Title: Rapid and Accurate Genetic Prediction Modeling for Genome-Wide
Association or Whole-Genome Sequencing Study Data
Description: Rapidly build accurate genetic prediction models for genome-wide association or whole-genome sequencing study data by smooth-threshold multivariate genetic prediction (STMGP) method. Variable selection is performed using marginal association test p-values with an optimal p-value cutoff selected by Cp-type criterion. Quantitative and binary traits are modeled respectively via linear and logistic regression models. A function that works through PLINK software (Purcell et al. 2007 <DOI:10.1086/519795>, Chang et al. 2015 <DOI:10.1186/s13742-015-0047-8>) <https://www.cog-genomics.org/plink2> is provided. Covariates can be included in regression model.
Author: Masao Ueki [aut, cre]
Maintainer: Masao Ueki <uekimrsd@nifty.com>
Diff between stmgp versions 1.0.4.1 dated 2025-02-11 and 1.0.4.2 dated 2025-10-02
stmgp-1.0.4.1/stmgp/R/stplink1.0.4.1.R |only stmgp-1.0.4.2/stmgp/DESCRIPTION | 8 ++++---- stmgp-1.0.4.2/stmgp/MD5 | 11 ++++++----- stmgp-1.0.4.2/stmgp/NAMESPACE | 2 +- stmgp-1.0.4.2/stmgp/NEWS.md | 3 +++ stmgp-1.0.4.2/stmgp/R/stplink1.0.4.2.R |only stmgp-1.0.4.2/stmgp/build/partial.rdb |binary stmgp-1.0.4.2/stmgp/man/dabic.Rd |only 8 files changed, 14 insertions(+), 10 deletions(-)
Title: Optimal Adaptive Allocation Using Deep Reinforcement Learning
Description: An implementation to compute an optimal adaptive allocation rule
using deep reinforcement learning in a dose-response study
(Matsuura et al. (2022) <doi:10.1002/sim.9247>).
The adaptive allocation rule can directly optimize a performance metric,
such as power, accuracy of the estimated target dose, or mean absolute error
over the estimated dose-response curve.
Author: Kentaro Matsuura [aut, cre, cph] ,
Koji Makiyama [aut, ctb]
Maintainer: Kentaro Matsuura <matsuurakentaro55@gmail.com>
Diff between RLoptimal versions 1.2.1 dated 2025-01-13 and 1.2.2 dated 2025-10-02
DESCRIPTION | 12 +- MD5 | 12 +- NAMESPACE | 1 R/allocation_rule.R | 4 build/vignette.rds |binary inst/doc/RLoptimal.R | 264 ++++++++++++++++++++++++------------------------ inst/doc/RLoptimal.html | 4 7 files changed, 150 insertions(+), 147 deletions(-)
Title: Bayesian Adaptive Trial Simulator Software (BATSS) for
Generalised Linear Models
Description: Defines operating characteristics of Bayesian Adaptive Trials considering a generalised linear model response via Monte Carlo simulations of Bayesian GLM fitted via integrated Laplace approximations (INLA).
Author: Dominique-Laurent Couturier [aut, cre] ,
Liz Ryan [aut] ,
Rainer Puhr [aut],
Thomas Jaki [aut] ,
Stephane Heritier [aut]
Maintainer: Dominique-Laurent Couturier <dominique.couturier@mrc-bsu.cam.ac.uk>
Diff between BATSS versions 1.1.0 dated 2025-09-21 and 1.1.1 dated 2025-10-02
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- R/plot.batss.R | 28 +++++++++++++++++++++++++--- R/summary.batss.R | 42 +++++++++++++++++++++++++++++++++--------- man/plot.batss.Rd | 3 +++ man/print.summary.batss.Rd |only man/summary.batss.Rd | 11 +++++++++++ 7 files changed, 81 insertions(+), 20 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut],
Zachary Deane-Mayer [aut],
David Chudzicki [aut],
Dallin Akagi [aut],
Sergey Yurgenson [aut],
Thakur Raj Anand [aut],
Peter Hurford [aut],
Chester Ismay [aut],
AJ Alon [aut, cre],
Andrew Watson [aut],
Gregory Williams [aut],
Anasta [...truncated...]
Maintainer: AJ Alon <api-maintainer@datarobot.com>
Diff between datarobot versions 2.18.6 dated 2024-03-13 and 2.18.7 dated 2025-10-02
DESCRIPTION | 77 +++- MD5 | 76 ++-- NEWS.md | 9 build/vignette.rds |binary inst/doc/AdvancedTuning.R | 16 - inst/doc/AdvancedTuning.html | 132 ++++---- inst/doc/AdvancedVignette.R | 220 +++++++------- inst/doc/AdvancedVignette.html | 374 ++++++++++++------------ inst/doc/Calendars.R | 46 +- inst/doc/Calendars.html | 168 +++++----- inst/doc/ComparingSubsets.R | 68 ++-- inst/doc/ComparingSubsets.html | 273 ++++++++--------- inst/doc/ComplianceDocumentation.R | 42 +- inst/doc/ComplianceDocumentation.html | 158 +++++----- inst/doc/DatetimePartitionedProjects.R | 110 +++---- inst/doc/DatetimePartitionedProjects.html | 226 +++++++------- inst/doc/Deployment.R | 52 +-- inst/doc/Deployment.html | 168 +++++----- inst/doc/IntroductionToDataRobot.R | 58 +-- inst/doc/IntroductionToDataRobot.html | 166 +++++----- inst/doc/Multiclass.R | 36 +- inst/doc/Multiclass.html | 220 +++++++------- inst/doc/PartialDependence.R | 32 +- inst/doc/PartialDependence.html | 327 ++++++++++---------- inst/doc/PredictionExplanations.R | 60 +-- inst/doc/PredictionExplanations.html | 182 +++++------ inst/doc/RatingTables.R | 62 +-- inst/doc/RatingTables.html | 180 +++++------ inst/doc/TimeSeries.R | 116 +++---- inst/doc/TimeSeries.html | 200 ++++++------ inst/doc/TrainingPredictions.R | 30 - inst/doc/TrainingPredictions.html | 146 ++++----- inst/doc/VariableImportance.R | 52 +-- inst/doc/VariableImportance.html | 325 ++++++++++---------- tests/testthat/test-CreateGroupPartition.R | 60 ++- tests/testthat/test-CreateRandomPartition.R | 56 ++- tests/testthat/test-CreateStratifiedPartition.R | 56 ++- tests/testthat/test-CreateUserPartition.R | 64 ++-- tests/testthat/test-StartAutopilot.R | 53 +-- 39 files changed, 2406 insertions(+), 2290 deletions(-)
Title: Simulation and Analysis Tools for Clinical Dose Response
Modeling
Description: Bayesian and ML Emax model fitting, graphics and simulation for clinical dose
response. The summary data from the dose response meta-analyses in
Thomas, Sweeney, and Somayaji (2014) <doi:10.1080/19466315.2014.924876> and
Thomas and Roy (2016) <doi:10.1080/19466315.2016.1256229>
Wu, Banerjee, Jin, Menon, Martin, and Heatherington(2017) <doi:10.1177/0962280216684528>
are included
in the package. The prior distributions for the Bayesian analyses default to
the posterior predictive distributions derived from these references.
Author: Neal Thomas [aut, cre] ,
Jing Wu [aut],
Mike K. Smith [aut]
Maintainer: Neal Thomas <snthomas99@gmail.com>
Diff between clinDR versions 2.4.1 dated 2023-08-09 and 2.5.2 dated 2025-10-02
DESCRIPTION | 10 - INDEX |only MD5 | 58 +++++----- NAMESPACE | 2 R/predict.fitEmaxB.R | 1 inst/NEWS | 4 inst/models/basemodel.stan | 14 +- inst/models/mrmodel.stan | 6 - inst/shiny/app.R | 28 ++++ inst/tests/Rplots.pdf |only inst/tests/extraGraphics/pdfoutput/output.densityplot_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.densityplot_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.fitEmax_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.fitEmax_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.plotB_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.plotB_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.plotD_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.plotD_old.pdf |binary inst/tests/extraGraphics/runGraphics.R | 1 inst/tests/imputeMIL2.stan | 18 +-- man/clinDR-package.Rd | 2 man/emaxsim.Rd | 19 ++- man/emaxsimB.Rd | 12 +- man/fitEmaxB.Rd | 8 - man/predict.fitEmaxB.Rd | 3 31 files changed, 113 insertions(+), 73 deletions(-)
Title: Bayesian Exposure-Response Analysis Tools
Description: Suite of tools that facilitate
exposure-response analysis using Bayesian methods. The package
provides a streamlined workflow for fitting types of models that are
commonly used in exposure-response analysis - linear and Emax for continuous
endpoints, logistic linear and logistic Emax for binary endpoints, as well
as performing simulation and visualization. Learn more about the workflow
at <https://genentech.github.io/BayesERbook/>.
