Title: A Logging Utility Focus on Clinical Trial Programming Workflows
Description: A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
Author: Nathan Kosiba [aut, cre],
Thomas Bermudez [aut],
Ben Straub [aut],
Michael Rimler [aut],
Nicholas Masel [aut],
Sam Parmar [aut],
GSK/Atorus JPT [cph, fnd]
Maintainer: Nathan Kosiba <nhkosiba@gmail.com>
Diff between logrx versions 0.3.0 dated 2023-10-17 and 0.3.1 dated 2024-04-11
logrx-0.3.0/logrx/tests/testthat/ref/ex1.html |only logrx-0.3.0/logrx/tests/testthat/ref/ex1.log |only logrx-0.3.0/logrx/tests/testthat/ref/ex2.log |only logrx-0.3.1/logrx/DESCRIPTION | 6 logrx-0.3.1/logrx/MD5 | 29 logrx-0.3.1/logrx/NAMESPACE | 1 logrx-0.3.1/logrx/NEWS.md | 4 logrx-0.3.1/logrx/R/writer.R | 9 logrx-0.3.1/logrx/build/vignette.rds |binary logrx-0.3.1/logrx/inst/doc/approved.R | 150 +-- logrx-0.3.1/logrx/inst/doc/approved.html | 1010 +++++++++++++------------- logrx-0.3.1/logrx/inst/doc/execution.R | 48 - logrx-0.3.1/logrx/inst/doc/execution.html | 938 ++++++++++++------------ logrx-0.3.1/logrx/inst/doc/logrx.R | 24 logrx-0.3.1/logrx/inst/doc/logrx.html | 906 +++++++++++------------ logrx-0.3.1/logrx/inst/doc/options.R | 46 - logrx-0.3.1/logrx/inst/doc/options.html | 660 ++++++++-------- 17 files changed, 1919 insertions(+), 1912 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.0.6 dated 2024-04-11 and 1.0.7 dated 2024-04-11
renv-1.0.6/renv/inst/repos/src/contrib/renv_1.0.6.tar.gz |only renv-1.0.7/renv/DESCRIPTION | 6 ++--- renv-1.0.7/renv/MD5 | 18 +++++++-------- renv-1.0.7/renv/NEWS.md | 6 +++++ renv-1.0.7/renv/R/bootstrap.R | 15 ++++++++++++ renv-1.0.7/renv/R/utils.R | 15 ------------ renv-1.0.7/renv/inst/repos/src/contrib/PACKAGES | 4 +-- renv-1.0.7/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.0.7/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.0.7/renv/inst/repos/src/contrib/renv_1.0.7.tar.gz |only renv-1.0.7/renv/inst/resources/activate.R | 15 ++++++++++++ 11 files changed, 50 insertions(+), 29 deletions(-)
Title: Kernel-Embedding-of-Probability Test for Elliptical Distribution
Description: Provides an implementation of a kernel-embedding of probability test for elliptical distribution. This is an asymptotic test for elliptical distribution under general alternatives, and the location and shape parameters are assumed to be unknown. Some side-products are posted, including the transformation between rectangular and polar coordinates and two product-type kernel functions. See Tang and Li (2024) <arXiv:2306.10594> for details.
Author: Yin Tang [aut, cre],
Bing Li [cph, aut]
Maintainer: Yin Tang <yqt5219@psu.edu>
Diff between KEPTED versions 0.1.0 dated 2024-03-27 and 0.1.1 dated 2024-04-11
DESCRIPTION | 6 MD5 | 8 - NEWS.md | 4 R/EllKEPT.R | 37 ++-- inst/doc/KEPTED.html | 391 +++++++++++++++++++++++++-------------------------- 5 files changed, 227 insertions(+), 219 deletions(-)
Title: Statistical Network Models for Dynamic Network Data
Description: Tools for fitting statistical network models to dynamic network data.
Can be used for fitting both dynamic network actor models ('DyNAMs') and
relational event models ('REMs').
Stadtfeld, Hollway, and Block (2017a) <doi:10.1177/0081175017709295>,
Stadtfeld, Hollway, and Block (2017b) <doi:10.1177/0081175017733457>,
Stadtfeld and Block (2017) <doi:10.15195/v4.a14>,
Hoffman et al. (2020) <doi:10.1017/nws.2020.3>.
Author: James Hollway [aut, dtc] ,
Christoph Stadtfeld [aut, dtc],
Marion Hoffman [aut],
Alvaro Uzaheta [cre, aut] ,
Mirko Reul [ctb],
Timon Elmer [ctb],
Kieran Mepham [ctb],
Per Block [ctb],
Xiaolei Zhang [ctb],
Weigutian Ou [ctb],
Emily Garvin [ctb],
Siwei [...truncated...]
Maintainer: Alvaro Uzaheta <ualvaro@ethz.ch>
Diff between goldfish versions 1.6.4 dated 2022-08-24 and 1.6.8 dated 2024-04-11
goldfish-1.6.4/goldfish/inst/doc/dynami-example.R |only goldfish-1.6.4/goldfish/inst/doc/teaching1.R |only goldfish-1.6.4/goldfish/inst/doc/teaching2.R |only goldfish-1.6.4/goldfish/src/DyNAM_rate_ordered_gather_compute.cpp_deprecated |only goldfish-1.6.4/goldfish/src/REM_gather_compute.cpp_deprecated |only goldfish-1.6.4/goldfish/src/REM_ordered_gather_compute.cpp_deprecated |only goldfish-1.6.4/goldfish/vignettes/teaching/examine-1.png |only goldfish-1.6.8/goldfish/DESCRIPTION | 33 goldfish-1.6.8/goldfish/MD5 | 214 - goldfish-1.6.8/goldfish/NAMESPACE | 35 goldfish-1.6.8/goldfish/NEWS.md | 31 goldfish-1.6.8/goldfish/R/RcppExports.R | 295 +- goldfish-1.6.8/goldfish/R/data_Fisheries_Treaties_6070.R | 62 goldfish-1.6.8/goldfish/R/data_RFID_Validity_Study.R | 48 goldfish-1.6.8/goldfish/R/data_Social_Evolution.R | 38 goldfish-1.6.8/goldfish/R/functions_checks.R | 611 +++- goldfish-1.6.8/goldfish/R/functions_data.R | 425 ++- goldfish-1.6.8/goldfish/R/functions_diagnostics.R | 96 goldfish-1.6.8/goldfish/R/functions_effects_DyNAM_choice.R | 757 +++-- goldfish-1.6.8/goldfish/R/functions_effects_DyNAM_choice_coordination.R | 236 - goldfish-1.6.8/goldfish/R/functions_effects_DyNAM_rate.R | 191 - goldfish-1.6.8/goldfish/R/functions_effects_DyNAMi_choice.R | 271 +- goldfish-1.6.8/goldfish/R/functions_effects_DyNAMi_rate.R | 666 +++-- goldfish-1.6.8/goldfish/R/functions_effects_REM.R | 483 ++- goldfish-1.6.8/goldfish/R/functions_estimation.R | 309 +- goldfish-1.6.8/goldfish/R/functions_estimation_engine.R | 680 ++--- goldfish-1.6.8/goldfish/R/functions_estimation_engine_c.r | 489 +-- goldfish-1.6.8/goldfish/R/functions_gather.R | 320 +- goldfish-1.6.8/goldfish/R/functions_group_interaction_utility.R | 227 + goldfish-1.6.8/goldfish/R/functions_output.R | 223 + goldfish-1.6.8/goldfish/R/functions_parsing.R | 250 + goldfish-1.6.8/goldfish/R/functions_postestimate.R | 49 goldfish-1.6.8/goldfish/R/functions_preprocessing.R | 503 ++- goldfish-1.6.8/goldfish/R/functions_preprocessing_interaction.R | 197 - goldfish-1.6.8/goldfish/R/functions_utility.R | 192 - goldfish-1.6.8/goldfish/R/goldfish-package.R | 26 goldfish-1.6.8/goldfish/R/testthat-helpers.R | 425 ++- goldfish-1.6.8/goldfish/R/zzz.R | 10 goldfish-1.6.8/goldfish/README.md | 300 +- goldfish-1.6.8/goldfish/build/partial.rdb |binary goldfish-1.6.8/goldfish/build/vignette.rds |binary goldfish-1.6.8/goldfish/configure | 501 --- goldfish-1.6.8/goldfish/configure.ac | 217 - goldfish-1.6.8/goldfish/inst/REFERENCES.bib |only goldfish-1.6.8/goldfish/inst/doc/dynami-example.Rmd | 334 +- goldfish-1.6.8/goldfish/inst/doc/dynami-example.html | 398 +-- goldfish-1.6.8/goldfish/inst/doc/goldfishEffects.R | 87 goldfish-1.6.8/goldfish/inst/doc/goldfishEffects.Rmd | 216 - goldfish-1.6.8/goldfish/inst/doc/goldfishEffects.html | 595 ++-- goldfish-1.6.8/goldfish/inst/doc/teaching1.Rmd | 337 +- goldfish-1.6.8/goldfish/inst/doc/teaching1.html | 1285 +++++----- goldfish-1.6.8/goldfish/inst/doc/teaching2.Rmd | 131 - goldfish-1.6.8/goldfish/inst/doc/teaching2.html | 797 +++--- goldfish-1.6.8/goldfish/man/Fisheries_Treaties_6070.Rd | 62 goldfish-1.6.8/goldfish/man/GatherPreprocessing.Rd |only goldfish-1.6.8/goldfish/man/RFID_Validity_Study.Rd | 46 goldfish-1.6.8/goldfish/man/Social_Evolution.Rd | 38 goldfish-1.6.8/goldfish/man/defineNodes.Rd | 2 goldfish-1.6.8/goldfish/man/estimate.Rd | 28 goldfish-1.6.8/goldfish/man/examine.Rd | 9 goldfish-1.6.8/goldfish/man/figures/lifecycle-archived.svg |only goldfish-1.6.8/goldfish/man/figures/lifecycle-defunct.svg |only goldfish-1.6.8/goldfish/man/figures/lifecycle-deprecated.svg |only goldfish-1.6.8/goldfish/man/figures/lifecycle-experimental.svg |only goldfish-1.6.8/goldfish/man/figures/lifecycle-maturing.svg |only goldfish-1.6.8/goldfish/man/figures/lifecycle-questioning.svg |only goldfish-1.6.8/goldfish/man/figures/lifecycle-stable.svg |only goldfish-1.6.8/goldfish/man/figures/lifecycle-superseded.svg |only goldfish-1.6.8/goldfish/man/goldfish-package.Rd | 46 goldfish-1.6.8/goldfish/man/update-method.Rd | 11 goldfish-1.6.8/goldfish/src/DyNAM_MM_default.cpp | 106 goldfish-1.6.8/goldfish/src/DyNAM_choice_default.cpp | 88 goldfish-1.6.8/goldfish/src/DyNAM_rate_default.cpp | 367 +- goldfish-1.6.8/goldfish/src/DyNAM_rate_ordered_default.cpp | 115 goldfish-1.6.8/goldfish/src/Makevars.in | 22 goldfish-1.6.8/goldfish/src/Makevars.win | 20 goldfish-1.6.8/goldfish/src/REM_default.cpp | 445 +-- goldfish-1.6.8/goldfish/src/REM_ordered_default.cpp | 125 goldfish-1.6.8/goldfish/src/compute_coordination_selection.cpp | 198 - goldfish-1.6.8/goldfish/src/compute_multinomial_selection.cpp | 45 goldfish-1.6.8/goldfish/src/compute_poisson_selection.cpp | 45 goldfish-1.6.8/goldfish/src/convert_rdata_to_cdata.cpp | 40 goldfish-1.6.8/goldfish/src/gather_progress.cpp | 3 goldfish-1.6.8/goldfish/src/gather_progress.hpp | 3 goldfish-1.6.8/goldfish/src/gather_receiver_model.cpp | 42 goldfish-1.6.8/goldfish/src/gather_sender_model.cpp | 350 +- goldfish-1.6.8/goldfish/src/gather_sender_receiver_model.cpp | 148 - goldfish-1.6.8/goldfish/tests/testthat/test-effects_preprocessing.R |only goldfish-1.6.8/goldfish/tests/testthat/test-effects_preprocessing_DyNAM_choice.R | 325 ++ goldfish-1.6.8/goldfish/tests/testthat/test-effects_preprocessing_DyNAM_rate.R |only goldfish-1.6.8/goldfish/tests/testthat/test-effects_preprocessing_DyNAMi_choice.R | 73 goldfish-1.6.8/goldfish/tests/testthat/test-effects_preprocessing_DyNAMi_rate.R | 217 + goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-init_default.R | 35 goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-update_alter.R | 33 goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-update_diff.R | 100 goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-update_four.R | 88 goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-update_indeg.R | 203 - goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-update_inertia.R | 92 goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-update_recip.R | 111 goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-update_same.R | 39 goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-update_sim.R | 115 goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_choice-update_trans.R | 65 goldfish-1.6.8/goldfish/tests/testthat/test-functions_effects_DyNAM_rate-update_ego.R | 4 goldfish-1.6.8/goldfish/tests/testthat/test-functions_estimation.R |only goldfish-1.6.8/goldfish/tests/testthat/test-functions_estimation_engine_c.R |only goldfish-1.6.8/goldfish/tests/testthat/test-functions_gather.R |only goldfish-1.6.8/goldfish/tests/testthat/test-functions_output.R |only goldfish-1.6.8/goldfish/tests/testthat/test-functions_postestimate.R | 32 goldfish-1.6.8/goldfish/vignettes/dynami-example.Rmd | 334 +- goldfish-1.6.8/goldfish/vignettes/dynami-example.Rmd.orig | 345 +- goldfish-1.6.8/goldfish/vignettes/goldfishEffects.Rmd | 216 - goldfish-1.6.8/goldfish/vignettes/teaching/plot-examine-1.png |only goldfish-1.6.8/goldfish/vignettes/teaching/plot-teaching1-1.png |binary goldfish-1.6.8/goldfish/vignettes/teaching/plot-teaching1-2.png |binary goldfish-1.6.8/goldfish/vignettes/teaching/plot-teaching1-3.png |binary goldfish-1.6.8/goldfish/vignettes/teaching/plot-teaching2-1.png |binary goldfish-1.6.8/goldfish/vignettes/teaching1.Rmd | 337 +- goldfish-1.6.8/goldfish/vignettes/teaching1.Rmd.orig | 222 + goldfish-1.6.8/goldfish/vignettes/teaching2.Rmd | 131 - goldfish-1.6.8/goldfish/vignettes/teaching2.Rmd.orig | 94 120 files changed, 11104 insertions(+), 8101 deletions(-)
Title: Geometrically Designed Spline Regression
Description: Spline Regression, Generalized Additive Models, and Component-wise Gradient
Boosting, utilizing Geometrically Designed (GeD) Splines. GeDS regression is a
non-parametric method inspired by geometric principles, for fitting spline regression
models with variable knots in one or two independent variables. It efficiently estimates
the number of knots and their positions, as well as the spline order, assuming the
response variable follows a distribution from the exponential family. GeDS models
integrate the broader category of Generalized (Non-)Linear Models, offering a flexible
approach to modeling complex relationships. A description of the method can be found in
Kaishev et al. (2016) <doi:10.1007/s00180-015-0621-7> and Dimitrova et al. (2023)
<doi:10.1016/j.amc.2022.127493>. Further extending its capabilities, GeDS's implementation
includes Generalized Additive Models (GAM) and Functional Gradient Boosting (FGB),
enabling versatile multivariate predictor modeling, as discuss [...truncated...]
