Title: Knock Errors Off Nice Guesses
Description: Miscellaneous functions and data used in psychological research and teaching. Keng
currently has a built-in dataset depress, and could (1) scale a vector; (2) compute the cut-off
values of Pearson's r with known sample size; (3) test the significance and compute the post-hoc
power for Pearson's r with known sample size; (4) conduct a priori power analysis and plan the
sample size for Pearson's r; (5) compare lm()'s fitted outputs using R-squared, f_squared,
post-hoc power, and PRE (Proportional Reduction in Error, also called partial R-squared or
partial Eta-squared); (6) calculate PRE from partial correlation, Cohen's f, or f_squared;
(7) conduct a priori power analysis and plan the sample size for one or a set of predictors in
regression analysis; (8) conduct post-hoc power analysis for one or a set of predictors in
regression analysis with known sample size; (9) randomly pick numbers for Chinese Super Lotto
and Double Color Balls.
Author: Qingyao Zhang [aut, cre]
Maintainer: Qingyao Zhang <qingyaozhang@outlook.com>
Diff between Keng versions 2024.12.15 dated 2024-12-15 and 2025.8.16 dated 2025-08-19
DESCRIPTION | 16 ++--- MD5 | 34 +++++++---- NAMESPACE | 2 NEWS.md | 13 +++- R/Scale.R | 122 ++++++++++++++++++++-------------------- R/data.R | 2 R/pick_dcb.R |only R/pick_sl.R |only R/power_lm.R | 22 +++---- R/power_r.R | 22 +++---- README.md | 22 +++---- build/vignette.rds |binary inst/doc/commonSampleSizes.R |only inst/doc/commonSampleSizes.Rmd |only inst/doc/commonSampleSizes.html |only man/depress.Rd | 2 man/pick_dcb.Rd |only man/pick_sl.Rd |only man/power_lm.Rd | 8 +- man/power_r.Rd | 8 +- tests/testthat/test-pick_dcb.R |only tests/testthat/test-pick_sl.R |only vignettes/commonSampleSizes.Rmd |only 23 files changed, 149 insertions(+), 124 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut],
Youngsun Park [aut] ,
Hyungwoo Jo [aut],
Jeongmin Seo [aut],
Hojun LEE [aut],
Sungho Choi [aut],
Yeji Ka [...truncated...]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.6.11 dated 2025-07-02 and 1.6.13 dated 2025-08-19
DESCRIPTION | 22 + MD5 | 33 +- NAMESPACE | 1 NEWS.md | 27 ++ R/bar.R | 164 ++++++++++--- R/box.R | 8 R/forestcox.R | 103 +++++--- R/forestglm.R | 86 +++++-- R/gee.R | 4 R/kaplan.R | 15 - R/roc.R | 396 ++++++++++++++++----------------- R/timeroc.R | 334 ++++++++++++++++++++------- build/vignette.rds |binary inst/doc/jsmodule.html | 26 +- inst/doc/jsmodule_subgroup_cmprsk.html | 16 - man/rocModule.Rd | 1 man/rocUI.Rd | 1 tests/testthat/test-timeroc.R |only 18 files changed, 794 insertions(+), 443 deletions(-)
Title: A Comprehensive Analysis of High Dimensional Longitudinal Data
Description: To provide a comprehensive analysis of high dimensional longitudinal
data,this package provides analysis for any combination of 1) simultaneous
variable selection and estimation, 2) mean regression or quantile regression
for heterogeneous data, 3) cross-sectional or longitudinal data, 4) balanced
or imbalanced data, 5) moderate, high or even ultra-high dimensional data,
via computationally efficient implementations of penalized generalized
estimating equations.
Author: Tianhai Zu [aut, cre],
Brittany Green [aut, ctb],
Yan Yu [aut, ctb]
Maintainer: Tianhai Zu <zuti@mail.uc.edu>
Diff between geeVerse versions 0.2.2 dated 2024-11-12 and 0.3.0 dated 2025-08-19
geeVerse-0.2.2/geeVerse/R/generateData.R |only geeVerse-0.2.2/geeVerse/R/qpgee_sim.R |only geeVerse-0.2.2/geeVerse/man/generateData.Rd |only geeVerse-0.2.2/geeVerse/man/predict.qpgee.Rd |only geeVerse-0.2.2/geeVerse/man/qpgee.est.Rd |only geeVerse-0.3.0/geeVerse/DESCRIPTION | 6 geeVerse-0.3.0/geeVerse/MD5 | 48 geeVerse-0.3.0/geeVerse/NAMESPACE | 23 geeVerse-0.3.0/geeVerse/R/CVfit.R | 4 geeVerse-0.3.0/geeVerse/R/PGEE.R | 11 geeVerse-0.3.0/geeVerse/R/generate_data.R |only geeVerse-0.3.0/geeVerse/R/qpgee.R | 1170 ++++------ geeVerse-0.3.0/geeVerse/R/summary.R |only geeVerse-0.3.0/geeVerse/R/utils.R | 39 geeVerse-0.3.0/geeVerse/R/yeastG1.R | 2 geeVerse-0.3.0/geeVerse/README.md | 24 geeVerse-0.3.0/geeVerse/inst/sim/replication_script_for_main.R | 488 ++-- geeVerse-0.3.0/geeVerse/inst/sim/replication_script_for_main_test.R |only geeVerse-0.3.0/geeVerse/inst/sim/test_new.R |only geeVerse-0.3.0/geeVerse/man/CVfit.Rd | 6 geeVerse-0.3.0/geeVerse/man/PGEE.Rd | 17 geeVerse-0.3.0/geeVerse/man/Siga_cov.Rd | 4 geeVerse-0.3.0/geeVerse/man/compile_result.Rd | 2 geeVerse-0.3.0/geeVerse/man/compile_result.default.Rd |only geeVerse-0.3.0/geeVerse/man/compile_result.qpgee.Rd |only geeVerse-0.3.0/geeVerse/man/dot-update_beta.Rd |only geeVerse-0.3.0/geeVerse/man/dot-update_correlation.Rd |only geeVerse-0.3.0/geeVerse/man/geeVerse.Rd |only geeVerse-0.3.0/geeVerse/man/generate_data.Rd |only geeVerse-0.3.0/geeVerse/man/pp_scad_lin.Rd |only geeVerse-0.3.0/geeVerse/man/print.summary.qpgee.Rd |only geeVerse-0.3.0/geeVerse/man/qpgee.Rd | 101 geeVerse-0.3.0/geeVerse/man/qpgeeControl.Rd |only geeVerse-0.3.0/geeVerse/man/yeastG1.Rd | 2 34 files changed, 958 insertions(+), 989 deletions(-)
Title: The Directed Prediction Index
Description: The Directed Prediction Index ('DPI') is
a simulation-based method
for quantifying the relative endogeneity (relative dependence)
of outcome (Y) versus predictor (X) variables
in multiple linear regression models.
By comparing the proportion of variance explained (R-squared)
between the Y-as-outcome model and the X-as-outcome model
while controlling for a sufficient number
of potential confounding variables,
it suggests a more plausible influence direction
from a more exogenous variable (X) to a more endogenous variable (Y).
Methodological details are provided at
<https://psychbruce.github.io/DPI/>.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between DPI versions 2025.6 dated 2025-06-18 and 2025.8 dated 2025-08-19
DPI-2025.6/DPI/man/plot.dpi.Rd |only DPI-2025.6/DPI/man/plot.dpi.curve.Rd |only DPI-2025.6/DPI/man/print.dpi.Rd |only DPI-2025.6/DPI/man/print.summary.dpi.Rd |only DPI-2025.6/DPI/man/summary.dpi.Rd |only DPI-2025.8/DPI/DESCRIPTION | 18 DPI-2025.8/DPI/MD5 | 26 DPI-2025.8/DPI/NAMESPACE | 6 DPI-2025.8/DPI/NEWS.md | 6 DPI-2025.8/DPI/R/DPI.R | 921 +++++++++++++++++++++++--------- DPI-2025.8/DPI/README.md | 9 DPI-2025.8/DPI/build |only DPI-2025.8/DPI/man/DPI-package.Rd |only DPI-2025.8/DPI/man/DPI.Rd | 31 - DPI-2025.8/DPI/man/DPI_curve.Rd | 14 DPI-2025.8/DPI/man/S3method.dpi.Rd |only DPI-2025.8/DPI/man/S3method.network.Rd |only DPI-2025.8/DPI/man/cor_network.Rd | 46 - DPI-2025.8/DPI/man/dag_network.Rd |only 19 files changed, 755 insertions(+), 322 deletions(-)
Title: Random Effects Meta-Analysis for Correlated Test Statistics
Description: Meta-analysis is widely used to summarize estimated effects sizes across multiple statistical tests. Standard fixed and random effect meta-analysis methods assume that the estimated of the effect sizes are statistically independent. Here we relax this assumption and enable meta-analysis when the correlation matrix between effect size estimates is known. Fixed effect meta-analysis uses the method of Lin and Sullivan (2009) <doi:10.1016/j.ajhg.2009.11.001>, and random effects meta-analysis uses the method of Han, et al. <doi:10.1093/hmg/ddw049>.
Author: Gabriel Hoffman [aut, cre]
Maintainer: Gabriel Hoffman <gabriel.hoffman@mssm.edu>
Diff between remaCor versions 0.0.18 dated 2024-02-08 and 0.0.20 dated 2025-08-19
remaCor-0.0.18/remaCor/vignettes/remaCor_cache/html/out_1ddc35650af5576c7585cdd0ca1f72de.RData |only remaCor-0.0.18/remaCor/vignettes/remaCor_cache/html/out_1ddc35650af5576c7585cdd0ca1f72de.rdb |only remaCor-0.0.18/remaCor/vignettes/remaCor_cache/html/out_1ddc35650af5576c7585cdd0ca1f72de.rdx |only remaCor-0.0.18/remaCor/vignettes/remaCor_cache/html/rema_c2b94817ad6f98d9ab1b0f4b282329d1.RData |only remaCor-0.0.18/remaCor/vignettes/remaCor_cache/html/rema_c2b94817ad6f98d9ab1b0f4b282329d1.rdb |only remaCor-0.0.18/remaCor/vignettes/remaCor_cache/html/rema_c2b94817ad6f98d9ab1b0f4b282329d1.rdx |only remaCor-0.0.18/remaCor/vignettes/remaCor_cache/html/sessionInfo_6b303b50b61848f54c05a32b0362481b.RData |only remaCor-0.0.18/remaCor/vignettes/remaCor_cache/html/sessionInfo_6b303b50b61848f54c05a32b0362481b.rdb |only remaCor-0.0.18/remaCor/vignettes/remaCor_cache/html/sessionInfo_6b303b50b61848f54c05a32b0362481b.rdx |only remaCor-0.0.20/remaCor/DESCRIPTION | 13 remaCor-0.0.20/remaCor/MD5 | 40 +- remaCor-0.0.20/remaCor/NEWS.md | 8 remaCor-0.0.20/remaCor/R/LS_empirical_pvalue.R | 20 - remaCor-0.0.20/remaCor/R/RE2C.R | 28 - remaCor-0.0.20/remaCor/README.md | 14 remaCor-0.0.20/remaCor/build/partial.rdb |binary remaCor-0.0.20/remaCor/build/vignette.rds |binary remaCor-0.0.20/remaCor/inst/REFERENCES.bib | 17 remaCor-0.0.20/remaCor/inst/doc/remaCor.html | 189 +++++----- remaCor-0.0.20/remaCor/man/LS.empirical.Rd | 12 remaCor-0.0.20/remaCor/man/RE2C.Rd | 13 remaCor-0.0.20/remaCor/vignettes/remaCor_cache/html/out_9cbbeef008c0d5dfb87530b1e6de5f80.RData |only remaCor-0.0.20/remaCor/vignettes/remaCor_cache/html/out_9cbbeef008c0d5dfb87530b1e6de5f80.rdb |only remaCor-0.0.20/remaCor/vignettes/remaCor_cache/html/out_9cbbeef008c0d5dfb87530b1e6de5f80.rdx |only remaCor-0.0.20/remaCor/vignettes/remaCor_cache/html/rema_2a44e1823be62314863a2857afd42512.RData |only remaCor-0.0.20/remaCor/vignettes/remaCor_cache/html/rema_2a44e1823be62314863a2857afd42512.rdb |only remaCor-0.0.20/remaCor/vignettes/remaCor_cache/html/rema_2a44e1823be62314863a2857afd42512.rdx |only remaCor-0.0.20/remaCor/vignettes/remaCor_cache/html/sessionInfo_3af1cf4a471171be852d8f2ce360fe27.RData |only remaCor-0.0.20/remaCor/vignettes/remaCor_cache/html/sessionInfo_3af1cf4a471171be852d8f2ce360fe27.rdb |only remaCor-0.0.20/remaCor/vignettes/remaCor_cache/html/sessionInfo_3af1cf4a471171be852d8f2ce360fe27.rdx |only 30 files changed, 200 insertions(+), 154 deletions(-)
Title: Genome-Wide Robust Analysis for Biobank Data (GRAB)
Description: Provides a comprehensive suite of genome-wide association study (GWAS) methods
specifically designed for biobank-scale data. The package offers computationally efficient
and robust association tests for time-to-event traits (e.g., Bi et al., 2020
<doi:10.1016/j.ajhg.2020.06.003>), ordinal categorical traits (e.g., Bi et al., 2021
<doi:10.1016/j.ajhg.2021.03.019>), and longitudinal traits (Xu et al., 2025
<doi:10.1038/s41467-025-56669-1>). Additionally, it includes functions for
simulating genotype and phenotype data to support research and method development.
Author: Wenjian Bi [aut],
Wei Zhou [aut],
Rounak Dey [aut],
Zhangchen Zhao [aut],
Seunggeun Lee [aut],
Woody Miao [cre]
Maintainer: Woody Miao <miaolin@pku.edu.cn>
Diff between GRAB versions 0.2.2 dated 2025-07-29 and 0.2.3 dated 2025-08-19
GRAB-0.2.2/GRAB/inst/PairwiseIBD |only GRAB-0.2.2/GRAB/inst/SparseGRM |only GRAB-0.2.2/GRAB/inst/results |only GRAB-0.2.3/GRAB/DESCRIPTION | 8 GRAB-0.2.3/GRAB/MD5 | 111 - GRAB-0.2.3/GRAB/NAMESPACE | 11 GRAB-0.2.3/GRAB/R/CCT.R | 2 GRAB-0.2.3/GRAB/R/DenseGRM.R | 3 GRAB-0.2.3/GRAB/R/GRAB_Marker.R | 490 ++--- GRAB-0.2.3/GRAB/R/GRAB_Null_Model.R | 368 ++-- GRAB-0.2.3/GRAB/R/GRAB_Region.R | 130 - GRAB-0.2.3/GRAB/R/GRAB_Simu.R | 86 GRAB-0.2.3/GRAB/R/Geno.R | 38 GRAB-0.2.3/GRAB/R/POLMM.R | 57 GRAB-0.2.3/GRAB/R/PairwiseIBD.R | 31 GRAB-0.2.3/GRAB/R/SAGELD.R | 49 GRAB-0.2.3/GRAB/R/SPACox.R | 26 GRAB-0.2.3/GRAB/R/SPAGRM.R | 64 GRAB-0.2.3/GRAB/R/SPAmix.R | 74 GRAB-0.2.3/GRAB/R/SparseGRM.R | 62 GRAB-0.2.3/GRAB/R/Util.R | 17 GRAB-0.2.3/GRAB/R/WtCoxG.R | 139 - GRAB-0.2.3/GRAB/R/control.R | 43 GRAB-0.2.3/GRAB/R/formula.R | 2 GRAB-0.2.3/GRAB/README.md | 70 GRAB-0.2.3/GRAB/inst/extdata/PairwiseIBD.txt |only GRAB-0.2.3/GRAB/inst/extdata/SparseGRM.txt |only GRAB-0.2.3/GRAB/inst/extdata/objPOLMMnull.RData |only GRAB-0.2.3/GRAB/inst/extdata/simuPHENO.txt | 2002 +++++++++++------------ GRAB-0.2.3/GRAB/inst/extdata/simuPLINK.frq |only GRAB-0.2.3/GRAB/inst/extdata/simuPLINK_RV.frq |only GRAB-0.2.3/GRAB/man/GRAB.Marker.Rd | 155 - GRAB-0.2.3/GRAB/man/GRAB.NullModel.Rd | 206 +- GRAB-0.2.3/GRAB/man/GRAB.POLMM.Rd | 44 GRAB-0.2.3/GRAB/man/GRAB.ReadGeno.Rd | 1 GRAB-0.2.3/GRAB/man/GRAB.Region.Rd | 32 GRAB-0.2.3/GRAB/man/GRAB.SPACox.Rd | 17 GRAB-0.2.3/GRAB/man/GRAB.SPAGRM.Rd | 5 GRAB-0.2.3/GRAB/man/GRAB.SPAmix.Rd | 34 GRAB-0.2.3/GRAB/man/GRAB.SimuGMat.Rd | 1 GRAB-0.2.3/GRAB/man/GRAB.SimuGMatFromGenoFile.Rd | 1 GRAB-0.2.3/GRAB/man/GRAB.SimubVec.Rd | 1 GRAB-0.2.3/GRAB/man/GRAB.WtCoxG.Rd | 19 GRAB-0.2.3/GRAB/man/GRAB.makePlink.Rd | 1 GRAB-0.2.3/GRAB/man/checkIfSampleIDsExist.Rd | 1 GRAB-0.2.3/GRAB/man/getSampleIDsFromBGEN.Rd | 1 GRAB-0.2.3/GRAB/man/getSparseGRM.Rd | 8 GRAB-0.2.3/GRAB/man/getTempFilesFullGRM.Rd | 3 GRAB-0.2.3/GRAB/man/getVersionFromBGEN.Rd | 1 GRAB-0.2.3/GRAB/man/handleFormula.Rd | 1 GRAB-0.2.3/GRAB/man/setDenseGRM.Rd | 1 GRAB-0.2.3/GRAB/src/BGEN.cpp | 38 GRAB-0.2.3/GRAB/src/DenseGRM.cpp | 32 GRAB-0.2.3/GRAB/src/Main.cpp | 140 - GRAB-0.2.3/GRAB/src/Makevars | 7 GRAB-0.2.3/GRAB/src/PLINK.cpp | 24 GRAB-0.2.3/GRAB/src/POLMM.cpp | 113 - GRAB-0.2.3/GRAB/src/UTIL.cpp | 12 GRAB-0.2.3/GRAB/src/WtCoxG.cpp | 14 59 files changed, 2400 insertions(+), 2396 deletions(-)
Title: Bivariate Zero-Inflated Count Models Using Copulas
Description: Maximum likelihood estimation of copula-based zero-inflated
(and non-inflated) Poisson and negative binomial count models, based on the
article <doi:10.18637/jss.v109.i01>. Supports Frank and Gaussian copulas.
Allows for mixed margins (e.g., one margin Poisson, the other zero-inflated
negative binomial), and several marginal link functions. Built-in methods for
publication-quality tables using 'texreg', post-estimation diagnostics using
'DHARMa', and testing for marginal zero-modification via <doi:10.1177/0962280217749991>.
For information on copula regression for count data, see Genest and Nešlehová (2007)
<doi:10.1017/S0515036100014963> as well as Nikoloulopoulos (2013) <doi:10.1007/978-3-642-35407-6_11>.
For information on zero-inflated count regression generally, see Lambert (1992)
<https://www.jstor.org/stable/1269547>. The author acknowledges
support by NSF DMS-1925119 and DMS-212324.
Author: John Niehaus [aut, cre]
Maintainer: John Niehaus <jniehaus2257@gmail.com>
Diff between bizicount versions 1.3.3 dated 2024-05-01 and 1.3.4 dated 2025-08-19
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 21 +++++++++++++++++++++ R/bizicount.R | 2 +- R/zicreg.R | 4 ++-- README.md | 2 +- man/bizicount.Rd | 2 +- man/zic.reg.Rd | 4 ++-- 8 files changed, 39 insertions(+), 18 deletions(-)
Title: 'shiny' Widgets for 'teal' Applications
Description: Collection of 'shiny' widgets to support 'teal' applications.
Enables the manipulation of application layout and plot or table
settings.
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.widgets versions 0.4.3 dated 2025-01-31 and 0.5.0 dated 2025-08-19
teal.widgets-0.4.3/teal.widgets/inst/optional-select-input |only teal.widgets-0.4.3/teal.widgets/man/get_bs_version.Rd |only teal.widgets-0.4.3/teal.widgets/man/plot_suppress.Rd |only teal.widgets-0.5.0/teal.widgets/DESCRIPTION | 18 teal.widgets-0.5.0/teal.widgets/MD5 | 111 +-- teal.widgets-0.5.0/teal.widgets/NEWS.md | 13 teal.widgets-0.5.0/teal.widgets/R/basic_table_args.R | 6 teal.widgets-0.5.0/teal.widgets/R/draggable_buckets.R | 6 teal.widgets-0.5.0/teal.widgets/R/get_dt_rows.R | 22 teal.widgets-0.5.0/teal.widgets/R/ggplot2_args.R | 6 teal.widgets-0.5.0/teal.widgets/R/nested_closeable_modal.R | 9 teal.widgets-0.5.0/teal.widgets/R/optionalInput.R | 166 ++--- teal.widgets-0.5.0/teal.widgets/R/panel_group.R | 122 ---- teal.widgets-0.5.0/teal.widgets/R/plot_with_settings.R | 264 ++------ teal.widgets-0.5.0/teal.widgets/R/standard_layout.R | 58 + teal.widgets-0.5.0/teal.widgets/R/table_with_settings.R | 56 - teal.widgets-0.5.0/teal.widgets/R/utils.R | 25 teal.widgets-0.5.0/teal.widgets/R/verbatim_popup.R | 64 +- teal.widgets-0.5.0/teal.widgets/R/white_small_well.R | 2 teal.widgets-0.5.0/teal.widgets/build/vignette.rds |binary teal.widgets-0.5.0/teal.widgets/inst/WORDLIST | 1 teal.widgets-0.5.0/teal.widgets/inst/draggable-buckets/draggable-buckets.js | 4 teal.widgets-0.5.0/teal.widgets/inst/plot-with-settings/plot-with-settings.css | 84 -- teal.widgets-0.5.0/teal.widgets/inst/plot-with-settings/plot-with-settings.js | 7 teal.widgets-0.5.0/teal.widgets/inst/standard-layout |only teal.widgets-0.5.0/teal.widgets/inst/table-with-settings/table-with-settings.css | 100 --- teal.widgets-0.5.0/teal.widgets/inst/verbatim-popup/verbatim-popup.css |only teal.widgets-0.5.0/teal.widgets/inst/verbatim-popup/verbatim-popup.js | 9 teal.widgets-0.5.0/teal.widgets/man/basic_table_args.Rd | 1 teal.widgets-0.5.0/teal.widgets/man/clean_brushedPoints.Rd | 1 teal.widgets-0.5.0/teal.widgets/man/draggable_buckets.Rd | 5 teal.widgets-0.5.0/teal.widgets/man/get_dt_rows.Rd | 19 teal.widgets-0.5.0/teal.widgets/man/ggplot2_args.Rd | 1 teal.widgets-0.5.0/teal.widgets/man/nested_closeable_modal.Rd | 4 teal.widgets-0.5.0/teal.widgets/man/optionalSelectInput.Rd | 30 teal.widgets-0.5.0/teal.widgets/man/optionalSliderInput.Rd | 15 teal.widgets-0.5.0/teal.widgets/man/optionalSliderInputValMinMax.Rd | 18 teal.widgets-0.5.0/teal.widgets/man/panel_group.Rd | 2 teal.widgets-0.5.0/teal.widgets/man/panel_item.Rd | 2 teal.widgets-0.5.0/teal.widgets/man/parse_basic_table_args.Rd | 1 teal.widgets-0.5.0/teal.widgets/man/parse_ggplot2_args.Rd | 1 teal.widgets-0.5.0/teal.widgets/man/plot_with_settings.Rd | 31 - teal.widgets-0.5.0/teal.widgets/man/resolve_basic_table_args.Rd | 1 teal.widgets-0.5.0/teal.widgets/man/resolve_ggplot2_args.Rd | 1 teal.widgets-0.5.0/teal.widgets/man/standard_layout.Rd | 1 teal.widgets-0.5.0/teal.widgets/man/table_with_settings.Rd | 3 teal.widgets-0.5.0/teal.widgets/man/verbatim_popup.Rd | 3 teal.widgets-0.5.0/teal.widgets/man/white_small_well.Rd | 1 teal.widgets-0.5.0/teal.widgets/tests/testthat/helpers-utils.R | 6 teal.widgets-0.5.0/teal.widgets/tests/testthat/test-draggable_buckets.R |only teal.widgets-0.5.0/teal.widgets/tests/testthat/test-get_dt_rows_ui.R |only teal.widgets-0.5.0/teal.widgets/tests/testthat/test-ggplot2_args.R | 97 ++- teal.widgets-0.5.0/teal.widgets/tests/testthat/test-optionalSelectInput_ui.R |only teal.widgets-0.5.0/teal.widgets/tests/testthat/test-optionalSliderInputValMinMax_ui.R |only teal.widgets-0.5.0/teal.widgets/tests/testthat/test-plot_with_settings.R | 36 - teal.widgets-0.5.0/teal.widgets/tests/testthat/test-plot_with_settings_ui.R | 301 ++++------ teal.widgets-0.5.0/teal.widgets/tests/testthat/test-standard_layout.R | 101 --- teal.widgets-0.5.0/teal.widgets/tests/testthat/test-table_with_settings_ui.R | 192 ++---- teal.widgets-0.5.0/teal.widgets/tests/testthat/test-utils.R | 4 teal.widgets-0.5.0/teal.widgets/tests/testthat/test-verbatim_popup.R | 4 teal.widgets-0.5.0/teal.widgets/tests/testthat/test-verbatim_popup_ui.R | 4 61 files changed, 804 insertions(+), 1235 deletions(-)
Title: Stratified Randomized Experiments
Description: Estimate average treatment effects (ATEs) in stratified randomized experiments. `sreg` supports a wide range of stratification designs, including matched pairs, n-tuple designs, and larger strata with many units — possibly of unequal size across strata. 'sreg' is designed to accommodate scenarios with multiple treatments and cluster-level treatment assignments, and accommodates optimal linear covariate adjustment based on baseline observable characteristics. 'sreg' computes estimators and standard errors based on Bugni, Canay, Shaikh (2018) <doi:10.1080/01621459.2017.1375934>; Bugni, Canay, Shaikh, Tabord-Meehan (2024+) <doi:10.48550/arXiv.2204.08356>; Jiang, Linton, Tang, Zhang (2023+) <doi:10.48550/arXiv.2201.13004>; Bai, Jiang, Romano, Shaikh, and Zhang (2024) <doi:10.1016/j.jeconom.2024.105740>; Liu (2024+) <doi:10.48550/arXiv.2301.09016>; and Cytrynbaum (2024) <doi:10.3982/QE2475>.
Author: Juri Trifonov [aut, cre, cph],
Yuehao Bai [aut],
Azeem Shaikh [aut],
Max Tabord-Meehan [aut]
Maintainer: Juri Trifonov <jutrifonov@u.northwestern.edu>
Diff between sreg versions 1.0.1 dated 2025-02-06 and 2.0.1 dated 2025-08-19
DESCRIPTION | 16 MD5 | 41 NAMESPACE | 6 NEWS.md | 14 R/2.0(dev) |only R/core.R | 459 ++++++++--- R/data_check.r | 190 ++++ R/dgp_obs.r | 277 ++++++ R/output.r | 355 +++++--- R/pi_hat.r | 159 +++ R/result.r | 291 +++++++ R/tau_hat.r | 282 ++++++ R/var_hat.r | 346 +++++++- R/zzz.r | 1 README.md | 236 ++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro-to-sreg.html | 14 man/figures |only man/plot.sreg.Rd |only man/sreg.Rd | 36 man/sreg.rgen.Rd | 13 tests/testthat/test-core.R | 1824 +++++++++++++++++++++++++++++++++++++++++--- 23 files changed, 4108 insertions(+), 452 deletions(-)
Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling.
Author: Markus Loecher [aut, cre]
Maintainer: Markus Loecher <markus.loecher@gmail.com>
Diff between RgoogleMaps versions 1.5.1 dated 2023-11-06 and 1.5.3 dated 2025-08-19
DESCRIPTION | 16 ++++++++---- MD5 | 8 +++--- R/ReadMapTile.R | 66 ++++++++++++++++++++++++++--------------------------- R/SpatialToPBS.R | 9 +++++-- man/ReadMapTile.Rd | 57 ++++++++++++++++++++++++++++++--------------- 5 files changed, 93 insertions(+), 63 deletions(-)
Title: Orthogonal Nonlinear Least-Squares Regression
Description: Fits two-dimensional data by means of orthogonal nonlinear least-squares using Levenberg-Marquardt minimization and provides functionality for fit diagnostics and plotting. Delivers the same results as the 'ODRPACK' Fortran implementation described in Boggs et al. (1989) <doi:10.1145/76909.76913>, but is implemented in pure R.
Author: Andrej-Nikolai Spiess [aut, cre]
Maintainer: Andrej-Nikolai Spiess <draspiess@gmail.com>
Diff between onls versions 0.1-2 dated 2022-10-31 and 0.1-3 dated 2025-08-19
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS | 4 ++++ build/partial.rdb |only build/vignette.rds |binary inst/doc/onls.pdf |binary man/onls.Rd | 10 +++++----- 7 files changed, 19 insertions(+), 14 deletions(-)
Title: Multiple-Instance Learning with Support Vector Machines
Description: Weakly supervised (WS), multiple instance (MI) data lives in
numerous interesting applications such as drug discovery, object
detection, and tumor prediction on whole slide images. The 'mildsvm'
package provides an easy way to learn from this data by training
Support Vector Machine (SVM)-based classifiers. It also contains
helpful functions for building and printing multiple instance data
frames. The core methods from 'mildsvm' come from the following
references: Kent and Yu (2024) <doi:10.1214/24-AOAS1876>; Xiao, Liu, and Hao
(2018) <doi:10.1109/TNNLS.2017.2766164>; Muandet et al. (2012)
<https://proceedings.neurips.cc/paper/2012/file/9bf31c7ff062936a96d3c8bd1f8f2ff3-Paper.pdf>;
Chu and Keerthi (2007) <doi:10.1162/neco.2007.19.3.792>; and Andrews
et al. (2003)
<https://papers.nips.cc/paper/2232-support-vector-machines-for-multiple-instance-learning.pdf>.
Many functions use the 'Gurobi' optimization back-end to improve the
optimization problem speed; the ' [...truncated...]
Author: Sean Kent [aut, cre] ,
Yifei Liou [aut]
Maintainer: Sean Kent <skent259@gmail.com>
Diff between mildsvm versions 0.4.0 dated 2022-07-14 and 0.4.1 dated 2025-08-19
DESCRIPTION | 12 MD5 | 56 ++-- NEWS.md | 7 R/mi_df.R | 2 R/summarize_samples.R | 8 R/utils-model.R | 2 README.md | 15 - build/partial.rdb |binary man/build_fm.Rd | 6 man/cv_misvm.Rd | 8 man/formatting.Rd | 2 man/kfm_nystrom.Rd | 6 man/kme.Rd | 6 man/mildsvm-package.Rd | 2 man/mior.Rd | 14 - man/mismm.Rd | 8 man/misvm.Rd | 10 man/misvm_orova.Rd | 8 man/omisvm.Rd | 13 man/smm.Rd | 8 man/summarize_samples.Rd | 6 man/svor_exc.Rd | 12 tests/testthat/_snaps/examples.md | 521 ++------------------------------------ tests/testthat/_snaps/mi_df.md | 2 tests/testthat/_snaps/mild_df.md | 2 tests/testthat/_snaps/smm.md | 12 tests/testthat/_snaps/svor_exc.md | 14 - tests/testthat/test-examples.R | 4 tests/testthat/test-smm.R | 6 29 files changed, 155 insertions(+), 617 deletions(-)
Title: Forced Choice in Item Response Theory
Description: Bayesian estimation of forced choice models in Item Response Theory using 'rstan' (See Stan Development Team (2020) <https://mc-stan.org/>).
Author: Naidan Tu [aut, cre] ,
Seang-Hwane Joo [aut] ,
Philseok Lee [aut] ,
Stephen Stark [aut]
Maintainer: Naidan Tu <naidantu1031@gmail.com>
Diff between fcirt versions 0.1.0 dated 2022-02-01 and 0.2.1 dated 2025-08-19
fcirt-0.1.0/fcirt/inst/doc/my-vignette.html |only fcirt-0.2.1/fcirt/DESCRIPTION | 22 fcirt-0.2.1/fcirt/MD5 | 51 - fcirt-0.2.1/fcirt/NAMESPACE | 2 fcirt-0.2.1/fcirt/NEWS.md |only fcirt-0.2.1/fcirt/R/fcirt-package.R | 5 fcirt-0.2.1/fcirt/R/fcirt.R | 66 +- fcirt-0.2.1/fcirt/R/methods_bayesplot.R | 19 fcirt-0.2.1/fcirt/R/methods_extract.R | 21 fcirt-0.2.1/fcirt/R/methods_information.R | 19 fcirt-0.2.1/fcirt/R/stanmodels.R | 2 fcirt-0.2.1/fcirt/README.md | 87 +- fcirt-0.2.1/fcirt/build/vignette.rds |binary fcirt-0.2.1/fcirt/inst/doc/my-vignette.R | 14 fcirt-0.2.1/fcirt/inst/doc/my-vignette.Rmd | 46 - fcirt-0.2.1/fcirt/inst/doc/my-vignette.pdf |only fcirt-0.2.1/fcirt/inst/stan/muppnocov.stan | 161 ++--- fcirt-0.2.1/fcirt/man/bayesplot.Rd | 19 fcirt-0.2.1/fcirt/man/extract.Rd | 19 fcirt-0.2.1/fcirt/man/fcirt-package.Rd | 20 fcirt-0.2.1/fcirt/man/fcirt.Rd | 19 fcirt-0.2.1/fcirt/man/figures/README-example-1.png |binary fcirt-0.2.1/fcirt/man/figures/README-example-2.png |binary fcirt-0.2.1/fcirt/man/information.Rd | 19 fcirt-0.2.1/fcirt/src/Makevars | 5 fcirt-0.2.1/fcirt/src/stanExports_muppnocov.cc | 2 fcirt-0.2.1/fcirt/src/stanExports_muppnocov.h | 645 ++++++++++++++------- fcirt-0.2.1/fcirt/vignettes/my-vignette.Rmd | 46 - 28 files changed, 828 insertions(+), 481 deletions(-)
Title: Estimation of Extreme Conditional Quantiles and Probabilities
Description: Extreme value theory, nonparametric kernel estimation, tail
conditional probabilities, extreme conditional quantile, adaptive estimation,
quantile regression, survival probabilities.
Author: Gilles Durrieu [aut],
Ion Grama [aut],
Kevin Jaunatre [aut, cre],
Quang-Khoai Pham [aut],
Jean-Marie Tricot [aut]
Maintainer: Kevin Jaunatre <kevin.jaunatre@hotmail.fr>
Diff between extremefit versions 1.0.3 dated 2025-04-10 and 1.1.0 dated 2025-08-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/PackageOxygen.R | 31 ++++++++++++++++++++----------- inst/doc/extremefit.pdf |binary 4 files changed, 27 insertions(+), 18 deletions(-)
Title: Reinforcement Learning Tools for Two-Alternative Forced Choice
Tasks
Description: Tools for building Rescorla-Wagner Models for Two-Alternative
Forced Choice tasks, commonly employed in psychological research.
