Title: Data Set and Helper Functions for Wind Farm Layout Optimization
Problems
Description: Provides a convenient data set, a set of helper functions, and a benchmark function for
economically (profit) driven wind farm layout optimization. This enables researchers in the field
of the NP-hard (non-deterministic polynomial-time hard) problem of wind farm layout optimization
to focus on their optimization methodology contribution and also provides a realistic benchmark
setting for comparability among contributions. See Croonenbroeck, Carsten & Hennecke, David (2020)
<doi:10.1016/j.energy.2020.119244>.
Author: Carsten Croonenbroeck [aut, cre],
David Hennecke [ctb]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Diff between wflo versions 1.5 dated 2020-04-22 and 1.6 dated 2020-11-26
DESCRIPTION | 17 INDEX | 16 MD5 | 57 +- NAMESPACE | 6 NEWS | 16 R/Functions.R | 1292 +++++++++++++++++++++++++++++++++++++++++++--- R/zzz.R | 6 inst/CITATION |only inst/doc/wflo.R | 24 inst/doc/wflo.Rnw | 30 - inst/doc/wflo.pdf |binary man/AirDensity.Rd |only man/Area.Rd |only man/Cost.Rd | 5 man/FarmData.Rd | 5 man/FarmVars.Rd | 7 man/GK2Index.Rd |only man/GK2LonLat.Rd |only man/GaussWS.Rd |only man/GenerateGauss.Rd |only man/GetFarmFromLonLat.Rd |only man/Height.Rd |only man/Index2GK.Rd |only man/JensenTrapezoid.Rd | 9 man/LonLat2GK.Rd |only man/MosettiTurbineCost.Rd |only man/PairPenalty.Rd | 3 man/PartialJensen.Rd |only man/PointInPolygon.Rd | 4 man/Profit.Rd | 11 man/QuickGauss3D.Rd |only man/ShowWakePenalizers.Rd | 65 ++ man/SwitchProfile.Rd |only man/WindspeedHellmann.Rd |only man/WindspeedLog.Rd |only man/Yield.Rd | 9 vignettes/refs.bib | 45 + vignettes/wflo.Rnw | 30 - 38 files changed, 1472 insertions(+), 185 deletions(-)
Title: Partially Separable Quasi-Newton
Description: Provides quasi-Newton methods to minimize partially separable
functions. The methods are largely described by
Nocedal and Wright (2006) <doi:10.1007/978-0-387-40065-5>.
Author: Benjamin Christoffersen [cre, aut]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between psqn versions 0.1.3 dated 2020-11-14 and 0.1.4 dated 2020-11-26
DESCRIPTION | 6 ++-- MD5 | 12 ++++----- inst/doc/psqn.html | 44 ++++++++++++++++----------------- inst/include/lp.h | 56 ++++++++++++++++++++++++++++++++++++++++++ inst/include/psqn.h | 50 +++++++++++++++++++++++++++++--------- src/r-api.cpp | 68 +++++++++++++++++++++++++++++++++------------------- src/test-lp.cpp | 26 +++++++++++++++++++ 7 files changed, 195 insertions(+), 67 deletions(-)
Title: A Collection of Models that Employ a Prior Distribution on
Partitions
Description: Provides functions that fit hierarchical Gaussian and probit ordinal models.
A (covariate dependent) product partition model is used as a prior.
If a covariate dependent product partition model is selected,
then all the options detailed in Page, G.L.; Quintana, F.A.; (2018)
<doi:10.1007/s11222-017-9777-z> are available. In addition, a function
that fits a Gaussian likelihood spatial product partition model that is
detailed in Page, G.L.; Quintana, F.A.; (2016) <doi:10.1214/15-BA971> is
also provided.
Author: Garritt L. Page [aut, cre, cph],
S. McKay Curtis [ctb, cph],
Radford M. Neal [ctb, cph]
Maintainer: Garritt L. Page <page@stat.byu.edu>
Diff between ppmSuite versions 0.1.0 dated 2020-11-23 and 0.1.1 dated 2020-11-26
DESCRIPTION | 6 +- MD5 | 20 +++--- src/Rutil.c | 106 ++++--------------------------------- src/init.c | 9 +-- src/matrix.c | 4 - src/mcmcloop.missing.c | 19 +++--- src/mcmcloop.ordinal.missing.pmx.c | 33 +++++------ src/mcmcloop.ordinal.ppmx.c | 14 ++-- src/mcmcloop.ppmx.c | 20 +++--- src/mcmcloop.sppm.c | 7 +- src/routine.rppmx.c | 4 - 11 files changed, 82 insertions(+), 160 deletions(-)
Title: Genetics and Independence Testing of Mixed Genetic Panels
Description: Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package.
Author: Bing Song
Maintainer: Bing Song <bingsong@my.unthsc.edu>
Diff between mixIndependR versions 0.4.0 dated 2020-11-25 and 0.4.2 dated 2020-11-26
DESCRIPTION | 12 +- MD5 | 33 +++-- NEWS.md | 12 ++ R/GenotypeFreq.R | 6 - R/mixexample-data.R |only data |only inst/doc/BasicGenetics.R | 43 +++---- inst/doc/BasicGenetics.Rmd | 59 ++++----- inst/doc/BasicGenetics.html | 154 ++------------------------ inst/doc/DistributionBuildingNComparison.R | 33 ++--- inst/doc/DistributionBuildingNComparison.Rmd | 33 ++--- inst/doc/DistributionBuildingNComparison.html | 40 +----- inst/doc/HypothesisTest.R | 35 +++-- inst/doc/HypothesisTest.Rmd | 35 +++-- inst/doc/HypothesisTest.html | 15 +- man/mixexample.Rd |only vignettes/BasicGenetics.Rmd | 59 ++++----- vignettes/DistributionBuildingNComparison.Rmd | 33 ++--- vignettes/HypothesisTest.Rmd | 35 +++-- 19 files changed, 256 insertions(+), 381 deletions(-)
Title: Statistics of Extremes
Description: Conducts inference in statistical models for extreme values (de Carvalho et al (2012), <doi:10.1080/03610926.2012.709905>; de Carvalho and Davison (2014), <10.1080/01621459.2013.872651>; Einmahl et al (2016), <doi:10.1111/rssb.12099>).
Author: Miguel de Carvalho [aut, cre],
Rodrigo Rubio [aut],
Vianey Palacios [aut],
Alejandro Jara [ctb],
Tim Hanson [ctb]
Maintainer: Miguel de Carvalho <miguel.decarvalho@ed.ac.uk>
Diff between extremis versions 1.0 dated 2020-11-20 and 1.2 dated 2020-11-26
DESCRIPTION | 6 +- MD5 | 16 +++--- R/cPTdensity.R | 81 ++++++++++++++++++++++++---------- R/cdensity.R | 2 man/cPTdensity.Rd | 18 +++---- src/PTudensitybetapmh.f | 109 +++++++++++++++++++++++------------------------ src/ToolsDistributions.f | 6 -- src/ToolsRfun.c | 10 ++++ src/init.c | 2 9 files changed, 142 insertions(+), 108 deletions(-)
Title: Clustering of Micro Panel Data
Description: Two-step feature-based clustering method designed for micro panel (longitudinal) data with the artificial panel data generator. See Sobisek, Stachova, Fojtik (2018) <arXiv:1807.05926>.
