Wed, 31 Mar 2021

Package microbial updated to version 0.0.18 with previous version 0.0.17 dated 2020-12-07

Title: Do 16s Data Analysis and Generate Figures
Description: Provides functions to enhance the available statistical analysis procedures in R by providing simple functions to analysis and visualize the 16S rRNA data.Here we present a tutorial with minimum working examples to demonstrate usage and dependencies.
Author: Kai Guo [aut, cre], Pan Gao [aut]
Maintainer: Kai Guo <guokai8@gmail.com>

Diff between microbial versions 0.0.17 dated 2020-12-07 and 0.0.18 dated 2021-03-31

 DESCRIPTION             |   16 ++---
 MD5                     |   18 +++---
 R/Functions.R           |    8 ++
 R/misc.R                |    4 +
 R/plot.R                |   12 ++--
 README.md               |  136 ++++++++++++++++++++++++++++++++----------------
 inst/doc/microbial.html |    6 +-
 man/difftest.Rd         |    3 +
 man/distcolor.Rd        |    2 
 tests                   |only
 10 files changed, 133 insertions(+), 72 deletions(-)

More information about microbial at CRAN
Permanent link

Package deepdep updated to version 0.2.2 with previous version 0.2.1 dated 2020-05-06

Title: Visualise and Explore the Deep Dependencies of R Packages
Description: Provides tools for exploration of R package dependencies. The main deepdep() function allows to acquire deep dependencies of any package and plot them in an elegant way. It also adds some popularity measures for the packages e.g. in the form of download count through the 'cranlogs' package. Uses the CRAN metadata database <http://crandb.r-pkg.org> and Bioconductor metadata <http://bioconductor.org>. Other data acquire functions are: get_dependencies(), get_downloads() and get_description(). The deepdep_shiny() function runs shiny application that helps to produce a nice 'deepdep' plot.
Author: Dominik Rafacz [aut, cre] (<https://orcid.org/0000-0003-0925-1909>), Hubert Baniecki [aut], Szymon Maksymiuk [aut], Mateusz Bakala [aut]
Maintainer: Dominik Rafacz <dominikrafacz@gmail.com>

Diff between deepdep versions 0.2.1 dated 2020-05-06 and 0.2.2 dated 2021-03-31

 deepdep-0.2.1/deepdep/inst/doc/deepdep-comparison.R                |only
 deepdep-0.2.1/deepdep/inst/doc/deepdep-package.R                   |only
 deepdep-0.2.1/deepdep/tests/testthat/test_deepdep.R                |only
 deepdep-0.2.1/deepdep/tests/testthat/test_development.R            |only
 deepdep-0.2.1/deepdep/tests/testthat/test_get_available_packages.R |only
 deepdep-0.2.1/deepdep/tests/testthat/test_get_dependencies.R       |only
 deepdep-0.2.1/deepdep/tests/testthat/test_get_description.R        |only
 deepdep-0.2.1/deepdep/tests/testthat/test_get_downloads.R          |only
 deepdep-0.2.1/deepdep/tests/testthat/test_plot.R                   |only
 deepdep-0.2.2/deepdep/DESCRIPTION                                  |   17 
 deepdep-0.2.2/deepdep/MD5                                          |   76 -
 deepdep-0.2.2/deepdep/R/deepdep.R                                  |    3 
 deepdep-0.2.2/deepdep/R/get_available_packages.R                   |    4 
 deepdep-0.2.2/deepdep/R/get_dependencies.R                         |    4 
 deepdep-0.2.2/deepdep/R/get_description.R                          |    4 
 deepdep-0.2.2/deepdep/R/get_downloads.R                            |    2 
 deepdep-0.2.2/deepdep/R/plot_deepdep.R                             |    9 
 deepdep-0.2.2/deepdep/R/plot_downloads.R                           |    3 
 deepdep-0.2.2/deepdep/R/print_package_description.R                |    2 
 deepdep-0.2.2/deepdep/build/vignette.rds                           |binary
 deepdep-0.2.2/deepdep/inst/doc/deepdep-comparison.Rmd              |   39 
 deepdep-0.2.2/deepdep/inst/doc/deepdep-comparison.html             |  282 -----
 deepdep-0.2.2/deepdep/inst/doc/deepdep-package.Rmd                 |  209 +++
 deepdep-0.2.2/deepdep/inst/doc/deepdep-package.html                |  556 +++-------
 deepdep-0.2.2/deepdep/man/deepdep.Rd                               |    3 
 deepdep-0.2.2/deepdep/man/get_available_packages.Rd                |    4 
 deepdep-0.2.2/deepdep/man/get_dependencies.Rd                      |    4 
 deepdep-0.2.2/deepdep/man/get_description.Rd                       |    4 
 deepdep-0.2.2/deepdep/man/get_downloads.Rd                         |    2 
 deepdep-0.2.2/deepdep/man/plot_deepdep.Rd                          |    9 
 deepdep-0.2.2/deepdep/man/plot_downloads.Rd                        |    3 
 deepdep-0.2.2/deepdep/man/print.package_description.Rd             |    2 
 deepdep-0.2.2/deepdep/tests/fixtures                               |only
 deepdep-0.2.2/deepdep/tests/testthat/setup-deepdep.R               |only
 deepdep-0.2.2/deepdep/tests/testthat/test-deepdep.R                |only
 deepdep-0.2.2/deepdep/tests/testthat/test-development.R            |only
 deepdep-0.2.2/deepdep/tests/testthat/test-get_available_packages.R |only
 deepdep-0.2.2/deepdep/tests/testthat/test-plot.R                   |only
 deepdep-0.2.2/deepdep/vignettes/deepdep-comparison.Rmd             |   39 
 deepdep-0.2.2/deepdep/vignettes/deepdep-package.Rmd                |  209 +++
 deepdep-0.2.2/deepdep/vignettes/miniCRAN-1.png                     |only
 deepdep-0.2.2/deepdep/vignettes/plot_dependencies1-1.png           |only
 deepdep-0.2.2/deepdep/vignettes/plot_dependencies1-2.png           |only
 deepdep-0.2.2/deepdep/vignettes/plot_dependencies2-1.png           |only
 deepdep-0.2.2/deepdep/vignettes/plot_dependencies3-1.png           |only
 deepdep-0.2.2/deepdep/vignettes/plot_dependencies4-1.png           |only
 deepdep-0.2.2/deepdep/vignettes/plot_dependencies5-1.png           |only
 47 files changed, 746 insertions(+), 743 deletions(-)

More information about deepdep at CRAN
Permanent link

Package bgumbel updated to version 0.0.3 with previous version 0.0.2.2 dated 2021-03-23

Title: Bimodal Gumbel Distribution
Description: Bimodal Gumbel distribution. General functions for performing extreme value analysis.
Author: Pedro C. Brom [aut, cre, cph] (<https://orcid.org/0000-0002-1288-7695>, http://lattes.cnpq.br/0154064396756002), Cira E. G. Otiniano [aut, cph] (<https://orcid.org/0000-0002-5619-0478>, http://lattes.cnpq.br/0307717595727716), Roberto Vila [aut, cph] (<https://orcid.org/0000-0003-1073-0114>, http://lattes.cnpq.br/4978745622057574), Marcelo B. Pereira [aut, cph] (<https://orcid.org/0000-0002-1182-5193>, https://lattes.cnpq.br/9358366674842900)
Maintainer: Pedro C. Brom <pcbrom@gmail.com>

Diff between bgumbel versions 0.0.2.2 dated 2021-03-23 and 0.0.3 dated 2021-03-31

 DESCRIPTION       |   12 ++++++------
 MD5               |   12 ++++++------
 NAMESPACE         |    1 +
 NEWS.md           |    8 ++++++--
 R/mlebgumbel.R    |   29 ++++++++++++++++++++++++++---
 README.md         |   15 ++++++++++++---
 man/mlebgumbel.Rd |   16 ++++++++++++++--
 7 files changed, 71 insertions(+), 22 deletions(-)

More information about bgumbel at CRAN
Permanent link

Package Taba updated to version 1.0.0 with previous version 0.2.0 dated 2020-07-22

Title: Taba Robust Correlations
Description: Calculates the robust Taba linear, Taba rank (monotonic), TabWil, and TabWil rank correlations. Test statistics as well as one sided or two sided p-values are provided for all correlations. Multiple correlations and p-values can be calculated simultaneously across multiple variables. In addition, users will have the option to use the partial, semipartial, and generalized partial correlations; where the partial and semipartial correlations use linear, logistic, or Poisson regression to modify the specified variable.
Author: Mohammad Tabatabai [aut], Derek Wilus [aut, cre]
Maintainer: Derek Wilus <dwilus@mmc.edu>

Diff between Taba versions 0.2.0 dated 2020-07-22 and 1.0.0 dated 2021-03-31

 DESCRIPTION          |    8 ++++----
 MD5                  |   23 ++++++++++++-----------
 R/Taba.R             |    4 +++-
 R/TabaGpartial.R     |   12 +++++++-----
 R/TabaMatrix.R       |    4 +++-
 R/TabaPartial.R      |    4 +++-
 R/TabaTest.R         |   48 +++++++++++++++++++++++++++++++++++++++++-------
 build                |only
 man/taba.Rd          |    4 +++-
 man/taba.gpartial.Rd |   12 +++++++-----
 man/taba.matrix.Rd   |    4 +++-
 man/taba.partial.Rd  |    4 +++-
 man/taba.test.Rd     |   11 ++++++++---
 13 files changed, 97 insertions(+), 41 deletions(-)

More information about Taba at CRAN
Permanent link

Package plantecophys updated to version 1.4-6 with previous version 1.4-4 dated 2019-03-13

Title: Modelling and Analysis of Leaf Gas Exchange Data
Description: Coupled leaf gas exchange model, A-Ci curve simulation and fitting, Ball-Berry stomatal conductance models, leaf energy balance using Penman-Monteith, Cowan-Farquhar optimization, humidity unit conversions. See Duursma (2015) <doi:10.1371/journal.pone.0143346>.
Author: Remko Duursma [aut, cre]
Maintainer: Remko Duursma <remkoduursma@gmail.com>

Diff between plantecophys versions 1.4-4 dated 2019-03-13 and 1.4-6 dated 2021-03-31

 DESCRIPTION                          |   12 -
 MD5                                  |   47 ++---
 R/fitBB.R                            |   21 +-
 R/fitaci_methods.R                   |   86 ++++++----
 build/partial.rdb                    |binary
 build/vignette.rds                   |binary
 inst/doc/Introduction_to_fitaci.R    |   30 +--
 inst/doc/Introduction_to_fitaci.html |  284 +++++++----------------------------
 inst/doc/fitaci-FAQ.R                |    8 
 inst/doc/fitaci-FAQ.Rmd              |    2 
 inst/doc/fitaci-FAQ.html             |  280 +++++++---------------------------
 inst/doc/new_T_responses.R           |    2 
 inst/doc/new_T_responses.html        |  215 +++-----------------------
 man/AciC4.Rd                         |   26 ++-
 man/FARAO.Rd                         |   17 +-
 man/Photosyn.Rd                      |   50 ++++--
 man/PhotosynEB.Rd                    |   12 +
 man/PhotosynTuzet.Rd                 |    3 
 man/acidata1.Rd                      |    6 
 man/fitBB.Rd                         |   12 +
 man/fitaci.Rd                        |   59 +++++--
 man/fitacis.Rd                       |   31 ++-
 man/manyacidat.Rd                    |    6 
 tests/testthat/Rplots.pdf            |only
 vignettes/fitaci-FAQ.Rmd             |    2 
 25 files changed, 444 insertions(+), 767 deletions(-)

More information about plantecophys at CRAN
Permanent link

New package spatsurv with initial version 1.6
Package: spatsurv
Title: Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models
Version: 1.6
Date: 2021-03-26
Author: Benjamin M. Taylor and Barry S. Rowlingson Additional contributions Ziyu Zheng
Maintainer: Benjamin M. Taylor <benjamin.taylor.software@gmail.com>
Description: Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models. See Benjamin M. Taylor, Barry S. Rowlingson (2017) <doi:10.18637/jss.v077.i04>.
License: GPL-3
Imports: survival, sp, spatstat.geom, spatstat.core, spatstat (>= 2.0-0), raster, iterators, RandomFields, fields, Matrix, stringr, rgeos, RColorBrewer, methods, lubridate
Suggests: rgdal, rgl, OpenStreetMap
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-03-31 16:06:38 UTC; ben
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2021-03-31 16:30:03 UTC

More information about spatsurv at CRAN
Permanent link

Package fpeek updated to version 0.1.2 with previous version 0.1.1 dated 2019-04-16

Title: Check Text Files Content at a Glance
Description: Tools to help text files importation. It can return the number of lines; print the first and last lines; convert encoding. Operations are made without reading the entire file before starting, resulting in good performances with large files. This package provides an alternative to a simple use of the 'head', 'tail', 'wc' and 'iconv' programs that are not always available on machine where R is installed.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@ardata.fr>

Diff between fpeek versions 0.1.1 dated 2019-04-16 and 0.1.2 dated 2021-03-31

 DESCRIPTION |    9 ++++-----
 MD5         |    7 ++++---
 NEWS.md     |    4 ++++
 README.md   |   19 ++++++-------------
 man/figures |only
 5 files changed, 18 insertions(+), 21 deletions(-)

More information about fpeek at CRAN
Permanent link

Package ClustAssess updated to version 0.1.1 with previous version 0.1.0 dated 2021-03-31

Title: Tools for Assessing Clustering
Description: A set of tools for evaluating clustering similarity across methods and method stability using element-centric clustering comparison (Gates et al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package enables data-wide assessment of clustering robustness using proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014) <doi:10.1038/srep06207>), which can be used to infer the optimal number of clusters in the data.
Author: Arash Shahsavari [aut, cre], Irina Mohorianu [aut]
Maintainer: Arash Shahsavari <as3006@cam.ac.uk>

Diff between ClustAssess versions 0.1.0 dated 2021-03-31 and 0.1.1 dated 2021-03-31

 DESCRIPTION                                   |    8 ++++----
 MD5                                           |    8 ++++----
 README.md                                     |   11 ++++++++++-
 inst/doc/ClustAssess.html                     |    2 +-
 inst/doc/comparing-soft-and-hierarchical.html |    2 +-
 5 files changed, 20 insertions(+), 11 deletions(-)

More information about ClustAssess at CRAN
Permanent link

Package aRbs updated to version 0.1.2 with previous version 0.1.1 dated 2021-03-27

Title: Find Arbitrage Opportunities for Sports Matches
Description: Money doesn't grow on trees. Arbitrage opportunities do. Find the best arbitrage opportunities (arbs) in sports matches through <https://www.oddschecker.com/>. This package allows the user to input the URLs of <https://www.oddschecker.com/> subdomains in order to extract any opportunities for arbitrage. The majority of the functionality is implemented using the function `get_arbs_shiny()`, which simply provides an easy-to-use interface wrapping the functionality of the `get_arbs()` function. This function first finds all subdomains of the URL entered, then filters to only include those that look like event betting pages. Next, odds are scraped from the various bookmakers listed for that event, before returning combinations of bookmakers, odds or outcomes that could be used for arbitrage. Bets placed subsequently are done so at bettor's risk. Please see package README for full details.
Author: Andrew Little [aut, cre]
Maintainer: Andrew Little <andrewlittlebristol@gmail.com>

Diff between aRbs versions 0.1.1 dated 2021-03-27 and 0.1.2 dated 2021-03-31

 aRbs-0.1.1/aRbs/inst               |only
 aRbs-0.1.2/aRbs/DESCRIPTION        |    9 +++++----
 aRbs-0.1.2/aRbs/MD5                |   19 ++++++++++---------
 aRbs-0.1.2/aRbs/NAMESPACE          |    1 +
 aRbs-0.1.2/aRbs/NEWS.md            |    9 +++++++--
 aRbs-0.1.2/aRbs/R/get_arbs.R       |   17 +++++++++++++++--
 aRbs-0.1.2/aRbs/R/get_arbs_shiny.R |   18 +++++++++++-------
 aRbs-0.1.2/aRbs/R/print.arb.R      |   22 ++++++++++++----------
 aRbs-0.1.2/aRbs/R/server.R         |only
 aRbs-0.1.2/aRbs/R/ui.R             |only
 aRbs-0.1.2/aRbs/man/get_arbs.Rd    |    2 +-
 aRbs-0.1.2/aRbs/man/print.arb.Rd   |    4 ++--
 12 files changed, 64 insertions(+), 37 deletions(-)

More information about aRbs at CRAN
Permanent link

Package tiff updated to version 0.1-8 with previous version 0.1-7 dated 2021-03-02

Title: Read and Write TIFF Images
Description: Functions to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors, including native image representation.
Author: Simon Urbanek <Simon.Urbanek@r-project.org> [aut, cre], Kent Johnson <kjohnson@akoyabio.com> [ctb]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>

Diff between tiff versions 0.1-7 dated 2021-03-02 and 0.1-8 dated 2021-03-31

 DESCRIPTION     |    9 +-
 MD5             |   14 +--
 NEWS            |   27 +++++-
 R/read.R        |   31 ++++++-
 R/write.R       |    2 
 man/readTIFF.Rd |   72 +++++++++++-----
 src/read.c      |  243 +++++++++++++++++++++++++++++++++++++++++++++++---------
 src/reg.c       |    5 -
 8 files changed, 324 insertions(+), 79 deletions(-)

More information about tiff at CRAN
Permanent link

Package RAQSAPI updated to version 2.0.1 with previous version 2.0.0 dated 2021-03-13

Title: A R Interface to the US EPA Air Quality System Data Mart API
Description: Retrieve air monitoring data and associated metadata from the US Environmental Protection Agency's Air Quality System service using functions. See <https://aqs.epa.gov/aqsweb/documents/data_api.html> for details about the US EPA Data Mart API.
Author: Clinton Mccrowey [cre, aut] (United States Enviornmental Protection Agency Region 3 Air and Radiation Division), Timothy Sharac [ctb, rev] (United States Enviornmental Protection Agency), Nick Mangus [rev] (United States Enviornmental Protection Agency), Doug Jager [ctb, rev] (United States Enviornmental Protection Agency), Ryan Brown [ctb, rev] (United States Enviornmental Protection Agency), Daniel Garver [ctb, rev] (United States Enviornmental Protection Agency), Benjamin Wells [ctb, rev] (United States Enviornmental Protection Agency)
Maintainer: Clinton Mccrowey <mccrowey.clinton@epa.gov>

