                  |   54 -
 man/dgp_spsur.Rd             |  510 +++++++++--------
 man/impacts.Rd               |  290 ++++------
 man/lmtestspsur.Rd           |  377 ++++++-------
 man/lr_betas_spsur.Rd        |  368 ++++++------
 man/lrtestspsur.Rd           |  389 ++++++-------
 man/print.summary.spsur.Rd   |   67 +-
 man/spc.Rd                   |   76 +-
 man/spsur-package.Rd         |  356 ++++++------
 man/spsur3sls.Rd             |  449 +++++++--------
 man/spsurml.Rd               |  685 ++++++++++++-----------
 man/spsurtime.Rd             |  422 +++++++-------
 man/summary.spsur.Rd         |   78 +-
 man/wald_betas.Rd            |  220 +++----
 man/wald_deltas.Rd           |  252 ++++----
 vignettes/rsconnect          |only
 36 files changed, 6170 insertions(+), 6170 deletions(-)

More information about spsur at CRAN
Permanent link

Package Seurat updated to version 3.1.2 with previous version 3.1.1 dated 2019-10-03

Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>), Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>), Jeff Farrell [ctb], Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Patrick Roelli [ctb], Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>

Diff between Seurat versions 3.1.1 dated 2019-10-03 and 3.1.2 dated 2019-12-12

 Seurat-3.1.1/Seurat/man/MapQuery.Rd                             |only
 Seurat-3.1.1/Seurat/man/PairwiseIntegrateReference.Rd           |only
 Seurat-3.1.2/Seurat/DESCRIPTION                                 |   13 
 Seurat-3.1.2/Seurat/MD5                                         |  214 +--
 Seurat-3.1.2/Seurat/NAMESPACE                                   |   12 
 Seurat-3.1.2/Seurat/NEWS.md                                     |   11 
 Seurat-3.1.2/Seurat/R/clustering.R                              |   58 
 Seurat-3.1.2/Seurat/R/differential_expression.R                 |    6 
 Seurat-3.1.2/Seurat/R/dimensional_reduction.R                   |   39 
 Seurat-3.1.2/Seurat/R/generics.R                                |   30 
 Seurat-3.1.2/Seurat/R/integration.R                             |  669 +++++-----
 Seurat-3.1.2/Seurat/R/objects.R                                 |  629 ++++++---
 Seurat-3.1.2/Seurat/R/preprocessing.R                           |   44 
 Seurat-3.1.2/Seurat/R/utilities.R                               |  121 +
 Seurat-3.1.2/Seurat/R/visualization.R                           |   37 
 Seurat-3.1.2/Seurat/README.md                                   |    2 
 Seurat-3.1.2/Seurat/man/AddMetaData.Rd                          |    1 
 Seurat-3.1.2/Seurat/man/AddModuleScore.Rd                       |   18 
 Seurat-3.1.2/Seurat/man/Assay-class.Rd                          |    3 
 Seurat-3.1.2/Seurat/man/AverageExpression.Rd                    |   15 
 Seurat-3.1.2/Seurat/man/BuildClusterTree.Rd                     |   14 
 Seurat-3.1.2/Seurat/man/CalculateBarcodeInflections.Rd          |   10 
 Seurat-3.1.2/Seurat/man/CellCycleScoring.Rd                     |    3 
 Seurat-3.1.2/Seurat/man/CellScatter.Rd                          |   12 
 Seurat-3.1.2/Seurat/man/CellsByIdentities.Rd                    |only
 Seurat-3.1.2/Seurat/man/CollapseEmbeddingOutliers.Rd            |   10 
 Seurat-3.1.2/Seurat/man/CollapseSpeciesExpressionMatrix.Rd      |    8 
 Seurat-3.1.2/Seurat/man/ColorDimSplit.Rd                        |   53 
 Seurat-3.1.2/Seurat/man/CreateDimReducObject.Rd                 |   17 
 Seurat-3.1.2/Seurat/man/CreateGeneActivityMatrix.Rd             |   12 
 Seurat-3.1.2/Seurat/man/CreateSeuratObject.Rd                   |   13 
 Seurat-3.1.2/Seurat/man/DefaultAssay.Rd                         |    9 
 Seurat-3.1.2/Seurat/man/DietSeurat.Rd                           |   12 
 Seurat-3.1.2/Seurat/man/DimHeatmap.Rd                           |   21 
 Seurat-3.1.2/Seurat/man/DimPlot.Rd                              |   28 
 Seurat-3.1.2/Seurat/man/DimReduc-class.Rd                       |   14 
 Seurat-3.1.2/Seurat/man/DoHeatmap.Rd                            |   27 
 Seurat-3.1.2/Seurat/man/DotPlot.Rd                              |   19 
 Seurat-3.1.2/Seurat/man/ExpMean.Rd                              |    4 
 Seurat-3.1.2/Seurat/man/ExportToCellbrowser.Rd                  |   19 
 Seurat-3.1.2/Seurat/man/FeaturePlot.Rd                          |   34 
 Seurat-3.1.2/Seurat/man/FeatureScatter.Rd                       |   16 
 Seurat-3.1.2/Seurat/man/FindAllMarkers.Rd                       |   27 
 Seurat-3.1.2/Seurat/man/FindClusters.Rd                         |   49 
 Seurat-3.1.2/Seurat/man/FindConservedMarkers.Rd                 |   14 
 Seurat-3.1.2/Seurat/man/FindIntegrationAnchors.Rd               |   24 
 Seurat-3.1.2/Seurat/man/FindMarkers.Rd                          |   61 
 Seurat-3.1.2/Seurat/man/FindNeighbors.Rd                        |   72 -
 Seurat-3.1.2/Seurat/man/FindTransferAnchors.Rd                  |   26 
 Seurat-3.1.2/Seurat/man/FindVariableFeatures.Rd                 |   59 
 Seurat-3.1.2/Seurat/man/GetResidual.Rd                          |   11 
 Seurat-3.1.2/Seurat/man/Graph-class.Rd                          |    8 
 Seurat-3.1.2/Seurat/man/HTODemux.Rd                             |   16 
 Seurat-3.1.2/Seurat/man/HTOHeatmap.Rd                           |   13 
 Seurat-3.1.2/Seurat/man/HVFInfo.Rd                              |    3 
 Seurat-3.1.2/Seurat/man/Idents.Rd                               |   13 
 Seurat-3.1.2/Seurat/man/IntegrateData.Rd                        |   21 
 Seurat-3.1.2/Seurat/man/IsGlobal.Rd                             |only
 Seurat-3.1.2/Seurat/man/JackStraw.Rd                            |   13 
 Seurat-3.1.2/Seurat/man/JackStrawPlot.Rd                        |    3 
 Seurat-3.1.2/Seurat/man/LabelClusters.Rd                        |   11 
 Seurat-3.1.2/Seurat/man/LabelPoints.Rd                          |   11 
 Seurat-3.1.2/Seurat/man/Loadings.Rd                             |    3 
 Seurat-3.1.2/Seurat/man/LocalStruct.Rd                          |   13 
 Seurat-3.1.2/Seurat/man/LogVMR.Rd                               |    4 
 Seurat-3.1.2/Seurat/man/MULTIseqDemux.Rd                        |   12 
 Seurat-3.1.2/Seurat/man/MetaFeature.Rd                          |   10 
 Seurat-3.1.2/Seurat/man/MixingMetric.Rd                         |   12 
 Seurat-3.1.2/Seurat/man/NormalizeData.Rd                        |   35 
 Seurat-3.1.2/Seurat/man/OldWhichCells.Rd                        |   30 
 Seurat-3.1.2/Seurat/man/PCASigGenes.Rd                          |    9 
 Seurat-3.1.2/Seurat/man/PercentageFeatureSet.Rd                 |    9 
 Seurat-3.1.2/Seurat/man/PolyDimPlot.Rd                          |    9 
 Seurat-3.1.2/Seurat/man/PolyFeaturePlot.Rd                      |   14 
 Seurat-3.1.2/Seurat/man/PrepSCTIntegration.Rd                   |    9 
 Seurat-3.1.2/Seurat/man/ProjectDim.Rd                           |   13 
 Seurat-3.1.2/Seurat/man/RenameAssays.Rd                         |only
 Seurat-3.1.2/Seurat/man/RenameCells.Rd                          |    9 
 Seurat-3.1.2/Seurat/man/RidgePlot.Rd                            |   19 
 Seurat-3.1.2/Seurat/man/RowMergeSparseMatrices.Rd               |only
 Seurat-3.1.2/Seurat/man/RunALRA.Rd                              |   34 
 Seurat-3.1.2/Seurat/man/RunCCA.Rd                               |   34 
 Seurat-3.1.2/Seurat/man/RunICA.Rd                               |   56 
 Seurat-3.1.2/Seurat/man/RunLSI.Rd                               |   47 
 Seurat-3.1.2/Seurat/man/RunPCA.Rd                               |   64 
 Seurat-3.1.2/Seurat/man/RunTSNE.Rd                              |   67 -
 Seurat-3.1.2/Seurat/man/RunUMAP.Rd                              |  101 +
 Seurat-3.1.2/Seurat/man/SCTransform.Rd                          |   26 
 Seurat-3.1.2/Seurat/man/ScaleData.Rd                            |   69 -
 Seurat-3.1.2/Seurat/man/ScoreJackStraw.Rd                       |   16 
 Seurat-3.1.2/Seurat/man/SelectIntegrationFeatures.Rd            |   10 
 Seurat-3.1.2/Seurat/man/SetAssayData.Rd                         |    3 
 Seurat-3.1.2/Seurat/man/SeuratCommand-class.Rd                  |    2 
 Seurat-3.1.2/Seurat/man/SeuratTheme.Rd                          |   10 
 Seurat-3.1.2/Seurat/man/SubsetData.Rd                           |   30 
 Seurat-3.1.2/Seurat/man/TopFeatures.Rd                          |   10 
 Seurat-3.1.2/Seurat/man/TransferData.Rd                         |   16 
 Seurat-3.1.2/Seurat/man/UpdateSymbolList.Rd                     |   18 
 Seurat-3.1.2/Seurat/man/VariableFeaturePlot.Rd                  |   10 
 Seurat-3.1.2/Seurat/man/VariableFeatures.Rd                     |    3 
 Seurat-3.1.2/Seurat/man/VizDimLoadings.Rd                       |   14 
 Seurat-3.1.2/Seurat/man/VlnPlot.Rd                              |   23 
 Seurat-3.1.2/Seurat/man/WhichCells.Rd                           |   19 
 Seurat-3.1.2/Seurat/man/as.Seurat.Rd                            |   27 
 Seurat-3.1.2/Seurat/man/as.loom.Rd                              |   15 
 Seurat-3.1.2/Seurat/man/as.sparse.Rd                            |   13 
 Seurat-3.1.2/Seurat/man/h5ad.Rd                                 |   17 
 Seurat-3.1.2/Seurat/man/merge.Seurat.Rd                         |   13 
 Seurat-3.1.2/Seurat/man/print.DimReduc.Rd                       |    3 
 Seurat-3.1.2/Seurat/man/subset.Seurat.Rd                        |    3 
 Seurat-3.1.2/Seurat/tests/testthat/test_dimensional_reduction.R |   38 
 111 files changed, 2557 insertions(+), 1196 deletions(-)

More information about Seurat at CRAN
Permanent link

Package rtika updated to version 1.23 with previous version 1.22 dated 2019-08-02

Title: R Interface to 'Apache Tika'
Description: Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Author: Sasha Goodman [aut, cre], The Apache Software Foundation [aut, cph], Julia Silge [rev] (Reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/191), David Gohel [rev] (Reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/191)
Maintainer: Sasha Goodman <goodmansasha@gmail.com>

Diff between rtika versions 1.22 dated 2019-08-02 and 1.23 dated 2019-12-12

 DESCRIPTION                      |   10 -
 LICENSE                          |    2 
 MD5                              |   28 ++--
 NEWS.md                          |    7 +
 R/install_tika.R                 |    8 -
 R/tika.R                         |   29 ++--
 R/zzz.R                          |    2 
 README.md                        |   10 -
 build/vignette.rds               |binary
 inst/doc/rtika_introduction.R    |   30 ++--
 inst/doc/rtika_introduction.html |  259 +++++++++++++++++++--------------------
 man/install_tika.Rd              |   17 +-
 man/rtika.Rd                     |    1 
 man/tika.Rd                      |   22 ++-
 man/tika_fetch.Rd                |    9 +
 15 files changed, 231 insertions(+), 203 deletions(-)

More information about rtika at CRAN
Permanent link

Package metricTester updated to version 1.3.6 with previous version 1.3.4 dated 2017-10-31

Title: Test Metric and Null Model Statistical Performance
Description: Explore the behavior and statistical performance of 13 pre-defined phylogenetic metrics and 11 null models, and of user-defined metrics and null models, as detailed in Miller et al. (2017) <doi:10.1111/ecog.02070>.
Author: Eliot Miller, Chris Trisos & Damien Farine
Maintainer: Eliot Miller <eliot.isaac@gmail.com>

Diff between metricTester versions 1.3.4 dated 2017-10-31 and 1.3.6 dated 2019-12-12

 DESCRIPTION                                |   12 ++++-----
 MD5                                        |   38 ++++++++++++++---------------
 NAMESPACE                                  |    1 
 NEWS.md                                    |    8 ++++++
 R/calcField.R                              |    4 +--
 R/defineMetrics.R                          |   10 ++++++-
 R/utils.R                                  |    7 +++++
 man/betaLinker.Rd                          |    3 +-
 man/betaMetricSims.Rd                      |    3 +-
 man/betaMetricsNnulls.Rd                   |    4 +--
 man/betaMultiLinker.Rd                     |    8 +++---
 man/defineMetrics.Rd                       |    5 +++
 man/dispersalNull.Rd                       |    4 +--
 man/expectations.Rd                        |    4 +--
 man/linker.Rd                              |    4 +--
 man/metricsNnulls.Rd                       |    4 +--
 man/multiLinker.Rd                         |    4 +--
 man/sesTraitField.Rd                       |    4 +--
 man/varyX.Rd                               |    4 +--
 tests/testthat/test_calc_metric_null_sim.R |    2 -
 20 files changed, 80 insertions(+), 53 deletions(-)

More information about metricTester at CRAN
Permanent link

Package EpiILMCT updated to version 1.1.5 with previous version 1.1.4 dated 2019-10-13

Title: Continuous Time Distance-Based and Network-Based Individual Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks.
Author: Waleed Almutiry [aut, cre], Rob Deardon [aut, ths], Vineetha Warriyar K. V. [ctb]
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>

Diff between EpiILMCT versions 1.1.4 dated 2019-10-13 and 1.1.5 dated 2019-12-12

 DESCRIPTION             |    8 
 MD5                     |   16 -
 R/datgen.r              |  244 ++++++++++++------------
 R/epictmcmc.r           |  479 +++++++++++++++++++++++-------------------------
 R/epictmcmcsinr.r       |  206 ++++++++++----------
 R/epictmcmcsir.r        |  164 ++++++++--------
 R/epiplot.r             |  142 +++++++-------
 R/loglikelihoodepiILM.r |  178 ++++++++---------
 R/netdis.r              |   53 ++---
 9 files changed, 745 insertions(+), 745 deletions(-)

More information about EpiILMCT at CRAN
Permanent link

Package caretEnsemble updated to version 2.0.1 with previous version 2.0.0 dated 2016-02-07

Title: Ensembles of Caret Models
Description: Functions for creating ensembles of caret models: caretList() and caretStack(). caretList() is a convenience function for fitting multiple caret::train() models to the same dataset. caretStack() will make linear or non-linear combinations of these models, using a caret::train() model as a meta-model, and caretEnsemble() will make a robust linear combination of models using a GLM.
Author: Zachary A. Deane-Mayer [aut, cre], Jared E. Knowles [aut]
Maintainer: Zachary A. Deane-Mayer <zach.mayer@gmail.com>

Diff between caretEnsemble versions 2.0.0 dated 2016-02-07 and 2.0.1 dated 2019-12-12

 DESCRIPTION                          |   25 
 LICENSE                              |    2 
 MD5                                  |  132 ++--
 NAMESPACE                            |    7 
 R/S3GenericExtenstions.R             |    8 
 R/caretEnsemble-package.R            |    1 
 R/caretEnsemble.R                    |    2 
 R/caretList.R                        |  116 +++-
 R/caretStack.R                       |   23 
 R/helper_functions.R                 |   95 +++
 README.md                            |   14 
 build/vignette.rds                   |binary
 inst/doc/caretEnsemble-intro.R       |    9 
 inst/doc/caretEnsemble-intro.Rmd     |    2 
 inst/doc/caretEnsemble-intro.html    |  956 ++++++++++++++++++++++-------------
 man/as.caretList.Rd                  |only
 man/as.caretList.default.Rd          |only
 man/as.caretList.list.Rd             |only
 man/autoplot.Rd                      |    1 
 man/bestPreds.Rd                     |    1 
 man/c.caretList.Rd                   |    1 
 man/c.train.Rd                       |    1 
 man/caretEnsemble.Rd                 |    1 
 man/caretList.Rd                     |    1 
 man/caretModelSpec.Rd                |    1 
 man/caretStack.Rd                    |    1 
 man/check_bestpreds_indexes.Rd       |    1 
 man/check_bestpreds_obs.Rd           |    1 
 man/check_bestpreds_preds.Rd         |    1 
 man/check_bestpreds_resamples.Rd     |    1 
 man/check_caretList_classes.Rd       |    1 
 man/check_caretList_model_types.Rd   |    1 
 man/data.Rd                          |   10 
 man/dotplot.caretStack.Rd            |    1 
 man/extractBestPreds.Rd              |    1 
 man/extractCaretTarget.Rd            |    1 
 man/extractCaretTarget.default.Rd    |    1 
 man/extractCaretTarget.formula.Rd    |    1 
 man/extractModFrame.Rd               |    1 
 man/extractModRes.Rd                 |    1 
 man/extractModelName.Rd              |only
 man/extractModelTypes.Rd             |    1 
 man/fortify.Rd                       |    1 
 man/getBinaryTargetLevel.Rd          |only
 man/is.caretEnsemble.Rd              |    1 
 man/is.caretList.Rd                  |    1 
 man/is.caretStack.Rd                 |    1 
 man/makePredObsMatrix.Rd             |    1 
 man/methodCheck.Rd                   |    1 
 man/metrics.Rd                       |    3 
 man/multiResiduals.Rd                |    1 
 man/plot.caretEnsemble.Rd            |    1 
 man/plot.caretStack.Rd               |    1 
 man/predict.caretList.Rd             |    4 
 man/predict.caretStack.Rd            |    5 
 man/print.caretStack.Rd              |    1 
 man/residuals.caretEnsemble.Rd       |    1 
 man/setBinaryTargetLevel.Rd          |only
 man/sub-.caretList.Rd                |only
 man/summary.caretEnsemble.Rd         |    1 
 man/summary.caretStack.Rd            |    1 
 man/trControlCheck.Rd                |    1 
 man/tuneCheck.Rd                     |    1 
 man/validateBinaryTargetLevel.Rd     |only
 man/validateCustomModel.Rd           |only
 man/varImp.caretEnsemble.Rd          |    1 
 man/wtd.sd.Rd                        |    1 
 tests/testthat/test-caretList.R      |   13 
 tests/testthat/test-caretStack.R     |   17 
 tests/testthat/test-classSelection.R |only
 tests/testthat/test-ensemble.R       |   58 ++
 vignettes/caretEnsemble-intro.Rmd    |    2 
 72 files changed, 1018 insertions(+), 525 deletions(-)

More information about caretEnsemble at CRAN
Permanent link

Package ppcong updated to version 0.0.2 with previous version 0.0.1 dated 2019-11-28

Title: Interfacing with ProPublica's 'Congress' API
Description: A simple interface for interacting with ProPublica's 'Congress' API, which provides data about current and former members of both chambers of the U.S. Congress and can be found at the following URL: <https://projects.propublica.org/api-docs/congress-api/>.
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>), Lingshu Hu [ctb] (<https://orcid.org/0000-0003-0304-882X>), Alieva Iuliia [ctb] (<https://orcid.org/0000-0001-6270-8985>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>

Diff between ppcong versions 0.0.1 dated 2019-11-28 and 0.0.2 dated 2019-12-12

 DESCRIPTION               |   14 ++++----
 MD5                       |   18 +++++------
 NAMESPACE                 |    2 +
 NEWS.md                   |    5 +++
 R/ppc_members.R           |   74 ++++++++++++++++++++++++++++++++++++++++++----
 R/utils.R                 |    6 +++
 man/ppc_committees.Rd     |    8 +++-
 man/ppc_members.Rd        |   12 ++++---
 man/ppc_votes.Rd          |    3 -
 tests/testthat/test-ppc.R |   11 ++++++
 10 files changed, 123 insertions(+), 30 deletions(-)

More information about ppcong at CRAN
Permanent link

Package polymapR updated to version 1.0.20 with previous version 1.0.19 dated 2019-02-01

Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>.
Author: Peter Bourke [aut, cre], Geert van Geest [aut], Roeland Voorrips [ctb]
Maintainer: Peter Bourke <pbourkey@gmail.com>

Diff between polymapR versions 1.0.19 dated 2019-02-01 and 1.0.20 dated 2019-12-12

 polymapR-1.0.19/polymapR/man/createMap.Rd                          |only
 polymapR-1.0.19/polymapR/vignettes/figures/map_diagnostics.png     |only
 polymapR-1.0.20/polymapR/DESCRIPTION                               |   17 
 polymapR-1.0.20/polymapR/MD5                                       |   99 
 polymapR-1.0.20/polymapR/NAMESPACE                                 |    2 
 polymapR-1.0.20/polymapR/R/aiding_functions.R                      |   16 
 polymapR-1.0.20/polymapR/R/exported_functions.R                    | 1493 ++--------
 polymapR-1.0.20/polymapR/R/p4_functions.R                          |   52 
 polymapR-1.0.20/polymapR/R/r6_functions.R                          |  210 -
 polymapR-1.0.20/polymapR/R/roxygen_datasets.R                      |    7 
 polymapR-1.0.20/polymapR/data/datalist                             |    3 
 polymapR-1.0.20/polymapR/data/map1.rda                             |only
 polymapR-1.0.20/polymapR/data/map2.rda                             |only
 polymapR-1.0.20/polymapR/data/map3.rda                             |only
 polymapR-1.0.20/polymapR/inst/doc/Vignette_polymapR.R              |   19 
 polymapR-1.0.20/polymapR/inst/doc/Vignette_polymapR.Rmd            |   45 
 polymapR-1.0.20/polymapR/inst/doc/Vignette_polymapR.html           |   71 
 polymapR-1.0.20/polymapR/man/MDSMap_from_list.Rd                   |    2 
 polymapR-1.0.20/polymapR/man/SNSN_LOD_deviations.Rd                |    2 
 polymapR-1.0.20/polymapR/man/assign_linkage_group.Rd               |    6 
 polymapR-1.0.20/polymapR/man/bridgeHomologues.Rd                   |    2 
 polymapR-1.0.20/polymapR/man/check_map.Rd                          |   16 
 polymapR-1.0.20/polymapR/man/cluster_SN_markers.Rd                 |   10 
 polymapR-1.0.20/polymapR/man/compare_maps.Rd                       |only
 polymapR-1.0.20/polymapR/man/consensus_LG_assignment.Rd            |    6 
 polymapR-1.0.20/polymapR/man/convert_marker_dosages.Rd             |    8 
 polymapR-1.0.20/polymapR/man/createTetraOriginInput.Rd             |    3 
 polymapR-1.0.20/polymapR/man/create_phased_maplist.Rd              |    3 
 polymapR-1.0.20/polymapR/man/finish_linkage_analysis.Rd            |    6 
 polymapR-1.0.20/polymapR/man/get_markertype_combinations.Rd        |    2 
 polymapR-1.0.20/polymapR/man/homologue_lg_assignment.Rd            |   11 
 polymapR-1.0.20/polymapR/man/linkage.Rd                            |    8 
 polymapR-1.0.20/polymapR/man/map1.Rd                               |only
 polymapR-1.0.20/polymapR/man/map2.Rd                               |only
 polymapR-1.0.20/polymapR/man/map3.Rd                               |only
 polymapR-1.0.20/polymapR/man/marker_data_summary.Rd                |    6 
 polymapR-1.0.20/polymapR/man/merge_homologues.Rd                   |    6 
 polymapR-1.0.20/polymapR/man/merge_marker_assignments.Rd           |    2 
 polymapR-1.0.20/polymapR/man/orient_and_merge_maps.Rd              |    8 
 polymapR-1.0.20/polymapR/man/overviewSNlinks.Rd                    |    8 
 polymapR-1.0.20/polymapR/man/parental_quantities.Rd                |    3 
 polymapR-1.0.20/polymapR/man/phase_SN_diploid.Rd                   |    6 
 polymapR-1.0.20/polymapR/man/plot_phased_maplist.Rd                |    4 
 polymapR-1.0.20/polymapR/man/screen_for_NA_values.Rd               |    7 
 polymapR-1.0.20/polymapR/man/screen_for_duplicate_individuals.Rd   |    6 
 polymapR-1.0.20/polymapR/man/split_linkage_info.Rd                 |    2 
 polymapR-1.0.20/polymapR/man/test_prefpairing.Rd                   |    3 
 polymapR-1.0.20/polymapR/man/write.TSNPM.Rd                        |    3 
 polymapR-1.0.20/polymapR/man/write.mct.Rd                          |    3 
 polymapR-1.0.20/polymapR/man/write.pwd.Rd                          |    3 
 polymapR-1.0.20/polymapR/man/write_nested_list.Rd                  |    3 
 polymapR-1.0.20/polymapR/man/write_pwd_list.Rd                     |    3 
 polymapR-1.0.20/polymapR/vignettes/Vignette_polymapR.Rmd           |   45 
 polymapR-1.0.20/polymapR/vignettes/figures/LG1_check_map_plotA.png |only
 polymapR-1.0.20/polymapR/vignettes/figures/LG1_check_map_plotB.png |only
 polymapR-1.0.20/polymapR/vignettes/polymapR_vignette.RData         |binary
 56 files changed, 787 insertions(+), 1453 deletions(-)

More information about polymapR at CRAN
Permanent link

Package gluvarpro updated to version 2.0 with previous version 1.0 dated 2019-04-09

Title: Glucose Variability Measures from Continuous Glucose Monitoring Data
Description: Calculate different glucose variability measures, including average measures of glycemia, measures of glycemic variability and measures of glycemic risk, from continuous glucose monitoring data. Boris P. Kovatchev, Erik Otto, Daniel Cox, Linda Gonder-Frederick, and William Clarke (2006) <doi:10.2337/dc06-1085>. Jean-Pierre Le Floch, Philippe Escuyer, Eric Baudin, Dominique Baudon, and Leon Perlemuter (1990) <doi:10.2337/diacare.13.2.172>. C.M. McDonnell, S.M. Donath, S.I. Vidmar, G.A. Werther, and F.J. Cameron (2005) <doi:10.1089/dia.2005.7.253>. Everitt, Brian (1998) <doi:10.1111/j.1751-5823.2011.00149_2.x>. Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) <doi:10.2307/2234167>. Dougherty, R. L., Edelman, A. and Hyman, J. M. (1989) <doi:10.1090/S0025-5718-1989-0962209-1>. Tukey, J. W. (1977) <doi:10.1016/0377-2217(86)90209-2>. F. John Service (2013) <doi:10.2337/db12-1396>. Edmond A. Ryan, Tami Shandro, Kristy Green, Breay W. Paty, Peter A. Senior, David Bigam, A.M. James Shapiro, and Marie-Christine Vantyghem (2004) <doi:10.2337/diabetes.53.4.955>. Seniz Sevimer Tuncan, Mehmet Uzunlulu, Ozge telci caklili, Hasan Huseyin Mutlu, and Aytekin Oguz (2016) <doi:10.5152/cjms.2016.109>. Sarah E. Siegelaar, Frits Holleman, Joost B. L. Hoekstra, and J. Hans DeVries (2010) <doi:10.1210/er.2009-0021>. Gabor Marics, Zsofia Lendvai, Csaba Lodi, Levente Koncz, David Zakarias, Gyorgy Schuster, Borbala Mikos, Csaba Hermann, Attila J. Szabo, and Peter Toth-Heyn (2015) <doi:10.1186/s12938-015-0035-3>.
Author: Sergio Contador
Maintainer: Sergio Contador <scontador@ucm.es>

Diff between gluvarpro versions 1.0 dated 2019-04-09 and 2.0 dated 2019-12-12

 DESCRIPTION     |   13 +++++++------
 MD5             |   46 +++++++++++++++++++++++++---------------------
 NAMESPACE       |   20 +++++++++++---------
 R/avggvp.R      |only
 R/mplotgvp.R    |only
 R/plotgvp.R     |   18 ++++++------------
 man/adrrgvp.Rd  |    4 ++--
 man/aucgvp.Rd   |    2 +-
 man/avggvp.Rd   |only
 man/bgigvp.Rd   |    4 ++--
 man/congagvp.Rd |    2 +-
 man/cvgvp.Rd    |    2 +-
 man/datagvp1.Rd |    2 +-
 man/datagvp2.Rd |    2 +-
 man/datagvp3.Rd |    2 +-
 man/fillgvp.Rd  |    2 +-
 man/iqrgvp.Rd   |    2 +-
 man/jigvp.Rd    |    2 +-
 man/ligvp.Rd    |    2 +-
 man/magegvp.Rd  |    2 +-
 man/meangvp.Rd  |    2 +-
 man/mplotgvp.Rd |only
 man/mvgvp.Rd    |    2 +-
 man/plotgvp.Rd  |    2 +-
 man/pstrgvp.Rd  |    2 +-
 man/sdgvp.Rd    |    2 +-
 26 files changed, 69 insertions(+), 68 deletions(-)

More information about gluvarpro at CRAN
Permanent link

Package ecotox updated to version 1.4.1 with previous version 1.4.0 dated 2019-03-26

Title: Analysis of Ecotoxicology
Description: A simple approach to using a probit or logit analysis to calculate lethal concentration (LC) or time (LT) and the appropriate fiducial confidence limits desired for selected LC or LT for ecotoxicology studies (Finney 1971; Wheeler et al. 2006; Robertson et al. 2007). The simplicity of 'ecotox' comes from the syntax it implies within its functions which are similar to functions like glm() and lm(). In addition to the simplicity of the syntax, a comprehensive data frame is produced which gives the user a predicted LC or LT value for the desired level and a suite of important parameters such as fiducial confidence limits and slope. Finney, D.J. (1971, ISBN: 052108041X); Wheeler, M.W., Park, R.M., and Bailer, A.J. (2006) <doi:10.1897/05-320R.1>; Robertson, J.L., Savin, N.E., Russell, R.M., and Preisler, H.K. (2007, ISBN: 0849323312).
Author: Benjamin L Hlina [aut, cre]
Maintainer: Benjamin L Hlina <benjamin.hlina@gmail.com>

Diff between ecotox versions 1.4.0 dated 2019-03-26 and 1.4.1 dated 2019-12-12

 DESCRIPTION                      |   13 +-
 MD5                              |   44 +++----
 NAMESPACE                        |    3 
 R/LCx.R                          |  180 +++++++++++++----------------
 R/LTx.R                          |   30 +---
 R/lampreytime.R                  |    2 
 R/lampreytox.R                   |    5 
 R/ratio_test.R                   |   72 +++++++----
 README.md                        |   42 ++++++
 data/lamprey_tox.rda             |binary
 inst/CITATION                    |   21 +--
 man/LC_logit.Rd                  |  237 +++++++++++++++++++--------------------
 man/LC_probit.Rd                 |  232 +++++++++++++++++++-------------------
 man/LT_logit.Rd                  |  126 ++++++++++----------
 man/LT_probit.Rd                 |  126 ++++++++++----------
 man/lamprey_time.Rd              |   58 ++++-----
 man/lamprey_tox.Rd               |   58 ++++-----
 man/ratio_test.Rd                |  127 ++++++++++----------
 tests/testthat/test-LC_logit.R   |   38 +++++-
 tests/testthat/test-LC_probit.R  |   70 ++++++++---
 tests/testthat/test-LT_logit.R   |   27 ++++
 tests/testthat/test-LT_probit.R  |   28 ++++
 tests/testthat/test-ratio_test.R |  160 +++++++++++++++++++++++---
 23 files changed, 976 insertions(+), 723 deletions(-)

More information about ecotox at CRAN
Permanent link

Package rmarkdown updated to version 2.0 with previous version 1.18 dated 2019-11-27

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Andrew Dunning [ctb], Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Barret Schloerke [ctb], Christophe Dervieux [ctb], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Jeff Allen [ctb], Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak lua filter), Albert Krewinkel [ctb, cph] (pagebreak lua filter)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between rmarkdown versions 1.18 dated 2019-11-27 and 2.0 dated 2019-12-12

 rmarkdown-1.18/rmarkdown/inst/rmd/latex/compact-title.tex                       |only
 rmarkdown-2.0/rmarkdown/DESCRIPTION                                             |   10 
 rmarkdown-2.0/rmarkdown/MD5                                                     |  111 +++++-----
 rmarkdown-2.0/rmarkdown/NAMESPACE                                               |    1 
 rmarkdown-2.0/rmarkdown/NEWS.md                                                 |   28 ++
 rmarkdown-2.0/rmarkdown/R/context_document.R                                    |only
 rmarkdown-2.0/rmarkdown/R/html_dependencies.R                                   |   13 +
 rmarkdown-2.0/rmarkdown/R/html_document.R                                       |    4 
 rmarkdown-2.0/rmarkdown/R/html_document_base.R                                  |    9 
 rmarkdown-2.0/rmarkdown/R/html_notebook.R                                       |    6 
 rmarkdown-2.0/rmarkdown/R/html_resources.R                                      |   32 +-
 rmarkdown-2.0/rmarkdown/R/md_document.R                                         |    6 
 rmarkdown-2.0/rmarkdown/R/output_format.R                                       |  109 +++------
 rmarkdown-2.0/rmarkdown/R/params.R                                              |    5 
 rmarkdown-2.0/rmarkdown/R/pdf_document.R                                        |   47 ++--
 rmarkdown-2.0/rmarkdown/R/powerpoint_presentation.R                             |    4 
 rmarkdown-2.0/rmarkdown/R/render.R                                              |   72 ++----
 rmarkdown-2.0/rmarkdown/R/render_site.R                                         |   75 +++---
 rmarkdown-2.0/rmarkdown/R/shiny.R                                               |   55 +---
 rmarkdown-2.0/rmarkdown/R/shiny_prerendered.R                                   |   21 -
 rmarkdown-2.0/rmarkdown/R/slidy_presentation.R                                  |   16 +
 rmarkdown-2.0/rmarkdown/R/util.R                                                |   22 -
 rmarkdown-2.0/rmarkdown/inst/rmd/h/pandoc                                       |only
 rmarkdown-2.0/rmarkdown/inst/rmd/ioslides/ioslides-13.5.1/theme/css/default.css |    6 
 rmarkdown-2.0/rmarkdown/inst/rmd/lua/pagebreak.lua                              |    5 
 rmarkdown-2.0/rmarkdown/inst/rmd/slidy/slidy_shiny.js                           |only
 rmarkdown-2.0/rmarkdown/man/all_output_formats.Rd                               |    4 
 rmarkdown-2.0/rmarkdown/man/beamer_presentation.Rd                              |   12 -
 rmarkdown-2.0/rmarkdown/man/context_document.Rd                                 |only
 rmarkdown-2.0/rmarkdown/man/default_output_format.Rd                            |    4 
 rmarkdown-2.0/rmarkdown/man/find_external_resources.Rd                          |    2 
 rmarkdown-2.0/rmarkdown/man/github_document.Rd                                  |   12 -
 rmarkdown-2.0/rmarkdown/man/html_document.Rd                                    |   12 -
 rmarkdown-2.0/rmarkdown/man/html_fragment.Rd                                    |   12 -
 rmarkdown-2.0/rmarkdown/man/html_vignette.Rd                                    |   12 -
 rmarkdown-2.0/rmarkdown/man/ioslides_presentation.Rd                            |   12 -
 rmarkdown-2.0/rmarkdown/man/knit_params_ask.Rd                                  |    2 
 rmarkdown-2.0/rmarkdown/man/md_document.Rd                                      |   17 -
 rmarkdown-2.0/rmarkdown/man/output_format.Rd                                    |   56 ++---
 rmarkdown-2.0/rmarkdown/man/parse_html_notebook.Rd                              |    4 
 rmarkdown-2.0/rmarkdown/man/pdf_document.Rd                                     |   12 -
 rmarkdown-2.0/rmarkdown/man/powerpoint_presentation.Rd                          |   12 -
 rmarkdown-2.0/rmarkdown/man/render.Rd                                           |    3 
 rmarkdown-2.0/rmarkdown/man/render_site.Rd                                      |   14 -
 rmarkdown-2.0/rmarkdown/man/resolve_output_format.Rd                            |    5 
 rmarkdown-2.0/rmarkdown/man/slidy_presentation.Rd                               |   12 -
 rmarkdown-2.0/rmarkdown/man/word_document.Rd                                    |   12 -
 rmarkdown-2.0/rmarkdown/man/yaml_front_matter.Rd                                |    2 
 rmarkdown-2.0/rmarkdown/tests/rmd/raw-header.Rmd                                |only
 rmarkdown-2.0/rmarkdown/tests/rmd/two-authors.Rmd                               |only
 rmarkdown-2.0/rmarkdown/tests/rmd/yaml-r-code.Rmd                               |only
 rmarkdown-2.0/rmarkdown/tests/testrmd.R                                         |   12 +
 rmarkdown-2.0/rmarkdown/tests/testthat/resources/file-exists.Rmd                |    3 
 rmarkdown-2.0/rmarkdown/tests/testthat/site/PageD.R                             |only
 rmarkdown-2.0/rmarkdown/tests/testthat/site/_site.yml                           |    3 
 rmarkdown-2.0/rmarkdown/tests/testthat/test-formats.R                           |    1 
 rmarkdown-2.0/rmarkdown/tests/testthat/test-formats.Rmd                         |    1 
 rmarkdown-2.0/rmarkdown/tests/testthat/test-ioslides.R                          |    2 
 rmarkdown-2.0/rmarkdown/tests/testthat/test-lua-filters.R                       |    2 
 rmarkdown-2.0/rmarkdown/tests/testthat/test-notebook.R                          |    2 
 rmarkdown-2.0/rmarkdown/tests/testthat/test-site.R                              |    7 
 61 files changed, 479 insertions(+), 444 deletions(-)

