Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Synthesize Bio [aut, cre]
Maintainer: Synthesize Bio <candace@synthesize.bio>
Diff between rsynthbio versions 3.0.2 dated 2025-10-29 and 4.0.0 dated 2025-12-03
rsynthbio-3.0.2/rsynthbio/R/data-handlers.R |only rsynthbio-3.0.2/rsynthbio/man/MODEL_MODALITIES.Rd |only rsynthbio-3.0.2/rsynthbio/man/MODEL_MODES.Rd |only rsynthbio-3.0.2/rsynthbio/man/extract_expression_data.Rd |only rsynthbio-3.0.2/rsynthbio/man/get_valid_modalities.Rd |only rsynthbio-3.0.2/rsynthbio/man/get_valid_modes.Rd |only rsynthbio-3.0.2/rsynthbio/man/get_valid_query.Rd |only rsynthbio-3.0.2/rsynthbio/man/log_cpm.Rd |only rsynthbio-3.0.2/rsynthbio/man/resolve_api_slug.Rd |only rsynthbio-3.0.2/rsynthbio/man/validate_modality.Rd |only rsynthbio-3.0.2/rsynthbio/man/validate_query.Rd |only rsynthbio-4.0.0/rsynthbio/DESCRIPTION | 20 rsynthbio-4.0.0/rsynthbio/MD5 | 55 - rsynthbio-4.0.0/rsynthbio/NAMESPACE | 10 rsynthbio-4.0.0/rsynthbio/NEWS.md | 52 - rsynthbio-4.0.0/rsynthbio/R/call_model_api.R | 349 ++------ rsynthbio-4.0.0/rsynthbio/R/output-transformers.R |only rsynthbio-4.0.0/rsynthbio/R/utils.R | 27 rsynthbio-4.0.0/rsynthbio/README.md | 48 - rsynthbio-4.0.0/rsynthbio/build/vignette.rds |binary rsynthbio-4.0.0/rsynthbio/inst/doc/getting-started.R | 52 - rsynthbio-4.0.0/rsynthbio/inst/doc/getting-started.Rmd | 89 -- rsynthbio-4.0.0/rsynthbio/inst/doc/getting-started.html | 89 -- rsynthbio-4.0.0/rsynthbio/man/OUTPUT_TRANSFORMERS.Rd |only rsynthbio-4.0.0/rsynthbio/man/default_output_transformer.Rd |only rsynthbio-4.0.0/rsynthbio/man/get_example_query.Rd |only rsynthbio-4.0.0/rsynthbio/man/get_output_transformer.Rd |only rsynthbio-4.0.0/rsynthbio/man/list_models.Rd |only rsynthbio-4.0.0/rsynthbio/man/make_api_request.Rd |only rsynthbio-4.0.0/rsynthbio/man/predict_query.Rd | 29 rsynthbio-4.0.0/rsynthbio/man/start_model_query.Rd | 4 rsynthbio-4.0.0/rsynthbio/man/transform_baseline_output.Rd |only rsynthbio-4.0.0/rsynthbio/tests/testthat/helper-mocks.R | 2 rsynthbio-4.0.0/rsynthbio/tests/testthat/test-call_model_api.R | 296 ++---- rsynthbio-4.0.0/rsynthbio/tests/testthat/test-data-handlers.R | 119 -- rsynthbio-4.0.0/rsynthbio/tests/testthat/test-integration-predict-metadata.R |only rsynthbio-4.0.0/rsynthbio/tests/testthat/test-integration-reference-conditioning.R |only rsynthbio-4.0.0/rsynthbio/tests/testthat/test-live-api.R | 433 +++------- rsynthbio-4.0.0/rsynthbio/vignettes/getting-started.Rmd | 89 -- 39 files changed, 582 insertions(+), 1181 deletions(-)
Title: Create Randomization Lists
Description: Randomization lists are an integral component of randomized clinical trials. 'randotools' provides tools to easily create such lists.
Author: Alan G Haynes [aut, cre]
Maintainer: Alan G Haynes <alan.haynes@unibe.ch>
Diff between randotools versions 0.2.3 dated 2025-11-07 and 0.2.4 dated 2025-12-03
DESCRIPTION | 6 MD5 | 42 +-- NEWS.md | 68 +++-- R/blockrand.R | 172 +++++++------- R/check_plan.R | 249 ++++++++++---------- R/imbalance_seq_plots.R | 356 +++++++++++++++--------------- R/imbalance_test.R | 320 +++++++++++++------------- R/imbalance_test_plot.R | 162 ++++++------- R/randolist.R | 186 +++++++-------- R/randolist_to_db.R | 190 ++++++++-------- README.md | 54 +++- tests/testthat/_snaps/randolist_to_db.md | 60 ++--- tests/testthat/_snaps/summary.md | 134 +++++------ tests/testthat/test-blockrand.R | 108 ++++----- tests/testthat/test-check_plan.R | 120 +++++----- tests/testthat/test-imbalance_seq_plots.R | 150 ++++++------ tests/testthat/test-imbalance_test.R | 218 +++++++++--------- tests/testthat/test-imbalance_test_plot.R | 146 ++++++------ tests/testthat/test-imbplot.R | 102 ++++---- tests/testthat/test-randolist.R | 126 +++++----- tests/testthat/test-randolist_to_db.R | 218 +++++++++--------- tests/testthat/test-summary.R | 182 +++++++-------- 22 files changed, 1709 insertions(+), 1660 deletions(-)
Title: Compact Inline Widgets for 'shiny' Apps
Description: Provides a basic set of compact widgets for 'shiny' apps which
occupy less space and can appear inline with surrounding text.
Author: Nick Davies [aut, cre]
Maintainer: Nick Davies <nicholas.davies@lshtm.ac.uk>
Diff between inshiny versions 0.1.0 dated 2025-09-09 and 0.1.1 dated 2025-12-03
inshiny-0.1.0/inshiny/tests/testthat/_snaps/action.md |only inshiny-0.1.1/inshiny/DESCRIPTION | 6 +-- inshiny-0.1.1/inshiny/MD5 | 17 ++++----- inshiny-0.1.1/inshiny/NEWS.md | 4 ++ inshiny-0.1.1/inshiny/R/action.R | 4 +- inshiny-0.1.1/inshiny/R/helper.R | 16 +++++++- inshiny-0.1.1/inshiny/README.md | 7 +++ inshiny-0.1.1/inshiny/inst/doc/inshiny.html | 10 +++-- inshiny-0.1.1/inshiny/tests/testthat/_snaps/shiny-1.10.0 |only inshiny-0.1.1/inshiny/tests/testthat/_snaps/shiny-1.12.0 |only inshiny-0.1.1/inshiny/tests/testthat/test-action.R | 28 +++++++++++---- 11 files changed, 67 insertions(+), 25 deletions(-)
Title: Bayesian Inference for Neyman-Scott Point Processes
Description: The Bayesian MCMC estimation of parameters for Thomas-type cluster
point process with various inhomogeneities. It allows for inhomogeneity in
(i) distribution of parent points, (ii) mean number of points in a cluster,
(iii) cluster spread. The package also allows for the Bayesian MCMC
algorithm for the homogeneous generalized Thomas process. The cluster size
is allowed to have a variance that is greater or less than the expected
value (cluster sizes are over or under dispersed). Details are described in
Dvořák, Remeš, Beránek & Mrkvička (2022) <arXiv: 10.48550/arXiv.2205.07946>.
Author: Mrkvicka Tomas [aut],
Dvorak Jiri [aut],
Beranek Ladislav [aut],
Remes Radim [aut, cre],
Park Jaewoo [ctb],
Lee Sujeong [ctb]
Maintainer: Remes Radim <inrem@jcu.cz>
Diff between binspp versions 0.2.2 dated 2025-05-05 and 0.2.3 dated 2025-12-03
binspp-0.2.2/binspp/R/rgenpois.R |only binspp-0.2.2/binspp/man/plot_outputs.Rd |only binspp-0.2.2/binspp/man/print_outputs.Rd |only binspp-0.2.2/binspp/man/print_outputs_internsp.Rd |only binspp-0.2.3/binspp/DESCRIPTION | 10 binspp-0.2.3/binspp/MD5 | 40 binspp-0.2.3/binspp/NAMESPACE | 14 binspp-0.2.3/binspp/R/binspp-package.R | 6 binspp-0.2.3/binspp/R/binspp_auxiliary.R | 2611 +++++++++++--------- binspp-0.2.3/binspp/R/estgtp.R | 354 +- binspp-0.2.3/binspp/R/estinternsp.R | 16 binspp-0.2.3/binspp/R/rgenp.R |only binspp-0.2.3/binspp/R/rgtp.R | 183 - binspp-0.2.3/binspp/build/partial.rdb |binary binspp-0.2.3/binspp/man/estgtp.Rd | 3 binspp-0.2.3/binspp/man/estinternsp.Rd | 2 binspp-0.2.3/binspp/man/estintp.Rd | 82 binspp-0.2.3/binspp/man/first_step.Rd | 23 binspp-0.2.3/binspp/man/plot.output_estintp.Rd |only binspp-0.2.3/binspp/man/print.output_estinternsp.Rd |only binspp-0.2.3/binspp/man/print.output_estintp.Rd |only binspp-0.2.3/binspp/man/rThomasInhom.Rd | 12 binspp-0.2.3/binspp/man/rawMCMCoutput.Rd |only binspp-0.2.3/binspp/man/re_estimate.Rd | 60 binspp-0.2.3/binspp/man/rgtp.Rd | 10 binspp-0.2.3/binspp/man/simulate.output_estintp.Rd |only 26 files changed, 1868 insertions(+), 1558 deletions(-)
Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.modules.general versions 0.5.1 dated 2025-10-22 and 0.6.0 dated 2025-12-03
teal.modules.general-0.5.1/teal.modules.general/tests/testthat/test-shinytest2-tm_misssing_data.R |only teal.modules.general-0.6.0/teal.modules.general/DESCRIPTION | 34 teal.modules.general-0.6.0/teal.modules.general/MD5 | 213 teal.modules.general-0.6.0/teal.modules.general/NAMESPACE | 71 teal.modules.general-0.6.0/teal.modules.general/NEWS.md | 732 +- teal.modules.general-0.6.0/teal.modules.general/R/geom_mosaic.R |only teal.modules.general-0.6.0/teal.modules.general/R/teal.modules.general.R | 35 teal.modules.general-0.6.0/teal.modules.general/R/tm_a_pca.R | 2295 +++---- teal.modules.general-0.6.0/teal.modules.general/R/tm_a_regression.R | 2083 +++---- teal.modules.general-0.6.0/teal.modules.general/R/tm_data_table.R | 698 +- teal.modules.general-0.6.0/teal.modules.general/R/tm_file_viewer.R | 513 - teal.modules.general-0.6.0/teal.modules.general/R/tm_front_page.R | 528 - teal.modules.general-0.6.0/teal.modules.general/R/tm_g_association.R | 1128 +-- teal.modules.general-0.6.0/teal.modules.general/R/tm_g_bivariate.R | 2201 +++---- teal.modules.general-0.6.0/teal.modules.general/R/tm_g_distribution.R | 2825 ++++----- teal.modules.general-0.6.0/teal.modules.general/R/tm_g_response.R | 1222 ++-- teal.modules.general-0.6.0/teal.modules.general/R/tm_g_scatterplot.R | 2166 +++---- teal.modules.general-0.6.0/teal.modules.general/R/tm_g_scatterplotmatrix.R | 1188 +--- teal.modules.general-0.6.0/teal.modules.general/R/tm_missing_data.R | 2894 +++++----- teal.modules.general-0.6.0/teal.modules.general/R/tm_outliers.R | 2715 ++++----- teal.modules.general-0.6.0/teal.modules.general/R/tm_rmarkdown.R |only teal.modules.general-0.6.0/teal.modules.general/R/tm_t_crosstable.R | 1003 +-- teal.modules.general-0.6.0/teal.modules.general/R/tm_variable_browser.R | 2616 ++++----- teal.modules.general-0.6.0/teal.modules.general/R/utils.R | 839 +- teal.modules.general-0.6.0/teal.modules.general/build/vignette.rds |binary teal.modules.general-0.6.0/teal.modules.general/inst/WORDLIST | 34 teal.modules.general-0.6.0/teal.modules.general/inst/doc/decorate-module-output.R | 840 +- teal.modules.general-0.6.0/teal.modules.general/inst/doc/decorate-module-output.html | 1750 +++--- teal.modules.general-0.6.0/teal.modules.general/inst/doc/teal-modules-general.R | 154 teal.modules.general-0.6.0/teal.modules.general/inst/doc/teal-modules-general.html | 998 +-- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-association-plot.R | 544 - teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-association-plot.html | 1320 ++-- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-bivariate-plot.R | 1182 ++-- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-bivariate-plot.html | 1958 +++--- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-cross-table.R | 224 teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-cross-table.html | 992 +-- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-data-table.R | 162 teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-data-table.html | 934 +-- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-outliers-module.R | 326 - teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-outliers-module.html | 1100 +-- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-regression-plots.R | 478 - teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-regression-plots.html | 1254 ++-- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-response-plot.R | 698 +- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-response-plot.html | 1474 ++--- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-scatterplot-matrix.R | 254 teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-scatterplot-matrix.html | 1032 +-- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-scatterplot.R | 686 +- teal.modules.general-0.6.0/teal.modules.general/inst/doc/using-scatterplot.html | 1462 ++--- teal.modules.general-0.6.0/teal.modules.general/inst/sample_files/co2_example.Rmd |only teal.modules.general-0.6.0/teal.modules.general/man/dot-markdown_internal.Rd |only teal.modules.general-0.6.0/teal.modules.general/man/dot-scale_x_mosaic.Rd |only teal.modules.general-0.6.0/teal.modules.general/man/filter_outliers.Rd |only teal.modules.general-0.6.0/teal.modules.general/man/geom_mosaic.Rd |only teal.modules.general-0.6.0/teal.modules.general/man/is_tab_active_js.Rd |only teal.modules.general-0.6.0/teal.modules.general/man/plot_var_summary.Rd | 10 teal.modules.general-0.6.0/teal.modules.general/man/set_chunk_attrs.Rd |only teal.modules.general-0.6.0/teal.modules.general/man/set_chunk_dims.Rd |only teal.modules.general-0.6.0/teal.modules.general/man/srv_decorate_teal_data.Rd | 71 teal.modules.general-0.6.0/teal.modules.general/man/tm_a_pca.Rd | 430 - 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teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_a_pca.R | 519 - teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_a_regression.R | 367 - teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_data_table.R | 206 teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_file_viewer.R | 208 teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_front_page.R | 144 teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_association.R | 229 teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_bivariate.R | 487 - teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_distribution.R | 254 teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_response.R | 227 teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_scatterplot.R | 412 - teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_scatterplotmatrix.R | 235 teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_missing_data.R |only teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_outliers.R | 646 +- teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_t_crosstable.R | 219 teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-shinytest2-tm_variable_browser.R | 469 - teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-tm_rmarkdown.R |only teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test-utils.R |only teal.modules.general-0.6.0/teal.modules.general/tests/testthat/test_bivariate_ggplot_call.R | 185 91 files changed, 29314 insertions(+), 29163 deletions(-)
More information about teal.modules.general at CRAN
Permanent link
Title: Spectroscopy Related Utilities
Description: Utility functions for spectroscopy. 1. Functions to simulate
spectra for use in teaching or testing. 2. Functions to process files created by
'LoggerPro' and 'SpectraSuite' software.
Author: Bryan A. Hanson [aut, cre]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between SpecHelpers versions 0.3.1 dated 2025-03-06 and 0.3.2 dated 2025-12-03
DESCRIPTION | 13 ++-- MD5 | 14 ++--- NEWS | 3 + R/multiplet.R | 151 +++++++++++++++++++++++++++++++++--------------------- R/sysdata.rda |binary build/partial.rdb |binary data/CIExyz.RData |binary man/multiplet.Rd | 13 ++++ 8 files changed, 125 insertions(+), 69 deletions(-)
Title: Constrained Single Index Model Estimation
Description: Estimation of function and index vector in single index model ('sim')
with (and w/o) shape constraints including different smoothness conditions.
See, e.g., Kuchibhotla and Patra (2020) <doi:10.3150/19-BEJ1183>.
Author: Arun Kumar Kuchibhotla [aut] ,
Rohit Kumar Patra [aut],
Martin Maechler [ctb, cre]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
This is a re-admission after prior archival of version 0.4 dated 2017-04-25
Diff between simest versions 0.4 dated 2017-04-25 and 0.4-1-1 dated 2025-12-03
simest-0.4-1-1/simest/DESCRIPTION | 37 ++ simest-0.4-1-1/simest/MD5 | 61 ++-- simest-0.4-1-1/simest/NAMESPACE | 39 +-- simest-0.4-1-1/simest/R/CvxLipReg.R |only simest-0.4-1-1/simest/R/CvxLseConReg.r | 70 ++--- simest-0.4-1-1/simest/R/CvxLseReg.r | 183 +++++++------- simest-0.4-1-1/simest/R/CvxPenReg.r | 146 +++++------ simest-0.4-1-1/simest/R/SimEst.r | 319 +++++++++++-------------- simest-0.4-1-1/simest/R/SimEstGcv.r | 127 ++++----- simest-0.4-1-1/simest/R/SmoothPenReg.r | 152 +++++------ simest-0.4-1-1/simest/R/SolvePenta.R |only simest-0.4-1-1/simest/R/merge.r | 38 +- simest-0.4-1-1/simest/README | 9 simest-0.4-1-1/simest/build |only simest-0.4-1-1/simest/inst/CITATION | 40 +-- simest-0.4-1-1/simest/inst/NEWS.Rd |only simest-0.4-1-1/simest/inst/TODO.md |only simest-0.4-1-1/simest/man/cpen.Rd |only simest-0.4-1-1/simest/man/cvx.lip.reg.Rd | 107 +++++--- simest-0.4-1-1/simest/man/cvx.lse.con.reg.Rd |only simest-0.4-1-1/simest/man/cvx.lse.reg.Rd | 106 +++++--- simest-0.4-1-1/simest/man/cvx.pen.reg.Rd | 102 ++++--- simest-0.4-1-1/simest/man/derivcvxpec.Rd | 8 simest-0.4-1-1/simest/man/fastmerge.Rd | 65 +++-- simest-0.4-1-1/simest/man/penta.Rd | 6 simest-0.4-1-1/simest/man/predcvxpen.Rd | 8 simest-0.4-1-1/simest/man/sim.est.Rd | 183 +++++++------- simest-0.4-1-1/simest/man/simest-deprecated.Rd |only simest-0.4-1-1/simest/man/simestgcv.Rd | 127 +++++---- simest-0.4-1-1/simest/man/smooth.pen.reg.Rd | 124 ++++++--- simest-0.4-1-1/simest/man/solve.pentadiag.Rd | 46 +-- simest-0.4-1-1/simest/man/spen_egcv.Rd | 9 simest-0.4-1-1/simest/tests |only simest-0.4/simest/R/CvxLipReg.r |only simest-0.4/simest/R/SolvePenta.r |only simest-0.4/simest/man/cpen.rd |only simest-0.4/simest/man/cvx.lse.con.reg.rd |only 37 files changed, 1125 insertions(+), 987 deletions(-)
Title: Radiation Safety
Description: Provides functions for radiation safety, also known as
"radiation protection" and "radiological control". The science of
radiation protection is called "health physics" and its engineering
functions are called "radiological engineering". Functions in this
package cover many of the computations needed by radiation safety
professionals. Examples include: obtaining updated calibration and
source check values for radiation monitors to account for radioactive
decay in a reference source, simulating instrument readings to better
understand measurement uncertainty, correcting instrument readings
for geometry and ambient atmospheric conditions. Many of these
functions are described in Johnson and Kirby (2011, ISBN-13:
978-1609134198). Utilities are also included for developing inputs
and processing outputs with radiation transport codes, such as MCNP,
a general-purpose Monte Carlo N-Particle code that can be used for
neutron, photon, electron, or coupled neutron/photon/electron transport
(Wern [...truncated...]
