Tue, 02 Jun 2020

Package oceanis updated to version 1.7.3 with previous version 1.0.7 dated 2020-04-02

Title: Cartography for Statistical Analysis
Description: Creating maps for statistical analysis such as proportional circles, chroropleth, typology and flows. Some functions use 'shiny' or 'leaflet' technologies for dynamism and interactivity. The great features are : - Create maps in a web environment where the parameters are modifiable on the fly ('shiny' and 'leaflet' technology). - Create interactive maps through zoom and pop-up ('leaflet' technology). - Create frozen maps with the possibility to add labels.
Author: Sébastien CALVET - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [cre, aut], Sophie AUDRIC - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [aut], SED - DR Hauts-de-France - INSEE [ctb], PSAR-SL - DR Auvergne-Rhone-Alpes - INSEE [ctb], PSAR-EEP - DR Occitanie - INSEE [ctb], SED - DR Pays-de-la-Loire - INSEE [ctb]
Maintainer: Sébastien CALVET <sebastien.calvet@insee.fr>

Diff between oceanis versions 1.0.7 dated 2020-04-02 and 1.7.3 dated 2020-06-02

 DESCRIPTION                     |   18 ++--
 MD5                             |   84 +++++++++---------
 NAMESPACE                       |  180 ++++++++++++++++++++--------------------
 NEWS                            |   31 ++++++
 R/leaflet_classes.R             |    4 
 R/leaflet_classes_ronds.R       |    4 
 R/leaflet_joignantes.R          |    6 -
 R/leaflet_oursins.R             |    4 
 R/leaflet_ronds.R               |    4 
 R/leaflet_ronds_classes.R       |    4 
 R/leaflet_saphirs.R             |    4 
 R/leaflet_typo.R                |    4 
 R/plot_classes.R                |   39 +++++---
 R/plot_classes_ronds.R          |   74 ++++++++++------
 R/plot_joignantes.R             |   28 ++++--
 R/plot_ronds.R                  |   28 ++++--
 R/plot_ronds_classes.R          |   70 +++++++++------
 R/plot_saphirs.R                |   29 ++++--
 R/plot_typo.R                   |   57 +++++++-----
 R/plot_typo_symboles.R          |   79 ++++++++++-------
 R/sf_pays973.R                  |    5 +
 R/sf_paysm.R                    |    5 +
 R/sf_reg01.R                    |    3 
 R/sf_reg02.R                    |    3 
 R/sf_reg03.R                    |    5 +
 R/sf_reg04.R                    |    5 +
 R/sf_reg06.R                    |    5 +
 R/shiny_classes.R               |    4 
 R/shiny_classes_ronds.R         |    4 
 R/shiny_joignantes.R            |    4 
 R/shiny_oursins.R               |    4 
 R/shiny_ronds.R                 |    4 
 R/shiny_ronds_classes.R         |    4 
 R/shiny_saphirs.R               |    4 
 R/shiny_typo.R                  |    4 
 build/vignette.rds              |binary
 inst/doc/integration_shiny.html |    4 
 inst/doc/oceanis.html           |   19 +---
 inst/extdata/pays973.dbf        |binary
 inst/extdata/pays973.prj        |    2 
 inst/extdata/pays973.shp        |binary
 inst/extdata/pays973.shx        |binary
 man/donnees.Rd                  |    6 -
 43 files changed, 499 insertions(+), 346 deletions(-)

More information about oceanis at CRAN
Permanent link

Package CornerstoneR updated to version 2.0.1 with previous version 2.0.0 dated 2020-05-17

Title: Collection of Scripts for Interface Between 'Cornerstone' and 'R'
Description: Collection of generic 'R' scripts which enable you to use existing 'R' routines in 'Cornerstone'. The desktop application 'Cornerstone' (<https://www.camline.com/en/products/cornerstone/cornerstone-core.html>) is a data analysis software provided by 'camLine' that empowers engineering teams to find solutions even faster. The engineers incorporate intensified hands-on statistics into their projects. They benefit from an intuitive and uniquely designed graphical Workmap concept: you design experiments (DoE) and explore data, analyze dependencies, and find answers you can act upon, immediately, interactively, and without any programming. While 'Cornerstone's' interface to the statistical programming language 'R' has been available since version 6.0, the latest interface with 'R' is even much more efficient. 'Cornerstone' release 7.1.1 allows you to integrate user defined 'R' packages directly into the standard 'Cornerstone' GUI. Your engineering team stays in 'Cornerstone's' graphical working environment and can apply 'R' routines, immediately and without the need to deal with programming code. Additionally, your 'R' programming team develops corresponding 'R' packages detached from 'Cornerstone' in their favorite 'R' environment. Learn how to use 'R' packages in 'Cornerstone' 7.1.1 on 'camLineTV' YouTube channel (<https://www.youtube.com/watch?v=HEQHwq_laXU>) (available in German).
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@camline.academy>

Diff between CornerstoneR versions 2.0.0 dated 2020-05-17 and 2.0.1 dated 2020-06-02

 CornerstoneR-2.0.0/CornerstoneR/tests/testthat/test_functionList.R   |only
 CornerstoneR-2.0.1/CornerstoneR/DESCRIPTION                          |    6 
 CornerstoneR-2.0.1/CornerstoneR/MD5                                  |   44 +-
 CornerstoneR-2.0.1/CornerstoneR/NAMESPACE                            |    1 
 CornerstoneR-2.0.1/CornerstoneR/NEWS.md                              |    6 
 CornerstoneR-2.0.1/CornerstoneR/R/matchNearestNeighbor.R             |    1 
 CornerstoneR-2.0.1/CornerstoneR/R/reshapeWide.R                      |    7 
 CornerstoneR-2.0.1/CornerstoneR/R/showVersions.R                     |only
 CornerstoneR-2.0.1/CornerstoneR/build/vignette.rds                   |binary
 CornerstoneR-2.0.1/CornerstoneR/inst/csdata/functionList.txt         |    2 
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/fitFunction.html            |  134 ++------
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/matchNearestNeighbor.html   |   58 +--
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/mosaicPlot.html             |   40 --
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/randomForest.html           |  106 ++----
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/redirectDataset.html        |   52 +--
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/reshape.R                   |    7 
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/reshape.Rmd                 |   19 -
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/reshape.html                |  163 ++++------
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/showVersions.R              |only
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/showVersions.Rmd            |only
 CornerstoneR-2.0.1/CornerstoneR/inst/doc/showVersions.html           |only
 CornerstoneR-2.0.1/CornerstoneR/inst/variablesdialog/reshapeWide.xml |    2 
 CornerstoneR-2.0.1/CornerstoneR/man/showVersions.Rd                  |only
 CornerstoneR-2.0.1/CornerstoneR/tests/testthat/test_misc.R           |only
 CornerstoneR-2.0.1/CornerstoneR/tests/testthat/test_reshape.R        |   20 +
 CornerstoneR-2.0.1/CornerstoneR/vignettes/reshape.Rmd                |   19 -
 CornerstoneR-2.0.1/CornerstoneR/vignettes/showVersions.Rmd           |only
 27 files changed, 292 insertions(+), 395 deletions(-)

More information about CornerstoneR at CRAN
Permanent link

Package contact updated to version 1.2.3 with previous version 1.2.2 dated 2020-04-13

Title: Creating Contact and Social Networks
Description: Process spatially- and temporally-discrete data into contact and social networks, and facilitate network analysis by randomizing individuals' movement paths and/or related categorical variables. To use this package, users need only have a dataset containing spatial data (i.e., latitude/longitude, or planar x & y coordinates), individual IDs relating spatial data to specific individuals, and date/time information relating spatial locations to temporal locations. The functionality of this package ranges from data "cleaning" via multiple filtration functions, to spatial and temporal data interpolation, and network creation and analysis. Functions within this package are not limited to describing interpersonal contacts. Package functions can also identify and quantify "contacts" between individuals and fixed areas (e.g., home ranges, water bodies, buildings, etc.). As such, this package is an incredibly useful resource for facilitating epidemiological, ecological, ethological and sociological research.
Author: Trevor Farthing [aut, cre], Daniel Dawson [aut], Cristina Lanzas [ctb]
Maintainer: Trevor Farthing <tsfarthi@ncsu.edu>

Diff between contact versions 1.2.2 dated 2020-04-13 and 1.2.3 dated 2020-06-02

 contact-1.2.2/contact/inst/doc/Using_the_contact_package_v1_2_2.R    |only
 contact-1.2.2/contact/inst/doc/Using_the_contact_package_v1_2_2.Rmd  |only
 contact-1.2.2/contact/inst/doc/Using_the_contact_package_v1_2_2.html |only
 contact-1.2.2/contact/vignettes/Using_the_contact_package_v1_2_2.Rmd |only
 contact-1.2.3/contact/DESCRIPTION                                    |    6 
 contact-1.2.3/contact/MD5                                            |   32 ++---
 contact-1.2.3/contact/NAMESPACE                                      |    2 
 contact-1.2.3/contact/R/contactCompare_binom.R                       |only
 contact-1.2.3/contact/R/contactCompare_chisq.R                       |   64 +++++++---
 contact-1.2.3/contact/R/ntwrkEdges.R                                 |   51 +++++--
 contact-1.2.3/contact/R/socialEdges.R                                |only
 contact-1.2.3/contact/R/tempAggregate.R                              |    6 
 contact-1.2.3/contact/R/timeBlock.append.R                           |    2 
 contact-1.2.3/contact/build/vignette.rds                             |binary
 contact-1.2.3/contact/inst/doc/Using_the_contact_package_v1_2_3.R    |only
 contact-1.2.3/contact/inst/doc/Using_the_contact_package_v1_2_3.Rmd  |only
 contact-1.2.3/contact/inst/doc/Using_the_contact_package_v1_2_3.html |only
 contact-1.2.3/contact/man/contactCompare_binom.Rd                    |only
 contact-1.2.3/contact/man/contactCompare_chisq.Rd                    |   41 ++++--
 contact-1.2.3/contact/man/ntwrkEdges.Rd                              |    2 
 contact-1.2.3/contact/man/socialEdges.Rd                             |only
 contact-1.2.3/contact/man/timeBlock.append.Rd                        |    2 
 contact-1.2.3/contact/vignettes/Using_the_contact_package_v1_2_3.Rmd |only
 23 files changed, 137 insertions(+), 71 deletions(-)

More information about contact at CRAN
Permanent link

Package omicwas updated to version 0.7.0 with previous version 0.3.1 dated 2020-02-19

Title: Cell-Type-Specific Association Testing in Bulk Omics Experiments
Description: In bulk epigenome/transcriptome experiments, molecular expression is measured in a tissue, which is a mixture of multiple types of cells. This package tests association of a disease/phenotype with a molecular marker for each cell type. The proportion of cell types in each sample needs to be given as input. The package is applicable to epigenome-wide association study (EWAS) and differential gene expression analysis. Takeuchi and Kato (submitted) "omicwas: cell-type-specific epigenome-wide and transcriptome association study".
Author: Fumihiko Takeuchi [aut, cre] (<https://orcid.org/0000-0003-3185-5661>)
Maintainer: Fumihiko Takeuchi <fumihiko@takeuchi.name>

Diff between omicwas versions 0.3.1 dated 2020-02-19 and 0.7.0 dated 2020-06-02

 omicwas-0.3.1/omicwas/data/datalist                    |only
 omicwas-0.7.0/omicwas/DESCRIPTION                      |   18 
 omicwas-0.7.0/omicwas/MD5                              |   42 
 omicwas-0.7.0/omicwas/NAMESPACE                        |   11 
 omicwas-0.7.0/omicwas/R/GSE42861small.R                |    2 
 omicwas-0.7.0/omicwas/R/GTExsmall.R                    |only
 omicwas-0.7.0/omicwas/R/ctcisQTL.R                     |  149 --
 omicwas-0.7.0/omicwas/R/lmridgeLW76.R                  |only
 omicwas-0.7.0/omicwas/R/omicwas.R                      |  882 +++++++++++++++--
 omicwas-0.7.0/omicwas/README.md                        |   14 
 omicwas-0.7.0/omicwas/build                            |only
 omicwas-0.7.0/omicwas/data/GSE79262small.RData         |binary
 omicwas-0.7.0/omicwas/data/GTExsmall.RData             |only
 omicwas-0.7.0/omicwas/inst                             |only
 omicwas-0.7.0/omicwas/man/GSE42861small.Rd             |    6 
 omicwas-0.7.0/omicwas/man/GSE79262small.Rd             |    4 
 omicwas-0.7.0/omicwas/man/GTExsmall.Rd                 |only
 omicwas-0.7.0/omicwas/man/ctassoc.Rd                   |  102 +
 omicwas-0.7.0/omicwas/man/ctcisQTL.Rd                  |   46 
 omicwas-0.7.0/omicwas/tests/GSE42861smallresult.RData  |binary
 omicwas-0.7.0/omicwas/tests/GSE42861smallresult2.RData |only
 omicwas-0.7.0/omicwas/tests/GTExsmallresult.RData      |only
 omicwas-0.7.0/omicwas/tests/ctcisQTL.out.txt           |  202 +--
 omicwas-0.7.0/omicwas/tests/testthat/testctcisQTL.R    |    4 
 omicwas-0.7.0/omicwas/tests/testthat/testomicwas.R     |   31 
 omicwas-0.7.0/omicwas/vignettes                        |only
 26 files changed, 1108 insertions(+), 405 deletions(-)

More information about omicwas at CRAN
Permanent link

Package mixAK updated to version 5.3 with previous version 5.2 dated 2020-02-10

Title: Multivariate Normal Mixture Models and Mixtures of Generalized Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between mixAK versions 5.2 dated 2020-02-10 and 5.3 dated 2020-06-02

 DESCRIPTION      |    8 ++++----
 MD5              |   12 ++++++------
 NAMESPACE        |   10 +++++++---
 NEWS             |    3 +++
 data/Acidity.rda |binary
 data/Enzyme.rda  |binary
 data/Galaxy.rda  |binary
 7 files changed, 20 insertions(+), 13 deletions(-)

More information about mixAK at CRAN
Permanent link

Package poppr updated to version 2.8.6 with previous version 2.8.5 dated 2020-02-25

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 2.8.5 dated 2020-02-25 and 2.8.6 dated 2020-06-02

 DESCRIPTION                  |   11 -
 MD5                          |   69 +++---
 NEWS.md                      |   25 ++
 R/Index_calculations.r       |   76 ++++---
 R/bitwise.r                  |   89 ++++----
 R/check_data.R               |    2 
 R/distances.r                |    2 
 R/file_handling.r            |   54 +++--
 R/ia_jackknife.R             |   93 ++++-----
 R/internal.r                 |   45 +---
 R/pipe.R                     |    2 
 R/print_methods.r            |    2 
 R/sample_schemes.r           |   12 -
 R/zzz.r                      |    2 
 build/vignette.rds           |binary
 data/Aeut.rda                |binary
 data/Pinf.rda                |binary
 data/Pram.rda                |binary
 data/monpop.rda              |binary
 data/old_Pinf.rda            |binary
 data/old_partial_clone.rda   |binary
 data/partial_clone.rda       |binary
 inst/doc/algo.pdf            |binary
 inst/doc/mlg.html            |  392 +++++++++++++++++++------------------
 inst/doc/poppr_manual.html   |  444 ++++++++++++++++++++++---------------------
 man/Aeut.Rd                  |    6 
 man/Pinf.Rd                  |    6 
 man/Pram.Rd                  |    6 
 man/genetic_distance.Rd      |    4 
 man/monpop.Rd                |    6 
 man/partial_clone.Rd         |    6 
 man/win.ia.Rd                |    2 
 tests/testthat/genalex       |only
 tests/testthat/test-import.R |   15 +
 tests/testthat/test-plots.R  |    2 
 tests/testthat/test-winia.R  |    5 
 36 files changed, 750 insertions(+), 628 deletions(-)

More information about poppr at CRAN
Permanent link

Package metaBMA updated to version 0.6.3 with previous version 0.6.2 dated 2019-09-16

Title: Bayesian Model Averaging for Random and Fixed Effects Meta-Analysis
Description: Computes the posterior model probabilities for standard meta-analysis models (null model vs. alternative model assuming either fixed- or random-effects, respectively). These posterior probabilities are used to estimate the overall mean effect size as the weighted average of the mean effect size estimates of the random- and fixed-effect model as proposed by Gronau, Van Erp, Heck, Cesario, Jonas, & Wagenmakers (2017, <doi:10.1080/23743603.2017.1326760>). The user can define a wide range of non-informative or informative priors for the mean effect size and the heterogeneity coefficient. Moreover, using pre-compiled Stan models, meta-analysis with continuous and discrete moderators with Jeffreys-Zellner-Siow (JZS) priors can be fitted and tested. This allows to compute Bayes factors and perform Bayesian model averaging across random- and fixed-effects meta-analysis with and without moderators. For a primer on Bayesian model-averaged meta-analysis, see Gronau, Heck, Berkhout, Haaf, & Wagenmakers (2020, <doi:10.31234/osf.io/97qup>).
Author: Daniel W. Heck [aut, cre] (<https://orcid.org/0000-0002-6302-9252>), Quentin F. Gronau [ctb], Eric-Jan Wagenmakers [ctb]
Maintainer: Daniel W. Heck <dheck@uni-marburg.de>

Diff between metaBMA versions 0.6.2 dated 2019-09-16 and 0.6.3 dated 2020-06-02

 DESCRIPTION                               |   23 +++++++-----
 MD5                                       |   55 +++++++++++++++---------------
 NEWS                                      |    6 +++
 R/bma.R                                   |   54 +++++++++++++++++++----------
 R/metaBMA.R                               |    4 +-
 R/meta_bma.R                              |   10 +++++
 R/meta_stan.R                             |    3 +
 build/vignette.rds                        |binary
 inst/CITATION                             |only
 inst/doc/metaBMA.R                        |   10 ++---
 inst/doc/metaBMA.html                     |   45 ++++++++++--------------
 man/bma.Rd                                |   10 ++++-
 man/facial_feedback.Rd                    |    6 ++-
 man/metaBMA-package.Rd                    |    5 ++
 man/meta_bma.Rd                           |   27 ++++++++++++--
 man/meta_default.Rd                       |    3 -
 man/meta_fixed.Rd                         |   20 ++++++++--
 man/meta_ordered.Rd                       |   22 +++++++++---
 man/meta_random.Rd                        |   24 +++++++++----
 man/plot_forest.Rd                        |   12 +++++-
 man/plot_posterior.Rd                     |   10 ++++-
 man/power_pose.Rd                         |   10 ++++-
 man/prior.Rd                              |   10 ++++-
 man/towels.Rd                             |    6 ++-
 tests/testthat/test_H0_logml.R            |    6 ++-
 tests/testthat/test_bma.R                 |   14 ++++---
 tests/testthat/test_gronau2017powerpose.R |   14 +++----
 tests/testthat/test_integrate.R           |    8 +++-
 tests/testthat/test_stan.R                |    8 ++--
 29 files changed, 282 insertions(+), 143 deletions(-)

More information about metaBMA at CRAN
Permanent link

Package jsonify updated to version 1.2.1 with previous version 1.2.0 dated 2020-05-30

Title: Convert Between 'R' Objects and Javascript Object Notation (JSON)
Description: Conversions between 'R' objects and Javascript Object Notation (JSON) using the 'rapidjsonr' library <https://CRAN.R-project.org/package=rapidjsonr>.
Author: David Cooley [aut, cre], Chris Muir [ctb], Brendan Knapp [ctb] (<https://orcid.org/0000-0003-3284-4972>)
Maintainer: David Cooley <dcooley@symbolix.com.au>

Diff between jsonify versions 1.2.0 dated 2020-05-30 and 1.2.1 dated 2020-06-02

 DESCRIPTION                                          |    8 -
 MD5                                                  |   10 +-
 NEWS.md                                              |    4 
 inst/doc/jsonify.html                                |    4 
 inst/include/jsonify/from_json/from_json.hpp         |   59 +++++++++++-
 inst/include/jsonify/from_json/simplify/simplify.hpp |   90 ++++++++++---------
 6 files changed, 119 insertions(+), 56 deletions(-)

More information about jsonify at CRAN
Permanent link

Package geoknife updated to version 1.6.4 with previous version 1.6.3 dated 2019-01-30

Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey Geo Data Portal web application or elsewhere, using a web-enabled workflow that eliminates the need to download and store large datasets that are reliably hosted on the Internet. The package provides access to several data subset and summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut, cre], Jordan Walker [aut], Alison Appling [aut], David Blodgett [aut], Emily Read [aut], Luke Winslow [aut], Lindsay Carr [aut], David Watkins [aut]
Maintainer: Jordan Read <jread@usgs.gov>

Diff between geoknife versions 1.6.3 dated 2019-01-30 and 1.6.4 dated 2020-06-02

 DESCRIPTION                       |   12 
 MD5                               |   74 ++--
 NEWS.md                           |    6 
 R/06-simplegeom-obj.R             |    7 
 R/bufferPoint.R                   |    2 
 R/start-geojob.R                  |    9 
 build/vignette.rds                |binary
 inst/doc/custom_data_sources.R    |   94 +++---
 inst/doc/custom_data_sources.html |  372 +++++++++++++++++++------
 inst/doc/geoknife.html            |  563 ++++++++++++++++++++++++++------------
 inst/doc/plot_geotiff.R           |   48 +--
 inst/doc/plot_geotiff.html        |  371 ++++++++++++++++++++-----
 man/XML-method.Rd                 |    1 
 man/abstract-datagroup.Rd         |    1 
 man/algorithm-webprocess.Rd       |    1 
 man/attribute.Rd                  |    1 
 man/bufferPoint.Rd                |    2 
 man/check-geojob.Rd               |    1 
 man/datagroup-methods.Rd          |    1 
 man/download.Rd                   |    1 
 man/email-method.Rd               |    1 
 man/geojob-methods.Rd             |    3 
 man/geom.Rd                       |    1 
 man/inputs-webprocess.Rd          |    3 
 man/parseTimeseries.Rd            |    2 
 man/query.Rd                      |    1 
 man/simplegeom-methods.Rd         |    1 
 man/start-methods.Rd              |    2 
 man/times-webdata.Rd              |    1 
 man/times_query-method.Rd         |    1 
 man/url.Rd                        |    1 
 man/values.Rd                     |    1 
 man/variables_query-method.Rd     |    1 
 man/version.Rd                    |    1 
 man/wait.Rd                       |    1 
 man/webdata-methods.Rd            |    7 
 man/webgeom-methods.Rd            |    5 
 man/webprocess-methods.Rd         |    9 
 38 files changed, 1130 insertions(+), 479 deletions(-)

More information about geoknife at CRAN
Permanent link

Package geiger updated to version 2.0.7 with previous version 2.0.6.4 dated 2020-01-25

Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Author: Luke Harmon, Matthew Pennell, Chad Brock, Joseph Brown, Wendell Challenger, Jon Eastman, Rich FitzJohn, Rich Glor, Gene Hunt, Liam Revell, Graham Slater, Josef Uyeda, and Jason Weir
Maintainer: Luke Harmon <lukeh@uidaho.edu>

Diff between geiger versions 2.0.6.4 dated 2020-01-25 and 2.0.7 dated 2020-06-02

 ChangeLog                |   68 
 DESCRIPTION              |   18 
 MD5                      |  156 -
 NAMESPACE                |  336 ++--
 R/TESTING.R              | 1202 +++++++-------
 R/congruify.R            |  910 +++++------
 R/deprecated.R           |  318 +--
 R/disparity.R            |  533 +++---
 R/diversification.R      |  496 +++---
 R/diversitree.R          |    4 
 R/edges.R                |  452 ++---
 R/examples.R             |  222 +-
 R/glomogram.R            |  312 +--
 R/internal.R             |  254 +--
 R/likelihood.R           |  865 +++++-----
 R/mecca.R                | 3028 ++++++++++++++++++-------------------
 R/medusa.R               | 2647 ++++++++++++++++----------------
 R/plotting.R             | 1446 ++++++++---------
 R/postpred.R             |  560 +++---
 R/proposals.R            | 1741 ++++++++++-----------
 R/rjmcmc.R               |  552 +++---
 R/simulation.R           |  556 +++---
 R/traits-fossil.R        | 1533 +++++++++----------
 R/traits.R               | 2125 +++++++++++++-------------
 R/utilities-misc.R       |   16 
 R/utilities-phylo.R      | 3781 +++++++++++++++++++++++------------------------
 R/utilities-print.R      |  645 ++++----
 R/utilities-stat.R       |  316 +--
 README.md                |   86 -
 inst/CITATION            |  145 -
 man/aicm.Rd              |   86 -
 man/aicw.Rd              |   66 
 man/aov.phylo.Rd         |  114 -
 man/bd.ms.Rd             |  152 -
 man/calibrate.mecca.Rd   |  178 +-
 man/calibrate.rjmcmc.Rd  |   88 -
 man/congruify.phylo.Rd   |  112 -
 man/dcount.Rd            |   86 -
 man/drop.extinct.Rd      |   96 -
 man/dtt.Rd               |  154 -
 man/fitContinuous.Rd     |  394 ++--
 man/fitContinuousMCMC.Rd |  212 +-
 man/fitDiscrete.Rd       |  251 +--
 man/gbresolve.Rd         |  124 -
 man/geiger-data.Rd       |  234 +-
 man/geiger-defunct.Rd    |  156 -
 man/geiger-examples.Rd   |   22 
 man/geiger-internal.Rd   |  183 +-
 man/geiger-package.Rd    |   48 
 man/load.rjmcmc.Rd       |  116 -
 man/make.gbm.Rd          |  148 -
 man/mecca.Rd             |  296 +--
 man/medusa.Rd            |  172 +-
 man/name.check.Rd        |   94 -
 man/nh.test.Rd           |  152 -
 man/nodelabel.phylo.Rd   |  250 +--
 man/plot.medusa.Rd       |  106 -
 man/pp.mcmc.Rd           |  283 +--
 man/r8s.phylo.Rd         |  150 -
 man/ratematrix.Rd        |   82 -
 man/rc.Rd                |  116 -
 man/rescale.Rd           |  182 +-
 man/rjmcmc.bm.Rd         |  228 +-
 man/sim.bd.Rd            |   90 -
 man/sim.bdtree.Rd        |  116 -
 man/sim.char.Rd          |  126 -
 man/startingpt.mecca.Rd  |  132 -
 man/subset.phylo.Rd      |   66 
 man/tips.Rd              |   64 
 man/to.auteur.Rd         |   70 
 man/treedata.Rd          |   76 
 src/APE_reorder_phylo.c  |    1 
 src/branches.cpp         |  110 -
 src/init.c               |    1 
 src/mkn.c                |   30 
 src/mkn.h                |    2 
 src/pic.c                |    4 
 src/util.c               |   33 
 src/utilities.cpp        |  203 +-
 79 files changed, 15858 insertions(+), 15720 deletions(-)

More information about geiger at CRAN
Permanent link

Package simplevis updated to version 1.1.4 with previous version 1.1.3 dated 2020-05-14

Title: Simple Visualisation with 'ggplot2' and 'leaflet' Wrappers
Description: Provides 'ggplot2' and 'leaflet' wrapper functions designed to simplify the creation of high quality graph and map visualisations. These functions only require inputs of data, variables and titles to provide beautiful interactive or image visualisations. However they allow for more flexibility if required. The intent is that high quality well-designed graphs and maps can be made more consistently with less effort, code and expertise than would otherwise be required.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>), Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>

Diff between simplevis versions 1.1.3 dated 2020-05-14 and 1.1.4 dated 2020-06-02

 simplevis-1.1.3/simplevis/data/nz_region.rda      |only
 simplevis-1.1.3/simplevis/man/nz_region.Rd        |only
 simplevis-1.1.4/simplevis/DESCRIPTION             |    6 +++---
 simplevis-1.1.4/simplevis/MD5                     |   16 +++++++---------
 simplevis-1.1.4/simplevis/NEWS.md                 |    4 ++++
 simplevis-1.1.4/simplevis/R/data.R                |   13 -------------
 simplevis-1.1.4/simplevis/R/other.R               |   10 ----------
 simplevis-1.1.4/simplevis/inst/doc/simplevis.html |    4 ++--
 simplevis-1.1.4/simplevis/man/pal_point_set1.Rd   |    8 +-------
 simplevis-1.1.4/simplevis/man/pal_snz.Rd          |    8 +-------
 10 files changed, 18 insertions(+), 51 deletions(-)

More information about simplevis at CRAN
Permanent link

Package postHoc updated to version 0.1.3 with previous version 0.1.1 dated 2020-03-24

Title: Tools for Post-Hoc Analysis
Description: Implements a range of facilities for post-hoc analysis and summarizing linear models, generalized linear models and generalized linear mixed models, including grouping and clustering via pairwise comparisons using graph representations and efficient algorithms for finding maximal cliques of a graph. Includes also non-parametric toos for post-hoc analysis. It has S3 methods for printing summarizing, and producing plots, line and barplots suitable for post-hoc analyses.
Author: Rodrigo Labouriau [aut, cre] (<https://orcid.org/0000-0001-8713-6864>)
Maintainer: Rodrigo Labouriau <rodrigo.labouriau@math.au.dk>

Diff between postHoc versions 0.1.1 dated 2020-03-24 and 0.1.3 dated 2020-06-02

 DESCRIPTION                    |   12 -
 MD5                            |   26 ++-
 NAMESPACE                      |   10 +
 R/AuxiliarFunctions.R          |   21 ++
 R/GroupClustering.R            |  298 +++++++++++++++++++++++++++++++++++++----
 R/Methods4PostHoc.R            |    2 
 R/OldCompatibility.R           |only
 build                          |only
 inst                           |only
 man/ExtractCI.Rd               |    5 
 man/FormGroupsClusters.Rd      |    3 
 man/GroupClusterEffects.Rd     |only
 man/KruskalWallisAllPvalues.Rd |only
 man/MedianBootCI.Rd            |only
 man/posthoc.Rd                 |   16 +-
 man/posthocKW.Rd               |only
 vignettes                      |only
 17 files changed, 342 insertions(+), 51 deletions(-)

More information about postHoc at CRAN
Permanent link

Package Pade updated to version 1.0.1 with previous version 1.0.0 dated 2019-12-08

Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order (Baker, 1975) <ISBN:9780120748556>.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

Diff between Pade versions 1.0.0 dated 2019-12-08 and 1.0.1 dated 2020-06-02

 DESCRIPTION                |   12 ++---
 MD5                        |   14 +++---
 R/Pade.R                   |   14 +++---
 README.md                  |  102 +++++++++++++++++++++++++++++++++------------
 build                      |only
 inst/CITATION              |only
 inst/NEWS.Rd               |   43 +++++++++++++-----
 man/Pade-package.Rd        |   23 +++++++---
 tests/testthat/test-Pade.R |    8 +++
 9 files changed, 156 insertions(+), 60 deletions(-)

More information about Pade at CRAN
Permanent link

Package jmvcore updated to version 1.2.23 with previous version 1.2.19 dated 2020-05-14

Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>

Diff between jmvcore versions 1.2.19 dated 2020-05-14 and 1.2.23 dated 2020-06-02

 DESCRIPTION  |    8 ++++----
 MD5          |   10 +++++-----
 R/analysis.R |   30 +++++++++++++++++++-----------
 R/array.R    |    3 ++-
 R/group.R    |    3 ++-
 R/table.R    |   58 ++++++++++++++++++++++++++++++----------------------------
 6 files changed, 62 insertions(+), 50 deletions(-)

More information about jmvcore at CRAN
Permanent link

Package isqg updated to version 1.3 with previous version 1.2 dated 2019-02-13

Title: In Silico Quantitative Genetics
Description: Accomplish high performance simulations in quantitative genetics. The molecular genetic components are represented by R6/C++ classes and methods. The core computational algorithm is implemented using bitsets according to <doi:10.1534/g3.119.400373>. A mix between low and high level interfaces provides great flexibility and allows user defined extensions and a wide range of applications.
Author: Fernando H. Toledo [aut, cre] (<https://orcid.org/0000-0003-0158-643X>) International Maize and Wheat Improvement Center [cph]
Maintainer: Fernando H. Toledo <f.toledo@cgiar.org>

Diff between isqg versions 1.2 dated 2019-02-13 and 1.3 dated 2020-06-02

 isqg-1.2/isqg/inst/include/isqg/Sifter.hpp  |only
 isqg-1.2/isqg/src/Sifter.cpp                |only
 isqg-1.3/isqg/DESCRIPTION                   |   24 +-
 isqg-1.3/isqg/MD5                           |   49 +++---
 isqg-1.3/isqg/NAMESPACE                     |    4 
 isqg-1.3/isqg/R/Functions.R                 |   45 +----
 isqg-1.3/isqg/R/Hooks.R                     |    1 
 isqg-1.3/isqg/R/ISQG.R                      |    7 
 isqg-1.3/isqg/R/Mating.R                    |    9 -
 isqg-1.3/isqg/R/R6Classes.R                 |   96 ++++++++---
 isqg-1.3/isqg/R/Trait.R                     |    2 
 isqg-1.3/isqg/build                         |only
 isqg-1.3/isqg/inst/CITATION                 |only
 isqg-1.3/isqg/inst/REFERENCES.bib           |only
 isqg-1.3/isqg/inst/extdata                  |only
 isqg-1.3/isqg/inst/include/isqg.h           |    2 
 isqg-1.3/isqg/inst/include/isqg/FwdDefs.hpp |   11 -
 isqg-1.3/isqg/inst/include/isqg/isqg.hpp    |   21 +-
 isqg-1.3/isqg/man/Data.Rd                   |    4 
 isqg-1.3/isqg/man/Genotype.Rd               |    2 
 isqg-1.3/isqg/man/ISQG.Rd                   |    6 
 isqg-1.3/isqg/man/Specie.Rd                 |  125 +++++++++++++++
 isqg-1.3/isqg/man/Specimen.Rd               |  227 +++++++++++++++++++++++++++-
 isqg-1.3/isqg/man/Trait.Rd                  |   92 ++++++++++-
 isqg-1.3/isqg/man/dot-decode.Rd             |only
 isqg-1.3/isqg/man/dot-fuse.Rd               |only
 isqg-1.3/isqg/man/set_specie.Rd             |   44 +----
 isqg-1.3/isqg/src/Makevars                  |    2 
 isqg-1.3/isqg/src/Makevars.win              |    2 
 29 files changed, 605 insertions(+), 170 deletions(-)

More information about isqg at CRAN
Permanent link

Package install.load updated to version 1.2.3 with previous version 1.2.1 dated 2016-07-12

Title: Check, Install and Load CRAN & USGS GRAN Packages
Description: The function `install_load` checks the local R library(ies) to see if the required package(s) is/are installed or not. If the package(s) is/are not installed, then the package(s) will be installed along with the required dependency(ies). This function pulls source or binary packages from the Rstudio-sponsored CRAN mirror and/or the USGS GRAN Repository. Lastly, the chosen package(s) is/are loaded. The function `load_package` simply loads the provided packages. If this package does not fit your needs, then you may want to consider these other R packages: 'needs', 'easypackages', 'pacman', 'pak', 'anyLib', and/or 'librarian'.
Author: maloneypatr [aut, cre], Irucka Embry [aut, ctb]
Maintainer: Irucka Embry <iembry@ecoccs.com>

Diff between install.load versions 1.2.1 dated 2016-07-12 and 1.2.3 dated 2020-06-02

 install.load-1.2.1/install.load/LICENSE.note        |only
 install.load-1.2.3/install.load/DESCRIPTION         |   24 +++++++++---------
 install.load-1.2.3/install.load/LICENSE             |only
 install.load-1.2.3/install.load/MD5                 |   21 +++++++++-------
 install.load-1.2.3/install.load/NAMESPACE           |    3 ++
 install.load-1.2.3/install.load/NEWS.md             |   10 ++++++-
 install.load-1.2.3/install.load/R/install.load.R    |only
 install.load-1.2.3/install.load/R/install_load.R    |   26 +++++++++++++-------
 install.load-1.2.3/install.load/R/load_package.R    |   10 +++++--
 install.load-1.2.3/install.load/README.md           |    8 +++---
 install.load-1.2.3/install.load/inst                |only
 install.load-1.2.3/install.load/man/install.load.Rd |only
 install.load-1.2.3/install.load/man/install_load.Rd |   20 ++++++++-------
 install.load-1.2.3/install.load/man/load_package.Rd |   12 +++------
 14 files changed, 82 insertions(+), 52 deletions(-)

More information about install.load at CRAN
Permanent link

Package IndexConstruction updated to version 0.1-3 with previous version 0.1-2 dated 2019-10-24

Title: Index Construction for Time Series Data
Description: Derivation of indexes for benchmarking purposes. A methodology with flexible number of constituents is implemented. Also functions for market capitalization and volume weighted indexes with fixed number of constituents are available. The main function of the package, indexComp(), provides the derived index, suitable for analysis purposes. The functions indexUpdate(), indexMemberSelection() and indexMembersUpdate() are components of indexComp() and enable one to construct and continuously update an index, e.g. for display on a website. The methodology behind the functions provided gets introduced in Trimborn and Haerdle (2018) <doi:10.1016/j.jempfin.2018.08.004>.
Author: Simon Trimborn <trimborn.econometrics@gmail.com>
Maintainer: Simon Trimborn <trimborn.econometrics@gmail.com>

Diff between IndexConstruction versions 0.1-2 dated 2019-10-24 and 0.1-3 dated 2020-06-02

 DESCRIPTION           |   12 ++++++------
 MD5                   |    8 ++++----
 NAMESPACE             |    4 +---
 data/CryptoData.RData |binary
 data/datalist         |    2 +-
 5 files changed, 12 insertions(+), 14 deletions(-)

More information about IndexConstruction at CRAN
Permanent link

Package DLMtool updated to version 5.4.4 with previous version 5.4.3 dated 2020-04-16

Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management procedures for data-limited fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Tom Carruthers [aut, cre], Adrian Hordyk [aut], M. Bryan [ctb], HF. Geremont [ctb], C. Grandin [ctb], W. Harford [ctb], Q. Huynh [ctb], C. Walters [ctb]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>

Diff between DLMtool versions 5.4.3 dated 2020-04-16 and 5.4.4 dated 2020-06-02

 DLMtool-5.4.3/DLMtool/data/Generic_Fleet.RData                   |only
 DLMtool-5.4.3/DLMtool/data/Generic_Obs.RData                     |only
 DLMtool-5.4.3/DLMtool/data/datalist                              |only
 DLMtool-5.4.4/DLMtool/DESCRIPTION                                |   12 
 DLMtool-5.4.4/DLMtool/MD5                                        |  259 ++---
 DLMtool-5.4.4/DLMtool/NAMESPACE                                  |    2 
 DLMtool-5.4.4/DLMtool/NEWS.md                                    |   15 
 DLMtool-5.4.4/DLMtool/R/Data_make_update.R                       |   42 
 DLMtool-5.4.4/DLMtool/R/DefineClasses.r                          |   58 -
 DLMtool-5.4.4/DLMtool/R/MPs_SupportingFunctions.R                |    1 
 DLMtool-5.4.4/DLMtool/R/MSE_functions.R                          |   93 +
 DLMtool-5.4.4/DLMtool/R/Misc_Exported.R                          |   14 
 DLMtool-5.4.4/DLMtool/R/Misc_Internal.R                          |   51 -
 DLMtool-5.4.4/DLMtool/R/PMobjects.R                              |    6 
 DLMtool-5.4.4/DLMtool/R/SampleOM.R                               |  120 +-
 DLMtool-5.4.4/DLMtool/R/Turing.R                                 |    4 
 DLMtool-5.4.4/DLMtool/R/popdyn.R                                 |   14 
 DLMtool-5.4.4/DLMtool/R/runMSE.r                                 |   73 +
 DLMtool-5.4.4/DLMtool/R/sysdata.rda                              |binary
 DLMtool-5.4.4/DLMtool/data/Albacore.RData                        |binary
 DLMtool-5.4.4/DLMtool/data/Atlantic_mackerel.RData               |binary
 DLMtool-5.4.4/DLMtool/data/Blue_shark.RData                      |binary
 DLMtool-5.4.4/DLMtool/data/Bluefin_tuna.RData                    |binary
 DLMtool-5.4.4/DLMtool/data/Bluefin_tuna_WAtl.RData               |binary
 DLMtool-5.4.4/DLMtool/data/Butterfish.RData                      |binary
 DLMtool-5.4.4/DLMtool/data/China_rockfish.RData                  |binary
 DLMtool-5.4.4/DLMtool/data/Cobia.RData                           |binary
 DLMtool-5.4.4/DLMtool/data/DataDescription.RData                 |binary
 DLMtool-5.4.4/DLMtool/data/DecE_Dom.RData                        |binary
 DLMtool-5.4.4/DLMtool/data/DecE_HDom.RData                       |binary
 DLMtool-5.4.4/DLMtool/data/DecE_NDom.RData                       |binary
 DLMtool-5.4.4/DLMtool/data/Example_datafile.RData                |binary
 DLMtool-5.4.4/DLMtool/data/FlatE_Dom.RData                       |binary
 DLMtool-5.4.4/DLMtool/data/FlatE_HDom.RData                      |binary
 DLMtool-5.4.4/DLMtool/data/FlatE_NDom.RData                      |binary
 DLMtool-5.4.4/DLMtool/data/FleetDescription.RData                |binary
 DLMtool-5.4.4/DLMtool/data/Generic_DecE.RData                    |binary
 DLMtool-5.4.4/DLMtool/data/Generic_FlatE.RData                   |binary
 DLMtool-5.4.4/DLMtool/data/Generic_IncE.RData                    |binary
 DLMtool-5.4.4/DLMtool/data/Generic_fleet.RData                   |only
 DLMtool-5.4.4/DLMtool/data/Generic_obs.RData                     |only
 DLMtool-5.4.4/DLMtool/data/Gulf_blue_tilefish.RData              |binary
 DLMtool-5.4.4/DLMtool/data/Herring.RData                         |binary
 DLMtool-5.4.4/DLMtool/data/ImpDescription.RData                  |binary
 DLMtool-5.4.4/DLMtool/data/Imprecise_Biased.RData                |binary
 DLMtool-5.4.4/DLMtool/data/Imprecise_Unbiased.RData              |binary
 DLMtool-5.4.4/DLMtool/data/IncE_HDom.RData                       |binary
 DLMtool-5.4.4/DLMtool/data/IncE_NDom.RData                       |binary
 DLMtool-5.4.4/DLMtool/data/LHdatabase.RData                      |binary
 DLMtool-5.4.4/DLMtool/data/Low_Effort_Non_Target.RData           |binary
 DLMtool-5.4.4/DLMtool/data/MSEDescription.RData                  |binary
 DLMtool-5.4.4/DLMtool/data/Mackerel.RData                        |binary
 DLMtool-5.4.4/DLMtool/data/OMDescription.RData                   |binary
 DLMtool-5.4.4/DLMtool/data/ObsDescription.RData                  |binary
 DLMtool-5.4.4/DLMtool/data/Overages.RData                        |binary
 DLMtool-5.4.4/DLMtool/data/Perfect_Imp.RData                     |binary
 DLMtool-5.4.4/DLMtool/data/Perfect_Info.RData                    |binary
 DLMtool-5.4.4/DLMtool/data/Porgy.RData                           |binary
 DLMtool-5.4.4/DLMtool/data/Precise_Biased.RData                  |binary
 DLMtool-5.4.4/DLMtool/data/Precise_Unbiased.RData                |binary
 DLMtool-5.4.4/DLMtool/data/Red_snapper.RData                     |binary
 DLMtool-5.4.4/DLMtool/data/ReqData.RData                         |binary
 DLMtool-5.4.4/DLMtool/data/Rockfish.RData                        |binary
 DLMtool-5.4.4/DLMtool/data/SimulatedData.RData                   |binary
 DLMtool-5.4.4/DLMtool/data/Simulation_1.RData                    |binary
 DLMtool-5.4.4/DLMtool/data/Snapper.RData                         |binary
 DLMtool-5.4.4/DLMtool/data/Sole.RData                            |binary
 DLMtool-5.4.4/DLMtool/data/StockDescription.RData                |binary
 DLMtool-5.4.4/DLMtool/data/Target_All_Fish.RData                 |binary
 DLMtool-5.4.4/DLMtool/data/Targeting_Small_Fish.RData            |binary
 DLMtool-5.4.4/DLMtool/data/Toothfish.RData                       |binary
 DLMtool-5.4.4/DLMtool/data/ourReefFish.RData                     |binary
 DLMtool-5.4.4/DLMtool/data/testOM.RData                          |binary
 DLMtool-5.4.4/DLMtool/data/tiny.RData                            |binary
 DLMtool-5.4.4/DLMtool/man/AvC.Rd                                 |  122 +-
 DLMtool-5.4.4/DLMtool/man/AvC_MLL.Rd                             |  124 +-
 DLMtool-5.4.4/DLMtool/man/BK.Rd                                  |  228 ++--
 DLMtool-5.4.4/DLMtool/man/CC1.Rd                                 |  214 ++--
 DLMtool-5.4.4/DLMtool/man/CompSRA.Rd                             |  150 +-
 DLMtool-5.4.4/DLMtool/man/DBSRA.Rd                               |  224 ++--
 DLMtool-5.4.4/DLMtool/man/DCAC.Rd                                |  354 +++----
 DLMtool-5.4.4/DLMtool/man/DD.Rd                                  |  174 +--
 DLMtool-5.4.4/DLMtool/man/DDe.Rd                                 |  166 +--
 DLMtool-5.4.4/DLMtool/man/DTe40.Rd                               |  132 +-
 DLMtool-5.4.4/DLMtool/man/Data-class.Rd                          |  446 ++++----
 DLMtool-5.4.4/DLMtool/man/DataDescription.Rd                     |    2 
 DLMtool-5.4.4/DLMtool/man/DynF.Rd                                |  168 +--
 DLMtool-5.4.4/DLMtool/man/EtargetLopt.Rd                         |  120 +-
 DLMtool-5.4.4/DLMtool/man/FMSYref.Rd                             |  132 +-
 DLMtool-5.4.4/DLMtool/man/Fadapt.Rd                              |  210 ++--
 DLMtool-5.4.4/DLMtool/man/Fdem.Rd                                |  174 +--
 DLMtool-5.4.4/DLMtool/man/Fratio.Rd                              |  244 ++--
 DLMtool-5.4.4/DLMtool/man/GB_CC.Rd                               |  140 +-
 DLMtool-5.4.4/DLMtool/man/GB_slope.Rd                            |  164 +--
 DLMtool-5.4.4/DLMtool/man/GB_target.Rd                           |  176 +--
 DLMtool-5.4.4/DLMtool/man/Gcontrol.Rd                            |  172 +--
 DLMtool-5.4.4/DLMtool/man/ICI.Rd                                 |  200 +--
 DLMtool-5.4.4/DLMtool/man/IT5.Rd                                 |  154 +--
 DLMtool-5.4.4/DLMtool/man/ITM.Rd                                 |  106 +-
 DLMtool-5.4.4/DLMtool/man/ITe5.Rd                                |  142 +-
 DLMtool-5.4.4/DLMtool/man/Imp-class.Rd                           |   82 -
 DLMtool-5.4.4/DLMtool/man/Iratio.Rd                              |  152 +--
 DLMtool-5.4.4/DLMtool/man/Islope1.Rd                             |  202 ++--
 DLMtool-5.4.4/DLMtool/man/Itarget1.Rd                            |  226 ++--
 DLMtool-5.4.4/DLMtool/man/Itarget1_MPA.Rd                        |  176 +--
 DLMtool-5.4.4/DLMtool/man/ItargetE1.Rd                           |  210 ++--
 DLMtool-5.4.4/DLMtool/man/LBSPR.Rd                               |  200 +--
 DLMtool-5.4.4/DLMtool/man/Lratio_BHI.Rd                          |  198 +--
 DLMtool-5.4.4/DLMtool/man/LstepCC1.Rd                            |  306 +++---
 DLMtool-5.4.4/DLMtool/man/LstepCE1.Rd                            |  210 ++--
 DLMtool-5.4.4/DLMtool/man/Ltarget1.Rd                            |  266 ++---
 DLMtool-5.4.4/DLMtool/man/LtargetE1.Rd                           |  180 +--
 DLMtool-5.4.4/DLMtool/man/MCD.Rd                                 |  138 +-
 DLMtool-5.4.4/DLMtool/man/MRreal.Rd                              |  122 +-
 DLMtool-5.4.4/DLMtool/man/MSEDescription.Rd                      |   32 
 DLMtool-5.4.4/DLMtool/man/OM-class.Rd                            |  504 +++++-----
 DLMtool-5.4.4/DLMtool/man/Rcontrol.Rd                            |  216 ++--
 DLMtool-5.4.4/DLMtool/man/Rec-class.Rd                           |   98 -
 DLMtool-5.4.4/DLMtool/man/SBT1.Rd                                |  238 ++--
 DLMtool-5.4.4/DLMtool/man/SPMSY.Rd                               |  150 +-
 DLMtool-5.4.4/DLMtool/man/SPSRA.Rd                               |  168 +--
 DLMtool-5.4.4/DLMtool/man/SPmod.Rd                               |  162 +--
 DLMtool-5.4.4/DLMtool/man/SPslope.Rd                             |  186 +--
 DLMtool-5.4.4/DLMtool/man/YPR.Rd                                 |  184 +--
 DLMtool-5.4.4/DLMtool/man/checkMSE.Rd                            |  124 +-
 DLMtool-5.4.4/DLMtool/man/curE.Rd                                |  122 +-
 DLMtool-5.4.4/DLMtool/man/matlenlim.Rd                           |  230 ++--
 DLMtool-5.4.4/DLMtool/man/runCOSEWIC.Rd                          |  280 ++---
 DLMtool-5.4.4/DLMtool/man/summary-Data.Rd                        |   62 -
 DLMtool-5.4.4/DLMtool/man/testOM.Rd                              |   32 
 DLMtool-5.4.4/DLMtool/src/genLenComp.cpp                         |    3 
 DLMtool-5.4.4/DLMtool/tests/manual/test-code/test-OM_functions.R |   12 
 DLMtool-5.4.4/DLMtool/tests/manual/test-code/test-cpars.R        |    6 
 133 files changed, 5556 insertions(+), 5323 deletions(-)

More information about DLMtool at CRAN
Permanent link

Package ddpcr updated to version 1.15 with previous version 1.14 dated 2020-03-23

Title: Analysis and Visualization of Droplet Digital PCR in R and on the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

Diff between ddpcr versions 1.14 dated 2020-03-23 and 1.15 dated 2020-06-02

 DESCRIPTION                     |    6 
 MD5                             |   18 
 NEWS.md                         |    6 
 R/aaa.R                         |   12 
 R/outliers.R                    |    2 
 inst/doc/algorithm.html         |  420 +++++++------
 inst/doc/extend.html            |  825 +++++++++++++------------
 inst/doc/overview.html          | 1272 ++++++++++++++++++----------------------
 inst/doc/technical_details.html |  409 +++++++-----
 tests/testthat/test-utils.R     |    4 
 10 files changed, 1521 insertions(+), 1453 deletions(-)

More information about ddpcr at CRAN
Permanent link

Package pubh updated to version 1.1.14 with previous version 1.1.12 dated 2020-04-26

Title: A Toolbox for Public Health and Epidemiology
Description: A toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand 'ggplot2' plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.
Author: Josie Athens [aut, cre], Frank Harell [ctb], John Fox [ctb], R-Core [ctb]
Maintainer: Josie Athens <josie.athens@otago.ac.nz>

Diff between pubh versions 1.1.12 dated 2020-04-26 and 1.1.14 dated 2020-06-02

 DESCRIPTION                |   16 -
 MD5                        |   40 +--
 NAMESPACE                  |    4 
 R/descriptive_functions.R  |    7 
 R/display_functions.R      |    6 
 R/epi_functions.R          |    6 
 R/plot_functions.R         |   13 -
 build/vignette.rds         |binary
 data/Oncho.rda             |binary
 inst/doc/introduction.R    |    9 
 inst/doc/introduction.Rmd  |   19 -
 inst/doc/introduction.html |  119 ++++------
 inst/doc/regression.R      |   49 ++--
 inst/doc/regression.Rmd    |   55 ++--
 inst/doc/regression.html   |  513 ++++++++++++++++++++++-----------------------
 man/cross_tab.Rd           |    8 
 man/glm_coef.Rd            |    4 
 man/multiple.Rd            |    7 
 man/odds_trend.Rd          |    6 
 vignettes/introduction.Rmd |   19 -
 vignettes/regression.Rmd   |   55 ++--
 21 files changed, 486 insertions(+), 469 deletions(-)

More information about pubh at CRAN
Permanent link

Package pccc updated to version 1.0.5 with previous version 1.0.4 dated 2020-05-15

Title: Pediatric Complex Chronic Conditions
Description: An implementation of the pediatric complex chronic conditions (CCC) classification system using R and C++.
Author: Peter DeWitt [aut], Tell Bennett [aut], James Feinstein [aut], Seth Russell [aut, cre]
Maintainer: Seth Russell <seth.russell@ucdenver.edu>

Diff between pccc versions 1.0.4 dated 2020-05-15 and 1.0.5 dated 2020-06-02

 DESCRIPTION                  |    8 
 MD5                          |   22 -
 NEWS.md                      |    8 
 R/ccc.R                      |    2 
 R/get_codes.R                |    2 
 data/comparability.rda       |binary
 data/pccc_icd10_dataset.rda  |binary
 data/pccc_icd9_dataset.rda   |binary
 inst/doc/pccc-example.html   |    4 
 inst/doc/pccc-icd-codes.html |  759 +++++++++++++++++++++++++++++++++++++++++--
 inst/doc/pccc-overview.html  |    4 
 man/ccc.Rd                   |   15 
 12 files changed, 774 insertions(+), 50 deletions(-)

More information about pccc at CRAN
Permanent link

Package LHD updated to version 1.1.0 with previous version 0.1.3 dated 2020-04-14

Title: Latin Hypercube Designs (LHDs) Algorithms
Description: Contains different algorithms for efficient Latin Hypercube Designs (LHDs) with flexible sizes. Our package is comprehensive since it is capable of generating nearly orthogonal LHDs, maximin distance LHDs, and maximum projection LHDs. Documentation for each algorithm includes useful information and explanation along with corresponding references. This package is particularly useful in the area of Design and Analysis of Experiments (DAE). More specifically, design of computer experiments.
Author: Hongzhi Wang, Qian Xiao, Abhyuday Mandal
Maintainer: Hongzhi Wang <hw34508@uga.edu>

Diff between LHD versions 0.1.3 dated 2020-04-14 and 1.1.0 dated 2020-06-02

 DESCRIPTION                            |    8 
 MD5                                    |   64 +-
 NAMESPACE                              |    3 
 NEWS.md                                |   21 
 R/AvgAbsCor.R                          |only
 R/GA.R                                 |  393 ++++++++++++--
 R/LaPSO.R                              |  416 +++++++++++++--
 R/MaxAbsCor.R                          |only
 R/MaxProCriterion.R                    |only
 R/OA2LHD.R                             |   25 
 R/OASA.R                               |  256 +++++++--
 R/SA.R                                 |  181 +++++-
 R/SA2008.R                             |  360 +++++++++++--
 R/SLHD.R                               |  877 +++++++++++++++++++++++++++++----
 R/dij.R                                |    2 
 R/phi_p.R                              |   12 
 R/rLHD.R                               |    3 
 inst/doc/Vignette_for_LHD.R            |   88 ++-
 inst/doc/Vignette_for_LHD.Rmd          |  134 +++--
 inst/doc/Vignette_for_LHD.html         |  490 +++++++++---------
 man/AvgAbsCor.Rd                       |only
 man/GA.Rd                              |   35 -
 man/LaPSO.Rd                           |   49 +
 man/MaxAbsCor.Rd                       |only
 man/MaxProCriterion.Rd                 |only
 man/OA2LHD.Rd                          |   24 
 man/OASA.Rd                            |   60 +-
 man/SA.Rd                              |   44 +
 man/SA2008.Rd                          |   46 +
 man/SLHD.Rd                            |   58 +-
 man/dij.Rd                             |    2 
 man/phi_p.Rd                           |   12 
 man/rLHD.Rd                            |    3 
 tests/testthat/testmyfunctions_part1.R |   24 
 tests/testthat/testmyfunctions_part2.R |   24 
 vignettes/Vignette_for_LHD.Rmd         |  134 +++--
 36 files changed, 2905 insertions(+), 943 deletions(-)

More information about LHD at CRAN
Permanent link

Package drake updated to version 7.12.2 with previous version 7.12.1 dated 2020-05-14

Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://docs.ropensci.org/drake/> and the online manual <https://books.ropensci.org/drake/>.
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Alex Axthelm [ctb], Jasper Clarkberg [ctb], Kirill Müller [ctb], Ben Bond-Lamberty [ctb] (<https://orcid.org/0000-0001-9525-4633>), Tristan Mahr [ctb] (<https://orcid.org/0000-0002-8890-5116>), Miles McBain [ctb] (<https://orcid.org/0000-0003-2865-2548>), Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>), Ellis Hughes [ctb], Matthew Mark Strasiotto [ctb], Ben Marwick [rev], Peter Slaughter [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

Diff between drake versions 7.12.1 dated 2020-05-14 and 7.12.2 dated 2020-06-02

 DESCRIPTION                       |    6 ++--
 MD5                               |   22 +++++++-------
 NEWS.md                           |    7 ++++
 R/dynamic.R                       |    1 
 R/store_outputs.R                 |   15 ++++++++++
 R/transform_plan.R                |   42 ++++++++++++++++------------
 build/drake.pdf                   |binary
 tests/scenarios/run.sh            |    1 
 tests/testthat/test-6-visuals.R   |    2 +
 tests/testthat/test-7-deprecate.R |    1 
 tests/testthat/test-7-dsl.R       |   19 ++++++++++++
 tests/testthat/test-9-dynamic.R   |   57 ++++++++++++++++++++++++++++++++++++--
 12 files changed, 139 insertions(+), 34 deletions(-)

More information about drake at CRAN
Permanent link

Mon, 01 Jun 2020

Package vpc updated to version 1.2.1 with previous version 1.2.0 dated 2020-05-07

Title: Create Visual Predictive Checks
Description: Visual predictive checks are a commonly used diagnostic plot in pharmacometrics, showing how certain statistics (percentiles) for observed data compare to those same statistics for data simulated from a model. The package can generate VPCs for continuous, categorical, censored, and (repeated) time-to-event data.
Author: Ron Keizer <ronkeizer@gmail.com>
Maintainer: Ron Keizer <ronkeizer@gmail.com>

Diff between vpc versions 1.2.0 dated 2020-05-07 and 1.2.1 dated 2020-06-01

 DESCRIPTION           |   11 ++++-----
 MD5                   |   14 +++++------
 NEWS.md               |    3 ++
 R/plot_vpc.R          |    2 -
 R/vpc_cat.R           |   61 +++++++++++++++++++++++++++++++-------------------
 R/vpc_cens.R          |   40 +++++++++++++++-----------------
 tests/test-vpc_cat.R  |    4 ++-
 tests/test-vpc_cens.R |    5 +++-
 8 files changed, 81 insertions(+), 59 deletions(-)

More information about vpc at CRAN
Permanent link

Package StratigrapheR updated to version 1.1.0 with previous version 1.0.1 dated 2020-03-20

Title: Integrated Stratigraphy
Description: Includes bases for litholog generation: graphical functions based on R base graphics, interval management functions and svg importation functions among others. Also include stereographic projection functions, and other functions made to deal with large datasets while keeping options to get into the details of the data. When using for publication please cite Wouters, S., Da Silva, A.C. Crucifix, M., Sinnesael, M., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2019, Litholog generation with the StratigrapheR package and signal decomposition for cyclostratigraphic purposes. Geophysical Research Abstracts Vol. 21, EGU2019-5520, 2019, EGU General Assembly 2019. <http://hdl.handle.net/2268/234402> The palaeomagnetism functions are based on: Tauxe, L., 2010. Essentials of Paleomagnetism. University of California Press. <https://earthref.org/MagIC/books/Tauxe/Essentials/>; Allmendinger, R. W., Cardozo, N. C., and Fisher, D., 2013, Structural Geology Algorithms: Vectors & Tensors: Cambridge, England, Cambridge University Press, 289 pp.; Cardozo, N., and Allmendinger, R. W., 2013, Spherical projections with OSXStereonet: Computers & Geosciences, v. 51, no. 0, p. 193 - 205, <doi: 10.1016/j.cageo.2012.07.021>.
Author: Sebastien Wouters [aut, cre], Adam D. Smith [ctb]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>

Diff between StratigrapheR versions 1.0.1 dated 2020-03-20 and 1.1.0 dated 2020-06-01

 StratigrapheR-1.0.1/StratigrapheR/R/mat.lag.R          |only
 StratigrapheR-1.0.1/StratigrapheR/man/mat.lag.Rd       |only
 StratigrapheR-1.1.0/StratigrapheR/DESCRIPTION          |   12 ++---
 StratigrapheR-1.1.0/StratigrapheR/MD5                  |   19 ++++----
 StratigrapheR-1.1.0/StratigrapheR/NAMESPACE            |    4 -
 StratigrapheR-1.1.0/StratigrapheR/NEWS                 |only
 StratigrapheR-1.1.0/StratigrapheR/R/StratigrapheR.R    |    2 
 StratigrapheR-1.1.0/StratigrapheR/R/tie.lim.R          |   16 ++++---
 StratigrapheR-1.1.0/StratigrapheR/man/StratigrapheR.Rd |    2 
 StratigrapheR-1.1.0/StratigrapheR/man/earinc.Rd        |   38 ++++++++---------
 StratigrapheR-1.1.0/StratigrapheR/man/formFunction.Rd  |   36 ++++++++--------
 StratigrapheR-1.1.0/StratigrapheR/man/tie.lim.Rd       |    2 
 12 files changed, 65 insertions(+), 66 deletions(-)

More information about StratigrapheR at CRAN
Permanent link

Package LPKsample updated to version 2.1 with previous version 2.0 dated 2018-09-20

Title: LP Nonparametric High Dimensional K-Sample Comparison
Description: LP nonparametric high-dimensional K-sample comparison method that includes (i) confirmatory test, (ii) exploratory analysis, and (iii) options to output a data-driven LP-transformed matrix for classification. The primary reference is Mukhopadhyay, S. and Wang, K. (2020, Biometrika); <arXiv:1810.01724>.
Author: Subhadeep Mukhopadhyay, Kaijun Wang
Maintainer: Kaijun Wang <kaijunwang.19@gmail.com>

Diff between LPKsample versions 2.0 dated 2018-09-20 and 2.1 dated 2020-06-01

 DESCRIPTION              |   18 -
 MD5                      |   20 +-
 NAMESPACE                |    2 
 R/GLP.R                  |  443 +++++++++++++++++++++++++++++++----------------
 build/partial.rdb        |binary
 data/leukemia.rda        |binary
 man/GLP.Rd               |   38 ++--
 man/LP.comean.Rd         |    2 
 man/LPKsample-package.Rd |    4 
 man/LPT.Rd               |    2 
 man/W.Gen.Rd             |    2 
 11 files changed, 342 insertions(+), 189 deletions(-)

More information about LPKsample at CRAN
Permanent link

Package DisImpact updated to version 0.0.9 with previous version 0.0.8 dated 2020-04-28

Title: Calculates Disproportionate Impact When Binary Success Data are Disaggregated by Subgroups
Description: Implements methods for calculating disproportionate impact: the percentage point gap, proportionality index, and the 80% index. California Community Colleges Chancellor's Office (2017). Percentage Point Gap Method. <https://www.cccco.edu/-/media/CCCCO-Website/About-Us/Divisions/Digital-Innovation-and-Infrastructure/Research/Files/PercentagePointGapMethod2017.ashx>. California Community Colleges Chancellor's Office (2014). Guidelines for Measuring Disproportionate Impact in Equity Plans. <https://www.cccco.edu/-/media/CCCCO-Website/Files/DII/guidelines-for-measuring-disproportionate-impact-in-equity-plans-tfa-ada.pdf>.
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>

Diff between DisImpact versions 0.0.8 dated 2020-04-28 and 0.0.9 dated 2020-06-01

 DESCRIPTION              |    8 ++---
 MD5                      |   16 +++++-----
 NEWS                     |    4 ++
 R/percentage_point_gap.R |   69 ++++++++++++++++++++++++++++++++++++-----------
 inst/doc/Tutorial.html   |   26 ++++++++---------
 man/di_ppg.Rd            |   15 ++--------
 man/di_ppg_iterate.Rd    |   18 ++++--------
 man/ppg_moe.Rd           |    3 +-
 man/student_equity.Rd    |    4 --
 9 files changed, 94 insertions(+), 69 deletions(-)

More information about DisImpact at CRAN
Permanent link

Package smoothedLasso updated to version 1.2 with previous version 1.1 dated 2020-05-31

Title: Smoothed LASSO Regression via Nesterov Smoothing
Description: We provide full functionality to compute smoothed LASSO regression estimates. For this, the LASSO objective function is first smoothed using Nesterov smoothing (see Y. Nesterov (2005) <doi:10.1007/s10107-004-0552-5>), resulting in a modified LASSO objective function with explicit gradients everywhere. The smoothed objective function and its gradient are used to minimize it via BFGS, and the obtained minimizer is returned. Using Nesterov smoothing, the smoothed LASSO objective function can be made arbitrarily close to the original (unsmoothed) one. In particular, the Nesterov approach has the advantage that it comes with explicit accuracy bounds, both on the L1/L2 difference of the unsmoothed to the smoothed LASSO objective function as well as on their respective minimizers. A progressive smoothing approach is provided which iteratively smoothes the LASSO, resulting in more stable regression estimates.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Nilanjana Laha [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>

Diff between smoothedLasso versions 1.1 dated 2020-05-31 and 1.2 dated 2020-06-01

 DESCRIPTION       |    8 ++++----
 MD5               |    4 ++--
 R/smoothedLasso.r |   12 ++++--------
 3 files changed, 10 insertions(+), 14 deletions(-)

More information about smoothedLasso at CRAN
Permanent link

Package bujar updated to version 0.2-8 with previous version 0.2-7 dated 2019-11-12

Title: Buckley-James Regression for Survival Data with High-Dimensional Covariates
Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Implementations for survival data include boosting with componentwise linear least squares, componentwise smoothing splines, regression trees and MARS. Other high-dimensional tools include penalized regression for survival data. See Wang and Wang (2010) <doi:10.2202/1544-6115.1550>.
Author: Zhu Wang <https://orcid.org/0000-0002-0773-0052> and others (see COPYRIGHTS)
Maintainer: Zhu Wang <wangz1@uthscsa.edu>

Diff between bujar versions 0.2-7 dated 2019-11-12 and 0.2-8 dated 2020-06-01

 DESCRIPTION        |   10 +++++-----
 MD5                |   10 +++++-----
 NAMESPACE          |    3 ---
 NEWS               |    4 ++++
 build/vignette.rds |binary
 inst/doc/dlbcl.pdf |binary
 6 files changed, 14 insertions(+), 13 deletions(-)

More information about bujar at CRAN
Permanent link

Package bimets updated to version 1.5.1 with previous version 1.5.0 dated 2020-05-29

Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, endogenous targeting and model renormalization.
Author: Andrea Luciani [aut, cre], Roberto Stok [aut], Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>

Diff between bimets versions 1.5.0 dated 2020-05-29 and 1.5.1 dated 2020-06-01

 DESCRIPTION             |    8 ++++----
 MD5                     |   20 ++++++++++----------
 NEWS.md                 |    4 ++++
 R/bimets_ts_functions.R |    2 +-
 README.md               |   47 ++++++++++++++++++++++++-----------------------
 inst/doc/bimets.R       |   41 +++++++++++++++++++----------------------
 inst/doc/bimets.Rnw     |    7 ++-----
 inst/doc/bimets.pdf     |binary
 man/MDL.Rd              |    7 ++-----
 man/bimets-package.Rd   |    7 ++-----
 vignettes/bimets.Rnw    |    7 ++-----
 11 files changed, 70 insertions(+), 80 deletions(-)

More information about bimets at CRAN
Permanent link

Package tidyRSS updated to version 2.0.2 with previous version 2.0.1 dated 2020-03-07

Title: Tidy RSS for R
Description: With the objective of including data from RSS feeds into your analysis, 'tidyRSS' parses RSS, Atom and JSON feeds and returns a tidy data frame.
Author: Robert Myles McDonnell
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>

Diff between tidyRSS versions 2.0.1 dated 2020-03-07 and 2.0.2 dated 2020-06-01

 DESCRIPTION                   |   15 ++++----
 MD5                           |   25 +++++++-------
 NAMESPACE                     |    6 +++
 NEWS.md                       |    5 ++
 R/atom_parse.R                |   71 +++++++++++++++++++++++++-----------------
 R/clean_up.R                  |   22 ++++++++++---
 R/json_parse.R                |    4 +-
 R/rss_parse.R                 |   25 ++++++++++++--
 R/tidyfeed.R                  |    9 +++--
 R/utils.R                     |   40 +++++++++++++++--------
 R/zzz.R                       |    4 +-
 README.md                     |    2 +
 inst                          |only
 tests/testthat/test_general.R |   38 +++++++++++++++++++++-
 14 files changed, 190 insertions(+), 76 deletions(-)

More information about tidyRSS at CRAN
Permanent link

Package phytools updated to version 0.7-47 with previous version 0.7-20 dated 2020-03-19

Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>

Diff between phytools versions 0.7-20 dated 2020-03-19 and 0.7-47 dated 2020-06-01

 DESCRIPTION                  |   12 -
 MD5                          |  284 ++++++++++++++++++++++---------------------
 NAMESPACE                    |   88 ++++++++-----
 R/anc.Bayes.R                |   33 ++++
 R/anc.ML.R                   |    8 +
 R/ancThresh.R                |    8 -
 R/bmPlot.R                   |   17 +-
 R/branching.diffusion.R      |   18 +-
 R/collapseTree.R             |    3 
 R/contMap.R                  |    2 
 R/cospeciation.R             |    6 
 R/evol.vcv.R                 |    3 
 R/evolvcv.lite.R             |    4 
 R/fancyTree.R                |   14 +-
 R/fitMk.R                    |  131 ++++++++++++-------
 R/fitPagel.R                 |   52 +++++--
 R/fitmultiMk.R               |    6 
 R/fitpolyMk.R                |    6 
 R/ltt.R                      |   10 +
 R/make.simmap.R              |    8 -
 R/map.to.singleton.R         |    4 
 R/mcmcMk.R                   |  188 ++++++++++++++++++++++------
 R/phylo.heatmap.R            |    5 
 R/phylomorphospace.R         |    4 
 R/plotSimmap.R               |    3 
 R/sim.history.R              |   55 ++++++--
 R/threshBayes.R              |  225 ++++++++++++++++++++++++++--------
 R/utilities.R                |  120 +++++++++---------
 data/anole.data.rda          |only
 data/anoletree.rda           |binary
 data/datalist                |only
 data/mammal.data.rda         |only
 data/mammal.tree.rda         |only
 data/salamanders.rda         |only
 data/sunfish.data.rda        |only
 data/sunfish.tree.rda        |only
 data/wasp.data.rda           |only
 data/wasp.trees.rda          |only
 man/Dtest.Rd                 |    1 
 man/add.arrow.Rd             |   29 ++++
 man/add.color.bar.Rd         |    1 
 man/add.random.Rd            |    2 
 man/add.simmap.legend.Rd     |    2 
 man/aic.w.Rd                 |    3 
 man/allFurcTrees.Rd          |   11 +
 man/anc.Bayes.Rd             |   43 +++++-
 man/anc.ML.Rd                |   16 +-
 man/anc.trend.Rd             |   43 +++++-
 man/ancThresh.Rd             |   19 ++
 man/anoletree.Rd             |   46 ++++++
 man/as.Qmatrix.Rd            |only
 man/ave.rates.Rd             |    6 
 man/averageTree.Rd           |    1 
 man/bd.Rd                    |    2 
 man/bind.tip.Rd              |    9 -
 man/bmPlot.Rd                |   30 +++-
 man/branching.diffusion.Rd   |    8 -
 man/brownie.lite.Rd          |   21 ++-
 man/brownieREML.Rd           |    6 
 man/collapseTree.Rd          |    7 -
 man/consensus.edges.Rd       |    3 
 man/contMap.Rd               |   21 +++
 man/cophylo.Rd               |   18 +-
 man/cospeciation.Rd          |   19 ++
 man/countSimmap.Rd           |   11 -
 man/ctt.Rd                   |    5 
 man/density.multiSimmap.Rd   |    2 
 man/densityMap.Rd            |   19 ++
 man/describe.simmap.Rd       |    2 
 man/dotTree.Rd               |   13 +
 man/edgeProbs.Rd             |    2 
 man/estDiversity.Rd          |    2 
 man/evol.rate.mcmc.Rd        |    5 
 man/evol.vcv.Rd              |   11 +
 man/evolvcv.lite.Rd          |   11 +
 man/exhaustiveMP.Rd          |    2 
 man/expand.clade.Rd          |    1 
 man/fancyTree.Rd             |   22 ++-
 man/fastAnc.Rd               |   14 +-
 man/fastBM.Rd                |   11 +
 man/findMRCA.Rd              |   11 +
 man/fit.bd.Rd                |   35 ++++-
 man/fitBayes.Rd              |    1 
 man/fitDiversityModel.Rd     |    4 
 man/fitMk.Rd                 |   25 +++
 man/fitPagel.Rd              |    7 -
 man/genSeq.Rd                |   12 -
 man/get.treepos.Rd           |    1 
 man/getStates.Rd             |    1 
 man/lambda.transform.Rd      |    7 -
 man/likMlambda.Rd            |    1 
 man/locate.fossil.Rd         |    3 
 man/locate.yeti.Rd           |    3 
 man/ls.tree.Rd               |    3 
 man/ltt.Rd                   |   26 ++-
 man/ltt95.Rd                 |    2 
 man/make.era.map.Rd          |    1 
 man/make.simmap.Rd           |   26 +++
 man/map.overlap.Rd           |    2 
 man/map.to.singleton.Rd      |    1 
 man/markChanges.Rd           |    3 
 man/mergeMappedStates.Rd     |    2 
 man/midpoint.root.Rd         |    1 
 man/mrp.supertree.Rd         |    3 
 man/multi.mantel.Rd          |    1 
 man/multiRF.Rd               |    1 
 man/optim.phylo.ls.Rd        |    2 
 man/paintSubTree.Rd          |    1 
 man/pbtree.Rd                |    1 
 man/pgls.Ives.Rd             |    6 
 man/phenogram.Rd             |   26 +--
 man/phyl.RMA.Rd              |    4 
 man/phyl.cca.Rd              |    1 
 man/phyl.pairedttest.Rd      |    1 
 man/phyl.pca.Rd              |   11 +
 man/phylo.heatmap.Rd         |   20 ++-
 man/phylo.impute.Rd          |    1 
 man/phylo.to.map.Rd          |    2 
 man/phyloDesign.Rd           |    2 
 man/phylomorphospace.Rd      |   17 ++
 man/phylomorphospace3d.Rd    |   17 +-
 man/phylosig.Rd              |   34 ++++-
 man/phytools-package.Rd      |    8 -
 man/plotBranchbyTrait.Rd     |    2 
 man/plotSimmap.Rd            |   23 ++-
 man/plotThresh.Rd            |    2 
 man/plotTree.datamatrix.Rd   |    1 
 man/plotTree.wBars.Rd        |   17 ++
 man/posterior.evolrate.Rd    |    1 
 man/ratebystate.Rd           |    2 
 man/ratebytree.Rd            |    2 
 man/rateshift.Rd             |    2 
 man/read.simmap.Rd           |    1 
 man/reorder.backbonePhylo.Rd |    2 
 man/rerootingMethod.Rd       |    1 
 man/roundPhylogram.Rd        |    6 
 man/rstate.Rd                |    2 
 man/sampleFrom.Rd            |    1 
 man/sim.corrs.Rd             |    1 
 man/sim.history.Rd           |    7 -
 man/sim.ratebystate.Rd       |    1 
 man/sim.rates.Rd             |    5 
 man/simBMphylo.Rd            |    8 -
 man/skewers.Rd               |    1 
 man/threshBayes.Rd           |   12 +
 man/threshDIC.Rd             |    2 
 man/threshState.Rd           |    2 
 man/tree.grow.Rd             |    4 
 148 files changed, 1622 insertions(+), 640 deletions(-)

More information about phytools at CRAN
Permanent link

Package mpath updated to version 0.3-26 with previous version 0.3-25 dated 2020-04-22

Title: Regularized Linear Models
Description: Algorithms optimize penalized models. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson, zero-inflated negative binomial regression models and robust models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD), minimax concave penalty (MCP), and each possibly combining with L_2 penalty. See Wang et al. (2014) <doi:10.1002/sim.6314>, Wang et al. (2015) <doi:10.1002/bimj.201400143>, Wang et al. (2016) <doi:10.1177/0962280214530608>, Wang (2019) <arXiv:1912.11119>.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <wangz1@uthscsa.edu>

Diff between mpath versions 0.3-25 dated 2020-04-22 and 0.3-26 dated 2020-06-01

 DESCRIPTION           |    8 ++++----
 MD5                   |   12 ++++++------
 NAMESPACE             |    2 --
 build/vignette.rds    |binary
 inst/doc/brcancer.pdf |binary
 inst/doc/german.pdf   |binary
 inst/doc/kkt.pdf      |binary
 7 files changed, 10 insertions(+), 12 deletions(-)

More information about mpath at CRAN
Permanent link

Package malariaAtlas updated to version 1.0.1 with previous version 1.0.0 dated 2020-02-24

Title: An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'
Description: A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.
Author: Daniel Pfeffer [aut] (<https://orcid.org/0000-0002-2204-3488>), Tim Lucas [aut, cre] (<https://orcid.org/0000-0003-4694-8107>), Daniel May [aut] (<https://orcid.org/0000-0003-0005-2452>), Suzanne Keddie [aut] (<https://orcid.org/0000-0003-1254-7794>), Jen Rozier [aut] (<https://orcid.org/0000-0002-2610-7557>), Oliver Watson [aut] (<https://orcid.org/0000-0003-2374-0741>), Harry Gibson [aut] (<https://orcid.org/0000-0001-6779-3250>), Nick Golding [ctb], David Smith [ctb]
Maintainer: Tim Lucas <timcdlucas@gmail.com>

Diff between malariaAtlas versions 1.0.0 dated 2020-02-24 and 1.0.1 dated 2020-06-01

 DESCRIPTION                     |    8 +-
 MD5                             |   48 ++++++------
 R/listShp.R                     |    7 +
 build/vignette.rds              |binary
 inst/doc/overview.html          |  158 ++++++++++++++++++++--------------------
 man/autoplot.MAPraster.Rd       |   16 ++--
 man/autoplot.MAPshp.Rd          |    3 
 man/autoplot.pr.points.Rd       |   18 +++-
 man/autoplot.vector.points.Rd   |   15 ++-
 man/autoplot_MAPraster.Rd       |    2 
 man/convertPrevalence.Rd        |   13 ++-
 man/extractRaster.Rd            |    8 +-
 man/fillDHSCoordinates.Rd       |   20 +++--
 man/getPR.Rd                    |    3 
 man/getRaster.Rd                |   11 ++
 man/getShp.Rd                   |   12 ++-
 man/getVecOcc.Rd                |    9 +-
 man/isAvailable.Rd              |    9 +-
 man/isAvailable_pr.Rd           |    9 +-
 man/isAvailable_vec.Rd          |    9 +-
 man/malariaAtlas.Rd             |    1 
 tests/testthat/test_as.class.R  |    2 
 tests/testthat/test_getPR.R     |   13 +--
 tests/testthat/test_getVecOcc.R |    8 +-
 tests/testthat/test_listData.R  |   12 +--
 25 files changed, 243 insertions(+), 171 deletions(-)

More information about malariaAtlas at CRAN
Permanent link

Package FKF updated to version 0.1.6 with previous version 0.1.5 dated 2018-07-20

Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman filter, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in BLAS and LAPACK. Due to the speed of the filter, the fitting of high-dimensional linear state space models to large datasets becomes possible. This package also contains a plot function for the visualization of the state vector and graphical diagnostics of the residuals.
Author: David Luethi [aut], Philipp Erb [aut], Simon Otziger [aut], Paul Smith [cre] (<https://orcid.org/0000-0002-0034-3412>)
Maintainer: Paul Smith <paul@waternumbers.co.uk>

Diff between FKF versions 0.1.5 dated 2018-07-20 and 0.1.6 dated 2020-06-01

 DESCRIPTION     |   38 ++++++++++++++++++++++++++------------
 MD5             |   18 ++++++++++++------
 NAMESPACE       |    1 -
 R/FKF-package.R |    2 +-
 R/fkf.R         |   10 +++++-----
 README.md       |only
 build           |only
 inst/doc        |only
 man/fkf.Rd      |    8 ++++----
 man/plot.fkf.Rd |   10 ++++++++--
 vignettes       |only
 11 files changed, 56 insertions(+), 31 deletions(-)

More information about FKF at CRAN
Permanent link

Package rstantools updated to version 2.1.0 with previous version 2.0.0 dated 2019-09-14

Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing with 'Stan' <https://mc-stan.org>, including functions to set up the required package structure, S3 generics and default methods to unify function naming across 'Stan'-based R packages, and vignettes with recommendations for developers.
Author: Jonah Gabry [aut, cre], Ben Goodrich [aut], Martin Lysy [aut], Stefan Siegert [ctb], Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>

Diff between rstantools versions 2.0.0 dated 2019-09-14 and 2.1.0 dated 2020-06-01

 DESCRIPTION                         |   12 -
 MD5                                 |   40 ++---
 NAMESPACE                           |    1 
 NEWS.md                             |   17 ++
 R/posterior_epred.R                 |only
 R/rstan_create_package.R            |   17 +-
 R/use_rstan.R                       |    2 
 inst/doc/developer-guidelines.html  |   28 ++-
 inst/doc/minimal-rstan-package.R    |   48 +++---
 inst/doc/minimal-rstan-package.Rmd  |    3 
 inst/doc/minimal-rstan-package.html |  282 ++++++++++++++++++++----------------
 inst/include/sys/DESCRIPTION        |    4 
 inst/include/sys/Makevars           |   10 -
 inst/include/sys/Makevars.win       |   11 -
 man/init_cpp.Rd                     |   10 -
 man/posterior_epred.Rd              |only
 man/posterior_interval.Rd           |    6 
 man/predictive_interval.Rd          |    6 
 man/rstan_config.Rd                 |    2 
 man/rstan_create_package.Rd         |   33 ++--
 man/use_rstan.Rd                    |    2 
 vignettes/minimal-rstan-package.Rmd |    3 
 22 files changed, 301 insertions(+), 236 deletions(-)

More information about rstantools at CRAN
Permanent link

Package mrbin updated to version 1.4.2 with previous version 1.4.1 dated 2020-05-20

Title: Magnetic Resonance Binning, Integration and Normalization
Description: Nuclear Magnetic Resonance is widely used in Life Science research. The package (<http://www.kleinomicslab.com/software>) converts 1D or 2D data into a matrix of values suitable for further data analysis and performs basic processing steps in a reproducible way. Negative values, a common issue in such data, are replaced by positive values. All used parameters are stored in a readable text file and can be restored from that file to enable exact reproduction of the data at a later time.
Author: Matthias Klein [aut, cre] (<https://orcid.org/0000-0001-7455-5381>)
Maintainer: Matthias Klein <klein.663@osu.edu>

Diff between mrbin versions 1.4.1 dated 2020-05-20 and 1.4.2 dated 2020-06-01

 DESCRIPTION         |    6 -
 MD5                 |   12 +-
 NEWS.md             |    9 ++
 R/mrbin.R           |  224 +++++++++++++++++++++++++++++++---------------------
 inst/doc/mrbin.Rnw  |    4 
 inst/doc/mrbin.pdf  |binary
 vignettes/mrbin.Rnw |    4 
 7 files changed, 160 insertions(+), 99 deletions(-)

More information about mrbin at CRAN
Permanent link

Package Umpire updated to version 2.0.3 with previous version 2.0.1 dated 2020-04-27

Title: Simulating Realistic Gene Expression and Clinical Data
Description: The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with links to associated outcomes. See Zhang and Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the ability to simulate realistic mixed-typed clinical data.
Author: Kevin R. Coombes, Jiexin Zhang, Caitlin E. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>

Diff between Umpire versions 2.0.1 dated 2020-04-27 and 2.0.3 dated 2020-06-01

 DESCRIPTION                     |    8 
 MD5                             |   28 +-
 R/e07-2-cancerModel.R           |    8 
 R/e11-clinical.R                |    2 
 build/vignette.rds              |binary
 inst/doc/Umpire.pdf             |binary
 inst/doc/Umpire2.R              |    3 
 inst/doc/Umpire2.Rmd            |    5 
 inst/doc/Umpire2.html           |  406 +++++++++++++++++++---------------------
 inst/doc/surv.R                 |only
 inst/doc/surv.Rmd               |only
 inst/doc/surv.html              |only
 man/e13-CancerModel-class.Rd    |    6 
 tests/t07-cancerModel.Rout.save |  148 +++++++-------
 tests/t22-survModel.R           |   30 ++
 vignettes/Umpire2.Rmd           |    5 
 vignettes/surv.Rmd              |only
 17 files changed, 341 insertions(+), 308 deletions(-)

More information about Umpire at CRAN
Permanent link

Package tadaatoolbox updated to version 0.17.0 with previous version 0.16.1 dated 2018-11-23

Title: Helpers for Data Analysis and Presentation Focused on Undergrad Psychology
Description: A teaching project for the display of statistical tests as well as some convenience functions for data cleanup. The primary components are the functions prefixed with 'tadaa_', which are built to work in an interactive environment, but also print markdown tables powered by 'pixiedust' for the creation of 'RMarkdown' reports. This package is no longer actively developed.
Author: Lukas Burk [aut, cre] (<https://orcid.org/0000-0001-7528-3795>), Tobias Anton [aut], Daniel Lüdecke [ctb], Gesa Graf [ctb]
Maintainer: Lukas Burk <lukas@tadaa-data.de>