More information about rmarkdown at CRAN
Permanent link

Package lazytrade updated to version 0.3.8 with previous version 0.3.7 dated 2019-12-03

Title: Learn Computer and Data Science using Algorithmic Trading
Description: Provide sets of functions and methods to learn and practice data science using idea of algorithmic trading. Main goal is to process information within "Decision Support System" to come up with analysis or predictions. There are several utilities such as dynamic and adaptive risk management using reinforcement learning and even functions to generate predictions of price changes using pattern recognition deep regression learning.
Author: Vladimir Zhbanko
Maintainer: Vladimir Zhbanko <vladimir.zhbanko@gmail.com>

Diff between lazytrade versions 0.3.7 dated 2019-12-03 and 0.3.8 dated 2019-12-12

 DESCRIPTION                                  |    8 -
 MD5                                          |  103 +++++++-------
 NAMESPACE                                    |    3 
 NEWS.md                                      |    7 +
 R/util_generate_password.R                   |only
 R/zzz.R                                      |    3 
 README.md                                    |   42 ++++--
 man/DFR.Rd                                   |   50 +++----
 man/EURUSDM15X75.Rd                          |   34 ++--
 man/TradeStatePolicy.Rd                      |   34 ++--
 man/aml_collect_data.Rd                      |  158 +++++++++++-----------
 man/aml_make_model.Rd                        |  150 ++++++++++-----------
 man/aml_score_data.Rd                        |  177 +++++++++++++------------
 man/aml_test_model.Rd                        |  186 +++++++++++++--------------
 man/check_if_optimize.Rd                     |  137 ++++++++++---------
 man/create_labelled_data.Rd                  |  104 +++++++--------
 man/create_transposed_data.Rd                |   84 ++++++------
 man/data_trades.Rd                           |   46 +++---
 man/decrypt_mykeys.Rd                        |   78 +++++------
 man/evaluate_macroeconomic_event.Rd          |  141 ++++++++++----------
 man/evaluate_market_type.Rd                  |  106 +++++++--------
 man/generate_RL_policy.Rd                    |   94 ++++++-------
 man/generate_RL_policy_mt.Rd                 |   84 ++++++------
 man/get_profit_factorDF.Rd                   |   60 ++++----
 man/import_data.Rd                           |   78 +++++------
 man/import_data_mt.Rd                        |   75 +++++-----
 man/indicator_dataset.Rd                     |   34 ++--
 man/load_asset_data.Rd                       |  108 ++++++++-------
 man/log_RL_progress.Rd                       |   76 +++++------
 man/log_RL_progress_mt.Rd                    |   78 +++++------
 man/macd_df.Rd                               |   32 ++--
 man/opt_aggregate_results.Rd                 |   72 +++++-----
 man/opt_create_graphs.Rd                     |   86 ++++++------
 man/policy_tr_systDF.Rd                      |   34 ++--
 man/price_dataset.Rd                         |   34 ++--
 man/profit_factor.Rd                         |   68 ++++-----
 man/profit_factorDF.Rd                       |   46 +++---
 man/profit_factor_data.Rd                    |   46 +++---
 man/record_policy.Rd                         |   95 +++++++------
 man/record_policy_mt.Rd                      |   82 ++++++-----
 man/result_R.Rd                              |   34 ++--
 man/result_prev.Rd                           |   32 ++--
 man/self_learn_ai_R.Rd                       |  151 +++++++++++----------
 man/test_data_pattern.Rd                     |   36 ++---
 man/test_model.Rd                            |   90 ++++++-------
 man/to_m.Rd                                  |   54 +++----
 man/trading_systemDF.Rd                      |   50 +++----
 man/util_generate_password.Rd                |only
 man/writeCommandViaCSV.Rd                    |   98 +++++++-------
 man/write_command_via_csv.Rd                 |   99 +++++++-------
 man/write_control_parameters.Rd              |   80 +++++------
 man/write_control_parameters_mt.Rd           |   84 ++++++------
 man/x_test_model.Rd                          |   34 ++--
 tests/testthat/test-util_generate_password.R |only
 54 files changed, 1923 insertions(+), 1852 deletions(-)

More information about lazytrade at CRAN
Permanent link

Package conStruct updated to version 1.0.4 with previous version 1.0.3 dated 2019-01-03

Title: Models Spatially Continuous and Discrete Population Genetic Structure
Description: A method for modeling genetic data as a combination of discrete layers, within each of which relatedness may decay continuously with geographic distance. This package contains code for running analyses (which are implemented in the modeling language 'rstan') and visualizing and interpreting output. See the paper for more details on the model and its utility.
Author: Gideon Bradburd [aut, cre]
Maintainer: Gideon Bradburd <bradburd@msu.edu>

Diff between conStruct versions 1.0.3 dated 2019-01-03 and 1.0.4 dated 2019-12-12

 DESCRIPTION                         |   10 +++---
 MD5                                 |   54 ++++++++++++++++++------------------
 NEWS.md                             |    6 ++++
 R/format.data.R                     |   18 ++++++++----
 R/model.comparison.R                |   19 ++++++++----
 R/plot.output.R                     |    6 ++--
 R/process.model.fit.R               |   10 +++---
 R/run.conStruct.R                   |   11 ++++---
 R/zzz.R                             |    2 -
 build/vignette.rds                  |binary
 inst/doc/format-data.R              |   18 ++++++------
 inst/doc/format-data.Rmd            |    5 ++-
 inst/doc/format-data.html           |   30 ++++++++++++--------
 inst/doc/model-comparison.R         |   28 +++++++++---------
 inst/doc/model-comparison.html      |   34 +++++++++++++---------
 inst/doc/run-conStruct.R            |   14 ++++-----
 inst/doc/run-conStruct.html         |   22 +++++++++-----
 inst/doc/visualize-results.R        |   22 +++++++-------
 inst/doc/visualize-results.html     |   18 ++++++++----
 man/calculate.layer.contribution.Rd |    3 --
 man/compare.two.runs.Rd             |   10 +++++-
 man/conStruct.Rd                    |   16 ++++++++--
 man/make.admix.pie.plot.Rd          |   13 ++++++--
 man/make.all.the.plots.Rd           |    5 +--
 man/make.structure.plot.Rd          |   12 ++++++--
 man/structure2conStruct.Rd          |   22 ++++++++++----
 man/x.validation.Rd                 |   20 ++++++++++---
 vignettes/format-data.Rmd           |    5 ++-
 28 files changed, 268 insertions(+), 165 deletions(-)

More information about conStruct at CRAN
Permanent link

Package SEERaBomb updated to version 2019.2 with previous version 2019.1 dated 2019-05-07

Title: SEER and Atomic Bomb Survivor Data Analysis Tools
Description: Creates SEER (Surveillance, Epidemiology and End Results) and A-bomb data binaries from ASCII sources and provides tools for estimating SEER second cancer risks. Methods are described in <doi:10.1038/leu.2015.258>.
Author: Tomas Radivoyevitch [aut, cre], R. Molenaar [ctb]
Maintainer: Tomas Radivoyevitch <radivot@ccf.org>

Diff between SEERaBomb versions 2019.1 dated 2019-05-07 and 2019.2 dated 2019-12-12

 DESCRIPTION                                       |    8 ++---
 MD5                                               |   31 +++++++++++-----------
 NAMESPACE                                         |    2 -
 NEWS                                              |    7 ++++
 R/csd.R                                           |   12 ++++++--
 R/getE.R                                          |    3 +-
 R/incidSEER.R                                     |    2 -
 R/mk2D.R                                          |    7 ++--
 R/mkExcelCsd.R                                    |    2 -
 R/pickFields.R                                    |   12 ++++++++
 R/simSeerSet.R                                    |    4 +-
 inst/docs/examples/mkDataBinaries.R               |    4 ++
 inst/docs/papers/attic/leukemia2016/mkExcelDemo.R |   15 +++++++++-
 inst/docs/papers/attic/leukemia2016/tables.R      |    4 +-
 inst/docs/papers/misc                             |only
 man/mkExcelCsd.Rd                                 |    2 -
 man/simSeerSet.Rd                                 |    2 -
 17 files changed, 79 insertions(+), 38 deletions(-)

More information about SEERaBomb at CRAN
Permanent link

Package PCMBase updated to version 1.2.11 with previous version 1.2.10 dated 2019-09-11

Title: Simulation and Likelihood Calculation of Phylogenetic Comparative Models
Description: Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above models can be associated with different branches of the tree. The PCMBase package is limited to trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for ML and Bayesian fit of these models to tree and trait data. The package web-site <https://venelin.github.io/PCMBase/> provides access to the documentation and other resources.
Author: Venelin Mitov [aut, cre, cph] (<a href="https://venelin.github.io">venelin.github.io</a>), Krzysztof Bartoszek [ctb], Georgios Asimomitis [ctb], Tanja Stadler [ths]
Maintainer: Venelin Mitov <vmitov@gmail.com>

Diff between PCMBase versions 1.2.10 dated 2019-09-11 and 1.2.11 dated 2019-12-12

 PCMBase-1.2.10/PCMBase/man/UpperChol.Rd                       |only
 PCMBase-1.2.11/PCMBase/DESCRIPTION                            |   13 
 PCMBase-1.2.11/PCMBase/MD5                                    |   66 -
 PCMBase-1.2.11/PCMBase/NAMESPACE                              |    8 
 PCMBase-1.2.11/PCMBase/NEWS.md                                |   19 
 PCMBase-1.2.11/PCMBase/R/GaussianPCM.R                        |   35 
 PCMBase-1.2.11/PCMBase/R/MixedGaussian.R                      |   82 +-
 PCMBase-1.2.11/PCMBase/R/PCM.R                                |  400 +++++++++-
 PCMBase-1.2.11/PCMBase/R/PCMParam.R                           |  123 +--
 PCMBase-1.2.11/PCMBase/R/PCMTree.R                            |   70 -
 PCMBase-1.2.11/PCMBase/R/Utilities.R                          |   60 -
 PCMBase-1.2.11/PCMBase/R/matrixparametrizations.R             |    9 
 PCMBase-1.2.11/PCMBase/README.md                              |   23 
 PCMBase-1.2.11/PCMBase/inst/CITATION                          |   18 
 PCMBase-1.2.11/PCMBase/inst/doc/PCMBase.html                  |   46 -
 PCMBase-1.2.11/PCMBase/inst/doc/PCMCreateModel.html           |   12 
 PCMBase-1.2.11/PCMBase/inst/doc/PCMParam.html                 |    8 
 PCMBase-1.2.11/PCMBase/inst/doc/PCMTracePruning.html          |    8 
 PCMBase-1.2.11/PCMBase/man/MatchListMembers.Rd                |only
 PCMBase-1.2.11/PCMBase/man/MixedGaussian.Rd                   |   42 -
 PCMBase-1.2.11/PCMBase/man/PCMAddToListAttribute.Rd           |only
 PCMBase-1.2.11/PCMBase/man/PCMCombineListAttribute.Rd         |only
 PCMBase-1.2.11/PCMBase/man/PCMGetAttribute.Rd                 |only
 PCMBase-1.2.11/PCMBase/man/PCMGetVecParamsRegimesAndModels.Rd |    4 
 PCMBase-1.2.11/PCMBase/man/PCMLik.Rd                          |   31 
 PCMBase-1.2.11/PCMBase/man/PCMListMembers.Rd                  |only
 PCMBase-1.2.11/PCMBase/man/PCMOptions.Rd                      |    2 
 PCMBase-1.2.11/PCMBase/man/PCMParamLocateInShortVector.Rd     |   11 
 PCMBase-1.2.11/PCMBase/man/PCMParamSetByName.Rd               |    4 
 PCMBase-1.2.11/PCMBase/man/PCMParseErrorMessage.Rd            |   16 
 PCMBase-1.2.11/PCMBase/man/PCMSetAttribute.Rd                 |only
 PCMBase-1.2.11/PCMBase/man/PCMSim.Rd                          |   14 
 PCMBase-1.2.11/PCMBase/man/PCMTreeListCladePartitions.Rd      |    6 
 PCMBase-1.2.11/PCMBase/man/PCMVar.Rd                          |    6 
 PCMBase-1.2.11/PCMBase/man/UpperTriFactor.Rd                  |only
 PCMBase-1.2.11/PCMBase/tests/testthat/test-PCMTree.R          |    2 
 PCMBase-1.2.11/PCMBase/vignettes/REFERENCES-R.bib             |    2 
 PCMBase-1.2.11/PCMBase/vignettes/REFERENCES.bib               |   14 
 38 files changed, 753 insertions(+), 401 deletions(-)

More information about PCMBase at CRAN
Permanent link

Package amap updated to version 0.8-18 with previous version 0.8-17 dated 2019-05-13

Title: Another Multidimensional Analysis Package
Description: Tools for Clustering and Principal Component Analysis (With robust methods, and parallelized functions).
Author: Antoine Lucas
Maintainer: Antoine Lucas <antoinelucas@gmail.com>

Diff between amap versions 0.8-17 dated 2019-05-13 and 0.8-18 dated 2019-12-12

 amap-0.8-17/amap/configure          |only
 amap-0.8-17/amap/configure.ac       |only
 amap-0.8-17/amap/src/distance_T.inl |only
 amap-0.8-17/amap/src/hclust_T.inl   |only
 amap-0.8-18/amap/DESCRIPTION        |    8 ++++----
 amap-0.8-18/amap/MD5                |   27 ++++++++++++++-------------
 amap-0.8-18/amap/R/Kmeans.R         |    2 +-
 amap-0.8-18/amap/R/dist.R           |    2 +-
 amap-0.8-18/amap/R/hcluster.R       |    2 +-
 amap-0.8-18/amap/build/vignette.rds |binary
 amap-0.8-18/amap/inst/doc/amap.pdf  |binary
 amap-0.8-18/amap/inst/doc/vignettes |only
 amap-0.8-18/amap/inst/po/po         |only
 amap-0.8-18/amap/src/Makevars.in    |    4 +---
 amap-0.8-18/amap/src/distance_T.h   |    2 +-
 amap-0.8-18/amap/src/distance_T.h.h |only
 amap-0.8-18/amap/src/hclust_T.h     |    2 +-
 amap-0.8-18/amap/src/hclust_T.h.h   |only
 18 files changed, 24 insertions(+), 25 deletions(-)

More information about amap at CRAN
Permanent link

Package treeHMM updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-13

Title: Tree Structured Hidden Markov Model
Description: Used for Inference, Prediction and Parameter learning for tree structured Hidden Markov Model. The package propose a new architecture of Hidden Markov Model(HMM) known as Tree Structured HMM which could be used in various applications which involves graphs, trees etc.
Author: Prajwal Bende [aut, cre], Russ Greiner [ths], Pouria Ramazi [ths]
Maintainer: Prajwal Bende <pbende@ualberta.ca>

Diff between treeHMM versions 0.1.0 dated 2019-10-13 and 0.1.1 dated 2019-12-12

 DESCRIPTION |   12 +++++++-----
 MD5         |    2 +-
 2 files changed, 8 insertions(+), 6 deletions(-)

More information about treeHMM at CRAN
Permanent link

Package miWQS updated to version 0.2.0 with previous version 0.1.0 dated 2019-07-31

Title: Multiple Imputation Using Weighted Quantile Sum Regression
Description: The `miWQS` package handles the uncertainty due to below the detection limit in a correlated component mixture problem. Researchers want to determine if a set/mixture of continuous and correlated components/chemicals is associated with an outcome and if so, which components are important in that mixture. These components share a common outcome but are interval-censored between zero and low thresholds, or detection limits, that may be different across the components. The `miWQS` package applies the multiple imputation (MI) procedure to the weighted quantile sum regression (WQS) methodology for continuous, binary, or count outcomes. The imputation models are: bootstrapping imputation (Lubin et.al (2004) <doi:10.1289/ehp.7199>) and Bayesian imputation.
Author: Paul M. Hargarten [aut, cre], David C. Wheeler [aut, rev, ths]
Maintainer: Paul M. Hargarten <hargartenp@vcu.edu>

Diff between miWQS versions 0.1.0 dated 2019-07-31 and 0.2.0 dated 2019-12-12

 miWQS-0.1.0/miWQS/R/impute_multivariate_bayesian_mi_part.R         |only
 miWQS-0.2.0/miWQS/DESCRIPTION                                      |   34 
 miWQS-0.2.0/miWQS/MD5                                              |   96 -
 miWQS-0.2.0/miWQS/NAMESPACE                                        |    6 
 miWQS-0.2.0/miWQS/NEWS.md                                          |   52 
 miWQS-0.2.0/miWQS/R/analyze_individually.R                         |    6 
 miWQS-0.2.0/miWQS/R/check_miWQS_Functions.R                        |  604 +++++-----
 miWQS-0.2.0/miWQS/R/coef_wqs_helper.R                              |    3 
 miWQS-0.2.0/miWQS/R/combine_AIC.R                                  |    7 
 miWQS-0.2.0/miWQS/R/do_many_wqs.R                                  |   39 
 miWQS-0.2.0/miWQS/R/estimate_wqs_WQS.R                             |  238 +--
 miWQS-0.2.0/miWQS/R/estimate_wqs_formula.R                         |only
 miWQS-0.2.0/miWQS/R/formatIQR.R                                    |    2 
 miWQS-0.2.0/miWQS/R/formatZ.R                                      |   37 
 miWQS-0.2.0/miWQS/R/head_array.R                                   |    5 
 miWQS-0.2.0/miWQS/R/impute_Lubin.R                                 |  121 --
 miWQS-0.2.0/miWQS/R/impute_boot.R                                  |  150 +-
 miWQS-0.2.0/miWQS/R/impute_multivariate_bayesian_part.R            |only
 miWQS-0.2.0/miWQS/R/impute_sub.R                                   |   14 
 miWQS-0.2.0/miWQS/R/impute_univariate_bayesian_imputation_stage1.R |   68 -
 miWQS-0.2.0/miWQS/R/is_integer.R                                   |   50 
 miWQS-0.2.0/miWQS/R/make_quantile_matrix_WQS.R                     |    4 
 miWQS-0.2.0/miWQS/R/plot_wqs_ggplot2_helper.R                      |   40 
 miWQS-0.2.0/miWQS/R/pool_mi_stage3.R                               |   99 -
 miWQS-0.2.0/miWQS/R/print_wqs_helper.R                             |    2 
 miWQS-0.2.0/miWQS/R/simdata87.R                                    |    6 
 miWQS-0.2.0/miWQS/R/specify_init_WQS.R                             |    3 
 miWQS-0.2.0/miWQS/R/wqs.pool.test_data.R                           |    6 
 miWQS-0.2.0/miWQS/build/vignette.rds                               |binary
 miWQS-0.2.0/miWQS/inst/WORDLIST                                    |   11 
 miWQS-0.2.0/miWQS/inst/doc/README.R                                |    3 
 miWQS-0.2.0/miWQS/inst/doc/README.Rmd                              |    7 
 miWQS-0.2.0/miWQS/inst/doc/README.pdf                              |binary
 miWQS-0.2.0/miWQS/man/analyze.individually.Rd                      |    6 
 miWQS-0.2.0/miWQS/man/coef.wqs.Rd                                  |    4 
 miWQS-0.2.0/miWQS/man/combine.AIC.Rd                               |    8 
 miWQS-0.2.0/miWQS/man/do.many.wqs.Rd                               |   26 
 miWQS-0.2.0/miWQS/man/estimate.wqs.Rd                              |   53 
 miWQS-0.2.0/miWQS/man/estimate.wqs.formula.Rd                      |only
 miWQS-0.2.0/miWQS/man/impute.Lubin.Rd                              |   41 
 miWQS-0.2.0/miWQS/man/impute.boot.Rd                               |   33 
 miWQS-0.2.0/miWQS/man/impute.multivariate.bayesian.Rd              |   15 
 miWQS-0.2.0/miWQS/man/impute.sub.Rd                                |   19 
 miWQS-0.2.0/miWQS/man/impute.univariate.bayesian.mi.Rd             |   24 
 miWQS-0.2.0/miWQS/man/make.quantile.matrix.Rd                      |    9 
 miWQS-0.2.0/miWQS/man/plot.wqs.Rd                                  |   10 
 miWQS-0.2.0/miWQS/man/pool.mi.Rd                                   |   24 
 miWQS-0.2.0/miWQS/man/print.wqs.Rd                                 |    1 
 miWQS-0.2.0/miWQS/man/simdata87.Rd                                 |    6 
 miWQS-0.2.0/miWQS/man/wqs.pool.test.Rd                             |    4 
 miWQS-0.2.0/miWQS/vignettes/README.Rmd                             |    7 
 51 files changed, 974 insertions(+), 1029 deletions(-)

More information about miWQS at CRAN
Permanent link

Package datasets.load updated to version 1.0.0 with previous version 0.3.0 dated 2018-09-10

Title: Interfaces for Loading Datasets
Description: Visual interface for loading datasets in RStudio from all installed (unloaded) packages, also includes command line interfaces.
Author: Bastiaan quast [aut, cre]
Maintainer: Bastiaan quast <bquast@gmail.com>

Diff between datasets.load versions 0.3.0 dated 2018-09-10 and 1.0.0 dated 2019-12-12

 DESCRIPTION |   12 ++++++------
 MD5         |    2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

More information about datasets.load at CRAN
Permanent link

Package spam64 updated to version 2.5-1 with previous version 2.4-0 dated 2019-11-02

Title: 64-Bit Extension of the SPArse Matrix R Package 'spam'
Description: Provides the Fortran code of the R package 'spam' with 64-bit integers. Loading this package together with the R package spam enables the sparse matrix class spam to handle huge sparse matrices with more than 2^31-1 non-zero elements. Documentation is provided in Gerber, Moesinger and Furrer (2017) <doi:10.1016/j.cageo.2016.11.015>.
Author: Reinhard Furrer [aut, cre], Florian Gerber [aut], Roman Flury [aut], Daniel Gerber [ctb], Kaspar Moesinger [ctb], Youcef Saad [ctb] (SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/), Esmond G. Ng [ctb] (Fortran Cholesky routines), Barry W. Peyton [ctb] (Fortran Cholesky routines), Joseph W.H. Liu [ctb] (Fortran Cholesky routines), Alan D. George [ctb] (Fortran Cholesky routines), Lehoucq B. Rich [ctb] (ARPACK), Maschhoff Kristi [ctb] (ARPACK), Sorensen C. Danny [ctb] (ARPACK), Yang Chao [ctb] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>

Diff between spam64 versions 2.4-0 dated 2019-11-02 and 2.5-1 dated 2019-12-12

 spam64-2.4-0/spam64/src/dn_eigen.f       |only
 spam64-2.4-0/spam64/src/ds_eigen.f       |only
 spam64-2.4-0/spam64/src/stat.h           |only
 spam64-2.5-1/spam64/DESCRIPTION          |   10 
 spam64-2.5-1/spam64/MD5                  |   35 -
 spam64-2.5-1/spam64/src/bckslvmodified.f |   16 
 spam64-2.5-1/spam64/src/cholmodified.f   |  458 ++++++++++++------------
 spam64-2.5-1/spam64/src/dgetv0.f         |   64 ---
 spam64-2.5-1/spam64/src/dist.f           |  184 ++++-----
 spam64-2.5-1/spam64/src/dn_ARPACK.f      |  461 +++---------------------
 spam64-2.5-1/spam64/src/dn_eigen64.f     |only
 spam64-2.5-1/spam64/src/ds_ARPACK.f      |  523 +++++----------------------
 spam64-2.5-1/spam64/src/ds_eigen64.f     |only
 spam64-2.5-1/spam64/src/fromsparsekit.f  |   33 -
 spam64-2.5-1/spam64/src/init.c           |    8 
 spam64-2.5-1/spam64/src/kronecker.f      |    4 
 spam64-2.5-1/spam64/src/permutation.f    |  290 +++++++--------
 spam64-2.5-1/spam64/src/rowcolstats.f    |   50 +-
 spam64-2.5-1/spam64/src/spamown.f        |  586 +++++++++++++++----------------
 spam64-2.5-1/spam64/src/spamown2.f       |   54 +-
 spam64-2.5-1/spam64/src/xybind.f         |    8 
 21 files changed, 1038 insertions(+), 1746 deletions(-)

More information about spam64 at CRAN
Permanent link

Package spam updated to version 2.5-1 with previous version 2.5-0 dated 2019-12-06

Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64). Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.
Author: Reinhard Furrer [aut, cre], Florian Gerber [aut], Roman Flury [aut], Daniel Gerber [ctb], Kaspar Moesinger [ctb], Youcef Saad [ctb] (SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/), Esmond G. Ng [ctb] (Fortran Cholesky routines), Barry W. Peyton [ctb] (Fortran Cholesky routines), Joseph W.H. Liu [ctb] (Fortran Cholesky routines), Alan D. George [ctb] (Fortran Cholesky routines), Lehoucq B. Rich [ctb] (ARPACK), Maschhoff Kristi [ctb] (ARPACK), Sorensen C. Danny [ctb] (ARPACK), Yang Chao [ctb] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>

Diff between spam versions 2.5-0 dated 2019-12-06 and 2.5-1 dated 2019-12-12

 spam-2.5-0/spam/src/compare.f                             |only
 spam-2.5-1/spam/DESCRIPTION                               |    8 +--
 spam-2.5-1/spam/MD5                                       |   35 ++++++--------
 spam-2.5-1/spam/NEWS.md                                   |    7 ++
 spam-2.5-1/spam/inst/doc/spam.R                           |   26 +++++-----
 spam-2.5-1/spam/inst/doc/spam.pdf                         |binary
 spam-2.5-1/spam/src/dist.f                                |    6 --
 spam-2.5-1/spam/src/ds_ARPACK.f                           |   26 ++++++++++
 spam-2.5-1/spam/src/ds_eigen.f                            |   16 ------
 spam-2.5-1/spam/src/spamown.f                             |   10 +---
 spam-2.5-1/spam/tests/demo_article-jss-example1.Rout.save |    4 -
 spam-2.5-1/spam/tests/demo_article-jss-example2.Rout.save |    6 +-
 spam-2.5-1/spam/tests/demo_article-jss.Rout.save          |    4 -
 spam-2.5-1/spam/tests/demo_cholesky.Rout.save             |    4 -
 spam-2.5-1/spam/tests/demo_jss15-BYM.Rout.save            |    4 -
 spam-2.5-1/spam/tests/demo_jss15-Leroux.Rout.save         |    4 -
 spam-2.5-1/spam/tests/demo_spam.Rout.save                 |    4 -
 spam-2.5-1/spam/tests/demo_timing.Rout.save               |    4 -
 spam-2.5-1/spam/tests/jss_areal_counts.Rout.save          |    4 -
 19 files changed, 93 insertions(+), 79 deletions(-)

More information about spam at CRAN
Permanent link

New package metaboGSE with initial version 1.2.2
Package: metaboGSE
Type: Package
Title: Gene Set Enrichment Analysis via Integration of Metabolic Networks and RNA-Seq Data
Version: 1.2.2
Depends: R (>= 3.4.0), sybil (>= 2.0.4), ape (>= 3.3)
Suggests: glpkAPI (>= 1.3.0), clpAPI (>= 1.2.7), topGO (>= 2.24.0), unix, KernSmooth, KEGGREST, survival, ctc, knitr, rmarkdown
Imports: utils, stats, methods, parallel, grDevices, graphics, Matrix, AnnotationDbi (>= 1.32.3)
Packaged: 2019-12-12 08:22:16 UTC; ttran
Author: Van Du T. Tran [aut, cre], Marco Pagni [aut]
Maintainer: Van Du T. Tran <thuong.tran@sib.swiss>
Description: Integrates metabolic networks and RNA-seq data to construct condition-specific series of metabolic sub-networks and applies to gene set enrichment analysis (Tran et al. (2018) <doi:10.1093/bioinformatics/bty929>).
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.2
VignetteBuilder: knitr
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2019-12-12 16:30:02 UTC

More information about metaboGSE at CRAN
Permanent link

Package idiogramFISH updated to version 1.11.1 with previous version 1.9.1 dated 2019-11-29

Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of several karyotypes having a set of dataframes for chromosome data and optionally mark data. Includes also a function to plot holocentrics and its marks supporting micrometers and Mb. Marks can have square or dot form, its legend (label) can be drawn inline or to the right of karyotypes. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x> , karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre], Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>

Diff between idiogramFISH versions 1.9.1 dated 2019-11-29 and 1.11.1 dated 2019-12-12

 DESCRIPTION                               |    8 
 MD5                                       |   91 +--
 NEWS.md                                   |   11 
 R/chrbasicdataHolo.R                      |    5 
 R/markdataholo.R                          |    4 
 R/plotIdiograms.R                         |  475 +++++++++++-------
 R/plotlabelsright.R                       |   55 +-
 README.md                                 |  140 ++---
 data/bigdfOfChrSize3Mb.rda                |only
 data/bigdfOfMarks3Mb.rda                  |only
 inst/doc/AplotIdiogramsVig.R              |  228 +++++---
 inst/doc/AplotIdiogramsVig.Rmd            |  246 +++++----
 inst/doc/AplotIdiogramsVig.html           |  764 +++++++++++++++++++++++-------
 inst/doc/BplotIdiogramsHoloVig.R          |  154 ++----
 inst/doc/BplotIdiogramsHoloVig.Rmd        |  154 ++----
 inst/doc/BplotIdiogramsHoloVig.html       |  206 +++-----
 inst/doc/CgroupsVig.R                     |   70 --
 inst/doc/CgroupsVig.Rmd                   |   71 --
 inst/doc/CgroupsVig.html                  |  144 ++---
 inst/doc/DphylogenyVig.R                  |   84 +--
 inst/doc/DphylogenyVig.Rmd                |   84 +--
 inst/doc/DphylogenyVig.html               |  220 ++++----
 inst/doc/EhumanVig.R                      |   69 +-
 inst/doc/EhumanVig.Rmd                    |   72 +-
 inst/doc/EhumanVig.html                   |  161 +++---
 inst/doc/index.R                          |  122 ++--
 inst/doc/index.Rmd                        |  130 ++---
 inst/doc/index.html                       |  183 +++----
 man/chrbasicdataHolo.Rd                   |    5 
 man/figures/README-example-1.svg          |  351 +++++++------
 man/figures/README-example2-1.png         |binary
 man/figures/README-unnamed-chunk-14-1.png |binary
 man/figures/README-unnamed-chunk-15-1.png |binary
 man/figures/crandownload.svg              |    4 
 man/figures/cranversion.svg               |    4 
 man/figures/gitbadge.svg                  |    2 
 man/markdataholo.Rd                       |    5 
 man/plotIdiograms.Rd                      |   81 +--
 vignettes/AplotIdiogramsVig.Rmd           |  246 +++++----
 vignettes/BplotIdiogramsHoloVig.Rmd       |  154 ++----
 vignettes/CgroupsVig.Rmd                  |   71 --
 vignettes/DphylogenyVig.Rmd               |   84 +--
 vignettes/DphylogenyVig_files             |only
 vignettes/EhumanVig.Rmd                   |   72 +-
 vignettes/index.Rmd                       |  130 ++---
 45 files changed, 2818 insertions(+), 2342 deletions(-)

More information about idiogramFISH at CRAN
Permanent link

Package rpact updated to version 2.0.6 with previous version 2.0.5 dated 2019-11-08

Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut], Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>

