Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Eamon B. O'Dea [c [...truncated...]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 4.6 dated 2023-01-11 and 4.7 dated 2023-03-02
pomp-4.6/pomp/R/deprecated.R |only pomp-4.6/pomp/man/pomp-deprecated.Rd |only pomp-4.7/pomp/DESCRIPTION | 16 +-- pomp-4.7/pomp/MD5 | 124 +++++++++++++++--------------- pomp-4.7/pomp/NAMESPACE | 5 - pomp-4.7/pomp/R/abc.R | 6 - pomp-4.7/pomp/R/as_data_frame.R | 3 pomp-4.7/pomp/R/blowflies.R | 6 - pomp-4.7/pomp/R/bsmc2.R | 10 +- pomp-4.7/pomp/R/conc.R |only pomp-4.7/pomp/R/concat.R | 143 +++-------------------------------- pomp-4.7/pomp/R/cond_logLik.R | 17 ++++ pomp-4.7/pomp/R/covariate_table.R | 10 -- pomp-4.7/pomp/R/covmat.R | 10 +- pomp-4.7/pomp/R/defunct.R |only pomp-4.7/pomp/R/eff_sample_size.R | 17 ++++ pomp-4.7/pomp/R/extract.R | 3 pomp-4.7/pomp/R/filter_mean.R | 2 pomp-4.7/pomp/R/filter_traj.R | 30 ++----- pomp-4.7/pomp/R/flow.R | 4 pomp-4.7/pomp/R/kalman.R | 14 +-- pomp-4.7/pomp/R/listie.R | 62 +++++++-------- pomp-4.7/pomp/R/load.R | 8 - pomp-4.7/pomp/R/melt.R | 20 ++++ pomp-4.7/pomp/R/mif2.R | 18 ++-- pomp-4.7/pomp/R/nlf.R | 46 +++++------ pomp-4.7/pomp/R/obs.R | 23 ++++- pomp-4.7/pomp/R/ou2.R | 4 pomp-4.7/pomp/R/parameter_trans.R | 6 - pomp-4.7/pomp/R/pfilter.R | 8 - pomp-4.7/pomp/R/plot.R | 23 ++--- pomp-4.7/pomp/R/pmcmc.R | 8 - pomp-4.7/pomp/R/pomp.R | 6 - pomp-4.7/pomp/R/probe.R | 6 - pomp-4.7/pomp/R/probe_match.R | 6 - pomp-4.7/pomp/R/saved_states.R | 16 +-- pomp-4.7/pomp/R/simulate.R | 8 - pomp-4.7/pomp/R/spect.R | 24 ++--- pomp-4.7/pomp/R/spect_match.R | 16 +-- pomp-4.7/pomp/R/states.R | 19 +++- pomp-4.7/pomp/R/time.R | 4 pomp-4.7/pomp/R/traces.R | 8 - pomp-4.7/pomp/R/traj_match.R | 12 +- pomp-4.7/pomp/R/trajectory.R | 8 - pomp-4.7/pomp/R/workhorses.R | 44 +++++----- pomp-4.7/pomp/R/wpfilter.R | 20 +--- pomp-4.7/pomp/inst/CITATION | 4 pomp-4.7/pomp/inst/NEWS | 27 ++++++ pomp-4.7/pomp/inst/NEWS.Rd | 14 +++ pomp-4.7/pomp/man/conc.Rd |only pomp-4.7/pomp/man/concat.Rd | 54 ++++++------- pomp-4.7/pomp/man/cond_logLik.Rd | 5 - pomp-4.7/pomp/man/ebola.Rd | 23 +---- pomp-4.7/pomp/man/eff_sample_size.Rd | 5 - pomp-4.7/pomp/man/filter_mean.Rd | 2 pomp-4.7/pomp/man/filter_traj.Rd | 9 -- pomp-4.7/pomp/man/forecast.Rd | 2 pomp-4.7/pomp/man/obs.Rd | 6 - pomp-4.7/pomp/man/ou2.Rd | 4 pomp-4.7/pomp/man/pfilter.Rd | 2 pomp-4.7/pomp/man/plot.Rd | 1 pomp-4.7/pomp/man/pmcmc.Rd | 2 pomp-4.7/pomp/man/pomp-defunct.Rd |only pomp-4.7/pomp/man/pred_mean.Rd | 2 pomp-4.7/pomp/man/pred_var.Rd | 2 pomp-4.7/pomp/man/states.Rd | 6 - 66 files changed, 496 insertions(+), 517 deletions(-)
Title: Pedigree/Family-Based Genetic Association Tests Analysis and
Power
Description: This R package provides power calculations via internal simulation methods. The package also provides a frontend to the now abandoned PBAT program (developed by Christoph Lange), and reads in the corresponding output and displays results and figures when appropriate. The license of this R package itself is GPL. However, to have the program interact with the PBAT program for some functionality of the R package, users must additionally obtain the PBAT program from Christoph Lange, and accept his license. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.
Author: Thomas Hoffmann <tjhoffm@gmail.com>, with contributions from Christoph Lange <clange@hsph.harvard.edu>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between pbatR versions 2.2-15 dated 2023-02-03 and 2.2-16 dated 2023-03-02
DESCRIPTION | 8 ++--- MD5 | 4 +- R/help.R | 84 ++++++++++++++++++++++++++++++++---------------------------- 3 files changed, 51 insertions(+), 45 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: Lennart Schneider [cre, aut] ,
Jakob Richter [aut] ,
Marc Becker [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: Lennart Schneider <lennart.sch@web.de>
Diff between mlr3mbo versions 0.1.1 dated 2022-11-18 and 0.1.2 dated 2023-03-02
DESCRIPTION | 24 MD5 | 116 +- NAMESPACE | 1 NEWS.md | 11 R/AcqFunction.R | 31 R/AcqFunctionAEI.R |only R/AcqFunctionCB.R | 4 R/AcqFunctionEI.R | 3 R/AcqFunctionEIPS.R | 3 R/AcqFunctionMean.R | 2 R/AcqFunctionPI.R | 3 R/AcqFunctionSmsEgo.R | 2 R/OptimizerMbo.R | 4 R/Surrogate.R | 9 R/SurrogateLearner.R | 16 R/SurrogateLearnerCollection.R | 27 R/TunerMbo.R | 2 R/aaa.R |only R/bayesopt_ego.R | 2 R/bayesopt_mpcl.R | 2 R/bayesopt_parego.R | 2 R/bayesopt_smsego.R | 2 R/bibentries.R | 12 R/helper.R | 18 R/mbo_defaults.R | 16 R/zzz.R | 27 README.md | 11 inst/doc/mlr3mbo.R | 2 inst/doc/mlr3mbo.Rmd | 2 inst/doc/mlr3mbo.html | 995 +++++++++++------------ man/AcqFunction.Rd | 8 man/Surrogate.Rd | 3 man/SurrogateLearner.Rd | 5 man/SurrogateLearnerCollection.Rd | 3 man/default_surrogate.Rd | 3 man/mlr_acqfunctions.Rd | 1 man/mlr_acqfunctions_aei.Rd |only man/mlr_acqfunctions_cb.Rd | 1 man/mlr_acqfunctions_ei.Rd | 4 man/mlr_acqfunctions_eips.Rd | 4 man/mlr_acqfunctions_mean.Rd | 1 man/mlr_acqfunctions_pi.Rd | 4 man/mlr_acqfunctions_smsego.Rd | 1 man/mlr_loop_functions_ego.Rd | 2 man/mlr_loop_functions_mpcl.Rd | 4 man/mlr_loop_functions_parego.Rd | 2 man/mlr_loop_functions_smsego.Rd | 2 man/mlr_optimizers_mbo.Rd | 2 tests/testthat/test_AcqFunction.R | 16 tests/testthat/test_AcqFunctionAEI.R |only tests/testthat/test_AcqFunctionCB.R | 1 tests/testthat/test_AcqFunctionEI.R | 1 tests/testthat/test_AcqFunctionEIPS.R | 3 tests/testthat/test_AcqFunctionMean.R | 1 tests/testthat/test_AcqFunctionPI.R | 1 tests/testthat/test_AcqFunctionSmsEgo.R | 1 tests/testthat/test_SurrogateLearner.R | 6 tests/testthat/test_SurrogateLearnerCollection.R | 11 tests/testthat/test_TunerMbo.R | 10 tests/testthat/test_mbo_defaults.R | 8 vignettes/mlr3mbo.Rmd | 2 61 files changed, 805 insertions(+), 655 deletions(-)
Title: R Interface for Google 'Cloud Pub/Sub' REST API
Description: Provides an easy to use interface to the 'Google
Pub/Sub' REST API <https://cloud.google.com/pubsub/docs/reference/rest>.
