Title: Fast EM and Best-Subset Selection for CUB Models for Rating Data
Description: For ordinal rating data, consider the accelerated Expectation-Maximization algorithm to estimate and test models within the family of CUB models (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions). The procedure is built upon Louis' identity for the observed information matrix. Best-subset variable selection for CUB regression models is then implemented on such basis. The methods here implemented are illustrated and discussed in the preprint available from Researchgate by Simone R. (2020) <https://tinyurl.com/vvk563e>.
Author: Rosaria Simone <rosaria.simone@unina.it>
Maintainer: Rosaria Simone <rosaria.simone@unina.it>
Diff between FastCUB versions 0.0.1 dated 2020-01-31 and 0.0.2 dated 2020-02-12
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/fastCUB.R | 2 +- R/fastCUB_package.R | 2 +- R/fastcub0q.R | 6 +++--- R/fastcubp0.R | 6 +++--- R/fastcubpq.R | 6 +++--- man/fastCUB_package.Rd | 2 +- 8 files changed, 22 insertions(+), 22 deletions(-)
Title: R Interface to the 'UNU.RAN' Random Variate Generators
Description: Interface to the 'UNU.RAN' library for Universal Non-Uniform RANdom variate generators.
Thus it allows to build non-uniform random number generators from quite arbitrary
distributions. In particular, it provides an algorithm for fast numerical inversion
for distribution with given density function.
In addition, the package contains densities, distribution functions and quantiles
from a couple of distributions.
Author: Josef Leydold [aut, cre],
Wolfgang H"ormann [aut]
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Runuran versions 0.28 dated 2020-02-04 and 0.30 dated 2020-02-12
Runuran-0.28/Runuran/tests/test-all.R |only Runuran-0.28/Runuran/tests/test_auxurng.R |only Runuran-0.28/Runuran/tests/test_details.R |only Runuran-0.28/Runuran/tests/test_details.Rout.save |only Runuran-0.28/Runuran/tests/test_packed.R |only Runuran-0.30/Runuran/DESCRIPTION | 8 +-- Runuran-0.30/Runuran/MD5 | 47 ++++++++++++++------- Runuran-0.30/Runuran/NEWS | 22 +++++++++ Runuran-0.30/Runuran/R/Runuran.R | 22 ++++++++- Runuran-0.30/Runuran/R/unuran_cmv.R | 3 + Runuran-0.30/Runuran/inst/doc/Runuran.pdf |binary Runuran-0.30/Runuran/man/Runuran-package.Rd | 4 - Runuran-0.30/Runuran/src/Runuran.c | 25 ++++++++++- Runuran-0.30/Runuran/tests/run_testthat.R |only Runuran-0.30/Runuran/tests/testthat/saves |only Runuran-0.30/Runuran/tests/testthat/test_auxurng.R |only Runuran-0.30/Runuran/tests/testthat/test_details.R |only Runuran-0.30/Runuran/tests/testthat/test_distr.R |only Runuran-0.30/Runuran/tests/testthat/test_options.R | 12 ++--- Runuran-0.30/Runuran/tests/testthat/test_packed.R |only Runuran-0.30/Runuran/vignettes/inputs/version.tex | 2 21 files changed, 112 insertions(+), 33 deletions(-)
Title: Enterprise Streamlined 'Shiny' Application Framework
Description: An enterprise-targeted scalable and UI-standardized 'shiny' framework
including a variety of developer convenience functions with the goal of both
streamlining robust application development while assisting with creating a
consistent user experience regardless of application or developer.
Author: Constance Brett [aut, cre],
Isaac Neuhaus [aut] (canvasXpress JavaScript Library Maintainer),
Ger Inberg [ctb],
Bristol-Meyers Squibb (BMS) [cph]
Maintainer: Constance Brett <connie@aggregate-genius.com>
Diff between periscope versions 0.4.7 dated 2019-12-10 and 0.4.8 dated 2020-02-12
DESCRIPTION | 10 +- MD5 | 69 +++++++++------ NAMESPACE | 3 NEWS.md | 9 +- R/convert_template.R |only R/downloadFile.R | 10 ++ R/fw_helpers_external.R | 17 ++- R/generate_template.R | 12 +- build/vignette.rds |binary inst/doc/downloadFile-module.html | 4 inst/doc/downloadablePlot-module.html | 4 inst/doc/downloadableTable-module.html | 4 inst/doc/new-application.Rmd | 4 inst/doc/new-application.html | 6 - inst/fw_templ/p_example/plots.R | 1 man/add_reset_button.Rd |only man/add_right_sidebar.Rd |only man/add_ui_sidebar_advanced.Rd | 7 + man/add_ui_sidebar_basic.Rd | 3 man/create_new_application.Rd | 9 +- man/downloadFile.Rd | 11 ++ man/downloadablePlot.Rd | 12 ++ man/downloadablePlotUI.Rd | 17 ++- man/downloadableTable.Rd | 15 ++- man/downloadableTableUI.Rd | 9 +- man/periscope.Rd | 1 man/remove_reset_button.Rd |only man/set_app_parameters.Rd | 9 +- tests/testthat/sample_app |only tests/testthat/test_convert_application.R |only tests/testthat/test_ui_functions.R | 131 +++++++++++++++++++++++++++--- tests/testthat/test_ui_misc_functions.R | 8 + vignettes/new-application.Rmd | 4 33 files changed, 301 insertions(+), 88 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-30 1.1-221.2
2019-04-18 1.1-221.1
2014-08-05 1.1-221
2014-04-02 1.1-20
2012-11-08 1.1-13
2012-05-16 1.1-12
2012-04-10 1.1-11
2012-01-23 1.1-9
2011-01-20 1.1-5
2010-05-04 1.1
2009-12-10 1.0
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Author: Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut] (<https://orcid.org/0000-0002-1994-3581>),
Pedro Despouy [aut],
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.9.1 dated 2019-11-07 and 4.9.2 dated 2020-02-12
DESCRIPTION | 8 MD5 | 870 +++++----- NAMESPACE | 1 NEWS.md | 15 R/add.R | 39 R/embed.R | 2 R/ggplotly.R | 4 R/layers2traces.R | 15 R/layout.R | 12 R/plotly.R | 22 R/plotly_build.R | 2 R/sf.R | 2 R/sysdata.rda |binary inst/docker/Dockerfile.vtest | 1 inst/examples/shiny/event_data/tests/mytest-expected/001.json | 21 inst/examples/shiny/event_data/tests/mytest-expected/002.json | 21 inst/examples/shiny/event_data/tests/mytest-expected/003.json | 21 inst/examples/shiny/event_data/tests/mytest-expected/004.json | 21 inst/htmlwidgets/lib/plotlyjs/LICENSE | 2 inst/htmlwidgets/lib/plotlyjs/locales/af.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/am.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/ar-dz.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/ar-eg.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/ar.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/az.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/bg.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/bs.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/ca.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/cs.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/cy.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/da.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/de-ch.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/de.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/el.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/eo.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/es-ar.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/es-pe.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/es.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/et.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/eu.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/fa.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/fi.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/fo.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/fr-ch.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/fr.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/gl.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/gu.js | 2 inst/htmlwidgets/lib/plotlyjs/locales/he.js | 2 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Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. Users can collect open-access avian recordings or enter their own data into a workflow that facilitates spectrographic visualization and measurement of acoustic parameters. 'warbleR' makes use of the basic sound analysis tools from the package 'seewave', and offers new tools for acoustic structure analysis. The main features of the package are the use of loops to apply tasks through acoustic signals referenced in a selection (annotation) table and the production of spectrograms in image files that allow to organize data and verify acoustic analyzes. The package offers functions to explore, organize and manipulate multiple sound files, explore and download 'Xeno-Canto' recordings, detect signals automatically, create spectrograms of complete recordings or individual signals, run different measures of acoustic signal structure, evaluate the performance of measurement methods, catalog signals, characterize different structural levels in acoustic signals, run statistical analysis of duet coordination and consolidate databases and annotation tables, among others.
Author: Marcelo Araya-Salas [aut, cre]
(<https://orcid.org/0000-0003-3594-619X>),
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between warbleR versions 1.1.21 dated 2020-02-04 and 1.1.22 dated 2020-02-12
DESCRIPTION | 8 +++--- MD5 | 36 ++++++++++++++-------------- R/find_peaks.R | 2 - R/rename_waves_est.R | 10 +++---- data/comp_matrix.rda |binary data/lbh_selec_table.rda |binary data/lbh_selec_table2.rda |binary data/new_function_names.rda |binary data/selec.table.rda |binary data/sim.coor.sing.rda |binary data/sim_coor_sing.rda |binary inst/doc/Intro_to_warbleR.R | 5 --- inst/doc/Intro_to_warbleR.Rmd | 5 --- inst/doc/Intro_to_warbleR.html | 48 +++++++++++++++++++------------------- inst/doc/warbleR_workflow_01.html | 2 - inst/doc/warbleR_workflow_02.html | 4 +-- inst/doc/warbleR_workflow_03.html | 4 +-- man/rename_waves_est.Rd | 10 +++---- vignettes/Intro_to_warbleR.Rmd | 5 --- 19 files changed, 65 insertions(+), 74 deletions(-)
Title: Exponential Random Graph Models for Small Networks
Description: Simulation and estimation of Exponential Random Graph Models (ERGMs)
for small networks using exact statistics. As a difference from the 'ergm'
package, 'ergmito' circumvents using Markov-Chain Maximum Likelihood Estimator
(MC-MLE) and instead uses Maximum Likelihood Estimator (MLE) to fit ERGMs
for small networks. As exhaustive enumeration is computationally feasible for
small networks, this R package takes advantage of this and provides tools for
calculating likelihood functions, and other relevant functions, directly,
meaning that in many cases both estimation and simulation of ERGMs for
small networks can be faster and more accurate than simulation-based
algorithms.
Author: George Vega Yon [cre, aut] (<https://orcid.org/0000-0002-3171-0844>),
Kayla de la Haye [ths] (<https://orcid.org/0000-0002-2536-7701>),
Army Research Laboratory and the U.S. Army Research Office [fnd] (Grant
Number W911NF-15-1-0577)
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between ergmito versions 0.2-0 dated 2020-02-01 and 0.2-1 dated 2020-02-12
ergmito-0.2-0/ergmito/data/fivesamplers.rda |only ergmito-0.2-0/ergmito/man/fivesamplers.Rd |only ergmito-0.2-1/ergmito/DESCRIPTION | 10 +- ergmito-0.2-1/ergmito/MD5 | 26 ++--- ergmito-0.2-1/ergmito/R/data.R | 21 ++-- ergmito-0.2-1/ergmito/R/ergmito-checkers.R | 60 ++++++++---- ergmito-0.2-1/ergmito/build/ergmito.pdf |binary ergmito-0.2-1/ergmito/inst/doc/ergm-equations.Rmd | 4 ergmito-0.2-1/ergmito/inst/doc/ergm-equations.html | 14 +- ergmito-0.2-1/ergmito/inst/doc/extending-ergmito.html | 26 ++--- ergmito-0.2-1/ergmito/inst/test-data-for-tests.R | 4 ergmito-0.2-1/ergmito/inst/test-data-for-tests.rda |binary ergmito-0.2-1/ergmito/inst/tinytest/test-ergmito-checkers.R | 44 ++++---- ergmito-0.2-1/ergmito/man/fivenets.Rd | 3 ergmito-0.2-1/ergmito/vignettes/ergm-equations.Rmd | 4 15 files changed, 113 insertions(+), 103 deletions(-)
Title: Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
Description: Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.
