Title: Velocity and Accuracy of the LOg-RAnk TEst
Description: The algorithm implemented in this package was
designed to quickly estimates the distribution of the
log-rank especially for heavy unbalanced groups. VALORATE
estimates the null distribution and the p-value of the
log-rank test based on a recent formulation. For a given
number of alterations that define the size of survival
groups, the estimation involves a weighted sum of
distributions that are conditional on a co-occurrence term
where mutations and events are both present. The estimation
of conditional distributions is quite fast allowing the
analysis of large datasets in few minutes
<https://bioinformatics.mx/index.php/bioinfo-tools/>.
Author: Victor Trevino [aut, cre]
Maintainer: Victor Trevino <vtrevino@itesm.mx>
Diff between valorate versions 1.0-1 dated 2016-10-09 and 1.0-5 dated 2025-03-26
DESCRIPTION | 12 +-- MD5 | 29 +++---- NAMESPACE | 6 + R/valorate.R | 125 +++++++++++++++++++++++++++++--- man/New_Valorate.Rd | 10 +- man/prepare.n1.Rd | 2 man/valorate-internal.Rd | 2 man/valorate.p.value.Rd | 2 man/valorate.plot.empirical.Rd | 2 man/valorate.plot.kaplan.Rd | 2 man/valorate.plot.sampling.densities.Rd | 2 man/valorate.plot.subpop.Rd | 4 - man/valorate.random.n1.Rd |only man/valorate.risk.Rd | 4 - man/valorate.survdiff.Rd | 6 - src/valorate_samplings.c | 109 ++++++++++++++++++++++----- 16 files changed, 249 insertions(+), 68 deletions(-)
Title: Sampling Design for Spatially Explicit Capture-Recapture
Description: Tools for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'. Extensions in version 2.5.0 include costing and evaluation of detector spacing.
Author: Murray Efford [aut, cre] ,
Ian Durbach [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secrdesign versions 2.9.2 dated 2024-09-27 and 2.9.3 dated 2025-03-26
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NEWS | 9 +++++++++ R/optimalSpacing.R | 2 +- R/run.scenarios.R | 3 ++- build |only man/GAoptim.Rd | 6 +++--- man/Lambda.Rd | 2 +- man/optimalSpacing.Rd | 2 +- man/secrdesign-internal.Rd | 4 +++- man/secrdesign-package.Rd | 8 ++++---- src/Makevars |only 12 files changed, 39 insertions(+), 25 deletions(-)
Title: Access Formula 1 Data
Description: Obtain Formula 1 data via the 'Jolpica API' <https://jolpi.ca> and the unofficial API <https://www.formula1.com/en/timing/f1-live> via the 'fastf1' 'Python' library <https://docs.fastf1.dev/>.
Author: Santiago Casanova [aut, cre, cph],
Philip Bulsink [aut]
Maintainer: Santiago Casanova <santiago.casanova@yahoo.com>
Diff between f1dataR versions 2.0.0 dated 2025-03-01 and 2.0.1 dated 2025-03-26
DESCRIPTION | 8 +-- MD5 | 22 ++++---- NEWS.md | 7 ++ R/load_results.R | 23 +++++++-- R/load_schedule.R | 7 ++ R/utils.R | 70 ---------------------------- man/load_results.Rd | 11 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/test-load_driver_telemetry.R | 3 - tests/testthat/test-load_laps.R | 2 tests/testthat/test-load_results.R | 4 + tests/testthat/test-load_session_laps.R | 2 12 files changed, 58 insertions(+), 101 deletions(-)
Title: Bayesian Generalized Linear Regression
Description: Bayesian Generalized Linear Regression.
Author: Gustavo de los Campos [aut],
Paulino Perez Rodriguez [aut, cre]
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Diff between BGLR versions 1.1.3 dated 2024-10-07 and 1.1.4 dated 2025-03-26
CHANGELOG | 3 DESCRIPTION | 7 - MD5 | 18 +- R/BGLR.R | 241 +++++++++++++++++++++++++++++----- R/Multitrait.R | 62 +++++--- demo/00Index | 2 demo/BRR_Sparse.R |only inst/md/BGLR_SPARSE.md |only inst/md/GBLUP.md | 68 +++++++++ src/init.c | 4 src/util_sample.c | 339 +++++++++++++++++++++++++++++++++++++++++++------ 11 files changed, 635 insertions(+), 109 deletions(-)
Title: Measuring Association with Recursive Binning
Description: An iterative implementation of a recursive binary partitioning algorithm to measure pairwise dependence with a modular design that allows user specification of the splitting logic and stop criteria. Helper functions provide suggested versions of both and support visualization and the computation of summary statistics on final binnings. For a complete description of the functionality and algorithm, see Salahub and Oldford (2023) <doi:10.48550/arXiv.2311.08561>.
Author: Chris Salahub [aut, cre]
Maintainer: Chris Salahub <chris.salahub@uwaterloo.ca>
Diff between AssocBin versions 1.0-2 dated 2024-12-09 and 1.1-0 dated 2025-03-26
DESCRIPTION | 8 +- MD5 | 34 ++++++------ NAMESPACE | 11 +++- R/covariances.R |only R/degreesOfFreedom.R |only R/dispatch.R | 131 +++++++++++++++++++++++++++++++++++++++--------- R/generating_blocks.R |only R/plotBinning.R | 41 ++++++++++++++- R/splitters.R | 14 ++--- R/stats.R | 16 +++-- build/vignette.rds |binary data/heart.rda |binary data/sp500pseudo.rda |binary inst/doc/AssocBin.html | 28 +++++----- inst/doc/complex.html | 24 ++++---- man/binstatistics.Rd | 6 +- man/degreesoffreedom.Rd |only man/inDep.Rd | 34 +++++++++--- man/methods.Rd | 23 ++++++++ man/shadings.Rd | 18 ++++++ 20 files changed, 292 insertions(+), 96 deletions(-)
Title: Secure Shell (SSH) Client for R
Description: Connect to a remote server over SSH to transfer files via SCP,
setup a secure tunnel, or run a command or script on the host while
streaming stdout and stderr directly to the client.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between ssh versions 0.9.3 dated 2024-09-19 and 0.9.4 dated 2025-03-26
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- build/vignette.rds |binary src/Makevars.in | 6 +++--- src/Makevars.win | 15 ++++++++------- tools/winlibs.R | 11 ++++++----- 6 files changed, 25 insertions(+), 23 deletions(-)
Title: Joint Statistical Models for Preference Learning with Rankings
and Ratings
Description: Statistical tools for the Mallows-Binomial model, the first joint statistical model for preference learning for rankings and ratings. This project was supported by the National Science Foundation under Grant No. 2019901.
Author: Michael Pearce [aut, cre, cph]
Maintainer: Michael Pearce <pearce790@gmail.com>
Diff between rankrate versions 1.2.0 dated 2023-08-17 and 1.2.1 dated 2025-03-26
DESCRIPTION | 12 +++++++----- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ README.md | 5 +++++ inst/doc/overview.R | 3 --- inst/doc/overview.Rmd | 7 ++++--- inst/doc/overview.html | 5 +++++ inst/doc/tutorial.html | 4 ++-- vignettes/overview.Rmd | 7 ++++--- 9 files changed, 39 insertions(+), 24 deletions(-)
Title: Interaction Selection in Logistic Regression
Description: Logistic regression model with data-driven screening for significant two-way interactions.
Author: Yi Lian [aut, cre],
Tianze Jiao [aut],
Guanbo Wang [aut],
Archer Y. Yang [aut],
Julien Mairal [ctb],
Yuansi Chen [ctb]
Maintainer: Yi Lian <yi.lian@pennmedicine.upenn.edu>
Diff between intsel versions 1.0 dated 2025-03-10 and 1.0.1 dated 2025-03-26
DESCRIPTION | 8 ++--- MD5 | 18 ++++++------ R/RcppExports.R | 8 ++--- R/intsel.R | 4 ++ R/intsel_cv.R | 9 +++++- man/intsel.Rd | 3 ++ man/intsel_cv.Rd | 3 ++ src/RcppExports.cpp | 18 ++++++------ src/main.cpp | 16 ++++++---- tests/testthat/test-intsel.R | 63 ++++++++++++++++++++++++++++++++++++++++++- 10 files changed, 117 insertions(+), 33 deletions(-)
Title: Data for "R Graphics Cookbook"
Description: Data sets used in the book "R Graphics Cookbook" by Winston
Chang, published by O'Reilly Media.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>
Diff between gcookbook versions 2.0 dated 2018-11-06 and 2.0.1 dated 2025-03-26
gcookbook-2.0.1/gcookbook/DESCRIPTION | 16 ++++++++++------ gcookbook-2.0.1/gcookbook/MD5 | 15 +++++++-------- gcookbook-2.0.1/gcookbook/R/gcookbook.r | 15 +++++++-------- gcookbook-2.0.1/gcookbook/man/cabbage_exp.Rd | 4 ++-- gcookbook-2.0.1/gcookbook/man/climate.Rd | 4 ++-- gcookbook-2.0.1/gcookbook/man/countries.Rd | 2 +- gcookbook-2.0.1/gcookbook/man/gcookbook.Rd | 6 +++++- gcookbook-2.0.1/gcookbook/man/isabel.Rd | 2 +- gcookbook-2.0/gcookbook/data/datalist |only 9 files changed, 35 insertions(+), 29 deletions(-)
Title: Download Files over HTTP and HTTPS
Description: Provides a wrapper for the download.file function,
making it possible to download files over HTTPS on Windows, Mac OS X, and
other Unix-like platforms. The 'RCurl' package provides this functionality
(and much more) but can be difficult to install because it must be compiled
with external dependencies. This package has no external dependencies, so
it is much easier to install.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>
Diff between downloader versions 0.4 dated 2015-07-09 and 0.4.1 dated 2025-03-26
downloader-0.4.1/downloader/DESCRIPTION | 13 +++++++---- downloader-0.4.1/downloader/MD5 | 24 ++++++++++----------- downloader-0.4.1/downloader/NAMESPACE | 2 - downloader-0.4.1/downloader/R/downloader-package.r | 3 -- downloader-0.4.1/downloader/R/sha_url.r | 2 - downloader-0.4.1/downloader/R/source_url.r | 2 - downloader-0.4.1/downloader/man/download.Rd | 22 +++++++++---------- downloader-0.4.1/downloader/man/downloader.Rd | 15 +++++++++++-- downloader-0.4.1/downloader/man/sha_url.Rd | 9 ++++--- downloader-0.4.1/downloader/man/source_url.Rd | 7 +++--- downloader-0.4.1/downloader/tests/testthat |only downloader-0.4.1/downloader/tests/testthat.R |only downloader-0.4/downloader/inst |only downloader-0.4/downloader/tests/test-all.R |only 14 files changed, 58 insertions(+), 41 deletions(-)
Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based
inventory data from the U.S. Department of Agriculture, Forest Service,
Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut],
Gretchen Moisen [aut],
Paul Patterson [aut],
Chris Toney [aut],
Grayson White [aut, cre] ,
Joshua Yamamoto [aut]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTA versions 3.7.0 dated 2025-02-04 and 3.7.1 dated 2025-03-26
FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_datSum_examples.R |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_datSum_examples.Rmd |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_datSum_examples.html |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_manual_mod_est.R |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_manual_mod_est.Rmd |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_manual_mod_est.html |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_manual_mod_pop.R |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_manual_mod_pop.Rmd |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_manual_mod_pop.html |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_tutorial_DB.R |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_tutorial_DB.Rmd |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_tutorial_DB.html |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_tutorial_dat.R |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_tutorial_dat.Rmd |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_tutorial_dat.html |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_tutorial_sp.R |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_tutorial_sp.Rmd |only FIESTA-3.7.0/FIESTA/inst/doc/FIESTA_tutorial_sp.html |only FIESTA-3.7.0/FIESTA/vignettes/FIESTA_datSum_examples.Rmd |only FIESTA-3.7.0/FIESTA/vignettes/FIESTA_manual_mod_est.Rmd |only FIESTA-3.7.0/FIESTA/vignettes/FIESTA_manual_mod_pop.Rmd |only FIESTA-3.7.0/FIESTA/vignettes/FIESTA_tutorial_DB.Rmd |only FIESTA-3.7.0/FIESTA/vignettes/FIESTA_tutorial_dat.Rmd |only FIESTA-3.7.0/FIESTA/vignettes/FIESTA_tutorial_sp.Rmd |only FIESTA-3.7.1/FIESTA/DESCRIPTION | 10 FIESTA-3.7.1/FIESTA/MD5 | 133 FIESTA-3.7.1/FIESTA/R/DBgetCSV.R | 112 FIESTA-3.7.1/FIESTA/R/DBgetEvalid.R | 111 FIESTA-3.7.1/FIESTA/R/DBgetPlots.R | 67 FIESTA-3.7.1/FIESTA/R/DBgetXY.R | 37 FIESTA-3.7.1/FIESTA/R/DBqryCSV.R | 6 FIESTA-3.7.1/FIESTA/R/check.cond.R | 5 FIESTA-3.7.1/FIESTA/R/check.estdata.R | 9 FIESTA-3.7.1/FIESTA/R/check.estdataP2VEG.R | 58 FIESTA-3.7.1/FIESTA/R/check.popdataCHNG.R | 7 FIESTA-3.7.1/FIESTA/R/check.popdataP2VEG.R | 235 - FIESTA-3.7.1/FIESTA/R/check.popdataPLT.R | 8 FIESTA-3.7.1/FIESTA/R/check.rowcol.R | 1787 ------- FIESTA-3.7.1/FIESTA/R/check.tabvar.R |only FIESTA-3.7.1/FIESTA/R/check.tree.R | 2 FIESTA-3.7.1/FIESTA/R/datLUTnm.R | 11 FIESTA-3.7.1/FIESTA/R/datLUTspp.R | 59 FIESTA-3.7.1/FIESTA/R/datSumTree.R | 1123 ++-- FIESTA-3.7.1/FIESTA/R/datSumTreeDom.R | 275 - FIESTA-3.7.1/FIESTA/R/est.outtabs.R | 33 FIESTA-3.7.1/FIESTA/R/modGBarea.R | 30 FIESTA-3.7.1/FIESTA/R/modGBchng.R | 9 FIESTA-3.7.1/FIESTA/R/modGBp2veg.R | 149 FIESTA-3.7.1/FIESTA/R/modGBpop.R | 70 FIESTA-3.7.1/FIESTA/R/modGBratio.R | 13 FIESTA-3.7.1/FIESTA/R/modGBtree.R | 9 FIESTA-3.7.1/FIESTA/R/modMAarea.R | 8 FIESTA-3.7.1/FIESTA/R/modMAratio.R | 2 FIESTA-3.7.1/FIESTA/R/modMAtree.R | 4 FIESTA-3.7.1/FIESTA/R/modSAarea.R | 4 FIESTA-3.7.1/FIESTA/R/modSAtree.R | 6 FIESTA-3.7.1/FIESTA/R/spExtractRast.R | 5 FIESTA-3.7.1/FIESTA/R/zzz.R | 2 FIESTA-3.7.1/FIESTA/build/vignette.rds |binary FIESTA-3.7.1/FIESTA/inst/doc/FIESTA_tutorial_GB.R | 16 FIESTA-3.7.1/FIESTA/inst/doc/FIESTA_tutorial_GB.Rmd | 18 FIESTA-3.7.1/FIESTA/inst/doc/FIESTA_tutorial_GB.html | 3500 +++++++-------- FIESTA-3.7.1/FIESTA/inst/doc/FIESTA_tutorial_MA.html | 139 FIESTA-3.7.1/FIESTA/inst/doc/FIESTA_tutorial_PB.html | 152 FIESTA-3.7.1/FIESTA/inst/doc/FIESTA_tutorial_SA.html | 4 FIESTA-3.7.1/FIESTA/man/datLUTnm.Rd | 5 FIESTA-3.7.1/FIESTA/man/datLUTspp.Rd | 7 FIESTA-3.7.1/FIESTA/man/datSumTree.Rd | 32 FIESTA-3.7.1/FIESTA/man/datSumTreeDom.Rd | 14 FIESTA-3.7.1/FIESTA/man/ref_codes.Rd | 2 FIESTA-3.7.1/FIESTA/tests/testthat/_snaps/modGBarea.md | 3 FIESTA-3.7.1/FIESTA/tests/testthat/_snaps/modGBratio.md | 6 FIESTA-3.7.1/FIESTA/tests/testthat/_snaps/modGBtree.md | 9 FIESTA-3.7.1/FIESTA/tests/testthat/test-modGBarea.R | 4 FIESTA-3.7.1/FIESTA/tests/testthat/test-modGBratio.R | 5 FIESTA-3.7.1/FIESTA/tests/testthat/test-modGBtree.R | 5 FIESTA-3.7.1/FIESTA/tests/testthat/test-spExtractRast.R | 36 FIESTA-3.7.1/FIESTA/tests/testthat/test-spGetPlots.R | 3 FIESTA-3.7.1/FIESTA/tests/testthat/test-spGetXY.R | 3 FIESTA-3.7.1/FIESTA/vignettes/FIESTA_tutorial_GB.Rmd | 18 80 files changed, 3464 insertions(+), 4916 deletions(-)
Title: Datasets and Functions to Accompany Analisis De Datos Con R
Description: Datasets and functions to accompany the book 'Analisis de datos con el programa
estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109).
The package helps carry out data management, exploratory analyses, and model fitting.
Author: Christian Salas-Eljatib [aut, cre]
,
Pino Nicolas [ctb] ,
Riquelme Joaquin [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Diff between datana versions 1.0.5 dated 2024-09-07 and 1.0.6 dated 2025-03-26
datana-1.0.5/datana/R/describe_datas.R |only datana-1.0.5/datana/data/airnyc.rda |only datana-1.0.5/datana/data/airnyc2.rda |only datana-1.0.5/datana/data/baiTreelines.rda |only datana-1.0.5/datana/data/baiTreelines2.rda |only datana-1.0.5/datana/data/bearsDepu.rda |only datana-1.0.5/datana/data/bearsDepu2.rda |only datana-1.0.5/datana/data/carbohydrateTreelines.rda |only datana-1.0.5/datana/data/deadForestCA.rda |only datana-1.0.5/datana/data/deadForestCA2.rda |only datana-1.0.5/datana/data/deadLianas.rda |only datana-1.0.5/datana/data/deadLianas2.rda |only datana-1.0.5/datana/data/forestFire.rda |only datana-1.0.5/datana/data/forestFire2.rda |only datana-1.0.5/datana/data/forestHawaii.rda |only datana-1.0.5/datana/data/landCoverSantiago.rda |only datana-1.0.5/datana/data/landCoverSantiago2.rda |only datana-1.0.5/datana/data/pinusContorta.rda |only datana-1.0.5/datana/data/pinusContorta2.rda |only datana-1.0.5/datana/data/plantsHawaii.rda |only datana-1.0.5/datana/data/presidentChile.rda |only datana-1.0.5/datana/data/presidentChile2.rda |only datana-1.0.5/datana/data/primary2.rda |only datana-1.0.5/datana/data/pspLlancahue.rda |only datana-1.0.5/datana/data/pspLlancahue2.rda |only datana-1.0.5/datana/data/pspRuca.rda |only datana-1.0.5/datana/data/pspRuca2.rda |only datana-1.0.5/datana/data/snaspeChile.rda |only datana-1.0.5/datana/data/snaspeChile2.rda |only datana-1.0.5/datana/data/spatAustria.rda |only datana-1.0.5/datana/data/speciesList.rda |only datana-1.0.5/datana/data/trailCameraTrap.rda |only datana-1.0.5/datana/man/airnyc.Rd |only datana-1.0.5/datana/man/airnyc2.Rd |only datana-1.0.5/datana/man/baiTreelines.Rd |only datana-1.0.5/datana/man/baiTreelines2.Rd |only datana-1.0.5/datana/man/bearsDepu.Rd |only datana-1.0.5/datana/man/bearsDepu2.Rd |only datana-1.0.5/datana/man/carbohydrateTreelines.Rd |only datana-1.0.5/datana/man/deadForestCA.Rd |only datana-1.0.5/datana/man/deadForestCA2.Rd |only datana-1.0.5/datana/man/deadLianas.Rd |only datana-1.0.5/datana/man/deadLianas2.Rd |only datana-1.0.5/datana/man/forestFire.Rd |only datana-1.0.5/datana/man/forestFire2.Rd |only datana-1.0.5/datana/man/forestHawaii.Rd |only datana-1.0.5/datana/man/landCoverSantiago.Rd |only datana-1.0.5/datana/man/landCoverSantiago2.Rd |only datana-1.0.5/datana/man/pinusContorta.Rd |only datana-1.0.5/datana/man/pinusContorta2.Rd |only datana-1.0.5/datana/man/plantsHawaii.Rd |only datana-1.0.5/datana/man/presidentChile.Rd |only datana-1.0.5/datana/man/presidentChile2.Rd |only datana-1.0.5/datana/man/primary2.Rd |only datana-1.0.5/datana/man/pspLlancahue.Rd |only datana-1.0.5/datana/man/pspLlancahue2.Rd |only datana-1.0.5/datana/man/pspRuca.Rd |only datana-1.0.5/datana/man/pspRuca2.Rd |only datana-1.0.5/datana/man/snaspeChile.Rd |only datana-1.0.5/datana/man/snaspeChile2.Rd |only datana-1.0.5/datana/man/spatAustria.Rd |only datana-1.0.5/datana/man/speciesList.Rd |only datana-1.0.5/datana/man/trailCameraTrap.Rd |only datana-1.0.6/datana/DESCRIPTION | 13 datana-1.0.6/datana/MD5 | 522 ++++++++++----------- datana-1.0.6/datana/NAMESPACE | 8 datana-1.0.6/datana/R/cdf.R | 33 - datana-1.0.6/datana/R/contrast.R | 20 datana-1.0.6/datana/R/deleteRight.R | 17 datana-1.0.6/datana/R/describeDatas.R |only datana-1.0.6/datana/R/descstat.R | 31 - datana-1.0.6/datana/R/findColumn.byname.R | 14 datana-1.0.6/datana/R/gmean.R | 14 datana-1.0.6/datana/R/kurto.R | 12 datana-1.0.6/datana/R/lrt.R | 12 datana-1.0.6/datana/R/pvalt.R | 17 datana-1.0.6/datana/R/pvalz.R | 13 datana-1.0.6/datana/R/skew.R | 15 datana-1.0.6/datana/R/timeserplot.R | 461 ++++++++---------- datana-1.0.6/datana/R/xyboxplot.R | 45 + datana-1.0.6/datana/R/xyhist.R | 24 datana-1.0.6/datana/R/xymultiplot.R | 139 +++-- datana-1.0.6/datana/build/partial.rdb |binary datana-1.0.6/datana/data/ChickWeight.rda |only datana-1.0.6/datana/data/aboutrsq.rda |binary datana-1.0.6/datana/data/aboutrsq2.rda |binary datana-1.0.6/datana/data/airquality.rda |only datana-1.0.6/datana/data/airquality2.rda |only datana-1.0.6/datana/data/annualppCities.rda |binary datana-1.0.6/datana/data/annualppCities2.rda |binary datana-1.0.6/datana/data/araucaria.rda |binary datana-1.0.6/datana/data/araucaria2.rda |binary datana-1.0.6/datana/data/baitreeline.rda |only datana-1.0.6/datana/data/baitreeline2.rda |only datana-1.0.6/datana/data/bears.rda |binary datana-1.0.6/datana/data/bears2.rda |binary datana-1.0.6/datana/data/bearsdepu.rda |only datana-1.0.6/datana/data/bearsdepu2.rda |only datana-1.0.6/datana/data/beetles.rda |binary datana-1.0.6/datana/data/beetles2.rda |binary datana-1.0.6/datana/data/biomass.rda |binary datana-1.0.6/datana/data/biomass2.rda |binary datana-1.0.6/datana/data/cameratrap.rda |only datana-1.0.6/datana/data/cameratrap2.rda |only datana-1.0.6/datana/data/carbohtrees.rda |only datana-1.0.6/datana/data/carbohtrees2.rda |only datana-1.0.6/datana/data/casen.rda |only datana-1.0.6/datana/data/chicksw.rda |binary datana-1.0.6/datana/data/chicksw2.rda |only datana-1.0.6/datana/data/co2temp.rda |only datana-1.0.6/datana/data/corkoak.rda |binary datana-1.0.6/datana/data/corkoak2.rda |binary datana-1.0.6/datana/data/crown.rda |binary datana-1.0.6/datana/data/crown2.rda |binary datana-1.0.6/datana/data/demograph.rda |binary datana-1.0.6/datana/data/election.rda |binary datana-1.0.6/datana/data/election2.rda |binary datana-1.0.6/datana/data/eucaleaf.rda |binary datana-1.0.6/datana/data/eucaleaf2.rda |binary datana-1.0.6/datana/data/eucaleafAll.rda |binary datana-1.0.6/datana/data/eucaleafAll2.rda |binary datana-1.0.6/datana/data/eucaplot.rda |binary datana-1.0.6/datana/data/eucaplot2.rda |binary datana-1.0.6/datana/data/eucaplotr.rda |only datana-1.0.6/datana/data/eucaplotr2.rda |only datana-1.0.6/datana/data/fertiliza.rda |binary datana-1.0.6/datana/data/fertiliza2.rda |binary datana-1.0.6/datana/data/ficdiamgr.rda |binary datana-1.0.6/datana/data/ficdiamgr2.rda |binary datana-1.0.6/datana/data/fishgrowth.rda |binary datana-1.0.6/datana/data/fishgrowth2.rda |binary datana-1.0.6/datana/data/floraChile.rda |binary datana-1.0.6/datana/data/floraChile2.rda |binary datana-1.0.6/datana/data/football.rda |binary datana-1.0.6/datana/data/football2.rda |binary datana-1.0.6/datana/data/forestfire.rda |only datana-1.0.6/datana/data/forestfire2.rda |only datana-1.0.6/datana/data/hawaii.rda |binary datana-1.0.6/datana/data/hawaii2.rda |binary datana-1.0.6/datana/data/hgrdfir.rda |binary datana-1.0.6/datana/data/hgrdfir2.rda |binary datana-1.0.6/datana/data/idahohd.rda |binary datana-1.0.6/datana/data/idahohd2.rda |binary datana-1.0.6/datana/data/invasivesRCI.rda |binary datana-1.0.6/datana/data/landcover.rda |only datana-1.0.6/datana/data/landcover2.rda |only datana-1.0.6/datana/data/largetrees.rda |only datana-1.0.6/datana/data/largetrees2.rda |only datana-1.0.6/datana/data/llancahue.rda |only datana-1.0.6/datana/data/llancahue2.rda |only datana-1.0.6/datana/data/lleuque.rda |binary datana-1.0.6/datana/data/lleuque2.rda |only datana-1.0.6/datana/data/pcontorta.rda |only datana-1.0.6/datana/data/pcontorta2.rda |only datana-1.0.6/datana/data/pinaster.rda |binary datana-1.0.6/datana/data/pinaster2.rda |binary datana-1.0.6/datana/data/pinusSpp.rda |binary datana-1.0.6/datana/data/pinusSpp2.rda |binary datana-1.0.6/datana/data/presenceIce.rda |binary datana-1.0.6/datana/data/president.rda |only datana-1.0.6/datana/data/primary.rda |binary datana-1.0.6/datana/data/pspruca.rda |only datana-1.0.6/datana/data/pspruca2.rda |only datana-1.0.6/datana/data/ptaeda.rda |binary datana-1.0.6/datana/data/ptaeda2.rda |binary datana-1.0.6/datana/data/radiatapl.rda |binary datana-1.0.6/datana/data/radiatapl2.rda |binary datana-1.0.6/datana/data/raulihg.rda |binary datana-1.0.6/datana/data/raulihg2.rda |binary datana-1.0.6/datana/data/regNothofagus.rda |binary datana-1.0.6/datana/data/simula.rda |binary datana-1.0.6/datana/data/slashpine.rda |binary datana-1.0.6/datana/data/slashpine2.rda |binary datana-1.0.6/datana/data/sludge.rda |binary datana-1.0.6/datana/data/sludge2.rda |only datana-1.0.6/datana/data/snaspe.rda |only datana-1.0.6/datana/data/snaspe2.rda |only datana-1.0.6/datana/data/soiltreat.rda |binary datana-1.0.6/datana/data/soiltreat2.rda |binary datana-1.0.6/datana/data/spataustria.rda |only datana-1.0.6/datana/data/species.rda |only datana-1.0.6/datana/data/species2.rda |only datana-1.0.6/datana/data/sppAbundance.rda |binary datana-1.0.6/datana/data/sppTraits.rda |binary datana-1.0.6/datana/data/standLleuque.rda |binary datana-1.0.6/datana/data/standLleuque2.rda |binary datana-1.0.6/datana/data/traits.rda |binary datana-1.0.6/datana/data/traits2.rda |binary datana-1.0.6/datana/data/treegr.rda |binary datana-1.0.6/datana/data/treegr2.rda |binary datana-1.0.6/datana/data/treelistinve.rda |binary datana-1.0.6/datana/data/treelistinve2.rda |binary datana-1.0.6/datana/data/treevol.rda |binary datana-1.0.6/datana/data/treevol2.rda |binary datana-1.0.6/datana/data/treevolroble.rda |binary datana-1.0.6/datana/data/treevolroble2.rda |binary datana-1.0.6/datana/data/treevolruca.rda |binary datana-1.0.6/datana/data/treevolruca2.rda |binary datana-1.0.6/datana/inst/CITATION | 14 datana-1.0.6/datana/man/ChickWeight.Rd |only datana-1.0.6/datana/man/aboutrsq.Rd | 9 datana-1.0.6/datana/man/aboutrsq2.Rd | 18 datana-1.0.6/datana/man/airquality.Rd |only datana-1.0.6/datana/man/airquality2.Rd |only datana-1.0.6/datana/man/annualppCities.Rd | 5 datana-1.0.6/datana/man/annualppCities2.Rd | 5 datana-1.0.6/datana/man/araucaria.Rd | 50 +- datana-1.0.6/datana/man/araucaria2.Rd | 44 - datana-1.0.6/datana/man/baitreeline.Rd |only datana-1.0.6/datana/man/baitreeline2.Rd |only datana-1.0.6/datana/man/bears.Rd | 17 datana-1.0.6/datana/man/bears2.Rd | 26 - datana-1.0.6/datana/man/bearsdepu.Rd |only datana-1.0.6/datana/man/bearsdepu2.Rd |only datana-1.0.6/datana/man/beetles.Rd | 30 - datana-1.0.6/datana/man/beetles2.Rd | 31 - datana-1.0.6/datana/man/biomass.Rd | 11 datana-1.0.6/datana/man/biomass2.Rd | 22 datana-1.0.6/datana/man/cameratrap.Rd |only datana-1.0.6/datana/man/cameratrap2.Rd |only datana-1.0.6/datana/man/carbohtrees.Rd |only datana-1.0.6/datana/man/carbohtrees2.Rd |only datana-1.0.6/datana/man/casen.Rd |only datana-1.0.6/datana/man/cdf.Rd | 30 - datana-1.0.6/datana/man/chicksw.Rd | 24 datana-1.0.6/datana/man/chicksw2.Rd |only datana-1.0.6/datana/man/co2temp.Rd |only datana-1.0.6/datana/man/contrast.Rd | 14 datana-1.0.6/datana/man/corkoak.Rd | 12 datana-1.0.6/datana/man/corkoak2.Rd | 12 datana-1.0.6/datana/man/crown.Rd | 24 datana-1.0.6/datana/man/crown2.Rd | 23 datana-1.0.6/datana/man/datana-package.Rd | 33 - datana-1.0.6/datana/man/deleteRight.Rd | 18 datana-1.0.6/datana/man/demograph.Rd | 15 datana-1.0.6/datana/man/descstat.Rd | 23 datana-1.0.6/datana/man/election.Rd | 7 datana-1.0.6/datana/man/election2.Rd | 4 datana-1.0.6/datana/man/eucaleaf.Rd | 23 datana-1.0.6/datana/man/eucaleaf2.Rd | 31 - datana-1.0.6/datana/man/eucaleafAll.Rd | 26 - datana-1.0.6/datana/man/eucaleafAll2.Rd | 28 - datana-1.0.6/datana/man/eucaplot.Rd | 18 datana-1.0.6/datana/man/eucaplot2.Rd | 29 - datana-1.0.6/datana/man/eucaplotr.Rd |only datana-1.0.6/datana/man/eucaplotr2.Rd |only datana-1.0.6/datana/man/fertiliza.Rd | 15 datana-1.0.6/datana/man/fertiliza2.Rd | 14 datana-1.0.6/datana/man/ficdiamgr.Rd | 14 datana-1.0.6/datana/man/ficdiamgr2.Rd | 5 datana-1.0.6/datana/man/findColumn.byname.Rd | 15 datana-1.0.6/datana/man/fishgrowth.Rd | 7 datana-1.0.6/datana/man/fishgrowth2.Rd | 7 datana-1.0.6/datana/man/floraChile.Rd | 11 datana-1.0.6/datana/man/floraChile2.Rd | 10 datana-1.0.6/datana/man/football.Rd | 5 datana-1.0.6/datana/man/football2.Rd | 8 datana-1.0.6/datana/man/forestfire.Rd |only datana-1.0.6/datana/man/forestfire2.Rd |only datana-1.0.6/datana/man/gmean.Rd | 15 datana-1.0.6/datana/man/hawaii.Rd | 20 datana-1.0.6/datana/man/hawaii2.Rd | 20 datana-1.0.6/datana/man/hgrdfir.Rd | 17 datana-1.0.6/datana/man/hgrdfir2.Rd | 15 datana-1.0.6/datana/man/idahohd.Rd | 15 datana-1.0.6/datana/man/idahohd2.Rd | 7 datana-1.0.6/datana/man/invasivesRCI.Rd | 26 - datana-1.0.6/datana/man/kurto.Rd | 12 datana-1.0.6/datana/man/landcover.Rd |only datana-1.0.6/datana/man/landcover2.Rd |only datana-1.0.6/datana/man/largetrees.Rd |only datana-1.0.6/datana/man/largetrees2.Rd |only datana-1.0.6/datana/man/llancahue.Rd |only datana-1.0.6/datana/man/llancahue2.Rd |only datana-1.0.6/datana/man/lleuque.Rd | 26 - datana-1.0.6/datana/man/lleuque2.Rd |only datana-1.0.6/datana/man/lrt.Rd | 12 datana-1.0.6/datana/man/pcontorta.Rd |only datana-1.0.6/datana/man/pcontorta2.Rd |only datana-1.0.6/datana/man/pinaster.Rd | 11 datana-1.0.6/datana/man/pinaster2.Rd | 8 datana-1.0.6/datana/man/pinusSpp.Rd | 21 datana-1.0.6/datana/man/pinusSpp2.Rd | 22 datana-1.0.6/datana/man/presenceIce.Rd | 17 datana-1.0.6/datana/man/president.Rd |only datana-1.0.6/datana/man/primary.Rd | 54 +- datana-1.0.6/datana/man/pspruca.Rd |only datana-1.0.6/datana/man/pspruca2.Rd |only datana-1.0.6/datana/man/ptaeda.Rd | 23 datana-1.0.6/datana/man/ptaeda2.Rd | 15 datana-1.0.6/datana/man/pvalt.Rd | 17 datana-1.0.6/datana/man/pvalz.Rd | 13 datana-1.0.6/datana/man/radiatapl.Rd | 13 datana-1.0.6/datana/man/radiatapl2.Rd | 18 datana-1.0.6/datana/man/raulihg.Rd | 19 datana-1.0.6/datana/man/raulihg2.Rd | 20 datana-1.0.6/datana/man/regNothofagus.Rd | 23 datana-1.0.6/datana/man/simula.Rd | 36 - datana-1.0.6/datana/man/skew.Rd | 15 datana-1.0.6/datana/man/slashpine.Rd | 11 datana-1.0.6/datana/man/slashpine2.Rd | 11 datana-1.0.6/datana/man/sludge.Rd | 10 datana-1.0.6/datana/man/sludge2.Rd |only datana-1.0.6/datana/man/snaspe.Rd |only datana-1.0.6/datana/man/snaspe2.Rd |only datana-1.0.6/datana/man/soiltreat.Rd | 8 datana-1.0.6/datana/man/soiltreat2.Rd | 21 datana-1.0.6/datana/man/spataustria.Rd |only datana-1.0.6/datana/man/species.Rd |only datana-1.0.6/datana/man/species2.Rd |only datana-1.0.6/datana/man/sppAbundance.Rd | 25 - datana-1.0.6/datana/man/sppTraits.Rd | 10 datana-1.0.6/datana/man/standLleuque.Rd | 12 datana-1.0.6/datana/man/standLleuque2.Rd | 29 - datana-1.0.6/datana/man/timeserplot.Rd | 106 ++-- datana-1.0.6/datana/man/traits.Rd | 15 datana-1.0.6/datana/man/traits2.Rd | 11 datana-1.0.6/datana/man/treegr.Rd | 23 datana-1.0.6/datana/man/treegr2.Rd | 30 - datana-1.0.6/datana/man/treelistinve.Rd | 32 - datana-1.0.6/datana/man/treelistinve2.Rd | 30 - datana-1.0.6/datana/man/treevol.Rd | 11 datana-1.0.6/datana/man/treevol2.Rd | 8 datana-1.0.6/datana/man/treevolroble.Rd | 16 datana-1.0.6/datana/man/treevolroble2.Rd | 18 datana-1.0.6/datana/man/treevolruca.Rd | 22 datana-1.0.6/datana/man/treevolruca2.Rd | 17 datana-1.0.6/datana/man/xyboxplot.Rd | 36 - datana-1.0.6/datana/man/xyhist.Rd | 21 datana-1.0.6/datana/man/xymultiplot.Rd | 99 ++- 330 files changed, 1981 insertions(+), 1378 deletions(-)
Title: Miscellaneous Functions for Southwest Fisheries Science Center
Description: Collection of conversion, analytical, geodesic, mapping, and
plotting functions. Used to support packages and code written by
researchers at the Southwest Fisheries Science Center of the National
Oceanic and Atmospheric Administration.
Author: Eric Archer [aut, cre]
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between swfscMisc versions 1.6.5 dated 2023-09-08 and 1.6.6 dated 2025-03-26
swfscMisc-1.6.5/swfscMisc/R/diversity.R |only swfscMisc-1.6.5/swfscMisc/man/diversity.Rd |only swfscMisc-1.6.6/swfscMisc/DESCRIPTION | 16 ++-- swfscMisc-1.6.6/swfscMisc/MD5 | 30 +++++--- swfscMisc-1.6.6/swfscMisc/NAMESPACE | 6 + swfscMisc-1.6.6/swfscMisc/R/betaParams.R |only swfscMisc-1.6.6/swfscMisc/R/gammaParams.R |only swfscMisc-1.6.6/swfscMisc/R/ggBiplot.R | 12 +-- swfscMisc-1.6.6/swfscMisc/R/mcmc2list.R |only swfscMisc-1.6.6/swfscMisc/R/plotAssignments.R | 4 - swfscMisc-1.6.6/swfscMisc/R/runjags2list.R | 92 ++++++++++++++------------ swfscMisc-1.6.6/swfscMisc/R/sn.params.R | 21 ++++- swfscMisc-1.6.6/swfscMisc/R/stan2list.R |only swfscMisc-1.6.6/swfscMisc/R/swfscMisc.R | 4 - swfscMisc-1.6.6/swfscMisc/README.md | 43 ++++++++---- swfscMisc-1.6.6/swfscMisc/man/betaParams.Rd |only swfscMisc-1.6.6/swfscMisc/man/gammaParams.Rd |only swfscMisc-1.6.6/swfscMisc/man/mcmc2list.Rd |only swfscMisc-1.6.6/swfscMisc/man/runjags2list.Rd | 6 - swfscMisc-1.6.6/swfscMisc/man/stan2list.Rd |only swfscMisc-1.6.6/swfscMisc/man/swfscMisc.Rd | 12 +++ 21 files changed, 149 insertions(+), 97 deletions(-)
Title: A Client for 'ChromaDB'
Description: Client for 'ChromaDB', a vector database for storing and querying embeddings. This package provides a convenient interface to interact with the REST API of 'ChromaDB' <https://docs.trychroma.com>.
