Title: Spatial Designs for Ecological and Environmental Surveys
Description: Provides spatially survey balanced designs using the quasi-random number method described Robinson et al. (2013) <doi:10.1111/biom.12059>. These designs can accommodate, without substantial detrimental effects on spatial balance, legacy sites (Foster et al., 2017 <doi:10.1111/2041-210X.12782>), and for both point samples and transect samples (Foster et al. 2020, <doi:10.1111/2041-210X.13321>). Additional information about the package use itself is given in Foster (2021) <doi:10.1111/2041-210X.13535>.
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@data61.csiro.au>
Diff between MBHdesign versions 2.1.11 dated 2021-10-26 and 2.2.2 dated 2022-01-24
MBHdesign-2.1.11/MBHdesign/INDEX |only MBHdesign-2.2.2/MBHdesign/DESCRIPTION | 9 ++-- MBHdesign-2.2.2/MBHdesign/MD5 | 19 ++++---- MBHdesign-2.2.2/MBHdesign/NAMESPACE | 15 ++++-- MBHdesign-2.2.2/MBHdesign/NEWS | 8 +++ MBHdesign-2.2.2/MBHdesign/R/MBHdesign4.R | 51 ++++++++++++++++++++++- MBHdesign-2.2.2/MBHdesign/R/onLoad.R | 2 MBHdesign-2.2.2/MBHdesign/build/vignette.rds |binary MBHdesign-2.2.2/MBHdesign/inst/doc/MBHdesign.pdf |binary MBHdesign-2.2.2/MBHdesign/man/modEsti.Rd | 2 MBHdesign-2.2.2/MBHdesign/man/quasiSamp.Rd | 25 +++++++++-- 11 files changed, 103 insertions(+), 28 deletions(-)
Title: Graphical Tools for Exploring Data with 'iNZight'
Description: Simple plotting function(s) for exploratory data analysis with flexible options allowing for easy plot customisation. The goal is to make it easy for beginners to start exploring a dataset through simple R function calls, as well as provide a similar interface to summary statistics and inference information. Includes functionality to generate interactive HTML-driven graphs. Used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions.
Author: Tom Elliott [aut, cre] (<https://orcid.org/0000-0002-7815-6318>),
Yu Han Soh [aut],
Daniel Barnett [aut],
Simon Anastasiadis [ctb] (Social Wellbeing Agency, NZ)
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>
Diff between iNZightPlots versions 2.13.3 dated 2021-07-01 and 2.14.0 dated 2022-01-24
DESCRIPTION | 29 - MD5 | 91 ++-- NAMESPACE | 1 R/addSmoother.R | 26 + R/addTrend.R | 6 R/colourpalettes.R | 6 R/general.R | 6 R/getSummary.R | 144 ++++++ R/iNZGG.R | 8 R/iNZightPlot.R | 14 R/inference.R | 708 +++++++++++++++++++-------------- R/inzDataframe.R | 1 R/inzbarplot.R | 29 - R/inzdotplot.R | 36 + R/inzhexplot.R | 3 R/inzinference.R | 11 R/inzpar.R | 10 R/inzplot.R | 2 R/inzscatterplot.R | 4 R/inzsummary.R | 11 R/inztransform.R | 5 R/privacy_controls.R |only R/summary.R | 300 +++++++++++-- R/sysdata.rda |binary man/figures/README-colours-1.png |binary man/figures/README-demo-1.png |binary man/figures/README-demo-inf.png |binary man/figures/README-demo-usage-2.png |binary man/figures/README-demo-usage-3.png |binary man/figures/README-demo-usage-4.png |binary man/figures/README-trends-2.png |binary man/getPlotSummary.Rd | 17 man/inzpar.Rd | 4 man/snz_privacy_controls.Rd |only tests/testthat/test_bar.R | 2 tests/testthat/test_bar2.R | 2 tests/testthat/test_dot.R | 24 + tests/testthat/test_epi.R | 42 - tests/testthat/test_frequencies.R | 4 tests/testthat/test_inference.R | 131 +++++- tests/testthat/test_poststrat.R | 4 tests/testthat/test_privacy_controls.R |only tests/testthat/test_repweights.R | 29 - tests/testthat/test_scatter.R | 31 - tests/testthat/test_summary.R | 23 + tests/testthat/test_survey.R | 14 tests/testthat/test_survey_inference.R | 139 +++--- tests/testthat/test_survey_methods.R | 8 48 files changed, 1349 insertions(+), 576 deletions(-)
Title: Flexible Genotyping for Polyploids
Description: Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allele bias, overdispersion, and sequencing
error. The main functions are flexdog() and multidog(),
which allow the specification
of many different genotype distributions. Also provided are functions to
simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as
functions to calculate oracle genotyping error rates, oracle_mis(), and
correlation with the true genotypes, oracle_cor(). These latter two
functions are useful for read depth calculations. Run
browseVignettes(package = "updog") in R for example usage. See
Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and
Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for details
on the implemented methods.
Author: David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between updog versions 2.1.1 dated 2021-10-25 and 2.1.2 dated 2022-01-24
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/ashdog.R | 20 +++++++++++++------- R/oracle.R | 8 ++++++-- R/rflexdog.R | 5 ++++- README.md | 9 ++++----- build/partial.rdb |binary build/vignette.rds |binary tests/testthat/test_dbetabinom.R | 6 ++++-- 10 files changed, 49 insertions(+), 29 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio, PBC [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.15.1 dated 2022-01-13 and 0.15.2 dated 2022-01-24
renv-0.15.1/renv/vignettes/renv.md |only renv-0.15.2/renv/DESCRIPTION | 6 renv-0.15.2/renv/MD5 | 39 ++--- renv-0.15.2/renv/NEWS.md | 2 renv-0.15.2/renv/R/namespace.R | 4 renv-0.15.2/renv/inst/doc/bioconductor.html | 31 +++- renv-0.15.2/renv/inst/doc/cellar.html | 62 +++++++-- renv-0.15.2/renv/inst/doc/ci.html | 61 +++++++-- renv-0.15.2/renv/inst/doc/collaborating.html | 72 ++++++++-- renv-0.15.2/renv/inst/doc/docker.html | 119 ++++++++++++++---- renv-0.15.2/renv/inst/doc/faq.html | 131 +++++++++++++++----- renv-0.15.2/renv/inst/doc/lockfile.html | 22 ++- renv-0.15.2/renv/inst/doc/mran.html | 78 +++++++++-- renv-0.15.2/renv/inst/doc/packages.html | 66 +++++++--- renv-0.15.2/renv/inst/doc/profiles.html | 71 ++++++++-- renv-0.15.2/renv/inst/doc/python.html | 52 ++++++- renv-0.15.2/renv/inst/doc/renv.html | 6 renv-0.15.2/renv/inst/doc/rsconnect.html | 46 ++++++- renv-0.15.2/renv/inst/doc/use.html | 31 +++- renv-0.15.2/renv/tests/testthat/test-dependencies.R | 4 renv-0.15.2/renv/tests/testthat/test-install.R | 4 21 files changed, 702 insertions(+), 205 deletions(-)
Title: Construct Modeling Packages
Description: Building modeling packages is hard. A large amount
of effort generally goes into providing an implementation for a new
method that is efficient, fast, and correct, but often less emphasis
is put on the user interface. A good interface requires specialized
knowledge about S3 methods and formulas, which the average package
developer might not have. The goal of 'hardhat' is to reduce the
burden around building new modeling packages by providing
functionality for preprocessing, predicting, and validating input.