Diff between RAQSAPI versions 2.0.0 dated 2021-03-13 and 2.0.1 dated 2021-03-31

 RAQSAPI-2.0.0/RAQSAPI/R/AQSAPI.R                                     |only
 RAQSAPI-2.0.1/RAQSAPI/DESCRIPTION                                    |   16 
 RAQSAPI-2.0.1/RAQSAPI/MD5                                            |  193 
 RAQSAPI-2.0.1/RAQSAPI/NEWS.md                                        |   10 
 RAQSAPI-2.0.1/RAQSAPI/R/RAQSAPIlistfunctions.R                       |only
 RAQSAPI-2.0.1/RAQSAPI/R/bybox.R                                      |only
 RAQSAPI-2.0.1/RAQSAPI/R/bycbsa.R                                     |only
 RAQSAPI-2.0.1/RAQSAPI/R/bycounty.R                                   |only
 RAQSAPI-2.0.1/RAQSAPI/R/byma.R                                       |only
 RAQSAPI-2.0.1/RAQSAPI/R/bypqao.R                                     |only
 RAQSAPI-2.0.1/RAQSAPI/R/bysite.R                                     |only
 RAQSAPI-2.0.1/RAQSAPI/R/bystate.R                                    |only
 RAQSAPI-2.0.1/RAQSAPI/R/setupfunctions.R                             |only
 RAQSAPI-2.0.1/RAQSAPI/build/RAQSAPI.pdf                              |13822 +++++-----
 RAQSAPI-2.0.1/RAQSAPI/inst/WORDLIST                                  |  206 
 RAQSAPI-2.0.1/RAQSAPI/inst/codecov.yml                               |only
 RAQSAPI-2.0.1/RAQSAPI/inst/doc/InstallandSetup.Rmd                   |   18 
 RAQSAPI-2.0.1/RAQSAPI/inst/doc/InstallandSetup.html                  |   30 
 RAQSAPI-2.0.1/RAQSAPI/inst/doc/RAQSAPIFunctions-Brief.Rmd            |  147 
 RAQSAPI-2.0.1/RAQSAPI/inst/doc/RAQSAPIFunctions-Brief.html           |   39 
 RAQSAPI-2.0.1/RAQSAPI/inst/doc/RAQSAPIvignette.html                  |   34 
 RAQSAPI-2.0.1/RAQSAPI/inst/doc/UsingRAQSAPI.Rmd                      |  114 
 RAQSAPI-2.0.1/RAQSAPI/inst/doc/UsingRAQSAPI.html                     |   98 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_annualsummary_by_box.Rd                |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_annualsummary_by_cbsa.Rd               |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_annualsummary_by_county.Rd             |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_annualsummary_by_site.Rd               |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_annualsummary_by_state.Rd              |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_cbsas.Rd                               |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_classes.Rd                             |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_counties_by_state.Rd                   |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_credentials.Rd                         |    4 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_dailysummary_by_box.Rd                 |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_dailysummary_by_cbsa.Rd                |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_dailysummary_by_county.Rd              |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_dailysummary_by_site.Rd                |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_dailysummary_by_state.Rd               |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_fields_by_service.Rd                   |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_isavailable.Rd                         |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_knownissues.Rd                         |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_mas.Rd                                 |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_monitors_by_box.Rd                     |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_monitors_by_cbsa.Rd                    |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_monitors_by_county.Rd                  |    6 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_monitors_by_site.Rd                    |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_monitors_by_state.Rd                   |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_parameters_by_class.Rd                 |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_pqaos.Rd                               |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_blanks_by_MA.Rd                     |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_blanks_by_county.Rd                 |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_blanks_by_pqao.Rd                   |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_blanks_by_site.Rd                   |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_blanks_by_state.Rd                  |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_collocated_assessments_by_MA.Rd     |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_collocated_assessments_by_county.Rd |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_collocated_assessments_by_pqao.Rd   |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_collocated_assessments_by_site.Rd   |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_collocated_assessments_by_state.Rd  |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateaudit_by_MA.Rd              |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateaudit_by_county.Rd          |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateaudit_by_pqao.Rd            |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateaudit_by_site.Rd            |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateaudit_by_state.Rd           |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateverification_by_MA.Rd       |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateverification_by_county.Rd   |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateverification_by_pqao.Rd     |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateverification_by_site.Rd     |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_flowrateverification_by_state.Rd    |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_one_point_qc_by_MA.Rd               |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_one_point_qc_by_county.Rd           |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_one_point_qc_by_pqao.Rd             |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_one_point_qc_by_site.Rd             |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_one_point_qc_by_state.Rd            |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_pep_audit_by_MA.Rd                  |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_pep_audit_by_county.Rd              |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_pep_audit_by_pqao.Rd                |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_pep_audit_by_site.Rd                |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_qa_pep_audit_by_state.Rd               |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_removeheader.Rd                        |    4 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_revisionhistory.Rd                     |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_sampledata_by_box.Rd                   |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_sampledata_by_cbsa.Rd                  |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_sampledata_by_county.Rd                |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_sampledata_by_site.Rd                  |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_sampledata_by_state.Rd                 |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_sign_up.Rd                             |    4 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_sites_by_county.Rd                     |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_states.Rd                              |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_transactionsample_by_MA.Rd             |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_transactionsample_by_county.Rd         |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_transactionsample_by_site.Rd           |    2 
 RAQSAPI-2.0.1/RAQSAPI/man/aqs_transactionsample_by_state.Rd          |    2 
 RAQSAPI-2.0.1/RAQSAPI/tests/testthat/test-RAQSAPlistfunctions.R      |    8 
 RAQSAPI-2.0.1/RAQSAPI/tests/testthat/test-byCBSA.R                   |  112 
 RAQSAPI-2.0.1/RAQSAPI/tests/testthat/test-byMA.R                     |  174 
 RAQSAPI-2.0.1/RAQSAPI/tests/testthat/test-bybox.R                    |   54 
 RAQSAPI-2.0.1/RAQSAPI/tests/testthat/test-bycounty.R                 |  234 
 RAQSAPI-2.0.1/RAQSAPI/tests/testthat/test-bypqao.R                   |    8 
 RAQSAPI-2.0.1/RAQSAPI/tests/testthat/test-bysite.R                   |  260 
 RAQSAPI-2.0.1/RAQSAPI/tests/testthat/test-bystate.R                  |  246 
 RAQSAPI-2.0.1/RAQSAPI/vignettes/InstallandSetup.Rmd                  |   18 
 RAQSAPI-2.0.1/RAQSAPI/vignettes/RAQSAPIFunctions-Brief.Rmd           |  147 
 RAQSAPI-2.0.1/RAQSAPI/vignettes/UsingRAQSAPI.Rmd                     |  114 
 103 files changed, 8197 insertions(+), 8053 deletions(-)

More information about RAQSAPI at CRAN
Permanent link

New package HierDpart with initial version 1.5.0
Package: HierDpart
Version: 1.5.0
Date: 2021-03-31
Title: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems
Description: Miscellaneous R functions for calculating and decomposing hierarchical diversity metrics, including hierarchical allele richness, hierarchical exponential Shannon entropy (true diversity of order q=1), hierarchical heterozygosity and genetic differentiation (Jaccard dissimilarity, Delta D, Fst and Jost's D). In addition,a new approach to identify population structure based on the homogeneity of multivariate variances of Shannon differentiation is presented. This package allows users to analyse spatial structured genetic data or species data under a unifying framework (Gaggiotti, O. E. et al, 2018, Evol Appl, 11:1176-1193; <DOI:10.1111/eva.12593>), which partitions diversity and differentiation into any hierarchical levels. It helps you easily structure and format your data. In summary,it implements the analyses of true diversity profiles (q=0, 1, 2), hierarchical diversities and differentiation decomposition, visualization of population structure, as well as the estimation of correlation between geographic distance and genetic differentiation.
Author: Xinghu Qin
Maintainer: Xinghu Qin <qinxinghu@gmail.com>
Depends: R (>= 3.0)
License: GPL (>= 3)
SystemRequirements: GNU make
URL: https://github.com/xinghuq/HierDpart
BugReports: https://github.com/xinghuq/HierDpart/issues
Imports: GGally, adegenet, diveRsity, entropart, mmod,ggplot2, hierfstat, reshape2, tibble,ade4,vegan,ape,pegas,permute
VignetteBuilder: knitr
NeedsCompilation: no
Suggests: knitr,testthat,rmarkdown
Packaged: 2021-03-31 14:30:24 UTC; xq5
Repository: CRAN
Date/Publication: 2021-03-31 15:20:05 UTC

More information about HierDpart at CRAN
Permanent link

Package aopdata updated to version 0.2.0 with previous version 0.1.0 dated 2021-03-08

Title: Data from the 'Access to Opportunities Project (AOP)'
Description: Download data from the 'Access to Opportunities Project (AOP)'. The 'aopdata' package brings annual estimates of access to employment, health and education services by transport mode, as well as data on the spatial distribution of population, schools and health-care facilities at a fine spatial resolution for all cities included in the study. More info on the 'AOP' website <https://www.ipea.gov.br/acessooportunidades/en/>.
Author: Rafael H. M. Pereira [aut, cre] (<https://orcid.org/0000-0003-2125-7465>), Daniel Herszenhut [aut] (<https://orcid.org/0000-0001-8066-1105>), Marcus Saraiva [aut] (<https://orcid.org/0000-0001-6218-2338>), Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>

Diff between aopdata versions 0.1.0 dated 2021-03-08 and 0.2.0 dated 2021-03-31

 DESCRIPTION                     |   13 
 LICENSE                         |    2 
 MD5                             |   82 ++---
 NAMESPACE                       |    2 
 NEWS.md                         |   11 
 R/download_metadata.R           |   23 -
 R/read_access.R                 |   14 
 R/read_grid.R                   |    5 
 R/read_landuse.R                |   24 +
 R/read_population.R             |only
 R/utils.R                       |  223 ++++++++++---
 README.md                       |   38 +-
 build/vignette.rds              |binary
 inst/doc/access_inequality.R    |    1 
 inst/doc/access_inequality.Rmd  |    3 
 inst/doc/access_inequality.html |  639 +++++++++++++++++++++++++++++++++++++--
 inst/doc/access_maps.R          |   16 
 inst/doc/access_maps.Rmd        |   16 
 inst/doc/access_maps.html       |  651 ++++++++++++++++++++++++++++++++++++++--
 inst/doc/intro_to_aopdata.R     |only
 inst/doc/intro_to_aopdata.Rmd   |only
 inst/doc/intro_to_aopdata.html  |only
 inst/doc/landuse_maps.R         |   20 -
 inst/doc/landuse_maps.Rmd       |   18 -
 inst/doc/landuse_maps.html      |  262 ++++++++++++++--
 man/aop_merge.Rd                |    7 
 man/aop_spatial_join.Rd         |    1 
 man/check_connection.Rd         |only
 man/download_data.Rd            |    1 
 man/load_data.Rd                |    1 
 man/read_access.Rd              |    9 
 man/read_grid.Rd                |    2 
 man/read_landuse.Rd             |   10 
 man/read_population.Rd          |only
 man/rm_accent.Rd                |    1 
 man/select_city_input.Rd        |    1 
 man/select_metadata.Rd          |    1 
 man/select_mode_input.Rd        |    1 
 man/select_year_input.Rd        |    1 
 tests                           |only
 vignettes/access_inequality.Rmd |    3 
 vignettes/access_maps.Rmd       |   16 
 vignettes/intro_to_aopdata.Rmd  |only
 vignettes/landuse_maps.Rmd      |   18 -
 44 files changed, 1846 insertions(+), 290 deletions(-)

More information about aopdata at CRAN
Permanent link

Package volcano3D updated to version 1.2.0 with previous version 1.1.0 dated 2021-02-22

Title: Interactive Plotting of Three-Way Differential Expression Analysis
Description: Differential expression (DE) analysis can be used to discover quantitative changes in expression levels between experimental groups. Such results are typically visualised using volcano plots, however in cases where more than two experimental groups are involved, visualising results can become convoluted and it quickly becomes difficult to see the wood for the trees. This package provides easy-to-use functions to extract and visualise outputs from DE between three groups (primarily aimed at 'limma' and 'DESeq2' outputs). We present novel methods to map DE results into polar coordinates to enable users to combine and simultaneously view three sets of results. These graphics also possess optional 'plotly' outputs for interactive and three-dimensional functionality, as seen in Lewis et. al. (2019) <doi:10.1016/j.celrep.2019.07.091>.
Author: Katriona Goldmann [aut, cre] (<https://orcid.org/0000-0002-9073-6323>), Myles Lewis [aut] (<https://orcid.org/0000-0001-9365-5345>)
Maintainer: Katriona Goldmann <k.goldmann@qmul.ac.uk>

Diff between volcano3D versions 1.1.0 dated 2021-02-22 and 1.2.0 dated 2021-03-31

 DESCRIPTION            |   16 +
 MD5                    |   10 -
 NEWS.md                |    4 
 R/volcano3D.R          |   18 +-
 inst/doc/Vignette.html |  434 +------------------------------------------------
 man/volcano3D.Rd       |   10 +
 6 files changed, 52 insertions(+), 440 deletions(-)

More information about volcano3D at CRAN
Permanent link

New package lgcp with initial version 1.7
Package: lgcp
Maintainer: Benjamin M. Taylor <benjamin.taylor.software@gmail.com>
License: GPL-2 | GPL-3
Title: Log-Gaussian Cox Process
LazyLoad: yes
Author: Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle. Additional code contributions from Edzer Pebesma, Dominic Schumacher.
Description: Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo. See Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle (2015) <doi:10.18637/jss.v063.i07>.
Version: 1.7
Date: 2021-03-26
Imports: spatstat.geom, spatstat.core, spatstat (>= 2.0-0), spatstat.utils, sp, raster, tcltk, RandomFields, iterators, ncdf4, methods, rpanel (>= 1.1-3), fields, maptools, Matrix, rgeos
Suggests: sparr, rgdal, gpclib
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-03-31 13:29:28 UTC; ben
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2021-03-31 14:50:02 UTC

More information about lgcp at CRAN
Permanent link

Package gamlss updated to version 5.3-4 with previous version 5.3-2 dated 2021-03-16

Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Author: Mikis Stasinopoulos [aut, cre, cph], Bob Rigby [aut], Vlasios Voudouris [ctb], Calliope Akantziliotou [ctb], Marco Enea [ctb], Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>

Diff between gamlss versions 5.3-2 dated 2021-03-16 and 5.3-4 dated 2021-03-31

 DESCRIPTION       |    8 ++++----
 MD5               |    8 ++++----
 R/gamlss-5.R      |    2 +-
 build/partial.rdb |binary
 inst/doc/NEWS.txt |    6 ++++++
 5 files changed, 15 insertions(+), 9 deletions(-)

More information about gamlss at CRAN
Permanent link

Package SoundShape updated to version 1.1.0 with previous version 1.0 dated 2020-10-29

Title: Sound Waves Onto Morphometric Data
Description: Implement a promising, and yet little explored protocol for bioacoustical analysis, the eigensound method by MacLeod, Krieger and Jones (2013) <doi:10.4404/hystrix-24.1-6299>. Eigensound is a multidisciplinary method focused on the direct comparison between stereotyped sounds from different species. 'SoundShape', in turn, provide the tools required for anyone to go from sound waves to Principal Components Analysis, using tools extracted from traditional bioacoustics (i.e. 'tuneR' and 'seewave' packages), geometric morphometrics (i.e. 'geomorph' package) and multivariate analysis (e.g. 'stats' package). For more information, please see Rocha and Romano (2021) and check 'SoundShape' repository on GitHub for news and updates <https://github.com/p-rocha/SoundShape>.
Author: Pedro Rocha [aut, cre]
Maintainer: Pedro Rocha <p.rocha1990@gmail.com>

Diff between SoundShape versions 1.0 dated 2020-10-29 and 1.1.0 dated 2021-03-31

 DESCRIPTION                   |   16 +-
 MD5                           |   18 +-
 R/hypo.surf.R                 |    5 
 README.md                     |  276 ++++++++++++++++++++++++------------------
 build/vignette.rds            |binary
 inst/doc/Getting-started.Rmd  |  114 +++++++++++------
 inst/doc/Getting-started.html |  156 ++++++++++++++++-------
 man/SoundShape.Rd             |    5 
 man/hypo.surf.Rd              |    4 
 vignettes/Getting-started.Rmd |  114 +++++++++++------
 10 files changed, 440 insertions(+), 268 deletions(-)

More information about SoundShape at CRAN
Permanent link

New package sapa with initial version 2.0-3
Package: sapa
Title: Spectral Analysis for Physical Applications
Version: 2.0-3
Authors@R: c(person("Donald", "Percival", email = "dbpercival@gmail.com", role = c("cre", "aut")), person("William", "Constantine", email = "wlbconstan@gmail.com", role = "aut"))
Depends: R (>= 3.0.2)
Description: Software for book "Spectral Analysis for Physical Applications", Donald B. Percival and Andrew T. Walden (1993), <doi:10.1017/CBO9780511622762>, Cambridge University Press. Contains functionality for nonparametric spectral density estimation of time series, including direct spectral estimators, lag window estimators, estimators based on Welch's overlapped segment averaging (WOSA) and multitaper estimators based on discrete prolate spheroidal sequences (DPSS) and on sinusoidal tapers.
License: GPL-2
Imports: ifultools (>= 2.0-22), splus2R (>= 1.3-3), methods
NeedsCompilation: yes
Packaged: 2021-03-31 04:09:32 UTC; ied
Author: Donald Percival [cre, aut], William Constantine [aut]
Maintainer: Donald Percival <dbpercival@gmail.com>
Repository: CRAN
Date/Publication: 2021-03-31 13:20:03 UTC

