Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 3.5.0 dated 2025-11-05 and 3.5.1 dated 2025-11-16
DESCRIPTION | 8 +++---- MD5 | 17 ++++++++-------- R/opal.R | 41 +++++++++++++++++++++++++++++----------- build/vignette.rds |binary inst/doc/datashield-admin.html | 4 +-- inst/doc/opal-files.html | 4 +-- inst/doc/opal-projects.html | 4 +-- inst/doc/opal-rsession.html | 4 +-- man/dot-extractOpalCSRFToken.Rd |only man/opalr-package.Rd | 2 - 10 files changed, 52 insertions(+), 32 deletions(-)
Title: Visualise OMOP Results using 'shiny' Applications
Description: Visualise results obtained from analysing data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model using
'shiny' applications.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Edward Burn [ctb] ,
Nuria Mercade-Besora [ctb] ,
Elin Rowlands [ctb] ,
Cecilia Campanile [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between OmopViewer versions 0.4.0 dated 2025-07-08 and 0.5.0 dated 2025-11-16
OmopViewer-0.4.0/OmopViewer/inst/logos/hds_logo_noline.svg |only OmopViewer-0.5.0/OmopViewer/DESCRIPTION | 10 OmopViewer-0.5.0/OmopViewer/MD5 | 53 - OmopViewer-0.5.0/OmopViewer/NAMESPACE | 1 OmopViewer-0.5.0/OmopViewer/NEWS.md |only OmopViewer-0.5.0/OmopViewer/R/appDynamic.R | 11 OmopViewer-0.5.0/OmopViewer/R/appStatic.R | 16 OmopViewer-0.5.0/OmopViewer/R/buttons.R | 44 - OmopViewer-0.5.0/OmopViewer/R/createServer.R | 26 OmopViewer-0.5.0/OmopViewer/R/createUi.R | 46 + OmopViewer-0.5.0/OmopViewer/R/defaultPanels.R | 24 OmopViewer-0.5.0/OmopViewer/R/sysdata.rda |binary OmopViewer-0.5.0/OmopViewer/R/theme.R | 87 ++ OmopViewer-0.5.0/OmopViewer/R/utilities.R | 8 OmopViewer-0.5.0/OmopViewer/data/omopViewerPanels.rda |binary OmopViewer-0.5.0/OmopViewer/data/omopViewerResults.rda |binary OmopViewer-0.5.0/OmopViewer/inst/brand |only OmopViewer-0.5.0/OmopViewer/inst/doc/dynamic_app.R | 2 OmopViewer-0.5.0/OmopViewer/inst/doc/edit_static_content.R | 4 OmopViewer-0.5.0/OmopViewer/inst/doc/edit_static_content.html | 6 OmopViewer-0.5.0/OmopViewer/inst/doc/export_static_app.R | 22 OmopViewer-0.5.0/OmopViewer/inst/doc/export_static_app.html | 332 +++++----- OmopViewer-0.5.0/OmopViewer/inst/functions.R | 5 OmopViewer-0.5.0/OmopViewer/man/exportStaticApp.Rd | 4 OmopViewer-0.5.0/OmopViewer/man/omopViewerThemes.Rd |only OmopViewer-0.5.0/OmopViewer/man/panelDetailsFromResult.Rd | 5 OmopViewer-0.5.0/OmopViewer/tests/testthat/test-appStatic.R | 34 - 27 files changed, 440 insertions(+), 300 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gert versions 2.1.5 dated 2025-03-24 and 2.2.0 dated 2025-11-16
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS | 4 ++++ R/pr.R | 2 +- build/vignette.rds |binary configure | 2 +- inst/doc/gert.html | 22 +++++++++++----------- src/Makevars.win | 6 +++++- tests/testthat/test-commit.R | 3 ++- tests/testthat/test-merge.R | 13 +++++++------ tools/winlibs.R | 6 +++--- 11 files changed, 49 insertions(+), 39 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 0.2.1 dated 2025-11-06 and 0.2.2 dated 2025-11-16