Diff between rpact versions 2.0.5 dated 2019-11-08 and 2.0.6 dated 2019-12-12

 rpact-2.0.5/rpact/R/f_analysis.R                                             |only
 rpact-2.0.5/rpact/R/f_analysis_means.R                                       |only
 rpact-2.0.5/rpact/R/f_analysis_means_multiarmed.R                            |only
 rpact-2.0.5/rpact/R/f_analysis_rates.R                                       |only
 rpact-2.0.5/rpact/R/f_analysis_survival.R                                    |only
 rpact-2.0.5/rpact/inst/tests/testthat/test-f_analysis_means.R                |only
 rpact-2.0.5/rpact/inst/tests/testthat/test-f_analysis_rates.R                |only
 rpact-2.0.5/rpact/inst/tests/testthat/test-f_analysis_survival.R             |only
 rpact-2.0.5/rpact/man/sub-TrialDesignSet-ANY-ANY-ANY-method.Rd               |only
 rpact-2.0.5/rpact/tests/testthat/test-f_analysis_means.R                     |only
 rpact-2.0.5/rpact/tests/testthat/test-f_analysis_rates.R                     |only
 rpact-2.0.5/rpact/tests/testthat/test-f_analysis_survival.R                  |only
 rpact-2.0.6/rpact/DESCRIPTION                                                |   16 
 rpact-2.0.6/rpact/MD5                                                        |  302 +--
 rpact-2.0.6/rpact/NAMESPACE                                                  |    2 
 rpact-2.0.6/rpact/NEWS.md                                                    |   11 
 rpact-2.0.6/rpact/R/class_analysis_dataset.R                                 |  442 +++--
 rpact-2.0.6/rpact/R/class_analysis_results.R                                 |   79 
 rpact-2.0.6/rpact/R/class_analysis_stage_results.R                           |  218 ++
 rpact-2.0.6/rpact/R/class_core_parameter_set.R                               |   84 
 rpact-2.0.6/rpact/R/class_design.R                                           |   38 
 rpact-2.0.6/rpact/R/class_design_plan.R                                      |   27 
 rpact-2.0.6/rpact/R/class_design_set.R                                       |    2 
 rpact-2.0.6/rpact/R/class_simulation_results.R                               |   10 
 rpact-2.0.6/rpact/R/class_summary.R                                          |   40 
 rpact-2.0.6/rpact/R/class_time.R                                             |   14 
 rpact-2.0.6/rpact/R/f_analysis_base.R                                        |only
 rpact-2.0.6/rpact/R/f_analysis_base_means.R                                  |only
 rpact-2.0.6/rpact/R/f_analysis_base_rates.R                                  |only
 rpact-2.0.6/rpact/R/f_analysis_base_survival.R                               |only
 rpact-2.0.6/rpact/R/f_core_assertions.R                                      |   74 
 rpact-2.0.6/rpact/R/f_core_constants.R                                       |   28 
 rpact-2.0.6/rpact/R/f_core_utilities.R                                       |   63 
 rpact-2.0.6/rpact/R/f_design_group_sequential.R                              |  116 -
 rpact-2.0.6/rpact/R/f_design_sample_size_calculator.R                        |   83 
 rpact-2.0.6/rpact/inst/tests/testthat/helper-f_analysis_rates.R              |    1 
 rpact-2.0.6/rpact/inst/tests/testthat/helper-f_analysis_survival.R           |    2 
 rpact-2.0.6/rpact/inst/tests/testthat/test-class_analysis_dataset.R          |  265 +++
 rpact-2.0.6/rpact/inst/tests/testthat/test-class_summary.R                   |  225 +-
 rpact-2.0.6/rpact/inst/tests/testthat/test-f_analysis_base_means.R           |only
 rpact-2.0.6/rpact/inst/tests/testthat/test-f_analysis_base_rates.R           |only
 rpact-2.0.6/rpact/inst/tests/testthat/test-f_analysis_base_survival.R        |only
 rpact-2.0.6/rpact/inst/tests/testthat/test-f_core_assertions.R               |   35 
 rpact-2.0.6/rpact/inst/tests/testthat/test-f_core_output_formats.R           |    2 
 rpact-2.0.6/rpact/inst/tests/testthat/test-f_design_power_calculator.R       |  100 -
 rpact-2.0.6/rpact/inst/tests/testthat/test-f_design_sample_size_calculator.R |  230 ++
 rpact-2.0.6/rpact/inst/tests/testthat/test_generic_functions.R               |only
 rpact-2.0.6/rpact/man/AccrualTime.Rd                                         |   26 
 rpact-2.0.6/rpact/man/AnalysisResults.Rd                                     |   38 
 rpact-2.0.6/rpact/man/AnalysisResultsFisher.Rd                               |   28 
 rpact-2.0.6/rpact/man/AnalysisResultsGroupSequential.Rd                      |   30 
 rpact-2.0.6/rpact/man/AnalysisResultsInverseNormal.Rd                        |   30 
 rpact-2.0.6/rpact/man/AnalysisResults_as.data.frame.Rd                       |   36 
 rpact-2.0.6/rpact/man/AnalysisResults_names.Rd                               |   35 
 rpact-2.0.6/rpact/man/Dataset.Rd                                             |   58 
 rpact-2.0.6/rpact/man/DatasetMeans.Rd                                        |   58 
 rpact-2.0.6/rpact/man/DatasetRates.Rd                                        |   54 
 rpact-2.0.6/rpact/man/DatasetSurvival.Rd                                     |   58 
 rpact-2.0.6/rpact/man/EventProbabilities.Rd                                  |   26 
 rpact-2.0.6/rpact/man/FieldSet.Rd                                            |   26 
 rpact-2.0.6/rpact/man/FieldSet_names.Rd                                      |   30 
 rpact-2.0.6/rpact/man/FieldSet_print.Rd                                      |   30 
 rpact-2.0.6/rpact/man/FrameSet_as.matrix.Rd                                  |   30 
 rpact-2.0.6/rpact/man/NumberOfSubjects.Rd                                    |   26 
 rpact-2.0.6/rpact/man/ParameterSet.Rd                                        |   26 
 rpact-2.0.6/rpact/man/ParameterSet_as.data.frame.Rd                          |   41 
 rpact-2.0.6/rpact/man/ParameterSet_print.Rd                                  |   44 
 rpact-2.0.6/rpact/man/ParameterSet_summary.Rd                                |   61 
 rpact-2.0.6/rpact/man/PiecewiseSurvivalTime.Rd                               |   26 
 rpact-2.0.6/rpact/man/PlotSettings.Rd                                        |  108 -
 rpact-2.0.6/rpact/man/PowerAndAverageSampleNumberResult.Rd                   |   28 
 rpact-2.0.6/rpact/man/PowerAndAverageSampleNumberResult_as.data.frame.Rd     |   41 
 rpact-2.0.6/rpact/man/SimulationResults.Rd                                   |   36 
 rpact-2.0.6/rpact/man/SimulationResultsMeans.Rd                              |   26 
 rpact-2.0.6/rpact/man/SimulationResultsRates.Rd                              |   26 
 rpact-2.0.6/rpact/man/SimulationResultsSurvival.Rd                           |   26 
 rpact-2.0.6/rpact/man/StageResults.Rd                                        |   70 
 rpact-2.0.6/rpact/man/StageResultsMeans.Rd                                   |   70 
 rpact-2.0.6/rpact/man/StageResultsRates.Rd                                   |   70 
 rpact-2.0.6/rpact/man/StageResultsSurvival.Rd                                |   70 
 rpact-2.0.6/rpact/man/StageResults_as.data.frame.Rd                          |   42 
 rpact-2.0.6/rpact/man/StageResults_names.Rd                                  |   30 
 rpact-2.0.6/rpact/man/TrialDesign.Rd                                         |   36 
 rpact-2.0.6/rpact/man/TrialDesignCharacteristics.Rd                          |   38 
 rpact-2.0.6/rpact/man/TrialDesignCharacteristics_as.data.frame.Rd            |   55 
 rpact-2.0.6/rpact/man/TrialDesignConditionalDunnett.Rd                       |   26 
 rpact-2.0.6/rpact/man/TrialDesignFisher.Rd                                   |   34 
 rpact-2.0.6/rpact/man/TrialDesignGroupSequential.Rd                          |   36 
 rpact-2.0.6/rpact/man/TrialDesignInverseNormal.Rd                            |   36 
 rpact-2.0.6/rpact/man/TrialDesignPlan.Rd                                     |   36 
 rpact-2.0.6/rpact/man/TrialDesignPlanMeans.Rd                                |   28 
 rpact-2.0.6/rpact/man/TrialDesignPlanRates.Rd                                |   28 
 rpact-2.0.6/rpact/man/TrialDesignPlanSurvival.Rd                             |   28 
 rpact-2.0.6/rpact/man/TrialDesignPlanSurvival_summary.Rd                     |   33 
 rpact-2.0.6/rpact/man/TrialDesignPlan_as.data.frame.Rd                       |   41 
 rpact-2.0.6/rpact/man/TrialDesignSet.Rd                                      |   62 
 rpact-2.0.6/rpact/man/TrialDesignSet_as.data.frame.Rd                        |   45 
 rpact-2.0.6/rpact/man/TrialDesignSet_length.Rd                               |   30 
 rpact-2.0.6/rpact/man/TrialDesignSet_names.Rd                                |   30 
 rpact-2.0.6/rpact/man/TrialDesign_as.data.frame.Rd                           |   55 
 rpact-2.0.6/rpact/man/getAccrualTime.Rd                                      |  558 +++---
 rpact-2.0.6/rpact/man/getAnalysisResults.Rd                                  |  227 +-
 rpact-2.0.6/rpact/man/getAvailablePlotTypes.Rd                               |   65 
 rpact-2.0.6/rpact/man/getConditionalPower.Rd                                 |   94 -
 rpact-2.0.6/rpact/man/getConditionalRejectionProbabilities.Rd                |   78 
 rpact-2.0.6/rpact/man/getData.Rd                                             |   38 
 rpact-2.0.6/rpact/man/getDataset.Rd                                          |  292 +--
 rpact-2.0.6/rpact/man/getDesignCharacteristics.Rd                            |   58 
 rpact-2.0.6/rpact/man/getDesignFisher.Rd                                     |  182 +-
 rpact-2.0.6/rpact/man/getDesignGroupSequential.Rd                            |  213 +-
 rpact-2.0.6/rpact/man/getDesignInverseNormal.Rd                              |  218 +-
 rpact-2.0.6/rpact/man/getDesignSet.Rd                                        |   82 
 rpact-2.0.6/rpact/man/getEventProbabilities.Rd                               |  154 -
 rpact-2.0.6/rpact/man/getFinalConfidenceInterval.Rd                          |  170 -
 rpact-2.0.6/rpact/man/getFinalPValue.Rd                                      |   48 
 rpact-2.0.6/rpact/man/getLogLevel.Rd                                         |   42 
 rpact-2.0.6/rpact/man/getNumberOfSubjects.Rd                                 |   78 
 rpact-2.0.6/rpact/man/getPiecewiseSurvivalTime.Rd                            |  235 +-
 rpact-2.0.6/rpact/man/getPowerAndAverageSampleNumber.Rd                      |   67 
 rpact-2.0.6/rpact/man/getPowerMeans.Rd                                       |  155 -
 rpact-2.0.6/rpact/man/getPowerRates.Rd                                       |  164 +
 rpact-2.0.6/rpact/man/getPowerSurvival.Rd                                    |  477 ++---
 rpact-2.0.6/rpact/man/getRawData.Rd                                          |   44 
 rpact-2.0.6/rpact/man/getRepeatedConfidenceIntervals.Rd                      |   54 
 rpact-2.0.6/rpact/man/getRepeatedPValues.Rd                                  |   54 
 rpact-2.0.6/rpact/man/getSampleSizeMeans.Rd                                  |  154 -
 rpact-2.0.6/rpact/man/getSampleSizeRates.Rd                                  |  159 -
 rpact-2.0.6/rpact/man/getSampleSizeSurvival.Rd                               |  525 +++---
 rpact-2.0.6/rpact/man/getSimulationMeans.Rd                                  |  404 ++--
 rpact-2.0.6/rpact/man/getSimulationRates.Rd                                  |  408 ++--
 rpact-2.0.6/rpact/man/getSimulationSurvival.Rd                               |  854 +++++-----
 rpact-2.0.6/rpact/man/getStageResults.Rd                                     |  124 -
 rpact-2.0.6/rpact/man/getTestActions.Rd                                      |   44 
 rpact-2.0.6/rpact/man/plot.AnalysisResults.Rd                                |  205 +-
 rpact-2.0.6/rpact/man/plot.Dataset.Rd                                        |  135 -
 rpact-2.0.6/rpact/man/plot.SimulationResults.Rd                              |  161 +
 rpact-2.0.6/rpact/man/plot.StageResults.Rd                                   |  210 +-
 rpact-2.0.6/rpact/man/plot.TrialDesign.Rd                                    |  195 +-
 rpact-2.0.6/rpact/man/plot.TrialDesignPlan.Rd                                |  172 +-
 rpact-2.0.6/rpact/man/plot.TrialDesignSet.Rd                                 |  184 +-
 rpact-2.0.6/rpact/man/printCitation.Rd                                       |   46 
 rpact-2.0.6/rpact/man/readDataset.Rd                                         |  118 -
 rpact-2.0.6/rpact/man/readDatasets.Rd                                        |  114 -
 rpact-2.0.6/rpact/man/resetLogLevel.Rd                                       |   42 
 rpact-2.0.6/rpact/man/rpact.Rd                                               |  114 -
 rpact-2.0.6/rpact/man/setLogLevel.Rd                                         |   55 
 rpact-2.0.6/rpact/man/sub-TrialDesignSet-method.Rd                           |   31 
 rpact-2.0.6/rpact/man/testPackage.Rd                                         |   87 -
 rpact-2.0.6/rpact/man/utilitiesForPiecewiseExponentialDistribution.Rd        |  204 +-
 rpact-2.0.6/rpact/man/utilitiesForSurvivalTrials.Rd                          |   89 -
 rpact-2.0.6/rpact/man/writeDataset.Rd                                        |  134 -
 rpact-2.0.6/rpact/man/writeDatasets.Rd                                       |  132 -
 rpact-2.0.6/rpact/tests/testthat/helper-f_analysis_rates.R                   |    1 
 rpact-2.0.6/rpact/tests/testthat/helper-f_analysis_survival.R                |    2 
 rpact-2.0.6/rpact/tests/testthat/test-class_analysis_dataset.R               |  265 +++
 rpact-2.0.6/rpact/tests/testthat/test-class_summary.R                        |  225 +-
 rpact-2.0.6/rpact/tests/testthat/test-f_analysis_base_means.R                |only
 rpact-2.0.6/rpact/tests/testthat/test-f_analysis_base_rates.R                |only
 rpact-2.0.6/rpact/tests/testthat/test-f_analysis_base_survival.R             |only
 rpact-2.0.6/rpact/tests/testthat/test-f_core_assertions.R                    |   35 
 rpact-2.0.6/rpact/tests/testthat/test-f_core_output_formats.R                |    2 
 rpact-2.0.6/rpact/tests/testthat/test-f_design_power_calculator.R            |  100 -
 rpact-2.0.6/rpact/tests/testthat/test-f_design_sample_size_calculator.R      |  230 ++
 rpact-2.0.6/rpact/tests/testthat/test_generic_functions.R                    |only
 164 files changed, 8016 insertions(+), 6437 deletions(-)

More information about rpact at CRAN
Permanent link

Package RandomFields updated to version 3.3.7 with previous version 3.3.6 dated 2019-03-06

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields. Main geostatistical parts are based on the books by Christian Lantuejoul <doi:10.1007/978-3-662-04808-5>, Jean-Paul Chiles and Pierre Delfiner <doi:10.1002/9781118136188> and Noel A. Cressie <doi:10.1002/9781119115151>. For the extreme value random fields see Oesting, Schlather, Schillings (2019) <doi.org/10.1002/sta4.228> and Schlather (2002) <doi.org/10.1023/A:1020977924878>.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Brian D. Ripley [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.3.6 dated 2019-03-06 and 3.3.7 dated 2019-12-12

 DESCRIPTION                |    8 ++++----
 MD5                        |   26 +++++++++++++-------------
 R/RMmodels-Methods-plots.R |    5 ++++-
 R/fitgauss.R               |    3 +--
 man/RMpoissonpoly.Rd       |    2 +-
 man/RMtrafo.Rd             |    4 ++--
 src/InternalCov.cc         |    2 +-
 src/Machine.h              |    4 ++--
 src/RF.h                   |    2 +-
 src/cubicsolver.cc         |    2 +-
 src/questions.cc           |    6 +++++-
 src/trend.cc               |    2 +-
 src/variogramAndCo.cc      |    2 +-
 src/variogramAndCo.h       |    2 +-
 14 files changed, 38 insertions(+), 32 deletions(-)

More information about RandomFields at CRAN
Permanent link

Package phylin updated to version 2.0.2 with previous version 2.0.1 dated 2019-11-19

Title: Spatial Interpolation of Genetic Data
Description: The spatial interpolation of genetic distances between samples is based on a modified kriging method that accepts a genetic distance matrix and generates a map of probability of lineage presence. This package also offers tools to generate a map of potential contact zones between groups with user-defined thresholds in the tree to account for old and recent divergence. Additionally, it has functions for IDW interpolation using genetic data and midpoints.
Author: Pedro Tarroso, Guillermo Velo-Anton, Silvia Carvalho
Maintainer: Pedro Tarroso <ptarroso@cibio.up.pt>

Diff between phylin versions 2.0.1 dated 2019-11-19 and 2.0.2 dated 2019-12-12

 DESCRIPTION                      |    6 +++---
 MD5                              |   18 +++++++++---------
 R/gen.variogram.R                |    8 ++++----
 R/krig.R                         |    2 +-
 R/mtest.gv.R                     |    2 +-
 inst/CITATION                    |    8 +++++---
 inst/doc/phylin_tutorial.pdf     |binary
 inst/doc/resistance_tutorial.pdf |binary
 man/mtest.gv.Rd                  |    2 +-
 man/simul.gen.dist.Rd            |    2 +-
 10 files changed, 25 insertions(+), 23 deletions(-)

More information about phylin at CRAN
Permanent link

Package OncoBayes2 updated to version 0.5-8 with previous version 0.5-4 dated 2019-11-19

Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional EXchangeability-NonEXchangeability parameter modelling for flexible borrowing from historical or concurrent data-sources. The safety model can guide dose-escalation decisions for adaptive oncology Phase I dose-escalation trials which involve an arbitrary number of drugs. Please refer to Neuenschwander et al. (2008) <doi:10.1002/sim.3230> and Neuenschwander et al. (2016) <doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph], Sebastian Weber [aut, cre], Andrew Bean [aut], Lukas A. Widmer [aut], Trustees of Columbia University [cph] (R/stanmodels.R, configure, configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>

Diff between OncoBayes2 versions 0.5-4 dated 2019-11-19 and 0.5-8 dated 2019-12-12

 DESCRIPTION                            |   16 
 MD5                                    |   43 -
 NAMESPACE                              |    1 
 R/blrm_exnex.R                         |  174 ++++---
 R/blrm_trial.R                         |   31 +
 R/posterior_predict.R                  |    2 
 R/pp_data.R                            |   11 
 R/summary.R                            |    4 
 R/sysdata.rda                          |binary
 inst/NEWS                              |   23 
 inst/doc/OncoBayes2.pdf                |binary
 inst/doc/introduction.html             |  262 +++++-----
 inst/sbc/calibration.md5               |    6 
 inst/sbc/sbc_report.html               |  244 +++++-----
 inst/sbc/sbc_tools.R                   |    3 
 inst/stan/blrm_exnex.stan              |   78 ++-
 man/blrm_exnex.Rd                      |  173 ++++---
 man/log_inv_logit.Rd                   |only
 src/stanExports_blrm_exnex.h           |  789 +++++++++++++++++----------------
 tests/testthat/helper-sampling.R       |    4 
 tests/testthat/helper-trial_examples.R |   67 +-
 tests/testthat/test-blrm_exnex.R       |   37 +
 tests/testthat/test-blrm_trial.R       |   96 +++-
 23 files changed, 1204 insertions(+), 860 deletions(-)

More information about OncoBayes2 at CRAN
Permanent link

Package virtualspecies updated to version 1.5.1 with previous version 1.5 dated 2019-05-06

Title: Generation of Virtual Species Distributions
Description: Provides a framework for generating virtual species distributions, a procedure increasingly used in ecology to improve species distribution models. This package integrates the existing methodological approaches with the objective of generating virtual species distributions with increased ecological realism.
Author: Boris Leroy [cre, aut], Christine N. Meynard [ctb], Celine Bellard [ctb], Franck Courchamp [ctb], Robin Delsol [ctb], Willson Gaul [ctb]
Maintainer: Boris Leroy <leroy.boris@gmail.com>

Diff between virtualspecies versions 1.5 dated 2019-05-06 and 1.5.1 dated 2019-12-12

 DESCRIPTION                   |   13 
 MD5                           |   58 +--
 NAMESPACE                     |    2 
 NEWS                          |    8 
 R/convertToPA.R               |   10 
 R/generateRandomSp.R          |    9 
 R/generateSpFromFun.R         |    2 
 R/limitDistribution.R         |   12 
 R/plotSuitabilityToProba.R    |    2 
 R/removeCollinearity.R        |    9 
 R/sampleOccurrences.R         |   24 -
 R/utilityFunctions.R          |    4 
 man/betaFun.Rd                |  114 +++----
 man/convertToPA.Rd            |  562 +++++++++++++++++++-------------------
 man/custnorm.Rd               |  104 +++----
 man/formatFunctions.Rd        |  150 +++++-----
 man/generateRandomSp.Rd       |  356 ++++++++++++------------
 man/generateSpFromBCA.Rd      |  330 +++++++++++-----------
 man/generateSpFromFun.Rd      |  290 ++++++++++---------
 man/generateSpFromPCA.Rd      |  319 +++++++++++----------
 man/limitDistribution.Rd      |  281 +++++++++----------
 man/linearFun.Rd              |   70 ++--
 man/logisticFun.Rd            |  118 ++++----
 man/plotResponse.Rd           |  209 +++++++-------
 man/plotSuitabilityToProba.Rd |  136 ++++-----
 man/quadraticFun.Rd           |   76 ++---
 man/removeCollinearity.Rd     |  191 ++++++------
 man/sampleOccurrences.Rd      |  619 +++++++++++++++++++++---------------------
 man/synchroniseNA.Rd          |   82 ++---
 man/virtualspecies-package.Rd |  140 ++++-----
 30 files changed, 2190 insertions(+), 2110 deletions(-)

More information about virtualspecies at CRAN
Permanent link

New package SCtools with initial version 0.3.0
Package: SCtools
Title: Extensions for Synthetic Controls Analysis
Version: 0.3.0
Authors@R: c( person(given = 'Bruno', family = 'Castanho Silva', role = c('aut', 'cre'), email = 'bcsilva@wiso.uni-koeln.de', comment = c(ORCID = '0000-0001-9363-4704')), person(given = 'Michael', family = 'DeWitt', role = c('aut'), email = 'me.dewitt.jr@gmail.com', comment = c(ORCID = '0000-0001-8940-1967')))
Description: Extensions to the synthetic controls analyses performed by the package 'Synth' as detailed in Abadie, Diamond, and Hainmueller (2011) <doi:10.18637/jss.v042.i13>. Includes generating and plotting placebos, post/pre-MSPE (mean squared prediction error) significance tests and plots, and calculating average treatment effects for multiple treated units. This package represents an implementation of those methods suggested in Abadie, Diamond,and Hainmueller (2010) <doi:10.1198/jasa.2009.ap08746> for use in synthetic control analysis.
BugReports: https://github.com/bcastanho/SCtools/issues
Maintainer: Bruno Castanho Silva <bcsilva@wiso.uni-koeln.de>
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5), future (>= 1.6.2)
Imports: ggplot2, Synth, stringr, stats, cvTools, furrr, dplyr, purrr
Suggests: testthat, covr, knitr, tidyr, rmarkdown
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-12-03 16:00:23 UTC; 54011
Author: Bruno Castanho Silva [aut, cre] (<https://orcid.org/0000-0001-9363-4704>), Michael DeWitt [aut] (<https://orcid.org/0000-0001-8940-1967>)
Repository: CRAN
Date/Publication: 2019-12-12 13:40:02 UTC

More information about SCtools at CRAN
Permanent link

Package APIS updated to version 1.0.0 with previous version 0.1.0 dated 2019-08-19

Title: Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents
Description: Parentage assignment package. Parentage assignment is performed based on observed average Mendelian transmission probability distributions. The main function of this package is the function APIS(), which is the parentage assignment function.
Author: Ronan Griot, François Allal, Romain Morvezen, Sophie Brard-Fudulea, Pierrick Haffray, Florence Phocas and Marc Vandeputte
Maintainer: Ronan Griot <ronan.griot@gmail.com>

Diff between APIS versions 0.1.0 dated 2019-08-19 and 1.0.0 dated 2019-12-12

 DESCRIPTION                 |    8 ++++----
 MD5                         |    8 ++++----
 NAMESPACE                   |    1 +
 R/APIS_functions.R          |    7 ++++---
 inst/doc/APIS_vignette.html |    8 ++++----
 5 files changed, 17 insertions(+), 15 deletions(-)

More information about APIS at CRAN
Permanent link

Package Rfast updated to version 1.9.8 with previous version 1.9.7 dated 2019-11-24

Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>

Diff between Rfast versions 1.9.7 dated 2019-11-24 and 1.9.8 dated 2019-12-12

 Rfast-1.9.7/Rfast/R/source.R                     |only
 Rfast-1.9.8/Rfast/DESCRIPTION                    |   10 +-
 Rfast-1.9.8/Rfast/MD5                            |   33 +++---
 Rfast-1.9.8/Rfast/NEWS.md                        |    2 
 Rfast-1.9.8/Rfast/R/system_and_package.R         |   51 ++++++++++
 Rfast-1.9.8/Rfast/R/variable_selection.R         |   16 ++-
 Rfast-1.9.8/Rfast/inst/include/Rfast/helpers.hpp |    1 
 Rfast-1.9.8/Rfast/inst/include/Rfast/matrix.hpp  |    4 
 Rfast-1.9.8/Rfast/inst/include/Rfast/vector.hpp  |    2 
 Rfast-1.9.8/Rfast/man/Rfast-package.Rd           |  114 +++++++++++++----------
 Rfast-1.9.8/Rfast/src/dir_knn.cpp                |   35 ++++---
 Rfast-1.9.8/Rfast/src/dists.cpp                  |    2 
 Rfast-1.9.8/Rfast/src/dists_vec.cpp              |   21 ++--
 Rfast-1.9.8/Rfast/src/init.c                     |    4 
 Rfast-1.9.8/Rfast/src/my_k_sorted_array.cpp      |   42 +++++---
 Rfast-1.9.8/Rfast/src/reg_lib.cpp                |   35 ++++---
 Rfast-1.9.8/Rfast/src/system_files.cpp           |    2 
 Rfast-1.9.8/Rfast/src/topological_sort.cpp       |   14 +-
 18 files changed, 249 insertions(+), 139 deletions(-)

More information about Rfast at CRAN
Permanent link

Package paleotree updated to version 3.3.25 with previous version 3.3.0 dated 2019-06-04

Title: Paleontological and Phylogenetic Analyses of Evolution
Description: Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.
Author: David W. Bapst, Peter J. Wagner
Maintainer: David W. Bapst <dwbapst@gmail.com>

Diff between paleotree versions 3.3.0 dated 2019-06-04 and 3.3.25 dated 2019-12-12

 CHANGELOG                                                     |  639 -
 DESCRIPTION                                                   |   23 
 MD5                                                           |  376 
 NAMESPACE                                                     |  328 
 R/DiversityCurves.R                                           | 1042 +-
 R/RaiaCopesRule.R                                             |  543 -
 R/SamplingConv.R                                              |  414 -
 R/SongZhangDicrano.R                                          |  238 
 R/binTimeData.R                                               |  406 -
 R/branchClasses.R                                             |  211 
 R/cal3TimePaleoPhy.R                                          | 3533 ++++-----
 R/cladogeneticTraitCont.R                                     |  226 
 R/communityEcology.R                                          |  562 -
 R/compareTimescaling.R                                        |  498 -
 R/constrainParPaleo.R                                         |  813 +-
 R/createMrBayesConstraints.R                                  |  255 
 R/createMrBayesTipCalibrations.R                              |  839 +-
 R/createMrBayesTipDatingNexus.R                               | 2190 ++---
 R/dateNodes.R                                                 |  179 
 R/dateTaxonTreePBDB.R                                         |  787 +-
 R/degradeTree.R                                               |  330 
 R/depthRainbow.R                                              |   68 
 R/divCurveFossilRecordSim.R                                   |  198 
 R/durationFreq.R                                              |  824 +-
 R/equation2function.R                                         |  134 
 R/exhaustationFunctions.R                                     | 3916 +++++-----
 R/expandTaxonTree.R                                           |  270 
 R/fixRootTime.R                                               |  464 -
 R/footeValues.R                                               |  492 -
 R/fourDateFunctions.R                                         |  226 
 R/freqRat.R                                                   |  618 -
 R/getDataPBDB.R                                               |  628 -
 R/getFixedAgesFromNexus.R                                     |  176 
 R/graptDisparity.R                                            |  430 -
 R/graptPBDB.R                                                 |  350 
 R/hidden.gettingPhyloPicFunctions.R                           |  405 -
 R/hidden.makePBDBtaxonTree.Functions.R                        | 1202 +--
 R/hidden.modelExpressionModification.R                        |  254 
 R/hidden.plotTaxonStratDurations.R                            |  160 
 R/hidden.plottingPhyloPicFunctions.R                          |  576 -
 R/horizonSampRate.R                                           |  256 
 R/inverseSurv.R                                               |  985 +-
 R/isTimeListSequential.R                                      |   54 
 R/kanto.R                                                     |  541 -
 R/macroperforateForam.R                                       |  756 -
 R/makePBDBtaxonTree.R                                         |  844 +-
 R/minBranchLength.R                                           |  357 
 R/minCharChange.R                                             | 1644 ++--
 R/modelMethods.R                                              |  683 -
 R/modifyTerminalBranches.R                                    |  965 +-
 R/multiDiv.R                                                  | 1037 +-
 R/nearestNeighborDist.R                                       |  205 
 R/nodeDates2branchLengths.R                                   |  346 
 R/obtainDatedPosteriorTreesMrB.R                              | 1059 +-
 R/occData2timeList.R                                          |  494 -
 R/optimPaleo.R                                                |   80 
 R/paleotree-package.R                                         |  225 
 R/parentChild2TaxonTree.R                                     |  708 -
 R/parseNexusFile.R                                            |  236 
 R/perCapitaRates.R                                            |  532 -
 R/perfectParsCharTree.R                                       |  156 
 R/plotOccData.R                                               |  269 
 R/plotPhyloPicTree.R                                          | 1444 +--
 R/plotTraitgram.R                                             |  292 
 R/pqr2Ps.R                                                    |  250 
 R/probAnc.R                                                   |  403 -
 R/resolveTreeChar.R                                           |  792 +-
 R/retiolitinae.R                                              |  174 
 R/reverseList.R                                               |   90 
 R/rootSplit.R                                                 |   65 
 R/sampleRanges.R                                              |  986 +-
 R/seqTimeList.R                                               |  329 
 R/setRootAge.R                                                |  240 
 R/simFossilRecord.R                                           | 3294 ++++----
 R/simFossilRecordInternal.R                                   | 1227 +--
 R/simFossilRecordMethods.R                                    |  830 +-
 R/taxa2cladogram.R                                            |  292 
 R/taxa2phylo.R                                                |  750 +
 R/taxonSortPBDBocc.R                                          |  824 +-
 R/taxonTable2TaxonTree.R                                      |  331 
 R/termTaxa.R                                                  |  854 +-
 R/testEdgeMat.R                                               |  584 -
 R/timeLadderTree.R                                            |  274 
 R/timePaleoPhy.R                                              | 2766 +++----
 R/timeSliceTree.R                                             |  318 
 R/tipDatingCompatabilitySummaryMrB.R                          |  269 
 R/treeContradiction.R                                         |  393 -
 R/twoWayEcologyCluster.R                                      |  546 -
 R/unitLengthTree.R                                            |   95 
 R/writeSimpleSumtNexus.R                                      |  120 
 README.md                                                     |  110 
 inst/CITATION                                                 |   22 
 inst/WORDLIST                                                 |only
 man/DiversityCurves.Rd                                        |  525 -
 man/RaiaCopesRule.Rd                                          |  537 -
 man/SamplingConv.Rd                                           |  240 
 man/SongZhangDicrano.Rd                                       |  238 
 man/binTimeData.Rd                                            |  277 
 man/branchClasses.Rd                                          |  139 
 man/cal3TimePaleoPhy.Rd                                       | 1404 +--
 man/cladogeneticTraitCont.Rd                                  |  214 
 man/communityEcology.Rd                                       |  362 
 man/compareTimescaling.Rd                                     |  240 
 man/constrainParPaleo.Rd                                      |  528 -
 man/createMrBayesConstraints.Rd                               |  154 
 man/createMrBayesTipCalibrations.Rd                           |  317 
 man/createMrBayesTipDatingNexus.Rd                            |  794 +-
 man/dateNodes.Rd                                              |  151 
 man/dateTaxonTreePBDB.Rd                                      |  337 
 man/degradeTree.Rd                                            |  213 
 man/depthRainbow.Rd                                           |   64 
 man/divCurveFossilRecordSim.Rd                                |  127 
 man/durationFreq.Rd                                           |  410 -
 man/equation2function.Rd                                      |  103 
 man/exhaustionFunctions.Rd                                    |  395 -
 man/expandTaxonTree.Rd                                        |  192 
 man/fixRootTime.Rd                                            |  200 
 man/footeValues.Rd                                            |  223 
 man/freqRat.Rd                                                |  560 -
 man/getDataPBDB.Rd                                            |  312 
 man/graptDisparity.Rd                                         |  424 -
 man/graptPBDB.Rd                                              |  352 
 man/horizonSampRate.Rd                                        |  171 
 man/inverseSurv.Rd                                            |  576 -
 man/kanto.Rd                                                  |  526 -
 man/macroperforateForam.Rd                                    |  744 -
 man/makePBDBtaxonTree.Rd                                      |  524 -
 man/minBranchLength.Rd                                        |  227 
 man/minCharChange.Rd                                          |  907 +-
 man/modelMethods.Rd                                           |  369 
 man/modifyTerminalBranches.Rd                                 |  607 -
 man/multiDiv.Rd                                               |  497 -
 man/nearestNeighborDist.Rd                                    |  168 
 man/nodeDates2branchLengths.Rd                                |  250 
 man/obtainDatedPosteriorTreesMrB.Rd                           |  480 -
 man/occData2timeList.Rd                                       |  320 
 man/optimPaleo.Rd                                             |   78 
 man/paleotree-package.Rd                                      |  201 
 man/parentChild2taxonTree.Rd                                  |  277 
 man/perCapitaRates.Rd                                         |  291 
 man/perfectParsCharTree.Rd                                    |  104 
 man/plotOccData.Rd                                            |  170 
 man/plotPhyloPicTree.Rd                                       |  737 -
 man/plotTraitgram.Rd                                          |  166 
 man/pqr2Ps.Rd                                                 |  230 
 man/probAnc.Rd                                                |  218 
 man/resolveTreeChar.Rd                                        |  459 -
 man/retiolitinae.Rd                                           |  166 
 man/reverseList.Rd                                            |   89 
 man/rootSplit.Rd                                              |   67 
 man/sampleRanges.Rd                                           |  597 -
 man/seqTimeList.Rd                                            |  206 
 man/setRootAge.Rd                                             |  140 
 man/simFossilRecord.Rd                                        | 2402 +++---
 man/simFossilRecordMethods.Rd                                 |  369 
 man/taxa2cladogram.Rd                                         |  223 
 man/taxa2phylo.Rd                                             |  230 
 man/taxonSortPBDBocc.Rd                                       |  409 -
 man/taxonTable2taxonTree.Rd                                   |  145 
 man/termTaxa.Rd                                               |  579 -
 man/testEdgeMat.Rd                                            |  136 
 man/timeLadderTree.Rd                                         |  144 
 man/timeList2fourDate.Rd                                      |  143 
 man/timePaleoPhy.Rd                                           | 1516 +--
 man/timeSliceTree.Rd                                          |  218 
 man/tipDatingCompatabilitySummaryMrB.Rd                       |  243 
 man/treeContradiction.Rd                                      |  281 
 man/twoWayEcologyCluster.Rd                                   |  298 
 man/unitLengthTree.Rd                                         |  104 
 tests/spelling.R                                              |only
 tests/testthat.R                                              |    8 
 tests/testthat/data/retio_dating.nex                          |  316 
 tests/testthat/data/retio_dating.run1.p                       |  206 
 tests/testthat/data/retio_dating.run1.t                       |  258 
 tests/testthat/data/retio_dating.run2.p                       |  206 
 tests/testthat/data/retio_dating.run2.t                       |  258 
 tests/testthat/references                                     |only
 tests/testthat/test_Contradiction_05-25-17.R                  |  111 
 tests/testthat/test_cal3_dateTreatment_Armin.R                |  589 -
 tests/testthat/test_cladogeneticTraitCont.R                   |   67 
 tests/testthat/test_inverseSurv.R                             |   58 
 tests/testthat/test_minBranchLength_check_10-09-15.R          |   69 
 tests/testthat/test_obtainDatedPosteriorTreesMrB.R            |  125 
 tests/testthat/test_simFossilRecord_countFinalTaxa_07-15-19.R |only
 tests/testthat/test_simFossilRecord_negative_dates_07-06-19.R |only
 tests/testthat/test_simFossilRecord_rejection.R               |only
 tests/testthat/test_simFossilRecord_returnAllRuns_output.R    |only
 tests/testthat/test_simFossilRecord_return_extant_taxa.R      |only
 tests/testthat/test_simFossilRecord_return_extinct_taxa.R     |only
 tests/testthat/test_simFossilRecord_simple.R                  |only
 tests/testthat/test_timeSlice_dropExtinct_shifts_root_age.R   |only
 tests/testthat/test_timeSlice_tip_labels_differ.R             |only
 192 files changed, 45686 insertions(+), 41838 deletions(-)

More information about paleotree at CRAN
Permanent link

Package mpr updated to version 1.0.5 with previous version 1.0.4 dated 2016-10-12

Title: Multi-Parameter Regression (MPR)
Description: Package for fitting Multi-Parameter Regression (MPR) models to right-censored survival data. These are flexible parametric regression models which extend standard models, for example, proportional hazards.
Author: Kevin Burke
Maintainer: Kevin Burke <kevin.burke@ul.ie>

Diff between mpr versions 1.0.4 dated 2016-10-12 and 1.0.5 dated 2019-12-12

 DESCRIPTION           |    8 ++++----
 MD5                   |    4 ++--
 R/print.summary.mpr.R |    8 +++++---
 3 files changed, 11 insertions(+), 9 deletions(-)

More information about mpr at CRAN
Permanent link

Package FunnelPlotR updated to version 0.2.2 with previous version 0.2.1 dated 2019-10-09

Title: Funnel Plots for Indirectly-Standardised Ratios
Description: An implementation of the Spiegelhalter (2005) <doi:10.1002/sim.1970> Funnel plots for reporting standardised ratios, with overdispersion adjustment.
Author: Chris Mainey [aut, cre] (<https://orcid.org/0000-0002-3018-6171>), Matthew Bass [ctb]
Maintainer: Chris Mainey <chris.mainey@uhb.nhs.uk>

Diff between FunnelPlotR versions 0.2.1 dated 2019-10-09 and 0.2.2 dated 2019-12-12

 DESCRIPTION                               |    8 -
 MD5                                       |   39 +++--
 NAMESPACE                                 |    2 
 NEWS.md                                   |    6 
 R/build_limits_lookup.R                   |    6 
 R/draw_plot.R                             |    2 
 R/funnel_plot.R                           |    2 
 README.md                                 |    2 
 inst/CITATION                             |only
 inst/doc/funnel_plots.R                   |   10 -
 inst/doc/funnel_plots.Rmd                 |    2 
 inst/doc/funnel_plots.html                |    9 -
 man/OD_adjust_func.Rd                     |   59 ++++----
 man/aggregate_func.Rd                     |   36 ++---
 man/build_limits_lookup.Rd                |   79 ++++++-----
 man/draw_plot.Rd                          |   95 +++++++-------
 man/figures/README-funnel1-1.png          |binary
 man/figures/README-funnel2-1.png          |binary
 man/funnel_plot.Rd                        |  199 +++++++++++++++---------------
 tests/testthat/test-build_limits_lookup.R |    4 
 vignettes/funnel_plots.Rmd                |    2 
 21 files changed, 301 insertions(+), 261 deletions(-)

More information about FunnelPlotR at CRAN
Permanent link

Package clickR updated to version 0.4.40 with previous version 0.4.32 dated 2019-04-19

Title: Fix Data and Create Report Tables from Different Objects
Description: Tools for assessing data quality, performing exploratory analysis, fixing data errors in numerical, factor and date variables and creating report tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>

Diff between clickR versions 0.4.32 dated 2019-04-19 and 0.4.40 dated 2019-12-12

 DESCRIPTION             |    6 +++---
 MD5                     |   14 ++++++++------
 NAMESPACE               |    2 ++
 R/check_quality.R       |   35 ++++++++++++++++++++++++++++++++++-
 R/descriptive.R         |    9 +++++++--
 R/report_model.R        |    2 +-
 man/search_scripts.Rd   |    2 +-
 man/workspace.Rd        |only
 man/workspace_sapply.Rd |only
 9 files changed, 56 insertions(+), 14 deletions(-)

More information about clickR at CRAN
Permanent link

Package AID updated to version 2.5 with previous version 2.4 dated 2019-05-16

Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre], Ozgur Asar [aut], Ozlem Ilk [aut]
Maintainer: Osman Dag <osman.dag@outlook.com>

Diff between AID versions 2.4 dated 2019-05-16 and 2.5 dated 2019-12-12

 DESCRIPTION   |    8 ++++----
 MD5           |    6 +++---
 R/boxcoxlm.R  |    2 +-
 inst/citation |    2 +-
 4 files changed, 9 insertions(+), 9 deletions(-)

More information about AID at CRAN
Permanent link

Package seminr updated to version 1.0.1 with previous version 1.0.0 dated 2019-09-27

Title: Domain-Specific Language for Building PLS Structural Equation Models
Description: A powerful, easy to write and easy to modify syntax for specifying and estimating Partial Least Squares (PLS) path models allowing for the latest estimation methods for Consistent PLS as per Dijkstra & Henseler (2015, MISQ 39(2): 297-316), adjusted interactions as per Henseler & Chin (2010) <doi:10.1080/10705510903439003> and bootstrapping utilizing parallel processing as per Hair et al. (2017, ISBN:978-1483377445).
Author: Soumya Ray [aut, ths], Nicholas Patrick Danks [aut, cre], Juan Manuel Velasquez Estrada [aut]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>

Diff between seminr versions 1.0.0 dated 2019-09-27 and 1.0.1 dated 2019-12-12

 DESCRIPTION          |   14 +-
 MD5                  |    8 -
 R/library.R          |    4 
 build/vignette.rds   |binary
 inst/doc/SEMinR.html |  344 +++++++++++++++++++++++++--------------------------
 5 files changed, 185 insertions(+), 185 deletions(-)