Author: Davis Vaughan [aut, cre],
Max Kuhn [aut],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between hardhat versions 0.1.6 dated 2021-07-14 and 0.2.0 dated 2022-01-24
DESCRIPTION | 8 +-- MD5 | 37 ++++++++------- NAMESPACE | 3 + NEWS.md | 13 +++++ R/blueprint-formula-default.R | 88 ++++++++++++++++++++++++++++++------- R/delete-response.R | 2 R/extract.R | 20 +++++++- R/tune.R |only README.md | 7 +- build/hardhat.pdf |binary build/vignette.rds |binary inst/doc/forge.html | 20 ++++---- inst/doc/mold.html | 30 ++++++------ inst/doc/package.html | 10 ++-- man/default_formula_blueprint.Rd | 8 ++- man/delete_response.Rd | 2 man/hardhat-extract.Rd | 10 +++- man/hardhat-package.Rd | 9 --- man/tune.Rd |only tests/testthat/test-mold-formula.R | 31 ++++++++++++- tests/testthat/test-tune.R |only 21 files changed, 211 insertions(+), 87 deletions(-)
Title: Fair Models in Machine Learning
Description: Fair machine learning regression models which take sensitive attributes into account in
model estimation. Currently implementing Komiyama et al. (2018)
<http://proceedings.mlr.press/v80/komiyama18a/komiyama18a.pdf>, Zafar et al.
(2019) <https://www.jmlr.org/papers/volume20/18-262/18-262.pdf> and my own
approach that uses ridge regression to enforce fairness.
Author: Marco Scutari [aut, cre]
Maintainer: Marco Scutari <marco.scutari@gmail.com>
Diff between fairml versions 0.6 dated 2021-08-09 and 0.6.1 dated 2022-01-24
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/comparisons.R | 20 ++++++++++---------- R/crossvalidation.R | 12 ++++++------ R/getters.R | 22 +++++++++++----------- R/parallel.R | 2 +- R/predict.R | 20 ++++++++++---------- R/print.R | 4 ++-- R/profile-plots.R | 4 ++-- R/sanitization-data.R | 2 +- R/sanitization-misc.R | 2 +- R/summary.R | 2 +- 12 files changed, 60 insertions(+), 60 deletions(-)
Title: Universal Storage Engine for Sparse and Dense Multidimensional
Arrays
Description: The universal storage engine 'TileDB' introduces a
powerful on-disk format for multi-dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.10.2 dated 2021-12-19 and 0.11.0 dated 2022-01-24
DESCRIPTION | 6 MD5 | 80 NAMESPACE | 9 NEWS.md | 29 R/Array.R | 4 R/ArraySchema.R | 284 +++ R/Attribute.R | 34 R/Dim.R | 50 R/Domain.R | 35 R/Filter.R | 33 R/FilterList.R | 24 R/Query.R | 13 R/RcppExports.R | 18 R/TileDBArray.R | 12 R/Utils.R | 81 R/generics.R | 2 R/zzz.R | 5 README.md | 6 inst/doc/documentation.html | 1692 +++++++++----------- inst/doc/introduction.html | 16 inst/doc/tiledb-mariadb-examples.html | 337 +-- inst/tinytest/test_attr.R | 13 inst/tinytest/test_dimsubset.R | 1 inst/tinytest/test_tiledbarray.R | 2 man/attrs-tiledb_array_schema-numeric-method.Rd | 2 man/describe.Rd |only man/dim.tiledb_array_schema.Rd | 2 man/dimensions-tiledb_array_schema-method.Rd | 2 man/generics.Rd | 5 man/raw_dump-tiledb_array_schema-method.Rd |only man/raw_dump-tiledb_attr-method.Rd |only man/raw_dump-tiledb_domain-method.Rd |only man/save_allocation_size_preference.Rd |only man/show-tiledb_dim-method.Rd |only man/show-tiledb_domain-method.Rd | 6 man/show-tiledb_filter-method.Rd |only man/show-tiledb_filter_list-method.Rd |only man/tiledb_array_schema.Rd | 3 man/tiledb_array_schema_set_validity_filter_list.Rd |only man/tiledb_dim_get_cell_val_num.Rd |only man/tiledb_filter_set_option.Rd | 7 man/tiledb_ndim-tiledb_array_schema-method.Rd | 2 man/tiledb_query_ctx.Rd |only man/tiledb_schema_object.Rd |only src/RcppExports.cpp | 53 src/libtiledb.cpp | 59 tools/tiledbVersion.txt | 4 47 files changed, 1787 insertions(+), 1144 deletions(-)
Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut, cre],
Brian Ripley [trl] (producer of the initial R port, maintainer
1999-2017)
Maintainer: Beth Atkinson <atkinson@mayo.edu>
Diff between rpart versions 4.1-15 dated 2019-04-12 and 4.1.16 dated 2022-01-24
ChangeLog | 10 ++++--- DESCRIPTION | 8 +++--- MD5 | 48 +++++++++++++++++++------------------- R/plot.rpart.R | 6 +++- R/print.rpart.R | 6 ++-- R/prune.rpart.R | 2 - R/rpart.R | 6 +++- R/rpart.class.R | 4 +-- R/rpart.matrix.R | 13 +++++++--- R/xpred.rpart.R | 6 +++- build/vignette.rds |binary data/solder.rda |binary inst/doc/longintro.pdf |binary inst/doc/usercode.Rnw | 2 - inst/doc/usercode.pdf |binary man/path.rpart.Rd | 2 - man/plot.rpart.Rd | 12 ++++++++- man/print.rpart.Rd | 6 +++- man/rpart.Rd | 2 - src/free_tree.c | 4 +-- src/insert_split.c | 4 +-- src/xval.c | 4 +-- tests/Examples/rpart-Ex.Rout.save | 2 - tests/minus_in_formula.R |only tests/minus_in_formula.Rout.save |only vignettes/usercode.Rnw | 2 - 26 files changed, 89 insertions(+), 60 deletions(-)
Title: Pattern Support for 'qtl2' Package
Description: Routines in 'qtl2' to study allele patterns in quantitative trait loci (QTL)
mapping over a chromosome.
Useful in crosses with more than two alleles to identify how sets of alleles,
genetically different strands at the same locus, have different response levels.
Plots show profiles over a chromosome.
Can handle multiple traits together.
See <https://github.com/byandell/qtl2pattern>.