DESCRIPTION | 12 - MD5 | 130 +++++++++------ NAMESPACE | 38 ++++ NEWS.md | 359 ++++++++++++++++++++++-------------------- R/RcppExports.R | 15 + R/ipcw.R | 86 +++++----- R/ipe.R | 97 ++++++----- R/liferegr.R | 51 ----- R/logisregr.R | 49 ----- R/msm.R | 84 +++++---- R/phregr.R | 62 +------ R/plot.ipcw.R |only R/plot.ipe.R |only R/plot.msm.R |only R/plot.rpsftm.R |only R/plot.tsegest.R |only R/plot.tsesimp.R |only R/print.ipcw.R |only R/print.ipe.R |only R/print.liferegr.R | 28 +-- R/print.logisregr.R | 28 +-- R/print.msm.R |only R/print.phregr.R | 26 +-- R/print.rpsftm.R |only R/print.tsegest.R |only R/print.tsesimp.R |only R/residuals_liferegr.R | 23 +- R/residuals_phregr.R | 23 +- R/rpsftm.R | 114 +++++++------ R/survfit_phregr.R | 15 + R/trtswitch-package.R | 9 - R/tsegest.R | 135 +++++++++------ R/tsesimp.R | 83 +++++---- inst/doc/rpsftm.R | 2 inst/doc/rpsftm.Rmd | 2 inst/doc/rpsftm.html | 2 inst/doc/tsegest.R | 3 inst/doc/tsegest.Rmd | 6 inst/doc/tsegest.html | 18 +- man/ipcw.Rd | 32 --- man/ipe.Rd | 40 +--- man/liferegr.Rd | 16 - man/logisregr.Rd | 16 - man/lrtest.Rd | 8 man/msm.Rd | 30 --- man/phregr.Rd | 19 -- man/plot.ipcw.Rd |only man/plot.ipe.Rd |only man/plot.msm.Rd |only man/plot.rpsftm.Rd |only man/plot.tsegest.Rd |only man/plot.tsesimp.Rd |only man/print.ipcw.Rd |only man/print.ipe.Rd |only man/print.msm.Rd |only man/print.rpsftm.Rd |only man/print.tsegest.Rd |only man/print.tsesimp.Rd |only man/rpsftm.Rd | 56 ++---- man/tsegest.Rd | 66 +++---- man/tsesimp.Rd | 34 +-- src/RcppExports.cpp | 9 - src/ipcw.cpp | 172 ++++++++++++++++---- src/ipe.cpp | 158 ++++++++++++++---- src/msm.cpp | 146 +++++++++++++---- src/recensor_sim_rpsftm.cpp | 4 src/rpsftm.cpp | 216 +++++++++++++++++-------- src/survival_analysis.cpp | 66 ++++++- src/survival_analysis.h | 1 src/tsegest.cpp | 333 +++++++++++++++++++++++++------------- src/tsesimp.cpp | 231 ++++++++++++++++++++------- src/utilities.cpp | 61 +++++-- src/utilities.h | 4 tests/testthat.R | 16 - tests/testthat/test-rpsftm.R | 2 tests/testthat/test-tsegest.R | 3 vignettes/rpsftm.Rmd | 2 vignettes/tsegest.Rmd | 6 78 files changed, 1944 insertions(+), 1303 deletions(-)
Title: Functions to Efficiently Simulate and Evaluate NFL Seasons
Description: A set of functions to simulate National Football League
seasons including the sophisticated tie-breaking procedures.
Author: Sebastian Carl [cre, aut, cph],
Lee Sharpe [aut]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between nflseedR versions 2.0.1 dated 2025-08-18 and 2.0.2 dated 2025-11-16
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 6 +++++- R/nflseedR-package.R | 3 +++ R/standings_prettify.R | 4 ++-- R/summary_nflseedR.R | 2 +- R/utils.R | 3 +-- README.md | 7 +++---- man/nfl_standings_prettify.Rd | 4 ++-- man/summary.nflseedR_simulation.Rd | 2 +- 10 files changed, 31 insertions(+), 26 deletions(-)
Title: Add Standardized Regression Coefficients to Linear-Model-Objects
Description: Adds standardized regression coefficients to objects created by 'lm'. Also extends the S3 methods 'print', 'summary' and 'coef' with additional boolean argument 'standardized' and provides 'xtable'-support.
