Title: Build 'pkgdown' Websites Offline
Description: Provides support for building 'pkgdown' websites without an
internet connection. Works by bundling cached dependencies and
implementing drop-in replacements for key 'pkgdown' functions.
Enables package documentation websites to be built in environments
where internet access is unavailable or restricted.
For more details on generating 'pkgdown' websites, see
Wickham et al. (2025) <doi:10.32614/CRAN.package.pkgdown>.
Author: Nan Xiao [aut, cre, cph] ,
John Blischak [aut] ,
Algolia, Inc. and other contributors [ctb, cph] ,
Aidan Feldman [ctb, cph] ,
Zeno Rocha [ctb, cph] ,
Nick Williams [ctb, cph] ,
Julian Kuehnel [ctb, cph] ,
Kiro Risk [ctb, cph] ,
Khan Academy and other [...truncated...]
Maintainer: Nan Xiao <me@nanx.me>
Diff between pkgdown.offline versions 0.1.1 dated 2025-05-25 and 0.1.2 dated 2025-11-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/build.R | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/cache/MD5 | 7 +++++++ 7 files changed, 28 insertions(+), 10 deletions(-)
More information about pkgdown.offline at CRAN
Permanent link
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.5.1 dated 2025-10-21 and 0.6.0 dated 2025-11-08
DESCRIPTION | 18 +++++++-------- MD5 | 34 +++++++++++++++++++----------- NAMESPACE | 9 +++++++ NEWS.md | 13 +++++++++++ R/grouped_tbl_pivot_wider.R | 4 +-- R/gtsummary_utilities.R |only R/long_to_periods.R | 2 - R/plot_multiple_answers.R | 4 +-- R/plot_proportions.R | 9 ++++--- R/plot_trajectories.R |only R/proportion.R | 34 ++++++++++++++++-------------- R/view_dictionary.R |only README.md | 2 - inst/WORDLIST | 4 +++ inst/rstudio |only man/gtsummary_utilities.Rd |only man/plot_multiple_answers.Rd | 2 - man/plot_proportions.Rd | 2 - man/plot_trajectories.Rd |only man/view_dictionary.Rd |only tests/testthat/test-gtsummary-utilities.R |only tests/testthat/test-plot_trajectories.R |only tests/testthat/test-view_dictionary.R |only 23 files changed, 89 insertions(+), 48 deletions(-)
Title: Sparse Principal Component Regression
Description: The sparse principal component regression is computed. The regularization parameters are optimized by cross-validation.
Author: Shuichi Kawano
Maintainer: Shuichi Kawano <skawano@math.kyushu-u.ac.jp>
This is a re-admission after prior archival of version 2.1.1 dated 2022-10-16
Diff between spcr versions 2.1.1 dated 2022-10-16 and 2.1.1 dated 2025-11-08
0 files changed
Title: Sparse Group Partial Least Square Methods
Description: Regularized version of partial least square approaches
providing sparse, group, and sparse group versions of partial
least square regression models (Liquet, B., Lafaye de Micheaux, P.,
Hejblum B., Thiebaut, R. (2016) <doi:10.1093/bioinformatics/btv535>).
Version of PLS Discriminant analysis is also provided.
Author: Benoit Liquet [aut, cre],
Pierre Lafaye de Micheaux [aut],
Camilo Broc [aut]
Maintainer: Benoit Liquet <benoit.liquet@univ-pau.fr>
Diff between sgPLS versions 1.8 dated 2023-10-05 and 1.8.1 dated 2025-11-08
DESCRIPTION | 28 +++++++++++++++++++--------- MD5 | 10 +++++----- man/gPLS.Rd | 2 +- man/gPLSda.Rd | 4 ++-- man/sPLSda.Rd | 4 ++-- man/sgPLSda.Rd | 4 ++-- 6 files changed, 31 insertions(+), 21 deletions(-)
Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to calculate the fold change (FC, Delta Delta Ct method) or relative expression (RE, Delta Ct method). The functions further provide standard errors and confidence intervals for means, a [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
This is a re-admission after prior archival of version 2.0.3 dated 2025-06-04
Diff between rtpcr versions 2.0.3 dated 2025-06-04 and 2.0.3 dated 2025-11-08
0 files changed
Title: Histone ChIP-Seq qPCR Analyzer
Description: Quality control of chromatin immunoprecipitation libraries (ChIP-seq) by quantitative polymerase chain reaction (qPCR). This function calculates Enrichment value with respect to reference for each histone modification (specific to 'Vii7' software <http://www.thermofisher.com/ca/en/home/life-science/pcr/real-time-pcr/real-time-pcr-instruments/viia-7-real-time-pcr-system/viia-7-software.html>). This function is applicable to full panel of histone modifications described by International Human Epigenomic Consortium (IHEC).
Author: Alireza Lorzadeh
Maintainer: Alireza Lorzadeh <alorzadeh@bcgsc.ca>
This is a re-admission after prior archival of version 1.5 dated 2018-02-08
Diff between qcQpcr versions 1.5 dated 2018-02-08 and 1.5 dated 2025-11-08
0 files changed
Title: Shared Memory Multithreading
Description: This project extends 'R' with a mechanism for efficient parallel data access by utilizing 'C++' shared memory. Large data objects can be accessed and manipulated directly from 'R' without redundant copying, providing both speed and memory efficiency.
Author: Julian Maerte [aut, ctr] ,
Romain Francois [ctb],
Michael Thrun [aut, ths, rev, cph, cre]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between memshare versions 1.0.3 dated 2025-11-08 and 1.0.3.1 dated 2025-11-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/memshare.Rmd | 2 +- vignettes/memshare.Rmd | 2 +- 6 files changed, 11 insertions(+), 11 deletions(-)
Title: Bayesian Analysis of qRT-PCR Data
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: <https://matzlab.weebly.com/uploads/7/6/2/2/76229469/mcmc.qpcr.tutorial.v1.2.4.pdf>.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
This is a re-admission after prior archival of version 1.2.4 dated 2020-03-29
Diff between MCMC.qpcr versions 1.2.4 dated 2020-03-29 and 1.2.4 dated 2025-11-08
0 files changed
Title: Land Use Change Modelling in R
Description: Classes and methods for spatially explicit land use change
modelling in R.
Author: Simon Moulds <sim.moulds@gmail.com>
Maintainer: Simon Moulds <sim.moulds@gmail.com>
This is a re-admission after prior archival of version 1.0.4 dated 2019-03-01
Diff between lulcc versions 1.0.4 dated 2019-03-01 and 1.0.4 dated 2025-11-08
0 files changed
Title: Generalized Supervised Principal Component Regression
Description: Generalization of supervised principal component regression (SPCR;
Bair et al., 2006, <doi:10.1198/016214505000000628>) to support continuous,
binary, and discrete variables as outcomes and predictors
(inspired by the 'superpc' R package <https://cran.r-project.org/package=superpc>).
Author: Edoardo Costantini [aut, cre]
Maintainer: Edoardo Costantini <costantini.edoardo@yahoo.com>
This is a re-admission after prior archival of version 0.9.5 dated 2024-04-12
Diff between gspcr versions 0.9.5 dated 2024-04-12 and 0.9.5 dated 2025-11-08
0 files changed
Title: Estimates Allele Frequency on qPCR DeltaDeltaCq from Bulk
Samples
Description: Interval estimation of the population allele frequency from qPCR analysis based on the restriction enzyme digestion (RED)-DeltaDeltaCq method (Osakabe et al. 2017, <doi:10.1016/j.pestbp.2017.04.003>), as well as general DeltaDeltaCq analysis. Compatible with the Cq measurement of DNA extracted from multiple individuals at once, so called "group-testing", this model assumes that the quantity of DNA extracted from an individual organism follows a gamma distribution. Therefore, the point estimate is robust regarding the uncertainty of the DNA yield.
Author: Masaaki Sudo [aut, cre]
Maintainer: Masaaki Sudo <masaaki@sudori.info>
This is a re-admission after prior archival of version 0.4.0 dated 2022-01-27
Diff between freqpcr versions 0.4.0 dated 2022-01-27 and 0.4.0 dated 2025-11-08
0 files changed
Title: Analysis and Visualization of Droplet Digital PCR in R and on
the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR
(ddPCR) data in R. This is the first non-proprietary software for analyzing
two-channel ddPCR data. An interactive tool was also created and is available
online to facilitate this analysis for anyone who is not comfortable with
using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
This is a re-admission after prior archival of version 1.15.2 dated 2023-08-20
Diff between ddpcr versions 1.15.2 dated 2023-08-20 and 1.15.2 dated 2025-11-08
0 files changed
Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <doi:10.1016/j.jprot.2019.103613>.
Author: Mohamed Soudy [aut, cre],
Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between UniprotR versions 2.5.0 dated 2025-06-15 and 2.5.1 dated 2025-11-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/GetSequences.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Acquiring and Processing Data from Japan Institute for Health
Security
Description: Download and post process the infectious disease case data
from Japan Institute for Health Security. Also the package included
ready-to-analyse datasets. See the data source website for further details
<https://id-info.jihs.go.jp/>.
Author: Tomonori Hoshi [aut, cre],
Erina Ishigaki [aut],
Satoshi Kaneko [aut]
Maintainer: Tomonori Hoshi <tomonori.hoshi.japan@gmail.com>
Diff between jpinfect versions 0.1.5 dated 2025-10-08 and 0.1.6 dated 2025-11-08
DESCRIPTION | 6 - MD5 | 14 +- build/vignette.rds |binary data/bullet.rda |binary data/place_prefecture.rda |binary data/sex_prefecture.rda |binary inst/doc/jpinfect.html | 204 +++++++++++++++++++++---------------------- inst/extdata/1999_Syu_11.xls |binary 8 files changed, 112 insertions(+), 112 deletions(-)
Title: Accounting Analysis
Description: Provides methods for processing corporate balance sheets with a focus on the Brazilian reporting format. Includes data standardization, classification by accounting categories, and aggregation of values. Supports accounting and financial analyses of companies, improving efficiency and ensuring reproducibility of empirical studies.
Author: Lissandro Costa de Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Costa de Sousa <lisandrosousa54@gmail.com>
Diff between adcontabil versions 1.0.4 dated 2025-10-03 and 1.1.0 dated 2025-11-08
adcontabil-1.0.4/adcontabil/man/categorias.Rd |only adcontabil-1.0.4/adcontabil/man/classificar_conta.Rd |only adcontabil-1.1.0/adcontabil/DESCRIPTION | 6 adcontabil-1.1.0/adcontabil/MD5 | 28 + adcontabil-1.1.0/adcontabil/NAMESPACE | 2 adcontabil-1.1.0/adcontabil/R/AV_AH.R | 21 - adcontabil-1.1.0/adcontabil/R/indicadores.R | 238 ++++++++++----- adcontabil-1.1.0/adcontabil/R/padronizar_balanco.R | 8 adcontabil-1.1.0/adcontabil/R/padronizar_dre.R |only adcontabil-1.1.0/adcontabil/R/zzz.R | 103 +++++- adcontabil-1.1.0/adcontabil/man/calcular_AV_AH.Rd | 7 adcontabil-1.1.0/adcontabil/man/categorias_bp.Rd |only adcontabil-1.1.0/adcontabil/man/categorias_dre.Rd |only adcontabil-1.1.0/adcontabil/man/classificar_conta_bp.Rd |only adcontabil-1.1.0/adcontabil/man/classificar_conta_dre.Rd |only adcontabil-1.1.0/adcontabil/man/indicadores.Rd | 86 +++-- adcontabil-1.1.0/adcontabil/man/normalizar_texto.Rd | 10 adcontabil-1.1.0/adcontabil/man/padronizar_balanco.Rd | 2 adcontabil-1.1.0/adcontabil/man/padronizar_dre.Rd |only 19 files changed, 344 insertions(+), 167 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] ,
Gregor Gorjanc [ctb] ,
John Hickey [ctb] ,
Daniel Money [ctb] ,
David Wilson [ctb],
Thiago Oliveira [ctb] ,
Audrey Martin [ctb] ,
Philip Greenspoon [ctb] ,
Ros Craddock [ctb] ,
Jana Obsteter [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 2.0.0 dated 2025-09-01 and 2.1.0 dated 2025-11-08
DESCRIPTION | 21 +++--- MD5 | 42 ++++++------ NAMESPACE | 3 NEWS.md | 16 ++++ R/AlphaSimR.R | 34 +++++----- R/Class-Pop.R | 16 +++- R/RcppExports.R | 6 - R/misc.R | 19 +++++ R/popSummary.R | 129 ++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 2 inst/doc/AlphaSimR.html | 11 +-- inst/doc/traits.pdf |binary man/AlphaSimR-package.Rd | 27 ++++---- man/mendelianSampling.Rd |only man/parentAverage.Rd |only man/popVar.Rd | 2 man/popVarCpp.Rd |only src/RcppExports.cpp | 10 +-- src/misc.cpp | 4 - src/packHaplo.cpp | 4 + src/simulator.cpp | 5 + tests/testthat/test-popSummary.R |only 24 files changed, 270 insertions(+), 81 deletions(-)
Title: Multivariate Bayesian Sparse Group Selection with Spike and Slab
Description: An implementation of a Bayesian sparse group model using spike and slab priors in a regression context. It is designed for regression with a multivariate response variable, but also provides an implementation for univariate response.
Author: Benoit Liquet [aut, cre],
Matthew Sutton [aut]
Maintainer: Benoit Liquet <benoit.liquet@univ-pau.fr>
Diff between MBSGS versions 1.1.0 dated 2017-08-09 and 1.2.0 dated 2025-11-08
DESCRIPTION | 14 +++++++++----- MD5 | 8 ++++---- R/MBSGS-internal.R | 4 ++-- man/BGLSS.Rd | 4 +--- man/BSGSSS.Rd | 2 +- 5 files changed, 17 insertions(+), 15 deletions(-)
Title: Processing Hemispherical Canopy Images
Description: Import and classify canopy fish-eye images, estimate angular gap fraction and derive canopy attributes like leaf area index and openness. Additional information is provided in the study by Chianucci F., Macek M. (2023) <doi:10.1016/j.agrformet.2023.109470>.
Author: Francesco Chianucci [aut, cre] ,
Martin Macek [aut]
Maintainer: Francesco Chianucci <fchianucci@gmail.com>
Diff between hemispheR versions 1.1.7 dated 2025-09-03 and 1.1.8 dated 2025-11-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS.md | 4 ++++ R/binarize_fisheye.R | 10 +++++++++- R/import_fisheye.R | 6 ++++-- 6 files changed, 26 insertions(+), 11 deletions(-)
Title: Exponential Integral and Incomplete Gamma Function
Description: The exponential integrals E_1(x), E_2(x), E_n(x) and
Ei(x), and the incomplete gamma function G(a, x) defined for
negative values of its first argument. The package also gives easy
access to the underlying C routines through an API; see the package
vignette for details. A test package included in sub-directory
example_API provides an implementation. C routines derived from the
GNU Scientific Library <https://www.gnu.org/software/gsl/>.
Author: Vincent Goulet [cre, aut],
Gerard Jungman [aut] ,
Brian Gough [aut] ,
Jeffrey A. Ryan [aut] ,
Robert Gentleman [aut] ,
Ross Ihaka [aut] ,
R Core Team [aut] ,
R Foundation [aut]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between expint versions 0.1-8 dated 2022-10-28 and 0.1-9 dated 2025-11-08
expint-0.1-8/expint/vignettes/auto |only expint-0.1-9/expint/DESCRIPTION | 8 +-- expint-0.1-9/expint/MD5 | 27 ++++++------ expint-0.1-9/expint/build/partial.rdb |binary expint-0.1-9/expint/build/vignette.rds |binary expint-0.1-9/expint/inst/CITATION | 19 +------- expint-0.1-9/expint/inst/NEWS.Rd | 13 +++++- expint-0.1-9/expint/inst/doc/expint.R | 18 ++++---- expint-0.1-9/expint/inst/doc/expint.Rnw | 66 ------------------------------- expint-0.1-9/expint/inst/doc/expint.pdf |binary expint-0.1-9/expint/src/expint.c | 33 +++++---------- expint-0.1-9/expint/src/expint.h | 8 +-- expint-0.1-9/expint/src/gamma_inc.c | 18 ++------ expint-0.1-9/expint/vignettes/Makefile |only expint-0.1-9/expint/vignettes/expint.Rnw | 66 ------------------------------- expint-0.1-9/expint/vignettes/share |only 16 files changed, 67 insertions(+), 209 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: CRAN Team [ctb, cre] ,
Duncan Temple Lang [aut] ,
Tomas Kalibera [ctb],
Ivan Krylov [ctb]
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between XML versions 3.99-0.19 dated 2025-08-22 and 3.99-0.20 dated 2025-11-08
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 7 +++++++ R/tree.R | 2 +- src/DocParse.c | 3 +++ src/RUtils.c | 2 +- src/XMLEventParse.c | 11 +++++++++++ 8 files changed, 37 insertions(+), 12 deletions(-)
Title: Shared Memory Multithreading
Description: This project extends 'R' with a mechanism for efficient parallel data access by utilizing 'C++' shared memory. Large data objects can be accessed and manipulated directly from 'R' without redundant copying, providing both speed and memory efficiency.
Author: Julian Maerte [aut, ctr] ,
Romain Francois [ctb],
Michael Thrun [aut, ths, rev, cph, cre]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between memshare versions 1.0.2 dated 2025-09-10 and 1.0.3 dated 2025-11-08
memshare-1.0.2/memshare/src/Makevars |only memshare-1.0.2/memshare/src/Makevars.win |only memshare-1.0.3/memshare/DESCRIPTION | 11 + memshare-1.0.3/memshare/MD5 | 34 +++-- memshare-1.0.3/memshare/README.md | 52 ++++++++ memshare-1.0.3/memshare/build/partial.rdb |binary memshare-1.0.3/memshare/build/vignette.rds |only memshare-1.0.3/memshare/inst |only memshare-1.0.3/memshare/man/memApply.Rd | 134 ++++++++++++++-------- memshare-1.0.3/memshare/man/memLapply.Rd | 134 ++++++++++++++-------- memshare-1.0.3/memshare/man/memshare-package.Rd | 58 +++++++++ memshare-1.0.3/memshare/man/pageList.Rd | 87 +++++++------- memshare-1.0.3/memshare/man/releaseVariables.Rd | 85 +++++++------- memshare-1.0.3/memshare/man/releaseViews.Rd | 106 +++++++++-------- memshare-1.0.3/memshare/man/retrieveMetadata.Rd | 111 +++++++++--------- memshare-1.0.3/memshare/man/retrieveViews.Rd | 144 +++++++++++++----------- memshare-1.0.3/memshare/man/viewList.Rd | 109 +++++++++--------- memshare-1.0.3/memshare/src/memory_page.cpp | 20 ++- memshare-1.0.3/memshare/src/memory_page.h | 22 ++- memshare-1.0.3/memshare/vignettes |only 20 files changed, 662 insertions(+), 445 deletions(-)
Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: A joint model for large-scale, competing risks time-to-event data with singular or multiple longitudinal biomarkers, implemented with the efficient algorithms developed by Li and colleagues (2022) <doi:10.1155/2022/1362913> and <doi:10.48550/arXiv.2506.12741>.
The time-to-event data is modelled using a (cause-specific) Cox
proportional hazards regression model with time-fixed covariates.
The longitudinal biomarkers are modelled using a linear mixed
effects model. The association between the longitudinal submodel
and the survival submodel is captured through shared random
effects. It allows researchers to analyze large-scale data to
model biomarker trajectories, estimate their effects on event
outcomes, and dynamically predict future events from patients’
past histories. A function for simulating survival and longitudinal
data for multiple biomarkers is also included alongside built-in
datasets.
Author: Shanpeng Li [aut, cre],
Ning Li [ctb],
Emily Ouyang [ctb],
Hong Wang [ctb],
Jin Zhou [ctb],
Hua Zhou [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.5.2 dated 2025-10-18 and 1.5.3 dated 2025-11-08
DESCRIPTION | 29 +++-- MD5 | 29 ++--- NAMESPACE | 4 NEWS.md | 5 R/CIF1mv.SF.R |only R/FastJM.R | 2 R/MAEQjmcs.R | 4 R/Pkmv.us_SF.R |only R/logLikCRmv.R | 2 R/logLikSFmv.R |only R/print.jmcs.R | 207 +++++++++++++++++++----------------- R/print.survfitmvjmcs.R |only R/summary.jmcs.R | 29 +++-- R/survfitmvjmcs.R | 258 ++++++++++++++++++++++----------------------- README.md | 162 ++++++++++++++++++++++++++-- inst/WORDLIST | 6 + man/print.survfitmvjmcs.Rd |only man/survfitmvjmcs.Rd | 2 18 files changed, 469 insertions(+), 270 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and
Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>.
'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 5.1.1 dated 2025-09-02 and 5.2.0 dated 2025-11-08
DESCRIPTION | 19 MD5 | 94 NAMESPACE | 31 NEWS | 27 R/apiOA2df.R | 294 R/apply_citation_matching.R |only R/assignEvolutionColors.R |only R/authorBio.r |only R/convert2df.R | 110 R/csvScopus2df.R | 48 R/findAuthorWorks.r |only R/histNetwork.R | 127 R/lifeCycle.R |only R/ltwa.R |only R/networkPlot.R | 401 - R/plotThematicEvolution.R | 315 R/thematicEvolution.R | 219 R/thematicMap.R | 860 +- R/zzz.R | 291 build/partial.rdb |binary data/bibtag.rda |binary data/countries.rda |binary data/customTheme.rda |binary data/logo.rda |binary data/ltwa.rda |only data/stopwords.rda |binary inst/biblioshiny/article_summary.R |only inst/biblioshiny/biblioAI.R | 2147 ++++- inst/biblioshiny/biblioShot.R | 3 inst/biblioshiny/contentAnalysisServer.R |only inst/biblioshiny/contentAnalysisUI.R |only inst/biblioshiny/cssTags.R |only inst/biblioshiny/helpContent.R | 2110 +++++ inst/biblioshiny/libraries.R | 16 inst/biblioshiny/lifeCycleUI.R |only inst/biblioshiny/openalex_api.R |only inst/biblioshiny/pubmed_api.R |only inst/biblioshiny/server.R |11235 ++++++++++++++++++++++--------- inst/biblioshiny/ui.R |10324 ++++++++++++++++++++-------- inst/biblioshiny/utils.R | 2503 +++++- inst/biblioshiny/utils_old.R |only inst/biblioshiny/www/ORCID.jpg |only inst/biblioshiny/www/openalex.jpg |only man/abbreviate_journal_title.Rd |only man/abbreviate_term.Rd |only man/applyCitationMatching.Rd |only man/assignEvolutionColors.Rd |only man/authorBio.Rd |only man/convert_scopus_new_to_classic.Rd |only man/create_journal_iso4_lookup.Rd |only man/findAuthorWorks.Rd |only man/get_authors_summary.Rd |only man/get_iso4_stop_words.Rd |only man/lifeCycle.Rd |only man/ltwa.Rd |only man/mergeKeywords.Rd | 4 man/networkPlot.Rd | 16 man/normalize_citations.Rd |only man/normalize_journal_to_iso4.Rd |only man/plotThematicEvolution.Rd | 40 man/prepare_ltwa_lookup.Rd |only man/print_author_works_summary.Rd |only man/remove_diacritics.Rd |only man/thematicEvolution.Rd | 13 man/thematicMap.Rd | 22 65 files changed, 23084 insertions(+), 8185 deletions(-)
Title: Drug Response Prediction from Differential Multi-Omics Networks
Description: While it has been well established that drugs affect and help
patients differently, personalized drug response predictions remain
challenging. Solutions based on single omics measurements have been proposed,
and networks provide means to incorporate molecular interactions into reasoning.
However, how to integrate the wealth of information contained in multiple omics
layers still poses a complex problem.
We present a novel network analysis pipeline, DrDimont, Drug response prediction
from Differential analysis of multi-omics networks. It allows for comparative
conclusions between two conditions and translates them into differential drug
response predictions. DrDimont focuses on molecular interactions. It establishes
condition-specific networks from correlation within an omics layer that are
then reduced and combined into heterogeneous, multi-omics molecular networks.
A novel semi-local, path-based integration step ensures integrative conclusions.
Differential predictions are derived fro [...truncated...]
