Title: R Interface to 'Redatam' Library
Description: Provides an API to work with 'Redatam' (see <https://redatam.org>)
databases in both formats: 'RXDB' (new format) and 'DICX' (old format) and running
'Redatam' programs written in 'SPC' language. It's a wrapper around 'Redatam'
core and provides functions to open/close a database (redatam_open()/redatam_close()),
list entities and variables from the database (redatam_entities(), redatam_variables())
and execute a 'SPC' program and gets the results as data frames
(redatam_query(), redatam_run()).
Author: Jaime Salvador [aut, cre] ,
CELADE [cph]
Maintainer: Jaime Salvador <jaime.salvador@ideasybits.com>
Diff between redatamx versions 1.2.0 dated 2025-11-02 and 1.2.1 dated 2025-11-22
DESCRIPTION | 6 MD5 | 68 +++--- NAMESPACE | 30 +-- NEWS.md | 115 ++++++----- R/cpp11.R | 106 +++++----- R/output-env.R | 82 ++++---- R/redatam-api.R | 414 +++++++++++++++++++++--------------------- R/redatam-package.R | 16 - R/redatam-plugins.R | 76 +++---- R/redatam-query.R | 206 ++++++++++---------- R/redatam-run.R | 200 ++++++++++---------- R/zzz.R | 34 +-- README.md | 238 ++++++++++++------------ configure | 2 configure.win | 84 ++++---- inst/COPYRIGHTS | 16 - inst/License.txt | 40 ++-- man/outputs.Rd | 62 +++--- man/redatam_close.Rd | 56 ++--- man/redatam_create.Rd | 54 ++--- man/redatam_destroy_.Rd | 48 ++-- man/redatam_entities.Rd | 52 ++--- man/redatam_info.Rd | 40 ++-- man/redatam_init_.Rd | 54 ++--- man/redatam_internal_query.Rd | 58 ++--- man/redatam_internal_run.Rd | 58 ++--- man/redatam_load_plugin.Rd | 58 ++--- man/redatam_open.Rd | 52 ++--- man/redatam_query.Rd | 70 +++---- man/redatam_run.Rd | 70 +++---- man/redatam_save.Rd | 60 +++--- man/redatam_variables.Rd | 56 ++--- man/redatam_version.Rd | 40 ++-- man/redatamx-package.Rd | 58 ++--- src/red_initialize.cpp | 2 35 files changed, 1343 insertions(+), 1338 deletions(-)
Title: Mass-Preserving Spline Functions for Soil Data
Description: A low-dependency implementation of GSIF::mpspline() <https://r-forge.r-project.org/scm/viewvc.php/pkg/R/mpspline.R?view=markup&revision=240&root=gsif>,
which applies a mass-preserving spline to soil attributes. Splining soil data
is a safe way to make continuous down-profile estimates of attributes measured
over discrete, often discontinuous depth intervals.
Author: Lauren O'Brien [aut, cre] ,
Brendan Malone [ctb] ,
Tomislav Hengl [ctb] ,
Tom Bishop [ctb],
David Rossiter [ctb],
Dylan Beaudette [ctb],
Andrew Brown [ctb]
Maintainer: Lauren O'Brien <obrlsoilau@gmail.com>
Diff between mpspline2 versions 0.1.6 dated 2022-04-03 and 0.1.9 dated 2025-11-22
mpspline2-0.1.6/mpspline2/man/mpspline_compact.Rd |only mpspline2-0.1.6/mpspline2/man/mpspline_tidy.Rd |only mpspline2-0.1.9/mpspline2/DESCRIPTION | 22 mpspline2-0.1.9/mpspline2/MD5 | 32 - mpspline2-0.1.9/mpspline2/NEWS.md | 14 mpspline2-0.1.9/mpspline2/R/mpspline.R | 61 +- mpspline2-0.1.9/mpspline2/R/wrappers.R | 355 ++++++++------- mpspline2-0.1.9/mpspline2/README.md | 10 mpspline2-0.1.9/mpspline2/build/partial.rdb |binary mpspline2-0.1.9/mpspline2/man/mpspline-wrappers.Rd |only mpspline2-0.1.9/mpspline2/man/mpspline.Rd | 13 mpspline2-0.1.9/mpspline2/man/mpspline_datchk.Rd | 2 mpspline2-0.1.9/mpspline2/man/mpspline_est1.Rd | 2 mpspline2-0.1.9/mpspline2/man/mpspline_fit1.Rd | 2 mpspline2-0.1.9/mpspline2/man/mpspline_one.Rd | 2 mpspline2-0.1.9/mpspline2/man/mpspline_rmse1.Rd | 2 mpspline2-0.1.9/mpspline2/tests/testthat/test_mpspline.R | 11 mpspline2-0.1.9/mpspline2/tests/testthat/test_multivar.R |only mpspline2-0.1.9/mpspline2/tests/testthat/test_wrappers.R | 6 19 files changed, 333 insertions(+), 201 deletions(-)
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Description: The following several classes of frailty models using a
penalized likelihood estimation on the hazard function but also a
parametric estimation can be fit using this R package: 1) A shared
frailty model (with gamma or log-normal frailty distribution) and Cox
proportional hazard model. Clustered and recurrent survival times can
be studied. 2) Additive frailty models for proportional hazard models
with two correlated random effects (intercept random effect with
random slope). 3) Nested frailty models for hierarchically clustered
data (with 2 levels of clustering) by including two iid gamma random
effects. 4) Joint frailty models in the context of the joint
modelling for recurrent events with terminal event for clustered data
or not. A joint frailty model for two semi-competing risks and
clustered data is also proposed. 5) Joint general frailty models in
the context of the joint modelling for recurrent events with terminal
event data with two independent frailty terms. 6) Joint Neste [...truncated...]
Author: Virginie Rondeau [aut, cre] ,
Juan R. Gonzalez [aut],
Yassin Mazroui [aut],
Audrey Mauguen [aut],
Amadou Diakite [aut],
Alexandre Laurent [aut],
Myriam Lopez [aut],
Agnieszka Krol [aut],
Casimir L. Sofeu [aut],
Julien Dumerc [aut],
Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>
Diff between frailtypack versions 3.7.1 dated 2025-10-15 and 3.8.0 dated 2025-11-22
DESCRIPTION | 19 MD5 | 240 - NAMESPACE | 16 NEWS | 17 R/GenfrailtyPenal.R | 24 R/additivePenal.R | 36 R/dataHelp.R | 152 + R/frailtyCmprsk.R |only R/frailtyIllnessDeath.R |only R/frailtyPenal.R | 4920 +++++++++++++++++++----------------- R/jointSurroCopPenal.R | 18 R/jointSurroPenal.R | 14 R/longiPenal.R | 2 R/multivPenal.R | 3628 +++++++++++++------------- R/plot.frailtyCmprsk.R |only R/plot.frailtyIllnessDeath.R |only R/prediction.R | 34 R/print.frailtyCmprsk.R |only R/print.frailtyIllnessDeath.R |only R/print.jointPenal.R | 1839 ++++++------- R/ste.R | 4 R/summary.frailtyCmprsk.R |only R/summary.frailtyIllnessDeath.R |only R/summary.jointPenal.R | 413 +-- R/trivPenal.R | 4 R/trivPenalNL.R | 6 build/vignette.rds |binary data/CPRSKbmtcrr.rda |only data/Paq810.rda |only data/readmission.rda |binary data/readmission2.rda |only inst/doc/Package_summary.Rmd | 64 inst/doc/Package_summary.html | 2300 ++++++++-------- man/CPRSKbmtcrr.Rd |only man/Cmeasures.Rd | 304 +- man/Diffepoce.Rd | 262 - man/GenfrailtyPenal.Rd | 1926 +++++++------- man/Paq810.Rd |only man/SurvIC.Rd | 124 man/additivePenal.Rd | 519 +-- man/bcos.Rd | 60 man/cluster.Rd | 80 man/colorectal.Rd | 96 man/colorectalLongi.Rd | 94 man/dataAdditive.Rd | 68 man/dataMultiv.Rd | 58 man/dataNCC.Rd | 52 man/dataNested.Rd | 72 man/dataOvarian.Rd | 76 man/epoce.Rd | 382 +- man/event2.Rd | 56 man/figures/CMPRSKSCHEME.png |only man/figures/IDSCHEME.png |only man/frailtyCmprsk.Rd |only man/frailtyIllnessDeath.Rd |only man/frailtyPenal.Rd | 2103 ++++++++------- man/frailtypack-package.Rd | 472 +-- man/gastadj.Rd | 84 man/hazard.Rd | 74 man/jointSurrCopSimul.Rd | 430 +-- man/jointSurrSimul.Rd | 374 +- man/jointSurroCopPenal.Rd | 1094 ++++---- man/jointSurroPenal.Rd | 14 man/jointSurroPenalSimul.Rd | 880 +++--- man/jointSurroTKendall.Rd | 220 - man/longDat.Rd | 44 man/longiPenal.Rd | 1198 ++++---- man/loocv.Rd | 190 - man/multivPenal.Rd | 4 man/num.id.Rd | 110 man/plot.Diffepoce.Rd | 66 man/plot.additivePenal.Rd | 146 - man/plot.epoce.Rd | 84 man/plot.frailtyCmprsk.Rd |only man/plot.frailtyIllnessDeath.Rd |only man/plot.frailtyPenal.Rd | 164 - man/plot.jointNestedPenal.Rd | 172 - man/plot.jointPenal.Rd | 176 - man/plot.jointSurroPenal.Rd | 194 - man/plot.jointSurroPenalloocv.Rd | 172 - man/plot.longiPenal.Rd | 182 - man/plot.multivPenal.Rd | 140 - man/plot.nestedPenal.Rd | 144 - man/plot.predFrailty.Rd | 76 man/plot.predJoint.Rd | 86 man/plot.predLongi.Rd | 80 man/plot.trivPenal.Rd | 168 - man/plot.trivPenalNL.Rd | 168 - man/plotTreatPredJointSurro.Rd | 400 +- man/predict.jointSurroPenal.Rd | 266 - man/prediction.Rd | 1916 +++++++------- man/print.Cmeasures.Rd | 48 man/print.additivePenal.Rd | 54 man/print.frailtyCmprsk.Rd |only man/print.frailtyIllnessDeath.Rd |only man/print.frailtyPenal.Rd | 52 man/print.jointNestedPenal.Rd | 58 man/print.jointPenal.Rd | 54 man/print.jointSurroPenal.Rd | 182 - man/print.longiPenal.Rd | 64 man/print.multivPenal.Rd | 58 man/print.nestedPenal.Rd | 74 man/print.trivPenal.Rd | 58 man/print.trivPenalNL.Rd | 60 man/readmission.Rd | 66 man/readmission2.Rd |only man/runShiny.Rd | 50 man/slope.Rd | 126 man/ste.Rd | 274 +- man/subcluster.Rd | 104 man/summary.additivePenal.Rd | 106 man/summary.frailtyCmprsk.Rd |only man/summary.frailtyIllnessDeath.Rd |only man/summary.frailtyPenal.Rd | 132 man/summary.jointNestedPenal.Rd | 112 man/summary.jointPenal.Rd | 124 man/summary.jointSurroPenal.Rd | 162 - man/summary.jointSurroPenalSimul.Rd | 158 - man/summary.longiPenal.Rd | 156 - man/summary.multivPenal.Rd | 72 man/summary.nestedPenal.Rd | 110 man/summary.trivPenal.Rd | 136 man/summary.trivPenalNL.Rd | 138 - man/survDat.Rd | 44 man/survival.Rd | 76 man/terminal.Rd | 54 man/timedep.Rd | 198 - man/trivPenal.Rd | 976 +++---- man/trivPenalNL.Rd | 1052 +++---- man/wts.Rd | 84 src/Adonnees.f90 | 70 src/joint.f90 | 18 vignettes/Package_summary.Rmd | 64 133 files changed, 18164 insertions(+), 17330 deletions(-)
Title: Creating Chronological Charts
Description: Easy way to draw chronological charts from tables, aiming to include an intuitive environment for anyone new to R. Includes 'ggplot2' geoms and theme for chronological charts.
