Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to
make it easy to download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rvest versions 0.3.4 dated 2019-05-15 and 0.3.5 dated 2019-11-08
DESCRIPTION | 6 +- MD5 | 30 +++++------ NEWS.md | 4 + R/selectors.R | 6 +- README.md | 4 + build/vignette.rds |binary inst/doc/selectorgadget.R | 23 +++++++-- inst/doc/selectorgadget.Rmd | 29 +++++++++-- inst/doc/selectorgadget.html | 103 +++++++++++++++++++++++++++-------------- man/html_nodes.Rd | 6 +- vignettes/selectorgadget-1.png |binary vignettes/selectorgadget-2.png |binary vignettes/selectorgadget-3.png |binary vignettes/selectorgadget-4.png |binary vignettes/selectorgadget-5.png |binary vignettes/selectorgadget.Rmd | 29 +++++++++-- 16 files changed, 168 insertions(+), 72 deletions(-)
Title: Fisheries Stock Assessment Simulation Testing with Stock
Synthesis
Description: Develops a framework for fisheries stock assessment simulation
testing with Stock Synthesis (SS) as described in Anderson et al.
(2014) <doi:10.1371/journal.pone.0092725>.
Author: Kelli F. Johnson [aut, cre],
Sean C. Anderson [aut] (<https://orcid.org/0000-0001-9563-1937>),
Kathryn Doering [aut],
Cole Monnahan [aut],
Christine Stawitz [aut],
Ian Taylor [aut],
Curry Cunningham [ctb],
Allan Hicks [ctb],
Felipe Hurtado-Ferro [ctb],
Peter Kuriyama [ctb],
Roberto Licandeo [ctb],
Carey McGilliard [ctb],
Melissa Murdian [ctb],
Kotaro Ono [ctb],
Merrill Rudd [ctb],
Cody Szuwalski [ctb],
Juan Valero [ctb],
Athol Whitten [ctb]
Maintainer: Kelli F. Johnson <kelli.johnson@noaa.gov>
Diff between ss3sim versions 0.9.5 dated 2017-04-18 and 1.0.3 dated 2019-11-08
ss3sim-0.9.5/ss3sim/R/bias_ss3.r |only ss3sim-0.9.5/ss3sim/R/change_fltname.r |only ss3sim-0.9.5/ss3sim/R/change_maturity.R |only ss3sim-0.9.5/ss3sim/R/change_year.R |only ss3sim-0.9.5/ss3sim/R/extract_expected_data.r |only ss3sim-0.9.5/ss3sim/R/pastef.r |only ss3sim-0.9.5/ss3sim/R/run_bias_ss3.r |only ss3sim-0.9.5/ss3sim/inst/doc/making-functions.Rmd |only ss3sim-0.9.5/ss3sim/inst/doc/making-functions.html |only ss3sim-0.9.5/ss3sim/inst/extdata/Simple |only ss3sim-0.9.5/ss3sim/inst/extdata/cases |only ss3sim-0.9.5/ss3sim/inst/extdata/eg-cases/agecomp100-cod.txt |only ss3sim-0.9.5/ss3sim/inst/extdata/example-om/data.ss_new |only ss3sim-0.9.5/ss3sim/inst/extdata/models/cod-om/ss3.par |only ss3sim-0.9.5/ss3sim/inst/extdata/output |only ss3sim-0.9.5/ss3sim/inst/extdata/time-varying-case-tests |only ss3sim-0.9.5/ss3sim/man/bias_ss3.Rd |only ss3sim-0.9.5/ss3sim/man/calculate_runtime.Rd |only ss3sim-0.9.5/ss3sim/man/change_agecomp.Rd |only ss3sim-0.9.5/ss3sim/man/change_fltname.Rd |only ss3sim-0.9.5/ss3sim/man/change_index.Rd |only ss3sim-0.9.5/ss3sim/man/change_lcomp.Rd |only ss3sim-0.9.5/ss3sim/man/change_maturity.Rd |only ss3sim-0.9.5/ss3sim/man/change_year.Rd |only ss3sim-0.9.5/ss3sim/man/extract_expected_data.Rd |only ss3sim-0.9.5/ss3sim/man/pastef.Rd |only ss3sim-0.9.5/ss3sim/man/run_bias_ss3.Rd |only ss3sim-0.9.5/ss3sim/vignettes/making-functions.Rmd |only ss3sim-1.0.3/ss3sim/DESCRIPTION | 85 ss3sim-1.0.3/ss3sim/LICENSE | 4 ss3sim-1.0.3/ss3sim/MD5 | 409 -- ss3sim-1.0.3/ss3sim/NAMESPACE | 182 - ss3sim-1.0.3/ss3sim/NEWS.md | 65 ss3sim-1.0.3/ss3sim/R/add_colnames.R |only ss3sim-1.0.3/ss3sim/R/add_nulls.R | 2 ss3sim-1.0.3/ss3sim/R/calculate_re.R | 66 ss3sim-1.0.3/ss3sim/R/case-parsing.r | 11 ss3sim-1.0.3/ss3sim/R/case-write.R | 10 ss3sim-1.0.3/ss3sim/R/change_data.r | 288 - ss3sim-1.0.3/ss3sim/R/change_e.r | 366 +- ss3sim-1.0.3/ss3sim/R/change_em_binning.r | 197 - ss3sim-1.0.3/ss3sim/R/change_f.r | 167 - ss3sim-1.0.3/ss3sim/R/change_f_par.r |only ss3sim-1.0.3/ss3sim/R/change_lcomp_constant.R | 14 ss3sim-1.0.3/ss3sim/R/change_o.R |only ss3sim-1.0.3/ss3sim/R/change_q.R |only ss3sim-1.0.3/ss3sim/R/change_rec_devs.r | 171 - ss3sim-1.0.3/ss3sim/R/change_rec_devs_par.r |only ss3sim-1.0.3/ss3sim/R/change_retro.r | 13 ss3sim-1.0.3/ss3sim/R/change_tail_compression.R | 13 ss3sim-1.0.3/ss3sim/R/change_tv.r | 563 +-- ss3sim-1.0.3/ss3sim/R/clean_data.r | 156 ss3sim-1.0.3/ss3sim/R/copy_ss3models.r | 12 ss3sim-1.0.3/ss3sim/R/create_argfiles.r | 2 ss3sim-1.0.3/ss3sim/R/expand_scenarios.r | 16 ss3sim-1.0.3/ss3sim/R/fill_across.r | 7 ss3sim-1.0.3/ss3sim/R/get-results.r | 296 - ss3sim-1.0.3/ss3sim/R/get_bin.R | 6 ss3sim-1.0.3/ss3sim/R/get_bin_info.r | 2 ss3sim-1.0.3/ss3sim/R/get_model_folder.r | 2 ss3sim-1.0.3/ss3sim/R/get_sigma.r | 18 ss3sim-1.0.3/ss3sim/R/get_ss_version.R |only ss3sim-1.0.3/ss3sim/R/growth_estimation.R | 4 ss3sim-1.0.3/ss3sim/R/make_dummy_data.r | 38 ss3sim-1.0.3/ss3sim/R/profile_fmsy.r | 164 ss3sim-1.0.3/ss3sim/R/run_ss3model.r | 39 ss3sim-1.0.3/ss3sim/R/run_ss3sim.r | 144 ss3sim-1.0.3/ss3sim/R/sample_agecomp.R | 266 - ss3sim-1.0.3/ss3sim/R/sample_calcomp.R | 33 ss3sim-1.0.3/ss3sim/R/sample_comp.R |only ss3sim-1.0.3/ss3sim/R/sample_index.r | 245 - ss3sim-1.0.3/ss3sim/R/sample_lcomp.R | 207 - ss3sim-1.0.3/ss3sim/R/sample_mlacomp.R | 60 ss3sim-1.0.3/ss3sim/R/sample_wtatage.R | 46 ss3sim-1.0.3/ss3sim/R/ss3sim_base.r | 576 +-- ss3sim-1.0.3/ss3sim/R/standardize_bounds.R | 22 ss3sim-1.0.3/ss3sim/R/verify_input.r | 48 ss3sim-1.0.3/ss3sim/README.md | 101 ss3sim-1.0.3/ss3sim/build/vignette.rds |binary ss3sim-1.0.3/ss3sim/data/scalar_dat.rda |binary ss3sim-1.0.3/ss3sim/data/ts_dat.rda |binary