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Title: Loading Screen for 'Shiny'
Description: Full screen and partial loading screens for 'Shiny' with spinners, progress bars, and notifications.
Author: John Coene [aut, cre],
Jinhwan Kim [ctb],
Victor Granda [ctb] (<https://orcid.org/0000-0002-0469-1991>)
Maintainer: John Coene <jcoenep@gmail.com>
Diff between waiter versions 0.2.3 dated 2021-07-21 and 0.2.4 dated 2021-10-04
waiter-0.2.3/waiter/inst/assets/butler |only waiter-0.2.3/waiter/inst/assets/hostess |only waiter-0.2.3/waiter/inst/assets/waiter |only waiter-0.2.4/waiter/DESCRIPTION | 12 ++-- waiter-0.2.4/waiter/MD5 | 45 +++++++++------- waiter-0.2.4/waiter/NAMESPACE | 12 ++++ waiter-0.2.4/waiter/NEWS.md | 17 ++++++ waiter-0.2.4/waiter/R/attendant.R |only waiter-0.2.4/waiter/R/hostess.R | 25 ++------- waiter-0.2.4/waiter/R/httr.R |only waiter-0.2.4/waiter/R/print.R | 5 - waiter-0.2.4/waiter/R/progress.R |only waiter-0.2.4/waiter/R/utils.R | 4 - waiter-0.2.4/waiter/R/waiter.R | 61 +++++++++++++++++++++-- waiter-0.2.4/waiter/R/waitress.R | 35 +++++++++++++ waiter-0.2.4/waiter/README.md | 18 +++--- waiter-0.2.4/waiter/build/vignette.rds |binary waiter-0.2.4/waiter/inst/packer/attendant.js |only waiter-0.2.4/waiter/inst/packer/hostess.js |only waiter-0.2.4/waiter/inst/packer/waiter.js | 2 waiter-0.2.4/waiter/inst/packer/waitress.js | 2 waiter-0.2.4/waiter/man/Attendant.Rd |only waiter-0.2.4/waiter/man/attendantBar.Rd |only waiter-0.2.4/waiter/man/httr_progress.Rd |only waiter-0.2.4/waiter/man/useAttendant.Rd |only waiter-0.2.4/waiter/man/waitressClass.Rd | 51 +++++++++++++++++++ waiter-0.2.4/waiter/man/withProgressAttendant.Rd |only waiter-0.2.4/waiter/man/withProgressWaitress.Rd |only waiter-0.2.4/waiter/man/withWaiter.Rd |only 29 files changed, 222 insertions(+), 67 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter@zoology.ubc.ca>
Diff between phylopath versions 1.1.2 dated 2019-12-06 and 1.1.3 dated 2021-10-04
DESCRIPTION | 10 - MD5 | 42 ++-- NEWS.md | 15 + R/DAG.R | 3 R/internal.R | 35 ++- R/phylopath.R | 20 +- R/print_and_plot.R | 21 +- build/vignette.rds |binary inst/doc/binary_models.html | 329 +++++++++---------------------------- inst/doc/intro_to_phylopath.html | 343 ++++++++++----------------------------- man/average.Rd | 6 man/cichlids.Rd | 4 man/cichlids_tree.Rd | 4 man/est_DAG.Rd | 2 man/phylo_path.Rd | 2 man/plot.DAG.Rd | 2 man/plot.fitted_DAG.Rd | 2 man/plot_model_set.Rd | 2 man/red_list.Rd | 4 man/red_list_tree.Rd | 4 man/rhino.Rd | 4 man/rhino_tree.Rd | 4 22 files changed, 287 insertions(+), 571 deletions(-)
Title: Create Interactive Graphs with 'Echarts JavaScript' Version 5
Description: Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes
36 chart types, themes, 'Shiny' proxies and animations.
Author: John Coene [aut, cre, cph],
Wei Su [ctb],
Helgasoft [ctb],
Xianying Tan [ctb] (<https://orcid.org/0000-0002-6072-3521>),
Robin Cura [ctb] (<https://orcid.org/0000-0001-5926-1828>),
Mathida Chuk [ctb]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between echarts4r versions 0.4.1 dated 2021-07-14 and 0.4.2 dated 2021-10-04
echarts4r-0.4.1/echarts4r/man/e_add.Rd |only echarts4r-0.4.2/echarts4r/DESCRIPTION | 16 echarts4r-0.4.2/echarts4r/MD5 | 123 +++---- echarts4r-0.4.2/echarts4r/NAMESPACE | 6 echarts4r-0.4.2/echarts4r/NEWS.md | 22 + echarts4r-0.4.2/echarts4r/R/add.R | 76 +++- echarts4r-0.4.2/echarts4r/R/add_.R | 6 echarts4r-0.4.2/echarts4r/R/color.R | 23 + echarts4r-0.4.2/echarts4r/R/echarts4r.R | 81 ++++ echarts4r-0.4.2/echarts4r/R/globe.R | 2 echarts4r-0.4.2/echarts4r/R/map.R | 2 echarts4r-0.4.2/echarts4r/R/mark.R | 23 - echarts4r-0.4.2/echarts4r/R/nesting.R | 74 ++++ echarts4r-0.4.2/echarts4r/R/opts.R | 88 ++++- echarts4r-0.4.2/echarts4r/R/utils.R | 47 ++ echarts4r-0.4.2/echarts4r/inst/htmlwidgets/echarts4r.js | 23 + echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/echarts-en.min.js | 4 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/i18n |only echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/azul.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/bee-inspired.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/blue.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/caravan.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/carp.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/cool.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/dark-blue.js | 10 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/dark-bold.js | 10 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/dark-digerati.js | 10 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/dark-fresh-cut.js | 10 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/dark-mushroom.js | 10 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/dark.js | 171 ++++++---- echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/eduardo.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/forest.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/fresh-cut.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/fruit.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/gray.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/green.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/helianthus.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/infographic.js | 6 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/inspired.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/jazz.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/london.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/macarons.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/macarons2.js | 38 +- echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/mint.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/red-velvet.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/red.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/roma.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/royal.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/sakura.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/shine.js | 14 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/tech-blue.js | 2 echarts4r-0.4.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/themes/vintage.js | 2 echarts4r-0.4.2/echarts4r/man/e_bar.Rd | 7 echarts4r-0.4.2/echarts4r/man/e_color.Rd | 12 echarts4r-0.4.2/echarts4r/man/e_dims.Rd |only echarts4r-0.4.2/echarts4r/man/e_gauge.Rd | 9 echarts4r-0.4.2/echarts4r/man/e_locale.Rd |only echarts4r-0.4.2/echarts4r/man/graph.Rd | 12 echarts4r-0.4.2/echarts4r/man/mark.Rd | 23 - echarts4r-0.4.2/echarts4r/man/nesting.Rd |only 60 files changed, 710 insertions(+), 298 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-20 0.2.1
2021-09-16 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-06 0.1.0
Title: Summary Plots with Adjusted Error Bars
Description: Computes standard error and confidence interval of various descriptive statistics under
various designs and sampling schemes. The main function, superbPlot(), can either return a plot
or a dataframe with the statistic and its precision interval so that other plotting package
can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109>
or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005)
<doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012)
<doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>,
Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding
<doi:10.20982/tqmp.15.1.p001> for specific references.