Author: Kenta Yoshida [aut, cre] ,
Francois Mercier [aut] ,
Danielle Navarro [aut] ,
Genentech, Inc. [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between BayesERtools versions 0.2.3 dated 2025-06-16 and 0.2.4 dated 2025-10-02
BayesERtools-0.2.3/BayesERtools/tests/testthat/Rplots.pdf |only BayesERtools-0.2.4/BayesERtools/DESCRIPTION | 6 BayesERtools-0.2.4/BayesERtools/MD5 | 27 +- BayesERtools-0.2.4/BayesERtools/NEWS.md | 12 BayesERtools-0.2.4/BayesERtools/R/coveff.R | 130 ++++++++-- BayesERtools-0.2.4/BayesERtools/R/yyy.R | 2 BayesERtools-0.2.4/BayesERtools/README.md | 8 BayesERtools-0.2.4/BayesERtools/inst/doc/overview_of_the_package.html | 2 BayesERtools-0.2.4/BayesERtools/man/build_spec_coveff.Rd | 2 BayesERtools-0.2.4/BayesERtools/man/plot_coveff.Rd | 16 + BayesERtools-0.2.4/BayesERtools/man/print_coveff.Rd | 17 + BayesERtools-0.2.4/BayesERtools/man/sim_coveff.Rd | 17 + BayesERtools-0.2.4/BayesERtools/tests/testthat/test-coveff.R | 76 +++++ BayesERtools-0.2.4/BayesERtools/tests/testthat/test-loo_kfold.R | 2 BayesERtools-0.2.4/BayesERtools/vignettes/data/supported_models.csv | 2 15 files changed, 265 insertions(+), 54 deletions(-)
Title: Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indexes, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [aut] ,
Ned Horning [aut],
Jakob Schwalb-Willmann [aut] ,
Robert J. Hijmans [ctb] ,
Konstantin Mueller [aut, cre]
Maintainer: Konstantin Mueller <konstantinfinn.mueller@gmx.de>
Diff between RStoolbox versions 1.0.2.1 dated 2025-02-03 and 1.0.2.2 dated 2025-10-02
DESCRIPTION | 21 ++++++++++++--------- MD5 | 24 ++++++++++++------------ R/coregisterImages.R | 8 ++++---- R/ggRGB.R | 4 ++-- R/histMatch.R | 5 +++-- R/superClass.R | 5 +++-- README.md | 1 + man/spectralIndices.Rd | 2 +- man/superClass.Rd | 3 +++ src/predictMlc.cpp | 3 +-- tests/testthat/test-ggplot.R | 8 ++++---- tests/testthat/test-spectralIndices.R | 3 ++- tests/testthat/test-superClass.R | 21 +++++++++++++++++++++ 13 files changed, 69 insertions(+), 39 deletions(-)
Title: Manipulate 'JDemetra+' Workspaces
Description: Set of tools to manipulate the 'JDemetra+' workspaces. Based
on the 'RJDemetra' package (which interfaces with version 2 of the
'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal
adjustment software officially recommended to the members of the
European Statistical System (ESS) and the European System of Central
Banks). This package provides access to additional workspace
manipulation functions such as metadata manipulation, raw paths and
wrangling of several workspaces simultaneously. These additional
functionalities are useful as part of a CVS data production chain.
Author: Tanguy Barthelemy [aut, cre, art],
Alain Quartier-la-Tente [aut] ,
Institut national de la statistique et des etudes economiques [cph]
,
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjdworkspace versions 1.1.9 dated 2025-01-21 and 1.2.0 dated 2025-10-02
DESCRIPTION | 52 +++++------ MD5 | 13 +- NEWS.md | 43 ++++++--- R/update_path.R | 241 ++++++++++++++++------------------------------------- man/update_path.Rd | 25 ++--- tests |only 6 files changed, 151 insertions(+), 223 deletions(-)
Title: River Hydrograph Separation and Analysis
Description: River hydrograph separation and daily runoff time series analysis. Provides
various filters to separate baseflow and quickflow. Implements advanced separation
technique by Rets et al. (2022) <doi:10.1134/S0097807822010146> which involves
meteorological data to reveal genetic components of the runoff: ground, rain, thaw
and spring (seasonal thaw). High-performance C++17 computation, annually aggregated
variables, statistical testing and numerous plotting functions for high-quality
visualization.
Author: Timofey Samsonov [aut, cre] ,
Ekaterina Rets [ctb] ,
Maria Kireeva [ctb]
Maintainer: Timofey Samsonov <tsamsonov@geogr.msu.ru>
Diff between grwat versions 0.0.4 dated 2023-10-27 and 0.1 dated 2025-10-02
grwat-0.0.4/grwat/R/utils-pipe.R |only grwat-0.0.4/grwat/R/utils.R |only grwat-0.0.4/grwat/man/pipe.Rd |only grwat-0.1/grwat/DESCRIPTION | 28 grwat-0.1/grwat/MD5 | 102 +- grwat-0.1/grwat/NAMESPACE | 4 grwat-0.1/grwat/NEWS.md | 9 grwat-0.1/grwat/R/Utils.R |only grwat-0.1/grwat/R/plot.R | 192 ++- grwat-0.1/grwat/R/process.R | 62 - grwat-0.1/grwat/R/report.R | 2 grwat-0.1/grwat/R/separate.R | 66 - grwat-0.1/grwat/R/summarize.R | 20 grwat-0.1/grwat/R/test.R | 36 grwat-0.1/grwat/README.md | 15 grwat-0.1/grwat/build/vignette.rds |binary grwat-0.1/grwat/inst/doc/baseflow.R | 10 grwat-0.1/grwat/inst/doc/baseflow.Rmd | 10 grwat-0.1/grwat/inst/doc/baseflow.html | 38 grwat-0.1/grwat/inst/doc/grwat.R | 2 grwat-0.1/grwat/inst/doc/grwat.Rmd | 4 grwat-0.1/grwat/inst/doc/grwat.html | 55 - grwat-0.1/grwat/inst/doc/separation.html | 16 grwat-0.1/grwat/inst/doc/summaries.html | 854 ++++++++--------- grwat-0.1/grwat/inst/examples/gr_baseflow.R | 12 grwat-0.1/grwat/inst/examples/gr_fill_gaps.R | 2 grwat-0.1/grwat/inst/examples/gr_from_pardf.R |only grwat-0.1/grwat/inst/examples/gr_get_gaps.R | 2 grwat-0.1/grwat/inst/examples/gr_join_rean.R | 2 grwat-0.1/grwat/inst/examples/gr_plot_sep.R | 5 grwat-0.1/grwat/inst/examples/gr_separate.R | 14 grwat-0.1/grwat/inst/examples/gr_to_pardf.R |only grwat-0.1/grwat/man/gr_baseflow.Rd | 12 grwat-0.1/grwat/man/gr_fill_gaps.Rd | 2 grwat-0.1/grwat/man/gr_from_pardf.Rd |only grwat-0.1/grwat/man/gr_get_gaps.Rd | 2 grwat-0.1/grwat/man/gr_join_rean.Rd | 2 grwat-0.1/grwat/man/gr_plot_sep.Rd | 10 grwat-0.1/grwat/man/gr_separate.Rd | 14 grwat-0.1/grwat/man/gr_summarize.Rd | 2 grwat-0.1/grwat/man/gr_to_pardf.Rd |only grwat-0.1/grwat/tests/testthat/Rplots.pdf |binary grwat-0.1/grwat/tests/testthat/test-gr_baseflow.R | 74 - grwat-0.1/grwat/tests/testthat/test-gr_fill_gaps.R | 4 grwat-0.1/grwat/tests/testthat/test-gr_get_gaps.R | 4 grwat-0.1/grwat/tests/testthat/test-gr_plot_acf.R | 16 grwat-0.1/grwat/tests/testthat/test-gr_plot_hori.R | 13 grwat-0.1/grwat/tests/testthat/test-gr_plot_matrix.R | 41 grwat-0.1/grwat/tests/testthat/test-gr_plot_minmonth.R | 32 grwat-0.1/grwat/tests/testthat/test-gr_plot_periods.R | 39 grwat-0.1/grwat/tests/testthat/test-gr_plot_ridge.R | 17 grwat-0.1/grwat/tests/testthat/test-gr_plot_sep.R | 94 + grwat-0.1/grwat/tests/testthat/test-gr_plot_tests.R | 11 grwat-0.1/grwat/tests/testthat/test-gr_plot_vars.R | 74 - grwat-0.1/grwat/vignettes/baseflow.Rmd | 10 grwat-0.1/grwat/vignettes/grwat.Rmd | 4 56 files changed, 1137 insertions(+), 902 deletions(-)
Title: Result Model Manager
Description: Database data model management utilities for R packages in the Observational Health Data Sciences and
Informatics programme. 'ResultModelManager' provides utility functions to allow package
maintainers to migrate existing SQL database models, export and import results in consistent patterns.