Author: Adrian Dragulescu [aut],
Cole Arendt [aut, cre]
Maintainer: Cole Arendt <cole.arendt@outlook.com>
Diff between xlsx versions 0.6.1 dated 2018-06-11 and 0.6.2 dated 2020-02-12
xlsx-0.6.1/xlsx/inst/doc/xlsx.Rnw |only xlsx-0.6.1/xlsx/inst/doc/xlsx.pdf |only xlsx-0.6.1/xlsx/vignettes/xlsx.Rnw |only xlsx-0.6.2/xlsx/DESCRIPTION | 31 xlsx-0.6.2/xlsx/MD5 | 172 +- xlsx-0.6.2/xlsx/NAMESPACE | 89 + xlsx-0.6.2/xlsx/NEWS | 102 - xlsx-0.6.2/xlsx/R/Alignment.R | 74 - xlsx-0.6.2/xlsx/R/Border.R | 89 + xlsx-0.6.2/xlsx/R/Cell.R | 362 +++--- xlsx-0.6.2/xlsx/R/CellBlock.R | 508 +++++--- xlsx-0.6.2/xlsx/R/CellProtection.R | 52 xlsx-0.6.2/xlsx/R/CellStyle.R | 521 +++++--- xlsx-0.6.2/xlsx/R/DataFormat.R | 61 - xlsx-0.6.2/xlsx/R/Fill.R | 68 - xlsx-0.6.2/xlsx/R/Font.R | 143 +- xlsx-0.6.2/xlsx/R/NamedRanges.R | 298 ++-- xlsx-0.6.2/xlsx/R/Picture.R | 109 + xlsx-0.6.2/xlsx/R/PrintSetup.R | 135 +- xlsx-0.6.2/xlsx/R/Row.R | 807 +++++++------ xlsx-0.6.2/xlsx/R/Workbook.R | 383 +++--- xlsx-0.6.2/xlsx/R/addDataFrame.R | 97 + xlsx-0.6.2/xlsx/R/autoRefresh.R | 34 xlsx-0.6.2/xlsx/R/comment.R | 148 +- xlsx-0.6.2/xlsx/R/otherEffects.R | 453 ++++--- xlsx-0.6.2/xlsx/R/read.xlsx.R | 294 +++- xlsx-0.6.2/xlsx/R/read.xlsx2.R | 114 - xlsx-0.6.2/xlsx/R/readColumns.R | 99 + xlsx-0.6.2/xlsx/R/readRows.R | 122 +- xlsx-0.6.2/xlsx/R/utilities.R | 369 +++--- xlsx-0.6.2/xlsx/R/write.xlsx.R | 236 ++- xlsx-0.6.2/xlsx/R/write.xlsx2.R | 54 xlsx-0.6.2/xlsx/R/xlsx-package.R |only xlsx-0.6.2/xlsx/README.md | 75 + xlsx-0.6.2/xlsx/build/vignette.rds |binary xlsx-0.6.2/xlsx/inst/doc/excel_report.R |only xlsx-0.6.2/xlsx/inst/doc/excel_report.Rmd |only xlsx-0.6.2/xlsx/inst/doc/excel_report.html |only xlsx-0.6.2/xlsx/inst/doc/xlsx.R | 14 xlsx-0.6.2/xlsx/inst/doc/xlsx.Rmd |only xlsx-0.6.2/xlsx/inst/doc/xlsx.html |only xlsx-0.6.2/xlsx/inst/tests/crash_write_xlsx.R | 44 xlsx-0.6.2/xlsx/inst/tests/lib_tests_xlsx.R | 1560 +++++++++++++------------- xlsx-0.6.2/xlsx/inst/tests/test.import.R | 278 ++-- xlsx-0.6.2/xlsx/man/Alignment.Rd | 81 - xlsx-0.6.2/xlsx/man/Border.Rd | 73 - xlsx-0.6.2/xlsx/man/Cell.Rd | 110 - xlsx-0.6.2/xlsx/man/CellBlock.Rd | 237 ++- xlsx-0.6.2/xlsx/man/CellProtection.Rd | 51 xlsx-0.6.2/xlsx/man/CellStyle-plus.Rd | 45 xlsx-0.6.2/xlsx/man/CellStyle.Rd | 131 +- xlsx-0.6.2/xlsx/man/Comment.Rd | 64 - xlsx-0.6.2/xlsx/man/DataFormat.Rd | 68 - xlsx-0.6.2/xlsx/man/Fill.Rd | 79 - xlsx-0.6.2/xlsx/man/Font.Rd | 112 - xlsx-0.6.2/xlsx/man/NamedRanges.Rd | 86 - xlsx-0.6.2/xlsx/man/OtherEffects.Rd | 165 +- xlsx-0.6.2/xlsx/man/POI_constants.Rd | 26 xlsx-0.6.2/xlsx/man/Picture.Rd | 58 xlsx-0.6.2/xlsx/man/PrintSetup.Rd | 89 - xlsx-0.6.2/xlsx/man/Row.Rd | 70 - xlsx-0.6.2/xlsx/man/Sheet.Rd | 50 xlsx-0.6.2/xlsx/man/Workbook.Rd | 75 - xlsx-0.6.2/xlsx/man/addDataFrame.Rd | 136 +- xlsx-0.6.2/xlsx/man/addHyperlink.Rd | 61 - xlsx-0.6.2/xlsx/man/autoRefresh.Rd | 49 xlsx-0.6.2/xlsx/man/read.xlsx.Rd | 224 ++- xlsx-0.6.2/xlsx/man/readColumns.Rd | 134 +- xlsx-0.6.2/xlsx/man/readRows.Rd | 67 - xlsx-0.6.2/xlsx/man/write.xlsx.Rd | 124 +- xlsx-0.6.2/xlsx/man/xlsx-package.Rd | 115 - xlsx-0.6.2/xlsx/tests |only xlsx-0.6.2/xlsx/vignettes/excel_report.Rmd |only xlsx-0.6.2/xlsx/vignettes/excel_report.png |only xlsx-0.6.2/xlsx/vignettes/xlsx.Rmd |only xlsx-0.6.2/xlsx/vignettes/xlsx.bib |only 76 files changed, 6110 insertions(+), 4465 deletions(-)
Title: SIMulated Structural Equation Modeling
Description: Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Author: Sunthud Pornprasertmanit [aut],
Patrick Miller [aut],
Alexander Schoemann [aut],
Terrence D. Jorgensen [aut, cre]
(<https://orcid.org/0000-0001-5111-6773>),
Corbin Quick [ctb]
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>
Diff between simsem versions 0.5-14 dated 2018-06-03 and 0.5-15 dated 2020-02-12
DESCRIPTION | 29 - MD5 | 18 R/createData.R | 11 R/drawParam.R | 220 ++++----- R/generate.R | 6 R/imposeMissing.R | 1301 +++++++++++++++++++++++++++--------------------------- R/model.R | 23 R/sim.R | 30 + man/bindDist.Rd | 2 man/sim.Rd | 100 ++-- 10 files changed, 897 insertions(+), 843 deletions(-)
Title: Connecting R and 'Raven' Sound Analysis Software
Description: A tool to exchange data between R and 'Raven' sound analysis software (Cornell Lab of Ornithology). Functions work on data formats compatible with the R package 'warbleR'.
Author: Marcelo Araya-Salas [aut, cre]
(<https://orcid.org/0000-0003-3594-619X>)
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between Rraven versions 1.0.8 dated 2019-11-02 and 1.0.9 dated 2020-02-12
Rraven-1.0.8/Rraven/man/Rraven.Rd |only Rraven-1.0.9/Rraven/DESCRIPTION | 12 Rraven-1.0.9/Rraven/MD5 | 64 Rraven-1.0.9/Rraven/NAMESPACE | 10 Rraven-1.0.9/Rraven/NEWS.md | 6 Rraven-1.0.9/Rraven/R/Rraven-package.R | 14 Rraven-1.0.9/Rraven/R/exp_empty_sels.R | 17 Rraven-1.0.9/Rraven/R/exp_est.R | 29 Rraven-1.0.9/Rraven/R/exp_raven.R | 14 Rraven-1.0.9/Rraven/R/extract_ts.R | 2 Rraven-1.0.9/Rraven/R/fix_path.R | 10 Rraven-1.0.9/Rraven/R/imp_corr_mat.R | 14 Rraven-1.0.9/Rraven/R/imp_raven.R | 9 Rraven-1.0.9/Rraven/R/match_wav_case.R | 14 Rraven-1.0.9/Rraven/R/raven_batch_detec.R | 158 - Rraven-1.0.9/Rraven/R/run_raven.R | 29 Rraven-1.0.9/Rraven/README.md | 4 Rraven-1.0.9/Rraven/inst/doc/Rraven.R | 9 Rraven-1.0.9/Rraven/inst/doc/Rraven.Rmd | 42 Rraven-1.0.9/Rraven/inst/doc/Rraven.html | 1374 ---------- Rraven-1.0.9/Rraven/man/exp_empty_sels.Rd | 17 Rraven-1.0.9/Rraven/man/exp_est.Rd | 11 Rraven-1.0.9/Rraven/man/exp_raven.Rd | 14 Rraven-1.0.9/Rraven/man/fix_path.Rd | 10 Rraven-1.0.9/Rraven/man/imp_corr_mat.Rd | 14 Rraven-1.0.9/Rraven/man/imp_raven.Rd | 6 Rraven-1.0.9/Rraven/man/match_wav_case.Rd | 14 Rraven-1.0.9/Rraven/man/raven_batch_detec.Rd | 4 Rraven-1.0.9/Rraven/man/run_raven.Rd | 19 Rraven-1.0.9/Rraven/vignettes/Catalog.jpeg |binary Rraven-1.0.9/Rraven/vignettes/Rraven.Rmd | 42 Rraven-1.0.9/Rraven/vignettes/opt2_short_exp_raven1.gif |only Rraven-1.0.9/Rraven/vignettes/opt2_short_exp_raven2.gif |only Rraven-1.0.9/Rraven/vignettes/opt2_short_raven_batch_detec.gif |only Rraven-1.0.9/Rraven/vignettes/opt2_short_raven_correlator.gif |only Rraven-1.0.9/Rraven/vignettes/opt2_short_run_raven1.gif |only 36 files changed, 385 insertions(+), 1597 deletions(-)
Title: Geometries to Plot Networks with 'ggplot2'
Description: Geometries to plot network objects with 'ggplot2'.
Author: François Briatte [aut, cre] (<https://orcid.org/0000-0001-6494-9774>),
Michał Bojanowski [ctb] (<https://orcid.org/0000-0001-7503-852X>),
Mickaël Canouil [ctb] (<https://orcid.org/0000-0002-3396-4549>),
Zachary Charlop-Powers [ctb] (<https://orcid.org/0000-0001-8816-4680>),
Jacob C. Fisher [ctb] (<https://orcid.org/0000-0003-0299-0346>),
Kipp Johnson [ctb] (<https://orcid.org/0000-0002-5102-741X>),
Tyler Rinker [ctb]
Maintainer: François Briatte <f.briatte@gmail.com>
Diff between ggnetwork versions 0.5.1 dated 2016-03-24 and 0.5.8 dated 2020-02-12
ggnetwork-0.5.1/ggnetwork/README.md |only ggnetwork-0.5.1/ggnetwork/tests/testthat/test-fortify.R |only ggnetwork-0.5.1/ggnetwork/tests/testthat/test-geoms.R |only ggnetwork-0.5.8/ggnetwork/DESCRIPTION | 42 ggnetwork-0.5.8/ggnetwork/MD5 | 64 - ggnetwork-0.5.8/ggnetwork/NAMESPACE | 14 ggnetwork-0.5.8/ggnetwork/NEWS.md |only ggnetwork-0.5.8/ggnetwork/R/fortify-igraph.R | 61 - ggnetwork-0.5.8/ggnetwork/R/fortify-network.R | 202 +--- ggnetwork-0.5.8/ggnetwork/R/geom-edges.R | 322 +++--- ggnetwork-0.5.8/ggnetwork/R/geom-nodes.R | 423 ++++---- ggnetwork-0.5.8/ggnetwork/R/ggnetwork.R | 54 - ggnetwork-0.5.8/ggnetwork/R/utilities.R | 214 ++++ ggnetwork-0.5.8/ggnetwork/build/vignette.rds |binary ggnetwork-0.5.8/ggnetwork/inst/doc/ggnetwork.R | 66 - ggnetwork-0.5.8/ggnetwork/inst/doc/ggnetwork.Rmd | 10 ggnetwork-0.5.8/ggnetwork/inst/doc/ggnetwork.html | 496 +++++++--- ggnetwork-0.5.8/ggnetwork/man/format_fortify.Rd |only ggnetwork-0.5.8/ggnetwork/man/fortify.Rd |only ggnetwork-0.5.8/ggnetwork/man/fortify.igraph.Rd | 55 - ggnetwork-0.5.8/ggnetwork/man/fortify.network.Rd | 61 - ggnetwork-0.5.8/ggnetwork/man/geom_edges.Rd | 176 +-- ggnetwork-0.5.8/ggnetwork/man/geom_edgetext.Rd | 133 +- ggnetwork-0.5.8/ggnetwork/man/geom_edgetext_repel.Rd | 148 +- ggnetwork-0.5.8/ggnetwork/man/geom_nodes.Rd | 110 +- ggnetwork-0.5.8/ggnetwork/man/geom_nodetext.Rd | 177 ++- ggnetwork-0.5.8/ggnetwork/man/geom_nodetext_repel.Rd | 156 +-- ggnetwork-0.5.8/ggnetwork/man/ggnetwork.Rd | 17 ggnetwork-0.5.8/ggnetwork/man/scale_safely.Rd |only ggnetwork-0.5.8/ggnetwork/man/theme_blank.Rd | 1 ggnetwork-0.5.8/ggnetwork/man/theme_facet.Rd | 1 ggnetwork-0.5.8/ggnetwork/man/unit.Rd |only ggnetwork-0.5.8/ggnetwork/tests/testthat/test-fortify-igraph.R |only ggnetwork-0.5.8/ggnetwork/tests/testthat/test-fortify-network.R |only ggnetwork-0.5.8/ggnetwork/tests/testthat/test-geom-edges.R |only ggnetwork-0.5.8/ggnetwork/tests/testthat/test-geom-nodes.R |only ggnetwork-0.5.8/ggnetwork/tests/testthat/test-ggnetwork.R | 72 + ggnetwork-0.5.8/ggnetwork/tests/testthat/test-utilities.R | 35 ggnetwork-0.5.8/ggnetwork/vignettes/ggnetwork.Rmd | 10 39 files changed, 1921 insertions(+), 1199 deletions(-)
Title: Weighting and Weighted Statistics
Description: Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial correlations, Chi-Squared statistics, histograms, and t-tests. Also now includes some software for quickly recoding survey data and plotting point estimates from interaction terms in regressions (and multiply imputed regressions). NOTE: Weighted partial correlation calculations pulled to address a bug.
Author: Josh Pasek [aut, cre], with some assistance from Alex Tahk and some code modified from R-core; Additional contributions by Gene Culter and Marcus Schwemmle.