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>,
Emilio S. Guillen <Emilio.Saenz-Guillen@bayes.city.ac.uk>,
Vladimir K. Kaishev <V.Kaishev@city.ac.uk>,
Andrea Lattuada <andrea.lattuada@hotmail.com> and
Richard J. Verrall <R.J.Verrall@city.ac.uk>
Maintainer: Emilio S. Guillen <Emilio.Saenz-Guillen@bayes.city.ac.uk>
Diff between GeDS versions 0.2.0 dated 2024-03-24 and 0.2.1 dated 2024-04-11
DESCRIPTION | 6 MD5 | 34 ++-- R/BivariateFitter.R | 215 ++++++++++++++++++++----------- R/GGeDS.R | 50 +++++-- R/NGeDS.R | 6 R/NGeDSboost.R | 2 R/NGeDSgam.R | 2 R/S3methods.R | 8 - R/SplineReg.R | 8 - R/UnivariateFitter.R | 260 +++++++++++++++++++++----------------- R/plot_GeDSMethod.R | 67 +++++---- R/read.formula.R | 9 + README.md | 2 man/BivariateFitters.Rd | 15 +- man/GGeDS.Rd | 45 +++++- man/GeDS-package.Rd | 1 man/NGeDS.Rd | 3 man/plot-GeDS-method.Rd | 327 ++++++++++++++++++++++++------------------------ 18 files changed, 615 insertions(+), 445 deletions(-)
Title: Import, Recompute and Analyze Data from Portable Gas Analyzers
Description: Provides functions to import data from several instruments
commonly used by plant physiologists to measure characteristics
related to photosynthesis. It provides a standardized list of variable
names, and several sets of equations to calculate additional variables
based on the measurements. These equations have been described by von
Caemmerer and Farquhar (1981) <doi:10.1007/BF00384257>, Busch et al.
(2020) <doi:10.1038/s41477-020-0606-6> and Márquez et al. (2021)
<doi:10.1038/s41477-021-00861-w>. In addition, this package
facilitates performing sensitivity analyses on variables or
assumptions used in the calculations.
Author: Danny Tholen [aut, cre]
Maintainer: Danny Tholen <thalecress+p@gmail.com>
Diff between gasanalyzer versions 0.3.4 dated 2024-01-10 and 0.4.0 dated 2024-04-11
DESCRIPTION | 10 MD5 | 59 +- NAMESPACE | 2 NEWS.md | 9 R/calc_data.R | 223 +++++++++- R/equations.R | 3 R/factory.R | 2 R/matching.R | 15 R/raw.R | 4 R/read_6400.R | 53 +- R/read_6800.R | 83 ++-- R/read_ciras3_xml.R | 3 R/read_ciras4.R |only R/read_gfs.R | 220 +++++----- R/readwrite_gasanalyzer.R | 2 R/sysdata.rda |binary R/utils.R | 49 +- R/xlsx_helpers.R | 4 README.md | 4 inst/WORDLIST | 8 inst/doc/gasanalyzer.R | 67 +-- inst/doc/gasanalyzer.Rmd | 75 +-- inst/doc/gasanalyzer.html | 943 +++++++++++++++++++++++----------------------- inst/extdata/ciras4.csv |only inst/extdata/d13C.tsv |binary inst/extdata/vars.tsv | 585 ++++++++++++++-------------- man/read_6400_txt.Rd | 6 man/read_6800_txt.Rd | 5 man/read_6800_xlsx.Rd | 4 man/read_ciras4.Rd |only man/read_gfs.Rd | 5 vignettes/gasanalyzer.Rmd | 75 +-- 32 files changed, 1373 insertions(+), 1145 deletions(-)
Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <https://www.tesourodireto.com.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetTDData versions 1.5.4 dated 2023-05-15 and 1.5.5 dated 2024-04-11
GetTDData-1.5.4/GetTDData/R/gtdd_download_TD_data.R |only GetTDData-1.5.4/GetTDData/R/gtdd_read_TD_files.R |only GetTDData-1.5.4/GetTDData/man/download.TD.data.Rd |only GetTDData-1.5.4/GetTDData/man/read.TD.files.Rd |only GetTDData-1.5.5/GetTDData/DESCRIPTION | 10 +++--- GetTDData-1.5.5/GetTDData/MD5 | 15 ++++------ GetTDData-1.5.5/GetTDData/NAMESPACE | 3 -- GetTDData-1.5.5/GetTDData/NEWS.md | 3 ++ GetTDData-1.5.5/GetTDData/R/globals.R |only GetTDData-1.5.5/GetTDData/R/td_get_current.R |only GetTDData-1.5.5/GetTDData/man/td_get_current.Rd |only GetTDData-1.5.5/GetTDData/tests/testthat/test-importing-data.R | 12 ++++++++ 12 files changed, 28 insertions(+), 15 deletions(-)
Title: Recursive Partitioning Based on Psychometric Models
Description: Recursive partitioning based on psychometric models,
employing the general MOB algorithm (from package partykit) to obtain
Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and
MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial
credit models.
Author: Achim Zeileis [aut, cre] ,
Carolin Strobl [aut] ,
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut] ,
David Dreifuss [aut],
Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotree versions 0.16-0 dated 2022-05-06 and 0.16-1 dated 2024-04-11
psychotree-0.16-0/psychotree/NEWS |only psychotree-0.16-1/psychotree/DESCRIPTION | 12 psychotree-0.16-1/psychotree/MD5 | 28 - psychotree-0.16-1/psychotree/NEWS.md |only psychotree-0.16-1/psychotree/R/bttree.R | 2 psychotree-0.16-1/psychotree/R/gpcmtree.R | 6 psychotree-0.16-1/psychotree/R/graphics.R | 321 ------------------- psychotree-0.16-1/psychotree/R/mpttree.R | 2 psychotree-0.16-1/psychotree/R/npltree.R | 2 psychotree-0.16-1/psychotree/R/pctree.R | 2 psychotree-0.16-1/psychotree/R/raschtree.R | 2 psychotree-0.16-1/psychotree/R/rstree.R | 2 psychotree-0.16-1/psychotree/build/partial.rdb |binary psychotree-0.16-1/psychotree/build/vignette.rds |binary psychotree-0.16-1/psychotree/inst/doc/raschtree.pdf |binary psychotree-0.16-1/psychotree/man/node_profileplot.Rd | 168 ++++----- 16 files changed, 125 insertions(+), 422 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.3.1 dated 2024-03-28 and 1.4.0 dated 2024-04-11
DESCRIPTION | 8 MD5 | 48 R/GPModel.R | 16 configure.ac | 2 man/GPModel_shared_params.Rd | 12 man/fit.GPModel.Rd | 14 man/fit.Rd | 12 man/fitGPModel.Rd | 14 man/set_optim_params.GPModel.Rd | 12 man/set_optim_params.Rd | 12 src/include/GPBoost/Vecchia_utils.h | 2 src/include/GPBoost/cov_fcts.h | 12 src/include/GPBoost/likelihoods.h | 413 ++++--- src/include/GPBoost/optim_utils.h | 166 +- src/include/GPBoost/re_comp.h | 2 src/include/GPBoost/re_model_template.h | 688 +++++++----- src/include/LBFGS.h | 32 src/include/LBFGSpp/LineSearchBacktracking.h | 27 src/include/LBFGSpp/LineSearchNocedalWright.h | 39 src/include/LBFGSpp/Param.h | 7 tests/testthat/test_GPModel_gaussian_process.R | 177 ++- tests/testthat/test_GPModel_grouped_random_effects.R | 127 +- tests/testthat/test_GPModel_non_Gaussian_data.R | 410 +++---- tests/testthat/test_z_GPBoost_algorithm.R | 14 tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 28 25 files changed, 1425 insertions(+), 869 deletions(-)
Title: Interface to 'Travel Time' API
Description: 'Travel Time' API <https://docs.traveltime.com/api/overview/introduction> helps users find locations by journey time rather than using ‘as the crow flies’ distance.
Time-based searching gives users more opportunities for personalisation and delivers a more relevant search.
Author: TravelTime [aut, cre]
Maintainer: TravelTime <frontend@traveltime.com>
Diff between traveltimeR versions 1.1.5 dated 2024-04-10 and 1.2.0 dated 2024-04-11
DESCRIPTION | 8 ++++---- MD5 | 11 +++++++---- NAMESPACE | 2 ++ R/distance_map.R |only R/make_searches.R | 7 ++++++- README.md | 37 +++++++++++++++++++++++++++++++++++++ man/check_coords_for_error.Rd |only man/distance_map.Rd |only 8 files changed, 56 insertions(+), 9 deletions(-)
Title: An Extension of 'Tidymodels' Supporting Offset Terms
Description: Extend the 'tidymodels' ecosystem <https://www.tidymodels.org/> to
enable the creation of predictive models with offset terms. Models with
offsets are most useful when working with count data or when fitting an
adjustment model on top of an existing model with a prior expectation.
The former situation is common in insurance where data is often weighted by
exposures. The latter is common in life insurance where industry mortality
tables are often used as a starting point for setting assumptions.