More information about sapa at CRAN
Permanent link

New package rdecision with initial version 1.0.3
Package: rdecision
Title: Decision Analytic Modelling in Health Economics
Version: 1.0.3
Authors@R: c( person(given="Andrew", family="Sims", email = "andrew.sims@newcastle.ac.uk", role = c("aut", "cre"), comment = c(ORCID="0000-0002-9553-7278")), person(given="Kim", family="Fairbairn", email="kim.fairbairn@nhs.net", role=c("aut"), comment = c(ORCID="0000-0001-5108-6279")))
Description: Classes and functions for modelling health care interventions using cohort models (decision trees). Mechanisms are provided for associating an uncertainty distribution with each source variable and for ensuring transparency of the mathematical relationships between variables. The package terminology follows Briggs "Decision Modelling for Health Economic Evaluation" (2006, ISBN:978-0-19-852662-9).
Depends: R (>= 3.1.0)
Imports: grid, R6, rlang (>= 0.4.2), stats, utils
Suggests: covr, knitr, pander, rmarkdown, testthat (>= 3.0.0), utf8
License: GPL-3
LazyData: false
Language: en-GB
Encoding: UTF-8
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2021-03-30 21:56:10 UTC; andrew
Author: Andrew Sims [aut, cre] (<https://orcid.org/0000-0002-9553-7278>), Kim Fairbairn [aut] (<https://orcid.org/0000-0001-5108-6279>)
Maintainer: Andrew Sims <andrew.sims@newcastle.ac.uk>
Repository: CRAN
Date/Publication: 2021-03-31 13:20:06 UTC

More information about rdecision at CRAN
Permanent link

Package document updated to version 3.3.1 with previous version 3.3.0 dated 2020-10-30

Title: Run 'roxygen2' on (Chunks of) Single Code Files
Description: Have you ever been tempted to create 'roxygen2'-style documentation comments for one of your functions that was not part of one of your packages (yet)? This is exactly what this package is about: running 'roxygen2' on (chunks of) a single code file.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

Diff between document versions 3.3.0 dated 2020-10-30 and 3.3.1 dated 2021-03-31

 document-3.3.0/document/R/test_helpers.R                       |only
 document-3.3.0/document/man/get_RUN_R_TESTS.Rd                 |only
 document-3.3.0/document/man/is_running_on_fvafrcu_machines.Rd  |only
 document-3.3.0/document/man/is_running_on_gitlab_com.Rd        |only
 document-3.3.0/document/man/set_RUN_R_TESTS.Rd                 |only
 document-3.3.1/document/DESCRIPTION                            |   11 -
 document-3.3.1/document/MD5                                    |   26 +--
 document-3.3.1/document/NAMESPACE                              |    4 
 document-3.3.1/document/NEWS.md                                |   10 +
 document-3.3.1/document/R/document.R                           |   34 ++--
 document-3.3.1/document/inst/doc/Introduction_to_document.html |   75 +---------
 document-3.3.1/document/inst/expected_files/simple.html        |only
 document-3.3.1/document/inst/runit_tests/expected_files.r      |   23 +--
 document-3.3.1/document/tests/testthat.R                       |    4 
 document-3.3.1/document/tests/testthat/test_basic.R            |    6 
 document-3.3.1/document/tests/testthat/test_check.R            |    2 
 document-3.3.1/document/tests/testthat/test_parse.R            |    2 
 17 files changed, 76 insertions(+), 121 deletions(-)

More information about document at CRAN
Permanent link

Package BioVenn updated to version 1.1.2 with previous version 1.1.1 dated 2021-01-07

Title: Create Area-Proportional Venn Diagrams from Biological Lists
Description: Creates an area-proportional Venn diagram of 2 or 3 circles. 'BioVenn' is the only R package that can automatically generate an accurate area-proportional Venn diagram by having only lists of (biological) identifiers as input. Also offers the option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Based on the BioVenn web interface available at <https://www.biovenn.nl>. Hulsen (2021) <doi:10.3233/DS-210032>.
Author: Tim Hulsen [aut, cre] (<https://orcid.org/0000-0002-0208-8443>)
Maintainer: Tim Hulsen <thulsen@gmail.com>

Diff between BioVenn versions 1.1.1 dated 2021-01-07 and 1.1.2 dated 2021-03-31

 DESCRIPTION        |    9 
 MD5                |   10 
 R/draw.venn.R      | 1516 ++++++++++++++++++++++++++---------------------------
 build/vignette.rds |binary
 inst/CITATION      |   20 
 man/draw.venn.Rd   |    4 
 6 files changed, 779 insertions(+), 780 deletions(-)

More information about BioVenn at CRAN
Permanent link

Package wrMisc updated to version 1.5.4 with previous version 1.5.3 dated 2021-02-26

Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Many times large experimental datasets need some additional filtering, adequate functions are provided. Batch reading (or writing) of sets of files and combining data to arrays is supported, too. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>

Diff between wrMisc versions 1.5.3 dated 2021-02-26 and 1.5.4 dated 2021-03-31

 DESCRIPTION                   |    7 -
 MD5                           |   22 +--
 NAMESPACE                     |    1 
 R/coordOfFilt.R               |only
 R/linModelSelect.R            |   67 ++++-----
 R/moderTestXgrp.R             |    2 
 build/vignette.rds            |binary
 inst/doc/wrMiscVignette1.R    |   15 +-
 inst/doc/wrMiscVignette1.Rmd  |   33 +++-
 inst/doc/wrMiscVignette1.html |  286 +++++++++++++++++++-----------------------
 man/coordOfFilt.Rd            |only
 man/linModelSelect.Rd         |   39 +++--
 vignettes/wrMiscVignette1.Rmd |   33 +++-
 13 files changed, 263 insertions(+), 242 deletions(-)

More information about wrMisc at CRAN
Permanent link

Package spatstat.gui updated to version 2.0-0 with previous version 1.2-0 dated 2021-02-16

Title: Interactive Graphics Functions for the 'spatstat' Package
Description: Extension to the 'spatstat' package, containing interactive graphics capabilities.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>), Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>), Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.gui versions 1.2-0 dated 2021-02-16 and 2.0-0 dated 2021-03-31

 DESCRIPTION |   15 +++++++--------
 MD5         |    2 +-
 2 files changed, 8 insertions(+), 9 deletions(-)

More information about spatstat.gui at CRAN
Permanent link

Package shapes updated to version 1.2.6 with previous version 1.2.5 dated 2019-12-01

Title: Statistical Shape Analysis
Description: Routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons.
Author: Ian L. Dryden
Maintainer: Ian Dryden <ian.dryden@nottingham.ac.uk>

Diff between shapes versions 1.2.5 dated 2019-12-01 and 1.2.6 dated 2021-03-31

 DESCRIPTION                |    8 -
 MD5                        |   76 +++++------
 NAMESPACE                  |    3 
 NEWS.md                    |    4 
 R/shapes.R                 |  294 ++++++++++++++++++++++++++++++++++++++++++++-
 data/apes.rda              |binary
 data/brains.rda            |binary
 data/cortical.rda          |binary
 data/digit3.dat.rda        |binary
 data/dna.dat.rda           |binary
 data/gels.rda              |binary
 data/gorf.dat.rda          |binary
 data/gorm.dat.rda          |binary
 data/humanmove.rda         |binary
 data/macaques.rda          |binary
 data/macf.dat.rda          |binary
 data/macm.dat.rda          |binary
 data/mice.rda              |binary
 data/nsa.rda               |binary
 data/panf.dat.rda          |binary
 data/panm.dat.rda          |binary
 data/pongof.dat.rda        |binary
 data/pongom.dat.rda        |binary
 data/protein.rda           |binary
 data/qcet2.dat.rda         |binary
 data/qlet2.dat.rda         |binary
 data/qset2.dat.rda         |binary
 data/rats.rda              |binary
 data/sand.rda              |binary
 data/schizophrenia.dat.rda |binary
 data/schizophrenia.rda     |binary
 data/shells.rda            |binary
 data/sooty.dat.rda         |binary
 data/sooty.rda             |binary
 data/steroids.rda          |binary
 man/plot3darcs.Rd          |only
 man/pns.Rd                 |    5 
 man/pns4pc.Rd              |    5 
 man/pnss3d.Rd              |only
 man/shapes-internal.Rd     |    3 
 40 files changed, 348 insertions(+), 50 deletions(-)

More information about shapes at CRAN
Permanent link

Package prioritizr updated to version 7.0.1 with previous version 5.0.3 dated 2020-11-24

Title: Systematic Conservation Prioritization in R
Description: Systematic conservation prioritization using mixed integer linear programming (MILP). It provides a flexible interface for building and solving conservation planning problems. Once built, conservation planning problems can be solved using a variety of commercial and open-source exact algorithm solvers. By using exact algorithm solvers, solutions can be generated that are guaranteed to be optimal (or within a pre-specified optimality gap). Furthermore, conservation problems can be constructed to optimize the spatial allocation of different management actions or zones, meaning that conservation practitioners can identify solutions that benefit multiple stakeholders. To solve large-scale or complex conservation planning problems, users should install the Gurobi optimization software (available from <https://www.gurobi.com/>) and the 'gurobi' R package (see Gurobi Installation Guide vignette for details). Additionally, the 'rcbc' R package (available at <https://github.com/dirkschumacher/rcbc>) can be used to generate solutions using the CBC optimization software (<https://projects.coin-or.org/Cbc>).
Author: Jeffrey O Hanson [aut] (<https://orcid.org/0000-0002-4716-6134>), Richard Schuster [aut, cre] (<https://orcid.org/0000-0003-3191-7869>), Nina Morrell [aut], Matthew Strimas-Mackey [aut] (<https://orcid.org/0000-0001-8929-7776>), Matthew E Watts [aut], Peter Arcese [aut] (<https://orcid.org/0000-0002-8097-482X>), Joseph Bennett [aut] (<https://orcid.org/0000-0002-3901-9513>), Hugh P Possingham [aut] (<https://orcid.org/0000-0001-7755-996X>)
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>

Diff between prioritizr versions 5.0.3 dated 2020-11-24 and 7.0.1 dated 2021-03-31