Author: Thomas Rose [aut, cre] ,
Chiara Girotto [aut]
Maintainer: Thomas Rose <roseth@posteo.com>
Diff between chronochrt versions 0.1.3 dated 2024-01-14 and 0.1.4 dated 2025-11-22
DESCRIPTION | 22 +- MD5 | 81 +++---- NEWS.md | 13 - R/chronochrt-package.R | 7 R/chronochrt_add_chron.R | 62 +++-- R/chronochrt_arrange_regions.R | 14 - R/chronochrt_convert_to_chron.R | 36 ++- R/chronochrt_geom.R | 342 ++++++++++++++++++--------------- R/chronochrt_geom_imagelabels.R | 123 ++++++----- R/chronochrt_import.R | 38 ++- R/chronochrt_label_image.R | 25 +- R/chronochrt_label_text.R | 13 - R/chronochrt_plot.R | 338 ++++++++++++++++++++++++++------ R/chronochrt_theme.R | 44 ++-- R/chronochrt_wrapper_import.R | 63 ++++-- README.md | 74 +++---- build/vignette.rds |binary inst/doc/ChronochRt.R | 281 +++++++++++++++------------ inst/doc/ChronochRt.Rmd | 274 +++++++++++++++----------- inst/doc/ChronochRt.html | 326 +++++++++++++++++-------------- inst/doc/Examples.R | 99 +++++---- inst/doc/Examples.Rmd | 98 +++++---- inst/doc/Examples.html | 98 +++++---- man/add_chron.Rd | 30 +- man/add_label_image.Rd | 17 - man/arrange_regions.Rd | 1 man/chronochrt-package.Rd | 102 ++++----- man/geom_chronochRt.Rd | 285 +++++++++++++-------------- man/geom_chronochRtImage.Rd | 183 +++++++++-------- man/import_chron_delim.Rd | 4 man/import_chron_excel.Rd | 3 man/plot_chronochrt.Rd | 5 tests/testthat/Rplots.pdf |only tests/testthat/setup.R | 149 ++++++++------ tests/testthat/test_add.R | 8 tests/testthat/test_geoms_chronochrt.R | 28 ++ tests/testthat/test_geoms_image.R | 2 tests/testthat/test_import.R | 256 +++++++++++++++++------- tests/testthat/test_label_image.R | 54 ++--- tests/testthat/test_plot.R | 10 vignettes/ChronochRt.Rmd | 274 +++++++++++++++----------- vignettes/Examples.Rmd | 98 +++++---- 42 files changed, 2376 insertions(+), 1604 deletions(-)
Title: A Framework for Planning and Executing Analyses
Description: A comprehensive framework for planning and executing analyses in R.
It provides a structured approach to running the same function multiple times
with different arguments, executing multiple functions on the same datasets,
and creating systematic analyses across multiple strata or variables.
The framework is particularly useful for applying the same analysis across
multiple strata (e.g., locations, age groups), running statistical methods
on multiple variables (e.g., exposures, outcomes), generating multiple tables
or graphs for reports, and creating systematic surveillance analyses.
Key features include efficient data management, structured analysis planning,
flexible execution options, built-in debugging tools, and hash-based caching.
Author: Richard Aubrey White [aut, cre]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between plnr versions 2022.11.23 dated 2022-11-23 and 2025.11.22 dated 2025-11-22
DESCRIPTION | 42 +- LICENSE | 4 MD5 | 67 ++- NAMESPACE | 1 NEWS.md | 38 +- R/3_onAttach.R | 2 R/create_rmarkdown.R | 25 + R/expand_list.R | 25 + R/get_anything.R | 16 R/is_run_directly.R | 20 + R/plan.R | 368 +++++++++++---------- R/set_opts.R | 16 R/try_again.R | 40 +- README.md | 85 +++-- build/vignette.rds |binary inst/CITATION |only inst/doc/adding_analyses.R | 6 inst/doc/adding_analyses.Rmd | 20 - inst/doc/adding_analyses.html | 712 ++++++++++++++++++++++-------------------- inst/doc/plnr.R | 131 ++----- inst/doc/plnr.Rmd | 220 +++++------- inst/doc/plnr.html | 476 ++++++++++++---------------- man/Plan.Rd | 437 +++++++++++++++++-------- man/create_rmarkdown.Rd | 30 + man/example_action_fn.Rd | 22 + man/expand_list.Rd | 24 + man/figures/logo.png |binary man/get_anything.Rd | 17 - man/hash_it.Rd |only man/is_run_directly.Rd | 22 + man/set_opts.Rd | 18 - man/test_action_fn.Rd | 12 man/try_again.Rd | 41 ++ man/uuid_generator.Rd |only vignettes/adding_analyses.Rmd | 20 - vignettes/plnr.Rmd | 220 +++++------- 36 files changed, 1742 insertions(+), 1435 deletions(-)
Title: An Interface for Running 'ADMIXTOOLS' Analyses
Description: An interface for performing all stages of 'ADMIXTOOLS' analyses
(<https://github.com/dreichlab/admixtools>) entirely from R. Wrapper functions
(D, f4, f3, etc.) completely automate the generation of intermediate
configuration files, run 'ADMIXTOOLS' programs on the command-line, and
parse output files to extract values of interest. This allows users to focus
on the analysis itself instead of worrying about low-level technical details.
A set of complementary functions for processing and filtering of data in
the 'EIGENSTRAT' format is also provided.
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between admixr versions 0.9.1 dated 2020-07-03 and 0.9.2 dated 2025-11-22
admixr-0.9.1/admixr/inst/doc/qpAdm.R |only admixr-0.9.1/admixr/inst/doc/qpAdm.Rmd |only admixr-0.9.1/admixr/inst/doc/qpAdm.html |only admixr-0.9.1/admixr/inst/doc/tutorial.R |only admixr-0.9.1/admixr/inst/doc/tutorial.Rmd |only admixr-0.9.1/admixr/inst/doc/tutorial.html |only admixr-0.9.1/admixr/man/keep_transitions.Rd |only admixr-0.9.1/admixr/vignettes/qpAdm.Rmd |only admixr-0.9.1/admixr/vignettes/tutorial.Rmd |only admixr-0.9.2/admixr/DESCRIPTION | 16 - admixr-0.9.2/admixr/MD5 | 68 +++--- admixr-0.9.2/admixr/NAMESPACE | 1 admixr-0.9.2/admixr/NEWS.md | 105 +++++----- admixr-0.9.2/admixr/R/eigenstrat.R | 36 +-- admixr-0.9.2/admixr/R/io.R | 2 admixr-0.9.2/admixr/R/output_parsers.R | 22 +- admixr-0.9.2/admixr/R/qpAdm.R | 27 +- admixr-0.9.2/admixr/R/utils.R | 29 ++ admixr-0.9.2/admixr/R/wrappers.R | 23 ++ admixr-0.9.2/admixr/R/zzz.R | 24 +- admixr-0.9.2/admixr/README.md | 144 ++++++++------ admixr-0.9.2/admixr/build/admixr-00build.log |only admixr-0.9.2/admixr/build/vignette.rds |binary admixr-0.9.2/admixr/inst/doc/vignette-01-tutorial.R |only admixr-0.9.2/admixr/inst/doc/vignette-01-tutorial.Rmd |only admixr-0.9.2/admixr/inst/doc/vignette-01-tutorial.html |only admixr-0.9.2/admixr/inst/doc/vignette-02-qpAdm.R |only admixr-0.9.2/admixr/inst/doc/vignette-02-qpAdm.Rmd |only admixr-0.9.2/admixr/inst/doc/vignette-02-qpAdm.html |only admixr-0.9.2/admixr/man/f4ratio.Rd | 5 admixr-0.9.2/admixr/man/filter_bed.Rd | 11 - admixr-0.9.2/admixr/man/qpAdm.Rd | 5 admixr-0.9.2/admixr/man/qpAdm_rotation.Rd | 24 +- admixr-0.9.2/admixr/man/qpWave.Rd | 5 admixr-0.9.2/admixr/tests/testthat/helper-functions.R | 19 - admixr-0.9.2/admixr/tests/testthat/test-admixtools_cmds.R | 13 - admixr-0.9.2/admixr/tests/testthat/test-filtering.R | 57 +++++ admixr-0.9.2/admixr/tests/testthat/test-io.R | 4 admixr-0.9.2/admixr/tests/testthat/test-log.R | 4 admixr-0.9.2/admixr/tests/testthat/test-qpAdm.R | 49 ++++ admixr-0.9.2/admixr/tests/testthat/test-utils.R | 19 + admixr-0.9.2/admixr/tests/testthat/test-wrappers.R | 55 ++++- admixr-0.9.2/admixr/vignettes/vignette-01-tutorial.Rmd |only admixr-0.9.2/admixr/vignettes/vignette-02-qpAdm.Rmd |only 44 files changed, 512 insertions(+), 255 deletions(-)
Title: Compute Soil Carbon Fluxes for the National Ecological
Observatory Network Sites
Description: Acquires and synthesizes soil carbon fluxes at sites located in the National Ecological Observatory Network (NEON). Provides flux estimates and associated uncertainty as well as key environmental measurements (soil water, temperature, CO2 concentration) that are used to compute soil fluxes.
Author: John Zobitz [aut, cre] ,
Edward Ayres [aut] ,
Katie O'Rourke [ctb] ,
Zoey Werbin [ctb],
Lajntxiag Lee [ctb],
Ridwan Abdi [ctb] ,
Dijone Mehmeti [ctb] ,
Ly Xiong [ctb]
Maintainer: John Zobitz <zobitz@augsburg.edu>
Diff between neonSoilFlux versions 2.0.0 dated 2025-08-24 and 3.0.0 dated 2025-11-22
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Title: A Package for Working with ICD Codes and Comorbidity Algorithms
Description: Provides tools for working with medical coding schemas such as the
International Classification of Diseases (ICD). Includes functions for
comorbidity classification algorithms such as the Pediatric Complex Chronic
Conditions (PCCC), Charlson, and Elixhauser indices.
