Title: Download Weather Data from Environment and Climate Change Canada
Description: Provides means for downloading historical weather data from
the Environment and Climate Change Canada website
(<https://climate.weather.gc.ca/historical_data/search_historic_data_e.html>).
Data can be downloaded from multiple stations and over large date ranges
and automatically processed into a single dataset. Tools are also provided
to identify stations either by name or proximity to a location.
Author: Steffi LaZerte [aut, cre] (<https://orcid.org/0000-0002-7690-8360>),
Sam Albers [ctb] (<https://orcid.org/0000-0002-9270-7884>),
Nick Brown [ctb] (<https://orcid.org/0000-0002-2719-0671>),
Kevin Cazelles [ctb] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Steffi LaZerte <steffi@steffi.ca>
Diff between weathercan versions 0.5.0 dated 2021-01-15 and 0.6.0 dated 2021-05-14
weathercan-0.5.0/weathercan/data/stations.rda |only weathercan-0.5.0/weathercan/man/get_tz.Rd |only weathercan-0.5.0/weathercan/man/tz_calc.Rd |only weathercan-0.5.0/weathercan/tests/fixtures/normals_url_5010480.yml |only weathercan-0.5.0/weathercan/tests/testthat/helper-weathercan.R |only weathercan-0.5.0/weathercan/vignettes/normals_files |only weathercan-0.6.0/weathercan/DESCRIPTION | 26 weathercan-0.6.0/weathercan/MD5 | 166 weathercan-0.6.0/weathercan/NAMESPACE | 6 weathercan-0.6.0/weathercan/NEWS.md | 22 weathercan-0.6.0/weathercan/R/data.R | 31 weathercan-0.6.0/weathercan/R/interpolate.R | 9 weathercan-0.6.0/weathercan/R/normals.R | 161 weathercan-0.6.0/weathercan/R/stations.R | 277 weathercan-0.6.0/weathercan/R/utils.R | 34 weathercan-0.6.0/weathercan/R/weather.R | 66 weathercan-0.6.0/weathercan/R/weathercan-pkg.R | 21 weathercan-0.6.0/weathercan/build/vignette.rds |binary weathercan-0.6.0/weathercan/data/normals_measurements.rda |binary weathercan-0.6.0/weathercan/inst/WORDLIST | 50 weathercan-0.6.0/weathercan/inst/doc/flags.Rmd | 4 weathercan-0.6.0/weathercan/inst/doc/flags.html | 241 weathercan-0.6.0/weathercan/inst/doc/glossary.Rmd | 2 weathercan-0.6.0/weathercan/inst/doc/glossary.html | 213 weathercan-0.6.0/weathercan/inst/doc/glossary_normals.Rmd | 2 weathercan-0.6.0/weathercan/inst/doc/glossary_normals.html | 209 weathercan-0.6.0/weathercan/inst/doc/interpolate_data.Rmd | 2 weathercan-0.6.0/weathercan/inst/doc/interpolate_data.html | 471 weathercan-0.6.0/weathercan/inst/doc/normals.R | 8 weathercan-0.6.0/weathercan/inst/doc/normals.Rmd | 23 weathercan-0.6.0/weathercan/inst/doc/normals.html | 367 weathercan-0.6.0/weathercan/inst/doc/reproducibility.R |only weathercan-0.6.0/weathercan/inst/doc/reproducibility.Rmd |only weathercan-0.6.0/weathercan/inst/doc/reproducibility.html |only weathercan-0.6.0/weathercan/inst/doc/weathercan.R | 58 weathercan-0.6.0/weathercan/inst/doc/weathercan.Rmd | 74 weathercan-0.6.0/weathercan/inst/doc/weathercan.html | 642 weathercan-0.6.0/weathercan/inst/extdata |only weathercan-0.6.0/weathercan/man/check_eccc.Rd |only weathercan-0.6.0/weathercan/man/normals_dl.Rd | 74 weathercan-0.6.0/weathercan/man/normals_measurements.Rd | 3 weathercan-0.6.0/weathercan/man/stations.Rd | 33 weathercan-0.6.0/weathercan/man/stations_dl.Rd | 36 weathercan-0.6.0/weathercan/man/stations_meta.Rd |only weathercan-0.6.0/weathercan/man/stations_search.Rd | 34 weathercan-0.6.0/weathercan/man/weather_dl.Rd | 41 weathercan-0.6.0/weathercan/tests/fixtures/meta_raw1.yml | 6 weathercan-0.6.0/weathercan/tests/fixtures/meta_raw2.yml | 6 weathercan-0.6.0/weathercan/tests/fixtures/meta_raw3.yml | 6 weathercan-0.6.0/weathercan/tests/fixtures/normals_dl_1096450_2403500_5010480_1971.yml |only weathercan-0.6.0/weathercan/tests/fixtures/normals_dl_1096450_2403500_5010480_1981.yml |only weathercan-0.6.0/weathercan/tests/fixtures/normals_dl_2100517_1981.yml |only weathercan-0.6.0/weathercan/tests/fixtures/normals_dl_5010480_1971.yml |only weathercan-0.6.0/weathercan/tests/fixtures/normals_dl_5010480_1981.yml |only weathercan-0.6.0/weathercan/tests/fixtures/normals_html_5010480_1971.yml |only weathercan-0.6.0/weathercan/tests/fixtures/normals_html_5010480_1981.yml |only weathercan-0.6.0/weathercan/tests/fixtures/normals_http404.yml |only weathercan-0.6.0/weathercan/tests/fixtures/stations_http404.yml |only weathercan-0.6.0/weathercan/tests/fixtures/stations_normals.yml |only weathercan-0.6.0/weathercan/tests/fixtures/weather_day_1274_1275_2017.yml | 24 weathercan-0.6.0/weathercan/tests/fixtures/weather_day_42013_51423_2017.yml | 18 weathercan-0.6.0/weathercan/tests/fixtures/weather_day_4291_51423_1928.yml | 12 weathercan-0.6.0/weathercan/tests/fixtures/weather_day_51423_2018.yml | 6 weathercan-0.6.0/weathercan/tests/fixtures/weather_day_51423_54398_2016.yml | 6 weathercan-0.6.0/weathercan/tests/fixtures/weather_day_54398_2016_2017.yml | 18 weathercan-0.6.0/weathercan/tests/fixtures/weather_day_6819_51423_2017_2018.yml | 18 weathercan-0.6.0/weathercan/tests/fixtures/weather_hour_1274_1275_2012-11.yml | 12 weathercan-0.6.0/weathercan/tests/fixtures/weather_hour_1275_1001_2017-01.yml | 18 weathercan-0.6.0/weathercan/tests/fixtures/weather_hour_27534_2001-12_2002-01.yml | 18 weathercan-0.6.0/weathercan/tests/fixtures/weather_hour_42203_49909_2006-04.yml |12832 +++++----- weathercan-0.6.0/weathercan/tests/fixtures/weather_hour_42203_49909_2017-09.yml | 24 weathercan-0.6.0/weathercan/tests/fixtures/weather_hour_50821_2018.yml | 12 weathercan-0.6.0/weathercan/tests/fixtures/weather_hour_6556_1965.yml | 12 weathercan-0.6.0/weathercan/tests/fixtures/weather_hour_6819_2017.yml | 18 weathercan-0.6.0/weathercan/tests/fixtures/weather_hour_6819_51423_2017-08_2018-05.yml | 108 weathercan-0.6.0/weathercan/tests/fixtures/weather_month_1274.yml | 12 weathercan-0.6.0/weathercan/tests/fixtures/weather_month_1275_51423.yml | 12 weathercan-0.6.0/weathercan/tests/fixtures/weather_month_4291_27534.yml | 24 weathercan-0.6.0/weathercan/tests/fixtures/weather_month_5217.yml | 12 weathercan-0.6.0/weathercan/tests/fixtures/weather_month_5401_5940.yml | 12 weathercan-0.6.0/weathercan/tests/fixtures/weather_month_5410.yml | 12 weathercan-0.6.0/weathercan/tests/fixtures/weather_raw1.yml | 19 weathercan-0.6.0/weathercan/tests/fixtures/weather_raw2.yml | 6 weathercan-0.6.0/weathercan/tests/fixtures/weather_raw3.yml | 6 weathercan-0.6.0/weathercan/tests/testthat/setup-weathercan.R |only weathercan-0.6.0/weathercan/tests/testthat/test_00_onLoad.R |only weathercan-0.6.0/weathercan/tests/testthat/test_02_utils.R | 31 weathercan-0.6.0/weathercan/tests/testthat/test_03_station_dl.R | 141 weathercan-0.6.0/weathercan/tests/testthat/test_08_normals.R | 288 weathercan-0.6.0/weathercan/vignettes/flags.Rmd | 4 weathercan-0.6.0/weathercan/vignettes/glossary.Rmd | 2 weathercan-0.6.0/weathercan/vignettes/glossary_normals.Rmd | 2 weathercan-0.6.0/weathercan/vignettes/interpolate_data.Rmd | 2 weathercan-0.6.0/weathercan/vignettes/normals.Rmd | 23 weathercan-0.6.0/weathercan/vignettes/reproducibility.Rmd |only weathercan-0.6.0/weathercan/vignettes/weathercan.Rmd | 74 96 files changed, 8364 insertions(+), 8898 deletions(-)
Title: Single Cell Mapper
Description: The single cell mapper (scMappR) R package contains a suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes (DEG). The function "scMappR_and_pathway_analysis" reranks DEGs to generate cell-type specificity scores called cell-weighted fold-changes. Users input a list of DEGs, normalized counts, and a signature matrix into this function. scMappR then re-weights bulk DEGs by cell-type specific expression from the signature matrix, cell-type proportions from RNA-seq deconvolution and the ratio of cell-type proportions between the two conditions to account for changes in cell-type proportion. With cwFold-changes calculated, scMappR uses two approaches to utilize cwFold-changes to complete cell-type specific pathway analysis. The "process_dgTMatrix_lists" function in the scMappR package contains an automated scRNA-seq processing pipeline where users input scRNA-seq count data, which is made compatible for scMappR and other R packages that analyze scRNA-seq data. We further used this to store hundreds up regularly updating signature matrices. The functions "tissue_by_celltype_enrichment", "tissue_scMappR_internal", and "tissue_scMappR_custom" combine these consistently processed scRNAseq count data with gene-set enrichment tools to allow for cell-type marker enrichment of a generic gene list (e.g. GWAS hits). Reference: Sokolowski,D.J., Faykoo-Martinez,M., Erdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A. and Wilson,M.D. (2021) Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. NAR Genomics and Bioinformatics. 3(1). Iqab011. <doi:10.1093/nargab/lqab011>.
Author: Dustin Sokolowski [aut, cre],
Mariela Faykoo-Martinez [aut],
Lauren Erdman [aut],
Houyun Hou [aut],
Cadia Chan [aut],
Helen Zhu [aut],
Melissa Holmes [aut],
Anna Goldenberg [aut],
Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Diff between scMappR versions 1.0.1 dated 2021-03-29 and 1.0.2 dated 2021-05-14
DESCRIPTION | 6 - MD5 | 30 +++--- R/gsva_cellIdentify.R | 2 R/process_dgTMatrix_lists.R | 2 R/process_from_count.R | 2 R/seurat_to_generes.R | 2 README.md | 14 ++ data/sm.rda |binary inst/doc/scMappR_Vignette.R | 34 ++++++- inst/doc/scMappR_Vignette.Rmd | 52 ++++++++++ inst/doc/scMappR_Vignette.html | 198 +++++++++++++++++++++++------------------ man/gsva_cellIdentify.Rd | 2 man/process_dgTMatrix_lists.Rd | 2 man/process_from_count.Rd | 2 man/seurat_to_generes.Rd | 2 vignettes/scMappR_Vignette.Rmd | 52 ++++++++++ 16 files changed, 283 insertions(+), 119 deletions(-)
Title: Solver for Partially Observable Markov Decision Processes
(POMDP)
Description: Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Processes (POMDP) models. The package includes pomdp-solve to solve POMDPs using a variety of exact and approximate value iteration algorithms. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Author: Michael Hahsler [aut, cph, cre],
Hossein Kamalzadeh [aut, cph],
Anthony R. Cassandra [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between pomdp versions 0.99.1 dated 2021-05-14 and 0.99.2 dated 2021-05-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ inst/doc/POMDP.html | 2 +- src/pomdp-solve/Makefile | 28 ++++++++++++---------------- src/pomdp-solve/laspack/Makefile | 7 ++++--- src/pomdp-solve/lp-solve/Makefile | 4 ++-- src/pomdp-solve/mdp/Makefile | 4 ++-- 8 files changed, 37 insertions(+), 35 deletions(-)
Title: Multivariate Data Analysis Laboratory
Description: An open-source implementation of latent variable methods and multivariate modeling tools. The focus is on exploratory analyses using dimensionality reduction methods including low dimensional embedding, classical multivariate statistical tools, and tools for enhanced interpretation of machine learning methods (i.e. intelligible models to provide important information for end-users). Target domains include extension to dedicated applications e.g. for manufacturing process modeling, spectroscopic analyses, and data mining.
Author: Nelson Lee Afanador, Thanh Tran, Lionel Blanchet, and Richard Baumgartner
Maintainer: Nelson Lee Afanador <nelson.afanador@gmail.com>
Diff between mvdalab versions 1.4 dated 2017-10-16 and 1.5 dated 2021-05-14
DESCRIPTION | 10 +- MD5 | 18 ++-- NEWS.md | 7 + R/R2s.R | 17 +--- R/plsFit.R | 211 +++++++++++++++++++++++++--------------------------- R/predict.mvdareg.R | 64 +++++++-------- R/summary.mvdareg.R | 3 README.md | 5 - man/plsFit.Rd | 4 man/wrtpls.fit.Rd | 121 ++++++++++++++--------------- 10 files changed, 228 insertions(+), 232 deletions(-)
Title: Calculate Multivariate Richness via UTC and sUTC
Description: Functions to calculate Unique Trait Combinations (UTC) and scaled
Unique Trait Combinations (sUTC) as measures of multivariate richness. The
package can also calculate beta-diversity for trait richness and can
partition this into nestedness-related and turnover components. The code
will also calculate several measures of overlap. See Keyel and Wiegand
(2016) <doi:10.1111/2041-210X.12558> for more details.