Author: Katharina Baum [cre] ,
Pauline Hiort [aut] ,
Julian Hugo [aut] ,
Spoorthi Kashyap [aut] ,
Nataniel Mueller [aut] ,
Justus Zeinert [aut]
Maintainer: Katharina Baum <katharina.baum@fu-berlin.de>
Diff between DrDimont versions 0.1.4 dated 2022-09-23 and 0.1.6 dated 2025-11-08
DrDimont-0.1.4/DrDimont/man/calculate_interaction_score.Rd |only DrDimont-0.1.4/DrDimont/man/check_connection.Rd |only DrDimont-0.1.4/DrDimont/man/check_drug_target.Rd |only DrDimont-0.1.4/DrDimont/man/check_drug_targets_in_layers.Rd |only DrDimont-0.1.4/DrDimont/man/check_layer.Rd |only DrDimont-0.1.4/DrDimont/man/check_sensible_connections.Rd |only DrDimont-0.1.4/DrDimont/man/chunk.Rd |only DrDimont-0.1.4/DrDimont/man/chunk_2gether.Rd |only DrDimont-0.1.4/DrDimont/man/combine_graphs.Rd |only DrDimont-0.1.4/DrDimont/man/corPvalueStudentParallel.Rd |only DrDimont-0.1.4/DrDimont/man/create_unique_layer_node_ids.Rd |only DrDimont-0.1.4/DrDimont/man/find_targets.Rd |only DrDimont-0.1.4/DrDimont/man/generate_reduced_graph.Rd |only DrDimont-0.1.4/DrDimont/man/get_layer.Rd |only DrDimont-0.1.4/DrDimont/man/get_layer_setting.Rd |only DrDimont-0.1.4/DrDimont/man/graph_metrics.Rd |only DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_id.Rd |only DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_table.Rd |only DrDimont-0.1.4/DrDimont/man/load_interaction_score_output.Rd |only DrDimont-0.1.4/DrDimont/man/network_reduction_by_p_value.Rd |only DrDimont-0.1.4/DrDimont/man/network_reduction_by_pickHardThreshold.Rd |only DrDimont-0.1.4/DrDimont/man/sample_size.Rd |only DrDimont-0.1.4/DrDimont/man/set_cluster.Rd |only DrDimont-0.1.4/DrDimont/man/shutdown_cluster.Rd |only DrDimont-0.1.4/DrDimont/man/target_edge_list.Rd |only DrDimont-0.1.4/DrDimont/man/write_interaction_score_input.Rd |only DrDimont-0.1.6/DrDimont/DESCRIPTION | 36 DrDimont-0.1.6/DrDimont/LICENSE | 2 DrDimont-0.1.6/DrDimont/MD5 | 148 DrDimont-0.1.6/DrDimont/NAMESPACE | 26 DrDimont-0.1.6/DrDimont/R/checks.R | 48 DrDimont-0.1.6/DrDimont/R/data_documentations.R | 90 DrDimont-0.1.6/DrDimont/R/drug_targets.R | 20 DrDimont-0.1.6/DrDimont/R/graph_combination.R | 10 DrDimont-0.1.6/DrDimont/R/interaction_score.R | 18 DrDimont-0.1.6/DrDimont/R/network_generation.R | 87 DrDimont-0.1.6/DrDimont/R/network_reduction.R | 66 DrDimont-0.1.6/DrDimont/R/pipeline_functions.R | 63 DrDimont-0.1.6/DrDimont/R/settings.R | 34 DrDimont-0.1.6/DrDimont/R/utilities.R | 114 DrDimont-0.1.6/DrDimont/R/utils-pipe.R | 4 DrDimont-0.1.6/DrDimont/build/vignette.rds |binary DrDimont-0.1.6/DrDimont/data/combined_graphs_example.rda |binary DrDimont-0.1.6/DrDimont/data/correlation_matrices_example.rda |binary DrDimont-0.1.6/DrDimont/data/differential_graph_example.rda |binary DrDimont-0.1.6/DrDimont/data/drug_gene_interactions.rda |binary DrDimont-0.1.6/DrDimont/data/drug_response_scores_example.rda |binary DrDimont-0.1.6/DrDimont/data/drug_target_edges_example.rda |binary DrDimont-0.1.6/DrDimont/data/individual_graphs_example.rda |binary DrDimont-0.1.6/DrDimont/data/interaction_score_graphs_example.rda |binary DrDimont-0.1.6/DrDimont/data/layers_example.rda |binary DrDimont-0.1.6/DrDimont/data/metabolite_data.rda |binary DrDimont-0.1.6/DrDimont/data/metabolite_protein_interactions.rda |binary DrDimont-0.1.6/DrDimont/data/mrna_data.rda |binary DrDimont-0.1.6/DrDimont/data/phosphosite_data.rda |binary DrDimont-0.1.6/DrDimont/data/protein_data.rda |binary DrDimont-0.1.6/DrDimont/inst/CITATION | 9 DrDimont-0.1.6/DrDimont/inst/doc/DrDimont_Vignette.R | 407 - DrDimont-0.1.6/DrDimont/inst/doc/DrDimont_Vignette.Rmd | 141 DrDimont-0.1.6/DrDimont/inst/doc/DrDimont_Vignette.html | 2197 +++++----- DrDimont-0.1.6/DrDimont/inst/python_igraph_interaction_score.py | 19 DrDimont-0.1.6/DrDimont/man/check_input.Rd | 2 DrDimont-0.1.6/DrDimont/man/combined_graphs_example.Rd | 6 DrDimont-0.1.6/DrDimont/man/compute_correlation_matrices.Rd | 2 DrDimont-0.1.6/DrDimont/man/compute_drug_response_scores.Rd | 2 DrDimont-0.1.6/DrDimont/man/correlation_matrices_example.Rd | 10 DrDimont-0.1.6/DrDimont/man/determine_drug_targets.Rd | 4 DrDimont-0.1.6/DrDimont/man/differential_graph_example.Rd | 2 DrDimont-0.1.6/DrDimont/man/drdimont_settings.Rd | 33 DrDimont-0.1.6/DrDimont/man/drug_gene_interactions.Rd | 6 DrDimont-0.1.6/DrDimont/man/drug_response_scores_example.Rd | 8 DrDimont-0.1.6/DrDimont/man/drug_target_edges_example.Rd | 8 DrDimont-0.1.6/DrDimont/man/generate_combined_graphs.Rd | 2 DrDimont-0.1.6/DrDimont/man/generate_individual_graphs.Rd | 6 DrDimont-0.1.6/DrDimont/man/generate_interaction_score_graphs.Rd | 4 DrDimont-0.1.6/DrDimont/man/individual_graphs_example.Rd | 10 DrDimont-0.1.6/DrDimont/man/interaction_score_graphs_example.Rd | 4 DrDimont-0.1.6/DrDimont/man/layers_example.Rd | 10 DrDimont-0.1.6/DrDimont/man/make_drug_target.Rd | 2 DrDimont-0.1.6/DrDimont/man/make_layer.Rd | 6 DrDimont-0.1.6/DrDimont/man/metabolite_data.Rd | 8 DrDimont-0.1.6/DrDimont/man/metabolite_protein_interactions.Rd | 6 DrDimont-0.1.6/DrDimont/man/mrna_data.Rd | 4 DrDimont-0.1.6/DrDimont/man/phosphosite_data.Rd | 4 DrDimont-0.1.6/DrDimont/man/pipe.Rd | 4 DrDimont-0.1.6/DrDimont/man/protein_data.Rd | 2 DrDimont-0.1.6/DrDimont/man/run_pipeline.Rd | 4 DrDimont-0.1.6/DrDimont/vignettes/DrDimont_Vignette.Rmd | 141 88 files changed, 1927 insertions(+), 1912 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-24 1.6.0
2025-10-08 1.5.5
2025-08-25 1.5.4
2025-08-18 1.5.3
2025-07-24 1.5.2
2025-07-15 1.5.0
2025-07-07 1.4.4
2025-07-07 1.4.5
Title: Plot Null Hypothesis Significance Tests
Description: Illustrate graphically the most common Null Hypothesis Significance Testing procedures. More specifically, this package provides functions to plot Chi-Squared, F, t (one- and two-tailed) and z (one- and two-tailed) tests, by plotting the probability density under the null hypothesis as a function of the different test statistic values. Although highly flexible (color theme, fonts, etc.), only the minimal number of arguments (observed test statistic, degrees of freedom) are necessary for a clear and useful graph to be plotted, with the observed test statistic and the p value, as well as their corresponding value labels. The axes are automatically scaled to present the relevant part and the overall shape of the probability density function. This package is especially intended for education purposes, as it provides a helpful support to help explain the Null Hypothesis Significance Testing process, its use and/or shortcomings.
Author: Nils Myszkowski [aut, cre]
Maintainer: Nils Myszkowski <nilsmyszkowskiscience@gmail.com>
Diff between nhstplot versions 1.4.0 dated 2025-07-30 and 1.4.1 dated 2025-11-08
DESCRIPTION | 6 ++-- MD5 | 16 +++++------ NEWS.md | 5 ++- R/plot.chisqtest.R | 10 +++---- R/plot.ftest.R | 10 +++---- R/plot.ttest.R | 32 +++++++++++------------ R/plot.ztest.R | 34 ++++++++++++------------ build/vignette.rds |binary inst/doc/nhstplot.html | 67 +++++++++++++++++++++++++++---------------------- 9 files changed, 96 insertions(+), 84 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb],
Zoe Clarke [ctb]
Maintainer: Samuel Marsh <sccustomize@gmail.com>
Diff between scCustomize versions 3.2.0 dated 2025-09-10 and 3.2.1 dated 2025-11-08
scCustomize-3.2.0/scCustomize/man/Liger_to_Seurat.Rd |only scCustomize-3.2.0/scCustomize/man/deprecated.Rd |only scCustomize-3.2.1/scCustomize/DESCRIPTION | 10 scCustomize-3.2.1/scCustomize/MD5 | 72 - scCustomize-3.2.1/scCustomize/NAMESPACE | 5 scCustomize-3.2.1/scCustomize/NEWS.md | 33 scCustomize-3.2.1/scCustomize/R/Color_Palettes.R | 11 scCustomize-3.2.1/scCustomize/R/Deprecated.R | 18 scCustomize-3.2.1/scCustomize/R/Generics.R | 3 scCustomize-3.2.1/scCustomize/R/Internal_Utilities.R | 633 ++++++++-- scCustomize-3.2.1/scCustomize/R/LIGER_Internal_Utilities.R | 16 scCustomize-3.2.1/scCustomize/R/LIGER_Plotting.R | 1 scCustomize-3.2.1/scCustomize/R/LIGER_Utilities.R | 56 scCustomize-3.2.1/scCustomize/R/Object_Conversion.R | 483 +++---- scCustomize-3.2.1/scCustomize/R/Object_Utilities.R | 337 ++++- scCustomize-3.2.1/scCustomize/R/Plotting_Nebulosa.R | 7 scCustomize-3.2.1/scCustomize/R/Plotting_QC_Seq_10X.R | 30 scCustomize-3.2.1/scCustomize/R/Plotting_QC_Seurat.R | 2 scCustomize-3.2.1/scCustomize/R/Plotting_Seurat.R | 265 +++- scCustomize-3.2.1/scCustomize/R/Plotting_Seurat_Iterative.R | 14 scCustomize-3.2.1/scCustomize/R/Plotting_Shared.R | 1 scCustomize-3.2.1/scCustomize/R/Plotting_Statistics.R | 8 scCustomize-3.2.1/scCustomize/R/Plotting_Utilities_Internal.R | 39 scCustomize-3.2.1/scCustomize/R/QC_Utilities_Seurat.R | 12 scCustomize-3.2.1/scCustomize/R/Read_&_Write_Data.R | 54 scCustomize-3.2.1/scCustomize/R/Statistics.R | 5 scCustomize-3.2.1/scCustomize/R/Utilities.R | 39 scCustomize-3.2.1/scCustomize/R/zzz.R | 2 scCustomize-3.2.1/scCustomize/man/Clustered_DotPlot.Rd | 6 scCustomize-3.2.1/scCustomize/man/DimPlot_scCustom.Rd | 10 scCustomize-3.2.1/scCustomize/man/ElbowPlot_scCustom.Rd |only scCustomize-3.2.1/scCustomize/man/Extract_Sample_Meta.Rd | 7 scCustomize-3.2.1/scCustomize/man/Fetch_Meta.Rd | 8 scCustomize-3.2.1/scCustomize/man/Map_New_Meta.Rd |only scCustomize-3.2.1/scCustomize/man/NavyAndOrange.Rd | 2 scCustomize-3.2.1/scCustomize/man/Random_Cells_Downsample.Rd | 4 scCustomize-3.2.1/scCustomize/man/Read_CellBender_h5_Multi_Directory.Rd | 3 scCustomize-3.2.1/scCustomize/man/Stacked_VlnPlot.Rd | 4 scCustomize-3.2.1/scCustomize/man/VlnPlot_scCustom.Rd | 2 39 files changed, 1465 insertions(+), 737 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, surface slope, and orientation patch count for teeth using scans of
enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph],
Edward Fuselier [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 5.3 dated 2023-01-26 and 6.0 dated 2025-11-08
molaR-5.3/molaR/R/ARC_Legend.R |only molaR-5.3/molaR/R/DNE_Discard_Legend.R |only molaR-5.3/molaR/R/DNE_Legend.R |only molaR-5.3/molaR/R/OPC_Legend.R |only molaR-5.3/molaR/R/RFI_Legend.R |only molaR-5.3/molaR/R/Slope_Legend.R |only molaR-5.3/molaR/R/molaR_bgplot.R |only molaR-6.0/molaR/DESCRIPTION | 12 molaR-6.0/molaR/MD5 | 61 molaR-6.0/molaR/NAMESPACE | 2 molaR-6.0/molaR/R/ARC3d.R | 310 ++ molaR-6.0/molaR/R/Check2D.R | 218 + molaR-6.0/molaR/R/DNE3d.R | 490 ++-- molaR-6.0/molaR/R/DNE3dDiscard.R | 328 +- molaR-6.0/molaR/R/Face_Normals.R | 2 molaR-6.0/molaR/R/OPC3d.R | 644 +++-- molaR-6.0/molaR/R/RFI3d.R | 462 ++-- molaR-6.0/molaR/R/Slope3d.R | 375 ++- molaR-6.0/molaR/R/clipDisplay.R | 20 molaR-6.0/molaR/R/meshClip.R | 330 +- molaR-6.0/molaR/R/plyPlaneCut.R | 428 +-- molaR-6.0/molaR/R/zzz.R |only molaR-6.0/molaR/build/vignette.rds |binary molaR-6.0/molaR/inst/doc/molaR_vignette.R | 125 - molaR-6.0/molaR/inst/doc/molaR_vignette.Rmd | 45 molaR-6.0/molaR/inst/doc/molaR_vignette.html | 3067 +++++++++------------------ molaR-6.0/molaR/man/ARC3d.Rd | 86 molaR-6.0/molaR/man/Check2D.Rd | 84 molaR-6.0/molaR/man/DNE3d.Rd | 110 molaR-6.0/molaR/man/DNE3dDiscard.Rd | 104 molaR-6.0/molaR/man/OPC3d.Rd | 131 - molaR-6.0/molaR/man/RFI3d.Rd | 113 molaR-6.0/molaR/man/Slope3d.Rd | 91 molaR-6.0/molaR/man/meshClip.Rd |only molaR-6.0/molaR/man/plyPlaneCut.Rd | 151 - molaR-6.0/molaR/vignettes/molaR_vignette.Rmd | 45 36 files changed, 3914 insertions(+), 3920 deletions(-)
Title: Patient-Reported Outcome Data Analysis with Stan
Description: Algorithms and subroutines for patient-reported outcome data analysis.
Author: Bin Wang [aut, cre]
Maintainer: Bin Wang <bwang831@gmail.com>
Diff between prome versions 2.0.1.9 dated 2025-10-08 and 3.0.1.5 dated 2025-11-08
prome-2.0.1.9/prome/R/blindinglogit.R |only prome-2.0.1.9/prome/man/lslogit.Rd |only prome-3.0.1.5/prome/DESCRIPTION | 10 +++++----- prome-3.0.1.5/prome/MD5 | 20 +++++++++++++++----- prome-3.0.1.5/prome/NAMESPACE | 11 +++++++---- prome-3.0.1.5/prome/R/blindingCPE.R |only prome-3.0.1.5/prome/R/blindingTEST.R |only prome-3.0.1.5/prome/R/zzz.R |only prome-3.0.1.5/prome/data/bd010.rda |only prome-3.0.1.5/prome/data/bd011.rda |only prome-3.0.1.5/prome/data/bd012.rda |only prome-3.0.1.5/prome/data/datalist | 3 +++ prome-3.0.1.5/prome/inst/extdata |only prome-3.0.1.5/prome/man/blindingcpe.Rd |only prome-3.0.1.5/prome/man/blindingdata.Rd |only prome-3.0.1.5/prome/man/blindingtest.Rd |only 16 files changed, 30 insertions(+), 14 deletions(-)
Title: Run Any CLI Tool on a 'Conda' Environment
Description: Simplifies the execution of command line interface (CLI)
tools within isolated and reproducible environments. It enables users
to effortlessly manage 'Conda' environments, execute command line
tools, handle dependencies, and ensure reproducibility in their data
analysis workflows.
Author: Lucio Queiroz [aut, cre, cph] ,
Claudio Zanettini [aut, ctb]
Maintainer: Lucio Queiroz <luciorqueiroz@gmail.com>
Diff between condathis versions 0.1.2 dated 2025-06-02 and 0.1.3 dated 2025-11-08
DESCRIPTION | 19 - MD5 | 117 +++---- NAMESPACE | 1 NEWS.md | 70 +++- R/check_micromamba_version.R | 5 R/clean_cache.R | 42 +- R/create_base_env.R | 2 R/create_env.R | 93 +++-- R/define_platform.R | 16 R/env_exists.R | 2 R/format_channels_args.R | 1 R/get_best_micromamba_path.R | 22 + R/get_env_dir.R | 2 R/get_install_dir.R | 8 R/get_sys_arch.R | 2 R/install_micromamba.R | 64 ++- R/install_packages.R | 53 ++- R/list_envs.R | 4 R/list_packages.R | 41 +- R/micromamba_bin_path.R | 8 R/native_cmd.R | 49 +- R/packages_search_native.R | 25 - R/parse_output.R | 63 +++ R/parse_quiet_flag.R | 2 R/parse_strategy_verbose.R | 103 ++++-- R/remove_env.R | 33 + R/rethrow_error_run.R | 14 R/run.R | 146 +++++--- R/run_bin.R | 46 +- R/run_internal_native.R | 44 +- R/symlink_micromamba_bin.R | 8 README.md | 284 +++++------------ build |only inst/doc |only man/clean_cache.Rd |only man/condathis-package.Rd | 1 man/create_env.Rd | 26 + man/env_exists.Rd | 22 + man/get_install_dir.Rd | 8 man/install_micromamba.Rd | 8 man/install_packages.Rd | 24 + man/list_packages.Rd | 33 + man/parse_output.Rd | 25 + man/remove_env.Rd | 27 + man/run.Rd | 84 +++-- man/run_bin.Rd | 54 ++- tests/testthat.R | 2 tests/testthat/test-clean_cache.R |only tests/testthat/test-create_base_env.R | 6 tests/testthat/test-create_env.R | 76 ++-- tests/testthat/test-create_nested_env.R | 10 tests/testthat/test-format_channels_args.R | 5 tests/testthat/test-get_env_dir.R | 2 tests/testthat/test-get_sys_arch.R | 9 tests/testthat/test-is_micromamba_available_for_arch.R | 15 tests/testthat/test-parse_output.R |only tests/testthat/test-parse_strategy_verbose.R | 141 +++++++- tests/testthat/test-rethrow_error.R | 26 + tests/testthat/test-run_bin.R | 20 - tests/testthat/test-run_output_file.R | 26 - tests/testthat/test-run_verbose_levels.R |only vignettes |only 62 files changed, 1338 insertions(+), 701 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <https://www.canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.57.4 dated 2025-07-22 and 1.58.7 dated 2025-11-08
DESCRIPTION | 6 ++-- MD5 | 26 +++++++++--------- NEWS.md | 4 ++ build/vignette.rds |binary inst/README-known_issues.md | 2 + inst/doc/additional_examples.html | 4 +- inst/doc/getting_started.html | 4 +- inst/htmlwidgets/canvasXpress.yaml | 2 - inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 8 ++--- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 6 ++-- inst/ui-examples/cX-function.R.gz |binary tests/testthat/test-other-decorations.R | 7 ++++ tests/testthat/test-other-piping.R | 1 tests/testthat/test-ui-heatmap.R | 8 +++++ 14 files changed, 48 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-18 4.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-19 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-12 0.1.6
2023-04-25 0.1.5
2022-10-26 0.1.4
2020-08-25 0.1.3
2020-05-26 0.1.2
2020-04-08 0.1.1
2020-03-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-04 1.1.1
2022-02-10 1.0.1
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2022-04-22 0.1.2
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2022-04-01 0.2.1
2022-02-03 0.2
2021-09-12 0.1.1
2021-09-09 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-18 0.1.4
2020-12-03 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-11 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-13 1.3.0
2020-06-09 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-16 0.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-16 2.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-09 1.0.3
2022-01-10 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-04 2.0.3
2025-03-25 2.0.2
2025-02-13 2.0.1
2024-07-07 2.0.0
2024-05-30 1.0.9
2024-05-16 1.0.8
2024-05-10 1.0.7
2024-04-29 1.0.6
2024-04-21 1.0.5
2024-04-20 1.0.4
2024-04-13 1.0.3
2024-04-10 1.0.2
2024-04-05 1.0.1
2024-04-02 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-08 1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-12 0.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-19 0.3.0
2022-03-25 0.2.0
2021-05-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-28 1.5.0
2016-08-27 1.0.0
2016-04-26 0.0.3
2016-03-29 0.0.2
2016-03-03 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-14 0.1.3
2023-06-19 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-17 2.3.0
2016-01-21 2.2.1
2015-02-19 2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-03 0.6.1
2022-07-18 0.6.0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-05 1.1.0
2023-01-11 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-18 1.3.4
2021-08-13 1.3.2
2021-07-15 1.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-17 0.1.1
2022-06-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-01 1.0.4
2019-01-24 1.0.3
2017-03-27 1.0.2
2015-08-19 1.0.1
2015-07-30 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-19 0.5.0
2021-11-17 0.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-02 0.4.0
2017-03-28 0.3.3
2017-03-07 0.3.0
2016-07-12 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-25 1.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-02 0.5.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-01 1.2.2
2020-02-25 1.2.1
2019-10-03 1.2.0
2018-07-24 1.1.2
2018-06-23 1.1.1
2017-11-20 1.1.0
2017-11-03 1.0.0
2017-11-03 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-18 0.0.25
2024-07-17 0.0.22
2022-08-12 0.0.18
2022-07-11 0.0.17
2022-07-08 0.0.16
2022-03-02 0.0.15
2022-01-05 0.0.14
2021-11-19 0.0.12
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-25 0.3.0
2018-07-05 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-20 2.0.0
2023-02-09 1.0.2
2022-10-20 1.0.1
2022-09-22 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-16 0.2.5
2022-10-21 0.2.4
2022-06-27 0.2.2
2022-06-09 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-11 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-12 0.9.5
2023-11-21 0.9.4.1
2023-11-17 0.9.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-30 1.0.1
2024-06-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-09 0.4.0
2024-01-29 0.3.0
2016-12-05 0.2.0
2015-08-21 0.1.2
2012-09-09 0.1.1
2012-08-18 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-13 1.3
2014-08-09 1.2
2014-05-05 1.1
2014-03-29 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-06 1.1.88
2014-12-02 1.1.87
2014-02-11 1.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-01 1.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-29 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-27 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-11 2.3
2021-03-17 2.2
2020-06-16 2.1
2018-07-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-18 1.0.1
2017-09-04 0.9.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-28 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-15 0.0.3
2023-04-12 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-20 1.15.2
2023-04-02 1.15.1
2020-06-02 1.15
2020-03-23 1.14
2020-02-28 1.13
2020-01-13 1.12
2019-01-03 1.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-14 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-07 0.2.5
2020-02-29 0.2.4
2019-07-01 0.2.3-1
2019-06-29 0.2.3
2018-07-15 0.2.2
2017-04-03 0.2.0
2016-11-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-18 0.1.4
2021-04-16 0.1.3
2018-04-21 0.1.2
2018-02-11 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-20 0.3.0
2016-11-05 0.2
2014-05-05 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-24 1.1.3
2019-07-02 1.1.2
2018-07-14 1.1.1
2017-09-25 1.1.0
2017-07-23 1.0.0
2016-10-09 0.7.0
2016-09-13 0.6.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-10 0.1.11
2022-02-22 0.1.9
2021-12-06 0.1.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-28 1.0.2
2022-01-07 1.0.1
2021-06-14 1.0.0
2020-10-29 0.4.10
2020-02-23 0.4.9
2020-01-13 0.4.8
2019-09-08 0.4.7
2019-07-27 0.4.6
2018-09-10 0.4.5
2017-12-18 0.4.3
2017-10-19 0.4.2
2017-06-26 0.4.1
2017-04-12 0.4.0
2017-04-07 0.3.22
2016-10-31 0.3.18
2016-04-14 0.3.16
2015-09-15 0.3.15
2015-04-27 0.3.10
2015-03-17 0.3.9
2014-10-10 0.3.3
2014-10-01 0.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-14 0.1.1
2020-11-30 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-24 3.2-5
2020-09-01 3.2-3
2019-03-20 3.2-2
2019-01-08 3.2-1
2018-07-25 3.2-0
2017-10-05 3.1-5
2017-04-21 3.1-4
2017-03-16 3.1-3
2017-01-09 3.1-2
2016-12-20 3.1-1
2016-08-11 3.0-0
2016-02-22 2.4-1
2015-03-04 2.4-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-20 0.9.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-22 0.1.1
2024-05-13 0.1.0
2024-03-14 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-19 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-21 1.2.1
2021-04-27 1.2.0
2021-03-15 1.1.9
2020-08-07 1.1.8
2020-05-04 1.1.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-09 1.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-29 1.2.4
2019-02-04 1.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-13 0.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-19 2.3.1
2023-10-13 2.3.0
2022-06-15 2.2.0
2021-06-17 2.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-01 3.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-19 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-03 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-01 0.0.5
2021-02-13 0.0.4
2020-12-10 0.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-12 0.6.3
2020-07-16 0.6.2
2020-05-27 0.6.1
2020-04-02 0.6.0
2020-03-06 0.5.9
2019-06-14 0.5.7
2019-03-22 0.5.2
2019-03-21 0.5.0
2018-06-14 0.4
2018-04-19 0.3
2018-03-19 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-25 0.9.2
2021-06-28 0.9.1
2021-02-07 0.8.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-16 0.6.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-01 1.5
2022-05-23 1.4
2022-05-18 1.3
2022-04-15 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-19 1.2.0
2021-07-01 1.1.0
2021-01-21 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-12 0.1.0
Title: A Magical Framework for Collaborative & Reproducible Data
Analysis
Description: A comprehensive data analysis framework for NIH-funded research that streamlines workflows for both data cleaning and preparing and modifying NIH Data Archive ('NDA') data structures and submission templates. Provides unified access to multiple data sources ('REDCap', 'MongoDB', 'Qualtrics', 'SQL', 'ORACLE') through interfaces to their APIs, with specialized functions for data cleaning, filtering, merging, and parsing. Features automatic validation, field harmonization, and memory-aware processing to enhance reproducibility in multi-site collaborative research as described in Mittal et al. (2021) <doi:10.20900/jpbs.20210011>.