Author: Peter DeWitt [aut, cre, cov] ,
Tell Bennett [ctb] ,
Seth Russell [ctb] ,
Meg Rebull [ctb] ,
Vincent Rubinetti [cov]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between medicalcoder versions 0.6.0 dated 2025-10-15 and 0.7.0 dated 2025-11-22
medicalcoder-0.6.0/medicalcoder/man/figures/medicalcoder_600x600_hex.png |only medicalcoder-0.6.0/medicalcoder/man/figures/medicalcoder_600x600_square.png |only medicalcoder-0.6.0/medicalcoder/tests/test-charlson-codes.R |only medicalcoder-0.6.0/medicalcoder/tests/test-charlson-index-scores.R |only medicalcoder-0.6.0/medicalcoder/tests/test-elixhauser-codes.R |only medicalcoder-0.6.0/medicalcoder/tests/test-elixhauser-index-scores.R |only medicalcoder-0.6.0/medicalcoder/tests/test-elixhauser-poa.R |only medicalcoder-0.6.0/medicalcoder/tests/test-get_icd.R |only medicalcoder-0.6.0/medicalcoder/tests/test-icd-codes.R |only medicalcoder-0.6.0/medicalcoder/tests/test-pccc-codes.R |only medicalcoder-0.6.0/medicalcoder/tests/test-pccc-conditions.R |only medicalcoder-0.6.0/medicalcoder/tests/test-summary.R |only medicalcoder-0.7.0/medicalcoder/DESCRIPTION | 31 medicalcoder-0.7.0/medicalcoder/MD5 | 157 medicalcoder-0.7.0/medicalcoder/NEWS.md | 34 medicalcoder-0.7.0/medicalcoder/R/charlson.R | 33 medicalcoder-0.7.0/medicalcoder/R/comorbidities.R | 91 medicalcoder-0.7.0/medicalcoder/R/elixhauser.R | 230 + medicalcoder-0.7.0/medicalcoder/R/get_icd_codes.R | 2 medicalcoder-0.7.0/medicalcoder/R/lookup_icd_codes.R | 49 medicalcoder-0.7.0/medicalcoder/R/medicalcoder-pkg.R | 26 medicalcoder-0.7.0/medicalcoder/R/pccc.R | 8 medicalcoder-0.7.0/medicalcoder/R/summary.R | 75 medicalcoder-0.7.0/medicalcoder/R/sysdata.rda |binary medicalcoder-0.7.0/medicalcoder/R/utilities.R | 5 medicalcoder-0.7.0/medicalcoder/README.md | 320 + medicalcoder-0.7.0/medicalcoder/build/vignette.rds |binary medicalcoder-0.7.0/medicalcoder/data/mdcr.rda |binary medicalcoder-0.7.0/medicalcoder/data/mdcr_longitudinal.rda |binary medicalcoder-0.7.0/medicalcoder/inst/WORDLIST | 31 medicalcoder-0.7.0/medicalcoder/inst/doc/charlson.R | 8 medicalcoder-0.7.0/medicalcoder/inst/doc/charlson.Rmd | 14 medicalcoder-0.7.0/medicalcoder/inst/doc/charlson.html | 122 medicalcoder-0.7.0/medicalcoder/inst/doc/comorbidities.R | 113 medicalcoder-0.7.0/medicalcoder/inst/doc/comorbidities.Rmd | 142 medicalcoder-0.7.0/medicalcoder/inst/doc/comorbidities.html | 839 ++--- medicalcoder-0.7.0/medicalcoder/inst/doc/elixhauser.R | 5 medicalcoder-0.7.0/medicalcoder/inst/doc/elixhauser.Rmd | 17 medicalcoder-0.7.0/medicalcoder/inst/doc/elixhauser.html | 317 - medicalcoder-0.7.0/medicalcoder/inst/doc/icd.R | 34 medicalcoder-0.7.0/medicalcoder/inst/doc/icd.Rmd | 80 medicalcoder-0.7.0/medicalcoder/inst/doc/icd.html | 470 +- medicalcoder-0.7.0/medicalcoder/inst/doc/pccc.R | 342 +- medicalcoder-0.7.0/medicalcoder/inst/doc/pccc.Rmd | 456 +- medicalcoder-0.7.0/medicalcoder/inst/doc/pccc.html | 1646 +++++++--- medicalcoder-0.7.0/medicalcoder/man/comorbidities.Rd | 53 medicalcoder-0.7.0/medicalcoder/man/figures/hex.svg |only medicalcoder-0.7.0/medicalcoder/man/get_icd_codes.Rd | 2 medicalcoder-0.7.0/medicalcoder/man/medicalcoder-package.Rd | 29 medicalcoder-0.7.0/medicalcoder/tests/expected-ahrq-results.rds |only medicalcoder-0.7.0/medicalcoder/tests/expected-results-for-test-pccc/pccc_cumulative_v2.1.rds |binary medicalcoder-0.7.0/medicalcoder/tests/expected-results-for-test-pccc/pccc_cumulative_v3.0.rds |binary medicalcoder-0.7.0/medicalcoder/tests/expected-results-for-test-pccc/pccc_cumulative_v3.1.rds |binary medicalcoder-0.7.0/medicalcoder/tests/expected-results-for-test-pccc/pccc_current_v2.1.rds |binary medicalcoder-0.7.0/medicalcoder/tests/expected-results-for-test-pccc/pccc_current_v3.0.rds |binary medicalcoder-0.7.0/medicalcoder/tests/expected-results-for-test-pccc/pccc_current_v3.1.rds |binary medicalcoder-0.7.0/medicalcoder/tests/mdcr_subset_DF.rds |only medicalcoder-0.7.0/medicalcoder/tests/mdcr_subset_DT.rds |only medicalcoder-0.7.0/medicalcoder/tests/mdcr_subset_TBL.rds |only medicalcoder-0.7.0/medicalcoder/tests/results_pccc_1.0.6.rds |binary medicalcoder-0.7.0/medicalcoder/tests/test-asserts.R | 178 - medicalcoder-0.7.0/medicalcoder/tests/test-charlson.R | 42 medicalcoder-0.7.0/medicalcoder/tests/test-comorbidities.R | 94 medicalcoder-0.7.0/medicalcoder/tests/test-data-frame-tools.R |only medicalcoder-0.7.0/medicalcoder/tests/test-elixhauser-example.R | 33 medicalcoder-0.7.0/medicalcoder/tests/test-elixhauser.R | 16 medicalcoder-0.7.0/medicalcoder/tests/test-icd_compact_to_full.R | 8 medicalcoder-0.7.0/medicalcoder/tests/test-internal-data.R |only medicalcoder-0.7.0/medicalcoder/tests/test-is_icd.R | 104 medicalcoder-0.7.0/medicalcoder/tests/test-locked-bindings.R | 9 medicalcoder-0.7.0/medicalcoder/tests/test-longitudinal-comorbidities.R | 36 medicalcoder-0.7.0/medicalcoder/tests/test-longitudinal-pccc-v3.1.R | 7 medicalcoder-0.7.0/medicalcoder/tests/test-lookup_icd_codes.R | 56 medicalcoder-0.7.0/medicalcoder/tests/test-pccc-deltas.R | 1 medicalcoder-0.7.0/medicalcoder/tests/test-pccc.R | 46 medicalcoder-0.7.0/medicalcoder/tests/test-summary-charlson.R |only medicalcoder-0.7.0/medicalcoder/tests/test-summary-elixhauser.R |only medicalcoder-0.7.0/medicalcoder/tests/test-summary-pccc-subconditions.R |only medicalcoder-0.7.0/medicalcoder/tests/test-summary-pccc.R |only medicalcoder-0.7.0/medicalcoder/tests/test-tibble-datatable.R | 202 - medicalcoder-0.7.0/medicalcoder/tests/test-vs-ahrq.R |only medicalcoder-0.7.0/medicalcoder/tests/test-vs-pccc_1.0.6.R | 43 medicalcoder-0.7.0/medicalcoder/tests/test-zero-row-inputs.R | 165 - medicalcoder-0.7.0/medicalcoder/tests/utilities.R |only medicalcoder-0.7.0/medicalcoder/vignettes/articles |only medicalcoder-0.7.0/medicalcoder/vignettes/charlson.Rmd | 14 medicalcoder-0.7.0/medicalcoder/vignettes/comorbidities.Rmd | 142 medicalcoder-0.7.0/medicalcoder/vignettes/elixhauser.Rmd | 17 medicalcoder-0.7.0/medicalcoder/vignettes/icd.Rmd | 80 medicalcoder-0.7.0/medicalcoder/vignettes/pccc.Rmd | 456 +- medicalcoder-0.7.0/medicalcoder/vignettes/references.bib | 43 91 files changed, 4922 insertions(+), 2651 deletions(-)
Title: Combined miRNA- And mRNA-Testing
Description: Package for combined miRNA- and mRNA-testing.
Author: Stephan Artmann [aut, cre],
Klaus Jung [aut],
Tim Beissbarth [aut]
Maintainer: Stephan Artmann <stephanartmann@gmx.net>
Diff between miRtest versions 2.1 dated 2024-02-05 and 2.2 dated 2025-11-22
DESCRIPTION | 15 +++-- MD5 | 12 ++-- R/miRtest.R | 144 +++++++++++++++++++++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/miRtest.Rnw | 4 - inst/doc/miRtest.pdf |binary vignettes/miRtest.Rnw | 4 - 7 files changed, 156 insertions(+), 23 deletions(-)
Title: Dataset of the 'Contoso' Company
Description: A collection of synthetic datasets simulating sales transactions from a fictional company. The dataset includes various related tables that contain essential business and operational data, useful for analyzing sales performance and other business insights. Key tables included in the package are:
- "sales": Contains data on individual sales transactions, including order details, pricing, quantities, and customer information.
- "customer": Stores customer-specific details such as demographics, geographic location, occupation, and birthday.
- "store": Provides information about stores, including location, size, status, and operational dates.
- "orders": Contains details about customer orders, including order and delivery dates, store, and customer data.
- "product": Contains data on products, including attributes such as product name, category, price, cost, and weight.
- "date": A time-based table that includes date-related attributes like year, month, quarter, day, and working day indica [...truncated...]
Author: Alejandro Hagan [aut, cre]
Maintainer: Alejandro Hagan <alejandro.hagan@outlook.com>
Diff between contoso versions 1.1.1 dated 2025-11-12 and 1.2.0 dated 2025-11-22
contoso-1.1.1/contoso/data/date.rda |only contoso-1.1.1/contoso/man/date.Rd |only contoso-1.2.0/contoso/DESCRIPTION | 8 ++++---- contoso-1.2.0/contoso/MD5 | 12 ++++++------ contoso-1.2.0/contoso/NEWS.md | 3 +++ contoso-1.2.0/contoso/R/data.R | 6 +++--- contoso-1.2.0/contoso/README.md | 9 ++++----- contoso-1.2.0/contoso/data/calendar.rda |only contoso-1.2.0/contoso/man/calendar.Rd |only 9 files changed, 20 insertions(+), 18 deletions(-)
Title: Tools for Reading and Writing ISO/OGC Geographic Metadata
Description: Provides facilities to read, write and validate geographic metadata
defined with ISO TC211 / OGC ISO geographic information metadata standards, and
encoded using the ISO 19139 and ISO 19115-3 (XML) standard technical specifications.
This includes ISO 19110 (Feature cataloguing), 19115 (dataset metadata), 19119 (service metadata)
and 19136 (GML). Other interoperable schemas from the OGC are progressively supported
as well, such as the Sensor Web Enablement (SWE) Common Data Model, the OGC GML
Coverage Implementation Schema (GMLCOV), or the OGC GML Referenceable Grid (GMLRGRID).
Author: Emmanuel Blondel [aut, cre] ,
R Consortium [fnd]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
This is a re-admission after prior archival of version 0.9.2 dated 2025-06-05
Diff between geometa versions 0.9.2 dated 2025-06-05 and 0.9.3 dated 2025-11-22
DESCRIPTION | 10 MD5 | 22 R/INSPIREMetadataValidator.R | 7 R/ISOAbstractObject.R | 22 README.md | 2 inst/extdata/examples/metadata_19115-3.xml | 1496 +++++++++++----------- inst/extdata/schemas/gml/coordinateOperations.xsd | 2 man/GMLTimeInstant.Rd | 2 man/INSPIREMetadataValidator.Rd | 8 man/ISOAbstractObject.Rd | 12 man/ISOImageryMetadata.Rd | 2 man/ISOMetadata.Rd | 42 12 files changed, 852 insertions(+), 775 deletions(-)
Title: Methods for ''A Fast Alternative for the R x C Ecological
Inference Case''
Description: Estimates the probability matrix for the R×C Ecological Inference problem using the Expectation-Maximization Algorithm with four approximation methods for the E-Step, and an exact method as well. It also provides a bootstrap function to estimate the standard deviation of the estimated probabilities. In addition, it has functions that aggregate rows optimally to have more reliable estimates in cases of having few data points. For comparing the probability estimates of two groups, a Wald test routine is implemented. The library has data from the first round of the Chilean Presidential Election 2021 and can also generate synthetic election data. Methods described in Thraves, Charles; Ubilla, Pablo; Hermosilla, Daniel (2024) ''A Fast Ecological Inference Algorithm for the R×C case'' <doi:10.2139/ssrn.4832834>.