More information about seminr at CRAN
Permanent link

Package random.polychor.pa updated to version 1.1.4-3 with previous version 1.1.4-2 dated 2016-07-26

Title: A Parallel Analysis with Polychoric Correlation Matrices
Description: The Function performs a parallel analysis using simulated polychoric correlation matrices. The nth-percentile of the eigenvalues distribution obtained from both the randomly generated and the real data polychoric correlation matrices is returned. A plot comparing the two types of eigenvalues (real and simulated) will help determine the number of real eigenvalues that outperform random data. The function is based on the idea that if real data are non-normal and the polychoric correlation matrix is needed to perform a Factor Analysis, then the Parallel Analysis method used to choose a non-random number of factors should also be based on randomly generated polychoric correlation matrices and not on Pearson correlation matrices. Random data sets are simulated assuming or a uniform or a multinomial distribution or via the bootstrap method of resampling (i.e., random permutations of cases). Also Multigroup Parallel analysis is made available for random (uniform and multinomial distribution and with or without difficulty factor) and bootstrap methods. An option to choose between default or full output is also available as well as a parameter to print Fit Statistics (Chi-squared, TLI, RMSEA, RMR and BIC) for the factor solutions indicated by the Parallel Analysis.
Author: Fabio Presaghi [aut, cre], Marta Desimoni [ctb]
Maintainer: Fabio Presaghi <fabio.presaghi@uniroma1.it>

Diff between random.polychor.pa versions 1.1.4-2 dated 2016-07-26 and 1.1.4-3 dated 2019-12-12

 DESCRIPTION                       |   10 +++++-----
 MD5                               |   10 +++++-----
 R/random.polychor.pa.r            |   21 ++++++++++++++-------
 man/NEWS.Rd                       |    6 ++++++
 man/random.polychor.pa-package.Rd |    8 +++++---
 man/random.polychor.pa.Rd         |   21 +++++++++++++++------
 6 files changed, 50 insertions(+), 26 deletions(-)

More information about random.polychor.pa at CRAN
Permanent link

Package ProjectManagement updated to version 1.2.3 with previous version 1.2.1 dated 2019-04-08

Title: Management of Deterministic and Stochastic Projects
Description: Management problems of deterministic and stochastic projects. It obtains the duration of a project and the appropriate slack for each activity in a deterministic context. In addition it obtains a schedule of activities' time (Castro, Gómez & Tejada (2007) <doi:10.1016/j.orl.2007.01.003>). It also allows the management of resources. When the project is done, and the actual duration for each activity is known, then it can know how long the project is delayed and make a fair delivery of the delay between each activity (Bergantiños, Valencia-Toledo & Vidal-Puga (2018) <doi:10.1016/j.dam.2017.08.012>). In a stochastic context it can estimate the average duration of the project and plot the density of this duration, as well as, the density of the early and last times of the chosen activities. As in the deterministic case, it can make a distribution of the delay generated by observing the project already carried out.
Author: Juan Carlos Gonçalves Dosantos [aut, cre], Ignacio García Jurado [aut], Julián Costa Bouzas [aut]
Maintainer: Juan Carlos Gonçalves Dosantos <juan.carlos.goncalves@udc.es>

Diff between ProjectManagement versions 1.2.1 dated 2019-04-08 and 1.2.3 dated 2019-12-12

 DESCRIPTION                   |    8 -
 MD5                           |    8 -
 R/function_mce.R              |  254 +++++++++++++++++++++++-------------------
 R/function_pert_estocastico.R |    4 
 man/mce.Rd                    |    2 
 5 files changed, 157 insertions(+), 119 deletions(-)

More information about ProjectManagement at CRAN
Permanent link

Package mlr3misc updated to version 0.1.6 with previous version 0.1.5 dated 2019-09-28

Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions used in 'mlr3' and its companion packages. Comes with helper functions for functional programming, for printing, to work with 'data.table', as well as some generally useful 'R6' classes. This package also supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3misc versions 0.1.5 dated 2019-09-28 and 0.1.6 dated 2019-12-12

 DESCRIPTION                 |    8 -
 MD5                         |   39 +++---
 NEWS.md                     |    6 +
 R/Dictionary.R              |   89 +++++++--------
 R/cite_bib.R                |   42 ++++---
 R/dictionary_sugar.R        |    7 +
 README.md                   |    3 
 man/Dictionary.Rd           |  257 ++++++++++++++++++++++++++++++++++++--------
 man/cite_bib.Rd             |   13 +-
 man/compat-map.Rd           |   14 +-
 man/dictionary_sugar_get.Rd |    3 
 man/encapsulate.Rd          |   12 +-
 man/figures                 |only
 man/invoke.Rd               |    2 
 man/keep_in_bounds.Rd       |    4 
 man/mlr3misc-package.Rd     |    4 
 man/modify_if.Rd            |    4 
 man/require_namespaces.Rd   |    6 -
 man/set_names.Rd            |    2 
 man/str_collapse.Rd         |    3 
 man/str_indent.Rd           |    5 
 21 files changed, 368 insertions(+), 155 deletions(-)

More information about mlr3misc at CRAN
Permanent link

Package imagefluency updated to version 0.2.2 with previous version 0.2.1 dated 2019-09-27

Title: Image Statistics Based on Processing Fluency
Description: Get image statistics based on processing fluency theory. The functions provide scores for several basic aesthetic principles that facilitate fluent cognitive processing of images: contrast, complexity / simplicity, self-similarity, symmetry, and typicality. See Mayer & Landwehr (2018) <doi:10.1037/aca0000187> and Mayer & Landwehr (2018) <doi:10.31219/osf.io/gtbhw> for the theoretical background of the methods.
Author: Stefan Mayer [aut, cre] (<https://orcid.org/0000-0003-0034-7090>)
Maintainer: Stefan Mayer <stefan@mayer-de.com>

Diff between imagefluency versions 0.2.1 dated 2019-09-27 and 0.2.2 dated 2019-12-12

 DESCRIPTION                           |   13 ++---
 MD5                                   |   32 +++++++------
 NEWS.md                               |    6 ++
 R/self-similarity.R                   |    2 
 R/typicality.R                        |    6 --
 R/utils.R                             |    4 -
 README.md                             |    7 ++
 build/vignette.rds                    |binary
 inst/doc/imagefluency.R               |   28 +++++------
 inst/doc/imagefluency.html            |   39 +++++++---------
 man/figures                           |only
 man/imagefluency-package.Rd           |    2 
 tests/testthat/Rplots.pdf             |only
 tests/testthat/test_complexity.R      |   51 ++++++++++++++++++++-
 tests/testthat/test_contrast.R        |   17 ++++++-
 tests/testthat/test_self_similarity.R |   81 +++++++++++++++++++++++++++++++--
 tests/testthat/test_symmetry.R        |   71 ++++++++++++++++++++++++++---
 tests/testthat/test_typicality.R      |   82 +++++++++++++++++++++++++++++++++-
 18 files changed, 361 insertions(+), 80 deletions(-)

More information about imagefluency at CRAN
Permanent link

Package congressbr updated to version 0.2.2 with previous version 0.2.1 dated 2019-05-08

Title: Downloads, Unpacks and Tidies Legislative Data from the Brazilian Federal Senate and Chamber of Deputies
Description: Downloads and tidies data from the Brazilian Federal Senate and Chamber of Deputies Application Programming Interfaces available at <http:// legis.senado.gov.br/dadosabertos/> and <https://dadosabertos.camara.leg.br/> respectively.
Author: Robert McDonnell [aut, cre], Guilherme Jardim Duarte [aut], Danilo Freire [aut], Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>

Diff between congressbr versions 0.2.1 dated 2019-05-08 and 0.2.2 dated 2019-12-12

 DESCRIPTION                 |   10 +-
 MD5                         |   64 +++++++-------
 NAMESPACE                   |    4 
 NEWS.md                     |    4 
 R/cham_votes.R              |  194 ++++++++++++++++++++++++++++++++++----------
 R/sen_agenda.R              |    6 -
 R/sen_various.R             |    4 
 R/sen_votes.R               |   84 ++++++++++++++++---
 R/util.R                    |    4 
 README.md                   |    3 
 build/vignette.rds          |binary
 inst/doc/chamber.R          |   22 ++--
 inst/doc/chamber.html       |  168 +++++++++++++++++++-------------------
 inst/doc/senate.R           |   32 +++----
 inst/doc/senate.html        |  178 +++++++++++++++++++---------------------
 man/cham_bills.Rd           |   21 +++-
 man/cham_votes.Rd           |    4 
 man/cham_votes_year.Rd      |only
 man/congressbr.Rd           |    1 
 man/sen_agenda.Rd           |   12 ++
 man/sen_bill_search.Rd      |   28 ++++--
 man/sen_bills.Rd            |    9 +-
 man/sen_bills_current.Rd    |   10 +-
 man/sen_bills_passing.Rd    |    9 +-
 man/sen_bills_updates.Rd    |   10 +-
 man/sen_commissions_type.Rd |    3 
 man/sen_plenary_agenda.Rd   |    3 
 man/sen_senator.Rd          |    9 +-
 man/sen_senator_legis.Rd    |    9 +-
 man/sen_senator_list.Rd     |    3 
 man/sen_votes.Rd            |    3 
 man/sen_votes_year.Rd       |   10 +-
 man/sen_votes_year_file.Rd  |only
 man/vote_to_rollcall.Rd     |    3 
 34 files changed, 579 insertions(+), 345 deletions(-)

More information about congressbr at CRAN
Permanent link

Package BIOdry updated to version 0.7 with previous version 0.6 dated 2019-05-28

Title: Multilevel Modeling of Dendroclimatical Fluctuations
Description: Multilevel ecological data series (MEDS) are sequences of observations ordered according to temporal/spatial hierarchies that are defined by sample designs, with sample variability confined to ecological factors. Dendroclimatic MEDS of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity. Modeled fluctuations (model frames) are compared with Mantel correlograms on multiple levels defined by sample design. Package implementation can be understood by running examples in modelFrame(), and muleMan() functions.
Author: Wilson Lara <wilarhen@gmail.com>, Felipe Bravo <fbravo@pvs.uva.es>
Maintainer: Wilson Lara <wilarhen@gmail.com>

Diff between BIOdry versions 0.6 dated 2019-05-28 and 0.7 dated 2019-12-12

 DESCRIPTION               |    8 ++---
 MD5                       |   38 +++++++++++++--------------
 NEWS                      |    3 ++
 R/anova.modelFrame.R      |   23 ++++++++++------
 R/frametoLme.R            |   64 +++++++++++++++++++++++++---------------------
 R/modelFrame.R            |   25 ++++++++++-------
 R/muleMan.R               |   33 +++++++++++++----------
 R/plot.modelFrame.R       |   15 +++++-----
 R/plot.muleMan.R          |   35 ++++++++++++++-----------
 R/summary.modelFrame.R    |   16 ++++++-----
 R/wlai.R                  |    2 -
 build/partial.rdb         |binary
 man/anova.modelFrame.Rd   |   23 ++++++++++------
 man/frametoLme.Rd         |   64 +++++++++++++++++++++++++---------------------
 man/modelFrame.Rd         |   55 ++++++++++++++++++++-------------------
 man/muleMan.Rd            |   33 +++++++++++++----------
 man/plot.modelFrame.Rd    |   15 +++++-----
 man/plot.muleMan.Rd       |   35 ++++++++++++++-----------
 man/summary.modelFrame.Rd |   16 ++++++-----
 man/wlai.Rd               |    2 -
 20 files changed, 281 insertions(+), 224 deletions(-)

More information about BIOdry at CRAN
Permanent link

Package tm updated to version 0.7-7 with previous version 0.7-6 dated 2018-12-21

Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] (<https://orcid.org/0000-0001-7656-8338>), Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>), Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>

Diff between tm versions 0.7-6 dated 2018-12-21 and 0.7-7 dated 2019-12-12

 DESCRIPTION             |    8 ++++----
 MD5                     |   20 ++++++++++----------
 R/matrix.R              |   14 +++++++++-----
 build/vignette.rds      |binary
 data/acq.rda            |binary
 data/crude.rda          |binary
 inst/doc/extensions.pdf |binary
 inst/doc/tm.pdf         |binary
 src/copy.c              |    3 ++-
 src/init.c              |    2 +-
 src/tdm.cpp             |    8 ++++++--
 11 files changed, 32 insertions(+), 23 deletions(-)

More information about tm at CRAN
Permanent link

Package graph4lg updated to version 0.2.0 with previous version 0.1.1 dated 2019-07-23

Title: Build Graphs for Landscape Genetics Analysis
Description: Build graphs for landscape genetics analysis. This set of functions can be used to import and convert spatial and genetic data initially in different formats, import landscape graphs created with 'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>, make diagnosis plots of isolation by distance relationships in order to choose how to build genetic graphs, create graphs with a large range of pruning methods, weight their links with several genetic distances, plot and analyse graphs, compare them with other graphs. It uses functions from other packages such as 'adegenet' (Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi et Nepusz, 2006) <https://bit.ly/35a3V3H>. It also implements methods commonly used in landscape genetics to create graphs, described by Dyer et Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data (van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.
Author: Paul Savary
Maintainer: Paul Savary <savarypaul660@gmail.com>

Diff between graph4lg versions 0.1.1 dated 2019-07-23 and 0.2.0 dated 2019-12-12

 DESCRIPTION                     |   17 +-
 MD5                             |  173 ++++++++++++-----------
 NAMESPACE                       |    7 
 NEWS.md                         |    6 
 R/add_nodes_attr.R              |   34 ++--
 R/aux_25_09.R                   |    3 
 R/compar_r_fisher.R             |    3 
 R/convert_cd.R                  |   43 +++--
 R/data.R                        |   31 ++--
 R/df_to_pw_mat.R                |only
 R/dist_max_corr.R               |   34 ++--
 R/g_percol.R                    |   24 +--
 R/gen_graph_indep.R             |   77 ++++++----
 R/gen_graph_thr.R               |    5 
 R/gen_graph_topo.R              |   11 -
 R/genepop_to_genind.R           |   19 +-
 R/genind_to_genepop.R           |   13 +
 R/graph_modul_compar.R          |  124 ++++++++++------
 R/graph_node_compar.R           |   59 ++++----
 R/graph_plan.R                  |only
 R/graph_plot_compar.R           |   37 ++---
 R/graph_to_df.R                 |only
 R/graph_to_shp.R                |   58 ++++---
 R/graph_topo_compar.R           |   62 ++++----
 R/graphab_to_igraph.R           |   34 ++--
 R/gstud_to_genind.R             |   18 +-
 R/kernel_param.R                |only
 R/loci_to_genind.R              |    5 
 R/mat_gen_dist.R                |   57 ++++---
 R/mat_geo_dist.R                |   28 ++-
 R/mat_pw_d_jost.R               |   14 +
 R/mat_pw_dps.R                  |    8 -
 R/mat_pw_fst.R                  |   16 +-
 R/mat_pw_gst.R                  |   14 +
 R/plot_graph_lg.R               |   99 +++++++------
 R/plot_graph_modul.R            |  162 ++++++++++++----------
 R/plot_w_hist.R                 |   10 -
 R/pop_gen_index.R               |  123 ++++++++++------
 R/pw_mat_to_df.R                |only
 R/reorder_mat.R                 |   15 +-
 R/scatter_dist.R                |   13 -
 R/scatter_dist_g.R              |   34 ++--
 R/structure_to_genind.R         |   47 +++---
 build/partial.rdb               |binary
 inst/doc/vignette_graph4lg.R    |   88 +++++------
 inst/doc/vignette_graph4lg.html |  102 ++++++-------
 man/add_nodes_attr.Rd           |  157 +++++++++++----------
 man/compar_r_fisher.Rd          |   96 ++++++-------
 man/convert_cd.Rd               |  184 ++++++++++++-------------
 man/data_pc_genind.Rd           |   56 +++----
 man/data_pc_gpop.Rd             |   76 +++++-----
 man/data_pc_gstud.Rd            |   80 +++++-----
 man/data_pc_loci.Rd             |   68 ++++-----
 man/data_pc_str.Rd              |   72 ++++-----
 man/data_simul_genind.Rd        |   69 ++++-----
 man/data_tuto.Rd                |   50 +++---
 man/df_to_pw_mat.Rd             |only
 man/dist_max_corr.Rd            |  212 ++++++++++++++--------------
 man/g_percol.Rd                 |   70 ++++-----
 man/gen_graph_indep.Rd          |  263 ++++++++++++++++++-----------------
 man/gen_graph_thr.Rd            |  105 +++++++-------
 man/gen_graph_topo.Rd           |  125 ++++++++---------
 man/genepop_to_genind.Rd        |  111 +++++++--------
 man/genind_to_genepop.Rd        |  174 +++++++++++------------
 man/graph_modul_compar.Rd       |  294 +++++++++++++++++++++-------------------
 man/graph_node_compar.Rd        |  188 +++++++++++++------------
 man/graph_plan.Rd               |only
 man/graph_plot_compar.Rd        |  115 +++++++--------
 man/graph_to_df.Rd              |only
 man/graph_to_shp.Rd             |  157 +++++++++++----------
 man/graph_topo_compar.Rd        |  211 ++++++++++++++--------------
 man/graphab_to_igraph.Rd        |  161 +++++++++++----------
 man/gstud_to_genind.Rd          |   87 +++++------
 man/kernel_param.Rd             |only
 man/loci_to_genind.Rd           |   61 ++++----
 man/mat_gen_dist.Rd             |  164 +++++++++++-----------
 man/mat_geo_dist.Rd             |   90 ++++++------
 man/mat_pw_d_j.Rd               |  122 ++++++++--------
 man/mat_pw_dps.Rd               |   98 ++++++-------
 man/mat_pw_fst.Rd               |  120 ++++++++--------
 man/mat_pw_gst.Rd               |  120 ++++++++--------
 man/plot_graph_lg.Rd            |  134 +++++++++---------
 man/plot_graph_modul.Rd         |  213 +++++++++++++++-------------
 man/plot_w_hist.Rd              |   62 ++++----
 man/pop_gen_index.Rd            |  109 +++++++-------
 man/pts_pop_pc.Rd               |   78 +++++-----
 man/pts_pop_simul.Rd            |   56 +++----
 man/pw_mat_to_df.Rd             |only
 man/reorder_mat.Rd              |   72 ++++-----
 man/scatter_dist.Rd             |  159 +++++++++++----------
 man/scatter_dist_g.Rd           |  175 ++++++++++++-----------
 man/structure_to_genind.Rd      |  139 +++++++++---------
 vignettes/data_gpop_test.txt    |only
 93 files changed, 3630 insertions(+), 3250 deletions(-)

More information about graph4lg at CRAN
Permanent link

Package CARBayesST updated to version 3.0.2 with previous version 3.0.1 dated 2019-01-08

Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, or Poisson, but for some models only the binomial and Poisson data likelihoods are available. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) style prior distributions. A number of different random effects structures are available, including Bernardinelli et al. (1995) <doi:10.1002/sim.4780142112>, Rushworth et al. (2014) <doi:10.1016/j.sste.2014.05.001> and Lee et al. (2016) <doi:10.1214/16-AOAS941>. Full details are given in the vignette accompanying this package. The creation of this package was supported by the Engineering and Physical Sciences Research Council (EPSRC) grant EP/J017442/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee, Alastair Rushworth and Gary Napier
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>

Diff between CARBayesST versions 3.0.1 dated 2019-01-08 and 3.0.2 dated 2019-12-12

 DESCRIPTION               |    8 ++++----
 MD5                       |   20 ++++++++++----------
 R/binomial.CARadaptive.R  |    8 ++++----
 R/common.functions.R      |    8 ++++----
 R/gaussian.CARadaptive.R  |    8 ++++----
 R/poisson.CARadaptive.R   |    8 ++++----
 build/vignette.rds        |binary
 inst/doc/CARBayesST.Rnw   |    8 ++++----
 inst/doc/CARBayesST.pdf   |binary
 man/CARBayesST-package.Rd |    4 ++--
 vignettes/CARBayesST.Rnw  |    8 ++++----
 11 files changed, 40 insertions(+), 40 deletions(-)

More information about CARBayesST at CRAN
Permanent link

Package sismonr updated to version 2.0.0 with previous version 1.1.4 dated 2019-07-21

Title: Simulation of in Silico Multi-Omic Networks
Description: A tool for the simulation of gene expression profiles for in silico regulatory networks. The package generates gene regulatory networks, which include protein-coding and noncoding genes linked via different types of regulation: regulation of transcription, translation, RNA or protein decay, and post-translational modifications. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations, but is defined by the user. A choice of stochastic simulation algorithms allow us to simulate the expression profiles (RNA and if applicable protein abundance) of the genes in the in silico system for the different in silico individuals. A tutorial explaining how to use the package is available at <https://oliviaab.github.io/sismonr/>. Manuscript in preparation; see also Angelin-Bonnet O., Biggs P.J. and Vignes M. (2018) <doi:10.1109/BIBM.2018.8621131>. Note that sismonr relies on Julia code called internally by the functions. No knowledge of Julia is required in order to use sismonr, but Julia must be installed on the computer (instructions can be found in the tutorial, the GitHub page or the vignette of the package).
Author: Olivia Angelin-Bonnet [aut, cre] (<https://orcid.org/0000-0002-7708-2919>), Patrick Biggs [aut] (<https://orcid.org/0000-0002-0285-4101>), Matthieu Vignes [aut] (<https://orcid.org/0000-0001-8929-2975>), John M. Chambers [ctb]
Maintainer: Olivia Angelin-Bonnet <olivia.angelinbonnet@gmail.com>

Diff between sismonr versions 1.1.4 dated 2019-07-21 and 2.0.0 dated 2019-12-12

 DESCRIPTION                                 |   10 
 MD5                                         |   74 +++---
 NAMESPACE                                   |    2 
 NEWS.md                                     |   15 +
 R/args_classes.R                            |   19 -
 R/in_silico_population.R                    |  136 +++++++----
 R/in_silico_system.R                        |   30 +-
 R/stochastic_simulation.R                   |  345 ++++++++++++++++++++++++----
 build/vignette.rds                          |binary
 inst/doc/sismonr_vignette.R                 |   22 -
 inst/doc/sismonr_vignette.Rmd               |   36 --
 inst/doc/sismonr_vignette.html              |  145 +++++------
 inst/julia/stochastic_model.jl              |  282 +++++++++++++++++++---
 inst/julia/stochastic_simulation.jl         |   46 ++-
 inst/julia/testModules.jl                   |    4 
 man/callJuliaStochasticSimulation.Rd        |    4 
 man/createInSilicoPopulation.Rd             |   31 +-
 man/createInSilicoSystem.Rd                 |    2 
 man/createIndividual.Rd                     |   32 ++
 man/createStochSystem.Rd                    |   10 
 man/getRNAseqMatrix.Rd                      |only
 man/insilicoindividualargs.Rd               |    6 
 man/insilicosystemargs.Rd                   |    4 
 man/mergeAlleleAbundance.Rd                 |    4 
 man/mergeComplexesAbundance.Rd              |    4 
 man/mergePTMAbundance.Rd                    |    4 
 man/plotGRN.Rd                              |    4 
 man/plotHeatMap.Rd                          |   14 -
 man/plotMutations.Rd                        |    6 
 man/plotSimulation.Rd                       |   14 -
 man/sampleLibrarySize.Rd                    |only
 man/simulateInSilicoSystem.Rd               |    4 
 man/simulateParallelInSilicoSystem.Rd       |    4 
 man/steadyStateAbundance.Rd                 |    4 
 man/summariseSimulation.Rd                  |    6 
 tests/testthat/test-args_classes.R          |    8 
 tests/testthat/test-in_silico_population.R  |   53 +++-
 tests/testthat/test-stochastic_simulation.R |  101 +++++---
 vignettes/sismonr_vignette.Rmd              |   36 --
 39 files changed, 1077 insertions(+), 444 deletions(-)

More information about sismonr at CRAN
Permanent link

Package rprev updated to version 1.0.3 with previous version 1.0.2 dated 2019-03-12

Title: Estimating Disease Prevalence from Registry Data
Description: Estimates disease prevalence for a given index date, using existing registry data extended with Monte Carlo simulations.
Author: Stuart Lacy [cre, aut], Simon Crouch [aut], Stephanie Lax [aut]
Maintainer: Stuart Lacy <stuart.lacy@york.ac.uk>

Diff between rprev versions 1.0.2 dated 2019-03-12 and 1.0.3 dated 2019-12-12

 DESCRIPTION                          |   11 
 MD5                                  |   54 +-
 NAMESPACE                            |    2 
 NEWS.md                              |    4 
 build/vignette.rds                   |binary
 inst/doc/diagnostics.R               |   38 -
 inst/doc/diagnostics.html            |  517 +++++++++++++++++-------
 inst/doc/user_guide.R                |   72 +--
 inst/doc/user_guide.html             |  745 ++++++++++++++++++++++-------------
 man/UKmortality.Rd                   |   48 +-
 man/counted_prevalence.Rd            |   72 +--
 man/draw_incident_population.Rd      |   64 +--
 man/extract_covars.Rd                |   46 +-
 man/fixed_cure.Rd                    |  123 +++--
 man/plot.incdiag.Rd                  |   80 +--
 man/plot.survfit.prev.Rd             |   80 +--
 man/predict_survival_probability.Rd  |   52 +-
 man/prevalence.Rd                    |  357 ++++++++--------
 man/prevsim.Rd                       |   62 +-
 man/rprev.Rd                         |   61 +-
 man/sim_prevalence.Rd                |  104 ++--
 man/summary.survfit.prev.Rd          |   96 ++--
 man/survfit.prevalence.Rd            |   58 +-
 man/test_homogeneity.Rd              |  180 ++++----
 man/test_prevalence_fit.Rd           |   75 +--
 man/validate_incidence_model.Rd      |   56 +-
 man/validate_survival_model.Rd       |   65 +--
 tests/testthat/test_survival_model.R |    2 
 28 files changed, 1796 insertions(+), 1328 deletions(-)

More information about rprev at CRAN
Permanent link

Package RGCxGC updated to version 1.1.0 with previous version 1.0.0 dated 2019-01-20

Title: Preprocessing and Multivariate Analysis of Bidimensional Gas Chromatography Data
Description: Toolbox for chemometrics analysis of bidimensional gas chromatography data. This package import data for common scientific data format (NetCDF) and fold it to 2D chromatogram. Then, it can perform preprocessing and multivariate analysis. In the preprocessing algorithms, baseline correction, smoothing, and peak alignment are available. While in multivariate analysis, multiway principal component analysis is incorporated.
Author: Cristian Quiroz-Moreno [aut, cre], Guilherme L. Alexandrino [aut], Noroska G.S. Mogollón [aut]
Maintainer: Cristian Quiroz-Moreno <cristianquirozd1997@gmail.com>

Diff between RGCxGC versions 1.0.0 dated 2019-01-20 and 1.1.0 dated 2019-12-12

 RGCxGC-1.0.0/RGCxGC/vignettes/bioinformatics.csl         |only
 RGCxGC-1.0.0/RGCxGC/vignettes/images/basicWorkflow.png   |only
 RGCxGC-1.1.0/RGCxGC/DESCRIPTION                          |   25 
 RGCxGC-1.1.0/RGCxGC/MD5                                  |  106 ++-
 RGCxGC-1.1.0/RGCxGC/NAMESPACE                            |   13 
 RGCxGC-1.1.0/RGCxGC/R/A_classes.R                        |  104 +--
 RGCxGC-1.1.0/RGCxGC/R/MTBLS579.R                         |    6 
 RGCxGC-1.1.0/RGCxGC/R/Myrothecium.R                      |only
 RGCxGC-1.1.0/RGCxGC/R/baseline_corr.R                    |   32 -
 RGCxGC-1.1.0/RGCxGC/R/batchTwoDCOW.R                     |  147 ++--
 RGCxGC-1.1.0/RGCxGC/R/dephase_chrom.R                    |only
 RGCxGC-1.1.0/RGCxGC/R/get_metadata.R                     |only
 RGCxGC-1.1.0/RGCxGC/R/import_mixOmics.R                  |only
 RGCxGC-1.1.0/RGCxGC/R/join_chromatograms.R               |   39 -
 RGCxGC-1.1.0/RGCxGC/R/m_prcomp.R                         |   35 -
 RGCxGC-1.1.0/RGCxGC/R/make_loadings.R                    |only
 RGCxGC-1.1.0/RGCxGC/R/plot.R                             |   45 +
 RGCxGC-1.1.0/RGCxGC/R/plot_loading.R                     |  120 ++-
 RGCxGC-1.1.0/RGCxGC/R/print.R                            |    6 
 RGCxGC-1.1.0/RGCxGC/R/read_chrom.R                       |  106 ++-
 RGCxGC-1.1.0/RGCxGC/R/reference_chrom.R                  |only
 RGCxGC-1.1.0/RGCxGC/R/scores.R                           |    6 
 RGCxGC-1.1.0/RGCxGC/R/set_metadata.R                     |only
 RGCxGC-1.1.0/RGCxGC/R/twod_cow.R                         |   33 -
 RGCxGC-1.1.0/RGCxGC/R/unfold_chrom.R                     |only
 RGCxGC-1.1.0/RGCxGC/R/wsmooth.R                          |   16 
 RGCxGC-1.1.0/RGCxGC/build/partial.rdb                    |binary
 RGCxGC-1.1.0/RGCxGC/build/vignette.rds                   |binary
 RGCxGC-1.1.0/RGCxGC/data/MTBLS579.rda                    |binary
 RGCxGC-1.1.0/RGCxGC/data/Myrothecium.rda                 |only
 RGCxGC-1.1.0/RGCxGC/data/datalist                        |only
 RGCxGC-1.1.0/RGCxGC/inst/doc/Explanation.R               |   80 +-
 RGCxGC-1.1.0/RGCxGC/inst/doc/Explanation.Rmd             |  288 +++++----
 RGCxGC-1.1.0/RGCxGC/inst/doc/Explanation.html            |  469 ++++++++-------
 RGCxGC-1.1.0/RGCxGC/man/GCxGC-class.Rd                   |   14 
 RGCxGC-1.1.0/RGCxGC/man/MPCA-class.Rd                    |   18 
 RGCxGC-1.1.0/RGCxGC/man/MTBLS579.Rd                      |    6 
 RGCxGC-1.1.0/RGCxGC/man/Myrothecium.Rd                   |only
 RGCxGC-1.1.0/RGCxGC/man/PLSDA-class.Rd                   |only
 RGCxGC-1.1.0/RGCxGC/man/baseline_corr.Rd                 |   18 
 RGCxGC-1.1.0/RGCxGC/man/batch_2DCOW-class.Rd             |    4 
 RGCxGC-1.1.0/RGCxGC/man/batch_2DCOW.Rd                   |   68 +-
 RGCxGC-1.1.0/RGCxGC/man/dephase_chrom-methods.Rd         |only
 RGCxGC-1.1.0/RGCxGC/man/get_metadata-methods.Rd          |only
 RGCxGC-1.1.0/RGCxGC/man/import_mixOmics-methods.Rd       |only
 RGCxGC-1.1.0/RGCxGC/man/join_chromatograms.Rd            |   13 
 RGCxGC-1.1.0/RGCxGC/man/joined_chrom-class.Rd            |   12 
 RGCxGC-1.1.0/RGCxGC/man/m_prcomp.Rd                      |   22 
 RGCxGC-1.1.0/RGCxGC/man/make_loadings.Rd                 |only
 RGCxGC-1.1.0/RGCxGC/man/plot-methods.Rd                  |   23 
 RGCxGC-1.1.0/RGCxGC/man/plot_loading-methods.Rd          |   20 
 RGCxGC-1.1.0/RGCxGC/man/preproc_GCxGC-class.Rd           |    8 
 RGCxGC-1.1.0/RGCxGC/man/print-methods.Rd                 |    6 
 RGCxGC-1.1.0/RGCxGC/man/projected-class.Rd               |only
 RGCxGC-1.1.0/RGCxGC/man/raw_GCxGC-class.Rd               |   10 
 RGCxGC-1.1.0/RGCxGC/man/read_chrom.Rd                    |   41 -
 RGCxGC-1.1.0/RGCxGC/man/reference_chrom.Rd               |only
 RGCxGC-1.1.0/RGCxGC/man/scores-methods.Rd                |    6 
 RGCxGC-1.1.0/RGCxGC/man/set_metadata-methods.Rd          |only
 RGCxGC-1.1.0/RGCxGC/man/twod_cow.Rd                      |   26 
 RGCxGC-1.1.0/RGCxGC/man/unfold_chrom.Rd                  |only
 RGCxGC-1.1.0/RGCxGC/man/wsmooth.Rd                       |   16 
 RGCxGC-1.1.0/RGCxGC/vignettes/Explanation.Rmd            |  288 +++++----
 RGCxGC-1.1.0/RGCxGC/vignettes/analitica-chimica-acta.csl |only
 RGCxGC-1.1.0/RGCxGC/vignettes/images/basicWorkflow.jpg   |only
 RGCxGC-1.1.0/RGCxGC/vignettes/images/dataProcessing.png  |binary
 66 files changed, 1374 insertions(+), 921 deletions(-)

More information about RGCxGC at CRAN
Permanent link

Package RclusTool updated to version 0.91.1 with previous version 0.91 dated 2019-11-06

Title: Graphical Toolbox for Clustering and Classification of Data Frames
Description: Graphical toolbox for clustering and classification of data frames. It proposes a graphical interface to process clustering and classification methods on features data-frames, and to view initial data as well as resulted cluster or classes. According to the level of available labels, different approaches are proposed: unsupervised clustering, semi-supervised clustering and supervised classification. To assess the processed clusters or classes, the toolbox can import and show some supplementary data formats: either profile/time series, or images. These added information can help the expert to label clusters (clustering), or to constrain data frame rows (semi-supervised clustering), using Constrained spectral embedding algorithm by Wacquet et al. (2013) <doi:10.1016/j.patrec.2013.02.003> and the methodology provided by Wacquet et al. (2013) <doi:10.1007/978-3-642-35638-4_21>.
Author: Guillaume Wacquet [aut], Pierre-Alexandre Hebert [aut, cre], Emilie Poisson [aut], Pierre Talon [aut]
Maintainer: Pierre-Alexandre Hebert <hebert@univ-littoral.fr>

Diff between RclusTool versions 0.91 dated 2019-11-06 and 0.91.1 dated 2019-12-12

 DESCRIPTION                           |   10 +-
 MD5                                   |  148 +++++++++++++++++-----------------
 NAMESPACE                             |    3 
 R/RclusTool.R                         |    5 -
 R/batchTab.R                          |    2 
 R/importTab.R                         |    2 
 R/preprocessTab.R                     |    2 
 R/sampleBuilding.R                    |    1 
 R/sampleClustering.R                  |    1 
 R/sampleCompute.R                     |    9 +-
 R/sampleView.R                        |   17 +++
 R/semisupTab.R                        |    2 
 R/supTab.R                            |    2 
 R/unsupTab.R                          |    2 
 man/ElbowPlot.Rd                      |    3 
 man/KmeansAutoElbow.Rd                |    3 
 man/KwaySSSC.Rd                       |   10 +-
 man/MainWindow.Rd                     |    3 
 man/abdPlot.Rd                        |   27 +++---
 man/abdPlotTabs.Rd                    |    3 
 man/addClustering.Rd                  |    3 
 man/analyzePlot.Rd                    |   13 ++
 man/applyPreprocessing.Rd             |   10 +-
 man/buildBatchTab.Rd                  |    3 
 man/buildImportTab.Rd                 |    3 
 man/buildPreprocessTab.Rd             |    3 
 man/buildSemisupTab.Rd                |    3 
 man/buildUnsupTab.Rd                  |    3 
 man/buildsupTab.Rd                    |    3 
 man/clusterDensity.Rd                 |    8 +
 man/clusterSummary.Rd                 |    9 +-
 man/computeCKmeans.Rd                 |   11 ++
 man/computeCSC.Rd                     |   10 +-
 man/computeEM.Rd                      |   10 +-
 man/computeItemsGUI.Rd                |    3 
 man/computeKmeans.Rd                  |    3 
 man/computePcaSample.Rd               |   11 +-
 man/computeSampling.Rd                |   11 ++
 man/computeSemiSupervised.Rd          |   22 +++--
 man/computeSpectralEmbeddingSample.Rd |   12 ++
 man/computeSupervised.Rd              |    9 +-
 man/computeUnSupervised.Rd            |   17 ++-
 man/cor.mtest.Rd                      |    6 +
 man/dot-logoFrame.Rd                  |    3 
 man/extractProtos.Rd                  |    9 +-
 man/featSpaceNameConvert.Rd           |    7 +
 man/formatLabelSample.Rd              |    9 +-
 man/guessFileEncoding.Rd              |    2 
 man/importSample.Rd                   |   24 ++++-
 man/initBatchTab.Rd                   |    3 
 man/initImportTab.Rd                  |    6 -
 man/initPreprocessTab.Rd              |   13 ++
 man/initSemisupTab.Rd                 |    6 -
 man/initSupTab.Rd                     |    3 
 man/initUnsupTab.Rd                   |    3 
 man/itemsModel.Rd                     |    5 -
 man/listDerivableFeatureSpaces.Rd     |    8 +
 man/loadSample.Rd                     |    3 
 man/makeFeatureSpaceOperations.Rd     |   13 ++
 man/plotDensity2D.Rd                  |   28 +++---
 man/plotProfile.Rd                    |   16 ++-
 man/plotProfileExtract.Rd             |   16 ++-
 man/plotSampleFeatures.Rd             |   37 +++++---
 man/purgeSample.Rd                    |    8 +
 man/readTrainSet.Rd                   |    8 +
 man/saveLogFile.Rd                    |    3 
 man/spectralClustering.Rd             |   14 ++-
 man/tk2add.notetab.Rd                 |    3 
 man/tk2delete.notetab.Rd              |    3 
 man/tk2draw.notetab.Rd                |    3 
 man/tk2notetab.RclusTool.Rd           |    3 
 man/tkrplot.RclusTool.Rd              |    3 
 man/tkrreplot.RclusTool.Rd            |    3 
 man/toStringDataFrame.Rd              |    3 
 man/visualizeSampleClustering.Rd      |   20 +++-
 75 files changed, 515 insertions(+), 214 deletions(-)

