Title: Methods for Computing Spatial, Temporal, and Spatiotemporal
Statistics
Description: Methods for computing spatial, temporal, and spatiotemporal
statistics as described in Gouhier and Guichard (2014)
<doi:10.1111/2041-210X.12188>. These methods include
empirical univariate, bivariate and multivariate
variograms; fitting variogram models; phase locking and synchrony analysis;
generating autocorrelated and cross-correlated matrices.
Author: Tarik C. Gouhier
Maintainer: Tarik C. Gouhier <tarik.gouhier@gmail.com>
Diff between synchrony versions 0.3.7 dated 2018-05-19 and 0.3.8 dated 2019-12-05
synchrony-0.3.7/synchrony/R/synchrony-internal.R |only synchrony-0.3.8/synchrony/DESCRIPTION | 12 +++++++----- synchrony-0.3.8/synchrony/MD5 | 13 ++++++------- synchrony-0.3.8/synchrony/R/correlated.matrix.R | 2 +- synchrony-0.3.8/synchrony/R/vario.fit.R | 14 +++++++------- synchrony-0.3.8/synchrony/README.md | 2 +- synchrony-0.3.8/synchrony/inst/NEWS.Rd | 8 ++++++++ synchrony-0.3.8/synchrony/man/synchrony-package.Rd | 16 +++++++++------- 8 files changed, 39 insertions(+), 28 deletions(-)
Title: A Soil Survey Toolkit
Description: Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
Author: Dylan Beaudette [cre],
Jay Skovlin [aut],
Stephen Roecker [aut],
USDA-NRCS Soil Survey Staff [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between sharpshootR versions 1.5 dated 2019-11-20 and 1.5.1 dated 2019-12-05
DESCRIPTION | 10 ++--- MD5 | 12 +++--- R/PCP_plot.R | 1 R/PLSS2LL.R | 52 ++++++++++++++--------------- R/multinominal2logical.R | 4 +- tests/testthat/test-FFD.R | 8 ++-- tests/testthat/test-multinominal2logical.R | 2 - 7 files changed, 45 insertions(+), 44 deletions(-)
Title: Length-Based Spawning Potential Ratio
Description: Simulate expected equilibrium length composition, yield-per-recruit, and
the spawning potential ratio (SPR) using the length-based SPR (LBSPR) model. Fit the LBSPR
model to length data to estimate selectivity, relative apical fishing mortality, and
the spawning potential ratio for data-limited fisheries.
See Hordyk et al (2016) <doi:10.1139/cjfas-2015-0422> for more information about the
LBSPR assessment method.
Author: Adrian Hordyk [aut, cre]
Maintainer: Adrian Hordyk <ar.hordyk@gmail.com>
Diff between LBSPR versions 0.1.4 dated 2019-08-26 and 0.1.5 dated 2019-12-05
LBSPR-0.1.4/LBSPR/inst/shiny_apps/Sim |only LBSPR-0.1.5/LBSPR/DESCRIPTION | 6 ++-- LBSPR-0.1.5/LBSPR/MD5 | 18 ++++++------ LBSPR-0.1.5/LBSPR/R/LBSPRfit_.r | 22 +++++++------- LBSPR-0.1.5/LBSPR/R/Shiny.r | 2 - LBSPR-0.1.5/LBSPR/R/defineMeths.r | 4 +- LBSPR-0.1.5/LBSPR/inst/doc/LBSPR.html | 5 +-- LBSPR-0.1.5/LBSPR/inst/shiny_apps/LBSPR/server.r | 34 +++++++++++++++-------- LBSPR-0.1.5/LBSPR/inst/shiny_apps/YPRSim |only 9 files changed, 51 insertions(+), 40 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex
macroevolutionary dynamics on phylogenetic trees. It is a companion
package to the command line program BAMM (Bayesian Analysis of
Macroevolutionary Mixtures) and is entirely oriented towards the analysis,
interpretation, and visualization of evolutionary rates. Functionality
includes visualization of rate shifts on phylogenies, estimating
evolutionary rates through time, comparing posterior distributions of
evolutionary rates across clades, comparing diversification models using
Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi,
Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.1.6 dated 2017-02-03 and 2.1.7 dated 2019-12-05
DESCRIPTION | 13 +- MD5 | 161 ++++++++++++++++++------------------- R/NU.branching.times.R | 2 R/addBAMMlegend.R | 45 +++++++++- R/addBAMMshifts.R | 2 R/as.phylo.bammdata.R | 2 R/bammLikelihood.R | 2 R/colorMap.R | 26 ++++- R/computeBayesFactors.R | 6 - R/cumulativeShiftProbsTree.R | 2 R/dtRates.R | 2 R/generateControlFile.R | 2 R/getBestShiftConfiguration.R | 30 +++--- R/getCladeRates.R | 2 R/getCohortMatrix.R | 2 R/getEventData.R | 6 - R/getMarginalBranchRateMatrix.R | 4 R/getMeanBranchLengthTree.R | 2 R/getRateThroughTimeMatrix.R | 4 R/getTipRates.R | 2 R/marginalOddsRatioBranches.R | 20 ---- R/marginalShiftProbsTree.R | 2 R/maximumShiftCredibility.R | 2 R/phylogeneticMean.R | 8 - R/plot.bammdata.R | 56 +++++++++++- R/plot.bammshifts.R | 4 R/plot.credibleshiftset.R | 2 R/plotPrior.R | 2 R/plotRateThroughTime.R | 8 - R/speciesByRatesMatrix.R | 26 +++-- R/stepBF.R | 8 - R/subsetEventData.R | 2 R/subtreeBAMM.R | 6 - R/traitDependentBAMM.R | 49 +++++++---- R/writeEventData.R | 2 man/BAMMlikelihood.Rd | 13 ++ man/BAMMtools-data.Rd | 15 +-- man/BAMMtools.Rd | 10 -- man/ShiftProbsTree.Rd | 10 +- man/addBAMMlegend.Rd | 28 ++++-- man/addBAMMshifts.Rd | 21 +++- man/assignColorBreaks.Rd | 17 ++- man/cohorts.Rd | 21 +++- man/computeBayesFactors.Rd | 1 man/credibleShiftSet.Rd | 16 ++- man/distinctShiftConfigurations.Rd | 7 - man/dtRates.Rd | 7 - man/generateControlFile.Rd | 14 ++- man/getBestShiftConfiguration.Rd | 7 - man/getBranchShiftPriors.Rd | 7 - man/getCladeRates.Rd | 7 - man/getCohortMatrix.Rd | 7 - man/getEventData.Rd | 17 ++- man/getJenksBreaks.Rd | 7 - man/getMarginalBranchRateMatrix.Rd | 1 man/getMeanBranchLengthTree.Rd | 7 - man/getRateThroughTimeMatrix.Rd | 17 ++- man/getShiftNodesFromIndex.Rd | 7 - man/getTipRates.Rd | 9 -- man/getmrca.Rd | 7 - man/marginalOddsRatioBranches.Rd | 27 +----- man/maximumShiftCredibility.Rd | 7 - man/plot.bammdata.Rd | 42 +++++++-- man/plot.bammshifts.Rd | 27 ++++-- man/plot.credibleshiftset.Rd | 31 ++++--- man/plotPrior.Rd | 12 ++ man/plotRateThroughTime.Rd | 44 +++++++--- man/ratesHistogram.Rd | 19 ++-- man/richColors.Rd | 1 man/samplingProbs.Rd | 11 +- man/setBAMMpriors.Rd | 11 +- man/speciesByRatesMatrix.Rd | 34 +++---- man/stepBF.Rd | 10 -- man/subsetEventData.Rd | 7 - man/subtreeBAMM.Rd | 7 - man/summary.bammdata.Rd | 7 - man/summary.credibleshiftset.Rd | 9 -- man/testTimeVariableBranches.Rd | 9 -- man/traitDependentBAMM.Rd | 26 +++-- man/transparentColor.Rd | 1 man/writeEventData.Rd | 1 src/BAMMtools_init.c |only 82 files changed, 670 insertions(+), 467 deletions(-)
Title: Local Time Space Kriging
Description: Implements local spatial and local spatiotemporal Kriging based on local spatial and local spatiotemporal variograms, respectively. The method is documented in Kumar et al (2013) <https://www.nature.com/articles/jes201352)>.
Author: Naresh Kumar, Dong Liang, Jin Chen, Jun Chen
Maintainer: Dong Liang <dliang@umces.edu>
Diff between ltsk versions 1.0.7 dated 2019-02-01 and 1.0.8 dated 2019-12-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/dnb.R | 4 ++-- R/ltsk.R | 2 +- R/working.ltsk.R | 2 +- man/ltsk.Rd | 4 ++-- 6 files changed, 15 insertions(+), 15 deletions(-)
Title: Environments Behaving (Almost) as Lists
Description: List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting, e.g. 'x <- listenv(a = 1, b = 2); for (i in seq_along(x)) x[[i]] <- x[[i]] ^ 2; y <- as.list(x)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between listenv versions 0.7.0 dated 2018-01-21 and 0.8.0 dated 2019-12-05
DESCRIPTION | 8 +- MD5 | 44 ++++++++-------- NAMESPACE | 1 NEWS | 98 ++++++++++++++++++++++++------------ R/get_variable.R | 4 - R/listenv,dims.R | 12 ++-- R/listenv.R | 68 +++++++++++++----------- R/parse_env_subset.R | 97 +++++++++++++++++++++++------------ R/undim.R | 2 R/utils.R | 16 +++++ build/vignette.rds |binary inst/WORDLIST |only inst/doc/listenv.html | 2 inst/doc/listenv.md.rsp | 2 man/cash-.listenv.Rd | 1 man/cash-set-.listenv.Rd | 1 man/listenv.Rd | 1 man/mapping.Rd | 5 + man/undim.Rd | 1 tests/lapply.R |only tests/listenv.R | 2 tests/parse_env_subset,dimensions.R | 28 ++++++++++ tests/parse_env_subset.R | 81 +++++++++++++++++++++++++++++ vignettes/listenv.md.rsp | 2 24 files changed, 339 insertions(+), 137 deletions(-)
Title: Moment-Free Estimation of Sharpe Ratios
Description: An efficient moment-free estimator of the Sharpe ratio, or signal-to-noise ratio, for heavy-tailed data (see <arXiv:1505.01333>).
Author: Damien Challet
Maintainer: Damien Challet <damien.challet@gmail.com>
Diff between sharpeRratio versions 1.1 dated 2016-10-07 and 1.2 dated 2019-12-05
sharpeRratio-1.1/sharpeRratio/data/a_vs_R0dN.rda |only sharpeRratio-1.1/sharpeRratio/man/a_vs_R0dN.Rd |only sharpeRratio-1.2/sharpeRratio/DESCRIPTION | 12 +-- sharpeRratio-1.2/sharpeRratio/MD5 | 22 +++-- sharpeRratio-1.2/sharpeRratio/NAMESPACE | 6 - sharpeRratio-1.2/sharpeRratio/NEWS |only sharpeRratio-1.2/sharpeRratio/R/RcppExports.R | 4 - sharpeRratio-1.2/sharpeRratio/R/estimateSNR.R | 54 ++++++++------ sharpeRratio-1.2/sharpeRratio/README.md |only sharpeRratio-1.2/sharpeRratio/data/a.rda |only sharpeRratio-1.2/sharpeRratio/data/f.rda |only sharpeRratio-1.2/sharpeRratio/man/a.Rd |only sharpeRratio-1.2/sharpeRratio/man/estimateSNR.Rd | 16 ++-- sharpeRratio-1.2/sharpeRratio/man/f.Rd |only sharpeRratio-1.2/sharpeRratio/man/sharpeRratio-package.Rd | 5 - sharpeRratio-1.2/sharpeRratio/src/RcppExports.cpp | 22 ++++- 16 files changed, 83 insertions(+), 58 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.8.3 dated 2019-11-11 and 0.9.0 dated 2019-12-05
DESCRIPTION | 8 - MD5 | 234 ++++++++++++++++++---------------- NAMESPACE | 7 + NEWS.md | 73 ++++++++++ R/bioconductor.R | 46 +++++- R/bootstrap.R | 4 R/cache.R | 49 +++---- R/condition.R |only R/config.R | 40 +++++ R/defer.R | 6 R/dependencies.R | 58 +++++++- R/description.R | 29 ++++ R/diagnostics.R | 4 R/download.R | 24 +-- R/files.R | 166 ++++++++++++++++++++---- R/globals.R | 7 - R/hash.R | 3 R/hydrate.R | 10 - R/infrastructure.R | 69 +++++++--- R/init.R | 2 R/install.R | 44 +++--- R/load.R | 22 +++ R/local-packages.R |only R/lockfile-api.R |only R/lockfile-diff.R | 2 R/lockfile-read.R | 2 R/lockfile.R | 153 +++++++--------------- R/lockfiles.R |only R/migrate.R | 3 R/packages.R | 2 R/path.R | 8 - R/paths.R | 24 ++- R/platform.R | 30 ++++ R/pretty.R | 3 R/project.R | 23 --- R/python.R | 5 R/record.R |only R/records.R | 46 +++++- R/rehash.R |only R/remotes.R | 12 + R/renvignore.R | 4 R/restore.R | 35 +++-- R/retrieve.R | 68 +++++++--- R/run.R | 10 + R/scope.R | 26 +++ R/snapshot.R | 203 +++++++++++++++++++++--------- R/status.R | 236 ++++++++++++++++++++++++++++------- R/system.R |only R/temp.R | 2 R/tests.R | 16 +- R/testthat-helpers.R | 18 ++ R/update.R | 3 R/upgrade.R | 4 R/utils-map.R | 38 +++++ R/utils.R | 8 - R/vector.R | 13 + R/zzz.R | 2 build/vignette.rds |binary inst/doc/ci.R | 2 inst/doc/ci.Rmd | 2 inst/doc/ci.html | 3 inst/doc/collaborating.R | 2 inst/doc/collaborating.Rmd | 5 inst/doc/collaborating.html | 5 inst/doc/docker.R | 4 inst/doc/docker.Rmd | 8 - inst/doc/docker.html | 26 +-- inst/doc/faq.R | 2 inst/doc/faq.Rmd | 34 +++-- inst/doc/faq.html | 104 ++++++++++++++- inst/doc/local-sources.R | 4 inst/doc/local-sources.Rmd | 33 +++- inst/doc/local-sources.html | 32 ++-- inst/doc/lockfile.R | 2 inst/doc/lockfile.Rmd | 25 ++- inst/doc/lockfile.html | 13 + inst/doc/packages.R |only inst/doc/packages.Rmd |only inst/doc/packages.html |only inst/doc/python.R | 2 inst/doc/python.html | 3 inst/doc/renv.R | 2 inst/doc/renv.Rmd | 114 ++++++++++------ inst/doc/renv.html | 90 ++++++------- inst/resources/activate.R | 30 ++++ man/activate.Rd | 3 man/config.Rd | 39 +++++ man/deactivate.Rd | 3 man/diagnostics.Rd | 3 man/history.Rd | 1 man/init.Rd | 1 man/lockfile.Rd | 127 ++++-------------- man/lockfiles.Rd |only man/paths.Rd | 2 man/record.Rd |only man/rehash.Rd |only man/remove.Rd | 1 man/restore.Rd | 12 + man/revert.Rd | 1 man/run.Rd | 11 - man/snapshot.Rd | 6 man/status.Rd | 7 - tests/testthat/test-bioconductor.R | 22 +-- tests/testthat/test-cache.R | 17 ++ tests/testthat/test-dependencies.R | 43 ++++++ tests/testthat/test-download.R | 21 ++- tests/testthat/test-files.R | 31 ++++ tests/testthat/test-infrastructure.R | 59 ++++++++ tests/testthat/test-install.R | 12 + tests/testthat/test-load.R | 1 tests/testthat/test-record.R |only tests/testthat/test-records.R | 40 +++++ tests/testthat/test-rehash.R |only tests/testthat/test-renvignore.R | 9 + tests/testthat/test-restore.R | 10 + tests/testthat/test-retrieve.R | 25 +++ tests/testthat/test-snapshot.R | 36 +++++ tests/testthat/test-status.R | 9 - vignettes/ci.Rmd | 2 vignettes/collaborating.Rmd | 5 vignettes/docker.Rmd | 8 - vignettes/faq.Rmd | 34 +++-- vignettes/local-sources.Rmd | 33 +++- vignettes/lockfile.Rmd | 25 ++- vignettes/packages.Rmd |only vignettes/renv.Rmd | 114 ++++++++++------ 126 files changed, 2267 insertions(+), 957 deletions(-)
Title: MST-kNN Clustering Algorithm
Description: Implements the MST-kNN clustering algorithm which was proposed by Inostroza-Ponta, M. (2008) <https://trove.nla.gov.au/work/28729389?selectedversion=NBD44634158>.
Author: Jorge Parraga-Alava [aut, cre],
Pablo Moscato [aut],
Mario Inostroza-Ponta [aut]
Maintainer: Jorge Parraga-Alava <jorge.parraga@usach.cl>
Diff between mstknnclust versions 0.1.0 dated 2019-02-06 and 0.2.0 dated 2019-12-05
DESCRIPTION | 8 MD5 | 18 R/main.R | 175 ++++--- build/vignette.rds |binary inst/doc/guide.R | 12 inst/doc/guide.html | 356 +++++++++++++--- man/generate.intersections.mst.knn.Rd | 4 man/generate.knn.Rd | 22 man/mst.knn.Rd | 7 vignettes/guide_files/figure-html/unnamed-chunk-6-1.png |binary 10 files changed, 445 insertions(+), 157 deletions(-)
Title: Functions to Facilitate the Simulation of Large Scale Assessment
Data
Description: Provides functions to simulate data from large-scale educational
assessments, including background questionnaire data and cognitive item
responses that adhere to a multiple-matrix sampled design.
Author: Tyler Matta [aut],
Leslie Rutkowski [aut],
David Rutkowski [aut],
Yuan-Ling Linda Liaw [aut],
Kondwani Kajera Mughogho [ctb],
Waldir Leoncio [aut, cre]
Maintainer: Waldir Leoncio <waldir.leoncio@gmail.com>
Diff between lsasim versions 2.0.0 dated 2019-09-12 and 2.0.1 dated 2019-12-05
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/cov_gen.R | 2 +- R/cov_yxw_gen.R | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Regional Frequency Analysis using L-Moments
Description: Functions for regional frequency analysis using the methods
of J. R. M. Hosking and J. R. Wallis (1997), "Regional frequency analysis:
an approach based on L-moments".
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking <jrmhosking@gmail.com>
Diff between lmomRFA versions 3.2 dated 2019-03-10 and 3.3 dated 2019-12-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 12 ++++++++++++ R/lmomRFA.r | 17 +++++++++++------ data/Appalach.rda |binary data/Cascades.rda |binary data/Maxwind.rda |binary inst/lmomRFA-manual.pdf |binary 8 files changed, 34 insertions(+), 17 deletions(-)
Title: Hidden Markov Model for Financial Time-Series Based on Lambda
Distribution
Description: Hidden Markov Model (HMM) based on symmetric lambda distribution
framework is implemented for the study of return time-series in the financial
market. Major features in the S&P500 index, such as regime identification,
volatility clustering, and anti-correlation between return and volatility,
can be extracted from HMM cleanly. Univariate symmetric lambda distribution
is essentially a location-scale family of exponential power distribution.
Such distribution is suitable for describing highly leptokurtic time series
obtained from the financial market. It provides a theoretically solid foundation
to explore such data where the normal distribution is not adequate. The HMM
implementation follows closely the book: "Hidden Markov Models for Time Series",
by Zucchini, MacDonald, Langrock (2016).