 prioritizr-5.0.3/prioritizr/R/feature_representation.R                                 |only
 prioritizr-5.0.3/prioritizr/R/ferrier_score.R                                          |only
 prioritizr-5.0.3/prioritizr/R/irreplaceability.R                                       |only
 prioritizr-5.0.3/prioritizr/R/rarity_weighted_richness.R                               |only
 prioritizr-5.0.3/prioritizr/R/replacement_cost.R                                       |only
 prioritizr-5.0.3/prioritizr/man/feature_representation.Rd                              |only
 prioritizr-5.0.3/prioritizr/man/ferrier_score.Rd                                       |only
 prioritizr-5.0.3/prioritizr/man/figures/README-unnamed-chunk-7-1.png                   |only
 prioritizr-5.0.3/prioritizr/man/figures/README-unnamed-chunk-8-1.png                   |only
 prioritizr-5.0.3/prioritizr/man/irreplaceability.Rd                                    |only
 prioritizr-5.0.3/prioritizr/man/rarity_weighted_richness.Rd                            |only
 prioritizr-5.0.3/prioritizr/man/replacement_cost.Rd                                    |only
 prioritizr-5.0.3/prioritizr/tests/testthat/test_add_min_shortfalls_objective.R         |only
 prioritizr-5.0.3/prioritizr/tests/testthat/test_feature_representation.R               |only
 prioritizr-5.0.3/prioritizr/tests/testthat/test_ferrier_score.R                        |only
 prioritizr-5.0.3/prioritizr/tests/testthat/test_rarity_weighted_richness.R             |only
 prioritizr-5.0.3/prioritizr/tests/testthat/test_replacement_cost.R                     |only
 prioritizr-5.0.3/prioritizr/tests/testthat/test_solvers.R                              |only
 prioritizr-7.0.1/prioritizr/DESCRIPTION                                                |   90 
 prioritizr-7.0.1/prioritizr/MD5                                                        |  450 +--
 prioritizr-7.0.1/prioritizr/NAMESPACE                                                  |   29 
 prioritizr-7.0.1/prioritizr/NEWS.md                                                    |only
 prioritizr-7.0.1/prioritizr/R/ArrayParameter-proto.R                                   |   19 
 prioritizr-7.0.1/prioritizr/R/Collection-proto.R                                       |   21 
 prioritizr-7.0.1/prioritizr/R/ConservationModifier-proto.R                             |   16 
 prioritizr-7.0.1/prioritizr/R/ConservationProblem-proto.R                              |   74 
 prioritizr-7.0.1/prioritizr/R/MiscParameter-proto.R                                    |   12 
 prioritizr-7.0.1/prioritizr/R/OptimizationProblem-proto.R                              |    1 
 prioritizr-7.0.1/prioritizr/R/Parameter-proto.R                                        |    3 
 prioritizr-7.0.1/prioritizr/R/Parameters-proto.R                                       |   22 
 prioritizr-7.0.1/prioritizr/R/Portfolio-proto.R                                        |    7 
 prioritizr-7.0.1/prioritizr/R/RcppExports.R                                            |   16 
 prioritizr-7.0.1/prioritizr/R/ScalarParameter-proto.R                                  |   25 
 prioritizr-7.0.1/prioritizr/R/Solver-proto.R                                           |    6 
 prioritizr-7.0.1/prioritizr/R/add_absolute_targets.R                                   |  105 
 prioritizr-7.0.1/prioritizr/R/add_binary_decisions.R                                   |    6 
 prioritizr-7.0.1/prioritizr/R/add_boundary_penalties.R                                 |  241 -
 prioritizr-7.0.1/prioritizr/R/add_cbc_solver.R                                         |only
 prioritizr-7.0.1/prioritizr/R/add_connectivity_penalties.R                             |  282 +-
 prioritizr-7.0.1/prioritizr/R/add_contiguity_constraints.R                             |   82 
 prioritizr-7.0.1/prioritizr/R/add_cplex_solver.R                                       |  103 
 prioritizr-7.0.1/prioritizr/R/add_cuts_portfolio.R                                     |    2 
 prioritizr-7.0.1/prioritizr/R/add_default_solver.R                                     |   27 
 prioritizr-7.0.1/prioritizr/R/add_feature_contiguity_constraints.R                     |   98 
 prioritizr-7.0.1/prioritizr/R/add_feature_weights.R                                    |   71 
 prioritizr-7.0.1/prioritizr/R/add_gurobi_solver.R                                      |  165 -
 prioritizr-7.0.1/prioritizr/R/add_linear_penalties.R                                   |  150 -
 prioritizr-7.0.1/prioritizr/R/add_locked_in_constraints.R                              |  129 -
 prioritizr-7.0.1/prioritizr/R/add_locked_out_constraints.R                             |   23 
 prioritizr-7.0.1/prioritizr/R/add_loglinear_targets.R                                  |    3 
 prioritizr-7.0.1/prioritizr/R/add_lpsymphony_solver.R                                  |  122 
 prioritizr-7.0.1/prioritizr/R/add_mandatory_allocation_constraints.R                   |    3 
 prioritizr-7.0.1/prioritizr/R/add_manual_bounded_constraints.R                         |   44 
 prioritizr-7.0.1/prioritizr/R/add_manual_locked_constraints.R                          |   52 
 prioritizr-7.0.1/prioritizr/R/add_manual_targets.R                                     |   80 
 prioritizr-7.0.1/prioritizr/R/add_max_cover_objective.R                                |    9 
 prioritizr-7.0.1/prioritizr/R/add_max_features_objective.R                             |   13 
 prioritizr-7.0.1/prioritizr/R/add_max_phylo_div_objective.R                            |   50 
 prioritizr-7.0.1/prioritizr/R/add_max_phylo_end_objective.R                            |   50 
 prioritizr-7.0.1/prioritizr/R/add_max_utility_objective.R                              |    6 
 prioritizr-7.0.1/prioritizr/R/add_min_largest_shortfall_objective.R                    |only
 prioritizr-7.0.1/prioritizr/R/add_min_set_objective.R                                  |   10 
 prioritizr-7.0.1/prioritizr/R/add_min_shortfall_objective.R                            |   24 
 prioritizr-7.0.1/prioritizr/R/add_neighbor_contraints.R                                |  103 
 prioritizr-7.0.1/prioritizr/R/add_proportion_decisions.R                               |   10 
 prioritizr-7.0.1/prioritizr/R/add_relative_targets.R                                   |   15 
 prioritizr-7.0.1/prioritizr/R/add_rsymphony_solver.R                                   |  139 -
 prioritizr-7.0.1/prioritizr/R/add_semicontinuous_decisions.R                           |   10 
 prioritizr-7.0.1/prioritizr/R/add_shuffle_portfolio.R                                  |    2 
 prioritizr-7.0.1/prioritizr/R/boundary_matrix.R                                        |    5 
 prioritizr-7.0.1/prioritizr/R/compile.R                                                |   17 
 prioritizr-7.0.1/prioritizr/R/constraints.R                                            |    6 
 prioritizr-7.0.1/prioritizr/R/decisions.R                                              |    5 
 prioritizr-7.0.1/prioritizr/R/deprecated.R                                             |  141 -
 prioritizr-7.0.1/prioritizr/R/eval_boundary_summary.R                                  |only
 prioritizr-7.0.1/prioritizr/R/eval_connectivity_summary.R                              |only
 prioritizr-7.0.1/prioritizr/R/eval_cost_summary.R                                      |only
 prioritizr-7.0.1/prioritizr/R/eval_feature_representation_summary.R                    |only
 prioritizr-7.0.1/prioritizr/R/eval_ferrier_importance.R                                |only
 prioritizr-7.0.1/prioritizr/R/eval_n_summary.R                                         |only
 prioritizr-7.0.1/prioritizr/R/eval_rare_richness_importance.R                          |only
 prioritizr-7.0.1/prioritizr/R/eval_replacement_importance.R                            |only
 prioritizr-7.0.1/prioritizr/R/eval_target_coverage_summary.R                           |only
 prioritizr-7.0.1/prioritizr/R/feature_abundances.R                                     |    8 
 prioritizr-7.0.1/prioritizr/R/importance.R                                             |only
 prioritizr-7.0.1/prioritizr/R/internal.R                                               |   27 
 prioritizr-7.0.1/prioritizr/R/marxan_problem.R                                         |   35 
 prioritizr-7.0.1/prioritizr/R/objectives.R                                             |   37 
 prioritizr-7.0.1/prioritizr/R/package.R                                                |    6 
 prioritizr-7.0.1/prioritizr/R/parameters.R                                             |   86 
 prioritizr-7.0.1/prioritizr/R/penalties.R                                              |    4 
 prioritizr-7.0.1/prioritizr/R/planning_unit_solution_status.R                          |only
 prioritizr-7.0.1/prioritizr/R/portfolios.R                                             |   24 
 prioritizr-7.0.1/prioritizr/R/presolve_check.R                                         |   20 
 prioritizr-7.0.1/prioritizr/R/problem.R                                                |   57 
 prioritizr-7.0.1/prioritizr/R/rij_matrix.R                                             |   10 
 prioritizr-7.0.1/prioritizr/R/run_calculations.R                                       |   18 
 prioritizr-7.0.1/prioritizr/R/solve.R                                                  |   47 
 prioritizr-7.0.1/prioritizr/R/solvers.R                                                |  112 
 prioritizr-7.0.1/prioritizr/R/summaries.R                                              |only
 prioritizr-7.0.1/prioritizr/R/targets.R                                                |   11 
 prioritizr-7.0.1/prioritizr/R/write_problem.R                                          |only
 prioritizr-7.0.1/prioritizr/R/zones.R                                                  |    6 
 prioritizr-7.0.1/prioritizr/R/zzz.R                                                    |    2 
 prioritizr-7.0.1/prioritizr/README.md                                                  |  217 -
 prioritizr-7.0.1/prioritizr/build/partial.rdb                                          |only
 prioritizr-7.0.1/prioritizr/build/vignette.rds                                         |binary
 prioritizr-7.0.1/prioritizr/inst/doc/gurobi_installation.Rmd                           |    4 
 prioritizr-7.0.1/prioritizr/inst/doc/gurobi_installation.html                          |  150 -
 prioritizr-7.0.1/prioritizr/inst/doc/prioritizr.Rmd                                    |  309 +-
 prioritizr-7.0.1/prioritizr/inst/doc/prioritizr.html                                   | 1254 +++++-----
 prioritizr-7.0.1/prioritizr/inst/doc/publication_record.Rmd                            |   18 
 prioritizr-7.0.1/prioritizr/inst/doc/publication_record.html                           |   67 
 prioritizr-7.0.1/prioritizr/inst/doc/saltspring.Rmd                                    |   45 
 prioritizr-7.0.1/prioritizr/inst/doc/saltspring.html                                   |  299 +-
 prioritizr-7.0.1/prioritizr/inst/doc/tasmania.Rmd                                      |    4 
 prioritizr-7.0.1/prioritizr/inst/doc/tasmania.html                                     |  358 +-
 prioritizr-7.0.1/prioritizr/inst/doc/zones.Rmd                                         |   14 
 prioritizr-7.0.1/prioritizr/inst/doc/zones.html                                        |  783 +++---
 prioritizr-7.0.1/prioritizr/man/ArrayParameter-class.Rd                                |    8 
 prioritizr-7.0.1/prioritizr/man/Collection-class.Rd                                    |   10 
 prioritizr-7.0.1/prioritizr/man/ConservationModifier-class.Rd                          |   10 
 prioritizr-7.0.1/prioritizr/man/ConservationProblem-class.Rd                           |   44 
 prioritizr-7.0.1/prioritizr/man/MiscParameter-class.Rd                                 |    9 
 prioritizr-7.0.1/prioritizr/man/Parameter-class.Rd                                     |    2 
 prioritizr-7.0.1/prioritizr/man/Parameters-class.Rd                                    |   12 
 prioritizr-7.0.1/prioritizr/man/ScalarParameter-class.Rd                               |    9 
 prioritizr-7.0.1/prioritizr/man/add_absolute_targets.Rd                                |   45 
 prioritizr-7.0.1/prioritizr/man/add_binary_decisions.Rd                                |    6 
 prioritizr-7.0.1/prioritizr/man/add_boundary_penalties.Rd                              |  135 -
 prioritizr-7.0.1/prioritizr/man/add_cbc_solver.Rd                                      |only
 prioritizr-7.0.1/prioritizr/man/add_connectivity_penalties.Rd                          |   99 
 prioritizr-7.0.1/prioritizr/man/add_contiguity_constraints.Rd                          |   28 
 prioritizr-7.0.1/prioritizr/man/add_cplex_solver.Rd                                    |   89 
 prioritizr-7.0.1/prioritizr/man/add_cuts_portfolio.Rd                                  |    2 
 prioritizr-7.0.1/prioritizr/man/add_default_solver.Rd                                  |   17 
 prioritizr-7.0.1/prioritizr/man/add_feature_contiguity_constraints.Rd                  |   17 
 prioritizr-7.0.1/prioritizr/man/add_feature_weights.Rd                                 |   46 
 prioritizr-7.0.1/prioritizr/man/add_gurobi_solver.Rd                                   |  186 +
 prioritizr-7.0.1/prioritizr/man/add_linear_penalties.Rd                                |   63 
 prioritizr-7.0.1/prioritizr/man/add_locked_in_constraints.Rd                           |   24 
 prioritizr-7.0.1/prioritizr/man/add_locked_out_constraints.Rd                          |   23 
 prioritizr-7.0.1/prioritizr/man/add_loglinear_targets.Rd                               |    3 
 prioritizr-7.0.1/prioritizr/man/add_lsymphony_solver.Rd                                |   95 
 prioritizr-7.0.1/prioritizr/man/add_mandatory_allocation_constraints.Rd                |    3 
 prioritizr-7.0.1/prioritizr/man/add_manual_bounded_constraints.Rd                      |   25 
 prioritizr-7.0.1/prioritizr/man/add_manual_locked_constraints.Rd                       |   23 
 prioritizr-7.0.1/prioritizr/man/add_manual_targets.Rd                                  |   60 
 prioritizr-7.0.1/prioritizr/man/add_max_cover_objective.Rd                             |    9 
 prioritizr-7.0.1/prioritizr/man/add_max_features_objective.Rd                          |   13 
 prioritizr-7.0.1/prioritizr/man/add_max_phylo_div_objective.Rd                         |   50 
 prioritizr-7.0.1/prioritizr/man/add_max_phylo_end_objective.Rd                         |   50 
 prioritizr-7.0.1/prioritizr/man/add_max_utility_objective.Rd                           |    6 
 prioritizr-7.0.1/prioritizr/man/add_min_largest_shortfall_objective.Rd                 |only
 prioritizr-7.0.1/prioritizr/man/add_min_set_objective.Rd                               |   10 
 prioritizr-7.0.1/prioritizr/man/add_min_shortfall_objective.Rd                         |   22 
 prioritizr-7.0.1/prioritizr/man/add_neighbor_constraints.Rd                            |   15 
 prioritizr-7.0.1/prioritizr/man/add_proportion_decisions.Rd                            |   10 
 prioritizr-7.0.1/prioritizr/man/add_relative_targets.Rd                                |   49 
 prioritizr-7.0.1/prioritizr/man/add_rsymphony_solver.Rd                                |   89 
 prioritizr-7.0.1/prioritizr/man/add_semicontinuous_decisions.Rd                        |   10 
 prioritizr-7.0.1/prioritizr/man/add_shuffle_portfolio.Rd                               |    2 
 prioritizr-7.0.1/prioritizr/man/boundary_matrix.Rd                                     |    3 
 prioritizr-7.0.1/prioritizr/man/constraints.Rd                                         |    6 
 prioritizr-7.0.1/prioritizr/man/decisions.Rd                                           |    5 
 prioritizr-7.0.1/prioritizr/man/eval_boundary_summary.Rd                               |only
 prioritizr-7.0.1/prioritizr/man/eval_connectivity_summary.Rd                           |only
 prioritizr-7.0.1/prioritizr/man/eval_cost_summary.Rd                                   |only
 prioritizr-7.0.1/prioritizr/man/eval_feature_representation_summary.Rd                 |only
 prioritizr-7.0.1/prioritizr/man/eval_ferrier_importance.Rd                             |only
 prioritizr-7.0.1/prioritizr/man/eval_n_summary.Rd                                      |only
 prioritizr-7.0.1/prioritizr/man/eval_rare_richness_importance.Rd                       |only
 prioritizr-7.0.1/prioritizr/man/eval_replacement_importance.Rd                         |only
 prioritizr-7.0.1/prioritizr/man/eval_target_coverage_summary.Rd                        |only
 prioritizr-7.0.1/prioritizr/man/feature_abundances.Rd                                  |    8 
 prioritizr-7.0.1/prioritizr/man/importance.Rd                                          |only
 prioritizr-7.0.1/prioritizr/man/marxan_problem.Rd                                      |   35 
 prioritizr-7.0.1/prioritizr/man/misc_parameter.Rd                                      |   13 
 prioritizr-7.0.1/prioritizr/man/objectives.Rd                                          |   36 
 prioritizr-7.0.1/prioritizr/man/penalties.Rd                                           |    4 
 prioritizr-7.0.1/prioritizr/man/portfolios.Rd                                          |   23 
 prioritizr-7.0.1/prioritizr/man/presolve_check.Rd                                      |   20 
 prioritizr-7.0.1/prioritizr/man/prioritizr-deprecated.Rd                               |   96 
 prioritizr-7.0.1/prioritizr/man/prioritizr.Rd                                          |    6 
 prioritizr-7.0.1/prioritizr/man/problem.Rd                                             |   54 
 prioritizr-7.0.1/prioritizr/man/rij_matrix.Rd                                          |   10 
 prioritizr-7.0.1/prioritizr/man/run_calculations.Rd                                    |   18 
 prioritizr-7.0.1/prioritizr/man/scalar_parameters.Rd                                   |    5 
 prioritizr-7.0.1/prioritizr/man/solve.Rd                                               |   30 
 prioritizr-7.0.1/prioritizr/man/solvers.Rd                                             |  110 
 prioritizr-7.0.1/prioritizr/man/summaries.Rd                                           |only
 prioritizr-7.0.1/prioritizr/man/targets.Rd                                             |    7 
 prioritizr-7.0.1/prioritizr/man/write_problem.Rd                                       |only
 prioritizr-7.0.1/prioritizr/man/zones.Rd                                               |    6 
 prioritizr-7.0.1/prioritizr/src/RcppExports.cpp                                        |   53 
 prioritizr-7.0.1/prioritizr/src/init.c                                                 |    8 
 prioritizr-7.0.1/prioritizr/src/rcpp_absolute_amount_held_by_solution.cpp              |only
 prioritizr-7.0.1/prioritizr/src/rcpp_apply_min_largest_shortfall_objective.cpp         |only
 prioritizr-7.0.1/prioritizr/src/rcpp_boundary.cpp                                      |only
 prioritizr-7.0.1/prioritizr/src/rcpp_connectivity.cpp                                  |only
 prioritizr-7.0.1/prioritizr/tests/testthat.R                                           |   16 
 prioritizr-7.0.1/prioritizr/tests/testthat/helper_boundary.R                           |only
 prioritizr-7.0.1/prioritizr/tests/testthat/helper_connectivity.R                       |only
 prioritizr-7.0.1/prioritizr/tests/testthat/helper_skip.R                               |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_Id.R                                   |    2 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_Waiver.R                               |    3 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_boundary_penalties.R               |   14 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_cbc_solver.R                       |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_connectivity_penalties.R           |   39 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_contiguity_constraints.R           |   10 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_cplex_solver.R                     |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_cuts_portfolio.R                   |  119 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_default_solver.R                   |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_extra_portfolio.R                  |  145 -
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_feature_contiguity_constraints.R   |   27 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_feature_weights.R                  |   40 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_gap_portfolio.R                    |  145 -
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_gurobi_solver.R                    |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_linear_penalties.R                 |    6 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_locked_in_constraints.R            |   39 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_locked_out_constraints.R           |   57 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_lpsymphony_solver.R                |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_mandatory_allocation_constraints.R |    8 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_manual_bounded_constraints.R       |   24 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_manual_locked_constraints.R        |    6 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_max_cover_objective.R              |   22 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_max_features_objective.R           |   38 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_max_phylo_div_objective.R          |   48 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_max_phylo_end_objective.R          |   48 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_max_utility_objective.R            |   22 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_min_largest_shortfall_objective.R  |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_min_set_objective.R                |   35 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_min_shortfall_objective.R          |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_neighbor_constraints.R             |    6 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_rsymphony_solver.R                 |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_shuffle_portfolio.R                |  169 -
 prioritizr-7.0.1/prioritizr/tests/testthat/test_add_top_portfolio.R                    |  145 -
 prioritizr-7.0.1/prioritizr/tests/testthat/test_boundary_matrix.R                      |    4 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_decisions.R                            |   22 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_defaults.R                             |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_documentation.R                        |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_eval_boundary_summary.R                |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_eval_connectivity_summary.R            |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_eval_cost_summary.R                    |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_eval_feature_representation_summary.R  |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_eval_ferrier_importance.R              |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_eval_n_summary.R                       |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_eval_rare_richness_importance.R        |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_eval_replacement_importance.R          |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_eval_target_coverage_summary.R         |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_marxan_problem.R                       |   15 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_parameters.R                           |   28 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_planning_unit_solution_status.R        |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_problem.R                              |   84 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_problem_negative.R                     |   20 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_run_calculations.R                     |only
 prioritizr-7.0.1/prioritizr/tests/testthat/test_solve.R                                |   69 
 prioritizr-7.0.1/prioritizr/tests/testthat/test_write_problem.R                        |only
 prioritizr-7.0.1/prioritizr/vignettes/gurobi_installation.Rmd                          |    4 
 prioritizr-7.0.1/prioritizr/vignettes/prioritizr.Rmd                                   |  309 +-
 prioritizr-7.0.1/prioritizr/vignettes/publication_record.Rmd                           |   18 
 prioritizr-7.0.1/prioritizr/vignettes/references.bib                                   |    2 
 prioritizr-7.0.1/prioritizr/vignettes/saltspring.Rmd                                   |   45 
 prioritizr-7.0.1/prioritizr/vignettes/tasmania.Rmd                                     |    4 
 prioritizr-7.0.1/prioritizr/vignettes/zones.Rmd                                        |   14 
 265 files changed, 5631 insertions(+), 5450 deletions(-)

More information about prioritizr at CRAN
Permanent link

Package cat.dt updated to version 0.3.1 with previous version 0.3.0 dated 2021-03-29

Title: Computerized Adaptive Testing and Decision Trees
Description: Implements the Merged Tree-CAT method (Javier Rodriguez-Cuadrado et al., 2020, <doi:10.1016/j.eswa.2019.113066>) to generate Computerized Adaptive Tests (CATs) based on a decision tree. The tree growth is controlled by merging branches with similar trait distributions and estimations. This package has the necessary tools for creating CATs and estimate the subject's ability level.
Author: Javier Rodriguez-Cuadrado [aut, cre], Juan C. Laria [aut], David Delgado-Gomez [aut]
Maintainer: Javier Rodriguez-Cuadrado <javierro@est-econ.uc3m.es>

Diff between cat.dt versions 0.3.0 dated 2021-03-29 and 0.3.1 dated 2021-03-31

 DESCRIPTION                               |    6 +-
 MD5                                       |   24 ++++----
 R/CAT_ability_est_group.R                 |   12 ++--
 R/CAT_summary.R                           |   88 ++++++++++++++---------------
 R/allocate_sons.R                         |   74 ++++++++++++------------
 R/create_E_MFI.R                          |   68 +++++++++++-----------
 README.md                                 |   90 ++++++++++++++++--------------
 man/CAT_ability_est_group.Rd              |   12 ++--
 man/allocate_sons.Rd                      |    2 
 man/create_E_MFI.Rd                       |    2 
 man/figures/README-unnamed-chunk-13-1.png |binary
 man/figures/README-unnamed-chunk-7-1.png  |binary
 man/summary.cat.dt.Rd                     |    2 
 13 files changed, 193 insertions(+), 187 deletions(-)

More information about cat.dt at CRAN
Permanent link

Package HDiR updated to version 1.1.1 with previous version 1.1 dated 2021-01-28

Title: Directional Highest Density Regions
Description: We provide an R tool for nonparametric plug-in estimation of Highest Density Regions (HDRs) in the directional setting. Concretely, circular and spherical regions can be reconstructed from a data sample following Saavedra-Nieves and Crujeiras (2020) <arXiv:2009.08915>. This library also contains two real datasets in the circular and spherical settings. The first one concerns a problem from animal orientation studies and the second one is related to earthquakes occurrences.
Author: Paula Saavedra-Nieves [aut, cre], Rosa M Crujeiras [aut], Andrés Prieto [ctb], Felicita Scapini [dtc]
Maintainer: Paula Saavedra-Nieves <paula.saavedra@usc.es>

Diff between HDiR versions 1.1 dated 2021-01-28 and 1.1.1 dated 2021-03-31

 DESCRIPTION              |    6 +++---
 MD5                      |   28 ++++++++++++++--------------
 R/circ.boot.bw.R         |    8 ++++----
 R/circ.hdr.R             |    8 ++++----
 R/circ.plugin.hdr.R      |   19 ++++++++++---------
 R/circ.scatterplot.R     |    5 +++--
 R/sphere.hdr.R           |    6 +++---
 R/sphere.plugin.hdr.R    |    6 +++---
 man/circ.boot.bw.Rd      |    2 +-
 man/circ.hdr.Rd          |    6 +++---
 man/circ.plugin.hdr.Rd   |   20 ++++++++++++--------
 man/circ.scatterplot.Rd  |    2 +-
 man/earthquakes.Rd       |    4 ++--
 man/sphere.hdr.Rd        |    6 +++---
 man/sphere.plugin.hdr.Rd |   10 +++++-----
 15 files changed, 71 insertions(+), 65 deletions(-)

