Title: Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis.
Risk regression models for survival endpoints also in the presence of competing
risks are fitted using binomial regression based on a time sequence of binary
event status variables. A formula interface for the Fine-Gray regression model
and an interface for the combination of cause-specific Cox regression models.
A toolbox for assessing and comparing performance of risk predictions (risk
markers and risk prediction models). Prediction performance is measured by the
Brier score and the area under the ROC curve for binary possibly time-dependent
outcome. Inverse probability of censoring weighting and pseudo values are used
to deal with right censored data. Lists of risk markers and lists of risk models
are assessed simultaneously. Cross-validation repeatedly splits the data, trains
the risk prediction models on one part of each split and then summarizes and
compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre],
Johan Sebastian Ohlendorff [aut],
Paul Blanche [ctb],
Rikke Mortensen [ctb],
Marvin Wright [ctb],
Nikolaj Tollenaar [ctb],
John Muschelli [ctb],
Ulla Brasch Mogensen [ctb],
Asbjoern Risom [ctb],
Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 2026.02.13 dated 2026-02-16 and 2026.03.11 dated 2026-03-12
riskRegression-2026.02.13/riskRegression/tests/testthat/test-phreg.R |only riskRegression-2026.03.11/riskRegression/DESCRIPTION | 12 riskRegression-2026.03.11/riskRegression/MD5 | 29 riskRegression-2026.03.11/riskRegression/R/AUC.binary.R | 6 riskRegression-2026.03.11/riskRegression/R/CSC.R | 125 +++- riskRegression-2026.03.11/riskRegression/R/GLMnet.R | 307 +++++----- riskRegression-2026.03.11/riskRegression/R/coxLP.R | 31 - riskRegression-2026.03.11/riskRegression/R/coxStrata.R | 21 riskRegression-2026.03.11/riskRegression/R/plotCalibration.R | 8 riskRegression-2026.03.11/riskRegression/R/predict.CauseSpecificCox.R | 5 riskRegression-2026.03.11/riskRegression/R/predictRisk.R | 88 +- riskRegression-2026.03.11/riskRegression/R/print.CauseSpecificCox.R | 9 riskRegression-2026.03.11/riskRegression/man/CSC.Rd | 35 - riskRegression-2026.03.11/riskRegression/man/GLMnet.Rd | 79 +- riskRegression-2026.03.11/riskRegression/src/Makevars | 2 riskRegression-2026.03.11/riskRegression/src/Makevars.win | 1 16 files changed, 466 insertions(+), 292 deletions(-)
More information about riskRegression at CRAN
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Title: Computes Statistics for Relational Event History Data
Description: Computes a variety of statistics for relational event models. Relational event models enable researchers to investigate both exogenous and endogenous factors influencing the evolution of a time-ordered sequence of events. These models are categorized into tie-oriented models (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>), where the probability of a dyad interacting next is modeled in a single step, and actor-oriented models (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>), which first model the probability of a sender initiating an interaction and subsequently the probability of the sender's choice of receiver. The package is designed to compute a variety of statistics that summarize exogenous and endogenous influences on the event stream for both types of models.
Author: Marlyne Meijerink-Bosman [aut],
Giuseppe Arena [ctb],
Diana Karimova [ctb],
Rumana Lakdawala [ctb],
Mahdi Shafiee Kamalabad [ctb],
Fabio Generoso Vieira [ctb],
Roger Leenders [ctb],
Joris Mulder [aut, cre]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between remstats versions 3.2.4 dated 2025-01-29 and 3.2.5 dated 2026-03-12
DESCRIPTION | 41 ++++++++++++++++++----------------------- LICENSE | 2 +- MD5 | 10 +++++----- build/partial.rdb |binary build/vignette.rds |binary src/RcppExports.cpp | 12 ++++++------ 6 files changed, 30 insertions(+), 35 deletions(-)
Title: Highly Optimized Protocol Buffer Serializers
Description: Pure C++ implementations for reading and writing several common data
formats based on Google protocol-buffers. Currently supports 'rexp.proto' for
serialized R objects, 'geobuf.proto' for binary geojson, and 'mvt.proto' for
vector tiles. This package uses the auto-generated C++ code by protobuf-compiler,
hence the entire serialization is optimized at compile time. The 'RProtoBuf'
package on the other hand uses the protobuf runtime library to provide a general-
purpose toolkit for reading and writing arbitrary protocol-buffer data in R.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between protolite versions 2.3.1 dated 2024-10-04 and 2.4.0 dated 2026-03-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 35 ++++++++++++++++++++++++++--------- 4 files changed, 36 insertions(+), 16 deletions(-)
Title: Interpolate Munsell Renotation Data from Hue Value/Chroma to
CIE/RGB
Description: Methods for interpolating data in the Munsell color system following the ASTM D-1535 standard. Hues and chromas with decimal values can be interpolated and converted to/from the Munsell color system and CIE xyY, CIE XYZ, CIE Lab, CIE Luv, or RGB. Includes ISCC-NBS color block lookup. Based on the work by Paul Centore, "The Munsell and Kubelka-Munk Toolbox".
Author: Jose Gama [aut, trl],
Paul Centore [aut, cph],
Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between munsellinterpol versions 3.2-0 dated 2025-06-18 and 3.3-2 dated 2026-03-12
DESCRIPTION | 8 +- MD5 | 78 ++++++++++---------- NEWS.md | 14 +++ R/ISCC-NBS.R | 15 ++- R/round.R | 33 ++++---- R/sysdata.rda |binary build/vignette.rds |binary data/munsellinterpol.rda |binary inst/doc/dental.html | 12 +-- inst/doc/lightness.pdf |binary inst/doc/lightness.rnw | 2 inst/doc/lociHC.pdf |binary inst/doc/lociHC.rnw | 2 inst/doc/munsellinterpol-guide.html | 24 +++--- inst/doc/soil.R | 23 ++--- inst/doc/soil.Rmd | 53 +++++++++---- inst/doc/soil.html | 132 +++++++++++++++++++--------------- inst/extdata/PantoneCoY.txt | 2 inst/extdata/Supplement1_3.6.2024.csv | 2 inst/extdata/glossybook-Centore.txt |only inst/extdata/mattebook-Joensuu.txt |only man/LabtoMunsell.Rd | 2 man/LuvtoMunsell.Rd | 2 man/MunsellBooks.Rd |only man/MunsellToLab.Rd | 2 man/MunsellToLuv.Rd | 2 man/MunsellToRGB.Rd | 2 man/MunsellToXYZ.Rd | 2 man/MunsellTosRGB.Rd | 2 man/MunsellToxyY.Rd | 4 - man/RGBtoMunsell.Rd | 2 man/XYZtoMunsell.Rd | 2 man/macros/macros.Rd | 2 man/round.Rd | 96 ++++++------------------ man/sRGBtoMunsell.Rd | 2 man/xyYtoMunsell.Rd | 4 - tests/test-rounding.R | 5 - tools/books.R |only tools/datasets.R | 94 +++++++++--------------- vignettes/lightness.rnw | 2 vignettes/lociHC.rnw | 2 vignettes/soil.Rmd | 53 +++++++++---- 42 files changed, 353 insertions(+), 329 deletions(-)
More information about munsellinterpol at CRAN
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Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] ,
Christoph Burow [aut, trl, dtc] ,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 1.1.2 dated 2025-12-12 and 1.2.0 dated 2026-03-12
Luminescence-1.1.2/Luminescence/R/github.R |only Luminescence-1.1.2/Luminescence/R/install_DevelopmentVersion.R |only Luminescence-1.1.2/Luminescence/inst/include |only Luminescence-1.1.2/Luminescence/man/GitHub-API.Rd |only Luminescence-1.1.2/Luminescence/man/install_DevelopmentVersion.Rd |only Luminescence-1.1.2/Luminescence/tests/testthat/test_github.R |only Luminescence-1.1.2/Luminescence/tests/testthat/test_install_DevelopmentVersion.R |only Luminescence-1.2.0/Luminescence/DESCRIPTION | 14 Luminescence-1.2.0/Luminescence/MD5 | 838 ++++---- Luminescence-1.2.0/Luminescence/NAMESPACE | 14 Luminescence-1.2.0/Luminescence/NEWS.md | 696 +++++++ Luminescence-1.2.0/Luminescence/R/Luminescence-generics.R | 276 ++ Luminescence-1.2.0/Luminescence/R/Luminescence-package.R | 129 - Luminescence-1.2.0/Luminescence/R/RLum-class.R | 29 Luminescence-1.2.0/Luminescence/R/RLum.Analysis-class.R | 121 - Luminescence-1.2.0/Luminescence/R/RLum.Data-class.R | 14 Luminescence-1.2.0/Luminescence/R/RLum.Data.Curve-class.R | 69 Luminescence-1.2.0/Luminescence/R/RLum.Data.Image-class.R | 60 Luminescence-1.2.0/Luminescence/R/RLum.Data.Spectrum-class.R | 37 Luminescence-1.2.0/Luminescence/R/RLum.Results-class.R | 22 Luminescence-1.2.0/Luminescence/R/Risoe.BINfileData-class.R | 26 Luminescence-1.2.0/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 25 Luminescence-1.2.0/Luminescence/R/Risoe.BINfileData2RLum.Data.Curve.R | 30 Luminescence-1.2.0/Luminescence/R/addins_RLum.R | 13 Luminescence-1.2.0/Luminescence/R/analyse_Al2O3C_CrossTalk.R | 44 Luminescence-1.2.0/Luminescence/R/analyse_Al2O3C_ITC.R | 53 Luminescence-1.2.0/Luminescence/R/analyse_Al2O3C_Measurement.R | 48 Luminescence-1.2.0/Luminescence/R/analyse_FadingMeasurement.R | 97 - Luminescence-1.2.0/Luminescence/R/analyse_IRSAR.RF.R | 30 Luminescence-1.2.0/Luminescence/R/analyse_SAR.CWOSL.R | 934 +++++----- Luminescence-1.2.0/Luminescence/R/analyse_SAR.TL.R | 94 - 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Luminescence-1.2.0/Luminescence/R/convert_XSYG2CSV.R | 17 Luminescence-1.2.0/Luminescence/R/correct_PMTLinearity.R | 19 Luminescence-1.2.0/Luminescence/R/extract_IrradiationTimes.R | 95 - Luminescence-1.2.0/Luminescence/R/extract_ROI.R | 14 Luminescence-1.2.0/Luminescence/R/fit_CWCurve.R | 44 Luminescence-1.2.0/Luminescence/R/fit_DoseResponseCurve.R | 146 - Luminescence-1.2.0/Luminescence/R/fit_EmissionSpectra.R | 19 Luminescence-1.2.0/Luminescence/R/fit_IsothermalHolding.R | 16 Luminescence-1.2.0/Luminescence/R/fit_LMCurve.R | 103 - Luminescence-1.2.0/Luminescence/R/fit_OSLLifeTimes.R | 13 Luminescence-1.2.0/Luminescence/R/fit_SurfaceExposure.R | 25 Luminescence-1.2.0/Luminescence/R/fit_ThermalQuenching.R | 2 Luminescence-1.2.0/Luminescence/R/import_Data.R | 16 Luminescence-1.2.0/Luminescence/R/internal_as.latex.table.R | 12 Luminescence-1.2.0/Luminescence/R/internals_RLum.R | 529 ++++- Luminescence-1.2.0/Luminescence/R/internals_Thermochronometry.R | 20 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| 8 Luminescence-1.2.0/Luminescence/man/calc_CosmicDoseRate.Rd | 5 Luminescence-1.2.0/Luminescence/man/calc_EED_Model.Rd | 10 Luminescence-1.2.0/Luminescence/man/calc_FadingCorr.Rd | 7 Luminescence-1.2.0/Luminescence/man/calc_FastRatio.Rd | 2 Luminescence-1.2.0/Luminescence/man/calc_FiniteMixture.Rd | 6 Luminescence-1.2.0/Luminescence/man/calc_FuchsLang2001.Rd | 8 Luminescence-1.2.0/Luminescence/man/calc_HomogeneityTest.Rd | 6 Luminescence-1.2.0/Luminescence/man/calc_Huntley2006.Rd | 13 Luminescence-1.2.0/Luminescence/man/calc_IEU.Rd | 6 Luminescence-1.2.0/Luminescence/man/calc_Lamothe2003.Rd | 23 Luminescence-1.2.0/Luminescence/man/calc_MaxDose.Rd | 25 Luminescence-1.2.0/Luminescence/man/calc_MinDose.Rd | 83 Luminescence-1.2.0/Luminescence/man/calc_MoransI.Rd | 13 Luminescence-1.2.0/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 12 Luminescence-1.2.0/Luminescence/man/calc_OSLLxTxRatio.Rd | 88 Luminescence-1.2.0/Luminescence/man/calc_SourceDoseRate.Rd | 22 Luminescence-1.2.0/Luminescence/man/calc_Statistics.Rd | 4 Luminescence-1.2.0/Luminescence/man/calc_TLLxTxRatio.Rd | 37 Luminescence-1.2.0/Luminescence/man/calc_ThermalLifetime.Rd | 4 Luminescence-1.2.0/Luminescence/man/calc_WodaFuchs2008.Rd | 4 Luminescence-1.2.0/Luminescence/man/calc_gSGC.Rd | 6 Luminescence-1.2.0/Luminescence/man/calc_gSGC_feldspar.Rd | 4 Luminescence-1.2.0/Luminescence/man/combine_De_Dr.Rd | 42 Luminescence-1.2.0/Luminescence/man/convert_Activity2Concentration.Rd | 18 Luminescence-1.2.0/Luminescence/man/convert_BIN2CSV.Rd | 4 Luminescence-1.2.0/Luminescence/man/convert_CW2pHMi.Rd | 38 Luminescence-1.2.0/Luminescence/man/convert_CW2pLM.Rd | 23 Luminescence-1.2.0/Luminescence/man/convert_CW2pLMi.Rd | 33 Luminescence-1.2.0/Luminescence/man/convert_CW2pPMi.Rd | 34 Luminescence-1.2.0/Luminescence/man/convert_Concentration2DoseRate.Rd | 38 Luminescence-1.2.0/Luminescence/man/convert_Daybreak2CSV.Rd | 7 Luminescence-1.2.0/Luminescence/man/convert_PSL2CSV.Rd | 10 Luminescence-1.2.0/Luminescence/man/convert_PSL2Risoe.BINfileData.Rd | 8 Luminescence-1.2.0/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 4 Luminescence-1.2.0/Luminescence/man/convert_SG2MG.Rd | 27 Luminescence-1.2.0/Luminescence/man/convert_Second2Gray.Rd | 12 Luminescence-1.2.0/Luminescence/man/convert_Wavelength2Energy.Rd | 4 Luminescence-1.2.0/Luminescence/man/convert_XSYG2CSV.Rd | 6 Luminescence-1.2.0/Luminescence/man/correct_PMTLinearity.Rd | 10 Luminescence-1.2.0/Luminescence/man/dot-as.latex.table.Rd | 4 Luminescence-1.2.0/Luminescence/man/extract_IrradiationTimes.Rd | 9 Luminescence-1.2.0/Luminescence/man/extract_ROI.Rd | 11 Luminescence-1.2.0/Luminescence/man/fit_CWCurve.Rd | 18 Luminescence-1.2.0/Luminescence/man/fit_DoseResponseCurve.Rd | 80 Luminescence-1.2.0/Luminescence/man/fit_EmissionSpectra.Rd | 12 Luminescence-1.2.0/Luminescence/man/fit_LMCurve.Rd | 40 Luminescence-1.2.0/Luminescence/man/fit_OSLLifeTimes.Rd | 4 Luminescence-1.2.0/Luminescence/man/fit_SurfaceExposure.Rd | 10 Luminescence-1.2.0/Luminescence/man/fit_ThermalQuenching.Rd | 4 Luminescence-1.2.0/Luminescence/man/get_Layout.Rd | 2 Luminescence-1.2.0/Luminescence/man/get_RLum.Rd | 13 Luminescence-1.2.0/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-1.2.0/Luminescence/man/import_Data.Rd | 8 Luminescence-1.2.0/Luminescence/man/length_RLum.Rd | 9 Luminescence-1.2.0/Luminescence/man/melt_RLum.Rd | 4 Luminescence-1.2.0/Luminescence/man/merge_RLum.Analysis.Rd | 10 Luminescence-1.2.0/Luminescence/man/merge_RLum.Data.Curve.Rd | 11 Luminescence-1.2.0/Luminescence/man/merge_RLum.Data.Spectrum.Rd | 7 Luminescence-1.2.0/Luminescence/man/merge_RLum.Rd | 7 Luminescence-1.2.0/Luminescence/man/merge_RLum.Results.Rd | 6 Luminescence-1.2.0/Luminescence/man/merge_Risoe.BINfileData.Rd | 15 Luminescence-1.2.0/Luminescence/man/metadata.Rd | 8 Luminescence-1.2.0/Luminescence/man/methods_RLum.Rd | 28 Luminescence-1.2.0/Luminescence/man/names_RLum.Rd | 7 Luminescence-1.2.0/Luminescence/man/normalise_RLum.Rd |only Luminescence-1.2.0/Luminescence/man/plot_AbanicoPlot.Rd | 67 Luminescence-1.2.0/Luminescence/man/plot_DRCSummary.Rd | 20 Luminescence-1.2.0/Luminescence/man/plot_DRTResults.Rd | 38 Luminescence-1.2.0/Luminescence/man/plot_DetPlot.Rd | 41 Luminescence-1.2.0/Luminescence/man/plot_DoseResponseCurve.Rd | 13 Luminescence-1.2.0/Luminescence/man/plot_FilterCombinations.Rd | 9 Luminescence-1.2.0/Luminescence/man/plot_GrowthCurve.Rd | 45 Luminescence-1.2.0/Luminescence/man/plot_Histogram.Rd | 5 Luminescence-1.2.0/Luminescence/man/plot_KDE.Rd | 16 Luminescence-1.2.0/Luminescence/man/plot_MoranScatterplot.Rd | 31 Luminescence-1.2.0/Luminescence/man/plot_NRt.Rd | 9 Luminescence-1.2.0/Luminescence/man/plot_OSLAgeSummary.Rd | 10 Luminescence-1.2.0/Luminescence/man/plot_RLum.Analysis.Rd | 6 Luminescence-1.2.0/Luminescence/man/plot_RLum.Data.Curve.Rd | 17 Luminescence-1.2.0/Luminescence/man/plot_RLum.Data.Image.Rd | 11 Luminescence-1.2.0/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 21 Luminescence-1.2.0/Luminescence/man/plot_RLum.Rd | 61 Luminescence-1.2.0/Luminescence/man/plot_RLum.Results.Rd | 4 Luminescence-1.2.0/Luminescence/man/plot_ROI.Rd | 52 Luminescence-1.2.0/Luminescence/man/plot_RadialPlot.Rd | 22 Luminescence-1.2.0/Luminescence/man/plot_Risoe.BINfileData.Rd | 11 Luminescence-1.2.0/Luminescence/man/plot_SingleGrainDisc.Rd | 17 Luminescence-1.2.0/Luminescence/man/plot_ViolinPlot.Rd | 14 Luminescence-1.2.0/Luminescence/man/read_BIN2R.Rd | 28 Luminescence-1.2.0/Luminescence/man/read_BINXLOG2R.Rd |only Luminescence-1.2.0/Luminescence/man/read_Daybreak2R.Rd | 24 Luminescence-1.2.0/Luminescence/man/read_HeliosOSL2R.Rd | 24 Luminescence-1.2.0/Luminescence/man/read_PSL2R.Rd | 24 Luminescence-1.2.0/Luminescence/man/read_RF2R.Rd | 23 Luminescence-1.2.0/Luminescence/man/read_SPE2R.Rd | 28 Luminescence-1.2.0/Luminescence/man/read_TIFF2R.Rd | 21 Luminescence-1.2.0/Luminescence/man/read_XSYG2R.Rd | 18 Luminescence-1.2.0/Luminescence/man/remove_RLum.Rd | 4 Luminescence-1.2.0/Luminescence/man/remove_SignalBackground.Rd | 7 Luminescence-1.2.0/Luminescence/man/replicate_RLum.Rd | 4 Luminescence-1.2.0/Luminescence/man/report_RLum.Rd | 6 Luminescence-1.2.0/Luminescence/man/sTeve.Rd | 2 Luminescence-1.2.0/Luminescence/man/scale_GammaDose.Rd | 13 Luminescence-1.2.0/Luminescence/man/set_RLum.Rd | 7 Luminescence-1.2.0/Luminescence/man/set_Risoe.BINfileData.Rd | 4 Luminescence-1.2.0/Luminescence/man/smooth_RLum.Rd | 17 Luminescence-1.2.0/Luminescence/man/sort_RLum.Rd | 5 Luminescence-1.2.0/Luminescence/man/structure_RLum.Rd | 7 Luminescence-1.2.0/Luminescence/man/subset_SingleGrainData.Rd | 22 Luminescence-1.2.0/Luminescence/man/template_DRAC.Rd | 18 Luminescence-1.2.0/Luminescence/man/trim_RLum.Data.Rd | 4 Luminescence-1.2.0/Luminescence/man/tune_Data.Rd | 4 Luminescence-1.2.0/Luminescence/man/use_DRAC.Rd | 8 Luminescence-1.2.0/Luminescence/man/verify_SingleGrainData.Rd | 14 Luminescence-1.2.0/Luminescence/man/view.Rd | 4 Luminescence-1.2.0/Luminescence/man/write_R2BIN.Rd | 6 Luminescence-1.2.0/Luminescence/man/write_R2TIFF.Rd | 7 Luminescence-1.2.0/Luminescence/man/write_RLum2CSV.Rd | 4 Luminescence-1.2.0/Luminescence/src/Makevars | 1 Luminescence-1.2.0/Luminescence/src/Makevars.win | 1 Luminescence-1.2.0/Luminescence/src/RcppExports.cpp | 9 Luminescence-1.2.0/Luminescence/src/create_UID.cpp | 3 Luminescence-1.2.0/Luminescence/src/src_ThermoChronometry.cpp | 3 Luminescence-1.2.0/Luminescence/src/src_analyse_IRSARRF_SRS.cpp | 44 Luminescence-1.2.0/Luminescence/src/src_fit_functions.cpp | 8 Luminescence-1.2.0/Luminescence/tests/testthat/_data/OSLdecomposed_1.2.0.rds |only Luminescence-1.2.0/Luminescence/tests/testthat/_data/daybreak-tests |only Luminescence-1.2.0/Luminescence/tests/testthat/setup.R | 17 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 26 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Data.Curve.R | 22 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Data.Image.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Data.Spectrum.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Results-class.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_Risoe.BINfileData-class.R | 12 Luminescence-1.2.0/Luminescence/tests/testthat/test_Risoe.BINfileData2RLum.Analysis.R | 10 Luminescence-1.2.0/Luminescence/tests/testthat/test_Risoe.BINfileData2RLum.Data.Curve.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 35 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R | 25 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R | 19 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 118 - Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 688 +++++-- Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 72 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_ThermochronometryData.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_baSAR.R | 320 ++- Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 191 -- Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_portableOSL.R | 84 Luminescence-1.2.0/Luminescence/tests/testthat/test_apply_EfficiencyCorrection.R | 59 Luminescence-1.2.0/Luminescence/tests/testthat/test_as_latex_table.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_bin_RLumData.R | 17 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_AverageDose.R | 28 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_CentralDose.R | 10 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_CobbleDoseRate.R | 27 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_CommonDose.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_CosmicDoseRate.R | 10 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_EED_Model.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_FastRatio.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_FiniteMixture.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_FuchsLang2001.R | 8 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_HomogeneityTest.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_Lamothe2003.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_MaxDose.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_MinDose.R | 84 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_MoransI.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_OSLLxTxDecomposed.R | 23 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_OSLLxTxRatio.R | 369 ++- Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_TLLxTxRatio.R | 89 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_ThermalLifetime.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_WodaFuchs2008.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_gSGC.