Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common univariate
statistics in concise tables available in a variety of
formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 0.8.3 dated 2018-04-16 and 0.8.4 dated 2018-06-07
DESCRIPTION | 10 ++++---- MD5 | 22 +++++++++---------- NAMESPACE | 2 - NEWS | 7 ++++++ R/dfSummary.R | 8 +++---- R/print.summarytools.R | 2 - inst/doc/Introduction.R | 2 - inst/doc/Introduction.Rmd | 4 +-- inst/doc/Introduction.html | 36 +++++++++++++++++++++++--------- inst/doc/Recommendations-rmarkdown.html | 8 +++---- man/print.summarytools.Rd | 2 - vignettes/Introduction.Rmd | 4 +-- 12 files changed, 65 insertions(+), 42 deletions(-)
Title: Easily Add Markdown Help Files to 'shiny' Inputs and Outputs
Description: Creates a lightweight way to add markdown helpfiles to 'shiny' apps,
using modal dialog boxes, with no need to observe each help button separately.
Author: Chris Thom [aut, cre]
Maintainer: Chris Thom <christopher.w.thom@outlook.com>
Diff between shinyhelper versions 0.1.1 dated 2018-05-30 and 0.2.0 dated 2018-06-07
DESCRIPTION | 7 ++-- MD5 | 38 ++++++++++++++-------- NAMESPACE | 1 NEWS.md | 42 +++++++++++++++++++++++++ R/create-help-files.R | 18 +++++++--- R/for-shiny.R | 43 ++++++++++++++++++------- R/helper.R | 41 +++++++++++++++++++++--- R/no-export.R | 47 +++++++++++----------------- R/shinyhelper-demo.R |only README.md | 78 ++++++++++++++++++++++++++++++++++++++++++----- inst/example |only man/create_help_files.Rd | 11 +++--- man/figures |only man/get_id.Rd | 2 - man/helper.Rd | 22 ++++++++++--- man/observe_helpers.Rd | 16 +++++---- man/shinyhelperDemo.Rd |only man/show_help_message.Rd | 14 +++----- man/use_shinyhelper.Rd | 7 ++-- 19 files changed, 281 insertions(+), 106 deletions(-)
Title: Tools for Antitrust Practitioners
Description: A collection of tools for antitrust practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of mergers under different competitive regimes.
Author: Charles Taragin and Michael Sandfort
Maintainer: Charles Taragin <charles.taragin@usdoj.gov>
Diff between antitrust versions 0.99.8 dated 2018-05-17 and 0.99.9 dated 2018-06-07
DESCRIPTION | 8 +++---- MD5 | 18 +++++++-------- R/antitrust_shiny.R | 1 R/auction2ndlogit.R | 48 +++--------------------------------------- build/partial.rdb |binary inst/antitrust_shiny/server.R | 23 +++++++++++--------- inst/antitrust_shiny/ui.R | 4 ++- inst/doc/manual.Rnw | 2 - inst/doc/manual.pdf |binary vignettes/manual.Rnw | 2 - 10 files changed, 36 insertions(+), 70 deletions(-)
Title: 'tigreBrowser' Database Writer
Description: Write modelling results into a database for
'tigreBrowser', a web-based tool for browsing figures and summary
data of independent model fits, such as Gaussian process models
fitted for each gene or other genomic element. The browser is
available at <https://github.com/PROBIC/tigreBrowser>.
Author: Antti Honkela [aut, cre],
Miika-Petteri Matikainen [aut]
Maintainer: Antti Honkela <antti.honkela@helsinki.fi>
Diff between tigreBrowserWriter versions 0.1.4 dated 2016-12-12 and 0.1.5 dated 2018-06-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/database.R | 2 +- README.md | 4 ++++ 4 files changed, 12 insertions(+), 8 deletions(-)
More information about tigreBrowserWriter at CRAN
Permanent link
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 1.1.0 dated 2017-08-29 and 1.1.4 dated 2018-06-07
DESCRIPTION | 15 +++---- MD5 | 27 +++++++------ NAMESPACE | 3 + NEWS.md |only R/defaults.R | 10 ++-- R/getTexPackages.R | 13 ++++++ R/texPreview.R | 53 +++++++++++++++++++++----- README.md | 3 - build/texPreview.pdf |binary inst/examples/rmarkdown/html/testCarousel.Rmd | 8 +-- inst/examples/rmarkdown/revealjs/revealjs.Rmd | 7 ++- man/texPreview.Rd | 8 +-- man/tex_opts.Rd | 4 + tests |only 14 files changed, 109 insertions(+), 42 deletions(-)
Title: Laboratory Sieve Test Reporting Functions
Description: Functions for making particle-size analysis. Sieve tests are widely used to obtain particle-size distribution of powders or granular materials.
Author: Petr Matousu
Maintainer: Petr Matousu <pmatousu@more-praha.cz>
Diff between sievetest versions 1.2.2 dated 2014-07-08 and 1.2.3 dated 2018-06-07
DESCRIPTION | 13 +++++++------ MD5 | 13 ++++++++++--- NAMESPACE | 19 ++++++++++++++++++- R/sieve_test.R | 49 ++++++++++++++++++++++++++++++++----------------- inst/ShinyApps |only 5 files changed, 67 insertions(+), 27 deletions(-)
Title: Efficient and Publishing-Oriented Workflow for Psychological
Science
Description: Toolbox for psychologists, neuropsychologists and neuroscientists.
It implements methods to create report-ready outputs for many statistical models,
as well as various convenient statistical functions used in psychological science,
such as correlation matrices and standardization.
Author: Dominique Makowski [aut, cre, cph],
Viliam Simko [ctb],
Sasha Epskamp [rev] (Sasha reviewed the package for JOSS, see
https://github.com/openjournals/joss-reviews/issues/470)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between psycho versions 0.2.3 dated 2018-05-11 and 0.2.8 dated 2018-06-07
psycho-0.2.3/psycho/R/interpret_d_posterior.R |only psycho-0.2.8/psycho/DESCRIPTION | 16 psycho-0.2.8/psycho/MD5 | 164 +- psycho-0.2.8/psycho/NAMESPACE | 43 psycho-0.2.8/psycho/NEWS.md | 48 psycho-0.2.8/psycho/R/analyze.R | 8 psycho-0.2.8/psycho/R/analyze.aov.R |only psycho-0.2.8/psycho/R/analyze.fa.R |only psycho-0.2.8/psycho/R/analyze.htest.R |only psycho-0.2.8/psycho/R/analyze.lavaan.R |only psycho-0.2.8/psycho/R/analyze.lm.R | 5 psycho-0.2.8/psycho/R/analyze.lmerModLmerTest.R | 8 psycho-0.2.8/psycho/R/analyze.stanreg.R | 792 ++++++---- psycho-0.2.8/psycho/R/assess.R | 54 psycho-0.2.8/psycho/R/bayes_cor.R |only psycho-0.2.8/psycho/R/correlation.R | 72 psycho-0.2.8/psycho/R/crawford.test.R | 15 psycho-0.2.8/psycho/R/crawford_dissociation.test.R | 4 psycho-0.2.8/psycho/R/create_intervals.R |only psycho-0.2.8/psycho/R/dprime.R | 4 psycho-0.2.8/psycho/R/find_best_model.stanreg.R | 4 psycho-0.2.8/psycho/R/find_matching_string.R |only psycho-0.2.8/psycho/R/formatting.R | 29 psycho-0.2.8/psycho/R/get_contrasts.stanreg.R | 4 psycho-0.2.8/psycho/R/get_predicted.stanreg.R | 8 psycho-0.2.8/psycho/R/hdi.R | 7 psycho-0.2.8/psycho/R/interpret_R2.R |only psycho-0.2.8/psycho/R/interpret_RMSEA.R |only psycho-0.2.8/psycho/R/interpret_bf.R | 102 + psycho-0.2.8/psycho/R/interpret_d.R | 174 ++ psycho-0.2.8/psycho/R/interpret_r.R |only psycho-0.2.8/psycho/R/model_to_priors.R |only psycho-0.2.8/psycho/R/n_factors.R | 43 psycho-0.2.8/psycho/R/power_analysis.R | 5 psycho-0.2.8/psycho/R/refdata.R |only psycho-0.2.8/psycho/R/remove_empty_cols.R |only psycho-0.2.8/psycho/R/rope.R |only psycho-0.2.8/psycho/R/summary.psychobject.R | 1 psycho-0.2.8/psycho/README.md | 57 psycho-0.2.8/psycho/inst/doc/bayesian.R | 69 psycho-0.2.8/psycho/inst/doc/bayesian.Rmd | 106 - psycho-0.2.8/psycho/inst/doc/bayesian.html | 521 ++---- psycho-0.2.8/psycho/inst/doc/overview.R | 3 psycho-0.2.8/psycho/inst/doc/overview.Rmd | 14 psycho-0.2.8/psycho/inst/doc/overview.html | 99 - psycho-0.2.8/psycho/man/analyze.Rd | 8 psycho-0.2.8/psycho/man/analyze.aov.Rd |only psycho-0.2.8/psycho/man/analyze.fa.Rd |only psycho-0.2.8/psycho/man/analyze.htest.Rd |only psycho-0.2.8/psycho/man/analyze.lavaan.Rd |only psycho-0.2.8/psycho/man/analyze.lm.Rd | 4 psycho-0.2.8/psycho/man/analyze.lmerModLmerTest.Rd | 5 psycho-0.2.8/psycho/man/analyze.stanreg.Rd | 23 psycho-0.2.8/psycho/man/assess.Rd | 2 psycho-0.2.8/psycho/man/bayes_adj_R2.Rd |only psycho-0.2.8/psycho/man/bayes_cor.Rd |only psycho-0.2.8/psycho/man/bayes_cor.test.Rd |only psycho-0.2.8/psycho/man/crawford_dissociation.test.Rd | 2 psycho-0.2.8/psycho/man/create_intervals.Rd |only psycho-0.2.8/psycho/man/find_matching_string.Rd |only psycho-0.2.8/psycho/man/format_bf.Rd |only psycho-0.2.8/psycho/man/format_digit.Rd | 4 psycho-0.2.8/psycho/man/format_loadings.Rd |only psycho-0.2.8/psycho/man/format_p.Rd | 4 psycho-0.2.8/psycho/man/get_cfa_model.Rd |only psycho-0.2.8/psycho/man/get_loadings_max.Rd |only psycho-0.2.8/psycho/man/get_std_posteriors.Rd |only psycho-0.2.8/psycho/man/interpret_R2.Rd |only psycho-0.2.8/psycho/man/interpret_R2_posterior.Rd |only psycho-0.2.8/psycho/man/interpret_RMSEA.Rd |only psycho-0.2.8/psycho/man/interpret_bf.Rd | 12 psycho-0.2.8/psycho/man/interpret_d.Rd | 16 psycho-0.2.8/psycho/man/interpret_d_posterior.Rd | 19 psycho-0.2.8/psycho/man/interpret_r.Rd |only psycho-0.2.8/psycho/man/interpret_r_posterior.Rd |only psycho-0.2.8/psycho/man/model_to_priors.Rd |only psycho-0.2.8/psycho/man/n_factors.Rd | 8 psycho-0.2.8/psycho/man/plot_loadings.Rd |only psycho-0.2.8/psycho/man/power_analysis.Rd | 4 psycho-0.2.8/psycho/man/refdata.Rd |only psycho-0.2.8/psycho/man/remove_empty_cols.Rd |only psycho-0.2.8/psycho/man/reorder_matrix.Rd |only psycho-0.2.8/psycho/man/rope.Rd |only psycho-0.2.8/psycho/tests/testthat/test-analyze.aov.R |only psycho-0.2.8/psycho/tests/testthat/test-analyze.fa.R |only psycho-0.2.8/psycho/tests/testthat/test-analyze.htest.R |only psycho-0.2.8/psycho/tests/testthat/test-analyze.lavaan.R |only psycho-0.2.8/psycho/tests/testthat/test-analyze.stanreg.R | 41 psycho-0.2.8/psycho/tests/testthat/test-assess.R | 2 psycho-0.2.8/psycho/tests/testthat/test-bayes_cor.R |only psycho-0.2.8/psycho/tests/testthat/test-correlation.R | 15 psycho-0.2.8/psycho/tests/testthat/test-create_intervals.R |only psycho-0.2.8/psycho/tests/testthat/test-dprime.R | 2 psycho-0.2.8/psycho/tests/testthat/test-find_matching_string.R |only psycho-0.2.8/psycho/tests/testthat/test-formatting.R | 4 psycho-0.2.8/psycho/tests/testthat/test-get_contrasts.stanreg.R | 4 psycho-0.2.8/psycho/tests/testthat/test-hdi.R | 1 psycho-0.2.8/psycho/tests/testthat/test-interpret_R2.R |only psycho-0.2.8/psycho/tests/testthat/test-interpret_RMSEA.R |only psycho-0.2.8/psycho/tests/testthat/test-interpret_bf.R | 5 psycho-0.2.8/psycho/tests/testthat/test-interpret_d.R |only psycho-0.2.8/psycho/tests/testthat/test-interpret_r.R |only psycho-0.2.8/psycho/tests/testthat/test-model_to_priors.R |only psycho-0.2.8/psycho/tests/testthat/test-odds_to_probs.R | 9 psycho-0.2.8/psycho/tests/testthat/test-power_analysis.R | 2 psycho-0.2.8/psycho/tests/testthat/test-refdata.R |only psycho-0.2.8/psycho/tests/testthat/test-remove_empty_cols.R |only psycho-0.2.8/psycho/tests/testthat/test-rnorm_perfect.R | 5 psycho-0.2.8/psycho/vignettes/bayesian.Rmd | 106 - psycho-0.2.8/psycho/vignettes/overview.Rmd | 14 110 files changed, 1730 insertions(+), 1070 deletions(-)
Title: Bindings for 'Tabula' PDF Table Extractor Library
Description: Bindings for the 'Tabula' <http://tabula.technology/> 'Java'
library, which can extract tables from PDF documents. The 'tabulizerjars'
package <https://github.com/ropensci/tabulizerjars> provides versioned
'Java' .jar files, including all dependencies, aligned to releases of
'Tabula'.
Author: Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>),
Tom Paskhalis [cre] (<https://orcid.org/0000-0001-9298-8850>),
David Gohel [ctb] (rOpenSci reviewer),
Lincoln Mullen [ctb] (rOpenSci reviewer)
Maintainer: Tom Paskhalis <tpaskhalis@gmail.com>
Diff between tabulizer versions 0.2.1 dated 2018-05-24 and 0.2.2 dated 2018-06-07
DESCRIPTION | 6 - MD5 | 20 +++--- NEWS.md | 6 + R/extract_tables.R | 22 +++++- R/output.R | 36 ++++++---- README.md | 118 +++++++++++++++++++----------------- inst/doc/tabulizer.Rmd | 26 ++++--- inst/doc/tabulizer.html | 12 +-- man/extract_tables.Rd | 11 ++- tests/testthat/test_write_methods.R | 15 +--- vignettes/tabulizer.Rmd | 26 ++++--- 11 files changed, 168 insertions(+), 130 deletions(-)
Title: Spatial Extent Tools
Description: Functions to produce a fully fledged 'geo-spatial' object extent as a
'SpatialPolygonsDataFrame'. Also included are functions to generate polygons
from raster data using 'quadmesh' techniques, a round number buffered extent, and
general spatial-extent and 'raster-like' extent helpers missing from the originating
packages. Some latitude-based tools for polar maps are included.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between spex versions 0.4.0 dated 2017-08-03 and 0.5.0 dated 2018-06-07
spex-0.4.0/spex/R/qm_rasterToPolygons.r |only spex-0.4.0/spex/R/spex-package.r |only spex-0.5.0/spex/DESCRIPTION | 12 +++---- spex-0.5.0/spex/MD5 | 32 +++++++++++-------- spex-0.5.0/spex/NAMESPACE | 5 ++ spex-0.5.0/spex/NEWS.md | 12 +++++++ spex-0.5.0/spex/R/latitude.R |only spex-0.5.0/spex/R/qm_rasterToPolygons.R |only spex-0.5.0/spex/R/spex-package.R |only spex-0.5.0/spex/R/spex.R | 14 ++------ spex-0.5.0/spex/data/ice.rda |only spex-0.5.0/spex/man/ice.Rd |only spex-0.5.0/spex/man/latitudecircle.Rd |only spex-0.5.0/spex/man/latmask.Rd |only spex-0.5.0/spex/man/lux.Rd | 2 - spex-0.5.0/spex/man/polygonize.Rd | 23 ++++++++----- spex-0.5.0/spex/man/psf.Rd | 2 - spex-0.5.0/spex/man/spex-package.Rd |only spex-0.5.0/spex/man/spex.Rd | 23 +------------ spex-0.5.0/spex/tests/testthat/Rplots.pdf |only spex-0.5.0/spex/tests/testthat/test-latitude.R |only spex-0.5.0/spex/tests/testthat/test-sf-from-raster.R | 13 +++++-- spex-0.5.0/spex/tests/testthat/test-spex-extent.R | 6 +-- 23 files changed, 79 insertions(+), 65 deletions(-)
Title: Access your Coletum's Data from API
Description: Get your data (forms, structures, answers) from Coletum
<https://coletum.com> to handle and analyse.