Author: Mark Hogue [aut, cre]
Maintainer: Mark Hogue <mark.hogue.chp@gmail.com>
Diff between radsafer versions 2.3.0 dated 2023-07-12 and 2.4.0 dated 2025-12-03
radsafer-2.3.0/radsafer/R/mcnp_si_sp_RD.R |only radsafer-2.3.0/radsafer/R/mcnp_si_sp_hist.R |only radsafer-2.3.0/radsafer/R/mcnp_si_sp_hist_scan.R |only radsafer-2.3.0/radsafer/man/mcnp_si_sp_RD.Rd |only radsafer-2.3.0/radsafer/man/mcnp_si_sp_hist.Rd |only radsafer-2.3.0/radsafer/man/mcnp_si_sp_hist_scan.Rd |only radsafer-2.4.0/radsafer/DESCRIPTION | 18 - radsafer-2.4.0/radsafer/MD5 | 88 ++--- radsafer-2.4.0/radsafer/NAMESPACE | 4 radsafer-2.4.0/radsafer/NEWS.md | 6 radsafer-2.4.0/radsafer/R/RN_plot_df.R |only radsafer-2.4.0/radsafer/R/RN_plot_search_results.R | 12 radsafer-2.4.0/radsafer/R/RN_plot_spectrum.R | 30 - radsafer-2.4.0/radsafer/R/RN_save_spectrum.R | 22 - radsafer-2.4.0/radsafer/R/mcnp_est_nps.R | 12 radsafer-2.4.0/radsafer/R/mcnp_matrix_rotations.R | 12 radsafer-2.4.0/radsafer/R/mcnp_mesh_bins.R | 4 radsafer-2.4.0/radsafer/R/mcnp_plot_out_spec.R | 2 radsafer-2.4.0/radsafer/R/mcnp_scan2plot.R | 18 - radsafer-2.4.0/radsafer/R/mcnp_scan_save.R | 24 - radsafer-2.4.0/radsafer/R/mcnp_sdef_erg_hist.R | 26 - radsafer-2.4.0/radsafer/R/mcnp_sdef_erg_line.R | 16 radsafer-2.4.0/radsafer/R/radsafer-package.R | 14 radsafer-2.4.0/radsafer/build/partial.rdb |binary radsafer-2.4.0/radsafer/build/vignette.rds |binary radsafer-2.4.0/radsafer/inst/doc/Introduction_to_radsafer.R | 2 radsafer-2.4.0/radsafer/inst/doc/Introduction_to_radsafer.html | 28 - radsafer-2.4.0/radsafer/man/RN_Spec_Act.Rd | 1 radsafer-2.4.0/radsafer/man/RN_bin_screen_phot.Rd | 141 ++++---- radsafer-2.4.0/radsafer/man/RN_index_screen.Rd | 1 radsafer-2.4.0/radsafer/man/RN_info.Rd | 1 radsafer-2.4.0/radsafer/man/RN_plot_df.Rd |only radsafer-2.4.0/radsafer/man/RN_plot_search_results.Rd | 11 radsafer-2.4.0/radsafer/man/RN_plot_spectrum.Rd | 3 radsafer-2.4.0/radsafer/man/RN_save_spectrum.Rd | 1 radsafer-2.4.0/radsafer/man/RN_search_alpha_by_E.Rd | 1 radsafer-2.4.0/radsafer/man/RN_search_beta_by_E.Rd | 1 radsafer-2.4.0/radsafer/man/RN_search_phot_by_E.Rd | 1 radsafer-2.4.0/radsafer/man/hvl.Rd | 46 +- radsafer-2.4.0/radsafer/man/mcnp_cone_angle.Rd | 5 radsafer-2.4.0/radsafer/man/mcnp_est_nps.Rd | 5 radsafer-2.4.0/radsafer/man/mcnp_matrix_rotations.Rd | 5 radsafer-2.4.0/radsafer/man/mcnp_mesh_bins.Rd | 149 ++++----- radsafer-2.4.0/radsafer/man/mcnp_plot_out_spec.Rd | 5 radsafer-2.4.0/radsafer/man/mcnp_scan2plot.Rd | 5 radsafer-2.4.0/radsafer/man/mcnp_scan_save.Rd | 5 radsafer-2.4.0/radsafer/man/mcnp_sdef_erg_hist.Rd | 115 +++---- radsafer-2.4.0/radsafer/man/mcnp_sdef_erg_line.Rd | 161 ++++------ radsafer-2.4.0/radsafer/man/radsafer-package.Rd | 42 +- 49 files changed, 523 insertions(+), 520 deletions(-)
Title: Additions and Extensions of the 'VGAM' Package
Description: Extending the functionalities of the 'VGAM' package with
additional functions and datasets. At present, 'VGAMextra'
comprises new family functions (ffs) to estimate several time
series models by maximum likelihood using Fisher scoring,
unlike popular packages in CRAN relying on optim(), including
ARMA-GARCH-like models, the Order-(p, d, q) ARIMAX model (non-
seasonal), the Order-(p) VAR model, error correction models
for cointegrated time series, and ARMA-structures with Student-t
errors. For independent data, new ffs to estimate the inverse-
Weibull, the inverse-gamma, the generalized beta of the second
kind and the general multivariate normal distributions are
available. In addition, 'VGAMextra' incorporates new VGLM-links
for the mean-function, and the quantile-function (as an alternative
to ordinary quantile modelling) of several 1-parameter distributions,
that are compatible with the class of VGLM/VGAM family functions.
Currently, only fixed-effects models are implemented. All fun [...truncated...]
Author: Victor Miranda [aut, cre, cph],
Thomas Yee [ctb, ths, cph]
Maintainer: Victor Miranda <victor.miranda@aut.ac.nz>
Diff between VGAMextra versions 0.0-8 dated 2025-08-21 and 0.0-9 dated 2025-12-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 9 +++++---- NEWS | 9 ++++++++- 4 files changed, 20 insertions(+), 12 deletions(-)
Title: Superefficient Estimation of Future Conditional Hazards Based on
Marker Information
Description: Provides univariate and indexed (multivariate) nonparametric smoothed kernel estimators for the future conditional hazard rate function when time-dependent covariates are present, a bandwidth selector for the estimator's implementation and pointwise and uniform confidence bands. Methods used in the package refer to Bagkavos, Isakson, Mammen, Nielsen and Proust-Lima (2025) <doi:10.1093/biomet/asaf008>.
Author: Dimitrios Bagkavos [aut, cre],
Alex Isakson [ctb],
Enno Mammen [ctb],
Jens Nielsen [ctb],
Cecile Proust-Lima [ctb]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between HQM versions 1.0 dated 2025-02-01 and 1.1 dated 2025-12-03
DESCRIPTION | 8 - MD5 | 50 +++++++-- NAMESPACE | 2 R/Boot.HRandIndex.param.R |only R/Boot.hqm.R |only R/BwB.HRandIndex.param.R |only R/Pivot.Index.CIs.R |only R/Quantile.Index.CIs.R |only R/Sim.True.Hazard.R |only R/SingleIndCondFutHaz.R |only R/StudentizedBwB.Index.CIs.R |only R/b_selection_index_optim.R |only R/index_optim.R |only R/lin_interpolate.R | 15 ++ R/lin_interpolate_plus.R |only R/prep_cv2.R |only build/partial.rdb |binary man/Boot.HRandIndex.param.Rd |only man/Boot.hqm.Rd |only man/BwB.HRandIndex.param.Rd |only man/Pivot.Index.CIs.Rd |only man/Quantile.Index.CIs.Rd |only man/Sim.True.Hazard.Rd |only man/SingleIndCondFutHaz.Rd |only man/StudentizedBwB.Index.CIs.Rd |only man/b_selection.Rd | 20 ++- man/b_selection_index_optim.Rd |only man/b_selection_prep_g.Rd | 8 - man/g_xt.Rd | 6 - man/get_h_x.Rd | 82 ++++++++++++++- man/get_h_xll.Rd | 112 +++++++++++++++++---- man/h_xt.Rd | 25 +++- man/h_xt_vec.Rd | 209 +++++++++++++++++++++++++++++++++++++++- man/h_xtll.Rd | 49 ++++++--- man/index_optim.Rd |only man/lin_interpolate_plus.Rd |only man/llK_b.Rd | 14 +- man/prep_cv2.Rd |only 38 files changed, 509 insertions(+), 91 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-26 2.4.1
2022-05-20 2.4
2022-04-27 2.3
2022-04-07 2.2
2021-09-13 2.1
2020-06-26 1.1
2019-01-09 1.0
Title: Density and Abundance from Distance-Sampling Surveys
Description: Distance-sampling (<doi:10.1007/978-3-319-19219-2>)
is a field survey and analytical method that estimates density and
abundance of survey targets (e.g., animals) when
detection probability declines with observation distance.
Distance-sampling is popular in ecology,
especially when survey targets are observed from aerial platforms (e.g.,
airplane or drone), surface vessels (e.g., boat or truck), or along
walking transects. Analysis involves fitting smooth (parametric) curves to
histograms of observation distances and using those functions to
adjust density estimates for missed targets. Routines included here
fit curves to observation distance histograms, estimate effective
sampling area, density of targets in surveyed areas, and the abundance
of targets in a surrounding study area. Confidence interval estimation
uses built-in bootstrap resampling. Help files are extensive and have been
vetted by multiple authors. Many tutorials are available on the package's
website (URL below).
Author: Trent McDonald [cre, aut],
Jason Carlisle [aut],
Aidan McDonald [aut] ,
Ryan Nielson [ctb] ,
Ben Augustine [ctb] ,
James Griswald [ctb] ,
Patrick McKann [ctb] ,
Lacey Jeroue [ctb] ,
Hoffman Abigail [ctb] ,
Kleinsausser Michael [ctb] ,
Joel Reynolds [ [...truncated...]
Maintainer: Trent McDonald <trent@mcdonalddatasciences.com>
Diff between Rdistance versions 4.0.5 dated 2025-04-10 and 4.1.1 dated 2025-12-03
Rdistance-4.0.5/Rdistance/R/likeParamNames.R |only Rdistance-4.0.5/Rdistance/R/secondDeriv.r |only Rdistance-4.1.1/Rdistance/DESCRIPTION | 44 - Rdistance-4.1.1/Rdistance/MD5 | 352 ++++++----- Rdistance-4.1.1/Rdistance/NAMESPACE | 47 - Rdistance-4.1.1/Rdistance/NEWS.md | 44 + Rdistance-4.1.1/Rdistance/R/AIC.dfunc.R | 7 Rdistance-4.1.1/Rdistance/R/EDR.R | 64 -- Rdistance-4.1.1/Rdistance/R/ESW.r | 86 -- Rdistance-4.1.1/Rdistance/R/HookesJeeves.R |only Rdistance-4.1.1/Rdistance/R/Nlminb.R |only Rdistance-4.1.1/Rdistance/R/Optim.R |only Rdistance-4.1.1/Rdistance/R/RdistDf.R | 6 Rdistance-4.1.1/Rdistance/R/RdistanceControls.R | 58 + Rdistance-4.1.1/Rdistance/R/abundEstim.R | 127 ++-- Rdistance-4.1.1/Rdistance/R/autoDistSamp.R | 16 Rdistance-4.1.1/Rdistance/R/bcCI.R | 3 Rdistance-4.1.1/Rdistance/R/bspline.expansion.R |only Rdistance-4.1.1/Rdistance/R/checkNEvalPts.R | 14 Rdistance-4.1.1/Rdistance/R/checkUnits.R | 50 - Rdistance-4.1.1/Rdistance/R/coef.dfunc.r | 5 Rdistance-4.1.1/Rdistance/R/colorize.R | 45 - Rdistance-4.1.1/Rdistance/R/cosine.expansion.R | 105 +-- Rdistance-4.1.1/Rdistance/R/dE.multi.R | 8 Rdistance-4.1.1/Rdistance/R/dE.single.R | 144 +++- Rdistance-4.1.1/Rdistance/R/dfuncEstim.R | 25 Rdistance-4.1.1/Rdistance/R/dfuncEstimErrMessage.R | 2 Rdistance-4.1.1/Rdistance/R/differentiableLikelihoods.R |only Rdistance-4.1.1/Rdistance/R/distances.R | 2 Rdistance-4.1.1/Rdistance/R/effectiveDistance.R | 27 Rdistance-4.1.1/Rdistance/R/effort.R | 2 Rdistance-4.1.1/Rdistance/R/errDataUnk.R | 2 Rdistance-4.1.1/Rdistance/R/estimateN.r | 50 - Rdistance-4.1.1/Rdistance/R/expansionTerms.R | 100 ++- Rdistance-4.1.1/Rdistance/R/groupSizes.R | 4 Rdistance-4.1.1/Rdistance/R/gxEstim.r | 15 Rdistance-4.1.1/Rdistance/R/halfnorm.like.R | 113 ++- Rdistance-4.1.1/Rdistance/R/halfnorm.start.limits.R | 10 Rdistance-4.1.1/Rdistance/R/hazrate.like.R | 52 - Rdistance-4.1.1/Rdistance/R/hazrate.start.limits.R | 17 Rdistance-4.1.1/Rdistance/R/hermite.expansion.R | 58 - Rdistance-4.1.1/Rdistance/R/insertOneStepBreaks.R |only Rdistance-4.1.1/Rdistance/R/integrateHalfnormLines.R |only Rdistance-4.1.1/Rdistance/R/integrateHalfnormPoints.R |only Rdistance-4.1.1/Rdistance/R/integrateHazrateLines.R |only Rdistance-4.1.1/Rdistance/R/integrateKey.R |only Rdistance-4.1.1/Rdistance/R/integrateNegexpLines.R |only Rdistance-4.1.1/Rdistance/R/integrateNegexpPoints.R |only Rdistance-4.1.1/Rdistance/R/integrateNumeric.R |only Rdistance-4.1.1/Rdistance/R/integrateOneStepLines.R |only Rdistance-4.1.1/Rdistance/R/integrateOneStepNumeric.R |only Rdistance-4.1.1/Rdistance/R/integrateOneStepPoints.R |only Rdistance-4.1.1/Rdistance/R/intercept.only.R | 6 Rdistance-4.1.1/Rdistance/R/is.RdistDf.R | 6 Rdistance-4.1.1/Rdistance/R/is.Unitless.R | 4 Rdistance-4.1.1/Rdistance/R/is.points.R | 4 Rdistance-4.1.1/Rdistance/R/is.smoothed.R | 4 Rdistance-4.1.1/Rdistance/R/likeParamNames.r |only Rdistance-4.1.1/Rdistance/R/lines.dfunc.R | 12 Rdistance-4.1.1/Rdistance/R/maximize.g.r | 20 Rdistance-4.1.1/Rdistance/R/mlEstimates.R | 78 -- Rdistance-4.1.1/Rdistance/R/model.matrix.dfunc.R | 3 Rdistance-4.1.1/Rdistance/R/nCovars.R | 4 Rdistance-4.1.1/Rdistance/R/nLL.R | 398 +++++++------ Rdistance-4.1.1/Rdistance/R/negexp.like.R | 21 Rdistance-4.1.1/Rdistance/R/negexp.start.limits.R | 11 Rdistance-4.1.1/Rdistance/R/observationType.R | 4 Rdistance-4.1.1/Rdistance/R/oneBsIter.R | 40 - Rdistance-4.1.1/Rdistance/R/oneStep.like.R |only Rdistance-4.1.1/Rdistance/R/oneStep.start.limits.R |only Rdistance-4.1.1/Rdistance/R/parseModel.R | 52 - Rdistance-4.1.1/Rdistance/R/plot.dfunc.para.R | 74 -- Rdistance-4.1.1/Rdistance/R/plot.dfunc.r | 17 Rdistance-4.1.1/Rdistance/R/predDensity.R | 8 Rdistance-4.1.1/Rdistance/R/predDfuncs.R | 45 + Rdistance-4.1.1/Rdistance/R/predLikelihood.R | 8 Rdistance-4.1.1/Rdistance/R/predict.dfunc.R | 43 - Rdistance-4.1.1/Rdistance/R/print.abund.r | 10 Rdistance-4.1.1/Rdistance/R/print.dfunc.r | 141 +++- Rdistance-4.1.1/Rdistance/R/secondDeriv.R |only Rdistance-4.1.1/Rdistance/R/simple.expansion.r | 55 - Rdistance-4.1.1/Rdistance/R/simpsonCoefs.R |only Rdistance-4.1.1/Rdistance/R/sine.expansion.R |only Rdistance-4.1.1/Rdistance/R/sparrowDetectionData.R | 5 Rdistance-4.1.1/Rdistance/R/sparrowDf.R | 5 Rdistance-4.1.1/Rdistance/R/sparrowDfuncObserver.R | 8 Rdistance-4.1.1/Rdistance/R/sparrowSiteData.R | 5 Rdistance-4.1.1/Rdistance/R/startLimits.R | 4 Rdistance-4.1.1/Rdistance/R/summary.abund.R | 13 Rdistance-4.1.1/Rdistance/R/summary.dfunc.R | 11 Rdistance-4.1.1/Rdistance/R/summary.rowwise_df.R | 34 - Rdistance-4.1.1/Rdistance/R/thrasherDetectionData.R | 5 Rdistance-4.1.1/Rdistance/R/thrasherDf.R | 5 Rdistance-4.1.1/Rdistance/R/thrasherSiteData.R | 7 Rdistance-4.1.1/Rdistance/R/transectType.R | 4 Rdistance-4.1.1/Rdistance/R/unitHelper_%#%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%acre%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%cm%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%ft%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%ha%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%inches%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%km%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%km^2%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%m%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%m^2%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%mi%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%mi^2%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_%yd%.