Author: Jan Fojtik [aut, cre],
Anna Grishko [aut],
Lukas Sobisek [aut, cph, rev]
Maintainer: Jan Fojtik <9afojtik@gmail.com>
Diff between CluMP versions 0.8 dated 2020-02-17 and 0.8.1 dated 2020-11-26
DESCRIPTION | 20 +- MD5 | 38 ++-- NAMESPACE | 1 NEWS.md | 6 R/Generate_Panel.R | 336 +++++++++++++++++++++--------------------- R/OptiNum.R | 349 ++++++++++++++++++++++---------------------- R/PanelPlot.R | 215 +++++++++++++-------------- R/clump.R | 300 +++++++++++++++++++------------------- R/clump_profiles.R | 393 +++++++++++++++++++++++++------------------------- R/clump_view.R | 271 +++++++++++++++++----------------- man/CluMP.Rd | 5 man/CluMP_profiles.Rd | 3 man/CluMP_view.Rd | 13 + man/GeneratePanel.Rd | 13 + man/OptiNum.Rd | 10 + man/PanelPlot.Rd | 15 + man/ParamCubic.Rd | 6 man/ParamExpon.Rd | 6 man/ParamLinear.Rd | 6 man/ParamQuadrat.Rd | 6 20 files changed, 1030 insertions(+), 982 deletions(-)
Title: User Friendly Bayesian Data Analysis for Psychology
Description: Contains several Bayesian models for data analysis of psychological tests. A user friendly interface for these models should enable students and researchers to perform professional level Bayesian data analysis without advanced knowledge in programming and Bayesian statistics. This package is based on the Stan platform (Carpenter et el. 2017 <doi:10.18637/jss.v076.i01>).
Author: Jure Demšar [cre, aut],
Grega Repovš [aut],
Erik Štrumbelj [aut],
Trustees of Columbia University [cph],
John Kruschke [cph] (R/shared_functions.R - mcmc_hdi,
src/stan_files/ttest.stan),
Rasmus Baath [cph] (R/b_bootstrap.R)
Maintainer: Jure Demšar <jure.demsar@fri.uni-lj.si>
Diff between bayes4psy versions 1.2.3 dated 2020-02-20 and 1.2.4 dated 2020-11-26
DESCRIPTION | 8 MD5 | 232 ++--- NAMESPACE | 2 NEWS.md | 47 - README.md | 2 build/vignette.rds |binary inst/doc/adaptation_level.R | 13 inst/doc/adaptation_level.Rmd | 13 inst/doc/adaptation_level.html | 279 ++---- inst/doc/afterimages.R | 5 inst/doc/afterimages.Rmd | 7 inst/doc/afterimages.html | 619 +++++---------- inst/doc/flanker.R | 10 inst/doc/flanker.Rmd | 10 inst/doc/flanker.html | 451 ++++------ inst/doc/stroop.R | 26 inst/doc/stroop.Rmd | 40 inst/doc/stroop.html | 348 ++------ man/b_bootstrap.Rd | 118 +- man/b_color.Rd | 228 ++--- man/b_linear.Rd | 154 +-- man/b_prior-class.Rd | 34 man/b_prior-get_prior_id.Rd | 34 man/b_reaction_time.Rd | 140 +-- man/b_results-class.Rd | 16 man/b_results-compare_distributions.Rd | 32 man/b_results-compare_means.Rd | 32 man/b_results-get_parameters.Rd | 26 man/b_results-get_subject_parameters.Rd | 26 man/b_results-plot_distributions.Rd | 32 man/b_results-plot_distributions_difference.Rd | 32 man/b_results-plot_fit.Rd | 32 man/b_results-plot_means.Rd | 30 man/b_results-plot_means_difference.Rd | 32 man/b_results-plot_trace.Rd | 26 man/b_success_rate.Rd | 130 +-- man/b_ttest.Rd | 126 +-- man/bayes4psy-datasets.Rd | 356 ++++---- man/bayes4psy-package.Rd | 30 man/color_class-class.Rd | 602 +++++++------- man/color_class-compare_distributions.Rd | 54 - man/color_class-compare_means.Rd | 54 - man/color_class-get_parameters.Rd | 50 - man/color_class-plot_distributions.Rd | 54 - man/color_class-plot_distributions_difference.Rd | 54 - man/color_class-plot_distributions_hsv.Rd | 60 - man/color_class-plot_fit.Rd | 54 - man/color_class-plot_fit_hsv.Rd | 56 - man/color_class-plot_hsv.Rd | 56 - man/color_class-plot_means.Rd | 54 - man/color_class-plot_means_difference.Rd | 54 - man/color_class-plot_means_hsv.Rd | 60 - man/color_class-plot_trace.Rd | 50 - man/linear_class-class.Rd | 326 +++---- man/linear_class-compare_distributions.Rd | 54 - man/linear_class-compare_means.Rd | 54 - man/linear_class-get_parameters.Rd | 50 - man/linear_class-get_subject_parameters.Rd | 50 - man/linear_class-plot_distributions.Rd | 54 - man/linear_class-plot_distributions_difference.Rd | 54 - man/linear_class-plot_fit.Rd | 54 - man/linear_class-plot_means.Rd | 54 - man/linear_class-plot_means_difference.Rd | 54 - man/linear_class-plot_trace.Rd | 50 - man/mcmc_hdi.Rd | 42 - man/plot-color_class-missing-method.Rd | 50 - man/plot-linear_class-missing-method.Rd | 50 - man/plot-reaction_time_class-missing-method.Rd | 50 - man/plot-success_rate_class-missing-method.Rd | 50 - man/plot-ttest_class-missing-method.Rd | 42 - man/reaction_time_class-class.Rd | 378 ++++----- man/reaction_time_class-compare_distributions.Rd | 54 - man/reaction_time_class-compare_means.Rd | 54 - man/reaction_time_class-get_parameters.Rd | 50 - man/reaction_time_class-get_subject_parameters.Rd | 50 - man/reaction_time_class-plot_distributions.Rd | 54 - man/reaction_time_class-plot_distributions_difference.Rd | 54 - man/reaction_time_class-plot_fit.Rd | 54 - man/reaction_time_class-plot_means.Rd | 54 - man/reaction_time_class-plot_means_difference.Rd | 54 - man/reaction_time_class-plot_trace.Rd | 50 - man/show-color_class-method.Rd | 42 - man/show-linear_class-method.Rd | 42 - man/show-reaction_time_class-method.Rd | 42 - man/show-success_rate_class-method.Rd | 42 - man/show-ttest_class-method.Rd | 42 - man/success_rate_class-class.Rd | 346 ++++---- man/success_rate_class-compare_distributions.Rd | 54 - man/success_rate_class-compare_means.Rd | 54 - man/success_rate_class-get_parameters.Rd | 50 - man/success_rate_class-get_subject_parameters.Rd | 50 - man/success_rate_class-plot_distributions.Rd | 54 - man/success_rate_class-plot_distributions_difference.Rd | 54 - man/success_rate_class-plot_fit.Rd | 54 - man/success_rate_class-plot_means.Rd | 54 - man/success_rate_class-plot_means_difference.Rd | 54 - man/success_rate_class-plot_trace.Rd | 50 - man/summary-color_class-method.Rd | 42 - man/summary-linear_class-method.Rd | 42 - man/summary-reaction_time_class-method.Rd | 42 - man/summary-success_rate_class-method.Rd | 42 - man/summary-ttest_class-method.Rd | 42 - man/ttest_class-class.Rd | 426 +++++----- man/ttest_class-compare_distributions.Rd | 54 - man/ttest_class-compare_means.Rd | 54 - man/ttest_class-get_parameters.Rd | 50 - man/ttest_class-plot_distributions.Rd | 54 - man/ttest_class-plot_distributions_difference.Rd | 54 - man/ttest_class-plot_fit.Rd | 50 - man/ttest_class-plot_means.Rd | 54 - man/ttest_class-plot_means_difference.Rd | 54 - man/ttest_class-plot_trace.Rd | 50 - tests/testthat/test_linear.R | 2 vignettes/adaptation_level.Rmd | 13 vignettes/afterimages.Rmd | 7 vignettes/flanker.Rmd | 10 vignettes/stroop.Rmd | 40 117 files changed, 4492 insertions(+), 4908 deletions(-)
Title: Distributed Representations of Words
Description: Learn vector representations of words by continuous bag of words and skip-gram implementations of the 'word2vec' algorithm.