Author: Matt Heaphy [aut, cre, cph]
Maintainer: Matt Heaphy <mattrmattrs@gmail.com>
Diff between offsetreg versions 1.0.0 dated 2024-01-23 and 1.1.0 dated 2024-04-11
offsetreg-1.0.0/offsetreg/R/offsetreg-data.R |only offsetreg-1.1.0/offsetreg/DESCRIPTION | 12 ++-- offsetreg-1.1.0/offsetreg/MD5 | 47 ++++++++++------ offsetreg-1.1.0/offsetreg/NAMESPACE | 15 +++++ offsetreg-1.1.0/offsetreg/NEWS.md | 16 ++++- offsetreg-1.1.0/offsetreg/R/boost_tree_data.R |only offsetreg-1.1.0/offsetreg/R/boost_tree_offset.R |only offsetreg-1.1.0/offsetreg/R/decision_tree_data.R |only offsetreg-1.1.0/offsetreg/R/decision_tree_exposure.R |only offsetreg-1.1.0/offsetreg/R/glm.R | 47 +++++++++------- offsetreg-1.1.0/offsetreg/R/poisson_reg_data.R |only offsetreg-1.1.0/offsetreg/R/poisson_reg_offset.R | 18 +++++- offsetreg-1.1.0/offsetreg/R/reexports.R | 4 + offsetreg-1.1.0/offsetreg/R/rpart.R |only offsetreg-1.1.0/offsetreg/R/xgboost.R |only offsetreg-1.1.0/offsetreg/R/zzz.R | 14 +++- offsetreg-1.1.0/offsetreg/README.md | 33 ++++++----- offsetreg-1.1.0/offsetreg/build |only offsetreg-1.1.0/offsetreg/inst |only offsetreg-1.1.0/offsetreg/man/boost_tree_offset.Rd |only offsetreg-1.1.0/offsetreg/man/decision_tree_exposure.Rd |only offsetreg-1.1.0/offsetreg/man/glm_offset.Rd | 10 ++- offsetreg-1.1.0/offsetreg/man/glmnet_offset.Rd | 2 offsetreg-1.1.0/offsetreg/man/offsetreg-package.Rd | 2 offsetreg-1.1.0/offsetreg/man/poisson_reg_offset.Rd | 2 offsetreg-1.1.0/offsetreg/man/reexports.Rd | 3 - offsetreg-1.1.0/offsetreg/man/rpart_exposure.Rd |only offsetreg-1.1.0/offsetreg/man/xgb_train_offset.Rd |only offsetreg-1.1.0/offsetreg/tests/testthat/test-poisson.R | 13 ++++ offsetreg-1.1.0/offsetreg/tests/testthat/test-rpart.R |only offsetreg-1.1.0/offsetreg/tests/testthat/test-xgboost.R |only offsetreg-1.1.0/offsetreg/vignettes |only 32 files changed, 168 insertions(+), 70 deletions(-)
Title: Interface to 'fastai'
Description: The 'fastai' <https://docs.fast.ai/index.html> library
simplifies training fast and accurate neural networks
using modern best practices. It is based on research
in to deep learning best practices undertaken
at 'fast.ai', including 'out of the box' support
for vision, text, tabular, audio, time series, and
collaborative filtering models.
Author: Turgut Abdullayev [ctb, cre, cph, aut]
Maintainer: Turgut Abdullayev <turqut.a.314@gmail.com>
Diff between fastai versions 2.2.1 dated 2023-03-11 and 2.2.2 dated 2024-04-11
DESCRIPTION | 8 MD5 | 2347 +-- NAMESPACE | 1926 +-- NEWS.md | 144 R/GAN.R | 1666 +- R/Learner_fits.R | 596 - R/Loss.R | 504 R/audio_aug_preprocess.R | 94 R/audio_aug_signal.R | 374 R/audio_aug_spectrogram.R | 296 R/audio_core_config.R | 668 - R/audio_core_signal.R | 336 R/audio_core_spectrogram.R | 206 R/audio_download_tar.R | 128 R/blocks.R | 882 - R/blurr_hugging_face.R | 1730 +- R/bs_finder.R | 122 R/callbacks.R | 786 - R/callbacks_data.R | 402 R/callbacks_hook.R | 524 R/callbacks_mixup_preds_rnn.R | 232 R/callbacks_schedule.R | 252 R/callbacks_training.R | 80 R/cnn_learner.R | 546 R/collab.R | 682 - R/custom_modules.R | 222 R/cycleGAN_models.R | 1092 - R/dataloader.R | 96 R/download_tar.R | 2114 +-- R/experimental.R | 254 R/fastaibuilt.R | 192 R/fastinference.R | 456 R/freeze.R | 84 R/generics_image.R | 44 R/generics_mask.R | 746 - R/generics_tensor.R | 932 - R/icevision_albumentations.R | 5935 ++++------ R/icevision_dataloaders.R | 516 R/icevision_dataset.R | 128 R/icevision_datasplitters.R | 168 R/icevision_efficentdet.R | 102 R/icevision_faster_rcnn.R | 100 R/icevision_mask_rcnn.R | 116 R/icevision_metrics.R | 84 R/icevision_models.R | 338 R/icevision_parsers.R | 364 R/icevision_utils.R | 308 R/image_loaders.R | 1160 - R/image_ops.R | 548 R/import_modules.R | 626 - R/install_fastai.R | 376 R/kaggle_wrappers.R | 336 R/layers.R | 1848 +-- R/losses.R | 74 R/medical.R | 636 - R/metric.R | 2644 ++-- R/optimizers.R | 1482 +- R/package.R | 544 R/predictions.R | 80 R/reexports.R | 102 R/splitters.R | 82 R/stats.R | 468 R/tabular.R | 430 R/tabular_model.R | 256 R/tabular_transform.R | 436 R/test.R | 1160 - R/text_core.R | 1254 +- R/text_data.R | 1646 +- R/text_learner.R | 812 - R/text_models.R | 1210 +- R/time_series_core.R | 184 R/time_series_data.R | 248 R/time_series_model.R | 336 R/time_series_tabular.R | 406 R/timm_loader.R | 70 R/unet.R | 514 R/vision_augment.R | 2042 +-- R/vision_core.R | 1478 +- R/vision_data.R | 458 R/vision_learner.R | 198 R/vision_models.R | 1892 +-- README.md | 3806 +++--- build/vignette.rds |binary inst/doc/Basic_Tabular.R | 114 inst/doc/Basic_Tabular.Rmd | 426 inst/doc/Basic_Tabular.html | 1032 - inst/doc/audio.R | 146 inst/doc/audio.Rmd | 340 inst/doc/audio.html | 932 - inst/doc/audio2tf.R | 100 inst/doc/audio2tf.Rmd | 270 inst/doc/audio2tf.html | 874 - inst/doc/basic_img_class.R | 100 inst/doc/basic_img_class.Rmd | 384 inst/doc/basic_img_class.html | 1002 - inst/doc/bayes_opt.R | 130 inst/doc/bayes_opt.Rmd | 176 inst/doc/bayes_opt.html | 868 - inst/doc/callbacks.R | 96 inst/doc/callbacks.Rmd | 294 inst/doc/callbacks.html | 894 - inst/doc/catalyst.R | 46 inst/doc/catalyst.Rmd | 140 inst/doc/catalyst.html | 800 - inst/doc/custom_img.R | 172 inst/doc/custom_img.Rmd | 332 inst/doc/custom_img.html | 948 - inst/doc/data_aug.R | 200 inst/doc/data_aug.Rmd | 462 inst/doc/data_aug.html | 1048 - inst/doc/gpt.R | 148 inst/doc/gpt.Rmd | 284 inst/doc/gpt.html | 948 - inst/doc/head_pose.R | 162 inst/doc/head_pose.Rmd | 334 inst/doc/head_pose.html | 944 - inst/doc/lightning.R | 32 inst/doc/lightning.Rmd | 96 inst/doc/lightning.html | 768 - inst/doc/low.R | 264 inst/doc/low.Rmd | 688 - inst/doc/low.html | 1240 +- inst/doc/medical_dcm.R | 118 inst/doc/medical_dcm.Rmd | 764 - inst/doc/medical_dcm.html | 1372 +- inst/doc/migrating_ignite.R | 28 inst/doc/migrating_ignite.Rmd | 92 inst/doc/migrating_ignite.html | 764 - inst/doc/migrating_pytorch.R | 30 inst/doc/migrating_pytorch.Rmd | 90 inst/doc/migrating_pytorch.html | 752 - inst/doc/multilabel.R | 150 inst/doc/multilabel.Rmd | 704 - inst/doc/multilabel.html | 1318 +- inst/doc/obj_detect.R | 104 inst/doc/obj_detect.Rmd | 236 inst/doc/obj_detect.html | 882 - inst/doc/optimizer.R | 502 inst/doc/optimizer.Rmd | 1078 - inst/doc/optimizer.html | 1524 +- inst/doc/question_answering.R | 208 inst/doc/question_answering.Rmd | 616 - inst/doc/question_answering.html | 1236 +- inst/doc/super_res_gan.R | 122 inst/doc/super_res_gan.Rmd | 250 inst/doc/super_res_gan.html | 884 - inst/doc/textclassification.R | 106 inst/doc/textclassification.Rmd | 858 - inst/doc/textclassification.html | 1484 +- inst/doc/textsummarize.R | 166 inst/doc/textsummarize.Rmd | 574 inst/doc/textsummarize.html | 1202 +- inst/doc/time_series.R | 104 inst/doc/time_series.Rmd | 578 inst/doc/time_series.html | 1198 +- inst/python/fastaibuilt/Module_test.py | 20 inst/python/fastaibuilt/Transformer.py | 42 inst/python/fastaibuilt/bs_finder.py | 320 inst/python/fastaibuilt/crappify.py | 46 inst/python/fastaibuilt/custom_loss.py | 22 inst/python/fastaibuilt/migrating_catalyst.py | 76 inst/python/fastaibuilt/migrating_ignite.py | 186 inst/python/fastaibuilt/migrating_lightning.py | 88 inst/python/fastaibuilt/migrating_pytorch.py | 136 inst/python/fastaibuilt/pretrained_timm_models.py | 164 inst/python/fastaibuilt/retinanet/inference.py | 132 inst/python/fastaibuilt/train_imagenette.py | 172 inst/python/fastaibuilt/train_imdbclassifier.py | 108 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man/win_brain_soft.Rd | 28 man/win_liver.Rd | 28 man/win_lungs.Rd | 28 man/win_mediastinum.Rd | 28 man/win_spine_bone.Rd | 28 man/win_spine_soft.Rd | 28 man/win_stroke.Rd | 28 man/win_subdural.Rd | 28 man/xla.Rd | 28 man/xresnet101.Rd | 34 man/xresnet152.Rd | 34 man/xresnet18.Rd | 34 man/xresnet18_deep.Rd | 34 man/xresnet18_deeper.Rd | 34 man/xresnet34.Rd | 34 man/xresnet34_deep.Rd | 34 man/xresnet34_deeper.Rd | 34 man/xresnet50.Rd | 34 man/xresnet50_deep.Rd | 34 man/xresnet50_deeper.Rd | 34 man/xresnext101.Rd | 34 man/xresnext18.Rd | 34 man/xresnext34.Rd | 34 man/xresnext50.Rd | 34 man/xse_resnet101.Rd | 34 man/xse_resnet152.Rd | 34 man/xse_resnet18.Rd | 34 man/xse_resnet34.Rd | 34 man/xse_resnet50.Rd | 34 man/xse_resnext101.Rd | 34 man/xse_resnext18.Rd | 34 man/xse_resnext18_deep.Rd | 34 man/xse_resnext18_deeper.Rd | 34 man/xse_resnext34.Rd | 34 man/xse_resnext34_deep.Rd | 34 man/xse_resnext34_deeper.Rd | 34 man/xse_resnext50.Rd | 34 man/xse_resnext50_deep.Rd | 34 man/xse_resnext50_deeper.Rd | 34 man/xsenet154.Rd | 34 man/zoom.Rd | 38 man/zoom_mat.Rd | 80 tests/testthat.R | 24 tests/testthat/test-GAN.R |only tests/testthat/test-collab.R |only tests/testthat/test-experimental.R |only tests/testthat/test-generics-tensor.R |only tests/testthat/test-image.R |only tests/testthat/test-medical.R |only tests/testthat/test-medical_image_render.R |only tests/testthat/test-model_load.R |only tests/testthat/test-modify.R |only tests/testthat/test-nn_module.R |only tests/testthat/test-predict_medical.R |only tests/testthat/test-pretrained_in_cnn_learner.R |only tests/testthat/test-regression.R |only tests/testthat/test-tabular.R |only tests/testthat/test-text-load.R |only tests/testthat/test-text.R | 52 tests/testthat/test-time-series.R | 82 tests/testthat/utils.R | 76 vignettes/Basic_Tabular.Rmd | 426 vignettes/audio.Rmd | 340 vignettes/audio2tf.Rmd | 270 vignettes/basic_img_class.Rmd | 384 vignettes/bayes_opt.Rmd | 176 vignettes/callbacks.Rmd | 294 vignettes/catalyst.Rmd | 140 vignettes/custom_img.Rmd | 332 vignettes/data_aug.Rmd | 462 vignettes/gpt.Rmd | 284 vignettes/head_pose.Rmd | 334 vignettes/lightning.Rmd | 96 vignettes/low.Rmd | 688 - vignettes/medical_dcm.Rmd | 764 - vignettes/migrating_ignite.Rmd | 92 vignettes/migrating_pytorch.Rmd | 90 vignettes/multilabel.Rmd | 704 - vignettes/obj_detect.Rmd | 236 vignettes/optimizer.Rmd | 1078 - vignettes/question_answering.Rmd | 616 - vignettes/super_res_gan.Rmd | 250 vignettes/textclassification.Rmd | 858 - vignettes/textsummarize.Rmd | 574 vignettes/time_series.Rmd | 578 1182 files changed, 80133 insertions(+), 80120 deletions(-)
Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's
Biostatistics: A Foundation for Analysis in the
Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DanielBiostatistics10th versions 0.1.11 dated 2024-04-03 and 0.2.0 dated 2024-04-11
DanielBiostatistics10th-0.1.11/DanielBiostatistics10th/data/data.rda |only DanielBiostatistics10th-0.1.11/DanielBiostatistics10th/inst |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/DESCRIPTION | 28 +- DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/MD5 | 91 ++++----- DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/NEWS.md | 3 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/0PACKAGE.R | 2 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/BooleanTable.R | 14 + DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/Gosset_Welch.R | 1 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/addProbs.R | 2 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp1.R | 2 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp10.R |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp11.R | 7 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp12.R | 4 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp13.R |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp14.R |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp2.R | 10 - DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp3.R | 6 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp4.R | 14 - DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp7.power.R | 2 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp8.R |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp9.R | 7 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/data/EXA.rda |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/data/EXR.rda |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/data/LDS.rda |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/data/REV.rda |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/BooleanTable.Rd | 1 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter01.Rd | 8 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter02.Rd | 29 +-- DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter03.Rd |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter04.Rd | 66 ++++--- DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter05to07.Rd | 94 +++++----- DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter07_power.Rd | 15 - DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter08.Rd |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter09.Rd | 33 +-- DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter10.Rd |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter11.Rd | 50 ++--- DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter12.Rd | 67 +++---- DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter13.Rd |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Chapter14.Rd |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/DanielBiostatistics10th-package.Rd | 3 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/Gosset_Welch.Rd | 1 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/addProbs.Rd | 2 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/autoplot.BooleanTable.Rd | 2 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/binom2pois.Rd | 5 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/freqs-class.Rd | 1 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/show-BooleanTable-method.Rd | 1 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/show-freqs-method.Rd | 1 DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/summary.BooleanTable.Rd | 3 48 files changed, 311 insertions(+), 264 deletions(-)
More information about DanielBiostatistics10th at CRAN
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Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks
(walk, bike, public transport and car) using 'R5', the Rapid Realistic
Routing on Real-world and Reimagined networks engine
<https://github.com/conveyal/r5>. The package allows users to generate
detailed routing analysis or calculate travel time matrices using
seamless parallel computing on top of the R5 Java machine. While R5
is developed by Conveyal, the package r5r is independently developed
by a team at the Institute for Applied Economic Research (Ipea) with
contributions from collaborators. Apart from the documentation in this
package, users will find additional information on R5 documentation at
<https://docs.conveyal.com/>. Although we try to keep new releases of
r5r in synchrony with R5, the development of R5 follows Conveyal's
independent update process. Hence, users should confirm the R5 version
implied by the Conveyal user manual (see
<https://docs.conveyal.com/changelog>) corresponds with the R5 ver [...truncated...]