Most concepts and ideas within this R package are referenced from
Sutton and Barto (2018) <ISBN:9780262039246>.
The package allows for the intuitive definition of RL models using simple
if-else statements and three basic models built into this R package are
referenced from
Niv et al. (2012)<doi:10.1523/JNEUROSCI.5498-10.2012>.
Our approach to constructing and evaluating these computational models
is informed by the guidelines proposed in
Wilson & Collins (2019) <doi:10.7554/eLife.49547>.
Example datasets included with the package are sourced from the work of
Mason et al. (2024) <doi:10.3758/s13423-023-02415-x>.
Author: YuKi [aut, cre]
Maintainer: YuKi <hmz1969a@gmail.com>
Diff between binaryRL versions 0.9.0 dated 2025-07-08 and 0.9.7 dated 2025-08-19
binaryRL-0.9.0/binaryRL/data/Mason_2024_Exp1.rda |only binaryRL-0.9.0/binaryRL/data/Mason_2024_Exp2.rda |only binaryRL-0.9.0/binaryRL/man/Mason_2024_Exp1.Rd |only binaryRL-0.9.0/binaryRL/man/Mason_2024_Exp2.Rd |only binaryRL-0.9.7/binaryRL/DESCRIPTION | 34 binaryRL-0.9.7/binaryRL/MD5 | 105 +- binaryRL-0.9.7/binaryRL/NAMESPACE | 5 binaryRL-0.9.7/binaryRL/R/1_unique_choice.R | 37 binaryRL-0.9.7/binaryRL/R/2_arrange_data.R | 20 binaryRL-0.9.7/binaryRL/R/3_add_NA.R | 36 binaryRL-0.9.7/binaryRL/R/4_set_initial_value.R | 22 binaryRL-0.9.7/binaryRL/R/5_decision_making.R | 325 ++----- binaryRL-0.9.7/binaryRL/R/6_model_fit.R | 135 +-- binaryRL-0.9.7/binaryRL/R/7_digits.R | 22 binaryRL-0.9.7/binaryRL/R/8_output.R | 155 +-- binaryRL-0.9.7/binaryRL/R/9_mode.R | 40 binaryRL-0.9.7/binaryRL/R/RcppExports.R |only binaryRL-0.9.7/binaryRL/R/binaryRL-package.R | 34 binaryRL-0.9.7/binaryRL/R/func_epsilon.R | 24 binaryRL-0.9.7/binaryRL/R/func_eta.R | 22 binaryRL-0.9.7/binaryRL/R/func_gamma.R | 9 binaryRL-0.9.7/binaryRL/R/func_logl.R |only binaryRL-0.9.7/binaryRL/R/func_pi.R | 72 + binaryRL-0.9.7/binaryRL/R/func_tau.R | 187 +++- binaryRL-0.9.7/binaryRL/R/model_RSTD.R | 29 binaryRL-0.9.7/binaryRL/R/model_TD.R | 27 binaryRL-0.9.7/binaryRL/R/model_Utility.R | 29 binaryRL-0.9.7/binaryRL/R/process_optimize_para.R | 212 ++++- binaryRL-0.9.7/binaryRL/R/process_recovery_data.R | 268 +++--- binaryRL-0.9.7/binaryRL/R/process_simulate_list.R | 51 - binaryRL-0.9.7/binaryRL/R/step1_run_m.R | 502 ++++++++---- binaryRL-0.9.7/binaryRL/R/step2_rcv_d.R | 281 ++++-- binaryRL-0.9.7/binaryRL/R/step3_fit_p.R | 659 ++++++++++++---- binaryRL-0.9.7/binaryRL/R/step4_rpl_e.R | 85 +- binaryRL-0.9.7/binaryRL/R/summary.binaryRL.R | 152 ++- binaryRL-0.9.7/binaryRL/R/tool_sign_numbers.R |only binaryRL-0.9.7/binaryRL/R/tool_update_priors.R |only binaryRL-0.9.7/binaryRL/R/zzz.R | 3 binaryRL-0.9.7/binaryRL/data/Mason_2024_G1.rda |only binaryRL-0.9.7/binaryRL/data/Mason_2024_G2.rda |only binaryRL-0.9.7/binaryRL/man/Mason_2024_G1.Rd |only binaryRL-0.9.7/binaryRL/man/Mason_2024_G2.Rd |only binaryRL-0.9.7/binaryRL/man/RSTD.Rd | 19 binaryRL-0.9.7/binaryRL/man/TD.Rd | 19 binaryRL-0.9.7/binaryRL/man/Utility.Rd | 20 binaryRL-0.9.7/binaryRL/man/binaryRL-package.Rd | 36 binaryRL-0.9.7/binaryRL/man/fit_p.Rd | 363 +++++++- binaryRL-0.9.7/binaryRL/man/func_epsilon.Rd | 393 ++++----- binaryRL-0.9.7/binaryRL/man/func_eta.Rd | 334 ++++---- binaryRL-0.9.7/binaryRL/man/func_gamma.Rd | 325 +++---- binaryRL-0.9.7/binaryRL/man/func_logl.Rd |only binaryRL-0.9.7/binaryRL/man/func_pi.Rd | 50 - binaryRL-0.9.7/binaryRL/man/func_tau.Rd | 370 +++++--- binaryRL-0.9.7/binaryRL/man/optimize_para.Rd | 166 +++- binaryRL-0.9.7/binaryRL/man/rcv_d.Rd | 271 ++++-- binaryRL-0.9.7/binaryRL/man/recovery_data.Rd | 97 +- binaryRL-0.9.7/binaryRL/man/rpl_e.Rd | 71 + binaryRL-0.9.7/binaryRL/man/run_m.Rd | 905 ++++++++++++---------- binaryRL-0.9.7/binaryRL/man/simulate_list.Rd | 31 binaryRL-0.9.7/binaryRL/src |only 60 files changed, 4263 insertions(+), 2789 deletions(-)
Title: Auto-GO: Reproducible, Robust and High Quality Ontology
Enrichment Visualizations
Description: Auto-GO is a framework that enables automated, high quality Gene Ontology enrichment analysis visualizations. It also features a handy wrapper for Differential Expression analysis around the 'DESeq2' package described in Love et al. (2014) <doi:10.1186/s13059-014-0550-8>. The whole framework is structured in different, independent functions, in order to let the user decide which steps of the analysis to perform and which plot to produce.
Author: Isabella Grassucci [aut] ,
Eleonora Sperandio [aut] ,
Fabio Ticconi [cre] ,
Alice Massacci [aut] ,
Lorenzo D'Ambrosio [aut] ,
Matteo Pallocca [aut]
Maintainer: Fabio Ticconi <fabio.ticconi@gmail.com>
This is a re-admission after prior archival of version 1.0.1 dated 2025-02-27
Diff between autoGO versions 1.0.1 dated 2025-02-27 and 1.0.3 dated 2025-08-19
DESCRIPTION | 24 ++++++++++++++---------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 1 - R/autoGO-package.R | 1 - R/sysdata.rda |binary build/partial.rdb |binary build/vignette.rds |binary inst/doc/autoGO-tutorial.html | 12 ++++++------ vignettes/imgs/barplot.png |binary vignettes/imgs/distrib_C1.png |binary vignettes/imgs/distrib_H.png |binary vignettes/imgs/heatmap.png |binary vignettes/imgs/lolligo.png |binary vignettes/imgs/volcano.png |binary vignettes/imgs/volcanoplot_highlighted.png |binary 15 files changed, 34 insertions(+), 32 deletions(-)
Title: Bootstrap Confidence Interval Estimation for 'ETAS' Model
Parameters
Description: The 2-D spatial and temporal Epidemic Type Aftershock Sequence ('ETAS') Model is
widely used to 'decluster' earthquake data catalogs. Usually, the calculation of standard
errors of the 'ETAS' model parameter estimates is based on the Hessian matrix derived from
the log-likelihood function of the fitted model. However, when an 'ETAS' model is fitted to
a local data set over a time period that is limited or short, the standard errors based on
the Hessian matrix may be inaccurate. It follows that the asymptotic confidence intervals
for parameters may not always be reliable. As an alternative, this package allows for the
construction of bootstrap confidence intervals based on empirical quantiles for the parameters
of the 2-D spatial and temporal 'ETAS' model. This version improves on Version 0.1.0 of the
package by enabling the study space window (renamed 'study region') to be polygonal rather
than merely rectangular. A Japan earthquake data catalog is used in a second example to
illustrat [...truncated...]
Author: Renjie Peng [aut, cre],
Pierre Dutilleul [aut] ,
Christian Genest [aut]
Maintainer: Renjie Peng <renjie.peng@mail.mcgill.ca>
Diff between ETASbootstrap versions 0.2.0 dated 2024-06-09 and 0.2.1 dated 2025-08-19
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/simulate_background_earthquakes.R | 2 +- man/simulate_background_earthquakes.Rd | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully
configurable HTTP/FTP requests where responses can be processed in memory, on
disk, or streaming via the callback or connection interfaces. Some knowledge
of 'libcurl' is recommended; for a more-user-friendly web client see the
'httr2' package which builds on this package with http specific tools and logic.
Author: Jeroen Ooms [aut, cre] ,
Hadley Wickham [ctb],
Posit Software, PBC [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between curl versions 6.4.0 dated 2025-06-22 and 7.0.0 dated 2025-08-19
curl-6.4.0/curl/src/typelist.h |only curl-6.4.0/curl/tools/ada.tar.gz |only curl-6.4.0/curl/tools/typelist.R |only curl-6.4.0/curl/tools/typelist.h.in |only curl-7.0.0/curl/DESCRIPTION | 8 +- curl-7.0.0/curl/MD5 | 54 +++++++------- curl-7.0.0/curl/NAMESPACE | 1 curl-7.0.0/curl/NEWS | 9 ++ curl-7.0.0/curl/R/nslookup.R | 4 + curl-7.0.0/curl/R/onload.R | 4 - curl-7.0.0/curl/R/options.R | 51 ++++--------- curl-7.0.0/curl/R/parser.R | 35 +-------- curl-7.0.0/curl/build/vignette.rds |binary curl-7.0.0/curl/cleanup | 1 curl-7.0.0/curl/configure | 39 ++++------ curl-7.0.0/curl/inst/doc/intro.html | 100 +++++++++++++-------------- curl-7.0.0/curl/man/curl_options.Rd | 3 curl-7.0.0/curl/man/curl_parse_url.Rd | 16 ++-- curl-7.0.0/curl/src/curl-common.h | 27 ------- curl-7.0.0/curl/src/handle.c | 53 ++------------ curl-7.0.0/curl/src/init.c | 4 - curl-7.0.0/curl/src/macos-polyfill.h | 3 curl-7.0.0/curl/src/multi.c | 2 curl-7.0.0/curl/src/options.c | 4 - curl-7.0.0/curl/src/typechecking.c | 28 ------- curl-7.0.0/curl/src/urlparser.c | 83 ++-------------------- curl-7.0.0/curl/src/version.c | 8 -- curl-7.0.0/curl/tests/spelling.Rout.save |only curl-7.0.0/curl/tests/testthat/test-auth.R | 9 ++ curl-7.0.0/curl/tests/testthat/test-parser.R | 8 +- curl-7.0.0/curl/tools/version.c |only 31 files changed, 191 insertions(+), 363 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.11.0 dated 2025-07-29 and 0.13.0 dated 2025-08-19
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Title: Data Model for 'teal' Applications
Description: Provides a 'teal_data' class as a unified data model for
'teal' applications focusing on reproducibility and relational data.
Author: Dawid Kaledkowski [aut, cre] ,
Aleksander Chlebowski [aut] ,
Marcin Kosinski [aut],
Andre Verissimo [aut] ,
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Junlue Zhao [aut],
Chendi Liao [re [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.data versions 0.7.0 dated 2025-01-28 and 0.8.0 dated 2025-08-19
teal.data-0.7.0/teal.data/R/testhat-helpers.R |only teal.data-0.7.0/teal.data/man/all.equal.join_keys.Rd |only teal.data-0.7.0/teal.data/man/rADAE.Rd |only teal.data-0.7.0/teal.data/man/rADCM.Rd |only teal.data-0.7.0/teal.data/man/rADEX.Rd |only teal.data-0.7.0/teal.data/man/rADLB.Rd |only teal.data-0.7.0/teal.data/man/rADRS.Rd |only teal.data-0.7.0/teal.data/man/rADSL.Rd |only teal.data-0.7.0/teal.data/man/rADTR.Rd |only teal.data-0.7.0/teal.data/man/rADTTE.Rd |only teal.data-0.7.0/teal.data/man/rADVS.Rd |only teal.data-0.7.0/teal.data/tests/testthat/helper-all.equal.R |only teal.data-0.8.0/teal.data/DESCRIPTION | 31 +- teal.data-0.8.0/teal.data/MD5 | 63 +--- teal.data-0.8.0/teal.data/NEWS.md | 10 teal.data-0.8.0/teal.data/R/cdisc_data.R | 1 teal.data-0.8.0/teal.data/R/data.R | 140 +++++----- teal.data-0.8.0/teal.data/R/dummy_function.R | 5 teal.data-0.8.0/teal.data/R/join_key.R | 1 teal.data-0.8.0/teal.data/R/join_keys-utils.R | 3 teal.data-0.8.0/teal.data/R/join_keys.R | 3 teal.data-0.8.0/teal.data/R/teal_data-class.R | 25 - teal.data-0.8.0/teal.data/R/teal_data-constructor.R | 4 teal.data-0.8.0/teal.data/R/teal_data-show.R | 4 teal.data-0.8.0/teal.data/R/topological_sort.R | 2 teal.data-0.8.0/teal.data/build/vignette.rds |binary teal.data-0.8.0/teal.data/inst/WORDLIST | 5 teal.data-0.8.0/teal.data/inst/doc/teal-data-reproducibility.html | 20 - teal.data-0.8.0/teal.data/inst/doc/teal-data.html | 4 teal.data-0.8.0/teal.data/man/cdisc_data.Rd | 2 teal.data-0.8.0/teal.data/man/default_cdisc_join_keys.Rd | 11 teal.data-0.8.0/teal.data/man/example_cdisc_data.Rd | 5 teal.data-0.8.0/teal.data/man/join_key.Rd | 2 teal.data-0.8.0/teal.data/man/join_keys.Rd | 6 teal.data-0.8.0/teal.data/man/random_cdisc_data.Rd |only teal.data-0.8.0/teal.data/man/teal_data.Rd | 4 teal.data-0.8.0/teal.data/tests/testthat/test-join_keys-c.R | 5 teal.data-0.8.0/teal.data/tests/testthat/test-join_keys-extract.R | 25 + teal.data-0.8.0/teal.data/tests/testthat/test-join_keys.R | 40 +- 39 files changed, 220 insertions(+), 201 deletions(-)
Title: Database Preferences and Skyline Computation
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator (see Börzsönyi, et al.
(2001) <doi:10.1109/ICDE.2001.914855>), and some generalizations
known as database preferences (see Kießling (2002)
<doi:10.1016/B978-155860869-6/50035-4>).
Author: Patrick Roocks [aut, cre]
Maintainer: Patrick Roocks <mail@p-roocks.de>
Diff between rPref versions 1.4.0 dated 2023-01-30 and 1.5.0 dated 2025-08-19
DESCRIPTION | 24 +- MD5 | 74 +++---- NEWS | 8 R/base-pref-macros.r | 50 ++-- R/base-pref.r | 108 +++++----- R/complex-pref.r | 217 +++++++++++---------- R/general-pref.r | 70 +++--- R/pred-succ.r | 147 +++++++------- R/pref-eval.r | 446 ++++++++++++++++++++++++++------------------ R/rPref.r | 5 R/show-pref.r | 223 +++++++++++----------- R/visualize.r | 425 ++++++++++++++++++++--------------------- build/vignette.rds |binary inst/CITATION | 10 inst/doc/introduction.R | 26 +- inst/doc/introduction.Rmd | 10 inst/doc/introduction.html | 64 +++--- inst/doc/visualization.R | 16 - inst/doc/visualization.html | 72 +++---- inst/test/test-algorithms.r | 48 ++-- inst/test/test-psel.r | 120 +++++------ man/base_pref.Rd | 44 ++-- man/base_pref_macros.Rd | 24 +- man/complex_pref.Rd | 50 ++-- man/general_pref.Rd | 14 - man/get_hasse_diag.Rd | 4 man/plot_btg.Rd | 72 +++---- man/plot_front.Rd | 15 - man/pred_succ.Rd | 34 +-- man/psel.Rd | 141 ++++++++----- man/rPref.Rd | 10 man/show.pref.Rd | 18 - man/show.query.Rd | 25 +- src/Makevars | 1 src/Makevars.win | 2 src/psel-par-top.cpp | 244 ++++++++++++------------ src/scalagon.cpp | 2 vignettes/introduction.Rmd | 10 38 files changed, 1530 insertions(+), 1343 deletions(-)
Title: Retrieval-Augmented Generation (RAG) Workflows
Description: Provides tools for implementing Retrieval-Augmented
Generation (RAG) workflows with Large Language Models (LLM). Includes
functions for document processing, text chunking, embedding
generation, storage management, and content retrieval. Supports
various document types and embedding providers ('Ollama', 'OpenAI'),
with 'DuckDB' as the default storage backend. Integrates with the
'ellmer' package to equip chat objects with retrieval capabilities.
Designed to offer both sensible defaults and customization options
with transparent access to intermediate outputs. For a review of
retrieval-augmented generation methods, see Gao et al. (2023)
"Retrieval-Augmented Generation for Large Language Models: A Survey"
<doi:10.48550/arXiv.2312.10997>.
Author: Tomasz Kalinowski [aut, cre],
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between ragnar versions 0.2.0 dated 2025-07-12 and 0.2.1 dated 2025-08-19
ragnar-0.2.0/ragnar/man/ragnar_store_update.Rd |only ragnar-0.2.0/ragnar/man/reexports.Rd |only ragnar-0.2.0/ragnar/tools/configure_reticulate.R |only ragnar-0.2.1/ragnar/DESCRIPTION | 18 +- ragnar-0.2.1/ragnar/MD5 | 80 ++++++------- ragnar-0.2.1/ragnar/NAMESPACE | 7 - ragnar-0.2.1/ragnar/NEWS.md | 34 +++++ ragnar-0.2.1/ragnar/R/aaa-utils.R | 41 ++++++ ragnar-0.2.1/ragnar/R/ellmer.R | 47 ++++--- ragnar-0.2.1/ragnar/R/embed-gemini.R |only ragnar-0.2.1/ragnar/R/embed.R | 22 +++ ragnar-0.2.1/ragnar/R/legacy.R | 2 ragnar-0.2.1/ragnar/R/markdown-document.R | 2 ragnar-0.2.1/ragnar/R/markdown-segment.R | 4 ragnar-0.2.1/ragnar/R/ragnar-package.R | 4 ragnar-0.2.1/ragnar/R/read-html.R | 50 +++++++- ragnar-0.2.1/ragnar/R/read-markdown.R | 8 - ragnar-0.2.1/ragnar/R/retrieve.R | 24 ++- ragnar-0.2.1/ragnar/R/store-v1.R | 8 - ragnar-0.2.1/ragnar/R/store-v2.R | 21 ++- ragnar-0.2.1/ragnar/R/store.R | 40 +++--- ragnar-0.2.1/ragnar/README.md | 62 +++++----- ragnar-0.2.1/ragnar/configure | 2 ragnar-0.2.1/ragnar/configure.win | 2 ragnar-0.2.1/ragnar/inst/python/_ragnartools/markitdown.py | 9 + ragnar-0.2.1/ragnar/inst/store-inspector/modules.R | 30 ++++ ragnar-0.2.1/ragnar/man/MarkdownDocumentChunks.Rd | 2 ragnar-0.2.1/ragnar/man/embed_google_vertex.Rd | 36 +++++ ragnar-0.2.1/ragnar/man/embed_ollama.Rd | 16 ++ ragnar-0.2.1/ragnar/man/ragnar_find_links.Rd | 7 - ragnar-0.2.1/ragnar/man/ragnar_register_tool_retrieve.Rd | 2 ragnar-0.2.1/ragnar/man/ragnar_retrieve.Rd | 2 ragnar-0.2.1/ragnar/man/ragnar_retrieve_vss.Rd | 2 ragnar-0.2.1/ragnar/man/ragnar_retrieve_vss_and_bm25.Rd | 2 ragnar-0.2.1/ragnar/man/ragnar_store_create.Rd | 2 ragnar-0.2.1/ragnar/man/ragnar_store_insert.Rd | 29 +++- ragnar-0.2.1/ragnar/man/read_as_markdown.Rd | 8 - ragnar-0.2.1/ragnar/tests/testthat/_snaps/store.md | 12 + ragnar-0.2.1/ragnar/tests/testthat/helper-doc.R | 7 + ragnar-0.2.1/ragnar/tests/testthat/test-embed-gemini.R |only ragnar-0.2.1/ragnar/tests/testthat/test-extra-cols.R | 5 ragnar-0.2.1/ragnar/tests/testthat/test-retrieve.R | 45 +++++++ ragnar-0.2.1/ragnar/tests/testthat/test-store.R | 26 +++- ragnar-0.2.1/ragnar/tools/configure_deps.R |only 44 files changed, 527 insertions(+), 193 deletions(-)
Title: Diversity-Interactions (DI) Models
Description: The 'DImodels' package is suitable for analysing data from biodiversity and ecosystem function studies using the Diversity-Interactions (DI) modelling approach introduced by Kirwan et al. (2009) <doi:10.1890/08-1684.1>. Suitable data will contain proportions for each species and a community-level response variable, and may also include additional factors, such as blocks or treatments. The package can perform data manipulation tasks, such as computing pairwise interactions (the DI_data() function), can perform an automated model selection process (the autoDI() function) and has the flexibility to fit a wide range of user-defined DI models (the DI() function).
Author: Rafael de Andrade Moral [aut, cre],
John Connolly [aut],
Rishabh Vishwakarma [ctb],
Caroline Brophy [aut]
Maintainer: Rafael de Andrade Moral <rafael.deandrademoral@mu.ie>
Diff between DImodels versions 1.3.2 dated 2024-02-28 and 1.3.3 dated 2025-08-19
DESCRIPTION | 14 MD5 | 42 NAMESPACE | 6 R/DI.R | 5 R/autoDI.R | 11 R/autoDI_internal.R | 92 R/postfit_comparisons.R |only R/predictDI.R | 156 - README.md | 335 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/DImodels.R | 360 +-- inst/doc/DImodels.Rmd | 119 - inst/doc/DImodels.html | 3023 +++++++++++++++-------------- man/compare_communities.Rd |only man/contrasts_DI.Rd | 137 - man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-2.png |binary tests/testthat/test-DI.R | 8 tests/testthat/test-autoDI.R | 5 tests/testthat/test-post_fit_comparisons.R |only tests/testthat/test-predictDI.R | 118 - vignettes/DImodels.Rmd | 119 - 24 files changed, 2431 insertions(+), 2119 deletions(-)
Title: Robust Multi-Model Subset Selection
Description: Efficient algorithms for generating ensembles of robust, sparse and diverse models via robust
multi-model subset selection (RMSS). The robust ensembles are generated by minimizing the sum of
the least trimmed square loss of the models in the ensembles under constraints for the size of
the models and the sharing of the predictors. Tuning parameters for the robustness, sparsity and
diversity of the robust ensemble are selected by cross-validation.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RMSS versions 1.2.0 dated 2025-07-17 and 1.2.1 dated 2025-08-19
DESCRIPTION | 10 +-- MD5 | 14 ++--- NEWS | 6 +- R/cv.RMSS.R | 5 + man/cv.RMSS.Rd | 3 - src/EnsembleModel.cpp | 139 ++++++++++++++++++++++++++++++++++++++++++++++++-- src/EnsembleModel.hpp | 5 + src/RInterfaceCV.cpp | 13 +++- 8 files changed, 169 insertions(+), 26 deletions(-)
Title: Tools for Plant Image Analysis
Description: Tools for both single and batch image manipulation and
analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and
phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>).
The tools can be used for the quantification of leaf area, object
counting, extraction of image indexes, shape measurement, object
landmark identification, and Elliptical Fourier Analysis of object
outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package
also provides a comprehensive pipeline for generating shapefiles with
complex layouts and supports high-throughput phenotyping of RGB,
multispectral, and hyperspectral orthomosaics. This functionality
facilitates field phenotyping using UAV- or satellite-based imagery.
Author: Tiago Olivoto [aut, cre]
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between pliman versions 3.0.0 dated 2024-11-06 and 3.1.0 dated 2025-08-19
DESCRIPTION | 17 MD5 | 151 +- NAMESPACE | 28 NEWS.md | 22 R/RcppExports.R | 36 R/analyze_objects.R | 526 ++++++-- R/analyze_objects_minimal.R | 287 +++- R/apply_fun_to_imgs.R | 134 +- R/measure_disease.R | 200 ++- R/measure_disease_byl.R | 162 +- R/measure_injury.R | 199 +-- R/sad.R | 4 R/utilities.R | 478 +++++-- R/utils_efourier.R | 37 R/utils_file.R | 23 R/utils_imagem.R | 2673 ++++++++++++++++++++++++++++------------- R/utils_indexes.R | 27 R/utils_landmarks.R | 19 R/utils_mapedit.R | 32 R/utils_mask.R | 6 R/utils_measures.R | 121 + R/utils_mosaic.R | 1540 +++++++++++++++++++---- R/utils_objects.R | 703 +++++++--- R/utils_pick.R | 152 ++ R/utils_polygon.R | 16 R/utils_shapefile.R | 365 ++++- R/utils_shp.R | 637 ++++++--- R/zzz.R | 45 build/partial.rdb |binary inst/indexes.csv | 12 inst/tmp_images/shp1.rds |only inst/tmp_images/shp2.rds |only man/analyze_objects.Rd | 18 man/ccc.Rd |only man/efourier.Rd | 2 man/efourier_norm.Rd | 2 man/efourier_shape.Rd | 2 man/entropy.Rd |only man/get_uuid.Rd |only man/image_align.Rd | 2 man/image_augment.Rd | 7 man/image_binary.Rd | 302 ++-- man/image_canny_edge.Rd |only man/image_contour_line.Rd |only man/image_label.Rd |only man/image_line_segment.Rd |only man/image_thinning_guo_hall.Rd | 1 man/line_on_halfplot.Rd |only man/measure_disease.Rd | 8 man/mosaic_analyze.Rd | 2 man/mosaic_analyze_iter.Rd | 13 man/mosaic_chm.Rd | 7 man/mosaic_chm_extract.Rd | 46 man/mosaic_classify.Rd |only man/mosaic_clip.Rd |only man/mosaic_crop.Rd | 98 - man/mosaic_index.Rd | 13 man/mosaic_input.Rd | 2 man/mosaic_interpolate.Rd | 2 man/mosaic_rotate.Rd |only man/mosaic_vectorize.Rd | 6 man/object_bbox.Rd |only man/object_export.Rd | 5 man/object_export_shp.Rd | 7 man/object_to_color.Rd | 19 man/plot_bbox.Rd |only man/plot_line_segment.Rd |only man/shapefile_build.Rd | 8 man/shapefile_measures.Rd | 7 man/shapefile_operations.Rd |only man/utils_indexes.Rd | 4 man/utils_objects.Rd | 21 man/utils_pick.Rd | 11 man/utils_transform.Rd | 23 man/uuid.Rd |only src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 136 ++ src/adsf.c |only src/adsf.h |only src/canny.h |only src/code.cpp | 281 ++++ src/code_polygons.cpp | 38 src/line_segment_detector.cpp |only src/lsd.c |only src/lsd.h |only src/object_contours.cpp |only src/rcpp_canny.cpp |only src/smooth_contours.c |only src/smooth_contours.h |only src/tools.c |only 91 files changed, 7159 insertions(+), 2590 deletions(-)
Title: MAle Lineage ANalysis
Description: MAle Lineage ANalysis by simulating
genealogies backwards and imposing short tandem repeats (STR) mutations forwards.
Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses.
Numerous analyses are possible, e.g. number of matches and meiotic distance to matches.
Refer to papers mentioned in citation("malan") (DOI's:
<doi:10.1371/journal.pgen.1007028>,
<doi:10.21105/joss.00684> and
<doi:10.1016/j.fsigen.2018.10.004>).
Author: Mikkel Meyer Andersen [aut, cre]
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between malan versions 1.0.3 dated 2023-11-28 and 1.0.4 dated 2025-08-19
DESCRIPTION | 9 ++++--- MD5 | 24 +++++++++---------- NEWS | 4 +++ R/print.R | 6 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/case-study-partial.R | 4 +-- inst/doc/case-study-partial.html | 40 ++++++++++++++++++--------------- inst/doc/introduction.R | 4 +-- inst/doc/introduction.html | 34 ++++++++++++++-------------- man/as_tbl_graph.malan_pedigreelist.Rd | 4 +-- man/get_nodes_edges.Rd | 2 - man/malan-package.Rd | 1 13 files changed, 71 insertions(+), 61 deletions(-)
Title: Pre- And Post-Processing in Bayesian Evolutionary Analyses
Description: Functions are provided for prior specification in divergence time
estimation using fossils as well as other kinds of data. It
provides tools for interacting with the input and output of Bayesian
platforms in evolutionary biology such as 'BEAST2', 'MrBayes', 'RevBayes',
or 'MCMCTree'.
It Implements a simple measure similarity between probability
density functions for comparing prior and
posterior Bayesian densities, as well as code for calculating the
combination of distributions using conflation of Hill (2008). Functions for estimating the
origination time in collections of distributions using the x-intercept (e.g., Draper and Smith, 1998) and
stratigraphic intervals (Marshall 2010) are also available.
Hill, T. 2008. "Conflations of probability distributions". Transactions of the American Mathematical Society, 363:3351-3372. <doi:10.48550/arXiv.0808.1808>,
Draper, N. R. and Smith, H. 1998. "Applied Regression Analysis". 1--706. Wiley Interscience, New York. <DOI:10.1002/978111 [...truncated...]
Author: Gustavo A. Ballen [aut, cre],
Sandra Reinales [aut]
Maintainer: Gustavo A. Ballen <gustavo.a.ballen@gmail.com>
Diff between tbea versions 1.6.1 dated 2025-04-10 and 1.7.0 dated 2025-08-19
DESCRIPTION | 13 +-- MD5 | 64 +++++++++++++--- R/crossplot.R | 116 +++++++++++++++++++----------- R/data.R | 43 +++++++++++ README.md | 18 ++-- build/partial.rdb |binary build/vignette.rds |binary data/cynodontidae.posterior.rda |only data/cynodontidae.prior.rda |only inst/doc/concatenation.R |only inst/doc/concatenation.Rmd |only inst/doc/concatenation.html |only inst/doc/conflation.R |only inst/doc/conflation.Rmd |only inst/doc/conflation.html |only inst/doc/intro.Rmd | 2 inst/doc/intro.html | 8 +- inst/doc/l_calibration_mcmctree.R |only inst/doc/l_calibration_mcmctree.Rmd |only inst/doc/l_calibration_mcmctree.html |only inst/doc/node_calibration_density.R |only inst/doc/node_calibration_density.Rmd |only inst/doc/node_calibration_density.html |only inst/doc/posterior_tree_distribution.R |only inst/doc/posterior_tree_distribution.Rmd |only inst/doc/posterior_tree_distribution.html |only inst/doc/prior_posterior_comparisons.R |only inst/doc/prior_posterior_comparisons.Rmd |only inst/doc/prior_posterior_comparisons.html |only inst/doc/starting_tree.R |only inst/doc/starting_tree.Rmd |only inst/doc/starting_tree.html |only inst/doc/stratigraphic_intervals.R |only inst/doc/stratigraphic_intervals.Rmd |only inst/doc/stratigraphic_intervals.html |only inst/doc/whyInitVals.html | 20 ++--- inst/doc/x_intercept.R |only inst/doc/x_intercept.Rmd |only inst/doc/x_intercept.html |only man/crossplot.Rd | 46 +++++++++-- man/cynodontidae.posterior.Rd |only man/cynodontidae.prior.Rd |only man/tbea-package.Rd | 1 vignettes/concatenation.Rmd |only vignettes/conflation.Rmd |only vignettes/intro.Rmd | 2 vignettes/l_calibration_mcmctree.Rmd |only vignettes/node_calibration_density.Rmd |only vignettes/posterior_tree_distribution.Rmd |only vignettes/prior_posterior_comparisons.Rmd |only vignettes/starting_tree.Rmd |only vignettes/stratigraphic_intervals.Rmd |only vignettes/x_intercept.Rmd |only 53 files changed, 243 insertions(+), 90 deletions(-)
Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management
system developed by the New Zealand Institute of Language, Brain
and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>.
This package defines functions for accessing corpus data in a 'LaBB-CAT'
instance. You must have at least version 20230818.1400 of 'LaBB-CAT'
to use this package.
For more information about 'LaBB-CAT', see
Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142>
or
Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>
Diff between nzilbb.labbcat versions 1.4-0 dated 2025-05-22 and 1.5-0 dated 2025-08-19
nzilbb.labbcat-1.4-0/nzilbb.labbcat/R/expressionFromAttributeValuePattern.R |only nzilbb.labbcat-1.4-0/nzilbb.labbcat/R/expressionFromAttributeValueRange.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/DESCRIPTION | 11 nzilbb.labbcat-1.5-0/nzilbb.labbcat/MD5 | 98 +++-- nzilbb.labbcat-1.5-0/nzilbb.labbcat/NAMESPACE | 12 nzilbb.labbcat-1.5-0/nzilbb.labbcat/NEWS.md | 52 ++ nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/appendFromPraat.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/appendLabels.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/appendOffsets.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/fragmentAudio.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/fragmentData.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/fragmentLabels.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/fragmentTranscripts.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/generateLayer.R | 2 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/generateLayerUtterances.R | 7 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getAllUtterances.R | 10 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getDictionaries.R | 5 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getDictionaryEntries.R | 24 - nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getFragmentAnnotations.R | 24 - nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getFragments.R | 10 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getMatchAlignments.R | 72 +++ nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getMatchLabels.R | 71 +++ nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getMatches.R | 46 -- nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getParticipantAttributes.R | 16 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/getSoundFragments.R | 4 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/labbcatCredentials.R | 129 ++++-- nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/labbcatVersionInfo.R | 5 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/newTranscript.R | 2 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/nzilbb.labbcat.R | 190 +++++----- nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/processWithPraat.R | 2 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/transcriptUploadParameters.R | 2 nzilbb.labbcat-1.5-0/nzilbb.labbcat/R/updateTranscript.R | 2 nzilbb.labbcat-1.5-0/nzilbb.labbcat/build/partial.rdb |binary nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/appendFromPraat.Rd |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/appendLabels.Rd |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/appendOffsets.Rd |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/fragmentAudio.Rd |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/fragmentData.Rd |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/fragmentLabels.Rd |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/fragmentTranscripts.Rd |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/getFragments.Rd | 6 nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/getSoundFragments.Rd | 4 nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/labbcatCredentials.Rd | 11 nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/nzilbb.labbcat.Rd | 8 nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/praatScriptCentreOfGravity.Rd | 3 nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/praatScriptFastTrack.Rd | 3 nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/praatScriptFormants.Rd | 3 nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/praatScriptIntensity.Rd | 3 nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/praatScriptPitch.Rd | 3 nzilbb.labbcat-1.5-0/nzilbb.labbcat/man/processWithPraat.Rd | 3 nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-appendFromPraat.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-appendLabels.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-appendOffsets.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-fragmentAudio.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-fragmentData.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-fragmentLabels.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-fragmentTranscripts.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-getAllUtterances.R | 6 nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-getFragmentAnnotationData.R |only nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-getFragmentAnnotations.R | 6 nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-getMatchAlignments.R | 43 +- nzilbb.labbcat-1.5-0/nzilbb.labbcat/tests/testthat/test-layerDictionaryManagement.R | 8 62 files changed, 602 insertions(+), 304 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Mediation Analysis for Count and Zero-Inflated Count Data
Description: Performs causal mediation analysis for count and zero-inflated
count data without or with a post-treatment confounder; calculates power
to detect prespecified causal mediation effects, direct effects, and
total effects; performs sensitivity analysis when there is a treatment-
induced mediator-outcome confounder as described by Cheng, J., Cheng, N.F.,
Guo, Z., Gregorich, S., Ismail, A.I., Gansky, S.A. (2018)
<doi:10.1177/0962280216686131>. Implements Instrumental Variable (IV)
method to estimate the controlled (natural) direct and mediation effects,
and compute the bootstrap Confidence Intervals as described by Guo, Z.,
Small, D.S., Gansky, S.A., Cheng, J. (2018) <doi:10.1111/rssc.12233>. This
software was made possible by Grant R03DE028410 from the National
Institute of Dental and Craniofacial Research, a component of the National
Institutes of Health.