Author: Brian S Yandell [aut, cre]
Maintainer: Brian S Yandell <brian.yandell@wisc.edu>
Diff between qtl2pattern versions 1.0.17 dated 2021-09-22 and 1.2.0 dated 2022-01-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/read_probs_fast.R | 2 +- R/sdp_to_pattern.R | 13 +++++++++++-- build/vignette.rds |binary inst/doc/qtl2pattern.html | 14 +++++++------- man/sdp_to_pattern.Rd | 6 ++++-- 7 files changed, 33 insertions(+), 22 deletions(-)
Title: Data Visualization for QTL Experiments
Description: Functions to plot QTL (quantitative trait loci) analysis
results and related diagnostics.
Part of 'qtl2', an upgrade of the 'qtl'
package to better handle high-dimensional data and complex cross
designs.
Author: Brian S Yandell [aut, cre],
Karl W Broman [aut]
Maintainer: Brian S Yandell <brian.yandell@wisc.edu>
Diff between qtl2ggplot versions 1.1.0 dated 2021-09-08 and 1.2.1 dated 2022-01-24
DESCRIPTION | 10 ++++---- MD5 | 14 +++++------ R/ggplot_snpasso.R | 4 ++- R/sdp_to_pattern.R | 7 +++++ build/vignette.rds |binary inst/doc/qtl2ggplot.html | 56 +++++++++++++++++++++++------------------------ man/ggplot_snpasso.Rd | 4 ++- man/sdp_to_pattern.Rd | 4 ++- 8 files changed, 55 insertions(+), 44 deletions(-)
Title: Use LaTeX Expressions in Plots
Description: Parses and converts LaTeX math formulas to R's plotmath
expressions, used to enter mathematical formulas and symbols to be rendered as
text, axis labels, etc. throughout R's plotting system.
Author: Stefano Meschiari [aut, cre]
Maintainer: Stefano Meschiari <stefano.meschiari@gmail.com>
Diff between latex2exp versions 0.5.0 dated 2021-03-18 and 0.9.0 dated 2022-01-24
latex2exp-0.5.0/latex2exp/man/print.latextoken.Rd |only latex2exp-0.5.0/latex2exp/man/toString.latextoken.Rd |only latex2exp-0.5.0/latex2exp/tests/testthat/Rplots.pdf |only latex2exp-0.5.0/latex2exp/tests/testthat/test_latex2exp.r |only latex2exp-0.9.0/latex2exp/DESCRIPTION | 18 latex2exp-0.9.0/latex2exp/MD5 | 50 latex2exp-0.9.0/latex2exp/NAMESPACE | 37 latex2exp-0.9.0/latex2exp/NEWS.md | 46 latex2exp-0.9.0/latex2exp/R/demos.R |only latex2exp-0.9.0/latex2exp/R/latex2exp.R | 751 +------------ latex2exp-0.9.0/latex2exp/R/parser.R |only latex2exp-0.9.0/latex2exp/R/plots.R |only latex2exp-0.9.0/latex2exp/R/symbols.R |only latex2exp-0.9.0/latex2exp/R/utils.R |only latex2exp-0.9.0/latex2exp/build/vignette.rds |binary latex2exp-0.9.0/latex2exp/inst/doc/supported-commands.R |only latex2exp-0.9.0/latex2exp/inst/doc/supported-commands.Rmd |only latex2exp-0.9.0/latex2exp/inst/doc/supported-commands.html |only latex2exp-0.9.0/latex2exp/inst/doc/using-latex2exp.R | 102 - latex2exp-0.9.0/latex2exp/inst/doc/using-latex2exp.Rmd | 157 -- latex2exp-0.9.0/latex2exp/inst/doc/using-latex2exp.html | 168 -- latex2exp-0.9.0/latex2exp/man/TeX.Rd | 56 latex2exp-0.9.0/latex2exp/man/figures |only latex2exp-0.9.0/latex2exp/man/latex2exp.Rd | 8 latex2exp-0.9.0/latex2exp/man/latex2exp_examples.Rd | 12 latex2exp-0.9.0/latex2exp/man/latex2exp_supported.Rd | 14 latex2exp-0.9.0/latex2exp/man/plot.expression.Rd | 17 latex2exp-0.9.0/latex2exp/man/print.latexexpression.Rd |only latex2exp-0.9.0/latex2exp/man/print.latextoken2.Rd |only latex2exp-0.9.0/latex2exp/tests/testthat/setup.R |only latex2exp-0.9.0/latex2exp/tests/testthat/test_examples.r |only latex2exp-0.9.0/latex2exp/tests/testthat/test_simple.R |only latex2exp-0.9.0/latex2exp/vignettes/supported-commands.Rmd |only latex2exp-0.9.0/latex2exp/vignettes/using-latex2exp.Rmd | 157 -- 34 files changed, 470 insertions(+), 1123 deletions(-)
Title: Miscellaneous Functions for the USGS INL Project Office
Description: A collection of functions for creating high-level graphics,
performing raster-based analysis, processing MODFLOW-based models,
selecting subsets using a genetic algorithm, creating interactive web maps,
accessing color palettes, etc. Used to support packages and scripts written
by researchers at the United States Geological Survey (USGS)
Idaho National Laboratory (INL) Project Office.
Author: Jason C. Fisher [aut, cre] (<https://orcid.org/0000-0001-9032-8912>)
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between inlmisc versions 0.5.2 dated 2020-09-12 and 0.5.5 dated 2022-01-24
DESCRIPTION | 10 +- MD5 | 77 ++++++++++--------- NEWS.md | 18 ++++ R/AddColorKey.R | 2 R/AddPoints.R | 2 R/AddScaleBar.R | 2 R/CreateWebMap.R | 6 - R/ExtractAlongTransect.R | 6 + R/FindOptimalSubset.R | 4 - R/GetColors.R | 2 R/GetRegionOfInterest.R | 2 R/Grid2Polygons.R | 4 - R/POSIXct2Character.R | 2 R/PlotCrossSection.R | 2 R/PlotGraph.R | 8 +- R/PlotMap.R | 2 R/PrintTable.R | 3 R/RecreateLibrary.R | 17 ++-- R/SetPolygons.R | 1 R/sysdata.rda |binary README.md | 175 ++++++++++++++++++++------------------------- build |only man/AddColorKey.Rd | 2 man/AddScaleBar.Rd | 2 man/CreateWebMap.Rd | 6 - man/FindOptimalSubset.Rd | 4 - man/GetColors.Rd | 2 man/GetRegionOfInterest.Rd | 2 man/Grid2Polygons.Rd | 2 man/POSIXct2Character.Rd | 2 man/PlotCrossSection.Rd | 2 man/PlotGraph.Rd | 6 + man/PrintTable.Rd | 3 man/RecreateLibrary.Rd | 17 ++-- man/figures/table01.pdf |binary man/figures/table02.pdf |binary man/figures/table03.pdf |binary man/figures/table04.pdf |binary man/figures/table05.pdf |binary man/figures/table05.svg | 2 40 files changed, 204 insertions(+), 193 deletions(-)
Title: A Ternary Conditional Operator for R
Description: A small language extension for succinct conditional assignment using `?` and `:`, emulating the conditional ternary operator syntax using in C, Java, JavaScript and other languages.