Diff between tadaatoolbox versions 0.16.1 dated 2018-11-23 and 0.17.0 dated 2020-06-01

 tadaatoolbox-0.16.1/tadaatoolbox/R/tadaa_pairwise_games_howell.R      |only
 tadaatoolbox-0.16.1/tadaatoolbox/man/games_howell.Rd                  |only
 tadaatoolbox-0.16.1/tadaatoolbox/man/tadaa_normtest.Rd                |only
 tadaatoolbox-0.16.1/tadaatoolbox/man/tadaa_pairwise_gh.Rd             |only
 tadaatoolbox-0.17.0/tadaatoolbox/DESCRIPTION                          |   51 -
 tadaatoolbox-0.17.0/tadaatoolbox/MD5                                  |  115 +--
 tadaatoolbox-0.17.0/tadaatoolbox/NAMESPACE                            |    9 
 tadaatoolbox-0.17.0/tadaatoolbox/NEWS.md                              |   21 
 tadaatoolbox-0.17.0/tadaatoolbox/R/cleanup_helpers.R                  |   32 
 tadaatoolbox-0.17.0/tadaatoolbox/R/ggplot2_themes.R                   |    5 
 tadaatoolbox-0.17.0/tadaatoolbox/R/invert_scales.R                    |    1 
 tadaatoolbox-0.17.0/tadaatoolbox/R/misc_stats.R                       |    2 
 tadaatoolbox-0.17.0/tadaatoolbox/R/nom_stats.R                        |    6 
 tadaatoolbox-0.17.0/tadaatoolbox/R/ord_stats.R                        |    6 
 tadaatoolbox-0.17.0/tadaatoolbox/R/recode_helpers.R                   |    6 
 tadaatoolbox-0.17.0/tadaatoolbox/R/tadaa_assumptions.R                |   72 -
 tadaatoolbox-0.17.0/tadaatoolbox/R/tadaa_omnibus.R                    |   29 
 tadaatoolbox-0.17.0/tadaatoolbox/R/tadaa_one_sample.R                 |   19 
 tadaatoolbox-0.17.0/tadaatoolbox/R/tadaa_pairwise_t.R                 |    9 
 tadaatoolbox-0.17.0/tadaatoolbox/R/tadaa_pairwise_tukey.R             |   14 
 tadaatoolbox-0.17.0/tadaatoolbox/R/tadaa_plots.R                      |   38 -
 tadaatoolbox-0.17.0/tadaatoolbox/R/tadaa_two_sample.R                 |  164 +++-
 tadaatoolbox-0.17.0/tadaatoolbox/R/z_test.R                           |only
 tadaatoolbox-0.17.0/tadaatoolbox/README.md                            |  142 +--
 tadaatoolbox-0.17.0/tadaatoolbox/build/vignette.rds                   |binary
 tadaatoolbox-0.17.0/tadaatoolbox/inst/doc/overview.R                  |   29 
 tadaatoolbox-0.17.0/tadaatoolbox/inst/doc/overview.Rmd                |   28 
 tadaatoolbox-0.17.0/tadaatoolbox/inst/doc/overview.html               |  256 +++----
 tadaatoolbox-0.17.0/tadaatoolbox/inst/doc/test_output.R               |   24 
 tadaatoolbox-0.17.0/tadaatoolbox/inst/doc/test_output.html            |  361 ++++------
 tadaatoolbox-0.17.0/tadaatoolbox/man/delete_na.Rd                     |   21 
 tadaatoolbox-0.17.0/tadaatoolbox/man/effect_size_t.Rd                 |   10 
 tadaatoolbox-0.17.0/tadaatoolbox/man/generate_recodes.Rd              |    4 
 tadaatoolbox-0.17.0/tadaatoolbox/man/interval_labels.Rd               |    6 
 tadaatoolbox-0.17.0/tadaatoolbox/man/ngo.Rd                           |    4 
 tadaatoolbox-0.17.0/tadaatoolbox/man/ord_gamma.Rd                     |    6 
 tadaatoolbox-0.17.0/tadaatoolbox/man/pval_string.Rd                   |    5 
 tadaatoolbox-0.17.0/tadaatoolbox/man/reexports.Rd                     |    2 
 tadaatoolbox-0.17.0/tadaatoolbox/man/sidak_sd.Rd                      |    4 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_aov.Rd                     |   44 -
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_balance.Rd                 |    7 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_chisq.Rd                   |   28 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_int.Rd                     |   23 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_kruskal.Rd                 |   26 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_levene.Rd                  |   27 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_mean_ci.Rd                 |    6 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_nom.Rd                     |   19 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_one_sample.Rd              |   32 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_ord.Rd                     |   20 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_pairwise_t.Rd              |   36 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_pairwise_tukey.Rd          |   24 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_plot_tukey.Rd              |    8 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_t.test.Rd                  |   46 -
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_wilcoxon.Rd                |   31 
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaa_z.test.Rd                  |only
 tadaatoolbox-0.17.0/tadaatoolbox/man/tadaatoolbox-package.Rd          |   16 
 tadaatoolbox-0.17.0/tadaatoolbox/man/theme_readthedown.Rd             |   29 
 tadaatoolbox-0.17.0/tadaatoolbox/man/z.Rd                             |    2 
 tadaatoolbox-0.17.0/tadaatoolbox/man/z.test.Rd                        |only
 tadaatoolbox-0.17.0/tadaatoolbox/tests/testthat/test-assumptions.R    |    5 
 tadaatoolbox-0.17.0/tadaatoolbox/tests/testthat/test-pairwise_tests.R |   15 
 tadaatoolbox-0.17.0/tadaatoolbox/vignettes/overview.Rmd               |   28 
 62 files changed, 986 insertions(+), 987 deletions(-)

More information about tadaatoolbox at CRAN
Permanent link

Package smoothSurv updated to version 2.3 with previous version 2.2 dated 2020-05-18

Title: Survival Regression with Smoothed Error Distribution
Description: Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled C++ written using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between smoothSurv versions 2.2 dated 2020-05-18 and 2.3 dated 2020-06-01

 DESCRIPTION        |    8 ++++----
 MD5                |    8 ++++----
 NAMESPACE          |    2 +-
 NEWS               |    6 ++++++
 src/Scythe_Error.h |    4 +++-
 5 files changed, 18 insertions(+), 10 deletions(-)

More information about smoothSurv at CRAN
Permanent link

Package DecomposeR updated to version 1.0.2 with previous version 1.0.1 dated 2020-04-01

Title: Empirical Mode Decomposition for Cyclostratigraphy
Description: Tools to apply Ensemble Empirical Mode Decomposition (EEMD) for cyclostratigraphy purposes. Mainly: a new algorithm, extricate, that performs EEMD in seconds, a linear interpolation algorithm using the greatest rational common divisor of depth or time, different algorithms to compute instantaneous amplitude, frequency and ratios of frequencies, and functions to verify and visualise the outputs. The functions were developed during the CRASH project (Checking the Reproducibility of Astrochronology in the Hauterivian). When using for publication please cite Wouters, S., Da Silva, A.C. Crucifix, M., Sinnesael, M., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2019, "Litholog generation with the 'StratigrapheR' package and signal decomposition for cyclostratigraphic purposes". Geophysical Research Abstracts Vol. 21, EGU2019-5520, 2019, EGU General Assembly 2019. <http://hdl.handle.net/2268/234402>.
Author: Sebastien Wouters [aut, cre]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>

Diff between DecomposeR versions 1.0.1 dated 2020-04-01 and 1.0.2 dated 2020-06-01

 DESCRIPTION       |   10 +++++-----
 MD5               |   18 +++++++++---------
 NAMESPACE         |    4 +---
 NEWS              |    5 +++++
 R/DecomposeR.R    |    3 ++-
 R/gzc.algorithm.R |   31 +++++++++++++++----------------
 R/is.simp.emd.R   |    5 ++---
 R/parsimony.R     |    1 -
 man/DecomposeR.Rd |    2 +-
 man/ratios.Rd     |   40 ++++++++++++++++++++--------------------
 10 files changed, 60 insertions(+), 59 deletions(-)

More information about DecomposeR at CRAN
Permanent link

Package PKNCA updated to version 0.9.4 with previous version 0.9.3 dated 2020-04-12

Title: Perform Pharmacokinetic Non-Compartmental Analysis
Description: Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.
Author: Bill Denney [aut, cre] (<https://orcid.org/0000-0002-5759-428X>), Clare Buckeridge [aut], Sridhar Duvvuri [ctb]
Maintainer: Bill Denney <wdenney@humanpredictions.com>

Diff between PKNCA versions 0.9.3 dated 2020-04-12 and 0.9.4 dated 2020-06-01

 DESCRIPTION                                 |    8 
 MD5                                         |  236 +++++++++---------
 NEWS.md                                     |   10 
 R/001-add.interval.col.R                    |    2 
 R/check.intervals.R                         |    6 
 R/class-general.R                           |   24 -
 R/exclude.R                                 |    2 
 R/pk.calc.all.R                             |    2 
 R/pk.calc.simple.R                          |    2 
 R/superposition.R                           |    2 
 R/tss.stepwise.linear.R                     |    2 
 README.md                                   |    2 
 inst/doc/AUC-Calculation-with-PKNCA.R       |   22 -
 inst/doc/AUC-Calculation-with-PKNCA.Rmd     |   24 -
 inst/doc/AUC-Calculation-with-PKNCA.html    |   32 +-
 inst/doc/Example-theophylline.html          |    2 
 inst/doc/Introduction-and-Usage.R           |    2 
 inst/doc/Introduction-and-Usage.Rmd         |    8 
 inst/doc/Introduction-and-Usage.html        |    8 
 inst/doc/Options-for-Controlling-PKNCA.html |    2 
 inst/doc/PKNCA-validation.html              |   23 -
 inst/doc/Writing-Parameter-Functions.Rmd    |    2 
 inst/doc/Writing-Parameter-Functions.html   |    2 
 man/AIC.list.Rd                             |   58 ++--
 man/PKNCA.Rd                                |   76 +++---
 man/PKNCA.choose.option.Rd                  |   62 ++--
 man/PKNCA.options.Rd                        |  128 +++++-----
 man/PKNCA.set.summary.Rd                    |  132 +++++-----
 man/PKNCAconc.Rd                            |  170 ++++++-------
 man/PKNCAdata.Rd                            |  150 +++++------
 man/PKNCAdose.Rd                            |  164 ++++++------
 man/PKNCAresults.Rd                         |   68 ++---
 man/add.interval.col.Rd                     |  206 ++++++++--------
 man/addProvenance.Rd                        |   52 ++--
 man/as.data.frame.PKNCAresults.Rd           |   48 +--
 man/business.mean.Rd                        |  138 +++++-----
 man/check.conc.time.Rd                      |   74 ++---
 man/check.conversion.Rd                     |   46 +--
 man/check.interval.deps.Rd                  |   62 ++--
 man/check.interval.specification.Rd         |   76 +++---
 man/checkProvenance.Rd                      |   44 +--
 man/choose.auc.intervals.Rd                 |  120 ++++-----
 man/clean.conc.blq.Rd                       |  150 +++++------
 man/clean.conc.na.Rd                        |   74 ++---
 man/exclude.Rd                              |  124 ++++-----
 man/exclude_nca.Rd                          |  118 ++++-----
 man/find.tau.Rd                             |   84 +++---
 man/findOperator.Rd                         |   66 ++---
 man/fit_half_life.Rd                        |   60 ++--
 man/formula.PKNCAconc.Rd                    |   44 +--
 man/formula.parseFormula.Rd                 |   62 ++--
 man/geomean.Rd                              |   86 +++---
 man/get.best.model.Rd                       |   46 +--
 man/get.first.model.Rd                      |   38 +--
 man/get.interval.cols.Rd                    |   60 ++--
 man/get.parameter.deps.Rd                   |   56 ++--
 man/getAttributeColumn.Rd                   |   48 +--
 man/getColumnValueOrNot.Rd                  |   62 ++--
 man/getDataName.Rd                          |   94 +++----
 man/getDepVar.Rd                            |   54 ++--
 man/getGroups.PKNCAconc.Rd                  |   96 +++----
 man/getIndepVar.Rd                          |   54 ++--
 man/interp.extrap.conc.Rd                   |  354 ++++++++++++++--------------
 man/merge.splitlist.Rd                      |   58 ++--
 man/model.frame.PKNCAconc.Rd                |   52 ++--
 man/parseFormula.Rd                         |  102 ++++----
 man/pk.business.Rd                          |   74 ++---
 man/pk.calc.ae.Rd                           |   60 ++--
 man/pk.calc.aucint.Rd                       |  296 +++++++++++------------
 man/pk.calc.aucpext.Rd                      |   52 ++--
 man/pk.calc.auxc.Rd                         |  352 +++++++++++++--------------
 man/pk.calc.c0.Rd                           |  152 ++++++------
 man/pk.calc.cav.Rd                          |   48 +--
 man/pk.calc.ceoi.Rd                         |   50 +--
 man/pk.calc.cl.Rd                           |   68 ++---
 man/pk.calc.clast.obs.Rd                    |   46 +--
 man/pk.calc.clr.Rd                          |   58 ++--
 man/pk.calc.cmax.Rd                         |   58 ++--
 man/pk.calc.ctrough.Rd                      |   44 +--
 man/pk.calc.deg.fluc.Rd                     |   48 +--
 man/pk.calc.f.Rd                            |   50 +--
 man/pk.calc.fe.Rd                           |   56 ++--
 man/pk.calc.half.life.Rd                    |  222 ++++++++---------
 man/pk.calc.mrt.Rd                          |   78 +++---
 man/pk.calc.mrt.md.Rd                       |   72 ++---
 man/pk.calc.swing.Rd                        |   46 +--
 man/pk.calc.tlag.Rd                         |   46 +--
 man/pk.calc.tlast.Rd                        |   62 ++--
 man/pk.calc.tmax.Rd                         |   74 ++---
 man/pk.calc.vd.Rd                           |   70 ++---
 man/pk.nca.Rd                               |   70 ++---
 man/pk.nca.interval.Rd                      |  174 ++++++-------
 man/pk.tss.Rd                               |   60 ++--
 man/pk.tss.data.prep.Rd                     |  112 ++++----
 man/pk.tss.monoexponential.Rd               |  114 ++++-----
 man/pk.tss.monoexponential.individual.Rd    |   78 +++---
 man/pk.tss.monoexponential.population.Rd    |   82 +++---
 man/pk.tss.stepwise.linear.Rd               |  112 ++++----
 man/print.PKNCAconc.Rd                      |   66 ++---
 man/print.summary_PKNCAresults.Rd           |   46 +--
 man/roundString.Rd                          |   74 ++---
 man/roundingSummarize.Rd                    |   44 +--
 man/setAttributeColumn.Rd                   |   98 +++----
 man/setDuration.Rd                          |   58 ++--
 man/setExcludeColumn.Rd                     |   46 +--
 man/setRoute.Rd                             |   56 ++--
 man/signifString.Rd                         |   94 +++----
 man/split.PKNCAconc.Rd                      |   76 +++---
 man/summary.PKNCAdata.Rd                    |   36 +-
 man/summary.PKNCAresults.Rd                 |  140 +++++------
 man/superposition.Rd                        |  204 ++++++++--------
 man/time_calc.Rd                            |   64 ++---
 man/tss.monoexponential.generate.formula.Rd |   38 +--
 tests/testthat/test-class-PKNCAconc.R       |    2 
 tests/testthat/test-class-PKNCAdata.R       |    2 
 tests/testthat/test-class-PKNCAdose.R       |    2 
 vignettes/AUC-Calculation-with-PKNCA.Rmd    |   24 -
 vignettes/Introduction-and-Usage.Rmd        |    8 
 vignettes/Writing-Parameter-Functions.Rmd   |    2 
 119 files changed, 4253 insertions(+), 4252 deletions(-)

More information about PKNCA at CRAN
Permanent link

Package clean updated to version 2.0.0 with previous version 1.1.0 dated 2019-08-20

Title: Fast and Easy Data Cleaning
Description: A wrapper around the new 'cleaner' package, that allows data cleaning functions for classes 'logical', 'factor', 'numeric', 'character', 'currency' and 'Date' to make data cleaning fast and easy. Relying on very few dependencies, it provides smart guessing, but with user options to override anything if needed.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

Diff between clean versions 1.1.0 dated 2019-08-20 and 2.0.0 dated 2020-06-01

 clean-1.1.0/clean/R/clean.R            |only
 clean-1.1.0/clean/R/currency.R         |only
 clean-1.1.0/clean/R/data.R             |only
 clean-1.1.0/clean/R/format_datetime.R  |only
 clean-1.1.0/clean/R/freq.R             |only
 clean-1.1.0/clean/R/helpers.R          |only
 clean-1.1.0/clean/R/regex_true_false.R |only
 clean-1.1.0/clean/data                 |only
 clean-1.1.0/clean/man                  |only
 clean-1.1.0/clean/tests                |only
 clean-2.0.0/clean/DESCRIPTION          |   28 +-
 clean-2.0.0/clean/MD5                  |   27 --
 clean-2.0.0/clean/NAMESPACE            |  105 ----------
 clean-2.0.0/clean/NEWS.md              |   11 -
 clean-2.0.0/clean/R/import.R           |only
 clean-2.0.0/clean/README.md            |  321 ---------------------------------
 16 files changed, 29 insertions(+), 463 deletions(-)

More information about clean at CRAN
Permanent link

Package sergeant updated to version 0.9.0 with previous version 0.5.2 dated 2017-07-17

Title: Tools to Transform and Query Data with Apache Drill
Description: Apache Drill is a low-latency distributed query engine designed to enable data exploration and analysis on both relational and non-relational data stores, scaling to petabytes of data. Methods are provided that enable working with Apache Drill instances via the REST API, DBI methods and using 'dplyr'/'dbplyr' idioms. Helper functions are included to facilitate using official Drill Docker images/containers.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>), Edward Visel [ctb], Andy Hine [ctb], Scott Came [ctb], David Severski [ctb] (<https://orcid.org/0000-0001-7867-0459>), James Lamb [ctb]
Maintainer: Bob Rudis <bob@rud.is>

Diff between sergeant versions 0.5.2 dated 2017-07-17 and 0.9.0 dated 2020-06-01

 sergeant-0.5.2/sergeant/R/jdbc.r                                   |only
 sergeant-0.5.2/sergeant/R/sergeant.r                               |only
 sergeant-0.5.2/sergeant/inst/java                                  |only
 sergeant-0.5.2/sergeant/man/drill_jdbc.Rd                          |only
 sergeant-0.5.2/sergeant/tests/testthat                             |only
 sergeant-0.5.2/sergeant/tests/testthat.R                           |only
 sergeant-0.9.0/sergeant/DESCRIPTION                                |   58 
 sergeant-0.9.0/sergeant/LICENSE                                    |    2 
 sergeant-0.9.0/sergeant/MD5                                        |  115 -
 sergeant-0.9.0/sergeant/NAMESPACE                                  |   27 
 sergeant-0.9.0/sergeant/NEWS.md                                    |   42 
 sergeant-0.9.0/sergeant/R/ctas-profile.R                           |only
 sergeant-0.9.0/sergeant/R/custom.r                                 |    2 
 sergeant-0.9.0/sergeant/R/dbi.r                                    |  338 ++++
 sergeant-0.9.0/sergeant/R/dplyr.r                                  |  171 +-
 sergeant-0.9.0/sergeant/R/drill-docker.R                           |only
 sergeant-0.9.0/sergeant/R/query.r                                  |  182 ++
 sergeant-0.9.0/sergeant/R/rest-api.r                               |only
 sergeant-0.9.0/sergeant/R/schemas.R                                |   30 
 sergeant-0.9.0/sergeant/R/sergeant-package.r                       |   25 
 sergeant-0.9.0/sergeant/R/set.R                                    |   19 
 sergeant-0.9.0/sergeant/R/utils.r                                  |   29 
 sergeant-0.9.0/sergeant/R/zzz.R                                    |    5 
 sergeant-0.9.0/sergeant/README.md                                  |  718 ++++------
 sergeant-0.9.0/sergeant/inst/tinytest                              |only
 sergeant-0.9.0/sergeant/man/DrilDriver-class.Rd                    |   10 
 sergeant-0.9.0/sergeant/man/Drill.Rd                               |   30 
 sergeant-0.9.0/sergeant/man/DrillConnection-class.Rd               |   23 
 sergeant-0.9.0/sergeant/man/DrillDriver-class.Rd                   |    9 
 sergeant-0.9.0/sergeant/man/DrillResult-class.Rd                   |   37 
 sergeant-0.9.0/sergeant/man/ctas_profile.Rd                        |only
 sergeant-0.9.0/sergeant/man/dbDataType-DrillConnection-method.Rd   |   10 
 sergeant-0.9.0/sergeant/man/dbDisconnect-DrillConnection-method.Rd |    1 
 sergeant-0.9.0/sergeant/man/dbGetInfo.Rd                           |only
 sergeant-0.9.0/sergeant/man/drill_active.Rd                        |   25 
 sergeant-0.9.0/sergeant/man/drill_cancel.Rd                        |   23 
 sergeant-0.9.0/sergeant/man/drill_connection.Rd                    |   40 
 sergeant-0.9.0/sergeant/man/drill_custom_functions.Rd              |   23 
 sergeant-0.9.0/sergeant/man/drill_functions.Rd                     |only
 sergeant-0.9.0/sergeant/man/drill_metrics.Rd                       |   23 
 sergeant-0.9.0/sergeant/man/drill_options.Rd                       |   23 
 sergeant-0.9.0/sergeant/man/drill_opts.Rd                          |only
 sergeant-0.9.0/sergeant/man/drill_profile.Rd                       |   23 
 sergeant-0.9.0/sergeant/man/drill_profiles.Rd                      |   23 
 sergeant-0.9.0/sergeant/man/drill_query.Rd                         |   29 
 sergeant-0.9.0/sergeant/man/drill_set.Rd                           |   23 
 sergeant-0.9.0/sergeant/man/drill_settings_reset.Rd                |   21 
 sergeant-0.9.0/sergeant/man/drill_show_files.Rd                    |   15 
 sergeant-0.9.0/sergeant/man/drill_show_schemas.Rd                  |   11 
 sergeant-0.9.0/sergeant/man/drill_stats.Rd                         |   23 
 sergeant-0.9.0/sergeant/man/drill_status.Rd                        |   23 
 sergeant-0.9.0/sergeant/man/drill_storage.Rd                       |   68 
 sergeant-0.9.0/sergeant/man/drill_system_reset.Rd                  |   21 
 sergeant-0.9.0/sergeant/man/drill_threads.Rd                       |   23 
 sergeant-0.9.0/sergeant/man/drill_up.Rd                            |only
 sergeant-0.9.0/sergeant/man/drill_uplift.Rd                        |    8 
 sergeant-0.9.0/sergeant/man/drill_use.Rd                           |   11 
 sergeant-0.9.0/sergeant/man/drill_version.Rd                       |   23 
 sergeant-0.9.0/sergeant/man/format.DrillConnection.Rd              |only
 sergeant-0.9.0/sergeant/man/killall_drill.Rd                       |only
 sergeant-0.9.0/sergeant/man/print.drill_conn.Rd                    |only
 sergeant-0.9.0/sergeant/man/sergeant-exports.Rd                    |    1 
 sergeant-0.9.0/sergeant/man/sergeant.Rd                            |   17 
 sergeant-0.9.0/sergeant/man/showall_drill.Rd                       |only
 sergeant-0.9.0/sergeant/man/src_drill.Rd                           |   27 
 sergeant-0.9.0/sergeant/man/src_tbls.Rd                            |   10 
 sergeant-0.9.0/sergeant/tests/tinytest.R                           |only
 67 files changed, 1739 insertions(+), 701 deletions(-)

More information about sergeant at CRAN
Permanent link

Package haven updated to version 2.3.1 with previous version 2.3.0 dated 2020-05-24

Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between haven versions 2.3.0 dated 2020-05-24 and 2.3.1 dated 2020-06-01

 DESCRIPTION                    |    6 +--
 MD5                            |   16 +++++-----
 NAMESPACE                      |    9 +++++
 NEWS.md                        |    7 ++++
 R/labelled.R                   |   40 +++++++++++++++++++++++++-
 inst/doc/datetimes.html        |   13 --------
 inst/doc/semantics.html        |   62 ++++++++++++++++-------------------------
 src/readstat/readstat_iconv.h  |    2 -
 tests/testthat/test-labelled.R |   54 +++++++++++++++++++++++++++++++++++
 9 files changed, 145 insertions(+), 64 deletions(-)

More information about haven at CRAN
Permanent link

Package hexSticker updated to version 0.4.7 with previous version 0.4.6 dated 2019-05-20

Title: Create Hexagon Sticker in R
Description: Helper functions for creating reproducible hexagon sticker purely in R.
Author: Guangchuang Yu [aut, cre], Laurent Gatto [ctb], Johannes Rainer [ctb], Sebastian Gibb [ctb], Robert Corty [ctb], Thomas Neitmann [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between hexSticker versions 0.4.6 dated 2019-05-20 and 0.4.7 dated 2020-06-01

 hexSticker-0.4.6/hexSticker/README.md                               |only
 hexSticker-0.4.7/hexSticker/DESCRIPTION                             |   26 
 hexSticker-0.4.7/hexSticker/MD5                                     |   39 
 hexSticker-0.4.7/hexSticker/NAMESPACE                               |   71 -
 hexSticker-0.4.7/hexSticker/NEWS.md                                 |  112 -
 hexSticker-0.4.7/hexSticker/R/as-raster.R                           |only
 hexSticker-0.4.7/hexSticker/R/sticker.R                             |  695 +++++-----
 hexSticker-0.4.7/hexSticker/inst/figures/baseplot.png               |binary
 hexSticker-0.4.7/hexSticker/inst/figures/cat.png                    |only
 hexSticker-0.4.7/hexSticker/inst/figures/ggplot2-google-font.png    |binary
 hexSticker-0.4.7/hexSticker/inst/figures/ggplot2.png                |binary
 hexSticker-0.4.7/hexSticker/inst/figures/imgfile.png                |binary
 hexSticker-0.4.7/hexSticker/inst/figures/lattice.png                |binary
 hexSticker-0.4.7/hexSticker/inst/fonts/Aller/Aller_Font_License.txt |  182 +-
 hexSticker-0.4.7/hexSticker/man/geom_hexagon.Rd                     |   48 
 hexSticker-0.4.7/hexSticker/man/geom_pkgname.Rd                     |   73 -
 hexSticker-0.4.7/hexSticker/man/geom_url.Rd                         |   84 -
 hexSticker-0.4.7/hexSticker/man/reexports.Rd                        |   40 
 hexSticker-0.4.7/hexSticker/man/save_sticker.Rd                     |   42 
 hexSticker-0.4.7/hexSticker/man/sticker.Rd                          |  226 +--
 hexSticker-0.4.7/hexSticker/man/sticker_dev.Rd                      |   34 
 hexSticker-0.4.7/hexSticker/man/theme_sticker.Rd                    |   44 
 22 files changed, 897 insertions(+), 819 deletions(-)

More information about hexSticker at CRAN
Permanent link

Package cleaner updated to version 1.5.0 with previous version 1.4.0 dated 2020-04-01

Title: Fast and Easy Data Cleaning
Description: Data cleaning functions for classes logical, factor, numeric, character, currency and Date to make data cleaning fast and easy. Relying on very few dependencies, it provides smart guessing, but with user options to override anything if needed.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

Diff between cleaner versions 1.4.0 dated 2020-04-01 and 1.5.0 dated 2020-06-01

 DESCRIPTION         |    8 +++---
 MD5                 |   20 +++++++++-------
 NAMESPACE           |   63 +++++++++-------------------------------------------
 NEWS.md             |   30 ++++++++++++++++++++++++
 R/clean.R           |    5 +---
 R/currency.R        |   26 ++++++++++-----------
 R/format_names.R    |only
 R/freq.R            |   53 +++++++++++++++++++++++--------------------
 R/na_replace.R      |only
 R/percentage.R      |   28 +++++++++++------------
 man/format_names.Rd |only
 man/freq.Rd         |    2 -
 man/na_replace.Rd   |only
 13 files changed, 116 insertions(+), 119 deletions(-)

More information about cleaner at CRAN
Permanent link

Package aws.signature updated to version 0.6.0 with previous version 0.5.2 dated 2019-08-08

Title: Amazon Web Services Request Signatures
Description: Generates version 2 and version 4 request signatures for Amazon Web Services ('AWS') <https://aws.amazon.com/> Application Programming Interfaces ('APIs') and provides a mechanism for retrieving credentials from environment variables, 'AWS' credentials files, and 'EC2' instance metadata. For use on 'EC2' instances, users will need to install the suggested package 'aws.ec2metadata' <https://cran.r-project.org/package=aws.ec2metadata>.
Author: Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>), Jonathan Stott [cre, aut], Mike Kaminsky [ctb]
Maintainer: Jonathan Stott <jonathan.stott@magairports.com>

Diff between aws.signature versions 0.5.2 dated 2019-08-08 and 0.6.0 dated 2020-06-01

 DESCRIPTION                               |   16 -
 MD5                                       |   34 +-
 NEWS.md                                   |    8 
 R/canonical_request.R                     |    8 
 R/locate_credentials.R                    |  436 ++++++++++++++++--------------
 R/read_credentials.R                      |    2 
 R/utils.R                                 |    6 
 R/v4.R                                    |    7 
 man/canonical_request.Rd                  |   12 
 man/locate_credentials.Rd                 |   17 -
 man/read_credentials.Rd                   |   12 
 man/signature_v2_auth.Rd                  |   24 +
 man/signature_v4.Rd                       |   11 
 man/signature_v4_auth.Rd                  |   26 +
 man/string_to_sign.Rd                     |    9 
 tests/testthat/test-canonical_request.R   |only
 tests/testthat/test-v4.R                  |only
 tests/testthat/tests-locate_credentials.R |  171 +++++++++++
 tests/testthat/tests-read_credentials.R   |   11 
 19 files changed, 559 insertions(+), 251 deletions(-)

More information about aws.signature at CRAN
Permanent link

Package shinyWidgets updated to version 0.5.3 with previous version 0.5.2 dated 2020-05-14

Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications. Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph], Fanny Meyer [aut], David Granjon [aut], Ian Fellows [ctb] (Methods for mutating vertical tabs & updateMultiInput), Wil Davis [ctb] (numericRangeInput function), SnapAppointments [cph] (bootstrap-select), Mattia Larentis [ctb, cph] (Bootstrap Switch), Emanuele Marchi [ctb, cph] (Bootstrap Switch), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Flatlogic [cph] (Awesome Bootstrap Checkbox), mouse0270 [ctb, cph] (Material Design Switch), Tristan Edwards [ctb, cph] (SweetAlert), Fabian Lindfors [ctb, cph] (multi.js), Anthony Terrien [ctb, cph] (jQuery Knob), Daniel Eden [ctb, cph] (animate.css), Ganapati V S [ctb, cph] (bttn.css), Brian Grinstead [ctb, cph] (Spectrum), Lokesh Rajendran [ctb, cph] (pretty-checkbox), Leon Gersen [ctb, cph] (wnumb & noUiSlider), Timofey Marochkin [ctb, cph] (air-datepicker), Tobias Ahlin [ctb, cph] (CSS spin), atomiks [ctb, cph] (tippy.js)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between shinyWidgets versions 0.5.2 dated 2020-05-14 and 0.5.3 dated 2020-06-01

 shinyWidgets-0.5.2/shinyWidgets/inst/assets/checkboxGroupButtons         |only
 shinyWidgets-0.5.2/shinyWidgets/inst/assets/radioGroupButtons            |only
 shinyWidgets-0.5.3/shinyWidgets/DESCRIPTION                              |   14 
 shinyWidgets-0.5.3/shinyWidgets/MD5                                      |   71 
 shinyWidgets-0.5.3/shinyWidgets/NAMESPACE                                |    1 
 shinyWidgets-0.5.3/shinyWidgets/NEWS.md                                  |   10 
 shinyWidgets-0.5.3/shinyWidgets/R/actionBttn.R                           |   35 
 shinyWidgets-0.5.3/shinyWidgets/R/dependencies.R                         |   23 
 shinyWidgets-0.5.3/shinyWidgets/R/drop-menu.R                            |    1 
 shinyWidgets-0.5.3/shinyWidgets/R/input-airDatepicker.R                  |   39 
 shinyWidgets-0.5.3/shinyWidgets/R/input-checkboxgroupbuttons.R           |  118 -
 shinyWidgets-0.5.3/shinyWidgets/R/input-icon.R                           |   27 
 shinyWidgets-0.5.3/shinyWidgets/R/input-pretty.R                         | 1027 ++--------
 shinyWidgets-0.5.3/shinyWidgets/R/input-radiogroupbuttons.R              |  116 -
 shinyWidgets-0.5.3/shinyWidgets/R/progressBars.R                         |    5 
 shinyWidgets-0.5.3/shinyWidgets/R/utils.R                                |   13 
 shinyWidgets-0.5.3/shinyWidgets/inst/assets/buttons-group                |only
 shinyWidgets-0.5.3/shinyWidgets/inst/assets/numeric                      |only
 shinyWidgets-0.5.3/shinyWidgets/inst/assets/shinyWidgets-bindings.min.js |    2 
 shinyWidgets-0.5.3/shinyWidgets/man/checkboxGroupButtons.Rd              |    5 
 shinyWidgets-0.5.3/shinyWidgets/man/downloadBttn.Rd                      |    2 
 shinyWidgets-0.5.3/shinyWidgets/man/execute_safely.Rd                    |    1 
 shinyWidgets-0.5.3/shinyWidgets/man/numericInputIcon.Rd                  |    4 
 shinyWidgets-0.5.3/shinyWidgets/man/prettyCheckbox.Rd                    |  141 -
 shinyWidgets-0.5.3/shinyWidgets/man/prettyCheckboxGroup.Rd               |   63 
 shinyWidgets-0.5.3/shinyWidgets/man/prettyRadioButtons.Rd                |   64 
 shinyWidgets-0.5.3/shinyWidgets/man/prettySwitch.Rd                      |   31 
 shinyWidgets-0.5.3/shinyWidgets/man/prettyToggle.Rd                      |  131 -
 shinyWidgets-0.5.3/shinyWidgets/man/radioGroupButtons.Rd                 |    5 
 shinyWidgets-0.5.3/shinyWidgets/man/updateCheckboxGroupButtons.Rd        |    9 
 shinyWidgets-0.5.3/shinyWidgets/man/updatePrettyCheckbox.Rd              |   28 
 shinyWidgets-0.5.3/shinyWidgets/man/updatePrettyCheckboxGroup.Rd         |   45 
 shinyWidgets-0.5.3/shinyWidgets/man/updatePrettyRadioButtons.Rd          |   37 
 shinyWidgets-0.5.3/shinyWidgets/man/updatePrettySwitch.Rd                |   17 
 shinyWidgets-0.5.3/shinyWidgets/man/updatePrettyToggle.Rd                |   26 
 shinyWidgets-0.5.3/shinyWidgets/man/updateRadioGroupButtons.Rd           |    9 
 36 files changed, 935 insertions(+), 1185 deletions(-)

More information about shinyWidgets at CRAN
Permanent link

Package ggpmisc updated to version 0.3.5 with previous version 0.3.4 dated 2020-04-22

Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Specialization of method ggplot(): accept and convert on the fly time series data. Geom: "table", "plot" and "grob" add insets to plots using native data coordinates, while "table_npc", "plot_npc" and "grob_npc" do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: locate and tag peaks and valleys; count observations in different quadrants of a plot; select observations based on 2D density; label with the equation of a polynomial fitted with lm() or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

Diff between ggpmisc versions 0.3.4 dated 2020-04-22 and 0.3.5 dated 2020-06-01

 DESCRIPTION              |   10 
 MD5                      |   40 -
 NAMESPACE                |    9 
 NEWS                     |    5 
 R/geom-grob.R            |   23 
 R/geom-plot.R            |   26 
 R/geom-table.R           |  677 ++++++++++++++++++++++--
 R/stat-fit-broom-tb.R    |   30 -
 R/stat-fmt-tb.R          |   34 +
 inst/doc/user-guide.R    |   11 
 inst/doc/user-guide.Rmd  |   28 
 inst/doc/user-guide.html | 1317 +++++++++++++++++++++++------------------------
 man/geom_grob.Rd         |   26 
 man/geom_plot.Rd         |   29 -
 man/geom_table.Rd        |  145 ++++-
 man/ggpmisc-ggproto.Rd   |  198 +++----
 man/stat_fit_tb.Rd       |   29 -
 man/stat_fmt_tb.Rd       |   27 
 man/stat_poly_eq.Rd      |  618 +++++++++++-----------
 man/ttheme_gtdefault.Rd  |only
 man/ttheme_set.Rd        |only
 vignettes/user-guide.Rmd |   28 
 22 files changed, 2083 insertions(+), 1227 deletions(-)

More information about ggpmisc at CRAN
Permanent link

Package collections updated to version 0.3.2 with previous version 0.3.1 dated 2020-04-30

Title: High Performance Container Data Types
Description: Provides high performance container data types such as queues, stacks, deques, dicts and ordered dicts. Benchmarks <https://randy3k.github.io/collections/articles/benchmark.html> have shown that these containers are asymptotically more efficient than those offered by other packages.
Author: Randy Lai [aut, cre], Andrea Mazzoleni [cph] (tommy hash table library)
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

Diff between collections versions 0.3.1 dated 2020-04-30 and 0.3.2 dated 2020-06-01

 DESCRIPTION                |    9 ++--
 MD5                        |   12 ++---
 R/dict.R                   |   12 +++++
 README.md                  |   16 ++++---
 man/dict.Rd                |   11 +++++
 src/dict.c                 |   94 +++++++++++++++++++++++----------------------
 tests/testthat/test-dict.R |   38 +++++++++++-------
 7 files changed, 117 insertions(+), 75 deletions(-)

More information about collections at CRAN
Permanent link

Package sen2r updated to version 1.3.5 with previous version 1.3.4 dated 2020-04-22

Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images and perform preliminary processing operations. 'sen2r' provides the instruments required to easily perform (and eventually automate) the steps necessary to build a complete Sentinel-2 processing chain. A Graphical User Interface to facilitate data processing is also provided.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>), Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>

Diff between sen2r versions 1.3.4 dated 2020-04-22 and 1.3.5 dated 2020-06-01

 sen2r-1.3.4/sen2r/R/editModPoly.R                                    |only
 sen2r-1.3.4/sen2r/man/editModPoly.Rd                                 |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t05_load_binpaths.R            |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t06_scihub_login.R             |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t07_s2_dop.R                   |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t08_build_example_param_file.R |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t10_s2_list.R                  |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t11_s2_classes.R               |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t12_s2_download.R              |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t13_install_sen2cor.R          |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t14_sen2cor.R                  |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t15_s2_order.R                 |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t20_s2_merge.R                 |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t21_s2_warp.R                  |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t22_s2_mask.R                  |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t23_s2_indices.R               |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t24_s2_rgb.R                   |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t25_ignorelist.R               |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t30_create_s2_dop.R            |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t31_abs2rel.R                  |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t32_list_indices.R             |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t33_sen2r_getElements.R        |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t34_st_crs2.R                  |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t35_create_indices_db.R        |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t36_mountpoint.R               |only
 sen2r-1.3.4/sen2r/tests/testthat/test-t37_projpar.R                  |only
 sen2r-1.3.5/sen2r/DESCRIPTION                                        |   16 
 sen2r-1.3.5/sen2r/MD5                                                |  319 +++++-----
 sen2r-1.3.5/sen2r/NAMESPACE                                          |  135 ----
 sen2r-1.3.5/sen2r/NEWS.md                                            |   21 
 sen2r-1.3.5/sen2r/R/abs2rel.R                                        |    5 
 sen2r-1.3.5/sen2r/R/add_rgb_image.R                                  |   23 
 sen2r-1.3.5/sen2r/R/build_example_param_file.R                       |    5 
 sen2r-1.3.5/sen2r/R/calcindex.R                                      |only
 sen2r-1.3.5/sen2r/R/check_gdal.R                                     |   69 +-
 sen2r-1.3.5/sen2r/R/check_gui_deps.R                                 |only
 sen2r-1.3.5/sen2r/R/check_param_list.R                               |    5 
 sen2r-1.3.5/sen2r/R/check_sen2r_deps.R                               |  203 +++---
 sen2r-1.3.5/sen2r/R/compute_s2_paths.R                               |    5 
 sen2r-1.3.5/sen2r/R/comsub.R                                         |    5 
 sen2r-1.3.5/sen2r/R/create_indices_db.R                              |    7 
 sen2r-1.3.5/sen2r/R/create_s2_dop.R                                  |    5 
 sen2r-1.3.5/sen2r/R/expand_path.R                                    |   10 
 sen2r-1.3.5/sen2r/R/expect_equal_crs.R                               |    5 
 sen2r-1.3.5/sen2r/R/fix_envi_format.R                                |    5 
 sen2r-1.3.5/sen2r/R/gdalUtil.R                                       |    5 
 sen2r-1.3.5/sen2r/R/gdal_abs2rel.R                                   |    5 
 sen2r-1.3.5/sen2r/R/gdal_warp.R                                      |    5 
 sen2r-1.3.5/sen2r/R/gdalwarp_grid.R                                  |   18 
 sen2r-1.3.5/sen2r/R/gipp.R                                           |   10 
 sen2r-1.3.5/sen2r/R/give_write_permission.R                          |    5 
 sen2r-1.3.5/sen2r/R/helpers_extent.R                                 |   57 +
 sen2r-1.3.5/sen2r/R/ignorelist.R                                     |    5 
 sen2r-1.3.5/sen2r/R/init_python.R                                    |    7 
 sen2r-1.3.5/sen2r/R/install_aria2.R                                  |    5 
 sen2r-1.3.5/sen2r/R/install_sen2cor.R                                |    5 
 sen2r-1.3.5/sen2r/R/list_indices.R                                   |    5 
 sen2r-1.3.5/sen2r/R/load_binpaths.R                                  |    7 
 sen2r-1.3.5/sen2r/R/mountpoint.R                                     |    5 
 sen2r-1.3.5/sen2r/R/nn.R                                             |    5 
 sen2r-1.3.5/sen2r/R/path_check.R                                     |   48 -
 sen2r-1.3.5/sen2r/R/print_message.R                                  |    5 
 sen2r-1.3.5/sen2r/R/projpar.R                                        |    7 
 sen2r-1.3.5/sen2r/R/raster_metadata.R                                |    5 
 sen2r-1.3.5/sen2r/R/s2_calcindices.R                                 |  136 ----
 sen2r-1.3.5/sen2r/R/s2_dop.R                                         |    7 
 sen2r-1.3.5/sen2r/R/s2_download.R                                    |    5 
 sen2r-1.3.5/sen2r/R/s2_gui.R                                         |  216 +++++-
 sen2r-1.3.5/sen2r/R/s2_list.R                                        |    6 
 sen2r-1.3.5/sen2r/R/s2_mask.R                                        |    5 
 sen2r-1.3.5/sen2r/R/s2_merge.R                                       |    5 
 sen2r-1.3.5/sen2r/R/s2_order.R                                       |    5 
 sen2r-1.3.5/sen2r/R/s2_rgb.R                                         |   42 +
 sen2r-1.3.5/sen2r/R/s2_thumbnails.R                                  |  180 ++++-
 sen2r-1.3.5/sen2r/R/s2_tiles.R                                       |    5 
 sen2r-1.3.5/sen2r/R/s2_translate.R                                   |    7 
 sen2r-1.3.5/sen2r/R/safe_getMetadata.R                               |    5 
 sen2r-1.3.5/sen2r/R/safe_is_online.R                                 |    5 
 sen2r-1.3.5/sen2r/R/safe_shortname.R                                 |    5 
 sen2r-1.3.5/sen2r/R/safelist-class.R                                 |    5 
 sen2r-1.3.5/sen2r/R/scihub_login.R                                   |   26 
 sen2r-1.3.5/sen2r/R/sen2cor.R                                        |   16 
 sen2r-1.3.5/sen2r/R/sen2r.R                                          |   66 +-
 sen2r-1.3.5/sen2r/R/sen2r_getElements.R                              |    5 
 sen2r-1.3.5/sen2r/R/sen2r_process_report.R                           |    5 
 sen2r-1.3.5/sen2r/R/smooth_mask.R                                    |   19 
 sen2r-1.3.5/sen2r/R/st_crs2.R                                        |   20 
 sen2r-1.3.5/sen2r/R/str_pad2.R                                       |    5 
 sen2r-1.3.5/sen2r/R/tiles_intersects.R                               |    5 
 sen2r-1.3.5/sen2r/R/trace_functions.R                                |    5 
 sen2r-1.3.5/sen2r/R/zzz.R                                            |   29 
 sen2r-1.3.5/sen2r/inst/WORDLIST                                      |    3 
 sen2r-1.3.5/sen2r/inst/doc/installation.R                            |    5 
 sen2r-1.3.5/sen2r/inst/doc/installation.Rmd                          |  138 ++--
 sen2r-1.3.5/sen2r/inst/doc/installation.html                         |  132 ++--
 sen2r-1.3.5/sen2r/inst/doc/sen2r_gui.Rmd                             |    9 
 sen2r-1.3.5/sen2r/inst/doc/sen2r_gui.html                            |    9 
 sen2r-1.3.5/sen2r/man/abs2rel.Rd                                     |    7 
 sen2r-1.3.5/sen2r/man/add_rgb_image.Rd                               |    7 
 sen2r-1.3.5/sen2r/man/build_example_param_file.Rd                    |    7 
 sen2r-1.3.5/sen2r/man/calcindex.Rd                                   |only
 sen2r-1.3.5/sen2r/man/check_gdal.Rd                                  |   14 
 sen2r-1.3.5/sen2r/man/check_gui_deps.Rd                              |only
 sen2r-1.3.5/sen2r/man/check_param_list.Rd                            |    7 
 sen2r-1.3.5/sen2r/man/check_sen2r_deps.Rd                            |   18 
 sen2r-1.3.5/sen2r/man/compute_s2_paths.Rd                            |    7 
 sen2r-1.3.5/sen2r/man/comsub.Rd                                      |    7 
 sen2r-1.3.5/sen2r/man/create_indices_db.Rd                           |    7 
 sen2r-1.3.5/sen2r/man/create_s2_dop.Rd                               |    7 
 sen2r-1.3.5/sen2r/man/expand_path.Rd                                 |    7 
 sen2r-1.3.5/sen2r/man/expect_equal_crs.Rd                            |    7 
 sen2r-1.3.5/sen2r/man/fix_envi_format.Rd                             |    7 
 sen2r-1.3.5/sen2r/man/gdalUtil.Rd                                    |    7 
 sen2r-1.3.5/sen2r/man/gdal_abs2rel_rel2abs.Rd                        |    7 
 sen2r-1.3.5/sen2r/man/gdal_warp.Rd                                   |    7 
 sen2r-1.3.5/sen2r/man/gdalwarp_grid.Rd                               |    7 
 sen2r-1.3.5/sen2r/man/gipp.Rd                                        |    7 
 sen2r-1.3.5/sen2r/man/gipp_init.Rd                                   |    7 
 sen2r-1.3.5/sen2r/man/give_write_permission.Rd                       |    7 
 sen2r-1.3.5/sen2r/man/ignorelist.Rd                                  |    7 
 sen2r-1.3.5/sen2r/man/init_python.Rd                                 |    7 
 sen2r-1.3.5/sen2r/man/install_aria2.Rd                               |    7 
 sen2r-1.3.5/sen2r/man/install_sen2cor.Rd                             |    7 
 sen2r-1.3.5/sen2r/man/list_indices.Rd                                |    7 
 sen2r-1.3.5/sen2r/man/load_binpaths.Rd                               |    7 
 sen2r-1.3.5/sen2r/man/load_extent.Rd                                 |    7 
 sen2r-1.3.5/sen2r/man/mountpoint.Rd                                  |    7 
 sen2r-1.3.5/sen2r/man/nn.Rd                                          |    7 
 sen2r-1.3.5/sen2r/man/normalize_path.Rd                              |    7 
 sen2r-1.3.5/sen2r/man/print_message.Rd                               |    7 
 sen2r-1.3.5/sen2r/man/projpar.Rd                                     |    7 
 sen2r-1.3.5/sen2r/man/raster2rgb.Rd                                  |    7 
 sen2r-1.3.5/sen2r/man/raster_metadata.Rd                             |    7 
 sen2r-1.3.5/sen2r/man/s2_calcindices.Rd                              |    7 
 sen2r-1.3.5/sen2r/man/s2_dop.Rd                                      |    7 
 sen2r-1.3.5/sen2r/man/s2_download.Rd                                 |    7 
 sen2r-1.3.5/sen2r/man/s2_gui.Rd                                      |    7 
 sen2r-1.3.5/sen2r/man/s2_list.Rd                                     |    7 
 sen2r-1.3.5/sen2r/man/s2_mask.Rd                                     |    7 
 sen2r-1.3.5/sen2r/man/s2_merge.Rd                                    |    7 
 sen2r-1.3.5/sen2r/man/s2_order.Rd                                    |    7 
 sen2r-1.3.5/sen2r/man/s2_rgb.Rd                                      |   15 
 sen2r-1.3.5/sen2r/man/s2_thumbnails.Rd                               |   15 
 sen2r-1.3.5/sen2r/man/s2_tiles.Rd                                    |    7 
 sen2r-1.3.5/sen2r/man/s2_translate.Rd                                |    7 
 sen2r-1.3.5/sen2r/man/safe_getMetadata.Rd                            |    7 
 sen2r-1.3.5/sen2r/man/safe_is_online.Rd                              |    7 
 sen2r-1.3.5/sen2r/man/safe_shortname.Rd                              |    7 
 sen2r-1.3.5/sen2r/man/safelist-class.Rd                              |    7 
 sen2r-1.3.5/sen2r/man/scihub_login.Rd                                |    7 
 sen2r-1.3.5/sen2r/man/sen2cor.Rd                                     |    7 
 sen2r-1.3.5/sen2r/man/sen2r.Rd                                       |    7 
 sen2r-1.3.5/sen2r/man/sen2r_getElements.Rd                           |    7 
 sen2r-1.3.5/sen2r/man/sen2r_process_report.Rd                        |    7 
 sen2r-1.3.5/sen2r/man/smooth_mask.Rd                                 |    7 
 sen2r-1.3.5/sen2r/man/st_crs2.Rd                                     |    7 
 sen2r-1.3.5/sen2r/man/stack2rgb.Rd                                   |   16 
 sen2r-1.3.5/sen2r/man/str_pad2.Rd                                    |    7 
 sen2r-1.3.5/sen2r/man/tiles_intersects.Rd                            |    7 
 sen2r-1.3.5/sen2r/man/trace_function.Rd                              |    7 
 sen2r-1.3.5/sen2r/tests/testthat/test-abs2rel.R                      |only
 sen2r-1.3.5/sen2r/tests/testthat/test-build_example_param_file.R     |only
 sen2r-1.3.5/sen2r/tests/testthat/test-gdal_warp.R                    |only
 sen2r-1.3.5/sen2r/tests/testthat/test-gdalwarp_grid.R                |only
 sen2r-1.3.5/sen2r/tests/testthat/test-list_indices.R                 |only
 sen2r-1.3.5/sen2r/tests/testthat/test-load_binpaths.R                |only
 sen2r-1.3.5/sen2r/tests/testthat/test-mountpoint.R                   |only
 sen2r-1.3.5/sen2r/tests/testthat/test-projpar.R                      |only
 sen2r-1.3.5/sen2r/tests/testthat/test-s2_calcindices.R               |only
 sen2r-1.3.5/sen2r/tests/testthat/test-s2_dop.R                       |only
 sen2r-1.3.5/sen2r/tests/testthat/test-s2_download.R                  |only
 sen2r-1.3.5/sen2r/tests/testthat/test-s2_list.R                      |only
 sen2r-1.3.5/sen2r/tests/testthat/test-s2_mask.R                      |only
 sen2r-1.3.5/sen2r/tests/testthat/test-s2_order.R                     |only
 sen2r-1.3.5/sen2r/tests/testthat/test-s2_rgb.R                       |only
 sen2r-1.3.5/sen2r/tests/testthat/test-safelist-class.R               |only
 sen2r-1.3.5/sen2r/tests/testthat/test-scihub_login.R                 |only
 sen2r-1.3.5/sen2r/tests/testthat/test-sen2cor.R                      |only
 sen2r-1.3.5/sen2r/tests/testthat/test-sen2r-00_connection.R          |only
 sen2r-1.3.5/sen2r/tests/testthat/test-sen2r-01_merge.R               |only
 sen2r-1.3.5/sen2r/tests/testthat/test-sen2r-02_warp.R                |only
 sen2r-1.3.5/sen2r/tests/testthat/test-sen2r-03_mask.R                |only
 sen2r-1.3.5/sen2r/tests/testthat/test-sen2r-04_indices.R             |only
 sen2r-1.3.5/sen2r/tests/testthat/test-sen2r-05_rgb.R                 |only
 sen2r-1.3.5/sen2r/tests/testthat/test-sen2r-06_ignorelist.R          |only
 sen2r-1.3.5/sen2r/tests/testthat/test-sen2r_getElements.R            |only
 sen2r-1.3.5/sen2r/tests/testthat/test-st_crs2.R                      |only
 sen2r-1.3.5/sen2r/vignettes/installation.Rmd                         |  138 ++--
 sen2r-1.3.5/sen2r/vignettes/sen2r_gui.Rmd                            |    9 
 189 files changed, 1869 insertions(+), 941 deletions(-)

More information about sen2r at CRAN
Permanent link

Package Delaporte updated to version 7.0.3 with previous version 7.0.2 dated 2019-05-17

Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

Diff between Delaporte versions 7.0.2 dated 2019-05-17 and 7.0.3 dated 2020-06-01

 DESCRIPTION                   |   14 +--
 MD5                           |   18 ++-
 R/Delaporte.R                 |    2 
 README.md                     |   66 +++++++++++---
 build/partial.rdb             |binary
 inst/CITATION                 |only
 inst/NEWS.Rd                  |  192 ++++++++++++++++++++++++++++++++----------
 man/Delaporte-package.Rd      |   25 +++--
 src/Makevars                  |    2 
 src/utils_and_wrappers.c      |    1 
 tests/testthat/test-package.r |only
 11 files changed, 235 insertions(+), 85 deletions(-)

More information about Delaporte at CRAN
Permanent link

Package sigminer updated to version 1.0.6 with previous version 1.0.5 dated 2020-05-14

Title: Extract, Analyze and Visualize Signatures for Genomic Variations
Description: Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff, et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>), Tao Wu [aut, ctb], Ziyu Tao [aut, ctb], Geoffrey Macintyre [ctb], Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>

Diff between sigminer versions 1.0.5 dated 2020-05-14 and 1.0.6 dated 2020-06-01

 DESCRIPTION                     |   14 ++--
 MD5                             |   49 ++++++++-------
 NAMESPACE                       |    1 
 NEWS.md                         |   16 +++++
 R/generate_matrices.R           |   53 ++++++++++++++--
 R/get_groups.R                  |   74 ++++++++++++++++++-----
 R/get_sig_similarity.R          |   10 ++-
 R/show_cosmic_signatures.R      |   10 ++-
 R/show_groups.R                 |only
 R/show_sig_bootstrap.R          |  101 ++++++++++++++++++++++++--------
 R/show_sig_fit.R                |   33 ++++++++--
 R/show_sig_profile.R            |   32 ++++++++--
 R/sig_convert.R                 |    2 
 R/sig_fit.R                     |  125 +++++++++++++++++++++-------------------
 R/sig_fit_bootstrap.R           |    6 -
 R/sig_fit_bootstrap_batch.R     |   73 +++++++++++++++++++----
 inst/extdata/TSB_signatures.rds |only
 man/get_groups.Rd               |    5 -
 man/get_sig_similarity.Rd       |    7 +-
 man/show_cosmic_sig_profile.Rd  |    6 +
 man/show_groups.Rd              |only
 man/show_sig_bootstrap.Rd       |   39 ++++++++----
 man/show_sig_fit.Rd             |    3 
 man/sig_convert.Rd              |    2 
 man/sig_fit.Rd                  |   31 ++++-----
 man/sig_fit_bootstrap.Rd        |   15 ++--
 man/sig_fit_bootstrap_batch.Rd  |   26 +++++---
 27 files changed, 512 insertions(+), 221 deletions(-)

More information about sigminer at CRAN
Permanent link

Package blocksdesign updated to version 4.1 with previous version 4.0 dated 2020-05-06

Title: Nested and Crossed Block Designs for Factorial and Unstructured Treatment Sets
Description: Constructs D-optimal or near D-optimal treatment and block designs for linear treatment models with crossed or nested block factors. The treatment design can be any arbitrary linear model defined by a treatment model formula and the block design can be any feasible combination of crossed or nested block factors. The block design factors are optimized sequentially and the levels of each successive block factor are optimized within the levels of each preceding block factor. Crossed block designs with non-singular interaction effects are optimized using a weighting scheme that allows for differential weighting of first and second-order block effects. Outputs include a table showing the allocation of treatments to blocks and tables showing the achieved D-efficiency factors for each block and treatment design.
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>

Diff between blocksdesign versions 4.0 dated 2020-05-06 and 4.1 dated 2020-06-01

 DESCRIPTION   |    8 
 MD5           |   18 
 R/blocks.r    |  160 +++---
 R/design.r    | 1342 ++++++++++++++++++++++++++++------------------------------
 R/hcf.R       |    3 
 R/ppMOLS.R    |  436 +++++++++---------
 man/HCF.Rd    |    3 
 man/MOLS.Rd   |   15 
 man/blocks.Rd |   58 +-
 man/design.Rd |  172 +++----
 10 files changed, 1099 insertions(+), 1116 deletions(-)

More information about blocksdesign at CRAN
Permanent link

Package Evapotranspiration updated to version 1.15 with previous version 1.14 dated 2019-05-31

Title: Modelling Actual, Potential and Reference Crop Evapotranspiration
Description: Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo [aut, cre] <danlu.guo@adelaide.edu.au>, Seth Westra [aut] <swestra@civeng.adelaide.edu.au>, Tim Peterson [ctb] <tim.peterson@monash.edu>
Maintainer: Danlu Guo <danlu.guo@unimelb.edu.au>

Diff between Evapotranspiration versions 1.14 dated 2019-05-31 and 1.15 dated 2020-06-01

 Evapotranspiration-1.14/Evapotranspiration/man/data.Rd                  |only
 Evapotranspiration-1.15/Evapotranspiration/DESCRIPTION                  |   12 
 Evapotranspiration-1.15/Evapotranspiration/MD5                          |   76 
 Evapotranspiration-1.15/Evapotranspiration/NAMESPACE                    |    2 
 Evapotranspiration-1.15/Evapotranspiration/NEWS                         |   14 
 Evapotranspiration-1.15/Evapotranspiration/R/Evapotranspiration.R       | 1553 ++++------
 Evapotranspiration-1.15/Evapotranspiration/data/defaultconstants.RData  |binary
 Evapotranspiration-1.15/Evapotranspiration/data/processeddata.RData     |binary
 Evapotranspiration-1.15/Evapotranspiration/man/ET.Abtew.Rd              |   16 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.BlaneyCriddle.Rd      |   14 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.BrutsaertStrickler.Rd |   16 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.ChapmanAustralian.Rd  |   26 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.GrangerGray.Rd        |   20 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.Hamon.Rd              |   12 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.HargreavesSamani.Rd   |   12 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.JensenHaise.Rd        |   18 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.Linacre.Rd            |   14 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.Makkink.Rd            |   16 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.MattShuttleworth.Rd   |   18 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.McGuinnessBordne.Rd   |   14 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.MortonCRAE.Rd         |   22 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.MortonCRWE.Rd         |   20 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.PenPan.Rd             |   22 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.Penman.Rd             |   26 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.PenmanMonteith.Rd     |   22 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.PriestleyTaylor.Rd    |   18 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.Rd                    |   28 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.Romanenko.Rd          |   13 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.SzilagyiJozsa.Rd      |   18 
 Evapotranspiration-1.15/Evapotranspiration/man/ET.Turc.Rd               |   18 
 Evapotranspiration-1.15/Evapotranspiration/man/ETComparison.Rd          |   18 
 Evapotranspiration-1.15/Evapotranspiration/man/ETForcings.Rd            |    6 
 Evapotranspiration-1.15/Evapotranspiration/man/ETPlot.Rd                |   12 
 Evapotranspiration-1.15/Evapotranspiration/man/E_OBS.Rd                 |    2 
 Evapotranspiration-1.15/Evapotranspiration/man/ReadInputs.Rd            |    2 
 Evapotranspiration-1.15/Evapotranspiration/man/ReadOBSEvaporation.Rd    |    4 
 Evapotranspiration-1.15/Evapotranspiration/man/climatedata.Rd           |    4 
 Evapotranspiration-1.15/Evapotranspiration/man/constants.Rd             |    4 
 Evapotranspiration-1.15/Evapotranspiration/man/defaultconstants.Rd      |    2 
 Evapotranspiration-1.15/Evapotranspiration/man/processeddata.Rd         |only
 40 files changed, 1046 insertions(+), 1068 deletions(-)

More information about Evapotranspiration at CRAN
Permanent link

Sun, 31 May 2020

Package tidyjson updated to version 0.3.1 with previous version 0.3.0 dated 2020-05-28

Title: Tidy Complex 'JSON'
Description: Turn complex 'JSON' data into tidy data frames.
Author: Jeremy Stanley [aut], Cole Arendt [aut, cre]
Maintainer: Cole Arendt <cole@rstudio.com>

Diff between tidyjson versions 0.3.0 dated 2020-05-28 and 0.3.1 dated 2020-05-31

 DESCRIPTION                            |   10 +++---
 MD5                                    |   27 ++++++++--------
 NAMESPACE                              |    5 +++
 NEWS.md                                |   16 +++++++++
 R/data-worldbank.R                     |    2 +
 R/spread_all.R                         |    8 +++-
 R/tbl_json.R                           |   54 +++++++++++++++++++++++++++++++++
 inst/doc/introduction-to-tidyjson.html |   23 +++++++-------
 inst/doc/visualizing-json.html         |   27 ++++++++--------
 man/spread_all.Rd                      |    8 +++-
 man/worldbank.Rd                       |    2 +
 tests/testthat/test-examples.R         |only
 tests/testthat/test-gather_object.R    |    5 ---
 tests/testthat/test-json_structure.R   |    2 -
 tests/testthat/test-tbl_json.R         |   32 ++++++++++++++++++-
 15 files changed, 165 insertions(+), 56 deletions(-)

More information about tidyjson at CRAN
Permanent link

Package sundialr updated to version 0.1.4 with previous version 0.1.3 dated 2019-06-09

Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computation.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
Author: Satyaprakash Nayak [aut, cre, cph] (<https://orcid.org/0000-0001-7225-1317>), Lawrence Livermore National Security [cph], Southern Methodist University [cph]
Maintainer: Satyaprakash Nayak <sn248@cornell.edu>

Diff between sundialr versions 0.1.3 dated 2019-06-09 and 0.1.4 dated 2020-05-31

 sundialr-0.1.3/sundialr/inst/include/nvector/cuda                                       |only
 sundialr-0.1.3/sundialr/inst/include/nvector/nvector_cuda.h                             |only
 sundialr-0.1.3/sundialr/inst/include/nvector/nvector_mpicuda.h                          |only
 sundialr-0.1.3/sundialr/inst/include/nvector/nvector_mpiraja.h                          |only
 sundialr-0.1.3/sundialr/inst/include/nvector/nvector_parhyp.h                           |only
 sundialr-0.1.3/sundialr/inst/include/nvector/nvector_petsc.h                            |only
 sundialr-0.1.3/sundialr/inst/include/nvector/nvector_pthreads.h                         |only
 sundialr-0.1.3/sundialr/inst/include/nvector/nvector_raja.h                             |only
 sundialr-0.1.3/sundialr/inst/include/nvector/raja                                       |only
 sundialr-0.1.3/sundialr/inst/include/sundials/sundials_klu_impl.h                       |only
 sundialr-0.1.3/sundialr/inst/include/sundials/sundials_mpi.h                            |only
 sundialr-0.1.3/sundialr/inst/include/sundials/sundials_pcg.h                            |only
 sundialr-0.1.3/sundialr/inst/include/sundials/sundials_sparse.h                         |only
 sundialr-0.1.3/sundialr/inst/include/sundials/sundials_spbcgs.h                         |only
 sundialr-0.1.3/sundialr/inst/include/sundials/sundials_spfgmr.h                         |only
 sundialr-0.1.3/sundialr/inst/include/sundials/sundials_spgmr.h                          |only
 sundialr-0.1.3/sundialr/inst/include/sundials/sundials_sptfqmr.h                        |only
 sundialr-0.1.3/sundialr/inst/include/sundials/sundials_superlumt_impl.h                 |only
 sundialr-0.1.3/sundialr/src/sundials/cvode/F90                                          |only
 sundialr-0.1.3/sundialr/src/sundials/cvode/README                                       |only
 sundialr-0.1.3/sundialr/src/sundials/cvode/fcmix                                        |only
 sundialr-0.1.3/sundialr/src/sundials/cvodes/README                                      |only
 sundialr-0.1.3/sundialr/src/sundials/nvec_ser                                           |only
 sundialr-0.1.3/sundialr/src/sundials/sundials/sundials_mpi.c                            |only
 sundialr-0.1.3/sundialr/src/sundials/sundials/sundials_pcg.c                            |only
 sundialr-0.1.3/sundialr/src/sundials/sundials/sundials_sparse.c                         |only
 sundialr-0.1.3/sundialr/src/sundials/sundials/sundials_spbcgs.c                         |only
 sundialr-0.1.3/sundialr/src/sundials/sundials/sundials_spfgmr.c                         |only
 sundialr-0.1.3/sundialr/src/sundials/sundials/sundials_spgmr.c                          |only
 sundialr-0.1.3/sundialr/src/sundials/sundials/sundials_sptfqmr.c                        |only
 sundialr-0.1.3/sundialr/src/sundials/sunlinsol_band                                     |only
 sundialr-0.1.3/sundialr/src/sundials/sunlinsol_dense                                    |only
 sundialr-0.1.3/sundialr/src/sundials/sunmat_band                                        |only
 sundialr-0.1.3/sundialr/src/sundials/sunmat_dense                                       |only
 sundialr-0.1.3/sundialr/src/sundials/sunnonlinsol/fixedpoint/F90                        |only
 sundialr-0.1.3/sundialr/src/sundials/sunnonlinsol/newton/F90                            |only
 sundialr-0.1.4/sundialr/DESCRIPTION                                                     |   46 
 sundialr-0.1.4/sundialr/LICENSE                                                         |only
 sundialr-0.1.4/sundialr/MD5                                                             |  406 -
 sundialr-0.1.4/sundialr/NEWS                                                            |only
 sundialr-0.1.4/sundialr/R/RcppExports.R                                                 |   41 
 sundialr-0.1.4/sundialr/R/zzz.R                                                         |    6 
 sundialr-0.1.4/sundialr/README.md                                                       |   34 
 sundialr-0.1.4/sundialr/build/vignette.rds                                              |binary
 sundialr-0.1.4/sundialr/inst/COPYRIGHTS                                                 |only
 sundialr-0.1.4/sundialr/inst/doc/my-vignette.R                                          |   79 
 sundialr-0.1.4/sundialr/inst/doc/my-vignette.Rmd                                        |  158 
 sundialr-0.1.4/sundialr/inst/doc/my-vignette.html                                       |  440 -
 sundialr-0.1.4/sundialr/inst/examples/cv_Roberts_dns.r                                  |    1 
 sundialr-0.1.4/sundialr/inst/examples/cvs_Roberts_dns.r                                 |    3 
 sundialr-0.1.4/sundialr/inst/examples/cvsolve_1D.r                                      |only
 sundialr-0.1.4/sundialr/inst/examples/ida_Roberts_dns.r                                 |only
 sundialr-0.1.4/sundialr/inst/include/cvode/cvode.h                                      |  770 --
 sundialr-0.1.4/sundialr/inst/include/cvode/cvode_bandpre.h                              |  143 
 sundialr-0.1.4/sundialr/inst/include/cvode/cvode_bbdpre.h                               |  288 
 sundialr-0.1.4/sundialr/inst/include/cvode/cvode_diag.h                                 |  102 
 sundialr-0.1.4/sundialr/inst/include/cvode/cvode_direct.h                               |   68 
 sundialr-0.1.4/sundialr/inst/include/cvode/cvode_ls.h                                   |  367 -
 sundialr-0.1.4/sundialr/inst/include/cvode/cvode_spils.h                                |  107 
 sundialr-0.1.4/sundialr/inst/include/cvodes/cvodes.h                                    | 2008 ------
 sundialr-0.1.4/sundialr/inst/include/cvodes/cvodes_bandpre.h                            |  176 
 sundialr-0.1.4/sundialr/inst/include/cvodes/cvodes_bbdpre.h                             |  354 -
 sundialr-0.1.4/sundialr/inst/include/cvodes/cvodes_diag.h                               |  124 
 sundialr-0.1.4/sundialr/inst/include/cvodes/cvodes_direct.h                             |   66 
 sundialr-0.1.4/sundialr/inst/include/cvodes/cvodes_ls.h                                 |  506 -
 sundialr-0.1.4/sundialr/inst/include/cvodes/cvodes_spils.h                              |  152 
 sundialr-0.1.4/sundialr/inst/include/ida                                                |only
 sundialr-0.1.4/sundialr/inst/include/nvector/nvector_openmp.h                           |  228 
 sundialr-0.1.4/sundialr/inst/include/nvector/nvector_openmpdev.h                        |  234 
 sundialr-0.1.4/sundialr/inst/include/nvector/nvector_parallel.h                         |  253 
 sundialr-0.1.4/sundialr/inst/include/nvector/nvector_serial.h                           |  209 
 sundialr-0.1.4/sundialr/inst/include/rhs_func.h                                         |only
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_band.h                           |   61 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_config.h                         |   38 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_config.in                        |   30 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_dense.h                          |   65 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_direct.h                         |  116 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_fconfig.h                        |   11 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_fconfig.in                       |   11 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_fnvector.h                       |   27 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_futils.h                         |only
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_iterative.h                      |  305 -
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_lapack.h                         |  253 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_linearsolver.h                   |  422 -
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_math.h                           |   47 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_matrix.h                         |  205 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_mpi_types.h                      |   31 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_nonlinearsolver.h                |  159 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_nvector.h                        |  433 -
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_nvector_senswrapper.h            |   32 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_types.h                          |   55 
 sundialr-0.1.4/sundialr/inst/include/sundials/sundials_version.h                        |   52 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_band.h                         |   80 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_cusolversp_batchqr.h           |only
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_dense.h                        |   85 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_klu.h                          |  154 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_lapackband.h                   |   87 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_lapackdense.h                  |   87 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_pcg.h                          |  179 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_spbcgs.h                       |  183 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_spfgmr.h                       |  202 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_spgmr.h                        |  201 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_sptfqmr.h                      |  175 
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_superludist.h                  |only
 sundialr-0.1.4/sundialr/inst/include/sunlinsol/sunlinsol_superlumt.h                    |  112 
 sundialr-0.1.4/sundialr/inst/include/sunmatrix/sunmatrix_band.h                         |  256 
 sundialr-0.1.4/sundialr/inst/include/sunmatrix/sunmatrix_dense.h                        |  195 
 sundialr-0.1.4/sundialr/inst/include/sunmatrix/sunmatrix_slunrloc.h                     |only
 sundialr-0.1.4/sundialr/inst/include/sunmatrix/sunmatrix_sparse.h                       |  270 
 sundialr-0.1.4/sundialr/inst/include/sunnonlinsol/sunnonlinsol_fixedpoint.h             |   63 
 sundialr-0.1.4/sundialr/inst/include/sunnonlinsol/sunnonlinsol_newton.h                 |   20 
 sundialr-0.1.4/sundialr/inst/include/sunnonlinsol/sunnonlinsol_petscsnes.h              |only
 sundialr-0.1.4/sundialr/man/cvode.Rd                                                    |   15 
 sundialr-0.1.4/sundialr/man/cvodes.Rd                                                   |   19 
 sundialr-0.1.4/sundialr/man/cvsolve.Rd                                                  |only
 sundialr-0.1.4/sundialr/man/figures                                                     |only
 sundialr-0.1.4/sundialr/man/ida.Rd                                                      |only
 sundialr-0.1.4/sundialr/src/Makevars                                                    |   69 
 sundialr-0.1.4/sundialr/src/Makevars.win                                                |   69 
 sundialr-0.1.4/sundialr/src/RcppExports.cpp                                             |   37 
 sundialr-0.1.4/sundialr/src/check_retval.cpp                                            |   30 
 sundialr-0.1.4/sundialr/src/cvode.cpp                                                   |  201 
 sundialr-0.1.4/sundialr/src/cvodes.cpp                                                  |   43 
 sundialr-0.1.4/sundialr/src/cvsolve.cpp                                                 |only
 sundialr-0.1.4/sundialr/src/ida.cpp                                                     |only
 sundialr-0.1.4/sundialr/src/rhs_func.cpp                                                |only
 sundialr-0.1.4/sundialr/src/sortTimes.cpp                                               |only
 sundialr-0.1.4/sundialr/src/sundials/cvode/CMakeLists.txt                               |  111 
 sundialr-0.1.4/sundialr/src/sundials/cvode/LICENSE                                      |   77 
 sundialr-0.1.4/sundialr/src/sundials/cvode/NOTICE                                       |only
 sundialr-0.1.4/sundialr/src/sundials/cvode/README.md                                    |only
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode.c                                      |  636 +-
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_bandpre.c                              |  138 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_bandpre_impl.h                         |   18 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_bbdpre.c                               |  154 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_bbdpre_impl.h                          |   18 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_diag.c                                 |   16 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_diag_impl.h                            |   16 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_direct.c                               |only
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_impl.h                                 |   34 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_io.c                                   |   64 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_ls.c                                   |  514 +
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_ls_impl.h                              |   40 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_nls.c                                  |   37 
 sundialr-0.1.4/sundialr/src/sundials/cvode/cvode_spils.c                                |only
 sundialr-0.1.4/sundialr/src/sundials/cvodes/CMakeLists.txt                              |  112 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/LICENSE                                     |   77 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/NOTICE                                      |only
 sundialr-0.1.4/sundialr/src/sundials/cvodes/README.md                                   |only
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodea.c                                    |  328 -
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodea_io.c                                 |   29 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes.c                                    | 3037 +++++-----
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_bandpre.c                            |  138 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_bandpre_impl.h                       |   18 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_bbdpre.c                             |  180 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_bbdpre_impl.h                        |   18 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_diag.c                               |   16 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_diag_impl.h                          |   16 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_direct.c                             |only
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_impl.h                               |  233 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_io.c                                 |  271 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_ls.c                                 |  691 +-
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_ls_impl.h                            |   50 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_nls.c                                |   38 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_nls_sim.c                            |   59 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_nls_stg.c                            |   56 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_nls_stg1.c                           |   40 
 sundialr-0.1.4/sundialr/src/sundials/cvodes/cvodes_spils.c                              |only
 sundialr-0.1.4/sundialr/src/sundials/ida                                                |only
 sundialr-0.1.4/sundialr/src/sundials/nvector                                            |only
 sundialr-0.1.4/sundialr/src/sundials/sundials/CMakeLists.txt                            |   90 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_band.c                           |   16 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_dense.c                          |   16 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_direct.c                         |   16 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_futils.c                         |only
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_iterative.c                      |   16 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_linearsolver.c                   |  147 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_math.c                           |   16 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_matrix.c                         |  135 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_nonlinearsolver.c                |  111 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_nvector.c                        |  390 +
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_nvector_senswrapper.c            |   16 
 sundialr-0.1.4/sundialr/src/sundials/sundials/sundials_version.c                        |   16 
 sundialr-0.1.4/sundialr/src/sundials/sunlinsol                                          |only
 sundialr-0.1.4/sundialr/src/sundials/sunmatrix                                          |only
 sundialr-0.1.4/sundialr/src/sundials/sunnonlinsol/CMakeLists.txt                        |   20 
 sundialr-0.1.4/sundialr/src/sundials/sunnonlinsol/fixedpoint/CMakeLists.txt             |   26 
 sundialr-0.1.4/sundialr/src/sundials/sunnonlinsol/fixedpoint/fsunnonlinsol_fixedpoint.c |   18 
 sundialr-0.1.4/sundialr/src/sundials/sunnonlinsol/fixedpoint/fsunnonlinsol_fixedpoint.h |   18 
 sundialr-0.1.4/sundialr/src/sundials/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c  |  164 
 sundialr-0.1.4/sundialr/src/sundials/sunnonlinsol/newton/CMakeLists.txt                 |   24 
 sundialr-0.1.4/sundialr/src/sundials/sunnonlinsol/newton/fsunnonlinsol_newton.c         |   16 
 sundialr-0.1.4/sundialr/src/sundials/sunnonlinsol/newton/fsunnonlinsol_newton.h         |   16 
 sundialr-0.1.4/sundialr/src/sundials/sunnonlinsol/newton/sunnonlinsol_newton.c          |  121 
 sundialr-0.1.4/sundialr/tests                                                           |only
 sundialr-0.1.4/sundialr/vignettes/my-vignette.Rmd                                       |  158 
 196 files changed, 8584 insertions(+), 12816 deletions(-)

More information about sundialr at CRAN
Permanent link

Package robotstxt updated to version 0.7.4 with previous version 0.6.2 dated 2018-07-18

Title: A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler' Permissions Checker
Description: Provides functions to download and parse 'robots.txt' files. Ultimately the package makes it easy to check if bots (spiders, crawler, scrapers, ...) are allowed to access specific resources on a domain.
Author: Peter Meissner [aut, cre], Kun Ren [aut, cph] (Author and copyright holder of list_merge.R.), Oliver Keys [ctb] (original release code review), Rich Fitz John [ctb] (original release code review)
Maintainer: Peter Meissner <retep.meissner@gmail.com>

Diff between robotstxt versions 0.6.2 dated 2018-07-18 and 0.7.4 dated 2020-05-31

 robotstxt-0.6.2/robotstxt/R/valid_robotstxt.R                       |only
 robotstxt-0.7.4/robotstxt/DESCRIPTION                               |   29 
 robotstxt-0.7.4/robotstxt/LICENSE                                   |   12 
 robotstxt-0.7.4/robotstxt/MD5                                       |  102 
 robotstxt-0.7.4/robotstxt/NAMESPACE                                 |   38 
 robotstxt-0.7.4/robotstxt/NEWS.md                                   |  312 -
 robotstxt-0.7.4/robotstxt/R/as_list.R                               |only
 robotstxt-0.7.4/robotstxt/R/fix_url.R                               |only
 robotstxt-0.7.4/robotstxt/R/get_robotstxt.R                         |  240 -
 robotstxt-0.7.4/robotstxt/R/get_robotstxt_http_get.R                |   92 
 robotstxt-0.7.4/robotstxt/R/get_robotstxts.R                        |  220 -
 robotstxt-0.7.4/robotstxt/R/guess_domain.R                          |   27 
 robotstxt-0.7.4/robotstxt/R/http_domain_changed.R                   |only
 robotstxt-0.7.4/robotstxt/R/http_subdomain_changed.R                |only
 robotstxt-0.7.4/robotstxt/R/http_was_redirected.R                   |only
 robotstxt-0.7.4/robotstxt/R/is_suspect_robotstxt.R                  |only
 robotstxt-0.7.4/robotstxt/R/is_valid_robotstxt.R                    |only
 robotstxt-0.7.4/robotstxt/R/list_merge.R                            |only
 robotstxt-0.7.4/robotstxt/R/null_to_default.R                       |only
 robotstxt-0.7.4/robotstxt/R/parse_url.R                             |only
 robotstxt-0.7.4/robotstxt/R/paths_allowed.R                         |  228 -
 robotstxt-0.7.4/robotstxt/R/paths_allowed_worker_spiderbar.R        |    4 
 robotstxt-0.7.4/robotstxt/R/print_robotstxt_text.R                  |   39 
 robotstxt-0.7.4/robotstxt/R/request_handler_handler.R               |only
 robotstxt-0.7.4/robotstxt/R/robotstxt.R                             |   30 
 robotstxt-0.7.4/robotstxt/R/rt_get_fields.R                         |  142 
 robotstxt-0.7.4/robotstxt/R/rt_request_handler.R                    |only
 robotstxt-0.7.4/robotstxt/R/rt_request_handler_defaults.R           |only
 robotstxt-0.7.4/robotstxt/README.md                                 |  622 ++
 robotstxt-0.7.4/robotstxt/build/vignette.rds                        |binary
 robotstxt-0.7.4/robotstxt/inst/doc/using_robotstxt.R                |   22 
 robotstxt-0.7.4/robotstxt/inst/doc/using_robotstxt.Rmd              |    7 
 robotstxt-0.7.4/robotstxt/inst/doc/using_robotstxt.html             |  386 +
 robotstxt-0.7.4/robotstxt/inst/http_requests                        |only
 robotstxt-0.7.4/robotstxt/man/as.list.robotstxt_text.Rd             |only
 robotstxt-0.7.4/robotstxt/man/fix_url.Rd                            |only
 robotstxt-0.7.4/robotstxt/man/get_robotstxt.Rd                      |  100 
 robotstxt-0.7.4/robotstxt/man/get_robotstxt_http_get.Rd             |   57 
 robotstxt-0.7.4/robotstxt/man/get_robotstxts.Rd                     |  110 
 robotstxt-0.7.4/robotstxt/man/http_domain_changed.Rd                |only
 robotstxt-0.7.4/robotstxt/man/http_subdomain_changed.Rd             |only
 robotstxt-0.7.4/robotstxt/man/http_was_redirected.Rd                |only
 robotstxt-0.7.4/robotstxt/man/is_suspect_robotstxt.Rd               |only
 robotstxt-0.7.4/robotstxt/man/is_valid_robotstxt.Rd                 |    2 
 robotstxt-0.7.4/robotstxt/man/list_merge.Rd                         |only
 robotstxt-0.7.4/robotstxt/man/null_to_defeault.Rd                   |only
 robotstxt-0.7.4/robotstxt/man/parse_url.Rd                          |only
 robotstxt-0.7.4/robotstxt/man/paths_allowed.Rd                      |  139 
 robotstxt-0.7.4/robotstxt/man/paths_allowed_worker_spiderbar.Rd     |   48 
 robotstxt-0.7.4/robotstxt/man/request_handler_handler.Rd            |only
 robotstxt-0.7.4/robotstxt/man/robotstxt.Rd                          |  173 
 robotstxt-0.7.4/robotstxt/man/rt_cache.Rd                           |    4 
 robotstxt-0.7.4/robotstxt/man/rt_get_fields_worker.Rd               |   44 
 robotstxt-0.7.4/robotstxt/man/rt_request_handler.Rd                 |only
 robotstxt-0.7.4/robotstxt/tests/testthat/test_attribute_handling.R  |only
 robotstxt-0.7.4/robotstxt/tests/testthat/test_get_robotstxt.R       |only
 robotstxt-0.7.4/robotstxt/tests/testthat/test_http_event_handling.R |only
 robotstxt-0.7.4/robotstxt/tests/testthat/test_issue50.R             |only
 robotstxt-0.7.4/robotstxt/tests/testthat/test_paths_allowed.R       | 2085 +++++-----
 robotstxt-0.7.4/robotstxt/tests/testthat/test_robotstxt.R           |  176 
 robotstxt-0.7.4/robotstxt/tests/testthat/test_tools.R               |  192 
 robotstxt-0.7.4/robotstxt/vignettes/style.css                       |only
 robotstxt-0.7.4/robotstxt/vignettes/using_robotstxt.Rmd             |    7 
 63 files changed, 3492 insertions(+), 2197 deletions(-)

More information about robotstxt at CRAN
Permanent link

Package MCMCpack updated to version 1.4-8 with previous version 1.4-7 dated 2020-05-08

Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return 'coda' mcmc objects that can then be summarized using the 'coda' package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.
Author: Andrew D. Martin [aut], Kevin M. Quinn [aut], Jong Hee Park [aut,cre], Ghislain Vieilledent [ctb], Michael Malecki[ctb], Matthew Blackwell [ctb], Keith Poole [ctb], Craig Reed [ctb], Ben Goodrich [ctb], Ross Ihaka [cph], The R Development Core Team [cph], The R Foundation [cph], Pierre L'Ecuyer [cph], Makoto Matsumoto [cph], Takuji Nishimura [cph]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>

Diff between MCMCpack versions 1.4-7 dated 2020-05-08 and 1.4-8 dated 2020-05-31

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

More information about MCMCpack at CRAN
Permanent link

Package GNAR updated to version 1.1.0 with previous version 1.0 dated 2019-10-29

Title: Methods for Fitting Network Time Series Models
Description: Simulation of, and fitting models for, Generalised Network Autoregressive (GNAR) time series models which take account of network structure. Such models are described in Knight et al. (2016), see <arXiv:1603.03221>.
Author: Kathryn Leeming [aut], Guy Nason [aut], Matt Nunes [aut, cre], Marina Knight [ctb]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>

Diff between GNAR versions 1.0 dated 2019-10-29 and 1.1.0 dated 2020-05-31

 DESCRIPTION          |   10 +++++-----
 MD5                  |   28 ++++++++++++++--------------
 R/GNARdesign.R       |   17 +++++++++++------
 R/GNARsim.R          |    5 +++++
 R/NofNeighbours.R    |    9 +++++++--
 R/as.GNARnet.R       |    8 +++++++-
 R/is.GNARnet.R       |    9 ++++++++-
 R/matrixtoGNAR.R     |   15 ++++++++++++---
 R/simulate.GNARfit.R |    9 ++++++++-
 data/fiveNode.rda    |binary
 data/gdp.rda         |binary
 data/vswind.rda      |binary
 inst/CHANGES         |   10 +++++++++-
 man/is.GNARnet.Rd    |    4 +++-
 man/matrixtoGNAR.Rd  |    2 +-
 15 files changed, 90 insertions(+), 36 deletions(-)

More information about GNAR at CRAN
Permanent link

Package EMSS updated to version 1.0.1 with previous version 1.0.0 dated 2020-05-29

Title: Some EM-Type Estimation Methods for the Heckman Selection Model
Description: Some EM-type algorithms to estimate parameters for the well-known Heckman selection model are provided in the package. Such algorithms are as follow: ECM(Expectation/Conditional Maximization), ECM(NR)(the Newton-Raphson method is adapted to the ECM) and ECME(Expectation/Conditional Maximization Either). Since the algorithms are based on the EM algorithm, they also have EM’s main advantages, namely, stability and ease of implementation. Further details and explanations of the algorithms can be found in Zhao et al. (2020) <doi: 10.1016/j.csda.2020.106930>.
Author: Kexuan Yang <717260446@qq.com>, Sang Kyu Lee <leesa111@msu.edu>, Zhao Jun <zhaojun2021@hotmail.com>, and Hyoung-Moon Kim <hmk966a@gmail.com >
Maintainer: Sang Kyu Lee <leesa111@msu.edu>

Diff between EMSS versions 1.0.0 dated 2020-05-29 and 1.0.1 dated 2020-05-31

 DESCRIPTION |    6 
 MD5         |    4 
 R/EMSS.R    | 1932 ++++++++++++++++++++++++++++++------------------------------
 3 files changed, 972 insertions(+), 970 deletions(-)

More information about EMSS at CRAN
Permanent link

Package BGGM updated to version 2.0.0 with previous version 1.0.0 dated 2020-02-06

Title: Bayesian Gaussian Graphical Models
Description: Fit Bayesian Gaussian graphical models. The methods are separated into two Bayesian approaches for inference: hypothesis testing and estimation. There are extensions for confirmatory hypothesis testing, comparing Gaussian graphical models, and node wise predictability. These methods were recently introduced in the Gaussian graphical model literature, including Williams (2019) <doi:10.31234/osf.io/x8dpr>, Williams and Mulder (2019) <doi:10.31234/osf.io/ypxd8>, Williams, Rast, Pericchi, and Mulder (2019) <doi:10.31234/osf.io/yt386>.
Author: Donald Williams [aut, cre], Joris Mulder [aut]
Maintainer: Donald Williams <drwwilliams@ucdavis.edu>