More information about RclusTool at CRAN
Permanent link

Package interpret updated to version 0.1.24 with previous version 0.1.25 dated 2019-12-12

Title: Fit Interpretable Machine Learning Models and Explain Blackbox Machine Learning
Description: Package for training interpretable machine learning models and explaining blackbox systems. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretability. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut], Harsha Nori [aut], Paul Koch [aut], Rich Caruana [aut, cre], Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>

Diff between interpret versions 0.1.25 dated 2019-12-12 and 0.1.24 dated 2019-12-12

 DESCRIPTION |    8 ++++----
 MD5         |    2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

More information about interpret at CRAN
Permanent link

Package ifaTools updated to version 0.20 with previous version 0.19 dated 2019-03-09

Title: Toolkit for Item Factor Analysis with 'OpenMx'
Description: Tools, tutorials, and demos of Item Factor Analysis using 'OpenMx'.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between ifaTools versions 0.19 dated 2019-03-09 and 0.20 dated 2019-12-12

 DESCRIPTION                                |   10 +++++-----
 MD5                                        |   23 ++++++++++++++---------
 build/vignette.rds                         |binary
 inst/doc/pritikin-schmidt.pdf              |binary
 inst/itemModelExplorer/ui.R                |    2 +-
 man/iccPlot.Rd                             |    3 +--
 man/replicateModelBy.Rd                    |   14 +++++++++++---
 man/uniquenessPrior.Rd                     |    3 +--
 man/univariatePrior.Rd                     |    3 +--
 tests/testthat/test-addExploratoryFactor.R |   24 ++++++++++++++++++++----
 tools                                      |only
 11 files changed, 54 insertions(+), 28 deletions(-)

More information about ifaTools at CRAN
Permanent link

Package geepack updated to version 1.3-0 with previous version 1.2-1 dated 2016-09-24

Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can also handle clustered categorical responses.
Author: Søren Højsgaard [aut, cre, cph], Ulrich Halekoh [aut, cph], Jun Yan [aut, cph], Claus Ekstrøm [ctb]
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>

Diff between geepack versions 1.2-1 dated 2016-09-24 and 1.3-0 dated 2019-12-12

 geepack-1.2-1/geepack/data/dietox.txt.gz            |only
 geepack-1.2-1/geepack/data/koch.txt.gz              |only
 geepack-1.2-1/geepack/data/ohio.txt.gz              |only
 geepack-1.2-1/geepack/data/respdis.txt.gz           |only
 geepack-1.2-1/geepack/data/respiratory.txt.gz       |only
 geepack-1.2-1/geepack/data/seizure.txt.gz           |only
 geepack-1.2-1/geepack/data/sitka89.txt.gz           |only
 geepack-1.2-1/geepack/data/spruce.txt.gz            |only
 geepack-1.2-1/geepack/man/DATA-dietox.Rd            |only
 geepack-1.2-1/geepack/man/DATA-koch.Rd              |only
 geepack-1.2-1/geepack/man/DATA-ohio.Rd              |only
 geepack-1.2-1/geepack/man/DATA-respdis.Rd           |only
 geepack-1.2-1/geepack/man/DATA-respiratory.Rd       |only
 geepack-1.2-1/geepack/man/DATA-seizure.Rd           |only
 geepack-1.2-1/geepack/man/DATA-sitka89.Rd           |only
 geepack-1.2-1/geepack/man/DATA-spruce.Rd            |only
 geepack-1.2-1/geepack/man/SHDgeese-internal.Rd      |only
 geepack-1.2-1/geepack/man/geese-internal.Rd         |only
 geepack-1.3-0/geepack/ChangeLog                     |   18 
 geepack-1.3-0/geepack/DESCRIPTION                   |   35 
 geepack-1.3-0/geepack/MD5                           |  162 +-
 geepack-1.3-0/geepack/NAMESPACE                     |   17 
 geepack-1.3-0/geepack/R/data-geepack.R              |only
 geepack-1.3-0/geepack/R/fixed2Zcor.R                |   97 +
 geepack-1.3-0/geepack/R/geeglm-anova.R              |  718 +++++------
 geepack-1.3-0/geepack/R/geeglm.R                    | 1206 ++++++++++--------
 geepack-1.3-0/geepack/R/geem-interface.R            |only
 geepack-1.3-0/geepack/R/geepack-package.R           |only
 geepack-1.3-0/geepack/R/geese.R                     |  732 +++++++----
 geepack-1.3-0/geepack/R/internal.R                  |  164 +-
 geepack-1.3-0/geepack/R/ordgee.R                    |  410 +++---
 geepack-1.3-0/geepack/R/qic.R                       |only
 geepack-1.3-0/geepack/R/rrr.R                       |   49 
 geepack-1.3-0/geepack/R/summary.R                   |  228 +--
 geepack-1.3-0/geepack/R/zzz.R                       |    6 
 geepack-1.3-0/geepack/README.md                     |only
 geepack-1.3-0/geepack/build/vignette.rds            |binary
 geepack-1.3-0/geepack/data/dietox.rda               |only
 geepack-1.3-0/geepack/data/koch.RData               |only
 geepack-1.3-0/geepack/data/muscatine.rda            |only
 geepack-1.3-0/geepack/data/ohio.RData               |only
 geepack-1.3-0/geepack/data/respdis.RData            |only
 geepack-1.3-0/geepack/data/respiratory.RData        |only
 geepack-1.3-0/geepack/data/seizure.RData            |only
 geepack-1.3-0/geepack/data/sitka89.RData            |only
 geepack-1.3-0/geepack/data/spruce.RData             |only
 geepack-1.3-0/geepack/inst/CITATION                 |    4 
 geepack-1.3-0/geepack/inst/doc/geepack-manual.R     |   22 
 geepack-1.3-0/geepack/inst/doc/geepack-manual.Rnw   |  410 +++---
 geepack-1.3-0/geepack/inst/doc/geepack-manual.pdf   |binary
 geepack-1.3-0/geepack/inst/include/famstr.h         |  282 ++--
 geepack-1.3-0/geepack/inst/include/gee2.h           |  164 +-
 geepack-1.3-0/geepack/inst/include/geese.h          |   16 
 geepack-1.3-0/geepack/inst/include/geesubs.h        |  502 +++----
 geepack-1.3-0/geepack/inst/include/inter.h          |   84 -
 geepack-1.3-0/geepack/inst/include/ordgee.h         |  226 +--
 geepack-1.3-0/geepack/inst/include/param.h          |  216 +--
 geepack-1.3-0/geepack/inst/include/tnt/cholesky.h   |  192 +--
 geepack-1.3-0/geepack/inst/include/tnt/cmat.h       | 1210 +++++++++---------
 geepack-1.3-0/geepack/inst/include/tnt/fcscmat.h    |  330 ++---
 geepack-1.3-0/geepack/inst/include/tnt/fmat.h       | 1154 +++++++++---------
 geepack-1.3-0/geepack/inst/include/tnt/fortran.h    |  134 +-
 geepack-1.3-0/geepack/inst/include/tnt/fspvec.h     |  336 ++---
 geepack-1.3-0/geepack/inst/include/tnt/index.h      |  166 +-
 geepack-1.3-0/geepack/inst/include/tnt/lapack.h     |  386 +++---
 geepack-1.3-0/geepack/inst/include/tnt/lu.h         |  408 +++---
 geepack-1.3-0/geepack/inst/include/tnt/qr.h         |  458 +++----
 geepack-1.3-0/geepack/inst/include/tnt/region1d.h   |  742 +++++------
 geepack-1.3-0/geepack/inst/include/tnt/region2d.h   |  934 +++++++-------
 geepack-1.3-0/geepack/inst/include/tnt/stopwatch.h  |  166 +-
 geepack-1.3-0/geepack/inst/include/tnt/subscript.h  |  116 -
 geepack-1.3-0/geepack/inst/include/tnt/tnt.h        |  180 +-
 geepack-1.3-0/geepack/inst/include/tnt/tntmath.h    |  170 +-
 geepack-1.3-0/geepack/inst/include/tnt/tntreqs.h    |  140 +-
 geepack-1.3-0/geepack/inst/include/tnt/transv.h     |  320 ++---
 geepack-1.3-0/geepack/inst/include/tnt/triang.h     | 1276 ++++++++++----------
 geepack-1.3-0/geepack/inst/include/tnt/trisolve.h   |  368 ++---
 geepack-1.3-0/geepack/inst/include/tnt/vec.h        |  806 ++++++------
 geepack-1.3-0/geepack/inst/include/tnt/vecadaptor.h |  578 ++++-----
 geepack-1.3-0/geepack/inst/include/tnt/version.h    |   40 
 geepack-1.3-0/geepack/inst/include/tntsupp.h        | 1112 ++++++++---------
 geepack-1.3-0/geepack/inst/include/utils.h          |  128 +-
 geepack-1.3-0/geepack/man/QIC.Rd                    |only
 geepack-1.3-0/geepack/man/dietox.Rd                 |only
 geepack-1.3-0/geepack/man/fixed2Zcor.Rd             |  142 --
 geepack-1.3-0/geepack/man/geeglm.Rd                 |  263 ++--
 geepack-1.3-0/geepack/man/geepack-internal.Rd       |only
 geepack-1.3-0/geepack/man/geese.Rd                  |  509 +++----
 geepack-1.3-0/geepack/man/geese.control.Rd          |   82 -
 geepack-1.3-0/geepack/man/genZcor.Rd                |  140 +-
 geepack-1.3-0/geepack/man/koch.Rd                   |only
 geepack-1.3-0/geepack/man/muscatine.Rd              |only
 geepack-1.3-0/geepack/man/ohio.Rd                   |only
 geepack-1.3-0/geepack/man/ordgee.Rd                 |  234 +--
 geepack-1.3-0/geepack/man/respdis.Rd                |only
 geepack-1.3-0/geepack/man/respiratory.Rd            |only
 geepack-1.3-0/geepack/man/seizure.Rd                |only
 geepack-1.3-0/geepack/man/sitka89.Rd                |only
 geepack-1.3-0/geepack/man/spruce.Rd                 |only
 geepack-1.3-0/geepack/src/gee2.cc                   |   19 
 geepack-1.3-0/geepack/src/init.c                    |only
 geepack-1.3-0/geepack/src/inter.cc                  |   22 
 geepack-1.3-0/geepack/src/ordgee.cc                 |    9 
 geepack-1.3-0/geepack/vignettes/geepack-manual.Rnw  |  410 +++---
 104 files changed, 10111 insertions(+), 9337 deletions(-)

More information about geepack at CRAN
Permanent link

Package CARBayes updated to version 5.1.3 with previous version 5.1.2 dated 2019-06-21

Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, multinomial, Poisson or zero-inflated Poisson (ZIP), and spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution. A number of different models are available for univariate spatial data, including models with no random effects as well as random effects modelled by different types of CAR prior, including the BYM model (Besag et al. (1991) <doi:10.1007/BF00116466>), the Leroux model (Leroux et al. (2000) <doi:10.1007/978-1-4612-1284-3_4>) and the localised model (Lee et al. (2015) <doi:10.1002/env.2348>). Additionally, a multivariate CAR (MCAR) model for multivariate spatial data is available, as is a two-level hierarchical model for modelling data relating to individuals within areas. Full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development has been supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1, ESRC grant ES/K006460/1, Innovate UK / Natural Environment Research Council (NERC) grant NE/N007352/1 and the TB Alliance.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>

Diff between CARBayes versions 5.1.2 dated 2019-06-21 and 5.1.3 dated 2019-12-12

 DESCRIPTION                   |    8 
 MD5                           |   24 
 R/binomial.MVlerouxCAR.R      | 1014 ++++++++++++-------------
 R/binomial.dissimilarityCAR.R | 1063 +++++++++++++--------------
 R/common.functions.R          |   11 
 R/gaussian.MVlerouxCAR.R      |  962 ++++++++++++------------
 R/gaussian.dissimilarityCAR.R |  987 ++++++++++++-------------
 R/poisson.MVlerouxCAR.R       |  956 ++++++++++++------------
 R/poisson.dissimilarityCAR.R  | 1029 +++++++++++++-------------
 inst/doc/CARBayes.Rnw         | 1646 +++++++++++++++++++++---------------------
 inst/doc/CARBayes.pdf         |binary
 man/CARBayes-package.Rd       |    6 
 vignettes/CARBayes.Rnw        | 1646 +++++++++++++++++++++---------------------
 13 files changed, 4674 insertions(+), 4678 deletions(-)

More information about CARBayes at CRAN
Permanent link

Package texPreview updated to version 1.4.3 with previous version 1.4.2 dated 2019-12-05

Title: Compile and Preview Snippets of 'LaTeX'
Description: Compile snippets of 'LaTeX' directly into images from the R console to view in the 'RStudio' viewer pane, Shiny apps and 'RMarkdown' documents.
Author: Jonathan Sidi [aut, cre], Daniel Polhamus [aut]
Maintainer: Jonathan Sidi <yonis@metrumrg.com>

Diff between texPreview versions 1.4.2 dated 2019-12-05 and 1.4.3 dated 2019-12-12

 DESCRIPTION                       |   16 ++++-----
 MD5                               |   28 ++++++++---------
 NEWS.md                           |    3 +
 README.md                         |    6 ++-
 build/texPreview.pdf              |binary
 inst/doc/classes.html             |   10 +++---
 inst/doc/kable.html               |    4 +-
 inst/doc/rmarkdown.html           |    8 ++--
 inst/doc/slickr.html              |   14 ++++----
 inst/doc/tests_and_coverage.html  |    2 -
 inst/doc/tex_packages.html        |    4 +-
 inst/doc/tikz.html                |    4 +-
 tests/README.md                   |   62 +++++++++++++++++++-------------------
 tests/testthat/helper-functions.R |   14 +++++++-
 tests/testthat/test-rmd.R         |   12 +------
 15 files changed, 98 insertions(+), 89 deletions(-)

More information about texPreview at CRAN
Permanent link

Package interpret updated to version 0.1.25 with previous version 0.1.23 dated 2019-11-03

Title: Fit Interpretable Machine Learning Models and Explain Blackbox Machine Learning
Description: Package for training interpretable machine learning models and explaining blackbox systems. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretable characteristics. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut], Harsha Nori [aut], Paul Koch [aut], Rich Caruana [aut, cre], Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>

Diff between interpret versions 0.1.23 dated 2019-11-03 and 0.1.25 dated 2019-12-12

 interpret-0.1.23/interpret/man/get_best_model_feature_combination.Rd    |only
 interpret-0.1.23/interpret/man/get_current_model_feature_combination.Rd |only
 interpret-0.1.23/interpret/man/initialize_training_classification.Rd    |only
 interpret-0.1.23/interpret/man/initialize_training_regression.Rd        |only
 interpret-0.1.23/interpret/man/training_step.Rd                         |only
 interpret-0.1.23/interpret/src/core/EbmTrainingState.h                  |only
 interpret-0.1.23/interpret/src/core/Training.cpp                        |only
 interpret-0.1.25/interpret/DESCRIPTION                                  |   13 
 interpret-0.1.25/interpret/MD5                                          |   61 -
 interpret-0.1.25/interpret/NAMESPACE                                    |   12 
 interpret-0.1.25/interpret/R/interpret_core.R                           |  238 +---
 interpret-0.1.25/interpret/R/native_booster.R                           |only
 interpret-0.1.25/interpret/R/native_interactions.R                      |only
 interpret-0.1.25/interpret/man/ebm_classify.Rd                          |only
 interpret-0.1.25/interpret/man/ebm_feature.Rd                           |    4 
 interpret-0.1.25/interpret/man/ebm_feature_combination.Rd               |    4 
 interpret-0.1.25/interpret/man/ebm_predict_proba.Rd                     |only
 interpret-0.1.25/interpret/man/get_interaction_score.Rd                 |    2 
 interpret-0.1.25/interpret/man/initialize_interaction_classification.Rd |   10 
 interpret-0.1.25/interpret/man/initialize_interaction_regression.Rd     |    4 
 interpret-0.1.25/interpret/src/Makevars                                 |    2 
 interpret-0.1.25/interpret/src/core/Boosting.cpp                        |only
 interpret-0.1.25/interpret/src/core/CachedThreadResources.h             |   14 
 interpret-0.1.25/interpret/src/core/DataSetByFeature.cpp                |    7 
 interpret-0.1.25/interpret/src/core/DimensionMultiple.h                 |  114 +-
 interpret-0.1.25/interpret/src/core/DimensionSingle.h                   |   73 -
 interpret-0.1.25/interpret/src/core/EbmBoostingState.h                  |only
 interpret-0.1.25/interpret/src/core/EbmInteractionState.h               |    2 
 interpret-0.1.25/interpret/src/core/EbmInternal.h                       |   70 +
 interpret-0.1.25/interpret/src/core/EbmStatistics.h                     |   49 
 interpret-0.1.25/interpret/src/core/HistogramBucket.h                   |    2 
 interpret-0.1.25/interpret/src/core/InitializeResiduals.h               |    2 
 interpret-0.1.25/interpret/src/core/InteractionDetection.cpp            |   27 
 interpret-0.1.25/interpret/src/core/RandomStream.h                      |    3 
 interpret-0.1.25/interpret/src/core/SegmentedTensor.h                   |    4 
 interpret-0.1.25/interpret/src/core/TreeNode.h                          |    2 
 interpret-0.1.25/interpret/src/core/inc/ebmcore.h                       |   64 -
 interpret-0.1.25/interpret/src/interpret_R.cpp                          |  494 +++++-----
 38 files changed, 674 insertions(+), 603 deletions(-)

More information about interpret at CRAN
Permanent link

Package biomartr (with last version 0.9.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-12-10 0.9.1
2019-05-21 0.9.0

Permanent link
Package RMAWGEN updated to version 1.3.7 with previous version 1.3.6 dated 2019-11-15

Title: Multi-Site Auto-Regressive Weather GENerator
Description: S3 and S4 functions are implemented for spatial multi-site stochastic generation of daily time series of temperature and precipitation. These tools make use of Vector AutoRegressive models (VARs). The weather generator model is then saved as an object and is calibrated by daily instrumental "Gaussianized" time series through the 'vars' package tools. Once obtained this model, it can it can be used for weather generations and be adapted to work with several climatic monthly time series.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>

Diff between RMAWGEN versions 1.3.6 dated 2019-11-15 and 1.3.7 dated 2019-12-12

 DESCRIPTION       |   10 +++++-----
 MD5               |    6 +++---
 R/extractmonths.R |    2 +-
 data/trentino.rda |binary
 4 files changed, 9 insertions(+), 9 deletions(-)

More information about RMAWGEN at CRAN
Permanent link

Package partition updated to version 0.1.1 with previous version 0.1.0 dated 2019-05-17

Title: Agglomerative Partitioning Framework for Dimension Reduction
Description: A fast and flexible framework for agglomerative partitioning. 'partition' uses an approach called Direct-Measure-Reduce to create new variables that maintain the user-specified minimum level of information. Each reduced variable is also interpretable: the original variables map to one and only one variable in the reduced data set. 'partition' is flexible, as well: how variables are selected to reduce, how information loss is measured, and the way data is reduced can all be customized.
Author: Joshua Millstein [aut], Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>

Diff between partition versions 0.1.0 dated 2019-05-17 and 0.1.1 dated 2019-12-12

 DESCRIPTION                                    |   14 +--
 MD5                                            |   87 +++++++++++-----------
 NEWS.md                                        |only
 R/mappings.R                                   |    4 -
 R/metrics.R                                    |    1 
 R/plot.R                                       |    6 -
 README.md                                      |    9 ++
 build/vignette.rds                             |binary
 inst/WORDLIST                                  |    7 +
 inst/doc/extending-partition.R                 |   26 +++---
 inst/doc/extending-partition.html              |   38 +++++----
 inst/doc/introduction-to-partition.R           |   28 +++----
 inst/doc/introduction-to-partition.html        |   98 +++++++++++++------------
 man/as_director.Rd                             |    5 -
 man/as_measure.Rd                              |   22 +++--
 man/as_partition_step.Rd                       |   16 +++-
 man/as_partitioner.Rd                          |   11 +-
 man/as_reducer.Rd                              |   14 ++-
 man/assign_partition.Rd                        |    2 
 man/direct_distance.Rd                         |    5 -
 man/direct_k_cluster.Rd                        |   15 ++-
 man/hits.Rd                                    |    1 
 man/kmeans_helpers.Rd                          |    3 
 man/map_partition.Rd                           |    8 +-
 man/mapping_helpers.Rd                         |   11 ++
 man/measure_icc.Rd                             |   11 +-
 man/measure_min_icc.Rd                         |   10 +-
 man/measure_min_r2.Rd                          |   10 +-
 man/measure_std_mutualinfo.Rd                  |   10 +-
 man/measure_variance_explained.Rd              |   10 +-
 man/part_icc.Rd                                |   11 +-
 man/part_kmeans.Rd                             |   20 +++--
 man/part_minr2.Rd                              |   11 +-
 man/part_pc1.Rd                                |   11 +-
 man/part_stdmi.Rd                              |   11 +-
 man/partition.Rd                               |   17 +++-
 man/plot_partitions.Rd                         |   41 +++++++---
 man/plot_permutation.Rd                        |   12 ++-
 man/reduce_first_component.Rd                  |    7 +
 man/reduce_kmeans.Rd                           |   10 +-
 man/reduce_scaled_mean.Rd                      |    7 +
 man/replace_partitioner.Rd                     |   14 ++-
 man/simulate_block_data.Rd                     |   11 ++
 man/test_permutation.Rd                        |    9 +-
 tests/testthat/test-mappings-and-scores-work.R |    2 
 45 files changed, 402 insertions(+), 274 deletions(-)

More information about partition at CRAN
Permanent link

Package glmnetUtils updated to version 1.1.4 with previous version 1.1.3 dated 2019-11-18

Title: Utilities for 'Glmnet'
Description: Provides a formula interface for the 'glmnet' package for elasticnet regression, a method for cross-validating the alpha parameter, and other quality-of-life tools.
Author: Microsoft [cph], Hong Ooi [aut, cre]
Maintainer: Hong Ooi <hongooi@microsoft.com>

Diff between glmnetUtils versions 1.1.3 dated 2019-11-18 and 1.1.4 dated 2019-12-12

 DESCRIPTION         |    6 +--
 MD5                 |    8 ++--
 NEWS.md             |    4 ++
 R/glmnetFormula.r   |    2 -
 inst/doc/intro.html |  101 ++++------------------------------------------------
 5 files changed, 20 insertions(+), 101 deletions(-)

More information about glmnetUtils at CRAN
Permanent link

Package emojifont updated to version 0.5.3 with previous version 0.5.2 dated 2018-06-20

Title: Emoji and Font Awesome in Graphics
Description: An implementation of using emoji and fontawesome for using in both base and 'ggplot2' graphics.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), Claus Thorn Ekstrøm [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between emojifont versions 0.5.2 dated 2018-06-20 and 0.5.3 dated 2019-12-12

 DESCRIPTION             |    8 -
 MD5                     |   18 +--
 NEWS.md                 |    4 
 build/vignette.rds      |binary
 inst/doc/emojifont.R    |   18 +--
 inst/doc/emojifont.Rmd  |   12 --
 inst/doc/emojifont.html |  287 +++++++++++++++++++++++++++++-------------------
 man/geom_emoji.Rd       |   11 +
 man/geom_fontawesome.Rd |   10 +
 vignettes/emojifont.Rmd |   12 --
 10 files changed, 232 insertions(+), 148 deletions(-)

More information about emojifont at CRAN
Permanent link

Package StratifiedMedicine updated to version 0.2.1 with previous version 0.2.0 dated 2019-10-13

Title: Stratified Medicine
Description: A toolkit for stratified medicine, subgroup identification, and precision medicine. Current tools include (1) filtering models (reduce covariate space), (2) patient-level estimate models (counterfactual patient-level quantities, for example the individual treatment effect), (3) subgroup identification models (find subsets of patients with similar treatment effects), and (4) parameter estimation and inference (for the overall population and discovered subgroups). These tools can directly feed into stratified medicine algorithms including PRISM (patient response identifiers for stratified medicine; Jemielita and Mehrotra (2019) <arXiv:1912.03337>. PRISM is a flexible and general framework which accepts user-created models/functions. This package is in beta and will be continually updated.
Author: Thomas Jemielita [aut, cre]
Maintainer: Thomas Jemielita <thomasjemielita@gmail.com>

Diff between StratifiedMedicine versions 0.2.0 dated 2019-10-13 and 0.2.1 dated 2019-12-12

 StratifiedMedicine-0.2.0/StratifiedMedicine/R/model_template.R                      |only
 StratifiedMedicine-0.2.0/StratifiedMedicine/man/model_template.Rd                   |only
 StratifiedMedicine-0.2.1/StratifiedMedicine/DESCRIPTION                             |   16 
 StratifiedMedicine-0.2.1/StratifiedMedicine/MD5                                     |  104 +--
 StratifiedMedicine-0.2.1/StratifiedMedicine/NAMESPACE                               |    4 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/PRISM.R                               |   48 +
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/PRISM_resamp.R                        |    1 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/generate_subgrp_data.R                |   60 +-
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/param_dr.R                            |   32 -
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/param_ple.R                           |    5 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/param_rmst.R                          |    2 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/ple_bart.R                            |  181 ++++--
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/ple_ranger.R                          |   88 ++-
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/ple_rfsrc.R                           |only
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/ple_train.R                           |    3 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/plot.R                                |  154 ++++-
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_ctree.R                        |   11 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_glmtree.R                      |only
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_lmtree.R                       |   15 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_otr.R                          |    7 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_train.R                        |    3 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_weibull.R                      |   15 
 StratifiedMedicine-0.2.1/StratifiedMedicine/R/utils.R                               |  103 +--
 StratifiedMedicine-0.2.1/StratifiedMedicine/README.md                               |   80 +-
 StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_PRISM.R                     |   59 +-
 StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_PRISM.Rmd                   |  117 ++--
 StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_PRISM.html                  |  280 +++++-----
 StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_User_Models.R               |  108 ++-
 StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_User_Models.Rmd             |  110 ++-
 StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_User_Models.html            |  150 +++--
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/PRISM.Rd                            |   34 -
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/PRISM_resamp.Rd                     |   11 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/PRISM_train.Rd                      |    7 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-1.png        |binary
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-2.png        |binary
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-3.png        |binary
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-4.png        |binary
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-5.png        |binary
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-6.png        |binary
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/param_dr.Rd                         |   12 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/param_ple.Rd                        |    5 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/ple_bart.Rd                         |   16 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/ple_ranger.Rd                       |   13 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/ple_rfsrc.Rd                        |only
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/ple_train.Rd                        |    3 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/plot.PRISM.Rd                       |    7 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_ctree.Rd                     |   11 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_glmtree.Rd                   |only
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_lmtree.Rd                    |   13 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_otr.Rd                       |    7 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_train.Rd                     |    3 
 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_weibull.Rd                   |   12 
 StratifiedMedicine-0.2.1/StratifiedMedicine/tests/testthat/test-param_preds_plots.R |    2 
 StratifiedMedicine-0.2.1/StratifiedMedicine/tests/testthat/test-ple_preds_plots.R   |    4 
 StratifiedMedicine-0.2.1/StratifiedMedicine/vignettes/SM_PRISM.Rmd                  |  117 ++--
 StratifiedMedicine-0.2.1/StratifiedMedicine/vignettes/SM_User_Models.Rmd            |  110 ++-
 56 files changed, 1403 insertions(+), 740 deletions(-)

More information about StratifiedMedicine at CRAN
Permanent link

Package Rphylopars updated to version 0.2.12 with previous version 0.2.11 dated 2019-10-21

Title: Phylogenetic Comparative Tools for Missing Data and Within-Species Variation
Description: Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data. Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.
Author: Eric W. Goolsby, Jorn Bruggeman, Cecile Ane
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>

Diff between Rphylopars versions 0.2.11 dated 2019-10-21 and 0.2.12 dated 2019-12-12

 DESCRIPTION               |    8 ++---
 MD5                       |    8 ++---
 R/phylopars_main.R        |   64 ++++++++++++++++++++++++++++------------------
 R/phylopars_update.R      |   52 ++++++++++++++++++-------------------
 man/Rphylopars-package.Rd |    4 +-
 5 files changed, 75 insertions(+), 61 deletions(-)

More information about Rphylopars at CRAN
Permanent link

Package RFishBC updated to version 0.2.3 with previous version 0.2.2 dated 2019-05-02

Title: Back-Calculation of Fish Length
Description: Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated 'fishBC' software (<https://fisheries.org/bookstore/all-titles/software/70317/>).
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>)
Maintainer: Derek Ogle <derek@derekogle.com>

Diff between RFishBC versions 0.2.2 dated 2019-05-02 and 0.2.3 dated 2019-12-12

 DESCRIPTION               |   10 -
 MD5                       |   48 ++++----
 NAMESPACE                 |    2 
 NEWS.md                   |    4 
 R/digitizeRadii.R         |    2 
 R/getID.R                 |    2 
 man/FSA-internals.Rd      |   46 +++----
 man/RFBCoptions.Rd        |  184 +++++++++++++++----------------
 man/RFishBC.Rd            |   17 +-
 man/SMBassWB1.Rd          |   56 ++++-----
 man/SMBassWB2.Rd          |   70 +++++------
 man/StdIntLit.Rd          |   54 ++++-----
 man/aStandard.Rd          |   58 ++++-----
 man/addNote.Rd            |   58 ++++-----
 man/addRadCap.Rd          |   98 ++++++++--------
 man/backCalc.Rd           |  101 +++++++++--------
 man/bcFuns.Rd             |  144 ++++++++++++------------
 man/combineData.Rd        |   72 ++++++------
 man/digitizeRadii.Rd      |  269 +++++++++++++++++++++++++---------------------
 man/findNotes.Rd          |   54 ++++-----
 man/findScalingFactor.Rd  |  110 ++++++++++--------
 man/gConvert.Rd           |  135 +++++++++++------------
 man/getID.Rd              |  146 ++++++++++++------------
 man/listFiles.Rd          |   76 ++++++------
 man/showDigitizedImage.Rd |  147 +++++++++++++------------
 25 files changed, 1021 insertions(+), 942 deletions(-)

More information about RFishBC at CRAN
Permanent link

Package MBHdesign updated to version 2.1.6 with previous version 2.1.5 dated 2019-10-17

Title: Spatial Designs for Ecological and Environmental Surveys
Description: Provides spatially balanced designs from a set of (contiguous) potential sampling locations in a study region for point-based and for transect-based surveys. Accommodates, without detrimental effects on spatial balance, sites that the researcher wishes to include in the survey for reasons other than the current randomisation (legacy sites).
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@data61.csiro.au>

Diff between MBHdesign versions 2.1.5 dated 2019-10-17 and 2.1.6 dated 2019-12-12

 DESCRIPTION            |    6 +++---
 MD5                    |    8 ++++----
 R/FunsForTransect8.R   |    6 ++++--
 R/MBHdesign4.R         |    6 ++++--
 inst/doc/MBHdesign.pdf |binary
 5 files changed, 15 insertions(+), 11 deletions(-)

More information about MBHdesign at CRAN
Permanent link

Package BHSBVAR updated to version 2.0.1 with previous version 2.0.0 dated 2019-10-28

Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for estimating the parameters of Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>

Diff between BHSBVAR versions 2.0.0 dated 2019-10-28 and 2.0.1 dated 2019-12-12

 DESCRIPTION                    |   10 -
 MD5                            |   47 ++--
 NAMESPACE                      |   16 -
 NEWS                           |only
 R/BHSBVAR-package.R            |only
 R/BHSBVAR.R                    |  141 ++++++++------
 R/RcppExports.R                |    4 
 R/USLMData.R                   |    4 
 data/USLMData.rda              |binary
 inst/doc/BHSBVAR.R             |   12 -
 inst/doc/BHSBVAR.Rnw           |   35 +--
 inst/doc/BHSBVAR.pdf           |binary
 man/BHSBVAR-package.Rd         |only
 man/BH_SBVAR.Rd                |  390 +++++++++++++++++++++--------------------
 man/Dist_Plots.Rd              |  269 ++++++++++++++--------------
 man/HD_Plots.Rd                |  297 ++++++++++++++++---------------
 man/IRF_Plots.Rd               |  271 ++++++++++++++--------------
 man/USLMData.Rd                |   50 ++---
 src/BHSBVAR-init.c             |    4 
 src/BHSBVAR.cpp                |  143 +++++++--------
 src/RcppExports.cpp            |   10 -
 vignettes/BHSBVAR.Rnw          |   35 +--
 vignettes/fig/Dist_plots-1.pdf |binary
 vignettes/fig/HD_plots-1.pdf   |binary
 vignettes/fig/IRF_plots-1.pdf  |binary
 vignettes/fig/Model-1.pdf      |binary
 26 files changed, 896 insertions(+), 842 deletions(-)

More information about BHSBVAR at CRAN
Permanent link

Wed, 11 Dec 2019

Package tbm updated to version 0.3-2 with previous version 0.3-1 dated 2019-10-05

Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between tbm versions 0.3-1 dated 2019-10-05 and 0.3-2 dated 2019-12-11

 DESCRIPTION                 |    8 ++++----
 MD5                         |   12 ++++++------
 R/tbm.R                     |    4 +++-
 inst/NEWS.Rd                |    8 ++++++++
 inst/doc/tbm_supplement.pdf |binary
 tests/bodyfat.R             |    6 +++---
 tests/bodyfat.Rout.save     |   12 ++++++------
 7 files changed, 30 insertions(+), 20 deletions(-)

More information about tbm at CRAN
Permanent link

Package rmdfiltr updated to version 0.1.2 with previous version 0.1.1 dated 2019-12-09

Title: 'Lua' filters for R Markdown
Description: A collection of 'Lua' filters that extend the functionality of R Markdown templates (e.g., count words or post-process 'pandoc-citeproc'- citations).
Author: Frederik Aust [aut, cre] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>

Diff between rmdfiltr versions 0.1.1 dated 2019-12-09 and 0.1.2 dated 2019-12-11

 rmdfiltr-0.1.1/rmdfiltr/man/verify_pandoc_version.Rd                |only
 rmdfiltr-0.1.2/rmdfiltr/DESCRIPTION                                 |    6 -
 rmdfiltr-0.1.2/rmdfiltr/MD5                                         |   27 ++--
 rmdfiltr-0.1.2/rmdfiltr/NAMESPACE                                   |    1 
 rmdfiltr-0.1.2/rmdfiltr/R/add_lua_filter.R                          |    8 +
 rmdfiltr-0.1.2/rmdfiltr/R/utils.R                                   |   58 +++++-----
 rmdfiltr-0.1.2/rmdfiltr/inst/doc/replace_ampersands.R               |   16 +-
 rmdfiltr-0.1.2/rmdfiltr/inst/doc/replace_ampersands.Rmd             |    7 +
 rmdfiltr-0.1.2/rmdfiltr/inst/doc/replace_ampersands.html            |   21 +--
 rmdfiltr-0.1.2/rmdfiltr/inst/doc/wordcount.R                        |   16 +-
 rmdfiltr-0.1.2/rmdfiltr/inst/doc/wordcount.Rmd                      |    7 +
 rmdfiltr-0.1.2/rmdfiltr/inst/doc/wordcount.html                     |   23 +--
 rmdfiltr-0.1.2/rmdfiltr/tests/testthat/test_convenience_functions.R |    2 
 rmdfiltr-0.1.2/rmdfiltr/vignettes/replace_ampersands.Rmd            |    7 +
 rmdfiltr-0.1.2/rmdfiltr/vignettes/wordcount.Rmd                     |    7 +
 15 files changed, 118 insertions(+), 88 deletions(-)

More information about rmdfiltr at CRAN
Permanent link

Package openblender updated to version 0.3.4 with previous version 0.3.3 dated 2019-12-06

Title: Request <https://openblender.io> API Services
Description: Interface to make HTTP requests to 'OpenBlender' API services. Go to <https://openblender.io> for more information.
Author: Open Blender Inc. [cph], Daniel V. Pinacho [aut, cre]
Maintainer: Daniel V. Pinacho <danielvpinacho@gmail.com>

Diff between openblender versions 0.3.3 dated 2019-12-06 and 0.3.4 dated 2019-12-11

 DESCRIPTION          |    6 +++---
 MD5                  |    6 +++---
 R/get_observations.R |   16 ++++++++++++++++
 R/utils.R            |   10 ++--------
 4 files changed, 24 insertions(+), 14 deletions(-)

More information about openblender at CRAN
Permanent link

Package newsmap updated to version 0.7.0 with previous version 0.6.9 dated 2019-07-29

Title: Semi-Supervised Model for Geographical Document Classification
Description: Semi-supervised model for geographical document classification (Watanabe 2018) <doi:10.1080/21670811.2017.1293487>. This package currently contains seed dictionaries in English, German, French, Spanish, Russian, Hebrew, Arabic Japanese and Chinese (Simplified and Traditional).
Author: Kohei Watanabe [aut, cre, cph], Stefan Müller [aut], Dani Madrid-Morales [aut], Katerina Tertytchnaya [aut], Ke Cheng [aut], Chung-hong Chan [aut], Claude Grasland [aut], Giuseppe Carteny [aut], Elad Segev [aut], Dai Yamao [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>