Author: Denis Cousineau [aut, cre],
Bradley Harding [ctb],
Marc-Andre Goulet [ctb],
Jesika Walker [art, pre]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>
Diff between superb versions 0.9.7.5 dated 2021-06-23 and 0.9.7.6 dated 2021-10-04
DESCRIPTION | 26 - MD5 | 83 +-- NEWS.md | 27 - R/superbData.R | 2 R/superbPlot.R | 12 R/superbShiny.R | 16 README.md | 33 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 17 inst/REFERENCES.bib | 33 + inst/doc/TheMakingOf.R | 46 - inst/doc/TheMakingOf.Rmd | 54 +- inst/doc/TheMakingOf.html | 70 +- inst/doc/Vignette1.Rmd | 2 inst/doc/Vignette1.html | 5 inst/doc/Vignette2.Rmd | 4 inst/doc/Vignette2.html | 10 inst/doc/Vignette3.Rmd | 2 inst/doc/Vignette3.html | 7 inst/doc/Vignette4.html | 4 inst/doc/Vignette5.html | 22 inst/doc/Vignette6.html | 50 +- inst/doc/Vignette8.html | 2 inst/doc/Vignette9.html | 10 inst/doc/VignetteA.R | 204 ++++++++ inst/doc/VignetteA.Rmd | 206 ++++++++ inst/doc/VignetteA.html | 30 - inst/doc/VignetteB.html | 4 inst/doc/VignetteC.R |only inst/doc/VignetteC.Rmd |only inst/doc/VignetteC.html |only inst/superbShiny/App.R | 250 ++++++---- inst/superbShiny/rsconnect/shinyapps.io/superbplot/superbshiny.dcf | 6 man/superb-package.Rd | 7 man/superbData.Rd | 2 man/superbPlot.Rd | 2 man/superbShiny.Rd | 8 tests/testthat/test_compatibility.R |only vignettes/TheMakingOf.Rmd | 54 +- vignettes/Vignette1.Rmd | 2 vignettes/Vignette2.Rmd | 4 vignettes/Vignette3.Rmd | 2 vignettes/VignetteA.Rmd | 206 ++++++++ vignettes/VignetteC.Rmd |only 45 files changed, 1156 insertions(+), 368 deletions(-)
Title: Analysis and Visualisation of Benchmark Experiments
Description: Implements methods for post-hoc analysis and
visualisation of benchmark experiments, for 'mlr3' and beyond.
Author: Sonabend Raphael [cre, aut] (<https://orcid.org/0000-0001-9225-4654>),
Florian Pfisterer [aut] (<https://orcid.org/0000-0001-8867-762X>),
Michel Lang [ctb] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [ctb] (<https://orcid.org/0000-0001-6002-6980>)
Maintainer: Sonabend Raphael <raphaelsonabend@gmail.com>
Diff between mlr3benchmark versions 0.1.2 dated 2021-04-19 and 0.1.3 dated 2021-10-04
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/BenchmarkAggr.R | 8 ++++---- R/autoplot.BenchmarkAggr.R | 2 +- README.md | 3 +-- man/BenchmarkAggr.Rd | 2 +- man/autoplot.BenchmarkAggr.Rd | 2 +- tests/testthat/test_BenchmarkAggr.R | 2 +- tests/testthat/test_autoplot_BenchmarkAggr.R | 24 ++++++++++++++++++++++-- 10 files changed, 49 insertions(+), 25 deletions(-)
Title: Easily Process a Batch of Cox Models
Description: A tool to operate a batch of univariate or multivariate Cox
models and return tidy result.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>)
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between ezcox versions 1.0.0 dated 2021-09-12 and 1.0.1 dated 2021-10-04
DESCRIPTION | 8 +- MD5 | 22 ++++---- NAMESPACE | 1 NEWS.md | 6 ++ R/cox_panel.R | 8 ++ R/ezcox.R | 1 README.md | 25 +++++++-- build/vignette.rds |binary inst/doc/ezcox.html | 14 ++--- inst/doc/ezforest.html | 25 ++------- inst/doc/ezgroup.html | 85 ++++++++++++++----------------- man/figures/README-unnamed-chunk-2-1.png |binary 12 files changed, 105 insertions(+), 90 deletions(-)
Title: Estimates Economic Variables for Word-of-Mouth-Campaigns
Description: Methods for estimating profit, profit-maximizing price, demand and consumer surplus of Word-of-Mouth-campaigns on mean-field networks.
Author: Michael Scholz [cre, aut],
Thomas Woehner [aut],
Ralf Peters [ctb]
Maintainer: Michael Scholz <michael.scholz@th-deg.de>
Diff between WordOfMouth versions 1.0.0 dated 2020-03-30 and 1.1.0 dated 2021-10-04
DESCRIPTION | 10 +-- MD5 | 20 +++--- NAMESPACE | 3 NEWS.md |only R/Classes.r | 13 +++- R/Computation.r | 102 ++++++++++++++++++++++++++++++-- R/WordOfMouth-package.r | 2 man/WoMCampaign-class.Rd | 14 ++++ man/WoMNetwork-class.Rd | 10 ++- man/WordOfMouth-package.Rd | 2 man/compareToFIMarket.Rd |only man/computeInformationCostsThreshold.Rd |only man/computeWoMIntensity.Rd |only 13 files changed, 154 insertions(+), 22 deletions(-)
Title: Fast Computation of Latent Correlations for Mixed Data
Description: The first stand-alone R package for computation of latent correlation that takes into account all variable types (continuous/binary/ordinal/zero-inflated),
comes with an optimized memory footprint, and is computationally efficient, essentially making latent correlation estimation almost as fast as rank-based correlation estimation.
The estimation is based on latent copula Gaussian models.
For continuous/binary types, see Fan, J., Liu, H., Ning, Y., and Zou, H. (2017) <doi:10.1111/rssb.12168>.
For ternary type, see Quan X., Booth J.G. and Wells M.T. (2018) <arXiv:1809.06255>.
For truncated type or zero-inflated type, see Yoon G., Carroll R.J. and Gaynanova I. (2020) <doi:10.1093/biomet/asaa007>.
For approximation method of computation, see Yoon G., Müller C.L. and Gaynanova I. (2021) <doi:10.1080/10618600.2021.1882468>.
Author: Mingze Huang [aut, cre] (<https://orcid.org/0000-0003-3919-1564>),
Grace Yoon [aut] (<https://orcid.org/0000-0003-3263-1352>),
Christian Müller [aut] (<https://orcid.org/0000-0002-3821-7083>),
Irina Gaynanova [aut] (<https://orcid.org/0000-0002-4116-0268>)
Maintainer: Mingze Huang <mingzehuang@gmail.com>
Diff between latentcor versions 1.0.0 dated 2021-08-26 and 1.1.0 dated 2021-10-04
latentcor-1.0.0/latentcor/R/GenData.R |only latentcor-1.0.0/latentcor/R/estR.R |only latentcor-1.0.0/latentcor/man/GenData.Rd |only latentcor-1.0.0/latentcor/man/estR.Rd |only latentcor-1.0.0/latentcor/man/examples/estR_ex.R |only latentcor-1.0.0/latentcor/tests/testthat/test_GenData.R |only latentcor-1.0.0/latentcor/tests/testthat/test_estR.R |only latentcor-1.0.0/latentcor/vignettes/tutorials |only latentcor-1.1.0/latentcor/DESCRIPTION | 12 latentcor-1.1.0/latentcor/MD5 | 50 latentcor-1.1.0/latentcor/NAMESPACE | 5 latentcor-1.1.0/latentcor/NEWS.md |only latentcor-1.1.0/latentcor/R/gen_data.R |only latentcor-1.1.0/latentcor/R/get_types.R |only latentcor-1.1.0/latentcor/R/internal.R | 22 latentcor-1.1.0/latentcor/R/latentcor.R |only latentcor-1.1.0/latentcor/README.md | 79 + latentcor-1.1.0/latentcor/build/partial.rdb |binary latentcor-1.1.0/latentcor/build/vignette.rds |binary latentcor-1.1.0/latentcor/inst/doc/latentcor.R | 101 - latentcor-1.1.0/latentcor/inst/doc/latentcor.Rmd | 562 --------- latentcor-1.1.0/latentcor/inst/doc/latentcor.html | 874 ++------------ latentcor-1.1.0/latentcor/inst/doc/latentcor_math.R |only latentcor-1.1.0/latentcor/inst/doc/latentcor_math.Rmd |only latentcor-1.1.0/latentcor/inst/doc/latentcor_math.html |only latentcor-1.1.0/latentcor/man/examples/latentcor_ex.R |only latentcor-1.1.0/latentcor/man/gen_data.Rd |only latentcor-1.1.0/latentcor/man/get_types.Rd |only latentcor-1.1.0/latentcor/man/latentcor.Rd |only latentcor-1.1.0/latentcor/tests/testthat/test_encodeX.R | 4 latentcor-1.1.0/latentcor/tests/testthat/test_gen_data.R |only latentcor-1.1.0/latentcor/tests/testthat/test_get_types.R |only latentcor-1.1.0/latentcor/tests/testthat/test_latentcor.R |only latentcor-1.1.0/latentcor/tests/testthat/test_zratio.R | 8 latentcor-1.1.0/latentcor/vignettes/latentcor.Rmd | 562 --------- latentcor-1.1.0/latentcor/vignettes/latentcor.bib | 35 latentcor-1.1.0/latentcor/vignettes/latentcor_math.Rmd |only latentcor-1.1.0/latentcor/vignettes/timing_plot.png |only 38 files changed, 491 insertions(+), 1823 deletions(-)
Title: Creates Log Files
Description: Contains functions to help create log files. The
package aims to overcome the difficulty of the base R sink() command. The
log_print() function will print to both the console and the file log,
without interfering in other write operations.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between logr versions 1.2.5 dated 2021-07-30 and 1.2.6 dated 2021-10-04
DESCRIPTION | 10 MD5 | 29 +- NAMESPACE | 2 NEWS.md | 8 R/logr.R | 258 +++++++-------------- R/supplements.R |only README.md | 5 build/vignette.rds |binary man/log_code.Rd |only man/log_path.Rd | 2 man/log_status.Rd | 2 tests/testthat/log/test.log |only tests/testthat/log/test10.log |only tests/testthat/log/test6.log |only tests/testthat/log/test7.log |only tests/testthat/log/test8.log |only tests/testthat/log/test8_orig.log |only tests/testthat/log/test9.log |only tests/testthat/test-logr.R | 466 ++++++++++++++++++-------------------- tests/testthat/test-supplements.R |only tests/testthat/test-unicode.R |only 21 files changed, 353 insertions(+), 429 deletions(-)
Title: Character String Processing Facilities
Description: A collection of character string/text/natural language
processing tools for pattern searching (e.g., with 'Java'-like regular
expressions or the 'Unicode' collation algorithm), random string generation,
case mapping, string transliteration, concatenation, sorting, padding,
wrapping, Unicode normalisation, date-time formatting and parsing,
and many more. They are fast, consistent, convenient, and -
thanks to 'ICU' (International Components for Unicode) -
portable across all locales and platforms.