Author: Alexander Keyel
Maintainer: Alexander Keyel <skeyel@gmail.com>
Diff between multirich versions 2.1.1 dated 2015-09-17 and 2.1.3 dated 2021-05-14
DESCRIPTION | 14 - MD5 | 57 ++--- NAMESPACE | 2 NEWS | 6 R/MVR.r | 2 README.md |only build/vignette.rds |binary inst/doc/Sensitivity_analysis.R | 2 inst/doc/Sensitivity_analysis.Rmd | 2 inst/doc/Sensitivity_analysis.html | 411 ++++++++++++++++++++++++++++++------- man/calc.mvd.Rd | 6 man/calc.mvo.Rd | 4 man/check.breaks.Rd | 4 man/check.traits.Rd | 12 - man/data.preprocess.Rd | 4 man/df.categorize.Rd | 4 man/expand.breaks.Rd | 4 man/get.breaks.Rd | 4 man/get.traitspace.Rd | 4 man/listtotext.Rd | 4 man/make.trait.Rd | 4 man/matrix.check.Rd | 4 man/multirich-package.Rd | 12 - man/mvfd.Rd | 21 + man/part.mvr.beta.Rd | 12 - man/plot.sensitivity.Rd | 7 man/sensitivity.analysis.Rd | 15 - man/sensitivity.boxplots.Rd | 4 man/utc.sim.Rd | 14 - vignettes/Sensitivity_analysis.Rmd | 2 30 files changed, 470 insertions(+), 171 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
van Valkenhoef et al. (2012) <doi:10.1002/jrsm.1054>;
van Valkenhoef et al. (2015) <doi:10.1002/jrsm.1167>.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef <gert@gertvv.nl>
Diff between gemtc versions 1.0-0 dated 2021-04-30 and 1.0-1 dated 2021-05-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 8 ++++++++ R/ll.binom.log.R | 7 +++---- build/partial.rdb |binary tests/testthat/test-unit-mtc.model_inits.R | 24 ------------------------ 6 files changed, 20 insertions(+), 37 deletions(-)
Title: Obtain Suggested Coordinate Reference System Information for
Spatial Data
Description: Uses data from the 'EPSG' Registry to look up suitable coordinate reference
system transformations for spatial datasets in R. Returns a data frame with 'CRS' codes
that can be used for 'CRS' transformation and mapping projects. Please see
the 'EPSG' Dataset Terms of Use at <https://epsg.org/terms-of-use.html> for more information.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between crsuggest versions 0.3 dated 2021-05-10 and 0.3.1 dated 2021-05-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/suggest_crs.R | 10 ++++++++-- README.md | 10 +++++++++- man/suggest_crs.Rd | 13 +++++++++++-- 5 files changed, 36 insertions(+), 13 deletions(-)
Title: Semi-Automatic Grading of R and Rmd Scripts
Description: A customisable set of tools for assessing and grading
R or R-markdown scripts from students. It allows for checking correctness
of code output, runtime statistics and static code analysis. The latter
feature is made possible by representing R expressions using a tree
structure.
Author: Vik Gopal [aut, cre],
Samuel Seah [aut],
Viknesh Jeya Kumar [aut],
Gabriel Ang [aut],
Ruofan Liu [ctb],
National University of Singapore [cph]
Maintainer: Vik Gopal <vik.gopal@nus.edu.sg>
Diff between autoharp versions 0.0.6 dated 2021-05-02 and 0.0.7 dated 2021-05-14
autoharp-0.0.6/autoharp/inst/examples/soln_templates/soln_template_01.R |only autoharp-0.0.7/autoharp/DESCRIPTION | 6 autoharp-0.0.7/autoharp/MD5 | 23 +- autoharp-0.0.7/autoharp/NAMESPACE | 26 ++ autoharp-0.0.7/autoharp/NEWS | 4 autoharp-0.0.7/autoharp/R/generate_thumbnails.R | 18 - autoharp-0.0.7/autoharp/R/populate_soln_env.R | 1 autoharp-0.0.7/autoharp/R/run_tuner.R | 15 - autoharp-0.0.7/autoharp/R/write_html.R | 8 autoharp-0.0.7/autoharp/inst/doc/user-manual.R | 91 +--------- autoharp-0.0.7/autoharp/inst/doc/user-manual.Rmd | 28 +-- autoharp-0.0.7/autoharp/inst/doc/user-manual.html | 86 ++++----- autoharp-0.0.7/autoharp/vignettes/user-manual.Rmd | 28 +-- 13 files changed, 150 insertions(+), 184 deletions(-)
Title: Tree-Based Discriminant Analysis
Description: Performs sparse discriminant analysis on a combination of
node and leaf predictors when the predictor variables are
structured according to a tree, as described in Fukuyama et
al. (2017) <doi:10.1371/journal.pcbi.1005706>.
Author: Julia Fukuyama [aut, cre]
Maintainer: Julia Fukuyama <julia.fukuyama@gmail.com>
Diff between treeDA versions 0.0.4 dated 2018-06-26 and 0.0.5 dated 2021-05-14
DESCRIPTION | 12 MD5 | 23 NAMESPACE | 2 R/treeda-functions.R | 20 build/vignette.rds |binary inst/doc/treeda-vignette.R | 26 inst/doc/treeda-vignette.html | 1546 ++++++++++++++++++++++++++++++++++++++++-- man/getBranchLengths.Rd |only man/plot_coefficients.Rd | 8 man/predict.treeda.Rd | 3 man/treeda.Rd | 15 man/treeda_example.Rd | 6 man/treedacv.Rd | 15 13 files changed, 1563 insertions(+), 113 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.3.0 dated 2021-05-01 and 5.4.0 dated 2021-05-14
DESCRIPTION | 8 MD5 | 146 +++++++++-------- NEWS.md | 38 ++++ R/Workbook.R | 4 R/aaa-utils.R | 10 - R/bind-insert.R | 14 + R/brdr.R | 9 - R/clean-contents.R | 115 +++++++++---- R/dimnames.R | 3 R/flextable.R | 2 R/html.R | 2 R/latex.R | 6 R/mapping-functions.R | 10 + R/merge.R | 15 + R/misc.R | 3 R/number-format-functions.R | 8 R/package-docs.R | 30 +++ R/properties-cell.R | 58 +++++-- R/rtf.R | 2 R/screen.R | 15 - R/subset-extract-internal.R | 87 ++++++++-- R/subset-extract.R | 15 + R/zzz.R | 1 build/vignette.rds |binary inst/doc/design-principles.html | 4 inst/doc/huxreg.R | 3 inst/doc/huxreg.Rmd | 3 inst/doc/huxreg.html | 10 - inst/doc/huxtable.R | 25 ++- inst/doc/huxtable.Rmd | 80 +++++++-- inst/doc/huxtable.html | 157 ++++++++++++------- inst/doc/themes.html | 6 man/add_colnames.Rd | 3 man/add_rows.Rd | 2 man/align.Rd | 41 ++++ man/brdr.Rd | 6 man/by_colorspace.Rd | 3 man/by_ranges.Rd | 2 man/by_regex.Rd | 2 man/by_values.Rd | 3 man/cbind.huxtable.Rd | 6 man/fmt_percent.Rd | 4 man/huxtable-FAQ.Rd | 16 + man/huxtable-news.Rd | 44 ++++- man/huxtable-options.Rd | 6 man/insert_column.Rd | 2 man/merge_across.Rd | 4 man/merge_cells.Rd | 3 man/merge_repeated_rows.Rd | 8 man/subset-.brdr.Rd | 1 man/t.huxtable.Rd | 4 tests/testthat/file13d3a9992877.aux |only tests/testthat/file13d3a9992877.log |only tests/testthat/file13d3a9992877.pdf |only tests/testthat/file292256751fe0.aux |only tests/testthat/file292256751fe0.log |only tests/testthat/file292256751fe0.pdf |only tests/testthat/pdf-check-106271.pdf |only tests/testthat/pdf-check-127816.pdf |only tests/testthat/pdf-check-12928.pdf |only tests/testthat/pdf-check-15071.pdf |only tests/testthat/pdf-check-176135.pdf |only tests/testthat/pdf-check-185619.pdf |only tests/testthat/pdf-check-318500.pdf |only tests/testthat/pdf-check-72532.pdf |only tests/testthat/temp-artefacts/latex-siunitx-test.pdf |only tests/testthat/temp-artefacts/long-minus-test.docx |binary tests/testthat/temp-artefacts/long-minus-test.html | 8 tests/testthat/temp-artefacts/long-minus-test.pdf |binary tests/testthat/temp-artefacts/long-minus-test.pptx |binary tests/testthat/temp-artefacts/long-minus-test.rtf | 6 tests/testthat/temp-artefacts/long-minus-test.tex | 6 tests/testthat/temp-artefacts/long-minus-test.xlsx |binary tests/testthat/temp-artefacts/table-tester-2.tex | 18 +- tests/testthat/test-attributes.R | 11 + tests/testthat/test-number-formatting.R | 54 ++---- tests/testthat/test-subset-replace.R | 29 +-- tests/testthat/test-subset-spans.R |only tests/testthat/test-yy-end-to-end.R | 19 ++ tests/testthat/test-zz-fuzz.R | 2 vignettes/huxreg.Rmd | 3 vignettes/huxtable.Rmd | 80 +++++++-- 82 files changed, 884 insertions(+), 401 deletions(-)
Title: Hidden Markov Models of Character Evolution
Description: Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
Author: Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Jeffrey Oliver [aut],
James Boyko [aut]
Maintainer: Jeremy Beaulieu <jmbeauli@uark.edu>
Diff between corHMM versions 2.6 dated 2021-01-06 and 2.7 dated 2021-05-14
DESCRIPTION | 8 +- MD5 | 28 ++++----- R/ancRECON.R | 106 ++++++++++++++++++------------------- R/corHMM.R | 85 +++++++++++++++++------------ R/makeSimmap.R | 81 +++++++++++++++++++--------- inst/doc/corHMMv2.1-vignette.R | 4 - inst/doc/corHMMv2.1-vignette.Rmd | 4 - man/ancRECON.Rd | 9 ++- man/corHMM.Rd | 8 ++ man/getFullMat.Rd | 4 + man/makeSimmap.Rd | 10 +++ man/plotMKmodel.Rd | 5 + tests/testthat/testlikelihood.R | 2 vignettes/corHMMv2.1-vignette.Rmd | 4 - vignettes/corHMMv2.1-vignette.html | 41 ++++++++++++-- 15 files changed, 251 insertions(+), 148 deletions(-)
Title: Conduct Direction-Projection-Permutation Tests and Display Plots
Description: Conducts a direction-projection-permutation test and displays diagnostic plots to facilitate the visual assessment of the test. See Wei et al. (2016) <doi:10.1080/10618600.2015.1027773> and Lam et al. (2018) <doi:10.1080/10618600.2017.1366915> for more details.
Author: Andrew G. Allmon [aut, cre],
J.S. Marron [aut],
Michael G. Hudgens [aut]
Maintainer: Andrew G. Allmon <allmondrew@yahoo.com>
Diff between diproperm versions 0.1.0 dated 2020-09-01 and 0.2.0 dated 2021-05-14
DESCRIPTION | 10 +++---- MD5 | 23 +++++++++--------- R/DiProPerm.R | 69 ++++++++++++++++++++++++++++++++++++++++++++---------- R/data.R | 4 +-- R/dpp_functions.R | 26 ++++++++++++++++++-- R/loadings.R | 8 ++++-- R/plotdpp.R | 10 ++++++- README.md | 8 +++++- build |only man/DiProPerm.Rd | 22 ++++++++++------- man/loadings.Rd | 8 ++++-- man/mushrooms.Rd | 4 +-- man/plotdpp.Rd | 6 ++++ 13 files changed, 148 insertions(+), 50 deletions(-)
Title: Long Term Water Quality Trend Analysis
Description: Enable users to evaluate long-term trends using a Generalized
Additive Modeling (GAM) approach. The model development includes selecting a
GAM structure to describe nonlinear seasonally-varying changes over time,
incorporation of hydrologic variability via either a river flow or salinity,
the use of an intervention to deal with method or laboratory changes
suspected to impact data values, and representation of left- and
interval-censored data. The approach has been applied to water quality data
in the Chesapeake Bay, a major estuary on the east coast of the United
States to provide insights to a range of management- and research-focused
questions. Methodology described in Murphy (2019)
<doi:10.1016/j.envsoft.2019.03.027>.
Author: Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
Maintainer: Erik W Leppo <Erik.Leppo@tetratech.com>
Diff between baytrends versions 2.0.4 dated 2021-04-19 and 2.0.5 dated 2021-05-14
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++--------- NEWS | 25 +++++++++++++++++++++++- NEWS.md | 25 +++++++++++++++++++++++- R/analysisOrganizeData.R | 11 +++++----- R/layerAggregation.R | 9 ++++---- R/selectData.R | 9 ++++++-- README.md | 17 ++++++---------- inst/doc/Detrending_Flow_and_Salinity_Data.html | 6 ++--- inst/doc/Processing_Censored_Data.html | 6 ++--- 10 files changed, 91 insertions(+), 41 deletions(-)
Title: Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studies
Description: Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.
