Title: Penalised Regression with Multiple Sets of Prior Effects
('Transfer Learning')
Description: Improves the predictive performance of ridge and lasso regression exploiting one or more sources of prior information on the importance and direction of effects (Rauschenberger and others 2023, <doi:10.1093/bioinformatics/btad680>). For running the vignette (optional), install 'fwelnet' and 'ecpc' from <https://github.com/kjytay/fwelnet> and <https://github.com/Mirrelijn/ecpc>, respectively.
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <armin.rauschenberger@uni.lu>
Diff between transreg versions 1.0.4 dated 2025-06-10 and 1.0.5 dated 2025-07-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/functions.R | 8 ++++---- README.md | 7 +++---- 4 files changed, 14 insertions(+), 15 deletions(-)
Title: Compact and Flexible Summaries of Data
Description: A simple to use summary function that can be used with pipes
and displays nicely in the console. The default summary statistics may
be modified by the user as can the default formatting. Support for
data frames and vectors is included, and users can implement their own
skim methods for specific object types as described in a vignette.
Default summaries include support for inline spark graphs.
Instructions for managing these on specific operating systems are
given in the "Using skimr" vignette and the README.
Author: Elin Waring [cre, aut],
Michael Quinn [aut],
Amelia McNamara [aut],
Eduardo Arino de la Rubia [aut],
Hao Zhu [aut],
Julia Lowndes [ctb],
Shannon Ellis [aut],
Hope McLeod [ctb],
Hadley Wickham [ctb],
Kirill Mueller [ctb],
RStudio, Inc. [cph] ,
Connor K [...truncated...]
Maintainer: Elin Waring <elin.waring@gmail.com>
Diff between skimr versions 2.1.5 dated 2022-12-23 and 2.2.1 dated 2025-07-26
skimr-2.1.5/skimr/inst/doc/skimr.R |only skimr-2.1.5/skimr/inst/doc/skimr.Rmd |only skimr-2.1.5/skimr/inst/doc/skimr.html |only skimr-2.1.5/skimr/inst/rmarkdown/templates/fonts-in-skimr/skeleton/skeleton.log |only skimr-2.1.5/skimr/inst/rmarkdown/templates/fonts-in-skimr/skeleton/skeleton.pdf |only skimr-2.1.5/skimr/man/reexports.Rd |only skimr-2.1.5/skimr/tests/testthat/data.table |only skimr-2.1.5/skimr/tests/testthat/dplyr |only skimr-2.1.5/skimr/tests/testthat/print |only skimr-2.1.5/skimr/tests/testthat/skim_tee |only skimr-2.1.5/skimr/tests/testthat/summary |only skimr-2.1.5/skimr/tests/testthat/test-data.table.R |only skimr-2.1.5/skimr/vignettes/skimr.Rmd |only skimr-2.2.1/skimr/DESCRIPTION | 38 +- skimr-2.2.1/skimr/MD5 | 130 ++----- skimr-2.2.1/skimr/NAMESPACE | 19 - skimr-2.2.1/skimr/NEWS.md | 17 - skimr-2.2.1/skimr/R/deprecated.R | 2 skimr-2.2.1/skimr/R/get_skimmers.R | 15 skimr-2.2.1/skimr/R/package.R |only skimr-2.2.1/skimr/R/reshape.R | 29 - skimr-2.2.1/skimr/R/skim.R | 24 - skimr-2.2.1/skimr/R/skim_print.R | 10 skimr-2.2.1/skimr/R/skim_with.R | 15 skimr-2.2.1/skimr/R/skimr-package.R | 58 --- skimr-2.2.1/skimr/R/stats.R | 20 + skimr-2.2.1/skimr/R/utils.R | 28 - skimr-2.2.1/skimr/README.md | 76 ++-- skimr-2.2.1/skimr/build/vignette.rds |binary skimr-2.2.1/skimr/inst/doc/Skimr_defaults.html | 27 + skimr-2.2.1/skimr/inst/doc/extending_skimr.R | 12 skimr-2.2.1/skimr/inst/doc/extending_skimr.Rmd | 4 skimr-2.2.1/skimr/inst/doc/extending_skimr.html | 170 ++++------ skimr-2.2.1/skimr/inst/doc/using_skimr.R |only skimr-2.2.1/skimr/inst/doc/using_skimr.Rmd |only skimr-2.2.1/skimr/inst/doc/using_skimr.html |only skimr-2.2.1/skimr/man/fix_windows_histograms.Rd | 4 skimr-2.2.1/skimr/man/focus.Rd | 12 skimr-2.2.1/skimr/man/knit_print.Rd | 2 skimr-2.2.1/skimr/man/print.Rd | 4 skimr-2.2.1/skimr/man/skim.Rd | 24 - skimr-2.2.1/skimr/man/skimr-package.Rd | 78 +++- skimr-2.2.1/skimr/man/skimr-vctrs.Rd | 2 skimr-2.2.1/skimr/man/stats.Rd | 12 skimr-2.2.1/skimr/tests/testthat.R | 8 skimr-2.2.1/skimr/tests/testthat/_snaps |only skimr-2.2.1/skimr/tests/testthat/helper-expectations.R | 80 ---- skimr-2.2.1/skimr/tests/testthat/test-data-table.R |only skimr-2.2.1/skimr/tests/testthat/test-dplyr.R | 22 - skimr-2.2.1/skimr/tests/testthat/test-reshape.R | 18 - skimr-2.2.1/skimr/tests/testthat/test-sfl.R | 2 skimr-2.2.1/skimr/tests/testthat/test-skim.R | 120 +------ skimr-2.2.1/skimr/tests/testthat/test-skim_print.R | 68 +--- skimr-2.2.1/skimr/tests/testthat/test-skim_tee.R | 20 - skimr-2.2.1/skimr/tests/testthat/test-skim_with.R | 12 skimr-2.2.1/skimr/tests/testthat/test-summary.R | 14 skimr-2.2.1/skimr/tests/testthat/test-vctrs.R | 2 skimr-2.2.1/skimr/vignettes/extending_skimr.Rmd | 4 skimr-2.2.1/skimr/vignettes/using_skimr.Rmd |only 59 files changed, 520 insertions(+), 682 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super
Imposition by Translation And Rotation) growth curve models. SITAR is
a shape-invariant model with a regression B-spline mean curve and
subject-specific random effects on both the measurement and age
scales. The model was first described by Lindstrom (1995)
<doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole
et al (2010) <doi:10.1093/ije/dyq115>.