Author: Andrea Dodet [aut, cre]
Maintainer: Andrea Dodet <andodet@gmail.com>
Diff between googlePubsubR versions 0.0.3 dated 2022-01-16 and 0.0.4 dated 2023-03-02
DESCRIPTION | 8 - MD5 | 10 - NEWS.md | 4 R/zzz.R | 16 +- inst/doc/getting_started.html | 233 ++++++++++++++++++++++++++++++++++++++---- inst/doc/shiny_consumer.html | 233 ++++++++++++++++++++++++++++++++++++++---- 6 files changed, 448 insertions(+), 56 deletions(-)
Title: Feature Selection Algorithms for Computer Aided Diagnosis
Description: Contains a set of utilities for building and testing statistical models (linear, logistic,ordinal or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya, Israel Alanis and Jorge Orozco
Maintainer: Jose Gerardo Tamez-Pena <jose.tamezpena@tec.mx>
Diff between FRESA.CAD versions 3.4.3 dated 2022-10-09 and 3.4.4 dated 2023-03-02
FRESA.CAD-3.4.3/FRESA.CAD/R/supervisedDecorrelation.r |only FRESA.CAD-3.4.3/FRESA.CAD/man/supervisedDecorrelation.Rd |only FRESA.CAD-3.4.4/FRESA.CAD/DESCRIPTION | 8 FRESA.CAD-3.4.4/FRESA.CAD/MD5 | 54 +- FRESA.CAD-3.4.4/FRESA.CAD/NAMESPACE | 4 FRESA.CAD-3.4.4/FRESA.CAD/NEWS | 7 FRESA.CAD-3.4.4/FRESA.CAD/R/BSWiMS.r | 42 +- FRESA.CAD-3.4.4/FRESA.CAD/R/CoxBenchmark.R | 29 - FRESA.CAD-3.4.4/FRESA.CAD/R/FRESAModelingFunctions.R | 72 ++- FRESA.CAD-3.4.4/FRESA.CAD/R/IterativeDecorrelation.r |only FRESA.CAD-3.4.4/FRESA.CAD/R/baggedModel.R | 221 +++++++++--- FRESA.CAD-3.4.4/FRESA.CAD/R/plot.FRESABenchmark.R | 91 ---- FRESA.CAD-3.4.4/FRESA.CAD/R/predictForFresa.R | 16 FRESA.CAD-3.4.4/FRESA.CAD/R/predictionStats.R | 51 +- FRESA.CAD-3.4.4/FRESA.CAD/R/randomCV.R | 119 ++---- FRESA.CAD-3.4.4/FRESA.CAD/R/randomCVFunctions.R | 134 ++++++- FRESA.CAD-3.4.4/FRESA.CAD/R/summary.fitFRESA.R | 20 - FRESA.CAD-3.4.4/FRESA.CAD/R/uniRankVar.R | 76 +++- FRESA.CAD-3.4.4/FRESA.CAD/R/univariateCox.R | 97 +++-- FRESA.CAD-3.4.4/FRESA.CAD/inst/CITATION | 17 FRESA.CAD-3.4.4/FRESA.CAD/man/BSWiMS.Rd | 6 FRESA.CAD-3.4.4/FRESA.CAD/man/FRESA.CAD-package.Rd | 4 FRESA.CAD-3.4.4/FRESA.CAD/man/FilterUnivariate.Rd | 2 FRESA.CAD-3.4.4/FRESA.CAD/man/IterartiveDecorrelation.Rd |only FRESA.CAD-3.4.4/FRESA.CAD/man/benchmarking.Rd | 6 FRESA.CAD-3.4.4/FRESA.CAD/man/filteredFit.Rd | 2 FRESA.CAD-3.4.4/FRESA.CAD/man/getDerivedCoefficients.Rd | 23 - FRESA.CAD-3.4.4/FRESA.CAD/man/randomCV.Rd | 10 FRESA.CAD-3.4.4/FRESA.CAD/man/uniRankVar.Rd | 4 FRESA.CAD-3.4.4/FRESA.CAD/src/binaryFeatureSelectionCpp.cpp | 2 30 files changed, 675 insertions(+), 442 deletions(-)
Title: Exploration and Graphics for RivEr Trends
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut] ,
Laura DeCicco [aut, cre] ,
Tim Cohn [ctb],
David Watkins [ctb],
Lindsay Carr [ctb],
Jennifer Murphy [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRET versions 3.0.7 dated 2022-01-25 and 3.0.8 dated 2023-03-02
EGRET-3.0.7/EGRET/R/sysdata.rda |only EGRET-3.0.8/EGRET/DESCRIPTION | 26 EGRET-3.0.8/EGRET/MD5 | 251 +- EGRET-3.0.8/EGRET/NAMESPACE | 5 EGRET-3.0.8/EGRET/NEWS | 17 EGRET-3.0.8/EGRET/R/EGRET.R | 16 EGRET-3.0.8/EGRET/R/boxConcMonth.R | 105 EGRET-3.0.8/EGRET/R/boxConcThree.R | 57 EGRET-3.0.8/EGRET/R/boxResidMonth.R | 66 EGRET-3.0.8/EGRET/R/compressData.r | 27 EGRET-3.0.8/EGRET/R/estSurfaces.R | 11 EGRET-3.0.8/EGRET/R/flowDuration.R | 22 EGRET-3.0.8/EGRET/R/fluxBiasEight.R | 31 EGRET-3.0.8/EGRET/R/fluxUnit.R | 28 EGRET-3.0.8/EGRET/R/generalAxis.R | 19 EGRET-3.0.8/EGRET/R/kalman_functions.R | 50 EGRET-3.0.8/EGRET/R/mergeReport.r | 4 EGRET-3.0.8/EGRET/R/multiPlotDataOverview.R | 87 EGRET-3.0.8/EGRET/R/objectDefinitions.R | 85 EGRET-3.0.8/EGRET/R/plotConcHist.R | 89 EGRET-3.0.8/EGRET/R/plotConcPred.R | 134 - EGRET-3.0.8/EGRET/R/plotConcQ.R | 35 EGRET-3.0.8/EGRET/R/plotConcQSmooth.R | 105 EGRET-3.0.8/EGRET/R/plotConcTime.R | 201 + EGRET-3.0.8/EGRET/R/plotConcTimeDaily.R | 108 EGRET-3.0.8/EGRET/R/plotConcTimeSmooth.R | 66 EGRET-3.0.8/EGRET/R/plotContours.R | 46 EGRET-3.0.8/EGRET/R/plotDiffContours.R | 33 EGRET-3.0.8/EGRET/R/plotFlowSingle.R | 8 EGRET-3.0.8/EGRET/R/plotFluxHist.R | 27 EGRET-3.0.8/EGRET/R/plotFluxTimeDaily.R | 95 EGRET-3.0.8/EGRET/R/plotMonthTrend.R |only EGRET-3.0.8/EGRET/R/plotResidPred.R | 45 EGRET-3.0.8/EGRET/R/populateDaily.r | 11 EGRET-3.0.8/EGRET/R/populateDateColumns.r | 23 EGRET-3.0.8/EGRET/R/printSeries.R | 35 EGRET-3.0.8/EGRET/R/processQWData.r | 65 EGRET-3.0.8/EGRET/R/readDataFromFile.r | 32 EGRET-3.0.8/EGRET/R/readNWISDaily.r | 66 EGRET-3.0.8/EGRET/R/readNWISSample.r | 83 EGRET-3.0.8/EGRET/R/readUserDaily.r | 46 EGRET-3.0.8/EGRET/R/readUserSample.r | 31 EGRET-3.0.8/EGRET/R/readWQPSample.R | 35 EGRET-3.0.8/EGRET/R/runGroups.R | 91 EGRET-3.0.8/EGRET/R/runPairs.R | 176 + EGRET-3.0.8/EGRET/R/runSeries.R | 2 EGRET-3.0.8/EGRET/R/runSurvReg.R | 4 EGRET-3.0.8/EGRET/R/setSeasonLabel.R | 31 EGRET-3.0.8/EGRET/R/setSeasonLabelByUser.R | 49 EGRET-3.0.8/EGRET/R/setupYears.R | 24 EGRET-3.0.8/EGRET/R/stitch.R | 22 EGRET-3.0.8/EGRET/R/tableChange.R | 98 EGRET-3.0.8/EGRET/R/tableChangeSingle.R | 6 EGRET-3.0.8/EGRET/R/tableFlowChange.R | 8 EGRET-3.0.8/EGRET/R/tableResults.R | 33 EGRET-3.0.8/EGRET/README.md | 263 -- EGRET-3.0.8/EGRET/build/partial.rdb |binary EGRET-3.0.8/EGRET/build/vignette.rds |binary EGRET-3.0.8/EGRET/inst/CITATION | 24 EGRET-3.0.8/EGRET/inst/doc/EGRET.Rmd | 17 EGRET-3.0.8/EGRET/inst/doc/EGRET.html | 1435 ++++++++---- EGRET-3.0.8/EGRET/inst/doc/Overview.Rmd | 54 EGRET-3.0.8/EGRET/inst/doc/Overview.html | 496 +++- EGRET-3.0.8/EGRET/inst/doc/parallel.html | 208 + EGRET-3.0.8/EGRET/man/Constants.Rd | 3 EGRET-3.0.8/EGRET/man/EGRET-package.Rd | 2 EGRET-3.0.8/EGRET/man/boxConcMonth.Rd | 22 EGRET-3.0.8/EGRET/man/boxConcThree.Rd | 5 EGRET-3.0.8/EGRET/man/boxResidMonth.Rd | 8 EGRET-3.0.8/EGRET/man/cleanUp.Rd | 5 EGRET-3.0.8/EGRET/man/compressData.Rd | 8 EGRET-3.0.8/EGRET/man/concUnit-class.Rd |only EGRET-3.0.8/EGRET/man/decimalHighLow.Rd | 5 EGRET-3.0.8/EGRET/man/figures/README-fluxPlots-1.png |binary EGRET-3.0.8/EGRET/man/figures/README-multiPlots-1.png |binary EGRET-3.0.8/EGRET/man/figures/README-multiPlots-2.png |binary EGRET-3.0.8/EGRET/man/figures/README-plotFours-1.png |binary EGRET-3.0.8/EGRET/man/figures/README-plotFours-2.png |binary EGRET-3.0.8/EGRET/man/figures/README-runModel-10.png |binary EGRET-3.0.8/EGRET/man/figures/README-runModel-11.png |binary EGRET-3.0.8/EGRET/man/figures/README-runModel-9.png |binary EGRET-3.0.8/EGRET/man/figures/README-unnamed-chunk-4-1.png |binary EGRET-3.0.8/EGRET/man/figures/README-unnamed-chunk-4-2.png |binary EGRET-3.0.8/EGRET/man/figures/README-unnamed-chunk-4-3.png |binary EGRET-3.0.8/EGRET/man/figures/logo.png |binary EGRET-3.0.8/EGRET/man/flexPlotAddOn.Rd | 3 EGRET-3.0.8/EGRET/man/flowDuration.Rd | 6 EGRET-3.0.8/EGRET/man/fluxBiasMulti.Rd | 8 EGRET-3.0.8/EGRET/man/generalAxis.Rd | 6 EGRET-3.0.8/EGRET/man/genmissing.Rd | 7 EGRET-3.0.8/EGRET/man/multiPlotDataOverview.Rd | 34 EGRET-3.0.8/EGRET/man/plotConcHist.Rd | 15 EGRET-3.0.8/EGRET/man/plotConcPred.Rd | 5 EGRET-3.0.8/EGRET/man/plotConcQ.Rd | 5 EGRET-3.0.8/EGRET/man/plotConcQSmooth.Rd | 6 EGRET-3.0.8/EGRET/man/plotConcTime.Rd | 15 EGRET-3.0.8/EGRET/man/plotConcTimeDaily.Rd | 23 EGRET-3.0.8/EGRET/man/plotConcTimeSmooth.Rd | 18 EGRET-3.0.8/EGRET/man/plotContours.Rd | 7 EGRET-3.0.8/EGRET/man/plotDiffContours.Rd | 9 EGRET-3.0.8/EGRET/man/plotFluxHist.Rd | 3 EGRET-3.0.8/EGRET/man/plotFluxTimeDaily.Rd | 11 EGRET-3.0.8/EGRET/man/plotMonthTrend.Rd |only EGRET-3.0.8/EGRET/man/plotResidPred.Rd | 5 EGRET-3.0.8/EGRET/man/plotWRTDSKalman.Rd | 3 EGRET-3.0.8/EGRET/man/populateDaily.Rd | 4 EGRET-3.0.8/EGRET/man/populateDailySamp.Rd | 44 EGRET-3.0.8/EGRET/man/printGroups.Rd |only EGRET-3.0.8/EGRET/man/printPairs.Rd |only EGRET-3.0.8/EGRET/man/processQWData.Rd | 6 EGRET-3.0.8/EGRET/man/qUnit-class.Rd | 2 EGRET-3.0.8/EGRET/man/randomSubset.Rd | 5 EGRET-3.0.8/EGRET/man/readDataFromFile.Rd | 19 EGRET-3.0.8/EGRET/man/readNWISDaily.Rd | 11 EGRET-3.0.8/EGRET/man/readNWISSample.Rd | 14 EGRET-3.0.8/EGRET/man/readUserDaily.Rd | 29 EGRET-3.0.8/EGRET/man/readUserSample.Rd | 13 EGRET-3.0.8/EGRET/man/readWQPSample.Rd | 15 EGRET-3.0.8/EGRET/man/runGroups.Rd | 8 EGRET-3.0.8/EGRET/man/runPairs.Rd | 27 EGRET-3.0.8/EGRET/man/setSeasonLabel.Rd | 10 EGRET-3.0.8/EGRET/man/setSeasonLabelByUser.Rd | 13 EGRET-3.0.8/EGRET/man/wrtdsK.Rd | 2 EGRET-3.0.8/EGRET/tests/testthat/Rplots.pdf |binary EGRET-3.0.8/EGRET/tests/testthat/tests_flow_normalization.R | 16 EGRET-3.0.8/EGRET/tests/testthat/tests_imports.R | 32 EGRET-3.0.8/EGRET/tests/testthat/tests_utils.R | 28 EGRET-3.0.8/EGRET/vignettes/EGRET.Rmd | 17 EGRET-3.0.8/EGRET/vignettes/Overview.Rmd | 54 EGRET-3.0.8/EGRET/vignettes/logo.png |only 130 files changed, 4133 insertions(+), 1850 deletions(-)
Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple rectangular
data. The 'rtables' package provides a framework for declaring complex multi-level tabulations
and then applying them to data. This framework models both tabulation and the resulting
tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting
or grouping of data in row and column dimensions, cells containing multiple values,
and the concept of contextual summary computations. A convenient pipe-able interface is provided
for declaring table layouts and the corresponding computations, and then applying them to data.