Author: Gethin Davies [aut, cre]
Maintainer: Gethin Davies <grd.davies@gmail.com>
Diff between rtern versions 0.1.1 dated 2021-04-28 and 0.1.2 dated 2022-01-24
DESCRIPTION | 12 - MD5 | 20 - NAMESPACE | 1 NEWS.md | 38 ++- R/conditional_operator.R | 199 +++++++++--------- R/is_assignment.R | 2 README.md | 111 +++++----- inst/WORDLIST | 22 +- man/help.Rd | 4 man/is_assignment.Rd | 2 tests/testthat/test-conditional_operator.R | 306 ++++++++++++++++------------- 11 files changed, 386 insertions(+), 331 deletions(-)
Title: Interface to the 'Microsoft 365' Suite of Cloud Services
Description: An interface to the 'Microsoft 365' (formerly known as 'Office 365') suite of cloud services, building on the framework supplied by the 'AzureGraph' package. Enables access from R to data stored in 'Teams', 'SharePoint Online' and 'OneDrive', including the ability to list drive folder contents, upload and download files, send messages, and retrieve data lists. Also provides a full-featured 'Outlook' email client, with the ability to send emails and manage emails and mail folders.
Author: Hong Ooi [aut, cre],
Roman Zenka [ctb],
Robert Ashton [ctb],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between Microsoft365R versions 2.3.2 dated 2021-10-26 and 2.3.3 dated 2022-01-24
DESCRIPTION | 6 ++-- MD5 | 14 +++++----- NEWS.md | 4 +++ R/build_email_request.R | 36 +++++++++++++++++++++------- R/make_email_attachments.R | 20 ++++++++++----- R/ms_outlook_email.R | 2 - tests/testthat/test05b_outlook_email.R | 4 +-- tests/testthat/test05c_outlook_attachment.R | 2 - 8 files changed, 59 insertions(+), 29 deletions(-)
Title: Measuring Disparity
Description: A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics (Guillerme (2018) <doi:10.1111/2041-210X.13022>). The package also provides functions for looking at disparity in a serial way (e.g. disparity through time - Guillerme and Cooper (2018) <doi:10.1111/pala.12364>) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph],
Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>
Diff between dispRity versions 1.6.0 dated 2021-04-17 and 1.6.8 dated 2022-01-24
DESCRIPTION | 10 +- MD5 | 70 +++++++------- NAMESPACE | 3 NEWS.md | 51 +++++++--- R/chrono.subsets.R | 35 ++++--- R/chrono.subsets_fun.R | 12 +- R/custom.subsets.R | 152 +++---------------------------- R/custom.subsets_fun.R | 137 ++++++++++++++++++++++++--- R/dispRity.R | 2 R/dispRity.metric.R | 31 ++---- R/dispRity_fun.R | 7 - R/make.metric.R | 6 + R/null.test_fun.R | 22 +++- R/plot.dispRity.R | 22 +++- R/plot.dispRity_fun.R | 141 +++++++++++++++++++++++----- R/print.dispRity.R | 27 +++++ R/randtest.dispRity.R | 2 R/randtest.dist.R |only R/sanitizing.R | 11 +- R/select.axes.R |only R/summary.dispRity.R | 27 +++++ R/test.dispRity.R | 14 ++ R/zzz.R | 4 data/BeckLee_ages.rda |binary data/BeckLee_disparity.rda |binary data/BeckLee_mat50.rda |binary data/BeckLee_mat99.rda |binary data/BeckLee_tree.rda |binary data/demo_data.rda |binary data/disparity.rda |binary inst/vignettes/dispRity_workhop_code.Rmd | 3 man/chrono.subsets.Rd | 14 +- man/dispRity.metric.Rd | 8 - man/plot.dispRity.Rd | 6 - man/randtest.dispRity.Rd | 2 man/randtest.dist.Rd |only man/select.axes.Rd |only src/dispRity.h | 4 38 files changed, 515 insertions(+), 308 deletions(-)
Title: Estimate Univariate Gaussian and Student's t Mixture
Autoregressive Models
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2021) <doi:10.1080/03610926.2021.1916531>,
Savi Virolainen (2021) <doi:10.1515/snde-2020-0060>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.4.1 dated 2022-01-18 and 3.4.2 dated 2022-01-24
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/geneticAlgorithm.R | 18 +++++++++++++----- inst/doc/uGMARpaper.Rnw | 30 +++++++++++++++--------------- inst/doc/uGMARpaper.pdf |binary vignettes/uGMARpaper.Rnw | 30 +++++++++++++++--------------- 7 files changed, 57 insertions(+), 44 deletions(-)
Title: Extract Semantic Relations from Text by Querying and Reshaping
Syntax
Description: Various functions for querying and reshaping dependency trees,
as for instance created with the 'spacyr' or 'udpipe' packages.
This enables the automatic extraction of useful semantic relations from texts,
such as quotes (who said what) and clauses (who did what). Method proposed in
Van Atteveldt et al. (2017) <doi:10.1017/pan.2016.12>.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between rsyntax versions 0.1.2 dated 2021-06-13 and 0.1.3 dated 2022-01-24
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Armadillo requires a C++11 compiler.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.10.7.5.0 dated 2021-12-17 and 0.10.8.1.0 dated 2022-01-24
ChangeLog | 32 ++ DESCRIPTION | 8 MD5 | 84 ++--- build/partial.rdb |binary configure | 18 - configure.ac | 4 inst/NEWS.Rd | 26 + inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo | 2 inst/include/armadillo_bits/Cube_bones.hpp | 26 - inst/include/armadillo_bits/Cube_meat.hpp | 32 +- inst/include/armadillo_bits/Mat_bones.hpp | 46 +- inst/include/armadillo_bits/Mat_meat.hpp | 76 ++-- inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/auxlib_bones.hpp | 8 inst/include/armadillo_bits/auxlib_meat.hpp | 47 +-- inst/include/armadillo_bits/constants.hpp | 2 inst/include/armadillo_bits/diagmat_proxy.hpp | 284 ------------------ inst/include/armadillo_bits/fn_accu.hpp | 38 +- inst/include/armadillo_bits/fn_eig_sym.hpp | 20 - inst/include/armadillo_bits/fn_norm.hpp | 44 ++ inst/include/armadillo_bits/fn_rank.hpp | 51 +-- inst/include/armadillo_bits/fn_reshape.hpp | 16 - inst/include/armadillo_bits/glue_solve_meat.hpp | 2 inst/include/armadillo_bits/glue_times_meat.hpp | 60 ++- inst/include/armadillo_bits/gmm_diag_meat.hpp | 2 inst/include/armadillo_bits/gmm_full_meat.hpp | 2 inst/include/armadillo_bits/op_cond_meat.hpp | 2 inst/include/armadillo_bits/op_expmat_meat.hpp | 2 inst/include/armadillo_bits/op_find_meat.hpp | 95 ++++-- inst/include/armadillo_bits/op_inv_meat.hpp | 27 + inst/include/armadillo_bits/op_logmat_meat.hpp | 4 inst/include/armadillo_bits/op_pinv_bones.hpp | 4 inst/include/armadillo_bits/op_pinv_meat.hpp | 190 +++++++++--- inst/include/armadillo_bits/op_powmat_meat.hpp | 8 inst/include/armadillo_bits/op_rank_bones.hpp |only inst/include/armadillo_bits/op_rank_meat.hpp |only inst/include/armadillo_bits/op_reshape_bones.hpp | 16 - inst/include/armadillo_bits/op_reshape_meat.hpp | 355 ++++++++++++----------- inst/include/armadillo_bits/op_resize_bones.hpp | 13 inst/include/armadillo_bits/op_resize_meat.hpp | 161 +++++----- inst/include/armadillo_bits/op_sqrtmat_meat.hpp | 4 inst/include/armadillo_bits/sympd_helper.hpp | 217 +++++++++++++- 44 files changed, 1154 insertions(+), 880 deletions(-)
Title: Graph/Network Visualization
Description: Build graph/network structures using functions for stepwise addition and
deletion of nodes and edges. Work with data available in tables for bulk
addition of nodes, edges, and associated metadata. Use graph selections
and traversals to apply changes to specific nodes or edges. A wide
selection of graph algorithms allow for the analysis of graphs. Visualize
the graphs and take advantage of any aesthetic properties assigned to
nodes and edges.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>)
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 1.0.7 dated 2022-01-15 and 1.0.8 dated 2022-01-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 10 insertions(+), 6 deletions(-)
Title: A Graphical User Interface for Dexter
Description: Classical Test and Item analysis,
Item Response analysis and data management for educational and psychological tests.
