Title: Selection, Reverse-Engineering and Prediction in Cascade
Networks
Description: A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between Cascade versions 2.1 dated 2022-11-28 and 2.2 dated 2025-08-20
DESCRIPTION | 19 +-- MD5 | 26 ++-- R/Cascade-package.R | 15 -- R/micropredict.R | 4 R/network.R | 16 +- README.md | 308 ++++++++++++++++++++++++------------------------- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 19 +-- inst/_pkgdown.yml | 2 man/Cascade-package.Rd | 19 ++- tests |only 12 files changed, 224 insertions(+), 204 deletions(-)
Title: Utilities for the Application of a Polygenic Score to a VCF
Description: Simple and transparent parsing of genotype/dosage data
from an input Variant Call Format (VCF) file, matching of genotype
coordinates to the component Single Nucleotide Polymorphisms (SNPs)
of an existing polygenic score (PGS), and application of SNP weights
to dosages for the calculation of a polygenic score for each individual
in accordance with the additive weighted sum of dosages model. Methods
are designed in reference to best practices described by
Collister, Liu, and Clifton (2022) <doi:10.3389/fgene.2022.818574>.
Author: Paul Boutros [cre],
Nicole Zeltser [aut] ,
Rachel Dang [ctb],
Raag Agrawal [ctb]
Maintainer: Paul Boutros <PBoutros@mednet.ucla.edu>
Diff between ApplyPolygenicScore versions 3.0.1 dated 2025-03-05 and 4.0.0 dated 2025-08-20
DESCRIPTION | 19 MD5 | 69 NAMESPACE | 15 NEWS.md | 32 R/apply-pgs.R | 432 +++-- R/assess-strand-flip.R | 314 ++- R/calculate-dosage.R | 147 + R/combine-vcf-with-pgs.R | 152 + R/handle-multiallelic-sites.R | 150 + R/handle-vcf.R | 105 + R/plot-pgs.R | 380 ++++ R/run-pgs-statistics.R | 636 +++++++ R/variant-by-sample-matrix-utility.R | 151 + README.md | 25 inst/doc/UserGuide.R | 303 --- inst/doc/UserGuide.Rmd | 278 ++- inst/doc/UserGuide.html | 1073 +++++++------ man/analyze.pgs.binary.predictiveness.Rd |only man/apply.polygenic.score.Rd | 41 man/assess.pgs.vcf.allele.match.Rd | 8 man/combine.vcf.with.pgs.Rd | 8 man/create.pgs.boxplot.Rd |only man/create.pgs.density.plot.Rd | 12 man/create.pgs.with.continuous.phenotype.plot.Rd | 17 man/import.vcf.Rd | 43 tests/testthat/data/merged.multiallelic.site.test.data.Rda |binary tests/testthat/generate-test-data.R | 16 tests/testthat/helper-test-utils.R |only tests/testthat/test-dosage-calculator.R | 38 tests/testthat/test-pgs-application.R | 538 +++++- tests/testthat/test-pgs-statistics.R | 409 ++++ tests/testthat/test-plotting.R | 374 ++++ tests/testthat/test-sample-by-snp-matrix-utility.R | 180 ++ tests/testthat/test-strand-flip-handling.R | 57 tests/testthat/test-vcf-import.R | 124 + tests/testthat/test-vcf-pgs-merge.R | 143 + vignettes/UserGuide.Rmd | 278 ++- 37 files changed, 5069 insertions(+), 1498 deletions(-)
More information about ApplyPolygenicScore at CRAN
Permanent link
Title: Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry
Data
Description: Dirichlet process mixture of multivariate normal, skew normal or skew t-distributions
modeling oriented towards flow-cytometry data preprocessing applications. Method is
detailed in: Hejblum, Alkhassimn, Gottardo, Caron & Thiebaut (2019) <doi: 10.1214/18-AOAS1209>.
Author: Boris P Hejblum [aut, cre],
Chariff Alkhassim [aut],
Francois Caron [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between NPflow versions 0.13.5 dated 2024-01-13 and 0.13.6 dated 2025-08-20
DESCRIPTION | 14 ++++++++------ MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/NPflow-package.R | 4 ++-- README.md | 2 ++ build/partial.rdb |binary inst/CITATION | 2 +- man/NPflow-package.Rd | 5 +++-- 8 files changed, 27 insertions(+), 18 deletions(-)
Title: Local Partial Likelihood Estimation and Simultaneous Confidence
Band
Description: Local partial likelihood estimation by Fan, Lin and Zhou(2006)<doi:10.1214/009053605000000796> and simultaneous confidence band is a set of tools to test the covariates-biomarker interaction for survival data. Test for the covariates-biomarker interaction using the bootstrap method and the asymptotic method with simultaneous confidence band (Liu, Jiang and Chen (2015)<doi:10.1002/sim.6563>).
Author: Bingshu E. Chen [aut, cre],
Yicong Liu [aut],
Siwei Zhang [aut],
Teng Wen [aut],
Wenyu Jiang [aut]
Maintainer: Bingshu E. Chen <bingshu.chen@queensu.ca>
Diff between lpl versions 0.12 dated 2025-04-04 and 0.13 dated 2025-08-20
lpl-0.12/lpl/R/ibs.lple.R |only lpl-0.13/lpl/DESCRIPTION | 8 ++++---- lpl-0.13/lpl/MD5 | 20 ++++++++++++++++---- lpl-0.13/lpl/NAMESPACE | 12 ++++++++++-- lpl-0.13/lpl/R/ibs.R |only lpl-0.13/lpl/R/numScoreHess.R |only lpl-0.13/lpl/R/rSurv.R |only lpl-0.13/lpl/R/rmst.R |only lpl-0.13/lpl/README.md |only lpl-0.13/lpl/man/coxScoreHess.Rd |only lpl-0.13/lpl/man/ibs.Rd |only lpl-0.13/lpl/man/ipcw.Rd |only lpl-0.13/lpl/man/lple.Rd | 2 -- lpl-0.13/lpl/man/multiRoot.Rd |only lpl-0.13/lpl/man/numHessian.Rd |only lpl-0.13/lpl/man/numScore.Rd |only lpl-0.13/lpl/man/rSurv.Rd |only lpl-0.13/lpl/man/rmst.Rd |only 18 files changed, 30 insertions(+), 12 deletions(-)
Title: Improved Random Number Generator Seeding
Description: A procedure for seeding R's built in random number
generators using a variable-length sequence of values.
Accumulates input entropy into a 256-bit hash digest or "ironseed"
and is able to generate a variable-length sequence of output seeds
from an ironseed.
Author: Reed Cartwright [aut, cre] ,
National Science Foundation DBI-1929850 [fnd]
Maintainer: Reed Cartwright <racartwright@gmail.com>
Diff between ironseed versions 0.1.0 dated 2025-07-11 and 0.2.0 dated 2025-08-20
ironseed-0.1.0/ironseed/src/ironseed.h |only ironseed-0.2.0/ironseed/DESCRIPTION | 19 ironseed-0.2.0/ironseed/MD5 | 53 + ironseed-0.2.0/ironseed/NAMESPACE | 16 ironseed-0.2.0/ironseed/NEWS.md | 40 + ironseed-0.2.0/ironseed/R/aaa.R |only ironseed-0.2.0/ironseed/R/import-standalone-defer.R |only ironseed-0.2.0/ironseed/R/ironseed.R | 288 +++++---- ironseed-0.2.0/ironseed/R/set_seed.R |only ironseed-0.2.0/ironseed/R/stream.R |only ironseed-0.2.0/ironseed/R/utils.R |only ironseed-0.2.0/ironseed/R/with.R |only ironseed-0.2.0/ironseed/README.md | 69 +- ironseed-0.2.0/ironseed/build |only ironseed-0.2.0/ironseed/inst/tinytest/test_ironseed-values.R |only ironseed-0.2.0/ironseed/inst/tinytest/test_ironseed.R | 289 ++++++---- ironseed-0.2.0/ironseed/inst/tinytest/test_set-seed.R |only ironseed-0.2.0/ironseed/inst/tinytest/test_stream.R |only ironseed-0.2.0/ironseed/inst/tinytest/test_with.R |only ironseed-0.2.0/ironseed/man/figures/README-analysis_256-1.png |binary ironseed-0.2.0/ironseed/man/figures/README-analysis_32-1.png |binary ironseed-0.2.0/ironseed/man/fill_random_seed.Rd | 6 ironseed-0.2.0/ironseed/man/ironseed-package.Rd | 5 ironseed-0.2.0/ironseed/man/ironseed.Rd | 99 ++- ironseed-0.2.0/ironseed/man/ironseed_stream.Rd |only ironseed-0.2.0/ironseed/man/with_ironseed.Rd |only ironseed-0.2.0/ironseed/src/Makevars.win |only ironseed-0.2.0/ironseed/src/base58.c | 32 - ironseed-0.2.0/ironseed/src/compat.c | 170 +++++ ironseed-0.2.0/ironseed/src/config.h.in | 5 ironseed-0.2.0/ironseed/src/init.c | 10 ironseed-0.2.0/ironseed/src/init.h | 4 ironseed-0.2.0/ironseed/src/ironseed.c | 143 ++++ ironseed-0.2.0/ironseed/tests/tinytest.R | 7 ironseed-0.2.0/ironseed/tools/config/configure.R | 82 ++ 35 files changed, 936 insertions(+), 401 deletions(-)
Title: Initiation à La Statistique Avec R
Description: Datasets and functions for the book "Initiation à la Statistique avec R", F. Bertrand and M. Maumy-Bertrand (2022, ISBN:978-2100782826 Dunod, fourth edition).
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between BioStatR versions 4.0.1 dated 2023-03-21 and 4.0.2 dated 2025-08-20
BioStatR-4.0.1/BioStatR/man/BioStatR.Rd |only BioStatR-4.0.2/BioStatR/DESCRIPTION | 20 ++++++++---- BioStatR-4.0.2/BioStatR/MD5 | 38 ++++++++++++------------ BioStatR-4.0.2/BioStatR/NEWS.md | 4 ++ BioStatR-4.0.2/BioStatR/R/BioStatR-package.R | 19 +++--------- BioStatR-4.0.2/BioStatR/R/binom.ci.R | 4 +- BioStatR-4.0.2/BioStatR/R/cvar.R | 4 +- BioStatR-4.0.2/BioStatR/R/eta2.R | 4 +- BioStatR-4.0.2/BioStatR/R/gg_qqplot.R | 4 +- BioStatR-4.0.2/BioStatR/R/panel.hist.R | 4 +- BioStatR-4.0.2/BioStatR/R/plotcdf2.R | 4 +- BioStatR-4.0.2/BioStatR/R/poi.ci.R | 4 +- BioStatR-4.0.2/BioStatR/inst/CITATION | 4 +- BioStatR-4.0.2/BioStatR/man/BioStatR-package.Rd |only BioStatR-4.0.2/BioStatR/man/binom.ci.Rd | 4 +- BioStatR-4.0.2/BioStatR/man/cvar.Rd | 4 +- BioStatR-4.0.2/BioStatR/man/eta2.Rd | 4 +- BioStatR-4.0.2/BioStatR/man/gg_qqplot.Rd | 4 +- BioStatR-4.0.2/BioStatR/man/panel.hist.Rd | 4 +- BioStatR-4.0.2/BioStatR/man/plotcdf2.Rd | 4 +- BioStatR-4.0.2/BioStatR/man/poi.ci.Rd | 4 +- 21 files changed, 72 insertions(+), 69 deletions(-)
Title: Identifies Mean, Variance, and Hierarchically Clustered
Biclusters
Description: Identifies a bicluster, a submatrix of the data such that the features and observations within the submatrix differ from those not contained in submatrix, using a two-step method. In the first step, observations in the bicluster are identified to maximize the sum of weighted between cluster feature differences. The method is described in Helgeson et al. (2020) <doi:10.1111/biom.13136>. 'SCBiclust' can be used to identify biclusters which differ based on feature means, feature variances, or more general differences.
Author: Erika S. Helgeson [aut, cre],
Qian Liu [aut],
Guanhua Chen [aut],
Michael R. Kosorok [aut],
Eric Bair [aut]
Maintainer: Erika S. Helgeson <helge@umn.edu>
Diff between SCBiclust versions 1.0.1 dated 2022-06-09 and 1.0.2 dated 2025-08-20
DESCRIPTION | 41 ++++++++++++++++++++++-------- LICENSE |only MD5 | 25 +++++++++--------- NAMESPACE | 3 ++ R/SC-Biclust-SigClust-stop.R | 49 ++++++++++++++++++------------------ R/SC-Biclust-SigClust.R | 53 +++++++++++++++++++-------------------- R/SC-HBiclust-SigClust.R | 40 ++++++++++++++++------------- R/SC-Var-Biclust.R | 42 +++++++++++++++--------------- R/SCBiclust_beta_ks.R | 50 +++++++++++++++++++----------------- man/PermBiclust.beta.ks.Rd | 19 +++++++------ man/PermBiclust.sigclust.Rd | 24 ++++++++--------- man/PermBiclust.sigclust_stop.Rd | 26 +++++++++---------- man/PermHclust.sigclust.Rd | 20 +++++++------- man/VarPermBiclust.chisqdiff.Rd | 16 +++++------ 14 files changed, 221 insertions(+), 187 deletions(-)
Title: Construct Consistent Time Series from Textual Data
Description: A rolling version of the Latent Dirichlet Allocation, see Rieger et al. (2021) <doi:10.18653/v1/2021.findings-emnlp.201>. By a sequential approach, it enables the construction of LDA-based time series of topics that are consistent with previous states of LDA models. After an initial modeling, updates can be computed efficiently, allowing for real-time monitoring and detection of events or structural breaks.
Author: Jonas Rieger [aut, cre]
Maintainer: Jonas Rieger <jonas.rieger@tu-dortmund.de>
Diff between rollinglda versions 0.1.3 dated 2023-11-28 and 0.1.4 dated 2025-08-20
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- R/RollingLDA.R | 2 +- R/updateRollingLDA.R | 2 +- man/RollingLDA.Rd | 2 +- man/updateRollingLDA.Rd | 2 +- 6 files changed, 16 insertions(+), 15 deletions(-)
Title: Normalized Power Prior Bayesian Analysis
Description: Posterior sampling in several commonly used distributions using
normalized power prior as described in
Duan, Ye and Smith (2006) <doi:10.1002/env.752> and
Ibrahim et.al. (2015) <doi:10.1002/sim.6728>.
Sampling of the power parameter is achieved via
either independence Metropolis-Hastings or random walk Metropolis-Hastings
based on transformation.
Author: Zifei Han [aut, cre],
Qiang Zhang [aut],
Tianyu Bai [aut],
Yuyan Duan [aut],
Keying Ye [aut]
Maintainer: Zifei Han <hanzifei1@gmail.com>
Diff between NPP versions 0.6.0 dated 2023-12-11 and 0.7.0 dated 2025-08-20
DESCRIPTION | 29 +++++++++++++++++++++++++---- MD5 | 8 +++++--- NAMESPACE | 18 +++++++++--------- R/IRTNPP.R |only inst/NEWS.txt | 4 ++-- man/IRTNPP.Rd |only 6 files changed, 41 insertions(+), 18 deletions(-)
Title: A Unified Time Series Event Detection Framework
Description: By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Author: Eduardo Ogasawara [aut, ths, cre] ,
Antonio Castro [aut],
Antonio Mello [aut],
Diego Carvalho [ctb],
Eduardo Bezerra [ctb],
Ellen Paixao [aut],
Fernando Fraga [aut],
Heraldo Borges [aut],
Janio Lima [aut],
Jessica Souza [aut],
Lais Baroni [aut],
Luca [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between harbinger versions 1.2.727 dated 2025-06-29 and 1.2.737 dated 2025-08-20
harbinger-1.2.727/harbinger/R/hanr_red.R |only harbinger-1.2.727/harbinger/man/hanr_red.Rd |only harbinger-1.2.737/harbinger/DESCRIPTION | 20 ++++---------- harbinger-1.2.737/harbinger/MD5 | 10 +++---- harbinger-1.2.737/harbinger/NAMESPACE | 4 +- harbinger-1.2.737/harbinger/R/hanr_rtad.R |only harbinger-1.2.737/harbinger/README.md | 38 +++++++++++++-------------- harbinger-1.2.737/harbinger/man/hanr_rtad.Rd |only 8 files changed, 33 insertions(+), 39 deletions(-)
Title: Exact P-Values and Matching Confidence Intervals for Simple
Discrete Parametric Cases
Description: Calculates exact tests and confidence intervals for one-sample binomial and one- or two-sample Poisson cases (see Fay (2010) <doi:10.32614/rj-2010-008>).
Author: Michael P. Fay [aut, cre]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between exactci versions 1.4-4 dated 2023-08-24 and 1.4-5 dated 2025-08-20
ChangeLog | 4 ++++ DESCRIPTION | 16 ++++++++++------ MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/TwoSidedPoissonCIs.R | 4 ++-- inst/doc/exactci.pdf |binary man/powerBinom.Rd | 2 +- 7 files changed, 23 insertions(+), 15 deletions(-)
Title: Applied Statistical Hypothesis Tests
Description: Gives some hypothesis test functions (sign test, median and other quantile tests, Wilcoxon signed rank test, coefficient of variation test, test of normal variance, test on weighted sums of Poisson [see Fay and Kim <doi:10.1002/bimj.201600111>], sample size for t-tests with different variances and non-equal n per arm, Behrens-Fisher test, nonparametric ABC intervals, Wilcoxon-Mann-Whitney test [with effect estimates and confidence intervals, see Fay and Malinovsky <doi:10.1002/sim.7890>], two-sample melding tests [see Fay, Proschan, and Brittain <doi:10.1111/biom.12231>], one-way ANOVA allowing var.equal=FALSE [see Brown and Forsythe, 1974, Biometrics]), prevalence confidence intervals that adjust for sensitivity and specificity [see Lang and Reiczigel, 2014 <doi:10.1016/j.prevetmed.2013.09.015>] or Bayer, Fay, and Graubard, 2023 <doi:10.48550/arXiv.2205.13494>). The focus is on hypothesis tests that have compatible confidence intervals, but some functions [...truncated...]
Author: Michael P. Fay [aut, cre]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between asht versions 1.0.1 dated 2023-08-24 and 1.0.3 dated 2025-08-20
DESCRIPTION | 16 ++++++++++------ MD5 | 14 +++++++------- inst/NEWS.Rd | 18 ++++++++++++++++++ man/meldCD.Rd | 2 +- man/signTest.Rd | 14 +++++++------- man/simulateSS.Rd | 20 ++++++++++---------- man/wmwTest.Rd | 4 ++-- man/wsrTest.Rd | 6 +++--- 8 files changed, 58 insertions(+), 36 deletions(-)
Title: P-Spline Regression for Utility Functions and Derived Measures
Description: Predicts a smooth and continuous (individual) utility function from utility points, and computes measures of intensity for risk and higher-order risk measures (or any other measure computed with user-written function) based on this utility function and its derivatives according to the method introduced in Schneider (2017) <http://hdl.handle.net/21.11130/00-1735-0000-002E-E306-0>.
Author: Sebastian O. Schneider [aut, cre, prg],
Giulia Baldini [edt, prg],
Paul Eilers [ctb]
Maintainer: Sebastian O. Schneider <sschneider@coll.mpg.de>
Diff between utilityFunctionTools versions 0.1.1 dated 2021-03-29 and 1.0 dated 2025-08-20
DESCRIPTION | 10 ++++----- MD5 | 5 ++-- R/HigherOrderRiskPreferences.R | 42 +++++++++++++++++++++-------------------- man/figures |only 4 files changed, 30 insertions(+), 27 deletions(-)
More information about utilityFunctionTools at CRAN
Permanent link
Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.modules.general versions 0.4.1 dated 2025-04-01 and 0.5.0 dated 2025-08-20
teal.modules.general-0.4.1/teal.modules.general/inst/css |only teal.modules.general-0.4.1/teal.modules.general/man/include_css_files.Rd |only teal.modules.general-0.4.1/teal.modules.general/man/is_tab_active_js.Rd |only teal.modules.general-0.4.1/teal.modules.general/tests/testthat/man/include_css_files.Rd |only teal.modules.general-0.4.1/teal.modules.general/tests/testthat/man/is_tab_active_js.Rd |only teal.modules.general-0.5.0/teal.modules.general/DESCRIPTION | 38 - teal.modules.general-0.5.0/teal.modules.general/MD5 | 97 ++-- teal.modules.general-0.5.0/teal.modules.general/NEWS.md | 19 teal.modules.general-0.5.0/teal.modules.general/R/tm_a_pca.R | 20 teal.modules.general-0.5.0/teal.modules.general/R/tm_a_regression.R | 61 +- teal.modules.general-0.5.0/teal.modules.general/R/tm_data_table.R | 43 -- teal.modules.general-0.5.0/teal.modules.general/R/tm_file_viewer.R | 9 teal.modules.general-0.5.0/teal.modules.general/R/tm_front_page.R | 19 teal.modules.general-0.5.0/teal.modules.general/R/tm_g_association.R | 16 teal.modules.general-0.5.0/teal.modules.general/R/tm_g_bivariate.R | 28 - teal.modules.general-0.5.0/teal.modules.general/R/tm_g_distribution.R | 210 ++++------ teal.modules.general-0.5.0/teal.modules.general/R/tm_g_response.R | 12 teal.modules.general-0.5.0/teal.modules.general/R/tm_g_scatterplot.R | 24 - teal.modules.general-0.5.0/teal.modules.general/R/tm_g_scatterplotmatrix.R | 12 teal.modules.general-0.5.0/teal.modules.general/R/tm_missing_data.R | 127 ++---- teal.modules.general-0.5.0/teal.modules.general/R/tm_outliers.R | 153 ++++--- teal.modules.general-0.5.0/teal.modules.general/R/tm_t_crosstable.R | 75 ++- teal.modules.general-0.5.0/teal.modules.general/R/tm_variable_browser.R | 178 +++----- teal.modules.general-0.5.0/teal.modules.general/R/utils.R | 23 - teal.modules.general-0.5.0/teal.modules.general/build/vignette.rds |binary teal.modules.general-0.5.0/teal.modules.general/inst/WORDLIST | 3 teal.modules.general-0.5.0/teal.modules.general/man/srv_decorate_teal_data.Rd | 3 teal.modules.general-0.5.0/teal.modules.general/man/tm_g_distribution.Rd | 6 teal.modules.general-0.5.0/teal.modules.general/man/tm_missing_data.Rd | 4 teal.modules.general-0.5.0/teal.modules.general/man/tm_outliers.Rd | 4 teal.modules.general-0.5.0/teal.modules.general/man/tm_t_crosstable.Rd | 15 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/man/srv_decorate_teal_data.Rd | 3 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/man/tm_g_distribution.Rd | 6 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/man/tm_missing_data.Rd | 4 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/man/tm_outliers.Rd | 4 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/man/tm_t_crosstable.Rd | 15 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-examples.R | 1 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_a_pca.R | 11 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_a_regression.R | 9 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_data_table.R | 6 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_file_viewer.R | 12 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_front_page.R | 11 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_association.R | 6 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_bivariate.R | 4 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_distribution.R | 3 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_response.R | 4 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_scatterplot.R | 5 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_scatterplotmatrix.R | 10 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_misssing_data.R | 22 - teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_outliers.R | 12 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_t_crosstable.R | 10 teal.modules.general-0.5.0/teal.modules.general/tests/testthat/test-shinytest2-tm_variable_browser.R | 21 - 52 files changed, 741 insertions(+), 637 deletions(-)
More information about teal.modules.general at CRAN
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Title: Markdown-Based Programmable Surveys Using 'Quarto' and 'shiny'
Description: Generate programmable surveys using markdown and R code chunks. Surveys
are composed of two files: a survey.qmd 'Quarto' file defining the
survey content (pages, questions, etc), and an app.R file defining a
'shiny' app with global settings (libraries, database configuration,
etc.) and server configuration options (e.g., conditional skipping /
display, etc.). Survey data collected from respondents is stored in a
'PostgreSQL' database. Features include controls for conditional skip
logic (skip to a page based on an answer to a question), conditional
display logic (display a question based on an answer to a question), a
customizable progress bar, and a wide variety of question types,
including multiple choice (single choice and multiple choices),
select, text, numeric, multiple choice buttons, text area, and dates.
Because the surveys render into a 'shiny' app, designers can also
leverage the reactive capabilities of 'shiny' to create dynamic and
interactive surveys.
Author: John Paul Helveston [aut, cre, cph] ,
Pingfan Hu [aut, cph] ,
Bogdan Bunea [aut, cph] ,
Stefan Munnes [ctb]
Maintainer: John Paul Helveston <john.helveston@gmail.com>
Diff between surveydown versions 0.12.6 dated 2025-07-07 and 0.13.0 dated 2025-08-20
surveydown-0.12.6/surveydown/R/dashboard.R |only surveydown-0.13.0/surveydown/DESCRIPTION | 12 surveydown-0.13.0/surveydown/MD5 | 29 surveydown-0.13.0/surveydown/NEWS.md | 18 surveydown-0.13.0/surveydown/R/config.R | 846 ++++++-- surveydown-0.13.0/surveydown/R/db.R | 459 ++-- surveydown-0.13.0/surveydown/R/server.R | 1697 +++++++++++------ surveydown-0.13.0/surveydown/R/translation.R | 120 - surveydown-0.13.0/surveydown/R/ui.R | 1332 ++++++++----- surveydown-0.13.0/surveydown/R/util.R | 1054 ++++++++-- surveydown-0.13.0/surveydown/inst/css/surveydown.css | 11 surveydown-0.13.0/surveydown/man/sd_completion_code.Rd | 2 surveydown-0.13.0/surveydown/man/sd_dashboard.Rd | 41 surveydown-0.13.0/surveydown/man/sd_redirect.Rd | 11 surveydown-0.13.0/surveydown/man/sd_server.Rd | 44 surveydown-0.13.0/surveydown/man/sd_store_value.Rd | 41 16 files changed, 3924 insertions(+), 1793 deletions(-)
Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures with
quantile-based basis functions, possibly under linearity and
homogeneity assumptions. This approach estimates a regression line
corresponding to the expected change in the outcome (on the link
basis) given a simultaneous increase in the quantile-based category
for all exposures. Works with continuous, binary, and right-censored
time-to-event outcomes. Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and
Alexandra J. White (2019) A quantile-based g-computation approach to
addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <alex.keil@nih.gov>
Diff between qgcomp versions 2.18.4 dated 2025-03-28 and 2.18.7 dated 2025-08-20
DESCRIPTION | 8 ++-- MD5 | 40 +++++++++++----------- NAMESPACE | 2 + NEWS.md | 11 ++++++ R/base.R | 27 ++++++-------- R/base_esteq.R | 5 +- R/base_experimental.R | 24 +++++++++++++ R/base_hurdle.R | 27 ++++---------- R/base_multinomial.R | 9 ++-- R/base_surv.R | 46 +++++++++++++++---------- R/base_tobit.R | 9 +++- R/base_utility.R | 60 +++++++++++++++++++++++++++++++++ R/base_zi.R | 13 +++---- README.md | 2 - inst/doc/qgcomp-advanced-vignette.html | 28 +++++++-------- inst/doc/qgcomp-basic-vignette.html | 4 +- inst/doc/qgcomp-vignette.html | 2 - man/dot-qgcomp_object.Rd |only man/dot-qgcomp_object_add.Rd |only man/qgcomp.cch.noboot.Rd | 2 - man/qgcomp.cox.boot.Rd | 2 - man/qgcomp.cox.noboot.Rd | 2 - 22 files changed, 211 insertions(+), 112 deletions(-)
Title: Optimal Design and Statistical Power for Experimental Studies
Investigating Main, Mediation, and Moderation Effects
Description: Calculate the optimal sample size allocation that
uses the minimum resources to achieve targeted statistical
power in experiments.
Perform power analyses with and without accommodating
costs and budget. The designs cover single-level
and multilevel experiments detecting main, mediation,
and moderation effects (and some combinations).
The references for the proposed methods include:
(1) Shen, Z., & Kelcey, B. (2020).
Optimal sample allocation under unequal costs in
cluster-randomized trials.
Journal of Educational and Behavioral Statistics, 45(4): 446-474.
<doi:10.3102/1076998620912418>.
(2) Shen, Z., & Kelcey, B. (2022b). Optimal sample allocation for
three-level multisite cluster-randomized trials.
Journal of Research on Educational Effectiveness, 15 (1), 130-150.
<doi:10.1080/19345747.2021.1953200>.
(3) Shen, Z., & Kelcey, B. (2022a). Optimal sample allocation in
multisite randomized trials. The Journal of Experimental Education,
90(3), 693-711. <doi:10.108 [...truncated...]