Author: David Schoch [aut, cre] ,
Christoph Sax [aut],
cynkra LLC [cph]
Maintainer: David Schoch <david@schochastics.net>
Diff between rchroma versions 0.1.0 dated 2025-02-13 and 0.2.0 dated 2025-03-26
DESCRIPTION | 8 +- MD5 | 21 +++--- NAMESPACE | 4 + NEWS.md | 4 + R/connection.R | 150 ++++++++++++++++++++++++++++++++++++++++++- README.md | 22 ++++-- inst/doc/introduction.R | 18 ++--- inst/doc/introduction.Rmd | 30 +++----- inst/doc/introduction.html | 125 +++++++++++++++++------------------ man/chroma_docker_run.Rd |only man/chroma_docker_running.Rd |only man/chroma_docker_stop.Rd |only vignettes/introduction.Rmd | 30 +++----- 13 files changed, 277 insertions(+), 135 deletions(-)
Title: Tools Developed by the Long Term Ecological Research Community
Description: Set of the data science tools created by various members of the Long Term
Ecological Research (LTER) community. These functions were initially written largely
as standalone operations and have later been aggregated into this package.
Author: Nicholas Lyon [aut, cre] ,
Angel Chen [aut] ,
Miguel C. Leon [ctb] ,
National Science Foundation [fnd] ,
University of California, Santa Barbara [cph]
Maintainer: Nicholas Lyon <lyon@nceas.ucsb.edu>
Diff between ltertools versions 1.2.0 dated 2025-02-21 and 2.0.0 dated 2025-03-26
ltertools-1.2.0/ltertools/R/make_json.R |only ltertools-1.2.0/ltertools/man/make_json.Rd |only ltertools-1.2.0/ltertools/tests/testthat/test-make_json.R |only ltertools-2.0.0/ltertools/DESCRIPTION | 12 ltertools-2.0.0/ltertools/MD5 | 29 - ltertools-2.0.0/ltertools/NAMESPACE | 3 ltertools-2.0.0/ltertools/NEWS.md | 9 ltertools-2.0.0/ltertools/R/check_key.R |only ltertools-2.0.0/ltertools/R/harmonize.R | 115 +----- ltertools-2.0.0/ltertools/R/standardize.R |only ltertools-2.0.0/ltertools/README.md | 6 ltertools-2.0.0/ltertools/build/vignette.rds |binary ltertools-2.0.0/ltertools/inst/doc/ltertools.R | 16 ltertools-2.0.0/ltertools/inst/doc/ltertools.Rmd | 30 - ltertools-2.0.0/ltertools/inst/doc/ltertools.html | 252 +++++--------- ltertools-2.0.0/ltertools/man/check_key.Rd |only ltertools-2.0.0/ltertools/man/standardize.Rd |only ltertools-2.0.0/ltertools/tests/testthat/test-harmonize.R | 2 ltertools-2.0.0/ltertools/vignettes/ltertools.Rmd | 30 - 19 files changed, 159 insertions(+), 345 deletions(-)
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements methods which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
An accompanying 'Python' wrapper ('shaprpy') is available through the GitHub repository.
Author: Martin Jullum [cre, aut] ,
Lars Henry Berge Olsen [aut] ,
Annabelle Redelmeier [aut],
Jon Lachmann [aut] ,
Nikolai Sellereite [aut] ,
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
Diff between shapr versions 1.0.2 dated 2025-02-06 and 1.0.3 dated 2025-03-26
DESCRIPTION | 12 MD5 | 187 NEWS.md | 369 - R/approach.R | 4 R/approach_categorical.R | 8 R/approach_vaeac.R | 5820 ++++++++++++------------- R/approach_vaeac_torch_modules.R | 123 R/asymmetric_and_casual_Shapley.R | 70 R/check_convergence.R | 2 R/cli.R | 6 R/compute_estimates.R | 2 R/compute_vS.R | 4 R/explain.R | 1246 ++--- R/explain_forecast.R | 4 R/finalize_explanation.R | 2 R/model.R | 2 R/model_arima.R | 4 R/plot.R | 3940 ++++++++-------- R/prepare_next_iteration.R | 2 R/print.R | 1 R/print_iter.R | 2 R/save_results.R | 3 R/setup.R | 28 R/shapley_setup.R | 12 R/testthat-helpers.R | 63 R/timing.R | 2 README.md | 528 +- inst/REFERENCES.bib | 14 inst/doc/asymmetric_causal.Rmd | 42 inst/doc/asymmetric_causal.html | 1586 +++--- inst/doc/general_usage.Rmd | 43 inst/doc/general_usage.html | 1213 ++--- inst/doc/regression.Rmd | 65 inst/doc/regression.html | 3281 +++++++------- inst/doc/vaeac.Rmd | 18 inst/doc/vaeac.html | 984 ++-- man/additional_regression_setup.Rd | 3 man/append_vS_list.Rd | 3 man/check_convergence.Rd | 3 man/cli_compute_vS.Rd | 3 man/cli_iter.Rd | 3 man/cli_startup.Rd | 3 man/compute_estimates.Rd | 3 man/compute_time.Rd | 3 man/compute_vS.Rd | 3 man/create_coalition_table.Rd | 10 man/create_marginal_data_training.Rd | 20 man/explain.Rd | 32 man/explain_forecast.Rd | 6 man/figures/nrlogo_new.jpg |only man/finalize_explanation.Rd | 3 man/get_S_causal_steps.Rd | 42 man/get_data_specs.Rd | 14 man/get_extra_comp_args_default.Rd | 7 man/get_iterative_args_default.Rd | 3 man/get_max_n_coalitions_causal.Rd | 10 man/get_output_args_default.Rd | 3 man/get_supported_models.Rd | 3 man/mcar_mask_generator.Rd | 8 man/memory_layer.Rd | 22 man/paired_sampler.Rd | 28 man/plot.shapr.Rd | 2 man/plot_MSEv_eval_crit.Rd | 178 man/plot_SV_several_approaches.Rd | 174 man/plot_vaeac_eval_crit.Rd | 194 man/plot_vaeac_imputed_ggpairs.Rd | 284 - man/prepare_next_iteration.Rd | 3 man/print.shapr.Rd | 3 man/print_iter.Rd | 3 man/regression.train_model.Rd | 2 man/save_results.Rd | 3 man/setup.Rd | 6 man/setup_approach.Rd | 5 man/shapley_setup.Rd | 3 man/specified_masks_mask_generator.Rd | 14 man/specified_prob_mask_generator.Rd | 11 man/testing_cleanup.Rd | 3 man/vaeac_dataset.Rd | 29 man/vaeac_postprocess_data.Rd | 10 tests/testthat/helper-ar-arima.R | 10 tests/testthat/test-asymmetric-causal-output.R | 1044 ++-- tests/testthat/test-asymmetric-causal-setup.R | 19 tests/testthat/test-forecast-output.R | 548 -- tests/testthat/test-forecast-setup.R | 1303 +++-- tests/testthat/test-iterative-output.R | 543 -- tests/testthat/test-iterative-setup.R | 654 +- tests/testthat/test-plot.R | 630 +- tests/testthat/test-regression-output.R | 614 +- tests/testthat/test-regression-setup.R | 19 tests/testthat/test-regular-output.R | 1150 ++-- tests/testthat/test-regular-setup.R | 3530 +++++++-------- vignettes/asymmetric_causal.Rmd | 42 vignettes/general_usage.Rmd | 43 vignettes/regression.Rmd | 65 vignettes/vaeac.Rmd | 18 95 files changed, 15755 insertions(+), 15334 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis' (included as a fallback) with
'MsgPack' encoding provided via 'RcppMsgPack' headers. It now also
includes the pub/sub functions from the 'rredis' package.
Author: Dirk Eddelbuettel [aut, cre] ,
Bryan Lewis [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.2.4 dated 2023-08-19 and 0.2.5 dated 2025-03-26
RcppRedis-0.2.4/RcppRedis/demo |only RcppRedis-0.2.5/RcppRedis/ChangeLog | 44 + RcppRedis-0.2.5/RcppRedis/DESCRIPTION | 18 RcppRedis-0.2.5/RcppRedis/MD5 | 37 RcppRedis-0.2.5/RcppRedis/README.md | 8 RcppRedis-0.2.5/RcppRedis/build/vignette.rds |binary RcppRedis-0.2.5/RcppRedis/configure | 605 +++++++------- RcppRedis-0.2.5/RcppRedis/configure.ac | 6 RcppRedis-0.2.5/RcppRedis/inst/NEWS.Rd | 13 RcppRedis-0.2.5/RcppRedis/inst/demos |only RcppRedis-0.2.5/RcppRedis/inst/doc/market-monitoring.pdf |binary RcppRedis-0.2.5/RcppRedis/inst/doc/redis-introduction.pdf |binary RcppRedis-0.2.5/RcppRedis/src/Makevars.in | 2 RcppRedis-0.2.5/RcppRedis/src/Redis.cpp | 34 RcppRedis-0.2.5/RcppRedis/src/hiredis/hiredis.c | 8 15 files changed, 438 insertions(+), 337 deletions(-)
Title: A Bias Bound Approach to Non-Parametric Inference
Description: A novel bias-bound approach for non-parametric inference is introduced,
focusing on both density and conditional expectation estimation.
It constructs valid confidence intervals that account for the presence of
a non-negligible bias and thus make it possible to perform inference with
optimal mean squared error minimizing bandwidths.
This package is based on Schennach (2020) <doi:10.1093/restud/rdz065>.
Author: Xinyu DAI [aut, cre],
Susanne M Schennach [aut]
Maintainer: Xinyu DAI <xinyu_dai@brown.edu>
Diff between rbbnp versions 0.1.0 dated 2024-02-01 and 0.2.0 dated 2025-03-26
rbbnp-0.1.0/rbbnp/build |only rbbnp-0.2.0/rbbnp/DESCRIPTION | 8 rbbnp-0.2.0/rbbnp/MD5 | 87 +++++---- rbbnp-0.2.0/rbbnp/NAMESPACE | 2 rbbnp-0.2.0/rbbnp/NEWS.md |only rbbnp-0.2.0/rbbnp/R/config.R |only rbbnp-0.2.0/rbbnp/R/kernel_factory.R |only rbbnp-0.2.0/rbbnp/R/kernels.R | 4 rbbnp-0.2.0/rbbnp/R/main.R | 156 ++++++----------- rbbnp-0.2.0/rbbnp/R/rbbnp-pkg.R | 2 rbbnp-0.2.0/rbbnp/R/utils.R | 82 ++++++--- rbbnp-0.2.0/rbbnp/inst/CITATION |only rbbnp-0.2.0/rbbnp/man/DATA_PATH.Rd | 22 +- rbbnp-0.2.0/rbbnp/man/EXT_DATA_PATH.Rd | 24 +- rbbnp-0.2.0/rbbnp/man/W_kernel.Rd | 42 ++-- rbbnp-0.2.0/rbbnp/man/W_kernel_ft.Rd | 44 ++--- rbbnp-0.2.0/rbbnp/man/biasBound_condExpectation.Rd | 174 +++++++++---------- rbbnp-0.2.0/rbbnp/man/biasBound_density.Rd | 184 ++++++++++----------- rbbnp-0.2.0/rbbnp/man/create_biasBound_config.Rd |only rbbnp-0.2.0/rbbnp/man/create_kernel_functions.Rd |only rbbnp-0.2.0/rbbnp/man/epanechnikov_kernel.Rd | 34 +-- rbbnp-0.2.0/rbbnp/man/epanechnikov_kernel_ft.Rd | 34 +-- rbbnp-0.2.0/rbbnp/man/fun_approx.Rd | 82 ++++----- rbbnp-0.2.0/rbbnp/man/gen_sample_data.Rd | 58 +++--- rbbnp-0.2.0/rbbnp/man/get_avg_f1x.Rd | 46 ++--- rbbnp-0.2.0/rbbnp/man/get_avg_fyx.Rd | 50 ++--- rbbnp-0.2.0/rbbnp/man/get_avg_phi.Rd | 44 ++--- rbbnp-0.2.0/rbbnp/man/get_avg_phi_log.Rd | 44 ++--- rbbnp-0.2.0/rbbnp/man/get_conditional_var.Rd | 51 ++--- rbbnp-0.2.0/rbbnp/man/get_est_Ar.Rd | 68 +++---- rbbnp-0.2.0/rbbnp/man/get_est_B.Rd | 34 +-- rbbnp-0.2.0/rbbnp/man/get_est_b1x.Rd | 38 ++-- rbbnp-0.2.0/rbbnp/man/get_est_byx.Rd | 42 ++-- rbbnp-0.2.0/rbbnp/man/get_est_vy.Rd | 28 +-- rbbnp-0.2.0/rbbnp/man/get_sigma.Rd | 46 ++--- rbbnp-0.2.0/rbbnp/man/get_sigma_yx.Rd | 51 ++--- rbbnp-0.2.0/rbbnp/man/get_xi_interval.Rd | 58 +++--- rbbnp-0.2.0/rbbnp/man/kernel_reg.Rd | 50 ++--- rbbnp-0.2.0/rbbnp/man/normal_kernel.Rd | 34 +-- rbbnp-0.2.0/rbbnp/man/normal_kernel_ft.Rd | 34 +-- rbbnp-0.2.0/rbbnp/man/plot_ft.Rd | 64 +++---- rbbnp-0.2.0/rbbnp/man/rpoly01.Rd | 42 ++-- rbbnp-0.2.0/rbbnp/man/sample_data.Rd | 40 ++-- rbbnp-0.2.0/rbbnp/man/sinc.Rd | 34 +-- rbbnp-0.2.0/rbbnp/man/sinc_ft.Rd | 34 +-- rbbnp-0.2.0/rbbnp/man/true_density_2fold.Rd | 34 +-- rbbnp-0.2.0/rbbnp/tests |only 47 files changed, 1005 insertions(+), 1000 deletions(-)
Title: Creates Log Files
Description: Contains functions to help create log files. The
package aims to overcome the difficulty of the base R sink() command. The
log_print() function will print to both the console and the file log,
without interfering in other write operations.