ss3sim-1.0.3/ss3sim/inst/CITATION | 24 ss3sim-1.0.3/ss3sim/inst/doc/introduction.R | 470 +- ss3sim-1.0.3/ss3sim/inst/doc/introduction.Rmd | 1314 +------ ss3sim-1.0.3/ss3sim/inst/doc/introduction.html | 1657 +++++----- ss3sim-1.0.3/ss3sim/inst/doc/making-models.Rmd | 146 ss3sim-1.0.3/ss3sim/inst/doc/making-models.html | 321 - ss3sim-1.0.3/ss3sim/inst/doc/modifying-models.Rmd | 88 ss3sim-1.0.3/ss3sim/inst/doc/modifying-models.html | 169 - ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/E0-cod.txt | 12 ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/E1-cod.txt | 12 ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/E100-cod.txt | 12 ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/E101-cod.txt | 12 ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/F0-cod.txt | 2 ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/F1-cod.txt |only ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/G0-cod.txt | 1 ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/M0-cod.txt | 1 ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/O0-cod.txt |only ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/S0-cod.txt | 1 ss3sim-1.0.3/ss3sim/inst/extdata/eg-cases/calcomp0-cod.txt |only ss3sim-1.0.3/ss3sim/inst/extdata/example-om/ss3_exp_vals_comps.dat |only ss3sim-1.0.3/ss3sim/inst/extdata/example-om/ss3_expected_values.dat |only ss3sim-1.0.3/ss3sim/inst/extdata/models/cod-em/codEM.ctl | 324 + ss3sim-1.0.3/ss3sim/inst/extdata/models/cod-em/forecast.ss | 94 ss3sim-1.0.3/ss3sim/inst/extdata/models/cod-em/starter.ss | 34 ss3sim-1.0.3/ss3sim/inst/extdata/models/cod-om/codOM.ctl | 532 +-- ss3sim-1.0.3/ss3sim/inst/extdata/models/cod-om/codOM.dat | 1401 ++++---- ss3sim-1.0.3/ss3sim/inst/extdata/models/cod-om/forecast.ss | 94 ss3sim-1.0.3/ss3sim/inst/extdata/models/cod-om/starter.ss | 38 ss3sim-1.0.3/ss3sim/man/add_CPUE.Rd |only ss3sim-1.0.3/ss3sim/man/add_colnames.Rd |only ss3sim-1.0.3/ss3sim/man/add_nulls.Rd | 4 ss3sim-1.0.3/ss3sim/man/add_tv_parlines.Rd |only ss3sim-1.0.3/ss3sim/man/calculate_data_units.Rd | 14 ss3sim-1.0.3/ss3sim/man/calculate_re.Rd | 52 ss3sim-1.0.3/ss3sim/man/case_comp.Rd | 4 ss3sim-1.0.3/ss3sim/man/case_fishing.Rd | 4 ss3sim-1.0.3/ss3sim/man/case_tv.Rd | 8 ss3sim-1.0.3/ss3sim/man/change_data.Rd | 91 ss3sim-1.0.3/ss3sim/man/change_e.Rd | 100 ss3sim-1.0.3/ss3sim/man/change_e_fcast_yrs.Rd |only ss3sim-1.0.3/ss3sim/man/change_em_binning.Rd | 103 ss3sim-1.0.3/ss3sim/man/change_f.Rd | 91 ss3sim-1.0.3/ss3sim/man/change_f_par.Rd |only ss3sim-1.0.3/ss3sim/man/change_lcomp_constant.Rd | 13 ss3sim-1.0.3/ss3sim/man/change_o.Rd |only ss3sim-1.0.3/ss3sim/man/change_pop_bin.Rd |only ss3sim-1.0.3/ss3sim/man/change_rec_devs.Rd | 52 ss3sim-1.0.3/ss3sim/man/change_rec_devs_par.Rd |only ss3sim-1.0.3/ss3sim/man/change_retro.Rd | 9 ss3sim-1.0.3/ss3sim/man/change_tail_compression.Rd | 12 ss3sim-1.0.3/ss3sim/man/change_tv.Rd | 65 ss3sim-1.0.3/ss3sim/man/check_data.Rd | 6 ss3sim-1.0.3/ss3sim/man/check_data_str_range.Rd |only ss3sim-1.0.3/ss3sim/man/clean_data.Rd | 5 ss3sim-1.0.3/ss3sim/man/cleanup_ss3.Rd | 14 ss3sim-1.0.3/ss3sim/man/copy_ss3models.Rd | 2 ss3sim-1.0.3/ss3sim/man/create_argfiles.Rd | 9 ss3sim-1.0.3/ss3sim/man/expand_scenarios.Rd | 12 ss3sim-1.0.3/ss3sim/man/get_bin.Rd | 6 ss3sim-1.0.3/ss3sim/man/get_caseargs.Rd | 4 ss3sim-1.0.3/ss3sim/man/get_results_all.Rd | 9 ss3sim-1.0.3/ss3sim/man/get_results_derived.Rd | 1 ss3sim-1.0.3/ss3sim/man/get_results_scalar.Rd | 1 ss3sim-1.0.3/ss3sim/man/get_results_scenario.Rd | 29 ss3sim-1.0.3/ss3sim/man/get_results_timeseries.Rd | 1 ss3sim-1.0.3/ss3sim/man/get_sigmar.Rd | 6 ss3sim-1.0.3/ss3sim/man/get_ss_ver_dl.Rd |only ss3sim-1.0.3/ss3sim/man/get_ss_ver_file.Rd |only ss3sim-1.0.3/ss3sim/man/plot_scalar_boxplot.Rd | 7 ss3sim-1.0.3/ss3sim/man/plot_scalar_points.Rd | 8 ss3sim-1.0.3/ss3sim/man/plot_ts_boxplot.Rd | 5 ss3sim-1.0.3/ss3sim/man/plot_ts_lines.Rd | 6 ss3sim-1.0.3/ss3sim/man/plot_ts_points.Rd | 6 ss3sim-1.0.3/ss3sim/man/profile_fmsy.Rd | 64 ss3sim-1.0.3/ss3sim/man/remove_CPUE.Rd |only ss3sim-1.0.3/ss3sim/man/remove_q_ctl.Rd |only ss3sim-1.0.3/ss3sim/man/run_ss3model.Rd | 24 ss3sim-1.0.3/ss3sim/man/run_ss3sim.Rd | 109 ss3sim-1.0.3/ss3sim/man/sample_agecomp.Rd | 147 ss3sim-1.0.3/ss3sim/man/sample_calcomp.Rd | 28 ss3sim-1.0.3/ss3sim/man/sample_comp.Rd |only ss3sim-1.0.3/ss3sim/man/sample_index.Rd | 92 ss3sim-1.0.3/ss3sim/man/sample_lcomp.Rd | 122 ss3sim-1.0.3/ss3sim/man/sample_mlacomp.Rd | 49 ss3sim-1.0.3/ss3sim/man/sample_wtatage.Rd | 28 ss3sim-1.0.3/ss3sim/man/ss3sim_base.Rd | 170 - ss3sim-1.0.3/ss3sim/man/standardize_bounds.Rd | 11 ss3sim-1.0.3/ss3sim/man/vbgf_func.Rd | 2 ss3sim-1.0.3/ss3sim/man/verify_input.Rd | 11 ss3sim-1.0.3/ss3sim/man/verify_plot_arguments.Rd | 2 ss3sim-1.0.3/ss3sim/vignettes/introduction.Rmd | 1314 +------ ss3sim-1.0.3/ss3sim/vignettes/making-models.Rmd | 146 ss3sim-1.0.3/ss3sim/vignettes/modifying-models.Rmd | 88 174 files changed, 6367 insertions(+), 8694 deletions(-)
More information about NPBayesImputeCat at CRAN
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Title: Compute Krippendorff's Alpha
Description: Provides functions to compute and plot Krippendorff's inter-coder
reliability coefficient alpha and bootstrapped uncertainty estimates
(Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to
make use of parallel threads where supported.