Author: Tim Cole [cre, aut, cph]
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.4.0 dated 2023-06-23 and 1.5.0 dated 2025-07-26
DESCRIPTION | 18 MD5 | 52 +- NAMESPACE | 16 NEWS | 34 + R/BICadj.R | 9 R/anova.sitar.R | 6 R/getDV.R |only R/getPeakTrough.R | 19 R/plot.sitar.R | 592 ++++++++++++----------- R/predict.sitar.R | 302 +++++------ R/sitar-package.R | 34 - R/sitar.R | 239 +++++---- R/sitarlib.R | 8 R/xyadj.R | 44 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/Fitting_models_with_SITAR.R | 18 inst/doc/Fitting_models_with_SITAR.html | 14 inst/doc/Optimal_design_for_centile_studies.R | 6 inst/doc/Optimal_design_for_centile_studies.html | 12 man/anova.sitar.Rd | 6 man/getDV.Rd |only man/getPeakTrough.Rd | 10 man/plot.sitar.Rd | 215 ++++---- man/predict.sitar.Rd | 63 +- man/sitar-package.Rd | 40 + man/sitar.Rd | 119 ++-- man/summary.sitar.Rd | 8 28 files changed, 1037 insertions(+), 847 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow [aut, cre]
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 3.1.2 dated 2024-02-26 and 3.1.3 dated 2025-07-26
DESCRIPTION | 12 +++++--- MD5 | 42 +++++++++++++++---------------- NEWS.md | 4 ++ R/palette.R | 2 - inst/slowtests/rpart.report.bat | 2 - inst/slowtests/test.describe.col.bat | 2 - inst/slowtests/test.imports.bat | 2 - inst/slowtests/test.na.bat | 2 - inst/slowtests/test.palette.bat | 2 - inst/slowtests/test.rpart.plot.Rout.save | 30 +++++++++------------- inst/slowtests/test.rpart.plot.bat | 2 - inst/slowtests/test.rpart.rules.bat | 2 - inst/slowtests/test.type5.bat | 2 - inst/slowtests/usersplits.bat | 2 - inst/slowtests/vignette.Rout.save | 2 - inst/slowtests/vignette.bat | 2 - inst/slowtests/webpage.figs.bat | 2 - man/prp.Rd | 14 +++++----- man/ptitanic.Rd | 3 -- man/rpart.plot.Rd | 14 +++++----- man/rpart.predict.Rd | 10 +++---- man/rpart.rules.Rd | 2 - 22 files changed, 79 insertions(+), 78 deletions(-)
Title: Visualize Outputs from the 'Johnson-Neyman' Technique
Description: Aids in the calculation and visualization of regions of non-significance using the 'Johnson-Neyman' technique and its extensions as described by Bauer and Curran (2005) <doi:10.1207/s15327906mbr4003_5> to assess the influence of categorical and continuous moderators. Allows correcting for phylogenetic relatedness.
Author: Ken Toyama [cre, aut]
Maintainer: Ken Toyama <ken.toyama7@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2023-11-24
Diff between JNplots versions 0.1.1 dated 2023-11-24 and 0.1.2 dated 2025-07-26
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/jnt_cat.R | 8 ++++---- R/jnt_cont.R | 8 ++++---- build/partial.rdb |binary man/jnt_cat.Rd | 8 ++++---- man/jnt_cont.Rd | 8 ++++---- 8 files changed, 37 insertions(+), 30 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic-process movement models to animal tracking data.
The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced and detailed in
Fleming & Calabrese et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>,
Fleming et al (2019) <doi:10.1111/2041-21 [...truncated...]