Author: David Bosak [aut, cre],
Rikard Isaksson [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between logr versions 1.3.8 dated 2024-05-09 and 1.3.9 dated 2025-03-26
DESCRIPTION | 8 MD5 | 61 +++--- NAMESPACE | 1 NEWS.md | 11 + R/logr.R | 176 ++++++++++++++++--- R/unicode.R | 4 R/utilities.R | 12 - build/vignette.rds |binary inst/doc/logr-example1.R | 15 - inst/doc/logr-example1.Rmd | 197 +++++++++++---------- inst/doc/logr-example1.html | 373 ++++++++++++++++++++--------------------- inst/doc/logr-faq.Rmd | 16 + inst/doc/logr-faq.html | 14 + inst/doc/logr-globals.R | 16 + inst/doc/logr-globals.Rmd | 27 ++ inst/doc/logr-globals.html | 20 ++ inst/doc/logr-integration.R |only inst/doc/logr-integration.Rmd |only inst/doc/logr-integration.html |only inst/doc/logr-put.html | 2 inst/doc/logr-tidylog.Rmd | 2 inst/doc/logr-tidylog.html | 4 inst/doc/logr.html | 2 man/log_info.Rd |only man/log_open.Rd | 27 ++ tests/testthat/log/test.log | 19 +- tests/testthat/log/test13.log | 138 +++++++++------ tests/testthat/myspdir |only tests/testthat/test-logr.R | 133 ++++++++++++++ tests/testthat/test.log |only vignettes/logr-example1.Rmd | 197 +++++++++++---------- vignettes/logr-faq.Rmd | 16 + vignettes/logr-globals.Rmd | 27 ++ vignettes/logr-integration.Rmd |only vignettes/logr-tidylog.Rmd | 2 35 files changed, 998 insertions(+), 522 deletions(-)
Title: Core Functions for Data Quality Assessment
Description: Perform data quality assessment ('DQA') of electronic health
records ('EHR'). Publication: Kapsner et al. (2021)
<doi:10.1055/s-0041-1733847>.
Author: Lorenz A. Kapsner [cre, aut] ,
Jonathan M. Mang [aut] ,
Helene Koester [ctb],
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between DQAstats versions 0.3.7 dated 2025-02-07 and 0.3.8 dated 2025-03-26
DQAstats-0.3.7/DQAstats/man/parallel.Rd |only DQAstats-0.3.8/DQAstats/DESCRIPTION | 8 DQAstats-0.3.8/DQAstats/MD5 | 59 DQAstats-0.3.8/DQAstats/NAMESPACE | 1 DQAstats-0.3.8/DQAstats/R/DQA.R | 1020 +-- DQAstats-0.3.8/DQAstats/R/mdr.R | 784 +- DQAstats-0.3.8/DQAstats/R/simple_summary.R | 48 DQAstats-0.3.8/DQAstats/R/utils.R | 25 DQAstats-0.3.8/DQAstats/inst/doc/DQAstats2SHIPdataset.R | 9 DQAstats-0.3.8/DQAstats/inst/doc/DQAstats2SHIPdataset.html | 3097 ---------- DQAstats-0.3.8/DQAstats/inst/doc/DQAstats2SHIPdataset.qmd | 12 DQAstats-0.3.8/DQAstats/tests/testthat.R | 24 DQAstats-0.3.8/DQAstats/tests/testthat/test-DQA.R | 116 DQAstats-0.3.8/DQAstats/tests/testthat/test-MDR.R | 192 DQAstats-0.3.8/DQAstats/tests/testthat/test-check_date_restriction_requirements.R | 104 DQAstats-0.3.8/DQAstats/tests/testthat/test-completeness.R | 256 DQAstats-0.3.8/DQAstats/tests/testthat/test-conformance.R | 308 DQAstats-0.3.8/DQAstats/tests/testthat/test-dataloading.R | 326 - DQAstats-0.3.8/DQAstats/tests/testthat/test-datamap.R | 262 DQAstats-0.3.8/DQAstats/tests/testthat/test-datetime_restrictions.R | 222 DQAstats-0.3.8/DQAstats/tests/testthat/test-descriptive_results.R | 624 +- DQAstats-0.3.8/DQAstats/tests/testthat/test-etl_and_differences_checks.R | 262 DQAstats-0.3.8/DQAstats/tests/testthat/test-export.R | 300 DQAstats-0.3.8/DQAstats/tests/testthat/test-helper_vars.R | 294 DQAstats-0.3.8/DQAstats/tests/testthat/test-import.R | 212 DQAstats-0.3.8/DQAstats/tests/testthat/test-plausibilities.R | 290 DQAstats-0.3.8/DQAstats/tests/testthat/test-readme.R | 96 DQAstats-0.3.8/DQAstats/tests/testthat/test-reduce_cat.R | 256 DQAstats-0.3.8/DQAstats/tests/testthat/test-render_conformance.R | 326 - DQAstats-0.3.8/DQAstats/tests/testthat/test-time_compare.R | 210 DQAstats-0.3.8/DQAstats/vignettes/DQAstats2SHIPdataset.qmd | 12 31 files changed, 3619 insertions(+), 6136 deletions(-)
Title: Search and Retrieve Data from the BC Data Catalogue
Description: Search, query, and download tabular and
'geospatial' data from the British Columbia Data Catalogue
(<https://catalogue.data.gov.bc.ca/>). Search catalogue data records
based on keywords, data licence, sector, data format, and B.C.
government organization. View metadata directly in R, download many
data formats, and query 'geospatial' data available via the B.C.
government Web Feature Service ('WFS') using 'dplyr' syntax.
Author: Andy Teucher [aut, cre] ,
Sam Albers [aut, ctb] ,
Stephanie Hazlitt [aut, ctb] ,
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gmail.com>
Diff between bcdata versions 0.5.0 dated 2024-12-11 and 0.5.1 dated 2025-03-26
DESCRIPTION | 6 MD5 | 98 +-- NEWS.md | 9 R/bcdata-package.R | 3 R/bcdc-get-citation.R | 15 R/bcdc-web-services.R | 98 ++- R/bcdc_browse.R | 25 - R/bcdc_options.R | 79 ++- R/bcdc_search.R | 188 ++++--- R/cli.R | 1 R/cql-geom-predicates.R | 99 ++- R/cql-translator.R | 51 +- R/describe-feature.R | 47 - R/get_data.R | 120 +++- R/utils-classes.R | 305 ++++++++---- R/utils-filter.R | 6 R/utils-is.R | 1 R/utils-select.R | 6 R/utils.R | 192 ++++--- build/vignette.rds |binary inst/doc/explore-silviculture-data-using-bcdata.Rmd | 2 inst/doc/explore-silviculture-data-using-bcdata.html | 2 inst/doc/service_documentation.Rmd | 12 inst/doc/service_documentation.html | 6 man/bcdc_options.Rd | 15 man/bcdc_query_geodata.Rd | 20 tests/testthat/helper-bcdata.R | 2 tests/testthat/setup.R | 2 tests/testthat/test-bcdc-get-citation.R | 2 tests/testthat/test-browse.R | 12 tests/testthat/test-cql-string.R | 60 +- tests/testthat/test-describe-feature.R | 60 +- tests/testthat/test-edge-cases.R | 7 tests/testthat/test-geom-operators.R | 4 tests/testthat/test-get-data.R | 41 + tests/testthat/test-get_record.R | 48 + tests/testthat/test-options.R | 38 + tests/testthat/test-print-methods.R | 26 - tests/testthat/test-query-geodata-base-methods.R | 11 tests/testthat/test-query-geodata-collect.R | 36 + tests/testthat/test-query-geodata-filter.R | 350 +++++++++----- tests/testthat/test-query-geodata-mutate.R | 2 tests/testthat/test-query-geodata-select.R | 34 - tests/testthat/test-query-geodata.R | 27 - tests/testthat/test-search.R | 40 + tests/testthat/test-utils.R | 27 - vignettes/explore-silviculture-data-using-bcdata.Rmd | 2 vignettes/explore-silviculture-data-using-bcdata.Rmd.orig | 2 vignettes/precompile.R | 21 vignettes/service_documentation.Rmd | 12 50 files changed, 1515 insertions(+), 757 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements into groups (i.e., anticlusters) with the goal of maximizing between-group similarity or within-group heterogeneity. The anticlustering approach thereby reverses the logic of cluster analysis that strives for high within-group homogeneity and clear separation between groups. Computationally, anticlustering is accomplished by maximizing instead of minimizing a clustering objective function, such as the intra-cluster variance (used in k-means clustering) or the sum of pairwise distances within clusters. The main function anticlustering() gives access to optimal and heuristic anticlustering methods described in Papenberg and Klau (2021; <doi:10.1037/met0000301>), Brusco et al. (2020; <doi:10.1111/bmsp.12186>), Papenberg (2024; <doi:10.1111/bmsp.12315>), and Papenberg et al. (2025; <doi:10.1101/2025.03.03.641320>). The optimal algorithms require that an integer linear programming solver is installed. This p [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb] ,
Hannah Hengelbrock [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.10 dated 2025-03-13 and 0.8.10-1 dated 2025-03-26
DESCRIPTION | 6 +- MD5 | 6 +- inst/doc/Speeding_up_anticlustering.html | 26 ++++++------ inst/tinytest/test-2pml.R | 66 +++++++++++++++++++------------ 4 files changed, 61 insertions(+), 43 deletions(-)
Title: Estimate Haplotype Relative Risks in Case-Control Data
Description: Haplotype and covariate relative risks in case-control data are estimated by weighted logistic regression. Diplotype probabilities, which are estimated by EM computation with progressive insertion of loci, are utilized as weights. French et al. (2006) <doi:10.1002/gepi.20161>.
Author: Benjamin French [cre, aut] ,
Shawn Garbett [ctb] ,
Thomas Lumley [aut]
Maintainer: Benjamin French <b.french@vumc.org>
Diff between haplo.ccs versions 1.3.2 dated 2022-04-28 and 1.3.3 dated 2025-03-26
DESCRIPTION | 22 +++++++++++++++------- MD5 | 4 ++-- README.md | 15 ++++++++------- 3 files changed, 25 insertions(+), 16 deletions(-)
Title: Supervised Component Generalized Linear Regression
Description: An extension of the Fisher Scoring Algorithm to combine PLS regression with GLM
estimation in the multivariate context. Covariates can also be grouped in themes.