Author: Alexander Staudt [aut, cre], Pierre L'Ecuyer [ctb] (author of the C++ RNG code)
Maintainer: Alexander Staudt <staudtlex@live.de>
Diff between icr versions 0.6.0 dated 2019-06-23 and 0.6.1 dated 2019-11-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/plot_icr.R | 4 ++-- R/print_icr.R | 18 ++++++++---------- cleanup | 2 +- 5 files changed, 19 insertions(+), 21 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The
package should add new functionality to R such as the possibility to
manipulate 'NeXML' objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Hilmar Lapp [aut] (<https://orcid.org/0000-0001-9107-0714>),
Kseniia Shumelchyk [aut],
Rutger Vos [aut] (<https://orcid.org/0000-0001-9254-7318>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.3.0 dated 2019-01-24 and 2.4.0 dated 2019-11-08
DESCRIPTION | 11 MD5 | 57 - NAMESPACE | 1 NEWS.md | 16 R/add_characters.R | 7 R/get_metadata.R | 4 R/nexml_methods.R | 273 ++++++- R/nexml_validate.R | 8 R/nexml_write.R | 9 R/utils.R | 15 README.md | 12 build/vignette.rds |binary inst/doc/S4.html | 17 inst/doc/intro.R | 8 inst/doc/intro.Rmd | 16 inst/doc/intro.html | 185 +++- inst/doc/metadata.html | 1398 ++++++++++++++++-------------------- inst/doc/simmap.html | 19 inst/doc/sparql.html | 19 man/charzero_as_empty.Rd |only man/nexml_write.Rd | 9 man/summary-nexml-method.Rd |only tests/testthat/helper-RNeXML.R | 4 tests/testthat/test_02_summary.R |only tests/testthat/test_characters.R | 3 tests/testthat/test_comp_analysis.R | 13 tests/testthat/test_global_ids.R | 2 tests/testthat/test_meta_extract.R | 48 - tests/testthat/test_rdf.R | 34 tests/testthat/test_taxonomy.R | 2 vignettes/intro.Rmd | 16 31 files changed, 1256 insertions(+), 950 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,
Nathan Russell, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.0.2 dated 2019-07-25 and 1.0.3 dated 2019-11-08
Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-FAQ.R |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-FAQ.Rmd |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-attributes.R |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-attributes.Rmd |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-extending.R |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-extending.Rmd |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-introduction.R |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-introduction.Rmd |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-jss-2011.R |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-modules.R |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-modules.Rmd |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-package.Rmd |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-quickref.R |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-quickref.Rmd |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-sugar.R |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp-sugar.Rmd |only Rcpp-1.0.2/Rcpp/inst/doc/Rcpp.bib |only Rcpp-1.0.2/Rcpp/vignettes/.install_extras |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp-FAQ.Rmd |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp-attributes.Rmd |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp-extending.Rmd |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp-introduction.Rmd |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp-modules.Rmd |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp-package.Rmd |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp-quickref.Rmd |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp-sugar.Rmd |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp-unitTests.pdf |only Rcpp-1.0.2/Rcpp/vignettes/Rcpp.bib |only Rcpp-1.0.2/Rcpp/vignettes/figures |only Rcpp-1.0.3/Rcpp/ChangeLog | 141 ++ Rcpp-1.0.3/Rcpp/DESCRIPTION | 8 Rcpp-1.0.3/Rcpp/MD5 | 126 +- Rcpp-1.0.3/Rcpp/R/Module.R | 6 Rcpp-1.0.3/Rcpp/README.md | 23 Rcpp-1.0.3/Rcpp/build/vignette.rds |binary Rcpp-1.0.3/Rcpp/cleanup | 7 Rcpp-1.0.3/Rcpp/inst/NEWS.Rd | 43 Rcpp-1.0.3/Rcpp/inst/bib/Rcpp.bib | 28 Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-FAQ.Rnw |only Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-attributes.Rnw |only Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-attributes.pdf |binary Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-extending.Rnw |only Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-introduction.Rnw |only Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-jss-2011.Rnw | 1078 ------------------- Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-jss-2011.pdf |binary Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-modules.Rnw |only Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-package.Rnw |only Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-quickref.Rnw |only Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-sugar.Rnw |only Rcpp-1.0.3/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-1.0.3/Rcpp/inst/include/Rcpp.h | 2 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/DataFrame.h | 4 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/Environment.h | 12 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/Reference.h | 5 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/XPtr.h | 31 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/api/meat/is.h | 4 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/api/meat/meat.h | 2 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/config.h | 4 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/exceptions.h | 7 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/proxy/FieldProxy.h | 9 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/r/headers.h | 10 Rcpp-1.0.3/Rcpp/inst/include/Rcpp/r_cast.h | 3 Rcpp-1.0.3/Rcpp/inst/unitTests/cpp/XPtr.cpp | 11 Rcpp-1.0.3/Rcpp/inst/unitTests/runit.XPTr.R | 11 Rcpp-1.0.3/Rcpp/inst/unitTests/runit.exposeClass.R | 8 Rcpp-1.0.3/Rcpp/tests/doRUnit.R | 4 Rcpp-1.0.3/Rcpp/vignettes/Rcpp-FAQ.Rnw |only Rcpp-1.0.3/Rcpp/vignettes/Rcpp-attributes.Rnw |only Rcpp-1.0.3/Rcpp/vignettes/Rcpp-extending.Rnw |only Rcpp-1.0.3/Rcpp/vignettes/Rcpp-introduction.Rnw |only Rcpp-1.0.3/Rcpp/vignettes/Rcpp-jss-2011.Rnw | 1078 ------------------- Rcpp-1.0.3/Rcpp/vignettes/Rcpp-modules.Rnw |only Rcpp-1.0.3/Rcpp/vignettes/Rcpp-package.Rnw |only Rcpp-1.0.3/Rcpp/vignettes/Rcpp-quickref.Rnw |only Rcpp-1.0.3/Rcpp/vignettes/Rcpp-sugar.Rnw |only Rcpp-1.0.3/Rcpp/vignettes/pdf |only 82 files changed, 400 insertions(+), 2265 deletions(-)
Title: Weighted Metrics, Scoring Functions and Performance Measures for
Machine Learning
Description: Provides weighted versions of several metrics,
scoring functions and performance measures used in machine learning,
including average unit deviances of the Bernoulli, Tweedie, Poisson,
and Gamma distributions, see Jorgensen B. (1997, ISBN:
978-0412997112). The package also contains a weighted version of
generalized R-squared, see e.g. Cohen, J. et al. (2002, ISBN:
978-0805822236). Furthermore, 'dplyr' chains are supported.
Author: Michael Mayer [aut, cre, cph],
Christian Lorentzen [rev]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between MetricsWeighted versions 0.2.0 dated 2019-08-19 and 0.3.0 dated 2019-11-08
DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++------ NAMESPACE | 3 +++ NEWS.md | 17 +++++++++++++---- R/weighted_mean.R | 3 +-- R/weighted_variance.R |only inst/doc/MetricsWeighted.html | 4 ++-- man/weighted_mean.Rd | 3 +-- man/weighted_var.Rd |only 9 files changed, 32 insertions(+), 20 deletions(-)
More information about MetricsWeighted at CRAN
Permanent link
Title: Clustering with Matrix Gaussian and Matrix Transformation
Mixture Models
Description: Provides matrix Gaussian mixture models, matrix transformation mixture models and their model-based clustering results. The parsimonious models of the mean matrices and variance covariance matrices are implemented with a total of 196 variations.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Shuchismita Sarkar [ctb],
Michael Hutt [ctb, cph],
Stephen Moshier [ctb, cph],
Rouben Rostamian [ctb, cph],
Carl Edward Rasmussen [ctb, cph],
Dianne Cook [ctb, cph]
Maintainer: Xuwen Zhu <xzhu20@cba.ua.edu>