Author: Stefan Behrendt [aut, cre]
Maintainer: Stefan Behrendt <r@behrendt-stefan.de>
Diff between lm.beta versions 1.7-2 dated 2023-03-12 and 1.7-3 dated 2025-11-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 5 +++++ build/vignette.rds |binary inst/doc/comparison.R | 12 ++++++------ inst/doc/comparison.pdf |binary inst/doc/implementation.pdf |binary man/xtable.lm.beta.Rd | 18 +++++++++--------- 8 files changed, 31 insertions(+), 26 deletions(-)
Title: Investigating the Functional Characteristics of Selected
Variants and Their Vicinity Genomic Region
Description: To investigate the functional characteristics of selected SNPs and their vicinity genomic region. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
Author: Alireza Ani [aut, cre],
Zoha Kamali [aut],
Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between SNPannotator versions 0.2.6.0 dated 2023-01-12 and 1.4.0 dated 2025-11-16
SNPannotator-0.2.6.0/SNPannotator/R/CADD.R |only SNPannotator-0.2.6.0/SNPannotator/R/checkReturnedVariantData.R |only SNPannotator-0.2.6.0/SNPannotator/R/codes.R |only SNPannotator-0.2.6.0/SNPannotator/R/getGeneFile.R |only SNPannotator-0.2.6.0/SNPannotator/R/getVariantData.R |only SNPannotator-0.2.6.0/SNPannotator/R/returnVariantDatatable.R |only SNPannotator-0.2.6.0/SNPannotator/inst/extdata/cytoband_GRCh37.rds |only SNPannotator-0.2.6.0/SNPannotator/man/LDlist.Rd |only SNPannotator-0.2.6.0/SNPannotator/man/annotate.Rd |only SNPannotator-0.2.6.0/SNPannotator/man/listDatabases.Rd |only SNPannotator-0.2.6.0/SNPannotator/man/pingServer.Rd |only SNPannotator-0.2.6.0/SNPannotator/man/releaseVersion.Rd |only SNPannotator-1.4.0/SNPannotator/DESCRIPTION | 26 SNPannotator-1.4.0/SNPannotator/MD5 | 70 SNPannotator-1.4.0/SNPannotator/NAMESPACE | 42 SNPannotator-1.4.0/SNPannotator/R/aaa.R |only SNPannotator-1.4.0/SNPannotator/R/annotate_shiny.R |only SNPannotator-1.4.0/SNPannotator/R/cadd_functions.R |only SNPannotator-1.4.0/SNPannotator/R/configFile_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/data_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/demo.R |only SNPannotator-1.4.0/SNPannotator/R/ensembl_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/eqtl_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/eqtl_graph_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/fgrepo_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/getVariantLDs.R | 303 ++ SNPannotator-1.4.0/SNPannotator/R/gwascat_graph_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/inSilicoSeqPipeline.R | 104 - SNPannotator-1.4.0/SNPannotator/R/join_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/logger_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/misc_files.R |only SNPannotator-1.4.0/SNPannotator/R/parse_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/runPipelineOnlist.R | 1017 ++++++++-- SNPannotator-1.4.0/SNPannotator/R/stringDB_funcs.R |only SNPannotator-1.4.0/SNPannotator/R/string_network.R |only SNPannotator-1.4.0/SNPannotator/R/zzz.R | 76 SNPannotator-1.4.0/SNPannotator/build |only SNPannotator-1.4.0/SNPannotator/inst/doc |only SNPannotator-1.4.0/SNPannotator/inst/extdata/cytoband_grch37.rda |only SNPannotator-1.4.0/SNPannotator/inst/extdata/cytoband_grch38.rda |only SNPannotator-1.4.0/SNPannotator/inst/extdata/demo_config.ini |only SNPannotator-1.4.0/SNPannotator/inst/extdata/demo_input.txt |only SNPannotator-1.4.0/SNPannotator/inst/extdata/gene_names_grch37.rda |only