More information about HDiR at CRAN
Permanent link

New package EmissV with initial version 0.665.5.2
Package: EmissV
Title: Tools for Create Emissions for Air Quality Models
Date: 2021-03-30
Version: 0.665.5.2
Authors@R: c( person(given = "Daniel", family = "Schuch", role = c("aut", "cre"), email = "underschuch@gmail.com", comment = c(ORCID = "0000-0001-5977-4519")), person(given = "Sergio", family = "Ibarra-Espinosa", role = c("aut"), email = "sergio.ibarra@usp.br", comment = c(ORCID = "0000-0002-3162-1905")) )
Maintainer: Daniel Schuch <underschuch@gmail.com>
Description: Processing tools to create emissions for use in numerical air quality models. Emissions can be calculated both using emission factors and activity data (Schuch et al 2018) <doi:10.21105/joss.00662> or using pollutant inventories (Schuch et al., 2018) <doi:10.30564/jasr.v1i1.347>. Functions to process individual point emissions, line emissions and area emissions of pollutants are available as well as methods to incorporate alternative data for Spatial distribution of emissions such as satellite images (Martins et al, 2012) <doi:10.3389/fenvs.2015.00009> or openstreetmap data (Andrade et al, 2015) <doi:10.3389/fenvs.2015.00009>.
Depends: R (>= 3.4)
Imports: ncdf4, units(>= 0.5-1), raster, sp, sf, methods, data.table, rgdal
Suggests: testthat (>= 2.1.0), covr, osmar, RCurl, eixport, lwgeom
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://atmoschem.github.io/EmissV/
BugReports: https://github.com/atmoschem/EmissV/issues
NeedsCompilation: no
Packaged: 2021-03-30 16:28:10 UTC; under
Author: Daniel Schuch [aut, cre] (<https://orcid.org/0000-0001-5977-4519>), Sergio Ibarra-Espinosa [aut] (<https://orcid.org/0000-0002-3162-1905>)
Repository: CRAN
Date/Publication: 2021-03-31 11:10:02 UTC

More information about EmissV at CRAN
Permanent link

New package ClustAssess with initial version 0.1.0
Package: ClustAssess
Type: Package
Title: Tools for Assessing Clustering
Version: 0.1.0
Authors@R: c(person("Arash", "Shahsavari", email="as3006@cam.ac.uk", role = c("aut", "cre")), person("Irina", "Mohorianu", email="iim22@cam.ac.uk", role="aut"))
Maintainer: Arash Shahsavari <as3006@cam.ac.uk>
Description: A set of tools for evaluating clustering similarity across methods and method stability using element-centric clustering comparison (Gates et al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package enables data-wide assessment of clustering robustness using proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014) <doi:10.1038/srep06207>), which can be used to infer the optimal number of clusters in the data.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: ggplot2, dplyr, fastcluster, rlang, Matrix, igraph, magrittr, Rcpp, methods, stats
RoxygenNote: 7.1.1
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, e1071, dbscan, dendextend, Seurat
URL: https://github.com/moodymudskipper/inops
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-03-30 16:38:04 UTC; Arash
Author: Arash Shahsavari [aut, cre], Irina Mohorianu [aut]
Repository: CRAN
Date/Publication: 2021-03-31 12:00:05 UTC

More information about ClustAssess at CRAN
Permanent link

Package MARVEL updated to version 1.1.0 with previous version 1.0.0 dated 2021-03-01

Title: Revealing Splicing Dynamics at Single-Cell Resolution
Description: Alternative splicing represents an additional and underappreciated layer of complexity underlying gene expression profiles. Nevertheless, there remains hitherto a paucity of softwares to investigate splicing dynamics at single-cell resolution. 'MARVEL' quantifies percent spliced-in (PSI) values for the five primary exon-level splicing events, namely skipped-exon (SE), mutually exclusive exons (MXE), retained intron (RI), alternative 5' and 3' splice sites (A5SS and A3SS, respectively). Additionally, 'MARVEL' performs differential splicing analysis to identify splicing events whose PSI distribution differ between groups of cells. Finally, 'MARVEL' models the PSI distribution for each event as a beta distribution and categorises each distribution into modalities (inspired by Song (2017) <doi:10.1016/j.molcel.2017.06.003>).
Author: Sean Wen
Maintainer: Sean Wen <sean.wenwx@gmail.com>

Diff between MARVEL versions 1.0.0 dated 2021-03-01 and 1.1.0 dated 2021-03-31

 MARVEL-1.0.0/MARVEL/inst/extdata/Data/Counts_per_Base_Validated.txt |only
 MARVEL-1.1.0/MARVEL/DESCRIPTION                                     |    6 
 MARVEL-1.1.0/MARVEL/MD5                                             |   12 -
 MARVEL-1.1.0/MARVEL/R/Script_01_0_ComputePSI.R                      |    8 -
 MARVEL-1.1.0/MARVEL/R/Script_01_5_ComputePSI_RI.R                   |   68 +++++-----
 MARVEL-1.1.0/MARVEL/inst/extdata/Data/Counts_by_Region.txt          |only
 MARVEL-1.1.0/MARVEL/man/ComputePSI.RI.Rd                            |    9 -
 MARVEL-1.1.0/MARVEL/man/ComputePSI.Rd                               |    4 
 8 files changed, 56 insertions(+), 51 deletions(-)

More information about MARVEL at CRAN
Permanent link

New package complexNet with initial version 0.1.0
Package: complexNet
Type: Package
Title: Complex Network Generation
Version: 0.1.0
Authors@R: c(person("Marco", "Smolla", , "drsmolla@icloud.com", role = c("aut", "cre"),comment = c(ORCID = "0000-0001-6367-8765")))
Description: Providing a set of functions to easily generate and iterate complex networks. The functions can be used to generate realistic networks with a wide range of different clustering, density, and average path length. For more information consult research articles by Amiyaal Ilany and Erol Akcay (2016) <doi:10.1093/icb/icw068> and Ilany and Erol Akcay (2016) <doi:10.1101/026120>, which have inspired many methods in this package.
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: methods
URL: https://marcosmolla.github.io/complexNet/, https://github.com/marcosmolla/complexNet
BugReports: https://github.com/marcosmolla/complexNet/issues
Date: 2021-03-30 09:00:02 UTC
NeedsCompilation: no
Packaged: 2021-03-30 14:04:05 UTC; marco
Author: Marco Smolla [aut, cre] (<https://orcid.org/0000-0001-6367-8765>)
Maintainer: Marco Smolla <drsmolla@icloud.com>
Repository: CRAN
Date/Publication: 2021-03-31 11:00:02 UTC

More information about complexNet at CRAN
Permanent link

Package spotoroo updated to version 0.1.1 with previous version 0.1.0 dated 2021-03-22

Title: Spatiotemporal Clustering of Satellite Hot Spot Data
Description: An algorithm to cluster satellite hot spot data spatially and temporally.
Author: Weihao Li [aut, cre] (<https://orcid.org/0000-0003-4959-106X>), Di Cook [ctb] (<https://orcid.org/0000-0002-3813-7155>), Emily Dodwell [ctb]
Maintainer: Weihao Li <llreczx@gmail.com>

Diff between spotoroo versions 0.1.0 dated 2021-03-22 and 0.1.1 dated 2021-03-31

 DESCRIPTION                              |    6 
 MD5                                      |   62 -
 NEWS.md                                  |   72 -
 R/hotspot_cluster.R                      |    2 
 R/plot_vic_map.R                         |    1 
 R/summary_spotoroo.R                     |    2 
 README.md                                |  433 +++++-----
 build/vignette.rds                       |binary
 inst/doc/Clustering-hot-spots.R          |  298 +++----
 inst/doc/Clustering-hot-spots.Rmd        |  799 +++++++++----------
 inst/doc/Clustering-hot-spots.html       | 1287 +++++++++++++------------------
 man/extract_fire.Rd                      |  148 +--
 man/figures/README-unnamed-chunk-6-1.png |binary
 man/figures/README-unnamed-chunk-7-1.png |binary
 man/figures/README-unnamed-chunk-8-1.png |binary
 man/figures/README-unnamed-chunk-9-1.png |binary
 man/get_fire_mov.Rd                      |  136 +--
 man/handle_noise.Rd                      |   90 +-
 man/hotspot_cluster.Rd                   |  346 ++++----
 man/ignition_point.Rd                    |  138 +--
 man/plot.spotoroo.Rd                     |  106 +-
 man/plot_def.Rd                          |  146 +--
 man/plot_fire_mov.Rd                     |  138 +--
 man/plot_spotoroo.Rd                     |  326 +++----
 man/plot_timeline.Rd                     |  172 ++--
 man/plot_vic_map.Rd                      |   52 -
 man/print.spotoroo.Rd                    |   94 +-
 man/spotoroo.Rd                          |   98 +-
 man/summary.spotoroo.Rd                  |   92 +-
 man/summary_spotoroo.Rd                  |  102 +-
 tests/testthat/test-plot_spotoroo.R      |  140 +--
 vignettes/Clustering-hot-spots.Rmd       |  799 +++++++++----------
 32 files changed, 2959 insertions(+), 3126 deletions(-)

More information about spotoroo at CRAN
Permanent link

New package kindisperse with initial version 0.9.2
Package: kindisperse
Title: Simulate and Estimate Close-Kin Dispersal Kernels
Version: 0.9.2
Authors@R: person(given = "Moshe-Elijah", family = "Jasper", role = c("aut", "cre"), email = "moshe.jasper@unimelb.edu.au", comment = c(ORCID = "0000-0003-4541-3223"))
Description: Functions for simulating and estimating kinship-related dispersal. Based on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A. Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito". Assumes an additive variance model of dispersal in two dimensions, compatible with Wright's neighbourhood area. Simple and composite dispersal simulations are supplied, as well as the functions needed to estimate parent-offspring dispersal for simulated or empirical data, and to undertake sampling design for future field studies of dispersal. For ease of use an integrated Shiny app is also included.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/moshejasper/kindisperse
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown
Imports: ggplot2, readr, shiny, shinythemes, ggrepel, fitdistrplus, LaplacesDemon, here, stats, methods, tibble, grid, magrittr, plotly, dplyr, rlang, tidyselect, stringr
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-03-30 10:53:42 UTC; mossu
Author: Moshe-Elijah Jasper [aut, cre] (<https://orcid.org/0000-0003-4541-3223>)
Maintainer: Moshe-Elijah Jasper <moshe.jasper@unimelb.edu.au>
Repository: CRAN
Date/Publication: 2021-03-31 09:10:02 UTC

More information about kindisperse at CRAN
Permanent link

New package ggfx with initial version 1.0.0
Package: ggfx
Title: Pixel Filters for 'ggplot2' and 'grid'
Version: 1.0.0
Authors@R: c(person(given = "Thomas Lin", family = "Pedersen", role = c("aut", "cre"), email = "thomasp85@gmail.com", comment = c(ORCID = "0000-0002-5147-4711")), person(given = "RStudio", role = c("cph", "fnd")))
Description: Provides a range of filters that can be applied to layers from the 'ggplot2' package and its extensions, along with other graphic elements such as guides and theme elements. The filters are applied at render time and thus uses the exact pixel dimensions needed.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: magick (>= 2.7.1), ragg, grid, ggplot2, grDevices, gtable, rlang
RoxygenNote: 7.1.1.9001
URL: https://ggfx.data-imaginist.com, https://github.com/thomasp85/ggfx
BugReports: https://github.com/thomasp85/ggfx/issues
Suggests: covr, knitr, rmarkdown, farver (>= 2.1.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-03-29 18:40:29 UTC; thomas
Author: Thomas Lin Pedersen [aut, cre] (<https://orcid.org/0000-0002-5147-4711>), RStudio [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Repository: CRAN
Date/Publication: 2021-03-31 09:20:02 UTC

More information about ggfx at CRAN
Permanent link

Package fairness updated to version 1.2.1 with previous version 1.2.0 dated 2020-11-19

Title: Algorithmic Fairness Metrics
Description: Offers calculation, visualization and comparison of algorithmic fairness metrics. Fair machine learning is an emerging topic with the overarching aim to critically assess whether ML algorithms reinforce existing social biases. Unfair algorithms can propagate such biases and produce predictions with a disparate impact on various sensitive groups of individuals (defined by sex, gender, ethnicity, religion, income, socioeconomic status, physical or mental disabilities). Fair algorithms possess the underlying foundation that these groups should be treated similarly or have similar prediction outcomes. The fairness R package offers the calculation and comparisons of commonly and less commonly used fairness metrics in population subgroups. These methods are described by Calders and Verwer (2010) <doi:10.1007/s10618-010-0190-x>, Chouldechova (2017) <doi:10.1089/big.2016.0047>, Feldman et al. (2015) <doi:10.1145/2783258.2783311> , Friedler et al. (2018) <doi:10.1145/3287560.3287589> and Zafar et al. (2017) <doi:10.1145/3038912.3052660>. The package also offers convenient visualizations to help understand fairness metrics.
Author: Nikita Kozodoi [aut, cre], Tibor V. Varga [aut] (<https://orcid.org/0000-0002-2383-699X>)
Maintainer: Nikita Kozodoi <n.kozodoi@icloud.com>

Diff between fairness versions 1.2.0 dated 2020-11-19 and 1.2.1 dated 2021-03-31

 DESCRIPTION                     |    8 
 MD5                             |   74 ++---
 NEWS.md                         |    7 
 R/acc_parity.R                  |   64 ++--
 R/dem_parity.R                  |   50 +--
 R/equal_odds.R                  |   50 +--
 R/fairness-package.R            |    4 
 R/fnr_parity.R                  |   68 ++---
 R/fpr_parity.R                  |   68 ++---
 R/mcc_parity.R                  |   68 ++---
 R/npv_parity.R                  |   68 ++---
 R/pred_rate_parity.R            |   68 ++---
 R/prop_parity.R                 |   56 +---
 R/roc_parity.R                  |   17 -
 R/spec_parity.R                 |   66 ++--
 build/vignette.rds              |binary
 inst/doc/fairness.R             |  114 +++-----
 inst/doc/fairness.Rmd           |  238 ++++++++++-------
 inst/doc/fairness.html          |  541 ++++++++++++++--------------------------
 man/acc_parity.Rd               |   30 +-
 man/dem_parity.Rd               |   30 +-
 man/equal_odds.Rd               |   30 +-
 man/fairness.Rd                 |    4 
 man/fnr_parity.Rd               |   30 +-
 man/fpr_parity.Rd               |   30 +-
 man/mcc_parity.Rd               |   30 +-
 man/npv_parity.Rd               |   30 +-
 man/pred_rate_parity.Rd         |   32 +-
 man/prop_parity.Rd              |   30 +-
 man/roc_parity.Rd               |   27 -
 man/spec_parity.Rd              |   30 +-
 tests/testthat/test.errors.R    |   54 ++-
 tests/testthat/test.outputs.R   |   78 ++---
 tests/testthat/test.preds-col.R |   38 +-
 tests/testthat/test.preds-vec.R |   38 +-
 tests/testthat/test.probs-col.R |   41 +--
 tests/testthat/test.probs-vec.R |   41 +--
 vignettes/fairness.Rmd          |  238 ++++++++++-------
 38 files changed, 1159 insertions(+), 1331 deletions(-)

More information about fairness at CRAN
Permanent link

Package doconv updated to version 0.1.1 with previous version 0.1.0 dated 2021-03-30

Title: Document Conversion to 'PDF' or 'PNG'
Description: Functions to convert 'Microsoft Word' or 'Microsoft PowerPoint' documents to 'PDF' format and also for converting them into a thumbnail. In order to work, 'LibreOffice' must be installed on the machine and possibly 'python' and 'Microsoft Word'. If the latter is available, it can be used to produce PDF documents identical to the originals, otherwise, 'LibreOffice' is used.
Author: David Gohel [aut, cre], ArData [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>

Diff between doconv versions 0.1.0 dated 2021-03-30 and 0.1.1 dated 2021-03-31

 DESCRIPTION                         |    7 +++--
 MD5                                 |   17 ++++++++------
 NAMESPACE                           |    1 
 NEWS.md                             |only
 R/to_miniature.R                    |    4 +--
 R/to_pdf.R                          |   43 +++++++++++++++++++++++++++++++++++-
 README.md                           |    8 ++++++
 inst/doc-examples/minimal-word.docx |only
 man/check_libreoffice_export.Rd     |only
 man/to_miniature.Rd                 |    4 +--
 man/to_pdf.Rd                       |    2 -
 11 files changed, 70 insertions(+), 16 deletions(-)

More information about doconv at CRAN
Permanent link

New package codeCollection with initial version 0.1.2
Package: codeCollection
Type: Package
Title: Collection of Codes with Labels
Version: 0.1.2
Authors@R: person(given = "Jari", family = "Haukka", role = c("aut", "cre"), email = "jari.haukka@helsinki.fi", comment = c(ORCID = "0000-0003-1450-6208"))
Description: Includes several classifications such as International Statistical Classification of Diseases and Related Health Problems 10th Revision (ICD10), Anatomical Therapeutic Chemical (ATC) Classification, The International Classification of Diseases for Oncology (ICD-O-3), and International Classification of Primary Care (ICPC). Includes function that adds descriptive label to code value. Depending on classification following languages are available: English, Finnish, Swedish, and Latin.
Depends: R (>= 3.5)
Imports: Epi
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-03-30 10:51:51 UTC; jkhaukka
Author: Jari Haukka [aut, cre] (<https://orcid.org/0000-0003-1450-6208>)
Maintainer: Jari Haukka <jari.haukka@helsinki.fi>
Repository: CRAN
Date/Publication: 2021-03-31 09:10:09 UTC

More information about codeCollection at CRAN
Permanent link

New package BayesRGMM with initial version 1.0
Package: BayesRGMM
Type: Package
Title: Bayesian Robust Generalized Mixed Models for Longitudinal Data
Version: 1.0
Depends: R (>= 3.5.0)
Date: 2021-03-18
Authors@R: c(person(given = "Kuo-Jung", family = "Lee", role = c("aut", "cre"), email = "kuojunglee@ncku.edu.tw", comment = c(ORCID = "0000-0002-7388-4738")), person(given = "Ray-Bing", family = "Chen", role = "ctb"), person(given = "Keunbaik", family = "Lee", role = "ctb"), person(given = "Chanmin", family = "Kim", role = "ctb"))
Description: To perform model estimation using MCMC algorithms with Bayesian methods for incomplete longitudinal studies on binary outcomes that are measured repeatedly on subjects over time with drop-outs. Details about the method can be found in the vignette or <https://sites.google.com/view/kuojunglee/r-packages/bayesrgmm>.
License: GPL-2
URL: https://sites.google.com/view/kuojunglee/r-packages
Encoding: UTF-8
Imports: Rcpp (>= 1.0.1), MASS, batchmeans, abind, reshape, msm, mvtnorm, plyr, Rdpack
RdMacros: Rdpack
LinkingTo: Rcpp, RcppArmadillo, RcppDist
Suggests: testthat
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2021-03-30 12:24:57 UTC; kuo-junglee
Author: Kuo-Jung Lee [aut, cre] (<https://orcid.org/0000-0002-7388-4738>), Ray-Bing Chen [ctb], Keunbaik Lee [ctb], Chanmin Kim [ctb]
Maintainer: Kuo-Jung Lee <kuojunglee@ncku.edu.tw>
Repository: CRAN
Date/Publication: 2021-03-31 09:40:02 UTC