Diff between MatTransMix versions 0.1.4 dated 2019-07-18 and 0.1.6 dated 2019-11-08
DESCRIPTION | 12 +-- MD5 | 20 +++--- NAMESPACE | 6 + NEWS | 8 ++ R/libMatTransFull.R | 166 +++++++++++++++++++++++++++++++++++++-------------- R/print.R |only demo/EMalgorithm1.R | 12 --- demo/EMalgorithm2.R | 18 +++-- man/MatTrans.EM.Rd | 32 +++++---- man/print.summary.Rd |only src/libFull.c | 26 +++++-- src/runFull.c | 2 12 files changed, 205 insertions(+), 97 deletions(-)
Title: Drawing SVG Graphics to Visualize and Map Genome-Wide Data on
Idiograms
Description: For whole-genome analysis, idiograms are virtually the most intuitive and effective way to map and visualize the genome-wide information. RIdeogram was developed to visualize and map whole-genome data on idiograms with no restriction of species.
Author: Zhaodong Hao [aut, cre],
Dekang Lv [aut],
Ying Ge [aut],
Jisen Shi [aut],
Weijers Dolf [aut],
Guangchuang Yu [aut],
Jinhui Chen [aut]
Maintainer: Zhaodong Hao <haozd1992@163.com>
Diff between RIdeogram versions 0.1.1 dated 2019-01-15 and 0.2.0 dated 2019-11-08
DESCRIPTION | 17 MD5 | 71 + NAMESPACE | 3 R/GFFex.R |only R/convertSVG.R | 2 R/ideogram.R | 1270 ++++++++++++++++++++------- README.md | 14 build/vignette.rds |binary data/Fst_between_CE_and_CW.rda |only data/LTR_density.rda |binary data/Pi_for_CE.rda |only data/Pi_for_CE_and_CW.rda |only data/gene_density.rda |binary data/karyotype_dual_comparison.rda |only data/karyotype_ternary_comparison.rda |only data/liriodendron_karyotype.rda |only data/synteny_dual_comparison.rda |only data/synteny_ternary_comparison.rda |only data/synteny_ternary_comparison_graident.rda |only inst/doc/RIdeogram.R | 29 inst/doc/RIdeogram.Rmd | 150 ++- inst/doc/RIdeogram.html | 240 ++++- man/Fst_between_CE_and_CW.Rd |only man/GFFex.Rd |only man/Pi_for_CE.Rd |only man/Pi_for_CE_and_CW.Rd |only man/convertSVG.Rd | 2 man/ideogram.Rd | 20 man/karyotype_dual_comparison.Rd |only man/karyotype_ternary_comparison.Rd |only man/liriodendron_karyotype.Rd |only man/synteny_dual_comparison.Rd |only man/synteny_ternary_comparison.Rd |only man/synteny_ternary_comparison_graident.Rd |only vignettes/RIdeogram.Rmd | 150 ++- vignettes/figures/example1.png |binary vignettes/figures/example10.png |binary vignettes/figures/example11.png |only vignettes/figures/example12.png |only vignettes/figures/example13.png |only vignettes/figures/example14.png |only vignettes/figures/example15.png |only vignettes/figures/example16.png |only vignettes/figures/example17.png |only vignettes/figures/example2.png |binary vignettes/figures/example5.png |binary vignettes/figures/example6.png |binary vignettes/figures/example7.png |binary vignettes/figures/example8.png |binary vignettes/figures/example9.png |binary 50 files changed, 1529 insertions(+), 439 deletions(-)
Title: Managing and Visualizing Brain Surface Data
Description: Provides high-level access to 'FreeSurfer' <http://freesurfer.net/> neuroimaging data on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize the results directly in 'R'.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between fsbrain versions 0.0.1 dated 2019-10-30 and 0.0.2 dated 2019-11-08
fsbrain-0.0.1/fsbrain/README.md |only fsbrain-0.0.1/fsbrain/vignettes/rgl_brain_aparc.jpg |only fsbrain-0.0.1/fsbrain/vignettes/rgl_brain_ct.jpg |only fsbrain-0.0.2/fsbrain/DESCRIPTION | 12 fsbrain-0.0.2/fsbrain/MD5 | 113 +- fsbrain-0.0.2/fsbrain/NAMESPACE | 21 fsbrain-0.0.2/fsbrain/R/coloredmesh.R |only fsbrain-0.0.2/fsbrain/R/fsdir_abstraction_subject.R | 93 ++ fsbrain-0.0.2/fsbrain/R/helpers.R | 26 fsbrain-0.0.2/fsbrain/R/metadata_io.R | 299 ++++++ fsbrain-0.0.2/fsbrain/R/morph_atlas_agg.R | 29 fsbrain-0.0.2/fsbrain/R/optdata.R | 87 +- fsbrain-0.0.2/fsbrain/R/vis.R | 431 +++++++--- fsbrain-0.0.2/fsbrain/R/vis_meshes.R | 77 + fsbrain-0.0.2/fsbrain/R/vis_multiview.R | 99 +- fsbrain-0.0.2/fsbrain/inst/doc/fsbrain.R | 191 ++++ fsbrain-0.0.2/fsbrain/inst/doc/fsbrain.Rmd | 371 +++++++- fsbrain-0.0.2/fsbrain/inst/doc/fsbrain.html | 342 ++++++- fsbrain-0.0.2/fsbrain/inst/extdata/demographics.tsv | 2 fsbrain-0.0.2/fsbrain/man/brainview.si.Rd | 9 fsbrain-0.0.2/fsbrain/man/brainview.sr.Rd | 9 fsbrain-0.0.2/fsbrain/man/brainview.t4.Rd | 9 fsbrain-0.0.2/fsbrain/man/brainview.t9.Rd | 9 fsbrain-0.0.2/fsbrain/man/brainviews.Rd | 9 fsbrain-0.0.2/fsbrain/man/check.for.coloredmeshes.colormap.Rd |only fsbrain-0.0.2/fsbrain/man/clip.data.Rd |only fsbrain-0.0.2/fsbrain/man/coloredmesh.from.annot.Rd | 6 fsbrain-0.0.2/fsbrain/man/coloredmesh.from.label.Rd |only fsbrain-0.0.2/fsbrain/man/coloredmesh.from.mask.Rd |only fsbrain-0.0.2/fsbrain/man/coloredmesh.from.morph.native.Rd | 10 fsbrain-0.0.2/fsbrain/man/coloredmesh.from.morph.standard.Rd |only fsbrain-0.0.2/fsbrain/man/coloredmesh.from.morphdata.Rd | 6 fsbrain-0.0.2/fsbrain/man/combine.coloredmeshes.data.Rd |only fsbrain-0.0.2/fsbrain/man/download_fsaverage.Rd |only fsbrain-0.0.2/fsbrain/man/download_optional_data.Rd | 2 fsbrain-0.0.2/fsbrain/man/draw.colorbar.Rd |only fsbrain-0.0.2/fsbrain/man/find.subjectsdir.of.Rd | 4 fsbrain-0.0.2/fsbrain/man/get_optional_data_filepath.Rd | 2 fsbrain-0.0.2/fsbrain/man/group.label.Rd | 4 fsbrain-0.0.2/fsbrain/man/labeldata.from.mask.Rd |only fsbrain-0.0.2/fsbrain/man/mask.from.labeldata.for.hemi.Rd |only fsbrain-0.0.2/fsbrain/man/perform.rglactions.Rd |only fsbrain-0.0.2/fsbrain/man/read.md.demographics.Rd | 8 fsbrain-0.0.2/fsbrain/man/report.on.demographics.Rd |only fsbrain-0.0.2/fsbrain/man/rglactions.has.key.Rd |only fsbrain-0.0.2/fsbrain/man/subject.annot.Rd | 3 fsbrain-0.0.2/fsbrain/man/subject.label.Rd | 4 fsbrain-0.0.2/fsbrain/man/test.numerical.meandiff.Rd |only fsbrain-0.0.2/fsbrain/man/test.numerical.meandiff.paired.Rd |only fsbrain-0.0.2/fsbrain/man/test.numerical.meandiff.unpaired.Rd |only fsbrain-0.0.2/fsbrain/man/unify.coloredmeshes.colormaps.Rd |only fsbrain-0.0.2/fsbrain/man/vis.coloredmeshes.Rd | 7 fsbrain-0.0.2/fsbrain/man/vis.coloredmeshes.rotating.Rd | 10 fsbrain-0.0.2/fsbrain/man/vis.data.on.fsaverage.Rd | 13 fsbrain-0.0.2/fsbrain/man/vis.data.on.subject.Rd | 16 fsbrain-0.0.2/fsbrain/man/vis.mask.on.subject.Rd |only fsbrain-0.0.2/fsbrain/man/vis.region.values.on.subject.Rd |only fsbrain-0.0.2/fsbrain/man/vis.rotated.coloredmeshes.Rd | 4 fsbrain-0.0.2/fsbrain/man/vis.subject.annot.Rd | 12 fsbrain-0.0.2/fsbrain/man/vis.subject.label.Rd |only fsbrain-0.0.2/fsbrain/man/vis.subject.morph.native.Rd | 15 fsbrain-0.0.2/fsbrain/man/vis.subject.morph.standard.Rd |only fsbrain-0.0.2/fsbrain/man/write.region.values.fsaverage.Rd | 2 fsbrain-0.0.2/fsbrain/tests/testthat/test-fsdir-abstraction-subject.R | 68 + fsbrain-0.0.2/fsbrain/tests/testthat/test-helpers.R | 10 fsbrain-0.0.2/fsbrain/tests/testthat/test-metadata-io.R | 30 fsbrain-0.0.2/fsbrain/tests/testthat/test-vis-multiview.R | 149 +++ fsbrain-0.0.2/fsbrain/vignettes/fsbrain.Rmd | 371 +++++++- fsbrain-0.0.2/fsbrain/vignettes/fsbrain_aparc.jpg |only fsbrain-0.0.2/fsbrain/vignettes/fsbrain_ct.jpg |only fsbrain-0.0.2/fsbrain/vignettes/fsbrain_vis_surfaces.jpg |only fsbrain-0.0.2/fsbrain/vignettes/fsbrain_vis_views.jpg |only 72 files changed, 2530 insertions(+), 464 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects from statistical models and returns the
result as tidy data frames. These data frames are ready to use with the
'ggplot2'-package. Marginal effects can be calculated for many different
models. Interaction terms, splines and polynomial terms are also supported.
The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a
generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 0.12.0 dated 2019-09-03 and 0.13.0 dated 2019-11-08