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_gSGC_feldspar.R | 3 Luminescence-1.2.0/Luminescence/tests/testthat/test_combine_De_Dr.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_Activity2Concentration.R | 3 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_CW2pX.R | 101 - Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_Concentration2DoseRate.R | 36 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_Daybreak2CSV.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_PSL2CSV.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_PSL2RisoeBINfiledata.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_RLum2Risoe.BINfileData.R | 23 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_SG2MG.R | 44 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_Second2Gray.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_XSYG2CSV.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_correct_PMTLinearity.R | 64 Luminescence-1.2.0/Luminescence/tests/testthat/test_extract_IrradiationTimes.R | 29 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_CWCurve.R | 17 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_DoseResponseCurve.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_IsothermalHolding.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_LMCurve.R | 54 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_SurfaceExposure.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_internals.R | 263 ++ Luminescence-1.2.0/Luminescence/tests/testthat/test_internals_Thermochronometry.R | 8 Luminescence-1.2.0/Luminescence/tests/testthat/test_merge_RLum.Data.Spectrum.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_merge_RLum.Results.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_merge_Risoe.BINfileData.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_methods_S3.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_names_RLum.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_normalise_RLum.R |only Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 25 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_DRCSummary.R | 22 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_DRTResults.R | 29 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_DetPlot.R | 146 + Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_DoseResponseCurve.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_GrowthCurve.R | 17 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_Histogram.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_KDE.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_NRt.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.Analysis.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.Data.Curve.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 37 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.R | 43 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.Results.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RadialPlot.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_Risoe.BINfileData.R | 11 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_ViolinPlot.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_BIN2R.R | 39 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_BINXLOG2R.R |only Luminescence-1.2.0/Luminescence/tests/testthat/test_read_Daybreak2R.R | 48 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_HeliosOSL2R.R | 11 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_PSL2R.R | 57 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_RF2R.R | 10 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_SPE2R.R | 37 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_TIFF2R.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_XSYG2R.R | 29 Luminescence-1.2.0/Luminescence/tests/testthat/test_remove_SignalBackground.R | 23 Luminescence-1.2.0/Luminescence/tests/testthat/test_report_RLum.R | 12 Luminescence-1.2.0/Luminescence/tests/testthat/test_subset_RLum.R | 44 Luminescence-1.2.0/Luminescence/tests/testthat/test_subset_SingleGrainData.R | 25 Luminescence-1.2.0/Luminescence/tests/testthat/test_trim_RLum.Data.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_use_DRAC.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_write_R2TIFF.R | 5 Luminescence-1.2.0/Luminescence/tests/testthat/test_write_RLum2CSV.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_zzz.R | 1 427 files changed, 10871 insertions(+), 7497 deletions(-)
Title: Read Hierarchical Fixed Width Files
Description: Read hierarchical fixed width files like those commonly used by
many census data providers. Also allows for reading of data in chunks,
and reading 'gzipped' files without storing the full file in memory.
Author: Greg Freedman Ellis [aut],
Derek Burk [aut, cre],
Joe Grover [ctb],
Mark Padgham [ctb],
Hadley Wickham [ctb] ,
Jim Hester [ctb] ,
Romain Francois [ctb] ,
R Core Team [ctb] ,
RStudio [cph, fnd] ,
Jukka Jylaenki [ctb, cph] ,
Mikkel Joergensen [ctb, cph] [...truncated...]
Maintainer: Derek Burk <ipums+cran@umn.edu>
Diff between hipread versions 0.2.5 dated 2025-06-19 and 0.2.6 dated 2026-03-12
DESCRIPTION | 8 - MD5 | 10 +- NEWS.md | 4 R/col_specs.R | 242 +++++++++++++++++++++++++++++----------------------------- man/hip_rt.Rd | 2 src/iconv.cpp | 2 6 files changed, 136 insertions(+), 132 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Includes implementation for the kidney hierarchical composite endpoint as defined in Heerspink HL et al (2023) “Development and validation of a new hierarchical composite end point for clinical trials of kidney disease progression” (Journal of the American Society of Nephrology 34 (2): 2025–2038, <doi:10.1681/ASN.0000000000000243>). Win odds, also called Wilcoxon-Mann-Whitney or success odds, is the main analysis method. Other win statistics (win probability, win ratio, net benefit) are also implemented in the univariate case, provided there is no censoring. The win probability analysis is based on the Brunner-Munzel test and uses the DeLong-DeLong-Clarke-Pearson variance estimator, as described by Brunner and Konietschke (2025) in “An unbiased rank-based estimator of the Mann–Whitney variance including the case of ties” (Statistical Papers 66 (1): 20, <doi:10.1007/s00362-024-01635-0>). Includes implementation of a new [...truncated...]
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.9.0 dated 2026-01-29 and 0.9.1 dated 2026-03-12
DESCRIPTION | 8 - MD5 | 28 ++-- NEWS.md | 21 +++ R/simKHCE.R | 66 +++++----- R/simTTE.R | 7 - inst/doc/Introduction.html | 2 inst/doc/Wins.Rmd | 6 inst/doc/Wins.html | 18 ++ inst/doc/hce.R | 39 ++++- inst/doc/hce.Rmd | 142 ++++++++++++++++----- inst/doc/hce.html | 297 +++++++++++++++++++++++++++++++-------------- inst/doc/maraca.html | 2 man/simKHCE.Rd | 23 +-- vignettes/Wins.Rmd | 6 vignettes/hce.Rmd | 142 ++++++++++++++++----- 15 files changed, 575 insertions(+), 232 deletions(-)
Title: Fast Agent-Based Epi Models
Description: A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Author: George Vega Yon [aut, cre] ,
Derek Meyer [aut] ,
Andrew Pulsipher [aut] ,
Susan Holmes [rev] ,
Abinash Satapathy [rev] ,
Carinogurjao [rev],
Centers for Disease Control and Prevention [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between epiworldR versions 0.12.0.0 dated 2026-02-21 and 0.13.0.0 dated 2026-03-12
DESCRIPTION | 6 MD5 | 126 +++--- NEWS.md | 13 R/agents-methods.R | 6 build/vignette.rds |binary inst/doc/advanced-modeling.html | 28 - inst/doc/getting-started.html | 60 +- inst/doc/likelihood-free-mcmc.html | 26 - inst/doc/mixing.html | 40 - inst/doc/run-multiple.html | 20 inst/include/epiworld/adjlist-meat.hpp | 8 inst/include/epiworld/agent-bones.hpp | 69 +-- inst/include/epiworld/agent-events-meat.hpp | 32 - inst/include/epiworld/agent-meat-state.hpp | 12 inst/include/epiworld/agent-meat-virus-sampling.hpp | 34 - inst/include/epiworld/agent-meat.hpp | 222 ++++------- inst/include/epiworld/agentssample-bones.hpp | 4 inst/include/epiworld/config.hpp | 9 inst/include/epiworld/entity-bones.hpp | 22 - inst/include/epiworld/entity-distribute-meat.hpp | 10 inst/include/epiworld/entity-meat.hpp | 50 -- inst/include/epiworld/epiworld.hpp | 45 ++ inst/include/epiworld/globalevent-bones.hpp | 4 inst/include/epiworld/globalevent-meat.hpp | 6 inst/include/epiworld/math/lfmcmc/lfmcmc-bones.hpp | 9 inst/include/epiworld/math/lfmcmc/lfmcmc-meat.hpp | 8 inst/include/epiworld/model-bones.hpp | 63 +-- inst/include/epiworld/model-meat-print.hpp | 6 inst/include/epiworld/model-meat.hpp | 171 +++++--- inst/include/epiworld/models/diffnet.hpp | 25 - inst/include/epiworld/models/globalevents.hpp | 8 inst/include/epiworld/models/init-functions.hpp | 30 - inst/include/epiworld/models/measlesmixing.hpp | 137 +++--- inst/include/epiworld/models/measlesmixingriskquarantine.hpp | 115 ++--- inst/include/epiworld/models/measlesschool.hpp | 107 ++--- inst/include/epiworld/models/seir.hpp | 24 - inst/include/epiworld/models/seirconnected.hpp | 51 +- inst/include/epiworld/models/seird.hpp | 28 - inst/include/epiworld/models/seirdconnected.hpp | 56 +- inst/include/epiworld/models/seirmixing.hpp | 64 +-- inst/include/epiworld/models/seirmixingquarantine.hpp | 122 ++---- inst/include/epiworld/models/sir.hpp | 10 inst/include/epiworld/models/sirconnected.hpp | 46 +- inst/include/epiworld/models/sird.hpp | 10 inst/include/epiworld/models/sirdconnected.hpp | 52 +- inst/include/epiworld/models/sirlogit.hpp | 42 -- inst/include/epiworld/models/sirmixing.hpp | 50 +- inst/include/epiworld/models/sis.hpp | 10 inst/include/epiworld/models/sisd.hpp | 10 inst/include/epiworld/models/surveillance.hpp | 59 +- inst/include/epiworld/randgraph.hpp | 16 inst/include/epiworld/random_graph.hpp | 12 inst/include/epiworld/rng-utils.hpp |only inst/include/epiworld/tool-bones.hpp | 41 +- inst/include/epiworld/tool-distribute-meat.hpp | 9 inst/include/epiworld/tool-meat.hpp | 10 inst/include/epiworld/tools |only inst/include/epiworld/virus-bones.hpp | 2 inst/include/epiworld/virus-distribute-meat.hpp | 9 inst/include/epiworld/virus-meat.hpp | 14 inst/tinytest/test-lfmcmc.R | 21 - inst/tinytest/test-sird.R | 7 src/agents.cpp | 14 src/entities.cpp | 6 src/lfmcmc.cpp | 2 65 files changed, 1177 insertions(+), 1151 deletions(-)
Title: Linear Programming Discriminant Analysis
Description: Classification method obtained through linear programming.