Author: André Smaniotto [aut, cre],
Marcelo Magnani [aut],
Rodrigo Sant'Ana [aut],
GeoSapiens [cph, fnd]
Maintainer: André Smaniotto <smaniotto@geosapiens.com.br>
Diff between RColetum versions 0.1.0 dated 2018-06-06 and 0.1.1 dated 2018-06-07
DESCRIPTION | 10 +++++++--- MD5 | 4 ++-- man/RColetum-package.Rd | 6 ++++++ 3 files changed, 15 insertions(+), 5 deletions(-)
Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes. It can import and export data in
ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi',
'POPDIST', 'STRand', and binary presence/absence formats. It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account. These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R. Allelic diversity
statistics and Polymorphic Information Content are also available. polysat can
assist the user in estimating the ploidy of samples, and it can estimate allele
frequencies in populations, calculate pairwise or global differentiation statistics
based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'.
Functions are also included for assigning alleles to isoloci in cases where one pair
of microsatellite primers amplifies alleles from two or more independently
segregating isoloci. polysat is described by Clark and Jasieniuk (2011)
<doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier (2017)
<doi:10.1111/1755-0998.12639>.
Author: Lindsay V. Clark [aut, cre],
Handunnethi Nihal de Silva [ctb]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polysat versions 1.7-2 dated 2017-08-17 and 1.7-3 dated 2018-06-07
polysat-1.7-2/polysat/vignettes/allopolyVignette.pdf |only polysat-1.7-2/polysat/vignettes/polysattutorial.pdf |only polysat-1.7-3/polysat/DESCRIPTION | 21 polysat-1.7-3/polysat/MD5 | 49 - polysat-1.7-3/polysat/NAMESPACE | 5 polysat-1.7-3/polysat/NEWS | 16 polysat-1.7-3/polysat/R/RcppExports.R |only polysat-1.7-3/polysat/R/classes_generics_methods.R | 10 polysat-1.7-3/polysat/R/individual_distance.R | 26 polysat-1.7-3/polysat/R/population_stats.R | 762 +++++++------------ polysat-1.7-3/polysat/build |only polysat-1.7-3/polysat/inst/CITATION | 3 polysat-1.7-3/polysat/inst/doc/allopolyVignette.R |only polysat-1.7-3/polysat/inst/doc/allopolyVignette.Rnw |only polysat-1.7-3/polysat/inst/doc/allopolyVignette.pdf |binary polysat-1.7-3/polysat/inst/doc/polysattutorial.R | 319 +++++++ polysat-1.7-3/polysat/inst/doc/polysattutorial.Rnw |only polysat-1.7-3/polysat/inst/doc/polysattutorial.pdf |binary polysat-1.7-3/polysat/man/alleleCorrelations.Rd | 2 polysat-1.7-3/polysat/man/deSilvaFreq.Rd | 2 polysat-1.7-3/polysat/man/gendata.to.genind.Rd | 16 polysat-1.7-3/polysat/man/genotypeProbs.Rd | 2 polysat-1.7-3/polysat/man/meandistance.matrix.Rd | 2 polysat-1.7-3/polysat/man/plotSSAllo.Rd | 2 polysat-1.7-3/polysat/man/polysat-internal.Rd | 46 - polysat-1.7-3/polysat/man/recodeAllopoly.Rd | 2 polysat-1.7-3/polysat/man/simAllopoly.Rd | 2 polysat-1.7-3/polysat/src |only polysat-1.7-3/polysat/vignettes/polysattutorial.Rnw | 4 29 files changed, 700 insertions(+), 591 deletions(-)
Title: Panel-Corrected Standard Error Estimation in R
Description: A function to estimate
panel-corrected standard errors. Data may contain balanced or
unbalanced panels.
Author: Delia Bailey <delia.bailey@gmail.com> and Jonathan N. Katz
<jkatz@caltech.edu>
Maintainer: Delia Bailey <delia.bailey@gmail.com>
Diff between pcse versions 1.9.1 dated 2018-04-03 and 1.9.1.1 dated 2018-06-07
DESCRIPTION | 10 +++++----- MD5 | 9 ++++++--- build |only inst/doc/pcse.pdf |binary man/pcse-package.Rd | 39 ++++++++++++++------------------------- man/pcse.Rd |only 6 files changed, 25 insertions(+), 33 deletions(-)
Title: Computation of Parameters Used in Preliminary Assessment of
Conservation Status
Description: Multi-species estimation of geographical range parameters
for preliminary assessment of conservation status following Criterion B of the
International Union for Conservation of Nature (IUCN,
see <http://www.iucnredlist.org>).
Author: Gilles Dauby
Maintainer: Gilles Dauby <gildauby@gmail.com>
Diff between ConR versions 1.2.1 dated 2017-06-13 and 1.2.2 dated 2018-06-07
DESCRIPTION | 8 MD5 | 40 - NAMESPACE | 8 R/IUCNeval.functionv11.R | 216 +++++--- README.md |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/my-vignette.R | 6 inst/doc/my-vignette.Rmd | 38 + inst/doc/my-vignette.html | 318 ++++++------ man/EOO.computing.Rd | 17 man/IUCN.eval.Rd | 23 man/subpop.comp.Rd | 2 tests/testthat/EOO.results.csv |only tests/testthat/test-3.R | 4 vignettes/IUCN__results_map/IUCN_Berlinia_bruneelii.png |binary vignettes/IUCN__results_map/IUCN_Oncocalamus_mannii.png |binary vignettes/IUCN__results_map/IUCN_Platycoryne_guingangae.png |binary vignettes/IUCN__results_map/IUCN_Psychotria_minuta.png |binary vignettes/IUCN__results_map/number_threatened_sp.png |binary vignettes/IUCN__results_map/proportion_threatened_sp.png |binary vignettes/my-vignette.Rmd | 38 + 22 files changed, 460 insertions(+), 258 deletions(-)
Title: Biological Risk Assessment
Description: A spatio-temporal exposure-hazard model for assessing biological
risk and impact. The model is based on stochastic geometry for describing
the landscape and the exposed individuals, a dispersal kernel for the
dissemination of contaminants and an ecotoxicological equation.
Walker E, Leclerc M, Rey JF, Beaudouin R, Soubeyrand S, and Messean A, (2017),
A Spatio-Temporal Exposure-Hazard Model for Assessing Biological Risk and Impact,
Risk Analysis, <doi:10.1111/risa.12941>.
Author: Emily Walker [aut],
Jean-Francois Rey [aut, cre],
Melen Leclerc [aut],
Samuel Soubeyrand [ctb],
Marc Bourotte [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inra.fr>
Diff between briskaR versions 0.1.1 dated 2017-09-04 and 0.1.2 dated 2018-06-07
DESCRIPTION | 21 + MD5 | 18 - R/briskaR.R | 4 build/vignette.rds |binary data/Precipitation.rda |binary data/maize.emitted_pollen.rda |binary data/maize.proportion_pollen.rda |binary data/maize_65.rda |binary inst/doc/demonstrations.html | 428 ++++++++++++++++++++++++++------------- man/briskaR-package.Rd | 4 10 files changed, 312 insertions(+), 163 deletions(-)
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Can calculate various string distances based on edits
(Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q-
gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An
implementation of soundex is provided as well. Distances can be computed between
character vectors while taking proper care of encoding or between integer
vectors representing generic sequences. Stringdist is built for speed and
paralellizes computation using 'openMP'. An API for C or C++ is exposed as well.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb],
Chris Muir [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.4.7 dated 2018-03-13 and 0.9.5.0 dated 2018-06-07
DESCRIPTION | 18 ++++++++++------ MD5 | 26 +++++++++++++++--------- NEWS | 8 ++++++- R/doc_api.R |only R/stringdist.R | 43 +++++++++++----------------------------- inst/doc |only inst/include |only man/stringdist-api.Rd |only man/stringdist.Rd | 19 +++-------------- src/Makevars | 2 - src/Makevars.win |only src/R_register_native.c | 12 ++++++++++- src/Rstringdist.c | 2 - src/stringdist.c | 2 - src/stringdist_pkg.h |only tests/testthat/testStringdist.R | 3 -- 16 files changed, 65 insertions(+), 70 deletions(-)
Title: Build and Run Spatially Explicit Agent-Based Models
Description: Build and run spatially explicit
agent-based models using only the R platform. 'NetLogoR' follows the same
framework as the 'NetLogo' software
(Wilensky, 1999 <http://ccl.northwestern.edu/netlogo/>) and is a translation
in R of the structure and functions of 'NetLogo'.
'NetLogoR' provides new R classes to define model agents and functions to
implement spatially explicit agent-based models in the R environment.
This package allows benefiting of the fast and easy coding phase from the
highly developed 'NetLogo' framework, coupled with the versatility, power
and massive resources of the R software.
Examples of three models (Ants <http://ccl.northwestern.edu/netlogo/models/Ants>,
Butterfly (Railsback and Grimm, 2012) and Wolf-Sheep-Predation
<http://ccl.northwestern.edu/netlogo/models/WolfSheepPredation>) written using
'NetLogoR' are available. The 'NetLogo' code of the original version of these
models is provided alongside.
A programming guide inspired from the 'NetLogo' Programming Guide
(<https://ccl.northwestern.edu/netlogo/docs/programming.html>) and a dictionary
of 'NetLogo' primitives (<https://ccl.northwestern.edu/netlogo/docs/dictionary.html>)
equivalences are also available.
NOTE: To increment 'time', these functions can use a for loop or can be
integrated with a discrete event simulator, such as 'SpaDES'
(<https://cran.r-project.org/package=SpaDES>).
The suggested package 'fastshp' can be installed with
'install.packages("fastshp", repos = "https://rforge.net", type = "source")'.
Author: Sarah Bauduin [aut, cre],
Eliot J B McIntire [aut],
Alex M Chubaty [aut],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Sarah Bauduin <sarahbauduin@hotmail.fr>
Diff between NetLogoR versions 0.3.2 dated 2018-02-12 and 0.3.3 dated 2018-06-07
.aspell/defaults.R | 12 DESCRIPTION | 54 MD5 | 310 NAMESPACE | 488 NEWS.md | 60 R/Agent-classes.R | 80 R/Classes.R | 130 R/NetLogoR-package.R | 40 R/agentMatrix-Class-methods.R | 1560 +- R/agentset-functions.R | 4088 +++--- R/function-arguments.R | 176 R/patch-functions.R | 1645 +- R/plot.R | 148 R/quickPlot.R | 362 R/spades-functions.R | 518 R/turtle-functions.R | 6299 ++++------ R/world-functions.R | 1138 - R/worldNLR-classes-methods.R | 1112 - README.md | 54 build/vignette.rds |binary inst/doc/NLR-Dictionary.Rmd | 1862 +- inst/doc/NLR-Dictionary.html | 1354 +- inst/doc/ProgrammingGuide.R | 88 inst/doc/ProgrammingGuide.Rmd | 510 inst/doc/ProgrammingGuide.html | 438 inst/examples/Ants/Ants.R | 528 inst/examples/Ants/Ants.nlogo | 1276 +- inst/examples/Butterfly/Butterfly-1.R | 132 inst/examples/Butterfly/Butterfly-1.nlogo | 946 - inst/examples/Wolf-Sheep-Predation/README.txt | 8 inst/examples/Wolf-Sheep-Predation/Wolf-Sheep-Predation-SpaDES.R | 100 inst/examples/Wolf-Sheep-Predation/Wolf-Sheep-Predation.R | 638 - inst/examples/Wolf-Sheep-Predation/Wolf-Sheep-Predation.nlogo | 1652 +- inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/LICENSE | 42 inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/README.txt | 6 inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.R | 922 - inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/WolfSheepPredation.Rmd | 154 inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/citation.bib | 18 inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/tests/testthat/test-template.R | 166 inst/examples/Wolf-Sheep-Predation/WolfSheepPredation/tests/unitTests.R | 18 man/NLall.Rd | 152 man/NLany.Rd | 106 man/NLcount.Rd | 96 man/NLdist.Rd | 174 man/NLset.Rd | 176 man/NLwith.Rd | 168 man/NLworldIndex.Rd | 82 man/NetLogoR-package.Rd | 68 man/PxcorPycorFromCell.Rd | 74 man/Subsetting.Rd | 64 man/agentClasses-class.Rd | 38 man/agentMatrix-bind-methods.Rd | 46 man/agentMatrix-class.Rd | 116 man/agentMatrix-compare-methods.Rd | 40 man/agentMatrix-show-methods.Rd | 70 man/agentMatrix.Rd | 96 man/bbox.Rd | 90 man/bk.Rd | 168 man/canMove.Rd | 90 man/cellFromPxcorPycor.Rd | 74 man/clearPatches.Rd | 94 man/coordinates.Rd | 38 man/createOTurtles.Rd | 124 man/createTurtles.Rd | 150 man/createWorld.Rd | 120 man/die.Rd | 94 man/diffuse.Rd | 148 man/downhill.Rd | 158 man/dx.Rd | 108 man/dy.Rd | 108 man/extract-methods.Rd | 256 man/face.Rd | 146 man/fargs.Rd | 176 man/fd.Rd | 154 man/hatch.Rd | 120 man/home.Rd | 126 man/inCone.Rd | 174 man/inRadius.Rd | 160 man/initialize-agentMatrix-method.Rd | 50 man/inspect.Rd | 84 man/isNLclass.Rd | 136 man/layoutCircle.Rd | 130 man/left.Rd | 94 man/maxNof.Rd | 168 man/maxOneOf.Rd | 172 man/maxPxcor.Rd | 76 man/maxPycor.Rd | 76 man/minNof.Rd | 168 man/minOneOf.Rd | 172 man/minPxcor.Rd | 76 man/minPycor.Rd | 76 man/moveTo.Rd | 124 man/nOf.Rd | 158 man/neighbors.Rd | 133 man/noPatches.Rd | 62 man/noTurtles.Rd | 62 man/of.Rd | 152 man/oneOf.Rd | 148 man/other.Rd | 130 man/pExist.Rd | 90 man/patch.Rd | 148 man/patchAhead.Rd | 116 man/patchAt.Rd | 144 man/patchDistDir.Rd | 142 man/patchHere.Rd | 98 man/patchLeft.Rd | 132 man/patchRight.Rd | 134 man/patchSet.Rd | 92 man/patches.Rd | 80 man/plotMethods.Rd | 112 man/projNowhere.Rd | 34 man/quickPlot-methods.Rd | 176 man/quickPlottables-class.Rd | 66 man/randomPxcor.Rd | 80 man/randomPycor.Rd | 80 man/randomXYcor.Rd | 72 man/randomXcor.Rd | 88 man/randomYcor.Rd | 88 man/raster2world.Rd | 96 man/right.Rd | 94 man/setXY.Rd | 140 man/show-methods.Rd | 36 man/sortOn.Rd | 156 man/spdf2turtles.Rd | 76 man/sprout.Rd | 148 man/stackWorlds.Rd | 68 man/subHeadings.Rd | 146 man/tExist.Rd | 108 man/towards.Rd | 152 man/turtle.Rd | 116 man/turtleSet.Rd | 100 man/turtles2spdf.Rd | 64 man/turtlesAt.Rd | 175 man/turtlesOn.Rd | 154 man/turtlesOwn.Rd | 96 man/updateList.Rd | 98 man/uphill.Rd | 158 man/withMax.Rd | 156 man/withMin.Rd | 156 man/world2raster.Rd | 82 man/worldArray-class.Rd | 36 man/worldHeight.Rd | 76 man/worldMatrix-class.Rd | 98 man/worldNLR-class.Rd | 28 man/worldWidth.Rd | 76 man/wrap.Rd | 192 tests/test-all.R | 8 tests/testthat/test-NetLogoR-classes.R | 290 tests/testthat/test-agentMatrix.R | 796 - tests/testthat/test-agentset-functions.R | 1644 +- tests/testthat/test-patch-functions.R | 1238 - tests/testthat/test-plotting.R | 168 tests/testthat/test-spelling.R | 58 tests/testthat/test-turtle-functions.R | 2436 +-- tests/testthat/test-world-functions.R | 156 vignettes/NLR-Dictionary.Rmd | 1862 +- vignettes/ProgrammingGuide.Rmd | 510 157 files changed, 25123 insertions(+), 25117 deletions(-)
Title: Goodness of Fit Test for Continuous Distribution Functions
Description: Computes the test statistic and p-value of the Cramer-von Mises and Anderson-Darling test for some continuous distribution functions proposed by Chen and Balakrishnan (1995) <http://asq.org/qic/display-item/index.html?item=11407>. In addition to our classic distribution functions here, we calculate the Goodness of Fit (GoF) test to dataset which follows the extreme value distribution function, without remembering the formula of distribution/density functions. Calculates the Value at Risk (VaR) and Average VaR are another important risk factors which are estimated by using well-known distribution functions. Pflug and Romisch (2007, ISBN: 9812707409) is a good reference to study the properties of risk measures.