The techniques are detailed in the paper "Distributed Representations of Words and Phrases and their Compositionality" by Mikolov et al. (2013), available at <arXiv:1310.4546>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
BNOSAC [cph] (R wrapper),
Max Fomichev [ctb, cph] (Code in src/word2vec)
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between word2vec versions 0.3.2 dated 2020-10-10 and 0.3.3 dated 2020-11-26
DESCRIPTION | 6 MD5 | 16 +- NAMESPACE | 1 NEWS.md | 5 R/doc2vec.R | 2 R/utils.R |only man/read.word2vec.Rd | 84 ++++++------ man/txt_clean_word2vec.Rd |only man/word2vec.Rd | 312 +++++++++++++++++++++++----------------------- man/write.word2vec.Rd | 108 +++++++-------- 10 files changed, 271 insertions(+), 263 deletions(-)
Title: 'sf'-Based Interface to the 'HERE' REST APIs
Description: Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
(1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API;
(2) route directions, travel distance or time matrices and isolines using the 'Routing' API;
(3) request real-time traffic flow and incident information from the 'Traffic' API;
(4) find request public transport connections and nearby stations from the 'Public Transit' API;
(5) request intermodal routes using the 'Intermodal Routing' API;
(6) get weather forecasts, reports on current weather conditions, astronomical
information and alerts at a specific location from the 'Destination Weather' API.
Locations, routes and isolines are returned as 'sf' objects.
Author: Merlin Unterfinger [aut, cre] (<https://orcid.org/0000-0003-2020-2366>),
Daniel Possenriede [ctb] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between hereR versions 0.5.1 dated 2020-10-20 and 0.5.2 dated 2020-11-26
DESCRIPTION | 6 MD5 | 30 +- NEWS.md | 11 R/geocode.R | 24 + R/sysdata.rda |binary R/utils.R | 9 build/vignette.rds |binary inst/doc/authentication.html | 266 -------------------- inst/doc/geocoder.html | 366 ++++----------------------- inst/doc/intermodal.html | 346 +++----------------------- inst/doc/routing.html | 448 +++++++-------------------------- inst/doc/traffic.html | 302 +--------------------- inst/doc/transit.html | 428 ++++++-------------------------- inst/doc/weather.html | 557 +++++++++++------------------------------- man/geocode.Rd | 12 tests/testthat/test-geocode.R | 3 16 files changed, 541 insertions(+), 2267 deletions(-)
Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running
program that seeks to monitor the status and trends of the breeding birds in
North America. Since its start in 1966, the BBS has accumulated over 50 years
of data for over 500 species of North American Birds. Given the temporal and
spatial structure of the data, hierarchical Bayesian models are used to assess
the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform
hierarchical Bayesian analysis of BBS data. You can run a full
model analysis for one or more species that you choose, or you can take
more control and specify how the data should be stratified, prepared
for 'JAGS', or modelled. The functions provided here allow you to replicate
analyses performed by the United State Geological Survey (USGS, see Link
and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service
(CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre],
Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <edwardsb@uoguelph.ca>
Diff between bbsBayes versions 2.3.4.2020 dated 2020-10-22 and 2.3.5.2020 dated 2020-11-26
DESCRIPTION | 8 MD5 | 8 R/prepare-jags-data.R | 2 R/stratify.R | 9 - README.md | 407 ++++++++++++++++++++++++++++---------------------- 5 files changed, 247 insertions(+), 187 deletions(-)
Title: Efficient Designs for Discrete Choice Experiments
Description: Generates efficient designs for discrete choice experiments based on the multinomial logit model, and individually adapted designs for the mixed multinomial logit model. The generated designs can be presented on screen and choice data can be gathered using a shiny application. Traets F, Sanchez G, and Vandebroek M (2020) <doi:10.18637/jss.v096.i03>.
Author: Frits Traets [aut, cre],
Daniel Gil [ctb]
Maintainer: Frits Traets <frits.traets@kuleuven.be>
Diff between idefix versions 0.4.3 dated 2020-04-07 and 1.0.1 dated 2020-11-26
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- R/CEA.R | 1 + R/efficiency_algorithms.R | 2 ++ R/idefix.R | 2 +- build/partial.rdb |binary inst/CITATION |only inst/REFERENCES.bib | 13 +++++++++++-- man/Modfed.Rd | 3 +++ man/SeqCEA.Rd | 2 ++ man/SeqMOD.Rd | 2 ++ man/idefix-package.Rd | 4 +++- 12 files changed, 40 insertions(+), 18 deletions(-)
More information about affinitymatrix at CRAN
Permanent link
Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in
high dimensions.
Author: Marius Hofert [aut, cre],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrng versions 0.0-7 dated 2019-09-09 and 0.0-8 dated 2020-11-26
DESCRIPTION | 9 ++++++--- MD5 | 12 +++++++----- NAMESPACE | 1 + R/auxiliaries.R |only R/qrng.R | 1 + R/test_functions.R | 16 ++++++++++++++-- man/qrng.Rd | 14 +++++++------- man/to_array.Rd |only 8 files changed, 36 insertions(+), 17 deletions(-)
Title: Fetch Data from 'National Stock Exchange (India)'
Description: Fetch data related to stocks, index, futures & options from the
'NSE (National Stock Exchange, India)'. This package is community maintained
and is not officially supported by 'NSE'. The accuracy of data is only as
correct as provided on <https://www.nseindia.com>.
Author: Lokesh Kumar [aut],
Aravind Hebbali [aut, cre],
Lionel Pinto [ctb]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between nse2r versions 0.1.2 dated 2020-06-18 and 0.1.3 dated 2020-11-26
DESCRIPTION | 6 MD5 | 8 NEWS.md | 6 R/nse-stock.R | 10 README.md | 2004 ++++++++++++++++++++++++++++++++-------------------------- 5 files changed, 1144 insertions(+), 890 deletions(-)
Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in 'movebank.org'
as well as tools to visualize and statistically analyze animal movement data,
among others functions to calculate dynamic Brownian Bridge Movement Models.
Move helps addressing movement ecology questions.
Author: Bart Kranstauber [aut, cre],
Marco Smolla [aut],
Anne K Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move versions 4.0.4 dated 2020-09-12 and 4.0.6 dated 2020-11-26
DESCRIPTION | 6 MD5 | 18 +- R/WebImport.R | 4 build/vignette.rds |binary inst/doc/browseMovebank.R | 2 inst/doc/browseMovebank.Rmd | 2 inst/doc/browseMovebank.html | 6 inst/doc/move.html | 381 +++++++++++++++++++++---------------------- tests/testthat/test.web.R | 48 ++--- vignettes/browseMovebank.Rmd | 2 10 files changed, 240 insertions(+), 229 deletions(-)
Title: Markov Chains
Description: Computation of various Markovian models for categorical data
including homogeneous Markov chains of any order, MTD models, Hidden Markov
models, and Double Chain Markov Models.