Author: Marek Gagolewski [aut, cre, cph] (<https://orcid.org/0000-0003-0637-6028>),
Bartek Tartanus [ctb], and others (stringi source code);
Unicode, Inc. and others (ICU4C source code, Unicode Character Database)
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringi versions 1.7.4 dated 2021-08-25 and 1.7.5 dated 2021-10-04
DESCRIPTION | 22 ++-- INSTALL | 2 MD5 | 31 +++--- NEWS | 29 +++++- R/stringi-package.R | 12 +- configure | 36 ++++--- configure.ac | 36 +++---- inst/AUTHORS | 2 inst/CITATION | 12 ++ man/about_stringi.Rd | 12 +- src/stri_container_utf8.cpp | 1 src/stri_cpp.txt | 1 src/stri_external.h | 4 src/stri_string8.cpp |only src/stri_string8.h | 199 +++----------------------------------------- tools/AC_CXX_HAVE_STL.m4 | 33 +++---- tools/AC_CXX_NAMESPACES.m4 | 10 +- 17 files changed, 164 insertions(+), 278 deletions(-)
Title: 'sf'-Based Interface to the 'HERE' REST APIs
Description: Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
(1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API;
(2) route directions, travel distance or time matrices and isolines using the 'Routing', 'Matrix Routing' and 'Isoline Routing' APIs;
(3) request real-time traffic flow and incident information from the 'Traffic' API;
(4) find request public transport connections and nearby stations from the 'Public Transit' API;
(5) request intermodal routes using the 'Intermodal Routing' API;
(6) get weather forecasts, reports on current weather conditions, astronomical
information and alerts at a specific location from the 'Destination Weather' API.
Locations, routes and isolines are returned as 'sf' objects.
Author: Merlin Unterfinger [aut, cre] (<https://orcid.org/0000-0003-2020-2366>),
Daniel Possenriede [ctb] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between hereR versions 0.8.0 dated 2021-09-28 and 0.8.1 dated 2021-10-04
DESCRIPTION | 12 +- MD5 | 8 - NEWS.md | 79 +++++++------- README.md | 286 +++++++++++++++++++++++++-------------------------- man/hereR-package.Rd | 6 - 5 files changed, 198 insertions(+), 193 deletions(-)
Title: Functional Regression for Irregularly Timed Data
Description: Performs functional regression, and some related
approaches, for intensive longitudinal data (see the book by Walls & Schafer,
2006, Models for Intensive Longitudinal Data, Oxford) when such data is not
necessarily observed on an equally spaced grid of times. The
approach generally follows the ideas of Goldsmith, Bobb, Crainiceanu,
Caffo, and Reich (2011)<DOI:10.1198/jcgs.2010.10007> and the approach taken in their sample code, but
with some modifications to make it more feasible to use with long rather
than wide, non-rectangular longitudinal datasets with unequal and
potentially random measurement times. It also allows easy plotting of the
correlation between the smoothed covariate and the outcome as a function of
time, which can add additional insights on how to interpret a functional
regression. Additionally, it also provides several permutation tests for
the significance of the functional predictor. The heuristic interpretation
of ``time'' is used to describe the index of the functional predictor, but
the same methods can equally be used for another unidimensional continuous
index, such as space along a north-south axis. Note that most of the functionality
of this package has been superseded by added features after 2016 in the 'pfr' function by
Jonathan Gellar, Mathew W. McLean, Jeff Goldsmith, and Fabian Scheipl, in the
'refund' package built by Jeff Goldsmith and co-authors and maintained by Julia Wrobel.
The development of the funreg package in 2015 and 2016 was part of a research
project supported by Award R03 CA171809-01 from the National Cancer Institute and Award P50
DA010075 from the National Institute on Drug Abuse. The content is solely the responsibility of the
authors and does not necessarily represent the official views of the
National Institute on Drug Abuse, the National Cancer Institute, or the
National Institutes of Health.
Author: John Dziak [aut, cre] (<https://orcid.org/0000-0003-0762-5495>),
Mariya Shiyko [aut]
Maintainer: John Dziak <dziakj1@gmail.com>
Diff between funreg versions 1.2 dated 2016-08-24 and 1.2.2 dated 2021-10-04
DESCRIPTION | 32 +++++++++------- MD5 | 60 +++++++++++++++--------------- NAMESPACE | 26 ++++++++++--- R/CoefFunReg.r | 3 - R/FittedFunEigen.r | 1 R/FittedFunReg.r | 2 - R/FunEigen.r | 4 +- R/FunReg.r | 12 +++--- R/FunRegPermutation.r | 7 +-- R/GenerateDataForDemonstration.r | 1 R/MarginalCorFuneigen.r | 3 + R/PlotFunEigen.r | 2 - R/PlotFunReg.r | 2 - R/SummaryFunReg.r | 4 +- man/SampleFunregData.Rd | 27 +++++++------ man/coef.funreg.Rd | 3 - man/fitted.funeigen.Rd | 27 ++++++------- man/fitted.funreg.Rd | 11 ++--- man/funeigen.Rd | 12 ++---- man/funreg.Rd | 65 +++++++++++++++++++-------------- man/funreg.permutation.Rd | 39 +++++++++---------- man/generate.data.for.demonstration.Rd | 40 +++++++++++--------- man/make.funreg.basis.Rd | 21 +++++----- man/marginal.cor.Rd | 9 ++-- man/marginal.cor.funeigen.Rd | 29 +++++++------- man/num.functional.covs.in.model.Rd | 7 +-- man/plot.funeigen.Rd | 20 ++++------ man/plot.funreg.Rd | 13 +++--- man/print.funreg.Rd | 5 +- man/redo.funreg.Rd | 11 ++--- man/summary.funreg.Rd | 19 ++++----- 31 files changed, 269 insertions(+), 248 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses. The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: František Bartoš [aut, cre] (<https://orcid.org/0000-0002-0018-5573>)
Maintainer: František Bartoš <f.bartos96@gmail.com>
Diff between BayesTools versions 0.1.1 dated 2021-07-13 and 0.1.2 dated 2021-10-04
DESCRIPTION | 6 MD5 | 39 ++-- NAMESPACE | 1 NEWS.md | 11 + R/JAGS-fit.R | 4 R/JAGS-marglik.R | 27 +-- R/interpret.R |only R/model-averaging-plots.R | 88 ++++++---- R/model-averaging.R | 4 R/priors-density.R | 2 R/priors-plot.R | 14 - R/summary-tables.R | 4 man/interpret.Rd |only man/plot_models.Rd | 13 + tests/testthat/_snaps/model-averaging-plots/model-averaging-plot-models-10.svg |only tests/testthat/_snaps/model-averaging-plots/model-averaging-plot-models-9.svg |only tests/testthat/_snaps/model-averaging-plots/model-averaging-plot-posterior-simple-8.svg | 26 +- tests/testthat/_snaps/model-averaging-plots/model-averaging-plot-prior-simple-3.svg | 26 +- tests/testthat/_snaps/model-averaging-plots/model-averaging-plot-prior-simple-4.svg | 16 - tests/testthat/_snaps/priors-plot/priors-plot-6-7.svg |only tests/testthat/test-model-averaging-plots.R | 12 + tests/testthat/test-priors-plot.R | 1 tests/testthat/test-summary-tables.R | 38 ++++ 23 files changed, 207 insertions(+), 125 deletions(-)
Title: Tropical Fisheries Analysis
Description: A compilation of fish stock assessment methods for the
analysis of length-frequency data in the context of data-poor
fisheries. Includes methods and examples included in the FAO
Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish
stock assessment" (<http://www.fao.org/documents/card/en/c/9bb12a06-2f05-5dcb-a6ca-2d6dd3080f65/>),
as well as other more recent methods.