Author: Charles Thraves [aut] ,
Pablo Ubilla [aut] ,
Daniel Hermosilla [aut, cre],
Hanson Troy [ctb, cph]
Maintainer: Daniel Hermosilla <daniel.hermosilla.r@ug.uchile.cl>
Diff between fastei versions 0.0.0.10 dated 2025-09-15 and 0.0.0.11 dated 2025-11-22
DESCRIPTION | 10 - MD5 | 56 ++--- R/RcppExports.R | 12 - R/eim-class.R | 158 ++++++++++++++-- R/internal.R | 66 ++++++ inst/doc/demonstration.html | 430 ++++++++++++++++++++++---------------------- man/bootstrap.Rd | 4 man/fastei-package.Rd | 2 man/get_agg_opt.Rd | 2 man/get_agg_proxy.Rd | 2 man/run_em.Rd | 21 +- src/LP.c | 355 ++++++++++++------------------------ src/RcppExports.cpp | 27 +- src/bootstrap.c | 7 src/bootstrap.h | 2 src/dynamic_program.c | 26 +- src/dynamic_program.h | 8 src/exact.c | 311 +++++++++++++++++++++++-------- src/exact.h | 2 src/globals.h | 2 src/main.c | 195 +++++++++++++++---- src/main.h | 2 src/multivariate-cdf.c | 119 +++++++----- src/multivariate-cdf.h | 5 src/multivariate-pdf.c | 177 +++++++++++++----- src/utils_multivariate.c | 42 ++++ src/utils_multivariate.h | 8 src/wrapper.cpp | 48 ++++ src/wrapper.h | 10 - 29 files changed, 1333 insertions(+), 776 deletions(-)
Title: IEEG (Intracranial Electroencephalography) Epoch Data Tools
Description: Provides tools for working with iEEG matrix data, including downloading curated iEEG data from OSF (The Open Science Framework <https://osf.io/>) (EpochDownloader()), making new objects (Epoch()), processing (crop() and resample()), and visualizing the data (plot()).
Author: Jiefei Wang [aut, cre]
Maintainer: Jiefei Wang <szwjf08@gmail.com>
Diff between Epoch versions 1.0.3 dated 2025-09-03 and 1.0.7 dated 2025-11-22
DESCRIPTION | 8 MD5 | 25 NAMESPACE | 1 NEWS.md |only R/EpochDownloader.r | 21 R/method-Epoch-plot.r | 25 R/utils.r | 47 + R/zzz.r | 2 README.md | 7 build/vignette.rds |binary inst/doc/Epoch.html | 1233 +++++++++++++++------------------------ man/EpochDownloader-method.Rd | 21 man/dot-standardizeIEEG.Rd | 6 man/plot-Epoch-missing-method.Rd | 13 14 files changed, 613 insertions(+), 796 deletions(-)
Title: Automatic Marking of R Assignments
Description: Automatic marking of R assignments for students and teachers based
on 'testthat' test suites.
Author: Mans Magnusson [aut, cre],
Oscar Pettersson [aut]
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between markmyassignment versions 0.8.8 dated 2024-01-29 and 0.8.9 dated 2025-11-22
markmyassignment-0.8.8/markmyassignment/R/markmyassignment.R |only markmyassignment-0.8.8/markmyassignment/man/markmyassignment.Rd |only markmyassignment-0.8.9/markmyassignment/DESCRIPTION | 18 markmyassignment-0.8.9/markmyassignment/MD5 | 18 markmyassignment-0.8.9/markmyassignment/R/markmyassignment-package.R |only markmyassignment-0.8.9/markmyassignment/build/vignette.rds |binary markmyassignment-0.8.9/markmyassignment/inst/doc/markmyassignment-teacher.R | 30 - markmyassignment-0.8.9/markmyassignment/inst/doc/markmyassignment-teacher.html | 5 markmyassignment-0.8.9/markmyassignment/inst/doc/markmyassignment.R | 16 markmyassignment-0.8.9/markmyassignment/inst/doc/markmyassignment.html | 232 +++++----- markmyassignment-0.8.9/markmyassignment/man/markmyassignment-package.Rd |only markmyassignment-0.8.9/markmyassignment/tests/testthat/test-expectation.R | 12 12 files changed, 180 insertions(+), 151 deletions(-)
More information about markmyassignment at CRAN
Permanent link
Title: Multi-Context Colocalization Analysis for QTL and GWAS Studies
Description: A multi-task learning approach to variable selection regression with highly correlated predictors and sparse effects,
based on frequentist statistical inference. It provides statistical evidence to identify which subsets of predictors have non-zero
effects on which subsets of response variables, motivated and designed for colocalization analysis across genome-wide association studies (GWAS)
and quantitative trait loci (QTL) studies.
The ColocBoost model is described in Cao et. al. (2025) <doi:10.1101/2025.04.17.25326042>.
Author: Xuewei Cao [cre, aut, cph],
Haochen Sun [aut, cph],
Ru Feng [aut, cph],
Daniel Nachun [aut, cph],
Kushal Dey [aut, cph],
Gao Wang [aut, cph]
Maintainer: Xuewei Cao <xc2270@cumc.columbia.edu>
Diff between colocboost versions 1.0.6 dated 2025-09-09 and 1.0.7 dated 2025-11-22
DESCRIPTION | 8 MD5 | 113 ++--- R/colocboost.R | 438 ++++++++++++++++----- R/colocboost_assemble.R | 6 R/colocboost_check_update_jk.R | 91 +++- R/colocboost_inference.R | 20 - R/colocboost_init.R | 5 R/colocboost_one_causal.R | 10 R/colocboost_plot.R | 148 ++++--- R/colocboost_update.R | 3 R/colocboost_utils.R | 76 +++ R/colocboost_workhorse.R | 6 inst/doc/Ambiguous_Colocalization.R | 2 inst/doc/Ambiguous_Colocalization.Rmd | 2 inst/doc/Ambiguous_Colocalization.html | 6 inst/doc/ColocBoost_Wrapper_Pipeline.R | 160 ++++++-- inst/doc/ColocBoost_Wrapper_Pipeline.Rmd | 274 ++++++++++--- inst/doc/ColocBoost_Wrapper_Pipeline.html | 458 ++++++++++++++++------- inst/doc/Disease_Prioritized_Colocalization.R | 2 inst/doc/Disease_Prioritized_Colocalization.Rmd | 2 inst/doc/Disease_Prioritized_Colocalization.html | 30 - inst/doc/FineBoost_Special_Case.html | 20 - inst/doc/Individual_Level_Colocalization.R | 2 inst/doc/Individual_Level_Colocalization.Rmd | 2 inst/doc/Individual_Level_Colocalization.html | 91 ++-- inst/doc/Interpret_ColocBoost_Output.R | 2 inst/doc/Interpret_ColocBoost_Output.Rmd | 2 inst/doc/Interpret_ColocBoost_Output.html | 46 +- inst/doc/LD_Free_Colocalization.R | 2 inst/doc/LD_Free_Colocalization.Rmd | 2 inst/doc/LD_Free_Colocalization.html | 51 +- inst/doc/Partial_Overlap_Variants.R | 2 inst/doc/Partial_Overlap_Variants.Rmd | 2 inst/doc/Partial_Overlap_Variants.html | 60 +-- inst/doc/Summary_Statistics_Colocalization.R | 2 inst/doc/Summary_Statistics_Colocalization.Rmd | 2 inst/doc/Summary_Statistics_Colocalization.html | 102 ++--- inst/doc/Visualization_ColocBoost_Output.R | 9 inst/doc/Visualization_ColocBoost_Output.Rmd | 15 inst/doc/Visualization_ColocBoost_Output.html | 57 +- inst/doc/announcements.Rmd | 8 inst/doc/announcements.html | 13 man/colocboost.Rd | 11 man/colocboost_plot.Rd | 11 man/colocboost_validate_input_data.Rd |only tests/testthat/test_plot.R | 4 tests/testthat/test_sumstats.R | 77 +++ tests/testthat/test_utils.R | 14 vignettes/Ambiguous_Colocalization.Rmd | 2 vignettes/ColocBoost_Wrapper_Pipeline.Rmd | 274 ++++++++++--- vignettes/Disease_Prioritized_Colocalization.Rmd | 2 vignettes/Individual_Level_Colocalization.Rmd | 2 vignettes/Interpret_ColocBoost_Output.Rmd | 2 vignettes/LD_Free_Colocalization.Rmd | 2 vignettes/Partial_Overlap_Variants.Rmd | 2 vignettes/Summary_Statistics_Colocalization.Rmd | 2 vignettes/Visualization_ColocBoost_Output.Rmd | 15 vignettes/announcements.Rmd | 8 58 files changed, 1931 insertions(+), 849 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-05 0.9.2
2025-02-21 0.9.1
2025-01-29 0.9
2024-04-18 0.8-0
2022-10-27 0.7-1
2022-08-19 0.7
2022-01-26 0.6-6
2021-12-06 0.6-5
2021-09-16 0.6-4
2020-08-04 0.6-3
2020-05-14 0.6-2
2019-10-31 0.6-1
2019-09-27 0.6-0
2019-05-26 0.5-0
2018-12-17 0.4-0
2018-08-22 0.3-0
2017-11-28 0.2-0
2017-05-26 0.1-0
Title: Object-Oriented Interface for Offline Change-Point Detection
Description: A collection of efficient implementations of popular offline change-point detection algorithms, featuring a consistent, object-oriented interface for practical use.
Author: Minh Long Nguyen [aut, cre],
Toby Hocking [aut],
Charles Truong [aut]
Maintainer: Minh Long Nguyen <edelweiss611428@gmail.com>
Diff between rupturesRcpp versions 1.0.0 dated 2025-11-21 and 1.0.1 dated 2025-11-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/zzz.R | 2 +- README.md | 2 ++ src/tmplBinSeg.cpp | 32 +++++++++++++++----------------- src/tmplPelt.cpp | 34 +++++++++++++++------------------- src/tmplWindow.cpp | 33 +++++++++++++++++---------------- 7 files changed, 60 insertions(+), 63 deletions(-)
Title: Models Hurricane Wind Speed, Wind Direction, and Wind Damage
Description: The HURRECON model estimates wind speed, wind direction, enhanced
Fujita scale wind damage, and duration of EF0 to EF5 winds as a function
of hurricane location and maximum sustained wind speed. Results may be
generated for a single site or an entire region. Hurricane track and
intensity data may be imported directly from the US National Hurricane
Center's HURDAT2 database. For details on the original version of the
model written in Borland Pascal, see: Boose, Chamberlin, and Foster (2001)
<doi:10.1890/0012-9615(2001)071[0027:LARIOH]2.0.CO;2> and Boose, Serrano,
and Foster (2004) <doi:10.1890/02-4057>.
Author: Emery Boose [aut, cre],
President and Fellows of Harvard College [cph]
Maintainer: Emery Boose <boose@fas.harvard.edu>
Diff between HurreconR versions 1.1 dated 2023-06-13 and 1.2 dated 2025-11-22
HurreconR-1.1/HurreconR/inst/region/land_water_summary.expected |only HurreconR-1.1/HurreconR/inst/site/site_summary.expected |only HurreconR-1.2/HurreconR/DESCRIPTION | 10 +- HurreconR-1.2/HurreconR/MD5 | 10 +- HurreconR-1.2/HurreconR/build/vignette.rds |binary HurreconR-1.2/HurreconR/tests/testthat/_snaps |only HurreconR-1.2/HurreconR/tests/testthat/test_HurreconR.R | 46 +++++----- 7 files changed, 36 insertions(+), 30 deletions(-)
Title: Generalized Linear Mixed Model Association Tests
Description: Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) <DOI:10.1016/j.ajhg.2016.02.012>. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) <DOI:10.1016/j.ajhg.2018.12.012>, including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.