Diff between newsmap versions 0.6.9 dated 2019-07-29 and 0.7.0 dated 2019-12-11

 DESCRIPTION                             |   23 +++++++++++----------
 MD5                                     |   20 ++++++++++--------
 NEWS.md                                 |    4 +++
 R/data.R                                |   16 ++++++++++++++
 README.md                               |   19 ++++++++---------
 data/data_dictionary_newsmap_ar.RData   |only
 data/data_dictionary_newsmap_he.RData   |only
 man/data_dictionary_newsmap_ar.Rd       |only
 man/data_dictionary_newsmap_he.Rd       |only
 man/predict.textmodel_newsmap.Rd        |   10 +++++++--
 man/textmodel_newsmap.Rd                |    3 --
 tests/testthat/test-data.R              |   31 +++++++++++++++++++---------
 tests/testthat/test-textmodel_newsmap.R |   35 +++++++++++++++++++++++++++++++-
 13 files changed, 118 insertions(+), 43 deletions(-)

More information about newsmap at CRAN
Permanent link

Package dslabs updated to version 0.7.2 with previous version 0.7.1 dated 2019-07-14

Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Author: Rafael A. Irizarry, Amy Gill
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>

Diff between dslabs versions 0.7.1 dated 2019-07-14 and 0.7.2 dated 2019-12-11

 DESCRIPTION                          |    8 ++++----
 MD5                                  |    6 +++---
 data/divorce_margarine.rda           |binary
 inst/script/make-divorce_margarine.R |    6 +++---
 4 files changed, 10 insertions(+), 10 deletions(-)

More information about dslabs at CRAN
Permanent link

Package LPower updated to version 0.1.1 with previous version 0.1.0 dated 2018-05-11

Title: Calculates Power, Sample Size, or Detectable Effect for Longitudinal Analyses
Description: Computes power, or sample size or the detectable difference for a repeated measures model with attrition. It requires the variance covariance matrix of the observations but can compute this matrix for several common random effects models. See Diggle, P, Liang, KY and Zeger, SL (1994, ISBN:9780198522843).
Author: David A. Schoenfeld
Maintainer: David A. Schoenfeld <Dschoenfeld@mgh.harvard.edu>

Diff between LPower versions 0.1.0 dated 2018-05-11 and 0.1.1 dated 2019-12-11

 DESCRIPTION        |    6 +++---
 MD5                |    5 +++--
 R/powslopes_new1.R |    8 ++++----
 R/powslopes_new2.R |only
 4 files changed, 10 insertions(+), 9 deletions(-)

More information about LPower at CRAN
Permanent link

Package qgcomp updated to version 1.3.0 with previous version 1.2.0 dated 2019-11-12

Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures with quantile-based basis functions, possibly under linearity and homogeneity assumptions. This approach estimates a regression line corresponding to the expected change in the outcome (on the link basis) given a simultaneous increase in the quantile-based category for all exposures. Works with continuous, binary, and right-censored time-to-event outcomes. Reference: Alexander P. Keil, Jessie P. Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao Alexandra J. White (2019) A quantile-based g-computation approach to addressing the effects of exposure mixtures; <arXiv:1902.04200> [stat.ME].
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>

Diff between qgcomp versions 1.2.0 dated 2019-11-12 and 1.3.0 dated 2019-12-11

 DESCRIPTION                   |    8 -
 MD5                           |   44 +++---
 NAMESPACE                     |    4 
 NEWS.md                       |   12 +
 R/base.R                      |  291 +++++++++++++++++++++++++++++-------------
 R/base_surv.R                 |   97 ++++++++------
 R/data.R                      |    3 
 inst/doc/qgcomp-vignette.R    |   47 ++++--
 inst/doc/qgcomp-vignette.Rmd  |  126 +++++++++++-------
 inst/doc/qgcomp-vignette.html |  197 +++++++++++++++++-----------
 man/coxmsm.fit.Rd             |    4 
 man/metals.Rd                 |    3 
 man/msm.fit.Rd                |    2 
 man/msm.predict.Rd            |    2 
 man/plot.qgcompfit.Rd         |   18 ++
 man/predict.qgcompfit.Rd      |    3 
 man/qgcomp.Rd                 |   20 ++
 man/qgcomp.cox.boot.Rd        |   26 ++-
 man/qgcomp.cox.noboot.Rd      |   14 +-
 man/se_comb.Rd                |   30 ++--
 tests/test_asis.R             |only
 tests/test_boot_vs_noboot.R   |    9 -
 tests/test_cox_msmtest.R      |only
 vignettes/qgcomp-vignette.Rmd |  126 +++++++++++-------
 24 files changed, 724 insertions(+), 362 deletions(-)

More information about qgcomp at CRAN
Permanent link

Package paleofire updated to version 1.2.4 with previous version 1.2.3 dated 2019-01-08

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@gmail.com>
Maintainer: Olivier Blarquez <blarquez@gmail.com>

Diff between paleofire versions 1.2.3 dated 2019-01-08 and 1.2.4 dated 2019-12-11

 DESCRIPTION                  |   12 +-
 MD5                          |   84 ++++++++++----------
 NEWS                         |    6 +
 R/SEA.R                      |   16 +++
 R/kdffreq.R                  |   17 ++--
 R/paleofire-package.R        |    6 +
 R/pfCircular.R               |    2 
 R/pfCompositeLF.R            |   23 +++--
 R/pfDotMap.r                 |    2 
 R/pfGridding.R               |  174 +++++++++++++++++++++++--------------------
 R/pfSimpleGrid.r             |    2 
 R/pfSiteSel.R                |    4 
 R/pfTransform.R              |   95 ++++++++++++-----------
 R/potveg.R                   |    1 
 R/pretreatment.R             |    6 -
 R/zzz.R                      |    1 
 build/vignette.rds           |binary
 inst/doc/paleofire-paper.pdf |binary
 man/SEA.Rd                   |   17 +++-
 man/checkGCDversion.Rd       |    2 
 man/kdffreq.Rd               |   18 +++-
 man/paleofire-package.Rd     |   10 +-
 man/pfAddData.Rd             |   14 ++-
 man/pfCircular.Rd            |    3 
 man/pfComposite.Rd           |    9 +-
 man/pfCompositeLF.Rd         |   13 ++-
 man/pfDiagnostic.Rd          |   21 +++--
 man/pfDotMap.Rd              |   20 +++-
 man/pfGridding.Rd            |   19 +++-
 man/pfKruskal.Rd             |    3 
 man/pfSimpleGrid.Rd          |   33 +++++---
 man/pfTransform.Rd           |   22 ++++-
 man/plot.CHAR.Rd             |   16 +++
 man/plot.kdffreq.Rd          |   14 ++-
 man/plot.pfCircular.Rd       |   12 ++
 man/plot.pfComposite.Rd      |   12 ++
 man/plot.pfCompositeLF.Rd    |   16 +++
 man/plot.pfGridding.Rd       |   21 ++++-
 man/plot.pfKruskal.Rd        |    3 
 man/plot.pfSiteSel.Rd        |   16 +++
 man/plot.potveg.Rd           |   11 ++
 man/potveg.Rd                |    2 
 man/pretreatment.Rd          |   10 +-
 43 files changed, 513 insertions(+), 275 deletions(-)

More information about paleofire at CRAN
Permanent link

Package nima updated to version 0.6.1 with previous version 0.5.0 dated 2018-05-21

Title: Nima Hejazi's R Toolbox
Description: Miscellaneous R functions developed as collateral damage over the course of work in statistical and scientific computing for research. These include, for example, utilities that supplement existing idiosyncrasies of the R language, extend existing plotting functionality and aesthetics, help prepare data objects for imputation, and extend access to command line tools and systems-level information.
Author: Nima Hejazi [aut, cre, cph] (<https://orcid.org/0000-0002-7127-2789>)
Maintainer: Nima Hejazi <nh@nimahejazi.org>

Diff between nima versions 0.5.0 dated 2018-05-21 and 0.6.1 dated 2019-12-11

 nima-0.5.0/nima/R/compare.R                                |only
 nima-0.5.0/nima/R/factornum.R                              |only
 nima-0.5.0/nima/R/mse.R                                    |only
 nima-0.5.0/nima/R/qrDecomp.R                               |only
 nima-0.5.0/nima/R/utilities.R                              |only
 nima-0.5.0/nima/man/compFun.Rd                             |only
 nima-0.5.0/nima/man/factornum.Rd                           |only
 nima-0.5.0/nima/man/lmPlots_gg.Rd                          |only
 nima-0.5.0/nima/man/qqPlot_gg.Rd                           |only
 nima-0.5.0/nima/man/qrD.Rd                                 |only
 nima-0.5.0/nima/tests/testthat/test-compare.R              |only
 nima-0.5.0/nima/tests/testthat/test-factornum.R            |only
 nima-0.5.0/nima/tests/testthat/test-ggPlots.R              |only
 nima-0.5.0/nima/tests/testthat/test-qrDecomp.R             |only
 nima-0.6.1/nima/DESCRIPTION                                |   29 +-
 nima-0.6.1/nima/LICENSE                                    |    2 
 nima-0.6.1/nima/MD5                                        |   79 +++---
 nima-0.6.1/nima/NAMESPACE                                  |   21 +
 nima-0.6.1/nima/NEWS.md                                    |   65 ++++-
 nima-0.6.1/nima/R/absmax.R                                 |    1 
 nima-0.6.1/nima/R/attribute_names.R                        |    3 
 nima-0.6.1/nima/R/commas.R                                 |    1 
 nima-0.6.1/nima/R/discrete_by_quantile.R                   |   10 
 nima-0.6.1/nima/R/factor_to_numeric.R                      |only
 nima-0.6.1/nima/R/missing_ind.R                            |    1 
 nima-0.6.1/nima/R/plots.R                                  |  156 +++++++------
 nima-0.6.1/nima/R/risk.R                                   |only
 nima-0.6.1/nima/R/simulation_tools.R                       |only
 nima-0.6.1/nima/R/theme_jetblack.R                         |    8 
 nima-0.6.1/nima/R/theme_nima.R                             |    1 
 nima-0.6.1/nima/R/uniqlen.R                                |    1 
 nima-0.6.1/nima/R/utils.R                                  |only
 nima-0.6.1/nima/man/attrnames.Rd                           |    2 
 nima-0.6.1/nima/man/clear.Rd                               |    7 
 nima-0.6.1/nima/man/discrete_by_quantile.Rd                |    6 
 nima-0.6.1/nima/man/exit.Rd                                |    2 
 nima-0.6.1/nima/man/factor_to_num.Rd                       |only
 nima-0.6.1/nima/man/hweb.Rd                                |    6 
 nima-0.6.1/nima/man/lm_plot.Rd                             |only
 nima-0.6.1/nima/man/mse.Rd                                 |    6 
 nima-0.6.1/nima/man/nll.Rd                                 |only
 nima-0.6.1/nima/man/openfile.Rd                            |    7 
 nima-0.6.1/nima/man/qq_plot.Rd                             |only
 nima-0.6.1/nima/man/sim_plot.Rd                            |only
 nima-0.6.1/nima/man/summarize_sim.Rd                       |only
 nima-0.6.1/nima/man/theme_jetblack.Rd                      |    1 
 nima-0.6.1/nima/man/theme_nima.Rd                          |    1 
 nima-0.6.1/nima/tests/testthat/test-absmax.R               |    1 
 nima-0.6.1/nima/tests/testthat/test-commas.R               |    1 
 nima-0.6.1/nima/tests/testthat/test-discrete_by_quantile.R |    1 
 nima-0.6.1/nima/tests/testthat/test-factor_to_num.R        |only
 nima-0.6.1/nima/tests/testthat/test-missing_ind.R          |   18 -
 nima-0.6.1/nima/tests/testthat/test-uniqlen.R              |    1 
 53 files changed, 261 insertions(+), 177 deletions(-)

More information about nima at CRAN
Permanent link

Package GCD updated to version 4.0.5 with previous version 4.0.4 dated 2018-11-28

Title: Global Charcoal Database
Description: Contains the Global Charcoal database data. Data include charcoal series (age, depth, charcoal quantity, associated units and methods) and information on sedimentary sites (localisation, depositional environment, biome, etc.) as well as publications informations. Since 4.0.0 the GCD mirrors the online SQL database at <http://paleofire.org>.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>

Diff between GCD versions 4.0.4 dated 2018-11-28 and 4.0.5 dated 2019-12-11

 DESCRIPTION             |   10 +++---
 MD5                     |   26 ++++++++++-------
 NEWS                    |   33 +++++++++++++++++++++-
 R/GCD-package.R         |   70 +++++++++++++++++++++++++++++++++++++++++++++++-
 data/datalist           |    3 ++
 data/date.rda           |only
 data/date_type.rda      |only
 data/mat_dated.rda      |only
 data/paleofiredata.rda  |binary
 data/paleofiresites.rda |binary
 data/pub.rda            |binary
 data/pub_key.rda        |binary
 data/release.rda        |binary
 man/GCD-package.Rd      |   10 +++---
 man/date.Rd             |only
 man/date_type.Rd        |only
 man/mat_dated.Rd        |only
 17 files changed, 130 insertions(+), 22 deletions(-)

More information about GCD at CRAN
Permanent link

Package RgoogleMaps updated to version 1.4.5 with previous version 1.4.4 dated 2019-08-20

Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>

Diff between RgoogleMaps versions 1.4.4 dated 2019-08-20 and 1.4.5 dated 2019-12-11

 DESCRIPTION               |   12 ++-
 MD5                       |   39 ++++++-----
 R/GetBingMap.R            |    2 
 R/GetMap.R                |    9 +-
 R/GetMap.bbox.R           |    7 +-
 R/GetMapTiles.R           |  145 ++++++++++++++++++++++++++++++-------------
 R/LatLon2XY.centered.R    |   26 +++----
 R/PlotOnMapTiles.R        |   36 ++++++++--
 R/PlotOnStaticMap.R       |   10 +--
 R/genStaticMap.R          |   18 ++++-
 R/getGeoCode.R            |  153 ++++++++++++++++++++++++++--------------------
 R/plotOSM.R               |only
 man/GetBingMap.Rd         |    2 
 man/GetMap.Rd             |   12 ++-
 man/GetMap.bbox.Rd        |   11 ++-
 man/GetMapTiles.Rd        |  109 ++++++++++++++++++++++----------
 man/PlotOnMapTiles.Rd     |   10 +--
 man/genStaticMap.Rd       |   13 ++-
 man/geosphere_mercator.Rd |only
 man/getGeoCode.Rd         |    8 +-
 man/osmtile_bbox.Rd       |only
 man/plotOSM.Rd            |only
 man/plotOSMtile.Rd        |only
 23 files changed, 399 insertions(+), 223 deletions(-)

More information about RgoogleMaps at CRAN
Permanent link

Package DatabionicSwarm updated to version 1.1.2 with previous version 1.1.1 dated 2019-01-27

Title: Swarm Intelligence for Self-Organized Clustering
Description: Algorithms implementing populations of agents that interact with one another and sense their environment may exhibit emergent behavior such as self-organization and swarm intelligence. Here, a swarm system called databionic swarm (DBS) is introduced. DBS is able to adapt itself to structures of high-dimensional data such as natural clusters characterized by distance and/or density based structures in the data space. The first module is the parameter-free projection method called Pswarm (Pswarm()), which exploits the concepts of self-organization and emergence, game theory, swarm intelligence and symmetry considerations. The second module is the parameter-free high-dimensional data visualization technique, which generates projected points on the topographic map with hypsometric tints defined by the generalized U-matrix (GeneratePswarmVisualization()). The third module is the clustering method itself with non-critical parameters (DBSclustering()). Clustering can be verified by the visualization and vice versa. The term DBS refers to the method as a whole. It enables even a non-professional in the field of data mining to apply its algorithms for visualization and/or clustering to data sets with completely different structures drawn from diverse research fields. The package is based on the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>. A comparison to 26 common clustering algorithms on 15 datasets is presented on the website.
Author: Michael Thrun [aut, cre, cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>

Diff between DatabionicSwarm versions 1.1.1 dated 2019-01-27 and 1.1.2 dated 2019-12-11

 DatabionicSwarm-1.1.1/DatabionicSwarm/R/MultipleSwarms.R            |only
 DatabionicSwarm-1.1.2/DatabionicSwarm/DESCRIPTION                   |   10 
 DatabionicSwarm-1.1.2/DatabionicSwarm/MD5                           |   33 
 DatabionicSwarm-1.1.2/DatabionicSwarm/NAMESPACE                     |    2 
 DatabionicSwarm-1.1.2/DatabionicSwarm/R/DBSclustering.R             |   23 
 DatabionicSwarm-1.1.2/DatabionicSwarm/R/Delaunay4Points.R           |    2 
 DatabionicSwarm-1.1.2/DatabionicSwarm/R/RobustNorm_BackTrafo.R      |only
 DatabionicSwarm-1.1.2/DatabionicSwarm/R/RobustNormalization.R       |   57 
 DatabionicSwarm-1.1.2/DatabionicSwarm/build/partial.rdb             |binary
 DatabionicSwarm-1.1.2/DatabionicSwarm/build/vignette.rds            |binary
 DatabionicSwarm-1.1.2/DatabionicSwarm/inst/NEWS                     |   11 
 DatabionicSwarm-1.1.2/DatabionicSwarm/inst/doc/DatabionicSwarm.R    |   42 
 DatabionicSwarm-1.1.2/DatabionicSwarm/inst/doc/DatabionicSwarm.Rmd  |  131 
 DatabionicSwarm-1.1.2/DatabionicSwarm/inst/doc/DatabionicSwarm.html | 1798 +++++++++-
 DatabionicSwarm-1.1.2/DatabionicSwarm/man/Hepta.Rd                  |    6 
 DatabionicSwarm-1.1.2/DatabionicSwarm/man/RobustNorm_BackTrafo.Rd   |only
 DatabionicSwarm-1.1.2/DatabionicSwarm/man/RobustNormalization.Rd    |   29 
 DatabionicSwarm-1.1.2/DatabionicSwarm/man/setGridSize.Rd            |    5 
 DatabionicSwarm-1.1.2/DatabionicSwarm/vignettes/DatabionicSwarm.Rmd |  131 
 19 files changed, 1946 insertions(+), 334 deletions(-)

More information about DatabionicSwarm at CRAN
Permanent link

Package erhcv (with last version 0.1.4) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-12-10 0.1.4
2018-10-07 0.1.3
2018-06-12 0.1.2
2018-06-10 0.1.1

Permanent link
Package uGMAR updated to version 3.2.1 with previous version 3.2.0 dated 2019-08-27

Title: Estimate Univariate Gaussian or Student's t Mixture Autoregressive Model
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR), Student's t Mixture Autoregressive (StMAR) and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models, quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes. Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>, Mika Meitz, Daniel Preve, Pentti Saikkonen (2018) <arXiv:1805.04010>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>

Diff between uGMAR versions 3.2.0 dated 2019-08-27 and 3.2.1 dated 2019-12-11

 DESCRIPTION                          |    6 +++---
 MD5                                  |    8 ++++----
 NEWS.md                              |    4 ++++
 inst/doc/intro-to-uGMAR.html         |    4 ++--
 tests/testthat/test_standardErrors.R |   28 ++++++++++++++--------------
 5 files changed, 27 insertions(+), 23 deletions(-)

More information about uGMAR at CRAN
Permanent link

Package spacesRGB updated to version 1.3-0 with previous version 1.2-2 dated 2019-01-30

Title: Standard and User-Defined RGB Color Spaces, with Conversion Between RGB and CIE XYZ
Description: Standard RGB spaces included are sRGB, 'Adobe' RGB, 'ProPhoto' RGB, BT.709, and others. User-defined RGB spaces are also possible. There is partial support for ACES Color workflows.
Author: Glenn Davis [aut,cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>

Diff between spacesRGB versions 1.2-2 dated 2019-01-30 and 1.3-0 dated 2019-12-11

 DESCRIPTION                   |    8 ++---
 MD5                           |   14 +++++----
 NEWS.md                       |    4 ++
 build/vignette.rds            |binary
 inst/doc/spacesRGB-guide.R    |only
 inst/doc/spacesRGB-guide.html |   62 ++++++++++++++++++++++++++++++------------
 tests/CGATS.RR                |only
 tests/test-ACES.R             |    7 +++-
 tests/test-conversions.R      |    4 +-
 9 files changed, 68 insertions(+), 31 deletions(-)

More information about spacesRGB at CRAN
Permanent link

Package landscapemetrics updated to version 1.4 with previous version 1.3 dated 2019-11-07

Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>) and new ones from the current literature on landscape metrics. This package supports 'raster' spatial objects and takes RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the 'raster' package as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre] (<https://orcid.org/0000-0003-1125-9918>), Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>), Laura J. Graham [ctb] (Input on package structure), Jeffrey Hollister [ctb] (Input on package structure), Kimberly A. With [ctb] (Input on package structure), Florian Privé [ctb] (Original author of underlying C++ code for get_nearestneighbour() function), Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>

Diff between landscapemetrics versions 1.3 dated 2019-11-07 and 1.4 dated 2019-12-11

 landscapemetrics-1.3/landscapemetrics/src/cclabel_4.c                                   |only
 landscapemetrics-1.3/landscapemetrics/src/cclabel_8.c                                   |only
 landscapemetrics-1.4/landscapemetrics/DESCRIPTION                                       |   15 
 landscapemetrics-1.4/landscapemetrics/MD5                                               | 1043 +-
 landscapemetrics-1.4/landscapemetrics/NAMESPACE                                         | 1888 ++--
 landscapemetrics-1.4/landscapemetrics/NEWS.md                                           |  278 
 landscapemetrics-1.4/landscapemetrics/R/RcppExports.R                                   |  206 
 landscapemetrics-1.4/landscapemetrics/R/calculate_correlation.R                         |  364 
 landscapemetrics-1.4/landscapemetrics/R/calculate_lsm.R                                 |  932 +-
 landscapemetrics-1.4/landscapemetrics/R/check_landscape.R                               |  325 
 landscapemetrics-1.4/landscapemetrics/R/construct_buffer.R                              |  374 
 landscapemetrics-1.4/landscapemetrics/R/data.R                                          |  250 
 landscapemetrics-1.4/landscapemetrics/R/data_info.R                                     |   84 
 landscapemetrics-1.4/landscapemetrics/R/extract_lsm.R                                   |  869 +-
 landscapemetrics-1.4/landscapemetrics/R/get_adjacencies.R                               |  533 -
 landscapemetrics-1.4/landscapemetrics/R/get_boundaries.R                                |  524 -
 landscapemetrics-1.4/landscapemetrics/R/get_circumscribingcircle.R                      |  402 -
 landscapemetrics-1.4/landscapemetrics/R/get_nearestneighbour.R                          |  452 -
 landscapemetrics-1.4/landscapemetrics/R/get_patches.R                                   |  672 -
 landscapemetrics-1.4/landscapemetrics/R/get_unique_values.R                             |  501 -
 landscapemetrics-1.4/landscapemetrics/R/landscapemetrics-package.R                      |  110 
 landscapemetrics-1.4/landscapemetrics/R/list_lsm.R                                      |  410 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_ai.R                                      |  351 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_area_cv.R                                 |  303 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_area_mn.R                                 |  305 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_area_sd.R                                 |  303 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_ca.R                                      |  301 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_cai_cv.R                                  |  341 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_cai_mn.R                                  |  335 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_cai_sd.R                                  |  339 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_circle_cv.R                               |  323 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_circle_mn.R                               |  317 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_circle_sd.R                               |  318 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_clumpy.R                                  |  393 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_cohesion.R                                |  364 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_contig_cv.R                               |  320 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_contig_mn.R                               |  319 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_contig_sd.R                               |  321 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_core_cv.R                                 |  334 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_core_mn.R                                 |  328 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_core_sd.R                                 |  332 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_cpland.R                                  |  361 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_dcad.R                                    |  357 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_dcore_cv.R                                |  339 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_dcore_mn.R                                |  332 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_dcore_sd.R                                |  342 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_division.R                                |  318 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_ed.R                                      |  364 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_enn_cv.R                                  |  328 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_enn_mn.R                                  |  330 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_enn_sd.R                                  |  330 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_frac_cv.R                                 |  310 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_frac_mn.R                                 |  303 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_frac_sd.R                                 |  308 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_gyrate_cv.R                               |  315 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_gyrate_mn.R                               |  314 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_gyrate_sd.R                               |  313 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_iji.R                                     |  356 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_lpi.R                                     |  307 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_lsi.R                                     |  367 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_mesh.R                                    |  323 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_ndca.R                                    |  337 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_nlsi.R                                    |  393 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_np.R                                      |  315 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_pafrac.R                                  |  402 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_para_cv.R                                 |  303 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_para_mn.R                                 |  303 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_para_sd.R                                 |  304 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_pd.R                                      |  322 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_pladj.R                                   |  305 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_pland.R                                   |  295 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_shape_cv.R                                |  312 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_shape_mn.R                                |  311 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_shape_sd.R                                |  312 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_split.R                                   |  319 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_tca.R                                     |  330 
 landscapemetrics-1.4/landscapemetrics/R/lsm_c_te.R                                      |  488 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_ai.R                                      |  308 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_area_cv.R                                 |  301 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_area_mn.R                                 |  307 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_area_sd.R                                 |  305 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_cai_cv.R                                  |  369 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_cai_mn.R                                  |  364 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_cai_sd.R                                  |  368 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_circle_cv.R                               |  315 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_circle_mn.R                               |  313 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_circle_sd.R                               |  318 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_cohesion.R                                |  336 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_condent.R                                 |  361 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_contag.R                                  |  358 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_contig_cv.R                               |  321 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_contig_mn.R                               |  319 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_contig_sd.R                               |  321 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_core_cv.R                                 |  363 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_core_mn.R                                 |  359 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_core_sd.R                                 |  361 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_dcad.R                                    |  381 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_dcore_cv.R                                |  369 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_dcore_mn.R                                |  363 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_dcore_sd.R                                |  367 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_division.R                                |  313 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_ed.R                                      |  354 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_enn_cv.R                                  |  325 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_enn_mn.R                                  |  325 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_enn_sd.R                                  |  325 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_ent.R                                     |  315 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_frac_cv.R                                 |  309 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_frac_mn.R                                 |  307 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_frac_sd.R                                 |  307 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_gyrate_cv.R                               |  315 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_gyrate_mn.R                               |  312 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_gyrate_sd.R                               |  313 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_iji.R                                     |  360 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_joinent.R                                 |  343 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_lpi.R                                     |  301 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_lsi.R                                     |  361 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_mesh.R                                    |  311 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_msidi.R                                   |  312 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_msiei.R                                   |  302 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_mutinf.R                                  |  359 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_ndca.R                                    |  361 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_np.R                                      |  283 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_pafrac.R                                  |  388 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_para_cv.R                                 |  303 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_para_mn.R                                 |  303 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_para_sd.R                                 |  303 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_pd.R                                      |  328 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_pladj.R                                   |  295 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_pr.R                                      |  259 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_prd.R                                     |  299 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_rpr.R                                     |  320 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_shape_cv.R                                |  311 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_shape_mn.R                                |  309 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_shape_sd.R                                |  309 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_shdi.R                                    |  287 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_shei.R                                    |  287 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_sidi.R                                    |  295 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_siei.R                                    |  299 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_split.R                                   |  307 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_ta.R                                      |  287 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_tca.R                                     |  357 
 landscapemetrics-1.4/landscapemetrics/R/lsm_l_te.R                                      |  383 
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_area.R                                    |  355 
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_cai.R                                     |  408 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_circle.R                                  |  453 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_contig.R                                  |  435 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_core.R                                    |  464 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_enn.R                                     |  473 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_frac.R                                    |  346 
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_gyrate.R                                  |  413 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_ncore.R                                   |  569 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_para.R                                    |  331 
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_perim.R                                   |  437 -
 landscapemetrics-1.4/landscapemetrics/R/lsm_p_shape.R                                   |  373 
 landscapemetrics-1.4/landscapemetrics/R/matrix_to_raster.R                              |  164 
 landscapemetrics-1.4/landscapemetrics/R/onUnload.R                                      |   16 
 landscapemetrics-1.4/landscapemetrics/R/options_landscapemetrics.R                      |   64 
 landscapemetrics-1.4/landscapemetrics/R/pad_raster.R                                    |  548 -
 landscapemetrics-1.4/landscapemetrics/R/proj_info.R                                     |  104 
 landscapemetrics-1.4/landscapemetrics/R/raster_to_points.R                              |  317 
 landscapemetrics-1.4/landscapemetrics/R/sample_lsm.R                                    | 1083 +-
 landscapemetrics-1.4/landscapemetrics/R/scale_sample.R                                  |  798 +-
 landscapemetrics-1.4/landscapemetrics/R/scale_window.R                                  |  763 -
 landscapemetrics-1.4/landscapemetrics/R/show_cores.R                                    |  578 -
 landscapemetrics-1.4/landscapemetrics/R/show_correlation.R                              |  588 -
 landscapemetrics-1.4/landscapemetrics/R/show_lsm.R                                      |  624 -
 landscapemetrics-1.4/landscapemetrics/R/show_patches.R                                  |  446 -
 landscapemetrics-1.4/landscapemetrics/R/spatialize_lsm.R                                |  612 -
 landscapemetrics-1.4/landscapemetrics/R/unpad_raster.R                                  |  478 -
 landscapemetrics-1.4/landscapemetrics/R/window_lsm.R                                    | 1102 +-
 landscapemetrics-1.4/landscapemetrics/build/vignette.rds                                |binary
 landscapemetrics-1.4/landscapemetrics/inst/CITATION                                     |   30 
 landscapemetrics-1.4/landscapemetrics/inst/doc/getstarted.R                             |  190 
 landscapemetrics-1.4/landscapemetrics/inst/doc/getstarted.Rmd                           |  364 
 landscapemetrics-1.4/landscapemetrics/inst/doc/getstarted.html                          | 1197 +--
 landscapemetrics-1.4/landscapemetrics/man/augusta_nlcd.Rd                               |   42 
 landscapemetrics-1.4/landscapemetrics/man/calculate_correlation.Rd                      |   72 
 landscapemetrics-1.4/landscapemetrics/man/calculate_lsm.Rd                              |  329 
 landscapemetrics-1.4/landscapemetrics/man/check_landscape.Rd                            |   96 
 landscapemetrics-1.4/landscapemetrics/man/construct_buffer.Rd                           |  113 
 landscapemetrics-1.4/landscapemetrics/man/data_info.Rd                                  |   54 
 landscapemetrics-1.4/landscapemetrics/man/extract_lsm.Rd                                |  257 
 landscapemetrics-1.4/landscapemetrics/man/figures/README-unnamed-chunk-1-1.png          |binary
 landscapemetrics-1.4/landscapemetrics/man/figures/REAsDME-unnamed-chunk-1-1.png         |only
 landscapemetrics-1.4/landscapemetrics/man/fragstats_class_augusta_nlcd.Rd               |   32 
 landscapemetrics-1.4/landscapemetrics/man/fragstats_class_landscape.Rd                  |   32 
 landscapemetrics-1.4/landscapemetrics/man/fragstats_class_podlasie.Rd                   |   32 
 landscapemetrics-1.4/landscapemetrics/man/fragstats_landscape_augusta_nlcd.Rd           |   32 
 landscapemetrics-1.4/landscapemetrics/man/fragstats_landscape_landscape.Rd              |   32 
 landscapemetrics-1.4/landscapemetrics/man/fragstats_landscape_podlasie.Rd               |   32 
 landscapemetrics-1.4/landscapemetrics/man/fragstats_patch_augusta_nlcd.Rd               |   32 
 landscapemetrics-1.4/landscapemetrics/man/fragstats_patch_landscape.Rd                  |   32 
 landscapemetrics-1.4/landscapemetrics/man/fragstats_patch_podlasie.Rd                   |   32 
 landscapemetrics-1.4/landscapemetrics/man/get_adjacencies.Rd                            |  150 
 landscapemetrics-1.4/landscapemetrics/man/get_boundaries.Rd                             |  163 
 landscapemetrics-1.4/landscapemetrics/man/get_circumscribingcircle.Rd                   |  116 
 landscapemetrics-1.4/landscapemetrics/man/get_nearestneighbour.Rd                       |  104 
 landscapemetrics-1.4/landscapemetrics/man/get_patches.Rd                                |  210 
 landscapemetrics-1.4/landscapemetrics/man/get_unique_values.Rd                          |  122 
 landscapemetrics-1.4/landscapemetrics/man/landscape.Rd                                  |   36 
 landscapemetrics-1.4/landscapemetrics/man/landscapemetrics.Rd                           |   91 
 landscapemetrics-1.4/landscapemetrics/man/list_lsm.Rd                                   |  119 
 landscapemetrics-1.4/landscapemetrics/man/lsm_abbreviations_names.Rd                    |   50 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_ai.Rd                                   |  126 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_area_cv.Rd                              |  134 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_area_mn.Rd                              |  136 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_area_sd.Rd                              |  142 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_ca.Rd                                   |  134 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_cai_cv.Rd                               |  186 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_cai_mn.Rd                               |  180 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_cai_sd.Rd                               |  184 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_circle_cv.Rd                            |  150 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_circle_mn.Rd                            |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_circle_sd.Rd                            |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_clumpy.Rd                               |  122 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_cohesion.Rd                             |  136 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_contig_cv.Rd                            |  156 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_contig_mn.Rd                            |  154 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_contig_sd.Rd                            |  156 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_core_cv.Rd                              |  178 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_core_mn.Rd                              |  174 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_core_sd.Rd                              |  176 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_cpland.Rd                               |  170 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_dcad.Rd                                 |  176 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_dcore_cv.Rd                             |  184 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_dcore_mn.Rd                             |  178 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_dcore_sd.Rd                             |  184 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_division.Rd                             |  128 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_ed.Rd                                   |  143 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_enn_cv.Rd                               |  155 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_enn_mn.Rd                               |  155 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_enn_sd.Rd                               |  155 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_frac_cv.Rd                              |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_frac_mn.Rd                              |  138 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_frac_sd.Rd                              |  144 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_gyrate_cv.Rd                            |  148 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_gyrate_mn.Rd                            |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_gyrate_sd.Rd                            |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_iji.Rd                                  |  132 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_lpi.Rd                                  |  128 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_lsi.Rd                                  |  134 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_mesh.Rd                                 |  138 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_ndca.Rd                                 |  178 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_nlsi.Rd                                 |  132 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_np.Rd                                   |  120 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_pafrac.Rd                               |  149 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_para_cv.Rd                              |  140 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_para_mn.Rd                              |  140 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_para_sd.Rd                              |  140 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_pd.Rd                                   |  130 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_pladj.Rd                                |  114 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_pland.Rd                                |  126 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_shape_cv.Rd                             |  142 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_shape_mn.Rd                             |  142 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_shape_sd.Rd                             |  142 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_split.Rd                                |  134 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_tca.Rd                                  |  151 
 landscapemetrics-1.4/landscapemetrics/man/lsm_c_te.Rd                                   |  135 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_ai.Rd                                   |  130 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_area_cv.Rd                              |  134 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_area_mn.Rd                              |  136 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_area_sd.Rd                              |  132 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_cai_cv.Rd                               |  186 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_cai_mn.Rd                               |  180 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_cai_sd.Rd                               |  184 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_circle_cv.Rd                            |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_circle_mn.Rd                            |  144 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_circle_sd.Rd                            |  148 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_cohesion.Rd                             |  126 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_condent.Rd                              |  128 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_contag.Rd                               |  136 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_contig_cv.Rd                            |  156 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_contig_mn.Rd                            |  154 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_contig_sd.Rd                            |  156 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_core_cv.Rd                              |  180 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_core_mn.Rd                              |  176 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_core_sd.Rd                              |  178 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_dcad.Rd                                 |  176 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_dcore_cv.Rd                             |  184 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_dcore_mn.Rd                             |  178 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_dcore_sd.Rd                             |  182 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_division.Rd                             |  134 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_ed.Rd                                   |  143 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_enn_cv.Rd                               |  155 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_enn_mn.Rd                               |  155 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_enn_sd.Rd                               |  155 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_ent.Rd                                  |  113 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_frac_cv.Rd                              |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_frac_mn.Rd                              |  144 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_frac_sd.Rd                              |  144 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_gyrate_cv.Rd                            |  148 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_gyrate_mn.Rd                            |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_gyrate_sd.Rd                            |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_iji.Rd                                  |  134 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_joinent.Rd                              |  123 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_lpi.Rd                                  |  128 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_lsi.Rd                                  |  134 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_mesh.Rd                                 |  138 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_msidi.Rd                                |  132 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_msiei.Rd                                |  122 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_mutinf.Rd                               |  125 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_ndca.Rd                                 |  178 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_np.Rd                                   |  122 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_pafrac.Rd                               |  149 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_para_cv.Rd                              |  140 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_para_mn.Rd                              |  140 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_para_sd.Rd                              |  140 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_pd.Rd                                   |  130 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_pladj.Rd                                |  114 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_pr.Rd                                   |  110 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_prd.Rd                                  |  120 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_rpr.Rd                                  |  132 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_shape_cv.Rd                             |  142 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_shape_mn.Rd                             |  142 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_shape_sd.Rd                             |  142 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_shdi.Rd                                 |  122 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_shei.Rd                                 |  126 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_sidi.Rd                                 |  132 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_siei.Rd                                 |  132 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_split.Rd                                |  134 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_ta.Rd                                   |  124 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_tca.Rd                                  |  149 
 landscapemetrics-1.4/landscapemetrics/man/lsm_l_te.Rd                                   |  124 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_area.Rd                                 |  138 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_cai.Rd                                  |  161 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_circle.Rd                               |  148 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_contig.Rd                               |  158 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_core.Rd                                 |  184 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_enn.Rd                                  |  155 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_frac.Rd                                 |  146 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_gyrate.Rd                               |  142 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_ncore.Rd                                |  186 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_para.Rd                                 |  140 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_perim.Rd                                |  118 
 landscapemetrics-1.4/landscapemetrics/man/lsm_p_shape.Rd                                |  144 
 landscapemetrics-1.4/landscapemetrics/man/matrix_to_raster.Rd                           |   88 
 landscapemetrics-1.4/landscapemetrics/man/options_landscapemetrics.Rd                   |   56 
 landscapemetrics-1.4/landscapemetrics/man/pad_raster.Rd                                 |  172 
 landscapemetrics-1.4/landscapemetrics/man/podlasie_ccilc.Rd                             |   36 
 landscapemetrics-1.4/landscapemetrics/man/proj_info.Rd                                  |   54 
 landscapemetrics-1.4/landscapemetrics/man/raster_to_points.Rd                           |   86 
 landscapemetrics-1.4/landscapemetrics/man/rcpp_cell_from_xy.Rd                          |   38 
 landscapemetrics-1.4/landscapemetrics/man/rcpp_create_neighborhood.Rd                   |   38 
 landscapemetrics-1.4/landscapemetrics/man/rcpp_get_nearest_neighbor.Rd                  |   44 
 landscapemetrics-1.4/landscapemetrics/man/rcpp_xy_from_matrix.Rd                        |   36 
 landscapemetrics-1.4/landscapemetrics/man/sample_lsm.Rd                                 |  283 
 landscapemetrics-1.4/landscapemetrics/man/scale_sample.Rd                               |  210 
 landscapemetrics-1.4/landscapemetrics/man/scale_window.Rd                               |  221 
 landscapemetrics-1.4/landscapemetrics/man/show_cores.Rd                                 |  191 
 landscapemetrics-1.4/landscapemetrics/man/show_correlation.Rd                           |   96 
 landscapemetrics-1.4/landscapemetrics/man/show_lsm.Rd                                   |  195 
 landscapemetrics-1.4/landscapemetrics/man/show_patches.Rd                               |  142 
 landscapemetrics-1.4/landscapemetrics/man/spatialize_lsm.Rd                             |  180 
 landscapemetrics-1.4/landscapemetrics/man/unpad_raster.Rd                               |  146 
 landscapemetrics-1.4/landscapemetrics/man/window_lsm.Rd                                 |  212 
 landscapemetrics-1.4/landscapemetrics/src/RcppExports.cpp                               |   17 
 landscapemetrics-1.4/landscapemetrics/src/rcpp_cclabel.cpp                              |only
 landscapemetrics-1.4/landscapemetrics/src/rcpp_cclabel.h                                |only
 landscapemetrics-1.4/landscapemetrics/tests/testthat.R                                  |   10 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/helper-brick.R                     |    8 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/helper-landscapes.R                |   38 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/helper-points.R                    |   36 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-calculate-lsm.R               |  250 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-calculate_correlation.R       |  140 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-check-landscape.R             |  149 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-construct-buffer.R            |   71 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-different-classes.R           |only
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-extract-lsm.R                 |  272 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-get-adjacencies.R             |  141 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-get-boundaries.R              |  102 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-get-circumscribungcircle.R    |  146 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-get-nearestneighbour.R        |   66 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-get-patches.R                 |   52 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-get-unique-values.R           |  182 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-list-lsm.R                    |  182 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-ai.R                    |   68 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-area-cv.R               |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-area-mn.R               |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-area-sd.R               |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-ca.R                    |   52 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-cai-cv.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-cai-mn.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-cai-sd.R                |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-circle-cv.R             |   52 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-circle-mn.R             |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-circle-sd.R             |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-clumpy.R                |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-cohesion.R              |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-contig-cv.R             |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-contig-mn.R             |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-contig-sd.R             |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-core-cv.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-core-mn.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-core-sd.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-cpland.R                |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-dcad.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-dcore_cv.R              |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-dcore_mn.R              |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-dcore_sd.R              |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-division.R              |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-ed.R                    |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-enn-cv.R                |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-enn-mn.R                |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-enn-sd.R                |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-frac-cv.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-frac-mn.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-frac-sd.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-gyrate-cv.R             |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-gyrate-mn.R             |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-gyrate-sd.R             |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-iji.R                   |   68 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-lpi.R                   |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-lsi.R                   |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-mesh.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-ndca.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-nlsi.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-np.R                    |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-pafrac.R                |   76 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-para-cv.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-para-mn.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-para-sd.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-pd.R                    |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-pladj.R                 |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-pland.R                 |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-shape-cv.R              |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-shape-mn.R              |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-shape-sd.R              |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-split.R                 |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-tca.R                   |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-c-te.R                    |   64 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-ai.R                    |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-area-cv.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-area-mn.R               |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-area-sd.R               |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-cai-cv.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-cai-mn.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-cai-sd.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-circle-cv.R             |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-circle-mn.R             |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-circle-sd.R             |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-cohesion.R              |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-condent.R               |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-contag.R                |   66 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-contig-cv.R             |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-contig-mn.R             |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-contig-sd.R             |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-core-cv.R               |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-core-mn.R               |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-core-sd.R               |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-dcad.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-dcore-cv.R              |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-dcore-mn.R              |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-dcore-sd.R              |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-division.R              |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-ed.R                    |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-enn-cv.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-enn-mn.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-enn-sd.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-ent.R                   |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-frac-cv.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-frac-mn.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-frac-sd.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-gyrate-cv.R             |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-gyrate-mn.R             |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-gyrate-sd.R             |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-iji.R                   |   68 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-joinent.R               |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-lpi.R                   |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-lsi.R                   |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-mesh.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-msidi.R                 |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-msiei.R                 |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-mutinf.R                |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-ndca.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-np.R                    |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-pafrac.R                |   66 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-para-cv.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-para-mn.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-para-sd.R               |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-pd.R                    |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-pladj.R                 |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-pr.R                    |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-prd.R                   |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-rpr.R                   |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shape-cv.R              |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shape-mn.R              |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shape-sd.R              |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shdi.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shei.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-sidi.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-siei.R                  |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-split.R                 |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-ta.R                    |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-tca.R                   |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-te.R                    |   66 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-area.R                  |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-cai.R                   |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-circle.R                |   54 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-contig.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-core.R                  |   68 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-enn.R                   |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-frac.R                  |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-gyrate.R                |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-nca.R                   |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-para.R                  |   50 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-perim.R                 |   54 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-shape.R                 |   48 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-matrix-to-raster.R            |   96 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-options-landscapemetrics.R    |   25 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-pad-raster.R                  |   92 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-raster-to-points.R            |   84 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-rcpp-get-coocurrence-matrix.R |  204 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-rcpp-get-entropy.R            |   46 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-sample-lsm.R                  |  428 -
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-scale-sample.R                |  200 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-scale-window.R                |  172 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-show-cores.R                  |  106 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-show-correlation.R            |  117 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-show-lsm.R                    |   96 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-show-patches.R                |   74 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-spatialize-lsm.R              |  152 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-unique-values.R               |   26 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-unpad-raster.R                |only
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-window-lsm.R                  |   84 
 landscapemetrics-1.4/landscapemetrics/tests/testthat/test_fragstats.R                   | 3884 +++++-----
 landscapemetrics-1.4/landscapemetrics/vignettes/getstarted.Rmd                          |  364 
 526 files changed, 52835 insertions(+), 50810 deletions(-)