Author: Stephen H-T. Lihn [aut, cre]
Maintainer: Stephen H-T. Lihn <stevelihn@gmail.com>
Diff between ldhmm versions 0.4.5 dated 2018-02-28 and 0.5.1 dated 2019-12-05
ldhmm-0.4.5/ldhmm/R/sldhmm-class.R |only ldhmm-0.4.5/ldhmm/build |only ldhmm-0.4.5/ldhmm/man/sldhmm-class.Rd |only ldhmm-0.4.5/ldhmm/vignettes |only ldhmm-0.5.1/ldhmm/DESCRIPTION | 15 +++---- ldhmm-0.5.1/ldhmm/MD5 | 42 +++++++++------------ ldhmm-0.5.1/ldhmm/NAMESPACE | 1 ldhmm-0.5.1/ldhmm/NEWS.md | 5 ++ ldhmm-0.5.1/ldhmm/R/ldhmm-conditional_prob.R | 2 - ldhmm-0.5.1/ldhmm/R/ldhmm-constructor.R | 2 - ldhmm-0.5.1/ldhmm/R/ldhmm-forecast_prob.R | 4 +- ldhmm-0.5.1/ldhmm/R/ldhmm-gamma_init.R | 19 +++++---- ldhmm-0.5.1/ldhmm/R/ldhmm-log_forward.R | 4 +- ldhmm-0.5.1/ldhmm/R/ldhmm-mllk.R | 2 - ldhmm-0.5.1/ldhmm/R/ldhmm-oxford_man_plot_obs.R | 8 ++-- ldhmm-0.5.1/ldhmm/R/ldhmm-plot_spx_vix_obs.R | 8 ++-- ldhmm-0.5.1/ldhmm/R/ldhmm-sma.R | 2 - ldhmm-0.5.1/ldhmm/R/ldhmm-ts_log_rtn.R | 28 +++++++++----- ldhmm-0.5.1/ldhmm/R/ldhmm-viterbi.R | 2 - ldhmm-0.5.1/ldhmm/man/ldhmm.gamma_init.Rd | 13 +++--- ldhmm-0.5.1/ldhmm/man/ldhmm.mle.Rd | 6 +-- ldhmm-0.5.1/ldhmm/man/ldhmm.oxford_man_plot_obs.Rd | 6 +-- 22 files changed, 89 insertions(+), 80 deletions(-)
Title: Loglikelihood Adjustment for Extreme Value Models
Description: Performs adjusted inferences based on model objects fitted, using
maximum likelihood estimation, by the extreme value analysis packages
'evd' <https://cran.r-project.org/package=evd>,
'evir' <https://cran.r-project.org/package=evir>,
'extRemes' <https://cran.r-project.org/package=extRemes>,
'fExtremes' <https://cran.r-project.org/package=fExtremes>,
'ismev' <https://cran.r-project.org/package=ismev>,
'mev' <https://cran.r-project.org/package=mev>,
'POT' <https://cran.r-project.org/package=POT> and
'texmex' <https://cran.r-project.org/package=texmex>.
Adjusted standard errors and an adjusted loglikelihood are provided, using
the 'chandwich' package <https://cran.r-project.org/package=chandwich>
and the object-oriented features of the 'sandwich' package
<https://cran.r-project.org/package=sandwich>. The adjustment is based on a
robust sandwich estimator of the parameter covariance matrix, based on the
methodology in Chandler and Bate (2007) <doi:10.1093/biomet/asm015>. This
can be used for cluster correlated data when interest lies in the
parameters of the marginal distributions, or for performing inferences that
are robust to certain types of model misspecification. Univariate extreme
value models, including regression models, are supported.
Author: Paul J. Northrop [aut, cre, cph],
Camellia Yin [aut, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between lax versions 1.0.0 dated 2019-08-24 and 1.1.0 dated 2019-12-05
DESCRIPTION | 20 - MD5 | 107 ++++---- NAMESPACE | 50 +++ NEWS.md |only R/POT.R | 4 R/alogLik_methods.R | 5 R/estfun.R | 44 +++ R/evd.R | 3 R/evir.R | 8 R/evir_gpd.R | 135 ++++------ R/extRemes.R | 12 R/fExtremes.R | 3 R/ismev.R | 100 ++++++- R/ismev_gev_fit.R | 2 R/ismev_gpd_fit.R | 2 R/ismev_methods.R | 217 +++++++++------- R/ismev_refits.R | 126 +++++++++ R/ismev_rlarg_fit.R |only R/lax-internal.R | 13 - R/lax.R | 6 R/mev.R |only R/mev_egp.R |only R/mev_gev.R |only R/mev_gpd.R |only R/mev_pp.R |only R/mev_rlarg.R |only R/texmex.R | 3 README.md | 4 inst/doc/lax-vignette.R | 66 +++-- inst/doc/lax-vignette.Rmd | 38 ++ inst/doc/lax-vignette.html | 68 ++--- man/POT.Rd | 191 +++++--------- man/alogLik.Rd | 315 ++++++++++++------------ man/anova.lax.Rd | 176 ++++++------- man/evd.Rd | 242 +++++++----------- man/evir.Rd | 249 ++++++++----------- man/extRemes.Rd | 341 +++++++++++--------------- man/fExtremes.Rd | 240 +++++++----------- man/ismev.Rd | 403 +++++++++++++++---------------- man/ismev_refits.Rd | 336 +++++++++++++++---------- man/lax-internal.Rd | 62 ++-- man/lax.Rd | 201 +++++++-------- man/logLik.logLikVec.Rd | 32 +- man/logLikVec.Rd | 32 +- man/mev.Rd |only man/ow.Rd | 64 ++-- man/plot.retlev.Rd | 117 ++++----- man/pot_refit.Rd | 111 ++++---- man/print.retlev.Rd | 73 ++--- man/print.summary.retlev.Rd | 68 ++--- man/return_level.Rd | 253 ++++++++++--------- man/summary.retlev.Rd | 70 ++--- man/texmex.Rd | 304 ++++++++++------------- tests/testthat/test-bc-deriv.R | 37 ++ tests/testthat/test-ismev-gev-vs-rlarg.R |only tests/testthat/test-logLik-extRemes.R | 52 ++-- tests/testthat/test-logLik-ismev.R | 50 +++ tests/testthat/test-logLik-mev.R |only vignettes/lax-vignette.Rmd | 38 ++ vignettes/lax.bib | 23 + 60 files changed, 2690 insertions(+), 2426 deletions(-)
Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.utils versions 2.9.0 dated 2019-06-13 and 2.9.1 dated 2019-12-05
DESCRIPTION | 8 ++--- MD5 | 16 +++++----- NAMESPACE | 2 - NEWS | 15 +++++++++ R/fileAccess.R | 29 +++++++++++-------- R/withSeed.R | 80 +++++++++++++++++++++++++++++++---------------------- R/wrap.array.R | 2 - tests/fileAccess.R | 14 +++++++++ tests/withSeed.R | 7 ++++ 9 files changed, 115 insertions(+), 58 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed
('plotly.js' is able to handle larger size matrix), the ability to zoom from
the 'dendrogram' panes, and the placing of factor variables in the sides of the
'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Alan O'Callaghan [aut] (https://github.com/Alanocallaghan),
Jonathan Sidi [ctb] (https://github.com/yonicd),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 0.16.0 dated 2019-05-11 and 1.0.0 dated 2019-12-05
ChangeLog | 332 ++++ DESCRIPTION | 16 MD5 | 75 NAMESPACE | 191 +- NEWS | 963 ++++++------ NEWS.md | 963 ++++++------ R/RColorBrewer.R | 726 ++++----- R/distfuns.R | 14 R/ggheatmap.R |only R/heatmaply.R | 2769 +++++++++++++++++------------------ R/heatmapr.R | 1113 +++++++------- R/is.na10.R | 108 - R/percentize.R | 362 ++-- R/plots.R | 1733 ++++++++++----------- R/zzz.R | 615 +++---- README.md | 370 ++-- build/vignette.rds |binary inst/CITATION | 38 inst/doc/heatmaply.R | 570 ++++--- inst/doc/heatmaply.Rmd | 1182 ++++++++------ inst/doc/heatmaply.html | 1462 ++++++++++-------- man/RColorBrewer_colors.Rd | 302 +-- man/ggheatmap.Rd |only man/ggplot_side_color_plot.Rd | 77 man/heatmaply.Rd | 1143 +++++++------- man/heatmapr.Rd | 349 ++-- man/is.heatmapr.Rd | 34 man/is.na10.Rd | 92 - man/is.plotly.Rd | 34 man/normalize.Rd | 90 - man/percentize.Rd | 92 - tests/testthat.R | 24 tests/testthat/test_RColorBrewer.R | 74 tests/testthat/test_ggheatmap.R |only tests/testthat/test_heatmaply.R | 323 ++-- tests/testthat/test_heatmaply_misc.R | 295 +-- tests/testthat/test_heatmapr.R | 65 tests/testthat/test_misc.R | 48 tests/testthat/test_plots.R | 340 ++-- vignettes/heatmaply.Rmd | 1182 ++++++++------ 40 files changed, 9716 insertions(+), 8450 deletions(-)
Title: Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Description: Compute the median ranking according to the Kemeny's axiomatic approach.
Rankings can or cannot contain ties, rankings can be both complete or incomplete.
The package contains both branch-and-bound algorithms and heuristic solutions recently proposed.
The searching space of the solution can either be restricted to the universe of the permutations or unrestricted to all possible ties.
The package also provide some useful utilities for deal with preference rankings.
This release declare as deprecated some functions that are still in the package for compatibility. Next release will not contains these functions.
Please type '?ConsRank-deprecated'
Essential references:
Emond, E.J., and Mason, D.W. (2002) <doi:10.1002/mcda.313>;
D'Ambrosio, A., Amodio, S., and Iorio, C. (2015) <doi:10.1285/i20705948v8n2p198>;
Amodio, S., D'Ambrosio, A., and Siciliano R. (2016) <doi:10.1016/j.ejor.2015.08.048>;
D'Ambrosio, A., Mazzeo, G., Iorio, C., and Siciliano, R. (2017) <doi:10.1016/j.cor.2017.01.017>.
Author: Antonio D'Ambrosio [aut, cre],
Sonia Amodio [ctb],
Giulio Mazzeo [ctb]
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRank versions 2.0.1 dated 2017-04-28 and 2.1.0 dated 2019-12-05
ConsRank-2.0.1/ConsRank/R/ALL.r |only ConsRank-2.0.1/ConsRank/R/BBconsensus.R |only ConsRank-2.0.1/ConsRank/R/BBconsensus2.R |only ConsRank-2.0.1/ConsRank/R/DECORcore.R |only ConsRank-2.0.1/ConsRank/R/Penalty.R |only ConsRank-2.0.1/ConsRank/R/PenaltyBB2.R |only ConsRank-2.0.1/ConsRank/R/ReorderingBB.R |only ConsRank-2.0.1/ConsRank/R/Tau_X.R |only ConsRank-2.0.1/ConsRank/R/branches.R |only ConsRank-2.0.1/ConsRank/R/childclosint.R |only ConsRank-2.0.1/ConsRank/R/childtie.R |only ConsRank-2.0.1/ConsRank/R/combincost.R |only ConsRank-2.0.1/ConsRank/R/crossover.R |only ConsRank-2.0.1/ConsRank/R/findbranches.R |only ConsRank-2.0.1/ConsRank/R/findconsensusBB.R |only ConsRank-2.0.1/ConsRank/R/mutaterand1.R |only ConsRank-2.0.1/ConsRank/man/BBconsensus.Rd |only ConsRank-2.0.1/ConsRank/man/BBconsensus2.Rd |only ConsRank-2.0.1/ConsRank/man/DECORcore.Rd |only ConsRank-2.0.1/ConsRank/man/Penalty.Rd |only ConsRank-2.0.1/ConsRank/man/PenaltyBB2.Rd |only ConsRank-2.0.1/ConsRank/man/ReorderingBB.Rd |only ConsRank-2.0.1/ConsRank/man/Tau_X.Rd |only ConsRank-2.0.1/ConsRank/man/branches.Rd |only ConsRank-2.0.1/ConsRank/man/childclosint.Rd |only ConsRank-2.0.1/ConsRank/man/childtie.Rd |only ConsRank-2.0.1/ConsRank/man/combincost.Rd |only ConsRank-2.0.1/ConsRank/man/crossover.Rd |only ConsRank-2.0.1/ConsRank/man/findbranches.Rd |only ConsRank-2.0.1/ConsRank/man/findconsensusBB.Rd |only ConsRank-2.0.1/ConsRank/man/mutaterand1.Rd |only ConsRank-2.1.0/ConsRank/DESCRIPTION | 25 +- ConsRank-2.1.0/ConsRank/MD5 | 117 +++++------ ConsRank-2.1.0/ConsRank/NAMESPACE | 28 +- ConsRank-2.1.0/ConsRank/R/BBFULL.R | 95 +-------- ConsRank-2.1.0/ConsRank/R/DECOR.R | 85 +------- ConsRank-2.1.0/ConsRank/R/EMCons.R | 98 --------- ConsRank-2.1.0/ConsRank/R/FASTDECOR.R | 111 +---------- ConsRank-2.1.0/ConsRank/R/FASTcons.R | 98 --------- ConsRank-2.1.0/ConsRank/R/QuickCons.R | 100 +--------- ConsRank-2.1.0/ConsRank/R/combinpmatr.R | 12 - ConsRank-2.1.0/ConsRank/R/consrank.R |only ConsRank-2.1.0/ConsRank/R/deprecated.R |only ConsRank-2.1.0/ConsRank/R/kemenyd.R | 30 +-- ConsRank-2.1.0/ConsRank/R/kemenydesign.R | 16 - ConsRank-2.1.0/ConsRank/R/kemenyscore.R | 30 +-- ConsRank-2.1.0/ConsRank/R/labels.R | 56 +++-- ConsRank-2.1.0/ConsRank/R/order2rank.R |only ConsRank-2.1.0/ConsRank/R/partitions.R |only ConsRank-2.1.0/ConsRank/R/polyplot.R | 208 +++++++++++++-------- ConsRank-2.1.0/ConsRank/R/rank2order.R |only ConsRank-2.1.0/ConsRank/R/reordering.R | 34 +-- ConsRank-2.1.0/ConsRank/R/scorematrix.R | 36 +-- ConsRank-2.1.0/ConsRank/R/stirling2.R |only ConsRank-2.1.0/ConsRank/R/tabulaterows.R | 52 ++--- ConsRank-2.1.0/ConsRank/R/tau_x.R |only ConsRank-2.1.0/ConsRank/R/univranks.R |only ConsRank-2.1.0/ConsRank/man/BBFULL.Rd | 93 ++++----- ConsRank-2.1.0/ConsRank/man/ConsRank-deprecated.Rd |only ConsRank-2.1.0/ConsRank/man/ConsRank-package.Rd | 34 ++- ConsRank-2.1.0/ConsRank/man/DECOR.Rd | 127 ++++++------ ConsRank-2.1.0/ConsRank/man/EMCons.Rd | 101 ++++------ ConsRank-2.1.0/ConsRank/man/EMD.Rd | 2 ConsRank-2.1.0/ConsRank/man/FASTDECOR.Rd | 124 +++++++----- ConsRank-2.1.0/ConsRank/man/FASTcons.Rd | 118 ++++++----- ConsRank-2.1.0/ConsRank/man/Idea.Rd | 2 ConsRank-2.1.0/ConsRank/man/QuickCons.Rd | 92 ++++----- ConsRank-2.1.0/ConsRank/man/combinpmatr.Rd | 70 +++---- ConsRank-2.1.0/ConsRank/man/consrank.Rd |only ConsRank-2.1.0/ConsRank/man/kemenyd.Rd | 76 +++---- ConsRank-2.1.0/ConsRank/man/kemenydesign.Rd | 46 ++-- ConsRank-2.1.0/ConsRank/man/kemenyscore.Rd | 68 +++--- ConsRank-2.1.0/ConsRank/man/labels.Rd | 78 ++++--- ConsRank-2.1.0/ConsRank/man/order2rank.Rd |only ConsRank-2.1.0/ConsRank/man/partitions.Rd |only ConsRank-2.1.0/ConsRank/man/polyplot.Rd | 92 ++++----- ConsRank-2.1.0/ConsRank/man/rank2order.Rd |only ConsRank-2.1.0/ConsRank/man/reordering.Rd | 40 ++-- ConsRank-2.1.0/ConsRank/man/scorematrix.Rd | 68 +++--- ConsRank-2.1.0/ConsRank/man/stirling2.Rd |only ConsRank-2.1.0/ConsRank/man/tabulaterows.Rd | 98 +++++---- ConsRank-2.1.0/ConsRank/man/tau_x.Rd |only ConsRank-2.1.0/ConsRank/man/univranks.Rd |only 83 files changed, 1097 insertions(+), 1463 deletions(-)
Title: Contextualization and Evaluation of COI-5P Barcode Data
Description: Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI).
It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing
the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences
against nucleotide and amino acid profile hidden Markov models (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically
diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted
analysis of barcode data.
Author: Cameron M. Nugent
Maintainer: Cameron M. Nugent <nugentc@uoguelph.ca>
Diff between coil versions 1.0.1 dated 2019-10-16 and 1.1.0 dated 2019-12-05
DESCRIPTION | 6 +++--- MD5 | 23 ++++++++++++----------- R/coi5p.r | 38 +++++++++++++++++++++++++++++++++++--- R/deploy_PHMMs.r | 17 ++++++++++++++--- R/print.r | 28 ++++++++++++++++++++-------- README.md | 27 +++++++++++++++++++-------- inst/doc/coil-vignette.R | 6 +++--- inst/doc/coil-vignette.Rmd | 12 ++++++------ inst/doc/coil-vignette.html | 33 ++++++++++++++++++--------------- tests/testthat/test_frameNotes.r |only tests/testthat/test_longSeq.r | 10 ++++++++++ tests/testthat/test_print.r | 20 +++++++++++++++----- vignettes/coil-vignette.Rmd | 12 ++++++------ 13 files changed, 161 insertions(+), 71 deletions(-)
Title: Convert Between Spatial Objects and Well-Known Binary Geometry
Description: Utility functions to convert between the 'Spatial' classes
specified by the package 'sp', and the well-known binary '(WKB)'
representation for geometry specified by the 'Open Geospatial Consortium'.
Supports 'Spatial' objects of class 'SpatialPoints',
'SpatialPointsDataFrame', 'SpatialLines', 'SpatialLinesDataFrame',
'SpatialPolygons', and 'SpatialPolygonsDataFrame'. Supports 'WKB' geometry
types 'Point', 'LineString', 'Polygon', 'MultiPoint', 'MultiLineString', and
'MultiPolygon'. Includes extensions to enable creation of maps with
'TIBCO Spotfire'.
Author: TIBCO Software Inc.
Maintainer: Ian Cook <ianmcook@gmail.com>
Diff between wkb versions 0.3-0 dated 2016-03-24 and 0.4-0 dated 2019-12-05
wkb-0.3-0/wkb/R/XYListToWKBLineString.R |only wkb-0.3-0/wkb/R/contourLinesToWKB.R |only wkb-0.3-0/wkb/R/coordPairsStringToWKBPolygon.R |only wkb-0.4-0/wkb/DESCRIPTION | 26 +++---- wkb-0.4-0/wkb/LICENSE | 2 wkb-0.4-0/wkb/MD5 | 31 ++++---- wkb-0.4-0/wkb/NAMESPACE | 2 wkb-0.4-0/wkb/NEWS.md |only wkb-0.4-0/wkb/R/SpatialPolygonsToWKBPolygon.R | 88 ++++++++++++++++++++++++ wkb-0.4-0/wkb/R/hex2raw.R | 2 wkb-0.4-0/wkb/R/readWKB.R | 24 ++++-- wkb-0.4-0/wkb/R/writeWKB.R | 35 ++++++++- wkb-0.4-0/wkb/README.md |only wkb-0.4-0/wkb/man/hex2raw.Rd | 5 - wkb-0.4-0/wkb/man/readWKB.Rd | 3 wkb-0.4-0/wkb/man/writeEnvelope.Rd | 3 wkb-0.4-0/wkb/man/writeWKB.Rd | 11 +-- wkb-0.4-0/wkb/tests/testthat/testmultipolygon.R | 24 ++++++ wkb-0.4-0/wkb/tests/testthat/testpolygon.R | 41 ++++------- 19 files changed, 218 insertions(+), 79 deletions(-)
Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Sebastien Da Veiga, Thibault Delage, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Amandine Marrel, Anouar Meynaoui, Barry L. Nelson, Filippo Monari, Roelof Oomen, Oldrich Rakovec, Bernardo Ramos, Olivier Roustant, Eunhye Song, Jeremy Staum, Roman Sueur, Taieb Touati, Frank Weber
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between sensitivity versions 1.16.2 dated 2019-10-09 and 1.16.3 dated 2019-12-05
DESCRIPTION | 6 MD5 | 36 +- NEWS | 18 + R/morris.R | 18 - R/morris_oat.R | 12 R/shapleyPermEx.R | 432 +++++++++++++-------------- R/shapleyPermRand.R | 408 +++++++++++++------------- R/soboljansen.R | 615 +++++++++++++++++++-------------------- R/sobolmartinez.R | 684 ++++++++++++++++++++++---------------------- R/sobolroalhs.R | 1 man/PLI.Rd | 6 man/PLIquantile.Rd | 10 man/PLIquantile_multivar.Rd | 4 man/PLIsuperquantile.Rd | 10 man/morris.Rd | 2 man/sensiHSIC.Rd | 2 man/soboljansen.Rd | 3 man/sobolmartinez.Rd | 2 man/sobolroalhs.Rd | 4 19 files changed, 1149 insertions(+), 1124 deletions(-)
Title: PHATE - Potential of Heat-Diffusion for Affinity-Based
Transition Embedding
Description: PHATE is a tool for visualizing high dimensional single-cell data
with natural progressions or trajectories. PHATE uses a novel conceptual framework
for learning and visualizing the manifold inherent to biological systems in which
smooth transitions mark the progressions of cells from one state to another.