Diff between BGGM versions 1.0.0 dated 2020-02-06 and 2.0.0 dated 2020-05-31

 BGGM-1.0.0/BGGM/R/diagnostics.R                            |only
 BGGM-1.0.0/BGGM/R/fitted.R                                 |only
 BGGM-1.0.0/BGGM/R/metrics.R                                |only
 BGGM-1.0.0/BGGM/R/plot_adjacency.R                         |only
 BGGM-1.0.0/BGGM/R/posterior_predict.R                      |only
 BGGM-1.0.0/BGGM/R/pp_check.estimate.R                      |only
 BGGM-1.0.0/BGGM/R/residuals.R                              |only
 BGGM-1.0.0/BGGM/R/shiny_bggm.explore.R                     |only
 BGGM-1.0.0/BGGM/README.md                                  |only
 BGGM-1.0.0/BGGM/inst/doc/credible_intervals.R              |only
 BGGM-1.0.0/BGGM/inst/doc/credible_intervals.Rmd            |only
 BGGM-1.0.0/BGGM/inst/doc/credible_intervals.html           |only
 BGGM-1.0.0/BGGM/inst/doc/network_plot_1.R                  |only
 BGGM-1.0.0/BGGM/inst/doc/network_plot_1.Rmd                |only
 BGGM-1.0.0/BGGM/inst/doc/network_plot_1.html               |only
 BGGM-1.0.0/BGGM/inst/doc/ppc1.R                            |only
 BGGM-1.0.0/BGGM/inst/doc/ppc1.Rmd                          |only
 BGGM-1.0.0/BGGM/inst/doc/ppc1.html                         |only
 BGGM-1.0.0/BGGM/inst/doc/predict.R                         |only
 BGGM-1.0.0/BGGM/inst/doc/predict.Rmd                       |only
 BGGM-1.0.0/BGGM/inst/doc/predict.html                      |only
 BGGM-1.0.0/BGGM/man/assess_predictability.Rd               |only
 BGGM-1.0.0/BGGM/man/bayes_R2.Rd                            |only
 BGGM-1.0.0/BGGM/man/diagnostics.Rd                         |only
 BGGM-1.0.0/BGGM/man/figures/README-example-1.png           |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-10-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-12-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-13-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-15-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-17-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-18-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-19-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-2-1.png   |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-20-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-21-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-22-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-24-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-25-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-26-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-27-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-29-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-29-2.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-29-3.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-3-1.png   |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-30-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-31-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-32-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-33-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-37-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-38-1.png  |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-4-1.png   |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-5-1.png   |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-6-1.png   |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-7-1.png   |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-9-1.png   |only
 BGGM-1.0.0/BGGM/man/figures/README-unnamed-chunk-9-2.png   |only
 BGGM-1.0.0/BGGM/man/figures/logo.jpg                       |only
 BGGM-1.0.0/BGGM/man/figures/logo.pdf                       |only
 BGGM-1.0.0/BGGM/man/figures/logo2.jpg                      |only
 BGGM-1.0.0/BGGM/man/fisher_r2z.Rd                          |only
 BGGM-1.0.0/BGGM/man/fisher_z2r.Rd                          |only
 BGGM-1.0.0/BGGM/man/fitted.estimate.Rd                     |only
 BGGM-1.0.0/BGGM/man/ggm_compare_bf.Rd                      |only
 BGGM-1.0.0/BGGM/man/ggm_compare_estimate.default.Rd        |only
 BGGM-1.0.0/BGGM/man/ggm_compare_ppc.default.Rd             |only
 BGGM-1.0.0/BGGM/man/mae.Rd                                 |only
 BGGM-1.0.0/BGGM/man/mape.Rd                                |only
 BGGM-1.0.0/BGGM/man/mse.Rd                                 |only
 BGGM-1.0.0/BGGM/man/plot.metric.Rd                         |only
 BGGM-1.0.0/BGGM/man/plot.select.estimate.Rd                |only
 BGGM-1.0.0/BGGM/man/plot.select.explore.Rd                 |only
 BGGM-1.0.0/BGGM/man/plot.select.ggm_compare_bf.Rd          |only
 BGGM-1.0.0/BGGM/man/plot_adjacency.Rd                      |only
 BGGM-1.0.0/BGGM/man/posterior_predict.Rd                   |only
 BGGM-1.0.0/BGGM/man/pp_check.estimate.Rd                   |only
 BGGM-1.0.0/BGGM/man/print.coef.estimate.Rd                 |only
 BGGM-1.0.0/BGGM/man/print.confirm.Rd                       |only
 BGGM-1.0.0/BGGM/man/print.estimate.Rd                      |only
 BGGM-1.0.0/BGGM/man/print.explore.Rd                       |only
 BGGM-1.0.0/BGGM/man/print.fitted.estimate.Rd               |only
 BGGM-1.0.0/BGGM/man/print.ggm_compare_bf.Rd                |only
 BGGM-1.0.0/BGGM/man/print.ggm_compare_estimate.Rd          |only
 BGGM-1.0.0/BGGM/man/print.ggm_compare_ppc.Rd               |only
 BGGM-1.0.0/BGGM/man/print.map.Rd                           |only
 BGGM-1.0.0/BGGM/man/print.metric.Rd                        |only
 BGGM-1.0.0/BGGM/man/print.post.pred.Rd                     |only
 BGGM-1.0.0/BGGM/man/print.predict.estimate.Rd              |only
 BGGM-1.0.0/BGGM/man/print.select.estimate.Rd               |only
 BGGM-1.0.0/BGGM/man/print.select.explore.Rd                |only
 BGGM-1.0.0/BGGM/man/print.select.ggm_compare_bf.Rd         |only
 BGGM-1.0.0/BGGM/man/print.select.ggm_compare_estimate.Rd   |only
 BGGM-1.0.0/BGGM/man/print.summary.estimate.Rd              |only
 BGGM-1.0.0/BGGM/man/print.summary.explore.Rd               |only
 BGGM-1.0.0/BGGM/man/print.summary.ggm_compare_ppc.Rd       |only
 BGGM-1.0.0/BGGM/man/print.summary.ggm_estimate_bf.Rd       |only
 BGGM-1.0.0/BGGM/man/print.summary.ggm_estimate_compare.Rd  |only
 BGGM-1.0.0/BGGM/man/print.summary.metric.Rd                |only
 BGGM-1.0.0/BGGM/man/residuals.estimate.Rd                  |only
 BGGM-1.0.0/BGGM/man/rmse.Rd                                |only
 BGGM-1.0.0/BGGM/man/select.ggm_compare_bf.Rd               |only
 BGGM-1.0.0/BGGM/man/shiny_bggm.Rd                          |only
 BGGM-1.0.0/BGGM/man/shiny_bggm.explore.Rd                  |only
 BGGM-1.0.0/BGGM/man/summary.confirm.Rd                     |only
 BGGM-1.0.0/BGGM/man/summary.ggm_compare_bf.Rd              |only
 BGGM-1.0.0/BGGM/man/summary.ggm_compare_ppc.Rd             |only
 BGGM-1.0.0/BGGM/man/summary.metric.Rd                      |only
 BGGM-1.0.0/BGGM/man/summary.select.estimate.Rd             |only
 BGGM-1.0.0/BGGM/man/summary.select.ggm_compare_bf.Rd       |only
 BGGM-1.0.0/BGGM/man/summary.select.ggm_compare_estimate.Rd |only
 BGGM-1.0.0/BGGM/vignettes/credible_intervals.Rmd           |only
 BGGM-1.0.0/BGGM/vignettes/network_plot_1.Rmd               |only
 BGGM-1.0.0/BGGM/vignettes/ppc1.Rmd                         |only
 BGGM-1.0.0/BGGM/vignettes/predict.Rmd                      |only
 BGGM-2.0.0/BGGM/DESCRIPTION                                |   29 
 BGGM-2.0.0/BGGM/MD5                                        |  352 +
 BGGM-2.0.0/BGGM/NAMESPACE                                  |  208 -
 BGGM-2.0.0/BGGM/NEWS.md                                    |only
 BGGM-2.0.0/BGGM/R/BGGM-package.R                           |only
 BGGM-2.0.0/BGGM/R/RcppExports.R                            |only
 BGGM-2.0.0/BGGM/R/bggm_missing.R                           |only
 BGGM-2.0.0/BGGM/R/coef.estimate.R                          |  499 ++
 BGGM-2.0.0/BGGM/R/confirm.R                                | 1186 +++---
 BGGM-2.0.0/BGGM/R/convergence.R                            |  186 -
 BGGM-2.0.0/BGGM/R/datasets.R                               | 1381 ++++---
 BGGM-2.0.0/BGGM/R/estimate.R                               |  934 +++--
 BGGM-2.0.0/BGGM/R/explore.default.R                        |  917 +++-
 BGGM-2.0.0/BGGM/R/fisher_r2z.R                             |   32 
 BGGM-2.0.0/BGGM/R/fisher_z2r.R                             |   26 
 BGGM-2.0.0/BGGM/R/gen_ordinal.R                            |only
 BGGM-2.0.0/BGGM/R/ggm_compare_bf.default.R                 |  867 +++-
 BGGM-2.0.0/BGGM/R/ggm_compare_confirm.R                    |only
 BGGM-2.0.0/BGGM/R/ggm_compare_estimate.default.R           |  687 ++-
 BGGM-2.0.0/BGGM/R/ggm_compare_ppc.default.R                | 1455 ++++---
 BGGM-2.0.0/BGGM/R/helpers.R                                | 2387 +++++++------
 BGGM-2.0.0/BGGM/R/map.R                                    |   96 
 BGGM-2.0.0/BGGM/R/pcor_2_cor.BGGM.R                        |only
 BGGM-2.0.0/BGGM/R/pcor_mat.R                               |only
 BGGM-2.0.0/BGGM/R/plot.select.R                            |only
 BGGM-2.0.0/BGGM/R/plot_prior.R                             |only
 BGGM-2.0.0/BGGM/R/posterior_samples.R                      |only
 BGGM-2.0.0/BGGM/R/posterior_sum.R                          |only
 BGGM-2.0.0/BGGM/R/predict.estimate.R                       |  445 +-
 BGGM-2.0.0/BGGM/R/predictability.R                         |  622 ++-
 BGGM-2.0.0/BGGM/R/print_BGGM.R                             |only
 BGGM-2.0.0/BGGM/R/regression_summary.R                     |only
 BGGM-2.0.0/BGGM/R/roll_your_own.R                          |only
 BGGM-2.0.0/BGGM/R/select.estimate.R                        |  746 +---
 BGGM-2.0.0/BGGM/R/select.explore.R                         | 2020 +++--------
 BGGM-2.0.0/BGGM/R/select.ggm_compare_bf.R                  |  406 --
 BGGM-2.0.0/BGGM/R/select.ggm_compare_estimate.R            |  430 --
 BGGM-2.0.0/BGGM/R/weighted_adj_mat.R                       |only
 BGGM-2.0.0/BGGM/R/zero_order.R                             |only
 BGGM-2.0.0/BGGM/build/partial.rdb                          |only
 BGGM-2.0.0/BGGM/build/vignette.rds                         |binary
 BGGM-2.0.0/BGGM/cleanup                                    |only
 BGGM-2.0.0/BGGM/configure                                  |only
 BGGM-2.0.0/BGGM/configure.ac                               |only
 BGGM-2.0.0/BGGM/data/Sachs.rda                             |only
 BGGM-2.0.0/BGGM/data/asd_ocd.rda                           |only
 BGGM-2.0.0/BGGM/data/bfi.rda                               |binary
 BGGM-2.0.0/BGGM/data/depression_anxiety_t1.rda             |only
 BGGM-2.0.0/BGGM/data/depression_anxiety_t2.rda             |only
 BGGM-2.0.0/BGGM/data/gss.rda                               |only
 BGGM-2.0.0/BGGM/data/women_math.rda                        |only
 BGGM-2.0.0/BGGM/inst/CITATION                              |only
 BGGM-2.0.0/BGGM/inst/REFERENCES.bib                        |only
 BGGM-2.0.0/BGGM/inst/doc/control.Rmd                       |only
 BGGM-2.0.0/BGGM/inst/doc/control.html                      |only
 BGGM-2.0.0/BGGM/inst/doc/hyp_3_ways.R                      |only
 BGGM-2.0.0/BGGM/inst/doc/hyp_3_ways.Rmd                    |only
 BGGM-2.0.0/BGGM/inst/doc/hyp_3_ways.html                   |only
 BGGM-2.0.0/BGGM/inst/doc/in_tandem.R                       |only
 BGGM-2.0.0/BGGM/inst/doc/in_tandem.Rmd                     |only
 BGGM-2.0.0/BGGM/inst/doc/in_tandem.html                    |only
 BGGM-2.0.0/BGGM/inst/doc/installation.R                    |only
 BGGM-2.0.0/BGGM/inst/doc/installation.Rmd                  |only
 BGGM-2.0.0/BGGM/inst/doc/installation.html                 |only
 BGGM-2.0.0/BGGM/inst/doc/mcmc_diagnostics.R                |only
 BGGM-2.0.0/BGGM/inst/doc/mcmc_diagnostics.Rmd              |only
 BGGM-2.0.0/BGGM/inst/doc/mcmc_diagnostics.html             |only
 BGGM-2.0.0/BGGM/inst/doc/netplot.R                         |only
 BGGM-2.0.0/BGGM/inst/doc/netplot.Rmd                       |only
 BGGM-2.0.0/BGGM/inst/doc/netplot.html                      |only
 BGGM-2.0.0/BGGM/inst/doc/netstat_custom.R                  |only
 BGGM-2.0.0/BGGM/inst/doc/netstat_custom.Rmd                |only
 BGGM-2.0.0/BGGM/inst/doc/netstat_custom.html               |only
 BGGM-2.0.0/BGGM/inst/doc/ppc_custom.R                      |only
 BGGM-2.0.0/BGGM/inst/doc/ppc_custom.Rmd                    |only
 BGGM-2.0.0/BGGM/inst/doc/ppc_custom.html                   |only
 BGGM-2.0.0/BGGM/inst/doc/predictability.R                  |only
 BGGM-2.0.0/BGGM/inst/doc/predictability.Rmd                |only
 BGGM-2.0.0/BGGM/inst/doc/predictability.html               |only
 BGGM-2.0.0/BGGM/inst/doc/test_sum.R                        |only
 BGGM-2.0.0/BGGM/inst/doc/test_sum.Rmd                      |only
 BGGM-2.0.0/BGGM/inst/doc/test_sum.html                     |only
 BGGM-2.0.0/BGGM/man/BGGM-package.Rd                        |only
 BGGM-2.0.0/BGGM/man/Sachs.Rd                               |only
 BGGM-2.0.0/BGGM/man/asd_ocd.Rd                             |only
 BGGM-2.0.0/BGGM/man/bfi.Rd                                 |   16 
 BGGM-2.0.0/BGGM/man/bggm_missing.Rd                        |only
 BGGM-2.0.0/BGGM/man/coef.estimate.Rd                       |   66 
 BGGM-2.0.0/BGGM/man/coef.explore.Rd                        |only
 BGGM-2.0.0/BGGM/man/confirm.Rd                             |  240 +
 BGGM-2.0.0/BGGM/man/convergence.Rd                         |   48 
 BGGM-2.0.0/BGGM/man/csws.Rd                                |   26 
 BGGM-2.0.0/BGGM/man/depression_anxiety_t1.Rd               |only
 BGGM-2.0.0/BGGM/man/depression_anxiety_t2.Rd               |only
 BGGM-2.0.0/BGGM/man/estimate.Rd                            |  217 -
 BGGM-2.0.0/BGGM/man/explore.Rd                             |  183 
 BGGM-2.0.0/BGGM/man/figures/acf.png                        |only
 BGGM-2.0.0/BGGM/man/figures/acf_new.png                    |only
 BGGM-2.0.0/BGGM/man/figures/acf_new2.png                   |only
 BGGM-2.0.0/BGGM/man/figures/acf_problem.png                |only
 BGGM-2.0.0/BGGM/man/figures/binary_r2_error.png            |only
 BGGM-2.0.0/BGGM/man/figures/binary_r2_ridge.png            |only
 BGGM-2.0.0/BGGM/man/figures/hyp_3ways_hist.png             |only
 BGGM-2.0.0/BGGM/man/figures/hyp_3ways_pie.png              |only
 BGGM-2.0.0/BGGM/man/figures/hyp_3ways_ppc.png              |only
 BGGM-2.0.0/BGGM/man/figures/hyp_plot.png                   |only
 BGGM-2.0.0/BGGM/man/figures/index_hist.png                 |only
 BGGM-2.0.0/BGGM/man/figures/index_summ.png                 |only
 BGGM-2.0.0/BGGM/man/figures/logo.png                       |only
 BGGM-2.0.0/BGGM/man/figures/netplot_1.png                  |only
 BGGM-2.0.0/BGGM/man/figures/netplot_2.png                  |only
 BGGM-2.0.0/BGGM/man/figures/netplot_3.png                  |only
 BGGM-2.0.0/BGGM/man/figures/netplot_index.png              |only
 BGGM-2.0.0/BGGM/man/figures/netstat_assort.png             |only
 BGGM-2.0.0/BGGM/man/figures/netstat_bridge.png             |only
 BGGM-2.0.0/BGGM/man/figures/netstat_ridge.png              |only
 BGGM-2.0.0/BGGM/man/figures/ordinal_r2_error.png           |only
 BGGM-2.0.0/BGGM/man/figures/test_sum_hist.png              |only
 BGGM-2.0.0/BGGM/man/figures/trace.png                      |only
 BGGM-2.0.0/BGGM/man/fisher_r_to_z.Rd                       |only
 BGGM-2.0.0/BGGM/man/fisher_z_to_r.Rd                       |only
 BGGM-2.0.0/BGGM/man/gen_ordinal.Rd                         |only
 BGGM-2.0.0/BGGM/man/ggm_compare_confirm.Rd                 |only
 BGGM-2.0.0/BGGM/man/ggm_compare_estimate.Rd                |  191 +
 BGGM-2.0.0/BGGM/man/ggm_compare_explore.Rd                 |only
 BGGM-2.0.0/BGGM/man/ggm_compare_ppc.Rd                     |only
 BGGM-2.0.0/BGGM/man/gss.Rd                                 |only
 BGGM-2.0.0/BGGM/man/iri.Rd                                 |    6 
 BGGM-2.0.0/BGGM/man/map.Rd                                 |    6 
 BGGM-2.0.0/BGGM/man/pcor_mat.Rd                            |only
 BGGM-2.0.0/BGGM/man/pcor_sum.Rd                            |only
 BGGM-2.0.0/BGGM/man/pcor_to_cor.Rd                         |only
 BGGM-2.0.0/BGGM/man/plot.confirm.Rd                        |only
 BGGM-2.0.0/BGGM/man/plot.ggm_compare_ppc.Rd                |   68 
 BGGM-2.0.0/BGGM/man/plot.pcor_sum.Rd                       |only
 BGGM-2.0.0/BGGM/man/plot.predictability.Rd                 |only
 BGGM-2.0.0/BGGM/man/plot.roll_your_own.Rd                  |only
 BGGM-2.0.0/BGGM/man/plot.select.Rd                         |only
 BGGM-2.0.0/BGGM/man/plot.summary.estimate.Rd               |   36 
 BGGM-2.0.0/BGGM/man/plot.summary.explore.Rd                |   38 
 BGGM-2.0.0/BGGM/man/plot.summary.ggm_compare_estimate.Rd   |only
 BGGM-2.0.0/BGGM/man/plot.summary.ggm_compare_explore.Rd    |only
 BGGM-2.0.0/BGGM/man/plot.summary.select.explore.Rd         |only
 BGGM-2.0.0/BGGM/man/plot_prior.Rd                          |only
 BGGM-2.0.0/BGGM/man/posterior_samples.Rd                   |only
 BGGM-2.0.0/BGGM/man/predict.estimate.Rd                    |   36 
 BGGM-2.0.0/BGGM/man/predict.explore.Rd                     |only
 BGGM-2.0.0/BGGM/man/predictability.Rd                      |only
 BGGM-2.0.0/BGGM/man/print.BGGM.Rd                          |only
 BGGM-2.0.0/BGGM/man/ptsd.Rd                                |   12 
 BGGM-2.0.0/BGGM/man/ptsd_cor1.Rd                           |   23 
 BGGM-2.0.0/BGGM/man/ptsd_cor2.Rd                           |   20 
 BGGM-2.0.0/BGGM/man/ptsd_cor3.Rd                           |   22 
 BGGM-2.0.0/BGGM/man/ptsd_cor4.Rd                           |   21 
 BGGM-2.0.0/BGGM/man/regression_summary.Rd                  |only
 BGGM-2.0.0/BGGM/man/roll_your_own.Rd                       |only
 BGGM-2.0.0/BGGM/man/rsa.Rd                                 |    6 
 BGGM-2.0.0/BGGM/man/select.Rd                              |    4 
 BGGM-2.0.0/BGGM/man/select.estimate.Rd                     |   97 
 BGGM-2.0.0/BGGM/man/select.explore.Rd                      |  156 
 BGGM-2.0.0/BGGM/man/select.ggm_compare_estimate.Rd         |   79 
 BGGM-2.0.0/BGGM/man/select.ggm_compare_explore.Rd          |only
 BGGM-2.0.0/BGGM/man/summary.coef.Rd                        |only
 BGGM-2.0.0/BGGM/man/summary.estimate.Rd                    |   33 
 BGGM-2.0.0/BGGM/man/summary.explore.Rd                     |   35 
 BGGM-2.0.0/BGGM/man/summary.ggm_compare_estimate.Rd        |   44 
 BGGM-2.0.0/BGGM/man/summary.ggm_compare_explore.Rd         |only
 BGGM-2.0.0/BGGM/man/summary.predictability.Rd              |only
 BGGM-2.0.0/BGGM/man/summary.select.explore.Rd              |   38 
 BGGM-2.0.0/BGGM/man/tas.Rd                                 |    6 
 BGGM-2.0.0/BGGM/man/weighted_adj_mat.Rd                    |only
 BGGM-2.0.0/BGGM/man/women_math.Rd                          |only
 BGGM-2.0.0/BGGM/man/zero_order_cors.Rd                     |only
 BGGM-2.0.0/BGGM/src                                        |only
 BGGM-2.0.0/BGGM/vignettes/control.Rmd                      |only
 BGGM-2.0.0/BGGM/vignettes/hyp_3_ways.Rmd                   |only
 BGGM-2.0.0/BGGM/vignettes/in_tandem.Rmd                    |only
 BGGM-2.0.0/BGGM/vignettes/installation.Rmd                 |only
 BGGM-2.0.0/BGGM/vignettes/mcmc_diagnostics.Rmd             |only
 BGGM-2.0.0/BGGM/vignettes/netplot.Rmd                      |only
 BGGM-2.0.0/BGGM/vignettes/netstat_custom.Rmd               |only
 BGGM-2.0.0/BGGM/vignettes/netstat_fit.rda                  |only
 BGGM-2.0.0/BGGM/vignettes/ppc_custom.Rmd                   |only
 BGGM-2.0.0/BGGM/vignettes/predictability.Rmd               |only
 BGGM-2.0.0/BGGM/vignettes/test_sum.Rmd                     |only
 298 files changed, 10398 insertions(+), 7286 deletions(-)

More information about BGGM at CRAN
Permanent link

Package sars updated to version 1.2.3 with previous version 1.2.1 dated 2020-01-07

Title: Fit and Compare Species-Area Relationship Models Using Multimodel Inference
Description: Implements the basic elements of the multi-model inference paradigm for up to twenty species-area relationship models (SAR), using simple R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>. The package is scalable and users can easily create their own model and data objects. Additional SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] (<https://orcid.org/0000-0002-7624-244X>), Francois Guilhaumon [aut] (<https://orcid.org/0000-0003-4707-8932>), Kevin Cazelles [rev] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Thomas J. Matthews <txm676@gmail.com>

Diff between sars versions 1.2.1 dated 2020-01-07 and 1.2.3 dated 2020-05-31

 DESCRIPTION                              |    8 
 MD5                                      |  182 ++++-----
 NAMESPACE                                |    2 
 NEWS.md                                  |   18 
 R/class_plot.R                           |  102 ++++-
 R/class_print.R                          |   28 -
 R/class_summary.R                        |   12 
 R/data_aegean.R                          |   13 
 R/data_coleman.R                         |    2 
 R/data_galap.R                           |   15 
 R/data_niering.R                         |   15 
 R/obs_shape.R                            |   16 
 R/optim.R                                |  200 +++++++---
 R/sar_asymp.R                            |   30 -
 R/sar_average.R                          |  199 +++++++---
 R/sar_betap.R                            |   28 -
 R/sar_chapman.R                          |   28 -
 R/sar_conf_int.R                         |   91 ++--
 R/sar_epm1.R                             |   28 -
 R/sar_epm2.R                             |   28 -
 R/sar_gompertz.R                         |   28 -
 R/sar_heleg.R                            |   28 -
 R/sar_koba.R                             |   28 -
 R/sar_linear.R                           |    7 
 R/sar_loga.R                             |   28 -
 R/sar_mmf.R                              |   28 -
 R/sar_monod.R                            |   28 -
 R/sar_negexpo.R                          |   30 -
 R/sar_p1.R                               |   28 -
 R/sar_p2.R                               |   28 -
 R/sar_power.R                            |   28 -
 R/sar_powerR.R                           |   28 -
 R/sar_ratio.R                            |   28 -
 R/sar_weibull3.R                         |   28 -
 R/sar_weibull4.R                         |   28 -
 README.md                                |  141 +++++--
 inst/CITATION                            |    6 
 inst/doc/sars-r-package.R                |   13 
 inst/doc/sars-r-package.Rmd              |   85 +++-
 inst/doc/sars-r-package.html             |  602 +++++++++++++++++++++----------
 inst/model_factory.R                     |   44 +-
 inst/non_lin_models/Mod_asymp.R          |    2 
 inst/non_lin_models/Mod_negexpo.R        |    2 
 man/aegean.Rd                            |   53 +-
 man/cole_sim.Rd                          |   46 +-
 man/coleman.Rd                           |  108 ++---
 man/display_sars_models.Rd               |   40 +-
 man/figures/README-unnamed-chunk-5-1.png |binary
 man/galap.Rd                             |   55 +-
 man/gdm.Rd                               |  216 +++++------
 man/lin_pow.Rd                           |  140 +++----
 man/niering.Rd                           |   51 +-
 man/plot.coleman.Rd                      |  151 ++++---
 man/plot.multi.Rd                        |  329 +++++++++-------
 man/plot.sars.Rd                         |  206 +++++-----
 man/sar_asymp.Rd                         |  170 ++++----
 man/sar_average.Rd                       |  348 +++++++++--------
 man/sar_betap.Rd                         |  170 ++++----
 man/sar_chapman.Rd                       |  170 ++++----
 man/sar_epm1.Rd                          |  170 ++++----
 man/sar_epm2.Rd                          |  170 ++++----
 man/sar_gompertz.Rd                      |  170 ++++----
 man/sar_heleg.Rd                         |  170 ++++----
 man/sar_koba.Rd                          |  170 ++++----
 man/sar_linear.Rd                        |  128 +++---
 man/sar_loga.Rd                          |  170 ++++----
 man/sar_mmf.Rd                           |  170 ++++----
 man/sar_monod.Rd                         |  170 ++++----
 man/sar_multi.Rd                         |  120 +++---
 man/sar_negexpo.Rd                       |  170 ++++----
 man/sar_p1.Rd                            |  170 ++++----
 man/sar_p2.Rd                            |  170 ++++----
 man/sar_power.Rd                         |  170 ++++----
 man/sar_powerR.Rd                        |  170 ++++----
 man/sar_pred.Rd                          |  130 +++---
 man/sar_ratio.Rd                         |  170 ++++----
 man/sar_weibull3.Rd                      |  170 ++++----
 man/sar_weibull4.Rd                      |  170 ++++----
 man/sars-package.Rd                      |  160 ++++----
 man/sars_models.Rd                       |   28 -
 man/summary.sars.Rd                      |  128 +++---
 tests/testthat/test_crit_method.R        |only
 tests/testthat/test_grid_start.R         |only
 tests/testthat/test_loga.R               |    2 
 tests/testthat/test_monod.R              |    2 
 tests/testthat/test_multi.R              |   16 
 tests/testthat/test_p2.R                 |    2 
 tests/testthat/test_power.R              |   14 
 tests/testthat/test_pred.R               |    4 
 tests/testthat/test_sar_linear.R         |    2 
 tests/testthat/test_shape.R              |    4 
 tests/testthat/test_weibull3.R           |    2 
 vignettes/sars-r-package.Rmd             |   85 +++-
 93 files changed, 4540 insertions(+), 3601 deletions(-)

More information about sars at CRAN
Permanent link

Package lessR updated to version 3.9.5 with previous version 3.9.4 dated 2020-05-07

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

Diff between lessR versions 3.9.4 dated 2020-05-07 and 3.9.5 dated 2020-05-31

 lessR-3.9.4/lessR/R/av.brief.R             |only
 lessR-3.9.4/lessR/R/cr.brief.R             |only
 lessR-3.9.4/lessR/R/rd.brief.R             |only
 lessR-3.9.4/lessR/R/rd_brief.R             |only
 lessR-3.9.4/lessR/inst/doc/getColors.R     |only
 lessR-3.9.4/lessR/inst/doc/getColors.Rmd   |only
 lessR-3.9.4/lessR/inst/doc/getColors.html  |only
 lessR-3.9.4/lessR/vignettes/getColors.Rmd  |only
 lessR-3.9.5/lessR/DESCRIPTION              |    8 
 lessR-3.9.5/lessR/MD5                      |  122 +--
 lessR-3.9.5/lessR/NAMESPACE                |    6 
 lessR-3.9.5/lessR/NEWS                     |   37 +
 lessR-3.9.5/lessR/R/BarChart.R             |    2 
 lessR-3.9.5/lessR/R/Help.R                 | 1073 -----------------------------
 lessR-3.9.5/lessR/R/Histogram.R            |   31 
 lessR-3.9.5/lessR/R/Plot.R                 |   53 -
 lessR-3.9.5/lessR/R/SummaryStats.R         |   18 
 lessR-3.9.5/lessR/R/bc.zmain.R             |    4 
 lessR-3.9.5/lessR/R/cr.zmain.R             |   35 
 lessR-3.9.5/lessR/R/dn.zmain.R             |    3 
 lessR-3.9.5/lessR/R/plt.zmain.R            |    2 
 lessR-3.9.5/lessR/R/plt.ztxt.R             |   21 
 lessR-3.9.5/lessR/R/style.R                |    4 
 lessR-3.9.5/lessR/R/style.zshow.R          |    2 
 lessR-3.9.5/lessR/R/ttest.R                |    2 
 lessR-3.9.5/lessR/R/zzz.R                  |   36 
 lessR-3.9.5/lessR/build/vignette.rds       |binary
 lessR-3.9.5/lessR/inst/doc/BarChart.R      |   17 
 lessR-3.9.5/lessR/inst/doc/BarChart.Rmd    |   71 +
 lessR-3.9.5/lessR/inst/doc/BarChart.html   |  197 +++--
 lessR-3.9.5/lessR/inst/doc/Customize.R     |only
 lessR-3.9.5/lessR/inst/doc/Customize.Rmd   |only
 lessR-3.9.5/lessR/inst/doc/Customize.html  |only
 lessR-3.9.5/lessR/inst/doc/Data.R          |only
 lessR-3.9.5/lessR/inst/doc/Data.Rmd        |only
 lessR-3.9.5/lessR/inst/doc/Data.html       |only
 lessR-3.9.5/lessR/inst/doc/Extract.Rmd     |   22 
 lessR-3.9.5/lessR/inst/doc/Extract.html    |   99 +-
 lessR-3.9.5/lessR/inst/doc/Histogram.Rmd   |   13 
 lessR-3.9.5/lessR/inst/doc/Histogram.html  |   64 -
 lessR-3.9.5/lessR/inst/doc/Means.R         |only
 lessR-3.9.5/lessR/inst/doc/Means.Rmd       |only
 lessR-3.9.5/lessR/inst/doc/Means.html      |only
 lessR-3.9.5/lessR/inst/doc/Plot.R          |   32 
 lessR-3.9.5/lessR/inst/doc/Plot.Rmd        |   69 +
 lessR-3.9.5/lessR/inst/doc/Plot.html       |  235 ++++--
 lessR-3.9.5/lessR/inst/doc/Regression.R    |only
 lessR-3.9.5/lessR/inst/doc/Regression.Rmd  |only
 lessR-3.9.5/lessR/inst/doc/Regression.html |only
 lessR-3.9.5/lessR/inst/doc/pivot.Rmd       |   14 
 lessR-3.9.5/lessR/inst/doc/pivot.html      |   67 -
 lessR-3.9.5/lessR/inst/img/DataExcel.png   |binary
 lessR-3.9.5/lessR/man/ANOVA.Rd             |   33 
 lessR-3.9.5/lessR/man/BarChart.Rd          |    6 
 lessR-3.9.5/lessR/man/Correlation.Rd       |    4 
 lessR-3.9.5/lessR/man/Help.Rd              |  101 --
 lessR-3.9.5/lessR/man/Histogram.Rd         |   10 
 lessR-3.9.5/lessR/man/PieChart.Rd          |    3 
 lessR-3.9.5/lessR/man/Plot.Rd              |    4 
 lessR-3.9.5/lessR/man/Read.Rd              |   16 
 lessR-3.9.5/lessR/man/SummaryStats.Rd      |   17 
 lessR-3.9.5/lessR/man/Write.Rd             |    8 
 lessR-3.9.5/lessR/man/getColors.Rd         |    4 
 lessR-3.9.5/lessR/man/style.Rd             |    2 
 lessR-3.9.5/lessR/man/ttest.Rd             |    6 
 lessR-3.9.5/lessR/vignettes/BarChart.Rmd   |   71 +
 lessR-3.9.5/lessR/vignettes/Customize.Rmd  |only
 lessR-3.9.5/lessR/vignettes/Data.Rmd       |only
 lessR-3.9.5/lessR/vignettes/Extract.Rmd    |   22 
 lessR-3.9.5/lessR/vignettes/Histogram.Rmd  |   13 
 lessR-3.9.5/lessR/vignettes/Means.Rmd      |only
 lessR-3.9.5/lessR/vignettes/Plot.Rmd       |   69 +
 lessR-3.9.5/lessR/vignettes/Regression.Rmd |only
 lessR-3.9.5/lessR/vignettes/pivot.Rmd      |   14 
 74 files changed, 1070 insertions(+), 1692 deletions(-)

More information about lessR at CRAN
Permanent link

Package smoothedLasso updated to version 1.1 with previous version 1.0 dated 2020-04-03

Title: Smoothed LASSO Regression via Nesterov Smoothing
Description: We provide full functionality to compute smoothed LASSO regression estimates. For this, the LASSO objective function is first smoothed using Nesterov smoothing (see Y. Nesterov (2005) <doi:10.1007/s10107-004-0552-5>), resulting in a modified LASSO objective function with explicit gradients everywhere. The smoothed objective function and its gradient are used to minimize it via BFGS, and the obtained minimizer is returned. Using Nesterov smoothing, the smoothed LASSO objective function can be made arbitrarily close to the original (unsmoothed) one. In particular, the Nesterov approach has the advantage that it comes with explicit accuracy bounds, both on the L1/L2 difference of the unsmoothed to the smoothed LASSO objective function as well as on their respective minimizers. A progressive smoothing approach is provided which iteratively smoothes the LASSO, resulting in more stable regression estimates.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Nilanjana Laha [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>

Diff between smoothedLasso versions 1.0 dated 2020-04-03 and 1.1 dated 2020-05-31

 DESCRIPTION       |   10 +++++-----
 MD5               |    6 +++---
 NAMESPACE         |    1 +
 R/smoothedLasso.r |    7 ++++---
 4 files changed, 13 insertions(+), 11 deletions(-)

More information about smoothedLasso at CRAN
Permanent link

Package spmoran updated to version 0.2.0-1 with previous version 0.2.0 dated 2020-05-20

Title: Moran Eigenvector-Based Scalable Spatial Additive Mixed Modeling
Description: Functions for estimating Moran eigenvector-based spatial additive mixed models, and other spatial regression models. For details see Murakami (2020) <arXiv:1703.04467>.
Author: Daisuke Murakami
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>

Diff between spmoran versions 0.2.0 dated 2020-05-20 and 0.2.0-1 dated 2020-05-31

 DESCRIPTION                      |    8 +++----
 MD5                              |   41 ++++++++++++++++++++-------------------
 R/plot_qr.R                      |    2 -
 R/resf_qr.R                      |   28 ++++++++++++++++----------
 build/vignette.rds               |binary
 inst/doc/boston_sample.pdf       |only
 inst/doc/boston_sample.pdf.asis  |only
 inst/doc/vignettes.pdf           |binary
 inst/doc/vignettes.pdf.asis      |    6 ++---
 man/besf.Rd                      |    2 -
 man/besf_vc.Rd                   |    2 -
 man/esf.Rd                       |    2 -
 man/lsem.Rd                      |    2 -
 man/lslm.Rd                      |    2 -
 man/plot_qr.Rd                   |    2 -
 man/predict0.Rd                  |    4 +--
 man/predict0_vc.Rd               |    4 +--
 man/resf.Rd                      |    2 -
 man/resf_qr.Rd                   |    2 -
 man/resf_vc.Rd                   |    2 -
 man/weigen.Rd                    |    4 +--
 vignettes/boston_sample.pdf.asis |only
 vignettes/vignettes.pdf.asis     |    6 ++---
 23 files changed, 65 insertions(+), 56 deletions(-)

More information about spmoran at CRAN
Permanent link

Package RDFTensor updated to version 1.2 with previous version 1.1 dated 2019-01-11

Title: Different Tensor Factorization (Decomposition) Techniques for RDF Tensors (Three-Mode-Tensors)
Description: Different Tensor Factorization techniques suitable for RDF Tensors. RDF Tensors are three-mode-tensors, binary tensors and usually very sparse. Currently implemented methods are 'RESCAL' Maximilian Nickel, Volker Tresp, and Hans-Peter Kriegel (2012) <doi:10.1145/2187836.2187874>, 'NMU' Daniel D. Lee and H. Sebastian Seung (1999) <doi:10.1038/44565>, 'ALS', Alternating Least Squares 'parCube' Papalexakis, Evangelos, C. Faloutsos, and N. Sidiropoulos (2012) <doi:10.1007/978-3-642-33460-3_39>, 'CP_APR' C. Chi and T. G. Kolda (2012) <doi.org/10.1137/110859063>. The code is mostly converted from MATLAB and Python implementations of these methods. The package also contains functions to get Boolean (Binary) transformation of the real-number-decompositions. These methods also are for general tensors, so with few modifications they can be applied for other types of tensor.
Author: Abdelmoneim Amer Desouki
Maintainer: Abdelmoneim Amer Desouki <desouki@mail.upb.de>

Diff between RDFTensor versions 1.1 dated 2019-01-11 and 1.2 dated 2020-05-31

 DESCRIPTION                      |   15 ++++++----
 MD5                              |   32 ++++++++++++++++-----
 NAMESPACE                        |   13 ++++++++
 NEWS                             |   11 +++++++
 R/RDF2Tensor.R                   |   58 ++++++++++++++++++++++++++++++++++-----
 R/RescalReconstructBack.R        |only
 R/recon_1prd_topn_par.R          |only
 R/rescal.R                       |   35 +++++++++++------------
 R/rescal_Trp_Val.R               |only
 R/scRescal.R                     |only
 build/partial.rdb                |binary
 build/vignette.rds               |only
 data/umls_tnsr.RData             |binary
 inst/doc                         |only
 man/RescalReconstructBack.Rd     |only
 man/inv_rescal_sf_prd_chnkgrp.Rd |only
 man/recon_1prd_topn_par.Rd       |only
 man/rescal.Rd                    |    2 -
 man/rescal_SO_Val.Rd             |only
 man/rescal_Trp_Val.Rd            |only
 man/scRescal.Rd                  |only
 man/tensor2mat.Rd                |only
 vignettes                        |only
 23 files changed, 125 insertions(+), 41 deletions(-)

More information about RDFTensor at CRAN
Permanent link

Package ggasym updated to version 0.1.4 with previous version 0.1.3 dated 2020-04-03

Title: Asymmetric Matrix Plotting in 'ggplot2'
Description: Plots a symmetric matrix with three different fill aesthetics for the top-left and bottom-right triangles and along the diagonal. It operates within the Grammar of Graphics paradigm implemented in 'ggplot2'.
Author: Joshua H Cook [aut, cre] (<https://orcid.org/0000-0001-9815-6879>)
Maintainer: Joshua H Cook <joshuacook0023@gmail.com>

Diff between ggasym versions 0.1.3 dated 2020-04-03 and 0.1.4 dated 2020-05-31

 DESCRIPTION                                 |    6 +-
 MD5                                         |   26 +++++++-----
 NEWS.md                                     |    4 +
 R/asymmetrise.R                             |    4 -
 R/asymmetrise_stats.R                       |   60 ++++++++++++++++++----------
 R/utils.R                                   |    2 
 build/vignette.rds                          |binary
 inst/doc/ggasym-corrr.html                  |   28 ++++++++-----
 inst/doc/ggasym-stats.html                  |   46 +++++++++++++--------
 man/asymmetrise_stats.Rd                    |   24 ++++++-----
 man/figures/README-adj_colorbars-1.png      |only
 man/figures/README-example1-1.png           |only
 man/figures/README-example2-1.png           |only
 man/figures/README-example3-1.png           |only
 man/figures/README-faceting_plot-1.png      |only
 man/figures/README-stats_example_plot-1.png |only
 tests/testthat/test-asymmetrise_stats.R     |   17 +++++--
 17 files changed, 137 insertions(+), 80 deletions(-)

More information about ggasym at CRAN
Permanent link

Package europepmc updated to version 0.4 with previous version 0.3 dated 2018-04-20

Title: R Interface to the Europe PubMed Central RESTful Web Service
Description: An R Client for the Europe PubMed Central RESTful Web Service (see <https://europepmc.org/RestfulWebService> for more information). It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible. No registration or API key is required. See the vignettes for usage examples.
Author: Najko Jahn [aut, cre, cph], Maëlle Salmon [ctb]
Maintainer: Najko Jahn <najko.jahn@gmail.com>

Diff between europepmc versions 0.3 dated 2018-04-20 and 0.4 dated 2020-05-31

 europepmc-0.3/europepmc/R/epmc_tm.r                              |only
 europepmc-0.3/europepmc/R/epmc_tm_count.r                        |only
 europepmc-0.3/europepmc/inst/image                               |only
 europepmc-0.3/europepmc/inst/imageunnamed-chunk-4-1.png          |only
 europepmc-0.3/europepmc/man/epmc_tm.Rd                           |only
 europepmc-0.3/europepmc/man/epmc_tm_count.Rd                     |only
 europepmc-0.4/europepmc/DESCRIPTION                              |   18 
 europepmc-0.4/europepmc/MD5                                      |  101 -
 europepmc-0.4/europepmc/NAMESPACE                                |   15 
 europepmc-0.4/europepmc/NEWS.md                                  |   20 
 europepmc-0.4/europepmc/R/annotations_by_id.R                    |only
 europepmc-0.4/europepmc/R/defunct.r                              |   12 
 europepmc-0.4/europepmc/R/epmc_citations.r                       |    4 
 europepmc-0.4/europepmc/R/epmc_datalinks.r                       |only
 europepmc-0.4/europepmc/R/epmc_db.r                              |    8 
 europepmc-0.4/europepmc/R/epmc_db_count.r                        |    2 
 europepmc-0.4/europepmc/R/epmc_details.r                         |    9 
 europepmc-0.4/europepmc/R/epmc_ftxt.r                            |   20 
 europepmc-0.4/europepmc/R/epmc_ftxt_book.r                       |    2 
 europepmc-0.4/europepmc/R/epmc_hits_trend.R                      |    5 
 europepmc-0.4/europepmc/R/epmc_lablinks.r                        |    4 
 europepmc-0.4/europepmc/R/epmc_lablinks_count.r                  |    3 
 europepmc-0.4/europepmc/R/epmc_profile.r                         |    2 
 europepmc-0.4/europepmc/R/epmc_refs.r                            |    6 
 europepmc-0.4/europepmc/R/epmc_search.r                          |   13 
 europepmc-0.4/europepmc/R/epmc_search_by_doi.r                   |only
 europepmc-0.4/europepmc/R/europepmc.r                            |   13 
 europepmc-0.4/europepmc/R/utils.r                                |   48 
 europepmc-0.4/europepmc/README.md                                |  117 -
 europepmc-0.4/europepmc/build/vignette.rds                       |binary
 europepmc-0.4/europepmc/inst/doc/evergreenreviewgraphs.R         |   12 
 europepmc-0.4/europepmc/inst/doc/evergreenreviewgraphs.html      |  332 ++--
 europepmc-0.4/europepmc/inst/doc/introducing-europepmc.R         |   41 
 europepmc-0.4/europepmc/inst/doc/introducing-europepmc.Rmd       |   58 
 europepmc-0.4/europepmc/inst/doc/introducing-europepmc.html      |  794 +++++-----
 europepmc-0.4/europepmc/man/epmc_annotations_by_id.Rd            |only
 europepmc-0.4/europepmc/man/epmc_citations.Rd                    |   37 
 europepmc-0.4/europepmc/man/epmc_db.Rd                           |   43 
 europepmc-0.4/europepmc/man/epmc_details.Rd                      |    3 
 europepmc-0.4/europepmc/man/epmc_ftxt.Rd                         |    5 
 europepmc-0.4/europepmc/man/epmc_hits_trend.Rd                   |    6 
 europepmc-0.4/europepmc/man/epmc_lablinks.Rd                     |    9 
 europepmc-0.4/europepmc/man/epmc_refs.Rd                         |   34 
 europepmc-0.4/europepmc/man/epmc_search.Rd                       |   15 
 europepmc-0.4/europepmc/man/epmc_search_.Rd                      |    9 
 europepmc-0.4/europepmc/man/epmc_search_by_doi.Rd                |only
 europepmc-0.4/europepmc/man/epmc_search_by_doi_.Rd               |only
 europepmc-0.4/europepmc/man/europepmc.Rd                         |    7 
 europepmc-0.4/europepmc/man/figures                              |only
 europepmc-0.4/europepmc/tests/testthat/test_annotations_by_id.r  |only
 europepmc-0.4/europepmc/tests/testthat/test_epmc_db.r            |   10 
 europepmc-0.4/europepmc/tests/testthat/test_epmc_details.r       |   14 
 europepmc-0.4/europepmc/tests/testthat/test_epmc_ftxt.r          |    3 
 europepmc-0.4/europepmc/tests/testthat/test_epmc_ftxt_book.r     |   20 
 europepmc-0.4/europepmc/tests/testthat/test_epmc_refs.r          |    4 
 europepmc-0.4/europepmc/tests/testthat/test_epmc_search_by_doi.r |only
 europepmc-0.4/europepmc/tests/testthat/test_epmc_tm.r            |   24 
 europepmc-0.4/europepmc/tests/testthat/test_epmc_tm_count.r      |   15 
 europepmc-0.4/europepmc/vignettes/introducing-europepmc.Rmd      |   58 
 59 files changed, 1032 insertions(+), 943 deletions(-)

More information about europepmc at CRAN
Permanent link

Package TreeBUGS updated to version 1.4.5 with previous version 1.4.4 dated 2019-12-05

Title: Hierarchical Multinomial Processing Tree Modeling
Description: User-friendly analysis of hierarchical multinomial processing tree (MPT) models that are often used in cognitive psychology. Implements the latent-trait MPT approach (Klauer, 2010) <DOI:10.1007/s11336-009-9141-0> and the beta-MPT approach (Smith & Batchelder, 2010) <DOI:10.1016/j.jmp.2009.06.007> to model heterogeneity of participants. MPT models are conveniently specified by an .eqn-file as used by other MPT software and data are provided by a .csv-file or directly in R. Models are either fitted by calling JAGS or by an MPT-tailored Gibbs sampler in C++ (only for nonhierarchical and beta MPT models). Provides tests of heterogeneity and MPT-tailored summaries and plotting functions. A detailed documentation is available in Heck, Arnold, & Arnold (2018) <DOI:10.3758/s13428-017-0869-7>.
Author: Daniel W. Heck [aut, cre] (<https://orcid.org/0000-0002-6302-9252>), Nina R. Arnold [aut, dtc], Denis Arnold [aut], Alexander Ly [ctb], Marius Barth [ctb] (<https://orcid.org/0000-0002-3421-6665>)
Maintainer: Daniel W. Heck <dheck@uni-marburg.de>

Diff between TreeBUGS versions 1.4.4 dated 2019-12-05 and 1.4.5 dated 2020-05-31

 DESCRIPTION                       |   10 ++++-----
 MD5                               |   34 ++++++++++++++++-----------------
 NAMESPACE                         |    2 -
 NEWS                              |    8 +++++++
 R/BFslope.R                       |   23 +++++++++++-----------
 R/covPredictorHandling.R          |   39 +++++++++++++++++++++++++++++++++++++-
 R/fitBetaMPT.R                    |    3 +-
 R/fitTraitMPT.R                   |    7 ++----
 R/plotDistribution.R              |    1 
 R/plotFit.R                       |    7 +++---
 R/posteriorPredictive.R           |   10 +++++++--
 R/transformedParPosthoc.R         |    1 
 build/vignette.rds                |binary
 inst/doc/TreeBUGS_1_intro.html    |   12 ++++-------
 inst/doc/TreeBUGS_2_extended.html |   12 ++++-------
 man/arnold2013.Rd                 |    6 +++--
 man/betaMPT.Rd                    |    3 +-
 man/traitMPT.Rd                   |   12 +++++------
 18 files changed, 120 insertions(+), 70 deletions(-)

More information about TreeBUGS at CRAN
Permanent link

Package timetk updated to version 2.0.0 with previous version 1.0.0 dated 2020-04-19

Title: A Tool Kit for Working with Time Series in R
Description: Easy visualization, wrangling, and preprocessing of time series data for forecasting and machine learning prediction. Methods discussed herein are commonplace in machine learning, and have been cited in various literature. Refer to "Calendar Effects" in papers such as Taieb, Souhaib Ben. "Machine learning strategies for multi-step-ahead time series forecasting." Universit Libre de Bruxelles, Belgium (2014): 75-86. <http://souhaib-bentaieb.com/pdf/2014_phd.pdf>.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

Diff between timetk versions 1.0.0 dated 2020-04-19 and 2.0.0 dated 2020-05-31

 timetk-1.0.0/timetk/R/augment-tk_augment_roll_apply.R                           |only
 timetk-1.0.0/timetk/R/diagnostics-tk_time_series_cv_plan.R                      |only
 timetk-1.0.0/timetk/R/plot-time_series_cv_plan.R                                |only
 timetk-1.0.0/timetk/R/recipes-step_impute_ts.R                                  |only
 timetk-1.0.0/timetk/R/recipes-step_roll_apply.R                                 |only
 timetk-1.0.0/timetk/R/vec-impute_ts.R                                           |only
 timetk-1.0.0/timetk/R/vec-roll-apply.R                                          |only
 timetk-1.0.0/timetk/man/impute_ts_vec.Rd                                        |only
 timetk-1.0.0/timetk/man/roll_apply_vec.Rd                                       |only
 timetk-1.0.0/timetk/man/step_impute_ts.Rd                                       |only
 timetk-1.0.0/timetk/man/step_roll_apply.Rd                                      |only
 timetk-1.0.0/timetk/man/tk_augment_roll_apply.Rd                                |only
 timetk-1.0.0/timetk/tests/testthat/test_recipes-step_timeseries_signature.R     |only
 timetk-1.0.0/timetk/tests/testthat/test_tk_augment_timeseries.R                 |only
 timetk-1.0.0/timetk/tests/testthat/test_tk_get_timeseries.R                     |only
 timetk-1.0.0/timetk/tests/testthat/test_tk_index.R                              |only
 timetk-1.0.0/timetk/tests/testthat/test_tk_make_future_timeseries.R             |only
 timetk-1.0.0/timetk/tests/testthat/test_tk_tbl.R                                |only
 timetk-1.0.0/timetk/tests/testthat/test_tk_ts.R                                 |only
 timetk-1.0.0/timetk/tests/testthat/test_tk_xts.R                                |only
 timetk-1.0.0/timetk/tests/testthat/test_tk_zoo.R                                |only
 timetk-1.0.0/timetk/tests/testthat/test_tk_zooreg.R                             |only
 timetk-2.0.0/timetk/DESCRIPTION                                                 |   18 
 timetk-2.0.0/timetk/MD5                                                         |  225 +--
 timetk-2.0.0/timetk/NAMESPACE                                                   |   61 
 timetk-2.0.0/timetk/NEWS.md                                                     |   95 +
 timetk-2.0.0/timetk/R/00_global_vars.R                                          |    7 
 timetk-2.0.0/timetk/R/augment-tk_augment_differences.R                          |    3 
 timetk-2.0.0/timetk/R/augment-tk_augment_fourier.R                              |    2 
 timetk-2.0.0/timetk/R/augment-tk_augment_holiday_signature.R                    |    2 
 timetk-2.0.0/timetk/R/augment-tk_augment_lags.R                                 |    2 
 timetk-2.0.0/timetk/R/augment-tk_augment_slidify.R                              |only
 timetk-2.0.0/timetk/R/augment-tk_augment_timeseries.R                           |    2 
 timetk-2.0.0/timetk/R/diagnostics-tk_acf_diagnostics.R                          |   59 
 timetk-2.0.0/timetk/R/diagnostics-tk_anomaly_diagnostics.R                      |only
 timetk-2.0.0/timetk/R/diagnostics-tk_stl_diagnostics.R                          |    1 
 timetk-2.0.0/timetk/R/dplyr-future_frame.R                                      |only
 timetk-2.0.0/timetk/R/dplyr-pad_by_time.R                                       |   41 
 timetk-2.0.0/timetk/R/dplyr-slidify.R                                           |    8 
 timetk-2.0.0/timetk/R/get-tk_get_timeseries.R                                   |   13 
 timetk-2.0.0/timetk/R/index-tk_index.R                                          |   46 
 timetk-2.0.0/timetk/R/lubridate-date_parsers.R                                  |only
 timetk-2.0.0/timetk/R/make-tk_make_timeseries.R                                 |   15 
 timetk-2.0.0/timetk/R/make-tk_make_timeseries_future.R                          |  626 +++++++---
 timetk-2.0.0/timetk/R/plot-acf_diagnostics.R                                    |   43 
 timetk-2.0.0/timetk/R/plot-anomaly_diagnostics.R                                |only
 timetk-2.0.0/timetk/R/plot-seasonal_diagnostics.R                               |    4 
 timetk-2.0.0/timetk/R/plot-stl_diagnostics.R                                    |    2 
 timetk-2.0.0/timetk/R/plot-time_series.R                                        |    7 
 timetk-2.0.0/timetk/R/recipes-step_box_cox.R                                    |    6 
 timetk-2.0.0/timetk/R/recipes-step_diff.R                                       |   12 
 timetk-2.0.0/timetk/R/recipes-step_fourier.R                                    |    5 
 timetk-2.0.0/timetk/R/recipes-step_holiday_signature.R                          |    5 
 timetk-2.0.0/timetk/R/recipes-step_slidify.R                                    |only
 timetk-2.0.0/timetk/R/recipes-step_smooth.R                                     |   16 
 timetk-2.0.0/timetk/R/recipes-step_timeseries_signature.R                       |    5 
 timetk-2.0.0/timetk/R/recipes-step_ts_clean.R                                   |only
 timetk-2.0.0/timetk/R/recipes-step_ts_impute.R                                  |only
 timetk-2.0.0/timetk/R/recipes-step_ts_pad.R                                     |only
 timetk-2.0.0/timetk/R/rsample-plot_time_series_cv_plan.R                        |only
 timetk-2.0.0/timetk/R/rsample-time_series_cv.R                                  |  165 +-
 timetk-2.0.0/timetk/R/rsample-tk_time_series_cv_plan.R                          |only
 timetk-2.0.0/timetk/R/utils-dates.R                                             |   15 
 timetk-2.0.0/timetk/R/vec-box_cox.R                                             |    4 
 timetk-2.0.0/timetk/R/vec-diff.R                                                |   50 
 timetk-2.0.0/timetk/R/vec-fourier.R                                             |    4 
 timetk-2.0.0/timetk/R/vec-lag.R                                                 |   10 
 timetk-2.0.0/timetk/R/vec-normalize.R                                           |only
 timetk-2.0.0/timetk/R/vec-slidify.R                                             |only
 timetk-2.0.0/timetk/R/vec-smooth.R                                              |    8 
 timetk-2.0.0/timetk/R/vec-standardize.R                                         |only
 timetk-2.0.0/timetk/R/vec-ts_clean.R                                            |only
 timetk-2.0.0/timetk/R/vec-ts_impute.R                                           |only
 timetk-2.0.0/timetk/README.md                                                   |   43 
 timetk-2.0.0/timetk/inst/doc/TK03_Forecasting_Using_Time_Series_Signature.R     |    2 
 timetk-2.0.0/timetk/inst/doc/TK03_Forecasting_Using_Time_Series_Signature.Rmd   |    2 
 timetk-2.0.0/timetk/inst/doc/TK03_Forecasting_Using_Time_Series_Signature.html  |   12 
 timetk-2.0.0/timetk/inst/doc/TK04_Plotting_Time_Series.R                        |   11 
 timetk-2.0.0/timetk/inst/doc/TK04_Plotting_Time_Series.Rmd                      |   23 
 timetk-2.0.0/timetk/inst/doc/TK04_Plotting_Time_Series.html                     |  100 -
 timetk-2.0.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.R        |    4 
 timetk-2.0.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.Rmd      |    4 
 timetk-2.0.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.html     |    4 
 timetk-2.0.0/timetk/inst/doc/TK07_Time_Series_Data_Wrangling.R                  |    6 
 timetk-2.0.0/timetk/inst/doc/TK07_Time_Series_Data_Wrangling.Rmd                |   12 
 timetk-2.0.0/timetk/inst/doc/TK07_Time_Series_Data_Wrangling.html               |   16 
 timetk-2.0.0/timetk/man/box_cox_vec.Rd                                          |    4 
 timetk-2.0.0/timetk/man/diff_vec.Rd                                             |   30 
 timetk-2.0.0/timetk/man/figures/README-unnamed-chunk-4-1.png                    |binary
 timetk-2.0.0/timetk/man/figures/README-unnamed-chunk-5-1.png                    |binary
 timetk-2.0.0/timetk/man/figures/README-unnamed-chunk-6-1.png                    |only
 timetk-2.0.0/timetk/man/fourier_vec.Rd                                          |    4 
 timetk-2.0.0/timetk/man/future_frame.Rd                                         |only
 timetk-2.0.0/timetk/man/is_date_class.Rd                                        |only
 timetk-2.0.0/timetk/man/lag_vec.Rd                                              |   12 
 timetk-2.0.0/timetk/man/normalize_vec.Rd                                        |only
 timetk-2.0.0/timetk/man/pad_by_time.Rd                                          |    6 
 timetk-2.0.0/timetk/man/parse_date2.Rd                                          |only
 timetk-2.0.0/timetk/man/plot_acf_diagnostics.Rd                                 |   27 
 timetk-2.0.0/timetk/man/plot_anomaly_diagnostics.Rd                             |only
 timetk-2.0.0/timetk/man/plot_time_series_cv_plan.Rd                             |   20 
 timetk-2.0.0/timetk/man/slidify.Rd                                              |    8 
 timetk-2.0.0/timetk/man/slidify_vec.Rd                                          |only
 timetk-2.0.0/timetk/man/smooth_vec.Rd                                           |    8 
 timetk-2.0.0/timetk/man/standardize_vec.Rd                                      |only
 timetk-2.0.0/timetk/man/step_box_cox.Rd                                         |    5 
 timetk-2.0.0/timetk/man/step_diff.Rd                                            |    5 
 timetk-2.0.0/timetk/man/step_fourier.Rd                                         |    5 
 timetk-2.0.0/timetk/man/step_holiday_signature.Rd                               |    5 
 timetk-2.0.0/timetk/man/step_slidify.Rd                                         |only
 timetk-2.0.0/timetk/man/step_smooth.Rd                                          |   14 
 timetk-2.0.0/timetk/man/step_timeseries_signature.Rd                            |    5 
 timetk-2.0.0/timetk/man/step_ts_clean.Rd                                        |only
 timetk-2.0.0/timetk/man/step_ts_impute.Rd                                       |only
 timetk-2.0.0/timetk/man/step_ts_pad.Rd                                          |only
 timetk-2.0.0/timetk/man/time_series_cv.Rd                                       |   92 -
 timetk-2.0.0/timetk/man/tk_acf_diagnostics.Rd                                   |   15 
 timetk-2.0.0/timetk/man/tk_anomaly_diagnostics.Rd                               |only
 timetk-2.0.0/timetk/man/tk_augment_differences.Rd                               |    2 
 timetk-2.0.0/timetk/man/tk_augment_fourier.Rd                                   |    2 
 timetk-2.0.0/timetk/man/tk_augment_holiday.Rd                                   |    2 
 timetk-2.0.0/timetk/man/tk_augment_lags.Rd                                      |    2 
 timetk-2.0.0/timetk/man/tk_augment_slidify.Rd                                   |only
 timetk-2.0.0/timetk/man/tk_augment_timeseries.Rd                                |    2 
 timetk-2.0.0/timetk/man/tk_make_future_timeseries.Rd                            |   55 
 timetk-2.0.0/timetk/man/tk_stl_diagnostics.Rd                                   |   10 
 timetk-2.0.0/timetk/man/tk_time_series_cv_plan.Rd                               |    6 
 timetk-2.0.0/timetk/man/ts_clean_vec.Rd                                         |only
 timetk-2.0.0/timetk/man/ts_impute_vec.Rd                                        |only
 timetk-2.0.0/timetk/tests/testthat/test-recipes-step_timeseries_signature.R     |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_augment_timeseries.R                 |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_get_timeseries.R                     |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_index.R                              |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_make_timeseries.R                    |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_make_timeseries_future-OLD.R         |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_make_timeseries_future.R             |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_tbl.R                                |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_ts.R                                 |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_xts.R                                |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_zoo.R                                |only
 timetk-2.0.0/timetk/tests/testthat/test-tk_zooreg.R                             |only
 timetk-2.0.0/timetk/vignettes/TK03_Forecasting_Using_Time_Series_Signature.Rmd  |    2 
 timetk-2.0.0/timetk/vignettes/TK04_Plotting_Time_Series.Rmd                     |   23 
 timetk-2.0.0/timetk/vignettes/TK05_Plotting_Seasonality_and_Correlation.Rmd     |    4 
 timetk-2.0.0/timetk/vignettes/TK07_Time_Series_Data_Wrangling.Rmd               |   12 
 timetk-2.0.0/timetk/vignettes/temp_archive/TK02_Time_Series_Date_Sequences.Rmd  |    4 
 timetk-2.0.0/timetk/vignettes/temp_archive/TK08_Automatic_Anomaly_Detection.Rmd |only
 147 files changed, 1405 insertions(+), 812 deletions(-)

More information about timetk at CRAN
Permanent link

Package taxlist updated to version 0.1.9 with previous version 0.1.8 dated 2020-04-29

Title: Handling Taxonomic Lists
Description: Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.
Author: Miguel Alvarez [aut, cre] (<https://orcid.org/0000-0003-1500-1834>), Zachary Foster [ctb] (<https://orcid.org/0000-0002-5075-0948>)
Maintainer: Miguel Alvarez <kamapu78@gmail.com>

Diff between taxlist versions 0.1.8 dated 2020-04-29 and 0.1.9 dated 2020-05-31

 DESCRIPTION                 |    6 +++---
 MD5                         |   10 +++++-----
 NEWS.md                     |   10 +++++++++-
 R/taxlist-class.R           |    3 ++-
 data/Easplist.rda           |binary
 inst/doc/taxlist-intro.html |   16 ++++++++--------
 6 files changed, 27 insertions(+), 18 deletions(-)

More information about taxlist at CRAN
Permanent link

Package rmarkdown updated to version 2.2 with previous version 2.1 dated 2020-01-20

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Andrew Dunning [ctb] (<https://orcid.org/0000-0003-0464-5036>), Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Barret Schloerke [ctb], Christophe Dervieux [ctb], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Jeff Allen [ctb], JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], RStudio, PBC [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak lua filter), Albert Krewinkel [ctb, cph] (pagebreak lua filter)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between rmarkdown versions 2.1 dated 2020-01-20 and 2.2 dated 2020-05-31

 DESCRIPTION                              |   14 ++--
 MD5                                      |   99 ++++++++++++++++---------------
 NAMESPACE                                |    2 
 NEWS.md                                  |   32 ++++++++++
 R/beamer_presentation.R                  |    5 -
 R/context_document.R                     |    3 
 R/html_document.R                        |    8 --
 R/html_document_base.R                   |   11 +--
 R/html_fragment.R                        |    3 
 R/html_notebook.R                        |    2 
 R/html_paged.R                           |   20 +++++-
 R/html_resources.R                       |    2 
 R/html_vignette.R                        |   20 ++++++
 R/ioslides_presentation.R                |    5 +
 R/output_format.R                        |    7 --
 R/pandoc.R                               |   88 ++++++++++++++++++---------
 R/pdf_document.R                         |   35 ++++++++--
 R/powerpoint_presentation.R              |    5 -
 R/render.R                               |   40 ++++++------
 R/render_html.R                          |   12 +--
 R/render_site.R                          |   13 +---
 R/slidy_presentation.R                   |    5 -
 R/tufte_handout.R                        |    2 
 R/word_document.R                        |    8 --
 README.md                                |    2 
 build/vignette.rds                       |binary
 inst/doc/lua-filters.html                |   54 ++++++++--------
 inst/rmd/h/default.html                  |    8 ++
 inst/rmd/h/navigation-1.1/codefolding.js |    4 -
 inst/rmd/lua/latex-div.lua               |   26 +++++---
 man/beamer_presentation.Rd               |   10 +--
 man/context_document.Rd                  |    8 +-
 man/find_pandoc.Rd                       |only
 man/html_document.Rd                     |    5 -
 man/html_document_base.Rd                |    9 --
 man/html_fragment.Rd                     |    5 -
 man/html_notebook.Rd                     |    5 -
 man/metadata.Rd                          |    4 -
 man/odt_document.Rd                      |    4 -
 man/paged_table.Rd                       |   20 +++++-
 man/pandoc_args.Rd                       |    3 
 man/pandoc_convert.Rd                    |    4 -
 man/pdf_document.Rd                      |   15 ++--
 man/powerpoint_presentation.Rd           |    5 -
 man/slidy_presentation.Rd                |   11 ---
 man/tufte_handout.Rd                     |    6 +
 man/word_document.Rd                     |    5 -
 tests/testthat/test-notebook.R           |   23 +++++++
 tests/testthat/test-output_format.R      |only
 tests/testthat/test-site.R               |    6 -
 tests/testthat/test-spin.R               |only
 tests/testthat/test-utils.R              |only
 tests/testthat/test-vignette.R           |only
 53 files changed, 403 insertions(+), 280 deletions(-)

More information about rmarkdown at CRAN
Permanent link

Package ipmisc updated to version 3.0.0 with previous version 2.0.0 dated 2020-04-11

Title: Miscellaneous Functions for Data Cleaning and Analysis
Description: Provides functions needed for data cleaning and formatting and forms data cleaning and wrangling backend for the following packages: 'broomExtra', 'ggstatsplot', 'groupedstats', 'pairwiseComparisons', 'statsExpressions', and 'tidyBF'.
Author: Indrajeet Patil [aut, cre, cph] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

Diff between ipmisc versions 2.0.0 dated 2020-04-11 and 3.0.0 dated 2020-05-31

 ipmisc-2.0.0/ipmisc/R/helpers_messages.R                  |only
 ipmisc-2.0.0/ipmisc/R/sort_xy.R                           |only
 ipmisc-2.0.0/ipmisc/data/movies_long.rdata                |only
 ipmisc-2.0.0/ipmisc/data/movies_wide.rdata                |only
 ipmisc-2.0.0/ipmisc/man/bartlett_message.Rd               |only
 ipmisc-2.0.0/ipmisc/man/movies_long.Rd                    |only
 ipmisc-2.0.0/ipmisc/man/movies_wide.Rd                    |only
 ipmisc-2.0.0/ipmisc/man/normality_message.Rd              |only
 ipmisc-2.0.0/ipmisc/man/sort_xy.Rd                        |only
 ipmisc-2.0.0/ipmisc/tests/testthat/test-helper_messages.R |only
 ipmisc-2.0.0/ipmisc/tests/testthat/test-sort_xy.R         |only
 ipmisc-3.0.0/ipmisc/DESCRIPTION                           |   15 +-
 ipmisc-3.0.0/ipmisc/MD5                                   |   21 ---
 ipmisc-3.0.0/ipmisc/NAMESPACE                             |    9 -
 ipmisc-3.0.0/ipmisc/NEWS.md                               |   10 +
 ipmisc-3.0.0/ipmisc/R/data.R                              |   76 --------------
 ipmisc-3.0.0/ipmisc/inst/WORDLIST                         |    7 -
 17 files changed, 23 insertions(+), 115 deletions(-)

More information about ipmisc at CRAN
Permanent link

Package Disequilibrium updated to version 1.1 with previous version 1.0 dated 2020-01-20

Title: Disequilibrium Models
Description: Estimate, summarize, and perform predictions with the market in disequilibrium model, as found in Gourieroux, C. (2000) <doi:10.1017/CBO9780511805608> and Maddala, G. (1983) <doi:10.1017/CBO9780511810176>. The parameters are estimated with maximum likelihood.
Author: Nate Latshaw [aut, cre], Michael Guggisberg [aut], Institute for Defense Analyses [cph]
Maintainer: Nate Latshaw <dcms2015@gmail.com>

Diff between Disequilibrium versions 1.0 dated 2020-01-20 and 1.1 dated 2020-05-31

 DESCRIPTION                     |   19 -
 MD5                             |   40 +-
 NAMESPACE                       |    6 
 R/Disequilibrium.R              |  690 +++++++++++++++++++++++++++++++++++-----
 README.md                       |only
 build                           |only
 data                            |only
 inst                            |only
 man/DE.Rd                       |   70 ++--
 man/DllhoodDatanhrho.Rd         |    2 
 man/DllhoodDbeta1.Rd            |    2 
 man/DllhoodDlogsigma11.Rd       |    2 
 man/GetDeltaMethodParameters.Rd |only
 man/GradientDE.Rd               |    6 
 man/LLikelihoodDE.Rd            |   17 
 man/TransformSigma_PDtoR2.Rd    |only
 man/TransformSigma_R2toPD.Rd    |only
 man/estfun.DE.Rd                |only
 man/fjdata.Rd                   |only
 man/nGradientDE.Rd              |    6 
 man/nLLikelihoodDE.Rd           |only
 man/nobs.DE.Rd                  |only
 man/predict.DE.Rd               |    4 
 man/residuals.DE.Rd             |only
 man/summary.DE.Rd               |    6 
 man/vcov.DE.Rd                  |only
 vignettes                       |only
 27 files changed, 722 insertions(+), 148 deletions(-)

More information about Disequilibrium at CRAN
Permanent link

Sat, 30 May 2020

Package ukpolice updated to version 0.2.1 with previous version 0.2.0 dated 2020-05-24

Title: Download Data on UK Police and Crime
Description: Downloads data from the 'UK Police' public data API, the full docs of which are available at <https://data.police.uk/docs/>. Includes data on police forces and police force areas, crime reports, and the use of stop-and-search powers.
Author: Evan Odell [aut, cre] (<https://orcid.org/0000-0003-1845-808X>), Tierney Nicholas [aut] (<https://orcid.org/0000-0003-1460-8722>)
Maintainer: Evan Odell <evanodell91@gmail.com>

Diff between ukpolice versions 0.2.0 dated 2020-05-24 and 0.2.1 dated 2020-05-30

 DESCRIPTION                           |    6 +++---
 LICENSE                               |    2 +-
 MD5                                   |   12 ++++++------
 NEWS.md                               |   10 +++++++++-
 inst/doc/introduction.html            |    4 ++--
 tests/testthat/test-empty-functions.R |    2 +-
 tests/testthat/test-stop-and-search.R |   13 ++++++++++---
 7 files changed, 32 insertions(+), 17 deletions(-)

More information about ukpolice at CRAN
Permanent link

Package Rmixmod updated to version 2.1.4 with previous version 2.1.2.2 dated 2019-03-11

Title: Classification with Mixture Modelling
Description: Interface of 'MIXMOD' software for supervised, unsupervised and semi-supervised classification with mixture modelling.
Author: Florent Langrognet [aut], Remi Lebret [aut], Christian Poli [aut], Serge Iovleff [aut], Benjamin Auder [aut], Parmeet Bhatia [ctb], Anwuli Echenim [ctb], Serge Iovleff [aut], Christophe Biernacki [ctb], Gilles Celeux [ctb], Gerard Govaert [ctb], Quentin Grimonprez [cre]
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>

Diff between Rmixmod versions 2.1.2.2 dated 2019-03-11 and 2.1.4 dated 2020-05-30

 Rmixmod-2.1.2.2/Rmixmod/src/Makevars                                        |only
 Rmixmod-2.1.2.2/Rmixmod/src/XmlMakevars                                     |only
 Rmixmod-2.1.2.2/Rmixmod/src/XmlMakevars.in                                  |only
 Rmixmod-2.1.4/Rmixmod/DESCRIPTION                                           |   49 
 Rmixmod-2.1.4/Rmixmod/MD5                                                   |  207 +--
 Rmixmod-2.1.4/Rmixmod/NAMESPACE                                             |    1 
 Rmixmod-2.1.4/Rmixmod/R/A_NAMESPACE.R                                       |    2 
 Rmixmod-2.1.4/Rmixmod/R/CompositeModel.R                                    |  266 +---
 Rmixmod-2.1.4/Rmixmod/R/CompositeParameter.R                                |  100 -
 Rmixmod-2.1.4/Rmixmod/R/GaussianModel.R                                     |  219 +--
 Rmixmod-2.1.4/Rmixmod/R/GaussianParameter.R                                 |   95 -
 Rmixmod-2.1.4/Rmixmod/R/Mixmod.R                                            |  351 ++---
 Rmixmod-2.1.4/Rmixmod/R/MixmodCluster.R                                     |  257 +--
 Rmixmod-2.1.4/Rmixmod/R/MixmodDAResults.R                                   |   72 -
 Rmixmod-2.1.4/Rmixmod/R/MixmodLearn.R                                       |  220 +--
 Rmixmod-2.1.4/Rmixmod/R/MixmodPredict.R                                     |  207 +--
 Rmixmod-2.1.4/Rmixmod/R/MixmodResults.R                                     |  286 ++--
 Rmixmod-2.1.4/Rmixmod/R/MixmodXml.R                                         |   30 
 Rmixmod-2.1.4/Rmixmod/R/Model.R                                             |   65 -
 Rmixmod-2.1.4/Rmixmod/R/MultinomialModel.R                                  |  179 +-
 Rmixmod-2.1.4/Rmixmod/R/MultinomialParameter.R                              |  104 -
 Rmixmod-2.1.4/Rmixmod/R/Parameter.R                                         |   34 
 Rmixmod-2.1.4/Rmixmod/R/Rmixmod.R                                           |  644 ++++------
 Rmixmod-2.1.4/Rmixmod/R/Strategy.R                                          |  307 ++--
 Rmixmod-2.1.4/Rmixmod/R/global.R                                            |  423 +++---
 Rmixmod-2.1.4/Rmixmod/cleanup                                               |only
 Rmixmod-2.1.4/Rmixmod/configure                                             |   38 
 Rmixmod-2.1.4/Rmixmod/configure.ac                                          |   22 
 Rmixmod-2.1.4/Rmixmod/data/birds.rda                                        |binary
 Rmixmod-2.1.4/Rmixmod/data/car.rda                                          |binary
 Rmixmod-2.1.4/Rmixmod/data/finance.rda                                      |binary
 Rmixmod-2.1.4/Rmixmod/data/geyser.rda                                       |binary
 Rmixmod-2.1.4/Rmixmod/data/heterodata.rda                                   |binary
 Rmixmod-2.1.4/Rmixmod/data/heterodatatest.rda                               |binary
 Rmixmod-2.1.4/Rmixmod/data/heterodatatrain.rda                              |binary
 Rmixmod-2.1.4/Rmixmod/data/titanic.rda                                      |binary
 Rmixmod-2.1.4/Rmixmod/man/CompositeModel-class.Rd                           |    1 
 Rmixmod-2.1.4/Rmixmod/man/CompositeParameter-class.Rd                       |    1 
 Rmixmod-2.1.4/Rmixmod/man/GaussianModel-class.Rd                            |    1 
 Rmixmod-2.1.4/Rmixmod/man/GaussianParameter-class.Rd                        |    1 
 Rmixmod-2.1.4/Rmixmod/man/Mixmod-class.Rd                                   |    1 
 Rmixmod-2.1.4/Rmixmod/man/MixmodCluster-class.Rd                            |    1 
 Rmixmod-2.1.4/Rmixmod/man/MixmodDAResults-class.Rd                          |    1 
 Rmixmod-2.1.4/Rmixmod/man/MixmodLearn-class.Rd                              |    1 
 Rmixmod-2.1.4/Rmixmod/man/MixmodPredict-class.Rd                            |    1 
 Rmixmod-2.1.4/Rmixmod/man/MixmodResults-class.Rd                            |    1 
 Rmixmod-2.1.4/Rmixmod/man/MixmodXmlCheck-class.Rd                           |    1 
 Rmixmod-2.1.4/Rmixmod/man/MixmodXmlInput-class.Rd                           |    1 
 Rmixmod-2.1.4/Rmixmod/man/Model-class.Rd                                    |    1 
 Rmixmod-2.1.4/Rmixmod/man/MultinomialModel-class.Rd                         |    7 
 Rmixmod-2.1.4/Rmixmod/man/MultinomialParameter-class.Rd                     |    1 
 Rmixmod-2.1.4/Rmixmod/man/Parameter-class.Rd                                |    1 
 Rmixmod-2.1.4/Rmixmod/man/Rmixmod-package.Rd                                |   13 
 Rmixmod-2.1.4/Rmixmod/man/Strategy-class.Rd                                 |    1 
 Rmixmod-2.1.4/Rmixmod/man/asQualitative.Rd                                  |    1 
 Rmixmod-2.1.4/Rmixmod/man/barplot-methods.Rd                                |    1 
 Rmixmod-2.1.4/Rmixmod/man/barplotCluster.Rd                                 |   10 
 Rmixmod-2.1.4/Rmixmod/man/birds.Rd                                          |    7 
 Rmixmod-2.1.4/Rmixmod/man/car.Rd                                            |    7 
 Rmixmod-2.1.4/Rmixmod/man/clusteringMain.Rd                                 |    1 
 Rmixmod-2.1.4/Rmixmod/man/composeModelName.Rd                               |    1 
 Rmixmod-2.1.4/Rmixmod/man/ellipse.Rd                                        |    1 
 Rmixmod-2.1.4/Rmixmod/man/extract-methods.Rd                                |   94 -
 Rmixmod-2.1.4/Rmixmod/man/finance.Rd                                        |    7 
 Rmixmod-2.1.4/Rmixmod/man/geyser.Rd                                         |    9 
 Rmixmod-2.1.4/Rmixmod/man/heterodata.Rd                                     |    7 
 Rmixmod-2.1.4/Rmixmod/man/heterodatatest.Rd                                 |    7 
 Rmixmod-2.1.4/Rmixmod/man/heterodatatrain.Rd                                |    7 
 Rmixmod-2.1.4/Rmixmod/man/hist-methods.Rd                                   |    1 
 Rmixmod-2.1.4/Rmixmod/man/histCluster.Rd                                    |   13 
 Rmixmod-2.1.4/Rmixmod/man/initialize-methods.Rd                             |  131 +-
 Rmixmod-2.1.4/Rmixmod/man/is.dataType.Rd                                    |    1 
 Rmixmod-2.1.4/Rmixmod/man/is.wholenumber.Rd                                 |    1 
 Rmixmod-2.1.4/Rmixmod/man/isQualitative.Rd                                  |    1 
 Rmixmod-2.1.4/Rmixmod/man/learnMain.Rd                                      |    1 
 Rmixmod-2.1.4/Rmixmod/man/matrix2binary.Rd                                  |    1 
 Rmixmod-2.1.4/Rmixmod/man/mixmodCluster.Rd                                  |    1 
 Rmixmod-2.1.4/Rmixmod/man/mixmodCompositeModel.Rd                           |   17 
 Rmixmod-2.1.4/Rmixmod/man/mixmodGaussianModel.Rd                            |   15 
 Rmixmod-2.1.4/Rmixmod/man/mixmodLearn.Rd                                    |    1 
 Rmixmod-2.1.4/Rmixmod/man/mixmodLearn.default.Rd                            |   12 
 Rmixmod-2.1.4/Rmixmod/man/mixmodMultinomialModel.Rd                         |   17 
 Rmixmod-2.1.4/Rmixmod/man/mixmodPredict.Rd                                  |    1 
 Rmixmod-2.1.4/Rmixmod/man/mixmodStrategy.Rd                                 |   21 
 Rmixmod-2.1.4/Rmixmod/man/mixmodXmlCheck.Rd                                 |    1 
 Rmixmod-2.1.4/Rmixmod/man/mixmodXmlInput.Rd                                 |    1 
 Rmixmod-2.1.4/Rmixmod/man/mixmodXmlLoad.Rd                                  |    1 
 Rmixmod-2.1.4/Rmixmod/man/nbFactorFromData.Rd                               |    1 
 Rmixmod-2.1.4/Rmixmod/man/oldmixmodPredict.Rd                               |    6 
 Rmixmod-2.1.4/Rmixmod/man/plot-methods.Rd                                   |    4 
 Rmixmod-2.1.4/Rmixmod/man/plotCluster.Rd                                    |   16 
 Rmixmod-2.1.4/Rmixmod/man/predictMain.Rd                                    |    1 
 Rmixmod-2.1.4/Rmixmod/man/print-methods.Rd                                  |   16 
 Rmixmod-2.1.4/Rmixmod/man/show-methods.Rd                                   |   16 
 Rmixmod-2.1.4/Rmixmod/man/sortByCriterion-methods.Rd                        |    1 
 Rmixmod-2.1.4/Rmixmod/man/summary-methods.Rd                                |   11 
 Rmixmod-2.1.4/Rmixmod/man/titanic.Rd                                        |    7 
 Rmixmod-2.1.4/Rmixmod/man/vector2binary.Rd                                  |    1 
 Rmixmod-2.1.4/Rmixmod/man/xMain.Rd                                          |    1 
 Rmixmod-2.1.4/Rmixmod/src/ClusteringInputHandling.cpp                       |   12 
 Rmixmod-2.1.4/Rmixmod/src/InputHandling.cpp                                 |    4 
 Rmixmod-2.1.4/Rmixmod/src/Makevars.in                                       |only
 Rmixmod-2.1.4/Rmixmod/src/Makevars.win                                      |    6 
 Rmixmod-2.1.4/Rmixmod/src/mixmod/Kernel/Parameter/GaussianEDDAParameter.cpp |    2 
 Rmixmod-2.1.4/Rmixmod/src/mixmod/mixmod_r.mk                                |    8 
 Rmixmod-2.1.4/Rmixmod/src/mixmod_iostream/mixmod_iostream_r.mk              |    1 
 Rmixmod-2.1.4/Rmixmod/tests/heterogeneousDAtest.R                           |   39 
 107 files changed, 2256 insertions(+), 2509 deletions(-)

More information about Rmixmod at CRAN
Permanent link

Package PINSPlus updated to version 2.0.4 with previous version 2.0.3 dated 2020-05-28

Title: Clustering Algorithm for Data Integration and Disease Subtyping
Description: Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et.al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et.al. (2017)<DOI: 10.1101/gr.215129.116>).
Author: Hung Nguyen, Bang Tran, Duc Tran and Tin Nguyen
Maintainer: Hung Nguyen <hungnp@nevada.unr.edu>

Diff between PINSPlus versions 2.0.3 dated 2020-05-28 and 2.0.4 dated 2020-05-30

 DESCRIPTION                    |    8 ++++----
 MD5                            |    8 ++++----
 R/perturbation-clustering.R    |   26 +++++++++++++-------------
 R/stopping-criteria-handlers.R |    4 ++--
 vignettes/PINSPlus.html        |   14 +++++++-------
 5 files changed, 30 insertions(+), 30 deletions(-)

More information about PINSPlus at CRAN
Permanent link

Package MatTransMix updated to version 0.1.9 with previous version 0.1.8 dated 2020-04-08

Title: Clustering with Matrix Gaussian and Matrix Transformation Mixture Models
Description: Provides matrix Gaussian mixture models, matrix transformation mixture models and their model-based clustering results. The parsimonious models of the mean matrices and variance covariance matrices are implemented with a total of 196 variations.
Author: Xuwen Zhu [aut, cre], Volodymyr Melnykov [aut], Shuchismita Sarkar [ctb], Michael Hutt [ctb, cph], Stephen Moshier [ctb, cph], Rouben Rostamian [ctb, cph], Carl Edward Rasmussen [ctb, cph], Dianne Cook [ctb, cph]
Maintainer: Xuwen Zhu <xzhu20@cba.ua.edu>

Diff between MatTransMix versions 0.1.8 dated 2020-04-08 and 0.1.9 dated 2020-05-30

 DESCRIPTION       |    8 ++++----
 MD5               |    6 +++---
 NEWS              |    4 ++++
 data/Salary.RData |binary
 4 files changed, 11 insertions(+), 7 deletions(-)

More information about MatTransMix at CRAN
Permanent link

Package loon.data updated to version 0.1.0 with previous version 0.0.9 dated 2020-05-19

Title: Data Used to Illustrate 'Loon' Functionality
Description: Data used as examples in the 'loon' package.
Author: R. Wayne Oldford [aut, cre], Adrian Waddell [aut]
Maintainer: R. Wayne Oldford <rwoldford@uwaterloo.ca>

Diff between loon.data versions 0.0.9 dated 2020-05-19 and 0.1.0 dated 2020-05-30

 DESCRIPTION               |    6 +++---
 MD5                       |   20 +++++++++++++-------
 NEWS.md                   |    8 +++++++-
 R/covidNZ.R               |only
 R/medicalRecords.R        |    2 +-
 R/pandemic.R              |    2 +-
 R/placenamesCanada.R      |only
 data/covidNZ.rda          |only
 data/datalist             |    2 ++
 data/placenamesCanada.rda |only
 man/covidNZ.Rd            |only
 man/medicalRecords.Rd     |    2 +-
 man/pandemic.Rd           |    2 +-
 man/placenamesCanada.Rd   |only
 14 files changed, 29 insertions(+), 15 deletions(-)

More information about loon.data at CRAN
Permanent link

Package GMSE updated to version 0.6.0.4 with previous version 0.4.0.13 dated 2020-02-04

Title: Generalised Management Strategy Evaluation Simulator
Description: Integrates game theory and ecological theory to construct social-ecological models that simulate the management of populations and stakeholder actions. These models build off of a previously developed management strategy evaluation (MSE) framework to simulate all aspects of management: population dynamics, manager observation of populations, manager decision making, and stakeholder responses to management decisions. The newly developed generalised management strategy evaluation (GMSE) framework uses genetic algorithms to mimic the decision-making process of managers and stakeholders under conditions of change, uncertainty, and conflict. Simulations can be run using gmse(), gmse_apply(), and gmse_gui() functions.
Author: A. Bradley Duthie [aut, cre] (<https://orcid.org/0000-0001-8343-4995>), Adrian Bach [ctb], Nils Bunnefeld [ctb, fnd] (<https://orcid.org/0000-0002-1349-4463>), Jeremy Cusack [ctb] (<https://orcid.org/0000-0003-3004-1586>), Isabel Jones [ctb] (<https://orcid.org/0000-0002-8361-1370>), Jeroen Minderman [ctb] (<https://orcid.org/0000-0002-8451-5540>), Erlend Nilsen [ctb] (<https://orcid.org/0000-0002-5119-8331>), Rocio Pozo [ctb] (<https://orcid.org/0000-0002-7546-8076>), Sarobidy Rakotonarivo [ctb] (<https://orcid.org/0000-0002-8032-1431>), Bram Van Moorter [ctb] (<https://orcid.org/0000-0002-3196-1993>)
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>

Diff between GMSE versions 0.4.0.13 dated 2020-02-04 and 0.6.0.4 dated 2020-05-30