Author: Nancy Cheng [aut, cre],
Zijian Guo [aut],
Jing Cheng [aut]
Maintainer: Nancy Cheng <Nancy.Cheng@ucsf.edu>
Diff between maczic versions 1.0.0 dated 2023-09-11 and 1.1.0 dated 2025-08-19
maczic-1.0.0/maczic/build/maczic.pdf |only maczic-1.0.0/maczic/build/maczic_1.0.0.pdf |only maczic-1.1.0/maczic/DESCRIPTION | 26 ++++++++++++++++++++------ maczic-1.1.0/maczic/MD5 | 21 ++++++++++----------- maczic-1.1.0/maczic/NEWS.md | 9 +++++++-- maczic-1.1.0/maczic/R/mediate_iv.R | 2 +- maczic-1.1.0/maczic/R/mediate_zi.R | 8 ++++---- maczic-1.1.0/maczic/R/mediate_zi_vcoef.R | 2 +- maczic-1.1.0/maczic/build/maczic_1.1.0.pdf |only maczic-1.1.0/maczic/build/stage23.rdb |binary maczic-1.1.0/maczic/man/mediate_iv.Rd | 2 +- maczic-1.1.0/maczic/man/mediate_zi.Rd | 8 ++++---- maczic-1.1.0/maczic/man/mediate_zi_vcoef.Rd | 2 +- 13 files changed, 49 insertions(+), 31 deletions(-)
Title: Forest Attributes in U.S. States
Description: A small subset of plots throughout the U.S. are sampled and
assessed "on-the-ground" as forested or non-forested by the U.S.
Department of Agriculture, Forest Service, Forest Inventory and
Analysis (FIA) Program, but the FIA also has access to remotely sensed
data for all land in the country. The 'forested' package contains data
frames intended for use in predictive modeling applications where the more
easily-accessible remotely sensed data can be used to predict whether a plot
is forested or non-forested. Currently, the package provides data for
Washington and Georgia.
Author: Grayson White [aut] ,
Hannah Frick [aut] ,
Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between forested versions 0.1.0 dated 2024-07-31 and 0.2.0 dated 2025-08-19
DESCRIPTION | 51 ++++++++++++++++++++++++---------------------- LICENSE | 2 - MD5 | 18 +++++++++------- NEWS.md | 12 ++++++++++ R/forested.R | 48 +++++++++++++++++++++++++++++++++---------- README.md | 23 +++++++++----------- data/forested.rda |binary data/forested_ga.rda |only data/forested_wa.rda |only man/forested-package.Rd | 6 ++--- man/forested.Rd | 53 ++++++++++++++++++++++++++++++++++++++---------- 11 files changed, 143 insertions(+), 70 deletions(-)
Title: A Flexible Interface for 'LLM' API Interactions
Description: Provides a flexible interface for interacting with Large Language Model ('LLM')
providers including 'OpenAI', 'Groq', 'Anthropic', 'DeepSeek', 'DashScope', 'Gemini', 'Grok'
and 'GitHub Models'. Supports both synchronous and asynchronous chat-completion APIs, with
features such as retry logic, dynamic model selection, customizable parameters, and
multi-message conversation handling. Designed to streamline integration with
state-of-the-art LLM services across multiple platforms.
Author: Kwadwo Daddy Nyame Owusu Boakye [aut, cre]
Maintainer: Kwadwo Daddy Nyame Owusu Boakye <kwadwo.owusuboakye@outlook.com>
Diff between chatLLM versions 0.1.2 dated 2025-05-20 and 0.1.3 dated 2025-08-19
DESCRIPTION | 8 +-- MD5 | 11 ++-- NEWS.md |only R/chatLLM.R | 112 ++++++++++++++++++++++++++++++---------------- README.md | 6 +- man/call_llm.Rd | 4 - tests/testthat/00_setup.R | 5 ++ 7 files changed, 96 insertions(+), 50 deletions(-)
Title: Accessing Statistics Canada Data Table and Vectors
Description: Searches for, accesses, and retrieves Statistics Canada data
tables, as well as individual vectors, as tidy data frames.
This package enriches the tables with metadata, deals
with encoding issues, allows for bilingual English or French language data retrieval, and bundles
convenience functions to make it easier to work with retrieved table data. For more efficient data
access the package allows for caching data in a local database and database level filtering, data
manipulation and summarizing.
Author: Jens von Bergmann [aut, cre],
Dmitry Shkolnik [aut]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cansim versions 0.4.3 dated 2025-05-30 and 0.4.4 dated 2025-08-19
DESCRIPTION | 6 +- MD5 | 59 +++++++++++++------------ NAMESPACE | 2 NEWS.md | 7 ++ R/cansim.R | 12 ++--- R/cansim_helpers.R | 47 +++++++++---------- R/cansim_metadata.R | 26 +++++++---- R/cansim_parquet.R | 47 ++++++++++--------- R/cansim_sql.R | 12 ++--- R/cansim_tables_list.R | 4 - R/cansim_vectors.R | 10 ++-- R/user_settings.R |only README.md | 11 ++-- build/vignette.rds |binary inst/doc/cansim.R | 5 ++ inst/doc/cansim.Rmd | 10 ++++ inst/doc/cansim.html | 34 +++++++++++++- inst/doc/working_with_large_tables.Rmd | 2 inst/doc/working_with_large_tables.html | 40 +++++++++++----- man/cansim_repartition_cached_table.Rd | 4 - man/get_cansim_connection.Rd | 4 - man/get_cansim_data_for_table_coord_periods.Rd | 2 man/get_cansim_sqlite.Rd | 4 - man/get_cansim_table_template.Rd | 6 ++ man/list_cansim_cached_tables.Rd | 4 - man/list_cansim_sqlite_cached_tables.Rd | 4 - man/remove_cansim_cached_tables.Rd | 4 - man/remove_cansim_sqlite_cached_table.Rd | 4 - man/set_cansim_cache_path.Rd |only man/show_cansim_cache_path.Rd |only vignettes/cansim.Rmd | 10 ++++ vignettes/working_with_large_tables.Rmd | 2 32 files changed, 235 insertions(+), 147 deletions(-)
Title: Word Embedding Research Framework for Psychological Science
Description: An integrative toolbox of word embedding research that provides:
(1) a collection of 'pre-trained' static word vectors in the '.RData'
compressed format <https://psychbruce.github.io/WordVector_RData.pdf>;
(2) a group of functions to process, analyze, and visualize word vectors;
(3) a range of tests to examine conceptual associations, including
the Word Embedding Association Test <doi:10.1126/science.aal4230>
and the Relative Norm Distance <doi:10.1073/pnas.1720347115>,
with permutation test of significance; and
(4) a set of training methods to locally train (static) word vectors
from text corpora, including 'Word2Vec' <doi:10.48550/arXiv.1301.3781>,
'GloVe' <doi:10.3115/v1/D14-1162>, and 'FastText' <doi:10.48550/arXiv.1607.04606>.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between PsychWordVec versions 2025.3 dated 2025-03-30 and 2025.8 dated 2025-08-19
DESCRIPTION | 15 MD5 | 62 +- NAMESPACE | 1 NEWS.md | 5 R/00-utils.R | 6 R/01-basic.R | 911 +++++++++++++++----------------------------- R/02-static.R | 195 ++------- README.md | 11 build |only man/PsychWordVec-package.Rd |only man/as_embed.Rd | 20 man/cosine_similarity.Rd | 9 man/data_transform.Rd | 55 -- man/data_wordvec_load.Rd | 25 - man/data_wordvec_subset.Rd | 45 -- man/demodata.Rd | 4 man/dict_expand.Rd | 25 - man/dict_reliability.Rd | 73 +-- man/get_wordvec.Rd | 23 - man/most_similar.Rd | 75 +-- man/normalize.Rd | 30 - man/orth_procrustes.Rd | 63 --- man/pair_similarity.Rd | 25 - man/plot_network.Rd | 49 -- man/plot_similarity.Rd | 54 -- man/plot_wordvec.Rd | 21 - man/plot_wordvec_tSNE.Rd | 47 -- man/sum_wordvec.Rd | 51 +- man/tab_similarity.Rd | 36 - man/test_RND.Rd | 96 +--- man/test_WEAT.Rd | 120 ++--- man/tokenize.Rd | 27 - man/train_wordvec.Rd | 159 ++----- 33 files changed, 821 insertions(+), 1517 deletions(-)
Title: Data for Mathematical Modeling and Applied Calculus
Description: Contains the data sets for the first and second editions of the textbook
"Mathematical Modeling and Applied Calculus" by Joel Kilty and Alex M. McAllister.
The first edition of the book was published by Oxford University Press in 2018 with
ISBN-13: 978-019882472. The second edition is expected to be published in January
2027.
Author: Joel Kilty [aut, cre],
McAllister Alex [aut]
Maintainer: Joel Kilty <joel.kilty@centre.edu>
Diff between MMAC versions 0.1.2 dated 2018-07-05 and 1.0 dated 2025-08-19
MMAC-0.1.2/MMAC/R/namespaceDoc.R |only MMAC-0.1.2/MMAC/man/MMAC.Rd |only MMAC-1.0/MMAC/DESCRIPTION | 28 MMAC-1.0/MMAC/MD5 | 280 +- MMAC-1.0/MMAC/NEWS.md | 6 MMAC-1.0/MMAC/R/MMAC-package.R |only MMAC-1.0/MMAC/R/datasetsDoc.R | 2774 +++++++++++++++++++++----- MMAC-1.0/MMAC/README.md | 7 MMAC-1.0/MMAC/data/AAPLStockMonthly.rda |binary MMAC-1.0/MMAC/data/Abalone.rda |only MMAC-1.0/MMAC/data/AddidasProfit.rda |only MMAC-1.0/MMAC/data/Advertising.rda |only MMAC-1.0/MMAC/data/AutoMPG.rda |only MMAC-1.0/MMAC/data/AverageCO2Levels.rda |only MMAC-1.0/MMAC/data/AvianFemur.rda |only MMAC-1.0/MMAC/data/BlastData.rda |binary MMAC-1.0/MMAC/data/CHIPExpenditures.rda |only MMAC-1.0/MMAC/data/CaliforniaHousing.rda |only MMAC-1.0/MMAC/data/CarSales.rda |only MMAC-1.0/MMAC/data/CellularSubscriptions.rda |only MMAC-1.0/MMAC/data/CellularSubscriptions2.rda |only MMAC-1.0/MMAC/data/ChildLabor.rda |only MMAC-1.0/MMAC/data/CigaretteSales.rda |only MMAC-1.0/MMAC/data/DJIA.rda |only MMAC-1.0/MMAC/data/DaylengthFairbanks.rda |only MMAC-1.0/MMAC/data/DuluthDayLength.rda |only MMAC-1.0/MMAC/data/DunkinDonuts.rda |only MMAC-1.0/MMAC/data/EVMarketShare.rda |only MMAC-1.0/MMAC/data/ElectricityDemand.rda |only MMAC-1.0/MMAC/data/EngineBore.rda |only MMAC-1.0/MMAC/data/FiddlerCrabs.rda |only MMAC-1.0/MMAC/data/FishWeights.rda |only MMAC-1.0/MMAC/data/FlightsWorldwide.rda |only MMAC-1.0/MMAC/data/GaltonMale.rda |only MMAC-1.0/MMAC/data/GlobalCO2Emissions.rda |only MMAC-1.0/MMAC/data/Happiness.rda |only MMAC-1.0/MMAC/data/HenWeight.rda |only MMAC-1.0/MMAC/data/JuniperTrees.rda |only MMAC-1.0/MMAC/data/KeyWestTides.rda |only MMAC-1.0/MMAC/data/MammalEnergy.rda |only MMAC-1.0/MMAC/data/MediterraneanSeaTemp.rda |only MMAC-1.0/MMAC/data/MusselsMetabolic.rda |only MMAC-1.0/MMAC/data/NASDAQ.rda |only MMAC-1.0/MMAC/data/NYCHousingPrices.rda |only MMAC-1.0/MMAC/data/NikeRevenue.rda |only MMAC-1.0/MMAC/data/NintendoSwitch.rda |only MMAC-1.0/MMAC/data/OnlineAdvertising.rda |only MMAC-1.0/MMAC/data/OrganicFood.rda |only MMAC-1.0/MMAC/data/PaypalAccounts.rda |only MMAC-1.0/MMAC/data/PaypalUsers.rda |only MMAC-1.0/MMAC/data/PesticideConsumption.rda |only MMAC-1.0/MMAC/data/RoosterWeight.rda |only MMAC-1.0/MMAC/data/SeaTemperature.rda |only MMAC-1.0/MMAC/data/SmartphoneUsers.rda |only MMAC-1.0/MMAC/data/SolarCapacity.rda |only MMAC-1.0/MMAC/data/StJohnsTides.rda |only MMAC-1.0/MMAC/data/StudentLoans.rda |only MMAC-1.0/MMAC/data/SunflowerHeight.rda |only MMAC-1.0/MMAC/data/SunriseCancun.rda |only MMAC-1.0/MMAC/data/TemperaturesLexington.rda |only MMAC-1.0/MMAC/data/TeslaRevenue.rda |only MMAC-1.0/MMAC/data/TherapodLength.rda |only MMAC-1.0/MMAC/data/ThreadfinBream.rda |only MMAC-1.0/MMAC/data/Transistors.rda |only MMAC-1.0/MMAC/data/UKOnlineSales.rda |only MMAC-1.0/MMAC/data/USGDPDebt.rda |only MMAC-1.0/MMAC/data/USGrossDomesticProduct.rda |only MMAC-1.0/MMAC/data/USInflationRate.rda |only MMAC-1.0/MMAC/data/USMilitarySpending.rda |only MMAC-1.0/MMAC/data/USNationalDebt.rda |only MMAC-1.0/MMAC/data/USNuclearTests.rda |only MMAC-1.0/MMAC/data/USPopulationDecade.rda |only MMAC-1.0/MMAC/data/USPowerProduction.rda |only MMAC-1.0/MMAC/data/USTaxReceipts.rda |only MMAC-1.0/MMAC/data/UnemploymentRate.rda |only MMAC-1.0/MMAC/data/UrbanPopulation.rda |only MMAC-1.0/MMAC/data/VO2Max.rda |only MMAC-1.0/MMAC/data/VehicleRegistrations.rda |only MMAC-1.0/MMAC/data/VerizonEmployees.rda |only MMAC-1.0/MMAC/data/WineQuality.rda |only MMAC-1.0/MMAC/data/WineSales.rda |only MMAC-1.0/MMAC/data/XUsers.rda |only MMAC-1.0/MMAC/man/AAPLStockMonthly.Rd | 14 MMAC-1.0/MMAC/man/APCalculus.Rd | 13 MMAC-1.0/MMAC/man/APCalculus2.Rd | 13 MMAC-1.0/MMAC/man/Abalone.Rd |only MMAC-1.0/MMAC/man/AddidasProfit.Rd |only MMAC-1.0/MMAC/man/Advertising.Rd |only MMAC-1.0/MMAC/man/AutoMPG.Rd |only MMAC-1.0/MMAC/man/AverageCO2Levels.Rd |only MMAC-1.0/MMAC/man/AvianFemur.Rd |only MMAC-1.0/MMAC/man/BlastData.Rd | 15 MMAC-1.0/MMAC/man/BodyMassMetabolicRate.Rd | 14 MMAC-1.0/MMAC/man/CHIPExpenditures.Rd |only MMAC-1.0/MMAC/man/CaliforniaHousing.Rd |only MMAC-1.0/MMAC/man/CarSales.Rd |only MMAC-1.0/MMAC/man/CellularSubscriptions.Rd |only MMAC-1.0/MMAC/man/CellularSubscriptions2.Rd |only MMAC-1.0/MMAC/man/ChildLabor.Rd |only MMAC-1.0/MMAC/man/CigaretteSales.Rd |only MMAC-1.0/MMAC/man/DJIA.Rd |only MMAC-1.0/MMAC/man/DJIACloseQuarterly.Rd | 14 MMAC-1.0/MMAC/man/DaylengthFairbanks.Rd |only MMAC-1.0/MMAC/man/DuluthDayLength.Rd |only MMAC-1.0/MMAC/man/DunkinDonuts.Rd |only MMAC-1.0/MMAC/man/EVMarketShare.Rd |only MMAC-1.0/MMAC/man/EbolaSierraLeone.Rd | 14 MMAC-1.0/MMAC/man/ElectricBill.Rd | 14 MMAC-1.0/MMAC/man/ElectricityDemand.Rd |only MMAC-1.0/MMAC/man/ElectronicMailOrderSales.Rd | 14 MMAC-1.0/MMAC/man/EngineBore.Rd |only MMAC-1.0/MMAC/man/EngineRPM.Rd | 13 MMAC-1.0/MMAC/man/FacebookUsers.Rd | 14 MMAC-1.0/MMAC/man/FiddlerCrabs.Rd |only MMAC-1.0/MMAC/man/FishWeights.Rd |only MMAC-1.0/MMAC/man/FlightsWorldwide.Rd |only MMAC-1.0/MMAC/man/FordMarketVolume1.Rd | 14 MMAC-1.0/MMAC/man/FordMarketVolume2.Rd | 14 MMAC-1.0/MMAC/man/GaltonMale.Rd |only MMAC-1.0/MMAC/man/GenderRatio1.Rd | 13 MMAC-1.0/MMAC/man/GenderRatio2.Rd | 13 MMAC-1.0/MMAC/man/GlobalCO2Emissions.Rd |only MMAC-1.0/MMAC/man/HSDropoutRate.Rd | 13 MMAC-1.0/MMAC/man/HSGradsInCollege.Rd | 14 MMAC-1.0/MMAC/man/Happiness.Rd |only MMAC-1.0/MMAC/man/Hawaii.Rd | 14 MMAC-1.0/MMAC/man/HealthExpenditure.Rd | 14 MMAC-1.0/MMAC/man/HenWeight.Rd |only MMAC-1.0/MMAC/man/HispanicPopulation.Rd | 13 MMAC-1.0/MMAC/man/JuniperTrees.Rd |only MMAC-1.0/MMAC/man/KeyWestTides.Rd |only MMAC-1.0/MMAC/man/LifeExpectancyPhysicians.Rd | 14 MMAC-1.0/MMAC/man/MMAC-package.Rd |only MMAC-1.0/MMAC/man/MammalEnergy.Rd |only MMAC-1.0/MMAC/man/MaunaLoaCO2.Rd | 14 MMAC-1.0/MMAC/man/McDBurgers1.Rd | 13 MMAC-1.0/MMAC/man/McDBurgers2.Rd | 13 MMAC-1.0/MMAC/man/MediterraneanSeaTemp.Rd |only MMAC-1.0/MMAC/man/MonthlyUnemployment.Rd | 13 MMAC-1.0/MMAC/man/Mortgage15YrAnnual.Rd | 14 MMAC-1.0/MMAC/man/Mortgage30YrAnnual.Rd | 14 MMAC-1.0/MMAC/man/Mortgage30YrMonthly1.Rd | 14 MMAC-1.0/MMAC/man/Mortgage30YrMonthly2.Rd | 14 MMAC-1.0/MMAC/man/MusselsMetabolic.Rd |only MMAC-1.0/MMAC/man/NASDAQ.Rd |only MMAC-1.0/MMAC/man/NASDAQQuarterly.Rd | 14 MMAC-1.0/MMAC/man/NYCHousingPrices.Rd |only MMAC-1.0/MMAC/man/NaturalGasConsumption.Rd | 14 MMAC-1.0/MMAC/man/NaturalGasConsumption2.Rd | 14 MMAC-1.0/MMAC/man/NetherlandsPopulation.Rd | 14 MMAC-1.0/MMAC/man/NikeRevenue.Rd |only MMAC-1.0/MMAC/man/NintendoSwitch.Rd |only MMAC-1.0/MMAC/man/OilProductionAnnual1.Rd | 14 MMAC-1.0/MMAC/man/OilProductionAnnual2.Rd | 14 MMAC-1.0/MMAC/man/OnlineAdvertising.Rd |only MMAC-1.0/MMAC/man/OrganicFood.Rd |only MMAC-1.0/MMAC/man/PaypalAccounts.Rd |only MMAC-1.0/MMAC/man/PaypalUsers.Rd |only MMAC-1.0/MMAC/man/PesticideConsumption.Rd |only MMAC-1.0/MMAC/man/PollenCountLA.Rd | 13 MMAC-1.0/MMAC/man/PopulationBelgium.Rd | 13 MMAC-1.0/MMAC/man/RoosterWeight.Rd |only MMAC-1.0/MMAC/man/RunningSpeed.Rd | 14 MMAC-1.0/MMAC/man/SATMathKentucky.Rd | 13 MMAC-1.0/MMAC/man/SeaTemperature.Rd |only MMAC-1.0/MMAC/man/SmartphoneUsers.Rd |only MMAC-1.0/MMAC/man/SolarCapacity.Rd |only MMAC-1.0/MMAC/man/StJohnsTides.Rd |only MMAC-1.0/MMAC/man/StudentDebt1.Rd | 14 MMAC-1.0/MMAC/man/StudentDebt2.Rd | 14 MMAC-1.0/MMAC/man/StudentLoans.Rd |only MMAC-1.0/MMAC/man/SunPositionAlaska.Rd | 14 MMAC-1.0/MMAC/man/SunflowerHeight.Rd |only MMAC-1.0/MMAC/man/SunriseCancun.Rd |only MMAC-1.0/MMAC/man/SunriseLA.Rd | 15 MMAC-1.0/MMAC/man/SunsetGreenwich.Rd | 14 MMAC-1.0/MMAC/man/SunsetLA.Rd | 15 MMAC-1.0/MMAC/man/SwimmingSpeed.Rd | 14 MMAC-1.0/MMAC/man/TemperaturesDanville.Rd | 14 MMAC-1.0/MMAC/man/TemperaturesLexington.Rd |only MMAC-1.0/MMAC/man/TeslaRevenue.Rd |only MMAC-1.0/MMAC/man/TherapodLength.Rd |only MMAC-1.0/MMAC/man/ThreadfinBream.Rd |only MMAC-1.0/MMAC/man/ToyotaMonthly.Rd | 13 MMAC-1.0/MMAC/man/Transistors.Rd |only MMAC-1.0/MMAC/man/TwitterUsers.Rd | 14 MMAC-1.0/MMAC/man/TwitterUsers1.Rd | 14 MMAC-1.0/MMAC/man/TwitterUsers2.Rd | 14 MMAC-1.0/MMAC/man/TwitterUsers3.Rd | 14 MMAC-1.0/MMAC/man/UKOnlineSales.Rd |only MMAC-1.0/MMAC/man/USCO2Emissions.Rd | 14 MMAC-1.0/MMAC/man/USGDPDebt.Rd |only MMAC-1.0/MMAC/man/USGrossDomesticProduct.Rd |only MMAC-1.0/MMAC/man/USInflationRate.Rd |only MMAC-1.0/MMAC/man/USMilitarySpending.Rd |only MMAC-1.0/MMAC/man/USNationalDebt.Rd |only MMAC-1.0/MMAC/man/USNuclearTests.Rd |only MMAC-1.0/MMAC/man/USPopulationDecade.Rd |only MMAC-1.0/MMAC/man/USPowerProduction.Rd |only MMAC-1.0/MMAC/man/USRetailTax.Rd | 13 MMAC-1.0/MMAC/man/USTaxReceipts.Rd |only MMAC-1.0/MMAC/man/USTotalPopulation.Rd | 16 MMAC-1.0/MMAC/man/UnemploymentRate.Rd |only MMAC-1.0/MMAC/man/UrbanPopulation.Rd |only MMAC-1.0/MMAC/man/VO2Max.Rd |only MMAC-1.0/MMAC/man/VehicleRegistrations.Rd |only MMAC-1.0/MMAC/man/VerizonEmployees.Rd |only MMAC-1.0/MMAC/man/WaterLevelsEastportMaine.Rd | 15 MMAC-1.0/MMAC/man/WeightChange.Rd | 14 MMAC-1.0/MMAC/man/WineQuality.Rd |only MMAC-1.0/MMAC/man/WineSales.Rd |only MMAC-1.0/MMAC/man/WorldPopulation.Rd | 13 MMAC-1.0/MMAC/man/WorldPopulationChange.Rd | 14 MMAC-1.0/MMAC/man/XUsers.Rd |only MMAC-1.0/MMAC/man/YellowCards.Rd | 14 215 files changed, 2845 insertions(+), 1080 deletions(-)
Title: The Fill-Mask Association Test
Description: The Fill-Mask Association Test ('FMAT')
<doi:10.1037/pspa0000396>
is an integrative and probability-based method using
Masked Language Models to measure conceptual associations
(e.g., attitudes, biases, stereotypes, social norms, cultural values)
as propositions in natural language.
Supported language models include 'BERT'
<doi:10.48550/arXiv.1810.04805> and its variants available at 'Hugging Face'
<https://huggingface.co/models?pipeline_tag=fill-mask>.
Methodological references and installation guidance are provided at
<https://psychbruce.github.io/FMAT/>.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between FMAT versions 2025.4 dated 2025-04-08 and 2025.8 dated 2025-08-19
DESCRIPTION | 15 +- MD5 | 34 +++-- NEWS.md | 4 R/FMAT.R | 282 ++++++++++++++---------------------------------- README.md | 15 +- build |only man/BERT_download.Rd | 9 - man/BERT_info.Rd | 4 man/BERT_vocab.Rd | 27 +--- man/FMAT-package.Rd |only man/FMAT_query.Rd | 31 +---- man/FMAT_query_bind.Rd | 6 - man/FMAT_run.Rd | 81 ++++--------- man/ICC_models.Rd | 6 - man/LPR_reliability.Rd | 9 - man/dot-.Rd | 1 man/fill_mask.Rd | 17 -- man/set_cache_folder.Rd | 12 -- man/summary.fmat.Rd | 24 +--- 19 files changed, 194 insertions(+), 383 deletions(-)
Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based
decision making processes using Monte Carlo simulations. Decision support
is given on two levels: (i) The actual decision level is to choose between
two alternatives under probabilistic uncertainty. This package calculates
the optimal decision based on maximizing expected welfare. (ii) The meta
decision level is to allocate resources to reduce the uncertainty in the
underlying decision problem, i.e to increase the current information to
improve the actual decision making process. This problem is dealt with
using the Value of Information Analysis. The Expected Value of
Information for arbitrary prospective estimates can be calculated as
well as Individual Expected Value of Perfect Information.
The probabilistic calculations are done via Monte Carlo
simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] ,
Lutz Goehring [aut] ,
Katja Schiffers [aut] ,
Cory Whitney [aut] ,
Eduardo Fernandez [aut]
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between decisionSupport versions 1.114 dated 2024-04-08 and 1.115 dated 2025-08-19
DESCRIPTION | 10 +- MD5 | 32 ++++---- R/decisionSupport-package.R | 7 + R/plot_cashflow.R | 10 +- R/plot_evpi.R | 2 R/plot_pls.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/example_decision_function.R | 2 inst/doc/example_decision_function.html | 38 ++++----- inst/doc/wildfire_example.html | 125 ++++++++++++++++---------------- man/decisionSupport-package.Rd | 21 ++++- man/plot_cashflow.Rd | 10 +- man/plot_evpi.Rd | 2 man/plot_pls.Rd | 2 vignettes/vignettes.bib | 2 vignettes/wildfire.bib | 2 17 files changed, 140 insertions(+), 127 deletions(-)
More information about decisionSupport at CRAN
Permanent link
Title: Spatial Interpolation using Bayesian Maximum Entropy (BME)
Description: Provides an accessible and robust implementation of core BME
methodologies for spatial prediction. It enables the systematic integration
of heterogeneous data sources including both hard data (precise
measurements) and soft interval data (bounded or uncertain observations)
while incorporating prior knowledge and supporting variogram-based spatial
modeling. The BME methodology is described in Christakos (1990)
<doi:10.1007/BF00890661> and Serre and Christakos (1999)
<doi:10.1007/s004770050029>.
Author: Kinspride Duah [aut, cre, cph] ,
Yan Sun [aut]
Maintainer: Kinspride Duah <kinspride2020@gmail.com>
Diff between BMEmapping versions 1.2.0 dated 2025-07-27 and 1.2.2 dated 2025-08-19
DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- NEWS.md | 2 ++ R/extended_range.R | 6 +++--- R/plot.BMEmapping.R | 1 - inst/doc/Introduction_to_BMEmapping.html | 6 +++--- tests/testthat/test-bme_cv.R |only tests/testthat/test-prob_zk.R |only 8 files changed, 18 insertions(+), 15 deletions(-)
Title: Interface to the Algorithm Selection Benchmark Library
Description: Provides an interface to the algorithm selection benchmark library
at <https://www.coseal.net/aslib/> and the 'LLAMA' package
(<https://cran.r-project.org/package=llama>) for building
algorithm selection models; see Bischl et al. (2016)
<doi:10.1016/j.artint.2016.04.003>.
Author: Bernd Bischl [aut],
Lars Kotthoff [aut, cre],
Pascal Kerschke [ctb, aut],
Damir Pulatov [ctb, aut]
Maintainer: Lars Kotthoff <larsko@uwyo.edu>
Diff between aslib versions 0.1.2 dated 2022-08-25 and 0.1.3 dated 2025-08-19
DESCRIPTION | 33 +++++++++++++++++++++++++-------- MD5 | 20 ++++++++++---------- NEWS | 3 +++ R/convertAlgoPerfToWideFormat.R | 2 +- R/createCVSplits.R | 2 +- R/parseASScenario.R | 8 ++++---- R/summarizeLlamaExps.R | 6 +++--- man/convertAlgoPerfToWideFormat.Rd | 2 +- man/createCVSplits.Rd | 2 +- man/parseASScenario.Rd | 8 ++++---- man/summarizeLlamaExps.Rd | 6 +++--- 11 files changed, 56 insertions(+), 36 deletions(-)
Title: Affymetrix SNP Probe-Summarization using Non-Negative Matrix
Factorization
Description: A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).
Author: Maria Ortiz [aut],
Henrik Bengtsson [aut, cre, cph],
Angel Rubio [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between ACNE versions 0.9.1 dated 2024-02-17 and 0.9.2 dated 2025-08-19
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/doACNE.R | 11 ++++++----- man/doACNE.Rd | 11 ++++++----- 5 files changed, 26 insertions(+), 17 deletions(-)
Title: Parametric Mixture Models for Uncertainty Estimation of
Fatalities in UCDP Conflict Data
Description: Provides functions for estimating uncertainty in the number of fatalities in the Uppsala Conflict Data Program (UCDP) data. The package implements a parametric reported-value Gumbel mixture distribution that accounts for the uncertainty in the number of fatalities in the UCDP data. The model is based on information from a survey on UCDP coders and how they view the uncertainty of the number of fatalities from UCDP events. The package provides functions for making random draws of fatalities from the mixture distribution, as well as to estimate percentiles, quantiles, means, and other statistics of the distribution. Full details on the survey and estimation procedure can be found in Vesco et al (2024).
Author: David Randahl [cre, aut]
Maintainer: David Randahl <david.randahl@pcr.uu.se>
Diff between uncertainUCDP versions 0.5.2 dated 2024-07-02 and 0.6.1 dated 2025-08-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/uncertainUCDP.R | 11 +++++++++-- 3 files changed, 14 insertions(+), 7 deletions(-)
Title: Maxwell Control Charts
Description: Computes Control limits, coefficients of control limits, various performance metrics and depicts control charts for monitoring Maxwell-distributed quality characteristics.
Author: Zahid Khan [aut],
Zsolt T. Kosztyan [aut, cre]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between mxcc versions 0.0.3 dated 2025-06-13 and 0.0.4 dated 2025-08-19
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Item Maker
Description: This is an Automatic Item Generator for Psychological Assessment. Items created with the 'IMak' package should not be used in applied settings as part of the working protocol without ensuring first that the items meet the required psychometric quality standards (see Blum & Holling, 2018) <DOI:10.3389/fpsyg.2018.01286>.
Author: Diego Blum [aut, cre]
Maintainer: Diego Blum <blumworx@gmail.com>
Diff between IMak versions 2.1.1 dated 2025-07-25 and 2.1.2 dated 2025-08-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 52 ++++++++++++++++++++++++++++------------------------ R/afs.R | 56 ++++++++++++++++++++++++++++---------------------------- man/afs.Rd | 56 ++++++++++++++++++++++++++++---------------------------- 5 files changed, 92 insertions(+), 88 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms. See <doi:10.7717/peerj.8451> for tsd functions; see <doi:10.1016/j.jtherbio.2014.08.005> for thermal reaction norm of embryo growth.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between embryogrowth versions 10.2 dated 2025-06-16 and 10.3 dated 2025-08-19
DESCRIPTION | 8 MD5 | 30 +- NEWS | 16 + R/HatchingSuccess.MHmcmc.R | 51 +++- R/HatchingSuccess.lnL.R | 4 R/HeterogeneityNests.R | 471 ++++++++++++++++++++++++---------------- R/embryogrowth-package.R | 4 R/plot.HatchingSuccess.R | 4 R/plot.Nests.R | 2 R/searchR.R | 8 build/partial.rdb |binary data/resultNest_mcmc_4p_SSM.rda |binary man/HatchingSuccess.MHmcmc.Rd | 5 man/HeterogeneityNests.Rd | 57 ++++ man/embryogrowth-package.Rd | 4 man/searchR.Rd | 6 16 files changed, 435 insertions(+), 235 deletions(-)
Title: Setting Download Method to 'wget'
Description: Provides function, wget_set(), to change the method (default to 'wget -c') using in download.file().
Using 'wget -c' allowing continued downloading, which is especially useful for slow internet connection and for downloading large files.
User can run wget_unset() to restore previous setting.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between wget versions 0.0.3 dated 2024-09-24 and 0.0.4 dated 2025-08-19
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 1 + R/wget.R | 9 ++++----- 4 files changed, 14 insertions(+), 13 deletions(-)
Title: Simple Implementation of Semantic Versioning (SemVer)
Description: Simple implementation of Semantic Versioning 2.0.0 ('SemVer') on the
'vctrs' package. This package provides a simple way to create,
compare, and manipulate semantic versions in R. It is designed to be
lightweight and easy to use.