Author: Zuchao Shen [aut, cre] ,
Benjamin Kelcey [aut]
Maintainer: Zuchao Shen <zuchao.shen@gmail.com>
Diff between odr versions 1.5.0 dated 2025-05-29 and 1.6.3 dated 2025-08-20
odr-1.5.0/odr/R/od.2m.111m.R |only odr-1.5.0/odr/R/power.2m.111m.R |only odr-1.5.0/odr/man/od.2m.111m.Rd |only odr-1.5.0/odr/man/power.2m.111m.Rd |only odr-1.6.3/odr/DESCRIPTION | 8 +-- odr-1.6.3/odr/MD5 | 60 +++++++++++++----------- odr-1.6.3/odr/NAMESPACE | 8 ++- odr-1.6.3/odr/R/gen.design.pars.R | 13 +++-- odr-1.6.3/odr/R/od.1.111.R | 2 odr-1.6.3/odr/R/od.1.111m.R |only odr-1.6.3/odr/R/od.2.221m.R | 13 ++--- odr-1.6.3/odr/R/od.2m.R | 17 ++++-- odr-1.6.3/odr/R/od.2m.mod.R |only odr-1.6.3/odr/R/od.2m.only.mod.R |only odr-1.6.3/odr/R/plot.power.R |only odr-1.6.3/odr/R/power.1.111.R | 8 +-- odr-1.6.3/odr/R/power.1.111m.R |only odr-1.6.3/odr/R/power.1.R | 87 ++++++++++++++++++++++------------- odr-1.6.3/odr/R/power.2m.R | 51 ++++++-------------- odr-1.6.3/odr/R/power.2m.mod.R |only odr-1.6.3/odr/build/vignette.rds |binary odr-1.6.3/odr/inst/doc/odr.R | 11 ++++ odr-1.6.3/odr/inst/doc/odr.Rmd | 52 ++++++++++++++++++-- odr-1.6.3/odr/inst/doc/odr.html | 86 +++++++++++++++++++++++++++++----- odr-1.6.3/odr/man/gen.design.pars.Rd | 13 ++--- odr-1.6.3/odr/man/od.1.111.Rd | 2 odr-1.6.3/odr/man/od.1.111m.Rd |only odr-1.6.3/odr/man/od.2.221m.Rd | 17 +++--- odr-1.6.3/odr/man/od.2m.Rd | 11 ++-- odr-1.6.3/odr/man/od.2m.mod.Rd |only odr-1.6.3/odr/man/od.2m.only.mod.Rd |only odr-1.6.3/odr/man/od.3m.Rd | 5 +- odr-1.6.3/odr/man/plot.power.Rd |only odr-1.6.3/odr/man/power.1.111.Rd | 10 ++-- odr-1.6.3/odr/man/power.1.111m.Rd |only odr-1.6.3/odr/man/power.1.Rd | 4 - odr-1.6.3/odr/man/power.2m.Rd | 8 +-- odr-1.6.3/odr/man/power.2m.mod.Rd |only odr-1.6.3/odr/vignettes/odr.Rmd | 52 ++++++++++++++++++-- 39 files changed, 361 insertions(+), 177 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical
models and returns the result as tidy data frames. These data frames are
ready to use with the 'ggplot2'-package. Effects and predictions can be
calculated for many different models. Interaction terms, splines and
polynomial terms are also supported. The main functions are ggpredict(),
ggemmeans() and ggeffect(). There is a generic plot()-method to plot the
results using 'ggplot2'.
Author: Daniel Luedecke [aut, cre] ,
Frederik Aust [ctb] ,
Sam Crawley [ctb] ,
Mattan S. Ben-Shachar [ctb] ,
Sean C. Anderson [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between ggeffects versions 2.3.0 dated 2025-06-13 and 2.3.1 dated 2025-08-20
DESCRIPTION | 8 ++--- LICENSE | 4 +- MD5 | 12 +++---- NEWS.md | 4 ++ R/print.R | 8 ----- build/vignette.rds |binary man/install_latest.Rd | 80 +++++++++++++++++++++++++------------------------- 7 files changed, 56 insertions(+), 60 deletions(-)
Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups preprocessed through
matching, weighting or subclassification, for example, using propensity scores. Includes
integration with 'MatchIt', 'WeightIt', 'MatchThem', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal',
'cem', 'sbw', and 'designmatch' for assessing balance on the output of their preprocessing
functions. Users can also specify data for balance assessment not generated through
the above packages. Also included are methods for assessing balance in clustered or
multiply imputed data sets or data sets with multi-category, continuous, or longitudinal treatments.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between cobalt versions 4.6.0 dated 2025-04-15 and 4.6.1 dated 2025-08-20
DESCRIPTION | 9 - MD5 | 94 ++++++------ NAMESPACE | 1 NEWS.md | 10 + R/bal.compute.R | 279 ++++++++++++++++++++++-------------- R/bal.plot.R | 59 ++++--- R/bal.tab.R | 3 R/bal.tab.cem.match.R | 1 R/bal.tab.designmatch.R | 7 R/balance-statistics.R | 4 R/balance-summary.R | 4 R/base.bal.tab.R | 2 R/chk-functions.R | 2 R/class-bal.tab.msm.R | 5 R/class-bal.tab.multi.R | 6 R/class-bal.tab.subclass.R | 6 R/f.build.R | 2 R/functions_for_processing.R | 122 ++++++++------- R/get.w.R | 10 - R/lalonde.R | 5 R/love.plot.R | 61 +++---- R/print.bal.tab.R | 24 +-- R/splitfactor.R | 6 R/utils.R | 75 ++++++--- R/var.names.R | 6 R/x2base.R | 14 - R/zzz.R | 5 README.md | 2 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/cobalt.Rmd | 14 - inst/doc/cobalt.html | 67 ++++---- inst/doc/longitudinal-treat.html | 4 inst/doc/love.plot.Rmd | 17 +- inst/doc/love.plot.html | 169 ++++++++++----------- inst/doc/optimizing-balance.Rmd | 2 inst/doc/other-packages.html | 44 ++--- inst/doc/segmented-data.html | 4 man/bal.tab.Rd | 2 man/bal.tab.designmatch.Rd | 4 man/lalonde.Rd | 3 tests/testthat/Rplots.pdf |binary tests/testthat/helpers.R | 2 tests/testthat/test-bal.compute.R | 149 +++++++++++++++++++ tests/testthat/test-github-issues.R | 5 vignettes/cobalt.Rmd | 14 - vignettes/love.plot.Rmd | 17 +- vignettes/optimizing-balance.Rmd | 2 48 files changed, 813 insertions(+), 530 deletions(-)
Title: Bayesian MI-LASSO for Variable Selection on Multiply-Imputed
Datasets
Description: Provides a suite of Bayesian MI-LASSO for variable selection methods for multiply-imputed datasets. The package includes four Bayesian MI-LASSO models using shrinkage (Multi-Laplace, Horseshoe, ARD) and Spike-and-Slab (Spike-and-Laplace) priors, along with tools for model fitting via MCMC, four-step projection predictive variable selection, and hyperparameter calibration. Methods are suitable for both continuous and binary covariates under missing-at-random assumptions. See Zou, J., Wang, S. and Chen, Q. (2025), Bayesian MI-LASSO for Variable Selection on Multiply-Imputed Data. ArXiv, 2211.00114. <doi:10.48550/arXiv.2211.00114> for more details. We also provide the frequentist`s MI-LASSO function.
Author: Jungang Zou [aut, cre],
Sijian Wang [aut],
Qixuan Chen [aut]
Maintainer: Jungang Zou <jungang.zou@gmail.com>
Diff between BMIselect versions 1.0.1 dated 2025-07-09 and 1.0.2 dated 2025-08-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/bmiselect.R | 2 +- man/BMI_LASSO.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Functions and Datasets for Forest Biometrics and Modelling
Description: A system of functions and data aiming to apply quantitative analyses to forest
ecology, silviculture and decision-making. Besides, the package helps to carry out data
management, exploratory analysis, and model assessment.
Author: Christian Salas-Eljatib [aut, cre] ,
Campos Nicolas [ctb] ,
Marivil Marcos [ctb] ,
Riquelme Joaquin [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Diff between biometrics versions 1.0.1 dated 2025-04-01 and 1.0.2 dated 2025-08-20
biometrics-1.0.1/biometrics/R/describeDataBiometrics.r |only biometrics-1.0.1/biometrics/R/interp.a.r |only biometrics-1.0.1/biometrics/R/interp.b.r |only biometrics-1.0.1/biometrics/R/qmd.r |only biometrics-1.0.1/biometrics/R/valesta.r |only biometrics-1.0.1/biometrics/man/biometrics-package.Rd |only biometrics-1.0.1/biometrics/man/interp.a.Rd |only biometrics-1.0.1/biometrics/man/interp.b.Rd |only biometrics-1.0.1/biometrics/man/qmd.Rd |only biometrics-1.0.1/biometrics/man/valesta.Rd |only biometrics-1.0.2/biometrics/DESCRIPTION | 37 +-- biometrics-1.0.2/biometrics/MD5 | 167 ++++++++++++----- biometrics-1.0.2/biometrics/NAMESPACE | 20 +- biometrics-1.0.2/biometrics/R/barplotgr.r |only biometrics-1.0.2/biometrics/R/data-biomass.r |only biometrics-1.0.2/biometrics/R/data-biomass2.r |only biometrics-1.0.2/biometrics/R/data-deadlianas.r |only biometrics-1.0.2/biometrics/R/data-deadlianas2.r |only biometrics-1.0.2/biometrics/R/data-hawaii.r |only biometrics-1.0.2/biometrics/R/data-hawaii2.r |only biometrics-1.0.2/biometrics/R/data-largeplot.r |only biometrics-1.0.2/biometrics/R/data-mortaforest.r |only biometrics-1.0.2/biometrics/R/data-mortaforest2.r |only biometrics-1.0.2/biometrics/R/data-pinaster.r |only biometrics-1.0.2/biometrics/R/data-pinaster2.r |only biometrics-1.0.2/biometrics/R/data-pinusSpp.r |only biometrics-1.0.2/biometrics/R/data-pinusSpp2.r |only biometrics-1.0.2/biometrics/R/data-plantshawaii.r |only biometrics-1.0.2/biometrics/R/data-popvol.r |only biometrics-1.0.2/biometrics/R/data-popvol2.r |only biometrics-1.0.2/biometrics/R/data-spataustria.r |only biometrics-1.0.2/biometrics/R/data-spatimepsp.r |only biometrics-1.0.2/biometrics/R/data-standtabRauli.r |only biometrics-1.0.2/biometrics/R/data-standtabRauli2.r |only biometrics-1.0.2/biometrics/R/data-tapereuca2.r |only biometrics-1.0.2/biometrics/R/data-treegrowth.r |only biometrics-1.0.2/biometrics/R/data-treegrowth2.r |only biometrics-1.0.2/biometrics/R/data-treelistinve.r |only biometrics-1.0.2/biometrics/R/data-treelistinve2.r |only biometrics-1.0.2/biometrics/R/data-treevolruca.r |only biometrics-1.0.2/biometrics/R/data-treevolruca2.r |only biometrics-1.0.2/biometrics/R/data-trlhawaii.r |only biometrics-1.0.2/biometrics/R/data-trlpsptime.r |only biometrics-1.0.2/biometrics/R/data-trlremeasu.r |only biometrics-1.0.2/biometrics/R/data-trlsmoopsp.r |only biometrics-1.0.2/biometrics/R/dg.r |only biometrics-1.0.2/biometrics/R/domvar.r | 53 +++-- biometrics-1.0.2/biometrics/R/gtree.r | 51 +++-- biometrics-1.0.2/biometrics/R/interpy1.r |only biometrics-1.0.2/biometrics/R/interpy2.r |only biometrics-1.0.2/biometrics/R/kozak.r |only biometrics-1.0.2/biometrics/R/kozaklast.r |only biometrics-1.0.2/biometrics/R/kozakln.r |only biometrics-1.0.2/biometrics/R/nele.list.r | 14 - biometrics-1.0.2/biometrics/R/powerfx.r |only biometrics-1.0.2/biometrics/R/uestimator.r | 27 +- biometrics-1.0.2/biometrics/build/partial.rdb |binary biometrics-1.0.2/biometrics/data/biomass.rda |only biometrics-1.0.2/biometrics/data/biomass2.rda |only biometrics-1.0.2/biometrics/data/deadlianas.rda |binary biometrics-1.0.2/biometrics/data/deadlianas2.rda |binary biometrics-1.0.2/biometrics/data/hawaii.rda |only biometrics-1.0.2/biometrics/data/hawaii2.rda |only biometrics-1.0.2/biometrics/data/largeplot.rda |binary biometrics-1.0.2/biometrics/data/mortaforest.rda |binary biometrics-1.0.2/biometrics/data/mortaforest2.rda |binary biometrics-1.0.2/biometrics/data/pinaster.rda |only biometrics-1.0.2/biometrics/data/pinaster2.rda |only biometrics-1.0.2/biometrics/data/pinusSpp.rda |only biometrics-1.0.2/biometrics/data/pinusSpp2.rda |only biometrics-1.0.2/biometrics/data/plantshawaii.rda |binary biometrics-1.0.2/biometrics/data/popvol.rda |binary biometrics-1.0.2/biometrics/data/popvol2.rda |only biometrics-1.0.2/biometrics/data/spataustria.rda |binary biometrics-1.0.2/biometrics/data/spatimepsp.rda |binary biometrics-1.0.2/biometrics/data/standtabRauli.rda |only biometrics-1.0.2/biometrics/data/standtabRauli2.rda |only biometrics-1.0.2/biometrics/data/tapereuca2.rda |only biometrics-1.0.2/biometrics/data/treegrowth.rda |only biometrics-1.0.2/biometrics/data/treegrowth2.rda |only biometrics-1.0.2/biometrics/data/treelistinve.rda |only biometrics-1.0.2/biometrics/data/treelistinve2.rda |only biometrics-1.0.2/biometrics/data/treevolruca.rda |only biometrics-1.0.2/biometrics/data/treevolruca2.rda |only biometrics-1.0.2/biometrics/data/trlhawaii.rda |binary biometrics-1.0.2/biometrics/data/trlpsptime.rda |binary biometrics-1.0.2/biometrics/data/trlremeasu.rda |binary biometrics-1.0.2/biometrics/data/trlsmoopsp.rda |binary biometrics-1.0.2/biometrics/inst/CITATION | 4 biometrics-1.0.2/biometrics/man/barplotgr.Rd |only biometrics-1.0.2/biometrics/man/biomass.Rd |only biometrics-1.0.2/biometrics/man/biomass2.Rd |only biometrics-1.0.2/biometrics/man/deadlianas.Rd | 65 +++--- biometrics-1.0.2/biometrics/man/deadlianas2.Rd | 72 +++---- biometrics-1.0.2/biometrics/man/dg.Rd |only biometrics-1.0.2/biometrics/man/domvar.Rd | 36 ++- biometrics-1.0.2/biometrics/man/gtree.Rd | 35 ++- biometrics-1.0.2/biometrics/man/hawaii.Rd |only biometrics-1.0.2/biometrics/man/hawaii2.Rd |only biometrics-1.0.2/biometrics/man/interpy1.Rd |only biometrics-1.0.2/biometrics/man/interpy2.Rd |only biometrics-1.0.2/biometrics/man/kozak.Rd |only biometrics-1.0.2/biometrics/man/kozaklast.Rd |only biometrics-1.0.2/biometrics/man/kozakln.Rd |only biometrics-1.0.2/biometrics/man/largeplot.Rd | 30 +-- biometrics-1.0.2/biometrics/man/mortaforest.Rd | 83 ++++---- biometrics-1.0.2/biometrics/man/mortaforest2.Rd | 123 ++++++------ biometrics-1.0.2/biometrics/man/pinaster.Rd |only biometrics-1.0.2/biometrics/man/pinaster2.Rd |only biometrics-1.0.2/biometrics/man/pinusSpp.Rd |only biometrics-1.0.2/biometrics/man/pinusSpp2.Rd |only biometrics-1.0.2/biometrics/man/plantshawaii.Rd | 36 +-- biometrics-1.0.2/biometrics/man/popvol.Rd | 31 +-- biometrics-1.0.2/biometrics/man/popvol2.Rd |only biometrics-1.0.2/biometrics/man/powerfx.Rd |only biometrics-1.0.2/biometrics/man/spataustria.Rd | 43 ++-- biometrics-1.0.2/biometrics/man/spatimepsp.Rd | 37 +-- biometrics-1.0.2/biometrics/man/standtabRauli.Rd |only biometrics-1.0.2/biometrics/man/standtabRauli2.Rd |only biometrics-1.0.2/biometrics/man/tapereuca2.Rd |only biometrics-1.0.2/biometrics/man/treegrowth.Rd |only biometrics-1.0.2/biometrics/man/treegrowth2.Rd |only biometrics-1.0.2/biometrics/man/treelistinve.Rd |only biometrics-1.0.2/biometrics/man/treelistinve2.Rd |only biometrics-1.0.2/biometrics/man/treevolruca.Rd |only biometrics-1.0.2/biometrics/man/treevolruca2.Rd |only biometrics-1.0.2/biometrics/man/trlhawaii.Rd | 56 ++--- biometrics-1.0.2/biometrics/man/trlpsptime.Rd | 97 ++++----- biometrics-1.0.2/biometrics/man/trlremeasu.Rd | 28 +- biometrics-1.0.2/biometrics/man/trlsmoopsp.Rd | 51 ++--- biometrics-1.0.2/biometrics/man/uestimator.Rd | 18 + 131 files changed, 678 insertions(+), 536 deletions(-)
Title: 2D Cartesian Coordinate Transformation
Description: Applies affine and similarity transformations on vector spatial data (sp objects). Transformations can be defined from control points or directly from parameters. If redundant control points are provided Least Squares is applied allowing to obtain residuals and RMSE.
Author: German Carrillo [cre, aut]
Maintainer: German Carrillo <geotux_tuxman@linuxmail.org>
Diff between vec2dtransf versions 1.1.3 dated 2023-08-23 and 1.1.5 dated 2025-08-20
DESCRIPTION | 16 ++++++++++------ MD5 | 8 ++++---- NEWS.md | 8 ++++++++ README.md | 6 +++--- man/applyTransformation.Rd | 2 +- 5 files changed, 26 insertions(+), 14 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] ,
Romain Lesur [aut, cph] ,
Christophe Dervieux [ctb] ,
Brent Thorne [aut] ,
Xianying Tan [aut] ,
Atsushi Yasumoto [ctb] ,
Posit Software, PBC [cph, fnd],
Adam Hyde [ctb] ,
Min-Zhong Lu [ctb] ,
Zulko [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.22 dated 2025-01-07 and 0.23 dated 2025-08-20
DESCRIPTION | 20 +++++++++++--------- MD5 | 8 ++++---- NEWS.md | 5 +++++ inst/resources/js/hooks.js | 4 ++-- tests/test-ci/test-chrome.R | 2 +- 5 files changed, 23 insertions(+), 16 deletions(-)
Title: Exact Tests and Confidence Intervals for 2x2 Tables
Description: Calculates conditional exact tests (Fisher's exact test, Blaker's exact test, or exact McNemar's test) and unconditional exact tests (including score-based tests on differences in proportions, ratios of proportions, and odds ratios, and Boshcloo's test) with appropriate matching confidence intervals, and provides power and sample size calculations. Gives melded confidence intervals for the binomial case (Fay, et al, 2015, <DOI:10.1111/biom.12231>). Gives boundary-optimized rejection region test (Gabriel, et al, 2018, <DOI:10.1002/sim.7579>), an unconditional exact test for the situation where the controls are all expected to fail. Gives confidence intervals compatible with exact McNemar's or sign tests (Fay and Lumbard, 2021, <DOI:10.1002/sim.8829>). For review of these kinds of exact tests see Fay and Hunsberger (2021, <DOI:10.1214/21-SS131>).
Author: Michael P. Fay [aut, cre],
Sally A. Hunsberger [ctb],
Martha Nason [ctb],
Erin Gabriel [ctb],
Keith Lumbard [ctb]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between exact2x2 versions 1.6.9 dated 2024-01-25 and 1.7.0 dated 2025-08-20
ChangeLog | 4 +++ DESCRIPTION | 36 +++++++++++++++++++++++--------- MD5 | 24 ++++++++++----------- R/uncondExact2x2.R | 26 +++++++++++++++++++++++ build/vignette.rds |binary inst/doc/exact2x2.pdf |binary inst/doc/exact2x2Validation.pdf |binary inst/doc/exactMcNemar.pdf |binary inst/doc/midpAdjustment.pdf |binary inst/doc/unconditionalExact2x2Tests.pdf |binary man/exact2x2-package.Rd | 4 +-- man/power2x2.Rd | 10 ++++---- man/unirootGrid.Rd | 10 ++++---- 13 files changed, 80 insertions(+), 34 deletions(-)
Title: Vintage Sparse PCA for Semi-Parametric Factor Analysis
Description: Provides fast spectral estimation of latent factors in random
dot product graphs using the vsp estimator. Under mild assumptions,
the vsp estimator is consistent for (degree-corrected) stochastic
blockmodels, (degree-corrected) mixed-membership stochastic
blockmodels, and degree-corrected overlapping stochastic blockmodels.
Author: Karl Rohe [aut],
Muzhe Zeng [aut],
Alex Hayes [aut, cre, cph] ,
Fan Chen [aut]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between vsp versions 0.1.2 dated 2024-11-05 and 0.1.3 dated 2025-08-20
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/bff.html | 4 ++-- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Time Series Prediction with Integrated Tuning
Description: Time series prediction is a critical task in data analysis, requiring not only the selection of appropriate models, but also suitable data preprocessing and tuning strategies.
TSPredIT (Time Series Prediction with Integrated Tuning) is a framework that provides a seamless integration of data preprocessing, decomposition, model training, hyperparameter optimization, and evaluation.
Unlike other frameworks, TSPredIT emphasizes the co-optimization of both preprocessing and modeling steps, improving predictive performance.
It supports a variety of statistical and machine learning models, filtering techniques, outlier detection, data augmentation, and ensemble strategies.
More information is available in Salles et al. <doi:10.1007/978-3-662-68014-8_2>.
Author: Eduardo Ogasawara [aut, ths, cre] ,
Cristiane Gea [aut],
Diego Carvalho [ctb],
Diogo Santos [aut],
Eduardo Bezerra [ctb],
Esther Pacitti [ctb],
Fabio Porto [ctb],
Fernando Alexandrino [aut],
Rebecca Salles [aut],
Vitoria Birindiba [aut],
CEFET/RJ [cp [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between tspredit versions 1.2.727 dated 2025-06-22 and 1.2.737 dated 2025-08-20
tspredit-1.2.727/tspredit/R/ts_maintune.R |only tspredit-1.2.727/tspredit/man/ts_maintune.Rd |only tspredit-1.2.737/tspredit/DESCRIPTION | 24 ++++++++---------- tspredit-1.2.737/tspredit/MD5 | 14 +++++----- tspredit-1.2.737/tspredit/NAMESPACE | 6 ++-- tspredit-1.2.737/tspredit/R/ts_integtune.R |only tspredit-1.2.737/tspredit/R/ts_tune.R | 24 +++++++++--------- tspredit-1.2.737/tspredit/README.md | 34 +++++++++++++------------- tspredit-1.2.737/tspredit/man/ts_integtune.Rd |only tspredit-1.2.737/tspredit/man/ts_tune.Rd | 10 ++++--- 10 files changed, 56 insertions(+), 56 deletions(-)
Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for ordering objects with an implementation of several
seriation/sequencing/ordination techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Author: Michael Hahsler [aut, cre, cph] ,
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph] ,
David Barnett [ctb],
Michael Brusco [ctb, cph],
Michael Friendly [ctb],
Hans-Friedrich Koehn [ctb, cph],
Fionn Murtagh [ctb, cph],
Stephanie Stahl [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.5.7 dated 2024-12-05 and 1.5.8 dated 2025-08-20
DESCRIPTION | 14 +++++++------- MD5 | 42 +++++++++++++++++++++--------------------- NEWS.md | 7 +++++++ R/SupremeCourt.R | 6 +++--- R/bertinplot.R | 25 +++++++++++++++---------- R/criterion.R | 7 +++---- R/criterion.dist.R | 12 ++++++++++-- R/dissplot.R | 39 +++++++++++++++++++++------------------ R/ggdissplot.R | 2 +- R/pimage.R | 11 ++++++----- R/ser_dist.R | 8 ++++---- R/seriate_best.R | 6 +++--- README.md | 12 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/seriation.pdf |binary man/SupremeCourt.Rd | 6 +++--- man/bertinplot.Rd | 23 ++++++++++++++--------- man/criterion.Rd | 7 +++---- man/dissplot.Rd | 28 ++++++++++++++++------------ man/pimage.Rd | 11 ++++++----- man/ser_dist.Rd | 8 ++++---- 22 files changed, 153 insertions(+), 121 deletions(-)
Title: Noninferiority Tests with Variable Margins
Description: Noninferiority tests for difference in failure rates at a prespecified control rate or prespecified time. For details, see Fay and Follmann, 2016 <DOI:10.1177/1740774516654861>.
Author: Michael P. Fay [aut, cre]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between nivm versions 0.5 dated 2024-01-25 and 0.6 dated 2025-08-20
DESCRIPTION | 16 ++++++++++------ MD5 | 10 +++++----- NEWS | 4 ++++ man/nicqControl.Rd | 2 +- man/nicqTest.Rd | 2 +- man/powerNicqTest.Rd | 8 ++++---- 6 files changed, 25 insertions(+), 17 deletions(-)
Title: Geostatistics for Compositional Analysis
Description: Support for geostatistical analysis of multivariate data,
in particular data with restrictions, e.g. positive amounts,
compositions, distributional data, microstructural data, etc.
It includes descriptive analysis and modelling for such data, both
from a two-point Gaussian perspective and multipoint perspective.
The methods mainly follow Tolosana-Delgado, Mueller and van den
Boogaart (2018) <doi:10.1007/s11004-018-9769-3>.
Author: Raimon Tolosana-Delgado [aut] ,
Ute Mueller [aut],
K. Gerald van den Boogaart [ctb, cre],
Hassan Talebi [ctb, cph],
Helmholtz-Zentrum Dresden-Rossendorf [cph],
Edith Cowan University [cph]
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between gmGeostats versions 0.11.3 dated 2023-04-18 and 0.11.4 dated 2025-08-20
DESCRIPTION | 13 MD5 | 61 - NAMESPACE | 1 NEWS.md | 11 R/compositionsCompatibility.R | 4 R/data.R | 10 R/genDiag.R | 14 R/gmSpatialModel.R | 2 R/gstatCompatibility.R | 2 R/preparations.R | 23 R/spSupport.R | 7 R/variograms.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/gmGeostats.R | 2 inst/doc/gmGeostats.html | 520 ++++++++++++-- inst/doc/register_new_layer_datatype.R | 12 inst/doc/register_new_layer_datatype.html | 1044 +++++++++++++++++++----------- man/Maf.data.frame.Rd | 10 man/NGSAustralia.Rd | 60 - man/as.gmEVario.Rd | 3 man/coloredBiplot.genDiag.Rd | 6 man/getTellus.Rd | 4 man/gmSpatialModel-class.Rd | 2 man/gsi.EVario2D.Rd | 5 man/gsi.EVario3D.Rd | 5 man/ndirections.Rd | 3 man/plot.gmEVario.Rd | 3 man/plot.logratioVariogramAnisotropy.Rd | 2 man/variogram.Rd |only man/variogramModelPlot.gmEVario.Rd | 3 src/gmGeostats.c | 2 32 files changed, 1282 insertions(+), 556 deletions(-)
Title: Floristic Quality Assessment Tools for R
Description: Tools for downloading and analyzing floristic quality assessment data.
See Freyman et al. (2015) <doi:10.1111/2041-210X.12491> for more information
about floristic quality assessment and the associated database.
Author: Andrew Gard [aut, cre] ,
Alexia Myers [aut],
Irene Luwabelwa [aut]
Maintainer: Andrew Gard <agard@lakeforest.edu>
Diff between fqar versions 0.5.5 dated 2025-06-21 and 0.5.6 dated 2025-08-20
DESCRIPTION | 6 +-- MD5 | 42 ++++++++++++------------- NEWS.md | 6 ++- R/assessment_list_inventory.R | 5 +- R/download_assessment.R | 3 + R/download_assessment_internal.R | 24 +++++++------- R/download_assessment_list.R | 16 +++++++-- R/download_database.R | 3 + R/download_database_internal.R | 1 R/download_transect.R | 3 + R/download_transect_list.R | 12 +++++-- R/index_fqa_assessments.R | 3 + R/index_fqa_assessments_internal.R | 2 + R/index_fqa_databases.R | 2 - R/index_fqa_transects.R | 3 + R/transect_list_inventory.R | 5 +- build/vignette.rds |binary man/download_assessment_list.Rd | 4 +- man/download_transect_list.Rd | 4 +- man/index_fqa_databases.Rd | 2 - tests/testthat/test-download_assessment_list.R | 4 +- tests/testthat/test-download_transect_list.R | 5 ++ 22 files changed, 96 insertions(+), 59 deletions(-)
Title: EcoPhyloMapper
Description: Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.