Author: Tobias K. Mildenberger [aut, cre], Marc H. Taylor [aut], Matthias Wolff [aut]
Maintainer: Tobias K. Mildenberger <t.k.mildenberger@gmail.com>
Diff between TropFishR versions 1.6.2 dated 2020-01-28 and 1.6.3 dated 2021-10-04
DESCRIPTION | 24 MD5 | 119 +- NAMESPACE | 3 NEWS.md |only R/Bhattacharya.R | 6 R/ELEFAN.R | 13 R/ELEFAN_SA.R | 362 +++---- R/VBGF.R | 10 R/VPA.R | 60 - R/Z_CPUE.R | 17 R/catchCurve.R | 5 R/growth_length_age.R | 68 - R/lfqCreate.R | 2 R/lfqModify.R | 2 R/plot.VPA.R | 2 R/plot.lfq.R | 1 R/plot.predict_mod.R | 206 ++-- R/predict_mod.R | 447 +++++++-- R/stock_sim.R | 168 ++- README.md | 15 build/vignette.rds |binary inst/doc/Using_TropFishR_ELEFAN_functions.R | 1 inst/doc/Using_TropFishR_ELEFAN_functions.Rmd | 66 - inst/doc/Using_TropFishR_ELEFAN_functions.html | 1214 ++++++++++++------------- inst/doc/lfqData.Rmd | 60 - inst/doc/lfqData.html | 579 +++++------ inst/doc/tutorial.R | 303 +++--- inst/doc/tutorial.Rmd | 529 ++++++---- inst/doc/tutorial.html | 1110 +++++++++++----------- man/VBGF.Rd | 4 man/alba.Rd | 6 man/bream.Rd | 6 man/catchCurve.Rd | 1 man/emperor.Rd | 6 man/gillnet.Rd | 6 man/goatfish.Rd | 6 man/growth_length_age.Rd | 8 man/haddock.Rd | 6 man/hake.Rd | 6 man/plot.predict_mod.Rd | 73 - man/predict_mod.Rd | 6 man/shrimps.Rd | 6 man/synCAA1.Rd | 6 man/synCAA2.Rd | 6 man/synCPUE.Rd | 6 man/synLFQ1.Rd | 6 man/synLFQ2.Rd | 6 man/synLFQ3.Rd | 6 man/synLFQ4.Rd | 6 man/synLFQ5.Rd | 6 man/synLFQ6.Rd | 6 man/synLFQ7.Rd | 6 man/synLFQ8.Rd | 6 man/tilapia.Rd | 6 man/trammelnet.Rd | 6 man/trawl_fishery_Java.Rd | 6 man/whiting.Rd | 6 vignettes/TropFishR.bib | 8 vignettes/Using_TropFishR_ELEFAN_functions.Rmd | 66 - vignettes/lfqData.Rmd | 60 - vignettes/tutorial.Rmd | 529 ++++++---- 61 files changed, 3392 insertions(+), 2893 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing
framework for R that is easy to learn and use, and integrates with
your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd],
R Core team [ctb] (Implementation of utils::recover())
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 3.0.4 dated 2021-07-01 and 3.1.0 dated 2021-10-04
DESCRIPTION | 17 +- MD5 | 157 ++++++++++++++------------ NEWS.md | 100 ++++++++++++++++- R/compare.R | 2 R/expect-condition.R | 6 - R/expect-self-test.R | 8 - R/expectation.R | 36 +++--- R/local.R | 18 +-- R/mock.R | 27 ---- R/quasi-label.R | 47 ++++++-- R/reporter-check.R | 12 +- R/reporter-progress.R | 60 ++++++---- R/reporter-stop.R | 11 + R/reporter-zzz.R | 16 +- R/skip.R | 45 +++++-- R/snapshot-cleanup.R |only R/snapshot-file-snaps.R |only R/snapshot-file.R | 38 +----- R/snapshot-reporter.R | 168 +++++++++------------------- R/snapshot-serialize.R | 24 ++++ R/snapshot.R | 125 +++++++++++++++------ R/test-files.R | 2 R/test-that.R | 32 ++--- R/utils.R | 7 + README.md | 3 build/vignette.rds |binary inst/doc/custom-expectation.html | 2 inst/doc/skipping.html | 2 inst/doc/snapshotting.R | 10 - inst/doc/snapshotting.Rmd | 13 -- inst/doc/snapshotting.html | 169 +++++++++++++++++------------ inst/doc/test-fixtures.Rmd | 2 inst/doc/test-fixtures.html | 22 +-- inst/doc/third-edition.R | 29 ++++ inst/doc/third-edition.Rmd | 48 ++++++++ inst/doc/third-edition.html | 114 +++++++++++++------ man/StopReporter.Rd | 4 man/compare.Rd | 2 man/expect_error.Rd | 2 man/expect_snapshot.Rd | 47 ++++++-- man/expect_snapshot_file.Rd | 8 + man/local_snapshotter.Rd | 2 man/local_test_context.Rd | 11 + man/skip.Rd | 11 + man/test_that.Rd | 28 ++-- man/with_mock.Rd | 28 ---- tests/testthat/_snaps/R4.0 |only tests/testthat/_snaps/quasi-label.md |only tests/testthat/_snaps/reporter-check.md | 16 +- tests/testthat/_snaps/reporter-junit.md | 9 + tests/testthat/_snaps/reporter-location.md | 1 tests/testthat/_snaps/reporter-minimal.md | 2 tests/testthat/_snaps/reporter-progress.md | 159 ++++++++++++++++----------- tests/testthat/_snaps/reporter-rstudio.md | 5 tests/testthat/_snaps/reporter-silent.md | 2 tests/testthat/_snaps/reporter-stop.md | 21 --- tests/testthat/_snaps/reporter-summary.md | 20 ++- tests/testthat/_snaps/reporter-tap.md | 7 - tests/testthat/_snaps/reporter-teamcity.md | 5 tests/testthat/_snaps/reporter.md | 4 tests/testthat/_snaps/skip.md | 7 + tests/testthat/_snaps/snapshot-cleanup.md |only tests/testthat/_snaps/snapshot.md | 24 ++++ tests/testthat/reporters/fail-many.R | 2 tests/testthat/reporters/skips.R |only tests/testthat/test-expect-condition.R | 34 +++++ tests/testthat/test-expectation.R | 8 + tests/testthat/test-local.R | 1 tests/testthat/test-parallel.R | 4 tests/testthat/test-quasi-label.R | 38 ++++++ tests/testthat/test-reporter-list.R | 2 tests/testthat/test-reporter-progress.R | 16 ++ tests/testthat/test-reporter-stop.R | 11 + tests/testthat/test-skip.R | 23 +++ tests/testthat/test-snapshot-cleanup.R |only tests/testthat/test-snapshot-file-snaps.R |only tests/testthat/test-snapshot-file.R | 65 +++-------- tests/testthat/test-snapshot-manage.R | 4 tests/testthat/test-snapshot-reporter.R | 32 ++--- tests/testthat/test-snapshot.R | 23 +++ vignettes/snapshotting.Rmd | 13 -- vignettes/test-fixtures.Rmd | 2 vignettes/third-edition.Rmd | 48 ++++++++ 83 files changed, 1340 insertions(+), 783 deletions(-)
Title: Predict Dominant Direction of Reactions of a Biochemical Network
Description: Biologically relevant, yet mathematically sound constraints are used
to compute the propensity and thence infer the dominant direction of reactions
of a generic biochemical network. The reactions must be unique and their
number must exceed that of the reactants,i.e., reactions >= reactants + 2.