Author: Tatsuya Shima [aut, cre]
Maintainer: Tatsuya Shima <ts1s1andn@gmail.com>
Diff between smvr versions 0.2.0 dated 2025-07-05 and 0.2.1 dated 2025-08-19
DESCRIPTION | 6 ++--- MD5 | 25 ++++++++++++------------ NEWS.md | 7 ++++++ R/parse.R | 20 +++++-------------- R/pre_release_identifier.R | 20 ++++++++++--------- R/smvr.R | 2 - R/utils.R | 16 ++++++++++++++- man/pre_release_identifier.Rd | 2 - tests/testthat/_snaps/parse.md | 19 +++++++++++++++--- tests/testthat/_snaps/pre_release_identifier.md | 12 +++++++++-- tests/testthat/_snaps/smvr.md | 2 - tests/testthat/test-parse.R | 9 +++++++- tests/testthat/test-pre_release_identifier.R | 9 +++++++- tests/testthat/test-utils.R |only 14 files changed, 100 insertions(+), 49 deletions(-)
Title: Sequence Generalization Through Similarity Network
Description: Proposes an application for sequence prediction generalizing the similarity within the network of previous sequences.
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between segen versions 1.1.0 dated 2022-08-15 and 2.0.0 dated 2025-08-19
DESCRIPTION | 16 - MD5 | 12 NAMESPACE | 8 NEWS.md | 30 + R/main.R | 931 ++++++++++++++++++++++++++++++++++++++--------------------- man/segen.Rd | 41 +- tests |only 7 files changed, 689 insertions(+), 349 deletions(-)
Title: Compute the Rectangular Statistical Cartogram
Description: Implements the RecMap MP2 construction heuristic
<doi:10.1109/INFVIS.2004.57>.
This algorithm draws maps according to a given statistical
value, e.g., election results, population, or epidemiological data.
The basic idea of the RecMap algorithm is that each map region,
e.g., different countries, is represented by a rectangle.
The area of each rectangle represents the statistical value provided
as input to maintain zero cartographic error.
Computationally intensive tasks are implemented in C++.
The included vignette documents recmap algorithm usage.
Author: Christian Panse [aut, cre]
Maintainer: Christian Panse <Christian.Panse@gmail.com>
Diff between recmap versions 1.0.17 dated 2023-09-23 and 1.0.20 dated 2025-08-19
DESCRIPTION | 22 ++-- MD5 | 41 ++++----- NAMESPACE | 3 R/RcppExports.R | 101 +++++++++++----------- R/recmap.R | 102 ++++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 7 - inst/doc/recmap.R | 20 ++-- inst/doc/recmap.html | 136 ++++++++++++++++++------------ inst/shiny-examples/server.R | 4 man/as.SpatialPolygonsDataFrame.recmap.Rd | 4 man/as.recmap.SpatialPolygonsDataFrame.Rd | 8 - man/dot-getUS_map.Rd |only man/dot-get_7triangles.Rd | 2 man/plot.recmap.Rd | 13 ++ man/recmap.Rd | 77 +++++++++------- man/recmapGA.Rd | 36 +------ man/recmapGRASP.Rd | 100 ++++++---------------- man/summary.recmap.Rd | 10 +- src/Recmap.cpp | 101 +++++++++++----------- vignettes/recmap.bib | 2 22 files changed, 406 insertions(+), 383 deletions(-)
Title: Formal Parser and Related Tools for R Markdown Documents
Description: An implementation of a formal grammar and parser for R Markdown documents
using the Boost Spirit X3 library. It also includes a collection of high level
functions for working with the resulting abstract syntax tree.
Author: Colin Rundel [aut, cre]
Maintainer: Colin Rundel <rundel@gmail.com>
Diff between parsermd versions 0.1.3 dated 2024-01-16 and 0.2.0 dated 2025-08-19
parsermd-0.1.3/parsermd/R/rmd_subset.R |only parsermd-0.1.3/parsermd/R/rmd_subset_util.R |only parsermd-0.1.3/parsermd/R/util_create.R |only parsermd-0.1.3/parsermd/inst/doc/parsermd.Rmd |only parsermd-0.1.3/parsermd/inst/doc/templates.Rmd |only parsermd-0.1.3/parsermd/inst/empty_sections.Rmd |only parsermd-0.1.3/parsermd/inst/hw01-student.Rmd |only parsermd-0.1.3/parsermd/inst/hw01.Rmd |only parsermd-0.1.3/parsermd/inst/hw02-complex.Rmd |only parsermd-0.1.3/parsermd/inst/minimal.Rmd |only parsermd-0.1.3/parsermd/inst/raw_attr.Rmd |only parsermd-0.1.3/parsermd/inst/reverse_sections.Rmd |only parsermd-0.1.3/parsermd/man/rmd_node.Rd |only parsermd-0.1.3/parsermd/man/rmd_subset.Rd |only parsermd-0.1.3/parsermd/man/rmd_subset_util.Rd |only parsermd-0.1.3/parsermd/src/parser_rcpp_wrap.cpp |only parsermd-0.1.3/parsermd/src/parser_rcpp_wrap.h |only parsermd-0.1.3/parsermd/src/util.h |only parsermd-0.1.3/parsermd/tests/testthat/_snaps/parse-options.md |only parsermd-0.1.3/parsermd/tests/testthat/knitr-examples |only parsermd-0.1.3/parsermd/tests/testthat/test-parse-options.R |only parsermd-0.1.3/parsermd/vignettes/parsermd.Rmd |only parsermd-0.1.3/parsermd/vignettes/templates.Rmd |only parsermd-0.2.0/parsermd/DESCRIPTION | 16 parsermd-0.2.0/parsermd/MD5 | 632 +++++-- parsermd-0.2.0/parsermd/NAMESPACE | 199 ++ parsermd-0.2.0/parsermd/NEWS.md | 36 parsermd-0.2.0/parsermd/R/RcppExports.R | 68 parsermd-0.2.0/parsermd/R/as_ast.R | 107 + parsermd-0.2.0/parsermd/R/as_document.R | 276 ++- parsermd-0.2.0/parsermd/R/as_tibble.R | 56 parsermd-0.2.0/parsermd/R/parse_collection.R |only parsermd-0.2.0/parsermd/R/parse_rmd.R | 74 parsermd-0.2.0/parsermd/R/parse_yaml.R |only parsermd-0.2.0/parsermd/R/print_tree.R | 259 ++- parsermd-0.2.0/parsermd/R/render.R | 81 parsermd-0.2.0/parsermd/R/rmd_ast_append.R |only parsermd-0.2.0/parsermd/R/rmd_check_template.R | 6 parsermd-0.2.0/parsermd/R/rmd_chunk_options.R | 73 parsermd-0.2.0/parsermd/R/rmd_classes_s7.R |only parsermd-0.2.0/parsermd/R/rmd_fenced_div_wrap.R |only parsermd-0.2.0/parsermd/R/rmd_inline_code_utils.R |only parsermd-0.2.0/parsermd/R/rmd_insert.R |only parsermd-0.2.0/parsermd/R/rmd_modify.R |only parsermd-0.2.0/parsermd/R/rmd_node.R | 386 +++- parsermd-0.2.0/parsermd/R/rmd_node_sections.R | 102 + parsermd-0.2.0/parsermd/R/rmd_select.R | 61 parsermd-0.2.0/parsermd/R/rmd_select_helpers.R | 314 +++ parsermd-0.2.0/parsermd/R/rmd_shortcode_utils.R |only parsermd-0.2.0/parsermd/R/rmd_source.R | 8 parsermd-0.2.0/parsermd/R/rmd_span_utils.R |only parsermd-0.2.0/parsermd/R/rmd_template.R | 4 parsermd-0.2.0/parsermd/R/tests.R |only parsermd-0.2.0/parsermd/R/util_other.R |only parsermd-0.2.0/parsermd/R/util_subset.R | 67 parsermd-0.2.0/parsermd/R/zzz.R |only parsermd-0.2.0/parsermd/README.md | 78 parsermd-0.2.0/parsermd/build/vignette.rds |binary parsermd-0.2.0/parsermd/inst/doc/assignment-with-key.R |only parsermd-0.2.0/parsermd/inst/doc/assignment-with-key.html |only parsermd-0.2.0/parsermd/inst/doc/assignment-with-key.qmd |only parsermd-0.2.0/parsermd/inst/doc/editing-documents.R |only parsermd-0.2.0/parsermd/inst/doc/editing-documents.html |only parsermd-0.2.0/parsermd/inst/doc/editing-documents.qmd |only parsermd-0.2.0/parsermd/inst/doc/know-your-nodes.R |only parsermd-0.2.0/parsermd/inst/doc/know-your-nodes.html |only parsermd-0.2.0/parsermd/inst/doc/know-your-nodes.qmd |only parsermd-0.2.0/parsermd/inst/doc/parsermd.R | 83 parsermd-0.2.0/parsermd/inst/doc/parsermd.html | 835 +++------- parsermd-0.2.0/parsermd/inst/doc/parsermd.qmd |only parsermd-0.2.0/parsermd/inst/doc/templates.R | 41 parsermd-0.2.0/parsermd/inst/doc/templates.html | 472 +---- parsermd-0.2.0/parsermd/inst/doc/templates.qmd |only parsermd-0.2.0/parsermd/inst/examples |only parsermd-0.2.0/parsermd/man/as_ast.Rd | 2 parsermd-0.2.0/parsermd/man/as_document.Rd | 6 parsermd-0.2.0/parsermd/man/chunk_options.Rd | 13 parsermd-0.2.0/parsermd/man/figures/logo |only 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parsermd-0.2.0/parsermd/man/rmd_raw_chunk.Rd |only parsermd-0.2.0/parsermd/man/rmd_select.Rd | 12 parsermd-0.2.0/parsermd/man/rmd_select_helpers.Rd | 54 parsermd-0.2.0/parsermd/man/rmd_shortcode.Rd |only parsermd-0.2.0/parsermd/man/rmd_source.Rd | 2 parsermd-0.2.0/parsermd/man/rmd_span.Rd |only parsermd-0.2.0/parsermd/man/rmd_template.Rd | 2 parsermd-0.2.0/parsermd/man/shortcode_utils.Rd |only parsermd-0.2.0/parsermd/man/span_utils.Rd |only parsermd-0.2.0/parsermd/src/RcppExports.cpp | 205 ++ parsermd-0.2.0/parsermd/src/parse_R_type.h |only parsermd-0.2.0/parsermd/src/parse_R_type_ast.h |only parsermd-0.2.0/parsermd/src/parse_cbrace.h |only parsermd-0.2.0/parsermd/src/parse_chunk.h | 110 - parsermd-0.2.0/parsermd/src/parse_chunk_ast.h | 10 parsermd-0.2.0/parsermd/src/parse_code_block.h |only parsermd-0.2.0/parsermd/src/parse_code_block_ast.h |only parsermd-0.2.0/parsermd/src/parse_code_block_literal.h |only parsermd-0.2.0/parsermd/src/parse_code_block_literal_ast.h |only parsermd-0.2.0/parsermd/src/parse_expr.h | 1 parsermd-0.2.0/parsermd/src/parse_fenced_div.h |only parsermd-0.2.0/parsermd/src/parse_fenced_div_ast.h |only parsermd-0.2.0/parsermd/src/parse_heading.h |only parsermd-0.2.0/parsermd/src/parse_inline_code.h |only parsermd-0.2.0/parsermd/src/parse_inline_code_ast.h |only parsermd-0.2.0/parsermd/src/parse_markdown.h |only parsermd-0.2.0/parsermd/src/parse_markdown_ast.h |only parsermd-0.2.0/parsermd/src/parse_option.h | 8 parsermd-0.2.0/parsermd/src/parse_pandoc_attr.h |only parsermd-0.2.0/parsermd/src/parse_pandoc_attr_ast.h |only parsermd-0.2.0/parsermd/src/parse_qstring.h | 18 parsermd-0.2.0/parsermd/src/parse_rmd.h | 48 parsermd-0.2.0/parsermd/src/parse_rmd_ast.h | 21 parsermd-0.2.0/parsermd/src/parse_shortcode.h |only parsermd-0.2.0/parsermd/src/parse_shortcode_ast.h |only parsermd-0.2.0/parsermd/src/parse_span.h |only parsermd-0.2.0/parsermd/src/parse_span_ast.h |only parsermd-0.2.0/parsermd/src/parse_ticks.h |only parsermd-0.2.0/parsermd/src/parse_yaml.h | 26 parsermd-0.2.0/parsermd/src/parser.cpp | 577 ++++++ parsermd-0.2.0/parsermd/src/parser_error_handler.h | 334 +++- parsermd-0.2.0/parsermd/src/rcpp_wrap.h |only parsermd-0.2.0/parsermd/tests/testthat/_snaps/as_document.md | 25 parsermd-0.2.0/parsermd/tests/testthat/_snaps/as_tibble.md | 123 - parsermd-0.2.0/parsermd/tests/testthat/_snaps/error-formatting.md |only parsermd-0.2.0/parsermd/tests/testthat/_snaps/parse-chunk.md | 126 + parsermd-0.2.0/parsermd/tests/testthat/_snaps/parse-code_block.md |only parsermd-0.2.0/parsermd/tests/testthat/_snaps/parse-code_block_literal.md |only parsermd-0.2.0/parsermd/tests/testthat/_snaps/parse-fenced_divs.md |only parsermd-0.2.0/parsermd/tests/testthat/_snaps/parse-span.md |only parsermd-0.2.0/parsermd/tests/testthat/_snaps/parse-yaml.md | 75 parsermd-0.2.0/parsermd/tests/testthat/_snaps/print_tree.md | 141 + parsermd-0.2.0/parsermd/tests/testthat/_snaps/rmd_chunk_options.md |only 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parsermd-0.2.0/parsermd/tests/testthat/examples |only parsermd-0.2.0/parsermd/tests/testthat/helper-tests.R |only parsermd-0.2.0/parsermd/tests/testthat/test-as_document-yaml_opts.R |only parsermd-0.2.0/parsermd/tests/testthat/test-as_document.R | 23 parsermd-0.2.0/parsermd/tests/testthat/test-as_tibble.R | 21 parsermd-0.2.0/parsermd/tests/testthat/test-error-formatting.R |only parsermd-0.2.0/parsermd/tests/testthat/test-examples-knitr-round-trip.R |only parsermd-0.2.0/parsermd/tests/testthat/test-examples-quarto-cli-round-trip.R |only parsermd-0.2.0/parsermd/tests/testthat/test-examples-quarto-web-round-trip.R |only parsermd-0.2.0/parsermd/tests/testthat/test-examples-shortcodes.R |only parsermd-0.2.0/parsermd/tests/testthat/test-examples-spans.R |only parsermd-0.2.0/parsermd/tests/testthat/test-extract-inline-codes.R |only parsermd-0.2.0/parsermd/tests/testthat/test-extract-shortcodes.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-R-value.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-chunk.R | 344 ++-- parsermd-0.2.0/parsermd/tests/testthat/test-parse-chunk_options.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-code_block.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-code_block_literal.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-exprs.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-fenced_divs.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-headings.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-inline_code.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-markdown.R | 103 - parsermd-0.2.0/parsermd/tests/testthat/test-parse-qstring.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-shortcode.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-span.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse-yaml.R | 134 + parsermd-0.2.0/parsermd/tests/testthat/test-parse-yaml_options.R |only parsermd-0.2.0/parsermd/tests/testthat/test-parse_rmd.R | 82 parsermd-0.2.0/parsermd/tests/testthat/test-print_tree.R | 33 parsermd-0.2.0/parsermd/tests/testthat/test-rmd_ast_append.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_check_template.R | 4 parsermd-0.2.0/parsermd/tests/testthat/test-rmd_chunk_options.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_fenced_div_wrap.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_insert.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_modify.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_node.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_node_sections.R | 28 parsermd-0.2.0/parsermd/tests/testthat/test-rmd_s7_classes.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_select-by_fdiv.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_select-by_section.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_select-has_code.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_select-has_heading.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_select-has_inline_code.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_select-has_label.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_select-has_option.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_select-has_shortcode.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_select-has_type.R |only parsermd-0.2.0/parsermd/tests/testthat/test-rmd_source.R | 47 parsermd-0.2.0/parsermd/tests/testthat/test-util_subset.R | 54 parsermd-0.2.0/parsermd/vignettes/assignment-with-key.qmd |only parsermd-0.2.0/parsermd/vignettes/editing-documents.qmd |only parsermd-0.2.0/parsermd/vignettes/know-your-nodes.qmd |only parsermd-0.2.0/parsermd/vignettes/parsermd.qmd |only parsermd-0.2.0/parsermd/vignettes/templates.qmd |only 218 files changed, 4845 insertions(+), 2333 deletions(-)
Title: A Comprehensive Toolkit for Clinical HLA Informatics
Description: A comprehensive toolkit for clinical Human Leukocyte Antigen (HLA) informatics, built on 'tidyverse' <https://tidyverse.tidyverse.org/> principles and making use of genotype list string (GL string, Mack et al. (2023) <doi:10.1111/tan.15126>) for storing and computing HLA genotype data. Specific functionalities include: coercion of HLA data in tabular format to and from GL string; calculation of matching and mismatching in all directions, with multiple output formats; automatic formatting of HLA data for searching within a GL string; truncation of molecular HLA data to a specific number of fields; and reading HLA genotypes in HML files and extracting the GL string.
Author: Nicholas Brown [cre, aut] ,
Busra Coskun [aut]
Maintainer: Nicholas Brown <nicholas.brown@pennmedicine.upenn.edu>
Diff between immunogenetr versions 0.3.1 dated 2025-06-25 and 1.0.0 dated 2025-08-19
DESCRIPTION | 12 +++++++----- MD5 | 13 ++++++++----- NAMESPACE | 1 + NEWS.md | 4 ++++ R/HLA_mismatch_alleles.R |only R/HLA_mismatched_alleles.R | 2 ++ man/HLA_mismatch_alleles.Rd |only man/HLA_mismatched_alleles.Rd | 2 ++ tests/testthat/test-HLA_mismatch_alleles.R |only 9 files changed, 24 insertions(+), 10 deletions(-)
More information about confidenceCurves at CRAN
Permanent link
Title: Chinese Name Database 1930-2008
Description: A database of Chinese surnames and given names (1930-2008).
This database contains nationwide frequency statistics of
1,806 Chinese surnames and 2,614 Chinese characters used in given names,
covering about 1.2 billion Han Chinese population
(96.8 percent of the Han Chinese household-registered population
born from 1930 to 2008 and still alive in 2008).
This package also contains a function for computing multiple indices of
Chinese surnames and given names for social science research (e.g.,
name uniqueness, name gender, name valence, and name warmth/competence).
Details are provided at
<https://psychbruce.github.io/ChineseNames/>.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between ChineseNames versions 2023.8 dated 2023-08-08 and 2025.8 dated 2025-08-19
ChineseNames-2023.8/ChineseNames/build |only ChineseNames-2023.8/ChineseNames/man/ChineseNames.Rd |only ChineseNames-2025.8/ChineseNames/DESCRIPTION | 27 - ChineseNames-2025.8/ChineseNames/MD5 | 17 ChineseNames-2025.8/ChineseNames/NEWS.md | 6 ChineseNames-2025.8/ChineseNames/R/ChineseNames.R | 239 ++++------- ChineseNames-2025.8/ChineseNames/README.md | 28 - ChineseNames-2025.8/ChineseNames/man/ChineseNames-package.Rd |only ChineseNames-2025.8/ChineseNames/man/compute_name_index.Rd | 63 +- ChineseNames-2025.8/ChineseNames/man/familyname.Rd | 14 ChineseNames-2025.8/ChineseNames/man/givenname.Rd | 30 - 11 files changed, 189 insertions(+), 235 deletions(-)
Title: Time-Based Rolling Functions
Description: Provides rolling statistical functions based
on date and time windows instead of n-lagged observations.
Author: Michael Schramm [aut, cre, cph] ,
Frank Harrell [ctb],
Bob Rudis [ctb]
Maintainer: Michael Schramm <mpschramm@gmail.com>
Diff between tbrf versions 0.1.6 dated 2025-04-02 and 0.1.7 dated 2025-08-19
DESCRIPTION | 22 +++--- MD5 | 80 +++++++++++++------------ NAMESPACE | 4 - NEWS.md | 18 +++++ R/data.R | 26 +++++++- R/ggproto-classes.R |only R/stat-stepribbon.R |only R/tbr_binom.R | 43 ++++++++----- R/tbr_gmean.R | 57 +++++++---------- R/tbr_mean.R | 61 ++++++++----------- R/tbr_median.R | 14 ++-- R/tbr_misc.R | 16 ++--- R/tbr_sd.R | 17 ++--- R/tbr_sum.R | 22 +++--- R/tbrf-package.R |only R/utils.R | 30 ++++++--- README.md | 23 ++++--- data/Entero.rda |only inst/doc/intro_to_tbrf.R | 33 +++++----- inst/doc/intro_to_tbrf.Rmd | 33 +++++----- inst/doc/intro_to_tbrf.html | 105 ++++++++++++++++----------------- man/Dissolved_Oxygen.Rd | 2 man/Entero.Rd |only man/figures/README-tbr_hour-1.png |binary man/figures/README-tbr_threehour-1.png |binary man/open_window.Rd | 4 - man/stat_stepribbon.Rd |only man/tbr_binom.Rd | 6 + man/tbr_binom_window.Rd | 4 - man/tbr_gmean.Rd | 6 + man/tbr_gmean_window.Rd | 2 man/tbr_mean.Rd | 6 + man/tbr_mean_window.Rd | 4 - man/tbr_median.Rd | 6 + man/tbr_median_window.Rd | 4 - man/tbr_misc.Rd | 7 +- man/tbr_sd.Rd | 6 + man/tbr_sd_window.Rd | 4 - man/tbr_sum.Rd | 6 + man/tbr_sum_window.Rd | 4 - man/tbrf-ggproto.Rd |only man/tbrf.Rd |only tests/testthat/test-expectedClass.R | 6 + tests/testthat/test-expectedValues.R | 15 +++- vignettes/intro_to_tbrf.Rmd | 33 +++++----- 45 files changed, 418 insertions(+), 311 deletions(-)
Title: Plot Raster Images Interactively on a Plain HTML Canvas
Description: Provides methods for plotting potentially large (raster) images
interactively on a plain HTML canvas. In contrast to package 'mapview'
data are plotted without background map, but data can be projected to
any spatial coordinate reference system.
Supports plotting of classes 'RasterLayer', 'RasterStack', 'RasterBrick'
(from package 'raster') as well as 'png' files located on disk.
Interactivity includes zooming, panning, and mouse location information.
In case of multi-layer 'RasterStacks' or 'RasterBricks', RGB image plots
are created (similar to 'raster::plotRGB' - but interactive).
Author: Tim Appelhans [cre, aut],
Stefan Woellauer [aut]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between plainview versions 0.2.1 dated 2023-07-11 and 0.2.2 dated 2025-08-19
DESCRIPTION | 12 +- MD5 | 16 +-- NEWS | 7 + NEWS.md | 7 + R/plainView.R | 195 +++++++++++------------------------------------ R/plainview-package.R | 4 man/plainView.Rd | 15 +-- man/plainViewOutput.Rd | 2 man/plainview-package.Rd | 11 ++ 9 files changed, 96 insertions(+), 173 deletions(-)
Title: Owen Q-Function
Description: Evaluates the Owen Q-function for an integer value of the
degrees of freedom, by applying Owen's algorithm (1965)
<doi:10.1093/biomet/52.3-4.437>. It is useful for the calculation of
the power of equivalence tests.
Author: Stephane Laurent [aut],
Alex Ball [cre]
Maintainer: Alex Ball <alex_keith_ball@hotmail.com>
This is a re-admission after prior archival of version 1.0.7 dated 2023-04-11
Diff between OwenQ versions 1.0.7 dated 2023-04-11 and 1.0.8 dated 2025-08-19
DESCRIPTION | 16 MD5 | 32 NEWS.md | 66 R/RcppExports.R | 126 - build/vignette.rds |binary inst/doc/OwenQ.R | 164 - inst/doc/OwenQ.html | 1346 ++++++------ inst/doc/Validation.R | 784 +++---- inst/doc/Validation.html | 3894 ++++++++++++++++++------------------- tests/testthat/test-OwenQ1_algo1.R | 190 - tests/testthat/test-OwenQ1_algo2.R | 190 - tests/testthat/test-OwenQ2_algo1.R | 4 tests/testthat/test-OwenQ2_algo2.R | 4 tests/testthat/test-pOwen_algo1.R | 820 +++---- tests/testthat/test-pOwen_algo2.R | 820 +++---- tests/testthat/test-ptOwen.R | 2 tests/testthat/test-spowen2.R | 32 17 files changed, 4249 insertions(+), 4241 deletions(-)
Title: Java Graphics Device
Description: Graphics device routing all graphics commands to a Java
program. The actual functionality of the JavaGD depends
on the Java-side implementation. Simple AWT and Swing
implementations are included.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@R-project.org>
Diff between JavaGD versions 0.6-5 dated 2022-11-30 and 0.6-6 dated 2025-08-19
DESCRIPTION | 10 ++++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ inst/java/javaGD.jar |binary src/jGDtalk.c | 7 ++++--- src/javaGD.c | 9 ++++++++- src/javaGD.h | 2 +- 7 files changed, 31 insertions(+), 15 deletions(-)
More information about invitroTKstats at CRAN
Permanent link
Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO (or more generally elastic net), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Oblique Random Forest ('aorsf'), Artificial Neural Network (ANN), Recursive Partitioning ('RPART') or step wise regression models are fit. Cross validation leave out samples (leading to nested cross validation) or bootstrap out-of-bag samples are used to evaluate and compare performances between these models with results presented in tabular or graphical means. Calibration plots can also be generated, again based upon (outer nested) cross validation or bootstrap leave out (out of bag) samples.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied by using the [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.6-1 dated 2025-05-10 and 0.6-2 dated 2025-08-19
glmnetr-0.6-1/glmnetr/R/calplot_240404.R |only glmnetr-0.6-1/glmnetr/R/cv.glmnetr_250418.R |only glmnetr-0.6-1/glmnetr/R/cv.glmnetr_perf_250504.R |only glmnetr-0.6-1/glmnetr/R/nested.cis_250416.R |only glmnetr-0.6-1/glmnetr/R/nested.compare_250428.R |only glmnetr-0.6-1/glmnetr/R/nested.glmnetr_250424.R |only glmnetr-0.6-1/glmnetr/R/plot_perf_glmnetr_250328.R |only glmnetr-0.6-1/glmnetr/R/predict.cv.glmnetr_250404.R |only glmnetr-0.6-1/glmnetr/R/summary.cv.glmnetr_250502.R |only glmnetr-0.6-1/glmnetr/R/summary.nested.glmnetr_250328.R |only glmnetr-0.6-1/glmnetr/inst/doc/An_Overview_of_glmnetr_250510.pdf |only glmnetr-0.6-1/glmnetr/inst/doc/An_Overview_of_glmnetr_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/inst/doc/Calibration_250510.pdf |only glmnetr-0.6-1/glmnetr/inst/doc/Calibration_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/inst/doc/Elastic_net_models_250510.pdf |only glmnetr-0.6-1/glmnetr/inst/doc/Elastic_net_models_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/inst/doc/Ridge_and_Lasso_250510.pdf |only glmnetr-0.6-1/glmnetr/inst/doc/Ridge_and_Lasso_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/inst/doc/Using_ann_tab_cv_250510.pdf |only glmnetr-0.6-1/glmnetr/inst/doc/Using_ann_tab_cv_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/inst/doc/Using_stepreg_250510.pdf |only glmnetr-0.6-1/glmnetr/inst/doc/Using_stepreg_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/man/nested.compare_0_5_1.Rd |only glmnetr-0.6-1/glmnetr/man/plot_perf_glmnetr_0_5_5.Rd |only glmnetr-0.6-1/glmnetr/man/summary.cv.glmnetr_0_6_1.Rd |only glmnetr-0.6-1/glmnetr/vignettes/An_Overview_of_glmnetr_250510.Rmd |only glmnetr-0.6-1/glmnetr/vignettes/An_Overview_of_glmnetr_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/vignettes/Calibration_250510.Rmd |only glmnetr-0.6-1/glmnetr/vignettes/Calibration_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/vignettes/Elastic_net_models_250510.Rmd |only glmnetr-0.6-1/glmnetr/vignettes/Elastic_net_models_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/vignettes/Ridge_and_Lasso_250510.Rmd |only glmnetr-0.6-1/glmnetr/vignettes/Ridge_and_Lasso_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/vignettes/Using_ann_tab_cv_250510.Rmd |only glmnetr-0.6-1/glmnetr/vignettes/Using_ann_tab_cv_250510.pdf.asis |only glmnetr-0.6-1/glmnetr/vignettes/Using_stepreg_250510.Rmd |only glmnetr-0.6-1/glmnetr/vignettes/Using_stepreg_250510.pdf.asis |only glmnetr-0.6-2/glmnetr/DESCRIPTION | 16 - glmnetr-0.6-2/glmnetr/MD5 | 119 +++++----- glmnetr-0.6-2/glmnetr/NAMESPACE | 4 glmnetr-0.6-2/glmnetr/R/calplot_250814.R |only glmnetr-0.6-2/glmnetr/R/cv.glmnetr_250804.R |only glmnetr-0.6-2/glmnetr/R/cv.glmnetr_perf_250525.R |only glmnetr-0.6-2/glmnetr/R/elastic_tools_250818.R |only glmnetr-0.6-2/glmnetr/R/nested.cis_250528.R |only glmnetr-0.6-2/glmnetr/R/nested.compare_0_5_1_241224.R | 24 +- glmnetr-0.6-2/glmnetr/R/nested.compare_0_6_2_250527.R |only glmnetr-0.6-2/glmnetr/R/nested.compare_250527.R |only glmnetr-0.6-2/glmnetr/R/nested.glmnetr_250804.R |only glmnetr-0.6-2/glmnetr/R/plot.cv.glmnetr_0_6_2_250525.R |only glmnetr-0.6-2/glmnetr/R/plot.cv.glmnetr_250503.R | 7 glmnetr-0.6-2/glmnetr/R/plot_perf_glmnetr_0_5_5_241104.R | 2 glmnetr-0.6-2/glmnetr/R/plot_perf_glmnetr_0_6_2_250525.R |only glmnetr-0.6-2/glmnetr/R/plot_perf_glmnetr_250525.R |only glmnetr-0.6-2/glmnetr/R/predict.cv.glmnetr_250804.R |only glmnetr-0.6-2/glmnetr/R/summary.cv.glmnetr_0_5_5_250404.R | 2 glmnetr-0.6-2/glmnetr/R/summary.cv.glmnetr_0_6_1_250501.R | 2 glmnetr-0.6-2/glmnetr/R/summary.cv.glmnetr_0_6_2_250525.R |only glmnetr-0.6-2/glmnetr/R/summary.cv.glmnetr_250818.R |only glmnetr-0.6-2/glmnetr/R/summary.nested.glmnetr_0_6_2_250804.R |only glmnetr-0.6-2/glmnetr/R/summary.nested.glmnetr_250525.R |only glmnetr-0.6-2/glmnetr/build/vignette.rds |binary glmnetr-0.6-2/glmnetr/inst/doc/An_Overview_of_glmnetr_250818.pdf |only glmnetr-0.6-2/glmnetr/inst/doc/An_Overview_of_glmnetr_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/inst/doc/Calibration_250818.pdf |only glmnetr-0.6-2/glmnetr/inst/doc/Calibration_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/inst/doc/Elastic_net_models_250818.pdf |only glmnetr-0.6-2/glmnetr/inst/doc/Elastic_net_models_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/inst/doc/Ridge_and_Lasso_250818.pdf |only glmnetr-0.6-2/glmnetr/inst/doc/Ridge_and_Lasso_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/inst/doc/Using_ann_tab_cv_250818.pdf |only glmnetr-0.6-2/glmnetr/inst/doc/Using_ann_tab_cv_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/inst/doc/Using_stepreg_250818.pdf |only glmnetr-0.6-2/glmnetr/inst/doc/Using_stepreg_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/man/calplot.Rd | 16 - glmnetr-0.6-2/glmnetr/man/cv.glmnetr.Rd | 6 glmnetr-0.6-2/glmnetr/man/glmnetr.cis.Rd | 2 glmnetr-0.6-2/glmnetr/man/glmnetr.compcv.Rd | 2 glmnetr-0.6-2/glmnetr/man/nested.cis.Rd | 14 + glmnetr-0.6-2/glmnetr/man/nested.compare.Rd | 6 glmnetr-0.6-2/glmnetr/man/nested.glmnetr.Rd | 21 - glmnetr-0.6-2/glmnetr/man/plot_perf_glmnetr.Rd | 2 glmnetr-0.6-2/glmnetr/man/predict.cv.glmnetr.Rd | 2 glmnetr-0.6-2/glmnetr/man/print.nested.glmnetr.Rd | 2 glmnetr-0.6-2/glmnetr/man/roundperf.Rd | 2 glmnetr-0.6-2/glmnetr/man/summary.cv.glmnetr.Rd | 2 glmnetr-0.6-2/glmnetr/man/summary.nested.glmnetr.Rd | 2 glmnetr-0.6-2/glmnetr/vignettes/An_Overview_of_glmnetr_250818.Rmd |only glmnetr-0.6-2/glmnetr/vignettes/An_Overview_of_glmnetr_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/vignettes/Calibration_250818.Rmd |only glmnetr-0.6-2/glmnetr/vignettes/Calibration_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/vignettes/Elastic_net_models_250818.Rmd |only glmnetr-0.6-2/glmnetr/vignettes/Elastic_net_models_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/vignettes/Ridge_and_Lasso_250818.Rmd |only glmnetr-0.6-2/glmnetr/vignettes/Ridge_and_Lasso_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/vignettes/Using_ann_tab_cv_250818.Rmd |only glmnetr-0.6-2/glmnetr/vignettes/Using_ann_tab_cv_250818.pdf.asis |only glmnetr-0.6-2/glmnetr/vignettes/Using_stepreg_250818.Rmd |only glmnetr-0.6-2/glmnetr/vignettes/Using_stepreg_250818.pdf.asis |only 99 files changed, 141 insertions(+), 114 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service <https://crunch.io/> provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Greg Freedman Ellis [aut, cre],
Jonathan Keane [aut],
Mike Malecki [aut],
Neal Richardson [aut],
Gordon Shotwell [aut],
Aljaz Sluga [aut]
Maintainer: Greg Freedman Ellis <greg@crunch.io>
Diff between crunch versions 1.31.0 dated 2025-03-18 and 1.31.1 dated 2025-08-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/export-dataset.R | 35 +++++++++++++++++++++++++++++++++-- R/show.R | 2 ++ tests/testthat/test-api.R | 8 -------- tests/testthat/test-as-data-frame.R | 1 + tests/testthat/test-export-dataset.R | 25 ++++++------------------- 7 files changed, 51 insertions(+), 38 deletions(-)
Title: Crafting Print-Ready Maps and Layered Visualizations
Description: Simplifying the creation of print-ready maps, this package offers a user-friendly interface derived from 'ggplot2' for handling OpenStreetMap data. It streamlines the map-making process, allowing users to focus on the story their maps tell. Transforming raw geospatial data into informative visualizations is made easy with simple features 'sf' geometries. Whether for urban planning, environmental studies, or impactful public presentations, this tool facilitates straightforward and effective map creation. Enhance the dissemination of spatial information with high-quality, narrative-driven visualizations!