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Bjoern Reineking [ctb],
Guillaume Peron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Chad J. Wilhite [ctb],
Eliezer Gurarie [ctb],
Kamran Sa [...truncated...]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 1.2.0 dated 2023-09-23 and 1.3.0 dated 2025-07-26
ctmm-1.2.0/ctmm/man/RSF.fit.Rd |only ctmm-1.3.0/ctmm/DESCRIPTION | 11 ctmm-1.3.0/ctmm/MD5 | 205 +++--- ctmm-1.3.0/ctmm/NAMESPACE | 5 ctmm-1.3.0/ctmm/NEWS.md | 39 + ctmm-1.3.0/ctmm/R/QP.R | 2 ctmm-1.3.0/ctmm/R/acf.R | 3 ctmm-1.3.0/ctmm/R/bandwidth.R | 12 ctmm-1.3.0/ctmm/R/cde.R |only ctmm-1.3.0/ctmm/R/change.point.R | 4 ctmm-1.3.0/ctmm/R/convex.R | 108 ++- ctmm-1.3.0/ctmm/R/corridor.R | 2 ctmm-1.3.0/ctmm/R/covm.R | 28 ctmm-1.3.0/ctmm/R/ctmm.R | 53 + ctmm-1.3.0/ctmm/R/cv.R | 3 ctmm-1.3.0/ctmm/R/dexp.R |only ctmm-1.3.0/ctmm/R/diff.R | 31 - ctmm-1.3.0/ctmm/R/distance.R | 8 ctmm-1.3.0/ctmm/R/emulate.R | 45 + ctmm-1.3.0/ctmm/R/encounter.R | 286 +++------ ctmm-1.3.0/ctmm/R/export.R | 134 ++-- ctmm-1.3.0/ctmm/R/fit.R | 33 - ctmm-1.3.0/ctmm/R/generic.R | 80 +- ctmm-1.3.0/ctmm/R/grid.R | 16 ctmm-1.3.0/ctmm/R/homerange.R | 6 ctmm-1.3.0/ctmm/R/kalman.R | 50 - ctmm-1.3.0/ctmm/R/kde.R | 64 +- ctmm-1.3.0/ctmm/R/krige.R | 76 +- ctmm-1.3.0/ctmm/R/likelihood.R | 61 +- ctmm-1.3.0/ctmm/R/log.R | 149 ++++ ctmm-1.3.0/ctmm/R/log.ctmm.R | 28 ctmm-1.3.0/ctmm/R/math.R | 37 + ctmm-1.3.0/ctmm/R/matrix.R | 126 ++-- ctmm-1.3.0/ctmm/R/mean.R | 873 ++++++++++++++++------------- ctmm-1.3.0/ctmm/R/mean.UD.R | 13 ctmm-1.3.0/ctmm/R/mean.ctmm.R | 301 +++++---- ctmm-1.3.0/ctmm/R/mean.mu.R |only ctmm-1.3.0/ctmm/R/meta.chisq.R | 185 +++--- ctmm-1.3.0/ctmm/R/meta.normal.R | 644 ++++++++++++++++----- ctmm-1.3.0/ctmm/R/modes.R | 2 ctmm-1.3.0/ctmm/R/npr.R | 53 - ctmm-1.3.0/ctmm/R/numDeriv.R | 2 ctmm-1.3.0/ctmm/R/occurrence.R | 31 - ctmm-1.3.0/ctmm/R/optim.R | 24 ctmm-1.3.0/ctmm/R/outlier.R | 4 ctmm-1.3.0/ctmm/R/overlap.R | 6 ctmm-1.3.0/ctmm/R/parameters.R | 47 + ctmm-1.3.0/ctmm/R/periodogram.R | 3 ctmm-1.3.0/ctmm/R/plot.telemetry.R | 48 - ctmm-1.3.0/ctmm/R/plot.variogram.R | 5 ctmm-1.3.0/ctmm/R/plot3d.R | 4 ctmm-1.3.0/ctmm/R/projection.R | 108 +++ ctmm-1.3.0/ctmm/R/ridge.R | 203 +----- ctmm-1.3.0/ctmm/R/rsf.R | 734 +++++++++++++----------- ctmm-1.3.0/ctmm/R/rsf.select.R | 10 ctmm-1.3.0/ctmm/R/sdm.R | 16 ctmm-1.3.0/ctmm/R/select.R | 22 ctmm-1.3.0/ctmm/R/series.R | 19 ctmm-1.3.0/ctmm/R/speed.R | 103 ++- ctmm-1.3.0/ctmm/R/stats.R | 50 + ctmm-1.3.0/ctmm/R/suitability.R | 24 ctmm-1.3.0/ctmm/R/summary.ctmm.R | 21 ctmm-1.3.0/ctmm/R/telemetry.R | 250 +++++--- ctmm-1.3.0/ctmm/R/time.R | 86 +- ctmm-1.3.0/ctmm/R/transition.R | 10 ctmm-1.3.0/ctmm/R/uere.R | 4 ctmm-1.3.0/ctmm/R/units.R | 3 ctmm-1.3.0/ctmm/R/variogram.fit.R | 2 ctmm-1.3.0/ctmm/README.md | 18 ctmm-1.3.0/ctmm/TODO | 45 + ctmm-1.3.0/ctmm/build/partial.rdb |binary ctmm-1.3.0/ctmm/build/vignette.rds |binary ctmm-1.3.0/ctmm/inst/doc/akde.R | 18 ctmm-1.3.0/ctmm/inst/doc/akde.html | 58 - ctmm-1.3.0/ctmm/inst/doc/error.html | 50 - ctmm-1.3.0/ctmm/inst/doc/interactions.R | 11 ctmm-1.3.0/ctmm/inst/doc/interactions.Rmd | 15 ctmm-1.3.0/ctmm/inst/doc/interactions.html | 165 ++--- ctmm-1.3.0/ctmm/inst/doc/periodogram.html | 138 ++-- ctmm-1.3.0/ctmm/inst/doc/variogram.html | 36 - ctmm-1.3.0/ctmm/man/akde.Rd | 3 ctmm-1.3.0/ctmm/man/as.telemetry.Rd | 6 ctmm-1.3.0/ctmm/man/ctmm-FAQ.Rd | 32 - ctmm-1.3.0/ctmm/man/ctmm-package.Rd | 7 ctmm-1.3.0/ctmm/man/ctmm.boot.Rd | 5 ctmm-1.3.0/ctmm/man/distance.Rd | 2 ctmm-1.3.0/ctmm/man/encounter.Rd | 18 ctmm-1.3.0/ctmm/man/export.Rd | 10 ctmm-1.3.0/ctmm/man/log.Rd | 5 ctmm-1.3.0/ctmm/man/mean.Rd | 3 