Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.
Author: Oeyvind Langsrud [aut, cre],
Johan Heldal [aut]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SmallCountRounding versions 1.0.3 dated 2022-11-16 and 1.0.5 dated 2024-09-05
DESCRIPTION | 16 - LICENSE |only MD5 | 43 ++--- NEWS.md | 5 R/PLSrounding.R | 2 R/PLSroundingFits.R | 4 R/RoundViaDummy.R | 10 - R/SmallCountData.R | 4 R/SmallCountRounding-package.R | 3 R/aggrtab.R | 6 R/makeroundtabs.R | 4 R/redcube.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_SmallCountRounding.html | 192 +++++++++++------------ man/PLSrounding.Rd | 2 man/PLSroundingFits.Rd | 4 man/RoundViaDummy.Rd | 10 - man/SmallCountData.Rd | 4 man/SmallCountRounding-package.Rd | 17 ++ man/aggrtab.Rd | 4 man/makeroundtabs.Rd | 2 man/redcube.Rd | 2 23 files changed, 180 insertions(+), 158 deletions(-)
More information about SmallCountRounding at CRAN
Permanent link
Title: Tools for Processing and Analyzing Files from the Hydrological
Catchment Model HYPE
Description: Work with model files (setup, input, output) from
the hydrological catchment model HYPE: Streamlined file import and export, standard
evaluation plot routines, diverse post-processing and aggregation routines
for hydrological model analysis. The HYPEtools package is also archived at <doi:10.5281/zenodo.7627955>
and can be cited in publications with Brendel et al. (2024) <doi:10.1016/j.envsoft.2024.106094>.
Author: Rene Capell [aut, cre] ,
Conrad Brendel [aut] ,
Jafet Andersson [ctb],
David Gustafsson [ctb],
Jude Musuuza [ctb],
Jude Lubega [ctb]
Maintainer: Rene Capell <hypetools.rene@smhi.se>
Diff between HYPEtools versions 1.6.2 dated 2024-05-23 and 1.6.3 dated 2024-09-05
DESCRIPTION | 9 - MD5 | 71 ++++++------- NAMESPACE | 2 NEWS.md | 13 ++ R/distinctColorPalette.R | 2 R/function_CompareFiles.R | 6 - R/function_PlotMapOutput.R | 32 ++--- R/function_PlotMapPoints.R | 44 ++++---- R/function_PlotPerformanceByAttribute.R | 168 +++++++++++++++++++------------ R/function_ReadWsOutput.R | 2 R/function_SubidAttributeSummary.R | 4 R/functioncollection_Harmonized.R | 16 ++ R/functioncollection_export.R | 2 R/functioncollection_import.R | 18 +-- R/sysdata.rda |binary README.md | 43 ++++--- build/partial.rdb |only build/vignette.rds |binary inst/doc/basin_network.html | 2 inst/doc/plot_map_statistics.html | 4 man/CompareFiles.Rd | 6 - man/HYPEtools-package.Rd | 2 man/PlotMapOutput.Rd | 32 ++--- man/PlotMapPoints.Rd | 44 ++++---- man/PlotPerformanceByAttribute.Rd | 58 +++++----- man/ReadBasinOutput.Rd | 4 man/ReadGeoData.Rd | 2 man/ReadMapOutput.Rd | 4 man/ReadObs.Rd | 2 man/ReadTimeOutput.Rd | 4 man/ReadWsOutput.Rd | 2 man/ReadXobs.Rd | 2 man/SubidAttributeSummary.Rd | 4 man/WriteHarmonizedData.Rd | 4 man/WriteHarmonizedSpatialDescription.Rd | 4 man/WriteXobs.Rd | 2 man/distinctColorPalette.Rd | 2 37 files changed, 347 insertions(+), 269 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predicti [...truncated...]
Author: John Wambaugh [aut, cre] ,
Sarah Davidson-Fritz [aut] ,
Robert Pearce [aut] ,
Caroline Ring [aut] ,
Greg Honda [aut] ,
Mark Sfeir [aut],
Matt Linakis [aut] ,
Dustin Kapraun [aut] ,
Nathan Pollesch [ctb] ,
Miyuki Breen [ctb] ,
Shannon Bell [ctb] ,
Xia [...truncated...]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 2.3.1 dated 2024-03-26 and 2.4.0 dated 2024-09-05
httk-2.3.1/httk/R/convert_httkpop_1comp.R |only httk-2.3.1/httk/R/get_fabsgut.R |only httk-2.3.1/httk/man/convert_httkpop_1comp.Rd |only httk-2.3.1/httk/man/get_fabsgut.Rd |only httk-2.4.0/httk/DESCRIPTION | 15 httk-2.4.0/httk/MD5 | 313 +-- httk-2.4.0/httk/NAMESPACE | 2 httk-2.4.0/httk/NEWS.md | 59 httk-2.4.0/httk/R/armitage.R | 22 httk-2.4.0/httk/R/available_rblood2plasma.R | 11 httk-2.4.0/httk/R/benchmark_httk.R | 131 + httk-2.4.0/httk/R/calc_analytic_css.R | 190 +- httk-2.4.0/httk/R/calc_analytic_css_1comp.R | 112 - httk-2.4.0/httk/R/calc_analytic_css_3comp.R | 178 +- httk-2.4.0/httk/R/calc_analytic_css_3compss.R | 113 + httk-2.4.0/httk/R/calc_analytic_css_pbtk.R | 106 - httk-2.4.0/httk/R/calc_css.R | 62 httk-2.4.0/httk/R/calc_elimination_rate.R | 4 httk-2.4.0/httk/R/calc_half_life.R | 4 httk-2.4.0/httk/R/calc_hep_bioavailability.R | 16 httk-2.4.0/httk/R/calc_hep_clearance.R | 64 httk-2.4.0/httk/R/calc_kair.R | 42 httk-2.4.0/httk/R/calc_mc_css.R | 8 httk-2.4.0/httk/R/calc_mc_oral_equiv.R | 4 httk-2.4.0/httk/R/calc_mc_tk.R | 28 httk-2.4.0/httk/R/calc_oral_bioavailability.R | 393 ++++ httk-2.4.0/httk/R/calc_rblood2plasma.R | 8 httk-2.4.0/httk/R/calc_volume_of_distribution.R | 6 httk-2.4.0/httk/R/check_model.R |only httk-2.4.0/httk/R/convert_solve_x.R | 2 httk-2.4.0/httk/R/create_mc_samples.R | 88 - httk-2.4.0/httk/R/data.R | 82 - httk-2.4.0/httk/R/get_caco2.R | 4 httk-2.4.0/httk/R/get_chem_id.R | 7 httk-2.4.0/httk/R/get_cheminfo.R | 33 httk-2.4.0/httk/R/get_fbio.R |only httk-2.4.0/httk/R/get_weight_class.R | 2 httk-2.4.0/httk/R/httkpop_generate.R | 42 httk-2.4.0/httk/R/httkpop_mc.R | 21 httk-2.4.0/httk/R/invitro_mc.R | 10 httk-2.4.0/httk/R/load_dawson2021.R | 2 httk-2.4.0/httk/R/load_honda2023.R | 2 httk-2.4.0/httk/R/load_pradeep2020.R | 2 httk-2.4.0/httk/R/modelinfo_1comp.R | 67 httk-2.4.0/httk/R/modelinfo_3comp.R | 155 - httk-2.4.0/httk/R/modelinfo_3compss.R | 43 httk-2.4.0/httk/R/modelinfo_fetal_pbtk.R | 58 httk-2.4.0/httk/R/modelinfo_gas_pbtk.R | 86 - httk-2.4.0/httk/R/modelinfo_pbtk.R | 85 - httk-2.4.0/httk/R/onAtttach.R |only httk-2.4.0/httk/R/parameterize_1comp.R | 4 httk-2.4.0/httk/R/parameterize_3comp.R | 6 httk-2.4.0/httk/R/parameterize_fetal_pbtk.R | 5 httk-2.4.0/httk/R/parameterize_gas_pbtk.R | 30 httk-2.4.0/httk/R/parameterize_pbtk.R | 32 httk-2.4.0/httk/R/parameterize_schmitt.R | 58 httk-2.4.0/httk/R/parameterize_steadystate.R | 23 httk-2.4.0/httk/R/predict_partitioning_schmitt.R | 47 httk-2.4.0/httk/R/scale_dosing.R | 2 httk-2.4.0/httk/R/solve_1comp.R | 18 httk-2.4.0/httk/R/solve_3comp.R | 46 httk-2.4.0/httk/R/solve_fetal_pbtk.R | 91 - httk-2.4.0/httk/R/solve_gas_pbtk.R | 44 httk-2.4.0/httk/R/solve_model.R | 123 + httk-2.4.0/httk/R/solve_pbtk.R | 74 httk-2.4.0/httk/R/sysdata.rda |binary httk-2.4.0/httk/build/partial.rdb |binary httk-2.4.0/httk/build/vignette.rds |binary httk-2.4.0/httk/data/Tables.RData |binary httk-2.4.0/httk/inst/REFERENCES.bib | 165 ++ httk-2.4.0/httk/inst/doc/V1_IntroToHTTK.html | 138 - httk-2.4.0/httk/inst/doc/V2_IntrotoIVIVE.R | 246 +-- httk-2.4.0/httk/inst/doc/V2_IntrotoIVIVE.Rmd | 44 httk-2.4.0/httk/inst/doc/V2_IntrotoIVIVE.html | 702 ++------ httk-2.4.0/httk/inst/doc/Va_Pearce2017.R | 9 httk-2.4.0/httk/inst/doc/Va_Pearce2017.Rmd | 13 httk-2.4.0/httk/inst/doc/Va_Pearce2017.html | 619 +++---- httk-2.4.0/httk/inst/doc/Vb_Ring2017.html | 4 httk-2.4.0/httk/inst/doc/Ve_Wambaugh2018.html | 4 httk-2.4.0/httk/inst/doc/Vg_Wambaugh2019.html | 4 httk-2.4.0/httk/inst/doc/Vh_Linakis2020.R | 219 +- httk-2.4.0/httk/inst/doc/Vh_Linakis2020.Rmd | 228 ++ httk-2.4.0/httk/inst/doc/Vh_Linakis2020.html | 1448 +++++++++--------- httk-2.4.0/httk/inst/doc/Vi_Kapraun2022.html | 4 httk-2.4.0/httk/man/available_rblood2plasma.Rd | 4 httk-2.4.0/httk/man/calc_analytic_css.Rd | 24 httk-2.4.0/httk/man/calc_analytic_css_1comp.Rd | 13 httk-2.4.0/httk/man/calc_analytic_css_3comp.Rd | 39 httk-2.4.0/httk/man/calc_analytic_css_3compss.Rd | 38 httk-2.4.0/httk/man/calc_analytic_css_pbtk.Rd | 30 httk-2.4.0/httk/man/calc_css.Rd | 11 httk-2.4.0/httk/man/calc_elimination_rate.Rd | 2 httk-2.4.0/httk/man/calc_fbio.oral.Rd | 57 httk-2.4.0/httk/man/calc_half_life.Rd | 2 httk-2.4.0/httk/man/calc_hep_clearance.Rd | 52 httk-2.4.0/httk/man/calc_kair.Rd | 12 httk-2.4.0/httk/man/calc_mc_css.Rd | 7 httk-2.4.0/httk/man/calc_mc_oral_equiv.Rd | 4 httk-2.4.0/httk/man/calc_mc_tk.Rd | 5 httk-2.4.0/httk/man/calc_rblood2plasma.Rd | 4 httk-2.4.0/httk/man/check_model.Rd |only httk-2.4.0/httk/man/chem.invivo.PK.aggregate.data.Rd | 52 httk-2.4.0/httk/man/concentration_data_Linakis2020.Rd | 37 httk-2.4.0/httk/man/convert_solve_x.Rd | 2 httk-2.4.0/httk/man/create_mc_samples.Rd | 33 httk-2.4.0/httk/man/get_caco2.Rd | 4 httk-2.4.0/httk/man/get_cheminfo.Rd | 9 httk-2.4.0/httk/man/get_fbio.Rd |only httk-2.4.0/httk/man/get_weight_class.Rd | 2 httk-2.4.0/httk/man/honda2023.data.Rd | 4 httk-2.4.0/httk/man/httk-package.Rd | 3 httk-2.4.0/httk/man/httk.performance.Rd | 2 httk-2.4.0/httk/man/httkpop_generate.Rd | 42 httk-2.4.0/httk/man/invitro_mc.Rd | 5 httk-2.4.0/httk/man/load_dawson2021.Rd | 2 httk-2.4.0/httk/man/load_honda2023.Rd | 2 httk-2.4.0/httk/man/load_pradeep2020.Rd | 2 httk-2.4.0/httk/man/metabolism_data_Linakis2020.Rd | 3 httk-2.4.0/httk/man/parameterize_1comp.Rd | 4 httk-2.4.0/httk/man/parameterize_3comp.Rd | 4 httk-2.4.0/httk/man/parameterize_gas_pbtk.Rd | 8 httk-2.4.0/httk/man/parameterize_pbtk.Rd | 10 httk-2.4.0/httk/man/parameterize_schmitt.Rd | 4 httk-2.4.0/httk/man/parameterize_steadystate.Rd | 6 httk-2.4.0/httk/man/physiology.data.Rd | 36 httk-2.4.0/httk/man/predict_partitioning_schmitt.Rd | 2 httk-2.4.0/httk/man/solve_1comp.Rd | 24 httk-2.4.0/httk/man/solve_3comp.Rd | 42 httk-2.4.0/httk/man/solve_fetal_pbtk.Rd | 66 httk-2.4.0/httk/man/solve_gas_pbtk.Rd | 44 httk-2.4.0/httk/man/solve_model.Rd | 22 httk-2.4.0/httk/man/solve_pbtk.Rd | 51 httk-2.4.0/httk/src/init.c | 90 - httk-2.4.0/httk/src/model3comp.c | 30 httk-2.4.0/httk/src/model_gas_pbtk.c | 2 httk-2.4.0/httk/src/modelpbtk.c | 2 httk-2.4.0/httk/tests/1comp_test.R | 6 httk-2.4.0/httk/tests/1comp_test.Rout.save | 407 ++--- httk-2.4.0/httk/tests/3comp_test.R | 15 httk-2.4.0/httk/tests/3comp_test.Rout.save | 675 ++++---- httk-2.4.0/httk/tests/3compss_test.R | 4 httk-2.4.0/httk/tests/3compss_test.Rout.save | 128 + httk-2.4.0/httk/tests/adddata_test.Rout.save | 14 httk-2.4.0/httk/tests/caco2_test.R | 16 httk-2.4.0/httk/tests/caco2_test.Rout.save | 413 ++--- httk-2.4.0/httk/tests/cheminfo_test.Rout.save | 44 httk-2.4.0/httk/tests/fetal_pbtk_testing.R | 4 httk-2.4.0/httk/tests/fetal_pbtk_testing.Rout.save | 411 +++-- httk-2.4.0/httk/tests/ivive_test.R | 2 httk-2.4.0/httk/tests/ivive_test.Rout.save | 36 httk-2.4.0/httk/tests/montecarlo_tests.R | 14 httk-2.4.0/httk/tests/montecarlo_tests.Rout.save | 779 +++++---- httk-2.4.0/httk/tests/other_tests.Rout.save | 414 ++--- httk-2.4.0/httk/tests/pbtk_test.R | 9 httk-2.4.0/httk/tests/pbtk_test.Rout.save | 489 +++--- httk-2.4.0/httk/tests/solve_gas_test.R | 4 httk-2.4.0/httk/tests/solve_gas_test.Rout.save | 433 ++--- httk-2.4.0/httk/tests/unit_test.Rout.save | 40 httk-2.4.0/httk/vignettes/V2_IntrotoIVIVE.Rmd | 44 httk-2.4.0/httk/vignettes/Va_Pearce2017.Rmd | 13 httk-2.4.0/httk/vignettes/Vh_Linakis2020.Rmd | 228 ++ httk-2.4.0/httk/vignettes/supptab1.csv |only httk-2.4.0/httk/vignettes/supptab2.csv |only 163 files changed, 7417 insertions(+), 5312 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets,
regression models, and more. The code to create the tables is concise
and highly customizable. Data frames can be summarized with any
function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] ,
Joseph Larmarange [aut] ,
Michael Curry [aut] ,
Jessica Lavery [aut] ,
Karissa Whiting [aut] ,
Emily C. Zabor [aut] ,
Xing Bai [ctb],
Esther Drill [ctb] ,
Jessica Flynn [ctb] ,
Margie Hannum [ctb] ,
Stephanie Lobaugh [c [...truncated...]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 2.0.1 dated 2024-08-17 and 2.0.2 dated 2024-09-05
gtsummary-2.0.1/gtsummary/inst/doc/inline_text.R |only gtsummary-2.0.1/gtsummary/inst/doc/inline_text.Rmd |only gtsummary-2.0.1/gtsummary/inst/doc/inline_text.html |only gtsummary-2.0.1/gtsummary/inst/doc/themes.R |only gtsummary-2.0.1/gtsummary/inst/doc/themes.Rmd |only gtsummary-2.0.1/gtsummary/inst/doc/themes.html |only gtsummary-2.0.1/gtsummary/vignettes/inline_text.Rmd |only gtsummary-2.0.1/gtsummary/vignettes/themes.Rmd |only gtsummary-2.0.2/gtsummary/DESCRIPTION | 12 gtsummary-2.0.2/gtsummary/MD5 | 237 +-- gtsummary-2.0.2/gtsummary/NAMESPACE | 8 gtsummary-2.0.2/gtsummary/NEWS.md | 34 gtsummary-2.0.2/gtsummary/R/add_ci.R | 4 gtsummary-2.0.2/gtsummary/R/add_ci.tbl_svysummary.R | 4 gtsummary-2.0.2/gtsummary/R/add_glance.R | 39 gtsummary-2.0.2/gtsummary/R/add_n.R | 4 gtsummary-2.0.2/gtsummary/R/add_overall_ard.R |only gtsummary-2.0.2/gtsummary/R/add_p.R | 2 gtsummary-2.0.2/gtsummary/R/add_p.tbl_survfit.R | 12 gtsummary-2.0.2/gtsummary/R/add_stat.R | 4 gtsummary-2.0.2/gtsummary/R/add_stat_label.R | 4 gtsummary-2.0.2/gtsummary/R/add_vif.R | 2 gtsummary-2.0.2/gtsummary/R/brdg_continuous.R | 3 gtsummary-2.0.2/gtsummary/R/brdg_summary.R | 146 +- gtsummary-2.0.2/gtsummary/R/combine_terms.R | 2 gtsummary-2.0.2/gtsummary/R/gather_ard.R |only gtsummary-2.0.2/gtsummary/R/glance_fun.R |only gtsummary-2.0.2/gtsummary/R/import-standalone-checks.R | 85 + gtsummary-2.0.2/gtsummary/R/modify.R | 69 - gtsummary-2.0.2/gtsummary/R/select_helpers.R | 4 gtsummary-2.0.2/gtsummary/R/tbl_ard_continuous.R | 54 gtsummary-2.0.2/gtsummary/R/tbl_ard_summary.R | 50 gtsummary-2.0.2/gtsummary/R/tbl_ard_wide_summary.R | 27 gtsummary-2.0.2/gtsummary/R/tbl_continuous.R | 10 gtsummary-2.0.2/gtsummary/R/tbl_cross.R | 2 gtsummary-2.0.2/gtsummary/R/tbl_custom_summary.R | 1 gtsummary-2.0.2/gtsummary/R/tbl_likert.R |only gtsummary-2.0.2/gtsummary/R/tbl_summary.R | 4 gtsummary-2.0.2/gtsummary/R/tbl_svysummary.R | 2 gtsummary-2.0.2/gtsummary/R/tbl_uvregression.R | 15 gtsummary-2.0.2/gtsummary/R/tibble_as_cli.R |only gtsummary-2.0.2/gtsummary/R/utils-cards.R | 2 gtsummary-2.0.2/gtsummary/README.md | 3 gtsummary-2.0.2/gtsummary/build/gtsummary.pdf |binary gtsummary-2.0.2/gtsummary/build/stage23.rdb |binary gtsummary-2.0.2/gtsummary/build/vignette.rds |binary gtsummary-2.0.2/gtsummary/inst/doc/gtsummary_definition.html | 664 +++++----- gtsummary-2.0.2/gtsummary/man/add_glance.Rd | 19 gtsummary-2.0.2/gtsummary/man/add_n_summary.Rd | 10 gtsummary-2.0.2/gtsummary/man/add_overall_ard.Rd |only gtsummary-2.0.2/gtsummary/man/add_p.tbl_survfit.Rd | 14 gtsummary-2.0.2/gtsummary/man/gather_ard.Rd |only gtsummary-2.0.2/gtsummary/man/glance_fun_s3.Rd |only gtsummary-2.0.2/gtsummary/man/modify.Rd | 4 gtsummary-2.0.2/gtsummary/man/select_helpers.Rd | 4 gtsummary-2.0.2/gtsummary/man/tbl_ard_continuous.Rd | 8 gtsummary-2.0.2/gtsummary/man/tbl_ard_summary.Rd | 12 gtsummary-2.0.2/gtsummary/man/tbl_ard_wide_summary.Rd | 12 gtsummary-2.0.2/gtsummary/man/tbl_likert.Rd 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Title: Regression Models with Break-Points / Change-Points Estimation
(with Possibly Random Effects)
Description: Fitting regression models where, in addition to possible linear terms, one or more covariates have segmented (i.e., broken-line or piece-wise linear) or stepmented (i.e. piece-wise constant) effects. Multiple breakpoints for the same variable are allowed.