More information about BayesRGMM at CRAN
Permanent link

Package BayesLN updated to version 0.2.2 with previous version 0.2.1 dated 2020-10-28

Title: Bayesian Inference for Log-Normal Data
Description: Bayesian inference under log-normality assumption must be performed very carefully. In fact, under the common priors for the variance, useful quantities in the original data scale (like mean and quantiles) do not have posterior moments that are finite (Fabrizi et al. 2012 <doi:10.1214/12-BA733>). This package allows to easily carry out a proper Bayesian inferential procedure by fixing a suitable distribution (the generalized inverse Gaussian) as prior for the variance. Functions to estimate several kind of means (unconditional, conditional and conditional under a mixed model) and quantiles (unconditional and conditional) are provided.
Author: Aldo Gardini [aut, cre] (<https://orcid.org/0000-0002-2164-5815>), Enrico Fabrizi [aut] (<https://orcid.org/0000-0003-2504-7043>), Carlo Trivisano [aut] (<https://orcid.org/0000-0002-5991-4902>)
Maintainer: Aldo Gardini <aldo.gardini2@unibo.it>

Diff between BayesLN versions 0.2.1 dated 2020-10-28 and 0.2.2 dated 2021-03-31

 DESCRIPTION                  |    8 
 MD5                          |   32 +-
 R/Est_quant.R                |  108 ++++++-
 R/Hier_model.R               |    6 
 R/LN_mean.R                  |   17 +
 R/RcppExports.R              |    4 
 build/vignette.rds           |binary
 inst/doc/BayesLogNormal.R    |    2 
 inst/doc/BayesLogNormal.Rmd  |    2 
 inst/doc/BayesLogNormal.html |  594 +++++++++++++++----------------------------
 inst/include                 |only
 man/LN_Quant.Rd              |    4 
 man/LN_QuantReg.Rd           |    4 
 man/LN_hierarchical.Rd       |    2 
 src/RcppExports.cpp          |  111 +++++++-
 src/gibbs.cpp                |    3 
 vignettes/BayesLogNormal.Rmd |    2 
 17 files changed, 453 insertions(+), 446 deletions(-)

More information about BayesLN at CRAN
Permanent link

New package tidypaleo with initial version 0.1.0
Package: tidypaleo
Title: Tidy Tools for Paleoenvironmental Archives
Version: 0.1.0
Authors@R: person("Dewey", "Dunnington", email = "dewey@fishandwhistle.net", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-9415-4582"))
Description: Provides a set of functions with a common framework for age-depth model management, stratigraphic visualization, and common statistical transformations. The focus of the package is stratigraphic visualization, for which 'ggplot2' components are provided to reproduce the scales, geometries, facets, and theme elements commonly used in publication-quality stratigraphic diagrams. Helpers are also provided to reproduce the exploratory statistical summaries that are frequently included on stratigraphic diagrams.
Depends: R (>= 3.4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown, vegan, patchwork, forcats, vdiffr
URL: https://paleolimbot.github.io/tidypaleo/, https://github.com/paleolimbot/tidypaleo
BugReports: https://github.com/paleolimbot/tidypaleo/issues
Imports: rlang, tidyselect, dplyr, vctrs, tibble, scales, ggplot2 (>= 3.0.0), styler, purrr, ggstance, stringr, withr, tidyr (>= 1.0.2), digest, rioja
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-03-29 16:14:04 UTC; dewey
Author: Dewey Dunnington [aut, cre, cph] (<https://orcid.org/0000-0002-9415-4582>)
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Repository: CRAN
Date/Publication: 2021-03-31 08:50:03 UTC

More information about tidypaleo at CRAN
Permanent link

New package survmixer with initial version 1.3
Package: survmixer
Title: Design of Clinical Trials with Survival Endpoints Based on Binary Responses
Version: 1.3
Author: Marta Bofill Roig [aut, cre], Guadalupe Gomez Melis [ctb], Yu Shen [ctb]
Maintainer: Marta Bofill Roig <marta.bofillroig@meduniwien.ac.at>
Description: Sample size and effect size calculations for survival endpoints based on mixture survival-by-response model. The methods implemented can be found in Bofill, Shen & Gómez (2021) <arXiv:2008.12887>.
License: GPL-3
Encoding: UTF-8
LazyData: false
Imports: stats
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-03-30 08:32:40 UTC; marta.bofill
Repository: CRAN
Date/Publication: 2021-03-31 08:40:02 UTC

More information about survmixer at CRAN
Permanent link

New package SpatialKWD with initial version 0.3.0
Package: SpatialKWD
Type: Package
Title: Spatial KWD for Large Spatial Maps
Version: 0.3.0
Date: 2021-03-29
Author: Stefano Gualandi [aut, cre]
Authors@R: c(person("Stefano", "Gualandi", role = c("aut", "cre"), email = "stefano.gualandi@gmail.com") )
Maintainer: Stefano Gualandi <stefano.gualandi@gmail.com>
Description: Contains efficient implementations of Discrete Optimal Transport algorithms for the computation of Kantorovich-Wasserstein distances between pairs of large spatial maps (Bassetti, Gualandi, Veneroni (2020), <doi:10.1137/19M1261195>). All the algorithms are based on an ad-hoc implementation of the Network Simplex algorithm. The package has three main helper functions: compareOneToOne() (to compare two spatial maps), compareOneToMany() (to compare a reference maps with a list of other maps), and compareAll() (to compute a matrix of distances between a list of maps). In case of non-convex maps, the helper functions first build the convex-hull of the input bins and pads the weights with zeros.
License: EUPL (>= 1.2)
Imports: methods, Rcpp
SystemRequirements: C++11
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2021-03-29 15:16:31 UTC; stegua
Repository: CRAN
Date/Publication: 2021-03-31 08:30:02 UTC

More information about SpatialKWD at CRAN
Permanent link

New package rSAFE with initial version 0.1.2
Package: rSAFE
Title: Surrogate-Assisted Feature Extraction
Version: 0.1.2
Authors@R: c(person("Alicja", "Gosiewska", role = c("aut", "cre"), email = "alicjagosiewska@gmail.com"), person("Anna", "Gierlak", role = c("aut"), email = "anna.gierlak@op.pl"), person("Przemyslaw", "Biecek", role = c("aut", "ths")), person("Michal", "Burdukiewicz", role = c("ctb"), comment = c(ORCID = "0000-0001-8926-582X")))
Description: Provides a model agnostic tool for white-box model trained on features extracted from a black-box model. For more information see: Gosiewska et al. (2020) <arXiv:2002.04267>.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: DALEX, dendextend, ggplot2, ggpubr, grDevices, ingredients, sets, stats
Suggests: gbm, knitr, pander, randomForest, rmarkdown, spelling, testthat, vdiffr
VignetteBuilder: knitr
URL: https://github.com/ModelOriented/rSAFE
BugReports: https://github.com/ModelOriented/rSAFE/issues
Language: en-US
NeedsCompilation: no
Packaged: 2021-03-29 14:27:35 UTC; user
Author: Alicja Gosiewska [aut, cre], Anna Gierlak [aut], Przemyslaw Biecek [aut, ths], Michal Burdukiewicz [ctb] (<https://orcid.org/0000-0001-8926-582X>)
Maintainer: Alicja Gosiewska <alicjagosiewska@gmail.com>
Repository: CRAN
Date/Publication: 2021-03-31 08:20:02 UTC

More information about rSAFE at CRAN
Permanent link

New package OpenSpecy with initial version 0.8.2
Package: OpenSpecy
Type: Package
Title: Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra
Version: 0.8.2
Date: 2021-03-29
Authors@R: c(person("Win", "Cowger", role = c("cre", "aut"), email = "wincowger@gmail.com", comment = c(ORCID = "0000-0001-9226-3104")), person("Zacharias", "Steinmetz", role = c("aut"), email = "steinmetz-z@uni-landau.de", comment = c(ORCID = "0000-0001-6675-5033")), person("Andrew", "Gray", role = c("ctb"), comment = c(ORCID = "0000-0003-2252-7367")), person("Hannah", "Hapich", role = c("ctb"), comment = c(ORCID = "0000-0003-0000-6632")), person("Jennifer", "Lynch", role = c("ctb","dtc"), comment = c(ORCID = "0000-0003-3572-8782")), person("Hannah", "De Frond", role = c("ctb", "dtc"), comment = c(ORCID = "0000-0003-1199-0727")), person("Keenan", "Munno", role = c("ctb", "dtc"), comment = c(ORCID = "0000-0003-2916-5944")), person("Chelsea", "Rochman", role = c("ctb", "dtc"), comment = c(ORCID = "0000-0002-7624-711X")), person("Sebastian", "Primpke", role = c("ctb", "dtc"), comment = c(ORCID = "0000-0001-7633-8524")), person("Orestis", "Herodotou", role = c("ctb", "dtc")))
Description: Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples. Supported features include reading spectral data files (.asp, .csv, .jdx, .spc, .spa, .0), Savitzky-Golay smoothing of spectral intensities with smooth_intens(), correcting background noise with subtr_bg() in accordance with Zhao et al. (2007) <doi:10.1366/000370207782597003>, and identifying spectra using an onboard reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>). Analyzed spectra can be shared with the Open Specy community. A Shiny app is available via run_app() or online at <https://wincowger.shinyapps.io/OpenSpecy/>.
URL: https://github.com/wincowgerDEV/OpenSpecy
BugReports: https://github.com/wincowgerDEV/OpenSpecy/issues
License: CC BY 4.0
Encoding: UTF-8
LazyLoad: true
LazyData: true
VignetteBuilder: knitr
Depends: R (>= 4.0.0)
Imports: magrittr, rlang, dplyr, osfr, hyperSpec, hexView, digest, signal, shiny
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), config, shinyjs, shinythemes, shinyBS, shinyWidgets, ggplot2, plotly, data.table, DT, curl, rdrop2
RoxygenNote: 7.1.1
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2021-03-29 09:05:55 UTC; steinmetz-z
Author: Win Cowger [cre, aut] (<https://orcid.org/0000-0001-9226-3104>), Zacharias Steinmetz [aut] (<https://orcid.org/0000-0001-6675-5033>), Andrew Gray [ctb] (<https://orcid.org/0000-0003-2252-7367>), Hannah Hapich [ctb] (<https://orcid.org/0000-0003-0000-6632>), Jennifer Lynch [ctb, dtc] (<https://orcid.org/0000-0003-3572-8782>), Hannah De Frond [ctb, dtc] (<https://orcid.org/0000-0003-1199-0727>), Keenan Munno [ctb, dtc] (<https://orcid.org/0000-0003-2916-5944>), Chelsea Rochman [ctb, dtc] (<https://orcid.org/0000-0002-7624-711X>), Sebastian Primpke [ctb, dtc] (<https://orcid.org/0000-0001-7633-8524>), Orestis Herodotou [ctb, dtc]
Maintainer: Win Cowger <wincowger@gmail.com>
Repository: CRAN
Date/Publication: 2021-03-31 08:50:16 UTC

More information about OpenSpecy at CRAN
Permanent link

New package NonParRolCor with initial version 0.4.0
Package: NonParRolCor
Type: Package
Title: a Non-Parametric Statistical Significance Test for Rolling Correlation
Version: 0.4.0
Authors@R: c(person(given = "Josue M.", family = "Polanco-Martinez", role = c("aut", "cph", "cre"), email = "josue.m.polanco@gmail.com", comment = c(ORCID = "0000-0001-7164-0185")), person(given = "Jose L.", family = "Lopez-Martinez", role = c("ctb"), email = "jose.lopez@correo.uady.mx", comment = c(ORCID = "0000-0002-2489-7559")))
Maintainer: Josue M. Polanco-Martinez <josue.m.polanco@gmail.com>
Depends: R (>= 3.5.0), gtools, pracma, colorspace, doParallel
Imports: foreach, scales
Description: Estimates and plots (as a heat map) the statistical significance of rolling window correlation coefficients, which is carried out through a non-parametric computing-intensive method. This method addresses the effects due to the multiple testing (inflation of the Type I error) when the statistical significance is estimated for the rolling window correlation coefficients. The method is based on Monte Carlo simulations by permuting one of the variables (dependent) under analysis and keeping fixed the other variable (independent). We improve the computational efficiency of this method to reduce the computation time through parallel computing. The 'NonParRolCor' package also provides examples with synthetic and real-life ecological time series to exemplify its use. Methods derived from R. Telford (2013) <https://quantpalaeo.wordpress.com/2013/01/04/> and J.M. Polanco-Martinez (2020) <doi:10.1016/j.ecoinf.2020.101163>.
License: GPL (>= 2)
Repository: CRAN
Encoding: UTF-8
LazyData: true
Date/Publication: 2021-03-31 09:00:05 UTC
NeedsCompilation: no
Packaged: 2021-03-30 10:37:43 UTC; jomopo
Author: Josue M. Polanco-Martinez [aut, cph, cre] (<https://orcid.org/0000-0001-7164-0185>), Jose L. Lopez-Martinez [ctb] (<https://orcid.org/0000-0002-2489-7559>)

More information about NonParRolCor at CRAN
Permanent link

New package nflseedR with initial version 1.0.1
Package: nflseedR
Title: Functions to Efficiently Simulate and Evaluate NFL Seasons
Version: 1.0.1
Authors@R: c(person(given = "Lee", family = "Sharpe", role = c("aut", "cph")), person(given = "Sebastian", family = "Carl", role = c("cre", "aut"), email = "mrcaseb@gmail.com"))
Description: A set of functions to simulate National Football League seasons including the sophisticated tie-breaking procedures.
License: MIT + file LICENSE
URL: https://nflseedr.com, https://github.com/leesharpe/nflseedR
BugReports: https://github.com/leesharpe/nflseedR/issues
Depends: R (>= 3.5.0)
Imports: cli, crayon, curl, dplyr, furrr, future, glue, gsubfn, magrittr, progressr, purrr, readr, rlang, tibble, tidyr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), tidyverse
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-03-30 09:51:58 UTC; ne48wop
Author: Lee Sharpe [aut, cph], Sebastian Carl [cre, aut]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Repository: CRAN
Date/Publication: 2021-03-31 08:50:06 UTC

More information about nflseedR at CRAN
Permanent link

New package hawkesbow with initial version 1.0.0
Package: hawkesbow
Title: Estimation of Hawkes Processes from Binned Observations
Version: 1.0.0
Authors@R: person(given = "Felix", family = "Cheysson", role = c("aut", "cre"), email = "felix@cheysson.fr", comment = c(ORCID = "0000-0002-9095-2878"))
Description: Implements an estimation method for Hawkes processes when count data are only observed in discrete time, using a spectral approach derived from the Bartlett spectrum, see Cheysson and Lang (2020) <arXiv:2003.04314>. Some general use functions for Hawkes processes are also included: simulation of (in)homogeneous Hawkes process, maximum likelihood estimation, residual analysis, etc.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.0
Depends: Rcpp
Imports: methods, nloptr
Suggests: testthat (>= 2.1.0), knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo, BH
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-03-29 16:41:25 UTC; Pheliks
Author: Felix Cheysson [aut, cre] (<https://orcid.org/0000-0002-9095-2878>)
Maintainer: Felix Cheysson <felix@cheysson.fr>
Repository: CRAN
Date/Publication: 2021-03-31 08:50:10 UTC

More information about hawkesbow at CRAN
Permanent link

New package forplo with initial version 0.1.0
Package: forplo
Type: Package
Title: Flexible Forest Plots
Version: 0.1.0
Authors@R: person("Vincent", "ten Cate, PhD", email = "vincent10kd@gmail.com", role = c("cre","aut"))
Description: Simplifies the creation and customization of forest plots (alternatively called dot-and-whisker plots). Input classes accepted by 'forplo' are data.frame, matrix, lm, glm, and coxph. 'forplo' was written in base R and does not depend on other packages.
License: GPL-3
Encoding: UTF-8
Language: en-US
Depends: R (>= 3.5.0)
VignetteBuilder: knitr, rmarkdown, lattice
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, lattice, MASS, meta, survival
NeedsCompilation: no
Packaged: 2021-03-30 10:32:10 UTC; arinetencate-hoek
Author: Vincent ten Cate, PhD [cre, aut]
Maintainer: "Vincent ten Cate, PhD" <vincent10kd@gmail.com>
Repository: CRAN
Date/Publication: 2021-03-31 09:00:02 UTC

More information about forplo at CRAN
Permanent link

New package cmR with initial version 1.0.1
Package: cmR
Type: Package
Title: Analysis of Cardiac Magnetic Resonance Images
Version: 1.0.1
Date: 2021-03-29
Author: Volker Schmid [aut, cre]
Authors@R: c(person("Volker", "Schmid", role = c("aut", "cre"), email = "volker.schmid@lmu.de"))
Maintainer: Volker Schmid <volker.schmid@lmu.de>
Depends: R (>= 3.5.0)
Imports: Matrix, splines, fields, graphics, parallel
Description: Computes maximum response from Cardiac Magnetic Resonance Images using spatial and voxel wise spline based Bayesian model. This is an implementation of the methods described in Schmid (2011) <doi:10.1109/TMI.2011.2109733> "Voxel-Based Adaptive Spatio-Temporal Modelling of Perfusion Cardiovascular MRI". IEEE TMI 30(7) p. 1305 - 1313.
License: GPL-3
RoxygenNote: 7.1.1
Encoding: UTF-8
LazyData: true
URL: https://bioimaginggroup.github.io/cmr/
Suggests: knitr, rmarkdown, codetools, testthat (>= 3.0.0), R.rsp
VignetteBuilder: knitr, R.rsp
BugReports: https://github.com/bioimaginggroup/cmR/issues
NeedsCompilation: no
Packaged: 2021-03-30 09:09:47 UTC; ri45lat2
Repository: CRAN
Date/Publication: 2021-03-31 08:50:13 UTC