Author: David Willinger [aut, cre, cph]
Maintainer: David Willinger <david.willinger@gmail.com>
Diff between cartographr versions 0.2.2 dated 2024-06-28 and 0.2.3 dated 2025-08-19
DESCRIPTION | 10 ++++----- MD5 | 14 ++++++------- NEWS.md | 10 ++++++++- build/vignette.rds |binary inst/doc/cartographr.R | 40 +++++++++++++++++++------------------- inst/doc/cartographr.html | 4 +-- tests/testthat/test-cartographr.R | 2 - tests/testthat/test-utils.R | 2 - 8 files changed, 45 insertions(+), 37 deletions(-)
Title: Bayesian Parameter Estimation and Forecasting for
Epidemiological Models
Description: Methods for Bayesian parameter estimation and forecasting in epidemiological models.
Functions enable model fitting using Bayesian methods and generate forecasts with uncertainty quantification.
Implements approaches described in <doi:10.48550/arXiv.2411.05371> and <doi:10.1002/sim.9164>.
Author: Hamed Karami [aut],
Amanda Bleichrodt [aut],
Ruiyan Luo [aut],
Gerardo Chowell [aut, cre]
Maintainer: Gerardo Chowell <gchowell@gsu.edu>
Diff between BayesianFitForecast versions 1.0.0 dated 2024-12-05 and 1.1.0 dated 2025-08-19
DESCRIPTION | 9 MD5 | 16 - build/vignette.rds |binary inst/extdata/option.R | 5 inst/scripts/run_MCMC.R | 36 +-- inst/scripts/run_analyzeResults.R | 343 +++++++++++++++++++++++++----- inst/scripts/stancreator.R | 431 ++++++++++++++++++++------------------ man/Run_MCMC.Rd | 2 man/Run_analyzeResults.Rd | 6 9 files changed, 557 insertions(+), 291 deletions(-)
More information about BayesianFitForecast at CRAN
Permanent link
Title: Nonparametric Estimation of the Yield Curve Evolution
Description: Nonparametric estimation of discount functions and yield curves from
transaction data of coupon paying bonds.
Koo, B., La Vecchia, D., & Linton, O. B. (2021) <doi:10.1016/j.jeconom.2020.04.014>
describe an application of this package using the Center for Research in
Security Prices (CRSP) Bond Data and document its implementation.
Author: Bonsoo Koo [aut],
Nathaniel Tomasetti [ctb],
Kai-Yang Goh [ctb],
Yangzhuoran Fin Yang [aut, cre]
Maintainer: Yangzhuoran Fin Yang <yangyangzhuoran@gmail.com>
Diff between ycevo versions 0.2.1 dated 2024-06-05 and 0.3.0 dated 2025-08-19
DESCRIPTION | 18 +- MD5 | 36 ++--- NAMESPACE | 5 NEWS.md | 7 R/assertion.R | 67 +++++---- R/augment.R | 199 ++++++++++++++++++++------- R/autoplot.R | 239 ++++++++++++++++++++++++++++++--- R/epa.R | 59 ++++---- R/estimation.R | 359 ++++++++++++++++++++++++++++++++------------------ R/preparation.R | 76 ++++++---- R/simulation.R | 183 ++++++++++++++++++------- R/util.R | 168 ++++++++++++++--------- R/ycevo-package.R | 8 - R/ycevo.R | 150 ++++++++++++-------- README.md | 326 ++++++++++++++++++++++----------------------- man/augment.ycevo.Rd | 2 man/autoplot.ycevo.Rd | 4 man/plot.ycevo.Rd |only man/predict.ycevo.Rd |only man/ycevo.Rd | 4 20 files changed, 1265 insertions(+), 645 deletions(-)
Title: Streamline Population Genomic and Genetic Analyses
Description: Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.
Author: Keaka Farleigh [aut, cph, cre] ,
Mason Murphy [aut, cph, ctb] ,
Christopher Blair [aut, cph, ctb] ,
Tereza Jezkova [aut, cph, ctb]
Maintainer: Keaka Farleigh <keakafarleigh@gmail.com>
Diff between PopGenHelpR versions 1.4.0 dated 2025-07-02 and 1.4.1 dated 2025-08-19
DESCRIPTION | 6 MD5 | 20 - NEWS.md | 10 R/Differentiation.R | 350 +++++++++++++------------ R/Heterozygosity.R | 32 +- R/Private.alleles.R | 5 README.md | 4 inst/doc/PopGenHelpR_vignette.R | 16 - inst/doc/PopGenHelpR_vignette.Rmd | 518 ++++++++++++++++++------------------- inst/doc/PopGenHelpR_vignette.html | 22 - vignettes/PopGenHelpR_vignette.Rmd | 518 ++++++++++++++++++------------------- 11 files changed, 772 insertions(+), 729 deletions(-)
Title: Predictor-Assisted Graphical Models under Error-in-Variables
Description: We consider the network structure detection for variables Y with auxiliary variables X accommodated, which are possibly subject to measurement error. The following three functions are designed to address various structures by different methods : one is NP_Graph() that is used for handling the nonlinear relationship between the responses and the covariates, another is Joint_Gaussian() that is used for correction in linear regression models via the Gaussian maximum likelihood, and the other Cond_Gaussian() is for linear regression models via conditional likelihood function.
Author: Wan-Yi Chang [aut, cre],
Li-Pang Chen [aut]
Maintainer: Wan-Yi Chang <jessica306a@gmail.com>
Diff between PAGE versions 0.3.0 dated 2025-07-30 and 0.4.0 dated 2025-08-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/Con_Gaussian.R | 39 ++++++++++++++++++++++++++++----------- man/Cond_Gaussian.Rd | 9 ++++++--- 4 files changed, 40 insertions(+), 20 deletions(-)
Title: Working with 'MCSim' Models
Description: Tools that facilitate ordinary differential equation (ODE) modeling in 'R'. This package allows one to perform simulations for ODE models that are encoded in the GNU 'MCSim' model specification language (Bois, 2009) <doi:10.1093/bioinformatics/btp162> using ODE solvers from the 'R' package 'deSolve' (Soetaert et al., 2010) <doi:10.18637/jss.v033.i09>.
Author: Dustin F. Kapraun [aut, cre] ,
Todd J. Zurlinden [aut] ,
Andrew J. Shapiro [aut] ,
Ryan D. Friese [aut] ,
Frederic Y. Bois [ctb] ,
Free Software Foundation, Inc. [cph]
Maintainer: Dustin F. Kapraun <kapraun.dustin@epa.gov>
Diff between MCSimMod versions 0.9.1 dated 2025-04-17 and 1.0 dated 2025-08-19
MCSimMod-0.9.1/MCSimMod/inst/doc/exponential_demo.R |only MCSimMod-0.9.1/MCSimMod/inst/doc/exponential_demo.Rmd |only MCSimMod-0.9.1/MCSimMod/inst/doc/exponential_demo.html |only MCSimMod-0.9.1/MCSimMod/inst/doc/quickstart.R |only MCSimMod-0.9.1/MCSimMod/inst/doc/quickstart.Rmd |only MCSimMod-0.9.1/MCSimMod/inst/doc/quickstart.html |only MCSimMod-0.9.1/MCSimMod/vignettes/exponential_demo.Rmd |only MCSimMod-0.9.1/MCSimMod/vignettes/quickstart.Rmd |only MCSimMod-1.0/MCSimMod/DESCRIPTION | 36 ++-- MCSimMod-1.0/MCSimMod/MD5 | 86 ++++++---- MCSimMod-1.0/MCSimMod/R/compileModel.R | 39 ++-- MCSimMod-1.0/MCSimMod/build/vignette.rds |binary MCSimMod-1.0/MCSimMod/inst/CITATION |only MCSimMod-1.0/MCSimMod/inst/doc/details.R |only MCSimMod-1.0/MCSimMod/inst/doc/details.Rmd |only MCSimMod-1.0/MCSimMod/inst/doc/details.html |only MCSimMod-1.0/MCSimMod/inst/doc/events_demo.R | 18 +- MCSimMod-1.0/MCSimMod/inst/doc/events_demo.Rmd | 26 +-- MCSimMod-1.0/MCSimMod/inst/doc/events_demo.html | 20 +- MCSimMod-1.0/MCSimMod/inst/doc/inputs_demo.R | 16 - MCSimMod-1.0/MCSimMod/inst/doc/inputs_demo.Rmd | 34 +-- MCSimMod-1.0/MCSimMod/inst/doc/inputs_demo.html | 33 +-- MCSimMod-1.0/MCSimMod/inst/doc/intro.R |only MCSimMod-1.0/MCSimMod/inst/doc/intro.Rmd |only MCSimMod-1.0/MCSimMod/inst/doc/intro.html |only MCSimMod-1.0/MCSimMod/inst/doc/model_specification.R |only MCSimMod-1.0/MCSimMod/inst/doc/model_specification.Rmd |only MCSimMod-1.0/MCSimMod/inst/doc/model_specification.html |only MCSimMod-1.0/MCSimMod/inst/doc/newt_cool_demo.R | 18 +- MCSimMod-1.0/MCSimMod/inst/doc/newt_cool_demo.Rmd | 30 +-- MCSimMod-1.0/MCSimMod/inst/doc/newt_cool_demo.html | 27 +-- MCSimMod-1.0/MCSimMod/inst/doc/pbpk_demo.R |only MCSimMod-1.0/MCSimMod/inst/doc/pbpk_demo.Rmd |only MCSimMod-1.0/MCSimMod/inst/doc/pbpk_demo.html |only MCSimMod-1.0/MCSimMod/inst/doc/pbpk_demo_plots.R |only MCSimMod-1.0/MCSimMod/inst/doc/pk1_demo.R | 24 +- MCSimMod-1.0/MCSimMod/inst/doc/pk1_demo.Rmd | 38 ++-- MCSimMod-1.0/MCSimMod/inst/doc/pk1_demo.html | 27 +-- MCSimMod-1.0/MCSimMod/inst/doc/pred_prey_demo.R | 22 +- MCSimMod-1.0/MCSimMod/inst/doc/pred_prey_demo.Rmd | 34 +-- MCSimMod-1.0/MCSimMod/inst/doc/pred_prey_demo.html | 29 +-- MCSimMod-1.0/MCSimMod/inst/extdata/pbpk_simple.model |only MCSimMod-1.0/MCSimMod/src/mod.c | 2 MCSimMod-1.0/MCSimMod/vignettes/ModelFiles.png |only MCSimMod-1.0/MCSimMod/vignettes/ModelFiles.pptx |only MCSimMod-1.0/MCSimMod/vignettes/ModelObjectFigure.png |only MCSimMod-1.0/MCSimMod/vignettes/ModelObjectFigure.pptx |only MCSimMod-1.0/MCSimMod/vignettes/ModelSpecificationComponents.png |only MCSimMod-1.0/MCSimMod/vignettes/ModelSpecificationComponents.pptx |only MCSimMod-1.0/MCSimMod/vignettes/amount_lost_vs_time.png |only MCSimMod-1.0/MCSimMod/vignettes/conc_comp_vs_time.png |only MCSimMod-1.0/MCSimMod/vignettes/conc_vb_vs_time.png |only MCSimMod-1.0/MCSimMod/vignettes/details.Rmd |only MCSimMod-1.0/MCSimMod/vignettes/events_demo.Rmd | 26 +-- MCSimMod-1.0/MCSimMod/vignettes/inputs_demo.Rmd | 34 +-- MCSimMod-1.0/MCSimMod/vignettes/intro.Rmd |only MCSimMod-1.0/MCSimMod/vignettes/model_specification.Rmd |only MCSimMod-1.0/MCSimMod/vignettes/newt_cool_demo.Rmd | 30 +-- MCSimMod-1.0/MCSimMod/vignettes/pbpk_basic_model_schematic.png |only MCSimMod-1.0/MCSimMod/vignettes/pbpk_basic_model_schematic.pptx |only MCSimMod-1.0/MCSimMod/vignettes/pbpk_demo.Rmd |only MCSimMod-1.0/MCSimMod/vignettes/pk1_demo.Rmd | 38 ++-- MCSimMod-1.0/MCSimMod/vignettes/pred_prey_demo.Rmd | 34 +-- 63 files changed, 360 insertions(+), 361 deletions(-)
Title: Continuous Time SEM - 'OpenMx' Based Functions
Description: Original 'ctsem' (continuous time structural equation modelling)
functionality, based on the 'OpenMx' software, as described in
Driver, Oud, Voelkle (2017) <doi:10.18637/jss.v077.i05>, with updated details in vignette.
Combines stochastic differential equations representing latent processes with
structural equation measurement models. These functions were split off from
the main package of 'ctsem', as the main package uses the 'rstan' package as a backend now --
offering estimation options from max likelihood to Bayesian.
There are nevertheless use cases for the wide format SEM style approach as offered here,
particularly when there are no individual differences in observation timing and the
number of individuals is large. For the main 'ctsem' package, see <https://cran.r-project.org/package=ctsem>.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsemOMX versions 1.0.6 dated 2023-12-05 and 1.0.7 dated 2025-08-19
ctsemOMX-1.0.6/ctsemOMX/R/ctPostPredict.R |only ctsemOMX-1.0.6/ctsemOMX/R/ctsem.R |only ctsemOMX-1.0.6/ctsemOMX/inst/doc/ctsem.R |only ctsemOMX-1.0.6/ctsemOMX/inst/doc/ctsem.pdf |only ctsemOMX-1.0.6/ctsemOMX/inst/doc/ctsem.rnw |only ctsemOMX-1.0.6/ctsemOMX/man/ctPostPredict.Rd |only ctsemOMX-1.0.6/ctsemOMX/vignettes/ctsem-concordance.tex |only ctsemOMX-1.0.6/ctsemOMX/vignettes/ctsem.rnw |only ctsemOMX-1.0.7/ctsemOMX/DESCRIPTION | 10 ctsemOMX-1.0.7/ctsemOMX/MD5 | 55 - ctsemOMX-1.0.7/ctsemOMX/NAMESPACE | 1 ctsemOMX-1.0.7/ctsemOMX/R/ctCI.R | 2 ctsemOMX-1.0.7/ctsemOMX/R/ctFit.R | 18 ctsemOMX-1.0.7/ctsemOMX/R/ctModelFromFit.R | 6 ctsemOMX-1.0.7/ctsemOMX/R/ctMultigroupFit.R | 14 ctsemOMX-1.0.7/ctsemOMX/R/ctRefineTo.R | 6 ctsemOMX-1.0.7/ctsemOMX/R/ctsemOMX-package.R | 8 ctsemOMX-1.0.7/ctsemOMX/R/plot.ctsemFit.R | 12 ctsemOMX-1.0.7/ctsemOMX/R/summary.ctsemFit.R | 12 ctsemOMX-1.0.7/ctsemOMX/build/vignette.rds |binary ctsemOMX-1.0.7/ctsemOMX/inst/doc/ctsemOMX.R |only ctsemOMX-1.0.7/ctsemOMX/inst/doc/ctsemOMX.pdf |only ctsemOMX-1.0.7/ctsemOMX/inst/doc/ctsemOMX.rnw |only ctsemOMX-1.0.7/ctsemOMX/man/ctFit.Rd | 398 ++++++------- ctsemOMX-1.0.7/ctsemOMX/man/ctModelFromFit.Rd | 52 - ctsemOMX-1.0.7/ctsemOMX/man/ctMultigroupFit.Rd | 206 +++--- ctsemOMX-1.0.7/ctsemOMX/man/ctPlot.Rd | 136 ++-- ctsemOMX-1.0.7/ctsemOMX/man/ctRefineTo.Rd | 56 - ctsemOMX-1.0.7/ctsemOMX/man/ctsemOMX.Rd | 110 +-- ctsemOMX-1.0.7/ctsemOMX/man/plot.ctsemFit.Rd | 168 ++--- ctsemOMX-1.0.7/ctsemOMX/man/plot.ctsemMultigroupFit.Rd | 42 - ctsemOMX-1.0.7/ctsemOMX/man/summary.ctsemFit.Rd | 108 +-- ctsemOMX-1.0.7/ctsemOMX/man/summary.ctsemMultigroupFit.Rd | 42 - ctsemOMX-1.0.7/ctsemOMX/vignettes/ctsemOMX-concordance.tex |only ctsemOMX-1.0.7/ctsemOMX/vignettes/ctsemOMX.rnw |only 35 files changed, 720 insertions(+), 742 deletions(-)
Title: Alternative and Fast ROC Analysis
Description: Alternative and fast algorithms for the analysis of receiver operating
characteristics curves (ROC curves) as described in Thomas et al. (2017)
<doi:10.1186/s41512-017-0017-y> and Thomas et al. (2023) <doi:10.1016/j.ajogmf.2023.101110>.
Author: Gregoire Thomas [aut, cre] ,
Robin Tuytten [ctb] ,
Jef Moerman [ctb],
Xavier Robin [cph] ,
Stefan Siegert [cph]
Maintainer: Gregoire Thomas <gregoire.thomas@SQU4RE.com>
Diff between alternativeROC versions 1.0.0 dated 2025-06-29 and 1.0.1 dated 2025-08-19
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS | 5 +++++ R/ci.R | 8 ++------ R/rocperf.R | 6 ++---- R/rocsesp.R |only build/partial.rdb |binary tests/testthat/test_rocperf_fun.R | 19 +++++++++++++++++-- 8 files changed, 37 insertions(+), 22 deletions(-)
More information about alternativeROC at CRAN
Permanent link
Title: Scalable Gaussian Process Regression with Hierarchical Shrinkage
Priors
Description: Efficient variational inference methods for fully Bayesian Gaussian
Process Regression (GPR) models with hierarchical shrinkage priors,
including the triple gamma prior for effective variable selection and
covariance shrinkage in high-dimensional settings. The package leverages normalizing
flows to approximate complex posterior distributions. For details on implementation,
see Knaus (2025) <doi:10.48550/arXiv.2501.13173>.
Author: Peter Knaus [aut, cre]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>
Diff between shrinkGPR versions 1.0.0 dated 2025-01-30 and 1.1 dated 2025-08-19
DESCRIPTION | 12 MD5 | 41 ++- NAMESPACE | 65 ++-- NEWS.md |only R/GPR_class.R | 34 -- R/TPR_class.R |only R/internal_utils.R | 2 R/kernel_funcs.R | 32 -- R/plot_functions.R |only R/pred_functions.R | 306 +++++++++++++++++++++- R/shrinkGPR.R | 20 - R/shrinkGPR_package.R | 139 ++++++++++ R/shrinkTPR.R |only R/simGPR.R | 29 +- R/sylvester.R | 50 +-- man/gen_marginal_samples.Rd |only man/gen_posterior_samples.Rd | 2 man/plot.shrinkGPR.Rd |only man/plot.shrinkGPR_marg_samples_1D.Rd |only man/plot.shrinkGPR_marg_samples_2D.Rd |only man/plot.shrinkTPR.Rd |only man/predict.shrinkTPR.Rd |only man/shrinkGPR.Rd | 459 +++++++++++++++++----------------- man/shrinkTPR.Rd |only man/simGPR.Rd | 173 ++++++------ tests/testthat/Rplots.pdf |only tests/testthat/test_shrinkGPR.R | 33 ++ tests/testthat/test_shrinkTPR.R |only 28 files changed, 931 insertions(+), 466 deletions(-)
Title: Pedigree Inference from SNPs
Description: Multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>
Diff between sequoia versions 2.11.2 dated 2024-05-28 and 3.0.3 dated 2025-08-19
sequoia-2.11.2/sequoia/man/CountAgeDif.Rd |only sequoia-2.11.2/sequoia/man/GetDummifiable.Rd |only sequoia-3.0.3/sequoia/DESCRIPTION | 10 sequoia-3.0.3/sequoia/MD5 | 162 sequoia-3.0.3/sequoia/NAMESPACE | 4 sequoia-3.0.3/sequoia/NEWS.md | 39 sequoia-3.0.3/sequoia/R/CalcBYprobs.R | 12 sequoia-3.0.3/sequoia/R/CalcMaxMismatch.R | 20 sequoia-3.0.3/sequoia/R/CalcOHLLR.R | 16 sequoia-3.0.3/sequoia/R/CalcPairLL.R | 195 sequoia-3.0.3/sequoia/R/CalcParentProbs.R |only sequoia-3.0.3/sequoia/R/CalcRped.R | 1 sequoia-3.0.3/sequoia/R/CheckGeno.R | 6 sequoia-3.0.3/sequoia/R/CheckLifeHist.R | 3 sequoia-3.0.3/sequoia/R/ComparePairs.R | 38 sequoia-3.0.3/sequoia/R/ComparePeds.R | 51 sequoia-3.0.3/sequoia/R/ConfProb.R | 176 sequoia-3.0.3/sequoia/R/CountGenerations.R | 3 sequoia-3.0.3/sequoia/R/DuplicateCheck.R | 16 sequoia-3.0.3/sequoia/R/ErrToM.R | 4 sequoia-3.0.3/sequoia/R/Err_RADseq.R |only sequoia-3.0.3/sequoia/R/EstEr.R | 2 sequoia-3.0.3/sequoia/R/GenoConvert.R | 11 sequoia-3.0.3/sequoia/R/GetMaybeRel.R | 16 sequoia-3.0.3/sequoia/R/MkAgePrior.R | 55 sequoia-3.0.3/sequoia/R/PedPolish.R | 13 sequoia-3.0.3/sequoia/R/PedToNum.R | 13 sequoia-3.0.3/sequoia/R/PlotAgePrior.R | 2 sequoia-3.0.3/sequoia/R/PlotPairLL.R | 2 sequoia-3.0.3/sequoia/R/PlotPedComp.R | 2 sequoia-3.0.3/sequoia/R/Prepare.R | 25 sequoia-3.0.3/sequoia/R/RelPlot.R | 2 sequoia-3.0.3/sequoia/R/SNPstats.R | 48 sequoia-3.0.3/sequoia/R/SeqListSummary.R | 4 sequoia-3.0.3/sequoia/R/Sequoia_F90wrappers.R | 8 sequoia-3.0.3/sequoia/R/Sequoia_Main.R | 170 sequoia-3.0.3/sequoia/R/SimGeno.R | 25 sequoia-3.0.3/sequoia/R/Utils.R | 13 sequoia-3.0.3/sequoia/R/WriteToFiles.R | 11 sequoia-3.0.3/sequoia/R/getAssignable.R | 153 sequoia-3.0.3/sequoia/R/getRelM.R | 16 sequoia-3.0.3/sequoia/build/vignette.rds |binary sequoia-3.0.3/sequoia/inst/doc/PedComp.html | 4 sequoia-3.0.3/sequoia/inst/doc/quick_start_example1.html | 46 sequoia-3.0.3/sequoia/inst/doc/vignette-age.R | 2 sequoia-3.0.3/sequoia/inst/doc/vignette-age.Rmd | 2 sequoia-3.0.3/sequoia/inst/doc/vignette-age.pdf |binary sequoia-3.0.3/sequoia/inst/doc/vignette-main.Rmd | 2094 +++-- sequoia-3.0.3/sequoia/inst/doc/vignette-main.pdf |binary sequoia-3.0.3/sequoia/inst/doc/vignette_mtDNA.pdf |binary sequoia-3.0.3/sequoia/man/CalcBYprobs.Rd | 12 sequoia-3.0.3/sequoia/man/CalcMaxMismatch.Rd | 12 sequoia-3.0.3/sequoia/man/CalcOHLLR.Rd | 28 sequoia-3.0.3/sequoia/man/CalcPairLL.Rd | 96 sequoia-3.0.3/sequoia/man/CalcParentProbs.Rd |only sequoia-3.0.3/sequoia/man/CheckLH.Rd | 3 sequoia-3.0.3/sequoia/man/ComparePairs.Rd | 7 sequoia-3.0.3/sequoia/man/DuplicateCheck.Rd | 5 sequoia-3.0.3/sequoia/man/ErrToM.Rd | 1 sequoia-3.0.3/sequoia/man/Err_RADseq.Rd |only sequoia-3.0.3/sequoia/man/EstConf.Rd | 36 sequoia-3.0.3/sequoia/man/EstEr.Rd | 1 sequoia-3.0.3/sequoia/man/FortifyPairs.Rd | 4 sequoia-3.0.3/sequoia/man/GenoConvert.Rd | 9 sequoia-3.0.3/sequoia/man/GetLLRAge.Rd | 13 sequoia-3.0.3/sequoia/man/GetMaybeRel.Rd | 23 sequoia-3.0.3/sequoia/man/GetRelM.Rd | 6 sequoia-3.0.3/sequoia/man/LLtoProb.Rd |only sequoia-3.0.3/sequoia/man/MakeAgePrior.Rd | 5 sequoia-3.0.3/sequoia/man/MkFortParams.Rd | 1 sequoia-3.0.3/sequoia/man/PedCompare.Rd | 2 sequoia-3.0.3/sequoia/man/PedPolish.Rd | 7 sequoia-3.0.3/sequoia/man/PedToNum.Rd | 4 sequoia-3.0.3/sequoia/man/ReOrderDums.Rd |only sequoia-3.0.3/sequoia/man/SimGeno.Rd | 15 sequoia-3.0.3/sequoia/man/SnpStats.Rd | 8 sequoia-3.0.3/sequoia/man/SummarySeq.Rd | 2 sequoia-3.0.3/sequoia/man/getAssignCat.Rd | 41 sequoia-3.0.3/sequoia/man/sequoia.Rd | 55 sequoia-3.0.3/sequoia/man/writeSeq.Rd | 4 sequoia-3.0.3/sequoia/src/Sequoia.f90 | 6216 ++++++++------- sequoia-3.0.3/sequoia/src/init.c | 56 sequoia-3.0.3/sequoia/src/pretty_R_print.c | 19 sequoia-3.0.3/sequoia/vignettes/sequoia_refs.bib | 11 sequoia-3.0.3/sequoia/vignettes/vignette-age.Rmd | 2 sequoia-3.0.3/sequoia/vignettes/vignette-main.Rmd | 2094 +++-- 86 files changed, 7828 insertions(+), 4465 deletions(-)
Title: Save and Retrieve Name-Value Pairs to and from a File
Description: Facilitates secret management by storing credentials in a dedicated file,
keeping them out of your code base.
The secrets are stored without encryption.
This package is compatible with secrets stored by the 'SecretsProvider' 'Python' package <https://pypi.org/project/SecretsProvider/>.
Author: Koen Greuell [aut, cre]
Maintainer: Koen Greuell <vlic@lifewatch.eu>
Diff between SecretsProvider versions 1.0.0 dated 2025-04-02 and 1.0.1 dated 2025-08-19
DESCRIPTION | 12 +++++++----- MD5 | 6 +++--- NEWS.md | 5 +++++ R/SecretsProvider.R | 2 +- 4 files changed, 16 insertions(+), 9 deletions(-)
More information about SecretsProvider at CRAN
Permanent link
Title: Graphical User Interface with Integrated 'Diagrammer' for
'Lavaan'
Description: Provides a graphical user interface with an
integrated diagrammer for latent variables from the 'lavaan' package.
It offers two core functions: first, lavaangui() launches a web application
that allows users to specify models by drawing path diagrams, fitting them,
assessing model fit, and more; second, plot_lavaan() creates
interactive path diagrams from models specified in 'lavaan'.
Karch (2024) <doi: 10.31234/osf.io/f4ary> contains a tutorial.
Author: Julian D. Karch [aut, cre, cph]
Maintainer: Julian D. Karch <j.d.karch@fsw.leidenuniv.nl>
Diff between lavaangui versions 0.2.5 dated 2025-07-15 and 0.2.6 dated 2025-08-19
lavaangui-0.2.5/lavaangui/inst/www/assets/index-cf36f4da.js |only lavaangui-0.2.6/lavaangui/DESCRIPTION | 8 +++--- lavaangui-0.2.6/lavaangui/MD5 | 10 ++++---- lavaangui-0.2.6/lavaangui/NEWS.md | 14 ++++++++---- lavaangui-0.2.6/lavaangui/R/start_app.R | 1 lavaangui-0.2.6/lavaangui/inst/www/assets/index-f9f1a2f2.js |only lavaangui-0.2.6/lavaangui/inst/www/index.html | 2 - 7 files changed, 21 insertions(+), 14 deletions(-)
Title: Lattice-Based Space-Filling Designs
Description: Lattice-based space-filling designs with fill or separation distance properties including
interleaved lattice-based minimax distance designs proposed in Xu He (2017)
<doi:10.1093/biomet/asx036>, interleaved lattice-based maximin distance designs
proposed in Xu He (2018) <doi:10.1093/biomet/asy069>, interleaved lattice-based
designs with low fill and high separation distance properties proposed in
Xu He (2024) <doi:10.1137/23M156940X>, (sliced) rotated sphere packing designs
proposed in Xu He (2017) <doi:10.1080/01621459.2016.1222289> and Xu He (2019)
<doi:10.1080/00401706.2018.1458655>, densest packing-based maximum projections
designs proposed in Xu He (2020) <doi:10.1093/biomet/asaa057> and Xu He (2018)
<doi:10.48550/arXiv.1709.02062>, maximin distance designs for mixed continuous,
ordinal, and binary variables proposed in Hui Lan and Xu He (2025)
<doi:10.48550/arXiv.2507.23405>, and optimized and regularly repeated lattice-based
Latin [...truncated...]
Author: Xu He [aut, cre],
Hui Lan [aut],
Junpeng Gong [aut],
Zhaohui Li [aut]
Maintainer: Xu He <hexu@amss.ac.cn>
Diff between LatticeDesign versions 3.0-1 dated 2025-02-07 and 4.0-1 dated 2025-08-19
LatticeDesign-3.0-1/LatticeDesign/man/LatticeDesign-package.Rd |only LatticeDesign-4.0-1/LatticeDesign/DESCRIPTION | 39 +- LatticeDesign-4.0-1/LatticeDesign/MD5 | 27 + LatticeDesign-4.0-1/LatticeDesign/NAMESPACE | 7 LatticeDesign-4.0-1/LatticeDesign/R/ILMmDMixVars.R |only LatticeDesign-4.0-1/LatticeDesign/R/InterleavedMaximinD.r | 137 +++++----- LatticeDesign-4.0-1/LatticeDesign/R/InterleavedMinimaxD.r | 36 -- LatticeDesign-4.0-1/LatticeDesign/R/LLHD.r |only LatticeDesign-4.0-1/LatticeDesign/man/CoprimeNumbers.Rd |only LatticeDesign-4.0-1/LatticeDesign/man/CriterionLLHD.Rd |only LatticeDesign-4.0-1/LatticeDesign/man/DPMPD.Rd | 2 LatticeDesign-4.0-1/LatticeDesign/man/InterleavedFillSepD.Rd | 14 - LatticeDesign-4.0-1/LatticeDesign/man/InterleavedMaximinMixedD.Rd |only LatticeDesign-4.0-1/LatticeDesign/man/LLHD.Rd |only LatticeDesign-4.0-1/LatticeDesign/man/LLHDpoints.Rd |only LatticeDesign-4.0-1/LatticeDesign/man/LRS.Rd | 4 LatticeDesign-4.0-1/LatticeDesign/man/ProjSepD.Rd | 2 LatticeDesign-4.0-1/LatticeDesign/src/Criterion.c |only LatticeDesign-4.0-1/LatticeDesign/src/init.c | 20 + 19 files changed, 152 insertions(+), 136 deletions(-)
Title: German Election Database (GERDA)
Description: Provides tools to download comprehensive datasets of local,
state, and federal election results in Germany from 1990 to 2025. The package
facilitates access to data on turnout, vote shares for major parties, and
demographic information across different levels of government (municipal, state,
and federal). It offers access to geographically harmonized datasets
that account for changes in municipal boundaries over time and incorporate
mail-in voting districts. Users can easily retrieve, clean, and standardize
German electoral data, making it ready for analysis. Data is sourced from
<https://github.com/awiedem/german_election_data>.
Author: Hanno Hilbig [aut, cre]
Maintainer: Hanno Hilbig <hhilbig@ucdavis.edu>
Diff between gerda versions 0.1.0 dated 2024-11-20 and 0.2.0 dated 2025-08-19
DESCRIPTION | 16 ++++--- MD5 | 30 ++++++++----- NAMESPACE | 1 NEWS.md |only R/gerda_data_list.R | 15 +++--- R/load_gerda_web.R | 28 ++++++++---- R/party_crosswalk.R |only R/sysdata.rda |only README.md | 16 +++++-- inst/doc/gerda.R | 10 ++++ inst/doc/gerda.Rmd | 40 +++++++++++++++++ inst/doc/gerda.html | 110 +++++++++++++++++++++++++++++++++++-------------- man/load_gerda_web.Rd | 4 + man/party_crosswalk.Rd |only tests |only vignettes/gerda.Rmd | 40 +++++++++++++++++ 16 files changed, 243 insertions(+), 67 deletions(-)
Title: Streamlining Data Access in Clinical Research
Description: Provides a consistent interface for connecting R to various
data sources including file systems and databases.
Designed for clinical research, 'connector' streamlines access to 'ADAM',
'SDTM' for example. It helps to deal with multiple data formats through a standardized API and centralized
configuration.