SNPannotator-1.4.0/SNPannotator/inst/extdata/gene_names_grch38.rda |only SNPannotator-1.4.0/SNPannotator/inst/extdata/inSilicoSeqConfig.ini |only SNPannotator-1.4.0/SNPannotator/inst/rmd/style.css | 18 SNPannotator-1.4.0/SNPannotator/inst/rmd/variantReport.Rmd | 582 +++-- SNPannotator-1.4.0/SNPannotator/man/EnsemblDatabases.Rd |only SNPannotator-1.4.0/SNPannotator/man/EnsemblReleases.Rd |only SNPannotator-1.4.0/SNPannotator/man/annotate_shiny.Rd |only SNPannotator-1.4.0/SNPannotator/man/demo_annotation.Rd |only SNPannotator-1.4.0/SNPannotator/man/findGenomicPos.Rd |only SNPannotator-1.4.0/SNPannotator/man/findPairwiseLD.Rd |only SNPannotator-1.4.0/SNPannotator/man/findProxy.Rd |only SNPannotator-1.4.0/SNPannotator/man/findRSID.Rd |only SNPannotator-1.4.0/SNPannotator/man/getConfigFile.Rd |only SNPannotator-1.4.0/SNPannotator/man/mergeResultFiles.Rd |only SNPannotator-1.4.0/SNPannotator/man/pingEnsembl.Rd |only SNPannotator-1.4.0/SNPannotator/man/run_annotation.Rd |only SNPannotator-1.4.0/SNPannotator/man/run_stringdb_annotation.Rd |only SNPannotator-1.4.0/SNPannotator/vignettes |only 61 files changed, 1798 insertions(+), 440 deletions(-)
Title: Twang Causal Mediation Modeling via Weighting
Description: Provides functions for estimating natural direct and indirect effects for mediation analysis. It uses weighting where the weights are functions of estimates of the probability of exposure or treatment assignment (Hong, G (2010). <https://cepa.stanford.edu/sites/default/files/workshops/GH_JSM%20Proceedings%202010.pdf> Huber, M. (2014). <doi:10.1002/jae.2341>). Estimation of probabilities can use generalized boosting or logistic regression. Additional functions provide diagnostics of the model fit and weights. The vignette provides details and examples.
Author: Dan McCaffrey [aut, cre],
Katherine Castellano [aut],
Donna Coffman [aut],
Brian Vegetabile [aut],
Megan Schuler [aut],
Haoyu Zhou [aut]
Maintainer: Dan McCaffrey <dmccaffrey@ets.org>
Diff between twangMediation versions 1.2 dated 2022-08-16 and 1.2.1 dated 2025-11-16
twangMediation-1.2.1/twangMediation/DESCRIPTION | 17 twangMediation-1.2.1/twangMediation/MD5 | 78 twangMediation-1.2.1/twangMediation/NAMESPACE | 46 twangMediation-1.2.1/twangMediation/NEWS.md |only twangMediation-1.2.1/twangMediation/R/bal.table.mediation.R | 450 +--- twangMediation-1.2.1/twangMediation/R/data.R | 128 - twangMediation-1.2.1/twangMediation/R/desc.effects.R | 64 twangMediation-1.2.1/twangMediation/R/desc.effects.mediation.R | 277 +- twangMediation-1.2.1/twangMediation/R/diag.plot.color.R | 408 ++-- twangMediation-1.2.1/twangMediation/R/dx.wts.mediation.R | 396 ++-- twangMediation-1.2.1/twangMediation/R/makePlotDat.R | 276 +- twangMediation-1.2.1/twangMediation/R/plot.mediation.R | 681 ++++--- twangMediation-1.2.1/twangMediation/R/print.bal.table.mediation.R | 158 - twangMediation-1.2.1/twangMediation/R/print.mediation.R | 228 +- twangMediation-1.2.1/twangMediation/R/summary.mediation.R | 314 +-- twangMediation-1.2.1/twangMediation/R/twangMediation-package.R | 14 twangMediation-1.2.1/twangMediation/R/twang_functions.R | 316 +-- twangMediation-1.2.1/twangMediation/R/utils_mediation.R | 350 +-- twangMediation-1.2.1/twangMediation/R/wgtmed.R | 965 ++++------ twangMediation-1.2.1/twangMediation/build/partial.rdb |only twangMediation-1.2.1/twangMediation/build/vignette.rds |binary twangMediation-1.2.1/twangMediation/inst/doc/twangMediation.pdf |binary