Author: Ogier Maitre and Kevin Emery, with contributions from Oliver Buschor and Andre Berchtold
Maintainer: Andre Berchtold <andre.berchtold@unil.ch>
Diff between march versions 3.1 dated 2019-08-18 and 3.3.2 dated 2020-11-26
march-3.1/march/man/march.name-march.Dcmm-method.Rd |only march-3.1/march/man/march.name-march.Indep-method.Rd |only march-3.1/march/man/march.name-march.Mc-method.Rd |only march-3.1/march/man/march.name-march.Mtd-method.Rd |only march-3.1/march/man/march.name.Rd |only march-3.1/march/man/march.thompson-march.Dcmm-numeric-method.Rd |only march-3.1/march/man/march.thompson-march.Indep-numeric-method.Rd |only march-3.1/march/man/march.thompson-march.Mc-numeric-method.Rd |only march-3.1/march/man/march.thompson-march.Mtd-numeric-method.Rd |only march-3.1/march/man/march.thompson.Rd |only march-3.3.2/march/DESCRIPTION | 19 march-3.3.2/march/MD5 | 91 march-3.3.2/march/NAMESPACE | 9 march-3.3.2/march/R/march.AllGenerics.R | 1496 ++++++---- march-3.3.2/march/R/march.ci.R | 70 march-3.3.2/march/R/march.dcmm.R | 13 march-3.3.2/march/R/march.dcmm.em.R | 21 march-3.3.2/march/R/march.diagnostic.R | 90 march-3.3.2/march/R/march.mtd.R | 84 march-3.3.2/march/data/Employment.2.rda |only march-3.3.2/march/data/pewee.rda |binary march-3.3.2/march/data/pewee_df.rda |binary march-3.3.2/march/data/sleep.rda |binary march-3.3.2/march/data/sleep_df.rda |binary march-3.3.2/march/man/Employment.2.Rd |only march-3.3.2/march/man/march.AIC.Rd | 64 march-3.3.2/march/man/march.BIC.Rd | 52 march-3.3.2/march/man/march.Dataset-class.Rd | 68 march-3.3.2/march/man/march.Dcmm-class.Rd | 74 march-3.3.2/march/man/march.Indep-class.Rd | 46 march-3.3.2/march/man/march.Mc-class.Rd | 50 march-3.3.2/march/man/march.Model-class.Rd | 44 march-3.3.2/march/man/march.Mtd-class.Rd | 66 march-3.3.2/march/man/march.Rd | 2 march-3.3.2/march/man/march.dataset.loadFromDataFrame.Rd | 145 march-3.3.2/march/man/march.dataset.loadFromFile.Rd | 61 march-3.3.2/march/man/march.dcmm.construct.Rd | 201 - march-3.3.2/march/man/march.dcmm.viterbi.Rd | 56 march-3.3.2/march/man/march.indep.bailey.Rd |only march-3.3.2/march/man/march.indep.construct.Rd | 64 march-3.3.2/march/man/march.indep.thompson.Rd |only march-3.3.2/march/man/march.mc.bailey.Rd |only march-3.3.2/march/man/march.mc.construct.Rd | 72 march-3.3.2/march/man/march.mc.thompson.Rd |only march-3.3.2/march/man/march.mtd.bailey.Rd |only march-3.3.2/march/man/march.mtd.construct.Rd | 113 march-3.3.2/march/man/march.mtd.thompson.Rd |only march-3.3.2/march/man/march.write.Rd | 42 march-3.3.2/march/man/pewee.Rd | 2 march-3.3.2/march/man/pewee_df.Rd | 2 march-3.3.2/march/man/pewee_t.Rd | 2 march-3.3.2/march/man/sleep.Rd | 2 march-3.3.2/march/man/sleep_df.Rd | 2 march-3.3.2/march/tests/examples/march.bailey.example.R |only march-3.3.2/march/tests/examples/march.dcmm.construct.example.R | 4 march-3.3.2/march/tests/examples/march.thompson.example.R | 4 56 files changed, 1830 insertions(+), 1301 deletions(-)
Title: Analyzing Data with Cellwise Outliers
Description: Tools for detecting cellwise outliers and robust methods to analyze
data which may contain them. Contains the implementation of the algorithms described in
Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access)
Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access),
Raymaekers and Rousseeuw (2019) <doi:10.1080/00401706.2019.1677270> (open access),
Raymaekers and Rousseeuw (2020) <arXiv:2005.07946> (open access),
Raymaekers and Rousseeuw (2020) <arXiv:1912.12446> (open access).
Examples can be found in the vignettes:
"DDC_examples", "MacroPCA_examples", "wrap_examples" and "transfo_examples".
Author: Jakob Raymaekers [aut, cre],
Peter Rousseeuw [aut],
Wannes Van den Bossche [ctb],
Mia Hubert [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between cellWise versions 2.2.1 dated 2020-11-11 and 2.2.2 dated 2020-11-26
cellWise-2.2.1/cellWise/inst/doc/Wrap_examples.R |only cellWise-2.2.1/cellWise/inst/doc/Wrap_examples.Rmd |only cellWise-2.2.1/cellWise/inst/doc/Wrap_examples.html |only cellWise-2.2.1/cellWise/vignettes/Wrap_examples.Rmd |only cellWise-2.2.2/cellWise/DESCRIPTION | 15 cellWise-2.2.2/cellWise/MD5 | 27 - cellWise-2.2.2/cellWise/NAMESPACE | 7 cellWise-2.2.2/cellWise/R/RcppExports.R | 4 cellWise-2.2.2/cellWise/R/TVCN.R | 2 cellWise-2.2.2/cellWise/R/cellHandler.R |only cellWise-2.2.2/cellWise/build/vignette.rds |binary cellWise-2.2.2/cellWise/inst/doc/wrap_examples.R |only cellWise-2.2.2/cellWise/inst/doc/wrap_examples.Rmd |only cellWise-2.2.2/cellWise/inst/doc/wrap_examples.html |only cellWise-2.2.2/cellWise/man/DI.Rd |only cellWise-2.2.2/cellWise/man/cellHandler.Rd |only cellWise-2.2.2/cellWise/man/transfo.Rd | 2 cellWise-2.2.2/cellWise/src/Main.cpp | 423 +++++++++++++++++++- cellWise-2.2.2/cellWise/src/RcppExports.cpp | 16 cellWise-2.2.2/cellWise/vignettes/wrap_examples.Rmd |only 20 files changed, 454 insertions(+), 42 deletions(-)
Title: Modelling of Microbial Growth
Description: Modelling of microbial growth under isothermal and dynamic conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions using methods (algorithms & models) common in
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] (<https://orcid.org/0000-0002-4404-3550>),
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 0.1.1 dated 2020-11-11 and 0.1.2 dated 2020-11-26
biogrowth-0.1.1/biogrowth/R/S3_plotting.R |only biogrowth-0.1.1/biogrowth/man/plot.DynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitDynamicGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitIsoGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitMultipleDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitMultipleGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitSecondaryGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.IsothermalGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.MCMCgrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.StochasticGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.TimeDistribution.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitDynamicGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitIsoGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitMultipleDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitMultipleGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitSecondaryGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitDynamicGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitIsoGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitMultipleDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitMultipleGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitSecondaryGrowth.Rd |only biogrowth-0.1.2/biogrowth/DESCRIPTION | 8 biogrowth-0.1.2/biogrowth/MD5 | 157 biogrowth-0.1.2/biogrowth/NAMESPACE | 235 biogrowth-0.1.2/biogrowth/NEWS.md | 45 biogrowth-0.1.2/biogrowth/R/DynamicGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/FitDynamicGrowthMCMC_class.R |only biogrowth-0.1.2/biogrowth/R/FitDynamicGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/FitIsoGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/FitMultipleDynamicGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/FitMultipleGrowthMCMC_class.R |only biogrowth-0.1.2/biogrowth/R/FitSecondaryGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/IsothermalGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/MCMCgrowth_class.R |only biogrowth-0.1.2/biogrowth/R/S3_methods.R | 474 - biogrowth-0.1.2/biogrowth/R/StochasticGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/TimeDistribution_class.R |only biogrowth-0.1.2/biogrowth/R/baranyi_model.R | 116 biogrowth-0.1.2/biogrowth/R/data.R | 110 biogrowth-0.1.2/biogrowth/R/fit_dynamic_growth.R | 556 +- biogrowth-0.1.2/biogrowth/R/fit_iso_growth.R | 256 biogrowth-0.1.2/biogrowth/R/fit_multi_dynamic.R | 522 -- biogrowth-0.1.2/biogrowth/R/fit_secondary_models.R | 474 - biogrowth-0.1.2/biogrowth/R/functions_counts.R | 270 - biogrowth-0.1.2/biogrowth/R/gamma_models.R | 234 biogrowth-0.1.2/biogrowth/R/helpers.R | 223 biogrowth-0.1.2/biogrowth/R/meatinfo_primary.R | 244 biogrowth-0.1.2/biogrowth/R/metainfo_secondary.R | 236 biogrowth-0.1.2/biogrowth/R/predict_MCMC_growth.R | 297 - biogrowth-0.1.2/biogrowth/R/predict_dynamic_growth.R | 274 - biogrowth-0.1.2/biogrowth/R/predict_isothermal_growth.R | 291 - biogrowth-0.1.2/biogrowth/R/predict_stochastic_growth.R | 336 - biogrowth-0.1.2/biogrowth/README.md | 126 biogrowth-0.1.2/biogrowth/build/vignette.rds |binary biogrowth-0.1.2/biogrowth/data/example_dynamic_growth.rda |binary biogrowth-0.1.2/biogrowth/inst/doc/Publication-ready-figures-with-biogrowth.R | 524 +- biogrowth-0.1.2/biogrowth/inst/doc/Publication-ready-figures-with-biogrowth.Rmd | 778 +- biogrowth-0.1.2/biogrowth/inst/doc/Publication-ready-figures-with-biogrowth.html | 1294 ++-- biogrowth-0.1.2/biogrowth/inst/doc/biogrowth_basics.R | 909 +-- biogrowth-0.1.2/biogrowth/inst/doc/biogrowth_basics.Rmd | 2475 ++++----- biogrowth-0.1.2/biogrowth/inst/doc/biogrowth_basics.html | 2594 +++++----- biogrowth-0.1.2/biogrowth/man/DynamicGrowth.Rd |only biogrowth-0.1.2/biogrowth/man/FitDynamicGrowth.Rd |only biogrowth-0.1.2/biogrowth/man/FitDynamicGrowthMCMC.Rd |only biogrowth-0.1.2/biogrowth/man/FitIsoGrowth.Rd |only biogrowth-0.1.2/biogrowth/man/FitMultipleDynamicGrowth.Rd |only biogrowth-0.1.2/biogrowth/man/FitMultipleGrowthMCMC.Rd |only biogrowth-0.1.2/biogrowth/man/FitSecondaryGrowth.Rd |only biogrowth-0.1.2/biogrowth/man/IsothermalGrowth.Rd |only biogrowth-0.1.2/biogrowth/man/MCMCgrowth.Rd |only biogrowth-0.1.2/biogrowth/man/StochasticGrowth.Rd |only biogrowth-0.1.2/biogrowth/man/TimeDistribution.Rd |only biogrowth-0.1.2/biogrowth/man/check_primary_pars.Rd | 40 biogrowth-0.1.2/biogrowth/man/check_secondary_pars.Rd | 30 biogrowth-0.1.2/biogrowth/man/dBaranyi.Rd | 62 biogrowth-0.1.2/biogrowth/man/distribution_to_logcount.Rd | 6 biogrowth-0.1.2/biogrowth/man/extract_secondary_pars.Rd | 52 biogrowth-0.1.2/biogrowth/man/figures |only biogrowth-0.1.2/biogrowth/man/fit_MCMC_growth.Rd | 11 biogrowth-0.1.2/biogrowth/man/fit_dynamic_growth.Rd | 11 biogrowth-0.1.2/biogrowth/man/fit_isothermal_growth.Rd | 144 biogrowth-0.1.2/biogrowth/man/fit_multiple_growth.Rd | 162 biogrowth-0.1.2/biogrowth/man/fit_multiple_growth_MCMC.Rd | 172 biogrowth-0.1.2/biogrowth/man/fit_secondary_growth.Rd | 177 biogrowth-0.1.2/biogrowth/man/full_Ratkowski.Rd | 40 biogrowth-0.1.2/biogrowth/man/get_dyna_residuals.Rd | 72 biogrowth-0.1.2/biogrowth/man/get_multi_dyna_residuals.Rd | 58 biogrowth-0.1.2/biogrowth/man/is.FitMultipleDynamicGrowth.Rd |only biogrowth-0.1.2/biogrowth/man/is.FitMultipleDynamicGrowthMCMC.Rd |only biogrowth-0.1.2/biogrowth/man/iso_Baranyi.Rd | 56 biogrowth-0.1.2/biogrowth/man/multiple_experiments.Rd | 52 biogrowth-0.1.2/biogrowth/man/predict_MCMC_growth.Rd | 146 biogrowth-0.1.2/biogrowth/man/predict_dynamic_growth.Rd | 195 biogrowth-0.1.2/biogrowth/man/predict_isothermal_growth.Rd | 87 biogrowth-0.1.2/biogrowth/man/predict_stochastic_growth.Rd | 11 biogrowth-0.1.2/biogrowth/man/primary_model_data.Rd | 38 biogrowth-0.1.2/biogrowth/man/secondary_model_data.Rd | 38 biogrowth-0.1.2/biogrowth/man/zwietering_gamma.Rd | 48 biogrowth-0.1.2/biogrowth/vignettes/Publication-ready-figures-with-biogrowth.Rmd | 778 +- biogrowth-0.1.2/biogrowth/vignettes/biogrowth_basics.Rmd | 2475 ++++----- 103 files changed, 9476 insertions(+), 9543 deletions(-)
Title: Small Example Response and Response Time Data from PISA 2018
Description: Scored responses and responses times from the Canadian subsample of the PISA 2018 assessment, accessible as the "Cognitive Item Data File" by OECD (2019) <https://www.oecd.org/pisa/data/2018database/>.
Author: Benjamin Becker [aut, cre],
Esther Ulitzsch [ctb],
Christoph Koenig [ctb]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>
Diff between pisaRT versions 1.0.0 dated 2020-07-01 and 2.0.0 dated 2020-11-26
DESCRIPTION | 12 ++++----- MD5 | 25 ++++++++++---------- NAMESPACE | 4 +-- NEWS.md |only R/pisaL.R | 6 +++- R/pisaRT-package.R | 10 ++++---- R/pisaW.R | 6 +++- README.md | 9 +++---- data/pisaL.rda |binary data/pisaW.rda |binary man/pisaL.Rd | 56 +++++++++++++++++++++++---------------------- man/pisaRT.Rd | 50 ++++++++++++++++++++-------------------- man/pisaW.Rd | 54 ++++++++++++++++++++++--------------------- tests/testthat/test_pisa.R | 27 ++++++++++++++++++--- 14 files changed, 145 insertions(+), 114 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 1.0.0 dated 2020-11-01 and 1.0.1 dated 2020-11-26
DESCRIPTION | 8 +-- MD5 | 10 +-- NEWS.md | 5 + R/forestglm.R | 14 ++--- build/vignette.rds |binary inst/doc/jstable.html | 130 ++++++++++++++++++++------------------------------ 6 files changed, 74 insertions(+), 93 deletions(-)
Title: Imputation of Count Data using Side Information
Description: Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear model where main row and column effects are decomposed as regression terms on known covariates. A residual low-rank interaction term is also fitted. LORI returns estimates of covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure.
Author: Genevieve Robin [aut, cre]
Maintainer: Genevieve Robin <genevieve.robin@polytechnique.edu>
Diff between lori versions 2.2.0 dated 2019-12-10 and 2.2.1 dated 2020-11-26
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/altmin.R | 32 ++++++++++++++++---------------- R/cv.lori.R | 15 +++++++++------ R/lori.R | 9 ++++++--- R/mcgd.R | 10 +++++----- man/cv.lori.Rd | 21 ++++++++++++++++++--- man/lori.Rd | 20 +++++++++++++++++--- man/mi.lori.Rd | 19 +++++++++++++++---- 10 files changed, 102 insertions(+), 55 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-14 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-16 1.01
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-01 1.4
2013-06-18 1.3
2013-02-04 1.2
2012-09-26 1.1
2012-08-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-11 0.15
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-19 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-04 0.11
2017-02-28 0.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-12 3.0.0
2020-04-19 2.6.1
2020-01-20 2.6.0
2019-07-30 2.5.1
2019-07-01 2.5.0
2019-04-07 2.4.5
2019-03-18 2.4.4
2018-09-11 2.4.3
2018-03-11 2.4.2
2017-10-16 2.4.1
2017-06-06 2.4
2016-08-23 2.3
2016-02-25 2.2
2015-03-20 2.1
2014-11-18 2.0
2012-11-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-26 0.1-41
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-07 2.4
2014-07-21 2.3
2012-08-22 1.0
Title: Row by Row Data Processing Tool, Using 'DataSailr' Script
Description: A row by row data processing tool. You can write data processing code in 'DataSailr' script which is specially intended for data manipulation. The package uses 'libsailr' (C/C++ library) for its 'DataSailr' code parsing and its execution.