'ReDirection', computes the null space of a user-defined stoichiometry
matrix. The spanning non-zero and unique reaction vectors (RVs) are
combinatorially summed to generate one or more subspaces recursively.
Every reaction is represented as a sequence of identical components
across all RVs of a particular subspace. The terms are evaluated with
(biologically relevant bounds, linear maps, tests of convergence, descriptive
statistics, vector norms) and the terms are classified into forward-, reverse-
and equivalent-subsets. Since, these are mutually exclusive the probability
of occurrence is binary (all, 1; none, 0).
The combined propensity of a reaction is the p1-norm of the
sub-propensities, i.e., sum of the products of the probability and maximum
numeric value of a subset (least upper bound, greatest lower bound). This,
if strictly positive is the probable rate constant, is used to infer dominant
direction and annotate a reaction as "Forward (f)", "Reverse (b)" or
"Equivalent (e)".
The inherent computational complexity (NP-hard) per iteration suggests
that a suitable value for the number of reactions is around 20.
Three functions comprise ReDirection. These are check_matrix() and
reaction_vector() which are internal, and calculate_reaction_vector()
which is external.
Author: Siddhartha Kundu <2021: Manuscript Under Preparation>
Maintainer: Siddhartha Kundu <siddhartha_kundu@aiims.edu>
Diff between ReDirection versions 1.0.0 dated 2021-09-29 and 1.0.1 dated 2021-10-04
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/calculate_reaction_vector.R | 11 ++++++----- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: Quality Report Generation for MaxQuant and mzTab Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015)
<doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow [aut, cre],
Juliane Schmachtenberg [ctb],
Swenja Wagner [ctb],
Patricia Scheil [ctb],
Tom Waschischek [ctb],
Guido Mastrobuoni [dtc, rev]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between PTXQC versions 1.0.10 dated 2021-06-02 and 1.0.11 dated 2021-10-04
PTXQC-1.0.10/PTXQC/inst/examples/report_v1.0.0__txt_5files_withMatch-100min.html |only PTXQC-1.0.10/PTXQC/inst/examples/report_v1.0.0__txt_5files_withMatch-100min.pdf |only PTXQC-1.0.11/PTXQC/DESCRIPTION | 12 PTXQC-1.0.11/PTXQC/MD5 | 92 +-- PTXQC-1.0.11/PTXQC/NAMESPACE | 11 PTXQC-1.0.11/PTXQC/NEWS | 5 PTXQC-1.0.11/PTXQC/R/MzQC_classes.R | 105 ++- PTXQC-1.0.11/PTXQC/R/PTXQC.R | 3 PTXQC-1.0.11/PTXQC/R/createReport.R | 68 +- PTXQC-1.0.11/PTXQC/R/createYaml.R | 6 PTXQC-1.0.11/PTXQC/R/fcn_MQ.R | 2 PTXQC-1.0.11/PTXQC/R/fcn_MQalign.R | 2 PTXQC-1.0.11/PTXQC/R/fcn_misc.R | 55 + PTXQC-1.0.11/PTXQC/R/fcn_mqpar.R | 41 - PTXQC-1.0.11/PTXQC/R/fcn_plots.R | 13 PTXQC-1.0.11/PTXQC/R/fcn_qualities.R | 2 PTXQC-1.0.11/PTXQC/R/mzQC.R | 291 +++++++++- PTXQC-1.0.11/PTXQC/R/qcMetric.R | 20 PTXQC-1.0.11/PTXQC/R/qcMetric_EVD.R | 12 PTXQC-1.0.11/PTXQC/R/qcMetric_MSMS.R | 41 - PTXQC-1.0.11/PTXQC/R/qcMetric_MSMSScans.R | 10 PTXQC-1.0.11/PTXQC/README.md | 10 PTXQC-1.0.11/PTXQC/inst/cv |only PTXQC-1.0.11/PTXQC/inst/doc/PTXQC-Basic_Guide_for_R_users.html | 68 -- PTXQC-1.0.11/PTXQC/inst/doc/PTXQC-CustomizeReport.html | 68 -- PTXQC-1.0.11/PTXQC/inst/doc/PTXQC-DragNDrop.html | 68 -- PTXQC-1.0.11/PTXQC/inst/doc/PTXQC-FAQ.html | 68 -- PTXQC-1.0.11/PTXQC/inst/doc/PTXQC-Input_And_Output_Data.html | 68 -- PTXQC-1.0.11/PTXQC/inst/doc/PTXQC-ListOfMetrics.html | 68 -- PTXQC-1.0.11/PTXQC/inst/examples/README.md | 4 PTXQC-1.0.11/PTXQC/inst/examples/report_ecoli_small.mzQC |only PTXQC-1.0.11/PTXQC/inst/examples/report_v1.0.10__txt_5files_withMatch-100min.html |only PTXQC-1.0.11/PTXQC/inst/examples/report_v1.0.10__txt_5files_withMatch-100min.pdf |only PTXQC-1.0.11/PTXQC/man/CVDictionarySingleton.Rd |only PTXQC-1.0.11/PTXQC/man/MzQCcontrolledVocabulary-class.Rd | 58 - PTXQC-1.0.11/PTXQC/man/MzQCmetadata-class.Rd | 46 - PTXQC-1.0.11/PTXQC/man/MzQCmzQC-class.Rd | 62 +- PTXQC-1.0.11/PTXQC/man/QCMetaFilenames.Rd |only PTXQC-1.0.11/PTXQC/man/assembleMZQC.Rd |only PTXQC-1.0.11/PTXQC/man/fromDatatoMzQC.Rd | 48 - PTXQC-1.0.11/PTXQC/man/getCVDictionary.Rd |only PTXQC-1.0.11/PTXQC/man/getCVTemplate.Rd |only PTXQC-1.0.11/PTXQC/man/getMQPARValue.Rd | 60 +- PTXQC-1.0.11/PTXQC/man/getQualityMetricTemplate.Rd |only PTXQC-1.0.11/PTXQC/man/getReportFilenames.Rd | 74 +- PTXQC-1.0.11/PTXQC/man/getRunQualityTemplate.Rd |only PTXQC-1.0.11/PTXQC/man/hasFileSuffix.Rd |only PTXQC-1.0.11/PTXQC/man/isValidMzQC.Rd | 73 +- PTXQC-1.0.11/PTXQC/man/parseOBO.Rd | 34 - PTXQC-1.0.11/PTXQC/man/qcMetric-class.Rd | 126 ++-- PTXQC-1.0.11/PTXQC/man/qualUniform.Rd | 92 +-- PTXQC-1.0.11/PTXQC/man/removeSuffix.Rd |only PTXQC-1.0.11/PTXQC/man/suffixToCV.Rd |only PTXQC-1.0.11/PTXQC/man/writeMZQC.Rd |only PTXQC-1.0.11/PTXQC/tests/testthat/test_computeQC.R | 24 55 files changed, 1124 insertions(+), 786 deletions(-)
Title: Cytobank API Wrapper for R
Description: Tools to interface with Cytobank's API via R, organized by various
endpoints that represent various areas of Cytobank functionality. Learn more
about Cytobank at <https://www.beckman.com/flow-cytometry/software/cytobank-premium>.