 GMSE-0.4.0.13/GMSE/R/scratch.R                           |only
 GMSE-0.6.0.4/GMSE/DESCRIPTION                            |   10 
 GMSE-0.6.0.4/GMSE/MD5                                    |  118 -
 GMSE-0.6.0.4/GMSE/NAMESPACE                              |    3 
 GMSE-0.6.0.4/GMSE/NEWS.md                                |only
 GMSE-0.6.0.4/GMSE/R/gmse.R                               |  206 +-
 GMSE-0.6.0.4/GMSE/R/gmse_apply.R                         | 1401 +++++++++------
 GMSE-0.6.0.4/GMSE/R/gmse_gui.R                           |   99 -
 GMSE-0.6.0.4/GMSE/R/gmse_summary.R                       |    7 
 GMSE-0.6.0.4/GMSE/R/initialise.R                         |  229 ++
 GMSE-0.6.0.4/GMSE/R/landscape.R                          |   83 
 GMSE-0.6.0.4/GMSE/R/manager.R                            |    4 
 GMSE-0.6.0.4/GMSE/R/observation.R                        |    4 
 GMSE-0.6.0.4/GMSE/R/plotting.R                           |   69 
 GMSE-0.6.0.4/GMSE/R/resource.R                           |    2 
 GMSE-0.6.0.4/GMSE/R/user.R                               |    4 
 GMSE-0.6.0.4/GMSE/README.md                              |    4 
 GMSE-0.6.0.4/GMSE/build/vignette.rds                     |binary
 GMSE-0.6.0.4/GMSE/inst/doc/SI1.pdf                       |binary
 GMSE-0.6.0.4/GMSE/inst/doc/SI2.pdf                       |binary
 GMSE-0.6.0.4/GMSE/inst/doc/SI3.pdf                       |binary
 GMSE-0.6.0.4/GMSE/inst/doc/SI4.pdf                       |binary
 GMSE-0.6.0.4/GMSE/inst/doc/SI5.pdf                       |binary
 GMSE-0.6.0.4/GMSE/inst/doc/SI6.pdf                       |binary
 GMSE-0.6.0.4/GMSE/inst/doc/SI7.pdf                       |binary
 GMSE-0.6.0.4/GMSE/inst/doc/SI8.pdf                       |only
 GMSE-0.6.0.4/GMSE/inst/doc/SI8.pdf.asis                  |only
 GMSE-0.6.0.4/GMSE/inst/doc/ms.pdf                        |binary
 GMSE-0.6.0.4/GMSE/man/anecdotal.Rd                       |   15 
 GMSE-0.6.0.4/GMSE/man/case01plot.Rd                      |   15 
 GMSE-0.6.0.4/GMSE/man/count_agent_cells.Rd               |only
 GMSE-0.6.0.4/GMSE/man/gmse.Rd                            |  136 +
 GMSE-0.6.0.4/GMSE/man/gmse_apply.Rd                      |   12 
 GMSE-0.6.0.4/GMSE/man/gmse_replicates.Rd                 |    3 
 GMSE-0.6.0.4/GMSE/man/make_agents.Rd                     |   78 
 GMSE-0.6.0.4/GMSE/man/make_interaction_array.Rd          |   17 
 GMSE-0.6.0.4/GMSE/man/make_landscape.Rd                  |   26 
 GMSE-0.6.0.4/GMSE/man/make_resource.Rd                   |   18 
 GMSE-0.6.0.4/GMSE/man/manager.Rd                         |   15 
 GMSE-0.6.0.4/GMSE/man/manager_user_budgets.Rd            |only
 GMSE-0.6.0.4/GMSE/man/observation.Rd                     |   19 
 GMSE-0.6.0.4/GMSE/man/owner_land_ssa.Rd                  |only
 GMSE-0.6.0.4/GMSE/man/rec.n.Rd                           |    4 
 GMSE-0.6.0.4/GMSE/man/resource.Rd                        |    3 
 GMSE-0.6.0.4/GMSE/man/ssb.n.Rd                           |    4 
 GMSE-0.6.0.4/GMSE/man/user.Rd                            |   14 
 GMSE-0.6.0.4/GMSE/src/game.c                             |  139 -
 GMSE-0.6.0.4/GMSE/src/gmse_init.c                        |   12 
 GMSE-0.6.0.4/GMSE/src/landscape.c                        |only
 GMSE-0.6.0.4/GMSE/src/manager.c                          |  152 +
 GMSE-0.6.0.4/GMSE/src/resource.c                         |  201 +-
 GMSE-0.6.0.4/GMSE/src/user.c                             |   74 
 GMSE-0.6.0.4/GMSE/src/utilities.c                        |  309 ++-
 GMSE-0.6.0.4/GMSE/src/utilities.h                        |   18 
 GMSE-0.6.0.4/GMSE/tests/testthat/test-gmse_apply.R       |  143 -
 GMSE-0.6.0.4/GMSE/tests/testthat/test-gmse_apply_loops.R |only
 GMSE-0.6.0.4/GMSE/tests/testthat/test-make_agents.R      |   19 
 GMSE-0.6.0.4/GMSE/tests/testthat/test-make_landscape.R   |   69 
 GMSE-0.6.0.4/GMSE/tests/testthat/test-make_resource.R    |    2 
 GMSE-0.6.0.4/GMSE/tests/testthat/test-manager.R          |   88 
 GMSE-0.6.0.4/GMSE/tests/testthat/test-observation.R      |   60 
 GMSE-0.6.0.4/GMSE/tests/testthat/test-resource.R         |   82 
 GMSE-0.6.0.4/GMSE/tests/testthat/test-summary.R          |    8 
 GMSE-0.6.0.4/GMSE/tests/testthat/test-user.R             |  110 -
 GMSE-0.6.0.4/GMSE/vignettes/SI8.pdf.asis                 |only
 65 files changed, 2885 insertions(+), 1223 deletions(-)

More information about GMSE at CRAN
Permanent link

Package bbsBayes updated to version 2.2.2 with previous version 2.2.1 dated 2020-05-27

Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running program that seeks to monitor the status and trends of the breeding birds in North America. Since its start in 1966, the BBS has accumulated over 50 years of data for over 300 species of North American Birds. Given the temporal and spatial structure of the data, hierarchical Bayesian models are used to assess the status and trends of these 300+ species of birds. 'bbsBayes' allows you to perform hierarchical Bayesian analysis of BBS data. You can run a full model analysis for one or more species that you choose, or you can take more control and specify how the data should be stratified, prepared for 'JAGS', or modelled. The functions provided here allow you to replicate analyses performed by the United State Geological Survey (USGS, see Link and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service (CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre], Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <edwardsb@uoguelph.ca>

Diff between bbsBayes versions 2.2.1 dated 2020-05-27 and 2.2.2 dated 2020-05-30

 DESCRIPTION                            |    8 ++++----
 MD5                                    |   12 ++++++------
 R/generate-indices.R                   |    5 ++++-
 R/generate-regional-indices.R          |   12 ++++++++++--
 README.md                              |   10 ++++------
 inst/CITATION                          |   12 ++++++++++++
 man/figures/WOTH_status_assessment.png |binary
 7 files changed, 40 insertions(+), 19 deletions(-)

More information about bbsBayes at CRAN
Permanent link

Package bayest updated to version 1.4 with previous version 1.3 dated 2020-05-27

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

Diff between bayest versions 1.3 dated 2020-05-27 and 1.4 dated 2020-05-30

 DESCRIPTION       |   11 ++++++-----
 MD5               |    4 ++--
 build/partial.rdb |binary
 3 files changed, 8 insertions(+), 7 deletions(-)

More information about bayest at CRAN
Permanent link

Package bayesanova updated to version 1.4 with previous version 1.3 dated 2020-02-11

Title: Bayesian Inference in the Analysis of Variance via Markov Chain Monte Carlo in Gaussian Mixture Models
Description: Provides a Bayesian version of the analysis of variance based on a three-component Gaussian mixture for which a Gibbs sampler produces posterior draws. For details about the Bayesian ANOVA based on Gaussian mixtures, see Kelter (2019) <arXiv:1906.07524>.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>

Diff between bayesanova versions 1.3 dated 2020-02-11 and 1.4 dated 2020-05-30

 DESCRIPTION       |   11 ++++++-----
 MD5               |    4 ++--
 build/partial.rdb |binary
 3 files changed, 8 insertions(+), 7 deletions(-)

More information about bayesanova at CRAN
Permanent link

Package volesti updated to version 1.1.0 with previous version 1.0.3 dated 2019-09-10

Title: Volume Approximation and Sampling of Convex Polytopes
Description: Provides an R interface for 'volesti' C++ package. 'volesti' computes estimations of volume of polytopes given by (i) a set of points, (ii) linear inequalities or (iii) Minkowski sum of segments (a.k.a. zonotopes). There are three algorithms for volume estimation as well as algorithms for sampling, rounding and rotating polytopes. Moreover, 'volesti' provides algorithms for estimating copulas useful in computational finance.
Author: Vissarion Fisikopoulos <vissarion.fisikopoulos@gmail.com> [aut, cph, cre], Apostolos Chalkis <tolis.chal@gmail.com> [cph, aut], contributors in file inst/AUTHORS
Maintainer: Vissarion Fisikopoulos <vissarion.fisikopoulos@gmail.com>

Diff between volesti versions 1.0.3 dated 2019-09-10 and 1.1.0 dated 2020-05-30

 volesti-1.0.3/volesti/R/GenCross.R                                             |only
 volesti-1.0.3/volesti/R/GenCube.R                                              |only
 volesti-1.0.3/volesti/R/GenProdSimplex.R                                       |only
 volesti-1.0.3/volesti/R/GenRandHpoly.R                                         |only
 volesti-1.0.3/volesti/R/GenRandVpoly.R                                         |only
 volesti-1.0.3/volesti/R/GenSimplex.R                                           |only
 volesti-1.0.3/volesti/R/GenSkinnyCube.R                                        |only
 volesti-1.0.3/volesti/R/GenZonotope.R                                          |only
 volesti-1.0.3/volesti/R/fileToMatrix.R                                         |only
 volesti-1.0.3/volesti/R/rand_rotate.R                                          |only
 volesti-1.0.3/volesti/man/GenCross.Rd                                          |only
 volesti-1.0.3/volesti/man/GenCube.Rd                                           |only
 volesti-1.0.3/volesti/man/GenProdSimplex.Rd                                    |only
 volesti-1.0.3/volesti/man/GenRandHpoly.Rd                                      |only
 volesti-1.0.3/volesti/man/GenRandVpoly.Rd                                      |only
 volesti-1.0.3/volesti/man/GenSimplex.Rd                                        |only
 volesti-1.0.3/volesti/man/GenSkinnyCube.Rd                                     |only
 volesti-1.0.3/volesti/man/GenZonotope.Rd                                       |only
 volesti-1.0.3/volesti/man/InnerBall.Rd                                         |only
 volesti-1.0.3/volesti/man/IntVP.Rd                                             |only
 volesti-1.0.3/volesti/man/Rcpp_IntVP.Rd                                        |only
 volesti-1.0.3/volesti/man/SliceOfSimplex.Rd                                    |only
 volesti-1.0.3/volesti/man/copula1.Rd                                           |only
 volesti-1.0.3/volesti/man/copula2.Rd                                           |only
 volesti-1.0.3/volesti/man/fileToMatrix.Rd                                      |only
 volesti-1.0.3/volesti/man/rand_rotate.Rd                                       |only
 volesti-1.0.3/volesti/src/InnerBall.cpp                                        |only
 volesti-1.0.3/volesti/src/SliceOfSimplex.cpp                                   |only
 volesti-1.0.3/volesti/src/copula1.cpp                                          |only
 volesti-1.0.3/volesti/src/copula2.cpp                                          |only
 volesti-1.0.3/volesti/src/include/annealing                                    |only
 volesti-1.0.3/volesti/src/include/convex_bodies/polytopes.h                    |only
 volesti-1.0.3/volesti/src/include/generators/polytope_generators.h             |only
 volesti-1.0.3/volesti/src/include/rotating.h                                   |only
 volesti-1.0.3/volesti/src/include/samplers                                     |only
 volesti-1.0.3/volesti/src/include/solve_lp.h                                   |only
 volesti-1.0.3/volesti/src/include/volume/vars.h                                |only
 volesti-1.0.3/volesti/src/include/volume/volume.h                              |only
 volesti-1.1.0/volesti/DESCRIPTION                                              |   23 
 volesti-1.1.0/volesti/MD5                                                      |  205 ++-
 volesti-1.1.0/volesti/NAMESPACE                                                |   31 
 volesti-1.1.0/volesti/NEWS.md                                                  |   11 
 volesti-1.1.0/volesti/R/RcppExports.R                                          |  350 +++---
 volesti-1.1.0/volesti/R/compute_indicators.R                                   |only
 volesti-1.1.0/volesti/R/file_to_polytope.R                                     |only
 volesti-1.1.0/volesti/R/gen_cross.R                                            |only
 volesti-1.1.0/volesti/R/gen_cube.R                                             |only
 volesti-1.1.0/volesti/R/gen_prod_simplex.R                                     |only
 volesti-1.1.0/volesti/R/gen_rand_hpoly.R                                       |only
 volesti-1.1.0/volesti/R/gen_rand_vpoly.R                                       |only
 volesti-1.1.0/volesti/R/gen_rand_zonotope.R                                    |only
 volesti-1.1.0/volesti/R/gen_simplex.R                                          |only
 volesti-1.1.0/volesti/R/gen_skinny_cube.R                                      |only
 volesti-1.1.0/volesti/R/rotate_polytope.R                                      |only
 volesti-1.1.0/volesti/R/round_polytope.R                                       |   32 
 volesti-1.1.0/volesti/R/zonotope_approximation.R                               |only
 volesti-1.1.0/volesti/README.md                                                |   26 
 volesti-1.1.0/volesti/man/Hpolytope.Rd                                         |    8 
 volesti-1.1.0/volesti/man/Rcpp_Hpolytope.Rd                                    |    8 
 volesti-1.1.0/volesti/man/Rcpp_Vpolytope.Rd                                    |    5 
 volesti-1.1.0/volesti/man/Rcpp_VpolytopeIntersection.Rd                        |only
 volesti-1.1.0/volesti/man/Rcpp_Zonotope.Rd                                     |    5 
 volesti-1.1.0/volesti/man/Vpolytope.Rd                                         |    4 
 volesti-1.1.0/volesti/man/VpolytopeIntersection.Rd                             |only
 volesti-1.1.0/volesti/man/Zonotope.Rd                                          |    4 
 volesti-1.1.0/volesti/man/compute_indicators.Rd                                |only
 volesti-1.1.0/volesti/man/copula.Rd                                            |only
 volesti-1.1.0/volesti/man/direct_sampling.Rd                                   |only
 volesti-1.1.0/volesti/man/exact_vol.Rd                                         |   26 
 volesti-1.1.0/volesti/man/file_to_polytope.Rd                                  |only
 volesti-1.1.0/volesti/man/frustum_of_simplex.Rd                                |only
 volesti-1.1.0/volesti/man/gen_cross.Rd                                         |only
 volesti-1.1.0/volesti/man/gen_cube.Rd                                          |only
 volesti-1.1.0/volesti/man/gen_prod_simplex.Rd                                  |only
 volesti-1.1.0/volesti/man/gen_rand_hpoly.Rd                                    |only
 volesti-1.1.0/volesti/man/gen_rand_vpoly.Rd                                    |only
 volesti-1.1.0/volesti/man/gen_rand_zonotope.Rd                                 |only
 volesti-1.1.0/volesti/man/gen_simplex.Rd                                       |only
 volesti-1.1.0/volesti/man/gen_skinny_cube.Rd                                   |only
 volesti-1.1.0/volesti/man/inner_ball.Rd                                        |only
 volesti-1.1.0/volesti/man/poly_gen.Rd                                          |   14 
 volesti-1.1.0/volesti/man/rotate_polytope.Rd                                   |only
 volesti-1.1.0/volesti/man/rotating.Rd                                          |   12 
 volesti-1.1.0/volesti/man/round_polytope.Rd                                    |   27 
 volesti-1.1.0/volesti/man/rounding.Rd                                          |   16 
 volesti-1.1.0/volesti/man/sample_points.Rd                                     |   70 -
 volesti-1.1.0/volesti/man/volume.Rd                                            |   64 -
 volesti-1.1.0/volesti/man/zono_approx.Rd                                       |only
 volesti-1.1.0/volesti/man/zonotope_approximation.Rd                            |only
 volesti-1.1.0/volesti/src/Makevars                                             |    2 
 volesti-1.1.0/volesti/src/Makevars.win                                         |    2 
 volesti-1.1.0/volesti/src/RcppExports.cpp                                      |  160 +-
 volesti-1.1.0/volesti/src/copula.cpp                                           |only
 volesti-1.1.0/volesti/src/direct_sampling.cpp                                  |only
 volesti-1.1.0/volesti/src/exact_vol.cpp                                        |  138 --
 volesti-1.1.0/volesti/src/external/lpsolve/build/lp_solve/lp_presolve.c        |    8 
 volesti-1.1.0/volesti/src/frustum_of_simplex.cpp                               |only
 volesti-1.1.0/volesti/src/include/cartesian_geom/point.h                       |  231 ++-
 volesti-1.1.0/volesti/src/include/convex_bodies/ball.h                         |only
 volesti-1.1.0/volesti/src/include/convex_bodies/ballintersectconvex.h          |  244 ++--
 volesti-1.1.0/volesti/src/include/convex_bodies/ellipsoids.h                   |   17 
 volesti-1.1.0/volesti/src/include/convex_bodies/hpolytope.h                    |only
 volesti-1.1.0/volesti/src/include/convex_bodies/vpolyintersectvpoly.h          |  243 ++--
 volesti-1.1.0/volesti/src/include/convex_bodies/vpolytope.h                    |only
 volesti-1.1.0/volesti/src/include/convex_bodies/zonoIntersecthpoly.h           |only
 volesti-1.1.0/volesti/src/include/convex_bodies/zpolytope.h                    |only
 volesti-1.1.0/volesti/src/include/generators/boost_random_number_generator.hpp |only
 volesti-1.1.0/volesti/src/include/generators/h_polytopes_generator.h           |only
 volesti-1.1.0/volesti/src/include/generators/known_polytope_generators.h       |only
 volesti-1.1.0/volesti/src/include/generators/v_polytopes_generators.h          |only
 volesti-1.1.0/volesti/src/include/generators/z_polytopes_generators.h          |only
 volesti-1.1.0/volesti/src/include/lp_oracles                                   |only
 volesti-1.1.0/volesti/src/include/misc                                         |only
 volesti-1.1.0/volesti/src/include/random_walks                                 |only
 volesti-1.1.0/volesti/src/include/rounding.h                                   |  169 ++
 volesti-1.1.0/volesti/src/include/sampling                                     |only
 volesti-1.1.0/volesti/src/include/volume/copulas.h                             |   23 
 volesti-1.1.0/volesti/src/include/volume/exact_vols.h                          |   65 -
 volesti-1.1.0/volesti/src/include/volume/rotating.hpp                          |only
 volesti-1.1.0/volesti/src/include/volume/rounding.hpp                          |only
 volesti-1.1.0/volesti/src/include/volume/sampling_policies.hpp                 |only
 volesti-1.1.0/volesti/src/include/volume/volume_cooling_balls.hpp              |only
 volesti-1.1.0/volesti/src/include/volume/volume_cooling_gaussians.hpp          |only
 volesti-1.1.0/volesti/src/include/volume/volume_cooling_hpoly.hpp              |only
 volesti-1.1.0/volesti/src/include/volume/volume_sequence_of_balls.hpp          |only
 volesti-1.1.0/volesti/src/inner_ball.cpp                                       |only
 volesti-1.1.0/volesti/src/poly_gen.cpp                                         |   44 
 volesti-1.1.0/volesti/src/polytopes_modules.cpp                                |   98 -
 volesti-1.1.0/volesti/src/rotating.cpp                                         |   55 
 volesti-1.1.0/volesti/src/rounding.cpp                                         |  113 -
 volesti-1.1.0/volesti/src/sample_points.cpp                                    |  578 +++++-----
 volesti-1.1.0/volesti/src/volume.cpp                                           |  397 +++---
 volesti-1.1.0/volesti/src/zonotope_approximation.cpp                           |only
 volesti-1.1.0/volesti/tests/testthat.R                                         |    1 
 volesti-1.1.0/volesti/tests/testthat/test_Hvol.R                               |  173 --
 volesti-1.1.0/volesti/tests/testthat/test_InnerBall.R                          |   40 
 volesti-1.1.0/volesti/tests/testthat/test_Vvol.R                               |   65 -
 volesti-1.1.0/volesti/tests/testthat/test_Zvol.R                               |   55 
 volesti-1.1.0/volesti/tests/testthat/test_copulas.R                            |    4 
 volesti-1.1.0/volesti/tests/testthat/test_rounding.R                           |   40 
 volesti-1.1.0/volesti/tests/testthat/test_sampling.R                           |   81 -
 141 files changed, 2035 insertions(+), 1952 deletions(-)

More information about volesti at CRAN
Permanent link

Package gratia updated to version 0.4.1 with previous version 0.3.1 dated 2020-03-29

Title: Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'
Description: Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.
Author: Gavin L. Simpson [aut, cre] (<https://orcid.org/0000-0002-9084-8413>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>)
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>

Diff between gratia versions 0.3.1 dated 2020-03-29 and 0.4.1 dated 2020-05-30

 gratia-0.3.1/gratia/man/figures/appraise-figure.png                                                               |only
 gratia-0.3.1/gratia/man/figures/draw-gam-figure.png                                                               |only
 gratia-0.4.1/gratia/DESCRIPTION                                                                                   |   14 
 gratia-0.4.1/gratia/MD5                                                                                           |  235 ++--
 gratia-0.4.1/gratia/NAMESPACE                                                                                     |   46 
 gratia-0.4.1/gratia/NEWS.md                                                                                       |  117 ++
 gratia-0.4.1/gratia/R/add-methods.R                                                                               |only
 gratia-0.4.1/gratia/R/basis-funs.R                                                                                |    6 
 gratia-0.4.1/gratia/R/data-sim.R                                                                                  |only
 gratia-0.4.1/gratia/R/data-slice.R                                                                                |   44 
 gratia-0.4.1/gratia/R/datagen-methods.R                                                                           |   76 -
 gratia-0.4.1/gratia/R/datasets.R                                                                                  |   31 
 gratia-0.4.1/gratia/R/derivatives.R                                                                               |  117 +-
 gratia-0.4.1/gratia/R/diagnose.R                                                                                  |  181 ++-
 gratia-0.4.1/gratia/R/draw-methods.R                                                                              |  482 +++++++-
 gratia-0.4.1/gratia/R/evaluate_smooth.R                                                                           |   82 +
 gratia-0.4.1/gratia/R/family-utils.R                                                                              |  555 +++++-----
 gratia-0.4.1/gratia/R/posterior-samples.R                                                                         |   15 
 gratia-0.4.1/gratia/R/smooth-differences.R                                                                        |only
 gratia-0.4.1/gratia/R/subsetting.R                                                                                |    9 
 gratia-0.4.1/gratia/R/utililties.R                                                                                |  163 ++
 gratia-0.4.1/gratia/README.md                                                                                     |  127 +-
 gratia-0.4.1/gratia/data/gss_vocab.rda                                                                            |only
 gratia-0.4.1/gratia/data/ref_sims.rda                                                                             |only
 gratia-0.4.1/gratia/man/add_fitted.Rd                                                                             |only
 gratia-0.4.1/gratia/man/add_fitted.gam.Rd                                                                         |only
 gratia-0.4.1/gratia/man/add_residuals.Rd                                                                          |only
 gratia-0.4.1/gratia/man/add_residuals.gam.Rd                                                                      |only
 gratia-0.4.1/gratia/man/appraise.Rd                                                                               |   36 
 gratia-0.4.1/gratia/man/basis.Rd                                                                                  |    6 
 gratia-0.4.1/gratia/man/data_sim.Rd                                                                               |only
 gratia-0.4.1/gratia/man/data_slice.Rd                                                                             |    5 
 gratia-0.4.1/gratia/man/datagen.Rd                                                                                |   41 
 gratia-0.4.1/gratia/man/difference_smooths.Rd                                                                     |only
 gratia-0.4.1/gratia/man/draw.difference_smooth.Rd                                                                 |only
 gratia-0.4.1/gratia/man/draw.evaluated_smooth.Rd                                                                  |   25 
 gratia-0.4.1/gratia/man/draw.gam.Rd                                                                               |   29 
 gratia-0.4.1/gratia/man/draw.smooth_samples.Rd                                                                    |    4 
 gratia-0.4.1/gratia/man/evaluate_smooth.Rd                                                                        |    7 
 gratia-0.4.1/gratia/man/family.gam.Rd                                                                             |    5 
 gratia-0.4.1/gratia/man/figures/README-appraise-figure-1.png                                                      |only
 gratia-0.4.1/gratia/man/figures/README-draw-gam-figure-1.png                                                      |only
 gratia-0.4.1/gratia/man/figures/README-draw-gam-figure-2d-1.png                                                   |only
 gratia-0.4.1/gratia/man/gss_vocab.Rd                                                                              |only
 gratia-0.4.1/gratia/man/is_factor_term.Rd                                                                         |only
 gratia-0.4.1/gratia/man/link.Rd                                                                                   |   34 
 gratia-0.4.1/gratia/man/observed_fitted_plot.Rd                                                                   |   11 
 gratia-0.4.1/gratia/man/posterior_samples.Rd                                                                      |    3 
 gratia-0.4.1/gratia/man/predicted_samples.Rd                                                                      |    3 
 gratia-0.4.1/gratia/man/qq_plot.Rd                                                                                |   19 
 gratia-0.4.1/gratia/man/ref_sims.Rd                                                                               |only
 gratia-0.4.1/gratia/man/residuals_linpred_plot.Rd                                                                 |   14 
 gratia-0.4.1/gratia/man/smooth_samples.Rd                                                                         |    6 
 gratia-0.4.1/gratia/man/term_variables.Rd                                                                         |only
 gratia-0.4.1/gratia/man/vars_from_label.Rd                                                                        |only
 gratia-0.4.1/gratia/tests/Examples/gratia-Ex.Rout.save                                                            |  351 ++++--
 gratia-0.4.1/gratia/tests/figs/derivatives-methods/draw-issue-47-derivatives-for-complex-factor-by.svg            |    4 
 gratia-0.4.1/gratia/tests/figs/derivatives-methods/draw-issue-47-derivatives-for-complex-ordered-factor-by.svg    |    4 
 gratia-0.4.1/gratia/tests/figs/derivatives-methods/draw-issue-47-derivatives-for-factor-by.svg                    |    4 
 gratia-0.4.1/gratia/tests/figs/derivatives-methods/draw-issue-47-derivatives-for-gamm-factor-by.svg               |    8 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-1d-smooth-for-selected-smooth-with-overall-uncertainty-false.svg |   24 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-1d-smooth-for-selected-smooth.svg                                |   28 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-2d-smooth-diff-contour-colour.svg                                |only
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-2d-smooth-with-20-contour-bins.svg                               |only
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-2d-smooth-with-5-contour-bins.svg                                |only
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-2d-smooth-without-contours.svg                                   |only
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-2d-smooth.svg                                                    |   20 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-am-with-2d-smooth.svg                                            |   20 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-am-with-continuous-by-var-fixed-scale.svg                        |   34 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-am-with-continuous-by-variable-smooth.svg                        |   34 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-am-with-factor-by-variable-smooth-with-fixed-scales.svg          |  174 +--
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-am-with-factor-by-variable-smooth.svg                            |  214 +--
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-derivatives-for-a-gam-with-fixed-scales.svg                      |  356 +++---
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-evaluated-parametric-term-with-linear-parametric-term.svg        |  448 ++++----
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-evaluated-re-smooth-with-factor-by.svg                           |    2 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-evaluated-re-smooth.svg                                          |    2 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-evaulated-2d-smooth-standard-errors.svg                          |   86 -
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-model-with-fs-smooth-fixed-scales.svg                        |  150 +-
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-model-with-fs-smooth.svg                                     |   76 -
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-model-with-non-standard-names.svg                            |   40 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-model-with-ranef-smooth-factor-by-fixed-scales.svg           |  386 +++---
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-model-with-ranef-smooth-factor-by.svg                        |  174 +--
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-model-with-ranef-smooth-fixed-scales.svg                     |  266 ++--
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-model-with-ranef-smooth.svg                                  |  176 +--
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-smooth-for-selected-smooth-character.svg                     |   32 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-smooth-for-selected-smooth-logical.svg                       |   38 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-smooth-for-selected-smooth-numeric.svg                       |   32 
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-smooth-for-two-selected-smooths-character.svg                |   70 -
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-smooth-for-two-selected-smooths-logical.svg                  |   70 -
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-smooth-for-two-selected-smooths-numeric.svg                  |   70 -
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-with-factor-parametric-term.svg                              |  138 +-
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-with-linear-parametric-term.svg                              |  138 +-
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-with-overall-uncertainty-false.svg                           |  156 +-
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-with-partial-match-true.svg                                  |  114 +-
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-with-select-and-parametric-is-false.svg                      |  114 +-
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-with-select-and-parametric-is-null.svg                       |  114 +-
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-with-select-and-parametric-is-true.svg                       |  174 +--
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-without-select-and-parametric-is-false.svg                   |  154 +-
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-gam-without-select-and-parametric-is-true.svg                    |  214 +--
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-issue-39-empty-plots.svg                                         |  196 +--
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-simple-multi-smooth-am-with-fixed-scales.svg                     |  184 +--
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-simple-multi-smooth-am.svg                                       |  147 +-
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-simple-partial-residuals-with-fixed-scales.svg                   |only
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-simple-partial-residuals.svg                                     |only
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-std-error-of-2d-smooth.svg                                       |   86 -
 gratia-0.4.1/gratia/tests/figs/draw-methods/draw-ziplss-parametric-terms-issue-45.svg                             |  188 +--
 gratia-0.4.1/gratia/tests/figs/draw-methods/issue-22-draw-with-mixed-random-effects.svg                           |only
 gratia-0.4.1/gratia/tests/figs/draw-methods/issue-73-draw-uses-fixed-scales-if-asked-for-them.svg                 |only
 gratia-0.4.1/gratia/tests/figs/qq-plot-methods/qq-plot-data-simulation-pearson-residuals.svg                      |    2 
 gratia-0.4.1/gratia/tests/figs/qq-plot-methods/qq-plot-data-simulation-response-residuals.svg                     |    2 
 gratia-0.4.1/gratia/tests/figs/qq-plot-methods/qq-plot-data-simulation.svg                                        |    2 
 gratia-0.4.1/gratia/tests/figs/test-by-variables/continuous-by-variable-smmoth.svg                                |   40 
 gratia-0.4.1/gratia/tests/figs/test-by-variables/draw-gam-user-select-and-parametric-true.svg                     |   92 -
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-bird-move-model-1.svg                            |   40 
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-bird-move-model-2.svg                            |   82 -
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-bird-move-model-3.svg                            |  405 +++----
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-bird-move-model-5.svg                            |  343 +++---
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-co2-model-1.svg                                  |   42 
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-co2-model-2.svg                                  |   40 
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-co2-model-3.svg                                  |  535 ++++-----
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-co2-model-5.svg                                  |  446 ++++----
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-zoop-model-4.svg                                 |    2 
 gratia-0.4.1/gratia/tests/figs/test-hgam-paper-models/hgam-paper-zoop-model-5.svg                                 |  342 +++---
 gratia-0.4.1/gratia/tests/testthat/test-add-functions.R                                                           |only
 gratia-0.4.1/gratia/tests/testthat/test-data-sim.R                                                                |only
 gratia-0.4.1/gratia/tests/testthat/test-data-slice.R                                                              |    2 
 gratia-0.4.1/gratia/tests/testthat/test-datagen.R                                                                 |only
 gratia-0.4.1/gratia/tests/testthat/test-derivatives.R                                                             |    5 
 gratia-0.4.1/gratia/tests/testthat/test-difference-smooths.R                                                      |only
 gratia-0.4.1/gratia/tests/testthat/test-draw-methods.R                                                            |   64 +
 gratia-0.4.1/gratia/tests/testthat/test-evaluate-parametric-terms.R                                               |only
 gratia-0.4.1/gratia/tests/testthat/test-evaluate-smooth-methods.R                                                 |   39 
 gratia-0.4.1/gratia/tests/testthat/test-family-utils.R                                                            |  427 +++++++
 gratia-0.4.1/gratia/tests/testthat/test-hgam-paper.R                                                              |   13 
 gratia-0.4.1/gratia/tests/testthat/test-posterior-samples.R                                                       |   13 
 gratia-0.4.1/gratia/tests/testthat/test-utilities.R                                                               |   14 
 136 files changed, 6475 insertions(+), 4575 deletions(-)

More information about gratia at CRAN
Permanent link

Package MrSGUIDE updated to version 0.1.1 with previous version 0.1.0 dated 2020-05-29

Title: Multiple Responses Subgroup Identification using 'GUIDE' Algorithm
Description: An R implementation of 'GUIDE' style algorithm focusing on subgroup identification problem under multiple responses of Loh et al. (2019) <doi:10.1002/widm.1326>. This package is intended for use for randomized trials and observational studies.
Author: Peigen Zhou [aut, cre] (<https://orcid.org/0000-0003-4609-0374>), Wei-Yin Loh [aut] (<https://orcid.org/0000-0001-6983-2495>)
Maintainer: Peigen Zhou <pzhou9@wisc.edu>

Diff between MrSGUIDE versions 0.1.0 dated 2020-05-29 and 0.1.1 dated 2020-05-30

 DESCRIPTION                   |    8 -
 MD5                           |    8 -
 NEWS.md                       |    4 
 inst/doc/UsageOfMrSGUIDE.html |  226 ++++++++++++++++++++++--------------------
 src/regression.cpp            |    6 -
 5 files changed, 135 insertions(+), 117 deletions(-)

More information about MrSGUIDE at CRAN
Permanent link

Package ggstatsplot updated to version 0.5.0 with previous version 0.4.0 dated 2020-04-15

Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It is targeted primarily at behavioral sciences community to provide a one-line code to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms, dot plots, dot-and-whisker plots) or categorical (pie and bar charts) data. Currently, it supports only the most common types of statistical tests: parametric, nonparametric, robust, and bayesian versions of t-test/anova, correlation analyses, contingency table analysis, meta-analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, cph] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

Diff between ggstatsplot versions 0.4.0 dated 2020-04-15 and 0.5.0 dated 2020-05-30

 ggstatsplot-0.4.0/ggstatsplot/man/figures/README-theme_ggstatsplot-1.png   |only
 ggstatsplot-0.4.0/ggstatsplot/tests/testthat/test-helpers_ggbetweenstats.R |only
 ggstatsplot-0.5.0/ggstatsplot/DESCRIPTION                                  |   28 
 ggstatsplot-0.5.0/ggstatsplot/MD5                                          |  164 +-
 ggstatsplot-0.5.0/ggstatsplot/NAMESPACE                                    |    9 
 ggstatsplot-0.5.0/ggstatsplot/NEWS.md                                      |   54 
 ggstatsplot-0.5.0/ggstatsplot/R/attach.R                                   |only
 ggstatsplot-0.5.0/ggstatsplot/R/ggbarstats.R                               |   17 
 ggstatsplot-0.5.0/ggstatsplot/R/ggbetweenstats.R                           |   28 
 ggstatsplot-0.5.0/ggstatsplot/R/ggcoefstats.R                              |  135 --
 ggstatsplot-0.5.0/ggstatsplot/R/ggcorrmat.R                                |   28 
 ggstatsplot-0.5.0/ggstatsplot/R/ggdotplotstats.R                           |   11 
 ggstatsplot-0.5.0/ggstatsplot/R/gghistostats.R                             |   14 
 ggstatsplot-0.5.0/ggstatsplot/R/ggpiestats.R                               |   34 
 ggstatsplot-0.5.0/ggstatsplot/R/ggwithinstats.R                            |   47 
 ggstatsplot-0.5.0/ggstatsplot/R/helpers_ggbetweenstats_graphics.R          |  100 -
 ggstatsplot-0.5.0/ggstatsplot/R/helpers_ggcoefstats_graphics.R             |   37 
 ggstatsplot-0.5.0/ggstatsplot/R/helpers_messages.R                         |    2 
 ggstatsplot-0.5.0/ggstatsplot/R/helpers_theme_ggstatsplot.R                |   41 
 ggstatsplot-0.5.0/ggstatsplot/R/reexports.R                                |   10 
 ggstatsplot-0.5.0/ggstatsplot/README.md                                    |  115 -
 ggstatsplot-0.5.0/ggstatsplot/inst/CITATION                                |    8 
 ggstatsplot-0.5.0/ggstatsplot/inst/WORDLIST                                |    2 
 ggstatsplot-0.5.0/ggstatsplot/inst/doc/additional.html                     |   17 
 ggstatsplot-0.5.0/ggstatsplot/man/aesthetic_addon.Rd                       |  135 --
 ggstatsplot-0.5.0/ggstatsplot/man/cat_counter.Rd                           |    4 
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggbarstats1-1.png         |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggbetweenstats1-1.png     |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggbetweenstats2-1.png     |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggbetweenstats3-1.png     |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggcoefstats1-1.png        |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggcoefstats2-1.png        |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggcorrmat1-1.png          |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggcorrmat2-1.png          |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggdotplotstats1-1.png     |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggdotplotstats2-1.png     |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-gghistostats1-1.png       |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-gghistostats2-1.png       |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggpiestats1-1.png         |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggpiestats2-1.png         |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggpiestats3-1.png         |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggscatterstats1-1.png     |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggscatterstats3-1.png     |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggwithinstats1-1.png      |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ggwithinstats2-1.png      |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/README-ridgeplot-1.png           |binary
 ggstatsplot-0.5.0/ggstatsplot/man/figures/ggstatsverse.jpg                 |only
 ggstatsplot-0.5.0/ggstatsplot/man/figures/logo.png                         |binary
 ggstatsplot-0.5.0/ggstatsplot/man/ggbarstats.Rd                            |   38 
 ggstatsplot-0.5.0/ggstatsplot/man/ggbetweenstats.Rd                        |    8 
 ggstatsplot-0.5.0/ggstatsplot/man/ggcoefstats.Rd                           |   70 -
 ggstatsplot-0.5.0/ggstatsplot/man/ggcoefstats_label_maker.Rd               |   18 
 ggstatsplot-0.5.0/ggstatsplot/man/ggcorrmat.Rd                             |   49 
 ggstatsplot-0.5.0/ggstatsplot/man/ggdotplotstats.Rd                        |    5 
 ggstatsplot-0.5.0/ggstatsplot/man/gghistostats.Rd                          |    7 
 ggstatsplot-0.5.0/ggstatsplot/man/ggpiestats.Rd                            |   45 
 ggstatsplot-0.5.0/ggstatsplot/man/ggsignif_adder.Rd                        |    4 
 ggstatsplot-0.5.0/ggstatsplot/man/ggstatsplot-package.Rd                   |    5 
 ggstatsplot-0.5.0/ggstatsplot/man/ggwithinstats.Rd                         |    7 
 ggstatsplot-0.5.0/ggstatsplot/man/grouped_ggbarstats.Rd                    |   31 
 ggstatsplot-0.5.0/ggstatsplot/man/grouped_ggbetweenstats.Rd                |    3 
 ggstatsplot-0.5.0/ggstatsplot/man/grouped_ggcorrmat.Rd                     |   59 
 ggstatsplot-0.5.0/ggstatsplot/man/grouped_ggdotplotstats.Rd                |    5 
 ggstatsplot-0.5.0/ggstatsplot/man/grouped_gghistostats.Rd                  |    5 
 ggstatsplot-0.5.0/ggstatsplot/man/grouped_ggpiestats.Rd                    |   87 -
 ggstatsplot-0.5.0/ggstatsplot/man/grouped_ggwithinstats.Rd                 |    3 
 ggstatsplot-0.5.0/ggstatsplot/man/histo_labeller.Rd                        |    2 
 ggstatsplot-0.5.0/ggstatsplot/man/reexports.Rd                             |    4 
 ggstatsplot-0.5.0/ggstatsplot/tests/testthat/test-ggbarstats.R             |    1 
 ggstatsplot-0.5.0/ggstatsplot/tests/testthat/test-ggbetweenstats.R         |   53 
 ggstatsplot-0.5.0/ggstatsplot/tests/testthat/test-ggcoefstats.R            |  379 -----
 ggstatsplot-0.5.0/ggstatsplot/tests/testthat/test-ggpiestats.R             |    4 
 ggstatsplot-0.5.0/ggstatsplot/tests/testthat/test-ggwithinstats.R          |   22 
 ggstatsplot-0.5.0/ggstatsplot/tests/testthat/test-helper_messages.R        |    2 
 ggstatsplot-0.5.0/ggstatsplot/tests/testthat/test-pairwise_ggsignif.R      |   23 
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/faq.Rmd                   |   21 
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/ggbetweenstats.Rmd        |   53 
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/ggcoefstats.Rmd           |  674 +++++-----
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/ggcorrmat.Rmd             |    3 
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/ggdotplotstats.Rmd        |    1 
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/gghistostats.Rmd          |    9 
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/ggpiestats.Rmd            |   12 
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/ggscatterstats.Rmd        |    3 
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/ggwithinstats.Rmd         |    8 
 ggstatsplot-0.5.0/ggstatsplot/vignettes/web_only/purrr_examples.Rmd        |   32 
 85 files changed, 1000 insertions(+), 1795 deletions(-)

More information about ggstatsplot at CRAN
Permanent link

Package worcs updated to version 0.1.2 with previous version 0.1.1 dated 2020-05-18

Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R', with a minimal amount of code. This package is based on the Workflow for Open Reproducible Code in Science (WORCS), a step-by-step procedure based on best practices for Open Science. It includes an 'RStudio' project template, several convenience functions, and all dependencies required to make your project reproducible and transparent. WORCS is explained in the tutorial paper by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2020). <doi:10.17605/OSF.IO/ZCVBS>.
Author: Caspar J. van Lissa [aut, cre] (<https://orcid.org/0000-0002-0808-5024>), Aaron Peikert [aut] (<https://orcid.org/0000-0001-7813-818X>), Andreas M. Brandmaier [aut] (<https://orcid.org/0000-0001-8765-6982>)
Maintainer: Caspar J. van Lissa <c.j.vanlissa@uu.nl>

Diff between worcs versions 0.1.1 dated 2020-05-18 and 0.1.2 dated 2020-05-30

 worcs-0.1.1/worcs/inst/rstudio/templates/project/resources/worcs_badge.png |only
 worcs-0.1.2/worcs/DESCRIPTION                                              |   21 -
 worcs-0.1.2/worcs/MD5                                                      |   70 ++-
 worcs-0.1.2/worcs/NAMESPACE                                                |    2 
 worcs-0.1.2/worcs/R/citations.R                                            |  208 +++++-----
 worcs-0.1.2/worcs/R/export.R                                               |   29 -
 worcs-0.1.2/worcs/R/github.R                                               |   86 ++--
 worcs-0.1.2/worcs/R/misc.R                                                 |   13 
 worcs-0.1.2/worcs/R/save_load.R                                            |  154 +++++--
 worcs-0.1.2/worcs/R/synthetic.R                                            |   27 +
 worcs-0.1.2/worcs/R/worcs_checklist.R                                      |    3 
 worcs-0.1.2/worcs/R/worcs_project.R                                        |  118 +++--
 worcs-0.1.2/worcs/build/vignette.rds                                       |binary
 worcs-0.1.2/worcs/inst/doc/citation.R                                      |only
 worcs-0.1.2/worcs/inst/doc/citation.Rmd                                    |only
 worcs-0.1.2/worcs/inst/doc/citation.html                                   |only
 worcs-0.1.2/worcs/inst/doc/git_cloud.R                                     |only
 worcs-0.1.2/worcs/inst/doc/git_cloud.Rmd                                   |only
 worcs-0.1.2/worcs/inst/doc/git_cloud.html                                  |only
 worcs-0.1.2/worcs/inst/doc/setup.R                                         |    7 
 worcs-0.1.2/worcs/inst/doc/setup.Rmd                                       |   30 -
 worcs-0.1.2/worcs/inst/doc/setup.html                                      |  110 -----
 worcs-0.1.2/worcs/inst/doc/workflow.R                                      |only
 worcs-0.1.2/worcs/inst/doc/workflow.Rmd                                    |only
 worcs-0.1.2/worcs/inst/doc/workflow.html                                   |only
 worcs-0.1.2/worcs/inst/rstudio/templates/project/resources/README.md       |   75 +--
 worcs-0.1.2/worcs/inst/rstudio/templates/project/resources/references.bib  |   29 -
 worcs-0.1.2/worcs/inst/rstudio/templates/project/resources/worcs_icon.png  |only
 worcs-0.1.2/worcs/inst/rstudio/templates/project/worcs.dcf                 |    4 
 worcs-0.1.2/worcs/man/closed_data.Rd                                       |   15 
 worcs-0.1.2/worcs/man/git_user.Rd                                          |   10 
 worcs-0.1.2/worcs/man/has_git_user.Rd                                      |only
 worcs-0.1.2/worcs/man/load_data.Rd                                         |    1 
 worcs-0.1.2/worcs/man/open_data.Rd                                         |   15 
 worcs-0.1.2/worcs/man/synthetic.Rd                                         |    6 
 worcs-0.1.2/worcs/man/worcs_checklist.Rd                                   |    3 
 worcs-0.1.2/worcs/man/worcs_project.Rd                                     |   10 
 worcs-0.1.2/worcs/tests/testthat/test-test-closed_data.R                   |   11 
 worcs-0.1.2/worcs/vignettes/citation.Rmd                                   |only
 worcs-0.1.2/worcs/vignettes/gh_release.png                                 |only
 worcs-0.1.2/worcs/vignettes/git_cloud.Rmd                                  |only
 worcs-0.1.2/worcs/vignettes/scholar_bib.png                                |only
 worcs-0.1.2/worcs/vignettes/setup.Rmd                                      |   30 -
 worcs-0.1.2/worcs/vignettes/vignettes.bib                                  |only
 worcs-0.1.2/worcs/vignettes/workflow.Rmd                                   |only
 45 files changed, 602 insertions(+), 485 deletions(-)

More information about worcs at CRAN
Permanent link

Package OCA updated to version 0.2 with previous version 0.1 dated 2017-02-07

Title: Optimal Capital Allocations
Description: Computes optimal capital allocations based on some standard principles such as Haircut, Overbeck type II and the Covariance Allocation Principle. It also provides some shortcuts for obtaining the Value at Risk and the Expectation Shortfall, using both the normal and the t-student distribution, see Urbina and Guillén (2014)<doi:10.1016/j.eswa.2014.05.017> and Urbina (2013)<http://hdl.handle.net/2099.1/19443>.
Author: Jilber Urbina
Maintainer: Jilber Urbina <JilberUrbina@banpro.com.ni>

Diff between OCA versions 0.1 dated 2017-02-07 and 0.2 dated 2020-05-30

 DESCRIPTION |   10 ++---
 MD5         |    6 +--
 R/VaR.R     |  101 ++++++++++++++++++++++++++++++++++++++----------------------
 man/VaR.Rd  |    8 +---
 4 files changed, 75 insertions(+), 50 deletions(-)

More information about OCA at CRAN
Permanent link

Package glca updated to version 0.1.1 with previous version 0.1.0 dated 2020-05-29

Title: Latent Class Analysis with Grouped Data
Description: Fits latent class analysis (LCA) including group variable and covariates. The group variable can be handled either by multilevel LCA described in Vermunt (2003) <DOI:10.1111/j.0081-1750.2003.t01-1-00131.x> or standard LCA at each level of group variable. The covariates can be incorporated in the form of logistic regression (Bandeen-Roche et al. (1997) <DOI:10.1080/01621459.1997.10473658>).
Author: Youngsun Kim, Hwan Chung
Maintainer: Youngsun Kim <kim0sun@korea.ac.kr>

Diff between glca versions 0.1.0 dated 2020-05-29 and 0.1.1 dated 2020-05-30

 DESCRIPTION       |    8 ++++----
 MD5               |    6 +++---
 build/partial.rdb |binary
 src/glca.cpp      |    2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)

More information about glca at CRAN
Permanent link

Package tripack updated to version 1.3-9.1 with previous version 1.3-9 dated 2020-03-06

Title: Triangulation of Irregularly Spaced Data
Description: A constrained two-dimensional Delaunay triangulation package providing both triangulation and generation of voronoi mosaics of irregular spaced data.
Author: Fortran code by R. J. Renka. R functions by Albrecht Gebhardt <albrecht.gebhardt@aau.at>. With contributions from Stephen Eglen <stephen@anc.ed.ac.uk>, Sergei Zuyev <sergei@stams.strath.ac.uk> and Denis White <white.denis@epamail.epa.gov>
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>

Diff between tripack versions 1.3-9 dated 2020-03-06 and 1.3-9.1 dated 2020-05-30

 DESCRIPTION   |    6 +++---
 MD5           |    4 ++--
 src/tripack.h |    4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

More information about tripack at CRAN
Permanent link

Package akima updated to version 0.6-2.1 with previous version 0.6-2 dated 2016-12-19

Title: Interpolation of Irregularly and Regularly Spaced Data
Description: Several cubic spline interpolation methods of H. Akima for irregular and regular gridded data are available through this package, both for the bivariate case (irregular data: ACM 761, regular data: ACM 760) and univariate case (ACM 433 and ACM 697). Linear interpolation of irregular gridded data is also covered by reusing D. J. Renkas triangulation code which is part of Akimas Fortran code. A bilinear interpolator for regular grids was also added for comparison with the bicubic interpolator on regular grids.
Author: Hiroshi Akima [aut, cph] (Fortran code (TOMS 760, 761, 697 and 433)), Albrecht Gebhardt [aut, cre, cph] (R port (interp* functions), bicubic* functions), Thomas Petzold [ctb, cph] (aspline function), Martin Maechler [ctb, cph] (interp2xyz function + enhancements), YYYY Association for Computing Machinery, Inc. [cph] (covers code from TOMS 760, 761, 697 and 433)
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>

Diff between akima versions 0.6-2 dated 2016-12-19 and 0.6-2.1 dated 2020-05-30

 DESCRIPTION      |    6 +++---
 MD5              |    7 ++++---
 src/akima.h      |   32 +++++++++++++++++---------------
 src/akima.h.keep |only
 src/init.c       |    1 +
 5 files changed, 25 insertions(+), 21 deletions(-)

More information about akima at CRAN
Permanent link

Package jsonify updated to version 1.2.0 with previous version 1.1.1 dated 2020-03-14

Title: Convert Between 'R' Objects and Javascript Object Notation (JSON)
Description: Conversions between 'R' objects and Javascript Object Notation (JSON) using the 'rapidjsonr' library <https://CRAN.R-project.org/package=rapidjsonr>.
Author: David Cooley [aut, cre], Chris Muir [ctb], Brendan Knapp [ctb] (<https://orcid.org/0000-0003-3284-4972>)
Maintainer: David Cooley <dcooley@symbolix.com.au>

Diff between jsonify versions 1.1.1 dated 2020-03-14 and 1.2.0 dated 2020-05-30

 DESCRIPTION                                          |   18 
 LICENSE                                              |only
 MD5                                                  |   31 -
 NEWS.md                                              |    5 
 README.md                                            |   16 
 build/vignette.rds                                   |binary
 inst/doc/jsonify.html                                |   14 
 inst/include/jsonify/from_json/api.hpp               |   26 -
 inst/include/jsonify/from_json/from_json.hpp         |  289 ++++-------
 inst/include/jsonify/from_json/from_json_utils.hpp   |   20 
 inst/include/jsonify/from_json/simplify/simplify.hpp |  472 +++++++------------
 inst/include/jsonify/jsonify.hpp                     |    4 
 inst/include/jsonify/to_json/utils.hpp               |    5 
 src/from_json.cpp                                    |    2 
 src/read_json.cpp                                    |    6 
 tests/testthat/test-from_json.R                      |    3 
 tests/testthat/test-from_json_simplify.R             |   12 
 17 files changed, 399 insertions(+), 524 deletions(-)

More information about jsonify at CRAN
Permanent link

Package pmdplyr updated to version 0.3.3 with previous version 0.3.1.1 dated 2020-05-15

Title: 'dplyr' Extension for Common Panel Data Maneuvers
Description: Using the 'dplyr' package as a base, adds a family of functions designed to make manipulating panel data easier. Allows the addition of indexing variables to a tibble to create a pibble, and the manipulation of data based on those indexing variables.
Author: Nick Huntington-Klein [aut, cre] (<https://orcid.org/0000-0002-7352-3991>), Philip Khor [aut] (<https://orcid.org/0000-0002-8333-1256>)
Maintainer: Nick Huntington-Klein <nhuntington-klein@fullerton.edu>

Diff between pmdplyr versions 0.3.1.1 dated 2020-05-15 and 0.3.3 dated 2020-05-30

 DESCRIPTION                             |   14 
 MD5                                     |   54 +--
 NAMESPACE                               |    2 
 NEWS.md                                 |    8 
 R/inexact_join.R                        |   33 +
 R/major_mutate_variations.R             |    2 
 R/panel_consistency.R                   |   59 ++-
 R/panel_convert.R                       |   40 +-
 R/pibble.R                              |    2 
 R/tbl_pb_methods.R                      |   31 +
 R/tlag.R                                |    6 
 build/vignette.rds                      |binary
 inst/doc/dplyr_variants.html            |  524 +++++++++++++++---------------
 inst/doc/panel_tools.R                  |    2 
 inst/doc/panel_tools.Rmd                |    2 
 inst/doc/panel_tools.html               |  550 ++++++++++++++++----------------
 inst/doc/pmdplyr.html                   |  338 +++++++++----------
 man/SPrail.Rd                           |    6 
 man/Scorecard.Rd                        |    6 
 man/join.Rd                             |   47 +-
 man/mutate_cascade.Rd                   |    2 
 man/pipe.Rd                             |   24 -
 tests/testthat/test-bad_input.R         |    1 
 tests/testthat/test-inexact_join.R      |   17 
 tests/testthat/test-panel_consistency.R |    9 
 tests/testthat/test-panel_convert.R     |    1 
 tests/testthat/test-pibble.R            |    4 
 vignettes/panel_tools.Rmd               |    2 
 28 files changed, 973 insertions(+), 813 deletions(-)

More information about pmdplyr at CRAN
Permanent link

Package exiftoolr updated to version 0.1.3 with previous version 0.1.2 dated 2019-06-07

Title: ExifTool Functionality from R
Description: Reads, writes, and edits EXIF and other file metadata using ExifTool <https://exiftool.org/>, returning read results as a data frame. ExifTool supports many different metadata formats including EXIF, GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP and ID3, as well as the maker notes of many digital cameras by Canon, Casio, DJI, FLIR, FujiFilm, GE, GoPro, HP, JVC/Victor, Kodak, Leaf, Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson, Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung, Sanyo, Sigma/Foveon and Sony.
Author: Joshua O'Brien [aut, cre]
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>

Diff between exiftoolr versions 0.1.2 dated 2019-06-07 and 0.1.3 dated 2020-05-30

 DESCRIPTION                |   14 ++--
 MD5                        |   17 ++---
 NAMESPACE                  |    2 
 R/exif_read.R              |   46 +++++++-------
 R/install.R                |only
 R/utils.R                  |  145 ++++++++-------------------------------------
 man/configure_exiftoolr.Rd |   58 +++++++++---------
 man/exif_call.Rd           |  143 ++++++++++++++++++++++----------------------
 man/exif_read.Rd           |  141 +++++++++++++++++++++----------------------
 man/install_exiftool.Rd    |   77 +++++++++++++----------
 10 files changed, 280 insertions(+), 363 deletions(-)

More information about exiftoolr at CRAN
Permanent link

Package spaMM updated to version 3.3.0 with previous version 3.2.0 dated 2020-04-20

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 3.2.0 dated 2020-04-20 and 3.3.0 dated 2020-05-30

 spaMM-3.2.0/spaMM/tests/testthat/test-Matern-spprec.R             |only
 spaMM-3.3.0/spaMM/DESCRIPTION                                     |   15 
 spaMM-3.3.0/spaMM/MD5                                             |  234 +++++----
 spaMM-3.3.0/spaMM/NAMESPACE                                       |    4 
 spaMM-3.3.0/spaMM/R/COMPoisson.R                                  |    2 
 spaMM-3.3.0/spaMM/R/HLCor.R                                       |   35 -
 spaMM-3.3.0/spaMM/R/HLCor_body.R                                  |   78 ---
 spaMM-3.3.0/spaMM/R/HLFactorList.R                                |   83 +--
 spaMM-3.3.0/spaMM/R/HLfit.R                                       |   26 -
 spaMM-3.3.0/spaMM/R/HLfit_Internals.R                             |  235 ++++++----
 spaMM-3.3.0/spaMM/R/HLfit_body.R                                  |  209 ++++----
 spaMM-3.3.0/spaMM/R/HLframes.R                                    |   63 +-
 spaMM-3.3.0/spaMM/R/LR.R                                          |   75 ++-
 spaMM-3.3.0/spaMM/R/LevM_v_h.R                                    |    7 
 spaMM-3.3.0/spaMM/R/LevM_v_h_spprec.R                             |    7 
 spaMM-3.3.0/spaMM/R/MakeCovEst.R                                  |   31 -
 spaMM-3.3.0/spaMM/R/RcppExports.R                                 |    4 
 spaMM-3.3.0/spaMM/R/bloc_lambda.R                                 |   12 
 spaMM-3.3.0/spaMM/R/calc_LRT.R                                    |    4 
 spaMM-3.3.0/spaMM/R/calc_logdisp_cov.R                            |   31 -
 spaMM-3.3.0/spaMM/R/confint.R                                     |   76 ++-
 spaMM-3.3.0/spaMM/R/corrHLfit.R                                   |  198 ++------
 spaMM-3.3.0/spaMM/R/corrHLfit_body.R                              |    1 
 spaMM-3.3.0/spaMM/R/corrMM.LRT.R                                  |    3 
 spaMM-3.3.0/spaMM/R/corrPars.R                                    |   18 
 spaMM-3.3.0/spaMM/R/correlationFns.R                              |    2 
 spaMM-3.3.0/spaMM/R/cov_new_fix.R                                 |   66 +-
 spaMM-3.3.0/spaMM/R/determine_spprec.R                            |  106 +---
 spaMM-3.3.0/spaMM/R/extractors.R                                  |  181 ++-----
 spaMM-3.3.0/spaMM/R/fit_as_ZX.R                                   |   14 
 spaMM-3.3.0/spaMM/R/fit_as_sparsePrecision.R                      |    7 
 spaMM-3.3.0/spaMM/R/fitme.R                                       |  175 +------
 spaMM-3.3.0/spaMM/R/fitme_body.R                                  |    3 
 spaMM-3.3.0/spaMM/R/fitmecorrHLfit_body_internals.R               |    9 
 spaMM-3.3.0/spaMM/R/geo_info.R                                    |    6 
 spaMM-3.3.0/spaMM/R/get_cPredVar.R                                |    8 
 spaMM-3.3.0/spaMM/R/hatvalues.R                                   |only
 spaMM-3.3.0/spaMM/R/locoptim.R                                    |    1 
 spaMM-3.3.0/spaMM/R/multiFRK.R                                    |    4 
 spaMM-3.3.0/spaMM/R/negbin.R                                      |   26 +
 spaMM-3.3.0/spaMM/R/newPLS.R                                      |    8 
 spaMM-3.3.0/spaMM/R/plot.HLfit.R                                  |    8 
 spaMM-3.3.0/spaMM/R/postfit_internals.R                           |   57 +-
 spaMM-3.3.0/spaMM/R/predict.R                                     |   88 ++-
 spaMM-3.3.0/spaMM/R/predict_marg.R                                |    4 
 spaMM-3.3.0/spaMM/R/preprocess.R                                  |  205 ++++----
 spaMM-3.3.0/spaMM/R/preprocess_internals.R                        |  215 +++++++--
 spaMM-3.3.0/spaMM/R/sXaug_EigenDense_QRP_Chol_scaled.R            |    2 
 spaMM-3.3.0/spaMM/R/sXaug_Matrix_QRP_CHM.R                        |   11 
 spaMM-3.3.0/spaMM/R/sXaug_sparsePrecisions.R                      |   41 +
 spaMM-3.3.0/spaMM/R/save.R                                        |   14 
 spaMM-3.3.0/spaMM/R/separator.R                                   |  128 +++--
 spaMM-3.3.0/spaMM/R/simulate.HL.R                                 |   13 
 spaMM-3.3.0/spaMM/R/source_MV.R                                   |    2 
 spaMM-3.3.0/spaMM/R/spaMM.data.R                                  |   14 
 spaMM-3.3.0/spaMM/R/spaMM_boot.R                                  |   74 ++-
 spaMM-3.3.0/spaMM/R/summary.HL.R                                  |   49 +-
 spaMM-3.3.0/spaMM/R/update.HL.R                                   |   13 
 spaMM-3.3.0/spaMM/R/utils.R                                       |   29 +
 spaMM-3.3.0/spaMM/build/partial.rdb                               |binary
 spaMM-3.3.0/spaMM/inst/NEWS.Rd                                    |   47 ++
 spaMM-3.3.0/spaMM/man/AIC.Rd                                      |    3 
 spaMM-3.3.0/spaMM/man/COMPoisson.Rd                               |   19 
 spaMM-3.3.0/spaMM/man/CauchyCorr.Rd                               |    4 
 spaMM-3.3.0/spaMM/man/HLCor.Rd                                    |   15 
 spaMM-3.3.0/spaMM/man/HLfit.Rd                                    |   64 --
 spaMM-3.3.0/spaMM/man/IMRF.Rd                                     |   52 +-
 spaMM-3.3.0/spaMM/man/Loaloa.Rd                                   |   14 
 spaMM-3.3.0/spaMM/man/Matern.corr.Rd                              |   16 
 spaMM-3.3.0/spaMM/man/anova.HLfit.Rd                              |   15 
 spaMM-3.3.0/spaMM/man/arabidopsis.Rd                              |   12 
 spaMM-3.3.0/spaMM/man/autoregressive.Rd                           |   44 -
 spaMM-3.3.0/spaMM/man/confint.Rd                                  |   36 -
 spaMM-3.3.0/spaMM/man/convergence.Rd                              |    2 
 spaMM-3.3.0/spaMM/man/corrHLfit.Rd                                |   28 -
 spaMM-3.3.0/spaMM/man/corrMatrix.Rd                               |   10 
 spaMM-3.3.0/spaMM/man/covStruct.Rd                                |   42 -
 spaMM-3.3.0/spaMM/man/dopar.Rd                                    |   10 
 spaMM-3.3.0/spaMM/man/extractors.Rd                               |    6 
 spaMM-3.3.0/spaMM/man/fitme.Rd                                    |   13 
 spaMM-3.3.0/spaMM/man/fixed.LRT.Rd                                |   11 
 spaMM-3.3.0/spaMM/man/get_inits_from_fit.Rd                       |    7 
 spaMM-3.3.0/spaMM/man/get_matrix.Rd                               |    6 
 spaMM-3.3.0/spaMM/man/get_ranPars.Rd                              |    7 
 spaMM-3.3.0/spaMM/man/hatvalues.HLfit.Rd                          |only
 spaMM-3.3.0/spaMM/man/how.Rd                                      |    2 
 spaMM-3.3.0/spaMM/man/is_separated.Rd                             |    6 
 spaMM-3.3.0/spaMM/man/libraries.Rd                                |only
 spaMM-3.3.0/spaMM/man/make.scaled.dist.Rd                         |   13 
 spaMM-3.3.0/spaMM/man/mapMM.Rd                                    |   17 
 spaMM-3.3.0/spaMM/man/method.Rd                                   |only
 spaMM-3.3.0/spaMM/man/options.Rd                                  |    2 
 spaMM-3.3.0/spaMM/man/phiHGLM.Rd                                  |   33 -
 spaMM-3.3.0/spaMM/man/plot.HL.Rd                                  |   12 
 spaMM-3.3.0/spaMM/man/predict.Rd                                  |   11 
 spaMM-3.3.0/spaMM/man/random-effects.Rd                           |only
 spaMM-3.3.0/spaMM/man/salamander.Rd                               |   13 
 spaMM-3.3.0/spaMM/man/scotlip.Rd                                  |    5 
 spaMM-3.3.0/spaMM/man/seaMask.Rd                                  |   34 -
 spaMM-3.3.0/spaMM/man/seeds.Rd                                    |   10 
 spaMM-3.3.0/spaMM/man/simulate.Rd                                 |    3 
 spaMM-3.3.0/spaMM/man/spaMM.Rd                                    |  115 ++--
 spaMM-3.3.0/spaMM/man/spaMM_boot.Rd                               |   17 
 spaMM-3.3.0/spaMM/man/sparse_precision.Rd                         |    5 
 spaMM-3.3.0/spaMM/man/vcov.Rd                                     |   15 
 spaMM-3.3.0/spaMM/src/RcppExports.cpp                             |   15 
 spaMM-3.3.0/spaMM/src/spaMM_linear.cpp                            |  102 +++-
 spaMM-3.3.0/spaMM/tests/test-all.R                                |    3 
 spaMM-3.3.0/spaMM/tests/testthat/test-CAR.R                       |    2 
 spaMM-3.3.0/spaMM/tests/testthat/test-IsoriX.R                    |    2 
 spaMM-3.3.0/spaMM/tests/testthat/test-augZXy.R                    |    6 
 spaMM-3.3.0/spaMM/tests/testthat/test-confint.R                   |    8 
 spaMM-3.3.0/spaMM/tests/testthat/test-dhglm.R                     |    1 
 spaMM-3.3.0/spaMM/tests/testthat/test-negbin1.R                   |    2 
 spaMM-3.3.0/spaMM/tests/testthat/test-predVar-Matern-corrMatrix.R |only
 spaMM-3.3.0/spaMM/tests/testthat/test-predVar.R                   |    3 
 spaMM-3.3.0/spaMM/tests/testthat/test-ranCoefs.R                  |    2 
 spaMM-3.3.0/spaMM/tests/testthat/test-random-slope.R              |    8 
 spaMM-3.3.0/spaMM/tests/testthat/test-separation.R                |    2 
 spaMM-3.3.0/spaMM/tests/testthat/test-simulate.R                  |    2 
 spaMM-3.3.0/spaMM/tests/testthat/test-truncated.R                 |    2 
 spaMM-3.3.0/spaMM/tests/testthat/test_outer.R                     |only
 122 files changed, 2201 insertions(+), 1789 deletions(-)

More information about spaMM at CRAN
Permanent link

Package SWMPrExtension updated to version 1.1.5 with previous version 1.1.4 dated 2020-05-04

Title: Functions for Analyzing and Plotting Estuary Monitoring Data
Description: Tools for performing routine analysis and plotting tasks with environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System <http://cdmo.baruch.sc.edu/>. This package builds on the functionality of the SWMPr package <https://cran.r-project.org/package=SWMPr>, which is used to retrieve and organize the data. The combined set of tools address common challenges associated with continuous time series data for environmental decision making, and are intended for use in annual reporting activities. References: Beck, Marcus W. (2016) <ISSN 2073-4859><https://journal.r-project.org/archive/2016-1/beck.pdf> Rudis, Bob (2014) <https://rud.is/b/2014/11/16/moving-the-earth-well-alaska-hawaii-with-r/>. United States Environmental Protection Agency (2015) <https://cfpub.epa.gov/si/si_public_record_Report.cfm?dirEntryId=327030>. United States Environmental Protection Agency (2012) <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.646.1973&rep=rep1&type=pdf>.
Author: Julie Padilla [aut, ctb], Marcus Beck [ctb], Kimberly Cressman [ctb], Dave Eslinger [cre, ctb], Bob Rudis [ctb]
Maintainer: Dave Eslinger <dave.eslinger@noaa.gov>

Diff between SWMPrExtension versions 1.1.4 dated 2020-05-04 and 1.1.5 dated 2020-05-30

 DESCRIPTION                          |    9 -
 MD5                                  |   45 ++++----
 NAMESPACE                            |    3 
 NEWS.md                              |    3 
 R/lm_p_labs.R                        |   83 +++++++++++----
 R/seasonal_dot.R                     |    2 
 data/datalist                        |only
 man/cbm_spatial.Rd                   |   44 ++++----
 man/create_sk_national_ft_results.Rd |   82 +++++++--------
 man/elk_spatial.Rd                   |   44 ++++----
 man/elknmnut.Rd                      |   44 ++++----
 man/elksmwq.Rd                       |   44 ++++----
 man/historical_range.Rd              |  180 +++++++++++++++++-----------------
 man/lm_p_labs.Rd                     |    2 
 man/load_shp_file.Rd                 |   52 +++++-----
 man/national_sk_map.Rd               |  116 +++++++++++-----------
 man/res_custom_sk_map.Rd             |  142 +++++++++++++--------------
 man/res_local_map.Rd                 |  182 +++++++++++++++++------------------
 man/res_national_map.Rd              |  120 +++++++++++------------
 man/res_sk_map.Rd                    |  182 +++++++++++++++++------------------
 man/reserve_locs.Rd                  |   52 +++++-----
 man/sampling_stations.Rd             |   44 ++++----
 man/seasonal_dot.Rd                  |    2 
 man/us_laea.Rd                       |   44 ++++----
 24 files changed, 782 insertions(+), 739 deletions(-)

More information about SWMPrExtension at CRAN
Permanent link

Package spiderbar updated to version 0.2.3 with previous version 0.2.2 dated 2019-08-19

Title: Parse and Test Robots Exclusion Protocol Files and Rules
Description: The 'Robots Exclusion Protocol' <https://www.robotstxt.org/orig.html> documents a set of standards for allowing or excluding robot/spider crawling of different areas of site content. Tools are provided which wrap The 'rep-cpp' <https://github.com/seomoz/rep-cpp> C++ library for processing these 'robots.txt' files.
Author: Bob Rudis (bob@rud.is) [aut, cre], SEOmoz, Inc [aut]
Maintainer: Bob Rudis <bob@rud.is>

Diff between spiderbar versions 0.2.2 dated 2019-08-19 and 0.2.3 dated 2020-05-30

 spiderbar-0.2.2/spiderbar/tests/test-all.R    |only
 spiderbar-0.2.2/spiderbar/tests/testthat      |only
 spiderbar-0.2.3/spiderbar/DESCRIPTION         |   12 ++++++------
 spiderbar-0.2.3/spiderbar/MD5                 |   24 ++++++++++++------------
 spiderbar-0.2.3/spiderbar/NEWS.md             |    6 ++++++
 spiderbar-0.2.3/spiderbar/R/can-fetch.r       |    3 ++-
 spiderbar-0.2.3/spiderbar/R/crawl-delay.r     |    2 +-
 spiderbar-0.2.3/spiderbar/R/robxp.r           |    8 +++++---
 spiderbar-0.2.3/spiderbar/inst/tinytest       |only
 spiderbar-0.2.3/spiderbar/man/can_fetch.Rd    |    5 ++++-
 spiderbar-0.2.3/spiderbar/man/crawl_delays.Rd |    8 ++++----
 spiderbar-0.2.3/spiderbar/man/robxp.Rd        |    8 +++-----
 spiderbar-0.2.3/spiderbar/man/sitemaps.Rd     |    2 +-
 spiderbar-0.2.3/spiderbar/man/spiderbar.Rd    |    1 -
 spiderbar-0.2.3/spiderbar/tests/tinytest.R    |only
 15 files changed, 44 insertions(+), 35 deletions(-)

More information about spiderbar at CRAN
Permanent link

Package influenceAUC updated to version 0.1.2 with previous version 0.1.1 dated 2020-02-19

Title: Identify Influential Observations in Binary Classification
Description: Ke, B. S., Chiang, A. J., & Chang, Y. C. I. (2018) <doi:10.1080/10543406.2017.1377728> provide two theoretical methods (influence function and local influence) based on the area under the receiver operating characteristic curve (AUC) to quantify the numerical impact of each observation to the overall AUC. Alternative graphical tools, cumulative lift charts, are proposed to reveal the existences and approximate locations of those influential observations through data visualization.
Author: Bo-Shiang Ke [cre, aut, cph], Yuan-chin Ivan Chang [aut], Wen-Ting Wang [aut]
Maintainer: Bo-Shiang Ke <naivete0907@gmail.com>

Diff between influenceAUC versions 0.1.1 dated 2020-02-19 and 0.1.2 dated 2020-05-30

 influenceAUC-0.1.1/influenceAUC/README.md                   |only
 influenceAUC-0.1.2/influenceAUC/DESCRIPTION                 |    8 
 influenceAUC-0.1.2/influenceAUC/MD5                         |   29 -
 influenceAUC-0.1.2/influenceAUC/NAMESPACE                   |    3 
 influenceAUC-0.1.2/influenceAUC/R/reporter.R                |   37 ++
 influenceAUC-0.1.2/influenceAUC/R/utils.R                   |  197 +++++++-----
 influenceAUC-0.1.2/influenceAUC/man/IAUC.Rd                 |  146 ++++----
 influenceAUC-0.1.2/influenceAUC/man/LAUC.Rd                 |  108 +++---
 influenceAUC-0.1.2/influenceAUC/man/fetch_output_indeces.Rd |only
 influenceAUC-0.1.2/influenceAUC/man/pinpoint.Rd             |only
 influenceAUC-0.1.2/influenceAUC/man/plot.IAUC.Rd            |    2 
 influenceAUC-0.1.2/influenceAUC/man/plot.ICLC.Rd            |    2 
 influenceAUC-0.1.2/influenceAUC/man/plot.LAUC.Rd            |    2 
 influenceAUC-0.1.2/influenceAUC/man/plot_sequentially.Rd    |   28 -
 influenceAUC-0.1.2/influenceAUC/man/print.IAUC.Rd           |    2 
 influenceAUC-0.1.2/influenceAUC/man/print.LAUC.Rd           |    2 
 influenceAUC-0.1.2/influenceAUC/man/print_output.Rd         |    2 
 17 files changed, 323 insertions(+), 245 deletions(-)

More information about influenceAUC at CRAN
Permanent link

Package FrF2 updated to version 2.2-2 with previous version 2.2-1 dated 2020-05-29

Title: Fractional Factorial Designs with 2-Level Factors
Description: Regular and non-regular Fractional Factorial 2-level designs can be created. Furthermore, analysis tools for Fractional Factorial designs with 2-level factors are offered (main effects and interaction plots for all factors simultaneously, cube plot for looking at the simultaneous effects of three factors, full or half normal plot, alias structure in a more readable format than with the built-in function alias).
Author: Ulrike Groemping
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>

Diff between FrF2 versions 2.2-1 dated 2020-05-29 and 2.2-2 dated 2020-05-30

 DESCRIPTION      |    6 +++---
 MD5              |    8 ++++----
 R/makecatlg.R    |   11 +++++++----
 inst/NEWS        |    6 ++++++
 man/makecatlg.Rd |   10 +++++-----
 5 files changed, 25 insertions(+), 16 deletions(-)

More information about FrF2 at CRAN
Permanent link

Package drat updated to version 0.1.6 with previous version 0.1.5 dated 2019-03-28

Title: 'Drat' R Archive Template
Description: Creation and use of R Repositories via helper functions to insert packages into a repository, and to add repository information to the current R session. Two primary types of repositories are support: gh-pages at GitHub, as well as local repositories on either the same machine or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel with contributions by Carl Boettiger, Neal Fultz, Sebastian Gibb, Colin Gillespie, Jan Górecki, Matt Jones, Thomas Leeper, Steven Pav, Jan Schulz, Christoph Stepper and Felix G.M. Ernst.
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between drat versions 0.1.5 dated 2019-03-28 and 0.1.6 dated 2020-05-30

 drat-0.1.5/drat/man/getPathForPackage.Rd             |only
 drat-0.1.6/drat/ChangeLog                            |  395 ++++++++++---------
 drat-0.1.6/drat/DESCRIPTION                          |   12 
 drat-0.1.6/drat/MD5                                  |   43 +-
 drat-0.1.6/drat/R/archivePackages.R                  |   22 -
 drat-0.1.6/drat/R/insertPackage.R                    |   91 ++--
 drat-0.1.6/drat/R/pruneRepo.R                        |   14 
 drat-0.1.6/drat/README.md                            |   27 -
 drat-0.1.6/drat/build/vignette.rds                   |binary
 drat-0.1.6/drat/inst/NEWS.Rd                         |   12 
 drat-0.1.6/drat/inst/doc/CombiningDratAndTravis.html |   36 +
 drat-0.1.6/drat/inst/doc/DratFAQ.html                |   65 +--
 drat-0.1.6/drat/inst/doc/DratForPackageAuthors.R     |    6 
 drat-0.1.6/drat/inst/doc/DratForPackageAuthors.html  |   71 ++-
 drat-0.1.6/drat/inst/doc/DratForPackageUsers.R       |    4 
 drat-0.1.6/drat/inst/doc/DratForPackageUsers.html    |   63 +--
 drat-0.1.6/drat/inst/doc/WhyDrat.R                   |    6 
 drat-0.1.6/drat/inst/doc/WhyDrat.html                |   67 +--
 drat-0.1.6/drat/man/addRepo.Rd                       |    1 
 drat-0.1.6/drat/man/archivePackages.Rd               |   16 
 drat-0.1.6/drat/man/identifyPackageType.Rd           |    4 
 drat-0.1.6/drat/man/insertPackage.Rd                 |   11 
 drat-0.1.6/drat/man/pruneRepo.Rd                     |   16 
 23 files changed, 572 insertions(+), 410 deletions(-)

More information about drat at CRAN
Permanent link

Package Brq updated to version 3.0 with previous version 2.5 dated 2019-04-15

Title: Bayesian Analysis of Quantile Regression Models
Description: Bayesian estimation and variable selection for quantile regression models.
Author: Rahim Alhamzawi
Maintainer: Rahim Alhamzawi (University of Al-Qadisiyah) <rahim.alhamzawi@qu.edu.iq>

Diff between Brq versions 2.5 dated 2019-04-15 and 3.0 dated 2020-05-30

 DESCRIPTION     |   10 ++--
 MD5             |   22 ++++----
 R/Brq.default.R |   44 +++++++++++++++--
 R/model.R       |   22 ++++++++
 R/plot.Brq.R    |  137 +++++++++++++++++++++++++++++---------------------------
 R/summary.Brq.R |   23 +++++++++
 data/wheat.rda  |binary
 man/DIC.Rd      |    5 +-
 man/ImmunogG.Rd |    3 -
 man/USgirl.Rd   |    3 -
 man/plot.Brq.Rd |    4 -
 man/wheat.Rd    |   28 ++++-------
 12 files changed, 189 insertions(+), 112 deletions(-)

More information about Brq at CRAN
Permanent link

Fri, 29 May 2020

Package nimbleEcology updated to version 0.3.0 with previous version 0.2.2 dated 2020-05-12

Title: Distributions for Ecological Models in 'nimble'
Description: Common ecological distributions for 'nimble' models in the form of nimbleFunction objects. Includes Cormack-Jolly-Seber, occupancy, dynamic occupancy, hidden Markov, dynamic hidden Markov, and N-mixture models. (Jolly (1965) <DOI: 10.2307/2333826>, Seber (1965) <DOI: 10.2307/2333827>, Turek et al. (2016) <doi:10.1007/s10651-016-0353-z>).
Author: Benjamin R. Goldstein [aut, cre], Daniel Turek [aut], Lauren Ponisio [aut], Perry de Valpine [aut]
Maintainer: Benjamin R. Goldstein <ben.goldstein@berkeley.edu>

Diff between nimbleEcology versions 0.2.2 dated 2020-05-12 and 0.3.0 dated 2020-05-29

 DESCRIPTION                                 |   11 
 MD5                                         |   44 ++-
 NAMESPACE                                   |    1 
 R/dCJS.R                                    |    9 
 R/dDHMM.R                                   |  239 +++++++++++++++----
 R/dDynOcc.R                                 |   17 -
 R/dHMM.R                                    |  207 ++++++++++++++--
 R/dNmixture.R                               |    9 
 R/dOcc.R                                    |   12 
 R/zzz.R                                     |   34 +-
 README.md                                   |    5 
 build                                       |only
 inst/CITATION                               |only
 inst/NEWS                                   |only
 inst/doc/Introduction_to_nimbleEcology.R    |only
 inst/doc/Introduction_to_nimbleEcology.Rmd  |only
 inst/doc/Introduction_to_nimbleEcology.html |  177 +++++++-------
 man/dCJS.Rd                                 |    9 
 man/dDHMM.Rd                                |   71 +++--
 man/dDynOcc.Rd                              |   17 -
 man/dHMM.Rd                                 |   50 ++--
 man/dNmixture.Rd                            |    9 
 man/dOcc.Rd                                 |   11 
 tests/testthat/test-DHMM.R                  |  343 +++++++++++++++++++++++++++-
 tests/testthat/test-HMM.R                   |  200 +++++++++++++++-
 vignettes                                   |only
 26 files changed, 1144 insertions(+), 331 deletions(-)

More information about nimbleEcology at CRAN
Permanent link

Package lotri updated to version 0.2.2 with previous version 0.2.1 dated 2020-02-12

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 0.2.1 dated 2020-02-12 and 0.2.2 dated 2020-05-29

 DESCRIPTION                    |   16 
 MD5                            |   32 
 NAMESPACE                      |   29 
 NEWS.md                        |   29 
 R/lotri.R                      | 1385 +++++++++++++++++++++++++----------------
 README.md                      |  337 +++++++--
 build/vignette.rds             |binary
 inst/doc/lotri-motivation.R    |  146 ++--
 inst/doc/lotri-motivation.Rmd  |  256 ++++---
 inst/doc/lotri-motivation.html |  666 +++++++++++++------
 man/as.lotri.Rd                |only
 man/figures                    |only
 man/lotri.Rd                   |  191 +++--
 man/lotriMat.Rd                |only
 man/lotriSep.Rd                |only
 src                            |only
 tests/testthat.R               |    8 
 tests/testthat/test-lotri.R    | 1245 +++++++++++++++++++++++++++---------
 vignettes/lotri-motivation.Rmd |  256 ++++---
 19 files changed, 3082 insertions(+), 1514 deletions(-)

More information about lotri at CRAN
Permanent link

Package chk updated to version 0.5.0 with previous version 0.4.0 dated 2020-03-04

Title: Check User-Supplied Function Arguments
Description: For developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), Ayla Pearson [ctb] (<https://orcid.org/0000-0001-7388-1222>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between chk versions 0.4.0 dated 2020-03-04 and 0.5.0 dated 2020-05-29

 chk-0.4.0/chk/man/chk_datetime.Rd                           |only
 chk-0.4.0/chk/tests/testthat/tests-chk-character.R          |only
 chk-0.5.0/chk/DESCRIPTION                                   |    8 
 chk-0.5.0/chk/MD5                                           |  138 +++++++-----
 chk-0.5.0/chk/NAMESPACE                                     |   19 +
 chk-0.5.0/chk/NEWS.md                                       |   16 +
 chk-0.5.0/chk/R/check-dirs.R                                |only
 chk-0.5.0/chk/R/check-files.R                               |only
 chk-0.5.0/chk/R/check-values.R                              |   19 +
 chk-0.5.0/chk/R/chk-character-or-factor.R                   |only
 chk-0.5.0/chk/R/chk-chr.R                                   |only
 chk-0.5.0/chk/R/chk-datetime.R                              |   52 +++-
 chk-0.5.0/chk/R/chk-dbl.R                                   |only
 chk-0.5.0/chk/R/chk-factor.R                                |only
 chk-0.5.0/chk/R/chk-is.R                                    |only
 chk-0.5.0/chk/R/chk-not-subset.R                            |only
 chk-0.5.0/chk/R/chk-null-or.R                               |only
 chk-0.5.0/chk/R/chk-orderset.R                              |only
 chk-0.5.0/chk/R/chk-wnum.R                                  |only
 chk-0.5.0/chk/R/deprecated.R                                |   38 ---
 chk-0.5.0/chk/R/template.R                                  |    1 
 chk-0.5.0/chk/README.md                                     |   25 --
 chk-0.5.0/chk/build/chk.pdf                                 |binary
 chk-0.5.0/chk/build/vignette.rds                            |binary
 chk-0.5.0/chk/inst/doc/chk-families.html                    |   13 -
 chk-0.5.0/chk/inst/doc/chk.html                             |   26 --
 chk-0.5.0/chk/man/check_data.Rd                             |    2 
 chk-0.5.0/chk/man/check_dim.Rd                              |    2 
 chk-0.5.0/chk/man/check_dirs.Rd                             |only
 chk-0.5.0/chk/man/check_files.Rd                            |only
 chk-0.5.0/chk/man/check_key.Rd                              |    2 
 chk-0.5.0/chk/man/check_names.Rd                            |    2 
 chk-0.5.0/chk/man/check_values.Rd                           |    6 
 chk-0.5.0/chk/man/chk_array.Rd                              |    1 
 chk-0.5.0/chk/man/chk_atomic.Rd                             |    1 
 chk-0.5.0/chk/man/chk_character.Rd                          |    2 
 chk-0.5.0/chk/man/chk_character_or_factor.Rd                |only
 chk-0.5.0/chk/man/chk_chr.Rd                                |only
 chk-0.5.0/chk/man/chk_data.Rd                               |    1 
 chk-0.5.0/chk/man/chk_date.Rd                               |    2 
 chk-0.5.0/chk/man/chk_date_time.Rd                          |only
 chk-0.5.0/chk/man/chk_dbl.Rd                                |only
 chk-0.5.0/chk/man/chk_deprecated.Rd                         |   20 -
 chk-0.5.0/chk/man/chk_double.Rd                             |    2 
 chk-0.5.0/chk/man/chk_environment.Rd                        |    2 
 chk-0.5.0/chk/man/chk_factor.Rd                             |only
 chk-0.5.0/chk/man/chk_function.Rd                           |    1 
 chk-0.5.0/chk/man/chk_integer.Rd                            |    2 
 chk-0.5.0/chk/man/chk_is.Rd                                 |only
 chk-0.5.0/chk/man/chk_join.Rd                               |    8 
 chk-0.5.0/chk/man/chk_list.Rd                               |    2 
 chk-0.5.0/chk/man/chk_logical.Rd                            |    2 
 chk-0.5.0/chk/man/chk_matrix.Rd                             |    1 
 chk-0.5.0/chk/man/chk_not_subset.Rd                         |only
 chk-0.5.0/chk/man/chk_null_or.Rd                            |only
 chk-0.5.0/chk/man/chk_number.Rd                             |    2 
 chk-0.5.0/chk/man/chk_numeric.Rd                            |    1 
 chk-0.5.0/chk/man/chk_orderset.Rd                           |only
 chk-0.5.0/chk/man/chk_s3_class.Rd                           |    1 
 chk-0.5.0/chk/man/chk_s4_class.Rd                           |    1 
 chk-0.5.0/chk/man/chk_scalar.Rd                             |    2 
 chk-0.5.0/chk/man/chk_setequal.Rd                           |   21 +
 chk-0.5.0/chk/man/chk_string.Rd                             |    2 
 chk-0.5.0/chk/man/chk_subset.Rd                             |   19 +
 chk-0.5.0/chk/man/chk_superset.Rd                           |    6 
 chk-0.5.0/chk/man/chk_tz.Rd                                 |    2 
 chk-0.5.0/chk/man/chk_vector.Rd                             |    1 
 chk-0.5.0/chk/man/chk_whole_number.Rd                       |    2 
 chk-0.5.0/chk/man/chk_whole_numeric.Rd                      |    1 
 chk-0.5.0/chk/man/chk_wnum.Rd                               |only
 chk-0.5.0/chk/man/expect_chk_error.Rd                       |   33 +-
 chk-0.5.0/chk/man/params.Rd                                 |    2 
 chk-0.5.0/chk/tests/testthat/test-aaa-deprecated.R          |   52 ++--
 chk-0.5.0/chk/tests/testthat/test-check-data.R              |    4 
 chk-0.5.0/chk/tests/testthat/test-check-dirs.R              |only
 chk-0.5.0/chk/tests/testthat/test-check-files.R             |only
 chk-0.5.0/chk/tests/testthat/test-check-values.R            |   35 +++
 chk-0.5.0/chk/tests/testthat/test-chk-character-or-factor.R |only
 chk-0.5.0/chk/tests/testthat/test-chk-character.R           |only
 chk-0.5.0/chk/tests/testthat/test-chk-chr.R                 |only
 chk-0.5.0/chk/tests/testthat/test-chk-date.R                |   14 -
 chk-0.5.0/chk/tests/testthat/test-chk-dbl.R                 |only
 chk-0.5.0/chk/tests/testthat/test-chk-factor.R              |only
 chk-0.5.0/chk/tests/testthat/test-chk-is.R                  |only
 chk-0.5.0/chk/tests/testthat/test-chk-not-subset.R          |only
 chk-0.5.0/chk/tests/testthat/test-chk-null-or.R             |only
 chk-0.5.0/chk/tests/testthat/test-chk-orderset.R            |only
 chk-0.5.0/chk/tests/testthat/test-chk-wnum.R                |only
 chk-0.5.0/chk/tests/testthat/test-date-time.R               |only
 89 files changed, 363 insertions(+), 254 deletions(-)