Author: Toshihiro Umehara [aut, cre],
Troy Hanson [cph, ctb] (uthash),
Howard Hinnant [cph, ctb] (date.h),
Adrian Colomitchi [cph, ctb] (date.h),
Florian Dang [cph, ctb] (date.h),
Paul Thompson [cph, ctb] (date.h),
Tomasz Kamiński [cph, ctb] (date.h),
Nemanja Trifunovic [cph, ctb] (utfcpp),
Kim Grasman [cph, ctb] (getopt_port),
Jon Clayden [cph, ctb] (ore package),
K.Kosako [cph, ctb] (onigmo author),
K.Takata [cph, ctb] (onigmo author),
Byte [cph, ctb] (onigmo contributor),
KUBO Takehiro [cph, ctb] (onigmo contributor),
Free Software Foundation, Inc [cph],
X Consortium [cph]
Maintainer: Toshihiro Umehara <toshi@niceume.com>
Diff between datasailr versions 0.8.6 dated 2020-08-26 and 0.8.7 dated 2020-11-26
DESCRIPTION | 12 +++--- MD5 | 36 +++++++++---------- NEWS.md | 13 +++++++ R/data_sailr_main.R | 27 ++++++++++---- README.md | 78 ++++++++++++++++++++++-------------------- configure | 61 +++++++++++++++++++++++++++----- configure.ac | 27 +++++++++++++- man/datasailr-package.Rd | 6 +-- man/sail.Rd | 12 +++--- src/Makevars.in | 10 ++--- src/Onigmo/Makefile.in | 9 ++-- src/Onigmo/aclocal.m4 | 36 +++++++++++++++++++ src/Onigmo/configure | 34 ++++++++++++++++++ src/Onigmo/configure.ac | 1 src/Onigmo/sample/Makefile.in | 7 ++- src/data_sailr_cpp_main.cpp | 1 src/libsailr/HISTORY.md | 6 +++ src/libsailr/tree_free.c | 5 ++ src/libsailr/vm/vm.c | 16 +++++--- 19 files changed, 291 insertions(+), 106 deletions(-)
Title: Efficient Computation of Ordinary and Generalized Poisson
Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between PoissonBinomial versions 1.2.0 dated 2020-11-25 and 1.2.1 dated 2020-11-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 15 +++++++++++++-- inst/doc/proc_approx.html | 22 +++++++++++----------- inst/doc/proc_exact.html | 14 +++++++------- src/PoissonBinomial.cpp | 16 ++++++++-------- 6 files changed, 48 insertions(+), 37 deletions(-)
More information about PoissonBinomial at CRAN
Permanent link
Title: Bayesian Model Selection and Averaging for Non-Local and Local
Priors
Description: Bayesian model selection and averaging for regression and mixtures for non-local and selected local priors.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck, Oriol Abril
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 2.2.9 dated 2019-12-06 and 3.0.1 dated 2020-11-26
ChangeLog | 18 DESCRIPTION | 8 MD5 | 63 - R/bms_ortho.R | 8 R/emomLM.R | 10 R/greedyGLM.R | 2 R/modelSelection.R | 390 +++++- R/modelSelectionGLM.R | 23 R/modelsearch.R | 3 R/msPriorSpec.R | 76 - R/nlpMarginal.R | 28 R/pmomLM.R | 4 R/pmomPM.R | 14 build/vignette.rds |binary data/hald.rda |binary inst/doc/mombf.pdf |binary man/modelSelection.Rd | 50 man/msPriorSpec-class.Rd | 37 man/nlpMarginals.Rd | 17 src/RcppExports.cpp | 16 src/cstat.cpp | 2 src/glm.cpp |only src/glm.h |only src/modelSel.cpp | 1773 +++++++++++++++++++++++------ src/modelSel.h | 133 +- src/modselFunction.cpp | 377 ++++++ src/modselFunction.h | 64 - src/nlpMarg.cpp | 38 src/nlpMarg.h | 4 tests/testthat/data-for-tests.R | 1 tests/testthat/test-modelSelection-enum.R | 31 tests/testthat/test-modelSelection-gibbs.R | 20 tests/testthat/test-mspriorspec.R |only tests/testthat/test-nlpMarginal-groups.R | 17 34 files changed, 2619 insertions(+), 608 deletions(-)
Title: Media News Extraction for Text Analysis
Description: Extract textual data from different media channels
through its source based on users choice of keywords.
These data can be used to perform text analysis to
identify patterns in respective media reporting.
The media channels used in this package are print media.
The data (or news) used are publicly available to consumers.
Author: Vatsal Aima [aut, cre]
Maintainer: Vatsal Aima <vaima75@hotmail.com>
Diff between MediaNews versions 0.2.0 dated 2020-11-24 and 0.2.1 dated 2020-11-26
DESCRIPTION | 20 ++++++++++---------- MD5 | 13 ++++++++----- NAMESPACE | 2 ++ R/TOI_News_Articles.R | 8 ++++++-- R/TOI_News_Dataset.R | 1 + R/emoji_Data.R |only README.md | 4 +++- data |only man/emoji_Data.Rd |only 9 files changed, 30 insertions(+), 18 deletions(-)
Title: Convert Between R Objects and Geometric Structures
Description: Geometry shapes in 'R' are typically represented by matrices (points, lines), with more complex
shapes being lists of matrices (polygons). 'Geometries' will convert various 'R' objects into these shapes.
Conversion functions are available at both the 'R' level, and through 'Rcpp'.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <david.cooley.au@gmail.com>
Diff between geometries versions 0.1.0 dated 2020-08-14 and 0.2.0 dated 2020-11-26
DESCRIPTION | 12 +- MD5 | 59 ++++++----- NEWS.md |only R/RcppExports.R | 20 ++- R/geometries.R | 6 - README.md | 92 +++++++++++++++++- build/vignette.rds |binary inst/doc/geometries.html | 64 ++++++++++++ inst/include/geometries/coordinates/dimensions.hpp | 69 ++++++------- inst/include/geometries/geometries.hpp | 17 +-- inst/include/geometries/nest/nest.hpp | 104 ++++++++++---------- inst/include/geometries/utils/close/close.hpp | 28 ++++- inst/include/geometries/utils/columns/columns.hpp | 41 ++++---- inst/include/geometries/utils/reshape |only inst/include/geometries/utils/sexp/sexp.hpp | 21 +++- inst/include/geometries/utils/split/split.hpp | 65 +++++++++--- inst/include/geometries/utils/vectors/vectors.hpp | 82 +++++++--------- inst/tinytest/test_attributes.R | 50 +++++++++ inst/tinytest/test_columns.R | 5 inst/tinytest/test_coordinates.R | 39 +++++-- inst/tinytest/test_geometries.R | 4 inst/tinytest/test_nest.R | 106 ++++++++++----------- inst/tinytest/test_sexp.R | 2 inst/tinytest/test_split.R |only man/gm_geometries.Rd | 6 - src/RcppExports.cpp | 70 ++++++++++--- src/columns.cpp | 21 ++++ src/coordinates.cpp | 4 src/geometries.cpp | 5 src/shapes.cpp | 46 ++++----- src/tests.cpp | 26 ++++- src/utils.cpp | 12 -- 32 files changed, 725 insertions(+), 351 deletions(-)
Title: Nonparametric Methods for Generating High Quality Comparative
Effectiveness Evidence
Description: Implements novel nonparametric approaches to address
biases and confounding when comparing treatments or exposures in
observational studies of outcomes. While designed and appropriate for use
in studies involving medicine and the life sciences, the package can be
used in other situations involving outcomes with multiple confounders.