Author: Joshua G. Kenney [aut, cre],
Trevor F. Williams [aut],
Minerva K. Pappu [aut],
Michael J. Spilka [aut],
Danielle N. Pratt [ctb],
Victor J. Pokorny [ctb],
Santiago Castiello de Obeso [ctb],
Praveen Suthaharan [ctb],
Christian R. Horgan [ctb]
Maintainer: Joshua G. Kenney <joshua.kenney@yale.edu>
Diff between wizaRdry versions 0.2.6 dated 2025-06-17 and 0.5.0 dated 2025-11-07
DESCRIPTION | 15 MD5 | 103 +- NAMESPACE | 16 R/ConfigEnv.R | 60 + R/SecretsEnv.R | 121 +-- R/checkColumnPrefix.R | 18 R/checkInterviewAge.R | 35 R/checkQualtricsDuplicates.R | 33 R/cleanDataFrameExists.R | 19 R/createCsv.R | 14 R/createNda.R | 4 R/createNdaDataDefinition.R |only R/createNdaSubmissionTemplate.R |only R/createRda.R | 14 R/createSpss.R | 15 R/dataFilter.R | 11 R/dataMerge.R | 9 R/dataParse.R | 6 R/dataRequest.R | 43 - R/deprecated.R |only R/getMongo.R | 506 ++++++------- R/getOracle.R |only R/getQualtrics.R | 287 +++++-- R/getRedcap.R | 88 +- R/getSql.R |only R/ndaRequest.R | 890 +++++++++++++++++++++-- R/ndaRequiredVariablesExist.R | 31 R/ndaValidator.R | 1502 ++++++++++++++++++++++++++++++++++++++-- R/processCaprData.R | 200 ++++- R/scry.R | 87 +- R/testSuite.R | 16 R/zzz.R | 3 man/createCsv.Rd | 18 man/createRds.Rd | 18 man/createSpss.Rd | 18 man/dataFilter.Rd | 84 -- man/dataMerge.Rd | 27 man/dataRequest.Rd | 17 man/getRedcap.Rd | 40 - man/getSurvey.Rd | 22 man/getTask.Rd | 28 man/mongo.Rd | 14 man/mongo.index.Rd | 4 man/ndaRequest.Rd | 24 man/oracle.Rd |only man/oracle.desc.Rd |only man/oracle.index.Rd |only man/oracle.query.Rd |only man/oracle.test.Rd |only man/qualtrics.index.Rd | 15 man/redcap.Rd | 4 man/redcap.rune.Rd | 4 man/scry.Rd | 2 man/sql.Rd |only man/sql.desc.Rd |only man/sql.index.Rd |only man/sql.query.Rd |only man/to.nda.Rd | 41 + man/wizaRdry-deprecated.Rd |only man/wizaRdry-package.Rd | 2 60 files changed, 3495 insertions(+), 1033 deletions(-)
Title: Salary Analysis by the Swiss Federal Office for Gender Equality
Description: Implementation of the Swiss Confederation's standard analysis
model for salary analyses
<www.ebg.admin.ch/en/equal-pay-analysis-with-logib> in R. The
analysis is run at company-level and the model is intended for
medium-sized and large companies. It can technically be used with 50
or more employees (apprentices, trainees/interns and expats are not
included in the analysis). Employees with at least 100 employees are
required by the Gender Equality Act to conduct an equal pay analysis.
This package allows users to run the equal salary analysis in R,
providing additional transparency with respect to the methodology and
simple automation possibilities.
Author: Marc Stoeckli [aut, cre],
Silvia Strub [ctb],
Jonathan Chassot [aut],
Jeremy Kolly [aut],
Federal Office for Gender Equality of Switzerland [cph, fnd]
Maintainer: Marc Stoeckli <marc.stoeckli@ebg.admin.ch>
Diff between logib versions 0.2.0 dated 2024-12-20 and 0.2.1 dated 2025-11-07
DESCRIPTION | 16 +- MD5 | 30 ++--- NEWS.md | 8 + R/analysis.R | 36 ++++-- R/data.R | 6 - R/data_check.R | 22 ++- R/data_preparation.R | 122 +++++++++++++++------- R/datalists.R | 6 - README.md | 2 data/datalist_example.rda |binary man/datalist_example.Rd | 6 - tests/testthat/Beispiel_Datenblatt_M1.xlsx |binary tests/testthat/Esempio_foglio_di_dati_M1.xlsx |binary tests/testthat/Example_data_sheet_M1.xlsx |binary tests/testthat/Exemple_feuille_de_donnees_M1.xlsx |binary tests/testthat/test-analysis.R | 21 +-- 16 files changed, 175 insertions(+), 100 deletions(-)
Title: G-Formula for Causal Inference via Multiple Imputation
Description: Implements the G-Formula method for causal inference with time-varying treatments and
confounders using Bayesian multiple imputation methods, as described by
Bartlett et al (2025) <doi:10.1177/09622802251316971>. It creates multiple synthetic imputed
datasets under treatment regimes of interest using the 'mice' package. These can then be analysed
using rules developed for analysing multiple synthetic datasets.
Author: Jonathan Bartlett [aut, cre] ,
Camila Olarte Parra [ctb] ,
Erik van Zwet [ctb]
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Diff between gFormulaMI versions 1.0.2 dated 2025-07-03 and 1.0.3 dated 2025-11-07
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/gFormulaImpute.R | 2 +- inst/doc/gFormulaMI.Rmd | 4 ++-- inst/doc/gFormulaMI.html | 20 +++++++++++--------- man/gFormulaImpute.Rd | 2 +- vignettes/gFormulaMI.Rmd | 4 ++-- 8 files changed, 31 insertions(+), 25 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-07 0.2.2
2025-10-26 0.2.1
2025-10-22 0.2
Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography
formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and
'Bibentry'. Includes a port of the 'bibutils' utilities by Chris
Putnam <https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] , comment.ORCID: 0000-0003-2839-346X),
Chris Putman [aut] ,
Richard Mathar [ctb] ,
Johannes Wilm [ctb] ,
R Core Team [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 2.3 dated 2024-10-04 and 2.4 dated 2025-11-07
rbibutils-2.3/rbibutils/inst/bib/Putnam1992.end |only rbibutils-2.3/rbibutils/tests/testthat/test-convert.Rsav |only rbibutils-2.4/rbibutils/DESCRIPTION | 12 rbibutils-2.4/rbibutils/MD5 | 175 - rbibutils-2.4/rbibutils/NAMESPACE | 61 rbibutils-2.4/rbibutils/NEWS.md | 822 +++-- rbibutils-2.4/rbibutils/R/bib.R | 627 ++-- rbibutils-2.4/rbibutils/R/bibentry.R | 1419 +++++----- rbibutils-2.4/rbibutils/R/convert.R | 126 rbibutils-2.4/rbibutils/R/import.R | 152 - rbibutils-2.4/rbibutils/R/zzz.R | 31 rbibutils-2.4/rbibutils/build/partial.rdb |binary rbibutils-2.4/rbibutils/build/vignette.rds |binary rbibutils-2.4/rbibutils/inst/bib/00README.org | 8 rbibutils-2.4/rbibutils/inst/bib/Cousquer_1991_PCE.bib | 2 rbibutils-2.4/rbibutils/inst/bib/Cousquer_1991_PCE2.bib | 2 rbibutils-2.4/rbibutils/inst/bib/Cousquer_1991_PCE2_e.bib | 2 rbibutils-2.4/rbibutils/inst/bib/Cousquer_1991_PCE4.bib | 2 rbibutils-2.4/rbibutils/inst/bib/Cousquer_1991_PCE5.bib | 2 rbibutils-2.4/rbibutils/inst/bib/Cousquer_1991_PCE5_e.bib | 2 rbibutils-2.4/rbibutils/inst/bib/Cousquer_1991_PCE_e.bib | 2 rbibutils-2.4/rbibutils/inst/bib/WuertzEtalGarch.bib | 20 rbibutils-2.4/rbibutils/inst/bib/latin1accents_utf8.bib | 18 rbibutils-2.4/rbibutils/inst/bib/litprog280.bib | 13 rbibutils-2.4/rbibutils/inst/bib/litprog280macros_only.bib | 13 rbibutils-2.4/rbibutils/inst/doc/rbibutils.R | 154 - 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Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Cross Validation and similar, or using iterated nested Laplace
approximation for fully Bayesian inference. See Wood (2025)
<doi:10.1146/annurev-statistics-112723-034249> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood [aut, cre]
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.9-3 dated 2025-04-04 and 1.9-4 dated 2025-11-07
mgcv-1.9-3/mgcv/man/full.score.Rd |only mgcv-1.9-4/mgcv/ChangeLog | 54 mgcv-1.9-4/mgcv/DESCRIPTION | 18 mgcv-1.9-4/mgcv/MD5 | 150 - mgcv-1.9-4/mgcv/NAMESPACE | 28 mgcv-1.9-4/mgcv/R/bam.r | 65 mgcv-1.9-4/mgcv/R/deprecated.r |only mgcv-1.9-4/mgcv/R/efam.r | 1385 ++++++++++++++++- mgcv-1.9-4/mgcv/R/fast-REML.r | 4 mgcv-1.9-4/mgcv/R/gam.fit3.r | 6 mgcv-1.9-4/mgcv/R/gam.fit4.r | 13 mgcv-1.9-4/mgcv/R/gamlss.r | 205 +- mgcv-1.9-4/mgcv/R/gfam.r | 2 mgcv-1.9-4/mgcv/R/jagam.r | 2 mgcv-1.9-4/mgcv/R/mgcv.r | 564 ++---- mgcv-1.9-4/mgcv/R/misc.r | 28 mgcv-1.9-4/mgcv/R/plots.r | 218 +- mgcv-1.9-4/mgcv/R/scasm.r |only mgcv-1.9-4/mgcv/R/smooth.r | 9 mgcv-1.9-4/mgcv/R/soap.r | 32 mgcv-1.9-4/mgcv/man/NCV.Rd | 2 mgcv-1.9-4/mgcv/man/Predict.matrix.soap.film.Rd | 15 mgcv-1.9-4/mgcv/man/Tweedie.Rd | 3 mgcv-1.9-4/mgcv/man/bam.Rd | 2 mgcv-1.9-4/mgcv/man/bam.update.Rd | 5 mgcv-1.9-4/mgcv/man/bcg.Rd |only mgcv-1.9-4/mgcv/man/choose.k.Rd | 1 mgcv-1.9-4/mgcv/man/concurvity.Rd | 4 mgcv-1.9-4/mgcv/man/dpnorm.Rd | 3 mgcv-1.9-4/mgcv/man/dppois.Rd |only mgcv-1.9-4/mgcv/man/exclude.too.far.Rd | 4 mgcv-1.9-4/mgcv/man/extract.lme.cov.Rd | 2 mgcv-1.9-4/mgcv/man/family.mgcv.Rd | 2 mgcv-1.9-4/mgcv/man/formXtViX.Rd | 2 mgcv-1.9-4/mgcv/man/gam.Rd | 19 mgcv-1.9-4/mgcv/man/gam.check.Rd | 2 mgcv-1.9-4/mgcv/man/gam.control.Rd | 7 mgcv-1.9-4/mgcv/man/gam.fit.Rd | 4 mgcv-1.9-4/mgcv/man/gam.fit3.Rd | 4 mgcv-1.9-4/mgcv/man/gam.outer.Rd | 5 mgcv-1.9-4/mgcv/man/gam.selection.Rd | 3 mgcv-1.9-4/mgcv/man/gam.vcomp.Rd | 38 mgcv-1.9-4/mgcv/man/gam2objective.Rd | 2 mgcv-1.9-4/mgcv/man/gamm.Rd | 1 mgcv-1.9-4/mgcv/man/gammals.Rd | 4 mgcv-1.9-4/mgcv/man/gaulss.Rd | 2 mgcv-1.9-4/mgcv/man/get.var.Rd | 4 mgcv-1.9-4/mgcv/man/gumbls.Rd | 2 mgcv-1.9-4/mgcv/man/in.out.Rd | 4 mgcv-1.9-4/mgcv/man/inSide.Rd | 16 mgcv-1.9-4/mgcv/man/interpret.gam.Rd | 3 mgcv-1.9-4/mgcv/man/k.check.Rd | 1 mgcv-1.9-4/mgcv/man/ls.size.Rd | 4 mgcv-1.9-4/mgcv/man/magic.Rd | 1 mgcv-1.9-4/mgcv/man/mgcv-package.Rd | 13 mgcv-1.9-4/mgcv/man/mono.con.Rd | 1 mgcv-1.9-4/mgcv/man/new.name.Rd | 4 mgcv-1.9-4/mgcv/man/notExp.Rd | 4 mgcv-1.9-4/mgcv/man/notExp2.Rd | 5 mgcv-1.9-4/mgcv/man/null.space.dimension.Rd | 1 mgcv-1.9-4/mgcv/man/pcls.Rd | 15 mgcv-1.9-4/mgcv/man/pdIdnot.Rd | 2 mgcv-1.9-4/mgcv/man/pdTens.Rd | 2 mgcv-1.9-4/mgcv/man/place.knots.Rd | 4 mgcv-1.9-4/mgcv/man/plot.gam.Rd | 39 mgcv-1.9-4/mgcv/man/predict.gam.Rd | 4 mgcv-1.9-4/mgcv/man/print.gam.Rd | 3 mgcv-1.9-4/mgcv/man/qq.gam.Rd | 1 mgcv-1.9-4/mgcv/man/random.effects.Rd | 10 mgcv-1.9-4/mgcv/man/rig.Rd | 1 mgcv-1.9-4/mgcv/man/s.Rd | 6 mgcv-1.9-4/mgcv/man/scasm.Rd |only mgcv-1.9-4/mgcv/man/smooth.construct.Rd | 1 mgcv-1.9-4/mgcv/man/smooth.construct.ad.smooth.spec.Rd | 5 mgcv-1.9-4/mgcv/man/smooth.construct.bs.smooth.spec.Rd | 9 mgcv-1.9-4/mgcv/man/smooth.construct.so.smooth.spec.Rd | 2 mgcv-1.9-4/mgcv/man/smooth.terms.Rd | 2 mgcv-1.9-4/mgcv/man/smoothCon.Rd | 4 mgcv-1.9-4/mgcv/man/te.Rd | 5 79 files changed, 2201 insertions(+), 896 deletions(-)
Title: Pointcloud Interactive Computation
Description: Provides advanced algorithms for analyzing pointcloud data from terrestrial laser scanner in
forestry applications. Key features include fast voxelization of
large datasets; segmentation of point clouds into forest floor,
understorey, canopy, and wood components. The package enables
efficient processing of large-scale forest pointcloud data, offering
insights into forest structure, connectivity, and fire risk
assessment. Algorithms to analyze pointcloud data (.xyz input file).
For more details, see Ferrara & Arrizza (2025) <https://hdl.handle.net/20.500.14243/533471>.
For single tree segmentation details, see Ferrara et al. (2018)
<doi:10.1016/j.agrformet.2018.04.008>.
Author: Roberto Ferrara [aut, cre] ,
Stefano Arrizza [ctb]
Maintainer: Roberto Ferrara <roberto.ferrara@cnr.it>
Diff between PiC versions 1.2.6 dated 2025-10-11 and 1.2.7 dated 2025-11-07
PiC-1.2.6/PiC/R/SegOne.R |only PiC-1.2.7/PiC/DESCRIPTION | 6 PiC-1.2.7/PiC/MD5 | 26 +- PiC-1.2.7/PiC/NAMESPACE | 3 PiC-1.2.7/PiC/NEWS.md | 72 +++++++ PiC-1.2.7/PiC/R/Floseg.R | 41 ++-- PiC-1.2.7/PiC/R/SegOne_v4_1_2.R |only PiC-1.2.7/PiC/R/Voxels.R | 8 PiC-1.2.7/PiC/R/globals.R | 22 ++ PiC-1.2.7/PiC/README.md | 253 ++++++++++++++++++++++++++- PiC-1.2.7/PiC/man/Floseg.Rd | 2 PiC-1.2.7/PiC/man/SegOne.Rd | 271 +++++++++++++++++++++++++++-- PiC-1.2.7/PiC/tests/testthat/test-Floseg.R | 4 PiC-1.2.7/PiC/tests/testthat/test-SegOne.R | 118 +++++------- PiC-1.2.7/PiC/tests/testthat/test-voxel.R | 110 ++++++----- 15 files changed, 768 insertions(+), 168 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 2.22.9 dated 2025-08-20 and 2.22.10 dated 2025-11-07
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/MxVersion.R | 2 +- build/stage23.rdb |binary inst/doc/deriv.html | 16 ++++++++-------- inst/doc/factor_analysis.html | 12 ++++++------ inst/doc/reg_mimic.html | 10 +++++----- inst/doc/regularization.html | 2 +- 8 files changed, 33 insertions(+), 33 deletions(-)
Title: Predicted Values and Discrete Changes for Regression Models
Description: Functions to calculate predicted values and the difference between
the two cases with confidence interval for lm() [linear model], glm() [generalized linear model], glm.nb() [negative binomial model],
polr() [ordinal logistic model], vglm() [generalized ordinal logistic model], multinom() [multinomial model], tobit() [tobit model],
svyglm() [survey-weighted generalised linear models] and lmer() [linear multilevel models] using Monte Carlo simulations or bootstrap. Reference: Bennet A. Zelner (2009) <doi:10.1002/smj.783>.
Author: Benjamin E. Schlegel [aut, cre]
Maintainer: Benjamin E. Schlegel <kontakt@benjaminschlegel.ch>
Diff between glm.predict versions 4.3-0 dated 2024-01-15 and 4.3-2 dated 2025-11-07
DESCRIPTION | 19 ++++++++++----- MD5 | 50 ++++++++++++++++++++-------------------- R/basepredict.glm.R | 7 ++++- R/basepredict.lm.R | 8 +++++- R/basepredict.lmerMod.R | 7 ++++- R/basepredict.mlogit.R | 12 +++++++-- R/basepredict.multinom.R | 8 +++++- R/basepredict.polr.R | 7 ++++- R/basepredict.vglm.R | 9 +++++-- R/dc.glm.R | 7 ++++- R/dc.lm.R | 7 ++++- R/dc.lmerMod.R | 7 ++++- R/dc.mlogit.R | 11 +++++++- R/dc.multinom.R | 8 +++++- R/dc.polr.R | 7 ++++- R/dc.vglm.R | 9 +++++-- R/getBaseCombinations.R | 52 ++++++++++++++++++++++++++++++++--------- R/getCombinations.R | 6 ++-- R/getProducts.R | 4 ++- R/getValues.R | 25 +++++++++++++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/glm.predict.html | 57 +++++++++++++++++++++++----------------------- man/basepredict.mlogit.Rd | 12 ++++----- man/dc.mlogit.Rd | 18 ++++++-------- man/predicts.Rd | 1 26 files changed, 246 insertions(+), 112 deletions(-)
Title: Bayesian Hierarchical Modelling of Spatio-Temporal Health Data
Description: Supports modeling health outcomes using Bayesian hierarchical
spatio-temporal models with complex covariate effects (e.g., linear,
non-linear, interactions, distributed lag linear and non-linear
models) in the 'INLA' framework. It is designed to help users identify key
drivers and predictors of disease risk by enabling streamlined model
exploration, comparison, and visualization of complex covariate effects.
See an application of the modelling framework in Lowe, Lee, O'Reilly et al. (2021)
<doi:10.1016/S2542-5196(20)30292-8>.
Author: Carles Mila [aut, cre] ,
Giovenale Moirano [aut] ,
Anna B. Kawiecki [aut] ,
Rachel Lowe [aut]
Maintainer: Carles Mila <carles.milagarcia@bsc.es>
Diff between GHRmodel versions 0.1.0 dated 2025-10-21 and 0.1.1 dated 2025-11-07
DESCRIPTION | 6 - MD5 | 32 +++---- NEWS.md | 6 + R/plot_coef_crosspred.R | 164 ++++++++++++++++++++++++++++---------- README.md | 18 +++- build/vignette.rds |binary inst/doc/GHRmodel_DLNM.R | 7 - inst/doc/GHRmodel_DLNM.Rmd | 17 ++- inst/doc/GHRmodel_DLNM.html | 22 ++--- inst/doc/GHRmodel_covariates.Rmd | 4 inst/doc/GHRmodel_covariates.html | 4 inst/doc/GHRmodel_overview.Rmd | 14 +-- inst/doc/GHRmodel_overview.html | 14 +-- man/GHRmodel-package.Rd | 2 vignettes/GHRmodel_DLNM.Rmd | 17 ++- vignettes/GHRmodel_covariates.Rmd | 4 vignettes/GHRmodel_overview.Rmd | 14 +-- 17 files changed, 223 insertions(+), 122 deletions(-)
Title: Motif Discovery in Functional Data
Description: Efficiently implementing two complementary methodologies for discovering motifs in functional data: ProbKMA and FunBIalign.
Cremona and Chiaromonte (2023) "Probabilistic K-means with Local Alignment for Clustering and Motif Discovery in Functional Data" <doi:10.1080/10618600.2022.2156522> is a probabilistic K-means algorithm that leverages local alignment and fuzzy clustering to identify recurring patterns (candidate functional motifs) across and within curves, allowing different portions of the same curve to belong to different clusters. It includes a family of distances and a normalization to discover various motif types and learns motif lengths in a data-driven manner. It can also be used for local clustering of misaligned data.
Di Iorio, Cremona, and Chiaromonte (2023) "funBIalign: A Hierarchical Algorithm for Functional Motif Discovery Based on Mean Squared Residue Scores" <doi:10.48550/arXiv.2306.04254> applies hierarchical agglomerative clustering with a functional g [...truncated...]