More information about landscapemetrics at CRAN
Permanent link

Package JWileymisc updated to version 1.0.1 with previous version 1.0.0 dated 2019-11-22

Title: Miscellaneous Utilities and Functions
Description: Miscellaneous tools and functions, including: generate descriptive statistics tables, format output, visualize relations among variables or check distributions, and generic functions for residual and model diagnostics.
Author: Joshua F. Wiley [aut, cre] (<https://orcid.org/0000-0002-0271-6702>)
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>

Diff between JWileymisc versions 1.0.0 dated 2019-11-22 and 1.0.1 dated 2019-12-11

 DESCRIPTION                        |   15 ++---
 MD5                                |   29 +++++-----
 NAMESPACE                          |    2 
 NEWS.md                            |    9 +++
 R/diagnostics.R                    |  103 +++++++++++++++++++++++++++++++------
 R/models.R                         |   25 +++++---
 R/plotting.R                       |   97 ++++++++++++++++++++++++++--------
 inst/doc/diagnostics-vignette.html |    8 +-
 inst/doc/model-test-vignette.html  |    4 -
 man/dot-quantilePercentiles.Rd     |    6 +-
 man/modelDiagnostics.Rd            |   14 ++++-
 man/modelPerformance.Rd            |   25 +++++---
 man/plot.modelDiagnostics.lm.Rd    |    9 +--
 man/plot.residualDiagnostics.Rd    |only
 man/residualDiagnostics.Rd         |   18 ++++++
 tests/testthat/test-scoring.R      |    8 +-
 16 files changed, 276 insertions(+), 96 deletions(-)

More information about JWileymisc at CRAN
Permanent link

Package glmnet updated to version 3.0-2 with previous version 3.0-1 dated 2019-11-15

Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial regression. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers listed in the URL below.
Author: Jerome Friedman [aut], Trevor Hastie [aut, cre], Rob Tibshirani [aut], Balasubramanian Narasimhan [aut], Noah Simon [aut], Junyang Qian [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>

Diff between glmnet versions 3.0-1 dated 2019-11-15 and 3.0-2 dated 2019-12-11

 DESCRIPTION          |    8 ++++----
 MD5                  |   30 +++++++++++++++---------------
 NEWS.md              |   12 ++++++++++++
 R/assess.glmnet.R    |   42 +++++++++++++++++++++++++++---------------
 R/confusion.glmnet.R |    4 +++-
 R/cv.mrelnet.R       |    2 +-
 R/cv.multnet.R       |    2 +-
 R/lambda.interp.R    |    6 ++++--
 R/pb.R               |    2 +-
 R/predict.multnet.R  |    3 ++-
 inst/doc/Coxnet.pdf  |binary
 inst/doc/glmnet.pdf  |binary
 inst/doc/relax.pdf   |binary
 man/assess.glmnet.Rd |   42 +++++++++++++++++++++++++++---------------
 src/glmnet_init.c    |    4 ++--
 src/pb.c             |    3 ++-
 16 files changed, 101 insertions(+), 59 deletions(-)

More information about glmnet at CRAN
Permanent link

Package GFGM.copula updated to version 1.0.4 with previous version 1.0.3 dated 2018-04-02

Title: Generalized Farlie-Gumbel-Morgenstern Copula
Description: Compute bivariate dependence measures and perform bivariate competing risks analysis under the generalized Farlie-Gumbel-Morgenstern (FGM) copula. See Shih and Emura (2018) <doi:10.1007/s00180-018-0804-0> and Shih and Emura (2019) <doi:10.1007/s00362-016-0865-5> for details.
Author: Jia-Han Shih
Maintainer: Jia-Han Shih <tommy355097@gmail.com>

Diff between GFGM.copula versions 1.0.3 dated 2018-04-02 and 1.0.4 dated 2019-12-11

 DESCRIPTION               |   12 +-
 MD5                       |   34 +++----
 NAMESPACE                 |    2 
 R/CvM.GFGM.BurrIII.R      |    2 
 R/Depmeasure.GFGM.R       |    4 
 R/GFGM.BurrIII.R          |    4 
 R/MLE.GFGM.BurrIII.R      |    4 
 R/MLE.GFGM.spline.R       |   19 +---
 R/Sdist.GFGM.BurrIII.R    |    4 
 R/Sdist.GFGM.spline.R     |    4 
 build/partial.rdb         |binary
 man/CvM.GFGM.BurrIII.Rd   |  187 ++++++++++++++++++++++--------------------
 man/Dependence.GFGM.Rd    |   70 +++++++--------
 man/GFGM.BurrIII.Rd       |   90 ++++++++++----------
 man/MLE.GFGM.BurrIII.Rd   |  202 ++++++++++++++++++++++++----------------------
 man/MLE.GFGM.spline.Rd    |  162 +++++++++++++++++-------------------
 man/Sdist.GFGM.BurrIII.Rd |   98 +++++++++++-----------
 man/Sdist.GFGM.spline.Rd  |  100 +++++++++++-----------
 18 files changed, 503 insertions(+), 495 deletions(-)

More information about GFGM.copula at CRAN
Permanent link

Package exactRankTests updated to version 0.8-31 with previous version 0.8-30 dated 2019-04-28

Title: Exact Distributions for Rank and Permutation Tests
Description: Computes exact conditional p-values and quantiles using an implementation of the Shift-Algorithm by Streitberg & Roehmel.
Author: Torsten Hothorn [aut, cre], Kurt Hornik [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between exactRankTests versions 0.8-30 dated 2019-04-28 and 0.8-31 dated 2019-12-11

 DESCRIPTION                       |    8 ++++----
 MD5                               |   28 ++++++++++++++--------------
 data/ASAT.rda                     |binary
 data/bloodp.rda                   |binary
 data/ears.rda                     |binary
 data/glioma.rda                   |binary
 data/globulin.rda                 |binary
 data/lungcancer.rda               |binary
 data/neuropathy.rda               |binary
 data/ocarcinoma.rda               |binary
 data/rotarod.rda                  |binary
 data/sal.rda                      |binary
 inst/NEWS                         |    6 +++++-
 tests/exactRankTests-Ex.R         |    2 +-
 tests/exactRankTests-Ex.Rout.save |   12 ++++++------
 15 files changed, 30 insertions(+), 26 deletions(-)

More information about exactRankTests at CRAN
Permanent link

Package dexter updated to version 1.0.2 with previous version 1.0.1 dated 2019-11-22

Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris, Timo Bechger, Jesse Koops, Ivailo Partchev
Maintainer: Jesse Koops <jesse.koops@cito.nl>

Diff between dexter versions 1.0.1 dated 2019-11-22 and 1.0.2 dated 2019-12-11

 DESCRIPTION                               |    6 +--
 MD5                                       |   34 +++++++++---------
 NEWS                                      |    6 +++
 R/anon_plausible_values.R                 |    8 ++--
 R/plausible_scores.R                      |    3 +
 R/plausible_values.R                      |   17 +++++----
 R/resp_data.R                             |   12 +++---
 inst/doc/DIF_vignette.html                |    4 +-
 inst/doc/Equating.html                    |   10 ++---
 inst/doc/Plausible_Values.R               |    4 +-
 inst/doc/Plausible_Values.Rmd             |    4 +-
 inst/doc/Plausible_Values.html            |   18 ++++-----
 inst/doc/Test_Individual_differences.html |   12 +++---
 inst/doc/dexter.html                      |   56 +++++++++++++++---------------
 inst/doc/profile-plots.html               |    4 +-
 tests/testthat/test_data_selection.R      |   20 ++++++++++
 tests/testthat/test_plausible_scores.R    |    4 +-
 vignettes/Plausible_Values.Rmd            |    4 +-
 18 files changed, 130 insertions(+), 96 deletions(-)

More information about dexter at CRAN
Permanent link

Package bmotif updated to version 2.0.0 with previous version 1.0.0 dated 2018-01-29

Title: Motif Analyses of Bipartite Networks
Description: Counts occurrences of motifs in bipartite networks, as well as the number of times each node or link appears in each unique position within motifs. Has support for both binary and weighted motifs: can calculate the mean weight of motifs and the standard deviation of their mean weights. Intended for use in ecology, but its methods are general and can be applied to any bipartite network.
Author: Benno Simmons [aut, cre], Michelle Sweering [aut], Maybritt Schillinger [aut], Riccardo Di Clemente [aut]
Maintainer: Benno Simmons <benno.simmons@gmail.com>

Diff between bmotif versions 1.0.0 dated 2018-01-29 and 2.0.0 dated 2019-12-11

 bmotif-1.0.0/bmotif/R/normalise_positions.R                        |only
 bmotif-1.0.0/bmotif/R/positions.R                                  |only
 bmotif-1.0.0/bmotif/man/positions.Rd                               |only
 bmotif-1.0.0/bmotif/tests/testthat/test_positions.R                |only
 bmotif-2.0.0/bmotif/DESCRIPTION                                    |   33 +
 bmotif-2.0.0/bmotif/LICENSE                                        |    4 
 bmotif-2.0.0/bmotif/MD5                                            |   61 ++-
 bmotif-2.0.0/bmotif/NAMESPACE                                      |    5 
 bmotif-2.0.0/bmotif/NEWS                                           |   30 +
 bmotif-2.0.0/bmotif/R/RcppExports.R                                |only
 bmotif-2.0.0/bmotif/R/large_tensor.r                               |only
 bmotif-2.0.0/bmotif/R/link_positions.r                             |only
 bmotif-2.0.0/bmotif/R/mcount.R                                     |  191 +++++++---
 bmotif-2.0.0/bmotif/R/mean_weight.R                                |only
 bmotif-2.0.0/bmotif/R/motif_info.R                                 |only
 bmotif-2.0.0/bmotif/R/motif_sd.R                                   |only
 bmotif-2.0.0/bmotif/R/name_edge.R                                  |only
 bmotif-2.0.0/bmotif/R/node_positions.R                             |only
 bmotif-2.0.0/bmotif/R/normalise_link_positions.R                   |only
 bmotif-2.0.0/bmotif/R/normalise_node_positions.R                   |only
 bmotif-2.0.0/bmotif/R/pop_sd.r                                     |only
 bmotif-2.0.0/bmotif/R/sysdata.rda                                  |binary
 bmotif-2.0.0/bmotif/R/testing_functions.R                          |only
 bmotif-2.0.0/bmotif/R/weighted_node_positions_output_row_names.R   |only
 bmotif-2.0.0/bmotif/README.md                                      |  170 ++++++++
 bmotif-2.0.0/bmotif/build                                          |only
 bmotif-2.0.0/bmotif/inst                                           |only
 bmotif-2.0.0/bmotif/man/figures                                    |only
 bmotif-2.0.0/bmotif/man/link_positions.Rd                          |only
 bmotif-2.0.0/bmotif/man/mcount.Rd                                  |   81 +++-
 bmotif-2.0.0/bmotif/man/node_positions.Rd                          |only
 bmotif-2.0.0/bmotif/src                                            |only
 bmotif-2.0.0/bmotif/tests/testthat/test_check_motif.R              |only
 bmotif-2.0.0/bmotif/tests/testthat/test_link_positions.R           |only
 bmotif-2.0.0/bmotif/tests/testthat/test_link_positions_weights.R   |only
 bmotif-2.0.0/bmotif/tests/testthat/test_mcount.R                   |   80 +++-
 bmotif-2.0.0/bmotif/tests/testthat/test_mean_weight.R              |only
 bmotif-2.0.0/bmotif/tests/testthat/test_motif_info.R               |only
 bmotif-2.0.0/bmotif/tests/testthat/test_node_positions.R           |only
 bmotif-2.0.0/bmotif/tests/testthat/test_normalise_node_positions.R |only
 bmotif-2.0.0/bmotif/tests/testthat/test_sd.R                       |only
 bmotif-2.0.0/bmotif/tests/testthat/test_weighted_node_pos_v2.R     |only
 bmotif-2.0.0/bmotif/vignettes                                      |only
 43 files changed, 532 insertions(+), 123 deletions(-)

More information about bmotif at CRAN
Permanent link

Package shinymanager updated to version 1.0.100 with previous version 1.0 dated 2019-06-19

Title: Authentication Management for 'Shiny' Applications
Description: Simple and secure authentification mechanism for single 'Shiny' applications. Credentials are stored in an encrypted 'SQLite' database. Source code of main application is protected until authentication is successful.
Author: Benoit Thieurmel [aut, cre], Victor Perrier [aut]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>

Diff between shinymanager versions 1.0 dated 2019-06-19 and 1.0.100 dated 2019-12-11

 DESCRIPTION                        |   11 -
 MD5                                |   56 ++++---
 NAMESPACE                          |    2 
 NEWS.md                            |only
 R/language.R                       |    2 
 R/module-admin.R                   |   20 ++
 R/module-auth.R                    |   92 ------------
 R/module-pwd.R                     |   51 -------
 R/secure-app.R                     |  119 ++++++----------
 README.md                          |   21 ++
 build                              |only
 inst/assets/styles-auth.css        |    2 
 inst/assets/timeout.js             |    2 
 inst/doc                           |only
 inst/sticker                       |only
 man/check_credentials.Rd           |  126 ++++++++---------
 man/create_db.Rd                   |  118 ++++++++--------
 man/db-crypted.Rd                  |  184 ++++++++++++-------------
 man/fab_button.Rd                  |  150 ++++++++++----------
 man/figures/add_user.png           |only
 man/figures/password_table.png     |only
 man/figures/popup.png              |only
 man/figures/shinymanager-login.png |binary
 man/figures/shinymanager-pwd.png   |binary
 man/figures/user_table.png         |only
 man/generate_pwd.Rd                |   42 ++---
 man/module-authentication.Rd       |  268 ++++++++++++++++++-------------------
 man/module-password.Rd             |  185 +++++++++++++------------
 man/secure-app.Rd                  |  187 +++++++++++++------------
 tests/testthat/test-language.R     |only
 tests/testthat/test-modules-ui.R   |   13 +
 vignettes                          |only
 32 files changed, 786 insertions(+), 865 deletions(-)

More information about shinymanager at CRAN
Permanent link

New package pavo with initial version 2.3.0
Package: pavo
Title: Perceptual Analysis, Visualization and Organization of Spectral Colour Data
Version: 2.3.0
Authors@R: c(person(given = "Rafael", family = "Maia", role = c("aut", "cre"), email = "rm72@zips.uakron.edu", comment = c(ORCID = "0000-0002-7563-9795")), person(given = "Thomas", family = "White", role = "aut", email = "thomas.white026@gmail.com", comment = c(ORCID = "0000-0002-3976-1734")), person(given = "Hugo", family = "Gruson", role = "aut", email = "hugo.gruson+R@normalesup.org", comment = c(ORCID = "0000-0002-4094-1476")), person(given = "John", family = "Endler", role = "aut", email = "john.endler@deakin.edu.au"), person(given = "Chad", family = "Eliason", role = "aut", email = "cme16@zips.uakron.edu"), person(given = "Pierre-Paul", family = "Bitton", role = "aut", email = "bittonp@uwindsor.ca", comment = c(ORCID = "0000-0001-5984-2331")))
Description: A cohesive framework for parsing, analyzing and organizing colour from spectral data.
License: GPL (>= 2)
URL: http://rafaelmaia.net/pavo/, https://github.com/rmaia/pavo/
BugReports: https://github.com/rmaia/pavo/issues
Depends: R (>= 3.5.0)
Imports: cluster, geometry(>= 0.4.0), magick, pbmcapply, plot3D, sp, viridisLite
Suggests: digest, imager, knitr, mapproj, NbClust, rgl, rmarkdown, testthat, xml2
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
RoxygenNote: 7.0.2
NeedsCompilation: no
Packaged: 2019-12-11 07:12:43 UTC; rafaelmaia
Author: Rafael Maia [aut, cre] (<https://orcid.org/0000-0002-7563-9795>), Thomas White [aut] (<https://orcid.org/0000-0002-3976-1734>), Hugo Gruson [aut] (<https://orcid.org/0000-0002-4094-1476>), John Endler [aut], Chad Eliason [aut], Pierre-Paul Bitton [aut] (<https://orcid.org/0000-0001-5984-2331>)
Maintainer: Rafael Maia <rm72@zips.uakron.edu>
Repository: CRAN
Date/Publication: 2019-12-11 15:30:02 UTC

More information about pavo at CRAN
Permanent link

Package Bivariate.Pareto updated to version 1.0.3 with previous version 1.0.2 dated 2018-04-02

Title: Bivariate Pareto Models
Description: Perform competing risks analysis under bivariate Pareto models. See Shih et al. (2019) <doi:10.1080/03610926.2018.1425450> for details.
Author: Jia-Han Shih, Wei Lee
Maintainer: Jia-Han Shih <tommy355097@gmail.com>

Diff between Bivariate.Pareto versions 1.0.2 dated 2018-04-02 and 1.0.3 dated 2019-12-11

 DESCRIPTION                 |   14 -
 MD5                         |   30 ++--
 NAMESPACE                   |    3 
 R/Frank.Pareto.R            |    2 
 R/Kendall.SNBP.R            |    4 
 R/MLE.Frank.Pareto.R        |    4 
 R/MLE.Frank.Pareto.com.R    |   15 +-
 R/MLE.SN.Pareto.R           |   19 --
 R/SN.Pareto.R               |    2 
 build/partial.rdb           |binary
 man/Frank.Pareto.Rd         |   70 ++++-----
 man/Kendall.SNBP.Rd         |   70 ++++-----
 man/MLE.Frank.Pareto.Rd     |  301 +++++++++++++++++++++--------------------
 man/MLE.Frank.Pareto.com.Rd |  293 +++++++++++++++++++++-------------------
 man/MLE.SN.Pareto.Rd        |  317 ++++++++++++++++++++++----------------------
 man/SN.Pareto.Rd            |   76 +++++-----
 16 files changed, 619 insertions(+), 601 deletions(-)

More information about Bivariate.Pareto at CRAN
Permanent link

Package TaxicabCA updated to version 0.1.1 with previous version 0.1.0 dated 2018-07-18

Title: Taxicab Correspondence Analysis
Description: Computation and visualization of Taxicab Correspondence Analysis, Choulakian (2006) <doi:10.1007/s11336-004-1231-4>. Classical correspondence analysis (CA) is a statistical method to analyse 2-dimensional tables of positive numbers and is typically applied to contingency tables (Benzecri, J.-P. (1973). L'Analyse des Donnees. Volume II. L'Analyse des Correspondances. Paris, France: Dunod). Classical CA is based on the Euclidean distance. Taxicab CA is like classical CA but is based on the Taxicab or Manhattan distance. For some tables, Taxicab CA gives more informative results than classical CA.
Author: Jacques Allard and Vartan Choulakian
Maintainer: Jacques Allard <jacques.allard@gmail.com>

Diff between TaxicabCA versions 0.1.0 dated 2018-07-18 and 0.1.1 dated 2019-12-11

 DESCRIPTION                                |    8 -
 MD5                                        |   45 ++++----
 NAMESPACE                                  |    2 
 R/CombineCollinearRowsCols.R               |    2 
 R/data.R                                   |    2 
 R/saveTCA.r                                |    1 
 R/tca.R                                    |   80 +++++++++++----
 man/CombineCollinearRowsCols.Rd            |   80 +++++++--------
 man/ComputeLambda.Rd                       |   52 +++++-----
 man/CreateAllBinaries.Rd                   |   52 +++++-----
 man/JitterPosition.Rd                      |   60 +++++------
 man/ListToObjects.Rd                       |   50 ++++-----
 man/RemoveRowsColumns0sAndDuplicates.Rd    |   66 ++++++------
 man/SearchCrissCross.Rd                    |   56 +++++-----
 man/SearchExhaustive.Rd                    |   52 +++++-----
 man/SearchGeneticAlgoritm.Rd               |   52 +++++-----
 man/milazzese.Rd                           |   48 ++++-----
 man/plot.tca.Rd                            |  101 ++++++++++---------
 man/print.tca.Rd                           |   42 ++++----
 man/rodent.Rd                              |   48 ++++-----
 man/saveTCA.Rd                             |   77 +++++++-------
 man/summary.tca.Rd                         |   48 ++++-----
 man/tca.Rd                                 |  150 +++++++++++++++--------------
 tests/testthat/test.rodent.transposed.ex.r |only
 24 files changed, 616 insertions(+), 558 deletions(-)

More information about TaxicabCA at CRAN
Permanent link

Package spmoran updated to version 0.1.7.2 with previous version 0.1.7.1 dated 2019-07-24

Title: Moran Eigenvector-Based Spatial Regression Models
Description: Functions for estimating Moran's eigenvector-based spatial regression models. For details see Murakami (2019) <arXiv:1703.04467>.
Author: Daisuke Murakami
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>

Diff between spmoran versions 0.1.7.1 dated 2019-07-24 and 0.1.7.2 dated 2019-12-11

 DESCRIPTION        |    8 
 MD5                |   18 
 R/besf.R           |  390 ++++++++--------
 R/besf_vc.R        | 1228 ++++++++++++++++++++++++++---------------------------
 R/lsem.R           |    7 
 R/lslm.R           |    6 
 R/resf.R           |  444 +++++++++----------
 R/resf_qr.R        |  432 +++++++++---------
 R/resf_vc.R        |    4 
 build/vignette.rds |binary
 10 files changed, 1267 insertions(+), 1270 deletions(-)

More information about spmoran at CRAN
Permanent link

New package rhierbaps with initial version 1.1.3
Package: rhierbaps
Type: Package
Title: Clustering Genetic Sequence Data Using the HierBAPS Algorithm
Version: 1.1.3
Authors@R: person("Gerry", "Tonkin-Hill", email = "g.tonkinhill@gmail.com", role = c("cre", "aut"))
Description: Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ape, purrr, utils, ggplot2, matrixStats, patchwork
RoxygenNote: 7.0.1
Suggests: knitr, rmarkdown, ggtree, phytools, testthat, formatR
VignetteBuilder: knitr
URL: https://github.com/gtonkinhill/rhierbaps
BugReports: https://github.com/gtonkinhill/rhierbaps/issues
NeedsCompilation: no
Packaged: 2019-12-11 06:42:07 UTC; gt4
Author: Gerry Tonkin-Hill [cre, aut]
Maintainer: Gerry Tonkin-Hill <g.tonkinhill@gmail.com>
Repository: CRAN
Date/Publication: 2019-12-11 14:20:05 UTC

More information about rhierbaps at CRAN
Permanent link

Package rebmix updated to version 2.11.0 with previous version 2.10.3 dated 2018-09-27

Title: Finite Mixture Modeling, Clustering & Classification
Description: R functions for random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac or circular von Mises parametric families.
Author: Marko Nagode [aut, cre], Branislav Panic [ctb]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>

Diff between rebmix versions 2.10.3 dated 2018-09-27 and 2.11.0 dated 2019-12-11

 DESCRIPTION               |   14 
 MD5                       |  115 ++--
 NAMESPACE                 |   25 
 R/AllClasses.R            |  180 ++++++-
 R/AllGenerics.R           |   22 
 R/RCLRMIX.R               |    2 
 R/RCLSMIX.R               |   13 
 R/REBMIX.R                |  367 ++++++++------
 R/RNGMIX.R                |    2 
 R/defaults.R              |   15 
 R/dfmix.R                 |   12 
 R/dfmix.x.R               |   12 
 R/dfmix.xy.R              |   24 
 R/pfmix.R                 |   12 
 R/pfmix.x.R               |   30 -
 R/pfmix.xy.R              |   24 
 R/plot.RCLSMIX.R          |   28 -
 R/split.R                 |   69 +-
 R/zaccessors.R            |  208 ++++++++
 build/vignette.rds        |binary
 data/adult.rda            |binary
 data/galaxy.rda           |binary
 data/iris.rda             |binary
 data/truck.rda            |binary
 data/weibull.rda          |binary
 data/weibullnormal.rda    |binary
 data/wine.rda             |binary
 inst/NEWS.Rd              |   11 
 inst/doc/rebmix.R         |  207 +++++++-
 inst/doc/rebmix.Rnw       |  235 ++++++++-
 inst/doc/rebmix.pdf       |binary
 man/BFSMIX.Rd             |    4 
 man/EM.Control-class.Rd   |only
 man/RCLRMIX.Rd            |    4 
 man/RCLS.chunk-class.Rd   |    5 
 man/RCLSMIX.Rd            |    4 
 man/REBMIX-class.Rd       |   22 
 man/REBMIX.Rd             |   51 +-
 man/REBMIX.boot.Rd        |    4 
 man/RNGMIX-class.Rd       |    6 
 man/RNGMIX.Rd             |   10 
 man/RNGMIX.Theta-class.Rd |    8 
 man/adult.Rd              |    2 
 man/galaxy.Rd             |   14 
 man/rebmix-internal.Rd    |   35 +
 src/Rrebmix.cpp           |  365 ++++++++++----
 src/Rrebmvnorm.cpp        |   75 ++
 src/base.cpp              |  290 +++++------
 src/base.h                |   71 ++
 src/emf.cpp               |only
 src/emf.h                 |only
 src/init.c                |   25 
 src/rebmix.cpp            |    6 
 src/rebmixf.cpp           | 1151 ++++++++++++++++++++++++++++++++++++++++++++--
 src/rebmixf.h             |   58 --
 src/rebmvnormf.cpp        |  247 +++++----
 src/rebmvnormf.h          |    3 
 src/rngmixf.cpp           |    7 
 vignettes/rebmix.Rnw      |  235 ++++++++-
 vignettes/rebmix.bib      |   26 -
 60 files changed, 3473 insertions(+), 882 deletions(-)

More information about rebmix at CRAN
Permanent link

Package mirtjml updated to version 1.3.0 with previous version 1.2 dated 2018-12-21

Title: Joint Maximum Likelihood Estimation for High-Dimensional Item Factor Analysis
Description: Provides constrained joint maximum likelihood estimation algorithms for item factor analysis (IFA) based on multidimensional item response theory models. So far, we provide functions for exploratory and confirmatory IFA based on the multidimensional two parameter logistic (M2PL) model for binary response data. Comparing with traditional estimation methods for IFA, the methods implemented in this package scale better to data with large numbers of respondents, items, and latent factors. The computation is facilitated by multiprocessing 'OpenMP' API. For more information, please refer to: 1. Chen, Y., Li, X., & Zhang, S. (2018). Joint Maximum Likelihood Estimation for High-Dimensional Exploratory Item Factor Analysis. Psychometrika, 1-23. <doi:10.1007/s11336-018-9646-5>; 2. Chen, Y., Li, X., & Zhang, S. (2019). Structured Latent Factor Analysis for Large-scale Data: Identifiability, Estimability, and Their Implications. Journal of the American Statistical Association, <doi: 10.1080/01621459.2019.1635485>.
Author: Siliang Zhang [aut, cre], Yunxiao Chen [aut], Xiaoou Li [aut]
Maintainer: Siliang Zhang <zhangsiliang123@gmail.com>

Diff between mirtjml versions 1.2 dated 2018-12-21 and 1.3.0 dated 2019-12-11

 DESCRIPTION           |   15 +++--
 MD5                   |   40 ++++++++-------
 NAMESPACE             |    3 +
 NEWS.md               |   15 +++++
 R/RcppExports.R       |   40 +++++++++++++--
 R/mirtjml_conf.R      |   15 +++--
 R/mirtjml_expr.R      |   81 ++++++++++++++++++++++++++++--
 R/utilities.R         |   20 +++++++
 R/zzz.R               |only
 README.md             |    6 +-
 man/getMIRTthreads.Rd |only
 man/mirtjml_conf.Rd   |   16 +++---
 man/mirtjml_expr.Rd   |   11 ++--
 man/setMIRTthreads.Rd |only
 src/Makevars          |    6 +-
 src/Makevars.win      |    5 +
 src/RcppExports.cpp   |  131 ++++++++++++++++++++++++++++++++++++++++++++++----
 src/cjmle_conf.cpp    |   84 ++++++++++++++++++++------------
 src/cjmle_expr.cpp    |   87 ++++++++++++++++++++-------------
 src/depend_funcs.cpp  |   63 +++++++++++++++---------
 src/depend_funcs.h    |    4 +
 src/mirtjml_omp.h     |   29 ++++-------
 src/openmp-utils.cpp  |only
 23 files changed, 497 insertions(+), 174 deletions(-)

More information about mirtjml at CRAN
Permanent link

Package MASSTIMATE updated to version 1.4 with previous version 1.3 dated 2016-01-13

Title: Body Mass Estimation Equations for Vertebrates
Description: Estimation equations are from a variety of sources but are, in general, based on regressions between skeletal measurements (e.g., stylopodial circumference) and body mass in living taxa (Campione and Evans, 2012).
Author: Nicolas E. Campione
Maintainer: Nicolas E. Campione <ncampion@une.edu.au>

Diff between MASSTIMATE versions 1.3 dated 2016-01-13 and 1.4 dated 2019-12-11

 DESCRIPTION               |   12 ++--
 MD5                       |   20 ++++---
 R/DME.R                   |only
 README.md                 |    2 
 data/dinos.csv.gz         |binary
 data/dinosbip.csv.gz      |binary
 man/DME.Rd                |only
 man/MASSTIMATE-package.Rd |   72 ++++++++++++++--------------
 man/QE.Rd                 |  110 +++++++++++++++++++++----------------------
 man/bipeds.Rd             |   90 +++++++++++++++++------------------
 man/cQE.Rd                |  116 +++++++++++++++++++++++-----------------------
 man/quadrupeds.Rd         |   90 +++++++++++++++++------------------
 12 files changed, 258 insertions(+), 254 deletions(-)

More information about MASSTIMATE at CRAN
Permanent link

Package lfe updated to version 2.8-4 with previous version 2.8-3 dated 2019-03-27

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors with many levels as pure control variables. Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>), Grant McDermott [ctb], Karl Dunkle Werner [ctb], Matthieu Stigler [ctb], Daniel Lüdecke [ctb]
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>