To see how PHATE can be applied to single-cell RNA-seq datasets from hematopoietic
stem cells, human embryonic stem cells, and bone marrow samples, check out our publication in Nature Biotechnology
at <doi:10.1038/s41587-019-0336-3>.
Author: Krishnan Srinivasan [aut],
Scott Gigante [cre] (<https://orcid.org/0000-0002-4544-2764>)
Maintainer: Scott Gigante <scott.gigante@yale.edu>
Diff between phateR versions 0.4.1 dated 2019-04-26 and 1.0.0 dated 2019-12-05
phateR-0.4.1/phateR/inst/examples/BMMSC_data_R_PCA.png |only phateR-0.4.1/phateR/inst/examples/BMMSC_data_R_phate.png |only phateR-0.4.1/phateR/inst/examples/BMMSC_data_R_phate_colored_by_Ifitm1_after_MAGIC.png |only phateR-0.4.1/phateR/inst/examples/BMMSC_data_R_phate_colored_by_Ifitm1_before_MAGIC.png |only phateR-1.0.0/phateR/DESCRIPTION | 12 phateR-1.0.0/phateR/LICENSE | 562 - phateR-1.0.0/phateR/MD5 | 58 phateR-1.0.0/phateR/NAMESPACE | 29 phateR-1.0.0/phateR/R/cluster.R | 84 phateR-1.0.0/phateR/R/phate.R | 815 +- phateR-1.0.0/phateR/R/preprocessing.R | 52 phateR-1.0.0/phateR/R/tree.data.R | 38 phateR-1.0.0/phateR/R/utils.R | 211 phateR-1.0.0/phateR/README.md | 453 - phateR-1.0.0/phateR/data/datalist | 4 phateR-1.0.0/phateR/inst/CITATION | 44 phateR-1.0.0/phateR/inst/examples/bonemarrow_tutorial.Rmd | 364 phateR-1.0.0/phateR/inst/examples/bonemarrow_tutorial.html | 3618 ++++----- phateR-1.0.0/phateR/inst/examples/bonemarrow_tutorial.nb.html | 3934 +++++----- phateR-1.0.0/phateR/inst/extdata/generate_treedata.R | 28 phateR-1.0.0/phateR/man/as.data.frame.Rd | 32 phateR-1.0.0/phateR/man/as.matrix.Rd | 34 phateR-1.0.0/phateR/man/cluster_phate.Rd | 80 phateR-1.0.0/phateR/man/ggplot.Rd | 56 phateR-1.0.0/phateR/man/install.phate.Rd | 71 phateR-1.0.0/phateR/man/library.size.normalize.Rd | 54 phateR-1.0.0/phateR/man/phate.Rd | 318 phateR-1.0.0/phateR/man/plot.Rd | 56 phateR-1.0.0/phateR/man/print.Rd | 66 phateR-1.0.0/phateR/man/summary.Rd | 62 phateR-1.0.0/phateR/man/tree.data.Rd | 36 phateR-1.0.0/phateR/man/tree.data.small.Rd | 36 32 files changed, 5660 insertions(+), 5547 deletions(-)
Title: Tools for Matrix Algebra, Optimization and Inference
Description: Matrix is an universal and sometimes primary object/unit in applied mathematics and statistics. We provide a number of algorithms for selected problems in optimization and statistical inference. For general exposition to the topic with focus on statistical context, see the book by Banerjee and Roy (2014, ISBN:9781420095388).
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyoustat@gmail.com>
Diff between maotai versions 0.1.1 dated 2019-10-25 and 0.1.2 dated 2019-12-05
maotai-0.1.1/maotai/R/distecdf.R |only maotai-0.1.1/maotai/man/distecdf.Rd |only maotai-0.1.2/maotai/DESCRIPTION | 8 ++-- maotai-0.1.2/maotai/MD5 | 47 +++++++++++++++------------ maotai-0.1.2/maotai/NAMESPACE | 7 +++- maotai-0.1.2/maotai/NEWS.md | 13 ++++--- maotai-0.1.2/maotai/R/RcppExports.R | 4 ++ maotai-0.1.2/maotai/R/aux_computation.R | 55 +++++++++++++++++++++++++++++++- maotai-0.1.2/maotai/R/aux_ecdf.R | 32 ++++++++++++++---- maotai-0.1.2/maotai/R/ecdfdist.R |only maotai-0.1.2/maotai/R/ecdfdist2.R |only maotai-0.1.2/maotai/R/epmeans.R |only maotai-0.1.2/maotai/R/mmd2test.R |only maotai-0.1.2/maotai/R/package-maotai.R | 7 ++-- maotai-0.1.2/maotai/R/shortestpath.R | 5 +- maotai-0.1.2/maotai/R/zzz.R | 6 +-- maotai-0.1.2/maotai/README.md | 5 +- maotai-0.1.2/maotai/build/partial.rdb |binary maotai-0.1.2/maotai/inst/REFERENCES.bib | 26 +++++++++++++++ maotai-0.1.2/maotai/man/dpmeans.Rd | 9 ++++- maotai-0.1.2/maotai/man/ecdfdist.Rd |only maotai-0.1.2/maotai/man/ecdfdist2.Rd |only maotai-0.1.2/maotai/man/epmeans.Rd |only maotai-0.1.2/maotai/man/lyapunov.Rd | 2 - maotai-0.1.2/maotai/man/maotai.Rd | 5 ++ maotai-0.1.2/maotai/man/mmd2test.Rd |only maotai-0.1.2/maotai/man/sylvester.Rd | 2 - maotai-0.1.2/maotai/man/trio.Rd | 11 +++++- maotai-0.1.2/maotai/src/RcppExports.cpp | 13 +++++++ maotai-0.1.2/maotai/src/cpp_kmeans.cpp |only 30 files changed, 203 insertions(+), 54 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Mohammadi and Wit (2019) <doi:10.18637/jss.v089.i03>.
Author: Reza Mohammadi [aut, cre] <https://orcid.org/0000-0001-9538-0648>,
Ernst Wit [aut] <https://orcid.org/0000-0002-3671-9610>,
Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.61 dated 2019-09-05 and 2.62 dated 2019-12-05
DESCRIPTION | 8 ++--- MD5 | 60 +++++++++++++++++++-------------------- NEWS | 7 ++-- R/adj2link.R | 28 +++++++++--------- R/bdgraph.R | 50 ++++++++++++++++----------------- R/bdgraph.mpl.R | 36 +++++++++++------------ R/bdgraph.npn.R | 38 +++++++++++++------------ R/bdgraph.sim.R | 62 ++++++++++++++++++++--------------------- R/bf.R | 30 +++++++++---------- R/compare.R | 32 ++++++++++----------- R/covariance.R | 30 +++++++++---------- R/detect_cores.R | 18 +++++++++-- R/get_things.R | 70 +++++++++++++++++++++++----------------------- R/gnorm.R | 42 ++++++++++++++------------- R/graph.sim.R | 34 +++++++++++----------- R/hill_climb_algorithm.R | 71 +++++++++++++++++++++++------------------------ R/hill_climb_binary.R | 71 +++++++++++++++++++++++------------------------ R/link2adj.R | 28 +++++++++--------- R/pgraph.R | 31 ++++++++++---------- R/plinks.R | 34 +++++++++++----------- R/plotcoda.R | 30 +++++++++---------- R/plotroc.R | 44 ++++++++++++++--------------- R/precision.R | 30 +++++++++---------- R/rgwish.R | 40 +++++++++++++------------- R/rmvnorm.R | 29 +++++++++---------- R/rwish.R | 28 +++++++++--------- R/select.R | 39 +++++++++++++------------ R/traceplot.R | 29 +++++++++---------- R/transfer.R | 32 +++++++++++---------- build/vignette.rds |binary inst/doc/vignette.pdf |binary 31 files changed, 554 insertions(+), 527 deletions(-)
Title: Covariate-Adjusted Receiver Operating Characteristic Curve
Inference
Description: Estimates the covariate-adjusted Receiver Operating Characteristic (AROC) curve and pooled (unadjusted) ROC curve by different methods. Inacio de Carvalho, V., and Rodriguez-Alvarez, M. X. (2018) <arXiv:1806.00473>.
Author: Maria Xose Rodriguez-Alvarez [aut, cre]
(<https://orcid.org/0000-0002-1329-9238>),
Vanda Inacio de Carvalho [aut]
(<https://orcid.org/0000-0001-8084-1616>)
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>
Diff between AROC versions 1.0-1 dated 2019-11-15 and 1.0-2 dated 2019-12-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/bddp.R | 2 +- build/partial.rdb |binary man/AROC-package.Rd | 4 ++-- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut, cre],
Hadley Wickham [aut],
lexicalunit [cph] (nanodbc library),
Google Inc. [cph] (cctz library),
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between odbc versions 1.2.0 dated 2019-11-28 and 1.2.1 dated 2019-12-05
DESCRIPTION | 8 ++-- MD5 | 20 +++++------ NEWS.md | 7 ++++ build/odbc.pdf |binary configure | 34 ++++++++++---------- man/OdbcConnection.Rd | 2 - man/dbListFields-OdbcConnection-character-method.Rd | 8 ++-- man/dbListTables-OdbcConnection-method.Rd | 4 +- man/odbc-tables.Rd | 6 +-- man/odbcSetTransactionIsolationLevel.Rd | 2 - src/Makevars.in | 3 + 11 files changed, 51 insertions(+), 43 deletions(-)
Title: Geometric Morphometrics Analysis and Virtual Anthropology
Description: Tools for geometric morphometric analysis. The package includes tools of virtual anthropology to align two not articulated parts belonging to the same specimen, to build virtual cavities as endocast (Profico et al, 2018 <doi:10.1002/ajpa.23493>).
Author: Antonio Profico, Costantino Buzi, Marina Melchionna, Paolo Piras, Pasquale Raia, Alessio Veneziano
Maintainer: Antonio Profico <antonio.profico@york.ac.uk>
Diff between Arothron versions 1.1.0 dated 2019-10-26 and 1.1.1 dated 2019-12-05
DESCRIPTION | 14 +++++----- MD5 | 10 +++---- NAMESPACE | 3 ++ R/Arothron.R | 3 ++ R/aro.clo.points.R | 48 ++++++++++++++++------------------- R/volendo.R | 71 +++++++++++++++++++++++------------------------------ 6 files changed, 72 insertions(+), 77 deletions(-)
Title: Compile and Preview Snippets of 'LaTeX' in 'RStudio'
Description: Compile and preview snippets of 'LaTeX'. Can be
used directly from the R console, from 'RStudio', in Shiny apps and R
Markdown documents. Must have 'pdflatex' or 'xelatex' or 'lualatex' in
'PATH'.
Author: Jonathan Sidi [aut, cre],
Daniel Polhamus [aut]
Maintainer: Jonathan Sidi <yonis@metrumrg.com>
Diff between texPreview versions 1.4.1 dated 2019-10-29 and 1.4.2 dated 2019-12-05
DESCRIPTION | 15 MD5 | 38 - NAMESPACE | 1 NEWS.md | 3 R/build_lines.R | 2 R/tex_image.R | 2 R/tex_viewer.R | 5 R/utils.R | 4 README.md | 4 build/texPreview.pdf |binary inst/doc/classes.html | 10 inst/doc/kable.html | 4 inst/doc/rmarkdown.html | 8 inst/doc/slickr.html | 1264 ++++----------------------------------- inst/doc/tests_and_coverage.html | 2 inst/doc/tex_packages.html | 4 inst/doc/tikz.html | 4 inst/tmpl.tex | 2 tests/testthat/test-print.R | 2 tests/testthat/test-tex.R | 2 20 files changed, 214 insertions(+), 1162 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX <https://sdmx.org>) Web Services
(<https://ec.europa.eu/eurostat/web/sdmx-web-services/about-this-service>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Mátyás Mészáros [aut, cre]
Maintainer: Mátyás Mészáros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.4.0 dated 2019-10-12 and 0.6.0 dated 2019-12-05
DESCRIPTION | 10 MD5 | 60 ++-- R/clean_restatapi_cache.R | 4 R/extract_data.R | 67 ++++- R/extract_dsd.R | 2 R/extract_toc.R | 6 R/get_compressed_sdmx.R | 15 - R/get_eurostat_bulk.R | 175 +++++++++----- R/get_eurostat_cache.R | 20 + R/get_eurostat_data.R | 534 ++++++++++++++++++++++++------------------- R/get_eurostat_dsd.R | 19 + R/get_eurostat_raw.R | 303 ++++++++++++++---------- R/get_eurostat_toc.R | 50 ++-- R/load_cfg.R | 59 +++- R/put_eurostat_cache.R | 2 R/search_eurostat_toc.R | 14 - README.md | 2 man/clean_restatapi_cache.Rd | 4 man/extract_data.Rd | 11 man/extract_dsd.Rd | 2 man/extract_toc.Rd | 6 man/get_compressed_sdmx.Rd | 4 man/get_eurostat_bulk.Rd | 50 ++-- man/get_eurostat_data.Rd | 32 +- man/get_eurostat_dsd.Rd | 2 man/get_eurostat_raw.Rd | 44 ++- man/get_eurostat_toc.Rd | 23 - man/load_cfg.Rd | 29 +- man/put_eurostat_cache.Rd | 2 man/search_eurostat_toc.Rd | 14 - tests/testthat/test-all.R | 500 +++++++++++++++++++++++++++------------- 31 files changed, 1292 insertions(+), 773 deletions(-)
Title: Piecewise Structural Equation Modeling
Description: Implements piecewise structural equation modeling from a single
list of structural equations, with new methods for non-linear, latent, and
composite variables, standardized coefficients, query-based prediction and
indirect effects. See <http://jslefche.github.io/piecewiseSEM/> for more.
Author: Jon Lefcheck [aut, cre],
Jarrett Byrnes [aut],
James Grace [aut]
Maintainer: Jon Lefcheck <lefcheckj@si.edu>
Diff between piecewiseSEM versions 2.0.2 dated 2018-07-24 and 2.1.0 dated 2019-12-05
piecewiseSEM-2.0.2/piecewiseSEM/R/Dag.R |only piecewiseSEM-2.0.2/piecewiseSEM/R/oldFunctions.R |only piecewiseSEM-2.0.2/piecewiseSEM/man/Dag.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/KRp.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/cyclic.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/endogenous.reverse.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/filter.exogenous.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/get.basis.set.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/get.dag.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/get.formula.list.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/get.model.control.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/get.random.formula.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/get.scaled.data.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/get.scaled.model.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/get.sort.dag.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/partial.resid.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/scaleFam.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/sem.aic.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/sem.basis.set.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/sem.coefs.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/sem.fisher.c.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/sem.fit.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/sem.missing.paths.Rd |only piecewiseSEM-2.0.2/piecewiseSEM/man/sem.model.fits.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/DESCRIPTION | 16 piecewiseSEM-2.1.0/piecewiseSEM/MD5 | 223 +- piecewiseSEM-2.1.0/piecewiseSEM/NAMESPACE | 25 piecewiseSEM-2.1.0/piecewiseSEM/NEWS.md | 15 piecewiseSEM-2.1.0/piecewiseSEM/R/anova_psem.R |only piecewiseSEM-2.1.0/piecewiseSEM/R/basisSet.R | 125 - piecewiseSEM-2.1.0/piecewiseSEM/R/cerror.R | 41 piecewiseSEM-2.1.0/piecewiseSEM/R/coefs.R | 625 ++++- piecewiseSEM-2.1.0/piecewiseSEM/R/dSep.R | 273 +- piecewiseSEM-2.1.0/piecewiseSEM/R/data.R | 26 piecewiseSEM-2.1.0/piecewiseSEM/R/fisherC.R | 5 piecewiseSEM-2.1.0/piecewiseSEM/R/getDAG.R |only piecewiseSEM-2.1.0/piecewiseSEM/R/helpers.R | 312 ++ piecewiseSEM-2.1.0/piecewiseSEM/R/import.R | 9 piecewiseSEM-2.1.0/piecewiseSEM/R/infCrit.R | 5 piecewiseSEM-2.1.0/piecewiseSEM/R/multigroup.R |only piecewiseSEM-2.1.0/piecewiseSEM/R/partialResid.R | 35 piecewiseSEM-2.1.0/piecewiseSEM/R/piecewiseSEM-package.R | 18 piecewiseSEM-2.1.0/piecewiseSEM/R/plot_psem.R |only piecewiseSEM-2.1.0/piecewiseSEM/R/psem.R | 49 piecewiseSEM-2.1.0/piecewiseSEM/R/rsquared.R | 210 + piecewiseSEM-2.1.0/piecewiseSEM/R/summary.R | 48 piecewiseSEM-2.1.0/piecewiseSEM/R/zzz.R | 6 piecewiseSEM-2.1.0/piecewiseSEM/README.md | 36 piecewiseSEM-2.1.0/piecewiseSEM/build/vignette.rds |binary piecewiseSEM-2.1.0/piecewiseSEM/data/meadows.rda |only piecewiseSEM-2.1.0/piecewiseSEM/inst/doc/piecewiseSEM.R | 82 piecewiseSEM-2.1.0/piecewiseSEM/inst/doc/piecewiseSEM.Rmd | 35 piecewiseSEM-2.1.0/piecewiseSEM/inst/doc/piecewiseSEM.html | 1065 +++++----- piecewiseSEM-2.1.0/piecewiseSEM/man/AIC.psem.Rd | 34 piecewiseSEM-2.1.0/piecewiseSEM/man/BIC.psem.Rd | 30 piecewiseSEM-2.1.0/piecewiseSEM/man/GetData.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/GetOLRE.Rd | 26 piecewiseSEM-2.1.0/piecewiseSEM/man/GetSDx.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/GetSDy.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/GetSingleData.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/GetVarCov.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/all.vars.merMod.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/all.vars_notrans.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/all.vars_trans.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/anova.psem.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/anovaLRT.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/anovaTable.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/as.psem.Rd | 30 piecewiseSEM-2.1.0/piecewiseSEM/man/basisSet.Rd | 106 piecewiseSEM-2.1.0/piecewiseSEM/man/captureTable.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/cbind_fill.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/cerror.Rd | 148 - piecewiseSEM-2.1.0/piecewiseSEM/man/coefs.Rd | 176 - piecewiseSEM-2.1.0/piecewiseSEM/man/dSep.Rd | 122 - piecewiseSEM-2.1.0/piecewiseSEM/man/dataTrans.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/dupOutput.Rd | 26 piecewiseSEM-2.1.0/piecewiseSEM/man/evaluateClasses.Rd | 26 piecewiseSEM-2.1.0/piecewiseSEM/man/filterExisting.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/filterExogenous.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/filterInteractions.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/findbars.lme.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/fisherC.Rd | 73 piecewiseSEM-2.1.0/piecewiseSEM/man/formatpsem.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/getAnova.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/getCoefficients.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/getDAG.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/getResidModels.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/get_response.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/grapes-twiddle-twiddle-grapes.Rd | 115 - piecewiseSEM-2.1.0/piecewiseSEM/man/handleCategoricalCoefs.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/infCrit.Rd | 78 piecewiseSEM-2.1.0/piecewiseSEM/man/isSig.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/keeley.Rd | 48 piecewiseSEM-2.1.0/piecewiseSEM/man/listFormula.Rd | 32 piecewiseSEM-2.1.0/piecewiseSEM/man/meadows.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/multigroup.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/nObs.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/onlyBars.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/partialCorr.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/partialResid.Rd | 114 - piecewiseSEM-2.1.0/piecewiseSEM/man/piecewiseSEM-package.Rd | 106 piecewiseSEM-2.1.0/piecewiseSEM/man/plot.psem.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/print.anova.psem.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/print.attr.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/print.basisSet.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/print.multigroup.psem.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/print.psem.Rd | 30 piecewiseSEM-2.1.0/piecewiseSEM/man/print.summary.psem.Rd | 30 piecewiseSEM-2.1.0/piecewiseSEM/man/psem.Rd | 85 piecewiseSEM-2.1.0/piecewiseSEM/man/removeCerror.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/removeData.Rd | 28 piecewiseSEM-2.1.0/piecewiseSEM/man/resid.lme.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/residuals.psem.Rd | 36 piecewiseSEM-2.1.0/piecewiseSEM/man/reverseAddVars.Rd | 38 piecewiseSEM-2.1.0/piecewiseSEM/man/reverseNonLin.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/rsquared.Rd | 204 - piecewiseSEM-2.1.0/piecewiseSEM/man/rsquared.glm.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/rsquared.glmerMod.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/rsquared.glmmPQL.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/rsquared.gls.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/rsquared.lm.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/rsquared.lme.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/rsquared.merMod.Rd | 30 piecewiseSEM-2.1.0/piecewiseSEM/man/rsquared.negbin.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/scaleGLM.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/scaleInt.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/shipley.Rd | 50 piecewiseSEM-2.1.0/piecewiseSEM/man/sortDag.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/specifyDir.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/stdCoefs.Rd | 31 piecewiseSEM-2.1.0/piecewiseSEM/man/stripTransformations.Rd | 22 piecewiseSEM-2.1.0/piecewiseSEM/man/summary.psem.Rd | 216 +- piecewiseSEM-2.1.0/piecewiseSEM/man/testBasisSetElements.Rd |only piecewiseSEM-2.1.0/piecewiseSEM/man/unstdCoefs.Rd | 28 piecewiseSEM-2.1.0/piecewiseSEM/man/update.psem.Rd | 30 piecewiseSEM-2.1.0/piecewiseSEM/vignettes/piecewiseSEM.Rmd | 35 136 files changed, 3527 insertions(+), 2666 deletions(-)
Title: Shed Light on Black Box Machine Learning Models
Description: Shed light on black box machine learning models by
the help of model performance, permutation variable importance (Fisher
et al. (2018) <arxiv:1801.01489>), ICE profiles, partial dependence
(Friedman J. H. (2001) <doi:10.1214/aos/1013203451>), accumulated
local effects (Apley D. W. (2016) <arXiv:1612.08468>), further effects
plots, interaction strength, and variable contribution breakdown
(approximate SHAP) for single observations (Gosiewska and Biecek
(2019) <arxiv:1903.11420>). All tools are implemented to work with
case weights and allow for stratified analysis. Furthermore, multiple
flashlights can be combined and analyzed together.