ggeffects-0.12.0/ggeffects/R/emm.R |only ggeffects-0.12.0/ggeffects/man/emm.Rd |only ggeffects-0.13.0/ggeffects/DESCRIPTION | 19 ggeffects-0.13.0/ggeffects/MD5 | 147 +++---- ggeffects-0.13.0/ggeffects/NAMESPACE | 14 ggeffects-0.13.0/ggeffects/NEWS.md | 29 + ggeffects-0.13.0/ggeffects/R/get_predictions_MixMod.R | 8 ggeffects-0.13.0/ggeffects/R/get_predictions_bamlss.R |only ggeffects-0.13.0/ggeffects/R/get_predictions_bayesx.R |only ggeffects-0.13.0/ggeffects/R/get_predictions_gam.R | 6 ggeffects-0.13.0/ggeffects/R/get_predictions_gamlss.R | 19 ggeffects-0.13.0/ggeffects/R/get_predictions_glmmTMB.R | 5 ggeffects-0.13.0/ggeffects/R/get_predictions_lm.R | 3 ggeffects-0.13.0/ggeffects/R/get_predictions_multinom.R | 6 ggeffects-0.13.0/ggeffects/R/get_predictions_ols.R | 1 ggeffects-0.13.0/ggeffects/R/get_predictions_polr.R | 4 ggeffects-0.13.0/ggeffects/R/get_predictions_stan.R | 3 ggeffects-0.13.0/ggeffects/R/get_predictions_zeroinfl.R | 26 - ggeffects-0.13.0/ggeffects/R/getter.R | 3 ggeffects-0.13.0/ggeffects/R/ggeffect.R | 36 + ggeffects-0.13.0/ggeffects/R/ggemmeans.R | 132 ++---- ggeffects-0.13.0/ggeffects/R/ggemmeans_add_confint.R | 73 ++- ggeffects-0.13.0/ggeffects/R/ggemmeans_predict_models.R | 12 ggeffects-0.13.0/ggeffects/R/ggemmeans_zi_predictions.R | 22 + ggeffects-0.13.0/ggeffects/R/ggpredict.R | 108 +---- ggeffects-0.13.0/ggeffects/R/moderator_pattern.R | 5 ggeffects-0.13.0/ggeffects/R/plot.R | 98 +++- ggeffects-0.13.0/ggeffects/R/post_processing_labels.R |only ggeffects-0.13.0/ggeffects/R/post_processing_predictions.R |only ggeffects-0.13.0/ggeffects/R/predict_standard_errors_from_vcov.R | 49 -- ggeffects-0.13.0/ggeffects/R/predict_zero_inflation.R | 7 ggeffects-0.13.0/ggeffects/R/predictions.R | 10 ggeffects-0.13.0/ggeffects/R/print.R | 28 - ggeffects-0.13.0/ggeffects/R/select_helpers.R | 4 ggeffects-0.13.0/ggeffects/R/themes.R | 66 +-- ggeffects-0.13.0/ggeffects/R/utils.R | 39 + ggeffects-0.13.0/ggeffects/R/utils_colors.R | 36 - ggeffects-0.13.0/ggeffects/R/utils_get_data_grid.R | 7 ggeffects-0.13.0/ggeffects/R/utils_ggpredict.R | 27 - ggeffects-0.13.0/ggeffects/R/utils_handle_labels.R | 21 - ggeffects-0.13.0/ggeffects/R/utils_model_function.R | 10 ggeffects-0.13.0/ggeffects/R/utils_set_attr.R | 4 ggeffects-0.13.0/ggeffects/R/vcov.R |only ggeffects-0.13.0/ggeffects/README.md | 30 - ggeffects-0.13.0/ggeffects/build/partial.rdb |binary ggeffects-0.13.0/ggeffects/inst/doc/ggeffects.html | 4 ggeffects-0.13.0/ggeffects/inst/doc/introduction_effectsatvalues.html | 6 ggeffects-0.13.0/ggeffects/inst/doc/introduction_plotcustomize.R | 2 ggeffects-0.13.0/ggeffects/inst/doc/introduction_plotcustomize.Rmd | 2 ggeffects-0.13.0/ggeffects/inst/doc/introduction_plotcustomize.html | 8 ggeffects-0.13.0/ggeffects/inst/doc/introduction_plotmethod.R | 3 ggeffects-0.13.0/ggeffects/inst/doc/introduction_plotmethod.Rmd | 3 ggeffects-0.13.0/ggeffects/inst/doc/introduction_plotmethod.html | 17 ggeffects-0.13.0/ggeffects/inst/doc/introduction_randomeffects.html | 62 +-- ggeffects-0.13.0/ggeffects/inst/doc/practical_logisticmixedmodel.html | 4 ggeffects-0.13.0/ggeffects/inst/doc/technical_differencepredictemmeans.html | 58 +- ggeffects-0.13.0/ggeffects/inst/doc/technical_stata.R | 70 --- ggeffects-0.13.0/ggeffects/inst/doc/technical_stata.Rmd | 107 ----- ggeffects-0.13.0/ggeffects/inst/doc/technical_stata.html | 130 ------ ggeffects-0.13.0/ggeffects/man/figures/unnamed-chunk-3-1.png |binary ggeffects-0.13.0/ggeffects/man/figures/unnamed-chunk-4-1.png |binary ggeffects-0.13.0/ggeffects/man/figures/unnamed-chunk-5-1.png |binary ggeffects-0.13.0/ggeffects/man/figures/unnamed-chunk-6-1.png |binary ggeffects-0.13.0/ggeffects/man/ggpredict.Rd | 13 ggeffects-0.13.0/ggeffects/man/plot.Rd | 12 ggeffects-0.13.0/ggeffects/man/values_at.Rd | 3 ggeffects-0.13.0/ggeffects/man/vcov.Rd |only ggeffects-0.13.0/ggeffects/tests/testthat/test-MixMod.R | 13 ggeffects-0.13.0/ggeffects/tests/testthat/test-clm.R | 34 - ggeffects-0.13.0/ggeffects/tests/testthat/test-clm2.R | 24 - ggeffects-0.13.0/ggeffects/tests/testthat/test-clmm.R | 12 ggeffects-0.13.0/ggeffects/tests/testthat/test-correct_se_sorting.R |only ggeffects-0.13.0/ggeffects/tests/testthat/test-decimals.R | 198 +++++----- ggeffects-0.13.0/ggeffects/tests/testthat/test-gamm.R | 8 ggeffects-0.13.0/ggeffects/tests/testthat/test-polr.R | 10 ggeffects-0.13.0/ggeffects/tests/testthat/test-vglm.R | 94 ++-- ggeffects-0.13.0/ggeffects/vignettes/introduction_plotcustomize.Rmd | 2 ggeffects-0.13.0/ggeffects/vignettes/introduction_plotmethod.Rmd | 3 ggeffects-0.13.0/ggeffects/vignettes/technical_stata.Rmd | 107 ----- 79 files changed, 843 insertions(+), 1283 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.14.0 dated 2019-07-02 and 1.15.0 dated 2019-11-08
DESCRIPTION | 6 +- MD5 | 64 +++++++++++------------ NEWS | 48 ++++++++++++++++- R/ClusterFuture-class.R | 7 +- R/Future-class.R | 51 +++++++++--------- R/FutureCondition-class.R | 12 +--- R/FutureRegistry.R | 4 - R/MulticoreFuture-class.R | 7 +- R/future.R | 2 R/futureAssign_OP.R | 8 ++ R/globals.R | 3 - R/makeClusterPSOCK.R | 51 ++++++++++++++++-- R/options.R | 12 ++-- R/resolve.R | 26 +++++---- R/signalConditions.R | 52 +++++++++++++++++- R/utils.R | 12 +++- R/uuid.R | 4 - build/vignette.rds |binary demo/mandelbrot.R | 27 ++++----- inst/doc/future-4-issues.html | 17 ++++++ inst/doc/future-4-issues.md.rsp | 17 +++++- inst/doc/future-4-non-exportable-objects.html | 34 ++++++++++++ inst/doc/future-4-non-exportable-objects.md.rsp | 33 +++++++++++ man/autoStopCluster.Rd | 2 man/future.options.Rd | 12 ++-- man/makeClusterPSOCK.Rd | 49 ++++++++++++++++- man/resolve.Rd | 5 - tests/cluster.R | 12 ---- tests/immediateCondition.R | 15 ++++- tests/multiprocess.R | 10 --- tests/multisession.R | 5 - vignettes/future-4-issues.md.rsp | 17 +++++- vignettes/future-4-non-exportable-objects.md.rsp | 33 +++++++++++ 33 files changed, 496 insertions(+), 161 deletions(-)
Title: Exploring Election and Census Highly Informative Data Nationally
for Australia
Description: Data from the seven Australian Federal Elections (House of
Representatives) between 2001 and 2019, and from the four Australian
Censuses over the same period. Includes tools for visualizing and
analysing the data, as well as imputing Census data for years in
which a Census does not occur. This package incorporates
data that is copyright Commonwealth of Australia (Australian
Electoral Commission and Australian Bureau of Statistics) 2019.
Author: Di Cook [aut],
Anthony Ebert [aut],
Jeremy Forbes [aut, cre],
Heike Hofmann [aut],
Rob Hyndman [aut],
Thomas Lumley [aut],
Ben Marwick [aut],
Carson Sievert [aut],
Mingzhu Sun [aut],
Dilini Talagala [aut],
Nicholas Tierney [aut],
Nathaniel Tomasetti [aut],
Earo Wang [aut],
Fang Zhou [aut],
Commonwealth of Australia AEC [cph],
Australian Bureau of Statistics ABS [cph]
Maintainer: Jeremy Forbes <jeremyforbes1995@gmail.com>
Diff between eechidna versions 1.3.0 dated 2019-03-17 and 1.4.0 dated 2019-11-08
eechidna-1.3.0/eechidna/data/abs2006_e07.rda |only eechidna-1.3.0/eechidna/data/datalist |only eechidna-1.3.0/eechidna/man/abs2006_e07.Rd |only eechidna-1.3.0/eechidna/vignettes/fig |only eechidna-1.4.0/eechidna/DESCRIPTION | 19 eechidna-1.4.0/eechidna/MD5 | 201 ++--- eechidna-1.4.0/eechidna/NAMESPACE | 10 eechidna-1.4.0/eechidna/R/cartogram.R | 18 eechidna-1.4.0/eechidna/R/data.R | 393 +++++++--- eechidna-1.4.0/eechidna/R/git-download.R | 293 +++++-- eechidna-1.4.0/eechidna/R/global.R | 2 eechidna-1.4.0/eechidna/R/imports.R | 6 eechidna-1.4.0/eechidna/R/interpolation.R | 266 ++++++ eechidna-1.4.0/eechidna/R/shapefiles.R | 2 eechidna-1.4.0/eechidna/data/abs2004.rda |binary eechidna-1.4.0/eechidna/data/abs2007.rda |binary eechidna-1.4.0/eechidna/data/abs2010.rda |binary eechidna-1.4.0/eechidna/data/abs2013.rda |binary eechidna-1.4.0/eechidna/data/abs2019.rda |only eechidna-1.4.0/eechidna/data/fp01.rda |binary eechidna-1.4.0/eechidna/data/fp04.rda |binary 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eechidna-1.4.0/eechidna/man/twoparty_pollingbooth_download.Rd | 6 eechidna-1.4.0/eechidna/man/weighted_avg_census.Rd | 8 eechidna-1.4.0/eechidna/man/weighted_avg_census_sa1.Rd |only eechidna-1.4.0/eechidna/tests/testthat/test-census.R | 5 eechidna-1.4.0/eechidna/tests/testthat/test-imputation.R | 40 - eechidna-1.4.0/eechidna/vignettes/eechidna-intro.Rmd | 27 112 files changed, 1184 insertions(+), 452 deletions(-)
Title: A Minimal Tool Set for Gathering USDA Quick Stat Data for
Analysis and Visualization
Description: Provides a consistent API to pull United States
Department of Agriculture census and survey data from the National
Agricultural Statistics Service (NASS) QuickStats service
<https://quickstats.nass.usda.gov>.