Author: Jamie Gilbert [aut, cre]
Maintainer: Jamie Gilbert <gilbert@ohdsi.org>
Diff between ResultModelManager versions 0.6.1 dated 2025-09-25 and 0.6.2 dated 2025-10-02
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 7 +++++++ R/DataMigrationManager.R | 2 +- inst/doc/CreatingMigrations.pdf |binary inst/doc/PackageDesign.pdf |binary inst/doc/UploadFunctionality.pdf |binary inst/doc/UsingAnExportManager.pdf |binary inst/doc/UsingConnectionHandlers.pdf |binary inst/doc/UsingPythonUploads.pdf |binary inst/doc/UsingQueryNamespaces.pdf |binary tests/testthat/setup.R | 1 - 12 files changed, 22 insertions(+), 16 deletions(-)
More information about ResultModelManager at CRAN
Permanent link
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with
interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut] ,
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3learners versions 0.12.0 dated 2025-05-23 and 0.13.0 dated 2025-10-02
DESCRIPTION | 18 - MD5 | 92 +++--- NAMESPACE | 3 NEWS.md | 7 R/LearnerClassifRanger.R | 17 - R/LearnerClassifXgboost.R | 12 R/LearnerRegrKM.R | 3 R/LearnerRegrRanger.R | 96 ++++-- R/LearnerRegrXgboost.R | 8 R/bibentries.R | 13 R/helpers_ranger.R | 19 - R/zzz.R | 3 README.md | 4 build/partial.rdb |binary inst/paramtest/test_paramtest_classif.xgboost.R | 6 inst/paramtest/test_paramtest_regr.ranger.R | 6 inst/paramtest/test_paramtest_regr.xgboost.R | 6 man/mlr_learners_classif.cv_glmnet.Rd | 11 man/mlr_learners_classif.glmnet.Rd | 11 man/mlr_learners_classif.kknn.Rd | 11 man/mlr_learners_classif.lda.Rd | 11 man/mlr_learners_classif.log_reg.Rd | 11 man/mlr_learners_classif.multinom.Rd | 11 man/mlr_learners_classif.naive_bayes.Rd | 11 man/mlr_learners_classif.nnet.Rd | 11 man/mlr_learners_classif.qda.Rd | 11 man/mlr_learners_classif.ranger.Rd | 11 man/mlr_learners_classif.svm.Rd | 11 man/mlr_learners_classif.xgboost.Rd | 8 man/mlr_learners_regr.cv_glmnet.Rd | 11 man/mlr_learners_regr.glmnet.Rd | 11 man/mlr_learners_regr.kknn.Rd | 11 man/mlr_learners_regr.km.Rd | 11 man/mlr_learners_regr.lm.Rd | 11 man/mlr_learners_regr.nnet.Rd | 11 man/mlr_learners_regr.ranger.Rd | 34 +- man/mlr_learners_regr.svm.Rd | 11 man/mlr_learners_regr.xgboost.Rd | 8 src |only tests/testthat/helper.R | 52 +++ tests/testthat/setup.R | 16 + tests/testthat/teardown.R | 3 tests/testthat/test_classif_cv_glmnet.R | 3 tests/testthat/test_classif_qda.R | 3 tests/testthat/test_classif_ranger.R | 9 tests/testthat/test_regr_cv_glmnet.R | 3 tests/testthat/test_regr_ranger.R | 348 +++++++++++++++++++++++- 47 files changed, 764 insertions(+), 234 deletions(-)
Title: Unifying Multiple Biplot Visualisations into a Single Display
Description: Aligning multiple visualisations by utilising generalised orthogonal Procrustes analysis (GPA) before combining coordinates into a single biplot display as described in Nienkemper-Swanepoel, le Roux and Lubbe (2023)<doi:10.1080/03610918.2021.1914089>. This is mainly suitable to combine visualisations constructed from multiple imputations, however, it can be generalised to combine variations of visualisations from the same datasets (i.e. resamples).
Author: Johane Nienkemper-Swanepoel [aut, cre, cph]
Maintainer: Johane Nienkemper-Swanepoel <nienkemperj@sun.ac.za>
Diff between GPAbin versions 1.1.0 dated 2025-07-16 and 1.1.1 dated 2025-10-02
DESCRIPTION | 7 +++-- MD5 | 28 +++++++++++----------- NEWS.md | 26 ++++++++++++++++++++- R/DRT.R | 4 ++- R/Procrustes.R | 4 +++ R/eval_meas.R | 24 ++++++++++++++++--- R/imputation.R | 3 ++ R/missmi.R | 2 - R/plotting.R | 69 ++++++++++++++++++++++++++++++++++++++++++-------------- man/DRT.Rd | 3 ++ man/GPAbin.Rd | 5 ++++ man/biplFig.Rd | 5 +++- man/evalMeas.Rd | 18 ++++++++++---- man/impute.Rd | 3 ++ man/missmi.Rd | 2 - 15 files changed, 155 insertions(+), 48 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Susanna Marquez [cre, aut],
Namita Gupta [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Edel Aron [ctb],
Cole Jensen [aut],
Gisela Gabernet [ctb],
Caroline Sullivan [ctb],
Hailong Meng [ [...truncated...]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between alakazam versions 1.4.0 dated 2025-09-25 and 1.4.1 dated 2025-10-02
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 8 ++++++++ R/Diversity.R | 2 +- R/Gene.R | 10 +++++----- inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.pdf |binary inst/doc/Fastq-Vignette.pdf |binary inst/doc/Files-Vignette.pdf |binary inst/doc/GeneUsage-Vignette.pdf |binary 10 files changed, 27 insertions(+), 19 deletions(-)
Title: Identify External Packages Used in a Project
Description: Screens all '.R', '.Rmd', and '.qmd' files to extract the name of
packages used in a project. This package detects packages called with
'library(foo)', 'require(foo)', 'foo::bar()' and 'use("foo", "bar")' and
adds these dependencies in the DESCRIPTION file in the sections Depends,
Imports, and Suggests.
Author: Nicolas Casajus [aut, cre, cph]
Maintainer: Nicolas Casajus <nicolas.casajus@fondationbiodiversite.fr>
Diff between rdeps versions 0.3 dated 2025-04-23 and 0.4 dated 2025-10-02
DESCRIPTION | 12 ++-- MD5 | 20 +++---- NAMESPACE | 1 NEWS.md | 4 + R/add_to_rdepsignore.R |only R/utils-deps.R | 129 +++++++++++++++++++++++++++++++++++++--------- R/utils-io.R | 18 ++++++ R/utils-proj.R | 36 ++++++++++++ README.md | 19 ++++-- inst/CITATION | 2 man/add_to_rdepsignore.Rd |only man/rdeps-package.Rd | 2 12 files changed, 196 insertions(+), 47 deletions(-)
Title: Comprehensive Single-Cell Annotation and Transcriptomic Analysis
Toolkit
Description: Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi: 10.1093/nar/gkac947>). Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi: 10.1101/2024.09.14.609619> for more details.
Author: Wei Cui [aut, cre, cph]
Maintainer: Wei Cui <m2c.w@outlook.com>
Diff between easybio versions 1.2.2 dated 2025-09-01 and 1.2.3 dated 2025-10-02
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 7 ++++++- R/sc.R | 2 +- inst/doc/example-sc-seq-workflow.Rmd | 2 +- inst/doc/example-sc-seq-workflow.html | 3 +-- inst/doc/example_limma.html | 4 ++-- vignettes/example-sc-seq-workflow.Rmd | 2 +- 8 files changed, 24 insertions(+), 20 deletions(-)
Title: Multidimensional Scaling of Asymmetric Proximities
Description: Multidimensional scaling models and methods for the visualization and analysis of asymmetric proximity data. An asymmetric data matrix has the same number of rows and columns, and these rows and columns refer to the same set of objects. At least some elements in the upper-triangle are different from the corresponding elements in the lower triangle. An example of an asymmetric matrix is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. This package provides algorithms for three multidimensional scaling models, the slide-vector model, a scaling model with unique dimensions and the asymscal model.Furthermore, some other procedures, such as a heat map for skew-symmetric data, and the decomposition of asymmetry are also provided for the exploratory analysis of asymmetric tables.
Author: Berrie Zielman [aut, cre]
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Diff between asymmetry versions 2.0.4 dated 2022-06-22 and 2.0.5 dated 2025-10-02
DESCRIPTION | 16 +- MD5 | 46 +++--- NAMESPACE | 6 R/asymscal.R | 139 ++++++++++++-------- R/hmap.R | 43 ++++-- R/mdsunique.R | 157 ++++++++++++++--------- R/plot.skewsymmetry.R | 42 ++++-- R/plot.slidevector.R | 39 +++-- R/skewsymmetry.R | 44 ++++-- R/slidevector.R | 138 +++++++++++++------- R/summary.skewsymmetry.R | 17 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/asymmetry.R | 64 +++++++++ inst/doc/asymmetry.Rmd | 93 +++++++++++++- inst/doc/asymmetry.html | 312 ++++++++++++++++++++++++++--------------------- man/asymmetry-package.Rd | 10 + man/asymscal.Rd | 7 - man/hmap.Rd | 2 man/mdsunique.Rd | 2 man/plot.Rd | 2 man/slidevector.Rd | 12 + man/studentmigration.Rd | 2 vignettes/asymmetry.Rmd | 93 +++++++++++++- 24 files changed, 867 insertions(+), 419 deletions(-)
Title: Retrieve, Harmonise and Map Open Data Regarding the Italian
School System
Description: Compiles and displays the available data sets regarding the Italian school system, with a focus on the infrastructural aspects.
Input datasets are downloaded from the web, with the aim of updating everything to real time.
The functions are divided in four main modules, namely
'Get', to scrape raw data from the web
'Util', various utilities needed to process raw data
'Group', to aggregate data at the municipality or province level
'Map', to visualize the output datasets.
