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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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 - 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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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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 codeCollection at CRAN
Permanent link
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(-)
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
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
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(-)
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(-)
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(-)
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
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(-)
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
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(-)
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(-)
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(-)
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],
SĂ©bastien 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(-)
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
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