Author: Marzia Angela Cremona [aut],
Francesca Chiaromonte [aut],
Jacopo Di Iorio [aut, cre],
Niccolo Feresini [aut],
Riccardo Lazzarini [aut]
Maintainer: Jacopo Di Iorio <jacopo.di.iorio@emory.edu>
Diff between funMoDisco versions 1.0.0 dated 2025-04-15 and 1.1.0 dated 2025-11-07
funMoDisco-1.0.0/funMoDisco/R/shiny.R |only funMoDisco-1.0.0/funMoDisco/man/motifSimulationApp.Rd |only funMoDisco-1.1.0/funMoDisco/DESCRIPTION | 16 funMoDisco-1.1.0/funMoDisco/MD5 | 74 - funMoDisco-1.1.0/funMoDisco/NAMESPACE | 114 + funMoDisco-1.1.0/funMoDisco/R/S4_constructor.R | 348 +++++ funMoDisco-1.1.0/funMoDisco/R/S4_methods.R | 400 +++++- funMoDisco-1.1.0/funMoDisco/R/S4_utilities.R | 35 funMoDisco-1.1.0/funMoDisco/R/cluster_candidate_motifs.R | 4 funMoDisco-1.1.0/funMoDisco/R/compare_nodes.R | 2 funMoDisco-1.1.0/funMoDisco/R/discoverMotifs.R | 403 ++++-- funMoDisco-1.1.0/funMoDisco/R/find_recommended_path.R | 8 funMoDisco-1.1.0/funMoDisco/R/funMoDisco-pkg.R | 2 funMoDisco-1.1.0/funMoDisco/R/get_parents.R | 2 funMoDisco-1.1.0/funMoDisco/R/get_path_complete.R | 23 funMoDisco-1.1.0/funMoDisco/R/padding.R | 2 funMoDisco-1.1.0/funMoDisco/R/probKMA_plot.R | 586 +++++----- funMoDisco-1.1.0/funMoDisco/R/probKMA_silhouette_plot.R | 1 funMoDisco-1.1.0/funMoDisco/R/recommend_node.R | 2 funMoDisco-1.1.0/funMoDisco/build/partial.rdb |binary funMoDisco-1.1.0/funMoDisco/build/vignette.rds |binary funMoDisco-1.1.0/funMoDisco/man/discoverMotifs.Rd | 110 - funMoDisco-1.1.0/funMoDisco/man/dot-generate_coefficients.Rd | 5 funMoDisco-1.1.0/funMoDisco/man/generateCurves-motifSimulation-method.Rd | 13 funMoDisco-1.1.0/funMoDisco/man/generateCurves.Rd | 7 funMoDisco-1.1.0/funMoDisco/man/motifSimulationBuilder.Rd | 9 funMoDisco-1.1.0/funMoDisco/man/plot_motifs-motifSimulation-method.Rd | 5 funMoDisco-1.1.0/funMoDisco/man/plot_motifs.Rd | 8 funMoDisco-1.1.0/funMoDisco/man/to_motifDiscovery-list-method.Rd | 3 funMoDisco-1.1.0/funMoDisco/man/to_motifDiscovery.Rd | 7 funMoDisco-1.1.0/funMoDisco/src/Makevars | 16 funMoDisco-1.1.0/funMoDisco/src/Makevars.win | 3 funMoDisco-1.1.0/funMoDisco/src/SobolDiss.cpp | 4 funMoDisco-1.1.0/funMoDisco/src/include/Dissimilarity.hpp | 1 funMoDisco-1.1.0/funMoDisco/src/include/Motif.hpp | 1 funMoDisco-1.1.0/funMoDisco/src/include/Motif.ipp | 42 funMoDisco-1.1.0/funMoDisco/src/include/ProbKMA.hpp | 1 funMoDisco-1.1.0/funMoDisco/src/include/Utilities.hpp | 17 funMoDisco-1.1.0/funMoDisco/src/probKMAImpl.cpp | 70 - 39 files changed, 1551 insertions(+), 793 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Procedures are available for choosing models that
conform to the hierarchy or marginality principle, for fitting and choosing between
two-dimensional spatial models using correlation, natural cubic smoothing spline and
P-spline models. A history of the fitting of a sequence of models is kept in a data frame.
Also used to compute functions and contrasts of, to investigate differences between and
to plot predictions obtained using any model fitting function. The content falls into
the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model
selection and description functions, (iv) Model diagnostics and simulation functions,
(v) Prediction production and presentation functions, (vi) Response transformation
functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions
(for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.4.51 dated 2025-08-21 and 4.4.55 dated 2025-11-07
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Title: Graphs and Tables for OMOP Results
Description: Provides methods to transform omop_result objects into
formatted tables and figures, facilitating the visualisation of study
results working with the Observational Medical Outcomes Partnership
(OMOP) Common Data Model.
Author: Marti Catala [aut] ,
Nuria Mercade-Besora [aut, cre] ,
Yuchen Guo [ctb] ,
Elin Rowlands [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Edward Burn [ctb]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between visOmopResults versions 1.3.1 dated 2025-10-09 and 1.4.0 dated 2025-11-07
visOmopResults-1.3.1/visOmopResults/man/tableStyleCode.Rd |only visOmopResults-1.4.0/visOmopResults/DESCRIPTION | 8 visOmopResults-1.4.0/visOmopResults/MD5 | 130 visOmopResults-1.4.0/visOmopResults/NAMESPACE | 1 visOmopResults-1.4.0/visOmopResults/NEWS.md | 103 visOmopResults-1.4.0/visOmopResults/R/datatableInternal.R | 26 visOmopResults-1.4.0/visOmopResults/R/documentationHelper.R | 45 visOmopResults-1.4.0/visOmopResults/R/formatTable.R | 59 visOmopResults-1.4.0/visOmopResults/R/fxTable.R | 7 visOmopResults-1.4.0/visOmopResults/R/gtTable.R | 13 visOmopResults-1.4.0/visOmopResults/R/helperFunctions.R | 44 visOmopResults-1.4.0/visOmopResults/R/plot.R | 62 visOmopResults-1.4.0/visOmopResults/R/plottingThemes.R | 213 visOmopResults-1.4.0/visOmopResults/R/reactableInternal.R | 40 visOmopResults-1.4.0/visOmopResults/R/styles.R |only visOmopResults-1.4.0/visOmopResults/R/tidy.R | 132 visOmopResults-1.4.0/visOmopResults/R/tinyTable.R | 9 visOmopResults-1.4.0/visOmopResults/R/utilities.R | 117 visOmopResults-1.4.0/visOmopResults/R/visOmopTable.R | 15 visOmopResults-1.4.0/visOmopResults/R/visTable.R | 73 visOmopResults-1.4.0/visOmopResults/build/vignette.rds |binary visOmopResults-1.4.0/visOmopResults/inst/brand |only visOmopResults-1.4.0/visOmopResults/inst/createMockReportData.R | 138 visOmopResults-1.4.0/visOmopResults/inst/doc/a01_tables.R | 231 visOmopResults-1.4.0/visOmopResults/inst/doc/a01_tables.Rmd | 440 visOmopResults-1.4.0/visOmopResults/inst/doc/a01_tables.html | 5676 +++++----- visOmopResults-1.4.0/visOmopResults/inst/doc/a02_plots.Rmd | 592 - visOmopResults-1.4.0/visOmopResults/inst/doc/a02_plots.html | 20 visOmopResults-1.4.0/visOmopResults/inst/doc/a03_quarto_reports.R | 1 visOmopResults-1.4.0/visOmopResults/inst/doc/a03_quarto_reports.Rmd | 539 visOmopResults-1.4.0/visOmopResults/inst/doc/a03_quarto_reports.html | 15 visOmopResults-1.4.0/visOmopResults/inst/doc/a04_shiny_apps.Rmd | 738 - visOmopResults-1.4.0/visOmopResults/inst/doc/a05_style.R |only visOmopResults-1.4.0/visOmopResults/inst/doc/a05_style.Rmd |only visOmopResults-1.4.0/visOmopResults/inst/doc/a05_style.html |only visOmopResults-1.4.0/visOmopResults/man/barPlot.Rd | 26 visOmopResults-1.4.0/visOmopResults/man/boxPlot.Rd | 26 visOmopResults-1.4.0/visOmopResults/man/emptyPlot.Rd | 17 visOmopResults-1.4.0/visOmopResults/man/emptyTable.Rd | 24 visOmopResults-1.4.0/visOmopResults/man/figures/README-unnamed-chunk-5-1.png |binary visOmopResults-1.4.0/visOmopResults/man/figures/README-unnamed-chunk-6-1.png |binary visOmopResults-1.4.0/visOmopResults/man/formatTable.Rd | 33 visOmopResults-1.4.0/visOmopResults/man/plotDoc.Rd | 20 visOmopResults-1.4.0/visOmopResults/man/scatterPlot.Rd | 26 visOmopResults-1.4.0/visOmopResults/man/setGlobalPlotOptions.Rd | 17 visOmopResults-1.4.0/visOmopResults/man/setGlobalTableOptions.Rd | 25 visOmopResults-1.4.0/visOmopResults/man/tableDoc.Rd | 25 visOmopResults-1.4.0/visOmopResults/man/themeVisOmop.Rd | 12 visOmopResults-1.4.0/visOmopResults/man/visOmopTable.Rd | 29 visOmopResults-1.4.0/visOmopResults/man/visTable.Rd | 29 visOmopResults-1.4.0/visOmopResults/tests/testthat/_snaps/datatableInternal.md | 5 visOmopResults-1.4.0/visOmopResults/tests/testthat/_snaps/formatTable.md | 2 visOmopResults-1.4.0/visOmopResults/tests/testthat/_snaps/reactableInternal.md | 16 visOmopResults-1.4.0/visOmopResults/tests/testthat/_snaps/tinyTable.md | 8 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-datatableInternal.R | 3 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-formatTable.R | 133 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-fxTable.R | 47 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-gtTable.R | 160 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-helperFunctions.R | 177 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-plot.R | 2 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-reactableInternal.R | 4 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-tinyTable.R | 6 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-visOmopTable.R | 36 visOmopResults-1.4.0/visOmopResults/tests/testthat/test-visTable.R | 15 visOmopResults-1.4.0/visOmopResults/vignettes/a01_tables.Rmd | 440 visOmopResults-1.4.0/visOmopResults/vignettes/a02_plots.Rmd | 592 - visOmopResults-1.4.0/visOmopResults/vignettes/a03_quarto_reports.Rmd | 539 visOmopResults-1.4.0/visOmopResults/vignettes/a04_shiny_apps.Rmd | 738 - visOmopResults-1.4.0/visOmopResults/vignettes/a05_style.Rmd |only 69 files changed, 6658 insertions(+), 6061 deletions(-)
More information about visOmopResults at CRAN
Permanent link
Title: Evolutionary Transcriptomics
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) <doi:10.1093/bioinformatics/btx835>). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.
Author: Hajk-Georg Drost [aut, cre] ,
Stefan Manolache [aut, ctb] ,
Jaruwatana Sodai Lotharukpong [aut, ctb] ,
Nikola Kalabova [aut, ctb] ,
Filipa Martins Costa [aut, ctb],
Kristian K Ullrich [aut, ctb]
Maintainer: Hajk-Georg Drost <hajk-georg.drost@tuebingen.mpg.de>
This is a re-admission after prior archival of version 0.9.3 dated 2021-02-24
Diff between myTAI versions 0.9.3 dated 2021-02-24 and 2.3.3 dated 2025-11-07
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Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.6.3 dated 2025-10-10 and 1.6.4 dated 2025-11-07
DESCRIPTION | 8 MD5 | 88 R/GPModel.R | 306 +-- R/gpb.Booster.R | 27 R/gpb.plot.partial.dependence.R | 22 README.md | 4 configure.ac | 2 demo/GPBoost_algorithm.R | 10 demo/compare_usage_lme4_gpboost.R | 8 demo/examples_in_R_package_documentation.R | 14 demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 95 - man/GPModel.Rd | 5 man/GPModel_shared_params.Rd | 13 man/fit.GPModel.Rd | 8 man/fit.Rd | 4 man/fitGPModel.Rd | 19 man/get_coef.GPModel.Rd | 8 man/get_coef.Rd | 8 man/get_cov_pars.GPModel.Rd | 8 man/get_cov_pars.Rd | 8 man/get_nested_categories.Rd | 2 man/gpb.plot.part.dep.interact.Rd | 8 man/gpb.plot.partial.dependence.Rd | 14 man/predict.GPModel.Rd | 4 man/set_optim_params.GPModel.Rd | 4 man/set_optim_params.Rd | 4 man/summary.GPModel.Rd | 4 src/CG_utils.cpp | 12 src/c_api.cpp | 34 src/gpboost_R.cpp | 35 src/gpboost_R.h | 29 src/include/GPBoost/cov_fcts.h | 49 src/include/GPBoost/likelihoods.h | 158 + src/include/GPBoost/re_comp.h | 17 src/include/GPBoost/re_model.h | 35 src/include/GPBoost/re_model_template.h | 895 +++++----- src/include/LightGBM/c_api.h | 23 src/objective/regression_objective.hpp | 20 src/re_model.cpp | 206 +- tests/testthat/_snaps |only tests/testthat/test_GPModel_combined_GP_random_effects.R | 34 tests/testthat/test_GPModel_gaussian_process.R | 693 +++---- tests/testthat/test_GPModel_grouped_random_effects.R | 158 + tests/testthat/test_GPModel_non_Gaussian_data.R | 601 +++--- tests/testthat/test_z_GPBoost_algorithm.R | 7 tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 4 46 files changed, 2117 insertions(+), 1598 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 0.10.1 dated 2025-08-20 and 0.10.2 dated 2025-11-07
DESCRIPTION | 13 +++++------ MD5 | 13 ++++++----- NEWS.md | 56 ++++++++++++++++++++++++++++++++++++++------------ R/importNOAA.R | 50 ++++++++++++++++++-------------------------- R/importNOAAlite.R | 7 ++---- R/utils.R |only man/importNOAA.Rd | 13 +++++------ man/importNOAAlite.Rd | 4 --- 8 files changed, 87 insertions(+), 69 deletions(-)
Title: Analyze Data from the Truth Commission in Colombia
Description: Facilitates use and analysis of data about the armed conflict
in Colombia resulting from the joint project between La Jurisdicción
Especial para la Paz (JEP), La Comisión para el Esclarecimiento de la
Verdad, la Convivencia y la No repetición (CEV), and the Human Rights Data
Analysis Group (HRDAG). The data are 100 replicates from a multiple
imputation through chained equations as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. With the replicates
the user can examine four human rights violations that occurred in the
Colombian conflict accounting for the impact of missing fields and fully
missing observations.
Author: Maria Gargiulo [aut, cre],
Maria Juliana Duran [aut],
Paula Andrea Amado [aut],
Patrick Ball [rev]
Maintainer: Maria Gargiulo <mariag@hrdag.org>
Diff between verdata versions 1.0.0 dated 2025-04-24 and 1.0.1 dated 2025-11-07
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ README.md | 16 ++++++++++++---- build/partial.rdb |binary inst/WORDLIST | 18 ++++++++++++++++-- inst/docs/README-en.md | 20 ++++++++++++++------ tests/testthat/test-estimate_mse.R | 2 +- 8 files changed, 57 insertions(+), 23 deletions(-)
Title: Urban Centrality Index
Description: Calculates the Urban Centrality Index (UCI) as in Pereira et al.,
(2013) <doi:10.1111/gean.12002>. The UCI measures the
extent to which the spatial organization of a city or region varies
from extreme polycentric to extreme monocentric in a continuous
scale from 0 to 1. Values closer to 0 indicate more polycentric patterns
and values closer to 1 indicate a more monocentric urban form.
Author: Rafael H. M. Pereira [aut, cre]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between uci versions 0.3.0 dated 2023-09-23 and 0.3.1 dated 2025-11-07
DESCRIPTION | 12 ++++---- MD5 | 22 ++++++++-------- NEWS.md | 6 ++++ R/uci.R | 13 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/uci.R | 12 ++++---- inst/doc/uci.Rmd | 11 ++------ inst/doc/uci.html | 52 +++++++++++++------------------------- man/uci.Rd | 3 -- tests/tests_rafa/max_uci_sparse.R | 10 +++++-- vignettes/uci.Rmd | 11 ++------ 12 files changed, 73 insertions(+), 79 deletions(-)
Title: Estimation of the Proportion of Treatment Effect Explained by
Surrogate Outcome Information
Description: Estimates the proportion of treatment effect on a censored primary outcome that is explained by the treatment effect on a censored surrogate outcome/event. All methods are described in detail in Parast, et al (2020) "Assessing the Value of a Censored Surrogate Outcome" <doi:10.1007/s10985-019-09473-1> and Wang et al (2025) "Model-free Approach to Evaluate a Censored Intermediate Outcome as a Surrogate for Overall Survival" <doi:10.1002/sim.70268>. A tutorial for this package can be found at <https://www.laylaparast.com/surrogateoutcome>.
Author: Layla Parast [aut, cre],
Xuan Wang [aut]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between SurrogateOutcome versions 1.1 dated 2021-11-15 and 1.2 dated 2025-11-07
SurrogateOutcome-1.1/SurrogateOutcome/build |only SurrogateOutcome-1.1/SurrogateOutcome/man/SurrogateOutcome-package.Rd |only SurrogateOutcome-1.2/SurrogateOutcome/DESCRIPTION | 15 SurrogateOutcome-1.2/SurrogateOutcome/MD5 | 12 SurrogateOutcome-1.2/SurrogateOutcome/NAMESPACE | 10 SurrogateOutcome-1.2/SurrogateOutcome/R/SurrogateOutcome.R | 452 +++++++++- SurrogateOutcome-1.2/SurrogateOutcome/man/R.opt.event.Rd |only SurrogateOutcome-1.2/SurrogateOutcome/man/WEIGHT.Rd |only SurrogateOutcome-1.2/SurrogateOutcome/man/WEIGHT.p.Rd |only SurrogateOutcome-1.2/SurrogateOutcome/man/resam.Rd |only 10 files changed, 462 insertions(+), 27 deletions(-)
More information about SurrogateOutcome at CRAN
Permanent link
Title: SM/LM EGARCH & GARCH, VaR/ES Backtesting & Dual LM Extensions
Description: Implement and fit a variety of short-memory (SM) and long-memory
(LM) models from a very broad family of exponential generalized autoregressive
conditional heteroskedasticity (EGARCH) models, such as a MEGARCH (modified
EGARCH), FIEGARCH (fractionally integrated EGARCH), FIMLog-GARCH (fractionally
integrated modulus Log-GARCH), and more. The FIMLog-GARCH as part of the
EGARCH family is discussed in Feng et al. (2023)
<https://econpapers.repec.org/paper/pdnciepap/156.htm>. For convenience and
the purpose of comparison, a variety of other popular SM and LM GARCH-type
models, like an APARCH model, a fractionally integrated
APARCH (FIAPARCH) model, standard GARCH and fractionally integrated GARCH
(FIGARCH) models, GJR-GARCH and FIGJR-GARCH models, TGARCH and FITGARCH
models, are implemented as well as dual models with simultaneous modelling of
the mean, including dual long-memory models with a fractionally integrated
autoregressive moving average (FARIMA) model in the mean and a long [...truncated...]
Author: Dominik Schulz [aut, cre] ,
Yuanhua Feng [aut] ,
Christian Peitz [aut] ),
Oliver Kojo Ayensu [aut] ,
Thomas Gries [ctb] ,
Sikandar Siddiqui [ctb] ,
Shujie Li [ctb]
Maintainer: Dominik Schulz <dominik.schulz@uni-paderborn.de>
Diff between fEGarch versions 1.0.2 dated 2025-09-11 and 1.0.3 dated 2025-11-07
fEGarch-1.0.2/fEGarch/man/fEGarch_fit-egarch_type_spec-method.Rd |only fEGarch-1.0.2/fEGarch/man/fEGarch_fit-loggarch_type_spec-method.Rd |only fEGarch-1.0.2/fEGarch/man/fEGarch_fit.Rd |only fEGarch-1.0.2/fEGarch/man/forecasting-model-methods.Rd |only fEGarch-1.0.3/fEGarch/DESCRIPTION | 6 fEGarch-1.0.3/fEGarch/MD5 | 74 ++--- fEGarch-1.0.3/fEGarch/NAMESPACE | 5 fEGarch-1.0.3/fEGarch/NEWS.md | 10 fEGarch-1.0.3/fEGarch/R/class-egarch-spec.R | 116 ++++----- fEGarch-1.0.3/fEGarch/R/distr_est.R | 6 fEGarch-1.0.3/fEGarch/R/forecasting-functions.R | 56 ++-- fEGarch-1.0.3/fEGarch/R/general_garch_fitting.R | 6 fEGarch-1.0.3/fEGarch/R/generics.R | 58 ++-- fEGarch-1.0.3/fEGarch/R/popular-methods.R | 2 fEGarch-1.0.3/fEGarch/R/sysdata.rda |binary fEGarch-1.0.3/fEGarch/R/ufRisk-functions.R | 14 - fEGarch-1.0.3/fEGarch/README.md | 120 ++++----- fEGarch-1.0.3/fEGarch/man/SP500.Rd | 50 +-- fEGarch-1.0.3/fEGarch/man/UKinflation.Rd | 52 ++-- fEGarch-1.0.3/fEGarch/man/accessor_methods_distr_est.Rd | 94 +++---- fEGarch-1.0.3/fEGarch/man/autoplot-fEGarch_risk-method.Rd | 72 ++--- fEGarch-1.0.3/fEGarch/man/backtest-generics.Rd | 82 +++--- fEGarch-1.0.3/fEGarch/man/backtest-tests.Rd | 12 fEGarch-1.0.3/fEGarch/man/figures/README-unnamed-chunk-12-1.png |binary fEGarch-1.0.3/fEGarch/man/figures/README-unnamed-chunk-15-1.png |binary fEGarch-1.0.3/fEGarch/man/figures/README-unnamed-chunk-25-1.png |binary fEGarch-1.0.3/fEGarch/man/figures/README-unnamed-chunk-9-1.png |binary fEGarch-1.0.3/fEGarch/man/fit-test-generics.Rd | 126 +++++----- fEGarch-1.0.3/fEGarch/man/fit_test_suite-fEGarch_fit-method.Rd | 102 ++++---- fEGarch-1.0.3/fEGarch/man/fitted.Rd | 72 ++--- fEGarch-1.0.3/fEGarch/man/forecasting-generics.Rd | 12 fEGarch-1.0.3/fEGarch/man/loss_functions.Rd | 46 +-- fEGarch-1.0.3/fEGarch/man/mean_spec_methods.Rd | 96 +++---- fEGarch-1.0.3/fEGarch/man/measure_risk.Rd | 2 fEGarch-1.0.3/fEGarch/man/nonpar-generics.Rd | 84 +++--- fEGarch-1.0.3/fEGarch/man/plot-fEGarch_fit-ANY-method.Rd | 118 ++++----- fEGarch-1.0.3/fEGarch/man/plot-fEGarch_risk-ANY-method.Rd | 78 +++--- fEGarch-1.0.3/fEGarch/man/plot.Rd | 42 +-- fEGarch-1.0.3/fEGarch/man/residuals.Rd | 66 ++--- fEGarch-1.0.3/fEGarch/man/sigma.Rd | 72 ++--- 40 files changed, 870 insertions(+), 881 deletions(-)
Title: Risk Assessments for Ecosystems or Ecosystem Components
Description: Implementation of a modular framework for ecosystem risk assessments,
combining existing risk assessment approaches tailored to semi-quantitative and
quantitative analyses.
Author: Helene Gutte [aut, cre, cph] ,
Saskia A. Otto [aut]
Maintainer: Helene Gutte <helenegutte96@gmail.com>
Diff between ecorisk versions 0.1.1 dated 2025-05-27 and 0.2.1 dated 2025-11-07
DESCRIPTION | 8 ++++---- LICENSE |only MD5 | 15 ++++++++------- NEWS.md | 4 ++++ R/plot_heatmap.R | 12 ++++++++---- R/plot_radar.R | 11 +++++++++-- build/vignette.rds |binary man/plot_heatmap.Rd | 12 ++++++++---- man/plot_radar.Rd | 9 ++++++++- 9 files changed, 49 insertions(+), 22 deletions(-)
Title: Processing and Analysing Animal Trajectories
Description: Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' <https://www.movebank.org/cms/movebank-main> and files is facilitated.