Author: Leonardo Cefalo [aut, cre] ,
Alessio Pollice [ctb, ths] ,
Paolo Maranzano [ctb]
Maintainer: Leonardo Cefalo <leonardo.cefalo@uniba.it>
Diff between SchoolDataIT versions 0.2.7 dated 2025-07-11 and 0.2.8 dated 2025-10-02
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/Get_Shapefile.R | 6 +++++- R/Map_School_Buildings.R | 2 +- R/Set_DB.R | 15 ++++++++++----- R/Util_DB_MIUR_num.R | 13 +++++++++++-- README.md | 7 +++++-- man/Map_School_Buildings.Rd | 2 +- man/Set_DB.Rd | 6 ++++++ man/Util_DB_MIUR_num.Rd | 7 ++++++- 11 files changed, 64 insertions(+), 26 deletions(-)
Title: Download and Analyze Crash Data
Description: Download crash data from the National Highway Traffic Safety Administration and prepare it for research.
Author: Steve Jackson [aut, cre]
Maintainer: Steve Jackson <steve.jackson@toxcel.com>
Diff between rfars versions 2.0.0 dated 2025-09-20 and 2.0.1 dated 2025-10-02
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- R/download_fars.R | 11 +++++++++-- R/download_gescrss.R | 10 +++++++++- R/get_fars.R | 21 ++++++++++++++++++++- R/get_gescrss.R | 21 ++++++++++++++++++++- R/helpers.R | 29 +++++++++++++++++++++++++++++ inst/doc/Searchable_Codebooks.html | 4 ++-- man/check_internet_connection.Rd |only 9 files changed, 100 insertions(+), 17 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 11.6 dated 2025-09-26 and 11.6.1 dated 2025-10-02
DESCRIPTION | 8 MD5 | 70 +++--- R/Partial_Moments.R | 25 ++ R/RcppExports.R | 28 -- README.md | 4 inst/doc/NNSvignette_Classification.R | 3 inst/doc/NNSvignette_Classification.Rmd | 3 inst/doc/NNSvignette_Classification.html | 57 +--- inst/doc/NNSvignette_Clustering_and_Regression.R | 3 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 4 inst/doc/NNSvignette_Comparing_Distributions.R | 3 inst/doc/NNSvignette_Comparing_Distributions.Rmd | 3 inst/doc/NNSvignette_Correlation_and_Dependence.R | 3 inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 4 inst/doc/NNSvignette_Forecasting.R | 3 inst/doc/NNSvignette_Forecasting.Rmd | 3 inst/doc/NNSvignette_Overview.R | 3 inst/doc/NNSvignette_Overview.Rmd | 3 inst/doc/NNSvignette_Overview.html | 104 +++------ inst/doc/NNSvignette_Partial_Moments.R | 3 inst/doc/NNSvignette_Partial_Moments.Rmd | 3 inst/doc/NNSvignette_Sampling.R | 3 inst/doc/NNSvignette_Sampling.Rmd | 4 man/PM.matrix.Rd | 25 -- src/fast_lm.cpp | 219 ++++++++++--------- src/partial_moments.cpp | 2 src/partial_moments_rcpp.cpp | 37 --- src/partial_moments_rcpp.h | 23 + vignettes/NNSvignette_Classification.Rmd | 3 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 4 vignettes/NNSvignette_Comparing_Distributions.Rmd | 3 vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 4 vignettes/NNSvignette_Forecasting.Rmd | 3 vignettes/NNSvignette_Overview.Rmd | 3 vignettes/NNSvignette_Partial_Moments.Rmd | 3 vignettes/NNSvignette_Sampling.Rmd | 4 36 files changed, 290 insertions(+), 390 deletions(-)
Title: Detecting Outliers in Network Meta-Analysis
Description: A set of functions providing several outlier (i.e., studies with extreme findings) and influential detection measures and methodologies in network meta-analysis :
- simple outlier and influential detection measures
- outlier and influential detection measures by considering study deletion (shift the mean)
- plots for outlier and influential detection measures
- Q-Q plot for network meta-analysis
- Forward Search algorithm in network meta-analysis.
- forward plots to monitor statistics in each step of the forward search algorithm
- forward plots for summary estimates and their confidence intervals in each step of forward search algorithm.
Author: Maria Petropoulou [aut, cre] ,
Guido Schwarzer [aut] ,
Agapios Panos [aut],
Dimitris Mavridis [aut]
Maintainer: Maria Petropoulou <m.petropoulou.a@gmail.com>
Diff between NMAoutlier versions 0.2.0 dated 2025-02-10 and 0.2.1 dated 2025-10-02
DESCRIPTION | 22 ++++++++------ MD5 | 44 ++++++++++++++--------------- R/NMAoutlier-package.R | 4 +- R/NMAoutlier.R | 8 ++++- R/NMAoutlier.measures.R | 25 +++++++++++----- R/Qnetplot.R | 2 - R/fwdplot.R | 2 - R/fwdplotest.R | 2 - R/measplot.R | 8 ++--- R/plotesthelper.R | 2 - R/plothelper.R | 2 - R/print.NMAoutlier.R | 9 +++--- R/print.NMAoutlier.measures.R | 63 ++++++++++++++++++++++++++---------------- R/res_multi.R | 2 - man/NMAoutlier-package.Rd | 4 +- man/NMAoutlier.Rd | 2 - man/NMAoutlier.measures.Rd | 4 +- man/Qnetplot.Rd | 2 - man/fwdplot.Rd | 2 - man/fwdplotest.Rd | 2 - man/measplot.Rd | 2 - man/plotesthelper.Rd | 2 - man/plothelper.Rd | 2 - 23 files changed, 125 insertions(+), 92 deletions(-)
Title: Broadcasted Array Operations Like 'NumPy'
Description: Implements efficient 'NumPy'-like broadcasted operations for atomic and recursive arrays.
In the context of operations involving 2 (or more) arrays,
“broadcasting” refers to efficiently recycling array dimensions without allocating additional memory.
Besides linking to 'Rcpp',
'broadcast' does not use any external libraries in any way;
'broadcast' was essentially made from scratch and can be installed out-of-the-box.
The implementations available in 'broadcast' include, but are not limited to, the following.
1) Broadcasted element-wise operations on any 2 arrays;
they support a large set of
relational, arithmetic, Boolean, string, and bit-wise operations.
2) A faster, more memory efficient, and broadcasted abind-like function,
for binding arrays along an arbitrary dimension.
3) Broadcasted ifelse-like, and apply-like functions.
4) Casting functions,
that cast subset-groups of an array to a new dimension, cast nested lists to dimensional lists, and vice-versa.
5) A few linear algebra fu [...truncated...]