Author: Brad Lindblad [aut, cre],
Michael Thomas [ctb],
Alex Mindeman [ctb]
Maintainer: Brad Lindblad <bradley.lindblad@gmail.com>
Diff between tidyUSDA versions 0.2.3 dated 2019-11-02 and 0.2.4 dated 2019-11-08
DESCRIPTION | 6 +- MD5 | 10 ++-- NEWS.md | 4 + R/getQuickstat.R | 92 ++++++++++++++++++++++++++++++------------- inst/doc/using_tidyusda.html | 4 - man/getQuickstat.Rd | 6 ++ 6 files changed, 83 insertions(+), 39 deletions(-)
Title: Scatter Pie Plot
Description: Creates scatterpie plots, especially useful for plotting pies on a map.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scatterpie versions 0.1.3 dated 2019-09-26 and 0.1.4 dated 2019-11-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 4 ++++ R/geom_scatterpie.R | 16 ++++++++++------ inst/doc/scatterpie.html | 22 +++++++++++----------- man/geom_scatterpie.Rd | 6 ++++-- 6 files changed, 37 insertions(+), 27 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 2.0.4 dated 2019-10-02 and 2.0.5 dated 2019-11-08
DESCRIPTION | 24 - MD5 | 137 +++--- NAMESPACE | 1 NEWS.md | 12 R/class_analysis_dataset.R | 6 R/class_analysis_results.R | 6 R/class_analysis_stage_results.R | 6 R/class_core_parameter_set.R | 79 +--- R/class_core_plot_settings.R | 6 R/class_design.R | 22 - R/class_design_plan.R | 91 ++-- R/class_design_power_and_asn.R | 6 R/class_design_set.R | 6 R/class_event_probabilities.R | 12 R/class_simulation_results.R | 42 +- R/class_summary.R |only R/class_time.R | 235 ++++++++---- R/f_analysis_means_multiarmed.R | 54 +- R/f_core_assertions.R | 13 R/f_core_constants.R | 29 - R/f_core_output_formats.R | 10 R/f_core_utilities.R | 38 + R/f_design_group_sequential.R | 19 R/f_design_sample_size_calculator.R | 195 ++++++--- R/f_design_utilities.R | 235 ------------ R/f_simulation_means.R | 8 R/f_simulation_survival.R | 20 - inst/tests/testthat/test-class_analysis_dataset.R | 2 inst/tests/testthat/test-class_summary.R |only inst/tests/testthat/test-class_time.R | 235 +++++++++++- inst/tests/testthat/test-f_analysis_means.R | 111 +++-- inst/tests/testthat/test-f_analysis_rates.R | 2 inst/tests/testthat/test-f_analysis_survival.R | 2 inst/tests/testthat/test-f_core_assertions.R | 2 inst/tests/testthat/test-f_core_output_formats.R | 8 inst/tests/testthat/test-f_core_utilities.R | 9 inst/tests/testthat/test-f_design_fisher_combination_test.R | 2 inst/tests/testthat/test-f_design_group_sequential_design.R | 2 inst/tests/testthat/test-f_design_power_calculator.R | 33 - inst/tests/testthat/test-f_design_sample_size_calculator.R | 140 ++++++- inst/tests/testthat/test-f_design_utilities.R | 2 inst/tests/testthat/test-f_simulation_means.R | 2 inst/tests/testthat/test-f_simulation_rates.R | 2 inst/tests/testthat/test-f_simulation_survival.R | 2 man/ParameterSet_summary.Rd | 17 man/TrialDesignPlanSurvival_summary.Rd | 3 man/getDesignGroupSequential.Rd | 3 man/getPiecewiseSurvivalTime.Rd | 9 man/getPowerRates.Rd | 13 man/getPowerSurvival.Rd | 32 - man/getSampleSizeSurvival.Rd | 37 + man/getSimulationSurvival.Rd | 19 man/printCitation.Rd |only man/sub-TrialDesignSet-ANY-ANY-ANY-method.Rd |only man/testPackage.Rd | 2 tests/testthat/test-class_analysis_dataset.R | 2 tests/testthat/test-class_summary.R |only tests/testthat/test-class_time.R | 235 +++++++++++- tests/testthat/test-f_analysis_means.R | 111 +++-- tests/testthat/test-f_analysis_rates.R | 2 tests/testthat/test-f_analysis_survival.R | 2 tests/testthat/test-f_core_assertions.R | 2 tests/testthat/test-f_core_output_formats.R | 8 tests/testthat/test-f_core_utilities.R | 9 tests/testthat/test-f_design_fisher_combination_test.R | 2 tests/testthat/test-f_design_group_sequential_design.R | 2 tests/testthat/test-f_design_power_calculator.R | 33 - tests/testthat/test-f_design_sample_size_calculator.R | 140 ++++++- tests/testthat/test-f_design_utilities.R | 2 tests/testthat/test-f_simulation_means.R | 2 tests/testthat/test-f_simulation_rates.R | 2 tests/testthat/test-f_simulation_survival.R | 2 72 files changed, 1664 insertions(+), 895 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. pathfindR is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
pathfindR also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in pathfindR are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for
Comprehensive Identification of Enriched Pathways in Omics Data Through
Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.
Author: Ege Ulgen, Ozan Ozisik
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 1.3.0 dated 2018-11-20 and 1.4.0 dated 2019-11-08
pathfindR-1.3.0/pathfindR/R/clustering.R |only pathfindR-1.3.0/pathfindR/R/scores.R |only pathfindR-1.3.0/pathfindR/data/biocarta_pathways.rda |only pathfindR-1.3.0/pathfindR/data/datalist |only pathfindR-1.3.0/pathfindR/data/go_all_pathways.rda |only pathfindR-1.3.0/pathfindR/data/go_bp_genes.rda |only pathfindR-1.3.0/pathfindR/data/go_bp_pathways.rda |only pathfindR-1.3.0/pathfindR/data/go_cc_genes.rda |only pathfindR-1.3.0/pathfindR/data/go_cc_pathways.rda |only pathfindR-1.3.0/pathfindR/data/go_mf_genes.rda |only pathfindR-1.3.0/pathfindR/data/go_mf_pathways.rda |only pathfindR-1.3.0/pathfindR/data/kegg_pathways.rda |only pathfindR-1.3.0/pathfindR/data/reactome_pathways.rda |only pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_manual_exec.R |only pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_manual_exec.Rmd |only pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_manual_exec.html |only pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_vignette.R |only 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pathfindR-1.4.0/pathfindR/R/active_snw_functions.R | 258 - pathfindR-1.4.0/pathfindR/R/clustering_functions.R |only pathfindR-1.4.0/pathfindR/R/core_functions.R | 844 ++-- pathfindR-1.4.0/pathfindR/R/data.R | 383 + pathfindR-1.4.0/pathfindR/R/enrichment_functions.R | 368 + pathfindR-1.4.0/pathfindR/R/pathfindR.R | 59 pathfindR-1.4.0/pathfindR/R/scoring.R |only pathfindR-1.4.0/pathfindR/R/sysdata.rda |only pathfindR-1.4.0/pathfindR/R/visualization_functions.R | 953 +++- pathfindR-1.4.0/pathfindR/build/vignette.rds |binary pathfindR-1.4.0/pathfindR/data/RA_clustered.rda |binary pathfindR-1.4.0/pathfindR/data/RA_input.rda |binary pathfindR-1.4.0/pathfindR/data/RA_output.rda |binary pathfindR-1.4.0/pathfindR/data/biocarta_descriptions.rda |only pathfindR-1.4.0/pathfindR/data/biocarta_genes.rda |binary pathfindR-1.4.0/pathfindR/data/custom_result.rda |binary pathfindR-1.4.0/pathfindR/data/example_active_snws.rda |binary pathfindR-1.4.0/pathfindR/data/go_all_genes.rda |binary 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pathfindR-1.4.0/pathfindR/java/Application/Parameters.java | 4 pathfindR-1.4.0/pathfindR/java/File/ExperimentFileReader.java | 2 pathfindR-1.4.0/pathfindR/java/File/SIFReader.java | 4 pathfindR-1.4.0/pathfindR/java/Network/Network.java | 6 pathfindR-1.4.0/pathfindR/man/GO_all_terms_df.Rd |only pathfindR-1.4.0/pathfindR/man/RA_clustered.Rd | 42 pathfindR-1.4.0/pathfindR/man/RA_exp_mat.Rd | 16 pathfindR-1.4.0/pathfindR/man/RA_input.Rd | 20 pathfindR-1.4.0/pathfindR/man/RA_output.Rd | 33 pathfindR-1.4.0/pathfindR/man/active_snw_search.Rd | 94 pathfindR-1.4.0/pathfindR/man/annotate_term_genes.Rd |only pathfindR-1.4.0/pathfindR/man/biocarta_descriptions.Rd |only pathfindR-1.4.0/pathfindR/man/biocarta_genes.Rd | 8 pathfindR-1.4.0/pathfindR/man/biogrid_adj_list.Rd |only pathfindR-1.4.0/pathfindR/man/cluster_enriched_terms.Rd |only pathfindR-1.4.0/pathfindR/man/cluster_graph_vis.Rd | 32 pathfindR-1.4.0/pathfindR/man/color_kegg_pathway.Rd |only pathfindR-1.4.0/pathfindR/man/create_kappa_matrix.Rd | 25 pathfindR-1.4.0/pathfindR/man/custom_result.Rd | 4 pathfindR-1.4.0/pathfindR/man/enrichment.Rd | 41 pathfindR-1.4.0/pathfindR/man/enrichment_analyses.Rd | 54 pathfindR-1.4.0/pathfindR/man/enrichment_chart.Rd | 54 pathfindR-1.4.0/pathfindR/man/example_active_snws.Rd | 7 pathfindR-1.4.0/pathfindR/man/fetch_gene_set.Rd |only pathfindR-1.4.0/pathfindR/man/filterActiveSnws.Rd | 31 pathfindR-1.4.0/pathfindR/man/fuzzy_term_clustering.Rd |only