Author: Pascal Title [aut, cre] ,
Donald Swiderski [aut],
Miriam Zelditch [aut]
Maintainer: Pascal Title <pascal.title@stonybrook.edu>
Diff between epm versions 1.1.5 dated 2025-07-03 and 1.1.6 dated 2025-08-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/createEPMgrid.R | 16 ++++++++++++---- 3 files changed, 18 insertions(+), 10 deletions(-)
Title: Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms
of the DBSCAN family. Includes the clustering algorithms DBSCAN
(density-based spatial clustering of applications with noise) and
HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering
points to identify the clustering structure), shared nearest neighbor
clustering, and the outlier detection algorithms LOF (local outlier
factor) and GLOSH (global-local outlier score from hierarchies). The
implementations use the kd-tree data structure (from library ANN) for
faster k-nearest neighbor search. An R interface to fast kNN and
fixed-radius NN search is also provided. Hahsler, Piekenbrock and
Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph] ,
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph],
Claudia Malzer [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.2.2 dated 2025-01-25 and 1.2.3 dated 2025-08-20
DESCRIPTION | 12 ++++++------ MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 8 ++++++++ R/dbscan.R | 37 ++++++++++++++----------------------- R/hdbscan.R | 30 ++++++++++++++++-------------- R/hullplot.R | 2 +- R/optics.R | 27 +++++++-------------------- R/pointdensity.R | 3 ++- R/reachability.R | 2 +- README.md | 17 +++++++++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/dbscan.pdf |binary man/dbscan.Rd | 2 +- man/hdbscan.Rd | 12 +++++++++++- man/hullplot.Rd | 2 +- man/optics.Rd | 2 +- man/reachability.Rd | 2 +- tests/testthat/test-mst.R | 1 - 19 files changed, 101 insertions(+), 94 deletions(-)
Title: Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Description: Provides low-level access to 'GDAL' functionality.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable
developing further tools.
Author: Michael Sumner [aut, cre] ,
Simon Wotherspoon [ctb] ,
Mark Padgham [ctb] ),
Edzer Pebesma [ctb] ,
Roger Bivand [ctb] ,
Jim Hester [ctb, cph] ,
Timothy Keitt [ctb] ,
Jeroen Ooms [ctb] ,
Dale Maschette [ctb] ,
Joseph Stachelek [ctb],
Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.11.0 dated 2025-04-04 and 0.12.0 dated 2025-08-20
DESCRIPTION | 14 +++++++------- MD5 | 22 +++++++++++----------- NEWS.md | 8 ++++++++ R/read_stream_internal.R | 10 +--------- R/vapour_vrt.R | 2 +- build/vignette.rds |binary inst/WORDLIST | 1 + inst/doc/vapour.html | 24 ++++++++++++------------ inst/include/gdalarrowstream/gdalvectorstream.h | 19 +++++++------------ inst/include/gdalreadwrite/gdalreadwrite.h | 10 +++++++--- src/00_raster_block_io.cpp | 4 ++++ tests/testthat/test-warper.R | 6 ++++-- 12 files changed, 63 insertions(+), 57 deletions(-)
Title: Density Estimation and Visualization of 2D Scatter Plots
Description: The user has the option to utilize the two-dimensional density estimation techniques called smoothed density published by Eilers and Goeman (2004) <doi:10.1093/bioinformatics/btg454>, and pareto density which was evaluated for univariate data by Thrun, Gehlert and Ultsch, 2020 <doi:10.1371/journal.pone.0238835>. Moreover, it provides visualizations of the density estimation in the form of two-dimensional scatter plots in which the points are color-coded based on increasing density. Colors are defined by the one-dimensional clustering technique called 1D distribution cluster algorithm (DDCAL) published by Lux and Rinderle-Ma (2023) <doi:10.1007/s00357-022-09428-6>.
Author: Michael Thrun [aut, cre, cph] ,
Felix Pape [aut, rev],
Luca Brinkman [aut],
Quirin Stier [aut]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between ScatterDensity versions 0.1.0 dated 2025-04-15 and 0.1.1 dated 2025-08-20
DESCRIPTION | 15 - MD5 | 16 - NAMESPACE | 5 R/PDEscatter.R | 458 +++++++++++++++++++++++---------------------- R/SmoothedDensitiesXY.R | 263 ++++++++++++++++++++----- R/fast_table_num.R |only build/partial.rdb |binary man/PDEscatter.Rd | 3 man/SmoothedDensitiesXY.Rd | 6 man/fast_table_num.Rd |only 10 files changed, 473 insertions(+), 293 deletions(-)
More information about ScatterDensity at CRAN
Permanent link
Title: Hopfield Artificial Neural Networks
Description: Builds and optimizes Hopfield artificial neural networks (Hopfield, 1982, <doi:10.1073/pnas.79.8.2554>). One-layer and three-layer models are implemented. The energy of the Hopfield network is minimized with formula from Krotov and Hopfield (2016, <doi:10.48550/ARXIV.1606.01164>). Optimization (supervised learning) is done through a gradient-based method. Classification is done with S3 methods predict(). Parallelization with 'OpenMP' is used if available during compilation.
Author: Emmanuel Paradis [aut, cre, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between hann versions 1.0 dated 2025-07-25 and 1.1 dated 2025-08-20
DESCRIPTION | 8 +++---- MD5 | 6 ++--- inst/doc/IntroductionHopfieldNetworks.pdf |binary src/prototype_7.c | 34 ++++++++++++++++-------------- 4 files changed, 26 insertions(+), 22 deletions(-)
Title: Parse XML
Description: Bindings to 'libxml2' for working with XML data using a simple,
consistent interface based on 'XPath' expressions. Also supports XML schema
validation; for 'XSLT' transformations see the 'xslt' package.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Jeroen Ooms [aut, cre],
Posit Software, PBC [cph, fnd],
R Foundation [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between xml2 versions 1.3.8 dated 2025-03-14 and 1.4.0 dated 2025-08-20
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + NEWS.md | 8 ++++++++ R/xml_parse.R | 12 ++++++++++-- build/partial.rdb |binary build/vignette.rds |binary configure | 2 +- inst/doc/modification.html | 12 ++++++------ man/read_xml.Rd | 7 ++++++- src/xml2_doc.cpp | 7 +++++-- src/xml2_init.c | 9 +++++++++ src/xml2_output.cpp | 4 ++-- tests/testthat/test-xml_parse.R | 18 ++++++++++++++++-- 14 files changed, 81 insertions(+), 33 deletions(-)
Title: An Introduction to Statistical Modeling of Extreme Values
Description: Functions to support the computations carried out in
`An Introduction to Statistical Modeling of Extreme Values' by
Stuart Coles. The functions may be divided into the following
groups; maxima/minima, order statistics, peaks over thresholds
and point processes.
Author: Eric Gilleland [cre] ,
Janet E. Heffernan [aut],
Alec G. Stephenson [ctb]
Maintainer: Eric Gilleland <eric.gilleland@colostate.edu>
Diff between ismev versions 1.42 dated 2018-05-10 and 1.43 dated 2025-08-20
ismev-1.42/ismev/INDEX |only ismev-1.43/ismev/DESCRIPTION | 21 +++++++++++++-------- ismev-1.43/ismev/MD5 | 3 +-- 3 files changed, 14 insertions(+), 10 deletions(-)
Title: A Lightweight and Flexible Web Framework
Description: A very flexible framework for building server side logic in
R. The framework is unopinionated when it comes to how HTTP requests
and WebSocket messages are handled and supports all levels of app
complexity; from serving static content to full-blown dynamic
web-apps. Fiery does not hold your hand as much as e.g. the shiny
package does, but instead sets you free to create your web app the way
you want.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between fiery versions 1.2.1 dated 2024-02-05 and 1.3.0 dated 2025-08-20
fiery-1.2.1/fiery/R/FutureStack.R |only fiery-1.2.1/fiery/inst/doc/delayed.R |only fiery-1.2.1/fiery/inst/doc/delayed.Rmd |only fiery-1.2.1/fiery/inst/doc/delayed.html |only fiery-1.2.1/fiery/tests/testthat/test-FutureStack.R |only fiery-1.2.1/fiery/vignettes/delayed.Rmd |only fiery-1.3.0/fiery/DESCRIPTION | 25 fiery-1.3.0/fiery/MD5 | 73 - fiery-1.3.0/fiery/NAMESPACE | 21 fiery-1.3.0/fiery/NEWS.md | 59 - fiery-1.3.0/fiery/R/Fire.R | 691 +++++++++++---- fiery-1.3.0/fiery/R/HandlerStack.R | 44 fiery-1.3.0/fiery/R/PromiseStack.R |only fiery-1.3.0/fiery/R/aaa.R | 103 +- fiery-1.3.0/fiery/R/additional_type_checks.R | 4 fiery-1.3.0/fiery/R/fake_request.R | 108 +- fiery-1.3.0/fiery/R/fiery-package.R | 1 fiery-1.3.0/fiery/R/loggers.R | 279 ++++-- fiery-1.3.0/fiery/R/request_store.R |only fiery-1.3.0/fiery/R/zzz.R | 6 fiery-1.3.0/fiery/README.md | 66 - fiery-1.3.0/fiery/build/vignette.rds |binary fiery-1.3.0/fiery/inst/doc/events.R | 24 fiery-1.3.0/fiery/inst/doc/events.Rmd | 84 - fiery-1.3.0/fiery/inst/doc/events.html | 9 fiery-1.3.0/fiery/inst/doc/plugins.R | 58 - fiery-1.3.0/fiery/inst/doc/plugins.html | 1 fiery-1.3.0/fiery/man/Fire.Rd | 131 ++ fiery-1.3.0/fiery/man/fake_request.Rd | 9 fiery-1.3.0/fiery/man/figures/lifecycle-deprecated.svg |only fiery-1.3.0/fiery/man/figures/lifecycle-experimental.svg |only fiery-1.3.0/fiery/man/figures/lifecycle-stable.svg |only fiery-1.3.0/fiery/man/figures/lifecycle-superseded.svg |only fiery-1.3.0/fiery/man/loggers.Rd | 8 fiery-1.3.0/fiery/man/session_id_cookie.Rd |only fiery-1.3.0/fiery/tests/testthat/_snaps/Fire.md | 674 ++++++++++++++ fiery-1.3.0/fiery/tests/testthat/_snaps/HandlerStack.md |only fiery-1.3.0/fiery/tests/testthat/_snaps/PromiseStack.md |only fiery-1.3.0/fiery/tests/testthat/_snaps/fake_request.md |only fiery-1.3.0/fiery/tests/testthat/_snaps/loggers.md |only fiery-1.3.0/fiery/tests/testthat/helper.R |only fiery-1.3.0/fiery/tests/testthat/test-Fire.R | 522 +++++++---- fiery-1.3.0/fiery/tests/testthat/test-HandlerStack.R | 45 fiery-1.3.0/fiery/tests/testthat/test-PromiseStack.R |only fiery-1.3.0/fiery/tests/testthat/test-fake_request.R | 24 fiery-1.3.0/fiery/tests/testthat/test-loggers.R | 83 + fiery-1.3.0/fiery/vignettes/events.Rmd | 84 - 47 files changed, 2317 insertions(+), 919 deletions(-)
Title: Statistical Approaches for Time-to-Event Data in Agriculture
Description: A specific and comprehensive framework for the analyses of time-to-event data in agriculture. Fit non-parametric and parametric time-to-event models. Compare time-to-event curves for different experimental groups. Plots and other displays. It is particularly tailored to the analyses of data from germination and emergence assays. The methods are described in Onofri et al. (2022) "A unified framework for the analysis of germination, emergence, and other time-to-event data in weed science", Weed Science, 70, 259-271 <doi:10.1017/wsc.2022.8>.
Author: Andrea Onofri [aut, cre]
Maintainer: Andrea Onofri <andrea.onofri@unipg.it>
Diff between drcte versions 1.0.30 dated 2023-05-08 and 1.0.65 dated 2025-08-20
DESCRIPTION | 13 - MD5 | 52 ++--- NAMESPACE | 9 NEWS.md | 10 R/ED.drcte.R | 4 R/EDpar.R | 4 R/compCDF.R | 51 ++-- R/compParmte.R |only R/dist_exponential.R |only R/dist_loglogistic.R | 5 R/dist_lognormal.R | 156 ++++++++++----- R/drm_te.R | 225 ++------------------- R/drm_te_lik.R |only R/drm_te_separate.R | 36 ++- R/plot.drcte.R | 526 +++++++++------------------------------------------ R/plotData.R | 2 R/quantile.drcte.R | 3 R/reshape.te.R | 6 R/summary.drcte.R | 25 +- README.md | 10 inst |only man/ED.drcte.Rd | 2 man/KDE.Rd | 2 man/NPMLE.Rd | 2 man/compParmte.Rd |only man/drmte.Rd | 32 +-- man/drmteControl.Rd | 5 man/exponential.Rd |only man/lognormal.Rd | 17 - man/plot.drcte.Rd | 60 ----- 30 files changed, 409 insertions(+), 848 deletions(-)
Title: Dynamic Factor Models
Description: Efficient estimation of Dynamic Factor Models using the Expectation Maximization (EM) algorithm
or Two-Step (2S) estimation, supporting datasets with missing data. Factors are assumed to follow a stationary VAR
process of order p. The estimation options follow advances in the econometric literature: either running the Kalman
Filter and Smoother once with initial values from PCA - 2S estimation as in Doz, Giannone and Reichlin (2011)
<doi:10.1016/j.jeconom.2011.02.012> - or via iterated Kalman Filtering and Smoothing until EM convergence - following
Doz, Giannone and Reichlin (2012) <doi:10.1162/REST_a_00225> - or using the adapted EM algorithm of Banbura and
Modugno (2014) <doi:10.1002/jae.2306>, allowing arbitrary patterns of missing data. The implementation makes heavy
use of the 'Armadillo' 'C++' library and the 'collapse' package, providing for particularly speedy estimation.
A comprehensive set of methods supports interpretation and visualization of the model as [...truncated...]
Author: Sebastian Krantz [aut, cre],
Rytis Bagdziunas [aut],
Santtu Tikka [rev],
Eli Holmes [rev]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between dfms versions 0.3.0 dated 2025-05-18 and 0.3.1 dated 2025-08-20
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/EMBM_MQ.R | 2 +- R/EMBM_MQ_idio.R | 1 + R/init_cond.R | 2 +- inst/doc/dynamic_factor_models.pdf |binary inst/doc/introduction.html | 4 ++-- tests/testthat/test-DFM.R | 10 ++++++++++ 9 files changed, 32 insertions(+), 16 deletions(-)
Title: Leveraging Experiment Lines to Data Analytics
Description: The natural increase in the complexity of current research experiments and data demands better tools to enhance productivity in Data Analytics. The package is a framework designed to address the modern challenges in data analytics workflows. The package is inspired by Experiment Line concepts. It aims to provide seamless support for users in developing their data mining workflows by offering a uniform data model and method API. It enables the integration of various data mining activities, including data preprocessing, classification, regression, clustering, and time series prediction. It also offers options for hyper-parameter tuning and supports integration with existing libraries and languages. Overall, the package provides researchers with a comprehensive set of functionalities for data science, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_2 [...truncated...]
Author: Eduardo Ogasawara [aut, ths, cre] ,
Ana Carolina Sa [aut],
Antonio Castro [aut],
Caio Santos [aut],
Diego Carvalho [ctb],
Diego Salles [aut],
Eduardo Bezerra [ctb],
Esther Pacitti [ctb],
Fabio Porto [ctb],
Janio Lima [aut],
Lucas Tavares [aut],
Rafae [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolbox versions 1.2.727 dated 2025-06-28 and 1.2.737 dated 2025-08-20
DESCRIPTION | 26 ++++++++++++++----- MD5 | 22 ++++++++-------- R/cla_tune.R | 16 ++++++------ R/clu_tune.R | 16 +++++++----- R/dal_tune.R | 4 ++- R/reg_tune.R | 12 +++++---- README.md | 68 ++++++++++++++++++++++++++-------------------------- man/cla_tune.Rd | 10 ++++--- man/clu_tune.Rd | 12 ++++++--- man/dal_tune.Rd | 4 ++- man/fit.cla_tune.Rd | 4 --- man/reg_tune.Rd | 7 +++-- 12 files changed, 115 insertions(+), 86 deletions(-)
Title: Detect Aberrant Behavior in Test Data
Description: Detect several types of aberrant behavior, including answer
copying, answer similarity, change point, nonparametric misfit, parametric
misfit, preknowledge, rapid guessing, and test tampering.
Author: Kylie Gorney [aut, cre] ,
Jiayi Deng [aut]
Maintainer: Kylie Gorney <kgorney@msu.edu>
Diff between aberrance versions 0.2.1 dated 2025-03-07 and 0.3.0 dated 2025-08-20
DESCRIPTION | 19 - MD5 | 54 +-- NAMESPACE | 1 NEWS.md | 10 R/checks.R | 43 +- R/compute.R | 123 ++++++- R/detect-ac.R | 17 R/detect-as.R | 90 ++--- R/detect-cp.R |only R/detect-nm.R | 727 +++++++++++++++++++++--------------------- R/detect-pk.R | 200 ++++++----- R/detect-pm.R | 200 ++++------- R/detect-rg.R | 804 +++++++++++++++++++++++------------------------ R/detect-tt.R | 140 +++++--- R/est.R | 190 +++++------ R/irt.R | 276 ++++++++-------- R/sim.R | 629 ++++++++++++++++++------------------ R/utils.R | 86 ++--- README.md | 5 man/aberrance-package.Rd | 56 +-- man/detect_ac.Rd | 304 ++++++++--------- man/detect_as.Rd | 468 ++++++++++++--------------- man/detect_cp.Rd |only man/detect_nm.Rd | 380 +++++++++++----------- man/detect_pk.Rd | 364 +++++++++------------ man/detect_pm.Rd | 455 ++++++++++++-------------- man/detect_rg.Rd | 494 ++++++++++++++-------------- man/detect_tt.Rd | 418 ++++++++++++------------ man/sim.Rd | 537 +++++++++++++++---------------- 29 files changed, 3587 insertions(+), 3503 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero-or-One Inflated
Beta Regression
Description: Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu [aut, cre],
Yunchuan Kong [ctb]
Maintainer: Fang Liu <fang.liu.131@nd.edu>
Diff between zoib versions 1.6 dated 2023-05-21 and 1.6.1 dated 2025-08-20
DESCRIPTION | 20 ++++++++++++++------ MD5 | 8 ++++---- NAMESPACE | 3 ++- man/zoib-package.Rd | 4 ++-- man/zoib.Rd | 2 +- 5 files changed, 23 insertions(+), 14 deletions(-)
Title: Interface to 'TensorFlow' Datasets
Description: Interface to 'TensorFlow' Datasets, a high-level library for
building complex input pipelines from simple, re-usable pieces.
See <https://www.tensorflow.org/guide> for additional
details.
Author: Tomasz Kalinowski [ctb, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
Yuan Tang [aut] ,
Kevin Ushey [aut],
RStudio [cph, fnd],
Google Inc. [cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between tfdatasets versions 2.17.0 dated 2024-07-16 and 2.18.0 dated 2025-08-20
tfdatasets-2.17.0/tfdatasets/R/input_fn.R |only tfdatasets-2.17.0/tfdatasets/man/input_fn.Rd |only tfdatasets-2.17.0/tfdatasets/tests/testthat/test-input-fn.R |only tfdatasets-2.18.0/tfdatasets/DESCRIPTION | 12 tfdatasets-2.18.0/tfdatasets/MD5 | 76 - tfdatasets-2.18.0/tfdatasets/NAMESPACE | 3 tfdatasets-2.18.0/tfdatasets/NEWS.md | 8 tfdatasets-2.18.0/tfdatasets/R/dataset_methods.R | 102 +- tfdatasets-2.18.0/tfdatasets/R/package.R | 4 tfdatasets-2.18.0/tfdatasets/R/sample_from_datasets.R | 2 tfdatasets-2.18.0/tfdatasets/R/text_line_dataset.R | 71 + tfdatasets-2.18.0/tfdatasets/R/utils.R | 98 + tfdatasets-2.18.0/tfdatasets/build/vignette.rds |binary tfdatasets-2.18.0/tfdatasets/inst/doc/introduction.R | 504 +++++----- tfdatasets-2.18.0/tfdatasets/inst/doc/introduction.html | 3 tfdatasets-2.18.0/tfdatasets/man/dataset_batch.Rd | 6 tfdatasets-2.18.0/tfdatasets/man/dataset_cache.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_collect.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_concatenate.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_decode_delim.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_filter.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_interleave.Rd | 28 tfdatasets-2.18.0/tfdatasets/man/dataset_map.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_map_and_batch.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_padded_batch.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_prefetch.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_prefetch_to_device.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_prepare.Rd | 3 tfdatasets-2.18.0/tfdatasets/man/dataset_rebatch.Rd |only tfdatasets-2.18.0/tfdatasets/man/dataset_reduce.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_repeat.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_shuffle.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_shuffle_and_repeat.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_skip.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_take.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_take_while.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/dataset_window.Rd | 1 tfdatasets-2.18.0/tfdatasets/man/text_line_dataset.Rd | 31 tfdatasets-2.18.0/tfdatasets/man/tfrecord_dataset.Rd | 4 tfdatasets-2.18.0/tfdatasets/tests/testthat.R | 3 tfdatasets-2.18.0/tfdatasets/tests/testthat/helper-utils.R | 4 41 files changed, 601 insertions(+), 379 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: With high-dimensional omics features, repeated measure ANOVA leads to longitudinal gene-environment interaction studies that have intra-cluster correlations, outlying observations and structured sparsity arising from the ANOVA design. In this package, we have developed robust sparse Bayesian mixed effect models tailored for the above studies (Fan et al. (2025) <doi:10.1093/jrsssc/qlaf027>). An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between mixedBayes versions 0.1.10 dated 2025-07-08 and 0.1.11 dated 2025-08-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/mixedBayes.R | 3 ++- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Extended Agglomerative Hierarchical Clustering
Description: A comprehensive collection of linkage methods for agglomerative
hierarchical clustering on a matrix of proximity data (distances or
similarities), returning a multifurcated dendrogram or multidendrogram.
Multidendrograms can group more than two clusters when ties in proximity data
occur, and therefore they do not depend on the order of the input data.
Descriptive measures to analyze the resulting dendrogram are additionally
provided.
Author: Alberto Fernandez [aut, cre] ,
Sergio Gomez [aut]
Maintainer: Alberto Fernandez <alberto.fernandez@urv.cat>
Diff between mdendro versions 2.2.1 dated 2024-01-08 and 2.2.2 dated 2025-08-20
DESCRIPTION | 13 - MD5 | 10 build/vignette.rds |binary inst/doc/Introduction.R | 46 ++-- inst/doc/Introduction.html | 482 ++++++++++++++++++++++----------------------- man/linkage.Rd | 4 6 files changed, 275 insertions(+), 280 deletions(-)
Title: Geographic Display of Survey Data Statistics
Description: Automated calculation and visualization of survey data statistics on a color-coded (choropleth) map.
Author: Samuel Ackerman [aut, cre]
Maintainer: Samuel Ackerman <smackrmn@gmail.com>
Diff between mapStats versions 3.1 dated 2023-11-10 and 3.2 dated 2025-08-20
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/mapStats.Rd | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to
visualize the fit of regression models arising from a wide variety
of models in R ('lm', 'glm', 'coxph', 'rlm', 'gam', 'locfit', 'lmer',
'randomForest', etc.)
Author: Patrick Breheny [aut, cre] ,
Woodrow Burchett [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between visreg versions 2.7.0 dated 2020-06-04 and 2.8.0 dated 2025-08-20
visreg-2.7.0/visreg/NEWS |only visreg-2.7.0/visreg/inst/doc/quick-start.R |only visreg-2.7.0/visreg/inst/doc/quick-start.Rmd |only visreg-2.7.0/visreg/inst/doc/quick-start.html |only visreg-2.7.0/visreg/inst/tests |only visreg-2.7.0/visreg/man/subset-visreg.Rd |only visreg-2.7.0/visreg/man/visreg-faq.Rd |only visreg-2.7.0/visreg/tests/run |only visreg-2.7.0/visreg/vignettes/quick-start.Rmd |only visreg-2.8.0/visreg/DESCRIPTION | 34 ++ visreg-2.8.0/visreg/MD5 | 158 ++++++------- visreg-2.8.0/visreg/NAMESPACE | 23 + visreg-2.8.0/visreg/NEWS.md |only visreg-2.8.0/visreg/R/Terms.R | 16 - visreg-2.8.0/visreg/R/collapseVisregList.R | 11 visreg-2.8.0/visreg/R/getXY.R | 9 visreg-2.8.0/visreg/R/ggContPlot.R | 7 visreg-2.8.0/visreg/R/plot-visreg.R | 87 +++++++ visreg-2.8.0/visreg/R/plotVisreg2d.R | 59 +++++ visreg-2.8.0/visreg/R/plotVisregList.R | 1 visreg-2.8.0/visreg/R/setupCond.R | 7 visreg-2.8.0/visreg/R/setupD.R | 8 visreg-2.8.0/visreg/R/setupF.R | 17 - visreg-2.8.0/visreg/R/setupV.R | 2 visreg-2.8.0/visreg/R/setupX.R | 34 +- visreg-2.8.0/visreg/R/subset.R | 23 + visreg-2.8.0/visreg/R/toplegend.R | 15 - visreg-2.8.0/visreg/R/visreg-package.R |only visreg-2.8.0/visreg/R/visreg.R | 164 ++++++++++++++ visreg-2.8.0/visreg/R/visreg2d.R | 78 ++++++ visreg-2.8.0/visreg/R/visregLatticePlot.R | 2 visreg-2.8.0/visreg/R/visregList.R | 36 +++ visreg-2.8.0/visreg/R/visregPred.R | 17 + visreg-2.8.0/visreg/R/visregResid.R | 4 visreg-2.8.0/visreg/R/visreg_coef.R |only visreg-2.8.0/visreg/README.md | 56 ++-- visreg-2.8.0/visreg/build/partial.rdb |only visreg-2.8.0/visreg/build/vignette.rds |binary visreg-2.8.0/visreg/inst/CITATION | 14 - visreg-2.8.0/visreg/inst/doc/visreg.R |only visreg-2.8.0/visreg/inst/doc/visreg.html |only visreg-2.8.0/visreg/inst/doc/visreg.rmd |only visreg-2.8.0/visreg/inst/tinytest |only visreg-2.8.0/visreg/man/plot.visreg.Rd | 227 ++++++++----------- visreg-2.8.0/visreg/man/plot.visreg2d.Rd | 124 +++++----- visreg-2.8.0/visreg/man/subset.visreg.Rd |only visreg-2.8.0/visreg/man/visreg-package.Rd | 59 ++--- visreg-2.8.0/visreg/man/visreg.Rd | 303 +++++++++++--------------- visreg-2.8.0/visreg/man/visreg2d.Rd | 176 +++++++-------- visreg-2.8.0/visreg/man/visregList.Rd | 52 ++-- visreg-2.8.0/visreg/tests/test.R |only visreg-2.8.0/visreg/vignettes/visreg.rmd |only 52 files changed, 1122 insertions(+), 701 deletions(-)
Title: Simulate and Diagnose (Generalized) Linear Models
Description: Simulate samples from populations with known covariate
distributions, generate response variables according to common linear and
generalized linear model families, draw from sampling distributions of
regression estimates, and perform visual inference on diagnostics from model
fits.
Author: Alex Reinhart [aut, cre]
Maintainer: Alex Reinhart <areinhar@stat.cmu.edu>
Diff between regressinator versions 0.2.0 dated 2024-08-16 and 0.3.0 dated 2025-08-20
DESCRIPTION | 13 + MD5 | 69 +++++---- NAMESPACE | 2 NEWS.md | 26 +++ R/diagnose.R | 27 +++ R/residuals.R | 98 ++++++++++---- README.md | 32 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/linear-regression-diagnostics.R | 28 ++-- inst/doc/linear-regression-diagnostics.Rmd | 49 ++++--- inst/doc/linear-regression-diagnostics.html | 45 +++--- inst/doc/logistic-regression-diagnostics.R | 20 +- inst/doc/logistic-regression-diagnostics.Rmd | 56 ++++++-- inst/doc/logistic-regression-diagnostics.html | 27 ++- inst/doc/other-glm-diagnostics.R | 26 +-- inst/doc/other-glm-diagnostics.Rmd | 62 +++++++- inst/doc/other-glm-diagnostics.html | 34 ++-- inst/doc/regressinator.R | 16 +- inst/doc/regressinator.Rmd | 69 ++++++--- inst/doc/regressinator.html | 146 ++++++++++----------- man/augment_longer.Rd | 6 man/augment_quantile.Rd | 29 ++++ man/bin_by_interval.Rd | 6 man/figures/README-example-regression-lineup-1.png |binary man/model_lineup.Rd | 6 man/parametric_boot_distribution.Rd | 8 - man/partial_residuals.Rd | 32 ++-- man/sampling_distribution.Rd | 6 tests/testthat/test-diagnose.R | 19 ++ tests/testthat/test-residuals.R | 34 ++++ vignettes/linear-regression-diagnostics.Rmd | 49 ++++--- vignettes/logistic-regression-diagnostics.Rmd | 56 ++++++-- vignettes/other-glm-diagnostics.Rmd | 62 +++++++- vignettes/regressinator.Rmd | 69 ++++++--- 36 files changed, 830 insertions(+), 397 deletions(-)
Title: Identify Naturally Continuous Lines in a Spatial Network
Description: Provides functionality to group lines that form naturally
continuous lines in a spatial network. The algorithm implemented is based
on the Continuity in Street Networks (COINS) method from Tripathy et al.