Author: Ali Saeb
Maintainer: Ali Saeb <ali.saeb@gmail.com>
Diff between gnFit versions 0.1.0 dated 2017-11-05 and 0.2.0 dated 2018-06-07
DESCRIPTION | 8 ++++---- MD5 | 11 +++++++---- NAMESPACE | 5 +++-- R/gnfit.R | 4 ++-- R/rskFac.R |only README.md |only man/gnfit.Rd | 4 ++-- man/rskFac.Rd |only 8 files changed, 18 insertions(+), 14 deletions(-)
Title: Fast Hierarchical Clustering Routines for R and 'Python'
Description: This is a two-in-one package which provides interfaces to
both R and 'Python'. It implements fast hierarchical, agglomerative
clustering routines. Part of the functionality is designed as drop-in
replacement for existing routines: linkage() in the 'SciPy' package
'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the
'flashClust' package. It provides the same functionality with the
benefit of a much faster implementation. Moreover, there are
memory-saving routines for clustering of vector data, which go beyond
what the existing packages provide. For information on how to install
the 'Python' files, see the file INSTALL in the source distribution.
Based on the present package, Christoph Dalitz also wrote a pure 'C++'
interface to 'fastcluster':
<http://informatik.hsnr.de/~dalitz/data/hclust>.
Author: Daniel Müllner [aut, cph, cre],
Google Inc. [cph]
Maintainer: Daniel Müllner <daniel@danifold.net>
Diff between fastcluster versions 1.1.23 dated 2017-08-21 and 1.1.25 dated 2018-06-07
DESCRIPTION | 30 +++++--- INSTALL | 5 - LICENSE | 4 - MD5 | 38 +++++----- NEWS | 19 ++++- R/fastcluster.R | 9 +- README | 8 +- build/vignette.rds |binary inst/doc/fastcluster.Rtex | 16 +++- inst/doc/fastcluster.pdf |binary src/fastcluster.cpp | 96 ------------------------- src/fastcluster_R.cpp | 109 ++++++++++++----------------- src/python/fastcluster.py | 9 +- src/python/fastcluster_python.cpp | 141 -------------------------------------- src/python/setup.py | 12 +-- src/python/tests/nantest.py | 6 + src/python/tests/test.py | 6 + src/python/tests/vectortest.py | 6 + tests/test_fastcluster.R | 5 - vignettes/fastcluster.Rtex | 16 +++- 20 files changed, 178 insertions(+), 357 deletions(-)
Title: Scrape Lake Metadata Tables from Wikipedia
Description: Scrape lake metadata tables from Wikipedia <http://www.wikipedia.org>.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>)
Maintainer: Joseph Stachelek <stachel2@msu.edu>
Diff between wikilake versions 0.3 dated 2017-07-10 and 0.4 dated 2018-06-07
DESCRIPTION | 12 +- MD5 | 31 +++---- NAMESPACE | 3 NEWS.md | 4 R/get.R | 37 -------- R/units.R |only R/utils.R | 159 ++++++++++++++++++++++++++++++++---- R/wikilake-package.R | 2 README.md | 72 ++++++++++------ build/vignette.rds |binary data/milakes.rda |binary inst/doc/scrape_michigan_lakes.html | 6 - tests/testthat/test-lake_wiki.R | 12 ++ tools/images/mapping-1.png |binary tools/images/mapping2-1.png |binary tools/images/mapping3-1.png |binary tools/images/worldmapping-1.png |binary 17 files changed, 235 insertions(+), 103 deletions(-)
Title: Blind Source Separation and Supervised Dimension Reduction for
Time Series
Description: Different estimates are provided to solve the blind source separation problem for multivariate time series with stochastic volatility (Matilainen, Nordhausen and Oja (2015) <doi:10.1016/j.spl.2015.04.033>; Matilainen, Miettinen, Nordhausen, Oja and Taskinen (2017) <doi:10.17713/ajs.v46i3-4.671>) and supervised dimension reduction problem for multivariate time series (Matilainen, Croux, Nordhausen and Oja (2017) <doi:10.1016/j.ecosta.2017.04.002>). Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace.
Author: Markus Matilainen, Christophe Croux, Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen, Joni Virta
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>
Diff between tsBSS versions 0.4.1 dated 2018-05-06 and 0.5.0 dated 2018-06-07
DESCRIPTION | 14 +++--- MD5 | 25 ++++++++-- NAMESPACE | 6 +- R/AMUSEasymp.r |only R/AMUSEboot.R |only R/AMUSEladle.R |only R/LADLEinternal.R |only R/SOBIasymp.R |only R/SOBIboot.R |only R/SOBIladle.R |only inst/ChangeLog | 3 + man/AMUSEasymp.Rd |only man/AMUSEboot.Rd |only man/AMUSEladle.Rd |only man/SOBIasymp.Rd |only man/SOBIboot.Rd |only man/SOBIladle.Rd |only man/tsBSS-package.Rd | 23 +++++++-- src/bb.c | 20 ++++++++ src/tsBSS.cpp | 119 +++++++++++++++++++++++++++++++++++++++++++++++++++ 20 files changed, 188 insertions(+), 22 deletions(-)
Title: Data-Driven Identification of SVAR Models
Description: Implements data-driven identification methods for structural vector autoregressive (SVAR) models.
Based on an existing VAR model object (provided by e.g. VAR() from the 'vars' package), the structural
impact matrix is obtained via data-driven identification techniques (i.e. changes in volatility (Rigobon, R. (2003) <doi:10.1162/003465303772815727>),
least dependent innovations (Herwartz, H., Ploedt, M., (2016) <doi:10.1016/j.jimonfin.2015.11.001>) or non-Gaussian maximum likelihood (Lanne, M., Meitz, M., Saikkonen, P. (2017) <doi:10.1016/j.jeconom.2016.06.002>).
Author: Alexander Lange [aut, cre],
Bernhard Dalheimer [aut],
Helmut Herwartz [aut],
Simone Maxand [aut],
Hannes Riebl [ctb]
Maintainer: Alexander Lange <alexander.lange@uni-goettingen.de>
Diff between svars versions 1.1.2 dated 2018-03-06 and 1.2.0 dated 2018-06-07
svars-1.1.2/svars/R/likelihoodFunction.R |only svars-1.2.0/svars/DESCRIPTION | 11 svars-1.2.0/svars/MD5 | 87 +++--- svars-1.2.0/svars/NAMESPACE | 3 svars-1.2.0/svars/R/Wald.test.R | 6 svars-1.2.0/svars/R/bootstrap_mb.R | 102 ++++---- svars-1.2.0/svars/R/bootstrap_wild.R | 106 ++++---- svars-1.2.0/svars/R/chow.test.R | 4 svars-1.2.0/svars/R/fev.R | 4 svars-1.2.0/svars/R/hd.R | 10 svars-1.2.0/svars/R/id.cv.R | 18 - svars-1.2.0/svars/R/id.cvm.R | 15 - svars-1.2.0/svars/R/id.ngml.R | 107 +------- svars-1.2.0/svars/R/id.st.R |only svars-1.2.0/svars/R/id_ngml_boot.R | 90 ------- svars-1.2.0/svars/R/id_st_boot.R |only svars-1.2.0/svars/R/identifyVolatility.R | 51 ++-- svars-1.2.0/svars/R/identifyVolatility_boot.R | 4 svars-1.2.0/svars/R/imrf.R | 2 svars-1.2.0/svars/R/iterative_smooth_transition.R |only svars-1.2.0/svars/R/js_test.R | 2 svars-1.2.0/svars/R/ld.dc.R | 19 - svars-1.2.0/svars/R/likelihood_cv.R |only svars-1.2.0/svars/R/likelihood_ngml.R |only svars-1.2.0/svars/R/likelihood_st.R |only svars-1.2.0/svars/R/plot.svars.R |only svars-1.2.0/svars/R/plot_hd.R | 20 + svars-1.2.0/svars/R/summary.svars.R | 33 ++ svars-1.2.0/svars/R/y_lag_cr.R |only svars-1.2.0/svars/README.md | 3 svars-1.2.0/svars/data/LN.rda |only svars-1.2.0/svars/man/LN.Rd |only svars-1.2.0/svars/man/chow.test.Rd | 4 svars-1.2.0/svars/man/fev.Rd | 5 svars-1.2.0/svars/man/hd.Rd | 5 svars-1.2.0/svars/man/id.cv.Rd | 2 svars-1.2.0/svars/man/id.cvm.Rd | 8 svars-1.2.0/svars/man/id.dc.Rd | 4 svars-1.2.0/svars/man/id.ngml.Rd | 4 svars-1.2.0/svars/man/id.st.Rd |only svars-1.2.0/svars/man/imrf.Rd | 3 svars-1.2.0/svars/man/js.test.Rd | 2 svars-1.2.0/svars/man/mb.boot.Rd | 3 svars-1.2.0/svars/man/svars-package.Rd | 9 svars-1.2.0/svars/man/wild.boot.Rd | 5 svars-1.2.0/svars/tests/testthat/test-id_cv.R | 92 +++---- svars-1.2.0/svars/tests/testthat/test-id_ngml.R | 98 +++---- svars-1.2.0/svars/tests/testthat/test-likelihood_cv.R |only svars-1.2.0/svars/tests/testthat/test-likelihood_ngml.R |only svars-1.2.0/svars/tests/testthat/test-likelihood_st.R |only svars-1.2.0/svars/tests/testthat/test-mb_boot.R | 204 ++++++++-------- svars-1.2.0/svars/tests/testthat/test-wild_boot.R | 204 ++++++++-------- 52 files changed, 652 insertions(+), 697 deletions(-)
Title: Compact and Flexible Summaries of Data
Description: A simple to use summary function that can be used with pipes
and displays nicely in the console. The default summary statistics may be
modified by the user as can the default formatting. Support for data frames
and vectors is included, and users can implement their own skim methods for
specific object types as described in a vignette. Default summaries include
support for inline spark graphs. Instructions for managing these on
specific operating systems are given in the "Using skimr" vignette and the
README.
Author: Amelia McNamara [aut],
Eduardo Arino de la Rubia [aut],
Hao Zhu [aut],
Julia Lowndes [ctb],
Shannon Ellis [aut],
Elin Waring [cre],
Michael Quinn [aut],
Hope McLeod [ctb],
Hadley Wickham [ctb],
Kirill Müller [ctb],
RStudio, Inc. [cph] (Spark functions),
Connor Kirkpatrick [ctb],
Scott Brenstuhl [ctb],
Patrick Schratz [ctb],
lbusett [ctb],
Mikko Korpela [ctb],
Jennifer Thompson [ctb],
Harris McGehee [ctb]
Maintainer: Elin Waring <elin.waring@gmail.com>
Diff between skimr versions 1.0.2 dated 2018-04-02 and 1.0.3 dated 2018-06-07
DESCRIPTION | 12 - MD5 | 56 ++++---- NAMESPACE | 8 - NEWS.md | 17 ++ R/formats.R | 25 +++ R/functions.R | 26 +++- R/kable.R | 11 + R/options.R | 7 - R/pander.R | 15 +- R/skim.R | 13 -- R/skim_print.R | 19 +- R/skim_v.R | 5 R/skimr-package.R | 4 R/utils.R | 20 +++ README.md | 181 +++++++++++++--------------- inst/doc/Skimr_defaults.html | 10 - inst/doc/Supporting_additional_objects.html | 4 inst/doc/Using_skimr.html | 88 +++++++------ man/fix_windows_histograms.Rd |only man/pander.Rd | 18 +- man/skim.Rd | 2 man/skim_format.Rd | 20 ++- man/skim_with.Rd | 19 ++ tests/testthat/helper-options.R |only tests/testthat/test-formats.R | 36 ++++- tests/testthat/test-functions.R | 152 ++++++++++------------- tests/testthat/test-skim.R | 4 tests/testthat/test-skim_print.R | 52 ++++---- tests/testthat/test-skim_v.R | 34 +++-- tests/testthat/test-summary.R | 16 +- 30 files changed, 506 insertions(+), 368 deletions(-)
Title: The ScottKnott Clustering Algorithm
Description: Division of an ANOVA experiment treatment means into homogeneous distinct groups using the clustering method of Scott & Knott.
Author: Enio Jelihovschi, José Cláudio Faria and Ivan Bezerra Allaman
Maintainer: Ivan Bezerra Allaman <ivanalaman@gmail.com>
Diff between ScottKnott versions 1.2-5 dated 2014-09-29 and 1.2-7 dated 2018-06-07
ChangeLog | 8 ++++++++ DESCRIPTION | 16 ++++++---------- MD5 | 10 +++++----- NAMESPACE | 15 ++++++++++++++- R/SK.nest.aov.R | 4 ++-- inst/CITATION | 6 +++--- 6 files changed, 38 insertions(+), 21 deletions(-)
Title: Regularized Simultaneous Component Based Data Integration
Description: It performs regularized simultaneous component based data
integration for multiblock data.
Author: Zhengguo Gu [aut, cre],
Katrijn Van Deun [aut]
Maintainer: Zhengguo Gu <z.gu@uvt.nl>
Diff between RegularizedSCA versions 0.5.3 dated 2018-04-12 and 0.5.4 dated 2018-06-07
DESCRIPTION | 6 +-- MD5 | 12 +++--- R/maxLGlasso.R | 76 ++++++++++++++++++++++++-------------------- README.md | 5 ++ build/vignette.rds |binary inst/doc/RSCA-vignette.html | 4 +- man/maxLGlasso.Rd | 2 - 7 files changed, 58 insertions(+), 47 deletions(-)
More information about RegularizedSCA at CRAN
Permanent link
Title: Interpolate Munsell Renotation Data from Hue/Chroma to CIE/RGB
Description: Methods for interpolating data in the Munsell color system following the ASTM D-1535 standard. Hues and chromas with decimal values can be interpolated and converted to/from the Munsell color system and CIE xyY, CIE XYZ, CIE Lab, CIE Luv, or RGB. Based on the work by Paul Centore, "The Munsell and Kubelka-Munk Toolbox".