ctmm-1.3.0/ctmm/man/meta.Rd | 4 ctmm-1.3.0/ctmm/man/npr.Rd | 4 ctmm-1.3.0/ctmm/man/optimizer.Rd | 2 ctmm-1.3.0/ctmm/man/outlie.Rd | 6 ctmm-1.3.0/ctmm/man/overlap.Rd | 6 ctmm-1.3.0/ctmm/man/pd.matrix.Rd |only ctmm-1.3.0/ctmm/man/plot.telemetry.Rd | 10 ctmm-1.3.0/ctmm/man/projection.Rd | 5 ctmm-1.3.0/ctmm/man/residuals.Rd | 2 ctmm-1.3.0/ctmm/man/revisitation.Rd | 6 ctmm-1.3.0/ctmm/man/rsf.Rd |only ctmm-1.3.0/ctmm/man/sdm.fit.Rd | 6 ctmm-1.3.0/ctmm/man/sigfig.Rd | 2 ctmm-1.3.0/ctmm/man/speed.Rd | 2 ctmm-1.3.0/ctmm/man/summary.ctmm.Rd | 3 ctmm-1.3.0/ctmm/man/transition.Rd |only ctmm-1.3.0/ctmm/vignettes/interactions.Rmd | 15 107 files changed, 3848 insertions(+), 2485 deletions(-)
Title: Bayesian Recurrent Events Analysis
Description: Functions to produce MCMC samples for posterior inference in semiparametric Bayesian discrete time competing risks recurrent events models and multistate models.
Author: Adam J King [aut, cre]
Maintainer: Adam J King <king@cpp.edu>
Diff between brea versions 0.3.1 dated 2024-07-22 and 0.4.1 dated 2025-07-26
DESCRIPTION | 14 +- MD5 | 14 +- R/brea_mcmc.R | 270 ++++++++++++++++++++++++++++++++++++++++++----------- inst/doc/brea.R | 2 inst/doc/brea.Rmd | 4 inst/doc/brea.html | 18 +-- man/brea_mcmc.Rd | 4 vignettes/brea.Rmd | 4 8 files changed, 249 insertions(+), 81 deletions(-)
Title: Easy Interface to Search 'SciELO' Database
Description: Provides a simple interface to search and retrieve scientific articles
from the 'SciELO' (Scientific Electronic Library Online) database <https://scielo.org>.
It allows querying, filtering, and visualizing results in an interactive table.
Author: Pablo Ixcamparij [aut, cre],
Keneth Masis Leandro [aut]
Maintainer: Pablo Ixcamparij <jose.sorto@ucr.ac.cr>
Diff between easyScieloPack versions 0.1.0 dated 2025-07-18 and 0.1.1 dated 2025-07-26
DESCRIPTION | 23 +++++++++++++---------- MD5 | 2 +- 2 files changed, 14 insertions(+), 11 deletions(-)
More information about easyScieloPack at CRAN
Permanent link
Title: Identifying Unique Multilocus Genotypes where Genotyping Error
and Missing Data may be Present
Description: Tools for the identification of unique of multilocus genotypes when both genotyping error and missing data may be present; targeted for use with large datasets and databases containing multiple samples of each individual (a common situation in conservation genetics, particularly in non-invasive wildlife sampling applications). Functions explicitly incorporate missing data and can tolerate allele mismatches created by genotyping error. If you use this package, please cite the original publication in Molecular Ecology Resources (Galpern et al., 2012), the details for which can be generated using citation('allelematch'). For a complete vignette, please access via the Data S1 Supplementary documentation and tutorials (PDF) located at <doi:10.1111/j.1755-0998.2012.03137.x>.
Author: Paul Galpern [aut],
Micheline Manseau [aut],
Pete Hettinga [aut],
Karen Smith [aut],
Paul Wilson [aut],
Todd Cross [cre]
Maintainer: Todd Cross <todd.cross@gmail.com>
Diff between allelematch versions 2.5.4 dated 2024-03-28 and 2.5.5 dated 2025-07-26
DESCRIPTION | 41 ++++++++++++++++++++++++++++++++++++----- MD5 | 8 ++++---- R/allelematch.r | 4 ++-- build/partial.rdb |binary man/amCluster.Rd | 5 ++--- 5 files changed, 44 insertions(+), 14 deletions(-)
Title: Lightweight, General-Purpose Data Analysis Pipelines
Description: A lightweight yet powerful framework for building robust data
analysis pipelines. With 'pipeflow', you initialize a pipeline with your
dataset and construct workflows step by step by adding R functions.