Maintainer: Josh Pasek <josh@joshpasek.com>
Diff between weights versions 1.0 dated 2018-10-16 and 1.0.1 dated 2020-02-12
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/findwtdinteraction.list.R |only man/plotwtdinteraction.Rd | 1 + src/init.c | 2 +- 5 files changed, 10 insertions(+), 8 deletions(-)
Title: Subgroup Specific Optimal Dose Assignment
Description: Chooses subgroup specific optimal doses in a phase I dose finding clinical trial allowing for subgroup combination and simulates clinical trials under the subgroup specific time to event continual reassessment method. Chapple, A.G., Thall, P.F. (2018) <doi:10.1002/pst.1891>.
Author: Andrew Chapple
Maintainer: Andrew Chapple <achapp@lsuhsc.edu>
Diff between SubTite versions 3.0.0 dated 2019-11-03 and 3.0.1 dated 2020-02-12
DESCRIPTION | 12 ++++-------- MD5 | 4 ++-- src/SUBGROUP.cpp | 16 ++++++++-------- 3 files changed, 14 insertions(+), 18 deletions(-)
Title: Mixed-Effect Models, Particularly Spatial Models
Description: Inference based on mixed-effect models, including generalized linear mixed models with spatial correlations and models with non-Gaussian random effects (e.g., Beta). Both classical geostatistical models, and Markov random field models on irregular grids, can be fitted. Variation in residual variance (heteroscedasticity) can itself be represented by a generalized linear mixed model. Various approximations of likelihood or restricted likelihood are implemented, in particular h-likelihood (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) and Laplace approximation.
Author: François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>),
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut] (<https://orcid.org/0000-0003-0637-2959>),
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 3.0.0 dated 2019-06-21 and 3.1.2 dated 2020-02-12
spaMM-3.0.0/spaMM/data/oceanmask.RData |only spaMM-3.0.0/spaMM/data/worldcountries.RData |only spaMM-3.0.0/spaMM/man/separation.Rd |only spaMM-3.0.0/spaMM/man/simulate.HLCor.Rd |only spaMM-3.1.2/spaMM/DESCRIPTION | 21 spaMM-3.1.2/spaMM/MD5 | 246 +-- spaMM-3.1.2/spaMM/NAMESPACE | 9 spaMM-3.1.2/spaMM/R/COMPoisson.R | 62 spaMM-3.1.2/spaMM/R/GLM.fit.R | 68 spaMM-3.1.2/spaMM/R/HLFactorList.R | 1 spaMM-3.1.2/spaMM/R/HLfit_Internals.R | 457 ++++-- spaMM-3.1.2/spaMM/R/HLfit_b_internals.R | 40 spaMM-3.1.2/spaMM/R/HLfit_body.R | 243 +-- spaMM-3.1.2/spaMM/R/HLfit_body_augZXy.R | 7 spaMM-3.1.2/spaMM/R/IRLS_internals.R |only spaMM-3.1.2/spaMM/R/LR.R | 304 ++-- spaMM-3.1.2/spaMM/R/LevM_v_h.R |only spaMM-3.1.2/spaMM/R/LevM_v_h_spprec.R |only spaMM-3.1.2/spaMM/R/LevenbergMstep.R | 4 spaMM-3.1.2/spaMM/R/MakeCovEst.R | 157 +- spaMM-3.1.2/spaMM/R/bloc_lambda.R | 3 spaMM-3.1.2/spaMM/R/calc_LRT.R | 129 + spaMM-3.1.2/spaMM/R/calc_logdisp_cov.R | 4 spaMM-3.1.2/spaMM/R/confint.R | 3 spaMM-3.1.2/spaMM/R/corrHLfit-internals.R | 101 - spaMM-3.1.2/spaMM/R/corrHLfit.R | 2 spaMM-3.1.2/spaMM/R/corrHLfit_body.R | 4 spaMM-3.1.2/spaMM/R/corrMM.LRT.R | 19 spaMM-3.1.2/spaMM/R/correlationFns.R | 20 spaMM-3.1.2/spaMM/R/cov_new_fix.R | 32 spaMM-3.1.2/spaMM/R/dispGammaGLM.R | 4 spaMM-3.1.2/spaMM/R/extractors.R | 118 + spaMM-3.1.2/spaMM/R/fit_as_ZX.R | 751 +++++++--- spaMM-3.1.2/spaMM/R/fit_as_sparsePrecision.R | 760 +++++++---- spaMM-3.1.2/spaMM/R/fitme.R | 2 spaMM-3.1.2/spaMM/R/fitme_body.R | 32 spaMM-3.1.2/spaMM/R/fitmecorrHLfit_body_internals.R | 181 +- spaMM-3.1.2/spaMM/R/geo_info.R | 6 spaMM-3.1.2/spaMM/R/get_cPredVar.R |only spaMM-3.1.2/spaMM/R/locoptim.R | 103 - spaMM-3.1.2/spaMM/R/makeLowerUpper.R | 2 spaMM-3.1.2/spaMM/R/mapMM.R | 10 spaMM-3.1.2/spaMM/R/newPLS.R | 79 - spaMM-3.1.2/spaMM/R/plot_effects.R | 13 spaMM-3.1.2/spaMM/R/postfit_internals.R | 11 spaMM-3.1.2/spaMM/R/predict.R | 289 ++-- spaMM-3.1.2/spaMM/R/predict_marg.R | 5 spaMM-3.1.2/spaMM/R/preprocess.R | 201 +- spaMM-3.1.2/spaMM/R/profile.R | 14 spaMM-3.1.2/spaMM/R/sXaug_EigenDense_QRP_Chol_scaled.R | 49 spaMM-3.1.2/spaMM/R/sXaug_Matrix_QRP_CHM.R | 75 - spaMM-3.1.2/spaMM/R/sXaug_sparsePrecisions.R | 47 spaMM-3.1.2/spaMM/R/safe_opt.R |only spaMM-3.1.2/spaMM/R/separator.R | 51 spaMM-3.1.2/spaMM/R/simulate.HL.R | 102 - spaMM-3.1.2/spaMM/R/spaMM.data.R | 108 + spaMM-3.1.2/spaMM/R/spaMM_boot.R | 179 +- spaMM-3.1.2/spaMM/R/summary.HL.R | 6 spaMM-3.1.2/spaMM/R/sysdata.rda |only spaMM-3.1.2/spaMM/R/utils.R | 57 spaMM-3.1.2/spaMM/build/partial.rdb |binary spaMM-3.1.2/spaMM/inst/NEWS.Rd | 69 spaMM-3.1.2/spaMM/man/COMPoisson.Rd | 4 spaMM-3.1.2/spaMM/man/HLCor.Rd | 2 spaMM-3.1.2/spaMM/man/HLfit.Rd | 6 spaMM-3.1.2/spaMM/man/anova.HLfit.Rd | 20 spaMM-3.1.2/spaMM/man/confint.Rd | 2 spaMM-3.1.2/spaMM/man/convergence.Rd |only spaMM-3.1.2/spaMM/man/corrHLfit.Rd | 12 spaMM-3.1.2/spaMM/man/covStruct.Rd | 2 spaMM-3.1.2/spaMM/man/eval_replicate.Rd |only spaMM-3.1.2/spaMM/man/fitme.Rd | 22 spaMM-3.1.2/spaMM/man/fix_predVar.Rd |only spaMM-3.1.2/spaMM/man/fixed.LRT.Rd | 31 spaMM-3.1.2/spaMM/man/get_cPredVar.Rd |only spaMM-3.1.2/spaMM/man/get_inits_from_fit.Rd |only spaMM-3.1.2/spaMM/man/get_ranPars.Rd | 7 spaMM-3.1.2/spaMM/man/how.Rd | 5 spaMM-3.1.2/spaMM/man/is_separated.Rd | 6 spaMM-3.1.2/spaMM/man/make.scaled.dist.Rd | 2 spaMM-3.1.2/spaMM/man/mapMM.Rd | 22 spaMM-3.1.2/spaMM/man/options.Rd | 38 spaMM-3.1.2/spaMM/man/plot_effect.Rd | 6 spaMM-3.1.2/spaMM/man/post-fit.Rd |only spaMM-3.1.2/spaMM/man/predict.Rd | 44 spaMM-3.1.2/spaMM/man/seaMask.Rd | 28 spaMM-3.1.2/spaMM/man/simulate.Rd |only spaMM-3.1.2/spaMM/man/spaMM-S3.Rd | 1 spaMM-3.1.2/spaMM/man/spaMM-internal.Rd | 3 spaMM-3.1.2/spaMM/man/spaMM_boot.Rd | 40 spaMM-3.1.2/spaMM/man/summary.HL.Rd | 4 spaMM-3.1.2/spaMM/src/Makevars.win | 4 spaMM-3.1.2/spaMM/tests/test-all.R | 14 spaMM-3.1.2/spaMM/tests/testthat/test-AR1.R | 12 spaMM-3.1.2/spaMM/tests/testthat/test-CAR.R | 12 spaMM-3.1.2/spaMM/tests/testthat/test-COMPoisson.R | 7 spaMM-3.1.2/spaMM/tests/testthat/test-HLCor.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-HLfit.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-IMRF.R | 5 spaMM-3.1.2/spaMM/tests/testthat/test-Infusion.R | 8 spaMM-3.1.2/spaMM/tests/testthat/test-IsoriX.R | 13 spaMM-3.1.2/spaMM/tests/testthat/test-LRT-boot.R | 12 spaMM-3.1.2/spaMM/tests/testthat/test-MSFDR.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-Matern-spprec.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-Nugget.R | 5 spaMM-3.1.2/spaMM/tests/testthat/test-Rasch.R | 4 spaMM-3.1.2/spaMM/tests/testthat/test-adjacency-corrMatrix.R | 10 spaMM-3.1.2/spaMM/tests/testthat/test-adjacency-long.R | 29 spaMM-3.1.2/spaMM/tests/testthat/test-augZXy.R | 4 spaMM-3.1.2/spaMM/tests/testthat/test-blackbox.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-cloglog.R | 10 spaMM-3.1.2/spaMM/tests/testthat/test-confint.R | 17 spaMM-3.1.2/spaMM/tests/testthat/test-corMatern.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-dhglm.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-filled.mapMM.R | 10 spaMM-3.1.2/spaMM/tests/testthat/test-fixedLRT.R | 4 spaMM-3.1.2/spaMM/tests/testthat/test-inverse.Gamma.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-more-predict.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-multinomial.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-negbin1.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-pedigree.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-poly.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-predVar.R | 34 spaMM-3.1.2/spaMM/tests/testthat/test-ranCoefs.R | 60 spaMM-3.1.2/spaMM/tests/testthat/test-random-slope.R | 24 spaMM-3.1.2/spaMM/tests/testthat/test-rank.R | 14 spaMM-3.1.2/spaMM/tests/testthat/test-salamander.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-simulate.R | 28 spaMM-3.1.2/spaMM/tests/testthat/test-spaMM.R | 19 spaMM-3.1.2/spaMM/tests/testthat/test-spaMM.filled.contour.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-spaMM_glm.R | 2 spaMM-3.1.2/spaMM/tests/testthat/test-truncated.R | 5 spaMM-3.1.2/spaMM/tests/testthat/test_init_NaN.R |only 133 files changed, 3644 insertions(+), 2319 deletions(-)
Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2018) <arXiv:1810.03136> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] (<https://orcid.org/0000-0002-5516-5107>),
Sander Devriendt [aut],
Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>
Diff between smurf versions 1.0.3 dated 2020-02-07 and 1.0.4 dated 2020-02-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- inst/NEWS.Rd | 15 +++++++++++++++ inst/doc/smurf.html | 2 +- inst/examples/Rent_example2.R | 2 +- man/plot_lambda.Rd | 2 +- tests/testthat/test_input.R | 5 ----- tests/testthat/test_p.R | 3 +-- 8 files changed, 30 insertions(+), 21 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Originally described in Kamvar, Tabima, and Grünwald (2014)
<doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and
Grünwald (2015) <doi:10.3389/fgene.2015.00208>.