Author: Jose Gama [aut, trl],
Paul Centore [aut, cph],
Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between munsellinterpol versions 1.0.2 dated 2015-07-23 and 2.0.1 dated 2018-06-07
munsellinterpol-1.0.2/munsellinterpol/R/munsellinterpol.R |only munsellinterpol-1.0.2/munsellinterpol/data/MunsellRenotation.rda |only munsellinterpol-1.0.2/munsellinterpol/data/OptimalColoursForIlluminantC.rda |only munsellinterpol-1.0.2/munsellinterpol/data/OptimalColoursForIlluminantD65.rda |only munsellinterpol-1.0.2/munsellinterpol/man/MunsellHVC.Rd |only munsellinterpol-1.0.2/munsellinterpol/man/MunsellRenotation.Rd |only munsellinterpol-1.0.2/munsellinterpol/man/OptimalColoursForIlluminantC.Rd |only munsellinterpol-1.0.2/munsellinterpol/man/hypot.Rd |only munsellinterpol-1.0.2/munsellinterpol/man/munsellinterpolation-internal.Rd |only munsellinterpol-2.0.1/munsellinterpol/DESCRIPTION | 38 - munsellinterpol-2.0.1/munsellinterpol/MD5 | 119 ++++- munsellinterpol-2.0.1/munsellinterpol/NAMESPACE | 57 ++ munsellinterpol-2.0.1/munsellinterpol/NEWS.md |only munsellinterpol-2.0.1/munsellinterpol/R/Colorlab.R |only munsellinterpol-2.0.1/munsellinterpol/R/ISCC-NBS.R |only munsellinterpol-2.0.1/munsellinterpol/R/MunsellName.R |only munsellinterpol-2.0.1/munsellinterpol/R/MunsellToxyY.R |only munsellinterpol-2.0.1/munsellinterpol/R/RGB.R |only munsellinterpol-2.0.1/munsellinterpol/R/VandY.R |only munsellinterpol-2.0.1/munsellinterpol/R/adaption.R |only munsellinterpol-2.0.1/munsellinterpol/R/conversions.R |only munsellinterpol-2.0.1/munsellinterpol/R/datasets.R |only munsellinterpol-2.0.1/munsellinterpol/R/events.R |only munsellinterpol-2.0.1/munsellinterpol/R/inversions.R |only munsellinterpol-2.0.1/munsellinterpol/R/logging.R |only munsellinterpol-2.0.1/munsellinterpol/R/lookup.R |only munsellinterpol-2.0.1/munsellinterpol/R/optimals.R |only munsellinterpol-2.0.1/munsellinterpol/R/plots.R |only munsellinterpol-2.0.1/munsellinterpol/R/reparam.R |only munsellinterpol-2.0.1/munsellinterpol/R/spline.R |only munsellinterpol-2.0.1/munsellinterpol/R/sysdata.rda |only munsellinterpol-2.0.1/munsellinterpol/R/utils.R |only munsellinterpol-2.0.1/munsellinterpol/R/xyYtoMunsell.R |only munsellinterpol-2.0.1/munsellinterpol/build |only munsellinterpol-2.0.1/munsellinterpol/data/munsellinterpol.rda |only munsellinterpol-2.0.1/munsellinterpol/inst |only munsellinterpol-2.0.1/munsellinterpol/man/CentroidsISCCNBS.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/ColorBlockFromMunsell.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/ColorlabFormatToMunsellSpec.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/HVCfromMunsellName.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/IsWithinMacAdamLimits.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/Munsell2xy.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/MunsellNameFromHVC.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/MunsellSpecToColorlabFormat.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/MunsellToLab.Rd | 88 ++-- munsellinterpol-2.0.1/munsellinterpol/man/MunsellToLuv.Rd | 87 ++-- munsellinterpol-2.0.1/munsellinterpol/man/MunsellToRGB.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/MunsellToXYZ.Rd | 83 ++- munsellinterpol-2.0.1/munsellinterpol/man/MunsellTosRGB.Rd | 97 +++- munsellinterpol-2.0.1/munsellinterpol/man/MunsellToxyY.Rd | 210 ++++++++-- munsellinterpol-2.0.1/munsellinterpol/man/RGBtoMunsell.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/VandY.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/XYZ2xyY.Rd | 70 ++- munsellinterpol-2.0.1/munsellinterpol/man/XYZtoMunsell.Rd | 76 ++- munsellinterpol-2.0.1/munsellinterpol/man/adaption.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/figures |only munsellinterpol-2.0.1/munsellinterpol/man/lab2xyz.Rd | 65 +-- munsellinterpol-2.0.1/munsellinterpol/man/labtoMunsell.Rd | 75 ++- munsellinterpol-2.0.1/munsellinterpol/man/luv2xyz.Rd | 63 +-- munsellinterpol-2.0.1/munsellinterpol/man/luvtoMunsell.Rd | 74 ++- munsellinterpol-2.0.1/munsellinterpol/man/macros |only munsellinterpol-2.0.1/munsellinterpol/man/plotLociHC.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/plotPatchesH.Rd |only munsellinterpol-2.0.1/munsellinterpol/man/sRGBtoMunsell.Rd | 97 +++- munsellinterpol-2.0.1/munsellinterpol/man/srgb2xyz.Rd | 76 ++- munsellinterpol-2.0.1/munsellinterpol/man/xyY2XYZ.Rd | 72 ++- munsellinterpol-2.0.1/munsellinterpol/man/xyYtoMunsell.Rd | 163 ++++++- munsellinterpol-2.0.1/munsellinterpol/man/xyz2lab.Rd | 69 +-- munsellinterpol-2.0.1/munsellinterpol/man/xyz2luv.Rd | 68 +-- munsellinterpol-2.0.1/munsellinterpol/man/xyz2srgb.Rd | 77 ++- munsellinterpol-2.0.1/munsellinterpol/tests |only munsellinterpol-2.0.1/munsellinterpol/vignettes |only 72 files changed, 1219 insertions(+), 605 deletions(-)
More information about munsellinterpol at CRAN
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Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed);
- generalised linear mixed models (if R packages 'metafor', 'lme4', 'numDeriv', and 'BiasedUrn' are installed);
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.9-1 dated 2018-03-22 and 4.9-2 dated 2018-06-07
DESCRIPTION | 8 ++-- MD5 | 45 +++++++++++----------- NEWS | 18 +++++++++ R/forest.meta.R | 67 ++++++++++++++++++++------------- R/metabias.rm5.R | 20 ++++++---- R/metabin.R | 97 +++++++++++++++++++++++++++---------------------- R/metabind.R | 19 ++++++--- R/metagen.R | 2 - R/metareg.R | 93 +++++++++++++++++++++++++++------------------- R/print.summary.meta.R | 78 +++++++++++++++++++++------------------ R/replaceNULL.R |only R/subgroup.R | 16 +++++++- R/summary.meta.R | 39 ++++++++++--------- R/update.meta.R | 6 +-- man/metabin.Rd | 22 +++++++++-- man/metabind.Rd | 3 + man/metacont.Rd | 16 ++++++-- man/metacor.Rd | 16 ++++++-- man/metagen.Rd | 17 +++++++- man/metainc.Rd | 21 +++++++++- man/metamean.Rd | 16 ++++++-- man/metaprop.Rd | 22 +++++++++-- man/metarate.Rd | 22 +++++++++-- man/metareg.Rd | 17 +++++--- 24 files changed, 443 insertions(+), 237 deletions(-)
Title: Merging Linkage Maps by Linear Programming
Description: Creates a consensus genetic map by merging linkage maps from different populations. The software uses linear programming (LP) to efficiently minimize the mean absolute error between the consensus map and the linkage maps. This minimization is performed subject to linear inequality constraints that ensure the ordering of the markers in the linkage maps is preserved. When marker order is inconsistent between linkage maps, a minimum set of ordinal constraints is deleted to resolve the conflicts.
Author: Jeffrey Endelman
Maintainer: Jeffrey Endelman <endelman@wisc.edu>
Diff between LPmerge versions 1.6 dated 2014-08-16 and 1.7 dated 2018-06-07
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 ++ R/LPmerge.R | 14 +++++++------- man/LPmerge.Rd | 2 +- 5 files changed, 19 insertions(+), 17 deletions(-)
Title: Some Latent Variable Models
Description: Includes some procedures for latent variable modeling with a
particular focus on multilevel data.
The 'LAM' package contains mean and covariance structure modelling
for multivariate normally distributed data (mlnormal(); Longford, 1987;
<doi:10.1093/biomet/74.4.817>), a general Metropolis-Hastings algorithm
(amh(); Roberts & Rosenthal, 2001, <doi:10.1214/ss/1015346320>) and
penalized maximum likelihood estimation (pmle(); Cole, Chu & Greenland,
2014; <doi:10.1093/aje/kwt245>).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between LAM versions 0.2-9 dated 2018-03-20 and 0.3-48 dated 2018-06-07
LAM-0.2-9/LAM/R/amh_eval_prior.R |only LAM-0.2-9/LAM/src/mlnormal_helper_functions.cpp |only LAM-0.3-48/LAM/DESCRIPTION | 24 LAM-0.3-48/LAM/MD5 | 207 ++--- LAM-0.3-48/LAM/NAMESPACE | 6 LAM-0.3-48/LAM/R/RcppExports.R | 26 LAM-0.3-48/LAM/R/amh.R | 308 +++----- LAM-0.3-48/LAM/R/amh_compare_estimators.R | 44 - LAM-0.3-48/LAM/R/amh_eval_priors.R |only LAM-0.3-48/LAM/R/amh_ic.R | 41 - LAM-0.3-48/LAM/R/amh_init_acceptance_parameters.R |only LAM-0.3-48/LAM/R/amh_loglike.R | 4 LAM-0.3-48/LAM/R/amh_posterior.R | 25 LAM-0.3-48/LAM/R/amh_proc_methods.R |only LAM-0.3-48/LAM/R/amh_proposal_refresh.R | 42 - LAM-0.3-48/LAM/R/amh_sampling.R | 122 +-- LAM-0.3-48/LAM/R/coef.amh.R | 2 LAM-0.3-48/LAM/R/coef.mlnormal.R | 2 LAM-0.3-48/LAM/R/coef.pmle.R | 2 LAM-0.3-48/LAM/R/confint.amh.R | 39 - LAM-0.3-48/LAM/R/confint.mlnormal.R | 41 - LAM-0.3-48/LAM/R/confint.pmle.R | 36 LAM-0.3-48/LAM/R/lam_moving_average.R |only LAM-0.3-48/LAM/R/logLik.amh.R | 13 LAM-0.3-48/LAM/R/logLik.mlnormal.R | 13 LAM-0.3-48/LAM/R/logLik.pmle.R | 13 LAM-0.3-48/LAM/R/logLik_lam.R |only LAM-0.3-48/LAM/R/loglike_mvnorm.R | 34 LAM-0.3-48/LAM/R/loglike_mvnorm_NA_pattern.R | 31 LAM-0.3-48/LAM/R/loglike_mvnorm_NA_pattern_R.R |only LAM-0.3-48/LAM/R/loglike_mvnorm_R.R |only LAM-0.3-48/LAM/R/mlnormal.R | 494 ++++++------- LAM-0.3-48/LAM/R/mlnormal_abs_approx.R | 38 - LAM-0.3-48/LAM/R/mlnormal_adjust_numdiff_parameter.R | 9 LAM-0.3-48/LAM/R/mlnormal_as_vector_names.R | 6 LAM-0.3-48/LAM/R/mlnormal_check_matrix_list_difference.R | 18 LAM-0.3-48/LAM/R/mlnormal_covmat_add_ridge.R | 4 LAM-0.3-48/LAM/R/mlnormal_create_disp.R | 6 LAM-0.3-48/LAM/R/mlnormal_equal_list_matrices.R | 27 LAM-0.3-48/LAM/R/mlnormal_equal_matrix.R | 14 LAM-0.3-48/LAM/R/mlnormal_eval_penalty.R | 12 LAM-0.3-48/LAM/R/mlnormal_eval_penalty_update_theta.R | 102 +- LAM-0.3-48/LAM/R/mlnormal_eval_priors.R | 34 LAM-0.3-48/LAM/R/mlnormal_eval_priors_derivative.R | 18 LAM-0.3-48/LAM/R/mlnormal_eval_priors_derivative2.R | 28 LAM-0.3-48/LAM/R/mlnormal_fill_matrix_from_list.R | 16 LAM-0.3-48/LAM/R/mlnormal_fit_function_ml.R | 139 +-- LAM-0.3-48/LAM/R/mlnormal_ic.R | 38 - LAM-0.3-48/LAM/R/mlnormal_information_matrix_reml.R | 127 +-- LAM-0.3-48/LAM/R/mlnormal_linear_regression_bayes.R | 12 LAM-0.3-48/LAM/R/mlnormal_log_2pi.R | 2 LAM-0.3-48/LAM/R/mlnormal_log_det.R | 2 LAM-0.3-48/LAM/R/mlnormal_matrix2list.R | 12 LAM-0.3-48/LAM/R/mlnormal_parameter_change.R | 4 LAM-0.3-48/LAM/R/mlnormal_postproc_eval_posterior.R | 82 +- LAM-0.3-48/LAM/R/mlnormal_postproc_parameters.R | 127 +-- LAM-0.3-48/LAM/R/mlnormal_proc.R | 185 ++-- LAM-0.3-48/LAM/R/mlnormal_proc_control.R | 54 - LAM-0.3-48/LAM/R/mlnormal_proc_variance_shortcut.R | 139 +-- LAM-0.3-48/LAM/R/mlnormal_proc_variance_shortcut_XY_R.R | 20 LAM-0.3-48/LAM/R/mlnormal_proc_variance_shortcut_XY_Rcpp.R | 19 LAM-0.3-48/LAM/R/mlnormal_proc_variance_shortcut_Z_R.R | 56 - LAM-0.3-48/LAM/R/mlnormal_proc_variance_shortcut_Z_Rcpp.R | 55 - LAM-0.3-48/LAM/R/mlnormal_process_prior.R | 130 +-- LAM-0.3-48/LAM/R/mlnormal_soft_thresholding.R | 2 LAM-0.3-48/LAM/R/mlnormal_sqrt_diag.R | 4 LAM-0.3-48/LAM/R/mlnormal_summary_round_helper.R | 48 - LAM-0.3-48/LAM/R/mlnormal_update_V_R.R | 82 +- LAM-0.3-48/LAM/R/mlnormal_update_V_Rcpp.R | 34 LAM-0.3-48/LAM/R/mlnormal_update_beta.R | 145 +-- LAM-0.3-48/LAM/R/mlnormal_update_beta_GLS.R | 6 LAM-0.3-48/LAM/R/mlnormal_update_beta_XVX_R.R | 48 - LAM-0.3-48/LAM/R/mlnormal_update_beta_XVX_Rcpp.R | 17 LAM-0.3-48/LAM/R/mlnormal_update_beta_iterations_penalty.R | 66 - LAM-0.3-48/LAM/R/mlnormal_update_beta_iterations_priors.R | 54 - LAM-0.3-48/LAM/R/mlnormal_update_control_list.R | 22 LAM-0.3-48/LAM/R/mlnormal_update_ml_derivative_V.R | 100 +- LAM-0.3-48/LAM/R/mlnormal_update_theta_ml.R | 323 ++++---- LAM-0.3-48/LAM/R/mlnormal_update_theta_newton_step.R | 24 LAM-0.3-48/LAM/R/mlnormal_verbose_f0.R | 17 LAM-0.3-48/LAM/R/mlnormal_verbose_f1.R | 13 LAM-0.3-48/LAM/R/mlnormal_verbose_f2.R | 28 LAM-0.3-48/LAM/R/plot.amh.R | 292 +++---- LAM-0.3-48/LAM/R/pmle.R | 202 +++-- LAM-0.3-48/LAM/R/pmle_data_proc.R | 22 LAM-0.3-48/LAM/R/pmle_eval_posterior.R | 40 - LAM-0.3-48/LAM/R/pmle_eval_prior.R |only LAM-0.3-48/LAM/R/pmle_eval_prior_deriv.R |only LAM-0.3-48/LAM/R/pmle_ic.R | 29 LAM-0.3-48/LAM/R/pmle_prior_extract_density.R | 60 - LAM-0.3-48/LAM/R/pmle_process_prior.R | 60 - LAM-0.3-48/LAM/R/print.mlnormal.R | 82 +- LAM-0.3-48/LAM/R/suff_stat_NA_pattern.R | 48 - LAM-0.3-48/LAM/R/summary.amh.R | 164 ++-- LAM-0.3-48/LAM/R/summary.mlnormal.R | 131 +-- LAM-0.3-48/LAM/R/summary.pmle.R | 110 +- LAM-0.3-48/LAM/R/vcov.amh.R | 2 LAM-0.3-48/LAM/R/vcov.mlnormal.R | 2 LAM-0.3-48/LAM/R/vcov.pmle.R | 2 LAM-0.3-48/LAM/R/zzz.R | 31 LAM-0.3-48/LAM/README.md | 5 LAM-0.3-48/LAM/inst/NEWS | 22 LAM-0.3-48/LAM/man/LAM-package.Rd | 48 - LAM-0.3-48/LAM/man/amh.Rd | 281 ++++--- LAM-0.3-48/LAM/man/data.HT.Rd | 4 LAM-0.3-48/LAM/man/loglike_mvnorm.Rd | 26 LAM-0.3-48/LAM/man/mlnormal.Rd | 159 ++-- LAM-0.3-48/LAM/man/suff_stat_NA_pattern.Rd | 12 LAM-0.3-48/LAM/src/RcppExports.cpp | 84 +- LAM-0.3-48/LAM/src/lam_rcpp_loglike_mvnorm.cpp |only LAM-0.3-48/LAM/src/lam_rcpp_mlnormal.cpp |only 111 files changed, 3055 insertions(+), 3000 deletions(-)
Title: Tools for Working with ICD-9 and ICD-10 Codes, and Finding
Comorbidities
Description: Calculate comorbidities, Charlson scores, perform
fast and accurate validation, conversion, manipulation, filtering and
comparison of ICD-9 and ICD-10 codes. This package enables a work flow
from raw lists of ICD codes in hospital databases to
comorbidities. ICD-9 and ICD-10 comorbidity mappings from Quan (Deyo
and Elixhauser versions), Elixhauser and AHRQ included. Common
ambiguities and code formats are handled.