Author: Qihao Qi [aut, cre],
Stefanie Trop [aut],
Louis Liu [aut]
Maintainer: Qihao Qi <qqi@beckman.com>
Diff between CytobankAPI versions 1.3.0 dated 2018-11-23 and 1.4.0 dated 2021-10-04
DESCRIPTION | 41 +- MD5 | 128 +++---- NAMESPACE | 10 R/AdvancedAnalysis-class.R | 5 R/CITRUS-class.R | 5 R/DimensionalityReduction-class.R |only R/FlowSOM-class.R | 7 R/SPADE-class.R | 5 R/UMAP-class.R |only R/UserSession-class.R | 5 R/attachments.R | 23 - R/authenticate.R | 24 - R/citrus.R | 27 - R/compensations.R | 13 R/dimensionality_reduction.R |only R/drop.R | 9 R/experiments.R | 33 + R/fcs_files.R | 21 - R/flowsom.R | 28 - R/gates.R | 99 ++++- R/helper_functions.R | 10 R/optSNE-class.R |only R/panels.R | 11 R/populations.R | 11 R/private_helper_functions.R | 5 R/sample_tags.R | 11 R/scales.R | 13 R/spade.R | 48 +- R/startup.R | 5 R/statistics.R | 11 R/tSNE-class.R |only R/users.R | 11 R/viSNE-class.R | 41 +- R/visne.R | 37 +- README.md | 33 + build/vignette.rds |binary inst/NEWS | 12 inst/doc/cytobank-advanced-analyses.R | 20 - inst/doc/cytobank-advanced-analyses.Rmd | 370 ++++++++++++++------- inst/doc/cytobank-advanced-analyses.html | 541 ++++++++++++++++++++----------- inst/doc/cytobank-quickstart.R | 18 - inst/doc/cytobank-quickstart.Rmd | 3 inst/doc/cytobank-quickstart.html | 265 +++++++++------ man/DimensionalityReduction-class.Rd |only man/FlowSOM-class.Rd | 2 man/UMAP-class.Rd |only man/attachments.Rd | 89 +++-- man/authentication.Rd | 44 +- man/citrus.Rd | 109 +++--- man/compensations.Rd | 38 +- man/dimensionality_reduction.Rd |only man/drop.Rd | 19 - man/experiments.Rd | 167 ++++++--- man/fcs_files.Rd | 92 +++-- man/flowsom.Rd | 110 ++++-- man/gates.Rd | 79 +++- man/helper_functions.Rd | 12 man/optSNE-class.Rd |only man/panels.Rd | 26 - man/populations.Rd | 26 - man/sample_tags.Rd | 25 - man/scales.Rd | 38 +- man/spade.Rd | 223 ++++++++---- man/statistics.Rd | 37 +- man/tSNE-class.Rd |only man/users.Rd | 24 - man/viSNE-class.Rd | 24 - man/visne.Rd | 99 +++-- vignettes/cytobank-advanced-analyses.Rmd | 370 ++++++++++++++------- vignettes/cytobank-quickstart.Rmd | 3 70 files changed, 2386 insertions(+), 1229 deletions(-)
Title: Working with 'Sapfluxnet' Project Data
Description: Access, modify, aggregate and plot data from the 'Sapfluxnet' project
(<http://sapfluxnet.creaf.cat>), the first global database of sap flow measurements.
Author: Victor Granda [aut, cre] (<https://orcid.org/0000-0002-0469-1991>),
Rafael Poyatos [aut] (<https://orcid.org/0000-0003-0521-2523>),
Victor Flo [aut] (<https://orcid.org/0000-0003-1908-4577>),
Jacob Nelson [ctb] (<https://orcid.org/0000-0002-4663-2420>),
Sapfluxnet Core Team [cph]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between sapfluxnetr versions 0.1.1 dated 2020-08-27 and 0.1.2 dated 2021-10-04
DESCRIPTION | 6 MD5 | 46 - NEWS.md | 5 R/metrics.R | 19 R/sfn_dplyr.R | 20 README.md | 11 build/vignette.rds |binary inst/doc/custom-aggregation.R | 13 inst/doc/custom-aggregation.Rmd | 21 inst/doc/custom-aggregation.html | 675 ++++++---------- inst/doc/data-flags.html | 210 ----- inst/doc/memory-and-parallelization.html | 380 ++------- inst/doc/metadata-and-data-units.Rmd | 6 inst/doc/metadata-and-data-units.html | 314 +------ inst/doc/sapfluxnetr-quick-guide.html | 1238 ++++++++++++----------------- inst/doc/sfn-data-classes.html | 1290 +++++++++++++------------------ man/dot-fixed_metrics_funs.Rd | 17 man/figures/README-example_multi-1.png |binary man/figures/README-example_multi-2.png |binary man/figures/README-example_single-1.png |binary man/metrics.Rd | 2 man/sfn_metrics.Rd | 4 vignettes/custom-aggregation.Rmd | 21 vignettes/metadata-and-data-units.Rmd | 6 24 files changed, 1681 insertions(+), 2623 deletions(-)
Title: Fitting Linear Quantile Regression Mixed Models with
Relationship Matrix
Description: Fit a quantile regression mixed model involved Relationship Matrix using a sparse implementation of the
Frisch-Newton interior-point algorithm as described in
Portnoy and Koenker (1977, Statistical Science) <https://www.jstor.org/stable/2246216>.
Author: Sayyed Reza Alavian[aut,cre]
Majid Sarmad[ths]
Mehdi Jabbari Nooghabi[ths]
Hani Rezaee[ctb]
Saeed Zerehdaran[ctb]
Ferdowsi University Of Mashhad [cph]
Maintainer: Sayyed Reza Alavian <s.rezaalavian@mail.um.ac.ir>
Diff between LRQMM versions 1.2.2 dated 2020-08-02 and 1.2.3 dated 2021-10-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/STDE.R | 16 ++++++++-------- R/lrqmm.R | 28 ++++++++++++++-------------- R/lrqmm_m.R | 27 +++++++++++++-------------- man/lrqmm.Rd | 12 ++++++------ man/lrqmm_m.Rd | 14 +++++++------- 7 files changed, 57 insertions(+), 58 deletions(-)
Title: Indices of Effect Size and Standardized Parameters
Description: Provide utilities to work with indices of effect size and
standardized parameters for a wide variety of models (see list of
supported models using the function 'insight::supported_models()'),
allowing computation of and conversion between indices such as Cohen's
d, r, odds, etc.