Author: Zhian N. Kamvar [cre, aut] (<https://orcid.org/0000-0003-1458-7108>),
Javier F. Tabima [aut] (<https://orcid.org/0000-0002-3603-2691>),
Sydney E. Everhart [ctb, dtc] (<https://orcid.org/0000-0002-5773-1280>),
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb]
(<https://orcid.org/0000-0002-7324-7448>),
Erik Sotka [ctb],
Brian J. Knaus [ctb] (<https://orcid.org/0000-0003-1665-4343>),
Patrick G. Meirmans [ctb] (<https://orcid.org/0000-0002-6395-8107>),
Frédéric D. Chevalier [ctb] (<https://orcid.org/0000-0003-2611-8106>),
Niklaus J. Grünwald [ths] (<https://orcid.org/0000-0003-1656-7602>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.8.3 dated 2019-06-18 and 2.8.4 dated 2020-02-12
DESCRIPTION | 9 MD5 | 109 ++++----- NEWS.md |only R/aaaMLGmethods.R | 1 R/ia_jackknife.R | 1 R/poppr.R | 6 README.md | 2 build/vignette.rds |binary inst/doc/algo.R | 6 inst/doc/algo.pdf |binary inst/doc/mlg.R | 86 +++---- inst/doc/mlg.html | 454 +++++++++++++++++++-------------------- inst/doc/poppr_manual.R | 22 - inst/doc/poppr_manual.Rmd | 4 inst/doc/poppr_manual.html | 444 +++++++++++++++++++------------------- man/aboot.Rd | 17 + man/bitwise.dist.Rd | 13 - man/bitwise.ia.Rd | 3 man/bootgen-methods.Rd | 1 man/bruvo.boot.Rd | 16 + man/bruvo.dist.Rd | 3 man/bruvo.msn.Rd | 27 +- man/bruvomat-methods.Rd | 1 man/diversity_boot.Rd | 17 + man/diversity_ci.Rd | 16 + man/diversity_stats.Rd | 3 man/filter_stats.Rd | 17 + man/genclone-method.Rd | 6 man/genetic_distance.Rd | 5 man/genind2genalex.Rd | 19 + man/genotype_curve.Rd | 12 - man/getfile.Rd | 2 man/greycurve.Rd | 9 man/ia.Rd | 29 +- man/info_table.Rd | 15 + man/locus_table.Rd | 11 man/missingno.Rd | 3 man/mlg.Rd | 28 +- man/mlg.filter.Rd | 26 +- man/plot_filter_stats.Rd | 10 man/plot_poppr_msn.Rd | 30 ++ man/poppr-package.Rd | 7 man/poppr.Rd | 25 +- man/poppr.amova.Rd | 26 +- man/poppr.msn.Rd | 25 +- man/poppr.plot.Rd | 14 - man/popsub.Rd | 3 man/private_alleles.Rd | 12 - man/psex.Rd | 19 + man/read.genalex.Rd | 17 + man/rraf.Rd | 3 man/snpclone-coercion-methods.Rd | 3 man/snpclone-method.Rd | 4 man/unique-methods.Rd | 1 man/win.ia.Rd | 11 vignettes/poppr_manual.Rmd | 4 56 files changed, 954 insertions(+), 703 deletions(-)
Title: House Price Indexes
Description: Compute house price indexes and series using a variety of different methods and
models common through the real estate literature. Evaluate index 'goodness' based
on accuracy, volatility and revision statistics. Background on basic model construction
for repeat sales models can be found at: Case and Quigley (1991)
<https://ideas.repec.org/a/tpr/restat/v73y1991i1p50-58.html> and for hedonic pricing models at:
Bourassa et al (2006) <doi:10.1016/j.jhe.2006.03.001>. The package author's working paper on the
random forest approach to house price indexes can be found at: <http://www.github.com/andykrause/hpi_research>.
Author: Andy Krause [aut, cre]
Maintainer: Andy Krause <andyxkrause@gmail.com>
Diff between hpiR versions 0.3.0 dated 2020-01-11 and 0.3.1 dated 2020-02-12
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 1 - NEWS.md | 13 +++---------- R/calcForecastError.R | 1 - R/calcKFoldError.R | 15 +++++---------- inst/doc/classstructure.html | 4 ++-- inst/doc/introduction.html | 10 +++++----- man/buildForecastIDs.Rd | 2 -- man/createKFoldData.Rd | 6 ++---- 10 files changed, 32 insertions(+), 50 deletions(-)
Title: Distribution Optimization
Description: Fits Gaussian Mixtures by applying evolution. As fitness function a mixture of the chi square test for distributions and a novel measure for approximating the common area under curves between multiple Gaussians is used. The package presents an alternative to the commonly used Likelihood Maximization as is used in Expectation Maximization. The algorithm and applications of this package are published under: Lerch, F., Ultsch, A., Lotsch, J. (2020) <doi:10.1038/s41598-020-57432-w>. The evolution is based on the 'GA' package: Scrucca, L. (2013) <doi:10.18637/jss.v053.i04> while the Gaussian Mixture Logic stems from 'AdaptGauss': Ultsch, A, et al. (2015) <doi:10.3390/ijms161025897>.
Author: Florian Lerch, Jorn Lotsch, Alfred Ultsch
Maintainer: Florian Lerch <lerch@mathematik.uni-marburg.de>
Diff between DistributionOptimization versions 1.2.4 dated 2019-11-25 and 1.2.6 dated 2020-02-12
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 3 ++- R/BinProb4Mixtures.R | 4 ++-- R/DistributionOptimization.R | 26 ++++++++++++++++++++------ R/MixedDistributionError.R | 24 +++++++++++++++++------- R/OverlapErrorByDensity.R | 10 ++++++++-- man/BinProb4Mixtures.Rd | 3 +-- 8 files changed, 62 insertions(+), 32 deletions(-)
More information about DistributionOptimization at CRAN
Permanent link
Title: Estimating Dark Diversity and Site-Specific Species Pools
Description: Estimation of dark diversity and site-specific species pools using species co-occurrences.
It includes implementations of probabilistic dark diversity based on the
Hypergeometric distribution, as well as estimations based on the Beals index,
which can be transformed to binary predictions using different thresholds,
or transformed into a favorability index. All methods include the possibility of
using a calibration dataset that is used to estimate the indication matrix
between pairs of species, or to estimate dark diversity directly on a single
dataset. See De Caceres and Legendre (2008) <doi:10.1007/s00442-008-1017-y>,
Lewis et al. (2016) <doi:10.1111/2041-210X.12443>,
Partel et al. (2011) <doi:10.1016/j.tree.2010.12.004>, Real et al. (2017) <doi:10.1093/sysbio/syw072>
for further information.
Author: Carlos P. Carmona
Maintainer: Carlos P. Carmona <perezcarmonacarlos@gmail.com>
Diff between DarkDiv versions 0.1.0 dated 2019-04-27 and 0.2.0 dated 2020-02-12
DarkDiv-0.1.0/DarkDiv/tests/testthat.R |only DarkDiv-0.2.0/DarkDiv/DESCRIPTION | 10 +++++----- DarkDiv-0.2.0/DarkDiv/MD5 | 6 +++--- DarkDiv-0.2.0/DarkDiv/R/utility_functions.R | 2 +- DarkDiv-0.2.0/DarkDiv/tests/testthat |only 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Read Data Files from ActiGraph Monitors
Description: Standardize the process of bringing various modes of output files
into R. Additionally, processes are provided to read and minimally pre-
process raw data from primary accelerometer and inertial measurement unit files,
as well as binary .gt3x files. ActiGraph monitors are used to estimate physical
activity outcomes via body-worn sensors that measure (e.g.) acceleration or
rotational velocity.
Author: Paul R. Hibbing [aut, cre],
Vincent T. van Hees [ctb],
Samuel R. LaMunion [ctb],
John Muschelli [ctb],
Daniel Judge [ctb],
Judge Maygarden [ctb],
ActiGraph LLC [cph]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
Diff between AGread versions 1.0.0 dated 2019-09-18 and 1.1.0 dated 2020-02-12
AGread-1.0.0/AGread/R/check_gaps.R |only AGread-1.0.0/AGread/man/AG_round.Rd |only AGread-1.0.0/AGread/man/check_gaps.Rd |only AGread-1.0.0/AGread/man/test_VM.Rd |only AGread-1.0.0/AGread/man/test_times.Rd |only AGread-1.1.0/AGread/DESCRIPTION | 14 AGread-1.1.0/AGread/MD5 | 127 ++- AGread-1.1.0/AGread/NAMESPACE | 4 AGread-1.1.0/AGread/NEWS.md | 22 AGread-1.1.0/AGread/R/AG_insert.R |only AGread-1.1.0/AGread/R/AG_merge.R |only AGread-1.1.0/AGread/R/AGread-deprecated.R | 27 AGread-1.1.0/AGread/R/AGread.R | 2 AGread-1.1.0/AGread/R/AGread_utils.R | 19 AGread-1.1.0/AGread/R/RcppExports.R | 112 +++ AGread-1.1.0/AGread/R/Read_Counts.R | 353 ++-------- AGread-1.1.0/AGread/R/Read_Counts_Utils.R |only AGread-1.1.0/AGread/R/Read_IMU_Magnetometer_Directions.R | 72 +- AGread-1.1.0/AGread/R/Reintegrate.R | 11 AGread-1.1.0/AGread/R/collapse_gt3x.R | 199 ++++- AGread-1.1.0/AGread/R/format_sleep_events.R |only AGread-1.1.0/AGread/R/impute_IMU.R |only AGread-1.1.0/AGread/R/impute_primary.R |only AGread-1.1.0/AGread/R/parse_info_txt.R | 5 AGread-1.1.0/AGread/R/parse_log_bin.R | 33 AGread-1.1.0/AGread/R/parse_log_bin_utils.R | 13 AGread-1.1.0/AGread/R/parse_packet_set_ACTIVITY2.R | 84 -- AGread-1.1.0/AGread/R/parse_packet_set_EVENT.R |only AGread-1.1.0/AGread/R/parse_packet_set_SENSOR_DATA.R | 51 - AGread-1.1.0/AGread/R/parse_packet_set_SENSOR_SCHEMA.R | 4 AGread-1.1.0/AGread/R/parse_packet_set__generic_&_simple_methods.R | 28 AGread-1.1.0/AGread/R/read_gt3x.R | 48 - AGread-1.1.0/AGread/R/read_gt3x_utils.R | 82 +- AGread-1.1.0/AGread/R/zzz.R | 6 AGread-1.1.0/AGread/man/AG_col_names.Rd | 2 AGread-1.1.0/AGread/man/AG_insert.Rd |only AGread-1.1.0/AGread/man/AG_merge.Rd |only AGread-1.1.0/AGread/man/AG_meta.Rd | 2 AGread-1.1.0/AGread/man/AG_time.Rd | 4 AGread-1.1.0/AGread/man/capitalize.Rd |only AGread-1.1.0/AGread/man/check_inc.Rd | 6 AGread-1.1.0/AGread/man/classify_magnetometer.Rd | 2 AGread-1.1.0/AGread/man/collapse_gt3x.Rd | 6 AGread-1.1.0/AGread/man/empty_raw.Rd |only AGread-1.1.0/AGread/man/format_sleep_events.Rd |only AGread-1.1.0/AGread/man/get_VM.Rd | 21 AGread-1.1.0/AGread/man/get_duration-deprecated.Rd | 2 AGread-1.1.0/AGread/man/get_headersC.Rd |only AGread-1.1.0/AGread/man/get_times.Rd |only AGread-1.1.0/AGread/man/impute_IMU.Rd |only AGread-1.1.0/AGread/man/impute_primary.Rd |only AGread-1.1.0/AGread/man/mid_round.Rd |only AGread-1.1.0/AGread/man/next_separator.Rd |only AGread-1.1.0/AGread/man/parse_info_txt.Rd | 4 AGread-1.1.0/AGread/man/parse_packet_set.Rd | 13 AGread-1.1.0/AGread/man/payload_parse_activity2_26C.Rd | 5 AGread-1.1.0/AGread/man/payload_parse_sensor_data_25C.Rd | 4 AGread-1.1.0/AGread/man/reintegrate.Rd | 4 AGread-1.1.0/AGread/src/RcppExports.cpp | 167 ++++ AGread-1.1.0/AGread/src/get_VM_C.cpp |only AGread-1.1.0/AGread/src/get_headersC.cpp | 105 ++ AGread-1.1.0/AGread/src/get_latch.cpp |only AGread-1.1.0/AGread/src/get_times.cpp |only AGread-1.1.0/AGread/src/helpers.cpp | 42 + AGread-1.1.0/AGread/src/helpers.h | 1 AGread-1.1.0/AGread/src/impute_C.cpp |only AGread-1.1.0/AGread/src/imu_payload.h | 4 AGread-1.1.0/AGread/src/imu_wrapper.cpp | 17 AGread-1.1.0/AGread/src/interpolate_IMU.cpp | 39 - AGread-1.1.0/AGread/src/parseSensorC.cpp | 165 ++-- AGread-1.1.0/AGread/src/primary_payload.cpp | 53 - AGread-1.1.0/AGread/src/primary_payload.h | 3 AGread-1.1.0/AGread/src/primary_wrapper.cpp | 18 AGread-1.1.0/AGread/tests/testthat/read_3x_imu.rds |binary AGread-1.1.0/AGread/tests/testthat/read_3x_imu_1s.rds |binary AGread-1.1.0/AGread/tests/testthat/read_3x_raw.rds |binary AGread-1.1.0/AGread/tests/testthat/read_3x_raw_1s.rds |binary AGread-1.1.0/AGread/tests/testthat/test_equivalence.R | 21 78 files changed, 1264 insertions(+), 762 deletions(-)
Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>
Diff between RgoogleMaps versions 1.4.5.2 dated 2020-01-26 and 1.4.5.3 dated 2020-02-12
DESCRIPTION | 13 - MD5 | 14 - NAMESPACE | 3 R/PlotOnStaticMap.R | 2 R/PlotPolysOnStaticMap.R | 2 man/GetMapTiles.Rd | 329 ++++++++++++++------------------------------ man/PlotPolysOnStaticMap.Rd | 2 man/plotmap.Rd | 174 +++++++---------------- 8 files changed, 186 insertions(+), 353 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256',
'crc32', 'xxhash', 'murmurhash' and 'spookyhash' algorithms) permitting easy
comparison of R language objects, as well as functions such as'hmac()' to
create hash-based message authentication code. Please note that this package
is not meant to be deployed for cryptographic purposes for which more
comprehensive (and widely tested) libraries such as 'OpenSSL' should be
used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx,
Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, Kendon Bell,
Matthew de Queljoe, Ion Suruceanu, and Bill Denney.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.23 dated 2019-11-23 and 0.6.24 dated 2020-02-12
ChangeLog | 41 +++++ DESCRIPTION | 8 - MD5 | 25 +-- R/digest.R | 6 R/init.R | 25 ++- R/sha1.R | 66 +++----- R/vdigest.R | 2 build/vignette.rds |binary inst/doc/sha1.html | 227 ++++++++++++++---------------- inst/tinytest/test_new_matrix_behaviour.R |only inst/tinytest/test_sha1.R | 10 + man/digest2int.Rd | 2 man/sha1.Rd | 4 src/init.c | 10 - 14 files changed, 235 insertions(+), 191 deletions(-)
Title: Disease-Related Differential Proteins and Co-Expression Network
Analysis
Description: Functions designed to connect disease-related differential proteins and
co-expression network. It provides the basic statics analysis included t test, ANOVA analysis.