More information about chk at CRAN
Permanent link

Package V8 updated to version 3.1.0 with previous version 3.0.2 dated 2020-03-14

Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8: Google's open source JavaScript and WebAssembly engine. This package can be compiled either with V8 version 6 and up, a NodeJS shared library, or the legacy 3.14/3.15 branch of V8.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between V8 versions 3.0.2 dated 2020-03-14 and 3.1.0 dated 2020-05-29

 DESCRIPTION            |    6 +++---
 MD5                    |   16 ++++++++--------
 NEWS                   |    4 ++++
 build/partial.rdb      |binary
 build/vignette.rds     |binary
 configure              |   18 +++++++++++++++---
 inst/doc/npm.html      |    4 ++--
 inst/doc/v8_intro.html |    8 ++++----
 src/Makevars.in        |    2 +-
 9 files changed, 37 insertions(+), 21 deletions(-)

More information about V8 at CRAN
Permanent link

Package groupedstats updated to version 1.0.1 with previous version 1.0.0 dated 2020-05-05

Title: Grouped Statistical Analyses in a Tidy Way
Description: Collection of functions to run statistical tests across all combinations of multiple grouping variables.
Author: Indrajeet Patil [aut, cre, cph] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

Diff between groupedstats versions 1.0.0 dated 2020-05-05 and 1.0.1 dated 2020-05-29

 groupedstats-1.0.0/groupedstats/R/data.R                    |only
 groupedstats-1.0.0/groupedstats/R/groupedstats-package.R    |only
 groupedstats-1.0.0/groupedstats/data                        |only
 groupedstats-1.0.0/groupedstats/man/Titanic_full.Rd         |only
 groupedstats-1.0.0/groupedstats/man/groupedstats-package.Rd |only
 groupedstats-1.0.0/groupedstats/man/intent_morality.Rd      |only
 groupedstats-1.0.0/groupedstats/man/movies_long.Rd          |only
 groupedstats-1.0.0/groupedstats/man/movies_wide.Rd          |only
 groupedstats-1.0.0/groupedstats/tests/README.md             |only
 groupedstats-1.0.0/groupedstats/tests/testthat              |only
 groupedstats-1.0.0/groupedstats/tests/testthat.R            |only
 groupedstats-1.0.1/groupedstats/DESCRIPTION                 |   12 
 groupedstats-1.0.1/groupedstats/MD5                         |   73 ++----
 groupedstats-1.0.1/groupedstats/NAMESPACE                   |    7 
 groupedstats-1.0.1/groupedstats/NEWS.md                     |    5 
 groupedstats-1.0.1/groupedstats/R/grouped_aov.R             |   15 -
 groupedstats-1.0.1/groupedstats/R/grouped_glm.R             |   63 ++---
 groupedstats-1.0.1/groupedstats/R/grouped_glmer.R           |   24 -
 groupedstats-1.0.1/groupedstats/R/grouped_lm.R              |    1 
 groupedstats-1.0.1/groupedstats/R/grouped_lmer.R            |   11 
 groupedstats-1.0.1/groupedstats/R/grouped_p_value.R         |   12 
 groupedstats-1.0.1/groupedstats/R/grouped_proptest.R        |    9 
 groupedstats-1.0.1/groupedstats/R/grouped_slr.R             |    1 
 groupedstats-1.0.1/groupedstats/R/grouped_summary.R         |   13 -
 groupedstats-1.0.1/groupedstats/R/grouped_ttest.R           |    1 
 groupedstats-1.0.1/groupedstats/R/grouped_wilcox.R          |    1 
 groupedstats-1.0.1/groupedstats/README.md                   |  146 +++++-------
 groupedstats-1.0.1/groupedstats/inst/WORDLIST               |   11 
 groupedstats-1.0.1/groupedstats/man/grouped_aov.Rd          |   17 -
 groupedstats-1.0.1/groupedstats/man/grouped_glm.Rd          |   24 -
 groupedstats-1.0.1/groupedstats/man/grouped_glmer.Rd        |   28 --
 groupedstats-1.0.1/groupedstats/man/grouped_lm.Rd           |    3 
 groupedstats-1.0.1/groupedstats/man/grouped_lmer.Rd         |    4 
 groupedstats-1.0.1/groupedstats/man/grouped_proptest.Rd     |    3 
 groupedstats-1.0.1/groupedstats/man/grouped_slr.Rd          |    3 
 groupedstats-1.0.1/groupedstats/man/grouped_summary.Rd      |    5 
 groupedstats-1.0.1/groupedstats/man/grouped_ttest.Rd        |    3 
 groupedstats-1.0.1/groupedstats/man/grouped_wilcox.Rd       |    3 
 38 files changed, 166 insertions(+), 332 deletions(-)

More information about groupedstats at CRAN
Permanent link

Package tidytable updated to version 0.5.1 with previous version 0.5.0 dated 2020-05-23

Title: Tidy Interface to 'data.table'
Description: Tidy interface to 'data.table'. 'rlang' compatible, which allows the user to build custom functions much like they would in the tidyverse.
Author: Mark Fairbanks [aut, cre], Tyson Barrett [ctb], Ivan Leung [ctb], Ross Kennedy [ctb], Lionel Henry [ctb], Matt Carlson [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>

Diff between tidytable versions 0.5.0 dated 2020-05-23 and 0.5.1 dated 2020-05-29

 DESCRIPTION                            |    6 ++---
 MD5                                    |   31 ++++++++++++++++-------------
 NAMESPACE                              |    7 +++++-
 NEWS.md                                |    7 ++++++
 R/bind.R                               |   21 ++++---------------
 R/distinct.R                           |    5 +++-
 R/fill.R                               |    8 +++----
 R/map.R                                |    5 ++--
 R/map2.R                               |   14 +------------
 R/mutate_across.R                      |    3 --
 R/summarize_across.R                   |only
 R/tidytable_package.R                  |    7 +++---
 README.md                              |   35 ++++++++++++++++-----------------
 man/map..Rd                            |    5 ++--
 man/mutate_across..Rd                  |    3 --
 man/summarize_across..Rd               |only
 tests/testthat/test-distinct.R         |    4 +--
 tests/testthat/test-summarize_across.R |only
 18 files changed, 79 insertions(+), 82 deletions(-)

More information about tidytable at CRAN
Permanent link

Package iSTATS updated to version 1.3 with previous version 1.2 dated 2020-02-11

Title: A Graphical Interface to Perform STOCSY Analyses on NMR Data
Description: Launches a 'shiny' based application for Nuclear Magnetic Resonance (NMR) data importation and Statistical TOtal Correlation SpectroscopY (STOCSY) analyses in a full interactive approach. The theoretical background and applications of STOCSY method could be found at Cloarec, O., Dumas, M. E., Craig, A., Barton, R. H., Trygg, J., Hudson, J., Blancher, C., Gauguier, D., Lindon, J. C., Holmes, E. & Nicholson, J. (2005) <doi:10.1021/ac048630x>.
Author: Luiz Henrique Keng Queiroz Junior[aut,cre], Vitor Mendes de Oliveira [aut]
Maintainer: Luiz Henrique Keng Queiroz Junior <keng@ufg.br>

Diff between iSTATS versions 1.2 dated 2020-02-11 and 1.3 dated 2020-05-29

 iSTATS-1.2/iSTATS/data/datalist                     |only
 iSTATS-1.2/iSTATS/inst/app/www/ISTATS.1.png         |only
 iSTATS-1.2/iSTATS/inst/app/www/ISTATS.2.png         |only
 iSTATS-1.2/iSTATS/inst/app/www/ISTATS.png           |only
 iSTATS-1.2/iSTATS/inst/app/www/epsspec.png          |only
 iSTATS-1.2/iSTATS/inst/app/www/fluxogram.png        |only
 iSTATS-1.2/iSTATS/inst/app/www/jpegspec.png         |only
 iSTATS-1.3/iSTATS/DESCRIPTION                       |   15 
 iSTATS-1.3/iSTATS/MD5                               |   62 -
 iSTATS-1.3/iSTATS/R/main.R                          |   68 -
 iSTATS-1.3/iSTATS/inst/app/Pretreatment_server.R    |only
 iSTATS-1.3/iSTATS/inst/app/Pretreatment_ui.R        |only
 iSTATS-1.3/iSTATS/inst/app/about_ui.R               |   26 
 iSTATS-1.3/iSTATS/inst/app/example_data_server.R    |   13 
 iSTATS-1.3/iSTATS/inst/app/functions.R              |  500 +++++++++---
 iSTATS-1.3/iSTATS/inst/app/global.R                 |   83 +-
 iSTATS-1.3/iSTATS/inst/app/home_ui.R                |    2 
 iSTATS-1.3/iSTATS/inst/app/plot_interativo_server.R |  458 +++++------
 iSTATS-1.3/iSTATS/inst/app/select_signals_server.R  |  533 +++----------
 iSTATS-1.3/iSTATS/inst/app/select_signals_ui.R      |   30 
 iSTATS-1.3/iSTATS/inst/app/server.R                 |   13 
 iSTATS-1.3/iSTATS/inst/app/stocsy_i_server.R        |  812 ++++++++------------
 iSTATS-1.3/iSTATS/inst/app/stocsy_i_ui.R            |  268 +++---
 iSTATS-1.3/iSTATS/inst/app/stocsy_is_server.R       |   10 
 iSTATS-1.3/iSTATS/inst/app/stocsy_is_ui.R           |    2 
 iSTATS-1.3/iSTATS/inst/app/stocsy_rt_server.R       |   14 
 iSTATS-1.3/iSTATS/inst/app/stocsy_rt_ui.R           |    2 
 iSTATS-1.3/iSTATS/inst/app/ui.R                     |  148 +--
 iSTATS-1.3/iSTATS/inst/app/uploader_server.R        |  317 ++-----
 iSTATS-1.3/iSTATS/inst/app/uploader_server_CSV.R    |  466 +++++------
 iSTATS-1.3/iSTATS/inst/app/uploader_server_Rdata.R  |  222 ++---
 iSTATS-1.3/iSTATS/inst/app/www/download_buckets.png |only
 iSTATS-1.3/iSTATS/inst/app/www/download_points.png  |only
 iSTATS-1.3/iSTATS/inst/app/www/istats1.gif          |only
 iSTATS-1.3/iSTATS/inst/app/www/zoo.css              |  275 +++---
 iSTATS-1.3/iSTATS/man/CS_values_real.Rd             |    4 
 iSTATS-1.3/iSTATS/man/NMRData.Rd                    |    4 
 iSTATS-1.3/iSTATS/man/file_names.Rd                 |    4 
 38 files changed, 2066 insertions(+), 2285 deletions(-)

More information about iSTATS at CRAN
Permanent link

Package ArchaeoPhases updated to version 1.4.5 with previous version 1.4 dated 2019-01-02

Title: Post-Processing of the Markov Chain Simulated by 'ChronoModel', 'Oxcal' or 'BCal'
Description: Provides a list of functions for the statistical analysis of archaeological dates and groups of dates (see <doi:10.18637/jss.v093.c01> for a description). It is based on the post-processing of the Markov Chains whose stationary distribution is the posterior distribution of a series of dates. Such output can be simulated by different applications as for instance 'ChronoModel' (see <http://www.chronomodel.fr>), 'Oxcal' (see <https://c14.arch.ox.ac.uk/oxcal.html>) or 'BCal' (see <http://bcal.shef.ac.uk/>). The only requirement is to have a csv file containing a sample from the posterior distribution.
Author: Anne Philippe [aut, cre], Marie-Anne Vibet [aut], Thomas S. Dye [ctb]
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>

Diff between ArchaeoPhases versions 1.4 dated 2019-01-02 and 1.4.5 dated 2020-05-29

 DESCRIPTION                 |   12 +++++------
 MD5                         |   48 ++++++++++++++++++++++----------------------
 build/vignette.rds          |binary
 inst/CITATION               |   32 ++++++++++++++++-------------
 inst/doc/GroupsOfDates.Rmd  |    4 +--
 inst/doc/GroupsOfDates.html |    8 +++----
 inst/doc/Introduction.Rmd   |    4 +--
 inst/doc/Introduction.html  |   10 ++++-----
 inst/doc/SeriesOfDates.Rmd  |    4 +--
 inst/doc/SeriesOfDates.html |   33 +++++++++++++++++++++++++-----
 man/CreateMinMaxGroup.Rd    |    2 -
 man/ImportCSV.BCal.Rd       |    4 +--
 man/ImportCSV.Rd            |   12 +++++------
 man/MarginalPlot.Rd         |    2 -
 man/MultiPhasePlot.Rd       |    2 -
 man/MultiSuccessionPlot.Rd  |    5 +++-
 man/OccurrencePlot.Rd       |    3 ++
 man/PhasePlot.Rd            |    9 +++++---
 man/PhaseTimeRange.Rd       |    8 +++++++
 man/PhasesGap.Rd            |    3 ++
 man/PhasesTransition.Rd     |    4 ++-
 man/SuccessionPlot.Rd       |    4 +--
 vignettes/GroupsOfDates.Rmd |    4 +--
 vignettes/Introduction.Rmd  |    4 +--
 vignettes/SeriesOfDates.Rmd |    4 +--
 25 files changed, 135 insertions(+), 90 deletions(-)

More information about ArchaeoPhases at CRAN
Permanent link

Package rfacebookstat updated to version 2.1.1 with previous version 2.1.0 dated 2020-05-27

Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager from Facebook Marketing API into R. For more details see official documents by Facebook Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>)
Maintainer: Alexey Seleznev <selesnow@gmail.com>

Diff between rfacebookstat versions 2.1.0 dated 2020-05-27 and 2.1.1 dated 2020-05-29

 DESCRIPTION                                |    8 
 MD5                                        |   14 -
 NEWS.md                                    |    6 
 R/fbGetCostData.R                          |    2 
 build/partial.rdb                          |binary
 inst/doc/rfacebookstat-authorization.html  |   60 +++----
 inst/doc/rfacebookstat-cost-data.html      |   86 +++++-----
 inst/doc/rfacebookstat-get-statistics.html |  238 ++++++++++++++---------------
 8 files changed, 213 insertions(+), 201 deletions(-)

More information about rfacebookstat at CRAN
Permanent link

Package nucim updated to version 1.0.9 with previous version 1.0.6 dated 2018-10-09

Title: Nucleome Imaging Toolbox
Description: Tools for 4D nucleome imaging. Quantitative analysis of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy. See Volker J. Schmid, Marion Cremer, Thomas Cremer (2017) <doi:10.1016/j.ymeth.2017.03.013>.
Author: Volker Schmid [aut, cre]
Maintainer: Volker Schmid <stats@volkerschmid.de>

Diff between nucim versions 1.0.6 dated 2018-10-09 and 1.0.9 dated 2020-05-29

 nucim-1.0.6/nucim/inst/doc/publications.R                  |only
 nucim-1.0.6/nucim/inst/doc/publications.Rmd                |only
 nucim-1.0.6/nucim/inst/doc/publications.html               |only
 nucim-1.0.9/nucim/DESCRIPTION                              |   21 
 nucim-1.0.9/nucim/MD5                                      |   77 +-
 nucim-1.0.9/nucim/NEWS                                     |    8 
 nucim-1.0.9/nucim/R/classes.R                              |    1 
 nucim-1.0.9/nucim/R/colorsinclasses.R                      |   14 
 nucim-1.0.9/nucim/R/plot_classify_folder.R                 |    1 
 nucim-1.0.9/nucim/R/plot_nearest_class_folder.R            |    2 
 nucim-1.0.9/nucim/R/splitchannels.R                        |    4 
 nucim-1.0.9/nucim/R/spots_combined.R                       |   13 
 nucim-1.0.9/nucim/README.md                                |   10 
 nucim-1.0.9/nucim/build/vignette.rds                       |binary
 nucim-1.0.9/nucim/inst/doc/DAPIclassification.Rmd          |    4 
 nucim-1.0.9/nucim/inst/doc/DAPIclassification.html         |  217 ++++++
 nucim-1.0.9/nucim/inst/doc/workflow.html                   |  426 ++++++++++---
 nucim-1.0.9/nucim/inst/doc/workflow_many.Rmd               |    4 
 nucim-1.0.9/nucim/inst/doc/workflow_many.html              |  217 ++++++
 nucim-1.0.9/nucim/man/barplot_with_interval.Rd             |   11 
 nucim-1.0.9/nucim/man/barplot_with_interval_23.Rd          |   10 
 nucim-1.0.9/nucim/man/classify.folder.Rd                   |    3 
 nucim-1.0.9/nucim/man/colors.in.classes.Rd                 |   26 
 nucim-1.0.9/nucim/man/colors.in.classes.folder.Rd          |   17 
 nucim-1.0.9/nucim/man/compute.distance2border.Rd           |   10 
 nucim-1.0.9/nucim/man/dapimask.Rd                          |   10 
 nucim-1.0.9/nucim/man/dapimask.file.Rd                     |   10 
 nucim-1.0.9/nucim/man/dapimask.folder.Rd                   |    9 
 nucim-1.0.9/nucim/man/find.spots.file.Rd                   |   12 
 nucim-1.0.9/nucim/man/find.spots.folder.Rd                 |   10 
 nucim-1.0.9/nucim/man/nearestClassDistances.folder.Rd      |    9 
 nucim-1.0.9/nucim/man/plot_classify.folder.Rd              |    9 
 nucim-1.0.9/nucim/man/plot_nearestClassDistances.folder.Rd |   11 
 nucim-1.0.9/nucim/man/splitchannels.Rd                     |    2 
 nucim-1.0.9/nucim/man/splitchannels.file.Rd                |    2 
 nucim-1.0.9/nucim/man/splitchannels.folder.Rd              |    8 
 nucim-1.0.9/nucim/man/spots.combined.Rd                    |   19 
 nucim-1.0.9/nucim/man/spots.combined.file.Rd               |   17 
 nucim-1.0.9/nucim/man/spots.combined.folder.Rd             |   17 
 nucim-1.0.9/nucim/vignettes/DAPIclassification.Rmd         |    4 
 nucim-1.0.9/nucim/vignettes/workflow_many.Rmd              |    4 
 41 files changed, 1022 insertions(+), 227 deletions(-)

More information about nucim at CRAN
Permanent link

Package fresh updated to version 0.2.0 with previous version 0.1.0 dated 2019-10-21

Title: Create Custom 'Bootstrap' Themes to Use in 'Shiny'
Description: Customize 'Bootstrap' and 'Bootswatch' themes, like colors, fonts, grid layout, to use in 'Shiny' applications, 'rmarkdown' documents and 'flexdashboard'.
Author: Victor Perrier [aut, cre, cph], Fanny Meyer [aut], Thomas Park [ctb, cph] (Bootswatch themes), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), onkbear [ctb, cph] (admin-lte-2-sass), Colorlib [ctb, cph] (AdminLTE)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between fresh versions 0.1.0 dated 2019-10-21 and 0.2.0 dated 2020-05-29

 fresh-0.1.0/fresh/inst/assets/adminlte                                |only
 fresh-0.1.0/fresh/inst/assets/bootstrap3                              |only
 fresh-0.1.0/fresh/inst/doc/shiny.R                                    |only
 fresh-0.1.0/fresh/inst/doc/shiny.Rmd                                  |only
 fresh-0.1.0/fresh/inst/doc/shiny.html                                 |only
 fresh-0.1.0/fresh/inst/examples/default                               |only
 fresh-0.1.0/fresh/inst/examples/shiny-fluid/www                       |only
 fresh-0.1.0/fresh/man/vars_file.Rd                                    |only
 fresh-0.1.0/fresh/vignettes/shiny.Rmd                                 |only
 fresh-0.2.0/fresh/DESCRIPTION                                         |   22 
 fresh-0.2.0/fresh/MD5                                                 |  827 ++++++----
 fresh-0.2.0/fresh/NAMESPACE                                           |   21 
 fresh-0.2.0/fresh/NEWS.md                                             |    9 
 fresh-0.2.0/fresh/R/create_theme.R                                    |   74 
 fresh-0.2.0/fresh/R/search-vars.R                                     |only
 fresh-0.2.0/fresh/R/use_vars_template.R                               |   42 
 fresh-0.2.0/fresh/R/utils.R                                           |   33 
 fresh-0.2.0/fresh/R/vars-adminlte.R                                   |   89 -
 fresh-0.2.0/fresh/R/vars-bootstrap.R                                  |  190 +-
 fresh-0.2.0/fresh/R/vars-bs4dash.R                                    |only
 fresh-0.2.0/fresh/README.md                                           |  141 +
 fresh-0.2.0/fresh/build/fresh.pdf                                     |only
 fresh-0.2.0/fresh/build/vignette.rds                                  |binary
 fresh-0.2.0/fresh/inst/assets/AdminLTE-2.4.10                         |only
 fresh-0.2.0/fresh/inst/assets/AdminLTE-3.0.4                          |only
 fresh-0.2.0/fresh/inst/assets/bootstrap-3.4.1                         |only
 fresh-0.2.0/fresh/inst/assets/bootstrap-4.3.1                         |only
 fresh-0.2.0/fresh/inst/assets/default                                 |only
 fresh-0.2.0/fresh/inst/doc/fresh.R                                    |only
 fresh-0.2.0/fresh/inst/doc/fresh.Rmd                                  |only
 fresh-0.2.0/fresh/inst/doc/fresh.html                                 |only
 fresh-0.2.0/fresh/inst/doc/vars-bs4dash.R                             |only
 fresh-0.2.0/fresh/inst/doc/vars-bs4dash.Rmd                           |only
 fresh-0.2.0/fresh/inst/doc/vars-bs4dash.html                          |only
 fresh-0.2.0/fresh/inst/doc/vars-shiny.R                               |only
 fresh-0.2.0/fresh/inst/doc/vars-shiny.Rmd                             |only
 fresh-0.2.0/fresh/inst/doc/vars-shiny.html                            |only
 fresh-0.2.0/fresh/inst/doc/vars-shinydashboard.R                      |only
 fresh-0.2.0/fresh/inst/doc/vars-shinydashboard.Rmd                    |only
 fresh-0.2.0/fresh/inst/doc/vars-shinydashboard.html                   |only
 fresh-0.2.0/fresh/inst/examples/bs4Dash                               |only
 fresh-0.2.0/fresh/inst/examples/create/app.R                          |    2 
 fresh-0.2.0/fresh/inst/examples/demo-vignette                         |only
 fresh-0.2.0/fresh/inst/examples/flexdashboard/create-theme-flex.R     |   11 
 fresh-0.2.0/fresh/inst/examples/flexdashboard/index.Rmd               |    2 
 fresh-0.2.0/fresh/inst/examples/shiny-fluid/app.R                     |   15 
 fresh-0.2.0/fresh/inst/examples/shinydashboard                        |only
 fresh-0.2.0/fresh/man/adminlte_color.Rd                               |   85 -
 fresh-0.2.0/fresh/man/adminlte_global.Rd                              |    6 
 fresh-0.2.0/fresh/man/adminlte_sidebar.Rd                             |   23 
 fresh-0.2.0/fresh/man/adminlte_vars.Rd                                |only
 fresh-0.2.0/fresh/man/bs4Dash-sidebar.Rd                              |only
 fresh-0.2.0/fresh/man/bs4dash_button.Rd                               |only
 fresh-0.2.0/fresh/man/bs4dash_color.Rd                                |only
 fresh-0.2.0/fresh/man/bs4dash_font.Rd                                 |only
 fresh-0.2.0/fresh/man/bs4dash_layout.Rd                               |only
 fresh-0.2.0/fresh/man/bs4dash_status.Rd                               |only
 fresh-0.2.0/fresh/man/bs4dash_vars.Rd                                 |only
 fresh-0.2.0/fresh/man/bs4dash_yiq.Rd                                  |only
 fresh-0.2.0/fresh/man/bs_vars.Rd                                      |only
 fresh-0.2.0/fresh/man/bs_vars_alert.Rd                                |   25 
 fresh-0.2.0/fresh/man/bs_vars_badge.Rd                                |   15 
 fresh-0.2.0/fresh/man/bs_vars_button.Rd                               |   38 
 fresh-0.2.0/fresh/man/bs_vars_color.Rd                                |   29 
 fresh-0.2.0/fresh/man/bs_vars_component.Rd                            |only
 fresh-0.2.0/fresh/man/bs_vars_dropdown.Rd                             |   20 
 fresh-0.2.0/fresh/man/bs_vars_file.Rd                                 |only
 fresh-0.2.0/fresh/man/bs_vars_font.Rd                                 |   18 
 fresh-0.2.0/fresh/man/bs_vars_global.Rd                               |   16 
 fresh-0.2.0/fresh/man/bs_vars_input.Rd                                |   17 
 fresh-0.2.0/fresh/man/bs_vars_modal.Rd                                |   23 
 fresh-0.2.0/fresh/man/bs_vars_nav.Rd                                  |   11 
 fresh-0.2.0/fresh/man/bs_vars_navbar.Rd                               |   59 
 fresh-0.2.0/fresh/man/bs_vars_panel.Rd                                |   39 
 fresh-0.2.0/fresh/man/bs_vars_pills.Rd                                |    9 
 fresh-0.2.0/fresh/man/bs_vars_progress.Rd                             |   15 
 fresh-0.2.0/fresh/man/bs_vars_state.Rd                                |   21 
 fresh-0.2.0/fresh/man/bs_vars_table.Rd                                |only
 fresh-0.2.0/fresh/man/bs_vars_tabs.Rd                                 |   12 
 fresh-0.2.0/fresh/man/bs_vars_wells.Rd                                |    6 
 fresh-0.2.0/fresh/man/create_pretty.Rd                                |   11 
 fresh-0.2.0/fresh/man/create_theme.Rd                                 |   12 
 fresh-0.2.0/fresh/man/figures/bs4dash.png                             |only
 fresh-0.2.0/fresh/man/figures/fresh-logo.png                          |only
 fresh-0.2.0/fresh/man/figures/shinydashboard.png                      |only
 fresh-0.2.0/fresh/man/fresh.Rd                                        |    1 
 fresh-0.2.0/fresh/man/search_vars.Rd                                  |only
 fresh-0.2.0/fresh/man/search_vars_adminlte2.Rd                        |only
 fresh-0.2.0/fresh/man/search_vars_bs.Rd                               |only
 fresh-0.2.0/fresh/man/search_vars_bs4dash.Rd                          |only
 fresh-0.2.0/fresh/man/use_vars_template.Rd                            |   28 
 fresh-0.2.0/fresh/tests/testthat/test-create_theme.R                  |   19 
 fresh-0.2.0/fresh/tests/testthat/test-search-vars.R                   |only
 fresh-0.2.0/fresh/tests/testthat/test-use_vars_template.R             |   59 
 fresh-0.2.0/fresh/tests/testthat/test-utils.R                         |only
 fresh-0.2.0/fresh/tests/testthat/test-vars-adminlte.R                 |   13 
 fresh-0.2.0/fresh/tests/testthat/test-vars-bootstrap.R                |   43 
 fresh-0.2.0/fresh/tests/testthat/test-vars-bs4dash.R                  |only
 fresh-0.2.0/fresh/vignettes/assets                                    |only
 fresh-0.2.0/fresh/vignettes/figures/bs4dash-color-custom.png          |only
 fresh-0.2.0/fresh/vignettes/figures/bs4dash-layout-custom.png         |only
 fresh-0.2.0/fresh/vignettes/figures/bs4dash-navbar-custom.png         |only
 fresh-0.2.0/fresh/vignettes/figures/bs4dash-sidebar-custom.png        |only
 fresh-0.2.0/fresh/vignettes/figures/bs4dash-status-custom.png         |only
 fresh-0.2.0/fresh/vignettes/figures/bs4dash-status-default.png        |only
 fresh-0.2.0/fresh/vignettes/figures/bs4dash-yiq-custom.png            |only
 fresh-0.2.0/fresh/vignettes/figures/font-custom.png                   |only
 fresh-0.2.0/fresh/vignettes/figures/font-default.png                  |only
 fresh-0.2.0/fresh/vignettes/figures/modal-custom.png                  |only
 fresh-0.2.0/fresh/vignettes/figures/modal-default.png                 |only
 fresh-0.2.0/fresh/vignettes/figures/shinydashboard-body-custom.png    |only
 fresh-0.2.0/fresh/vignettes/figures/shinydashboard-colors-custom.png  |only
 fresh-0.2.0/fresh/vignettes/figures/shinydashboard-default.png        |only
 fresh-0.2.0/fresh/vignettes/figures/shinydashboard-sidebar-custom.png |only
 fresh-0.2.0/fresh/vignettes/fresh.Rmd                                 |only
 fresh-0.2.0/fresh/vignettes/vars-bs4dash.Rmd                          |only
 fresh-0.2.0/fresh/vignettes/vars-shiny.Rmd                            |only
 fresh-0.2.0/fresh/vignettes/vars-shinydashboard.Rmd                   |only
 118 files changed, 1506 insertions(+), 645 deletions(-)

More information about fresh at CRAN
Permanent link

Package dplyr updated to version 1.0.0 with previous version 0.8.5 dated 2020-03-07

Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>), Lionel Henry [aut], Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between dplyr versions 0.8.5 dated 2020-03-07 and 1.0.0 dated 2020-05-29

 dplyr-0.8.5/dplyr/R/RcppExports.R                                 |only
 dplyr-0.8.5/dplyr/R/bench-compare.r                               |only
 dplyr-0.8.5/dplyr/R/compat-lifecycle.R                            |only
 dplyr-0.8.5/dplyr/R/data-nasa.r                                   |only
 dplyr-0.8.5/dplyr/R/dataframe.R                                   |only
 dplyr-0.8.5/dplyr/R/do.r                                          |only
 dplyr-0.8.5/dplyr/R/dr.R                                          |only
 dplyr-0.8.5/dplyr/R/failwith.r                                    |only
 dplyr-0.8.5/dplyr/R/group-indices.R                               |only
 dplyr-0.8.5/dplyr/R/group-size.r                                  |only
 dplyr-0.8.5/dplyr/R/group_keys.R                                  |only
 dplyr-0.8.5/dplyr/R/hybrid.R                                      |only
 dplyr-0.8.5/dplyr/R/id.r                                          |only
 dplyr-0.8.5/dplyr/R/inline.r                                      |only
 dplyr-0.8.5/dplyr/R/join-vars.R                                   |only
 dplyr-0.8.5/dplyr/R/lengths.R                                     |only
 dplyr-0.8.5/dplyr/R/location.R                                    |only
 dplyr-0.8.5/dplyr/R/manip.r                                       |only
 dplyr-0.8.5/dplyr/R/match-vars.R                                  |only
 dplyr-0.8.5/dplyr/R/reexport-tidyselect.R                         |only
 dplyr-0.8.5/dplyr/R/src-local.r                                   |only
 dplyr-0.8.5/dplyr/R/tbl-cube.r                                    |only
 dplyr-0.8.5/dplyr/R/tbl-df.r                                      |only
 dplyr-0.8.5/dplyr/R/utils-bindings.R                              |only
 dplyr-0.8.5/dplyr/data/nasa.rda                                   |only
 dplyr-0.8.5/dplyr/inst/include                                    |only
 dplyr-0.8.5/dplyr/man/as.table.tbl_cube.Rd                        |only
 dplyr-0.8.5/dplyr/man/as.tbl_cube.Rd                              |only
 dplyr-0.8.5/dplyr/man/dr_dplyr.Rd                                 |only
 dplyr-0.8.5/dplyr/man/failwith.Rd                                 |only
 dplyr-0.8.5/dplyr/man/group_indices.Rd                            |only
 dplyr-0.8.5/dplyr/man/group_size.Rd                               |only
 dplyr-0.8.5/dplyr/man/groups.Rd                                   |only
 dplyr-0.8.5/dplyr/man/hybrid_call.Rd                              |only
 dplyr-0.8.5/dplyr/man/id.Rd                                       |only
 dplyr-0.8.5/dplyr/man/init_logging.Rd                             |only
 dplyr-0.8.5/dplyr/man/join.Rd                                     |only
 dplyr-0.8.5/dplyr/man/join.tbl_df.Rd                              |only
 dplyr-0.8.5/dplyr/man/n.Rd                                        |only
 dplyr-0.8.5/dplyr/man/nasa.Rd                                     |only
 dplyr-0.8.5/dplyr/man/sample.Rd                                   |only
 dplyr-0.8.5/dplyr/man/tally.Rd                                    |only
 dplyr-0.8.5/dplyr/man/tbl_cube.Rd                                 |only
 dplyr-0.8.5/dplyr/man/tidyeval.Rd                                 |only
 dplyr-0.8.5/dplyr/src/Makevars                                    |only
 dplyr-0.8.5/dplyr/src/Makevars.win                                |only
 dplyr-0.8.5/dplyr/src/RcppExports.cpp                             |only
 dplyr-0.8.5/dplyr/src/address.cpp                                 |only
 dplyr-0.8.5/dplyr/src/api.cpp                                     |only
 dplyr-0.8.5/dplyr/src/arrange.cpp                                 |only
 dplyr-0.8.5/dplyr/src/between.cpp                                 |only
 dplyr-0.8.5/dplyr/src/bind.cpp                                    |only
 dplyr-0.8.5/dplyr/src/distinct.cpp                                |only
 dplyr-0.8.5/dplyr/src/encoding.cpp                                |only
 dplyr-0.8.5/dplyr/src/group_indices.cpp                           |only
 dplyr-0.8.5/dplyr/src/hybrid.cpp                                  |only
 dplyr-0.8.5/dplyr/src/join.cpp                                    |only
 dplyr-0.8.5/dplyr/src/join_exports.cpp                            |only
 dplyr-0.8.5/dplyr/src/pch.h                                       |only
 dplyr-0.8.5/dplyr/src/rlang-export.c                              |only
 dplyr-0.8.5/dplyr/src/rlang.cpp                                   |only
 dplyr-0.8.5/dplyr/src/select.cpp                                  |only
 dplyr-0.8.5/dplyr/src/set.cpp                                     |only
 dplyr-0.8.5/dplyr/src/test.cpp                                    |only
 dplyr-0.8.5/dplyr/src/utils-bindings.cpp                          |only
 dplyr-0.8.5/dplyr/src/utils.cpp                                   |only
 dplyr-0.8.5/dplyr/src/window.cpp                                  |only
 dplyr-0.8.5/dplyr/tests/testthat/helper-astyle.R                  |only
 dplyr-0.8.5/dplyr/tests/testthat/helper-combine.R                 |only
 dplyr-0.8.5/dplyr/tests/testthat/helper-groups.R                  |only
 dplyr-0.8.5/dplyr/tests/testthat/helper-hybrid.R                  |only
 dplyr-0.8.5/dplyr/tests/testthat/test-active-bindings.R           |only
 dplyr-0.8.5/dplyr/tests/testthat/test-astyle.R                    |only
 dplyr-0.8.5/dplyr/tests/testthat/test-between.R                   |only
 dplyr-0.8.5/dplyr/tests/testthat/test-binds.R                     |only
 dplyr-0.8.5/dplyr/tests/testthat/test-combine.R                   |only
 dplyr-0.8.5/dplyr/tests/testthat/test-copy_to.R                   |only
 dplyr-0.8.5/dplyr/tests/testthat/test-copying.R                   |only
 dplyr-0.8.5/dplyr/tests/testthat/test-data_frame.R                |only
 dplyr-0.8.5/dplyr/tests/testthat/test-do.R                        |only
 dplyr-0.8.5/dplyr/tests/testthat/test-equality.r                  |only
 dplyr-0.8.5/dplyr/tests/testthat/test-group-indices.R             |only
 dplyr-0.8.5/dplyr/tests/testthat/test-group-size.R                |only
 dplyr-0.8.5/dplyr/tests/testthat/test-group_keys.R                |only
 dplyr-0.8.5/dplyr/tests/testthat/test-hybrid-traverse.R           |only
 dplyr-0.8.5/dplyr/tests/testthat/test-hybrid.R                    |only
 dplyr-0.8.5/dplyr/tests/testthat/test-internals.r                 |only
 dplyr-0.8.5/dplyr/tests/testthat/test-joins.r                     |only
 dplyr-0.8.5/dplyr/tests/testthat/test-lazyeval-compat.R           |only
 dplyr-0.8.5/dplyr/tests/testthat/test-new_grouped_df.R            |only
 dplyr-0.8.5/dplyr/tests/testthat/test-overscope.R                 |only
 dplyr-0.8.5/dplyr/tests/testthat/test-tbl-cube.R                  |only
 dplyr-0.8.5/dplyr/tests/testthat/test-ts.R                        |only
 dplyr-0.8.5/dplyr/tests/testthat/test-underscore.R                |only
 dplyr-0.8.5/dplyr/vignettes/colwise.html                          |only
 dplyr-0.8.5/dplyr/vignettes/future                                |only
 dplyr-0.8.5/dplyr/vignettes/patterns.html                         |only
 dplyr-0.8.5/dplyr/vignettes/tidyeval-further.html                 |only
 dplyr-0.8.5/dplyr/vignettes/tidyeval-introduction.html            |only
 dplyr-0.8.5/dplyr/vignettes/tidyeval-recipes-dplyr.html           |only
 dplyr-0.8.5/dplyr/vignettes/tidyeval-recipes.html                 |only
 dplyr-1.0.0/dplyr/DESCRIPTION                                     |   54 
 dplyr-1.0.0/dplyr/LICENSE                                         |    2 
 dplyr-1.0.0/dplyr/MD5                                             |  738 ++---
 dplyr-1.0.0/dplyr/NAMESPACE                                       |  174 -
 dplyr-1.0.0/dplyr/NEWS.md                                         |  378 ++
 dplyr-1.0.0/dplyr/R/across.R                                      |only
 dplyr-1.0.0/dplyr/R/all-equal.r                                   |   78 
 dplyr-1.0.0/dplyr/R/arrange.R                                     |only
 dplyr-1.0.0/dplyr/R/bind.r                                        |  137 -
 dplyr-1.0.0/dplyr/R/case_when.R                                   |   14 
 dplyr-1.0.0/dplyr/R/coalesce.R                                    |   21 
 dplyr-1.0.0/dplyr/R/colwise-arrange.R                             |   24 
 dplyr-1.0.0/dplyr/R/colwise-distinct.R                            |   28 
 dplyr-1.0.0/dplyr/R/colwise-filter.R                              |   27 
 dplyr-1.0.0/dplyr/R/colwise-funs.R                                |only
 dplyr-1.0.0/dplyr/R/colwise-group-by.R                            |   33 
 dplyr-1.0.0/dplyr/R/colwise-mutate.R                              |  231 -
 dplyr-1.0.0/dplyr/R/colwise-select.R                              |   96 
 dplyr-1.0.0/dplyr/R/colwise.R                                     |  100 
 dplyr-1.0.0/dplyr/R/compat-lazyeval.R                             |    2 
 dplyr-1.0.0/dplyr/R/compat-name-repair.R                          |   16 
 dplyr-1.0.0/dplyr/R/compat-purrr.R                                |    4 
 dplyr-1.0.0/dplyr/R/compat-tibble.R                               |only
 dplyr-1.0.0/dplyr/R/compute-collect.r                             |   25 
 dplyr-1.0.0/dplyr/R/conditions.R                                  |only
 dplyr-1.0.0/dplyr/R/context.R                                     |  134 +
 dplyr-1.0.0/dplyr/R/copy-to.r                                     |    7 
 dplyr-1.0.0/dplyr/R/count-tally.R                                 |  333 +-
 dplyr-1.0.0/dplyr/R/data-bands.R                                  |    2 
 dplyr-1.0.0/dplyr/R/data-mask.R                                   |only
 dplyr-1.0.0/dplyr/R/data-starwars.R                               |    5 
 dplyr-1.0.0/dplyr/R/defunct.r                                     |only
 dplyr-1.0.0/dplyr/R/deprec-bench-compare.r                        |only
 dplyr-1.0.0/dplyr/R/deprec-combine.R                              |only
 dplyr-1.0.0/dplyr/R/deprec-dbi.R                                  |only
 dplyr-1.0.0/dplyr/R/deprec-do.r                                   |only
 dplyr-1.0.0/dplyr/R/deprec-funs.R                                 |only
 dplyr-1.0.0/dplyr/R/deprec-lazyeval.R                             |only
 dplyr-1.0.0/dplyr/R/deprec-location.R                             |only
 dplyr-1.0.0/dplyr/R/deprec-src-local.r                            |only
 dplyr-1.0.0/dplyr/R/deprec-tibble.R                               |only
 dplyr-1.0.0/dplyr/R/deprec-tidyselect.R                           |only
 dplyr-1.0.0/dplyr/R/distinct.R                                    |  150 -
 dplyr-1.0.0/dplyr/R/doc-methods.R                                 |only
 dplyr-1.0.0/dplyr/R/doc-params.R                                  |only
 dplyr-1.0.0/dplyr/R/dplyr.r                                       |   42 
 dplyr-1.0.0/dplyr/R/error.R                                       |   25 
 dplyr-1.0.0/dplyr/R/filter.R                                      |only
 dplyr-1.0.0/dplyr/R/funs-predicates.R                             |    4 
 dplyr-1.0.0/dplyr/R/funs.R                                        |  250 -
 dplyr-1.0.0/dplyr/R/generics.R                                    |only
 dplyr-1.0.0/dplyr/R/group-by.r                                    |  212 -
 dplyr-1.0.0/dplyr/R/group_data.R                                  |  151 -
 dplyr-1.0.0/dplyr/R/group_map.R                                   |   64 
 dplyr-1.0.0/dplyr/R/group_nest.R                                  |   26 
 dplyr-1.0.0/dplyr/R/group_split.R                                 |   77 
 dplyr-1.0.0/dplyr/R/group_trim.R                                  |   11 
 dplyr-1.0.0/dplyr/R/grouped-df.r                                  |  413 +--
 dplyr-1.0.0/dplyr/R/groups-with.R                                 |only
 dplyr-1.0.0/dplyr/R/helper-error-msg.R                            |only
 dplyr-1.0.0/dplyr/R/if_else.R                                     |    2 
 dplyr-1.0.0/dplyr/R/join-cols.R                                   |only
 dplyr-1.0.0/dplyr/R/join-common-by.R                              |only
 dplyr-1.0.0/dplyr/R/join-rows.R                                   |only
 dplyr-1.0.0/dplyr/R/join.r                                        |  492 ++-
 dplyr-1.0.0/dplyr/R/lead-lag.R                                    |   87 
 dplyr-1.0.0/dplyr/R/mutate.R                                      |only
 dplyr-1.0.0/dplyr/R/na_if.R                                       |    2 
 dplyr-1.0.0/dplyr/R/nest_by.R                                     |only
 dplyr-1.0.0/dplyr/R/nth-value.R                                   |    2 
 dplyr-1.0.0/dplyr/R/order-by.R                                    |   20 
 dplyr-1.0.0/dplyr/R/progress.R                                    |   11 
 dplyr-1.0.0/dplyr/R/pull.R                                        |   38 
 dplyr-1.0.0/dplyr/R/rank.R                                        |   32 
 dplyr-1.0.0/dplyr/R/rbind.R                                       |   19 
 dplyr-1.0.0/dplyr/R/recode.R                                      |   31 
 dplyr-1.0.0/dplyr/R/relocate.R                                    |only
 dplyr-1.0.0/dplyr/R/rename.R                                      |only
 dplyr-1.0.0/dplyr/R/rows.R                                        |only
 dplyr-1.0.0/dplyr/R/rowwise.r                                     |  200 -
 dplyr-1.0.0/dplyr/R/sample.R                                      |  136 -
 dplyr-1.0.0/dplyr/R/select-helpers.R                              |only
 dplyr-1.0.0/dplyr/R/select.R                                      |only
 dplyr-1.0.0/dplyr/R/sets.r                                        |  144 +
 dplyr-1.0.0/dplyr/R/slice.R                                       |only
 dplyr-1.0.0/dplyr/R/src.r                                         |    8 
 dplyr-1.0.0/dplyr/R/src_dbi.R                                     |  161 -
 dplyr-1.0.0/dplyr/R/summarise.R                                   |only
 dplyr-1.0.0/dplyr/R/tbl.r                                         |   17 
 dplyr-1.0.0/dplyr/R/top-n.R                                       |   78 
 dplyr-1.0.0/dplyr/R/ts.R                                          |    6 
 dplyr-1.0.0/dplyr/R/utils-format.r                                |    7 
 dplyr-1.0.0/dplyr/R/utils-replace-with.R                          |    8 
 dplyr-1.0.0/dplyr/R/utils-tidy-eval.R                             |   73 
 dplyr-1.0.0/dplyr/R/utils.r                                       |   33 
 dplyr-1.0.0/dplyr/R/zzz.r                                         |    4 
 dplyr-1.0.0/dplyr/README.md                                       |   88 
 dplyr-1.0.0/dplyr/build/dplyr.pdf                                 |binary
 dplyr-1.0.0/dplyr/build/vignette.rds                              |binary
 dplyr-1.0.0/dplyr/data/starwars.rda                               |binary
 dplyr-1.0.0/dplyr/inst/doc/base.R                                 |only
 dplyr-1.0.0/dplyr/inst/doc/base.Rmd                               |only
 dplyr-1.0.0/dplyr/inst/doc/base.html                              |only
 dplyr-1.0.0/dplyr/inst/doc/colwise.R                              |only
 dplyr-1.0.0/dplyr/inst/doc/colwise.Rmd                            |only
 dplyr-1.0.0/dplyr/inst/doc/colwise.html                           |only
 dplyr-1.0.0/dplyr/inst/doc/compatibility.R                        |    2 
 dplyr-1.0.0/dplyr/inst/doc/compatibility.Rmd                      |    5 
 dplyr-1.0.0/dplyr/inst/doc/compatibility.html                     |   28 
 dplyr-1.0.0/dplyr/inst/doc/dplyr.R                                |  199 -
 dplyr-1.0.0/dplyr/inst/doc/dplyr.Rmd                              |  446 +--
 dplyr-1.0.0/dplyr/inst/doc/dplyr.html                             |  982 +++----
 dplyr-1.0.0/dplyr/inst/doc/grouping.R                             |only
 dplyr-1.0.0/dplyr/inst/doc/grouping.Rmd                           |only
 dplyr-1.0.0/dplyr/inst/doc/grouping.html                          |only
 dplyr-1.0.0/dplyr/inst/doc/programming.R                          |  363 --
 dplyr-1.0.0/dplyr/inst/doc/programming.Rmd                        |  790 +-----
 dplyr-1.0.0/dplyr/inst/doc/programming.html                       |  791 ++----
 dplyr-1.0.0/dplyr/inst/doc/rowwise.R                              |only
 dplyr-1.0.0/dplyr/inst/doc/rowwise.Rmd                            |only
 dplyr-1.0.0/dplyr/inst/doc/rowwise.html                           |only
 dplyr-1.0.0/dplyr/inst/doc/two-table.R                            |   25 
 dplyr-1.0.0/dplyr/inst/doc/two-table.Rmd                          |   62 
 dplyr-1.0.0/dplyr/inst/doc/two-table.html                         |   98 
 dplyr-1.0.0/dplyr/inst/doc/window-functions.R                     |    2 
 dplyr-1.0.0/dplyr/inst/doc/window-functions.Rmd                   |    6 
 dplyr-1.0.0/dplyr/inst/doc/window-functions.html                  |   48 
 dplyr-1.0.0/dplyr/man/across.Rd                                   |only
 dplyr-1.0.0/dplyr/man/add_rownames.Rd                             |   10 
 dplyr-1.0.0/dplyr/man/all_equal.Rd                                |   23 
 dplyr-1.0.0/dplyr/man/all_vars.Rd                                 |   16 
 dplyr-1.0.0/dplyr/man/arrange.Rd                                  |   73 
 dplyr-1.0.0/dplyr/man/arrange_all.Rd                              |   14 
 dplyr-1.0.0/dplyr/man/backend_dbplyr.Rd                           |   23 
 dplyr-1.0.0/dplyr/man/band_members.Rd                             |    4 
 dplyr-1.0.0/dplyr/man/bench_compare.Rd                            |   46 
 dplyr-1.0.0/dplyr/man/between.Rd                                  |    5 
 dplyr-1.0.0/dplyr/man/bind.Rd                                     |   35 
 dplyr-1.0.0/dplyr/man/case_when.Rd                                |   10 
 dplyr-1.0.0/dplyr/man/coalesce.Rd                                 |    9 
 dplyr-1.0.0/dplyr/man/combine.Rd                                  |   27 
 dplyr-1.0.0/dplyr/man/common_by.Rd                                |    2 
 dplyr-1.0.0/dplyr/man/compute.Rd                                  |   21 
 dplyr-1.0.0/dplyr/man/context.Rd                                  |only
 dplyr-1.0.0/dplyr/man/copy_to.Rd                                  |    3 
 dplyr-1.0.0/dplyr/man/count.Rd                                    |only
 dplyr-1.0.0/dplyr/man/cumall.Rd                                   |    3 
 dplyr-1.0.0/dplyr/man/defunct.Rd                                  |only
 dplyr-1.0.0/dplyr/man/distinct.Rd                                 |   60 
 dplyr-1.0.0/dplyr/man/distinct_all.Rd                             |   18 
 dplyr-1.0.0/dplyr/man/do.Rd                                       |  106 
 dplyr-1.0.0/dplyr/man/dplyr-package.Rd                            |   47 
 dplyr-1.0.0/dplyr/man/dplyr_data_masking.Rd                       |only
 dplyr-1.0.0/dplyr/man/dplyr_extending.Rd                          |only
 dplyr-1.0.0/dplyr/man/dplyr_tidy_select.Rd                        |only
 dplyr-1.0.0/dplyr/man/figures/lifecycle-superseded.svg            |only
 dplyr-1.0.0/dplyr/man/figures/logo.png                            |binary
 dplyr-1.0.0/dplyr/man/filter-joins.Rd                             |only
 dplyr-1.0.0/dplyr/man/filter.Rd                                   |  117 
 dplyr-1.0.0/dplyr/man/filter_all.Rd                               |   19 
 dplyr-1.0.0/dplyr/man/funs.Rd                                     |   39 
 dplyr-1.0.0/dplyr/man/group_by.Rd                                 |   67 
 dplyr-1.0.0/dplyr/man/group_by_all.Rd                             |   57 
 dplyr-1.0.0/dplyr/man/group_by_drop_default.Rd                    |    1 
 dplyr-1.0.0/dplyr/man/group_by_prepare.Rd                         |   13 
 dplyr-1.0.0/dplyr/man/group_cols.Rd                               |   17 
 dplyr-1.0.0/dplyr/man/group_data.Rd                               |   78 
 dplyr-1.0.0/dplyr/man/group_map.Rd                                |   24 
 dplyr-1.0.0/dplyr/man/group_nest.Rd                               |   17 
 dplyr-1.0.0/dplyr/man/group_split.Rd                              |   31 
 dplyr-1.0.0/dplyr/man/group_trim.Rd                               |   15 
 dplyr-1.0.0/dplyr/man/grouped_df.Rd                               |    8 
 dplyr-1.0.0/dplyr/man/lead-lag.Rd                                 |   52 
 dplyr-1.0.0/dplyr/man/location.Rd                                 |   12 
 dplyr-1.0.0/dplyr/man/make_tbl.Rd                                 |    3 
 dplyr-1.0.0/dplyr/man/mutate-joins.Rd                             |only
 dplyr-1.0.0/dplyr/man/mutate.Rd                                   |  213 -
 dplyr-1.0.0/dplyr/man/mutate_all.Rd                               |   64 
 dplyr-1.0.0/dplyr/man/na_if.Rd                                    |    2 
 dplyr-1.0.0/dplyr/man/nest_by.Rd                                  |only
 dplyr-1.0.0/dplyr/man/nest_join.Rd                                |only
 dplyr-1.0.0/dplyr/man/new_grouped_df.Rd                           |    4 
 dplyr-1.0.0/dplyr/man/progress_estimated.Rd                       |    6 
 dplyr-1.0.0/dplyr/man/pull.Rd                                     |   35 
 dplyr-1.0.0/dplyr/man/ranking.Rd                                  |    7 
 dplyr-1.0.0/dplyr/man/recode.Rd                                   |   28 
 dplyr-1.0.0/dplyr/man/reexports.Rd                                |   16 
 dplyr-1.0.0/dplyr/man/relocate.Rd                                 |only
 dplyr-1.0.0/dplyr/man/rename.Rd                                   |only
 dplyr-1.0.0/dplyr/man/rmd                                         |only
 dplyr-1.0.0/dplyr/man/rows.Rd                                     |only
 dplyr-1.0.0/dplyr/man/rowwise.Rd                                  |   79 
 dplyr-1.0.0/dplyr/man/sample_n.Rd                                 |only
 dplyr-1.0.0/dplyr/man/scoped.Rd                                   |   22 
 dplyr-1.0.0/dplyr/man/se-deprecated.Rd                            |  107 
 dplyr-1.0.0/dplyr/man/select.Rd                                   |  335 +-
 dplyr-1.0.0/dplyr/man/select_all.Rd                               |   72 
 dplyr-1.0.0/dplyr/man/select_vars.Rd                              |   27 
 dplyr-1.0.0/dplyr/man/setops.Rd                                   |   12 
 dplyr-1.0.0/dplyr/man/slice.Rd                                    |  181 +
 dplyr-1.0.0/dplyr/man/src_dbi.Rd                                  |   92 
 dplyr-1.0.0/dplyr/man/src_local.Rd                                |   18 
 dplyr-1.0.0/dplyr/man/src_tbls.Rd                                 |    4 
 dplyr-1.0.0/dplyr/man/starwars.Rd                                 |   11 
 dplyr-1.0.0/dplyr/man/storms.Rd                                   |    6 
 dplyr-1.0.0/dplyr/man/summarise.Rd                                |  118 
 dplyr-1.0.0/dplyr/man/summarise_all.Rd                            |   72 
 dplyr-1.0.0/dplyr/man/summarise_each.Rd                           |   20 
 dplyr-1.0.0/dplyr/man/tbl.Rd                                      |    5 
 dplyr-1.0.0/dplyr/man/tbl_df.Rd                                   |   12 
 dplyr-1.0.0/dplyr/man/tbl_ptype.Rd                                |only
 dplyr-1.0.0/dplyr/man/tidyeval-compat.Rd                          |   28 
 dplyr-1.0.0/dplyr/man/top_n.Rd                                    |   71 
 dplyr-1.0.0/dplyr/man/vars.Rd                                     |   18 
 dplyr-1.0.0/dplyr/man/with_groups.Rd                              |only
 dplyr-1.0.0/dplyr/src/dplyr.h                                     |only
 dplyr-1.0.0/dplyr/src/filter.cpp                                  |  592 ----
 dplyr-1.0.0/dplyr/src/funs.cpp                                    |only
 dplyr-1.0.0/dplyr/src/group_by.cpp                                |only
 dplyr-1.0.0/dplyr/src/group_data.cpp                              |only
 dplyr-1.0.0/dplyr/src/imports.cpp                                 |only
 dplyr-1.0.0/dplyr/src/init.cpp                                    |  168 -
 dplyr-1.0.0/dplyr/src/mutate.cpp                                  |  536 ----
 dplyr-1.0.0/dplyr/src/slice.cpp                                   |only
 dplyr-1.0.0/dplyr/src/summarise.cpp                               |  280 --
 dplyr-1.0.0/dplyr/tests/testthat/helper-dplyr.R                   |   13 
 dplyr-1.0.0/dplyr/tests/testthat/helper-encoding.R                |   49 
 dplyr-1.0.0/dplyr/tests/testthat/helper-s3.R                      |only
 dplyr-1.0.0/dplyr/tests/testthat/test-DBI.R                       |    5 
 dplyr-1.0.0/dplyr/tests/testthat/test-across-errors.txt           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-across.R                    |only
 dplyr-1.0.0/dplyr/tests/testthat/test-all-equal.r                 |only
 dplyr-1.0.0/dplyr/tests/testthat/test-arrange-errors.txt          |only
 dplyr-1.0.0/dplyr/tests/testthat/test-arrange.r                   |  266 --
 dplyr-1.0.0/dplyr/tests/testthat/test-bind-errors.txt             |only
 dplyr-1.0.0/dplyr/tests/testthat/test-bind.R                      |only
 dplyr-1.0.0/dplyr/tests/testthat/test-case-when-errors.txt        |only
 dplyr-1.0.0/dplyr/tests/testthat/test-case-when.R                 |   70 
 dplyr-1.0.0/dplyr/tests/testthat/test-coalesce-errors.txt         |only
 dplyr-1.0.0/dplyr/tests/testthat/test-coalesce.R                  |   18 
 dplyr-1.0.0/dplyr/tests/testthat/test-colwise-errors.txt          |only
 dplyr-1.0.0/dplyr/tests/testthat/test-colwise-filter-errors.txt   |only
 dplyr-1.0.0/dplyr/tests/testthat/test-colwise-filter.R            |   32 
 dplyr-1.0.0/dplyr/tests/testthat/test-colwise-funs.R              |only
 dplyr-1.0.0/dplyr/tests/testthat/test-colwise-mutate-errors.txt   |only
 dplyr-1.0.0/dplyr/tests/testthat/test-colwise-mutate.R            |  297 --
 dplyr-1.0.0/dplyr/tests/testthat/test-colwise-select-errors.txt   |only
 dplyr-1.0.0/dplyr/tests/testthat/test-colwise-select.R            |  104 
 dplyr-1.0.0/dplyr/tests/testthat/test-colwise.R                   |   37 
 dplyr-1.0.0/dplyr/tests/testthat/test-context-error.txt           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-context.R                   |only
 dplyr-1.0.0/dplyr/tests/testthat/test-count-tally.r               |  250 -
 dplyr-1.0.0/dplyr/tests/testthat/test-count-tally.txt             |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-combine-errors.txt   |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-combine.R            |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-dbi-errors.txt       |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-dbi.R                |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-do.R                 |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-funs-errors.txt      |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-funs.R               |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-lazyeval.R           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-src-local-errors.txt |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-src-local.r          |only
 dplyr-1.0.0/dplyr/tests/testthat/test-deprec-tibble.R             |only
 dplyr-1.0.0/dplyr/tests/testthat/test-distinct-errors.txt         |only
 dplyr-1.0.0/dplyr/tests/testthat/test-distinct.R                  |  155 -
 dplyr-1.0.0/dplyr/tests/testthat/test-do-errors.txt               |only
 dplyr-1.0.0/dplyr/tests/testthat/test-empty-groups.R              |   17 
 dplyr-1.0.0/dplyr/tests/testthat/test-equality-errors.txt         |only
 dplyr-1.0.0/dplyr/tests/testthat/test-filter-errors.txt           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-filter.r                    |  258 +-
 dplyr-1.0.0/dplyr/tests/testthat/test-funs-predicates-errors.txt  |only
 dplyr-1.0.0/dplyr/tests/testthat/test-funs-predicates.R           |   11 
 dplyr-1.0.0/dplyr/tests/testthat/test-funs.R                      |  128 -
 dplyr-1.0.0/dplyr/tests/testthat/test-generics.R                  |only
 dplyr-1.0.0/dplyr/tests/testthat/test-group-by-errors.txt         |only
 dplyr-1.0.0/dplyr/tests/testthat/test-group-by.r                  |  299 +-
 dplyr-1.0.0/dplyr/tests/testthat/test-group_data.R                |  187 -
 dplyr-1.0.0/dplyr/tests/testthat/test-group_map-errors.txt        |only
 dplyr-1.0.0/dplyr/tests/testthat/test-group_map.R                 |   89 
 dplyr-1.0.0/dplyr/tests/testthat/test-group_nest.R                |   20 
 dplyr-1.0.0/dplyr/tests/testthat/test-group_split.R               |  102 
 dplyr-1.0.0/dplyr/tests/testthat/test-grouped-df-errors.txt       |only
 dplyr-1.0.0/dplyr/tests/testthat/test-grouped-df-validate.txt     |only
 dplyr-1.0.0/dplyr/tests/testthat/test-grouped-df.r                |only
 dplyr-1.0.0/dplyr/tests/testthat/test-groups-with.R               |only
 dplyr-1.0.0/dplyr/tests/testthat/test-if-else-errors.txt          |only
 dplyr-1.0.0/dplyr/tests/testthat/test-if-else.R                   |  115 
 dplyr-1.0.0/dplyr/tests/testthat/test-join-cols.R                 |only
 dplyr-1.0.0/dplyr/tests/testthat/test-join-cols.txt               |only
 dplyr-1.0.0/dplyr/tests/testthat/test-join-rows.R                 |only
 dplyr-1.0.0/dplyr/tests/testthat/test-join-rows.txt               |only
 dplyr-1.0.0/dplyr/tests/testthat/test-join.r                      |only
 dplyr-1.0.0/dplyr/tests/testthat/test-lead-lag-errors.txt         |only
 dplyr-1.0.0/dplyr/tests/testthat/test-lead-lag.R                  |   45 
 dplyr-1.0.0/dplyr/tests/testthat/test-mutate-errors.txt           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-mutate-windowed.R           |   12 
 dplyr-1.0.0/dplyr/tests/testthat/test-mutate.r                    | 1027 +-------
 dplyr-1.0.0/dplyr/tests/testthat/test-n_distinct.R                |   17 
 dplyr-1.0.0/dplyr/tests/testthat/test-na-if-errors.txt            |only
 dplyr-1.0.0/dplyr/tests/testthat/test-na-if.R                     |   24 
 dplyr-1.0.0/dplyr/tests/testthat/test-nest_by.R                   |only
 dplyr-1.0.0/dplyr/tests/testthat/test-order-by-errors.txt         |only
 dplyr-1.0.0/dplyr/tests/testthat/test-order-by.R                  |only
 dplyr-1.0.0/dplyr/tests/testthat/test-pull.R                      |   12 
 dplyr-1.0.0/dplyr/tests/testthat/test-rank.R                      |   49 
 dplyr-1.0.0/dplyr/tests/testthat/test-rbind.R                     |  215 -
 dplyr-1.0.0/dplyr/tests/testthat/test-recode-errors.txt           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-recode.R                    |   55 
 dplyr-1.0.0/dplyr/tests/testthat/test-relocate.R                  |only
 dplyr-1.0.0/dplyr/tests/testthat/test-rename.R                    |only
 dplyr-1.0.0/dplyr/tests/testthat/test-rows.R                      |only
 dplyr-1.0.0/dplyr/tests/testthat/test-rows.txt                    |only
 dplyr-1.0.0/dplyr/tests/testthat/test-rowwise-print.txt           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-rowwise.r                   |only
 dplyr-1.0.0/dplyr/tests/testthat/test-sample-errors.txt           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-sample.R                    |  124 
 dplyr-1.0.0/dplyr/tests/testthat/test-select-errors.txt           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-select-helpers.R            |only
 dplyr-1.0.0/dplyr/tests/testthat/test-select.r                    |   95 
 dplyr-1.0.0/dplyr/tests/testthat/test-sets-errors.txt             |only
 dplyr-1.0.0/dplyr/tests/testthat/test-sets.R                      |  102 
 dplyr-1.0.0/dplyr/tests/testthat/test-slice-errors.txt            |only
 dplyr-1.0.0/dplyr/tests/testthat/test-slice.r                     |  158 -
 dplyr-1.0.0/dplyr/tests/testthat/test-summarise-errors.txt        |only
 dplyr-1.0.0/dplyr/tests/testthat/test-summarise.r                 | 1274 +---------
 dplyr-1.0.0/dplyr/tests/testthat/test-tbl.R                       |    3 
 dplyr-1.0.0/dplyr/tests/testthat/test-transmute.R                 |   34 
 dplyr-1.0.0/dplyr/tests/testthat/test-utils-errors.txt            |only
 dplyr-1.0.0/dplyr/tests/testthat/test-utils.R                     |   19 
 dplyr-1.0.0/dplyr/tests/testthat/test-window-errors.txt           |only
 dplyr-1.0.0/dplyr/tests/testthat/test-window.R                    |    6 
 dplyr-1.0.0/dplyr/tests/testthat/utf-8.txt                        |   12 
 dplyr-1.0.0/dplyr/vignettes/base.Rmd                              |only
 dplyr-1.0.0/dplyr/vignettes/colwise.Rmd                           |only
 dplyr-1.0.0/dplyr/vignettes/compatibility.Rmd                     |    5 
 dplyr-1.0.0/dplyr/vignettes/dplyr.Rmd                             |  446 +--
 dplyr-1.0.0/dplyr/vignettes/grouping.Rmd                          |only
 dplyr-1.0.0/dplyr/vignettes/programming.Rmd                       |  790 +-----
 dplyr-1.0.0/dplyr/vignettes/rowwise.Rmd                           |only
 dplyr-1.0.0/dplyr/vignettes/two-table.Rmd                         |   62 
 dplyr-1.0.0/dplyr/vignettes/window-functions.Rmd                  |    6 
 443 files changed, 8921 insertions(+), 12213 deletions(-)

More information about dplyr at CRAN
Permanent link

Package microseq updated to version 2.1 with previous version 2.0 dated 2020-01-09

Title: Basic Biological Sequence Handling
Description: Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.
Author: Lars Snipen, Kristian Hovde Liland
Maintainer: Lars Snipen <lars.snipen@nmbu.no>

Diff between microseq versions 2.0 dated 2020-01-09 and 2.1 dated 2020-05-29

 microseq-2.0/microseq/src/read_file.cpp      |only
 microseq-2.1/microseq/DESCRIPTION            |   12 ++---
 microseq-2.1/microseq/MD5                    |   27 +++++------
 microseq-2.1/microseq/NAMESPACE              |    4 +
 microseq-2.1/microseq/R/RcppExports.R        |   20 --------
 microseq-2.1/microseq/R/fasta.R              |   52 +++++++++++++----------
 microseq-2.1/microseq/R/fastq.R              |   41 ++++++++++--------
 microseq-2.1/microseq/build/vignette.rds     |binary
 microseq-2.1/microseq/inst/doc/vignette.Rnw  |    4 -
 microseq-2.1/microseq/inst/doc/vignette.pdf  |binary
 microseq-2.1/microseq/man/readFasta.Rd       |   18 ++++---
 microseq-2.1/microseq/man/readFastq.Rd       |   12 +++--
 microseq-2.1/microseq/src/RcppExports.cpp    |   61 ---------------------------
 microseq-2.1/microseq/src/init.c             |   16 +++----
 microseq-2.1/microseq/vignettes/vignette.Rnw |    4 -
 15 files changed, 105 insertions(+), 166 deletions(-)

More information about microseq at CRAN
Permanent link

Package matsbyname updated to version 0.4.15 with previous version 0.4.14 dated 2020-05-01

Title: An Implementation of Matrix Mathematics
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>

Diff between matsbyname versions 0.4.14 dated 2020-05-01 and 0.4.15 dated 2020-05-29

 DESCRIPTION                          |    8 -
 MD5                                  |   47 +++++---
 NAMESPACE                            |    9 +
 NEWS.md                              |   27 +++++
 R/Apply.R                            |    9 +
 R/Unary.R                            |  175 +++++++++++++++++---------------
 R/Utilities.R                        |  188 +++++++++++++++--------------------
 R/notation.R                         |only
 README.md                            |    4 
 build/vignette.rds                   |binary
 inst/CITATION                        |    4 
 inst/doc/about-vector-arguments.R    |only
 inst/doc/about-vector-arguments.Rmd  |only
 inst/doc/about-vector-arguments.html |only
 inst/doc/applybyname-vignette.html   |    4 
 inst/doc/matsbyname.html             |    4 
 man/aggregate_to_pref_suff_byname.Rd |   38 ++-----
 man/clean_byname.Rd                  |   23 ++--
 man/matricize_byname.Rd              |   19 +--
 man/prep_vector_arg.Rd               |    2 
 man/prepare_.FUNdots.Rd              |    4 
 man/rename_to_pref_suff_byname.Rd    |   34 +-----
 man/row-col-notation.Rd              |only
 man/vectorize_byname.Rd              |   23 +---
 tests/testthat/test_Unary.R          |  114 +++++++++++++--------
 tests/testthat/test_Utilities.R      |   79 ++++++++++----
 tests/testthat/test_notation.R       |only
 vignettes/about-vector-arguments.Rmd |only
 28 files changed, 450 insertions(+), 365 deletions(-)

More information about matsbyname at CRAN
Permanent link

Package bioimagetools updated to version 1.1.5 with previous version 1.1.4 dated 2020-01-15

Title: Tools for Microscopy Imaging
Description: Tools for 3D imaging, mostly for biology/microscopy. Read and write TIFF stacks. Functions for segmentation, filtering and analyzing 3D point patterns.
Author: Volker Schmid [aut, cre], Priyanka Kukreja [ctb], Fabian Scheipl [ctb]
Maintainer: Volker Schmid <stats@volkerschmid.de>

Diff between bioimagetools versions 1.1.4 dated 2020-01-15 and 1.1.5 dated 2020-05-29

 DESCRIPTION                   |   10 +--
 MD5                           |   34 ++++++++--
 NEWS                          |    3 
 R/readtif.R                   |  130 +++++++++++++++++++++---------------------
 R/segmentoutside.R            |    3 
 README.md                     |    7 +-
 build/vignette.rds            |binary
 inst/doc/readwriteplot.html   |  105 +++++++++++++++++++--------------
 man/readTIF.Rd                |    2 
 man/segment.outside.Rd        |    2 
 vignettes/readwriteplot_cache |only
 11 files changed, 171 insertions(+), 125 deletions(-)

More information about bioimagetools at CRAN
Permanent link

Package bimets updated to version 1.5.0 with previous version 1.4.3 dated 2020-03-17

Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, endogenous targeting and model renormalization.
Author: Andrea Luciani [aut, cre], Roberto Stok [aut], Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>

Diff between bimets versions 1.4.3 dated 2020-03-17 and 1.5.0 dated 2020-05-29

 bimets-1.4.3/bimets/inst/Licence.pdf                        |only
 bimets-1.5.0/bimets/DESCRIPTION                             |    8 
 bimets-1.5.0/bimets/MD5                                     |  186 
 bimets-1.5.0/bimets/NEWS.md                                 |   18 
 bimets-1.5.0/bimets/R/bimets_model_functions.R              |14182 ++++++------
 bimets-1.5.0/bimets/R/bimets_ts_functions.R                 |   94 
 bimets-1.5.0/bimets/README.md                               |   47 
 bimets-1.5.0/bimets/build/vignette.rds                      |binary
 bimets-1.5.0/bimets/data/bimets_12F_YP2D__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_12L_YP2D__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_12_D2YP__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_1F_YP2D__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_1L_YP2D__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_1_D2YP__.RData              |binary
 bimets-1.5.0/bimets/data/bimets_24F_YP2D__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_24L_YP2D__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_24_D2YP__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_2F_YP2D__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_2L_YP2D__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_2_D2YP__.RData              |binary
 bimets-1.5.0/bimets/data/bimets_366_D2YP__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_366_YP2D__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_36F_YP2D__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_36L_YP2D__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_36_D2YP__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_3F_YP2D__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_3L_YP2D__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_3_D2YP__.RData              |binary
 bimets-1.5.0/bimets/data/bimets_4F_YP2D__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_4L_YP2D__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_4_D2YP__.RData              |binary
 bimets-1.5.0/bimets/data/bimets_53F_YP2D__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_53L_YP2D__.RData            |binary
 bimets-1.5.0/bimets/data/bimets_53_D2YP__.RData             |binary
 bimets-1.5.0/bimets/data/bimets_static_G90__.RData          |binary
 bimets-1.5.0/bimets/data/bimets_static_TD90__.RData         |binary
 bimets-1.5.0/bimets/data/bimets_static_startYear___.RData   |binary
 bimets-1.5.0/bimets/data/bimets_static_totalLength___.RData |binary
 bimets-1.5.0/bimets/inst/doc/bimets.R                       | 1085 
 bimets-1.5.0/bimets/inst/doc/bimets.Rnw                     |  122 
 bimets-1.5.0/bimets/inst/doc/bimets.pdf                     |binary
 bimets-1.5.0/bimets/man/A1D.Rd                              |   14 
 bimets-1.5.0/bimets/man/ANNUAL.Rd                           |    6 
 bimets-1.5.0/bimets/man/CUMPROD.Rd                          |   16 
 bimets-1.5.0/bimets/man/CUMSUM.Rd                           |   18 
 bimets-1.5.0/bimets/man/DAILY.Rd                            |    8 
 bimets-1.5.0/bimets/man/ELIMELS.Rd                          |    4 
 bimets-1.5.0/bimets/man/ESTIMATE.Rd                         |   61 
 bimets-1.5.0/bimets/man/GETDATE.Rd                          |   48 
 bimets-1.5.0/bimets/man/GETYEARPERIOD.Rd                    |   32 
 bimets-1.5.0/bimets/man/INTS.Rd                             |   16 
 bimets-1.5.0/bimets/man/LOAD_MODEL.Rd                       |   14 
 bimets-1.5.0/bimets/man/LOAD_MODEL_DATA.Rd                  |    8 
 bimets-1.5.0/bimets/man/LOCS.Rd                             |   10 
 bimets-1.5.0/bimets/man/MDL.Rd                              |  165 
 bimets-1.5.0/bimets/man/MONTHLY.Rd                          |    8 
 bimets-1.5.0/bimets/man/MOVAVG.Rd                           |   18 
 bimets-1.5.0/bimets/man/MOVTOT.Rd                           |   18 
 bimets-1.5.0/bimets/man/MULTMATRIX.Rd                       |   16 
 bimets-1.5.0/bimets/man/NAMELIST.Rd                         |   12 
 bimets-1.5.0/bimets/man/NOELS.Rd                            |   12 
 bimets-1.5.0/bimets/man/NUMPERIOD.Rd                        |    2 
 bimets-1.5.0/bimets/man/QUARTERLY.Rd                        |   16 
 bimets-1.5.0/bimets/man/RENORM.Rd                           |   43 
 bimets-1.5.0/bimets/man/SEMIANNUAL.Rd                       |   12 
 bimets-1.5.0/bimets/man/SIMULATE.Rd                         |   47 
 bimets-1.5.0/bimets/man/TABIT.Rd                            |   32 
 bimets-1.5.0/bimets/man/TSDELTA.Rd                          |   13 
 bimets-1.5.0/bimets/man/TSDELTALOG.Rd                       |only
 bimets-1.5.0/bimets/man/TSDELTAP.Rd                         |   14 
 bimets-1.5.0/bimets/man/TSERIES.Rd                          |   36 
 bimets-1.5.0/bimets/man/TSEXTEND.Rd                         |   24 
 bimets-1.5.0/bimets/man/TSINFO.Rd                           |   20 
 bimets-1.5.0/bimets/man/TSJOIN.Rd                           |   26 
 bimets-1.5.0/bimets/man/TSLAG.Rd                            |   16 
 bimets-1.5.0/bimets/man/TSLEAD.Rd                           |    8 
 bimets-1.5.0/bimets/man/TSLOOK.Rd                           |   14 
 bimets-1.5.0/bimets/man/TSMERGE.Rd                          |   24 
 bimets-1.5.0/bimets/man/TSPROJECT.Rd                        |    8 
 bimets-1.5.0/bimets/man/TSTRIM.Rd                           |   18 
 bimets-1.5.0/bimets/man/as.bimets.Rd                        |   56 
 bimets-1.5.0/bimets/man/bimets-package.Rd                   |  231 
 bimets-1.5.0/bimets/man/bimetsConf.Rd                       |   46 
 bimets-1.5.0/bimets/man/date2yp.Rd                          |   14 
 bimets-1.5.0/bimets/man/frequency.Rd                        |   16 
 bimets-1.5.0/bimets/man/fromBIMETStoTS.Rd                   |   34 
 bimets-1.5.0/bimets/man/fromBIMETStoXTS.Rd                  |   44 
 bimets-1.5.0/bimets/man/fromTStoXTS.Rd                      |   74 
 bimets-1.5.0/bimets/man/fromXTStoTS.Rd                      |   74 
 bimets-1.5.0/bimets/man/idxOver.Rd                          |  146 
 bimets-1.5.0/bimets/man/is.bimets.Rd                        |   94 
 bimets-1.5.0/bimets/man/normalizeYP.Rd                      |    2 
 bimets-1.5.0/bimets/man/summary.BIMETS_MODEL.Rd             |   14 
 bimets-1.5.0/bimets/man/ym2yp.Rd                            |    2 
 bimets-1.5.0/bimets/vignettes/bimets.Rnw                    |  122 
 95 files changed, 9449 insertions(+), 8139 deletions(-)

More information about bimets at CRAN
Permanent link

Package texreg updated to version 1.37.1 with previous version 1.36.23 dated 2017-03-03

Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. (If the Zelig package, which this package enhances, cannot be found on CRAN, you can find it at <https://github.com/IQSS/Zelig>.)
Author: Philip Leifeld [aut, cre], Claudia Zucca [ctb]
Maintainer: Philip Leifeld <philip.leifeld@essex.ac.uk>

Diff between texreg versions 1.36.23 dated 2017-03-03 and 1.37.1 dated 2020-05-29

 texreg-1.36.23/texreg/R/classDefinition.R                   |only
 texreg-1.36.23/texreg/R/internal.R                          |only
 texreg-1.36.23/texreg/R/plotreg.R                           |only
 texreg-1.36.23/texreg/inst/doc/texreg.R                     |only
 texreg-1.36.23/texreg/man/print-texregTable.Rd              |only
 texreg-1.37.1/texreg/DESCRIPTION                            |   48 
 texreg-1.37.1/texreg/MD5                                    |  181 
 texreg-1.37.1/texreg/NAMESPACE                              |  152 
 texreg-1.37.1/texreg/R/extract.R                            | 7247 +++++++++---
 texreg-1.37.1/texreg/R/praise.R                             |only
 texreg-1.37.1/texreg/R/texreg.R                             | 5083 +++++++-
 texreg-1.37.1/texreg/build/vignette.rds                     |binary
 texreg-1.37.1/texreg/inst/CITATION                          |   38 
 texreg-1.37.1/texreg/inst/doc/texreg.Rnw                    |  943 -
 texreg-1.37.1/texreg/inst/doc/texreg.pdf                    |binary
 texreg-1.37.1/texreg/man/coeftostring.Rd                    |   41 
 texreg-1.37.1/texreg/man/compute.width.Rd                   |only
 texreg-1.37.1/texreg/man/createTexreg.Rd                    |  141 
 texreg-1.37.1/texreg/man/customcolumnnames.Rd               |only
 texreg-1.37.1/texreg/man/extract-ANY-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-Arima-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-H2OBinomialModel-method.Rd |only
 texreg-1.37.1/texreg/man/extract-Zelig-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-aftreg-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-averaging-method.Rd        |only
 texreg-1.37.1/texreg/man/extract-bam-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-betamfx-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-betaor-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-betareg-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-bife-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-biglm-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-brglm-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-brmsfit-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-btergm-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-censReg-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-clm-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-clmm-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-clogit-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-coeftest-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-coxph-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-coxph.penal-method.Rd      |only
 texreg-1.37.1/texreg/man/extract-coxreg-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-dynlm-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-ergm-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-ergmm-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-ets-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-fGARCH-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-feglm-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-feis-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-felm-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-forecast-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-forecast_ARIMA-method.Rd   |only
 texreg-1.37.1/texreg/man/extract-gam-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-gamlss-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-gamlssZadj-method.Rd       |only
 texreg-1.37.1/texreg/man/extract-gee-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-geeglm-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-gel-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-glm-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-glm.cluster-method.Rd      |only
 texreg-1.37.1/texreg/man/extract-glmerMod-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-glmmPQL-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-glmmTMB-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-glmmadmb-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-glmrob-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-gls-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-gmm-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-gnls-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-gnm-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-hurdle-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-ivreg-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-lm-method.Rd               |only
 texreg-1.37.1/texreg/man/extract-lm.cluster-method.Rd       |only
 texreg-1.37.1/texreg/man/extract-lme-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-lme4-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-lmerMod-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-lmrob-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-lnam-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-logitmfx-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-logitor-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-lqmm-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-lrm-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-maBina-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-merMod-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-mhurdle-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-mlogit-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-mnlogit-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-model.selection-method.Rd  |only
 texreg-1.37.1/texreg/man/extract-mtergm-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-multinom-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-negbin-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-negbinirr-method.Rd        |only
 texreg-1.37.1/texreg/man/extract-negbinmfx-method.Rd        |only
 texreg-1.37.1/texreg/man/extract-netlogit-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-nlme-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-nlmerMod-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-oglmx-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-ols-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-panelAR-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-pglm-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-pgmm-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-phreg-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-plm-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-pmg-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-poissonirr-method.Rd       |only
 texreg-1.37.1/texreg/man/extract-poissonmfx-method.Rd       |only
 texreg-1.37.1/texreg/man/extract-polr-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-probitmfx-method.Rd        |only
 texreg-1.37.1/texreg/man/extract-rem.dyad-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-rlm-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-rq-method.Rd               |only
 texreg-1.37.1/texreg/man/extract-sarlm-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-sclm-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-selection-method.Rd        |only
 texreg-1.37.1/texreg/man/extract-sienaFit-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-simex-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-speedglm-method.Rd         |only
 texreg-1.37.1/texreg/man/extract-speedlm-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-stergm-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-summary.lm-method.Rd       |only
 texreg-1.37.1/texreg/man/extract-survreg-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-survreg.penal-method.Rd    |only
 texreg-1.37.1/texreg/man/extract-svyglm-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-systemfit-method.Rd        |only
 texreg-1.37.1/texreg/man/extract-texreg-method.Rd           |only
 texreg-1.37.1/texreg/man/extract-tobit-method.Rd            |only
 texreg-1.37.1/texreg/man/extract-vglm-method.Rd             |only
 texreg-1.37.1/texreg/man/extract-weibreg-method.Rd          |only
 texreg-1.37.1/texreg/man/extract-wls-method.Rd              |only
 texreg-1.37.1/texreg/man/extract-zeroinfl-method.Rd         |only
 texreg-1.37.1/texreg/man/extract.Rd                         | 1060 -
 texreg-1.37.1/texreg/man/get.data.Rd                        |only
 texreg-1.37.1/texreg/man/get_stars_note.Rd                  |only
 texreg-1.37.1/texreg/man/htmlreg.Rd                         |only
 texreg-1.37.1/texreg/man/huxtablereg.Rd                     |only
 texreg-1.37.1/texreg/man/knitreg.Rd                         |only
 texreg-1.37.1/texreg/man/matrixreg.Rd                       |only
 texreg-1.37.1/texreg/man/names2latex.Rd                     |only
 texreg-1.37.1/texreg/man/override.Rd                        |only
 texreg-1.37.1/texreg/man/plotreg.Rd                         |  373 
 texreg-1.37.1/texreg/man/praise.Rd                          |only
 texreg-1.37.1/texreg/man/print.texregTable.Rd               |only
 texreg-1.37.1/texreg/man/reorder.Rd                         |only
 texreg-1.37.1/texreg/man/screenreg.Rd                       |only
 texreg-1.37.1/texreg/man/show-texreg-method.Rd              |only
 texreg-1.37.1/texreg/man/texreg-class.Rd                    |only
 texreg-1.37.1/texreg/man/texreg-package.Rd                  |   60 
 texreg-1.37.1/texreg/man/texreg.Rd                          |  646 -
 texreg-1.37.1/texreg/man/wordreg.Rd                         |only
 texreg-1.37.1/texreg/tests                                  |only
 texreg-1.37.1/texreg/vignettes/texreg.Rnw                   |  943 -
 151 files changed, 12175 insertions(+), 4781 deletions(-)

More information about texreg at CRAN
Permanent link

Package restatapi updated to version 0.8.6 with previous version 0.8.0 dated 2020-04-29

Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe. Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/data/database>). The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX <https://sdmx.org>) Web Services (<https://ec.europa.eu/eurostat/web/sdmx-web-services/about-this-service>) to search and download data from the Eurostat database using the SDMX standard.
Author: Mátyás Mészáros [aut, cre]
Maintainer: Mátyás Mészáros <matyas.meszaros@ec.europa.eu>

Diff between restatapi versions 0.8.0 dated 2020-04-29 and 0.8.6 dated 2020-05-29

 DESCRIPTION               |    8 
 MD5                       |   18 -
 R/create_filter_table.R   |   37 ++-
 R/filter_raw_data.R       |   20 +-
 R/get_eurostat_bulk.R     |   35 +--
 R/get_eurostat_data.R     |  426 +++++++++++++++++++++++-----------------------
 R/get_eurostat_dsd.R      |    2 
 R/get_eurostat_raw.R      |  146 +++++++--------
 R/load_cfg.R              |    1 
 tests/testthat/test-all.R |  121 +++++++------
 10 files changed, 422 insertions(+), 392 deletions(-)

More information about restatapi at CRAN
Permanent link

Package rbiom updated to version 1.0.2 with previous version 1.0.0 dated 2020-05-26

Title: Read/Write, Transform, and Summarize 'BIOM' Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files. Features include reading/writing all 'BIOM' formats, rarefaction, alpha diversity, beta diversity (including 'UniFrac'), summarizing counts by taxonomic level, and sample subsetting. Standalone functions for reading, writing, and subsetting phylogenetic trees are also provided. All CPU intensive operations are encoded in C with multi-thread support.
Author: Daniel P. Smith [aut, cre, cph] (<https://orcid.org/0000-0002-2479-2044>)
Maintainer: Daniel P. Smith <dansmith@orst.edu>

Diff between rbiom versions 1.0.0 dated 2020-05-26 and 1.0.2 dated 2020-05-29

 rbiom-1.0.0/rbiom/inst/extdata/hmp50.biom            |only
 rbiom-1.0.2/rbiom/DESCRIPTION                        |   14 
 rbiom-1.0.2/rbiom/MD5                                |   84 
 rbiom-1.0.2/rbiom/R/accessors.r                      |  500 ++---
 rbiom-1.0.2/rbiom/R/alpha.div.r                      |    2 
 rbiom-1.0.2/rbiom/R/beta.div.r                       |    2 
 rbiom-1.0.2/rbiom/R/print.r                          |   82 
 rbiom-1.0.2/rbiom/R/rarefy.r                         |    2 
 rbiom-1.0.2/rbiom/R/rbiom.r                          |   59 
 rbiom-1.0.2/rbiom/R/read.biom.r                      | 1620 +++++++++----------
 rbiom-1.0.2/rbiom/R/select.r                         |  141 -
 rbiom-1.0.2/rbiom/R/subset.r                         |   54 
 rbiom-1.0.2/rbiom/R/taxa.rollup.r                    |    2 
 rbiom-1.0.2/rbiom/R/unifrac.r                        |    2 
 rbiom-1.0.2/rbiom/R/write.biom.r                     |   16 
 rbiom-1.0.2/rbiom/README.md                          |    4 
 rbiom-1.0.2/rbiom/inst/extdata/hmp50.bz2             |only
 rbiom-1.0.2/rbiom/man/alpha.div.Rd                   |    2 
 rbiom-1.0.2/rbiom/man/beta.div.Rd                    |    2 
 rbiom-1.0.2/rbiom/man/counts.Rd                      |    2 
 rbiom-1.0.2/rbiom/man/info.Rd                        |    2 
 rbiom-1.0.2/rbiom/man/metadata.Rd                    |    2 
 rbiom-1.0.2/rbiom/man/nsamples.Rd                    |    2 
 rbiom-1.0.2/rbiom/man/ntaxa.Rd                       |    2 
 rbiom-1.0.2/rbiom/man/phylogeny.Rd                   |    2 
 rbiom-1.0.2/rbiom/man/print.Rd                       |    2 
 rbiom-1.0.2/rbiom/man/rarefy.Rd                      |    2 
 rbiom-1.0.2/rbiom/man/rbiom.Rd                       |   16 
 rbiom-1.0.2/rbiom/man/read.biom.Rd                   |    7 
 rbiom-1.0.2/rbiom/man/sample.names.Rd                |    2 
 rbiom-1.0.2/rbiom/man/select.Rd                      |    2 
 rbiom-1.0.2/rbiom/man/sequences.Rd                   |    2 
 rbiom-1.0.2/rbiom/man/subset.Rd                      |    2 
 rbiom-1.0.2/rbiom/man/taxa.names.Rd                  |    2 
 rbiom-1.0.2/rbiom/man/taxa.ranks.Rd                  |    2 
 rbiom-1.0.2/rbiom/man/taxa.rollup.Rd                 |    2 
 rbiom-1.0.2/rbiom/man/taxonomy.Rd                    |    2 
 rbiom-1.0.2/rbiom/man/unifrac.Rd                     |    2 
 rbiom-1.0.2/rbiom/man/write.biom.Rd                  |    4 
 rbiom-1.0.2/rbiom/src/par_unifrac.cpp                |    7 
 rbiom-1.0.2/rbiom/src/rcpp_rarefy.cpp                |    5 
 rbiom-1.0.2/rbiom/tests/testthat.R                   |    6 
 rbiom-1.0.2/rbiom/tests/testthat/test_calculations.r |    5 
 rbiom-1.0.2/rbiom/tests/testthat/test_file_io.r      |   27 
 44 files changed, 1364 insertions(+), 1335 deletions(-)