Author: Bart Kranstauber [aut, cre] ,
Kamran Safi [aut] ,
Anne K. Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move2 versions 0.4.4 dated 2025-02-10 and 0.4.5 dated 2025-11-07
DESCRIPTION | 13 +- MD5 | 28 ++--- NEWS.md | 5 build/vignette.rds |binary inst/doc/albatross.html | 15 +- inst/doc/convert.html | 5 inst/doc/filtering_tracks.html | 43 ++++---- inst/doc/movebank.html | 85 ++++++++-------- inst/doc/programming_move2_object.html | 5 inst/doc/trajectory_analysis.R | 4 inst/doc/trajectory_analysis.Rmd | 4 inst/doc/trajectory_analysis.html | 19 ++- tests/testthat/test-mt_read_speed.R | 10 + tests/testthat/test-mt_sim_brownian_motion.R | 137 ++++++++++++++++++++------- vignettes/trajectory_analysis.Rmd | 4 15 files changed, 235 insertions(+), 142 deletions(-)
Title: Hyperparameter Optimization for 'mlr3'
Description: Hyperparameter optimization package of the 'mlr3' ecosystem.
It features highly configurable search spaces via the 'paradox'
package and finds optimal hyperparameter configurations for any 'mlr3'
learner. 'mlr3tuning' works with several optimization algorithms e.g.
Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo')
and Hyperband (in 'mlr3hyperband'). Moreover, it can automatically
optimize learners and estimate the performance of optimized models
with nested resampling.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 1.4.0 dated 2025-06-04 and 1.5.0 dated 2025-11-07
DESCRIPTION | 15 ++-- MD5 | 63 ++++++++++---------- NAMESPACE | 4 + NEWS.md | 8 ++ R/CallbackAsyncTuning.R | 18 +++++ R/ObjectiveTuning.R | 2 R/TunerBatchInternal.R | 2 R/TuningInstanceAsyncMulticrit.R | 45 +++++++++++++- R/TuningInstanceAsyncSingleCrit.R | 52 ++++++++++++++-- R/mlr_callbacks.R | 4 + README.md | 3 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only man/callback_async_tuning.Rd | 16 ++++- man/mlr3tuning.asnyc_mlflow.Rd | 2 man/mlr_tuners_gensa.Rd | 22 +++--- man/mlr_tuners_internal.Rd | 2 man/mlr_tuners_nloptr.Rd | 29 ++------- tests/testthat/helper.R | 19 ++++++ tests/testthat/test_ArchiveAsyncTuning.R | 9 ++ tests/testthat/test_ArchiveAsyncTuningFrozen.R | 1 tests/testthat/test_AutoTuner.R | 9 +- tests/testthat/test_CallbackAsyncTuning.R | 17 +++++ tests/testthat/test_Tuner.R | 10 +-- tests/testthat/test_TunerAsyncDesignPoints.R | 1 tests/testthat/test_TunerAsyncGridSearch.R | 1 tests/testthat/test_TunerAsyncRandomSearch.R | 1 tests/testthat/test_TunerBatchIrace.R | 8 +- tests/testthat/test_TuningInstanceAsyncMultiCrit.R | 61 +++++++++++++++++++ tests/testthat/test_TuningInstanceAsyncSingleCrit.R | 62 +++++++++++++++++++ tests/testthat/test_error_handling.R | 25 ++----- tests/testthat/test_mlr_callbacks.R | 2 33 files changed, 396 insertions(+), 117 deletions(-)
Title: Simulation, Estimation and Reliability of Semi-Markov Models
Description: Performs parametric and non-parametric estimation and simulation
for multi-state discrete-time semi-Markov processes. For the parametric
estimation, several discrete distributions are considered for the sojourn
times: Uniform, Geometric, Poisson, Discrete Weibull and Negative Binomial.
The non-parametric estimation concerns the sojourn time distributions,
where no assumptions are done on the shape of distributions. Moreover, the
estimation can be done on the basis of one or several sample paths, with or
without censoring at the beginning or/and at the end of the sample paths.
Reliability indicators such as reliability, maintainability, availability,
BMP-failure rate, RG-failure rate, mean time to failure and mean time to
repair are available as well. The implemented methods are described in
Barbu, V.S., Limnios, N. (2008) <doi:10.1007/978-0-387-73173-5>,
Barbu, V.S., Limnios, N. (2008) <doi:10.1080/10485250701261913> and
Trevezas, S., Limnios, N. (2011) <doi:10.1080/1048 [...truncated...]
Author: Vlad Stefan Barbu [aut] ,
Florian Lecocq [aut],
Corentin Lothode [aut] ,
Nicolas Vergne [aut, cre]
Maintainer: Nicolas Vergne <nicolas.vergne@univ-rouen.fr>
Diff between smmR versions 1.0.3 dated 2021-08-03 and 1.0.5 dated 2025-11-07
smmR-1.0.3/smmR/man/aic.Rd |only smmR-1.0.3/smmR/man/bic.Rd |only smmR-1.0.3/smmR/man/loglik.Rd |only smmR-1.0.5/smmR/DESCRIPTION | 32 smmR-1.0.5/smmR/MD5 | 131 ++- smmR-1.0.5/smmR/NAMESPACE | 56 + smmR-1.0.5/smmR/R/RcppExports.R | 16 smmR-1.0.5/smmR/R/allgenerics.R | 208 +++-- smmR-1.0.5/smmR/R/convolution.R |only smmR-1.0.5/smmR/R/fit.param.f.dweibull.R | 16 smmR-1.0.5/smmR/R/fit.param.f.geom.R | 12 smmR-1.0.5/smmR/R/fit.param.f.nbinom.R | 16 smmR-1.0.5/smmR/R/fit.param.f.pois.R | 12 smmR-1.0.5/smmR/R/fit.param.fi.dweibull.R | 16 smmR-1.0.5/smmR/R/fit.param.fi.geom.R | 12 smmR-1.0.5/smmR/R/fit.param.fi.nbinom.R | 16 smmR-1.0.5/smmR/R/fit.param.fi.pois.R | 12 smmR-1.0.5/smmR/R/fit.param.fij.dweibull.R | 8 smmR-1.0.5/smmR/R/fit.param.fij.endcensoring.R | 18 smmR-1.0.5/smmR/R/fit.param.fij.geom.R | 4 smmR-1.0.5/smmR/R/fit.param.fij.nbinom.R | 8 smmR-1.0.5/smmR/R/fit.param.fij.pois.R | 4 smmR-1.0.5/smmR/R/fit.param.fj.dweibull.R | 8 smmR-1.0.5/smmR/R/fit.param.fj.endcensoring.R | 24 smmR-1.0.5/smmR/R/fit.param.fj.geom.R | 4 smmR-1.0.5/smmR/R/fit.param.fj.nbinom.R | 8 smmR-1.0.5/smmR/R/fit.param.fj.pois.R | 4 smmR-1.0.5/smmR/R/fitmm.R | 6 smmR-1.0.5/smmR/R/fitsmm.R | 11 smmR-1.0.5/smmR/R/get.H.R |only smmR-1.0.5/smmR/R/get.Niuj.R |only smmR-1.0.5/smmR/R/get.psi.R |only smmR-1.0.5/smmR/R/getProcesses.R |only smmR-1.0.5/smmR/R/matrixConvolution.R |only smmR-1.0.5/smmR/R/mm.R | 89 +- smmR-1.0.5/smmR/R/mmfit.R | 41 - smmR-1.0.5/smmR/R/processes.R | 6 smmR-1.0.5/smmR/R/smm.R | 253 +++---- smmR-1.0.5/smmR/R/smmR-package.R | 5 smmR-1.0.5/smmR/R/smmfit.R | 97 +- smmR-1.0.5/smmR/R/smmnonparametric.R | 125 ++- smmR-1.0.5/smmR/R/smmparametric.R | 110 ++- smmR-1.0.5/smmR/R/utils.R | 32 smmR-1.0.5/smmR/README.md | 122 +++ smmR-1.0.5/smmR/build/vignette.rds |binary smmR-1.0.5/smmR/inst/doc/Textile-Factory.R | 16 smmR-1.0.5/smmR/inst/doc/Textile-Factory.Rmd | 14 smmR-1.0.5/smmR/inst/doc/Textile-Factory.html | 785 +++++++++++++++------- smmR-1.0.5/smmR/inst/doc/smmR.R |only smmR-1.0.5/smmR/inst/doc/smmR.Rmd |only smmR-1.0.5/smmR/inst/doc/smmR.html |only smmR-1.0.5/smmR/man/convolution.Rd |only smmR-1.0.5/smmR/man/dot-failureRateBMP.Rd |only smmR-1.0.5/smmR/man/fitmm.Rd | 2 smmR-1.0.5/smmR/man/fitsmm.Rd | 2 smmR-1.0.5/smmR/man/get.H.Rd |only smmR-1.0.5/smmR/man/get.Kpar.Rd |only smmR-1.0.5/smmR/man/get.Niuj.Rd |only smmR-1.0.5/smmR/man/get.P.Rd |only smmR-1.0.5/smmR/man/get.Py.Rd |only smmR-1.0.5/smmR/man/get.f.Rd |only smmR-1.0.5/smmR/man/get.limitDistribution.Rd |only smmR-1.0.5/smmR/man/get.psi.Rd |only smmR-1.0.5/smmR/man/get.qy.Rd |only smmR-1.0.5/smmR/man/get.stationaryDistribution.Rd |only smmR-1.0.5/smmR/man/getKernel.Rd | 2 smmR-1.0.5/smmR/man/getProcesses.Rd |only smmR-1.0.5/smmR/man/matrixConvolution.Rd |only smmR-1.0.5/smmR/man/plot.smmfit.Rd | 26 smmR-1.0.5/smmR/man/smmR-package.Rd | 18 smmR-1.0.5/smmR/man/smmnonparametric.Rd | 1 smmR-1.0.5/smmR/src/Makevars | 1 smmR-1.0.5/smmR/src/Makevars.win | 1 smmR-1.0.5/smmR/src/RcppExports.cpp | 39 - smmR-1.0.5/smmR/src/utils.cpp | 66 - smmR-1.0.5/smmR/tests |only smmR-1.0.5/smmR/vignettes/Textile-Factory.Rmd | 14 smmR-1.0.5/smmR/vignettes/smmR.Rmd |only smmR-1.0.5/smmR/vignettes/smmR.tex |only 79 files changed, 1666 insertions(+), 863 deletions(-)
Title: Get Executing Script's Path
Description: Determine the path of the executing script. Compatible
with several popular GUIs: 'Rgui', 'RStudio', 'Positron',
'VSCode', 'Jupyter', 'Emacs', and 'Rscript' (shell). Compatible
with several functions and packages: 'source()',
'sys.source()', 'debugSource()' in 'RStudio',
'compiler::loadcmp()', 'utils::Sweave()', 'box::use()',
'knitr::knit()', 'plumber::plumb()', 'shiny::runApp()',
'package:targets', and 'testthat::source_file()'.
Author: Iris Simmons [aut, cre]
Maintainer: Iris Simmons <ikwsimmo@gmail.com>
Diff between this.path versions 2.7.0 dated 2025-04-10 and 2.7.1 dated 2025-11-07
DESCRIPTION | 8 +-- MD5 | 46 ++++++++++----------- NEWS | 14 ++++++ R/ns-hooks.R | 85 ++++++++++++++++++++++++++++++++++------ R/promises.R | 5 -- R/thispath.R | 24 +++++------ build/stage23.rdb |binary build/this.path.pdf |binary configure | 2 configure.win | 2 inst/NEWS.in.Rd | 14 ++++++ man/ext.Rd | 4 - man/is.main.Rd | 35 +++++++++------- man/progArgs.Rd | 12 +++-- man/set.gui.path.Rd | 2 man/shFILE.Rd | 10 ++-- man/this.path.Rd | 16 ++++--- src/backports.h | 10 ++-- src/pathjoin.c | 4 - src/pathsplit.c | 2 src/rgui_path.c | 4 - src/shfile.c | 3 + tests/ext-tests.R | 8 +-- tests/faster-subsequent-times.R | 4 + 24 files changed, 211 insertions(+), 103 deletions(-)
Title: CAESAR: a Cross-Technology and Cross-Resolution Framework for
Spatial Omics Annotation
Description: Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. [...truncated...]
Author: Xiao Zhang [aut, cre],
Wei Liu [aut],
Jin Liu [aut]
Maintainer: Xiao Zhang <zhangxiao1994@cuhk.edu.cn>
This is a re-admission after prior archival of version 0.2.2 dated 2025-04-01
Diff between CAESAR.Suite versions 0.2.2 dated 2025-04-01 and 0.2.3 dated 2025-11-07
DESCRIPTION | 10 MD5 | 36 NAMESPACE | 1 R/caesar.R | 22 R/caesar_annotation.R | 16 data/Human_HK_genes.rda |binary data/Mouse_HK_genes.rda |binary data/toydata.rda |binary inst/doc/STMOB.R | 417 +++++----- inst/doc/STMOB.Rmd | 61 - inst/doc/STMOB.html | 928 +++++++---------------- inst/doc/XeniumBC.R | 537 ++++++------- inst/doc/XeniumBC.Rmd | 65 - inst/doc/XeniumBC.html | 1818 ++++++++++------------------------------------ man/CAESAR.annotation.Rd | 4 man/CAESAR.coembedding.Rd | 6 man/find.sig.genes.Rd | 5 vignettes/STMOB.Rmd | 61 - vignettes/XeniumBC.Rmd | 65 - 19 files changed, 1339 insertions(+), 2713 deletions(-)
Title: A Common Representation of Time Indices of Different Types
Description: Provides an easy-to-use tind class representing time indices
of different types (years, quarters, months, ISO 8601 weeks, dates,
time of day, date-time, and arbitrary integer/numeric indices).
Includes an extensive collection of functions for calendrical computations
(including business applications), index conversions, index parsing,
and other operations. Auxiliary classes representing time differences and
time intervals (with set operations and index matching functionality) are
also provided. All routines have been optimised for speed in order
to facilitate computations on large datasets. More details regarding
calendars in general and calendrical algorithms can be found in
"Calendar FAQ" by Claus Tøndering <https://www.tondering.dk/claus/calendar.html>.
Author: Grzegorz Klima [aut, cre, cph]
Maintainer: Grzegorz Klima <dever@post.pl>
This is a re-admission after prior archival of version 0.2.1 dated 2025-10-26
Diff between tind versions 0.2.1 dated 2025-10-26 and 0.2.2 dated 2025-11-07
DESCRIPTION | 8 MD5 | 72 +++--- inst/doc/calendar.html | 138 ++++++------- inst/po/en@quot/LC_MESSAGES/R-tind.mo |binary inst/po/pl/LC_MESSAGES/R-tind.mo |binary po/R-tind.pot | 4 tests/testthat/test-00-base-utils.R | 36 +-- tests/testthat/test-01-base-in.R | 48 ++-- tests/testthat/test-02-base-yqmwd.R | 276 +++++++++++++------------- tests/testthat/test-03-base-tz.R | 16 - tests/testthat/test-04-base-th.R | 270 +++++++++++++------------- tests/testthat/test-05-base-res.R | 110 +++++----- tests/testthat/test-06-base-pretty.R | 22 +- tests/testthat/test-07-base-locale.R | 24 +- tests/testthat/test-08-base-types.R | 56 ++--- tests/testthat/test-09-base-parse.R | 196 +++++++++---------- tests/testthat/test-10-tind.R | 72 +++--- tests/testthat/test-11-format_parse.R | 20 - tests/testthat/test-12-coercion.R | 144 ++++++------- tests/testthat/test-13-methods.R | 90 ++++---- tests/testthat/test-14-tdiff.R | 112 +++++----- tests/testthat/test-15-tinterval.R | 88 ++++---- tests/testthat/test-16-types.R | 22 +- tests/testthat/test-17-ops.R | 16 - tests/testthat/test-18-setops_match.R | 184 ++++++++--------- tests/testthat/test-19-tzone.R | 22 +- tests/testthat/test-20-tspan.R | 20 - tests/testthat/test-22-print_summ_str.R | 26 +- tests/testthat/test-23-round.R | 50 ++-- tests/testthat/test-24-cut.R | 10 tests/testthat/test-26-ord_reg.R | 78 +++---- tests/testthat/test-27-calendar.R | 330 ++++++++++++++++---------------- tests/testthat/test-28-calendars.R | 78 +++---- tests/testthat/test-29-business.R | 86 ++++---- tests/testthat/test-30-other.R | 78 +++---- tests/testthat/test-31-merge.R | 166 ++++++++-------- tests/testthat/test-32-pretty.R | 12 - 37 files changed, 1490 insertions(+), 1490 deletions(-)
Title: Interpolate Bathymetry and Quantify Physical Aquatic Habitat
Description: Offers bathymetric interpolation using Inverse Distance Weighted and Ordinary Kriging via the 'gstat' and 'terra' packages. Other functions focus on quantifying physical aquatic habitats (e.g., littoral, epliminion, metalimnion, hypolimnion) from interpolated digital elevation models (DEMs). Functions were designed to calculate these metrics across water levels for use in reservoirs but can be applied to any DEM and will provide values for fixed conditions. Parameters like Secchi disk depth or estimated photic zone, thermocline depth, and water level fluctuation depth are included in most functions.
Author: Tristan Blechinger [aut, cre] ,
Sean Bertalot [aut]
Maintainer: Tristan Blechinger <tblechin@uwyo.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2025-04-15
Diff between rLakeHabitat versions 1.0.0 dated 2025-04-15 and 1.0.1 dated 2025-11-07
DESCRIPTION | 15 ++++++++------- MD5 | 6 +++--- R/animBathy.R | 2 +- build/vignette.rds |binary 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.3.2 dated 2025-10-12 and 0.3.5 dated 2025-11-07
DESCRIPTION | 6 MD5 | 23 - NEWS.md | 7 R/cms_download_subset.r | 28 +- R/translate.R | 2 README.md | 416 +++++++++++++++---------------- inst/doc/translate.R | 2 inst/doc/translate.Rmd | 12 inst/doc/translate.html | 10 man/figures/README-download-subset-1.png |binary man/figures/README-leaflet-1.png |binary tests/testthat/test-translate.R |only vignettes/translate.Rmd | 12 13 files changed, 271 insertions(+), 247 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-29 0.6.1
2025-05-29 0.6.0
2025-01-27 0.5.0
2024-12-09 0.4.0
2024-08-26 0.3.0
2024-07-31 0.2.0
2024-07-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-16 0.11
2024-09-16 0.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-20 1.1-2
2025-05-07 1.1-1
2025-05-01 1.1-0
2022-08-13 1.0-8
2022-05-02 1.0-7
2021-11-18 1.0-5
2020-03-08 1.0-2
2020-01-30 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-29 0.1.0
Title: Calculate Sun Position, Sunrise, Sunset, Solar Noon and Twilight
Description: Provides a set of convenient functions for calculating sun-related information, including the sun's position (elevation and azimuth), and the times of sunrise, sunset, solar noon, and twilight for any given geographical location on Earth. These calculations are based on equations provided by the National Oceanic & Atmospheric Administration (NOAA) <https://gml.noaa.gov/grad/solcalc/calcdetails.html> as described in "Astronomical Algorithms" by Jean Meeus (1991, ISBN: 978-0-943396-35-4).
Author: Roger Bivand [aut] ,
Adriaan M. Dokter [ctb, cre] ,
Pieter Huybrechts [ctb] ,
Sebastian Luque [aut],
Greg Pelletier [ctb],
Alexander Tedeschi [ctb]
Maintainer: Adriaan M. Dokter <amd427@cornell.edu>
Diff between suntools versions 1.0.1 dated 2024-11-20 and 1.1.0 dated 2025-11-07
DESCRIPTION | 19 +++++++++++-------- MD5 | 17 +++++++++-------- NEWS.md | 8 ++++++-- R/crepuscule.R | 2 +- R/solarnoon.R | 2 +- R/sun.R | 14 ++++++++++++++ R/sunriset.R | 2 +- README.md | 2 +- man/dls_correction.Rd |only tests/testthat/test-sun-methods.R | 24 ++++++++++++++++++++++++ 10 files changed, 68 insertions(+), 22 deletions(-)
Title: Reliability Growth Analysis
Description: Modeling and plotting functions for Reliability Growth Analysis (RGA). Models include the Duane (1962) <doi:10.1109/TA.1964.4319640>, Non-Homogeneous Poisson Process (NHPP) by Crow (1975) <https://apps.dtic.mil/sti/citations/ADA020296>, Piecewise Weibull NHPP by Guo et al. (2010) <doi:10.1109/RAMS.2010.5448029>, and Piecewise Weibull NHPP with Change Point Detection based on the 'segmented' package by Muggeo (2024) <https://cran.r-project.org/package=segmented>.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between ReliaGrowR versions 0.2 dated 2025-09-21 and 0.3 dated 2025-11-07
ReliaGrowR-0.2/ReliaGrowR/inst/paper/paper.html |only ReliaGrowR-0.2/ReliaGrowR/tests/testthat/_snaps/gof |only ReliaGrowR-0.2/ReliaGrowR/tests/testthat/test-duane.R |only ReliaGrowR-0.2/ReliaGrowR/tests/testthat/test-gof.R |only ReliaGrowR-0.2/ReliaGrowR/tests/testthat/test-rdt.R |only ReliaGrowR-0.2/ReliaGrowR/tests/testthat/test-rga.R |only ReliaGrowR-0.2/ReliaGrowR/tests/testthat/test-weibull_to_rga.R |only ReliaGrowR-0.3/ReliaGrowR/DESCRIPTION | 10 ReliaGrowR-0.3/ReliaGrowR/MD5 | 81 +- ReliaGrowR-0.3/ReliaGrowR/NAMESPACE | 4 ReliaGrowR-0.3/ReliaGrowR/NEWS.md | 10 ReliaGrowR-0.3/ReliaGrowR/R/duane.R | 350 ++++++++- ReliaGrowR-0.3/ReliaGrowR/R/gof.R | 86 +- ReliaGrowR-0.3/ReliaGrowR/R/grwr_api.R |only ReliaGrowR-0.3/ReliaGrowR/R/rdt.R | 172 +++- ReliaGrowR-0.3/ReliaGrowR/R/rga.R | 372 +++++++++- ReliaGrowR-0.3/ReliaGrowR/R/srr-stats-standards.R |only ReliaGrowR-0.3/ReliaGrowR/R/testdata.r |only ReliaGrowR-0.3/ReliaGrowR/R/weibull_to_rga.R | 84 +- ReliaGrowR-0.3/ReliaGrowR/README.md | 24 ReliaGrowR-0.3/ReliaGrowR/build/vignette.rds |binary ReliaGrowR-0.3/ReliaGrowR/data |only ReliaGrowR-0.3/ReliaGrowR/inst/CITATION | 9 ReliaGrowR-0.3/ReliaGrowR/inst/WORDLIST | 7 ReliaGrowR-0.3/ReliaGrowR/inst/doc/RGA.R | 26 ReliaGrowR-0.3/ReliaGrowR/inst/doc/RGA.Rmd | 57 + ReliaGrowR-0.3/ReliaGrowR/inst/doc/RGA.html | 72 + ReliaGrowR-0.3/ReliaGrowR/inst/doc/data.R |only ReliaGrowR-0.3/ReliaGrowR/inst/doc/data.Rmd |only ReliaGrowR-0.3/ReliaGrowR/inst/doc/data.html |only ReliaGrowR-0.3/ReliaGrowR/inst/paper/paper.Rmd | 2 ReliaGrowR-0.3/ReliaGrowR/man/duane.Rd | 52 + ReliaGrowR-0.3/ReliaGrowR/man/grwr_api.Rd |only ReliaGrowR-0.3/ReliaGrowR/man/plot.rga.Rd | 6 ReliaGrowR-0.3/ReliaGrowR/man/ppplot.rga.Rd | 6 ReliaGrowR-0.3/ReliaGrowR/man/print.rdt.Rd | 2 ReliaGrowR-0.3/ReliaGrowR/man/print.rga.Rd | 2 ReliaGrowR-0.3/ReliaGrowR/man/qqplot.rga.Rd | 4 ReliaGrowR-0.3/ReliaGrowR/man/rdt.Rd | 16 ReliaGrowR-0.3/ReliaGrowR/man/rga.Rd | 64 + ReliaGrowR-0.3/ReliaGrowR/man/testdata.Rd |only ReliaGrowR-0.3/ReliaGrowR/man/weibull_to_rga.Rd | 28 ReliaGrowR-0.3/ReliaGrowR/tests/spelling.R | 9 ReliaGrowR-0.3/ReliaGrowR/tests/testthat/Rplots.pdf |binary ReliaGrowR-0.3/ReliaGrowR/tests/testthat/_snaps/srr-rga |only ReliaGrowR-0.3/ReliaGrowR/tests/testthat/test-srr-duane.R |only ReliaGrowR-0.3/ReliaGrowR/tests/testthat/test-srr-gof.R |only ReliaGrowR-0.3/ReliaGrowR/tests/testthat/test-srr-rga.R |only ReliaGrowR-0.3/ReliaGrowR/tests/testthat/test-srr-testdata.R |only ReliaGrowR-0.3/ReliaGrowR/tests/testthat/test-srr-weibull_to_rga.R |only ReliaGrowR-0.3/ReliaGrowR/tests/testthat/test-srr_rdt.R |only ReliaGrowR-0.3/ReliaGrowR/vignettes/RGA.Rmd | 57 + ReliaGrowR-0.3/ReliaGrowR/vignettes/data.Rmd |only 53 files changed, 1368 insertions(+), 244 deletions(-)
Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse
set of pipelining operators ('PipeOps') that can be composed into graphs.