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between flashlight versions 0.4.0 dated 2019-11-10 and 0.5.0 dated 2019-12-05
DESCRIPTION | 18 - MD5 | 130 +++++----- NAMESPACE | 14 - NEWS.md | 49 +++ R/auto_cut.R | 2 R/grouped_center.R |only R/grouped_counts.R |only R/grouped_weighted_mean.R |only R/light_breakdown.R | 121 ++++----- R/light_effects.R | 16 - R/light_ice.R | 62 ++-- R/light_importance.R | 12 R/light_interaction.R | 197 +++++++++++---- R/light_performance.R | 3 R/light_profile.R | 36 -- R/light_recode.R | 4 R/plot_counts.R | 4 R/plot_light_breakdown.R | 19 - R/plot_light_effects.R | 21 - R/plot_light_ice.R | 6 R/plot_light_importance.R | 11 R/plot_light_performance.R | 4 R/plot_light_profile.R | 19 - R/predict_multiflashlight.R |only R/residuals_flashlight.R | 2 R/residuals_multiflashlight.R |only R/response.R | 9 R/zap_small.R |only README.md | 4 inst/doc/flashlight.R | 109 +++----- inst/doc/flashlight.Rmd | 74 ++--- inst/doc/flashlight.html | 503 +++++++++++++++++++-------------------- man/ale_profile.Rd | 115 ++++---- man/all_identical.Rd | 54 ++-- man/auto_cut.Rd | 105 ++++---- man/cut3.Rd | 87 +++--- man/flashlight.Rd | 130 +++++----- man/grouped_center.Rd |only man/grouped_counts.Rd |only man/grouped_stats.Rd | 130 +++++----- man/grouped_weighted_mean.Rd |only man/is.flashlight.Rd | 190 +++++++------- man/light_breakdown.Rd | 234 +++++++++--------- man/light_check.Rd | 86 +++--- man/light_combine.Rd | 110 ++++---- man/light_effects.Rd | 268 ++++++++++---------- man/light_ice.Rd | 236 +++++++++--------- man/light_importance.Rd | 215 ++++++++-------- man/light_interaction.Rd | 202 ++++++++------- man/light_performance.Rd | 161 ++++++------ man/light_profile.Rd | 320 ++++++++++++------------ man/light_recode.Rd | 110 ++++---- man/midpoints.Rd | 42 +-- man/most_important.Rd | 84 +++--- man/multiflashlight.Rd | 114 ++++---- man/plot.light_breakdown.Rd | 77 ++--- man/plot.light_effects.Rd | 118 ++++----- man/plot.light_ice.Rd | 125 ++++----- man/plot.light_importance.Rd | 102 ++++--- man/plot.light_performance.Rd | 85 +++--- man/plot.light_profile.Rd | 113 +++----- man/plot_counts.Rd | 114 ++++---- man/predict.flashlight.Rd | 52 ++-- man/predict.multiflashlight.Rd |only man/print.flashlight.Rd | 52 ++-- man/print.light.Rd | 50 +-- man/print.multiflashlight.Rd | 58 ++-- man/residuals.flashlight.Rd | 54 ++-- man/residuals.multiflashlight.Rd |only man/response.Rd | 83 +++--- man/zap_small.Rd |only vignettes/flashlight.Rmd | 74 ++--- 72 files changed, 2846 insertions(+), 2753 deletions(-)
Title: Extended Empirical Saddlepoint Density Approximations
Description: Tools for fitting the Extended Empirical Saddlepoint (EES) density.
Author: Matteo Fasiolo and Simon N. Wood
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between esaddle versions 0.0.4 dated 2019-12-04 and 0.0.5 dated 2019-12-05
esaddle-0.0.4/esaddle/R/mstOptim.R |only esaddle-0.0.4/esaddle/inst/tests/test-mstOptim.R |only esaddle-0.0.4/esaddle/src/mst.cpp |only esaddle-0.0.5/esaddle/DESCRIPTION | 12 +-- esaddle-0.0.5/esaddle/MD5 | 23 ++---- esaddle-0.0.5/esaddle/R/dsaddle.R | 84 +++++++---------------- esaddle-0.0.5/esaddle/R/selectDecay.R | 7 - esaddle-0.0.5/esaddle/inst/doc/esaddle.html | 12 +-- esaddle-0.0.5/esaddle/man/dsaddle.Rd | 18 +++- esaddle-0.0.5/esaddle/man/findMode.Rd | 11 ++- esaddle-0.0.5/esaddle/man/rsaddle.Rd | 12 ++- esaddle-0.0.5/esaddle/man/selectDecay.Rd | 16 +++- esaddle-0.0.5/esaddle/src/esaddle.h | 3 esaddle-0.0.5/esaddle/src/init.c | 3 14 files changed, 97 insertions(+), 104 deletions(-)
Title: A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer
Maintainer: James Dalgleish <james.dalgleish@nih.gov>
Diff between CNVScope versions 2.8.2 dated 2019-10-25 and 2.9.2 dated 2019-12-05
DESCRIPTION | 10 +- MD5 | 12 +-- NEWS.md | 8 +- R/rebinGenomicInteractions.R | 148 ++++++++++++++++++++------------------- inst/doc/additonal_examples.Rmd | 5 + inst/doc/additonal_examples.html | 3 vignettes/additonal_examples.Rmd | 5 + 7 files changed, 105 insertions(+), 86 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photos, tabulates records of species and individuals, and creates detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station including GIS export) and can visualise species activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 1.1 dated 2019-03-13 and 1.2 dated 2019-12-05
DESCRIPTION | 13 MD5 | 106 +- NAMESPACE | 9 NEWS | 30 R/activityDensity.R | 16 R/activityHistogram.R | 13 R/activityOverlap.R | 28 R/activityRadial.R | 15 R/appendSpeciesNames.R | 10 R/cameraOperation.R | 376 ++++----- R/checkSpeciesIdentification.R | 17 R/checkSpeciesNames.R | 12 R/detectionHistory.R | 152 ++- R/detectionMaps.R | 41 R/exifTagNames.R | 61 + R/getSpeciesImages.R | 16 R/imageRename.R | 245 +++-- R/recordTable.R | 103 +- R/recordTableIndividual.R | 107 +- R/spatialDetectionHistory.R | 156 ++- R/surveyReport.R | 69 - R/timeShiftImages.R | 2 R/variousOtherHelperFunctions.R | 1079 ++++++++++++++++++-------- R/variousPlottingHelperFunctions.R | 4 build/vignette.rds |binary data/camtraps.rda |binary data/recordTableIndividualSample.rda |binary data/recordTableSample.rda |binary data/timeShiftTable.rda |binary inst/doc/DataExploration.R | 34 inst/doc/DataExploration.html | 38 inst/doc/DataExtraction.R | 221 ++++- inst/doc/DataExtraction.Rmd | 226 +++++ inst/doc/DataExtraction.html | 434 +++++++--- inst/doc/ImageOrganisation.R | 25 inst/doc/ImageOrganisation.Rmd | 43 - inst/doc/ImageOrganisation.html | 112 +- inst/doc/SpeciesIndividualIdentification.R | 16 inst/doc/SpeciesIndividualIdentification.html | 164 ++- man/activityDensity.Rd | 5 man/activityHistogram.Rd | 6 man/activityOverlap.Rd | 16 man/activityRadial.Rd | 5 man/cameraOperation.Rd | 45 + man/camtrapR-package.Rd | 22 man/checkSpeciesIdentification.Rd | 2 man/detectionHistory.Rd | 48 - man/exifTagNames.Rd | 37 man/recordTable.Rd | 35 man/recordTableIndividual.Rd | 38 man/spatialDetectionHistory.Rd | 8 man/surveyReport.Rd | 9 vignettes/DataExtraction.Rmd | 226 +++++ vignettes/ImageOrganisation.Rmd | 43 - 54 files changed, 3159 insertions(+), 1379 deletions(-)
Title: Turner Miscellaneous
Description: Miscellaneous utility functions for data manipulation,
data tidying, and working with gene expression data.
Author: Stephen Turner [aut, cre] (<https://orcid.org/0000-0001-9140-9028>)
Maintainer: Stephen Turner <vustephen@gmail.com>
Diff between Tmisc versions 0.1.20 dated 2019-03-25 and 0.1.22 dated 2019-12-05
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/counts2fpkm.R | 2 +- R/jsd.R | 5 +++-- R/mat2df.R | 2 +- R/rownames_to_symprobe.R | 2 +- man/Tmisc.Rd | 1 - man/lsa.Rd | 10 ++++++++-- 10 files changed, 33 insertions(+), 22 deletions(-)
Title: Interface to the 'iPTMnet' API
Description: Provides an R interface to the 'iPTMnet' database REST API, which can be used to retrieve
Post Translational Modification (PTM) data in systems biology context. This package handles all the aspects
of communicating with the API, which involve sending the request, checking the error codes and parsing the
response in a format that is ready to integrate into existing workflows.
Author: Sachin Gavali
Maintainer: Sachin Gavali <saching@udel.edu>
Diff between iptmnetr versions 0.1.6 dated 2019-10-24 and 0.1.8 dated 2019-12-05
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 2 ++ R/api.R | 49 ++++++++++++++++++++++++++++++++++++++----------- man/get_api_version.Rd |only man/set_api_version.Rd |only 6 files changed, 48 insertions(+), 17 deletions(-)
Title: Estimation Methods for Causal Inference Based on Inverse
Probability Weighting
Description: Various estimation methods for causal inference based on inverse probability weighting. Specifically, the package includes methods for estimating average treatment effects as well as direct and indirect effects in causal mediation analysis. The models refer to the studies of Froelich (2007) <doi:10.1016/j.jeconom.2006.06.004>, Huber (2012) <doi:10.3102/1076998611411917>, Huber (2014) <doi:10.1080/07474938.2013.806197>, Huber (2014) <doi:10.1002/jae.2341>, and Froelich and Huber (2017) <doi:10.1111/rssb.12232>.
Author: Hugo Bodory and Martin Huber
Maintainer: Hugo Bodory <hugo.bodory@unifr.ch>
Diff between causalweight versions 0.1.2 dated 2018-12-01 and 0.1.3 dated 2019-12-05
DESCRIPTION | 10 MD5 | 36 ++- NAMESPACE | 12 + R/attrlateweight.R |only R/didweight.R |only R/functions.R | 502 +++++++++++++++++++++++++++++++++++++++++++++- R/medDML.R |only R/medweightcont.R | 16 - R/swissexper.R |only R/treatweight.R | 2 R/wexpect.R |only build/vignette.rds |binary data |only inst/doc/bodory-huber.pdf |binary man/attrlateweight.Rd |only man/didweight.Rd |only man/lateweight.Rd | 161 +++++++------- man/medDML.Rd |only man/medlateweight.Rd | 161 +++++++------- man/medweight.Rd | 160 +++++++------- man/medweightcont.Rd | 144 +++++++------ man/swissexper.Rd |only man/treatweight.Rd | 190 +++++++++-------- man/wexpect.Rd |only 24 files changed, 985 insertions(+), 409 deletions(-)
Title: Bayesian Inference for Factor Modeling
Description: Collection of procedures to perform Bayesian analysis on a variety
of factor models. Currently, it includes: Bayesian Exploratory Factor
Analysis (befa), an approach to dedicated factor analysis with stochastic
search on the structure of the factor loading matrix. The number of latent
factors, as well as the allocation of the manifest variables to the factors,
are not fixed a priori but determined during MCMC sampling.
More approaches will be included in future releases of this package.
Author: Rémi Piatek [aut, cre] (<https://orcid.org/0000-0002-3474-1304>)
Maintainer: Rémi Piatek <remi.piatek@econ.ku.dk>
Diff between BayesFM versions 0.1.2 dated 2017-02-20 and 0.1.3 dated 2019-12-05
DESCRIPTION | 18 ++++++++++-------- MD5 | 38 +++++++++++++++++++------------------- NEWS | 4 ++++ R/befa.R | 2 +- R/plot.befa.R | 2 +- R/post.column.switch.R | 2 +- R/post.sign.switch.R | 2 +- R/simul.R.prior.R | 9 ++++----- R/simul.nfac.prior.R | 3 ++- R/summary.befa.R | 23 ++++++++++++++--------- R/utils.R | 2 +- man/BayesFM.Rd | 8 +++----- man/befa.Rd | 9 ++++----- man/plot.befa.Rd | 9 ++++----- man/post.column.switch.Rd | 9 ++++----- man/post.sign.switch.Rd | 9 ++++----- man/simul.R.prior.Rd | 13 ++++++------- man/simul.dedic.facmod.Rd | 7 +++---- man/simul.nfac.prior.Rd | 10 +++++----- man/summary.befa.Rd | 18 ++++++++++++++---- 20 files changed, 105 insertions(+), 92 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>),
Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>),
Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>),
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Diff between SDMtune versions 0.2.0 dated 2019-09-02 and 0.2.1 dated 2019-12-05
DESCRIPTION | 18 +- MD5 | 81 +++++----- NAMESPACE | 1 NEWS.md | 10 + R/auc.R | 22 +- R/chart-utils.R | 2 R/confMatrix.R | 5 R/mergeSWD.R | 55 +++++-- R/optimizeModel.R | 2 R/plotCor.R | 2 R/plotJk.R | 2 R/plotPA.R | 9 - R/plotPred.R | 2 R/plotROC.R | 2 R/plotResponse.R | 6 R/plotVarImp.R | 2 R/predict-SDMmodel.R | 23 ++ R/predict-SDMmodelCV.R |only R/thinData.R | 12 + R/train.R | 110 ++++++++------ R/tss.R | 20 +- R/varSel.R | 2 inst/doc/SDMtune.html | 33 ++-- man/auc.Rd | 17 +- man/mergeSWD.Rd | 17 +- man/optimizeModel.Rd | 2 man/plotResponse.Rd | 4 man/predict-SDMmodel-method.Rd | 16 +- man/predict-SDMmodelCV-method.Rd |only man/train.Rd | 29 ++- man/tss.Rd | 17 +- man/varSel.Rd | 2 tests/testthat/test-auc.R | 11 + tests/testthat/test-confMatrix.R | 5 tests/testthat/test-mergeSWD.R | 29 ++- tests/testthat/test-predict-SDMmodel.R | 18 +- tests/testthat/test-predict-SDMmodelCV.R |only tests/testthat/test-train.R | 11 + tests/testthat/test-tss.R | 7 vignettes/SDMtune.bib | 216 ++++++++++++++-------------- vignettes/articles/prepare-data.Rmd | 2 vignettes/articles/tune-hyperparameters.Rmd | 14 + vignettes/articles/variable-selection.Rmd | 2 43 files changed, 525 insertions(+), 315 deletions(-)
Title: Probability Associator Time (PASS-T)
Description: Simulates judgments of frequency and duration based on
the Probability Associator Time (PASS-T) model. PASS-T is a memory
model based on a simple competitive artificial neural network. It
can imitate human judgments of frequency and duration, which have
been extensively studied in cognitive psychology
(e.g. Hintzman (1970) <doi:10.1037/h0028865>, Betsch et al. (2010)
<https://psycnet.apa.org/record/2010-18204-003>). The PASS-T model
is an extension of the PASS model (Sedlmeier, 2002,
ISBN:0198508638). The package provides an easy way to run
simulations, which can then be compared with empirical data in
human judgments of frequency and duration.
Author: Johannes Titz [aut, cre]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Diff between passt versions 0.1.0 dated 2019-11-05 and 0.1.1 dated 2019-12-05
DESCRIPTION | 10 - MD5 | 18 +- NAMESPACE | 1 NEWS.md | 5 R/passt.R | 3 inst/doc/passt.R | 24 +-- inst/doc/passt.html | 109 +++++++++-------- man/run_exp.Rd | 13 +- man/run_sim.Rd | 14 +- vignettes/library.bib | 304 ++++++++++++++++++++++++++++++++++++++++++++------ 10 files changed, 383 insertions(+), 118 deletions(-)
Title: Multi-Model Inference
Description: Tools for performing model selection and model averaging. Automated
model selection through subsetting the maximum model, with optional
constraints for model inclusion. Model parameter and prediction
averaging based on model weights derived from information criteria
(AICc and alike) or custom model weighting schemes.