More information about rbiom at CRAN
Permanent link

Package pairwiseComparisons updated to version 1.0.0 with previous version 0.3.1 dated 2020-05-27

Title: Multiple Pairwise Comparison Tests
Description: Multiple pairwise comparison tests on tidy data for one-way analysis of variance for both between-subjects and within-subjects designs. Currently, it supports only the most common types of statistical analyses and tests: parametric (Welch's and Student's t-test), nonparametric (Durbin-Conover test Dunn test), robust (Yuen’s trimmed means test), and Bayes Factor (Student's t-test).
Author: Indrajeet Patil [cre, aut, cph] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

Diff between pairwiseComparisons versions 0.3.1 dated 2020-05-27 and 1.0.0 dated 2020-05-29

 DESCRIPTION                                |   18 -
 MD5                                        |   22 -
 NAMESPACE                                  |    9 
 NEWS.md                                    |    7 
 R/games_howell.R                           |    3 
 R/global_vars.R                            |    6 
 R/helpers.R                                |   33 ++
 R/pairwise_comparisons.R                   |  188 +++++++------
 README.md                                  |  301 +++++++--------------
 man/pairwise_comparisons.Rd                |  411 ++++++++++++++---------------
 tests/testthat/test-pairwise_caption.R     |   32 --
 tests/testthat/test-pairwise_comparisons.R |  240 +++++++++++++---
 12 files changed, 698 insertions(+), 572 deletions(-)

More information about pairwiseComparisons at CRAN
Permanent link

Package copula updated to version 1.0-0 with previous version 0.999-20 dated 2020-02-06

Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.
Author: Marius Hofert [aut] (<https://orcid.org/0000-0001-8009-4665>), Ivan Kojadinovic [aut] (<https://orcid.org/0000-0002-2903-1543>), Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Jun Yan [aut] (<https://orcid.org/0000-0003-4401-7296>), Johanna G. Nešlehová [ctb] (evTestK(), <https://orcid.org/0000-0001-9634-4796>), Rebecca Morger [ctb] (fitCopula.ml(): code for free mixCopula weight parameters)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

Diff between copula versions 0.999-20 dated 2020-02-06 and 1.0-0 dated 2020-05-29

 DESCRIPTION                      |   25 
 MD5                              |  103 +--
 NAMESPACE                        |    8 
 R/AllGeneric.R                   |   27 
 R/aux-acopula.R                  |    8 
 R/empCopula.R                    |   25 
 R/fitCopula.R                    |  218 +++++-
 R/fixedPar.R                     |    6 
 R/graphics.R                     |    2 
 R/mixCopula.R                    |   96 ++
 R/normalCopula.R                 |    4 
 R/pairsRosenblatt.R              |    2 
 R/sysdata.rda                    |binary
 R/tCopula.R                      |    2 
 TODO                             |    1 
 build/partial.rdb                |binary
 build/vignette.rds               |binary
 data/SMI.12.rda                  |binary
 data/gasoil.rda                  |binary
 data/rdj.rda                     |binary
 inst/NEWS.Rd                     |   29 
 inst/doc/AC_Liouville.R          |only
 inst/doc/AC_Liouville.html       |  544 ++++++----------
 inst/doc/AR_Clayton.R            |only
 inst/doc/AR_Clayton.html         |  597 +++++++-----------
 inst/doc/Frank-Rmpfr.pdf         |binary
 inst/doc/GIG.R                   |only
 inst/doc/GIG.Rmd                 |   61 +
 inst/doc/GIG.html                |  944 +++++++++++++----------------
 inst/doc/HAXC.R                  |only
 inst/doc/HAXC.html               |  966 ++++++++++++++----------------
 inst/doc/NALC.R                  |only
 inst/doc/NALC.html               |  909 ++++++++++++----------------
 inst/doc/copula_GARCH.R          |only
 inst/doc/copula_GARCH.html       |  663 ++++++++------------
 inst/doc/dNAC.R                  |only
 inst/doc/dNAC.html               |  805 +++++++++++--------------
 inst/doc/empiricial_copulas.R    |only
 inst/doc/empiricial_copulas.html |  880 ++++++++++++---------------
 inst/doc/logL_visualization.R    |only
 inst/doc/logL_visualization.html | 1250 +++++++++++++++++++--------------------
 inst/doc/nacopula-pkg.pdf        |binary
 inst/doc/qrng.R                  |only
 inst/doc/qrng.Rmd                |    9 
 inst/doc/qrng.html               | 1164 +++++++++++++++++-------------------
 inst/doc/rhoAMH-dilog.pdf        |binary
 inst/doc/wild_animals.R          |only
 inst/doc/wild_animals.Rmd        |    5 
 inst/doc/wild_animals.html       | 1165 +++++++++++++++++-------------------
 inst/rData/GIG_vign-nlogl-gr.rds |only
 man/fitCopula.Rd                 |   32 
 man/fitLambda.Rd                 |    2 
 man/getIniParam.Rd               |only
 man/mixCopula.Rd                 |   21 
 tests/fitting-ex.R               |   19 
 tests/mixCop-tst.R               |  155 +++-
 vignettes/GIG.Rmd                |   61 +
 vignettes/qrng.Rmd               |    9 
 vignettes/wild_animals.Rmd       |    5 
 59 files changed, 5297 insertions(+), 5525 deletions(-)

More information about copula at CRAN
Permanent link

Package QCA updated to version 3.8.1 with previous version 3.8 dated 2020-05-27

Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis: crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA') and fuzzy sets ('fsQCA'), using a GUI - graphical user interface. 'QCA' is a methodology that bridges the qualitative and quantitative divide in social science research. It uses a Boolean algorithm that results in a minimal causal combination that explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>), Ciprian Paduraru [ctb] (<https://orcid.org/0000-0002-4518-374X>), jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/gui/www/lib/jquery-AUTHORS.txt), lp_solve [cph] (http://lpsolve.sourceforge.net), Vasil Dinkov [ctb, cph] (jquery.smartmenus.js library), Dmitry Baranovskiy [ctb, cph] (raphael.js library), Emmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js library), Jimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library), Alrik Thiem [aut] (from version 1.0-0 up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

Diff between QCA versions 3.8 dated 2020-05-27 and 3.8.1 dated 2020-05-29

 DESCRIPTION                                   |    8 +-
 MD5                                           |   70 +++++++++++++-------------
 R/minimize.R                                  |    4 +
 inst/ChangeLog                                |    2 
 inst/gui/www/js/maincode.js                   |    2 
 inst/staticdocs/CV.html                       |    4 -
 inst/staticdocs/LegacyDatasets.html           |    4 -
 inst/staticdocs/Lipset.html                   |    4 -
 inst/staticdocs/QCA.package.html              |    8 +-
 inst/staticdocs/RS.html                       |    4 -
 inst/staticdocs/SOPexpressions.html           |    4 -
 inst/staticdocs/XYplot.html                   |    4 -
 inst/staticdocs/Xplot.html                    |    4 -
 inst/staticdocs/calibrate.html                |    4 -
 inst/staticdocs/causalChain.html              |    4 -
 inst/staticdocs/chartFunctions.html           |    4 -
 inst/staticdocs/export.html                   |    4 -
 inst/staticdocs/factorize.html                |    4 -
 inst/staticdocs/findRows.html                 |    4 -
 inst/staticdocs/findTh.html                   |    4 -
 inst/staticdocs/fuzzyops.html                 |    4 -
 inst/staticdocs/generate.html                 |    4 -
 inst/staticdocs/implicantMatrixFunctions.html |    4 -
 inst/staticdocs/index.html                    |    4 -
 inst/staticdocs/intersection.html             |    4 -
 inst/staticdocs/minimize.html                 |    4 -
 inst/staticdocs/modelFit.html                 |    4 -
 inst/staticdocs/negate.html                   |    4 -
 inst/staticdocs/pof.html                      |    4 -
 inst/staticdocs/recode.html                   |    4 -
 inst/staticdocs/retention.html                |    4 -
 inst/staticdocs/runGUI.html                   |    4 -
 inst/staticdocs/subsetsAndSupersets.html      |    4 -
 inst/staticdocs/truthTable.html               |    4 -
 man/QCA.package.Rd                            |    4 -
 src/Makevars                                  |    4 -
 36 files changed, 109 insertions(+), 105 deletions(-)

More information about QCA at CRAN
Permanent link

Package qad updated to version 0.2.0 with previous version 0.1.2 dated 2020-03-23

Title: Quantification of Asymmetric Dependence
Description: A copula-based measure for quantifying asymmetry in dependence and associations.
Author: Florian Griessenberger [aut, cre], Robert R. Junker [aut], Wolfgang Trutschnig [aut]
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>

Diff between qad versions 0.1.2 dated 2020-03-23 and 0.2.0 dated 2020-05-29

 DESCRIPTION                              |   25 +-
 MD5                                      |   31 ++-
 NAMESPACE                                |    5 
 R/emp_c_copula.R                         |   37 ++--
 R/plots.R                                |  178 ++++++-------------
 R/qad.R                                  |  276 +++++++++++++++++++++++--------
 R/sysdata.rda                            |only
 R/utility_functions.R                    |   48 +++++
 man/cci.Rd                               |   18 --
 man/figures/README-example-1.png         |binary
 man/figures/README-example-2.png         |binary
 man/figures/README-example-3.png         |binary
 man/figures/README-unnamed-chunk-2-1.png |only
 man/figures/README-unnamed-chunk-2-2.png |only
 man/heatmap.qad.Rd                       |    2 
 man/mcData_independence.Rd               |only
 man/pairwise.qad.Rd                      |   24 +-
 man/qad.Rd                               |   29 +--
 man/qad_distribution.Rd                  |only
 19 files changed, 404 insertions(+), 269 deletions(-)

More information about qad at CRAN
Permanent link

Package FrF2 updated to version 2.2-1 with previous version 2.2 dated 2020-04-23

Title: Fractional Factorial Designs with 2-Level Factors
Description: Regular and non-regular Fractional Factorial 2-level designs can be created. Furthermore, analysis tools for Fractional Factorial designs with 2-level factors are offered (main effects and interaction plots for all factors simultaneously, cube plot for looking at the simultaneous effects of three factors, full or half normal plot, alias structure in a more readable format than with the built-in function alias).
Author: Ulrike Groemping
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>

Diff between FrF2 versions 2.2 dated 2020-04-23 and 2.2-1 dated 2020-05-29

 DESCRIPTION                                |    8 
 MD5                                        |   22 
 R/colpick.R                                |    4 
 inst/NEWS                                  |    6 
 tests/FrF2test.R                           |    2 
 tests/FrF2test.Rout.save                   | 1374 +++++++++++++++++------------
 tests/addcentertest.Rout.save              |   36 
 tests/foldtest.Rout.save                   |   36 
 tests/generators.from.designtest.Rout.save |   52 -
 tests/generators.summary.test.Rout.save    |   36 
 tests/godolphintest.Rout.save              |   36 
 tests/pbtest.Rout.save                     |   36 
 12 files changed, 975 insertions(+), 673 deletions(-)

More information about FrF2 at CRAN
Permanent link

Package dmdScheme updated to version 1.1.3.1 with previous version 1.1.3 dated 2020-05-28

Title: Domain Specific MetaData Scheme
Description: Forms the core for developing own domain specific metadata schemes. It contains the basic functionality needed for all metadata schemes based on the 'dmdScheme'. See R.M. Krug and O.L. Petchey (2019) <DOI:10.5281/zenodo.3581970>.
Author: Rainer M. Krug [aut, cre] (<https://orcid.org/0000-0002-7490-0066>), Owen L. Petchey [ctb] (<https://orcid.org/0000-0002-7724-1633>)
Maintainer: Rainer M. Krug <Rainer.Krug@uzh.ch>

Diff between dmdScheme versions 1.1.3 dated 2020-05-28 and 1.1.3.1 dated 2020-05-29

 DESCRIPTION                                  |    8 ++++----
 MD5                                          |   14 ++++++++------
 R/report.dmdScheme_validation.R              |    3 ++-
 inst/doc/Howto_create_new_scheme.html        |   10 +++++-----
 inst/doc/minimum_requirements_dmdscheme.html |    4 ++--
 inst/doc/r_package_introduction.html         |   14 +++++++-------
 man/report.Rd                                |    3 ++-
 vignettes/custom_template.R                  |only
 vignettes/custom_template.html               |only
 9 files changed, 30 insertions(+), 26 deletions(-)

More information about dmdScheme at CRAN
Permanent link

Package covglasso updated to version 1.0.2 with previous version 1.0.1 dated 2020-02-08

Title: Sparse Covariance Matrix Estimation
Description: Direct sparse covariance matrix estimation via the covariance graphical lasso by Bien, Tibshirani (2011) <doi:10.1093/biomet/asr054> using the fast coordinate descent algorithm of Wang (2014) <doi:10.1007/s11222-013-9385-5>.
Author: Michael Fop [aut, cre] (<https://orcid.org/0000-0003-3936-2757>), Hao Wang [ctb]
Maintainer: Michael Fop <michael.fop@ucd.ie>

Diff between covglasso versions 1.0.1 dated 2020-02-08 and 1.0.2 dated 2020-05-29

 DESCRIPTION       |    8 ++++----
 MD5               |    6 +++---
 NEWS.md           |    4 ++++
 src/covglasso.cpp |    4 +++-
 4 files changed, 14 insertions(+), 8 deletions(-)

More information about covglasso at CRAN
Permanent link

Package EpiEstim updated to version 2.2-3 with previous version 2.2-1 dated 2019-07-08

Title: Estimate Time Varying Reproduction Numbers from Epidemic Curves
Description: Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.
Author: Anne Cori [aut, cre] (<https://orcid.org/0000-0002-8443-9162>), Simon Cauchemez [ctb], Neil M. Ferguson [ctb] (<https://orcid.org/0000-0002-1154-8093>), Christophe Fraser [ctb] (<https://orcid.org/0000-0003-2399-9657>), Elisabeth Dahlqwist [ctb] (<https://orcid.org/0000-0001-5797-6803>), P. Alex Demarsh [ctb], Thibaut Jombart [ctb] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>), Justin Lessler [ctb] (<https://orcid.org/0000-0002-9741-8109>), Shikun Li [ctb], Jonathan A. Polonsky [ctb] (<https://orcid.org/0000-0002-8634-4255>), Jake Stockwin [ctb], Robin Thompson [ctb] (<https://orcid.org/0000-0001-8545-5212>), Rolina van Gaalen [ctb]
Maintainer: Anne Cori <a.cori@imperial.ac.uk>

Diff between EpiEstim versions 2.2-1 dated 2019-07-08 and 2.2-3 dated 2020-05-29

 EpiEstim-2.2-1/EpiEstim/R/estimate_R.R                                 |only
 EpiEstim-2.2-3/EpiEstim/DESCRIPTION                                    |    9 -
 EpiEstim-2.2-3/EpiEstim/MD5                                            |   78 ++++-----
 EpiEstim-2.2-3/EpiEstim/NEWS.md                                        |   17 +-
 EpiEstim-2.2-3/EpiEstim/R/data.R                                       |    4 
 EpiEstim-2.2-3/EpiEstim/R/discr_si.R                                   |    5 
 EpiEstim-2.2-3/EpiEstim/R/estimate_r.R                                 |only
 EpiEstim-2.2-3/EpiEstim/R/plot.R                                       |    6 
 EpiEstim-2.2-3/EpiEstim/R/wallinga_teunis.R                            |    4 
 EpiEstim-2.2-3/EpiEstim/README.md                                      |    1 
 EpiEstim-2.2-3/EpiEstim/build/vignette.rds                             |binary
 EpiEstim-2.2-3/EpiEstim/data/Flu1918.rda                               |binary
 EpiEstim-2.2-3/EpiEstim/data/Measles1861.rda                           |binary
 EpiEstim-2.2-3/EpiEstim/data/MockRotavirus.rda                         |binary
 EpiEstim-2.2-3/EpiEstim/data/SARS2003.rda                              |binary
 EpiEstim-2.2-3/EpiEstim/data/Smallpox1972.rda                          |binary
 EpiEstim-2.2-3/EpiEstim/inst/doc/demo.R                                |   38 ++--
 EpiEstim-2.2-3/EpiEstim/inst/doc/demo.html                             |   71 +++-----
 EpiEstim-2.2-3/EpiEstim/man/EstimateR.Rd                               |   29 ++-
 EpiEstim-2.2-3/EpiEstim/man/Flu2009.Rd                                 |   18 ++
 EpiEstim-2.2-3/EpiEstim/man/MockRotavirus.Rd                           |    2 
 EpiEstim-2.2-3/EpiEstim/man/WT.Rd                                      |   15 +
 EpiEstim-2.2-3/EpiEstim/man/check_cdt_samples_convergence.Rd           |    2 
 EpiEstim-2.2-3/EpiEstim/man/coarse2estim.Rd                            |    3 
 EpiEstim-2.2-3/EpiEstim/man/discr_si.Rd                                |    2 
 EpiEstim-2.2-3/EpiEstim/man/estimate_R.Rd                              |   14 +
 EpiEstim-2.2-3/EpiEstim/man/flu_2009_NYC_school.Rd                     |    2 
 EpiEstim-2.2-3/EpiEstim/man/init_mcmc_params.Rd                        |   11 -
 EpiEstim-2.2-3/EpiEstim/man/make_config.Rd                             |   22 +-
 EpiEstim-2.2-3/EpiEstim/man/make_mcmc_control.Rd                       |   12 -
 EpiEstim-2.2-3/EpiEstim/man/mers_2014_15.Rd                            |    2 
 EpiEstim-2.2-3/EpiEstim/man/plot.estimate_R.Rd                         |   33 ++-
 EpiEstim-2.2-3/EpiEstim/man/wallinga_teunis.Rd                         |    9 -
 EpiEstim-2.2-3/EpiEstim/tests/expected_output/Example1.rda             |binary
 EpiEstim-2.2-3/EpiEstim/tests/expected_output/Example2.rda             |binary
 EpiEstim-2.2-3/EpiEstim/tests/expected_output/Example3.rda             |binary
 EpiEstim-2.2-3/EpiEstim/tests/expected_output/Example4.rda             |binary
 EpiEstim-2.2-3/EpiEstim/tests/figs/flu2009-incidence-import.svg        |   84 +++++-----
 EpiEstim-2.2-3/EpiEstim/tests/figs/flu2009-instantaneous-no-legend.svg |   44 ++---
 EpiEstim-2.2-3/EpiEstim/tests/figs/flu2009-rc.svg                      |    4 
 EpiEstim-2.2-3/EpiEstim/tests/figs/flu2009-ri.svg                      |    4 
 41 files changed, 301 insertions(+), 244 deletions(-)

More information about EpiEstim at CRAN
Permanent link

Package usefun updated to version 0.4.6 with previous version 0.4.5 dated 2020-04-22

Title: A Collection of Useful Functions by John
Description: A set of general functions that I have used in various projects and in other R packages. They support some miscellaneous operations on data frames, matrices and vectors like adding a row on a ternary (3-value) data.frame based on positive and negative vector-indicators, rearranging a list of data.frames by rownames, pruning rows or columns of a data.frame that contain only one specific value given by the user, pruning and reordering a vector according to the common elements between its names and elements of another given vector, finding the non-common elements between two vectors (outer-section), normalization of a vector, matrix or data.frame's numeric values in a specified range, pretty printing of vector names and values in an R Markdown document. Also included is a function that returns the statistics needed for plotting a ROC curve.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>

Diff between usefun versions 0.4.5 dated 2020-04-22 and 0.4.6 dated 2020-05-29

 usefun-0.4.5/usefun/man/plot_string_to_file.Rd |only
 usefun-0.4.6/usefun/DESCRIPTION                |    6 ++--
 usefun-0.4.6/usefun/MD5                        |   23 ++++++++--------
 usefun-0.4.6/usefun/NAMESPACE                  |    6 ----
 usefun-0.4.6/usefun/NEWS.md                    |    5 +++
 usefun-0.4.6/usefun/R/plot.R                   |   35 -------------------------
 usefun-0.4.6/usefun/R/roc.R                    |    2 -
 usefun-0.4.6/usefun/R/save.R                   |    3 ++
 usefun-0.4.6/usefun/README.md                  |    1 
 usefun-0.4.6/usefun/man/get_roc_stats.Rd       |    2 -
 usefun-0.4.6/usefun/man/save_df_to_file.Rd     |    2 +
 usefun-0.4.6/usefun/man/save_vector_to_file.Rd |    1 
 usefun-0.4.6/usefun/tests/testthat/test-plot.R |only
 usefun-0.4.6/usefun/tests/testthat/test-save.R |only
 14 files changed, 29 insertions(+), 57 deletions(-)

More information about usefun at CRAN
Permanent link

Package gcKrig updated to version 1.1.4 with previous version 1.1.3 dated 2018-12-21

Title: Analysis of Geostatistical Count Data using Gaussian Copulas
Description: Provides a variety of functions to analyze and model geostatistical count data with Gaussian copulas, including 1) data simulation and visualization; 2) correlation structure assessment (here also known as the Normal To Anything); 3) calculate multivariate normal rectangle probabilities; 4) likelihood inference and parallel prediction at predictive locations.
Author: Zifei Han
Maintainer: Zifei Han <hanzifei1@gmail.com>

Diff between gcKrig versions 1.1.3 dated 2018-12-21 and 1.1.4 dated 2020-05-29

 DESCRIPTION       |    6 +++---
 MD5               |    8 ++++----
 R/TwoMethods.R    |    7 +++++--
 build/partial.rdb |binary
 inst/NEWS.txt     |    3 +++
 5 files changed, 15 insertions(+), 9 deletions(-)

More information about gcKrig at CRAN
Permanent link

Package TopKLists updated to version 1.0.7 with previous version 1.0.6 dated 2015-11-13

Title: Inference, Aggregation and Visualization for Top-K Ranked Lists
Description: For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers (1) statistical inference on the lengths of informative top-k lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results.
Author: Michael G. Schimek, Eva Budinska, Jie Ding, Karl G. Kugler, Vendula Svendova, Shili Lin
Maintainer: Michael G. Schimek <michael.schimek@medunigraz.at>

Diff between TopKLists versions 1.0.6 dated 2015-11-13 and 1.0.7 dated 2020-05-29

 DESCRIPTION            |   10 +++++-----
 MD5                    |   13 +++++++------
 NAMESPACE              |    2 +-
 R/TopKGraphics.R       |    8 ++++----
 build/vignette.rds     |binary
 inst/doc/TopKLists.pdf |binary
 man/breast.Rd          |    2 +-
 src/init.c             |only
 8 files changed, 18 insertions(+), 17 deletions(-)

More information about TopKLists at CRAN
Permanent link

Package synthACS updated to version 1.6.0 with previous version 1.5.7 dated 2020-04-25

Title: Synthetic Microdata and Spatial MicroSimulation Modeling for ACS Data
Description: Provides access to curated American Community Survey (ACS) base tables via a wrapper to library(acs). Builds synthetic micro-datasets at any user-specified geographic level with ten default attributes; and, conducts spatial microsimulation modeling (SMSM) via simulated annealing. SMSM is conducted in parallel by default. Lastly, we provide functionality for data-extensibility of micro-datasets.
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>

Diff between synthACS versions 1.5.7 dated 2020-04-25 and 1.6.0 dated 2020-05-29

 synthACS-1.5.7/synthACS/tests/testthat/test-class_synthACS_methods.R  |only
 synthACS-1.5.7/synthACS/tests/testthat/test-combine_smsm.R            |only
 synthACS-1.5.7/synthACS/tests/testthat/test-sim_anneal_parallel.R     |only
 synthACS-1.6.0/synthACS/DESCRIPTION                                   |   11 
 synthACS-1.6.0/synthACS/MD5                                           |   25 
 synthACS-1.6.0/synthACS/R/pull_population.R                           |    4 
 synthACS-1.6.0/synthACS/inst/doc/jss_synthACS.pdf                     |binary
 synthACS-1.6.0/synthACS/inst/testdata                                 |only
 synthACS-1.6.0/synthACS/tests/testthat.R                              |   14 
 synthACS-1.6.0/synthACS/tests/testthat/local-class_synthACS_methods.R |only
 synthACS-1.6.0/synthACS/tests/testthat/local-combine_smsm.R           |only
 synthACS-1.6.0/synthACS/tests/testthat/local-derive_synthetic.R       |only
 synthACS-1.6.0/synthACS/tests/testthat/local-sim_anneal.R             |only
 synthACS-1.6.0/synthACS/tests/testthat/local-sim_anneal_parallel.R    |only
 synthACS-1.6.0/synthACS/tests/testthat/local-synth_new_attr.R         |only
 synthACS-1.6.0/synthACS/tests/testthat/setup-testdata.R               |only
 synthACS-1.6.0/synthACS/tests/testthat/test-derive_synthetic.R        |   30 
 synthACS-1.6.0/synthACS/tests/testthat/test-sim_anneal.R              |  402 ----------
 synthACS-1.6.0/synthACS/tests/testthat/test-synth_new_attr.R          |  138 ---
 19 files changed, 31 insertions(+), 593 deletions(-)

More information about synthACS at CRAN
Permanent link

Package runes updated to version 0.1.0 with previous version 0.0.1 dated 2020-02-22

Title: Convert Strings to Elder Futhark Runes
Description: Convert a string of text characters to Elder Futhark Runes <https://en.wikipedia.org/wiki/Elder_Futhark>.
Author: Bryan Jenks [aut, cre] (<https://orcid.org/0000-0002-9604-3069>)
Maintainer: Bryan Jenks <bryanjenks@protonmail.com>

Diff between runes versions 0.0.1 dated 2020-02-22 and 0.1.0 dated 2020-05-29

 DESCRIPTION                       |    6 
 MD5                               |   17 +
 NEWS.md                           |   42 ++++
 R/runes.R                         |  195 ++++++++++++++++++----
 R/runes_table.R                   |  327 +++++++++++++++++++++++++++++++++++---
 inst                              |only
 man/runes.Rd                      |   20 +-
 man/runes_table.Rd                |    9 -
 tests/testthat/test-runes.R       |   75 +-------
 tests/testthat/test-runes_table.R |    7 
 10 files changed, 558 insertions(+), 140 deletions(-)

More information about runes at CRAN
Permanent link

Package pkgload updated to version 1.1.0 with previous version 1.0.2 dated 2018-10-29

Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then attaching it. This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Winston Chang [aut], RStudio [cph], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Jim Hester <jim.hester@rstudio.com>

Diff between pkgload versions 1.0.2 dated 2018-10-29 and 1.1.0 dated 2020-05-29

 DESCRIPTION                                             |   16 +-
 MD5                                                     |   61 +++++-----
 NEWS.md                                                 |   15 ++
 R/dev-example.r                                         |   44 +++++--
 R/dev-help.r                                            |   15 ++
 R/dev-topic.r                                           |    3 
 R/load-dll.r                                            |   12 +-
 R/load.r                                                |   90 ++++++++++++++--
 R/namespace-env.r                                       |   34 ++++--
 R/package-deps.r                                        |    5 
 R/shims.r                                               |    2 
 R/utils.R                                               |    7 -
 README.md                                               |    7 -
 man/check_suggested.Rd                                  |    5 
 man/dev_example.Rd                                      |   26 +++-
 man/dev_help.Rd                                         |   12 +-
 man/help.Rd                                             |    8 -
 man/imports_env.Rd                                      |    2 
 man/load_all.Rd                                         |   32 ++++-
 man/ns_env.Rd                                           |    4 
 man/parse_deps.Rd                                       |    4 
 man/pkg_env.Rd                                          |    2 
 man/system.file.Rd                                      |    2 
 tests/testthat/test-examples.R                          |   26 ++++
 tests/testthat/test-extraction.R                        |    2 
 tests/testthat/test-help.r                              |    1 
 tests/testthat/test-load.r                              |   14 ++
 tests/testthat/testHelp/NAMESPACE                       |    2 
 tests/testthat/testHelp/R/foofoo.r                      |   14 ++
 tests/testthat/testHelp/man/macros                      |only
 tests/testthat/testHelp/man/testCustomMacro.Rd          |only
 tests/testthat/testHelp/man/testSysMacro.Rd             |only
 tests/testthat/testLoadHelpers/tests/testthat/helpers.R |    2 
 33 files changed, 349 insertions(+), 120 deletions(-)

More information about pkgload at CRAN
Permanent link

Package MortCast updated to version 2.3-0 with previous version 2.2-1 dated 2020-05-05

Title: Estimation and Projection of Age-Specific Mortality Rates
Description: Age-specific mortality rates are estimated and projected using the Kannisto, Lee-Carter and related methods as described in Sevcikova et al. (2016) <doi:10.1007/978-3-319-26603-9_15>.
Author: Hana Sevcikova, Nan Li and Patrick Gerland
Maintainer: Hana Sevcikova <hanas@uw.edu>

Diff between MortCast versions 2.2-1 dated 2020-05-05 and 2.3-0 dated 2020-05-29

 ChangeLog            |    6 ++-
 DESCRIPTION          |   10 ++---
 MD5                  |   29 ++++++++-------
 R/MortCast-data.R    |   12 ++++--
 R/other_methods.R    |   97 ++++++++++++++++++++++++++++++++++-----------------
 build/partial.rdb    |binary
 data/LQcoef.rda      |binary
 data/MLT1Ylookup.rda |only
 data/MLTlookup.rda   |binary
 data/PMDadjcoef.rda  |binary
 data/PMDrho.rda      |binary
 data/datalist        |only
 man/MLTlookup.Rd     |   11 +++--
 man/mltgroup.Rd      |   21 ++++++++---
 man/pmdgroup.Rd      |    5 ++
 src/Makevars         |only
 src/life_tables.c    |   34 +++++++++--------
 17 files changed, 146 insertions(+), 79 deletions(-)

More information about MortCast at CRAN
Permanent link

Thu, 28 May 2020

Package hyperSpec updated to version 0.99-20200527 with previous version 0.99-20200213.1 dated 2020-04-01

Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Description: Comfortable ways to work with hyperspectral data sets. I.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f (wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Author: Claudia Beleites [aut, cre, dtc], Valter Sergo [aut], Alois Bonifacio [ctb, dtc], Marcel Dahms [ctb], Björn Egert [ctb], Simon Fuller [ctb], Vilmantas Gegzna [ctb], Rustam Guliev [ctb], Bryan Hanson [ctb], Michael Hermes [ctb], Martin Kammer [dtc], Roman Kiselev [ctb], Sebastian Mellor [ctb]
Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.gmbh>

Diff between hyperSpec versions 0.99-20200213.1 dated 2020-04-01 and 0.99-20200527 dated 2020-05-28

 DESCRIPTION                 |   53 +++++++++++++++++++++---------------------
 MD5                         |   55 +++++++++++++++++++++++---------------------
 NAMESPACE                   |    1 
 R/apply.R                   |    5 +++-
 R/decomposition.R           |    2 +
 R/fix_spc_colnames.R        |only
 R/initialize.R              |    6 ++--
 R/read.spc.R                |   27 +++++++++++++++++++++
 R/read.spc.Shimadzu.R       |only
 R/sysdata.rda               |binary
 R/wl.R                      |    4 +--
 data/barbiturates.rda       |binary
 data/laser.rda              |binary
 data/paracetamol.rda        |binary
 inst/doc/baseline.pdf       |binary
 inst/doc/chondro.pdf        |binary
 inst/doc/fileio.pdf         |binary
 inst/doc/fileio.pdf.asis    |    2 -
 inst/doc/flu.pdf            |binary
 inst/doc/hyperspec.pdf      |binary
 inst/doc/laser.pdf          |binary
 inst/doc/plotting.pdf       |binary
 man/apply.Rd                |    5 +++-
 man/barbiturates.Rd         |    6 +++-
 man/chondro.Rd              |    9 +++++--
 man/dot-fix_spc_colnames.Rd |only
 man/flu.Rd                  |    6 +++-
 man/laser.Rd                |    6 +++-
 man/paracetamol.Rd          |    6 +++-
 vignettes/fileio.pdf.asis   |    2 -
 30 files changed, 124 insertions(+), 71 deletions(-)

More information about hyperSpec at CRAN
Permanent link

Package ggplot2 updated to version 3.3.1 with previous version 3.3.0 dated 2020-03-05

Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Description: A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Author: Hadley Wickham [aut, cre], Winston Chang [aut], Lionel Henry [aut], Thomas Lin Pedersen [aut], Kohske Takahashi [aut], Claus Wilke [aut], Kara Woo [aut], Hiroaki Yutani [aut], Dewey Dunnington [aut], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between ggplot2 versions 3.3.0 dated 2020-03-05 and 3.3.1 dated 2020-05-28

 DESCRIPTION                       |    8 
 MD5                               |   38 
 NEWS.md                           |    5 
 README.md                         |    2 
 build/vignette.rds                |binary
 inst/doc/extending-ggplot2.html   | 1500 +++++++++++++++++++-------------------
 inst/doc/ggplot2-in-packages.html |  238 +++---
 inst/doc/ggplot2-specs.html       |  220 ++---
 man/diamonds.Rd                   |    6 
 man/economics.Rd                  |    8 
 man/faithfuld.Rd                  |    6 
 man/graphical-units.Rd            |    6 
 man/luv_colours.Rd                |    6 
 man/midwest.Rd                    |    6 
 man/mpg.Rd                        |    6 
 man/msleep.Rd                     |    6 
 man/presidential.Rd               |    6 
 man/seals.Rd                      |    4 
 man/txhousing.Rd                  |    6 
 tests/testthat/Rplots.pdf         |binary
 20 files changed, 1057 insertions(+), 1020 deletions(-)

More information about ggplot2 at CRAN
Permanent link

Package cvms updated to version 1.0.2 with previous version 1.0.1 dated 2020-04-19

Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models and get relevant evaluation metrics in a tidy format. Validate the best model on a test set and compare it to a baseline evaluation. Alternatively, evaluate predictions from an external model. Currently supports regression and classification (binary and multiclass). Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R., & Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre], Benjamin Hugh Zachariae [aut]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>

Diff between cvms versions 1.0.1 dated 2020-04-19 and 1.0.2 dated 2020-05-28

 DESCRIPTION                                     |    6 +--
 MD5                                             |   46 ++++++++++++------------
 NEWS.md                                         |    4 ++
 R/evaluate_predictions_multinomial.R            |    9 ++++
 R/evaluate_residuals.R                          |   10 +++++
 R/fit_predict_model_fn.R                        |    1 
 R/helpers.R                                     |    7 +++
 R/run_prediction_process.R                      |   15 +++++++
 R/validate_list.R                               |    2 -
 build/cvms.pdf                                  |binary
 inst/doc/available_metrics.html                 |    4 +-
 inst/doc/creating_a_confusion_matrix.Rmd        |    4 +-
 inst/doc/creating_a_confusion_matrix.html       |   18 ++++-----
 inst/doc/cross_validating_custom_functions.Rmd  |    7 +--
 inst/doc/cross_validating_custom_functions.html |   24 ++++++------
 inst/doc/evaluate_by_id.html                    |   10 ++---
 tests/testthat/test_baseline.R                  |   10 +++--
 tests/testthat/test_compational_grid.R          |    2 -
 tests/testthat/test_cross_validate_fn.R         |   18 ++++-----
 tests/testthat/test_evaluate.R                  |   16 ++++----
 tests/testthat/test_select_metrics.R            |    6 ++-
 tests/testthat/test_validate_fn.R               |    4 +-
 vignettes/creating_a_confusion_matrix.Rmd       |    4 +-
 vignettes/cross_validating_custom_functions.Rmd |    7 +--
 24 files changed, 142 insertions(+), 92 deletions(-)

More information about cvms at CRAN
Permanent link

Package censusxy updated to version 1.0.0 with previous version 0.1.2 dated 2019-08-09

Title: Access the U.S. Census Bureau's Geocoding A.P.I. System
Description: Provides access to the U.S. Census Bureau's A.P.I for matching American street addresses with their longitude and latitude. This includes both single address matching as well as batch functionality for multiple addresses. Census geographies can be appended to addresses if desired, and reverse geocoding of point locations to census geographies is also supported.
Author: Christopher Prener [aut, cre] (<https://orcid.org/0000-0002-4310-9888>), Branson Fox [aut] (<https://orcid.org/0000-0002-4361-2811>)
Maintainer: Christopher Prener <chris.prener@slu.edu>

Diff between censusxy versions 0.1.2 dated 2019-08-09 and 1.0.0 dated 2020-05-28

 censusxy-0.1.2/censusxy/R/cxy_geocode.R                   |only
 censusxy-0.1.2/censusxy/R/cxy_geocoder.R                  |only
 censusxy-0.1.2/censusxy/R/cxy_id.R                        |only
 censusxy-0.1.2/censusxy/R/cxy_prep.R                      |only
 censusxy-0.1.2/censusxy/R/cxy_replace.R                   |only
 censusxy-0.1.2/censusxy/R/cxy_split.R                     |only
 censusxy-0.1.2/censusxy/inst/extdata                      |only
 censusxy-0.1.2/censusxy/tests/testthat/test_cxy_geocode.R |only
 censusxy-1.0.0/censusxy/DESCRIPTION                       |   27 +-
 censusxy-1.0.0/censusxy/MD5                               |   44 ++-
 censusxy-1.0.0/censusxy/NAMESPACE                         |   22 -
 censusxy-1.0.0/censusxy/NEWS.md                           |   13 +
 censusxy-1.0.0/censusxy/R/batch.R                         |only
 censusxy-1.0.0/censusxy/R/internal.R                      |only
 censusxy-1.0.0/censusxy/R/options.R                       |only
 censusxy-1.0.0/censusxy/R/single.R                        |only
 censusxy-1.0.0/censusxy/README.md                         |   50 +---
 censusxy-1.0.0/censusxy/build/vignette.rds                |binary
 censusxy-1.0.0/censusxy/inst/doc/censusxy.R               |    2 
 censusxy-1.0.0/censusxy/inst/doc/censusxy.Rmd             |  110 +++++++--
 censusxy-1.0.0/censusxy/inst/doc/censusxy.html            |  163 +++++++++-----
 censusxy-1.0.0/censusxy/man/cxy_benchmarks.Rd             |only
 censusxy-1.0.0/censusxy/man/cxy_geocode.Rd                |   82 ++++---
 censusxy-1.0.0/censusxy/man/cxy_geography.Rd              |only
 censusxy-1.0.0/censusxy/man/cxy_oneline.Rd                |only
 censusxy-1.0.0/censusxy/man/cxy_single.Rd                 |only
 censusxy-1.0.0/censusxy/man/cxy_vintages.Rd               |only
 censusxy-1.0.0/censusxy/man/stl_homicides.Rd              |    6 
 censusxy-1.0.0/censusxy/man/stl_homicides_small.Rd        |    6 
 censusxy-1.0.0/censusxy/tests/testthat/test_batch.R       |only
 censusxy-1.0.0/censusxy/tests/testthat/test_options.R     |only
 censusxy-1.0.0/censusxy/tests/testthat/test_single.R      |only
 censusxy-1.0.0/censusxy/vignettes/censusxy.Rmd            |  110 +++++++--
 33 files changed, 421 insertions(+), 214 deletions(-)

More information about censusxy at CRAN
Permanent link

Package CALF updated to version 1.0.15 with previous version 0.2.0 dated 2017-05-19

Title: Coarse Approximation Linear Function
Description: Forward selection linear regression greedy algorithm where selection is driven by optimization of Welch t-test p-value or AUC (binary dependent vector), or Pearson correlation (nonbinary). Functions now enabled include data outputs for permutation tests of several types plus cross-validation features. Please see preprint at <https://www.biorxiv.org/content/10.1101/2020.03.27.011700v1> or <doi:10.1101/2020.03.27.011700>.
Author: Stephanie Lane [aut, cre], John Ford [aut], Clark Jeffries [aut], Diana Perkins [aut]
Maintainer: John Ford <JoRuFo@gmail.com>

Diff between CALF versions 0.2.0 dated 2017-05-19 and 1.0.15 dated 2020-05-28

 DESCRIPTION                     |   20 -
 MD5                             |   30 +
 NAMESPACE                       |    9 
 R/CALF-data.R                   |    4 
 R/CALF-package.R                |   39 +-
 R/calf_internal.R               |  229 ++++++--------
 R/calf_wrappers.R               |  624 +++++++++++++++++++++++++++++++++++++---
 R/print.calf.R                  |   22 +
 man/CALF-package.Rd             |   70 ++--
 man/CaseControl.Rd              |   30 +
 man/calf.Rd                     |   67 ++--
 man/calf_exact_binary_subset.Rd |only
 man/calf_fractional.Rd          |only
 man/calf_randomize.Rd           |   80 ++---
 man/calf_subset.Rd              |   83 ++---
 man/cv.calf.Rd                  |only
 man/write.calf.Rd               |only
 man/write.calf_randomize.Rd     |only
 man/write.calf_subset.Rd        |only
 19 files changed, 945 insertions(+), 362 deletions(-)

More information about CALF at CRAN
Permanent link

Package beam updated to version 2.0.2 with previous version 2.0.1 dated 2020-01-28

Title: Fast Bayesian Inference in Large Gaussian Graphical Models
Description: Fast Bayesian inference of marginal and conditional independence structures from high-dimensional data. Leday and Richardson (2019), Biometrics, <doi:10.1111/biom.13064>.
Author: Gwenael G.R. Leday [cre, aut], Ilaria Speranza [aut], Harry Gray [ctb]
Maintainer: Gwenael G.R. Leday <gwenael.leday@wur.nl>

Diff between beam versions 2.0.1 dated 2020-01-28 and 2.0.2 dated 2020-05-28

 DESCRIPTION       |   14 +++++++-------
 MD5               |    8 ++++----
 NEWS.md           |   12 +++++++++---
 man/beam-class.Rd |    2 +-
 src/beam.cpp      |   17 +++++++++++++++--
 5 files changed, 36 insertions(+), 17 deletions(-)

More information about beam at CRAN
Permanent link

Package echo.find updated to version 4.0 with previous version 3.0 dated 2019-06-20

Title: Finding Rhythms Using Extended Circadian Harmonic Oscillators (ECHO)
Description: Provides a function (echo_find()) designed to find rhythms from data using extended harmonic oscillators. For more information, see H. De los Santos et al. (2020) <doi:10.1093/bioinformatics/btz617> .
Author: Hannah De los Santos [aut, cre], Emily Collins [aut], Kristin Bennett [aut], Jennifer Hurley [aut], R Development Core Team [aut]
Maintainer: Hannah De los Santos <delosh@rpi.edu>

Diff between echo.find versions 3.0 dated 2019-06-20 and 4.0 dated 2020-05-28

 DESCRIPTION                 |   14 
 MD5                         |   18 
 NAMESPACE                   |    5 
 R/echo_package_functions.R  |   21 
 R/echo_utils.R              | 1425 +++++++++++++++++++++++++++++---------------
 inst/CITATION               |   33 -
 inst/doc/echo-vignette.Rmd  |    4 
 inst/doc/echo-vignette.html |  721 ++++++++++++++--------
 man/echo_find.Rd            |    4 
 vignettes/echo-vignette.Rmd |    4 
 10 files changed, 1483 insertions(+), 766 deletions(-)

More information about echo.find at CRAN
Permanent link

Package pins updated to version 0.4.1 with previous version 0.4.0 dated 2020-04-07

Title: Pin, Discover and Share Resources
Description: Pin remote resources into a local cache to work offline, improve speed and avoid recomputing; discover and share resources in local folders, 'GitHub', 'Kaggle' or 'RStudio Connect'. Resources can be anything from 'CSV', 'JSON', or image files to arbitrary R objects.
Author: Javier Luraschi [aut, cre], RStudio [cph]
Maintainer: Javier Luraschi <javier@rstudio.com>

Diff between pins versions 0.4.0 dated 2020-04-07 and 0.4.1 dated 2020-05-28

 DESCRIPTION                        |    6 +--
 MD5                                |   36 ++++++++++---------
 NEWS.md                            |   34 ++++++++++++++++++
 R/board_kaggle.R                   |   46 ++++++++++++++++++++-----
 R/board_registration.R             |    6 ++-
 R/board_rsconnect.R                |    3 -
 R/pin.R                            |   63 ++++++++--------------------------
 R/pin_download.R                   |   46 +++++++++++++++++--------
 R/pin_extensions.R                 |   67 +++++++++++++++++++++++++------------
 R/pins_metadata.R                  |only
 R/ui_viewer.R                      |   10 ++++-
 R/utils.R                          |    2 -
 inst/doc/boards-kaggle.Rmd         |   35 +++++++++++++++++++
 inst/doc/boards-kaggle.html        |   24 +++++++++++++
 inst/doc/boards-rsconnect.Rmd      |    2 -
 inst/doc/boards-rsconnect.html     |    2 -
 man/custom-pins.Rd                 |    2 -
 tests/testthat/test-pin-metadata.R |only
 vignettes/boards-kaggle.Rmd        |   35 +++++++++++++++++++
 vignettes/boards-rsconnect.Rmd     |    2 -
 20 files changed, 300 insertions(+), 121 deletions(-)

More information about pins at CRAN
Permanent link

Package MALDIrppa updated to version 1.0.2 with previous version 1.0.1-2 dated 2018-11-09

Title: MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis
Description: Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data.
Author: Javier Palarea-Albaladejo
Maintainer: Javier Palarea-Albaladejo <javier.palarea@bioss.ac.uk>

Diff between MALDIrppa versions 1.0.1-2 dated 2018-11-09 and 1.0.2 dated 2020-05-28

 DESCRIPTION                      |   12 -
 MD5                              |   54 ++--
 NAMESPACE                        |    1 
 NEWS                             |    7 
 R/wavSmoothing.R                 |   11 
 build/vignette.rds               |binary
 inst/doc/MALDIrppa_vignette.R    |    2 
 inst/doc/MALDIrppa_vignette.Rmd  |    2 
 inst/doc/MALDIrppa_vignette.html |  434 ++++++++++++++++++++++++++++++---------
 man/MALDIrppa-package.Rd         |    6 
 man/addMetadata.Rd               |    3 
 man/alignPeaks.Rd                |    4 
 man/countPeaks.Rd                |    4 
 man/deletePeaks.Rd               |    4 
 man/detectOutliers.Rd            |    4 
 man/importSpectra.Rd             |    4 
 man/plot.scSpectra.Rd            |    4 
 man/rawToPeaks.Rd                |    6 
 man/rawToSpectra.Rd              |    4 
 man/screenSpectra.Rd             |    4 
 man/snrPeaks.Rd                  |    4 
 man/summary.scSpectra.Rd         |    4 
 man/summaryPeaks.Rd              |    4 
 man/summarySpectra.Rd            |    4 
 man/wavSmoothing.Rd              |   18 -
 man/writeIntensity.Rd            |    8 
 man/writeMetadata.Rd             |    8 
 vignettes/MALDIrppa_vignette.Rmd |    2 
 28 files changed, 406 insertions(+), 216 deletions(-)

More information about MALDIrppa at CRAN
Permanent link

Package smacpod updated to version 2.1 with previous version 2.0.4 dated 2018-05-14

Title: Statistical Methods for the Analysis of Case-Control Point Data
Description: Statistical methods for analyzing case-control point data. Methods include the ratio of kernel densities, the difference in K Functions, the spatial scan statistic, and q nearest neighbors of cases.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>

Diff between smacpod versions 2.0.4 dated 2018-05-14 and 2.1 dated 2020-05-28

 smacpod-2.0.4/smacpod/R/Kdest.R           |only
 smacpod-2.0.4/smacpod/R/tolenv.R          |only
 smacpod-2.1/smacpod/DESCRIPTION           |    9 ++--
 smacpod-2.1/smacpod/MD5                   |   62 ++++++++++++++--------------
 smacpod-2.1/smacpod/NAMESPACE             |   44 +++++++++-----------
 smacpod-2.1/smacpod/NEWS                  |    4 +
 smacpod-2.1/smacpod/R/circles.intersect.R |    2 
 smacpod-2.1/smacpod/R/kd.R                |   11 ++---
 smacpod-2.1/smacpod/R/kdest-print.R       |only
 smacpod-2.1/smacpod/R/kdest.R             |only
 smacpod-2.1/smacpod/R/kdplus.test.R       |   37 ++++++++++-------
 smacpod-2.1/smacpod/R/logrr.R             |   17 +++----
 smacpod-2.1/smacpod/R/logrr.test.R        |   35 +++++++---------
 smacpod-2.1/smacpod/R/nrenv.R             |only
 smacpod-2.1/smacpod/R/plot.kdenv.R        |   39 ++++++++----------
 smacpod-2.1/smacpod/R/plot.logrrenv.R     |   15 ++----
 smacpod-2.1/smacpod/R/plot.spscan.R       |    2 
 smacpod-2.1/smacpod/R/qnn.test.R          |   65 ++++++++++++++++--------------
 smacpod-2.1/smacpod/R/spdensity.R         |    1 
 smacpod-2.1/smacpod/R/spscan.test.R       |    1 
 smacpod-2.1/smacpod/man/circles.plot.Rd   |   15 ++++++
 smacpod-2.1/smacpod/man/grave.Rd          |    6 +-
 smacpod-2.1/smacpod/man/kd.Rd             |   17 ++++++-
 smacpod-2.1/smacpod/man/kdest.Rd          |   28 ++++++++----
 smacpod-2.1/smacpod/man/kdplus.test.Rd    |   19 ++++++--
 smacpod-2.1/smacpod/man/logrr.Rd          |   43 +++++++++++++------
 smacpod-2.1/smacpod/man/logrr.test.Rd     |   23 +++++-----
 smacpod-2.1/smacpod/man/nn.Rd             |    4 -
 smacpod-2.1/smacpod/man/plot.kdenv.Rd     |   38 ++++++++++-------
 smacpod-2.1/smacpod/man/plot.logrrenv.Rd  |    2 
 smacpod-2.1/smacpod/man/plot.spscan.Rd    |    3 -
 smacpod-2.1/smacpod/man/print.kdenv.Rd    |only
 smacpod-2.1/smacpod/man/qnn.test.Rd       |   30 ++++++-------
 smacpod-2.1/smacpod/man/spdensity.Rd      |   24 ++++++++---
 smacpod-2.1/smacpod/man/spscan.test.Rd    |   18 ++++++--
 35 files changed, 351 insertions(+), 263 deletions(-)

More information about smacpod at CRAN
Permanent link

Package rgeoprofile updated to version 0.2.0 with previous version 0.1.1 dated 2020-01-08

Title: Geographic Profiling Methods for Serial Crime Analysis
Description: An implementation of functions for the analysis of serial crime incidents. The package implements algorithms for the geographical profiling of serial incidents in attempt to prioritize the area in which the anchor point or home base of the perpetrator is located. The geographic profiling methods in the package are implemented based upon the 'Dragnet' software by Canter, Coffey, Huntley, and Missen (2000) <doi:10.1023/A:1007551316253>, the 'CrimeStat' software by Levine (2013) <https://nij.ojp.gov/topics/articles/crimestat-spatial-statistics-program-analysis-crime-incident-locations>, and the criminal geographic targeting model outlined in Rossmo (2000, ISBN:978-0849381294) and Rossmo (1995) <http://summit.sfu.ca/item/6820>.
Author: Jamie Spaulding and Keith Morris
Maintainer: Jamie Spaulding <jspauldi@mix.wvu.edu>

Diff between rgeoprofile versions 0.1.1 dated 2020-01-08 and 0.2.0 dated 2020-05-28

 DESCRIPTION                 |   12 +++++++-----
 MD5                         |   44 +++++++++++++++++++++++++++++---------------
 NAMESPACE                   |    4 ++++
 NEWS.md                     |only
 R/cgt_profile.R             |    2 +-
 R/circle_center.R           |only
 R/linear_profile.R          |    2 +-
 R/lognorm_profile.R         |    2 +-
 R/neg_exp_profile.R         |    2 +-
 R/norm_profile.R            |    2 +-
 R/trun_neg_exp_profile.R    |    2 +-
 build                       |only
 inst/doc                    |only
 man/cgt_profile.Rd          |    2 +-
 man/circle_center.Rd        |only
 man/desalvo.Rd              |    6 ++++--
 man/linear_profile.Rd       |    2 +-
 man/lognorm_profile.Rd      |    5 ++---
 man/neg_exp_profile.Rd      |   13 ++++++++++---
 man/norm_profile.Rd         |    5 ++---
 man/trun_neg_exp_profile.Rd |    5 ++---
 vignettes                   |only
 22 files changed, 68 insertions(+), 42 deletions(-)

More information about rgeoprofile at CRAN
Permanent link

Package mfbvar updated to version 0.5.4 with previous version 0.5.3 dated 2020-03-19

Title: Mixed-Frequency Bayesian VAR Models
Description: Estimation of mixed-frequency Bayesian vector autoregressive (VAR) models. The package implements a state space-based VAR model that handles mixed frequencies of the data. The model is estimated using Markov Chain Monte Carlo to numerically approximate the posterior distribution. Prior distributions that can be used include normal-inverse Wishart and normal-diffuse priors as well as steady-state priors. Stochastic volatility can be handled by common or factor stochastic volatility models.
Author: Sebastian Ankargren [cre, aut] (<https://orcid.org/0000-0003-4415-8734>), Yukai Yang [aut] (<https://orcid.org/0000-0002-2623-8549>), Gregor Kastner [ctb] (<https://orcid.org/0000-0002-8237-8271>)
Maintainer: Sebastian Ankargren <sebastian.ankargren@statistics.uu.se>

Diff between mfbvar versions 0.5.3 dated 2020-03-19 and 0.5.4 dated 2020-05-28

 mfbvar-0.5.3/mfbvar/R/mcmc_diffuse.R                         |only
 mfbvar-0.5.3/mfbvar/man/build_DD.Rd                          |only
 mfbvar-0.5.3/mfbvar/man/build_Lambda.Rd                      |only
 mfbvar-0.5.3/mfbvar/man/build_M_Lambda.Rd                    |only
 mfbvar-0.5.3/mfbvar/man/build_U.Rd                           |only
 mfbvar-0.5.3/mfbvar/man/build_Y_tilde.Rd                     |only
 mfbvar-0.5.3/mfbvar/man/build_Z.Rd                           |only
 mfbvar-0.5.3/mfbvar/man/build_companion.Rd                   |only
 mfbvar-0.5.3/mfbvar/man/create_prior_Pi_Omega.Rd             |only
 mfbvar-0.5.3/mfbvar/man/dmatt.Rd                             |only
 mfbvar-0.5.3/mfbvar/man/dmultn.Rd                            |only
 mfbvar-0.5.3/mfbvar/man/dnorm_trunc.Rd                       |only
 mfbvar-0.5.3/mfbvar/man/dnorminvwish.Rd                      |only
 mfbvar-0.5.3/mfbvar/man/estimate_mdd_ss_1.Rd                 |only
 mfbvar-0.5.3/mfbvar/man/eval_Pi_Sigma_RaoBlack.Rd            |only
 mfbvar-0.5.3/mfbvar/man/eval_psi_MargPost.Rd                 |only
 mfbvar-0.5.3/mfbvar/man/figures                              |only
 mfbvar-0.5.3/mfbvar/man/fill_na.Rd                           |only
 mfbvar-0.5.3/mfbvar/man/kf_loglike.Rd                        |only
 mfbvar-0.5.3/mfbvar/man/kf_ragged.Rd                         |only
 mfbvar-0.5.3/mfbvar/man/max_eig_cpp.Rd                       |only
 mfbvar-0.5.3/mfbvar/man/mcmc_sampler.Rd                      |only
 mfbvar-0.5.3/mfbvar/man/mdd.minn.Rd                          |only
 mfbvar-0.5.3/mfbvar/man/ols_initialization.Rd                |only
 mfbvar-0.5.3/mfbvar/man/ols_pi.Rd                            |only
 mfbvar-0.5.3/mfbvar/man/posterior_Pi_Sigma.Rd                |only
 mfbvar-0.5.3/mfbvar/man/posterior_psi.Rd                     |only
 mfbvar-0.5.3/mfbvar/man/posterior_psi_mean.Rd                |only
 mfbvar-0.5.3/mfbvar/man/prior_Pi_Sigma.Rd                    |only
 mfbvar-0.5.3/mfbvar/man/smoother.Rd                          |only
 mfbvar-0.5.4/mfbvar/DESCRIPTION                              |   15 
 mfbvar-0.5.4/mfbvar/MD5                                      |  141 +++----
 mfbvar-0.5.4/mfbvar/NAMESPACE                                |    2 
 mfbvar-0.5.4/mfbvar/NEWS.md                                  |    3 
 mfbvar-0.5.4/mfbvar/R/RcppExports.R                          |    9 
 mfbvar-0.5.4/mfbvar/R/builders.R                             |    7 
 mfbvar-0.5.4/mfbvar/R/data.R                                 |   48 +-
 mfbvar-0.5.4/mfbvar/R/densities.R                            |  156 ++++----
 mfbvar-0.5.4/mfbvar/R/eval.R                                 |  198 +++++------
 mfbvar-0.5.4/mfbvar/R/fill_na.R                              |   67 +--
 mfbvar-0.5.4/mfbvar/R/interface.R                            |  195 ++++------
 mfbvar-0.5.4/mfbvar/R/interval_to_moments.R                  |   41 +-
 mfbvar-0.5.4/mfbvar/R/list_to_matrix.R                       |only
 mfbvar-0.5.4/mfbvar/R/mcmc_sampler.R                         |    2 
 mfbvar-0.5.4/mfbvar/R/mcmc_sampler_csv.R                     |   12 
 mfbvar-0.5.4/mfbvar/R/mcmc_sampler_diffuse.R                 |only
 mfbvar-0.5.4/mfbvar/R/mcmc_sampler_fsv.R                     |   16 
 mfbvar-0.5.4/mfbvar/R/mcmc_sampler_iw.R                      |   12 
 mfbvar-0.5.4/mfbvar/R/mdd.R                                  |    3 
 mfbvar-0.5.4/mfbvar/R/ols.R                                  |  122 +++---
 mfbvar-0.5.4/mfbvar/R/posteriors.R                           |    4 
 mfbvar-0.5.4/mfbvar/R/prior_pi_sigma.R                       |    2 
 mfbvar-0.5.4/mfbvar/R/utils.R                                |    7 
 mfbvar-0.5.4/mfbvar/build/vignette.rds                       |binary
 mfbvar-0.5.4/mfbvar/data/mf_usa.RData                        |only
 mfbvar-0.5.4/mfbvar/inst/doc/mfbvar_jss.R                    |   35 +
 mfbvar-0.5.4/mfbvar/inst/doc/mfbvar_jss.Rnw                  |   94 +++--
 mfbvar-0.5.4/mfbvar/inst/doc/mfbvar_jss.pdf                  |binary
 mfbvar-0.5.4/mfbvar/inst/include/mvn.h                       |   35 +
 mfbvar-0.5.4/mfbvar/inst/include/simsm_adaptive_cv.h         |    8 
 mfbvar-0.5.4/mfbvar/inst/include/simsm_adaptive_sv.h         |    8 
 mfbvar-0.5.4/mfbvar/inst/include/simsm_adaptive_univariate.h |    9 
 mfbvar-0.5.4/mfbvar/inst/include/update_csv.h                |    1 
 mfbvar-0.5.4/mfbvar/man/estimate_mfbvar.Rd                   |    9 
 mfbvar-0.5.4/mfbvar/man/interval_to_moments.Rd               |    1 
 mfbvar-0.5.4/mfbvar/man/mf_sweden.Rd                         |    8 
 mfbvar-0.5.4/mfbvar/man/mf_usa.Rd                            |only
 mfbvar-0.5.4/mfbvar/man/mfbvar.Rd                            |    1 
 mfbvar-0.5.4/mfbvar/man/plot-mfbvar.Rd                       |   58 +--
 mfbvar-0.5.4/mfbvar/man/plot.mfbvar_prior.Rd                 |    3 
 mfbvar-0.5.4/mfbvar/man/predict.mfbvar.Rd                    |    8 
 mfbvar-0.5.4/mfbvar/man/print.mfbvar.Rd                      |    3 
 mfbvar-0.5.4/mfbvar/man/print.mfbvar_prior.Rd                |    3 
 mfbvar-0.5.4/mfbvar/man/set_prior.Rd                         |   53 +-
 mfbvar-0.5.4/mfbvar/man/summary.mfbvar.Rd                    |    3 
 mfbvar-0.5.4/mfbvar/man/summary.mfbvar_prior.Rd              |    3 
 mfbvar-0.5.4/mfbvar/src/builders.cpp                         |    1 
 mfbvar-0.5.4/mfbvar/src/kf_cpp.cpp                           |    3 
 mfbvar-0.5.4/mfbvar/src/max_eig_cpp.cpp                      |    1 
 mfbvar-0.5.4/mfbvar/src/rnd_numbers.cpp                      |    3 
 mfbvar-0.5.4/mfbvar/src/smoothing.cpp                        |    1 
 mfbvar-0.5.4/mfbvar/src/update_csv.cpp                       |   12 
 mfbvar-0.5.4/mfbvar/src/update_fsv.cpp                       |    4 
 mfbvar-0.5.4/mfbvar/src/update_ng.cpp                        |   12 
 mfbvar-0.5.4/mfbvar/tests/testthat/test_mfbvar.R             |   98 +++++
 mfbvar-0.5.4/mfbvar/tests/testthat/test_plot.R               |    4 
 mfbvar-0.5.4/mfbvar/tests/testthat/test_predict.R            |   66 +++
 mfbvar-0.5.4/mfbvar/vignettes/mfbvar_jss.Rnw                 |   94 +++--
 88 files changed, 1000 insertions(+), 704 deletions(-)

More information about mfbvar at CRAN
Permanent link

Package slider updated to version 0.1.4 with previous version 0.1.3 dated 2020-05-14

Title: Sliding Window Functions
Description: Provides type-stable rolling window functions over any R data type. Cumulative and expanding windows are also supported. For more advanced usage, an index can be used as a secondary vector that defines how sliding windows are to be created.
Author: Davis Vaughan [aut, cre], RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>

Diff between slider versions 0.1.3 dated 2020-05-14 and 0.1.4 dated 2020-05-28

 DESCRIPTION                             |    6 
 MD5                                     |   71 ++++----
 NEWS.md                                 |    7 
 R/hop-common.R                          |   10 -
 R/zzz.R                                 |    2 
 README.md                               |    3 
 build/vignette.rds                      |binary
 inst/doc/rowwise.html                   |   10 -
 inst/doc/slider.html                    |   15 -
 src/assign.h                            |only
 src/hop.c                               |  169 +++++++++-----------
 src/index.c                             |  261 +++++++++++++++-----------------
 src/init.c                              |   18 +-
 src/slide.c                             |  159 +++++++++----------
 src/slider-vctrs-private.c              |   10 -
 src/slider-vctrs-private.h              |    4 
 src/slider-vctrs-public.c               |    2 
 src/utils.c                             |   47 ++++-
 src/utils.h                             |   16 +
 tests/testthat/test-hop-index-vec.R     |    4 
 tests/testthat/test-hop-index2-vec.R    |    4 
 tests/testthat/test-hop-vec.R           |    4 
 tests/testthat/test-hop.R               |    2 
 tests/testthat/test-hop2-vec.R          |    4 
 tests/testthat/test-hop2.R              |    2 
 tests/testthat/test-phop-index-vec.R    |    4 
 tests/testthat/test-phop-vec.R          |    4 
 tests/testthat/test-phop.R              |    4 
 tests/testthat/test-pslide-index-vec.R  |   15 +
 tests/testthat/test-pslide-period-vec.R |    4 
 tests/testthat/test-pslide-vec.R        |   26 ++-
 tests/testthat/test-slide-index-vec.R   |   15 +
 tests/testthat/test-slide-index2-vec.R  |   15 +
 tests/testthat/test-slide-period-vec.R  |    4 
 tests/testthat/test-slide-period2-vec.R |    4 
 tests/testthat/test-slide-vec.R         |   26 ++-
 tests/testthat/test-slide2-vec.R        |   26 ++-
 37 files changed, 544 insertions(+), 433 deletions(-)

More information about slider at CRAN
Permanent link

Package ramsvm updated to version 2.2 with previous version 2.1 dated 2020-01-10

Title: Reinforced Angle-Based Multicategory Support Vector Machines
Description: Provides a solution path for Reinforced Angle-based Multicategory Support Vector Machines, with linear learning, polynomial learning, and Gaussian kernel learning. C. Zhang, Y. Liu, J. Wang and H. Zhu. (2016) <doi:10.1080/10618600.2015.1043010>.
Author: Chong Zhang, Yufeng Liu, and Shannon Holloway
Maintainer: Shannon Holloway <sthollow@ncsu.edu>

Diff between ramsvm versions 2.1 dated 2020-01-10 and 2.2 dated 2020-05-28

 DESCRIPTION       |    8 ++++----
 MD5               |    6 +++---
 NEWS              |    7 +++++++
 src/ramsvm_init.c |    2 +-
 4 files changed, 15 insertions(+), 8 deletions(-)

More information about ramsvm at CRAN
Permanent link

Package otpr updated to version 0.4.1 with previous version 0.4.0 dated 2020-05-01

Title: An R Wrapper for the 'OpenTripPlanner' REST API
Description: A wrapper for the 'OpenTripPlanner' <http://www.opentripplanner.org/> REST API. Queries are submitted to the relevant 'OpenTripPlanner' API resource, the response is parsed and useful R objects are returned.
Author: Marcus Young [aut, cre] (<https://orcid.org/0000-0003-4627-1116>)
Maintainer: Marcus Young <M.A.Young@soton.ac.uk>

Diff between otpr versions 0.4.0 dated 2020-05-01 and 0.4.1 dated 2020-05-28

 DESCRIPTION                       |   11 +-
 MD5                               |   10 +-
 R/otp_get_times.R                 |  140 ++++++++++++++++----------------------
 README.md                         |   35 +++++++--
 man/figures/unnamed-chunk-8-1.png |binary
 man/otp_get_times.Rd              |    4 -
 6 files changed, 99 insertions(+), 101 deletions(-)

More information about otpr at CRAN
Permanent link

Package mvord updated to version 1.0.1 with previous version 1.0.0 dated 2020-04-17

Title: Multivariate Ordinal Regression Models
Description: A flexible framework for fitting multivariate ordinal regression models with composite likelihood methods. Methodological details are given in Hirk, Hornik, Vana (2020) <doi:10.18637/jss.v093.i04>.
Author: Rainer Hirk [aut, cre], Kurt Hornik [aut], Laura Vana [aut], Alan Genz [ctb] (Fortran Code)
Maintainer: Rainer Hirk <rhirk@wu.ac.at>

Diff between mvord versions 1.0.0 dated 2020-04-17 and 1.0.1 dated 2020-05-28

 DESCRIPTION                   |   10 +++----
 MD5                           |   17 ++++++------
 NEWS                          |    3 ++
 inst/doc/vignette_mvord.pdf   |binary
 inst/doc/vignette_mvord2.R    |   18 ++++++++-----
 inst/doc/vignette_mvord2.Rmd  |    7 ++++-
 inst/doc/vignette_mvord2.html |    7 +++--
 tests/check_toy_example.R     |   55 ++++++++++++++++++------------------------
 vignettes/df.rda              |only
 vignettes/vignette_mvord2.Rmd |    7 ++++-
 10 files changed, 68 insertions(+), 56 deletions(-)

More information about mvord at CRAN
Permanent link

Package momentfit updated to version 0.1-1 with previous version 0.1-0 dated 2020-01-31

Title: Methods of Moments
Description: Several classes for moment-based models are defined. The classes are defined for moment conditions derived from a single equation or a system of equations. The conditions can also be expressed as functions or formulas. Several methods are also offered to facilitate the development of different estimation techniques. The methods that are currently provided are the Generalized method of moments (Hansen 1982; <doi:10.2307/1912775>), for single equations and systems of equation, and the Generalized Empirical Likelihood (Smith 1997; <doi:10.1111/j.0013-0133.1997.174.x>, Kitamura 1997; <doi:10.1214/aos/1069362388>, Newey and Smith 2004; <doi:10.1111/j.1468-0262.2004.00482.x>, and Anatolyev 2005 <doi:10.1111/j.1468-0262.2005.00601.x>).
Author: Pierre Chausse <pchausse@uwaterloo.ca>
Maintainer: Pierre Chausse <pchausse@uwaterloo.ca>

Diff between momentfit versions 0.1-0 dated 2020-01-31 and 0.1-1 dated 2020-05-28

 DESCRIPTION                  |   12 -
 MD5                          |   77 +++++-----
 NAMESPACE                    |    2 
 R/allClasses.R               |   45 +++++
 R/momentModel-methods.R      |   98 +++++--------
 R/rModel-methods.R           |   77 +++-------
 R/rsysMomentModel-methods.R  |  324 +++++++++++++++++++++++++++++++++++++++++--
 R/sgmmfit-methods.R          |   39 ++---
 R/sysMomentModel-methods.R   |  164 ++++++++++++++++-----
 build/vignette.rds           |binary
 data/CigarettesSW.rda        |binary
 data/ConsumptionG.rda        |binary
 data/Griliches.rda           |binary
 data/HealthRWM.rda           |binary
 data/Klein.rda               |binary
 data/LabourCR.rda            |binary
 data/ManufactCost.rda        |binary
 data/Mroz.rda                |binary
 data/simData.rda             |binary
 inst/doc/gelS4.pdf           |binary
 inst/doc/gmmS4.R             |   92 +++++++++++-
 inst/doc/gmmS4.Rnw           |  208 +++++++++++++++++++++++++--
 inst/doc/gmmS4.pdf           |binary
 man/Dresiduals-methods.Rd    |    5 
 man/coef-methods.Rd          |    5 
 man/evalDMoment-methods.Rd   |    3 
 man/evalGmm-methods.Rd       |    6 
 man/evalMoment-methods.Rd    |    4 
 man/getRestrict-methods.Rd   |    8 +
 man/model.matrix-methods.Rd  |    7 
 man/modelDims-methods.Rd     |    4 
 man/print-methods.Rd         |    4 
 man/printRestrict-methods.Rd |    4 
 man/residuals-methods.Rd     |    6 
 man/restModel-methods.Rd     |   10 +
 man/setCoef-methods.Rd       |only
 man/subsetting.Rd            |    6 
 src/Makevars                 |    2 
 src/momentfit.h              |    4 
 vignettes/gmmS4.Rnw          |  208 +++++++++++++++++++++++++--
 40 files changed, 1159 insertions(+), 265 deletions(-)

More information about momentfit at CRAN
Permanent link

Package glmmML updated to version 1.1.1 with previous version 1.1.0 dated 2019-04-30

Title: Generalized Linear Models with Clustering
Description: Binomial and Poisson regression for clustered data, fixed and random effects with bootstrapping.
Author: Göran Broström [aut, cre], Jianming Jin [ctb], Henrik Holmberg [ctb]
Maintainer: Göran Broström <goran.brostrom@umu.se>

Diff between glmmML versions 1.1.0 dated 2019-04-30 and 1.1.1 dated 2020-05-28

 glmmML-1.1.0/glmmML/inst/doc/vignettes  |only
 glmmML-1.1.1/glmmML/ChangeLog           |   13 ++++
 glmmML-1.1.1/glmmML/DESCRIPTION         |   18 ++++--
 glmmML-1.1.1/glmmML/MD5                 |   35 ++++++-------
 glmmML-1.1.1/glmmML/R/glmmMLBoot.R      |    3 -
 glmmML-1.1.1/glmmML/R/glmmboot.R        |    1 
 glmmML-1.1.1/glmmML/build               |only
 glmmML-1.1.1/glmmML/inst/doc/glmmML.Rnw |only
 glmmML-1.1.1/glmmML/inst/doc/glmmML.pdf |binary
 glmmML-1.1.1/glmmML/src/Makevars        |    4 -
 glmmML-1.1.1/glmmML/src/bfun.c          |   22 ++++----
 glmmML-1.1.1/glmmML/src/fun.c           |   86 +++++++++++++++++++-------------
 glmmML-1.1.1/glmmML/src/fun.h           |   16 -----
 glmmML-1.1.1/glmmML/src/ghq.f           |    5 +
 glmmML-1.1.1/glmmML/src/ghq.h           |    2 
 glmmML-1.1.1/glmmML/src/glmmb0.c        |   15 ++---
 glmmML-1.1.1/glmmML/src/glmmboot.c      |    7 +-
 glmmML-1.1.1/glmmML/src/glmmml.c        |   20 ++++---
 glmmML-1.1.1/glmmML/vignettes           |only
 19 files changed, 140 insertions(+), 107 deletions(-)

More information about glmmML at CRAN
Permanent link

Package bayescopulareg updated to version 0.1.2 with previous version 0.1.0 dated 2020-05-01

Title: Bayesian Copula Regression
Description: Tools for Bayesian copula generalized linear models (GLMs). The sampling scheme is based on Pitt, Chan, and Kohn (2006) <doi:10.1093/biomet/93.3.537>. Regression parameters (including coefficients and dispersion parameters) are estimated via the adaptive random walk Metropolis approach developed by Haario, Saksman, and Tamminen (1999) <doi:10.1007/s001800050022>. The prior for the correlation matrix is based on Hoff (2007) <doi:10.1214/07-AOAS107>.
Author: Ethan Alt [aut, cre], Yash Bhosale [aut]
Maintainer: Ethan Alt <ethanalt@live.unc.edu>

Diff between bayescopulareg versions 0.1.0 dated 2020-05-01 and 0.1.2 dated 2020-05-28

 DESCRIPTION                   |   15 ++++++++++-----
 MD5                           |   11 ++++++-----
 NEWS.md                       |only
 man/bayescopulareg-package.Rd |    9 +++++++++
 src/condnormal.cpp            |    2 +-
 src/copula_predict.cpp        |    2 +-
 src/sample_copula.cpp         |   10 ++++++----
 7 files changed, 33 insertions(+), 16 deletions(-)

More information about bayescopulareg at CRAN
Permanent link

Package almanac updated to version 0.1.1 with previous version 0.1.0 dated 2020-05-27

Title: Tools for Working with Recurrence Rules
Description: Provides tools for defining recurrence rules and recurrence bundles. Recurrence rules are a programmatic way to define a recurring event, like the first Monday of December. Multiple recurrence rules can be combined into larger recurrence bundles. Together, these provide a system for adjusting and generating sequences of dates while simultaneously skipping over dates in a recurrence bundle's event set.
Author: Davis Vaughan [aut, cre], RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>

Diff between almanac versions 0.1.0 dated 2020-05-27 and 0.1.1 dated 2020-05-28

 DESCRIPTION           |    6 +++---
 MD5                   |   13 +++++++------
 NAMESPACE             |    2 ++
 NEWS.md               |only
 R/almanac-package.R   |    6 ++++++
 build/vignette.rds    |binary
 inst/doc/almanac.html |    4 ++--
 src/adjustments.cc    |   30 +++++++++++++++++++-----------
 8 files changed, 39 insertions(+), 22 deletions(-)

More information about almanac at CRAN
Permanent link

Package RRPP updated to version 0.6.0 with previous version 0.5.2 dated 2020-01-26

Title: Linear Model Evaluation with Randomized Residuals in a Permutation Procedure
Description: Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. This packaged is described by Collyer & Adams (2018) <doi:10.1111/2041-210X.13029>. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre], Dean Adams [aut]
Maintainer: Michael Collyer <mlcollyer@gmail.com>

Diff between RRPP versions 0.5.2 dated 2020-01-26 and 0.6.0 dated 2020-05-28

 DESCRIPTION                   |   10 
 MD5                           |   48 ++-
 NAMESPACE                     |   10 
 NEWS.md                       |   16 +
 R/RRPP.support.code.r         |  593 ++++++++++++++++++++++--------------------
 R/RRPP.utils.r                |  159 +++++++++++
 R/add.tree.r                  |only
 R/anova.lm.rrpp.r             |    8 
 R/lm.rrpp.r                   |   47 +--
 R/ordinate.r                  |only
 R/pairwise.r                  |    6 
 R/shared.support.code.r       |  175 ++++++++++++
 R/trajectory.analysis.r       |    4 
 build/vignette.rds            |binary
 data/PlethMorph.rda           |binary
 inst/doc/ANOVA.vs.MANOVA.html |    4 
 inst/doc/Using.RRPP.R         |    2 
 inst/doc/Using.RRPP.Rmd       |    4 
 inst/doc/Using.RRPP.html      |   16 -
 man/add.tree.Rd               |only
 man/anova.lm.rrpp.Rd          |    8 
 man/lm.rrpp.Rd                |    8 
 man/ordinate.Rd               |only
 man/plot.ordinate.Rd          |only
 man/print.classify.Rd         |only
 man/print.ordinate.Rd         |only
 man/print.summary.ordinate.Rd |only
 man/summary.classify.Rd       |only
 man/summary.ordinate.Rd       |only
 vignettes/Using.RRPP.Rmd      |    4 
 30 files changed, 764 insertions(+), 358 deletions(-)

More information about RRPP at CRAN
Permanent link

Package implicitMeasures updated to version 0.1.3 with previous version 0.1.2 dated 2020-04-05

Title: Computes the Scores for Different Implicit Measures
Description: A tool for computing the scores for the Implicit Association Test (IAT; Greenwald, McGhee & Schwartz (1998) <doi:10.1037/0022-3514.74.6.1464>) and the Single Category-IAT (SC-IAT: Karpinski & Steinman (2006) <doi:10.1037/0022-3514.91.1.16>). Functions for preparing the data (both for the IAT and the SC-IAT), plotting the results, and obtaining a table with the scores of implicit measures descriptive statistics are provided.
Author: Ottavia M. Epifania [aut, cre], Pasquale Anselmi [ctb], Egidio Robusto [ctb]
Maintainer: Ottavia M. Epifania <otta.epifania@gmail.com>

Diff between implicitMeasures versions 0.1.2 dated 2020-04-05 and 0.1.3 dated 2020-05-28

 DESCRIPTION                              |   10 -
 MD5                                      |   45 +++---
 NEWS.md                                  |    6 
 R/computeD.R                             |    2 
 README.md                                |  159 ++++++++++++++++++-----
 inst/doc/IAT-example.R                   |   52 ++++---
 inst/doc/IAT-example.Rmd                 |  110 +++++++++------
 inst/doc/IAT-example.html                |  214 +++++++++++++++----------------
 inst/doc/SC-IAT-example.R                |   74 +++++-----
 inst/doc/SC-IAT-example.Rmd              |  134 +++++++++++--------
 inst/doc/SC-IAT-example.html             |  211 +++++++++++++-----------------
 inst/doc/implicitMeasures.R              |   15 +-
 inst/doc/implicitMeasures.Rmd            |   52 ++++---
 inst/doc/implicitMeasures.html           |   76 +++++------
 inst/joss                                |only
 inst/paper.bib                           |only
 man/figures/README-unnamed-chunk-2-1.png |binary
 man/figures/README-unnamed-chunk-3-1.png |binary
 tests/spelling.R                         |only
 vignettes/IAT-example.Rmd                |  110 +++++++++------
 vignettes/SC-IAT-example.Rmd             |  134 +++++++++++--------
 vignettes/implicitMeasures.Rmd           |   52 ++++---
 vignettes/vignette.bib                   |   20 ++
 23 files changed, 843 insertions(+), 633 deletions(-)

More information about implicitMeasures at CRAN
Permanent link

Package StanHeaders updated to version 2.21.0-3 with previous version 2.19.2 dated 2020-02-11

Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is only useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut], Joshua Pritikin [ctb], Andrew Gelman [aut], Bob Carpenter [aut], Matt Hoffman [aut], Daniel Lee [aut], Michael Betancourt [aut], Marcus Brubaker [aut], Jiqiang Guo [aut], Peter Li [aut], Allen Riddell [aut], Marco Inacio [aut], Mitzi Morris [aut], Jeffrey Arnold [aut], Rob Goedman [aut], Brian Lau [aut], Rob Trangucci [aut], Jonah Gabry [aut], Alp Kucukelbir [aut], Robert Grant [aut], Dustin Tran [aut], Michael Malecki [aut], Yuanjun Gao [aut], Trustees of Columbia University [cph], Lawrence Livermore National Security [cph] (CVODES), The Regents of the University of California [cph] (CVODES), Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

Diff between StanHeaders versions 2.19.2 dated 2020-02-11 and 2.21.0-3 dated 2020-05-28