Author: Gabriel Becker [aut, cre],
Adrian Waddell [aut],
Daniel Sabanes Bove [ctb],
Maximilian Mordig [ctb],
Davide Garolini [ctb]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between rtables versions 0.5.1 dated 2022-05-21 and 0.6.0 dated 2023-03-02
rtables-0.5.1/rtables/man/lab_name.Rd |only rtables-0.5.1/rtables/man/make_row_df.Rd |only rtables-0.5.1/rtables/man/title_footer.Rd |only rtables-0.6.0/rtables/DESCRIPTION | 39 rtables-0.6.0/rtables/MD5 | 385 - rtables-0.6.0/rtables/NAMESPACE | 28 rtables-0.6.0/rtables/NEWS.md | 98 rtables-0.6.0/rtables/R/00tabletrees.R | 715 - rtables-0.6.0/rtables/R/Viewer.R | 35 rtables-0.6.0/rtables/R/argument_conventions.R | 272 rtables-0.6.0/rtables/R/as_html.R | 56 rtables-0.6.0/rtables/R/colby_constructors.R | 1060 +- rtables-0.6.0/rtables/R/compare_rtables.R | 70 rtables-0.6.0/rtables/R/deprecated.R | 6 rtables-0.6.0/rtables/R/format_rcell.R | 85 rtables-0.6.0/rtables/R/indent.R | 17 rtables-0.6.0/rtables/R/index_footnotes.R | 6 rtables-0.6.0/rtables/R/make_split_fun.R |only rtables-0.6.0/rtables/R/make_subset_expr.R | 80 rtables-0.6.0/rtables/R/simple_analysis.R | 9 rtables-0.6.0/rtables/R/split_funs.R | 729 +- rtables-0.6.0/rtables/R/summary.R | 180 rtables-0.6.0/rtables/R/tree_accessors.R 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rtables-0.6.0/rtables/man/cinfo.Rd | 15 rtables-0.6.0/rtables/man/clear_imods.Rd | 14 rtables-0.6.0/rtables/man/col_accessors.Rd | 15 rtables-0.6.0/rtables/man/collect_leaves.Rd | 21 rtables-0.6.0/rtables/man/compare_rtables.Rd | 13 rtables-0.6.0/rtables/man/compat_args.Rd | 52 rtables-0.6.0/rtables/man/constr_args.Rd | 79 rtables-0.6.0/rtables/man/content_table.Rd | 9 rtables-0.6.0/rtables/man/counts_wpcts.Rd |only rtables-0.6.0/rtables/man/custom_split_funs.Rd | 99 rtables-0.6.0/rtables/man/cutsplits.Rd | 82 rtables-0.6.0/rtables/man/dimensions.Rd | 19 rtables-0.6.0/rtables/man/do_base_split.Rd | 27 rtables-0.6.0/rtables/man/drop_facet_levels.Rd |only rtables-0.6.0/rtables/man/export_as_pdf.Rd | 92 rtables-0.6.0/rtables/man/export_as_rtf.Rd |only rtables-0.6.0/rtables/man/export_as_txt.Rd | 74 rtables-0.6.0/rtables/man/figures |only rtables-0.6.0/rtables/man/format_rcell.Rd | 34 rtables-0.6.0/rtables/man/formatters_methods.Rd |only rtables-0.6.0/rtables/man/gen_args.Rd | 89 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rtables-0.6.0/rtables/man/ref_fnotes.Rd | 93 rtables-0.6.0/rtables/man/rheader.Rd | 22 rtables-0.6.0/rtables/man/row_paths_summary.Rd | 13 rtables-0.6.0/rtables/man/rowclasses.Rd | 38 rtables-0.6.0/rtables/man/rrow.Rd | 19 rtables-0.6.0/rtables/man/rrowl.Rd | 19 rtables-0.6.0/rtables/man/rtable.Rd | 32 rtables-0.6.0/rtables/man/rtables_aligns.Rd | 48 rtables-0.6.0/rtables/man/rtinner.Rd | 3 rtables-0.6.0/rtables/man/score_funs.Rd | 6 rtables-0.6.0/rtables/man/sf_args.Rd | 9 rtables-0.6.0/rtables/man/sort_at_path.Rd | 35 rtables-0.6.0/rtables/man/spl_context.Rd | 56 rtables-0.6.0/rtables/man/spl_context_to_disp_path.Rd |only rtables-0.6.0/rtables/man/spl_variable.Rd |only rtables-0.6.0/rtables/man/split_cols_by.Rd | 135 rtables-0.6.0/rtables/man/split_cols_by_multivar.Rd | 38 rtables-0.6.0/rtables/man/split_funcs.Rd | 108 rtables-0.6.0/rtables/man/split_rows_by.Rd | 142 rtables-0.6.0/rtables/man/summarize_row_groups.Rd | 71 rtables-0.6.0/rtables/man/summarize_rows.Rd | 2 rtables-0.6.0/rtables/man/tabclasses.Rd | 74 rtables-0.6.0/rtables/man/table_shell.Rd | 39 rtables-0.6.0/rtables/man/table_structure.Rd | 10 rtables-0.6.0/rtables/man/top_left.Rd | 2 rtables-0.6.0/rtables/man/tostring.Rd | 33 rtables-0.6.0/rtables/man/tree_children.Rd | 15 rtables-0.6.0/rtables/man/trim_levels_in_facets.Rd |only rtables-0.6.0/rtables/man/trim_levels_to_map.Rd | 52 rtables-0.6.0/rtables/man/trim_prune_funs.Rd | 105 rtables-0.6.0/rtables/man/trim_rows.Rd | 38 rtables-0.6.0/rtables/man/tsv_io.Rd | 11 rtables-0.6.0/rtables/man/tt_to_flextable.Rd | 28 rtables-0.6.0/rtables/man/ttap.Rd | 50 rtables-0.6.0/rtables/man/update_ref_indexing.Rd | 3 rtables-0.6.0/rtables/man/varcuts.Rd | 150 rtables-0.6.0/rtables/man/vil.Rd | 2 rtables-0.6.0/rtables/man/vpaginate_table.Rd |only rtables-0.6.0/rtables/tests/testthat.R | 4 rtables-0.6.0/rtables/tests/testthat/setup-fakedata.R | 108 rtables-0.6.0/rtables/tests/testthat/test-accessors.R | 16 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rtables-0.6.0/rtables/tests/testthat/test-structure-summary.R | 5 rtables-0.6.0/rtables/tests/testthat/test-subset-access.R | 187 rtables-0.6.0/rtables/vignettes/advanced_usage.Rmd |only rtables-0.6.0/rtables/vignettes/baseline.Rmd | 79 rtables-0.6.0/rtables/vignettes/clinical_trials.Rmd | 801 +- rtables-0.6.0/rtables/vignettes/custom_appearance.Rmd |only rtables-0.6.0/rtables/vignettes/format_precedence.Rmd |only rtables-0.6.0/rtables/vignettes/introduction.Rmd | 301 rtables-0.6.0/rtables/vignettes/manual_table_construction.Rmd | 26 rtables-0.6.0/rtables/vignettes/sorting_pruning.Rmd | 472 + rtables-0.6.0/rtables/vignettes/split_functions.Rmd |only rtables-0.6.0/rtables/vignettes/subsetting_tables.Rmd | 190 rtables-0.6.0/rtables/vignettes/tabulation_concepts.Rmd | 233 rtables-0.6.0/rtables/vignettes/tabulation_dplyr.Rmd | 120 rtables-0.6.0/rtables/vignettes/title_footer.Rmd |only 212 files changed, 21006 insertions(+), 10626 deletions(-)
Title: Integrating Ecosystem Remote Sensing Products to Derive EBV
Indicators
Description: Essential Biodiversity Variables (EBV) are state variables with dimensions on time, space, and biological organization that document biodiversity change. Freely available ecosystem remote sensing products (ERSP) are downloaded and integrated with data for national or regional domains to derive indicators for EBV in the class ecosystem structure (Pereira et al., 2013) <doi:10.1126/science.1229931>, including horizontal ecosystem extents, fragmentation, and information-theory indices. To process ERSP, users must provide a polygon or geographic administrative data map. Downloadable ERSP include Global Surface Water (Peckel et al., 2016) <doi:10.1038/nature20584>, Forest Change (Hansen et al., 2013) <doi:10.1126/science.1244693>, and Continuous Tree Cover data (Sexton et al., 2013) <doi:10.1080/17538947.2013.786146>.