You can modify, remove, or insert steps and parameters at any stage,
while 'pipeflow' ensures the pipeline's integrity.
Overall, this package offers a beginner-friendly framework that simplifies
and streamlines the development of data analysis pipelines by making
them modular, intuitive, and adaptable.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between pipeflow versions 0.2.2 dated 2024-12-22 and 0.2.3 dated 2025-07-26
DESCRIPTION | 7 - MD5 | 91 ++++++++-------- NEWS.md | 10 + R/log.R | 2 inst/doc/v01-get-started.html | 73 ++++++------- inst/doc/v02-modify-pipeline.R | 12 +- inst/doc/v02-modify-pipeline.Rmd | 20 +-- inst/doc/v02-modify-pipeline.html | 178 ++++++++++++++++----------------- inst/doc/v03-combine-pipelines.html | 73 ++++++------- inst/doc/v04-collect-output.R | 8 + inst/doc/v04-collect-output.Rmd | 10 + inst/doc/v04-collect-output.html | 44 +++----- inst/doc/v05-split-and-combine.html | 115 ++++++++++----------- inst/doc/v06-self-modify-pipeline.html | 115 ++++++++++----------- man/figures/cartoon.png |only man/pipe_add.Rd | 172 +++++++++++++++---------------- man/pipe_append.Rd | 114 ++++++++++----------- man/pipe_append_to_step_names.Rd | 62 +++++------ man/pipe_clone.Rd | 54 +++++----- man/pipe_collect_out.Rd | 106 +++++++++---------- man/pipe_discard_steps.Rd | 108 ++++++++++---------- man/pipe_get_data.Rd | 48 ++++---- man/pipe_get_depends.Rd | 138 ++++++++++++------------- man/pipe_get_graph.Rd | 68 ++++++------ man/pipe_get_out.Rd | 60 +++++------ man/pipe_get_params.Rd | 134 ++++++++++++------------ man/pipe_insert.Rd | 96 ++++++++--------- man/pipe_length.Rd | 48 ++++---- man/pipe_lock_unlock.Rd | 96 ++++++++--------- man/pipe_new.Rd | 118 ++++++++++----------- man/pipe_pop_step.Rd | 114 ++++++++++----------- man/pipe_print.Rd | 62 +++++------ man/pipe_remove_step.Rd | 76 +++++++------- man/pipe_rename_step.Rd | 66 ++++++------ man/pipe_replace_step.Rd | 130 ++++++++++++------------ man/pipe_reset.Rd | 58 +++++----- man/pipe_run.Rd | 162 +++++++++++++++--------------- man/pipe_run_step.Rd | 94 ++++++++--------- man/pipe_set_data.Rd | 54 +++++----- man/pipe_set_data_split.Rd | 148 +++++++++++++-------------- man/pipe_set_keep_out.Rd | 68 ++++++------ man/pipe_set_params.Rd | 82 +++++++-------- man/pipe_set_params_at_step.Rd | 66 ++++++------ man/pipe_split.Rd | 70 ++++++------ man/step_info.Rd | 120 +++++++++++----------- vignettes/v02-modify-pipeline.Rmd | 20 +-- vignettes/v04-collect-output.Rmd | 10 + 47 files changed, 1801 insertions(+), 1779 deletions(-)
Title: Simulate Data for Discrete Choice Experiments
Description: Supports simulating choice experiment data for given designs. It helps to quickly test different designs against each other and compare the performance of new models. The goal of 'simulateDCE' is to make it easy to simulate choice experiment datasets using designs from 'NGENE', 'idefix' or 'spdesign'. You have to store the design file(s) in a sub-directory and need to specify certain parameters and the utility functions for the data generating process. For more details on choice experiments see Mariel et al. (2021) <doi:10.1007/978-3-030-62669-3>.
Author: Julian Sagebiel [aut, cre]
Maintainer: Julian Sagebiel <julian.sagebiel@idiv.de>
Diff between simulateDCE versions 0.3.0 dated 2025-07-09 and 0.3.1 dated 2025-07-26
DESCRIPTION | 9 MD5 | 30 NEWS.md | 29 R/globals.R | 2 R/sim_choice.R | 5 R/simulate_choices.R | 104 README.md |92515 --------------------------- inst/doc/SE_Agri-vignette.html | 1165 inst/doc/SE_drive-vignette.html | 573 inst/doc/csa-vignette.html | 918 man/sim_all.Rd | 2 man/sim_choice.Rd | 2 man/simulate_choices.Rd | 5 tests/manual-tests/simple_simulate_choices.R |only tests/manual-tests/test_speedsimulatedce.R |only tests/testthat/Rplots.pdf |binary tests/testthat/test-simulate_choices.R | 231 17 files changed, 2033 insertions(+), 93557 deletions(-)
Title: Flexible, Extensible, & Reproducible Pupillometry Preprocessing
Description: Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris' provides a modular, performant, and extensible preprocessing framework for pupillometry data with BIDS-like organization and interactive output reports [Esteban et al. (2019) <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44>]. Development was supported, in part, by the S [...truncated...]