 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/json                                                        |only
 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar.hpp                            |only
 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar_def.hpp                        |only
 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar_inst.cpp                       |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/meta/ad_promotable.hpp                               |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/add.hpp                                                |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/constants.hpp                                          |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/zeros.hpp                                      |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/lower_tri_inverse.hpp                                  |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/subtract.hpp                                           |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/transpose.hpp                                          |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/err/check_opencl.hpp                                 |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/meta/contains_std_vector.hpp                         |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/meta/is_constant_struct.hpp                          |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/is_constant_struct.hpp                          |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/is_vector.hpp                                   |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/is_vector_like.hpp                              |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_nonconstant_struct.hpp                |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant_struct.hpp                         |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_nonconstant_struct.hpp                      |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/seq_view.hpp                                   |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_solver.hpp                            |only
 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/meta/ad_promotable.hpp                               |only
 StanHeaders-2.21.0-3/StanHeaders/DESCRIPTION                                                                        |   15 
 StanHeaders-2.21.0-3/StanHeaders/MD5                                                                                | 3449 +++++-----
 StanHeaders-2.21.0-3/StanHeaders/NAMESPACE                                                                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/R                                                                                  |only
 StanHeaders-2.21.0-3/StanHeaders/build/vignette.rds                                                                 |binary
 StanHeaders-2.21.0-3/StanHeaders/inst/CITATION                                                                      |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/doc/stanmath.R                                                                |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/doc/stanmath.Rmd                                                              |   62 
 StanHeaders-2.21.0-3/StanHeaders/inst/doc/stanmath.html                                                             |  444 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/kinsol                                                                |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/analyze/mcmc/autocovariance.hpp                              |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/analyze/mcmc/compute_effective_sample_size.hpp               |  292 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/analyze/mcmc/compute_potential_scale_reduction.hpp           |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/analyze/mcmc/split_chains.hpp                                |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/callbacks/interrupt.hpp                                      |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/callbacks/logger.hpp                                         |  182 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/callbacks/stream_logger.hpp                                  |  134 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/callbacks/stream_writer.hpp                                  |  191 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/callbacks/tee_writer.hpp                                     |  106 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/callbacks/writer.hpp                                         |   86 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/command/stanc_helper.hpp                                     |  221 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/array_var_context.hpp                                     |  626 +
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/chained_var_context.hpp                                   |  107 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/cmd_line.hpp                                              |  519 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/dump.hpp                                                  | 1470 ++--
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/empty_var_context.hpp                                     |  184 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/ends_with.hpp                                             |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/is_whitespace.hpp                                         |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/program_reader.hpp                                        |   79 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/random_var_context.hpp                                    |  479 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/read_line.hpp                                             |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/reader.hpp                                                |  139 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/stan_csv_reader.hpp                                       |  667 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/starts_with.hpp                                           |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/trim_spaces.hpp                                           |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/util.hpp                                                  |   51 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/validate_zero_buf.hpp                                     |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/var_context.hpp                                           |  485 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/io/writer.hpp                                                |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_is_data_vis.hpp                       |  152 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_is_data_vis_def.hpp                   |   68 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_order_id_vis.hpp                      |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_order_id_vis_def.hpp                  |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_set_is_data_vis.hpp                   |  136 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_set_is_data_vis_def.hpp               |   70 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_total_dims_vis.hpp                    |  138 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_total_dims_vis_def.hpp                |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_vis.hpp                               |  360 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_bounds_vis.hpp                       |  264 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_is_specialized_vis.hpp               |  267 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_offset_multiplier_vis_def.hpp        |   60 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/ends_with.hpp                                   |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/ends_with_def.hpp                               |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/fun_name_exists.hpp                             |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/fun_name_exists_def.hpp                         |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/generate_expression.hpp                         |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/get_ccdf.hpp                                    |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/get_ccdf_def.hpp                                |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/get_cdf.hpp                                     |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/get_cdf_def.hpp                                 |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/get_prob_fun.hpp                                |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/get_prob_fun_def.hpp                            |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_ccdf_suffix.hpp                             |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_ccdf_suffix_def.hpp                         |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_cdf_suffix.hpp                              |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_cdf_suffix_def.hpp                          |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_lp_suffix.hpp                               |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_lp_suffix_def.hpp                           |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var.hpp                           |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_def.hpp                       |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_vis.hpp                       |  386 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_vis_def.hpp                   |  296 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_prob_fun_suffix.hpp                         |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_prob_fun_suffix_def.hpp                     |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_rng_suffix.hpp                              |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_rng_suffix_def.hpp                          |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var.hpp                                     |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_def.hpp                                 |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_vis.hpp                                 |  418 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_vis_def.hpp                             |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/infer_type_indexing.hpp                         |   25 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/infer_type_indexing_def.hpp                     |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_assignable.hpp                               |   43 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_assignable_def.hpp                           |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_multi_index.hpp                              |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_multi_index_def.hpp                          |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_multi_index_vis.hpp                          |  110 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_multi_index_vis_def.hpp                      |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil.hpp                                      |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_def.hpp                                  |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_vis.hpp                                  |   94 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_vis_def.hpp                              |   98 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_no_op_statement_vis.hpp                      |  304 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_no_op_statement_vis_def.hpp                  |  134 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nonempty.hpp                                 |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nonempty_def.hpp                             |   18 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_space.hpp                                    |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_space_def.hpp                                |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_user_defined.hpp                             |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_user_defined_def.hpp                         |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_user_defined_prob_function.hpp               |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/is_user_defined_prob_function_def.hpp           |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/num_index_op_dims.hpp                           |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/print_scope.hpp                                 |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/print_scope_def.hpp                             |   66 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/promote_primitive.hpp                           |   58 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/promote_primitive_def.hpp                       |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type.hpp                                |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_vis.hpp                            |  415 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_vis_def.hpp                        |  208 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/strip_ccdf_suffix.hpp                           |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/strip_cdf_suffix.hpp                            |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/strip_prob_fun_suffix.hpp                       |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/template.hpp                                    |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/var_occurs_vis.hpp                              |  428 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/var_occurs_vis_def.hpp                          |  186 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg1_vis.hpp                           |  362 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg1_vis_def.hpp                       |  219 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg2_vis.hpp                           |  367 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg2_vis_def.hpp                       |  219 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/write_bare_expr_type.hpp                        |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/write_bare_expr_type_def.hpp                    |   61 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/write_block_var_type.hpp                        |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/fun/write_idx_vis_def.hpp                           |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/nil.hpp                                             |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/algebra_solver.hpp                             |  104 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/algebra_solver_control.hpp                     |  149 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/algebra_solver_control_def.hpp                 |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/algebra_solver_def.hpp                         |   23 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/assgn.hpp                                      |  155 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/assgn_def.hpp                                  |   41 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/binary_op.hpp                                  |   88 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/binary_op_def.hpp                              |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/block_var_decl_def.hpp                         |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/break_continue_statement.hpp                   |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/break_continue_statement_def.hpp               |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_op.hpp                             |  113 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_op_def.hpp                         |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_statement.hpp                      |   66 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_statement_def.hpp                  |   18 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/distribution.hpp                               |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/expression.hpp                                 |  151 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/expression_def.hpp                             |  104 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/for_array_statement.hpp                        |   77 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/for_array_statement_def.hpp                    |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/for_matrix_statement.hpp                       |   77 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/for_matrix_statement_def.hpp                   |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/for_statement.hpp                              |   76 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/for_statement_def.hpp                          |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/fun.hpp                                        |   91 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/fun_def.hpp                                    |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_def.hpp                          |  109 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_def_def.hpp                      |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_defs.hpp                         |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_defs_def.hpp                     |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/idx.hpp                                        |  143 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/idx_def.hpp                                    |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/increment_log_prob_statement.hpp               |   54 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/increment_log_prob_statement_def.hpp           |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/index_op.hpp                                   |   85 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/index_op_sliced.hpp                            |   87 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/index_op_sliced_def.hpp                        |   18 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/int_literal.hpp                                |   52 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/int_literal_def.hpp                            |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_1d.hpp                               |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_1d_def.hpp                           |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode.hpp                              |  145 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode_control.hpp                      |  190 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode_control_def.hpp                  |   38 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode_def.hpp                          |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/lb_idx.hpp                                     |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/lb_idx_def.hpp                                 |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/local_var_decl_def.hpp                         |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/lub_idx.hpp                                    |   63 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/lub_idx_def.hpp                                |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/map_rect.hpp                                   |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/map_rect_def.hpp                               |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/matrix_expr.hpp                                |   78 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/matrix_expr_def.hpp                            |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/multi_idx.hpp                                  |   38 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/multi_idx_def.hpp                              |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/no_op_statement.hpp                            |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/omni_idx.hpp                                   |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/omni_idx_def.hpp                               |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/print_statement.hpp                            |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/print_statement_def.hpp                        |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/printable.hpp                                  |  104 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/printable_def.hpp                              |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/program.hpp                                    |  177 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/program_def.hpp                                |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/range.hpp                                      |   92 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/range_def.hpp                                  |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/reject_statement.hpp                           |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/reject_statement_def.hpp                       |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/return_statement.hpp                           |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/return_statement_def.hpp                       |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/row_vector_expr.hpp                            |   78 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/row_vector_expr_def.hpp                        |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/sample.hpp                                     |  111 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/sample_def.hpp                                 |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/statement.hpp                                  |  414 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/statement_def.hpp                              |   53 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/statements.hpp                                 |   70 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/statements_def.hpp                             |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/ub_idx.hpp                                     |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/ub_idx_def.hpp                                 |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/unary_op.hpp                                   |   74 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/unary_op_def.hpp                               |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/uni_idx.hpp                                    |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/uni_idx_def.hpp                                |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/var_decl.hpp                                   |  152 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/var_decl_def.hpp                               |   45 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/variable.hpp                                   |   72 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/variable_def.hpp                               |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/variable_dims.hpp                              |   65 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/variable_dims_def.hpp                          |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/while_statement.hpp                            |   65 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/node/while_statement_def.hpp                        |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/origin_block.hpp                                    |  160 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/scope.hpp                                           |  294 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/scope_def.hpp                                       |  173 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signature_t.hpp                       |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signatures.hpp                        |  813 +-
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signatures_def.hpp                    |  921 +-
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/bare_array_type_def.hpp                        |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/block_array_type_def.hpp                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/cholesky_factor_corr_block_type.hpp            |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/cholesky_factor_cov_block_type.hpp             |   87 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/double_block_type_def.hpp                      |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/double_type.hpp                                |   58 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/double_type_def.hpp                            |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/ill_formed_type.hpp                            |   47 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/ill_formed_type_def.hpp                        |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/int_block_type_def.hpp                         |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/int_type.hpp                                   |   59 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/int_type_def.hpp                               |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/local_array_type_def.hpp                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/local_var_type.hpp                             |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/local_var_type_def.hpp                         |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/matrix_block_type_def.hpp                      |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/matrix_local_type.hpp                          |   83 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/matrix_type.hpp                                |   58 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/matrix_type_def.hpp                            |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/row_vector_block_type_def.hpp                  |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/row_vector_local_type_def.hpp                  |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/row_vector_type.hpp                            |   58 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/row_vector_type_def.hpp                        |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/vector_block_type_def.hpp                      |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/vector_type.hpp                                |   58 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/vector_type_def.hpp                            |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/void_type.hpp                                  |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/type/void_type_def.hpp                              |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/variable_map.hpp                                    |  167 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/ast/variable_map_def.hpp                                |   65 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/compile_functions.hpp                                   |   83 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/compiler.hpp                                            |   75 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/function_signatures.h                                   |  139 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/constants.hpp                                 |   84 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/expression_visgen.hpp                         |  603 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/fun_scalar_type.hpp                           |   90 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_arg_decl.hpp                         |   50 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_array_builder_adds.hpp               |   39 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_bare_type.hpp                        |   99 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_block_var.hpp                        |   89 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_catch_throw_located.hpp              |   51 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_class_decl.hpp                       |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_class_decl_end.hpp                   |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_comment.hpp                          |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_constrained_param_names_method.hpp   |   65 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_constructor.hpp                      |  217 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_cpp.hpp                              |   88 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_data_var_ctor.hpp                    |   52 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_data_var_init.hpp                    |   85 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_destructor.hpp                       |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_dims_method.hpp                      |   94 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_expression.hpp                       |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_fun_inst_templ_params.hpp            |  103 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function.hpp                         |   71 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_arguments.hpp               |  118 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_body.hpp                    |   75 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_functor.hpp                 |   83 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_inline_return_type.hpp      |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation.hpp           |   86 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation_body.hpp      |  110 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation_name.hpp      |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiations.hpp          |   39 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_name.hpp                    |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_function_template_parameters.hpp     |  106 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_functions.hpp                        |   38 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_functor_arguments.hpp                |   68 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_globals.hpp                          |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_idx.hpp                              |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_idx_user.hpp                         |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_idxs.hpp                             |   65 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_idxs_user.hpp                        |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_include.hpp                          |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_includes.hpp                         |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_indent.hpp                           |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_indexed_expr.hpp                     |  128 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_indexed_expr_user.hpp                |   54 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_initializer.hpp                      |   87 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_line_number.hpp                      |   41 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_local_var_decl_inits.hpp             |  122 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_log_prob.hpp                         |  204 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_member_var_decls.hpp                 |   64 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_member_var_decls_all.hpp             |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_model_name_method.hpp                |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_model_typedef.hpp                    |   38 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_namespace_end.hpp                    |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_namespace_start.hpp                  |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_param_names_array.hpp                |   77 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_param_names_method.hpp               |   53 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_param_var.hpp                        |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_printable.hpp                        |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_private_decl.hpp                     |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_program_reader_fun.hpp               |   53 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_propto_default_function.hpp          |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_propto_default_function_body.hpp     |   53 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_public_decl.hpp                      |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_quoted_expression.hpp                |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_quoted_string.hpp                    |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_read_transform_params.hpp            |  101 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_real_var_type.hpp                    |   39 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_register_mpi.hpp                     |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_set_param_ranges.hpp                 |   89 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_standalone_functions.hpp             |   82 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_statement.hpp                        |   43 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_statements.hpp                       |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_transform_inits_method.hpp           |  302 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_try.hpp                              |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_typedef.hpp                          |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_typedefs.hpp                         |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_unconstrained_param_names_array.hpp  |   80 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_unconstrained_param_names_method.hpp |   68 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_using.hpp                            |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_using_namespace.hpp                  |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_usings.hpp                           |   38 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_usings_standalone_functions.hpp      |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_block_var.hpp               |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_context_size.hpp            |   82 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_nonnegative.hpp             |   62 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_tparam_inits.hpp            |   93 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_var_decl.hpp                |  116 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_var_dims.hpp                |   69 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_var_constructor.hpp                  |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_var_fill_define.hpp                  |   61 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_version_comment.hpp                  |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_void_statement.hpp                   |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_write_array_method.hpp               |  283 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/generate_write_block_var.hpp                  |   41 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/get_block_var_dims.hpp                        |   55 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/get_typedef_var_type.hpp                      |   41 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/get_verbose_var_type.hpp                      |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/idx_user_visgen.hpp                           |   82 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/idx_visgen.hpp                                |   92 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/is_numbered_statement_vis.hpp                 |   68 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/printable_visgen.hpp                          |   64 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/statement_visgen.hpp                          |  699 +-
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/visgen.hpp                                    |  100 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_begin_all_dims_col_maj_loop.hpp         |  139 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_begin_all_dims_row_maj_loop.hpp         |  139 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_begin_array_dims_loop.hpp               |   68 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_begin_param_elements_loop.hpp           |  147 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_constraints_fn.hpp                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_end_loop.hpp                            |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_nested_resize_loop_begin.hpp            |  108 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_resize_var_idx.hpp                      |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_var_decl_arg.hpp                        |  130 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_var_decl_type.hpp                       |   70 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_var_idx_all_dims.hpp                    |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_var_idx_all_dims_msg.hpp                |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/generator/write_var_idx_array_dims.hpp                  |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/bare_type_grammar.hpp                          |   54 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/bare_type_grammar_def.hpp                      |   93 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp                     |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/block_var_decls_grammar_def.hpp                |  284 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/block_var_decls_grammar_inst.cpp               |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/common_adaptors_def.hpp                        |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/expression07_grammar.hpp                       |   51 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/expression07_grammar_def.hpp                   |   58 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/expression07_grammar_inst.cpp                  |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar.hpp                         |   70 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar_def.hpp                     |  157 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar_inst.cpp                    |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar.hpp                          |   72 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar_def.hpp                      |  167 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar_inst.cpp                     |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar.hpp                            |   91 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar_def.hpp                        |  158 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar_inst.cpp                       |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/iterator_typedefs.hpp                          |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/local_var_decls_grammar.hpp                    |  115 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/local_var_decls_grammar_def.hpp                |  248 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/local_var_decls_grammar_inst.cpp               |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar.hpp                            |  110 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar_def.hpp                        |  252 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar_inst.cpp                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions.hpp                           |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions_def.cpp                       |  439 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/statement_2_grammar.hpp                        |   52 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/statement_2_grammar_def.hpp                    |   92 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/statement_2_grammar_inst.cpp                   |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar.hpp                          |  190 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_def.hpp                      |  612 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_inst.cpp                     |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar.hpp                               |  169 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar_def.hpp                           |  654 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar_inst.cpp                          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/whitespace_grammar.hpp                         |   21 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/whitespace_grammar_def.hpp                     |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/grammars/whitespace_grammar_inst.cpp                    |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/parser.hpp                                              |  186 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/lang/rethrow_located.hpp                                     |  284 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/base_adaptation.hpp                                     |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/base_adapter.hpp                                        |   39 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/base_mcmc.hpp                                           |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/chains.hpp                                              | 1052 +--
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/covar_adaptation.hpp                                    |   54 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/fixed_param_sampler.hpp                                 |   21 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/base_hmc.hpp                                        |  337 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp                   |  173 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp                     |   97 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/dense_e_point.hpp                      |  113 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/diag_e_metric.hpp                      |   88 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/diag_e_point.hpp                       |  108 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/ps_point.hpp                           |  134 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/softabs_metric.hpp                     |  354 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/softabs_point.hpp                      |   55 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/unit_e_metric.hpp                      |   85 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/unit_e_point.hpp                       |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/base_integrator.hpp                     |   25 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/base_leapfrog.hpp                       |  228 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/expl_leapfrog.hpp                       |   50 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/impl_leapfrog.hpp                       |  173 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_dense_e_nuts.hpp                         |   79 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_diag_e_nuts.hpp                          |   79 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_softabs_nuts.hpp                         |   66 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_unit_e_nuts.hpp                          |   66 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/base_nuts.hpp                                  |  626 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/dense_e_nuts.hpp                               |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/diag_e_nuts.hpp                                |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/softabs_nuts.hpp                               |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/unit_e_nuts.hpp                                |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/adapt_dense_e_nuts_classic.hpp         |   84 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/adapt_diag_e_nuts_classic.hpp          |   86 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/adapt_unit_e_nuts_classic.hpp          |   67 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/base_nuts_classic.hpp                  |  368 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/dense_e_nuts_classic.hpp               |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/diag_e_nuts_classic.hpp                |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/unit_e_nuts_classic.hpp                |   37 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_dense_e_static_hmc.hpp                 |   92 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_diag_e_static_hmc.hpp                  |   87 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_softabs_static_hmc.hpp                 |   72 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_unit_e_static_hmc.hpp                  |   74 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static/base_static_hmc.hpp                          |  237 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static/dense_e_static_hmc.hpp                       |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static/diag_e_static_hmc.hpp                        |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static/softabs_static_hmc.hpp                       |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static/unit_e_static_hmc.hpp                        |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_dense_e_static_uniform.hpp     |   88 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_diag_e_static_uniform.hpp      |   87 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_softabs_static_uniform.hpp     |   63 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_unit_e_static_uniform.hpp      |   74 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/base_static_uniform.hpp              |  281 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/dense_e_static_uniform.hpp           |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/diag_e_static_uniform.hpp            |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/softabs_static_uniform.hpp           |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/unit_e_static_uniform.hpp            |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_dense_e_xhmc.hpp                         |   85 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_diag_e_xhmc.hpp                          |   85 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_softabs_xhmc.hpp                         |   66 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_unit_e_xhmc.hpp                          |   67 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/base_xhmc.hpp                                  |  522 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/dense_e_xhmc.hpp                               |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/diag_e_xhmc.hpp                                |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/softabs_xhmc.hpp                               |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/unit_e_xhmc.hpp                                |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/sample.hpp                                              |   83 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/stepsize_adaptation.hpp                                 |  169 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/stepsize_adapter.hpp                                    |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/stepsize_covar_adapter.hpp                              |   57 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/stepsize_var_adapter.hpp                                |   58 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/var_adaptation.hpp                                      |   52 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/mcmc/windowed_adaptation.hpp                                 |  231 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/finite_diff_grad.hpp                                   |   95 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/grad_hess_log_prob.hpp                                 |  120 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/grad_tr_mat_times_hessian.hpp                          |   25 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/gradient.hpp                                           |   50 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/gradient_dot_vector.hpp                                |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/hessian.hpp                                            |   25 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/hessian_times_vector.hpp                               |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/indexing/deep_copy.hpp                                 |  112 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/indexing/index.hpp                                     |  193 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/indexing/index_list.hpp                                |  123 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/indexing/lvalue.hpp                                    |  877 +-
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/indexing/rvalue.hpp                                    |  700 --
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/indexing/rvalue_at.hpp                                 |  130 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/indexing/rvalue_index_size.hpp                         |  118 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/indexing/rvalue_return.hpp                             |  410 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/log_prob_grad.hpp                                      |  165 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/log_prob_propto.hpp                                    |  178 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/model_base.hpp                                         |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/model_base_crtp.hpp                                    |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/model_functional.hpp                                   |   39 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/model_header.hpp                                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/prob_grad.hpp                                          |  113 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/standalone_functions_header.hpp                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/model/test_gradients.hpp                                     |  174 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/optimization/bfgs.hpp                                        |  785 +-
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/optimization/bfgs_linesearch.hpp                             |  547 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/optimization/bfgs_update.hpp                                 |  111 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/optimization/lbfgs_update.hpp                                |  206 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/optimization/newton.hpp                                      |  124 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/diagnose/defaults.hpp                               |  137 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/diagnose/diagnose.hpp                               |  100 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/error_codes.hpp                                     |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/experimental/advi/defaults.hpp                      |  630 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/experimental/advi/fullrank.hpp                      |  152 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/experimental/advi/meanfield.hpp                     |  152 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/optimize/bfgs.hpp                                   |  325 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/optimize/defaults.hpp                               |  624 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/optimize/lbfgs.hpp                                  |  329 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/optimize/newton.hpp                                 |  207 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/defaults.hpp                                 |  969 +-
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/fixed_param.hpp                              |  130 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_dense_e.hpp                         |  241 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_dense_e_adapt.hpp                   |  299 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_diag_e.hpp                          |  239 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_diag_e_adapt.hpp                    |  295 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_unit_e.hpp                          |  116 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_unit_e_adapt.hpp                    |  138 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_static_dense_e.hpp                       |  238 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_static_dense_e_adapt.hpp                 |  300 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_static_diag_e.hpp                        |  238 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_static_diag_e_adapt.hpp                  |  298 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_static_unit_e.hpp                        |  115 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/hmc_static_unit_e_adapt.hpp                  |  139 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/sample/standalone_gqs.hpp                           |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/create_rng.hpp                                 |   55 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/create_unit_e_dense_inv_metric.hpp             |   54 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/create_unit_e_diag_inv_metric.hpp              |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/experimental_message.hpp                       |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/generate_transitions.hpp                       |  127 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/gq_writer.hpp                                  |  165 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/initialize.hpp                                 |   95 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/mcmc_writer.hpp                                |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/read_dense_inv_metric.hpp                      |   67 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/read_diag_inv_metric.hpp                       |   68 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/run_adaptive_sampler.hpp                       |  157 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/run_sampler.hpp                                |  130 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/validate_dense_inv_metric.hpp                  |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/services/util/validate_diag_inv_metric.hpp                   |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/variational/advi.hpp                                         | 1043 +--
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/variational/base_family.hpp                                  |  196 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/variational/families/normal_fullrank.hpp                     |  970 +-
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/variational/families/normal_meanfield.hpp                    |  848 +-
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/variational/print_progress.hpp                               |   87 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/src/stan/version.hpp                                                  |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/arr.hpp                                                 |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/arr/fun/log_sum_exp.hpp                                 |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/arr/fun/sum.hpp                                         |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/arr/fun/to_fvar.hpp                                     |   37 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/core/fvar.hpp                                           |   43 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat.hpp                                                 |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/Eigen_NumTraits.hpp                             |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/columns_dot_product.hpp                         |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/columns_dot_self.hpp                            |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/crossprod.hpp                                   |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/determinant.hpp                                 |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/divide.hpp                                      |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/dot_product.hpp                                 |   38 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/dot_self.hpp                                    |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/inverse.hpp                                     |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/log_determinant.hpp                             |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/log_softmax.hpp                                 |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/log_sum_exp.hpp                                 |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_left.hpp                                |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_left_ldlt.hpp                           |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_left_tri_low.hpp                        |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_right.hpp                               |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_right_tri_low.hpp                       |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/multiply.hpp                                    |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/multiply_lower_tri_self_transpose.hpp           |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/qr_Q.hpp                                        |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/qr_R.hpp                                        |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/quad_form_sym.hpp                               |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/rows_dot_product.hpp                            |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/rows_dot_self.hpp                               |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/softmax.hpp                                     |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/squared_distance.hpp                            |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/sum.hpp                                         |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/tcrossprod.hpp                                  |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/to_fvar.hpp                                     |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/typedefs.hpp                                    |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/fun/unit_vector_constrain.hpp                       |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/functor/gradient.hpp                                |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/functor/hessian.hpp                                 |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/functor/jacobian.hpp                                |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/meta/operands_and_partials.hpp                      |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/mat/vectorize/apply_scalar_unary.hpp                    |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/meta.hpp                                                |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal.hpp                                                |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/Phi.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/Phi_approx.hpp                                 |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/abs.hpp                                        |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/acos.hpp                                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/acosh.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/asin.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/asinh.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/atan.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/atan2.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/atanh.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/bessel_first_kind.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/bessel_second_kind.hpp                         |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/beta.hpp                                       |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/binary_log_loss.hpp                            |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/binomial_coefficient_log.hpp                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/cbrt.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/ceil.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/cos.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/cosh.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/digamma.hpp                                    |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/erf.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/erfc.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/exp.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/exp2.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/expm1.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/fabs.hpp                                       |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/falling_factorial.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/fdim.hpp                                       |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/floor.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/fma.hpp                                        |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/fmax.hpp                                       |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/fmin.hpp                                       |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/fmod.hpp                                       |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/gamma_p.hpp                                    |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/gamma_q.hpp                                    |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/grad_inc_beta.hpp                              |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/hypot.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/inc_beta.hpp                                   |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv.hpp                                        |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_Phi.hpp                                    |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_cloglog.hpp                                |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_logit.hpp                                  |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_sqrt.hpp                                   |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_square.hpp                                 |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/is_inf.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/is_nan.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/lbeta.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/ldexp.hpp                                      |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/lgamma.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/lmgamma.hpp                                    |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log.hpp                                        |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log10.hpp                                      |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1m.hpp                                      |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1m_exp.hpp                                  |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1m_inv_logit.hpp                            |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1p.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1p_exp.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log2.hpp                                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_diff_exp.hpp                               |   25 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_falling_factorial.hpp                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_inv_logit.hpp                              |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_inv_logit_diff.hpp                         |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_mix.hpp                                    |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_rising_factorial.hpp                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_sum_exp.hpp                                |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/logit.hpp                                      |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/modified_bessel_first_kind.hpp                 |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/modified_bessel_second_kind.hpp                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/multiply_log.hpp                               |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/owens_t.hpp                                    |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/pow.hpp                                        |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/primitive_value.hpp                            |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/rising_factorial.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/round.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/sin.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/sinh.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/sqrt.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/square.hpp                                     |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/tan.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/tanh.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/tgamma.hpp                                     |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/to_fvar.hpp                                    |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/trigamma.hpp                                   |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/trunc.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/value_of.hpp                                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/fun/value_of_rec.hpp                               |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/meta/is_fvar.hpp                                   |   21 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/meta/operands_and_partials.hpp                     |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/fwd/scal/meta/partials_type.hpp                             |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/memory/stack_alloc.hpp                                      |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/arr.hpp                                                 |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat.hpp                                                 |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat/fun/typedefs.hpp                                    |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat/functor/finite_diff_grad_hessian.hpp                |   23 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat/functor/finite_diff_grad_hessian_auto.hpp           |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat/functor/grad_hessian.hpp                            |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat/functor/grad_tr_mat_times_hessian.hpp               |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat/functor/gradient_dot_vector.hpp                     |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat/functor/hessian.hpp                                 |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat/functor/hessian_times_vector.hpp                    |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/mat/functor/partial_derivative.hpp                      |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/meta.hpp                                                |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/mix/scal.hpp                                                |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/buffer_types.hpp                                     |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/cholesky_decompose.hpp                               |   89 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/copy.hpp                                             |  256 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/copy_triangular.hpp                                  |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/diagonal_multiply.hpp                                |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_diagonal_zeros.hpp                         |   23 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_invalid_matrix_view.hpp                    |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_mat_size_one.hpp                           |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_matching_dims.hpp                          |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_nan.hpp                                    |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_opencl.hpp                                 |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_square.hpp                                 |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_symmetric.hpp                              |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_triangular.hpp                             |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/err/check_vector.hpp                                 |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/identity.hpp                                         |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/is_matrix_cl.hpp                                     |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernel_cl.hpp                                        |  321 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/add.hpp                                      |   75 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/bernoulli_logit_glm_lpmf.hpp                 |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/categorical_logit_glm_lpmf.hpp               |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/check_diagonal_zeros.hpp                     |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/check_nan.hpp                                |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/check_symmetric.hpp                          |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/cholesky_decompose.hpp                       |   45 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/copy.hpp                                     |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/copy_triangular.hpp                          |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions                             |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/diag_inv.hpp                                 |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/divide_columns.hpp                           |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/fill.hpp                                     |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/gp_exp_quad_cov.hpp                          |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/helpers.hpp                                  |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/identity.hpp                                 |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/inv_lower_tri_multiply.hpp                   |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/matrix_multiply.hpp                          |  323 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/multiply_transpose.hpp                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/neg_binomial_2_log_glm_lpmf.hpp              |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/neg_rect_lower_tri_multiply.hpp              |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/normal_id_glm_lpdf.hpp                       |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/ordered_logistic_glm_lpmf.hpp                |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/pack.hpp                                     |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/poisson_log_glm_lpmf.hpp                     |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/rep_matrix.hpp                               |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/scalar_mul.hpp                               |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/scalar_mul_diagonal.hpp                      |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/sub_block.hpp                                |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/subtract.hpp                                 |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/transpose.hpp                                |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/triangular_transpose.hpp                     |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/kernels/unpack.hpp                                   |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/matrix_cl.hpp                                        |  536 +
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/matrix_cl_view.hpp                                   |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/multiply.hpp                                         |  135 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/multiply_transpose.hpp                               |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/opencl.hpp                                           |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/opencl_context.hpp                                   |   83 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/prim                                                 |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/scalar_type.hpp                                      |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/stringify.hpp                                        |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/sub_block.hpp                                        |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/tri_inverse.hpp                                      |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/triangular_transpose.hpp                             |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/value_type.hpp                                       |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/opencl/zeros.hpp                                            |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr.hpp                                                |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/err/check_matching_sizes.hpp                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/err/check_nonzero_size.hpp                         |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/err/check_ordered.hpp                              |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/err/is_matching_size.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/err/is_nonzero_size.hpp                            |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/err/is_ordered.hpp                                 |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/array_builder.hpp                              |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/common_type.hpp                                |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/dot.hpp                                        |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/dot_self.hpp                                   |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/fill.hpp                                       |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/inverse_softmax.hpp                            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/log_sum_exp.hpp                                |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_elements.hpp                           |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_scalar.hpp                             |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_scalar_type.hpp                        |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/rep_array.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/scaled_add.hpp                                 |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/sort_asc.hpp                                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/sort_desc.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/sub.hpp                                        |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/sum.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of.hpp                                   |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of_rec.hpp                               |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/fun/vec_concat.hpp                                 |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/functor/coupled_ode_observer.hpp                   |  136 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/functor/coupled_ode_system.hpp                     |   98 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/functor/integrate_1d.hpp                           |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp                     |   77 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/meta/VectorBuilderHelper.hpp                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/meta/index_type.hpp                                |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/meta/is_constant.hpp                               |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/meta/is_vector.hpp                                 |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/meta/scalar_type.hpp                               |   25 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/arr/meta/value_type.hpp                                |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/core                                                   |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/core.hpp                                               |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat.hpp                                                |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/eigen_plugins.h                                    |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor.hpp                      |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor_corr.hpp                 |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_column_index.hpp                         |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_consistent_size_mvt.hpp                  |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_consistent_sizes_mvt.hpp                 |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_corr_matrix.hpp                          |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_cov_matrix.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_finite.hpp                               |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_flag_sundials.hpp                        |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_ldlt_factor.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_lower_triangular.hpp                     |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_matching_dims.hpp                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_multiplicable.hpp                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_nonempty.hpp                             |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_ordered.hpp                              |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_definite.hpp                         |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_semidefinite.hpp                     |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_positive_ordered.hpp                     |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_range.hpp                                |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_row_index.hpp                            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_simplex.hpp                              |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_spsd_matrix.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_square.hpp                               |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_std_vector_index.hpp                     |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_symmetric.hpp                            |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_unit_vector.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/check_vector.hpp                               |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/constraint_tolerance.hpp                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_cholesky_factor.hpp                         |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_cholesky_factor_corr.hpp                    |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_column_index.hpp                            |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_corr_matrix.hpp                             |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_ldlt_factor.hpp                             |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_lower_triangular.hpp                        |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_mat_finite.hpp                              |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_matching_dims.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_pos_definite.hpp                            |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_square.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_symmetric.hpp                               |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/is_unit_vector.hpp                             |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/err/validate_non_negative_index.hpp                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/Eigen.hpp                                      |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/LDLT_factor.hpp                                |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/MatrixExponential.h                            |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/accumulator.hpp                                |   23 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/add.hpp                                        |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/add_diag.hpp                                   |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/append_array.hpp                               |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/append_col.hpp                                 |   45 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/append_row.hpp                                 |   39 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/assign.hpp                                     |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/autocorrelation.hpp                            |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/chol2inv.hpp                                   |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_corr_constrain.hpp                    |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_corr_free.hpp                         |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_decompose.hpp                         |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_factor_constrain.hpp                  |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_factor_free.hpp                       |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/common_type.hpp                                |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/corr_matrix_constrain.hpp                      |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/corr_matrix_free.hpp                           |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_exp_quad.hpp                               |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain.hpp                       |   25 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain_lkj.hpp                   |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_free.hpp                            |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_free_lkj.hpp                        |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_u.hpp                              |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_v.hpp                              |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_w.hpp                              |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_matrix_times_vector.hpp                    |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_to_dense_matrix.hpp                        |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/cumulative_sum.hpp                             |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_post_multiply.hpp                         |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_pre_multiply.hpp                          |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/digamma.hpp                                    |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/dims.hpp                                       |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/distance.hpp                                   |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/divide.hpp                                     |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/divide_columns.hpp                             |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/dot_product.hpp                                |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_divide.hpp                                 |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_multiply.hpp                               |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/exp2.hpp                                       |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/factor_U.hpp                                   |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/factor_cov_matrix.hpp                          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/get_lp.hpp                                     |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_dot_prod_cov.hpp                            |   38 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_exp_quad_cov.hpp                            |  588 +
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_exponential_cov.hpp                         |   89 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_matern32_cov.hpp                            |   99 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_matern52_cov.hpp                            |  138 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_periodic_cov.hpp                            |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/head.hpp                                       |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/initialize.hpp                                 |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/inverse_spd.hpp                                |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/log2.hpp                                       |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/log_mix.hpp                                    |  126 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/log_sum_exp.hpp                                |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/make_nu.hpp                                    |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_2x2.hpp                             |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp                  |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_pade.hpp                            |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/max.hpp                                        |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left.hpp                               |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_ldlt.hpp                          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_spd.hpp                           |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_tri.hpp                           |   99 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_tri_low.hpp                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right.hpp                              |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_ldlt.hpp                         |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_spd.hpp                          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_tri.hpp                          |   47 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_tri_low.hpp                      |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/mean.hpp                                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/min.hpp                                        |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/multiply.hpp                                   |   60 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/multiply_lower_tri_self_transpose.hpp          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/num_elements.hpp                               |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/ordered_constrain.hpp                          |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/ordered_free.hpp                               |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/positive_ordered_constrain.hpp                 |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/positive_ordered_free.hpp                      |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/prod.hpp                                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_elements.hpp                           |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_scalar.hpp                             |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_scalar_type.hpp                        |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_Q.hpp                                       |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_R.hpp                                       |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_thin_Q.hpp                                  |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_thin_R.hpp                                  |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form_diag.hpp                             |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/rank.hpp                                       |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/read_corr_L.hpp                                |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_matrix.hpp                                 |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_row_vector.hpp                             |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_vector.hpp                                 |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/resize.hpp                                     |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/sd.hpp                                         |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/segment.hpp                                    |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/simplex_constrain.hpp                          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/simplex_free.hpp                               |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices.hpp                               |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices_asc.hpp                           |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices_desc.hpp                          |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/stan_print.hpp                                 |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/sub_col.hpp                                    |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/sub_row.hpp                                    |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/subtract.hpp                                   |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/tail.hpp                                       |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/tcrossprod.hpp                                 |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/to_array_1d.hpp                                |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/to_array_2d.hpp                                |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/to_matrix.hpp                                  |   53 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/to_row_vector.hpp                              |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/to_vector.hpp                                  |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_gen_inv_quad_form_ldlt.hpp               |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_gen_quad_form.hpp                        |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_inv_quad_form_ldlt.hpp                   |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/typedefs.hpp                                   |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/unit_vector_constrain.hpp                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/unit_vector_free.hpp                           |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/value_of.hpp                                   |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/value_of_rec.hpp                               |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/variance.hpp                                   |   18 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/welford_covar_estimator.hpp                    |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/fun/welford_var_estimator.hpp                      |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_gradient.hpp                   |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_gradient_auto.hpp              |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_hessian.hpp                    |   83 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_hessian_auto.hpp               |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_hessian_helper.hpp             |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect.hpp                               |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_combine.hpp                       |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_concurrent.hpp                    |  130 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_mpi.hpp                           |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_reduce.hpp                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/functor/mpi_parallel_call.hpp                      |   37 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/append_return_type.hpp                        |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/as_array_or_scalar.hpp                        |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/as_column_vector_or_scalar.hpp                |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/as_scalar.hpp                                 |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/broadcast_array.hpp                           |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/index_type.hpp                                |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/is_constant.hpp                               |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/is_eigen.hpp                                  |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/operands_and_partials.hpp                     |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/scalar_type.hpp                               |   59 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/seq_view.hpp                                  |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/meta/value_type.hpp                                |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/bernoulli_logit_glm_log.hpp                   |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/bernoulli_logit_glm_lpmf.hpp                  |   73 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/bernoulli_logit_glm_rng.hpp                   |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_log.hpp                           |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_glm_lpmf.hpp                |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_log.hpp                     |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_lpmf.hpp                    |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_rng.hpp                     |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_lpmf.hpp                          |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_rng.hpp                           |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/dirichlet_log.hpp                             |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp                            |  103 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/dirichlet_rng.hpp                             |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/gaussian_dlm_obs_log.hpp                      |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/gaussian_dlm_obs_lpdf.hpp                     |   45 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp                      |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/inv_wishart_log.hpp                           |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/inv_wishart_lpdf.hpp                          |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/inv_wishart_rng.hpp                           |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_log.hpp                     |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_lpdf.hpp                    |   59 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_rng.hpp                     |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_log.hpp                              |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_lpdf.hpp                             |   83 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_rng.hpp                              |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_cov_log.hpp                               |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_cov_lpdf.hpp                              |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/matrix_normal_prec_log.hpp                    |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/matrix_normal_prec_lpdf.hpp                   |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/matrix_normal_prec_rng.hpp                    |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_cholesky_log.hpp                     |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_cholesky_lpdf.hpp                    |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_log.hpp                              |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_lpdf.hpp                             |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_log.hpp                 |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_lpdf.hpp                |   70 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_rng.hpp                 |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_log.hpp                          |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_lpdf.hpp                         |   39 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_log.hpp                     |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_lpdf.hpp                    |   47 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_rng.hpp                     |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_rng.hpp                          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_log.hpp                       |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_lpdf.hpp                      |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_rng.hpp                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_log.hpp                           |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_lpmf.hpp                          |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_rng.hpp                           |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/neg_binomial_2_log_glm_log.hpp                |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/neg_binomial_2_log_glm_lpmf.hpp               |  103 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/normal_id_glm_log.hpp                         |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/normal_id_glm_lpdf.hpp                        |  137 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_glm_lpmf.hpp                 |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_log.hpp                      |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_lpmf.hpp                     |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_rng.hpp                      |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_probit_log.hpp                        |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_probit_lpmf.hpp                       |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_probit_rng.hpp                        |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp                       |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp                      |   65 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/wishart_log.hpp                               |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/wishart_lpdf.hpp                              |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/prob/wishart_rng.hpp                               |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/mat/vectorize/apply_scalar_unary.hpp                   |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/meta.hpp                                               |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal.hpp                                               |   41 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_2F1_converges.hpp                       |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_3F2_converges.hpp                       |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_bounded.hpp                             |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_consistent_size.hpp                     |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_consistent_sizes.hpp                    |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_finite.hpp                              |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_greater.hpp                             |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_greater_or_equal.hpp                    |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_less.hpp                                |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_less_or_equal.hpp                       |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_nonnegative.hpp                         |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_not_nan.hpp                             |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive.hpp                            |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive_finite.hpp                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/check_size_match.hpp                          |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/domain_error.hpp                              |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/domain_error_vec.hpp                          |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/invalid_argument.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/invalid_argument_vec.hpp                      |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/is_less_or_equal.hpp                          |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/is_not_nan.hpp                                |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/is_positive.hpp                               |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/is_scal_finite.hpp                            |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/is_size_match.hpp                             |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/out_of_range.hpp                              |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/err/system_error.hpp                              |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/F32.hpp                                       |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/Phi.hpp                                       |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/Phi_approx.hpp                                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/abs.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/acosh.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/as_bool.hpp                                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/asinh.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/atanh.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/bessel_first_kind.hpp                         |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/bessel_second_kind.hpp                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/beta.hpp                                      |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/binary_log_loss.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/binomial_coefficient_log.hpp                  |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/boost_policy.hpp                              |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/cbrt.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/choose.hpp                                    |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/common_type.hpp                               |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/constants.hpp                                 |   57 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/corr_constrain.hpp                            |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/corr_free.hpp                                 |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/digamma.hpp                                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/distance.hpp                                  |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/divide.hpp                                    |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/erf.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/erfc.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/exp.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/exp2.hpp                                      |   18 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/expm1.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/falling_factorial.hpp                         |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/fdim.hpp                                      |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/fill.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/finite_diff_stepsize.hpp                      |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/fma.hpp                                       |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/fmax.hpp                                      |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/fmin.hpp                                      |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/gamma_p.hpp                                   |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/gamma_q.hpp                                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_2F1.hpp                                  |   21 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_F32.hpp                                  |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_inc_beta.hpp                             |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_inc_beta.hpp                         |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_inc_gamma.hpp                        |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_lower_inc_gamma.hpp                  |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/hypot.hpp                                     |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/ibeta.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/identity_constrain.hpp                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/identity_free.hpp                             |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/if_else.hpp                                   |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_dda.hpp                              |   43 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_ddb.hpp                              |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_ddz.hpp                              |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/int_step.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inv.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_Phi.hpp                                   |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_cloglog.hpp                               |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_logit.hpp                                 |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_sqrt.hpp                                  |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_square.hpp                                |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/is_any_nan.hpp                                |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/is_inf.hpp                                    |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/is_integer.hpp                                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/is_nan.hpp                                    |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/is_nonpositive_integer.hpp                    |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/is_uninitialized.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/lb_constrain.hpp                              |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/lb_free.hpp                                   |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/lbeta.hpp                                     |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/ldexp.hpp                                     |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/lgamma.hpp                                    |   67 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/lmgamma.hpp                                   |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/locscale_constrain.hpp                        |   23 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/locscale_free.hpp                             |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m.hpp                                     |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m_exp.hpp                                 |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m_inv_logit.hpp                           |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log1p.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log1p_exp.hpp                                 |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log2.hpp                                      |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log_diff_exp.hpp                              |   21 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log_falling_factorial.hpp                     |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log_inv_logit.hpp                             |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log_inv_logit_diff.hpp                        |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log_mix.hpp                                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log_modified_bessel_first_kind.hpp            |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log_rising_factorial.hpp                      |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/log_sum_exp.hpp                               |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_and.hpp                               |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_eq.hpp                                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_gt.hpp                                |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_gte.hpp                               |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_lt.hpp                                |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_lte.hpp                               |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_negation.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_neq.hpp                               |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_or.hpp                                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/logit.hpp                                     |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/lub_constrain.hpp                             |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/lub_free.hpp                                  |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/modified_bessel_first_kind.hpp                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/modified_bessel_second_kind.hpp               |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/modulus.hpp                                   |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/multiply_log.hpp                              |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/offset_multiplier_constrain.hpp               |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/offset_multiplier_free.hpp                    |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/owens_t.hpp                                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/positive_constrain.hpp                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/positive_free.hpp                             |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/primitive_value.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/prob_constrain.hpp                            |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/prob_free.hpp                                 |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/promote_elements.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/promote_scalar.hpp                            |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/promote_scalar_type.hpp                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/rising_factorial.hpp                          |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/round.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/sign.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/size_zero.hpp                                 |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/sqrt.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/square.hpp                                    |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/squared_distance.hpp                          |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/step.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/sum.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/tgamma.hpp                                    |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/trigamma.hpp                                  |   23 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/trunc.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/ub_constrain.hpp                              |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/ub_free.hpp                                   |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/value_of.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/fun/value_of_rec.hpp                              |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/StdVectorBuilder.hpp                         |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/VectorBuilder.hpp                            |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/VectorBuilderHelper.hpp                      |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/ad_promotable.hpp                            |  146 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/bool_constant.hpp                            |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/child_type.hpp                               |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/conjunction.hpp                              |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_fvar.hpp                            |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_std_vector.hpp                      |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_vector.hpp                          |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/disjunction.hpp                              |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/include_summand.hpp                          |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/index_type.hpp                               |   18 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant.hpp                              |   21 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/is_eigen.hpp                                 |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/is_fvar.hpp                                  |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/is_var.hpp                                   |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/is_var_or_arithmetic.hpp                     |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/is_vector.hpp                                |   77 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/is_vector_like.hpp                           |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/operands_and_partials.hpp                    |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/partials_return_type.hpp                     |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/partials_type.hpp                            |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/promote_args.hpp                             |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/require_generics.hpp                         |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/return_type.hpp                              |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_seq_view.hpp                          |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_type.hpp                              |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_type_pre.hpp                          |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/meta/value_type.hpp                               |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_ccdf_log.hpp                       |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_cdf.hpp                            |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_cdf_log.hpp                        |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_lccdf.hpp                          |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_lcdf.hpp                           |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_log.hpp                            |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_log.hpp                      |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_lpmf.hpp                     |   45 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_rng.hpp                      |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_lpmf.hpp                           |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_rng.hpp                            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_ccdf_log.hpp                   |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_cdf.hpp                        |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_cdf_log.hpp                    |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_lccdf.hpp                      |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_lcdf.hpp                       |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_log.hpp                        |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_lpmf.hpp                       |  140 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_rng.hpp                        |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_ccdf_log.hpp                            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_cdf.hpp                                 |   64 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_cdf_log.hpp                             |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lccdf.hpp                               |   50 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lcdf.hpp                                |   50 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_log.hpp                                 |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lpdf.hpp                                |   95 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_ccdf_log.hpp                 |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_cdf_log.hpp                  |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_lccdf.hpp                    |   53 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_lcdf.hpp                     |   52 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_log.hpp                      |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_lpdf.hpp                     |   71 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_rng.hpp                      |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_rng.hpp                                 |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_ccdf_log.hpp                        |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_cdf.hpp                             |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_cdf_log.hpp                         |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_lccdf.hpp                           |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_lcdf.hpp                            |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_log.hpp                             |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_logit_log.hpp                       |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_logit_lpmf.hpp                      |   51 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_lpmf.hpp                            |   50 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_rng.hpp                             |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_ccdf_log.hpp                          |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_cdf.hpp                               |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_cdf_log.hpp                           |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lccdf.hpp                             |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lcdf.hpp                              |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_log.hpp                               |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lpdf.hpp                              |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_rng.hpp                               |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_ccdf_log.hpp                      |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_cdf.hpp                           |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_cdf_log.hpp                       |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lccdf.hpp                         |   37 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lcdf.hpp                          |   37 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_log.hpp                           |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lpdf.hpp                          |   74 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_rng.hpp                           |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_ccdf_log.hpp              |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_cdf.hpp                   |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_cdf_log.hpp               |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lccdf.hpp                 |   37 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lcdf.hpp                  |   37 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_log.hpp                   |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lpdf.hpp                  |   56 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_rng.hpp                   |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_ccdf_log.hpp                  |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_cdf.hpp                       |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_cdf_log.hpp                   |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lccdf.hpp                     |   39 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lcdf.hpp                      |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_log.hpp                       |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lpdf.hpp                      |   53 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_rng.hpp                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_ccdf_log.hpp                     |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_cdf.hpp                          |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_cdf_log.hpp                      |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_lccdf.hpp                        |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_lcdf.hpp                         |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_log.hpp                          |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_lpdf.hpp                         |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_rng.hpp                          |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_ccdf_log.hpp                         |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_cdf.hpp                              |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_cdf_log.hpp                          |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_lccdf.hpp                            |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_lcdf.hpp                             |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_log.hpp                              |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_lpdf.hpp                             |   85 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_rng.hpp                              |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_ccdf_log.hpp                           |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_cdf.hpp                                |   56 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_cdf_log.hpp                            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lccdf.hpp                              |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lcdf.hpp                               |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_log.hpp                                |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lpdf.hpp                               |   69 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_rng.hpp                                |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_ccdf_log.hpp                          |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_cdf.hpp                               |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_cdf_log.hpp                           |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lccdf.hpp                             |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lcdf.hpp                              |   31 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_log.hpp                               |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lpdf.hpp                              |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_rng.hpp                               |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/hypergeometric_log.hpp                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/hypergeometric_lpmf.hpp                      |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/hypergeometric_rng.hpp                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_ccdf_log.hpp                  |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_cdf.hpp                       |   53 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_cdf_log.hpp                   |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lccdf.hpp                     |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lcdf.hpp                      |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_log.hpp                       |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lpdf.hpp                      |   73 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_rng.hpp                       |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_ccdf_log.hpp                       |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_cdf.hpp                            |   65 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_cdf_log.hpp                        |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lccdf.hpp                          |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lcdf.hpp                           |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_log.hpp                            |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lpdf.hpp                           |   86 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_rng.hpp                            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_ccdf_log.hpp                        |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_cdf.hpp                             |   51 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_cdf_log.hpp                         |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_lccdf.hpp                           |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_lcdf.hpp                            |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_log.hpp                             |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_lpdf.hpp                            |   72 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_rng.hpp                             |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_ccdf_log.hpp                       |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_cdf.hpp                            |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_cdf_log.hpp                        |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lccdf.hpp                          |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lcdf.hpp                           |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_log.hpp                            |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lpdf.hpp                           |   88 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_rng.hpp                            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_ccdf_log.hpp                  |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_cdf.hpp                       |   44 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_cdf_log.hpp                   |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_lccdf.hpp                     |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_lcdf.hpp                      |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log.hpp                       |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log_log.hpp                   |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log_lpmf.hpp                  |   63 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log_rng.hpp                   |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_lpmf.hpp                      |   67 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_rng.hpp                       |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_ccdf_log.hpp                    |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_cdf.hpp                         |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_cdf_log.hpp                     |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_lccdf.hpp                       |   45 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_lcdf.hpp                        |   49 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_log.hpp                         |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_lpmf.hpp                        |   93 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_rng.hpp                         |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_ccdf_log.hpp                          |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_cdf.hpp                               |   55 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_cdf_log.hpp                           |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lccdf.hpp                             |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lcdf.hpp                              |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_log.hpp                               |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lpdf.hpp                              |   51 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_rng.hpp                               |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_sufficient_log.hpp                    |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_sufficient_lpdf.hpp                   |   45 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_ccdf_log.hpp                          |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_cdf.hpp                               |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_cdf_log.hpp                           |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_lccdf.hpp                             |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_lcdf.hpp                              |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_log.hpp                               |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_lpdf.hpp                              |   81 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_rng.hpp                               |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_ccdf_log.hpp                   |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_cdf.hpp                        |   66 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_cdf_log.hpp                    |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_lccdf.hpp                      |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_lcdf.hpp                       |   37 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_log.hpp                        |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_lpdf.hpp                       |   68 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_rng.hpp                        |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_ccdf_log.hpp                         |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_cdf.hpp                              |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_cdf_log.hpp                          |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_lccdf.hpp                            |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_lcdf.hpp                             |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log.hpp                              |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log_log.hpp                          |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log_lpmf.hpp                         |   56 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log_rng.hpp                          |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_lpmf.hpp                             |   46 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_rng.hpp                              |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_ccdf_log.hpp                        |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_cdf.hpp                             |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_cdf_log.hpp                         |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lccdf.hpp                           |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lcdf.hpp                            |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_log.hpp                             |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lpdf.hpp                            |   45 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_rng.hpp                             |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_ccdf_log.hpp           |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_cdf.hpp                |   59 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_cdf_log.hpp            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_lccdf.hpp              |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_lcdf.hpp               |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_log.hpp                |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_lpdf.hpp               |   93 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_rng.hpp                |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_ccdf_log.hpp                     |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_cdf.hpp                          |   50 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_cdf_log.hpp                      |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lccdf.hpp                        |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lcdf.hpp                         |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_log.hpp                          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lpdf.hpp                         |   56 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_rng.hpp                          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/std_normal_log.hpp                           |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/std_normal_lpdf.hpp                          |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_ccdf_log.hpp                       |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_cdf.hpp                            |   85 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_cdf_log.hpp                        |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_lccdf.hpp                          |   60 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_lcdf.hpp                           |   64 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_log.hpp                            |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_lpdf.hpp                           |   78 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_rng.hpp                            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_ccdf_log.hpp                         |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_cdf.hpp                              |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_cdf_log.hpp                          |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_lccdf.hpp                            |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_lcdf.hpp                             |   34 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_log.hpp                              |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_lpdf.hpp                             |   51 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_rng.hpp                              |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_log.hpp                            |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_lpdf.hpp                           |   60 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_rng.hpp                            |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_ccdf_log.hpp                         |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_cdf.hpp                              |   51 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_cdf_log.hpp                          |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_lccdf.hpp                            |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_lcdf.hpp                             |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_log.hpp                              |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_lpdf.hpp                             |   91 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_rng.hpp                              |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/wiener_log.hpp                               |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/prim/scal/prob/wiener_lpdf.hpp                              |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/arr.hpp                                                 |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/arr/fun/log_sum_exp.hpp                                 |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/arr/fun/sum.hpp                                         |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/arr/fun/to_var.hpp                                      |   21 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/arr/functor/coupled_ode_system.hpp                      |  509 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/arr/functor/integrate_1d.hpp                            |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core.hpp                                                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/autodiffstackstorage.hpp                           |  146 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/build_vari_array.hpp                               |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/chainable_alloc.hpp                                |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/chainablestack.hpp                                 |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/empty_nested.hpp                                   |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/gevv_vvv_vari.hpp                                  |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/grad.hpp                                           |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/init_chainablestack.hpp                            |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/matrix_vari.hpp                                    |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/nested_size.hpp                                    |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_addition.hpp                              |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_divide_equal.hpp                          |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_division.hpp                              |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_minus_equal.hpp                           |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_multiplication.hpp                        |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_multiply_equal.hpp                        |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_plus_equal.hpp                            |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_subtraction.hpp                           |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_unary_decrement.hpp                       |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_unary_increment.hpp                       |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_unary_negative.hpp                        |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/operator_unary_plus.hpp                            |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/precomputed_gradients.hpp                          |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/print_stack.hpp                                    |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/recover_memory.hpp                                 |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/recover_memory_nested.hpp                          |   29 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/set_zero_all_adjoints.hpp                          |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp                   |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/start_nested.hpp                                   |   14 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/stored_gradient_vari.hpp                           |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/var.hpp                                            |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/vari.hpp                                           |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/core/vector_vari.hpp                                    |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat.hpp                                                 |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp                             |  185 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/LDLT_alloc.hpp                                  |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/LDLT_factor.hpp                                 |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/cholesky_decompose.hpp                          |   79 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/columns_dot_product.hpp                         |   18 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/columns_dot_self.hpp                            |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/cov_exp_quad.hpp                                |   43 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/crossprod.hpp                                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/determinant.hpp                                 |   40 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/divide.hpp                                      |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/dot_product.hpp                                 |  100 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/dot_self.hpp                                    |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/gp_exp_quad_cov.hpp                             |   56 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/gp_periodic_cov.hpp                             |   35 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/grad.hpp                                        |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/initialize_variable.hpp                         |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/inverse.hpp                                     |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant.hpp                             |   25 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant_ldlt.hpp                        |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant_spd.hpp                         |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/log_softmax.hpp                                 |   62 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/log_sum_exp.hpp                                 |   26 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/matrix_exp_multiply.hpp                         |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left.hpp                                |  225 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_ldlt.hpp                           |  133 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_spd.hpp                            |  182 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_tri.hpp                            |  354 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/multiply.hpp                                    |  371 -
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/multiply_lower_tri_self_transpose.hpp           |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/ordered_constrain.hpp                           |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp                  |    7 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/quad_form.hpp                                   |   23 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/quad_form_sym.hpp                               |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/rows_dot_product.hpp                            |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/scale_matrix_exp_multiply.hpp                   |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/sd.hpp                                          |   48 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/simplex_constrain.hpp                           |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/softmax.hpp                                     |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/squared_distance.hpp                            |   69 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/stan_print.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/sum.hpp                                         |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/tcrossprod.hpp                                  |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/to_var.hpp                                      |   75 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_gen_inv_quad_form_ldlt.hpp                |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_gen_quad_form.hpp                         |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_inv_quad_form_ldlt.hpp                    |   78 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_quad_form.hpp                             |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/typedefs.hpp                                    |   27 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/unit_vector_constrain.hpp                       |   28 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/fun/variance.hpp                                    |   39 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/adj_jac_apply.hpp                           |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_solver_fp.hpp                       |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_solver_newton.hpp                   |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_solver_powell.hpp                   |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_system.hpp                          |   33 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_integrator.hpp                       |   92 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_ode_data.hpp                         |   32 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_utils.hpp                            |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/gradient.hpp                                |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/idas_forward_system.hpp                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/idas_integrator.hpp                         |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/idas_system.hpp                             |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/integrate_dae.hpp                           |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp                     |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/integrate_ode_bdf.hpp                       |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/jacobian.hpp                                |   21 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/kinsol_data.hpp                             |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/kinsol_solve.hpp                            |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/map_rect_concurrent.hpp                     |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/functor/map_rect_reduce.hpp                         |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/meta/operands_and_partials.hpp                      |   30 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/mat/vectorize/apply_scalar_unary.hpp                    |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/meta.hpp                                                |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal.hpp                                                |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/Phi.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/Phi_approx.hpp                                 |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/abs.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/acos.hpp                                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/acosh.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/as_bool.hpp                                    |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/asin.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/asinh.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/atan.hpp                                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/atan2.hpp                                      |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/atanh.hpp                                      |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/bessel_first_kind.hpp                          |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/bessel_second_kind.hpp                         |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/beta.hpp                                       |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/binary_log_loss.hpp                            |    8 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_fpclassify.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isfinite.hpp                             |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isnormal.hpp                             |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/calculate_chain.hpp                            |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/cbrt.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/ceil.hpp                                       |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/cos.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/cosh.hpp                                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/digamma.hpp                                    |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/erf.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/erfc.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/exp.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/exp2.hpp                                       |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/expm1.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/fabs.hpp                                       |   10 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/falling_factorial.hpp                          |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/fdim.hpp                                       |   16 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/floor.hpp                                      |    5 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/fma.hpp                                        |   42 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/fmax.hpp                                       |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/fmin.hpp                                       |   20 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/fmod.hpp                                       |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/gamma_p.hpp                                    |   13 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/gamma_q.hpp                                    |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/grad_inc_beta.hpp                              |    9 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/hypot.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/ibeta.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/if_else.hpp                                    |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/inc_beta.hpp                                   |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/inv.hpp                                        |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_Phi.hpp                                    |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_cloglog.hpp                                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_logit.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_sqrt.hpp                                   |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_square.hpp                                 |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/is_inf.hpp                                     |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/is_nan.hpp                                     |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/is_uninitialized.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/lbeta.hpp                                      |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/ldexp.hpp                                      |only
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/lgamma.hpp                                     |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/lmgamma.hpp                                    |    6 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log10.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m_exp.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m_inv_logit.hpp                            |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log1p.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log1p_exp.hpp                                  |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log2.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log_diff_exp.hpp                               |   24 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log_falling_factorial.hpp                      |   15 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log_inv_logit.hpp                              |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log_inv_logit_diff.hpp                         |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log_mix.hpp                                    |   17 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log_rising_factorial.hpp                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/log_sum_exp.hpp                                |   18 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/logit.hpp                                      |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/modified_bessel_first_kind.hpp                 |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/modified_bessel_second_kind.hpp                |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/multiply_log.hpp                               |   22 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/owens_t.hpp                                    |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/pow.hpp                                        |   36 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/primitive_value.hpp                            |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/rising_factorial.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/round.hpp                                      |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/sin.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/sinh.hpp                                       |    2 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/sqrt.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/square.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/squared_distance.hpp                           |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/step.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/tan.hpp                                        |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/tanh.hpp                                       |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/tgamma.hpp                                     |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/to_var.hpp                                     |   19 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/trigamma.hpp                                   |    3 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/trunc.hpp                                      |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/value_of.hpp                                   |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/fun/value_of_rec.hpp                               |    1 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/meta/is_var.hpp                                    |   12 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/meta/operands_and_partials.hpp                     |    4 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/rev/scal/meta/partials_type.hpp                             |   11 
 StanHeaders-2.21.0-3/StanHeaders/inst/include/stan/math/version.hpp                                                 |    7 
 StanHeaders-2.21.0-3/StanHeaders/man                                                                                |only
 StanHeaders-2.21.0-3/StanHeaders/src/Makevars                                                                       |   10 
 StanHeaders-2.21.0-3/StanHeaders/src/Makevars.win                                                                   |    3 
 StanHeaders-2.21.0-3/StanHeaders/src/kinsol                                                                         |only
 StanHeaders-2.21.0-3/StanHeaders/tests/rstan.R                                                                      |   12 
 StanHeaders-2.21.0-3/StanHeaders/vignettes/stanmath.Rmd                                                             |   62 
 1751 files changed, 42490 insertions(+), 43148 deletions(-)

More information about StanHeaders at CRAN
Permanent link

Package sjmisc updated to version 2.8.5 with previous version 2.8.4 dated 2020-04-03

Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data, and all integrate seamlessly into a 'tidyverse'-workflow.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Iago Giné-Vázquez [ctb], Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between sjmisc versions 2.8.4 dated 2020-04-03 and 2.8.5 dated 2020-05-28

 DESCRIPTION                     |    6 
 MD5                             |   32 -
 NAMESPACE                       |    1 
 NEWS.md                         |   11 
 R/descr.R                       |   22 -
 R/prop_table.R                  |   35 +
 R/rec.R                         |   24 -
 build/partial.rdb               |binary
 build/vignette.rds              |binary
 inst/doc/design_philosophy.html |  414 +++++++++----------
 inst/doc/exploringdatasets.html |  306 ++++++--------
 inst/doc/recodingvariables.html |  838 +++++++++++++++++++---------------------
 man/descr.Rd                    |  190 ++++-----
 man/find_var.Rd                 |  258 ++++++------
 man/flat_table.Rd               |    7 
 man/rec.Rd                      |   11 
 tests/testthat/test-rec.R       |    2 
 17 files changed, 1083 insertions(+), 1074 deletions(-)

More information about sjmisc at CRAN
Permanent link

Package rgbif updated to version 2.3 with previous version 2.2.0 dated 2020-03-09

Title: Interface to the Global 'Biodiversity' Information Facility API
Description: A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'; <https://www.gbif.org/developer/summary>). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the 'GBIF' tile map service to make 'rasters' summarizing huge amounts of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>), Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>), Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>), Laurens Geffert [ctb], Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>), Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rgbif versions 2.2.0 dated 2020-03-09 and 2.3 dated 2020-05-28

 DESCRIPTION                               |   12 ++--
 MD5                                       |   64 ++++++++++++------------
 NAMESPACE                                 |    1 
 NEWS.md                                   |   18 ++++++
 R/download_predicate_dsl.R                |   18 ++++--
 R/name_usage.r                            |    2 
 R/occ_data.R                              |   14 +++--
 R/occ_download_get.r                      |    9 +--
 R/occ_download_import.R                   |   13 +++-
 R/occ_download_meta.R                     |   19 ++++---
 R/occ_download_queue.R                    |   18 ++++--
 R/occ_search.r                            |   26 ++++++---
 R/rgbif-package.r                         |    1 
 README.md                                 |   80 +++++++++++++++---------------
 build/vignette.rds                        |binary
 inst/doc/downloads.html                   |    4 -
 inst/doc/issues.Rmd                       |    2 
 inst/doc/issues.html                      |    6 +-
 inst/doc/rgbif.Rmd                        |    6 +-
 inst/doc/rgbif.html                       |    7 +-
 inst/doc/taxonomic_names.html             |    4 -
 man/DownReq.Rd                            |    5 +
 man/GbifQueue.Rd                          |    9 +++
 man/occ_data.Rd                           |   34 ++++++++++++
 man/occ_download_get.Rd                   |    7 +-
 man/occ_download_import.Rd                |   16 ++++--
 man/occ_download_queue.Rd                 |   14 ++++-
 man/occ_search.Rd                         |   22 +++++++-
 tests/fixtures/occ_download_meta.yml      |only
 tests/testthat/test-occ_download_import.R |only
 tests/testthat/test-occ_download_meta.R   |only
 tests/testthat/test-occ_download_prep.R   |only
 tests/testthat/test-predicate_builders.R  |   20 +++++++
 vignettes/issues.Rmd                      |    2 
 vignettes/rgbif.Rmd                       |    6 +-
 35 files changed, 312 insertions(+), 147 deletions(-)

More information about rgbif at CRAN
Permanent link

Package mrbayes updated to version 0.2.0 with previous version 0.1.0 dated 2019-09-04

Title: Bayesian Summary Data Models for Mendelian Randomization Studies
Description: Bayesian estimation of inverse variance weighted (IVW), Burgess et al. (2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden et al. (2015) <doi:10.1093/ije/dyv080>, summary data models for Mendelian randomization analyses.
Author: Okezie Uche-Ikonne [aut, cre] (<https://orcid.org/0000-0002-8461-8099>), Frank Dondelinger [aut] (<https://orcid.org/0000-0003-1816-6300>), Tom Palmer [aut] (<https://orcid.org/0000-0003-4655-4511>)
Maintainer: Okezie Uche-Ikonne <o.uche-ikonne@lancaster.ac.uk>

Diff between mrbayes versions 0.1.0 dated 2019-09-04 and 0.2.0 dated 2020-05-28

 DESCRIPTION                                |   35 +++++++-----
 MD5                                        |   63 +++++++++++++++-------
 NAMESPACE                                  |    7 ++
 NEWS.md                                    |only
 R/do_data.R                                |   17 ++---
 R/mr_egger_rjags.R                         |   32 ++++++-----
 R/mr_egger_stan.R                          |only
 R/mr_ivw_rjags.R                           |   25 +++++---
 R/mr_ivw_stan.R                            |only
 R/mr_radialegger_rjags.R                   |   33 ++++++-----
 R/mr_radialegger_stan.R                    |only
 R/mrbayes-package.r                        |   10 +++
 R/stanmodels.R                             |only
 README.md                                  |   27 ++++++++-
 configure                                  |only
 configure.win                              |only
 data/do_data.rda                           |binary
 inst                                       |only
 man/bmi_insulin.Rd                         |    6 +-
 man/do_data.Rd                             |   23 +++-----
 man/mr_egger_rjags.Rd                      |   42 +++++++++-----
 man/mr_egger_stan.Rd                       |only
 man/mr_ivw_rjags.Rd                        |   32 +++++++----
 man/mr_ivw_stan.Rd                         |only
 man/mr_radialegger_rjags.Rd                |   42 +++++++++-----
 man/mr_radialegger_stan.Rd                 |only
 man/mrbayes-package.Rd                     |    6 +-
 src                                        |only
 tests/testthat/test-mr_egger_rjags.R       |   83 ++++++++++++-----------------
 tests/testthat/test-mr_egger_stan.R        |only
 tests/testthat/test-mr_ivw_rjags.R         |   52 +++++-------------
 tests/testthat/test-mr_ivw_stan.R          |only
 tests/testthat/test-mr_radialegger_rjags.R |   80 ++++++++++++---------------
 tests/testthat/test-mr_radialegger_stan.R  |only
 34 files changed, 352 insertions(+), 263 deletions(-)

More information about mrbayes at CRAN
Permanent link

Package GD updated to version 1.8 with previous version 1.7 dated 2019-08-21

Title: Geographical Detectors
Description: Geographical detectors for measuring spatial stratified heterogeneity, as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the optimal discretization of continuous data, four primary functions of geographical detectors, comparison of size effects of spatial unit and the visualizations of results. To use the package and to refer the descriptions of the package, methods and case datasets, please cite Yongze Song (2020) <doi:10.1080/15481603.2020.1760434>.
Author: Yongze Song [aut, cre] (<https://orcid.org/0000-0003-3420-9622>)
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>

Diff between GD versions 1.7 dated 2019-08-21 and 1.8 dated 2020-05-28

 DESCRIPTION           |   17 -
 MD5                   |   27 +-
 R/disc.R              |   18 +
 R/optidisc.R          |    1 
 R/zzz.R               |only
 build/vignette.rds    |binary
 inst/CITATION         |   38 +--
 inst/doc/GD.R         |   50 +++-
 inst/doc/GD.Rmd       |  192 +++++++++++++++---
 inst/doc/GD.html      |  511 ++++++++++++++++++++++++++++++++++++--------------
 vignettes/Figure1.png |only
 vignettes/Figure2.png |only
 vignettes/Figure3.png |only
 vignettes/Figure4.png |only
 vignettes/Figure5.png |only
 vignettes/Figure6.png |only
 vignettes/Figure7.png |only
 vignettes/Figure8.png |only
 vignettes/GD.Rmd      |  192 +++++++++++++++---
 19 files changed, 789 insertions(+), 257 deletions(-)

More information about GD at CRAN
Permanent link

Package auditor updated to version 1.3.0 with previous version 1.2.0 dated 2020-02-18

Title: Model Audit - Verification, Validation, and Error Analysis
Description: Provides an easy to use unified interface for creating validation plots for any model. The 'auditor' helps to avoid repetitive work consisting of writing code needed to create residual plots. This visualizations allow to asses and compare the goodness of fit, performance, and similarity of models.
Author: Alicja Gosiewska [aut, cre] (<https://orcid.org/0000-0001-6563-5742>), Przemyslaw Biecek [aut, ths] (<https://orcid.org/0000-0001-8423-1823>), Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>), Tomasz Mikołajczyk [aut], Michal Burdukiewicz [ctb], Szymon Maksymiuk [ctb]
Maintainer: Alicja Gosiewska <alicjagosiewska@gmail.com>

Diff between auditor versions 1.2.0 dated 2020-02-18 and 1.3.0 dated 2020-05-28

 DESCRIPTION                               |   14 -
 MD5                                       |  305 +++++++++++++++---------------
 NAMESPACE                                 |    4 
 NEWS.md                                   |   12 +
 R/audit.R                                 |   58 ++---
 R/check_residuals.R                       |   32 +--
 R/model_cooksdistance.R                   |   24 +-
 R/model_evaluation.R                      |   55 +++--
 R/model_halfnormal.R                      |   27 +-
 R/model_performance.R                     |   31 +--
 R/model_residual.R                        |   29 +-
 R/plot.R                                  |   58 +++--
 R/plotD3.R                                |   27 +-
 R/plotD3_acf.R                            |   12 -
 R/plotD3_autocorrelation.R                |   10 
 R/plotD3_cooksdistance.R                  |   10 
 R/plotD3_halfnormal.R                     |   11 -
 R/plotD3_lift.R                           |   30 +-
 R/plotD3_prediction.R                     |   14 -
 R/plotD3_rec.R                            |   14 -
 R/plotD3_residual.R                       |   13 -
 R/plotD3_roc.R                            |   37 ++-
 R/plotD3_rroc.R                           |    9 
 R/plotD3_scalelocation.R                  |   24 +-
 R/plot_acf.R                              |   16 -
 R/plot_autocorrelation.R                  |   12 -
 R/plot_cooksdistance.R                    |   11 -
 R/plot_correlation.R                      |   17 -
 R/plot_halfnormal.R                       |   13 -
 R/plot_lift.R                             |   37 +--
 R/plot_pca.R                              |   22 --
 R/plot_prc.R                              |only
 R/plot_prediction.R                       |   22 --
 R/plot_radar.R                            |   24 --
 R/plot_rec.R                              |   12 -
 R/plot_residual.R                         |   19 -
 R/plot_residual_boxplot.R                 |   20 -
 R/plot_residual_density.R                 |   27 +-
 R/plot_roc.R                              |   36 +--
 R/plot_rroc.R                             |   14 -
 R/plot_scalelocation.R                    |   17 -
 R/plot_tsecdf.R                           |   12 -
 R/print.R                                 |   76 +++----
 R/score.R                                 |    5 
 R/score_F1.R                              |   61 +++---
 R/score_acc.R                             |   65 ++++--
 R/score_auc.R                             |   88 +++++---
 R/score_auprc.R                           |only
 R/score_cooksdistance.R                   |    8 
 R/score_dw.R                              |   25 +-
 R/score_gini.R                            |   55 +++--
 R/score_halfnormal.R                      |   16 -
 R/score_mae.R                             |   23 +-
 R/score_mse.R                             |   22 +-
 R/score_peak.R                            |   24 +-
 R/score_precision.R                       |   59 +++--
 R/score_r2.R                              |   14 -
 R/score_rec.R                             |   28 +-
 R/score_recall.R                          |   60 +++--
 R/score_rmse.R                            |   21 +-
 R/score_rroc.R                            |   21 +-
 R/score_runs.R                            |   21 +-
 R/score_specificity.R                     |   61 +++---
 R/support_function_plot.R                 |    3 
 R/theme_drwhy.R                           |   13 -
 inst/CITATION                             |   21 --
 inst/doc/model_evaluation_audit.R         |   45 ++--
 inst/doc/model_evaluation_audit.Rmd       |   33 +--
 inst/doc/model_evaluation_audit.html      |   53 ++---
 inst/doc/model_fit_audit.R                |   14 -
 inst/doc/model_fit_audit.html             |    6 
 inst/doc/model_performance_audit.R        |   14 -
 inst/doc/model_performance_audit.html     |   47 +++-
 inst/doc/model_residuals_audit.R          |   46 ++--
 inst/doc/model_residuals_audit.Rmd        |    1 
 inst/doc/model_residuals_audit.html       |   32 +--
 inst/doc/observation_influence_audit.R    |   12 -
 inst/doc/observation_influence_audit.html |    2 
 man/audit.Rd                              |   55 ++---
 man/check_residuals.Rd                    |   16 -
 man/check_residuals_autocorrelation.Rd    |    6 
 man/check_residuals_outliers.Rd           |    6 
 man/figures/demo.png                      |only
 man/figures/logo.png                      |binary
 man/model_cooksdistance.Rd                |   20 +
 man/model_evaluation.Rd                   |   21 +-
 man/model_halfnormal.Rd                   |   21 +-
 man/model_performance.Rd                  |   32 ++-
 man/model_residual.Rd                     |   29 +-
 man/plot.Rd                               |   55 ++---
 man/plotD3.Rd                             |   26 +-
 man/plotD3_acf.Rd                         |   16 -
 man/plotD3_autocorrelation.Rd             |   38 ++-
 man/plotD3_cooksdistance.Rd               |   30 +-
 man/plotD3_halfnormal.Rd                  |   14 -
 man/plotD3_lift.Rd                        |   28 +-
 man/plotD3_prediction.Rd                  |   44 ++--
 man/plotD3_rec.Rd                         |   12 -
 man/plotD3_residual.Rd                    |   45 +++-
 man/plotD3_roc.Rd                         |   37 ++-
 man/plotD3_rroc.Rd                        |    9 
 man/plotD3_scalelocation.Rd               |   52 +++--
 man/plot_acf.Rd                           |   14 -
 man/plot_autocorrelation.Rd               |   10 
 man/plot_cooksdistance.Rd                 |    9 
 man/plot_correlation.Rd                   |   13 -
 man/plot_halfnormal.Rd                    |   10 
 man/plot_lift.Rd                          |   26 +-
 man/plot_pca.Rd                           |   18 -
 man/plot_prediction.Rd                    |   24 --
 man/plot_radar.Rd                         |   19 -
 man/plot_rec.Rd                           |    9 
 man/plot_residual.Rd                      |   38 ++-
 man/plot_residual_boxplot.Rd              |   18 -
 man/plot_residual_density.Rd              |   20 -
 man/plot_roc.Rd                           |   71 +++++-
 man/plot_rroc.Rd                          |   10 
 man/plot_scalelocation.Rd                 |   26 +-
 man/plot_tsecdf.Rd                        |   32 ++-
 man/print.auditor_model_cooksdistance.Rd  |    4 
 man/print.auditor_model_evaluation.Rd     |   14 -
 man/print.auditor_model_halfnormal.Rd     |   12 -
 man/print.auditor_model_performance.Rd    |   14 -
 man/print.auditor_model_residual.Rd       |   13 -
 man/print.auditor_score.Rd                |   14 -
 man/score.Rd                              |    5 
 man/score_acc.Rd                          |   25 +-
 man/score_auc.Rd                          |   22 +-
 man/score_auprc.Rd                        |only
 man/score_cooksdistance.Rd                |    4 
 man/score_dw.Rd                           |   16 -
 man/score_f1.Rd                           |   26 +-
 man/score_gini.Rd                         |   21 +-
 man/score_halfnormal.Rd                   |   12 -
 man/score_mae.Rd                          |   14 -
 man/score_mse.Rd                          |   15 -
 man/score_one_minus_acc.Rd                |   26 +-
 man/score_one_minus_auc.Rd                |   23 +-
 man/score_one_minus_auprc.Rd              |only
 man/score_one_minus_f1.Rd                 |   25 +-
 man/score_one_minus_gini.Rd               |   22 +-
 man/score_one_minus_precision.Rd          |   24 +-
 man/score_one_minus_recall.Rd             |   24 +-
 man/score_one_minus_specificity.Rd        |   26 +-
 man/score_peak.Rd                         |   17 +
 man/score_precision.Rd                    |   25 +-
 man/score_r2.Rd                           |   15 -
 man/score_rec.Rd                          |   17 +
 man/score_recall.Rd                       |   26 +-
 man/score_rmse.Rd                         |   14 -
 man/score_rroc.Rd                         |   14 -
 man/score_runs.Rd                         |   14 -
 man/score_specificity.Rd                  |   23 +-
 tests/testthat/test_scores.R              |    7 
 vignettes/model_evaluation_audit.Rmd      |   33 +--
 vignettes/model_residuals_audit.Rmd       |    1 
 156 files changed, 2144 insertions(+), 1728 deletions(-)

More information about auditor at CRAN
Permanent link

Package seewave updated to version 2.1.6 with previous version 2.1.5 dated 2019-12-06

Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.
Author: Jerome Sueur <sueur@mnhn.fr> [cre, au], Thierry Aubin [au], Caroline Simonis [au], Laurent Lellouch [main ctrb], Ethan C. Brown [ctrb], Marion Depraetere [ctrb], Camille Desjonqueres [ctrb], Francois Fabianek [ctrb], Amandine Gasc [ctrb], Eric Kasten [ctrb], Stefanie LaZerte [ctrb], Jonathan Lees [ctrb], Jean Marchal [ctrb], Andre Mikulec [ctrb], Sandrine Pavoine [ctrb], David Pinaud [ctrb], Alicia Stotz [ctrb], Luis J. Villanueva-Rivera [ctrb], Zev Ross [ctrb], Carl G. Witthoft [ctrb], Hristo Zhivomirov [ctrb].
Maintainer: Jerome Sueur <sueur@mnhn.fr>

Diff between seewave versions 2.1.5 dated 2019-12-06 and 2.1.6 dated 2020-05-28

 DESCRIPTION                   |   13 
 MD5                           |   44 +-
 NEWS                          |   20 +
 R/seewave.r                   |  639 ++++++++++++++++++++++++++++++++----------
 build/vignette.rds            |binary
 inst/doc/seewave_IO.R         |    1 
 inst/doc/seewave_IO.pdf       |binary
 inst/doc/seewave_analysis.R   |    1 
 inst/doc/seewave_analysis.pdf |binary
 man/ACI.Rd                    |    2 
 man/audiomoth.Rd              |only
 man/audiomoth.rename.Rd       |only
 man/beep.Rd                   |only
 man/gammatone.Rd              |only
 man/lts.Rd                    |   17 -
 man/melfilterbank.Rd          |    2 
 man/pastew.Rd                 |    5 
 man/read.audacity.Rd          |only
 man/seewave.internal.Rd       |    1 
 man/seewave.package.Rd        |    9 
 man/songmeter.Rd              |   31 +-
 man/specflux.Rd               |only
 man/spectro.Rd                |   10 
 man/spectro3D.Rd              |    3 
 man/synth.Rd                  |   10 
 man/timelapse.Rd              |only
 man/write.audacity.Rd         |only
 27 files changed, 604 insertions(+), 204 deletions(-)

More information about seewave at CRAN
Permanent link

Package gtfs2gps updated to version 1.2-0 with previous version 1.1-0 dated 2020-04-12

Title: Converting Transport Data from GTFS Format to GPS-Like Records
Description: Convert general transit feed specification (GTFS) data to global positioning system (GPS) records in 'data.table' format. It also has some functions to subset GTFS data in time and space and to convert both representations to simple feature format.
Author: Rafael H. M. Pereira [aut] (<https://orcid.org/0000-0003-2125-7465>), Pedro R. Andrade [aut, cre] (<https://orcid.org/0000-0001-8675-4046>), Joao Bazzo [aut] (<https://orcid.org/0000-0003-4536-5006>), Marcin Stepniak [ctb], Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro R. Andrade <pedro.andrade@inpe.br>

Diff between gtfs2gps versions 1.1-0 dated 2020-04-12 and 1.2-0 dated 2020-05-28

 gtfs2gps-1.1-0/gtfs2gps/R/gps_as_sf.R                             |only
 gtfs2gps-1.1-0/gtfs2gps/man/gps_as_sf.Rd                          |only
 gtfs2gps-1.1-0/gtfs2gps/tests/testthat/test_gps_as_sf.R           |only
 gtfs2gps-1.2-0/gtfs2gps/DESCRIPTION                               |   14 
 gtfs2gps-1.2-0/gtfs2gps/MD5                                       |   68 
 gtfs2gps-1.2-0/gtfs2gps/NAMESPACE                                 |   10 
 gtfs2gps-1.2-0/gtfs2gps/R/append_height.R                         |    3 
 gtfs2gps-1.2-0/gtfs2gps/R/filter_gtfs.R                           |  279 ++-
 gtfs2gps-1.2-0/gtfs2gps/R/gps_as_sflinestring.R                   |only
 gtfs2gps-1.2-0/gtfs2gps/R/gps_as_sfpoints.R                       |only
 gtfs2gps-1.2-0/gtfs2gps/R/gtfs2gps.R                              |   22 
 gtfs2gps-1.2-0/gtfs2gps/R/merge_gtfs_feeds.R                      |only
 gtfs2gps-1.2-0/gtfs2gps/R/mod_updates.R                           |   30 
 gtfs2gps-1.2-0/gtfs2gps/R/read_gtfs.R                             |   40 
 gtfs2gps-1.2-0/gtfs2gps/R/simplify_shapes.R                       |only
 gtfs2gps-1.2-0/gtfs2gps/R/test_gtfs_freq.R                        |    4 
 gtfs2gps-1.2-0/gtfs2gps/R/zzz.R                                   |    5 
 gtfs2gps-1.2-0/gtfs2gps/build/vignette.rds                        |binary
 gtfs2gps-1.2-0/gtfs2gps/inst/doc/intro_to_gtfs2gps.R              |   30 
 gtfs2gps-1.2-0/gtfs2gps/inst/doc/intro_to_gtfs2gps.Rmd            |   34 
 gtfs2gps-1.2-0/gtfs2gps/inst/doc/intro_to_gtfs2gps.html           |  700 +++++++++-
 gtfs2gps-1.2-0/gtfs2gps/inst/extdata/warsaw.zip                   |only
 gtfs2gps-1.2-0/gtfs2gps/man/append_height.Rd                      |    3 
 gtfs2gps-1.2-0/gtfs2gps/man/filter_by_agency_id.Rd                |    5 
 gtfs2gps-1.2-0/gtfs2gps/man/filter_by_route_id.Rd                 |only
 gtfs2gps-1.2-0/gtfs2gps/man/filter_by_route_type.Rd               |only
 gtfs2gps-1.2-0/gtfs2gps/man/filter_by_shape_id.Rd                 |    5 
 gtfs2gps-1.2-0/gtfs2gps/man/filter_single_trip.Rd                 |    5 
 gtfs2gps-1.2-0/gtfs2gps/man/filter_valid_stop_times.Rd            |    5 
 gtfs2gps-1.2-0/gtfs2gps/man/filter_week_days.Rd                   |    5 
 gtfs2gps-1.2-0/gtfs2gps/man/gps_as_sflinestring.Rd                |only
 gtfs2gps-1.2-0/gtfs2gps/man/gps_as_sfpoints.Rd                    |only
 gtfs2gps-1.2-0/gtfs2gps/man/merge_gtfs_feeds.Rd                   |only
 gtfs2gps-1.2-0/gtfs2gps/man/read_gtfs.Rd                          |    5 
 gtfs2gps-1.2-0/gtfs2gps/man/remove_invalid.Rd                     |   21 
 gtfs2gps-1.2-0/gtfs2gps/man/simplify_shapes.Rd                    |only
 gtfs2gps-1.2-0/gtfs2gps/tests/testthat/test_append_height.R       |    3 
 gtfs2gps-1.2-0/gtfs2gps/tests/testthat/test_filter_gtfs.R         |   67 
 gtfs2gps-1.2-0/gtfs2gps/tests/testthat/test_gps_as_sflinestring.R |only
 gtfs2gps-1.2-0/gtfs2gps/tests/testthat/test_gps_as_sfpoints.R     |only
 gtfs2gps-1.2-0/gtfs2gps/tests/testthat/test_merge_gtfs_feeds.R    |only
 gtfs2gps-1.2-0/gtfs2gps/tests/testthat/test_read_gtfs.R           |   15 
 gtfs2gps-1.2-0/gtfs2gps/tests/testthat/test_simplify_shapes.R     |only
 gtfs2gps-1.2-0/gtfs2gps/vignettes/intro_to_gtfs2gps.Rmd           |   34 
 44 files changed, 1134 insertions(+), 278 deletions(-)

More information about gtfs2gps at CRAN
Permanent link

Package DJL updated to version 3.4 with previous version 3.3 dated 2020-04-29

Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the Econometrics & Technometrics. Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, Malmquist productivity analysis, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, Ph.D. <technometrics.org>
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>

Diff between DJL versions 3.3 dated 2020-04-29 and 3.4 dated 2020-05-28

 DESCRIPTION            |   10 +++++-----
 MD5                    |    8 ++++----
 NEWS                   |   11 +++++++++++
 R/target.spec.dea.R    |   47 +++++++++++++++++++++++++++--------------------
 man/target.spec.dea.Rd |    3 ++-
 5 files changed, 49 insertions(+), 30 deletions(-)

More information about DJL at CRAN
Permanent link

Package tidyjson updated to version 0.3.0 with previous version 0.2.4 dated 2019-12-02

Title: Tidy Complex 'JSON'
Description: Turn complex 'JSON' data into tidy data frames.
Author: Jeremy Stanley [aut], Cole Arendt [aut, cre]
Maintainer: Cole Arendt <cole@rstudio.com>

Diff between tidyjson versions 0.2.4 dated 2019-12-02 and 0.3.0 dated 2020-05-28

 tidyjson-0.2.4/tidyjson/inst/doc/multiple-apis.R               |only
 tidyjson-0.2.4/tidyjson/inst/doc/multiple-apis.Rmd             |only
 tidyjson-0.2.4/tidyjson/inst/doc/multiple-apis.html            |only
 tidyjson-0.2.4/tidyjson/vignettes/multiple-apis.Rmd            |only
 tidyjson-0.3.0/tidyjson/DESCRIPTION                            |   17 
 tidyjson-0.3.0/tidyjson/MD5                                    |  123 -
 tidyjson-0.3.0/tidyjson/NAMESPACE                              |   10 
 tidyjson-0.3.0/tidyjson/NEWS.md                                |   34 
 tidyjson-0.3.0/tidyjson/R/append_values.R                      |   18 
 tidyjson-0.3.0/tidyjson/R/enter_object.R                       |    2 
 tidyjson-0.3.0/tidyjson/R/gather.R                             |    3 
 tidyjson-0.3.0/tidyjson/R/is_json.R                            |    1 
 tidyjson-0.3.0/tidyjson/R/json_complexity.R                    |    2 
 tidyjson-0.3.0/tidyjson/R/json_lengths.R                       |    2 
 tidyjson-0.3.0/tidyjson/R/json_schema.R                        |   14 
 tidyjson-0.3.0/tidyjson/R/json_structure.R                     |    6 
 tidyjson-0.3.0/tidyjson/R/json_types.R                         |    3 
 tidyjson-0.3.0/tidyjson/R/path.R                               |    1 
 tidyjson-0.3.0/tidyjson/R/spread_all.R                         |    8 
 tidyjson-0.3.0/tidyjson/R/spread_values.R                      |    3 
 tidyjson-0.3.0/tidyjson/R/tbl_json.R                           |  254 ++-
 tidyjson-0.3.0/tidyjson/R/tidyjson-package.R                   |    7 
 tidyjson-0.3.0/tidyjson/R/utils.R                              |    3 
 tidyjson-0.3.0/tidyjson/README.md                              |  140 +-
 tidyjson-0.3.0/tidyjson/build/vignette.rds                     |binary
 tidyjson-0.3.0/tidyjson/inst/doc/introduction-to-tidyjson.R    |   48 
 tidyjson-0.3.0/tidyjson/inst/doc/introduction-to-tidyjson.html |  412 +++---
 tidyjson-0.3.0/tidyjson/inst/doc/visualizing-json.R            |   50 
 tidyjson-0.3.0/tidyjson/inst/doc/visualizing-json.Rmd          |   12 
 tidyjson-0.3.0/tidyjson/inst/doc/visualizing-json.html         |  670 +++++-----
 tidyjson-0.3.0/tidyjson/inst/json_array.gif                    |only
 tidyjson-0.3.0/tidyjson/inst/json_object.gif                   |only
 tidyjson-0.3.0/tidyjson/inst/json_value.gif                    |only
 tidyjson-0.3.0/tidyjson/man/allowed_json_types.Rd              |    4 
 tidyjson-0.3.0/tidyjson/man/append_values.Rd                   |   12 
 tidyjson-0.3.0/tidyjson/man/append_values_factory.Rd           |    1 
 tidyjson-0.3.0/tidyjson/man/append_values_type.Rd              |    1 
 tidyjson-0.3.0/tidyjson/man/as_tibble.Rd                       |    1 
 tidyjson-0.3.0/tidyjson/man/as_tibble.tbl_json.Rd              |    4 
 tidyjson-0.3.0/tidyjson/man/bind_rows.Rd                       |   39 
 tidyjson-0.3.0/tidyjson/man/commits.Rd                         |    4 
 tidyjson-0.3.0/tidyjson/man/companies.Rd                       |    4 
 tidyjson-0.3.0/tidyjson/man/determine_types.Rd                 |    1 
 tidyjson-0.3.0/tidyjson/man/gather_factory.Rd                  |    9 
 tidyjson-0.3.0/tidyjson/man/has_names.Rd                       |    1 
 tidyjson-0.3.0/tidyjson/man/is_data_list.Rd                    |    1 
 tidyjson-0.3.0/tidyjson/man/is_json_factory.Rd                 |    1 
 tidyjson-0.3.0/tidyjson/man/issues.Rd                          |    4 
 tidyjson-0.3.0/tidyjson/man/json_factory.Rd                    |    1 
 tidyjson-0.3.0/tidyjson/man/json_get.Rd                        |only
 tidyjson-0.3.0/tidyjson/man/json_get_column.Rd                 |only
 tidyjson-0.3.0/tidyjson/man/json_schema.Rd                     |    8 
 tidyjson-0.3.0/tidyjson/man/json_structure.Rd                  |   16 
 tidyjson-0.3.0/tidyjson/man/list_or_dots.Rd                    |    1 
 tidyjson-0.3.0/tidyjson/man/my_unlist.Rd                       |    1 
 tidyjson-0.3.0/tidyjson/man/path.Rd                            |    1 
 tidyjson-0.3.0/tidyjson/man/tbl_json.Rd                        |   14 
 tidyjson-0.3.0/tidyjson/man/tidyjson.Rd                        |    6 
 tidyjson-0.3.0/tidyjson/man/worldbank.Rd                       |    4 
 tidyjson-0.3.0/tidyjson/man/wrap_dplyr_verb.Rd                 |    5 
 tidyjson-0.3.0/tidyjson/tests/testthat/test-append_values.R    |   20 
 tidyjson-0.3.0/tidyjson/tests/testthat/test-gather_object.R    |   18 
 tidyjson-0.3.0/tidyjson/tests/testthat/test-json_structure.R   |   25 
 tidyjson-0.3.0/tidyjson/tests/testthat/test-read_json.R        |    8 
 tidyjson-0.3.0/tidyjson/tests/testthat/test-spread_all.R       |   14 
 tidyjson-0.3.0/tidyjson/tests/testthat/test-tbl_json.R         |  214 ++-
 tidyjson-0.3.0/tidyjson/vignettes/visualizing-json.Rmd         |   12 
 67 files changed, 1359 insertions(+), 939 deletions(-)

More information about tidyjson at CRAN
Permanent link

Package dmdScheme updated to version 1.1.3 with previous version 1.1.2 dated 2020-04-30