Author: Cervan Girard [aut, cre],
Aksel Thomsen [aut],
Vladimir Obucina [aut],
Novo Nordisk A/S [cph]
Maintainer: Cervan Girard <cgid@novonordisk.com>
Diff between connector versions 0.1.1 dated 2025-05-09 and 1.0.0 dated 2025-08-19
connector-0.1.1/connector/R/cnt_logger_add_logs.R |only connector-0.1.1/connector/R/cnt_logger_generics.R |only connector-0.1.1/connector/R/cnt_logger_log_dbi.R |only connector-0.1.1/connector/R/cnt_logger_log_fs.R |only connector-0.1.1/connector/R/utils-docs.R |only connector-0.1.1/connector/R/utils-roxygen.R |only connector-0.1.1/connector/man/list_content_cnt.ConnectorLogger.Rd |only connector-0.1.1/connector/man/log_list_content_connector.Rd |only connector-0.1.1/connector/man/log_read_connector.ConnectorDBI.Rd |only connector-0.1.1/connector/man/log_read_connector.ConnectorFS.Rd |only connector-0.1.1/connector/man/log_read_connector.Rd |only connector-0.1.1/connector/man/log_read_connector.default.Rd |only connector-0.1.1/connector/man/log_remove_connector.ConnectorDBI.Rd |only connector-0.1.1/connector/man/log_remove_connector.ConnectorFS.Rd |only connector-0.1.1/connector/man/log_remove_connector.Rd |only connector-0.1.1/connector/man/log_remove_connector.default.Rd |only connector-0.1.1/connector/man/log_write_connector.ConnectorDBI.Rd |only connector-0.1.1/connector/man/log_write_connector.ConnectorFS.Rd |only connector-0.1.1/connector/man/log_write_connector.Rd |only connector-0.1.1/connector/man/log_write_connector.default.Rd |only connector-0.1.1/connector/man/print.ConnectorLogger.Rd |only connector-0.1.1/connector/man/read_cnt.ConnectorLogger.Rd |only connector-0.1.1/connector/man/remove_cnt.ConnectorLogger.Rd |only connector-0.1.1/connector/man/write_cnt.ConnectorLogger.Rd |only connector-1.0.0/connector/DESCRIPTION | 13 connector-1.0.0/connector/MD5 | 191 ++-- connector-1.0.0/connector/NAMESPACE | 10 connector-1.0.0/connector/NEWS.md | 27 connector-1.0.0/connector/R/cnt_generics.R | 57 - connector-1.0.0/connector/R/connect.R | 31 connector-1.0.0/connector/R/connect_utils.R | 1 connector-1.0.0/connector/R/connector-options.R | 18 connector-1.0.0/connector/R/connector.R | 6 connector-1.0.0/connector/R/connector_check_ressource.R |only connector-1.0.0/connector/R/connectors.R | 73 - connector-1.0.0/connector/R/conts_datasources.R | 74 + connector-1.0.0/connector/R/dbi_methods.R | 16 connector-1.0.0/connector/R/fs.R | 33 connector-1.0.0/connector/R/fs_methods.R | 128 ++- connector-1.0.0/connector/R/fs_read.R | 3 connector-1.0.0/connector/R/fs_write.R | 8 connector-1.0.0/connector/R/logger_add_logs.R |only connector-1.0.0/connector/R/logger_generics.R |only connector-1.0.0/connector/R/logger_log_dbi.R |only connector-1.0.0/connector/R/logger_log_fs.R |only connector-1.0.0/connector/R/use_connector.R |only connector-1.0.0/connector/R/utils_config.R | 135 +++ connector-1.0.0/connector/R/utils_docs.R |only connector-1.0.0/connector/R/utils_files.R | 30 connector-1.0.0/connector/R/utils_roxygen.R |only connector-1.0.0/connector/README.md | 45 - connector-1.0.0/connector/build/vignette.rds |binary connector-1.0.0/connector/inst/WORDLIST | 109 ++ connector-1.0.0/connector/inst/config/_connector.yml | 2 connector-1.0.0/connector/inst/config/_nested_connector.yml | 6 connector-1.0.0/connector/inst/doc/Consistent-API.R |only connector-1.0.0/connector/inst/doc/Consistent-API.Rmd |only connector-1.0.0/connector/inst/doc/Consistent-API.html |only connector-1.0.0/connector/inst/doc/connector.R | 157 --- connector-1.0.0/connector/inst/doc/connector.Rmd | 316 +------- connector-1.0.0/connector/inst/doc/connector.html | 394 ++-------- connector-1.0.0/connector/inst/doc/customize.Rmd | 15 connector-1.0.0/connector/inst/doc/customize.html | 191 ++-- connector-1.0.0/connector/inst/doc/without-yaml.R |only connector-1.0.0/connector/inst/doc/without-yaml.Rmd |only connector-1.0.0/connector/inst/doc/without-yaml.html |only connector-1.0.0/connector/man/ConnectorFS.Rd | 29 connector-1.0.0/connector/man/ConnectorLogger.Rd | 14 connector-1.0.0/connector/man/add_datasource.Rd | 3 connector-1.0.0/connector/man/add_logs.Rd | 8 connector-1.0.0/connector/man/add_metadata.Rd | 3 connector-1.0.0/connector/man/connect.Rd | 17 connector-1.0.0/connector/man/connector-options-params.Rd | 14 connector-1.0.0/connector/man/connector-options.Rd | 20 connector-1.0.0/connector/man/connectors.Rd | 8 connector-1.0.0/connector/man/create_directory_cnt.Rd | 3 connector-1.0.0/connector/man/datasources.Rd | 24 connector-1.0.0/connector/man/download_cnt.Rd | 32 connector-1.0.0/connector/man/download_directory_cnt.Rd | 28 connector-1.0.0/connector/man/extract_metadata.Rd |only connector-1.0.0/connector/man/list_content_cnt.Rd | 29 connector-1.0.0/connector/man/list_datasources.Rd |only connector-1.0.0/connector/man/log-functions.Rd |only connector-1.0.0/connector/man/read_cnt.Rd | 30 connector-1.0.0/connector/man/read_file.Rd | 3 connector-1.0.0/connector/man/remove_cnt.Rd | 24 connector-1.0.0/connector/man/remove_datasource.Rd | 10 connector-1.0.0/connector/man/remove_directory_cnt.Rd | 3 connector-1.0.0/connector/man/remove_metadata.Rd | 10 connector-1.0.0/connector/man/resource-validation.Rd |only connector-1.0.0/connector/man/tbl_cnt.Rd | 11 connector-1.0.0/connector/man/upload_cnt.Rd | 48 - connector-1.0.0/connector/man/upload_directory_cnt.Rd | 37 connector-1.0.0/connector/man/use_connector.Rd |only connector-1.0.0/connector/man/write_cnt.Rd | 28 connector-1.0.0/connector/man/write_datasources.Rd | 11 connector-1.0.0/connector/man/write_file.Rd | 2 connector-1.0.0/connector/tests/spelling.R | 3 connector-1.0.0/connector/tests/testthat/_snaps/connector.md | 216 +++++ connector-1.0.0/connector/tests/testthat/_snaps/metadata_connectors.md |only connector-1.0.0/connector/tests/testthat/_snaps/use_template.md |only connector-1.0.0/connector/tests/testthat/_snaps/utils_files.md | 106 ++ connector-1.0.0/connector/tests/testthat/helper.R | 3 connector-1.0.0/connector/tests/testthat/setup.R | 9 connector-1.0.0/connector/tests/testthat/test-cnt_logger_add_logs.R | 22 connector-1.0.0/connector/tests/testthat/test-cnt_logger_generics.R | 392 ++------- connector-1.0.0/connector/tests/testthat/test-cnt_logger_integration.R | 2 connector-1.0.0/connector/tests/testthat/test-cnt_logger_log_dbi.R | 5 connector-1.0.0/connector/tests/testthat/test-cnt_logger_log_fs.R | 18 connector-1.0.0/connector/tests/testthat/test-cnts_datasources.R | 21 connector-1.0.0/connector/tests/testthat/test-connect_utils.R | 20 connector-1.0.0/connector/tests/testthat/test-connector.R | 76 + connector-1.0.0/connector/tests/testthat/test-extract_function_info.R | 11 connector-1.0.0/connector/tests/testthat/test-fs.R | 21 connector-1.0.0/connector/tests/testthat/test-metadata_connectors.R |only connector-1.0.0/connector/tests/testthat/test-use_template.R |only connector-1.0.0/connector/tests/testthat/test-utils_files.R | 31 connector-1.0.0/connector/vignettes/Consistent-API.Rmd |only connector-1.0.0/connector/vignettes/connector.Rmd | 316 +------- connector-1.0.0/connector/vignettes/customize.Rmd | 15 connector-1.0.0/connector/vignettes/without-yaml.Rmd |only 121 files changed, 2081 insertions(+), 1744 deletions(-)
Title: Multivariate Lomax (Pareto Type II) and Its Related
Distributions
Description: Implements calculation of probability density function, cumulative distribution function, equicoordinate quantile function and survival function, and random numbers generation for the following multivariate distributions: Lomax (Pareto Type II), generalized Lomax, Mardia’s Pareto of Type I, Logistic, Burr, Cook-Johnson’s uniform, F and Inverted Beta. See Tapan Nayak (1987) <doi:10.2307/3214068>.
Author: Zhixin Lun [aut, cre] ,
Ravindra Khattree [aut]
Maintainer: Zhixin Lun <zhixin.lun@cuanschutz.edu>
This is a re-admission after prior archival of version 1.0.2 dated 2020-03-23
Diff between NonNorMvtDist versions 1.0.2 dated 2020-03-23 and 1.1.0 dated 2025-08-19
DESCRIPTION | 21 +++++------- MD5 | 16 ++++----- NAMESPACE | 94 +++++++++++++++++++++++++++--------------------------- R/MvtF.R | 2 - R/MvtGLomax.R | 2 - R/MvtInvBeta.R | 2 - man/MvtF.Rd | 2 - man/MvtGlomx.Rd | 2 - man/MvtInvBeta.Rd | 2 - 9 files changed, 71 insertions(+), 72 deletions(-)
Title: Generalized Additive Models for Location Scale and Shape
Description: Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Author: Mikis Stasinopoulos [aut, cre, cph] ,
Robert Rigby [aut] ,
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb],
Daniil Kiose [ctb] ,
Achim Zeileis [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>
Diff between gamlss versions 5.4-22 dated 2024-03-20 and 5.5-0 dated 2025-08-19
DESCRIPTION | 20 +- MD5 | 31 +-- NEWS.md | 9 + R/DropAddStepGAIC-Parallel.R | 13 - R/SUMMARY.R | 12 + R/chooseDistParallel.R | 177 ++++++++++----------- R/extra.R | 1 R/gamlss-5.R | 16 - R/gamlssVGD_23_12_21.R | 351 +++++++++++++++++++++++-------------------- R/gamlss_test.R |only R/lms.R | 106 +++++++----- R/predictAll_22_08_22.R | 11 - R/rqres.R | 14 + build/partial.rdb |binary man/LR.test.Rd | 5 man/acfResid.Rd | 2 man/gamlss.ps.Rd | 6 17 files changed, 426 insertions(+), 348 deletions(-)
Title: Download and Extract Data from US EPA's ECOTOX Database
Description: The US EPA ECOTOX database is a freely available database
with a treasure of aquatic and terrestrial ecotoxicological data.
As the online search interface doesn't come with an API, this
package provides the means to easily access and search the database
in R. To this end, all raw tables are downloaded from the EPA website
and stored in a local SQLite database <doi:10.1016/j.chemosphere.2024.143078>.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ECOTOXr versions 1.2.1 dated 2025-04-08 and 1.2.2 dated 2025-08-19
DESCRIPTION | 12 +-- MD5 | 30 ++++---- NEWS.md | 9 ++ README.md | 12 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ecotox-schema.html | 146 +++++++++++++++++++-------------------- inst/doc/reproducibility.html | 2 inst/doc/sanitising-ecotox.html | 18 ++-- inst/doc/searching-ecotox.R | 53 ++++++++++---- inst/doc/searching-ecotox.Rmd | 52 +++++++++++++ inst/doc/searching-ecotox.html | 97 ++++++++++++++++--------- tests/testthat/test_build.r | 2 tests/testthat/test_online.r | 6 - tests/testthat/test_sanitation.r | 2 vignettes/searching-ecotox.Rmd | 52 +++++++++++++ 16 files changed, 334 insertions(+), 159 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana [aut, cre] ,
Joan Salvador [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 4.9.1 dated 2024-10-30 and 4.10.0 dated 2025-08-19
DESCRIPTION | 17 MD5 | 70 +- NAMESPACE | 2 NEWS.md | 12 R/cGroupsWUI.R | 2 R/compare.i.R | 1162 ++++++++++++++++++----------------- R/compareGroups.R | 5 R/compareGroups.fit.R | 31 R/createTable.R | 5 R/descrTable.R | 2 R/export2md.R | 8 R/prepare.r | 13 R/table.i.R | 3 build/vignette.rds |binary inst/app/global.R | 9 inst/app/server.R | 32 inst/app/ui.R | 4 inst/doc/compareGroups_vignette.R | 32 inst/doc/compareGroups_vignette.Rmd | 47 - inst/doc/compareGroups_vignette.html | 778 +++++++++++------------ man/compareGroups-package.Rd | 4 man/compareGroups.Rd | 14 man/descrTable.Rd | 4 man/figures/var1age.pdf |binary man/figures/var1sex.pdf |binary vignettes/compareGroups_vignette.Rmd | 47 - vignettes/figures/bivar/age.png |binary vignettes/figures/bivar/sex.png |binary vignettes/figures/bivar/tmain.png |binary vignettes/figures/bivarsurv/age.png |binary vignettes/figures/bivarsurv/sex.png |binary vignettes/figures/example1.png |only vignettes/figures/example1docx.png |only vignettes/figures/example1pdf.png |only vignettes/figures/example1xlsx.png |only vignettes/figures/univar/age.png |binary vignettes/figures/univar/sex.png |binary vignettes/figures/univar/tmain.png |binary 38 files changed, 1219 insertions(+), 1084 deletions(-)
Title: Easy and Efficient Batch Processing of Regression Models
Description: Easily processes batches of univariate or multivariate
regression models. Returns results in a tidy format and generates
visualization plots for straightforward interpretation (Wang,
Shixiang, et al. (2021) <DOI:10.48550/arXiv.2110.14232>).
Author: Shixiang Wang [aut, cre] ,
Yun Peng [aut] ,
Chenyang Shu [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between bregr versions 1.0.0 dated 2025-06-28 and 1.2.0 dated 2025-08-19
DESCRIPTION | 15 MD5 | 109 - NAMESPACE | 24 NEWS.md | 35 R/00-bregr-package.R | 8 R/01-class.R | 78 R/02-pipeline.R | 436 +++- R/03-accessors.R | 168 + R/04-show-nomogram-helpers.R |only R/04-show.R | 1239 ++++++++++++- R/05-polar.R | 170 - R/06-avail.R | 74 R/07-diagnostics.R |only R/98-utils.R | 153 + README.md | 361 ++- build/vignette.rds |binary inst/doc/bregr-group-by.html | 16 inst/doc/model-config.R |only inst/doc/model-config.Rmd |only inst/doc/model-config.html |only inst/doc/quick-analyze-cancer-data.R |only inst/doc/quick-analyze-cancer-data.Rmd |only inst/doc/quick-analyze-cancer-data.html |only inst/doc/save-model-file.R |only inst/doc/save-model-file.Rmd |only inst/doc/save-model-file.html |only inst/doc/supported-models.R |only inst/doc/supported-models.Rmd |only inst/doc/supported-models.html |only man/accessors.Rd | 27 man/avails.Rd | 12 man/br_diagnose.Rd |only man/br_predict.Rd |only man/br_show_coxph_diagnostics.Rd |only man/br_show_fitted_line.Rd | 5 man/br_show_fitted_line_2d.Rd | 5 man/br_show_forest.Rd | 21 man/br_show_forest_circle.Rd |only man/br_show_forest_ggstats.Rd | 5 man/br_show_forest_ggstatsplot.Rd | 5 man/br_show_nomogram.Rd |only man/br_show_residuals.Rd |only man/br_show_risk_network.Rd | 5 man/br_show_survival_curves.Rd |only man/br_show_table.Rd | 5 man/br_show_table_gt.Rd | 7 man/bregr-package.Rd | 2 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-12-1.png |only man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/pipeline.Rd | 75 man/polar_connect.Rd | 8 man/polar_init.Rd | 20 man/print.breg.Rd | 2 tests/testthat/test-filter-variables.R |only tests/testthat/test-nomogram-interactions.R |only tests/testthat/test-nomogram.R |only tests/testthat/test-optimization.R |only tests/testthat/test-predict-survival.R |only tests/testthat/test-roxytest-testexamples-02-pipeline.R | 5 tests/testthat/test-roxytest-testexamples-03-accessors.R | 4 tests/testthat/test-roxytest-testexamples-04-show.R | 109 + tests/testthat/test-roxytest-testexamples-05-polar.R | 15 tests/testthat/test-roxytest-testexamples-07-diagnostics.R |only tests/testthat/test-survival-legend-order.R |only vignettes/model-config.Rmd |only vignettes/quick-analyze-cancer-data.Rmd |only vignettes/save-model-file.Rmd |only vignettes/supported-models.Rmd |only 72 files changed, 2686 insertions(+), 537 deletions(-)
Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).
Author: Rebecca Fisher [aut, cre] ,
Diego R. Barneche [aut] ,
Gerard F. Ricardo [aut] ,
David R. Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.1.3.0 dated 2024-08-19 and 2.1.3.1 dated 2025-08-19
DESCRIPTION | 19 +++++++++++-------- MD5 | 10 +++++----- R/bayesnec-package.R | 3 +-- build/vignette.rds |binary man/bayesnec-package.Rd | 19 +++++++++++++++++++ tests/testthat/test-model.frame.R | 24 ++++++++++++++++-------- 6 files changed, 52 insertions(+), 23 deletions(-)
Title: South Africa Macroeconomic Database API
Description: An R API providing access to a relational database with macroeconomic time series data for South Africa,
obtained from the South African Reserve Bank (SARB) and Statistics South Africa (STATSSA), and updated on a weekly basis
via the EconData <https://www.econdata.co.za/> platform and automated scraping of the SARB and STATSSA websites.
The database is maintained at the Department of Economics at Stellenbosch University.
Author: Sebastian Krantz [aut, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between samadb versions 0.3.0 dated 2024-05-24 and 0.3.1 dated 2025-08-19
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/accessdb.R | 8 ++++---- man/sm_expand_date.Rd | 2 +- man/sm_pivot_longer.Rd | 2 +- man/sm_pivot_wider.Rd | 2 +- man/sm_transpose.Rd | 2 +- 8 files changed, 22 insertions(+), 18 deletions(-)
Title: Markdown Parser and Renderer for R Graphics
Description: Provides the mean to parse and render markdown text with grid
along with facilities to define the styling of the text.
Author: Thomas Lin Pedersen [aut, cre] ,
Martin Mitas [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between marquee versions 1.0.0 dated 2025-01-20 and 1.1.0 dated 2025-08-19
DESCRIPTION | 34 - LICENSE | 2 MD5 | 92 +-- NEWS.md | 18 R/backports.R | 8 R/classic_style.R | 128 +++- R/element_marquee.R | 197 +++++-- R/geom_marquee.R | 116 +++- R/glue.R | 101 ++- R/grob.R | 830 ++++++++++++++++++++++--------- R/guide_marquee.R | 133 +++- R/images.R | 48 + R/ink.R | 8 R/parse.R | 13 R/style.R | 160 ++++- R/style_helpers.R | 24 R/style_set.R | 48 + README.md | 2 build/vignette.rds |binary inst/doc/marquee.R | 14 inst/doc/marquee.Rmd | 24 inst/doc/marquee.html | 9 inst/doc/marquee_style.R | 4 inst/doc/marquee_style.Rmd | 6 inst/doc/marquee_style.html | 7 inst/doc/marquee_syntax.R | 2 inst/doc/marquee_syntax.Rmd | 3 man/classic_style.Rd | 6 man/figures/README-unnamed-chunk-2-1.png |binary man/geom_marquee.Rd | 24 man/guide_marquee.Rd | 14 man/marquee-package.Rd | 2 man/marquee_parse.Rd | 7 man/style.Rd | 18 src/marquee.cpp | 14 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/parse/parsed.csv | 122 ++-- tests/testthat/test-element_marquee.R | 41 + tests/testthat/test-geom_marquee.R | 10 tests/testthat/test-glue.R | 25 tests/testthat/test-grob.R | 14 tests/testthat/test-guide_marquee.R | 23 tests/testthat/test-images.R | 4 tests/testthat/test-parse.R | 5 vignettes/marquee.Rmd | 24 vignettes/marquee_style.Rmd | 6 vignettes/marquee_syntax.Rmd | 3 47 files changed, 1761 insertions(+), 632 deletions(-)
Title: Estimate Functional and Stochastic Parameters of Linear Models
with Correlated Residuals and Missing Data
Description: Implements the Generalized Method of Wavelet Moments with Exogenous Inputs estimator (GMWMX) presented in Voirol, L., Xu, H., Zhang, Y., Insolia, L., Molinari, R. and Guerrier, S. (2024) <doi:10.48550/arXiv.2409.05160>.
The GMWMX estimator allows to estimate functional and stochastic parameters of linear models with correlated residuals in presence of missing data.
The 'gmwmx2' package provides functions to load and plot Global Navigation Satellite System (GNSS) data from the Nevada Geodetic Laboratory and functions to estimate linear model model with correlated residuals in presence of missing data.
Author: Lionel Voirol [aut, cre] ,
Haotian Xu [aut] ,
Yuming Zhang [aut] ,
Luca Insolia [aut] ,
Roberto Molinari [aut] ,
Stephane Guerrier [aut]
Maintainer: Lionel Voirol <lionelvoirol@hotmail.com>
Diff between gmwmx2 versions 0.0.2 dated 2025-04-10 and 0.0.3 dated 2025-08-19
DESCRIPTION | 22 ++++---- MD5 | 16 +++--- NEWS.md | 4 + R/gmwmx2.R | 43 ++++++++-------- build/vignette.rds |binary inst/doc/estimate_small_network.html | 90 +++++++++++++++++------------------ inst/doc/fit_model.html | 6 +- inst/doc/load_plot_data_ngl.html | 8 +-- man/plot.fit_gnss_ts_ngl.Rd | 2 9 files changed, 99 insertions(+), 92 deletions(-)
Title: Clinical Publication
Description: Accelerate the process from clinical data to medical publication,
including clinical data cleaning, significant result screening, and the
generation of publish-ready tables and figures.
Author: Yue Niu [aut, cre, cph] ,
Keyun Wang [aut]
Maintainer: Yue Niu <niuyuesam@163.com>
Diff between clinpubr versions 1.0.1 dated 2025-06-23 and 1.0.2 dated 2025-08-19
clinpubr-1.0.1/clinpubr/R/split_multichoice.r |only clinpubr-1.0.1/clinpubr/R/value_initial_cleaning.r |only clinpubr-1.0.1/clinpubr/tests/testthat/_snaps/split_multichoice.md |only clinpubr-1.0.1/clinpubr/tests/testthat/test-num_simple_cleaning.R |only clinpubr-1.0.1/clinpubr/tests/testthat/test-split_multichoice.r |only clinpubr-1.0.2/clinpubr/DESCRIPTION | 22 - clinpubr-1.0.2/clinpubr/LICENSE | 4 clinpubr-1.0.2/clinpubr/MD5 | 89 +++---- clinpubr-1.0.2/clinpubr/NAMESPACE | 5 clinpubr-1.0.2/clinpubr/NEWS.md | 30 ++ clinpubr-1.0.2/clinpubr/R/baseline_table.r | 122 +++++++--- clinpubr-1.0.2/clinpubr/R/classif_model_compare.r | 6 clinpubr-1.0.2/clinpubr/R/cut_by.r | 73 +++++ clinpubr-1.0.2/clinpubr/R/get_valid_subset.r | 10 clinpubr-1.0.2/clinpubr/R/initial_cleaning.r |only clinpubr-1.0.2/clinpubr/R/misc.r | 44 +++ clinpubr-1.0.2/clinpubr/R/multichoice.r |only clinpubr-1.0.2/clinpubr/R/rcs_plot.r | 31 +- clinpubr-1.0.2/clinpubr/R/subgroup_forest.r | 2 clinpubr-1.0.2/clinpubr/R/utils.R | 20 + clinpubr-1.0.2/clinpubr/README.md | 19 + clinpubr-1.0.2/clinpubr/man/baseline_table.Rd | 6 clinpubr-1.0.2/clinpubr/man/check_package.Rd |only clinpubr-1.0.2/clinpubr/man/combine_multichoice.Rd |only clinpubr-1.0.2/clinpubr/man/common_prefix.Rd |only clinpubr-1.0.2/clinpubr/man/cut_by.Rd | 20 + clinpubr-1.0.2/clinpubr/man/figures/README-example_3.2-1.png |binary clinpubr-1.0.2/clinpubr/man/figures/README-example_3.3-1.png |binary clinpubr-1.0.2/clinpubr/man/figures/README-example_3.3-2.png |binary clinpubr-1.0.2/clinpubr/man/figures/README-example_3.4-1.png |binary clinpubr-1.0.2/clinpubr/man/figures/README-example_3.4-2.png |binary clinpubr-1.0.2/clinpubr/man/figures/README-example_3.5-1.png |binary clinpubr-1.0.2/clinpubr/man/figures/README-example_3.6-1.png |binary clinpubr-1.0.2/clinpubr/man/figures/README-example_3.6-2.png |binary clinpubr-1.0.2/clinpubr/man/figures/README-example_3.6-3.png |binary clinpubr-1.0.2/clinpubr/man/figures/README-example_3.7-1.png |binary clinpubr-1.0.2/clinpubr/man/fill_with_last.Rd | 40 +-- clinpubr-1.0.2/clinpubr/man/first_mode.Rd | 46 +-- clinpubr-1.0.2/clinpubr/man/get_valid_subset.Rd | 3 clinpubr-1.0.2/clinpubr/man/indicate_duplicates.Rd |only clinpubr-1.0.2/clinpubr/man/rcs_plot.Rd | 4 clinpubr-1.0.2/clinpubr/man/split_multichoice.Rd | 2 clinpubr-1.0.2/clinpubr/man/str_match_replace.Rd | 56 ++-- clinpubr-1.0.2/clinpubr/man/test_normality.Rd |only clinpubr-1.0.2/clinpubr/man/value_initial_cleaning.Rd | 25 +- clinpubr-1.0.2/clinpubr/tests/testthat.R | 24 - clinpubr-1.0.2/clinpubr/tests/testthat/_snaps/multichoice.md |only clinpubr-1.0.2/clinpubr/tests/testthat/test-baseline_table.R | 3 clinpubr-1.0.2/clinpubr/tests/testthat/test-classif_model_compare.r | 16 + clinpubr-1.0.2/clinpubr/tests/testthat/test-cut_by.R | 55 ++++ clinpubr-1.0.2/clinpubr/tests/testthat/test-initial_cleaning.R |only clinpubr-1.0.2/clinpubr/tests/testthat/test-misc.R | 55 ++++ clinpubr-1.0.2/clinpubr/tests/testthat/test-multichoice.r |only 53 files changed, 611 insertions(+), 221 deletions(-)
Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses. See Sueur et al. (2008) <doi:10.1080/09524622.2008.9753600> and Sueur (2018) <doi:10.1007/978-3-319-77647-7>.
Author: Jerome Sueur [aut, cre],
Thierry Aubin [aut],
Caroline Simonis [aut],
Laurent Lellouch [ctr],
Pierre Aumond [ctr],
Adele de Baudouin [ctr],
Ethan C. Brown [ctr],
Guillaume Corbeau [ctr],
Marion Depraetere [ctr],
Camille Desjonqueres [ctr],
Francois F [...truncated...]
Maintainer: Jerome Sueur <sueur@mnhn.fr>
Diff between seewave versions 2.2.3 dated 2023-10-19 and 2.2.4 dated 2025-08-19
DESCRIPTION | 8 ++-- MD5 | 23 +++++++------ NEWS | 10 +++++- R/seewave.r | 70 ++++++++++++++++++++++++++++++++++++++++-- build/vignette.rds |binary inst/doc/seewave_IO.pdf |binary inst/doc/seewave_analysis.pdf |binary man/bstd.Rd |only man/noisew.Rd | 2 - man/oscillo.Rd | 2 - man/scd.Rd | 2 - man/synth.Rd | 2 - man/synth2.Rd | 2 - 13 files changed, 97 insertions(+), 24 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Utilities for common medical-statistics graphics
and tables, including automatic creation of publication-ready "Table 1"
summaries; transition (Sankey) plots; flow-chart helpers that extend the
grid package; Bézier lines and arrows; and a singular-value-decomposition-
based variable-selection method.
Author: Max Gordon [aut, cre]
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 3.0.3 dated 2023-08-25 and 3.0.4 dated 2025-08-19
DESCRIPTION | 28 ++-- MD5 | 56 ++++----- NEWS.md | 5 R/Gmisc.R | 3 R/bezierArrowGradient.R | 8 + R/descriptionStats.R | 4 R/mergeDesc.R | 2 build/vignette.rds |binary inst/doc/Descriptives.R | 6 - inst/doc/Descriptives.html | 8 - inst/doc/Grid-based_flowcharts.R | 4 inst/doc/Grid-based_flowcharts.html | 32 ++--- inst/doc/Transition-class.R | 2 inst/doc/Transition-class.Rmd | 4 inst/doc/Transition-class.html | 16 +- inst/doc/transitionPlot.R | 8 - inst/doc/transitionPlot.html | 22 +-- man/Gmisc-package.Rd | 13 ++ man/descGetMissing.Rd | 2 man/describeFactors.Rd | 4 man/describeMean.Rd | 2 man/describeMedian.Rd | 2 man/describeProp.Rd | 2 man/figCapNoLast.Rd | 4 man/figCapNoNext.Rd | 4 man/mergeDesc.Rd | 2 src/bezierArrowFn.cpp | 112 ++++++++++--------- tests/testthat/test-getDescriptionStats_tidyselect.R | 4 vignettes/Transition-class.Rmd | 4 29 files changed, 201 insertions(+), 162 deletions(-)
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 1.0.2 dated 2025-02-05 and 1.1.0 dated 2025-08-19
aifeducation-1.0.2/aifeducation/R/AIFEBaseModel.R |only aifeducation-1.0.2/aifeducation/R/DataManager.R |only aifeducation-1.0.2/aifeducation/R/FeatureExtractor.R |only aifeducation-1.0.2/aifeducation/R/LargeDataSetBase.R |only aifeducation-1.0.2/aifeducation/R/LargeDataSetForTextEmbeddings.R |only aifeducation-1.0.2/aifeducation/R/LargeDataSetForTexts.R |only aifeducation-1.0.2/aifeducation/R/TEClassifierProtoNet.R |only aifeducation-1.0.2/aifeducation/R/TEClassifierRegular.R |only aifeducation-1.0.2/aifeducation/R/TextEmbeddingModel.R |only aifeducation-1.0.2/aifeducation/R/dotAIFEDebertaTransformer.R |only aifeducation-1.0.2/aifeducation/R/sustainability.R |only aifeducation-1.0.2/aifeducation/R/utils_LargeDataSets.R |only aifeducation-1.0.2/aifeducation/R/utils_TeClassifier.R |only aifeducation-1.0.2/aifeducation/R/utils_doc_helpers.R |only aifeducation-1.0.2/aifeducation/R/utils_python_conda.R |only aifeducation-1.0.2/aifeducation/data/vignette_classifier.rda |only 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aifeducation-1.1.0/aifeducation/R/Studio_BaseModel_Train.R | 363 ++-- aifeducation-1.1.0/aifeducation/R/Studio_Classifier_Create.R | 650 +------ aifeducation-1.1.0/aifeducation/R/Studio_Classifier_Use.R | 7 aifeducation-1.1.0/aifeducation/R/Studio_DocumentationPage.R | 8 aifeducation-1.1.0/aifeducation/R/Studio_Error_Checks.R | 180 +- aifeducation-1.1.0/aifeducation/R/Studio_ExtendedTasks.R | 430 ---- aifeducation-1.1.0/aifeducation/R/Studio_FeatureExtractor_Create.R | 189 -- aifeducation-1.1.0/aifeducation/R/Studio_FeatureExtractor_Use.R | 4 aifeducation-1.1.0/aifeducation/R/Studio_License.R | 4 aifeducation-1.1.0/aifeducation/R/Studio_ProgressModal.R | 89 - aifeducation-1.1.0/aifeducation/R/Studio_Tabs_Classifier_Predict.R | 1 aifeducation-1.1.0/aifeducation/R/Studio_Tabs_DM_CreateTextDataSet.R | 13 aifeducation-1.1.0/aifeducation/R/Studio_Tabs_Description.R | 4 aifeducation-1.1.0/aifeducation/R/Studio_Tabs_Embed.R | 8 aifeducation-1.1.0/aifeducation/R/Studio_Tabs_Fill_Mask.R | 4 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Title: Adsorption Isotherm Model Fitting
Description: The Langmuir and Freundlich adsorption isotherms are pivotal in characterizing adsorption processes, essential across various scientific disciplines. Proper interpretation of adsorption isotherms involves robust fitting of data to the models, accurate estimation of parameters, and efficiency evaluation of the models, both in linear and non-linear forms. For researchers and practitioners in the fields of chemistry, environmental science, soil science, and engineering, a comprehensive package that satisfies all these requirements would be ideal for accurate and efficient analysis of adsorption data, precise model selection and validation for rigorous scientific inquiry and real-world applications. Details can be found in Langmuir (1918) <doi:10.1021/ja02242a004> and Giles (1973) <doi:10.1111/j.1478-4408.1973.tb03158.x>.
Author: Debopam Rakshit [aut, cre],
Arkaprava Roy [aut],
K. M. Manjaiah [aut],
Siba Prasad Datta [aut],
Ritwika Das [aut]
Maintainer: Debopam Rakshit <rakshitdebopam@yahoo.com>
Diff between AdIsMF versions 0.1.0 dated 2024-07-26 and 0.1.1 dated 2025-08-19
DESCRIPTION | 8 +- MD5 | 12 ++-- R/AdIsMF.R | 176 ++++++++++++++++++++++++++++++++---------------------------- man/FLM.Rd | 2 man/FNLM.Rd | 3 + man/LLM.Rd | 2 man/LNLM.Rd | 3 + 7 files changed, 115 insertions(+), 91 deletions(-)
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between yulab.utils versions 0.2.0 dated 2025-01-29 and 0.2.1 dated 2025-08-19
DESCRIPTION | 13 +++++++------ MD5 | 13 +++++++------ NAMESPACE | 3 +++ NEWS.md | 4 ++++ R/bib-ggtree.R | 4 ++-- R/os.R | 12 +++++++++++- R/utilities.R | 14 ++++++++++++++ man/user_dir.Rd |only 8 files changed, 48 insertions(+), 15 deletions(-)
Title: Force-Directed Euclidean Embedding of Dissimilarity Data
Description: A robust implementation of Topolow algorithm. It embeds objects into a low-dimensional Euclidean space from a matrix of pairwise dissimilarities, even when the data do not satisfy metric or Euclidean axioms. The package is particularly well-suited for sparse, incomplete, and censored (thresholded) datasets such as antigenic relationships. The core is a physics-inspired, gradient-free optimization framework that models objects as particles in a physical system, where observed dissimilarities define spring rest lengths and unobserved pairs exert repulsive forces. The package also provides functions specific to antigenic mapping to transform cross-reactivity and binding affinity measurements into accurate spatial representations in a phenotype space.
Key features include:
* Robust Embedding from Sparse Data: Effectively creates complete and consistent maps (in optimal dimensions) even with high proportions of missing data (e.g., >95%).
* Physics-Inspired Optimization: Models objects (e [...truncated...]
Author: Omid Arhami [aut, cre, cph]
Maintainer: Omid Arhami <omid.arhami@uga.edu>
Diff between topolow versions 1.0.0 dated 2025-07-11 and 2.0.0 dated 2025-08-19
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Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake',
'Azure Synapse Analytics Dedicated', 'Apache Spark', 'SQLite', and 'InterSystems IRIS'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.19.2 dated 2025-03-13 and 1.19.3 dated 2025-08-19
DESCRIPTION | 8 - MD5 | 10 - NEWS.md | 8 + inst/csv/replacementPatterns.csv | 7 - inst/doc/UsingSqlRender.pdf |binary tests/testthat/test-translate-iris.R | 242 ++++++++++++++++++----------------- 6 files changed, 149 insertions(+), 126 deletions(-)
Title: Sparse Projected Averaged Regression
Description: A flexible framework combining
variable screening and random projection techniques for fitting ensembles of
predictive generalized linear models to high-dimensional data.
Designed for extensibility, the package implements
key techniques as S3 classes with user-friendly constructors,
enabling easy integration and development of new procedures for
high-dimensional applications. For more details see
Parzer et al (2024a) <doi:10.48550/arXiv.2312.00130> and
Parzer et al (2024b) <doi:10.48550/arXiv.2410.00971>.