Author: Wilson Lara Henao [aut, cre],
Victor Gutierrez-Velez [aut],
Ivan Gonzalez [ctb],
Maria C. Londono [ctb]
Maintainer: Wilson Lara Henao <wilarhen@gmail.com>
Diff between ecochange versions 2.9.3 dated 2023-02-07 and 2.9.3.1 dated 2023-03-02
DESCRIPTION | 8 - MD5 | 8 - NEWS | 4 R/internal.R | 27 ++++- inst/doc/EcochangeTutorial.html | 193 ++++++++++++++++------------------------ 5 files changed, 111 insertions(+), 129 deletions(-)
Title: 'Amazon Web Service S3' File System
Description: Access 'Amazon Web Service Simple Storage Service' ('S3') <https://aws.amazon.com/s3/>
as if it were a file system. Interface based on the R package 'fs'.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between s3fs versions 0.1.2 dated 2023-02-14 and 0.1.3 dated 2023-03-02
DESCRIPTION | 6 MD5 | 22 - NEWS.md | 6 R/file_system.R | 6 R/s3filesystem_class.R | 672 ++++++++++++++++++++----------------- R/utils.R | 64 ++- R/zzz.R | 5 README.md | 9 man/S3FileSystem.Rd | 2 man/info.Rd | 2 man/touch.Rd | 2 tests/testthat/test-file-methods.R | 12 12 files changed, 463 insertions(+), 345 deletions(-)
Title: Finding Recurrent DNA Copy Number Alterations and Differences
Description: In tumor tissue, underlying genomic instability can lead to DNA copy number alterations,
e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the
genome, whereas recurrent alterations are observed in the same genomic region across multiple
independent samples, perhaps because they provide a selective growth advantage. Here we use
cyclic shift permutations to identify recurrent copy number alterations in a single cohort or
recurrent copy number differences in two cohorts based on a common set of genomic markers.
Additional functionality is provided to perform downstream analyses, including the creation of
summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al.
(2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al.
(2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022)
can be found at <doi: 10.1093/bioinformatics/ [...truncated...]
Author: Vonn Walter [aut, cre] ,
Hyo Young Choi [aut] ,
Xiaobei Zhao [aut] ,
Yan Gao [aut] ,
David Neil Hayes [aut]
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>
Diff between DiNAMIC.Duo versions 1.0.1 dated 2022-05-17 and 1.0.2 dated 2023-03-02
DiNAMIC.Duo-1.0.1/DiNAMIC.Duo/R/onAttach.R |only DiNAMIC.Duo-1.0.1/DiNAMIC.Duo/man/miniconda_installation.Rd |only DiNAMIC.Duo-1.0.2/DiNAMIC.Duo/DESCRIPTION | 15 ++++--- DiNAMIC.Duo-1.0.2/DiNAMIC.Duo/MD5 | 10 ++--- DiNAMIC.Duo-1.0.2/DiNAMIC.Duo/NEWS.md | 19 ++++++++++ DiNAMIC.Duo-1.0.2/DiNAMIC.Duo/build/vignette.rds |binary DiNAMIC.Duo-1.0.2/DiNAMIC.Duo/inst/doc/DiNAMICDuo_vignette.pdf |binary 7 files changed, 31 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-12 1.3.4
Title: Synthetic Likelihood Methods for Intractable Likelihoods
Description: Framework to perform synthetic likelihood inference
for models where the likelihood function is unavailable or
intractable.
Author: Matteo Fasiolo and Simon Wood
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between synlik versions 0.1.5 dated 2022-04-14 and 0.1.6 dated 2023-03-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/on_load.R | 13 ------------- build/vignette.rds |binary inst/CITATION | 22 ++++++++-------------- inst/doc/synlik.html | 34 +++++++++++++++++----------------- 6 files changed, 34 insertions(+), 53 deletions(-)
Title: A Very Nice Interface to 'WordNet'
Description: A very nice interface to Princeton's 'WordNet' without 'rJava' dependency. 'WordNet' data is not included. Princeton University makes 'WordNet' available to research and commercial users free of charge provided the terms of their license (<https://wordnet.princeton.edu/license-and-commercial-use>) are followed, and proper reference is made to the project using an appropriate citation (<https://wordnet.princeton.edu/citing-wordnet>).
Author: Chung-hong Chan [aut, cre]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between sehrnett versions 0.0.3 dated 2022-01-17 and 0.1.0 dated 2023-03-02
DESCRIPTION | 8 - MD5 | 10 - R/download.R | 20 +-- R/sehr.R | 7 + README.md | 266 +++++++++++++++++++++++++----------------------- man/download_wordnet.Rd | 4 6 files changed, 167 insertions(+), 148 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired by the end of 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] ,
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Daniel Baston [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.6-4 dated 2023-01-12 and 1.6-5 dated 2023-03-02
DESCRIPTION | 8 - MD5 | 22 ++--- NEWS.md | 8 + configure | 63 ++++++-------- configure.ac | 39 +++------ inst/SVN_VERSION | 2 inst/doc/CRS_projections_transformations.html | 110 +++++++++++++------------- inst/doc/OGR_shape_encoding.pdf |binary inst/doc/PROJ6_GDAL3.html | 34 ++++---- src/Makevars.in | 2 src/Makevars.ucrt | 2 src/Makevars.win | 4 12 files changed, 138 insertions(+), 156 deletions(-)
Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R.
The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange
with R. This provides a reliable and scalable foundation for statistical services or
building R web applications. The OpenCPU server runs either as a single-user development
server within the interactive R session, or as a multi-user Linux stack based on Apache2.
The entire system is fully open source and permissively licensed. The OpenCPU website
has detailed documentation and example apps.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between opencpu versions 2.2.8 dated 2022-05-18 and 2.2.9 dated 2023-03-02
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS | 3 +++ R/config.R | 2 +- R/parse_post.R | 6 ++++-- build/vignette.rds |binary inst/CITATION | 12 +++--------- inst/doc/opencpu-paper.pdf |binary man/figures |only 9 files changed, 22 insertions(+), 22 deletions(-)
Title: A Simple XML Tree Parser and Generator
Description: Provides a simple XML tree parser/generator. It includes
functions to read XML files into R objects, get information out of
and into nodes, and write R objects back to XML code. It's not as
powerful as the 'XML' package and doesn't aim to be, but for simple
XML handling it could be useful. It was originally developed for
the R GUI and IDE 'RKWard' <https://rkward.kde.org>, to make plugin
development easier.
Author: Meik Michalke [aut, cre]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between XiMpLe versions 0.10-3 dated 2020-09-19 and 0.11-1 dated 2023-03-02
XiMpLe-0.10-3/XiMpLe/R/XMLValidity.R |only XiMpLe-0.10-3/XiMpLe/man/XMLValidity.Rd |only XiMpLe-0.10-3/XiMpLe/man/XiMpLe.doc-class.Rd |only XiMpLe-0.10-3/XiMpLe/man/XiMpLe.node-class.Rd |only XiMpLe-0.10-3/XiMpLe/tests/testthat/sample_XML_tree_changed.RData |only XiMpLe-0.10-3/XiMpLe/tests/testthat/sample_XML_tree_changed_value.RData |only XiMpLe-0.11-1/XiMpLe/ChangeLog | 81 + XiMpLe-0.11-1/XiMpLe/DESCRIPTION | 18 XiMpLe-0.11-1/XiMpLe/MD5 | 107 + XiMpLe-0.11-1/XiMpLe/NAMESPACE | 14 XiMpLe-0.11-1/XiMpLe/R/00_class_01_XiMpLe.node.R | 98 + XiMpLe-0.11-1/XiMpLe/R/00_class_02_XiMpLe.doc.R | 104 + XiMpLe-0.11-1/XiMpLe/R/00_class_03_XiMpLe.validity.R | 12 XiMpLe-0.11-1/XiMpLe/R/01_method_01_pasteXML.R | 283 +++-- XiMpLe-0.11-1/XiMpLe/R/01_method_02_node.R | 81 + XiMpLe-0.11-1/XiMpLe/R/01_method_03_show.R | 12 XiMpLe-0.11-1/XiMpLe/R/01_method_04_validXML.R | 361 +++--- XiMpLe-0.11-1/XiMpLe/R/01_method_05_XMLgenerators.R | 12 XiMpLe-0.11-1/XiMpLe/R/XMLNode.R | 179 ++- XiMpLe-0.11-1/XiMpLe/R/XMLTree.R | 10 XiMpLe-0.11-1/XiMpLe/R/XiMpLe-internal.R | 541 ++++++++-- XiMpLe-0.11-1/XiMpLe/R/XiMpLe-package.R | 12 XiMpLe-0.11-1/XiMpLe/R/gen_tag_functions.R |only XiMpLe-0.11-1/XiMpLe/R/parseXMLTree.R | 38 XiMpLe-0.11-1/XiMpLe/R/pasteXMLTag.R | 288 ++++- XiMpLe-0.11-1/XiMpLe/R/provide_file.R |only XiMpLe-0.11-1/XiMpLe/R/zzz_is_get_utils.R | 242 +++- XiMpLe-0.11-1/XiMpLe/R/zzz_is_get_utils_deprecated.R |only XiMpLe-0.11-1/XiMpLe/build/partial.rdb |binary XiMpLe-0.11-1/XiMpLe/build/vignette.rds |binary XiMpLe-0.11-1/XiMpLe/inst/CITATION | 8 XiMpLe-0.11-1/XiMpLe/inst/NEWS.Rd | 92 + XiMpLe-0.11-1/XiMpLe/inst/doc/XiMpLe_vignette.R | 55 - XiMpLe-0.11-1/XiMpLe/inst/doc/XiMpLe_vignette.Rmd | 135 +- XiMpLe-0.11-1/XiMpLe/inst/doc/XiMpLe_vignette.html | 402 +++++-- XiMpLe-0.11-1/XiMpLe/man/XMLGetters-methods.Rd | 120 +- XiMpLe-0.11-1/XiMpLe/man/XMLNode.Rd | 67 - XiMpLe-0.11-1/XiMpLe/man/XMLTree.Rd | 4 XiMpLe-0.11-1/XiMpLe/man/XMLgenerators.Rd | 2 XiMpLe-0.11-1/XiMpLe/man/XiMpLe-package.Rd | 4 XiMpLe-0.11-1/XiMpLe/man/XiMpLe.validity-class.Rd | 9 XiMpLe-0.11-1/XiMpLe/man/XiMpLe_doc-class.Rd |only XiMpLe-0.11-1/XiMpLe/man/XiMpLe_node-class.Rd |only XiMpLe-0.11-1/XiMpLe/man/deprecated.Rd |only XiMpLe-0.11-1/XiMpLe/man/gen_tag_functions.Rd |only XiMpLe-0.11-1/XiMpLe/man/node.Rd | 12 XiMpLe-0.11-1/XiMpLe/man/parseXMLTree.Rd | 15 XiMpLe-0.11-1/XiMpLe/man/pasteXML-methods.Rd | 42 XiMpLe-0.11-1/XiMpLe/man/pasteXMLTag.Rd | 21 XiMpLe-0.11-1/XiMpLe/man/provide_file.Rd |only XiMpLe-0.11-1/XiMpLe/man/show-methods.Rd | 12 XiMpLe-0.11-1/XiMpLe/man/validXML.Rd | 10 XiMpLe-0.11-1/XiMpLe/tests/testthat/sample_RSS_changed.RData |only XiMpLe-0.11-1/XiMpLe/tests/testthat/sample_RSS_changed_value.RData |only XiMpLe-0.11-1/XiMpLe/tests/testthat/sample_RSS_parsed.RData |binary XiMpLe-0.11-1/XiMpLe/tests/testthat/sample_XML_node_attrs.RData |binary XiMpLe-0.11-1/XiMpLe/tests/testthat/sample_XML_node_closed_dput.txt | 2 XiMpLe-0.11-1/XiMpLe/tests/testthat/sample_XML_node_empty_dput.txt | 2 XiMpLe-0.11-1/XiMpLe/tests/testthat/sample_XML_node_extracted.RData |binary XiMpLe-0.11-1/XiMpLe/tests/testthat/sample_XML_tree.RData |binary XiMpLe-0.11-1/XiMpLe/tests/testthat/sample_XML_tree_old.RData |only XiMpLe-0.11-1/XiMpLe/tests/testthat/tests.R | 87 + XiMpLe-0.11-1/XiMpLe/vignettes/XiMpLe_vignette.Rmd | 135 +- 63 files changed, 2780 insertions(+), 949 deletions(-)
Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. Please note that 'rgeos' will be retired during 2023, plan transition to sf functions using 'GEOS' at your earliest convenience. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if i [...truncated...]