Operations exist for data preprocessing, model fitting, and ensemble
learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can
therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre],
Florian Pfisterer [aut] ,
Lennart Schneider [aut] ,
Bernd Bischl [aut] ,
Michel Lang [aut] ,
Sebastian Fischer [aut] ,
Susanne Dandl [aut],
Keno Mersmann [ctb],
Maximilian Muecke [ctb] ,
Lona Koers [ctb],
Alexander Winterstet [...truncated...]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr3pipelines versions 0.9.0 dated 2025-07-31 and 0.10.0 dated 2025-11-07
DESCRIPTION | 49 +- MD5 | 288 +++++++------- NAMESPACE | 6 NEWS.md | 16 R/FilterEnsemble.R |only R/Graph.R | 59 +-- R/GraphLearner.R | 12 R/PipeOp.R | 25 - R/PipeOpBoxCox.R | 3 R/PipeOpClassifAvg.R | 42 +- R/PipeOpDateFeatures.R | 221 ++++++----- R/PipeOpEnsemble.R | 19 R/PipeOpFeatureUnion.R | 13 R/PipeOpFixFactors.R | 22 + R/PipeOpInfo.R |only R/PipeOpIsomap.R |only R/PipeOpLearnerCV.R | 289 ++++++++++++++ R/PipeOpLearnerQuantiles.R | 2 R/PipeOpNMF.R | 60 ++- R/PipeOpPCA.R | 4 R/PipeOpRegrAvg.R | 177 ++++++++- R/PipeOpRemoveConstants.R | 2 R/PipeOpTrafo.R | 31 + R/PipeOpVtreat.R | 26 - R/TaskRegr_boston_housing.R | 4 R/bibentries.R | 10 R/mlr_graphs.R | 2 R/mlr_pipeops.R | 2 R/multiplicity.R | 2 R/preproc.R | 7 R/zzz.R | 24 + inst/doc/extending.html | 11 inst/testthat/helper_functions.R | 2 man/PipeOp.Rd | 2 man/PipeOpEncodePL.Rd | 2 man/PipeOpEnsemble.Rd | 2 man/PipeOpImpute.Rd | 2 man/PipeOpTargetTrafo.Rd | 2 man/PipeOpTaskPreproc.Rd | 2 man/PipeOpTaskPreprocSimple.Rd | 2 man/mlr_filters_ensemble.Rd |only man/mlr_graphs.Rd | 2 man/mlr_graphs_bagging.Rd | 2 man/mlr_graphs_ovr.Rd | 2 man/mlr_graphs_robustify.Rd | 2 man/mlr_graphs_stacking.Rd | 2 man/mlr_graphs_targettrafo.Rd | 2 man/mlr_learners_graph.Rd | 2 man/mlr_pipeops.Rd | 4 man/mlr_pipeops_adas.Rd | 4 man/mlr_pipeops_blsmote.Rd | 4 man/mlr_pipeops_boxcox.Rd | 4 man/mlr_pipeops_branch.Rd | 2 man/mlr_pipeops_chunk.Rd | 2 man/mlr_pipeops_classbalancing.Rd | 2 man/mlr_pipeops_classifavg.Rd | 34 + man/mlr_pipeops_classweights.Rd | 2 man/mlr_pipeops_colapply.Rd | 2 man/mlr_pipeops_collapsefactors.Rd | 2 man/mlr_pipeops_colroles.Rd | 2 man/mlr_pipeops_copy.Rd | 2 man/mlr_pipeops_datefeatures.Rd | 47 +- man/mlr_pipeops_decode.Rd | 2 man/mlr_pipeops_encode.Rd | 2 man/mlr_pipeops_encodeimpact.Rd | 2 man/mlr_pipeops_encodelmer.Rd | 4 man/mlr_pipeops_encodeplquantiles.Rd | 2 man/mlr_pipeops_encodepltree.Rd | 4 man/mlr_pipeops_featureunion.Rd | 2 man/mlr_pipeops_filter.Rd | 4 man/mlr_pipeops_fixfactors.Rd | 20 + man/mlr_pipeops_histbin.Rd | 2 man/mlr_pipeops_ica.Rd | 4 man/mlr_pipeops_imputeconstant.Rd | 2 man/mlr_pipeops_imputehist.Rd | 2 man/mlr_pipeops_imputelearner.Rd | 4 man/mlr_pipeops_imputemean.Rd | 2 man/mlr_pipeops_imputemedian.Rd | 2 man/mlr_pipeops_imputemode.Rd | 2 man/mlr_pipeops_imputeoor.Rd | 2 man/mlr_pipeops_imputesample.Rd | 2 man/mlr_pipeops_info.Rd |only man/mlr_pipeops_isomap.Rd |only man/mlr_pipeops_kernelpca.Rd | 4 man/mlr_pipeops_learner.Rd | 4 man/mlr_pipeops_learner_cv.Rd | 31 + man/mlr_pipeops_learner_pi_cvplus.Rd | 4 man/mlr_pipeops_learner_quantiles.Rd | 4 man/mlr_pipeops_missind.Rd | 2 man/mlr_pipeops_modelmatrix.Rd | 2 man/mlr_pipeops_multiplicityexply.Rd | 2 man/mlr_pipeops_multiplicityimply.Rd | 2 man/mlr_pipeops_mutate.Rd | 2 man/mlr_pipeops_nearmiss.Rd | 4 man/mlr_pipeops_nmf.Rd | 9 man/mlr_pipeops_nop.Rd | 2 man/mlr_pipeops_ovrsplit.Rd | 4 man/mlr_pipeops_ovrunite.Rd | 4 man/mlr_pipeops_pca.Rd | 6 man/mlr_pipeops_proxy.Rd | 4 man/mlr_pipeops_quantilebin.Rd | 2 man/mlr_pipeops_randomprojection.Rd | 2 man/mlr_pipeops_randomresponse.Rd | 4 man/mlr_pipeops_regravg.Rd | 94 ++++ man/mlr_pipeops_removeconstants.Rd | 2 man/mlr_pipeops_renamecolumns.Rd | 2 man/mlr_pipeops_replicate.Rd | 2 man/mlr_pipeops_rowapply.Rd | 2 man/mlr_pipeops_scale.Rd | 2 man/mlr_pipeops_scalemaxabs.Rd | 2 man/mlr_pipeops_scalerange.Rd | 2 man/mlr_pipeops_select.Rd | 2 man/mlr_pipeops_smote.Rd | 4 man/mlr_pipeops_smotenc.Rd | 4 man/mlr_pipeops_spatialsign.Rd | 2 man/mlr_pipeops_subsample.Rd | 2 man/mlr_pipeops_targetinvert.Rd | 36 + man/mlr_pipeops_targetmutate.Rd | 4 man/mlr_pipeops_targettrafoscalerange.Rd | 4 man/mlr_pipeops_textvectorizer.Rd | 4 man/mlr_pipeops_threshold.Rd | 4 man/mlr_pipeops_tomek.Rd | 4 man/mlr_pipeops_tunethreshold.Rd | 4 man/mlr_pipeops_unbranch.Rd | 2 man/mlr_pipeops_updatetarget.Rd | 4 man/mlr_pipeops_vtreat.Rd | 4 man/mlr_pipeops_yeojohnson.Rd | 4 man/po.Rd | 2 man/ppl.Rd | 2 man/preproc.Rd | 9 tests/testthat/_snaps |only tests/testthat/test_Graph.R | 14 tests/testthat/test_PipeOp.R | 23 - tests/testthat/test_filter_ensemble.R |only tests/testthat/test_meta.R | 4 tests/testthat/test_mlr_graphs_robustify.R | 29 + tests/testthat/test_multiplicities.R | 2 tests/testthat/test_pipeop_classifavg.R |only tests/testthat/test_pipeop_classweights.R | 24 + tests/testthat/test_pipeop_datefeatures.R | 104 ++--- tests/testthat/test_pipeop_featureunion.R | 31 + tests/testthat/test_pipeop_impute.R | 26 + tests/testthat/test_pipeop_imputelearner.R | 26 + tests/testthat/test_pipeop_info.R |only tests/testthat/test_pipeop_isomap.R |only tests/testthat/test_pipeop_learnercv.R | 522 ++++++++++++++++++++++++++- tests/testthat/test_pipeop_nmf.R | 85 ++++ tests/testthat/test_pipeop_regravg.R |only tests/testthat/test_pipeop_removeconstants.R | 16 tests/testthat/test_pipeop_task_preproc.R | 139 +++++++ tests/testthat/test_pipeop_textvectorizer.R | 5 151 files changed, 2458 insertions(+), 536 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', 'PowerPoint', 'typst', SVG and PNG. Simple, modern
interface to manipulate borders, size, position, captions, colours,
text styles and number formatting. Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function to create regression tables, and 'quick_*'
one-liners to print tables to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.7.0 dated 2025-08-18 and 5.8.0 dated 2025-11-07
huxtable-5.7.0/huxtable/R/roxygen-functions.R |only huxtable-5.7.0/huxtable/inst/doc/design-principles-html.html |only huxtable-5.7.0/huxtable/inst/doc/design-principles-html.html.asis |only huxtable-5.7.0/huxtable/inst/doc/design-principles-pdf.pdf |only huxtable-5.7.0/huxtable/inst/doc/design-principles-pdf.pdf.asis |only huxtable-5.7.0/huxtable/inst/doc/huxreg-html.html |only huxtable-5.7.0/huxtable/inst/doc/huxreg-html.html.asis |only huxtable-5.7.0/huxtable/inst/doc/huxreg-pdf.pdf |only huxtable-5.7.0/huxtable/inst/doc/huxreg-pdf.pdf.asis |only huxtable-5.7.0/huxtable/inst/doc/huxtable-html.html |only huxtable-5.7.0/huxtable/inst/doc/huxtable-html.html.asis |only huxtable-5.7.0/huxtable/inst/doc/huxtable-pdf.pdf |only huxtable-5.7.0/huxtable/inst/doc/huxtable-pdf.pdf.asis |only huxtable-5.7.0/huxtable/inst/doc/themes-html.html |only huxtable-5.7.0/huxtable/inst/doc/themes-html.html.asis |only huxtable-5.7.0/huxtable/vignettes/design-principles-html.html.asis |only huxtable-5.7.0/huxtable/vignettes/design-principles-pdf.pdf.asis |only huxtable-5.7.0/huxtable/vignettes/huxreg-html.html.asis |only huxtable-5.7.0/huxtable/vignettes/huxreg-pdf.pdf.asis |only huxtable-5.7.0/huxtable/vignettes/huxtable-html.html.asis |only huxtable-5.7.0/huxtable/vignettes/huxtable-pdf.pdf.asis |only huxtable-5.7.0/huxtable/vignettes/themes-html.html.asis |only huxtable-5.8.0/huxtable/DESCRIPTION | 22 - huxtable-5.8.0/huxtable/MD5 | 54 +--- huxtable-5.8.0/huxtable/NEWS.md | 9 huxtable-5.8.0/huxtable/R/clean-contents.R | 2 huxtable-5.8.0/huxtable/R/misc.R | 120 +++++----- huxtable-5.8.0/huxtable/R/properties-cell.R | 2 huxtable-5.8.0/huxtable/R/property-helpers.R | 4 huxtable-5.8.0/huxtable/README.md | 73 +++--- huxtable-5.8.0/huxtable/build/vignette.rds |binary huxtable-5.8.0/huxtable/inst/doc/huxreg.R |only huxtable-5.8.0/huxtable/inst/doc/huxreg.Rmd |only huxtable-5.8.0/huxtable/inst/doc/huxreg.html |only huxtable-5.8.0/huxtable/inst/doc/huxtable.R |only huxtable-5.8.0/huxtable/inst/doc/huxtable.Rmd |only huxtable-5.8.0/huxtable/inst/doc/huxtable.html |only huxtable-5.8.0/huxtable/man/hux_logo.Rd | 12 - huxtable-5.8.0/huxtable/man/huxtable-news.Rd | 11 huxtable-5.8.0/huxtable/man/number_format.Rd | 2 huxtable-5.8.0/huxtable/tests/testthat/table-tester-2.Rmd | 2 huxtable-5.8.0/huxtable/vignettes/huxreg.Rmd |only huxtable-5.8.0/huxtable/vignettes/huxtable.Rmd |only 43 files changed, 161 insertions(+), 152 deletions(-)
Title: Client for Rserve
Description: Client for Rserve, allowing to connect to Rserve instances and issue commands.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between RSclient versions 0.7-10 dated 2023-11-28 and 0.7-11 dated 2025-11-06
DESCRIPTION | 13 ++++++++----- MD5 | 15 ++++++++------- NEWS | 7 +++++++ man/RCC.Rd | 5 ++++- src/cli.c | 30 +++++++++++++++++++++++++++++- src/qap.h | 1 + src/qap_decode.c | 10 +++++++--- src/qap_encode.c | 1 - src/rcompat.h |only 9 files changed, 64 insertions(+), 18 deletions(-)
Title: Fit Growth Curves to Fish Data
Description: Fit growth models to otoliths and/or tagging data, using the 'RTMB'
package and maximum likelihood. The otoliths (or similar measurements of age)
provide direct observed coordinates of age and length. The tagging data
provide information about the observed length at release and length at
recapture at a later time, where the age at release is unknown and estimated
as a vector of parameters. The growth models provided by this package can be
fitted to otoliths only, tagging data only, or a combination of the two.
Growth variability can be modelled as constant or increasing with length.
Author: Arni Magnusson [aut, cre],
Mark Maunder [aut]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between fishgrowth versions 1.0.3 dated 2025-10-01 and 1.0.4 dated 2025-11-06
DESCRIPTION | 8 ++++---- MD5 | 39 ++++++++++++++++++++------------------- NEWS.md | 9 +++++++++ R/gcm.R | 10 +++++++++- R/gompertz.R | 10 +++++++++- R/gompertzo.R | 10 +++++++++- R/na_omit.R |only R/richards.R | 10 +++++++++- R/richardso.R | 10 +++++++++- R/schnute3.R | 10 +++++++++- R/vonbert.R | 10 +++++++++- R/vonberto.R | 10 +++++++++- build/partial.rdb |binary man/gcm.Rd | 5 ++++- man/gompertz.Rd | 5 ++++- man/gompertzo.Rd | 5 ++++- man/richards.Rd | 5 ++++- man/richardso.Rd | 5 ++++- man/schnute3.Rd | 5 ++++- man/vonbert.Rd | 5 ++++- man/vonberto.Rd | 5 ++++- 21 files changed, 137 insertions(+), 39 deletions(-)
Title: Spatial Projection of Network Signals along Geodesic Paths
Description: For a given graph containing vertices, edges, and a signal associated with the vertices, the 'PathwaySpace' package performs a convolution operation, which involves a weighted combination of neighboring vertices and their associated signals. The package then uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' could have various applications, such as visualizing network data in a graphical format that highlights the relationships and signal strengths between vertices. It can be particularly useful for understanding the influence of signals through complex networks. By combining graph theory, signal processing, and visualization, the 'PathwaySpace' package provides a novel way of representing graph data.
Author: Victor Apolonio [ctb],
Vinicius Chagas [ctb],
Sysbiolab and Collaborators [fnd],
Mauro Castro [aut, cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between PathwaySpace versions 1.0.2 dated 2025-07-27 and 1.1.0 dated 2025-11-06
PathwaySpace-1.0.2/PathwaySpace/vignettes/figures/fig10.png |only PathwaySpace-1.0.2/PathwaySpace/vignettes/figures/fig11.png |only PathwaySpace-1.0.2/PathwaySpace/vignettes/figures/fig12.png |only PathwaySpace-1.0.2/PathwaySpace/vignettes/figures/fig13.png |only PathwaySpace-1.0.2/PathwaySpace/vignettes/figures/fig9.png |only PathwaySpace-1.1.0/PathwaySpace/DESCRIPTION | 28 PathwaySpace-1.1.0/PathwaySpace/MD5 | 88 - PathwaySpace-1.1.0/PathwaySpace/NAMESPACE | 6 PathwaySpace-1.1.0/PathwaySpace/R/pspaceChecks.R | 235 +-- PathwaySpace-1.1.0/PathwaySpace/R/pspaceClasses.R | 4 PathwaySpace-1.1.0/PathwaySpace/R/pspaceDecay.R | 616 +++++++--- PathwaySpace-1.1.0/PathwaySpace/R/pspaceGenerics.R | 8 PathwaySpace-1.1.0/PathwaySpace/R/pspaceMethods.R | 300 ++-- PathwaySpace-1.1.0/PathwaySpace/R/pspaceMisc.R | 13 PathwaySpace-1.1.0/PathwaySpace/R/pspacePlots.R | 108 - PathwaySpace-1.1.0/PathwaySpace/R/pspaceSupplements.R | 590 ++++++--- PathwaySpace-1.1.0/PathwaySpace/R/pspaceWatershed.R | 8 PathwaySpace-1.1.0/PathwaySpace/build/partial.rdb |binary PathwaySpace-1.1.0/PathwaySpace/build/vignette.rds |binary PathwaySpace-1.1.0/PathwaySpace/inst/doc/PathwaySpace.R | 121 - PathwaySpace-1.1.0/PathwaySpace/inst/doc/PathwaySpace.Rmd | 340 +---- PathwaySpace-1.1.0/PathwaySpace/inst/doc/PathwaySpace.html | 462 ++----- PathwaySpace-1.1.0/PathwaySpace/man/PathwaySpace-class.Rd | 2 PathwaySpace-1.1.0/PathwaySpace/man/PathwaySpace-package.Rd | 1 PathwaySpace-1.1.0/PathwaySpace/man/buildPathwaySpace.Rd | 16 PathwaySpace-1.1.0/PathwaySpace/man/circularProjection-methods.Rd | 52 PathwaySpace-1.1.0/PathwaySpace/man/expDecay.Rd | 66 - PathwaySpace-1.1.0/PathwaySpace/man/getPathwaySpace-methods.Rd | 2 PathwaySpace-1.1.0/PathwaySpace/man/linearDecay.Rd | 66 - PathwaySpace-1.1.0/PathwaySpace/man/plotPathwaySpace-methods.Rd | 6 PathwaySpace-1.1.0/PathwaySpace/man/polarDecay.Rd |only PathwaySpace-1.1.0/PathwaySpace/man/polarProjection-methods.Rd | 77 - PathwaySpace-1.1.0/PathwaySpace/man/signalAggregation.Rd | 13 PathwaySpace-1.1.0/PathwaySpace/man/signalDecay.Rd | 32 PathwaySpace-1.1.0/PathwaySpace/man/silhouetteMapping-methods.Rd | 24 PathwaySpace-1.1.0/PathwaySpace/man/summitMapping-methods.Rd | 4 PathwaySpace-1.1.0/PathwaySpace/man/summitWatershed.Rd | 2 PathwaySpace-1.1.0/PathwaySpace/man/vertexSignal-accessors.Rd | 6 PathwaySpace-1.1.0/PathwaySpace/man/weibullDecay.Rd | 76 - PathwaySpace-1.1.0/PathwaySpace/vignettes/PathwaySpace.Rmd | 340 +---- PathwaySpace-1.1.0/PathwaySpace/vignettes/bibliography.bib | 21 PathwaySpace-1.1.0/PathwaySpace/vignettes/figures/fig1.png |binary PathwaySpace-1.1.0/PathwaySpace/vignettes/figures/fig3.png |binary PathwaySpace-1.1.0/PathwaySpace/vignettes/figures/fig4.png |binary PathwaySpace-1.1.0/PathwaySpace/vignettes/figures/fig5.png |binary PathwaySpace-1.1.0/PathwaySpace/vignettes/figures/fig6.png |binary PathwaySpace-1.1.0/PathwaySpace/vignettes/figures/fig7.png |binary PathwaySpace-1.1.0/PathwaySpace/vignettes/figures/fig8.png |binary 48 files changed, 1848 insertions(+), 1885 deletions(-)
Title: Analyze Mathematical Models of Healthcare Facility Transmission
Description: Calculate useful quantities for a user-defined differential equation
model of infectious disease transmission among individuals in a healthcare
facility. Input rates of transition between states of individuals with and
without the disease-causing organism, distributions of states at facility
admission, relative infectivity of transmissible states, and the facility length
of stay distribution. Calculate the model equilibrium and the basic facility
reproduction number, as described in Toth et al. (2025)
<doi:10.1371/journal.pcbi.1013577>.
Author: Damon Toth [aut, cre, cph] ,
Centers for Disease Control and Prevention [fnd]
Maintainer: Damon Toth <damon.toth@hsc.utah.edu>
Diff between facilityepimath versions 0.1.0 dated 2025-03-07 and 0.2.1 dated 2025-11-06
facilityepimath-0.1.0/facilityepimath/inst/figure1results.R |only facilityepimath-0.1.0/facilityepimath/inst/figure2results.R |only facilityepimath-0.1.0/facilityepimath/inst/table3and4results.R |only facilityepimath-0.2.1/facilityepimath/DESCRIPTION | 16 +-- facilityepimath-0.2.1/facilityepimath/MD5 | 21 ++- facilityepimath-0.2.1/facilityepimath/NEWS.md | 10 + facilityepimath-0.2.1/facilityepimath/README.md | 53 +++++----- facilityepimath-0.2.1/facilityepimath/build/vignette.rds |binary facilityepimath-0.2.1/facilityepimath/inst/Toth2025figure1.R |only facilityepimath-0.2.1/facilityepimath/inst/Toth2025figure2.R |only facilityepimath-0.2.1/facilityepimath/inst/Toth2025figure3.R |only facilityepimath-0.2.1/facilityepimath/inst/Toth2025table3and4.R |only facilityepimath-0.2.1/facilityepimath/inst/doc/equilibrium-and-R0.Rmd | 6 - facilityepimath-0.2.1/facilityepimath/inst/doc/equilibrium-and-R0.html | 15 +- facilityepimath-0.2.1/facilityepimath/vignettes/equilibrium-and-R0.Rmd | 6 - 15 files changed, 73 insertions(+), 54 deletions(-)
More information about facilityepimath at CRAN
Permanent link
Title: Functions to Scrape Rugby Data
Description: Provides a set of functions to scrape and analyze rugby data.
Supports competitions including the National Rugby League, New South Wales Cup,
Queensland Cup, Super League, and various representative and women's competitions.
Includes functions to fetch player statistics, match results, ladders, venues, and coaching data.
Designed to assist analysts, fans, and researchers in exploring historical and current rugby league data.
See Woods et al. (2017) <doi:10.1123/ijspp.2016-0187> for an example of rugby league performance analysis methodology.