Author: Marcus Saraiva [aut] ,
Rafael H. M. Pereira [aut, cre]
,
Daniel Herszenhut [aut] ,
Carlos Kaue Vieira Braga [aut]
,
Matthew Wigginton Bhagat-Conway [aut]
,
Luyu Liu [ctb] ,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between r5r versions 1.1.0 dated 2023-08-08 and 2.0 dated 2024-04-11
r5r-1.1.0/r5r/inst/jar/JRI.jar |only r5r-1.1.0/r5r/inst/jar/r5r_1_0_0.jar |only r5r-1.1.0/r5r/man/check_connection.Rd |only r5r-1.1.0/r5r/tests/tests_rafa/create_sample_points.R |only r5r-1.1.0/r5r/tests/tests_rafa/isochrone.R |only r5r-1.1.0/r5r/tests/tests_rafa/r5r_coverage.rds |only r5r-1.1.0/r5r/tests/tests_rafa/test_iso.R |only r5r-2.0/r5r/DESCRIPTION | 23 r5r-2.0/r5r/MD5 | 150 +- r5r-2.0/r5r/NAMESPACE | 1 r5r-2.0/r5r/NEWS.md | 29 r5r-2.0/r5r/R/accessibility.R | 560 ++++---- r5r-2.0/r5r/R/detailed_itineraries.R | 13 r5r-2.0/r5r/R/download_r5.R | 192 +- r5r-2.0/r5r/R/fare_structure.R | 221 +-- r5r-2.0/r5r/R/isochrone.R | 2 r5r-2.0/r5r/R/onLoad.R |only r5r-2.0/r5r/R/pareto_frontier.R | 411 ++--- r5r-2.0/r5r/R/r5r.R | 10 r5r-2.0/r5r/R/r5r_cache.R |only r5r-2.0/r5r/R/r5r_sitrep.R | 6 r5r-2.0/r5r/R/set.R | 1031 +++++++-------- r5r-2.0/r5r/R/setup_r5.R | 392 ++--- r5r-2.0/r5r/R/travel_time_matrix.R | 484 +++---- r5r-2.0/r5r/R/utils.R | 132 - r5r-2.0/r5r/build/partial.rdb |binary r5r-2.0/r5r/build/vignette.rds |binary r5r-2.0/r5r/inst/doc/accessibility.R | 274 +-- r5r-2.0/r5r/inst/doc/accessibility.html | 286 ++-- r5r-2.0/r5r/inst/doc/detailed_itineraries.R | 134 - r5r-2.0/r5r/inst/doc/detailed_itineraries.Rmd | 2 r5r-2.0/r5r/inst/doc/detailed_itineraries.html | 185 +- r5r-2.0/r5r/inst/doc/faq.R | 2 r5r-2.0/r5r/inst/doc/faq.html | 4 r5r-2.0/r5r/inst/doc/fare_structure.R | 407 +++-- r5r-2.0/r5r/inst/doc/fare_structure.Rmd | 983 +++++++------- r5r-2.0/r5r/inst/doc/fare_structure.html | 456 ++++-- r5r-2.0/r5r/inst/doc/isochrones.R | 240 +-- r5r-2.0/r5r/inst/doc/isochrones.html | 226 +-- r5r-2.0/r5r/inst/doc/pareto_frontier.R | 224 +-- r5r-2.0/r5r/inst/doc/pareto_frontier.html | 146 +- r5r-2.0/r5r/inst/doc/r5r.R | 221 +-- r5r-2.0/r5r/inst/doc/r5r.Rmd | 29 r5r-2.0/r5r/inst/doc/r5r.html | 308 ++-- r5r-2.0/r5r/inst/doc/time_window.R | 190 +- r5r-2.0/r5r/inst/doc/time_window.Rmd | 17 r5r-2.0/r5r/inst/doc/time_window.html | 269 ++- r5r-2.0/r5r/inst/doc/travel_time_matrix.R | 153 +- r5r-2.0/r5r/inst/doc/travel_time_matrix.Rmd | 6 r5r-2.0/r5r/inst/doc/travel_time_matrix.html | 198 +- r5r-2.0/r5r/inst/extdata/metadata_r5r.csv | 2 r5r-2.0/r5r/inst/extdata/poa/network_settings.json | 2 r5r-2.0/r5r/inst/extdata/spo/network_settings.json | 2 r5r-2.0/r5r/inst/jar/r5r.jar |only r5r-2.0/r5r/man/accessibility.Rd | 36 r5r-2.0/r5r/man/detailed_itineraries.Rd | 49 r5r-2.0/r5r/man/download_r5.Rd | 8 r5r-2.0/r5r/man/expanded_travel_time_matrix.Rd | 36 r5r-2.0/r5r/man/fileurl_from_metadata.Rd | 8 r5r-2.0/r5r/man/isochrone.Rd | 2 r5r-2.0/r5r/man/pareto_frontier.Rd | 36 r5r-2.0/r5r/man/r5r.Rd | 4 r5r-2.0/r5r/man/r5r_cache.Rd |only r5r-2.0/r5r/man/roxygen/templates/common_arguments.R | 130 - r5r-2.0/r5r/man/stop_r5.Rd | 1 r5r-2.0/r5r/man/travel_time_matrix.Rd | 36 r5r-2.0/r5r/tests/tests_marcus/debug_fare_calculator.R | 4 r5r-2.0/r5r/tests/tests_marcus/debug_fares_itineraries.R |only r5r-2.0/r5r/tests/tests_marcus/pareto_itineraries.R | 2 r5r-2.0/r5r/tests/tests_marcus/test_ttm2.R |only r5r-2.0/r5r/tests/tests_rafa/r5r_arrow.R |only r5r-2.0/r5r/tests/tests_rafa/test_rafa.R | 41 r5r-2.0/r5r/tests/tests_rafa/v7.0_vs_7.1.R |only r5r-2.0/r5r/tests/testthat/setup.R | 9 r5r-2.0/r5r/tests/testthat/test-accessibility.R | 444 +++--- r5r-2.0/r5r/tests/testthat/test-download_r5.R | 57 r5r-2.0/r5r/tests/testthat/test-setup_r5.R | 20 r5r-2.0/r5r/tests/testthat/test-write_fare_structure.R | 65 r5r-2.0/r5r/tests/testthat/test-z_r5r_cache.R |only r5r-2.0/r5r/vignettes/detailed_itineraries.Rmd | 2 r5r-2.0/r5r/vignettes/fare_structure.Rmd | 983 +++++++------- r5r-2.0/r5r/vignettes/r5r.Rmd | 29 r5r-2.0/r5r/vignettes/time_window.Rmd | 17 r5r-2.0/r5r/vignettes/travel_time_matrix.Rmd | 6 84 files changed, 5687 insertions(+), 4961 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [ctb] ,
Xintong Li [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 0.7.0 dated 2024-03-28 and 0.8.0 dated 2024-04-11
PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-plotCharacteristics.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-plotLargeScaleCharacteristics.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-plotSummarised.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseCharacteristics.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseCohortIntersect.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseCohortOverlap.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseCohortTiming.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseDemographics.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseLargeScaleCharacteristics.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-tableSummarised.R |only PatientProfiles-0.8.0/PatientProfiles/DESCRIPTION | 11 PatientProfiles-0.8.0/PatientProfiles/MD5 | 184 + PatientProfiles-0.8.0/PatientProfiles/NAMESPACE | 4 PatientProfiles-0.8.0/PatientProfiles/R/PatientProfiles-package.R | 2 PatientProfiles-0.8.0/PatientProfiles/R/addCategories.R | 2 PatientProfiles-0.8.0/PatientProfiles/R/addCohortIntersect.R | 2 PatientProfiles-0.8.0/PatientProfiles/R/addConceptIntersect.R | 2 PatientProfiles-0.8.0/PatientProfiles/R/addDateOfBirth.R | 2 PatientProfiles-0.8.0/PatientProfiles/R/addDeath.R |only PatientProfiles-0.8.0/PatientProfiles/R/addDemographics.R | 34 PatientProfiles-0.8.0/PatientProfiles/R/addIntersect.R | 9 PatientProfiles-0.8.0/PatientProfiles/R/addTableIntersect.R | 2 PatientProfiles-0.8.0/PatientProfiles/R/checks.R | 19 PatientProfiles-0.8.0/PatientProfiles/R/formats.R | 2 PatientProfiles-0.8.0/PatientProfiles/R/gtResult.R | 42 PatientProfiles-0.8.0/PatientProfiles/R/mockPatientProfiles.R | 14 PatientProfiles-0.8.0/PatientProfiles/R/plotCharacteristics.R | 30 PatientProfiles-0.8.0/PatientProfiles/R/plotLargeScaleCharacteristics.R | 933 +++++++--- PatientProfiles-0.8.0/PatientProfiles/R/plotSummarised.R | 531 ++--- PatientProfiles-0.8.0/PatientProfiles/R/reexports-omopgenerics.R | 2 PatientProfiles-0.8.0/PatientProfiles/R/summariseCharacteristics.R | 73 PatientProfiles-0.8.0/PatientProfiles/R/summariseCohortIntersect.R | 14 PatientProfiles-0.8.0/PatientProfiles/R/summariseCohortOverlap.R | 24 PatientProfiles-0.8.0/PatientProfiles/R/summariseCohortTiming.R | 40 PatientProfiles-0.8.0/PatientProfiles/R/summariseDemographics.R | 10 PatientProfiles-0.8.0/PatientProfiles/R/summariseLargeScaleCharacteristics.R | 16 PatientProfiles-0.8.0/PatientProfiles/R/summariseResult.R | 132 - PatientProfiles-0.8.0/PatientProfiles/R/summariseTableIntersect.R | 9 PatientProfiles-0.8.0/PatientProfiles/R/sysdata.rda |binary PatientProfiles-0.8.0/PatientProfiles/R/tableSummarised.R | 18 PatientProfiles-0.8.0/PatientProfiles/R/utilities.R | 15 PatientProfiles-0.8.0/PatientProfiles/R/utils-pipe.R | 2 PatientProfiles-0.8.0/PatientProfiles/README.md | 4 PatientProfiles-0.8.0/PatientProfiles/build |only PatientProfiles-0.8.0/PatientProfiles/inst/doc |only PatientProfiles-0.8.0/PatientProfiles/man/addDeathDate.Rd |only PatientProfiles-0.8.0/PatientProfiles/man/addDeathDays.Rd |only PatientProfiles-0.8.0/PatientProfiles/man/addDeathFlag.Rd |only PatientProfiles-0.8.0/PatientProfiles/man/addIntersect.Rd | 4 PatientProfiles-0.8.0/PatientProfiles/man/addLargeScaleCharacteristics.Rd | 3 PatientProfiles-0.8.0/PatientProfiles/man/formatCharacteristics.Rd | 4 PatientProfiles-0.8.0/PatientProfiles/man/gtCharacteristics.Rd | 23 PatientProfiles-0.8.0/PatientProfiles/man/mockPatientProfiles.Rd | 3 PatientProfiles-0.8.0/PatientProfiles/man/plotCharacteristics.Rd | 22 PatientProfiles-0.8.0/PatientProfiles/man/plotCohortIntersect.Rd | 26 PatientProfiles-0.8.0/PatientProfiles/man/plotCohortOverlap.Rd | 15 PatientProfiles-0.8.0/PatientProfiles/man/plotCohortTiming.Rd | 20 PatientProfiles-0.8.0/PatientProfiles/man/plotDemographics.Rd | 20 PatientProfiles-0.8.0/PatientProfiles/man/plotLargeScaleCharacteristics.Rd | 47 PatientProfiles-0.8.0/PatientProfiles/man/plotTableIntersect.Rd | 20 PatientProfiles-0.8.0/PatientProfiles/man/summariseCharacteristics.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/summariseCohortCounts.Rd |only PatientProfiles-0.8.0/PatientProfiles/man/summariseCohortIntersect.Rd | 4 PatientProfiles-0.8.0/PatientProfiles/man/summariseCohortOverlap.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/summariseCohortTiming.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/summariseConceptIntersect.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/summariseDemographics.