Author: Roger Bivand [cre, aut] ,
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb],
Patrick Giraudoux [ctb],
Martin Davis [cph, ctb],
Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.6-1 dated 2022-12-14 and 0.6-2 dated 2023-03-02
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 6 +++++- configure | 18 +++++++++--------- inst/SVN_VERSION | 2 +- man/wkt-functions.Rd | 2 +- src/Makevars.ucrt | 2 +- src/Makevars.win | 2 +- 8 files changed, 29 insertions(+), 25 deletions(-)
Title: Fast Computation of Romano-Wolf Corrected p-Values for Linear
Regression Models
Description: Fast Routines to Compute Romano-Wolf corrected p-Values
(Romano and Wolf (2005a) <DOI:10.1198/016214504000000539>,
Romano and Wolf (2005b) <DOI:10.1111/j.1468-0262.2005.00615.x>)
for objects of type 'fixest' and 'fixest_multi' from the 'fixest'
package via a wild (cluster) bootstrap.
Author: Alexander Fischer [aut, cre]
Maintainer: Alexander Fischer <alexander-fischer1801@t-online.de>
Diff between wildrwolf versions 0.6.0 dated 2023-02-27 and 0.6.1 dated 2023-03-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 9 +++++++++ tests/testthat/tests_vs_stata.R | 2 +- 4 files changed, 16 insertions(+), 7 deletions(-)
Title: Calculation of the Standardized Precipitation-Evapotranspiration
Index
Description: A set of functions for computing potential evapotranspiration and several widely used drought indices including the Standardized Precipitation-Evapotranspiration Index (SPEI).
Author: Santiago Begueria [aut, cre],
Sergio M. Vicente-Serrano [aut]
Maintainer: Santiago Begueria <santiago.begueria@csic.es>
Diff between SPEI versions 1.8.0 dated 2023-01-20 and 1.8.1 dated 2023-03-02
SPEI-1.8.0/SPEI/tests/testthat/testthat-problems.rds |only SPEI-1.8.1/SPEI/DESCRIPTION | 6 ++-- SPEI-1.8.1/SPEI/MD5 | 7 ++--- SPEI-1.8.1/SPEI/tests/testthat/test_spei.R | 24 +++++++++---------- SPEI-1.8.1/SPEI/tests/testthat/test_spi.R | 24 +++++++++---------- 5 files changed, 30 insertions(+), 31 deletions(-)
Title: Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations
Description: Simulate dose regimens for pharmacokinetic-pharmacodynamic (PK-PD)
models described by differential equation (DE) systems. Simulation using
ADVAN-style analytical equations is also supported (Abuhelwa et al. (2015)
<doi:10.1016/j.vascn.2015.03.004>).
Author: Ron Keizer [aut, cre],
Jasmine Hughes [aut],
Dominic Tong [aut],
Kara Woo [aut],
InsightRX [cph, fnd]
Maintainer: Ron Keizer <ron@insight-rx.com>
Diff between PKPDsim versions 1.1.1 dated 2022-04-01 and 1.3.0 dated 2023-03-02
DESCRIPTION | 16 +- MD5 | 222 ++++++++++++++++++----------- NAMESPACE | 2 NEWS.md | 4 R/PKPDsim-package.R | 1 R/add_ruv_to_quantile.R | 4 R/advan.R | 11 + R/analytical_eqn_wrapper.R | 2 R/check_iov_specification.R | 4 R/check_mixture_model.R | 2 R/compile_sim_cpp.R | 14 + R/create_event_table.R | 12 + R/create_obs_data.R | 1 R/define_tdm_init_model.R | 4 R/get_fixed_parameters.R |only R/get_t_obs_from_regimen.R | 3 R/get_var_y.R | 2 R/is_newer_package.R | 2 R/join_regimen.R | 4 R/misc.R | 32 ++-- R/model_from_api.R | 8 - R/mvrnorm2.R | 2 R/new_covariate.R | 19 +- R/new_ode_model.R | 93 +++++++----- R/new_regimen.R | 8 - R/object_to_R_code.R | 4 R/parse_obs_types.R | 54 +++++-- R/print.PKPDsim.R | 1 R/print.covariate.R | 1 R/print.regimen.R | 1 R/read_model_json.R | 11 + R/shift_state_indices.R | 4 R/sim.R | 12 - R/triangle_to_full.R | 22 +- README.md | 50 +++++- build |only inst/cpp/sim.cpp | 12 + inst/cpp/sim_header.cpp | 4 inst/doc |only inst/models |only inst/template/R/model.R | 1 man/OneCompIVbolus.Rd | 1 man/OneCompIVinfusion.Rd | 1 man/OneCompOral.Rd | 1 man/PKPDsim-package.Rd | 1 man/ThreeCompIVbolus.Rd | 1 man/ThreeCompIVinfusion.Rd | 1 man/ThreeCompIVinfusionMetab.Rd | 1 man/ThreeCompOral.Rd | 1 man/ThreeCompOralMetab.Rd | 1 man/TwoCompIVbolus.Rd | 1 man/TwoCompIVinfusion.Rd | 1 man/TwoCompOral.Rd | 1 man/add_ruv_to_quantile.Rd | 2 man/analytical_eqn_wrapper.Rd | 1 man/bioavailability_to_R_code.Rd | 1 man/check_iov_specification.Rd | 1 man/check_mixture_model.Rd | 1 man/check_obs_input.Rd |only man/create_event_table.Rd | 1 man/create_obs_data.Rd | 1 man/define_tdm_init_model.Rd | 1 man/figures |only man/get_fixed_parameters.Rd |only man/get_t_obs_from_regimen.Rd | 3 man/get_var_y.Rd | 2 man/is_newer_package.Rd | 1 man/lower_triangle_mat_size.Rd |only man/mvrnorm2.Rd | 2 man/new_covariate.Rd | 3 man/new_ode_model.Rd | 10 + man/new_regimen.Rd | 2 man/now_utc.Rd | 1 man/parse_obs_types.Rd | 11 + man/print.PKPDsim.Rd | 1 man/print.covariate.Rd | 1 man/print.regimen.Rd | 1 man/print_list.Rd | 4 man/search_replace_in_file.Rd | 2 man/shift_state_indices.Rd | 3 man/sim.Rd | 2 man/vector_to_R_code.Rd | 1 src/Makevars | 1 tests/testthat/test_get_fixed_parameters.R |only tests/testthat/test_iov.R | 117 +++++++++++---- tests/testthat/test_join_regimen.R | 8 + tests/testthat/test_misc.R | 31 ++++ tests/testthat/test_model_from_api.R | 6 tests/testthat/test_multi_obs.R | 98 ++++++++++++ tests/testthat/test_new_covariate.R | 13 + tests/testthat/test_new_ode_model.R | 80 ++++++++++ tests/testthat/test_new_regimen.R | 12 + tests/testthat/test_parse_obs_types.R | 60 ++++--- vignettes |only 94 files changed, 852 insertions(+), 294 deletions(-)
Title: Hyperband for 'mlr3'
Description: Successive Halving (Jamieson and Talwalkar (2016)
<arXiv:1502.07943>) and Hyperband (Li et al. 2018 <arXiv:1603.06560>)
optimization algorithm for the mlr3 ecosystem. The implementation in
mlr3hyperband features improved scheduling and parallelizes the evaluation
of configurations. The package includes tuners for hyperparameter
optimization in mlr3tuning and optimizers for black-box optimization in
bbotk.