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_dropUnits.R |only Rdistance-4.1.1/Rdistance/R/unitHelper_setUnits.R |only Rdistance-4.1.1/Rdistance/R/unnest.R | 2 Rdistance-4.1.1/Rdistance/R/varcovarEstim.R |only Rdistance-4.1.1/Rdistance/R/zzz.R | 24 Rdistance-4.1.1/Rdistance/build/partial.rdb |binary Rdistance-4.1.1/Rdistance/data/sparrowDfuncObserver.rda |binary Rdistance-4.1.1/Rdistance/man/AIC.dfunc.Rd | 3 Rdistance-4.1.1/Rdistance/man/EDR.Rd | 33 - Rdistance-4.1.1/Rdistance/man/ESW.Rd | 45 - Rdistance-4.1.1/Rdistance/man/HookeJeeves.Rd |only Rdistance-4.1.1/Rdistance/man/Nlminb.Rd |only Rdistance-4.1.1/Rdistance/man/Optim.Rd |only Rdistance-4.1.1/Rdistance/man/RdistDf.Rd | 13 Rdistance-4.1.1/Rdistance/man/Rdistance-package.Rd | 2 Rdistance-4.1.1/Rdistance/man/RdistanceControls.Rd | 58 + Rdistance-4.1.1/Rdistance/man/abundEstim.Rd | 10 Rdistance-4.1.1/Rdistance/man/autoDistSamp.Rd | 32 - Rdistance-4.1.1/Rdistance/man/bcCI.Rd | 2 Rdistance-4.1.1/Rdistance/man/bspline.expansion.Rd |only Rdistance-4.1.1/Rdistance/man/checkNEvalPts.Rd | 8 Rdistance-4.1.1/Rdistance/man/checkUnits.Rd | 2 Rdistance-4.1.1/Rdistance/man/coef.dfunc.Rd | 5 Rdistance-4.1.1/Rdistance/man/colorize.Rd | 90 +- Rdistance-4.1.1/Rdistance/man/cosine.expansion.Rd | 50 - Rdistance-4.1.1/Rdistance/man/dE.multi.Rd | 47 - Rdistance-4.1.1/Rdistance/man/dE.single.Rd | 75 +- Rdistance-4.1.1/Rdistance/man/dfuncEstim.Rd | 60 + Rdistance-4.1.1/Rdistance/man/dfuncEstimErrMessage.Rd | 2 Rdistance-4.1.1/Rdistance/man/differentiableLikelihoods.Rd |only Rdistance-4.1.1/Rdistance/man/distances.Rd | 2 Rdistance-4.1.1/Rdistance/man/effectiveDistance.Rd | 27 Rdistance-4.1.1/Rdistance/man/effort.Rd | 2 Rdistance-4.1.1/Rdistance/man/errDataUnk.Rd | 2 Rdistance-4.1.1/Rdistance/man/estimateN.Rd | 2 Rdistance-4.1.1/Rdistance/man/expansionTerms.Rd | 51 - Rdistance-4.1.1/Rdistance/man/groupSizes.Rd | 2 Rdistance-4.1.1/Rdistance/man/gxEstim.Rd | 7 Rdistance-4.1.1/Rdistance/man/halfnorm.like.Rd | 88 +- Rdistance-4.1.1/Rdistance/man/halfnorm.start.limits.Rd | 2 Rdistance-4.1.1/Rdistance/man/hazrate.like.Rd | 64 +- Rdistance-4.1.1/Rdistance/man/hazrate.start.limits.Rd | 2 Rdistance-4.1.1/Rdistance/man/hermite.expansion.Rd | 50 - Rdistance-4.1.1/Rdistance/man/insertOneStepBreaks.Rd |only Rdistance-4.1.1/Rdistance/man/integrateHalfnormLines.Rd |only Rdistance-4.1.1/Rdistance/man/integrateHalfnormPoints.Rd |only Rdistance-4.1.1/Rdistance/man/integrateHazrateLines.Rd |only Rdistance-4.1.1/Rdistance/man/integrateKey.Rd |only Rdistance-4.1.1/Rdistance/man/integrateNegexpLines.Rd |only Rdistance-4.1.1/Rdistance/man/integrateNegexpPoints.Rd |only Rdistance-4.1.1/Rdistance/man/integrateNumeric.Rd |only Rdistance-4.1.1/Rdistance/man/integrateOneStepLines.Rd |only Rdistance-4.1.1/Rdistance/man/integrateOneStepNumeric.Rd |only Rdistance-4.1.1/Rdistance/man/integrateOneStepPoints.Rd |only Rdistance-4.1.1/Rdistance/man/intercept.only.Rd | 2 Rdistance-4.1.1/Rdistance/man/is.RdistDf.Rd | 2 Rdistance-4.1.1/Rdistance/man/is.Unitless.Rd | 4 Rdistance-4.1.1/Rdistance/man/is.points.Rd | 2 Rdistance-4.1.1/Rdistance/man/is.smoothed.Rd | 2 Rdistance-4.1.1/Rdistance/man/likeParamNames.Rd | 68 +- Rdistance-4.1.1/Rdistance/man/lines.dfunc.Rd | 5 Rdistance-4.1.1/Rdistance/man/maximize.g.Rd | 3 Rdistance-4.1.1/Rdistance/man/mlEstimates.Rd | 2 Rdistance-4.1.1/Rdistance/man/model.matrix.dfunc.Rd | 2 Rdistance-4.1.1/Rdistance/man/nCovars.Rd | 2 Rdistance-4.1.1/Rdistance/man/nLL.Rd | 51 - Rdistance-4.1.1/Rdistance/man/negexp.like.Rd | 63 +- Rdistance-4.1.1/Rdistance/man/negexp.start.limits.Rd | 2 Rdistance-4.1.1/Rdistance/man/observationType.Rd | 2 Rdistance-4.1.1/Rdistance/man/oneBsIter.Rd | 49 + Rdistance-4.1.1/Rdistance/man/oneStep.like.Rd |only Rdistance-4.1.1/Rdistance/man/oneStep.start.limits.Rd |only Rdistance-4.1.1/Rdistance/man/parseModel.Rd | 68 +- Rdistance-4.1.1/Rdistance/man/plot.dfunc.Rd | 15 Rdistance-4.1.1/Rdistance/man/plot.dfunc.para.Rd | 8 Rdistance-4.1.1/Rdistance/man/predDensity.Rd | 2 Rdistance-4.1.1/Rdistance/man/predDfuncs.Rd | 2 Rdistance-4.1.1/Rdistance/man/predLikelihood.Rd | 2 Rdistance-4.1.1/Rdistance/man/predict.dfunc.Rd | 6 Rdistance-4.1.1/Rdistance/man/print.abund.Rd | 6 Rdistance-4.1.1/Rdistance/man/print.dfunc.Rd | 2 Rdistance-4.1.1/Rdistance/man/secondDeriv.Rd | 2 Rdistance-4.1.1/Rdistance/man/simple.expansion.Rd | 38 - Rdistance-4.1.1/Rdistance/man/simpsonCoefs.Rd |only Rdistance-4.1.1/Rdistance/man/sine.expansion.Rd |only Rdistance-4.1.1/Rdistance/man/sparrowDetectionData.Rd | 1 Rdistance-4.1.1/Rdistance/man/sparrowDf.Rd | 1 Rdistance-4.1.1/Rdistance/man/sparrowDfuncObserver.Rd | 4 Rdistance-4.1.1/Rdistance/man/sparrowSiteData.Rd | 1 Rdistance-4.1.1/Rdistance/man/startLimits.Rd | 3 Rdistance-4.1.1/Rdistance/man/summary.abund.Rd | 5 Rdistance-4.1.1/Rdistance/man/summary.dfunc.Rd | 1 Rdistance-4.1.1/Rdistance/man/summary.rowwise_df.Rd | 22 Rdistance-4.1.1/Rdistance/man/thrasherDetectionData.Rd | 1 Rdistance-4.1.1/Rdistance/man/thrasherDf.Rd | 1 Rdistance-4.1.1/Rdistance/man/thrasherSiteData.Rd | 3 Rdistance-4.1.1/Rdistance/man/transectType.Rd | 2 Rdistance-4.1.1/Rdistance/man/unitHelpers.Rd |only Rdistance-4.1.1/Rdistance/man/unnest.Rd | 2 Rdistance-4.1.1/Rdistance/man/varcovarEstim.Rd |only 208 files changed, 2293 insertions(+), 1908 deletions(-)
Title: Parametric Simplex Method for Sparse Learning
Description: Implements a unified framework of parametric simplex method for a variety of sparse learning problems (e.g., Dantzig selector (for linear regression), sparse quantile regression, sparse support vector machines, and compressive sensing) combined with efficient hyper-parameter selection strategies. The core algorithm is implemented in C++ with Eigen3 support for portable high performance linear algebra. For more details about parametric simplex method, see Haotian Pang (2017) <https://papers.nips.cc/paper/6623-parametric-simplex-method-for-sparse-learning.pdf>.
Author: Zichong Li [aut, cre],
Qianli Shen [aut]
Maintainer: Zichong Li <zichongli5@gmail.com>
Diff between PRIMAL versions 1.0.2 dated 2020-01-22 and 1.0.3 dated 2025-12-03
DESCRIPTION | 16 +++++++++++----- MD5 | 10 ++++++---- build |only inst/doc/vignette.pdf |binary src/Makevars | 3 +-- src/Makevars.win | 3 +-- src/init.c |only 7 files changed, 19 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-05 0.3.4
2015-01-16 0.3.3
2014-08-27 0.3.2
2014-04-25 0.3.1
2014-04-07 0.3
2014-03-04 0.2-6
2012-05-11 0.2-5
2012-04-01 0.2-3
2012-02-09 0.2-2
2012-02-02 0.2-1
2012-01-30 0.1-2
Title: Companion Application for the 'surveydown' Survey Platform
Description: Companion package that supports the 'surveydown' survey platform (<https://surveydown.org>). The default method for working with a 'surveydown' survey is to edit the plain text 'survey.qmd' and 'app.R' files. With 'sdstudio', you can create, preview and manage surveys with a 'shiny' application as a graphical user interface.
Author: Pingfan Hu [aut, cre, cph] ,
John Paul Helveston [aut, cph] ,
Bogdan Bunea [aut, cph]
Maintainer: Pingfan Hu <pingfan0727@gmail.com>
Diff between sdstudio versions 0.1.3 dated 2025-11-11 and 0.1.4 dated 2025-12-03
DESCRIPTION | 6 +-- MD5 | 10 +++--- NEWS.md | 17 +++++++++++ R/util.R | 15 +++------ README.md | 68 +++++++++++++++++++++++++++++++++++---------- tests/testthat/test-util.R | 13 +++----- 6 files changed, 89 insertions(+), 40 deletions(-)
Title: R Interface to the 'Yacas' Computer Algebra System
Description: Interface to the 'yacas' computer algebra system (<http://www.yacas.org/>).
Author: Mikkel Meyer Andersen [aut, cre, cph],
Rob Goedman [aut, cph],
Gabor Grothendieck [aut, cph],
Soeren Hoejsgaard [aut, cph],
Grzegorz Mazur [aut, cph],
Ayal Pinkus [aut, cph],
Nemanja Trifunovic [cph] )
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between Ryacas versions 1.1.5 dated 2023-01-16 and 1.1.6 dated 2025-12-03
DESCRIPTION | 9 - MD5 | 56 +++---- NAMESPACE | 1 R/ryacas-package.R | 3 R/yac-symbol.R | 23 ++ build/vignette.rds |binary inst/CITATION | 34 ++-- inst/NEWS | 5 inst/doc/arbitrary-precision.R | 4 inst/doc/arbitrary-precision.html | 146 +++++++++--------- inst/doc/getting-started.R | 14 - inst/doc/getting-started.html | 198 ++++++++++++------------- inst/doc/high-level.R | 2 inst/doc/high-level.html | 218 ++++++++++++++-------------- inst/doc/latent-variable-model.R | 6 inst/doc/latent-variable-model.html | 66 ++++---- inst/doc/low-level.R | 2 inst/doc/low-level.html | 240 +++++++++++++++---------------- inst/doc/ssm-matrix.R | 6 inst/doc/ssm-matrix.html | 130 ++++++++-------- inst/doc/yacas-rules.R | 2 inst/doc/yacas-rules.html | 26 +-- man/Ryacas-package.Rd | 28 +++ man/matrix_product.Rd |only man/pipe.Rd | 12 - src/yacas/include/yacas/utf8.h | 4 src/yacas/include/yacas/utf8/checked.h | 21 ++ src/yacas/include/yacas/utf8/core.h | 17 ++ src/yacas/include/yacas/utf8/cpp17.h |only src/yacas/include/yacas/utf8/unchecked.h | 7 30 files changed, 682 insertions(+), 598 deletions(-)
Title: Estimates of Standard Errors for Risk and Performance Measures
Description: Estimates of standard errors of popular risk and performance
measures for asset or portfolio returns using methods as described in
Chen and Martin (2021) <doi:10.21314/JOR.2020.446>.
Author: Anthony Christidis [aut, cre],
Xin Chen [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPESE versions 1.2.5 dated 2022-09-08 and 1.2.6 dated 2025-12-03
DESCRIPTION | 23 ++++++++++++++++------- MD5 | 8 ++++---- NEWS.md | 3 +++ README.md | 5 +++-- build/vignette.rds |binary 5 files changed, 26 insertions(+), 13 deletions(-)
Title: Interface to the Pan-STARRS API
Description: An interface to the API for 'Pan-STARRS1', a data archive of
the PS1 wide-field astronomical survey. The package allows access to
the PS1 catalog and to the PS1 images. (see
<https://outerspace.stsci.edu/display/PANSTARRS/> for more
information). You can use it to plan astronomical observations, make
guidance pictures, find magnitudes in five broadband filters (g, r, i,
z, y) and more.
Author: Grigory Uskov [cre, aut]
Maintainer: Grigory Uskov <uskov.russia@gmail.com>
Diff between panstarrs versions 0.2.2 dated 2024-05-02 and 0.2.3 dated 2025-12-03
DESCRIPTION | 11 ++++++----- LICENSE | 2 +- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/object_catalog_search.R | 22 ++++++++++++++++++++-- R/sysdata.rda |binary README.md | 2 +- build/vignette.rds |binary inst/doc/PS1_Cat.html | 7 ++++--- inst/doc/PS1_Images.html | 5 +++-- 10 files changed, 50 insertions(+), 23 deletions(-)
Title: Draw Samples of Truncated Multivariate Normal Distributions
Description: Draw samples from truncated multivariate normal distribution using the sequential nearest neighbor (SNN) method introduced in "Scalable Sampling of Truncated Multivariate Normals Using Sequential Nearest-Neighbor Approximation" <doi:10.48550/arXiv.2406.17307>.
Author: Jian Cao [aut, cre],
Matthias Katzfuss [aut]
Maintainer: Jian Cao <jcao2416@gmail.com>
Diff between nntmvn versions 1.2.0 dated 2025-02-08 and 1.3.0 dated 2025-12-03
DESCRIPTION | 11 ++++++----- MD5 | 10 ++++++++-- NAMESPACE | 9 +++++++++ NEWS.md |only R/check_screening.R |only man/plot.nntmvn_1stmmt_error.Rd |only man/plot.nntmvn_1stmmt_pred.Rd |only man/ptmvn_check_converge.Rd |only man/tmvn_check_converge.Rd |only 9 files changed, 23 insertions(+), 7 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 1.2.0 dated 2025-09-13 and 1.3.0 dated 2025-12-03
DESCRIPTION | 10 - MD5 | 194 ++++++++++++++-------------- NEWS.md | 14 ++ R/BenchmarkResult.R | 25 +-- R/DataBackendCbind.R | 2 R/DataBackendDataTable.R | 2 R/DataBackendRbind.R | 2 R/DataBackendRename.R | 4 R/HotstartStack.R | 8 - R/Learner.R | 30 ++-- R/LearnerClassif.R | 2 R/LearnerClassifDebug.R | 29 +--- R/LearnerClassifFeatureless.R | 4 R/LearnerClassifRpart.R | 4 R/LearnerRegr.R | 6 R/LearnerRegrDebug.R | 18 +- R/LearnerRegrFeatureless.R | 4 R/LearnerRegrRpart.R | 4 R/Measure.R | 75 ++++++++-- R/MeasureAIC.R | 6 R/MeasureBIC.R | 6 R/MeasureRegrPinball.R | 4 R/MeasureRegrRQR.R | 6 R/MeasureSelectedFeatures.R | 2 R/MeasureSimple.R | 69 +++++++-- R/Prediction.R | 25 ++- R/PredictionClassif.R | 27 +++ R/PredictionData.R | 4 R/PredictionDataClassif.R | 31 +++- R/PredictionDataRegr.R | 43 +++++- R/PredictionRegr.R | 24 +++ R/ResampleResult.R | 19 +- R/Resampling.R | 4 R/ResamplingCustomCV.R | 2 R/Task.R | 56 ++++---- R/TaskClassif.R | 8 - R/TaskRegr.R | 2 R/as_data_backend.R | 2 R/as_prediction_classif.R | 2 R/as_prediction_data.R | 3 R/as_result_data.R | 12 - R/as_task.R | 2 R/as_task_classif.R | 6 R/as_task_regr.R | 6 R/as_task_unsupervised.R | 2 R/assertions.R | 95 +++++++------ R/auto_convert.R | 2 R/benchmark.R | 10 - R/benchmark_grid.R | 10 - R/default_fallback.R | 12 - R/helper.R | 29 +--- R/helper_exec.R | 2 R/mlr_reflections.R | 5 R/partition.R | 2 R/predict.R | 4 R/resample.R | 2 R/set_validate.R | 2 R/warn_deprecated.R | 2 R/worker.R | 32 ++-- R/zzz.R | 17 ++ README.md | 8 - inst/testthat/helper_expectations.R | 14 +- man/BenchmarkResult.Rd | 12 - man/Measure.Rd | 56 +++++++- man/MeasureClassif.Rd | 3 man/MeasureRegr.Rd | 3 man/MeasureSimilarity.Rd | 3 man/Prediction.Rd | 15 +- man/PredictionClassif.Rd | 6 man/PredictionData.Rd | 3 man/PredictionRegr.Rd | 6 man/ResampleResult.Rd | 12 - man/mlr3-package.Rd | 23 +++ man/mlr_measures_aic.Rd | 3 man/mlr_measures_bic.Rd | 3 man/mlr_measures_classif.costs.Rd | 3 man/mlr_measures_debug_classif.Rd | 3 man/mlr_measures_elapsed_time.Rd | 3 man/mlr_measures_internal_valid_score.Rd | 3 man/mlr_measures_oob_error.Rd | 3 man/mlr_measures_regr.pinball.Rd | 3 man/mlr_measures_regr.rqr.Rd | 3 man/mlr_measures_regr.rsq.Rd | 3 man/mlr_measures_selected_features.Rd | 3 man/print.roc_measures.Rd | 2 tests/testthat/test_DataBackendRename.R | 8 - tests/testthat/test_Learner.R | 38 ++++- tests/testthat/test_Measure.R | 86 +++++++----- tests/testthat/test_PredictionClassif.R | 58 ++++++++ tests/testthat/test_PredictionDataClassif.R | 53 +++++++ tests/testthat/test_PredictionDataRegr.R | 49 +++++++ tests/testthat/test_PredictionRegr.R | 59 +++++++- tests/testthat/test_Task.R | 20 ++ tests/testthat/test_benchmark.R | 53 +++++-- tests/testthat/test_encapsulate.R | 2 tests/testthat/test_mlr_reflections.R | 1 tests/testthat/test_predict.R | 2 tests/testthat/test_resample.R | 42 +++--- 98 files changed, 1130 insertions(+), 576 deletions(-)
Title: Interval-Censored Sequence Kernel Association Test
Description: Implements the Interval-Censored Sequence Kernel Association (ICSKAT) test for testing the association between interval-censored time-to-event outcomes and groups of single nucleotide polymorphisms (SNPs). Interval-censored time-to-event data occur when the event time is not known exactly but can be deduced to fall within a given interval. For example, some medical conditions like bone mineral density deficiency are generally only diagnosed at clinical visits. If a patient goes for clinical checkups yearly and is diagnosed at, say, age 30, then the onset of the deficiency is only known to fall between the date of their age 29 checkup and the date of the age 30 checkup. Interval-censored data include right- and left-censored data as special cases. This package also implements the interval-censored Burden test and the ICSKATO test, which is the optimal combination of the ICSKAT and Burden tests. Please see the vignette for a quickstart guide. The paper describing these methods is " Infer [...truncated...]