Author: Han Chen [aut, cre],
Matthew Conomos [aut],
Duy Pham [aut],
Arthor Gilly [ctb],
Robert Gentleman [ctb, cph] ,
Ross Ihaka [ctb, cph] ,
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Eric Biggers [ctb, cph] ,
Tino Reichardt [ctb, cph] library), [...truncated...]
Maintainer: Han Chen <hanchenphd@gmail.com>
Diff between GMMAT versions 1.4.2 dated 2023-11-17 and 1.5.0 dated 2025-11-22
DESCRIPTION | 12 ++--- MD5 | 30 ++++++------- NAMESPACE | 10 +++- R/glmm.wald.R | 4 + R/glmmkin.R | 96 ++++++++++++++++++++++++++++++++++++++---- build/vignette.rds |binary configure | 30 ++++++------- configure.ac | 2 data/example.rda |binary inst/doc/GMMAT.Rnw | 13 ++++- inst/doc/GMMAT.pdf |binary man/GMMAT-package.Rd | 4 - man/glmmkin.Rd | 1 src/fitglmm.cpp | 2 tests/testthat/test_glmmkin.R | 12 ++--- vignettes/GMMAT.Rnw | 13 ++++- 16 files changed, 166 insertions(+), 63 deletions(-)
Title: Process Command Line Arguments
Description: Process command line arguments, as part of a data analysis
workflow. 'command' makes it easier to construct a workflow consisting
of lots of small, self-contained scripts, all run from a Makefile or
shell script. The aim is a workflow that is modular, transparent,
and reliable.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between command versions 0.1.2 dated 2025-10-16 and 0.1.3 dated 2025-11-22
command-0.1.2/command/inst/extdata/swiss1/Makefile |only command-0.1.2/command/inst/extdata/swiss1/out |only command-0.1.2/command/man/figures/README-pressure-1.png |only command-0.1.2/command/tests/testthat/test-extact_shell.R |only command-0.1.3/command/DESCRIPTION | 14 ++-- command-0.1.3/command/MD5 | 42 ++++++-------- command-0.1.3/command/NEWS.md | 22 +++++++ command-0.1.3/command/R/cmd_assign.R | 2 command-0.1.3/command/R/command-package.R | 2 command-0.1.3/command/R/extract_make.R | 4 - command-0.1.3/command/R/extract_shell.R | 4 - command-0.1.3/command/R/makefile.R | 2 command-0.1.3/command/R/shell_script.R | 2 command-0.1.3/command/README.md | 23 +++++-- command-0.1.3/command/inst/extdata/airmiles/Makefile | 4 - command-0.1.3/command/inst/extdata/swiss1/src/model.R | 4 + command-0.1.3/command/man/cmd_assign.Rd | 2 command-0.1.3/command/man/command-package.Rd | 2 command-0.1.3/command/man/extract_make.Rd | 2 command-0.1.3/command/man/extract_shell.Rd | 2 command-0.1.3/command/man/figures/sticker.png |only command-0.1.3/command/tests/testthat/test-extract_make.R | 2 command-0.1.3/command/tests/testthat/test-extract_shell.R |only 23 files changed, 80 insertions(+), 55 deletions(-)
Title: Access and Manipulate Amiga Disk Files
Description: Amiga Disk Files (ADF) are virtual
representations of 3.5 inch floppy disks for the
Commodore Amiga. Most disk drives from other systems
(including modern drives) are not able to read these
disks. The 'adfExplorer' package enables you to
establish R connections to files on such
virtual DOS-formatted disks, which can be use to
read from and write to those files.
Author: Pepijn de Vries [aut, cre] ,
Laurent Clevy [aut, cph]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between adfExplorer versions 2.0.3 dated 2025-01-10 and 2.1.0 dated 2025-11-22
adfExplorer-2.0.3/adfExplorer/R/deprecated.R |only adfExplorer-2.0.3/adfExplorer/man/deprecated.Rd |only adfExplorer-2.0.3/adfExplorer/tests/testthat/test_deprecated.R |only adfExplorer-2.0.3/adfExplorer/tests/testthat/test_examples.R |only adfExplorer-2.1.0/adfExplorer/DESCRIPTION | 23 adfExplorer-2.1.0/adfExplorer/MD5 | 107 +- adfExplorer-2.1.0/adfExplorer/NAMESPACE | 37 adfExplorer-2.1.0/adfExplorer/NEWS.md | 21 adfExplorer-2.1.0/adfExplorer/R/adfExplorer-package.R | 5 adfExplorer-2.1.0/adfExplorer/R/bitmap.R |only adfExplorer-2.1.0/adfExplorer/R/blocks.R | 188 ++-- adfExplorer-2.1.0/adfExplorer/R/compress.R | 92 +- adfExplorer-2.1.0/adfExplorer/R/connect_adf.R | 276 +++--- adfExplorer-2.1.0/adfExplorer/R/cpp11.R | 16 adfExplorer-2.1.0/adfExplorer/R/demo.R | 38 adfExplorer-2.1.0/adfExplorer/R/device_create.R | 204 ++-- adfExplorer-2.1.0/adfExplorer/R/device_info.R | 410 ++++----- adfExplorer-2.1.0/adfExplorer/R/entry_info.R | 6 adfExplorer-2.1.0/adfExplorer/R/helpers.R | 8 adfExplorer-2.1.0/adfExplorer/R/remove.R | 2 adfExplorer-2.1.0/adfExplorer/R/s3_conn.R | 3 adfExplorer-2.1.0/adfExplorer/R/undelete.R |only adfExplorer-2.1.0/adfExplorer/R/virtual_path.R | 70 - adfExplorer-2.1.0/adfExplorer/README.md | 4 adfExplorer-2.1.0/adfExplorer/build/vignette.rds |binary adfExplorer-2.1.0/adfExplorer/configure.win | 30 adfExplorer-2.1.0/adfExplorer/inst/doc/adf_objects.R | 3 adfExplorer-2.1.0/adfExplorer/inst/doc/adf_objects.Rmd | 440 +++++----- adfExplorer-2.1.0/adfExplorer/inst/doc/adf_objects.html | 15 adfExplorer-2.1.0/adfExplorer/inst/doc/file_system_modes.html | 4 adfExplorer-2.1.0/adfExplorer/inst/doc/version2.Rmd | 2 adfExplorer-2.1.0/adfExplorer/inst/doc/version2.html | 41 adfExplorer-2.1.0/adfExplorer/inst/doc/virtual_paths.html | 4 adfExplorer-2.1.0/adfExplorer/inst/example.adz |binary adfExplorer-2.1.0/adfExplorer/man/close_all_devices.Rd | 30 adfExplorer-2.1.0/adfExplorer/man/demo_adf.Rd | 40 adfExplorer-2.1.0/adfExplorer/man/get_adf_bitmap.Rd |only adfExplorer-2.1.0/adfExplorer/man/read_write.Rd | 12 adfExplorer-2.1.0/adfExplorer/man/remove_adf_entry.Rd | 4 adfExplorer-2.1.0/adfExplorer/man/salvage_adf_entry.Rd |only adfExplorer-2.1.0/adfExplorer/src/adf_file_info.cpp | 40 adfExplorer-2.1.0/adfExplorer/src/adf_file_operators.cpp | 14 adfExplorer-2.1.0/adfExplorer/src/adflib/adf_salv.c | 3 adfExplorer-2.1.0/adfExplorer/src/bitmap.cpp |only adfExplorer-2.1.0/adfExplorer/src/block_adf.cpp | 134 +-- adfExplorer-2.1.0/adfExplorer/src/cpp11.cpp | 32 adfExplorer-2.1.0/adfExplorer/src/dev_info.cpp | 2 adfExplorer-2.1.0/adfExplorer/src/undelete.cpp |only adfExplorer-2.1.0/adfExplorer/tests/testthat.R | 8 adfExplorer-2.1.0/adfExplorer/tests/testthat/test_bitmap.R |only adfExplorer-2.1.0/adfExplorer/tests/testthat/test_block.R |only adfExplorer-2.1.0/adfExplorer/tests/testthat/test_compress.R |only adfExplorer-2.1.0/adfExplorer/tests/testthat/test_devinfo.R |only adfExplorer-2.1.0/adfExplorer/tests/testthat/test_directory.R | 14 adfExplorer-2.1.0/adfExplorer/tests/testthat/test_entryinfo.R | 12 adfExplorer-2.1.0/adfExplorer/tests/testthat/test_exceptions.R | 16 adfExplorer-2.1.0/adfExplorer/tests/testthat/test_move.R | 26 adfExplorer-2.1.0/adfExplorer/tests/testthat/test_prep.R |only adfExplorer-2.1.0/adfExplorer/tests/testthat/test_remove.R | 36 adfExplorer-2.1.0/adfExplorer/tests/testthat/test_s3.R | 34 adfExplorer-2.1.0/adfExplorer/vignettes/adf_objects.Rmd | 440 +++++----- adfExplorer-2.1.0/adfExplorer/vignettes/version2.Rmd | 2 62 files changed, 1573 insertions(+), 1375 deletions(-)
Title: Building and Managing Local Databases from 'Google Earth Engine'
Description: Simplifies the creation, management, and updating of local databases using data extracted from 'Google Earth Engine' ('GEE'). It integrates with 'GEE' to store, aggregate, and process spatio-temporal data, leveraging 'SQLite' for efficient, serverless storage. The 'geeLite' package provides utilities for data transformation and supports real-time monitoring and analysis of geospatial features, making it suitable for researchers and practitioners in geospatial science. For details, see Kurbucz and Andrée (2025) "Building and Managing Local Databases from Google Earth Engine with the geeLite R Package" <https://hdl.handle.net/10986/43165>.