Author: Laura Vana-Guer [aut, cre] ,
Roman Parzer [aut] ,
Peter Filzmoser [aut]
Maintainer: Laura Vana-Guer <laura.vana.guer@tuwien.ac.at>
Diff between spareg versions 1.1.0 dated 2025-07-18 and 1.1.1 dated 2025-08-19
DESCRIPTION | 6 +- MD5 | 92 ++++++++++++++++++------------------ NEWS.md | 4 + R/rp_classes.R | 34 +++++++++---- R/screening_classes.R | 25 +++++++-- R/spareg.R | 84 +++++++++++++++++++++++++------- R/sparegcv.R | 50 ++++++++++++++++--- R/sparmodel_classes.R | 35 ++++++++++++- build/partial.rdb |binary inst/doc/spareg.R | 10 +-- inst/doc/spareg.Rnw | 12 ++-- inst/doc/spareg.pdf |binary man/coef.spar.Rd | 13 ++++- man/coef.spar.cv.Rd | 10 +++ man/constructor_randomprojection.Rd | 20 +++++++ man/constructor_screencoef.Rd | 18 ++++++- man/constructor_sparmodel.Rd | 21 +++++++- man/generate_cw.Rd | 4 - man/generate_gaussian.Rd | 4 - man/generate_sparse.Rd | 4 - man/get_coef.Rd | 11 +++- man/get_intercept.Rd | 11 +++- man/get_measure.Rd | 6 +- man/get_model.Rd | 10 ++- man/plot.spar.Rd | 15 +++++ man/plot.spar.cv.Rd | 17 ++++++ man/predict.spar.Rd | 8 ++- man/predict.spar.cv.Rd | 10 +++ man/print.coefspar.Rd | 6 +- man/print.randomprojection.Rd | 2 man/print.screencoef.Rd | 2 man/print.spar.Rd | 8 ++- man/print.spar.cv.Rd | 10 +++ man/rp_cw.Rd | 2 man/rp_gaussian.Rd | 2 man/rp_sparse.Rd | 2 man/screen_cor.Rd | 2 man/screen_glmnet.Rd | 2 man/screen_marglik.Rd | 2 man/spar.cv.Rd | 6 +- man/spar_glm.Rd | 8 ++- man/spar_glmnet.Rd | 9 +++ man/summary.coefspar.Rd | 6 +- tests/testthat/test-spareg.R | 56 ++++++++++++--------- tests/testthat/test-sparegcv.R | 82 +++++++++++--------------------- vignettes/spareg.Rnw | 12 ++-- vignettes/spareg.bib | 2 47 files changed, 519 insertions(+), 236 deletions(-)
Title: Classes and Methods for Simple Feature Objects that Have a Time
Column
Description: Classes and methods for spatial objects that have a registered time
column, in particular for irregular spatiotemporal data. The time column can
be of any type, but needs to be ordinal. Regularly laid out spatiotemporal
data (vector or raster data cubes) are handled by package 'stars'.
Author: Henning Teickner [aut, cre, cph] ,
Edzer Pebesma [aut, cph] ,
Benedikt Graeler [aut, cph]
Maintainer: Henning Teickner <henning.teickner@uni-muenster.de>
Diff between sftime versions 0.3.0 dated 2024-09-11 and 0.3.1 dated 2025-08-19
DESCRIPTION | 18 +++++----- MD5 | 10 ++--- NEWS.md | 4 ++ R/sftime.R | 4 +- inst/doc/sftime.html | 87 +++++++++++++++++++++++++-------------------------- man/st_as_sftime.Rd | 2 - 6 files changed, 66 insertions(+), 59 deletions(-)
Title: Regression Model Processing Port
Description: Provides R6 classes, methods and utilities to construct,
analyze, summarize, and visualize regression models.
Author: Shixiang Wang [aut, cre]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between regport versions 0.3.0 dated 2022-05-10 and 0.3.1 dated 2025-08-19
DESCRIPTION | 11 MD5 | 22 NEWS.md | 4 R/utils.R | 58 - README.md | 364 +++++------ man/REGModel.Rd | 488 +++++++-------- man/REGModelList.Rd | 390 +++++------ man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary tests/testthat/test-roxytest-testexamples-REGModel.R | 152 ++-- tests/testthat/test-roxytest-testexamples-REGModelList.R | 50 - 12 files changed, 773 insertions(+), 766 deletions(-)
Title: Public Key Infrastucture for R Based on the X.509 Standard
Description: Public Key Infrastucture functions such as verifying certificates, RSA encription and signing which can be used to build PKI infrastructure and perform cryptographic tasks.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between PKI versions 0.1-14 dated 2024-06-15 and 0.1-15 dated 2025-08-19
DESCRIPTION | 10 MD5 | 10 NEWS | 6 configure | 640 ++++++++++++++++++++++++++++++------------------------- configure.ac | 10 src/Makevars.win | 6 6 files changed, 390 insertions(+), 292 deletions(-)
Title: Pathways Longitudinal and Differential Analysis in Metabolomics
Description: Perform a differential analysis at pathway level based on
metabolite quantifications and information on pathway metabolite
composition. The method, described in Guilmineau et al (2025)
<doi:10.1186/s12859-025-06118-z> is based on a Principal Component
Analysis step and on a linear mixed model.
Automatic query of metabolic pathways is also implemented.
Author: Camille Guilmineau [aut],
Remi Servien [aut, cre] ,
Nathalie Vialaneix [aut]
Maintainer: Remi Servien <remi.servien@inrae.fr>
Diff between phoenics versions 0.5 dated 2025-01-29 and 0.6 dated 2025-08-19
DESCRIPTION | 33 MD5 | 48 - NAMESPACE | 80 - NEWS.md | 65 - R/data.R | 126 +- R/from_ASICS_to_PHOENICS.R | 128 +- R/overlap_coefficient.R | 262 ++--- R/pathwayRes-class.R | 500 +++++------ R/pathway_search.R | 212 ++-- R/test_pathway.R | 652 +++++++------- R/use_KEGGREST.R | 22 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 40 inst/adddata/ASICS_library_codes.txt | 438 ++++----- inst/doc/Introduction.R | 132 +-- inst/doc/Introduction.Rmd | 350 ++++--- inst/doc/Introduction.html | 1534 +++++++++++++++++------------------ man/MTBLS422.Rd | 128 +- man/from_ASICS_to_PHOENICS.Rd | 88 +- man/overlap_coefficient.Rd | 138 +-- man/pathwayRes.Rd | 188 ++-- man/pathway_search.Rd | 102 +- man/test_pathway.Rd | 243 ++--- vignettes/Introduction.Rmd | 350 ++++--- 25 files changed, 2939 insertions(+), 2920 deletions(-)
Title: Analyzing Survival Data from an Illness-Death Model
Description: Contains functions for data preparation,
prediction of transition probabilities,
estimating semi-parametric regression models
and for implementing nonparametric estimators
for other quantities. See Meira-Machado and
Roca-Pardiñas (2011) <doi:10.18637/jss.v038.i03>.
Author: Luis Meira-Machado [aut] ,
Javier Roca-Pardinas [aut] ,
Artur Araujo [ctb] ,
Gustavo Soutinho [ctb, cre]
Maintainer: Gustavo Soutinho <gustavosoutinho@sapo.pt>
Diff between p3state.msm versions 1.3.2 dated 2023-01-20 and 1.3.3 dated 2025-08-19
DESCRIPTION | 32 +++- MD5 | 26 +-- NAMESPACE | 24 ++- R/Biv.R | 1 R/data.creation.reg.R | 2 R/p3state.R | 8 + R/pLIDA.R | 1 R/plot.p3state.R | 344 +++++++++++++++++++++++++++----------------------- R/summary.p3state.R | 2 build/partial.rdb |binary inst/CITATION | 80 +++++------ inst/NEWS.Rd | 8 + man/heart2.Rd | 2 man/plot.p3state.Rd | 142 +++++++++----------- 14 files changed, 366 insertions(+), 306 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Marc Becker [cre, aut] ,
Lennart Schneider [aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3mbo versions 0.3.0 dated 2025-06-03 and 0.3.1 dated 2025-08-19
DESCRIPTION | 30 +++++++++---------- MD5 | 40 +++++++++++++------------- NEWS.md | 9 +++++ R/InputTrafoUnitcube.R | 2 - R/OptimizerADBO.R | 4 +- R/OptimizerAsyncMbo.R | 4 +- R/TunerADBO.R | 4 +- R/TunerAsyncMbo.R | 4 +- build/partial.rdb |binary man/mlr_optimizers_adbo.Rd | 4 +- man/mlr_optimizers_async_mbo.Rd | 4 +- man/mlr_tuners_adbo.Rd | 4 +- man/mlr_tuners_async_mbo.Rd | 4 +- tests/testthat/helper.R | 17 ++++++----- tests/testthat/test_AcqFunctionStochasticCB.R | 15 ++++++--- tests/testthat/test_AcqFunctionStochasticEI.R | 9 +++-- tests/testthat/test_OptimizerADBO.R | 3 + tests/testthat/test_OptimizerAsyncMbo.R | 8 +++-- tests/testthat/test_TunerADBO.R | 3 + tests/testthat/test_TunerAsyncMbo.R | 3 + tests/testthat/test_mbo_defaults.R | 25 ++++++++-------- 21 files changed, 118 insertions(+), 78 deletions(-)
Title: Translate R Expressions to 'MathML' and 'LaTeX'/'MathJax'
Description: Translate R expressions to 'MathML' or 'MathJax'/'LaTeX' so that
they can be rendered in R markdown documents and shiny apps. This package
depends on R package 'rolog', which requires an installation of the
'SWI'-'Prolog' runtime either from 'swi-prolog.org' or from R
package 'rswipl'.
Author: Matthias Gondan [aut, cre, cph] ,
Irene Alfarone [aut] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between mathml versions 1.5 dated 2025-06-13 and 1.6 dated 2025-08-19
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/mathml.R | 2 +- README.md | 16 ++++++++++++++-- build/vignette.rds |binary inst/doc/mathml.html | 5 +++-- inst/pl/lib/op.pl | 2 +- 8 files changed, 36 insertions(+), 17 deletions(-)
Title: Quasi Analysis of Variance for K-Functions
Description: One-way and two-way analysis of variance for replicated point
patterns, grouped by one or two classification factors, on the
basis of the corresponding K-functions.
Author: Rolf Turner [aut, cre]
Maintainer: Rolf Turner <rolfturner@posteo.net>
Diff between kanova versions 0.3-19 dated 2025-07-13 and 0.3-20 dated 2025-08-19
ChangeLog | 25 +++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 29 ++++++++++++++++------------- R/buildV.R | 1 - R/estSigsq.R | 21 ++++++++++++--------- R/iEngine.R | 2 +- R/permSumFns.R | 7 ++++++- R/resAndFit.R | 1 + inst/doc/testStat.pdf |binary inst/preVignettes/kanova.bib | 2 +- inst/preVignettes/testStat.bbl | 2 +- inst/preVignettes/testStat.blg | 2 +- inst/preVignettes/testStat.dvi |only inst/preVignettes/testStat.log | 4 ++-- inst/preVignettes/testStat.pdf |only inst/preVignettes/testStat.ps |only inst/preVignettes/testStat.tex | 2 +- 17 files changed, 71 insertions(+), 35 deletions(-)
Title: Genesys PGR Client
Description: Access data on plant genetic resources from genebanks around the world published on Genesys (<https://www.genesys-pgr.org>).
Your use of data is subject to terms and conditions available at <https://www.genesys-pgr.org/content/legal/terms>.
Author: Global Crop Diversity Trust [cph],
Matija Obreza [aut, cre],
Nora Castaneda [ctb]
Maintainer: Matija Obreza <matija.obreza@croptrust.org>
Diff between genesysr versions 2.1.1 dated 2024-02-23 and 2.2.0 dated 2025-08-19
genesysr-2.1.1/genesysr/man/api1_url.Rd |only genesysr-2.1.1/genesysr/man/dot-fetch_accessions_page.Rd |only genesysr-2.1.1/genesysr/man/dot-fetch_json_page.Rd |only genesysr-2.1.1/genesysr/man/fetch_accessions.Rd |only genesysr-2.2.0/genesysr/DESCRIPTION | 11 genesysr-2.2.0/genesysr/MD5 | 41 - genesysr-2.2.0/genesysr/NAMESPACE | 8 genesysr-2.2.0/genesysr/NEWS.md | 4 genesysr-2.2.0/genesysr/R/api-client.R | 48 + genesysr-2.2.0/genesysr/R/genesys.R | 324 ++++++------- genesysr-2.2.0/genesysr/R/validator.R | 47 - genesysr-2.2.0/genesysr/build/vignette.rds |binary genesysr-2.2.0/genesysr/inst/doc/tutorial.Rmd | 139 +++-- genesysr-2.2.0/genesysr/inst/doc/tutorial.html | 373 +++++++++++---- genesysr-2.2.0/genesysr/inst/doc/validation.Rmd | 4 genesysr-2.2.0/genesysr/inst/doc/validation.html | 8 genesysr-2.2.0/genesysr/man/SELECT_ALL_FIELDS.Rd |only genesysr-2.2.0/genesysr/man/SELECT_GEO_FIELDS.Rd |only genesysr-2.2.0/genesysr/man/SELECT_INFO_FIELDS.Rd |only genesysr-2.2.0/genesysr/man/dot-fieldsToSelect.Rd |only genesysr-2.2.0/genesysr/man/dot-list_accessions_page.Rd | 13 genesysr-2.2.0/genesysr/man/dot-postForm.Rd |only genesysr-2.2.0/genesysr/man/get_accessions.Rd | 44 - genesysr-2.2.0/genesysr/man/user_login.Rd | 12 genesysr-2.2.0/genesysr/vignettes/tutorial.Rmd | 139 +++-- genesysr-2.2.0/genesysr/vignettes/validation.Rmd | 4 26 files changed, 726 insertions(+), 493 deletions(-)
Title: Data Utilities for Congressional Research
Description: Provides easy-to-understand and consistent interfaces for
accessing data on the U.S. Congress. The functions in 'filibustr'
streamline the process for importing data on Congress into R, removing
the need to download and work from CSV files and the like. Data
sources include 'Voteview' (<https://voteview.com/>), the U.S. Senate
website (<https://www.senate.gov/>), and more.
Author: Max Feinleib [aut, cre, cph]
Maintainer: Max Feinleib <mhfeinleib@gmail.com>
Diff between filibustr versions 0.4.0 dated 2025-05-11 and 0.4.1 dated 2025-08-19
DESCRIPTION | 8 +++--- MD5 | 44 ++++++++++++++++++------------------- NEWS.md | 6 +++++ R/get_hvw_data.R | 4 +-- R/get_les.R | 4 +-- R/get_senate_cloture_votes.R | 2 - R/get_senate_sessions.R | 2 - R/get_voteview_member_votes.R | 4 +-- R/get_voteview_members.R | 6 ++--- R/get_voteview_parties.R | 6 ++--- R/get_voteview_rollcall_votes.R | 6 ++--- R/read_html_table.R | 3 +- R/utils_data_reading.R | 2 - build/partial.rdb |binary man/get_hvw_data.Rd | 4 ++- man/get_les.Rd | 4 ++- man/get_senate_cloture_votes.Rd | 2 + man/get_senate_sessions.Rd | 2 + man/get_voteview_member_votes.Rd | 5 ++-- man/get_voteview_members.Rd | 7 +++-- man/get_voteview_parties.Rd | 7 +++-- man/get_voteview_rollcall_votes.Rd | 7 +++-- man/read_html_table.Rd | 5 +++- 23 files changed, 81 insertions(+), 59 deletions(-)
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of spatially varying binomial probabilities, together with its extension, the Dirichlet Kernel Process (DKP), for categorical or multinomial data.
The package provides functions for model fitting, predictive inference with uncertainty quantification, posterior simulation, and visualization in one-and two-dimensional input spaces.
Multiple kernel functions (Gaussian, Matern 5/2, and Matern 3/2) are supported, with hyperparameters optimized through multi-start gradient-based search.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.1.0 dated 2025-07-23 and 0.1.1 dated 2025-08-19
BKP-0.1.0/BKP/man/figures/README-BKP-example-1.png |only BKP-0.1.0/BKP/man/figures/README-DKP-example-1.png |only BKP-0.1.0/BKP/man/figures/README-DKP-example-2.png |only BKP-0.1.0/BKP/man/figures/README-DKP-example-3.png |only BKP-0.1.1/BKP/DESCRIPTION | 32 - BKP-0.1.1/BKP/MD5 | 105 +++-- BKP-0.1.1/BKP/NAMESPACE | 79 ++-- BKP-0.1.1/BKP/NEWS.md | 9 BKP-0.1.1/BKP/R/BKP-package.R | 34 - BKP-0.1.1/BKP/R/fit_BKP.R | 404 +++++++++++---------- BKP-0.1.1/BKP/R/fit_DKP.R | 361 +++++++++--------- BKP-0.1.1/BKP/R/get_prior.R | 190 +++++---- BKP-0.1.1/BKP/R/get_prior_dkp.R | 8 BKP-0.1.1/BKP/R/kernel_matrix.R | 284 +++++++------- BKP-0.1.1/BKP/R/loss_fun.R | 160 ++++---- BKP-0.1.1/BKP/R/loss_fun_dkp.R | 145 +++---- BKP-0.1.1/BKP/R/plot_BKP.R | 102 +++-- BKP-0.1.1/BKP/R/plot_DKP.R | 139 ++++--- BKP-0.1.1/BKP/R/predict_BKP.R | 355 +++++++++--------- BKP-0.1.1/BKP/R/predict_DKP.R | 272 +++++++------- BKP-0.1.1/BKP/R/print_BKP.R | 11 BKP-0.1.1/BKP/R/print_DKP.R | 226 ++++++----- BKP-0.1.1/BKP/R/simulate_BKP.R | 312 ++++++++-------- BKP-0.1.1/BKP/R/summary_BKP.R | 184 ++++----- BKP-0.1.1/BKP/R/utils.R | 80 +++- BKP-0.1.1/BKP/README.md | 136 ++----- BKP-0.1.1/BKP/build |only BKP-0.1.1/BKP/inst |only BKP-0.1.1/BKP/man/BKP-package.Rd | 120 +++--- BKP-0.1.1/BKP/man/figures/elapsed_time.pdf |only BKP-0.1.1/BKP/man/figures/ex1.pdf |only BKP-0.1.1/BKP/man/figures/ex1_sim.pdf |only BKP-0.1.1/BKP/man/figures/ex1class001.pdf |only BKP-0.1.1/BKP/man/figures/ex1class2.pdf |only BKP-0.1.1/BKP/man/figures/ex2.pdf |only BKP-0.1.1/BKP/man/figures/ex2_sim.pdf |only BKP-0.1.1/BKP/man/figures/ex3.pdf |only BKP-0.1.1/BKP/man/figures/ex3_true.pdf |only BKP-0.1.1/BKP/man/figures/ex4.pdf |only BKP-0.1.1/BKP/man/figures/ex4LGP.pdf |only BKP-0.1.1/BKP/man/figures/ex4roc.pdf |only BKP-0.1.1/BKP/man/figures/ex4rocLGP.pdf |only BKP-0.1.1/BKP/man/figures/ex5.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class1.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class1_true.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class2.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class2_true.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class3.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class3_true.pdf |only BKP-0.1.1/BKP/man/figures/ex7.pdf |only BKP-0.1.1/BKP/man/figures/ex7LGP.pdf |only BKP-0.1.1/BKP/man/figures/ex7roc.pdf |only BKP-0.1.1/BKP/man/figures/ex7rocLGP.pdf |only BKP-0.1.1/BKP/man/fit.BKP.Rd | 21 - BKP-0.1.1/BKP/man/fit.DKP.Rd | 282 +++++++------- BKP-0.1.1/BKP/man/get_prior.Rd | 153 ++++--- BKP-0.1.1/BKP/man/get_prior_dkp.Rd | 169 ++++---- BKP-0.1.1/BKP/man/kernel_matrix.Rd | 186 ++++----- BKP-0.1.1/BKP/man/loss_fun.Rd | 133 +++--- BKP-0.1.1/BKP/man/loss_fun_dkp.Rd | 129 +++--- BKP-0.1.1/BKP/man/plot.Rd | 386 ++++++++++---------- BKP-0.1.1/BKP/man/predict.Rd | 368 +++++++++---------- BKP-0.1.1/BKP/man/print.Rd | 305 ++++++++------- BKP-0.1.1/BKP/man/simulate.Rd | 247 ++++++------ BKP-0.1.1/BKP/man/summary.Rd | 305 ++++++++------- BKP-0.1.1/BKP/tests/testthat/test-get_prior.R |only BKP-0.1.1/BKP/tests/testthat/test-get_prior_dkp.R |only BKP-0.1.1/BKP/vignettes |only 68 files changed, 3378 insertions(+), 3054 deletions(-)
Title: Beta Regression
Description: Beta regression for modeling beta-distributed dependent variables on the open unit interval (0, 1),
e.g., rates and proportions, see Cribari-Neto and Zeileis (2010) <doi:10.18637/jss.v034.i02>.
Moreover, extended-support beta regression models can accommodate dependent variables with
boundary observations at 0 and/or 1, see Kosmidis and Zeileis (2025) <doi:10.1093/jrsssc/qlaf039>.
For the classical beta regression model, alternative specifications are provided:
Bias-corrected and bias-reduced estimation, finite mixture models, and recursive partitioning for
beta regression, see Grün, Kosmidis, and Zeileis (2012) <doi:10.18637/jss.v048.i11>.
Author: Achim Zeileis [aut, cre] ,
Francisco Cribari-Neto [aut] ,
Bettina Gruen [aut] ,
Ioannis Kosmidis [aut] ,
Alexandre B. Simas [ctb] ,
Andrea V. Rocha [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between betareg versions 3.2-3 dated 2025-05-10 and 3.2-4 dated 2025-08-19
DESCRIPTION | 10 +++---- MD5 | 30 +++++++++++----------- NEWS.md | 16 ++++++++++++ R/betareg.R | 15 ++++++----- README.md | 32 ++++++++++++------------ inst/CITATION | 12 +++------ inst/doc/betareg.html | 8 +++--- inst/doc/betareg.qmd | 4 +-- man/LossAversion.Rd | 8 +++--- man/ReadingSkills.Rd | 10 +++---- man/betar_family.Rd | 12 ++++----- man/betareg.Rd | 8 +++--- man/residuals.betareg.Rd | 6 ++-- tests/Examples/betareg-Ex.Rout.save | 48 ++++++++++++++++++------------------ vignettes/betareg.bib | 4 +-- vignettes/betareg.qmd | 4 +-- 16 files changed, 122 insertions(+), 105 deletions(-)
Title: Collection of Utility Functions for Data Analysis and Computing
Description: Provides utility functions for data analysis and scientific computing. Includes functions for parallel processing, and other computational tasks to streamline workflows.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.0.7 dated 2025-07-20 and 0.1.2 dated 2025-08-19
thisutils-0.0.7/thisutils/R/import.R |only thisutils-0.0.7/thisutils/src/asMatrix.cpp |only thisutils-0.1.2/thisutils/DESCRIPTION | 8 thisutils-0.1.2/thisutils/MD5 | 67 thisutils-0.1.2/thisutils/NAMESPACE | 3 thisutils-0.1.2/thisutils/NEWS.md |only thisutils-0.1.2/thisutils/R/RcppExports.R | 86 + thisutils-0.1.2/thisutils/R/add_pkg_file.R | 33 thisutils-0.1.2/thisutils/R/as_matrix.R | 77 - thisutils-0.1.2/thisutils/R/computation.R | 118 + thisutils-0.1.2/thisutils/R/figlet.R | 27 thisutils-0.1.2/thisutils/R/log_message.R | 1105 +++++++++------- thisutils-0.1.2/thisutils/R/parallelize_fun.R | 15 thisutils-0.1.2/thisutils/R/reexport.R |only thisutils-0.1.2/thisutils/R/sparse_cor.R | 15 thisutils-0.1.2/thisutils/R/thisutils-package.R | 3 thisutils-0.1.2/thisutils/R/utils.R | 86 - thisutils-0.1.2/thisutils/README.md | 17 thisutils-0.1.2/thisutils/man/add_pkg_file.Rd | 32 thisutils-0.1.2/thisutils/man/as_matrix.Rd | 38 thisutils-0.1.2/thisutils/man/capitalize.Rd | 6 thisutils-0.1.2/thisutils/man/check_sparsity.Rd | 2 thisutils-0.1.2/thisutils/man/download.Rd | 5 thisutils-0.1.2/thisutils/man/figlet.Rd | 24 thisutils-0.1.2/thisutils/man/log_message.Rd | 325 +++- thisutils-0.1.2/thisutils/man/matrix_process.Rd |only thisutils-0.1.2/thisutils/man/matrix_to_table.Rd |only thisutils-0.1.2/thisutils/man/normalization.Rd | 6 thisutils-0.1.2/thisutils/man/parallelize_fun.Rd | 8 thisutils-0.1.2/thisutils/man/r_square.Rd | 6 thisutils-0.1.2/thisutils/man/remove_space.Rd | 8 thisutils-0.1.2/thisutils/man/simulate_sparse_matrix.Rd | 12 thisutils-0.1.2/thisutils/man/sparse_cor.Rd | 8 thisutils-0.1.2/thisutils/man/table_to_matrix.Rd |only thisutils-0.1.2/thisutils/man/thisutils-package.Rd | 3 thisutils-0.1.2/thisutils/man/try_get.Rd | 18 thisutils-0.1.2/thisutils/src/RcppExports.cpp | 52 thisutils-0.1.2/thisutils/src/matrix_to_table.cpp |only thisutils-0.1.2/thisutils/src/table_to_matrix.cpp |only 39 files changed, 1334 insertions(+), 879 deletions(-)
Title: Metabolomics Data Analysis Toolbox
Description: Functions for metabolomics data analysis: data preprocessing,
orthogonal signal correction, PCA analysis, PCA-DA analysis,
PLS-DA analysis, classification, feature selection, correlation
analysis, data visualisation and re-sampling strategies.
Author: Wanchang Lin [aut, cre]
Maintainer: Wanchang Lin <wanchanglin@hotmail.com>
Diff between mt versions 2.0-1.20 dated 2024-02-12 and 2.0-1.21 dated 2025-08-19
DESCRIPTION | 18 ++++++++++-------- MD5 | 22 +++++++++++----------- NEWS.md | 13 +++++++++---- man/cor.util.Rd | 2 +- man/data.visualisation.Rd | 2 +- man/grpplot.Rd | 2 +- man/mdsplot.Rd | 2 +- man/panel.elli.Rd | 4 ++-- man/panel.smooth.line.Rd | 2 +- man/pcaplot.Rd | 2 +- man/plot.pcalda.Rd | 2 +- man/plot.plsc.Rd | 2 +- 12 files changed, 40 insertions(+), 33 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd],
sungho Choi [aut],
Mingu Jee [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.5.14 dated 2025-07-30 and 0.5.16 dated 2025-08-19
DESCRIPTION | 10 - MD5 | 16 +- NAMESPACE | 15 ++ NEWS.md | 8 + R/jskm.R | 334 ++++++++++++++++++++++++++--------------------------- R/svyjskm.R | 87 +++++++------ inst/doc/jskm.html | 38 +++--- man/jskm.Rd | 2 man/svyjskm.Rd | 2 9 files changed, 269 insertions(+), 243 deletions(-)
Title: Query the GTEx Portal API
Description: A convenient R interface to the Genotype-Tissue Expression (GTEx)
Portal API. The GTEx project is a comprehensive public resource for studying
tissue-specific gene expression and regulation in human tissues. Through
systematic analysis of RNA sequencing data from 54 non-diseased tissue sites
across nearly 1000 individuals, GTEx provides crucial insights into the
relationship between genetic variation and gene expression. This data is
accessible through the GTEx Portal API enabling programmatic access to human
gene expression data. For more information on the API, see
<https://gtexportal.org/api/v2/redoc>.
Author: Alasdair Warwick [aut, cre, cph] ,
Benjamin Zuckerman [aut] ,
Abraham Olvera-Barrios [aut] ,
Chuin Ying Ung [aut] ,
Robert Luben [aut] ,
Zhian N. Kamvar [rev]
Maintainer: Alasdair Warwick <alasdair.warwick.19@ucl.ac.uk>
Diff between gtexr versions 0.2.0 dated 2025-04-23 and 0.2.1 dated 2025-08-19
DESCRIPTION | 22 - MD5 | 238 ++++++++--------- NEWS.md | 9 R/calculate_expression_quantitative_trait_loci.R | 4 R/calculate_ieqtls.R | 4 R/calculate_isqtls.R | 4 R/calculate_splicing_quantitative_trait_loci.R | 4 R/download.R | 4 R/get_annotation.R | 4 R/get_clustered_median_exon_expression.R | 4 R/get_clustered_median_gene_expression.R | 4 R/get_clustered_median_junction_expression.R | 4 R/get_clustered_median_transcript_expression.R | 4 R/get_collapsed_gene_model_exon.R | 4 R/get_dataset_info.R | 4 R/get_downloads_page_data.R | 4 R/get_eqtl_genes.R | 4 R/get_exons.R | 4 R/get_expression_pca.R | 4 R/get_file_list.R | 4 R/get_fine_mapping.R | 4 R/get_full_get_collapsed_gene_model_exon.R | 4 R/get_functional_annotation.R | 4 R/get_gene_expression.R | 4 R/get_gene_search.R | 4 R/get_genes.R | 4 R/get_genomic_features.R | 4 R/get_gwas_catalog_by_location.R | 4 R/get_image.R | 4 R/get_independent_eqtl.R | 4 R/get_linkage_disequilibrium_by_variant_data.R | 2 R/get_linkage_disequilibrium_data.R | 2 R/get_maintenance_message.R | 4 R/get_median_exon_expression.R | 4 R/get_median_gene_expression.R | 4 R/get_median_junction_expression.R | 4 R/get_median_transcript_expression.R | 4 R/get_multi_tissue_eqtls.R | 4 R/get_neighbor_gene.R | 4 R/get_news_item.R | 4 R/get_sample_biobank_data.R | 4 R/get_sample_datasets.R | 20 + R/get_service_info.R | 4 R/get_significant_single_tissue_eqtls.R | 4 R/get_significant_single_tissue_eqtls_by_location.R | 4 R/get_significant_single_tissue_ieqtls.R | 4 R/get_significant_single_tissue_isqtls.R | 4 R/get_significant_single_tissue_sqtls.R | 4 R/get_single_nucleus_gex.R | 4 R/get_single_nucleus_gex_summary.R | 4 R/get_sqtl_genes.R | 4 R/get_subject.R | 4 R/get_tissue_site_detail.R | 4 R/get_top_expressed_genes.R | 4 R/get_transcripts.R | 4 R/get_variant.R | 2 R/get_variant_by_location.R | 2 README.md | 5 inst/CITATION | 32 ++ inst/app/app.R | 35 ++ inst/doc/gtexr.R | 154 +++++------ inst/doc/gtexr.Rmd | 2 inst/doc/gtexr.html | 113 -------- inst/paper/paper.md | 12 man/calculate_expression_quantitative_trait_loci.Rd | 4 man/calculate_ieqtls.Rd | 4 man/calculate_isqtls.Rd | 4 man/calculate_splicing_quantitative_trait_loci.Rd | 4 man/download.Rd | 4 man/get_annotation.Rd | 4 man/get_clustered_median_exon_expression.Rd | 4 man/get_clustered_median_gene_expression.Rd | 4 man/get_clustered_median_junction_expression.Rd | 4 man/get_clustered_median_transcript_expression.Rd | 4 man/get_collapsed_gene_model_exon.Rd | 4 man/get_dataset_info.Rd | 4 man/get_downloads_page_data.Rd | 4 man/get_eqtl_genes.Rd | 4 man/get_exons.Rd | 4 man/get_expression_pca.Rd | 4 man/get_file_list.Rd | 4 man/get_fine_mapping.Rd | 4 man/get_full_get_collapsed_gene_model_exon.Rd | 4 man/get_functional_annotation.Rd | 4 man/get_gene_expression.Rd | 4 man/get_gene_search.Rd | 4 man/get_genes.Rd | 4 man/get_genomic_features.Rd | 4 man/get_gwas_catalog_by_location.Rd | 4 man/get_image.Rd | 4 man/get_independent_eqtl.Rd | 4 man/get_linkage_disequilibrium_by_variant_data.Rd | 2 man/get_linkage_disequilibrium_data.Rd | 2 man/get_maintenance_message.Rd | 4 man/get_median_exon_expression.Rd | 4 man/get_median_gene_expression.Rd | 4 man/get_median_junction_expression.Rd | 4 man/get_median_transcript_expression.Rd | 4 man/get_multi_tissue_eqtls.Rd | 4 man/get_neighbor_gene.Rd | 4 man/get_news_item.Rd | 4 man/get_sample_biobank_data.Rd | 4 man/get_sample_datasets.Rd | 4 man/get_service_info.Rd | 4 man/get_significant_single_tissue_eqtls.Rd | 4 man/get_significant_single_tissue_eqtls_by_location.Rd | 4 man/get_significant_single_tissue_ieqtls.Rd | 4 man/get_significant_single_tissue_isqtls.Rd | 4 man/get_significant_single_tissue_sqtls.Rd | 4 man/get_single_nucleus_gex.Rd | 4 man/get_single_nucleus_gex_summary.Rd | 4 man/get_sqtl_genes.Rd | 4 man/get_subject.Rd | 4 man/get_tissue_site_detail.Rd | 4 man/get_top_expressed_genes.Rd | 4 man/get_transcripts.Rd | 4 man/get_variant.Rd | 2 man/get_variant_by_location.Rd | 2 tests/testthat/test-get_sample_datasets.R | 59 ++-- vignettes/gtexr.Rmd | 2 120 files changed, 512 insertions(+), 603 deletions(-)
Title: Regression Helper Functions
Description: Methods for manipulating regression models and for describing these in a style adapted for medical journals.
Contains functions for generating an HTML table with crude and adjusted estimates, plotting hazard ratio, plotting model
estimates and confidence intervals using forest plots, extending this to comparing multiple models in a single forest plots.
In addition to the descriptive methods, there are functions for the robust covariance matrix provided by the 'sandwich'
package, a function for adding non-linearities to a model, and a wrapper around the 'Epi' package's Lexis() functions for
time-splitting a dataset when modeling non-proportional hazards in Cox regressions.
Author: Max Gordon [aut, cre],
Reinhard Seifert [aut]
Maintainer: Max Gordon <max@gforge.se>
Diff between Greg versions 2.0.2 dated 2024-01-29 and 2.0.3 dated 2025-08-19
DESCRIPTION | 8 +-- MD5 | 47 +++++++++---------- NEWS.md | 5 ++ R/Greg.R | 75 ++++++++++++++----------------- R/forestplotRegrObj_prForestplotPrep.R | 4 - R/printCrudeAndAdjustedModel.R | 6 +- R/private_functions.R | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/printCrudeAndAdjustedModel.html | 8 +-- inst/doc/timeSplitter.html | 58 +++++++++++------------ man/Greg-package.Rd | 59 ++++++++++++------------ man/caDescribeOpts.Rd | 6 +- man/prCaAddRefAndStat.Rd | 2 man/prCaAddReference.Rd | 2 man/prCaAddUserReferences.Rd | 2 man/prCaGetImputationCols.Rd | 2 man/prCaGetRowname.Rd | 2 man/prCaGetVnStats.Rd | 2 man/prCaPrepareCrudeAndAdjusted.Rd | 2 man/prCaSelectAndOrderVars.Rd | 2 man/prCaSetRownames.Rd | 2 man/prGetStatistics.Rd | 4 - tests/testthat/Rplots.pdf |only tests/testthat/test-forestplotRegrObj.R | 1 25 files changed, 153 insertions(+), 150 deletions(-)
Title: Codon Usage Bias Analysis
Description: A suite of functions for rapid and flexible analysis of codon
usage bias. It provides in-depth analysis at the codon level, including
relative synonymous codon usage (RSCU), tRNA weight calculations, machine
learning predictions for optimal or preferred codons, and visualization of
codon-anticodon pairing. Additionally, it can calculate various gene-
specific codon indices such as codon adaptation index (CAI), effective
number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation
index (tAI), mean codon stabilization coefficients (CSCg), and GC contents
(GC/GC3s/GC4d). It also supports both standard and non-standard genetic
code tables found in NCBI, as well as custom genetic code tables.