Author: Ryan Sun [aut, cre],
Liang Zhu [aut]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Diff between ICSKAT versions 0.2.0 dated 2021-11-25 and 0.3.0 dated 2025-12-03
ICSKAT-0.2.0/ICSKAT/src/Makevars |only ICSKAT-0.2.0/ICSKAT/src/Makevars.win |only ICSKAT-0.3.0/ICSKAT/DESCRIPTION | 8 ICSKAT-0.3.0/ICSKAT/MD5 | 8 ICSKAT-0.3.0/ICSKAT/build/vignette.rds |binary ICSKAT-0.3.0/ICSKAT/inst/doc/ICSKAT_tutorial.html | 382 ++++++++++++++-------- 6 files changed, 255 insertions(+), 143 deletions(-)
Title: High-Dimensional Cure Models
Description: Provides functions for fitting various penalized parametric and semi-parametric mixture cure models with different penalty functions, testing for a significant cure fraction, and testing for sufficient follow-up as described in Fu et al (2022)<doi:10.1002/sim.9513> and Archer et al (2024)<doi:10.1186/s13045-024-01553-6>. False discovery rate controlled variable selection is provided using model-X knock-offs.
Author: Han Fu [aut],
Kellie J. Archer [aut, cre] ,
Tung Lam Nguyen [rev] ,
Panagiotis Papastamoulis [rev]
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between hdcuremodels versions 0.0.5 dated 2025-07-31 and 0.0.6 dated 2025-12-03
DESCRIPTION | 20 +- MD5 | 39 +++-- R/cv_cureem.R | 18 +- R/data.R | 221 ++++++++++++++++++++++++++++++- R/generate_cure_data.R | 26 ++- R/utils.R |only README.md | 12 + build/partial.rdb |only build/vignette.rds |binary data/pediatric_flt3.rda |only inst/CITATION | 2 inst/doc/hdcuremodels.R | 1 inst/doc/hdcuremodels.Rmd | 3 inst/doc/hdcuremodels.html | 11 + man/cv_cureem.Rd | 16 +- man/generate_cure_data.Rd | 9 + man/hdcuremodels-package.Rd |only man/pediatric_flt3.Rd |only tests/testthat/test-formula.R | 2 tests/testthat/test-generate_cure_data.R | 5 tests/testthat/test-logLik.R | 4 tests/testthat/test-nobs.R | 2 vignettes/hdcuremodels.Rmd | 3 23 files changed, 328 insertions(+), 66 deletions(-)
Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share
computation summaries rather than actual data over HTTP with a master R process (using
'opencpu', for example). A stratified Cox model and a singular value decomposition are
provided. The former makes direct use of code from the R 'survival' package. (That is,
the underlying Cox model code is derived from that in the R 'survival' package.)
Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
design allows for new methods to be added in the future and includes facilities
for local prototyping and testing. Web applications are provided (via 'shiny') for
the implemented methods to help in designing and deploying the computations.
Author: Balasubramanian Narasimhan [aut, cre],
Marina Bendersky [aut],
Sam Gross [aut],
Terry M. Therneau [ctb],
Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between distcomp versions 1.3-3 dated 2022-09-01 and 1.3-4 dated 2025-12-03
distcomp-1.3-3/distcomp/R/distcomp.R |only distcomp-1.3-3/distcomp/man/distcomp.Rd |only distcomp-1.3-4/distcomp/DESCRIPTION | 8 distcomp-1.3-4/distcomp/MD5 | 100 +-- distcomp-1.3-4/distcomp/NEWS.md | 12 distcomp-1.3-4/distcomp/R/distcomp-package.R |only distcomp-1.3-4/distcomp/R/master.R | 7 distcomp-1.3-4/distcomp/README.md | 2 distcomp-1.3-4/distcomp/build/vignette.rds |binary distcomp-1.3-4/distcomp/inst/doc/prototyping.html | 159 ++--- distcomp-1.3-4/distcomp/inst/ex/Rprofile |only distcomp-1.3-4/distcomp/inst/stuff |only distcomp-1.3-4/distcomp/man/HEQueryCountMaster.Rd | 2 distcomp-1.3-4/distcomp/man/HEQueryCountWorker.Rd | 2 distcomp-1.3-4/distcomp/man/availableComputations.Rd | 2 distcomp-1.3-4/distcomp/man/availableDataSources.Rd | 2 distcomp-1.3-4/distcomp/man/createHEWorkerInstance.Rd | 2 distcomp-1.3-4/distcomp/man/createNCPInstance.Rd | 2 distcomp-1.3-4/distcomp/man/createWorkerInstance.Rd | 2 distcomp-1.3-4/distcomp/man/defineNewComputation.Rd | 2 distcomp-1.3-4/distcomp/man/destroyInstanceObject.Rd | 2 distcomp-1.3-4/distcomp/man/distcomp-internal.Rd | 2 distcomp-1.3-4/distcomp/man/distcomp-package.Rd |only distcomp-1.3-4/distcomp/man/distcompSetup.Rd | 2 distcomp-1.3-4/distcomp/man/executeHEMethod.Rd | 2 distcomp-1.3-4/distcomp/man/executeMethod.Rd | 2 distcomp-1.3-4/distcomp/man/generateId.Rd | 2 distcomp-1.3-4/distcomp/man/getComputationInfo.Rd | 2 distcomp-1.3-4/distcomp/man/getConfig.Rd | 2 distcomp-1.3-4/distcomp/man/makeDefinition.Rd | 2 distcomp-1.3-4/distcomp/man/makeHEMaster.Rd | 2 distcomp-1.3-4/distcomp/man/makeMaster.Rd | 2 distcomp-1.3-4/distcomp/man/makeNCP.Rd | 2 distcomp-1.3-4/distcomp/man/makeWorker.Rd | 2 distcomp-1.3-4/distcomp/man/resetComputationInfo.Rd | 2 distcomp-1.3-4/distcomp/man/runDistcompApp.Rd | 2 distcomp-1.3-4/distcomp/man/saveNewComputation.Rd | 2 distcomp-1.3-4/distcomp/man/saveNewNCP.Rd | 2 distcomp-1.3-4/distcomp/man/setComputationInfo.Rd | 2 distcomp-1.3-4/distcomp/man/setupMaster.Rd | 2 distcomp-1.3-4/distcomp/man/setupWorker.Rd | 2 distcomp-1.3-4/distcomp/man/uploadNewComputation.Rd | 2 distcomp-1.3-4/distcomp/man/uploadNewNCP.Rd | 2 distcomp-1.3-4/distcomp/man/writeCode.Rd | 2 distcomp-1.3-4/distcomp/src/chinv2.c | 6 distcomp-1.3-4/distcomp/src/cholesky2.c | 12 distcomp-1.3-4/distcomp/src/chsolve2.c | 6 distcomp-1.3-4/distcomp/src/coxcount1.c | 259 +++++--- distcomp-1.3-4/distcomp/src/coxfit6.c | 561 +++++++----------- distcomp-1.3-4/distcomp/src/coxmart.c | 5 distcomp-1.3-4/distcomp/src/dmatrix.c | 39 - distcomp-1.3-4/distcomp/src/init.c | 1 distcomp-1.3-4/distcomp/src/survS.h | 72 -- distcomp-1.3-4/distcomp/src/survproto.h | 199 ++++-- 54 files changed, 753 insertions(+), 757 deletions(-)
Title: Spatial Surplus Production Model Framework for Northern Shrimp
Populations
Description: Implement a GAM-based (Generalized Additive Models) spatial surplus
production model (spatial SPM), aimed at modeling northern shrimp population
in Atlantic Canada but potentially to any stock in any location. The package
is opinionated in its implementation of SPMs as it internally makes the choice
to use penalized spatial gams with time lags. However, it also aims to provide
options for the user to customize their model. The methods are described in
Pedersen et al. (2022, <https://www.dfo-mpo.gc.ca/csas-sccs/Publications/ResDocs-DocRech/2022/2022_062-eng.html>).
Author: Valentin Lucet [aut, cre, cph],
Eric Pedersen [aut]
Maintainer: Valentin Lucet <valentin.lucet@gmail.com>
This is a re-admission after prior archival of version 1.0.3 dated 2025-02-12
Diff between sspm versions 1.0.3 dated 2025-02-12 and 1.1.0 dated 2025-12-03
DESCRIPTION | 6 - MD5 | 10 +- NEWS.md | 4 build/vignette.rds |binary inst/doc/An_example_with_simulated_data.html | 135 ++++++++++++--------------- tests/testthat/test-fit.R | 2 6 files changed, 75 insertions(+), 82 deletions(-)
Title: Reconstruct Individual-Level Data from Published KM Plots
Description: Functions for reconstructing individual-level data (time, status, arm) from Kaplan-MEIER curves published in academic journals (e.g. NEJM, JCO, JAMA). The individual-level data can be used for re-analysis, meta-analysis, methodology development, etc. This package was used to generate the data for commentary such as Sun, Rich, & Wei (2018) <doi:10.1056/NEJMc1808567>. Please see the vignette for a quickstart guide.
Author: Ryan Sun [aut, cre]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Diff between reconstructKM versions 0.3.0 dated 2020-11-25 and 0.4.0 dated 2025-12-03
DESCRIPTION | 8 MD5 | 16 - R/format_raw_tabs.R | 9 build/vignette.rds |binary inst/doc/introduction.R | 2 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 442 +++++++++++++++++++++++++++------------------ man/format_raw_tabs.Rd | 4 vignettes/introduction.Rmd | 2 9 files changed, 290 insertions(+), 195 deletions(-)
Title: A Comprehensive Toolkit for Working with Encrypted Parquet Files
Description: Utilities for reading, writing, and managing RCDF files, including encryption and decryption support. It offers a flexible interface for handling data stored in encrypted Parquet format, along with metadata extraction, key management, and secure operations using Advanced Encryption Standard (AES) and Rivest-Shamir-Adleman (RSA) encryption.
Author: Bhas Abdulsamad [aut, cre, cph]
Maintainer: Bhas Abdulsamad <aeabdulsamad@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2025-10-12
Diff between rcdf versions 0.1.1 dated 2025-10-12 and 0.1.2 dated 2025-12-03
DESCRIPTION | 17 ++-- MD5 | 20 +++-- NEWS.md |only R/helpers.R | 2 R/read_rcdf.R | 50 +++++++++++--- R/write_parquet.R | 3 build/vignette.rds |binary inst/doc/rcdf.R | 146 ++++++++++++++++++++--------------------- inst/doc/rcdf.html | 1 man/figures |only man/read_rcdf.Rd | 5 - tests/testthat/test-read_env.R | 1 12 files changed, 139 insertions(+), 106 deletions(-)
Title: Access the Open Experience Sampling Method Database
Description: Provides programmatic access to the Open Experience Sampling Method ('openESM') database (<https://openesmdata.org>),
a collection of harmonized experience sampling datasets. The package enables researchers to discover, download,
and work with the datasets while ensuring proper citation and license compliance.
Author: Bjoern S. Siepe [aut, cre, cph] ,
Matthias Kloft [aut]
Maintainer: Bjoern S. Siepe <bjoernsiepe@gmail.com>
Diff between openesm versions 0.1.1 dated 2025-11-02 and 0.1.2 dated 2025-12-03
DESCRIPTION | 8 +-- MD5 | 20 +++---- NAMESPACE | 1 NEWS.md | 6 ++ R/S3_methods.R | 21 +++++++ R/utils.R | 8 +-- R/zenodo.R | 114 +++++++++++++++++++++++++++++++++++-------- README.md | 3 - man/cite.openesm_dataset.Rd | 11 +++- man/notes.openesm_dataset.Rd | 10 +++ tests/testthat/test-utils.R | 81 ++++++++++++++++++++++++++++++ 11 files changed, 239 insertions(+), 44 deletions(-)
Title: Metric Halfspace Depth
Description: Metric halfspace depth for object data, generalizing Tukey's depth for Euclidean data. Implementing the method described in Dai and Lopez-Pintado (2022) <doi:10.1080/01621459.2021.2011298>.
Author: Xiongtao Dai [aut, cre]
Maintainer: Xiongtao Dai <xiongtao.dai@hotmail.com>
This is a re-admission after prior archival of version 0.1.2 dated 2024-01-24
Diff between MHD versions 0.1.2 dated 2024-01-24 and 0.1.3 dated 2025-12-03
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Basic Functions to Investigate Metabolomics Data Matrices
Description: A set of functions to investigate raw data from (metabol)omics experiments intended to be used on a raw data matrix, i.e. following peak picking and signal deconvolution. Functions can be used to normalize data, detect biomarkers and perform sample classification. A detailed description of best practice usage may be found in the publication <doi:10.1007/978-1-4939-7819-9_20>.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between MetabolomicsBasics versions 1.4.5 dated 2024-01-31 and 1.4.7 dated 2025-12-03
DESCRIPTION | 18 ++++----- MD5 | 25 +++++++------ NAMESPACE | 1 R/Load_mzML.R | 8 ++-- R/MS2ExclusionList.R |only R/MetaboliteANOVA.R | 2 - R/PlotMetabolitePCA.R | 5 ++ R/PlotPValueHist.R | 2 - R/ReplaceMissingValues.R | 7 ++- R/msconvert.R | 84 ++++++++++++++++++++++++++++++++++++++------ R/read_msdial.R |only R/verify_suggested.R | 12 +++--- man/ReplaceMissingValues.Rd | 5 +- man/msconvert.Rd | 15 ++++++- man/read_msdial.Rd |only 15 files changed, 133 insertions(+), 51 deletions(-)
More information about MetabolomicsBasics at CRAN
Permanent link
Title: Extracts Knowledge from 'Git' Repositories
Description: Scan multiple 'Git' repositories, pull specified files content and process it with large language models. You can summarize the content in specific way, extract information and data, or find answers to your questions about the repositories. The output can be stored in vector database and used for semantic search or as a part of a RAG (Retrieval Augmented Generation) prompt.
Author: Kamil Wais [aut, cre],
Krystian Igras [aut],
Maciej Banas [aut]
Maintainer: Kamil Wais <kamil.wais@gmail.com>
This is a re-admission after prior archival of version 0.1.2 dated 2025-08-22
Diff between GitAI versions 0.1.2 dated 2025-08-22 and 0.1.3 dated 2025-12-03
DESCRIPTION | 12 MD5 | 107 +- NAMESPACE | 28 NEWS.md | 21 R/GitAI-package.R | 26 R/GitAI.R | 200 ++--- R/Pinecone.R | 472 ++++++------ R/VectorDatabase.R | 62 - R/add_files.R | 32 R/add_metadata.R | 96 +- R/find_records.R | 38 - R/global.R | 2 R/initialize_project.R | 18 R/process_content.R | 58 - R/process_repos.R | 222 ++--- R/run_demo.R | 12 R/set_database.R | 58 - R/set_llm.R | 104 +- R/set_repos.R | 98 +- R/test-helpers.R | 568 +++++++-------- R/verbose.R | 74 - README.md | 258 +++--- build/vignette.rds |binary inst/demo-app/app.R | 124 +-- inst/demo-app/rsconnect |only inst/doc/building-shiny-app-chatbot.R | 342 ++++----- inst/doc/building-shiny-app-chatbot.Rmd | 514 ++++++------- inst/doc/building-shiny-app-chatbot.html | 1155 +++++++++++++++---------------- man/GitAI-package.Rd | 51 - man/add_files.Rd | 40 - man/find_records.Rd | 42 - man/initialize_project.Rd | 34 man/is_verbose.Rd | 30 man/missing_deps_note_fix.Rd | 30 man/process_repos.Rd | 44 - man/set_database.Rd | 36 man/set_github_repos.Rd | 46 - man/set_gitlab_repos.Rd | 46 - man/set_llm.Rd | 52 - man/set_prompt.Rd | 38 - man/verbose_off.Rd | 24 man/verbose_on.Rd | 24 tests/testthat.R | 26 tests/testthat/setup.R | 180 ++-- tests/testthat/test-Pinecone.R | 192 ++--- tests/testthat/test-VectorDatabase.R | 20 tests/testthat/test-add_files.R | 52 - tests/testthat/test-add_metadata.R | 42 - tests/testthat/test-initialize_project.R | 20 tests/testthat/test-process_content.R | 98 +- tests/testthat/test-process_repos.R | 52 - tests/testthat/test-set_database.R | 48 - tests/testthat/test-set_llm.R | 225 ++---- tests/testthat/test-set_repos.R | 32 vignettes/building-shiny-app-chatbot.Rmd | 514 ++++++------- 55 files changed, 3374 insertions(+), 3365 deletions(-)
Title: Estimation in Difference-in-Difference Designs with Multiple
Groups and Periods
Description: Estimation of heterogeneity-robust difference-in-differences estimators, with a binary, discrete, or continuous treatment, in designs where past treatments may affect the current outcome.