pathfindR-1.4.0/pathfindR/man/genemania_adj_list.Rd |only pathfindR-1.4.0/pathfindR/man/go_all_genes.Rd | 10 pathfindR-1.4.0/pathfindR/man/hierarchical_term_clustering.Rd |only pathfindR-1.4.0/pathfindR/man/hyperg_test.Rd | 15 pathfindR-1.4.0/pathfindR/man/input_processing.Rd | 31 pathfindR-1.4.0/pathfindR/man/input_testing.Rd | 14 pathfindR-1.4.0/pathfindR/man/intact_adj_list.Rd |only pathfindR-1.4.0/pathfindR/man/kegg_adj_list.Rd |only pathfindR-1.4.0/pathfindR/man/kegg_descriptions.Rd |only 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pathfindR-1.4.0/pathfindR/man/visualize_terms.Rd |only pathfindR-1.4.0/pathfindR/tests |only pathfindR-1.4.0/pathfindR/vignettes/example_interaction_vis.png |only pathfindR-1.4.0/pathfindR/vignettes/intro_vignette.Rmd |only pathfindR-1.4.0/pathfindR/vignettes/man_enrichment_chart.png |only pathfindR-1.4.0/pathfindR/vignettes/manual_execution.Rmd |only pathfindR-1.4.0/pathfindR/vignettes/non_hs_analysis.Rmd |only pathfindR-1.4.0/pathfindR/vignettes/pathfindr.png |binary pathfindR-1.4.0/pathfindR/vignettes/score_hmap.png |only pathfindR-1.4.0/pathfindR/vignettes/term_clustering.png |only pathfindR-1.4.0/pathfindR/vignettes/term_gene.png |only 165 files changed, 3751 insertions(+), 2516 deletions(-)
Title: 'GeoNetwork' API R Interface
Description: Provides an R interface to the 'GeoNetwork' API (<https://geonetwork-opensource.org/#api>) allowing to upload and publish metadata in a 'GeoNetwork' web-application and exposte it to OGC CSW.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geonapi versions 0.2-2 dated 2019-10-18 and 0.3 dated 2019-11-08
DESCRIPTION | 8 +++--- MD5 | 15 ++++++----- R/GNManager.R | 71 ++++++++++++++++++++++++++++++++++++++++++------------- R/GNUtils.R | 41 +++++++++++++++---------------- R/geonapi.R | 4 +-- README.md | 2 - man/geonapi.Rd | 4 +-- tests/resources |only tests/test-all.R | 2 - 9 files changed, 93 insertions(+), 54 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2016) <arXiv:1604.04768>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <http://www.jstor.org/stable/2345592>. See Kosmidis et al (2019) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses (both ordinal and nominal), the adjusted score approaches return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>),
Kjell Konis [ctb],
Euloge Clovis Kenne Pagui [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 0.5.2 dated 2019-10-12 and 0.6.0 dated 2019-11-08
DESCRIPTION | 8 +- MD5 | 38 ++++++----- NEWS.md | 9 ++ R/brglm2-package.R | 39 ++++++------ R/brglmControl.R | 72 ++++++++++++++++++---- R/brglmFit.R | 149 +++++++++++++++++++++++++++++++++++----------- build/vignette.rds |binary inst/doc/adjacent.Rmd | 15 ---- inst/doc/adjacent.html | 2 inst/doc/iteration.Rmd | 45 ++++++++----- inst/doc/iteration.html | 28 +++++++- inst/doc/multinomial.Rmd | 10 --- inst/doc/multinomial.html | 4 - inst/empir_tests.R |only inst/empirical_br_tests.R |only man/brglm2.Rd | 39 ++++++------ man/brglmControl.Rd | 76 +++++++++++++++++++---- man/brglmFit.Rd | 124 ++++++++++++++++++++++++++++---------- vignettes/adjacent.Rmd | 15 ---- vignettes/iteration.Rmd | 45 ++++++++----- vignettes/multinomial.Rmd | 10 --- 21 files changed, 488 insertions(+), 240 deletions(-)
Title: Simple Interface to 'Microsoft Graph'
Description: A simple interface to the 'Microsoft Graph' API <https://docs.microsoft.com/en-us/graph/overview>. 'Graph' is a comprehensive framework for accessing data in various online Microsoft services. Currently, this package aims to provide an R interface only to the 'Azure Active Directory' part, with a view to supporting interoperability of R and 'Azure': users, groups, registered apps and service principals. However it can be easily extended to cover other services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureGraph versions 1.0.5 dated 2019-10-15 and 1.1.0 dated 2019-11-08
DESCRIPTION | 6 - MD5 | 25 ++-- NEWS.md | 9 + R/az_app.r | 98 ++++++++++++---- R/call_graph.R | 33 ++++- R/ms_graph.R | 49 +------- R/read_cert.R |only README.md | 2 inst/doc/intro.Rmd | 29 ++++ inst/doc/intro.html | 241 +++++++++++++++++++++-------------------- man/az_app.Rd | 25 +++- man/ms_graph.Rd | 4 tests/testthat/test02_app_sp.R | 34 +++++ vignettes/intro.Rmd | 29 ++++ 14 files changed, 371 insertions(+), 213 deletions(-)
More information about graphicalExtremes at CRAN
Permanent link
Title: Cyanobacteria Population Identification for Flow Cytometry
Description: An approach to filter out and/or identify synechococcus type cyanobacteria cells from all particles measured via flow cytometry.
It combines known characteristics of these cyanobacteria strains alongside gating techniques developed by Mehrnoush, M. et al. (2015) <doi:10.1093/bioinformatics/btu677>
in the 'flowDensity' package to identify and separate these cyanobacteria cells from other cell types.
Aside the gating techniques in the 'flowDensity' package, an EM style clustering technique
is also developed to identify these cyanobacteria cell populations.
Author: Oluwafemi Olusoji [aut, cre],
Aerts Marc [ctb],
Delaender Frederik [ctb],
Neyens Thomas [ctb],
Spaak jurg [aut]
Maintainer: Oluwafemi Olusoji <oluwafemi.olusoji@uhasselt.be>
Diff between cyanoFilter versions 0.1.1 dated 2019-08-09 and 0.1.2 dated 2019-11-08
DESCRIPTION | 13 ++-- MD5 | 36 ++++++------- R/Margin_Cells.R | 8 ++ R/bs4_nc.R | 51 +++++++++++------- R/bs5_nc.R | 51 ++++++++++-------- R/cell_gating.R | 111 ++++++++++++++++++++++++----------------- R/debris_invasion_nc.R | 8 +- R/debris_nc.R | 28 ++++++---- R/mvt_approach.R | 31 +++++++---- R/plotting_functions.R | 97 ++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/cyanoFilter.html | 38 ++++++++------ man/bs4_nc.Rd | 38 ++++++++------ man/bs5_nc.Rd | 38 ++++++++------ man/celldebris_emclustering.Rd | 12 ++-- man/celldebris_nc.Rd | 44 +++++++++------- man/cluster_plot.Rd | 10 +-- man/debris_inc.Rd | 4 - man/debris_nc.Rd | 19 ++++--- 19 files changed, 379 insertions(+), 258 deletions(-)
Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2. (See the vignette "AER" for a package overview.)
Author: Christian Kleiber [aut] (<https://orcid.org/0000-0002-6781-4733>),
Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between AER versions 1.2-7 dated 2019-07-30 and 1.2-8 dated 2019-11-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 12 +++++++----- NEWS | 10 ++++++++++ R/tobit.R | 27 +++++++++++++++++---------- inst/doc/AER.pdf |binary inst/doc/Sweave-journals.pdf |binary man/tobit.Rd | 3 --- 8 files changed, 45 insertions(+), 29 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-11 1.9
2016-09-15 1.7-2
2014-06-18 1.5-1
2013-06-12 1.5-0
2012-06-11 1.4-8
2011-10-24 1.4-6
2011-06-15 1.4-5
2011-03-08 1.4-4
2011-01-26 1.4-3
2010-11-10 1.4-2
2010-04-07 1.4-1
2010-02-23 1.4-0
2009-04-14 1.3
2008-05-19 1.2-6
2008-03-28 1.2-5
2007-11-23 1.2-3
2007-09-10 1.2-2
2007-04-23 1.2-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-30 1.4.2
2019-07-10 1.4.1
2019-05-09 1.4
2018-12-20 1.3-0.3
2016-10-10 1.2-6.1
2016-09-14 1.2-6
2016-02-09 1.2-4.1
2016-02-02 1.2-4
2014-12-16 1.2-0.1
2014-05-12 1.2-0
2013-11-26 1.1-7
2013-03-25 1.1-4
2012-11-28 1.1-0
2012-05-23 1.0-3
2011-12-07 1.0-0.1
2011-12-01 1.0-0
2011-10-24 0.9-6.3
2011-06-15 0.9-6.2
2011-03-24 0.9-5
2011-03-08 0.9-4
2010-11-11 0.9-3.1
2010-11-10 0.9-3
2010-07-24 0.9-2.1
2010-07-07 0.9-2
2010-05-10 0.9-1.1
2010-04-07 0.9-1
2010-02-23 0.9-0
2009-10-12 0.8-2
2009-09-09 0.8-1
2009-04-15 0.8-0
2008-12-04 0.6-0
2008-05-21 0.5-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-12 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-15 0.7.0
Title: Recurrent Event Regression
Description: A collection of regression models for recurrent event process and failure time data. Available methods include these from Xu et al. (2017) <doi:10.1080/01621459.2016.1173557>, Lin et al. (2000) <doi:10.1111/1467-9868.00259>, Wang et al. (2001) <doi:10.1198/016214501753209031>, Ghosh and Lin (2003) <doi:10.1111/j.0006-341X.2003.00102.x>, and Huang and Wang (2004) <doi:10.1198/016214504000001033>.