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/summariseLargeScaleCharacteristics.Rd | 3 PatientProfiles-0.8.0/PatientProfiles/man/summariseResult.Rd | 5 PatientProfiles-0.8.0/PatientProfiles/man/summariseTableIntersect.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/tableCharacteristics.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/tableCohortIntersect.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/tableCohortOverlap.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/tableCohortTiming.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/tableDemographics.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/man/tableLargeScaleCharacteristics.Rd | 4 PatientProfiles-0.8.0/PatientProfiles/man/tableTableIntersect.Rd | 2 PatientProfiles-0.8.0/PatientProfiles/tests/spelling.R | 3 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addAttributes.R | 1 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addCategories.R | 2 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addCohortIntersect.R | 108 + PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addConceptIntersect.R | 11 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addDeath.R |only PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addDemographics.R | 44 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addFutureObservation.R | 7 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addInObservation.R | 6 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addIntersect.R | 41 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addPriorObservation.R | 6 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-addTableIntersect.R | 799 ++++++-- PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-checks.R | 4 PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-mockPatientProfiles.R | 104 + PatientProfiles-0.8.0/PatientProfiles/tests/testthat/test-summariseResult.R | 9 PatientProfiles-0.8.0/PatientProfiles/vignettes |only 93 files changed, 2377 insertions(+), 1199 deletions(-)
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Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <d [...truncated...]
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 6.5 dated 2024-02-29 and 6.6 dated 2024-04-11
DESCRIPTION | 8 ++--- MD5 | 22 +++++++-------- R/cipc.reg.R | 6 +--- R/circpurka.reg.R | 14 ++++++--- R/esag.reg.R | 2 - R/gcpc.mle.R | 22 +++++++-------- R/gcpc.reg.R | 64 +++++++++++++++++++++++---------------------- R/hcfboot.R | 8 ++--- R/hetboot.R | 2 - R/matrixfisher.mle.R | 8 +++-- man/Directional-package.Rd | 4 +- man/matrixfisher.mle.Rd | 2 - 12 files changed, 85 insertions(+), 77 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Procedures are available for choosing models that
conform to the hierarchy or marginality principle, for fitting and choosing between
two-dimensional spatial models using correlation, natural cubic smoothing spline and
P-spline models. A history of the fitting of a sequence of models is kept in a data frame.
Also used to compute functions and contrasts of, to investigate differences between and
to plot predictions obtained using any model fitting function. The content falls into
the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model
selection and description functions, (iv) Model diagnostics and simulation functions,
(v) Prediction production and presentation functions, (vi) Response transformation
functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions
(for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.4.27 dated 2024-02-05 and 4.4.32 dated 2024-04-11
asremlPlus-4.4.27/asremlPlus/R/reml4.v10.r |only asremlPlus-4.4.32/asremlPlus/DESCRIPTION | 10 asremlPlus-4.4.32/asremlPlus/MD5 | 58 +- asremlPlus-4.4.32/asremlPlus/NAMESPACE | 17 asremlPlus-4.4.32/asremlPlus/R/REMLRTIC.v4.r | 282 +++++----- asremlPlus-4.4.32/asremlPlus/R/asremlPlusUtilities.r | 139 +++- asremlPlus-4.4.32/asremlPlus/R/bootREMLRT.v3.r | 3 asremlPlus-4.4.32/asremlPlus/R/estimateV.v3.R | 51 + asremlPlus-4.4.32/asremlPlus/R/reml4.v11.r |only asremlPlus-4.4.32/asremlPlus/R/spatial.funcs.v8.r | 25 asremlPlus-4.4.32/asremlPlus/R/spatial.utilities.v1.r | 15 asremlPlus-4.4.32/asremlPlus/R/variogram.faces.v7.r | 3 asremlPlus-4.4.32/asremlPlus/build/partial.rdb |binary asremlPlus-4.4.32/asremlPlus/inst/NEWS.Rd | 26 asremlPlus-4.4.32/asremlPlus/inst/doc/Ladybird.asreml.pdf |binary asremlPlus-4.4.32/asremlPlus/inst/doc/Ladybird.lm.pdf |binary asremlPlus-4.4.32/asremlPlus/inst/doc/Wheat.analysis.pdf |binary asremlPlus-4.4.32/asremlPlus/inst/doc/Wheat.infoCriteria.pdf |binary asremlPlus-4.4.32/asremlPlus/inst/doc/WheatSpatialModels.pdf |binary asremlPlus-4.4.32/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-4.4.32/asremlPlus/man/R2adj.asreml.Rd | 79 +- asremlPlus-4.4.32/asremlPlus/man/addSpatialModel.asrtests.Rd | 10 asremlPlus-4.4.32/asremlPlus/man/addSpatialModelOnIC.asrtests.Rd | 2 asremlPlus-4.4.32/asremlPlus/man/chooseSpatialModelOnIC.asrtests.Rd | 54 + asremlPlus-4.4.32/asremlPlus/man/estimateV.asreml.Rd | 7 asremlPlus-4.4.32/asremlPlus/tests/testthat/test42MET.r | 117 +++- asremlPlus-4.4.32/asremlPlus/tests/testthat/test42Orange.r | 22 asremlPlus-4.4.32/asremlPlus/tests/testthat/test42REMLRTIC.r | 16 asremlPlus-4.4.32/asremlPlus/tests/testthat/test42Selection.r | 2 asremlPlus-4.4.32/asremlPlus/tests/testthat/test42SpatialModels.r | 116 ++-- asremlPlus-4.4.32/asremlPlus/tests/testthat/test42WheatSpatialVignette.r | 22 31 files changed, 723 insertions(+), 353 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results [...truncated...]
Author: Emmanuel Paradis [aut, cre, cph]
,
Simon Blomberg [aut, cph] ,
Ben Bolker [aut, cph] ,
Joseph Brown [aut, cph] ,
Santiago Claramunt [aut, cph] ,
Julien Claude [aut, cph] ,
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph] [...truncated...]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 5.7-1 dated 2023-03-13 and 5.8 dated 2024-04-11
DESCRIPTION | 10 MD5 | 156 +++++++------- NAMESPACE | 3 NEWS | 5 R/Cheverud.R | 21 - R/DNA.R | 411 +++++++++++++++++++++++---------------- R/ace.R | 10 R/as.bitsplits.R | 6 R/as.phylo.formula.R | 2 R/binaryPGLMM.R | 66 ++---- R/chronopl.R | 2 R/collapse.singles.R | 3 R/comparePhylo.R | 13 - R/cophenetic.phylo.R | 11 - R/corphylo.R | 58 ++--- R/dist.topo.R | 116 +++++++---- R/drop.tip.R | 18 - R/evonet.R | 19 - R/extract.popsize.R | 10 R/howmanytrees.R | 2 R/is.compatible.R | 2 R/makeNodeLabel.R | 22 +- R/mcmc.popsize.R | 2 R/me.R | 9 R/njs.R | 4 R/node.dating.R | 150 +++++++------- R/nodelabels.R | 26 +- R/parafit.R | 12 - R/plot.phylo.R | 3 R/read.GenBank.R | 15 - R/read.nexus.R | 126 +---------- R/read.tree.R | 8 R/reconstruct.R | 7 R/reorder.phylo.R | 7 R/root.R | 83 ++++++- R/rtt.R | 4 R/summary.phylo.R | 11 - R/varcomp.R | 6 R/write.tree.R | 26 -- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/DrawingPhylogenies.Rnw | 2 inst/doc/DrawingPhylogenies.pdf |binary inst/doc/MoranI.pdf |binary inst/doc/RandomTopologies.Rnw | 4 inst/doc/RandomTopologies.pdf |binary man/AAbin.Rd | 6 man/DNAbin.Rd | 2 man/ace.Rd | 4 man/ape-package.Rd | 3 man/as.bitsplits.Rd | 9 man/bd.time.Rd | 16 - man/chronos.Rd | 22 +- man/corBrownian.Rd | 7 man/corClasses.Rd | 12 - man/del.gaps.Rd | 17 - man/delta.plot.Rd | 8 man/dist.dna.Rd | 60 ++--- man/dist.topo.Rd | 4 man/drop.tip.Rd | 12 - man/image.DNAbin.Rd | 11 - man/is.binary.tree.Rd | 4 man/makeNodeLabel.Rd | 21 + man/phymltest.Rd | 2 man/rTraitCont.Rd | 12 - man/rTraitDisc.Rd | 12 - man/read.GenBank.Rd | 7 man/read.dna.Rd | 16 - man/read.nexus.data.Rd | 28 +- man/read.tree.Rd | 4 man/root.Rd | 14 + man/stree.Rd | 12 - src/ape.c | 8 src/bitsplits.c | 31 ++ src/dist_nodes.c | 80 +++++-- src/nj.c | 38 ++- vignettes/DrawingPhylogenies.Rnw | 2 vignettes/RandomTopologies.Rnw | 4 79 files changed, 1063 insertions(+), 898 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre] ,
Victor Morales-Onate [aut] ,
Christian Caamano-Carrillo [aut]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.0.0 dated 2024-04-09 and 2.0.1 dated 2024-04-11
DESCRIPTION | 8 - MD5 | 26 +++--- NAMESPACE | 2 R/GeoCovmatrix.r | 23 +++-- R/GeoKrig.r | 2 R/GeoLik.r | 10 +- data/anomalies.rda |binary data/austemp.rda |binary data/spanish_wind.rda |binary data/winds.coords.rda |binary data/winds.rda |binary man/GeoVarestbootstrap.Rd | 5 - man/Matrixfun.Rd | 7 - src/TB.c | 197 +--------------------------------------------- 14 files changed, 52 insertions(+), 228 deletions(-)
Title: Electric Vehicle Charging Sessions Simulation
Description: Simulation of Electric Vehicles charging sessions using
Gaussian models, together with time-series power demand calculations.
The simulation methodology is published in
Cañigueral et al. (2023, ISBN:0957-4174) <doi:10.1016/j.eswa.2023.120318>.