Author: Anzony Quispe [aut, cre],
Diego Ciccia [aut],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut]
Maintainer: Anzony Quispe <anzony.quispe@gmail.com>
Diff between DIDmultiplegtDYN versions 2.1.2 dated 2025-01-22 and 2.2.0 dated 2025-12-03
DESCRIPTION | 21 LICENSE | 4 MD5 | 32 NAMESPACE | 71 R/did_multiplegt_bootstrap.R | 2 R/did_multiplegt_dyn.R | 2 R/did_multiplegt_dyn_core.R | 2701 +++++++++++++--------- R/did_multiplegt_dyn_normweights.R | 10 R/did_multiplegt_main.R | 4351 +++++++++++++++++++------------------ R/favara_imbs-data.R | 40 R/globals.R |only R/rnames.R | 24 README.md |only build/partial.rdb |binary man/did_multiplegt_dyn.Rd | 512 ++-- man/print.did_multiplegt_dyn.Rd | 38 man/rnames.did_multiplegt_dyn.Rd | 42 man/summary.did_multiplegt_dyn.Rd | 38 18 files changed, 4405 insertions(+), 3483 deletions(-)
More information about DIDmultiplegtDYN at CRAN
Permanent link
Title: Simple 'WebDAV' Client
Description: A simple 'WebDAV' client that provides functions to fetch and send
files or folders to servers using the 'WebDAV' protocol
(see 'RFC' 4918 <https://www.rfc-editor.org/rfc/rfc4918>).
Only a subset of the protocol is implemented (e.g. file locks are not yet
supported).
Author: Gunther Krauss [aut, cre]
Maintainer: Gunther Krauss <guntherkrauss@uni-bonn.de>
Diff between rdav versions 0.2.2 dated 2025-11-13 and 0.3.0 dated 2025-12-03
DESCRIPTION | 10 +-- MD5 | 31 ++++++------ NAMESPACE | 2 NEWS | 4 + R/ocs.R | 7 +- R/webdav.R | 83 +++++++++++++++++++++++++++++---- inst/doc/rdav.Rmd | 9 +-- inst/doc/rdav.html | 15 ++--- man/wd_connect.Rd | 9 +++ man/wd_getwd.Rd |only man/wd_setwd.Rd |only tests/testthat/helper-ocs.R | 8 +-- tests/testthat/helper-wd.R | 2 tests/testthat/test-ocs_create_share.R | 2 tests/testthat/test-ocs_shares.R | 2 tests/testthat/test-wd_setwd.R |only tests/testthat/test-wd_upload.R | 6 +- vignettes/rdav.Rmd | 9 +-- 18 files changed, 139 insertions(+), 60 deletions(-)
Title: Collection of Correlation and Association Estimators
Description: Compute correlation and other association matrices from
small to high-dimensional datasets with relative simple functions and
sensible defaults. Includes options for shrinkage and robustness to improve
results in noisy or high-dimensional settings (p >= n), plus convenient
print/plot methods for inspection. Implemented with optimised C++ backends
using BLAS/OpenMP and memory-aware symmetric updates. Works with base
matrices and data frames, returning standard R objects via a consistent S3
interface. Useful across genomics, agriculture, and machine-learning
workflows. Supports Pearson, Spearman, Kendall, distance correlation,
partial correlation, and robust biweight mid-correlation; Bland–Altman
analyses and Lin's concordance correlation coefficient (including
repeated-measures extensions). Methods based on Ledoit and Wolf (2004)
<doi:10.1016/S0047-259X(03)00096-4>; Schäfer and Strimmer (2005)
<doi:10.2202/1544-6115.1175>; Lin (1989) <doi:10.2307/2532051>.
Author: Thiago de Paula Oliveira [aut, cre]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@gmail.com>
Diff between matrixCorr versions 0.6.2 dated 2025-11-15 and 0.7.2 dated 2025-12-03
DESCRIPTION | 12 MD5 | 69 +- NAMESPACE | 7 R/RcppExports.R | 6 R/biweight_mid_corr.R | 120 ++--- R/bland_altman.R | 89 ++- R/bland_altman_repeated.R | 129 +++-- R/ccc_repeated.R | 741 ++++++++++++++++++-------------- R/concordance_corr.R | 106 ++-- R/distance_corr.R | 32 - R/kendall_corr.R | 85 +-- R/partial_correlation.R | 54 +- R/pearson_corr.R | 26 - R/schafer_corr.R | 45 - R/spearman_rho.R | 25 - R/utils.R |only R/validate_corr_input.R | 13 man/abort_bad_arg.Rd |only man/abort_internal.Rd |only man/ccc_pairwise_u_stat.Rd | 20 man/check_ar1_rho.Rd |only man/check_bool.Rd |only man/check_inherits.Rd |only man/check_matrix_dims.Rd |only man/check_prob_scalar.Rd |only man/check_required_cols.Rd |only man/check_same_length.Rd |only man/check_scalar_character.Rd |only man/check_scalar_int_pos.Rd |only man/check_scalar_nonneg.Rd |only man/check_scalar_numeric.Rd |only man/check_symmetric_matrix.Rd |only man/check_weights.Rd |only man/inform_if_verbose.Rd |only man/match_arg.Rd |only src/RcppExports.cpp | 13 src/ccc_repeated.cpp | 42 + tests/testthat.R | 6 tests/testthat/test-utils.R |only tests/testthat/test_biweight_mid_corr.R | 10 tests/testthat/test_bland_altman.R | 1 tests/testthat/test_ccc_repeated.R | 16 tests/testthat/test_kendall.R | 26 - tests/testthat/test_spearman_rho.R | 2 tests/testthat/tests_schafer_corr.R | 10 45 files changed, 973 insertions(+), 732 deletions(-)
Title: Empirical Bayes Estimation and Inference
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models
and some other density estimation and regression methods based on convex
optimization. See Koenker and Gu (2017) REBayes: An R Package for Empirical
Bayes Mixture Methods, Journal of Statistical Software, 82, 1--26,
<DOI:10.18637/jss.v082.i08>.
Author: Roger Koenker [aut, cre],
Jiaying Gu [ctb],
Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between REBayes versions 2.56 dated 2024-06-22 and 2.59 dated 2025-12-03
DESCRIPTION | 8 +- MD5 | 28 +++++--- NAMESPACE | 2 R/HodgesLehmann.R |only R/HuberSpline.R |only R/KWDual.R | 169 +++++++++++++++++++++++++++++++-------------------- R/medde.R | 8 +- build/vignette.rds |binary demo/00Index | 2 demo/HL1.R |only demo/Huber1.R |only inst/ChangeLog | 12 +++ inst/doc/Bdecon.pdf |binary inst/doc/medde.pdf |binary inst/doc/rebayes.pdf |binary man/HodgesLehmann.Rd |only man/HuberSpline.Rd |only man/KWDual.Rd | 8 +- 18 files changed, 153 insertions(+), 84 deletions(-)
Title: Pena-Yohai Initial Estimator for Robust S-Regression
Description: Deterministic Pena-Yohai initial estimator for robust S estimators
of regression. The procedure is described in detail in
Pena, D., & Yohai, V. (1999) <doi:10.2307/2670164>.
Author: David Kepplinger [aut, cre],
Matias Salibian-Barrera [aut],
Gabriela Cohen Freue [aut]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between pyinit versions 1.1.3 dated 2022-04-26 and 1.1.4 dated 2025-12-03
DESCRIPTION | 16 ++++++++-------- MD5 | 4 ++-- NEWS.md | 3 +++ 3 files changed, 13 insertions(+), 10 deletions(-)
Title: Trace Function Parameter Types
Description: The 'R' language includes a set of defined types, but the language
itself is "absurdly dynamic" (Turcotte & Vitek (2019)
<doi:10.1145/3340670.3342426>), and lacks any way to specify which types are
expected by any expression. The 'typetracer' package enables code to be
traced to extract detailed information on the properties of parameters
passed to 'R' functions. 'typetracer' can trace individual functions or
entire packages.
Author: Mark Padgham [aut, cre] ,
Filip Krikava [ctb] ,
covr authors [cph]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between typetracer versions 0.2.2 dated 2023-06-26 and 0.2.3 dated 2025-12-03
DESCRIPTION | 11 +- MD5 | 34 ++++---- NEWS.md | 9 ++ R/directory-fns.R | 1 R/load-and-clear-traces.R | 1 R/prepend-code.R | 1 R/testthat-fns.R | 1 R/trace-package.R | 1 R/tracer-define.R | 1 R/tracer-inject.R | 12 ++- R/zzz.R | 1 README.md | 71 ++++++++---------- build/vignette.rds |binary inst/doc/nse.html | 6 - src/utils.c | 141 +++++++++++++++++++++++++++++++++--- tests/testthat/test-trace-fns.R | 3 tests/testthat/test-trace-package.R | 1 tests/testthat/test-utils.R | 3 18 files changed, 211 insertions(+), 87 deletions(-)
Title: Interpreting High Resolution Mass Spectra
Description: High resolution mass spectrometry yields often large data sets of
spectra from compounds which are not present in available libraries. These
spectra need to be annotated and interpreted.
'InterpretMSSpectrum' provides a set of functions to perform such tasks for
Electrospray-Ionization and Atmospheric-Pressure-Chemical-Ionization derived
data in positive and negative ionization mode.
Author: Jan Lisec [aut, cre] ,
Jaeger Carsten [aut]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between InterpretMSSpectrum versions 1.4.5 dated 2024-01-31 and 1.5.2 dated 2025-12-03
DESCRIPTION | 12 +++---- MD5 | 34 ++++++++++---------- NAMESPACE | 1 R/InterpretMSSpectrum.R | 18 ++++++++++ R/PlausibleFormula.R | 7 +++- R/PlotSpec.R | 23 ++++++++----- R/findMAIN.r | 13 +++---- R/fml2expr.R |only README.md | 8 ++-- man/InterpretMSSpectrum.Rd | 16 +++++++++ man/PlotSpec.Rd | 9 ++++- man/fml2expr.Rd |only tests/testthat/_snaps/PlotSpec/plotspec-01.svg | 7 ++++ tests/testthat/_snaps/PlotSpec/plotspec-02.svg | 7 ++++ tests/testthat/_snaps/findMAIN/findmain-plot-01.svg | 29 +++++++++++------ tests/testthat/test-InterpretMSSpectrum.R | 1 tests/testthat/test-InterpretTP.R | 1 tests/testthat/test-PlotSpec.R | 2 + tests/testthat/test-findMAIN.R | 1 19 files changed, 133 insertions(+), 56 deletions(-)
More information about InterpretMSSpectrum at CRAN
Permanent link
Title: Evaluating Multinomial Order Restrictions with Bridge Sampling
Description: Evaluate hypotheses concerning the distribution of multinomial
proportions using bridge sampling. The bridge sampling routine is able to
compute Bayes factors for hypotheses that entail inequality constraints,
equality constraints, free parameters, and mixtures of all three. These
hypotheses are tested against the encompassing hypothesis, that all parameters
vary freely or against the null hypothesis that all category proportions are equal.
For more information see Sarafoglou et al. (2020) <doi:10.31234/osf.io/bux7p>.
Author: Alexandra Sarafoglou [aut, cre] ,
Frederik Aust [aut] ,
Julia M. Haaf [aut] ,
Joris Goosen [aut],
Quentin F. Gronau [aut],
Maarten Marsman [aut]
Maintainer: Alexandra Sarafoglou <alexandra.sarafoglou@gmail.com>
Diff between multibridge versions 1.2.0 dated 2022-11-01 and 1.3.0 dated 2025-12-03
DESCRIPTION | 20 +-- MD5 | 40 +++--- NEWS.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 33 +++-- inst/doc/MemoryOfLifestresses.html | 125 +++++++++---------- inst/doc/MendelianLawsOfInheritance.html | 123 ++++++++---------- inst/doc/PrevalenceOfStatisticalReportingErrors.html | 123 ++++++++---------- man/bayes_factor.Rd | 2 man/bayes_factor.bmult.Rd | 2 man/binom_bf_inequality.Rd | 7 - man/binom_bf_informed.Rd | 2 man/journals.Rd | 2 man/lifestresses.Rd | 2 man/mult_bf_inequality.Rd | 7 - man/mult_bf_informed.Rd | 2 man/peas.Rd | 2 man/plot.summary.bmult.Rd | 4 src/Makevars | 2 src/Makevars.win | 2 21 files changed, 252 insertions(+), 254 deletions(-)
Title: Addons for the 'mclust' Package
Description: Extend the functionality of the 'mclust' package for Gaussian
finite mixture modeling by including: density estimation for data with
bounded support (Scrucca, 2019 <doi:10.1002/bimj.201800174>); modal
clustering using MEM (Modal EM) algorithm for Gaussian mixtures
(Scrucca, 2021 <doi:10.1002/sam.11527>); entropy estimation via
Gaussian mixture modeling (Robin & Scrucca, 2023
<doi:10.1016/j.csda.2022.107582>); Gaussian mixtures modeling of
financial log-returns (Scrucca, 2024 <doi:10.3390/e26110907>).
Author: Luca Scrucca [aut, cre, cph]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between mclustAddons versions 0.9.2 dated 2025-04-03 and 0.10 dated 2025-12-03
DESCRIPTION | 13 ++++--- MD5 | 34 ++++++++++++-------- NAMESPACE | 6 +++ NEWS.md | 6 +++ R/GMM_finance.R | 28 +++++++++++++--- R/MclustBounded.R | 13 ++++++- R/RcppExports.R | 75 +++++++++++++++++++++++++++++++++++++++++++++ R/densityMclustBounded.R | 3 + R/hypvolgmm.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/mclustAddons.html | 43 +++++++++++++------------ man/GMMlogreturn.Rd | 4 +- man/hypcube_lhs.Rd |only man/hypcube_smc.Rd |only man/hypvolgmm.Rd |only man/hypvolgmm_hdlevel.Rd |only man/hypvoltmvnorm.Rd |only man/hypvolunif.Rd |only src/RcppExports.cpp | 51 ++++++++++++++++++++++++++++++ src/hypvolgmm.cpp |only src/init.c | 20 ++++++++---- 22 files changed, 239 insertions(+), 57 deletions(-)
Title: Air Pollution Tolerance Index (APTI) Calculator
Description: It calculates the Air Pollution Tolerance Index (APTI) of plant species using biochemical parameters such as chlorophyll content, leaf extract pH, relative water content, and ascorbic acid content. It helps in identifying tolerant species for greenbelt development and pollution mitigation studies. It includes a 'shiny' app for interactive APTI calculation and visualisation. For method details see, Sahu et al. (2020).<DOI:10.1007/s42452-020-3120-6>.
Author: Nobin Chandra Paul [aut, cre, cph],
Rupali Singh [aut, cph],
Sangram B Chavan [aut, cph],
Navyasree Ponnaganti [aut, cph],
K. Sammi Reddy [aut, cph]
Maintainer: Nobin Chandra Paul <ncp375@gmail.com>
Diff between APTIcalc versions 0.1.0 dated 2025-05-29 and 0.1.1 dated 2025-12-03
DESCRIPTION | 11 +++-- MD5 | 4 +- inst/shiny/app.R | 105 +++++++++++++++++++++++++++++++++++++++++++++---------- 3 files changed, 95 insertions(+), 25 deletions(-)
Title: Maximum Likelihood Multiple Imputation
Description: Implements proper and so-called Maximum Likelihood Multiple Imputation as described by von Hippel and Bartlett (2021) <doi:10.1214/20-STS793>. A number of different imputation methods are available, by utilising the 'norm', 'cat' and 'mix' packages. Inferences can be performed either using Rubin's rules (for proper imputation), or a modified version for maximum likelihood imputation. For maximum likelihood imputations a likelihood score based approach based on theory by Wang and Robins (1998) <doi:10.1093/biomet/85.4.935> is also available.
Author: Jonathan Bartlett [aut, cre]
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Diff between mlmi versions 1.1.2 dated 2023-06-02 and 1.1.3 dated 2025-12-03
DESCRIPTION | 18 MD5 | 58 - NAMESPACE | 20 NEWS.md | 22 R/catimp.R | 274 ++++---- R/common.r | 46 - R/data.r | 38 - R/miximp.R | 383 ++++++----- R/normUniImp.r | 148 ++-- R/normimp.R | 152 ++-- R/refBasedCts.r | 850 ++++++++++++------------- R/sb.r | 198 +++--- R/wb.r | 242 +++---- README.md | 20 build/partial.rdb |binary man/catImp.Rd | 190 ++--- man/ctsTrialWide.Rd | 54 - man/mixImp.Rd | 214 +++--- man/normUniImp.Rd | 102 +-- man/refBasedCts.Rd | 196 ++--- man/scoreBased.Rd | 150 ++-- man/withinBetween.Rd | 126 +-- tests/testthat.R | 8 tests/testthat/test_catimp.r | 219 ++++-- tests/testthat/test_miximp.r | 472 ++++++++------ tests/testthat/test_normimp.r | 152 ++-- tests/testthat/test_refBasedCts.R | 1250 +++++++++++++++++++------------------- tests/testthat/test_sb.R | 56 - tests/testthat/test_uniimp.r | 114 +-- tests/testthat/test_wb.r | 78 +- 30 files changed, 3007 insertions(+), 2843 deletions(-)
Title: Constrained Groupwise Additive Index Models
Description: Fits constrained groupwise additive index models and provides functions for inference and interpretation of these models. The method is described in Masselot, Chebana, Campagna, Lavigne, Ouarda, Gosselin (2022) "Constrained groupwise additive index models" <doi:10.1093/biostatistics/kxac023>.
Author: Pierre Masselot [aut, cre]
Maintainer: Pierre Masselot <pierre.masselot@lshtm.ac.uk>
Diff between cgaim versions 1.0.2 dated 2025-06-30 and 1.0.3 dated 2025-12-03
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/predict.cgaim.R | 9 +++++---- man/predict.cgaim.Rd | 2 ++ 5 files changed, 20 insertions(+), 12 deletions(-)
Title: Interactive 'shiny' Dashboard for 'nlmixr2'
Description: An R shiny user interface for the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) package,
designed to simplify the modeling process for users. Additionally, this package includes supplementary functions
to further enhances the usage of 'nlmixr2'.
Author: Richard Hooijmaijers [aut, cre, cph],
Teun Post [aut, cph],
LAPP Consultants [fnd, cph],
Matthew Fidler [ctb],
Veerle van Leemput [ctb]
Maintainer: Richard Hooijmaijers <richardhooijmaijers@gmail.com>
Diff between shinyMixR versions 0.5.2 dated 2025-08-22 and 0.5.3 dated 2025-12-03
DESCRIPTION | 11 ++- MD5 | 28 +++++----- NEWS.md | 4 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting_started.html | 7 +- inst/other/run1.res.rds |binary inst/other/run1.ressum.rds |binary tests/testthat/_snaps/shinymixr-02-parameter-table/run2-model-001.json | 12 ++-- tests/testthat/_snaps/shinymixr-02-parameter-table/run2-model-001_.new.png |only tests/testthat/_snaps/shinymixr-02-parameter-table/run2-model-001_.png |binary tests/testthat/_snaps/shinymixr-02-parameter-table/run2-model-002.json | 12 ++-- tests/testthat/_snaps/shinymixr-02-parameter-table/run2-model-002_.new.png |only tests/testthat/_snaps/shinymixr-02-parameter-table/run2-model-002_.png |binary tests/testthat/_snaps/shinymixr-03-create-newmodel/run3-model-001_.new.png |only tests/testthat/_snaps/shinymixr-03-create-newmodel/run3-model-002_.new.png |only tests/testthat/test-par_table.R | 8 ++ 17 files changed, 48 insertions(+), 34 deletions(-)
Title: Forensic Authorship Analysis
Description: Carry out comparative authorship analysis of disputed and undisputed texts within the Likelihood Ratio Framework for expressing evidence in forensic science. This package contains implementations of well-known algorithms for comparative authorship analysis, such as Smith and Aldridge's (2011) Cosine Delta <doi:10.1080/09296174.2011.533591> or Koppel and Winter's (2014) Impostors Method <doi:10.1002/asi.22954>, as well as functions to measure their performance and to calibrate their outputs into Log-Likelihood Ratios.