Author: Youyi Fong [cre],
Krisztian Sebestyen [aut],
Han Sunwoo [aut],
Jason Becker [ctb],
Bendix Carstensen [ctb],
Daryl Morris [ctb],
Josh Pasek [ctb],
Dennis Chao [ctb],
Andri Signorell [ctb],
Sue Li [ctb],
Jonathan Bartlett [ctb],
Christophe Dutang [ctb]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between kyotil versions 2020.10-12 dated 2020-10-13 and 2021.5-14 dated 2021-05-14
kyotil-2020.10-12/kyotil/R/marginal.risk.R |only kyotil-2020.10-12/kyotil/inst/doc/kyotil-vignette.pdf.asis |only kyotil-2020.10-12/kyotil/man/marginal.risk.Rd |only kyotil-2021.5-14/kyotil/ChangeLog | 45 ++++++ kyotil-2021.5-14/kyotil/DESCRIPTION | 11 - kyotil-2021.5-14/kyotil/MD5 | 37 ++--- kyotil-2021.5-14/kyotil/NAMESPACE | 7 - kyotil-2021.5-14/kyotil/R/P.adj.perm.R | 2 kyotil-2021.5-14/kyotil/R/base.R | 2 kyotil-2021.5-14/kyotil/R/cross_validation.R |only kyotil-2021.5-14/kyotil/R/iorw.R | 2 kyotil-2021.5-14/kyotil/R/plotting.R | 84 +++++++------ kyotil-2021.5-14/kyotil/R/print.R | 8 - kyotil-2021.5-14/kyotil/R/regression.model.functions.R | 69 ++++++---- kyotil-2021.5-14/kyotil/R/string.R | 5 kyotil-2021.5-14/kyotil/README.md |only kyotil-2021.5-14/kyotil/build/vignette.rds |binary kyotil-2021.5-14/kyotil/inst/doc/kyotil-vignette.pdf |binary kyotil-2021.5-14/kyotil/man/misc.Rd | 5 kyotil-2021.5-14/kyotil/man/plotting.Rd | 28 ++-- kyotil-2021.5-14/kyotil/man/print.Rd | 7 - kyotil-2021.5-14/kyotil/man/regression.model.functions.Rd | 11 + 22 files changed, 215 insertions(+), 108 deletions(-)
Title: Tools for Modeling Rate-Dependent Hysteretic Processes and
Ellipses
Description: Fit, summarize and plot sinusoidal hysteretic processes using:
two-step simple harmonic least squares, ellipse-specific non-linear least
squares, the direct method, geometric least squares or linear least squares.
Author: Spencer Maynes, Fan Yang, and Anne Parkhurst
Maintainer: Anne Parkhurst <aparkhurst@unl.edu>
Diff between hysteresis versions 2.6 dated 2017-12-13 and 2.7 dated 2021-05-14
DESCRIPTION | 10 MD5 | 360 ++++++++++++++----------- NAMESPACE | 186 ++++++------- NEWS | 24 - R/coef.ellipsefit.R | 2 R/coef.ellipsefitlist.R | 2 R/coef.ellipsesummary.R | 2 R/coef.ellipsesummarylist.R | 2 R/coef.fittedloop.R | 2 R/coef.fittedlooplist.R | 2 R/coef.fittedlooplist2r.R | 2 R/coef.loop2r.R | 2 R/coef.loop2rsummary.R | 2 R/coef.loopsummary.R | 2 R/coef.loopsummarylist.R | 2 R/coef.loopsummarylist2r.R | 2 R/delta.error.R | 192 ++++++------- R/delta.error.loop.R | 130 ++++----- R/delta.error.loop2r.R | 162 +++++------ R/derived.1.r | 14 R/derived.2.r | 16 - R/derived.amps.R | 18 - R/derived.focus.r | 16 - R/direct.R | 112 +++---- R/direct_renorm.R | 116 ++++---- R/directboot.R | 60 ++-- R/directsummary.R | 130 ++++----- R/ellipsespot.R | 10 R/fel.R | 192 ++++++------- R/fel.direct.R | 48 +-- R/fel.direct2harmonic.R | 102 +++---- R/fel.geometric.R | 92 +++--- R/fel.harmonic2.R | 70 ++-- R/fel.lm.R | 96 +++--- R/fel.nls.R | 106 +++---- R/fel.repeated.R | 48 +-- R/felReflect.R | 10 R/fitstatistics.R | 34 +- R/fitted.ellipsefit.R | 6 R/fitted.ellipsefitlist.R | 24 - R/fitted.ellipsesummary.R | 6 R/fitted.ellipsesummarylist.R | 26 - R/fitted.fittedloop.R | 6 R/fitted.fittedlooplist.R | 26 - R/fitted.fittedlooplist2r.R | 26 - R/fitted.loop2r.R | 6 R/fitted.loop2rsummary.R | 8 R/fitted.loopsummary.R | 8 R/fitted.loopsummarylist.R | 54 +-- R/floop.R | 284 ++++++++++---------- R/floop.repeated.R | 48 +-- R/floop2r.R | 310 +++++++++++----------- R/floop2r.repeated.R | 48 +-- R/floopCauchyLoss.R | 40 +- R/floopCauchyLoss2r.R | 42 +- R/floopReflect.R | 10 R/geom_ellipse.R | 58 ++-- R/geom_step.R | 62 ++-- R/geometric_distance.R | 48 +-- R/geometricboot.R | 104 +++---- R/geometricbootwrapper.R | 18 - R/geometricsummary.R | 134 ++++----- R/halir.R | 30 +- R/harmonic2boot.R | 84 ++--- R/harmonic2summary.R | 124 ++++---- R/harmonic2summaryEBS.r | 236 ++++++++-------- R/harmonicOptPoint.R | 62 ++-- R/harmonicspot.R | 10 R/internal.1.r | 16 - R/internal.2.r | 16 - R/internal.3.r | 12 R/lmboot.R | 116 ++++---- R/lmbootwrapper.R | 18 - R/lmsummary.R | 130 ++++----- R/loopboot.R | 110 +++---- R/loopbootgeom.R | 130 ++++----- R/m_ellipse.R | 32 +- R/mel.r | 22 - R/mel1.r | 28 - R/mel2.r | 26 - R/mel3.R | 30 +- R/mel4.R | 68 ++-- R/mloop.r | 52 +-- R/mloop2r.R | 66 ++-- R/nlsboot.R | 116 ++++---- R/nlsbootwrapper.R | 16 - R/nlssummary.R | 134 ++++----- R/plot.ellipsefit.R | 196 ++++++------- R/plot.ellipsefitlist.R | 20 - R/plot.ellipsesummary.R | 170 ++++++------ R/plot.ellipsesummarylist.R | 20 - R/plot.fittedloop.R | 144 +++++----- R/plot.fittedlooplist.R | 42 +- R/plot.loop2r.R | 118 ++++---- R/plot.loop2rsummary.R | 122 ++++---- R/plot.loopsummary.R | 140 ++++----- R/plot.loopsummarylist.R | 42 +- R/print.ellipsefit.R | 34 +- R/print.ellipsefitlist.R | 18 - R/print.ellipsemake.r | 8 R/print.ellipsesummary.r | 62 ++-- R/print.ellipsesummarylist.R | 76 ++--- R/print.fittedloop.R | 12 R/print.fittedlooplist.R | 38 +- R/print.loop2r.R | 14 R/print.loop2rsummary.R | 18 - R/print.loopsummary.R | 18 - R/print.loopsummarylist.R | 120 ++++---- R/renorm_ellipse.R | 34 +- R/residuals.ellipsefit.R | 16 - R/residuals.ellipsefitlist.R | 36 +- R/residuals.ellipsesummary.R | 14 R/residuals.ellipsesummarylist.R | 30 +- R/residuals.fittedloop.R | 14 R/residuals.fittedlooplist.R | 62 ++-- R/residuals.loop2r.R | 14 R/residuals.loop2rsummary.R | 14 R/residuals.loopsummary.R | 14 R/residuals.loopsummarylist.R | 62 ++-- R/rstudent.ellipsefit.R | 30 +- R/rstudent.ellipsefitlist.R | 28 - R/rstudent.ellipsesummary.R | 30 +- R/rstudent.ellipsesummarylist.R | 28 - R/rstudent.fittedloop.R | 34 +- R/rstudent.fittedlooplist.R | 54 +-- R/rstudent.loop2r.R | 44 +-- R/rstudent.loop2rsummary.R | 44 +-- R/rstudent.loopsummary.R | 34 +- R/rstudent.loopsummarylist.R | 56 +-- R/sandwich.error.R | 24 - R/splitloopboot.R | 124 ++++---- R/splitloopbootgeom.R | 140 ++++----- R/summary.ellipsefit.R | 46 +-- R/summary.ellipsefitlist.R | 120 ++++---- R/summary.fittedloop.R | 104 +++---- R/summary.fittedlooplist.R | 82 ++--- R/summary.fittedlooplist2r.R | 82 ++--- R/summary.loop2r.R | 108 +++---- R/tprofile.error.R | 12 README.md | 8 build/vignette.rds |binary inst/doc/index.R | 38 +- inst/doc/index.Rmd | 548 +++++++++++++++++++-------------------- inst/doc/index.html | 471 ++++++++++++++------------------- man/EllipseData.Rd | 98 +++--- man/HysteresisData.Rd | 96 +++--- man/fel.Rd | 230 ++++++++-------- man/fel.repeated.Rd | 212 +++++++-------- man/floop.Rd | 278 +++++++++---------- man/floop.repeated.Rd | 242 ++++++++--------- man/floopReflect.Rd | 82 ++--- man/hysteresis-package.Rd | 4 man/loop.parameters.Rd | 208 +++++++------- man/mel.rd | 284 ++++++++++---------- man/mloop.Rd | 202 +++++++------- man/plot.fittedloop.Rd | 216 +++++++-------- man/residuals.fittedloop.Rd | 278 +++++++++---------- man/summary.fittedloop.Rd | 214 +++++++-------- vignettes/boottest-1.png |only vignettes/boottest.png |only vignettes/bx-1.png |only vignettes/bx-2.png |only vignettes/bx-3.png |only vignettes/bx1.png |only vignettes/bx2.png |only vignettes/bx3.png |only vignettes/by-1.png |only vignettes/by-2.png |only vignettes/by-3.png |only vignettes/by1.png |only vignettes/by2.png |only vignettes/by3.png |only vignettes/geometric-1.png |only vignettes/geometric.png |only vignettes/index.Rmd | 548 +++++++++++++++++++-------------------- vignettes/mandn-1.png |only vignettes/mandn.png |only vignettes/moremandn-1.png |only vignettes/moremandn.png |only vignettes/multiple-1.png |only vignettes/multiple-2.png |only vignettes/multiple-3.png |only vignettes/multiple1.png |only vignettes/multiple2.png |only vignettes/multiple3.png |only vignettes/retention-1.png |only vignettes/retention-2.png |only vignettes/retention-3.png |only vignettes/retention1.png |only vignettes/retention2.png |only vignettes/retention3.png |only vignettes/tests-1.png |only vignettes/tests.png |only vignettes/unnamed-chunk-1-1.png |only vignettes/unnamed-chunk-1.png |only vignettes/unnamed-chunk-2-1.png |only vignettes/unnamed-chunk-2.png |only vignettes/unnamed-chunk-6-1.png |only vignettes/unnamed-chunk-6.png |only vignettes/unnamed-chunk-7-1.png |only vignettes/unnamed-chunk-7.png |only vignettes/unnamed-chunk-9-1.png |only vignettes/unnamed-chunk-9.png |only 203 files changed, 6334 insertions(+), 6353 deletions(-)
Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with
parametric or nonparametric pair-copulas. See
Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
Schallhorn et al. (2017) <arXiv:1705.08310>.
Author: Thomas Nagler [aut, cre],
Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between vinereg versions 0.7.3 dated 2021-02-24 and 0.7.4 dated 2021-05-14
DESCRIPTION | 7 MD5 | 18 - NEWS.md | 6 R/generics.R | 2 R/vinereg.R | 2 build/vignette.rds |binary inst/doc/abalone-example.html | 729 ++++++++++++++++++++++------------------- inst/doc/bike-rental.html | 732 ++++++++++++++++++++++++------------------ man/plot_effects.Rd | 2 man/vinereg.Rd | 2 10 files changed, 838 insertions(+), 662 deletions(-)
Title: Spatial Analysis and Modelling Utilities
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization, statistical
exploratory tools and raster-based metrics.
Author: Jeffrey S. Evans [aut, cre],
Melanie A. Murphy [ctb],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 1.3-6 dated 2021-03-28 and 1.3-7 dated 2021-05-14
spatialEco-1.3-6/spatialEco/man/date.seq.Rd |only spatialEco-1.3-7/spatialEco/DESCRIPTION | 10 - spatialEco-1.3-7/spatialEco/MD5 | 59 +++--- spatialEco-1.3-7/spatialEco/NAMESPACE | 5 spatialEco-1.3-7/spatialEco/R/breeding.density.R | 2 spatialEco-1.3-7/spatialEco/R/cgls_urls.R |only spatialEco-1.3-7/spatialEco/R/chen-data.R |only spatialEco-1.3-7/spatialEco/R/crossCorrelation.R | 133 +++++++++------ spatialEco-1.3-7/spatialEco/R/date_seq.R | 18 -- spatialEco-1.3-7/spatialEco/R/download.prism.R | 129 -------------- spatialEco-1.3-7/spatialEco/R/extract_vertices.R | 17 + spatialEco-1.3-7/spatialEco/R/insert.R | 10 - spatialEco-1.3-7/spatialEco/R/logistic.regression.R | 2 spatialEco-1.3-7/spatialEco/R/overlap.R | 2 spatialEco-1.3-7/spatialEco/R/polygon_extract.R |only spatialEco-1.3-7/spatialEco/R/pu-data.R | 2 spatialEco-1.3-7/spatialEco/R/random.raster.R | 18 +- spatialEco-1.3-7/spatialEco/R/raster.modified.ttest.R | 2 spatialEco-1.3-7/spatialEco/R/time_to_event.R |only spatialEco-1.3-7/spatialEco/R/zonal.stats.R | 5 spatialEco-1.3-7/spatialEco/data/chen.rda |only spatialEco-1.3-7/spatialEco/inst/NEWS | 13 + spatialEco-1.3-7/spatialEco/man/cgls_urls.Rd |only spatialEco-1.3-7/spatialEco/man/chen.Rd |only spatialEco-1.3-7/spatialEco/man/crossCorrelation.Rd | 130 +++++++++----- spatialEco-1.3-7/spatialEco/man/date_seq.Rd |only spatialEco-1.3-7/spatialEco/man/download.prism.Rd | 53 ----- spatialEco-1.3-7/spatialEco/man/extract.vertices.Rd | 15 - spatialEco-1.3-7/spatialEco/man/logistic.regression.Rd | 2 spatialEco-1.3-7/spatialEco/man/overlap.Rd | 2 spatialEco-1.3-7/spatialEco/man/polygon_extract.Rd |only spatialEco-1.3-7/spatialEco/man/pu.Rd | 2 spatialEco-1.3-7/spatialEco/man/random.raster.Rd | 16 - spatialEco-1.3-7/spatialEco/man/raster.modified.ttest.Rd | 2 spatialEco-1.3-7/spatialEco/man/time_to_event.Rd |only spatialEco-1.3-7/spatialEco/man/zonal.stats.Rd | 5 36 files changed, 289 insertions(+), 365 deletions(-)
Title: Number-Theoretic Functions
Description: Provides number-theoretic functions for factorization, prime
numbers, twin primes, primitive roots, modular logarithm and
inverses, extended GCD, Farey series and continuous fractions.