Diff between lfe versions 2.8-3 dated 2019-03-27 and 2.8-4 dated 2019-12-11

 DESCRIPTION                 |   30 ++++--
 MD5                         |   78 +++++++++---------
 NAMESPACE                   |    3 
 R/felm.R                    |  190 +++++++++++++++++++++++++++++++++++++-------
 R/generics.R                |   85 +++++++++++++++++++
 R/nlexpect.R                |    4 
 R/utils.R                   |   21 +---
 build/autoconf/install-sh   |   36 +++++---
 build/vignette.rds          |binary
 cleanup                     |    2 
 inst/NEWS.Rd                |   12 ++
 inst/doc/biascorrection.pdf |binary
 inst/doc/identification.R   |   74 ++++++++---------
 inst/doc/identification.pdf |binary
 inst/doc/index.html         |   32 +++----
 inst/doc/lfehow.R           |   26 +++---
 inst/doc/lfehow.pdf         |binary
 inst/doc/speed.R            |   18 ++--
 inst/doc/speed.pdf          |binary
 man/bccorr.Rd               |   12 ++
 man/btrap.Rd                |   14 ++-
 man/cgsolve.Rd              |    3 
 man/demeanlist.Rd           |   19 +++-
 man/felm.Rd                 |  119 ++++++++++++++++++++++-----
 man/fevcov.Rd               |   10 +-
 man/getfe.Rd                |   14 ++-
 man/is.estimable.Rd         |   10 +-
 man/kaczmarz.Rd             |    9 +-
 man/nlexpect.Rd             |   22 +++--
 man/summary.felm.Rd         |    8 +
 man/varvars.Rd              |    3 
 man/waldtest.Rd             |   11 ++
 src/demean.c                |   56 +++++++++---
 src/factor.c                |    4 
 src/lfe.c                   |    6 +
 src/lfe.h                   |    6 -
 src/utils.c                 |   11 ++
 tests/comparelm.R           |   30 ++++++
 tests/comparelm.Rout.save   |   69 +++++++++------
 tests/testthat              |only
 tests/testthat.R            |only
 41 files changed, 754 insertions(+), 293 deletions(-)

More information about lfe at CRAN
Permanent link

Package HH updated to version 3.1-39 with previous version 3.1-37 dated 2019-08-29

Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>

Diff between HH versions 3.1-37 dated 2019-08-29 and 3.1-39 dated 2019-12-11

 HH-3.1-37/HH/R/hh.R                        |only
 HH-3.1-37/HH/R/hh.file.R                   |only
 HH-3.1-37/HH/man/hh.Rd                     |only
 HH-3.1-39/HH/DESCRIPTION                   |    8 +-
 HH-3.1-39/HH/MD5                           |   73 ++++++++++++--------------
 HH-3.1-39/HH/NAMESPACE                     |   11 ++--
 HH-3.1-39/HH/NEWS                          |   79 +++++++++++++++++++++++++++++
 HH-3.1-39/HH/R/HHscriptnames.R             |    5 +
 HH-3.1-39/HH/R/X.residuals.R               |    2 
 HH-3.1-39/HH/R/aov.sufficient.R            |    5 -
 HH-3.1-39/HH/R/likert.R                    |    5 +
 HH-3.1-39/HH/R/mmcplot.R                   |   13 ++--
 HH-3.1-39/HH/R/position.R                  |   14 +----
 HH-3.1-39/HH/R/residual.plots.lattice.R    |    2 
 HH-3.1-39/HH/R/vif.R                       |    5 +
 HH-3.1-39/HH/build/partial.rdb             |binary
 HH-3.1-39/HH/man/CIplot.Rd                 |    8 +-
 HH-3.1-39/HH/man/Discrete4.color.Rd        |   17 ++----
 HH-3.1-39/HH/man/HH-defunct.Rd             |   10 +++
 HH-3.1-39/HH/man/HH.package.Rd             |   14 ++---
 HH-3.1-39/HH/man/NormalAndT.Rd             |   17 ++++--
 HH-3.1-39/HH/man/NormalAndTplot.Rd         |    3 -
 HH-3.1-39/HH/man/ae.dotplot7.Rd            |    4 -
 HH-3.1-39/HH/man/ae.dotplot7a.Rd           |    2 
 HH-3.1-39/HH/man/bivariateNormal.Rd        |    6 +-
 HH-3.1-39/HH/man/col.hh.Rd                 |    2 
 HH-3.1-39/HH/man/col3x2.Rd                 |   36 ++++++++-----
 HH-3.1-39/HH/man/export.eps.Rd             |   14 ++---
 HH-3.1-39/HH/man/likert.Rd                 |    7 +-
 HH-3.1-39/HH/man/mmcPruneIsomeans.Rd       |    3 -
 HH-3.1-39/HH/man/mmcisomeans.Rd            |    8 +-
 HH-3.1-39/HH/man/mmcplot.Rd                |    6 +-
 HH-3.1-39/HH/man/normalApproxBinomial.Rd   |    9 ++-
 HH-3.1-39/HH/man/position.Rd               |   33 +-----------
 HH-3.1-39/HH/man/pyramidLikert.Rd          |    2 
 HH-3.1-39/HH/man/rbind.trellis.Rd          |    3 -
 HH-3.1-39/HH/man/residual.plots.lattice.Rd |   11 ++--
 HH-3.1-39/HH/man/useOuterScales.Rd         |    3 -
 HH-3.1-39/HH/man/vif.Rd                    |   13 ----
 39 files changed, 268 insertions(+), 185 deletions(-)

More information about HH at CRAN
Permanent link

Package ctmm updated to version 0.5.8 with previous version 0.5.7 dated 2019-10-07

Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data. The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced in Fleming & Calabrese et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>, Fleming et al (2015) <doi:10.1890/14-2010.1>, Fleming et al (2016) <doi:10.1890/15-1607>, Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>, Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>, Péron et al (2017) <doi:10.1002/ecm.1260>, Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>, Fleming et al (2018) <doi:10.1002/eap.1704>, Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>, Fleming et al (2019) <doi:10.1111/2041-210X.13270>, and Noonan & Fleming et al (2019) <doi:10.1186/s40462-019-0177-1>.
Author: Christen H. Fleming [aut, cre], Justin M. Calabrese [aut], Xianghui Dong [ctb], Kevin Winner [ctb], Guillaume Péron [ctb], Michael J. Noonan [ctb], Bart Kranstauber [ctb], Eliezer Gurarie [ctb], Kamran Safi [ctb], Paul C. Cross [dtc], Thomas Mueller [dtc], Rogério C. de Paula [dtc], Thomas Akre [dtc], Jonathan Drescher-Lehman [dtc], Autumn-Lynn Harrison [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>

Diff between ctmm versions 0.5.7 dated 2019-10-07 and 0.5.8 dated 2019-12-11

 DESCRIPTION               |   23 ++--
 MD5                       |  121 +++++++++++-----------
 NAMESPACE                 |    3 
 NEWS.md                   |   19 +++
 R/1.R                     |   49 ++++++++
 R/anonymize.R             |    4 
 R/color.R                 |    6 -
 R/covm.R                  |    7 -
 R/ctmm.R                  |    5 
 R/cv.R                    |   75 ++++++++-----
 R/encounter.R             |only
 R/export.R                |    2 
 R/extent.R                |   34 +++++-
 R/gaussian.R              |only
 R/generic.R               |   88 ++++++----------
 R/kalman.R                |    7 -
 R/kde.R                   |   46 +++-----
 R/krige.R                 |    6 -
 R/likelihood.R            |   84 ++++++++-------
 R/matrix.R                |    4 
 R/mean.R                  |   30 ++++-
 R/median.R                |    2 
 R/numDeriv.R              |   23 ++--
 R/optim.R                 |    8 -
 R/outlier.R               |   12 +-
 R/overlap.R               |   80 +-------------
 R/parameters.R            |   83 ++++++++++++---
 R/periodogram.R           |    2 
 R/plot.variogram.R        |    9 +
 R/projection.R            |   23 +++-
 R/select.R                |  251 ++++++++++++++++++++++++++++------------------
 R/summary.ctmm.R          |    2 
 R/telemetry.R             |   61 ++++++-----
 R/temp_unzip.R            |   10 -
 R/uere.R                  |   20 +--
 R/units.R                 |   51 +++++++--
 R/variogram.R             |    4 
 R/variogram.fit.R         |    2 
 TODO                      |   45 +++++---
 inst/doc/akde.html        |   18 +--
 inst/doc/error.R          |    5 
 inst/doc/error.Rmd        |    5 
 inst/doc/error.html       |   53 +++++----
 inst/doc/periodogram.R    |    6 -
 inst/doc/periodogram.Rmd  |    6 -
 inst/doc/periodogram.html |   66 ++++++------
 inst/doc/variogram.html   |   38 +++---
 man/akde.Rd               |    2 
 man/ctmm-package.Rd       |   12 +-
 man/ctmm.fit.Rd           |    9 +
 man/encounter.Rd          |only
 man/export.Rd             |   12 +-
 man/extent.Rd             |    6 +
 man/mean.variogram.Rd     |    2 
 man/occurrence.Rd         |    2 
 man/outlie.Rd             |    6 -
 man/plot.variogram.Rd     |    2 
 man/simulate.ctmm.Rd      |    2 
 man/speed.Rd              |    8 -
 man/unit.Rd               |    8 +
 man/variogram.Rd          |    2 
 vignettes/error.Rmd       |    5 
 vignettes/periodogram.Rmd |    6 -
 63 files changed, 931 insertions(+), 651 deletions(-)

More information about ctmm at CRAN
Permanent link

Package BLPestimatoR updated to version 0.3.2 with previous version 0.3.0 dated 2019-10-18

Title: Performs a BLP Demand Estimation
Description: Provides the estimation algorithm to perform the demand estimation described in Berry, Levinsohn and Pakes (1995) <DOI:10.2307/2171802> . The routine uses analytic gradients and offers a large number of implemented integration methods and optimization routines.
Author: Daniel Brunner (aut), Constantin Weiser (ctr), Andre Romahn (ctr)
Maintainer: Daniel Brunner <daniel.brunner@hhu.de>

Diff between BLPestimatoR versions 0.3.0 dated 2019-10-18 and 0.3.2 dated 2019-12-11

 DESCRIPTION             |    6 +++---
 MD5                     |    8 ++++----
 R/estimateBLP.R         |    6 +++---
 R/wrappers.R            |    4 ++--
 inst/doc/blp_intro.html |    4 ++--
 5 files changed, 14 insertions(+), 14 deletions(-)

More information about BLPestimatoR at CRAN
Permanent link

Package qrandom updated to version 1.2.1 with previous version 1.2 dated 2019-08-20

Title: True Random Numbers using the ANU Quantum Random Numbers Server
Description: The ANU Quantum Random Number Generator provided by the Australian National University generates true random numbers in real-time by measuring the quantum fluctuations of the vacuum. This package offers an interface using their API. The electromagnetic field of the vacuum exhibits random fluctuations in phase and amplitude at all frequencies. By carefully measuring these fluctuations, one is able to generate ultra-high bandwidth random numbers. The quantum Random Number Generator is based on the papers by Symul et al., (2011) <doi:10.1063/1.3597793> and Haw, et al. (2015) <doi:10.1103/PhysRevApplied.3.054004>. The package offers functions to retrieve a sequence of random integers or hexadecimals and true random samples from a normal or uniform distribution.
Author: Siegfried Köstlmeier [aut, cre] (<https://orcid.org/0000-0002-7221-6981>), Boris Steipe [ctb] (<https://orcid.org/0000-0002-1134-6758>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

Diff between qrandom versions 1.2 dated 2019-08-20 and 1.2.1 dated 2019-12-11

 DESCRIPTION                         |    8 ++++----
 MD5                                 |   20 ++++++++++----------
 R/qUUID.R                           |    5 +++++
 R/qrandom.R                         |   16 +++++++++++++++-
 R/qrandommaxint.R                   |    6 +++++-
 build/partial.rdb                   |binary
 tests/testthat/test-qUUID.R         |    5 +++++
 tests/testthat/test-qrandom.R       |    6 +++++-
 tests/testthat/test-qrandommaxint.R |    4 ++++
 tests/testthat/test-qrandomnorm.R   |    4 ++++
 tests/testthat/test-qrandomunif.R   |    4 ++++
 11 files changed, 61 insertions(+), 17 deletions(-)

More information about qrandom at CRAN
Permanent link

Package essurvey updated to version 1.0.5 with previous version 1.0.4 dated 2019-11-04

Title: Download Data from the European Social Survey on the Fly
Description: Download data from the European Social Survey directly from their website <http://www.europeansocialsurvey.org/>. There are two families of functions that allow you to download and interactively check all countries and rounds available.
Author: Jorge Cimentada [aut, cre], Thomas Leeper [rev] (Thomas reviewed the package for rOpensci,see https://github.com/ropensci/onboarding/issues/201), Nujcharee Haswell [rev] (Nujcharee reviewed the package for rOpensci, see https://github.com/ropensci/onboarding/issues/201), Jorge Lopez [ctb], François Briatte [ctb]
Maintainer: Jorge Cimentada <cimentadaj@gmail.com>

Diff between essurvey versions 1.0.4 dated 2019-11-04 and 1.0.5 dated 2019-12-11

 DESCRIPTION                             |   10 
 MD5                                     |   44 -
 NEWS.md                                 |   16 
 R/download_format.R                     |    8 
 R/show_any_rounds.R                     |   14 
 R/show_funs.R                           |   12 
 inst/doc/intro_ess.R                    |   34 -
 inst/doc/intro_ess.html                 |    7 
 man/import_country.Rd                   |    9 
 man/import_rounds.Rd                    |    8 
 man/import_sddf_country.Rd              |    9 
 man/show_countries.Rd                   |    3 
 man/show_country_rounds.Rd              |    4 
 man/show_rounds.Rd                      |    3 
 man/show_rounds_country.Rd              |    3 
 man/show_theme_rounds.Rd                |    3 
 man/show_themes.Rd                      |    2 
 tests/testthat/test-1-show_.R           |  437 +++++++-------
 tests/testthat/test-2-country.R         |  946 ++++++++++++++++----------------
 tests/testthat/test-3-rounds.R          |  274 ++++-----
 tests/testthat/test-4-recode_missings.R |  277 ++++-----
 tests/testthat/test-6-country_lookup.R  |    1 
 tests/testthat/test-7-set_email.R       |    2 
 23 files changed, 1114 insertions(+), 1012 deletions(-)

More information about essurvey at CRAN
Permanent link

Package mstate updated to version 0.2.12 with previous version 0.2.11 dated 2018-04-09

Title: Data Preparation, Estimation and Prediction in Multi-State Models
Description: Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.
Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco, with contributions by Ronald Geskus
Maintainer: Hein Putter <H.Putter@lumc.nl>

Diff between mstate versions 0.2.11 dated 2018-04-09 and 0.2.12 dated 2019-12-11

 ChangeLog             |    3 ++
 DESCRIPTION           |   10 ++++----
 MD5                   |   14 +++++------
 R/cuminc.R            |   62 ++++++++++++++++++++------------------------------
 build/vignette.rds    |binary
 inst/doc/Tutorial.pdf |binary
 man/cuminc.Rd         |    2 -
 man/msprep.Rd         |    2 -
 8 files changed, 43 insertions(+), 50 deletions(-)

More information about mstate at CRAN
Permanent link

Package IMIFA updated to version 2.1.1 with previous version 2.1.0 dated 2019-02-04

Title: Infinite Mixtures of Infinite Factor Analysers and Related Models
Description: Provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametrically clustering high-dimensional data, introduced by Murphy et al. (2019) <doi:10.1214/19-BA1179>. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results, conducting posterior inference on parameters of interest, posterior predictive checking, and quantifying uncertainty.
Author: Keefe Murphy [aut, cre], Cinzia Viroli [ctb], Isobel Claire Gormley [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>

Diff between IMIFA versions 2.1.0 dated 2019-02-04 and 2.1.1 dated 2019-12-11

 DESCRIPTION                                                 |   14 
 MD5                                                         |  120 ++--
 NAMESPACE                                                   |    7 
 R/Diagnostics.R                                             |  110 ++--
 R/FullConditionals.R                                        |  230 +++++---
 R/Gibbs_FA.R                                                |    8 
 R/Gibbs_IFA.R                                               |    1 
 R/Gibbs_IMFA.R                                              |   79 +--
 R/Gibbs_IMIFA.R                                             |  254 ++++++---
 R/Gibbs_MFA.R                                               |   34 -
 R/Gibbs_MIFA.R                                              |   98 ++-
 R/Gibbs_OMFA.R                                              |   42 -
 R/Gibbs_OMIFA.R                                             |  100 ++-
 R/IMIFA.R                                                   |   10 
 R/MainFunction.R                                            |   65 +-
 R/PlottingFunctions.R                                       |  116 ++--
 R/SimulateData.R                                            |   43 -
 R/data.R                                                    |   16 
 README.md                                                   |    4 
 build/vignette.rds                                          |binary
 inst/CITATION                                               |   24 
 inst/NEWS.md                                                |   26 
 inst/doc/IMIFA.R                                            |   75 +-
 inst/doc/IMIFA.Rmd                                          |   60 +-
 inst/doc/IMIFA.html                                         |  110 ++--
 man/G_moments.Rd                                            |  119 ++--
 man/G_priorDensity.Rd                                       |  114 ++--
 man/IMIFA-package.Rd                                        |  124 ++--
 man/IMIFA_news.Rd                                           |   34 -
 man/Ledermann.Rd                                            |   48 -
 man/MGP_check.Rd                                            |  142 ++---
 man/PGMM_dfree.Rd                                           |  102 +--
 man/Procrustes.Rd                                           |  136 ++---
 man/USPSdigits.Rd                                           |   88 +--
 man/Zsimilarity.Rd                                          |  124 ++--
 man/bnpControl.Rd                                           |  210 ++++----
 man/coffee.Rd                                               |   38 -
 man/get_IMIFA_results.Rd                                    |  288 +++++------
 man/gumbel_max.Rd                                           |  122 ++--
 man/heat_legend.Rd                                          |   84 +--
 man/is.cols.Rd                                              |   50 -
 man/is.posi_def.Rd                                          |   82 +--
 man/mat2cols.Rd                                             |  148 ++---
 man/mcmc_IMIFA.Rd                                           |  313 ++++++------
 man/mgpControl.Rd                                           |  187 +++----
 man/mixfaControl.Rd                                         |  243 ++++-----
 man/olive.Rd                                                |   41 -
 man/pareto_scale.Rd                                         |   60 +-
 man/plot.Results_IMIFA.Rd                                   |  270 +++++-----
 man/plot_cols.Rd                                            |  138 ++---
 man/post_conf_mat.Rd                                        |   86 +--
 man/psi_hyper.Rd                                            |  160 +++---
 man/rDirichlet.Rd                                           |   72 +-
 man/scores_MAP.Rd                                           |  107 ++--
 man/shift_GA.Rd                                             |   72 +-
 man/show_IMIFA_digit.Rd                                     |  125 ++--
 man/show_digit.Rd                                           |   78 +-
 man/sim_IMIFA.Rd                                            |  208 ++++---
 man/storeControl.Rd                                         |  124 ++--
 vignettes/IMIFA.Rmd                                         |   60 +-
 vignettes/res_olive_IMIFA__Edited-Vignette-only-Version.rda |binary
 61 files changed, 3215 insertions(+), 2828 deletions(-)

More information about IMIFA at CRAN
Permanent link

Package icesTAF updated to version 3.3-1 with previous version 3.3-0 dated 2019-12-03

Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework <https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.
Author: Arni Magnusson [aut, cre], Colin Millar [aut], Alexandros Kokkalis [ctb], Ibrahim Umar [ctb]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>

Diff between icesTAF versions 3.3-0 dated 2019-12-03 and 3.3-1 dated 2019-12-11

 DESCRIPTION            |   18 ++++++++++--------
 MD5                    |   39 ++++++++++++++++++++-------------------
 NEWS                   |   12 ++++++++++++
 R/access.vocab.R       |only
 R/catage.long.R        |    4 ++--
 R/catage.taf.R         |    4 ++--
 R/catage.xtab.R        |    4 ++--
 R/draft.data.R         |    2 +-
 R/ds.file.R            |    2 +-
 R/ds.package.R         |    2 +-
 R/icesTAF-package.R    |    2 +-
 R/parse.repo.R         |   17 +++++++++--------
 R/process.bib.R        |   13 +++++++++++--
 R/process.inner.R      |    4 +---
 R/summary.taf.R        |    4 ++--
 man/catage.long.Rd     |    4 ++--
 man/catage.taf.Rd      |    4 ++--
 man/catage.xtab.Rd     |    4 ++--
 man/icesTAF-package.Rd |    2 +-
 man/process.bib.Rd     |    5 +++--
 man/summary.taf.Rd     |    4 ++--
 21 files changed, 87 insertions(+), 63 deletions(-)

More information about icesTAF at CRAN
Permanent link

Package rvkstat updated to version 2.6.3 with previous version 2.6.2 dated 2019-07-28

Title: Interface to API 'vk.com'
Description: Load data from vk.com api about your communiti users and views, ads performance, post on user wall and etc. For more detail see <https://vk.com/dev/first_guide>.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>

Diff between rvkstat versions 2.6.2 dated 2019-07-28 and 2.6.3 dated 2019-12-11

 DESCRIPTION              |    8 ++++----
 MD5                      |   10 +++++-----
 NEWS.md                  |    8 ++++++++
 R/vkGetAdStatistics.R    |    4 ++++
 build/partial.rdb        |binary
 man/vkGetAdStatistics.Rd |    1 +
 6 files changed, 22 insertions(+), 9 deletions(-)

More information about rvkstat at CRAN
Permanent link

Package performance updated to version 0.4.2 with previous version 0.4.0 dated 2019-10-21

Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality, which are not directly provided by R's 'base' or 'stats' packages. These include e.g. measures like r-squared, intraclass correlation coefficient (Nakagawa, Johnson & Schielzeth (2017) <doi:10.1098/rsif.2017.0213>), root mean squared error or functions to check models for overdispersion, singularity or zero-inflation and more. Functions apply to a large variety of regression models, including generalized linear models, mixed effects models and Bayesian models.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>), Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between performance versions 0.4.0 dated 2019-10-21 and 0.4.2 dated 2019-12-11

 DESCRIPTION                                      |   14 
 MD5                                              |  263 ++++++++--------
 NAMESPACE                                        |   45 ++
 NEWS.md                                          |   26 +
 R/binned_residuals.R                             |   36 +-
 R/check_autocorrelation.R                        |    5 
 R/check_collinearity.R                           |  140 +++-----
 R/check_convergence.R                            |    4 
 R/check_distribution.R                           |    3 
 R/check_heteroscedasticity.R                     |    1 
 R/check_homogeneity.R                            |    9 
 R/check_model.R                                  |   22 -
 R/check_model_diagnostics.R                      |   63 ++-
 R/check_normality.R                              |    8 
 R/check_outliers.R                               |   85 +++--
 R/check_overdispersion.R                         |   44 +-
 R/check_singularity.R                            |   36 +-
 R/check_zeroinflation.R                          |    9 
 R/compare_performance.R                          |   65 +++
 R/cronbachs_alpha.R                              |   41 ++
 R/helpers.R                                      |   86 ++++-
 R/icc.R                                          |   21 -
 R/item_difficulty.R                              |    2 
 R/item_intercor.R                                |    2 
 R/item_reliability.R                             |    1 
 R/item_split_half.R                              |    1 
 R/logLik.R                                       |   20 -
 R/looic.R                                        |    5 
 R/model_performance.R                            |   30 +
 R/model_performance.bayesian.R                   |   14 
 R/model_performance.lavaan.R                     |   12 
 R/model_performance.lm.R                         |   14 
 R/model_performance.mixed.R                      |   25 -
 R/performance_accuracy.R                         |    8 
 R/performance_aicc.R                             |   11 
 R/performance_hosmer.R                           |    3 
 R/performance_logloss.R                          |   14 
 R/performance_mse.R                              |   20 -
 R/performance_pcp.R                              |   15 
 R/performance_rmse.R                             |   40 +-
 R/performance_roc.R                              |    6 
 R/performance_rse.R                              |    1 
 R/performance_score.R                            |   28 +
 R/plot-methods.R                                 |   27 +
 R/print-methods.R                                |  111 +++++-
 R/r2.R                                           |  374 +++++++++++++----------
 R/r2_bayes.R                                     |   90 ++---
 R/r2_coxsnell.R                                  |   81 ++--
 R/r2_kl.R                                        |    6 
 R/r2_loo.R                                       |   14 
 R/r2_mcfadden.R                                  |   56 ++-
 R/r2_mckelvey.R                                  |   15 
 R/r2_nagelkerke.R                                |   84 ++---
 R/r2_nakagawa.R                                  |    1 
 R/r2_tjur.R                                      |    1 
 R/r2_xu.R                                        |    1 
 R/r2_zeroinflated.R                              |    6 
 R/skewness_kurtosis.R                            |    2 
 README.md                                        |   66 +++-
 build/partial.rdb                                |binary
 man/binned_residuals.Rd                          |  125 +++----
 man/check_autocorrelation.Rd                     |   73 ++--
 man/check_collinearity.Rd                        |  122 +++----
 man/check_convergence.Rd                         |   97 ++---
 man/check_distribution.Rd                        |   87 ++---
 man/check_heteroscedasticity.Rd                  |   57 +--
 man/check_homogeneity.Rd                         |   73 ++--
 man/check_model.Rd                               |  115 +++----
 man/check_normality.Rd                           |   84 ++---
 man/check_outliers.Rd                            |  373 +++++++++++-----------
 man/check_overdispersion.Rd                      |  135 ++++----
 man/check_singularity.Rd                         |  149 ++++-----
 man/check_zeroinflation.Rd                       |   75 ++--
 man/classify_distribution.Rd                     |   26 -
 man/cronbachs_alpha.Rd                           |   67 ++--
 man/figures/unnamed-chunk-13-1.png               |only
 man/figures/unnamed-chunk-22-1.png               |only
 man/icc.Rd                                       |  249 +++++++--------
 man/item_difficulty.Rd                           |   70 ++--
 man/item_intercor.Rd                             |   96 ++---
 man/item_reliability.Rd                          |   87 ++---
 man/item_split_half.Rd                           |   75 ++--
 man/looic.Rd                                     |   49 +--
 man/model_performance.Rd                         |  157 +++++----
 man/model_performance.lavaan.Rd                  |  121 +++----
 man/model_performance.lm.Rd                      |   97 ++---
 man/model_performance.merMod.Rd                  |   71 ++--
 man/model_performance.stanreg.Rd                 |  115 +++----
 man/performance_accuracy.Rd                      |   98 ++----
 man/performance_aicc.Rd                          |   65 +--
 man/performance_hosmer.Rd                        |   67 ++--
 man/performance_logloss.Rd                       |   71 ++--
 man/performance_mse.Rd                           |   69 ++--
 man/performance_pcp.Rd                           |  121 +++----
 man/performance_rmse.Rd                          |   93 ++---
 man/performance_roc.Rd                           |  105 +++---
 man/performance_rse.Rd                           |   53 +--
 man/performance_score.Rd                         |  133 ++++----
 man/r2.Rd                                        |   87 ++---
 man/r2_bayes.Rd                                  |  123 +++----
 man/r2_coxsnell.Rd                               |   75 ++--
 man/r2_kullback.Rd                               |   55 +--
 man/r2_loo.Rd                                    |   57 +--
 man/r2_mcfadden.Rd                               |   65 +--
 man/r2_mckelvey.Rd                               |   83 ++---
 man/r2_nagelkerke.Rd                             |   51 +--
 man/r2_nakagawa.Rd                               |   83 ++---
 man/r2_tjur.Rd                                   |   57 +--
 man/r2_xu.Rd                                     |   59 +--
 man/r2_zeroinflated.Rd                           |   75 ++--
 tests/testthat/test-backticks.R                  |only
 tests/testthat/test-check_convergence.R          |    2 
 tests/testthat/test-check_overdispersion.R       |    2 
 tests/testthat/test-check_singularity.R          |    2 
 tests/testthat/test-check_zeroinflation.R        |    2 
 tests/testthat/test-compare_performance.R        |    2 
 tests/testthat/test-coxph.R                      |    6 
 tests/testthat/test-cronbachs_alpha.R            |    2 
 tests/testthat/test-icc.R                        |    2 
 tests/testthat/test-item_difficulty.R            |   11 
 tests/testthat/test-item_intercor.R              |    2 
 tests/testthat/test-item_reliability.R           |   11 
 tests/testthat/test-item_splithalf.R             |    5 
 tests/testthat/test-model_performance-various.R  |    2 
 tests/testthat/test-model_performance.bayesian.R |    5 
 tests/testthat/test-model_performance.lm.R       |    2 
 tests/testthat/test-model_performance.merMod.R   |    2 
 tests/testthat/test-r2_coxsnell.R                |    2 
 tests/testthat/test-r2_kullback.R                |    2 
 tests/testthat/test-r2_mcfadden.R                |    5 
 tests/testthat/test-r2_nagelkerke.R              |    3 
 tests/testthat/test-r2_nakagawa.R                |    5 
 tests/testthat/test-r2_tjur.R                    |    4 
 tests/testthat/test-r2_zeroinflated.R            |    2 
 134 files changed, 3715 insertions(+), 3191 deletions(-)

More information about performance at CRAN
Permanent link

Package ungroup updated to version 1.1.5 with previous version 1.1.1 dated 2018-10-15

Title: Penalized Composite Link Model for Efficient Estimation of Smooth Distributions from Coarsely Binned Data
Description: Versatile method for ungrouping histograms (binned count data) assuming that counts are Poisson distributed and that the underlying sequence on a fine grid to be estimated is smooth. The method is based on the composite link model and estimation is achieved by maximizing a penalized likelihood. Smooth detailed sequences of counts and rates are so estimated from the binned counts. Ungrouping binned data can be desirable for many reasons: Bins can be too coarse to allow for accurate analysis; comparisons can be hindered when different grouping approaches are used in different histograms; and the last interval is often wide and open-ended and, thus, covers a lot of information in the tail area. Age-at-death distributions grouped in age classes and abridged life tables are examples of binned data. Because of modest assumptions, the approach is suitable for many demographic and epidemiological applications. For a detailed description of the method and applications see Rizzi et al. (2015) <doi:10.1093/aje/kwv020>.
Author: Marius D. Pascariu [aut, cre] (<https://orcid.org/0000-0002-2568-6489>), Silvia Rizzi [aut], Jonas Schoeley [aut] (<https://orcid.org/0000-0002-3340-8518>), Maciej J. Danko [aut] (<https://orcid.org/0000-0002-7924-9022>)
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>

Diff between ungroup versions 1.1.1 dated 2018-10-15 and 1.1.5 dated 2019-12-11

 DESCRIPTION                    |   10 
 LICENSE                        |only
 MD5                            |  135 +++++-----
 NAMESPACE                      |  109 ++++----
 NEWS                           |   27 +-
 R/RcppExports.R                |   22 -
 R/pclm_1D.R                    |  527 ++++++++++++++++++++++-------------------
 R/pclm_2D.R                    |  416 ++++++++++++++++----------------
 R/pclm_CI.R                    |  293 +++++++++++-----------
 R/pclm_control.R               |  163 ++++++------
 R/pclm_fit.R                   |  424 +++++++++++++++++---------------
 R/pclm_graphics.R              |  345 +++++++++++++-------------
 R/pclm_optim.R                 |  173 +++++++------
 R/ungroup-data.R               |   78 +++---
 R/ungroup-package.r            |   44 +--
 R/utils.R                      |  289 +++++++++++-----------
 README.md                      |  116 ++++-----
 THANKS                         |   38 +-
 build/partial.rdb              |binary
 build/vignette.rds             |binary
 inst/CITATION                  |   68 ++---
 inst/REFERENCES.bib            |  193 +++++++--------
 inst/doc/Intro.R               |  118 ++++-----
 inst/doc/Intro.Rmd             |  292 +++++++++++-----------
 inst/doc/Intro.pdf             |binary
 man/AIC.pclm.Rd                |  160 ++++++------
 man/AIC.pclm2D.Rd              |  160 ++++++------
 man/BIC.pclm.Rd                |  154 +++++------
 man/BIC.pclm2D.Rd              |  160 ++++++------
 man/build_B_spline_basis.Rd    |   72 ++---
 man/build_C_matrix.Rd          |   64 ++--
 man/build_P_matrix.Rd          |   46 +--
 man/compute_standard_errors.Rd |   38 +-
 man/control.pclm.Rd            |  102 +++----
 man/control.pclm2D.Rd          |  102 +++----
 man/create.artificial.bin.Rd   |   43 +--
 man/delete.artificial.bin.Rd   |   30 +-
 man/frac.Rd                    |   30 +-
 man/map.bins.Rd                |   45 +--
 man/ofun.Rd                    |   40 +--
 man/optimize_par.Rd            |   52 ++--
 man/pclm.Rd                    |  268 ++++++++++----------
 man/pclm.confidence.Rd         |   65 ++---
 man/pclm.confidence.dx.Rd      |   30 +-
 man/pclm.confidence.mx.Rd      |   30 +-
 man/pclm.fit.Rd                |  109 ++++----
 man/pclm.input.check.Rd        |   30 +-
 man/pclm2D.Rd                  |  238 +++++++++---------
 man/plot.pclm.Rd               |  104 ++++----
 man/plot.pclm2D.Rd             |  107 ++++----
 man/print.pclm.Rd              |   34 +-
 man/print.pclm2D.Rd            |   34 +-
 man/print.summary.pclm.Rd      |   34 +-
 man/print.summary.pclm2D.Rd    |   34 +-
 man/print.ungroup.data.Rd      |   34 +-
 man/residuals.pclm.Rd          |   56 ++--
 man/residuals.pclm2D.Rd        |   74 ++---
 man/seqlast.Rd                 |   46 +--
 man/suggest.valid.out.step.Rd  |   38 +-
 man/summary.pclm.Rd            |   34 +-
 man/summary.pclm2D.Rd          |   42 +--
 man/ungroup.Rd                 |  100 +++----
 man/ungroup.data.Rd            |   62 ++--
 man/validate.nlast.Rd          |   49 +--
 tests/testthat.R               |    8 
 tests/testthat/test_pclm.R     |  198 +++++++--------
 tests/testthat/test_pclm2D.R   |  124 ++++-----
 vignettes/Intro.Rmd            |  292 +++++++++++-----------
 vignettes/REFERENCES.bib       |  192 +++++++-------
 69 files changed, 3922 insertions(+), 3722 deletions(-)

More information about ungroup at CRAN
Permanent link

Package scorecard updated to version 0.2.8.1 with previous version 0.2.8 dated 2019-12-04

Title: Credit Risk Scorecard
Description: The `scorecard` package makes the development of credit risk scorecard easier and efficient by providing functions for some common tasks, such as data partition, variable selection, woe binning, scorecard scaling, performance evaluation and report generation. These functions can also used in the development of machine learning models. The references including: 1. Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard: Development and Implementation Using SAS. 2. Siddiqi, N. (2006, ISBN: 9780471754510). Credit risk scorecards. Developing and Implementing Intelligent Credit Scoring.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>

Diff between scorecard versions 0.2.8 dated 2019-12-04 and 0.2.8.1 dated 2019-12-11

 DESCRIPTION        |    8 ++++----
 MD5                |   18 +++++++++---------
 NEWS.md            |    6 ++++++
 R/germancredit.R   |    2 +-
 R/perf.R           |    9 ++++++---
 R/report.R         |    4 ++--
 R/woebin.R         |   10 +++++++---
 inst/doc/demo.html |    7 +++----
 man/report.Rd      |    4 ++--
 man/woebin_adj.Rd  |    5 ++++-
 10 files changed, 44 insertions(+), 29 deletions(-)

More information about scorecard at CRAN
Permanent link

Package dtwclust updated to version 5.5.6 with previous version 5.5.5 dated 2019-09-19

Title: Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance
Description: Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>

Diff between dtwclust versions 5.5.5 dated 2019-09-19 and 5.5.6 dated 2019-12-11

 DESCRIPTION                                  |    8 
 MD5                                          |   18 -
 R/UTILS-as-methods.R                         |    4 
 inst/NEWS.Rd                                 |    4 
 inst/doc/dtwclust.pdf                        |binary
 inst/doc/parallelization-considerations.html |    3 
 inst/doc/timing-experiments.html             |    5 
 tests/testthat/integration/families.R        |   16 -
 tests/testthat/integration/proxy.R           |  280 +++++++++++++--------------
 tests/testthat/unit/methods.R                |    4 
 10 files changed, 170 insertions(+), 172 deletions(-)

More information about dtwclust at CRAN
Permanent link

Package dirichletprocess updated to version 0.3.1 with previous version 0.3.0 dated 2019-05-03

Title: Build Dirichlet Process Objects for Bayesian Modelling
Description: Perform nonparametric Bayesian analysis using Dirichlet processes without the need to program the inference algorithms. Utilise included pre-built models or specify custom models and allow the 'dirichletprocess' package to handle the Markov chain Monte Carlo sampling. Our Dirichlet process objects can act as building blocks for a variety of statistical models including and not limited to: density estimation, clustering and prior distributions in hierarchical models. See Teh, Y. W. (2011) <https://www.stats.ox.ac.uk/~teh/research/npbayes/Teh2010a.pdf>, among many other sources.
Author: Gordon J. Ross [aut], Dean Markwick [aut, cre], Kees Mulder [ctb] (<https://orcid.org/0000-0002-5387-3812>)
Maintainer: Dean Markwick <dean.markwick@talk21.com>

Diff between dirichletprocess versions 0.3.0 dated 2019-05-03 and 0.3.1 dated 2019-12-11

 DESCRIPTION                                   |    6 ++--
 MD5                                           |   29 ++++++++++++-----------
 NEWS.md                                       |   10 +++++++-
 R/dirichlet_process_mvnormal.R                |    9 ++++---
 R/initialise.R                                |   17 +++++++------
 R/mvnormal_normal_wishart.R                   |   26 ++++++++++++++-------
 R/mvnormal_semi_conjugate.R                   |    2 -
 R/stick_breaking.R                            |   26 +++++++++++++--------
 R/utilities.R                                 |    2 -
 inst/doc/dirichletprocess.Rnw                 |   19 ++++++++-------
 inst/doc/dirichletprocess.pdf                 |binary
 man/DirichletProcessMvnormal.Rd               |    5 +++-
 man/Initialise.Rd                             |    5 +++-
 tests/testthat/Rplots.pdf                     |only
 tests/testthat/test_mvnormal_normal_wishart.R |   32 ++++++++++++++++++++++++++
 vignettes/dirichletprocess.Rnw                |   19 ++++++++-------
 16 files changed, 138 insertions(+), 69 deletions(-)

More information about dirichletprocess at CRAN
Permanent link


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