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between broadcast versions 0.1.3 dated 2025-09-15 and 0.1.5 dated 2025-10-02
broadcast-0.1.3/broadcast/inst/tinytest/cast/test-acast-bycolumn.R |only broadcast-0.1.3/broadcast/inst/tinytest/cast/test-acast-bylayer.R |only broadcast-0.1.3/broadcast/inst/tinytest/cast/test-acast-byrow.R |only broadcast-0.1.3/broadcast/inst/tinytest/cast/test-acast-errors.R |only broadcast-0.1.3/broadcast/inst/tinytest/cast/test-acast-fill.R |only broadcast-0.1.5/broadcast/DESCRIPTION | 10 broadcast-0.1.5/broadcast/MD5 | 164 +++++---- broadcast-0.1.5/broadcast/NAMESPACE | 2 broadcast-0.1.5/broadcast/NEWS.md | 61 ++- broadcast-0.1.5/broadcast/R/RcppExports.R | 28 - broadcast-0.1.5/broadcast/R/aaa00_broadcast_help.R | 34 -- broadcast-0.1.5/broadcast/R/aaa01_broadcast_operators.R | 6 broadcast-0.1.5/broadcast/R/aaa02_broadcast_casting.R | 31 + broadcast-0.1.5/broadcast/R/aaa03_broadcast_bind.R | 26 + broadcast-0.1.5/broadcast/R/aaa05_broadcast_typecast.R | 3 broadcast-0.1.5/broadcast/R/acast.R | 1 broadcast-0.1.5/broadcast/R/bc_b.R | 9 broadcast-0.1.5/broadcast/R/bc_bit.R | 2 broadcast-0.1.5/broadcast/R/bc_cplx.R | 2 broadcast-0.1.5/broadcast/R/bc_d.R | 2 broadcast-0.1.5/broadcast/R/bc_i.R | 2 broadcast-0.1.5/broadcast/R/bc_ifelse.R | 2 broadcast-0.1.5/broadcast/R/bc_list.R | 2 broadcast-0.1.5/broadcast/R/bc_raw.R | 2 broadcast-0.1.5/broadcast/R/bc_rel.R | 2 broadcast-0.1.5/broadcast/R/bc_str.R | 2 broadcast-0.1.5/broadcast/R/bcapply.R | 2 broadcast-0.1.5/broadcast/R/broadcaster.R | 3 broadcast-0.1.5/broadcast/R/cast_dim2flat.R | 3 broadcast-0.1.5/broadcast/R/cast_dim2hier.R | 1 broadcast-0.1.5/broadcast/R/cast_hier2dim.R | 104 ------ broadcast-0.1.5/broadcast/R/dropnests.R | 24 - broadcast-0.1.5/broadcast/R/hier2dim.R |only broadcast-0.1.5/broadcast/R/internal_cast.R | 8 broadcast-0.1.5/broadcast/R/internal_functions.R | 8 broadcast-0.1.5/broadcast/R/meta_functions.R |only broadcast-0.1.5/broadcast/R/typecast.R | 41 +- broadcast-0.1.5/broadcast/R/zzz.R |only broadcast-0.1.5/broadcast/build/partial.rdb |binary broadcast-0.1.5/broadcast/inst/examples/broadcast_cast.R |only broadcast-0.1.5/broadcast/inst/examples/broadcaster.R | 11 broadcast-0.1.5/broadcast/inst/examples/cast_dim2flat.R |only broadcast-0.1.5/broadcast/inst/examples/cast_hier2dim.R | 37 -- broadcast-0.1.5/broadcast/inst/examples/dropnests.R | 10 broadcast-0.1.5/broadcast/inst/tinytest/acast |only broadcast-0.1.5/broadcast/inst/tinytest/bc_b/test-bc_b.R | 40 ++ broadcast-0.1.5/broadcast/inst/tinytest/bc_rel_attr/test-main.R | 2 broadcast-0.1.5/broadcast/inst/tinytest/bc_str/test-bc_str_dist.R | 16 broadcast-0.1.5/broadcast/inst/tinytest/cast/test-cast_hier2dim.R | 14 broadcast-0.1.5/broadcast/inst/tinytest/cast/test-cast_hier2dim_padding.R | 8 broadcast-0.1.5/broadcast/inst/tinytest/cast/test-dropnests.R | 34 +- broadcast-0.1.5/broadcast/inst/tinytest/cast/test-hier2dim.R | 10 broadcast-0.1.5/broadcast/inst/tinytest/cast/test-hiernames2dimnames-errors.R |only broadcast-0.1.5/broadcast/inst/tinytest/cast/test-hiernames2dimnames-nonames.R |only broadcast-0.1.5/broadcast/inst/tinytest/cast/test-hiernames2dimnames.R |only broadcast-0.1.5/broadcast/inst/tinytest/cast/test-listcast_general.R | 3 broadcast-0.1.5/broadcast/inst/tinytest/cast/test-rcpp_depth_range.R | 6 broadcast-0.1.5/broadcast/inst/tinytest/cast/test-rcpp_lenrange_atdepth.R | 2 broadcast-0.1.5/broadcast/inst/tinytest/test-ellipsis.R |only broadcast-0.1.5/broadcast/inst/tinytest/typecast/test-atomic_typecast.R | 2 broadcast-0.1.5/broadcast/inst/tinytest/typecast/test-broadcasterclass.R |only broadcast-0.1.5/broadcast/inst/tinytest/typecast/test-edgecases.R |only broadcast-0.1.5/broadcast/man/aaa00_broadcast_help.Rd | 39 -- broadcast-0.1.5/broadcast/man/aaa01_broadcast_operators.Rd | 17 - broadcast-0.1.5/broadcast/man/aaa02_broadcast_casting.Rd | 77 ++++ broadcast-0.1.5/broadcast/man/bc.b.Rd | 9 broadcast-0.1.5/broadcast/man/bc.bit.Rd | 2 broadcast-0.1.5/broadcast/man/bc.cplx.Rd | 2 broadcast-0.1.5/broadcast/man/bc.d.Rd | 2 broadcast-0.1.5/broadcast/man/bc.i.Rd | 2 broadcast-0.1.5/broadcast/man/bc.list.Rd | 2 broadcast-0.1.5/broadcast/man/bc.raw.Rd | 2 broadcast-0.1.5/broadcast/man/bc.rel.Rd | 2 broadcast-0.1.5/broadcast/man/bc.str.Rd | 2 broadcast-0.1.5/broadcast/man/bc_ifelse.Rd | 2 broadcast-0.1.5/broadcast/man/bcapply.Rd | 2 broadcast-0.1.5/broadcast/man/bind_array.Rd | 27 + broadcast-0.1.5/broadcast/man/broadcaster.Rd | 14 broadcast-0.1.5/broadcast/man/cast_dim2flat.Rd | 165 ---------- broadcast-0.1.5/broadcast/man/cast_hier2dim.Rd | 74 ---- broadcast-0.1.5/broadcast/man/dropnests.Rd | 16 broadcast-0.1.5/broadcast/man/figures/in2out-FALSE-red.svg |only broadcast-0.1.5/broadcast/man/figures/in2out-TRUE-green.svg |only broadcast-0.1.5/broadcast/man/hier2dim.Rd |only broadcast-0.1.5/broadcast/man/typecast.Rd | 3 broadcast-0.1.5/broadcast/src/RcppExports.cpp | 61 +-- broadcast-0.1.5/broadcast/src/broadcast.h | 90 +++++ broadcast-0.1.5/broadcast/src/rcpp_bcDist_str.cpp | 16 broadcast-0.1.5/broadcast/src/rcpp_bc_b.cpp | 69 ++-- broadcast-0.1.5/broadcast/src/rcpp_hier2dim.cpp | 142 +++++++- broadcast-0.1.5/broadcast/tests/tinytest.R | 3 91 files changed, 877 insertions(+), 747 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-22 1.0.1
2022-12-06 1.0.0
Title: Estimate Vaccine Effectiveness Based on Different Study Designs
Description: Provides tools for estimating vaccine effectiveness and
related metrics. The 'vaccineff_data' class manages key features for
preparing, visualizing, and organizing cohort data, as well as
estimating vaccine effectiveness. The results and model performance
are assessed using the 'vaccineff' class.
Author: David Santiago Quevedo [aut] ,
Zulma M. Cucunuba [aut, cre] ,
International Development Research Center [fnd] ,
Geraldine Gomez Millan [ctb] ,
Pratik Gupte [ctb] ,
Erika J Cantor [ctb] ,
Santiago Loaiza [ctb] ,
Jaime Pavlich-Mariscal [ctb] ,
Hugo Gr [...truncated...]
Maintainer: Zulma M. Cucunuba <tracelacdev@gmail.com>
Diff between vaccineff versions 1.0.0 dated 2024-11-29 and 1.0.1 dated 2025-10-02
vaccineff-1.0.0/vaccineff/tests/testthat/_snaps/coh_match_utils.md |only vaccineff-1.0.1/vaccineff/DESCRIPTION | 54 +++--- vaccineff-1.0.1/vaccineff/LICENSE | 2 vaccineff-1.0.1/vaccineff/MD5 | 57 +++--- vaccineff-1.0.1/vaccineff/NEWS.md | 86 +++++----- vaccineff-1.0.1/vaccineff/R/coh_data_wrangling.R | 2 vaccineff-1.0.1/vaccineff/R/coh_eff_utils.R | 2 vaccineff-1.0.1/vaccineff/R/coh_immunization.R | 11 - vaccineff-1.0.1/vaccineff/R/coh_match_iterate.R | 7 vaccineff-1.0.1/vaccineff/R/coh_match_static.R | 2 vaccineff-1.0.1/vaccineff/R/coh_match_utils.R | 12 - vaccineff-1.0.1/vaccineff/R/handler_validations.R | 6 vaccineff-1.0.1/vaccineff/R/utils_get_age_group.R | 2 vaccineff-1.0.1/vaccineff/README.md | 53 +++--- vaccineff-1.0.1/vaccineff/build/vignette.rds |binary vaccineff-1.0.1/vaccineff/inst/WORDLIST | 11 - vaccineff-1.0.1/vaccineff/inst/doc/cohort_design.R | 2 vaccineff-1.0.1/vaccineff/inst/doc/cohort_design.html | 54 +++--- vaccineff-1.0.1/vaccineff/inst/doc/other_designs.R | 2 vaccineff-1.0.1/vaccineff/inst/doc/vaccineff.R | 2 vaccineff-1.0.1/vaccineff/inst/doc/vaccineff.html | 24 +- vaccineff-1.0.1/vaccineff/man/figures/README-unnamed-chunk-4-1.png |binary vaccineff-1.0.1/vaccineff/man/vaccineff-package.Rd | 4 vaccineff-1.0.1/vaccineff/tests/spelling.R | 3 vaccineff-1.0.1/vaccineff/tests/testthat/setup-options.R | 5 vaccineff-1.0.1/vaccineff/tests/testthat/test-coh_data_wrangling.R | 4 vaccineff-1.0.1/vaccineff/tests/testthat/test-coh_match.R | 2 vaccineff-1.0.1/vaccineff/tests/testthat/test-coh_match_utils.R | 5 vaccineff-1.0.1/vaccineff/tests/testthat/test-handler_warnings.R | 4 vaccineff-1.0.1/vaccineff/tests/testthat/test-utils_coverage.R | 6 30 files changed, 221 insertions(+), 203 deletions(-)
Title: Statistical Reporting with 'Quarto'
Description: Provides statistical components, tables, and graphs
that are useful in 'Quarto' and 'RMarkdown' reports and that produce 'Quarto'
elements for special formatting such as tabs and marginal notes and graphs.