Includes Legendre and Jacobi symbols, some divisor functions,
Euler's Phi function, etc.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between numbers versions 0.8-1 dated 2021-04-11 and 0.8-2 dated 2021-05-14
DESCRIPTION | 13 +++++-------- MD5 | 8 ++++---- NEWS | 5 +++++ build/partial.rdb |binary man/ratFarey.Rd | 24 ++++++++++-------------- 5 files changed, 24 insertions(+), 26 deletions(-)
Title: Download, Analyze & Clean New Jersey Car Crash Data
Description: Download and analyze motor vehicle crash data released by the New Jersey Department of Transportation (NJDOT).
The data in this package is collected through the filing of NJTR-1 form by police officers, which provide a standardized way of documenting a motor vehicle crash that occurred in New Jersey.
3 different data tables containing data on crashes, vehicles & pedestrians released from 2001 to the present can be downloaded & cleaned using this package.
Author: Gavin Rozzi [aut, cre] (<https://orcid.org/0000-0002-9969-8175>)
Maintainer: Gavin Rozzi <gr@gavinrozzi.com>
Diff between njtr1 versions 0.2.0 dated 2021-04-20 and 0.3.0 dated 2021-05-14
DESCRIPTION | 8 +- MD5 | 20 +++--- NAMESPACE | 3 + NEWS.md | 8 ++ R/data.R | 3 - R/download_data.R | 144 ++++++++++++++++++++++++++++++++++++++++++++++++-- data/insurance.rda |binary inst/doc/njtr1.html | 23 +++---- inst/extdata/testdata |only man/get_njtr1.Rd | 4 + man/insurance.Rd | 3 - man/read_njtr1.Rd |only 12 files changed, 180 insertions(+), 36 deletions(-)
Title: Interface to the Greek National Data Bank for
Hydrometeorological Information
Description: R interface to the Greek National Data Bank for Hydrological and
Meteorological Information. It covers
Hydroscope's data sources and provides functions to transliterate,
translate and download them into tidy dataframes.
Author: Konstantinos Vantas [aut, cre]
(<https://orcid.org/0000-0001-6387-8791>),
Sharla Gelfand [ctb, rev] (Sharla Gelfand reviewed the package for
rOpenSci, see https://github.com/ropensci/onboarding/issues/185),
Tim Trice [rev] (Tim Trice reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/185)
Maintainer: Konstantinos Vantas <kon.vantas@gmail.com>
Diff between hydroscoper versions 1.4 dated 2021-03-21 and 1.4.1 dated 2021-05-14
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/enhydris_api.R | 1 - README.md | 18 +++++++++++++++++- build/vignette.rds |binary inst/doc/intro_hydroscoper.R | 20 ++++++++++---------- inst/doc/intro_hydroscoper.html | 30 ++++++++++++++++++++++++++---- inst/doc/stations_with_data.html | 4 ++-- man/figures/README-plot_time_series-1.png |binary 10 files changed, 71 insertions(+), 30 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>),
Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>),
John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>),
Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>),
David Wilson [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 0.13.0 dated 2020-10-11 and 1.0.1 dated 2021-05-14
AlphaSimR-0.13.0/AlphaSimR/src/init.c |only AlphaSimR-0.13.0/AlphaSimR/tests/testthat/test-ibdRecHaplo.R |only AlphaSimR-1.0.1/AlphaSimR/DESCRIPTION | 17 AlphaSimR-1.0.1/AlphaSimR/MD5 | 121 +-- AlphaSimR-1.0.1/AlphaSimR/NAMESPACE | 5 AlphaSimR-1.0.1/AlphaSimR/NEWS | 18 AlphaSimR-1.0.1/AlphaSimR/R/Class-HybridPop.R | 2 AlphaSimR-1.0.1/AlphaSimR/R/Class-Pop.R | 329 ++++++++- AlphaSimR-1.0.1/AlphaSimR/R/Class-SimParam.R | 204 ++++-- AlphaSimR-1.0.1/AlphaSimR/R/RcppExports.R | 28 AlphaSimR-1.0.1/AlphaSimR/R/crossing.R | 358 ++++++---- AlphaSimR-1.0.1/AlphaSimR/R/founderPop.R | 64 + AlphaSimR-1.0.1/AlphaSimR/R/hybrids.R | 109 +++ AlphaSimR-1.0.1/AlphaSimR/R/mergePops.R | 17 AlphaSimR-1.0.1/AlphaSimR/R/misc.R | 32 AlphaSimR-1.0.1/AlphaSimR/R/phenotypes.R | 10 AlphaSimR-1.0.1/AlphaSimR/R/polyploids.R | 1 AlphaSimR-1.0.1/AlphaSimR/R/popSummary.R | 6 AlphaSimR-1.0.1/AlphaSimR/R/pullGeno.R | 295 +------- AlphaSimR-1.0.1/AlphaSimR/R/selection.R | 75 +- AlphaSimR-1.0.1/AlphaSimR/R/writeRecords.R | 2 AlphaSimR-1.0.1/AlphaSimR/README.md | 28 AlphaSimR-1.0.1/AlphaSimR/build/vignette.rds |binary AlphaSimR-1.0.1/AlphaSimR/inst/CITATION |only AlphaSimR-1.0.1/AlphaSimR/inst/doc/intro.html | 366 ++--------- AlphaSimR-1.0.1/AlphaSimR/inst/doc/traits.Rmd | 2 AlphaSimR-1.0.1/AlphaSimR/inst/doc/traits.pdf |binary AlphaSimR-1.0.1/AlphaSimR/man/AlphaSimR-package.Rd | 8 AlphaSimR-1.0.1/AlphaSimR/man/HybridPop-class.Rd | 2 AlphaSimR-1.0.1/AlphaSimR/man/MapPop-class.Rd | 8 AlphaSimR-1.0.1/AlphaSimR/man/MegaPop-class.Rd |only AlphaSimR-1.0.1/AlphaSimR/man/NamedMapPop-class.Rd |only AlphaSimR-1.0.1/AlphaSimR/man/Pop-class.Rd | 4 AlphaSimR-1.0.1/AlphaSimR/man/SimParam.Rd | 72 +- AlphaSimR-1.0.1/AlphaSimR/man/attrition.Rd |only AlphaSimR-1.0.1/AlphaSimR/man/cChr.Rd | 6 AlphaSimR-1.0.1/AlphaSimR/man/mergePops.Rd | 3 AlphaSimR-1.0.1/AlphaSimR/man/newMapPop.Rd | 2 AlphaSimR-1.0.1/AlphaSimR/man/newMegaPop.Rd |only AlphaSimR-1.0.1/AlphaSimR/man/newPop.Rd | 25 AlphaSimR-1.0.1/AlphaSimR/man/pedigreeCross.Rd | 4 AlphaSimR-1.0.1/AlphaSimR/man/pullIbdHaplo.Rd | 36 - AlphaSimR-1.0.1/AlphaSimR/man/pullQtlGeno.Rd | 55 - AlphaSimR-1.0.1/AlphaSimR/man/pullQtlHaplo.Rd | 86 -- AlphaSimR-1.0.1/AlphaSimR/man/pullSegSiteHaplo.Rd | 2 AlphaSimR-1.0.1/AlphaSimR/man/pullSnpHaplo.Rd | 2 AlphaSimR-1.0.1/AlphaSimR/man/selectFam.Rd | 8 AlphaSimR-1.0.1/AlphaSimR/man/selectInd.Rd | 8 AlphaSimR-1.0.1/AlphaSimR/man/selectOP.Rd | 6 AlphaSimR-1.0.1/AlphaSimR/man/selectWithinFam.Rd | 8 AlphaSimR-1.0.1/AlphaSimR/man/setPheno.Rd | 2 AlphaSimR-1.0.1/AlphaSimR/man/setPhenoGCA.Rd | 2 AlphaSimR-1.0.1/AlphaSimR/man/setPhenoProgTest.Rd |only AlphaSimR-1.0.1/AlphaSimR/man/writeRecords.Rd | 2 AlphaSimR-1.0.1/AlphaSimR/src/RcppExports.cpp | 138 +++- AlphaSimR-1.0.1/AlphaSimR/src/alphaSuite.cpp | 1 AlphaSimR-1.0.1/AlphaSimR/src/calcGenParam.cpp | 1 AlphaSimR-1.0.1/AlphaSimR/src/getGeno.cpp | 54 - AlphaSimR-1.0.1/AlphaSimR/src/getGv.cpp | 1 AlphaSimR-1.0.1/AlphaSimR/src/getHybridGv.cpp | 1 AlphaSimR-1.0.1/AlphaSimR/src/ibd.cpp |only AlphaSimR-1.0.1/AlphaSimR/src/meiosis.cpp | 294 ++++---- AlphaSimR-1.0.1/AlphaSimR/src/misc.cpp | 1 AlphaSimR-1.0.1/AlphaSimR/src/plink.cpp | 1 AlphaSimR-1.0.1/AlphaSimR/tests/testthat/test-crossing.R | 42 - AlphaSimR-1.0.1/AlphaSimR/vignettes/traits.Rmd | 2 66 files changed, 1577 insertions(+), 1399 deletions(-)
Title: Calculate Indices and Theoretical Physicochemical Properties of
Protein Sequences
Description: Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>),
Paola Rondon-Villarreal [aut, ths]
(<https://orcid.org/0000-0001-8209-3885>),
Rodrigo Torres [aut, ths] (<https://orcid.org/0000-0003-1113-3020>),
J. Sebastian Paez [ctb] (<https://orcid.org/0000-0002-0065-1474>),
Luis Pedro Coelho [ctb] (<https://orcid.org/0000-0002-9280-7885>),
Richèl J.C. Bilderbeek [ctb] (<https://orcid.org/0000-0003-1107-7049>),
Florian C. Sigloch [ctb] (<https://orcid.org/0000-0001-8130-6885>)
Maintainer: Daniel Osorio <daniecos@uio.no>
Diff between Peptides versions 2.4.3 dated 2020-11-16 and 2.4.4 dated 2021-05-14
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/massShift.R | 16 +++++++++++----- R/mw.R | 37 ++++++++++++++++++++++++++++++++++--- R/mz.R | 7 ++++++- README.md | 2 ++ man/massShift.Rd | 4 +++- man/mw.Rd | 12 ++++++++++-- 9 files changed, 83 insertions(+), 25 deletions(-)
Title: Partial Orders in Socio-Economics
Description: Implements tools for the analysis of partially ordered data, with a particular focus on the evaluation of multidimensional systems of indicators and on the analysis of poverty. References, Fattore M. (2016) <doi:10.1007/s11205-015-1059-6> Fattore M., Arcagni A. (2016) <doi:10.1007/s11205-016-1501-4> Arcagni A. (2017) <doi:10.1007/978-3-319-45421-4_19>.
Author: Alberto Arcagni [aut, cre],
Marco Fattore [aut]
Maintainer: Alberto Arcagni <alberto.arcagni@uniroma1.it>
Diff between parsec versions 1.2.4 dated 2021-05-14 and 1.2.5 dated 2021-05-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/var2prof.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<https://ec.europa.eu/eurostat> together with search and
manipulation utilities.