Author: Jesse Koops [aut, cre],
Eva de Schipper [aut],
Ivailo Partchev [aut, ctb],
Gunter Maris [aut, ctb],
Timo Bechger [aut, ctb],
Gareth Watts [cph] (author of jquery.sparkline),
Hakim El Hattab [cph] (author of zoom.js)
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dextergui versions 0.2.3 dated 2021-05-05 and 0.2.4 dated 2022-01-24
dextergui-0.2.3/dextergui/vignettes/img/main_bar.PNG |only dextergui-0.2.4/dextergui/DESCRIPTION | 14 dextergui-0.2.4/dextergui/MD5 | 26 - dextergui-0.2.4/dextergui/NEWS.md | 7 dextergui-0.2.4/dextergui/R/gui.R | 35 + dextergui-0.2.4/dextergui/R/misc.R | 34 - dextergui-0.2.4/dextergui/R/serve.R | 163 +++++- dextergui-0.2.4/dextergui/README.md | 4 dextergui-0.2.4/dextergui/build/vignette.rds |binary dextergui-0.2.4/dextergui/inst/doc/dextergui.R | 19 dextergui-0.2.4/dextergui/inst/doc/dextergui.Rmd | 52 +- dextergui-0.2.4/dextergui/inst/doc/dextergui.html | 288 ++---------- dextergui-0.2.4/dextergui/inst/extdata/manual.html | 75 ++- dextergui-0.2.4/dextergui/vignettes/dextergui.Rmd | 52 +- dextergui-0.2.4/dextergui/vignettes/img/profile_buttons.PNG |only 15 files changed, 420 insertions(+), 349 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],
Sébastien Auclair [ctb],
Christophe Dutang [aut],
Walter Garcia-Fontes [ctb],
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 3.2-0 dated 2021-10-05 and 3.2-1 dated 2022-01-24
DESCRIPTION | 8 +-- MD5 | 26 ++++++------ inst/CITATION | 2 inst/NEWS.Rd | 24 +++++++---- 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 tests/dpqr-tests.R | 90 ++++++++++++++++++++++++++------------------ vignettes/actuar.bib | 14 +++--- vignettes/auto/actuar.el | 91 ++++++++++++++++++++++++--------------------- 14 files changed, 145 insertions(+), 110 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 1.8.0 dated 2021-12-14 and 1.8.1 dated 2022-01-24
DESCRIPTION | 6 - MD5 | 14 +-- R/pairsAsPropensMatr.R | 33 +++++--- inst/doc/wrMiscVignette1.R | 12 ++- inst/doc/wrMiscVignette1.Rmd | 55 +++++++------- inst/doc/wrMiscVignette1.html | 164 +++++++++++++++++++++--------------------- man/pairsAsPropensMatr.Rd | 28 +++++-- vignettes/wrMiscVignette1.Rmd | 55 +++++++------- 8 files changed, 208 insertions(+), 159 deletions(-)
Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures with
quantile-based basis functions, possibly under linearity and
homogeneity assumptions. This approach estimates a regression line
corresponding to the expected change in the outcome (on the link
basis) given a simultaneous increase in the quantile-based category
for all exposures. Works with continuous, binary, and right-censored
time-to-event outcomes. Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and
Alexandra J. White (2019) A quantile-based g-computation approach to
addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between qgcomp versions 2.8.5 dated 2021-12-12 and 2.8.6 dated 2022-01-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 10 ++++++++++ README.md | 2 +- inst/doc/qgcomp-vignette.html | 2 +- tests/test_asis.R | 16 ++++++++++++---- 6 files changed, 33 insertions(+), 15 deletions(-)
Title: Interface to 'X12-ARIMA'/'X13-ARIMA-SEATS' and Structure for
Batch Processing of Seasonal Adjustment
Description: The 'X13-ARIMA-SEATS' <https://www.census.gov/data/software/x13as.html> methodology and software is a widely used software and developed by the US Census Bureau. It can be accessed from 'R' with this package and 'X13-ARIMA-SEATS' binaries are provided by the 'R' package 'x13binary'.
Author: Alexander Kowarik <alexander.kowarik@statistik.gv.at>, Angelika Meraner
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between x12 versions 1.9.3 dated 2020-11-13 and 1.10.0 dated 2022-01-24
x12-1.10.0/x12/DESCRIPTION | 17 ++----- x12-1.10.0/x12/MD5 | 16 +++---- x12-1.10.0/x12/R/x12work.R | 12 ++++- x12-1.10.0/x12/inst/CITATION | 8 +-- x12-1.10.0/x12/inst/tinytest |only x12-1.10.0/x12/man/readSpc.Rd | 84 +++++++++++++++++++------------------- x12-1.10.0/x12/man/x12-methods.Rd | 2 x12-1.10.0/x12/man/x12work.Rd | 2 x12-1.10.0/x12/tests/tinytest.R |only x12-1.9.3/x12/tests/testthat |only x12-1.9.3/x12/tests/testthat.R |only 11 files changed, 71 insertions(+), 70 deletions(-)
Title: Interpretation of Heterogeneous Single-Cell Gene Expression Data
Description: We develop a novel matrix factorization tool named 'scINSIGHT' to jointly analyze multiple single-cell gene expression samples from biologically heterogeneous sources, such as different disease phases, treatment groups, or developmental stages. Given multiple gene expression samples from different biological conditions, 'scINSIGHT' simultaneously identifies common and condition-specific gene pathways and quantify their expression levels in each sample in a lower-dimensional space. With the factorized results, the inferred expression levels and memberships of common gene pathways can be used to cluster cells and detect cell identities, and the condition-specific gene pathways can help compare functional differences in transcriptomes from distinct conditions.