Author: Andrea Nini [aut, cre, cph] ,
David van Leeuwen [cph]
Maintainer: Andrea Nini <andrea.nini@manchester.ac.uk>
Diff between idiolect versions 1.0.1 dated 2024-08-28 and 1.1.1 dated 2025-12-03
DESCRIPTION | 11 - MD5 | 46 +++--- NEWS.md | 16 ++ R/concordance.R | 43 ++++-- R/globals.R | 2 R/lambdaG_visualize.R | 161 +++++++++++++++------- R/ngram_tracing.R | 7 R/performance.R | 59 +++++++- R/utils.R | 17 ++ inst/doc/idiolect.html | 19 +- man/concordance.Rd | 17 +- man/lambdaG_visualize.Rd | 8 - man/performance.Rd | 6 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/concordance.md | 205 +++++++++++++++++++++++++++++ tests/testthat/_snaps/contentmask.md | 10 - tests/testthat/_snaps/lambdaG_visualize.md | 2 tests/testthat/_snaps/ngram_tracing.md | 38 ++--- tests/testthat/_snaps/tokenize_sents.md | 2 tests/testthat/test-concordance.R | 14 + tests/testthat/test-impostors.R | 23 +-- tests/testthat/test-lambdaG_visualize.R | 16 +- tests/testthat/test-performance.R | 9 + vignettes/references.bib | 8 - 24 files changed, 569 insertions(+), 170 deletions(-)
Title: Solution Paths for Linear and Logistic Regression Models with
Categorical Predictors, with SCOPE Penalty
Description: Computes solutions for linear and logistic regression models with potentially high-dimensional categorical predictors. This is done by applying a nonconvex penalty (SCOPE) and computing solutions in an efficient path-wise fashion. The scaling of the solution paths is selected automatically. Includes functionality for selecting tuning parameter lambda by k-fold cross-validation and early termination based on information criteria. Solutions are computed by cyclical block-coordinate descent, iterating an innovative dynamic programming algorithm to compute exact solutions for each block.
Author: Benjamin Stokell [aut],
Daniel Grose [ctb, cre],
Rajen Shah [ctb]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between CatReg versions 2.0.3 dated 2021-06-14 and 2.0.4 dated 2025-12-03
CatReg-2.0.3/CatReg/src/Makevars |only CatReg-2.0.4/CatReg/DESCRIPTION | 10 +++++----- CatReg-2.0.4/CatReg/MD5 | 17 ++++++++--------- CatReg-2.0.4/CatReg/R/predict.scope.R | 2 +- CatReg-2.0.4/CatReg/R/predict.scope.logistic.R | 2 +- CatReg-2.0.4/CatReg/R/scope.R | 2 +- CatReg-2.0.4/CatReg/R/scope.logistic.R | 2 +- CatReg-2.0.4/CatReg/build/partial.rdb |binary CatReg-2.0.4/CatReg/inst/REFERENCES.bib | 5 ----- CatReg-2.0.4/CatReg/src/RcppExports.cpp | 5 +++++ 10 files changed, 22 insertions(+), 23 deletions(-)
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] ,
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifen [...truncated...]
Maintainer: Jiaming Yuan <jm.yuan@outlook.com>
Diff between xgboost versions 1.7.11.1 dated 2025-05-15 and 3.1.2.1 dated 2025-12-03
xgboost-1.7.11.1/xgboost/R/xgb.serialize.R |only xgboost-1.7.11.1/xgboost/R/xgb.unserialize.R |only xgboost-1.7.11.1/xgboost/demo |only xgboost-1.7.11.1/xgboost/inst/doc/discoverYourData.R |only xgboost-1.7.11.1/xgboost/inst/doc/discoverYourData.Rmd |only xgboost-1.7.11.1/xgboost/inst/doc/discoverYourData.html |only xgboost-1.7.11.1/xgboost/inst/doc/xgboost.R |only xgboost-1.7.11.1/xgboost/inst/doc/xgboost.Rnw |only xgboost-1.7.11.1/xgboost/inst/doc/xgboost.pdf |only xgboost-1.7.11.1/xgboost/inst/doc/xgboostPresentation.R |only xgboost-1.7.11.1/xgboost/inst/doc/xgboostPresentation.Rmd |only xgboost-1.7.11.1/xgboost/inst/doc/xgboostPresentation.html |only xgboost-1.7.11.1/xgboost/man/callbacks.Rd |only xgboost-1.7.11.1/xgboost/man/cb.cv.predict.Rd |only xgboost-1.7.11.1/xgboost/man/cb.early.stop.Rd |only xgboost-1.7.11.1/xgboost/man/cb.evaluation.log.Rd |only xgboost-1.7.11.1/xgboost/man/cb.gblinear.history.Rd |only xgboost-1.7.11.1/xgboost/man/cb.print.evaluation.Rd |only xgboost-1.7.11.1/xgboost/man/cb.reset.parameters.Rd |only xgboost-1.7.11.1/xgboost/man/cb.save.model.Rd |only xgboost-1.7.11.1/xgboost/man/normalize.Rd |only xgboost-1.7.11.1/xgboost/man/prepare.ggplot.shap.data.Rd |only xgboost-1.7.11.1/xgboost/man/setinfo.Rd |only xgboost-1.7.11.1/xgboost/man/slice.xgb.DMatrix.Rd |only xgboost-1.7.11.1/xgboost/man/xgb.Booster.complete.Rd |only xgboost-1.7.11.1/xgboost/man/xgb.parameters.Rd |only xgboost-1.7.11.1/xgboost/man/xgb.serialize.Rd |only xgboost-1.7.11.1/xgboost/man/xgb.shap.data.Rd |only xgboost-1.7.11.1/xgboost/man/xgb.unserialize.Rd |only xgboost-1.7.11.1/xgboost/man/xgboost-deprecated.Rd |only xgboost-1.7.11.1/xgboost/src/Makevars.win |only xgboost-1.7.11.1/xgboost/src/include/xgboost/generic_parameters.h |only xgboost-1.7.11.1/xgboost/src/rabit |only xgboost-1.7.11.1/xgboost/src/src/collective/communicator.cc |only xgboost-1.7.11.1/xgboost/src/src/collective/communicator.cu |only xgboost-1.7.11.1/xgboost/src/src/collective/communicator.h |only xgboost-1.7.11.1/xgboost/src/src/collective/device_communicator.cuh |only xgboost-1.7.11.1/xgboost/src/src/collective/device_communicator_adapter.cuh |only xgboost-1.7.11.1/xgboost/src/src/collective/nccl_device_communicator.cuh |only xgboost-1.7.11.1/xgboost/src/src/collective/noop_communicator.h |only xgboost-1.7.11.1/xgboost/src/src/collective/rabit_communicator.h |only xgboost-1.7.11.1/xgboost/src/src/data/arrow-cdi.h |only xgboost-1.7.11.1/xgboost/src/src/data/histogram_cut_format.h |only xgboost-1.7.11.1/xgboost/src/src/objective/rank_obj.cc |only xgboost-1.7.11.1/xgboost/src/src/objective/rank_obj.cu |only xgboost-1.7.11.1/xgboost/src/src/tree/updater_quantile_hist.h |only xgboost-1.7.11.1/xgboost/tests/testthat/test_gc_safety.R |only xgboost-1.7.11.1/xgboost/vignettes/discoverYourData.Rmd |only xgboost-1.7.11.1/xgboost/vignettes/vignette.css |only xgboost-1.7.11.1/xgboost/vignettes/xgboost.Rnw |only xgboost-1.7.11.1/xgboost/vignettes/xgboost.bib |only xgboost-1.7.11.1/xgboost/vignettes/xgboostPresentation.Rmd |only xgboost-3.1.2.1/xgboost/DESCRIPTION | 21 xgboost-3.1.2.1/xgboost/MD5 | 846 ++-- xgboost-3.1.2.1/xgboost/NAMESPACE | 58 xgboost-3.1.2.1/xgboost/R/callbacks.R | 1811 ++++++---- xgboost-3.1.2.1/xgboost/R/utils.R | 665 ++- xgboost-3.1.2.1/xgboost/R/xgb.Booster.R | 1504 +++++--- xgboost-3.1.2.1/xgboost/R/xgb.DMatrix.R | 1295 ++++++- xgboost-3.1.2.1/xgboost/R/xgb.DMatrix.save.R | 12 xgboost-3.1.2.1/xgboost/R/xgb.config.R | 17 xgboost-3.1.2.1/xgboost/R/xgb.create.features.R | 45 xgboost-3.1.2.1/xgboost/R/xgb.cv.R | 431 +- xgboost-3.1.2.1/xgboost/R/xgb.dump.R | 81 xgboost-3.1.2.1/xgboost/R/xgb.ggplot.R | 66 xgboost-3.1.2.1/xgboost/R/xgb.importance.R | 205 - xgboost-3.1.2.1/xgboost/R/xgb.load.R | 60 xgboost-3.1.2.1/xgboost/R/xgb.load.raw.R | 25 xgboost-3.1.2.1/xgboost/R/xgb.model.dt.tree.R | 166 xgboost-3.1.2.1/xgboost/R/xgb.plot.deepness.R | 100 xgboost-3.1.2.1/xgboost/R/xgb.plot.importance.R | 101 xgboost-3.1.2.1/xgboost/R/xgb.plot.multi.trees.R | 84 xgboost-3.1.2.1/xgboost/R/xgb.plot.shap.R | 318 + xgboost-3.1.2.1/xgboost/R/xgb.plot.tree.R | 177 xgboost-3.1.2.1/xgboost/R/xgb.save.R | 69 xgboost-3.1.2.1/xgboost/R/xgb.save.raw.R | 43 xgboost-3.1.2.1/xgboost/R/xgb.train.R | 1077 ++++- xgboost-3.1.2.1/xgboost/R/xgboost.R | 1583 ++++++++ xgboost-3.1.2.1/xgboost/build/vignette.rds |binary xgboost-3.1.2.1/xgboost/configure | 638 +++ xgboost-3.1.2.1/xgboost/configure.ac | 57 xgboost-3.1.2.1/xgboost/configure.win | 21 xgboost-3.1.2.1/xgboost/inst/doc/xgboost_introduction.R |only xgboost-3.1.2.1/xgboost/inst/doc/xgboost_introduction.Rmd |only xgboost-3.1.2.1/xgboost/inst/doc/xgboost_introduction.html |only xgboost-3.1.2.1/xgboost/inst/doc/xgboostfromJSON.R | 48 xgboost-3.1.2.1/xgboost/inst/doc/xgboostfromJSON.Rmd | 48 xgboost-3.1.2.1/xgboost/inst/doc/xgboostfromJSON.html | 183 - xgboost-3.1.2.1/xgboost/inst/make-r-def.R | 6 xgboost-3.1.2.1/xgboost/man/a-compatibility-note-for-saveRDS-save.Rd | 111 xgboost-3.1.2.1/xgboost/man/agaricus.test.Rd | 11 xgboost-3.1.2.1/xgboost/man/agaricus.train.Rd | 11 xgboost-3.1.2.1/xgboost/man/coef.xgb.Booster.Rd |only xgboost-3.1.2.1/xgboost/man/dim.xgb.DMatrix.Rd | 7 xgboost-3.1.2.1/xgboost/man/dimnames.xgb.DMatrix.Rd | 17 xgboost-3.1.2.1/xgboost/man/getinfo.Rd | 95 xgboost-3.1.2.1/xgboost/man/predict.xgb.Booster.Rd | 294 + xgboost-3.1.2.1/xgboost/man/predict.xgboost.Rd |only xgboost-3.1.2.1/xgboost/man/print.xgb.Booster.Rd | 32 xgboost-3.1.2.1/xgboost/man/print.xgb.DMatrix.Rd | 13 xgboost-3.1.2.1/xgboost/man/print.xgb.cv.Rd | 25 xgboost-3.1.2.1/xgboost/man/print.xgboost.Rd |only xgboost-3.1.2.1/xgboost/man/variable.names.xgb.Booster.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.Callback.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.DMatrix.Rd | 178 xgboost-3.1.2.1/xgboost/man/xgb.DMatrix.hasinfo.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.DMatrix.save.Rd | 10 xgboost-3.1.2.1/xgboost/man/xgb.DataBatch.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.DataIter.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.ExtMemDMatrix.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.QuantileDMatrix.from_iterator.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.attr.Rd | 67 xgboost-3.1.2.1/xgboost/man/xgb.cb.cv.predict.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.cb.early.stop.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.cb.evaluation.log.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.cb.gblinear.history.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.cb.print.evaluation.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.cb.reset.parameters.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.cb.save.model.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.config.Rd | 33 xgboost-3.1.2.1/xgboost/man/xgb.copy.Booster.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.create.features.Rd | 33 xgboost-3.1.2.1/xgboost/man/xgb.cv.Rd | 248 - xgboost-3.1.2.1/xgboost/man/xgb.dump.Rd | 68 xgboost-3.1.2.1/xgboost/man/xgb.gblinear.history.Rd | 37 xgboost-3.1.2.1/xgboost/man/xgb.get.DMatrix.data.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.get.DMatrix.num.non.missing.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.get.DMatrix.qcut.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.get.num.boosted.rounds.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.importance.Rd | 146 xgboost-3.1.2.1/xgboost/man/xgb.is.same.Booster.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.load.Rd | 43 xgboost-3.1.2.1/xgboost/man/xgb.load.raw.Rd | 10 xgboost-3.1.2.1/xgboost/man/xgb.model.dt.tree.Rd | 116 xgboost-3.1.2.1/xgboost/man/xgb.model.parameters.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.params.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.plot.deepness.Rd | 81 xgboost-3.1.2.1/xgboost/man/xgb.plot.importance.Rd | 83 xgboost-3.1.2.1/xgboost/man/xgb.plot.multi.trees.Rd | 71 xgboost-3.1.2.1/xgboost/man/xgb.plot.shap.Rd | 197 - xgboost-3.1.2.1/xgboost/man/xgb.plot.shap.summary.Rd | 54 xgboost-3.1.2.1/xgboost/man/xgb.plot.tree.Rd | 120 xgboost-3.1.2.1/xgboost/man/xgb.save.Rd | 66 xgboost-3.1.2.1/xgboost/man/xgb.save.raw.Rd | 43 xgboost-3.1.2.1/xgboost/man/xgb.slice.Booster.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.slice.DMatrix.Rd |only xgboost-3.1.2.1/xgboost/man/xgb.train.Rd | 409 +- xgboost-3.1.2.1/xgboost/man/xgbConfig.Rd | 15 xgboost-3.1.2.1/xgboost/man/xgboost-options.Rd |only xgboost-3.1.2.1/xgboost/man/xgboost.Rd |only xgboost-3.1.2.1/xgboost/src/Makevars.in | 70 xgboost-3.1.2.1/xgboost/src/Makevars.win.in |only xgboost-3.1.2.1/xgboost/src/config.h |only xgboost-3.1.2.1/xgboost/src/config.h.in |only xgboost-3.1.2.1/xgboost/src/dmlc-core/include/dmlc/build_config_default.h | 3 xgboost-3.1.2.1/xgboost/src/dmlc-core/include/dmlc/common.h | 1 xgboost-3.1.2.1/xgboost/src/dmlc-core/include/dmlc/endian.h | 3 xgboost-3.1.2.1/xgboost/src/dmlc-core/include/dmlc/filesystem.h | 4 xgboost-3.1.2.1/xgboost/src/dmlc-core/include/dmlc/io.h | 11 xgboost-3.1.2.1/xgboost/src/dmlc-core/include/dmlc/memory_io.h | 22 xgboost-3.1.2.1/xgboost/src/dmlc-core/include/dmlc/parameter.h | 15 xgboost-3.1.2.1/xgboost/src/dmlc-core/include/dmlc/threadediter.h | 6 xgboost-3.1.2.1/xgboost/src/dmlc-core/include/dmlc/timer.h | 4 xgboost-3.1.2.1/xgboost/src/dmlc-core/src/config.cc | 4 xgboost-3.1.2.1/xgboost/src/dmlc-core/src/data/csv_parser.h | 9 xgboost-3.1.2.1/xgboost/src/dmlc-core/src/io/hdfs_filesys.cc | 9 xgboost-3.1.2.1/xgboost/src/dmlc-core/src/io/local_filesys.cc | 11 xgboost-3.1.2.1/xgboost/src/dmlc-core/src/io/s3_filesys.cc | 16 xgboost-3.1.2.1/xgboost/src/dmlc-core/src/io/single_file_split.h | 3 xgboost-3.1.2.1/xgboost/src/include/xgboost/base.h | 127 xgboost-3.1.2.1/xgboost/src/include/xgboost/c_api.h | 1057 +++-- xgboost-3.1.2.1/xgboost/src/include/xgboost/cache.h |only xgboost-3.1.2.1/xgboost/src/include/xgboost/collective/poll_utils.h |only xgboost-3.1.2.1/xgboost/src/include/xgboost/collective/result.h |only xgboost-3.1.2.1/xgboost/src/include/xgboost/collective/socket.h | 540 ++ xgboost-3.1.2.1/xgboost/src/include/xgboost/context.h |only xgboost-3.1.2.1/xgboost/src/include/xgboost/data.h | 599 +-- xgboost-3.1.2.1/xgboost/src/include/xgboost/gbm.h | 191 - xgboost-3.1.2.1/xgboost/src/include/xgboost/global_config.h | 32 xgboost-3.1.2.1/xgboost/src/include/xgboost/host_device_vector.h | 42 xgboost-3.1.2.1/xgboost/src/include/xgboost/json.h | 251 - xgboost-3.1.2.1/xgboost/src/include/xgboost/json_io.h | 80 xgboost-3.1.2.1/xgboost/src/include/xgboost/learner.h | 208 - xgboost-3.1.2.1/xgboost/src/include/xgboost/linalg.h | 380 +- xgboost-3.1.2.1/xgboost/src/include/xgboost/linear_updater.h | 11 xgboost-3.1.2.1/xgboost/src/include/xgboost/logging.h | 6 xgboost-3.1.2.1/xgboost/src/include/xgboost/metric.h | 35 xgboost-3.1.2.1/xgboost/src/include/xgboost/model.h | 13 xgboost-3.1.2.1/xgboost/src/include/xgboost/multi_target_tree_model.h |only xgboost-3.1.2.1/xgboost/src/include/xgboost/objective.h | 167 xgboost-3.1.2.1/xgboost/src/include/xgboost/parameter.h | 2 xgboost-3.1.2.1/xgboost/src/include/xgboost/predictor.h | 157 xgboost-3.1.2.1/xgboost/src/include/xgboost/span.h | 148 xgboost-3.1.2.1/xgboost/src/include/xgboost/string_view.h | 60 xgboost-3.1.2.1/xgboost/src/include/xgboost/task.h | 8 xgboost-3.1.2.1/xgboost/src/include/xgboost/tree_model.h | 584 +-- xgboost-3.1.2.1/xgboost/src/include/xgboost/tree_updater.h | 67 xgboost-3.1.2.1/xgboost/src/include/xgboost/version_config.h | 10 xgboost-3.1.2.1/xgboost/src/include/xgboost/windefs.h |only xgboost-3.1.2.1/xgboost/src/init.c | 87 xgboost-3.1.2.1/xgboost/src/src/CMakeLists.txt | 28 xgboost-3.1.2.1/xgboost/src/src/c_api/c_api.cc | 1140 ++++-- xgboost-3.1.2.1/xgboost/src/src/c_api/c_api.cu | 93 xgboost-3.1.2.1/xgboost/src/src/c_api/c_api_error.cc | 18 xgboost-3.1.2.1/xgboost/src/src/c_api/c_api_error.h | 21 xgboost-3.1.2.1/xgboost/src/src/c_api/c_api_utils.h | 154 xgboost-3.1.2.1/xgboost/src/src/c_api/coll_c_api.cc |only xgboost-3.1.2.1/xgboost/src/src/cli_main.cc | 117 xgboost-3.1.2.1/xgboost/src/src/collective/aggregator.cuh |only xgboost-3.1.2.1/xgboost/src/src/collective/aggregator.h |only xgboost-3.1.2.1/xgboost/src/src/collective/allgather.cc |only xgboost-3.1.2.1/xgboost/src/src/collective/allgather.h |only xgboost-3.1.2.1/xgboost/src/src/collective/allreduce.cc |only