(2021) <doi:10.1177/2399808320967680>, which identifies continuous
"strokes" in the network as the line strings that maximize the angles
between consecutive segments.
Author: Francesco Nattino [aut, cre, cph] ,
Claudiu Forgaci [aut] ,
Fakhereh Alidoost [aut] ,
Thijs van Lankveld [ctb] ,
Netherlands eScience Center [fnd]
Maintainer: Francesco Nattino <f.nattino@esciencecenter.nl>
Diff between rcoins versions 0.3.2 dated 2025-05-29 and 0.4.0 dated 2025-08-20
rcoins-0.3.2/rcoins/inst/doc/using-rcoins.R |only rcoins-0.3.2/rcoins/man/figures/continuous-streets.png |only rcoins-0.3.2/rcoins/man/figures/streets.png |only rcoins-0.4.0/rcoins/DESCRIPTION | 8 rcoins-0.4.0/rcoins/MD5 | 33 ++- rcoins-0.4.0/rcoins/NEWS.md | 17 + rcoins-0.4.0/rcoins/R/example_data.R | 87 ++++++++-- rcoins-0.4.0/rcoins/R/stroke.R | 3 rcoins-0.4.0/rcoins/README.md | 83 ++++----- rcoins-0.4.0/rcoins/build/vignette.rds |binary rcoins-0.4.0/rcoins/inst/doc/using-rcoins.Rmd | 48 +---- rcoins-0.4.0/rcoins/inst/doc/using-rcoins.html | 16 + rcoins-0.4.0/rcoins/man/figures/README-continuous-streets-1.png |only rcoins-0.4.0/rcoins/man/figures/README-streets-1.png |only rcoins-0.4.0/rcoins/man/figures/logo.png |only rcoins-0.4.0/rcoins/man/get_example_data.Rd | 15 + rcoins-0.4.0/rcoins/man/get_example_data_file.Rd |only rcoins-0.4.0/rcoins/tests/testthat/test-stroke.R | 7 rcoins-0.4.0/rcoins/vignettes/figures |only rcoins-0.4.0/rcoins/vignettes/precompile.R |only rcoins-0.4.0/rcoins/vignettes/using-rcoins.Rmd | 48 +---- rcoins-0.4.0/rcoins/vignettes/using-rcoins.Rmd.orig |only 22 files changed, 210 insertions(+), 155 deletions(-)
Title: A Modern K-Means (MKMeans) Clustering Algorithm
Description: It's a Modern K-Means clustering algorithm which works for data of any number of dimensions, has no limit with number of clusters expected, and can start with any initial cluster centers.
Author: Yarong Yang [aut, cre],
Nader Ebrahimi [ctb],
Yoram Rubin [ctb],
Jacob Zhang [ctb]
Maintainer: Yarong Yang <Yi.YA_yaya@hotmail.com>
Diff between MKMeans versions 3.1 dated 2024-10-08 and 3.2 dated 2025-08-20
DESCRIPTION | 24 ++++++++-------- MD5 | 16 +++++----- NAMESPACE | 2 - R/MKMeans.R | 14 ++++++--- man/C.f.Rd | 2 - man/Dist.Rd | 3 -- man/MKMean-class.Rd | 4 +- man/MKMeans-package.Rd | 50 +++++++++++++++++++++++++++++----- man/MKMeans.Rd | 72 +++++++++++++++++++++++++++++++++++++++---------- 9 files changed, 133 insertions(+), 54 deletions(-)
Title: Generalized Beta Distribution of the Second Kind: Properties,
Likelihood, Estimation
Description: The GB2 package explores the Generalized Beta distribution of the second kind. Density, cumulative distribution function, quantiles and moments of the distribution are given. Functions for the full log-likelihood, the profile log-likelihood and the scores are provided. Formulas for various indicators of inequality and poverty under the GB2 are implemented. The GB2 is fitted by the methods of maximum pseudo-likelihood estimation using the full and profile log-likelihood, and non-linear least squares estimation of the model parameters. Various plots for the visualization and analysis of the results are provided. Variance estimation of the parameters is provided for the method of maximum pseudo-likelihood estimation. A mixture distribution based on the compounding property of the GB2 is presented (denoted as "compound" in the documentation). This mixture distribution is based on the discretization of the distribution of the underlying random scale parameter. The discretization can be left [...truncated...]
Author: Monique Graf [aut],
Desislava Nedyalkova. [aut],
Desislava Nedyalkova [cre]
Maintainer: Desislava Nedyalkova <desislava.nedyalkova@gmail.com>
Diff between GB2 versions 2.1.1 dated 2022-06-22 and 2.1.2 dated 2025-08-20
DESCRIPTION | 33 ++++++++++++++++++++++++--------- MD5 | 15 ++++++++------- NEWS.md |only man/CompoundAuxVarest.Rd | 4 ++-- man/CompoundDensPlot.Rd | 2 +- man/CompoundVarest.Rd | 6 +++--- man/Fisk.Rd | 2 +- man/MLfullGB2.Rd | 2 +- man/MLprofGB2.Rd | 2 +- 9 files changed, 41 insertions(+), 25 deletions(-)
Title: Extended Kalman Filters for Animal Movement
Description: Synthetic generation of 1-D and 2-D correlated random walks (CRWs) for animal movement with behavioral switching, and particle filter estimation of movement parameters from observed trajectories using Extended Kalman Filter (EKF) model. See Ackerman (2018) <https://digital.library.temple.edu/digital/collection/p245801coll10/id/499150>.
Author: Samuel Ackerman [aut, cre]
Maintainer: Samuel Ackerman <smackrmn@gmail.com>
Diff between animalEKF versions 1.2 dated 2023-09-29 and 1.3 dated 2025-08-20
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++--------- build/partial.rdb |binary data/bc_longlat_map.rda |binary data/bc_longlat_map_img_ras.rda |binary data/shark_data_longlat.rda |binary data/shark_data_raw.rda |binary man/EKF_1d_interp_joint.Rd | 2 +- man/EKF_interp_joint.Rd | 2 +- man/make_segments.Rd | 2 +- 10 files changed, 18 insertions(+), 17 deletions(-)
Title: Pediatrics Extension Package for ADaM in 'R' Asset Library
Description: A toolbox for programming Clinical Data Standards Interchange
Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
ADaM datasets are a mandatory part of any New Drug or Biologics
License Application submitted to the United States Food and Drug
Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>). The package is
an extension package of the 'admiral' package for pediatric clinical
trials.
Author: Fanny Gautier [aut, cre] ,
Ross Farrugia [aut],
Zelos Zhu [aut],
Sukalpo Saha [aut],
Lina Patil [aut],
Samia Kabi [aut],
Laura Liao [ctb],
Remigiusz Kudlacz [ctb],
Pierre Wallet [ctb],
Amin Sherzad [ctb],
David Freedman [ctb],
Mahmoud Hamza [ctb],
Cy [...truncated...]
Maintainer: Fanny Gautier <fanny.gautier@cytel.com>
Diff between admiralpeds versions 0.2.0 dated 2025-01-16 and 0.2.1 dated 2025-08-20
DESCRIPTION | 16 ++++--- MD5 | 34 +++++++++------- NEWS.md | 18 ++++++++ R/data.R | 80 +++++++++++++++++++-------------------- inst/WORDLIST | 2 man/admiralpeds-package.Rd | 4 - man/figures/atorus_logo.png |only man/figures/cytel_logo.png |only man/figures/pfizer_logo.png |only man/figures/roche_logo.png |only man/who_bmi_for_age_boys.Rd | 8 +-- man/who_bmi_for_age_girls.Rd | 8 +-- man/who_hc_for_age_boys.Rd | 8 +-- man/who_hc_for_age_girls.Rd | 8 +-- man/who_lgth_ht_for_age_boys.Rd | 8 +-- man/who_lgth_ht_for_age_girls.Rd | 8 +-- man/who_wt_for_age_boys.Rd | 8 +-- man/who_wt_for_age_girls.Rd | 8 +-- man/who_wt_for_lgth_boys.Rd | 8 +-- man/who_wt_for_lgth_girls.Rd | 8 +-- 20 files changed, 130 insertions(+), 104 deletions(-)
Title: Training Run Tools for 'TensorFlow'
Description: Create and manage unique directories for each 'TensorFlow'
training run. Provides a unique, time stamped directory for each run
along with functions to retrieve the directory of the latest run or
latest several runs.
Author: Tomasz Kalinowski [ctb, cre],
Daniel Falbel [ctb],
JJ Allaire [aut],
RStudio [cph, fnd],
Mike Bostock [cph] ,
Masayuki Tanaka [cph] ,
jQuery Foundation [cph] ,
jQuery contributors [cph] ,
Shaun Bowe [cph] ,
Materialize [cph] ,
Yuxi You [cph] ,
Kevin [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz@rstudio.com>
Diff between tfruns versions 1.5.3 dated 2024-04-19 and 1.5.4 dated 2025-08-20
DESCRIPTION | 8 ++--- MD5 | 22 +++++++-------- NEWS.md | 4 ++ R/flags.R | 2 - build/vignette.rds |binary inst/doc/managing.R | 12 ++++---- inst/doc/managing.html | 5 ++- inst/doc/overview.R | 24 ++++++++-------- inst/doc/overview.html | 19 +++++++------ inst/doc/tuning.R | 70 ++++++++++++++++++++++++------------------------- inst/doc/tuning.html | 3 +- man/flags.Rd | 2 - 12 files changed, 89 insertions(+), 82 deletions(-)
Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the density, EM, and censored EM version (Bartoš & Schimmack, 2022,
<doi:10.15626/MP.2021.2720>; Schimmack & Bartoš, 2023, <doi: 10.1371/journal.pone.0290084>),
as well as the original density z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>).
Furthermore, the package provides summarizing and plotting functions for the fitted z-curve objects.
See the aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: Frantisek Bartos [aut, cre],
Ulrich Schimmack [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between zcurve versions 2.4.3 dated 2025-05-16 and 2.4.4 dated 2025-08-20
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/zcurve_density.R | 4 ++-- build/partial.rdb |binary src/zcurveEM.cpp | 20 +++++++------------- tests/testthat/_snaps/zcurve/z-curve-em-ggplot.svg | 2 +- tests/testthat/_snaps/zcurve/z-curve-em.svg | 2 +- tests/testthat/test-zcurve.R | 18 +++++++++--------- 8 files changed, 30 insertions(+), 36 deletions(-)
Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic
and Atmospheric Administration (NOAA) Integrated Surface Database
(ISD, see
<https://www.ncei.noaa.gov/products/land-based-station/integrated-surface-database>).
Author: David Carslaw [aut, cre] ,
Jack Davison [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.10.0 dated 2025-07-30 and 0.10.1 dated 2025-08-20
DESCRIPTION | 6 LICENSE | 4 MD5 | 36 NAMESPACE | 16 NEWS.md | 12 R/exportADMS.R | 374 +++---- R/getMeta.R | 596 ++++++------ R/importNOAA.R | 2265 ++++++++++++++++++++++++------------------------ R/importNOAAlite.R | 402 ++++---- R/weatherCodes.R | 24 R/worldmet-package.R | 48 - README.md | 184 +-- man/exportADMS.Rd | 72 - man/getMeta.Rd | 196 ++-- man/getMetaLive.Rd | 60 - man/importNOAA.Rd | 314 +++--- man/importNOAAlite.Rd | 218 ++-- man/weatherCodes.Rd | 52 - man/worldmet-package.Rd | 86 - 19 files changed, 2554 insertions(+), 2411 deletions(-)
Title: Statistical Test App with R 'shiny'
Description: Provides a user-friendly R 'shiny' app for performing various statistical tests on datasets.
It allows users to upload data in numerous formats and perform statistical analyses.
The app dynamically adapts its options based on the selected columns and supports both single and multiple column comparisons.
The app's user interface is designed to streamline the process of selecting datasets, columns, and test options,
making it easy for users to explore and interpret their data. The underlying functions for statistical tests are well-organized and can be used independently within other R scripts.
Author: Tomer Iwan [aut, cre],
Corneel Den Hartogh [ctb] ,
Jesus Blanco [ctb],
VU Analytics [cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between vvdoctor versions 0.0.1 dated 2024-04-27 and 0.0.2 dated 2025-08-20
vvdoctor-0.0.1/vvdoctor/R/rsconnect |only vvdoctor-0.0.2/vvdoctor/DESCRIPTION | 13 - vvdoctor-0.0.2/vvdoctor/MD5 | 21 +- vvdoctor-0.0.2/vvdoctor/NEWS.md | 28 ++- vvdoctor-0.0.2/vvdoctor/R/global.R | 93 +++++++--- vvdoctor-0.0.2/vvdoctor/R/server.R | 79 ++++++-- vvdoctor-0.0.2/vvdoctor/R/ui.R | 88 +++++---- vvdoctor-0.0.2/vvdoctor/README.md | 9 vvdoctor-0.0.2/vvdoctor/man/create_dependent_variable_histogram.Rd | 34 +-- vvdoctor-0.0.2/vvdoctor/man/determine_dependent_variable.Rd | 34 +-- vvdoctor-0.0.2/vvdoctor/man/determine_independent_variable.Rd | 34 +-- vvdoctor-0.0.2/vvdoctor/man/perform_statistical_test.Rd | 38 ++-- 12 files changed, 310 insertions(+), 161 deletions(-)
Title: 'Serpstat' API Wrapper
Description: The primary goal of 'Serpstat' API <https://api-docs.serpstat.com/docs/serpstat-public-api/jenasqbwtxdlr-introduction-to-serpstat-api>
is to reduce manual SEO (search engine optimization) and PPC (pay-per-click)
tasks. You can automate your keywords research or competitors analysis
with this API wrapper.
Author: Alex Danilin [aut, cre]
Maintainer: Alex Danilin <alexnikdanilin@gmail.com>
Diff between serpstatr versions 0.3.0 dated 2024-08-16 and 0.4.0 dated 2025-08-20
DESCRIPTION | 11 - MD5 | 68 +++++----- NAMESPACE | 2 NEWS.md | 11 + R/audit.R | 16 -- R/backlinks.R | 20 +-- R/project_management.R | 31 ++-- R/rank_tracker.R | 41 +++--- R/search_analytics.R | 195 ++++++++++++++++++++++--------- R/utility_functions.R | 22 --- README.md | 17 +- man/serpstatr.Rd | 2 man/sst_au_get_summary.Rd | 11 - man/sst_au_start.Rd | 8 - man/sst_bl_domain_summary.Rd | 14 -- man/sst_bl_referring_domains.Rd | 14 -- man/sst_call_api_method.Rd | 20 --- man/sst_pm_create_project.Rd | 17 +- man/sst_pm_delete_project.Rd | 11 - man/sst_pm_list_projects.Rd | 17 +- man/sst_rt_competitors.Rd | 14 -- man/sst_rt_positions_history.Rd | 17 +- man/sst_rt_project_regions.Rd | 18 +- man/sst_rt_serp_history.Rd | 17 +- man/sst_sa_database_info.Rd | 12 + man/sst_sa_domain_history.Rd | 14 -- man/sst_sa_domain_keywords.Rd | 14 -- man/sst_sa_domain_keywords_per_region.Rd |only man/sst_sa_domain_organic_competitors.Rd | 14 -- man/sst_sa_domain_top_pages.Rd | 14 -- man/sst_sa_domains_info.Rd | 14 -- man/sst_sa_keyword_top.Rd | 24 ++- man/sst_sa_keywords.Rd | 14 -- man/sst_sa_keywords_info.Rd | 14 -- man/sst_sa_related_keywords.Rd |only man/sst_sa_stats.Rd | 9 - 36 files changed, 406 insertions(+), 351 deletions(-)
Title: Credit Risk Scorecard
Description: The `scorecard` package makes the development of credit risk scorecard
easier and efficient by providing functions for some common tasks,
such as data partition, variable selection, woe binning, scorecard scaling,
performance evaluation and report generation. These functions can also used
in the development of machine learning models.
The references including:
1. Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard:
Development and Implementation Using SAS.
2. Siddiqi, N. (2006, ISBN: 9780471754510). Credit risk scorecards.
Developing and Implementing Intelligent Credit Scoring.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between scorecard versions 0.4.4 dated 2024-04-13 and 0.4.5 dated 2025-08-20
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/one_hot.R | 3 ++- R/perf.R | 2 +- R/var_filter.R | 10 ++++++++-- R/woebin.R | 2 +- inst/doc/demo.html | 4 ++-- 8 files changed, 29 insertions(+), 18 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.6.1 dated 2025-07-18 and 0.6.2 dated 2025-08-20
DESCRIPTION | 6 +- MD5 | 24 ++++----- NEWS.md | 10 ++++ R/MaestroPipelineList.R | 15 ++++++ R/MaestroSchedule.R | 5 -- R/invoke.R | 2 build/vignette.rds |binary inst/doc/maestro-1-quick-start.html | 8 +-- inst/doc/maestro-3-advanced-scheduling.html | 16 +++--- inst/doc/maestro-4-directed-acyclic-graphs.html | 26 +++++----- inst/doc/maestro-5-logging.html | 60 ++++++++++++------------ man/MaestroPipelineList.Rd | 21 ++++++++ tests/testthat/test-invoke.R | 27 ++++++++++ 13 files changed, 145 insertions(+), 75 deletions(-)
Title: Mean Comparison in 'ggplot2'
Description: Add mean comparison annotations to a 'ggplot'.
This package provides an easy way to indicate if two or more groups are significantly different in a 'ggplot'.
Usually you do not need to specify the test method, you only need to tell stat_compare() whether you want to perform a parametric test or a nonparametric test, and stat_compare() will automatically choose the appropriate test method based on your data.
For comparisons between two groups, the p-value is calculated by t-test (parametric) or Wilcoxon rank sum test (nonparametric). For comparisons among more than two groups, the p-value is calculated by One-way ANOVA (parametric) or Kruskal-Wallis test (nonparametric).
Author: Hao Wang [aut, cre]
Maintainer: Hao Wang <wanghao8772@gmail.com>
Diff between ggcompare versions 0.0.3 dated 2024-12-09 and 0.0.4 dated 2025-08-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 +++++- R/GGExtensions.R | 13 ++++++------- 4 files changed, 18 insertions(+), 15 deletions(-)
Title: Code Sharing at the Department of Epidemiology Research at
Statens Serum Institut
Description: This is a collection of assorted functions and examples collected
from various projects. Currently we have functionalities for simplifying
overlapping time intervals, Charlson comorbidity score constructors for
Danish data, getting frequency for multiple variables, getting standardized
output from logistic and log-linear regressions, sibling design linear
regression functionalities a method for calculating the confidence intervals
for functions of parameters from a GLM, Bayes equivalent for hypothesis
testing with asymptotic Bayes factor, and several help functions for
generalized random forest analysis using 'grf'.
Author: Anders Husby [aut] ,
Anna Laksafoss [aut] ,
Emilia Myrup Thiesson [aut] ,
Kim Daniel Jakobsen [aut, cre] ,
Mikael Andersson [aut] ,
Klaus Rostgaard [aut]
Maintainer: Kim Daniel Jakobsen <kija@ssi.dk>
Diff between EpiForsk versions 0.1.1 dated 2024-02-26 and 0.2.0 dated 2025-08-20
DESCRIPTION | 27 MD5 | 64 NAMESPACE | 3 R/adls_flatten_date_intervals.R | 8 R/aso_charlson_score.R | 1688 +++++++++--------- R/aso_freq_function.R | 2900 +++++++++++++++---------------- R/aso_freq_function_repeated.R | 294 +-- R/aso_odds_ratio_function.R | 1820 +++++++++---------- R/aso_odds_ratio_function_repeated.R | 671 ++++--- R/kija_c_for_benefit.R | 850 ++++----- R/kija_cate_surface.R | 558 ++--- R/kija_causal_forest_dynamic_subgroups.R | 938 +++++----- R/kija_discrete_covariates_to_onehot.R | 2 R/kija_fct_confint.R | 365 --- R/kija_list_permute.R |only R/kija_lms.R | 6 R/kija_rate_omnibus_test.R | 825 +++++--- R/kija_rate_test.R | 236 +- README.md | 17 build/vignette.rds |binary inst/doc/Contributing.R | 18 inst/doc/Contributing.html | 2 inst/doc/Writing_functions.R | 2 inst/doc/andh_forest_plot.R | 12 inst/doc/andh_forest_plot.html | 32 man/DiscreteCovariatesToOneHot.Rd | 2 man/EpiForsk-package.Rd | 8 man/ListPermute.Rd |only man/RATEOmnibusTest.Rd | 70 man/RATETest.Rd | 2 man/charlson_score.Rd | 8 man/fct_confint.Rd | 26 man/flatten_date_intervals.Rd | 8 man/lms.Rd | 6 34 files changed, 5803 insertions(+), 5665 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and inference.
This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC,
Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu
Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete,
Gaussian and conditional Gaussian networks, along with many score functions and
conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented.
Some utility functions (model comparison and manipulation, random data generation, arc
orientation testing, simple and advanced plots) are included, as well as support for
parameter estimation (maximum likelihood and Bayesian) and inference, conditional
probability queries, cross-validation, bootstrap and model averaging.
Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre],
Tomi Silander [ctb]
Maintainer: Marco Scutari <scutari@bnlearn.com>
Diff between bnlearn versions 5.0.2 dated 2025-01-07 and 5.1 dated 2025-08-20
bnlearn-5.0.2/bnlearn/R/frontend-data.R |only bnlearn-5.0.2/bnlearn/R/sanitization-discretization.R |only bnlearn-5.0.2/bnlearn/src/graphs/is.dag.c |only bnlearn-5.0.2/bnlearn/src/inference/loss.c |only bnlearn-5.0.2/bnlearn/src/parameters/discrete/classic_discrete.c |only bnlearn-5.0.2/bnlearn/src/parameters/discrete/hierarchical_dirichlet.c |only bnlearn-5.0.2/bnlearn/src/parameters/rinterface/classic_discrete.c |only bnlearn-5.0.2/bnlearn/src/parameters/rinterface/hierarchical_dirichlet.c |only bnlearn-5.0.2/bnlearn/src/parameters/rinterface/mixture_ordinary_least_squares.c |only bnlearn-5.0.2/bnlearn/src/parameters/rinterface/ordinary_least_squares.c |only bnlearn-5.0.2/bnlearn/src/scores/nml_regret.c |only bnlearn-5.0.2/bnlearn/src/scores/nml_regret_table.c |only bnlearn-5.1/bnlearn/Changelog | 54 + bnlearn-5.1/bnlearn/DESCRIPTION | 8 bnlearn-5.1/bnlearn/MD5 | 255 +++---- bnlearn-5.1/bnlearn/NAMESPACE | 16 bnlearn-5.1/bnlearn/R/backend-indep.R | 6 bnlearn-5.1/bnlearn/R/backend-s4.R | 3 bnlearn-5.1/bnlearn/R/causal.R |only bnlearn-5.1/bnlearn/R/ci.test.R | 4 bnlearn-5.1/bnlearn/R/classifiers.R | 1 bnlearn-5.1/bnlearn/R/cpdag.R | 152 ++++ bnlearn-5.1/bnlearn/R/cpq.R | 2 bnlearn-5.1/bnlearn/R/cv.R | 19 bnlearn-5.1/bnlearn/R/enumeration.R | 96 ++ bnlearn-5.1/bnlearn/R/formula.R | 2 bnlearn-5.1/bnlearn/R/frontend-amat.R | 2 bnlearn-5.1/bnlearn/R/frontend-arcs.R | 9 bnlearn-5.1/bnlearn/R/frontend-bn.R | 155 ++-- bnlearn-5.1/bnlearn/R/frontend-bootstrap.R | 26 bnlearn-5.1/bnlearn/R/frontend-causal.R |only bnlearn-5.1/bnlearn/R/frontend-fit.R | 13 bnlearn-5.1/bnlearn/R/frontend-foreign.R | 4 bnlearn-5.1/bnlearn/R/frontend-formula.R | 7 bnlearn-5.1/bnlearn/R/frontend-graph.R | 101 ++ bnlearn-5.1/bnlearn/R/frontend-missingdata.R | 9 bnlearn-5.1/bnlearn/R/frontend-mvnorm.R | 2 bnlearn-5.1/bnlearn/R/frontend-nodes.R | 62 + bnlearn-5.1/bnlearn/R/frontend-packages.R | 6 bnlearn-5.1/bnlearn/R/frontend-plot.R | 14 bnlearn-5.1/bnlearn/R/frontend-predict.R | 3 bnlearn-5.1/bnlearn/R/frontend-preprocessing.R |only bnlearn-5.1/bnlearn/R/frontend-print.R | 11 bnlearn-5.1/bnlearn/R/frontend-queries.R | 2 bnlearn-5.1/bnlearn/R/frontend-score.R | 51 + bnlearn-5.1/bnlearn/R/frontend-simulation.R | 9 bnlearn-5.1/bnlearn/R/frontend-strength.R | 14 bnlearn-5.1/bnlearn/R/globals.R | 65 + bnlearn-5.1/bnlearn/R/graphviz-compare.R | 22 bnlearn-5.1/bnlearn/R/hill-climbing.R | 32 bnlearn-5.1/bnlearn/R/kullback.leibler.R | 21 bnlearn-5.1/bnlearn/R/learning-algorithms.R | 19 bnlearn-5.1/bnlearn/R/likelihood.R | 3 bnlearn-5.1/bnlearn/R/loss.R | 310 ++++++--- bnlearn-5.1/bnlearn/R/nparams.R | 3 bnlearn-5.1/bnlearn/R/predict.R | 23 bnlearn-5.1/bnlearn/R/sanitization-enumeration.R | 18 bnlearn-5.1/bnlearn/R/sanitization-fitting.R | 1 bnlearn-5.1/bnlearn/R/sanitization-graph.R | 58 + bnlearn-5.1/bnlearn/R/sanitization-loss.R | 43 - bnlearn-5.1/bnlearn/R/sanitization-preprocessing.R |only bnlearn-5.1/bnlearn/R/sanitization-queries.R | 75 +- bnlearn-5.1/bnlearn/R/sanitization-scores.R | 15 bnlearn-5.1/bnlearn/R/sanitization-strength.R | 60 + bnlearn-5.1/bnlearn/R/sid.R |only bnlearn-5.1/bnlearn/R/tabu.R | 2 bnlearn-5.1/bnlearn/R/utils-graph.R | 125 +-- bnlearn-5.1/bnlearn/R/utils-misc.R | 7 bnlearn-5.1/bnlearn/man/alarm.Rd | 6 bnlearn-5.1/bnlearn/man/alpha.star.Rd | 4 bnlearn-5.1/bnlearn/man/arc.strength.Rd | 6 bnlearn-5.1/bnlearn/man/asia.Rd | 4 bnlearn-5.1/bnlearn/man/bayesian.network.classifiers.Rd | 4 bnlearn-5.1/bnlearn/man/bn.cv.Rd | 65 - bnlearn-5.1/bnlearn/man/bn.fit.Rd | 33 bnlearn-5.1/bnlearn/man/bn.kcv.class.Rd | 4 bnlearn-5.1/bnlearn/man/bnboot.Rd | 4 bnlearn-5.1/bnlearn/man/bnlearn-package.Rd | 6 bnlearn-5.1/bnlearn/man/causal.inference.Rd |only bnlearn-5.1/bnlearn/man/compare.Rd | 34 - bnlearn-5.1/bnlearn/man/conditional.independence.tests.Rd | 29 bnlearn-5.1/bnlearn/man/coronary.Rd | 2 bnlearn-5.1/bnlearn/man/count.graphs.Rd | 36 - 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Title: Lorenz and Penalized Lorenz Regressions
Description: Inference for the Lorenz and penalized Lorenz regressions. More broadly, the package proposes functions to assess inequality and graphically represent it. The Lorenz Regression procedure is introduced in Heuchenne and Jacquemain (2022) <doi:10.1016/j.csda.2021.107347> and in Jacquemain, A., C. Heuchenne, and E. Pircalabelu (2024) <doi:10.1214/23-EJS2200>.