Author: Guillaume Cornu [aut, cre] ,
Frederic Mortier [aut] ,
Catherine Trottier [aut],
Xavier Bry [aut],
Jocelyn Chauvet [aut] ,
Sylvie Gourlet-Fleury [dtc] ,
Claude Garcia [dtc] ,
GAMBAS [fnd]
Maintainer: Guillaume Cornu <gcornu@cirad.fr>
Diff between SCGLR versions 3.0 dated 2018-09-28 and 3.1.0 dated 2025-03-26
SCGLR-3.0/SCGLR/data/genus.rda |only SCGLR-3.0/SCGLR/demo/scglrPrediction.r |only SCGLR-3.0/SCGLR/inst/examples/exPrediction.r |only SCGLR-3.1.0/SCGLR/DESCRIPTION | 80 + SCGLR-3.1.0/SCGLR/MD5 | 123 +- SCGLR-3.1.0/SCGLR/NAMESPACE | 11 SCGLR-3.1.0/SCGLR/NEWS.md | 73 + SCGLR-3.1.0/SCGLR/R/critConvergence.r | 28 SCGLR-3.1.0/SCGLR/R/customize.r | 140 +- SCGLR-3.1.0/SCGLR/R/data.r | 4 SCGLR-3.1.0/SCGLR/R/dataGen.R |only SCGLR-3.1.0/SCGLR/R/genus2.R |only SCGLR-3.1.0/SCGLR/R/infoCriterion.r | 98 + SCGLR-3.1.0/SCGLR/R/ingUtils.r | 300 ++--- SCGLR-3.1.0/SCGLR/R/kCompRand.R |only SCGLR-3.1.0/SCGLR/R/kComponents.r | 149 +- SCGLR-3.1.0/SCGLR/R/methods.r | 77 - SCGLR-3.1.0/SCGLR/R/metric.r | 45 SCGLR-3.1.0/SCGLR/R/mixedping.R |only SCGLR-3.1.0/SCGLR/R/multivariateFormula.r | 132 +- SCGLR-3.1.0/SCGLR/R/oneComponent.r | 464 ++++----- SCGLR-3.1.0/SCGLR/R/package.r | 4 SCGLR-3.1.0/SCGLR/R/parallel.R |only SCGLR-3.1.0/SCGLR/R/plot.r | 1068 ++++++++++----------- SCGLR-3.1.0/SCGLR/R/print.r | 2 SCGLR-3.1.0/SCGLR/R/scglr.r | 66 - SCGLR-3.1.0/SCGLR/R/scglrCrossVal.r | 173 +-- SCGLR-3.1.0/SCGLR/R/summary.r | 4 SCGLR-3.1.0/SCGLR/R/theme.r | 46 SCGLR-3.1.0/SCGLR/R/theme_backward.r | 429 ++++---- SCGLR-3.1.0/SCGLR/R/utils.r | 148 +- SCGLR-3.1.0/SCGLR/README.md | 119 +- SCGLR-3.1.0/SCGLR/data/dataGen.RData |only SCGLR-3.1.0/SCGLR/data/genus.RData |only SCGLR-3.1.0/SCGLR/data/genus2.RData |only SCGLR-3.1.0/SCGLR/demo/00Index | 7 SCGLR-3.1.0/SCGLR/demo/scglr.r | 48 SCGLR-3.1.0/SCGLR/demo/scglrCrossVal.r | 60 - SCGLR-3.1.0/SCGLR/demo/scglrPlots.r | 64 - SCGLR-3.1.0/SCGLR/inst/examples/exCrossVal.r | 60 - SCGLR-3.1.0/SCGLR/inst/examples/exPlots.r | 64 - SCGLR-3.1.0/SCGLR/inst/examples/exScglr.r | 48 SCGLR-3.1.0/SCGLR/man/barplot.SCGLR.Rd | 46 SCGLR-3.1.0/SCGLR/man/barplot.SCGLRTHM.Rd | 40 SCGLR-3.1.0/SCGLR/man/cash-.MultivariateFormula.Rd | 42 SCGLR-3.1.0/SCGLR/man/critConvergence.Rd | 40 SCGLR-3.1.0/SCGLR/man/customize.Rd | 152 +- SCGLR-3.1.0/SCGLR/man/dataGen.Rd |only SCGLR-3.1.0/SCGLR/man/figures |only SCGLR-3.1.0/SCGLR/man/genus.Rd | 76 - SCGLR-3.1.0/SCGLR/man/genus2.Rd |only SCGLR-3.1.0/SCGLR/man/infoCriterion.Rd | 66 - SCGLR-3.1.0/SCGLR/man/kCompRand.Rd |only SCGLR-3.1.0/SCGLR/man/methodSR.Rd | 61 - SCGLR-3.1.0/SCGLR/man/multivariateFormula.Rd | 105 +- SCGLR-3.1.0/SCGLR/man/multivariateGlm.fit.Rd | 178 +-- SCGLR-3.1.0/SCGLR/man/multivariatePredictGlm.Rd | 168 +-- SCGLR-3.1.0/SCGLR/man/pairs.SCGLR.Rd | 54 - SCGLR-3.1.0/SCGLR/man/plot.SCGLR.Rd | 124 +- SCGLR-3.1.0/SCGLR/man/plot.SCGLRTHM.Rd | 38 SCGLR-3.1.0/SCGLR/man/print.MultivariateFormula.Rd | 36 SCGLR-3.1.0/SCGLR/man/print.SCGLR.Rd | 34 SCGLR-3.1.0/SCGLR/man/scglr.Rd | 226 ++-- SCGLR-3.1.0/SCGLR/man/scglrCrossVal.Rd | 192 ++- SCGLR-3.1.0/SCGLR/man/scglrTheme.Rd | 167 +-- SCGLR-3.1.0/SCGLR/man/scglrThemeBackward.Rd | 194 ++- SCGLR-3.1.0/SCGLR/man/screeplot.SCGLR.Rd | 44 SCGLR-3.1.0/SCGLR/man/screeplot.SCGLRTHM.Rd | 38 SCGLR-3.1.0/SCGLR/man/summary.SCGLR.Rd | 66 - 69 files changed, 3289 insertions(+), 3032 deletions(-)
Title: Data and Methods Around Reference Values in Pediatrics
Description: Calculation of standard deviation scores and percentiles adduced from different
standards (WHO, UK, Germany, Italy, China, etc). Also, references for laboratory values in
children and adults are available, e.g., serum lipids, iron-related blood parameters, IGF, liver enzymes. See package documentation for full list.
Author: Mandy Vogel [aut, cre]
Maintainer: Mandy Vogel <mandy.vogel@googlemail.com>
Diff between childsds versions 0.9.8 dated 2025-01-28 and 0.9.11 dated 2025-03-26
DESCRIPTION | 12 +++++++----- MD5 | 38 ++++++++++++++++++++++++++++---------- NAMESPACE | 10 ++++++++++ NEWS.md | 6 ++++++ R/data.R | 10 +++++++++- R/misc.R | 1 - R/palletes.R |only R/ridits.R |only R/sdsvals.r | 8 ++++---- R/zzz.R | 2 +- build |only data/leptin.ref.rda |binary data/life_shbg.ref.rda |binary data/uchu.pal.rda |only inst |only man/adjust_colors.Rd |only man/life_shbg.ref.Rd | 4 ++-- man/mean_ridits.Rd |only man/mid.mean.ranks.Rd |only man/props.Rd |only man/prs_pal.Rd |only man/ridits.from.ranks.Rd |only man/scale_colour_prs.Rd |only man/scale_fill_prs.Rd |only man/scale_uchu.Rd |only man/uchu.pal.Rd |only vignettes |only 27 files changed, 67 insertions(+), 24 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 1.7.8.1 dated 2024-07-24 and 1.7.9.1 dated 2025-03-26
xgboost |only 1 file changed
Title: R Interface to the 'DieHarder' RNG Test Suite
Description: The 'RDieHarder' package provides an R interface to
the 'DieHarder' suite of random number generators and tests that
was developed by Robert G. Brown and David Bauer, extending
earlier work by George Marsaglia and others. The 'DieHarder'
library code is included.
Author: Dirk Eddelbuettel [aut, cre] ,
Robert G Brown [aut],
David Bauer [aut],
DieHarder Contributors [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RDieHarder versions 0.2.6 dated 2024-01-12 and 0.2.7 dated 2025-03-26
ChangeLog | 26 ++++ DESCRIPTION | 21 ++- MD5 | 16 +-- README.md | 2 build/vignette.rds |binary configure | 255 +++++++++++++++++++++++------------------------- configure.ac | 4 inst/doc/RDieHarder.pdf |binary src/parsecl.c | 6 - 9 files changed, 179 insertions(+), 151 deletions(-)
Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marti Catala [ctb] ,
Xihang Chen [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [ctb] ,
Danielle Newby [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 3.4.0 dated 2025-02-19 and 3.4.1 dated 2025-03-26
DESCRIPTION | 17 MD5 | 34 R/codesFromConceptSet.R | 4 R/getCandidateCodes.R | 59 R/getRoutes.R | 120 - R/stratifyByRoute.R | 266 ++-- R/subsetOnRouteCategory.R | 190 +-- inst/doc/a01_Introduction_to_CodelistGenerator.html | 2 inst/doc/a02_Candidate_codes_OA.R | 2 inst/doc/a02_Candidate_codes_OA.Rmd | 8 inst/doc/a02_Candidate_codes_OA.html | 21 inst/doc/a03_Options_for_CodelistGenerator.html | 18 inst/doc/a04_Vocab_based_codelists.html | 4 man/CodelistGenerator-package.Rd | 1 man/getCandidateCodes.Rd | 2 tests/testthat/test-dbms.R | 1217 ++++++++++---------- tests/testthat/test-getCandidateCodes.R | 50 vignettes/a02_Candidate_codes_OA.Rmd | 8 18 files changed, 1013 insertions(+), 1010 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: Linear Programming Discriminant Analysis
Description: Classification method obtained through linear programming.
It is advantageous with respect to the classical developments when the distribution of the variables
involved is unknown or when the number of variables is much greater than the number of individuals.
Mathematical details behind the method are published in Nueda, et al. (2022) "LPDA: A new classification method based on linear programming".
<doi:10.1371/journal.pone.0270403>.
Author: Maria Jose Nueda [aut, cre]
Maintainer: Maria Jose Nueda <mj.nueda@ua.es>
Diff between lpda versions 1.0.1 dated 2023-03-07 and 1.2.0 dated 2025-03-26
lpda-1.0.1/lpda/R/CVktest.R |only lpda-1.0.1/lpda/R/CVloo.R |only lpda-1.0.1/lpda/R/bestPC.R |only lpda-1.0.1/lpda/R/bestVariability.R |only lpda-1.0.1/lpda/man/CVktest.Rd |only lpda-1.0.1/lpda/man/CVloo.Rd |only lpda-1.0.1/lpda/man/bestPC.Rd |only lpda-1.0.1/lpda/man/bestVariability.Rd |only lpda-1.2.0/lpda/DESCRIPTION | 17 lpda-1.2.0/lpda/MD5 | 80 - lpda-1.2.0/lpda/NAMESPACE | 21 lpda-1.2.0/lpda/NEWS.md | 10 lpda-1.2.0/lpda/R/lpda.3D.R |only lpda-1.2.0/lpda/R/lpda.R | 14 lpda-1.2.0/lpda/R/lpda.pca.R | 71 - lpda-1.2.0/lpda/R/lpdaCV.3D.R |only lpda-1.2.0/lpda/R/lpdaCV.R | 89 + lpda-1.2.0/lpda/R/plot.lpda.3D.R |only lpda-1.2.0/lpda/R/plot.lpda.R | 9 lpda-1.2.0/lpda/R/predict.lpda.3D.R |only lpda-1.2.0/lpda/R/predict.lpda.R | 43 lpda-1.2.0/lpda/R/summary.lpda.3D.R |only lpda-1.2.0/lpda/R/summary.lpda.R |only lpda-1.2.0/lpda/build/vignette.rds |binary lpda-1.2.0/lpda/data/RNAseq.RData |binary lpda-1.2.0/lpda/inst/doc/lpdaUsersGuide.R | 120 +- lpda-1.2.0/lpda/inst/doc/lpdaUsersGuide.Rmd | 219 ++-- lpda-1.2.0/lpda/inst/doc/lpdaUsersGuide.html | 521 ++++++---- lpda-1.2.0/lpda/man/RNAseq.Rd | 8 lpda-1.2.0/lpda/man/lpda.3D.Rd |only lpda-1.2.0/lpda/man/lpda.Rd | 19 lpda-1.2.0/lpda/man/lpdaCV.3D.Rd |only lpda-1.2.0/lpda/man/lpdaCV.Rd | 21 lpda-1.2.0/lpda/man/plot.lpda.3D.Rd |only lpda-1.2.0/lpda/man/plot.lpda.Rd | 2 lpda-1.2.0/lpda/man/predict.lpda.3D.Rd |only lpda-1.2.0/lpda/man/predict.lpda.Rd | 6 lpda-1.2.0/lpda/man/summary.lpda.3D.Rd |only lpda-1.2.0/lpda/man/summary.lpda.Rd |only lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-10-1.png |binary lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-11-1.png |only lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-12-1.png |binary lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-13-1.png |only lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-14-1.png |only lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-17-1.png |only lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-18-1.png |only lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-19-1.png |binary lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-20-1.png |binary lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-21-1.png |binary lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-21-2.png |only lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-5-1.png |only lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-7-1.png |only lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-8-1.png |binary lpda-1.2.0/lpda/vignettes/figures/README-unnamed-chunk-9-1.png |binary lpda-1.2.0/lpda/vignettes/lpdaUsersGuide.Rmd | 219 ++-- 55 files changed, 941 insertions(+), 548 deletions(-)
Title: Relative Survival, AER and SMR Based on French Death Rates
Description: It computes Relative survival, AER and SMR based on French death rates.