It is advantageous with respect to the classical developments when the distribution of the variables
involved is unknown or when the number of variables is much greater than the number of individuals.
Mathematical details behind the method are published in Nueda, et al. (2022) "LPDA: A new classification method based on linear programming".
<doi:10.1371/journal.pone.0270403>.
Author: Maria Jose Nueda [aut, cre]
Maintainer: Maria Jose Nueda <mj.nueda@ua.es>
Diff between lpda versions 1.2.2 dated 2025-10-27 and 1.2.3 dated 2026-03-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/lpda.R | 2 +- build/vignette.rds |binary inst/doc/lpdaUsersGuide.html | 24 ++++++++++++------------ 6 files changed, 25 insertions(+), 21 deletions(-)
Title: Time-Varying Coefficient for Single and Multi-Equation
Regressions
Description: Fitting time-varying coefficient models for single and multi-equation regressions, using kernel smoothing techniques.
Author: Isabel Casas [aut, cre],
Ruben Fernandez-Casal [aut]
Maintainer: Isabel Casas <casasis@gmail.com>
Diff between tvReg versions 0.5.9 dated 2023-09-01 and 0.5.10 dated 2026-03-12
tvReg-0.5.10/tvReg/DESCRIPTION | 10 tvReg-0.5.10/tvReg/MD5 | 67 - tvReg-0.5.10/tvReg/NEWS.md | 208 ++-- tvReg-0.5.10/tvReg/R/bw.R | 178 +-- tvReg-0.5.10/tvReg/R/forecast_tvreg.R |only tvReg-0.5.10/tvReg/R/plot_tvReg.R | 6 tvReg-0.5.10/tvReg/R/tvBOOT.R | 329 +++--- tvReg-0.5.10/tvReg/R/tvIRF.R | 29 tvReg-0.5.10/tvReg/R/tvLM.R | 274 ++--- tvReg-0.5.10/tvReg/R/tvPsi.R | 25 tvReg-0.5.10/tvReg/R/tvReg-package.R | 11 tvReg-0.5.10/tvReg/R/tvSURE.R | 688 +++++++------- tvReg-0.5.10/tvReg/R/tvVAR.R | 286 ++--- tvReg-0.5.10/tvReg/README.md |only tvReg-0.5.10/tvReg/build/vignette.rds |binary tvReg-0.5.10/tvReg/inst/CITATION | 10 tvReg-0.5.10/tvReg/inst/doc/tvReg.R | 34 tvReg-0.5.10/tvReg/inst/doc/tvReg.Rmd | 19 tvReg-0.5.10/tvReg/inst/doc/tvReg.html | 1432 +++++++++++++++++++++--------- tvReg-0.5.10/tvReg/man/CEES.Rd | 1 tvReg-0.5.10/tvReg/man/FF5F.Rd | 1 tvReg-0.5.10/tvReg/man/OECD.Rd | 1 tvReg-0.5.10/tvReg/man/RV.Rd | 1 tvReg-0.5.10/tvReg/man/bw.Rd | 23 tvReg-0.5.10/tvReg/man/bwCov.Rd | 7 tvReg-0.5.10/tvReg/man/forecast-tvReg.Rd | 2 tvReg-0.5.10/tvReg/man/tvCor.Rd | 2 tvReg-0.5.10/tvReg/man/tvCov.Rd | 4 tvReg-0.5.10/tvReg/man/tvIRF.Rd | 16 tvReg-0.5.10/tvReg/man/tvPsi.Rd | 12 tvReg-0.5.10/tvReg/man/tvReg-internals.Rd | 3 tvReg-0.5.10/tvReg/man/tvReg-package.Rd | 7 tvReg-0.5.10/tvReg/man/tvSURE.Rd | 8 tvReg-0.5.10/tvReg/man/tvVAR.Rd | 6 tvReg-0.5.10/tvReg/vignettes/tvReg.Rmd | 19 tvReg-0.5.9/tvReg/R/forecast_tvReg.R |only 36 files changed, 2180 insertions(+), 1539 deletions(-)
Title: Optimum Sample Allocation in Stratified Sampling
Description: Provides exact analytical algorithms for computing optimum sample
allocations in stratified sampling.
Supports classical Neyman-Tschuprow allocation, minimum-cost allocation under
a variance constraint, and multi-domain allocation with controlled precision.
Handles lower and upper bounds, cost constraints, and multiple domains.
Includes helper functions for variance computation, allocation summaries,
rounding, and example datasets for testing and benchmarking.
Author: Wojciech Wojciak [aut, cre],
Jacek Wesolowski [sad],
Robert Wieczorkowski [ctb]
Maintainer: Wojciech Wojciak <wojciech.wojciak@gmail.com>
Diff between stratallo versions 3.0.0 dated 2026-03-12 and 3.0.1 dated 2026-03-12
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------ build/partial.rdb |binary inst/doc/stratallo.html | 4 +-- tests/testthat/test-alg_dca.R | 50 +++++++++++++++++++-------------------- tests/testthat/test-alg_rdca.R | 26 +++++++++----------- tests/testthat/test-alg_rna.R | 6 ++-- tests/testthat/test-alg_rnabox.R | 4 +-- tests/testthat/test-dopt.R | 5 +-- 9 files changed, 57 insertions(+), 60 deletions(-)
Title: Progression Models for Repeated Measures
Description: A progression model for repeated measures (PMRM)
is a continuous-time nonlinear mixed-effects model for
longitudinal clinical trials in progressive diseases.
Unlike mixed models for repeated measures (MMRMs),
which estimate treatment effects as linear combinations
of additive effects on the outcome scale,
PMRMs characterize treatment effects
in terms of the underlying disease trajectory.
This framing yields clinically interpretable quantities
such as average time saved
and percent reduction in decline due to treatment.
This package implements frequentist PMRMs by
Raket (2022) <doi:10.1002/sim.9581> using
'RTMB' by Kristensen (2016) <doi:10.18637/jss.v070.i05>.
Author: William Michael Landau [aut, cre] ,
Lars Lau Raket [aut] ,
Kasper Kristensen [aut] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between pmrm versions 0.0.2 dated 2026-01-30 and 0.0.3 dated 2026-03-12
DESCRIPTION | 6 +- MD5 | 36 +++++++------- NEWS.md | 6 ++ R/pmrm_data.R | 46 +++++++++++++----- R/predict.R | 75 +++++++++++++++++++++++------- README.md | 5 +- inst/CITATION | 1 inst/doc/models.html | 17 ++---- inst/doc/usage.html | 27 +++++----- inst/doc/validation.html | 5 +- man/pmrm_data.Rd | 20 +++++++- man/pmrm_model.Rd | 5 +- man/pmrm_model_decline_nonproportional.Rd | 5 +- man/pmrm_model_decline_proportional.Rd | 5 +- man/pmrm_model_slowing_nonproportional.Rd | 5 +- man/pmrm_model_slowing_proportional.Rd | 5 +- tests/testthat/test-predict.R | 2 vignettes/validation/coverage.png |binary vignettes/validation/version.csv | 2 19 files changed, 189 insertions(+), 84 deletions(-)
Title: Signal Component Analysis for Optically Stimulated Luminescence
Description: Function library for the identification and separation of exponentially
decaying signal components in continuous-wave optically stimulated luminescence measurements.
A special emphasis is laid on luminescence dating with quartz, which is known for
systematic errors due to signal components with unequal physical behaviour.
Also, this package enables an easy to use signal decomposition of
data sets imported and analysed with the R package 'Luminescence'.
This includes the optional automatic creation of HTML reports. Further information and tutorials
can be found at <https://luminescence.de>.