Author: Alexandre Jacquemain [aut, cre] ,
Xingjie Shi [ctb]
Maintainer: Alexandre Jacquemain <aljacquemain@gmail.com>
Diff between LorenzRegression versions 2.2.0 dated 2025-06-27 and 2.3.0 dated 2025-08-20
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/LR-plot.R | 11 +++++++---- R/Lorenz-graphs.R | 46 ++++++++++++---------------------------------- R/PLR-plot.R | 35 ++++++++++++++++++++++++++--------- man/Lorenz.graphs.Rd | 6 +++++- man/autoplot.LR.Rd | 12 +++++++++++- man/autoplot.PLR.Rd | 5 +++++ 9 files changed, 81 insertions(+), 60 deletions(-)
More information about LorenzRegression at CRAN
Permanent link
Title: Hartigan's Dip Test Statistic for Unimodality - Corrected
Description: Compute Hartigan's dip test statistic for unimodality /
multimodality and provide a test with simulation based p-values, where
the original public code has been corrected.
Author: Martin Maechler [aut, cre] ,
Dario Ringach [aut]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between diptest versions 0.77-1 dated 2024-04-10 and 0.77-2 dated 2025-08-20
diptest-0.77-1/diptest/TODO |only diptest-0.77-2/diptest/DESCRIPTION | 22 +++++++---- diptest-0.77-2/diptest/MD5 | 19 ++++----- diptest-0.77-2/diptest/build/vignette.rds |binary diptest-0.77-2/diptest/inst/doc/diptest-issues.R | 1 diptest-0.77-2/diptest/inst/doc/diptest-issues.Rnw | 6 +-- diptest-0.77-2/diptest/inst/doc/diptest-issues.pdf |binary diptest-0.77-2/diptest/man/dip.Rd | 2 - diptest-0.77-2/diptest/tests/ex1.R | 2 - diptest-0.77-2/diptest/tests/ex1.Rout.save | 40 ++++++++++---------- diptest-0.77-2/diptest/vignettes/diptest-issues.Rnw | 6 +-- 11 files changed, 53 insertions(+), 45 deletions(-)
Title: Optimizing Consistency and Coverage in Configurational Causal
Modeling
Description: This is an add-on to the 'cna' package <https://CRAN.R-project.org/package=cna> comprising various functions for optimizing consistency and coverage scores of models of configurational comparative methods as Coincidence Analysis (CNA) and Qualitative Comparative Analysis (QCA). The function conCovOpt() calculates con-cov optima, selectMax() selects con-cov maxima among the con-cov optima, DNFbuild() can be used to build models actually reaching those optima, and findOutcomes() identifies those factor values in analyzed data that can be modeled as outcomes. For a theoretical introduction to these functions see Baumgartner and Ambuehl (2021) <doi:10.1177/0049124121995554>.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cnaOpt versions 0.5.2 dated 2022-07-08 and 0.5.3 dated 2025-08-20
DESCRIPTION | 8 - MD5 | 14 +- inst/NEWS | 3 man/cnaOpt.Rd | 14 +- man/conCovOpt.Rd | 12 +- man/conCovOpt_utils.Rd | 231 ++++++++++++++++++++++++------------------------- man/ereduce.Rd | 2 man/findOutcomes.Rd | 148 +++++++++++++++---------------- 8 files changed, 218 insertions(+), 214 deletions(-)
Title: Exploratory Web Apps for Analyzing Clinical Trials Data
Description: A 'shiny' based interactive exploration framework for
analyzing clinical trials data. 'teal' currently provides a dynamic
filtering facility and different data viewers. 'teal' 'shiny'
applications are built using standard 'shiny' modules.
Author: Dawid Kaledkowski [aut, cre] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Kartikeya Kirar [aut],
Vedha Viyash [aut],
Marcin Kosinski [aut],
Adrian Waddell [aut],
Dony Unardi [rev],
Nina Qi [rev],
Nikolas Burkoff [aut],
M [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal versions 0.16.0 dated 2025-02-23 and 1.0.0 dated 2025-08-20
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Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between parameters versions 0.27.0 dated 2025-07-09 and 0.28.0 dated 2025-08-20
parameters-0.27.0/parameters/R/print_table.R |only parameters-0.28.0/parameters/DESCRIPTION | 16 parameters-0.28.0/parameters/MD5 | 72 +- parameters-0.28.0/parameters/NAMESPACE | 6 parameters-0.28.0/parameters/NEWS.md | 25 parameters-0.28.0/parameters/R/display.R | 251 +-------- parameters-0.28.0/parameters/R/equivalence_test.R | 70 ++ parameters-0.28.0/parameters/R/extract_random_parameters.R | 54 + parameters-0.28.0/parameters/R/extract_random_variances.R | 237 +------- parameters-0.28.0/parameters/R/format.R | 102 --- parameters-0.28.0/parameters/R/methods_coxme.R | 193 ++++++ parameters-0.28.0/parameters/R/methods_lme4.R | 192 ------ parameters-0.28.0/parameters/R/methods_nlme.R | 2 parameters-0.28.0/parameters/R/methods_selection.R | 33 - parameters-0.28.0/parameters/R/p_function.R | 40 - parameters-0.28.0/parameters/R/print.compare_parameters.R | 7 parameters-0.28.0/parameters/R/print.parameters_model.R | 136 +--- parameters-0.28.0/parameters/R/print_html.R | 229 +++++--- parameters-0.28.0/parameters/R/print_md.R | 199 ------- parameters-0.28.0/parameters/R/standardize_parameters.R | 22 parameters-0.28.0/parameters/R/utils_format.R | 276 ---------- parameters-0.28.0/parameters/R/utils_pca_efa.R | 8 parameters-0.28.0/parameters/README.md | 2 parameters-0.28.0/parameters/inst/WORDLIST | 2 parameters-0.28.0/parameters/man/display.parameters_model.Rd | 226 -------- parameters-0.28.0/parameters/man/model_parameters.Rd | 3 parameters-0.28.0/parameters/man/model_parameters.aov.Rd | 1 parameters-0.28.0/parameters/man/model_parameters.htest.Rd | 1 parameters-0.28.0/parameters/man/p_function.Rd | 65 ++ parameters-0.28.0/parameters/man/principal_components.Rd | 17 parameters-0.28.0/parameters/man/print.compare_parameters.Rd | 24 parameters-0.28.0/parameters/man/print.parameters_model.Rd | 28 - parameters-0.28.0/parameters/tests/testthat/test-compare_parameters.R | 98 ++- parameters-0.28.0/parameters/tests/testthat/test-include_reference.R | 4 parameters-0.28.0/parameters/tests/testthat/test-marginaleffects.R | 4 parameters-0.28.0/parameters/tests/testthat/test-model_parameters.coxme.R | 82 ++ parameters-0.28.0/parameters/tests/testthat/test-printing.R | 27 parameters-0.28.0/parameters/tests/testthat/test-sampleSelection.R |only 38 files changed, 1110 insertions(+), 1644 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares
or REML by adding the function r() to formulas of lm() and glm(). A collection of
text-book statistics for higher education is also included, e.g. modifications
of the functions lm(), glm() and associated summaries from the package 'stats'.
Author: Kristian Hovde Liland [aut, cre],
Solve Saeboe¸ [ctb],
R Core Team [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.4.2 dated 2025-01-14 and 1.4.3 dated 2025-08-20
DESCRIPTION | 14 +- MD5 | 19 +- NAMESPACE | 3 NEWS | 9 + R/anova.R |only R/hasse.R | 9 - R/lm.R | 327 ++++++-------------------------------------------- R/utilities.R | 2 man/AnovaMix.Rd | 13 + man/lm.Rd | 11 + man/print.AnovaMix.Rd | 16 ++ 11 files changed, 115 insertions(+), 308 deletions(-)
Title: Generate Publication Ready Visualizations of Single Cell
Transcriptomics Data
Description: A system that provides a streamlined way of generating
publication ready plots for known Single-Cell transcriptomics data in
a “publication ready” format. This is, the goal is to automatically
generate plots with the highest quality possible, that can be used
right away or with minimal modifications for a research article.
Author: Enrique Blanco-Carmona [cre, aut]
Maintainer: Enrique Blanco-Carmona <scpubr@gmail.com>
Diff between SCpubr versions 2.0.2 dated 2023-10-11 and 3.0.0 dated 2025-08-20
SCpubr-2.0.2/SCpubr/R/do_CopyNumberVariantPlot.R |only SCpubr-2.0.2/SCpubr/R/do_CorrelationPlot.R |only SCpubr-2.0.2/SCpubr/R/do_FunctionalAnnotationPlot.R |only SCpubr-2.0.2/SCpubr/R/do_GeyserPlot.R |only SCpubr-2.0.2/SCpubr/R/do_GroupedGOTermPlot.R |only SCpubr-2.0.2/SCpubr/R/do_GroupwiseDEPlot.R |only SCpubr-2.0.2/SCpubr/R/do_PathwayActivityPlot.R |only SCpubr-2.0.2/SCpubr/R/do_TFActivityPlot.R |only SCpubr-2.0.2/SCpubr/man/do_CopyNumberVariantPlot.Rd |only SCpubr-2.0.2/SCpubr/man/do_CorrelationPlot.Rd |only SCpubr-2.0.2/SCpubr/man/do_FunctionalAnnotationPlot.Rd |only SCpubr-2.0.2/SCpubr/man/do_GeyserPlot.Rd |only SCpubr-2.0.2/SCpubr/man/do_GroupedGOTermPlot.Rd |only SCpubr-2.0.2/SCpubr/man/do_GroupwiseDEPlot.Rd |only SCpubr-2.0.2/SCpubr/man/do_PathwayActivityPlot.Rd |only SCpubr-2.0.2/SCpubr/man/do_TFActivityPlot.Rd |only SCpubr-2.0.2/SCpubr/man/examples/examples_do_CopyNumberVariantPlot.R |only SCpubr-2.0.2/SCpubr/man/examples/examples_do_CorrelationPlot.R |only SCpubr-2.0.2/SCpubr/man/examples/examples_do_FunctionalAnnotationPlot.R |only SCpubr-2.0.2/SCpubr/man/examples/examples_do_GeyserPlot.R |only SCpubr-2.0.2/SCpubr/man/examples/examples_do_GroupedGOTermPlot.R |only SCpubr-2.0.2/SCpubr/man/examples/examples_do_GroupwiseDEPlot.R |only SCpubr-2.0.2/SCpubr/man/examples/examples_do_PathwayActivityPlot.R |only SCpubr-2.0.2/SCpubr/man/examples/examples_do_TFActivityPlot.R |only SCpubr-2.0.2/SCpubr/man/package_report.Rd |only SCpubr-2.0.2/SCpubr/tests/testthat/test-do_CopyNumberVariantPlot.R |only SCpubr-2.0.2/SCpubr/tests/testthat/test-do_CorrelationPlot.R |only SCpubr-2.0.2/SCpubr/tests/testthat/test-do_FunctionalAnnotationPlot.R |only SCpubr-2.0.2/SCpubr/tests/testthat/test-do_GeyserPlot.R |only SCpubr-2.0.2/SCpubr/tests/testthat/test-do_GroupedGOTermPlot.R |only SCpubr-2.0.2/SCpubr/tests/testthat/test-do_GroupwiseDEPlot.R |only SCpubr-2.0.2/SCpubr/tests/testthat/test-do_PathwayActivityPlot.R |only SCpubr-2.0.2/SCpubr/tests/testthat/test-do_TFActivityPlot.R |only SCpubr-3.0.0/SCpubr/DESCRIPTION | 28 SCpubr-3.0.0/SCpubr/MD5 | 226 + SCpubr-3.0.0/SCpubr/NAMESPACE | 26 SCpubr-3.0.0/SCpubr/NEWS.md | 150 + SCpubr-3.0.0/SCpubr/R/do_ActivityHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_AlluvialPlot.R | 31 SCpubr-3.0.0/SCpubr/R/do_BarPlot.R | 17 SCpubr-3.0.0/SCpubr/R/do_BeeSwarmPlot.R | 14 SCpubr-3.0.0/SCpubr/R/do_BoxPlot.R | 69 SCpubr-3.0.0/SCpubr/R/do_CNVHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_CellularStatesPlot.R | 1236 +++++----- SCpubr-3.0.0/SCpubr/R/do_ChordDiagramPlot.R | 89 SCpubr-3.0.0/SCpubr/R/do_ColorBlindCheck.R |only SCpubr-3.0.0/SCpubr/R/do_ColorPalette.R | 9 SCpubr-3.0.0/SCpubr/R/do_CorrelationHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_DimPlot.R | 195 + SCpubr-3.0.0/SCpubr/R/do_DotPlot.R | 431 ++- SCpubr-3.0.0/SCpubr/R/do_EnrichmentHeatmap.R | 61 SCpubr-3.0.0/SCpubr/R/do_ExpressionHeatmap.R | 42 SCpubr-3.0.0/SCpubr/R/do_FeaturePlot.R | 111 SCpubr-3.0.0/SCpubr/R/do_GroupwiseDEHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_LigandReceptorPlot.R |only SCpubr-3.0.0/SCpubr/R/do_LoadingsHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_MetadataHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_NebulosaPlot.R | 2 SCpubr-3.0.0/SCpubr/R/do_PathwayActivityHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_RankedEnrichmentHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_RankedExpressionHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_RidgePlot.R | 152 - SCpubr-3.0.0/SCpubr/R/do_SCEnrichmentHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_SCExpressionHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_StripPlot.R |only SCpubr-3.0.0/SCpubr/R/do_TFActivityHeatmap.R |only SCpubr-3.0.0/SCpubr/R/do_TermEnrichmentPlot.R | 392 +-- SCpubr-3.0.0/SCpubr/R/do_ViolinPlot.R | 77 SCpubr-3.0.0/SCpubr/R/do_VolcanoPlot.R | 82 SCpubr-3.0.0/SCpubr/R/do_WafflePlot.R |only SCpubr-3.0.0/SCpubr/R/utils.R | 1209 +++++---- SCpubr-3.0.0/SCpubr/R/zzz.R | 4 SCpubr-3.0.0/SCpubr/README.md | 27 SCpubr-3.0.0/SCpubr/build/partial.rdb |binary SCpubr-3.0.0/SCpubr/build/vignette.rds |binary SCpubr-3.0.0/SCpubr/inst/extdata/enriched_terms_example.rds |binary SCpubr-3.0.0/SCpubr/man/do_ActivityHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_AlluvialPlot.Rd | 5 SCpubr-3.0.0/SCpubr/man/do_BarPlot.Rd | 3 SCpubr-3.0.0/SCpubr/man/do_BeeSwarmPlot.Rd | 3 SCpubr-3.0.0/SCpubr/man/do_BoxPlot.Rd | 14 SCpubr-3.0.0/SCpubr/man/do_CNVHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_CellularStatesPlot.Rd | 5 SCpubr-3.0.0/SCpubr/man/do_ChordDiagramPlot.Rd | 7 SCpubr-3.0.0/SCpubr/man/do_ColorBlindCheck.Rd |only SCpubr-3.0.0/SCpubr/man/do_CorrelationHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_DimPlot.Rd | 9 SCpubr-3.0.0/SCpubr/man/do_DotPlot.Rd | 95 SCpubr-3.0.0/SCpubr/man/do_EnrichmentHeatmap.Rd | 14 SCpubr-3.0.0/SCpubr/man/do_ExpressionHeatmap.Rd | 12 SCpubr-3.0.0/SCpubr/man/do_FeaturePlot.Rd | 6 SCpubr-3.0.0/SCpubr/man/do_GroupwiseDEHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_LigandReceptorPlot.Rd |only SCpubr-3.0.0/SCpubr/man/do_LoadingsHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_MetadataHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_PackageReport.Rd |only SCpubr-3.0.0/SCpubr/man/do_PathwayActivityHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_RankedEnrichmentHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_RankedExpressionHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_RidgePlot.Rd | 48 SCpubr-3.0.0/SCpubr/man/do_SCEnrichmentHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_SCExpressionHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_StripPlot.Rd |only SCpubr-3.0.0/SCpubr/man/do_TFActivityHeatmap.Rd |only SCpubr-3.0.0/SCpubr/man/do_TermEnrichmentPlot.Rd | 101 SCpubr-3.0.0/SCpubr/man/do_ViolinPlot.Rd | 6 SCpubr-3.0.0/SCpubr/man/do_VolcanoPlot.Rd | 14 SCpubr-3.0.0/SCpubr/man/do_WafflePlot.Rd |only SCpubr-3.0.0/SCpubr/man/doc_function.Rd | 22 SCpubr-3.0.0/SCpubr/man/examples/examples_do_ActivityHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_CNVHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_ColorBlindCheck.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_CorrelationHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_DotPlot.R | 47 SCpubr-3.0.0/SCpubr/man/examples/examples_do_GroupwiseDEHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_LigandReceptorPlot.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_LoadingsHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_MetadataHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_PathwayActivityHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_RankedEnrichmentHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_RankedExpressionHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_RidgePlot.R | 23 SCpubr-3.0.0/SCpubr/man/examples/examples_do_SCEnrichmentHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_SCExpressionHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_StripPlot.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_TFActivityHeatmap.R |only SCpubr-3.0.0/SCpubr/man/examples/examples_do_TermEnrichmentPlot.R | 8 SCpubr-3.0.0/SCpubr/man/examples/examples_do_WafflePlot.R |only SCpubr-3.0.0/SCpubr/tests/testthat/setup.R | 46 SCpubr-3.0.0/SCpubr/tests/testthat/test-do_ActivityHeatmap.R |only SCpubr-3.0.0/SCpubr/tests/testthat/test-do_AlluvialPlot.R | 98 SCpubr-3.0.0/SCpubr/tests/testthat/test-do_BarPlot.R | 137 - SCpubr-3.0.0/SCpubr/tests/testthat/test-do_BeeSwarmPlot.R | 120 SCpubr-3.0.0/SCpubr/tests/testthat/test-do_BoxPlot.R | 57 SCpubr-3.0.0/SCpubr/tests/testthat/test-do_CNVHeatmap.R |only SCpubr-3.0.0/SCpubr/tests/testthat/test-do_CellularStatesPlot.R | 64 SCpubr-3.0.0/SCpubr/tests/testthat/test-do_ChordDiagramPlot.R | 59 SCpubr-3.0.0/SCpubr/tests/testthat/test-do_ColorBlindCheck.R |only SCpubr-3.0.0/SCpubr/tests/testthat/test-do_ColorPalette.R | 14 SCpubr-3.0.0/SCpubr/tests/testthat/test-do_CorrelationHeatmap.R |only SCpubr-3.0.0/SCpubr/tests/testthat/test-do_DimPlot.R | 140 - SCpubr-3.0.0/SCpubr/tests/testthat/test-do_DotPlot.R | 202 - SCpubr-3.0.0/SCpubr/tests/testthat/test-do_EnrichmentHeatmap.R | 37 SCpubr-3.0.0/SCpubr/tests/testthat/test-do_ExpressionHeatmap.R | 7 SCpubr-3.0.0/SCpubr/tests/testthat/test-do_FeaturePlot.R | 251 +- SCpubr-3.0.0/SCpubr/tests/testthat/test-do_GroupwiseDEHeatmap.R |only SCpubr-3.0.0/SCpubr/tests/testthat/test-do_LigandReceptorPlot.R |only SCpubr-3.0.0/SCpubr/tests/testthat/test-do_LoadingsHeatmap.R |only SCpubr-3.0.0/SCpubr/tests/testthat/test-do_MetadataHeatmap.R |only SCpubr-3.0.0/SCpubr/tests/testthat/test-do_NebulosaPlot.R | 157 - 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Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine (version 3.50.4) and for various extensions is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 2.4.2 dated 2025-07-18 and 2.4.3 dated 2025-08-20
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 7 +++++++ build/vignette.rds |binary src/vendor/sqlite3/sqlite3.c | 43 +++++++++++++++++++++++++++++++++++-------- src/vendor/sqlite3/sqlite3.h | 6 +++--- 6 files changed, 55 insertions(+), 21 deletions(-)
Title: Natural Language Processing for Meta Analysis
Description: Given a CSV file with titles and abstracts, the package creates a
document-term matrix that is lemmatized and stemmed and can directly be used to
train machine learning methods for automatic title-abstract screening in the
preparation of a meta analysis.
Author: Nico Bruder [aut] ,
Samuel Zimmermann [aut] ,
Johannes Vey [aut] ,
Maximilian Pilz [aut, cre] ,
Institute of Medical Biometry - University of Heidelberg [cph]
Maintainer: Maximilian Pilz <maximilian.pilz@itwm.fraunhofer.de>
Diff between MetaNLP versions 0.1.3 dated 2024-11-07 and 0.1.4 dated 2025-08-20
MetaNLP-0.1.3/MetaNLP/tests/testthat/_snaps/constructor/wordcloud-exclude.svg |only MetaNLP-0.1.3/MetaNLP/tests/testthat/_snaps/constructor/wordcloud-include.svg |only MetaNLP-0.1.3/MetaNLP/tests/testthat/_snaps/constructor/wordcloud.svg |only MetaNLP-0.1.4/MetaNLP/DESCRIPTION | 18 - MetaNLP-0.1.4/MetaNLP/MD5 | 37 ++- MetaNLP-0.1.4/MetaNLP/NAMESPACE | 3 MetaNLP-0.1.4/MetaNLP/NEWS.md | 8 MetaNLP-0.1.4/MetaNLP/R/MetaNLP.R | 105 ++++++--- MetaNLP-0.1.4/MetaNLP/R/useful_functions.R | 112 ++++++++-- MetaNLP-0.1.4/MetaNLP/man/MetaNLP.Rd | 7 MetaNLP-0.1.4/MetaNLP/man/plot-MetaNLP-missing-method.Rd | 25 +- MetaNLP-0.1.4/MetaNLP/man/summary.Rd | 6 MetaNLP-0.1.4/MetaNLP/man/wordcloud.Rd |only MetaNLP-0.1.4/MetaNLP/tests/testthat/_snaps/constructor/barplot-exclude.svg |only MetaNLP-0.1.4/MetaNLP/tests/testthat/_snaps/constructor/barplot-include.svg |only MetaNLP-0.1.4/MetaNLP/tests/testthat/_snaps/constructor/barplot-n.svg |only MetaNLP-0.1.4/MetaNLP/tests/testthat/_snaps/constructor/barplot-sw-f.svg |only MetaNLP-0.1.4/MetaNLP/tests/testthat/_snaps/constructor/barplot-sw-t.svg |only MetaNLP-0.1.4/MetaNLP/tests/testthat/_snaps/constructor/barplot.svg |only MetaNLP-0.1.4/MetaNLP/tests/testthat/_snaps/summary |only MetaNLP-0.1.4/MetaNLP/tests/testthat/data/test_data.csv | 8 MetaNLP-0.1.4/MetaNLP/tests/testthat/test_constructor.R | 63 +++++ MetaNLP-0.1.4/MetaNLP/tests/testthat/test_summary.R | 98 ++++++++ 23 files changed, 407 insertions(+), 83 deletions(-)
Title: Fused Partitioned Regression for Clinical and Omics Data
Description: Fit (generalized) linear regression models in each leaf node of a tree.
The tree is constructed using clinical variables only. The linear regression
models are constructed using (high-dimensional) omics variables only. The
leaf-node-specific regression models are estimated using the penalized likelihood
including a standard ridge (L2) penalty and a fusion penalty that links the
leaf-node-specific regression models to one another. The intercepts of the
leaf nodes reflect the effects of the clinical variables and are left
unpenalized. The tree, fitted with the clinical variables only,
should be constructed outside of the package with the 'rpart' 'R' package.
See Goedhart and others (2024) <doi:10.48550/arXiv.2411.02396> for details
on the method.
Author: Jeroen M. Goedhart [aut, cre, cph] ,
Wessel N. van Wieringen [aut] ,
Thomas Klausch [ths],
Mark A. van de Wiel [ths],
Hanarth Fonds [fnd]
Maintainer: Jeroen M. Goedhart <jeroengoed@gmail.com>
Diff between fusedTree versions 1.0.1 dated 2025-07-11 and 1.1.0 dated 2025-08-20
DESCRIPTION | 8 MD5 | 25 NEWS.md | 19 R/fusedTree.R | 987 ++++++++++++++++++-------------- README.md | 217 ++++++- man/CVfoldsTree.Rd | 8 man/Dat_Tree.Rd | 10 man/PenOpt.Rd | 16 man/figures/README-binary-example-1.png |binary man/figures/README-fit-fusedTree-1.png |binary man/figures/README-fit-tree-1.png |binary man/figures/README-survial-data-1.png |only man/fusedTree.Rd | 26 man/predict.fusedTree.Rd | 19 14 files changed, 865 insertions(+), 470 deletions(-)
Title: Co-Data Learning for Bayesian Additive Regression Trees
Description: Estimate prior variable weights for Bayesian Additive Regression
Trees (BART). These weights correspond to the probabilities of the variables
being selected in the splitting rules of the sum-of-trees.
Weights are estimated using empirical Bayes and external information on
the explanatory variables (co-data).
BART models are fitted using the 'dbarts' 'R' package.
See Goedhart and others (2023) <doi:10.1002/sim.70004> for details.
Author: Jeroen M. Goedhart [aut, cre, cph] ,
Thomas Klausch [aut],
Mark A. van de Wiel [aut],
Vincent Dorie [ctb] ,
Hanarth Fonds [fnd]
Maintainer: Jeroen M. Goedhart <jeroengoed@gmail.com>
Diff between EBcoBART versions 1.1.1 dated 2025-01-14 and 1.1.2 dated 2025-08-20
DESCRIPTION | 14 +++++++------- MD5 | 14 ++++++++------ NEWS.md | 6 ++++++ R/EBcoBART_Functions.R | 2 +- R/data.R | 2 +- build |only inst |only man/Bloodplatelet.Rd | 2 +- man/EBcoBART.Rd | 2 +- 9 files changed, 25 insertions(+), 17 deletions(-)
Title: Tidy Analysis Tools for Mortality, Fertility, Migration and
Population Data
Description: Analysing vital statistics based on tools
consistent with the tidyverse. Tools are provided for data visualization,
life table calculations, computing net migration numbers, Lee-Carter
modelling; functional data modelling and forecasting.