Author: Kamil Bartoń
Maintainer: Kamil Bartoń <kamil.barton@go2.pl>
Diff between MuMIn versions 1.43.6 dated 2019-04-09 and 1.43.10 dated 2019-12-05
DESCRIPTION | 16 ++++++------ MD5 | 30 +++++++++++------------ NAMESPACE | 20 +-------------- NEWS | 15 +++++++++++ R/averaging.R | 30 +++++++++++++++-------- R/class-gamlss.R | 9 ++++++ R/init.R | 2 - R/methods-nobs.R | 6 ---- R/methods-predict.R | 61 ----------------------------------------------- R/model.sel.R | 3 ++ R/r.squaredGLMM2.R | 24 +++++++++++++----- R/std.coef.R | 8 ++---- data/Beetle.rda |binary data/Cement.rda |binary data/GPA.rda |binary man/predict.averaging.Rd | 20 ++++++--------- 16 files changed, 100 insertions(+), 144 deletions(-)
Title: Process and Analyze Mouse-Tracking Data
Description: Mouse-tracking, the analysis of mouse movements in computerized
experiments, is a method that is becoming increasingly popular in the
cognitive sciences. The mousetrap package offers functions for importing,
preprocessing, analyzing, aggregating, and visualizing mouse-tracking data.
Author: Pascal J. Kieslich [aut, cre] (<https://orcid.org/0000-0002-0853-9364>),
Dirk U. Wulff [aut] (<https://orcid.org/0000-0002-4008-8022>),
Felix Henninger [aut] (<https://orcid.org/0000-0002-7730-9511>),
Jonas M. B. Haslbeck [aut],
Sarah Brockhaus [ctb]
Maintainer: Pascal J. Kieslich <kieslich@psychologie.uni-mannheim.de>
Diff between mousetrap versions 3.1.3 dated 2019-10-04 and 3.1.4 dated 2019-12-05
DESCRIPTION | 8 ++-- MD5 | 22 ++++++------ NEWS.md | 13 ++++++- R/heatmap.R | 16 ++++---- R/import.R | 4 +- R/measures.R | 97 +++++++++++++++++++++++++++++++++++++++++++---------- R/preprocess.R | 2 - R/quantileeffect.R | 2 - R/reshape.R | 6 +-- R/startupmessage.R | 2 - R/utils.R | 2 - man/mt_measures.Rd | 18 +++++++-- 12 files changed, 137 insertions(+), 55 deletions(-)
Title: Test for Monotonicity in Expected Asset Returns, Sorted by
Portfolios
Description: Test for monotonicity in financial variables sorted by portfolios. It is conventional practice in empirical research to form portfolios of assets ranked by a certain sort variable. A t-test is then used to consider the mean return spread between the portfolios with the highest and lowest values of the sort variable. Yet comparing only the average returns on the top and bottom portfolios does not provide a sufficient way to test for a monotonic relation between expected returns and the sort variable. This package provides nonparametric tests for the full set of monotonic patterns by Patton, A. and Timmermann, A. (2010) <doi:10.1016/j.jfineco.2010.06.006> and compares the proposed results with extant alternatives such as t-tests, Bonferroni bounds, and multivariate inequality tests through empirical applications and simulations.
Author: Siegfried Köstlmeier [aut, cre, trl]
(<https://orcid.org/0000-0002-7221-6981>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>
Diff between monotonicity versions 1.3 dated 2019-08-20 and 1.3.1 dated 2019-12-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary tests/testthat/test-matrix_conversion.R | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Statistical Tests for Assessing Trinormal ROC Data
Description: Several statistical test functions as well as a function for exploratory data analysis to investigate classifiers allocating individuals to one of three disjoint and ordered classes. In a single classifier assessment the discriminatory power is compared to classification by chance. In a comparison of two classifiers the null hypothesis corresponds to equal discriminatory power of the two classifiers.
Author: Samuel Noll [aut],
Reinhard Furrer [ctb, cre],
Benjamin Reiser [ctb],
Christos T. Nakas [ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between trinROC versions 0.3.1 dated 2019-10-03 and 0.4 dated 2019-12-05
DESCRIPTION | 8 MD5 | 46 - NEWS.md |only R/boot.test.R | 18 R/emp.vus.R | 2 R/roc.eda.R | 39 - R/roc3.test.R | 19 R/rocsurf.trin.R | 8 R/trinROC.R | 8 R/trinROC.test.R | 10 R/trinVUS.test.R | 10 inst/doc/trinROC_vignette.R | 4 inst/doc/trinROC_vignette.Rmd | 4 man/boot.test.Rd | 30 - man/boxcoxROC.Rd | 11 man/findmu.Rd | 3 man/roc.eda.Rd | 29 - man/roc3.test.Rd | 20 man/rocsurf.trin.Rd | 8 man/trinROC-package.Rd | 8 man/trinROC.test.Rd | 17 man/trinVUS.test.Rd | 21 tests/testthat/Rplots.pdf |only vignettes/trinROC_vignette.Rmd | 4 vignettes/trinROC_vignette.html | 1113 +++++++++++++++++++++------------------- 25 files changed, 778 insertions(+), 662 deletions(-)
Title: Ridge Estimation of Vector Auto-Regressive (VAR) Processes
Description: The ragt2ridges-package provides ridge maximum likelihood estimation of vector auto-regressive processes: the VAR(1), VAR(2) and VARX(1) model (more to be added). Prior knowledge may be incorporated in the estimation through a) specification of the edges believed to be absent in the time series chain graph, and b) a shrinkage target towards which the parameter estimate is shrunken for large penalty parameter values. Estimation functionality is accompanied by methodology for penalty parameter selection. In addition, the package offers supporting functionality for the exploitation of estimated models. Among others, i) a procedure to infer the support of the non-sparse ridge estimate (and thereby of the time series chain graph) is implemented, ii) a table of node-wise network summary statistics, iii) mutual information analysis, and iv) impulse response analysis. Cf. Miok et al. (2017) <DOI:10.1002/bimj.201500269> and Miok et al. (2019) <DOI:10.1002/bimj.201700195> for details on the implemented methods.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between ragt2ridges versions 0.3.2 dated 2018-12-20 and 0.3.3 dated 2019-12-05
DESCRIPTION | 10 +- MD5 | 132 ++++++++++++++++++------------------- NAMESPACE | 2 R/CIGofVAR1.r | 6 - R/CIGofVAR2.r | 8 +- R/centerVAR1data.r | 2 R/createA.R | 18 ++--- R/dataVAR1.r | 10 +- R/dataVAR2.r | 12 +-- R/dataVARX1.r | 6 - R/evaluateVAR1fit.r | 8 +- R/graphVAR1.r | 16 ++-- R/graphVAR2.r | 18 ++--- R/graphVARX1.r | 18 ++--- R/impulseResponseVAR1.r | 4 - R/impulseResponseVAR2.r | 6 - R/impulseResponseVARX1.r | 4 - R/loglikLOOCVVAR1.r | 6 - R/loglikLOOCVVAR1fused.r | 8 +- R/loglikLOOCVVAR2.r | 6 - R/loglikLOOCVVARX1.r | 8 +- R/loglikLOOCVcontourVAR1.r | 10 +- R/loglikLOOCVcontourVAR1fused.r | 12 +-- R/loglikLOOCVcontourVAR2.r | 12 +-- R/loglikLOOCVcontourVARX1.r | 14 +-- R/loglikVAR1.r | 8 +- R/mutualInfoVAR1.r | 6 - R/mutualInfoVAR2.r | 8 +- R/nodeStatsVAR1.r | 2 R/nodeStatsVAR2.r | 2 R/optPenaltyVAR1.r | 8 +- R/optPenaltyVAR1fused.r | 10 +- R/optPenaltyVAR2.r | 8 +- R/optPenaltyVARX1.r | 10 +- R/plotVAR1data.r | 4 - R/ridgePathVAR1.r | 14 +-- R/ridgeVAR1.r | 36 +++++----- R/ridgeVAR1fused.r | 44 ++++++------ R/ridgeVAR2.r | 46 ++++++------ R/ridgeVARX1.r | 48 ++++++------- R/sparsifyVAR1.r | 22 +++--- R/sparsifyVAR2.r | 18 ++--- R/sparsifyVARX1.r | 18 ++--- inst/CITATION | 12 +-- inst/NEWS.Rd | 7 + man/CIGofVAR2.Rd | 2 man/graphVAR2.Rd | 2 man/graphVARX1.Rd | 2 man/impulseResponseVAR2.Rd | 2 man/impulseResponseVARX1.Rd | 2 man/loglikLOOCVVAR1fused.Rd | 2 man/loglikLOOCVVAR2.Rd | 2 man/loglikLOOCVVARX1.Rd | 2 man/loglikLOOCVcontourVAR1fused.Rd | 2 man/loglikLOOCVcontourVAR2.Rd | 2 man/loglikLOOCVcontourVARX1.Rd | 2 man/mutualInfoVAR2.Rd | 2 man/nodeStatsVAR2.Rd | 2 man/optPenaltyVAR1fused.Rd | 2 man/optPenaltyVAR2.Rd | 2 man/optPenaltyVARX1.Rd | 2 man/ragt2ridges-package.Rd | 6 - man/ridgeVAR1fused.Rd | 2 man/ridgeVAR2.Rd | 2 man/ridgeVARX1.Rd | 2 man/sparsifyVAR2.Rd | 2 man/sparsifyVARX1.Rd | 2 67 files changed, 371 insertions(+), 364 deletions(-)
Title: Poisson Lognormal Models
Description: The Poisson-lognormal model and variants can be used for
a variety of multivariate problems when count data are at play, including
principal component analysis for count data (Chiquet, Mariadassou and Robin,
2018 <doi:10.1214/18-AOAS1177>), discriminant analysis and
network inference (Chiquet, Mariadassou and Robin, 2018 <arXiv:1806.03120>).
Implements variational algorithms to fit such models accompanied with a set of
functions for visualization and diagnostic.
Author: Julien Chiquet [aut, cre] (<https://orcid.org/0000-0002-3629-3429>),
Mahendra Mariadassou [aut] (<https://orcid.org/0000-0003-2986-354X>),
Stéphane Robin [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inra.fr>
Diff between PLNmodels versions 0.9.2 dated 2019-05-17 and 0.9.3 dated 2019-12-05
DESCRIPTION | 9 MD5 | 48 +- NEWS.md | 8 R/PLNfit-class.R | 1 R/PLNnetwork.R | 4 R/PLNnetworkfamily-class.R | 10 R/PLNnetworkfit-class.R | 2 R/utils.R | 2 build/vignette.rds |binary inst/CITATION | 12 inst/doc/Import_data.html | 10 inst/doc/PLN.html | 102 ++--- inst/doc/PLNLDA.html | 620 ++++++++++++++++----------------- inst/doc/PLNPCA.Rmd | 2 inst/doc/PLNPCA.html | 162 ++++---- inst/doc/PLNnetwork.html | 240 ++++++------ inst/doc/Trichoptera.html | 10 man/PLNnetwork.Rd | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-import-utils.R | 7 tests/testthat/test-plnfit.R | 4 tests/testthat/test-plnlda-fit.R | 4 tests/testthat/test-plnnetworkfamily.R | 49 ++ vignettes/PLNPCA.Rmd | 2 vignettes/article/PLNreferences.bib | 22 - 25 files changed, 715 insertions(+), 616 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 0.9.0 dated 2019-11-08 and 0.9.1 dated 2019-12-05
DESCRIPTION | 10 ++-- MD5 | 32 ++++++------- NEWS.md | 10 +++- R/cox2.R | 19 ++++++-- R/coxme.R | 2 R/glmshow.R | 2 R/lmer.R | 4 - R/svycox.R | 2 R/svyglm.R | 2 inst/doc/jstable.R | 20 ++++---- inst/doc/jstable.html | 100 +++++++++++++++++-------------------------- man/CreateTableOne2.Rd | 36 ++++++++++++--- man/CreateTableOneJS.Rd | 40 ++++++++++++----- man/TableSubgroupCox.Rd | 13 ++++- man/TableSubgroupMultiCox.Rd | 14 ++++-- man/svyCreateTableOne2.Rd | 23 ++++++++- man/svyCreateTableOneJS.Rd | 26 +++++++++-- 17 files changed, 220 insertions(+), 135 deletions(-)
Title: Mixed Computerized Adaptive Multistage Testing
Description: Provides functions to more easily analyze computerized adaptive tests. Currently, functions for computerized
adaptive tests (CAT), computer adaptive multistage tests (CMT), and mixed computer adaptive multistage tests (McaMST)
utilizing CAT item-level adaptation for the initial stage and traditional MST module-level adaptation for the subsequent
stages have been created, and a variation of Hybrid computer adaptive MST is planned as well. For an in-depth look at
CAT and MST, see Weiss & Kingsbury (1984) <doi:10.1111/j.1745-3984.1984.tb01040.x> and Luecht & Nungester
(2000) <doi:10.1007/0-306-47531-6_6> respectively.
Author: Anthony Raborn [aut, cre]
Maintainer: Anthony Raborn <anthony.w.raborn@gmail.com>
Diff between caMST versions 0.1.2 dated 2019-10-09 and 0.1.3 dated 2019-12-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + NEWS.md | 11 +++-------- R/transition_matrix_plot.R | 3 ++- 5 files changed, 14 insertions(+), 17 deletions(-)
Title: Data Files and Functions Accompanying the Book "Bayesian Data
Analysis in Ecology using R, BUGS and Stan"
Description: Data files and functions accompanying the book Korner-Nievergelt, Roth, von Felten, Guelat, Almasi, Korner-Nievergelt (2015) "Bayesian Data Analysis in Ecology using R, BUGS and Stan", Elsevier, New York.
Author: Fraenzi Korner-Nievergelt, Tobias Roth, Stefanie von Felten, Jerome Guelat, Bettina Almasi, Pius Korner-Nievergelt
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@oikostat.ch>
Diff between blmeco versions 1.3 dated 2019-05-04 and 1.4 dated 2019-12-05
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 - R/AICweights.R | 10 +++------- man/AICweights.Rd | 29 +++++++---------------------- 5 files changed, 19 insertions(+), 39 deletions(-)
Title: Locally Gaussian Distributions: Estimation and Methods
Description: An implementation of locally Gaussian distributions. It provides methods for
implementing locally Gaussian multivariate density estimation, conditional density
estimation, various independence tests for iid and time series data, a test for conditional
independence and a test for financial contagion.
Author: Håkon Otneim [aut, cre]
Maintainer: Håkon Otneim <hakon.otneim@nhh.no>
Diff between lg versions 0.4.0 dated 2019-09-03 and 0.4.1 dated 2019-12-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test_density_estimation.R | 1 - 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Hidden Markov Models with Discrete Non-Parametric Observation
Distributions
Description: Fits hidden Markov models with discrete non-parametric
observation distributions to data sets. The observations may
be univariate or bivariate. Simulates data from such models.
Finds most probable underlying hidden states, the most
probable sequences of such states, and the log likelihood
of a collection of observations given the parameters of
the model. Auxiliary predictors are accommodated in the
univariate setting.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between hmm.discnp versions 2.1-11 dated 2019-08-07 and 2.1-12 dated 2019-12-05
ChangeLog | 7 ++++ DESCRIPTION | 8 ++--- MD5 | 60 +++++++++++++++++++-------------------- R/mps.R | 19 +++++++++--- R/nafracCalc.R | 20 ++++++++++--- R/pr.R | 18 +++++++++-- R/predictEngineHmmDiscnp.R | 13 +++++++- R/sp.R | 13 +++++++- data/Bovine.rda |binary data/Cryptosporidiosis.rda |binary data/Downloads.rda |binary data/EricssonB_Jul2.rda |binary data/FattyLiver.rda |binary data/FattyLiver2.rda |binary data/Hanta.rda |binary data/IPs.rda |binary data/InfantEEGsleepstates.rda |binary data/LegionnairesDisease.rda |binary data/OffshoreRigcountsAlaska.rda |binary data/PriceStability.rda |binary data/Strikes.rda |binary data/SydColDisc.rda |binary data/WoodPeweeSong.rda |binary data/ccprSim.rda |binary data/ftLiardFlows.rda |binary data/goldparticle380.rda |binary data/lesionCount.rda |binary data/linLandFlows.rda |binary data/portMannFlows.rda |binary data/portMannSedCon.rda |binary data/portMannSedLoads.rda |binary 31 files changed, 107 insertions(+), 51 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>),
George Athanasopoulos [aut],
Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>),
Gabriel Caceres [aut],
Leanne Chhay [aut],
Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>),
Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>),
Slava Razbash [aut],
Earo Wang [aut],
Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>),
R Core Team [ctb, cph],
Ross Ihaka [ctb, cph],
Daniel Reid [ctb],
David Shaub [ctb],
Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>),
Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.9 dated 2019-08-22 and 8.10 dated 2019-12-05
forecast-8.10/forecast/DESCRIPTION | 8 forecast-8.10/forecast/MD5 | 148 ++++------ forecast-8.10/forecast/NAMESPACE | 1 forecast-8.10/forecast/NEWS.md | 4 forecast-8.10/forecast/R/arima.R | 1 forecast-8.10/forecast/R/attach.R | 72 ++-- forecast-8.10/forecast/R/clean.R | 2 forecast-8.10/forecast/R/ets.R | 13 forecast-8.10/forecast/R/forecast-package.R | 2 forecast-8.10/forecast/R/ggplot.R | 307 ++++++++++----------- forecast-8.10/forecast/R/naive.R | 7 forecast-8.10/forecast/R/newarima2.R | 9 forecast-8.10/forecast/R/simulate.R | 5 forecast-8.10/forecast/R/spline.R | 2 forecast-8.10/forecast/R/theta.R | 4 forecast-8.10/forecast/README.md | 9 forecast-8.10/forecast/inst/doc/JSS2008.R | 24 - forecast-8.10/forecast/inst/doc/JSS2008.pdf |binary forecast-8.10/forecast/man/Acf.Rd | 45 ++- forecast-8.10/forecast/man/Arima.Rd | 20 + forecast-8.10/forecast/man/BoxCox.lambda.Rd | 3 forecast-8.10/forecast/man/CVar.Rd | 11 forecast-8.10/forecast/man/accuracy.Rd | 7 forecast-8.10/forecast/man/arfima.Rd | 12 forecast-8.10/forecast/man/auto.arima.Rd | 47 ++- forecast-8.10/forecast/man/autolayer.Rd | 2 forecast-8.10/forecast/man/autoplot.acf.Rd | 49 ++- forecast-8.10/forecast/man/autoplot.seas.Rd | 6 forecast-8.10/forecast/man/autoplot.ts.Rd | 22 + forecast-8.10/forecast/man/baggedModel.Rd | 3 forecast-8.10/forecast/man/bats.Rd | 20 + forecast-8.10/forecast/man/bizdays.Rd | 3 forecast-8.10/forecast/man/dm.test.Rd | 9 forecast-8.10/forecast/man/dshw.Rd | 19 + forecast-8.10/forecast/man/ets.Rd | 35 +- forecast-8.10/forecast/man/forecast.Arima.Rd | 41 ++ forecast-8.10/forecast/man/forecast.HoltWinters.Rd | 12 forecast-8.10/forecast/man/forecast.Rd | 18 - forecast-8.10/forecast/man/forecast.StructTS.Rd | 12 forecast-8.10/forecast/man/forecast.baggedModel.Rd | 7 forecast-8.10/forecast/man/forecast.bats.Rd | 6 forecast-8.10/forecast/man/forecast.ets.Rd | 17 - forecast-8.10/forecast/man/forecast.lm.Rd | 14 forecast-8.10/forecast/man/forecast.mlm.Rd | 14 forecast-8.10/forecast/man/forecast.modelAR.Rd | 17 - forecast-8.10/forecast/man/forecast.mts.Rd | 16 - forecast-8.10/forecast/man/forecast.nnetar.Rd | 17 - forecast-8.10/forecast/man/forecast.stl.Rd | 66 +++- forecast-8.10/forecast/man/geom_forecast.Rd | 17 - forecast-8.10/forecast/man/gghistogram.Rd | 10 forecast-8.10/forecast/man/gglagplot.Rd | 27 + forecast-8.10/forecast/man/ggmonthplot.Rd | 3 forecast-8.10/forecast/man/meanf.Rd | 13 forecast-8.10/forecast/man/modelAR.Rd | 16 - forecast-8.10/forecast/man/msts.Rd | 3 forecast-8.10/forecast/man/na.interp.Rd | 7 forecast-8.10/forecast/man/naive.Rd | 37 ++ forecast-8.10/forecast/man/ndiffs.Rd | 10 forecast-8.10/forecast/man/nnetar.Rd | 16 - forecast-8.10/forecast/man/nsdiffs.Rd | 10 forecast-8.10/forecast/man/plot.Arima.Rd | 10 forecast-8.10/forecast/man/plot.forecast.Rd | 44 ++- forecast-8.10/forecast/man/plot.mforecast.Rd | 6 forecast-8.10/forecast/man/residuals.forecast.Rd | 24 - forecast-8.10/forecast/man/seasonplot.Rd | 32 +- forecast-8.10/forecast/man/ses.Rd | 58 +++ forecast-8.10/forecast/man/simulate.ets.Rd | 100 +++++- forecast-8.10/forecast/man/splinef.Rd | 12 forecast-8.10/forecast/man/subset.ts.Rd | 15 - forecast-8.10/forecast/man/tbats.Rd | 20 + forecast-8.10/forecast/man/thetaf.Rd | 9 forecast-8.10/forecast/man/tsCV.Rd | 3 forecast-8.10/forecast/man/tsdisplay.Rd | 31 +- forecast-8.9/forecast/vignettes/JSS2008_files |only 74 files changed, 1150 insertions(+), 571 deletions(-)
Title: Bio-Logging Toolbox
Description: An R-shiny application to plot datalogger time series at a microsecond precision as Acceleration, Temperature,
Pressure, Light intensity from CATS, AXY-TREK LUL and WACU bio-loggers. It is possible to link behavioral labels extracted
from 'BORIS' software <http://www.boris.unito.it> or manually written in a csv file.