The network construction is not offered by the package, you can used 'WGCNA' package which you
can learn in Peter et al. (2008) <doi:10.1186/1471-2105-9-559>. It also provides module analysis
included PCA analysis, two enrichment analysis, Planner maximally filtered graph extraction and
hub analysis.
Author: Kefu Liu [aut, cre]
Maintainer: Kefu Liu <liukefu19@163.com>
Diff between DDPNA versions 0.2.1 dated 2019-06-15 and 0.2.3 dated 2020-02-12
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/DEPextract.R | 12 ++++++++++-- R/missing_value_impute.R | 19 ++++++++++++++----- R/module_enrich.R | 9 ++++++--- R/plot.R | 8 +++++++- data/Sample_ID_data.rda |binary man/DEP_Mod_HeatMap.Rd | 5 ++++- man/ID_match.Rd | 8 ++++---- man/MaxquantDataconvert.Rd | 8 ++++---- man/SoftThresholdScaleGraph.Rd | 4 +++- 11 files changed, 66 insertions(+), 35 deletions(-)
Title: Automated Data Preparation
Description: Do most of the painful data preparation for a data science project with a minimum amount of code; Take advantages of data.table efficiency and use some algorithmic trick in order to perform data preparation in a time and RAM efficient way.
Author: Emmanuel-Lin Toulemonde [aut, cre]
Maintainer: Emmanuel-Lin Toulemonde <el.toulemonde@protonmail.com>
Diff between dataPreparation versions 0.4.2 dated 2019-11-14 and 0.4.3 dated 2020-02-12
DESCRIPTION | 8 +- MD5 | 16 ++-- NEWS | 7 +- NEWS.md | 7 +- R/sameShape.R | 35 ++++++++-- build/vignette.rds |binary inst/doc/dataPreparation.html | 40 +++++------- inst/doc/train_test_prep.html | 130 ++++++++++++++++++++++++++++++++++++---- tests/testthat/test_sameShape.R | 45 +++++++++++++ 9 files changed, 237 insertions(+), 51 deletions(-)
More information about dataPreparation at CRAN
Permanent link
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 3.4.1 dated 2020-01-24 and 3.4.2 dated 2020-02-12
DESCRIPTION | 6 MD5 | 74 +++--- NEWS.md | 7 R/errors.R | 107 +++++++--- R/hook.R | 7 R/package.R | 4 R/r-process.R | 44 +--- R/r-session.R | 223 +++++++++++--------- R/rcmd-process.R | 25 -- R/rscript.R | 22 -- inst/WORDLIST | 9 inst/doc |only man/callr.Rd | 28 ++ man/convert_and_check_my_args.Rd | 4 man/default_repos.Rd | 4 man/get_result.Rd | 4 man/new_callr_error.Rd | 4 man/r.Rd | 4 man/r_bg.Rd | 4 man/r_copycat.Rd | 4 man/r_process.Rd | 155 ++++++++++++-- man/r_process_options.Rd | 4 man/r_session.Rd | 417 ++++++++++++++++++++++++++++++++------- man/r_session_debug.Rd | 4 man/r_session_options.Rd | 4 man/r_vanilla.Rd | 4 man/rcmd.Rd | 4 man/rcmd_bg.Rd | 4 man/rcmd_copycat.Rd | 4 man/rcmd_process.Rd | 131 ++++++++++-- man/rcmd_process_options.Rd | 4 man/rcmd_safe.Rd | 4 man/reexports.Rd | 9 man/rscript.Rd | 4 man/rscript_process.Rd | 129 ++++++++++-- man/rscript_process_options.Rd | 4 tests/testthat/test-error.R | 13 + tests/testthat/test-rcmd.R | 2 38 files changed, 1130 insertions(+), 354 deletions(-)
Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface
Database (ISD, see <https://www.ncdc.noaa.gov/isd>).
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.8.7 dated 2019-04-17 and 0.8.8 dated 2020-02-12
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/getMeta.R | 2 +- R/sysdata.rda |binary data/weatherCodes.rda |binary man/getMeta.Rd | 14 +++++++++++--- man/importNOAA.Rd | 13 ++++++++++--- man/worldmet.Rd | 1 - 8 files changed, 34 insertions(+), 20 deletions(-)
Title: Dimensionality Reduction via Regression
Description: An Implementation of Dimensionality Reduction
via Regression using Kernel Ridge Regression.
Author: Guido Kraemer [aut, cre]
Maintainer: Guido Kraemer <gkraemer@bgc-jena.mpg.de>
Diff between DRR versions 0.0.3 dated 2018-01-06 and 0.0.4 dated 2020-02-12
DESCRIPTION | 8 ++--- MD5 | 14 +++++----- R/DRR.R | 4 ++ README.md | 1 build/vignette.rds |binary inst/doc/comparePCA.R | 12 ++++---- inst/doc/comparePCA.html | 63 ++++++++++++++++++++++++++++++++++------------- man/drr.Rd | 19 +++++++++++--- 8 files changed, 82 insertions(+), 39 deletions(-)
Title: Co-Ranking Matrix
Description: Calculates the co-ranking matrix to assess the
quality of a dimensionality reduction.
Author: Guido Kraemer
Maintainer: Guido Kraemer <gkraemer@bgc-jena.mpg.de>
Diff between coRanking versions 0.1.4 dated 2018-10-01 and 0.2.1 dated 2020-02-12
DESCRIPTION | 10 +++-- MD5 | 35 ++++++++++------- NAMESPACE | 3 + R/coranking-package.R | 16 +++++--- R/coranking.R | 79 +++++++++++++++++++--------------------- R/image.R | 18 ++++----- R/lcmc.R | 4 +- R/r_nx.R |only R/rankmatrix.R | 15 ++++--- README.md | 5 ++ build/vignette.rds |binary inst/doc/coranking.R | 10 ++--- inst/doc/coranking.html | 64 +++++++++++++++++++++++--------- man/AUC_ln_K.Rd |only man/R_NX.Rd |only man/coRanking-package.Rd | 10 +++-- man/coranking.Rd | 22 +++++++---- man/imageplot.Rd | 16 ++++++-- man/plot_R_NX.Rd |only tests/testthat/test_coranking.R | 7 +++ tests/testthat/test_rnx.R |only 21 files changed, 190 insertions(+), 124 deletions(-)
Title: Visualization of Structures in High-Dimensional Data
Description: By gaining the property of emergence through self-organization, the enhancement of SOMs(self organizing maps) is called Emergent SOM (ESOM). The result of the projection by ESOM is a grid of neurons which can be visualised as a three dimensional landscape in form of the Umatrix. Further details can be found in the referenced publications (see url). This package offers tools for calculating and visualising the ESOM as well as Umatrix, Pmatrix and UStarMatrix. All the functionality is also available through graphical user interfaces implemented in 'shiny'.
Author: Florian Lerch[aut,cre], Michael Thrun[aut], Felix Pape[ctb], Raphael Paebst[ctb], Alfred Ultsch[aut]
Maintainer: Florian Lerch <lerch@mathematik.uni-marburg.de>
Diff between Umatrix versions 3.1 dated 2017-12-18 and 3.3 dated 2020-02-12
Umatrix-3.1/Umatrix/R/xPDEplot.R |only Umatrix-3.3/Umatrix/DESCRIPTION | 10 Umatrix-3.3/Umatrix/MD5 | 67 - Umatrix-3.3/Umatrix/NAMESPACE | 3 Umatrix-3.3/Umatrix/R/RcppExports.R | 54 - Umatrix-3.3/Umatrix/R/ToroidUmatrix.R | 94 +- Umatrix-3.3/Umatrix/R/createMaskFromPolygon.R | 44 - Umatrix-3.3/Umatrix/R/drawPoliticalMap.R | 62 - Umatrix-3.3/Umatrix/R/esomTrain.R | 182 ++-- Umatrix-3.3/Umatrix/R/iEsomTrain.R | 654 ++++++++--------- Umatrix-3.3/Umatrix/R/iUmapIsland.R | 562 +++++++------- Umatrix-3.3/Umatrix/R/iUstarmatrix.R | 739 ++++++++++--------- Umatrix-3.3/Umatrix/R/plotMatrix.R | 866 +++++++++++------------ Umatrix-3.3/Umatrix/R/pmatrixForEsom.R | 228 +++--- Umatrix-3.3/Umatrix/R/showMatrix3D.R | 458 ++++++------ Umatrix-3.3/Umatrix/R/umatrixForEsom.R | 194 ++--- Umatrix-3.3/Umatrix/R/upscaleUmatrix.R | 180 ++-- Umatrix-3.3/Umatrix/R/ustarmatrixCalc.R | 174 ++-- Umatrix-3.3/Umatrix/R/xBayesDecisionBoundaries.R | 124 +-- Umatrix-3.3/Umatrix/R/xDelaunay4BestMatches.R | 154 ++-- Umatrix-3.3/Umatrix/R/xDelaunayGraphMatrix.R | 250 +++--- Umatrix-3.3/Umatrix/R/xTileBM.R | 74 - Umatrix-3.3/Umatrix/R/xgplot.R | 96 +- Umatrix-3.3/Umatrix/R/xuniquePoints.R | 200 ++--- Umatrix-3.3/Umatrix/R/xzeros.R | 40 - Umatrix-3.3/Umatrix/man/Hepta.Rd | 2 Umatrix-3.3/Umatrix/man/esomTrain.Rd | 108 +- Umatrix-3.3/Umatrix/man/iEsomTrain.Rd | 52 - Umatrix-3.3/Umatrix/man/iUmapIsland.Rd | 46 - Umatrix-3.3/Umatrix/man/iUstarmatrix.Rd | 40 - Umatrix-3.3/Umatrix/man/plotMatrix.Rd | 90 +- Umatrix-3.3/Umatrix/man/pmatrixForEsom.Rd | 76 +- Umatrix-3.3/Umatrix/man/showMatrix3D.Rd | 70 - Umatrix-3.3/Umatrix/man/umatrixForEsom.Rd | 52 - Umatrix-3.3/Umatrix/man/ustarmatrixCalc.Rd | 60 - 35 files changed, 3062 insertions(+), 3043 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.100.30 dated 2019-08-19 and 0.100.47 dated 2020-02-12
rgl-0.100.30/rgl/tests |only rgl-0.100.47/rgl/DESCRIPTION | 8 rgl-0.100.47/rgl/MD5 | 126 - rgl-0.100.47/rgl/NAMESPACE | 4 rgl-0.100.47/rgl/R/animate.R | 8 rgl-0.100.47/rgl/R/asy.R | 62 rgl-0.100.47/rgl/R/bgplot3d.R | 19 rgl-0.100.47/rgl/R/obj.R | 2 rgl-0.100.47/rgl/R/par3d.R | 21 rgl-0.100.47/rgl/R/playwidget.R | 2 rgl-0.100.47/rgl/R/plot3d.R | 22 rgl-0.100.47/rgl/R/r3d.rgl.R | 15 rgl-0.100.47/rgl/R/rglwidget.R | 9 rgl-0.100.47/rgl/R/tkpar3dsave.R |only rgl-0.100.47/rgl/R/tkspin3d.R |only rgl-0.100.47/rgl/build/vignette.rds |binary rgl-0.100.47/rgl/configure | 9 rgl-0.100.47/rgl/configure.ac | 10 rgl-0.100.47/rgl/demo/stereo.R | 32 rgl-0.100.47/rgl/inst/NEWS | 38 rgl-0.100.47/rgl/inst/doc/WebGL.R | 35 rgl-0.100.47/rgl/inst/doc/WebGL.Rmd | 9 rgl-0.100.47/rgl/inst/doc/WebGL.html | 129 - rgl-0.100.47/rgl/inst/doc/legacyWebGL.R | 48 rgl-0.100.47/rgl/inst/doc/legacyWebGL.Rmd | 16 rgl-0.100.47/rgl/inst/doc/legacyWebGL.html | 171 + rgl-0.100.47/rgl/inst/doc/rgl.R | 32 rgl-0.100.47/rgl/inst/doc/rgl.Rmd | 78 rgl-0.100.47/rgl/inst/doc/rgl.html | 582 +++-- rgl-0.100.47/rgl/inst/slowTests |only rgl-0.100.47/rgl/inst/textures/bump_dust.png |binary rgl-0.100.47/rgl/inst/textures/nightfire.png |binary rgl-0.100.47/rgl/inst/textures/particle.png |binary rgl-0.100.47/rgl/inst/textures/refmap.png |binary rgl-0.100.47/rgl/inst/textures/rgl2.png |binary rgl-0.100.47/rgl/inst/textures/sunsleep.png |binary rgl-0.100.47/rgl/inst/textures/world.png |binary rgl-0.100.47/rgl/inst/textures/worldsmall.png |binary rgl-0.100.47/rgl/man/as.mesh3d.ashape3d.Rd | 9 rgl-0.100.47/rgl/man/bgplot3d.Rd | 5 rgl-0.100.47/rgl/man/import.Rd | 2 rgl-0.100.47/rgl/man/par3d.Rd | 5 rgl-0.100.47/rgl/man/par3dinterp.Rd | 4 rgl-0.100.47/rgl/man/playwidget.Rd | 4 rgl-0.100.47/rgl/man/propertyControl.Rd | 2 rgl-0.100.47/rgl/man/rglMouse.Rd | 2 rgl-0.100.47/rgl/man/rglToLattice.Rd | 4 rgl-0.100.47/rgl/man/rglwidget.Rd | 2 rgl-0.100.47/rgl/man/thigmophobe3d.Rd | 2 rgl-0.100.47/rgl/man/tkpar3dsave.Rd |only rgl-0.100.47/rgl/man/tkrgl.Rd |only rgl-0.100.47/rgl/man/tkspin3d.Rd |only rgl-0.100.47/rgl/man/tkspinControl.Rd |only rgl-0.100.47/rgl/man/writeASY.Rd | 10 rgl-0.100.47/rgl/src/Makevars.in | 2 rgl-0.100.47/rgl/src/PlaneSet.cpp | 37 rgl-0.100.47/rgl/src/build/autoconf/config.guess | 967 +++++--- rgl-0.100.47/rgl/src/build/autoconf/config.sub | 2538 +++++++++++------------ rgl-0.100.47/rgl/src/gui.cpp | 8 rgl-0.100.47/rgl/src/gui.h | 6 rgl-0.100.47/rgl/src/rglview.cpp | 23 rgl-0.100.47/rgl/src/rglview.h | 4 rgl-0.100.47/rgl/src/scene.cpp | 2 rgl-0.100.47/rgl/src/win32gui.cpp | 4 rgl-0.100.47/rgl/src/x11gui.cpp | 6 rgl-0.100.47/rgl/vignettes/WebGL.Rmd | 9 rgl-0.100.47/rgl/vignettes/legacyWebGL.Rmd | 16 rgl-0.100.47/rgl/vignettes/rgl.Rmd | 78 68 files changed, 3011 insertions(+), 2227 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on 'Windows',