Author: Shawn Schwartz [aut, cre] ,
Mingjian He [ctb],
Haopei Yang [ctb],
Alice Xue [ctb],
Gustavo Santiago-Reyes [ctb]
Maintainer: Shawn Schwartz <shawn.t.schwartz@gmail.com>
Diff between eyeris versions 2.1.0 dated 2025-07-22 and 2.1.1 dated 2025-07-26
DESCRIPTION | 8 +- MD5 | 47 ++++++------- NEWS.md | 108 ++++++++++++++++++------------- R/pipeline-bidsify.R | 57 ++++++++++++++-- R/pipeline-glassbox.R | 2 R/pipeline-loadasc.R | 10 ++ README.md | 25 ++++--- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST |only inst/doc/anatomy.html | 5 - inst/doc/complete-pipeline.Rmd | 4 - inst/doc/complete-pipeline.html | 11 +-- inst/doc/custom-extensions.Rmd | 2 inst/doc/custom-extensions.html | 7 -- inst/doc/epoching-bids-reports.Rmd | 6 - inst/doc/epoching-bids-reports.html | 13 +-- inst/doc/reports.Rmd | 10 +- inst/doc/reports.html | 15 ++-- man/figures/README-unnamed-chunk-3-1.png |binary man/glassbox.Rd | 2 vignettes/complete-pipeline.Rmd | 4 - vignettes/custom-extensions.Rmd | 2 vignettes/epoching-bids-reports.Rmd | 6 - vignettes/reports.Rmd | 10 +- 25 files changed, 213 insertions(+), 141 deletions(-)
Title: Public Economic Data and Quantitative Analysis
Description: Provides an interface to access public economic and financial data for
economic research and quantitative analysis. The data sources including
NBS, FRED, Sina, Eastmoney and etc. It also provides quantitative
functions for trading strategies based on the 'data.table', 'TTR',
'PerformanceAnalytics' and etc packages.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between pedquant versions 0.2.4 dated 2024-01-10 and 0.2.5 dated 2025-07-26
DESCRIPTION | 12 +- MD5 | 48 ++++----- NAMESPACE | 4 NEWS.md | 14 ++ R/ed_fred.R | 2 R/ed_nbs.R | 31 ++++-- R/func_helper.R | 32 +++++- R/md_0query.R | 2 R/md_2chinamoney.R | 70 ++++++-------- R/md_future.R | 27 ++++- R/md_stock1_.R | 2 R/md_stock1_hist.R | 4 R/md_stock_symbol.R | 97 +++++-------------- R/md_stocka_real.R | 32 +++++- R/pq_addti.R | 14 ++ R/pq_orders.R | 25 ++++- R/pq_plot2.R | 215 ++++++++++++++++++++++++++++++-------------- R/sysdata.rda |binary README.md | 20 ++-- inst/extdata/md_stock_adj.R | 2 man/ed_nbs.Rd | 6 + man/md_stock_symbol.Rd | 2 man/md_symbol.Rd | 2 man/pq_addti.Rd | 1 man/pq_plot.Rd | 14 ++ 25 files changed, 408 insertions(+), 270 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes eaxis(), an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] ,
Werner Stahel [ctb] , f.robftest, last,
p.scales, p.dnorm),
Andreas Ruckstuhl [ctb] , p.profileTraces,
p.res.2x),
Christian Keller [ctb] , p.tachoPlot),
Kjetil Halvorsen [ctb] , ecdf.ksCI),
Alain Hauser [ctb] , is.whole,
[...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-20 dated 2024-11-05 and 1.1-21 dated 2025-07-26
DESCRIPTION | 15 ++++++++------- MD5 | 15 ++++++++------- NAMESPACE | 1 + R/misc-goodies.R | 3 ++- R/prime-numbers-fn.R | 31 ++++++++++++++++++++++++++++--- build/partial.rdb |binary inst/NEWS.Rd | 13 +++++++++++++ man/gcd.Rd |only man/vcat.Rd | 9 ++++----- 9 files changed, 64 insertions(+), 23 deletions(-)
Title: Heuristics for Solving the Traveling Salesman Problem in
Warehouse Layouts
Description: Heuristic methods to solve the routing problems in a warehouse management. Package includes several heuristics such as the Midpoint, Return, S-Shape and Semi-Optimal Heuristics for designation of the picker’s route in order picking. The heuristics aim to provide the acceptable travel distances while considering warehouse layout constraints such as aisles and shelves.
It also includes implementation of the COPRAS (COmplex PRoportional ASsessment) method for supporting selection of locations to be visited by the picker in shared storage systems. The package is designed to facilitate more efficient warehouse routing and logistics operations.
see:
Bartholdi, J. J., Hackman, S. T. (2019). "WAREHOUSE & DISTRIBUTION SCIENCE. Release 0.98.1."
The Supply Chain & Logistics Institute. H. Milton Stewart School of Industrial and Systems Engineering.
Georgia Institute of Technology.
<https://www.warehouse-science.com/book/editions/wh-sci-0.98.1.pdf>.
Author: Andrzej Dudek [aut, cre] ,
Krzysztof Dmytrow [aut]
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between warehouseTools versions 0.1.3 dated 2025-06-22 and 0.1.4 dated 2025-07-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/dd_heuristic.r | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
More information about warehouseTools at CRAN
Permanent link
Title: A Parametric Model for Estimating the Mean Number of Events
Description: Implementation of a parametric joint model for modelling recurrent
and competing event processes using generalised survival models as described in
Entrop et al., (2025) <doi:10.1002/bimj.70038>. The joint model can
subsequently be used to predict the mean number of events in the
presence of competing risks at different time points. Comparisons of the mean
number of event functions, e.g. the differences in mean number of events
between two exposure groups, are also available.