Author: Dirk Mittelstrass [aut, cre] ,
Sebastian Kreutzer [aut] ,
Christoph Schmidt [aut] ,
Marco Colombo [aut] ,
Jan Beyer [ths] ,
Johannes Heitmann [ths],
Arno Straessner [ths]
Maintainer: Dirk Mittelstrass <dirk.mittelstrass@luminescence.de>
Diff between OSLdecomposition versions 1.1.0 dated 2025-08-31 and 1.2 dated 2026-03-12
DESCRIPTION | 17 - MD5 | 66 +++--- NAMESPACE | 1 NEWS.md | 76 +++++++ R/OSLdecomposition-package.R | 3 R/RLum.OSL_correction.R | 206 +++++++++++++------ R/RLum.OSL_decomposition.R | 174 +++++++++++----- R/RLum.OSL_global_fitting.R | 80 ++++--- R/check_RLum.Data.R |only R/decompose_OSLcurve.R | 5 R/fit_OSLcurve.R | 93 ++++----- R/optimise_OSLintervals.R | 5 R/plot_MultiExponential.R | 8 R/plot_OSLcurve.R | 10 R/plot_PhotoCrosssections.R | 5 R/simulate_OSLcomponents.R | 5 R/sum_OSLcurves.R | 372 +++++++++++++++++++++--------------- README.md | 6 inst/examples/example_CW.OSL.Data.R | 6 inst/examples/example_FB.R | 10 inst/rmd/report_Step2.Rmd | 37 ++- man/OSLdecomposition-package.Rd | 4 man/RLum.OSL_correction.Rd | 46 ++-- man/RLum.OSL_decomposition.Rd | 23 +- man/RLum.OSL_global_fitting.Rd | 19 + man/check_RLum.Data.Rd |only man/decompose_OSLcurve.Rd | 5 man/fit_OSLcurve.Rd | 13 - man/optimise_OSLintervals.Rd | 5 man/plot_MultiExponential.Rd | 312 ++++++++++++++---------------- man/plot_OSLcurve.Rd | 7 man/plot_PhotoCrosssections.Rd | 5 man/simulate_OSLcomponents.Rd | 5 man/sum_OSLcurves.Rd | 50 ++-- tests |only 35 files changed, 988 insertions(+), 691 deletions(-)
More information about OSLdecomposition at CRAN
Permanent link
Title: An R Package of Minorization-Maximization Algorithm via the
Assembly--Decomposition Technology
Description: The minorization-maximization (MM) algorithm is a powerful tool for maximizing nonconcave target function. However, for most existing MM algorithms, the surrogate function in the minorization step is constructed in a case-specific manner and requires manual programming. To address this limitation, we develop the R package MMAD, which systematically integrates the assembly--decomposition technology in the MM framework. This new package provides a comprehensive computational toolkit for one-stop inference of complex target functions, including function construction, evaluation, minorization and optimization via MM algorithm. By representing the target function through a hierarchical composition of assembly functions, we design a hierarchical algorithmic structure that supports both bottom-up operations (construction, evaluation) and top-down operation (minorization).
Author: Xifen Huang [aut],
Jinfeng Xu [aut],
Jiaqi Gu [aut, cre]
Maintainer: Jiaqi Gu <jiaqigu@usf.edu>
Diff between MMAD versions 2.0 dated 2025-11-26 and 2.0.1 dated 2026-03-12
DESCRIPTION | 12 +++++++----- MD5 | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.4.4 dated 2026-02-26 and 0.4.5 dated 2026-03-12
DESCRIPTION | 6 +-- MD5 | 64 ++++++++++++++++++---------------- NEWS.md | 14 +++++++ R/cms_download_native.R | 6 +-- R/cms_download_subset.r | 72 +++++++++++++++++++++++++-------------- R/cms_product_details.r | 70 +++++++++++++++++++------------------ R/cms_product_metadata.r | 63 +++++++++++++++++----------------- R/cms_product_services.r | 1 R/cms_products_list.r | 3 + R/generics.r | 9 ++-- R/init.R | 10 ++--- README.md | 5 ++ build/vignette.rds |binary inst/doc/product-info.R |only inst/doc/product-info.Rmd |only inst/doc/product-info.html |only inst/doc/proxy.R | 13 +++++-- inst/doc/proxy.Rmd | 18 +++++++-- inst/doc/proxy.html | 68 +++++++++++++++++------------------- inst/doc/translate.R | 2 - inst/doc/translate.Rmd | 2 - inst/doc/translate.html | 6 ++- man/cms_download_subset.Rd | 16 +++----- man/cms_product_details.Rd | 3 + man/cms_product_metadata.Rd | 3 + man/cms_product_services.Rd | 3 + man/cms_products_list.Rd | 5 ++ man/cms_wmts.Rd | 2 - man/cms_zarr_proxy.Rd | 2 - man/figures/README-leaflet-1.png |binary tests/testthat/test_native.r | 13 +++++++ tests/testthat/test_subset.r | 33 +++++++++++++++++ vignettes/product-info.Rmd |only vignettes/proxy.Rmd | 18 +++++++-- vignettes/translate.Rmd | 2 - 35 files changed, 331 insertions(+), 201 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Estimation Statistics with Confidence Intervals
Description: A collection of functions and 'jamovi' module for the estimation approach to inferential statistics, the approach which emphasizes effect sizes, interval estimates, and meta-analysis. Nearly all functions are based on 'statpsych' and 'metafor'. This package is still under active development, and breaking changes are likely, especially with the plot and hypothesis test functions. Data sets are included for all examples from Cumming & Calin-Jageman (2024) <ISBN:9780367531508>.
Author: Robert Calin-Jageman [aut, cre, cph]
Maintainer: Robert Calin-Jageman <rcalinjageman@dom.edu>
Diff between esci versions 1.0.9 dated 2026-01-16 and 1.0.10 dated 2026-03-12
DESCRIPTION | 6 +-- MD5 | 72 ++++++++++++++++++++++---------------------- NEWS.md | 9 ++++- R/jamovi_meta_functions.R | 4 +- R/jamovimetamdiff.b.R | 1 R/jamovimetamdiff.h.R | 15 +++++++++ R/jamovimetamean.b.R | 1 R/jamovimetamean.h.R | 15 +++++++++ R/jamovimetapdiff.b.R | 1 R/jamovimetapdiff.h.R | 15 +++++++++ R/jamovimetaproportion.b.R | 1 R/jamovimetaproportion.h.R | 15 +++++++++ R/jamovimetar.b.R | 2 - R/jamovimetar.h.R | 15 +++++++++ R/meta_any.R | 12 +++++-- R/meta_d1.R | 6 +++ R/meta_d2.R | 5 +++ R/meta_mdiff_two.R | 5 +++ R/meta_mean.R | 5 +++ R/meta_pdiff_two.R | 5 +++ R/meta_proportion.R | 5 +++ R/meta_r.R | 5 +++ build/stage23.rdb |binary man/geom_meta_diamond_h.Rd | 8 +++- man/jamovimetamdiff.Rd | 3 + man/jamovimetamean.Rd | 3 + man/jamovimetapdiff.Rd | 3 + man/jamovimetaproportion.Rd | 3 + man/jamovimetar.Rd | 3 + man/meta_any.Rd | 4 ++ man/meta_d1.Rd | 4 ++ man/meta_d2.Rd | 4 ++ man/meta_mdiff_two.Rd | 4 ++ man/meta_mean.Rd | 4 ++ man/meta_pdiff_two.Rd | 4 ++ man/meta_proportion.Rd | 4 ++ man/meta_r.Rd | 4 ++ 37 files changed, 225 insertions(+), 50 deletions(-)
Title: A Graphical User Interface for the 'yuima' Package
Description: Provides a graphical user interface for the 'yuima' package.
Author: YUIMA Project Team [aut],
Emanuele Guidotti [cre]
Maintainer: Emanuele Guidotti <emanuele.guidotti@usi.ch>
Diff between yuimaGUI versions 1.3.1 dated 2022-08-11 and 1.4.0 dated 2026-03-12
yuimaGUI-1.3.1/yuimaGUI/inst/yuimaGUI/ui/load_data/yourData.R |only yuimaGUI-1.4.0/yuimaGUI/DESCRIPTION | 19 yuimaGUI-1.4.0/yuimaGUI/MD5 | 55 yuimaGUI-1.4.0/yuimaGUI/R/sourceCodeYuimaGUI.R | 2 yuimaGUI-1.4.0/yuimaGUI/README.md |only yuimaGUI-1.4.0/yuimaGUI/inst/CITATION | 110 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/global.R | 170 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/rsconnect |only yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/eda/changepoint_non_parametric.R | 315 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/eda/changepoint_parametric.R | 1065 +-- yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/eda/clustering.R | 448 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/eda/llag_and_corr.R | 522 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/finance/profit_and_loss.R | 550 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/functions.R | 3436 +++++----- yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/load_data/finance.R | 184 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/load_data/your_file.R | 274 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/modeling/multivariate_results.R | 663 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/modeling/multivariate_start_estimation.R | 1162 +-- yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/modeling/univariate_results.R | 650 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/modeling/univariate_start_estimation.R | 1205 +-- yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/multivariate_estimated.R | 676 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/multivariate_non_estimated.R | 334 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/multivariate_results.R | 494 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/univariate_estimated.R | 652 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/univariate_non_estimated.R | 318 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/univariate_results.R | 310 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/ui.R | 138 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/ui/eda/changepoint.R | 422 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/ui/load_data/finData.R | 94 yuimaGUI-1.4.0/yuimaGUI/man/yuimaGUI.Rd | 2 30 files changed, 7220 insertions(+), 7050 deletions(-)
Title: Sparse Learning with Convex and Concave Penalties
Description: Fast tools for fitting sparse generalized linear models with convex
penalties (lasso) and concave penalties (smoothly clipped absolute
deviation and minimax concave penalty). Computation uses multi-stage convex
relaxation and pathwise coordinate optimization with warm starts,
active-set updates, and screening rules. Core solvers are implemented in
C++, and coefficient paths are stored as sparse matrices for memory
efficiency.