Author: Hugo Varet [aut, cre],
Jean-Philippe Jais [aut]
Maintainer: Hugo Varet <varethugo@gmail.com>
Diff between survexp.fr versions 1.1 dated 2022-04-19 and 1.2 dated 2025-03-26
survexp.fr-1.1/survexp.fr/R/AER.r |only survexp.fr-1.1/survexp.fr/R/LR.r |only survexp.fr-1.1/survexp.fr/R/SMR.r |only survexp.fr-1.1/survexp.fr/R/survexp_plot.r |only survexp.fr-1.2/survexp.fr/DESCRIPTION | 18 +++++++++----- survexp.fr-1.2/survexp.fr/MD5 | 28 +++++++++++------------ survexp.fr-1.2/survexp.fr/NEWS | 5 ++++ survexp.fr-1.2/survexp.fr/R/AER.R |only survexp.fr-1.2/survexp.fr/R/LR.R |only survexp.fr-1.2/survexp.fr/R/SMR.R |only survexp.fr-1.2/survexp.fr/R/survexp.fr-package.r | 3 -- survexp.fr-1.2/survexp.fr/R/survexp.fr.r | 6 ++-- survexp.fr-1.2/survexp.fr/R/survexp_plot.R |only survexp.fr-1.2/survexp.fr/data/survexp.fr.rda |binary survexp.fr-1.2/survexp.fr/man/AER.Rd | 2 - survexp.fr-1.2/survexp.fr/man/LR.Rd | 2 - survexp.fr-1.2/survexp.fr/man/SMR.Rd | 2 - survexp.fr-1.2/survexp.fr/man/survexp.fr.Rd | 6 ++-- survexp.fr-1.2/survexp.fr/man/survexp_plot.Rd | 6 ++-- 19 files changed, 44 insertions(+), 34 deletions(-)
Title: Simulation, Estimation and Forecasting of Beta-Skew-t-EGARCH
Models
Description: Simulation, estimation and forecasting of first-order Beta-Skew-t-EGARCH models with leverage (one-component, two-component, skewed versions).
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between betategarch versions 3.3 dated 2016-10-16 and 3.4 dated 2025-03-26
betategarch-3.3/betategarch/R/STkurtosis.R |only betategarch-3.3/betategarch/R/STmean.R |only betategarch-3.3/betategarch/R/STskewness.R |only betategarch-3.3/betategarch/R/STvar.R |only betategarch-3.3/betategarch/R/coef.tegarch.R |only betategarch-3.3/betategarch/R/dST.R |only betategarch-3.3/betategarch/R/fitted.tegarch.R |only betategarch-3.3/betategarch/R/logLik.tegarch.R |only betategarch-3.3/betategarch/R/predict.tegarch.R |only betategarch-3.3/betategarch/R/print.tegarch.R |only betategarch-3.3/betategarch/R/rST.R |only betategarch-3.3/betategarch/R/residuals.tegarch.R |only betategarch-3.3/betategarch/R/summary.tegarch.R |only betategarch-3.3/betategarch/R/tegarch.R |only betategarch-3.3/betategarch/R/tegarchLogl.R |only betategarch-3.3/betategarch/R/tegarchLogl2.R |only betategarch-3.3/betategarch/R/tegarchRecursion.R |only betategarch-3.3/betategarch/R/tegarchRecursion2.R |only betategarch-3.3/betategarch/R/tegarchSim.R |only betategarch-3.3/betategarch/R/vcov.tegarch.R |only betategarch-3.3/betategarch/src/betategarch.cpp |only betategarch-3.4/betategarch/DESCRIPTION | 16 ++--- betategarch-3.4/betategarch/MD5 | 52 +++++------------ betategarch-3.4/betategarch/NAMESPACE | 20 ++++++ betategarch-3.4/betategarch/NEWS | 19 +++--- betategarch-3.4/betategarch/R/betategarch-internal.R | 38 +++++------- betategarch-3.4/betategarch/R/betategarch-source.R |only betategarch-3.4/betategarch/build |only betategarch-3.4/betategarch/data/nasdaq.rda |binary betategarch-3.4/betategarch/man/betategarch-package.Rd | 28 ++++----- betategarch-3.4/betategarch/man/coef.tegarch.Rd | 31 +++++----- betategarch-3.4/betategarch/man/dST.Rd | 8 +- betategarch-3.4/betategarch/man/nasdaq.Rd | 7 +- betategarch-3.4/betategarch/man/predict.tegarch.Rd | 14 ++-- betategarch-3.4/betategarch/man/tegarch.Rd | 27 ++++---- betategarch-3.4/betategarch/man/tegarchLogl.Rd | 13 ++-- betategarch-3.4/betategarch/man/tegarchSim.Rd | 12 ++- betategarch-3.4/betategarch/src/betategarch.c |only betategarch-3.4/betategarch/src/recursions.c |only betategarch-3.4/betategarch/src/recursions.h |only 40 files changed, 149 insertions(+), 136 deletions(-)
Title: Meta-Analysis of RNA-Seq Data
Description: Implementation of two p-value combination techniques (inverse normal and Fisher methods). A vignette is provided to explain how to perform a meta-analysis from two independent RNA-seq experiments.
Author: Guillemette Marot [aut],
Andrea Rau [aut],
Florence Jaffrezic [aut],
Samuel Blanck [ctb, cre]
Maintainer: Samuel Blanck <samuel.blanck@univ-lille.fr>
Diff between metaRNASeq versions 1.0.7 dated 2021-10-01 and 1.0.8 dated 2025-03-26
DESCRIPTION | 28 ++- MD5 | 14 - R/IDD.IRR.R | 30 +-- build/vignette.rds |binary inst/CITATION | 28 +-- inst/doc/metaRNASeq.R | 412 ++++++++++++++++++++++++------------------------ inst/doc/metaRNASeq.pdf |binary man/param.Rd | 68 +++---- 8 files changed, 298 insertions(+), 282 deletions(-)
Title: Multiform Seq2Seq Model for Time-Feature Analysis
Description: Seq2seq time-feature analysis based on variational model, with a wide range of distributions available for the latent variable.
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between proteus versions 1.1.4 dated 2023-10-21 and 1.1.5 dated 2025-03-26
DESCRIPTION | 15 MD5 | 16 NAMESPACE | 39 -- NEWS.md | 6 R/main1.R | 690 ++++++++++++++++++------------------------- R/main2.R | 31 - man/proteus.Rd | 18 - man/proteus_random_search.Rd | 5 tests/testthat/test-main.R | 45 -- 9 files changed, 343 insertions(+), 522 deletions(-)
Title: Statistical Tests for the Production of Reference Materials
Description: The production of certified reference materials (CRMs) requires
various statistical tests depending on the task and recorded data to ensure
that reported values of CRMs are appropriate.
Often these tests are performed according to the procedures described in
'ISO GUIDE 35:2017'. The 'eCerto' package contains a 'Shiny' app which
provides functionality to load, process, report and backup data recorded
during CRM production and facilitates following the recommended procedures.
It is described in Lisec et al (2023) <doi:10.1007/s00216-023-05099-3> and
can also be accessed online <https://apps.bam.de/shn00/eCerto/> without
package installation.
Author: Jan Lisec [cre, aut] ,
Frederik Kress [ctb]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between eCerto versions 0.5.14 dated 2024-09-02 and 0.8.4 dated 2025-03-26
eCerto-0.5.14/eCerto/R/fnc_check_RData.R |only eCerto-0.5.14/eCerto/R/fnc_load_xlsx.R |only eCerto-0.5.14/eCerto/README.md |only eCerto-0.5.14/eCerto/tests/testthat/test-fnc_load_xlsx.R |only eCerto-0.8.4/eCerto/DESCRIPTION | 20 eCerto-0.8.4/eCerto/MD5 | 129 +- eCerto-0.8.4/eCerto/NEWS.md |only eCerto-0.8.4/eCerto/R/app_inits.R | 16 eCerto-0.8.4/eCerto/R/app_server.R | 3 eCerto-0.8.4/eCerto/R/app_ui.R | 8 eCerto-0.8.4/eCerto/R/app_utils.R | 20 eCerto-0.8.4/eCerto/R/check_RData_with_res_object.R |only eCerto-0.8.4/eCerto/R/fnc_CertValPlot.R | 1 eCerto-0.8.4/eCerto/R/fnc_c_filter_data.R | 6 eCerto-0.8.4/eCerto/R/fnc_check_fmt_Vdata.R | 2 eCerto-0.8.4/eCerto/R/fnc_flt_Vdata.R | 4 eCerto-0.8.4/eCerto/R/fnc_list2rv.R | 4 eCerto-0.8.4/eCerto/R/fnc_plot_lts_data.R | 35 eCerto-0.8.4/eCerto/R/fnc_prepFigV1.R | 45 eCerto-0.8.4/eCerto/R/fnc_prepFigV3.R | 19 eCerto-0.8.4/eCerto/R/fnc_prepTabC0.R | 2 eCerto-0.8.4/eCerto/R/fnc_prepTabC2.R | 6 eCerto-0.8.4/eCerto/R/fnc_prepTabS1.R | 22 eCerto-0.8.4/eCerto/R/fnc_prepTabV1.R | 7 eCerto-0.8.4/eCerto/R/fnc_read_Vdata.R | 31 eCerto-0.8.4/eCerto/R/fnc_read_drmd_xml.R |only eCerto-0.8.4/eCerto/R/fnc_read_lts_input.R | 2 eCerto-0.8.4/eCerto/R/fnc_read_xlsx.R |only eCerto-0.8.4/eCerto/R/fnc_read_zenodo.R | 5 eCerto-0.8.4/eCerto/R/fnc_styleTabC3.R | 2 eCerto-0.8.4/eCerto/R/fnc_styleTabD1.R |only eCerto-0.8.4/eCerto/R/fnc_styleTabD2.R |only eCerto-0.8.4/eCerto/R/fnc_styleTabD3.R |only eCerto-0.8.4/eCerto/R/fnc_styleTabL1.R | 2 eCerto-0.8.4/eCerto/R/fnc_styleTabS1.R | 6 eCerto-0.8.4/eCerto/R/fnc_xml2df.R |only eCerto-0.8.4/eCerto/R/m_ExcelUpload.R | 3 eCerto-0.8.4/eCerto/R/m_Rdata_import.R | 2 eCerto-0.8.4/eCerto/R/m_analyte.R | 367 +++--- eCerto-0.8.4/eCerto/R/m_dataView.R | 28 eCerto-0.8.4/eCerto/R/m_materialtabelle.R | 62 - eCerto-0.8.4/eCerto/R/m_report.R | 59 - eCerto-0.8.4/eCerto/R/m_stability_arrhenius.R | 76 - eCerto-0.8.4/eCerto/R/m_xlsx_range_select.R | 14 eCerto-0.8.4/eCerto/R/page_DRMD.R |only eCerto-0.8.4/eCerto/R/page_LTS.R | 547 ++++------ eCerto-0.8.4/eCerto/R/page_certification.R | 329 ++---- eCerto-0.8.4/eCerto/R/page_homogeneity.R | 8 eCerto-0.8.4/eCerto/R/page_stability.R | 279 +++-- eCerto-0.8.4/eCerto/R/page_validation.R | 9 eCerto-0.8.4/eCerto/R/reactiveClass.R | 11 eCerto-0.8.4/eCerto/R/statistic_helper.R | 4 eCerto-0.8.4/eCerto/R/utils_drmd.R |only eCerto-0.8.4/eCerto/inst/app/www/reports/report_vorlage_drmd.Rmd |only eCerto-0.8.4/eCerto/inst/app/www/reports/report_vorlage_stability.Rmd | 36 eCerto-0.8.4/eCerto/inst/app/www/reports/report_vorlage_validation.Rmd | 12 eCerto-0.8.4/eCerto/inst/app/www/rmd/certification_analyte_options.Rmd | 8 eCerto-0.8.4/eCerto/inst/app/www/rmd/certification_materialtabelle.Rmd | 25 eCerto-0.8.4/eCerto/inst/app/www/rmd/drmd_dataupload.Rmd |only eCerto-0.8.4/eCerto/inst/app/www/rmd/drmd_tab_D1.Rmd |only eCerto-0.8.4/eCerto/inst/app/www/rmd/drmd_tab_D2.Rmd |only eCerto-0.8.4/eCerto/inst/app/www/rmd/fig/C_Modul_Tab1.png |binary eCerto-0.8.4/eCerto/inst/app/www/rmd/fig/C_Modul_Tab3.png |binary eCerto-0.8.4/eCerto/inst/app/www/rmd/fig/S_Modul_Tab1.png |binary eCerto-0.8.4/eCerto/inst/app/www/rmd/stability_plot.Rmd | 4 eCerto-0.8.4/eCerto/inst/app/www/rmd/start_gethelp.Rmd | 4 eCerto-0.8.4/eCerto/inst/app/www/rmd/v_fig_V1.Rmd | 2 eCerto-0.8.4/eCerto/inst/golem-config.yml | 2 eCerto-0.8.4/eCerto/tests/testthat/test-certification.R | 6 eCerto-0.8.4/eCerto/tests/testthat/test-fnc_read_xlsx.R |only eCerto-0.8.4/eCerto/tests/testthat/test-help_the_user_modal.R | 2 eCerto-0.8.4/eCerto/tests/testthat/test-materialtabelle.R | 4 eCerto-0.8.4/eCerto/tests/testthat/test-page_start.R | 3 eCerto-0.8.4/eCerto/tests/testthat/test-run_app.R | 8 eCerto-0.8.4/eCerto/tests/testthat/test-validation.R | 3 75 files changed, 1214 insertions(+), 1100 deletions(-)
Title: Optimal Transport for Gating Transfer in Cytometry Data with
Domain Adaptation
Description: Supervised learning from a source distribution (with known segmentation into cell sub-populations)
to fit a target distribution with unknown segmentation. It relies regularized optimal transport to directly
estimate the different cell population proportions from a biological sample characterized with flow cytometry
measurements. It is based on the regularized Wasserstein metric to compare cytometry measurements from
different samples, thus accounting for possible mis-alignment of a given cell population across sample
(due to technical variability from the technology of measurements). Supervised learning technique based
on the Wasserstein metric that is used to estimate an optimal re-weighting of class proportions in a
mixture model Details are presented in Freulon P, Bigot J and Hejblum BP (2023) <doi:10.1214/22-AOAS1660>.