Author: Daniel Tomaro [aut, cre]
Maintainer: Daniel Tomaro <danieltomaro@icloud.com>
Diff between nrlR versions 0.1.1 dated 2025-09-01 and 0.1.2 dated 2025-11-06
DESCRIPTION | 8 ++++-- MD5 | 6 ++--- NEWS.md | 66 ++++++++++++++++++++++++------------------------------- R/fetch_lineup.R | 56 +++++++++++++++++++++++++--------------------- 4 files changed, 67 insertions(+), 69 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.8.1 dated 2025-08-25 and 0.8.2 dated 2025-11-06
vcfppR-0.8.1/vcfppR/src/htslib-1.21/htslib-uninstalled.pc |only vcfppR-0.8.1/vcfppR/src/htslib-1.21/htslib_static.mk |only vcfppR-0.8.2/vcfppR/DESCRIPTION | 6 vcfppR-0.8.2/vcfppR/MD5 | 44 + vcfppR-0.8.2/vcfppR/NAMESPACE | 1 vcfppR-0.8.2/vcfppR/NEWS.md | 6 vcfppR-0.8.2/vcfppR/R/vcf-compare.R | 157 +++++- vcfppR-0.8.2/vcfppR/R/vcf-plot.R | 49 +- vcfppR-0.8.2/vcfppR/R/vcf-tables.R | 95 ++++ vcfppR-0.8.2/vcfppR/README.md | 35 + vcfppR-0.8.2/vcfppR/build/vignette.rds |binary vcfppR-0.8.2/vcfppR/inst/doc/concordance-of-two-vcf-files.html | 226 +++++----- vcfppR-0.8.2/vcfppR/inst/extdata/imputed.gt.vcf.gz.tbi |only vcfppR-0.8.2/vcfppR/inst/extdata/platinum.sv.vcf.gz |only vcfppR-0.8.2/vcfppR/inst/extdata/platinum.sv.vcf.gz.tbi |only vcfppR-0.8.2/vcfppR/inst/extdata/svupp.call.vcf.gz |only vcfppR-0.8.2/vcfppR/inst/extdata/svupp.call.vcf.gz.tbi |only vcfppR-0.8.2/vcfppR/man/figures/README-gtgq-1.png |only vcfppR-0.8.2/vcfppR/man/subset.vcftable.Rd |only vcfppR-0.8.2/vcfppR/man/vcfcomp.Rd | 62 +- vcfppR-0.8.2/vcfppR/man/vcfplot.Rd | 11 vcfppR-0.8.2/vcfppR/src/htslib-1.21/config.mk | 24 - vcfppR-0.8.2/vcfppR/src/htslib-1.21/config.status | 93 +--- vcfppR-0.8.2/vcfppR/src/htslib-1.21/htslib.pc.tmp | 8 vcfppR-0.8.2/vcfppR/tests/testthat/test-vcf-comp.R | 209 +++++++++ vcfppR-0.8.2/vcfppR/tests/testthat/test-vcf-errors.R |only vcfppR-0.8.2/vcfppR/tests/testthat/test-vcf-plot.R |only vcfppR-0.8.2/vcfppR/tests/testthat/test-vcf-subset.R |only vcfppR-0.8.2/vcfppR/tests/testthat/test-vcf-table.R | 222 +++++++++ 29 files changed, 1003 insertions(+), 245 deletions(-)
Title: Estimating Hidden Population Size using Respondent Driven
Sampling Data
Description: Estimate the size of a networked population based on
respondent-driven sampling data. The package is part of the "RDS Analyst"
suite of packages for the analysis of respondent-driven sampling data.
See Handcock, Gile and Mar (2014) <doi:10.1214/14-EJS923>,
Handcock, Gile and Mar (2015) <doi:10.1111/biom.12255>,
Kim and Handcock (2021) <doi:10.1093/jssam/smz055>, and
McLaughlin, et. al. (2023) <doi:10.1214/23-AOAS1807>.
Author: Mark S. Handcock [aut, cre, cph] ,
Krista J. Gile [aut, cph],
Brian Kim [ctb],
Katherine R. McLaughlin [ctb]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between sspse versions 1.1.0-3 dated 2025-11-04 and 1.1.0-4 dated 2025-11-06
DESCRIPTION | 8 +++---- MD5 | 20 +++++++++---------- R/impute.visibility.R | 8 +++++-- R/plot.sspse.R | 5 ++-- R/poscmpwp.R | 1 R/posteriorsize.R | 48 ++++++++++++++++++++++++++++------------------- build/partial.rdb |binary man/impute.visibility.Rd | 6 +++++ man/posize_warning.Rd | 14 ------------- man/posteriorsize.Rd | 10 ++++----- src/posteriorcmpwpvis.c | 21 +++++++++++++++----- 11 files changed, 81 insertions(+), 60 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.1.1 dated 2025-10-27 and 1.3.0 dated 2025-11-06
DESCRIPTION | 12 ++-- MD5 | 26 ++++----- R/SEQopts.R | 9 ++- R/class_definitions.R | 4 + R/class_setters.R | 4 + R/internal_covariates.R | 4 + R/internal_hazard.R | 9 ++- R/internal_survival.R | 20 +++++-- build/vignette.rds |binary man/SEQopts.Rd | 6 ++ tests/testthat/test_coefficients.R | 97 +++++++++++++++++-------------------- tests/testthat/test_covariates.R | 15 ++--- tests/testthat/test_misc.R | 8 +++ tests/testthat/test_multinomial.R | 50 ++++++++----------- 14 files changed, 147 insertions(+), 117 deletions(-)
Title: Post-Estimation Functions for Generalized Linear Mixed Models
Description: Several functions for working with mixed effects regression models for limited dependent variables. The functions facilitate post-estimation of model predictions or margins, and comparisons between model predictions for assessing or probing moderation. Additional helper functions facilitate model comparisons and implements simulation-based inference for model predictions of alternative-specific outcome models. See also, Melamed and Doan (2024, ISBN: 978-1032509518).
Author: David Melamed [aut, cre]
Maintainer: David Melamed <dmmelamed@gmail.com>
This is a re-admission after prior archival of version 1.2.2 dated 2024-09-04
Diff between catregs versions 1.2.2 dated 2024-09-04 and 1.2.4 dated 2025-11-06
DESCRIPTION | 9 +++++---- MD5 | 32 ++++++++++++++++---------------- R/functions.R | 8 ++++---- build/vignette.rds |binary inst/doc/compare.margins.R | 8 ++++++-- inst/doc/compare.margins.Rmd | 8 ++++++-- inst/doc/compare.margins.html | 23 +++++++++++------------ inst/doc/count.fit.html | 5 +++-- inst/doc/daign.html | 5 +++-- inst/doc/first.diff.fitted.html | 5 +++-- inst/doc/list.coef.html | 5 +++-- inst/doc/margins.dat.clogit.html | 11 ++++++----- inst/doc/margins.dat.html | 5 +++-- inst/doc/margins.des.html | 5 +++-- inst/doc/second.diff.fitted.html | 5 +++-- man/compare.margins.Rd | 11 +++++++---- vignettes/compare.margins.Rmd | 8 ++++++-- 17 files changed, 88 insertions(+), 65 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-01 0.5.0
2022-10-03 0.4.1
2022-08-29 0.4.0
2022-08-20 0.3.3
2021-09-05 0.3.2
2021-05-21 0.3.1
2021-04-21 0.3.0
Title: Build Species Distribution Modeling using 'caret'
Description: Use machine learning algorithms and advanced geographic information system tools to
build Species Distribution Modeling in a extensible and modern fashion.
Author: Dayani Bailly [aut] ,
Edivando Couto [aut] ,
Jose Hilario Delconte Ferreira [aut] ,
Marcos R. Lima [aut] ,
Reginaldo Re [aut] ,
Valeria Batista [aut] ,
Luiz Fernando Esser [aut, cre, cph]
Maintainer: Luiz Fernando Esser <luizesser@gmail.com>
Diff between caretSDM versions 1.1.4 dated 2025-08-29 and 1.2.3 dated 2025-11-06
DESCRIPTION | 17 MD5 | 67 - NAMESPACE | 16 NEWS.md | 21 R/add_predictors.R | 3 R/add_scenarios.R | 76 + R/change_sdm.r |only R/correlate_sdm.r |only R/gcms_ensembles.R | 5 R/generated-globals.R | 2 R/mahal.dist.R | 97 +- R/maxent.R | 300 +++++-- R/plot.R | 102 +- R/predict_sdm.R | 2 R/pseudoabsences.R | 147 +-- R/sdm_area.R | 63 - R/summary_sdm.R | 99 +- R/tidyverse.R | 8 R/train_sdm.R | 92 +- R/tuneGrid_sdm.r |only R/use_mem.R | 2 man/correlate_sdm.Rd |only man/gcms_ensembles.Rd | 2 man/plot_occurrences.Rd | 5 man/prediction_change_sdm.Rd |only man/pseudoabsences.Rd | 18 man/train_sdm.Rd | 7 man/tuneGrid_sdm.Rd |only man/use_mem.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/_snaps/predict_sdm.md | 234 +++-- tests/testthat/_snaps/sdm_area.md | 2 tests/testthat/_snaps/train_sdm.md | 1372 ++++------------------------------- tests/testthat/test-add_predictors.R | 2 tests/testthat/test-add_scenarios.R | 51 - tests/testthat/test-data_clean.R | 3 tests/testthat/test-plot.R | 10 tests/testthat/test-train_sdm.R | 45 - 38 files changed, 1110 insertions(+), 1762 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.6 dated 2025-10-08 and 0.1.8 dated 2025-11-06
xtdml-0.1.6/xtdml/README.md |only xtdml-0.1.8/xtdml/DESCRIPTION | 18 xtdml-0.1.8/xtdml/MD5 | 27 xtdml-0.1.8/xtdml/NAMESPACE | 1 xtdml-0.1.8/xtdml/R/dataset.R | 4 xtdml-0.1.8/xtdml/R/helper.R | 907 +++++++++----------- xtdml-0.1.8/xtdml/R/xtdml_data.R | 164 ++- xtdml-0.1.8/xtdml/R/xtdml_main.R | 145 +-- xtdml-0.1.8/xtdml/R/xtdml_plr.R | 127 -- xtdml-0.1.8/xtdml/R/zzz.R | 38 xtdml-0.1.8/xtdml/man/make_plpr_data.Rd | 4 xtdml-0.1.8/xtdml/man/xtdml.Rd | 120 +- xtdml-0.1.8/xtdml/man/xtdml_data.Rd | 16 xtdml-0.1.8/xtdml/man/xtdml_data_from_data_frame.Rd | 17 xtdml-0.1.8/xtdml/man/xtdml_plr.Rd | 166 --- 15 files changed, 869 insertions(+), 885 deletions(-)
Title: Reference Interval Estimation using Real-World Data
Description: Indirect method for the estimation of reference intervals (RIs)
using Real-World Data ('RWD') and methods for comparing and verifying RIs.
Estimates RIs by applying advanced statistical methods to routine
diagnostic test measurements, which include both pathological and
non-pathological samples, to model the distribution of non-pathological
samples. This distribution is then used to derive reference intervals
and support RI verification, i.e., deciding if a specific RI is suitable
for the local population. The package also provides functions for
printing and plotting algorithm results. See ?refineR for a detailed
description of features. Version 1.0 of the algorithm is described in
'Ammer et al. (2021)' <doi:10.1038/s41598-021-95301-2>. Additional
guidance is in 'Ammer et al. (2023)' <doi:10.1093/jalm/jfac101>. The
verification method is described in 'Beck et al. (2025)'
<doi:10.1515/cclm-2025-0728>.
Author: Matthias Beck [aut, cre] ,
Tatjana Ammer [aut] ,
Christopher M Rank [aut],
Andre Schuetzenmeister [aut]
Maintainer: Matthias Beck <matthias.beck.mb1@roche.com>
Diff between refineR versions 1.6.2 dated 2024-08-21 and 2.0.0 dated 2025-11-06
DESCRIPTION | 53 + MD5 | 95 ++- NAMESPACE | 4 NEWS.md | 13 R/plot.R | 850 ++++++++++++++++---------------- R/utils.R | 768 +++++++++++++++++----------- R/utilsRIVerification.R |only build/partial.rdb |only build/vignette.rds |binary inst/doc/refineR_package.R | 4 inst/doc/refineR_package.Rmd | 17 inst/doc/refineR_package.html | 116 ++-- inst/doc/verification.R |only inst/doc/verification.html |only inst/doc/verification.rmd |only man/BoxCox.Rd | 44 - man/addGrid.Rd | 54 +- man/alignVec.Rd |only man/as.rgb.Rd | 74 +- man/ashDensity.Rd | 60 +- man/calculateCostHist.Rd | 80 +-- man/cdfTruncatedBoxCox.Rd |only man/checkInvalidArgs.Rd |only man/createVerificationTab.Rd |only man/defineSearchRegions.Rd | 56 +- man/estimateAB.Rd | 42 - man/findMainPeak.Rd | 58 +- man/findPeaksAndValleys.Rd | 40 - man/findRI.Rd | 142 ++--- man/findRoundingBase.Rd | 40 - man/generateHistData.Rd | 48 - man/getEquivalenceLimits.Rd |only man/getRI.Rd | 79 +- man/getRIMargins.Rd |only man/getRISimilarity.Rd |only man/getRIfromRWDRI.Rd |only man/getSumForPArea.Rd | 86 +-- man/getVerificationArgs.Rd |only man/invBoxCox.Rd | 44 - man/optimizeGrid.Rd | 54 +- man/perc_ci_asymptotic.Rd |only man/plot.RWDRI.Rd | 152 +++-- man/plotRIVerification.Rd |only man/pnormApprox.Rd | 56 +- man/print.RWDRI.Rd | 85 +-- man/printDataFractionWithinOutsideRI.Rd |only man/printSimilarityTable.Rd |only man/printTableHeader.Rd |only man/printTableRows.Rd |only man/printVerificationTable.Rd |only man/refineR-Package.Rd | 24 man/testParam.Rd | 88 +-- man/testcase1.Rd | 34 - man/testcase2.Rd | 34 - man/testcase3.Rd | 34 - man/testcase4.Rd | 34 - man/testcase5.Rd | 34 - man/verifyRI.Rd |only vignettes/refineR_package.Rmd | 17 vignettes/verification.rmd |only 60 files changed, 1914 insertions(+), 1599 deletions(-)
Title: A Fast Permutation-Based Split-Half Reliability Algorithm
Description: Accurately estimates the reliability of cognitive tasks using a fast and flexible permutation-based split-half reliability algorithm that supports stratified splitting while maintaining equal split sizes. See Kahveci, Bathke, and Blechert (2025) <doi:10.3758/s13423-024-02597-y> for details.
Author: Sercan Kahveci [aut, cre]
Maintainer: Sercan Kahveci <sercan.kahveci@plus.ac.at>
Diff between rapidsplithalf versions 0.4 dated 2025-01-28 and 0.5 dated 2025-11-06
DESCRIPTION | 13 +- MD5 | 36 ++--- NAMESPACE | 13 -- R/data.R | 4 R/helpers.R | 99 ++++++++++------ R/rapidsplit.R | 235 ++++++++++++++++++++------------------ R/spearmanbrown.R | 2 R/zzz.R | 11 + inst/doc/rapidsplithalf.Rmd | 4 inst/doc/rapidsplithalf.html | 36 ++--- man/figures/README-iatrel-1.png |binary man/figures/README-plotter-1.png |binary man/figures/README-plotter2-1.png |binary man/foodAAT.Rd | 2 man/raceIAT.Rd | 2 man/rapidsplit.Rd | 41 +++--- man/rapidsplithalf.Rd | 4 src/corByColumns.cpp | 10 + vignettes/rapidsplithalf.Rmd | 4 19 files changed, 284 insertions(+), 232 deletions(-)
More information about rapidsplithalf at CRAN
Permanent link
Title: Statistical Methods for Survival Data with Dependent Censoring
Description: Several statistical methods for analyzing survival data under various forms of dependent
censoring are implemented in the package. In addition to accounting for dependent censoring, it
offers tools to adjust for unmeasured confounding factors. The implemented approaches allow
users to estimate the dependency between survival time and dependent censoring time, based
solely on observed survival data. For more details on the methods, refer to Deresa and Van
Keilegom (2021) <doi:10.1093/biomet/asaa095>, Czado and Van Keilegom (2023)
<doi:10.1093/biomet/asac067>, Crommen et al. (2024) <doi:10.1007/s11749-023-00903-9>,
Deresa and Van Keilegom (2024) <doi:10.1080/01621459.2022.2161387>, Willems et al. (2025)
<doi:10.48550/arXiv.2403.11860>, Ding and Van Keilegom (2025) and D'Haen et al. (2025)
<doi:10.1007/s10985-025-09647-0>.
Author: Ilias Willems [aut] ,
Gilles Crommen [aut] ,
Negera Wakgari Deresa [aut, cre] ,
Jie Ding [aut] ,
Claudia Czado [aut] ,
Myrthe D'Haen [aut] ,
Ingrid Van Keilegom [aut]
Maintainer: Negera Wakgari Deresa <negera.deresa@gmail.com>
Diff between depCensoring versions 0.1.7 dated 2025-03-11 and 0.1.8 dated 2025-11-06
depCensoring-0.1.7/depCensoring/man/A_step.Rd |only depCensoring-0.1.7/depCensoring/man/Bspline.unit.interval.Rd |only depCensoring-0.1.7/depCensoring/man/CompC.Rd |only depCensoring-0.1.7/depCensoring/man/D.hat.Rd |only depCensoring-0.1.7/depCensoring/man/DYJtrans.Rd |only depCensoring-0.1.7/depCensoring/man/EAM.Rd |only depCensoring-0.1.7/depCensoring/man/EAM.converged.Rd |only depCensoring-0.1.7/depCensoring/man/EI.Rd |only depCensoring-0.1.7/depCensoring/man/E_step.Rd |only depCensoring-0.1.7/depCensoring/man/G.box.Rd |only depCensoring-0.1.7/depCensoring/man/G.cd.Rd |only depCensoring-0.1.7/depCensoring/man/G.cd.mc.Rd |only depCensoring-0.1.7/depCensoring/man/G.hat.Rd |only depCensoring-0.1.7/depCensoring/man/G.spline.Rd |only depCensoring-0.1.7/depCensoring/man/IYJtrans.Rd |only depCensoring-0.1.7/depCensoring/man/Lambda_AFT_ll.Rd |only depCensoring-0.1.7/depCensoring/man/Lambda_Cox_wb.Rd |only depCensoring-0.1.7/depCensoring/man/Lambda_inverse_AFT_ll.Rd |only depCensoring-0.1.7/depCensoring/man/Lambda_inverse_Cox_wb.Rd |only depCensoring-0.1.7/depCensoring/man/LikCopInd.Rd |only depCensoring-0.1.7/depCensoring/man/LikF.cmprsk.Rd |only depCensoring-0.1.7/depCensoring/man/LikGamma1.Rd |only depCensoring-0.1.7/depCensoring/man/LikGamma2.Rd |only depCensoring-0.1.7/depCensoring/man/LikI.bis.Rd |only depCensoring-0.1.7/depCensoring/man/LikI.cmprsk.Cholesky.Rd |only depCensoring-0.1.7/depCensoring/man/LikI.cmprsk.Rd |only depCensoring-0.1.7/depCensoring/man/Longfun.Rd |only depCensoring-0.1.7/depCensoring/man/MSpoint.Rd |only depCensoring-0.1.7/depCensoring/man/M_step.Rd |only depCensoring-0.1.7/depCensoring/man/Omega.hat.Rd |only depCensoring-0.1.7/depCensoring/man/PseudoL.Rd |only depCensoring-0.1.7/depCensoring/man/S.func.Rd |only depCensoring-0.1.7/depCensoring/man/Sigma.hat.Rd |only depCensoring-0.1.7/depCensoring/man/YJtrans.Rd |only depCensoring-0.1.7/depCensoring/man/boot.fun.Rd |only depCensoring-0.1.7/depCensoring/man/boot.funI.Rd |only depCensoring-0.1.7/depCensoring/man/cbMV.Rd |only depCensoring-0.1.7/depCensoring/man/check.args.pisurv.Rd |only depCensoring-0.1.7/depCensoring/man/chol2par.Rd |only depCensoring-0.1.7/depCensoring/man/chol2par.elem.Rd |only depCensoring-0.1.7/depCensoring/man/clear.plt.wdw.Rd |only depCensoring-0.1.7/depCensoring/man/cr.lik.Rd |only depCensoring-0.1.7/depCensoring/man/dD.hat.Rd |only depCensoring-0.1.7/depCensoring/man/dLambda_AFT_ll.Rd |only depCensoring-0.1.7/depCensoring/man/dLambda_Cox_wb.Rd |only depCensoring-0.1.7/depCensoring/man/dat.sim.reg.comp.risks.Rd |only depCensoring-0.1.7/depCensoring/man/dchol2par.Rd |only depCensoring-0.1.7/depCensoring/man/dchol2par.elem.Rd |only depCensoring-0.1.7/depCensoring/man/dm.bar.Rd |only depCensoring-0.1.7/depCensoring/man/do.optimization.Mstep.Rd |only depCensoring-0.1.7/depCensoring/man/draw.sv.init.Rd |only depCensoring-0.1.7/depCensoring/man/estimate.cf.Rd |only depCensoring-0.1.7/depCensoring/man/feasible_point_search.Rd |only depCensoring-0.1.7/depCensoring/man/get.anchor.points.Rd |only depCensoring-0.1.7/depCensoring/man/get.cond.moment.evals.Rd |only depCensoring-0.1.7/depCensoring/man/get.cvLLn.Rd |only depCensoring-0.1.7/depCensoring/man/get.deriv.mom.func.Rd |only depCensoring-0.1.7/depCensoring/man/get.dmi.tens.Rd |only depCensoring-0.1.7/depCensoring/man/get.extra.Estep.points.Rd |only depCensoring-0.1.7/depCensoring/man/get.instrumental.function.evals.Rd |only depCensoring-0.1.7/depCensoring/man/get.mi.mat.Rd |only depCensoring-0.1.7/depCensoring/man/get.next.point.Rd |only depCensoring-0.1.7/depCensoring/man/get.starting.values.Rd |only depCensoring-0.1.7/depCensoring/man/get.test.statistic.Rd |only depCensoring-0.1.7/depCensoring/man/gridSearch.Rd |only depCensoring-0.1.7/depCensoring/man/gs.algo.bidir.Rd |only depCensoring-0.1.7/depCensoring/man/gs.binary.Rd |only depCensoring-0.1.7/depCensoring/man/gs.interpolation.Rd |only depCensoring-0.1.7/depCensoring/man/gs.regular.Rd |only depCensoring-0.1.7/depCensoring/man/insert.row.Rd |only depCensoring-0.1.7/depCensoring/man/lf.delta.beta1.Rd |only depCensoring-0.1.7/depCensoring/man/lf.ts.Rd |only depCensoring-0.1.7/depCensoring/man/likF.cmprsk.Cholesky.Rd |only depCensoring-0.1.7/depCensoring/man/likIFG.cmprsk.Cholesky.Rd |only depCensoring-0.1.7/depCensoring/man/log_transform.Rd |only depCensoring-0.1.7/depCensoring/man/m.bar.Rd |only depCensoring-0.1.7/depCensoring/man/normalize.covariates.Rd |only depCensoring-0.1.7/depCensoring/man/normalize.covariates2.Rd |only depCensoring-0.1.7/depCensoring/man/plot_addpte.Rd |only depCensoring-0.1.7/depCensoring/man/plot_addpte.eval.Rd |only depCensoring-0.1.7/depCensoring/man/plot_base.Rd |only depCensoring-0.1.7/depCensoring/man/power_transform.Rd |only depCensoring-0.1.7/depCensoring/man/set.EAM.hyperparameters.Rd |only depCensoring-0.1.7/depCensoring/man/set.GS.hyperparameters.Rd |only depCensoring-0.1.7/depCensoring/man/set.hyperparameters.Rd |only depCensoring-0.1.7/depCensoring/man/test.point_Bei.Rd |only depCensoring-0.1.7/depCensoring/man/test.point_Bei_MT.Rd |only depCensoring-0.1.7/depCensoring/man/uniformize.data.Rd |only depCensoring-0.1.7/depCensoring/man/variance.cmprsk.Rd |only depCensoring-0.1.8/depCensoring/DESCRIPTION | 38 - depCensoring-0.1.8/depCensoring/MD5 | 122 --- depCensoring-0.1.8/depCensoring/NAMESPACE | 4 depCensoring-0.1.8/depCensoring/R/BoundingCovariateEffects.R | 349 +++++++--- depCensoring-0.1.8/depCensoring/R/CopulaBasedCoxPH_pseudoLikelihoodFunctions.R | 27 depCensoring-0.1.8/depCensoring/R/CopulaCoxPHmodel_BootstrapMethods.R | 13 depCensoring-0.1.8/depCensoring/R/ParamTransfoCompRisks.R | 111 +-- depCensoring-0.1.8/depCensoring/R/QRdepcens.R |only depCensoring-0.1.8/depCensoring/R/SemiParametricCopulawithoutCovariates.R | 8 depCensoring-0.1.8/depCensoring/R/data.R |only depCensoring-0.1.8/depCensoring/R/dataGeneratingFunction.R | 2 depCensoring-0.1.8/depCensoring/R/preconditionChecks.R | 90 +- depCensoring-0.1.8/depCensoring/R/yeo-johnsonTransformation.R | 106 +-- depCensoring-0.1.8/depCensoring/data |only depCensoring-0.1.8/depCensoring/man/Distance.Rd | 7 depCensoring-0.1.8/depCensoring/man/QRdepCens.Rd |only depCensoring-0.1.8/depCensoring/man/SurvDC.Rd | 8 depCensoring-0.1.8/depCensoring/man/estimate.cmprsk.Rd | 6 depCensoring-0.1.8/depCensoring/man/liver.Rd |only depCensoring-0.1.8/depCensoring/man/pi.surv.Rd | 99 ++ 109 files changed, 599 insertions(+), 391 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.4 dated 2025-10-22 and 1.4.1 dated 2025-11-06
BAwiR-1.4.1/BAwiR/DESCRIPTION | 13 +- BAwiR-1.4.1/BAwiR/MD5 | 66 ++++++----- BAwiR-1.4.1/BAwiR/NAMESPACE | 14 ++ BAwiR-1.4.1/BAwiR/NEWS | 4 BAwiR-1.4.1/BAwiR/R/do_OE.R | 2 BAwiR-1.4.1/BAwiR/R/do_four_factors_df.R | 51 ++++++-- BAwiR-1.4.1/BAwiR/R/do_lineup.R | 5 BAwiR-1.4.1/BAwiR/R/do_possession.R | 22 ++- BAwiR-1.4.1/BAwiR/R/do_prepare_data_or.R | 2 BAwiR-1.4.1/BAwiR/R/do_prepare_data_to.R | 28 +++- BAwiR-1.4.1/BAwiR/R/do_preproc_period.R | 2 BAwiR-1.4.1/BAwiR/R/do_time_out_success.R | 7 - BAwiR-1.4.1/BAwiR/R/do_time_out_success_altern.R |only BAwiR-1.4.1/BAwiR/R/do_usage.R | 102 ++++++++++------- BAwiR-1.4.1/BAwiR/R/do_viz_shots_gradient.R | 22 +++ BAwiR-1.4.1/BAwiR/R/do_viz_shots_scatter.R | 30 ++++- BAwiR-1.4.1/BAwiR/R/get_donut_usage.R |only BAwiR-1.4.1/BAwiR/R/get_donut_usage_action.R |only BAwiR-1.4.1/BAwiR/R/get_roster_age_profile.R |only BAwiR-1.4.1/BAwiR/data/acb_age_profile_data_2526.RData |only BAwiR-1.4.1/BAwiR/data/acb_usage_act_data_2526.RData |only BAwiR-1.4.1/BAwiR/data/acb_usage_data_2526.RData |only BAwiR-1.4.1/BAwiR/inst/doc/BAwiR.R | 11 + BAwiR-1.4.1/BAwiR/inst/doc/BAwiR.Rmd | 11 + BAwiR-1.4.1/BAwiR/inst/doc/BAwiR.html | 87 ++++++++------ BAwiR-1.4.1/BAwiR/inst/doc/BAwiR_pbp.html | 4 BAwiR-1.4.1/BAwiR/inst/doc/BAwiR_sc.html | 4 BAwiR-1.4.1/BAwiR/man/acb_age_profile_data_2526.Rd |only BAwiR-1.4.1/BAwiR/man/acb_usage_act_data_2526.Rd |only BAwiR-1.4.1/BAwiR/man/acb_usage_data_2526.Rd |only BAwiR-1.4.1/BAwiR/man/do_OE.Rd | 2 BAwiR-1.4.1/BAwiR/man/do_four_factors_df.Rd | 12 +- BAwiR-1.4.1/BAwiR/man/do_prepare_data_to.Rd | 2 BAwiR-1.4.1/BAwiR/man/do_time_out_success_altern.Rd |only BAwiR-1.4.1/BAwiR/man/do_viz_shots_gradient.Rd | 4 BAwiR-1.4.1/BAwiR/man/do_viz_shots_scatter.Rd | 8 + BAwiR-1.4.1/BAwiR/man/get_donut_usage.Rd |only BAwiR-1.4.1/BAwiR/man/get_donut_usage_action.Rd |only BAwiR-1.4.1/BAwiR/man/get_roster_age_profile.Rd |only BAwiR-1.4.1/BAwiR/vignettes/BAwiR.Rmd | 11 + BAwiR-1.4/BAwiR/build/partial.rdb |only BAwiR-1.4/BAwiR/man/BAwiR-package.Rd |only 42 files changed, 357 insertions(+), 169 deletions(-)
Title: Nonparametric Bootstrap Test for Regression Monotonicity
Description: Implements nonparametric bootstrap tests for detecting monotonicity
in regression functions from Hall, P. and Heckman, N. (2000) <doi:10.1214/aos/1016120363>
Includes tools for visualizing results using Nadaraya-Watson kernel regression and supports
efficient computation with 'C++'. Tutorials and shiny application demo are
available at <https://www.laylaparast.com/monotonicitytest> and <https://parastlab.shinyapps.io/MonotonicityTest>.