Author: Rob Hyndman [aut, cre, cph] ,
Sixian Tang [aut] ,
Miles McBain [ctb] ,
Mitchell O'Hara-Wild [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between vital versions 1.1.0 dated 2024-06-21 and 2.0.0 dated 2025-08-20
vital-1.1.0/vital/R/australia.R |only vital-1.1.0/vital/data/aus_fertility.rda |only vital-1.1.0/vital/data/aus_mortality.rda |only vital-1.1.0/vital/man/aus_fertility.Rd |only vital-1.1.0/vital/man/aus_mortality.Rd |only vital-2.0.0/vital/DESCRIPTION | 29 vital-2.0.0/vital/MD5 | 196 ++-- vital-2.0.0/vital/NAMESPACE | 29 vital-2.0.0/vital/NEWS.md | 14 vital-2.0.0/vital/R/FDM.R | 174 ++- vital-2.0.0/vital/R/LC.R | 269 +++-- vital-2.0.0/vital/R/STMF.R |only vital-2.0.0/vital/R/STMOMO.R |only vital-2.0.0/vital/R/augment.R | 43 vital-2.0.0/vital/R/autoplot.R | 70 - vital-2.0.0/vital/R/collapse_ages.R | 69 - vital-2.0.0/vital/R/components.R | 50 - vital-2.0.0/vital/R/dplyr-verbs-fable.R | 50 - vital-2.0.0/vital/R/dplyr-verbs.R | 63 + vital-2.0.0/vital/R/dplyr-verbs_models.R | 1 vital-2.0.0/vital/R/fable.R | 16 vital-2.0.0/vital/R/fabletools.R | 516 ++++++----- vital-2.0.0/vital/R/fmean.R | 96 +- vital-2.0.0/vital/R/fnaive.R | 62 - vital-2.0.0/vital/R/forecast.R | 201 +++- vital-2.0.0/vital/R/generate.R | 82 + vital-2.0.0/vital/R/hfd.R | 14 vital-2.0.0/vital/R/hmd.R | 106 +- vital-2.0.0/vital/R/interpolate.R | 72 - vital-2.0.0/vital/R/ktdb.R |only vital-2.0.0/vital/R/life_expectancy.R | 6 vital-2.0.0/vital/R/life_table.R | 84 + vital-2.0.0/vital/R/make_pr.R | 60 - vital-2.0.0/vital/R/model.R | 162 ++- vital-2.0.0/vital/R/net_migration.R | 61 - vital-2.0.0/vital/R/norway.R | 14 vital-2.0.0/vital/R/parse.R | 247 +++-- vital-2.0.0/vital/R/popsim.R |only vital-2.0.0/vital/R/smooth.R | 508 ++++++---- vital-2.0.0/vital/R/smooth_mortality_law.R |only vital-2.0.0/vital/R/sysdata.rda |only vital-2.0.0/vital/R/total_fertility_rate.R | 27 vital-2.0.0/vital/R/transform.R | 345 ++++--- vital-2.0.0/vital/R/undo_pr.R | 60 - vital-2.0.0/vital/R/vital.R | 181 ++- vital-2.0.0/vital/R/vital_package.R | 4 vital-2.0.0/vital/R/vital_vars.R | 2 vital-2.0.0/vital/README.md | 327 ++---- vital-2.0.0/vital/build |only vital-2.0.0/vital/data/norway_births.rda |binary vital-2.0.0/vital/data/norway_fertility.rda |binary vital-2.0.0/vital/data/norway_mortality.rda |binary vital-2.0.0/vital/inst |only vital-2.0.0/vital/man/FDM.Rd | 7 vital-2.0.0/vital/man/FMEAN.Rd | 4 vital-2.0.0/vital/man/FNAIVE.Rd | 4 vital-2.0.0/vital/man/GAPC.Rd |only vital-2.0.0/vital/man/LC.Rd | 7 vital-2.0.0/vital/man/age_components.Rd | 4 vital-2.0.0/vital/man/as_vital.Rd | 2 vital-2.0.0/vital/man/autoplot.fbl_vtl_ts.Rd | 9 vital-2.0.0/vital/man/autoplot.mdl_vtl_df.Rd | 7 vital-2.0.0/vital/man/autoplot.vital.Rd | 2 vital-2.0.0/vital/man/cohort_components.Rd |only vital-2.0.0/vital/man/collapse_ages.Rd | 6 vital-2.0.0/vital/man/figures/README-autoplot-1.png |binary vital-2.0.0/vital/man/figures/README-e0-1.png |binary vital-2.0.0/vital/man/figures/README-lc3-1.png |binary vital-2.0.0/vital/man/figures/README-smoothing-1.png |binary vital-2.0.0/vital/man/forecast.Rd | 24 vital-2.0.0/vital/man/generate.Rd | 3 vital-2.0.0/vital/man/generate_population.Rd |only vital-2.0.0/vital/man/interpolate.Rd | 10 vital-2.0.0/vital/man/life_expectancy.Rd | 6 vital-2.0.0/vital/man/life_table.Rd | 8 vital-2.0.0/vital/man/make_pr.Rd | 6 vital-2.0.0/vital/man/model.Rd | 4 vital-2.0.0/vital/man/norway_births.Rd | 12 vital-2.0.0/vital/man/read_hmd.Rd | 7 vital-2.0.0/vital/man/read_ktdb.Rd |only vital-2.0.0/vital/man/read_ktdb_files.Rd |only vital-2.0.0/vital/man/read_stmf.Rd |only vital-2.0.0/vital/man/read_stmf_files.Rd |only vital-2.0.0/vital/man/reexports.Rd | 4 vital-2.0.0/vital/man/smooth_mortality_law.Rd |only vital-2.0.0/vital/man/smooth_vital.Rd | 12 vital-2.0.0/vital/man/time_components.Rd | 5 vital-2.0.0/vital/man/total_fertility_rate.Rd | 4 vital-2.0.0/vital/man/undo_pr.Rd | 4 vital-2.0.0/vital/man/vital-package.Rd | 8 vital-2.0.0/vital/man/vital_vars.Rd | 2 vital-2.0.0/vital/tests/testthat/AUSstmfout.csv |only vital-2.0.0/vital/tests/testthat/faustl.txt |only vital-2.0.0/vital/tests/testthat/maustl.txt |only vital-2.0.0/vital/tests/testthat/test-FDM.R | 52 - vital-2.0.0/vital/tests/testthat/test-FMEAN.R | 43 vital-2.0.0/vital/tests/testthat/test-FNAIVE.R | 43 vital-2.0.0/vital/tests/testthat/test-LC.R | 139 +- vital-2.0.0/vital/tests/testthat/test-coherent-forecast.R | 10 vital-2.0.0/vital/tests/testthat/test-coherent.R | 26 vital-2.0.0/vital/tests/testthat/test-collapse_ages.R | 14 vital-2.0.0/vital/tests/testthat/test-dplyr.R | 66 - vital-2.0.0/vital/tests/testthat/test-hmd.R | 28 vital-2.0.0/vital/tests/testthat/test-ktdb.R |only vital-2.0.0/vital/tests/testthat/test-lifetable.R | 13 vital-2.0.0/vital/tests/testthat/test-smooth-mortality-law.R |only vital-2.0.0/vital/tests/testthat/test-smooth.R | 28 vital-2.0.0/vital/tests/testthat/test-stmf.R |only vital-2.0.0/vital/tests/testthat/test_STMOMO.R |only vital-2.0.0/vital/vignettes |only 110 files changed, 3053 insertions(+), 1890 deletions(-)
Title: Trend Removal for Vector Autoregressive Workflows
Description: Detrending multivariate time-series to approximate stationarity when dealing with intensive longitudinal data, prior to Vector Autoregressive (VAR) or multilevel-VAR estimation. Classical VAR assumes weak stationarity (constant first two moments), and deterministic trends inflate spurious autocorrelation, biasing Granger-causality and impulse-response analyses. All functions operate on raw panel data and write detrended columns back to the data set, but differ in the level at which the trend is estimated. See, for instance, Wang & Maxwell (2015) <doi:10.1037/met0000030>; Burger et al. (2022) <doi:10.4324/9781003111238-13>; Epskamp et al. (2018) <doi:10.1177/2167702617744325>.
Author: Giuseppe Corbelli [aut, cre]
Maintainer: Giuseppe Corbelli <giuseppe.corbelli@uniroma1.it>
Diff between statioVAR versions 0.1.2 dated 2025-07-30 and 0.1.3 dated 2025-08-20
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- NEWS.md | 8 ++++++++ R/detrender.R | 47 +++++++++++++++++++++++++++++++---------------- R/pooled.R | 16 ++++++++-------- R/statioVAR-package.R | 21 +++++++++++---------- build |only inst/WORDLIST | 5 +++++ man/detrender.Rd | 37 ++++++++++++++++++++++++++----------- man/pooled.Rd | 12 ++++++------ man/statioVAR.Rd | 19 ++++++++++--------- 11 files changed, 118 insertions(+), 72 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-api>.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.12.0 dated 2025-01-13 and 2.13.1 dated 2025-08-20
DESCRIPTION | 17 +++++------ MD5 | 19 ++++++------ NAMESPACE | 1 NEWS.md | 12 +++++++ R/fbErrors.R |only R/fbGetAds.R | 66 ++++++++++++++++++++++++++++++++----------- R/zzz.R | 2 - README.md | 2 - build/partial.rdb |binary man/fbGetAds.Rd | 26 +++++++++++++--- man/rfacebookstat-package.Rd | 2 - 11 files changed, 106 insertions(+), 41 deletions(-)
Title: Powerful Classes for HTTP Requests and Responses
Description: In order to facilitate parsing of http requests and creating
appropriate responses this package provides two classes to handle a lot of
the housekeeping involved in working with http exchanges. The infrastructure
builds upon the 'rook' specification and is thus well suited to be combined
with 'httpuv' based web servers.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between reqres versions 0.2.5 dated 2022-08-19 and 1.0.0 dated 2025-08-20
DESCRIPTION | 29 MD5 | 61 + NAMESPACE | 38 - NEWS.md | 61 + R/aaa.R | 205 ++++++ R/formatters.R | 24 R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/parsers.R | 17 R/problems.R |only R/reqres-package.R | 9 R/request.R | 1039 +++++++++++++++++++++++---------- R/response.R | 656 +++++++++++++++----- R/sysdata.rda |binary R/zzz.R |only README.md | 63 +- man/Request.Rd | 486 ++++++++++++--- man/Response.Rd | 534 ++++++++++++++-- man/abort_http_problem.Rd |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/formatters.Rd | 6 man/mime_type_from_file.Rd |only man/parsers.Rd | 7 man/query_parser.Rd |only man/random_key.Rd |only man/reqres-package.Rd | 2 man/session_cookie.Rd |only src |only tests/testthat.R | 8 tests/testthat/_snaps |only tests/testthat/test-aaa.R |only tests/testthat/test-formatters.R |only tests/testthat/test-parsers.R |only tests/testthat/test-problems.R |only tests/testthat/test-request.R | 277 ++++++++ tests/testthat/test-response.R | 482 ++++++++++++++- tests/testthat/test-session-cookie.R |only 40 files changed, 3216 insertions(+), 788 deletions(-)
Title: Spatial Objects of the Czech Republic
Description: Administrative regions and other spatial objects of the Czech Republic.
Author: Jindra Lacko [aut, cre] ,
Nick Bearman [rev]
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between RCzechia versions 1.12.6 dated 2025-03-14 and 1.12.8 dated 2025-08-20
DESCRIPTION | 34 +++++++++++++++--------------- MD5 | 42 +++++++++++++++++++------------------- NEWS.md | 12 ++++++++++ R/chr_uzemi.R | 10 ++++----- R/katastry.R | 8 +++---- R/kraje.R | 6 ++--- R/obce_body.R | 9 +++++--- R/obce_polygony.R | 9 +++++--- R/okresy.R | 6 ++--- R/orp_polygony.R | 6 ++--- build/partial.rdb |binary build/vignette.rds |binary man/chr_uzemi.Rd | 8 +++---- man/katastry.Rd | 6 ++--- man/kraje.Rd | 4 +-- man/obce_body.Rd | 6 +++-- man/obce_polygony.Rd | 7 ++++-- man/okresy.Rd | 4 +-- man/orp_polygony.Rd | 4 +-- tests/testthat/test-1-chr-uzemi.R | 4 +-- tests/testthat/test-1-katastr.R | 2 - tests/testthat/test-1-obce.R | 8 ++++--- 22 files changed, 110 insertions(+), 85 deletions(-)
Title: Inference Based on Non-Probability Samples
Description: Statistical inference with non-probability samples when auxiliary information from external sources such as probability samples or population totals or means is available. The package implements various methods such as inverse probability (propensity score) weighting, mass imputation and doubly robust approach. Details can be found in: Chen et al. (2020) <doi:10.1080/01621459.2019.1677241>, Yang et al. (2020) <doi:10.1111/rssb.12354>, Kim et al. (2021) <doi:10.1111/rssa.12696>, Yang et al. (2021) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2021001/article/00004-eng.htm> and Wu (2022) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2022002/article/00002-eng.htm>. For details on the package and its functionalities see <doi:10.48550/arXiv.2504.04255>.
Author: Lukasz Chrostowski [aut, ctb],
Maciej Beresewicz [aut, cre] ,
Piotr Chlebicki [aut, ctb]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>
Diff between nonprobsvy versions 0.2.2 dated 2025-05-24 and 0.2.3 dated 2025-08-20
DESCRIPTION | 6 +-- MD5 | 76 +++++++++++++++++++++---------------------- NEWS.md | 5 ++ R/check_balance.R | 2 - R/control_inference.R | 2 - R/control_outcome.R | 2 - R/control_selection.R | 2 - R/data.R | 4 +- R/method_glm.R | 2 - R/method_nn.R | 2 - R/method_npar.R | 2 - R/method_pmm.R | 3 - R/methods.R | 14 +++---- R/nonprob_documentation.R | 6 +-- R/plot.R | 2 - R/prints.R | 9 ----- R/summary.R | 2 - inst/WORDLIST | 1 man/admin.Rd | 2 - man/check_balance.Rd | 2 - man/coef.nonprob.Rd | 2 - man/confint.nonprob.Rd | 2 - man/control_inf.Rd | 2 - man/control_out.Rd | 2 - man/control_sel.Rd | 2 - man/extract.Rd | 2 - man/jvs.Rd | 2 - man/method_glm.Rd | 2 - man/method_nn.Rd | 2 - man/method_npar.Rd | 2 - man/method_pmm.Rd | 2 - man/nobs.nonprob.Rd | 2 - man/nonprob.Rd | 6 +-- man/plot.nonprob.Rd | 2 - man/pop_size.Rd | 2 - man/print.nonprob_summary.Rd | 2 - man/summary.nonprob.Rd | 2 - man/update.nonprob.Rd | 2 - man/weights.nonprob.Rd | 2 - 39 files changed, 93 insertions(+), 95 deletions(-)
Title: Computation of Satellite Position
Description: Provides basic functionalities to calculate the position of
satellites given a known state vector. The package includes implementations
of the SGP4 and SDP4 simplified perturbation models to propagate orbital
state vectors, as well as utilities to read TLE files and convert coordinates
between different frames of reference. Several of the functionalities of the
package (including the high-precision numerical orbit propagator) require
the coefficients and data included in the 'asteRiskData' package, available
in a 'drat' repository. To install this data package, run
'install.packages("asteRiskData", repos="https://rafael-ayala.github.io/drat/")'.
Felix R. Hoots, Ronald L. Roehrich and T.S. Kelso (1988) <https://celestrak.org/NORAD/documentation/spacetrk.pdf>.
David Vallado, Paul Crawford, Richard Hujsak and T.S. Kelso (2012) <doi:10.2514/6.2006-6753>.
Felix R. Hoots, Paul W. Schumacher Jr. and Robert A. Glover (2014) <doi:10.2514/1.9161>.
Author: Rafael Ayala [aut, cre] ,
Daniel Ayala [aut] ,
David Ruiz [aut] ,
Lara Selles Vidal [aut]
Maintainer: Rafael Ayala <rafaelayalahernandez@gmail.com>
Diff between asteRisk versions 1.4.3 dated 2023-01-14 and 1.4.4 dated 2025-08-20
asteRisk-1.4.3/asteRisk/inst/testGLONASSRINEX.txt |only asteRisk-1.4.3/asteRisk/inst/testGPSRINEX.txt |only asteRisk-1.4.3/asteRisk/man/ECItoKOE.Rd |only asteRisk-1.4.3/asteRisk/man/KOEtoECI.Rd |only asteRisk-1.4.4/asteRisk/DESCRIPTION | 31 asteRisk-1.4.4/asteRisk/MD5 | 106 asteRisk-1.4.4/asteRisk/NAMESPACE | 17 asteRisk-1.4.4/asteRisk/NEWS | 6 asteRisk-1.4.4/asteRisk/R/RcppExports.R | 48 asteRisk-1.4.4/asteRisk/R/auxiliaryFunctions.R | 190 + asteRisk-1.4.4/asteRisk/R/checks.R | 32 asteRisk-1.4.4/asteRisk/R/constants.R | 89 asteRisk-1.4.4/asteRisk/R/coordinatesTransformations.R | 161 - asteRisk-1.4.4/asteRisk/R/coordinatesTransformations_auxiliaryFunctions.R | 287 + asteRisk-1.4.4/asteRisk/R/debug.R |only asteRisk-1.4.4/asteRisk/R/evaluateSPK.R |only asteRisk-1.4.4/asteRisk/R/fileParsers.R | 1445 +++++++++- asteRisk-1.4.4/asteRisk/R/hpop.R | 35 asteRisk-1.4.4/asteRisk/R/hpop_acceleration.R | 597 +++- asteRisk-1.4.4/asteRisk/R/hpop_auxiliaryFunctions.R | 112 asteRisk-1.4.4/asteRisk/R/models.R | 475 +++ asteRisk-1.4.4/asteRisk/R/naif_codes.R |only asteRisk-1.4.4/asteRisk/R/orbitalManeuvers.R |only asteRisk-1.4.4/asteRisk/R/timeTransformations.R |only asteRisk-1.4.4/asteRisk/R/utils.R | 271 + asteRisk-1.4.4/asteRisk/R/zzz.R | 2 asteRisk-1.4.4/asteRisk/build/vignette.rds |binary asteRisk-1.4.4/asteRisk/inst/CORL_DL_001_02_B_T19_00002.BSP |only asteRisk-1.4.4/asteRisk/inst/CORL_DL_001_02____A__00002.BSP |only asteRisk-1.4.4/asteRisk/inst/doc/asteRisk.R | 302 +- asteRisk-1.4.4/asteRisk/inst/doc/asteRisk.Rmd | 22 asteRisk-1.4.4/asteRisk/inst/doc/asteRisk.html | 357 -- asteRisk-1.4.4/asteRisk/inst/spk14b_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw02_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw03_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw05_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw08_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw09_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw10_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw12_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw13_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw15_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw17_ex1.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw20_ex.bsp |only asteRisk-1.4.4/asteRisk/inst/spkw21_ex.bsp |only asteRisk-1.4.4/asteRisk/inst/testGLONASSRINEXv2.txt |only asteRisk-1.4.4/asteRisk/inst/testGLONASSRINEXv3.txt |only asteRisk-1.4.4/asteRisk/inst/testGPSRINEXv2.txt |only asteRisk-1.4.4/asteRisk/inst/testGPSRINEXv3.txt |only asteRisk-1.4.4/asteRisk/inst/unitTests/test_all.R | 290 +- asteRisk-1.4.4/asteRisk/inst/vgr2_jup230.bsp |only asteRisk-1.4.4/asteRisk/man/BCItoKOE.Rd |only asteRisk-1.4.4/asteRisk/man/KOEtoBCI.Rd |only asteRisk-1.4.4/asteRisk/man/TEMEtoGCRF.Rd | 22 asteRisk-1.4.4/asteRisk/man/evaluateSPKSegment.Rd |only asteRisk-1.4.4/asteRisk/man/hpop.Rd | 34 asteRisk-1.4.4/asteRisk/man/lambert.Rd |only asteRisk-1.4.4/asteRisk/man/listAvailablePlanetaryEphemerides.Rd |only asteRisk-1.4.4/asteRisk/man/readBinDAF.Rd |only asteRisk-1.4.4/asteRisk/man/readBinSPK.Rd |only asteRisk-1.4.4/asteRisk/man/readGLONASSNavigationRINEX.Rd | 155 + asteRisk-1.4.4/asteRisk/man/readGPSNavigationRINEX.Rd | 116 asteRisk-1.4.4/asteRisk/man/readOEM.Rd | 6 asteRisk-1.4.4/asteRisk/man/registerPlanetaryEphemerides.Rd |only asteRisk-1.4.4/asteRisk/src/Makevars | 1 asteRisk-1.4.4/asteRisk/src/Makevars.win | 1 asteRisk-1.4.4/asteRisk/src/RcppExports.cpp | 174 + asteRisk-1.4.4/asteRisk/src/geometry.cpp |only asteRisk-1.4.4/asteRisk/src/oceanTides.cpp | 94 asteRisk-1.4.4/asteRisk/src/utils.cpp | 237 + asteRisk-1.4.4/asteRisk/tests/runTests.R | 15 asteRisk-1.4.4/asteRisk/vignettes/asteRisk.Rmd | 22 asteRisk-1.4.4/asteRisk/vignettes/figures |only 73 files changed, 4975 insertions(+), 777 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-23 0.2.8
2023-05-17 0.2.7
2022-10-05 0.2.6
2021-08-17 0.2.5
2021-05-10 0.2.4
2020-09-17 0.2.3
2020-08-01 0.2.2
2020-06-03 0.2.1
2020-03-26 0.1.9
2020-03-17 0.1.8
2020-03-04 0.1.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-11 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-17 0.1.2
2025-03-14 0.1.1
2025-03-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-11 0.1-12.7.1
2023-08-31 0.1-12.7
2023-05-24 0.1-12.6
2022-05-01 0.1-12.5
2020-01-10 0.1-12.4
2020-01-09 0.1-12.3
2019-04-22 0.1-12.2
2018-02-01 0.1-12.1
2017-04-19 0.1-12
2016-11-23 0.1-11
2015-08-26 0.1-10
2014-09-10 0.1-9
2013-12-12 0.1-8
2010-08-25 0.1-2
2009-09-03 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-14 0.2.0
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut],
Sungho Choi [aut],
Jaewoong Heo [aut],
Mingu Jee [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.13 dated 2025-07-01 and 1.3.16 dated 2025-08-20
DESCRIPTION | 19 MD5 | 32 NAMESPACE | 1 NEWS.md | 10 R/CreateTableOneJS.R | 152 ++-- R/cox2.R | 315 +++++++-- R/gee.R | 37 - R/lmer.R | 81 +- R/svyCreateTableOneJS.R | 134 ++-- build/vignette.rds |binary inst/doc/jstable.html | 674 ++++++++++---------- inst/doc/jstable_competing_risk_analysis.html | 80 +- inst/doc/jstable_options.html | 846 +++++++++++++------------- man/cox2.display.Rd | 10 man/geeglm.display.Rd | 9 man/lmer.display.Rd | 10 tests/testthat/test-regtable.R | 37 + 17 files changed, 1382 insertions(+), 1065 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: This is a set of functions to retrieve information about GIMMS
NDVI3g files currently available online; download (and re-arrange, in the
case of NDVI3g.v0) the half-monthly data sets; import downloaded files from
ENVI binary (NDVI3g.v0) or NetCDF format (NDVI3g.v1) directly into R based
on the widespread 'raster' package; conduct quality control; and generate
monthly composites (e.g., maximum values) from the half-monthly input data.
As a special gimmick, a method is included to conveniently apply the
Mann-Kendall trend test upon 'Raster*' images, optionally featuring
trend-free pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between gimms versions 1.2.2 dated 2023-08-09 and 1.2.3 dated 2025-08-20
DESCRIPTION | 9 LICENSE | 4 MD5 | 72 +-- NAMESPACE | 44 +- NEWS | 177 ++++----- NEWS.md | 177 ++++----- R/downloadGimms.R | 510 +++++++++++++-------------- R/gimms-package.R | 109 ++--- R/gimmsControls.R | 600 ++++++++++++++++---------------- R/monthlyComposite.R | 288 +++++++-------- R/monthlyIndices.R | 182 ++++----- R/oldNaming.R | 164 ++++---- R/qualityControl.R | 314 ++++++++-------- R/rasterizeGimms.R | 496 +++++++++++++------------- R/rearrangeFiles.R | 132 +++---- R/significantTau.R | 414 +++++++++++----------- R/updateInventory.R | 722 +++++++++++++++++++-------------------- README.md | 254 ++++++------- build/partial.rdb |binary data/bale3g.v1.rda |binary data/kili3g.v0.rda |binary inst/extdata/poles.html | 20 - inst/tinytest/test-getPolesFTP.R | 178 ++++----- inst/tinytest/tests.R | 206 +++++------ man/bale3g.v1.Rd | 32 - man/downloadGimms.Rd | 266 +++++++------- man/gimms-package.Rd | 75 ++-- man/kili3g.v0.Rd | 32 - man/monthlyComposite.Rd | 156 ++++---- man/monthlyIndices.Rd | 116 +++--- man/oldNaming.Rd | 98 ++--- man/qualityControl.Rd | 118 +++--- man/rasterizeGimms.Rd | 164 ++++---- man/rearrangeFiles.Rd | 82 ++-- man/significantTau.Rd | 248 ++++++------- man/updateInventory.Rd | 132 +++---- tests/tinytest.R | 10 37 files changed, 3310 insertions(+), 3291 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii)
Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v)
Matrix functions, (vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions. There is a vignette describing how to use the
design functions for randomizing and assessing designs available as a
vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of
information when the 'Error' function has been used in the call to 'aov'.
The package 'dae' can also be installed from
<http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between dae versions 3.2.30 dated 2024-12-01 and 3.2.32 dated 2025-08-20
dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/colfacets-bottom-switch-placement.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/colfacets-bottom.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/colfacets-placement.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/rowfacets-switch-placement.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/rowfacets-switch.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/rows-and-columns-indexed-by-2-factors.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/using-facetstrips-place-from-designblocksggplot.new.svg |only dae-3.2.32/dae/DESCRIPTION | 12 +- dae-3.2.32/dae/MD5 | 46 +++------ dae-3.2.32/dae/NAMESPACE | 1 dae-3.2.32/dae/R/fac.functions.r | 11 +- dae-3.2.32/dae/build/partial.rdb |binary dae-3.2.32/dae/build/vignette.rds |binary dae-3.2.32/dae/inst/NEWS.Rd | 8 + dae-3.2.32/dae/inst/doc/DesignNotes.pdf |binary dae-3.2.32/dae/inst/doc/dae-manual.pdf |binary dae-3.2.32/dae/man/Zncsspline.Rd | 28 ++--- dae-3.2.32/dae/man/fac.multinested.Rd | 7 - dae-3.2.32/dae/tests/testthat.R | 1 dae-3.2.32/dae/tests/testthat/_snaps/testDesignGGPlot/colfacets-bottom-switch-placement.svg | 2 dae-3.2.32/dae/tests/testthat/_snaps/testDesignGGPlot/colfacets-bottom.svg | 2 dae-3.2.32/dae/tests/testthat/_snaps/testDesignGGPlot/colfacets-placement.svg | 18 +-- dae-3.2.32/dae/tests/testthat/_snaps/testDesignGGPlot/rowfacets-switch-placement.svg | 6 - dae-3.2.32/dae/tests/testthat/_snaps/testDesignGGPlot/rowfacets-switch.svg | 6 - dae-3.2.32/dae/tests/testthat/_snaps/testDesignGGPlot/rows-and-columns-indexed-by-2-factors.svg | 16 +-- dae-3.2.32/dae/tests/testthat/_snaps/testDesignGGPlot/using-facetstrips-place-from-designblocksggplot.svg | 16 +-- dae-3.2.32/dae/tests/testthat/testNestedFacs.r | 51 ++++++++++ dae-3.2.32/dae/tests/vdiffr.Rout.fail |only 28 files changed, 147 insertions(+), 84 deletions(-)
Title: Tools for Behavior Change Researchers and Professionals
Description: Contains specialised analyses and
visualisation tools for behavior change science.
These facilitate conducting determinant studies
(for example, using confidence interval-based
estimation of relevance, CIBER, or CIBERlite
plots, see Crutzen, Noijen & Peters (2017)
<doi:10/ghtfz9>),
systematically developing, reporting,
and analysing interventions (for example, using
Acyclic Behavior Change Diagrams), and reporting
about intervention effectiveness (for example, using
the Numbers Needed for Change, see Gruijters & Peters
(2017) <doi:10/jzkt>), and computing the
required sample size (using the Meaningful Change
Definition, see Gruijters & Peters (2020)
<doi:10/ghpnx8>).
This package is especially useful for
researchers in the field of behavior change or
health psychology and to behavior change
professionals such as intervention developers and
prevention workers.
Author: Gjalt-Jorn Peters [aut, cre] ,
Rik Crutzen [ctb] ,
Jeroen Bruinsma [ctb] ,
Stefan Gruijters [ctb]
Maintainer: Gjalt-Jorn Peters <behaviorchange@opens.science>
Diff between behaviorchange versions 0.5.5 dated 2023-03-04 and 25.8.0 dated 2025-08-20
DESCRIPTION | 29 + MD5 | 45 +-- R/CIBER.R | 36 +- R/CIBERlite.R | 3 R/CIBORG.R |only R/binaryCIBER.R | 26 + R/determinantStructure.R | 4 R/opts.R | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/abcd-laagdrempelige_nederlandse_uitleg.R | 16 - inst/doc/abcd-laagdrempelige_nederlandse_uitleg.html | 86 +++-- inst/doc/abcd.R | 4 inst/doc/abcd.html | 49 +-- inst/doc/complecs.R | 16 - inst/doc/complecs.html | 71 ++-- inst/doc/determinant-selection-table.R | 20 - inst/doc/determinant-selection-table.html | 257 ++++++++--------- inst/doc/determinant-selection-tutorial.R | 14 inst/doc/determinant-selection-tutorial.html | 283 +++++++++---------- man/CIBER.Rd | 12 man/CIBERlite.Rd | 3 man/behaviorchange-package.Rd | 1 man/determinantStructure.Rd | 4 24 files changed, 550 insertions(+), 441 deletions(-)
More information about behaviorchange at CRAN
Permanent link
Title: Provide the 'x13ashtml' Seasonal Adjustment Binary
Description: The US Census Bureau provides a seasonal adjustment program now
called 'X-13ARIMA-SEATS' building on both earlier programs called X-11 and
X-12 as well as the SEATS program by the Bank of Spain. The US Census Bureau
offers both source and binary versions -- which this package integrates for
use by other R packages.