Some of the functions produce entire report sections with tabs, e.g.,
the missing data report created by missChk(). Functions for inserting
variables and tables inside 'graphviz' and 'mermaid' diagrams are included,
and so are special clinical trial graphics for adverse event reporting.
Author: Frank E Harrell Jr [aut, cre]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between qreport versions 1.0-2 dated 2025-04-11 and 1.1-0 dated 2025-10-02
DESCRIPTION | 26 +++++++++++++------------- MD5 | 10 ++++++---- NEWS | 4 ++++ R/makedot.r |only R/reptools.r | 2 +- man/makedot.Rd |only man/makegraphviz.Rd | 2 +- 7 files changed, 25 insertions(+), 19 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 1.9.1.0 dated 2023-09-12 and 2.0.1.4 dated 2025-10-02
prome-1.9.1.0/prome/inst/stan/cross.stan |only prome-2.0.1.4/prome/DESCRIPTION | 14 +++--- prome-2.0.1.4/prome/MD5 | 17 ++++--- prome-2.0.1.4/prome/NAMESPACE | 4 + prome-2.0.1.4/prome/R/blindinglogit.R |only prome-2.0.1.4/prome/R/crossover2x2.R | 27 ++++++----- prome-2.0.1.4/prome/inst/stan/blindlogit.stan |only prome-2.0.1.4/prome/inst/stan/cross0.stan |only prome-2.0.1.4/prome/inst/stan/cross1.stan | 58 ++++++++++++------------- prome-2.0.1.4/prome/inst/stan/proportion.stan | 4 - prome-2.0.1.4/prome/inst/stan/proportions.stan | 4 - prome-2.0.1.4/prome/man/lslogit.Rd |only 12 files changed, 69 insertions(+), 59 deletions(-)
Title: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model
Description: Fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and Poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
Author: Jelle Goeman [aut, cre],
Rosa Meijer [aut],
Nimisha Chaturvedi [aut],
Matthew Lueder [aut]
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between penalized versions 0.9-52 dated 2022-04-23 and 0.9-53 dated 2025-10-02
ChangeLog | 3 + DESCRIPTION | 28 ++++++++++--- MD5 | 19 ++++----- R/RcppExports.R |only build/vignette.rds |binary inst/CITATION | 70 ++++++++++++++++++++-------------- inst/doc/penalized.pdf |binary man/breslow.Rd | 100 ++++++++++++++++++++++++------------------------- src/Makevars | 3 - src/Makevars.win | 1 src/RcppExports.cpp | 5 ++ 11 files changed, 133 insertions(+), 96 deletions(-)
Title: A Self-Adaptive Approach for Demodulating Multi-Component Signal
Description: Local Mean Decomposition is an iterative and self-adaptive approach for demodulating, processing, and analyzing multi-component amplitude modulated and frequency modulated signals. This R package is based on the approach suggested by Smith (2005) <doi:10.1098/rsif.2005.0058> and the 'Python' library 'PyLMD'.
Author: Shubhra Prakash [trl, aut, cre]
Maintainer: Shubhra Prakash <shubhraprakash279@gmail.com>
Diff between LMD versions 1.0.0 dated 2022-09-20 and 1.2.1 dated 2025-10-02
DESCRIPTION | 15 MD5 | 38 +- NAMESPACE | 27 - NEWS.md | 20 - R/lmd_shiny.R |only R/plot_lmd.R | 31 + README.md | 2 build/vignette.rds |binary inst/doc/Getting_Started_with_LMD.R | 2 inst/doc/Getting_Started_with_LMD.Rmd | 2 inst/doc/Getting_Started_with_LMD.html | 515 ++++++++++++++++----------------- man/extract_product_function.Rd | 82 ++--- man/find_extrema.Rd | 60 +-- man/is_monotonous.Rd | 64 ++-- man/lmd.Rd | 126 ++++---- man/lmd_shiny.Rd |only man/local_mean_and_envelope.Rd | 68 ++-- man/moving_average_smooth.Rd | 82 ++--- man/plot_lmd.Rd | 84 ++--- tests/testthat.R | 24 - vignettes/Getting_Started_with_LMD.Rmd | 2 21 files changed, 642 insertions(+), 602 deletions(-)
Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of
Markov Chain Monte Carlo simulations, as well as for graphically display
results from full MCMC analysis. The package also facilitates the graphical
interpretation of models by providing flexible functions to plot the
results against observed variables, and functions to work with
hierarchical/multilevel batches of parameters
(Fernández-i-Marín, 2016 <doi:10.18637/jss.v070.i09>).
Author: Xavier Fernandez i Marin [aut, cre]
Maintainer: Xavier Fernandez i Marin <xavier.fim@gmail.com>
Diff between ggmcmc versions 1.5.1.1 dated 2021-02-10 and 1.5.1.2 dated 2025-10-02
DESCRIPTION | 14 MD5 | 46 +- NAMESPACE | 1 NEWS | 295 ++++++------ R/data.R | 2 R/functions.R | 20 R/ggs.R | 42 - R/ggs_caterpillar.R | 2 R/ggs_compare_partial.R | 4 R/ggs_effective.R | 2 R/ggs_geweke.R | 4 R/ggs_pairs.R | 4 R/help.R | 4 build/vignette.rds |binary inst/doc/using_ggmcmc.R | 28 - inst/doc/using_ggmcmc.Rmd | 5 inst/doc/using_ggmcmc.html | 1025 ++++++++++++++++++++++++++++++--------------- inst/doc/v70i09.R | 58 +- inst/doc/v70i09.pdf |binary man/ggmcmc.Rd | 1 man/gl_unq.Rd | 2 man/radon.Rd | 2 vignettes/bibliography.bib | 2 vignettes/using_ggmcmc.Rmd | 5 24 files changed, 970 insertions(+), 598 deletions(-)
Title: Lightweight Repackaging of 'Themes' for 'ggplot2'
Description: Themes for 'ggplot2' are a convenient way to style plots. The 'hrbrthemes' package
contains a particularly nice one, but brings along a significant tail of dependencies. So this
(currently experimental) package brings along just the 'theme_ipsum_rc' theme using the 'Roboto'
'Condensed' font. Should the font not be installed on your system, see the help in the package
'hrbrthemes' on how to install 'Roboto Condensed'. Note that 'hrbrthemes' is now archived at
CRAN.
Author: Dirk Eddelbuettel [aut, cre] ,
Bob Rudis [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tinythemes versions 0.0.3 dated 2025-03-29 and 0.0.4 dated 2025-10-02
ChangeLog | 7 +++++++ DESCRIPTION | 20 +++++++++++--------- MD5 | 10 +++++----- R/theme.R | 2 +- build/partial.rdb |binary man/theme_ipsum_rc.Rd | 2 +- 6 files changed, 25 insertions(+), 16 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code, automated
reporting or use an easy to remember set of tidy functions for low
code exploratory data analysis.
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 1.3.5 dated 2025-06-24 and 1.3.6 dated 2025-10-02
DESCRIPTION | 6 MD5 | 82 ++++---- NEWS.md | 15 + R/explore.R | 15 + build/vignette.rds |binary inst/doc/abtest.html | 41 ++-- inst/doc/clean-drop.html | 39 ++-- inst/doc/data.html | 385 ++++++++++++++++++++--------------------- inst/doc/describe.html | 49 ++--- inst/doc/explain.html | 95 +++++----- inst/doc/explore-mtcars.html | 49 ++--- inst/doc/explore-penguins.html | 29 +-- inst/doc/explore-titanic.html | 41 ++-- inst/doc/explore.R | 26 +- inst/doc/explore.html | 89 +++++---- inst/doc/predict.html | 105 +++++------ inst/doc/report-target.R | 2 inst/doc/report-target.html | 27 +- inst/doc/report-targetpct.R | 2 inst/doc/report-targetpct.html | 27 +- inst/doc/report.R | 2 inst/doc/report.html | 25 +- inst/doc/tips-tricks.R | 18 - inst/doc/tips-tricks.html | 67 +++---- man/check_vec_low_variance.Rd | 50 ++--- man/create_data_abtest.Rd | 90 ++++----- man/create_data_esoteric.Rd | 72 +++---- man/cut_vec_num_avg.Rd | 38 ++-- man/drop_obs_if.Rd | 46 ++-- man/drop_obs_with_na.Rd | 44 ++-- man/drop_var_by_names.Rd | 46 ++-- man/drop_var_low_variance.Rd | 46 ++-- man/drop_var_no_variance.Rd | 42 ++-- man/drop_var_not_numeric.Rd | 42 ++-- man/drop_var_with_na.Rd | 42 ++-- man/explore-package.Rd | 1 man/explore_col.Rd | 106 +++++------ man/get_color.Rd | 72 +++---- man/interact.Rd | 54 ++--- man/log_info_if.Rd | 38 ++-- man/show_color.Rd | 42 ++-- man/use_data_wordle.Rd | 42 ++-- 42 files changed, 1135 insertions(+), 1014 deletions(-)
Title: Hierarchical Methods for Differential Equations
Description: Wrapper for Stan that offers a number of in-built models to implement a hierarchical Bayesian longitudinal model for repeat observation data. Model choice selects the differential equation that is fit to the observations. Single and multi-individual models are available. O'Brien et al. (2024) <doi:10.1111/2041-210X.14463>.