xgboost-3.1.2.1/xgboost/src/src/collective/allreduce.h |only xgboost-3.1.2.1/xgboost/src/src/collective/broadcast.cc |only xgboost-3.1.2.1/xgboost/src/src/collective/broadcast.h |only xgboost-3.1.2.1/xgboost/src/src/collective/coll.cc |only xgboost-3.1.2.1/xgboost/src/src/collective/coll.cu |only xgboost-3.1.2.1/xgboost/src/src/collective/coll.cuh |only xgboost-3.1.2.1/xgboost/src/src/collective/coll.h |only xgboost-3.1.2.1/xgboost/src/src/collective/comm.cc |only xgboost-3.1.2.1/xgboost/src/src/collective/comm.cu |only xgboost-3.1.2.1/xgboost/src/src/collective/comm.cuh |only xgboost-3.1.2.1/xgboost/src/src/collective/comm.h |only xgboost-3.1.2.1/xgboost/src/src/collective/comm_group.cc |only xgboost-3.1.2.1/xgboost/src/src/collective/comm_group.h |only xgboost-3.1.2.1/xgboost/src/src/collective/communicator-inl.h | 224 - 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xgboost-3.1.2.1/xgboost/src/src/common/hist_util.cu | 443 +- xgboost-3.1.2.1/xgboost/src/src/common/hist_util.cuh | 415 +- xgboost-3.1.2.1/xgboost/src/src/common/hist_util.h | 257 - xgboost-3.1.2.1/xgboost/src/src/common/host_device_vector.cc | 26 xgboost-3.1.2.1/xgboost/src/src/common/host_device_vector.cu | 151 xgboost-3.1.2.1/xgboost/src/src/common/io.cc | 383 +- xgboost-3.1.2.1/xgboost/src/src/common/io.h | 540 ++ xgboost-3.1.2.1/xgboost/src/src/common/json.cc | 208 - xgboost-3.1.2.1/xgboost/src/src/common/json_utils.h |only xgboost-3.1.2.1/xgboost/src/src/common/linalg_op.cc |only xgboost-3.1.2.1/xgboost/src/src/common/linalg_op.cu |only xgboost-3.1.2.1/xgboost/src/src/common/linalg_op.cuh | 104 xgboost-3.1.2.1/xgboost/src/src/common/linalg_op.h | 138 xgboost-3.1.2.1/xgboost/src/src/common/math.h | 70 xgboost-3.1.2.1/xgboost/src/src/common/numa_topo.cc |only xgboost-3.1.2.1/xgboost/src/src/common/numa_topo.h |only xgboost-3.1.2.1/xgboost/src/src/common/numeric.cc | 22 xgboost-3.1.2.1/xgboost/src/src/common/numeric.cu | 20 xgboost-3.1.2.1/xgboost/src/src/common/numeric.h | 48 xgboost-3.1.2.1/xgboost/src/src/common/nvtx_utils.h |only xgboost-3.1.2.1/xgboost/src/src/common/observer.h | 6 xgboost-3.1.2.1/xgboost/src/src/common/optional_weight.cc |only xgboost-3.1.2.1/xgboost/src/src/common/optional_weight.cu |only xgboost-3.1.2.1/xgboost/src/src/common/optional_weight.h |only xgboost-3.1.2.1/xgboost/src/src/common/param_array.cc |only xgboost-3.1.2.1/xgboost/src/src/common/param_array.h |only xgboost-3.1.2.1/xgboost/src/src/common/partition_builder.h | 252 - xgboost-3.1.2.1/xgboost/src/src/common/pseudo_huber.cc | 2 xgboost-3.1.2.1/xgboost/src/src/common/pseudo_huber.h | 4 xgboost-3.1.2.1/xgboost/src/src/common/quantile.cc | 303 - xgboost-3.1.2.1/xgboost/src/src/common/quantile.cu | 231 - xgboost-3.1.2.1/xgboost/src/src/common/quantile.cuh | 155 xgboost-3.1.2.1/xgboost/src/src/common/quantile.h | 92 xgboost-3.1.2.1/xgboost/src/src/common/quantile_loss_utils.cc |only xgboost-3.1.2.1/xgboost/src/src/common/quantile_loss_utils.h |only xgboost-3.1.2.1/xgboost/src/src/common/random.cc | 44 xgboost-3.1.2.1/xgboost/src/src/common/random.cu |only xgboost-3.1.2.1/xgboost/src/src/common/random.h | 100 xgboost-3.1.2.1/xgboost/src/src/common/ranking_utils.cc |only xgboost-3.1.2.1/xgboost/src/src/common/ranking_utils.cu |only xgboost-3.1.2.1/xgboost/src/src/common/ranking_utils.cuh | 114 xgboost-3.1.2.1/xgboost/src/src/common/ranking_utils.h |only xgboost-3.1.2.1/xgboost/src/src/common/ref_resource_view.cuh |only xgboost-3.1.2.1/xgboost/src/src/common/ref_resource_view.h |only xgboost-3.1.2.1/xgboost/src/src/common/resource.cu |only xgboost-3.1.2.1/xgboost/src/src/common/resource.cuh |only xgboost-3.1.2.1/xgboost/src/src/common/row_set.h | 155 xgboost-3.1.2.1/xgboost/src/src/common/stats.cc |only xgboost-3.1.2.1/xgboost/src/src/common/stats.cu | 133 xgboost-3.1.2.1/xgboost/src/src/common/stats.cuh | 280 + xgboost-3.1.2.1/xgboost/src/src/common/stats.h | 146 xgboost-3.1.2.1/xgboost/src/src/common/threading_utils.cc | 122 xgboost-3.1.2.1/xgboost/src/src/common/threading_utils.cuh |only xgboost-3.1.2.1/xgboost/src/src/common/threading_utils.h | 172 xgboost-3.1.2.1/xgboost/src/src/common/threadpool.h |only xgboost-3.1.2.1/xgboost/src/src/common/timer.cc | 45 xgboost-3.1.2.1/xgboost/src/src/common/timer.h | 15 xgboost-3.1.2.1/xgboost/src/src/common/transform.h | 49 xgboost-3.1.2.1/xgboost/src/src/common/transform_iterator.h |only xgboost-3.1.2.1/xgboost/src/src/common/type.h |only xgboost-3.1.2.1/xgboost/src/src/common/utils.h |only xgboost-3.1.2.1/xgboost/src/src/context.cc |only xgboost-3.1.2.1/xgboost/src/src/context.cu |only xgboost-3.1.2.1/xgboost/src/src/data/adapter.cc |only xgboost-3.1.2.1/xgboost/src/src/data/adapter.h | 882 +--- xgboost-3.1.2.1/xgboost/src/src/data/array_interface.cc |only xgboost-3.1.2.1/xgboost/src/src/data/array_interface.cu | 19 xgboost-3.1.2.1/xgboost/src/src/data/array_interface.h | 204 - 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xgboost-3.1.2.1/xgboost/src/src/data/gradient_index_format.cc | 185 - xgboost-3.1.2.1/xgboost/src/src/data/gradient_index_format.h |only xgboost-3.1.2.1/xgboost/src/src/data/gradient_index_page_source.cc | 70 xgboost-3.1.2.1/xgboost/src/src/data/gradient_index_page_source.h | 94 xgboost-3.1.2.1/xgboost/src/src/data/iterative_dmatrix.cc | 315 - xgboost-3.1.2.1/xgboost/src/src/data/iterative_dmatrix.cu | 241 - xgboost-3.1.2.1/xgboost/src/src/data/iterative_dmatrix.h | 148 xgboost-3.1.2.1/xgboost/src/src/data/proxy_dmatrix.cc | 117 xgboost-3.1.2.1/xgboost/src/src/data/proxy_dmatrix.cu | 84 xgboost-3.1.2.1/xgboost/src/src/data/proxy_dmatrix.cuh | 75 xgboost-3.1.2.1/xgboost/src/src/data/proxy_dmatrix.h | 363 +- xgboost-3.1.2.1/xgboost/src/src/data/quantile_dmatrix.cc |only xgboost-3.1.2.1/xgboost/src/src/data/quantile_dmatrix.cu |only xgboost-3.1.2.1/xgboost/src/src/data/quantile_dmatrix.h |only xgboost-3.1.2.1/xgboost/src/src/data/simple_batch_iterator.h | 22 xgboost-3.1.2.1/xgboost/src/src/data/simple_dmatrix.cc | 374 +- xgboost-3.1.2.1/xgboost/src/src/data/simple_dmatrix.cu | 68 xgboost-3.1.2.1/xgboost/src/src/data/simple_dmatrix.cuh | 55 xgboost-3.1.2.1/xgboost/src/src/data/simple_dmatrix.h | 40 xgboost-3.1.2.1/xgboost/src/src/data/sparse_page_dmatrix.cc | 244 - xgboost-3.1.2.1/xgboost/src/src/data/sparse_page_dmatrix.cu | 100 xgboost-3.1.2.1/xgboost/src/src/data/sparse_page_dmatrix.h | 186 - xgboost-3.1.2.1/xgboost/src/src/data/sparse_page_raw_format.cc | 81 xgboost-3.1.2.1/xgboost/src/src/data/sparse_page_source.cc |only xgboost-3.1.2.1/xgboost/src/src/data/sparse_page_source.cu | 43 xgboost-3.1.2.1/xgboost/src/src/data/sparse_page_source.h | 595 ++- xgboost-3.1.2.1/xgboost/src/src/data/sparse_page_writer.h | 95 xgboost-3.1.2.1/xgboost/src/src/data/validation.cc |only xgboost-3.1.2.1/xgboost/src/src/data/validation.cu |only xgboost-3.1.2.1/xgboost/src/src/data/validation.h | 21 xgboost-3.1.2.1/xgboost/src/src/encoder |only xgboost-3.1.2.1/xgboost/src/src/gbm/gblinear.cc | 131 xgboost-3.1.2.1/xgboost/src/src/gbm/gblinear_model.cc | 14 xgboost-3.1.2.1/xgboost/src/src/gbm/gblinear_model.h | 51 xgboost-3.1.2.1/xgboost/src/src/gbm/gbm.cc | 14 xgboost-3.1.2.1/xgboost/src/src/gbm/gbtree.cc | 902 ++-- xgboost-3.1.2.1/xgboost/src/src/gbm/gbtree.cu | 44 xgboost-3.1.2.1/xgboost/src/src/gbm/gbtree.h | 355 - xgboost-3.1.2.1/xgboost/src/src/gbm/gbtree_model.cc | 182 - xgboost-3.1.2.1/xgboost/src/src/gbm/gbtree_model.h | 142 xgboost-3.1.2.1/xgboost/src/src/global_config.cc | 23 xgboost-3.1.2.1/xgboost/src/src/learner.cc | 1102 ++---- xgboost-3.1.2.1/xgboost/src/src/linear/coordinate_common.h | 134 xgboost-3.1.2.1/xgboost/src/src/linear/linear_updater.cc | 4 xgboost-3.1.2.1/xgboost/src/src/linear/updater_coordinate.cc | 57 xgboost-3.1.2.1/xgboost/src/src/linear/updater_gpu_coordinate.cu | 61 xgboost-3.1.2.1/xgboost/src/src/linear/updater_shotgun.cc | 36 xgboost-3.1.2.1/xgboost/src/src/logging.cc | 9 xgboost-3.1.2.1/xgboost/src/src/metric/auc.cc | 222 - xgboost-3.1.2.1/xgboost/src/src/metric/auc.cu | 285 - xgboost-3.1.2.1/xgboost/src/src/metric/auc.h | 63 xgboost-3.1.2.1/xgboost/src/src/metric/elementwise_metric.cu | 251 - xgboost-3.1.2.1/xgboost/src/src/metric/metric.cc | 34 xgboost-3.1.2.1/xgboost/src/src/metric/metric_common.h | 67 xgboost-3.1.2.1/xgboost/src/src/metric/multiclass_metric.cu | 80 xgboost-3.1.2.1/xgboost/src/src/metric/rank_metric.cc | 550 +-- xgboost-3.1.2.1/xgboost/src/src/metric/rank_metric.cu | 464 +- xgboost-3.1.2.1/xgboost/src/src/metric/rank_metric.h |only xgboost-3.1.2.1/xgboost/src/src/metric/survival_metric.cu | 139 xgboost-3.1.2.1/xgboost/src/src/objective/adaptive.cc | 165 xgboost-3.1.2.1/xgboost/src/src/objective/adaptive.cu | 129 xgboost-3.1.2.1/xgboost/src/src/objective/adaptive.h | 72 xgboost-3.1.2.1/xgboost/src/src/objective/aft_obj.cu | 57 xgboost-3.1.2.1/xgboost/src/src/objective/hinge.cu | 136 xgboost-3.1.2.1/xgboost/src/src/objective/init_estimation.cc |only xgboost-3.1.2.1/xgboost/src/src/objective/init_estimation.h |only xgboost-3.1.2.1/xgboost/src/src/objective/lambdarank_obj.cc |only xgboost-3.1.2.1/xgboost/src/src/objective/lambdarank_obj.cu |only xgboost-3.1.2.1/xgboost/src/src/objective/lambdarank_obj.cuh |only xgboost-3.1.2.1/xgboost/src/src/objective/lambdarank_obj.h |only xgboost-3.1.2.1/xgboost/src/src/objective/multiclass_obj.cu | 269 - xgboost-3.1.2.1/xgboost/src/src/objective/multiclass_param.h |only xgboost-3.1.2.1/xgboost/src/src/objective/objective.cc | 34 xgboost-3.1.2.1/xgboost/src/src/objective/quantile_obj.cc |only xgboost-3.1.2.1/xgboost/src/src/objective/quantile_obj.cu |only xgboost-3.1.2.1/xgboost/src/src/objective/regression_loss.h | 118 xgboost-3.1.2.1/xgboost/src/src/objective/regression_obj.cu | 568 +-- xgboost-3.1.2.1/xgboost/src/src/objective/regression_param.h |only xgboost-3.1.2.1/xgboost/src/src/predictor/array_tree_layout.h |only xgboost-3.1.2.1/xgboost/src/src/predictor/cpu_predictor.cc | 1448 +++++-- xgboost-3.1.2.1/xgboost/src/src/predictor/gpu_predictor.cu | 1259 ++++-- xgboost-3.1.2.1/xgboost/src/src/predictor/predict_fn.h | 71 xgboost-3.1.2.1/xgboost/src/src/predictor/predictor.cc | 142 xgboost-3.1.2.1/xgboost/src/src/predictor/predictor.cu |only xgboost-3.1.2.1/xgboost/src/src/predictor/treeshap.cc |only xgboost-3.1.2.1/xgboost/src/src/predictor/treeshap.h |only xgboost-3.1.2.1/xgboost/src/src/predictor/utils.h |only xgboost-3.1.2.1/xgboost/src/src/tree/common_row_partitioner.h | 316 + xgboost-3.1.2.1/xgboost/src/src/tree/constraints.cu | 53 xgboost-3.1.2.1/xgboost/src/src/tree/constraints.cuh | 4 xgboost-3.1.2.1/xgboost/src/src/tree/constraints.h | 8 xgboost-3.1.2.1/xgboost/src/src/tree/fit_stump.cc |only xgboost-3.1.2.1/xgboost/src/src/tree/fit_stump.cu |only xgboost-3.1.2.1/xgboost/src/src/tree/fit_stump.h |only xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/evaluate_splits.cu | 148 xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/evaluate_splits.cuh | 56 xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/evaluator.cu | 34 xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/expand_entry.cuh | 123 xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/feature_groups.cu | 53 xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/feature_groups.cuh | 148 xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/gradient_based_sampler.cu | 335 - xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/gradient_based_sampler.cuh | 134 xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/histogram.cu | 493 +- xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/histogram.cuh | 236 + xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/quantiser.cuh |only xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/row_partitioner.cu | 50 xgboost-3.1.2.1/xgboost/src/src/tree/gpu_hist/row_partitioner.cuh | 353 + xgboost-3.1.2.1/xgboost/src/src/tree/hist/evaluate_splits.h | 528 ++ xgboost-3.1.2.1/xgboost/src/src/tree/hist/expand_entry.h | 248 + xgboost-3.1.2.1/xgboost/src/src/tree/hist/hist_cache.h |only xgboost-3.1.2.1/xgboost/src/src/tree/hist/hist_param.cc |only xgboost-3.1.2.1/xgboost/src/src/tree/hist/hist_param.h |only xgboost-3.1.2.1/xgboost/src/src/tree/hist/histogram.cc |only xgboost-3.1.2.1/xgboost/src/src/tree/hist/histogram.h | 559 +-- xgboost-3.1.2.1/xgboost/src/src/tree/hist/sampler.h |only xgboost-3.1.2.1/xgboost/src/src/tree/io_utils.h |only xgboost-3.1.2.1/xgboost/src/src/tree/multi_target_tree_model.cc |only xgboost-3.1.2.1/xgboost/src/src/tree/param.h | 149 xgboost-3.1.2.1/xgboost/src/src/tree/sample_position.h |only xgboost-3.1.2.1/xgboost/src/src/tree/split_evaluator.h | 35 xgboost-3.1.2.1/xgboost/src/src/tree/tree_model.cc | 921 +---- xgboost-3.1.2.1/xgboost/src/src/tree/tree_updater.cc | 22 xgboost-3.1.2.1/xgboost/src/src/tree/updater_approx.cc | 243 - xgboost-3.1.2.1/xgboost/src/src/tree/updater_colmaker.cc | 135 xgboost-3.1.2.1/xgboost/src/src/tree/updater_gpu_common.cuh | 85 xgboost-3.1.2.1/xgboost/src/src/tree/updater_gpu_hist.cu | 1424 ++++--- xgboost-3.1.2.1/xgboost/src/src/tree/updater_prune.cc | 73 xgboost-3.1.2.1/xgboost/src/src/tree/updater_quantile_hist.cc | 803 ++-- xgboost-3.1.2.1/xgboost/src/src/tree/updater_refresh.cc | 107 xgboost-3.1.2.1/xgboost/src/src/tree/updater_sync.cc | 55 xgboost-3.1.2.1/xgboost/src/xgboost_R.cc | 1624 +++++++- xgboost-3.1.2.1/xgboost/src/xgboost_R.h | 288 + xgboost-3.1.2.1/xgboost/src/xgboost_custom.cc | 16 xgboost-3.1.2.1/xgboost/tests/testthat.R | 2 xgboost-3.1.2.1/xgboost/tests/testthat/helper_model.R |only xgboost-3.1.2.1/xgboost/tests/testthat/test_basic.R | 945 ++++- xgboost-3.1.2.1/xgboost/tests/testthat/test_booster_slicing.R |only xgboost-3.1.2.1/xgboost/tests/testthat/test_callbacks.R | 578 ++- xgboost-3.1.2.1/xgboost/tests/testthat/test_custom_objective.R | 147 xgboost-3.1.2.1/xgboost/tests/testthat/test_dmatrix.R | 649 +++ xgboost-3.1.2.1/xgboost/tests/testthat/test_feature_weights.R |only xgboost-3.1.2.1/xgboost/tests/testthat/test_glm.R | 46 xgboost-3.1.2.1/xgboost/tests/testthat/test_helpers.R | 629 ++- xgboost-3.1.2.1/xgboost/tests/testthat/test_interaction_constraints.R | 51 xgboost-3.1.2.1/xgboost/tests/testthat/test_interactions.R | 141 xgboost-3.1.2.1/xgboost/tests/testthat/test_io.R | 69 xgboost-3.1.2.1/xgboost/tests/testthat/test_model_compatibility.R | 188 - xgboost-3.1.2.1/xgboost/tests/testthat/test_monotone.R |only xgboost-3.1.2.1/xgboost/tests/testthat/test_parameter_exposure.R | 28 xgboost-3.1.2.1/xgboost/tests/testthat/test_poisson_regression.R |only xgboost-3.1.2.1/xgboost/tests/testthat/test_ranking.R | 57 xgboost-3.1.2.1/xgboost/tests/testthat/test_unicode.R | 14 xgboost-3.1.2.1/xgboost/tests/testthat/test_update.R | 94 xgboost-3.1.2.1/xgboost/tests/testthat/test_xgboost.R |only xgboost-3.1.2.1/xgboost/vignettes/xgboost_introduction.Rmd |only xgboost-3.1.2.1/xgboost/vignettes/xgboostfromJSON.Rmd | 48 523 files changed, 39361 insertions(+), 22992 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut] ,
Joe Cheng [aut],
JJ Allaire [aut],
Carson Sievert [aut, cre] ,
Barret Schloerke [aut] ,
Garrick Aden-Buie [aut] ,
Yihui Xie [aut],
Jeff Allen [aut],
Jonathan McPherson [aut],
Alan Dipert [aut],
Barbara Borges [aut],
Posit Softwa [...truncated...]