Author: Kun Qian [aut, ctb, cre] (<https://orcid.org/0000-0002-2354-2238>),
Wei Vivian Li [aut, ctb] (<https://orcid.org/0000-0002-2087-2709>)
Maintainer: Kun Qian <Kun_Qian@foxmail.com>
Diff between scINSIGHT versions 0.1.1 dated 2021-09-06 and 0.1.2 dated 2022-01-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/scinsight.R | 3 ++- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Interface for the RobinHood.com No Commission Investing Platform
Description: Execute API calls to the RobinHood <https://robinhood.com> investing platform. Functionality includes accessing account data and current holdings, retrieving investment statistics and quotes, placing and canceling orders, getting market trading hours, searching investments by popular tag, and interacting with watch lists.
Author: Joseph Blubaugh
Maintainer: Joseph Blubaugh <jestonblu@gmail.com>
Diff between RobinHood versions 1.6 dated 2021-03-01 and 1.6.2 dated 2022-01-24
DESCRIPTION | 8 +- MD5 | 92 ++++++++++++++-------------- NAMESPACE | 34 ++++++++++ R/RobinHood.R | 2 R/api_accounts.R | 2 R/api_accounts_crypto.R | 2 R/api_ach.R | 21 ++++-- R/api_contracts.R | 6 - R/api_currency_pairs.R | 2 R/api_endpoints.R | 67 ++++++++++---------- R/api_fundamentals.R | 2 R/api_historicals.R | 2 R/api_historicals_crypto.R | 4 - R/api_historicals_options.R |only R/api_instruments.R | 2 R/api_instruments_options.R | 132 +++++++++++++++++++++++++++++++++-------- R/api_login.R | 2 R/api_logout.R | 2 R/api_marketdata.R | 24 ++++--- R/api_markets.R | 2 R/api_orders.R | 2 R/api_orders_crypto.R | 4 - R/api_orders_options.R | 2 R/api_portfolio_crypto.R | 2 R/api_portfolios.R | 6 - R/api_positions.R | 2 R/api_positions_crypto.R | 2 R/api_positions_options.R | 8 +- R/api_quote.R | 2 R/api_quote_crypto.R | 2 R/api_ratings.R | 2 R/api_tag.R | 2 R/api_tickers.R | 2 R/api_user.R | 2 R/api_watchlist.R | 2 R/check_rh.R | 2 R/get_ach.R | 20 ++---- R/get_contracts.R | 25 ++----- R/get_historicals_crypto.R | 8 +- R/get_historicals_options.R |only R/get_portfolios.R | 20 +++--- R/get_positions_options.R | 13 ++-- R/mod_json.R | 2 R/place_order.R | 46 +++++++++----- R/place_order_crypto.R | 4 - man/api_historicals_options.Rd |only man/api_instruments_options.Rd | 32 ++++++++- man/get_historicals_options.Rd |only man/place_order.Rd | 43 +++++++++---- 49 files changed, 419 insertions(+), 246 deletions(-)
Title: Utilities for 'DIZ' R Package Development
Description: Utility functions used for the R package development
infrastructure inside the data integration centers ('DIZ') to
standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] (<https://orcid.org/0000-0003-0518-4710>),
Lorenz A. Kapsner [aut] (<https://orcid.org/0000-0003-1866-860X>),
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitätsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZutils versions 0.0.9 dated 2021-12-08 and 0.0.10 dated 2022-01-24
DESCRIPTION | 8 MD5 | 106 ++-- NAMESPACE | 51 +- R/check_if_table_exists.R | 126 ++--- R/clean_path_name.R | 82 +-- R/clear.R | 98 ++-- R/close_all_connections.R | 98 ++-- R/combine_stats.R | 316 +++++++------- R/db_connection.R | 556 ++++++++++++------------ R/equals2.R | 116 ++--- R/feedback.R | 784 +++++++++++++++++------------------ R/firstup.R | 60 +- R/format_POSIXct.R | 144 +++--- R/get_config.R | 144 +++--- R/get_config_env.R | 344 +++++++-------- R/get_current_timestamp.R | 88 +-- R/get_db_systems.R | 66 +- R/global_env_hack.R | 92 ++-- R/is_date_format.R | 62 +- R/notin.R | 82 +-- R/query_database.R | 172 +++---- R/set_env_vars.R | 106 ++-- R/setdiff_all.R | 98 ++-- R/setenv2.R |only R/string_replacements.R | 208 ++++----- R/xml_2_json.R | 56 +- man/check_if_table_exists.Rd | 54 +- man/clean_path_name.Rd | 54 +- man/cleanup_old_logfile.Rd | 50 +- man/clear.Rd | 46 +- man/close_all_connections.Rd | 64 +- man/combine_stats.Rd | 62 +- man/db_connection.Rd | 160 +++---- man/equals2.Rd | 96 ++-- man/feedback.Rd | 174 +++---- man/feedback_get_formatted_string.Rd | 80 +-- man/feedback_to_console.Rd | 114 ++--- man/feedback_to_logfile.Rd | 78 +-- man/feedback_to_logjs.Rd | 52 +- man/feedback_to_ui.Rd | 58 +- man/firstup.Rd | 42 - man/format_posixct.Rd | 76 +-- man/get_config.Rd | 80 +-- man/get_config_env.Rd | 112 ++--- man/get_current_timestamp.Rd | 62 +- man/get_db_systems.Rd | 44 - man/global_env_hack.Rd | 70 +-- man/grapes-notin-grapes.Rd | 48 +- man/is_date_format.Rd | 38 - man/query_database.Rd | 118 ++--- man/set_env_vars.Rd | 52 +- man/setdiff_all.Rd | 80 +-- man/setenv2.Rd |only man/string_replacements.Rd | 76 +-- man/xml_2_json.Rd | 34 - 55 files changed, 3074 insertions(+), 3063 deletions(-)
Title: Package for Environmental Statistics, Including US EPA Guidance
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4,
<https://link.springer.com/book/9781461484554>).