Author: Marcell T. Kurbucz [aut, cre],
Bo Pieter Johannes Andree [aut]
Maintainer: Marcell T. Kurbucz <m.kurbucz@ucl.ac.uk>
Diff between geeLite versions 1.0.2 dated 2025-07-21 and 1.0.3 dated 2025-11-22
DESCRIPTION | 11 MD5 | 88 NAMESPACE | 12 R/gee_install.R | 290 - R/run_geelite.R | 3533 ++++++++------- R/run_geelite._halfgoogleimportR.R |only R/utils.R | 984 ++-- README.md | 352 - build/vignette.rds |binary inst/doc/geeLite.R | 292 - inst/doc/geeLite.Rmd | 550 +- inst/doc/geeLite.html | 8295 +++++++++---------------------------- man/batch_drive_export.Rd | 23 man/compare_lists.Rd | 9 man/compare_vectors.Rd | 9 man/compile_db.Rd | 11 man/db_connect.Rd | 5 man/ee_as_tidyee.Rd |only man/extract_drive_stats.Rd | 22 man/gee_install.Rd | 4 man/gee_message.Rd | 23 man/gen_messages.Rd | 9 man/get_batch.Rd | 11 man/get_batches.Rd | 11 man/get_bins.Rd | 10 man/get_cases.Rd | 15 man/get_grid.Rd | 10 man/get_images.Rd | 17 man/get_reducers.Rd | 9 man/get_shapes.Rd | 11 man/get_task.Rd | 9 man/local_chunk_extract.Rd | 13 man/print_version.Rd | 7 man/process_vector.Rd | 17 man/read_grid.Rd | 10 man/remove_tables.Rd | 8 man/run_geelite.Rd | 23 man/set_depend.Rd | 28 man/set_dirs.Rd | 8 man/set_progress_bar.Rd | 10 man/update_grid_stats.Rd | 11 man/write_grid.Rd | 7 man/write_grid_stats.Rd | 7 man/write_log_file.Rd | 8 man/write_state_file.Rd | 8 vignettes/geeLite.Rmd | 550 +- 46 files changed, 5852 insertions(+), 9488 deletions(-)
Title: Exploratory Data Analysis for the 'spatstat' Family
Description: Functionality for exploratory data analysis and nonparametric analysis of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Warick Brown [cph],
Achmad Choiruddin [ctb],
Ya-Mei Chang [ctb],
Jean-Francois Coeurjolly [ctb],
Lucia Cobo Sanchez [ctb, cph],
Ottma [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.explore versions 3.5-3 dated 2025-09-22 and 3.6-0 dated 2025-11-22
DESCRIPTION | 15 ++-- MD5 | 72 +++++++++++---------- NAMESPACE | 14 ++++ NEWS | 40 +++++++++++ R/bermantest.R | 4 - R/cdftest.R | 1 R/eval.fv.R | 33 +++++++-- R/evidence.R | 4 - R/fv.R | 12 +-- R/hasenvelope.R | 2 R/laslett.R | 4 - R/localpcf.R | 4 - R/markcorr.R | 131 +++++++++++++++++++++++++++++---------- R/nncount.R |only R/pairs.im.R | 2 R/quadrattest.R | 57 +++++++++++++--- R/rho2hat.R | 2 R/rhohat.R | 2 R/roc.R | 47 +++++++++---- R/smoothfun.R | 2 R/spatialcdf.R | 2 R/ssf.R | 6 - R/tolcon.R |only build/partial.rdb |binary inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/Emark.Rd | 4 + man/auc.Rd | 4 - man/macros/defns.Rd | 3 man/markconnect.Rd | 10 ++ man/markcorr.Rd | 11 ++- man/markcrosscorr.Rd | 4 + man/markequal.Rd |only man/markvario.Rd | 5 + man/nncount.Rd |only man/nnequal.Rd |only man/relrisk.ppp.Rd | 19 ++--- man/roc.Rd | 4 - man/spatstat.explore-internal.Rd | 10 ++ man/tolcon.Rd |only 40 files changed, 380 insertions(+), 152 deletions(-)
More information about spatstat.explore at CRAN
Permanent link
Title: Test Theory Analysis and Biclustering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.6.5 dated 2025-11-06 and 1.7.0 dated 2025-11-22
DESCRIPTION | 6 +- MD5 | 38 ++++++++------- NAMESPACE | 4 + NEWS.md | 13 +++++ R/00_GridSearch.R | 13 ++--- R/00_exametrikaPlot.R | 6 +- R/00_exametrikaPrint.R | 2 R/02_TestItemFunctions.R | 1 R/04C_ParameterEstimation.R | 1 R/07_IRM.R | 43 +++++++++++------ R/08C_BNM_GA.R | 24 +++++++++- R/09B_LDLRA_GA.R | 11 ++++ R/12_LRA_ordinal.R | 1 R/13_LRA_rated.R | 1 README.md | 2 man/Biclustering_IRM.Rd |only man/IRM.Rd | 103 ++----------------------------------------- man/StrLearningGA_BNM.Rd |only man/StrLearningPBIL_BNM.Rd |only man/StrLearningPBIL_LDLRA.Rd |only man/plot.exametrika.Rd | 6 +- man/print.exametrika.Rd | 2 22 files changed, 122 insertions(+), 155 deletions(-)
Title: Stochastic Tree Ensembles (XBART and BART) for Supervised
Learning and Causal Inference
Description: Flexible stochastic tree ensemble software.
Robust implementations of Bayesian Additive Regression Trees (BART)
Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285>
for supervised learning and Bayesian Causal Forests (BCF)
Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195>
for causal inference. Enables model serialization and parallel sampling
and provides a low-level interface for custom stochastic forest samplers.
Author: Drew Herren [aut, cre] ,
Richard Hahn [aut],
Jared Murray [aut],
Carlos Carvalho [aut],
Jingyu He [aut],
Pedro Lima [ctb],
stochtree contributors [cph],
Eigen contributors [cph] ,
xgboost contributors [cph] ,
treelite contributors [cph] ,
Microsoft C [...truncated...]
Maintainer: Drew Herren <drewherrenopensource@gmail.com>
Diff between stochtree versions 0.1.1 dated 2025-02-08 and 0.2.0 dated 2025-11-22
stochtree-0.1.1/stochtree/src/Makevars |only stochtree-0.2.0/stochtree/DESCRIPTION | 10 stochtree-0.2.0/stochtree/MD5 | 222 stochtree-0.2.0/stochtree/NAMESPACE | 15 stochtree-0.2.0/stochtree/NEWS.md | 43 stochtree-0.2.0/stochtree/R/bart.R | 4293 ++++--- stochtree-0.2.0/stochtree/R/bcf.R | 6130 ++++++---- stochtree-0.2.0/stochtree/R/calibration.R | 36 stochtree-0.2.0/stochtree/R/config.R | 826 - stochtree-0.2.0/stochtree/R/cpp11.R | 100 stochtree-0.2.0/stochtree/R/data.R | 520 stochtree-0.2.0/stochtree/R/forest.R | 2091 ++- stochtree-0.2.0/stochtree/R/generics.R | 8 stochtree-0.2.0/stochtree/R/kernel.R | 481 stochtree-0.2.0/stochtree/R/model.R | 525 stochtree-0.2.0/stochtree/R/posterior_transformation.R |only stochtree-0.2.0/stochtree/R/random_effects.R | 845 - stochtree-0.2.0/stochtree/R/serialization.R | 1106 + stochtree-0.2.0/stochtree/R/stochtree-package.R | 7 stochtree-0.2.0/stochtree/R/utils.R | 1469 +- stochtree-0.2.0/stochtree/R/variance.R | 22 stochtree-0.2.0/stochtree/README.md | 2 stochtree-0.2.0/stochtree/cleanup |only stochtree-0.2.0/stochtree/configure |only stochtree-0.2.0/stochtree/configure.ac |only stochtree-0.2.0/stochtree/configure.win |only stochtree-0.2.0/stochtree/inst/COPYRIGHTS | 7 stochtree-0.2.0/stochtree/man/Forest.Rd | 54 stochtree-0.2.0/stochtree/man/ForestDataset.Rd | 62 stochtree-0.2.0/stochtree/man/ForestModel.Rd | 73 stochtree-0.2.0/stochtree/man/ForestModelConfig.Rd | 134 stochtree-0.2.0/stochtree/man/ForestSamples.Rd | 83 stochtree-0.2.0/stochtree/man/RandomEffectSamples.Rd | 17 stochtree-0.2.0/stochtree/man/RandomEffectsDataset.Rd | 97 stochtree-0.2.0/stochtree/man/bart.Rd | 31 stochtree-0.2.0/stochtree/man/bcf.Rd | 52 stochtree-0.2.0/stochtree/man/computeForestLeafIndices.Rd | 5 stochtree-0.2.0/stochtree/man/computeForestMaxLeafIndex.Rd | 15 stochtree-0.2.0/stochtree/man/compute_bart_posterior_interval.Rd |only stochtree-0.2.0/stochtree/man/compute_bcf_posterior_interval.Rd |only stochtree-0.2.0/stochtree/man/compute_contrast_bart_model.Rd |only stochtree-0.2.0/stochtree/man/compute_contrast_bcf_model.Rd |only stochtree-0.2.0/stochtree/man/createBARTModelFromCombinedJson.Rd | 8 stochtree-0.2.0/stochtree/man/createBARTModelFromCombinedJsonString.Rd | 8 stochtree-0.2.0/stochtree/man/createBARTModelFromJson.Rd | 8 stochtree-0.2.0/stochtree/man/createBARTModelFromJsonFile.Rd | 8 stochtree-0.2.0/stochtree/man/createBARTModelFromJsonString.Rd | 10 stochtree-0.2.0/stochtree/man/createBCFModelFromCombinedJson.Rd | 30 stochtree-0.2.0/stochtree/man/createBCFModelFromCombinedJsonString.Rd | 30 stochtree-0.2.0/stochtree/man/createBCFModelFromJson.Rd | 38 stochtree-0.2.0/stochtree/man/createBCFModelFromJsonFile.Rd | 38 stochtree-0.2.0/stochtree/man/createBCFModelFromJsonString.Rd | 30 stochtree-0.2.0/stochtree/man/createForestModel.Rd | 8 stochtree-0.2.0/stochtree/man/createForestModelConfig.Rd | 8 stochtree-0.2.0/stochtree/man/expand_dims_1d.Rd |only stochtree-0.2.0/stochtree/man/expand_dims_2d.Rd |only stochtree-0.2.0/stochtree/man/expand_dims_2d_diag.Rd |only stochtree-0.2.0/stochtree/man/getRandomEffectSamples.bartmodel.Rd | 16 stochtree-0.2.0/stochtree/man/getRandomEffectSamples.bcfmodel.Rd | 38 stochtree-0.2.0/stochtree/man/loadVectorJson.Rd | 2 stochtree-0.2.0/stochtree/man/predict.bartmodel.Rd | 22 stochtree-0.2.0/stochtree/man/predict.bcfmodel.Rd | 35 stochtree-0.2.0/stochtree/man/preprocessPredictionData.Rd | 8 stochtree-0.2.0/stochtree/man/preprocessTrainData.Rd | 6 stochtree-0.2.0/stochtree/man/resetForestModel.Rd | 22 stochtree-0.2.0/stochtree/man/resetRandomEffectsModel.Rd | 4 stochtree-0.2.0/stochtree/man/resetRandomEffectsTracker.Rd | 4 stochtree-0.2.0/stochtree/man/rootResetRandomEffectsModel.Rd | 4 stochtree-0.2.0/stochtree/man/rootResetRandomEffectsTracker.Rd | 4 stochtree-0.2.0/stochtree/man/sample_bart_posterior_predictive.Rd |only stochtree-0.2.0/stochtree/man/sample_bcf_posterior_predictive.Rd |only stochtree-0.2.0/stochtree/man/sample_without_replacement.Rd |only stochtree-0.2.0/stochtree/man/saveBARTModelToJson.Rd | 8 stochtree-0.2.0/stochtree/man/saveBARTModelToJsonFile.Rd | 8 stochtree-0.2.0/stochtree/man/saveBARTModelToJsonString.Rd | 8 stochtree-0.2.0/stochtree/man/saveBCFModelToJson.Rd | 38 stochtree-0.2.0/stochtree/man/saveBCFModelToJsonFile.Rd | 38 stochtree-0.2.0/stochtree/man/saveBCFModelToJsonString.Rd | 38 stochtree-0.2.0/stochtree/src/Makevars.in |only stochtree-0.2.0/stochtree/src/Makevars.win.in |only stochtree-0.2.0/stochtree/src/R_data.cpp | 126 stochtree-0.2.0/stochtree/src/R_random_effects.cpp | 8 stochtree-0.2.0/stochtree/src/container.cpp | 4 stochtree-0.2.0/stochtree/src/cpp11.cpp | 210 stochtree-0.2.0/stochtree/src/cutpoint_candidates.cpp | 1 stochtree-0.2.0/stochtree/src/data.cpp | 4 stochtree-0.2.0/stochtree/src/forest.cpp | 47 stochtree-0.2.0/stochtree/src/include/stochtree/category_tracker.h | 4 stochtree-0.2.0/stochtree/src/include/stochtree/common.h | 4 stochtree-0.2.0/stochtree/src/include/stochtree/container.h | 32 stochtree-0.2.0/stochtree/src/include/stochtree/cutpoint_candidates.h | 2 stochtree-0.2.0/stochtree/src/include/stochtree/data.h | 63 stochtree-0.2.0/stochtree/src/include/stochtree/discrete_sampler.h |only stochtree-0.2.0/stochtree/src/include/stochtree/ensemble.h | 54 stochtree-0.2.0/stochtree/src/include/stochtree/io.h | 2 stochtree-0.2.0/stochtree/src/include/stochtree/leaf_model.h | 148 stochtree-0.2.0/stochtree/src/include/stochtree/log.h | 2 stochtree-0.2.0/stochtree/src/include/stochtree/mainpage.h | 2 stochtree-0.2.0/stochtree/src/include/stochtree/meta.h | 1 stochtree-0.2.0/stochtree/src/include/stochtree/openmp_utils.h |only stochtree-0.2.0/stochtree/src/include/stochtree/partition_tracker.h | 31 stochtree-0.2.0/stochtree/src/include/stochtree/random.h | 1 stochtree-0.2.0/stochtree/src/include/stochtree/random_effects.h | 57 stochtree-0.2.0/stochtree/src/include/stochtree/tree.h | 37 stochtree-0.2.0/stochtree/src/include/stochtree/tree_sampler.h | 387 stochtree-0.2.0/stochtree/src/include/stochtree/variance_model.h | 6 stochtree-0.2.0/stochtree/src/io.cpp | 2 stochtree-0.2.0/stochtree/src/kernel.cpp | 4 stochtree-0.2.0/stochtree/src/partition_tracker.cpp | 10 stochtree-0.2.0/stochtree/src/sampler.cpp | 111 stochtree-0.2.0/stochtree/src/serialization.cpp | 3 stochtree-0.2.0/stochtree/src/stochtree_types.h | 1 stochtree-0.2.0/stochtree/src/tree.cpp | 4 stochtree-0.2.0/stochtree/tests/testthat/test-bart.R | 895 + stochtree-0.2.0/stochtree/tests/testthat/test-bcf.R | 1203 + stochtree-0.2.0/stochtree/tests/testthat/test-categorical.R | 237 stochtree-0.2.0/stochtree/tests/testthat/test-data-preprocessing.R | 74 stochtree-0.2.0/stochtree/tests/testthat/test-dataset.R |only stochtree-0.2.0/stochtree/tests/testthat/test-forest-container.R |only stochtree-0.2.0/stochtree/tests/testthat/test-forest.R |only stochtree-0.2.0/stochtree/tests/testthat/test-predict.R | 567 stochtree-0.2.0/stochtree/tests/testthat/test-residual.R | 189 stochtree-0.2.0/stochtree/tests/testthat/test-serialization.R | 317 stochtree-0.2.0/stochtree/tests/testthat/test-utils.R |only 124 files changed, 16287 insertions(+), 8471 deletions(-)
Title: Creates Statistical Reports
Description: Contains functions to create regulatory-style statistical reports.