The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and
illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Segmented mixed models, i.e. random effects in the change point, are discussed in Muggeo (2014, <doi:10.1177/1471082X13504721>).
Estimation of piecewise-constant relationships and changepoints (mean-shift models) is
discussed in Fasola et al. (2018, <doi:10.1007/s00180-017-0740-4>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 2.1-1 dated 2024-07-26 and 2.1-2 dated 2024-09-05
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ R/plot.stepmented.r | 31 +++++++++++++++---------------- R/predict.segmented.r | 1 + R/predict.stepmented.R | 2 ++ R/segreg.r | 10 +++++++++- R/stepreg.r | 2 ++ man/plot.stepmented.Rd | 2 +- man/segmented-package.Rd | 4 ++-- 10 files changed, 53 insertions(+), 33 deletions(-)
Title: Modules to Import and Manipulate Data in 'Shiny'
Description: 'Shiny' modules to import data into an application or 'addin'
from various sources, and to manipulate them after that.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
Samra Goumri [aut],
Zauad Shahreer Abeer [aut],
Eduard Szoecs [ctb]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between datamods versions 1.5.1 dated 2024-05-16 and 1.5.2 dated 2024-09-05
DESCRIPTION | 18 MD5 | 66 - NAMESPACE | 4 NEWS.md | 299 ++--- R/create-column.R | 840 +++++++------- R/cut-variable.R | 57 R/edit-data.R | 2 R/import-file.R | 142 +- R/sample-data.R | 332 ++--- R/show_data.R | 242 ++-- R/update-factor.R | 541 ++++----- R/utils-shiny.R | 10 README.md | 320 ++--- build/vignette.rds |binary inst/doc/datamods.R | 322 ++--- inst/doc/datamods.html | 1246 ++++++++++----------- inst/doc/i18n.R | 150 +- inst/doc/i18n.html | 1943 ++++++++++++++++++++++----------- inst/extdata/pop-fra-dep.txt | 202 +-- inst/i18n/al.csv | 286 ++-- inst/i18n/cn.csv | 286 ++-- inst/i18n/de.csv | 286 ++-- inst/i18n/es.csv | 292 ++-- inst/i18n/extract_labels.R | 2 inst/i18n/fr.csv | 286 ++-- inst/i18n/kr.csv | 286 ++-- inst/i18n/mk.csv | 286 ++-- inst/i18n/pl.csv | 286 ++-- inst/i18n/pt.csv | 286 ++-- inst/i18n/tr.csv | 286 ++-- man/import-file.Rd | 10 tests/testthat/test-import-copypaste.R | 34 tests/testthat/test-import-modal.R | 32 tests/testthat/test-validation.R | 50 34 files changed, 5275 insertions(+), 4455 deletions(-)
Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). It allows to easily visualize
count data and statistical thresholds: rank vs abundance plots,
heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Matthew Peeples [ctb] ,
Ben Marwick [ctb] ,
Anne Philippe [ctb] ,
Jean-Baptiste Fourvel [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 3.1.0 dated 2024-05-16 and 3.1.1 dated 2024-09-05
DESCRIPTION | 15 MD5 | 186 ++--- NAMESPACE | 12 NEWS.md | 4 R/AllGenerics.R | 74 ++ R/coerce.R | 8 R/diversity.R | 12 R/diversity_alpha.R | 39 + R/plot_bertin.R | 12 R/plot_diversity.R | 19 R/plot_ford.R | 6 R/plot_heatmap.R | 15 R/plot_matrix.R | 13 R/plot_rank.R | 22 R/plot_spot.R | 16 R/rarefaction.R | 17 R/reexport.R | 18 R/tabula-internal.R | 88 -- R/tabula-package.R | 2 README.md | 469 +++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/alpha.html | 4 inst/doc/beta.html | 10 inst/examples/ex-diversity.R | 1 inst/examples/ex-diversity_old.R | 7 inst/examples/ex-plot_diversity.R | 2 inst/examples/ex-plot_heatmap.R | 13 inst/examples/ex-plot_rank.R | 3 inst/examples/ex-profiles.R | 4 inst/examples/ex-rarefaction.R | 3 inst/tinytest/_tinysnapshot/plot_ford_count.svg | 132 +-- inst/tinytest/_tinysnapshot/plot_ford_weights.svg | 158 ++-- inst/tinytest/_tinysnapshot/plot_mtx_count.svg | 442 ++++++------- inst/tinytest/_tinysnapshot/plot_mtx_incid.svg | 440 ++++++------- inst/tinytest/_tinysnapshot/plot_mtx_notfixed.svg | 442 ++++++------- inst/tinytest/_tinysnapshot/plot_mtx_occ.svg | 32 inst/tinytest/_tinysnapshot/plot_mtx_prop1.svg | 442 ++++++------- inst/tinytest/_tinysnapshot/plot_mtx_prop2.svg | 442 ++++++------- inst/tinytest/_tinysnapshot/plot_mtx_sim.svg | 74 +- inst/tinytest/_tinysnapshot/plot_profiles.svg | 20 inst/tinytest/_tinysnapshot/plot_rank_log.svg | 470 +++++++------- inst/tinytest/_tinysnapshot/plot_rank_nolegend.svg | 450 ++++++------- inst/tinytest/_tinysnapshot/plot_rarefaction.svg | 20 inst/tinytest/_tinysnapshot/plot_rarefaction_nolegend.svg | 10 inst/tinytest/_tinysnapshot/plot_richness.svg | 2 inst/tinytest/_tinysnapshot/plot_seriograph.svg | 222 +++--- inst/tinytest/_tinysnapshot/plot_spot_occ.svg | 20 inst/tinytest/_tinysnapshot/plot_spot_plain.svg | 54 - inst/tinytest/_tinysnapshot/plot_spot_prop1.svg | 54 - inst/tinytest/_tinysnapshot/plot_spot_prop2.svg | 54 - inst/tinytest/_tinysnapshot/plot_spot_ring.svg | 54 - inst/tinytest/_tinysnapshot/plot_spot_sim_plain.svg | 74 +- inst/tinytest/_tinysnapshot/plot_spot_sim_ring.svg | 74 +- inst/tinytest/test_richness.R | 4 man/data.frame.Rd |only man/heterogeneity.Rd | 3 man/index_ace.Rd | 3 man/index_baxter.Rd | 3 man/index_berger.Rd | 3 man/index_boone.Rd | 3 man/index_brillouin.Rd | 3 man/index_chao1.Rd | 3 man/index_chao2.Rd | 3 man/index_hurlbert.Rd | 3 man/index_ice.Rd | 3 man/index_margalef.Rd | 3 man/index_mcintosh.Rd | 3 man/index_menhinick.Rd | 3 man/index_shannon.Rd | 3 man/index_simpson.Rd | 3 man/index_squares.Rd | 3 man/matrigraph.Rd | 2 man/mutators.Rd | 4 man/observed.Rd |only man/occurrence.Rd | 2 man/plot_bertin.Rd | 10 man/plot_diceleraas.Rd | 2 man/plot_diversity.Rd | 23 man/plot_ford.Rd | 2 man/plot_heatmap.Rd | 25 man/plot_matrix.Rd | 6 man/plot_rank.Rd | 16 man/plot_rarefaction.Rd | 35 - man/plot_spot.Rd | 12 man/profiles.Rd | 19 man/rarefaction.Rd | 7 man/reexports.Rd | 6 man/richness.Rd | 10 man/seriograph.Rd | 2 man/she.Rd | 2 man/similarity.Rd | 2 man/simulate.Rd | 4 man/tabula-package.Rd | 2 man/turnover.Rd | 2 95 files changed, 3078 insertions(+), 2445 deletions(-)
Title: "Eating the Liver of Data Science"
Description: Offers a suite of helper functions to simplify various data science techniques for non-experts. This package aims to enable individuals with only a minimal level of coding knowledge to become acquainted with these techniques in an accessible manner. Inspired by an ancient Persian idiom, we liken this process to "eating the liver of data science," suggesting a deep and intimate engagement with the field of data science. This package includes functions for tasks such as data partitioning for out-of-sample testing, calculating Mean Squared Error (MSE) to assess prediction accuracy, and data transformations (z-score and min-max). In addition to these helper functions, the 'liver' package also features several intriguing datasets valuable for multivariate analysis.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.15 dated 2023-11-01 and 1.16 dated 2024-09-05
DESCRIPTION | 6 MD5 | 98 +++--- build/vignette.rds |binary data/adult.RData |binary data/advertising.RData |binary data/bank.RData |binary data/cereal.RData |binary data/churn.RData |binary data/churnCredit.RData |binary data/churnTel.RData |binary data/corona.RData |binary data/fertilizer.RData |binary data/house.RData |binary data/housePrice.RData |binary data/insurance.RData |binary data/marketing.RData |binary data/redWines.RData |binary data/risk.RData |binary data/whiteWines.RData |binary inst/doc/liver-example.R | 4 inst/doc/liver-example.html | 635 +++++++++++++++++++++++++++++--------------- man/accuracy.Rd | 4 man/adult.Rd | 6 man/advertising.Rd | 6 man/bank.Rd | 6 man/cereal.Rd | 8 man/churn.Rd | 6 man/churnCredit.Rd | 6 man/churnTel.Rd | 14 man/conf.mat.Rd | 2 man/conf.mat.plot.Rd | 2 man/corona.Rd | 4 man/fertilizer.Rd | 4 man/figures/logo.png |binary man/house.Rd | 6 man/housePrice.Rd | 6 man/insurance.Rd | 6 man/kNN.Rd | 6 man/kNN.plot.Rd | 4 man/liver-package.Rd | 2 man/mae.Rd | 4 man/marketing.Rd | 6 man/minmax.Rd | 2 man/mse.Rd | 4 man/redWines.Rd | 8 man/risk.Rd | 6 man/skim.Rd | 2 man/transform.Rd | 2 man/whiteWines.Rd | 8 man/zscore.Rd | 2 50 files changed, 545 insertions(+), 340 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks API. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both CPU and GPU devices.