CATS bio-logger are manufactured by <http://www.cats.is>, AXY-TREK are manufactured by <http://www.technosmart.eu> and
LUL and WACU are manufactured by <http://www.iphc.cnrs.fr/-MIBE-.html>.
Author: Sebastien Geiger [aut, cre]
Maintainer: Sebastien Geiger <sebastien.geiger@iphc.cnrs.fr>
Diff between rblt versions 0.2.4.4 dated 2019-10-15 and 0.2.4.5 dated 2019-12-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- R/logger.R | 2 +- inst/doc/rblt.html | 8 ++++++-- 5 files changed, 16 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-17 1.5
2016-08-01 1.4
2015-12-12 1.3
2015-01-21 1.2
2014-08-27 1.1-1
2014-03-11 1.1
2013-02-26 1.0
2012-04-30 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-04 0.1.1
Title: The Phylogenetic Ornstein-Uhlenbeck Mixed Model
Description: The Phylogenetic Ornstein-Uhlenbeck Mixed Model (POUMM) allows to
estimate the phylogenetic heritability of continuous traits, to test
hypotheses of neutral evolution versus stabilizing selection, to quantify
the strength of stabilizing selection, to estimate measurement error and to
make predictions about the evolution of a phenotype and phenotypic variation
in a population. The package implements combined maximum likelihood and
Bayesian inference of the univariate Phylogenetic Ornstein-Uhlenbeck Mixed
Model, fast parallel likelihood calculation, maximum likelihood
inference of the genotypic values at the tips, functions for summarizing and
plotting traces and posterior samples, functions for simulation of a univariate
continuous trait evolution model along a phylogenetic tree. So far, the
package has been used for estimating the heritability of quantitative traits
in macroevolutionary and epidemiological studies, see e.g.
Bertels et al. (2017) <doi:10.1093/molbev/msx246> and
Mitov and Stadler (2018) <doi:10.1093/molbev/msx328>. The algorithm for
parallel POUMM likelihood calculation has been published in
Mitov and Stadler (2019) <doi:10.1111/2041-210X.13136>.
Author: Venelin Mitov [aut, cre, cph] (<a
href="https://venelin.github.io">venelin.github.io</a>),
Matt Dowle [ctb]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between POUMM versions 2.1.5 dated 2019-03-27 and 2.1.6 dated 2019-12-05
DESCRIPTION | 14 - MD5 | 56 ++-- NEWS.md | 6 R/POUMM.R | 18 + R/fitPOUMM.R | 25 + R/likPOUMM.R | 18 + R/paramsPOUMM.R | 19 + R/specPOUMM.R | 22 + R/summaryPOUMM.R | 20 + R/utilities.R | 8 R/vignetteCachedResults.R | 18 + README.md | 7 build/vignette.rds |binary data/vignetteCachedResults.rda |binary inst/doc/InterpretingPOUMM.Rmd | 19 + inst/doc/InterpretingPOUMM.html | 407 ++++++++++++++++++++++++------- inst/doc/UserGuide.Rmd | 19 + inst/doc/UserGuide.html | 505 ++++++++++++++++++++++++++++----------- src/AbcPOUMM.h | 6 src/Makevars | 4 src/Rcpp.cpp | 25 + src/SPLITT.h | 75 ++++- tests/test-all.R | 17 + tests/testthat/test-fit.R | 17 + tests/testthat/test-lik.R | 17 + tests/testthat/test-parameters.R | 17 + tests/testthat/test-specify.R | 17 + vignettes/InterpretingPOUMM.Rmd | 19 + vignettes/UserGuide.Rmd | 19 + 29 files changed, 1121 insertions(+), 293 deletions(-)
Title: Correcting the Coverage of Credible Sets from Bayesian Genetic
Fine Mapping
Description: Using a computationally efficient method, the package can
be used to find the corrected coverage estimate of a credible set
of putative causal variants from Bayesian genetic fine-mapping.
The package can also be used to obtain a corrected credible set
if required; that is, the smallest set of variants required such
that the corrected coverage estimate of the resultant credible set is
within some user defined accuracy of the desired coverage.
Maller et al. (2012) <doi:10.1038/ng.2435>,
Wakefield (2009) <doi:10.1002/gepi.20359>,
Fortune and Wallace (2018) <doi:10.1093/bioinformatics/bty898>.
Author: Anna Hutchinson [aut, cre],
Chris Wallace [aut],
Kevin Kunzmann [ctb]
Maintainer: Anna Hutchinson <anna.hutchinson@mrc-bsu.cam.ac.uk>
Diff between corrcoverage versions 1.1.0 dated 2019-09-05 and 1.2.0 dated 2019-12-05
DESCRIPTION | 11 +- MD5 | 50 +++++++------ NAMESPACE | 1 NEWS.md | 10 +- R/RcppExports.R | 13 +++ R/corrected_cov_functions.R | 2 R/extra_functions.R | 6 - R/func_utils.R | 26 +++---- R/posterior_prob_functions.R | 4 - README.md | 6 - inst/doc/New-Credible-Set.R | 48 +++++-------- inst/doc/New-Credible-Set.Rmd | 65 ++++++----------- inst/doc/New-Credible-Set.html | 144 ++++++++++++++++++--------------------- inst/doc/a01_gwas_to_cs.Rmd | 12 +-- inst/doc/a01_gwas_to_cs.html | 12 +-- inst/doc/corrected-coverage.R | 54 +++++++------- inst/doc/corrected-coverage.Rmd | 76 +++++++++----------- inst/doc/corrected-coverage.html | 142 +++++++++++++++++++------------------- inst/extdata/z0.RDS |only inst/extdata/z0.tmp.RDS |only inst/extdata/z0.tmp_2.RDS |only inst/extdata/z0_2.RDS |only man/zj_pp_arma.Rd |only src/RcppExports.cpp | 17 ++++ src/zj_pp.cpp |only tests/testthat/test_corrcov.R | 4 - vignettes/New-Credible-Set.Rmd | 65 ++++++----------- vignettes/a01_gwas_to_cs.Rmd | 12 +-- vignettes/corrected-coverage.Rmd | 76 +++++++++----------- 29 files changed, 423 insertions(+), 433 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-16 0.2.6
2017-11-24 0.2.5
2017-06-23 0.2.4
2016-12-05 0.2.3
2016-02-27 0.2.2
2015-12-28 0.2.1
2015-11-18 0.2.0
2015-06-07 0.1.1
2014-09-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-05 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-21 0.8.1
2019-02-21 0.8.0
2019-01-08 0.7.6
2018-12-04 0.7.5
2018-11-24 0.7.4
2018-08-01 0.6.3
2018-07-26 0.6.2
2018-05-22 0.5.9
2018-03-21 0.5.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-13 1.1.5
2018-05-26 1.1.0
2018-01-21 1.0.9
2017-12-17 1.0.7
2017-10-20 1.0.5
2017-07-28 1.0.4
Title: Improved Prediction Intervals for ARIMA Processes and Structural
Time Series
Description: Prediction intervals for ARIMA and structural time series
models using importance sampling approach with uninformative priors for model
parameters, leading to more accurate coverage probabilities in frequentist
sense. Instead of sampling the future observations and hidden states of the
state space representation of the model, only model parameters are sampled,
and the method is based solving the equations corresponding to the conditional
coverage probability of the prediction intervals. This makes method relatively
fast compared to for example MCMC methods, and standard errors of prediction
limits can also be computed straightforwardly.
Author: Jouni Helske
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between tsPI versions 1.0.2 dated 2017-08-07 and 1.0.3 dated 2019-12-05
ChangeLog | 21 +- DESCRIPTION | 8 MD5 | 44 ++-- NAMESPACE | 76 +++---- R/arima_pi.R | 404 ++++++++++++++++++++-------------------- R/information_arma.R | 48 ++-- R/priors.R | 184 +++++++++--------- R/struct_pi.R | 330 ++++++++++++++++---------------- R/tsPI-package.R | 66 +++--- inst/CITATION | 96 ++++----- man/acv_arma.Rd | 70 +++--- man/arima_pi.Rd | 184 +++++++++--------- man/avg_coverage_arima.Rd | 112 +++++------ man/avg_coverage_struct.Rd | 122 ++++++------ man/dacv_arma.Rd | 52 ++--- man/information_arma.Rd | 62 +++--- man/priors.Rd | 74 +++---- man/struct_pi.Rd | 154 +++++++-------- man/tsPI.Rd | 68 +++--- src/approxinfmat.f95 | 86 ++++---- tests/test-all.R | 4 tests/testthat/test-arima_pi.R | 144 +++++++------- tests/testthat/test-struct_pi.R | 102 +++++----- 23 files changed, 1258 insertions(+), 1253 deletions(-)
Title: Hierarchical Multinomial Processing Tree Modeling
Description: User-friendly analysis of hierarchical multinomial processing tree (MPT)
models that are often used in cognitive psychology. Implements the latent-trait
MPT approach (Klauer, 2010) <DOI:10.1007/s11336-009-9141-0> and the beta-MPT
approach (Smith & Batchelder, 2010) <DOI:10.1016/j.jmp.2009.06.007> to model
heterogeneity of participants. MPT models are conveniently specified by an
.eqn-file as used by other MPT software and data are provided by a .csv-file
or directly in R. Models are either fitted by calling JAGS or by an MPT-tailored
Gibbs sampler in C++ (only for nonhierarchical and beta MPT models). Provides
tests of heterogeneity and MPT-tailored summaries and plotting functions.
A detailed documentation is available in Heck, Arnold, & Arnold (2018)
<DOI:10.3758/s13428-017-0869-7>.
Author: Daniel W. Heck [aut, cre] (<https://orcid.org/0000-0002-6302-9252>),
Nina R. Arnold [aut, dtc],
Denis Arnold [aut],
Alexander Ly [ctb],
Marius Barth [ctb] (<https://orcid.org/0000-0002-3421-6665>)
Maintainer: Daniel W. Heck <dheck@uni-marburg.de>
Diff between TreeBUGS versions 1.4.3 dated 2019-04-04 and 1.4.4 dated 2019-12-05
DESCRIPTION | 22 - MD5 | 135 ++++---- NAMESPACE | 2 NEWS | 7 R/CollectionOfInputProcessingFunctions.R | 4 R/RcppExports.R | 8 R/WAIC.R | 2 R/betweenSubjects.R | 5 R/correlationBayesMCMC.R | 2 R/covDataRead.R | 2 R/extendMPT.R | 14 R/fitModelCpp.R | 42 +- R/getParam.R | 2 R/makeModelDescription.R | 8 R/plotDistribution.R | 4 R/plotFrequencies.R | 6 R/posteriorPredictive.R | 4 R/probitInverse.R | 2 R/readEQN.R | 2 R/summarizeMCMC.R | 4 R/thetaHandling.R | 2 R/transformedParModelfile.R | 2 R/transformedParPosthoc.R | 5 build/vignette.rds |binary inst/doc/TreeBUGS_1_intro.R | 14 inst/doc/TreeBUGS_1_intro.html | 109 +++--- inst/doc/TreeBUGS_2_extended.R | 10 inst/doc/TreeBUGS_2_extended.html | 85 ++--- man/BayesFactorMPT.Rd | 103 +++--- man/BayesFactorSlope.Rd | 120 +++---- man/PPP.Rd | 60 +-- man/TreeBUGS-package.Rd | 124 +++---- man/WAIC.Rd | 156 ++++----- man/arnold2013.Rd | 102 +++--- man/betaMPT.Rd | 330 ++++++++++--------- man/betaMPTcpp.Rd | 187 +++++------ man/betweenSubjectMPT.Rd | 78 ++-- man/correlationPosterior.Rd | 155 ++++----- man/extendMPT.Rd | 63 +-- man/genBetaMPT.Rd | 157 ++++----- man/genMPT.Rd | 96 ++--- man/genTraitMPT.Rd | 195 ++++++----- man/getGroupMeans.Rd | 83 ++-- man/getParam.Rd | 118 +++---- man/getSamples.Rd | 66 ++- man/marginalMPT.Rd | 228 +++++++------ man/plot.Rd | 100 ++--- man/plotDistribution.Rd | 54 +-- man/plotFit.Rd | 70 ++-- man/plotFreq.Rd | 71 ++-- man/plotParam.Rd | 84 ++--- man/plotPrior.Rd | 78 ++-- man/plotPriorPost.Rd | 62 ++- man/posteriorPredictive.Rd | 73 ++-- man/priorPredictive.Rd | 144 ++++---- man/probitInverse.Rd | 72 ++-- man/readEQN.Rd | 136 ++++---- man/simpleMPT.Rd | 174 +++++----- man/summarizeMCMC.Rd | 38 +- man/summarizeMPT.Rd | 64 +-- man/testHetChi.Rd | 84 ++--- man/testHetPerm.Rd | 104 +++--- man/traitMPT.Rd | 517 ++++++++++++++++--------------- man/transformedParameters.Rd | 78 ++-- man/withinSubjectEQN.Rd | 62 +-- src/RcppExports.cpp | 14 src/betaMPT.cpp | 22 - src/init.c | 10 tests/testthat/test_fitModelCpp.R |only 69 files changed, 2618 insertions(+), 2418 deletions(-)
Title: Integrated Stratigraphy
Description: Includes bases for litholog generation: graphical functions
based on R base graphics, interval management functions and svg importation
functions among others. Also include stereographic projection functions,
and other functions made to deal with large datasets while keeping options
to get into the details of the data.
When using for publication please cite Wouters, S., Da Silva, A.C. Crucifix,
M., Sinnesael, M., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2019,
Litholog generation with the StratigrapheR package and signal decomposition
for cyclostratigraphic purposes. Geophysical Research Abstracts Vol. 21,
EGU2019-5520, 2019, EGU General Assembly 2019.
<http://hdl.handle.net/2268/234402>
The palaeomagnetism functions are based on:
Tauxe, L., 2010. Essentials of Paleomagnetism. University of California
Press. <https://earthref.org/MagIC/books/Tauxe/Essentials/>;
Allmendinger, R. W., Cardozo, N. C., and Fisher, D., 2013, Structural
Geology Algorithms: Vectors & Tensors: Cambridge, England, Cambridge
University Press, 289 pp.;
Cardozo, N., and Allmendinger, R. W., 2013, Spherical projections
with OSXStereonet: Computers & Geosciences, v. 51, no. 0, p. 193 - 205,
<doi: 10.1016/j.cageo.2012.07.021>.
Author: Sebastien Wouters [aut, cre], Adam D. Smith [ctb]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>
Diff between StratigrapheR versions 0.0.6 dated 2019-06-19 and 0.0.7 dated 2019-12-05
StratigrapheR-0.0.6/StratigrapheR/R/fastPairs.R |only StratigrapheR-0.0.6/StratigrapheR/man/fastPairs.Rd |only StratigrapheR-0.0.7/StratigrapheR/DESCRIPTION | 14 - StratigrapheR-0.0.7/StratigrapheR/MD5 | 61 ++++---- StratigrapheR-0.0.7/StratigrapheR/NAMESPACE | 11 - StratigrapheR-0.0.7/StratigrapheR/R/StratigrapheR.R | 14 - StratigrapheR-0.0.7/StratigrapheR/R/as.lim.R | 18 +- StratigrapheR-0.0.7/StratigrapheR/R/divisor.R |only StratigrapheR-0.0.7/StratigrapheR/R/fmean.R | 3 StratigrapheR-0.0.7/StratigrapheR/R/homogenise.R |only StratigrapheR-0.0.7/StratigrapheR/R/mat.lag.R | 2 StratigrapheR-0.0.7/StratigrapheR/R/merge_list.R | 6 StratigrapheR-0.0.7/StratigrapheR/R/minorAxis.R | 7 StratigrapheR-0.0.7/StratigrapheR/R/planepoints.R | 2 StratigrapheR-0.0.7/StratigrapheR/R/seq_mult.R |only StratigrapheR-0.0.7/StratigrapheR/R/supporting.examples.R | 4 StratigrapheR-0.0.7/StratigrapheR/R/tie.lim.R | 71 ++++------ StratigrapheR-0.0.7/StratigrapheR/data/bed.example.rda |binary StratigrapheR-0.0.7/StratigrapheR/data/boundary.example.rda |binary StratigrapheR-0.0.7/StratigrapheR/data/chron.example.rda |binary StratigrapheR-0.0.7/StratigrapheR/data/example.lense.rda |binary StratigrapheR-0.0.7/StratigrapheR/data/fossil.example.rda |binary StratigrapheR-0.0.7/StratigrapheR/data/noise_emd.rda |only StratigrapheR-0.0.7/StratigrapheR/data/proxy.example.litho.rda |binary StratigrapheR-0.0.7/StratigrapheR/data/proxy.example.rda |binary StratigrapheR-0.0.7/StratigrapheR/man/StratigrapheR.Rd | 2 StratigrapheR-0.0.7/StratigrapheR/man/StratigrapheR.examples.Rd | 1 StratigrapheR-0.0.7/StratigrapheR/man/as.lim.Rd | 4 StratigrapheR-0.0.7/StratigrapheR/man/divisor.Rd |only StratigrapheR-0.0.7/StratigrapheR/man/fmean.Rd | 2 StratigrapheR-0.0.7/StratigrapheR/man/homogenise.Rd |only StratigrapheR-0.0.7/StratigrapheR/man/merge_list.Rd | 6 StratigrapheR-0.0.7/StratigrapheR/man/minorAxis.Rd | 3 StratigrapheR-0.0.7/StratigrapheR/man/planepoints.Rd | 2 StratigrapheR-0.0.7/StratigrapheR/man/seq_mult.Rd |only StratigrapheR-0.0.7/StratigrapheR/man/tie.lim.Rd | 4 36 files changed, 126 insertions(+), 111 deletions(-)
Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. 'sglasso' package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between sglasso versions 1.2.3 dated 2018-05-26 and 1.2.4 dated 2019-12-05
ChangeLog | 2 ++ DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/fglasso.R | 2 +- R/sglasso.R | 4 ++-- man/sglasso-package.Rd | 4 ++-- 6 files changed, 17 insertions(+), 15 deletions(-)
Title: Ridge-Type Penalized Estimation of a Potpourri of Models
Description: The name of the package is derived from the French, 'pour' ridge, and provides functionality for ridge-type estimation of a potpourri of models. Currently, this estimation concerns that of various Gaussian graphical models from different study designs. Among others it considers the regular Gaussian graphical model and a mixture of such models. The porridge-package implements the estimation of the former either from i) data with replicated observations by penalized loglikelihood maximization using the regular ridge penalty on the parameters (van Wieringen, Chen, 2019) or ii) from non-replicated data by means of the generalized ridge estimator that allows for both the inclusion of quantitative and qualitative prior information on the precision matrix via element-wise penalization and shrinkage (van Wieringen, 2019, <doi.org/10.1080/10618600.2019.1604374>). Additionally, the porridge-package facilitates the ridge penalized estimation of a mixture of Gaussian graphical models (Aflakparast et al., 2018, <doi.org/10.1002/bimj.201700102>).