Author: Joshua P. Entrop [aut, cre, cph] ,
Alessandro Gasparini [ctb],
Mark Clements [ctb]
Maintainer: Joshua P. Entrop <joshuaentrop@posteo.de>
Diff between JointFPM versions 1.2.2 dated 2025-02-20 and 1.3.0 dated 2025-07-26
DESCRIPTION | 14 +-- MD5 | 16 ++-- NEWS.md | 68 +++++++++--------- R/mean_no.R | 145 +++++++++++++++++++++++++++++++++++++-- build/partial.rdb |binary inst/CITATION | 2 man/mean_no.Rd | 20 +++++ tests/testthat/_snaps/mean_no.md | 65 +++++++++++++++++ tests/testthat/test-mean_no.R | 98 ++++++++++++++++++++++++++ 9 files changed, 373 insertions(+), 55 deletions(-)
Title: Latent Interaction Testing for Genome-Wide Studies
Description: Identifying latent genetic interactions in genome-wide association studies
using the Latent Interaction Testing (LIT) framework.
LIT is a flexible kernel-based approach that leverages information across
multiple traits to detect latent genetic interactions without specifying or
observing the interacting variable (e.g., environment). LIT accepts
standard PLINK files as inputs to analyze large genome-wide association studies.
Author: Andrew Bass [aut, cre],
Michael Epstein [aut]
Maintainer: Andrew Bass <ajbass@emory.edu>
Diff between lit versions 1.0.0 dated 2023-08-15 and 1.0.1 dated 2025-07-26
DESCRIPTION | 6 MD5 | 20 +- NEWS.md | 3 README.md | 55 +++++-- build/vignette.rds |binary inst/doc/lit.R | 22 +- inst/doc/lit.html | 382 +++++++++----------------------------------------- man/gamut_plink.Rd | 2 man/lit.Rd | 6 man/lit_plink.Rd | 8 - man/marginal_plink.Rd | 2 11 files changed, 147 insertions(+), 359 deletions(-)
Title: Distance-Based Statistics
Description: Prediction methods where explanatory information is coded as a matrix of distances between individuals. Distances can either be directly input as a distances matrix, a squared distances matrix, an inner-products matrix or computed from observed predictors.
Author: Eva Boj [aut, cre],
Adria Caballe [aut],
Pedro Delicado [aut],
Josep Fortiana [aut]
Maintainer: Eva Boj <evaboj@ub.edu>
Diff between dbstats versions 2.0.2 dated 2024-01-26 and 2.0.3 dated 2025-07-26
DESCRIPTION | 23 +++++++++++++++++------ MD5 | 14 +++++++------- NEWS | 6 ++++++ man/dbglm.Rd | 2 +- man/dblm.Rd | 4 ++-- man/dbplsr.Rd | 4 ++-- man/dbstats-package.Rd | 4 ++-- man/disttoD2.rd | 2 +- 8 files changed, 38 insertions(+), 21 deletions(-)
Title: Local Pattern Analysis
Description: Describes spatial patterns of categorical raster data for
any defined regular and irregular areas.
Patterns are described quantitatively using built-in signatures
based on co-occurrence matrices but also allows for
any user-defined functions.
It enables spatial analysis such as search, change detection,
and clustering to be performed on spatial patterns (Nowosad (2021) <doi:10.1007/s10980-020-01135-0>).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between motif versions 0.6.4 dated 2023-06-29 and 0.6.5 dated 2025-07-26
DESCRIPTION | 11 + MD5 | 26 ++-- NEWS.md | 8 + R/lsp_add_spatial.R | 204 ++++++++++++++++++++-------------- R/lsp_compare.R | 62 +++++++--- R/lsp_extract.R | 4 R/lsp_search.R | 45 +++++-- R/lsp_signature.R | 127 ++++++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/v1_intro.R | 8 - inst/doc/v1_intro.html | 153 ++++++++++++------------- man/lsp_extract.Rd | 4 tests/testthat/test-lsp_add_spatial.R | 2 14 files changed, 391 insertions(+), 263 deletions(-)
Title: Classical Age-Depth Modelling of Cores from Deposits
Description: Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010) <doi:10.1016/j.quageo.2010.01.002>.
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [ctb] ,
Judith Esquivel Vazquez [ctb],
Simon Goring [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between clam versions 2.6.2 dated 2025-01-11 and 2.6.3 dated 2025-07-26
DESCRIPTION | 15 ++++++++------- MD5 | 22 +++++++++++----------- NEWS.md | 6 +++++- R/clam.R | 48 +++++++++++++++++++++--------------------------- R/models.R | 33 +++++++++++++++++++++------------ R/plots.R | 18 ++++++++++-------- R/readwrite.R | 43 +++++++++++++++++++------------------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/clam.Rmd | 2 +- inst/doc/clam.html | 52 +++++++++++++++++++++------------------------------- vignettes/clam.Rmd | 2 +- 12 files changed, 118 insertions(+), 123 deletions(-)
Title: Regularized PQL for Joint Selection in GLMMs
Description: Performs joint selection in Generalized Linear Mixed Models (GLMMs) using penalized likelihood methods. Specifically, the Penalized Quasi-Likelihood (PQL) is used as a loss function, and penalties are then augmented to perform simultaneous fixed and random effects selection. Regularized PQL avoids the need for integration (or approximations such as the Laplace's method) during the estimation process, and so the full solution path for model selection can be constructed relatively quickly.