Author: Dirk Eddelbuettel [aut, cre] ,
Christoph Sax [aut] ,
Kirill Mueller [ctb] ,
Jeroen Ooms [ctb] ,
Michael Antonov [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between x13binary versions 1.1.61 dated 2024-06-24 and 1.1.61.1 dated 2025-08-20
ChangeLog | 16 +++++++++++++++- DESCRIPTION | 21 +++++++++++---------- MD5 | 12 ++++++------ README.md | 12 +++++++----- src/Makefile | 4 ++-- src/Makefile.win | 2 +- tools/x13as_html/htmlout.f | 2 +- 7 files changed, 43 insertions(+), 26 deletions(-)
Title: Functions for Extracting and Merging Data in the 'teal'
Framework
Description: A standardized user interface for column selection, that
facilitates dataset merging in 'teal' framework.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Junlue Zhao [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.transform versions 0.6.0 dated 2025-02-12 and 0.7.0 dated 2025-08-20
teal.transform-0.6.0/teal.transform/R/include_css_js.R |only teal.transform-0.6.0/teal.transform/inst/css/data_extract.css |only teal.transform-0.6.0/teal.transform/man/include_css_files.Rd |only teal.transform-0.7.0/teal.transform/DESCRIPTION | 30 +- teal.transform-0.7.0/teal.transform/MD5 | 140 ++++------ teal.transform-0.7.0/teal.transform/NAMESPACE | 1 teal.transform-0.7.0/teal.transform/NEWS.md | 6 teal.transform-0.7.0/teal.transform/R/Queue.R | 1 teal.transform-0.7.0/teal.transform/R/choices_labeled.R | 5 teal.transform-0.7.0/teal.transform/R/choices_selected.R | 7 teal.transform-0.7.0/teal.transform/R/column_functions.R | 2 teal.transform-0.7.0/teal.transform/R/data_extract_datanames.R | 3 teal.transform-0.7.0/teal.transform/R/data_extract_module.R | 49 ++- teal.transform-0.7.0/teal.transform/R/data_extract_spec.R | 1 teal.transform-0.7.0/teal.transform/R/delayed_choices.R | 1 teal.transform-0.7.0/teal.transform/R/filter_spec.R | 1 teal.transform-0.7.0/teal.transform/R/format_data_extract.R | 2 teal.transform-0.7.0/teal.transform/R/get_merge_call.R | 5 teal.transform-0.7.0/teal.transform/R/input_checks.R | 4 teal.transform-0.7.0/teal.transform/R/merge_datasets.R | 1 teal.transform-0.7.0/teal.transform/R/merge_expression_module.R | 19 - teal.transform-0.7.0/teal.transform/R/resolve.R | 2 teal.transform-0.7.0/teal.transform/R/resolve_delayed.R | 2 teal.transform-0.7.0/teal.transform/R/select_spec.R | 1 teal.transform-0.7.0/teal.transform/R/teal.transform-package.R | 1 teal.transform-0.7.0/teal.transform/R/utils.R | 10 teal.transform-0.7.0/teal.transform/build/vignette.rds |binary teal.transform-0.7.0/teal.transform/inst/WORDLIST | 5 teal.transform-0.7.0/teal.transform/inst/css/data-extract.css |only teal.transform-0.7.0/teal.transform/inst/doc/combining-data-extract-with-data-merge.R | 2 teal.transform-0.7.0/teal.transform/inst/doc/combining-data-extract-with-data-merge.Rmd | 2 teal.transform-0.7.0/teal.transform/inst/doc/combining-data-extract-with-data-merge.html | 4 teal.transform-0.7.0/teal.transform/inst/doc/data-extract.R | 2 teal.transform-0.7.0/teal.transform/inst/doc/data-extract.Rmd | 2 teal.transform-0.7.0/teal.transform/inst/doc/data-extract.html | 4 teal.transform-0.7.0/teal.transform/inst/doc/data-merge.R | 4 teal.transform-0.7.0/teal.transform/inst/doc/data-merge.Rmd | 4 teal.transform-0.7.0/teal.transform/inst/doc/data-merge.html | 8 teal.transform-0.7.0/teal.transform/man/Queue.Rd | 2 teal.transform-0.7.0/teal.transform/man/add_no_selected_choices.Rd | 2 teal.transform-0.7.0/teal.transform/man/check_no_multiple_selection.Rd | 3 teal.transform-0.7.0/teal.transform/man/choices_labeled.Rd | 4 teal.transform-0.7.0/teal.transform/man/choices_selected.Rd | 4 teal.transform-0.7.0/teal.transform/man/compose_and_enable_validators.Rd | 8 teal.transform-0.7.0/teal.transform/man/data_extract_multiple_srv.Rd | 10 teal.transform-0.7.0/teal.transform/man/data_extract_spec.Rd | 2 teal.transform-0.7.0/teal.transform/man/data_extract_srv.Rd | 16 - teal.transform-0.7.0/teal.transform/man/data_extract_ui.Rd | 8 teal.transform-0.7.0/teal.transform/man/datanames_input.Rd | 2 teal.transform-0.7.0/teal.transform/man/delayed_choices.Rd | 2 teal.transform-0.7.0/teal.transform/man/filter_spec.Rd | 2 teal.transform-0.7.0/teal.transform/man/format_data_extract.Rd | 2 teal.transform-0.7.0/teal.transform/man/get_anl_relabel_call.Rd | 2 teal.transform-0.7.0/teal.transform/man/get_dataset_prefixed_col_names.Rd | 2 teal.transform-0.7.0/teal.transform/man/get_extract_datanames.Rd | 2 teal.transform-0.7.0/teal.transform/man/get_merge_call.Rd | 2 teal.transform-0.7.0/teal.transform/man/get_relabel_call.Rd | 2 teal.transform-0.7.0/teal.transform/man/is_single_dataset.Rd | 2 teal.transform-0.7.0/teal.transform/man/list_extract_spec.Rd | 2 teal.transform-0.7.0/teal.transform/man/merge_datasets.Rd | 2 teal.transform-0.7.0/teal.transform/man/merge_expression_module.Rd | 10 teal.transform-0.7.0/teal.transform/man/merge_expression_srv.Rd | 11 teal.transform-0.7.0/teal.transform/man/no_selected_as_NULL.Rd | 2 teal.transform-0.7.0/teal.transform/man/resolve.Rd | 2 teal.transform-0.7.0/teal.transform/man/resolve_delayed.Rd | 2 teal.transform-0.7.0/teal.transform/man/select_spec.Rd | 2 teal.transform-0.7.0/teal.transform/man/split_by_sep.Rd | 2 teal.transform-0.7.0/teal.transform/man/value_choices.Rd | 2 teal.transform-0.7.0/teal.transform/man/variable_choices.Rd | 2 teal.transform-0.7.0/teal.transform/tests/testthat/test-data_extract_module.R | 8 teal.transform-0.7.0/teal.transform/vignettes/combining-data-extract-with-data-merge.Rmd | 2 teal.transform-0.7.0/teal.transform/vignettes/data-extract.Rmd | 2 teal.transform-0.7.0/teal.transform/vignettes/data-merge.Rmd | 4 73 files changed, 198 insertions(+), 267 deletions(-)
More information about teal.transform at CRAN
Permanent link
Title: Filter Module for 'teal' Applications
Description: Data filtering module for 'teal' applications. Allows for
interactive filtering of data stored in 'data.frame' and
'MultiAssayExperiment' objects. Also displays filtered and unfiltered
observation counts.
Author: Dawid Kaledkowski [aut, cre] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Kartikeya Kirar [aut],
Marcin Kosinski [aut],
Chendi Liao [rev],
Dony Unardi [rev],
Andrew Bates [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.slice versions 0.6.0 dated 2025-02-03 and 0.7.0 dated 2025-08-20
DESCRIPTION | 37 - MD5 | 142 ++-- NAMESPACE | 1 NEWS.md | 14 R/FilterState-utils.R | 2 R/FilterState.R | 213 +++--- R/FilterStateChoices.R | 60 + R/FilterStateDate.R | 69 +- R/FilterStateDatettime.R | 86 +- R/FilterStateExpr.R | 67 + R/FilterStateLogical.R | 60 + R/FilterStateRange.R | 126 +-- R/FilterStates-utils.R | 2 R/FilterStates.R | 189 ++--- R/FilterStatesDF.R | 66 + R/FilterStatesSE.R | 142 +--- R/FilteredData-utils.R | 2 R/FilteredData.R | 225 +++--- R/FilteredDataset-utils.R | 2 R/FilteredDataset.R | 319 +++++---- R/FilteredDatasetDataframe.R | 22 R/FilteredDatasetMAE.R | 8 R/choices_labeled.R | 2 R/count_labels.R | 57 + R/filter_panel_api.R | 4 R/teal.slice.R | 1 R/teal_slice.R | 2 R/teal_slices.R | 2 R/utils.R | 12 R/zzz.R | 1 build/vignette.rds |binary inst/WORDLIST | 4 inst/css/filter-panel.css | 476 ++++---------- inst/doc/filter-panel-for-developers.R | 27 inst/doc/filter-panel-for-developers.Rmd | 27 inst/doc/filter-panel-for-developers.html | 159 ++-- inst/js/count-bar-labels.js | 38 - man/ChoicesFilterState.Rd | 47 - man/DFFilterStates.Rd | 68 +- man/DataframeFilteredDataset.Rd | 2 man/DateFilterState.Rd | 49 - man/DatetimeFilterState.Rd | 49 - man/DefaultFilteredDataset.Rd | 2 man/EmptyFilterState.Rd | 2 man/FilterState.Rd | 25 man/FilterStateExpr.Rd | 52 - man/FilterStates.Rd | 29 man/FilteredData.Rd | 29 man/FilteredDataset.Rd | 34 - man/LogicalFilterState.Rd | 47 - man/MAEFilterStates.Rd | 2 man/MAEFilteredDataset.Rd | 2 man/MatrixFilterStates.Rd | 2 man/RangeFilterState.Rd | 53 - man/SEFilterStates.Rd | 2 man/choices_labeled.Rd | 2 man/countBar.Rd | 2 man/countBars.Rd | 4 man/filter_state_api.Rd | 2 man/get_filter_expr.Rd | 2 man/init_filter_state.Rd | 2 man/init_filter_states.Rd | 2 man/init_filtered_dataset.Rd | 2 man/teal_slices.Rd | 3 man/toggle_button.Rd | 2 tests/testthat/helpers-shinytest2.R |only tests/testthat/helpers-testing-depth.R |only tests/testthat/test-ChoicesFilterState.R | 11 tests/testthat/test-FilterStates.R | 2 tests/testthat/test-SEFilterStates.R | 4 tests/testthat/test-count_labels.R | 73 +- tests/testthat/test-shinytest2_DataframeFilteredDataset.R |only tests/testthat/test-shinytest2_MAEFilteredDataset.R |only vignettes/filter-panel-for-developers.Rmd | 27 74 files changed, 1610 insertions(+), 1692 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Hosszejni and Kastner (2021) <doi:10.18637/jss.v100.i12> and Kastner (2016) <doi:10.18637/jss.v069.i05> and the package examples.
Author: Darjus Hosszejni [aut, cre] ,
Gregor Kastner [aut]
Maintainer: Darjus Hosszejni <darjus.hosszejni@icloud.com>
Diff between stochvol versions 3.2.6 dated 2025-07-31 and 3.2.7 dated 2025-08-20
stochvol-3.2.6/stochvol/tests/testthat/setup_all.R |only stochvol-3.2.7/stochvol/DESCRIPTION | 6 +++--- stochvol-3.2.7/stochvol/MD5 | 11 +++++------ stochvol-3.2.7/stochvol/NEWS.md | 7 +++++++ stochvol-3.2.7/stochvol/inst/doc/article.pdf |binary stochvol-3.2.7/stochvol/inst/doc/article2.pdf |binary stochvol-3.2.7/stochvol/src/single_update.cc | 2 +- 7 files changed, 16 insertions(+), 10 deletions(-)
Title: Spatio-Temporal Analysis of Point Patterns on Linear Networks
Description: Statistical analysis of spatio-temporal point processes on linear networks. This packages provides tools to visualise and analyse spatio-temporal point patterns on linear networks using first, second, and higher-order summary statistics.
Author: Mehdi Moradi [aut, cre] ,
Ottmar Cronie [ctb],
Jorge Mateu [ctb]
Maintainer: Mehdi Moradi <m2.moradi@yahoo.com>
Diff between stlnpp versions 0.4.0 dated 2024-05-27 and 0.5.0 dated 2025-08-20
stlnpp-0.4.0/stlnpp/man/as.tpp.stlpp.Rd |only stlnpp-0.5.0/stlnpp/DESCRIPTION | 15 stlnpp-0.5.0/stlnpp/MD5 | 74 ++- stlnpp-0.5.0/stlnpp/NAMESPACE | 14 stlnpp-0.5.0/stlnpp/R/STLFinhom.R |only stlnpp-0.5.0/stlnpp/R/STLHinhom.R |only stlnpp-0.5.0/stlnpp/R/STLJinhom.R |only stlnpp-0.5.0/stlnpp/R/as.lpp.stlpp.R | 14 stlnpp-0.5.0/stlnpp/R/as.stlpp.R | 41 + stlnpp-0.5.0/stlnpp/R/as.stlpp.tpp.R | 2 stlnpp-0.5.0/stlnpp/R/as.tpp.stlpp.R | 19 stlnpp-0.5.0/stlnpp/R/countends.stlpp.R |only stlnpp-0.5.0/stlnpp/R/density.stlpp.R | 18 stlnpp-0.5.0/stlnpp/R/densityVoronoi.stlpp.R | 30 - stlnpp-0.5.0/stlnpp/R/densityVoronoi.tpp.R | 24 - stlnpp-0.5.0/stlnpp/R/grid.stlpp.R |only stlnpp-0.5.0/stlnpp/R/methods.stlpp.R | 17 stlnpp-0.5.0/stlnpp/R/plot.stlpp.R | 501 +++++++++++++++--------- stlnpp-0.5.0/stlnpp/R/print.stlpp.R | 97 ++++ stlnpp-0.5.0/stlnpp/R/rpoistlpp.R | 2 stlnpp-0.5.0/stlnpp/R/rthin.stlpp.R | 4 stlnpp-0.5.0/stlnpp/R/stlg.R | 2 stlnpp-0.5.0/stlnpp/R/stlk.R | 2 stlnpp-0.5.0/stlnpp/R/stlnpp-package.R |only stlnpp-0.5.0/stlnpp/R/stlpp.R | 8 stlnpp-0.5.0/stlnpp/R/superimpose.stlpp.R |only stlnpp-0.5.0/stlnpp/R/superimpose.tpp.R |only stlnpp-0.5.0/stlnpp/R/unique.stlpp.R | 4 stlnpp-0.5.0/stlnpp/man/STLFinhom.Rd |only stlnpp-0.5.0/stlnpp/man/STLHinhom.Rd |only stlnpp-0.5.0/stlnpp/man/STLJinhom.Rd |only stlnpp-0.5.0/stlnpp/man/STLK.Rd | 2 stlnpp-0.5.0/stlnpp/man/STLg.Rd | 2 stlnpp-0.5.0/stlnpp/man/as.lpp.stlpp.Rd | 12 stlnpp-0.5.0/stlnpp/man/as.stlpp.Rd | 16 stlnpp-0.5.0/stlnpp/man/as.tpp.Rd |only stlnpp-0.5.0/stlnpp/man/density.stlpp.Rd | 8 stlnpp-0.5.0/stlnpp/man/densityVoronoi.stlpp.Rd | 8 stlnpp-0.5.0/stlnpp/man/densityVoronoi.tpp.Rd | 7 stlnpp-0.5.0/stlnpp/man/methods.stlpp.Rd | 61 ++ stlnpp-0.5.0/stlnpp/man/rpoistlpp.Rd | 2 stlnpp-0.5.0/stlnpp/man/rthin.stlpp.Rd | 4 stlnpp-0.5.0/stlnpp/man/stlnpp-package.Rd |only stlnpp-0.5.0/stlnpp/man/stlpp.Rd | 8 stlnpp-0.5.0/stlnpp/man/superimpose.stlpp.Rd |only stlnpp-0.5.0/stlnpp/man/superimpose.tpp.Rd |only 46 files changed, 687 insertions(+), 331 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled. For regression versions of the methods, Monte Carlo and asymptotic methods are used.
Author: Ivair Ramos Silva [aut, cre],
Martin Kulldorff [aut]
Maintainer: Ivair Ramos Silva <ivair@ufop.edu.br>
Diff between Sequential versions 4.3.4 dated 2024-10-24 and 4.4 dated 2025-08-20
DESCRIPTION | 12 - MD5 | 56 +++-- NAMESPACE | 6 R/Analyze.Binomial.R | 287 +++++++++++++++++++++++++----- R/Analyze.CondPoisson.R | 225 +++++++++++++++++++---- R/Analyze.Multinomial.R |only R/Analyze.Poisson.R | 166 +++++++++++++---- R/AnalyzeRegression.Binomial.R |only R/AnalyzeRegression.CondPoisson.R |only R/AnalyzeRegression.Poisson.R |only R/AnalyzeSetUp.Binomial.R | 106 ++++++++++- R/AnalyzeSetUp.CondPoisson.R | 79 +++++++- R/AnalyzeSetUp.Multinomial.R |only R/AnalyzeSetUp.Poisson.R | 76 +++++++ R/AnalyzeSetUpRegression.Binomial.R |only R/AnalyzeSetUpRegression.CondPoisson.R |only R/AnalyzeSetUpRegression.Poisson.R |only R/ConfidenceInterval.Binomial.R | 2 R/Performance.Threshold.Poisson.R | 2 R/SampleSize.CondPoisson.R | 70 +++++++ man/Analyze.Binomial.Rd | 4 man/Analyze.Multinomial.Rd |only man/Analyze.Poisson.Rd | 4 man/AnalyzeRegression.Binomial.Rd |only man/AnalyzeRegression.CondPoisson.Rd |only man/AnalyzeRegression.Poisson.Rd |only man/AnalyzeSetUp.Binomial.Rd | 17 + man/AnalyzeSetUp.CondPoisson.Rd | 6 man/AnalyzeSetUp.Multinomial.Rd |only man/AnalyzeSetUp.Poisson.Rd | 7 man/AnalyzeSetUpRegression.Binomial.Rd |only man/AnalyzeSetUpRegression.CondPoisson.Rd |only man/AnalyzeSetUpRegression.Poisson.Rd |only man/Performance.AlphaSpend.Binomial.Rd | 2 man/Performance.Threshold.CondPoisson.Rd | 2 man/SampleSize.CondPoisson.Rd | 25 -- man/Sequential-package.Rd | 84 +++++++- 37 files changed, 1024 insertions(+), 214 deletions(-)
Title: Robust Stepwise Split Regularized Regression
Description: Functions to perform robust stepwise split regularized regression. The approach first
uses a robust stepwise algorithm to split the variables into the models of an ensemble.
An adaptive robust regularized estimator is then applied to each subset of predictors
in the models of an ensemble.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between robStepSplitReg versions 1.1.0 dated 2023-06-29 and 2.0.0 dated 2025-08-20
robStepSplitReg-1.1.0/robStepSplitReg/R/RcppExports.R |only robStepSplitReg-1.1.0/robStepSplitReg/R/autoconfig.R.in |only robStepSplitReg-1.1.0/robStepSplitReg/R/autoconfig.win.R.in |only robStepSplitReg-1.1.0/robStepSplitReg/cleanup |only robStepSplitReg-1.1.0/robStepSplitReg/configure |only robStepSplitReg-1.1.0/robStepSplitReg/configure.ac |only robStepSplitReg-1.1.0/robStepSplitReg/configure.win |only robStepSplitReg-1.1.0/robStepSplitReg/src |only robStepSplitReg-2.0.0/robStepSplitReg/DESCRIPTION | 13 robStepSplitReg-2.0.0/robStepSplitReg/MD5 | 39 - robStepSplitReg-2.0.0/robStepSplitReg/NAMESPACE | 4 robStepSplitReg-2.0.0/robStepSplitReg/NEWS | 5 robStepSplitReg-2.0.0/robStepSplitReg/R/Coefficients.R | 34 - robStepSplitReg-2.0.0/robStepSplitReg/R/DataCheck.R | 126 ++--- robStepSplitReg-2.0.0/robStepSplitReg/R/Predictions.R | 56 +- robStepSplitReg-2.0.0/robStepSplitReg/R/Robust_Stepwise_Split.R |only robStepSplitReg-2.0.0/robStepSplitReg/R/robStepSplitReg.R | 222 ++++------ robStepSplitReg-2.0.0/robStepSplitReg/README.md | 4 robStepSplitReg-2.0.0/robStepSplitReg/man/robustStepwiseSplit.Rd |only 19 files changed, 238 insertions(+), 265 deletions(-)
More information about robStepSplitReg at CRAN
Permanent link
Title: Client for Various 'CrossRef' 'APIs'
Description: Client for various 'CrossRef' 'APIs', including 'metadata' search
with their old and newer search 'APIs', get 'citations' in various formats
(including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs'
to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to
full text of articles when available.
Author: Scott Chamberlain [aut],
Hao Zhu [aut],
Najko Jahn [aut, cre] ,
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Najko Jahn <najko.jahn@gmail.com>
Diff between rcrossref versions 1.2.0 dated 2022-11-11 and 1.2.1 dated 2025-08-20
DESCRIPTION | 12 +++--- MD5 | 25 +++++++------ NEWS.md | 6 +++ R/cache.R |only R/cr_cn.r | 36 ++++++++++++++----- R/cr_members.r | 6 +++ R/cr_works.R | 7 +++ README.md | 13 ++----- man/cr_cn.Rd | 12 +++++- man/cr_members.Rd | 6 +++ tests/fixtures/cr_members_filter_examples.yml |only tests/fixtures/cr_works_doi_filter.yml |only tests/testthat/test-cr_cn.R | 17 ++++++++- tests/testthat/test-cr_members.R | 48 ++++++++++++++++++++++++++ tests/testthat/test-cr_works.R | 13 +++++++ 15 files changed, 163 insertions(+), 38 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 14.6.0-1 dated 2025-07-02 and 14.6.3-1 dated 2025-08-20
ChangeLog | 33 +++++++ DESCRIPTION | 8 - MD5 | 45 +++++----- configure | 18 ++-- configure.ac | 2 inst/NEWS.Rd | 31 +++++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/Cube_meat.hpp | 18 ++-- inst/include/armadillo_bits/Mat_meat.hpp | 12 +- inst/include/armadillo_bits/arma_config.hpp | 7 + inst/include/armadillo_bits/arma_forward.hpp | 4 inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/compiler_setup.hpp | 25 +---- inst/include/armadillo_bits/config.hpp | 19 +++- inst/include/armadillo_bits/debug.hpp | 1 inst/include/armadillo_bits/fn_accu.hpp | 8 - inst/include/armadillo_bits/fn_conv_to.hpp | 10 +- inst/include/armadillo_bits/op_mean_meat.hpp | 8 - inst/include/armadillo_bits/op_omit_meat.hpp | 4 inst/include/armadillo_bits/op_sum_bones.hpp | 7 + inst/include/armadillo_bits/op_sum_meat.hpp | 110 +++++-------------------- inst/include/armadillo_bits/sp_auxlib_meat.hpp | 1 inst/include/legacy |only 24 files changed, 191 insertions(+), 182 deletions(-)
Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically.
Models may be specified with matrices or paths (LISREL or RAM)
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares.
equations, state space, and many others.
Support and advanced package binaries available at <https://openmx.ssri.psu.edu>.
The software is described in Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
[...truncated...]
Maintainer: Robert M. Kirkpatrick <rkirkpatrick2@vcu.edu>
Diff between OpenMx versions 2.22.7 dated 2025-05-23 and 2.22.9 dated 2025-08-20
DESCRIPTION | 14 +- MD5 | 52 +++++----- R/MxAutoStart.R | 7 - R/MxEval.R | 14 ++ R/MxExpectationGREML.R | 4 R/MxOptions.R | 2 R/MxVersion.R | 2 R/zzz.R | 1 README.md | 2 build/stage23.rdb |binary inst/doc/deriv.html | 14 +- inst/doc/factor_analysis.html | 8 - inst/doc/reg_mimic.html | 10 - inst/doc/regularization.html | 2 inst/models/nightly/AnalyticGradientTest.R | 1 inst/models/passing/GREML--minimal_test_model.R | 2 inst/models/passing/GREML--testStarterFunctionWithMissingData.R | 36 +++++- man/OpenMx.Rd | 3 man/mxAutoStart.Rd | 4 man/mxCheckIdentification.Rd | 5 man/mxOption.Rd | 20 ++- man/summary.MxModel.Rd | 21 ++++ src/ComputeGD.cpp | 2 src/ComputeNR.cpp | 2 src/omxGREMLfitfunction.cpp | 4 src/omxMLFitFunction.cpp | 2 tests/testthat/test-GREML_Error_Detection.R | 14 ++ 27 files changed, 171 insertions(+), 77 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 11.4.1 dated 2025-07-15 and 11.5 dated 2025-08-20
NNS-11.4.1/NNS/src/central_tendencies.h |only NNS-11.5/NNS/DESCRIPTION | 8 NNS-11.5/NNS/MD5 | 168 +- NNS-11.5/NNS/NAMESPACE | 5 NNS-11.5/NNS/R/ANOVA.R | 53 NNS-11.5/NNS/R/ARMA.R | 8 NNS-11.5/NNS/R/ARMA_optim.R | 39 NNS-11.5/NNS/R/Binary_ANOVA.R | 387 ++--- NNS-11.5/NNS/R/Boost.R | 697 ++++----- NNS-11.5/NNS/R/Causal_matrix.R | 104 + NNS-11.5/NNS/R/Causation.R | 204 +- NNS-11.5/NNS/R/Central_tendencies.R | 134 - NNS-11.5/NNS/R/Copula.R | 104 - NNS-11.5/NNS/R/Dependence.R | 52 NNS-11.5/NNS/R/Internal_Functions.R | 12 NNS-11.5/NNS/R/Multivariate_Regression.R | 43 NNS-11.5/NNS/R/NNS_VAR.R | 2 NNS-11.5/NNS/R/Partial_Moments.R | 429 +++-- NNS-11.5/NNS/R/Partition_Map.R | 205 +- NNS-11.5/NNS/R/RcppExports.R | 319 ++-- NNS-11.5/NNS/R/Regression.R | 149 - NNS-11.5/NNS/R/SD_Efficient_Set.R | 68 NNS-11.5/NNS/R/Stack.R | 26 NNS-11.5/NNS/R/Uni_Causation.R | 139 + NNS-11.5/NNS/R/Uni_SD_Routines.R | 51 NNS-11.5/NNS/R/dy_d_wrt.R | 63 NNS-11.5/NNS/R/dy_dx.R | 26 NNS-11.5/NNS/R/gvload.R | 2 NNS-11.5/NNS/README.md | 4 NNS-11.5/NNS/build/vignette.rds |binary NNS-11.5/NNS/inst/doc/NNSvignette_Classification.R | 24 NNS-11.5/NNS/inst/doc/NNSvignette_Classification.Rmd | 30 NNS-11.5/NNS/inst/doc/NNSvignette_Classification.html | 100 - NNS-11.5/NNS/inst/doc/NNSvignette_Clustering_and_Regression.R | 16 NNS-11.5/NNS/inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 21 NNS-11.5/NNS/inst/doc/NNSvignette_Clustering_and_Regression.html | 290 +-- NNS-11.5/NNS/inst/doc/NNSvignette_Comparing_Distributions.R | 8 NNS-11.5/NNS/inst/doc/NNSvignette_Comparing_Distributions.Rmd | 8 NNS-11.5/NNS/inst/doc/NNSvignette_Comparing_Distributions.html | 116 - NNS-11.5/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.R | 8 NNS-11.5/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 8 NNS-11.5/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.html | 50 NNS-11.5/NNS/inst/doc/NNSvignette_Forecasting.R | 40 NNS-11.5/NNS/inst/doc/NNSvignette_Forecasting.Rmd | 40 NNS-11.5/NNS/inst/doc/NNSvignette_Forecasting.html | 44 NNS-11.5/NNS/inst/doc/NNSvignette_Overview.R |only NNS-11.5/NNS/inst/doc/NNSvignette_Overview.Rmd |only NNS-11.5/NNS/inst/doc/NNSvignette_Overview.html |only NNS-11.5/NNS/inst/doc/NNSvignette_Partial_Moments.html | 6 NNS-11.5/NNS/inst/doc/NNSvignette_Sampling.R | 20 NNS-11.5/NNS/inst/doc/NNSvignette_Sampling.Rmd | 20 NNS-11.5/NNS/inst/doc/NNSvignette_Sampling.html | 18 NNS-11.5/NNS/man/Co.LPM.Rd | 26 NNS-11.5/NNS/man/Co.LPM_nD.Rd |only NNS-11.5/NNS/man/Co.UPM.Rd | 26 NNS-11.5/NNS/man/Co.UPM_nD.Rd |only NNS-11.5/NNS/man/D.LPM.Rd | 28 NNS-11.5/NNS/man/D.UPM.Rd | 28 NNS-11.5/NNS/man/DPM_nD.Rd |only NNS-11.5/NNS/man/LPM.Rd | 4 NNS-11.5/NNS/man/LPM.ratio.Rd | 38 NNS-11.5/NNS/man/NNS.ANOVA.Rd | 37 NNS-11.5/NNS/man/NNS.ARMA.optim.Rd | 5 NNS-11.5/NNS/man/NNS.CDF.Rd | 6 NNS-11.5/NNS/man/NNS.boost.Rd | 200 +- NNS-11.5/NNS/man/NNS.caus.Rd | 32 NNS-11.5/NNS/man/NNS.reg.Rd | 6 NNS-11.5/NNS/man/PM.matrix.Rd | 44 NNS-11.5/NNS/man/UPM.Rd | 4 NNS-11.5/NNS/man/UPM.ratio.Rd | 27 NNS-11.5/NNS/man/dy.dx.Rd | 91 - NNS-11.5/NNS/src/RcppExports.cpp | 164 ++ NNS-11.5/NNS/src/SD.cpp |only NNS-11.5/NNS/src/central_tendencies.cpp |only NNS-11.5/NNS/src/fast_lm.cpp | 2 NNS-11.5/NNS/src/partial_moments.cpp | 387 ++++- NNS-11.5/NNS/src/partial_moments.h | 169 +- NNS-11.5/NNS/src/partial_moments_rcpp.cpp | 755 +++++----- NNS-11.5/NNS/src/partial_moments_rcpp.h | 4 NNS-11.5/NNS/tests/testthat/Rplots.pdf |binary NNS-11.5/NNS/tests/testthat/test_Copula.R | 8 NNS-11.5/NNS/tests/testthat/test_Partial_Moments.R | 2 NNS-11.5/NNS/tests/testthat/test_Partition_Map.R | 6 NNS-11.5/NNS/vignettes/NNSvignette_Classification.Rmd | 30 NNS-11.5/NNS/vignettes/NNSvignette_Clustering_and_Regression.Rmd | 21 NNS-11.5/NNS/vignettes/NNSvignette_Comparing_Distributions.Rmd | 8 NNS-11.5/NNS/vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 8 NNS-11.5/NNS/vignettes/NNSvignette_Forecasting.Rmd | 40 NNS-11.5/NNS/vignettes/NNSvignette_Overview.Rmd |only NNS-11.5/NNS/vignettes/NNSvignette_Sampling.Rmd | 20 90 files changed, 3530 insertions(+), 3064 deletions(-)
Title: Nonlinear Regression for Agricultural Applications
Description: Additional nonlinear regression functions using self-start (SS) algorithms. One of the functions is the Beta growth function proposed by Yin et al. (2003) <doi:10.1093/aob/mcg029>. There are several other functions with breakpoints (e.g. linear-plateau, plateau-linear, exponential-plateau, plateau-exponential, quadratic-plateau, plateau-quadratic and bilinear), a non-rectangular hyperbola and a bell-shaped curve. Twenty eight (28) new self-start (SS) functions in total. This package also supports the publication 'Nonlinear regression Models and applications in agricultural research' by Archontoulis and Miguez (2015) <doi:10.2134/agronj2012.0506>, a book chapter with similar material <doi:10.2134/appliedstatistics.2016.0003.c15> and a publication by Oddi et. al. (2019) in Ecology and Evolution <doi:10.1002/ece3.5543>. The function 'nlsLMList' uses 'nlsLM' for fitting, but it is otherwise almost identical to 'nlme::nlsList'.In addition, this release of the package [...truncated...]