Author: Wessel N. van Wieringen [aut, cre],
Mehran Aflakparast [ctb] (part of the R-code of the mixture
functionality)
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between porridge versions 0.0.2 dated 2019-11-13 and 0.0.3 dated 2019-12-05
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ R/ridgeGGMmixtureAndCo.R | 8 ++++---- R/ridgePgenAndCo.r | 20 ++++++++++---------- R/ridgePrepAndCo.R | 20 ++++++++++---------- inst/NEWS.Rd | 7 +++++++ man/optPenaltyGGMmixture.kCVauto.Rd | 9 --------- man/porridge-package.Rd | 4 ++-- 9 files changed, 48 insertions(+), 48 deletions(-)
Title: Integrative Analysis of Several Related Data Matrices
Description: A generalization of principal component analysis for integrative
analysis. The method finds principal components that describe single matrices
or that are common to several matrices. The solutions are sparse. Rank of
solutions is automatically selected using cross validation. The method is
described in Kallus, Johansson, Nelander and Jörnsten (2019)
<arXiv:1911.04927>.
Author: Jonatan Kallus [aut, cre]
Maintainer: Jonatan Kallus <kallus@chalmers.se>
Diff between mmpca versions 1.0.1 dated 2019-11-29 and 1.0.2 dated 2019-12-05
DESCRIPTION | 8 MD5 | 16 NAMESPACE | 6 R/c.R | 25 - configure | 982 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- configure.ac | 2 src/Makevars.in | 2 src/Makevars.win | 2 src/optim.cpp | 25 + 9 files changed, 1030 insertions(+), 38 deletions(-)
Title: Generic N-Dimensional Hyperplane Fitting with Heteroscedastic
Covariant Errors and Intrinsic Scatter
Description: Includes two main high level codes for hyperplane fitting (hyper.fit) and visualising (hyper.plot2d / hyper.plot3d). In simple terms this allows the user to produce robust 1D linear fits for 2D x vs y type data, and robust 2D plane fits to 3D x vs y vs z type data. This hyperplane fitting works generically for any N-1 hyperplane model being fit to a N dimension dataset. All fits include intrinsic scatter in the generative model orthogonal to the hyperplane.
Author: Aaron Robotham and Danail Obreschkow
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between hyper.fit versions 1.1.0 dated 2019-01-31 and 1.1.1 dated 2019-12-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ R/hyper.basics.R | 10 +++++----- R/hyper.fit.R | 4 ++-- R/hyper.plot.R | 6 +++--- build/partial.rdb |binary man/hyper.fit-package.Rd | 4 ++-- 8 files changed, 27 insertions(+), 23 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Charles Spanbauer [aut],
Matthew Pratola [aut],
Martyn Plummer [ctb],
Nicky Best [ctb],
Kate Cowles [ctb],
Karen Vines [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 2.6 dated 2019-10-02 and 2.7 dated 2019-12-05
DESCRIPTION | 10 +++--- MD5 | 60 ++++++++++++++++++++-------------------- NEWS | 9 ++++++ R/bartModelMatrix.R | 4 +- R/mc.abart.R | 2 - R/mc.crisk.pwbart.R | 4 +- R/mc.crisk2.pwbart.R | 4 +- R/mc.gbart.R | 2 - R/mc.gbmm.R | 2 - R/mc.lbart.R | 2 - R/mc.mbart.R | 2 - R/mc.mbart2.R | 2 - R/mc.pbart.R | 2 - R/mc.recur.pwbart.R | 2 - R/mc.surv.pwbart.R | 2 - R/mc.wbart.R | 2 - R/surv.pwbart.R | 2 - build/vignette.rds |binary data/ACTG175.rda |binary data/alligator.rda |binary data/arq.rda |binary data/bladder.rda |binary data/leukemia.rda |binary data/lung.rda |binary data/transplant.rda |binary data/xdm20.test.rda |binary data/xdm20.train.rda |binary data/ydm20.test.rda |binary data/ydm20.train.rda |binary inst/doc/the-BART-R-package.pdf |binary man/mc.crisk2.pwbart.Rd | 2 - 31 files changed, 61 insertions(+), 54 deletions(-)
Title: Threshold Indicator Taxa Analysis
Description: Uses indicator species scores across binary partitions of
a sample set to detect congruence in taxon-specific changes of abundance
and occurrence frequency along an environmental gradient as evidence of
an ecological community threshold. Relevant references include: Baker,
ME and RS King. 2010. A new method for detecting and interpreting
biodiversity and ecological community thresholds. Methods in Ecology and
Evolution 1(1): 25:37. King, RS and ME Baker. 2010. Considerations for
identifying and interpreting ecological community thresholds. Journal
of the North American Benthological Association 29(3):998-1008. Baker ME
and RS King. 2013. Of TITAN and straw men: an appeal for greater
understanding of community data. Freshwater Science 32(2):489-506.
Author: Matthew E. Baker [aut, cph] (<https://orcid.org/0000-0001-5069-0204>),
Ryan S. King [aut, cph] (<https://orcid.org/0000-0002-3159-9816>),
David Kahle [aut, cph, cre] (<https://orcid.org/0000-0002-9999-1558>)
Maintainer: David Kahle <david@kahle.io>
Diff between TITAN2 versions 2.3 dated 2019-08-28 and 2.4 dated 2019-12-05
DESCRIPTION | 10 - MD5 | 40 +++--- NEWS | 14 +- R/TITAN2.R | 3 R/plot_sumz.R | 6 R/plot_taxa_ridges.R | 2 R/titan.R | 2 inst/doc/titan2-intro.R | 96 +++++++-------- man/TITAN2.Rd | 1 man/boot.titan.Rd | 16 ++ man/getivz.Rd | 11 + man/plot-cps.Rd | 32 ++++- man/plot-sumz.Rd | 40 +++++- man/plot-taxa.Rd | 41 +++++- man/plot_sumz_density.Rd | 33 ++++- man/plot_taxa_ridges.Rd | 28 +++- man/smallBigBoot.Rd | 32 ++++- man/sumz.tab.Rd | 12 + man/tboot.Rd | 12 + man/titan.Rd | 21 ++- vignettes/titan2-intro.html | 274 ++++++++++++++++++++++---------------------- 21 files changed, 451 insertions(+), 275 deletions(-)
Title: Unconstrained Numerical Optimization Algorithms
Description: Optimization algorithms implemented in R, including
conjugate gradient (CG), Broyden-Fletcher-Goldfarb-Shanno (BFGS) and the
limited memory BFGS (L-BFGS) methods. Most internal parameters can be set
through the call interface. The solvers hold up quite well for
higher-dimensional problems.
Author: James Melville [aut, cre]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between mize versions 0.2.2 dated 2019-07-11 and 0.2.3 dated 2019-12-05
DESCRIPTION | 8 MD5 | 110 +- NAMESPACE | 2 NEWS.md | 9 R/adaptive_restart.R | 13 R/convergence.R | 3 R/gradient.R | 131 +-- R/hager_zhang.R | 222 +++-- R/learning_rate.R | 17 R/life_cycle.R | 18 R/mize.R | 607 ++++++++------ R/momentum.R | 22 R/more_thuente.R | 159 +-- R/nesterov.R | 30 R/optimize.R | 89 +- R/polation.R | 26 R/rasmussen.R | 53 - R/schmidt.R | 467 ++++++---- R/step_size.R | 95 +- R/util.R | 54 - R/validate.R | 36 R/wolfe.R | 254 +++-- build/vignette.rds |binary inst/doc/convergence.R | 24 inst/doc/convergence.html | 31 inst/doc/mize.R | 92 +- inst/doc/mize.html | 45 - inst/doc/mmds.R | 24 inst/doc/mmds.Rmd | 2 inst/doc/mmds.html | 39 inst/doc/stateful.R | 24 inst/doc/stateful.html | 13 man/check_mize_convergence.Rd | 105 +- man/make_mize.Rd | 527 ++++++------ man/mize.Rd | 1507 ++++++++++++++++++----------------- man/mize_init.Rd | 203 ++-- man/mize_step.Rd | 188 ++-- man/mize_step_summary.Rd | 171 ++- tests/testthat/helper_util.R | 22 tests/testthat/test_api.R | 279 +++--- tests/testthat/test_cg.R | 192 ++-- tests/testthat/test_hager_zhang.R | 41 tests/testthat/test_loop_api.R | 8 tests/testthat/test_minfunc_armijo.R | 112 +- tests/testthat/test_minfunc_wolfe.R | 36 tests/testthat/test_mizer.R | 521 +++++++----- tests/testthat/test_mmds.R | 103 +- tests/testthat/test_more_thuente.R | 42 tests/testthat/test_nesterov.R | 66 - tests/testthat/test_newton.R | 93 +- tests/testthat/test_polation.R | 5 tests/testthat/test_quadposdef.R | 124 +- tests/testthat/test_rasmussen.R | 27 tests/testthat/test_rasmussen_cg.R | 93 +- tests/testthat/test_tn.R | 82 + vignettes/mmds.Rmd | 2 56 files changed, 4046 insertions(+), 3222 deletions(-)
Title: Precision of Discrete Parameters in Transdimensional MCMC
Description: Estimates the precision of transdimensional Markov chain Monte Carlo
(MCMC) output, which is often used for Bayesian analysis of models with different
dimensionality (e.g., model selection). Transdimensional MCMC (e.g., reversible
jump MCMC) relies on sampling a discrete model-indicator variable to estimate
the posterior model probabilities. If only few switches occur between the models,
precision may be low and assessment based on the assumption of independent
samples misleading. Based on the observed transition matrix of the indicator
variable, the method of Heck, Overstall, Gronau, & Wagenmakers (2019,
Statistics & Computing, 29, 631-643) <doi:10.1007/s11222-018-9828-0> draws
posterior samples of the stationary distribution to (a) assess the uncertainty
in the estimated posterior model probabilities and (b) estimate the effective
sample size of the MCMC output.
Author: Daniel W. Heck [aut, cre] (<https://orcid.org/0000-0002-6302-9252>)
Maintainer: Daniel W. Heck <dheck@uni-marburg.de>
Diff between MCMCprecision versions 0.3.9 dated 2018-08-10 and 0.4.0 dated 2019-12-05
DESCRIPTION | 29 +-- MD5 | 36 ++-- NAMESPACE | 2 NEWS | 6 R/MCMCprecision.R | 8 R/transitions.R | 2 build/vignette.rds |binary inst/CITATION | 8 inst/doc/Heck_2018_Statistics_and_Computing.pdf |binary inst/include/MCMCprecision.h | 34 +-- man/MCMCprecision-package.Rd | 76 ++++---- man/best_models.Rd | 52 ++--- man/fit_dirichlet.Rd | 74 ++++---- man/rdirichlet.Rd | 44 ++-- man/rmarkov.Rd | 52 ++--- man/stationary.Rd | 216 ++++++++++++------------ man/stationary_mle.Rd | 117 ++++++------- man/summary.stationary.Rd | 98 +++++----- man/transitions.Rd | 60 +++--- 19 files changed, 467 insertions(+), 447 deletions(-)
Title: Manipulation of Linear Systems of (in)Equalities
Description: Variable elimination (Gaussian elimination, Fourier-Motzkin elimination),
Moore-Penrose pseudoinverse, reduction to reduced row echelon form, value substitution,
projecting a vector on the convex polytope described by a system of (in)equations,
simplify systems by removing spurious columns and rows and collapse implied equalities,
test if a matrix is totally unimodular, compute variable ranges implied by linear
(in)equalities.
Author: Mark van der Loo [aut, cre],
Edwin de Jonge [aut]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between lintools versions 0.1.2 dated 2018-07-30 and 0.1.3 dated 2019-12-05
lintools-0.1.2/lintools/tests/testthat |only lintools-0.1.2/lintools/tests/testthat.R |only lintools-0.1.3/lintools/DESCRIPTION | 10 ++-- lintools-0.1.3/lintools/MD5 | 40 ++++++++-------- lintools-0.1.3/lintools/NEWS | 4 + lintools-0.1.3/lintools/R/spa.R | 3 - lintools-0.1.3/lintools/R/sparseConstraints.R | 21 ++++---- lintools-0.1.3/lintools/R/utils.R | 2 lintools-0.1.3/lintools/build/vignette.rds |binary lintools-0.1.3/lintools/inst/doc/project.html | 55 ++++++++++++++++------ lintools-0.1.3/lintools/inst/tinytest |only lintools-0.1.3/lintools/man/sparse_constraints.Rd | 4 - lintools-0.1.3/lintools/tests/tinytest.R |only 13 files changed, 86 insertions(+), 53 deletions(-)
Title: Animal Dominance Hierarchies by Elo Rating
Description: Provides functions to quantify animal dominance hierarchies. The major focus is on Elo rating and its ability to deal with temporal dynamics in dominance interaction sequences. For static data, David's score and de Vries' I&SI are also implemented. In addition, the package provides functions to assess transitivity, linearity and stability of dominance networks. See Neumann et al (2011) <doi:10.1016/j.anbehav.2011.07.016> for an introduction.
Author: Christof Neumann [aut, cre] (<https://orcid.org/0000-0002-0236-1219>),
Lars Kulik [aut]
Maintainer: Christof Neumann <christofneumann1@gmail.com>
Diff between EloRating versions 0.46.8 dated 2019-06-14 and 0.46.10 dated 2019-12-05
DESCRIPTION | 24 ++++++++++++---- MD5 | 40 +++++++++++++-------------- NAMESPACE | 1 R/dommats-data.R | 2 - R/likelo.R | 57 ++++++++++++++++++++++++++++++++------- R/optimizek.R | 18 ++++++++---- R/optistart.R | 6 ++-- R/prunk.R | 17 ++++++++--- R/randomelo.R | 8 ++++- build/partial.rdb |binary inst/NEWS.Rd | 14 +++++++++ inst/REFERENCES.bib | 15 ++++++++++ inst/doc/EloRating_tutorial.R | 26 +++++++++++------ inst/doc/EloRating_tutorial.Rmd | 37 ++++++++++++++++--------- inst/doc/EloRating_tutorial.pdf |binary man/dommats.Rd | 2 - man/likelo.Rd | 23 +++++++++++---- man/optimizek.Rd | 11 +++++-- man/optistart.Rd | 6 ++-- tests/testthat/test_optimizek.R | 2 - vignettes/EloRating_tutorial.Rmd | 37 ++++++++++++++++--------- 21 files changed, 250 insertions(+), 96 deletions(-)
Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: MCMC algorithms & processing functions for non- and semi-parametric models: 1. Dirichlet process mixtures & 2. spike-slab for multivariate (and univariate) regression, with nonparametric models for the means, the variances and the correlation matrix.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 2.1.1 dated 2019-10-13 and 2.1.2 dated 2019-12-05
DESCRIPTION | 8 +- MD5 | 36 +++++---- NAMESPACE | 1 R/bnpMulti.R | 54 ++++++++------ R/matalg.R |only R/mvrm.R | 17 ++-- R/plot.R | 190 +++++++++++++++++++++++++++++++++++++++------------- man/BNSP-package.Rd | 2 man/chol.Rd |only man/plot.mvrm.Rd | 3 src/BNSP_init.c | 3 src/BayesMult.c | 23 +++--- src/BayesMultG.c | 44 ++++++------ src/BayesMultGV.c | 44 ++++++------ src/Makevars | 2 src/OneResLtnt.c | 8 +- src/bnsp.h | 5 + src/matalg.h | 32 ++++++-- src/mvrmGAM.c | 32 +++++--- src/spec.BCM.h | 88 +++++++++++++++--------- 20 files changed, 380 insertions(+), 212 deletions(-)
Title: Boltzmann Entropy of a Landscape Gradient
Description: Calculates the Boltzmann entropy of a landscape gradient.
This package uses the analytical method created by Gao, P., Zhang, H.
and Li, Z., 2018 (<doi:10.1111/tgis.12315>) and by Gao, P. and Li, Z., 2019
(<doi:10.1007/s10980-019-00854-3>). It also extend the original ideas by
allowing calculations on data with missing values.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Space Informatics Lab [cph]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between belg versions 1.0.0 dated 2019-09-19 and 1.0.1 dated 2019-12-05
DESCRIPTION | 8 ++-- MD5 | 20 +++++------ NAMESPACE | 1 NEWS.md | 4 ++ R/get_boltzmann.R | 10 +++++ build/vignette.rds |binary inst/CITATION | 6 +-- inst/doc/belg1.R | 40 +++++++++++----------- inst/doc/belg1.html | 91 +++++++++++++++++++++++++-------------------------- man/belg-package.Rd | 2 - man/get_boltzmann.Rd | 21 +++++------ 11 files changed, 107 insertions(+), 96 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle, Darshan Baral,
Ulrike Groemping, Bill Venables
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.7-6 dated 2019-06-21 and 3.7-7 dated 2019-12-05
plotrix-3.7-6/plotrix/demo |only plotrix-3.7-7/plotrix/DESCRIPTION | 8 +++--- plotrix-3.7-7/plotrix/MD5 | 28 +++++++++++------------- plotrix-3.7-7/plotrix/NEWS | 9 +++++++ plotrix-3.7-7/plotrix/R/barNest.R | 2 - plotrix-3.7-7/plotrix/R/barp.R | 4 +-- plotrix-3.7-7/plotrix/R/brkdn.plot.R | 2 - plotrix-3.7-7/plotrix/R/centipede.plot.R | 2 - plotrix-3.7-7/plotrix/R/color2D.matplot.R | 10 ++++++-- plotrix-3.7-7/plotrix/R/dendrite.R | 2 - plotrix-3.7-7/plotrix/R/intersectDiagram.R | 4 +-- plotrix-3.7-7/plotrix/R/twoord.plot.R | 31 ++++++++++++++++++--------- plotrix-3.7-7/plotrix/data/soils.rda |binary plotrix-3.7-7/plotrix/man/plotrix-package.Rd | 8 +++--- plotrix-3.7-7/plotrix/man/twoord.plot.Rd | 3 +- 15 files changed, 68 insertions(+), 45 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from <http://tamivox.org/dave/multinomial/index.html> and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here <http://jeromekelleher.net/category/combinatorics.html>. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between multicool versions 0.1-10 dated 2016-11-25 and 0.1-11 dated 2019-12-05
DESCRIPTION | 13 ++++--- MD5 | 36 +++++++++---------- R/RcppExports.R | 8 ++-- R/Stirling2.R | 58 +++++++++++++++++++++++++++++++ R/allPerm.R | 32 +++++++++++++++++ R/genComp.R | 52 +++++++++++++++++++++++++++- R/initMC.r | 34 ++++++++++++++++++ R/multinom.R | 64 ++++++++++++++++++++++++++++++++++- R/nextPerm.R | 29 +++++++++++++++ man/Bell.Rd | 32 ++++++++++------- man/Stirling2.Rd | 41 +++++++++++++--------- man/allPerm.Rd | 93 +++++++++++++++++++++++++++------------------------ man/genComp.Rd | 67 ++++++++++++++++++++++++------------ man/initMC.Rd | 47 ++++++++++++++----------- man/multinom.Rd | 70 +++++++++++++++++++++++--------------- man/nextPerm.Rd | 30 +++++++++------- src/RcppExports.cpp | 24 ++++++++++--- src/compositions.cpp | 2 - src/multicool.cpp | 14 ++++--- 19 files changed, 551 insertions(+), 195 deletions(-)
Title: An Implementation of Matrix Mathematics
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsbyname versions 0.4.10 dated 2019-02-16 and 0.4.11 dated 2019-12-05
DESCRIPTION | 10 ++++---- MD5 | 44 ++++++++++++++++++------------------- NEWS.md | 11 +++++++++ R/Unary.R | 4 +-- R/Utilities.R | 2 - R/mat_byname.R | 4 +-- build/vignette.rds |binary inst/doc/applybyname-vignette.R | 10 ++++---- inst/doc/applybyname-vignette.html | 28 +++++++++++++---------- inst/doc/matsbyname.R | 30 ++++++++++++------------- inst/doc/matsbyname.html | 28 +++++++++++++---------- man/binaryapply_byname.Rd | 11 +++++++-- man/compare_byname.Rd | 3 -- man/complete_and_sort.Rd | 10 ++++++-- man/complete_rows_cols.Rd | 10 ++++++-- man/count_vals_byname.Rd | 7 ++++- man/count_vals_incols_byname.Rd | 7 ++++- man/count_vals_inrows_byname.Rd | 7 ++++- man/make_pattern.Rd | 6 +++-- man/naryapply_byname.Rd | 10 ++++++-- man/naryapplylogical_byname.Rd | 11 ++++++--- man/unaryapply_byname.Rd | 8 +++++- tests/testthat/test_S3.R | 2 - 23 files changed, 163 insertions(+), 100 deletions(-)
Title: Extract and Visualize the Results of Multivariate Data Analyses
Description: Provides some easy-to-use functions to extract and visualize the
output of multivariate data analyses, including 'PCA' (Principal Component
Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence
Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis) and 'HMFA' (Hierarchical Multiple
Factor Analysis) functions from different R packages. It contains also functions
for simplifying some clustering analysis steps and provides 'ggplot2' - based
elegant data visualization.