Author: Leo Lahti [aut, cre] (<https://orcid.org/0000-0001-5537-637X>),
Janne Huovari [aut],
Markus Kainu [aut],
Przemyslaw Biecek [aut],
Daniel Antal [ctb],
Diego Hernangomez [ctb],
Joona Lehtomaki [ctb],
Francois Briatte [ctb],
Reto Stauffer [ctb],
Paul Rougieux [ctb],
Anna Vasylytsya [ctb],
Oliver Reiter [ctb],
Pyry Kantanen [ctb]
Maintainer: Leo Lahti <leo.lahti@iki.fi>
Diff between eurostat versions 3.6.83 dated 2020-11-19 and 3.7.5 dated 2021-05-14
eurostat-3.6.83/eurostat/vignettes/fig/map1ex-1.pdf |only eurostat-3.6.83/eurostat/vignettes/fig/maps2-1.pdf |only eurostat-3.7.5/eurostat/DESCRIPTION | 80 ++- eurostat-3.7.5/eurostat/LICENSE | 2 eurostat-3.7.5/eurostat/MD5 | 123 ++--- eurostat-3.7.5/eurostat/NAMESPACE | 24 - eurostat-3.7.5/eurostat/NEWS | 6 eurostat-3.7.5/eurostat/R/add_nuts_level.R | 9 eurostat-3.7.5/eurostat/R/check_access_to_data.R | 8 eurostat-3.7.5/eurostat/R/cut_to_classes.R | 12 eurostat-3.7.5/eurostat/R/data_countries.R | 4 eurostat-3.7.5/eurostat/R/data_spatial.R | 2 eurostat-3.7.5/eurostat/R/dic_order.R | 9 eurostat-3.7.5/eurostat/R/eurostat-package.R | 2 eurostat-3.7.5/eurostat/R/eurotime2date.R | 5 eurostat-3.7.5/eurostat/R/eurotime2num.R | 3 eurostat-3.7.5/eurostat/R/firstlib.R | 42 - eurostat-3.7.5/eurostat/R/get_bibentry.R | 7 eurostat-3.7.5/eurostat/R/get_eurostat.R | 12 eurostat-3.7.5/eurostat/R/get_eurostat_dic.R | 14 eurostat-3.7.5/eurostat/R/get_eurostat_geospatial.R | 227 ++++++---- eurostat-3.7.5/eurostat/R/get_eurostat_json.R | 9 eurostat-3.7.5/eurostat/R/get_eurostat_raw.R | 6 eurostat-3.7.5/eurostat/R/get_eurostat_toc.R | 2 eurostat-3.7.5/eurostat/R/harmonize_geo_code.R | 15 eurostat-3.7.5/eurostat/R/label_eurostat.R | 7 eurostat-3.7.5/eurostat/R/recode_to_nuts_2013.R | 7 eurostat-3.7.5/eurostat/R/recode_to_nuts_2016.R | 7 eurostat-3.7.5/eurostat/R/search_eurostat.R | 9 eurostat-3.7.5/eurostat/R/set_eurostat_toc.R | 3 eurostat-3.7.5/eurostat/R/tidy_eurostat.R | 7 eurostat-3.7.5/eurostat/R/utils.R | 2 eurostat-3.7.5/eurostat/README.md | 150 +++++- eurostat-3.7.5/eurostat/build/vignette.rds |binary eurostat-3.7.5/eurostat/inst/doc/vignette.Rmd | 2 eurostat-3.7.5/eurostat/inst/doc/vignette.html | 109 ++-- eurostat-3.7.5/eurostat/man/add_nuts_level.Rd | 1 eurostat-3.7.5/eurostat/man/check_access_to_data.Rd | 1 eurostat-3.7.5/eurostat/man/cut_to_classes.Rd | 1 eurostat-3.7.5/eurostat/man/eu_countries.Rd | 4 eurostat-3.7.5/eurostat/man/eurostat-package.Rd | 2 eurostat-3.7.5/eurostat/man/eurostat_geodata_60_2016.Rd | 2 eurostat-3.7.5/eurostat/man/eurotime2date.Rd | 1 eurostat-3.7.5/eurostat/man/eurotime2num.Rd | 1 eurostat-3.7.5/eurostat/man/get_bibentry.Rd | 1 eurostat-3.7.5/eurostat/man/get_eurostat.Rd | 10 eurostat-3.7.5/eurostat/man/get_eurostat_dic.Rd | 9 eurostat-3.7.5/eurostat/man/get_eurostat_geospatial.Rd | 67 ++ eurostat-3.7.5/eurostat/man/get_eurostat_json.Rd | 5 eurostat-3.7.5/eurostat/man/get_eurostat_raw.Rd | 3 eurostat-3.7.5/eurostat/man/get_eurostat_toc.Rd | 2 eurostat-3.7.5/eurostat/man/harmonize_geo_code.Rd | 1 eurostat-3.7.5/eurostat/man/label_eurostat.Rd | 1 eurostat-3.7.5/eurostat/man/recode_to_nuts_2013.Rd | 1 eurostat-3.7.5/eurostat/man/recode_to_nuts_2016.Rd | 1 eurostat-3.7.5/eurostat/tests/testthat/test_bibliography.R | 2 eurostat-3.7.5/eurostat/tests/testthat/test_get.R | 28 - eurostat-3.7.5/eurostat/tests/testthat/test_get_eurostat_geospatial.R |only eurostat-3.7.5/eurostat/tests/testthat/test_json.R | 33 - eurostat-3.7.5/eurostat/tests/testthat/test_regional.R | 8 eurostat-3.7.5/eurostat/vignettes/vignette.Rmd | 2 eurostat-3.7.5/eurostat/vignettes/vignette.md | 2 eurostat-3.7.5/eurostat/vignettes/website/eurostat_tutorial.Rmd | 2 eurostat-3.7.5/eurostat/vignettes/website/maps.Rmd | 2 64 files changed, 717 insertions(+), 402 deletions(-)
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are
cumulative probability distributions which are fitted to
toxicity concentrations for different species as described by
Posthuma et al.(2001) <isbn:9781566705783>.
The ssdtools package uses Maximum Likelihood to fit distributions
such as the log-normal, gamma, log-logistic,
log-Gumbel, Gompertz and Weibull.
The user can provide custom distributions.
Multiple distributions can be averaged using Information Criteria.
Confidence intervals on hazard concentrations and proportions are produced by
parametric bootstrapping.
Author: Joe Thorley [aut, cre, ctr] (<https://orcid.org/0000-0002-7683-4592>),
Carl Schwarz [aut, ctr],
Angeline Tillmanns [ctb],
Ali Azizishirazi [ctb],
Rebecca Fisher [ctb],
David Fox [ctb],
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Andy Teucher [ctb],
Emilie Doussantousse [ctb],
Stephanie Hazlitt [ctb],
Nadine Hussein [ctb],
Nan-Hung Hsieh [ctb],
Sergio Ibarra Espinosa [ctb],
Province of British Columbia [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 0.3.3 dated 2021-02-19 and 0.3.4 dated 2021-05-14
ssdtools-0.3.3/ssdtools/man/nobs.fitdistcens.Rd |only ssdtools-0.3.3/ssdtools/man/predict.fitdistcens.Rd |only ssdtools-0.3.3/ssdtools/man/predict.fitdists.Rd |only ssdtools-0.3.3/ssdtools/man/predict.fitdistscens.Rd |only ssdtools-0.3.4/ssdtools/DESCRIPTION | 6 ssdtools-0.3.4/ssdtools/LICENSE | 4 ssdtools-0.3.4/ssdtools/MD5 | 216 +--- ssdtools-0.3.4/ssdtools/NEWS.md | 4 ssdtools-0.3.4/ssdtools/R/autoplot.R | 10 ssdtools-0.3.4/ssdtools/R/boot.R | 2 ssdtools-0.3.4/ssdtools/R/burrIII2.R | 8 ssdtools-0.3.4/ssdtools/R/burrrIII3.R | 8 ssdtools-0.3.4/ssdtools/R/cis.R | 2 ssdtools-0.3.4/ssdtools/R/coef.R | 2 ssdtools-0.3.4/ssdtools/R/data.R | 25 ssdtools-0.3.4/ssdtools/R/exposure.R | 2 ssdtools-0.3.4/ssdtools/R/fit.R | 2 ssdtools-0.3.4/ssdtools/R/gamma.R | 2 ssdtools-0.3.4/ssdtools/R/ggplot.R | 12 ssdtools-0.3.4/ssdtools/R/ggproto.R | 28 ssdtools-0.3.4/ssdtools/R/gof.R | 2 ssdtools-0.3.4/ssdtools/R/gompertz.R | 2 ssdtools-0.3.4/ssdtools/R/hc.R | 2 ssdtools-0.3.4/ssdtools/R/hp.R | 2 ssdtools-0.3.4/ssdtools/R/internal.R | 2 ssdtools-0.3.4/ssdtools/R/is.R | 6 ssdtools-0.3.4/ssdtools/R/lgumbel.R | 4 ssdtools-0.3.4/ssdtools/R/llog.R | 2 ssdtools-0.3.4/ssdtools/R/llogis.R | 2 ssdtools-0.3.4/ssdtools/R/lnorm.R | 4 ssdtools-0.3.4/ssdtools/R/match-moments.R | 2 ssdtools-0.3.4/ssdtools/R/namespace.R | 2 ssdtools-0.3.4/ssdtools/R/nobs.R | 8 ssdtools-0.3.4/ssdtools/R/npars.R | 5 ssdtools-0.3.4/ssdtools/R/params.R | 2 ssdtools-0.3.4/ssdtools/R/pareto.R | 2 ssdtools-0.3.4/ssdtools/R/plot-cdf.R | 34 ssdtools-0.3.4/ssdtools/R/plot-cf.R | 2 ssdtools-0.3.4/ssdtools/R/plot.R | 2 ssdtools-0.3.4/ssdtools/R/predict.R | 72 - ssdtools-0.3.4/ssdtools/R/print.R | 2 ssdtools-0.3.4/ssdtools/R/ssd-plot.R | 39 ssdtools-0.3.4/ssdtools/R/ssdtools-package.R | 2 ssdtools-0.3.4/ssdtools/R/subset.R | 2 ssdtools-0.3.4/ssdtools/R/utils.R | 2 ssdtools-0.3.4/ssdtools/R/weibull.R | 2 ssdtools-0.3.4/ssdtools/R/zzz.R | 2 ssdtools-0.3.4/ssdtools/README.md | 50 ssdtools-0.3.4/ssdtools/build/vignette.rds |binary ssdtools-0.3.4/ssdtools/inst/WORDLIST | 105 - ssdtools-0.3.4/ssdtools/inst/doc/distributions.Rmd | 2 ssdtools-0.3.4/ssdtools/inst/doc/distributions.html | 256 ---- ssdtools-0.3.4/ssdtools/inst/doc/exposure-plots.Rmd | 2 ssdtools-0.3.4/ssdtools/inst/doc/exposure-plots.html | 290 ----- ssdtools-0.3.4/ssdtools/inst/doc/faqs.html | 266 ---- ssdtools-0.3.4/ssdtools/inst/doc/small-sample-bias-ref.html | 203 --- ssdtools-0.3.4/ssdtools/inst/doc/ssdtools.html | 534 +++------- ssdtools-0.3.4/ssdtools/man/autoplot.fitdist.Rd | 12 ssdtools-0.3.4/ssdtools/man/boron_data.Rd | 9 ssdtools-0.3.4/ssdtools/man/boron_dists.Rd | 8 ssdtools-0.3.4/ssdtools/man/boron_hc5.Rd | 10 ssdtools-0.3.4/ssdtools/man/boron_lnorm.Rd | 8 ssdtools-0.3.4/ssdtools/man/boron_pred.Rd | 10 ssdtools-0.3.4/ssdtools/man/burrIII2.Rd | 3 ssdtools-0.3.4/ssdtools/man/burrIII3.Rd | 2 ssdtools-0.3.4/ssdtools/man/figures/README-unnamed-chunk-10-1.png |binary ssdtools-0.3.4/ssdtools/man/figures/README-unnamed-chunk-5-1.png |binary ssdtools-0.3.4/ssdtools/man/fluazinam_dists.Rd | 7 ssdtools-0.3.4/ssdtools/man/fluazinam_lnorm.Rd | 7 ssdtools-0.3.4/ssdtools/man/fluazinam_pred.Rd | 10 ssdtools-0.3.4/ssdtools/man/geom_hcintersect.Rd | 6 ssdtools-0.3.4/ssdtools/man/geom_ssd.Rd | 8 ssdtools-0.3.4/ssdtools/man/geom_xribbon.Rd | 6 ssdtools-0.3.4/ssdtools/man/is.fitdist.Rd | 7 ssdtools-0.3.4/ssdtools/man/is.fitdistcens.Rd | 7 ssdtools-0.3.4/ssdtools/man/is.fitdists.Rd | 7 ssdtools-0.3.4/ssdtools/man/is.fitdistscens.Rd | 7 ssdtools-0.3.4/ssdtools/man/llogis.Rd | 7 ssdtools-0.3.4/ssdtools/man/nobs.fitdist.Rd | 7 ssdtools-0.3.4/ssdtools/man/npars.Rd | 2 ssdtools-0.3.4/ssdtools/man/predict.fitdist.Rd | 55 - ssdtools-0.3.4/ssdtools/man/ssd_plot.Rd | 2 ssdtools-0.3.4/ssdtools/man/ssd_plot_cdf.Rd | 2 ssdtools-0.3.4/ssdtools/man/ssdtools-ggproto.Rd | 4 ssdtools-0.3.4/ssdtools/man/stat_ssd.Rd | 2 ssdtools-0.3.4/ssdtools/tests/testthat.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-autoplot.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-burrIII2.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-burrIII3.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-data.R | 18 ssdtools-0.3.4/ssdtools/tests/testthat/test-exposure.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-fit.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-gof.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-gompertz.R | 25 ssdtools-0.3.4/ssdtools/tests/testthat/test-hc.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-hp.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-lgumbel.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-llogis.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-match-moments.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-pareto.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-plot-cdf.R | 4 ssdtools-0.3.4/ssdtools/tests/testthat/test-plot-cf.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-plot.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-predict.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-schwarz-tillmans.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-ssd-plot.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-subset.R | 2 ssdtools-0.3.4/ssdtools/tests/testthat/test-test-data.R | 6 ssdtools-0.3.4/ssdtools/tests/testthat/test-utils.R | 2 ssdtools-0.3.4/ssdtools/vignettes/distributions.Rmd | 2 ssdtools-0.3.4/ssdtools/vignettes/exposure-plots.Rmd | 2 111 files changed, 902 insertions(+), 1661 deletions(-)
Title: Recommender System using Matrix Factorization
Description: R wrapper of the 'libmf' library
<https://www.csie.ntu.edu.tw/~cjlin/libmf/> for recommender
system using matrix factorization. It is typically used to
approximate an incomplete matrix using the product of two
matrices in a latent space. Other common names for this task
include "collaborative filtering", "matrix completion",
"matrix recovery", etc. High performance multi-core parallel
computing is supported in this package.
Author: Yixuan Qiu, Chih-Jen Lin, Yu-Chin Juan, Wei-Sheng Chin,
Yong Zhuang, Bo-Wen Yuan, Meng-Yuan Yang, and other
contributors. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between recosystem versions 0.4.4 dated 2021-01-10 and 0.4.5 dated 2021-05-14
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/NEWS.Rd | 6 ++++++ inst/doc/introduction.html | 6 +++--- 4 files changed, 17 insertions(+), 11 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, and ANOVA. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.5.2 dated 2021-04-14 and 0.5.3 dated 2021-05-14
sasLM-0.5.2/sasLM/inst/doc/Report-Different-Simplest2104150030.pdf |only sasLM-0.5.2/sasLM/inst/doc/Report-NOT-OKs2104150027.pdf |only sasLM-0.5.2/sasLM/inst/doc/Validation-Report-ANOVA-2104150022.pdf |only sasLM-0.5.2/sasLM/inst/doc/Validation-Report-GLM-2104150017.pdf |only sasLM-0.5.3/sasLM/DESCRIPTION | 6 - sasLM-0.5.3/sasLM/MD5 | 32 +++++----- sasLM-0.5.3/sasLM/R/ANOVA.R | 8 ++ sasLM-0.5.3/sasLM/R/BasicUtil.R | 23 +++++-- sasLM-0.5.3/sasLM/R/GLM.R | 12 ++- sasLM-0.5.3/sasLM/R/aov1.R | 7 +- sasLM-0.5.3/sasLM/R/aov2.R | 7 +- sasLM-0.5.3/sasLM/R/aov3.R | 7 +- sasLM-0.5.3/sasLM/R/e2.R | 9 ++ sasLM-0.5.3/sasLM/inst/NEWS.Rd | 8 ++ sasLM-0.5.3/sasLM/inst/doc/Report-Different-Simplest2104212048.pdf |only sasLM-0.5.3/sasLM/inst/doc/Report-NOT-OKs2104212045.pdf |only sasLM-0.5.3/sasLM/inst/doc/Validation-Report-ANOVA-2104212041.pdf |only sasLM-0.5.3/sasLM/inst/doc/Validation-Report-GLM-2104212036.pdf |only sasLM-0.5.3/sasLM/inst/doc/sasLM-manual.pdf |binary sasLM-0.5.3/sasLM/man/REG.Rd | 1 sasLM-0.5.3/sasLM/man/sasLM-package.Rd | 4 - 21 files changed, 91 insertions(+), 33 deletions(-)
Title: Non-Parametric Sampling with Parallel Monte Carlo
Description: An implementation of a non-parametric statistical model using a
parallelised Monte Carlo sampling scheme. The method implemented in this
package allows non-parametric inference to be regularized for small sample
sizes, while also being more accurate than approximations such as
variational Bayes. The concentration parameter is an effective sample size
parameter, determining the faith we have in the model versus the data. When
the concentration is low, the samples are close to the exact Bayesian
logistic regression method; when the concentration is high, the samples are
close to the simplified variational Bayes logistic regression. The method is
described in full in the paper Lyddon, Walker, and Holmes (2018),
"Nonparametric learning from Bayesian models with randomized objective
functions" <arXiv:1806.11544>.