Author: Jason Ge [aut],
Xingguo Li [aut],
Haoming Jiang [aut],
Mengdi Wang [aut],
Tong Zhang [aut],
Han Liu [aut],
Tuo Zhao [aut, cre],
Gael Guennebaud [ctb] ,
Benoit Jacob [ctb] ,
Eigen Library Authors [cph]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between picasso versions 1.4.1 dated 2026-03-10 and 1.5 dated 2026-03-12
picasso-1.4.1/picasso/src/src |only picasso-1.5/picasso/DESCRIPTION | 6 picasso-1.5/picasso/MD5 | 56 - picasso-1.5/picasso/R/gaussian_solver.R | 30 - picasso-1.5/picasso/R/logit_solver.R | 52 - picasso-1.5/picasso/R/picasso.R | 36 - picasso-1.5/picasso/R/picasso.gaussian.R | 84 +- picasso-1.5/picasso/R/picasso.logit.R | 27 picasso-1.5/picasso/R/picasso.poisson.R | 30 - picasso-1.5/picasso/R/picasso.sqrtlasso.R | 28 picasso-1.5/picasso/R/picasso_utils.R | 19 picasso-1.5/picasso/R/poisson_solver.R | 49 - picasso-1.5/picasso/R/sqrtlasso_solver.R | 49 - picasso-1.5/picasso/inst/doc/vignette.pdf |binary picasso-1.5/picasso/man/picasso.Rd | 26 picasso-1.5/picasso/src/c_api |only picasso-1.5/picasso/src/include/picasso/actgd.hpp | 3 picasso-1.5/picasso/src/include/picasso/actnewton.hpp | 3 picasso-1.5/picasso/src/include/picasso/c_api.hpp | 10 picasso-1.5/picasso/src/include/picasso/objective.hpp | 52 + picasso-1.5/picasso/src/include/picasso/solver_params.hpp | 14 picasso-1.5/picasso/src/objective |only picasso-1.5/picasso/src/picasso-all0.cpp | 15 picasso-1.5/picasso/src/picasso_R.cpp | 411 ++++++++------ picasso-1.5/picasso/src/solver |only 25 files changed, 586 insertions(+), 414 deletions(-)
Title: Forecast Reconciliation
Description: Classical (bottom-up and top-down), optimal combination and heuristic
point (Di Fonzo and Girolimetto, 2023 <doi:10.1016/j.ijforecast.2021.08.004>) and
probabilistic (Girolimetto et al. 2024 <doi:10.1016/j.ijforecast.2023.10.003>)
forecast reconciliation procedures for linearly constrained time series
(e.g., hierarchical or grouped time series) in cross-sectional, temporal,
or cross-temporal frameworks.
Author: Daniele Girolimetto [aut, cre] ,
Tommaso Di Fonzo [aut] ,
Yangzhuoran Fin Yang [ctb]
Maintainer: Daniele Girolimetto <daniele.girolimetto@unipd.it>
Diff between FoReco versions 1.1.0 dated 2025-06-07 and 1.2.0 dated 2026-03-12
DESCRIPTION | 30 MD5 | 160 ++--- NAMESPACE | 19 NEWS.md | 163 +++-- R/FoReco-package.R | 2 R/boot.R | 179 +++-- R/bottomup.R | 225 ++++--- R/cov_cs.R | 193 ++++-- R/cov_ct.R | 813 +++++++++++++++++++-------- R/cov_te.R | 394 +++++++++---- R/data.R | 66 +- R/foreco_info.R |only R/fun.R | 22 R/fun_export.R | 747 +++++++++++++----------- R/fun_residuals.R | 71 +- R/matrix_layout.R |only R/middleout.R | 281 ++++++--- R/reco_fun.R | 1264 +++++++++++++++++++++++++++--------------- R/reco_gauss.R |only R/reco_heu.R | 617 ++++++++++++-------- R/reco_lcc.R | 559 ++++++++++++------ R/reco_opt.R | 995 ++++++++++++++++++++------------- R/reco_sample.R |only R/topdown.R | 194 ++++-- README.md | 20 build/partial.rdb |binary inst/CITATION | 84 +- man/FoReco-package.Rd | 10 man/FoReco2matrix.Rd | 33 - man/aggts.Rd | 24 man/balance_hierarchy.Rd | 39 - man/commat.Rd | 4 man/csboot.Rd | 12 man/csbu.Rd | 44 - man/cscov.Rd | 80 +- man/cslcc.Rd | 158 +++-- man/csmo.Rd | 21 man/csmvn.Rd |only man/csprojmat.Rd | 41 - man/csrec.Rd | 233 ++++--- man/cssmp.Rd |only man/cstd.Rd | 15 man/cstools.Rd | 24 man/ctboot.Rd | 21 man/ctbu.Rd | 65 +- man/ctcov.Rd | 116 ++- man/ctlcc.Rd | 193 +++--- man/ctmatrix_layouts.Rd |only man/ctmo.Rd | 41 - man/ctmvn.Rd |only man/ctprojmat.Rd | 58 + man/ctrec.Rd | 263 +++++--- man/ctsmp.Rd |only man/cttd.Rd | 29 man/cttools.Rd | 42 - man/df2aggmat.Rd | 27 man/figures/logo.svg | 455 +++------------ man/heuristic-reco.Rd | 29 man/itagdp.Rd | 30 man/iterec.Rd | 29 man/lcmat.Rd | 4 man/new_foreco_info.Rd |only man/recoinfo.Rd | 25 man/residuals.Rd | 46 - man/roxygen/meta.R | 1 man/set_bounds.Rd | 30 man/shrink_estim.Rd | 18 man/shrink_oasd.Rd | 24 man/teboot.Rd | 16 man/tebu.Rd | 56 + man/tecov.Rd | 82 +- man/telcc.Rd | 175 +++-- man/tematrix_layouts.Rd |only man/temo.Rd | 27 man/temvn.Rd |only man/teprojmat.Rd | 37 - man/terec.Rd | 198 ++++-- man/tesmp.Rd |only man/tetd.Rd | 21 man/tetools.Rd | 20 man/unbalance_hierarchy.Rd | 31 - man/vndata.Rd | 36 - tests/testthat/test-cs.R | 476 ++++++++++++--- tests/testthat/test-csprob.R |only tests/testthat/test-ct.R | 605 +++++++++++++++----- tests/testthat/test-fun_exp.R | 2 tests/testthat/test-fun_res.R | 22 tests/testthat/test-te.R | 309 ++++++++-- 88 files changed, 7283 insertions(+), 4212 deletions(-)
Title: Wrapper for the Computational Morphometry Toolkit ('CMTK')
Library
Description: Provides R bindings for selected components of the
Computational Morphometry Toolkit ('CMTK') for image registration and
point transformation. A subset of the 'C++' source code required for point
transforms is bundled with 'cmtkr'. This allows direct calls into the 'CMTK'
library, avoiding command-line invocations and providing
order-of-magnitude speed improvements. Additional 'CMTK' functionality may
be wrapped in future releases. 'CMTK' is described in Rohlfing T and
Maurer CR (2003) <doi:10.1109/titb.2003.808506>.
Author: Gregory Jefferis [aut, cre] ,
Torsten Rohlfing [aut] ),
SRI International [cph] ,
Google, Inc. [cph]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between cmtkr versions 0.2.2 dated 2026-03-08 and 0.2.3 dated 2026-03-12
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NEWS.md | 7 ++++ README.md | 34 ------------------------ src/Makevars.win | 3 ++ src/cmtk/Base/cmtkImageOperationReplace.h | 3 +- src/cmtk/Base/cmtkMathUtil.h | 3 +- src/cmtk/Base/cmtkSincInterpolator.h | 5 ++- src/cmtk/Base/cmtkTemplateArray.txx | 9 +++--- src/cmtk/Base/cmtkUniformVolumeInterpolator.txx | 6 ++-- 10 files changed, 38 insertions(+), 56 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12'
preprocessed datasets, 'HippUnfold' hippocampal outputs and 'SubCortexMesh'
subcortical outputs for a given sample by restructuring the data values into
a single file. The single file can then be used by the package for analyses
independently from its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.4.5 dated 2025-12-15 and 1.5.0 dated 2026-03-12
VertexWiseR-1.4.5/VertexWiseR/R/zzz.R |only VertexWiseR-1.4.5/VertexWiseR/data/MNImap_hip.rdata |only VertexWiseR-1.4.5/VertexWiseR/inst/extdata/hip_points_cells.pkl |only VertexWiseR-1.4.5/VertexWiseR/man/MNImap_hip.Rd |only VertexWiseR-1.4.5/VertexWiseR/man/figures/sexdiff.png |only VertexWiseR-1.4.5/VertexWiseR/man/figures/sigcluster.png |only VertexWiseR-1.4.5/VertexWiseR/vignettes/SPRENG_tstatmaps.png |only VertexWiseR-1.4.5/VertexWiseR/vignettes/VertexWiseR_plot_overlay.asis |only VertexWiseR-1.4.5/VertexWiseR/vignettes/VertexWiseR_plot_overlay.html |only VertexWiseR-1.5.0/VertexWiseR/DESCRIPTION | 20 VertexWiseR-1.5.0/VertexWiseR/MD5 | 109 - VertexWiseR-1.5.0/VertexWiseR/NAMESPACE | 3 VertexWiseR-1.5.0/VertexWiseR/NEWS.md | 15 VertexWiseR-1.5.0/VertexWiseR/R/ASEGvextract.R |only VertexWiseR-1.5.0/VertexWiseR/R/DTSERIESvextract.R | 6 VertexWiseR-1.5.0/VertexWiseR/R/FSLRvextract.R | 15 VertexWiseR-1.5.0/VertexWiseR/R/HIPvextract.R | 2 VertexWiseR-1.5.0/VertexWiseR/R/RFT_vertex_analysis.R | 16 VertexWiseR-1.5.0/VertexWiseR/R/SURFvextract.R | 2 VertexWiseR-1.5.0/VertexWiseR/R/TFCE_vertex_analysis.R | 33 VertexWiseR-1.5.0/VertexWiseR/R/TFCE_vertex_analysis_mixed.R | 8 VertexWiseR-1.5.0/VertexWiseR/R/VWRfirstrun.R | 14 VertexWiseR-1.5.0/VertexWiseR/R/classes.r | 12 VertexWiseR-1.5.0/VertexWiseR/R/data.R | 15 VertexWiseR-1.5.0/VertexWiseR/R/getting_started.r | 34 VertexWiseR-1.5.0/VertexWiseR/R/other_functions.R | 282 +++ VertexWiseR-1.5.0/VertexWiseR/R/plot_overlay_surf.r | 715 +++++++--- VertexWiseR-1.5.0/VertexWiseR/R/plot_surf.R | 136 + VertexWiseR-1.5.0/VertexWiseR/R/plot_surf3d.R | 644 ++++++--- VertexWiseR-1.5.0/VertexWiseR/R/smooth_surf.R | 13 VertexWiseR-1.5.0/VertexWiseR/README.md | 8 VertexWiseR-1.5.0/VertexWiseR/build/vignette.rds |binary VertexWiseR-1.5.0/VertexWiseR/inst/doc/Python_troubleshooting.html | 135 + VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_Example_1.html | 8 VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_Example_2.html | 37 VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_Example_3.html |only VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_Example_3.html.asis |only VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_plot_overlay.html |only VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_plot_overlay.html.asis |only VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_surface_extraction.html | 271 ++- VertexWiseR-1.5.0/VertexWiseR/inst/extdata/hip_points_cells.rds |only VertexWiseR-1.5.0/VertexWiseR/inst/python/hipp_plot.py | 2 VertexWiseR-1.5.0/VertexWiseR/inst/python/surfplot_subcortical.py |only VertexWiseR-1.5.0/VertexWiseR/man/ASEGvextract.Rd |only VertexWiseR-1.5.0/VertexWiseR/man/DTSERIESvextract.Rd | 6 VertexWiseR-1.5.0/VertexWiseR/man/FSLRvextract.Rd | 12 VertexWiseR-1.5.0/VertexWiseR/man/MNIsurface-class.Rd | 2 VertexWiseR-1.5.0/VertexWiseR/man/ROImap-class.Rd | 2 VertexWiseR-1.5.0/VertexWiseR/man/edgelist-class.Rd | 2 VertexWiseR-1.5.0/VertexWiseR/man/figures/Flowchart.JPG |binary VertexWiseR-1.5.0/VertexWiseR/man/figures/sexdiff.jpg |only VertexWiseR-1.5.0/VertexWiseR/man/figures/sigcluster.jpg |only VertexWiseR-1.5.0/VertexWiseR/man/hip_points_cells.Rd | 4 VertexWiseR-1.5.0/VertexWiseR/man/plot_overlay_surf.Rd | 17 VertexWiseR-1.5.0/VertexWiseR/man/plot_surf.Rd | 11 VertexWiseR-1.5.0/VertexWiseR/man/plot_surf3d.Rd | 17 VertexWiseR-1.5.0/VertexWiseR/vignettes/Python_troubleshooting.Rmd | 55 VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_Example_1.Rmd | 18 VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_Example_2.Rmd | 34 VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_Example_3.Rmd |only VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_Example_3.html.asis |only VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_plot_overlay.Rmd | 125 + VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_plot_overlay.html.asis |only VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_surface_extraction.Rmd | 119 + VertexWiseR-1.5.0/VertexWiseR/vignettes/allaseg_plotsurf3d.jpg |only VertexWiseR-1.5.0/VertexWiseR/vignettes/references.bib | 48 VertexWiseR-1.5.0/VertexWiseR/vignettes/surfextract.jpg |binary 67 files changed, 2216 insertions(+), 811 deletions(-)
Title: Easily Scrape and Process AFL Data
Description: An easy package for scraping and processing Australia Rules Football (AFL)
data. 'fitzRoy' provides a range of functions for accessing publicly available data
from 'AFL Tables' <https://afltables.com/afl/afl_index.html>, 'Footy Wire' <https://www.footywire.com> and
'The Squiggle' <https://squiggle.com.au>. Further functions allow for easy processing,
cleaning and transformation of this data into formats that can be used for analysis.