Author: Marc Becker [aut, cre] ,
Sebastian Gruber [aut] ,
Jakob Richter [aut] ,
Julia Moosbauer [aut] ,
Bernd Bischl [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3hyperband versions 0.4.4 dated 2022-11-27 and 0.4.5 dated 2023-03-02
DESCRIPTION | 27 ++--- MD5 | 34 +++---- NEWS.md | 6 + R/OptimizerHyperband.R | 71 +++++++------- R/OptimizerSuccessiveHalving.R | 67 ++++++-------- R/TunerHyperband.R | 72 +-------------- R/TunerSuccessiveHalving.R | 71 +------------- R/aaa.R |only R/bibentries.R | 2 R/zzz.R | 26 +++-- man/figures |only man/mlr3hyperband-package.Rd | 4 man/mlr_optimizers_hyperband.Rd | 62 ++++++------- man/mlr_optimizers_successive_halving.Rd | 73 ++++++++------- man/mlr_tuners_hyperband.Rd | 128 +++++++++++++-------------- man/mlr_tuners_successive_halving.Rd | 120 +++++++++++++------------ tests/testthat/helper.R | 12 -- tests/testthat/test_TunerHyperband.R | 26 ++--- tests/testthat/test_TunerSuccessiveHalving.R | 26 ++--- 19 files changed, 370 insertions(+), 457 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-41 dated 2022-10-21 and 1.8-42 dated 2023-03-02
ChangeLog | 3 DESCRIPTION | 6 MD5 | 28 +- R/gam.fit4.r | 58 ++++- R/gamlss.r | 592 +++++++++++++++++++++++++++++++++++++--------------- R/mgcv.r | 5 R/mvam.r | 1 man/bam.Rd | 2 man/cnorm.Rd | 2 man/gam.fit3.Rd | 2 man/twlss.Rd | 2 src/discrete.c | 2 src/matrix.c | 2 src/ncv.c | 106 +++++++-- src/sparse-smooth.c | 4 15 files changed, 593 insertions(+), 222 deletions(-)
Title: Joint Species Distribution Models
Description: Fits joint species distribution models ('jSDM')
in a hierarchical Bayesian framework (Warton and al. 2015
<doi:10.1016/j.tree.2015.09.007>). The Gibbs sampler is written
in C++. It uses 'Rcpp', 'Armadillo' and 'GSL' to maximize computation
efficiency.
Author: Jeanne Clement [aut, cre] ,
Ghislain Vieilledent [aut] ,
Frederic Gosselin [ctb] ,
CIRAD [cph, fnd]
Maintainer: Jeanne Clement <jeanne.clement16@laposte.net>
Diff between jSDM versions 0.2.1 dated 2022-03-21 and 0.2.2 dated 2023-03-02
DESCRIPTION | 21 MD5 | 185 - NAMESPACE | 2 NEWS.md | 10 R/RcppExports.R | 112 - R/get_enviro_cor.R | 32 R/get_residual_cor.R | 72 R/hidden.R | 723 +++--- R/jSDM-package.R | 2 R/jSDM_binomial_logit.R | 96 R/jSDM_binomial_probit.R | 30 R/jSDM_binomial_probit_long_format.R | 38 R/jSDM_binomial_probit_sp_constrained.R | 23 R/jSDM_gaussian.R |only R/jSDM_poisson_log.R | 110 - R/plot_associations.R | 17 R/predict.jSDM.R | 25 README.md | 10 build/partial.rdb |binary build/vignette.rds |binary data/madagascar.rda |only inst/doc/jSDM.R | 3 inst/doc/jSDM.Rmd | 32 inst/doc/jSDM.html | 864 ++++++-- inst/doc/proof.Rmd | 6 inst/doc/proof.html | 1044 +++++++--- man/get_enviro_cor.Rd | 2 man/get_residual_cor.Rd | 24 man/jSDM-package.Rd | 2 man/jSDM_binomial_logit.Rd | 12 man/jSDM_binomial_probit.Rd | 11 man/jSDM_binomial_probit_long_format.Rd | 10 man/jSDM_binomial_probit_sp_constrained.Rd | 13 man/jSDM_gaussian.Rd |only man/jSDM_poisson_log.Rd | 12 man/madagascar.Rd |only man/plot_associations.Rd | 10 man/predict.jSDM.Rd | 2 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 526 ++++- src/Rcpp_jSDM_binomial_logit.cpp | 4 src/Rcpp_jSDM_binomial_logit_fixed_site.cpp | 4 src/Rcpp_jSDM_binomial_logit_fixed_site_lv.cpp | 4 src/Rcpp_jSDM_binomial_logit_lv.cpp | 4 src/Rcpp_jSDM_binomial_logit_rand_site.cpp | 15 src/Rcpp_jSDM_binomial_logit_rand_site_lv.cpp | 15 src/Rcpp_jSDM_binomial_logit_traits.cpp | 4 src/Rcpp_jSDM_binomial_logit_traits_fixed_site.cpp | 4 src/Rcpp_jSDM_binomial_logit_traits_fixed_site_lv.cpp | 4 src/Rcpp_jSDM_binomial_logit_traits_lv.cpp | 4 src/Rcpp_jSDM_binomial_logit_traits_rand_site.cpp | 15 src/Rcpp_jSDM_binomial_logit_traits_rand_site_lv.cpp | 15 src/Rcpp_jSDM_binomial_probit_rand_site.cpp | 11 src/Rcpp_jSDM_binomial_probit_rand_site_long_format.cpp | 11 src/Rcpp_jSDM_binomial_probit_rand_site_lv.cpp | 11 src/Rcpp_jSDM_binomial_probit_rand_site_lv_long_format.cpp | 10 src/Rcpp_jSDM_binomial_probit_traits_lv.cpp | 5 src/Rcpp_jSDM_binomial_probit_traits_rand_site.cpp | 11 src/Rcpp_jSDM_binomial_probit_traits_rand_site_long_format.cpp | 11 src/Rcpp_jSDM_binomial_probit_traits_rand_site_lv.cpp | 11 src/Rcpp_jSDM_binomial_probit_traits_rand_site_lv_long_format.cpp | 10 src/Rcpp_jSDM_gaussian.cpp |only src/Rcpp_jSDM_gaussian_fixed_site.cpp |only src/Rcpp_jSDM_gaussian_fixed_site_lv.cpp |only src/Rcpp_jSDM_gaussian_lv.cpp |only src/Rcpp_jSDM_gaussian_rand_site.cpp |only src/Rcpp_jSDM_gaussian_rand_site_lv.cpp |only src/Rcpp_jSDM_gaussian_traits.cpp |only src/Rcpp_jSDM_gaussian_traits_fixed_site.cpp |only src/Rcpp_jSDM_gaussian_traits_fixed_site_lv.cpp |only src/Rcpp_jSDM_gaussian_traits_lv.cpp |only src/Rcpp_jSDM_gaussian_traits_rand_site.cpp |only src/Rcpp_jSDM_gaussian_traits_rand_site_lv.cpp |only src/Rcpp_jSDM_poisson_log.cpp | 4 src/Rcpp_jSDM_poisson_log_fixed_site.cpp | 4 src/Rcpp_jSDM_poisson_log_fixed_site_lv.cpp | 4 src/Rcpp_jSDM_poisson_log_lv.cpp | 4 src/Rcpp_jSDM_poisson_log_rand_site.cpp | 15 src/Rcpp_jSDM_poisson_log_rand_site_lv.cpp | 15 src/Rcpp_jSDM_poisson_log_traits.cpp | 4 src/Rcpp_jSDM_poisson_log_traits_fixed_site.cpp | 4 src/Rcpp_jSDM_poisson_log_traits_fixed_site_lv.cpp | 4 src/Rcpp_jSDM_poisson_log_traits_lv.cpp | 4 src/Rcpp_jSDM_poisson_log_traits_rand_site.cpp | 15 src/Rcpp_jSDM_poisson_log_traits_rand_site_lv.cpp | 15 src/Rcpp_jSDM_useful.h | 4 tests/testthat/test-get_enviro_cor.R |only tests/testthat/test-get_residual_cor.R |only tests/testthat/test-hidden.R |only tests/testthat/test-inv_logit.R | 2 tests/testthat/test-jSDM_binomial_logit.R | 758 +++++++ tests/testthat/test-jSDM_binomial_probit.R | 24 tests/testthat/test-jSDM_binomial_probit_long_format.R | 24 tests/testthat/test-jSDM_binomial_probit_sp_constrained.R | 16 tests/testthat/test-jSDM_gaussian.R |only tests/testthat/test-jSDM_poisson_log.R | 749 ++++++- tests/testthat/test-logit.R | 4 tests/testthat/test-predict.jSDM.R |only vignettes/bib/biblio-jSDM.bib | 52 vignettes/figures/alpine_plants_.png |only vignettes/figures/birds_.jpg |only vignettes/figures/oribatid-mites.png |binary vignettes/jSDM.Rmd | 32 vignettes/proof.Rmd | 6 105 files changed, 4462 insertions(+), 1567 deletions(-)
Title: Estimates Gross Output Functions
Description: Estimation of gross output production functions and productivity in the presence of numerous fixed (nonflexible) and a single flexible input using the nonparametric identification strategy specified in Gandhi, Navarro, and Rivers (2020) <doi:10.1086/707736>. Monte Carlo evidence from the paper demonstrates high performance in estimating production function elasticities.
Author: David J. Jin [aut, cre]
Maintainer: David J. Jin <jindavid@sas.upenn.edu>
Diff between gnrprod versions 1.0.0 dated 2022-01-13 and 1.1.0 dated 2023-03-02
DESCRIPTION | 16 ++++----- MD5 | 24 +++++++------- NEWS.md | 3 + R/gnrflex.R | 2 + R/gnriv.R | 86 ++++++++++++++++++++++++++++++--------------------- R/gnriv.control.R | 10 +++-- R/gnrprod.R | 6 ++- README.md | 2 - build/partial.rdb |binary man/gnrflex.Rd | 1 man/gnriv.Rd | 2 - man/gnriv.control.Rd | 6 ++- man/gnrprod.Rd | 3 + 13 files changed, 96 insertions(+), 65 deletions(-)
Title: Facilitation of Data Preparation and Plotting Procedures for RDA
and PCA Analyses
Description: Help to the occasional R user for synthesis and enhanced graphical visualization of redundancy analysis (RDA) and principal component analysis (PCA) methods and objects.