More information about cmR at CRAN
Permanent link

New package clock with initial version 0.1.0
Package: clock
Title: Date-Time Types and Tools
Version: 0.1.0
Authors@R: c(person(given = "Davis", family = "Vaughan", role = c("aut", "cre"), email = "davis@rstudio.com"), person(given = "Howard", family = "Hinnant", role = "cph", comment = "Author of the included date library"), person(given = "RStudio", role = c("cph", "fnd")))
Description: Provides a comprehensive library for date-time manipulations using a new family of orthogonal date-time classes (durations, time points, zoned-times, and calendars) that partition responsibilities so that the complexities of time zones are only considered when they are really needed. Capabilities include: date-time parsing, formatting, arithmetic, extraction and updating of components, and rounding.
License: MIT + file LICENSE
URL: https://github.com/r-lib/clock
BugReports: https://github.com/r-lib/clock/issues
Depends: R (>= 3.3)
Imports: ellipsis (>= 0.3.1), rlang (>= 0.4.10), tzdb (>= 0.1.0), vctrs (>= 0.3.7)
Suggests: covr, knitr, magrittr, pillar, rmarkdown, testthat (>= 3.0.0), withr
LinkingTo: cpp11 (>= 0.2.6)
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2021-03-29 13:34:43 UTC; davis
Author: Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), RStudio [cph, fnd]
Maintainer: Davis Vaughan <davis@rstudio.com>
Repository: CRAN
Date/Publication: 2021-03-31 08:20:05 UTC

More information about clock at CRAN
Permanent link

Package NHSDataDictionaRy (with last version 1.2.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-03-30 1.2.2
2021-02-17 1.2.1
2021-02-02 1.2.0
2021-01-25 0.1.2

Permanent link
Package seminr (with last version 2.0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-03-22 2.0.1
2021-03-10 2.0.0
2020-07-23 1.1.0
2020-05-08 1.0.2
2019-12-12 1.0.1
2019-09-27 1.0.0
2019-05-07 0.7.0
2019-03-20 0.6.0
2018-10-18 0.5.3
2018-09-19 0.5.2
2018-09-10 0.5.1
2018-06-26 0.5.0
2018-01-18 0.4.0
2018-01-05 0.3.1

Permanent link
Package echarty updated to version 0.1.3 with previous version 0.1.0 dated 2021-02-16

Title: Minimal R/Shiny Interface to Library 'ECharts JavaScript'
Description: The goal is to deliver the full functionality of 'ECharts' with minimal overhead. 'ECharts' is based on data structures and 'echarty' users build R lists for these same data structures. One to three 'echarty' commands are usually sufficient to produce any chart.
Author: Larry Helgason [aut, cre, cph], John Coene [aut, cph]
Maintainer: Larry Helgason <larry@helgasoft.com>

Diff between echarty versions 0.1.0 dated 2021-02-16 and 0.1.3 dated 2021-03-31

 echarty-0.1.0/echarty/inst/js/echarts-gl.min.js     |only
 echarty-0.1.0/echarty/man/ec.sband.Rd               |only
 echarty-0.1.3/echarty/DESCRIPTION                   |   16 
 echarty-0.1.3/echarty/MD5                           |   41 -
 echarty-0.1.3/echarty/NAMESPACE                     |   20 
 echarty-0.1.3/echarty/NEWS.md                       |   28 
 echarty-0.1.3/echarty/R/echarty.R                   |  748 +++++++++++++++-----
 echarty-0.1.3/echarty/R/examples.R                  |  240 ++++--
 echarty-0.1.3/echarty/inst/htmlwidgets/echarty.js   |  213 ++++-
 echarty-0.1.3/echarty/inst/htmlwidgets/echarty.yaml |    2 
 echarty-0.1.3/echarty/inst/js/echarts.min.js        |    2 
 echarty-0.1.3/echarty/inst/js/renderers.js          |   41 -
 echarty-0.1.3/echarty/man/ec.data.Rd                |   17 
 echarty-0.1.3/echarty/man/ec.examples.Rd            |  238 ++++--
 echarty-0.1.3/echarty/man/ec.fromJson.Rd            |   20 
 echarty-0.1.3/echarty/man/ec.init.Rd                |   48 -
 echarty-0.1.3/echarty/man/ec.inspect.Rd             |   10 
 echarty-0.1.3/echarty/man/ec.js2r.Rd                |only
 echarty-0.1.3/echarty/man/ec.plugjs.Rd              |only
 echarty-0.1.3/echarty/man/ec.theme.Rd               |    8 
 echarty-0.1.3/echarty/man/ec.timegrp.Rd             |only
 echarty-0.1.3/echarty/man/ecr.band.Rd               |only
 echarty-0.1.3/echarty/man/ecr.ebars.Rd              |only
 echarty-0.1.3/echarty/man/ecs.exec.Rd               |  167 ++--
 echarty-0.1.3/echarty/man/ecs.render.Rd             |    4 
 25 files changed, 1319 insertions(+), 544 deletions(-)

More information about echarty at CRAN
Permanent link

Package neurobase updated to version 1.32.0 with previous version 1.29.0 dated 2020-01-14

Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects
Description: Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>

Diff between neurobase versions 1.29.0 dated 2020-01-14 and 1.32.0 dated 2021-03-31

 DESCRIPTION                                |   12 
 MD5                                        |  165 ++---
 NAMESPACE                                  |   10 
 NEWS.md                                    |   11 
 R/applyEmptyImageDimensions.R              |   34 +
 R/boxplot.nifti.R                          |    2 
 R/check_nifti.R                            |   12 
 R/check_nifti_header.R                     |   14 
 R/checknii.R                               |   23 
 R/checkniigz.R                             |   23 
 R/density.nifti.R                          |    5 
 R/dropEmptyImageDimensions.R               |    8 
 R/emptyImageDimensionsMask.R               |   13 
 R/ensure_array.R                           |   33 +
 R/fast_readnii.R                           |    8 
 R/finite_img.R                             |   17 
 R/flip_img.R                               |    3 
 R/images2matrix.R                          |   16 
 R/img_color_df.R                           |    1 
 R/img_indices.R                            |   19 
 R/img_ts_to_list.R                         |   17 
 R/maskEmptyImageDimensions.R               |   30 
 R/mask_img.R                               |   16 
 R/minmax_img.R                             |   33 +
 R/orient_rpi.R                             |only
 R/ortho2.R                                 |   22 
 R/ortho_diff.R                             |   22 
 R/overlay2.R                               |   49 +
 R/quantile_img.R                           |   24 
 R/read_rpi.R                               |only
 R/remake_img.R                             |   12 
 R/replaceEmptyImageDimensions.R            |only
 R/replace_outside_hull.R                   |   13 
 R/rescale_img.R                            |   43 +
 R/separate_img.R                           |   33 +
 R/tempimg.R                                |    4 
 R/write_nifti.R                            |    9 
 R/writenii.R                               |   11 
 R/zero_pad.R                               |    2 
 R/zscore_img.R                             |    4 
 README.md                                  |    6 
 build/vignette.rds                         |binary
 inst/doc/neurobase.Rmd                     |    2 
 inst/doc/neurobase.html                    |  473 ++++-----------
 inst/doc/nifti_basics.Rmd                  |    2 
 inst/doc/nifti_basics.html                 |  907 ++++++-----------------------
 inst/doc/simple_io.html                    |  369 ++---------
 man/applyEmptyImageDimensions-methods.Rd   |   35 +
 man/boxplot.nifti.Rd                       |    2 
 man/check_nifti-methods.Rd                 |   12 
 man/check_nifti_header-methods.Rd          |   15 
 man/checknii-methods.Rd                    |   18 
 man/checkniigz-methods.Rd                  |   18 
 man/datatype.Rd                            |    6 
 man/density.nifti.Rd                       |    5 
 man/dropEmptyImageDimensions.Rd            |    8 
 man/emptyImageDimensionsMask.Rd            |   11 
 man/ensure_array.Rd                        |   16 
 man/fast_readnii.Rd                        |    9 
 man/finite_img-methods.Rd                  |   18 
 man/flip_img.Rd                            |    3 
 man/images2matrix.Rd                       |   17 
 man/img_colour_df.Rd                       |    1 
 man/img_indices.Rd                         |   18 
 man/img_ts_to_list.Rd                      |   13 
 man/maskEmptyImageDimensions-methods.Rd    |   31 
 man/mask_img.Rd                            |   16 
 man/minmax_img-methods.Rd                  |   27 
 man/multi_overlay.Rd                       |   19 
 man/orient_rpi.Rd                          |only
 man/ortho2.Rd                              |   22 
 man/ortho_diff.Rd                          |   20 
 man/quantile_img.Rd                        |   11 
 man/read_rpi.Rd                            |only
 man/remake_img.Rd                          |   13 
 man/replaceEmptyImageDimensions-methods.Rd |only
 man/replace_outside_surface.Rd             |   11 
 man/rescale_img.Rd                         |    7 
 man/reverse_orient_rpi.Rd                  |only
 man/separate_img-methods.Rd                |   23 
 man/tempimg.Rd                             |    4 
 man/writeNIfTI2.Rd                         |   10 
 man/write_nifti.Rd                         |   10 
 man/zero_pad.Rd                            |    2 
 man/zscore_img.Rd                          |    4 
 vignettes/neurobase.Rmd                    |    2 
 vignettes/nifti_basics.Rmd                 |    2 
 87 files changed, 1527 insertions(+), 1464 deletions(-)

More information about neurobase at CRAN
Permanent link

Package surveillance updated to version 1.19.1 with previous version 1.19.0 dated 2021-01-30

Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
Description: Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of H<f6>hle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by H<f6>hle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.
Author: Michael H<f6>hle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>), Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>), Michaela Paul [aut], Leonhard Held [ctb, ths], Howard Burkom [ctb], Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb], Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Saban<e9>s Bov<e9> [ctb], Ma<eb>lle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb], Mikko Virtanen [ctb], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb] (A few code segments are modified versions of code from base R)
Maintainer: Sebastian Meyer <seb.meyer@fau.de>

Diff between surveillance versions 1.19.0 dated 2021-01-30 and 1.19.1 dated 2021-03-31

 surveillance-1.19.0/surveillance/R/RcppExports.R                        |only
 surveillance-1.19.0/surveillance/inst/NEWS.Rd                           |only
 surveillance-1.19.0/surveillance/src/RcppExports.cpp                    |only
 surveillance-1.19.1/surveillance/DESCRIPTION                            |   12 
 surveillance-1.19.1/surveillance/MD5                                    |  128 ++++------
 surveillance-1.19.1/surveillance/NAMESPACE                              |    9 
 surveillance-1.19.1/surveillance/NEWS.md                                |only
 surveillance-1.19.1/surveillance/R/AllGeneric.R                         |    6 
 surveillance-1.19.1/surveillance/R/algo_farrington.R                    |    8 
 surveillance-1.19.1/surveillance/R/algo_glrnb.R                         |   22 -
 surveillance-1.19.1/surveillance/R/algo_twins.R                         |   47 +--
 surveillance-1.19.1/surveillance/R/backprojNP.R                         |  119 +--------
 surveillance-1.19.1/surveillance/R/epidataCS.R                          |    7 
 surveillance-1.19.1/surveillance/R/farringtonFlexible.R                 |    4 
 surveillance-1.19.1/surveillance/R/hcl.colors.R                         |    2 
 surveillance-1.19.1/surveillance/R/hhh4.R                               |   15 -
 surveillance-1.19.1/surveillance/R/ks.plot.unif.R                       |   32 +-
 surveillance-1.19.1/surveillance/R/stcd.R                               |   10 
 surveillance-1.19.1/surveillance/R/sts.R                                |    9 
 surveillance-1.19.1/surveillance/R/sts_coerce.R                         |    4 
 surveillance-1.19.1/surveillance/R/sts_ggplot.R                         |    5 
 surveillance-1.19.1/surveillance/R/stsplot_space.R                      |   16 -
 surveillance-1.19.1/surveillance/R/stsplot_time.R                       |  100 +++----
 surveillance-1.19.1/surveillance/R/sysdata.rda                          |binary
 surveillance-1.19.1/surveillance/R/twinSIR_profile.R                    |   32 +-
 surveillance-1.19.1/surveillance/R/twinstim_helper.R                    |   21 -
 surveillance-1.19.1/surveillance/R/twinstim_siaf_polyCub_iso.R          |    8 
 surveillance-1.19.1/surveillance/R/twinstim_simulation.R                |   13 -
 surveillance-1.19.1/surveillance/build/partial.rdb                      |binary
 surveillance-1.19.1/surveillance/build/vignette.rds                     |binary
 surveillance-1.19.1/surveillance/data/imdepi.RData                      |binary
 surveillance-1.19.1/surveillance/data/measlesWeserEms.RData             |binary
 surveillance-1.19.1/surveillance/inst/THANKS                            |    1 
 surveillance-1.19.1/surveillance/inst/doc/glrnb.pdf                     |binary
 surveillance-1.19.1/surveillance/inst/doc/hhh4.pdf                      |binary
 surveillance-1.19.1/surveillance/inst/doc/hhh4_spacetime.Rnw            |    6 
 surveillance-1.19.1/surveillance/inst/doc/hhh4_spacetime.pdf            |binary
 surveillance-1.19.1/surveillance/inst/doc/monitoringCounts.R            |    2 
 surveillance-1.19.1/surveillance/inst/doc/monitoringCounts.Rnw          |    2 
 surveillance-1.19.1/surveillance/inst/doc/monitoringCounts.pdf          |binary
 surveillance-1.19.1/surveillance/inst/doc/surveillance.pdf              |binary
 surveillance-1.19.1/surveillance/inst/doc/twinSIR.Rnw                   |   18 -
 surveillance-1.19.1/surveillance/inst/doc/twinSIR.pdf                   |binary
 surveillance-1.19.1/surveillance/inst/doc/twinstim.R                    |    2 
 surveillance-1.19.1/surveillance/inst/doc/twinstim.Rnw                  |   14 -
 surveillance-1.19.1/surveillance/inst/doc/twinstim.pdf                  |binary
 surveillance-1.19.1/surveillance/inst/shapes/districtsD.RData           |binary
 surveillance-1.19.1/surveillance/man/epidataCS.Rd                       |    2 
 surveillance-1.19.1/surveillance/man/measlesDE.Rd                       |   21 +
 surveillance-1.19.1/surveillance/man/nowcast.Rd                         |    2 
 surveillance-1.19.1/surveillance/man/sts-class.Rd                       |    6 
 surveillance-1.19.1/surveillance/man/stsNewport.Rd                      |    2 
 surveillance-1.19.1/surveillance/man/sts_ggplot.Rd                      |    2 
 surveillance-1.19.1/surveillance/man/surveillance-package.Rd            |   24 +
 surveillance-1.19.1/surveillance/man/twinstim_simulation.Rd             |    2 
 surveillance-1.19.1/surveillance/src/determineSources.cc                |   80 +-----
 surveillance-1.19.1/surveillance/src/init.c                             |   50 ++-
 surveillance-1.19.1/surveillance/src/ks.c                               |   39 ---
 surveillance-1.19.1/surveillance/src/surveillance.c                     |   10 
 surveillance-1.19.1/surveillance/src/twinstim_siaf_polyCub_iso.c        |    4 
 surveillance-1.19.1/surveillance/tests/testthat/test-determineSources.R |    2 
 surveillance-1.19.1/surveillance/vignettes/hhh4_spacetime.Rnw           |    6 
 surveillance-1.19.1/surveillance/vignettes/monitoringCounts.Rnw         |    2 
 surveillance-1.19.1/surveillance/vignettes/references.bib               |    9 
 surveillance-1.19.1/surveillance/vignettes/surveillance-hmm.pdf         |binary
 surveillance-1.19.1/surveillance/vignettes/twinSIR.Rnw                  |   18 -
 surveillance-1.19.1/surveillance/vignettes/twinstim.Rnw                 |   14 -
 67 files changed, 418 insertions(+), 551 deletions(-)

More information about surveillance at CRAN
Permanent link

Package spatstat.local updated to version 4.1-0 with previous version 4.0-0 dated 2021-01-24

Title: Extension to 'spatstat' for Local Composite Likelihood
Description: Extension to the 'spatstat' package, enabling the user to fit point process models to point pattern data by local composite likelihood ('geographically weighted regression').
Author: Adrian Baddeley [aut, cre]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.local versions 4.0-0 dated 2021-01-24 and 4.1-0 dated 2021-03-31

 DESCRIPTION |   16 ++++++++--------
 MD5         |    2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

More information about spatstat.local at CRAN
Permanent link

Package spatstat.Knet updated to version 2.0-0 with previous version 1.65-0 dated 2021-02-15

Title: Extension to 'spatstat' for Large Datasets on a Linear Network
Description: Extension to the 'spatstat' family of packages, for analysing large datasets of spatial points on a network. The geometrically- corrected K function is computed using a memory-efficient tree-based algorithm described by Rakshit, Baddeley and Nair (2019).
Author: Suman Rakshit [aut, cph] (<https://orcid.org/0000-0003-0052-128X>), Adrian Baddeley [cre, cph] (<https://orcid.org/0000-0001-9499-8382>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.Knet versions 1.65-0 dated 2021-02-15 and 2.0-0 dated 2021-03-31

 DESCRIPTION        |   16 ++++++++--------
 MD5                |    6 +++---
 build/partial.rdb  |binary
 data/wacrashes.rda |binary
 4 files changed, 11 insertions(+), 11 deletions(-)

More information about spatstat.Knet at CRAN
Permanent link

Package randomForestSRC updated to version 2.11.0 with previous version 2.10.1 dated 2021-02-10