Author: James Day [cre, aut],
Robert Nguyen [aut],
Matthew Erbs [ctb],
Oscar Lane [aut],
Jason Zivkovic [ctb],
Jacob Holden [ctb]
Maintainer: James Day <jamesthomasday@gmail.com>
Diff between fitzRoy versions 1.6.0 dated 2024-12-10 and 1.7.0 dated 2026-03-12
DESCRIPTION | 6 - MD5 | 69 ++++++++----- NAMESPACE | 10 + R/fetch-outofcontract.R |only R/fetch-player-details.R | 82 +++++++++++----- R/fetch-player-stats.R | 32 ++++-- R/fetch_awards.R |only R/fetch_supercoach_dreamteam.R |only R/fetch_team_stats.R |only R/helpers-afl.R | 97 ++++++++++++++----- R/helpers-afltables-playerstats.R | 6 - R/helpers-afltables.R | 1 R/helpers-footywire.R | 117 +++++++++-------------- R/helpers-general.R | 116 ++++++++++++++++++++++ R/plot-score-worm.R | 12 +- inst/WORDLIST | 11 +- inst/doc/elo-ratings-example.html | 4 inst/doc/main-fetch-functions.Rmd | 1 inst/doc/main-fetch-functions.html | 2 man/fetch_awards.Rd |only man/fetch_awards_allaustralian.Rd |only man/fetch_awards_brownlow.Rd |only man/fetch_fantasy_scores.Rd |only man/fetch_outofcontract.Rd |only man/fetch_outofcontract_footywire.Rd |only man/fetch_player_details.Rd | 17 ++- man/fetch_player_stats.Rd | 9 + man/fetch_rising_star.Rd |only man/fetch_scores.Rd |only man/fetch_supercoach_scores.Rd |only man/fetch_team_stats.Rd |only man/fetch_team_stats_afltables.Rd |only man/fetch_team_stats_footywire.Rd |only man/fetch_team_stats_vflstats.Rd |only man/fitzRoy-package.Rd | 2 man/plot_score_worm.Rd | 2 man/plot_score_worm_totals.Rd | 2 man/team_abr_afl.Rd | 4 tests/testthat/test-fetch-awards.R |only tests/testthat/test-fetch-outofcontract.R |only tests/testthat/test-fetch-player-details.R | 14 ++ tests/testthat/test-fetch-player-stats.R | 8 - tests/testthat/test-fetch_supercoach_dreamteam.R |only tests/testthat/test-fetch_team_stats.R |only tests/testthat/test-team_colour_palettes.R | 14 +- vignettes/main-fetch-functions.Rmd | 1 46 files changed, 454 insertions(+), 185 deletions(-)
Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya [aut, cre]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-21 dated 2026-01-22 and 1.2-22 dated 2026-03-12
scam-1.2-21/scam/R/derivative.smooth.R |only scam-1.2-21/scam/R/uni.smooth.const-with-po.r |only scam-1.2-22/scam/ChangeLog | 8 ++++++++ scam-1.2-22/scam/DESCRIPTION | 8 ++++---- scam-1.2-22/scam/MD5 | 11 +++++------ scam-1.2-22/scam/R/bfgs.r | 7 ++++--- scam-1.2-22/scam/R/uni.smooth.const.r |only scam-1.2-22/scam/build/partial.rdb |binary 8 files changed, 21 insertions(+), 13 deletions(-)
Title: 'Rcpp' Bindings for the Boost Date_Time Library
Description: Access to Boost Date_Time functionality for dates,
durations (both for days and date time objects), time zones, and
posix time ('ptime') is provided by using 'Rcpp modules'. The
posix time implementation can support high-resolution of up to
nano-second precision by using 96 bits (instead of 64 with R)
to present a 'ptime' object (but this needs recompilation with
a #define set).
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppBDT versions 0.2.7 dated 2025-01-25 and 0.2.8 dated 2026-03-12
ChangeLog | 20 ++++++++++++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- README.md | 2 +- inst/NEWS.Rd | 7 +++++++ inst/include/RcppBDTtz.h | 9 ++++----- src/RcppBDTdt.cpp | 15 +++++++-------- src/RcppBDTpt.cpp | 7 +++---- 8 files changed, 56 insertions(+), 31 deletions(-)
Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative
maps. The package is a dependency for mvp-type
packages that use the STL map class: it traps
plausible idiom that is ill-defined (implementation-specific) and
returns an informative error, rather than returning a possibly
incorrect result. To cite the package in publications please use
Hankin (2022) <doi:10.48550/ARXIV.2210.03856>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between disordR versions 0.9-8-5 dated 2025-11-03 and 0.9-8-6 dated 2026-03-12
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- NAMESPACE | 2 - R/disordR.R | 6 ++--- build/vignette.rds |binary inst/doc/disindex.html | 12 +++++----- inst/doc/disordR.html | 57 +++++++++++++++++++++++++++---------------------- 7 files changed, 51 insertions(+), 44 deletions(-)
Title: Log-Linear Modelling of Triad Genotype Data
Description: Triad Log-Linear modelling of Imprinting
Environmental interactions, and Maternal effects (TriLLIEM).
This is an implementation of the log-linear model described in a series of
papers, see for example Ainsworth et al. (2010) <doi:10.1002/gepi.20547>.
Author: Kevin Heda Zhao [aut, cre],
Kelly Burkett [aut]
Maintainer: Kevin Heda Zhao <trilliemmaintainer@gmail.com>
Diff between TriLLIEM versions 0.1.0 dated 2026-03-05 and 0.1.1 dated 2026-03-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/partial.rdb |binary tests/testthat/test-TriLLIEM.R | 4 +++- tests/testthat/test-anova.TriLLIEM.R | 4 +++- tests/testthat/test-fullview.R | 8 +++++--- tests/testthat/test-simulate.R | 10 ++++++---- tests/testthat/test-summary.TriLLIEM.R | 6 ++++-- 8 files changed, 32 insertions(+), 22 deletions(-)
Title: Optimum Sample Allocation in Stratified Sampling
Description: Provides exact analytical algorithms for computing optimum sample
allocations in stratified sampling.
Supports classical Neyman-Tschuprow allocation, minimum-cost allocation under
a variance constraint, and multi-domain allocation with controlled precision.
Handles lower and upper bounds, cost constraints, and multiple domains.
Includes helper functions for variance computation, allocation summaries,
rounding, and example datasets for testing and benchmarking.