Originally designed to create tables, listings, and figures for the
pharmaceutical, biotechnology, and medical device industries, these
reports are generalized enough that they could be used in any industry.
Generates text, rich-text, PDF, HTML, and Microsoft Word file formats.
The package specializes
in printing wide and long tables with automatic page wrapping and splitting.
Reports can be produced with a minimum of function calls, and without
relying on other table packages. The package supports titles, footnotes,
page header, page footers, spanning headers, page by variables,
and automatic page numbering.
Author: David Bosak [aut, cre],
Bill Huang [aut],
Kevin Kramer [ctb],
Duong Tran [ctb],
Raphael Huang [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between reporter versions 1.4.4 dated 2024-03-19 and 1.4.5 dated 2025-11-22
DESCRIPTION | 12 - MD5 | 195 ++++++++++++------------ NEWS.md | 12 + R/create_style.R | 4 R/create_table_docx.R | 157 ++++++++++++++++++- R/create_table_html.R | 133 ++++++++++++++-- R/create_table_pdf.R | 33 +++- R/create_table_rtf.R | 191 ++++++++++++++++++++++- R/create_table_text.R | 2 R/page_template_docx.R | 35 +++- R/page_template_html.R | 24 ++ R/page_template_pdf.R | 77 +++++++-- R/page_template_rtf.R | 25 ++- R/plot_spec.R | 40 +++- R/report_spec.r | 39 +++- R/sizing_functions.R | 170 ++++++++++++++++---- R/table_spec.r | 7 R/utilities.R | 141 ++++++++++++----- R/write_docx.R | 40 ++++ R/write_report_docx.R | 20 +- README.md | 3 build/vignette.rds |binary inst/doc/reporter-break.Rmd | 6 inst/doc/reporter-break.html | 7 inst/doc/reporter-faq.Rmd | 16 + inst/doc/reporter-faq.html | 17 ++ inst/doc/reporter-figure.Rmd | 2 inst/doc/reporter-figure.html | 3 inst/doc/reporter-fonts.Rmd | 2 inst/doc/reporter-fonts.html | 3 inst/doc/reporter-listing.Rmd | 6 inst/doc/reporter-listing.html | 6 inst/doc/reporter-pageby.Rmd | 6 inst/doc/reporter-pageby.html | 6 inst/doc/reporter-rtf.Rmd | 2 inst/doc/reporter-rtf.html | 3 inst/doc/reporter-spanning.Rmd | 2 inst/doc/reporter-spanning.html | 3 inst/doc/reporter-stub.Rmd | 2 inst/doc/reporter-stub.html | 3 inst/doc/reporter-styles.Rmd | 22 +- inst/doc/reporter-styles.html | 23 +- inst/doc/reporter-super.Rmd | 4 inst/doc/reporter-super.html | 5 inst/doc/reporter-table.Rmd | 2 inst/doc/reporter-table.html | 3 inst/doc/reporter-text.Rmd | 2 inst/doc/reporter-text.html | 3 inst/doc/reporter-title_header.Rmd | 2 inst/doc/reporter-title_header.html | 3 inst/doc/reporter-wrap.Rmd | 4 inst/doc/reporter-wrap.html | 5 inst/doc/reporter.R | 2 inst/doc/reporter.Rmd | 2 inst/doc/reporter.html | 3 man/create_plot.Rd | 16 + man/create_report.Rd | 8 man/define.Rd | 4 man/footnotes.Rd | 10 - man/reporter.Rd | 5 tests/testthat/data/pdf2_81_input.rds |only tests/testthat/docx/example10.emf |only tests/testthat/docx/test14.docx |only tests/testthat/docx/test20.docx |only tests/testthat/docx/test20.jpg |binary tests/testthat/docx/test57.zip |only tests/testthat/test-create_table_docx.R | 11 + tests/testthat/test-create_table_html.R | 8 tests/testthat/test-create_table_pdf.R | 27 +++ tests/testthat/test-create_table_rtf.R | 17 +- tests/testthat/test-docx.R | 232 ++++++++++++++++++++++++++++ tests/testthat/test-html.R | 140 +++++++++++++++++ tests/testthat/test-page_template_docx.R | 251 ++++++++++++++++++------------- tests/testthat/test-page_template_html.R | 64 +++++++ tests/testthat/test-page_template_pdf.R | 27 +++ tests/testthat/test-page_template_rtf.R | 69 ++++++++ tests/testthat/test-pdf.R | 183 ++++++++++++++++++---- tests/testthat/test-pdf2.R | 160 +++++++++++++++++++ tests/testthat/test-rtf.R | 229 +++++++++++++++++++++++----- tests/testthat/test-rtf2.R | 135 ++++++++++++++++ tests/testthat/test-sizing_functions.R | 83 +++++++++- tests/testthat/test-system.R | 114 +++++++++++++- tests/testthat/test-user.R | 13 - tests/testthat/test-utilities.R | 69 ++++++++ tests/testthat/test-write_docx.R | 18 ++ vignettes/reporter-break.Rmd | 6 vignettes/reporter-faq.Rmd | 16 + vignettes/reporter-figure.Rmd | 2 vignettes/reporter-fonts.Rmd | 2 vignettes/reporter-listing.Rmd | 6 vignettes/reporter-pageby.Rmd | 6 vignettes/reporter-rtf.Rmd | 2 vignettes/reporter-spanning.Rmd | 2 vignettes/reporter-stub.Rmd | 2 vignettes/reporter-styles.Rmd | 22 +- vignettes/reporter-super.Rmd | 4 vignettes/reporter-table.Rmd | 2 vignettes/reporter-text.Rmd | 2 vignettes/reporter-title_header.Rmd | 2 vignettes/reporter-wrap.Rmd | 4 vignettes/reporter.Rmd | 2 101 files changed, 2898 insertions(+), 617 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library aiming towards
a good balance between speed and ease of use. It provides high-level syntax and
functionality deliberately similar to Matlab. It is useful for algorithm development
directly in C++, or quick conversion of research code into production environments.
It provides efficient classes for vectors, matrices and cubes where dense and sparse
matrices are supported. Integer, floating point and complex numbers are supported.
A sophisticated expression evaluator (based on template meta-programming) automatically
combines several operations to increase speed and efficiency. Dynamic evaluation
automatically chooses optimal code paths based on detected matrix structures.