Author: Jack O. Wasey [aut, cre, cph] (<https://orcid.org/0000-0003-3738-4637>),
William Murphy [ctb] (Van Walraven scores),
Anobel Odisho [ctb] (Hierarchical Condition Codes),
Vitaly Druker [ctb] (AHRQ CCS),
Ed Lee [ctb] (explain codes in table format),
Kevin Ushey [ctb] (Code adapted for fast factor generation),
R Core Team [ctb, cph] (m4 macro for OpenMP detection in configure)
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between icd versions 3.1.2 dated 2018-05-09 and 3.2.0 dated 2018-06-07
icd-3.1.2/icd/data/datalist |only icd-3.1.2/icd/data/icd10_sub_chapters.RData |only icd-3.1.2/icd/data/icd10cm2016.RData |only icd-3.1.2/icd/data/icd9_majors.RData |only icd-3.1.2/icd/data/icd9_sub_chapters.RData |only icd-3.1.2/icd/data/icd9cm_billable.RData |only icd-3.1.2/icd/data/icd9cm_hierarchy.RData |only icd-3.1.2/icd/data/icd_chapters.rda |only icd-3.1.2/icd/data/uranium_pathology.RData |only icd-3.1.2/icd/data/vermont_dx.RData |only icd-3.1.2/icd/man/comorbid_common.Rd |only icd-3.1.2/icd/man/explain.Rd |only icd-3.1.2/icd/man/factor_fast.Rd |only icd-3.1.2/icd/man/fastIntToString.Rd |only icd-3.1.2/icd/man/icd9Comorbid_alt_Taskloop.Rd |only icd-3.1.2/icd/man/lookupComorbid_alt_ByChunkForTaskloop.Rd |only icd-3.1.2/icd/man/regexec32.Rd |only icd-3.1.2/icd/src/comorbidTaskloop_alt.cpp |only icd-3.1.2/icd/tests/testthat/test-lints.R |only icd-3.2.0/icd/DESCRIPTION | 9 icd-3.2.0/icd/MD5 | 447 +++--- icd-3.2.0/icd/NAMESPACE | 57 icd-3.2.0/icd/R/RcppExports.R | 227 ++- icd-3.2.0/icd/R/as_char_no_warn.R | 1 icd-3.2.0/icd/R/categorize.R |only icd-3.2.0/icd/R/children.R | 25 icd-3.2.0/icd/R/children_alt.R | 8 icd-3.2.0/icd/R/comorbid.R | 283 +--- icd-3.2.0/icd/R/comorbid_alt.R | 4 icd-3.2.0/icd/R/comorbid_pccc.R |only icd-3.2.0/icd/R/condense.R | 5 icd-3.2.0/icd/R/convert.R | 35 icd-3.2.0/icd/R/datadocs.R | 290 +--- icd-3.2.0/icd/R/diff_comorbid.R | 6 icd-3.2.0/icd/R/env.R | 12 icd-3.2.0/icd/R/explain-table.R | 4 icd-3.2.0/icd/R/explain.R | 98 - icd-3.2.0/icd/R/factor_nosort.R | 112 + icd-3.2.0/icd/R/generate_mappings.R | 3 icd-3.2.0/icd/R/generate_pccc.R |only icd-3.2.0/icd/R/generate_spelling.R | 11 icd-3.2.0/icd/R/generate_sysdata.R | 132 + icd-3.2.0/icd/R/hcc.R | 16 icd-3.2.0/icd/R/icd-package.R | 44 icd-3.2.0/icd/R/parse-ahrq-ccs.R | 21 icd-3.2.0/icd/R/parse-icd10.R | 51 icd-3.2.0/icd/R/parse-icd10cm-xml.R | 10 icd-3.2.0/icd/R/parse.R | 10 icd-3.2.0/icd/R/ranges.R | 8 icd-3.2.0/icd/R/real.R | 8 icd-3.2.0/icd/R/save_in_data_dir.R | 3 icd-3.2.0/icd/R/score.R | 6 icd-3.2.0/icd/R/to_data_raw.R | 28 icd-3.2.0/icd/R/unzip_single.R | 20 icd-3.2.0/icd/R/util-file.R | 51 icd-3.2.0/icd/R/util-test.R | 8 icd-3.2.0/icd/R/util.R | 77 - icd-3.2.0/icd/R/valid.R | 143 -- icd-3.2.0/icd/R/z-deprecated.R | 32 icd-3.2.0/icd/R/zzz.R | 29 icd-3.2.0/icd/README.md | 27 icd-3.2.0/icd/build/vignette.rds |binary icd-3.2.0/icd/configure | 28 icd-3.2.0/icd/data/icd10_map_ahrq_pcs.RData |only icd-3.2.0/icd/data/icd10_map_pccc_dx.RData |only icd-3.2.0/icd/data/icd10_map_pccc_pcs.RData |only icd-3.2.0/icd/data/icd10_sources.RData |only icd-3.2.0/icd/data/icd9_map_pccc_dx.RData |only icd-3.2.0/icd/data/icd9_map_pccc_pcs.RData |only icd-3.2.0/icd/data/icd9_map_quan_elix.RData |binary icd-3.2.0/icd/inst/doc/Charlson_and_other_scores.R | 4 icd-3.2.0/icd/inst/doc/Charlson_and_other_scores.Rmd | 4 icd-3.2.0/icd/inst/doc/Charlson_and_other_scores.html | 11 icd-3.2.0/icd/inst/doc/Comparing_Comorbidity_Mappings_Vignette.html | 3 icd-3.2.0/icd/inst/doc/Efficient_calculation_of_comorbidities_from_medical_codes.R | 15 icd-3.2.0/icd/inst/doc/Efficient_calculation_of_comorbidities_from_medical_codes.Rmd | 19 icd-3.2.0/icd/inst/doc/Efficient_calculation_of_comorbidities_from_medical_codes.pdf |binary icd-3.2.0/icd/inst/doc/Ranges.html | 3 icd-3.2.0/icd/inst/doc/Using_Hierarchical_Condition_Codes.html | 3 icd-3.2.0/icd/inst/doc/icd-10.R | 14 icd-3.2.0/icd/inst/doc/icd-10.Rmd | 30 icd-3.2.0/icd/inst/doc/icd-10.html | 33 icd-3.2.0/icd/inst/doc/introduction.R | 46 icd-3.2.0/icd/inst/doc/introduction.Rmd | 52 icd-3.2.0/icd/inst/doc/introduction.html | 72 - icd-3.2.0/icd/inst/doc/pccc.R |only icd-3.2.0/icd/inst/doc/pccc.Rmd |only icd-3.2.0/icd/inst/doc/pccc.html |only icd-3.2.0/icd/inst/include/icd_RcppExports.h | 325 +++- icd-3.2.0/icd/man/categorize.Rd |only icd-3.2.0/icd/man/charlson.Rd | 6 icd-3.2.0/icd/man/charlson_from_comorbid.Rd | 12 icd-3.2.0/icd/man/children.Rd | 17 icd-3.2.0/icd/man/comorbid.Rd | 67 icd-3.2.0/icd/man/comorbidMatMul.Rd | 6 icd-3.2.0/icd/man/comorbidMatMulSimple.Rd |only icd-3.2.0/icd/man/comorbid_df_to_mat.Rd | 8 icd-3.2.0/icd/man/comorbid_hcc.Rd | 7 icd-3.2.0/icd/man/comorbid_mat_to_df.Rd | 2 icd-3.2.0/icd/man/comorbid_pccc_dx.Rd |only icd-3.2.0/icd/man/condense.Rd | 8 icd-3.2.0/icd/man/count_codes.Rd | 6 icd-3.2.0/icd/man/count_codes_wide.Rd | 6 icd-3.2.0/icd/man/diff_comorbid.Rd | 6 icd-3.2.0/icd/man/expand_range.Rd | 6 icd-3.2.0/icd/man/expect_chap_equal.Rd | 2 icd-3.2.0/icd/man/explain_code.Rd |only icd-3.2.0/icd/man/explain_table.Rd | 6 icd-3.2.0/icd/man/factor_nosort.Rd | 29 icd-3.2.0/icd/man/factor_split_na.Rd |only icd-3.2.0/icd/man/factor_split_rcpp.Rd |only icd-3.2.0/icd/man/fastIntToStringRcpp.Rd |only icd-3.2.0/icd/man/fetch_icd10cm_all.Rd |only icd-3.2.0/icd/man/filter_poa.Rd | 6 icd-3.2.0/icd/man/filter_valid.Rd | 6 icd-3.2.0/icd/man/generate_icd10_sources.Rd |only icd-3.2.0/icd/man/generate_icd_chapters.Rd |only icd-3.2.0/icd/man/generate_maps_pccc.Rd |only icd-3.2.0/icd/man/get_billable.Rd | 6 icd-3.2.0/icd/man/get_defined.Rd | 6 icd-3.2.0/icd/man/get_icd_name.Rd | 9 icd-3.2.0/icd/man/get_invalid.Rd | 6 icd-3.2.0/icd/man/get_raw_data_dir.Rd | 5 icd-3.2.0/icd/man/get_valid.Rd | 9 icd-3.2.0/icd/man/icd-package.Rd | 34 icd-3.2.0/icd/man/icd10_chapters.Rd | 13 icd-3.2.0/icd/man/icd10_comorbid_reduce.Rd | 7 icd-3.2.0/icd/man/icd10_fetch_ahrq_ccs.Rd | 4 icd-3.2.0/icd/man/icd10_map_ahrq_pcs.Rd |only icd-3.2.0/icd/man/icd10_parse_ahrq_ccs.Rd | 2 icd-3.2.0/icd/man/icd10_pcs.Rd |only icd-3.2.0/icd/man/icd10_sub_chapters.Rd | 14 icd-3.2.0/icd/man/icd10cm2016.Rd | 11 icd-3.2.0/icd/man/icd9AddLeadingZeroes_alt_ShortSingle.Rd | 3 icd-3.2.0/icd/man/icd9MajMinToCode.Rd | 15 icd-3.2.0/icd/man/icd9RandomShort.Rd | 2 icd-3.2.0/icd/man/icd9_chapters.Rd | 13 icd-3.2.0/icd/man/icd9_chapters_to_map.Rd | 2 icd-3.2.0/icd/man/icd9_fetch_ahrq_ccs.Rd | 4 icd-3.2.0/icd/man/icd9_is_n.Rd | 3 icd-3.2.0/icd/man/icd9_map_pccc.Rd |only icd-3.2.0/icd/man/icd9_map_single_ccs.Rd | 4 icd-3.2.0/icd/man/icd9_sources.Rd | 4 icd-3.2.0/icd/man/icd9cm_billable.Rd | 14 icd-3.2.0/icd/man/icd9cm_hierarchy.Rd | 24 icd-3.2.0/icd/man/icd_long_data.Rd | 2 icd-3.2.0/icd/man/is.icd9.Rd | 6 icd-3.2.0/icd/man/is_billable.Rd | 6 icd-3.2.0/icd/man/is_defined.Rd | 6 icd-3.2.0/icd/man/is_valid.Rd | 6 icd-3.2.0/icd/man/long_to_wide.Rd | 6 icd-3.2.0/icd/man/match_rcpp.Rd |only icd-3.2.0/icd/man/poa_choices.Rd | 6 icd-3.2.0/icd/man/refactor.Rd |only icd-3.2.0/icd/man/refactor_worker.Rd |only icd-3.2.0/icd/man/set_icd_class.Rd | 6 icd-3.2.0/icd/man/set_re_globals.Rd | 4 icd-3.2.0/icd/man/short_to_decimal.Rd | 6 icd-3.2.0/icd/man/simplify_map_lex.Rd | 14 icd-3.2.0/icd/man/sort_icd.Rd | 6 icd-3.2.0/icd/man/str_match_all.Rd | 4 icd-3.2.0/icd/man/unzip_to_data_raw.Rd | 3 icd-3.2.0/icd/man/uranium_pathology.Rd | 6 icd-3.2.0/icd/man/van_walraven.Rd | 6 icd-3.2.0/icd/man/vermont_dx.Rd | 10 icd-3.2.0/icd/man/wide_to_long.Rd | 6 icd-3.2.0/icd/src/RcppExports.cpp | 502 +++++-- icd-3.2.0/icd/src/appendMinor-1e51abe0.o.tmp |only icd-3.2.0/icd/src/appendMinor.cpp | 16 icd-3.2.0/icd/src/appendMinor.h | 1 icd-3.2.0/icd/src/appendMinor_alt.cpp | 10 icd-3.2.0/icd/src/appendMinor_alt.h | 1 icd-3.2.0/icd/src/attr.cpp | 3 icd-3.2.0/icd/src/attr.h | 1 icd-3.2.0/icd/src/categorize.cpp |only icd-3.2.0/icd/src/children.cpp | 1 icd-3.2.0/icd/src/comorbid.cpp | 62 icd-3.2.0/icd/src/comorbidCommon.cpp | 7 icd-3.2.0/icd/src/comorbidIcd10.cpp | 55 icd-3.2.0/icd/src/comorbidMatMul.cpp | 449 +++++- icd-3.2.0/icd/src/comorbidMatMul.h | 38 icd-3.2.0/icd/src/comorbidSetup.cpp | 1 icd-3.2.0/icd/src/comorbidSetup.h | 1 icd-3.2.0/icd/src/comorbid_alt.h | 6 icd-3.2.0/icd/src/config.h.in | 6 icd-3.2.0/icd/src/convert.cpp | 1 icd-3.2.0/icd/src/convert.h | 3 icd-3.2.0/icd/src/convert_alt.cpp | 2 icd-3.2.0/icd/src/fastIntToString.cpp | 12 icd-3.2.0/icd/src/fastIntToString.h | 2 icd-3.2.0/icd/src/fastIntToString_alt_Std.cpp | 9 icd-3.2.0/icd/src/guess.cpp | 2 icd-3.2.0/icd/src/guess.h | 1 icd-3.2.0/icd/src/icd_types.h | 21 icd-3.2.0/icd/src/local.h | 109 - icd-3.2.0/icd/src/longToWide.cpp | 13 icd-3.2.0/icd/src/manip_alt.cpp | 5 icd-3.2.0/icd/src/manip_alt.h | 2 icd-3.2.0/icd/src/random.cpp |only icd-3.2.0/icd/src/ranges.cpp | 1 icd-3.2.0/icd/src/ranges.h | 1 icd-3.2.0/icd/src/ranges_alt.cpp | 1 icd-3.2.0/icd/src/ranges_alt.h | 2 icd-3.2.0/icd/src/registration.c | 162 +- icd-3.2.0/icd/src/test-cpp.cpp | 213 ++- icd-3.2.0/icd/src/test-cpp_alt.cpp | 1 icd-3.2.0/icd/src/util.cpp | 420 ++++-- icd-3.2.0/icd/src/util.h | 24 icd-3.2.0/icd/tests/test-all.R | 1 icd-3.2.0/icd/tests/test-build-data.R | 1 icd-3.2.0/icd/tests/test-deprecated.R | 1 icd-3.2.0/icd/tests/test-slow.R | 1 icd-3.2.0/icd/tests/tests-build-data/test-build-maps-icd9.R | 6 icd-3.2.0/icd/tests/tests-build-data/test-parse-icd10.R | 2 icd-3.2.0/icd/tests/tests-build-data/test-parse.R | 2 icd-3.2.0/icd/tests/tests-deprecated/test-class.R | 46 icd-3.2.0/icd/tests/tests-deprecated/test-comorbid-maps-icd9.R | 2 icd-3.2.0/icd/tests/tests-deprecated/test-condense.R | 2 icd-3.2.0/icd/tests/tests-deprecated/test-explain.R | 4 icd-3.2.0/icd/tests/tests-deprecated/test-filter-poa.R | 2 icd-3.2.0/icd/tests/tests-deprecated/test-github133.R | 4 icd-3.2.0/icd/tests/tests-deprecated/test-parse.R | 2 icd-3.2.0/icd/tests/tests-deprecated/test-util.R | 2 icd-3.2.0/icd/tests/tests-deprecated/test-valid.R | 10 icd-3.2.0/icd/tests/tests-slow/test-refactor-slow.R |only icd-3.2.0/icd/tests/testthat/helper-base.R | 64 icd-3.2.0/icd/tests/testthat/helper-icd10.R | 82 - icd-3.2.0/icd/tests/testthat/test-billable.R | 2 icd-3.2.0/icd/tests/testthat/test-ccs-calcs.R | 41 icd-3.2.0/icd/tests/testthat/test-class.R | 46 icd-3.2.0/icd/tests/testthat/test-comorbid-calcs-icd10.R | 188 ++ icd-3.2.0/icd/tests/testthat/test-comorbid-calcs-icd9.R | 683 +++++----- icd-3.2.0/icd/tests/testthat/test-comorbid-maps-icd9.R | 114 - icd-3.2.0/icd/tests/testthat/test-condense.R | 10 icd-3.2.0/icd/tests/testthat/test-explain-table.R | 4 icd-3.2.0/icd/tests/testthat/test-explain.R | 62 icd-3.2.0/icd/tests/testthat/test-factor.R |only icd-3.2.0/icd/tests/testthat/test-filter-poa.R | 2 icd-3.2.0/icd/tests/testthat/test-future-explain-icd10.R | 3 icd-3.2.0/icd/tests/testthat/test-github133.R | 72 - icd-3.2.0/icd/tests/testthat/test-guess.R | 2 icd-3.2.0/icd/tests/testthat/test-hcc.R | 22 icd-3.2.0/icd/tests/testthat/test-openmp.R | 1 icd-3.2.0/icd/tests/testthat/test-refactor.R |only icd-3.2.0/icd/tests/testthat/test-sample-data.R | 2 icd-3.2.0/icd/tests/testthat/test-util.R | 13 icd-3.2.0/icd/tests/testthat/test-valid.R | 10 icd-3.2.0/icd/vignettes/Charlson_and_other_scores.Rmd | 4 icd-3.2.0/icd/vignettes/Efficient_calculation_of_comorbidities_from_medical_codes.Rmd | 19 icd-3.2.0/icd/vignettes/icd-10.Rmd | 30 icd-3.2.0/icd/vignettes/introduction.Rmd | 52 icd-3.2.0/icd/vignettes/pccc.Rmd |only 252 files changed, 4294 insertions(+), 3041 deletions(-)
Title: Fuzzy Linear Regression
Description: Estimators for fuzzy linear regression. The functions estimate parameters of
fuzzy linear regression models with crisp or fuzzy independent variables (triangular
fuzzy numbers are supported). Implements multiple methods for parameter estimation and
algebraic operations with triangular fuzzy numbers. Includes functions for
summarising, printing and plotting the model fit. Calculates predictions from the
model.