Author: Fernando Miguez [aut, cre] ,
Caio dos Santos [ctb] ,
Jose Pinheiro [ctb, cph] ,
Douglas Bates [ctb, cph] ,
R-core [ctb, cph]
Maintainer: Fernando Miguez <femiguez@iastate.edu>
Diff between nlraa versions 1.9.7 dated 2023-12-19 and 1.9.10 dated 2025-08-20
DESCRIPTION | 11 MD5 | 102 ++- NAMESPACE | 7 R/IA_tab.R | 768 ++++++++++++++-------------- R/SSbell.R | 2 R/SSblin.R | 46 + R/SSdlogis.R |only R/SSgmicmen.R |only R/SSmoh.R | 222 ++++---- R/SSnrh.R | 10 R/SSprofd.R | 2 R/SSquadpq.R |only R/SSspherical.R |only R/confidence_intervals.R |only R/nlsLMList.R | 38 - R/predict_nlme.R | 4 R/predict_nls.R | 989 ++++++++++++++++++------------------- R/simulate_gam.R | 4 R/simulate_lme.R | 23 R/simulate_nlme_one.R | 23 R/simulate_nls.R | 586 +++++++++++---------- R/summary_simulate.R | 23 README.md | 180 ++++++ inst/doc/Bootstrapping.Rmd | 5 inst/doc/Bootstrapping.html | 471 ++++++++--------- inst/doc/Confidence-Bands.R | 136 ++--- inst/doc/Confidence-Bands.html | 44 - inst/doc/Models-and-Functions.html | 22 inst/doc/nlraa-AgronJ-paper.html | 94 +-- inst/doc/nlraa.R | 12 inst/doc/nlraa.Rmd | 3 inst/doc/nlraa.html | 57 +- man/IA_tab.Rd | 19 man/SSbell.Rd | 2 man/SSgmicmen.Rd |only man/SSmoh.Rd | 18 man/SSnrh.Rd | 10 man/SSprofd.Rd | 2 man/SSquadpq.Rd |only man/SSspherical.Rd |only man/confidence_intervals.Rd |only man/nlsLMList.Rd | 18 man/nlsLMList.formula.Rd | 20 man/predict_nlme.Rd | 4 man/predict_nls.Rd | 4 man/simulate_gam.Rd | 4 man/summary_simulate.Rd | 7 tests/test_SSdlogis.R |only tests/test_SSquadpq.R |only tests/test_boot_nlme.R | 381 +++++++------- tests/test_confidence_intervals.R |only tests/test_environments.R | 68 +- tests/test_predict_gam.R | 4 tests/test_predict_nls.R | 475 ++++++++++++----- tests/test_simulate_lme.R | 5 tests/tests_SSother.R | 3 vignettes/Bootstrapping.Rmd | 5 vignettes/nlraa.Rmd | 3 58 files changed, 2705 insertions(+), 2231 deletions(-)
Title: Linear Mixed Model Solver
Description: An efficient and flexible system to solve sparse mixed model
equations. Important applications are the use of splines to model spatial or temporal
trends as described in Boer (2023). (<doi:10.1177/1471082X231178591>).
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between LMMsolver versions 1.0.10 dated 2025-05-14 and 1.0.11 dated 2025-08-20
DESCRIPTION | 10 MD5 | 69 +- NAMESPACE | 1 NEWS.md | 7 R/LMMsolve-class.R | 67 ++ R/LMMsolve.R | 2 R/chkInputLMMsolve.R | 35 - R/chkResponse.R | 4 R/chkSplinesFormula.R | 4 R/constructFixed.R | 6 R/constructGinv.R | 4 R/constructRandom.R | 7 R/constructRinv.R | 2 R/fitLMM.R | 9 R/getWeights.R | 4 R/mLogLik.R |only R/predictFunctions.R | 2 R/sparseMixedModels.R | 18 R/utils.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Solving_Linear_Mixed_Models.R | 32 - inst/doc/Solving_Linear_Mixed_Models.Rmd | 53 + inst/doc/Solving_Linear_Mixed_Models.html | 914 +++++++++++++++--------------- inst/tinytest/binomial1 |binary inst/tinytest/binomial2 |binary inst/tinytest/binomial3 |binary inst/tinytest/mLogLik0 |only inst/tinytest/pred5 |binary inst/tinytest/pred6 |only inst/tinytest/test_LMMsolve.R | 26 inst/tinytest/test_binomial.R | 8 inst/tinytest/test_mLogLik.R |only inst/tinytest/test_multinomial.R | 8 inst/tinytest/test_predict.R | 15 man/mLogLik.Rd |only man/predict.LMMsolve.Rd | 20 vignettes/Solving_Linear_Mixed_Models.Rmd | 53 + 38 files changed, 816 insertions(+), 570 deletions(-)
Title: Utilities for Scheduling Functions to Execute Later with Event
Loops
Description: Executes arbitrary R or C functions some time after the
current time, after the R execution stack has emptied. The functions
are scheduled in an event loop.
Author: Winston Chang [aut],
Joe Cheng [aut],
Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Marcus Geelnard [ctb, cph] ,
Evan Nemerson [ctb, cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between later versions 1.4.2 dated 2025-04-08 and 1.4.3 dated 2025-08-20
DESCRIPTION | 51 +++++---- LICENSE | 2 MD5 | 63 ++++++----- NEWS.md | 8 + R/later-package.R |only R/later.R | 54 ++------- README.md | 127 ++++++++++++++++------ build/vignette.rds |binary inst/doc/later-cpp.html | 9 - man/create_loop.Rd | 5 man/later-package.Rd |only src/RcppExports.cpp | 18 --- src/callback_registry.cpp | 31 ++--- src/callback_registry.h | 11 + src/debug.cpp | 4 src/fd.cpp | 42 ++----- src/init.c | 22 --- src/later.cpp | 49 +++----- src/later.h | 4 src/later_posix.cpp | 24 ++-- src/later_win32.cpp | 8 - src/threadutils.h | 1 src/timeconv.h | 1 src/timer_posix.cpp | 3 src/timestamp_unix.cpp | 13 +- src/wref.c | 2 tests/testthat.R | 26 +--- tests/testthat/_snaps |only tests/testthat/test-c-api.R | 14 ++ tests/testthat/test-cancel.R | 111 +++++++++++++++----- tests/testthat/test-later-fd.R | 31 ++++- tests/testthat/test-private-loops.R | 199 +++++++++++++++++++++++++----------- tests/testthat/test-run_now.R | 114 +++++++++++++------- 33 files changed, 606 insertions(+), 441 deletions(-)
Title: Construct Modeling Packages
Description: Building modeling packages is hard. A large amount of effort
generally goes into providing an implementation for a new method that
is efficient, fast, and correct, but often less emphasis is put on the
user interface. A good interface requires specialized knowledge about
S3 methods and formulas, which the average package developer might not
have. The goal of 'hardhat' is to reduce the burden around building
new modeling packages by providing functionality for preprocessing,
predicting, and validating input.
Author: Hannah Frick [aut, cre] ,
Davis Vaughan [aut],
Max Kuhn [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>
Diff between hardhat versions 1.4.1 dated 2025-01-31 and 1.4.2 dated 2025-08-20
DESCRIPTION | 17 +- LICENSE | 2 MD5 | 136 ++++++++++---------- NAMESPACE | 1 NEWS.md | 4 R/blueprint-formula-default.R | 224 ++++++++++++++++++++++------------ R/blueprint-formula.R | 28 ++-- R/blueprint-recipe-default.R | 194 +++++++++++++++++++++-------- R/blueprint-recipe.R | 42 +++--- R/blueprint-xy-default.R | 114 +++++++++++++---- R/blueprint-xy.R | 24 ++- R/blueprint.R | 67 +++++----- R/case-weights.R | 24 +++ R/classes.R | 2 R/constructor.R | 14 +- R/extract.R | 11 + R/forge.R | 18 +- R/intercept.R | 16 +- R/model-frame.R | 2 R/model-matrix.R | 18 +- R/model-offset.R | 2 R/mold.R | 6 R/new.R | 9 - R/ptype.R | 2 R/quantile-pred.R | 13 + R/recompose.R | 8 - R/scream.R | 10 + R/shrink.R | 2 R/spruce.R | 12 + R/standardize.R | 4 R/tune.R | 4 R/use.R | 10 - R/util.R | 47 ++++--- R/validation.R | 41 ++++-- README.md | 2 build/vignette.rds |binary inst/doc/forge.R | 24 +-- inst/doc/forge.Rmd | 33 +++-- inst/doc/forge.html | 30 ++-- inst/doc/mold.R | 12 - inst/doc/mold.Rmd | 17 +- inst/doc/mold.html | 9 - inst/doc/package.R | 20 +-- inst/doc/package.Rmd | 44 +++++- inst/doc/package.html | 13 + man/contr_one_hot.Rd | 18 ++ man/default_recipe_blueprint.Rd | 10 - man/hardhat-extract.Rd | 5 man/hardhat-package.Rd | 2 man/rmd/one-hot.Rmd | 6 man/tune.Rd | 4 tests/testthat/_snaps/mold-formula.md | 4 tests/testthat/_snaps/print.md | 4 tests/testthat/test-blueprint.R | 10 + tests/testthat/test-case-weights.R | 5 tests/testthat/test-encoding.R | 41 +++++- tests/testthat/test-forge-formula.R | 132 +++++++++++++++----- tests/testthat/test-forge-recipe.R | 34 ++++- tests/testthat/test-forge-xy.R | 29 +++- tests/testthat/test-model-offset.R | 6 tests/testthat/test-mold-formula.R | 98 +++++++++++--- tests/testthat/test-mold-recipe.R | 47 +++++-- tests/testthat/test-mold-xy.R | 12 + tests/testthat/test-quantile-pred.R | 15 +- tests/testthat/test-spruce.R | 11 + tests/testthat/test-use.R | 15 +- vignettes/forge.Rmd | 33 +++-- vignettes/mold.Rmd | 17 +- vignettes/package.Rmd | 44 +++++- 69 files changed, 1314 insertions(+), 620 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb] ,
Joeseph Zemm [...truncated...]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.20 dated 2025-07-15 and 2.7.21 dated 2025-08-20
DESCRIPTION | 6 +-- MD5 | 62 ++++++++++++++++--------------- NAMESPACE | 1 NEWS | 8 ++++ R/AAA.R | 3 + R/constructNWISURL.R | 4 +- R/construct_api_requests.R | 19 ++++++--- R/getWebServiceData.R | 2 - R/importWaterML1.R | 2 - R/readNWISunit.R | 18 +++++---- R/read_waterdata.R | 13 ++++++ R/read_waterdata_field_measurements.R |only R/read_waterdata_metadata.R | 1 R/read_waterdata_ts_meta.R | 2 + R/walk_pages.R | 50 +++++++++++++++++++++++-- R/whatNWISsites.R | 2 - R/whatWQPdata.R | 33 ++++++++++++---- inst/CITATION | 2 - inst/doc/dataRetrieval.R | 16 +++++--- inst/doc/dataRetrieval.Rmd | 16 +++++--- inst/doc/dataRetrieval.html | 18 ++++----- man/readNWISgwl.Rd | 14 +++---- man/read_waterdata_daily.Rd | 2 - man/read_waterdata_field_measurements.Rd |only man/read_waterdata_latest_continuous.Rd | 2 - man/read_waterdata_metadata.Rd | 1 man/read_waterdata_ts_meta.Rd | 31 +++++++++++++-- man/whatWQPdata.Rd | 3 + tests/testthat/tests_general.R | 23 +++++++++-- tests/testthat/tests_nldi.R | 1 tests/testthat/tests_samples.R | 3 + tests/testthat/tests_userFriendly_fxns.R | 17 ++++++-- vignettes/dataRetrieval.Rmd | 16 +++++--- 33 files changed, 271 insertions(+), 120 deletions(-)
Title: Utilities for Certara's Nonlinear Mixed-Effects Modeling Engine
Description: Perform Nonlinear Mixed-Effects (NLME) Modeling using Certara's
NLME-Engine. Access the same Maximum Likelihood engines used in the Phoenix
platform, including algorithms for parametric methods, individual, and pooled
data analysis.
The Quasi-Random Parametric Expectation-Maximization Method (QRPEM) is also
supported <https://www.page-meeting.org/default.asp?abstract=2338>. Execution
is supported both locally or on remote machines. Remote execution includes
support for Linux Sun Grid Engine (SGE), Simple Linux Utility for Resource Management
(SLURM) grids, Linux and Windows multicore, and individual runs.
Author: Soltanshahi Fred [aut],
Michael Tomashevskiy [aut],
James Craig [aut, cre],
Shuhua Hu [ctb],
Certara USA, Inc. [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Diff between Certara.NLME8 versions 3.0.1 dated 2024-10-15 and 3.0.2 dated 2025-08-20
DESCRIPTION | 12 MD5 | 8 R/checkHostParams.R | 165 +++++++---- inst/extdata/performEstimationOnSortColumns/Overall.expected | 14 man/checkInstallDir.Rd | 31 +- 5 files changed, 153 insertions(+), 77 deletions(-)
Title: R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) Output
Description: R graphics device using cairographics library that can be used to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek [aut, cre, cph] ,
Jeffrey Horner [aut]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Cairo versions 1.6-2 dated 2023-11-28 and 1.6-5 dated 2025-08-20
DESCRIPTION | 11 MD5 | 24 - NEWS | 23 + configure | 777 ++++++++++++++++++++++++++++++----------------------- configure.ac | 48 ++- src/cairogd.c | 25 + src/cairogd.h | 2 src/cairotalk.c | 155 +++++++++- src/img-backend.c | 2 src/pdf-backend.c | 4 src/ps-backend.c | 2 src/svg-backend.c | 2 src/xlib-backend.c | 21 - 13 files changed, 697 insertions(+), 399 deletions(-)
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file;
import/export data from/to files in any format;
print tables to Microsoft Word);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 2024.6 dated 2024-06-13 and 2025.8 dated 2025-08-20
bruceR-2024.6/bruceR/man/grapes-notin-grapes.Rd |only bruceR-2024.6/bruceR/man/pkg_install_suggested.Rd |only bruceR-2025.8/bruceR/DESCRIPTION | 27 bruceR-2025.8/bruceR/MD5 | 127 +- bruceR-2025.8/bruceR/NAMESPACE | 2 bruceR-2025.8/bruceR/NEWS.md | 11 bruceR-2025.8/bruceR/R/bruceR-stats_1_basic.R | 433 +++----- bruceR-2025.8/bruceR/R/bruceR-stats_2_scale.R | 292 ++--- bruceR-2025.8/bruceR/R/bruceR-stats_3_manova.R | 456 +++------ bruceR-2025.8/bruceR/R/bruceR-stats_4_regress.R | 415 +++----- bruceR-2025.8/bruceR/R/bruceR-stats_5_advance.R | 470 +++------ bruceR-2025.8/bruceR/R/bruceR-stats_6_plot.R | 84 - bruceR-2025.8/bruceR/R/bruceR.R | 324 ++---- bruceR-2025.8/bruceR/R/bruceR_utils.R | 500 ++++------ bruceR-2025.8/bruceR/README.md | 8 bruceR-2025.8/bruceR/man/Alpha.Rd | 48 bruceR-2025.8/bruceR/man/CFA.Rd | 31 bruceR-2025.8/bruceR/man/Corr.Rd | 13 bruceR-2025.8/bruceR/man/Describe.Rd | 6 bruceR-2025.8/bruceR/man/EFA.Rd | 115 +- bruceR-2025.8/bruceR/man/EMMEANS.Rd | 184 +-- bruceR-2025.8/bruceR/man/Freq.Rd | 5 bruceR-2025.8/bruceR/man/GLM_summary.Rd | 23 bruceR-2025.8/bruceR/man/HLM_ICC_rWG.Rd | 110 -- bruceR-2025.8/bruceR/man/HLM_summary.Rd | 32 bruceR-2025.8/bruceR/man/LOOKUP.Rd | 15 bruceR-2025.8/bruceR/man/MANOVA.Rd | 148 +- bruceR-2025.8/bruceR/man/PROCESS.Rd | 287 ++--- bruceR-2025.8/bruceR/man/Print.Rd | 4 bruceR-2025.8/bruceR/man/RGB.Rd | 6 bruceR-2025.8/bruceR/man/Run.Rd | 3 bruceR-2025.8/bruceR/man/TTEST.Rd | 67 - bruceR-2025.8/bruceR/man/add.Rd | 58 - bruceR-2025.8/bruceR/man/bruceR-demodata.Rd | 45 bruceR-2025.8/bruceR/man/bruceR-package.Rd | 223 +--- bruceR-2025.8/bruceR/man/cc.Rd | 2 bruceR-2025.8/bruceR/man/ccf_plot.Rd | 14 bruceR-2025.8/bruceR/man/cor_diff.Rd | 4 bruceR-2025.8/bruceR/man/cor_multilevel.Rd | 6 bruceR-2025.8/bruceR/man/dtime.Rd | 2 bruceR-2025.8/bruceR/man/export.Rd | 46 bruceR-2025.8/bruceR/man/formatF.Rd | 4 bruceR-2025.8/bruceR/man/formatN.Rd | 4 bruceR-2025.8/bruceR/man/grand_mean_center.Rd | 8 bruceR-2025.8/bruceR/man/granger_causality.Rd | 29 bruceR-2025.8/bruceR/man/granger_test.Rd | 21 bruceR-2025.8/bruceR/man/grapes-allin-grapes.Rd | 9 bruceR-2025.8/bruceR/man/grapes-anyin-grapes.Rd | 9 bruceR-2025.8/bruceR/man/grapes-grapes-COMPUTE-grapes-grapes.Rd | 44 bruceR-2025.8/bruceR/man/grapes-nonein-grapes.Rd | 9 bruceR-2025.8/bruceR/man/grapes-partin-grapes.Rd | 9 bruceR-2025.8/bruceR/man/grapes-pow-grapes.Rd | 4 bruceR-2025.8/bruceR/man/group_mean_center.Rd | 11 bruceR-2025.8/bruceR/man/import.Rd | 71 - bruceR-2025.8/bruceR/man/lavaan_summary.Rd | 16 bruceR-2025.8/bruceR/man/med_summary.Rd | 9 bruceR-2025.8/bruceR/man/model_summary.Rd | 54 - bruceR-2025.8/bruceR/man/p.Rd | 12 bruceR-2025.8/bruceR/man/pkg_depend.Rd | 3 bruceR-2025.8/bruceR/man/print_table.Rd | 40 bruceR-2025.8/bruceR/man/reexports.Rd |only bruceR-2025.8/bruceR/man/regress.Rd | 38 bruceR-2025.8/bruceR/man/scaler.Rd | 2 bruceR-2025.8/bruceR/man/set.wd.Rd | 12 bruceR-2025.8/bruceR/man/show_colors.Rd | 18 bruceR-2025.8/bruceR/man/theme_bruce.Rd | 30 66 files changed, 2107 insertions(+), 3005 deletions(-)
Title: 'BLAS' and 'LAPACK' Routines for Native R Matrices and
'big.matrix' Objects
Description: Provides arithmetic functions for R matrix and 'big.matrix' objects as well as functions for QR factorization, Cholesky factorization, General eigenvalue, and Singular value decomposition (SVD). A method matrix multiplication and an arithmetic method -for matrix addition, matrix difference- allows for mixed type operation -a matrix class object and a big.matrix class object- and pure type operation for two big.matrix class objects.
Author: Frederic Bertrand [cre, ctb] ,
Michael J. Kane [aut],
Bryan Lewis [aut],
John W. Emerson [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between bigalgebra versions 1.1.2 dated 2024-09-23 and 2.0.0 dated 2025-08-20
DESCRIPTION | 13 - MD5 | 28 +- NEWS.md | 4 R/bigalgebra.R | 86 +------ R/wrappers.R | 50 ++-- man/daxpy.Rd | 2 man/dcopy.Rd | 3 man/dgeev.Rd | 3 man/dgeqrf.Rd | 5 man/dgesdd.Rd | 3 man/dscal.Rd | 5 src/R_init_bigalgebra.c | 23 +- src/bigalgebra.cpp | 543 ++++++++++++++++++++++++++---------------------- src/bigalgebra.h | 13 - tests |only 15 files changed, 405 insertions(+), 376 deletions(-)
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and
'BatchExperiments', this package provides a parallel implementation of
the Map function for high performance computing systems managed by
schedulers 'IBM Spectrum LSF'
(<https://www.ibm.com/products/hpc-workload-management>), 'Univa Grid
Engine'/'Oracle Grid Engine'
(<https://altair.com/hpc-cloud-applications/>), 'Slurm'
(<https://slurm.schedmd.com/>), 'TORQUE/PBS'
(<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>),
or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>). A
multicore and socket mode allow the parallelization on a local
machines, and multiple machines can be hooked up via SSH to create a
makeshift cluster. Moreover, the package provides an abstraction
mechanism to define large-scale computer experiments in a
well-organized and reproducible way.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [aut],
Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.17 dated 2023-04-20 and 0.9.18 dated 2025-08-20
DESCRIPTION | 63 ++-- MD5 | 126 ++++---- NEWS.md | 4 R/Algorithm.R | 2 R/Hooks.R | 2 R/JobCollection.R | 2 R/JobTables.R | 2 R/Joins.R | 2 R/Logs.R | 2 R/Worker.R | 2 R/addExperiments.R | 2 R/batchMap.R | 2 R/batchMapResults.R | 2 R/batchReduce.R | 2 R/clusterFunctionsSGE.R | 2 R/estimateRuntimes.R | 4 R/findJobs.R | 2 R/getErrorMessages.R | 2 R/killJobs.R | 2 R/removeExperiments.R | 2 R/resetJobs.R | 2 R/submitJobs.R | 2 R/summarizeExperiments.R | 2 R/unwrap.R | 2 R/waitForFiles.R | 2 R/zzz.R | 2 README.md | 180 ++++++++--- build/vignette.rds |binary inst/doc/batchtools.R | 24 - inst/doc/batchtools.Rmd | 208 ++++++------- inst/doc/batchtools.html | 518 ++++++++++++++++----------------- man/JobCollection.Rd | 2 man/JoinTables.Rd | 2 man/Worker.Rd | 2 man/addAlgorithm.Rd | 2 man/addExperiments.Rd | 2 man/batchMap.Rd | 2 man/batchMapResults.Rd | 6 man/batchReduce.Rd | 2 man/batchtools-package.Rd | 7 man/estimateRuntimes.Rd | 4 man/findJobs.Rd | 2 man/getErrorMessages.Rd | 2 man/getJobTable.Rd | 2 man/grepLogs.Rd | 2 man/killJobs.Rd | 2 man/loadResult.Rd | 4 man/makeClusterFunctionsDocker.Rd | 4 man/makeClusterFunctionsInteractive.Rd | 4 man/makeClusterFunctionsLSF.Rd | 4 man/makeClusterFunctionsMulticore.Rd | 4 man/makeClusterFunctionsOpenLava.Rd | 4 man/makeClusterFunctionsSGE.Rd | 6 man/makeClusterFunctionsSSH.Rd | 4 man/makeClusterFunctionsSlurm.Rd | 4 man/makeClusterFunctionsSocket.Rd | 4 man/makeClusterFunctionsTORQUE.Rd | 4 man/removeExperiments.Rd | 2 man/resetJobs.Rd | 2 man/runHook.Rd | 2 man/submitJobs.Rd | 2 man/summarizeExperiments.Rd | 2 man/unwrap.Rd | 2 vignettes/batchtools.Rmd | 208 ++++++------- 64 files changed, 776 insertions(+), 702 deletions(-)
Title: Dyadic Mixed Model for Pedigree Data
Description: Mixed model analysis for quantitative genetics
with multi-trait responses and pedigree-based partitioning
of individual variation into a range of environmental and
genetic variance components for individual and
maternal effects. Method documented in dmmOverview.pdf; dmm is an
implementation of dispersion mean model described by
Searle et al. (1992) "Variance Components", Wiley, NY.
Dmm() can do 'MINQUE', 'bias-corrected-ML', and 'REML' variance and
covariance component estimates.
Author: Neville Jackson [aut, cre]
Maintainer: Neville Jackson <nanddjackson@bigpond.com>
Diff between dmm versions 3.2-1 dated 2025-07-08 and 3.2-2 dated 2025-08-20
dmm-3.2-1/dmm/R/fgls.iter.siga.R |only dmm-3.2-1/dmm/R/fgls.update.R |only dmm-3.2-2/dmm/DESCRIPTION | 10 dmm-3.2-2/dmm/MD5 | 46 - dmm-3.2-2/dmm/R/csummary.dmm.R | 4 dmm-3.2-2/dmm/R/csummary_specific.R | 4 dmm-3.2-2/dmm/R/dmesolve.R | 947 +++++++++++++++++----------- dmm-3.2-2/dmm/R/fgls.iter.siga.multiv.R |only dmm-3.2-2/dmm/R/fgls.iter.siga.univ.R |only dmm-3.2-2/dmm/R/fgls.update.multiv.R |only dmm-3.2-2/dmm/R/fgls.update.univ.R |only dmm-3.2-2/dmm/R/gls.iter.b.R | 16 dmm-3.2-2/dmm/R/gsummary.dmm.R | 4 dmm-3.2-2/dmm/R/gsummary_specific.R | 4 dmm-3.2-2/dmm/R/print.csummary.dmm.R | 6 dmm-3.2-2/dmm/R/print.csumspecific.dmm.R | 6 dmm-3.2-2/dmm/R/print.gsummary.dmm.R | 18 dmm-3.2-2/dmm/R/print.gsumspecific.dmm.R | 6 dmm-3.2-2/dmm/R/print.summary.dmm.R | 6 dmm-3.2-2/dmm/R/summary.dmm.R | 4 dmm-3.2-2/dmm/inst/doc/bugs.txt | 2 dmm-3.2-2/dmm/inst/doc/dmmClassSpecific.pdf |binary dmm-3.2-2/dmm/inst/doc/dmmOverview.pdf |binary dmm-3.2-2/dmm/inst/doc/dmmSolveDME.pdf |binary dmm-3.2-2/dmm/inst/doc/mods.txt | 2 dmm-3.2-2/dmm/inst/doc/remlmultiv.pdf |binary dmm-3.2-2/dmm/man/dmm-internal.Rd | 12 27 files changed, 686 insertions(+), 411 deletions(-)