Author: Tomasz Kalinowski [aut, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
Francois Chollet [aut, cph],
Posit Software, PBC [cph, fnd],
Google [cph, fnd],
Yuan Tang [ctb, cph] ,
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigri [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between keras3 versions 1.1.0 dated 2024-07-17 and 1.2.0 dated 2024-09-05
DESCRIPTION | 6 MD5 | 687 ++++++------- NAMESPACE | 3 NEWS.md | 21 R/Layer.R | 10 R/Loss.R | 18 R/Metric.R | 8 R/callbacks.R | 4 R/dataset-utils.R | 17 R/layer-methods.R | 5 R/layers-convolutional.R | 16 R/layers-core.R | 10 R/layers-preprocessing.R | 4 R/layers-reshaping.R | 29 R/losses.R | 61 - R/metrics.R | 16 R/model-creation.R | 7 R/model-persistence.R | 5 R/ops.R | 130 ++ R/optimizers.R | 130 ++ R/preprocessing-image.R | 4 R/utils.R | 2 inst/doc/custom_train_step_in_tensorflow.Rmd | 24 inst/doc/custom_train_step_in_tensorflow.html | 24 inst/doc/distributed_training_with_tensorflow.Rmd | 14 inst/doc/distributed_training_with_tensorflow.html | 14 inst/doc/distribution.Rmd | 23 inst/doc/distribution.html | 63 - inst/doc/functional_api.Rmd | 16 inst/doc/functional_api.html | 16 inst/doc/getting_started.Rmd | 8 inst/doc/getting_started.html | 10 inst/doc/intro_to_keras_for_engineers.Rmd | 29 inst/doc/intro_to_keras_for_engineers.html | 26 inst/doc/making_new_layers_and_models_via_subclassing.Rmd | 6 inst/doc/making_new_layers_and_models_via_subclassing.html | 6 inst/doc/training_with_built_in_methods.Rmd | 82 - inst/doc/training_with_built_in_methods.html | 94 + inst/doc/transfer_learning.Rmd | 10 inst/doc/transfer_learning.html | 10 inst/doc/understanding_masking_and_padding.Rmd | 4 inst/doc/understanding_masking_and_padding.html | 4 inst/doc/writing_a_custom_training_loop_in_tensorflow.Rmd | 4 inst/doc/writing_a_custom_training_loop_in_tensorflow.html | 4 man/Layer.Rd | 10 man/Loss.Rd | 21 man/Metric.Rd | 8 man/callback_backup_and_restore.Rd | 4 man/image_dataset_from_directory.Rd | 13 man/image_smart_resize.Rd | 6 man/keras_input.Rd | 3 man/layer_conv_2d.Rd | 8 man/layer_conv_3d.Rd | 8 man/layer_dense.Rd | 4 man/layer_einsum_dense.Rd | 2 man/layer_embedding.Rd | 4 man/layer_feature_space.Rd | 6 man/layer_input.Rd | 3 man/layer_string_lookup.Rd | 4 man/layer_tfsm.Rd | 4 man/layer_zero_padding_1d.Rd | 32 man/loss_binary_crossentropy.Rd | 3 man/loss_binary_focal_crossentropy.Rd | 3 man/loss_categorical_crossentropy.Rd | 3 man/loss_categorical_focal_crossentropy.Rd | 3 man/loss_categorical_hinge.Rd | 3 man/loss_cosine_similarity.Rd | 3 man/loss_ctc.Rd | 3 man/loss_dice.Rd | 3 man/loss_hinge.Rd | 3 man/loss_huber.Rd | 3 man/loss_kl_divergence.Rd | 5 man/loss_log_cosh.Rd | 3 man/loss_mean_absolute_error.Rd | 3 man/loss_mean_absolute_percentage_error.Rd | 3 man/loss_mean_squared_error.Rd | 3 man/loss_mean_squared_logarithmic_error.Rd | 3 man/loss_poisson.Rd | 5 man/loss_sparse_categorical_crossentropy.Rd | 3 man/loss_squared_hinge.Rd | 3 man/loss_tversky.Rd | 3 man/metric_binary_iou.Rd | 20 man/metric_categorical_crossentropy.Rd | 1 man/metric_iou.Rd | 20 man/metric_mean_iou.Rd | 20 man/metric_one_hot_iou.Rd | 26 man/metric_one_hot_mean_iou.Rd | 11 man/op_abs.Rd | 2 man/op_add.Rd | 2 man/op_all.Rd | 2 man/op_any.Rd | 2 man/op_append.Rd | 2 man/op_arange.Rd | 2 man/op_arccos.Rd | 2 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vignettes/transfer_learning.Rmd | 10 vignettes/understanding_masking_and_padding.Rmd | 4 vignettes/writing_a_custom_training_loop_in_tensorflow.Rmd | 4 346 files changed, 1955 insertions(+), 897 deletions(-)
Title: Simulation and Plots for Fossil and Taxonomy Data
Description: Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic
models of speciation, preservation and sampling.
Author: Rachel Warnock [aut, cph],
Joelle Barido-Sottani [aut, cre, cph],
Walker Pett [aut, cph],
O'Reilly Joseph [aut, cph],
Ugnė Stolz [aut, cph]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Diff between FossilSim versions 2.3.3 dated 2024-04-29 and 2.4.0 dated 2024-09-05
DESCRIPTION | 24 MD5 | 53 NAMESPACE | 11 NEWS.md | 144 +- R/FossilSim.R | 102 - R/SAtree.R | 2 R/conversions.R | 22 R/fbdrange.R |only R/fossils.R | 14 R/plot.fbdrange.R |only R/sim.taxonomy.R | 1 R/sysdata.rda |only build/vignette.rds |binary inst/doc/SAtree.R | 42 inst/doc/SAtree.html | 947 ++++++++--------- inst/doc/fossils.R | 582 +++++----- inst/doc/fossils.html | 1978 ++++++++++++++++++------------------- inst/doc/intro.R | 62 - inst/doc/intro.html | 992 +++++++++--------- inst/doc/paleotree.R | 44 inst/doc/paleotree.html | 1050 +++++++++++-------- inst/doc/simfbd.R | 48 inst/doc/simfbd.html | 932 ++++++++--------- inst/doc/taxonomy.R | 112 +- inst/doc/taxonomy.html | 1308 ++++++++++++------------ inst/extdata |only man/FossilSim.Rd | 3 man/fbdrange.Rd |only man/get_fbdrange_from_file.Rd |only man/paleotree.record.to.fossils.Rd | 4 man/plot.fbdrange.Rd |only 31 files changed, 4342 insertions(+), 4135 deletions(-)
More information about twoStageDesignTMLE at CRAN
Permanent link
Title: Extension to 'spatstat' for Large Datasets on a Linear Network
Description: Extension to the 'spatstat' family of packages, for analysing
large datasets of spatial points on a network. The geometrically-
corrected K function is computed using a memory-efficient
tree-based algorithm described by Rakshit, Baddeley and Nair (2019).
Author: Suman Rakshit [aut, cph] ,
Adrian Baddeley [cre, cph]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.Knet versions 3.1-0 dated 2024-07-19 and 3.1-2 dated 2024-09-05
DESCRIPTION | 8 +- MD5 | 15 ++--- NEWS | 14 +++++ build/partial.rdb |binary src/Knet.c | 4 + src/KnetInhom.c | 3 + src/memory.h |only src/netKcode.h | 150 +++++++++++++++++++++++++++--------------------------- src/netbase.c | 25 ++++----- 9 files changed, 121 insertions(+), 98 deletions(-)
Title: Poisson Network Autoregressive Models
Description: Quasi likelihood-based methods for estimating linear and log-linear Poisson Network Autoregression models with p lags and covariates. Tools for testing the linearity versus several non-linear alternatives. Tools for simulation of multivariate count distributions, from linear and non-linear PNAR models, by using a specific copula construction. References include: Armillotta, M. and K. Fokianos (2023). "Nonlinear network autoregression". Annals of Statistics, 51(6): 2526--2552. <doi:10.1214/23-AOS2345>. Armillotta, M. and K. Fokianos (2024). "Count network autoregression". Journal of Time Series Analysis, 45(4): 584--612. <doi:10.1111/jtsa.12728>. Armillotta, M., Tsagris, M. and Fokianos, K. (2024). "Inference for Network Count Time Series with the R Package PNAR". The R Journal, 15/4: 255--269. <doi:10.32614/RJ-2023-094>.
Author: Michail Tsagris [aut, cre],
Mirko Armillotta [aut, cph],
Konstantinos Fokianos [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between PNAR versions 1.6 dated 2023-10-09 and 1.7 dated 2024-09-05
DESCRIPTION | 12 ++++---- MD5 | 52 +++++++++++++++++++------------------- man/PNAR-package.Rd | 20 +++++++++----- man/adja.Rd | 2 - man/adja_gnp.Rd | 2 - man/crime.Rd | 2 - man/crime_W.Rd | 2 - man/global_optimise_LM_stnarpq.Rd | 15 +++------- man/global_optimise_LM_tnarpq.Rd | 17 ++++-------- man/lin_estimnarpq.Rd | 9 ++---- man/lin_ic_plot.Rd | 7 +++-- man/lin_narpq_init.Rd | 9 ++++-- man/log_lin_estimnarpq.Rd | 9 ++---- man/log_lin_ic_plot.Rd | 7 +++-- man/log_lin_narpq_init.Rd | 7 +++-- man/poisson.MODpq.Rd | 11 +++++--- man/poisson.MODpq.log.Rd | 11 +++++--- man/poisson.MODpq.nonlin.Rd | 13 ++++----- man/poisson.MODpq.stnar.Rd | 13 ++++----- man/poisson.MODpq.tnar.Rd | 13 ++++----- man/score_test_nonlinpq_h0.Rd | 13 ++------- man/score_test_stnarpq_DV.Rd | 17 ++++-------- man/score_test_stnarpq_j.Rd | 15 +++------- man/score_test_tnarpq_j.Rd | 17 ++++-------- man/summary.DV.Rd | 13 +-------- man/summary.PNAR.Rd | 7 ----- man/summary.nonlin.Rd | 11 -------- 27 files changed, 146 insertions(+), 180 deletions(-)
Title: 'OpenStreetMap' API
Description: Interface to 'OpenStreetMap API' for fetching and saving data
from/to the 'OpenStreetMap' database
(<https://wiki.openstreetmap.org/wiki/API_v0.6>).