Author: Steven P. Millard [aut],
Alexander Kowarik [ctb, cre] (<https://orcid.org/0000-0001-8598-4130>)
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between EnvStats versions 2.4.0 dated 2020-10-21 and 2.5.0 dated 2022-01-24
EnvStats-2.4.0/EnvStats/tests/testthat |only EnvStats-2.4.0/EnvStats/tests/testthat.R |only EnvStats-2.5.0/EnvStats/DESCRIPTION | 12 EnvStats-2.5.0/EnvStats/MD5 | 47 EnvStats-2.5.0/EnvStats/R/calibrate.R | 264 +- EnvStats-2.5.0/EnvStats/R/chenTTest.R | 193 - EnvStats-2.5.0/EnvStats/R/ebinom.R | 161 - EnvStats-2.5.0/EnvStats/README.md | 4 EnvStats-2.5.0/EnvStats/build |only EnvStats-2.5.0/EnvStats/inst/tinytest |only EnvStats-2.5.0/EnvStats/man/Distribution.df.Rd | 2 EnvStats-2.5.0/EnvStats/man/EnvStats-package.Rd | 4 EnvStats-2.5.0/EnvStats/man/Olympic.NH4.df.Rd | 2 EnvStats-2.5.0/EnvStats/man/distChoose.Rd | 2 EnvStats-2.5.0/EnvStats/man/distChooseCensored.Rd | 2 EnvStats-2.5.0/EnvStats/man/egammaAltCensored.Rd | 1010 ++++----- EnvStats-2.5.0/EnvStats/man/egammaCensored.Rd | 1002 ++++----- EnvStats-2.5.0/EnvStats/man/elnormAltCensored.Rd | 1938 +++++++++--------- EnvStats-2.5.0/EnvStats/man/elnormCensored.Rd | 1148 +++++----- EnvStats-2.5.0/EnvStats/man/enormCensored.Rd | 2318 +++++++++++----------- EnvStats-2.5.0/EnvStats/man/epoisCensored.Rd | 940 ++++---- EnvStats-2.5.0/EnvStats/man/gofTest.Rd | 2 EnvStats-2.5.0/EnvStats/man/simulateMvMatrix.Rd | 2 EnvStats-2.5.0/EnvStats/man/simulateVector.Rd | 2 EnvStats-2.5.0/EnvStats/tests/tinytest.R |only 25 files changed, 4527 insertions(+), 4528 deletions(-)
Title: Compare and Merge Two Files with a 'Shiny' App
Description: A 'Shiny' app allowing to compare and merge two files, with syntax highlighting for several coding languages.
Author: Stéphane Laurent [aut, cre],
Jamie Peabody [ctb, cph] (Mergely),
Marijn Haverbeke [ctb, cph] (CodeMirror),
Leandro Vital [ctb, cph] (Bootstrap Flash Alert),
Daniel Eden [ctb, cph] (animate.css)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between shinyMergely versions 0.1.0 dated 2020-09-14 and 0.2.0 dated 2022-01-24
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Title: Interface Between R and the OpenStreetMap-Based Routing Service
OSRM
Description: An interface between R and the 'OSRM' API. 'OSRM' is a routing
service based on 'OpenStreetMap' data. See <http://project-osrm.org/> for more
information. This package allows to compute routes, trips, isochrones and
travel distances matrices (travel time and kilometric distance).
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>),
Robin Cura [ctb],
Matthieu Viry [ctb],
Robin Lovelace [ctb] (<https://orcid.org/0000-0001-5679-6536>)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between osrm versions 3.5.0 dated 2021-09-27 and 3.5.1 dated 2022-01-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 9 ++++++++- R/utils.R | 9 ++++++--- README.md | 26 ++++++++++---------------- 5 files changed, 31 insertions(+), 27 deletions(-)
Title: Model-Based Response Dimension Reduction
Description: Functions for model-based response dimension reduction. Usual dimension reduction methods in multivariate regression focus on the reduction of predictors, not responses. The response dimension reduction is theoretically founded in Yoo and Cook (2008) <doi:10.1016/j.csda.2008.07.029>. Later, three model-based response dimension reduction approaches are proposed in Yoo (2016) <doi:10.1080/02331888.2017.1410152> and Yoo (2019) <doi:10.1016/j.jkss.2019.02.001>. The method by Yoo and Cook (2008) is based on non-parametric ordinary least squares, but the model-based approaches are done through maximum likelihood estimation. For two model-based response dimension reduction methods called principal fitted response reduction and unstructured principal fitted response reduction, chi-squared tests are provided for determining the dimension of the response subspace.
Author: Jae Keun Yoo
Maintainer: Jae Keun Yoo <peter.yoo@ewha.ac.kr>
Diff between mbrdr versions 1.1.0 dated 2022-01-07 and 1.1.1 dated 2022-01-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 - man/SIGMAS.Rd | 1 - man/choose.fx.Rd | 1 - man/matpower.Rd | 1 - man/mbrdr.Rd | 12 ++++++++++++ man/mbrdr.x.Rd | 1 - man/mps.Rd | 2 +- 9 files changed, 25 insertions(+), 18 deletions(-)
Title: Accesses Google Maps APIs to Retrieve Data and Plot Maps
Description: Provides a mechanism to plot a 'Google Map' from 'R' and overlay
it with shapes and markers. Also provides access to 'Google Maps' APIs,
including places, directions, roads, distances, geocoding, elevation and
timezone.
Author: David Cooley [aut, cre],
Paulo Barcelos [ctb] (Author of c++ decode_pl),
Rstudio [ctb] (Functions written for the Leaflet pacakge)
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between googleway versions 2.7.5 dated 2022-01-17 and 2.7.6 dated 2022-01-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/google_map.R | 4 ++-- R/google_places.R | 4 ++-- inst/doc/googleway-vignette.html | 4 ++-- man/google_map.Rd | 2 +- man/update_style.Rd | 2 +- 7 files changed, 18 insertions(+), 18 deletions(-)
Title: Fatty Acid Metabolic Analysis
Description: Fatty acid metabolic analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.
Author: Maribel Alcoriza-Balaguer [aut, cre],
Juan Carlos Garcia-Cañaveras [ctb],
Agustin Lahoz [ths]
Maintainer: Maribel Alcoriza-Balaguer <maribel_alcoriza@iislafe.es>
Diff between FAMetA versions 0.1.1 dated 2021-12-17 and 0.1.2 dated 2022-01-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/FAMetA.R | 2 +- R/processing.R | 8 ++------ 4 files changed, 9 insertions(+), 13 deletions(-)
Title: Binary Expansion Testing
Description: Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921>, Kai Zhang, Zhigen Zhai, and Wen Zhou. (2021). BEAUTY Powered BEAST, <arXiv:2103.00674> and Zhigen Zhao, Michael Baiocchi, Kai Zhang. SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables.
Author: Wan Zhang [aut, cre],
Zhigen Zhao [aut],
Michael Baiocchi [aut],
Kai Zhang [aut]
Maintainer: Wan Zhang <wanz63@live.unc.edu>
Diff between BET versions 0.4.1 dated 2021-10-30 and 0.4.2 dated 2022-01-24
DESCRIPTION | 6 MD5 | 12 R/RcppExports.R | 38 +-- R/plot.R | 682 +++++++++++++++++++++++++++--------------------------- build/partial.rdb |binary man/Beast.Rd | 160 ++++++------ src/BET3.cpp | 2 7 files changed, 455 insertions(+), 445 deletions(-)
Title: Variable-Lag Time Series Causality Inference Framework
Description: A framework to infer causality on a pair of time series of real numbers based on variable-lag Granger causality and transfer entropy. Typically, Granger causality and transfer entropy have an assumption of a fixed and constant time delay between the cause and effect. However, for a non-stationary time series, this assumption is not true. For example, considering two time series of velocity of person A and person B where B follows A. At some time, B stops tying his shoes, then running to catch up A. The fixed-lag assumption is not true in this case. We propose a framework that allows variable-lags between cause and effect in Granger causality and transfer entropy to allow them to deal with variable-lag non-stationary time series. Please see Chainarong Amornbunchornvej, Elena Zheleva, and Tanya Berger-Wolf (2021) <doi:10.1145/3441452> when referring to this package in publications.
