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(-)