Maintainer: Carson Sievert <carson@posit.co>
Diff between shiny versions 1.11.1 dated 2025-07-03 and 1.12.0 dated 2025-12-03
shiny-1.11.1/shiny/inst/www/shared/showdown |only shiny-1.12.0/shiny/DESCRIPTION | 157 shiny-1.12.0/shiny/MD5 | 172 shiny-1.12.0/shiny/NAMESPACE | 5 shiny-1.12.0/shiny/NEWS.md | 106 shiny-1.12.0/shiny/R/bind-cache.R | 41 shiny-1.12.0/shiny/R/bind-event.R | 75 shiny-1.12.0/shiny/R/conditions.R | 13 shiny-1.12.0/shiny/R/extended-task.R | 66 shiny-1.12.0/shiny/R/globals.R | 4 shiny-1.12.0/shiny/R/imageutils.R | 2 shiny-1.12.0/shiny/R/input-action.R | 63 shiny-1.12.0/shiny/R/mock-session.R | 56 shiny-1.12.0/shiny/R/otel-attr-srcref.R |only shiny-1.12.0/shiny/R/otel-collect.R |only shiny-1.12.0/shiny/R/otel-enable.R |only shiny-1.12.0/shiny/R/otel-error.R |only shiny-1.12.0/shiny/R/otel-label.R |only shiny-1.12.0/shiny/R/otel-reactive-update.R |only shiny-1.12.0/shiny/R/otel-session.R |only shiny-1.12.0/shiny/R/otel-shiny.R |only shiny-1.12.0/shiny/R/react.R | 80 shiny-1.12.0/shiny/R/reactive-domains.R | 8 shiny-1.12.0/shiny/R/reactives.R | 610 ++ shiny-1.12.0/shiny/R/render-plot.R | 2 shiny-1.12.0/shiny/R/runapp.R | 23 shiny-1.12.0/shiny/R/server.R | 21 shiny-1.12.0/shiny/R/shiny-options.R | 17 shiny-1.12.0/shiny/R/shiny-package.R | 9 shiny-1.12.0/shiny/R/shiny.R | 45 shiny-1.12.0/shiny/R/shinywrappers.R | 34 shiny-1.12.0/shiny/R/showcase.R | 16 shiny-1.12.0/shiny/R/update-input.R | 7 shiny-1.12.0/shiny/R/utils-lang.R | 32 shiny-1.12.0/shiny/R/utils-tags.R |only shiny-1.12.0/shiny/R/utils.R | 18 shiny-1.12.0/shiny/R/version_bs_date_picker.R | 2 shiny-1.12.0/shiny/README.md | 2 shiny-1.12.0/shiny/inst/www/shared/busy-indicators/busy-indicators.css | 2 shiny-1.12.0/shiny/inst/www/shared/datepicker/css/bootstrap-datepicker3.css | 256 - 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Title: A 'ggplot2' Extension for Translating Plot Text
Description: Provides a simple way to translate text elements in 'ggplot2' plots using a dictionary-based approach.
Author: Mathias Leroy [aut, cre]
Maintainer: Mathias Leroy <mathias.leroy.rpkg@gmail.com>
Diff between ggtranslate versions 0.1.1 dated 2025-08-21 and 0.1.2 dated 2025-12-03
DESCRIPTION | 8 MD5 | 8 R/ggtranslate.R | 52 ++-- man/ggtranslate.Rd | 9 tests/testthat/test-ggtranslate.R | 398 +++++++++++++++++++++++++------------- 5 files changed, 310 insertions(+), 165 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-21 1.1.3
2023-02-02 1.1.1
2021-07-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-06 1.1
2019-07-03 1.0
Title: Data Access and Analytical Tools for 'VectorSurv' Users
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Diff between vectorsurvR versions 1.6.0 dated 2025-11-03 and 1.6.1 dated 2025-12-03
DESCRIPTION | 6 - MD5 | 12 +-- R/getArthroCollections.R | 4 - R/getInfectionRate.R | 138 ++++++++++++++++++++++---------------------- R/getPools.R | 15 ++-- inst/doc/vectorsurvR.html | 4 - man/getArthroCollections.Rd | 2 7 files changed, 90 insertions(+), 91 deletions(-)
Title: Interpretable Neural Network Based on Generalized Additive
Models
Description: Neural Additive Model framework based on Generalized Additive Models from Hastie & Tibshirani (1990, ISBN:9780412343902), which trains a different neural network to estimate the contribution of each feature to the response variable. The networks are trained independently leveraging the local scoring and backfitting algorithms to ensure that the Generalized Additive Model converges and it is additive. The resultant Neural Network is a highly accurate and interpretable deep learning model, which can be used for high-risk AI practices where decision-making should be based on accountable and interpretable algorithms.
Author: Ines Ortega-Fernandez [aut, cre, cph] ,
Marta Sestelo [aut, cph]
Maintainer: Ines Ortega-Fernandez <iortega@gradiant.org>
Diff between neuralGAM versions 2.0.0 dated 2025-10-08 and 2.0.1 dated 2025-12-03
neuralGAM-2.0.0/neuralGAM/man/NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/plot.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/predict.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/print.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/summary.NeuralGAM.Rd |only neuralGAM-2.0.1/neuralGAM/DESCRIPTION | 8 neuralGAM-2.0.1/neuralGAM/MD5 | 32 +- neuralGAM-2.0.1/neuralGAM/NAMESPACE | 154 +++++++------- neuralGAM-2.0.1/neuralGAM/NEWS.md | 5 neuralGAM-2.0.1/neuralGAM/R/NeuralGAM.R | 10 neuralGAM-2.0.1/neuralGAM/R/autoplot.neuralGAM.R | 1 neuralGAM-2.0.1/neuralGAM/R/plot.NeuralGAM.R | 2 neuralGAM-2.0.1/neuralGAM/R/predict.NeuralGAM.R | 1 neuralGAM-2.0.1/neuralGAM/man/neuralGAM.Rd |only neuralGAM-2.0.1/neuralGAM/man/plot.neuralGAM.Rd |only neuralGAM-2.0.1/neuralGAM/man/predict.neuralGAM.Rd |only neuralGAM-2.0.1/neuralGAM/man/print.neuralGAM.Rd |only neuralGAM-2.0.1/neuralGAM/man/reexports.Rd | 32 +- neuralGAM-2.0.1/neuralGAM/man/summary.neuralGAM.Rd |only neuralGAM-2.0.1/neuralGAM/tests/testthat/test-NeuralGAM.R | 4 neuralGAM-2.0.1/neuralGAM/tests/testthat/test-plot.R | 6 neuralGAM-2.0.1/neuralGAM/tests/testthat/test-predict.R | 52 ++++ 22 files changed, 183 insertions(+), 124 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-02 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-30 1.1.1
2025-03-07 1.0.3
2025-02-18 1.0.2
2025-02-03 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-17 0.2.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-18 0.1.0
Title: Functions for Extracting and Merging Data in the 'teal'
Framework
Description: A standardized user interface for column selection, that
facilitates dataset merging in 'teal' framework.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Junlue Zhao [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.transform versions 0.7.0 dated 2025-08-20 and 0.7.1 dated 2025-12-03
DESCRIPTION | 10 ++++----- MD5 | 17 ++++++++-------- NEWS.md | 6 +++++ R/call_utils.R | 30 +++++++++++++++++++++++++++++ R/data_extract_filter_module.R | 3 -- R/merge_datasets.R | 6 +++++ build/vignette.rds |binary man/call_uses_magrittr_pipe.Rd |only tests/testthat/test-dplyr_call_examples.R | 1 tests/testthat/test-merge_expression_srv.R | 3 +- 10 files changed, 60 insertions(+), 16 deletions(-)
More information about teal.transform at CRAN
Permanent link
Title: Nonparametric Failure Time Bayesian Additive Regression Trees
Description: Nonparametric Failure Time (NFT) Bayesian Additive Regression Trees (BART): Time-to-event Machine Learning with Heteroskedastic Bayesian Additive Regression Trees (HBART) and Low Information Omnibus (LIO) Dirichlet Process Mixtures (DPM). An NFT BART model is of the form Y = mu + f(x) + sd(x) E where functions f and sd have BART and HBART priors, respectively, while E is a nonparametric error distribution due to a DPM LIO prior hierarchy. See the following for a description of the model at <doi:10.1111/biom.13857>.
Author: Rodney Sparapani [aut, cre],
Robert McCulloch [aut],
Matthew Pratola [ctb],
Hugh Chipman [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between nftbart versions 2.2 dated 2025-08-23 and 2.3 dated 2025-12-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ src/Makevars.in | 3 ++- src/Makevars.win | 3 ++- src/dinfo.h | 8 +++++++- 6 files changed, 23 insertions(+), 12 deletions(-)
Title: 1d Water Level Interpolation along the Rivers Elbe and Rhine
Description: An S4 class and several functions which utilize internally stored
datasets and gauging data enable 1d water level interpolation. The S4 class
(WaterLevelDataFrame) structures the computation and visualisation
of 1d water level information along the German federal waterways Elbe and
Rhine. 'hyd1d' delivers 1d water level data - extracted from the 'FLYS'
database - and validated gauging data - extracted from the hydrological
database 'WISKI7' - package-internally. For computations near real time
gauging data are queried externally from the 'PEGELONLINE REST API'
<https://pegelonline.wsv.de/webservice/dokuRestapi>.
Author: Arnd Weber [aut, cre] ,
Marcus Hatz [aut],
Wolfgang Stuermer [ctb],
Wilfried Wiechmann [ctb],
Benjamin Eberhardt [ctb]
Maintainer: Arnd Weber <arnd.weber@bafg.de>
Diff between hyd1d versions 0.5.3 dated 2025-02-26 and 0.5.4 dated 2025-12-03
DESCRIPTION | 12 +++++------ MD5 | 42 ++++++++++++++++++++-------------------- NEWS.md | 10 +++++++++ R/WaterLevelDataFrame-methods.R | 7 +++--- R/data.R | 8 +++---- R/waterLevel.R | 5 ++++ R/waterLevelFlood1.R | 2 - R/waterLevelFlood2.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/hyd1d.Rmd | 2 - inst/doc/hyd1d.html | 38 ++++++++++++++++++------------------ inst/doc/vignette_DE.Rmd | 2 - inst/doc/vignette_DE.html | 36 +++++++++++++++++----------------- man/df.flys.Rd | 2 - man/df.gauging_data.Rd | 4 +-- man/getPegelonlineW.Rd | 2 - man/waterLevel.Rd | 2 - man/waterLevelFlood1.Rd | 2 - man/waterLevelFlood2.Rd | 2 - vignettes/hyd1d.Rmd | 2 - vignettes/vignette_DE.Rmd | 2 - 22 files changed, 100 insertions(+), 84 deletions(-)
Title: Convolute Probabilistic Distributions
Description: Convolute probabilistic distributions using the random generator
function of each distribution. A new random number generator function is created that
perform the mathematical operation on the individual random samples from the
random generator function of each distribution. See the documentation for examples.
Author: Aponte John [aut, cre]
Maintainer: Aponte John <john.j.aponte@gmail.com>
Diff between convdistr versions 1.6.2 dated 2024-05-05 and 1.6.3 dated 2025-12-03
DESCRIPTION | 13 +- MD5 | 18 +-- NAMESPACE | 1 NEWS.md | 9 + R/restrict_environment.R | 35 +++++- build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/sample_size.html | 83 ++++++++-------- inst/doc/using-convdistr.html | 215 ++++++++++++++++++------------------------ man/convdistr-package.Rd | 1 10 files changed, 191 insertions(+), 185 deletions(-)
Title: Bindings to the Calcite Design System 'JavaScript' Component
Library
Description: Provides access to the 'Calcite Design System' 'javascript'
components via integration with the 'htmltools' and 'shiny' packages.
Pre-built and interactive components can be used to generate either
static html or interactive web applications. Learn more about the
'Calcite Design System' at
<https://developers.arcgis.com/calcite-design-system/>.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between calcite versions 0.1.0 dated 2025-04-01 and 0.1.1 dated 2025-12-03
DESCRIPTION | 9 +++++---- MD5 | 12 +++++++----- NEWS.md |only R/utils.R | 2 +- inst/examples/button-click.R |only inst/examples/earthquake-app.R | 36 +++++++++++++++++++++++++++--------- inst/www/calcite-bindings.js | 10 +++++++--- man/update_calcite.Rd | 2 +- 8 files changed, 48 insertions(+), 23 deletions(-)
Title: Exploratory Data Analysis, Group Comparison Tools, and Other
Procedures
Description: Provides a comprehensive set of tools for descriptive statistics,
graphical data exploration, outlier detection, homoscedasticity testing, and
multiple comparison procedures. Includes manual implementations of Levene's test,
Bartlett's test, and the Fligner-Killeen test, as well as post hoc comparison
methods such as Tukey, Scheffé, Games-Howell, Brunner-Munzel, and others.
This version introduces two new procedures: the Jonckheere-Terpstra trend test
and the Jarque-Bera test with Glinskiy's (2024) correction. Designed for use in
teaching, applied statistical analysis, and reproducible research.
Additionally you can find a post hoc Test Planner, which helps you to make a
decision on which procedure is most suitable.
Author: Carlos Jimenez-Gallardo [aut, cre]
Maintainer: Carlos Jimenez-Gallardo <carlos.jimenez@ufrontera.cl>
Diff between Analitica versions 2.1.2 dated 2025-10-07 and 2.2.0 dated 2025-12-03
DESCRIPTION | 6 - MD5 | 62 ++++++++-------- NAMESPACE | 1 R/BonferroniNPTest.R | 1 R/Conover_ImanTest.R | 1 R/DSCFTest.R | 159 +++++++++++++++++++++++------------------- R/DunnTestNP.R | 2 R/GamesHowellTest.R | 154 +++++++++++++++++++++++++++++----------- R/HolmTest.R | 2 R/MannWhitneyTest.R | 1 R/MauchlyTest.R | 3 R/NemenyiTest.R | 1 R/T2Test.R | 151 +++++++++++++++++++++++++++++---------- R/T3Test.R | 153 +++++++++++++++++++++++++++++----------- R/plot_comparations.R | 110 ++++++++++++++++++++++------- R/posthoc_planner.R | 71 ++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Analitica-intro.html | 6 - man/BonferroniNPTest.Rd | 1 man/ConoverTest.Rd | 1 man/DSCFTest.Rd | 35 +++++---- man/DunnTest.Rd | 3 man/GHTest.Rd | 41 ++++++++-- man/HolmTest.Rd | 2 man/MWTest.Rd | 1 man/MauchlyTest.Rd | 1 man/NemenyiTest.Rd | 1 man/Posthoc_planner.Rd | 65 ++++++++++++++++- man/T2Test.Rd | 35 +++++++-- man/T3Test.Rd | 32 ++++++-- man/plot.comparaciones.Rd | 22 ++++- 32 files changed, 813 insertions(+), 311 deletions(-)