Author: Daniel Falster [aut, ctb] ,
Tess O'Brien [aut, cre, cph] ,
Fonti Kar [ctb] ,
David Warton [aut, ctb]
Maintainer: Tess O'Brien <tess_obrien@fastmail.com>
Diff between hmde versions 1.2.1 dated 2025-07-04 and 1.2.2 dated 2025-10-02
DESCRIPTION | 6 +- MD5 | 24 ++++---- NEWS.md | 5 + README.md | 21 +++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/canham.html | 2 inst/doc/constant-growth.html | 58 ++++++++++---------- inst/doc/here_be_dragons.html | 26 ++++----- inst/doc/hmde_for_mathematicians.html | 4 - inst/doc/von-bertalanffy.html | 75 ++++++++++++++------------- tests/testthat/test-hmde_plot_de_pieces.R | 4 - tests/testthat/test-hmde_plot_obs_est_inds.R | 5 - 13 files changed, 114 insertions(+), 116 deletions(-)
Title: Chunkwise Text-File Processing for 'dplyr'
Description: Data stored in text file can be processed chunkwise using 'dplyr' commands. These
are recorded and executed per data chunk, so large files can be processed with
limited memory using the 'LaF' package.
Author: Edwin de Jonge [aut, cre]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between chunked versions 0.6.0 dated 2022-03-07 and 0.6.1 dated 2025-10-02
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NAMESPACE | 3 +++ R/insert_chunk_into.R | 2 +- R/pkg.R | 2 +- R/unsupported.R | 3 +++ man/chunked-package.Rd | 13 +++++++++++++ man/insert_chunkwise_into.Rd | 2 +- 8 files changed, 35 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-22 0.1.0
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression. Specifically, the package implements robust least angle
regression (Khan, Van Aelst & Zamar, 2007; <doi:10.1198/016214507000000950>),
(robust) groupwise least angle regression (Alfons, Croux & Gelper, 2016;
<doi:10.1016/j.csda.2015.02.007>), and sparse least trimmed squares
regression (Alfons, Croux & Gelper, 2013; <doi:10.1214/12-AOAS575>).
Author: Andreas Alfons [aut, cre] ,
Dirk Eddelbuettel [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.8.1 dated 2024-06-30 and 0.8.2 dated 2025-10-02
DESCRIPTION | 15 MD5 | 118 +- NAMESPACE | 264 ++-- NEWS | 7 R/AIC.R | 328 ++--- R/accessors.R | 418 +++---- R/fastLasso.R | 100 - R/initialSubsets.R | 100 - R/nci60.R | 188 +-- R/perry.R | 314 ++--- R/plot.R | 1780 +++++++++++++++---------------- R/print.R | 374 +++--- R/regFun.R | 114 - R/robustHD-package.R | 58 - R/seqModel.R | 212 +-- R/setupCoefPlot.R | 570 ++++----- R/setupCritPlot.R | 478 ++++---- R/standardize.R | 260 ++-- R/test.R | 62 - R/tsBlocks.R | 180 +-- R/utils.R | 512 ++++---- R/weights.R | 124 +- build/partial.rdb |binary data/TopGear.RData |binary data/nci60.RData |binary man/AIC.seqModel.Rd | 216 +-- man/coef.seqModel.Rd | 230 ++-- man/coefPlot.Rd | 264 ++-- man/corHuber.Rd | 228 +-- man/critPlot.Rd | 246 ++-- man/diagnosticPlot.Rd | 400 +++--- man/fitted.seqModel.Rd | 222 +-- man/getScale.Rd | 138 +- man/grplars.Rd | 544 ++++----- man/lambda0.Rd | 230 ++-- man/nci60.Rd | 176 +-- man/partialOrder.Rd | 84 - man/perry.seqModel.Rd | 286 ++-- man/plot.seqModel.Rd | 190 +-- man/predict.seqModel.Rd | 242 ++-- man/residuals.seqModel.Rd | 238 ++-- man/rlars.Rd | 478 ++++---- man/robustHD-package.Rd | 68 - man/setupCoefPlot.Rd | 312 ++--- man/setupCritPlot.Rd | 296 ++--- man/setupDiagnosticPlot.Rd | 322 ++--- man/sparseLTS.Rd | 594 +++++----- man/standardize.Rd | 152 +- man/tsBlocks.Rd | 82 - man/tslars.Rd | 402 +++---- man/tslarsP.Rd | 458 +++---- man/weights.sparseLTS.Rd | 172 +- man/winsorize.Rd | 252 ++-- src/fastGrplars.cpp | 399 +++--- src/fastLars.cpp | 31 src/fastSparseLTS.cpp | 2 tests/testthat.R | 8 tests/testthat/test-fastLasso-highdim.R | 102 - tests/testthat/test-fastLasso-multiple.R | 132 +- tests/testthat/test-fastLasso-simple.R | 124 +- 60 files changed, 7451 insertions(+), 7445 deletions(-)
Title: (Robust) Canonical Correlation Analysis via Projection Pursuit
Description: Canonical correlation analysis and maximum correlation via
projection pursuit, as well as fast implementations of correlation
estimators, with a focus on robust and nonparametric methods.
Author: Andreas Alfons [aut, cre] ,
David Simcha [ctb] ) implementation of Kendall correlation)
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between ccaPP versions 0.3.4 dated 2024-09-04 and 0.3.5 dated 2025-10-02
DESCRIPTION | 15 ++++++++------- MD5 | 16 ++++++++-------- NEWS | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary data/diabetes.RData |binary inst/doc/ccaPP-intro.pdf |binary src/cca.cpp | 4 ++-- vignettes/maxCor.bib | 2 +- 9 files changed, 24 insertions(+), 18 deletions(-)
Title: Access the UNESCO Institute for Statistics API
Description: Retrieve data from the UNESCO Institute for Statistics (UIS) API
<https://api.uis.unesco.org/api/public/documentation/>. UIS provides public
access to more than 4,000 indicators focusing on education, science and
technology, culture, and communication.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between uisapi versions 0.1.0 dated 2025-03-06 and 0.1.1 dated 2025-10-02
DESCRIPTION | 10 ++--- MD5 | 8 ++-- NEWS.md | 4 ++ R/uis_get_indicators.R | 5 ++ README.md | 96 +++++++++++++++++++++++++++++++------------------ 5 files changed, 79 insertions(+), 44 deletions(-)
Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object
as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre],
Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyseurat versions 0.8.0 dated 2024-01-09 and 0.8.4 dated 2025-10-02
tidyseurat-0.8.0/tidyseurat/build/tidyseurat.pdf |only tidyseurat-0.8.0/tidyseurat/tests/testthat/Rplots.pdf |only tidyseurat-0.8.4/tidyseurat/DESCRIPTION | 20 tidyseurat-0.8.4/tidyseurat/MD5 | 42 - tidyseurat-0.8.4/tidyseurat/NAMESPACE | 3 tidyseurat-0.8.4/tidyseurat/R/dplyr_methods.R | 2 tidyseurat-0.8.4/tidyseurat/R/methods.R | 4 tidyseurat-0.8.4/tidyseurat/R/print_method.R | 1 tidyseurat-0.8.4/tidyseurat/R/tidyr_methods.R | 2 tidyseurat-0.8.4/tidyseurat/R/utilities.R | 23 tidyseurat-0.8.4/tidyseurat/README.md | 8 tidyseurat-0.8.4/tidyseurat/build/stage23.rdb |binary tidyseurat-0.8.4/tidyseurat/build/vignette.rds |binary tidyseurat-0.8.4/tidyseurat/inst/doc/figures_article.R | 316 +++++------ tidyseurat-0.8.4/tidyseurat/inst/doc/figures_article.html | 189 +++---- tidyseurat-0.8.4/tidyseurat/inst/doc/introduction.R | 286 +++++----- tidyseurat-0.8.4/tidyseurat/inst/doc/introduction.html | 372 ++++++-------- tidyseurat-0.8.4/tidyseurat/man/as_tibble.Rd | 2 tidyseurat-0.8.4/tidyseurat/man/formatting.Rd | 2 tidyseurat-0.8.4/tidyseurat/man/fragments/intro.Rmd | 3 tidyseurat-0.8.4/tidyseurat/man/ggplot.Rd | 3 tidyseurat-0.8.4/tidyseurat/man/slice.Rd | 4 tidyseurat-0.8.4/tidyseurat/tests/testthat/test-methods.R | 5 23 files changed, 623 insertions(+), 664 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled. For regression versions of the methods, Monte Carlo and asymptotic methods are used.