Author: Joan Maspons [aut, cre, cph] ,
Jon Harmon [rev] ,
Carlos Camara [rev]
Maintainer: Joan Maspons <joanmaspons@gmail.com>
Diff between osmapiR versions 0.1.0 dated 2024-06-28 and 0.2.1 dated 2024-09-05
osmapiR-0.1.0/osmapiR/tests/testthat/mock_full_object_json |only osmapiR-0.2.1/osmapiR/DESCRIPTION | 16 osmapiR-0.2.1/osmapiR/MD5 | 187 - osmapiR-0.2.1/osmapiR/NAMESPACE | 6 osmapiR-0.2.1/osmapiR/NEWS.md | 39 osmapiR-0.2.1/osmapiR/R/import-standalone-s3-register.R |only osmapiR-0.2.1/osmapiR/R/osm_get_changesets.R | 27 osmapiR-0.2.1/osmapiR/R/osm_get_gpx_metadata.R | 24 osmapiR-0.2.1/osmapiR/R/osm_get_notes.R | 25 osmapiR-0.2.1/osmapiR/R/osm_get_objects.R | 68 osmapiR-0.2.1/osmapiR/R/osm_get_points_gps.R | 50 osmapiR-0.2.1/osmapiR/R/osm_get_user_details.R | 32 osmapiR-0.2.1/osmapiR/R/osm_query_changesets.R | 37 osmapiR-0.2.1/osmapiR/R/osmapiR-package.R | 5 osmapiR-0.2.1/osmapiR/R/osmapiR_connection.R | 8 osmapiR-0.2.1/osmapiR/R/osmapiR_methods.R | 37 osmapiR-0.2.1/osmapiR/R/osmapiR_request.R | 2 osmapiR-0.2.1/osmapiR/R/osmapi_changesets.R | 9 osmapiR-0.2.1/osmapiR/R/osmapi_elements.R | 15 osmapiR-0.2.1/osmapiR/R/osmapi_gps_traces.R | 89 osmapiR-0.2.1/osmapiR/R/osmapi_map_notes.R | 40 osmapiR-0.2.1/osmapiR/R/osmapi_user_data.R | 5 osmapiR-0.2.1/osmapiR/R/osmchange.R | 7 osmapiR-0.2.1/osmapiR/R/st_as_sf.R |only osmapiR-0.2.1/osmapiR/R/tags_list-wide.r | 24 osmapiR-0.2.1/osmapiR/R/xml_to_R.R | 215 + osmapiR-0.2.1/osmapiR/R/zzz.R | 13 osmapiR-0.2.1/osmapiR/README.md | 89 osmapiR-0.2.1/osmapiR/inst/CITATION |only osmapiR-0.2.1/osmapiR/inst/WORDLIST | 77 osmapiR-0.2.1/osmapiR/inst/doc/how_to_edit_gps_traces.html | 2 osmapiR-0.2.1/osmapiR/inst/doc/how_to_edit_osm.html | 2 osmapiR-0.2.1/osmapiR/inst/doc/osmapiR.html | 17 osmapiR-0.2.1/osmapiR/man/figures/logo.svg | 886 +++--- osmapiR-0.2.1/osmapiR/man/osm_diff_upload_changeset.Rd | 3 osmapiR-0.2.1/osmapiR/man/osm_download_changeset.Rd | 2 osmapiR-0.2.1/osmapiR/man/osm_get_changesets.Rd | 9 osmapiR-0.2.1/osmapiR/man/osm_get_data_gpx.Rd | 26 osmapiR-0.2.1/osmapiR/man/osm_get_gpx_metadata.Rd | 8 osmapiR-0.2.1/osmapiR/man/osm_get_notes.Rd | 9 osmapiR-0.2.1/osmapiR/man/osm_get_objects.Rd | 2 osmapiR-0.2.1/osmapiR/man/osm_get_points_gps.Rd | 20 osmapiR-0.2.1/osmapiR/man/osm_get_user_details.Rd | 2 osmapiR-0.2.1/osmapiR/man/osm_history_object.Rd | 2 osmapiR-0.2.1/osmapiR/man/osm_list_gpxs.Rd | 9 osmapiR-0.2.1/osmapiR/man/osm_query_changesets.Rd | 9 osmapiR-0.2.1/osmapiR/man/osm_read_bbox_notes.Rd | 7 osmapiR-0.2.1/osmapiR/man/osm_search_notes.Rd | 9 osmapiR-0.2.1/osmapiR/man/osmapiR-package.Rd | 13 osmapiR-0.2.1/osmapiR/man/osmchange_delete.Rd | 2 osmapiR-0.2.1/osmapiR/man/osmchange_modify.Rd | 2 osmapiR-0.2.1/osmapiR/man/st_as_sf.Rd |only osmapiR-0.2.1/osmapiR/man/tags_list-wide.Rd | 8 osmapiR-0.2.1/osmapiR/tests/testthat/_snaps/changesets.md | 150 + osmapiR-0.2.1/osmapiR/tests/testthat/_snaps/elements.md | 1274 +++++++--- osmapiR-0.2.1/osmapiR/tests/testthat/_snaps/map_notes.md | 182 + osmapiR-0.2.1/osmapiR/tests/testthat/_snaps/miscellaneous.md | 929 ------- osmapiR-0.2.1/osmapiR/tests/testthat/mock_bbox_objects/osm.org/api/0.6/map-e6e175.xml | 384 +-- 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|only osmapiR-0.2.1/osmapiR/tests/testthat/mock_full_object/osm.org/api/0.6/way/235744929/full.xml | 2 osmapiR-0.2.1/osmapiR/tests/testthat/mock_get_data_gpx/osm.org/api/0.6/gpx/3458743/data.R | 10 osmapiR-0.2.1/osmapiR/tests/testthat/mock_get_data_gpx/osm.org/api/0.6/gpx/3458743/data.gpx.R | 19 osmapiR-0.2.1/osmapiR/tests/testthat/mock_get_data_gpx/osm.org/api/0.6/gpx/3498170 |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_history_object/osm.org/api/0.6/node/35308286/history.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_history_object/osm.org/api/0.6/node/35308286/history.xml | 19 osmapiR-0.2.1/osmapiR/tests/testthat/mock_history_object/osm.org/api/0.6/relation/40581/history.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_history_object/osm.org/api/0.6/relation/40581/history.xml | 398 +++ osmapiR-0.2.1/osmapiR/tests/testthat/mock_history_object/osm.org/api/0.6/way/13073736/history.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_history_object/osm.org/api/0.6/way/13073736/history.xml | 449 +++ osmapiR-0.2.1/osmapiR/tests/testthat/mock_permissions/osm.org/api/0.6/permissions.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_query_changesets_empty/osm.org/api/0.6/changesets.json-c44390.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_read_object/osm.org/api/0.6/node/35308286.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_read_object/osm.org/api/0.6/node/35308286.xml | 6 osmapiR-0.2.1/osmapiR/tests/testthat/mock_read_object/osm.org/api/0.6/relation/40581.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_read_object/osm.org/api/0.6/relation/40581.xml | 10 osmapiR-0.2.1/osmapiR/tests/testthat/mock_read_object/osm.org/api/0.6/way/13073736.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_read_object/osm.org/api/0.6/way/13073736.xml | 4 osmapiR-0.2.1/osmapiR/tests/testthat/mock_relations_object/osm.org/api/0.6/node/1470837704/relations.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_relations_object/osm.org/api/0.6/node/1470837704/relations.xml | 9 osmapiR-0.2.1/osmapiR/tests/testthat/mock_relations_object/osm.org/api/0.6/relation/342792/relations.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_relations_object/osm.org/api/0.6/relation/342792/relations.xml | 25 osmapiR-0.2.1/osmapiR/tests/testthat/mock_relations_object/osm.org/api/0.6/way/372011578/relations.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_relations_object/osm.org/api/0.6/way/372011578/relations.xml | 338 +- osmapiR-0.2.1/osmapiR/tests/testthat/mock_search_notes_empty/osm.org/api/0.6/notes/search.gpx-0acea5.R |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_search_notes_empty/osm.org/api/0.6/notes/search.json-0acea5.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_search_notes_empty/osm.org/api/0.6/notes/search.rss-0acea5.R |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_version_object/osm.org/api/0.6/node/35308286/1.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_version_object/osm.org/api/0.6/relation/40581/3.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_version_object/osm.org/api/0.6/way/13073736/2.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_ways_node/osm.org/api/0.6/node/35308286/ways.json.json |only osmapiR-0.2.1/osmapiR/tests/testthat/mock_ways_node/osm.org/api/0.6/node/35308286/ways.xml | 2 osmapiR-0.2.1/osmapiR/tests/testthat/setup.R | 5 osmapiR-0.2.1/osmapiR/tests/testthat/test-changesets.R | 111 osmapiR-0.2.1/osmapiR/tests/testthat/test-elements.R | 164 + osmapiR-0.2.1/osmapiR/tests/testthat/test-gps_traces.R | 232 + osmapiR-0.2.1/osmapiR/tests/testthat/test-map_notes.R | 89 osmapiR-0.2.1/osmapiR/tests/testthat/test-miscellaneous.R | 36 osmapiR-0.2.1/osmapiR/tests/testthat/test-tags_list-wide.R | 24 osmapiR-0.2.1/osmapiR/tests/testthat/test-user_data.R | 23 108 files changed, 4491 insertions(+), 2731 deletions(-)
Title: Reproducible and Flexible Label Design
Description: An open-source R package to deploys reproducible and flexible labels using layers.
The 'huito' package is part of the 'inkaverse' project for developing different procedures and
tools used in plant science and experimental designs.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between huito versions 0.2.4 dated 2023-10-25 and 0.2.5 dated 2024-09-05
DESCRIPTION | 14 +-- MD5 | 18 ++--- NEWS.md | 4 + build/vignette.rds |binary inst/doc/germinar.html | 4 - inst/doc/labels.R | 26 +++---- inst/doc/labels.Rmd | 26 +++---- inst/doc/labels.html | 174 +++++++++++++++++++++++++++---------------------- inst/doc/stickers.html | 4 - vignettes/labels.Rmd | 26 +++---- 10 files changed, 161 insertions(+), 135 deletions(-)
Title: Provides a Link Between the 'LSEG Datastream' System and R
Description: Provides a set of functions and a class to connect, extract and
upload information from the 'LSEG Datastream' database. This
package uses the 'DSWS' API and server used by the 'Datastream DFO addin'.
Details of this API are available at <https://www.lseg.com/en/data-analytics>.
Please report issues at <https://github.com/CharlesCara/DatastreamDSWS2R/issues>.