Author: Alboukadel Kassambara [aut, cre],
Fabian Mundt [aut]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between factoextra versions 1.0.5 dated 2017-08-22 and 1.0.6 dated 2019-12-05
DESCRIPTION | 11 - MD5 | 92 +++++----- NEWS.md | 15 + R/fviz.R | 6 R/fviz_cluster.R | 92 +++++----- R/fviz_dend.R | 3 R/fviz_mclust.R | 1 R/fviz_nbclust.R | 6 R/get_clust_tendency.R | 8 R/hkmeans.R | 8 R/zzz.R | 2 README.md | 10 - man/dist.Rd | 5 man/eclust.Rd | 10 - man/eigenvalue.Rd | 9 man/facto_summarize.Rd | 4 man/fviz.Rd | 19 +- man/fviz_add.Rd | 3 man/fviz_ca.Rd | 14 - man/fviz_cluster.Rd | 71 ++++--- man/fviz_contrib.Rd | 8 man/fviz_cos2.Rd | 8 man/fviz_dend.Rd | 6 man/fviz_famd.Rd | 21 +- man/fviz_hmfa.Rd | 20 +- man/fviz_mca.Rd | 15 - man/fviz_mclust.Rd | 23 +- man/fviz_mfa.Rd | 23 +- man/fviz_nbclust.Rd | 5 man/fviz_pca.Rd | 15 - man/get_clust_tendency.Rd | 10 - man/hkmeans.Rd | 5 tools/README-correspondence-analysis-biplot-1.png |binary tools/README-determine-the-number-of-clusters-gap-statistics-1.png |binary tools/README-hierarchical-clustering-1.png |binary tools/README-individuals-factor-map-color-by-groups-1.png |binary tools/README-mca-biplot-1.png |binary tools/README-mca-graph-of-individuals-1.png |binary tools/README-mca-graph-variables-1.png |binary tools/README-partitioning-clustering-1.png |binary tools/README-pca-eigenvalue-1.png |binary tools/README-pca-variable-colors-by-contributions-1.png |binary tools/README-pca-variable-contributions-1.png |binary tools/README-pca-variable-contributions-2.png |binary tools/README-pca-variables-1.png |binary tools/README-principal-component-analysis-data-mining-1.png |binary tools/README-principal-component-analysis-data-mining-2.png |binary 47 files changed, 300 insertions(+), 248 deletions(-)
Title: Functional Data Analysis for Density Functions by Transformation
to a Hilbert Space
Description: An implementation of the methodology described in
Petersen and Mueller (2016) <doi:10.1214/15-AOS1363> for the functional
data analysis of samples of density functions. Densities are first
transformed to their corresponding log quantile densities, followed by
ordinary Functional Principal Components Analysis (FPCA). Transformation
modes of variation yield improved interpretation of the variability in the
data as compared to FPCA on the densities themselves. The standard
fraction of variance explained (FVE) criterion commonly used for functional
data is adapted to the transformation setting, also allowing for an
alternative quantification of variability for density data through the
Wasserstein metric of optimal transport.
Author: A. Petersen, P. Z. Hadjipantelis and H.G. Mueller
Maintainer: Alexander Petersen <petersen@pstat.ucsb.edu>
Diff between fdadensity versions 0.1.1 dated 2018-02-08 and 0.1.2 dated 2019-12-05
DESCRIPTION | 11 ++++--- MD5 | 45 ++++++++++++++++--------------- NAMESPACE | 1 R/CreateModeOfVarPlotLQ2D.R | 2 - R/GetFVE.R | 7 ++-- R/RegulariseByAlpha.R | 2 - R/dens2lqd.R | 3 ++ R/dens2qd.R | 2 + R/dens2quantile.R | 2 + R/normaliseDensities.R |only man/CreateModeOfVarPlotLQ2D.Rd | 12 ++++++-- man/FPCAdens.Rd | 11 +++++-- man/GetFVE.Rd | 3 -- man/MakeDENsample.Rd | 10 ++++-- man/MakeLQDsample.Rd | 9 ++++-- man/RegulariseByAlpha.Rd | 2 - man/dens2lqd.Rd | 4 ++ man/dens2qd.Rd | 11 ++++++- man/dens2quantile.Rd | 11 ++++++- man/getWFmean.Rd | 10 +++++- man/lqd2dens.Rd | 8 ++++- man/lqd2quantile.Rd | 8 ++++- man/normaliseDensities.Rd |only man/qd2dens.Rd | 8 ++++- tests/testthat/test_normaliseDensities.R |only 25 files changed, 126 insertions(+), 56 deletions(-)
Title: Measuring Morphological Diversity and Evolutionary Tempo
Description: Measures morphological diversity from discrete character data and
estimates evolutionary tempo on phylogenetic trees. Imports morphological
data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>)
format with ReadMorphNexus(), and writes to both #NEXUS and TNT format
(Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main
functions are DiscreteCharacterRate(), which implements likelihood ratio
tests for discrete character rates introduced across Lloyd et al. (2012)
<doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014)
<doi:10.1016/j.cub.2014.08.034>, Close et al. (2015)
<doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>,
and MorphDistMatrix(), which implements multiple discrete character
distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998)
<doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and
Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. Multiple functions
implement various morphospace plots: ChronoPhyloMorphospacePlot() implements
Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>,
MorphospacePlot() implements Wills et al. (1994)
<doi:10.1017/S009483730001263X>, PlotCharacterChanges() implements Wang and
Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and StackPlot() implements Foote
(1993) <doi:10.1017/S0094837300015864>. Other functions include
SafeTaxonomicReduction(), which implements Wilkinson (1995)
<doi:10.1093/sysbio/44.4.501>, and DolloSCM() implements the Dollo
stochastic character mapping of Tarver et al. (2018)
<doi:10.1093/gbe/evy096>.
Author: Graeme T. Lloyd [aut, cre, cph],
Thomas Guillerme [aut, cph],
Emma Sherratt [aut, cph],
Steve C. Wang [aut, cph]
Maintainer: Graeme T. Lloyd <graemetlloyd@gmail.com>
Diff between Claddis versions 0.3.0 dated 2019-02-12 and 0.3.4 dated 2019-12-05
Claddis-0.3.0/Claddis/R/PhyloCharCompletenessInBins.r |only Claddis-0.3.4/Claddis/DESCRIPTION | 10 - Claddis-0.3.4/Claddis/MD5 | 82 ++++----- Claddis-0.3.4/Claddis/NAMESPACE | 2 Claddis-0.3.4/Claddis/R/AncStateEstMatrix.R | 4 Claddis-0.3.4/Claddis/R/BlockAligner.R |only Claddis-0.3.4/Claddis/R/ChronoPhyloMorphospacePlot.R | 20 +- Claddis-0.3.4/Claddis/R/Claddis-package.R | 5 Claddis-0.3.4/Claddis/R/CompactifyMatrix.R | 134 +++++++++++---- Claddis-0.3.4/Claddis/R/DiscreteCharacterRate.R | 28 ++- Claddis-0.3.4/Claddis/R/FindAncestor.R | 2 Claddis-0.3.4/Claddis/R/MakeMorphMatrix.R | 49 +++-- Claddis-0.3.4/Claddis/R/MatrixPruner.R | 2 Claddis-0.3.4/Claddis/R/MinSpanTreeEdges.R | 13 + Claddis-0.3.4/Claddis/R/MorphDistMatrix.R | 41 +++- Claddis-0.3.4/Claddis/R/MorphMatrix2PCoA.R | 4 Claddis-0.3.4/Claddis/R/MorphospacePlot.R | 12 - Claddis-0.3.4/Claddis/R/MultiMorphospacePlot.R | 2 Claddis-0.3.4/Claddis/R/PhyloCharCompletenessInBins.R |only Claddis-0.3.4/Claddis/R/ReadMorphNexus.R | 4 Claddis-0.3.4/Claddis/R/SafeTaxonomicReduction.R | 2 Claddis-0.3.4/Claddis/R/StackPlot.R | 2 Claddis-0.3.4/Claddis/R/TrimMorphDistMatrix.R | 14 + Claddis-0.3.4/Claddis/R/WriteMorphNexus.R | 15 - Claddis-0.3.4/Claddis/R/WriteMorphTNT.R | 16 - Claddis-0.3.4/Claddis/README.md | 15 + Claddis-0.3.4/Claddis/man/BlockAligner.Rd |only Claddis-0.3.4/Claddis/man/ChronoPhyloMorphospacePlot.Rd | 14 - Claddis-0.3.4/Claddis/man/Claddis-package.Rd | 1 Claddis-0.3.4/Claddis/man/CompactifyMatrix.Rd | 9 - Claddis-0.3.4/Claddis/man/DiscreteCharacterRate.Rd | 27 ++- Claddis-0.3.4/Claddis/man/FindAncestor.Rd | 1 Claddis-0.3.4/Claddis/man/MakeMorphMatrix.Rd | 9 - Claddis-0.3.4/Claddis/man/MatrixPruner.Rd | 1 Claddis-0.3.4/Claddis/man/MorphDistMatrix.Rd | 1 Claddis-0.3.4/Claddis/man/MorphMatrix2PCoA.Rd | 5 Claddis-0.3.4/Claddis/man/MorphospacePlot.Rd | 2 Claddis-0.3.4/Claddis/man/MultiMorphospacePlot.Rd | 2 Claddis-0.3.4/Claddis/man/PhyloCharCompletenessInBins.Rd | 2 Claddis-0.3.4/Claddis/man/ReadMorphNexus.Rd | 1 Claddis-0.3.4/Claddis/man/SafeTaxonomicReduction.Rd | 3 Claddis-0.3.4/Claddis/man/StackPlot.Rd | 2 Claddis-0.3.4/Claddis/man/WriteMorphNexus.Rd | 1 Claddis-0.3.4/Claddis/man/WriteMorphTNT.Rd | 1 44 files changed, 353 insertions(+), 207 deletions(-)
Title: Helper Functions to 'misc3d' and 'rgl' Packages for Brain
Imaging
Description: This includes functions for creating 3D and 4D images using
'WebGL', 'rgl', and 'JavaScript' commands.
This package relies on the X toolkit ('XTK',
<https://github.com/xtk/X#readme>).
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between brainR versions 1.5.1 dated 2017-10-12 and 1.6.0 dated 2019-12-05
DESCRIPTION | 11 ++++++----- MD5 | 23 ++++++++++++----------- NEWS.md | 8 ++++++++ R/brainR-package.R | 2 +- R/scene4d.R | 16 ++++++++++++---- R/write4D.R | 13 ++++++++++--- R/write4D.file.R | 18 ++++++++++++++---- README.md | 23 ++++++++++++++++------- inst/CITATION |only man/brainR-package.Rd | 2 +- man/scene4d.Rd | 31 ++++++++++++++++++++++++------- man/write4D.Rd | 24 +++++++++++++++++++----- man/write4D.file.Rd | 27 +++++++++++++++++++++------ 13 files changed, 144 insertions(+), 54 deletions(-)
Title: R Client for the BAN API
Description: A client for the "Base Adresses Nationale" (BAN) API, which allows to (batch)
geocode and reverse-geocode French addresses. For more information about the BAN and its API, please see <https://adresse.data.gouv.fr/api>.
Author: Joel Gombin [cre, aut],
Paul-Antoine Chevalier [aut]
Maintainer: Joel Gombin <joel.gombin@gmail.com>
Diff between banR versions 0.2.0 dated 2017-08-03 and 0.2.1 dated 2019-12-05
banR-0.2.0/banR/inst/doc/geocode.md |only banR-0.2.1/banR/DESCRIPTION | 16 banR-0.2.1/banR/LICENSE |only banR-0.2.1/banR/MD5 | 30 - banR-0.2.1/banR/NEWS.md | 6 banR-0.2.1/banR/R/data.R | 3 banR-0.2.1/banR/R/geocode_tbl.R | 10 banR-0.2.1/banR/R/utils.R | 7 banR-0.2.1/banR/README.md | 94 ++- banR-0.2.1/banR/build/vignette.rds |binary banR-0.2.1/banR/inst/doc/geocode.R | 14 banR-0.2.1/banR/inst/doc/geocode.Rmd | 2 banR-0.2.1/banR/inst/doc/geocode.html | 597 ++++++++++++++++------- banR-0.2.1/banR/man/format_object_size.Rd | 3 banR-0.2.1/banR/man/paris2012.Rd | 3 banR-0.2.1/banR/tests/testthat/test_geocodetbl.R | 24 banR-0.2.1/banR/vignettes/geocode.Rmd | 2 17 files changed, 557 insertions(+), 254 deletions(-)
Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/services/storage>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureStor versions 3.0.0 dated 2019-11-03 and 3.0.1 dated 2019-12-05
DESCRIPTION | 6 ++--- MD5 | 30 ++++++++++++++++------------- NEWS.md | 8 +++++++ R/adls_client_funcs.R | 16 ++++++++++----- R/adls_transfer_internal.R | 8 ++----- R/az_storage.R | 3 -- R/blob_client_funcs.R | 39 ++++++++++++++++++++++++++------------ R/file_client_funcs.R | 14 ++++++++++++- R/storage_utils.R | 8 ++++++- man/adls_filesystem.Rd | 2 - man/blob.Rd | 4 +-- man/blob_container.Rd | 2 - tests/testthat/test02_blob.R | 20 +++++++++++++++++++ tests/testthat/test06_props.R | 3 ++ tests/testthat/test08_interop1.R |only tests/testthat/test08a_interop2.R |only tests/testthat/test08b_interop3.R |only tests/testthat/test08c_interop4.R |only 18 files changed, 114 insertions(+), 49 deletions(-)
Title: A Multiple Testing Procedure for High-Dimensional Mediation
Hypotheses
Description: A multiple-testing procedure for high-dimensional mediation hypotheses. Mediation analysis is of rising interest in epidemiology and clinical trials. Among existing methods for mediation analyses, the popular joint significance (JS) test yields an overly conservative type I error rate and therefore low power. In the R package 'HDMT' we implement a multiple-testing procedure that accurately controls the family-wise error rate (FWER) and the false discovery rate (FDR) when using JS for testing high-dimensional mediation hypotheses. The core of our procedure is based on estimating the proportions of three component null hypotheses and deriving the corresponding mixture distribution of null p-values. Results of the data examples include better-behaved quantile-quantile plots and improved detection of novel mediation relationships on the role of DNA methylation in genetic regulation of gene expression. With increasing interest in mediation by molecular intermediaries such as gene expression and epigenetic markers, the proposed method addresses an unmet methodological challenge.
Author: James Dai [aut, cre],
Xiaoyu Wang [aut]
Maintainer: James Dai <jdai@fredhutch.org>
Diff between HDMT versions 1.0 dated 2019-04-16 and 1.0.1 dated 2019-12-05
HDMT-1.0.1/HDMT/DESCRIPTION | 8 - HDMT-1.0.1/HDMT/MD5 | 37 ++--- HDMT-1.0.1/HDMT/R/fdrest.R | 212 +++++++++++++++--------------- HDMT-1.0.1/HDMT/R/fwerest.R | 188 +++++++++++++------------- HDMT-1.0.1/HDMT/R/nullestimation.R | 158 +++++++++++----------- HDMT-1.0.1/HDMT/build/vignette.rds |binary HDMT-1.0.1/HDMT/data/datalist | 3 HDMT-1.0.1/HDMT/data/exercise_input.RData |only HDMT-1.0.1/HDMT/data/snp_input.RData |only HDMT-1.0.1/HDMT/inst/doc/HDMT.R | 6 HDMT-1.0.1/HDMT/inst/doc/HDMT.Rnw | 6 HDMT-1.0.1/HDMT/inst/doc/HDMT.bib |only HDMT-1.0.1/HDMT/inst/doc/HDMT.pdf |binary HDMT-1.0.1/HDMT/man/adjust_quantile.Rd | 6 HDMT-1.0.1/HDMT/man/correct_qqplot.Rd | 2 HDMT-1.0.1/HDMT/man/exercise_input.Rd |only HDMT-1.0.1/HDMT/man/fdrest.Rd | 6 HDMT-1.0.1/HDMT/man/fwerest.Rd | 6 HDMT-1.0.1/HDMT/man/nullestimation.Rd | 6 HDMT-1.0.1/HDMT/man/snp_input.Rd |only HDMT-1.0.1/HDMT/vignettes/HDMT.Rnw | 6 HDMT-1.0/HDMT/data/exampleinputdata.rda |only HDMT-1.0/HDMT/man/exampleinputdata.Rd |only 23 files changed, 334 insertions(+), 316 deletions(-)
Title: Processing Chill and Heat Models for Temperate Fruit Trees
Description: Calculates the chilling and heat accumulation for studies of the temperate fruit trees. The models in this package are: Utah (Richardson et al., 1974, ISSN:0018-5345), Positive Chill Units - PCU (Linsley-Noaks et al., 1995, ISSN:1017-0316), GDH-A - Growing Degree Hours by Anderson et al.(1986, ISSN:0567-7572), GDH-R - Growing Degree Hours by Richardson et al.(1975, ISSN:0018-5345), North Carolina (Shaltout e Unrath, 1983, ISSN:0003-1062), Landsberg Model (Landsberg, 1974, ISSN:0305-7364), Q10 Model (Bidabe, 1967, ISSN:0031-9368), Jones Model (Jones et al., 2013 <DOI:10.1111/j.1438-8677.2012.00590.x>), Low-Chill Model (Gilreath and Buchanan, 1981, ISSN:0003-1062), Model for Cherry "Sweetheart" (Guak and Nielsen, 2013 <DOI:10.1007/s13580-013-0140-9>), Model for apple "Gala" (Guak and Nielsen, 2013 <DOI:10.1007/s13580-013-0140-9>), Taiwan Model (Lu et al., 2012 <DOI:10.17660/ActaHortic.2012.962.35>), Dynamic Model (Fishman et al., 1987, ISSN:0022-5193) adapted from the function Dynamic_Model() of the 'chillR' package (Luedeling, 2018), Unified Model (Chuine et al., 2016 <DOI:10.1111/gcb.13383>) and Heat Restriction model.
Author: Rafael Henrique Pertille [aut, cre]
(<https://orcid.org/0000-0002-4888-2001>),
Marcos Robson Sachet [aut, ctb]
(<https://orcid.org/0000-0002-0395-2475>),
Idemir Citadin [aut, ctb] (<https://orcid.org/0000-0001-9416-2761>),
Marieli Teresinha Guerrezi [aut, ctb]
(<https://orcid.org/0000-0003-3314-4046>)
Maintainer: Rafael Henrique Pertille <henriquepertille@gmail.com>
Diff between ChillModels versions 1.0.0 dated 2019-03-07 and 1.0.1 dated 2019-12-05
DESCRIPTION | 25 ++++++++++++++----------- MD5 | 2 +- 2 files changed, 15 insertions(+), 12 deletions(-)