Author: Boris Hejblum [aut, cre],
Paul Freulon [aut],
Kalidou Ba [aut, trl]
Maintainer: Boris Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between CytOpT versions 0.9.4 dated 2022-02-09 and 0.9.6 dated 2025-03-26
CytOpT-0.9.4/CytOpT/inst/python/CytOpTpy/__pycache__ |only CytOpT-0.9.6/CytOpT/DESCRIPTION | 12 CytOpT-0.9.6/CytOpT/MD5 | 34 CytOpT-0.9.6/CytOpT/NEWS.md | 5 CytOpT-0.9.6/CytOpT/R/CytOpT.R | 69 + CytOpT-0.9.6/CytOpT/R/HIPC_Standford.R | 46 - CytOpT-0.9.6/CytOpT/README.md | 34 CytOpT-0.9.6/CytOpT/build/vignette.rds |binary CytOpT-0.9.6/CytOpT/inst/CITATION | 25 CytOpT-0.9.6/CytOpT/inst/doc/CytOpt_HIPC.R | 4 CytOpT-0.9.6/CytOpT/inst/doc/CytOpt_HIPC.Rmd | 5 CytOpT-0.9.6/CytOpT/inst/doc/CytOpt_HIPC.html | 497 +++++++++---- CytOpT-0.9.6/CytOpT/man/CytOpT.Rd | 20 CytOpT-0.9.6/CytOpT/man/HIPC_Stanford.Rd | 36 CytOpT-0.9.6/CytOpT/man/figures/README-BAplot-1.png |binary CytOpT-0.9.6/CytOpT/man/figures/README-summary-plots-1.png |binary CytOpT-0.9.6/CytOpT/vignettes/CytOpt_HIPC.Rmd | 5 17 files changed, 525 insertions(+), 267 deletions(-)
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common descriptive
(univariate) statistics in concise tables available in a
variety of formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 1.1.2 dated 2025-03-17 and 1.1.3 dated 2025-03-26
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/parse_call.R | 24 +++++++++++++++++------- build/vignette.rds |binary inst/doc/introduction.html | 14 +++++++------- inst/doc/rmarkdown.html | 42 +++++++++++++++++++++--------------------- 7 files changed, 60 insertions(+), 44 deletions(-)
Title: Modelling with Sparse and Dense Matrices
Description: Generalized Linear Modelling with sparse and dense 'Matrix' matrices, using
modular prediction and response module classes.
Author: Douglas Bates [aut] ,
Martin Maechler [aut, cre]
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between MatrixModels versions 0.5-3 dated 2023-11-06 and 0.5-4 dated 2025-03-26
ChangeLog | 5 +++++ DESCRIPTION | 23 +++++++++++++++-------- MD5 | 12 ++++++------ man/lm.fit.sparse.Rd | 6 +++--- man/model.Matrix.Rd | 8 ++++---- man/modelMatrix-class.Rd | 16 ++++++++-------- man/predModule-class.Rd | 4 ++-- 7 files changed, 43 insertions(+), 31 deletions(-)
Title: Estimation Methods for Causal Inference Based on Inverse
Probability Weighting and Doubly Robust Estimation
Description: Various estimators of causal effects based on inverse probability weighting, doubly robust estimation, and double machine learning. Specifically, the package includes methods for estimating average treatment effects, direct and indirect effects in causal mediation analysis, and dynamic treatment effects. The models refer to studies of Froelich (2007) <doi:10.1016/j.jeconom.2006.06.004>, Huber (2012) <doi:10.3102/1076998611411917>, Huber (2014) <doi:10.1080/07474938.2013.806197>, Huber (2014) <doi:10.1002/jae.2341>, Froelich and Huber (2017) <doi:10.1111/rssb.12232>, Hsu, Huber, Lee, and Lettry (2020) <doi:10.1002/jae.2765>, and others.
Author: Hugo Bodory [aut, cre] ,
Martin Huber [aut] ,
Jannis Kueck [aut]
Maintainer: Hugo Bodory <hugo.bodory@unisg.ch>
Diff between causalweight versions 1.1.2 dated 2025-03-22 and 1.1.3 dated 2025-03-26
DESCRIPTION | 12 MD5 | 37 NAMESPACE | 8 R/ATETDML.R |only R/creditcard.R |only R/didDML.R |only R/didcontDML.R |only R/didcontDMLpanel.R |only R/functions.R | 3794 +++++++++++++++++++++++++------------------------ R/labormarket.R |only R/medDML.R | 113 - R/medlateweight.R | 108 - R/paneltestDML.R |only R/testmedident.R |only R/treatDML.R | 2 data/creditcard.RData |only data/labormarket.RData |only inst |only man/ATETDML.Rd |only man/creditcard.Rd |only man/didDML.Rd |only man/didcontDML.Rd |only man/didcontDMLpanel.Rd |only man/india.Rd | 88 - man/labormarket.Rd |only man/medDML.Rd | 5 man/paneltestDML.Rd |only man/rkd.Rd | 172 +- man/testmedident.Rd |only 29 files changed, 2258 insertions(+), 2081 deletions(-)
Title: Simulate Quantities of Interest from Regression Models
Description: This is an all-encompassing suite to facilitate the simulation of
so-called quantities of interest by way of a multivariate normal distribution
of the regression model's coefficients and variance-covariance matrix.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Diff between simqi versions 0.1.0 dated 2025-02-17 and 0.2.0 dated 2025-03-26
DESCRIPTION | 8 +- MD5 | 19 +++---- NAMESPACE | 2 NEWS.md | 9 +++ R/sim_qi.R | 126 +++++++++++++++++++++++++++++++++-------------- R/sim_qi.clm.R | 142 +++++++++++++++++++++-------------------------------- R/sim_qi.glm.R | 36 +++++++++---- R/sim_qi.lm.R | 36 ++++++++++--- R/sim_qi.logistf.R |only README.md | 2 man/sim_qi.Rd | 93 +++++++++++++++++++++++----------- 11 files changed, 290 insertions(+), 183 deletions(-)
Title: Serialize R Objects to JSON, JavaScript Object Notation
Description: This is a package that allows conversion to and from
data in Javascript object notation (JSON) format.
This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code
and allows R programmers to read and convert JSON content to R objects.
This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON
and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases.
This package uses methods and is readily extensible by defining methods for different classes,
vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R.
The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional
options to allow customizing the generation and processing of JSON content.
This package uses libjson rather than implementing yet another JSON parser. The aim is to support
other general projects by building on [...truncated...]
Author: CRAN Team [ctb, cre] ,
Duncan Temple Lang [aut] ,
Jonathan Wallace [aut]
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between RJSONIO versions 1.3-1.10 dated 2025-03-24 and 1.3-1.11 dated 2025-03-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/RJSON.c | 7 ++++++- 3 files changed, 11 insertions(+), 6 deletions(-)
Title: Imputation Procedures and Quality Tests for Fuzzy Data
Description: Special procedures for the imputation of missing fuzzy numbers are still underdeveloped. The goal of the package is to provide the new d-imputation method (DIMP for short, Romaniuk, M. and Grzegorzewski, P. (2023) "Fuzzy Data Imputation with DIMP and FGAIN" RB/23/2023) and covert some classical ones applied in R packages ('missForest','miceRanger','knn') for use with fuzzy datasets. Additionally, specially tailored benchmarking tests are provided to check and compare these imputation procedures with fuzzy datasets.
Author: Maciej Romaniuk [cre, aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyImputationTest versions 0.4.0 dated 2025-01-24 and 0.5.0 dated 2025-03-26
DESCRIPTION | 8 MD5 | 30 R/CalculateFuzzyMeasures.R | 8 R/CalculateFuzzyMeasuresSingleVar.R | 26 R/CalculateSE.R |only R/FuzzyImputation.R | 27 R/MethodsComparison.R | 44 R/PrepareDataForComparison.R |only R/methodNames.R | 2 R/utils.R | 2 man/CalculateFuzzyMeasures.Rd | 5 man/FuzzyImputation.Rd | 7 man/MethodsComparison.Rd | 2 man/methodNames.Rd | 2 tests/testthat/_snaps/CalculateFuzzyMeasures.md | 68 - tests/testthat/_snaps/ImputationTests.md | 68 - tests/testthat/_snaps/MethodsComparison.md | 1299 +++++++++++++++--------- 17 files changed, 1022 insertions(+), 576 deletions(-)
More information about FuzzyImputationTest at CRAN
Permanent link
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript
and WebAssembly engine. This package can be compiled either with V8 version 6
and up or NodeJS when built as a shared library.
Author: Jeroen Ooms [aut, cre] ,
Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between V8 versions 6.0.2 dated 2025-03-14 and 6.0.3 dated 2025-03-26
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS | 3 +++ build/partial.rdb |binary inst/doc/npm.html | 4 ++-- inst/doc/v8_intro.html | 6 +++--- src/Makevars.in | 6 +++--- src/Makevars.win | 17 +++++++++-------- src/bindings.cpp | 1 + tools/winlibs.R | 10 +++++----- 10 files changed, 38 insertions(+), 33 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.1.1 dated 2025-03-08 and 1.1.2 dated 2025-03-26
DESCRIPTION | 10 - MD5 | 39 ++--- NEWS.md | 5 R/headers.R | 4 R/oauth.R | 14 + R/req-auth-aws.R | 8 - R/req-headers.R | 19 ++ R/resp-stream.R | 5 README.md | 4 inst/doc/httr2.html | 38 ++--- man/req_headers.Rd | 4 tests/testthat/_snaps/req-headers.md | 13 + tests/testthat/helper-sync.R |only tests/testthat/helper-webfakes.R | 10 + tests/testthat/test-headers.R | 7 tests/testthat/test-req-auth-aws.R | 15 + tests/testthat/test-req-headers.R | 21 ++ tests/testthat/test-req-perform-connection.R | 4 tests/testthat/test-req-perform-parallel.R | 8 - tests/testthat/test-req-perform.R | 4 tests/testthat/test-resp-stream.R | 204 ++++++++++++--------------- 21 files changed, 256 insertions(+), 180 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb]
,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-36 dated 2025-01-11 and 1.1-37 dated 2025-03-26
DESCRIPTION | 13 +- MD5 | 35 ++++--- R/lmer.R | 4 R/predict.R | 5 - build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 24 ++++- inst/doc/PLSvGLS.pdf |binary inst/doc/Theory.pdf |binary inst/doc/lmer.R | 187 ------------------------------------------ inst/doc/lmer.pdf |binary inst/doc/lmerperf.html | 4 inst/tinytest |only man/simulate.merMod.Rd | 9 +- tests/REMLdev.R | 15 ++- tests/glmmExt.R | 2 tests/nbinom.R | 4 tests/simulate.R | 18 +++- tests/testthat/test-methods.R | 26 +++-- 19 files changed, 112 insertions(+), 234 deletions(-)
Title: Miscellaneous Utilities and Functions
Description: Miscellaneous tools and functions,
including: generate descriptive statistics tables,
format output, visualize relations among variables or check
distributions, and generic functions for residual and
model diagnostics.
Author: Joshua F. Wiley [aut, cre]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between JWileymisc versions 1.4.1 dated 2023-10-05 and 1.4.2 dated 2025-03-26
DESCRIPTION | 20 MD5 | 85 - NAMESPACE | 22 NEWS.md | 23 R/descriptives.R | 204 ++-- R/diagnostics.R | 153 +-- R/geoms_themes.R |only R/models.R | 133 +- R/plotting.R | 1799 +++++++++++++++++++------------------ R/scoring.R | 2 R/styler.R | 1654 +++++++++++++++++----------------- R/utils.R | 1075 +++++++++++----------- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/diagnostics-vignette.Rmd | 2 inst/doc/diagnostics-vignette.html | 199 ++-- inst/doc/exploratory-vignette.R | 72 - inst/doc/exploratory-vignette.Rmd | 2 inst/doc/exploratory-vignette.html | 108 +- inst/doc/model-test-vignette.Rmd | 2 inst/doc/model-test-vignette.html | 148 +-- man/APAStyler.Rd | 32 man/SEMSummary.Rd | 28 man/SEMSummary.fit.Rd | 21 man/compareIVs.Rd | 14 man/diffCircular.Rd | 6 man/dot-fround.Rd | 38 man/dot-quantilePercentiles.Rd | 14 man/f.r2.Rd | 50 - man/geom_tufterange.Rd |only man/gglikert.Rd | 6 man/internalcompareIV.Rd | 6 man/lagk.Rd | 52 - man/modelDiagnostics.Rd | 2 man/moments.Rd | 3 man/residualDiagnostics.Rd | 17 man/scoring.Rd | 2 man/testDistribution.Rd | 338 +++--- man/theme_tufte.Rd |only man/winsorizor.Rd | 9 tests/testthat/test-diagnostics.R | 12 vignettes/diagnostics-vignette.Rmd | 2 vignettes/exploratory-vignette.Rmd | 2 vignettes/model-test-vignette.Rmd | 2 45 files changed, 3307 insertions(+), 3054 deletions(-)