Author: Sy Han (Steven) Chiou [aut, cre],
Chiung-Yu Huang [aut]
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Diff between reReg versions 1.1.6 dated 2018-10-22 and 1.2.0 dated 2019-11-08
reReg-1.1.6/reReg/ChangeLog |only reReg-1.1.6/reReg/R/reReg_data.R |only reReg-1.1.6/reReg/man/plot.reSurv.Rd |only reReg-1.1.6/reReg/man/simDat.Rd |only reReg-1.2.0/reReg/DESCRIPTION | 13 reReg-1.2.0/reReg/MD5 | 59 +-- reReg-1.2.0/reReg/NAMESPACE | 38 - reReg-1.2.0/reReg/NEWS.md |only reReg-1.2.0/reReg/R/Recur.R |only reReg-1.2.0/reReg/R/plot.R | 631 +++++++++++++++++---------------- reReg-1.2.0/reReg/R/reReg.R | 401 ++++++++++---------- reReg-1.2.0/reReg/R/reReg_pkg.R | 6 reReg-1.2.0/reReg/R/reSurv.R | 135 ------- reReg-1.2.0/reReg/R/simu.R | 41 +- reReg-1.2.0/reReg/R/summary.R | 14 reReg-1.2.0/reReg/R/util.R |only reReg-1.2.0/reReg/inst/bib/reReg.bib | 21 - reReg-1.2.0/reReg/inst/examples |only reReg-1.2.0/reReg/man/Recur-pipe.Rd |only reReg-1.2.0/reReg/man/Recur.Rd |only reReg-1.2.0/reReg/man/plot.Recur.Rd |only reReg-1.2.0/reReg/man/plot.reReg.Rd | 33 + reReg-1.2.0/reReg/man/plotCSM.Rd | 33 + reReg-1.2.0/reReg/man/plotEvents.Rd | 46 +- reReg-1.2.0/reReg/man/plotHaz.Rd | 31 - reReg-1.2.0/reReg/man/plotRate.Rd | 24 - reReg-1.2.0/reReg/man/reReg-package.Rd | 2 reReg-1.2.0/reReg/man/reReg.Rd | 26 - reReg-1.2.0/reReg/man/reSurv.Rd | 20 - reReg-1.2.0/reReg/man/simSC.Rd |only reReg-1.2.0/reReg/src/init.c | 3 31 files changed, 777 insertions(+), 800 deletions(-)
Title: Routines for Logspline Density Estimation
Description: Contains routines for logspline density estimation.
The function oldlogspline() uses the same algorithm as the logspline package
version 1.0.x; i.e. the Kooperberg and Stone (1992)
algorithm (with an improved interface). The recommended routine logspline()
uses an algorithm from Stone et al (1997) <DOI:10.1214/aos/1031594728>.
Author: Charles Kooperberg [aut, cre],
Cleve Moler [ctb] (LINPACK routines in src),
Jack Dongarra [ctb] (LINPACK routines in src)
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between logspline versions 2.1.14 dated 2019-10-04 and 2.1.15 dated 2019-11-08
DESCRIPTION | 20 ++++++++++++++------ MD5 | 2 +- 2 files changed, 15 insertions(+), 7 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 0.8.6 dated 2019-09-02 and 0.9.0 dated 2019-11-08
DESCRIPTION | 11 - MD5 | 20 +- NAMESPACE | 2 NEWS.md | 4 R/cox2.R | 38 +++-- R/svycox.R | 3 README.md | 163 +++++++--------------- inst/doc/jstable.R | 12 - inst/doc/jstable.Rmd | 12 - inst/doc/jstable.html | 365 ++++++++++---------------------------------------- vignettes/jstable.Rmd | 12 - 11 files changed, 197 insertions(+), 445 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.3.7 dated 2019-10-03 and 0.3.8 dated 2019-11-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/jskm.R | 10 +++++----- inst/doc/jskm.html | 4 ++-- 5 files changed, 19 insertions(+), 15 deletions(-)
Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the
embedded 'ReadStat' C library,
<https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] (Author of included ReadStat code),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between haven versions 2.1.1 dated 2019-07-04 and 2.2.0 dated 2019-11-08
haven-2.1.1/haven/vignettes/rsconnect |only haven-2.2.0/haven/DESCRIPTION | 10 haven-2.2.0/haven/LICENSE | 2 haven-2.2.0/haven/MD5 | 107 ++-- haven-2.2.0/haven/NAMESPACE | 1 haven-2.2.0/haven/NEWS.md | 33 + haven-2.2.0/haven/R/RcppExports.R | 44 - haven-2.2.0/haven/R/as_factor.R | 2 haven-2.2.0/haven/R/haven.R | 155 ++++-- haven-2.2.0/haven/R/labelled.R | 6 haven-2.2.0/haven/R/tagged_na.R | 2 haven-2.2.0/haven/R/zap_label.R | 8 haven-2.2.0/haven/R/zap_labels.R | 7 haven-2.2.0/haven/README.md | 15 haven-2.2.0/haven/inst/doc/semantics.html | 30 - haven-2.2.0/haven/man/read_dta.Rd | 38 + haven-2.2.0/haven/man/read_sas.Rd | 44 + haven-2.2.0/haven/man/read_spss.Rd | 33 + haven-2.2.0/haven/man/read_xpt.Rd | 27 + haven-2.2.0/haven/man/zap_label.Rd | 3 haven-2.2.0/haven/man/zap_labels.Rd | 8 haven-2.2.0/haven/src/DfReader.cpp | 254 ++++------ haven-2.2.0/haven/src/DfWriter.cpp | 51 +- haven-2.2.0/haven/src/RcppExports.cpp | 131 +++-- haven-2.2.0/haven/src/haven_types.cpp | 55 +- haven-2.2.0/haven/src/haven_types.h | 24 haven-2.2.0/haven/src/readstat/readstat.h | 7 haven-2.2.0/haven/src/readstat/readstat_error.c | 5 haven-2.2.0/haven/src/readstat/readstat_parser.c | 5 haven-2.2.0/haven/src/readstat/sas/readstat_sas.c | 4 haven-2.2.0/haven/src/readstat/sas/readstat_sas7bdat_read.c | 18 haven-2.2.0/haven/src/readstat/sas/readstat_xport_read.c | 14 haven-2.2.0/haven/src/readstat/sas/readstat_xport_write.c | 12 haven-2.2.0/haven/src/readstat/spss/readstat_por.h | 1 haven-2.2.0/haven/src/readstat/spss/readstat_por_read.c | 18 haven-2.2.0/haven/src/readstat/spss/readstat_por_write.c | 5 haven-2.2.0/haven/src/readstat/spss/readstat_sav.h | 1 haven-2.2.0/haven/src/readstat/spss/readstat_sav_parse_timestamp.c | 4 haven-2.2.0/haven/src/readstat/spss/readstat_sav_parse_timestamp.rl | 4 haven-2.2.0/haven/src/readstat/spss/readstat_sav_read.c | 32 + haven-2.2.0/haven/src/readstat/spss/readstat_sav_write.c | 23 haven-2.2.0/haven/src/readstat/spss/readstat_zsav_read.c | 4 haven-2.2.0/haven/src/readstat/stata/readstat_dta.h | 1 haven-2.2.0/haven/src/readstat/stata/readstat_dta_parse_timestamp.c | 2 haven-2.2.0/haven/src/readstat/stata/readstat_dta_parse_timestamp.rl | 2 haven-2.2.0/haven/src/readstat/stata/readstat_dta_read.c | 22 haven-2.2.0/haven/src/readstat/stata/readstat_dta_write.c | 11 haven-2.2.0/haven/tests/testthat/helper-roundtrip.R | 26 - haven-2.2.0/haven/tests/testthat/test-as-factor.R | 7 haven-2.2.0/haven/tests/testthat/test-read-sas.R | 102 ++++ haven-2.2.0/haven/tests/testthat/test-read-sav.R | 40 + haven-2.2.0/haven/tests/testthat/test-read-stata.R | 39 + haven-2.2.0/haven/tests/testthat/test-write-dta.R | 32 + haven-2.2.0/haven/tests/testthat/test-write-sas.R | 10 haven-2.2.0/haven/tests/testthat/test-zap_label.R | 5 55 files changed, 1080 insertions(+), 466 deletions(-)