Author: Simon Lyddon [aut],
Miguel Morin [aut],
James Robinson [aut, cre],
The Alan Turing Institute [cph]
Maintainer: James Robinson <james.em.robinson@gmail.com>
Diff between PosteriorBootstrap versions 0.1.0 dated 2019-10-09 and 0.1.1 dated 2021-05-14
PosteriorBootstrap-0.1.0/PosteriorBootstrap/tests/testthat/test_lintr.R |only PosteriorBootstrap-0.1.1/PosteriorBootstrap/DESCRIPTION | 15 PosteriorBootstrap-0.1.1/PosteriorBootstrap/MD5 | 34 PosteriorBootstrap-0.1.1/PosteriorBootstrap/NAMESPACE | 1 PosteriorBootstrap-0.1.1/PosteriorBootstrap/NEWS.md | 5 PosteriorBootstrap-0.1.1/PosteriorBootstrap/R/PosteriorBootstrap.R | 13 PosteriorBootstrap-0.1.1/PosteriorBootstrap/R/data_loader.R | 11 PosteriorBootstrap-0.1.1/PosteriorBootstrap/README.md | 60 PosteriorBootstrap-0.1.1/PosteriorBootstrap/build/vignette.rds |binary PosteriorBootstrap-0.1.1/PosteriorBootstrap/inst/doc/PosteriorBootstrap.Rmd | 4 PosteriorBootstrap-0.1.1/PosteriorBootstrap/inst/doc/PosteriorBootstrap.html | 820 +++------- PosteriorBootstrap-0.1.1/PosteriorBootstrap/man/PosteriorBootstrap.Rd | 12 PosteriorBootstrap-0.1.1/PosteriorBootstrap/man/draw_logit_samples.Rd | 17 PosteriorBootstrap-0.1.1/PosteriorBootstrap/man/draw_stick_breaks.Rd | 8 PosteriorBootstrap-0.1.1/PosteriorBootstrap/man/get_file.Rd |only PosteriorBootstrap-0.1.1/PosteriorBootstrap/man/get_german_credit_dataset.Rd | 7 PosteriorBootstrap-0.1.1/PosteriorBootstrap/tests/testthat/test_anpl.R | 20 PosteriorBootstrap-0.1.1/PosteriorBootstrap/tests/testthat/test_german_data.R | 7 PosteriorBootstrap-0.1.1/PosteriorBootstrap/vignettes/PosteriorBootstrap.Rmd | 4 19 files changed, 443 insertions(+), 595 deletions(-)
More information about PosteriorBootstrap at CRAN
Permanent link
Title: Tools to Visualize, Manipulate, and Summarize MCMC Output
Description: Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with 'Stan', 'NIMBLE', 'JAGS', and other software.
Author: Casey Youngflesh [aut, cre] (<https://orcid.org/0000-0001-6343-3311>),
Christian Che-Castaldo [aut] (<https://orcid.org/0000-0002-7670-2178>),
Tyler Hardy [ctb]
Maintainer: Casey Youngflesh <caseyyoungflesh@gmail.com>
Diff between MCMCvis versions 0.15.1 dated 2021-04-13 and 0.15.2 dated 2021-05-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/MCMCdiag.R | 2 +- R/MCMCtrace.R | 10 +++++----- build/vignette.rds |binary inst/doc/MCMCvis.Rmd | 4 ++-- inst/doc/MCMCvis.html | 49 ++++++++++++++++++++++++++++--------------------- vignettes/MCMCvis.Rmd | 4 ++-- 9 files changed, 55 insertions(+), 42 deletions(-)
Title: Bayesian Spatial Split Population Survival Model
Description: Parametric spatial split-population (SP) survival models for clustered
event processes. The models account for structural and spatial heterogeneity among
“at risk” and “immune” populations, and incorporate time-varying covariates.
This package currently implements Weibull, Exponential and Log-logistic forms for
the duration component. It also includes functions for a series of diagnostic
tests and plots to easily visualize spatial autocorrelation, convergence, and spatial effects. Users can
create their own spatial weights matrix based on their units and adjacencies of
interest, making the use of these models flexible and broadly applicable to a
variety of research areas. Joo et al. (2020) <https://github.com/Nicolas-Schmidt/BayesSPsurv/blob/master/man/figures/SPcure.pdf> describe
the estimators included in this package.
Author: Brandon L. Bolte [aut],
Nicolas Schmidt [aut, cre],
Sergio Bejar [aut],
Bumba Mukherjee [aut],
Minnie M. Joo [ctb],
Nguyen K. Huynh [ctb]
Maintainer: Nicolas Schmidt <nschmidt@cienciassociales.edu.uy>
Diff between BayesSPsurv versions 0.1.2 dated 2021-01-08 and 0.1.3 dated 2021-05-14
DESCRIPTION | 10 MD5 | 34 +- NEWS.md | 10 R/Walter_2015_JCR.R | 3 R/exchangeSPsurv.R | 91 ++++--- R/plots.R | 4 R/pooledSPsurv.R | 15 - R/spatialSPsurv.R | 70 +++-- R/utils.R | 261 ++++++++++++++------- README.md | 281 ++++++++++++++--------- data/Walter_2015_JCR.rda |binary man/Walter_2015_JCR.Rd | 3 man/exchangeSPsurv.Rd | 373 ++++++++++++++++--------------- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/plot_JoinCount.Rd | 2 man/pooledSPsurv.Rd | 256 ++++++++++----------- man/spatialSPsurv.Rd | 54 +++- 18 files changed, 857 insertions(+), 610 deletions(-)
Title: Diving Calculations and Decompression Models
Description: Code for describing and manipulating scuba diving profiles
(depth-time curves) and decompression models,
for calculating the predictions of decompression models,
for calculating maximum no-decompression time and decompression tables,
and for performing mixed gas calculations.
Author: Adrian Baddeley [aut, cre],
Vittorio Broglio [ctb, dtc],
Pedro Antonio Neves [ctb, dtc],
Andrew Bassom [ctb],
Peter Buzzacott [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between scuba versions 1.10-0 dated 2020-05-15 and 1.11-0 dated 2021-05-14
scuba-1.10-0/scuba/data/Bookspan.R |only scuba-1.10-0/scuba/data/BuehlmannL16A.tab |only scuba-1.10-0/scuba/data/Workman65.tab |only scuba-1.11-0/scuba/DESCRIPTION | 10 +- scuba-1.11-0/scuba/MD5 | 99 +++++++++++++-------------- scuba-1.11-0/scuba/NAMESPACE | 10 +- scuba-1.11-0/scuba/NEWS | 10 ++ scuba-1.11-0/scuba/R/haldane.R | 4 - scuba-1.11-0/scuba/build/vignette.rds |binary scuba-1.11-0/scuba/data/Bookspan.rda |only scuba-1.11-0/scuba/data/BuehlmannL16A.tab.gz |only scuba-1.11-0/scuba/data/Workman65.tab.gz |only scuba-1.11-0/scuba/data/baron.rda |binary scuba-1.11-0/scuba/data/deepmine.rda |binary scuba-1.11-0/scuba/data/pedro.rda |binary scuba-1.11-0/scuba/inst/doc/intro.pdf |binary scuba-1.11-0/scuba/man/Bookspan.Rd | 5 - scuba-1.11-0/scuba/man/BuehlmannL16A.Rd | 5 - scuba-1.11-0/scuba/man/END.Rd | 5 - scuba-1.11-0/scuba/man/Mmix.Rd | 5 - scuba-1.11-0/scuba/man/Workman65.Rd | 5 - scuba-1.11-0/scuba/man/air.Rd | 5 - scuba-1.11-0/scuba/man/ascent.Rd | 5 - scuba-1.11-0/scuba/man/bestdoubledive.Rd | 6 - scuba-1.11-0/scuba/man/chop.dive.Rd | 5 - scuba-1.11-0/scuba/man/deco.ceiling.Rd | 5 - scuba-1.11-0/scuba/man/depths.dive.Rd | 5 - scuba-1.11-0/scuba/man/descent.Rd | 5 - scuba-1.11-0/scuba/man/dive.Rd | 5 - scuba-1.11-0/scuba/man/durations.dive.Rd | 5 - scuba-1.11-0/scuba/man/ead.Rd | 5 - scuba-1.11-0/scuba/man/haldane.Rd | 5 - scuba-1.11-0/scuba/man/hm.Rd | 5 - scuba-1.11-0/scuba/man/is.nitrox.Rd | 5 - scuba-1.11-0/scuba/man/macros |only scuba-1.11-0/scuba/man/maxmix.Rd | 5 - scuba-1.11-0/scuba/man/mod.Rd | 5 - scuba-1.11-0/scuba/man/ndl.Rd | 5 - scuba-1.11-0/scuba/man/nitrox.Rd | 5 - scuba-1.11-0/scuba/man/oxtox.Rd | 5 - scuba-1.11-0/scuba/man/param.Rd | 5 - scuba-1.11-0/scuba/man/pickmodel.Rd | 6 - scuba-1.11-0/scuba/man/plot.dive.Rd | 5 - scuba-1.11-0/scuba/man/ppO2.Rd | 5 - scuba-1.11-0/scuba/man/print.dive.Rd | 5 - scuba-1.11-0/scuba/man/saturated.state.Rd | 5 - scuba-1.11-0/scuba/man/scuba-package.Rd | 5 - scuba-1.11-0/scuba/man/scuba.constants.Rd | 5 - scuba-1.11-0/scuba/man/scuba.disclaimer.Rd | 5 - scuba-1.11-0/scuba/man/showstates.Rd | 5 - scuba-1.11-0/scuba/man/tanklist.Rd | 5 - scuba-1.11-0/scuba/man/times.dive.Rd | 5 - scuba-1.11-0/scuba/man/trimix.Rd | 5 - scuba-1.11-0/scuba/man/whichtank.Rd | 5 - 54 files changed, 109 insertions(+), 211 deletions(-)
Title: Information Preserving Regression-Based Tools for Statistical
Disclosure Control
Description: Implementation of the methods described in the paper with the above title: Langsrud, Ø. (2019) <doi:10.1007/s11222-018-9848-9>. The package can be used to generate synthetic or hybrid continuous microdata, and the relationship to the original data can be controlled in several ways. A function for replacing suppressed tabular cell frequencies with decimal numbers is included.
Author: Øyvind Langsrud [aut, cre]
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between RegSDC versions 0.5.0 dated 2021-01-21 and 0.6.0 dated 2021-05-14
DESCRIPTION | 9 ++++----- MD5 | 4 ++-- R/RegSDCdata.R | 4 ++-- 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data structures
and functions that facilitate the plotting of missing values and examination
of imputations. This allows missing data dependencies to be explored with
minimal deviation from the common work patterns of 'ggplot2' and tidy data.
The work is fully discussed at Tierney & Cook (2018) <arXiv:1809.02264>.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>),
Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>),
Miles McBain [aut] (<https://orcid.org/0000-0003-2865-2548>),
Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>),
Mitchell O'Hara-Wild [ctb],
Jim Hester [ctb],
Luke Smith [ctb],
Andrew Heiss [ctb] (<https://orcid.org/0000-0002-3948-3914>)
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 0.6.0 dated 2020-09-02 and 0.6.1 dated 2021-05-14
DESCRIPTION | 21 MD5 | 55 +- NAMESPACE | 2 NEWS.md | 18 R/mcar-test.R |only R/miss-x-span.R | 33 - R/naniar-package.R | 1 R/shadow-recode.R | 7 R/utils.R | 4 README.md | 420 +++++++++-------- build/partial.rdb |only build/vignette.rds |binary data/common_na_strings.rda |binary inst/WORDLIST | 117 ++-- inst/doc/exploring-imputed-values.html | 610 ++++++++----------------- inst/doc/getting-started-w-naniar.Rmd | 2 inst/doc/getting-started-w-naniar.html | 552 +++++++--------------- inst/doc/naniar-visualisation.Rmd | 2 inst/doc/naniar-visualisation.html | 466 +++++-------------- inst/doc/replace-with-na.html | 551 +++++++--------------- inst/doc/special-missing-values.html | 348 +++----------- man/common_na_strings.Rd | 2 man/mcar_test.Rd |only man/miss_var_span.Rd | 10 tests/figs/gg-miss-span/gg-miss-span-group.svg | 4 tests/figs/gg-miss-span/gg-miss-span.svg | 4 tests/testthat/test-mcar-test.R |only tests/testthat/test-miss-var-span.R | 13 tests/testthat/test-shadow-expand-relevel.R |only vignettes/getting-started-w-naniar.Rmd | 2 vignettes/naniar-visualisation.Rmd | 2 31 files changed, 1239 insertions(+), 2007 deletions(-)
Title: Buffer Generation for Spatial Models
Description: Generates non-circular simple feature geometries e.g. for the use as buffers in model-building.