Author: Charles Cara [aut, cre]
Maintainer: Charles Cara <charles.cara@absolute-strategy.com>
Diff between DatastreamDSWS2R versions 1.9.7 dated 2024-01-15 and 1.9.10 dated 2024-09-05
DESCRIPTION | 20 ++-- MD5 | 44 +++++----- NEWS.md | 9 +- R/DatastreamDSWS2R.R | 4 R/classConstructor.R | 14 --- README.md | 10 ++ man/DatastreamDSWS2R.Rd | 7 + man/classconstructor.Rd | 8 - tests/testthat/test-cbindRobust.R | 2 tests/testthat/test-common.R | 4 tests/testthat/test-dsws-buildRequestListBundle.R | 24 ++--- tests/testthat/test-dsws-initialise.R | 10 +- tests/testthat/test-dsws-listRequest.R | 12 +- tests/testthat/test-dsws-snapshotRequest.R | 32 +++---- tests/testthat/test-dsws-timeSeriesRequest.R | 12 -- tests/testthat/test-dsws-timeSeriesRequestChunking.R | 6 - tests/testthat/test-dsws-tokenExpired.R | 2 tests/testthat/test-old-staticRequest.R | 4 tests/testthat/test-old-timeSeriesRequest.R | 26 ++--- tests/testthat/test-wrapper-staticListRequestSet.R | 4 tests/testthat/test-wrapper.R | 6 - tests/testthat/testData/test-dsws-timeSeriesRequest-test01.json |binary tests/testthat/testData/test-dsws-timeSeriesRequest-test02.json |binary 23 files changed, 136 insertions(+), 124 deletions(-)
More information about DatastreamDSWS2R at CRAN
Permanent link
Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Toph Allen [aut, cre],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Toph Allen <toph@posit.co>
Diff between connectapi versions 0.2.0 dated 2024-06-06 and 0.3.0 dated 2024-09-05
connectapi-0.2.0/connectapi/build/connectapi.pdf |only connectapi-0.2.0/connectapi/man/render.Rd |only connectapi-0.3.0/connectapi/DESCRIPTION | 45 - connectapi-0.3.0/connectapi/MD5 | 75 +- connectapi-0.3.0/connectapi/NAMESPACE | 4 connectapi-0.3.0/connectapi/NEWS.md | 32 + connectapi-0.3.0/connectapi/R/connect.R | 288 +++------- connectapi-0.3.0/connectapi/R/content.R | 161 ++++- connectapi-0.3.0/connectapi/R/deploy.R | 14 connectapi-0.3.0/connectapi/R/get.R | 50 + connectapi-0.3.0/connectapi/R/page.R | 2 connectapi-0.3.0/connectapi/R/parse.R | 56 + connectapi-0.3.0/connectapi/R/utils-ci.R | 6 connectapi-0.3.0/connectapi/R/utils.R | 10 connectapi-0.3.0/connectapi/R/variant.R | 50 - connectapi-0.3.0/connectapi/README.md | 1 connectapi-0.3.0/connectapi/build/stage23.rdb |binary connectapi-0.3.0/connectapi/build/vignette.rds |binary connectapi-0.3.0/connectapi/inst/doc/customize-http.html | 8 connectapi-0.3.0/connectapi/inst/doc/getting-started.html | 8 connectapi-0.3.0/connectapi/man/Content.Rd | 14 connectapi-0.3.0/connectapi/man/PositConnect.Rd | 180 +++--- connectapi-0.3.0/connectapi/man/connectapi-package.Rd | 4 connectapi-0.3.0/connectapi/man/content_render.Rd |only connectapi-0.3.0/connectapi/man/content_restart.Rd |only connectapi-0.3.0/connectapi/man/get_oauth_credentials.Rd |only connectapi-0.3.0/connectapi/man/variant.Rd | 8 connectapi-0.3.0/connectapi/man/variant_render.Rd |only connectapi-0.3.0/connectapi/tests/integrated/test-deploy.R | 3 connectapi-0.3.0/connectapi/tests/testthat/__api__/applications/951bf3ad |only connectapi-0.3.0/connectapi/tests/testthat/__api__/applications/f2f37341/variants.json | 3 connectapi-0.3.0/connectapi/tests/testthat/__api__/server_settings.json | 4 connectapi-0.3.0/connectapi/tests/testthat/__api__/v1/content-064d19.json | 2 connectapi-0.3.0/connectapi/tests/testthat/__api__/v1/content/8f37d6e0 |only connectapi-0.3.0/connectapi/tests/testthat/__api__/v1/content/8f37d6e0.json |only connectapi-0.3.0/connectapi/tests/testthat/__api__/v1/content/951bf3ad.json |only connectapi-0.3.0/connectapi/tests/testthat/__api__/v1/oauth |only connectapi-0.3.0/connectapi/tests/testthat/__api__/variants |only connectapi-0.3.0/connectapi/tests/testthat/setup.R | 20 connectapi-0.3.0/connectapi/tests/testthat/test-connect.R | 12 connectapi-0.3.0/connectapi/tests/testthat/test-content.R | 82 ++ connectapi-0.3.0/connectapi/tests/testthat/test-oauth.R |only connectapi-0.3.0/connectapi/tests/testthat/test-parse.R | 125 ++++ connectapi-0.3.0/connectapi/tests/testthat/test-variant.R | 9 44 files changed, 852 insertions(+), 424 deletions(-)
Title: Comparative Analysis with Annotation-Based Genomic Components
Description: A first-principle, phylogeny-aware comparative genomics tool for
investigating associations between terms used to annotate genomic
components (e.g., Pfam IDs, Gene Ontology terms,) with quantitative
or rank variables such as number of cell types, genome size, or
density of specific genomic elements. See the project website for
more information, documentation and examples, and
<doi:10.1016/j.patter.2023.100728> for the full paper.
Author: Francisco Lobo [aut],
Felipe Campelo [aut, cre],
Jorge Augusto Hongo [aut],
Giovanni Marques de Castro [aut],
Gabriel Almeida [sad, dnc]
Maintainer: Felipe Campelo <fcampelo@gmail.com>
Diff between CALANGO versions 1.0.16 dated 2023-04-26 and 1.0.20 dated 2024-09-05
DESCRIPTION | 18 MD5 | 135 NAMESPACE | 24 NEWS.md | 111 R/AddGenomeVectors.R | 188 R/AnnotateResults.R | 38 R/CALANGO_brewer_pal.R | 1808 R/FileAddition.R | 72 R/FindContrasts.R | 236 R/FindCorrelations.R | 144 R/GenerateGenomeVector.R | 114 R/GenerateTree.R | 18 R/GroupElementCount.R | 70 R/activate_CRAN_dependencies_from_Rmd_reports.R | 32 R/check_bioc_dependencies.R | 40 R/check_inputs_correlation.R | 12 R/check_inputs_significance.R | 12 R/clean_data.R | 84 R/clean_data_correlation.R | 84 R/clean_data_significance.R | 92 R/do_analysis.R | 68 R/do_analysis_correlation.R | 274 R/do_analysis_significance.R | 10 R/install_bioc_dependencies.R | 122 R/load_data.R | 158 R/load_data_correlation.R | 296 R/load_data_significance.R | 196 R/make_correlation_report.R | 358 R/make_report.R | 88 R/make_significance_report.R | 28 R/parse_GenomeMap.R | 12 R/print_results_correlations.R | 88 R/read_calango_file.R | 44 R/restore_relative_paths.R | 16 R/retrieve_calanguize_genomes.R | 126 R/retrieve_data_files.R | 128 R/run_CALANGO.R | 339 R/save_tsv_files.R | 114 R/set_absolute_paths.R | 75 R/utils_ontology_manipulation.R | 204 R/utils_taxize_functions.R |only README.md | 551 build/vignette.rds |binary inst/CITATION | 32 inst/doc/CALANGO_Parameters.Rmd | 660 inst/doc/CALANGO_Parameters.html |23774 ++++++++++++- inst/extdata/report_files/_site.yml | 66 inst/extdata/report_files/about.Rmd | 44 inst/extdata/report_files/heatmap_phylo_norm.Rmd | 330 inst/extdata/report_files/heatmap_phylo_perc.Rmd | 282 inst/extdata/report_files/heatmap_phylo_raw.Rmd | 276 inst/extdata/report_files/index.Rmd | 136 inst/extdata/report_files/q_value_scatter.Rmd | 108 inst/extdata/report_files/table.Rmd | 416 inst/scripts/count_GO_feature2GO.pl | 116 inst/scripts/count_GO_gene2GO.pl | 148 inst/scripts/generate_symbolic_link.pl | 24 inst/scripts/parse_busco.pl | 76 inst/scripts/parse_interproscan_output.pl | 150 inst/scripts/parse_interproscan_output_IPR.pl | 132 inst/scripts/parse_interproscan_output_feature2GO.pl | 140 inst/scripts/parse_interproscan_output_gene2GO.pl | 190 inst/scripts/parse_interproscan_output_gene2SUPERFAMILY.pl | 194 man/install_bioc_dependencies.Rd | 76 man/make_report.Rd | 64 man/retrieve_calanguize_genomes.Rd | 93 man/retrieve_data_files.Rd | 96 man/run_CALANGO.Rd | 235 vignettes/CALANGO_Parameters.Rmd | 660 69 files changed, 28934 insertions(+), 6211 deletions(-)
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data
from disparate sources. Metadata is managed throughout the process to facilitate
reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] ,
Cory Merow [aut] ,
Brian Maitner [aut] ,
Jamie M. Kass [aut] ,
Vijay Barve [aut] ,
Robert P. Guralnick [aut] ,
Damiano Oldoni [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/407>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between occCite versions 0.5.7 dated 2024-06-23 and 0.5.8 dated 2024-09-05
DESCRIPTION | 14 +- MD5 | 16 +-- NEWS.md | 5 R/taxonRectification.R | 159 +++++++++++++++++++------------ build/vignette.rds |binary inst/doc/a_Simple.html | 12 +- inst/doc/b_Advanced.html | 38 +++---- man/taxonRectification.Rd | 7 + tests/testthat/test-taxonRectification.R | 17 +++ 9 files changed, 165 insertions(+), 103 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.