Title: Domain Specific MetaData Scheme
Description: Forms the core for developing own domain specific metadata schemes. It contains the basic functionality needed for all metadata schemes based on the 'dmdScheme'. See R.M. Krug and O.L. Petchey (2019) <DOI:10.5281/zenodo.3581970>.
Author: Rainer M. Krug [aut, cre] (<https://orcid.org/0000-0002-7490-0066>), Owen L. Petchey [ctb] (<https://orcid.org/0000-0002-7724-1633>)
Maintainer: Rainer M. Krug <Rainer.Krug@uzh.ch>

Diff between dmdScheme versions 1.1.2 dated 2020-04-30 and 1.1.3 dated 2020-05-28

 DESCRIPTION                                  |    6 +++---
 MD5                                          |   10 +++++-----
 R/validate_func.R                            |   13 +++++++++++++
 inst/doc/Howto_create_new_scheme.html        |   10 +++++-----
 inst/doc/minimum_requirements_dmdscheme.html |    4 ++--
 inst/doc/r_package_introduction.html         |   14 +++++++-------
 6 files changed, 35 insertions(+), 22 deletions(-)

More information about dmdScheme at CRAN
Permanent link

Package AMR updated to version 1.2.0 with previous version 1.1.0 dated 2020-04-15

Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods, like those defined by Leclercq et al. (2013) <doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory Standards Institute (2014) <isbn: 1-56238-899-1>.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>), Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>), Alexander W. Friedrich [aut, ths] (<https://orcid.org/0000-0003-4881-038X>), Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>), Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>), Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>), Judith M. Fonville [ctb], Erwin E. A. Hassing [ctb], Eric H. L. C. M. Hazenberg [ctb], Annick Lenglet [ctb], Bart C. Meijer [ctb], Sofia Ny [ctb], Dennis Souverein [ctb]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

Diff between AMR versions 1.1.0 dated 2020-04-15 and 1.2.0 dated 2020-05-28

 AMR-1.1.0/AMR/R/extended.R                          |only
 AMR-1.1.0/AMR/R/freq.R                              |only
 AMR-1.1.0/AMR/R/progress_estimated.R                |only
 AMR-1.1.0/AMR/R/read.4d.R                           |only
 AMR-1.1.0/AMR/data/datalist                         |only
 AMR-1.1.0/AMR/man/extended-functions.Rd             |only
 AMR-1.1.0/AMR/man/read.4D.Rd                        |only
 AMR-1.1.0/AMR/man/reexports.Rd                      |only
 AMR-1.1.0/AMR/tests/testthat/test-extended.R        |only
 AMR-1.1.0/AMR/tests/testthat/test-freq.R            |only
 AMR-1.1.0/AMR/tests/testthat/test-read.4d.R         |only
 AMR-1.2.0/AMR/DESCRIPTION                           |   20 
 AMR-1.2.0/AMR/MD5                                   |  264 ++--
 AMR-1.2.0/AMR/NAMESPACE                             |  168 --
 AMR-1.2.0/AMR/NEWS.md                               |   40 
 AMR-1.2.0/AMR/R/aa_helper_functions.R               |  287 ++++
 AMR-1.2.0/AMR/R/aa_helper_functions_dplyr.R         |only
 AMR-1.2.0/AMR/R/ab.R                                |   52 
 AMR-1.2.0/AMR/R/ab_property.R                       |   34 
 AMR-1.2.0/AMR/R/age.R                               |    3 
 AMR-1.2.0/AMR/R/amr.R                               |    2 
 AMR-1.2.0/AMR/R/atc_online.R                        |   50 
 AMR-1.2.0/AMR/R/availability.R                      |    3 
 AMR-1.2.0/AMR/R/bug_drug_combinations.R             |  135 +-
 AMR-1.2.0/AMR/R/catalogue_of_life.R                 |   24 
 AMR-1.2.0/AMR/R/count.R                             |   73 -
 AMR-1.2.0/AMR/R/data.R                              |   26 
 AMR-1.2.0/AMR/R/deprecated.R                        |    7 
 AMR-1.2.0/AMR/R/disk.R                              |   60 
 AMR-1.2.0/AMR/R/eucast_rules.R                      |  280 ++--
 AMR-1.2.0/AMR/R/filter_ab_class.R                   |   82 -
 AMR-1.2.0/AMR/R/first_isolate.R                     |  307 ++---
 AMR-1.2.0/AMR/R/ggplot_pca.R                        |   48 
 AMR-1.2.0/AMR/R/ggplot_rsi.R                        |  116 -
 AMR-1.2.0/AMR/R/globals.R                           |    6 
 AMR-1.2.0/AMR/R/guess_ab_col.R                      |   42 
 AMR-1.2.0/AMR/R/join_microorganisms.R               |   22 
 AMR-1.2.0/AMR/R/key_antibiotics.R                   |   71 -
 AMR-1.2.0/AMR/R/kurtosis.R                          |    7 
 AMR-1.2.0/AMR/R/lifecycle.R                         |   24 
 AMR-1.2.0/AMR/R/like.R                              |   38 
 AMR-1.2.0/AMR/R/mdro.R                              |  213 +--
 AMR-1.2.0/AMR/R/mic.R                               |   59 
 AMR-1.2.0/AMR/R/mo.R                                | 1209 ++++++++------------
 AMR-1.2.0/AMR/R/mo_property.R                       |   38 
 AMR-1.2.0/AMR/R/mo_source.R                         |  149 +-
 AMR-1.2.0/AMR/R/pca.R                               |   39 
 AMR-1.2.0/AMR/R/proportion.R                        |  139 +-
 AMR-1.2.0/AMR/R/resistance_predict.R                |  163 +-
 AMR-1.2.0/AMR/R/rsi.R                               |  159 +-
 AMR-1.2.0/AMR/R/rsi_calc.R                          |  203 +--
 AMR-1.2.0/AMR/R/rsi_df.R                            |   32 
 AMR-1.2.0/AMR/R/skewness.R                          |    7 
 AMR-1.2.0/AMR/R/sysdata.rda                         |binary
 AMR-1.2.0/AMR/R/translate.R                         |   21 
 AMR-1.2.0/AMR/R/zzz.R                               |   85 -
 AMR-1.2.0/AMR/README.md                             |   32 
 AMR-1.2.0/AMR/build/vignette.rds                    |binary
 AMR-1.2.0/AMR/data/antibiotics.rda                  |binary
 AMR-1.2.0/AMR/data/example_isolates.rda             |binary
 AMR-1.2.0/AMR/data/microorganisms.codes.rda         |binary
 AMR-1.2.0/AMR/data/microorganisms.old.rda           |binary
 AMR-1.2.0/AMR/data/microorganisms.rda               |binary
 AMR-1.2.0/AMR/data/rsi_translation.rda              |binary
 AMR-1.2.0/AMR/inst/doc/AMR.R                        |   25 
 AMR-1.2.0/AMR/inst/doc/AMR.Rmd                      |   41 
 AMR-1.2.0/AMR/inst/doc/AMR.html                     |  769 ++++++------
 AMR-1.2.0/AMR/inst/doc/EUCAST.Rmd                   |    2 
 AMR-1.2.0/AMR/inst/doc/EUCAST.html                  |   86 -
 AMR-1.2.0/AMR/inst/doc/MDR.R                        |    4 
 AMR-1.2.0/AMR/inst/doc/MDR.Rmd                      |    4 
 AMR-1.2.0/AMR/inst/doc/MDR.html                     |  191 +--
 AMR-1.2.0/AMR/inst/doc/PCA.R                        |    1 
 AMR-1.2.0/AMR/inst/doc/PCA.Rmd                      |    1 
 AMR-1.2.0/AMR/inst/doc/PCA.html                     |  207 +--
 AMR-1.2.0/AMR/inst/doc/WHONET.R                     |    1 
 AMR-1.2.0/AMR/inst/doc/WHONET.Rmd                   |    3 
 AMR-1.2.0/AMR/inst/doc/WHONET.html                  |   86 -
 AMR-1.2.0/AMR/inst/doc/resistance_predict.Rmd       |    4 
 AMR-1.2.0/AMR/inst/doc/resistance_predict.html      |  191 +--
 AMR-1.2.0/AMR/man/AMR-deprecated.Rd                 |    5 
 AMR-1.2.0/AMR/man/ab_property.Rd                    |   16 
 AMR-1.2.0/AMR/man/age.Rd                            |    4 
 AMR-1.2.0/AMR/man/age_groups.Rd                     |    4 
 AMR-1.2.0/AMR/man/antibiotics.Rd                    |    2 
 AMR-1.2.0/AMR/man/as.ab.Rd                          |    2 
 AMR-1.2.0/AMR/man/as.disk.Rd                        |    6 
 AMR-1.2.0/AMR/man/as.mic.Rd                         |    5 
 AMR-1.2.0/AMR/man/as.mo.Rd                          |    7 
 AMR-1.2.0/AMR/man/as.rsi.Rd                         |   17 
 AMR-1.2.0/AMR/man/atc_online.Rd                     |    4 
 AMR-1.2.0/AMR/man/availability.Rd                   |    6 
 AMR-1.2.0/AMR/man/bug_drug_combinations.Rd          |    4 
 AMR-1.2.0/AMR/man/catalogue_of_life.Rd              |   10 
 AMR-1.2.0/AMR/man/catalogue_of_life_version.Rd      |    5 
 AMR-1.2.0/AMR/man/count.Rd                          |   74 -
 AMR-1.2.0/AMR/man/eucast_rules.Rd                   |   12 
 AMR-1.2.0/AMR/man/filter_ab_class.Rd                |   10 
 AMR-1.2.0/AMR/man/first_isolate.Rd                  |   18 
 AMR-1.2.0/AMR/man/g.test.Rd                         |    2 
 AMR-1.2.0/AMR/man/ggplot_pca.Rd                     |    6 
 AMR-1.2.0/AMR/man/ggplot_rsi.Rd                     |  103 -
 AMR-1.2.0/AMR/man/guess_ab_col.Rd                   |    2 
 AMR-1.2.0/AMR/man/join.Rd                           |   12 
 AMR-1.2.0/AMR/man/key_antibiotics.Rd                |   11 
 AMR-1.2.0/AMR/man/kurtosis.Rd                       |    2 
 AMR-1.2.0/AMR/man/lifecycle.Rd                      |   28 
 AMR-1.2.0/AMR/man/like.Rd                           |   21 
 AMR-1.2.0/AMR/man/mdro.Rd                           |    5 
 AMR-1.2.0/AMR/man/microorganisms.Rd                 |   15 
 AMR-1.2.0/AMR/man/microorganisms.codes.Rd           |    4 
 AMR-1.2.0/AMR/man/microorganisms.old.Rd             |    7 
 AMR-1.2.0/AMR/man/mo_property.Rd                    |   10 
 AMR-1.2.0/AMR/man/mo_source.Rd                      |   42 
 AMR-1.2.0/AMR/man/p_symbol.Rd                       |    2 
 AMR-1.2.0/AMR/man/pca.Rd                            |    6 
 AMR-1.2.0/AMR/man/proportion.Rd                     |  140 +-
 AMR-1.2.0/AMR/man/resistance_predict.Rd             |   33 
 AMR-1.2.0/AMR/man/skewness.Rd                       |    2 
 AMR-1.2.0/AMR/man/translate.Rd                      |   10 
 AMR-1.2.0/AMR/tests/testthat/Rplots.pdf             |binary
 AMR-1.2.0/AMR/tests/testthat/test-ab.R              |    6 
 AMR-1.2.0/AMR/tests/testthat/test-ab_property.R     |    3 
 AMR-1.2.0/AMR/tests/testthat/test-count.R           |    2 
 AMR-1.2.0/AMR/tests/testthat/test-data.R            |   20 
 AMR-1.2.0/AMR/tests/testthat/test-deprecated.R      |    3 
 AMR-1.2.0/AMR/tests/testthat/test-eucast_rules.R    |   44 
 AMR-1.2.0/AMR/tests/testthat/test-filter_ab_class.R |    5 
 AMR-1.2.0/AMR/tests/testthat/test-first_isolate.R   |  106 -
 AMR-1.2.0/AMR/tests/testthat/test-mdro.R            |  148 +-
 AMR-1.2.0/AMR/tests/testthat/test-mo.R              |   19 
 AMR-1.2.0/AMR/tests/testthat/test-mo_property.R     |   21 
 AMR-1.2.0/AMR/tests/testthat/test-pca.R             |   21 
 AMR-1.2.0/AMR/vignettes/AMR.Rmd                     |   41 
 AMR-1.2.0/AMR/vignettes/EUCAST.Rmd                  |    2 
 AMR-1.2.0/AMR/vignettes/MDR.Rmd                     |    4 
 AMR-1.2.0/AMR/vignettes/PCA.Rmd                     |    1 
 AMR-1.2.0/AMR/vignettes/WHONET.Rmd                  |    3 
 AMR-1.2.0/AMR/vignettes/resistance_predict.Rmd      |    4 
 139 files changed, 3750 insertions(+), 3832 deletions(-)

More information about AMR at CRAN
Permanent link

Package precrec updated to version 0.11.2 with previous version 0.11.1 dated 2020-05-15

Title: Calculate Accurate Precision-Recall and ROC (Receiver Operator Characteristics) Curves
Description: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.
Author: Takaya Saito [aut, cre], Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>

Diff between precrec versions 0.11.1 dated 2020-05-15 and 0.11.2 dated 2020-05-28

 DESCRIPTION                              |    8 -
 MD5                                      |   12 +-
 NEWS.md                                  |    4 
 R/mm4_format_nfold.R                     |    9 +
 inst/doc/introduction.html               |  160 +++++++++++++++----------------
 tests/testthat/test_mm4_1_format_nfold.R |   28 +----
 tests/testthat/test_uc1_usecases.R       |   38 +++++++
 7 files changed, 150 insertions(+), 109 deletions(-)

More information about precrec at CRAN
Permanent link

Package blorr updated to version 0.3.0 with previous version 0.2.2 dated 2020-02-03

Title: Tools for Developing Binary Logistic Regression Models
Description: Tools designed to make it easier for beginner and intermediate users to build and validate binary logistic regression models. Includes bivariate analysis, comprehensive regression output, model fit statistics, variable selection procedures, model validation techniques and a 'shiny' app for interactive model building.
Author: Aravind Hebbali [aut, cre] (<https://orcid.org/0000-0001-9220-9669>)
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>

Diff between blorr versions 0.2.2 dated 2020-02-03 and 0.3.0 dated 2020-05-28

 DESCRIPTION                                               |   17 
 MD5                                                       |  219 ++---
 NAMESPACE                                                 |   66 -
 NEWS.md                                                   |    4 
 R/blr-backward-elimination.R                              |  155 +---
 R/blr-bivariate-analysis.R                                |  218 ++---
 R/blr-collinearity-diagnostics.R                          |  106 --
 R/blr-error-messages.R                                    |   64 -
 R/blr-forward-selection.R                                 |  120 +--
 R/blr-gains-table.R                                       |  193 ++---
 R/blr-hosmer-lemeshow-test.R                              |  107 +-
 R/blr-launch-app.R                                        |    1 
 R/blr-linktest.R                                          |   24 
 R/blr-lorenz-curve.R                                      |   46 -
 R/blr-lrtest.R                                            |   42 -
 R/blr-model-fit-stats.R                                   |  139 ---
 R/blr-model-validation.R                                  |  110 ++
 R/blr-multi-model-fit-stats.R                             |   35 
 R/blr-output.R                                            |  469 ++----------
 R/blr-pairs.R                                             |   44 -
 R/blr-plots-data.R                                        |  142 +--
 R/blr-plots.R                                             |   80 --
 R/blr-regress-compute.R                                   |   19 
 R/blr-regress.R                                           |    5 
 R/blr-residual-diagnostics.R                              |   77 +-
 R/blr-roc-curve.R                                         |   22 
 R/blr-stepwise-backward-regression.R                      |   41 -
 R/blr-stepwise-forward-regression.R                       |   51 -
 R/blr-stepwise-regression.R                               |  104 --
 R/blr-stepwise-selection.R                                |   49 -
 R/blr-utils.R                                             |  147 ---
 R/blr-woe-iv.R                                            |  123 +--
 R/zzz.R                                                   |   11 
 README.md                                                 |   87 --
 build/vignette.rds                                        |binary
 inst/doc/introduction.R                                   |   52 -
 inst/doc/introduction.html                                |  300 +++-----
 man/bank_marketing.Rd                                     |    6 
 man/blorr.Rd                                              |    1 
 man/blr_bivariate_analysis.Rd                             |   14 
 man/blr_confusion_matrix.Rd                               |   25 
 man/blr_decile_capture_rate.Rd                            |   31 
 man/blr_decile_lift_chart.Rd                              |   30 
 man/blr_gains_table.Rd                                    |   33 
 man/blr_gini_index.Rd                                     |   17 
 man/blr_ks_chart.Rd                                       |   29 
 man/blr_linktest.Rd                                       |    2 
 man/blr_lorenz_curve.Rd                                   |   30 
 man/blr_model_fit_stats.Rd                                |   18 
 man/blr_multi_model_fit_stats.Rd                          |   18 
 man/blr_pairs.Rd                                          |   19 
 man/blr_plot_c_fitted.Rd                                  |    8 
 man/blr_plot_c_leverage.Rd                                |    8 
 man/blr_plot_deviance_fitted.Rd                           |   11 
 man/blr_plot_deviance_residual.Rd                         |   10 
 man/blr_plot_dfbetas_panel.Rd                             |    4 
 man/blr_plot_diag_c.Rd                                    |   10 
 man/blr_plot_diag_cbar.Rd                                 |   10 
 man/blr_plot_diag_difchisq.Rd                             |   10 
 man/blr_plot_diag_difdev.Rd                               |   10 
 man/blr_plot_diag_fit.Rd                                  |    9 
 man/blr_plot_diag_influence.Rd                            |    9 
 man/blr_plot_diag_leverage.Rd                             |    9 
 man/blr_plot_difchisq_fitted.Rd                           |    8 
 man/blr_plot_difchisq_leverage.Rd                         |    8 
 man/blr_plot_difdev_fitted.Rd                             |    8 
 man/blr_plot_difdev_leverage.Rd                           |   10 
 man/blr_plot_fitted_leverage.Rd                           |   10 
 man/blr_plot_leverage.Rd                                  |    9 
 man/blr_plot_leverage_fitted.Rd                           |   10 
 man/blr_plot_pearson_residual.Rd                          |   10 
 man/blr_plot_residual_fitted.Rd                           |    7 
 man/blr_roc_curve.Rd                                      |   36 
 man/blr_rsq_adj_count.Rd                                  |   18 
 man/blr_rsq_cox_snell.Rd                                  |   18 
 man/blr_rsq_effron.Rd                                     |   18 
 man/blr_rsq_mcfadden_adj.Rd                               |   18 
 man/blr_rsq_mckelvey_zavoina.Rd                           |   18 
 man/blr_rsq_nagelkerke.Rd                                 |   18 
 man/blr_segment.Rd                                        |   10 
 man/blr_segment_dist.Rd                                   |   25 
 man/blr_segment_twoway.Rd                                 |   13 
 man/blr_step_aic_backward.Rd                              |   23 
 man/blr_step_aic_both.Rd                                  |    9 
 man/blr_step_aic_forward.Rd                               |   23 
 man/blr_step_p_backward.Rd                                |   17 
 man/blr_step_p_both.Rd                                    |    7 
 man/blr_step_p_forward.Rd                                 |   16 
 man/blr_test_hosmer_lemeshow.Rd                           |   18 
 man/blr_test_lr.Rd                                        |   21 
 man/blr_woe_iv.Rd                                         |   28 
 man/blr_woe_iv_stats.Rd                                   |   12 
 man/hsb2.Rd                                               |    6 
 man/stepwise.Rd                                           |    4 
 tests/figs/test-blr-plots-r/ks-chart.svg                  |    4 
 tests/figs/test-blr-plots-r/segment-distribution-plot.svg |   72 -
 tests/testthat/test-backward-elimination.R                |   12 
 tests/testthat/test-bivariate-analysis.R                  |  123 +--
 tests/testthat/test-blr-gains-table.R                     |   13 
 tests/testthat/test-blr-lrtest.R                          |   13 
 tests/testthat/test-blr-pairs.R                           |    5 
 tests/testthat/test-blr-plots.R                           |  122 ---
 tests/testthat/test-coll-diag.R                           |   38 -
 tests/testthat/test-forward-selection.R                   |   12 
 tests/testthat/test-hosmer-lemeshow.R                     |    5 
 tests/testthat/test-linktest.R                            |   11 
 tests/testthat/test-model-fit-stats.R                     |   41 -
 tests/testthat/test-model-validation.R                    |only
 tests/testthat/test-stepwise-selection.R                  |  522 ++++++--------
 tests/testthat/test-utils.R                               |   38 -
 tools/README-kschart-1.png                                |binary
 111 files changed, 2330 insertions(+), 3027 deletions(-)

More information about blorr at CRAN
Permanent link

Package trelliscopejs updated to version 0.2.5 with previous version 0.2.4 dated 2020-02-10

Title: Create Interactive Trelliscope Displays
Description: Trelliscope is a scalable, flexible, interactive approach to visualizing data (Hafen, 2013 <doi:10.1109/LDAV.2013.6675164>). This package provides methods that make it easy to create a Trelliscope display specification for TrelliscopeJS. High-level functions are provided for creating displays from within 'tidyverse' or 'ggplot2' workflows. Low-level functions are also provided for creating new interfaces.
Author: Ryan Hafen [aut, cre] (<https://orcid.org/0000-0002-5516-8367>), Barret Schloerke [aut]
Maintainer: Ryan Hafen <rhafen@gmail.com>

Diff between trelliscopejs versions 0.2.4 dated 2020-02-10 and 0.2.5 dated 2020-05-28

 trelliscopejs-0.2.4/trelliscopejs/man/panel.Rd                      |only
 trelliscopejs-0.2.5/trelliscopejs/DESCRIPTION                       |   10 
 trelliscopejs-0.2.5/trelliscopejs/MD5                               |   51 +-
 trelliscopejs-0.2.5/trelliscopejs/NAMESPACE                         |    1 
 trelliscopejs-0.2.5/trelliscopejs/NEWS.md                           |    1 
 trelliscopejs-0.2.5/trelliscopejs/R/cog.R                           |   48 +-
 trelliscopejs-0.2.5/trelliscopejs/R/facet_trelliscope.R             |    3 
 trelliscopejs-0.2.5/trelliscopejs/R/helpers.R                       |   20 
 trelliscopejs-0.2.5/trelliscopejs/R/tidy.R                          |  117 ++---
 trelliscopejs-0.2.5/trelliscopejs/R/trelliscope.R                   |    2 
 trelliscopejs-0.2.5/trelliscopejs/build/vignette.rds                |binary
 trelliscopejs-0.2.5/trelliscopejs/inst/doc/trelliscopejs.R          |   22 -
 trelliscopejs-0.2.5/trelliscopejs/inst/doc/trelliscopejs.Rmd        |   44 +-
 trelliscopejs-0.2.5/trelliscopejs/inst/doc/trelliscopejs.html       |  210 +++++-----
 trelliscopejs-0.2.5/trelliscopejs/man/cog.Rd                        |   18 
 trelliscopejs-0.2.5/trelliscopejs/man/cog_href.Rd                   |   16 
 trelliscopejs-0.2.5/trelliscopejs/man/cogs.Rd                       |   21 -
 trelliscopejs-0.2.5/trelliscopejs/man/facet_trelliscope.Rd          |    4 
 trelliscopejs-0.2.5/trelliscopejs/man/map2_cog.Rd                   |   11 
 trelliscopejs-0.2.5/trelliscopejs/man/map2_plot.Rd                  |   22 -
 trelliscopejs-0.2.5/trelliscopejs/man/map_cog.Rd                    |   15 
 trelliscopejs-0.2.5/trelliscopejs/man/map_plot.Rd                   |   28 -
 trelliscopejs-0.2.5/trelliscopejs/man/mpg_labels.Rd                 |    4 
 trelliscopejs-0.2.5/trelliscopejs/man/panels.Rd                     |   12 
 trelliscopejs-0.2.5/trelliscopejs/man/trelliscope.Rd                |   53 --
 trelliscopejs-0.2.5/trelliscopejs/tests/testthat/test-trelliscope.R |  110 ++---
 trelliscopejs-0.2.5/trelliscopejs/vignettes/trelliscopejs.Rmd       |   44 +-
 27 files changed, 426 insertions(+), 461 deletions(-)

More information about trelliscopejs at CRAN
Permanent link

Package survminer updated to version 0.4.7 with previous version 0.4.6 dated 2019-09-03

Title: Drawing Survival Curves using 'ggplot2'
Description: Contains the function 'ggsurvplot()' for drawing easily beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot adjusted curves for `Cox` model and to visually examine 'Cox' model assumptions.
Author: Alboukadel Kassambara [aut, cre], Marcin Kosinski [aut], Przemyslaw Biecek [aut], Scheipl Fabian [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

Diff between survminer versions 0.4.6 dated 2019-09-03 and 0.4.7 dated 2020-05-28

 DESCRIPTION                                                                |   13 
 MD5                                                                        |   82 +-
 NAMESPACE                                                                  |    1 
 NEWS.md                                                                    |   77 +
 R/ggsurvplot_df.R                                                          |    2 
 R/surv_group_by.R                                                          |    5 
 R/utilities.R                                                              |    4 
 build/vignette.rds                                                         |binary
 inst/doc/Informative_Survival_Plots.Rmd                                    |    5 
 inst/doc/Informative_Survival_Plots.html                                   |  407 +++++++++-
 inst/doc/Playing_with_fonts_and_texts.html                                 |  401 +++++++++
 inst/doc/Specifiying_weights_in_log-rank_comparisons.html                  |  399 +++++++++
 man/BMT.Rd                                                                 |    6 
 man/BRCAOV.survInfo.Rd                                                     |    6 
 man/arrange_ggsurvplots.Rd                                                 |   14 
 man/ggadjustedcurves.Rd                                                    |   27 
 man/ggcompetingrisks.Rd                                                    |   13 
 man/ggcoxdiagnostics.Rd                                                    |   37 
 man/ggcoxfunctional.Rd                                                     |   23 
 man/ggcoxzph.Rd                                                            |   18 
 man/ggflexsurvplot.Rd                                                      |   16 
 man/ggforest.Rd                                                            |   12 
 man/ggsurvevents.Rd                                                        |   14 
 man/ggsurvplot.Rd                                                          |   42 -
 man/ggsurvplot_add_all.Rd                                                  |   10 
 man/ggsurvplot_combine.Rd                                                  |   22 
 man/ggsurvplot_df.Rd                                                       |   42 -
 man/ggsurvplot_facet.Rd                                                    |   30 
 man/ggsurvplot_list.Rd                                                     |   10 
 man/ggsurvtable.Rd                                                         |   50 -
 man/ggsurvtheme.Rd                                                         |   19 
 man/myeloma.Rd                                                             |    6 
 man/pairwise_survdiff.Rd                                                   |    3 
 man/surv_cutpoint.Rd                                                       |   13 
 man/surv_pvalue.Rd                                                         |   10 
 tools/README-ggplot2-basic-survival-plot-1.png                             |binary
 tools/README-ggplot2-customized-survival-plot-1.png                        |binary
 tools/README-ggplot2-more-customized-survival-plot-1.png                   |binary
 tools/README-ggplot2-uber-customized-survival-plot-1.png                   |binary
 tools/README-ggplot2-uber-platinium-customized-survival-plot-1.png         |binary
 tools/README-ggplot2-uber-platinium-premium-customized-survival-plot-1.png |binary
 vignettes/Informative_Survival_Plots.Rmd                                   |    5 
 42 files changed, 1601 insertions(+), 243 deletions(-)

More information about survminer at CRAN
Permanent link

Package rgdal updated to version 1.5-8 with previous version 1.4-8 dated 2019-11-27

Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. From 'rgdal' 1.4-1, provision is made for 'PROJ6' accommodation, with 'PROJ6' functionality to follow; from 1.4-1 'rgdal' will build and function when 'PROJ' >= 6. From 'rgdal' 1.5-1, attempts are made to adapt the handling of coordinate reference systems to 'GDAL' 3 and 'PROJ' 6, using 'WKT2_2019' strings. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Tim Keitt [aut], Barry Rowlingson [aut, ctb], Edzer Pebesma [ctb], Michael Sumner [ctb], Robert Hijmans [ctb], Even Rouault [cph, ctb], Frank Warmerdam [cph, ctb], Jeroen Ooms [ctb], Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between rgdal versions 1.4-8 dated 2019-11-27 and 1.5-8 dated 2020-05-28

 ChangeLog                                     |  644 ++++++++
 DESCRIPTION                                   |   15 
 MD5                                           |  112 -
 NAMESPACE                                     |   17 
 R/AAA.R                                       |   70 
 R/Class-CRSx.R                                |  102 +
 R/gdal.R                                      |  104 +
 R/list_coordOps.R                             |only
 R/ogr.R                                       |  102 +
 R/ogr_sp.R                                    |  251 +++
 R/ogr_write.R                                 |    9 
 R/project.R                                   |  549 ++++++-
 R/sgdf_gdal.R                                 |    7 
 R/sp_gdal.R                                   |   88 -
 R/subs.R                                      |    5 
 R/wrappers.R                                  |   52 
 build/vignette.rds                            |binary
 configure                                     | 1918 +++++++++++++++++++++++++-
 configure.ac                                  |  136 +
 data/GridsDatums.rda                          |binary
 inst/ChangeLog                                |  644 ++++++++
 inst/SVN_VERSION                              |    2 
 inst/doc/CRS_projections_transformations.R    |only
 inst/doc/CRS_projections_transformations.Rmd  |only
 inst/doc/CRS_projections_transformations.html |only
 inst/doc/OGR_shape_encoding.R                 |    1 
 inst/doc/OGR_shape_encoding.pdf               |binary
 inst/doc/PROJ6_GDAL3.R                        |only
 inst/doc/PROJ6_GDAL3.Rmd                      |only
 inst/doc/PROJ6_GDAL3.html                     |only
 inst/vectors/airports.gfs                     |only
 inst/vectors/b_pump.gpkg                      |only
 man/CRS-class.Rd                              |   19 
 man/GDALDriver-class.Rd                       |   10 
 man/GDALRasterBand-class.Rd                   |    3 
 man/GridsDatums.Rd                            |    2 
 man/list_coordOps.Rd                          |only
 man/llgrid.Rd                                 |    1 
 man/projInfo.Rd                               |   10 
 man/project.Rd                                |   27 
 man/readGDAL.Rd                               |   39 
 man/readOGR.Rd                                |   35 
 man/showWKT.Rd                                |   66 
 man/spTransform-methods.Rd                    |   44 
 man/wrappers.Rd                               |    4 
 man/writeOGR.Rd                               |    6 
 src/Makevars.win                              |   62 
 src/OGR_write.cpp                             |  106 +
 src/gdal-bindings.cpp                         |  204 ++
 src/init.c                                    |   15 
 src/inverser.c                                |    2 
 src/ogr_proj.cpp                              |  359 ++++
 src/proj_info6.cpp                            |  710 +++++++++
 src/proj_network7.cpp                         |only
 src/projectit.cpp                             |   47 
 src/rgdal.h                                   |   39 
 tests/srs_rendering.R                         |   68 
 tests/srs_rendering.Rout.save                 |  159 +-
 tests/test_proj.R                             |   11 
 tests/test_proj.Rout.save                     |   38 
 tools/winlibs.R                               |    9 
 vignettes/CRS_projections_transformations.Rmd |only
 vignettes/PROJ.bib                            |only
 vignettes/PROJ6_GDAL3.Rmd                     |only
 64 files changed, 6401 insertions(+), 522 deletions(-)

More information about rgdal at CRAN
Permanent link

Package symDMatrix updated to version 2.1.0 with previous version 2.0.2 dated 2018-08-25

Title: Partitioned Symmetric Matrices
Description: A matrix-like class to represent a symmetric matrix partitioned into file-backed blocks.
Author: Gustavo de los Campos [aut], Alexander Grueneberg [aut, cre]
Maintainer: Alexander Grueneberg <cran@agrueneberg.info>

Diff between symDMatrix versions 2.0.2 dated 2018-08-25 and 2.1.0 dated 2020-05-28

 symDMatrix-2.0.2/symDMatrix/R/package.R                         |only
 symDMatrix-2.0.2/symDMatrix/man/examples                        |only
 symDMatrix-2.0.2/symDMatrix/man/initialize-symDMatrix-method.Rd |only
 symDMatrix-2.0.2/symDMatrix/tests/testthat                      |only
 symDMatrix-2.0.2/symDMatrix/tests/testthat.R                    |only
 symDMatrix-2.1.0/symDMatrix/DESCRIPTION                         |   15 
 symDMatrix-2.1.0/symDMatrix/MD5                                 |   48 +-
 symDMatrix-2.1.0/symDMatrix/NAMESPACE                           |    3 
 symDMatrix-2.1.0/symDMatrix/NEWS.md                             |   15 
 symDMatrix-2.1.0/symDMatrix/R/symDMatrix.R                      |  186 ----------
 symDMatrix-2.1.0/symDMatrix/README.md                           |   20 -
 symDMatrix-2.1.0/symDMatrix/inst/CITATION                       |only
 symDMatrix-2.1.0/symDMatrix/inst/tinytest                       |only
 symDMatrix-2.1.0/symDMatrix/man/as.symDMatrix.Rd                |   27 -
 symDMatrix-2.1.0/symDMatrix/man/as.symDMatrix.character.Rd      |   40 +-
 symDMatrix-2.1.0/symDMatrix/man/as.symDMatrix.matrix.Rd         |   57 +--
 symDMatrix-2.1.0/symDMatrix/man/blockIndex.Rd                   |   20 -
 symDMatrix-2.1.0/symDMatrix/man/blockSize.Rd                    |   33 -
 symDMatrix-2.1.0/symDMatrix/man/load.symDMatrix.Rd              |   26 -
 symDMatrix-2.1.0/symDMatrix/man/nBlocks.Rd                      |   18 
 symDMatrix-2.1.0/symDMatrix/man/symDMatrix-class.Rd             |   38 --
 symDMatrix-2.1.0/symDMatrix/man/symDMatrix-package.Rd           |   37 +
 symDMatrix-2.1.0/symDMatrix/man/symDMatrix.Rd                   |only
 symDMatrix-2.1.0/symDMatrix/tests/tinytest.R                    |only
 24 files changed, 225 insertions(+), 358 deletions(-)

More information about symDMatrix at CRAN
Permanent link

Package ggmsa updated to version 0.0.4 with previous version 0.0.2 dated 2020-01-08

Title: Plot Multiple Sequence Alignment using 'ggplot2'
Description: Supports visualizing multiple sequence alignment of DNA and protein sequences using 'ggplot2'. It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as aligning a phylogenetic tree produced by 'ggtree' with multiple sequence alignment.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), Lang Zhou [aut], Huina Huang [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between ggmsa versions 0.0.2 dated 2020-01-08 and 0.0.4 dated 2020-05-28

 ggmsa-0.0.2/ggmsa/inst/extdata/dna_seq.fasta |only
 ggmsa-0.0.4/ggmsa/DESCRIPTION                |   13 -
 ggmsa-0.0.4/ggmsa/MD5                        |   56 ++++---
 ggmsa-0.0.4/ggmsa/NAMESPACE                  |   31 +++
 ggmsa-0.0.4/ggmsa/NEWS.md                    |   32 +++-
 ggmsa-0.0.4/ggmsa/R/available.R              |only
 ggmsa-0.0.4/ggmsa/R/color_else.R             |   25 +--
 ggmsa-0.0.4/ggmsa/R/facet_msa.R              |only
 ggmsa-0.0.4/ggmsa/R/geom_GC.R                |only
 ggmsa-0.0.4/ggmsa/R/geom_asterisk.R          |only
 ggmsa-0.0.4/ggmsa/R/geom_msa.R               |   43 ++++-
 ggmsa-0.0.4/ggmsa/R/geom_seed.R              |only
 ggmsa-0.0.4/ggmsa/R/geom_seqlogo.R           |only
 ggmsa-0.0.4/ggmsa/R/ggmotif.R                |only
 ggmsa-0.0.4/ggmsa/R/ggmsa.R                  |   68 +++++++-
 ggmsa-0.0.4/ggmsa/R/methods-ggplot_add.R     |only
 ggmsa-0.0.4/ggmsa/R/msa_data.R               |   78 ++++-----
 ggmsa-0.0.4/ggmsa/R/prepare_fasta.R          |    4 
 ggmsa-0.0.4/ggmsa/R/sysdata.rda              |binary
 ggmsa-0.0.4/ggmsa/build/vignette.rds         |binary
 ggmsa-0.0.4/ggmsa/inst/doc/ggmsa.R           |   93 ++++++-----
 ggmsa-0.0.4/ggmsa/inst/doc/ggmsa.Rmd         |  144 +++++++++---------
 ggmsa-0.0.4/ggmsa/inst/doc/ggmsa.html        |  215 ++++++++++++++-------------
 ggmsa-0.0.4/ggmsa/inst/extdata/seedSample.fa |only
 ggmsa-0.0.4/ggmsa/man/available_colors.Rd    |only
 ggmsa-0.0.4/ggmsa/man/available_fonts.Rd     |only
 ggmsa-0.0.4/ggmsa/man/available_msa.Rd       |only
 ggmsa-0.0.4/ggmsa/man/facet_msa.Rd           |only
 ggmsa-0.0.4/ggmsa/man/figures                |only
 ggmsa-0.0.4/ggmsa/man/geom_GC.Rd             |only
 ggmsa-0.0.4/ggmsa/man/geom_asterisk.Rd       |only
 ggmsa-0.0.4/ggmsa/man/geom_msa.Rd            |   25 ++-
 ggmsa-0.0.4/ggmsa/man/geom_seed.Rd           |only
 ggmsa-0.0.4/ggmsa/man/geom_seqlogo.Rd        |only
 ggmsa-0.0.4/ggmsa/man/ggmotif.Rd             |only
 ggmsa-0.0.4/ggmsa/man/ggmsa.Rd               |   44 ++++-
 ggmsa-0.0.4/ggmsa/vignettes/Extensions       |only
 ggmsa-0.0.4/ggmsa/vignettes/ggmsa.Rmd        |  144 +++++++++---------
 38 files changed, 620 insertions(+), 395 deletions(-)

More information about ggmsa at CRAN
Permanent link

Package RBesT updated to version 1.6-1 with previous version 1.6-0 dated 2020-03-28

Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This includes meta-analysis, (robust) prior derivation from historical data, operating characteristics and analysis (1 and 2 sample cases). Please refer to Neuenschwander et al. (2010) <doi:10.1177/1740774509356002> and Schmidli et al. (2014) <doi:10.1111/biom.12242> for details on the methodology.
Author: Novartis Pharma AG [cph], Sebastian Weber [aut, cre], Beat Neuenschwander [ctb], Heinz Schmidli [ctb], Baldur Magnusson [ctb], Yue Li [ctb], Satrajit Roychoudhury [ctb], Trustees of Columbia University [cph] (R/stanmodels.R, configure, configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>

Diff between RBesT versions 1.6-0 dated 2020-03-28 and 1.6-1 dated 2020-05-28

 DESCRIPTION                        |   10 -
 MD5                                |   87 +++++----
 R/dlink.R                          |   22 +-
 R/gMAP.R                           |   22 +-
 R/integrate_logit_log.R            |   57 +++++-
 R/log_inv_logit.R                  |only
 R/mix.R                            |    9 -
 R/mixess.R                         |   15 +
 R/mixplot.R                        |   14 -
 R/predict_gMAP.R                   |   26 +-
 R/sysdata.rda                      |binary
 inst/NEWS                          |    6 
 inst/doc/PoS_codata.Rmd            |   10 -
 inst/doc/PoS_codata.html           |   10 -
 inst/doc/PoS_interim.Rmd           |   11 -
 inst/doc/PoS_interim.html          |   10 -
 inst/doc/RBesT.pdf                 |binary
 inst/doc/customizing_plots.R       |    9 -
 inst/doc/customizing_plots.Rmd     |   19 +-
 inst/doc/customizing_plots.html    |  238 ++++++++++++---------------
 inst/doc/introduction.Rmd          |   10 -
 inst/doc/introduction.html         |   10 -
 inst/doc/introduction_normal.Rmd   |   10 -
 inst/doc/introduction_normal.html  |   10 -
 inst/doc/robustMAP.html            |    8 
 inst/doc/variances_MAP.Rmd         |   10 -
 inst/doc/variances_MAP.html        |   10 -
 inst/sbc/calibration.md5           |    6 
 inst/sbc/make_reference_rankhist.R |  122 +++++++++++--
 inst/sbc/sbc_report.R              |   37 +---
 inst/sbc/sbc_report.html           |  324 +++++++++++++++++++++++++++----------
 inst/sbc/sbc_report_plots.R        |only
 inst/sbc/sbc_tools.R               |   68 +++++++
 inst/stan/gMAP.stan                |    6 
 man/integrate_density_log.Rd       |    2 
 man/log_inv_logit.Rd               |only
 src/stanExports_gMAP.h             |   20 +-
 tests/testthat/test-oc2S.R         |   22 ++
 tests/testthat/test-utils.R        |    5 
 tools/build.sh                     |    4 
 vignettes/PoS_codata.Rmd           |   10 -
 vignettes/PoS_interim.Rmd          |   11 -
 vignettes/customizing_plots.Rmd    |   19 +-
 vignettes/introduction.Rmd         |   10 -
 vignettes/introduction_normal.Rmd  |   10 -
 vignettes/variances_MAP.Rmd        |   10 -
 46 files changed, 843 insertions(+), 486 deletions(-)

More information about RBesT at CRAN
Permanent link

Package tidyfst updated to version 0.9.7 with previous version 0.9.6 dated 2020-05-02

Title: Tidy Verbs for Fast Data Manipulation
Description: A toolkit of tidy data manipulation verbs with 'data.table' as the backend. Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table', 'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain. This package is an extension of 'data.table'. While enjoying a tidy syntax, it also wraps combinations of efficient functions to facilitate frequently-used data operations.
Author: Tian-Yuan Huang [aut, cre] (<https://orcid.org/0000-0002-3591-4203>)
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>

Diff between tidyfst versions 0.9.6 dated 2020-05-02 and 0.9.7 dated 2020-05-28

 tidyfst-0.9.6/tidyfst/R/join_dt.R                    |only
 tidyfst-0.9.6/tidyfst/R/slice_dt.R                   |only
 tidyfst-0.9.6/tidyfst/man/slice_dt.Rd                |only
 tidyfst-0.9.7/tidyfst/DESCRIPTION                    |    6 -
 tidyfst-0.9.7/tidyfst/MD5                            |   22 +--
 tidyfst-0.9.7/tidyfst/NAMESPACE                      |   13 +-
 tidyfst-0.9.7/tidyfst/R/complete.R                   |    1 
 tidyfst-0.9.7/tidyfst/R/join.R                       |only
 tidyfst-0.9.7/tidyfst/R/nest_dt.R                    |    2 
 tidyfst-0.9.7/tidyfst/R/separate.R                   |   53 ++++++---
 tidyfst-0.9.7/tidyfst/R/slice.R                      |only
 tidyfst-0.9.7/tidyfst/inst/doc/chinese_tutorial.html |   20 +--
 tidyfst-0.9.7/tidyfst/man/join.Rd                    |  107 ++++++++-----------
 tidyfst-0.9.7/tidyfst/man/separate_dt.Rd             |    3 
 tidyfst-0.9.7/tidyfst/man/slice.Rd                   |only
 15 files changed, 121 insertions(+), 106 deletions(-)

More information about tidyfst at CRAN
Permanent link

Package PINSPlus updated to version 2.0.3 with previous version 2.0.2 dated 2020-04-13

Title: Clustering Algorithm for Data Integration and Disease Subtyping
Description: Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et.al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et.al. (2017)<DOI: 10.1101/gr.215129.116>).
Author: Hung Nguyen, Bang Tran, Duc Tran and Tin Nguyen
Maintainer: Hung Nguyen <hungnp@nevada.unr.edu>

Diff between PINSPlus versions 2.0.2 dated 2020-04-13 and 2.0.3 dated 2020-05-28

 DESCRIPTION                      |   14 ++------
 MD5                              |   16 ++++-----
 R/perturb-functions.R            |    8 ----
 R/perturbation-clustering.R      |    9 +++--
 R/subtyping-omics-data-helpers.R |   67 ---------------------------------------
 R/subtyping-omics-data.R         |   13 ++++---
 man/PerturbationClustering.Rd    |    7 +++-
 man/SubtypingOmicsData.Rd        |    3 +
 vignettes/PINSPlus.html          |   18 +++++-----
 9 files changed, 45 insertions(+), 110 deletions(-)

More information about PINSPlus at CRAN
Permanent link

Package m2r updated to version 1.0.2 with previous version 1.0.1 dated 2020-05-06

Title: Interface to 'Macaulay2'
Description: Persistent interface to 'Macaulay2' <http://www.math.uiuc.edu/Macaulay2/> and front-end tools facilitating its use in the 'R' ecosystem. For details see Kahle et. al. (2020) <doi:10.18637/jss.v093.i09>.
Author: David Kahle [aut, cph, cre] (<https://orcid.org/0000-0002-9999-1558>), Christopher O'Neill [aut, cph], Jeff Sommars [aut, cph]
Maintainer: David Kahle <david@kahle.io>

Diff between m2r versions 1.0.1 dated 2020-05-06 and 1.0.2 dated 2020-05-28

 DESCRIPTION      |    9 +++++----
 MD5              |   12 ++++++------
 R/m2_parser.R    |    7 +++++--
 R/m2r-package.R  |    3 +++
 inst/CITATION    |   33 +++++++++++++++++++++------------
 man/m2_parser.Rd |    9 +++++++--
 man/m2r.Rd       |    5 +++++
 7 files changed, 52 insertions(+), 26 deletions(-)

More information about m2r at CRAN
Permanent link

Package hsrecombi updated to version 0.3.0 with previous version 0.1.3 dated 2020-03-04

Title: Estimation of Recombination Rate and Maternal LD in Half-Sibs
Description: Paternal recombination rate and maternal linkage disequilibrium (LD) are estimated for pairs of biallelic markers such as single nucleotide polymorphisms (SNPs) from progeny genotypes and sire haplotypes. At least one sire has to be double heterozygous at the investigated pairs of SNPs. The implementation relies on paternal half-sib families. If maternal half- sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of recombination rate and maternal linkage disequilibrium in half-sibs" <doi:10.3389/fgene.2018.00186>. Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium in half-sib families" <doi:10.1534/genetics.111.137521>.
Author: Dörte Wittenburg [aut, cre]
Maintainer: Dörte Wittenburg <wittenburg@fbn-dummerstorf.de>

Diff between hsrecombi versions 0.1.3 dated 2020-03-04 and 0.3.0 dated 2020-05-28

 DESCRIPTION            |    8 +-
 MD5                    |   23 ++++---
 NAMESPACE              |    5 +
 NEWS.md                |   11 +++
 R/functions.R          |  150 +++++++++++++++++++++++++++++++++++++++++++++----
 R/hsrecombi.R          |   72 ++++++++++++++++++++++-
 man/checkCandidates.Rd |only
 man/editraw.Rd         |    4 -
 man/geneticPosition.Rd |only
 man/hsrecombi.Rd       |    6 +
 man/makehap.Rd         |   10 +--
 man/makehaplist.Rd     |    5 -
 man/makehappm.Rd       |only
 man/startvalue.Rd      |    2 
 14 files changed, 257 insertions(+), 39 deletions(-)

More information about hsrecombi at CRAN
Permanent link

Package gmm updated to version 1.6-5 with previous version 1.6-4 dated 2019-12-04

Title: Generalized Method of Moments and Generalized Empirical Likelihood
Description: It is a complete suite to estimate models based on moment conditions. It includes the two step Generalized method of moments (Hansen 1982; <doi:10.2307/1912775>), the iterated GMM and continuous updated estimator (Hansen, Eaton and Yaron 1996; <doi:10.2307/1392442>) and several methods that belong to the Generalized Empirical Likelihood family of estimators (Smith 1997; <doi:10.1111/j.0013-0133.1997.174.x>, Kitamura 1997; <doi:10.1214/aos/1069362388>, Newey and Smith 2004; <doi:10.1111/j.1468-0262.2004.00482.x>, and Anatolyev 2005 <doi:10.1111/j.1468-0262.2005.00601.x>).
Author: Pierre Chausse <pchausse@uwaterloo.ca>
Maintainer: Pierre Chausse <pchausse@uwaterloo.ca>

Diff between gmm versions 1.6-4 dated 2019-12-04 and 1.6-5 dated 2020-05-28

 DESCRIPTION             |   21 +++++++--------------
 MD5                     |   16 ++++++++--------
 build/vignette.rds      |binary
 data/Finance.rda        |binary
 data/Growth.rda         |binary
 data/nsw.rda            |binary
 data/wage.rda           |binary
 inst/doc/gmm_with_R.pdf |binary
 src/gmm.h               |    4 ++--
 9 files changed, 17 insertions(+), 24 deletions(-)

More information about gmm at CRAN
Permanent link

Package WeightSVM updated to version 1.7-5 with previous version 1.7-4 dated 2020-04-18

Title: Subject Weighted Support Vector Machines
Description: Functions for subject/instance weighted support vector machines (SVM). It uses a modified version of 'libsvm' and is compatible with package 'e1071'.
Author: Tianchen Xu [aut, cre] (<https://orcid.org/0000-0002-0102-7630>), Chih-Chung Chang [ctb, cph] (libsvm C++-code), Chih-Chen Lin [ctb, cph] (libsvm C++-code), Ming-Wei Chang [ctb, cph] (libsvm C++-code), Hsuan-Tien Lin [ctb, cph] (libsvm C++-code), Ming-Hen Tsai [ctb, cph] (libsvm C++-code), Chia-Hua Ho [ctb, cph] (libsvm C++-code), Hsiang-Fu Yu [ctb, cph] (libsvm C++-code), David Meyer [ctb], Evgenia Dimitriadou [ctb], Kurt Hornik [ctb], Andreas Weingessel [ctb], Friedrich Leisch [ctb]
Maintainer: Tianchen Xu <tx2155@columbia.edu>

Diff between WeightSVM versions 1.7-4 dated 2020-04-18 and 1.7-5 dated 2020-05-28

 DESCRIPTION        |    9 +++++----
 MD5                |    8 +++++++-
 build              |only
 inst               |only
 tests/tune.wsvm.Rd |only
 vignettes          |only
 6 files changed, 12 insertions(+), 5 deletions(-)

More information about WeightSVM at CRAN
Permanent link

Package webchem updated to version 1.0.0 with previous version 0.5.0 dated 2020-03-02

Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemIDplus, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem, SRS, Wikidata.
Author: Eduard Szöcs [aut], Robert Allaway [ctb], Daniel Muench [ctb], Johannes Ranke [ctb], Andreas Scharmüller [ctb], Eric R Scott [ctb], Jan Stanstrup [ctb], Gordon Getzinger [ctb], Tamás Stirling [ctb, cre]
Maintainer: Tamás Stirling <stirling.tamas@gmail.com>

Diff between webchem versions 0.5.0 dated 2020-03-02 and 1.0.0 dated 2020-05-28

 webchem-0.5.0/webchem/NEWS                             |only
 webchem-0.5.0/webchem/data/aw_idx.rda                  |only
 webchem-0.5.0/webchem/man/aw_idx.Rd                    |only
 webchem-0.5.0/webchem/man/ping.Rd                      |only
 webchem-0.5.0/webchem/tests/testthat/test_fn.R         |only
 webchem-1.0.0/webchem/DESCRIPTION                      |   23 
 webchem-1.0.0/webchem/MD5                              |  162 ++--
 webchem-1.0.0/webchem/NAMESPACE                        |   31 
 webchem-1.0.0/webchem/NEWS.md                          |only
 webchem-1.0.0/webchem/R/alanwood.R                     |  221 +++--
 webchem-1.0.0/webchem/R/chebi.R                        |   68 +
 webchem-1.0.0/webchem/R/chemid.R                       |   18 
 webchem-1.0.0/webchem/R/chemspider.R                   |  151 ++-
 webchem-1.0.0/webchem/R/cir.R                          |    6 
 webchem-1.0.0/webchem/R/cts.R                          |   20 
 webchem-1.0.0/webchem/R/etox.R                         |  276 ++++--
 webchem-1.0.0/webchem/R/extractors.R                   |   88 +-
 webchem-1.0.0/webchem/R/flavornet.R                    |    5 
 webchem-1.0.0/webchem/R/nist.R                         |  333 +++++---
 webchem-1.0.0/webchem/R/opsin.R                        |   36 
 webchem-1.0.0/webchem/R/pan.R                          |    8 
 webchem-1.0.0/webchem/R/ping.R                         |  202 ++++-
 webchem-1.0.0/webchem/R/pubchem.R                      |  676 +++++++++++++----
 webchem-1.0.0/webchem/R/utils.R                        |  162 +++-
 webchem-1.0.0/webchem/R/webchem-package.R              |   20 
 webchem-1.0.0/webchem/R/wikidata.R                     |  169 +---
 webchem-1.0.0/webchem/build                            |only
 webchem-1.0.0/webchem/inst/CITATION                    |   33 
 webchem-1.0.0/webchem/inst/doc                         |only
 webchem-1.0.0/webchem/man/as.cas.Rd                    |    3 
 webchem-1.0.0/webchem/man/aw_query.Rd                  |   33 
 webchem-1.0.0/webchem/man/build_aw_idx.Rd              |   21 
 webchem-1.0.0/webchem/man/chebi_comp_entity.Rd         |    7 
 webchem-1.0.0/webchem/man/ci_query.Rd                  |    2 
 webchem-1.0.0/webchem/man/cir_query.Rd                 |    2 
 webchem-1.0.0/webchem/man/cs_check_key.Rd              |    2 
 webchem-1.0.0/webchem/man/cs_compinfo.Rd               |    2 
 webchem-1.0.0/webchem/man/cs_control.Rd                |    4 
 webchem-1.0.0/webchem/man/cs_convert.Rd                |    9 
 webchem-1.0.0/webchem/man/cs_datasources.Rd            |    2 
 webchem-1.0.0/webchem/man/cs_extcompinfo.Rd            |    2 
 webchem-1.0.0/webchem/man/cts_compinfo.Rd              |    2 
 webchem-1.0.0/webchem/man/cts_convert.Rd               |   10 
 webchem-1.0.0/webchem/man/cts_from.Rd                  |    2 
 webchem-1.0.0/webchem/man/etox_basic.Rd                |   26 
 webchem-1.0.0/webchem/man/etox_targets.Rd              |   24 
 webchem-1.0.0/webchem/man/etox_tests.Rd                |    4 
 webchem-1.0.0/webchem/man/extractors.Rd                |    6 
 webchem-1.0.0/webchem/man/fn_percept.Rd                |    2 
 webchem-1.0.0/webchem/man/get_chebiid.Rd               |   13 
 webchem-1.0.0/webchem/man/get_cid.Rd                   |  139 ++-
 webchem-1.0.0/webchem/man/get_csid.Rd                  |   45 -
 webchem-1.0.0/webchem/man/get_etoxid.Rd                |   26 
 webchem-1.0.0/webchem/man/get_wdid.Rd                  |   21 
 webchem-1.0.0/webchem/man/is.cas.Rd                    |   19 
 webchem-1.0.0/webchem/man/is.inchikey.Rd               |   13 
 webchem-1.0.0/webchem/man/is.inchikey_cs.Rd            |    2 
 webchem-1.0.0/webchem/man/is.inchikey_format.Rd        |    5 
 webchem-1.0.0/webchem/man/is.smiles.Rd                 |   10 
 webchem-1.0.0/webchem/man/jagst.Rd                     |    6 
 webchem-1.0.0/webchem/man/lc50.Rd                      |    6 
 webchem-1.0.0/webchem/man/nist_ri.Rd                   |   38 
 webchem-1.0.0/webchem/man/opsin_query.Rd               |    2 
 webchem-1.0.0/webchem/man/parse_mol.Rd                 |   26 
 webchem-1.0.0/webchem/man/pc_prop.Rd                   |   45 -
 webchem-1.0.0/webchem/man/pc_sect.Rd                   |only
 webchem-1.0.0/webchem/man/pc_synonyms.Rd               |   41 -
 webchem-1.0.0/webchem/man/ping_service.Rd              |only
 webchem-1.0.0/webchem/man/wd_ident.Rd                  |    2 
 webchem-1.0.0/webchem/man/webchem.Rd                   |    3 
 webchem-1.0.0/webchem/tests/testthat.R                 |    6 
 webchem-1.0.0/webchem/tests/testthat/test-alanwood.R   |   65 -
 webchem-1.0.0/webchem/tests/testthat/test-chebi.R      |   53 +
 webchem-1.0.0/webchem/tests/testthat/test-chemid.R     |   49 -
 webchem-1.0.0/webchem/tests/testthat/test-chemspider.R |  169 +++-
 webchem-1.0.0/webchem/tests/testthat/test-cir.R        |   24 
 webchem-1.0.0/webchem/tests/testthat/test-cts.R        |   57 -
 webchem-1.0.0/webchem/tests/testthat/test-etox.R       |  258 +++---
 webchem-1.0.0/webchem/tests/testthat/test-extractors.R |  116 +-
 webchem-1.0.0/webchem/tests/testthat/test-flavornet.R  |only
 webchem-1.0.0/webchem/tests/testthat/test-nist.R       |  169 +++-
 webchem-1.0.0/webchem/tests/testthat/test-opsin.R      |   21 
 webchem-1.0.0/webchem/tests/testthat/test-pan.R        |   31 
 webchem-1.0.0/webchem/tests/testthat/test-pubchem.R    |  174 +++-
 webchem-1.0.0/webchem/tests/testthat/test-utils.R      |   47 -
 webchem-1.0.0/webchem/tests/testthat/test-wikidata.R   |   43 -
 webchem-1.0.0/webchem/vignettes                        |only
 87 files changed, 3125 insertions(+), 1492 deletions(-)

More information about webchem at CRAN
Permanent link

Package reactable updated to version 0.2.0 with previous version 0.1.0.1 dated 2020-02-29

Title: Interactive Data Tables Based on 'React Table'
Description: Interactive data tables for R, based on the 'React Table' JavaScript library. Provides an HTML widget that can be used in 'R Markdown' documents and 'Shiny' applications, or viewed from an R console.
Author: Greg Lin [aut, cre], Tanner Linsley [ctb, cph] (React Table library), Emotion team and other contributors [ctb, cph] (Emotion library)
Maintainer: Greg Lin <glin@glin.io>

Diff between reactable versions 0.1.0.1 dated 2020-02-29 and 0.2.0 dated 2020-05-28

 DESCRIPTION                         |   18 
 MD5                                 |   52 +-
 NAMESPACE                           |   26 -
 NEWS.md                             |only
 R/columns.R                         |   16 
 R/language.R                        |only
 R/reactable.R                       |  164 ++++++--
 R/shiny.R                           |only
 R/theme.R                           |only
 R/utils.R                           |    5 
 README.md                           |  687 ++----------------------------------
 inst/examples/app/app.R             |   84 +++-
 inst/examples/app/assets/styles.css |   21 -
 inst/htmlwidgets/reactable.js       |    4 
 inst/htmlwidgets/reactable.js.map   |    2 
 inst/htmlwidgets/reactable.yaml     |    1 
 man/colDef.Rd                       |  259 +++++++------
 man/colFormat.Rd                    |  143 +++----
 man/colGroup.Rd                     |  109 +++--
 man/figures                         |only
 man/getReactableState.Rd            |only
 man/reactable-package.Rd            |   71 +--
 man/reactable-shiny.Rd              |  134 +++----
 man/reactable.Rd                    |  427 ++++++++++++----------
 man/reactableLang.Rd                |only
 man/reactableTheme.Rd               |only
 man/updateReactable.Rd              |only
 tests/testthat/test-columns.R       |    8 
 tests/testthat/test-language.R      |only
 tests/testthat/test-reactable.R     |  236 +++++++++++-
 tests/testthat/test-shiny.R         |only
 tests/testthat/test-theme.R         |only
 tests/testthat/test-utils.R         |   12 
 33 files changed, 1190 insertions(+), 1289 deletions(-)

More information about reactable at CRAN
Permanent link

Package bayesplot updated to version 1.7.2 with previous version 1.7.1 dated 2019-12-01

Title: Plotting for Bayesian Models
Description: Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow advocated in Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>. The package is designed not only to provide convenient functionality for users, but also a common set of functions that can be easily used by developers working on a variety of R packages for Bayesian modeling, particularly (but not exclusively) packages interfacing with 'Stan'.
Author: Jonah Gabry [aut, cre], Tristan Mahr [aut], Paul-Christian Bürkner [ctb], Martin Modrák [ctb], Malcolm Barrett [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>

Diff between bayesplot versions 1.7.1 dated 2019-12-01 and 1.7.2 dated 2020-05-28

 bayesplot-1.7.1/bayesplot/tests/figs                               |only
 bayesplot-1.7.1/bayesplot/tests/testthat/Rplots.pdf                |only
 bayesplot-1.7.2/bayesplot/DESCRIPTION                              |   12 
 bayesplot-1.7.2/bayesplot/MD5                                      |  146 +---------
 bayesplot-1.7.2/bayesplot/NEWS.md                                  |    6 
 bayesplot-1.7.2/bayesplot/R/available-module-functions.R           |    7 
 bayesplot-1.7.2/bayesplot/R/helpers-gg.R                           |    7 
 bayesplot-1.7.2/bayesplot/R/mcmc-distributions.R                   |   40 +-
 bayesplot-1.7.2/bayesplot/R/mcmc-intervals.R                       |   13 
 bayesplot-1.7.2/bayesplot/R/mcmc-scatterplots.R                    |    6 
 bayesplot-1.7.2/bayesplot/R/ppc-intervals.R                        |   10 
 bayesplot-1.7.2/bayesplot/R/ppc-loo.R                              |    4 
 bayesplot-1.7.2/bayesplot/inst/doc/graphical-ppcs.R                |   52 +--
 bayesplot-1.7.2/bayesplot/inst/doc/graphical-ppcs.html             |   43 +-
 bayesplot-1.7.2/bayesplot/inst/doc/plotting-mcmc-draws.R           |   68 ++--
 bayesplot-1.7.2/bayesplot/inst/doc/plotting-mcmc-draws.Rmd         |   33 ++
 bayesplot-1.7.2/bayesplot/inst/doc/plotting-mcmc-draws.html        |   90 +++---
 bayesplot-1.7.2/bayesplot/inst/doc/visual-mcmc-diagnostics.R       |   86 +++--
 bayesplot-1.7.2/bayesplot/inst/doc/visual-mcmc-diagnostics.Rmd     |   35 +-
 bayesplot-1.7.2/bayesplot/inst/doc/visual-mcmc-diagnostics.html    |   56 ++-
 bayesplot-1.7.2/bayesplot/man/MCMC-intervals.Rd                    |    2 
 bayesplot-1.7.2/bayesplot/man/MCMC-scatterplots.Rd                 |    6 
 bayesplot-1.7.2/bayesplot/man/MCMC-traces.Rd                       |    2 
 bayesplot-1.7.2/bayesplot/man/available_ppc.Rd                     |    4 
 bayesplot-1.7.2/bayesplot/tests/testthat/test-helpers-shared.R     |   20 -
 bayesplot-1.7.2/bayesplot/tests/testthat/test-mcmc-diagnostics.R   |    8 
 bayesplot-1.7.2/bayesplot/tests/testthat/test-mcmc-distributions.R |   11 
 bayesplot-1.7.2/bayesplot/tests/testthat/test-mcmc-intervals.R     |    4 
 bayesplot-1.7.2/bayesplot/vignettes/plotting-mcmc-draws.Rmd        |   33 ++
 bayesplot-1.7.2/bayesplot/vignettes/visual-mcmc-diagnostics.Rmd    |   35 +-
 30 files changed, 440 insertions(+), 399 deletions(-)

More information about bayesplot at CRAN
Permanent link

Package PRSim updated to version 1.2-2 with previous version 1.2-1 dated 2020-01-10

Title: Stochastic Simulation of Streamflow Time Series using Phase Randomization
Description: Provides a simulation framework to simulate streamflow time series with similar main characteristics as observed data. These characteristics include the distribution of daily streamflow values and their temporal correlation as expressed by short- and long-range dependence. The approach is based on the randomization of the phases of the Fourier transform or the phases of the wavelet transform. The function prsim() is applicable to single site simulation and uses the Fourier transform. The function prsim.wave() extends the approach to multiple sites and is based on the complex wavelet transform. We further use the flexible four-parameter Kappa distribution, which allows for the extrapolation to yet unobserved low and high flows. Alternatively, the empirical or any other distribution can be used. A detailed description of the simulation approach for single sites and an application example can be found in <https://www.hydrol-earth-syst-sci.net/23/3175/2019/>. A detailed description and evaluation of the wavelet-based multi-site approach can be found in <https://www.hydrol-earth-syst-sci-discuss.net/hess-2019-658/>.
Author: Manuela Brunner [aut, cre] (<https://orcid.org/0000-0001-8824-877X>), Reinhard Furrer [aut] (<https://orcid.org/0000-0002-6319-2332>)
Maintainer: Manuela Brunner <manuela.i.brunner@gmail.com>

Diff between PRSim versions 1.2-1 dated 2020-01-10 and 1.2-2 dated 2020-05-28

 DESCRIPTION                    |   29 +++--
 MD5                            |   24 ++--
 NAMESPACE                      |    8 +
 R/fun_stoch_sim_wave.R         |  229 +++++++++++++++++++++++++++++++++++++++--
 build/partial.rdb              |binary
 demo/PRSim_wave-validate.R     |    2 
 demo/PRSim_wave.R              |    2 
 man/PRSim-package.Rd           |    2 
 man/fun_stoch_sim_wave.Rd      |    3 
 man/runoff.Rd                  |    2 
 man/runoff_multi_sites.Rd      |    2 
 man/simulations.Rd             |    2 
 man/simulations_multi_sites.Rd |    2 
 13 files changed, 268 insertions(+), 39 deletions(-)

More information about PRSim at CRAN
Permanent link

Package ouxy updated to version 2.1 with previous version 1.1 dated 2019-09-20

Title: Model of Adaptive Trait Evolution
Description: Performs statistical inference on the models of adaptive trait evolution under approximate Bayesian computation. This can simulate traits from four models, compute trait data summary statistics. Parameters are estimated under Approximate Bayesian Computation, model selection as well as posterior parameter mean will be reported. Users need to enter a comparative dataset and a phylogenetic tree.
Author: Dwueng-Chwuan Jhwueng
Maintainer: Dwueng-Chwuan Jhwueng <dcjhwueng@fcu.edu.tw>

Diff between ouxy versions 1.1 dated 2019-09-20 and 2.1 dated 2020-05-28

 DESCRIPTION         |   12 
 MD5                 |   32 
 NAMESPACE           |   18 
 R/ouxy.r            | 1972 ++++++++++++++++++++++++++++++++++++++++++++--------
 man/oubmTrait.Rd    |only
 man/oubmbmprior.Rd  |    6 
 man/oubmcirprior.Rd |    6 
 man/oubmmodel.Rd    |only
 man/oubmprior.Rd    |only
 man/ougbmTrait.Rd   |only
 man/ougbmmodel.Rd   |only
 man/ougbmprior.Rd   |only
 man/ougouTrait.Rd   |only
 man/ougoumodel.Rd   |only
 man/ougouprior.Rd   |only
 man/ououTrait.Rd    |only
 man/ououbmprior.Rd  |    6 
 man/ououcirprior.Rd |    6 
 man/ououmodel.Rd    |only
 man/ououprior.Rd    |only
 man/ouqbmTrait.Rd   |only
 man/ouqbmmodel.Rd   |only
 man/ouqbmprior.Rd   |only
 man/ouqouTrait.Rd   |only
 man/ouqoumodel.Rd   |only
 man/ouqouprior.Rd   |only
 26 files changed, 1758 insertions(+), 300 deletions(-)

More information about ouxy at CRAN
Permanent link

Package abcrlda updated to version 1.0.3 with previous version 1.0.2 dated 2020-01-29

Title: Asymptotically Bias-Corrected Regularized Linear Discriminant Analysis
Description: Offers methods to perform asymptotically bias-corrected regularized linear discriminant analysis (ABC_RLDA) for cost-sensitive binary classification. The bias-correction is an estimate of the bias term added to regularized discriminant analysis (RLDA) that minimizes the overall risk. The default magnitude of misclassification costs are equal and set to 0.5; however, the package also offers the options to set them to some predetermined values or, alternatively, take them as hyperparameters to tune. A. Zollanvari, M. Abdirash, A. Dadlani and B. Abibullaev (2019) <doi:10.1109/LSP.2019.2918485>.
Author: Dmitriy Fedorov [aut, cre], Amin Zollanvari [aut], Aresh Dadlani [aut], Berdakh Abibullaev [aut]
Maintainer: Dmitriy Fedorov <dmitriy.fedorov@nu.edu.kz>

Diff between abcrlda versions 1.0.2 dated 2020-01-29 and 1.0.3 dated 2020-05-28

 abcrlda-1.0.2/abcrlda/inst/abcrlda_1.0.2.pdf   |only
 abcrlda-1.0.3/abcrlda/DESCRIPTION              |    8 +++----
 abcrlda-1.0.3/abcrlda/MD5                      |   18 ++++++++---------
 abcrlda-1.0.3/abcrlda/NAMESPACE                |    2 -
 abcrlda-1.0.3/abcrlda/R/abc_grid.R             |   26 +++++++++++++------------
 abcrlda-1.0.3/abcrlda/R/abcrlda.R              |    8 +++----
 abcrlda-1.0.3/abcrlda/inst/abcrlda_1.0.3.pdf   |only
 abcrlda-1.0.3/abcrlda/man/abcrlda.Rd           |    4 +--
 abcrlda-1.0.3/abcrlda/man/da_risk_estimator.Rd |   10 +--------
 abcrlda-1.0.3/abcrlda/man/grid_search.Rd       |    2 -
 abcrlda-1.0.3/abcrlda/man/predict.abcrlda.Rd   |    4 +--
 11 files changed, 39 insertions(+), 43 deletions(-)

More information about abcrlda at CRAN
Permanent link

Wed, 27 May 2020

Package yhat updated to version 2.0-2 with previous version 2.0-1 dated 2020-05-25

Title: Interpreting Regression Effects
Description: The purpose of this package is to provide methods to interpret multiple linear regression and canonical correlation results including beta weights,structure coefficients, validity coefficients, product measures, relative weights, all-possible-subsets regression, dominance analysis, commonality analysis, and adjusted effect sizes.
Author: Kim Nimon <kim.nimon@gmail.com>, Fred Oswald, and J. Kyle Roberts.
Maintainer: Kim Nimon <kim.nimon@gmail.com>

Diff between yhat versions 2.0-1 dated 2020-05-25 and 2.0-2 dated 2020-05-27

 DESCRIPTION         |   19 +++++++------------
 MD5                 |   10 +++++-----
 man/calc.yhat.rd    |    4 +++-
 man/commonality.rd  |    2 +-
 man/rlw.rd          |    4 +++-
 man/yhat-package.Rd |    4 ++--
 6 files changed, 21 insertions(+), 22 deletions(-)

More information about yhat at CRAN
Permanent link

Package NIRStat updated to version 1.1 with previous version 1.0 dated 2018-01-29

Title: Novel Statistical Methods for Studying Near-Infrared Spectroscopy (NIRS) Time Series Data
Description: Provides transfusion-related differential tests on Near-infrared spectroscopy (NIRS) time series with detection limit, which contains two testing statistics: Mean Area Under the Curve (MAUC) and slope statistic. This package applied a penalized spline method within imputation setting. Testing is conducted by a nested permutation approach within imputation. Refer to Guo et al (2018) <doi:10.1177/0962280218786302> for further details.
Author: Yikai Wang [Emory University], Xiao Wang [ICF]
Maintainer: Yikai Wang <johnzon.wyk@gmail.com>

Diff between NIRStat versions 1.0 dated 2018-01-29 and 1.1 dated 2020-05-27

 DESCRIPTION      |   15 +++++------
 MD5              |   10 +++----
 R/plotNIRS.R     |   75 +++++++++++++++++++++++++++++++++----------------------
 man/MAUCtest.Rd  |    6 ++--
 man/Slopetest.Rd |    6 ++--
 man/plotNIRS.Rd  |   66 ++++++++++++++++++++++++------------------------
 6 files changed, 98 insertions(+), 80 deletions(-)

More information about NIRStat at CRAN
Permanent link

Package CGPfunctions updated to version 0.6.1 with previous version 0.6.0 dated 2020-04-02

Title: Powell Miscellaneous Functions for Teaching and Learning Statistics
Description: Miscellaneous functions useful for teaching statistics as well as actually practicing the art. They typically are not new methods but rather wrappers around either base R or other packages.
Author: Chuck Powell [aut, cre] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Chuck Powell <ibecav@gmail.com>

Diff between CGPfunctions versions 0.6.0 dated 2020-04-02 and 0.6.1 dated 2020-05-27

 DESCRIPTION                         |   12 +-
 MD5                                 |   25 ++--
 NEWS.md                             |   11 +
 R/helpers.R                         |  131 +++++++++++++++++++---
 R/seedist.R                         |  214 ++++++++++++++++++++++++------------
 build/vignette.rds                  |binary
 inst/doc/Using-Plot2WayANOVA.html   |   12 +-
 inst/doc/Using-PlotXTabs.html       |    6 -
 inst/doc/Using-PlotXTabs2.html      |    6 -
 inst/doc/Using-chaid_table.html     |    6 -
 inst/doc/Using-newggslopegraph.html |    6 -
 man/SeeDist.Rd                      |   47 ++++++-
 man/bf_display.Rd                   |only
 man/exponent.Rd                     |only
 man/number_to_word.Rd               |only
 15 files changed, 351 insertions(+), 125 deletions(-)

More information about CGPfunctions at CRAN
Permanent link

Package autoimage updated to version 2.1.9 with previous version 2.1 dated 2020-03-28

Title: Multiple Heat Maps for Projected Coordinates
Description: Functions for displaying multiple images or scatterplots with a color scale, i.e., heat maps, possibly with projected coordinates. The package relies on the base graphics system, so graphics are rendered rapidly.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>

Diff between autoimage versions 2.1 dated 2020-03-28 and 2.1.9 dated 2020-05-27

 autoimage-2.1.9/autoimage/DESCRIPTION                       |   10 
 autoimage-2.1.9/autoimage/MD5                               |   55 
 autoimage-2.1.9/autoimage/NAMESPACE                         |    2 
 autoimage-2.1.9/autoimage/NEWS                              |   15 
 autoimage-2.1.9/autoimage/R/auto_setup_functions_internal.R |  247 ++
 autoimage-2.1.9/autoimage/R/autopoints.R                    |   80 
 autoimage-2.1.9/autoimage/R/heat_ppoints.R                  |   74 
 autoimage-2.1.9/autoimage/R/paxes.R                         |  392 ++--
 autoimage-2.1.9/autoimage/R/pimage.R                        | 1173 +++++-------
 autoimage-2.1.9/autoimage/R/plines.R                        |  176 -
 autoimage-2.1.9/autoimage/inst/doc/autoimage.R              |    8 
 autoimage-2.1.9/autoimage/inst/doc/autoimage.Rmd            |   15 
 autoimage-2.1.9/autoimage/inst/doc/autoimage.html           |  199 +-
 autoimage-2.1.9/autoimage/inst/doc/autopoints.R             |   22 
 autoimage-2.1.9/autoimage/inst/doc/autopoints.Rmd           |   47 
 autoimage-2.1.9/autoimage/inst/doc/autopoints.html          |  216 +-
 autoimage-2.1.9/autoimage/inst/doc/ggplot2-comparison.html  |   24 
 autoimage-2.1.9/autoimage/man/autopoints.Rd                 |   33 
 autoimage-2.1.9/autoimage/man/blank.plot.Rd                 |   44 
 autoimage-2.1.9/autoimage/man/canada.Rd                     |    6 
 autoimage-2.1.9/autoimage/man/copoly.Rd                     |    6 
 autoimage-2.1.9/autoimage/man/dot-legend.scale.args.Rd      |   26 
 autoimage-2.1.9/autoimage/man/heat_ppoints.Rd               |    4 
 autoimage-2.1.9/autoimage/man/inarccap.Rd                   |    6 
 autoimage-2.1.9/autoimage/man/narccap.Rd                    |    6 
 autoimage-2.1.9/autoimage/tests/testthat/test-autoimage.R   |  163 -
 autoimage-2.1.9/autoimage/vignettes/autoimage.Rmd           |   15 
 autoimage-2.1.9/autoimage/vignettes/autopoints.Rmd          |   47 
 autoimage-2.1/autoimage/README.md                           |only
 29 files changed, 1714 insertions(+), 1397 deletions(-)

More information about autoimage at CRAN
Permanent link

Package semTools updated to version 0.5-3 with previous version 0.5-2 dated 2019-08-30

Title: Useful Tools for Structural Equation Modeling
Description: Provides useful tools for structural equation modeling.
Author: Terrence D. Jorgensen [aut, cre] (<https://orcid.org/0000-0001-5111-6773>), Sunthud Pornprasertmanit [aut], Alexander M. Schoemann [aut] (<https://orcid.org/0000-0002-8479-8798>), Yves Rosseel [aut] (<https://orcid.org/0000-0002-4129-4477>), Patrick Miller [ctb], Corbin Quick [ctb], Mauricio Garnier-Villarreal [ctb] (<https://orcid.org/0000-0002-2951-6647>), James Selig [ctb], Aaron Boulton [ctb], Kristopher Preacher [ctb], Donna Coffman [ctb], Mijke Rhemtulla [ctb] (<https://orcid.org/0000-0003-2572-2424>), Alexander Robitzsch [ctb] (<https://orcid.org/0000-0002-8226-3132>), Craig Enders [ctb], Ruben Arslan [ctb] (<https://orcid.org/0000-0002-6670-5658>), Bell Clinton [ctb], Pavel Panko [ctb], Edgar Merkle [ctb] (<https://orcid.org/0000-0001-7158-0653>), Steven Chesnut [ctb], Jarrett Byrnes [ctb], Jason D. Rights [ctb], Ylenio Longo [ctb], Maxwell Mansolf [ctb] (<https://orcid.org/0000-0001-6861-8657>), Mattan S. Ben-Shachar [ctb] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>

Diff between semTools versions 0.5-2 dated 2019-08-30 and 0.5-3 dated 2020-05-27

 DESCRIPTION                    |   42 -
 MD5                            |  129 ++---
 NAMESPACE                      |    1 
 NEWS.md                        |   34 +
 R/NET.R                        |   83 ++-
 R/auxiliary.R                  |    3 
 R/discriminantValidity.R       |only
 R/efa.R                        |  417 +++++++++-------
 R/emmeans_lavaan.R             |only
 R/fitIndices.R                 |  273 ++++++++--
 R/htmt.R                       |    8 
 R/indProd.R                    |  185 +++----
 R/measEq.R                     | 1055 ++++++++++++++++++++++++++++++++++++-----
 R/permuteMeasEq.R              |  316 ++++++------
 R/probeInteraction.R           |  659 +++++++++++++++++++------
 R/reliability.R                |  223 ++++++--
 R/runMI-LRT.R                  |   11 
 R/runMI-Wald.R                 |   11 
 R/runMI-methods.R              |   66 ++
 R/runMI-modification.R         |   51 +
 R/runMI-score.R                |  106 ++--
 R/runMI.R                      |   17 
 R/tukeySEM.R                   |    2 
 R/zzz.R                        |    8 
 build/vignette.rds             |binary
 inst/doc/partialInvariance.pdf |binary
 inst/examples                  |only
 man/Net-class.Rd               |    2 
 man/PAVranking.Rd              |    9 
 man/bsBootMiss.Rd              |    7 
 man/chisqSmallN.Rd             |   81 +--
 man/dat2way.Rd                 |    6 
 man/dat3way.Rd                 |    6 
 man/datCat.Rd                  |    6 
 man/discriminantValidity.Rd    |only
 man/efaUnrotate.Rd             |   22 
 man/exLong.Rd                  |    6 
 man/findRMSEAsamplesize.Rd     |    3 
 man/htmt.Rd                    |    6 
 man/indProd.Rd                 |   22 
 man/lavTestLRT.mi.Rd           |    5 
 man/lavTestScore.mi.Rd         |   44 +
 man/lavTestWald.mi.Rd          |    5 
 man/lavaan.mi-class.Rd         |   22 
 man/lavaan2emmeans.Rd          |only
 man/measEq.syntax-class.Rd     |   50 +
 man/measEq.syntax.Rd           |   75 ++
 man/modindices.mi.Rd           |   44 -
 man/monteCarloMed.Rd           |    4 
 man/mvrnonnorm.Rd              |    3 
 man/net.Rd                     |   15 
 man/parcelAllocation.Rd        |    2 
 man/partialInvariance.Rd       |   16 
 man/permuteMeasEq-class.Rd     |    3 
 man/permuteMeasEq.Rd           |   31 -
 man/plotProbe.Rd               |    3 
 man/plotRMSEApower.Rd          |    4 
 man/probe2WayMC.Rd             |   49 +
 man/probe2WayRC.Rd             |   60 +-
 man/probe3WayMC.Rd             |   60 +-
 man/probe3WayRC.Rd             |   69 +-
 man/reliability.Rd             |   18 
 man/reliabilityL2.Rd           |   53 +-
 man/runMI.Rd                   |   15 
 man/semTools-deprecated.Rd     |    4 
 man/semTools.Rd                |    1 
 man/simParcel.Rd               |    6 
 man/twostage-class.Rd          |   10 
 68 files changed, 3226 insertions(+), 1321 deletions(-)

More information about semTools at CRAN
Permanent link

Package gmnl updated to version 1.1-3.2 with previous version 1.1-3.1 dated 2018-11-06

Title: Multinomial Logit Models with Random Parameters
Description: An implementation of maximum simulated likelihood method for the estimation of multinomial logit models with random coefficients as presented by Sarrias and Daziano (2017) <doi:10.18637/jss.v079.i02>. Specifically, it allows estimating models with continuous heterogeneity such as the mixed multinomial logit and the generalized multinomial logit. It also allows estimating models with discrete heterogeneity such as the latent class and the mixed-mixed multinomial logit model.
Author: Mauricio Sarrias [aut, cre] (<https://orcid.org/0000-0001-5932-4817>), Ricardo Daziano [aut], Yves Croissant [ctb]
Maintainer: Mauricio Sarrias <msarrias86@gmail.com>

Diff between gmnl versions 1.1-3.1 dated 2018-11-06 and 1.1-3.2 dated 2020-05-27

 DESCRIPTION            |   24 ++++++++--------
 MD5                    |   36 ++++++++++++------------
 NAMESPACE              |    4 --
 R/glogitform.R         |   20 ++++++++++++-
 R/gmnl.R               |    6 ++--
 R/gmnl.logliks.R       |   12 +++-----
 R/gmnl.methods.R       |   24 ++++------------
 inst/NEWS.Rd           |    9 ++++++
 man/AIC.gmnl.Rd        |    1 
 man/bread.gmnl.Rd      |    1 
 man/cov.gmnl.Rd        |   12 +++-----
 man/effect.gmnl.Rd     |    7 ++--
 man/estfun.gmnl.Rd     |    1 
 man/gFormula.Rd        |    1 
 man/getSummary.gmnl.Rd |   16 ----------
 man/gmnl.Rd            |   72 ++++++++++++++++++++++++++++++++++---------------
 man/plot.gmnl.Rd       |   27 ++++++++++++------
 man/vcov.gmnl.Rd       |   13 ++++++--
 man/wtp.gmnl.Rd        |    7 ++--
 19 files changed, 164 insertions(+), 129 deletions(-)

More information about gmnl at CRAN
Permanent link

Package timereg updated to version 1.9.5 with previous version 1.9.4 dated 2019-07-30

Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression Models for Survival Data', Springer Verlag. Plus more recent developments. Additive survival model, semiparametric proportional odds model, fast cumulative residuals, excess risk models and more. Flexible competing risks regression including GOF-tests. Two-stage frailty modelling. PLS for the additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy Silver and Klaus Holst
Maintainer: Thomas Scheike <ts@biostat.ku.dk>

Diff between timereg versions 1.9.4 dated 2019-07-30 and 1.9.5 dated 2020-05-27

 DESCRIPTION               |   10 
 MD5                       |   72 ++--
 NAMESPACE                 |    2 
 R/base.r                  |   28 +
 R/event.split.r           |    2 
 R/glm-comprisk.r          |    4 
 R/new.timecox.r           |  769 +++++++++++++++++++++++-----------------------
 R/sim-pc-hazard.r         |  477 +++++++++++++++-------------
 man/Gprop.odds.Rd         |   18 -
 man/aalen.Rd              |   26 +
 man/comp.risk.Rd          |   43 ++
 man/cox.aalen.Rd          |   37 +-
 man/cox.ipw.Rd            |   10 
 man/cum.residuals.Rd      |   13 
 man/dynreg.Rd             |   17 -
 man/event.split.Rd        |   16 
 man/invsubdist.Rd         |   33 -
 man/pe.sasieni.Rd         |   14 
 man/plot.aalen.Rd         |   23 +
 man/plot.cum.residuals.Rd |   25 +
 man/plot.dynreg.Rd        |   23 +
 man/predict.timereg.Rd    |   16 
 man/prep.comp.risk.Rd     |   19 -
 man/prop.excess.Rd        |   13 
 man/prop.odds.Rd          |   23 +
 man/prop.odds.subdist.Rd  |   28 +
 man/rchaz.Rd              |   26 +
 man/rcrisk.Rd             |   17 -
 man/res.mean.Rd           |   33 +
 man/sim.cause.cox.Rd      |   35 --
 man/sim.cif.Rd            |   49 ++
 man/sim.cox.Rd            |   12 
 man/simsubdist.Rd         |   17 -
 man/timecox.Rd            |   30 +
 man/two.stage.Rd          |   21 +
 man/wald.test.Rd          |   15 
 src/comprisk.c            |   11 
 37 files changed, 1176 insertions(+), 851 deletions(-)

More information about timereg at CRAN
Permanent link

Package ows4R updated to version 0.1-5 with previous version 0.1-4 dated 2019-11-12

Title: Interface to OGC Web-Services (OWS)
Description: Provides an Interface to Web-Services defined as standards by the Open Geospatial Consortium (OGC), including Web Feature Service (WFS) for vector data, Catalogue Service (CSW) for ISO/OGC metadata and associated standards such as the common web-service specification (OWS) and OGC Filter Encoding. The long-term purpose is to add support for additional OGC service standards such as Web Coverage Service (WCS) and Web Processing Service (WPS).
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>), Norbert Billet [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Diff between ows4R versions 0.1-4 dated 2019-11-12 and 0.1-5 dated 2020-05-27

 DESCRIPTION                            |    8 +++----
 MD5                                    |   36 ++++++++++++++++-----------------
 R/CSWGetRecordById.R                   |    2 -
 R/OGCAbstractObject.R                  |    1 
 R/OWSRequest.R                         |    1 
 R/WFSCapabilities.R                    |   27 ++++++++++--------------
 R/WFSClient.R                          |   16 ++++++++++----
 R/WFSFeatureType.R                     |   31 ++++++++++++++++++++++------
 R/WFSFeatureTypeElement.R              |   11 +++++++---
 R/WFSGetFeature.R                      |    8 ++++++-
 R/ows4R.R                              |    4 +--
 README.md                              |    4 +--
 man/WFSCapabilities.Rd                 |    4 +--
 man/WFSClient.Rd                       |    8 ++++---
 man/WFSFeatureType.Rd                  |    5 ++--
 man/ows4R.Rd                           |    4 +--
 tests/testthat/test_WFSClient_v1_0_0.R |    2 -
 tests/testthat/test_WFSClient_v1_1_0.R |    2 -
 tests/testthat/test_WFSClient_v2_0_0.R |    2 -
 19 files changed, 104 insertions(+), 72 deletions(-)

More information about ows4R at CRAN
Permanent link


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