Inputs are : data frame, RDA (package 'vegan') and PCA (package 'FactoMineR') objects.
Outputs are : synthesized results of RDA, displayed in console and saved in tables ; displayed and saved objects of PCA graphic visualization of individuals and variables projections with multiple graphic parameters.
Method note : for the RDA output synthesis, several functions of the package 'RVAideMemoire', developed by Maxime Hervé, are exploited.
Author: Gregoire Bianchetti [aut, cre]
Maintainer: Gregoire Bianchetti <auguste.blam@gmail.com>
Diff between GABB versions 0.1.4 dated 2023-02-24 and 0.2.0 dated 2023-03-02
DESCRIPTION | 6 MD5 | 8 R/PCA_RDA_graphics.R | 492 ++++++++++++++++++++++++++++++++++-------------- R/check_data_for_RDA.R | 12 - man/PCA_RDA_graphics.Rd | 41 +++- 5 files changed, 402 insertions(+), 157 deletions(-)
Title: Handling Hierarchically Structured Risk Factors using Random
Effects Models
Description: Using this package, you can fit a random effects model using either the hierarchical credibility model, a combination of the hierarchical credibility model with a generalized linear model or a Tweedie generalized linear mixed model. See Campo, B.D.C. and Antonio, K. (2023) <doi:10.1080/03461238.2022.2161413>.
Author: Campo Bavo D.C. [aut, cre]
Maintainer: Campo Bavo D.C. <bavo.decock@kuleuven.be>
Diff between actuaRE versions 0.1.3 dated 2023-02-24 and 0.1.4 dated 2023-03-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/printFunctions.R | 21 ++++++++------------- build/partial.rdb |binary inst/doc/actuaRE.html | 42 ++++++++++++++++++++++-------------------- 5 files changed, 37 insertions(+), 40 deletions(-)
Title: Search Spaces for 'mlr3'
Description: Collection of search spaces for hyperparameter optimization in the
'mlr3' ecosystem. It features ready-to-use search spaces for many popular
machine learning algorithms. The search spaces are from scientific articles
and work for a wide range of data sets.
Author: Marc Becker [cre, aut] ,
Michel Lang [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuningspaces versions 0.3.3 dated 2022-12-07 and 0.3.4 dated 2023-03-02
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ NEWS.md | 5 +++++ R/TuningSpace.R | 5 +++-- README.md | 24 +++++++++++++++++++++--- man/TuningSpace.Rd | 11 +++++++++-- man/figures |only man/mlr3tuningspaces-package.Rd | 4 +++- 8 files changed, 53 insertions(+), 19 deletions(-)
More information about mlr3tuningspaces at CRAN
Permanent link
Title: Feature Selection for 'mlr3'
Description: Feature selection package of the 'mlr3' ecosystem. It selects
the optimal feature set for any 'mlr3' learner. The package works with
several optimization algorithms e.g. Random Search, Recursive Feature
Elimination, and Genetic Search. Moreover, it can automatically
optimize learners and estimate the performance of optimized feature
sets with nested resampling.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 0.10.0 dated 2023-02-21 and 0.11.0 dated 2023-03-02
DESCRIPTION | 6 MD5 | 118 +++++++++---------- NEWS.md | 9 + R/ArchiveFSelect.R | 2 R/AutoFSelector.R | 18 +- R/CallbackFSelect.R | 4 R/ContextEval.R | 4 R/FSelectInstanceMultiCrit.R | 8 + R/FSelectInstanceSingleCrit.R | 25 +++- R/FSelector.R | 19 ++- R/FSelectorDesignPoints.R | 2 R/FSelectorRFE.R | 12 + R/FSelectorRFECV.R | 7 - R/FSelectorRandomSearch.R | 2 R/FSelectorSequential.R | 2 R/FSelectorShadowVariableSearch.R | 7 - R/ObjectiveFSelect.R | 2 R/auto_fselector.R | 20 --- R/extract_inner_fselect_archives.R | 2 R/extract_inner_fselect_results.R | 2 R/fselect.R | 24 +-- R/fselect_nested.R | 36 +++-- R/mlr_callbacks.R | 2 R/sugar.R | 1 README.md | 11 + inst/testthat/helper_fselector.R | 10 - man/ArchiveFSelect.Rd | 2 man/AutoFSelector.Rd | 20 +-- man/CallbackFSelect.Rd | 2 man/ContextEval.Rd | 4 man/FSelectInstanceMultiCrit.Rd | 6 man/FSelectInstanceSingleCrit.Rd | 26 +++- man/FSelector.Rd | 19 ++- man/ObjectiveFSelect.Rd | 2 man/auto_fselector.Rd | 30 ++-- man/callback_fselect.Rd | 2 man/extract_inner_fselect_archives.Rd | 2 man/extract_inner_fselect_results.Rd | 2 man/fselect.Rd | 33 +++-- man/fselect_nested.Rd | 44 +++++-- man/fsi.Rd | 26 +++- man/mlr3fselect.backup.Rd | 2 man/mlr_fselectors_design_points.Rd | 2 man/mlr_fselectors_exhaustive_search.Rd | 2 man/mlr_fselectors_genetic_search.Rd | 2 man/mlr_fselectors_random_search.Rd | 2 man/mlr_fselectors_rfe.Rd | 19 ++- man/mlr_fselectors_rfecv.Rd | 10 + man/mlr_fselectors_sequential.Rd | 4 man/mlr_fselectors_shadow_variable_search.Rd | 10 + tests/testthat/test_ArchiveFSelect.R | 12 - tests/testthat/test_AutoFSelector.R | 7 - tests/testthat/test_FSelectorRFE.R | 8 - tests/testthat/test_FSelectorRFECV.R | 2 tests/testthat/test_auto_fselector.R | 12 - tests/testthat/test_extract_inner_fselect_archives.R | 24 +-- tests/testthat/test_extract_inner_fselect_result.R | 30 ++-- tests/testthat/test_fselect.R | 29 ++++ tests/testthat/test_fselect_nested.R | 4 tests/testthat/test_mlr_callbacks.R | 5 60 files changed, 480 insertions(+), 281 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-13 1.0
Title: Biological Entity Dictionary (BED)
Description: An interface for the 'Neo4j' database providing
mapping between different identifiers of biological entities.
This Biological Entity Dictionary (BED)
has been developed to address three main challenges.
The first one is related to the completeness of identifier mappings.
Indeed, direct mapping information provided by the different systems
are not always complete and can be enriched by mappings provided by other
resources.
More interestingly, direct mappings not identified by any of these
resources can be indirectly inferred by using mappings to a third reference.
For example, many human Ensembl gene ID are not directly mapped to any
Entrez gene ID but such mappings can be inferred using respective mappings
to HGNC ID. The second challenge is related to the mapping of deprecated
identifiers. Indeed, entity identifiers can change from one resource
release to another. The identifier history is provided by some resources,
such as Ensembl or the NCBI, but it is generally not used by mapping [...truncated...]
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between BED versions 1.4.12 dated 2023-02-16 and 1.4.13 dated 2023-03-02
DESCRIPTION | 6 MD5 | 14 R/zzz.R | 3 inst/doc/BED.R | 3 inst/doc/BED.Rmd | 5 inst/doc/BED.html | 2269 +++++++++++++++++++++++++----------------------------- inst/pkgdown.yml | 2 vignettes/BED.Rmd | 5 8 files changed, 1104 insertions(+), 1203 deletions(-)
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stephane Dray <stephane.dray@univ-lyon1.fr> and Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferriere.
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-17 dated 2023-01-27 and 1.0-18 dated 2023-03-02
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ inst/CITATION | 18 ++++-------------- inst/doc/adegraphics.html | 14 +++++++------- man/addline.Rd | 4 ++-- man/addsegment.Rd | 4 ++-- tests/nbgraph.R | 3 ++- 7 files changed, 26 insertions(+), 35 deletions(-)
Title: Basic Routing for Shiny Web Applications
Description: It is a simple router for your Shiny apps.
The router allows you to create dynamic web applications with real-time
User Interface and easily share url to pages within your Shiny apps.
Author: Ryszard Szymanski [cre, aut],
Jakub Nowicki [aut],
Filip Stachura [aut],
Dominik Krzeminski [aut],
Krystian Igras [aut],
Servet Ahmet Cizmeli [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Ryszard Szymanski <opensource+ryszard@appsilon.com>
Diff between shiny.router versions 0.2.3 dated 2022-07-01 and 0.3.0 dated 2023-03-02
DESCRIPTION | 49 +++++----- MD5 | 61 ++++++------ NAMESPACE | 2 R/logger.R | 3 R/pages.R | 16 +-- R/paths.R | 19 ++- R/router.R | 158 ++++++++++++++++++++++++++------- R/zzz.R | 14 +- README.md | 105 +++++++-------------- inst/WORDLIST |only man/attach_attribs.Rd | 5 - man/callback_mapping.Rd | 1 man/change_page.Rd | 4 man/cleanup_hashpath.Rd | 7 - man/create_router_callback.Rd | 3 man/disable_bootstrap_on_bookmark.Rd | 2 man/dot-onAttach.Rd |only man/extract_link_name.Rd | 1 man/figures/router_demo |only man/get_url_hash.Rd | 1 man/grapes-colon-colon-colon-grapes.Rd | 1 man/is_page.Rd | 2 man/log_msg.Rd | 3 man/make_router.Rd | 5 - man/page404.Rd | 2 man/parse_url_path.Rd | 2 man/route.Rd | 4 man/router_server.Rd | 18 +++ man/router_server_internal.Rd |only man/router_ui.Rd | 34 +++++-- man/router_ui_internal.Rd |only man/valid_path.Rd | 1 tests/testthat/test-paths.R | 4 tests/testthat/test-router.R | 33 ------ 34 files changed, 325 insertions(+), 235 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII,
and a set of formatters for transforming values or sets of values into
ASCII-ready display strings.