The package implements a family of methods for non-parametric bias correction
when comparing treatments in observational studies, including survival
analysis settings, where competing risks and/or censoring may be present.
The approach extends to bias-corrected personalized predictions of treatment
outcome differences, and analysis of heterogeneity of treatment effect-sizes
across patient subgroups. For further details, please see:
Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl:
An R Package for Comparative Safety and Effectiveness Research.
Journal of Statistical Software. 2020. p. 1–32. Available from <doi:10.18637/jss.v096.i04>.
Author: Nicolas R. Lauve [aut] (<https://orcid.org/0000-0002-9348-0319>),
Stuart J. Nelson [aut] (<https://orcid.org/0000-0002-8756-0179>),
S. Stanley Young [aut] (<https://orcid.org/0000-0001-9449-5478>),
Robert L. Obenchain [aut] (<https://orcid.org/0000-0002-8395-1666>),
Melania Pintilie [ctb],
Martin Kutz [ctb],
Christophe G. Lambert [aut, cre]
(<https://orcid.org/0000-0003-1994-2893>)
Maintainer: Christophe G. Lambert <cglambert@unm.edu>
Diff between LocalControl versions 1.1.2.1 dated 2020-04-07 and 1.1.2.2 dated 2020-11-26
DESCRIPTION | 36 ++++++++++++---------- MD5 | 41 +++++++++++++------------- NEWS.md | 6 +++ R/localControl.R | 23 +++++++++++++- README.md | 4 +- build/vignette.rds |binary inst/CITATION |only inst/doc/LocalControl-jss-2018.R | 1 inst/doc/LocalControl-jss-2018.pdf |binary man/LocalControl-deprecated.Rd | 1 man/LocalControl.Rd | 26 ++++++++++++---- man/LocalControlClassic.Rd | 14 ++++++-- man/LocalControlCompetingRisksConfidence.Rd | 13 +++++--- man/LocalControlNearestNeighborsConfidence.Rd | 28 ++++++++++++++--- man/SPSloess.Rd | 13 ++++++-- man/UPSLTDdist.Rd | 9 +++-- man/UPSaltdd.Rd | 14 +++++++- man/cardSim.Rd | 6 ++- man/framingham.Rd | 6 ++- man/lindner.Rd | 6 ++- man/plot.LocalControlCR.Rd | 33 +++++++++++++++----- man/plot.LocalControlCS.Rd | 27 ++++++++++++----- 22 files changed, 218 insertions(+), 89 deletions(-)
Title: Utilities for Japanese Mesh Code
Description: Helpful functions for using mesh code (80km to 125m) data in Japan. Visualize mesh code using 'ggplot2' and 'leaflet', etc.
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>)
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jpmesh versions 1.2.1 dated 2020-05-06 and 2.0.0 dated 2020-11-26
DESCRIPTION | 15 MD5 | 124 NAMESPACE | 11 NEWS.md | 8 R/01_imports.R |only R/administration_mesh.R | 23 R/coords_to_mesh.R | 35 R/export_mesh.R | 75 R/find_neighbor_mesh.R | 119 R/fine_separate.R | 113 R/is_mesh.R | 72 R/mesh_convert.R | 191 - R/mesh_to_coords.R | 49 R/meshcode.R |only R/rmesh.R | 19 R/sysdata.rda |binary R/util.R | 235 + build/vignette.rds |binary data/jpnrect.rda |binary data/sf_jpmesh.rda |binary inst/doc/usage.Rmd | 2 inst/doc/usage.html | 296 - man/administration_mesh.Rd | 8 man/coarse_gather.Rd | 4 man/converter.Rd | 7 man/coords_to_mesh.Rd | 3 man/figures/README-jpn_simple_map-1.png |binary man/figures/README-jpn_simple_map_sf-1.png |binary man/fine_separate.Rd | 12 man/mesh_size.Rd | 7 man/mesh_to_coords.Rd | 1 man/meshcode.Rd |only man/meshcode_set.Rd | 8 man/neighbor_mesh.Rd | 2 man/rmesh.Rd | 3 tests/figs/administration-mesh/administration-10kmmesh-pref33-34.svg | 421 +- tests/figs/administration-mesh/administration-10kmmesh-pref35.svg | 229 - tests/figs/administration-mesh/administration-1kmmesh-city08220-08221.svg | 935 ++--- tests/figs/administration-mesh/administration-1kmmesh-city08220.svg | 675 ++-- tests/figs/administration-mesh/administration-1kmmesh-city35201.svg | 1623 ++++------ tests/figs/administration-mesh/administration-80kmmesh-pref08.svg | 23 tests/figs/data/japan-rectangle.svg | 94 tests/figs/deps.txt | 2 tests/figs/find/neighbor-mesh-10km-6meshes.svg | 25 tests/figs/find/neighbor-mesh-1km-self-contains-false.svg | 29 tests/figs/find/neighbor-mesh-1km-self-contains-true.svg | 31 tests/figs/find/neighbor-mesh-80km-7meshes.svg | 27 tests/figs/find/neighbor-mesh-80km.svg | 31 tests/figs/separate-more-fine-mesh-order/fine-separate-10km.svg | 213 - tests/figs/separate-more-fine-mesh-order/fine-separate-1km.svg | 21 tests/figs/separate-more-fine-mesh-order/fine-separate-80km.svg | 141 tests/testthat/test-administration_mesh.R | 30 tests/testthat/test-converter.R | 59 tests/testthat/test-coords_to_meshcode.R | 121 tests/testthat/test-data.R | 11 tests/testthat/test-export_mesh.R | 13 tests/testthat/test-find.R | 88 tests/testthat/test-fine_separate.R | 68 tests/testthat/test-internal.R | 65 tests/testthat/test-mesh_to_coords.R | 45 tests/testthat/test-meshcode.R |only tests/testthat/test-neighborhood.R | 34 tests/testthat/test-rmesh.R | 9 tests/testthat/test-utities.R | 42 vignettes/usage.Rmd | 2 65 files changed, 3378 insertions(+), 3171 deletions(-)
Title: FROC Analysis by Bayesian Approaches
Description: Execute BayesianFROC::fit_GUI_Shiny() (or fit_GUI_Shiny_MRMC()) for a graphical user interface via Shiny. Provides new methods for the so-called Free-response Receiver Operating Characteristic (FROC) analysis. The ultimate aim of FROC analysis is to compare observer performances, which means comparing characteristics, such as area under the curve (AUC) or figure of merit (FOM). In this package, we only use the notion of AUC for modality comparison, where by "modality", we mean imaging methods such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET), ..., etc. So there is a problem that which imaging method is better to detect lesions from shadows in radiographs. To solve modality comparison issues, this package provides new methods using hierarchical Bayesian models proposed by the author of this package. Using this package, one can obtain at least one conclusion that which imaging methods are better for finding lesions in radiographs with the case of your data. Fitting FROC statistical models is sometimes not so good, it can easily confirm by drawing FROC curves and comparing these curves and the points constructed by False Positive fractions (FPFs) and True Positive Fractions (TPFs), we can validate the goodness of fit intuitively. Such validation is also implemented by the Chi square goodness of fit statistics in the Bayesian context which means that the parameter is not deterministic, thus by integrating it with the posterior predictive measure, we get a desired value. To compare modalities (imaging methods: MRI, CT, PET, ... , etc), we evaluate AUCs for each modality. FROC is developed by Dev Chakraborty, his FROC model in his 1989 paper relies on the maximal likelihood methodology. The author modified and provided the alternative Bayesian FROC model. Strictly speaking, his model does not coincide with models in this package. In FROC context, we means by multiple reader and multiple case (MRMC) the case of the number of reader or modality is two or more. The MRMC data is available for functions of this package. I hope that medical researchers use not only the frequentist method but also alternative Bayesian methods. In medical research, many problems are considered under only frequentist methods, such as the notion of p-values. But p-value is sometimes misunderstood. Bayesian methods provide very simple, direct, intuitive answer for research questions. Combining frequentist methods with Bayesian methods, we can obtain more reliable answer for research questions. Please execute the following R scripts from the R (R studio) console, demo(demo_MRMC, package = "BayesianFROC"); demo(demo_srsc, package = "BayesianFROC"); demo(demo_stan, package = "BayesianFROC"); demo(demo_drawcurves_srsc, package = "BayesianFROC"); demo_Bayesian_FROC(); demo_Bayesian_FROC_without_pause(). References: Dev Chakraborty (1989) <doi:10.1118/1.596358> Maximum likelihood analysis of free - response receiver operating characteristic (FROC) data. Pre-print: Issei Tsunoda; Bayesian Models for free-response receiver operating characteristic analysis.