'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gábor Csárdi [aut, cre],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between ps versions 1.3.0 dated 2018-12-21 and 1.3.1 dated 2020-02-12
ps-1.3.0/ps/build |only ps-1.3.1/ps/DESCRIPTION | 8 - ps-1.3.1/ps/MD5 | 115 ++++++++--------- ps-1.3.1/ps/NEWS.md | 5 ps-1.3.1/ps/R/kill-tree.R | 17 ++ ps-1.3.1/ps/R/linux.R | 18 ++ ps-1.3.1/ps/R/low-level.R | 198 ++++-------------------------- ps-1.3.1/ps/R/system.R | 9 - ps-1.3.1/ps/R/utils.R | 27 ---- ps-1.3.1/ps/README.md | 62 +++++---- ps-1.3.1/ps/configure | 8 - ps-1.3.1/ps/inst/tools |only ps-1.3.1/ps/man/CleanupReporter.Rd | 8 - ps-1.3.1/ps/man/ps_children.Rd | 54 +++++--- ps-1.3.1/ps/man/ps_cmdline.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_connections.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_cpu_count.Rd | 8 - ps-1.3.1/ps/man/ps_cpu_times.Rd | 57 +++++--- ps-1.3.1/ps/man/ps_create_time.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_cwd.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_environ.Rd | 68 +++++----- ps-1.3.1/ps/man/ps_exe.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_handle.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_interrupt.Rd | 41 ++++-- ps-1.3.1/ps/man/ps_is_running.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_kill.Rd | 54 +++++--- ps-1.3.1/ps/man/ps_kill_tree.Rd | 19 ++ ps-1.3.1/ps/man/ps_memory_info.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_name.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_num_fds.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_num_threads.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_open_files.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_pid.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_ppid.Rd | 68 +++++----- ps-1.3.1/ps/man/ps_resume.Rd | 54 +++++--- ps-1.3.1/ps/man/ps_send_signal.Rd | 54 +++++--- ps-1.3.1/ps/man/ps_status.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_suspend.Rd | 54 +++++--- ps-1.3.1/ps/man/ps_terminal.Rd | 53 +++++--- ps-1.3.1/ps/man/ps_terminate.Rd | 54 +++++--- ps-1.3.1/ps/man/ps_uids.Rd | 73 +++++------ ps-1.3.1/ps/man/ps_username.Rd | 53 +++++--- ps-1.3.1/ps/src/api-common.c | 4 ps-1.3.1/ps/src/api-linux.c | 6 ps-1.3.1/ps/src/api-macos.c | 6 ps-1.3.1/ps/src/api-posix.c | 4 ps-1.3.1/ps/src/api-windows.c | 2 ps-1.3.1/ps/src/arch/macos/process_info.c | 3 ps-1.3.1/ps/src/common.c | 4 ps-1.3.1/ps/src/dummy.c | 109 ++++++++-------- ps-1.3.1/ps/src/extra.c | 4 ps-1.3.1/ps/src/init.c | 4 ps-1.3.1/ps/src/linux.c | 1 ps-1.3.1/ps/src/macos.c | 4 ps-1.3.1/ps/src/posix.c | 4 ps-1.3.1/ps/src/px.c | 5 ps-1.3.1/ps/src/windows.c | 2 ps-1.3.1/ps/tests/testthat.R | 3 ps-1.3.1/ps/tests/testthat/helpers.R | 2 ps-1.3.1/ps/tests/testthat/test-winver.R |only 60 files changed, 1193 insertions(+), 955 deletions(-)
Title: Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)
Description: Provides a framework to perform Non-negative Matrix
Factorization (NMF). The package implements a set of already published algorithms
and seeding methods, and provides a framework to test, develop and plug
new/custom algorithms. Most of the built-in algorithms have been optimized
in C++, and the main interface function provides an easy way of performing
parallel computations on multicore machines.
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Nicolas Sauwen <nicolas.sauwen@openanalytics.eu>
Diff between NMF versions 0.21.0 dated 2018-03-06 and 0.22.0 dated 2020-02-12
DESCRIPTION | 14 +- MD5 | 50 +++++----- NAMESPACE | 4 R/Bioc-layer.R | 11 +- R/NMF-class.R | 2 R/aheatmap.R | 7 - R/data.R | 4 R/nmf.R | 2 R/nmfModel.R | 2 build/vignette.rds |binary inst/doc/NMF-vignette.R | 224 ++++++++++++++++++++++----------------------- inst/doc/NMF-vignette.Rnw | 70 +++++++++++++- inst/doc/NMF-vignette.pdf |binary inst/doc/consensus.pdf |binary inst/doc/heatmaps.R | 56 +++-------- inst/doc/heatmaps.Rnw | 1 inst/doc/heatmaps.pdf |binary man/KL-nmf.Rd | 2 man/aheatmap.Rd | 17 +-- man/esGolub.Rd | 5 - man/heatmaps.Rd | 16 +-- man/nmf.Rd | 2 man/nmfModel.Rd | 4 vignettes/NMF-vignette.Rnw | 70 +++++++++++++- vignettes/heatmaps.Rnw | 1 vignettes/src/bmc.R | 1 26 files changed, 343 insertions(+), 222 deletions(-)
Title: Case-Wise and Cluster-Wise Derivatives for Mixed Effects Models
Description: Compute case-wise and cluster-wise derivative for mixed effects models with respect to fixed effects parameter, random effect (co)variances, and residual variance. This material is partially based on work supported by the National Science Foundation under Grant Number 1460719.
Author: Ting Wang [aut, cre],
Edgar Merkle [aut] (<https://orcid.org/0000-0001-7158-0653>),
Yves Rosseel [ctb]
Maintainer: Ting Wang <twb8d@mail.missouri.edu>
Diff between merDeriv versions 0.1-7 dated 2019-07-10 and 0.1-8 dated 2020-02-12
DESCRIPTION | 12 +++---- MD5 | 24 +++++++-------- NAMESPACE | 10 +++++- R/estfun.glmerMod.R | 74 +++++++++++++++++++++++++++++++++++++++++++------ R/estfun.lmerMod.R | 24 ++++++++++++++- R/vcov.glmerMod.R | 52 ++++++++++++++++++++++++++++++++++ R/vcov.lmerMod.R | 34 +++++++++++++++++++--- README.md | 5 +-- build/partial.rdb |binary man/estfun.glmerMod.Rd | 7 +++- man/estfun.lmerMod.Rd | 9 +++-- man/vcov.glmerMod.Rd | 9 +++-- man/vcov.lmerMod.Rd | 12 ++++--- 13 files changed, 221 insertions(+), 51 deletions(-)
Title: A Simple Way to Specify Symmetric, Block Diagonal Matrices
Description: Provides a simple mechanism to specify a symmetric block diagonal matrices (often
used for covariance matrices). This is based on the domain specific language implemented
in 'nlmixr' but expanded to create matrices in R generally instead of specifying parts of matrices
to estimate.
Author: Matthew L. Fidler [aut, cre] (<https://orcid.org/0000-0001-8538-6691>)
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between lotri versions 0.1.1 dated 2019-05-14 and 0.2.1 dated 2020-02-12
DESCRIPTION | 10 MD5 | 23 - NAMESPACE | 7 NEWS.md |only R/lotri.R | 575 ++++++++++++++++++++++++++++++++--------- README.md | 13 build/vignette.rds |binary inst/doc/lotri-motivation.R | 27 + inst/doc/lotri-motivation.Rmd | 36 ++ inst/doc/lotri-motivation.html | 74 ++++- man/lotri.Rd | 17 - tests/testthat/test-lotri.R | 243 ++++++++++++++++- vignettes/lotri-motivation.Rmd | 36 ++ 13 files changed, 889 insertions(+), 172 deletions(-)
Title: Fast Embedding Guided by Self-Organizing Map
Description: Provides a smooth mapping of multidimensional points into
low-dimensional space defined by a self-organizing map. Designed to work
with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019)
<doi:10.1101/496869>.
Author: Mirek Kratochvil [aut, cre],
Sofie Van Gassen [cph],
Britt Callebaut [cph],
Yvan Saeys [cph],
Ron Wehrens [cph]
Maintainer: Mirek Kratochvil <exa.exa@gmail.com>
Diff between EmbedSOM versions 1.9 dated 2019-08-19 and 2.1.1 dated 2020-02-12
EmbedSOM-1.9/EmbedSOM/inst/doc/embedding.R |only EmbedSOM-1.9/EmbedSOM/inst/doc/embedding.Rmd |only EmbedSOM-1.9/EmbedSOM/inst/doc/embedding.html |only EmbedSOM-1.9/EmbedSOM/vignettes/embedding.Rmd |only EmbedSOM-2.1.1/EmbedSOM/DESCRIPTION | 9 EmbedSOM-2.1.1/EmbedSOM/MD5 | 60 - EmbedSOM-2.1.1/EmbedSOM/NAMESPACE | 11 EmbedSOM-2.1.1/EmbedSOM/R/coords.R |only EmbedSOM-2.1.1/EmbedSOM/R/embed.R | 146 ++- EmbedSOM-2.1.1/EmbedSOM/R/som.R | 273 +++++-- EmbedSOM-2.1.1/EmbedSOM/R/utils.R | 124 ++- EmbedSOM-2.1.1/EmbedSOM/README.md | 29 EmbedSOM-2.1.1/EmbedSOM/build/vignette.rds |binary EmbedSOM-2.1.1/EmbedSOM/inst/CITATION |only EmbedSOM-2.1.1/EmbedSOM/inst/doc/UsingEmbedSOM.R |only EmbedSOM-2.1.1/EmbedSOM/inst/doc/UsingEmbedSOM.Rmd |only EmbedSOM-2.1.1/EmbedSOM/inst/doc/UsingEmbedSOM.html |only EmbedSOM-2.1.1/EmbedSOM/man/EmbedSOM.Rd | 31 EmbedSOM-2.1.1/EmbedSOM/man/ExprColors.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/ExpressionGradient.Rd | 2 EmbedSOM-2.1.1/EmbedSOM/man/GQTSOM.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/GraphCoords.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/MSTCoords.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/MapDataToCodes.Rd | 12 EmbedSOM-2.1.1/EmbedSOM/man/NormalizeColor.Rd | 8 EmbedSOM-2.1.1/EmbedSOM/man/PlotData.Rd | 9 EmbedSOM-2.1.1/EmbedSOM/man/PlotEmbed.Rd | 42 - EmbedSOM-2.1.1/EmbedSOM/man/PlotGG.Rd | 2 EmbedSOM-2.1.1/EmbedSOM/man/RandomMap.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/SOM.Rd | 53 - EmbedSOM-2.1.1/EmbedSOM/man/UMAPCoords.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/UMatrixCoords.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/kMeansMap.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/kNNCoords.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/tSNECoords.Rd |only EmbedSOM-2.1.1/EmbedSOM/man/uwotCoords.Rd |only EmbedSOM-2.1.1/EmbedSOM/src/distfs.h | 331 +++++++- EmbedSOM-2.1.1/EmbedSOM/src/embed.cpp | 655 ++++++++++------ EmbedSOM-2.1.1/EmbedSOM/src/som.cpp | 777 +++++++++++++++++--- EmbedSOM-2.1.1/EmbedSOM/src/som.h | 68 + EmbedSOM-2.1.1/EmbedSOM/src/use_intrins.h |only EmbedSOM-2.1.1/EmbedSOM/vignettes/UsingEmbedSOM.Rmd |only 42 files changed, 1981 insertions(+), 661 deletions(-)
Title: Request <https://openblender.io> API Services
Description: Interface to make HTTP requests to 'OpenBlender' API services. Go to <https://openblender.io> for more information.