Author: Francis K.C. Hui [aut, cre]
Maintainer: Francis K.C. Hui <fhui28@gmail.com>
Diff between rpql versions 0.8.1 dated 2023-08-19 and 0.8.2 dated 2025-07-26
rpql-0.8.1/rpql/inst/NEWS.Rd |only rpql-0.8.2/rpql/DESCRIPTION | 16 ++++++++++------ rpql-0.8.2/rpql/MD5 | 11 +++++------ rpql-0.8.2/rpql/R/auxilaryfunctions.R | 11 +++++++++++ rpql-0.8.2/rpql/build/partial.rdb |binary rpql-0.8.2/rpql/man/nb2.Rd | 3 --- rpql-0.8.2/rpql/man/rpql.Rd | 2 +- 7 files changed, 27 insertions(+), 16 deletions(-)
Title: MASCOTNUM / RT-UQ Algorithms Template Tools
Description: Helper functions for MASCOTNUM / RT-UQ <https://uq.math.cnrs.fr/> algorithm template, for design of numerical experiments practice:
algorithm template parser to support MASCOTNUM specification <https://github.com/MASCOTNUM/algorithms>,
'ask & tell' decoupling injection (inspired by <https://search.r-project.org/CRAN/refmans/sensitivity/html/decoupling.html>)
to use "crimped" algorithms (like uniroot(), optim(), ...) from outside R,
basic template examples: Brent algorithm for 1 dim root finding and L-BFGS-B from base optim().
Author: Yann Richet [aut, cre]
Maintainer: Yann Richet <yann.richet@asnr.fr>
Diff between templr versions 0.2-0 dated 2022-10-25 and 0.2-1 dated 2025-07-26
DESCRIPTION | 20 ++++++++++---------- MD5 | 4 ++-- R/algorithm.R | 23 +++++++++++++---------- 3 files changed, 25 insertions(+), 22 deletions(-)
Title: Bitmap Images / Pixel Maps
Description: Functions for import, export, visualization and other manipulations of bitmapped images.
Author: Roger Bivand [aut] ,
Friedrich Leisch [aut] ,
Martin Maechler [aut] ,
Achim Zeileis [cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between pixmap versions 0.4-13 dated 2024-05-03 and 0.4-14 dated 2025-07-26
DESCRIPTION | 16 ++++++++-------- MD5 | 9 +++++---- NEWS.md | 9 +++++++++ R/pixmap.R | 4 ++-- tests/bugs.R | 10 +++++----- tests/bugs.Rout.save |only 6 files changed, 29 insertions(+), 19 deletions(-)
Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
and Diversity
Description: Analysis of plant pathogen pathotype survey data. Functions
provided calculate distribution of susceptibilities, distribution of
complexities with statistics, pathotype frequency distribution, as
well as diversity indices for pathotypes. This package is meant to be
a direct replacement for Herrmann, Löwer and Schachtel's (1999)
<doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet,
'HaGiS', previously used for pathotype analysis.
Author: Austin G. McCoy [aut, ccp] ,
Zachary Noel [aut, ccp] ,
Adam H. Sparks [aut, cre] ,
Martin Chilvers [aut, ths] ,
Jari Oksanen [aut] ,
Zhian N. Kamvar [ctb, rev] ,
Michigan Soybean Promotion Committee [fnd, cph],
Project GREEEN [fnd, cph],
North Centra [...truncated...]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between hagis versions 3.1.12 dated 2024-05-16 and 4.0.0 dated 2025-07-26
DESCRIPTION | 54 ++++-- MD5 | 72 ++++---- NEWS.md | 146 +++++++++-------- R/calculate_complexities.R | 182 +++++++++++++--------- R/calculate_diversities.R | 132 ++++++++------- R/create_binary_matrix.R | 36 ++-- R/data.R | 8 R/globals.R | 1 R/internal_functions.R | 42 ++--- R/summarize_gene.R | 122 ++++++++------ README.md | 117 +++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 11 + inst/doc/betadiversity.html | 18 +- inst/doc/hagis.R | 26 +-- inst/doc/hagis.Rmd | 10 - inst/doc/hagis.html | 14 - man/P_sojae_survey.Rd | 10 - man/autoplot.hagis.complexities.Rd | 16 + man/autoplot.hagis.gene.summary.Rd | 16 + man/calculate_complexities.Rd | 16 + man/calculate_diversities.Rd | 34 ++-- man/create_binary_matrix.Rd | 2 man/diversities_table.Rd | 22 +- man/hagis-package.Rd | 12 - man/individual_pathotypes.Rd | 24 +- man/sample_meta.Rd | 2 man/summarize_gene.Rd | 20 +- tests/testthat/test-autoplot_hagis_complexities.R | 62 +++---- tests/testthat/test-autoplot_rps_summary.R | 49 ++--- tests/testthat/test-calculate_complexities.R | 55 +++--- tests/testthat/test-calculate_diversities.R | 27 +-- tests/testthat/test-create_binary_matrix.R | 1 tests/testthat/test-diversities_table.R | 17 +- tests/testthat/test-individual_pathotypes.R | 14 + vignettes/hagis.Rmd | 10 - 37 files changed, 747 insertions(+), 653 deletions(-)