Author: Ivair Ramos Silva [aut, cre],
Martin Kulldorff [aut]
Maintainer: Ivair Ramos Silva <ivair@ufop.edu.br>
Diff between Sequential versions 4.4 dated 2025-08-20 and 4.5 dated 2025-10-02
DESCRIPTION | 10 - MD5 | 18 +-- NAMESPACE | 3 R/Analyze.CondPoisson.R | 6 - R/Analyze.Multinomial.R | 214 +++++++++++++++++++++++++++------------- R/AnalyzeSetUp.CondPoisson.R | 4 R/AnalyzeSetUp.Multinomial.R | 15 +- man/Analyze.Multinomial.Rd | 128 +++++++++++++++-------- man/AnalyzeSetUp.Multinomial.Rd | 7 - man/Sequential-package.Rd | 14 ++ 10 files changed, 272 insertions(+), 147 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Marc Becker [cre, aut] ,
Lennart Schneider [aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3mbo versions 0.3.1 dated 2025-08-19 and 0.3.2 dated 2025-10-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test_mbo_defaults.R | 4 ++-- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: General Linear Mixed Models for Gene-Level Differential
Expression
Description: Using mixed effects models to analyse longitudinal gene expression can highlight differences between sample groups over time. The most widely used differential gene expression tools are unable to fit linear mixed effect models, and are less optimal for analysing longitudinal data. This package provides negative binomial and Gaussian mixed effects models to fit gene expression and other biological data across repeated samples. This is particularly useful for investigating changes in RNA-Sequencing gene expression between groups of individuals over time, as described in: Rivellese, F., Surace, A. E., Goldmann, K., Sciacca, E., Cubuk, C., Giorli, G., ... Lewis, M. J., & Pitzalis, C. (2022) Nature medicine <doi:10.1038/s41591-022-01789-0>.
Author: Myles Lewis [aut, cre] ,
Katriona Goldmann [aut] ,
Elisabetta Sciacca [aut] ,
Cankut Cubuk [ctb] ,
Anna Surace [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between glmmSeq versions 0.5.5 dated 2022-10-08 and 0.5.7 dated 2025-10-02
DESCRIPTION | 27 MD5 | 30 NAMESPACE | 3 NEWS.md | 9 R/AllClass.R | 6 R/glmmRefit.R | 2 R/glmmSeq.R | 17 R/lmmSeq.R | 12 README.md | 4 build/vignette.rds |binary inst/doc/glmmSeq.R | 132 +- inst/doc/glmmSeq.html | 2704 ++++++++++++++++++++++++++------------------------ inst/doc/glmmSeq.rmd | 4 man/glmmRefit.Rd | 2 man/lmmSeq.Rd | 2 vignettes/glmmSeq.rmd | 4 16 files changed, 1545 insertions(+), 1413 deletions(-)
Title: Accounting for Random Displacements of True GPS Coordinates of
Data
Description: The purpose is to account for the random displacements
(jittering) of true survey household cluster center coordinates in geostatistical
analyses of Demographic and Health Surveys program (DHS) data. Adjustment for
jittering can be implemented either in the spatial random effect, or in the
raster/distance based covariates, or in both. Detailed information about the methods
behind the package functionality can be found in our two papers.
Umut Altay, John Paige, Andrea Riebler, Geir-Arne Fuglstad (2024) <doi:10.32614/RJ-2024-027>.
Umut Altay, John Paige, Andrea Riebler, Geir-Arne Fuglstad (2023) <doi:10.1177/1471082X231219847>.
Author: Umut Altay [cre, aut],
John Paige [aut],
Geir-Arne Fuglstad [aut],
Andrea Riebler [aut]
Maintainer: Umut Altay <altayumut.ua@gmail.com>
Diff between GeoAdjust versions 2.0.0 dated 2023-09-15 and 2.0.1 dated 2025-10-02
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- R/plotPred.R | 4 ++-- 3 files changed, 11 insertions(+), 11 deletions(-)
Title: A Data Analysis GUI for R
Description: An intuitive, cross-platform graphical data analysis system. It uses menus and dialogs to guide the user efficiently through the data manipulation and analysis process, and has an excel like spreadsheet for easy data frame visualization and editing. Deducer works best when used with the Java based R GUI JGR, but the dialogs can be called from the command line. Dialogs have also been integrated into the Windows Rgui.
Author: Ian Fellows [aut, cre]
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between Deducer versions 0.9-0 dated 2025-05-07 and 0.9-1 dated 2025-10-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- inst/java/deducer.jar |binary java/org/deducer.jar |binary 5 files changed, 9 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-14 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-24 0.4.1
2019-02-15 0.4.0
2018-12-17 0.3.0
2018-09-27 0.2.2
2018-09-16 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-20 1.0.0
Title: Continuous Time Mediation
Description: Calculates effect sizes, standard errors and confidence intervals
in continuous-time mediation models
(Deboeck and Preacher, 2015 <doi:10.1080/10705511.2014.973960>;
Ryan and Hamaker, 2021 <doi:10.1007/s11336-021-09767-0>).
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between cTMed versions 1.0.6 dated 2025-02-21 and 1.0.7 dated 2025-10-02
DESCRIPTION | 25 ++-- MD5 | 178 ++++++++++++++--------------- NEWS.md | 6 R/cTMed-boot-beta-dot.R | 11 - R/cTMed-boot-beta-std-dot.R | 41 ++---- R/cTMed-boot-beta-std.R | 4 R/cTMed-boot-beta.R | 4 R/cTMed-boot-central-dot.R | 11 - R/cTMed-boot-ci-dot.R | 106 ++++++++--------- R/cTMed-boot-indirect-central.R | 4 R/cTMed-boot-med-dot.R | 11 - R/cTMed-boot-med-std-dot.R | 59 ++++----- R/cTMed-boot-med-std.R | 8 - R/cTMed-boot-med.R | 8 - R/cTMed-boot-total-central.R | 4 R/cTMed-delta-beta-dot.R | 28 +--- R/cTMed-delta-beta-std-dot.R | 28 +--- R/cTMed-delta-beta-std.R | 2 R/cTMed-delta-beta.R | 2 R/cTMed-delta-central-dot.R | 30 ++-- R/cTMed-delta-ci-dot.R | 90 +++++++------- R/cTMed-delta-indirect-central.R | 2 R/cTMed-delta-med-dot.R | 34 ++--- R/cTMed-delta-med-std-dot.R | 34 ++--- R/cTMed-delta-med-std.R | 6 R/cTMed-delta-med.R | 6 R/cTMed-delta-total-central.R | 2 R/cTMed-direct-std.R | 6 R/cTMed-direct.R | 6 R/cTMed-indirect-central.R | 2 R/cTMed-indirect-std.R | 6 R/cTMed-indirect.R | 6 R/cTMed-mc-beta-dot.R | 41 ++---- R/cTMed-mc-beta-std-dot.R | 71 ++++------- R/cTMed-mc-beta-std.R | 2 R/cTMed-mc-beta.R | 2 R/cTMed-mc-central-dot.R | 41 ++---- R/cTMed-mc-ci-dot.R | 64 +++++----- R/cTMed-mc-indirect-central.R | 2 R/cTMed-mc-med-dot.R | 41 ++---- R/cTMed-mc-med-std-dot.R | 89 ++++++-------- R/cTMed-mc-med-std.R | 6 R/cTMed-mc-med.R | 6 R/cTMed-mc-phi-sigma.R | 24 +-- R/cTMed-mc-phi.R | 24 +-- R/cTMed-mc-total-central.R | 2 R/cTMed-med-std.R | 6 R/cTMed-med.R | 6 R/cTMed-methods-ctmedboot.R | 42 ++---- R/cTMed-methods-ctmeddelta.R | 38 ++---- R/cTMed-methods-ctmedmc.R | 38 ++---- R/cTMed-methods-ctmedmcphi.R | 2 R/cTMed-methods-ctmedmed.R | 69 +++++------ R/cTMed-methods-ctmedposteriorphi.R | 10 - R/cTMed-methods-ctmedtraj.R | 18 -- R/cTMed-plot-beta-ci-dot.R | 1 R/cTMed-plot-central-ci-dot.R | 1 R/cTMed-plot-central-dot.R | 1 R/cTMed-plot-med-ci-dot.R | 1 R/cTMed-plot-med-dot.R | 1 R/cTMed-plot-trajectory-dot.R | 1 R/cTMed-posterior-beta-dot.R | 13 -- R/cTMed-posterior-beta.R | 2 R/cTMed-posterior-central-dot.R | 44 ++----- R/cTMed-posterior-indirect-central.R | 2 R/cTMed-posterior-med-dot.R | 44 ++----- R/cTMed-posterior-med.R | 6 R/cTMed-posterior-total-central.R | 2 R/cTMed-total-central.R | 2 R/cTMed-total-std.R | 2 R/cTMed-total.R | 2 R/cTMed-trajectory.R | 2 R/wald-ci-wald-dot.R | 4 R/wald-probs-of-alpha-dot.R | 10 - build/partial.rdb |binary inst/CITATION | 2 man/BootBeta.Rd | 2 man/BootBetaStd.Rd | 2 man/BootIndirectCentral.Rd | 2 man/BootMed.Rd | 2 man/BootMedStd.Rd | 2 man/BootTotalCentral.Rd | 2 man/cTMed-package.Rd | 2 src/source.cpp | 16 +- tests/testthat/test-cTMed-boot-beta-std.R | 20 --- tests/testthat/test-cTMed-boot-med-std.R | 16 -- tests/testthat/test-cTMed-delta-beta-std.R | 4 tests/testthat/test-cTMed-mc-beta-std.R | 4 tests/testthat/test-cTMed-mc-phi-sigma.R | 8 - tests/testthat/test-cTMed-total-std.R | 8 - 90 files changed, 709 insertions(+), 938 deletions(-)