Author: Open Blender Inc. [cph],
Daniel V. Pinacho [aut, cre]
Maintainer: Daniel V. Pinacho <danielvpinacho@gmail.com>
Diff between openblender versions 0.3.5 dated 2020-01-29 and 0.3.6 dated 2020-02-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/get_observations.R | 4 ---- tests/testthat.R | 12 +++++++----- 4 files changed, 14 insertions(+), 16 deletions(-)
Title: Build and Tune Several Models
Description: Frequently one needs a convenient way to build and tune
several models in one go.The goal is to provide a number of convenience functions useful in machine learning
applications. It provides the ability to build, tune and obtain predictions of
several models in one function. The models are built using 'caret' functions with
easier to read syntax.
Kuhn(2014) <arXiv:1405.6974>.
Kuhn(2008) <doi10.18637/jss.v028.i05>.
Chambers,J.M.(1992) <doi:10.1007/978-3-642-50096-1_48>.
Wilkinson,G.N. and Rogers, C. E. (1973) <doi:10.2307/2346786>.
Author: Nelson Gonzabato [aut, cre]
Maintainer: Nelson Gonzabato <gonzabato@hotmail.com>
Diff between manymodelr versions 0.2.3 dated 2020-02-05 and 0.2.4 dated 2020-02-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ inst/doc/a-gentle-introduction-to-manymodelr.html | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Unbiased Central Moment Estimates
Description: Calculates one-sample unbiased central moment estimates and
two-sample pooled estimates up to 6th order, including estimates of
powers and products of central moments. Provides the machinery for
obtaining unbiased central moment estimators beyond 6th order by generating
expressions for expectations of raw sample moments and their powers and
products.
Gerlovina and Hubbard (2019) <doi:10.1080/25742558.2019.1701917>.
Author: Inna Gerlovina [aut, cre],
Alan Hubbard [aut]
Maintainer: Inna Gerlovina <innager@berkeley.edu>
Diff between Umoments versions 0.1.0 dated 2019-04-01 and 0.1.1 dated 2020-02-12
DESCRIPTION | 28 ++++++++++++++++++---------- MD5 | 22 +++++++++++----------- R/expectStr.R | 13 +++++-------- R/unbGen.R | 5 ++++- R/unbmom1.R | 2 +- build/vignette.rds |binary inst/doc/vignetteUmom.Rnw | 9 ++++++++- inst/doc/vignetteUmom.pdf |binary man/uM.Rd | 5 +++++ man/uM2pow3.Rd | 2 +- man/uMpool.Rd | 5 +++++ vignettes/vignetteUmom.Rnw | 9 ++++++++- 12 files changed, 66 insertions(+), 34 deletions(-)
Title: Representative and Adequate Prioritization Toolkit in R
Description: Biodiversity is in crisis. The overarching aim of conservation
is to preserve biodiversity patterns and processes. To this end, protected
areas are established to buffer species and preserve biodiversity processes.
But resources are limited and so protected areas must be cost-effective.
This package contains tools to generate plans for protected areas
(prioritizations), using spatially explicit targets for biodiversity
patterns and processes. To obtain solutions in a feasible amount of time,
this package uses the commercial 'Gurobi' software package (obtained from
<http://www.gurobi.com/>). For more information on using
this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.
Author: Jeffrey O Hanson [aut, cre],
Jonathan R Rhodes [aut],
Hugh P Possingham [aut],
Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between raptr versions 0.1.4 dated 2019-04-11 and 0.1.5 dated 2020-02-12
DESCRIPTION | 6 - MD5 | 24 ++-- NEWS.md | 5 + R/calcBoundaryData.R | 2 R/data.R | 2 R/generics.R | 2 build/vignette.rds |binary inst/doc/raptr.Rmd | 2 inst/doc/raptr.html | 233 +++++++++++++++++++++++------------------------- man/calcBoundaryData.Rd | 2 man/casestudy_data.Rd | 2 man/selections.Rd | 2 vignettes/raptr.Rmd | 2 13 files changed, 137 insertions(+), 147 deletions(-)
Title: Weighted Cox-Regression for Nested Case-Control Data
Description: Fit Cox proportional hazard models with a weighted
partial likelihood. It handles one or multiple endpoints, additional matching
and makes it possible to reuse controls for other endpoints.
Author: Nathalie C. Stoer, Sven Ove Samuelsen
Maintainer: Nathalie C. Stoer <nathalie.c.stoer@kreftregisteret.no>
Diff between multipleNCC versions 1.2-1 dated 2016-04-19 and 1.2-2 dated 2020-02-12
multipleNCC-1.2-1/multipleNCC/R/wpl8.R |only multipleNCC-1.2-2/multipleNCC/DESCRIPTION | 10 +++++----- multipleNCC-1.2-2/multipleNCC/MD5 | 8 ++++---- multipleNCC-1.2-2/multipleNCC/R/wpl9.R |only multipleNCC-1.2-2/multipleNCC/man/multipleNCC-package.Rd | 2 +- multipleNCC-1.2-2/multipleNCC/man/wpl.Rd | 3 --- 6 files changed, 10 insertions(+), 13 deletions(-)
Title: Joint Analysis and Imputation of Incomplete Data
Description: Provides joint analysis and imputation of (generalized)
linear and cumulative logit regression models, (generalized) linear and
cumulative logit mixed models and parametric (Weibull) as well as Cox
proportional hazards survival models with incomplete (covariate) data in
the Bayesian framework.
The package performs some preprocessing of the data and creates a 'JAGS'
model, which will then automatically be passed to 'JAGS'
<http://mcmc-jags.sourceforge.net> with the help of
the package 'rjags'.
It also provides summary and plotting functions for the output and allows
the user to export imputed values.
Author: Nicole S. Erler [aut, cre] (<https://orcid.org/0000-0002-9370-6832>)
Maintainer: Nicole S. Erler <n.erler@erasmusmc.nl>
Diff between JointAI versions 0.6.0 dated 2019-08-31 and 0.6.1 dated 2020-02-12
DESCRIPTION | 12 MD5 | 120 +-- NAMESPACE | 2 NEWS.md | 10 R/add_samples.R | 18 R/helpfunctions_formulas.R | 53 + R/helpfunctions_prep_impmodels.R | 8 R/impmodels_ordinal.R | 6 R/old_stuff.R |only R/predict.R | 5 R/print_functions.R | 1 README.md | 61 - build/vignette.rds |binary inst/doc/AfterFitting.R | 2 inst/doc/AfterFitting.Rmd | 2 inst/doc/AfterFitting.html | 101 +- inst/doc/MCMCsettings.html | 11 inst/doc/MinimalExample.R | 6 inst/doc/MinimalExample.html | 11 inst/doc/ModelSpecification.html | 15 inst/doc/SelectingParameters.R | 36 - inst/doc/SelectingParameters.html | 72 -- inst/doc/TheoreticalBackground.html | 4 inst/doc/VisualizingIncompleteData.html | 11 man/GR_crit.Rd | 163 ++-- man/JointAI.Rd | 285 ++++---- man/JointAIObject.Rd | 164 ++-- man/MC_error.Rd | 207 +++--- man/NHANES.Rd | 94 +- man/add_samples.Rd | 151 ++-- man/check_tvar.Rd | 38 - man/default_hyperpars.Rd | 192 ++--- man/densplot.Rd | 225 +++--- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/get_MIdat.Rd | 156 ++-- man/get_models.Rd | 126 +-- man/list_models.Rd | 144 ++-- man/longDF.Rd | 74 +- man/md_pattern.Rd | 106 +-- man/model_imp.Rd | 1059 ++++++++++++++++++------------- man/parameters.Rd | 64 - man/plot.JointAI.Rd | 40 - man/plot_all.Rd | 116 +-- man/plot_imp_distr.Rd | 80 +- man/predDF.Rd | 92 +- man/predict.JointAI.Rd | 198 +++-- man/residuals.JointAI.Rd | 73 +- man/set_refcat.Rd | 102 +- man/sharedParams.Rd | 144 ++-- man/simLong.Rd | 162 ++-- man/sim_data.Rd | 152 ++-- man/summary.JointAI.Rd | 196 +++-- man/traceplot.Rd | 246 +++---- man/wideDF.Rd | 58 - tests/testthat/test_add_samples.R |only tests/testthat/test_bugfixes.R | 7 tests/testthat/test_helpfunctions.R |only tests/testthat/test_longModels.R | 13 tests/testthat/test_survival.R |only vignettes/AfterFitting.Rmd | 2 63 files changed, 2936 insertions(+), 2560 deletions(-)
Title: Wizardry Code Offensive Programming Test Generation
Description: Allows to generate automatically 'testthat' code files from offensive
programming test cases. Generated test files are complete and ready to run.
Using 'wyz.code.testthat' you will earn a lot of time, reduce the number of
errors in test case production, be able to test immediately generated files
without any need to view or modify them, and enter a zero time latency between
code implementation and industrial testing. As with 'testthat', you may
complete provided test cases according to your needs to push testing further,
but this need is nearly void when using 'wyz.code.offensiveProgramming'.
Refer to chapter 9 of Offensive Programming Book, Fabien GELINEAU (2019,
ISBN:979-10-699-4075-8), to learn about details and get value from this package.
Author: Fabien Gelineau <neonira@gmail.com>
Maintainer: Fabien Gelineau <neonira@gmail.com>
Diff between wyz.code.testthat versions 1.1.9 dated 2019-10-13 and 1.1.16 dated 2020-02-12
wyz.code.testthat-1.1.16/wyz.code.testthat/DESCRIPTION | 10 +-- wyz.code.testthat-1.1.16/wyz.code.testthat/MD5 | 30 ++++++---- wyz.code.testthat-1.1.16/wyz.code.testthat/NAMESPACE | 3 - wyz.code.testthat-1.1.16/wyz.code.testthat/R/opTestthatInformation.R |only wyz.code.testthat-1.1.16/wyz.code.testthat/R/outOfPackage.R | 6 ++ wyz.code.testthat-1.1.16/wyz.code.testthat/build/partial.rdb |binary wyz.code.testthat-1.1.16/wyz.code.testthat/build/vignette.rds |binary wyz.code.testthat-1.1.16/wyz.code.testthat/inst/doc/releases.R |only wyz.code.testthat-1.1.16/wyz.code.testthat/inst/doc/releases.Rmd |only wyz.code.testthat-1.1.16/wyz.code.testthat/inst/doc/releases.html |only wyz.code.testthat-1.1.16/wyz.code.testthat/man/generateAllUnitTestsFromObject.Rd | 12 ++++ wyz.code.testthat-1.1.16/wyz.code.testthat/man/generateUnitTestFile.Rd | 7 +- wyz.code.testthat-1.1.16/wyz.code.testthat/man/opTestthatInformation.Rd |only wyz.code.testthat-1.1.16/wyz.code.testthat/man/testthatFactory.Rd | 7 ++ wyz.code.testthat-1.1.16/wyz.code.testthat/tests/testthat/test_opTestthatInformation.R |only wyz.code.testthat-1.1.16/wyz.code.testthat/vignettes/images |only wyz.code.testthat-1.1.16/wyz.code.testthat/vignettes/releases.Rmd |only wyz.code.testthat-1.1.16/wyz.code.testthat/vignettes/style.css |only wyz.code.testthat-1.1.16/wyz.code.testthat/vignettes/vignette-common.R |only wyz.code.testthat-1.1.9/wyz.code.testthat/inst/doc/wyz.code.testthat.R |only wyz.code.testthat-1.1.9/wyz.code.testthat/inst/doc/wyz.code.testthat.Rmd |only wyz.code.testthat-1.1.9/wyz.code.testthat/inst/doc/wyz.code.testthat.html |only wyz.code.testthat-1.1.9/wyz.code.testthat/vignettes/wyz.code.testthat.Rmd |only 23 files changed, 53 insertions(+), 22 deletions(-)
More information about wyz.code.testthat at CRAN
Permanent link
Title: Moment-Free Estimation of Sharpe Ratios
Description: An efficient moment-free estimator of the Sharpe ratio, or signal-to-noise ratio, for heavy-tailed data (see <arXiv:1505.01333>).