Author: Dylan Huynh [aut, cre]
Maintainer: Dylan Huynh <dylanhuynh@utexas.edu>
Diff between MonotonicityTest versions 1.2 dated 2025-04-24 and 1.3 dated 2025-11-06
MonotonicityTest-1.2/MonotonicityTest/R/main.R |only MonotonicityTest-1.3/MonotonicityTest/DESCRIPTION | 11 MonotonicityTest-1.3/MonotonicityTest/MD5 | 26 +- MonotonicityTest-1.3/MonotonicityTest/NAMESPACE | 5 MonotonicityTest-1.3/MonotonicityTest/R/monotonicity-result.R | 102 ++++++-- MonotonicityTest-1.3/MonotonicityTest/R/monotonicity-test.R |only MonotonicityTest-1.3/MonotonicityTest/R/plots.R |only MonotonicityTest-1.3/MonotonicityTest/R/utils.R |only MonotonicityTest-1.3/MonotonicityTest/README.md | 14 + MonotonicityTest-1.3/MonotonicityTest/man/create_kernel_plot.Rd | 2 MonotonicityTest-1.3/MonotonicityTest/man/monotonicity_test.Rd | 26 -- MonotonicityTest-1.3/MonotonicityTest/src/HallTest.cpp | 119 +++------- MonotonicityTest-1.3/MonotonicityTest/src/RLSState.cpp |only MonotonicityTest-1.3/MonotonicityTest/src/RLSState.h |only MonotonicityTest-1.3/MonotonicityTest/src/RcppExports.cpp | 4 MonotonicityTest-1.3/MonotonicityTest/tests/testthat/Rplots.pdf |binary MonotonicityTest-1.3/MonotonicityTest/tests/testthat/test-main.R | 52 +++- 17 files changed, 212 insertions(+), 149 deletions(-)
More information about MonotonicityTest at CRAN
Permanent link
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.7.1 dated 2025-10-24 and 1.8.0 dated 2025-11-06
DESCRIPTION | 8 +-- MD5 | 28 +++++------ NEWS.md | 5 + R/CallbackAsync.R | 26 ++++++++++ R/ContextAsync.R | 4 - R/OptimInstanceAsync.R | 6 -- R/OptimizerAsync.R | 61 +++++++++++++++++++----- man/CallbackAsync.Rd | 8 +++ man/ContextAsync.Rd | 3 - man/OptimizerAsync.Rd | 38 ++++++++++++++ man/callback_async.Rd | 14 +++++ tests/testthat/helper.R | 8 +-- tests/testthat/test_OptimizerAsynDesignPoints.R | 1 tests/testthat/test_OptimizerAsync.R | 4 - tests/testthat/test_OptimizerBatchLocalSearch.R | 12 ++-- 15 files changed, 173 insertions(+), 53 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 1.0.0 dated 2025-08-20 and 1.1.0 dated 2025-11-06
DESCRIPTION | 10 MD5 | 33 - NEWS.md | 11 R/aaa.R | 56 ++- R/formatters.R | 65 ++- R/otel.R |only R/parsers.R | 35 + R/problems.R | 62 ++- R/request.R | 645 +++++++++++++++++++++++++++-------- R/response.R | 276 +++++++++++--- man/Request.Rd | 27 + tests/testthat/test-aaa.R | 17 tests/testthat/test-formatters.R | 13 tests/testthat/test-parsers.R | 12 tests/testthat/test-problems.R | 70 ++- tests/testthat/test-request.R | 27 + tests/testthat/test-response.R | 73 +++ tests/testthat/test-session-cookie.R | 36 + 18 files changed, 1141 insertions(+), 327 deletions(-)
Title: Treatment Switching
Description: Implements rank preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), marginal structural model (MSM), simple two-stage estimation (TSEsimp), and improved two-stage estimation with g-estimation (TSEgest) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.2.0 dated 2025-10-06 and 0.2.1 dated 2025-11-06
DESCRIPTION | 8 MD5 | 150 NEWS.md | 26 R/RcppExports.R | 116 R/ipcw.R | 192 R/ipe.R | 69 R/msm.R | 184 R/rpsftm.R | 88 R/trtswitch-package.R | 13 R/tsegest.R | 287 - R/tsesimp.R | 103 inst/doc/ipcw.R | 8 inst/doc/ipcw.Rmd | 20 inst/doc/ipcw.html | 261 - inst/doc/ipe.R | 2 inst/doc/ipe.Rmd | 2 inst/doc/ipe.html | 4 inst/doc/msm.R | 4 inst/doc/msm.Rmd | 8 inst/doc/msm.html | 76 inst/doc/rpsftm.R | 2 inst/doc/rpsftm.Rmd | 2 inst/doc/rpsftm.html | 4 inst/doc/tsegest.R | 18 inst/doc/tsegest.Rmd | 30 inst/doc/tsegest.html | 89 inst/doc/tsesimp.R | 6 inst/doc/tsesimp.Rmd | 6 inst/doc/tsesimp.html | 166 man/findInterval3.Rd | 8 man/ipcw.Rd | 109 man/ipe.Rd | 58 man/kmdiff.Rd | 4 man/kmest.Rd | 26 man/lrtest.Rd | 26 man/msm.Rd | 111 man/recensor_sim_rpsftm.Rd | 6 man/rmdiff.Rd | 6 man/rmest.Rd | 2 man/rpsftm.Rd | 72 man/survQuantile.Rd | 2 man/trtswitch-package.Rd | 11 man/tsegest.Rd | 175 man/tsegestsim.Rd | 4 man/tsesimp.Rd | 87 man/tssim.Rd | 8 src/RcppExports.cpp | 50 src/ipcw.cpp | 1071 ++-- src/ipe.cpp | 556 +- src/logistic_regression.cpp | 1151 +--- src/logistic_regression.h | 19 src/msm.cpp | 857 +-- src/recensor_sim_rpsftm.cpp | 53 src/rpsftm.cpp | 542 +- src/splines.cpp | 118 src/survival_analysis.cpp | 8012 +++++++++++++------------------ src/survival_analysis.h | 57 src/tsegest.cpp | 1047 ++-- src/tsegestsim.cpp | 33 src/tsesimp.cpp | 554 +- src/tssim.cpp | 8 src/utilities.cpp | 314 - tests/testthat/test-ipe.R | 2 tests/testthat/test-kmest.R | 4 tests/testthat/test-lrtest.R | 9 tests/testthat/test-residuals_liferegr.R | 15 tests/testthat/test-rmdiff.R | 11 tests/testthat/test-rpsftm.R | 10 tests/testthat/test-tsegest.R | 13 tests/testthat/test-tsesimp.R | 55 vignettes/ipcw.Rmd | 20 vignettes/ipe.Rmd | 2 vignettes/msm.Rmd | 8 vignettes/rpsftm.Rmd | 2 vignettes/tsegest.Rmd | 30 vignettes/tsesimp.Rmd | 6 76 files changed, 8376 insertions(+), 8912 deletions(-)
Title: Estimates and Plots Single-Level and Multilevel Latent Class
Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al. (2025) <doi:10.1080/00273171.2025.2473935>.
Author: Roberto Di Mari [aut, cre],
Johan Lyrvall [aut],
Zsuzsa Bakk [ctb],
Jennifer Oser [ctb],
Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>
Diff between multilevLCA versions 2.1.1 dated 2025-10-01 and 2.1.2 dated 2025-11-06
DESCRIPTION | 8 MD5 | 22 - R/RcppExports.R | 4 build/partial.rdb |binary data/dataIEA.rda |binary data/dataTOY.rda |binary man/multiLCA.Rd | 736 +++++++++++++++++++++++++------------------------- src/LCAfit.cpp | 19 - src/RcppExports.cpp | 14 src/Utils.cpp | 37 ++ src/Utils.h | 1 src/multilevLC_EM.cpp | 46 +-- 12 files changed, 473 insertions(+), 414 deletions(-)
Title: Tools for Customer Lifetime Value Estimation
Description: A set of state-of-the-art probabilistic modeling approaches to derive estimates of individual customer lifetime values (CLV).
Commonly, probabilistic approaches focus on modelling 3 processes, i.e. individuals' attrition, transaction, and spending process.
Latent customer attrition models, which are also known as "buy-'til-you-die models", model the attrition as well as the transaction process.
They are used to make inferences and predictions about transactional patterns of individual customers such as their future purchase behavior.
Moreover, these models have also been used to predict individuals’ long-term engagement in activities such as playing an online game or
posting to a social media platform. The spending process is usually modelled by a separate probabilistic model. Combining these results yields in
lifetime values estimates for individual customers.
This package includes fast and accurate implementations of various probabilistic models for non-contractual settings
(e.g., gr [...truncated...]
Author: Patrick Bachmann [cre, aut],
Niels Kuebler [aut],
Markus Meierer [aut],
Jeffrey Naef [aut],
E. Shin Oblander [aut],
Patrik Schilter [aut]
Maintainer: Patrick Bachmann <pbachma@ethz.ch>
Diff between CLVTools versions 0.12.0 dated 2025-09-22 and 0.12.1 dated 2025-11-06
DESCRIPTION | 8 MD5 | 30 +- NEWS.md | 7 R/f_generics_clvfittedtransactions.R | 3 R/f_generics_clvfittedtransactionsdyncov.R | 3 R/f_generics_clvfittedtransactionsstaticcov.R | 3 R/f_interface_newcustomer.R | 40 ++- build/vignette.rds |binary inst/doc/CLVTools.R | 154 +++++++------- inst/doc/CLVTools.Rmd | 15 + inst/doc/CLVTools.pdf |binary man/newcustomer.Rd | 36 ++- tests/testthat/helper_s3_fitted_plot.R | 2 tests/testthat/helper_testthat_correctness_transactions.R | 8 tests/testthat/test_correctness_pnbd_dyncov.R | 4 vignettes/CLVTools.Rmd | 15 + 16 files changed, 198 insertions(+), 130 deletions(-)
Title: Post-Process 'ggplot2' Plots with 'TikZ' Code Using Plot
Coordinates
Description: Annotation of 'ggplot2' plots with arbitrary 'TikZ' code, using absolute data or relative plot coordinates.
Author: Oliver Thomas [aut, cre]
Maintainer: Oliver Thomas <ost.dev@posteo.net>
Diff between ggtikz versions 0.1.4 dated 2025-09-12 and 0.1.5 dated 2025-11-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ggtikzTransform.R | 4 ++-- R/ggtikzUninfinite.R | 4 ++-- inst/doc/examples.pdf |binary tests/testthat/test-coord_utils.R | 2 +- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: Generate Summary Tables for Categorical, Ordinal, and Continuous
Data
Description: Provides functions for tabulating and summarizing
categorical, multiple response, ordinal, and continuous
variables in R data frames. Makes it easy to create clear,
structured summary tables, so you spend less time wrangling
data and more time interpreting it.
Author: Ama Nyame-Mensah [aut, cre]
Maintainer: Ama Nyame-Mensah <ama@anyamemensah.com>
Diff between summarytabl versions 0.2.0 dated 2025-11-05 and 0.2.1 dated 2025-11-06
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 12 insertions(+), 8 deletions(-)
Title: Regularized Estimation in Mixed Effects Model
Description: Implementation of an algorithm in two steps to estimate parameters of a model whose latent dynamics are inferred through latent processes, jointly regularized. This package uses 'Monolix' software (<https://monolixsuite.slp-software.com/>), which provide robust statistical method for non-linear mixed effects modeling. 'Monolix' must have been installed prior to use.
Author: Auriane Gabaut [aut, cre],
Ariane Bercu [aut],
Melanie Prague [aut],
Cecile Proust-Lima [aut]
Maintainer: Auriane Gabaut <auriane.gabaut@inria.fr>
Diff between REMixed versions 1.1.0 dated 2025-10-28 and 1.1.1 dated 2025-11-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/doc.pdf |binary vignettes/Vignette___REMixed.pdf |binary 5 files changed, 11 insertions(+), 7 deletions(-)
Title: Rapid Asynchronous and Distributed Computing
Description: Package to tackle large-scale problems asynchronously across
a distributed network. Employing a database centric model, rush
enables workers to communicate tasks and their results over a shared
'Redis' database. Key features include low task overhead, efficient
caching, and robust error handling. The package powers the
asynchronous optimization algorithms in the 'bbotk' and 'mlr3tuning'
packages.
Author: Marc Becker [cre, aut, cph]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between rush versions 0.4.0 dated 2025-10-08 and 0.4.1 dated 2025-11-06
DESCRIPTION | 6 ++-- MD5 | 10 +++---- NEWS.md | 5 +++ R/Rush.R | 41 +++++++++++++++++++++----------- man/Rush.Rd | 12 +++++++-- tests/testthat/test-Rush.R | 57 +++++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 106 insertions(+), 25 deletions(-)
Title: Simulation and Plots for Fossil and Taxonomy Data
Description: Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic
models of speciation, preservation and sampling.
Author: Rachel Warnock [aut, cph],
Joelle Barido-Sottani [aut, cre, cph],
Walker Pett [aut, cph],
O'Reilly Joseph [aut, cph],
Ugnė Stolz [aut, cph]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Diff between FossilSim versions 2.4.2 dated 2025-10-28 and 2.4.3 dated 2025-11-06
DESCRIPTION | 6 MD5 | 18 - NEWS.md | 183 +++++++++---------- R/plot.fbdrange.R | 455 +++++++++++++++++++++++++----------------------- inst/doc/SAtree.html | 36 ++- inst/doc/fossils.html | 4 inst/doc/intro.html | 4 inst/doc/paleotree.html | 4 inst/doc/simfbd.html | 4 inst/doc/taxonomy.html | 4 10 files changed, 379 insertions(+), 339 deletions(-)
Title: Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Description: Import, manipulate and explore results generated by 'Antares', a
powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems
(more information about 'Antares' here : <https://antares-simulator.org/>).
Author: Tatiana Vargas [aut, cre],
Jalal-Edine ZAWAM [aut],
Frederic Breant [ctb],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Victor Perrier [ctb],
Etienne Sanchez [ctb],
Assil Mansouri [ctb],
Clement Berthet [ctb],
Kamel Kemiha [c [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between antaresRead versions 2.9.2 dated 2025-09-23 and 2.9.3 dated 2025-11-06
DESCRIPTION | 9 MD5 | 33 - NAMESPACE | 2 NEWS.md | 21 R/importOutput.R | 94 +-- R/setSimulationPath.R | 309 ++++------ R/setSimulationPathAPI.R | 119 +-- R/utils_api.R | 18 R/zzz.R | 10 inst/doc/antaresRead.html | 4 inst/referential_properties/cluster_properties.csv | 1 inst/variables_selection/ref_thematic_by_version/api_ref_conversion.csv | 2 inst/variables_selection/ref_thematic_by_version/ref_930.csv |only man/setSimulationPath.Rd | 22 man/setTimeoutAPI.Rd | 4 tests/testthat/test-readClusterDesc.R | 90 ++ tests/testthat/test-readInputTS.R | 62 ++ tests/testthat/test-thematic_timming.R | 172 +++++ 18 files changed, 672 insertions(+), 300 deletions(-)
Title: Methods to Analyse Signed Networks
Description: Methods for the analysis of signed networks. This includes
several measures for structural balance as introduced by Cartwright
and Harary (1956) <doi:10.1037/h0046049>, blockmodeling algorithms
from Doreian (2008) <doi:10.1016/j.socnet.2008.03.005>, various
centrality indices, and projections of signed two-mode networks
introduced by Schoch (2020) <doi:10.1080/0022250X.2019.1711376>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between signnet versions 1.0.5 dated 2025-02-05 and 1.0.6 dated 2025-11-06
DESCRIPTION | 11 - MD5 | 74 +++++----- NEWS.md | 6 R/balance_scores.R | 166 ++++++++++++++--------- R/blockmodel.R | 14 +- R/centrality_indices.R | 6 R/data_tribes.R | 1 R/plot.R | 215 ++++++++++++++++++------------- R/random_graphs.R | 2 R/signed_triangles.R | 2 R/utils.R | 54 +++---- README.md | 15 +- build/vignette.rds |binary inst/doc/blockmodeling.R | 2 inst/doc/blockmodeling.Rmd | 2 inst/doc/blockmodeling.html | 7 - inst/doc/centrality.html | 9 - inst/doc/complex_matrices.R | 2 inst/doc/complex_matrices.Rmd | 2 inst/doc/complex_matrices.html | 7 - inst/doc/signed_2mode.html | 13 + inst/doc/signed_networks.R | 2 inst/doc/signed_networks.Rmd | 2 inst/doc/signed_networks.html | 11 - inst/doc/structural_balance.html | 5 man/balance_score.Rd | 2 man/figures/README-block_example-1.png |binary man/figures/README-general_example-1.png |binary tests/testthat/test-balance_scores.R | 16 +- tests/testthat/test-blockmodel.R | 24 +-- tests/testthat/test-centrality_indices.R | 186 +++++++++++++++++++------- tests/testthat/test-complex_matrices.R | 208 ++++++++++++++++++++++++----- tests/testthat/test-laplace_matrix.R | 51 +++++-- tests/testthat/test-random_graphs.R | 24 +-- tests/testthat/test-signed_triangles.R | 84 ++++++++---- vignettes/blockmodeling.Rmd | 2 vignettes/complex_matrices.Rmd | 2 vignettes/signed_networks.Rmd | 2 38 files changed, 799 insertions(+), 432 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac, uniform or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] ,
Branislav Panic [ctb] ,
Jernej Klemenc [ctb] ,
Simon Oman [ctb]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.16.0 dated 2024-07-10 and 2.17.0 dated 2025-11-06
DESCRIPTION | 15 MD5 | 98 NAMESPACE | 6 R/AllClasses.R | 4352 +++++++++++++++++++++--------------------- R/AllGenerics.R | 607 ++--- R/EMMIX.R | 986 ++++----- R/RCLRMIX.R | 2 R/RCLSMIX.R | 4 R/REBMIX.R | 8 R/RNGMIX.R | 2 R/defaults.R | 15 R/zaccessors.R | 66 build/partial.rdb |binary build/vignette.rds |binary demo/rebmix.fault.detection.R | 294 +- demo/rebmix.truck.R | 152 - demo/rebmix.weibullnormal.R | 152 - inst/NEWS.Rd | 669 +++--- inst/doc/rebmix.R | 232 +- inst/doc/rebmix.Rnw | 1834 +++++++++-------- inst/doc/rebmix.pdf |binary man/EM.Control-class.Rd | 169 - man/EMMIX.Rd | 284 +- man/EMMIX.Theta-class.Rd | 170 - man/Histogram-class.Rd | 118 - man/RCLRMIX-class.Rd | 252 +- man/RCLS.chunk-class.Rd | 88 man/RCLSMIX-class.Rd | 158 - man/REBMIX-class.Rd | 270 +- man/REBMIX.boot-class.Rd | 152 - man/RNGMIX-class.Rd | 106 - man/RNGMIX.Theta-class.Rd | 126 - man/bearings.Rd | 198 - man/rebmix-internal.Rd | 781 +++---- man/sensorlessdrive.Rd | 142 - man/steelplates.Rd | 278 +- src/Rrebmix.cpp | 121 - src/Rrebmvnorm.cpp | 119 - src/base.cpp | 52 src/base.h | 43 src/emf.cpp | 2457 +++++++++++++++++++++-- src/emf.h | 62 src/init.c | 12 src/rebmix.cpp | 15 src/rebmixf.cpp | 620 +++++ src/rebmixf.h | 9 src/rebmvnormf.cpp | 11 src/rngmixf.cpp | 2 vignettes/rebmix.Rnw | 1834 +++++++++-------- vignettes/rebmix.bib | 1562 +++++++-------- 50 files changed, 11485 insertions(+), 8220 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-06 1.0.4
2023-06-06 1.0.3
2023-04-02 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-26 0.2.1
2025-10-22 0.2