Author: Issei Tsunoda [aut, cre]
Maintainer: Issei Tsunoda <tsunoda.issei1111@gmail.com>
Diff between BayesianFROC versions 0.3.1 dated 2020-09-14 and 0.4.0 dated 2020-11-26
DESCRIPTION | 55 MD5 | 185 - NAMESPACE | 10 NEWS.md | 145 + R/BayesianFROC.R | 93 R/Color_Message.R |only R/CoronaVirus_Disease_2019.R | 4 R/DrawCurves.R | 22 R/StartupMessage.R | 44 R/check_cohomology.R |only R/check_rhat.R | 2 R/chi_square_goodness_of_fit.R | 60 R/convertFromJafroc.R | 8 R/create_dataset.R | 4 R/document_dataset_MRMC.R | 4 R/document_dataset_srsc.R | 264 ++ R/draw_latent_distribution.R | 2 R/error_plot.R |only R/extract_EAP_by_array.R | 25 R/fffaaabbb.R | 31 R/file_remove.R | 4 R/fit_Bayesian_FROC.R | 166 + R/fit_GUI.R | 2 R/fit_GUI_Shiny.R | 1371 +++++++---- R/fut_GUI_MRMC_shiny.R | 37 R/h_moll.R |only R/is_logical_0.R |only R/metadata.R | 10 R/p_value_visualization.R |only R/plot_empirical_ROC_curves.R |only R/ppp.R | 184 + R/ppp_vectorization.R |only R/showGraphicalModel.R | 36 R/stanfitExtended.R | 2 R/tracePlotFROC.R | 2 R/validation_MRMC_Create_dataList_MRMC_Hit_from_rate_etc.R | 9 R/validation_error_srsc.R | 2 README.md | 149 - build/vignette.rds |binary data/data_low_p_value.rda |only data/data_much_low_p_value.rda |only demo/00Index | 2 demo/demo_for_compilation_of_all_models.R | 2 demo/demo_ppp.R | 6 demo/demo_ppp_plot_new.R |only inst/CITATION | 12 inst/doc/Implemented_Models.R | 4 inst/doc/Implemented_Models.Rmd | 134 - inst/doc/Implemented_Models.html | 314 +- inst/doc/References.Rnw | 5 inst/doc/References.pdf |binary inst/extdata/Model_MRMC_Multinomial.stan |only inst/extdata/Model_srscVer2.stan | 12 inst/extdata/Model_srsc_multinomial.stan | 205 + man/BayesianFROC.Rd | 90 man/Confirm_hit_rates_are_correctly_made_in_case_of_MRMC.Rd | 9 man/CoronaVirus_Disease_2019.Rd | 2 man/CoronaVirus_Disease_2019_prevalence.Rd | 2 man/Credible_Interval_for_curve.Rd | 4 man/Empirical_FROC_via_ggplot.Rd | 4 man/ROC_data_creator.Rd |only man/array_of_hit_and_false_alarms_from_vector.Rd | 8 man/check_hit_is_less_than_NL.Rd | 4 man/check_rhat.Rd | 2 man/chi_square_at_replicated_data_and_MCMC_samples_MRMC.Rd | 2 man/chi_square_goodness_of_fit.Rd | 2 man/chi_square_goodness_of_fit_from_input_all_param.Rd | 55 man/chi_square_goodness_of_fit_from_input_all_param_MRMC.Rd | 4 man/color_message.Rd |only man/convertFromJafroc.Rd | 8 man/create_dataset.Rd | 4 man/data.nonconverge.srsc.Rd | 3 man/data_low_p_value.Rd |only man/data_much_low_p_value.Rd |only man/ddd.Rd | 2 man/dddddd.Rd | 2 man/draw.CFP.CTP.from.dataList.Rd | 4 man/draw_latent_signal_distribution.Rd | 2 man/extract_EAP_CI.Rd | 25 man/fffaaabbb.Rd | 11 man/fit_Bayesian_FROC.Rd | 104 man/fit_GUI_Shiny.Rd | 59 man/fit_MRMC.Rd | 4 man/fit_MRMC_versionTWO.Rd | 4 man/fit_a_model_to.Rd | 10 man/ggplotFROC.EAP.Rd | 4 man/ggplotFROC.Rd | 4 man/give_name_srsc_data.Rd | 4 man/grapes-greater-than-greater-than-grapes.Rd | 4 man/initial_values_specification_for_stan_in_case_of_MRMC.Rd | 4 man/is_length_zero.Rd |only man/is_logical_0.Rd |only man/is_stanfitExtended.Rd |only man/metadata_to_fit_MRMC.Rd | 8 man/p_value_visualization.Rd |only man/plot_FPF_and_TPF_from_a_dataset.Rd | 4 man/plot_dataset_of_ppp.Rd |only man/plot_dataset_of_ppp_MRMC.Rd |only man/plot_empirical_ROC_curves.Rd |only man/ppp_srsc.Rd | 86 man/showGM.Rd | 7 man/trace_Plot.Rd | 2 man/validation.dataset_srsc.Rd | 2 vignettes/Implemented_Models.Rmd | 134 - vignettes/References.Rnw | 5 105 files changed, 3148 insertions(+), 1178 deletions(-)
Title: Tables of Descriptive Statistics in HTML
Description: Create HTML tables of descriptive statistics, as one would expect
to see as the first table (i.e. "Table 1") in a medical/epidemiological journal
article.
Author: Benjamin Rich [aut, cre, cph]
Maintainer: Benjamin Rich <mail@benjaminrich.net>
Diff between table1 versions 1.2 dated 2020-03-23 and 1.2.1 dated 2020-11-26
DESCRIPTION | 13 - MD5 | 20 +- NEWS.md | 6 R/table1.R | 47 ++++-- build/vignette.rds |binary inst/doc/table1-examples.R | 13 - inst/doc/table1-examples.Rmd | 15 -- inst/doc/table1-examples.html | 146 +++++++++----------- man/signif_pad.Rd | 143 +++++++++---------- man/table1.Rd | 301 +++++++++++++++++++++--------------------- vignettes/table1-examples.Rmd | 15 -- 11 files changed, 356 insertions(+), 363 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 0.4.15 dated 2020-05-29 and 0.4.16 dated 2020-11-26
DESCRIPTION | 10 MD5 | 38 - NEWS.md | 21 + R/Unary.R | 89 +++- R/Utilities.R | 8 R/notation.R | 2 build/vignette.rds |binary inst/CITATION | 4 inst/doc/about-vector-arguments.html | 484 +++++++++++++----------- inst/doc/applybyname-vignette.Rmd | 4 inst/doc/applybyname-vignette.html | 140 +++++-- inst/doc/matsbyname.Rmd | 20 - inst/doc/matsbyname.html | 696 +++++++++++++++++++---------------- man/colsums_byname.Rd | 8 man/hatize_byname.Rd | 19 man/rowsums_byname.Rd | 8 tests/testthat/test_Unary.R | 77 +++ tests/testthat/test_Utilities.R | 1 vignettes/applybyname-vignette.Rmd | 4 vignettes/matsbyname.Rmd | 20 - 20 files changed, 1001 insertions(+), 652 deletions(-)