Author: Mattan S. Ben-Shachar [aut, cre]
(<https://orcid.org/0000-0002-4287-4801>, @mattansb),
Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Ken Kelley [ctb],
David Stanley [ctb],
Jessica Burnett [rev] (<https://orcid.org/0000-0002-0896-5099>),
Johannes Karreth [rev] (<https://orcid.org/0000-0003-4586-7153>)
Maintainer: Mattan S. Ben-Shachar <matanshm@post.bgu.ac.il>
Diff between effectsize versions 0.4.5 dated 2021-05-25 and 0.5 dated 2021-10-04
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effectsize-0.5/effectsize/R/xtab.R | 273 +++++---- effectsize-0.5/effectsize/R/zzz_deprecated.R | 77 +- effectsize-0.5/effectsize/README.md | 137 +--- effectsize-0.5/effectsize/build/partial.rdb |binary effectsize-0.5/effectsize/build/vignette.rds |binary effectsize-0.5/effectsize/inst/CITATION | 18 effectsize-0.5/effectsize/inst/doc/anovaES.html | 190 +++--- effectsize-0.5/effectsize/inst/doc/bayesian_models.html | 104 +-- effectsize-0.5/effectsize/inst/doc/convert.Rmd | 8 effectsize-0.5/effectsize/inst/doc/convert.html | 33 - effectsize-0.5/effectsize/inst/doc/from_test_statistics.html | 194 +++--- effectsize-0.5/effectsize/inst/doc/interpret.Rmd | 32 - effectsize-0.5/effectsize/inst/doc/interpret.html | 26 effectsize-0.5/effectsize/inst/doc/simple_htests.R | 17 effectsize-0.5/effectsize/inst/doc/simple_htests.Rmd | 34 - effectsize-0.5/effectsize/inst/doc/simple_htests.html | 286 +++++----- effectsize-0.5/effectsize/inst/doc/standardize_parameters.html | 49 - effectsize-0.5/effectsize/man/F_to_eta2.Rd | 139 ++-- effectsize-0.5/effectsize/man/chisq_to_phi.Rd | 147 +++-- effectsize-0.5/effectsize/man/cohens_d.Rd | 152 +++-- effectsize-0.5/effectsize/man/d_to_common_language.Rd | 2 effectsize-0.5/effectsize/man/d_to_r.Rd | 13 effectsize-0.5/effectsize/man/effectsize.Rd | 13 effectsize-0.5/effectsize/man/effectsize_CIs.Rd |only effectsize-0.5/effectsize/man/effectsize_deprecated.Rd |only effectsize-0.5/effectsize/man/equivalence_test.effectsize_table.Rd | 28 effectsize-0.5/effectsize/man/es_info.Rd | 2 effectsize-0.5/effectsize/man/eta_squared.Rd | 134 ++-- effectsize-0.5/effectsize/man/format_standardize.Rd | 10 effectsize-0.5/effectsize/man/interpret.Rd | 32 + effectsize-0.5/effectsize/man/interpret_bf.Rd | 3 effectsize-0.5/effectsize/man/interpret_cohens_d.Rd |only effectsize-0.5/effectsize/man/interpret_cohens_g.Rd |only effectsize-0.5/effectsize/man/interpret_direction.Rd | 1 effectsize-0.5/effectsize/man/interpret_ess.Rd | 2 effectsize-0.5/effectsize/man/interpret_icc.Rd |only effectsize-0.5/effectsize/man/interpret_oddsratio.Rd | 10 effectsize-0.5/effectsize/man/interpret_pd.Rd |only effectsize-0.5/effectsize/man/interpret_r.Rd | 17 effectsize-0.5/effectsize/man/interpret_vif.Rd |only effectsize-0.5/effectsize/man/is_effectsize_name.Rd | 41 - 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effectsize-0.5/effectsize/vignettes/simple_htests.Rmd | 34 - 147 files changed, 3018 insertions(+), 1972 deletions(-)
Title: Dose Response for Omics
Description: Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Larras et al (2018) <DOI:10.1021/acs.est.8b04752> at <https://hal.archives-ouvertes.fr/hal-02309919>.
Author: Marie-Laure Delignette-Muller [aut],
Elise Billoir [aut],
Floriane Larras [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between DRomics versions 2.2-0 dated 2021-02-09 and 2.3-0 dated 2021-10-04
DRomics-2.2-0/DRomics/inst/DRomics-shiny/www/logoLbbe.png |only DRomics-2.2-0/DRomics/tests/examplewithLprobit.R |only DRomics-2.3-0/DRomics/DESCRIPTION | 9 DRomics-2.3-0/DRomics/MD5 | 56 +- DRomics-2.3-0/DRomics/NAMESPACE | 4 DRomics-2.3-0/DRomics/R/bmdboot.R | 2 DRomics-2.3-0/DRomics/R/bmdcalc.R | 7 DRomics-2.3-0/DRomics/R/bmdplot.R |only DRomics-2.3-0/DRomics/R/bmdplotwithgradient.R | 121 +++- DRomics-2.3-0/DRomics/R/curvesplot.R | 68 ++ DRomics-2.3-0/DRomics/R/drcfit.R | 7 DRomics-2.3-0/DRomics/R/ecdfplotwithCI.R | 4 DRomics-2.3-0/DRomics/R/itemselect.R | 2 DRomics-2.3-0/DRomics/R/sensitivityplot.R |only DRomics-2.3-0/DRomics/R/trendplot.R |only DRomics-2.3-0/DRomics/build/partial.rdb |binary DRomics-2.3-0/DRomics/build/vignette.rds |binary DRomics-2.3-0/DRomics/inst/DRomics-shiny/server.R | 4 DRomics-2.3-0/DRomics/inst/DRomics-shiny/ui.R | 40 - DRomics-2.3-0/DRomics/inst/NEWS | 14 DRomics-2.3-0/DRomics/inst/doc/DRomics_vignette.R | 72 ++ DRomics-2.3-0/DRomics/inst/doc/DRomics_vignette.Rmd | 190 +++++-- DRomics-2.3-0/DRomics/inst/doc/DRomics_vignette.html | 350 ++++++++------ DRomics-2.3-0/DRomics/man/bmdboot.Rd | 16 DRomics-2.3-0/DRomics/man/bmdplot.Rd |only DRomics-2.3-0/DRomics/man/bmdplotwithgradient.Rd | 21 DRomics-2.3-0/DRomics/man/curvesplot.Rd | 36 + DRomics-2.3-0/DRomics/man/drcfit.Rd | 19 DRomics-2.3-0/DRomics/man/ecdfquantileplot.Rd | 6 DRomics-2.3-0/DRomics/man/sensitivityplot.Rd |only DRomics-2.3-0/DRomics/man/trendplot.Rd |only DRomics-2.3-0/DRomics/tests/testbmdcalc.R | 3 DRomics-2.3-0/DRomics/vignettes/DRomics_vignette.Rmd | 190 +++++-- 33 files changed, 839 insertions(+), 402 deletions(-)
Title: Easy Data Wrangling
Description: A lightweight package to easily manipulate, clean,
transform, and prepare your data for analysis. It also forms
the data wrangling backend for the packages in the 'easystats'
ecosystem.
Author: Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Brenton M. Wiernik [aut] (<https://orcid.org/0000-0001-9560-6336>,
@bmwiernik)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between datawizard versions 0.2.0.1 dated 2021-09-02 and 0.2.1 dated 2021-10-04
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 4 ++++ NEWS.md | 10 +++++++++- R/center.R | 15 +++++++++++---- R/data_rescale.R | 2 +- R/data_transpose.R | 4 ++-- R/demean.R | 4 ++-- R/standardize.R | 23 +++++------------------ R/unstandardize.R | 3 +++ R/visualisation_recipe.R | 10 +++++++++- inst/doc/demean.R | 5 +++++ inst/doc/demean.Rmd | 5 +++++ inst/doc/demean.html | 3 ++- man/center.Rd | 9 +++++++++ man/standardize.Rd | 44 +++++++++++++++++++++++--------------------- man/visualisation_recipe.Rd | 2 +- vignettes/demean.Rmd | 5 +++++ 18 files changed, 118 insertions(+), 74 deletions(-)
Title: A Colour Picker Tool for Shiny and for Selecting Colours in
Plots
Description: A colour picker that can be used as an input in 'Shiny' apps
or Rmarkdown documents. The colour picker supports alpha opacity, custom
colour palettes, and many more options. A Plot Colour Helper tool is
available as an 'RStudio' Addin, which helps you pick colours to use in your
plots. A more generic Colour Picker 'RStudio' Addin is also provided to let
you select colours to use in your R code.
Author: Dean Attali [aut, cre] (<https://orcid.org/0000-0002-5645-3493>),
David Griswold [ctb]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between colourpicker versions 1.1.0 dated 2020-09-14 and 1.1.1 dated 2021-10-04
colourpicker-1.1.0/colourpicker/build |only colourpicker-1.1.0/colourpicker/inst/doc |only colourpicker-1.1.0/colourpicker/vignettes |only colourpicker-1.1.1/colourpicker/DESCRIPTION | 16 colourpicker-1.1.1/colourpicker/MD5 | 17 colourpicker-1.1.1/colourpicker/NEWS.md | 16 colourpicker-1.1.1/colourpicker/R/colourPickerGadget.R | 2 colourpicker-1.1.1/colourpicker/R/plotHelper.R | 12 colourpicker-1.1.1/colourpicker/README.md | 431 +++------- colourpicker-1.1.1/colourpicker/inst/gadgets/colourpicker/css/app.css | 5 10 files changed, 185 insertions(+), 314 deletions(-)
Title: r Client for OpenRefine API
Description: 'OpenRefine' (formerly 'Google Refine') is a popular, open source data cleaning software. This package enables users to programmatically trigger data transfer between R and 'OpenRefine'. Available functionality includes project import, export and deletion.