Diamond (1988) <doi:10.1016/0020-0255(88)90047-3>,
Hung & Yang (2006) <doi:10.1016/j.fss.2006.08.004>,
Lee & Tanaka (1999) <doi:10.15807/jorsj.42.98>,
Nasrabadi, Nasrabadi & Nasrabady (2005) <doi:10.1016/j.amc.2004.02.008>,
Tanaka, Hayashi & Watada (1989) <doi:10.1016/0377-2217(89)90431-1>.
Author: Pavel Skrabanek [aut, cph],
Natalia Martinkova [aut, cre, cph]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between fuzzyreg versions 0.2 dated 2018-04-24 and 0.3 dated 2018-06-07
fuzzyreg-0.2/fuzzyreg/R/diamond.R |only fuzzyreg-0.2/fuzzyreg/R/hung.R |only fuzzyreg-0.2/fuzzyreg/R/lee.R |only fuzzyreg-0.2/fuzzyreg/R/nasrabadi.R |only fuzzyreg-0.2/fuzzyreg/R/tanaka.R |only fuzzyreg-0.3/fuzzyreg/DESCRIPTION | 26 ++++++------- fuzzyreg-0.3/fuzzyreg/MD5 | 45 +++++++++++++----------- fuzzyreg-0.3/fuzzyreg/NAMESPACE | 7 +++ fuzzyreg-0.3/fuzzyreg/R/data.R | 2 - fuzzyreg-0.3/fuzzyreg/R/fls.R |only fuzzyreg-0.3/fuzzyreg/R/fuzzylm.R | 44 ++++++++++++----------- fuzzyreg-0.3/fuzzyreg/R/moflr.R |only fuzzyreg-0.3/fuzzyreg/R/oplr.R |only fuzzyreg-0.3/fuzzyreg/R/plot.fuzzylm.R | 40 +++++++++++++-------- fuzzyreg-0.3/fuzzyreg/R/plr.R |only fuzzyreg-0.3/fuzzyreg/R/plrls.R |only fuzzyreg-0.3/fuzzyreg/R/predict.fuzzylm.R | 4 +- fuzzyreg-0.3/fuzzyreg/R/print.summary.fuzzylm.R | 2 - fuzzyreg-0.3/fuzzyreg/man/diamond.Rd | 22 ++--------- fuzzyreg-0.3/fuzzyreg/man/fls.Rd |only fuzzyreg-0.3/fuzzyreg/man/fuzzydat.Rd | 2 - fuzzyreg-0.3/fuzzyreg/man/fuzzylm.Rd | 21 +++++------ fuzzyreg-0.3/fuzzyreg/man/hung.Rd | 22 +++-------- fuzzyreg-0.3/fuzzyreg/man/lee.Rd | 17 ++------- fuzzyreg-0.3/fuzzyreg/man/moflr.Rd |only fuzzyreg-0.3/fuzzyreg/man/nasrabadi.Rd | 23 ++++-------- fuzzyreg-0.3/fuzzyreg/man/oplr.Rd |only fuzzyreg-0.3/fuzzyreg/man/plot.fuzzylm.Rd | 6 ++- fuzzyreg-0.3/fuzzyreg/man/plr.Rd |only fuzzyreg-0.3/fuzzyreg/man/plrls.Rd |only fuzzyreg-0.3/fuzzyreg/man/tanaka.Rd | 19 ++-------- 31 files changed, 143 insertions(+), 159 deletions(-)
Title: Construction, Simulation and Analysis of Boolean Networks
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, probabilistic and temporal Boolean networks, and to
analyze and visualize attractors in Boolean networks.
Author: Christoph Müssel [aut],
Martin Hopfensitz [aut],
Dao Zhou [aut],
Hans A. Kestler [aut, cre],
Armin Biere [ctb] (contributed PicoSAT code),
Troy D. Hanson [ctb] (contributed uthash macros)
Maintainer: Hans A. Kestler <hans.kestler@uni-ulm.de>
Diff between BoolNet versions 2.1.3 dated 2016-11-21 and 2.1.4 dated 2018-06-07
DESCRIPTION | 8 - MD5 | 35 +++--- NAMESPACE | 4 R/helpers.R | 6 - R/plotSequence.R | 7 - build/vignette.rds |binary inst/NEWS.Rd | 5 inst/doc/BoolNet_package_vignette.R | 186 ++++++++++++++++----------------- inst/doc/BoolNet_package_vignette.Snw | 4 inst/doc/BoolNet_package_vignette.pdf |binary man/BoolNet-package.Rd | 4 man/plotAttractors.Rd | 4 man/plotSequence.Rd | 8 - src/common.c | 8 - src/common.h | 9 + src/init.c |only src/reconstruct_network.c | 2 src/symbolic_simulator.c | 2 vignettes/BoolNet_package_vignette.Snw | 4 19 files changed, 152 insertions(+), 144 deletions(-)
Title: Resistome Predicter
Description: Predicts Escherichia coli's resistome for candidate drug. It utilizes two algorithms viz. deterministic model and stochastic model (manuscript under preparation) for the prediction of drug class. Once the drug class is predicted, the resistome is fetched from the database for the predicted class.
Author: Saurav Bhaskar Saha, Vipul Gupta, Pramod Wasudeo Ramteke
Maintainer: Saurav Bhaskar Saha <saurav.saha@shiats.edu.in>
Diff between uCAREChemSuiteCLI versions 0.1.1 dated 2018-05-29 and 0.1.2 dated 2018-06-07
DESCRIPTION | 6 ++--- MD5 | 4 +-- R/uCAREChemSuiteCLI.R | 51 +++++++++++++++++++++++++++++++++++++++++++++++++- 3 files changed, 55 insertions(+), 6 deletions(-)
More information about uCAREChemSuiteCLI at CRAN
Permanent link
Title: 'dplyr' Functionality for Matched Tree and Data Objects
Description: Matches phylogenetic trees and trait data, and
allows simultaneous manipulation of the tree and data using 'dplyr'.
Author: Josef Uyeda
Maintainer: Josef Uyeda <josef.uyeda@gmail.com>
Diff between treeplyr versions 0.1.3 dated 2017-07-08 and 0.1.4 dated 2018-06-07
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/treeplyr_functions.R | 3 ++- inst/tests/test-treedata.R | 11 +++++++++-- 4 files changed, 19 insertions(+), 11 deletions(-)
Title: Tools for Reshaping Text
Description: Tools that can be used to reshape and restructure text data.
Author: Tyler Rinker [aut, cre],
Joran Elias [ctb],
Matthew Flickinger [ctb],
Paul Foster [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between textshape versions 1.5.0 dated 2017-09-08 and 1.6.0 dated 2018-06-07
textshape-1.5.0/textshape/R/set_output.R |only textshape-1.6.0/textshape/DESCRIPTION | 30 textshape-1.6.0/textshape/MD5 | 110 + textshape-1.6.0/textshape/NAMESPACE | 2 textshape-1.6.0/textshape/NEWS | 24 textshape-1.6.0/textshape/R/bind_list.R | 13 textshape-1.6.0/textshape/R/bind_table.R | 9 textshape-1.6.0/textshape/R/bind_vector.R | 9 textshape-1.6.0/textshape/R/change_index.R | 9 textshape-1.6.0/textshape/R/cluster_matrix.R | 17 textshape-1.6.0/textshape/R/column_to_rownames.R | 2 textshape-1.6.0/textshape/R/combine.R | 8 textshape-1.6.0/textshape/R/duration.R | 21 textshape-1.6.0/textshape/R/flatten.R |only textshape-1.6.0/textshape/R/from_to.R | 15 textshape-1.6.0/textshape/R/mtabulate.R | 21 textshape-1.6.0/textshape/R/split_index.R | 52 textshape-1.6.0/textshape/R/split_match_regex_to_transcript.R | 74 - textshape-1.6.0/textshape/R/split_portion.R | 24 textshape-1.6.0/textshape/R/split_run.R | 14 textshape-1.6.0/textshape/R/split_sentence.R | 69 - textshape-1.6.0/textshape/R/split_sentence_token.R | 32 textshape-1.6.0/textshape/R/split_speaker.R | 11 textshape-1.6.0/textshape/R/split_token.R | 22 textshape-1.6.0/textshape/R/split_transcript.R | 14 textshape-1.6.0/textshape/R/split_word.R | 22 textshape-1.6.0/textshape/R/tidy_colo_dtm.R | 28 textshape-1.6.0/textshape/R/tidy_dtm.R | 35 textshape-1.6.0/textshape/R/tidy_list.R | 39 textshape-1.6.0/textshape/R/tidy_matrix.R | 8 textshape-1.6.0/textshape/R/unique_pairs.R | 15 textshape-1.6.0/textshape/R/unnest_text.R |only textshape-1.6.0/textshape/R/utils.R | 109 + textshape-1.6.0/textshape/README.md | 575 ++++++---- textshape-1.6.0/textshape/data/DATA.rda |binary textshape-1.6.0/textshape/data/golden_rules.rda |binary textshape-1.6.0/textshape/data/hamlet.rda |binary textshape-1.6.0/textshape/data/simple_dtm.rda |binary textshape-1.6.0/textshape/inst/CITATION | 8 textshape-1.6.0/textshape/man/change_index.Rd | 9 textshape-1.6.0/textshape/man/cluster_matrix.Rd | 17 textshape-1.6.0/textshape/man/duration.Rd | 4 textshape-1.6.0/textshape/man/flatten.Rd |only textshape-1.6.0/textshape/man/mtabulate.Rd | 15 textshape-1.6.0/textshape/man/split_index.Rd | 2 textshape-1.6.0/textshape/man/split_match_regex_to_transcript.Rd | 23 textshape-1.6.0/textshape/man/tidy_colo_dtm.Rd | 20 textshape-1.6.0/textshape/man/tidy_dtm.Rd | 22 textshape-1.6.0/textshape/man/tidy_list.Rd | 21 textshape-1.6.0/textshape/man/tidy_matrix.Rd | 5 textshape-1.6.0/textshape/man/unique_pairs.Rd | 3 textshape-1.6.0/textshape/man/unnest_text.Rd |only textshape-1.6.0/textshape/tools/figure/unnamed-chunk-10-1.png |binary textshape-1.6.0/textshape/tools/figure/unnamed-chunk-16-1.png |binary textshape-1.6.0/textshape/tools/figure/unnamed-chunk-17-1.png |binary textshape-1.6.0/textshape/tools/figure/unnamed-chunk-18-1.png |only textshape-1.6.0/textshape/tools/figure/unnamed-chunk-19-1.png |only textshape-1.6.0/textshape/tools/figure/unnamed-chunk-27-1.png |only textshape-1.6.0/textshape/tools/figure/unnamed-chunk-44-1.png |only textshape-1.6.0/textshape/tools/figure/unnamed-chunk-45-1.png |only textshape-1.6.0/textshape/tools/figure/unnamed-chunk-46-1.png |only textshape-1.6.0/textshape/tools/figure/unnamed-chunk-55-1.png |only 62 files changed, 1081 insertions(+), 501 deletions(-)
Title: Estimating Disease Prevalence from Registry Data
Description: Estimates disease prevalence for a given index date, using existing
registry data extended with Monte Carlo simulations.
Author: Stuart Lacy [cre, aut],
Simon Crouch [aut],
Stephanie Lax [aut]
Maintainer: Stuart Lacy <stuart.lacy@york.ac.uk>
Diff between rprev versions 0.2.4 dated 2017-09-22 and 1.0.0 dated 2018-06-07
rprev-0.2.4/rprev/R/survival.R |only rprev-0.2.4/rprev/man/determine_registry_years.Rd |only rprev-0.2.4/rprev/man/determine_yearly_endpoints.Rd |only rprev-0.2.4/rprev/man/functional_form_age.Rd |only rprev-0.2.4/rprev/man/incidence.Rd |only rprev-0.2.4/rprev/man/incidence_age_distribution.Rd |only rprev-0.2.4/rprev/man/mean_incidence_rate.Rd |only rprev-0.2.4/rprev/man/plot.incidence.Rd |only rprev-0.2.4/rprev/man/population_survival_rate.Rd |only rprev-0.2.4/rprev/man/prevalence_counted.Rd |only rprev-0.2.4/rprev/man/prevalence_simulated.Rd |only rprev-0.2.4/rprev/man/raw_incidence.Rd |only rprev-0.2.4/rprev/man/test_incidence_fit.Rd |only rprev-0.2.4/rprev/man/yearly_incidence.Rd |only rprev-0.2.4/rprev/tests/testthat/cache/diagnostics/functional_form_age.rds |only rprev-0.2.4/rprev/tests/testthat/cache/diagnostics/inspect_incidence.rds |only rprev-0.2.4/rprev/tests/testthat/cache/diagnostics/poisson_incidence_sim.rds |only rprev-0.2.4/rprev/tests/testthat/cache/diagnostics/prev_chisq.rds |only rprev-0.2.4/rprev/tests/testthat/cache/prevalence |only rprev-0.2.4/rprev/tests/testthat/cache/survival |only rprev-0.2.4/rprev/tests/testthat/test_survival.R |only rprev-1.0.0/rprev/DESCRIPTION | 28 rprev-1.0.0/rprev/MD5 | 152 - rprev-1.0.0/rprev/NAMESPACE | 59 rprev-1.0.0/rprev/NEWS.md | 9 rprev-1.0.0/rprev/R/data.R | 18 rprev-1.0.0/rprev/R/diagnostics.R | 152 - rprev-1.0.0/rprev/R/fixedcure.R |only rprev-1.0.0/rprev/R/flexsurv.R |only rprev-1.0.0/rprev/R/homogeneous_poisson.R |only rprev-1.0.0/rprev/R/inc_model.R |only rprev-1.0.0/rprev/R/incidence.R | 364 +--- rprev-1.0.0/rprev/R/point_estimate.R |only rprev-1.0.0/rprev/R/prevalence.R | 893 ++++------ rprev-1.0.0/rprev/R/rprev.R | 18 rprev-1.0.0/rprev/R/surv_model.R |only rprev-1.0.0/rprev/R/survfit.prev.R | 83 rprev-1.0.0/rprev/R/survregmin.R |only rprev-1.0.0/rprev/R/test_custom_models.R |only rprev-1.0.0/rprev/R/utils.R | 108 - rprev-1.0.0/rprev/README.md | 10 rprev-1.0.0/rprev/build/vignette.rds |binary rprev-1.0.0/rprev/data/UKmortality.rda |binary rprev-1.0.0/rprev/data/prevsim.rda |binary rprev-1.0.0/rprev/inst/doc/diagnostics.R |only rprev-1.0.0/rprev/inst/doc/diagnostics.Rmd |only rprev-1.0.0/rprev/inst/doc/diagnostics.html |only rprev-1.0.0/rprev/inst/doc/user_guide.R | 334 ++- rprev-1.0.0/rprev/inst/doc/user_guide.Rmd | 463 +++-- rprev-1.0.0/rprev/inst/doc/user_guide.html | 714 ++++--- rprev-1.0.0/rprev/man/UKmortality.Rd | 16 rprev-1.0.0/rprev/man/counted_prevalence.Rd |only rprev-1.0.0/rprev/man/draw_incident_population.Rd |only rprev-1.0.0/rprev/man/extract_covars.Rd |only rprev-1.0.0/rprev/man/fixed_cure.Rd |only rprev-1.0.0/rprev/man/plot.incdiag.Rd |only rprev-1.0.0/rprev/man/plot.survfit.prev.Rd | 13 rprev-1.0.0/rprev/man/predict_survival_probability.Rd |only rprev-1.0.0/rprev/man/prevalence.Rd | 182 +- rprev-1.0.0/rprev/man/prevsim.Rd | 2 rprev-1.0.0/rprev/man/rprev.Rd | 18 rprev-1.0.0/rprev/man/sim_prevalence.Rd |only rprev-1.0.0/rprev/man/survfit.prevalence.Rd | 16 rprev-1.0.0/rprev/man/test_homogeneity.Rd |only rprev-1.0.0/rprev/man/test_prevalence_fit.Rd | 5 rprev-1.0.0/rprev/man/validate_incidence_model.Rd |only rprev-1.0.0/rprev/man/validate_survival_model.Rd |only rprev-1.0.0/rprev/tests/testthat/cache/diagnostics/prev_pval.rds |only rprev-1.0.0/rprev/tests/testthat/test_curemodels.R |only rprev-1.0.0/rprev/tests/testthat/test_diagnostics.R | 94 - rprev-1.0.0/rprev/tests/testthat/test_incidence.R | 68 rprev-1.0.0/rprev/tests/testthat/test_incidence_model.R |only rprev-1.0.0/rprev/tests/testthat/test_prevalence.R | 477 ++--- rprev-1.0.0/rprev/tests/testthat/test_survival_model.R |only rprev-1.0.0/rprev/vignettes/bibliography.bib | 11 rprev-1.0.0/rprev/vignettes/diagnostics.Rmd |only rprev-1.0.0/rprev/vignettes/user_guide.Rmd | 463 +++-- 77 files changed, 2360 insertions(+), 2410 deletions(-)
Title: Inferring Latent Diffusion Networks
Description: This is an R implementation of the netinf algorithm (Gomez Rodriguez, Leskovec, and Krause, 2010)<doi:10.1145/1835804.1835933>. Given a set of events that spread between a set of nodes the algorithm infers the most likely stable diffusion network that is underlying the diffusion process.