Author: Gabriel Becker [aut, cre],
Adrian Waddell [aut],
Davide Garolini [ctb],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between formatters versions 0.3.2 dated 2022-06-08 and 0.4.0 dated 2023-03-02
formatters-0.3.2/formatters/man/matrix_print_form.Rd |only formatters-0.4.0/formatters/DESCRIPTION | 39 formatters-0.4.0/formatters/MD5 | 92 - formatters-0.4.0/formatters/NAMESPACE | 41 formatters-0.4.0/formatters/NEWS.md | 70 + formatters-0.4.0/formatters/R/format_value.R | 337 +++-- formatters-0.4.0/formatters/R/generics.R | 295 +++- formatters-0.4.0/formatters/R/labels.R | 26 formatters-0.4.0/formatters/R/matrix_form.R | 505 ++++--- formatters-0.4.0/formatters/R/mpf_exporters.R |only formatters-0.4.0/formatters/R/page_size.R |only formatters-0.4.0/formatters/R/pagination.R | 584 ++++++-- formatters-0.4.0/formatters/R/tostring.R | 604 +++++++-- formatters-0.4.0/formatters/R/utils.R | 6 formatters-0.4.0/formatters/README.md | 269 ++-- formatters-0.4.0/formatters/build/vignette.rds |binary formatters-0.4.0/formatters/inst/WORDLIST |only formatters-0.4.0/formatters/inst/doc/formatters.R | 80 - formatters-0.4.0/formatters/inst/doc/formatters.Rmd | 86 - formatters-0.4.0/formatters/inst/doc/formatters.html | 491 +++++-- formatters-0.4.0/formatters/man/MatrixPrintForm.Rd |only formatters-0.4.0/formatters/man/basemethods.Rd | 6 formatters-0.4.0/formatters/man/basic_matrix_form.Rd | 9 formatters-0.4.0/formatters/man/basic_pagdf.Rd | 12 formatters-0.4.0/formatters/man/font_lcpi.Rd |only formatters-0.4.0/formatters/man/format_value.Rd | 9 formatters-0.4.0/formatters/man/ifnotlen0.Rd | 8 formatters-0.4.0/formatters/man/lab_name.Rd | 19 formatters-0.4.0/formatters/man/make_row_df.Rd | 48 formatters-0.4.0/formatters/man/matrix_form.Rd | 30 formatters-0.4.0/formatters/man/mpf_accessors.Rd |only formatters-0.4.0/formatters/man/mpf_to_rtf.Rd |only formatters-0.4.0/formatters/man/nlines.Rd | 13 formatters-0.4.0/formatters/man/padstr.Rd | 9 formatters-0.4.0/formatters/man/pag_indices_inner.Rd | 83 + formatters-0.4.0/formatters/man/pagdfrow.Rd | 15 formatters-0.4.0/formatters/man/page_lcpp.Rd |only formatters-0.4.0/formatters/man/page_types.Rd |only formatters-0.4.0/formatters/man/pagination_algo.Rd |only formatters-0.4.0/formatters/man/propose_column_widths.Rd | 11 formatters-0.4.0/formatters/man/spans_to_viscell.Rd | 10 formatters-0.4.0/formatters/man/sprintf_format.Rd | 5 formatters-0.4.0/formatters/man/table_inset.Rd |only formatters-0.4.0/formatters/man/title_footer.Rd | 12 formatters-0.4.0/formatters/man/tostring.Rd | 47 formatters-0.4.0/formatters/man/var_labels-set.Rd | 4 formatters-0.4.0/formatters/man/var_labels.Rd | 2 formatters-0.4.0/formatters/man/vert_pag_indices.Rd | 27 formatters-0.4.0/formatters/man/with_label.Rd | 2 formatters-0.4.0/formatters/man/wrap_string.Rd |only formatters-0.4.0/formatters/tests/testthat/test-exporters.R |only formatters-0.4.0/formatters/tests/testthat/test-formatters.R | 735 +++++++---- formatters-0.4.0/formatters/tests/testthat/test-pagination.R |only formatters-0.4.0/formatters/tests/testthat/test-txt_wrap.R |only formatters-0.4.0/formatters/vignettes/formatters.Rmd | 86 - 55 files changed, 3218 insertions(+), 1509 deletions(-)
Title: Aligned Corpus Toolkit
Description: The Aligned Corpus Toolkit (act) is designed for linguists that work with time aligned transcription data. It offers functions to import and export various annotation file formats ('ELAN' .eaf, 'EXMARaLDA .exb and 'Praat' .TextGrid files), create print transcripts in the style of conversation analysis, search transcripts (span searches across multiple annotations, search in normalized annotations, make concordances etc.), export and re-import search results (.csv and 'Excel' .xlsx format), create cuts for the search results (print transcripts, audio/video cuts using 'FFmpeg' and video sub titles in 'Subrib title' .srt format), modify the data in a corpus (search/replace, delete, filter etc.), interact with 'Praat' using 'Praat'-scripts, and exchange data with the 'rPraat' package. The package is itself written in R and may be expanded by other users.
Author: Oliver Ehmer [aut, cre]
Maintainer: Oliver Ehmer <oliver.ehmer@uos.de>
Diff between act versions 1.2.4 dated 2023-02-08 and 1.2.7 dated 2023-03-02
DESCRIPTION | 8 MD5 | 42 +-- R/act_options.R | 2 R/class_corpus.R | 10 R/corpus_import.R | 14 - R/corpus_new.R | 6 R/media_assign.R | 15 - R/search_cuts_media.R | 25 + R/search_new.R | 20 - R/search_run.R | 11 R/search_transcript_content.R | 67 ++--- R/transcripts_filter.R | 34 ++ R/transcripts_filter_single.R | 21 + R/transcripts_update_fulltexts.R | 4 R/transcripts_update_normalization.R | 6 data/examplecorpus.RData |binary inst/doc/install_ffmpeg.html | 445 ++++++++++++++++++++++++++++------- inst/doc/install_sendpraat.html | 289 ++++++++++++++++++++-- man/corpus-class.Rd | 8 man/corpus_import.Rd | 9 man/corpus_new.Rd | 6 man/options_show.Rd | 1 22 files changed, 815 insertions(+), 228 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-29 1.2.0
2015-03-17 1.0.8441
Title: Probabilistic Forecast Combination Using CRPS Learning
Description: Combine probabilistic forecasts using CRPS learning algorithms proposed in Berrisch, Ziel (2021) <arXiv:2102.00968> <doi:10.1016/j.jeconom.2021.11.008>. The package implements multiple online learning algorithms like Bernstein online aggregation; see Wintenberger (2014) <arXiv:1404.1356>. Quantile regression is also implemented for comparison purposes. Model parameters can be tuned automatically with respect to the loss of the forecast combination. Methods like predict(), update(), plot() and print() are available for convenience. This package utilizes the optim C++ library for numeric optimization <https://github.com/kthohr/optim>.
Author: Jonathan Berrisch [aut, cre] ,
Florian Ziel [aut]
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>
Diff between profoc versions 1.1.0 dated 2023-01-13 and 1.1.1 dated 2023-03-02
DESCRIPTION | 15 +++++++-------- MD5 | 13 +++++++------ NEWS.md | 11 +++++++++-- R/splines.R | 17 ++++++----------- build/partial.rdb |binary inst/CITATION |only src/Makevars | 2 -- src/Makevars.win | 2 -- 8 files changed, 29 insertions(+), 31 deletions(-)
Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'DDIwR', 'QCA' and 'venn'.
Interprets and translates, factorizes and negates SOP - Sum of Products
expressions, for both binary and multi-value crisp sets, and extracts
information (set names, set values) from those expressions. Other functions
perform various other checks if possibly numeric (even if all numbers reside
in a character vector) and coerce to numeric, or check if the numbers are
whole. It also offers, among many others, a highly versatile recoding
routine and some more flexible alternatives to the base function 'with()'
and 'within()'.
SOP simplification functions in this package use related minimization from
package 'QCA', which is recommended to be installed despite not being listed
in the Imports field, due to circular dependency issues.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between admisc versions 0.30 dated 2022-09-18 and 0.31 dated 2023-03-02
DESCRIPTION | 14 ++--- MD5 | 130 +++++++++++++++++++++++++------------------------- NAMESPACE | 4 + R/asNumeric.R | 2 R/asSOP.R | 2 R/brackets.R | 2 R/checkMV.R | 2 R/checkSubset.R | 2 R/checkValid.R | 2 R/classify.R | 2 R/coerceMode.R | 2 R/combnk.R | 2 R/compute.R | 2 R/dashes.R | 2 R/equality.R | 2 R/expand.R | 2 R/export.R | 2 R/factorize.R | 2 R/finvert.R | 2 R/frelevel.R | 2 R/getInfo.R | 2 R/getLevels.R | 2 R/getMatrix.R | 2 R/getName.R | 2 R/hclr.R | 2 R/inside.R |only R/intersection.R | 2 R/invert.R | 2 R/listRDA.R | 2 R/mvSOP.R | 2 R/negate.R | 2 R/numdec.R | 37 +++++++++----- R/objRDA.R | 2 R/onLoad.R | 2 R/pad.R | 2 R/permutations.R | 2 R/possibleNumeric.R | 2 R/prettyString.R | 2 R/prettyTable.R | 2 R/print.R | 2 R/recode.R | 2 R/recreate.R | 2 R/reload.R | 2 R/replaceText.R | 95 +++++++++++++++++++++++------------- R/scan.clipboard.R |only R/simplify.R | 2 R/sortExpressions.R | 2 R/stopError.R | 2 R/string.R | 2 R/tagged.R | 2 R/tildae.R | 2 R/translate.R | 2 R/tryCatchWEM.R | 4 - R/uninstall.R | 2 R/unload.R | 2 R/unlockEnvironment.R | 2 R/using.R | 43 ++++++++++------ R/validateNames.R | 2 R/verify.R | 2 R/wholeNumeric.R | 2 R/writePrimeimp.R | 2 build/partial.rdb |binary inst/ChangeLog | 7 ++ man/admisc_package.Rd | 4 - man/inside.Rd |only man/replaceText.Rd | 5 + man/scan.clipboard.Rd |only man/using.Rd | 1 68 files changed, 257 insertions(+), 191 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-20 1.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-25 2.3
2014-04-26 2.2
2014-03-26 2.1
2014-02-25 2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-21 2.1-1.1
2017-01-07 2.1-1
2016-12-16 2.1-0
2012-08-13 2.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-25 2.192
2019-11-12 2.190
2017-09-29 2.186
2016-09-22 2.154
2016-07-29 2.141
2016-07-29 2.142
2013-11-02 1.4
2013-11-01 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-28 0.2.10
2018-07-20 0.2.8
2018-06-07 0.2.7
2018-04-12 0.2.0
2017-11-28 0.1.8
2017-08-08 0.1.6
2017-08-03 0.1.5