Author: Chainarong Amornbunchornvej [aut, cre]
(<https://orcid.org/0000-0003-3131-0370>)
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>
Diff between VLTimeCausality versions 0.1.3 dated 2021-05-08 and 0.1.4 dated 2022-01-24
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/TSNANNearestNeighborPropagation.R |only R/followingRelation.R | 3 +++ README.md | 4 ++-- inst/doc/VLTimeCausality_demo.html | 6 +++--- man/TSNANNearestNeighborPropagation.Rd |only 9 files changed, 24 insertions(+), 14 deletions(-)
More information about VLTimeCausality at CRAN
Permanent link
Title: Spatial Sampling Design and Analysis
Description: A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that are not spatially balanced, select panel samples, measure the amount of spatial balance in a sample, adjust design weights, and more.
Author: Michael Dumelle [aut, cre] (<https://orcid.org/0000-0002-3393-5529>),
Tom Kincaid [aut],
Tony Olsen [aut],
Marc Weber [aut],
Don Stevens [ctb],
Denis White [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spsurvey versions 5.1.0 dated 2021-12-15 and 5.2.0 dated 2022-01-24
DESCRIPTION | 6 +- MD5 | 58 ++++++++++---------- NEWS.md | 16 +++++ R/attrisk_analysis.R | 2 R/cont_cdfplot.R | 2 R/cont_cdftest.R | 2 R/dsgn_check.R | 40 -------------- R/grts.R | 125 +++++++++++++++++++++------------------------ R/grts_stratum.R | 15 ++--- R/irs.R | 86 +++++++++++++++++------------- R/irs_stratum.R | 15 ++--- R/ppd_plot.R | 2 R/revisit_dsgn.R | 2 README.md | 4 - inst/CITATION | 4 - inst/doc/start-here.R | 2 inst/doc/start-here.Rmd | 2 inst/doc/start-here.html | 6 +- man/attrisk_analysis.Rd | 2 man/cont_cdfplot.Rd | 2 man/cont_cdftest.Rd | 2 man/diffrisk_analysis.Rd | 2 man/grts.Rd | 43 +++++---------- man/irs.Rd | 43 +++++---------- man/ppd_plot.Rd | 2 man/relrisk_analysis.Rd | 2 man/revisit_dsgn.Rd | 2 tests/testthat/test-grts.R | 10 +-- tests/testthat/test-irs.R | 10 +-- vignettes/start-here.Rmd | 2 30 files changed, 235 insertions(+), 276 deletions(-)
Title: Leadership-Inference Framework for Multivariate Time Series
Description: A leadership-inference framework for multivariate time series. The framework for multiple-faction-leadership inference from coordinated activities or 'mFLICA' uses a notion of a leader as an individual who initiates collective patterns that everyone in a group follows. Given a set of time series of individual activities, our goal is to identify periods of coordinated activity, find factions of coordination if more than one exist, as well as identify leaders of each faction. For each time step, the framework infers following relations between individual time series, then identifying a leader of each faction whom many individuals follow but it follows no one. A faction is defined as a group of individuals that everyone follows the same leader. 'mFLICA' reports following relations, leaders of factions, and members of each faction for each time step. Please see Chainarong Amornbunchornvej and Tanya Berger-Wolf (2018) <doi:10.1137/1.9781611975321.62> for methodology and Chainarong Amornbunchornvej (2021) <doi:10.1016/j.softx.2021.100781> for software when referring to this package in publications.
Author: Chainarong Amornbunchornvej [aut, cre]
(<https://orcid.org/0000-0003-3131-0370>)
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>
Diff between mFLICA versions 0.1.4 dated 2021-12-09 and 0.1.5 dated 2022-01-24
DESCRIPTION | 6 - MD5 | 24 +++--- NAMESPACE | 1 NEWS.md | 5 + R/TSNANNearestNeighborPropagation.R |only R/followingRelation.R | 3 build/vignette.rds |binary inst/doc/mFLICA_demo.html | 8 +- man/TS.Rd | 44 ++++++------ man/TSNANNearestNeighborPropagation.Rd |only man/getDynamicFollNet.Rd | 92 +++++++++++++------------- man/getFactions.Rd | 68 +++++++++---------- man/getReachableNodes.Rd | 62 ++++++++--------- man/mFLICA.Rd | 114 ++++++++++++++++----------------- 14 files changed, 219 insertions(+), 208 deletions(-)
Title: Atlas of Living Australia (ALA) Data and Resources in R
Description: The Atlas of Living Australia ('ALA') provides tools to enable users
of biodiversity information to find, access, combine and visualise data on
Australian plants and animals. 'galah' enables the R community to directly
access data and resources hosted by the ALA and other living atlases.
Author: Martin Westgate [aut, cre],
Matilda Stevenson [aut],
Dax Kellie [aut],
Peggy Newman [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between galah versions 1.3.1 dated 2021-08-21 and 1.4.0 dated 2022-01-24
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deletions(-)
Title: R Tools for Text Matrices, Embeddings, and Networks
Description: This is a collection of functions optimized for working with
with various kinds of text matrices. Focusing on
the text matrix as the primary object - represented
either as a base R dense matrix or a 'Matrix' package sparse
matrix - allows for a consistent and intuitive interface
that stays close to the underlying mathematical foundation
of computational text analysis. In particular, the package
includes functions for working with word embeddings,
text networks, and document-term matrices. Methods developed in
Stoltz and Taylor (2019) <doi:10.1007/s42001-019-00048-6>,
Taylor and Stoltz (2020) <doi:10.1007/s42001-020-00075-8>,
Taylor and Stoltz (2020) <doi:10.15195/v7.a23>, and
Stoltz and Taylor (2021) <doi:10.1016/j.poetic.2021.101567>.
Author: Dustin Stoltz [aut, cre] (<https://orcid.org/0000-0002-4774-0765>),
Marshall Taylor [aut] (<https://orcid.org/0000-0002-7440-0723>)
Maintainer: Dustin Stoltz <dss219@lehigh.edu>
Diff between text2map versions 0.1.1 dated 2021-10-22 and 0.1.3 dated 2022-01-24
DESCRIPTION | 12 - MD5 | 40 ++-- NAMESPACE | 3 NEWS.md | 11 + R/CMDist.R | 22 +- R/utils-dtm.R | 75 ++++++--- R/utils-embedding.R | 225 ++++++++++++++++++++++----- README.md | 10 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/CMDist-concept-movers-distance.Rmd | 12 - inst/doc/CMDist-concept-movers-distance.html | 28 +-- inst/doc/concept-class-analysis.html | 4 man/CMDist.Rd | 19 +- man/dtm_melter.Rd |only man/find_transformation.Rd |only man/get_centroid.Rd | 23 +- man/get_direction.Rd | 13 - man/text2map-package.Rd | 2 tests/testthat/test-utils-dtm.R | 15 + tests/testthat/test-utils-embeddings.R | 23 ++ vignettes/CMDist-concept-movers-distance.Rmd | 12 - 22 files changed, 397 insertions(+), 152 deletions(-)