Author: Damien Challet
Maintainer: Damien Challet <damien.challet@gmail.com>
Diff between sharpeRratio versions 1.2 dated 2019-12-05 and 1.3 dated 2020-02-12
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS | 9 ++++++++- R/estimateSNR.R | 14 ++++++++++++-- 4 files changed, 28 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-29 1.3.0
2020-01-20 1.2.0
2020-01-19 1.1.0
Title: Wizardry Code Meta Testing
Description: Test R any R function without having to provide parameter values.
Values will be generated, based on semantic naming of parameters as
introduced by package 'wyz.code.offensiveProgramming'. Generated tests
can be saved and reused. Value generation logic can be completed with your
own specific data types and generation schemes, to meet your requirements.
Main benefits of 'wyz.code.metaTesting' is higher developer productivity,
reduced time to production, and industrial inference testing. Refer to
chapter 10 of Offensive Programming Book, Fabien GELINEAU (2019,
ISBN:979-10-699-4075-8), to learn about details and get value from this
package.
Author: Fabien Gelineau <neonira@gmail.com>
Maintainer: Fabien Gelineau <neonira@gmail.com>
Diff between wyz.code.metaTesting versions 1.1.4 dated 2019-10-13 and 1.1.11 dated 2020-02-12
wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/DESCRIPTION | 10 - wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/MD5 | 67 ++++------ wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/NAMESPACE | 11 - wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/R/DataFactory.R | 13 + wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/R/codePatcher.R | 6 wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/R/computeArgumentsCombination.R | 6 wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/R/opMetatTestingInformation.R |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/R/outOfPackage.R | 7 + wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/R/retrieveDataFactory.R | 17 +- wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/R/testFunction.R | 2 wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/build/partial.rdb |binary wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/build/vignette.rds |binary wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/inst/doc/releases.R |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/inst/doc/releases.Rmd |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/inst/doc/releases.html |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/inst/unit-testing |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/man/buildSemanticArgumentName.Rd | 3 wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/man/exploreSignatures.Rd | 2 wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/man/generateData.Rd | 4 wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/man/opMetaTestingInformation.Rd |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/man/retrieveDataFactory.Rd | 16 +- wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/man/testFunction.Rd | 2 wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/man/usesSemanticArgumentNames.Rd | 4 wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/tests/testthat/test_opMetaTestingInformation.R |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/tests/testthat/test_opwf.R | 10 - wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/tests/testthat/test_retrieveDataFactory.R | 6 wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/vignettes/images |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/vignettes/releases.Rmd |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/vignettes/style.css |only wyz.code.metaTesting-1.1.11/wyz.code.metaTesting/vignettes/vignette-common.R |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/R/packageFunctionsInformation.R |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/R/shareSameSignature.R |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/inst/doc/wyz.code.metaTesting.R |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/inst/doc/wyz.code.metaTesting.Rmd |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/inst/doc/wyz.code.metaTesting.html |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/man/DataFactory.Rd |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/man/packageFunctionsInformation.Rd |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/man/shareSameSignature.Rd |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/tests/testthat/test_packageFunctionsInformation.R |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/tests/testthat/test_shareSameSignature.R |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/tests/unit-testing |only wyz.code.metaTesting-1.1.4/wyz.code.metaTesting/vignettes/wyz.code.metaTesting.Rmd |only 42 files changed, 89 insertions(+), 97 deletions(-)
More information about wyz.code.metaTesting at CRAN
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Title: Calculate Predicted Means for Linear Models
Description: Providing functions to diagnose
and make inferences from various linear models, such as those obtained from 'aov',
'lm', 'glm', 'gls', 'lme', and 'lmer'. Inferences include predicted
means and standard errors, contrasts, multiple comparisons, permutation tests and graphs.
Author: Dongwen Luo, Siva Ganesh and John Koolaard
Maintainer: Dongwen Luo <dongwen.luo@agresearch.co.nz>
Diff between predictmeans versions 1.0.1 dated 2018-08-23 and 1.0.2 dated 2020-02-12
DESCRIPTION | 8 ++++---- MD5 | 48 ++++++++++++++++++++++++++---------------------- NAMESPACE | 2 +- R/CookD.R | 4 ++-- R/Kmatrix.R | 47 ++++++++++++++++++++++++++--------------------- R/PMplot.R | 2 +- R/anovalmer.R | 2 +- R/contrastmeans.R | 4 ++-- R/covariatemeans.R | 20 ++++++++++---------- R/misc.R | 37 ++++++++++++++++++------------------- R/mymodelparm.R | 6 +++--- R/permanova.lmer.R | 8 ++++---- R/permlmer.R | 14 ++++++++++---- R/permmodels.R |only R/predictmeans.R | 37 +++++++++++++++++++------------------ R/residplot.R | 12 ++++++------ R/rsplot.gls.R | 4 ++-- R/rsplot.lme.R | 12 ++++++------ R/varcomp.lmer.R |only man/Kmatrix.Rd | 18 ++++++++++++------ man/PMplot.Rd | 6 +----- man/covariatemeans.Rd | 13 +++++++++---- man/permanova.lmer.Rd | 7 +++++-- man/permlmer.Rd | 9 ++++++--- man/permmodels.Rd |only man/predictmeans.Rd | 9 +++++++-- man/varcomp.lmer.Rd |only 27 files changed, 181 insertions(+), 148 deletions(-)
Title: A Collection of Fluorescence Fluctuation Spectroscopy Methods
Description: A set of tools for fluorescence fluctuation spectroscopy data analysis performance is provided in this package.
It includes techniques such as single-point fluorescence correlation spectroscopy, autocorrelation and pair correlation functions, number & brightness (raster line scan) and a novel, recently developed method by Hinde and co-workers, pair correlation of molecular brightness (doi:10.1038/ncomms11047).
A set of simulations and real experimental data is used for the examples of each function provided in this package.
For an in-depth description of the basics behind each function here included and a detailed step-by-step guide on how to use them on your own data, please refer to the Supplementary Material file provided at (<https://github.com/RPintoC/FCSlib_Sup_Data>).
Author: Raul Pinto Camara, Adan Guerrero.
Maintainer: Raul Pinto Camara <vasto.lorde.rp@gmail.com>
Diff between FCSlib versions 1.0.0 dated 2019-08-05 and 1.1.0 dated 2020-02-12
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Title: Machine Learning Model Evaluation
Description: Straightforward and detailed evaluation of machine learning models. 'MLeval' can produce receiver operating characteristic (ROC) curves, precision-recall (PR) curves, calibration curves, and PR gain curves. 'MLeval' accepts a data frame of class probabilities and ground truth labels, or, it can automatically interpret the Caret train function results from repeated cross validation, then select the best model and analyse the results. 'MLeval' produces a range of evaluation metrics with confidence intervals.
Author: Christopher R John
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between MLeval versions 0.2 dated 2019-11-29 and 0.3 dated 2020-02-12
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/evalm.R | 8 +++++--- inst/doc/introduction.pdf |binary 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as getting database specific taxonomic identifiers, verifying
species names, getting taxonomic hierarchies, fetching downstream and
upstream taxonomic names, getting taxonomic synonyms, converting
scientific to common names and vice versa, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Eduard Szoecs [aut],
Zachary Foster [aut],
Zebulun Arendsee [aut],
Carl Boettiger [ctb],
Karthik Ram [ctb],
Ignasi Bartomeus [ctb],
John Baumgartner [ctb],
James O'Donnell [ctb],
Jari Oksanen [ctb],
Bastian Greshake Tzovaras [ctb],
Philippe Marchand [ctb],
Vinh Tran [ctb],
Maëlle Salmon [ctb],
Gaopeng Li [ctb],
Matthias Grenié [ctb],
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.9.91 dated 2019-11-15 and 0.9.92 dated 2020-02-12
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Title: Derive Polygenic Risk Score Based on Emprical Bayes Theory
Description: EB-PRS is a novel method that leverages information for effect sizes across all the markers to improve the prediction accuracy. No parameter tuning is needed in the method, and no external information is needed. This R-package provides the calculation of polygenic risk scores from the given training summary statistics and testing data. We can use EB-PRS to extract main information, estimate Empirical Bayes parameters, derive polygenic risk scores for each individual in testing data, and evaluate the PRS according to AUC and predictive r2. See Song et al. (2020) <doi:10.1371/journal.pcbi.1007565> for a detailed presentation of the method.
Author: Shuang Song [aut, cre], Wei Jiang [aut], Lin Hou [aut] and Hongyu Zhao [aut]
Maintainer: Shuang Song <song-s19@mails.tsinghua.edu.cn>
Diff between EBPRS versions 2.0.1 dated 2020-01-16 and 2.0.3 dated 2020-02-12
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++-------- R/agtc.R | 62 +++++++++++++++++++++++++++------------------------- R/exdata.R | 2 - R/findPara.R | 17 +++++++------- R/packageEBPRS.R | 5 +--- R/validate.R | 4 +-- man/EBPRS.Rd | 8 +++--- man/EBPRSpackage.Rd | 4 +-- man/traindat.Rd | 2 - man/validate.Rd | 2 - 11 files changed, 69 insertions(+), 65 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Michael D. Wilson [aut] (<https://orcid.org/0000-0003-4143-7308>),
Paul-Christian Bürkner [rev],
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Quentin F. Gronau [ctb] (<https://orcid.org/0000-0001-5510-6943>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.5.1 dated 2020-01-27 and 0.5.2 dated 2020-02-12
DESCRIPTION | 6 - MD5 | 134 +++++++++++++------------- R/bayesfactor_inclusion.R | 2 R/bayesfactor_models.R | 30 +++-- R/bayesfactor_parameters.R | 57 ++++++----- R/bayesfactor_restricted.R | 36 +++--- R/convert_bayesian_to_frequentist.R | 45 ++++---- R/describe_posterior.R | 41 ++++--- R/describe_prior.R | 23 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/bayes_factors.R | 16 +-- inst/doc/bayes_factors.Rmd | 16 +-- inst/doc/bayes_factors.html | 90 ++++++++--------- inst/doc/credible_interval.R | 4 inst/doc/credible_interval.Rmd | 4 inst/doc/example1.R | 6 - inst/doc/example1.Rmd | 6 - inst/doc/example1.html | 16 +-- inst/doc/example2.R | 12 +- inst/doc/example2.Rmd | 12 +- inst/doc/example2.html | 10 - inst/doc/indicesEstimationComparison.R | 8 - inst/doc/indicesEstimationComparison.Rmd | 8 - inst/doc/probability_of_direction.R | 17 +-- inst/doc/probability_of_direction.Rmd | 17 +-- inst/doc/probability_of_direction.html | 2 inst/doc/region_of_practical_equivalence.R | 3 inst/doc/region_of_practical_equivalence.Rmd | 3 man/bayesfactor.Rd | 2 man/bayesfactor_inclusion.Rd | 2 man/bayesfactor_models.Rd | 2 man/bayesfactor_parameters.Rd | 57 ++++++----- man/bayesfactor_restricted.Rd | 36 +++--- man/check_prior.Rd | 2 man/ci.Rd | 2 man/convert_bayesian_as_frequentist.Rd | 45 ++++---- man/describe_posterior.Rd | 43 ++++---- man/describe_prior.Rd | 22 ++-- man/diagnostic_posterior.Rd | 2 man/effective_sample.Rd | 2 man/estimate_density.Rd | 2 man/eti.Rd | 2 man/hdi.Rd | 2 man/map_estimate.Rd | 2 man/mcse.Rd | 2 man/mhdior.Rd | 2 man/p_direction.Rd | 2 man/p_map.Rd | 2 man/p_significance.Rd | 2 man/rope.Rd | 2 man/rope_range.Rd | 2 man/sensitivity_to_prior.Rd | 2 man/simulate_prior.Rd | 2 man/update.bayesfactor_models.Rd | 2 tests/testthat/test-bayesfactor_models.R | 4 tests/testthat/test-bayesfactor_parameters.R | 4 tests/testthat/test-bayesfactor_restricted.R | 2 tests/testthat/test-describe_posterior.R | 3 tests/testthat/test-emmGrid.R | 3 tests/testthat/test-estimate_density.R | 4 vignettes/bayes_factors.Rmd | 16 +-- vignettes/credible_interval.Rmd | 4 vignettes/example1.Rmd | 6 - vignettes/example2.Rmd | 12 +- vignettes/indicesEstimationComparison.Rmd | 8 - vignettes/probability_of_direction.Rmd | 17 +-- vignettes/region_of_practical_equivalence.Rmd | 3 68 files changed, 476 insertions(+), 479 deletions(-)
Title: Artificial Neural Network Training and Simulating
Description: Commands for training a simulating an artificial neural network.
Author: Manuel Castejon Limas, Joaquin B. Ordieres Mere, Ana Gonzalez
Marcos, Francisco Javier Martinez de Pison Ascacibar, Alpha V.
Pernia Espinoza, Fernando Alba Elias, Jose Maria Perez Ramos
Maintainer: Manuel Castejón-Limas <manuel.castejon@gmail.com>
Diff between AMORE versions 0.2-15 dated 2014-04-14 and 0.2-16 dated 2020-02-12
ChangeLog | 3 +++ DESCRIPTION | 19 +++++++------------ MD5 | 15 ++++++++------- NAMESPACE | 4 ++-- src/ADAPTgd.c | 5 ++--- src/ADAPTgdwm.c | 7 +++---- src/copynet.c | 2 +- src/init.c |only src/sim.c | 9 +++------ 9 files changed, 29 insertions(+), 35 deletions(-)