Author: Marc Canigueral [aut, cre]
Maintainer: Marc Canigueral <marc.canigueral@udg.edu>
Diff between evsim versions 1.4.0 dated 2024-03-14 and 1.5.0 dated 2024-04-11
evsim-1.4.0/evsim/man/get_ev_model.Rd |only evsim-1.5.0/evsim/DESCRIPTION | 6 evsim-1.5.0/evsim/MD5 | 24 +- evsim-1.5.0/evsim/NAMESPACE | 4 evsim-1.5.0/evsim/NEWS.md | 8 evsim-1.5.0/evsim/R/demand.R | 2 evsim-1.5.0/evsim/R/evmodel.R | 111 +--------- evsim-1.5.0/evsim/R/simulation.R | 19 + evsim-1.5.0/evsim/man/get_charging_rates_distribution.Rd | 6 evsim-1.5.0/evsim/man/get_connection_models_from_parameters.Rd | 33 -- evsim-1.5.0/evsim/man/get_custom_ev_model.Rd |only evsim-1.5.0/evsim/man/get_energy_models_from_parameters.Rd | 32 -- evsim-1.5.0/evsim/man/simulate_sessions.Rd | 1 evsim-1.5.0/evsim/tests/testthat/test-evmodel.R | 12 - 14 files changed, 67 insertions(+), 191 deletions(-)
Title: Model Butcher
Description: Provides a set of S3 generics to axe components of fitted
model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut] ,
Davis Vaughan [aut],
Max Kuhn [aut],
Alex Hayes [aut],
Julia Silge [cre, aut] ,
Posit, PBC [cph, fnd]
Maintainer: Julia Silge <julia.silge@posit.co>
Diff between butcher versions 0.3.3 dated 2023-08-22 and 0.3.4 dated 2024-04-11
DESCRIPTION | 12 - MD5 | 45 ++-- NAMESPACE | 1 NEWS.md | 4 R/docs.R | 2 README.md | 116 +++++------ build/butcher.pdf |binary build/stage23.rdb |only build/vignette.rds |binary inst/doc/adding-models-to-butcher.R | 10 - inst/doc/adding-models-to-butcher.Rmd | 28 +- inst/doc/adding-models-to-butcher.html | 75 +++---- inst/doc/available-axe-methods.R | 2 inst/doc/available-axe-methods.Rmd | 2 inst/doc/available-axe-methods.html | 3 inst/doc/butcher.R | 61 ++---- inst/doc/butcher.Rmd | 90 +++------ inst/doc/butcher.html | 321 +++++++++++++++------------------ man/butcher-package.Rd | 1 man/figures/logo.png |binary tests/testthat/test-mda.R | 26 +- vignettes/adding-models-to-butcher.Rmd | 28 +- vignettes/available-axe-methods.Rmd | 2 vignettes/butcher.Rmd | 90 +++------ 24 files changed, 433 insertions(+), 486 deletions(-)
Title: Tools for R Package Developers
Description: R-hub v2 uses GitHub Actions to run 'R CMD check' and
similar package checks. The 'rhub' package helps you set up
R-hub v2 for your R package, and start running checks.
Author: Gabor Csardi [aut, cre],
Maelle Salmon [aut] ,
R Consortium [fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rhub versions 1.1.2 dated 2022-08-31 and 2.0.0 dated 2024-04-11
rhub-1.1.2/rhub/R/build.R |only rhub-1.1.2/rhub/R/check-class.R |only rhub-1.1.2/rhub/R/check-cran.R |only rhub-1.1.2/rhub/R/check-shortcuts.R |only rhub-1.1.2/rhub/R/column-dt.R |only rhub-1.1.2/rhub/R/column-group-id.R |only rhub-1.1.2/rhub/R/column-id.R |only rhub-1.1.2/rhub/R/column-result.R |only rhub-1.1.2/rhub/R/column-status.R |only rhub-1.1.2/rhub/R/email.R |only rhub-1.1.2/rhub/R/env.R |only rhub-1.1.2/rhub/R/error.R |only rhub-1.1.2/rhub/R/handle.R |only rhub-1.1.2/rhub/R/last.R |only rhub-1.1.2/rhub/R/list.R |only rhub-1.1.2/rhub/R/livelog.R |only rhub-1.1.2/rhub/R/local.R |only rhub-1.1.2/rhub/R/platform.R |only rhub-1.1.2/rhub/R/print-status.R |only rhub-1.1.2/rhub/R/print.R |only rhub-1.1.2/rhub/R/rematch_all.R |only rhub-1.1.2/rhub/R/rhub-package.R |only rhub-1.1.2/rhub/R/submit.R |only rhub-1.1.2/rhub/build |only rhub-1.1.2/rhub/inst/bin |only rhub-1.1.2/rhub/inst/doc |only rhub-1.1.2/rhub/man/rhub-ids.Rd |only rhub-1.1.2/rhub/tests/testthat/test-build.R |only rhub-1.1.2/rhub/tests/testthat/test-email.R |only rhub-1.1.2/rhub/tests/testthat/test-error.R |only rhub-1.1.2/rhub/tests/testthat/test-print.R |only rhub-1.1.2/rhub/tests/testthat/test-submit.R |only rhub-1.1.2/rhub/vignettes |only rhub-2.0.0/rhub/DESCRIPTION | 31 +- rhub-2.0.0/rhub/LICENSE | 4 rhub-2.0.0/rhub/MD5 | 162 ++++++------ rhub-2.0.0/rhub/NAMESPACE | 75 +---- rhub-2.0.0/rhub/NEWS.md | 22 + rhub-2.0.0/rhub/R/a-rstudio-detect.R |only rhub-2.0.0/rhub/R/aa-assertthat.R |only rhub-2.0.0/rhub/R/aaa-async.R |only rhub-2.0.0/rhub/R/api.R | 159 ++++++------ rhub-2.0.0/rhub/R/assertions.R | 183 ++++++-------- rhub-2.0.0/rhub/R/check.R | 158 ++++-------- rhub-2.0.0/rhub/R/cli.R |only rhub-2.0.0/rhub/R/compat-vctrs.R |only rhub-2.0.0/rhub/R/doctor.R |only rhub-2.0.0/rhub/R/errors.R |only rhub-2.0.0/rhub/R/gh.R |only rhub-2.0.0/rhub/R/http-cache.R |only rhub-2.0.0/rhub/R/onload.R |only rhub-2.0.0/rhub/R/platforms.R |only rhub-2.0.0/rhub/R/rc.R |only rhub-2.0.0/rhub/R/rematch.R |only rhub-2.0.0/rhub/R/rhub-app.R |only rhub-2.0.0/rhub/R/rhubv1.R |only rhub-2.0.0/rhub/R/rhubv2.R |only rhub-2.0.0/rhub/R/setup.R |only rhub-2.0.0/rhub/R/utils.R | 221 +++++++++++------ rhub-2.0.0/rhub/inst/header.md |only rhub-2.0.0/rhub/man/check.Rd | 52 ---- rhub-2.0.0/rhub/man/check_for_cran.Rd | 65 ----- rhub-2.0.0/rhub/man/check_shortcuts.Rd | 51 +-- rhub-2.0.0/rhub/man/get_check.Rd | 35 -- rhub-2.0.0/rhub/man/last_check.Rd | 20 - rhub-2.0.0/rhub/man/list_my_checks.Rd | 59 ---- rhub-2.0.0/rhub/man/list_package_checks.Rd | 54 ---- rhub-2.0.0/rhub/man/list_validated_emails.Rd | 19 - rhub-2.0.0/rhub/man/local_check_linux.Rd | 51 --- rhub-2.0.0/rhub/man/local_check_linux_images.Rd | 12 rhub-2.0.0/rhub/man/platforms.Rd | 18 - rhub-2.0.0/rhub/man/rc_list_local_tokens.Rd |only rhub-2.0.0/rhub/man/rc_list_repos.Rd |only rhub-2.0.0/rhub/man/rc_new_token.Rd |only rhub-2.0.0/rhub/man/rc_submit.Rd |only rhub-2.0.0/rhub/man/rhub-package.Rd | 263 +++++++++++++++++++- rhub-2.0.0/rhub/man/rhub_check.Rd | 88 +----- rhub-2.0.0/rhub/man/rhub_doctor.Rd |only rhub-2.0.0/rhub/man/rhub_platforms.Rd |only rhub-2.0.0/rhub/man/rhub_setup.Rd |only rhub-2.0.0/rhub/man/rhubv2.Rd |only rhub-2.0.0/rhub/man/roxygen |only rhub-2.0.0/rhub/man/validate_email.Rd | 32 -- rhub-2.0.0/rhub/tests/testthat.R | 8 rhub-2.0.0/rhub/tests/testthat/_snaps |only rhub-2.0.0/rhub/tests/testthat/fixtures |only rhub-2.0.0/rhub/tests/testthat/helpers.R | 166 +++++++++++- rhub-2.0.0/rhub/tests/testthat/test-api.R | 107 ++++---- rhub-2.0.0/rhub/tests/testthat/test-assertions.R | 181 +++++++------- rhub-2.0.0/rhub/tests/testthat/test-check.R | 94 ++----- rhub-2.0.0/rhub/tests/testthat/test-cli.R |only rhub-2.0.0/rhub/tests/testthat/test-doctor.R |only rhub-2.0.0/rhub/tests/testthat/test-gh.R |only rhub-2.0.0/rhub/tests/testthat/test-http-cache.R |only rhub-2.0.0/rhub/tests/testthat/test-platforms.R | 296 ++++++++++------------- rhub-2.0.0/rhub/tests/testthat/test-rc.R |only rhub-2.0.0/rhub/tests/testthat/test-rematch.R |only rhub-2.0.0/rhub/tests/testthat/test-setup.R |only rhub-2.0.0/rhub/tests/testthat/test-utils.R | 264 ++++++++++++++++---- 99 files changed, 1529 insertions(+), 1421 deletions(-)
Title: R Tools for Text Matrices, Embeddings, and Networks
Description: This is a collection of functions optimized for working with
with various kinds of text matrices. Focusing on
the text matrix as the primary object - represented
either as a base R dense matrix or a 'Matrix' package sparse
matrix - allows for a consistent and intuitive interface
that stays close to the underlying mathematical foundation
of computational text analysis. In particular, the package
includes functions for working with word embeddings,
text networks, and document-term matrices. Methods developed in
Stoltz and Taylor (2019) <doi:10.1007/s42001-019-00048-6>,
Taylor and Stoltz (2020) <doi:10.1007/s42001-020-00075-8>,
Taylor and Stoltz (2020) <doi:10.15195/v7.a23>, and
Stoltz and Taylor (2021) <doi:10.1016/j.poetic.2021.101567>.
Author: Dustin Stoltz [aut, cre] ,
Marshall Taylor [aut]
Maintainer: Dustin Stoltz <dss219@lehigh.edu>
Diff between text2map versions 0.1.9 dated 2024-03-12 and 0.2.0 dated 2024-04-11
text2map-0.1.9/text2map/tests/testthat/test-CMDist-d-parallel.R |only text2map-0.1.9/text2map/tests/testthat/test-CoCA.R |only text2map-0.2.0/text2map/DESCRIPTION | 9 text2map-0.2.0/text2map/MD5 | 37 text2map-0.2.0/text2map/NEWS.md | 14 text2map-0.2.0/text2map/R/utils-embedding-vectors.R | 32 text2map-0.2.0/text2map/inst/REFERENCES.bib | 23 text2map-0.2.0/text2map/man/get_anchors.Rd | 11 text2map-0.2.0/text2map/man/test_anchors.Rd | 14 text2map-0.2.0/text2map/tests/testthat/helper-data.R | 165 +-- text2map-0.2.0/text2map/tests/testthat/test-CMDist-a-prep.R | 161 --- text2map-0.2.0/text2map/tests/testthat/test-CMDist-b-cmdist.R | 99 - text2map-0.2.0/text2map/tests/testthat/test-CMDist-e-sensitivity.R | 225 ++-- text2map-0.2.0/text2map/tests/testthat/test-utils-dtm.R | 123 -- text2map-0.2.0/text2map/tests/testthat/test-utils-embedding-vectors.R | 94 - text2map-0.2.0/text2map/tests/testthat/test-utils-embeddings.R | 534 ++++++---- text2map-0.2.0/text2map/tests/testthat/test-utils-stopper.R | 227 ++-- text2map-0.2.0/text2map/tests/testthat/test-utils-textnets.R | 45 text2map-0.2.0/text2map/tests/testthat/test-utils.R | 47 text2map-0.2.0/text2map/tests/testthat/test-x-nocran-dtm-pkgs.R |only text2map-0.2.0/text2map/tests/testthat/test-y-nocran-CoCA.R |only text2map-0.2.0/text2map/tests/testthat/test-z-nocran-CMDist-parallel.R |only 22 files changed, 949 insertions(+), 911 deletions(-)
Title: Read and Modify 'STICS' Input/Output Files
Description: Manipulating input and output files of the 'STICS' crop
model. Files are either 'JavaSTICS' XML files or text files used by
the model 'fortran' executable. Most basic functionalities are reading
or writing parameter names and values in both XML or text input files,
and getting data from output files. Advanced functionalities include
XML files generation from XML templates and/or spreadsheets, or text
files generation from XML files by using 'xslt' transformation.