Author: Edzer Pebesma [aut, cre] ,
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 2.1-1 dated 2023-04-06 and 2.1-2 dated 2024-09-05
DESCRIPTION | 9 +- MD5 | 91 +++++++++++++-------------- NEWS.md | 6 + R/panel.pointPairs.R | 2 R/predict.gstat.R | 6 - R/variogram.formula.R | 2 R/variogram.gstat.R | 2 R/variogramST.R | 31 +++++---- build/vignette.rds |binary data/DE_RB_2005.rda |binary data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary demo/00Index | 1 demo/pcb_sf.R |only inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.pdf |binary inst/doc/st.pdf |binary man/jura.Rd | 14 ++-- man/krigeST.Rd | 5 - man/krigeTg.Rd | 2 man/plot.gstatVariogram.Rd | 6 - man/variogramST.Rd | 12 +-- man/vgm.Rd | 7 +- man/vgm.panel.Rd | 2 src/Makevars | 1 src/mtrx.c | 24 +++---- src/s.c | 116 +++++++++++++++++------------------ src/userio.c | 8 +- tests/stars.R | 3 tests/stars.Rout.save | 60 +++++++----------- tests/unproj.R | 4 - tests/unproj.Rout.save | 25 +------ tests/vdist.R | 7 +- tests/vdist.Rout.save | 19 +++-- 47 files changed, 232 insertions(+), 233 deletions(-)
Title: Feature Extraction and Document Classification with Noisy Labels
Description: Extract features and classify documents with noisy labels given by document-meta data or keyword matching Watanabe & Zhou (2020) <doi:10.1177/0894439320907027>.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordmap versions 0.8.0 dated 2024-06-18 and 0.9.0 dated 2024-09-05
DESCRIPTION | 12 ++++---- MD5 | 17 +++++++----- NAMESPACE | 9 ++++++ NEWS.md | 8 +++++ R/textmodel.R | 56 +++++++++++++++++++++++++++++----------- R/textplot.R |only inst/WORDLIST | 3 ++ man/textmodel_wordmap.Rd | 41 +++++++++++++++++++---------- man/textplot_terms.Rd |only tests/testthat/test-textmodel.R | 31 +++++++++++++++++++++- tests/testthat/test-textplot.R |only 11 files changed, 134 insertions(+), 43 deletions(-)
Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>.
Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 1.3.2 dated 2024-07-03 and 1.4.0 dated 2024-09-05
seededlda-1.3.2/seededlda/inst/deftbb.R |only seededlda-1.3.2/seededlda/src/Makevars |only seededlda-1.4.0/seededlda/DESCRIPTION | 10 - seededlda-1.4.0/seededlda/MD5 | 43 ++-- seededlda-1.4.0/seededlda/NAMESPACE | 1 seededlda-1.4.0/seededlda/NEWS.md | 8 seededlda-1.4.0/seededlda/R/RcppExports.R | 4 seededlda-1.4.0/seededlda/R/lda.R | 41 +++- seededlda-1.4.0/seededlda/R/seededlda.R | 9 - seededlda-1.4.0/seededlda/R/utils.R | 8 seededlda-1.4.0/seededlda/cleanup |only seededlda-1.4.0/seededlda/configure |only seededlda-1.4.0/seededlda/configure.ac |only seededlda-1.4.0/seededlda/inst/libtbb.R | 14 - seededlda-1.4.0/seededlda/man/info_tbb.Rd |only seededlda-1.4.0/seededlda/man/textmodel_lda.Rd | 21 +- seededlda-1.4.0/seededlda/man/textmodel_seededlda.Rd | 8 seededlda-1.4.0/seededlda/src/Makevars.in |only seededlda-1.4.0/seededlda/src/RcppExports.cpp | 9 - seededlda-1.4.0/seededlda/src/array.h | 1 seededlda-1.4.0/seededlda/src/lda.cpp | 12 - seededlda-1.4.0/seededlda/src/lda.h | 88 ++++++---- seededlda-1.4.0/seededlda/tests/testthat/test-internal.R | 22 ++ seededlda-1.4.0/seededlda/tests/testthat/test-textmodel_lda.R | 51 +++++ seededlda-1.4.0/seededlda/tests/testthat/test-textmodel_seededlda.R | 3 seededlda-1.4.0/seededlda/tests/testthat/test-utils.R | 4 26 files changed, 248 insertions(+), 109 deletions(-)
Title: Benchmarking and Visualization Toolkit for Penalized Cox Models
Description: Creates nomogram visualizations for penalized Cox regression
models, with the support of reproducible survival model building,
validation, calibration, and comparison for high-dimensional data.
Author: Nan Xiao [aut, cre] ,
Qing-Song Xu [aut],
Miao-Zhu Li [aut],
Frank Harrell [ctb] ,
Sergej Potapov [ctb] ,
Werner Adler [ctb] ,
Matthias Schmid [ctb]
Maintainer: Nan Xiao <me@nanx.me>
Diff between hdnom versions 6.0.3 dated 2024-03-02 and 6.0.4 dated 2024-09-05
DESCRIPTION | 8 ++--- MD5 | 28 +++++++++--------- NEWS.md | 17 ++++++++-- README.md | 9 ++--- build/vignette.rds |binary inst/doc/hdnom.html | 20 ++++++------ man/figures/README-kmplot-1.png |binary man/figures/README-model-comparison-1.png |binary man/figures/README-model-validation-calibration-1.png |binary man/figures/README-nomogram-1.png |binary src/survAUC_Cham_Diao.c | 26 +++++++++------- src/survAUC_SongZhou.c | 22 +++++++------- src/survAUC_UNO.c | 22 +++++++------- src/utils.c | 28 +++++++++--------- src/utils.h | 2 + 15 files changed, 100 insertions(+), 82 deletions(-)
Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with spatially correlated errors by robust (Kuensch et al. (2011) <doi:10.3929/ethz-a-009900710>) and Gaussian (Harville (1977) <doi:10.1080/01621459.1977.10480998>) (Restricted) Maximum Likelihood and for computing robust and customary point and block external-drift Kriging predictions (Cressie (1993) <doi:10.1002/9781119115151>), along with utility functions for variogram modelling in ad hoc geostatistical analyses, model building, model evaluation by cross-validation, (conditional) simulation of Gaussian processes (Davies and Bryant (2013) <doi:10.18637/jss.v055.i09>), unbiased back-transformation of Kriging predictions of log-transformed data (Cressie (2006) <doi:10.1007/s11004-005-9022-8>).
Author: Andreas Papritz [aut, cre]
Maintainer: Andreas Papritz <papritz@retired.ethz.ch>
Diff between georob versions 0.3-19 dated 2024-03-10 and 0.3-20 dated 2024-09-05
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 12 ++++++++++++ inst/doc/georob_vignette.pdf |binary man/lgnpp.Rd | 2 +- 8 files changed, 27 insertions(+), 12 deletions(-)
Title: Fitting and Forecasting Gegenbauer ARMA Time Series Models
Description: Methods for estimating univariate long memory-seasonal/cyclical
Gegenbauer time series processes. See for example (2022) <doi:10.1007/s00362-022-01290-3>.
Refer to the vignette for details of fitting these processes.
Author: Richard Hunt [aut, cre]
Maintainer: Richard Hunt <maint@huntemail.id.au>
Diff between garma versions 0.9.20 dated 2024-08-23 and 0.9.22 dated 2024-09-05
garma-0.9.20/garma/tests/testthat/_snaps |only garma-0.9.20/garma/tests/testthat/test-predict.R |only garma-0.9.20/garma/tests/testthat/test_garma2.R |only garma-0.9.22/garma/DESCRIPTION | 8 garma-0.9.22/garma/MD5 | 14 garma-0.9.22/garma/NEWS.md | 27 - garma-0.9.22/garma/R/gg_raw_pgram.R | 5 garma-0.9.22/garma/inst/doc/introduction.html | 4 garma-0.9.22/garma/tests/testthat/test_garma.R | 492 +++++++++++------------ 9 files changed, 276 insertions(+), 274 deletions(-)
Title: One-Dimensional Probability Distribution Support for the
'spatstat' Family
Description: Estimation of one-dimensional probability distributions
including kernel density estimation, weighted empirical cumulative
distribution functions, Kaplan-Meier and reduced-sample estimators
for right-censored data, heat kernels, kernel properties,
quantiles and integration.
Author: Adrian Baddeley [aut, cre, cph]
,
Tilman M. Davies [aut, ctb, cph]
,
Martin L. Hazelton [aut, ctb, cph]
,
Ege Rubak [aut, cph] ,
Rolf Turner [aut, cph] ,
Greg McSwiggan [ctb, cph]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.univar versions 3.0-0 dated 2024-06-28 and 3.0-1 dated 2024-09-05
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- NAMESPACE | 4 ++ NEWS | 23 +++++++++++ R/ewcdf.R | 79 +++++++++++++++++++++++++++------------- inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/quantile.ewcdf.Rd | 2 - man/quantilefun.Rd | 2 - man/spatstat.univar-internal.Rd | 4 ++ 10 files changed, 103 insertions(+), 39 deletions(-)
More information about spatstat.univar at CRAN
Permanent link
Title: Scoring Rules for Parametric and Simulated Distribution
Forecasts
Description: Dictionary-like reference for computing scoring rules in a wide
range of situations. Covers both parametric forecast distributions (such as
mixtures of Gaussians) and distributions generated via simulation. Further
details can be found in the package vignettes <doi:10.18637/jss.v090.i12>,
<doi:10.18637/jss.v110.i08>.