Matrix decompositions are provided through integration with LAPACK, or one of its
high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can
automatically use 'OpenMP' multi-threading (parallelisation) to speed up
computationally expensive operations [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 15.0.2-2 dated 2025-09-19 and 15.2.2-1 dated 2025-11-22
ChangeLog | 78 + DESCRIPTION | 8 MD5 | 315 +++--- NAMESPACE | 1 R/RcppExports.R | 9 R/inline.R | 5 README.md | 17 build/partial.rdb |binary build/vignette.rds |binary configure | 333 +++--- configure.ac | 264 ++--- inst/NEWS.Rd | 38 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/RcppArmadillo/config/RcppArmadilloConfig.h | 13 inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h.in | 21 inst/include/current/armadillo | 1 inst/include/current/armadillo_bits/Base_meat.hpp | 8 inst/include/current/armadillo_bits/Col_bones.hpp | 7 inst/include/current/armadillo_bits/Col_meat.hpp | 44 inst/include/current/armadillo_bits/Cube_meat.hpp | 2 inst/include/current/armadillo_bits/Mat_bones.hpp | 31 inst/include/current/armadillo_bits/Mat_meat.hpp | 503 +++++++++- inst/include/current/armadillo_bits/Row_bones.hpp | 10 inst/include/current/armadillo_bits/Row_meat.hpp | 51 - inst/include/current/armadillo_bits/SpMat_bones.hpp | 4 inst/include/current/armadillo_bits/SpMat_meat.hpp | 4 inst/include/current/armadillo_bits/arma_forward.hpp | 4 inst/include/current/armadillo_bits/arma_rng.hpp | 127 ++ inst/include/current/armadillo_bits/arma_version.hpp | 4 inst/include/current/armadillo_bits/constants.hpp | 6 inst/include/current/armadillo_bits/distr_param.hpp | 20 inst/include/current/armadillo_bits/field_meat.hpp | 2 inst/include/current/armadillo_bits/fn_all.hpp | 6 inst/include/current/armadillo_bits/fn_any.hpp | 6 inst/include/current/armadillo_bits/fn_circshift.hpp | 18 inst/include/current/armadillo_bits/fn_cumprod.hpp | 8 inst/include/current/armadillo_bits/fn_cumsum.hpp | 8 inst/include/current/armadillo_bits/fn_det.hpp | 2 inst/include/current/armadillo_bits/fn_diagmat.hpp | 4 inst/include/current/armadillo_bits/fn_diagvec.hpp | 6 inst/include/current/armadillo_bits/fn_diff.hpp | 6 inst/include/current/armadillo_bits/fn_expmat.hpp | 2 inst/include/current/armadillo_bits/fn_flip.hpp | 8 inst/include/current/armadillo_bits/fn_hist.hpp | 6 inst/include/current/armadillo_bits/fn_histc.hpp | 4 inst/include/current/armadillo_bits/fn_index_max.hpp | 6 inst/include/current/armadillo_bits/fn_index_min.hpp | 6 inst/include/current/armadillo_bits/fn_kron.hpp | 4 inst/include/current/armadillo_bits/fn_logmat.hpp | 6 inst/include/current/armadillo_bits/fn_max.hpp | 12 inst/include/current/armadillo_bits/fn_mean.hpp | 8 inst/include/current/armadillo_bits/fn_median.hpp | 6 inst/include/current/armadillo_bits/fn_min.hpp | 12 inst/include/current/armadillo_bits/fn_normalise.hpp | 2 inst/include/current/armadillo_bits/fn_orth_null.hpp | 4 inst/include/current/armadillo_bits/fn_prod.hpp | 13 inst/include/current/armadillo_bits/fn_quantile.hpp | 4 inst/include/current/armadillo_bits/fn_rande.hpp |only inst/include/current/armadillo_bits/fn_range.hpp | 4 inst/include/current/armadillo_bits/fn_repelem.hpp | 4 inst/include/current/armadillo_bits/fn_shuffle.hpp | 6 inst/include/current/armadillo_bits/fn_sort.hpp | 4 inst/include/current/armadillo_bits/fn_sort_index.hpp | 4 inst/include/current/armadillo_bits/fn_sqrtmat.hpp | 6 inst/include/current/armadillo_bits/fn_symmat.hpp | 16 inst/include/current/armadillo_bits/glue_join_bones.hpp | 10 inst/include/current/armadillo_bits/glue_join_meat.hpp | 118 +- inst/include/current/armadillo_bits/glue_kron_bones.hpp | 4 inst/include/current/armadillo_bits/glue_kron_meat.hpp | 25 inst/include/current/armadillo_bits/glue_polyfit_bones.hpp | 4 inst/include/current/armadillo_bits/glue_polyfit_meat.hpp | 61 + inst/include/current/armadillo_bits/glue_polyval_bones.hpp | 3 inst/include/current/armadillo_bits/glue_polyval_meat.hpp | 36 inst/include/current/armadillo_bits/glue_quantile_bones.hpp | 6 inst/include/current/armadillo_bits/glue_quantile_meat.hpp | 44 inst/include/current/armadillo_bits/glue_times_bones.hpp | 29 inst/include/current/armadillo_bits/glue_times_meat.hpp | 82 + inst/include/current/armadillo_bits/glue_trapz_bones.hpp | 4 inst/include/current/armadillo_bits/glue_trapz_meat.hpp | 37 inst/include/current/armadillo_bits/op_accu_bones.hpp | 6 inst/include/current/armadillo_bits/op_accu_meat.hpp | 98 + inst/include/current/armadillo_bits/op_all_meat.hpp | 2 inst/include/current/armadillo_bits/op_any_meat.hpp | 2 inst/include/current/armadillo_bits/op_circshift_bones.hpp | 2 inst/include/current/armadillo_bits/op_circshift_meat.hpp | 23 inst/include/current/armadillo_bits/op_clamp_bones.hpp | 4 inst/include/current/armadillo_bits/op_clamp_meat.hpp | 65 - inst/include/current/armadillo_bits/op_cumprod_bones.hpp | 6 inst/include/current/armadillo_bits/op_cumprod_meat.hpp | 39 inst/include/current/armadillo_bits/op_cumsum_bones.hpp | 6 inst/include/current/armadillo_bits/op_cumsum_meat.hpp | 39 inst/include/current/armadillo_bits/op_diff_bones.hpp | 6 inst/include/current/armadillo_bits/op_diff_meat.hpp | 48 inst/include/current/armadillo_bits/op_flip_bones.hpp | 19 inst/include/current/armadillo_bits/op_flip_meat.hpp | 280 ++--- inst/include/current/armadillo_bits/op_htrans_bones.hpp | 6 inst/include/current/armadillo_bits/op_htrans_meat.hpp | 37 inst/include/current/armadillo_bits/op_max_bones.hpp | 3 inst/include/current/armadillo_bits/op_max_meat.hpp | 24 inst/include/current/armadillo_bits/op_mean_bones.hpp | 3 inst/include/current/armadillo_bits/op_mean_meat.hpp | 18 inst/include/current/armadillo_bits/op_median_bones.hpp | 3 inst/include/current/armadillo_bits/op_median_meat.hpp | 19 inst/include/current/armadillo_bits/op_min_bones.hpp | 3 inst/include/current/armadillo_bits/op_min_meat.hpp | 24 inst/include/current/armadillo_bits/op_nonzeros_bones.hpp | 3 inst/include/current/armadillo_bits/op_nonzeros_meat.hpp | 16 inst/include/current/armadillo_bits/op_repmat_bones.hpp | 2 inst/include/current/armadillo_bits/op_repmat_meat.hpp | 17 inst/include/current/armadillo_bits/op_reshape_bones.hpp | 2 inst/include/current/armadillo_bits/op_reshape_meat.hpp | 28 inst/include/current/armadillo_bits/op_reverse_bones.hpp | 6 inst/include/current/armadillo_bits/op_reverse_meat.hpp | 142 +- inst/include/current/armadillo_bits/op_sort_bones.hpp | 3 inst/include/current/armadillo_bits/op_sort_meat.hpp | 25 inst/include/current/armadillo_bits/op_stddev_bones.hpp | 3 inst/include/current/armadillo_bits/op_stddev_meat.hpp | 20 inst/include/current/armadillo_bits/op_strans_bones.hpp | 6 inst/include/current/armadillo_bits/op_strans_meat.hpp | 35 inst/include/current/armadillo_bits/op_sum_bones.hpp | 12 inst/include/current/armadillo_bits/op_sum_meat.hpp | 102 ++ inst/include/current/armadillo_bits/op_trimat_bones.hpp | 3 inst/include/current/armadillo_bits/op_trimat_meat.hpp | 25 inst/include/current/armadillo_bits/op_var_bones.hpp | 3 inst/include/current/armadillo_bits/op_var_meat.hpp | 20 inst/include/current/armadillo_bits/op_vectorise_bones.hpp | 4 inst/include/current/armadillo_bits/op_vectorise_meat.hpp | 48 inst/include/current/armadillo_bits/operator_ostream.hpp | 2 inst/include/current/armadillo_bits/spglue_join_bones.hpp | 6 inst/include/current/armadillo_bits/spglue_join_meat.hpp | 34 inst/include/current/armadillo_bits/spglue_kron_bones.hpp | 3 inst/include/current/armadillo_bits/spglue_kron_meat.hpp | 15 inst/include/current/armadillo_bits/spglue_minus_bones.hpp | 3 inst/include/current/armadillo_bits/spglue_minus_meat.hpp | 15 inst/include/current/armadillo_bits/spglue_plus_bones.hpp | 3 inst/include/current/armadillo_bits/spglue_plus_meat.hpp | 15 inst/include/current/armadillo_bits/spglue_schur_bones.hpp | 3 inst/include/current/armadillo_bits/spglue_schur_meat.hpp | 15 inst/include/current/armadillo_bits/spglue_times_bones.hpp | 6 inst/include/current/armadillo_bits/spglue_times_meat.hpp | 32 inst/include/current/armadillo_bits/spop_htrans_bones.hpp | 6 inst/include/current/armadillo_bits/spop_htrans_meat.hpp | 37 inst/include/current/armadillo_bits/spop_repmat_bones.hpp | 3 inst/include/current/armadillo_bits/spop_repmat_meat.hpp | 14 inst/include/current/armadillo_bits/spop_strans_bones.hpp | 6 inst/include/current/armadillo_bits/spop_strans_meat.hpp | 29 inst/include/current/armadillo_bits/spop_trimat_bones.hpp | 3 inst/include/current/armadillo_bits/spop_trimat_meat.hpp | 18 inst/include/current/armadillo_bits/subview_bones.hpp | 22 inst/include/current/armadillo_bits/subview_meat.hpp | 258 ++++- inst/include/current/armadillo_bits/unwrap.hpp | 24 inst/tinytest/test_Rlapack.R | 2 inst/tinytest/test_misc.R | 7 man/armadillo_version.Rd | 7 src/Makevars.in | 5 src/Makevars.win | 1 src/RcppArmadillo.cpp | 16 src/RcppExports.cpp | 11 159 files changed, 3368 insertions(+), 1167 deletions(-)
Title: Adaptive Multivariate Integration over Hypercubes
Description: R wrappers around the cubature C library of Steven
G. Johnson for adaptive multivariate integration over hypercubes
and the Cuba C library of Thomas Hahn for deterministic and
Monte Carlo integration. Scalar and vector interfaces for
cubature and Cuba routines are provided; the vector interfaces
are highly recommended as demonstrated in the package
vignette.
Author: Balasubramanian Narasimhan [aut, cre],
Manuel Koller [ctb],
Dirk Eddelbuettel [ctb],
Steven G. Johnson [aut],
Thomas Hahn [aut],
Annie Bouvier [aut],
Kien Kieu [aut],
Simen Gaure [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>
Diff between cubature versions 2.1.4 dated 2025-06-02 and 2.1.4-1 dated 2025-11-22
DESCRIPTION | 10 MD5 | 30 NEWS.md | 6 build/vignette.rds |binary inst/doc/cubature.R | 155 - inst/doc/cubature.Rmd | 159 - inst/doc/cubature.html | 1746 ++++++++++----------- inst/doc/version2.html | 41 src/Cuba/a.wasm |only src/Cuba/config.guess | 1802 ++++++++++++--------- src/Cuba/config.h.in | 57 src/Cuba/config.sub | 3173 ++++++++++++++++++++++---------------- src/Cuba/configure | 4031 ++++++++++++++++++++++++++----------------------- src/Cuba/configure.ac | 122 + src/Cuba/install-sh | 596 ++++--- src/Makevars.webr |only vignettes/cubature.Rmd | 159 - 17 files changed, 6712 insertions(+), 5375 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit()' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reducing adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>. See Kosmidis et al (2020) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bi [...truncated...]
Author: Ioannis Kosmidis [aut, cre] ,
Euloge Clovis Kenne Pagui [aut] ,
Federico Boiocchi [ctb],
Philipp Sterzinger [ctb] ,
Kjell Konis [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 1.0.0 dated 2025-08-29 and 1.0.1 dated 2025-11-22
DESCRIPTION | 8 MD5 | 52 ++--- NEWS.md | 24 ++ R/data.R | 2 R/expo.R | 8 R/mdyplFit.R | 318 ---------------------------------- R/ordinal_superiority.R | 2 R/plrtest.R | 6 R/se.R | 44 ++++ R/solve_se.R | 209 +++++++++------------- R/summary-mdyplFit.R |only README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/tinytest/test-mdyplFit.R | 2 inst/tinytest/test-se.R | 2 inst/tinytest/test-summary_mdyplFit.R | 10 - man/MultipleFeatures.Rd | 2 man/confint.mdyplFit.Rd | 15 - man/expo.brglmFit.Rd | 8 man/mdyplControl.Rd | 2 man/mdyplFit.Rd | 4 man/ordinal_superiority.bracl.Rd | 2 man/plrtest.mdyplFit.Rd | 10 - man/se0_ridge.Rd |only man/sloe.Rd | 2 man/solve_se.Rd | 18 + man/summary.mdyplFit.Rd | 55 +---- 28 files changed, 262 insertions(+), 547 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-05 1.0.4
2018-08-30 1.0.3
2018-07-10 1.0.2
2018-06-22 1.0.1
2018-06-06 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-10 1.0.0