Author: VP Nagraj [aut, cre]
Maintainer: VP Nagraj <nagraj@nagraj.net>
Diff between rrefine versions 1.1.1 dated 2021-09-03 and 1.1.2 dated 2021-10-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/refine_export.R | 7 ++++--- README.md | 1 + inst/doc/rrefine-vignette.html | 4 ++-- man/refine_export.Rd | 3 +++ 7 files changed, 28 insertions(+), 15 deletions(-)
Title: Calculation of 22 CAnonical Time-Series CHaracteristics
Description: Calculate 22 summary statistics coded in C on time-series vectors to enable
pattern detection, classification, and regression applications in the
feature space as proposed by Lubba et al. (2019) <doi:10.1007/s10618-019-00647-x>.
Author: Trent Henderson [cre, aut],
Carl Lubba [ctb]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between Rcatch22 versions 0.1.12 dated 2021-05-31 and 0.1.13 dated 2021-10-04
Rcatch22-0.1.12/Rcatch22/src/main.c |only Rcatch22-0.1.12/Rcatch22/src/main.h |only Rcatch22-0.1.13/Rcatch22/DESCRIPTION | 10 +-- Rcatch22-0.1.13/Rcatch22/MD5 | 34 ++++++----- Rcatch22-0.1.13/Rcatch22/NAMESPACE | 2 Rcatch22-0.1.13/Rcatch22/R/RcppExports.R | 28 +++++++++ Rcatch22-0.1.13/Rcatch22/R/catch22_all.R | 73 +++++++++++++----------- Rcatch22-0.1.13/Rcatch22/README.md | 38 +++++++----- Rcatch22-0.1.13/Rcatch22/inst/doc/Rcatch22.R | 5 + Rcatch22-0.1.13/Rcatch22/inst/doc/Rcatch22.Rmd | 10 ++- Rcatch22-0.1.13/Rcatch22/inst/doc/Rcatch22.html | 9 ++ Rcatch22-0.1.13/Rcatch22/man/DN_Mean.Rd |only Rcatch22-0.1.13/Rcatch22/man/DN_Spread_Std.Rd |only Rcatch22-0.1.13/Rcatch22/man/catch22_all.Rd | 10 +-- Rcatch22-0.1.13/Rcatch22/src/DN_Mean.c |only Rcatch22-0.1.13/Rcatch22/src/DN_Mean.h |only Rcatch22-0.1.13/Rcatch22/src/DN_Spread_Std.c |only Rcatch22-0.1.13/Rcatch22/src/DN_Spread_Std.h |only Rcatch22-0.1.13/Rcatch22/src/RcppExports.cpp | 29 +++++++++ Rcatch22-0.1.13/Rcatch22/src/catch22.cpp | 34 +++++++++++ Rcatch22-0.1.13/Rcatch22/tests/test.R | 11 ++- Rcatch22-0.1.13/Rcatch22/vignettes/Rcatch22.Rmd | 10 ++- 22 files changed, 226 insertions(+), 77 deletions(-)
Title: Set of Tools to Data Analysis using Generalized Linear Models
Description: Set of tools to the statistical analysis of data using: (1) normal linear models; (2) generalized linear models; (3) negative binomial regression models as alternative to the Poisson regression models under the presence of overdispersion; (4) beta-binomial regression models as alternative to the binomial regression models under the presence of overdispersion; (5) generalized estimating equations for cluster correlated data.
Author: Luis Hernando Vanegas [aut, cre],
Luz Marina Rondón [aut],
Gilberto A. Paula [aut]
Maintainer: Luis Hernando Vanegas <lhvanegasp@unal.edu.co>
Diff between glmtoolbox versions 0.1.1 dated 2021-06-09 and 0.1.2 dated 2021-10-04
glmtoolbox-0.1.1/glmtoolbox/data/spruce.rda |only glmtoolbox-0.1.1/glmtoolbox/man/spruce.Rd |only glmtoolbox-0.1.2/glmtoolbox/DESCRIPTION | 10 glmtoolbox-0.1.2/glmtoolbox/MD5 | 71 glmtoolbox-0.1.2/glmtoolbox/NAMESPACE | 13 glmtoolbox-0.1.2/glmtoolbox/R/data.R | 92 - glmtoolbox-0.1.2/glmtoolbox/R/geeglm.R | 1205 +++++++++---- glmtoolbox-0.1.2/glmtoolbox/R/glms.R | 1346 ++++++++++----- glmtoolbox-0.1.2/glmtoolbox/R/overglm.R | 488 +++-- glmtoolbox-0.1.2/glmtoolbox/data/GUIDE.rda |only glmtoolbox-0.1.2/glmtoolbox/data/depression.rda |binary glmtoolbox-0.1.2/glmtoolbox/data/rinse.rda |only glmtoolbox-0.1.2/glmtoolbox/data/spruces.rda |only glmtoolbox-0.1.2/glmtoolbox/man/AGPC.Rd | 2 glmtoolbox-0.1.2/glmtoolbox/man/CIC.Rd | 2 glmtoolbox-0.1.2/glmtoolbox/man/GHYC.Rd | 2 glmtoolbox-0.1.2/glmtoolbox/man/GUIDE.Rd |only glmtoolbox-0.1.2/glmtoolbox/man/QIC.Rd | 2 glmtoolbox-0.1.2/glmtoolbox/man/RJC.Rd | 2 glmtoolbox-0.1.2/glmtoolbox/man/SGPC.Rd | 2 glmtoolbox-0.1.2/glmtoolbox/man/anova.glmgee.Rd | 12 glmtoolbox-0.1.2/glmtoolbox/man/anova.overglm.Rd | 13 glmtoolbox-0.1.2/glmtoolbox/man/anova2.Rd | 10 glmtoolbox-0.1.2/glmtoolbox/man/confint2.Rd | 4 glmtoolbox-0.1.2/glmtoolbox/man/cooks.distance.glmgee.Rd | 21 glmtoolbox-0.1.2/glmtoolbox/man/dfbeta.glmgee.Rd | 17 glmtoolbox-0.1.2/glmtoolbox/man/estequa.glmgee.Rd | 2 glmtoolbox-0.1.2/glmtoolbox/man/glmgee.Rd | 43 glmtoolbox-0.1.2/glmtoolbox/man/leverage.Rd |only glmtoolbox-0.1.2/glmtoolbox/man/leverage.glmgee.Rd |only glmtoolbox-0.1.2/glmtoolbox/man/localInfluence.Rd |only glmtoolbox-0.1.2/glmtoolbox/man/localInfluence.glmgee.Rd |only glmtoolbox-0.1.2/glmtoolbox/man/overglm.Rd | 2 glmtoolbox-0.1.2/glmtoolbox/man/predict.glmgee.Rd | 13 glmtoolbox-0.1.2/glmtoolbox/man/residuals.glmgee.Rd | 6 glmtoolbox-0.1.2/glmtoolbox/man/residuals2.Rd |only glmtoolbox-0.1.2/glmtoolbox/man/rinse.Rd |only glmtoolbox-0.1.2/glmtoolbox/man/spruces.Rd |only glmtoolbox-0.1.2/glmtoolbox/man/stepCriterion.glm.Rd | 58 glmtoolbox-0.1.2/glmtoolbox/man/stepCriterion.glmgee.Rd | 72 glmtoolbox-0.1.2/glmtoolbox/man/stepCriterion.lm.Rd | 63 glmtoolbox-0.1.2/glmtoolbox/man/stepCriterion.overglm.Rd | 42 glmtoolbox-0.1.2/glmtoolbox/man/vcov.glmgee.Rd | 20 43 files changed, 2504 insertions(+), 1131 deletions(-)