Author: Hong Zhang [aut, cre] ,
Mengyue Liu [aut],
Bu Zi [aut]
Maintainer: Hong Zhang <mt1022.dev@gmail.com>
Diff between cubar versions 1.1.0 dated 2024-12-07 and 1.2.0 dated 2025-08-19
cubar-1.1.0/cubar/man/plot_ca_pairing.Rd |only cubar-1.1.0/cubar/tests/testthat/test-plot_ca_pairing.R |only cubar-1.2.0/cubar/DESCRIPTION | 10 cubar-1.2.0/cubar/MD5 | 98 +-- cubar-1.2.0/cubar/NAMESPACE | 7 cubar-1.2.0/cubar/NEWS.md | 18 cubar-1.2.0/cubar/R/codon_info.R | 81 ++ cubar-1.2.0/cubar/R/codon_weight.R | 389 ++++++++++---- cubar-1.2.0/cubar/R/gene_index.R | 247 +++++--- cubar-1.2.0/cubar/R/sequences.R | 81 +- cubar-1.2.0/cubar/R/utils.R | 251 ++++++++- cubar-1.2.0/cubar/R/window.R | 60 +- cubar-1.2.0/cubar/README.md | 216 +++++-- cubar-1.2.0/cubar/build/vignette.rds |binary cubar-1.2.0/cubar/data/yeast_trna_gcn.rda |binary cubar-1.2.0/cubar/inst/doc/codon_optimization.R |only cubar-1.2.0/cubar/inst/doc/codon_optimization.Rmd |only cubar-1.2.0/cubar/inst/doc/codon_optimization.html |only cubar-1.2.0/cubar/inst/doc/cubar.R | 6 cubar-1.2.0/cubar/inst/doc/cubar.Rmd | 45 + cubar-1.2.0/cubar/inst/doc/cubar.html | 129 +++- cubar-1.2.0/cubar/inst/doc/non_standard_genetic_code.html | 9 cubar-1.2.0/cubar/man/ca_pairs.Rd |only cubar-1.2.0/cubar/man/check_cds.Rd | 34 - cubar-1.2.0/cubar/man/codon_optimize.Rd | 114 +++- cubar-1.2.0/cubar/man/count_codons.Rd | 19 cubar-1.2.0/cubar/man/create_codon_table.Rd | 28 - cubar-1.2.0/cubar/man/est_aau.Rd |only cubar-1.2.0/cubar/man/est_csc.Rd | 2 cubar-1.2.0/cubar/man/est_optimal_codons.Rd | 46 + cubar-1.2.0/cubar/man/est_rscu.Rd | 48 + cubar-1.2.0/cubar/man/est_trna_weight.Rd | 50 + cubar-1.2.0/cubar/man/extract_trna_gcn.Rd |only cubar-1.2.0/cubar/man/get_aau.Rd |only cubar-1.2.0/cubar/man/get_cai.Rd | 28 - cubar-1.2.0/cubar/man/get_codon_table.Rd | 30 - cubar-1.2.0/cubar/man/get_cscg.Rd | 2 cubar-1.2.0/cubar/man/get_dp.Rd | 2 cubar-1.2.0/cubar/man/get_enc.Rd | 32 - cubar-1.2.0/cubar/man/get_fop.Rd | 31 - cubar-1.2.0/cubar/man/get_gc.Rd | 15 cubar-1.2.0/cubar/man/get_gc3s.Rd | 4 cubar-1.2.0/cubar/man/get_gc4d.Rd | 4 cubar-1.2.0/cubar/man/get_tai.Rd | 36 + cubar-1.2.0/cubar/man/plot_ca_pairs.Rd |only cubar-1.2.0/cubar/man/rev_comp.Rd | 12 cubar-1.2.0/cubar/man/seq_to_codons.Rd | 12 cubar-1.2.0/cubar/man/show_codon_tables.Rd | 15 cubar-1.2.0/cubar/man/slide.Rd | 28 - cubar-1.2.0/cubar/man/slide_codon.Rd | 28 - cubar-1.2.0/cubar/tests/testthat/test-ca_pairs.R |only cubar-1.2.0/cubar/tests/testthat/test-data.R | 11 cubar-1.2.0/cubar/tests/testthat/test-est_trna_weight.R | 30 + cubar-1.2.0/cubar/tests/testthat/test-seq_to_codons.R | 6 cubar-1.2.0/cubar/vignettes/codon_optimization.Rmd |only cubar-1.2.0/cubar/vignettes/cubar.Rmd | 45 + 56 files changed, 1750 insertions(+), 609 deletions(-)
Title: Multivariate Normal Probabilities using Vecchia Approximation
Description: Under a different representation of the multivariate normal (MVN) probability, we can use the Vecchia approximation to sample the integrand at a linear complexity with respect to n. Additionally, both the SOV algorithm from Genz (92) and the exponential-tilting method from Botev (2017) can be adapted to linear complexity. The reference for the method implemented in this package is Jian Cao and Matthias Katzfuss (2024) "Linear-Cost Vecchia Approximation of Multivariate Normal Probabilities" <doi:10.48550/arXiv.2311.09426>. Two major references for the development of our method are Alan Genz (1992) "Numerical Computation of Multivariate Normal Probabilities" <doi:10.1080/10618600.1992.10477010> and Z. I. Botev (2017) "The Normal Law Under Linear Restrictions: Simulation and Estimation via Minimax Tilting" <doi:10.48550/arXiv.1603.04166>.
Author: Jian Cao [aut, cre],
Matthias Katzfuss [aut]
Maintainer: Jian Cao <jcao2416@gmail.com>
Diff between VeccTMVN versions 1.3.0 dated 2025-07-14 and 1.3.1 dated 2025-08-19
DESCRIPTION | 8 +++--- MD5 | 10 +++---- NEWS.md | 9 ++++-- R/mvnrnd_cwrap.R | 72 ++++++++++++++++++++++++++++--------------------------- R/rnd_TMVN.R | 4 +-- R/rnd_TMVT.R | 4 +-- 6 files changed, 56 insertions(+), 51 deletions(-)
Title: Graph Community Detection Methods into Systematic Conservation
Planning
Description: An innovative tool-set that incorporates graph community detection
methods into systematic conservation planning. It is designed to
enhance spatial prioritization by focusing on the protection of
areas with high ecological connectivity. Unlike traditional
approaches that prioritize individual planning units, 'priorCON'
focuses on clusters of features that exhibit strong ecological
linkages. The 'priorCON' package is built upon the 'prioritizr'
package <doi:10.32614/CRAN.package.prioritizr>, using commercial
and open-source exact algorithm solvers that ensure optimal
solutions to prioritization problems.
Author: Christos Adam [aut, cre] ,
Aggeliki Doxa [aut] ,
Nikolaos Nagkoulis [aut] ,
Maria Papazekou [aut] ,
Antonios D. Mazaris [aut] ,
Stelios Katsanevakis [aut]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between priorCON versions 0.1.5 dated 2025-04-20 and 0.1.6 dated 2025-08-19
DESCRIPTION | 22 ++--- MD5 | 30 +++--- NAMESPACE | 2 NEWS.md | 15 +++ R/functions_connect.R | 100 ++++++++++++++++++++--- README.md | 54 ++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.Rmd | 54 ++++++++++++ inst/doc/Introduction.html | 46 ++++++++++ man/get_cost_raster.Rd | 5 - man/get_features_raster.Rd | 5 - man/get_metrics.Rd | 15 ++- man/graph_connectivity_rasters.Rd |only tests/testthat/test-graph_connectivity_rasters.r |only vignettes/Introduction.Rmd | 54 ++++++++++++ vignettes/normalized_connectivity.png |only vignettes/original_connectivity.png |only 18 files changed, 360 insertions(+), 42 deletions(-)
Title: Spectral Response of Water Wells to Harmonic Strain and Pressure
Signals
Description: Provides tools to calculate the theoretical hydrodynamic response
of an aquifer undergoing harmonic straining or pressurization, or analyze
measured responses. There are
two classes of models here, designed for use with confined
aquifers: (1) for sealed wells, based on the model of
Kitagawa et al (2011, <doi:10.1029/2010JB007794>),
and (2) for open wells, based on the models of
Cooper et al (1965, <doi:10.1029/JZ070i016p03915>),
Hsieh et al (1987, <doi:10.1029/WR023i010p01824>),
Rojstaczer (1988, <doi:10.1029/JB093iB11p13619>),
Liu et al (1989, <doi:10.1029/JB094iB07p09453>), and
Wang et al (2018, <doi:10.1029/2018WR022793>). Wang's
solution is a special exception which
allows for leakage out of the aquifer
(semi-confined); it is equivalent to Hsieh's model
when there is no leakage (the confined case).
These models treat strain (or aquifer head) as an input to the
physical system, and fluid-pressure (or water height) as the output. The
applicable fre [...truncated...]
Author: Andrew J. Barbour [aut, cre] ,
Jonathan Kennel [ctb]
Maintainer: Andrew J. Barbour <andy.barbour@gmail.com>
Diff between kitagawa versions 3.1.2 dated 2024-01-29 and 3.1.3 dated 2025-08-19
DESCRIPTION | 15 ++- MD5 | 24 +++--- R/cross.R | 2 README.md | 10 +- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 5 + inst/doc/ResponseModels-knitr.pdf |binary inst/doc/Tohoku.Rmd | 2 inst/doc/Tohoku.html | 31 ++++---- man/cross_spectrum.Rd | 2 vignettes/ResponseModels-knitr.tex | 140 ++++++++++++++++++------------------- vignettes/Tohoku.Rmd | 2 13 files changed, 119 insertions(+), 114 deletions(-)
Title: Tools for Processing and Analyzing Files from the Hydrological
Catchment Model HYPE
Description: Work with model files (setup, input, output) from
the hydrological catchment model HYPE: Streamlined file import and export, standard
evaluation plot routines, diverse post-processing and aggregation routines
for hydrological model analysis. The HYPEtools package is also archived at <doi:10.5281/zenodo.7627955>
and can be cited in publications with Brendel et al. (2024) <doi:10.1016/j.envsoft.2024.106094>.
Author: Rene Capell [aut, cre] ,
Conrad Brendel [aut] ,
Jafet Andersson [ctb],
David Gustafsson [ctb],
Jude Musuuza [ctb],
Jude Lubega [ctb]
Maintainer: Rene Capell <hypetools.rene@smhi.se>
Diff between HYPEtools versions 1.6.5 dated 2025-05-05 and 1.6.6 dated 2025-08-19
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 11 +++++++++-- R/function_PlotAnnualRegime.R | 11 ++++++----- R/function_RunHYPE.R | 2 +- R/functioncollection_import.R | 38 ++++++++++++++++++++++---------------- R/methods_hydroGOF.R | 2 +- R/sysdata.rda |binary inst/doc/analyze_hype_ts.html | 2 +- inst/doc/basin_network.html | 2 +- inst/doc/plot_map_statistics.html | 4 ++-- man/GOF.Rd | 2 +- man/PlotAnnualRegime.Rd | 3 +++ man/ReadTimeOutput.Rd | 5 +---- man/RunHYPE.Rd | 2 +- 15 files changed, 67 insertions(+), 53 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 3.2.2 dated 2024-02-18 and 3.2.3 dated 2025-08-19
DESCRIPTION | 19 - MD5 | 148 +++++----- NEWS | 5 R/AffymetrixFileSet.R | 2 R/ChipEffectSet.calculateBaseline.R | 2 R/MatSmoothing.R | 15 - R/SmoothMultiarrayModel.R | 4 R/doCRMAv1.R | 2 R/doCRMAv2.R | 2 R/doFIRMA.R | 2 R/doGCRMA.R | 2 R/doRMA.R | 2 R/justRMA.R | 2 inst/testScripts/futures/Mapping10K_Xba142/11.AllelicCrosstalkCalibration.R | 4 inst/testScripts/futures/Mapping10K_Xba142/11.BasePositionNormalization.R | 4 inst/testScripts/futures/Mapping10K_Xba142/11.UniqueCDF.R | 4 man/AbstractProbeSequenceNormalization.Rd | 2 man/AdditiveCovariatesNormalization.Rd | 2 man/AffymetrixCdfFile.Rd | 16 - man/AffymetrixCelFile.Rd | 20 - man/AffymetrixCelSet.Rd | 22 - man/AffymetrixCelSetReporter.Rd | 2 man/AffymetrixCnChpSet.Rd | 2 man/AffymetrixFileSet.Rd | 4 man/AffymetrixPgfFile.Rd | 2 man/AlleleSummation.Rd | 2 man/AllelicCrosstalkCalibration.Rd | 2 man/AromaChipTypeAnnotationFile.Rd | 4 man/ArrayExplorer.Rd | 6 man/BackgroundCorrection.Rd | 2 man/ChipEffectFile.Rd | 2 man/ChipEffectGroupMerge.Rd | 2 man/ChipEffectSet.Rd | 4 man/CnagCfhFile.Rd | 4 man/CnagCfhSet.Rd | 8 man/DChipDcpSet.Rd | 2 man/DChipGenomeInformation.Rd | 2 man/DChipQuantileNormalization.Rd | 2 man/DChipSnpInformation.Rd | 2 man/FirmaModel.Rd | 4 man/FragmentEquivalentClassNormalization.Rd | 2 man/FragmentLengthNormalization.Rd | 2 man/GcContentNormalization.Rd | 2 man/GcRmaBackgroundCorrection.Rd | 2 man/GenericReporter.Rd | 6 man/GenomeInformation.Rd | 10 man/LimmaBackgroundCorrection.Rd | 2 man/MatNormalization.Rd | 2 man/MatSmoothing.Rd | 7 man/Model.Rd | 14 man/OpticalBackgroundCorrection.Rd | 2 man/ParameterCelSet.Rd | 4 man/ProbeLevelModel.Rd | 6 man/QualityAssessmentModel.Rd | 4 man/QuantileNormalization.Rd | 2 man/ReseqCrosstalkCalibration.Rd | 2 man/RmaBackgroundCorrection.Rd | 2 man/ScaleNormalization.Rd | 2 man/ScaleNormalization3.Rd | 2 man/SingleArrayUnitModel.Rd | 2 man/SmoothMultiarrayModel.Rd | 4 man/SnpInformation.Rd | 6 man/SpatialReporter.Rd | 2 man/TransformReport.Rd | 12 man/UgpGenomeInformation.Rd | 2 man/UnitModel.Rd | 2 man/UnitTypeScaleNormalization.Rd | 2 man/byPath.AffymetrixFileSet.Rd | 2 man/calculateBaseline.ChipEffectSet.Rd | 2 man/doCRMAv1.Rd | 2 man/doCRMAv2.Rd | 2 man/doFIRMA.Rd | 2 man/doGCRMA.Rd | 2 man/doRMA.Rd | 2 man/justRMA.Rd | 2 75 files changed, 238 insertions(+), 224 deletions(-)
More information about aroma.affymetrix at CRAN
Permanent link
Title: Threshold Model and Unit Root Tests in Cross-Section and Time
Series Data
Description: Threshold model, panel version of Hylleberg et al. (1990) <DOI:10.1016/0304-4076(90)90080-D> seasonal unit root tests, and panel unit root test of Chang (2002) <DOI:10.1016/S0304-4076(02)00095-7>.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between pdR versions 1.9.3 dated 2024-08-18 and 1.9.4 dated 2025-08-19
pdR-1.9.3/pdR/man/HEGY.test.Rd |only pdR-1.9.3/pdR/man/SeasComponent.Rd |only pdR-1.9.3/pdR/man/contts.Rd |only pdR-1.9.3/pdR/man/hegy.reg.Rd |only pdR-1.9.3/pdR/man/interpolpval.Rd |only pdR-1.9.3/pdR/man/lookupCVtable.Rd |only pdR-1.9.3/pdR/man/ret.Rd |only pdR-1.9.3/pdR/man/selPabic.Rd |only pdR-1.9.3/pdR/man/selPsignf.Rd |only pdR-1.9.4/pdR/DESCRIPTION | 10 pdR-1.9.4/pdR/MD5 | 17 pdR-1.9.4/pdR/NAMESPACE | 4 pdR-1.9.4/pdR/R/hegy.R | 1032 ++++++++----------------------------- pdR-1.9.4/pdR/man/ipsHEGY.Rd | 34 - 14 files changed, 254 insertions(+), 843 deletions(-)
Title: Estimation Methods for Markets in Equilibrium and Disequilibrium
Description: Provides estimation methods for markets in equilibrium and
disequilibrium. Supports the estimation of an equilibrium and
four disequilibrium models with both correlated and independent shocks.
Also provides post-estimation analysis tools, such as aggregation,
marginal effect, and shortage calculations. See Karapanagiotis (2024)
<doi:10.18637/jss.v108.i02> for an overview of the functionality
and examples. The estimation methods are based on full information
maximum likelihood techniques given in
Maddala and Nelson (1974) <doi:10.2307/1914215>. They are implemented
using the analytic derivative expressions calculated in
Karapanagiotis (2020) <doi:10.2139/ssrn.3525622>. Standard
errors can be estimated by adjusting for heteroscedasticity or clustering.
The equilibrium estimation constitutes a case of a system of linear,
simultaneous equations. Instead, the disequilibrium models replace the
market-clearing condition with a non-linear,
short-side rule and allow for differ [...truncated...]
Author: Pantelis Karapanagiotis [aut, cre]
Maintainer: Pantelis Karapanagiotis <pikappa.devel@gmail.com>
Diff between markets versions 1.1.5 dated 2024-02-17 and 1.1.6 dated 2025-08-19
DESCRIPTION | 14 MD5 | 40 - NEWS.md | 7 R/market_fit.R | 2 R/markets.R | 8 README.md | 287 ++++--- build/partial.rdb |binary build/vignette.rds |binary configure | 481 ++++++------ configure.ac | 2 inst/WORDLIST | 40 - inst/doc/basic_usage.R | 4 inst/doc/basic_usage.Rmd | 4 inst/doc/basic_usage.html | 1152 ++++++++++++++++--------------- inst/doc/market_clearing_assessment.html | 921 ++++++++++++------------ inst/doc/model_details.html | 607 ++++++++-------- inst/doc/package.html | 35 man/estimate.Rd | 2 man/markets.Rd | 10 tests/testthat/helper-common.R | 2 vignettes/basic_usage.Rmd | 4 21 files changed, 1891 insertions(+), 1731 deletions(-)
Title: Fast and Scalable Single Cell Differential Expression Analysis
using Mixed-Effects Models
Description: A fast and scalable linear mixed-effects model (LMM) estimation algorithm
for analysis of single-cell differential expression. The algorithm uses
summary-level statistics and requires less computer memory to fit the LMM.
Author: Changjiang Xu [aut, cre],
Delaram Pouyabahar [ctb],
Veronique Voisin [ctb],
Gary Bader [ctb]
Maintainer: Changjiang Xu <changjiang.xu@utoronto.ca>
Diff between FLASHMM versions 1.2.1 dated 2025-04-09 and 1.2.2 dated 2025-08-19
DESCRIPTION | 14 MD5 | 40 - NEWS.md | 2 R/lmm.R | 93 ++- R/lmmfit.R | 48 + R/lmmtest.R | 6 R/simuRNAseq.R | 33 - R/sslmm.R | 52 + README.md | 187 ++++-- inst/doc/FLASHMM-vignette.R | 220 ++++--- inst/doc/FLASHMM-vignette.Rmd | 465 ++++++++++------ inst/doc/FLASHMM-vignette.html | 1137 ++++++++++++++++++++++++----------------- man/figures |only man/lmm.Rd | 54 - man/lmmfit.Rd | 62 +- man/lmmtest.Rd | 6 man/simuRNAseq.Rd | 37 - man/sslmm.Rd | 29 - vignettes/FLASHMM-vignette.Rmd | 465 ++++++++++------ vignettes/reference.bib | 30 - 20 files changed, 1857 insertions(+), 1123 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12' preprocessed
datasets and 'HippUnfold' hippocampal segmentation outputs for a given
sample by restructuring the data values into a single file. The single
file can then be used by the package for analyses independently from
its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.4.0 dated 2025-07-29 and 1.4.1 dated 2025-08-19
DESCRIPTION | 14 ++--- MD5 | 21 ++++---- NAMESPACE | 3 - NEWS.md | 18 +++++-- R/CAT12vextract.R | 4 - R/DTSERIESvextract.R | 47 +++++++++--------- R/FSLRvextract.R | 47 +++++++++++------- inst/doc/VertexWiseR_surface_extraction.html | 68 +++++++++++++++------------ inst/python/read_cifti.py |only man/DTSERIESvextract.Rd | 11 +--- man/FSLRvextract.Rd | 14 ++--- vignettes/VertexWiseR_surface_extraction.Rmd | 20 +++---- 12 files changed, 144 insertions(+), 123 deletions(-)
Title: Data Unit Testing for R
Description: Test your data! An extension of the 'testthat' unit testing
framework with a family of functions and reporting tools for checking
and validating data frames.
Author: Danny Smith [aut, cre],
Kinto Behr [aut],
The Social Research Centre [cph]
Maintainer: Danny Smith <danny@gorcha.org>
Diff between testdat versions 0.4.2 dated 2023-09-03 and 0.4.3 dated 2025-08-19
DESCRIPTION | 8 LICENSE | 4 MD5 | 176 +-- NAMESPACE | 194 ++-- NEWS.md | 438 ++++----- R/chk-filter.R | 194 ++-- R/chk.R | 502 +++++----- R/comparison.R | 22 R/deprec-chk.R | 148 +-- R/deprec-expect.R | 314 +++--- R/deprec-reporter.R | 46 R/expect-chk.R | 286 ++--- R/expect-conditional.R | 212 ++-- R/expect-data.R | 108 +- R/expect-datacomp.R | 320 +++--- R/expect-exclusive.R | 216 ++-- R/expect-generic.R | 300 +++--- R/expect-labels.R | 252 ++--- R/expect-make.R | 118 +- R/expect-proportion.R | 352 +++---- R/expect-unique.R | 332 +++--- R/expect_depends.R | 146 +-- R/expectation.R | 248 ++--- R/reporter-excel.R | 186 +-- R/reporter-zzz.R | 164 +-- R/testdat-package.R | 44 R/utils.R | 36 R/zzz.R | 30 README.md | 198 ++-- build/vignette.rds |binary inst/doc/testdat.R | 278 ++--- inst/doc/testdat.Rmd | 658 ++++++------- inst/doc/testdat.html | 1535 ++++++++++++++++---------------- inst/test-testdat_example_test.R | 82 - man/chk-dates.Rd | 102 +- man/chk-defunct.Rd | 70 - man/chk-deprec.Rd | 70 - man/chk-dummy.Rd | 72 - man/chk-helper.Rd | 190 +-- man/chk-labels.Rd | 154 +-- man/chk-patterns.Rd | 94 - man/chk-text.Rd | 106 +- man/chk-uniqueness.Rd | 84 - man/chk-values.Rd | 128 +- man/conditional-expectations.Rd | 188 +-- man/data-params.Rd | 62 - man/datacomp-expectations.Rd | 192 ++-- man/date-expectations.Rd | 134 +- man/exclusivity-expectations.Rd | 178 +-- man/expect-defunct.Rd | 96 +- man/expect-deprec.Rd | 190 +-- man/expect_custom.Rd | 140 +- man/expect_depends.Rd | 150 +-- man/expect_make.Rd | 98 +- man/generic-expectations.Rd | 242 ++--- man/global-data.Rd | 118 +- man/label-expectations.Rd | 192 ++-- man/output_results_excel.Rd | 60 - man/pattern-expectations.Rd | 128 +- man/proportion-expectations.Rd | 272 ++--- man/reexports.Rd | 52 - man/reporter-deprec.Rd | 46 man/testdat-package.Rd | 104 +- man/text-expectations.Rd | 156 +-- man/uniqueness-expectations.Rd | 242 ++--- man/value-expectations.Rd | 154 +-- tests/testthat.R | 8 tests/testthat/test-chk.R | 10 tests/testthat/test-chk_filter.R | 66 - tests/testthat/test-chk_max_length.R | 6 tests/testthat/test-chk_pattern.R | 6 tests/testthat/test-chk_range.R | 42 tests/testthat/test-chk_values.R | 18 tests/testthat/test-expect-labels.R | 250 ++--- tests/testthat/test-expect-proportion.R | 92 - tests/testthat/test-expect-unique.R | 120 +- tests/testthat/test-expect-value.R | 20 tests/testthat/test-expect_base.R | 22 tests/testthat/test-expect_custom.R | 6 tests/testthat/test-expect_datacomp.R | 60 - tests/testthat/test-expect_depends.R | 100 +- tests/testthat/test-expect_exclusive.R | 46 tests/testthat/test-expect_generic.R | 18 tests/testthat/test-expect_make.R | 66 - tests/testthat/test-expect_range.R | 46 tests/testthat/test-pipe.R | 90 - tests/testthat/test-reporter_excel.R | 100 +- tests/testthat/test-testdata.R | 94 - vignettes/testdat.Rmd | 658 ++++++------- 89 files changed, 7182 insertions(+), 7173 deletions(-)
Title: Perform Pharmacokinetic Non-Compartmental Analysis
Description: Compute standard Non-Compartmental Analysis (NCA) parameters for
typical pharmacokinetic analyses and summarize them.
Author: Bill Denney [aut, cre] ,
Clare Buckeridge [aut],
Gerardo Jose Rodriguez [aut] ,
Sridhar Duvvuri [ctb]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between PKNCA versions 0.12.0 dated 2025-05-08 and 0.12.1 dated 2025-08-19
DESCRIPTION | 17 - MD5 | 115 +++---- NAMESPACE | 2 NEWS.md | 24 + R/001-add.interval.col.R | 4 R/PKNCA.R | 7 R/PKNCA.options.R | 9 R/aucint.R | 10 R/class-PKNCAresults.R | 2 R/exclude_nca.R | 292 ++++++++++--------- R/half.life.R | 51 ++- R/pk.calc.all.R | 37 +- R/pk.calc.simple.R | 6 R/pk.calc.urine.R | 2 R/unit-support.R | 14 README.md | 12 build/vignette.rds |binary inst/CITATION | 2 inst/doc/v01-introduction-and-usage.R | 5 inst/doc/v01-introduction-and-usage.Rmd | 5 inst/doc/v01-introduction-and-usage.html | 162 +++++----- inst/doc/v02-example-theophylline.html | 220 ++++++++------ inst/doc/v03-selection-of-calculation-intervals.html | 83 ++--- inst/doc/v04-sparse.html | 23 - inst/doc/v05-auc-calculation-with-PKNCA.html | 18 - inst/doc/v06-half-life-calculation-tobit.html | 63 ---- inst/doc/v06-half-life-calculation.Rmd | 1 inst/doc/v06-half-life-calculation.html | 36 +- inst/doc/v07-post-processing.html | 261 ++++++++-------- inst/doc/v07-unit-conversion.R | 8 inst/doc/v07-unit-conversion.Rmd | 25 + inst/doc/v07-unit-conversion.html | 29 + inst/doc/v08-data-imputation.html | 4 inst/doc/v22-time-to-steady-state.html | 4 inst/doc/v30-training-session.Rmd | 12 inst/doc/v30-training-session.html | 179 +++++------ inst/doc/v40-options-for-controlling-PKNCA.html | 30 + inst/doc/v60-PKNCA-validation.Rmd | 2 inst/doc/v60-PKNCA-validation.html | 50 +-- man/PKNCA.Rd | 9 man/exclude_nca.Rd | 26 - man/exclude_nca_by_param.Rd |only man/get_halflife_points.Rd | 11 man/pk.calc.cmax.Rd | 4 man/pk.calc.half.life.Rd | 10 man/pk.calc.tmax.Rd | 4 man/pk.nca.interval.Rd | 18 - tests/testthat/test-PKNCA.options.R | 1 tests/testthat/test-aucint.R | 18 + tests/testthat/test-class-PKNCAresults.R | 41 +- tests/testthat/test-exclude_nca.R | 157 +++++++++- tests/testthat/test-half.life.R | 125 ++++++++ tests/testthat/test-pk.calc.all.R | 18 - tests/testthat/test-unit-support.R | 19 + vignettes/v01-introduction-and-usage.Rmd | 5 vignettes/v06-half-life-calculation.Rmd | 1 vignettes/v07-unit-conversion.Rmd | 25 + vignettes/v30-training-session.Rmd | 12 vignettes/v60-PKNCA-validation.Rmd | 2 59 files changed, 1425 insertions(+), 907 deletions(-)
Title: Kernel Density Estimation with a Markov Chain Monte Carlo Sample
Description: Provides methods for selecting the optimal bandwidth in kernel density estimation for dependent samples, such as those generated by Markov chain Monte Carlo (MCMC). Implements a modified biased cross-validation (mBCV) approach that accounts for sample dependence, improving the accuracy of estimated density functions.
Author: Juhee Lee [aut, cre],
Hang J. Kim [aut],
Young-Min Kim [aut]
Maintainer: Juhee Lee <ljh988488@gmail.com>
Diff between KDEmcmc versions 0.0.1 dated 2025-04-24 and 0.0.2 dated 2025-08-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/mBCV.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Download and Visualize Essential Climate Change Data
Description: Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, methane, emissions, instrumental and proxy temperature records, sea levels, Arctic/Antarctic sea-ice, Hurricanes, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.html>, Vostok Paleo carbon dio [...truncated...]
Author: Hernando Cortina [aut, cre]
Maintainer: Hernando Cortina <hch@alum.mit.edu>
Diff between hockeystick versions 0.8.5 dated 2024-11-25 and 0.8.6 dated 2025-08-19
DESCRIPTION | 17 + MD5 | 80 +++++---- NAMESPACE | 1 NEWS.md | 5 R/extra_viz.R | 1 R/icecurves.R | 30 +-- R/instrumental_temp.R | 4 R/seaice.R | 26 +-- R/sealevel.R | 294 +++++++++++++++++----------------- README.md | 104 ------------ build/partial.rdb |binary build/vignette.rds |only inst/doc |only man/figures/README-2ktemp-1.png |binary man/figures/README-carbon-1.png |binary man/figures/README-dailytemp-1.png |binary man/figures/README-emissions-1.png |binary man/figures/README-emissions-2.png |binary man/figures/README-emissionsmap-1.png |binary man/figures/README-grid-1.png |binary man/figures/README-hurricanes-1.png |binary man/figures/README-hurricanes-2.png |binary man/figures/README-icecurves-1.png |binary man/figures/README-methane-1.png |binary man/figures/README-paleo-1.png |binary man/figures/README-si-1.png |binary man/figures/README-sl-1.png |binary man/figures/README-stripes-1.png |binary man/figures/README-stripes2-1.png |binary man/figures/README-temp-1.png |binary man/figures/README-tempcarbon-1.png |binary man/get_seaice.Rd | 6 man/get_temp.Rd | 4 vignettes |only 34 files changed, 256 insertions(+), 316 deletions(-)
Title: Test Theory Analysis and Biclustering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.5.1 dated 2025-03-09 and 1.6.0 dated 2025-08-19
DESCRIPTION | 8 - MD5 | 59 ++++---- NAMESPACE | 9 + NEWS.md | 18 ++ R/00_BiclucterUtils.R |only R/00_GridSearch.R |only R/00_exametrikaPlot.R | 286 +++++++++++++++++++++++++++------------- R/00_exametrikaPrint.R | 114 +++++++++++++-- R/01_dataFormat.R | 53 +++---- R/02B_TestStatistics.R | 1 R/02_TestItemFunctions.R | 10 + R/05_LCA.R | 8 - R/06_LRA.R | 23 +-- R/07B_InfiniteRelationalModel.R | 2 R/07_Biclustering.R | 110 ++++++++------- R/09_LDLRA.R | 2 R/10_LDB.R | 2 R/11_BINET.R | 2 R/12_OrdinalLatentRank.R | 67 ++++----- R/13_RatedLatentRank.R | 75 ++++------ R/14_GRM.R | 2 R/15_NominalBiclustering.R |only R/16_OrdinalBiclustering.R |only README.md | 4 man/BINET.Rd | 1 man/Biclustering.Rd | 57 ++++++- man/GridSearch.Rd |only man/IRM.Rd | 1 man/LCA.Rd | 5 man/LDB.Rd | 1 man/LDLRA.Rd | 1 man/LRA.Rd | 7 man/plot.exametrika.Rd | 31 ++++ 33 files changed, 631 insertions(+), 328 deletions(-)
Title: Effect Size Estimation and Visualisation
Description: An easy-to-use yet powerful system for plotting grouped data effect sizes.
Various types of effect size can be estimated, then plotted together with a
representation of the original data. Select from many possible data representations
(box plots, violin plots, raw data points etc.), and combine as desired.
'Durga' plots are implemented in base R, so are compatible with base R methods
for combining plots, such as 'layout()'. See Khan & McLean (2023)
<doi:10.1101/2023.02.06.526960>.
Author: Kawsar Khan [aut] ,
Jim McLean [aut, cre]
Maintainer: Jim McLean <jim_mclean@optusnet.com.au>
Diff between Durga versions 2.0 dated 2023-12-17 and 2.1.0 dated 2025-08-19
Durga-2.0/Durga/TODO |only Durga-2.0/Durga/tests/testthat/Rplots.pdf |only Durga-2.1.0/Durga/DESCRIPTION | 14 Durga-2.1.0/Durga/MD5 | 53 - Durga-2.1.0/Durga/NAMESPACE | 20 Durga-2.1.0/Durga/NEWS.md | 15 Durga-2.1.0/Durga/R/brackets.R | 14 Durga-2.1.0/Durga/R/contrasts.R | 2 Durga-2.1.0/Durga/R/data.R | 10 Durga-2.1.0/Durga/R/differences.R | 42 Durga-2.1.0/Durga/R/plot.R | 86 +- Durga-2.1.0/Durga/README.md | 91 +- Durga-2.1.0/Durga/build/partial.rdb |binary Durga-2.1.0/Durga/build/vignette.rds |binary Durga-2.1.0/Durga/inst/doc/Durga-intro.R | 36 Durga-2.1.0/Durga/inst/doc/Durga-intro.html | 50 - Durga-2.1.0/Durga/man/Durga-package.Rd | 58 - Durga-2.1.0/Durga/man/DurgaBrackets.Rd | 228 ++--- Durga-2.1.0/Durga/man/DurgaDiff.Rd | 557 ++++++------- Durga-2.1.0/Durga/man/DurgaDiff.formula.Rd | 286 +++--- Durga-2.1.0/Durga/man/DurgaPlot.Rd | 883 ++++++++++----------- Durga-2.1.0/Durga/man/DurgaTransparent.Rd | 74 - Durga-2.1.0/Durga/man/damselfly.Rd | 62 - Durga-2.1.0/Durga/man/insulin.Rd | 80 - Durga-2.1.0/Durga/man/insulin.wide.Rd | 66 - Durga-2.1.0/Durga/man/petunia.Rd | 54 - Durga-2.1.0/Durga/tests/testthat/test-brackets.R | 12 Durga-2.1.0/Durga/tests/testthat/test-difference.R | 193 +--- Durga-2.1.0/Durga/tests/testthat/test-plot.R |only 29 files changed, 1496 insertions(+), 1490 deletions(-)