Author: Fridolin Linder [aut, cre],
Bruce Desmarais [ctb]
Maintainer: Fridolin Linder <fridolin.linder@gmail.com>
Diff between NetworkInference versions 1.2.0 dated 2018-06-05 and 1.2.1 dated 2018-06-07
DESCRIPTION | 8 MD5 | 12 NEWS.md | 17 - R/zzz.R | 2 inst/doc/quickstart_vignette.html | 368 +++++++++++++++++----- inst/doc/tutorial_vignette.html | 616 +++++++++++++++++++++++++------------- src/netinf.cpp | 4 7 files changed, 720 insertions(+), 307 deletions(-)
More information about NetworkInference at CRAN
Permanent link
Title: Analysis of Diffusion and Contagion Processes on Networks
Description: Empirical statistical analysis, visualization and simulation of
diffusion and contagion processes on networks. The package implements algorithms
for calculating network diffusion statistics such as transmission rate, hazard
rates, exposure models, network threshold levels, infectiousness (contagion),
and susceptibility. The package is inspired by work published in Valente,
et al., (2015) <DOI:10.1016/j.socscimed.2015.10.001>; Valente (1995) <ISBN:
9781881303213>, Myers (2000) <DOI:10.1086/303110>, Iyengar and others (2011)
<DOI:10.1287/mksc.1100.0566>, Burt (1987) <DOI:10.1086/228667>; among others.
Author: George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>,
Rewrite functions with Rcpp, plus new features),
Stephanie Dyal [ctb] (Package's first version),
Timothy Hayes [ctb] (Package's first version),
Thomas Valente [aut, cph] (R original code)
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between netdiffuseR versions 1.19.0 dated 2017-10-25 and 1.20.0 dated 2018-06-07
ChangeLog | 16 + DESCRIPTION | 41 ++-- MD5 | 205 ++++++++++++------------ NAMESPACE | 2 R/RcppExports.R | 13 - R/adjmat.r | 6 R/diffnet-methods.r | 75 ++++++-- R/formula.r |only R/igraph.r | 9 - R/imports.r | 1 R/misc.r | 2 R/moran.r | 29 +-- R/package-doc.r | 12 + R/plot_diffnet2.r | 5 R/rdiffnet.r | 3 R/select_egoalter.R | 2 R/stats.R | 8 R/struct_equiv.R | 2 R/struct_test.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 7 inst/NEWS | 115 ++++++++----- inst/doc/analyzing-medical-innovation-data.R | 6 inst/doc/analyzing-medical-innovation-data.Rmd | 8 inst/doc/analyzing-medical-innovation-data.html | 79 +++++++-- inst/doc/introduction-to-netdiffuser.html | 18 +- man/as.array.diffnet.Rd | 1 man/bass.Rd | 1 man/bootnet.Rd | 2 man/brfarmers.Rd | 1 man/brfarmersDiffNet.Rd | 1 man/c.diffnet.Rd | 1 man/classify_adopters.Rd | 1 man/cumulative_adopt_count.Rd | 3 man/dgr.Rd | 2 man/diffnet-arithmetic.Rd | 1 man/diffnet-class.Rd | 2 man/diffnet_index.Rd | 1 man/diffnetmatmult.Rd | 1 man/diffreg.Rd |only man/diffusion-data.Rd | 1 man/diffusionMap.Rd | 1 man/drawColorKey.Rd | 8 man/edgelist_to_adjmat.Rd | 3 man/edges_coords.Rd | 5 man/ego_variance.Rd | 1 man/egonet_attrs.Rd | 1 man/exposure.Rd | 4 man/fakeDynEdgelist.Rd | 1 man/fakeEdgelist.Rd | 1 man/fakesurvey.Rd | 1 man/fakesurveyDyn.Rd | 1 man/grid_distribution.Rd | 1 man/hazard_rate.Rd | 4 man/igraph.Rd | 1 man/infection.Rd | 2 man/isolated.Rd | 1 man/kfamily.Rd | 1 man/kfamilyDiffNet.Rd | 1 man/matrix_compare.Rd | 1 man/medInnovations.Rd | 1 man/medInnovationsDiffNet.Rd | 1 man/moran.Rd | 29 +-- man/netdiffuseR-graphs.Rd | 1 man/netdiffuseR.Rd | 14 + man/netmatch.Rd | 1 man/network.Rd | 1 man/permute_graph.Rd | 1 man/plot.diffnet.Rd | 1 man/plot_adopters.Rd | 1 man/plot_diffnet.Rd | 3 man/plot_diffnet2.Rd | 10 - man/plot_infectsuscep.Rd | 6 man/plot_threshold.Rd | 19 +- man/rdiffnet.Rd | 2 man/read_pajek.Rd | 4 man/read_ucinet_head.Rd | 1 man/rescale_vertex_igraph.Rd | 1 man/rewire_graph.Rd | 1 man/rgraph_ba.Rd | 18 -- man/rgraph_er.Rd | 8 man/rgraph_ws.Rd | 1 man/ring_lattice.Rd | 1 man/select_egoalter.Rd | 2 man/struct_equiv.Rd | 3 man/struct_test.Rd | 2 man/summary.diffnet.Rd | 1 man/survey_to_diffnet.Rd | 1 man/threshold.Rd | 3 man/toa_diff.Rd | 2 man/toa_mat.Rd | 2 man/vertex_covariate_compare.Rd | 1 man/vertex_covariate_dist.Rd | 3 src/RcppExports.cpp | 29 +-- src/adjmat.cpp | 22 +- src/infection.cpp | 34 +-- src/netdiffuser_extra.cpp | 8 src/plot.cpp | 79 ++++++--- src/rgraph.cpp | 48 ++--- src/stats.cpp | 45 +---- src/struct_test.cpp | 18 +- tests/testthat/test-formula.R |only tests/testthat/test-plot_diffnet2.R | 2 vignettes/analyzing-medical-innovation-data.Rmd | 8 105 files changed, 719 insertions(+), 447 deletions(-)
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data structures
and functions that facilitate the plotting of missing values and examination
of imputations. This allows missing data dependencies to be explored with
minimal deviation from the common work patterns of 'ggplot2' and tidy data.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>),
Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>),
Miles McBain [aut] (<https://orcid.org/0000-0003-2865-2548>),
Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>),
Jim Hester [ctb],
Luke Smith [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 0.2.0 dated 2018-02-09 and 0.3.0 dated 2018-06-07
naniar-0.2.0/naniar/R/miss-x-pct-prop.R |only naniar-0.2.0/naniar/man/miss_case_pct.Rd |only naniar-0.2.0/naniar/man/miss_case_prop.Rd |only naniar-0.2.0/naniar/man/miss_var_pct.Rd |only naniar-0.2.0/naniar/man/miss_var_prop.Rd |only naniar-0.2.0/naniar/man/which_var_na.Rd |only naniar-0.3.0/naniar/DESCRIPTION | 34 naniar-0.3.0/naniar/MD5 | 189 +- naniar-0.3.0/naniar/NAMESPACE | 34 naniar-0.3.0/naniar/NEWS.md | 297 ++- naniar-0.3.0/naniar/R/cast-shadows.R | 2 naniar-0.3.0/naniar/R/data-common-na-numbers.R |only naniar-0.3.0/naniar/R/data-common-na-strings.R |only naniar-0.3.0/naniar/R/geom-miss-point.R | 67 naniar-0.3.0/naniar/R/gg-miss-case.R | 42 naniar-0.3.0/naniar/R/gg-miss-fct.R | 5 naniar-0.3.0/naniar/R/gg-miss-span.R | 3 naniar-0.3.0/naniar/R/gg-miss-var.R | 74 naniar-0.3.0/naniar/R/gg-miss-which.R | 3 naniar-0.3.0/naniar/R/helpers.R |only naniar-0.3.0/naniar/R/impute_below.R |only naniar-0.3.0/naniar/R/impute_mean.R |only naniar-0.3.0/naniar/R/miss-complete-x-pct-prop.R |only naniar-0.3.0/naniar/R/miss-scan-count.R | 3 naniar-0.3.0/naniar/R/miss-x-summary.R | 38 naniar-0.3.0/naniar/R/n-prop-miss-complete.R | 2 naniar-0.3.0/naniar/R/n-var-miss.R |only naniar-0.3.0/naniar/R/naniar-ggproto.R | 2 naniar-0.3.0/naniar/R/naniar-package.R | 3 naniar-0.3.0/naniar/R/scoped-replace-with-na.R | 18 naniar-0.3.0/naniar/R/shadow-shifters.R | 75 naniar-0.3.0/naniar/R/shadows.R | 123 + naniar-0.3.0/naniar/R/stat-miss-point.R | 3 naniar-0.3.0/naniar/R/utils.R | 22 naniar-0.3.0/naniar/R/where-na.R | 16 naniar-0.3.0/naniar/README.md | 250 ++- naniar-0.3.0/naniar/build/vignette.rds |binary naniar-0.3.0/naniar/data/common_na_numbers.rda |only naniar-0.3.0/naniar/data/common_na_strings.rda |only naniar-0.3.0/naniar/inst/doc/getting-started-w-naniar.R | 30 naniar-0.3.0/naniar/inst/doc/getting-started-w-naniar.Rmd | 36 naniar-0.3.0/naniar/inst/doc/getting-started-w-naniar.html | 545 ++++--- naniar-0.3.0/naniar/inst/doc/naniar-visualisation.R | 24 naniar-0.3.0/naniar/inst/doc/naniar-visualisation.Rmd | 39 naniar-0.3.0/naniar/inst/doc/naniar-visualisation.html | 495 ++++-- naniar-0.3.0/naniar/inst/doc/replace-with-na.R | 30 naniar-0.3.0/naniar/inst/doc/replace-with-na.Rmd | 64 naniar-0.3.0/naniar/inst/doc/replace-with-na.html | 561 +++++-- naniar-0.3.0/naniar/man/all-is-miss-complete.Rd |only naniar-0.3.0/naniar/man/any-na.Rd |only naniar-0.3.0/naniar/man/are_shadow.Rd |only naniar-0.3.0/naniar/man/as_shadow_upset.Rd |only naniar-0.3.0/naniar/man/common_na_numbers.Rd |only naniar-0.3.0/naniar/man/common_na_strings.Rd |only naniar-0.3.0/naniar/man/figures/README-gg-miss-var-1.png |binary naniar-0.3.0/naniar/man/figures/README-upset-plot-1.png |only naniar-0.3.0/naniar/man/gg_miss_case.Rd | 10 naniar-0.3.0/naniar/man/gg_miss_var.Rd | 3 naniar-0.3.0/naniar/man/impute_below.Rd |only naniar-0.3.0/naniar/man/impute_below_at.Rd |only naniar-0.3.0/naniar/man/impute_below_if.Rd |only naniar-0.3.0/naniar/man/impute_mean.Rd |only naniar-0.3.0/naniar/man/is_shadow.Rd |only naniar-0.3.0/naniar/man/miss-complete-case-pct.Rd |only naniar-0.3.0/naniar/man/miss-complete-case-prop.Rd |only naniar-0.3.0/naniar/man/miss-complete-var-pct.Rd |only naniar-0.3.0/naniar/man/miss-complete-var-prop.Rd |only naniar-0.3.0/naniar/man/miss_case_summary.Rd | 15 naniar-0.3.0/naniar/man/miss_scan_count.Rd | 3 naniar-0.3.0/naniar/man/miss_summary.Rd | 2 naniar-0.3.0/naniar/man/miss_var_summary.Rd | 13 naniar-0.3.0/naniar/man/miss_var_which.Rd |only naniar-0.3.0/naniar/man/n-var-case-complete.Rd |only naniar-0.3.0/naniar/man/n-var-case-miss.Rd |only naniar-0.3.0/naniar/man/n_complete.Rd | 2 naniar-0.3.0/naniar/man/naniar-ggproto.Rd | 2 naniar-0.3.0/naniar/man/reexports.Rd | 6 naniar-0.3.0/naniar/man/replace_with_na_all.Rd | 3 naniar-0.3.0/naniar/man/replace_with_na_at.Rd | 7 naniar-0.3.0/naniar/man/replace_with_na_if.Rd | 3 naniar-0.3.0/naniar/man/scoped-impute_mean.Rd |only naniar-0.3.0/naniar/man/shadow_shift.numeric.Rd |only naniar-0.3.0/naniar/man/unbinders.Rd |only naniar-0.3.0/naniar/tests/figs/deps.txt | 2 naniar-0.3.0/naniar/tests/figs/gg-miss-case/gg-miss-case-group-and-sort-show-pct.svg |only naniar-0.3.0/naniar/tests/figs/gg-miss-case/gg-miss-case-group-and-sort.svg | 308 ++-- naniar-0.3.0/naniar/tests/figs/gg-miss-case/gg-miss-case-group-show-pct.svg |only naniar-0.3.0/naniar/tests/figs/gg-miss-case/gg-miss-case-group.svg | 762 +++++----- naniar-0.3.0/naniar/tests/figs/gg-miss-case/gg-miss-case-plot-show-pct.svg |only naniar-0.3.0/naniar/tests/figs/gg-miss-case/gg-miss-case-sort-show-pct.svg |only naniar-0.3.0/naniar/tests/figs/gg-miss-case/gg-miss-case-sort.svg | 308 ++-- naniar-0.3.0/naniar/tests/figs/gg-miss-case/gg-miss-case.svg | 308 ++-- naniar-0.3.0/naniar/tests/figs/gg-miss-fct/gg-miss-fct.svg | 668 ++++---- naniar-0.3.0/naniar/tests/figs/gg-miss-var-plot/gg-miss-var-group-pct.svg | 102 - 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Title: Animal Movement Modelling using Hidden Markov Models
Description: Provides tools for animal movement modelling using hidden Markov
models. These include processing of tracking data, fitting hidden Markov models
to movement data, visualization of data and fitted model, decoding of the state
process...