Author: Patrice Lecharpentier [aut, cre]
,
Remi Vezy [aut] ,
Samuel Buis [aut] ,
Michel Giner [aut] ,
Timothee Flutre [ctb],
Thomas Robine [ctb],
Amine Barkaoui [ctb],
Patrick Chabrier [ctb],
Julie Constantin [rev],
Dominique Ripoche [rev],
Marie Launay [rev [...truncated...]
Maintainer: Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>
Diff between SticsRFiles versions 1.2.0 dated 2024-02-23 and 1.3.0 dated 2024-04-11
DESCRIPTION | 19 MD5 | 50 - NAMESPACE | 2 NEWS.md | 21 R/compute_day_number.R |only R/convert_xml2txt.R | 2 R/gen_tec_doc.R | 15 R/gen_usms_xml2txt.R | 19 R/get_file.R | 134 ++- R/manage_stics_versions.R | 22 R/read_params_table.R | 12 build/vignette.rds |binary inst/doc/Generating_Stics_XML_files.R | 1 inst/doc/Generating_Stics_XML_files.Rmd | 1 inst/doc/Generating_Stics_XML_files.html | 401 ++++----- inst/doc/Generating_Stics_text_files.html | 262 +++--- inst/doc/Manipulating_Stics_XML_files.html | 1186 ++++++++++++++-------------- inst/doc/Manipulating_Stics_text_files.html | 322 +++---- inst/doc/SticsRFiles.html | 930 ++++++++++----------- inst/doc/Upgrading_STICS_XML_files.html | 18 man/compute_day_from_date.Rd |only man/read_params_table.Rd | 2 tests/testthat/test-compute_day_number.R |only tests/testthat/test-gen_tec_xml.R | 38 tests/testthat/test-get_obs.R | 2 tests/testthat/test-get_sim.R | 2 tests/testthat/test-str2regex.R |only vignettes/Generating_Stics_XML_files.Rmd | 1 28 files changed, 1808 insertions(+), 1654 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Diff between stevedata versions 1.1.0 dated 2023-10-25 and 1.2.0 dated 2024-04-11
DESCRIPTION | 10 +- MD5 | 201 +++++++++++++++++++++++-------------------- NEWS.md | 15 +++ R/rd-DAPO.R |only R/rd-DCE12.R |only R/rd-DJIA.R | 8 - R/rd-EBJ.R |only R/rd-ESS10NO.R | 4 R/rd-ESS9GB.R | 2 R/rd-OODTPT.R | 4 R/rd-PPGE.R | 2 R/rd-african_coups.R |only R/rd-anes_prochoice.R | 28 +++-- R/rd-commodity_prices.R | 4 R/rd-ghp100k.R | 14 ++ R/rd-states_war.R |only R/rd-therms.R | 6 - R/rd-usa_chn_gdp_forecasts.R | 12 +- R/rd-wbd_example.R | 4 build/partial.rdb |binary data/DAPO.rda |only data/DCE12.rda |only data/DJIA.rda |binary data/EBJ.rda |only data/ESS10NO.rda |binary data/african_coups.rda |only data/states_war.rda |only man/Arca.Rd | 2 man/CFT15.Rd | 6 - man/CP77.Rd | 14 +- man/DAPO.Rd |only man/DCE12.Rd |only man/DJIA.Rd | 12 +- man/DST.Rd | 6 - man/Datasaurus.Rd | 2 man/Dee04.Rd | 4 man/EBJ.Rd |only man/ESS10NO.Rd | 2 man/ESS9GB.Rd | 6 - man/ESSBE5.Rd | 26 ++--- man/GHR04.Rd | 6 - man/Guber99.Rd | 2 man/LOTI.Rd | 8 - man/LTPT.Rd | 6 - man/LTWT.Rd | 16 +-- man/Lipset59.Rd | 11 +- man/Newhouse77.Rd | 6 - man/ODGI.Rd | 10 +- man/OODTPT.Rd | 6 - man/PPGE.Rd | 16 +-- man/Presidents.Rd | 2 man/SBCD.Rd | 2 man/SCP16.Rd | 2 man/TV16.Rd | 46 ++++----- man/af_crime93.Rd | 4 man/african_coups.Rd |only man/aluminum_premiums.Rd | 10 +- man/anes_partytherms.Rd | 6 - man/anes_prochoice.Rd | 28 +++-- man/anes_vote84.Rd | 2 man/arcticseaice.Rd | 6 - man/arg_tariff.Rd | 2 man/asn_stats.Rd | 4 man/clemson_temps.Rd | 6 - man/co2emissions.Rd | 8 - man/coffee_price.Rd | 4 man/commodity_prices.Rd | 10 +- man/eight_schools.Rd | 6 - man/election_turnout.Rd | 2 man/eq_passengercars.Rd | 14 +- man/fakeAPI.Rd | 2 man/fakeHappiness.Rd | 18 +-- man/fakeTSCS.Rd | 12 +- man/fakeTSD.Rd | 6 - man/ghp100k.Rd | 19 ++-- man/gss_abortion.Rd | 20 ++-- man/gss_spending.Rd | 70 +++++++------- man/gss_wages.Rd | 2 man/inglehart03.Rd | 8 - man/mm_mlda.Rd | 4 man/mm_nhis.Rd | 6 - man/mm_randhie.Rd | 4 man/mvprod.Rd | 6 - man/nesarc_drinkspd.Rd | 29 ++---- man/pwt_sample.Rd | 2 man/quartets.Rd | 4 man/recessions.Rd | 2 man/scb_regions.Rd | 4 man/sealevels.Rd | 6 - man/so2concentrations.Rd | 6 - man/states_war.Rd |only man/steves_clothes.Rd | 4 man/sugar_price.Rd | 6 - man/thatcher_approval.Rd | 10 +- man/therms.Rd | 14 +- man/ukg_eeri.Rd | 10 +- man/uniondensity.Rd | 10 +- man/usa_chn_gdp_forecasts.Rd | 6 - man/usa_computers.Rd | 6 - man/usa_migration.Rd | 4 man/usa_states.Rd | 4 man/usa_tradegdp.Rd | 4 man/voteincome.Rd | 2 man/wbd_example.Rd | 4 man/wvs_ccodes.Rd | 4 man/wvs_immig.Rd | 4 man/wvs_justifbribe.Rd | 6 - man/wvs_usa_abortion.Rd | 10 +- man/yugo_sales.Rd | 2 109 files changed, 520 insertions(+), 465 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Ronkko [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.14 dated 2024-01-09 and 2.15 dated 2024-04-11
SimDesign-2.14/SimDesign/tests/tests/test-SimDesign.R |only SimDesign-2.15/SimDesign/DESCRIPTION | 22 - SimDesign-2.15/SimDesign/MD5 | 94 ++--- SimDesign-2.15/SimDesign/NAMESPACE | 8 SimDesign-2.15/SimDesign/NEWS.md | 43 ++ SimDesign-2.15/SimDesign/R/Design.R | 81 ++++ SimDesign-2.15/SimDesign/R/PBA.R | 24 + SimDesign-2.15/SimDesign/R/SFA.R | 6 SimDesign-2.15/SimDesign/R/SimDesign.R | 11 SimDesign-2.15/SimDesign/R/SimExtract.R | 22 + SimDesign-2.15/SimDesign/R/SimResults.R | 26 - SimDesign-2.15/SimDesign/R/SimSolve.R | 60 +-- SimDesign-2.15/SimDesign/R/aggregate_simulations.R | 256 +++++++++++--- SimDesign-2.15/SimDesign/R/analysis.R | 61 ++- SimDesign-2.15/SimDesign/R/functions.R | 6 SimDesign-2.15/SimDesign/R/getArrayID.R |only SimDesign-2.15/SimDesign/R/runArraySimulation.R |only SimDesign-2.15/SimDesign/R/runSimulation.R | 204 +++++++---- SimDesign-2.15/SimDesign/R/util.R | 213 +++++++++++ SimDesign-2.15/SimDesign/build/partial.rdb |binary SimDesign-2.15/SimDesign/build/vignette.rds |binary SimDesign-2.15/SimDesign/inst/doc/Catch_errors.html | 70 +-- SimDesign-2.15/SimDesign/inst/doc/Fixed_obj_fun.html | 39 -- SimDesign-2.15/SimDesign/inst/doc/HPC-computing.R |only SimDesign-2.15/SimDesign/inst/doc/HPC-computing.Rmd |only SimDesign-2.15/SimDesign/inst/doc/HPC-computing.html |only SimDesign-2.15/SimDesign/inst/doc/MultipleAnalyses.html | 62 +-- SimDesign-2.15/SimDesign/inst/doc/Parallel-computing.R | 18 SimDesign-2.15/SimDesign/inst/doc/Parallel-computing.Rmd | 131 +++---- SimDesign-2.15/SimDesign/inst/doc/Parallel-computing.html | 94 ++--- SimDesign-2.15/SimDesign/inst/doc/Saving-results.R | 8 SimDesign-2.15/SimDesign/inst/doc/Saving-results.Rmd | 20 - SimDesign-2.15/SimDesign/inst/doc/Saving-results.html | 86 +--- SimDesign-2.15/SimDesign/inst/doc/SimDesign-intro.R | 9 SimDesign-2.15/SimDesign/inst/doc/SimDesign-intro.Rmd | 12 SimDesign-2.15/SimDesign/inst/doc/SimDesign-intro.html | 108 ++--- SimDesign-2.15/SimDesign/man/SFA.Rd | 6 SimDesign-2.15/SimDesign/man/SimDesign.Rd | 6 SimDesign-2.15/SimDesign/man/SimExtract.Rd | 6 SimDesign-2.15/SimDesign/man/SimResults.Rd | 20 - SimDesign-2.15/SimDesign/man/SimSolve.Rd | 54 +- SimDesign-2.15/SimDesign/man/aggregate_simulations.Rd | 92 ++++- SimDesign-2.15/SimDesign/man/createDesign.Rd | 7 SimDesign-2.15/SimDesign/man/expandDesign.Rd |only SimDesign-2.15/SimDesign/man/gen_seeds.Rd |only SimDesign-2.15/SimDesign/man/getArrayID.Rd |only SimDesign-2.15/SimDesign/man/runArraySimulation.Rd |only SimDesign-2.15/SimDesign/man/runSimulation.Rd | 113 +++--- SimDesign-2.15/SimDesign/tests/tests/test-01-core.R |only SimDesign-2.15/SimDesign/tests/tests/test-02-aggregate.R |only SimDesign-2.15/SimDesign/tests/tests/test-03-array.R |only SimDesign-2.15/SimDesign/vignettes/HPC-computing.Rmd |only SimDesign-2.15/SimDesign/vignettes/Parallel-computing.Rmd | 131 +++---- SimDesign-2.15/SimDesign/vignettes/Saving-results.Rmd | 20 - SimDesign-2.15/SimDesign/vignettes/SimDesign-intro.Rmd | 12 55 files changed, 1487 insertions(+), 774 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 1.2.0 dated 2024-04-10 and 1.2.1 dated 2024-04-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ tests/testthat/test-textmodel_lda.R | 10 +++++----- tests/testthat/test-utils.R | 10 ++++++++-- 5 files changed, 24 insertions(+), 14 deletions(-)
Title: Scaling Models and Classifiers for Textual Data
Description: Scaling models and classifiers for sparse matrix objects representing
textual data in the form of a document-feature matrix. Includes original
implementations of 'Laver', 'Benoit', and Garry's (2003) <doi:10.1017/S0003055403000698>,
'Wordscores' model, the Perry and 'Benoit' (2017) <doi:10.48550/arXiv.1710.08963> class affinity scaling model,
and the 'Slapin' and 'Proksch' (2008) <doi:10.1111/j.1540-5907.2008.00338.x> 'wordfish'
model, as well as methods for correspondence analysis, latent semantic analysis,
and fast Naive Bayes and linear 'SVMs' specially designed for sparse textual data.