twangMediation-1.2.1/twangMediation/inst/doc/twangMediation.pdf.asis |only twangMediation-1.2.1/twangMediation/man/NSDUH_female.Rd | 114 - twangMediation-1.2.1/twangMediation/man/bal.table.mediation.Rd | 90 twangMediation-1.2.1/twangMediation/man/calculate_effects.Rd | 60 twangMediation-1.2.1/twangMediation/man/check_missing.Rd | 38 twangMediation-1.2.1/twangMediation/man/desc.effects.Rd | 86 twangMediation-1.2.1/twangMediation/man/desc.effects.mediation.Rd | 94 twangMediation-1.2.1/twangMediation/man/dx.wts.mediation.Rd | 178 - twangMediation-1.2.1/twangMediation/man/plot.mediation.Rd | 136 - twangMediation-1.2.1/twangMediation/man/print.bal.table.mediation.Rd | 82 twangMediation-1.2.1/twangMediation/man/print.mediation.Rd | 82 twangMediation-1.2.1/twangMediation/man/summary.mediation.Rd | 92 twangMediation-1.2.1/twangMediation/man/swapTxCtrl.Rd | 44 twangMediation-1.2.1/twangMediation/man/tMdat.Rd | 74 twangMediation-1.2.1/twangMediation/man/twangMediation-package.Rd | 50 twangMediation-1.2.1/twangMediation/man/weighted_mean.Rd | 56 twangMediation-1.2.1/twangMediation/man/wgtmed.Rd | 385 +-- twangMediation-1.2.1/twangMediation/vignettes/twangMediation.pdf.asis |only twangMediation-1.2/twangMediation/R/vignettename.R |only twangMediation-1.2/twangMediation/inst/doc/twangMediation.Rnw |only twangMediation-1.2/twangMediation/vignettes/twangMediation.Rnw |only twangMediation-1.2/twangMediation/vignettes/twangMediation_tutorial.pdf |only 44 files changed, 3320 insertions(+), 3507 deletions(-)
More information about twangMediation at CRAN
Permanent link
Title: Extract and Summarise Data from Published Figures
Description: High-throughput, flexible and reproducible extraction of data from figures in primary research papers. metaDigitise() can extract data and / or automatically calculate summary statistics for users from box plots, bar plots (e.g., mean and errors), scatter plots and histograms.
Author: Joel Pick [aut],
Shinichi Nakagawa [aut],
Daniel Noble [aut, cre]
Maintainer: Daniel Noble <daniel.wa.noble@gmail.com>
Diff between metaDigitise versions 1.0.1 dated 2020-03-13 and 1.0.2 dated 2025-11-16
metaDigitise-1.0.1/metaDigitise/tests |only metaDigitise-1.0.2/metaDigitise/DESCRIPTION | 11 metaDigitise-1.0.2/metaDigitise/MD5 | 38 metaDigitise-1.0.2/metaDigitise/NEWS.md | 12 metaDigitise-1.0.2/metaDigitise/R/edit_metaDigitise.R | 4 metaDigitise-1.0.2/metaDigitise/R/metaDigitise.R | 2 metaDigitise-1.0.2/metaDigitise/README.md | 26 metaDigitise-1.0.2/metaDigitise/build/vignette.rds |binary metaDigitise-1.0.2/metaDigitise/inst/CITATION | 16 metaDigitise-1.0.2/metaDigitise/inst/doc/metaDigitise.html | 510 +++++++++-- metaDigitise-1.0.2/metaDigitise/man/MB_extract.Rd | 10 metaDigitise-1.0.2/metaDigitise/man/group_scatter_extract.Rd | 8 metaDigitise-1.0.2/metaDigitise/man/histogram_extract.Rd | 3 metaDigitise-1.0.2/metaDigitise/man/internal_redraw.Rd | 19 metaDigitise-1.0.2/metaDigitise/man/metaDigitise.Rd | 2 metaDigitise-1.0.2/metaDigitise/man/redraw_calibration.Rd | 10 16 files changed, 534 insertions(+), 137 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems. See Mary C. Meyer (2013)<doi:10.1080/03610918.2012.659820> for more details.
Author: Mary C. Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between coneproj versions 1.21 dated 2025-10-11 and 1.22 dated 2025-11-16
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 1 - R/coneproj.R | 4 ++-- 4 files changed, 10 insertions(+), 11 deletions(-)