Author: Alexander I. Jordan [aut] ,
Fabian Krueger [aut, cre] ,
Sebastian Lerch [aut] ,
Sam Allen [aut] ,
Maximiliane Graeter [ctb]
Maintainer: Fabian Krueger <Fabian.Krueger83@gmail.com>
Diff between scoringRules versions 1.1.1 dated 2023-05-10 and 1.1.2 dated 2024-09-05
DESCRIPTION | 19 ++-- MD5 | 58 +++++++----- NAMESPACE | 6 + R/get_weight_func.R |only R/header.R | 2 R/helper_checks.R | 44 +++++++++ R/rps.R |only R/scores_quantiles.R |only R/scores_sample_multiv.R | 2 R/scores_sample_multiv_weighted.R | 54 +++++++++-- R/scores_sample_univ.R | 30 +++--- R/scores_sample_univ_weighted.R | 31 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 19 ++-- inst/doc/article.Rnw | 2 inst/doc/article.pdf |binary inst/doc/article_weighted_scores.R | 23 ++++- inst/doc/article_weighted_scores.Rnw | 151 +++++++++++++++++++-------------- inst/doc/article_weighted_scores.pdf |binary inst/doc/gettingstarted.pdf |binary man/get_weight_func.Rd |only man/rps_probs.Rd |only man/scores_quantiles.Rd |only man/scores_sample_multiv.Rd | 2 man/scores_sample_multiv_weighted.Rd | 55 +++--------- man/scores_sample_univ.Rd | 4 man/scores_sample_univ_weighted.Rd | 21 +++- tests/testthat/test-rps.R |only tests/testthat/test-scores_quantiles.R |only vignettes/article.Rnw | 2 vignettes/article_weighted_scores.Rnw | 151 +++++++++++++++++++-------------- vignettes/bibliography.bib | 8 + vignettes/bibliography_weighted.bib | 44 +++++++-- 34 files changed, 470 insertions(+), 258 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Tomasz Kalinowski [ctb, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between reticulate versions 1.38.0 dated 2024-06-19 and 1.39.0 dated 2024-09-05
reticulate-1.38.0/reticulate/inst/doc/arrays.R |only reticulate-1.38.0/reticulate/inst/doc/calling_python.R |only reticulate-1.38.0/reticulate/inst/doc/package.R |only reticulate-1.38.0/reticulate/inst/doc/python_packages.R |only reticulate-1.38.0/reticulate/inst/doc/python_primer.R |only reticulate-1.38.0/reticulate/inst/doc/r_markdown.R |only reticulate-1.38.0/reticulate/inst/doc/versions.R |only reticulate-1.39.0/reticulate/DESCRIPTION | 9 reticulate-1.39.0/reticulate/MD5 | 128 - reticulate-1.39.0/reticulate/NAMESPACE | 3 reticulate-1.39.0/reticulate/NEWS.md | 45 reticulate-1.39.0/reticulate/R/RcppExports.R | 4 reticulate-1.39.0/reticulate/R/array.R | 3 reticulate-1.39.0/reticulate/R/conda.R | 54 reticulate-1.39.0/reticulate/R/config.R | 4 reticulate-1.39.0/reticulate/R/knitr-engine.R | 14 reticulate-1.39.0/reticulate/R/package.R | 18 reticulate-1.39.0/reticulate/R/python.R | 111 + reticulate-1.39.0/reticulate/R/repl.R | 13 reticulate-1.39.0/reticulate/R/thread.R | 55 reticulate-1.39.0/reticulate/R/virtualenv.R | 6 reticulate-1.39.0/reticulate/R/zzz.R | 4 reticulate-1.39.0/reticulate/build/vignette.rds |binary reticulate-1.39.0/reticulate/inst/config/config.py | 4 reticulate-1.39.0/reticulate/inst/doc/arrays.Rmd | 3 reticulate-1.39.0/reticulate/inst/doc/arrays.html | 2 reticulate-1.39.0/reticulate/inst/doc/calling_python.Rmd | 33 reticulate-1.39.0/reticulate/inst/doc/calling_python.html | 2 reticulate-1.39.0/reticulate/inst/doc/package.Rmd | 26 reticulate-1.39.0/reticulate/inst/doc/package.html | 110 - reticulate-1.39.0/reticulate/inst/doc/python_dependencies.html | 2 reticulate-1.39.0/reticulate/inst/doc/python_packages.Rmd | 12 reticulate-1.39.0/reticulate/inst/doc/python_packages.html | 2 reticulate-1.39.0/reticulate/inst/doc/python_primer.Rmd | 300 ++- reticulate-1.39.0/reticulate/inst/doc/python_primer.html | 885 +++++----- reticulate-1.39.0/reticulate/inst/doc/r_markdown.Rmd | 4 reticulate-1.39.0/reticulate/inst/doc/r_markdown.html | 12 reticulate-1.39.0/reticulate/inst/doc/versions.Rmd | 15 reticulate-1.39.0/reticulate/inst/doc/versions.html | 2 reticulate-1.39.0/reticulate/inst/python/rpytools/generator.py | 2 reticulate-1.39.0/reticulate/inst/python/rpytools/run.py |only reticulate-1.39.0/reticulate/inst/python/rpytools/thread.py | 41 reticulate-1.39.0/reticulate/man/as.character.python.builtin.bytes.Rd | 41 reticulate-1.39.0/reticulate/man/as.character.python.builtin.str.Rd |only reticulate-1.39.0/reticulate/man/conda-tools.Rd | 3 reticulate-1.39.0/reticulate/man/conda_run2.Rd |only reticulate-1.39.0/reticulate/man/py_main_thread_func.Rd | 7 reticulate-1.39.0/reticulate/man/py_str.Rd | 5 reticulate-1.39.0/reticulate/man/virtualenv-tools.Rd | 2 reticulate-1.39.0/reticulate/src/RcppExports.cpp | 12 reticulate-1.39.0/reticulate/src/event_loop.cpp | 30 reticulate-1.39.0/reticulate/src/event_loop.h | 2 reticulate-1.39.0/reticulate/src/libpython.cpp | 4 reticulate-1.39.0/reticulate/src/libpython.h | 4 reticulate-1.39.0/reticulate/src/pending_py_calls_notifier.cpp |only reticulate-1.39.0/reticulate/src/pending_py_calls_notifier.h |only reticulate-1.39.0/reticulate/src/python.cpp | 426 +++- reticulate-1.39.0/reticulate/src/reticulate_types.h | 31 reticulate-1.39.0/reticulate/tests/testthat/_snaps/python-knitr-engine/test-chunking.md | 2 reticulate-1.39.0/reticulate/tests/testthat/resources/_snaps |only reticulate-1.39.0/reticulate/tests/testthat/resources/figure |only reticulate-1.39.0/reticulate/tests/testthat/resources/test-custom-root-dir.md |only reticulate-1.39.0/reticulate/tests/testthat/test-finalize.R |only reticulate-1.39.0/reticulate/tests/testthat/test-python-numpy.R | 1 reticulate-1.39.0/reticulate/tests/testthat/test-python-source.R | 2 reticulate-1.39.0/reticulate/tests/testthat/test-python-threads.R |only reticulate-1.39.0/reticulate/vignettes/arrays.Rmd | 3 reticulate-1.39.0/reticulate/vignettes/calling_python.Rmd | 33 reticulate-1.39.0/reticulate/vignettes/package.Rmd | 26 reticulate-1.39.0/reticulate/vignettes/python_packages.Rmd | 12 reticulate-1.39.0/reticulate/vignettes/python_primer.Rmd | 300 ++- reticulate-1.39.0/reticulate/vignettes/r_markdown.Rmd | 4 reticulate-1.39.0/reticulate/vignettes/versions.Rmd | 15 73 files changed, 1865 insertions(+), 1028 deletions(-)
Title: Doubly Robust Difference-in-Differences Estimators
Description: Implements the locally efficient doubly robust difference-in-differences (DiD)
estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020)
<doi:10.1016/j.jeconom.2020.06.003>. The estimator combines inverse probability weighting and outcome
regression estimators (also implemented in the package) to form estimators with
more attractive statistical properties. Two different estimation methods can be used
to estimate the nuisance functions.
Author: Pedro H. C. Sant'Anna [aut, cre, cph],
Jun Zhao [aut]
Maintainer: Pedro H. C. Sant'Anna <pedrosantanna@causal-solutions.com>
Diff between DRDID versions 1.0.7 dated 2024-07-05 and 1.1.0 dated 2024-09-05
DESCRIPTION | 17 - MD5 | 86 ++--- NEWS.md | 13 R/drdid_imp_panel.R | 2 R/drdid_imp_rc.R | 28 + R/drdid_imp_rc1.R | 2 R/drdid_panel.R | 27 + R/drdid_rc.R | 86 ++++- R/drdid_rc1.R | 16 R/ipw_did_panel.R | 7 R/ipw_did_rc.R | 5 R/pre_process_drdid.R | 8 R/pscore.cal.R | 4 R/reg_did_panel.R | 20 - R/reg_did_rc.R | 41 ++ R/std_ipw_did_panel.R | 8 R/std_ipw_did_rc.R | 5 R/twfe_did_panel.R | 10 R/twfe_did_rc.R | 9 R/wboot.dr.imp.panel.R | 38 +- R/wboot.dr.tr.panel.R | 54 +-- R/wboot.ipw.panel.R | 37 +- R/wboot.reg.panel.R | 45 +- R/wboot.std.ipw.panel.R | 47 +- R/wboot_drdid_imp_rc.R | 92 +++-- R/wboot_drdid_imp_rc1.R | 54 +-- R/wboot_drdid_rc.R | 121 ++++--- R/wboot_drdid_rc1.R | 77 ++-- R/wboot_ipw_rc.R | 39 +- R/wboot_reg_rc.R | 68 ++-- R/wboot_std_ipw_rc.R | 55 +-- R/wols.br.panel.R | 13 R/wols_rc.R | 16 inst/WORDLIST | 6 man/DRDID-package.Rd | 2 tests/testthat/test_boot_panel.R | 408 ++++++++++++------------- tests/testthat/test_boot_rc.R | 548 +++++++++++++++++----------------- tests/testthat/test_boot_twfe_panel.R | 264 ++++++++-------- tests/testthat/test_boot_twfe_rc.R | 304 +++++++++--------- tests/testthat/test_errors.R | 68 ++-- tests/testthat/test_nocovariates.R | 378 +++++++++++------------ tests/testthat/test_output.R | 386 +++++++++++------------ tests/testthat/test_rc.R | 366 +++++++++++----------- tests/testthat/test_widelong.R | 310 +++++++++---------- 44 files changed, 2241 insertions(+), 1949 deletions(-)
Title: Machine Learning
Description: Machine learning, containing several algorithms for supervised and unsupervised classification, in addition to a function that plots the Receiver Operating Characteristic (ROC) and Precision-Recall (PRC) curve graphs, and also a function that returns several metrics used for model evaluation, the latter can be used in ranking results from other packs.
Author: Paulo Cesar Ossani [aut, cre]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between Kira versions 1.0.5 dated 2024-07-05 and 1.0.6 dated 2024-09-05
Kira-1.0.5/Kira/R/brute.force.R |only Kira-1.0.5/Kira/R/vote.R |only Kira-1.0.5/Kira/man/brute.force.Rd |only Kira-1.0.5/Kira/man/vote.Rd |only Kira-1.0.6/Kira/DESCRIPTION | 10 +++++----- Kira-1.0.6/Kira/MD5 | 14 +++++--------- Kira-1.0.6/Kira/NAMESPACE | 2 +- Kira-1.0.6/Kira/man/Kira-package.Rd | 6 ++---- Kira-1.0.6/Kira/man/knn.Rd | 2 +- Kira-1.0.6/Kira/man/regression.Rd | 2 +- 10 files changed, 15 insertions(+), 21 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-31 0.2.1
2021-09-23 0.2.0
2020-10-22 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-28 0.4.0
2018-07-30 0.3.0
Title: Geographically-Conscious Taxonomic Assignment for Metabarcoding
Description: A bioinformatics pipeline for performing taxonomic
assignment of DNA metabarcoding sequence data while considering
geographic location. A detailed tutorial is available at
<https://urodelan.github.io/Local_Taxa_Tool_Tutorial/>.
A manuscript describing these methods is in preparation.
Author: Kenen Goodwin [aut, cre] ,
Taal Levi [aut]
Maintainer: Kenen Goodwin <urodelan@gmail.com>
Diff between LocaTT versions 1.1.1 dated 2023-10-30 and 1.1.2 dated 2024-09-05
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- inst/CITATION | 6 +++--- 3 files changed, 10 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-29 1.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-31 0.9.12
2024-01-23 0.9.6
2021-07-26 0.9.4