Author: Kenneth Benoit [cre, aut, cph]
,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Patrick O. Perry [aut] ,
Benjamin Lauderdale [aut] ,
Johannes Gruber [aut] ,
William Lowe [aut] ,
Vikas Sindhwani [cph] ,
European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda.textmodels versions 0.9.6 dated 2023-03-22 and 0.9.7 dated 2024-04-11
quanteda.textmodels-0.9.6/quanteda.textmodels/src/ca_mt.cpp |only quanteda.textmodels-0.9.6/quanteda.textmodels/src/utility.cpp |only quanteda.textmodels-0.9.6/quanteda.textmodels/src/wordfish_dense.cpp |only quanteda.textmodels-0.9.6/quanteda.textmodels/src/wordfish_mt.cpp |only quanteda.textmodels-0.9.7/quanteda.textmodels/DESCRIPTION | 16 quanteda.textmodels-0.9.7/quanteda.textmodels/MD5 | 66 +-- quanteda.textmodels-0.9.7/quanteda.textmodels/NAMESPACE | 2 quanteda.textmodels-0.9.7/quanteda.textmodels/NEWS.md | 16 quanteda.textmodels-0.9.7/quanteda.textmodels/R/RcppExports.R | 20 - quanteda.textmodels-0.9.7/quanteda.textmodels/R/quanteda.textmodels-package.R | 1 quanteda.textmodels-0.9.7/quanteda.textmodels/R/textmodel-methods.R | 2 quanteda.textmodels-0.9.7/quanteda.textmodels/R/textmodel_affinity.R | 19 - quanteda.textmodels-0.9.7/quanteda.textmodels/R/textmodel_ca.R | 2 quanteda.textmodels-0.9.7/quanteda.textmodels/R/textmodel_svm.R | 3 quanteda.textmodels-0.9.7/quanteda.textmodels/R/textmodel_svmlin.R | 2 quanteda.textmodels-0.9.7/quanteda.textmodels/R/textmodel_wordfish.R | 28 - quanteda.textmodels-0.9.7/quanteda.textmodels/R/textmodel_wordscores.R | 2 quanteda.textmodels-0.9.7/quanteda.textmodels/README.md | 2 quanteda.textmodels-0.9.7/quanteda.textmodels/build/partial.rdb |binary quanteda.textmodels-0.9.7/quanteda.textmodels/build/vignette.rds |binary quanteda.textmodels-0.9.7/quanteda.textmodels/inst/WORDLIST | 7 quanteda.textmodels-0.9.7/quanteda.textmodels/inst/doc/textmodel_performance.R | 28 + quanteda.textmodels-0.9.7/quanteda.textmodels/inst/doc/textmodel_performance.Rmd | 26 + quanteda.textmodels-0.9.7/quanteda.textmodels/inst/doc/textmodel_performance.html | 180 +++++----- quanteda.textmodels-0.9.7/quanteda.textmodels/man/as.matrix.csr.dfm.Rd | 4 quanteda.textmodels-0.9.7/quanteda.textmodels/man/textmodel_affinity.Rd | 5 quanteda.textmodels-0.9.7/quanteda.textmodels/man/textmodel_wordfish.Rd | 10 quanteda.textmodels-0.9.7/quanteda.textmodels/man/textmodel_wordscores.Rd | 2 quanteda.textmodels-0.9.7/quanteda.textmodels/man/textmodels.Rd | 3 quanteda.textmodels-0.9.7/quanteda.textmodels/src/Makevars | 3 quanteda.textmodels-0.9.7/quanteda.textmodels/src/Makevars.win | 4 quanteda.textmodels-0.9.7/quanteda.textmodels/src/RcppExports.cpp | 61 --- quanteda.textmodels-0.9.7/quanteda.textmodels/src/ca.cpp |only quanteda.textmodels-0.9.7/quanteda.textmodels/src/svmlin.cpp | 2 quanteda.textmodels-0.9.7/quanteda.textmodels/src/wordfish.cpp |only quanteda.textmodels-0.9.7/quanteda.textmodels/tests/testthat/test-textmodel_wordfish.R | 66 --- quanteda.textmodels-0.9.7/quanteda.textmodels/vignettes/textmodel_performance.Rmd | 26 + 37 files changed, 287 insertions(+), 321 deletions(-)
More information about quanteda.textmodels at CRAN
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Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph],
Constantin Ahlmann-Eltze [ctb],
Hector Corrada Bravo [ctb],
Robert Gentleman [ctb],
Jan Gleixner [ctb],
Peter Hickey [ctb],
Ola Hossjer [ctb],
Harris Jaffee [ctb],
Dongcan Jiang [ctb],
Peter Langfelder [ctb],
Brian M [...truncated...]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 1.2.0 dated 2023-12-11 and 1.3.0 dated 2024-04-11
matrixStats-1.2.0/matrixStats/R/validateIndices.R |only matrixStats-1.2.0/matrixStats/man/validateIndices.Rd |only matrixStats-1.2.0/matrixStats/tests/validateIndices.R |only matrixStats-1.3.0/matrixStats/DESCRIPTION | 10 matrixStats-1.3.0/matrixStats/MD5 | 29 - matrixStats-1.3.0/matrixStats/NAMESPACE | 1 matrixStats-1.3.0/matrixStats/NEWS.md | 29 + matrixStats-1.3.0/matrixStats/R/000.DEPRECATION.R | 150 ++++------ matrixStats-1.3.0/matrixStats/R/999.package.R | 3 matrixStats-1.3.0/matrixStats/R/options.R |only matrixStats-1.3.0/matrixStats/R/rowRanks.R | 10 matrixStats-1.3.0/matrixStats/R/rowVars.R | 4 matrixStats-1.3.0/matrixStats/R/zzz.R | 23 - matrixStats-1.3.0/matrixStats/build/vignette.rds |binary matrixStats-1.3.0/matrixStats/inst/doc/matrixStats-methods.html | 2 matrixStats-1.3.0/matrixStats/man/matrixStats-package.Rd | 8 matrixStats-1.3.0/matrixStats/man/matrixStats.options.Rd |only matrixStats-1.3.0/matrixStats/src/diff2.c | 8 18 files changed, 150 insertions(+), 127 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Lightweight parallel code execution and distributed computing.
Designed for simplicity, a 'mirai' evaluates an R expression asynchronously,
on local or network resources, resolving automatically upon completion.
State of the art networking and concurrency via 'nanonext' and 'NNG'
(Nanomsg Next Gen) offers reliable and efficient scheduling over fast
inter-process communications or TCP/IP secured by TLS.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 0.12.1 dated 2024-02-02 and 0.13.2 dated 2024-04-11
DESCRIPTION | 17 ++-- MD5 | 96 ++++++++++++----------- NAMESPACE | 18 ++-- NEWS.md | 21 +++++ R/daemon.R | 30 +++++-- R/daemons.R | 101 ++++++++++++++++++++---- R/dispatcher.R | 10 +- R/mirai-package.R | 56 +------------ R/mirai.R | 114 +++++++++++++++++----------- R/next.R | 3 R/parallel.R | 50 +++++++++--- R/promises.R | 48 +++++++++-- README.md | 107 +++++++++++++------------- build/vignette.rds |binary inst/doc/mirai.Rmd | 179 ++++++++++++++++++++++++++++++++------------ inst/doc/mirai.html | 159 +++++++++++++++++++++++++++------------ inst/doc/parallel.Rmd | 58 +++++++++++++- inst/doc/parallel.html | 47 ++++++++++- inst/doc/plumber.Rmd | 34 ++++---- inst/doc/plumber.html | 34 ++++---- inst/doc/promises.Rmd | 8 + inst/doc/promises.html | 6 + inst/doc/shiny.R | 85 +++++++++----------- inst/doc/shiny.Rmd | 117 ++++++++++++++-------------- inst/doc/shiny.html | 102 ++++++++++++------------- inst/doc/torch.Rmd | 59 +++++++------- inst/doc/torch.html | 57 +++++++------- man/call_mirai.Rd | 19 ++-- man/daemon.Rd | 2 man/daemons.Rd | 10 ++ man/everywhere.Rd | 13 +-- man/is_mirai_error.Rd | 4 man/mirai-package.Rd | 8 - man/mirai.Rd | 42 +++++----- man/nextstream.Rd | 3 man/register_cluster.Rd |only man/serialization.Rd | 21 +++-- man/with.miraiDaemons.Rd |only tests/tests.R | 12 ++ vignettes/mirai.Rmd | 179 ++++++++++++++++++++++++++++++++------------ vignettes/mirai.Rmd.orig | 70 +++++++++++++++-- vignettes/parallel.Rmd | 58 +++++++++++++- vignettes/parallel.Rmd.orig | 41 ++++++++++ vignettes/plumber.Rmd | 34 ++++---- vignettes/plumber.Rmd.orig | 2 vignettes/promises.Rmd | 8 + vignettes/promises.Rmd.orig | 6 + vignettes/shiny.Rmd | 117 ++++++++++++++-------------- vignettes/torch.Rmd | 59 +++++++------- vignettes/torch.Rmd.orig | 15 +-- 50 files changed, 1504 insertions(+), 835 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.0.5 dated 2024-02-28 and 1.0.6 dated 2024-04-11
renv-1.0.5/renv/inst/repos/src/contrib/renv_1.0.5.tar.gz |only renv-1.0.6/renv/DESCRIPTION | 6 renv-1.0.6/renv/MD5 | 122 +++++++-------- renv-1.0.6/renv/NEWS.md | 32 +++ renv-1.0.6/renv/R/available-packages.R | 2 renv-1.0.6/renv/R/bootstrap.R | 22 +- renv-1.0.6/renv/R/cache.R | 18 +- renv-1.0.6/renv/R/call.R | 1 renv-1.0.6/renv/R/description.R | 13 + renv-1.0.6/renv/R/diagnostics.R | 1 renv-1.0.6/renv/R/download.R | 8 renv-1.0.6/renv/R/expr.R |only renv-1.0.6/renv/R/hash.R | 8 renv-1.0.6/renv/R/init.R | 25 +-- renv-1.0.6/renv/R/install.R | 4 renv-1.0.6/renv/R/load.R | 39 ++++ renv-1.0.6/renv/R/lockfile.R | 21 ++ renv-1.0.6/renv/R/path.R | 3 renv-1.0.6/renv/R/paths.R | 3 renv-1.0.6/renv/R/record.R | 8 renv-1.0.6/renv/R/retrieve.R | 32 +-- renv-1.0.6/renv/R/run.R | 7 renv-1.0.6/renv/R/settings.R | 2 renv-1.0.6/renv/R/snapshot.R | 35 +--- renv-1.0.6/renv/R/update.R | 5 renv-1.0.6/renv/R/upgrade.R | 9 - renv-1.0.6/renv/R/use-python.R | 23 +- renv-1.0.6/renv/R/utils.R | 16 - renv-1.0.6/renv/R/watchdog.R | 12 - renv-1.0.6/renv/README.md | 2 renv-1.0.6/renv/build/vignette.rds |binary renv-1.0.6/renv/inst/doc/ci.html | 2 renv-1.0.6/renv/inst/doc/faq.html | 2 renv-1.0.6/renv/inst/doc/package-install.Rmd | 2 renv-1.0.6/renv/inst/doc/package-install.html | 7 renv-1.0.6/renv/inst/doc/package-sources.html | 2 renv-1.0.6/renv/inst/doc/packages.Rmd | 10 - renv-1.0.6/renv/inst/doc/packages.html | 12 - renv-1.0.6/renv/inst/doc/packrat.html | 2 renv-1.0.6/renv/inst/doc/profiles.html | 2 renv-1.0.6/renv/inst/doc/renv.html | 7 renv-1.0.6/renv/inst/doc/rsconnect.html | 2 renv-1.0.6/renv/inst/repos/src/contrib/PACKAGES | 4 renv-1.0.6/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.0.6/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.0.6/renv/inst/repos/src/contrib/renv_1.0.6.tar.gz |only renv-1.0.6/renv/inst/resources/activate.R | 26 +-- renv-1.0.6/renv/man/init.Rd | 25 +-- renv-1.0.6/renv/man/load.Rd | 5 renv-1.0.6/renv/man/paths.Rd | 3 renv-1.0.6/renv/man/update.Rd | 4 renv-1.0.6/renv/tests/testthat.R | 8 renv-1.0.6/renv/tests/testthat/_snaps/bootstrap.md | 12 + renv-1.0.6/renv/tests/testthat/helper-testthat.R | 44 +---- renv-1.0.6/renv/tests/testthat/test-bootstrap.R | 21 ++ renv-1.0.6/renv/tests/testthat/test-expr.R |only renv-1.0.6/renv/tests/testthat/test-init.R | 2 renv-1.0.6/renv/tests/testthat/test-load.R | 22 ++ renv-1.0.6/renv/tests/testthat/test-lock.R | 6 renv-1.0.6/renv/tests/testthat/test-records.R | 19 ++ renv-1.0.6/renv/tests/testthat/test-remotes.R | 1 renv-1.0.6/renv/tests/testthat/test-watchdog.R | 4 renv-1.0.6/renv/vignettes/package-install.Rmd | 2 renv-1.0.6/renv/vignettes/packages.Rmd | 10 - 64 files changed, 450 insertions(+), 297 deletions(-)