Author: Tilman Leo Hohenberger [aut, cre]
(<https://orcid.org/0000-0002-4372-8750>)
Maintainer: Tilman Leo Hohenberger <tlh@ust.hk>
Diff between buffeRs versions 0.21 dated 2021-02-16 and 0.30 dated 2021-05-14
DESCRIPTION | 11 ++++++----- MD5 | 17 ++++++++++++++--- NAMESPACE | 2 ++ R/buffer_rectangle.R |only R/buffer_square.R |only R/buffer_wedge.R | 2 +- R/rotation_f.R |only README.md |only build |only inst |only man/buffer_rectangle.Rd |only man/buffer_square.Rd |only vignettes |only 13 files changed, 23 insertions(+), 9 deletions(-)
Title: Representation of Archaeological Data
Description: A collection of classes that represent
archaeological data. This package provides a set of S4 classes that
represent different special types of matrix (absolute/relative
frequency, presence/absence data, co-occurrence matrix, etc.) upon
which package developers can build subclasses. It also provides a set
of generic methods (mutators and coercion mechanisms) and functions
(e.g. summary statistics, predicates). In addition, a few classes of
general interest (e.g. that represent stratigraphic relationships)
are implemented.
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>),
Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>)
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between arkhe versions 0.3.0 dated 2021-04-09 and 0.3.1 dated 2021-05-14
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/arkhe-package.R | 7 ++++--- README.md | 8 +++----- build/partial.rdb |binary inst/CITATION | 4 ++-- inst/doc/arkhe.html | 4 ++-- inst/examples/ex-coerce.R | 2 +- man/arkhe-package.Rd | 7 ++++--- man/coerce.Rd | 2 +- 11 files changed, 36 insertions(+), 30 deletions(-)
Title: Green Finance and Environmental Risk
Description: Focuses on data collecting, analyzing and visualization in green finance and environmental
risk research and analysis. Main function includes environmental data collecting from
official websites such as MEP (Ministry of Environmental Protection of China, <https://www.mee.gov.cn>), water
related projects identification and environmental data visualization.
Author: Yuanchao Xu [aut, cre]
Maintainer: Yuanchao Xu <xuyuanchao37@gmail.com>
Diff between gfer versions 0.1.10 dated 2018-03-11 and 0.1.11 dated 2021-05-14
gfer-0.1.10/gfer/inst/doc/gfer.html |only gfer-0.1.11/gfer/DESCRIPTION | 12 gfer-0.1.11/gfer/MD5 | 118 +- gfer-0.1.11/gfer/NAMESPACE | 110 +- gfer-0.1.11/gfer/NEWS | 148 +-- gfer-0.1.11/gfer/R/data.R | 48 - gfer-0.1.11/gfer/R/getCSRRating.R | 300 +++--- gfer-0.1.11/gfer/R/getENNames.R | 164 +-- gfer-0.1.11/gfer/R/getExchange.R | 172 +-- gfer-0.1.11/gfer/R/getIndex.R | 230 ++--- gfer-0.1.11/gfer/R/getMktCap.R | 176 ++-- gfer-0.1.11/gfer/R/getNBS.R | 1040 ++++++++++++------------ gfer-0.1.11/gfer/R/getPPPList.R | 308 +++---- gfer-0.1.11/gfer/R/getProxy.R | 42 gfer-0.1.11/gfer/R/getTickers.R | 220 ++--- gfer-0.1.11/gfer/R/getWQ.R | 292 +++--- gfer-0.1.11/gfer/R/listedInfo.R | 336 +++---- gfer-0.1.11/gfer/R/plotChord.R | 188 ++-- gfer-0.1.11/gfer/R/plotScatterPie.R | 760 ++++++++--------- gfer-0.1.11/gfer/README.md | 72 - gfer-0.1.11/gfer/build/vignette.rds |binary gfer-0.1.11/gfer/inst/doc/gfer.Rmd | 52 - gfer-0.1.11/gfer/inst/doc/gfer.pdf |only gfer-0.1.11/gfer/man/GDPmix.Rd | 36 gfer-0.1.11/gfer/man/checkHttpStatus.Rd | 42 gfer-0.1.11/gfer/man/cm.Rd | 36 gfer-0.1.11/gfer/man/dataJson2df.Rd | 50 - gfer-0.1.11/gfer/man/genDfwds.Rd | 52 - gfer-0.1.11/gfer/man/getCSRRating.Rd | 70 - gfer-0.1.11/gfer/man/getCSRRating_unit.Rd | 56 - gfer-0.1.11/gfer/man/getENNames.Rd | 60 - gfer-0.1.11/gfer/man/getENNames_unit.Rd | 46 - gfer-0.1.11/gfer/man/getExchange.Rd | 58 - gfer-0.1.11/gfer/man/getHisMktCap.Rd | 70 - gfer-0.1.11/gfer/man/getHisMktCap_unit.Rd | 54 - gfer-0.1.11/gfer/man/getIndex.Rd | 68 - gfer-0.1.11/gfer/man/getIndexConstnt.Rd | 34 gfer-0.1.11/gfer/man/getIndexData.Rd | 32 gfer-0.1.11/gfer/man/getNBS.Rd | 50 - gfer-0.1.11/gfer/man/getPPPList.Rd | 66 - gfer-0.1.11/gfer/man/getPPPList_unit.Rd | 40 gfer-0.1.11/gfer/man/getProxy.Rd | 40 gfer-0.1.11/gfer/man/getStockList.Rd | 36 gfer-0.1.11/gfer/man/getTickers.Rd | 50 - gfer-0.1.11/gfer/man/getTickers_unit.Rd | 40 gfer-0.1.11/gfer/man/getWaterQ_MEP_all.Rd | 78 - gfer-0.1.11/gfer/man/getWaterQ_MEP_all_unit.Rd | 58 - gfer-0.1.11/gfer/man/getWaternomicsData_NBS.Rd | 32 gfer-0.1.11/gfer/man/getWaternomicsData_goog.Rd | 26 gfer-0.1.11/gfer/man/is.listed.Rd | 38 gfer-0.1.11/gfer/man/milSec.Rd | 28 gfer-0.1.11/gfer/man/plotChord.Rd | 99 +- gfer-0.1.11/gfer/man/plotScatterPie.Rd | 103 +- gfer-0.1.11/gfer/man/statscnDbs.Rd | 48 - gfer-0.1.11/gfer/man/statscnQueryData.Rd | 93 +- gfer-0.1.11/gfer/man/statscnQueryLastN.Rd | 60 - gfer-0.1.11/gfer/man/statscnQueryZb.Rd | 64 - gfer-0.1.11/gfer/man/statscnRegions.Rd | 62 - gfer-0.1.11/gfer/man/statscnRowNamePrefix.Rd | 58 - gfer-0.1.11/gfer/man/updateNBS.Rd | 34 gfer-0.1.11/gfer/vignettes/gfer.Rmd | 52 - 61 files changed, 3421 insertions(+), 3386 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-29 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-07 1.1.0
2021-04-30 1.0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-10 2.1.0
2019-02-14 2.0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-19 0.1.1
2017-10-21 0.1.0
Title: Simulation of Simple and Complex Survival Data
Description: Simulation of simple and complex survival data including recurrent and multiple events and competing risks. See Moriña D, Navarro A. (2014) <doi:10.18637/jss.v059.i02>.
Author: David Moriña Soler [aut, cre] (<https://orcid.org/0000-0001-5949-7443>),
Albert Navarro [aut]
Maintainer: David Moriña Soler <dmorina@ub.edu>
Diff between survsim versions 1.1.5 dated 2018-05-17 and 1.1.6 dated 2021-05-14
DESCRIPTION | 24 ++++++++++++++------ MD5 | 18 +++++++-------- R/crisk.ncens.sim.R | 57 +++++++++++++++++++++++++------------------------ R/crisk.sim.R | 4 +-- R/mult.ev.sim.R | 4 +-- R/rec.ev.cens.sim.R | 6 ++--- R/rec.ev.ncens.sim.R | 6 ++--- R/simple.surv.sim.R | 4 +-- inst/CITATION | 2 - man/survsim-package.Rd | 10 ++++---- 10 files changed, 74 insertions(+), 61 deletions(-)
Title: Average Bioequivalence with Expanding Limits (ABEL)
Description: Performs comparative bioavailability calculations for Average Bioequivalence with
Expanding Limits (ABEL). Implemented are 'Method A' and 'Method B' and the detection of outliers.
If the design allows, assessment of the empiric Type I Error and iteratively adjusting alpha to
control the consumer risk.
Average Bioequivalence - optionally with a tighter (narrow therapeutic index drugs) or wider
acceptance range (Gulf Cooperation Council, South Africa: Cmax) - is implemented as well.
Author: Helmut Schütz [aut, cre] (<https://orcid.org/0000-0002-1167-7880>),
Michael Tomashevskiy [ctb],
Detlew Labes [ctb] (<https://orcid.org/0000-0003-2169-426X>)
Maintainer: Helmut Schütz <helmut.schuetz@bebac.at>
Diff between replicateBE versions 1.0.15 dated 2020-07-24 and 1.0.17 dated 2021-05-14
replicateBE-1.0.15/replicateBE/man/figures/README-unnamed-chunk-9-1.png |only replicateBE-1.0.17/replicateBE/DESCRIPTION | 8 replicateBE-1.0.17/replicateBE/MD5 | 28 replicateBE-1.0.17/replicateBE/NEWS.md | 11 replicateBE-1.0.17/replicateBE/R/method.B.R | 8 replicateBE-1.0.17/replicateBE/README.md | 473 ++++--- replicateBE-1.0.17/replicateBE/build/partial.rdb |binary replicateBE-1.0.17/replicateBE/build/vignette.rds |binary replicateBE-1.0.17/replicateBE/inst/doc/vignette.R | 34 replicateBE-1.0.17/replicateBE/inst/doc/vignette.Rmd | 150 +- replicateBE-1.0.17/replicateBE/inst/doc/vignette.html | 663 +++++----- replicateBE-1.0.17/replicateBE/man/ABE.Rd | 4 replicateBE-1.0.17/replicateBE/man/figures/README-example2-1.png |only replicateBE-1.0.17/replicateBE/man/method.A.Rd | 52 replicateBE-1.0.17/replicateBE/man/method.B.Rd | 33 replicateBE-1.0.17/replicateBE/vignettes/vignette.Rmd | 150 +- 16 files changed, 890 insertions(+), 724 deletions(-)
Title: Solver for Partially Observable Markov Decision Processes
(POMDP)
Description: Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Processes (POMDP) models. The package includes pomdp-solve to solve POMDPs using a variety of exact and approximate value iteration algorithms. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Author: Michael Hahsler [aut, cph, cre],
Hossein Kamalzadeh [aut, cph],
Anthony R. Cassandra [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between pomdp versions 0.99.0 dated 2020-05-07 and 0.99.1 dated 2021-05-14
DESCRIPTION | 35 +-- MD5 | 92 ++++----- NAMESPACE | 73 +++---- NEWS.md | 16 + R/AAAimports.R |only R/AAAinstalled.R |only R/MDP.R | 5 R/POMDP.R | 24 +- R/colors.R | 4 R/plot_belief_space.R | 12 - R/plot_policy_graph.R | 6 R/policy.R | 17 - R/policy_graph.R | 74 +++++-- R/print.text.R | 1 R/read_write_POMDP.R | 37 ++- R/read_write_pomdp_solve.R | 4 R/reward.R | 8 R/sample_belief_space.R | 2 R/solve_POMDP.R | 49 ++-- R/solve_SARSOP.R |only R/transition_matrix.R | 43 +++- R/update_belief.R | 28 +- README.md | 11 - build/vignette.rds |binary data/Three_doors.rda |binary data/Tiger.rda |binary inst/doc/POMDP.Rmd | 4 inst/doc/POMDP.html | 322 ++++++++++++++++++-------------- man/MDP.Rd | 2 man/POMDP.Rd | 8 man/plot_belief_space.Rd | 4 man/plot_policy_graph.Rd | 3 man/policy.Rd | 15 - man/reward.Rd | 4 man/simulate_POMDP.Rd | 12 - man/solve_POMDP.Rd | 33 +-- man/solve_SARSOP.Rd |only man/transition_matrix.Rd | 4 man/update_belief.Rd | 17 + man/write_POMDP.Rd | 2 src/Makevars | 11 - src/install.libs.R | 1 src/pomdp-solve/Makefile | 3 src/pomdp-solve/config-file.h | 2 src/pomdp-solve/program-options.h | 2 tests/testthat/test-matrix_extractors.R | 89 ++++++++ tests/testthat/test-read_write_POMDP.R |only tests/testthat/test-solve_POMDP.R | 4 tests/testthat/test-solve_SARSOP.R |only vignettes/POMDP.Rmd | 4 50 files changed, 671 insertions(+), 416 deletions(-)
Title: Partial Orders in Socio-Economics
Description: Implements tools for the analysis of partially ordered data, with a particular focus on the evaluation of multidimensional systems of indicators and on the analysis of poverty. References, Fattore M. (2016) <doi:10.1007/s11205-015-1059-6> Fattore M., Arcagni A. (2016) <doi:10.1007/s11205-016-1501-4> Arcagni A. (2017) <doi:10.1007/978-3-319-45421-4_19>.
Author: Alberto Arcagni [aut, cre],
Marco Fattore [aut]
Maintainer: Alberto Arcagni <alberto.arcagni@uniroma1.it>
Diff between parsec versions 1.2.3 dated 2019-04-29 and 1.2.4 dated 2021-05-14
parsec-1.2.3/parsec/R/parsec-internal.R |only parsec-1.2.4/parsec/DESCRIPTION | 12 ++++++------ parsec-1.2.4/parsec/MD5 | 9 ++++----- parsec-1.2.4/parsec/man/evaluation.Rd | 2 +- parsec-1.2.4/parsec/man/idn.Rd | 2 +- parsec-1.2.4/parsec/man/parsec-package.Rd | 3 ++- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: Easy Computation of Alpha Functional Diversity Indices
Description: Computes 5 alpha-functional diversity indices: Functional
Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic),
Functional Dispersion (FDis) and Rao's entropy (Q) (reviewed in Villéger
et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient and modular functions
to compute functional diversity indices.