Author: Theo Michelot, Roland Langrock, Toby Patterson, Brett McClintock, Eric Rexstad (ctb)
Maintainer: Theo Michelot <tmichelot1@sheffield.ac.uk>
Diff between moveHMM versions 1.5 dated 2017-07-21 and 1.6 dated 2018-06-07
DESCRIPTION | 10 ++-- MD5 | 46 ++++++++++++---------- NAMESPACE | 8 +++ R/AIC_moveHMM.R | 18 +++++++- R/RcppExports.R | 16 +++---- R/allProbs.R | 10 ++-- R/fitHMM.R | 21 +++++----- R/nLogLike.R | 6 -- R/plotPR.R | 28 +++++++++---- R/plotStationary.R |only R/plot_moveHMM.R | 90 ++++++++++++++++++++++++++++++++------------ R/pseudoRes.R | 57 ++++++++++++++++----------- R/simData.R | 10 ++-- R/stationary.R |only R/turnAngle.R | 4 + build/vignette.rds |binary inst/doc/moveHMM-guide.R | 7 ++- inst/doc/moveHMM-guide.Rnw | 16 ++++++- inst/doc/moveHMM-guide.pdf |binary man/AIC.moveHMM.Rd | 2 man/plot.moveHMM.Rd | 8 +++ man/plotStationary.Rd |only man/stationary.Rd |only src/RcppExports.cpp | 16 +++---- src/moveHMM_init.c | 36 ++++++++--------- vignettes/moveHMM-guide.Rnw | 16 ++++++- 26 files changed, 271 insertions(+), 154 deletions(-)
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling for both dichotomous and polytomous responses. Various cognitive diagnosis models can be estimated, include the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7>, the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070>, and many other models they subsume. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.
Author: Wenchao Ma [aut, cre, cph],
Jimmy de la Torre [aut, cph],
Miguel Sorrel [ctb]
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>
Diff between GDINA versions 2.1.7 dated 2018-05-03 and 2.1.15 dated 2018-06-07
DESCRIPTION | 9 +- MD5 | 41 ++++++------ NEWS.md | 7 +- R/Est.R | 21 +++++- R/GDI.R | 18 ++--- R/GDINA-package.R | 6 + R/GDINA.R | 16 ++-- R/dif.R | 21 +++--- R/ecpe.R | 10 ++ R/plotIRF.GDINA.R | 174 ++++++++++++++++++++++++++++----------------------- R/print.GDINA.R | 2 R/structuralparm.R | 83 +++++++++++++++--------- R/summary.GDINA.R | 1 R/zzz.R |only README.md | 12 --- inst/shiny/server.R | 6 - man/GDINA-package.Rd | 6 + man/GDINA.Rd | 16 ++-- man/dif.Rd | 28 ++------ man/ecpe.Rd | 10 ++ man/plot.GDINA.Rd | 33 ++++----- man/plot.itemfit.Rd | 9 ++ 22 files changed, 311 insertions(+), 218 deletions(-)
Title: Haar-Fisz Functions for Binomial Data
Description: Binomial Haar-Fisz transforms for Gaussianization.
Author: Matt Nunes <m.nunes@lancaster.ac.uk>
Maintainer: Matt Nunes <m.nunes@lancaster.ac.uk>
Diff between binhf versions 1.0-1 dated 2014-04-24 and 1.0-2 dated 2018-06-07
binhf-1.0-1/binhf/R/madmad.R |only binhf-1.0-1/binhf/R/wandafromx.R |only binhf-1.0-2/binhf/DESCRIPTION | 14 +++++++------- binhf-1.0-2/binhf/MD5 | 16 +++++++--------- binhf-1.0-2/binhf/NAMESPACE | 5 +++++ binhf-1.0-2/binhf/R/shift.R | 4 +++- binhf-1.0-2/binhf/data/chr20.rda |binary binhf-1.0-2/binhf/data/mhc.rda |binary binhf-1.0-2/binhf/data/pintens.rda |binary binhf-1.0-2/binhf/man/chr20.Rd | 2 +- 10 files changed, 23 insertions(+), 18 deletions(-)
Title: Better ALignment CONsensus analYsis
Description: Facilitates the evolutionary analysis and structure conservation study of specified amino acids in proteins.
Author: Michal Stolarczyk & Alicja Pluciennik
Maintainer: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Diff between BALCONY versions 0.2.0 dated 2018-04-12 and 0.2.7 dated 2018-06-07
DESCRIPTION | 9 MD5 | 15 NAMESPACE | 1 R/BALCONYfunctions.R | 825 +++++++++++++++++++++------------------- man/CRE_conservativity.Rd | 3 man/RealValET_conservativity.Rd | 4 man/calculate_AA_variation.Rd | 4 man/calculate_pseudo_counts.Rd | 13 man/get_seq_weights.Rd |only 9 files changed, 468 insertions(+), 406 deletions(-)
Title: Finite Mixture Modeling for Raw and Binned Data
Description: Performs maximum likelihood estimation for finite mixture models for families including Normal, Weibull, Gamma and Lognormal by using EM algorithm, together with Newton-Raphson algorithm or bisection method when necessary. It also conducts mixture model selection by using information criteria or bootstrap likelihood ratio test. The data used for mixture model fitting can be raw data or binned data. The model fitting process is accelerated by using R package 'Rcpp'.
Author: Youjiao Yu [aut, cre]
Maintainer: Youjiao Yu <jiaoisjiao@gmail.com>
Diff between mixR versions 0.1.0 dated 2017-02-24 and 0.1.1 dated 2018-06-07
mixR-0.1.0/mixR/src/registerDynamicSymbol.c |only mixR-0.1.1/mixR/DESCRIPTION | 8 mixR-0.1.1/mixR/MD5 | 78 ++++----- mixR-0.1.1/mixR/NEWS.md |only mixR-0.1.1/mixR/R/RcppExports.R | 88 +++++----- mixR-0.1.1/mixR/R/density.mixfitEM.R | 2 mixR-0.1.1/mixR/R/gammapar.R | 2 mixR-0.1.1/mixR/R/lnormpar.R | 2 mixR-0.1.1/mixR/R/main.R | 10 - mixR-0.1.1/mixR/R/package.R | 4 mixR-0.1.1/mixR/R/plot.R | 8 mixR-0.1.1/mixR/R/print.selectEM.R | 2 mixR-0.1.1/mixR/R/reinstate.R | 2 mixR-0.1.1/mixR/R/weibullpar.R | 2 mixR-0.1.1/mixR/man/Stamp.Rd | 36 ++-- mixR-0.1.1/mixR/man/Stamp2.Rd | 38 ++-- mixR-0.1.1/mixR/man/bin.Rd | 74 ++++---- mixR-0.1.1/mixR/man/bs.test.Rd | 160 +++++++++--------- mixR-0.1.1/mixR/man/density.mixfitEM.Rd | 96 +++++------ mixR-0.1.1/mixR/man/initz.Rd | 80 ++++----- mixR-0.1.1/mixR/man/mixR-package.Rd | 220 ++++++++++++------------- mixR-0.1.1/mixR/man/mixfit.Rd | 240 ++++++++++++++-------------- mixR-0.1.1/mixR/man/plot.bootEM.Rd | 62 +++---- mixR-0.1.1/mixR/man/plot.mixfitEM.Rd | 124 +++++++------- mixR-0.1.1/mixR/man/plot.selectEM.Rd | 68 +++---- mixR-0.1.1/mixR/man/print.mixfitEM.Rd | 66 +++---- mixR-0.1.1/mixR/man/print.selectEM.Rd | 50 ++--- mixR-0.1.1/mixR/man/reinstate.Rd | 70 ++++---- mixR-0.1.1/mixR/man/rmixgamma.Rd | 74 ++++---- mixR-0.1.1/mixR/man/rmixlnorm.Rd | 74 ++++---- mixR-0.1.1/mixR/man/rmixnormal.Rd | 74 ++++---- mixR-0.1.1/mixR/man/rmixweibull.Rd | 74 ++++---- mixR-0.1.1/mixR/man/select.Rd | 160 +++++++++--------- mixR-0.1.1/mixR/man/to_k_lambda_weibull.Rd | 74 ++++---- mixR-0.1.1/mixR/man/to_mu_sd_gamma.Rd | 68 +++---- mixR-0.1.1/mixR/man/to_mu_sd_lnorm.Rd | 68 +++---- mixR-0.1.1/mixR/man/to_mu_sd_weibull.Rd | 70 ++++---- mixR-0.1.1/mixR/man/to_mulog_sdlog_lnorm.Rd | 72 ++++---- mixR-0.1.1/mixR/man/to_shape_rate_gamma.Rd | 72 ++++---- mixR-0.1.1/mixR/src/RcppExports.cpp | 141 +++++++++++----- mixR-0.1.1/mixR/src/mixCpp.cpp | 108 ++++++------ 41 files changed, 1387 insertions(+), 1334 deletions(-)
Title: Lightning Fast Serialization of Data Frames for R
Description: Multithreaded serialization of compressed data frames using the
'fst' format. The 'fst' format allows for random access of stored data and
compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD
compression library is owned by Facebook Inc.
Author: Mark Klik [aut, cre, cph],
Yann Collet [ctb, cph] (Yann Collet is author of the bundled LZ4 and
ZSTD code and copyright holder of LZ4),
Facebook, Inc. [cph] (Bundled ZSTD code)
Maintainer: Mark Klik <markklik@gmail.com>
Diff between fst versions 0.8.6 dated 2018-05-16 and 0.8.8 dated 2018-06-07
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- src/fstcore/blockstreamer/blockstreamer_v2.cpp | 15 +++++++++++++-- src/fstcore/character/character_v6.cpp | 11 +++++++++-- src/fstcore/compression/compression.cpp | 20 +++++++++++++------- src/fstcore/interface/fststore.cpp | 8 ++++++++ src/fstcore/logical/logical_v10.cpp | 16 ++-------------- tests/testthat/FactorStore/data1.fst |binary tests/testthat/test_lintr.R | 4 ++++ tests/testthat/testdata |only 10 files changed, 63 insertions(+), 37 deletions(-)
Title: Compare Detrital Zircon Suites
Description: Compare detrital zircon suites by uploading univariate,
U-Pb age, or bivariate, U-Pb age and Lu-Hf data, in a 'shiny'-based
user-interface. Outputs publication quality figures using 'ggplot2', and
tables of statistics currently in use in the detrital zircon geochronology
community.
Author: Magnus Kristoffersen [aut, cre]
Maintainer: Magnus Kristoffersen <magnus.kristoffersen@geo.uio.no>
Diff between detzrcr versions 0.2.2 dated 2018-04-11 and 0.2.3 dated 2018-06-07
DESCRIPTION | 6 +-- MD5 | 16 ++++----- NEWS.md | 4 ++ R/plotting.R | 20 +++++++++--- build/vignette.rds |binary inst/doc/detzrcr-vignette.html | 4 +- inst/shiny-apps/detzrcr_app/app.R | 63 +++++++++++++++++++++----------------- man/plot_dens.Rd | 4 +- man/plot_dens_hist.Rd | 4 +- 9 files changed, 75 insertions(+), 46 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, with optional sampling techniques and kernel term.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 1.5.2 dated 2018-03-20 and 1.5.3 dated 2018-06-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/RcppExports.R | 16 ++++++++++++++++ man/bWGR.Rd | 4 ++-- man/em.Rd | 4 ++++ src/RcppExports.cpp | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++ src/wgr032018.cpp | 31 +++++++++++++++++++++++++++---- 7 files changed, 110 insertions(+), 16 deletions(-)
Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre] (<https://orcid.org/0000-0001-5052-066X>)
Maintainer: Matti Vuorre <mv2521@columbia.edu>
Diff between bmlm versions 1.3.5 dated 2017-11-29 and 1.3.6 dated 2018-06-07
DESCRIPTION | 10 MD5 | 12 NEWS.md | 4 R/utils.R | 7 README.md | 55 - man/tab2doc.Rd | 6 src/include/models.hpp | 1733 +++++++++++++++++++++++-------------------------- 7 files changed, 902 insertions(+), 925 deletions(-)
Title: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck
models to phylogenetic comparative data using Bayesian reversible-jump
methods.
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda <josef.uyeda@gmail.com>
Diff between bayou versions 1.1.0 dated 2015-10-25 and 2.1 dated 2018-06-07
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Title: Bayesian Methods for Image Segmentation using a Potts Model
Description: Various algorithms for segmentation of 2D and 3D images, such
as computed tomography and satellite remote sensing. This package implements
Bayesian image analysis using the hidden Potts model with external field
prior of Moores et al. (2015) <doi:10.1016/j.csda.2014.12.001>.
Latent labels are sampled using chequerboard updating or Swendsen-Wang.
Algorithms for the smoothing parameter include pseudolikelihood, path sampling,
the exchange algorithm, approximate Bayesian computation (ABC-MCMC and ABC-SMC),
and Bayesian indirect likelihood (BIL). Refer to <doi:10.1007/s11222-014-9525-6>
and <arXiv:1503.08066> for further details.
Author: Matt Moores [aut, cre] (<https://orcid.org/0000-0003-4531-3572>),
Kerrie Mengersen [aut, ths] (<https://orcid.org/0000-0001-8625-9168>),
Dai Feng [ctb]
Maintainer: Matt Moores <mmoores@gmail.com>
Diff between bayesImageS versions 0.5-1 dated 2018-02-02 and 0.5-2 dated 2018-06-07
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Title: Bayesian Variable Selection and Model Averaging using Bayesian
Adaptive Sampling
Description: Package for Bayesian Variable Selection and Model Averaging in linear models and
generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from Liang et al (2008)
<DOI:10.1198/016214507000001337>
for linear models or mixtures of g-priors in GLMs of Li and Clyde (2015)
<arXiv:1503.06913>. Other model
selection criteria include AIC, BIC and Empirical Bayes estimates of g.
Sampling probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an efficient MCMC algorithm
samples models using the BAS tree structure as an efficient hash table.
Uniform priors over all models or beta-binomial prior distributions on
model size are allowed, and for large p truncated priors on the model
space may be used. The user may force variables to always be included.
Details behind the sampling algorithm are provided in
Clyde, Ghosh and Littman (2010) <DOI:10.1198/jcgs.2010.09049>.
This material is based upon work supported by the National Science
Foundation under Grant DMS-1106891. Any opinions, findings, and
conclusions or recommendations expressed in this material are those of
the author(s) and do not necessarily reflect the views of the
National Science Foundation.
Author: Merlise Clyde [aut, cre, cph] (<https://orcid.org/-5469>),
Michael Littman [ctb],
Quanli Wang [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@duke.edu>
Diff between BAS versions 1.5.0 dated 2018-05-06 and 1.5.1 dated 2018-06-07
DESCRIPTION | 8 +- MD5 | 43 ++++++------ NAMESPACE | 1 NEWS.md | 10 ++ R/predict.bas.R | 143 ++++++++++++++++++++++++++++++----------- inst/doc/BAS-vignette.R | 6 - inst/doc/BAS-vignette.Rmd | 6 - inst/doc/BAS-vignette.html | 139 ++++++++++++++++++++------------------- man/BAS.Rd | 3 man/bas.lm.Rd | 3 man/coef.Rd | 3 man/confint.coef.Rd | 3 man/confint.pred.Rd | 3 man/diagnostics.Rd | 3 man/fitted.Rd | 6 + man/force.heredity.bas.Rd | 3 man/image.bas.Rd | 3 man/predict.bas.Rd | 48 +++++++++---- man/predict.basglm.Rd | 47 ++++++++----- man/summary.Rd | 3 man/update.Rd | 3 man/variable.names.pred.bas.Rd |only vignettes/BAS-vignette.Rmd | 6 - 23 files changed, 312 insertions(+), 181 deletions(-)
Title: Solving 1D Advection Bi-Flux Diffusion Equation
Description: This software solves an Advection Bi-Flux Diffusive Problem using the Finite Difference Method FDM. Vasconcellos, J.F.V., Marinho, G.M., Zanni, J.H., 2016, Numerical analysis of an anomalous diffusion with a bimodal flux distribution. <doi:10.1016/j.rimni.2016.05.001>. Silva, L.G., Knupp, D.C., Bevilacqua, L., Galeao, A.C.N.R., Silva Neto, A.J., 2014, Formulation and solution of an Inverse Anomalous Diffusion Problem with Stochastic Techniques. <doi:10.5902/2179460X13184>. In this version, it is possible to include a source as a function depending on space and time, that is, s(x,t).
Author: Jader Lugon Junior, Pedro Paulo Gomes Watts Rodrigues, Luiz Bevilacqua, Diego Campos Knupp, Joao Flavio Vieira Vasconcellos and Antonio Jose da Silva Neto.
Maintainer: Jader Lugon Junior <jlugonjr@gmail.com>
Diff between AdvDif4 versions 0.1.18 dated 2018-04-25 and 0.2.18 dated 2018-06-07
DESCRIPTION | 8 +- MD5 | 15 ++-- R/AdvDif4.R | 35 +++++----- inst/doc/News.md |only inst/doc/parse10.R | 17 ++++- inst/doc/parse11.R | 16 +++-- inst/doc/parse20.R | 16 +++-- inst/doc/parse21.R | 16 +++-- man/AdvDif4.Rd | 169 +++++++++++++++++++++++++++++++++++++++++++---------- 9 files changed, 219 insertions(+), 73 deletions(-)