Title: Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>

Diff between randomForestSRC versions 2.10.1 dated 2021-02-10 and 2.11.0 dated 2021-03-31

 randomForestSRC-2.10.1/randomForestSRC/R/anonymous.utilities.R       |only
 randomForestSRC-2.10.1/randomForestSRC/R/data.utilities.R            |only
 randomForestSRC-2.10.1/randomForestSRC/R/factor.utilities.R          |only
 randomForestSRC-2.11.0/randomForestSRC/DESCRIPTION                   |   10 
 randomForestSRC-2.11.0/randomForestSRC/MD5                           |   71 
 randomForestSRC-2.11.0/randomForestSRC/NAMESPACE                     |    3 
 randomForestSRC-2.11.0/randomForestSRC/R/find.interaction.rfsrc.R    |    5 
 randomForestSRC-2.11.0/randomForestSRC/R/generic.predict.rfsrc.R     |  239 
 randomForestSRC-2.11.0/randomForestSRC/R/get.tree.rfsrc.R            |   63 
 randomForestSRC-2.11.0/randomForestSRC/R/holdout.vimp.rfsrc.R        |   85 
 randomForestSRC-2.11.0/randomForestSRC/R/imbalanced.rfsrc.R          |    4 
 randomForestSRC-2.11.0/randomForestSRC/R/impute.rfsrc.R              |    5 
 randomForestSRC-2.11.0/randomForestSRC/R/partial.rfsrc.R             |   67 
 randomForestSRC-2.11.0/randomForestSRC/R/plot.survival.rfsrc.R       |    2 
 randomForestSRC-2.11.0/randomForestSRC/R/plot.variable.rfsrc.R       |   17 
 randomForestSRC-2.11.0/randomForestSRC/R/print.rfsrc.R               |    8 
 randomForestSRC-2.11.0/randomForestSRC/R/rfsrc.R                     |  219 
 randomForestSRC-2.11.0/randomForestSRC/R/rfsrc.anonymous.R           |only
 randomForestSRC-2.11.0/randomForestSRC/R/rfsrc.fast.R                |   12 
 randomForestSRC-2.11.0/randomForestSRC/R/subsample.rfsrc.R           |    5 
 randomForestSRC-2.11.0/randomForestSRC/R/utilities.R                 |  112 
 randomForestSRC-2.11.0/randomForestSRC/R/utilities.data.R            |only
 randomForestSRC-2.11.0/randomForestSRC/R/utilities.factor.R          |only
 randomForestSRC-2.11.0/randomForestSRC/R/utilities.multivariate.R    |only
 randomForestSRC-2.11.0/randomForestSRC/R/utilities.performance.R     |only
 randomForestSRC-2.11.0/randomForestSRC/R/utilities.tdc.R             |only
 randomForestSRC-2.11.0/randomForestSRC/R/utilities.unsupervised.R    |only
 randomForestSRC-2.11.0/randomForestSRC/R/var.select.rfsrc.R          |    3 
 randomForestSRC-2.11.0/randomForestSRC/R/vimp.rfsrc.R                |   17 
 randomForestSRC-2.11.0/randomForestSRC/configure                     |   18 
 randomForestSRC-2.11.0/randomForestSRC/configure.ac                  |    2 
 randomForestSRC-2.11.0/randomForestSRC/inst/NEWS                     |   12 
 randomForestSRC-2.11.0/randomForestSRC/man/find.interaction.rfsrc.Rd |    4 
 randomForestSRC-2.11.0/randomForestSRC/man/holdout.vimp.rfsrc.Rd     |   51 
 randomForestSRC-2.11.0/randomForestSRC/man/predict.rfsrc.Rd          |   91 
 randomForestSRC-2.11.0/randomForestSRC/man/rfsrc.Rd                  |   57 
 randomForestSRC-2.11.0/randomForestSRC/man/rfsrc.anonymous.Rd        |only
 randomForestSRC-2.11.0/randomForestSRC/man/rfsrc.fast.Rd             |    9 
 randomForestSRC-2.11.0/randomForestSRC/man/vimp.rfsrc.Rd             |   61 
 randomForestSRC-2.11.0/randomForestSRC/src/R_init_randomForestSRC.c  |    4 
 randomForestSRC-2.11.0/randomForestSRC/src/randomForestSRC.c         | 3229 ++++++----
 randomForestSRC-2.11.0/randomForestSRC/src/randomForestSRC.h         |  178 
 42 files changed, 3258 insertions(+), 1405 deletions(-)

More information about randomForestSRC at CRAN
Permanent link

Package nprcgenekeepr updated to version 1.0.5 with previous version 1.0.3 dated 2020-06-02

Title: Genetic Tools for Colony Management
Description: Provides genetic tools for colony management and is a derivation of the work in Amanda Vinson and Michael J Raboin (2015) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671785/> "A Practical Approach for Designing Breeding Groups to Maximize Genetic Diversity in a Large Colony of Captive Rhesus Macaques ('Macaca' 'mulatto')". It provides a 'Shiny' application with an exposed API. The application supports five groups of functions: (1) Quality control of studbooks contained in text files or 'Excel' workbooks and of pedigrees within 'LabKey' Electronic Health Records (EHR); (2) Creation of pedigrees from a list of animals using the 'LabKey' EHR integration; (3) Creation and display of an age by sex pyramid plot of the living animals within the designated pedigree; (4) Generation of genetic value analysis reports; and (5) Creation of potential breeding groups with and without proscribed sex ratios and defined maximum kinships.
Author: Michael Raboin [aut], Terry Therneau [aut], Amanda Vinson [aut, dtc], R. Mark Sharp [aut, cre, cph, dtc] (<https://orcid.org/0000-0002-6170-6942>), Southwest National Primate Research Center NIH grant P51 RR13986 [fnd], Oregon National Primate Research Center grant P51 OD011092 [fnd]
Maintainer: R. Mark Sharp <rmsharp@me.com>

Diff between nprcgenekeepr versions 1.0.3 dated 2020-06-02 and 1.0.5 dated 2021-03-31

 nprcgenekeepr-1.0.3/nprcgenekeepr/R/runGeneKeepR.R                              |only
 nprcgenekeepr-1.0.3/nprcgenekeepr/inst/application/server.R                     |only
 nprcgenekeepr-1.0.3/nprcgenekeepr/inst/doc/a4Development_Plans.R                |only
 nprcgenekeepr-1.0.3/nprcgenekeepr/inst/doc/a4Development_Plans.Rmd              |only
 nprcgenekeepr-1.0.3/nprcgenekeepr/inst/doc/a4Development_Plans.html             |only
 nprcgenekeepr-1.0.3/nprcgenekeepr/vignettes/a4Development_Plans.Rmd             |only
 nprcgenekeepr-1.0.5/nprcgenekeepr/DESCRIPTION                                   |   15 
 nprcgenekeepr-1.0.5/nprcgenekeepr/MD5                                           |  102 
 nprcgenekeepr-1.0.5/nprcgenekeepr/NAMESPACE                                     |   10 
 nprcgenekeepr-1.0.5/nprcgenekeepr/NEWS.md                                       |only
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/checkChangedColsLst.R                       |    4 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/checkParentAge.R                            |    3 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/convertFromCenter.R                         |only
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/createPedSix.R                              |    2 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/fixColumnNames.R                            |    9 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/getCurrentAge.R                             |    2 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/getEmptyErrorLst.R                          |   47 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/getProductionStatus.R                       |    1 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/getSiteInfo.R                               |    1 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/getVersion.R                                |    6 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/get_elapsed_time_str.R                      |    1 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/groupAddAssign.R                            |    2 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/insertSeparators.R                          |    4 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/is_valid_date_str.R                         |    2 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/kinship.R                                   |    2 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/mapIdsToObfuscated.R                        |    4 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/nprcgenekeeper.R                            |   31 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/obfuscatePed.R                              |    1 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/qcStudbook.R                                |    5 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/readExcelPOSIXToCharacter.R                 |    3 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/runGenekeepr.R                              |only
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/saveDataframesAsFiles.R                     |   14 
 nprcgenekeepr-1.0.5/nprcgenekeepr/R/str_detect_fixed_all.R                      |    4 
 nprcgenekeepr-1.0.5/nprcgenekeepr/README.md                                     |   14 
 nprcgenekeepr-1.0.5/nprcgenekeepr/build/vignette.rds                            |binary
 nprcgenekeepr-1.0.5/nprcgenekeepr/inst/_pkgdown.yml                             |    1 
 nprcgenekeepr-1.0.5/nprcgenekeepr/inst/application/server.r                     |only
 nprcgenekeepr-1.0.5/nprcgenekeepr/inst/application/ui.R                         |    1 
 nprcgenekeepr-1.0.5/nprcgenekeepr/inst/application/uitpBreedingGroupFormation.R |   14 
 nprcgenekeepr-1.0.5/nprcgenekeepr/inst/application/uitpInput.R                  |   14 
 nprcgenekeepr-1.0.5/nprcgenekeepr/inst/application/uitpPedigreeBrowser.R        |   12 
 nprcgenekeepr-1.0.5/nprcgenekeepr/inst/application/uitpSummaryStatistics.R      |   20 
 nprcgenekeepr-1.0.5/nprcgenekeepr/inst/doc/a2interactive.Rmd                    |   52 
 nprcgenekeepr-1.0.5/nprcgenekeepr/inst/doc/a2interactive.html                   | 1642 ----------
 nprcgenekeepr-1.0.5/nprcgenekeepr/man/convertFromCenter.Rd                      |only
 nprcgenekeepr-1.0.5/nprcgenekeepr/man/kinship.Rd                                |    2 
 nprcgenekeepr-1.0.5/nprcgenekeepr/man/nprcgenekeepr.Rd                          |   31 
 nprcgenekeepr-1.0.5/nprcgenekeepr/man/runGeneKeepR.Rd                           |    2 
 nprcgenekeepr-1.0.5/nprcgenekeepr/man/saveDataframesAsFiles.Rd                  |    7 
 nprcgenekeepr-1.0.5/nprcgenekeepr/tests/testthat/test_addBackSecondParents.R    |    2 
 nprcgenekeepr-1.0.5/nprcgenekeepr/tests/testthat/test_addSecondParents.R        |only
 nprcgenekeepr-1.0.5/nprcgenekeepr/tests/testthat/test_convertFromCenter.R       |only
 nprcgenekeepr-1.0.5/nprcgenekeepr/tests/testthat/test_filterKinMatrix.R         |    4 
 nprcgenekeepr-1.0.5/nprcgenekeepr/tests/testthat/test_getFocalAnimalPed.R       |   72 
 nprcgenekeepr-1.0.5/nprcgenekeepr/tests/testthat/test_getMinParentAge.R         |    2 
 nprcgenekeepr-1.0.5/nprcgenekeepr/tests/testthat/test_makeExamplePedigreeFile.R |   16 
 nprcgenekeepr-1.0.5/nprcgenekeepr/tests/testthat/test_qcStudbook.R              |    1 
 nprcgenekeepr-1.0.5/nprcgenekeepr/tests/testthat/test_saveDataframesAsFiles.R   |only
 nprcgenekeepr-1.0.5/nprcgenekeepr/vignettes/a2interactive.Rmd                   |   52 
 59 files changed, 469 insertions(+), 1767 deletions(-)

More information about nprcgenekeepr at CRAN
Permanent link

Package MatchThem updated to version 1.0.0 with previous version 0.9.3 dated 2020-03-23

Title: Matching and Weighting Multiply Imputed Datasets
Description: Provides the necessary tools for the pre-processing techniques of matching and weighting multiply imputed datasets to control for effects of confounders and to reduce the degree of dependence on certain modeling assumptions in studying the causal associations between an exposure and an outcome. This package includes functions to perform matching within and across the multiply imputed datasets using several matching methods, to estimate weights of units in the imputed datasets using several weighting methods, to calculate the causal effect estimate in each matched or weighted dataset using parametric or non-parametric statistical models, and to pool the obtained estimates from these models according to Rubin's rules (please see <https://github.com/FarhadPishgar/MatchThem> for details).
Author: Farhad Pishgar [aut, cre], Noah Greifer [aut], Clémence Leyrat [ctb], Elizabeth Stuart [ctb]
Maintainer: Farhad Pishgar <Farhad.Pishgar@Gmail.com>

Diff between MatchThem versions 0.9.3 dated 2020-03-23 and 1.0.0 dated 2021-03-31

 DESCRIPTION               |   14 
 MD5                       |   63 +--
 NAMESPACE                 |   43 --
 NEWS.md                   |  106 +++--
 R/cbind.R                 |only
 R/class.functions.R       |  831 ++++++++--------------------------------------
 R/complete.R              |  371 ++++++++------------
 R/internal.functions.R    |  285 +++------------
 R/is.R                    |  424 +++++++++++------------
 R/matchthem.R             |  485 +++++++++++---------------
 R/mimids.R                |   55 +--
 R/pool.R                  |  293 +++++++---------
 R/trim.R                  |only
 R/weightthem.R            |  430 ++++++++++-------------
 R/wimids.R                |   53 +-
 R/with.R                  |  373 +++++++++++---------
 README.md                 |  120 +++---
 build/vignette.rds        |binary
 data/osteoarthritis.rdata |binary
 man/cbind.Rd              |only
 man/complete.Rd           |   36 -
 man/figure/logo.png       |binary
 man/is.mimids.Rd          |    7 
 man/is.mimipo.Rd          |   29 +
 man/is.mimira.Rd          |   12 
 man/is.wimids.Rd          |   12 
 man/matchthem.Rd          |   66 ++-
 man/mimids.Rd             |    2 
 man/osteoarthritis.Rd     |    6 
 man/pool.Rd               |   53 +-
 man/trim.Rd               |only
 man/weightthem.Rd         |   66 ++-
 man/wimids.Rd             |    2 
 man/with.Rd               |   58 +--
 vignettes/vignette.rds    |only
 35 files changed, 1746 insertions(+), 2549 deletions(-)

More information about MatchThem at CRAN
Permanent link

Package covidsymptom updated to version 0.9.2 with previous version 0.9.1 dated 2021-03-18

Title: COVID Symptom Study Sweden Open Dataset
Description: The COVID Symptom Study is a non-commercial project that uses a free mobile app to facilitate real-time data collection of symptoms, exposures, and risk factors related to COVID19. The package allows easy access to summary statistics data from COVID Symptom Study Sweden.
Author: Hugo Fitipaldi [aut, cre]
Maintainer: Hugo Fitipaldi <hugo.fitipaldi@med.lu.se>

Diff between covidsymptom versions 0.9.1 dated 2021-03-18 and 0.9.2 dated 2021-03-31

 covidsymptom-0.9.1/covidsymptom/R/covidsymptomdata.R                     |only
 covidsymptom-0.9.2/covidsymptom/DESCRIPTION                              |    9 +-
 covidsymptom-0.9.2/covidsymptom/MD5                                      |   36 +++++-----
 covidsymptom-0.9.2/covidsymptom/NAMESPACE                                |    4 -
 covidsymptom-0.9.2/covidsymptom/NEWS.md                                  |    7 +
 covidsymptom-0.9.2/covidsymptom/R/data.R                                 |    6 -
 covidsymptom-0.9.2/covidsymptom/R/get_latest_data.R                      |    8 --
 covidsymptom-0.9.2/covidsymptom/R/update_csss_data.R                     |    8 --
 covidsymptom-0.9.2/covidsymptom/README.md                                |   15 +++-
 covidsymptom-0.9.2/covidsymptom/data/county_estimates.rda                |binary
 covidsymptom-0.9.2/covidsymptom/data/national_estimates.rda              |binary
 covidsymptom-0.9.2/covidsymptom/data/postcode_estimates.rda              |binary
 covidsymptom-0.9.2/covidsymptom/man/county_estimates.Rd                  |    2 
 covidsymptom-0.9.2/covidsymptom/man/covidsymptom.Rd                      |    2 
 covidsymptom-0.9.2/covidsymptom/man/figures/README-unnamed-chunk-3-1.png |binary
 covidsymptom-0.9.2/covidsymptom/man/figures/README-unnamed-chunk-4-1.png |binary
 covidsymptom-0.9.2/covidsymptom/man/figures/README-unnamed-chunk-6-1.png |binary
 covidsymptom-0.9.2/covidsymptom/man/figures/hex3.png                     |only
 covidsymptom-0.9.2/covidsymptom/man/national_estimates.Rd                |    2 
 covidsymptom-0.9.2/covidsymptom/man/postcode_estimates.Rd                |    2 
 20 files changed, 54 insertions(+), 47 deletions(-)

More information about covidsymptom at CRAN
Permanent link

Package actuar updated to version 3.1-2 with previous version 3.1-1 dated 2021-02-03

Title: Actuarial Functions and Heavy Tailed Distributions
Description: Functions and data sets for actuarial science: modeling of loss distributions; risk theory and ruin theory; simulation of compound models, discrete mixtures and compound hierarchical models; credibility theory. Support for many additional probability distributions to model insurance loss size and frequency: 23 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete distribution; zero-truncated and zero-modified extensions of the standard discrete distributions. Support for phase-type distributions commonly used to compute ruin probabilities.
Author: Vincent Goulet [cre, aut], Sébastien Auclair [ctb], Christophe Dutang [aut], Nicholas Langevin [ctb], Xavier Milhaud [ctb], Tommy Ouellet [ctb], Alexandre Parent [ctb], Mathieu Pigeon [aut], Louis-Philippe Pouliot [ctb], Jeffrey A. Ryan [aut] (Package API), Robert Gentleman [aut] (Parts of the R to C interface), Ross Ihaka [aut] (Parts of the R to C interface), R Core Team [aut] (Parts of the R to C interface), R Foundation [aut] (Parts of the R to C interface)
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>

Diff between actuar versions 3.1-1 dated 2021-02-03 and 3.1-2 dated 2021-03-31

 DESCRIPTION                |    8 -
 MD5                        |   32 ++--
 inst/NEWS.Rd               |   22 +++
 inst/doc/actuar.pdf        |binary
 inst/doc/coverage.pdf      |binary
 inst/doc/credibility.pdf   |binary
 inst/doc/distributions.pdf |binary
 inst/doc/modeling.pdf      |binary
 inst/doc/risk.pdf          |binary
 inst/doc/simulation.pdf    |binary
 man/Burr.Rd                |    4 
 man/emm.Rd                 |    3 
 src/invgauss.c             |    2 
 src/zmlogarithmic.c        |    6 
 tests/betaint-tests.R      |    6 
 tests/dpqr-tests.R         |  290 +++++++++++++++++++++++----------------------
 tests/rmixture-tests.R     |    8 -
 17 files changed, 209 insertions(+), 172 deletions(-)

More information about actuar at CRAN
Permanent link

Package KDViz (with last version 1.3.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-01-13 1.3.1
2019-01-11 1.3

Permanent link
Package HierDpart (with last version 0.5.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-10-03 0.5.0
2019-02-13 0.3.5
2019-01-31 0.2.0
2018-10-26 0.1.2

Permanent link

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