Author: Matthias Grenié [aut, cre] (<https://orcid.org/0000-0002-4659-7522>),
Hugo Gruson [aut] (<https://orcid.org/0000-0002-4094-1476>)
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>
Diff between fundiversity versions 0.0.1 dated 2021-02-15 and 0.2.0 dated 2021-05-14
DESCRIPTION | 19 - MD5 | 53 +++- NAMESPACE | 4 NEWS.md |only R/dev_utils.R |only R/fd_chull_intersect.R |only R/fd_fdis.R |only R/fd_fdiv.R | 6 R/fd_feve.R | 5 R/fd_fric.R | 18 + R/fd_fric_intersect.R |only R/zzz.R |only README.md | 95 ++++++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/fundiversity.R | 23 + inst/doc/fundiversity.Rmd | 110 +++++++-- inst/doc/fundiversity.html | 394 +++++++++++++++++++++------------- inst/doc/parallel.Rmd |only inst/doc/parallel.html |only man/fd_fdis.Rd |only man/fd_fdiv.Rd | 20 + man/fd_feve.Rd | 11 man/fd_fric.Rd | 20 + man/fd_fric_intersect.Rd |only man/fd_raoq.Rd | 3 man/rmdchunks |only tests/testthat.R | 7 tests/testthat/test-chull.R |only tests/testthat/test-chull_intersect.R |only tests/testthat/test-fdis.R |only tests/testthat/test-fdiv.R | 2 tests/testthat/test-fric_intersect.R |only vignettes/fundiversity.Rmd | 110 +++++++-- vignettes/parallel.Rmd |only 36 files changed, 646 insertions(+), 254 deletions(-)
Title: Generation of ENVIREM Variables
Description: Generation of bioclimatic rasters that are complementary to the typical 19 bioclim variables.
Author: Pascal O. Title, Jordan B. Bemmels
Maintainer: Pascal Title <pascal.title@stonybrook.edu>
Diff between envirem versions 2.2 dated 2020-06-04 and 2.3 dated 2021-05-14
DESCRIPTION | 13 +-- MD5 | 182 +++++++++++++++++++++--------------------- R/assignNames.R | 1 R/generateRasters.R | 57 +++++++++---- R/layerCreation.R | 52 +++++++++--- R/split_raster.R | 2 R/verifyFileStructure.R | 8 + inst/extdata/bio_1.tif |binary inst/extdata/bio_10.tif |binary inst/extdata/bio_11.tif |binary inst/extdata/bio_12.tif |binary inst/extdata/bio_13.tif |binary inst/extdata/bio_14.tif |binary inst/extdata/bio_15.tif |binary inst/extdata/bio_16.tif |binary inst/extdata/bio_17.tif |binary inst/extdata/bio_18.tif |binary inst/extdata/bio_19.tif |binary inst/extdata/bio_2.tif |binary inst/extdata/bio_3.tif |binary inst/extdata/bio_4.tif |binary inst/extdata/bio_5.tif |binary inst/extdata/bio_6.tif |binary inst/extdata/bio_7.tif |binary inst/extdata/bio_8.tif |binary inst/extdata/bio_9.tif |binary inst/extdata/elev.tif |binary inst/extdata/et_solrad_1.tif |binary inst/extdata/et_solrad_10.tif |binary inst/extdata/et_solrad_11.tif |binary inst/extdata/et_solrad_12.tif |binary inst/extdata/et_solrad_2.tif |binary inst/extdata/et_solrad_3.tif |binary inst/extdata/et_solrad_4.tif |binary inst/extdata/et_solrad_5.tif |binary inst/extdata/et_solrad_6.tif |binary inst/extdata/et_solrad_7.tif |binary inst/extdata/et_solrad_8.tif |binary inst/extdata/et_solrad_9.tif |binary inst/extdata/prec_1.tif |binary inst/extdata/prec_10.tif |binary inst/extdata/prec_11.tif |binary inst/extdata/prec_12.tif |binary inst/extdata/prec_2.tif |binary inst/extdata/prec_3.tif |binary inst/extdata/prec_4.tif |binary inst/extdata/prec_5.tif |binary inst/extdata/prec_6.tif |binary inst/extdata/prec_7.tif |binary inst/extdata/prec_8.tif |binary inst/extdata/prec_9.tif |binary inst/extdata/tmax_1.tif |binary inst/extdata/tmax_10.tif |binary inst/extdata/tmax_11.tif |binary inst/extdata/tmax_12.tif |binary inst/extdata/tmax_2.tif |binary inst/extdata/tmax_3.tif |binary inst/extdata/tmax_4.tif |binary inst/extdata/tmax_5.tif |binary inst/extdata/tmax_6.tif |binary inst/extdata/tmax_7.tif |binary inst/extdata/tmax_8.tif |binary inst/extdata/tmax_9.tif |binary inst/extdata/tmean_1.tif |binary inst/extdata/tmean_10.tif |binary inst/extdata/tmean_11.tif |binary inst/extdata/tmean_12.tif |binary inst/extdata/tmean_2.tif |binary inst/extdata/tmean_3.tif |binary inst/extdata/tmean_4.tif |binary inst/extdata/tmean_5.tif |binary inst/extdata/tmean_6.tif |binary inst/extdata/tmean_7.tif |binary inst/extdata/tmean_8.tif |binary inst/extdata/tmean_9.tif |binary inst/extdata/tmin_1.tif |binary inst/extdata/tmin_10.tif |binary inst/extdata/tmin_11.tif |binary inst/extdata/tmin_12.tif |binary inst/extdata/tmin_2.tif |binary inst/extdata/tmin_3.tif |binary inst/extdata/tmin_4.tif |binary inst/extdata/tmin_5.tif |binary inst/extdata/tmin_6.tif |binary inst/extdata/tmin_7.tif |binary inst/extdata/tmin_8.tif |binary inst/extdata/tmin_9.tif |binary man/assignNames.Rd | 1 man/generateRasters.Rd | 2 man/layerCreation.Rd | 12 ++ man/split_raster.Rd | 2 man/verifyFileStructure.Rd | 9 +- 92 files changed, 204 insertions(+), 137 deletions(-)
Title: Random Network Model Estimation, Selection and Parameter Tuning
Description: Model selection and parameter tuning procedures for a class of random network models. The model selection can be done by a general cross-validation framework called ECV from Li et. al. (2016) <arXiv:1612.04717> . Several other model-based and task-specific methods are also included, such as NCV from Chen and Lei (2016) <arXiv:1411.1715>, likelihood ratio method from Wang and Bickel (2015) <arXiv:1502.02069>, spectral methods from Le and Levina (2015) <arXiv:1507.00827>. Many network analysis methods are also implemented, such as the regularized spectral clustering (Amini et. al. 2013 <doi:10.1214/13-AOS1138>) and its degree corrected version and graphon neighborhood smoothing (Zhang et. al. 2015 <arXiv:1509.08588>). It also includes the consensus clustering of Gao et. al. (2014) <arXiv:1410.5837> and the method of moments estimation of nomination SBM of Li et. al. (2020) <arxiv:2008.03652>.
Author: Tianxi Li, Elizaveta Levina, Ji Zhu
Maintainer: Tianxi Li <tianxili@virginia.edu>
Diff between randnet versions 0.2 dated 2019-02-12 and 0.3 dated 2021-05-14
DESCRIPTION | 14 ++-- MD5 | 41 ++++++------ NAMESPACE | 4 - R/RCode.R | 145 +++++++++++++++++++++++++++++++++++++++++---- man/BHMC.estimate.Rd | 2 man/BlockModel.Gen.Rd | 4 - man/ConcensusClust.Rd | 2 man/DCSBM.estimate.Rd | 2 man/ECV.Rank.Rd | 4 - man/ECV.block.Rd | 4 - man/ECV.nSmooth.lowrank.Rd | 4 - man/LRBIC.Rd | 2 man/NCV.select.Rd | 2 man/NMI.Rd | 2 man/NSBM.Gen.Rd |only man/NSBM.estimate.Rd |only man/RDPG.Gen.Rd | 4 - man/RightSC.Rd |only man/SBM.estimate.Rd | 2 man/nSmooth.Rd | 2 man/randnet-package.Rd | 13 ++-- man/reg.SP.Rd | 10 ++- man/reg.SSP.Rd | 10 ++- 23 files changed, 207 insertions(+), 66 deletions(-)
Title: Projected Polya Tree for Circular Data
Description: Provides functionality for the prior and posterior projected Polya tree for the analysis of circular data (Nieto-Barajas and Nunez-Antonio (2019) <arXiv:1902.06020>).
Author: Karla Mayra Perez [aut, cre], Luis E. Nieto-Barajas [aut]
Maintainer: Karla Mayra Perez <karla.mayra25@gmail.com>
Diff between PPTcirc versions 0.1.0 dated 2020-11-09 and 0.2.0 dated 2021-05-14
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md |only R/dsimpostppt.R | 50 ++++++++++++++++++++++++++------------------------ R/postppt.plot.R | 38 +++++++++++++++++++++++++------------- man/postppt.plot.Rd | 14 ++++++++++++-- 6 files changed, 71 insertions(+), 46 deletions(-)
Title: Client for the 'Pangaea' Database
Description: Tools to interact with the 'Pangaea' Database
(<https://www.pangaea.de>), including functions for searching for data,
fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea'
'OAI-PMH' service.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Kara Woo [aut],
Andrew MacDonald [aut],
Naupaka Zimmerman [aut],
Gavin Simpson [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between pangaear versions 1.0.0 dated 2020-01-22 and 1.1.0 dated 2021-05-14
DESCRIPTION | 13 +++---- LICENSE | 4 +- MD5 | 16 ++++----- NEWS.md | 8 ++++ R/pg_data.R | 2 - R/pg_search_es.R | 2 - README.md | 90 ++++++++++++++++++++++++---------------------------- build/vignette.rds |binary man/pg_search_es.Rd | 4 -- 9 files changed, 68 insertions(+), 71 deletions(-)
Title: Text Analysis with Emphasis on POS Tagging, Readability, and
Lexical Diversity
Description: A set of tools to analyze texts. Includes, amongst others, functions for
automatic language detection, hyphenation, several indices of lexical diversity
(e.g., type token ratio, HD-D/vocd-D, MTLD) and readability (e.g., Flesch,
SMOG, LIX, Dale-Chall). Basic import functions for language corpora are also
provided, to enable frequency analyses (supports Celex and Leipzig Corpora
Collection file formats) and measures like tf-idf. Note: For full functionality
a local installation of TreeTagger is recommended. It is also recommended to
not load this package directly, but by loading one of the available language
support packages from the 'l10n' repository
<https://undocumeantit.github.io/repos/l10n/>. 'koRpus' also includes a plugin
for the R GUI and IDE RKWard, providing graphical dialogs for its basic
features. The respective R package 'rkward' cannot be installed directly from a
repository, as it is a part of RKWard. To make full use of this feature, please
install RKWard from <https://rkward.kde.org> (plugins are detected
automatically). Due to some restrictions on CRAN, the full package sources are
only available from the project homepage. To ask for help, report bugs, request
features, or discuss the development of the package, please subscribe to the
koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Author: Meik Michalke [aut, cre],
Earl Brown [ctb],
Alberto Mirisola [ctb],
Alexandre Brulet [ctb],
Laura Hauser [ctb]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between koRpus versions 0.13-6 dated 2021-05-09 and 0.13-7 dated 2021-05-14
ChangeLog | 10 ++++++++++ DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/02_method_readTagged.R | 4 ++-- R/koRpus-internal.R | 4 ++-- R/koRpus-internal.rdb.formulae.R | 4 ++-- R/koRpus-package.R | 4 ++-- R/read.corp.LCC.R | 12 ++++++------ R/read.corp.celex.R | 4 ++-- build/partial.rdb |binary inst/CITATION | 4 ++-- inst/NEWS.Rd | 13 +++++++++++++ inst/doc/koRpus_vignette.html | 4 ++-- man/koRpus-package.Rd | 4 ++-- man/readTagged-methods.Rd | 2 +- 15 files changed, 64 insertions(+), 41 deletions(-)
Title: Customize Your Web Apps with Fancy Effects
Description: Add fancy CSS effects to your 'shinydashboards' or 'shiny' apps.
100% compatible with 'shinydashboardPlus' and 'bs4Dash'.
Author: David Granjon [aut, cre],
RinteRface [cph]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between shinyEffects versions 0.1.0 dated 2018-11-18 and 0.2.0 dated 2021-05-14
shinyEffects-0.1.0/shinyEffects/build |only shinyEffects-0.1.0/shinyEffects/inst/doc |only shinyEffects-0.1.0/shinyEffects/vignettes |only shinyEffects-0.2.0/shinyEffects/DESCRIPTION | 28 +-- shinyEffects-0.2.0/shinyEffects/LICENSE |only shinyEffects-0.2.0/shinyEffects/MD5 | 45 +++-- shinyEffects-0.2.0/shinyEffects/NAMESPACE | 3 shinyEffects-0.2.0/shinyEffects/NEWS.md | 8 - shinyEffects-0.2.0/shinyEffects/R/deps.R |only shinyEffects-0.2.0/shinyEffects/R/manipulateCSS.R |only shinyEffects-0.2.0/shinyEffects/R/setBlur.R |only shinyEffects-0.2.0/shinyEffects/R/setPersp.R |only shinyEffects-0.2.0/shinyEffects/R/setPulse.R | 127 ++++++++++++---- shinyEffects-0.2.0/shinyEffects/R/setShadow.R | 37 +--- shinyEffects-0.2.0/shinyEffects/R/setShake.R | 37 +--- shinyEffects-0.2.0/shinyEffects/R/setZoom.R | 37 +--- shinyEffects-0.2.0/shinyEffects/R/shinyEffectsGallery.R | 2 shinyEffects-0.2.0/shinyEffects/R/utils.R |only shinyEffects-0.2.0/shinyEffects/R/zzz.R |only shinyEffects-0.2.0/shinyEffects/README.md | 20 +- shinyEffects-0.2.0/shinyEffects/inst/assets |only shinyEffects-0.2.0/shinyEffects/inst/examples/app.R | 70 ++------ shinyEffects-0.2.0/shinyEffects/man/blurContainer.Rd |only shinyEffects-0.2.0/shinyEffects/man/setBlur.Rd |only shinyEffects-0.2.0/shinyEffects/man/setPersp.Rd |only shinyEffects-0.2.0/shinyEffects/man/setPulse.Rd | 38 +--- shinyEffects-0.2.0/shinyEffects/man/setShadow.Rd | 37 +--- shinyEffects-0.2.0/shinyEffects/man/setShake.Rd | 37 +--- shinyEffects-0.2.0/shinyEffects/man/setZoom.Rd | 37 +--- 29 files changed, 269 insertions(+), 294 deletions(-)