Author: Wojciech Wojciak [aut, cre],
Jacek Wesolowski [sad],
Robert Wieczorkowski [ctb]
Maintainer: Wojciech Wojciak <wojciech.wojciak@gmail.com>
Diff between stratallo versions 2.2.1 dated 2023-11-26 and 3.0.0 dated 2026-03-12
stratallo-2.2.1/stratallo/R/algorithms_1sided.R |only stratallo-2.2.1/stratallo/R/algorithms_2sided.R |only stratallo-2.2.1/stratallo/R/algorithms_of_other_authors.R |only stratallo-2.2.1/stratallo/R/helpers.R |only stratallo-2.2.1/stratallo/data/pop10_mM.rda |only stratallo-2.2.1/stratallo/data/pop507.rda |only stratallo-2.2.1/stratallo/data/pop969.rda |only stratallo-2.2.1/stratallo/man/CapacityScaling.Rd |only stratallo-2.2.1/stratallo/man/SimpleGreedy.Rd |only stratallo-2.2.1/stratallo/man/asummary.Rd |only stratallo-2.2.1/stratallo/man/opt_1sided.Rd |only stratallo-2.2.1/stratallo/man/pop10_mM.Rd |only stratallo-2.2.1/stratallo/man/pop507.Rd |only stratallo-2.2.1/stratallo/man/pop969.Rd |only stratallo-2.2.1/stratallo/man/ran_round.Rd |only stratallo-2.2.1/stratallo/man/rna_prior.Rd |only stratallo-2.2.1/stratallo/man/rna_rec.Rd |only stratallo-2.2.1/stratallo/man/round_oric.Rd |only stratallo-2.2.1/stratallo/man/stratallo-package.Rd |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_coma.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_rna.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_rna_rec.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_rnabox.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_sga.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_sgaplus.md |only stratallo-2.2.1/stratallo/tests/testthat/helper-dataobjects.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_coma.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_rna.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_rna_rec.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_rnabox.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_sga.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_sgaplus.R |only stratallo-2.2.1/stratallo/tests/testthat/test-helpers.R |only stratallo-3.0.0/stratallo/DESCRIPTION | 57 stratallo-3.0.0/stratallo/MD5 | 136 + stratallo-3.0.0/stratallo/NAMESPACE | 14 stratallo-3.0.0/stratallo/NEWS.md | 14 stratallo-3.0.0/stratallo/R/alg_dca.R |only stratallo-3.0.0/stratallo/R/alg_other_authors.R |only stratallo-3.0.0/stratallo/R/alg_rdca.R |only stratallo-3.0.0/stratallo/R/alg_rna-sga-coma.R |only stratallo-3.0.0/stratallo/R/alg_rnabox.R |only stratallo-3.0.0/stratallo/R/alloc_summary.R |only stratallo-3.0.0/stratallo/R/check_rdca.R |only stratallo-3.0.0/stratallo/R/data.R | 92 - stratallo-3.0.0/stratallo/R/dopt.R |only stratallo-3.0.0/stratallo/R/helpers_dca_rdca.R |only stratallo-3.0.0/stratallo/R/opt.R | 213 +- stratallo-3.0.0/stratallo/R/rounding.R |only stratallo-3.0.0/stratallo/R/stratallo-package.R | 54 stratallo-3.0.0/stratallo/R/utils.R |only stratallo-3.0.0/stratallo/R/var.R |only stratallo-3.0.0/stratallo/README.md | 239 --- stratallo-3.0.0/stratallo/build/partial.rdb |binary stratallo-3.0.0/stratallo/build/vignette.rds |binary stratallo-3.0.0/stratallo/data/pop10s_bounds_ucost.rda |only stratallo-3.0.0/stratallo/data/pop2d4s.rda |only stratallo-3.0.0/stratallo/data/pop507s_ucost.rda |only stratallo-3.0.0/stratallo/data/pop969s_ucost.rda |only stratallo-3.0.0/stratallo/data/pop9d278s.rda |only stratallo-3.0.0/stratallo/inst/REFERENCES.bib |only stratallo-3.0.0/stratallo/inst/WORDLIST | 66 stratallo-3.0.0/stratallo/inst/doc/stratallo.R | 123 - stratallo-3.0.0/stratallo/inst/doc/stratallo.Rmd | 602 ++++---- stratallo-3.0.0/stratallo/inst/doc/stratallo.html | 744 +++++----- stratallo-3.0.0/stratallo/man/alg_1sided.Rd |only stratallo-3.0.0/stratallo/man/alloc_summary.Rd |only stratallo-3.0.0/stratallo/man/check_rdca.Rd |only stratallo-3.0.0/stratallo/man/data.Rd |only stratallo-3.0.0/stratallo/man/dca.Rd |only stratallo-3.0.0/stratallo/man/dca_M.Rd |only stratallo-3.0.0/stratallo/man/dopt.Rd |only stratallo-3.0.0/stratallo/man/fpia.Rd | 79 - stratallo-3.0.0/stratallo/man/has_mixed_signs.Rd |only stratallo-3.0.0/stratallo/man/helpers_dca_rdca.Rd |only stratallo-3.0.0/stratallo/man/is_equal.Rd |only stratallo-3.0.0/stratallo/man/obj_emptiness.Rd |only stratallo-3.0.0/stratallo/man/opt.Rd | 153 +- stratallo-3.0.0/stratallo/man/optcost.Rd | 90 - stratallo-3.0.0/stratallo/man/rdca.Rd |only stratallo-3.0.0/stratallo/man/rdca_iter.Rd |only stratallo-3.0.0/stratallo/man/rna_experimental.Rd |only stratallo-3.0.0/stratallo/man/rnabox.Rd | 173 +- stratallo-3.0.0/stratallo/man/rounding.Rd |only stratallo-3.0.0/stratallo/man/simplegreedy-capacityscaling.Rd |only stratallo-3.0.0/stratallo/man/stratallo.Rd |only stratallo-3.0.0/stratallo/man/var_st.Rd | 64 stratallo-3.0.0/stratallo/tests/spelling.R | 9 stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_coma.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_dca.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_dca0.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_rdca.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_rna.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_rna_rec.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_rnabox.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_sga.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_sgaplus.md |only stratallo-3.0.0/stratallo/tests/testthat/helper-data.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_coma.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_dca.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_dca0.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_rdca.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_rna.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_rna_rec.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_rnabox.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_sga.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_sgaplus.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alloc_summary.R |only stratallo-3.0.0/stratallo/tests/testthat/test-check_rdca.R |only stratallo-3.0.0/stratallo/tests/testthat/test-dopt.R |only stratallo-3.0.0/stratallo/tests/testthat/test-helpers_dca_rdca.R |only stratallo-3.0.0/stratallo/tests/testthat/test-opt.R | 4 stratallo-3.0.0/stratallo/tests/testthat/test-rounding.R |only stratallo-3.0.0/stratallo/tests/testthat/test-utils.R |only stratallo-3.0.0/stratallo/tests/testthat/test-var.R |only stratallo-3.0.0/stratallo/vignettes/stratallo.Rmd | 602 ++++---- 116 files changed, 1819 insertions(+), 1709 deletions(-)
Title: Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
Description: Algorithms for accelerating the convergence of slow, monotone
sequences from smooth, contraction mappings such as the EM algorithm.
It can be used to accelerate any smooth, linearly convergent scheme.
A tutorial-style introduction is available in vignette("SQUAREM").
See also: Varadhan & Roland (2008) <doi:10.18637/jss.v092.i07>.
Author: Ravi Varadhan [aut, cre]
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between SQUAREM versions 2021.1 dated 2021-01-13 and 2026.1 dated 2026-03-12
DESCRIPTION | 34 ++++++------- MD5 | 6 +- man/fpiter.Rd | 32 ++++++------ man/squarem.Rd | 148 +++++++++++++++++++++++++++++---------------------------- 4 files changed, 113 insertions(+), 107 deletions(-)
Title: Accessing and Validating Marine Environmental Data from 'SHARK'
and Related Databases
Description: Provides functions to retrieve, process, analyze, and
quality-control marine physical, chemical, and biological data. The
main focus is on Swedish monitoring data available through the 'SHARK'
database <https://shark.smhi.se/en/>, with additional API support for 'Nordic
Microalgae' <https://nordicmicroalgae.org/>, 'Dyntaxa'
<https://artfakta.se/>, World Register of Marine Species ('WoRMS') <https://www.marinespecies.org>,
'AlgaeBase' <https://www.algaebase.org>, OBIS 'xylookup' web service
<https://iobis.github.io/xylookup/> and Intergovernmental Oceanographic Commission (IOC) -
UNESCO databases on harmful algae <https://www.marinespecies.org/hab/> and toxins
<https://toxins.hais.ioc-unesco.org/>.
Author: Markus Lindh [aut] ,
Anders Torstensson [aut, cre] ,
Mikael Hedblom [ctb] ,
Bengt Karlson [ctb] ,
SHARK [cph],
SBDI [fnd]
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Diff between SHARK4R versions 1.1.0 dated 2026-03-09 and 1.1.1 dated 2026-03-12
DESCRIPTION | 6 MD5 | 50 ++-- NEWS.md | 9 inst/CITATION | 4 inst/doc/quality_control.R | 171 +++++++++++--- inst/doc/quality_control.Rmd | 139 ++++++++++- inst/doc/quality_control.html | 79 +++--- inst/doc/retrieve_hab_data.R | 50 +++- inst/doc/retrieve_hab_data.Rmd | 36 ++- inst/doc/retrieve_hab_data.html | 8 inst/doc/retrieve_nordic_microalgae_data.R | 156 +++++++++---- inst/doc/retrieve_nordic_microalgae_data.Rmd | 105 ++++++++ inst/doc/retrieve_nordic_microalgae_data.html | 54 ++-- inst/doc/retrieve_shark_data.R | 84 ++++--- inst/doc/retrieve_shark_data.Rmd | 46 +++ inst/doc/retrieve_shark_data.html | 44 +-- inst/doc/retrieve_worms_data.R | 307 ++++++++++++++++++-------- inst/doc/retrieve_worms_data.Rmd | 166 +++++++++++++- inst/doc/retrieve_worms_data.html | 259 +++++++++++---------- tests/testthat/test-worms_api_functions.R | 2 tests/testthat/test-xylookup.R | 1 vignettes/quality_control.Rmd | 139 ++++++++++- vignettes/retrieve_hab_data.Rmd | 36 ++- vignettes/retrieve_nordic_microalgae_data.Rmd | 105 ++++++++ vignettes/retrieve_shark_data.Rmd | 46 +++ vignettes/retrieve_worms_data.Rmd | 166 +++++++++++++- 26 files changed, 1746 insertions(+), 522 deletions(-)
Title: A Two-Step Approach to Testing Overall Effect of
Gene-Environment Interaction for Multiple Phenotypes
Description: Interaction between a genetic variant (e.g., a single nucleotide polymorphism) and an environmental variable (e.g., physical activity) can have a shared effect on multiple phenotypes (e.g., blood lipids). We implement a two-step method to test for an overall interaction effect on multiple phenotypes. In first step, the method tests for an overall marginal genetic association between the genetic variant and the multivariate phenotype. The genetic variants which show an evidence of marginal overall genetic effect in the first step are prioritized while testing for an overall gene-environment interaction effect in the second step. Methodology is available from: A Majumdar, KS Burch, T Haldar, S Sankararaman, B Pasaniuc, WJ Gauderman, JS Witte (2020) <doi:10.1093/bioinformatics/btaa1083>.
Author: Arunabha Majumdar [aut, cre],
Tanushree Haldar [aut]
Maintainer: Arunabha Majumdar <statgen.arunabha@gmail.com>
Diff between MPGE versions 1.0.0 dated 2020-10-23 and 1.0.1 dated 2026-03-12
DESCRIPTION | 18 - MD5 | 50 ++-- NEWS.md | 6 R/MPGE.R | 8 R/data.R | 4 R/mv_G_GE_P.R | 4 R/mv_G_GE_P_base.R | 2 R/sst.R | 4 R/whmt.R | 4 README.md | 50 ++-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/mpge.R | 4 inst/doc/mpge.Rmd | 4 inst/doc/mpge.html | 441 +++++++++++++++++++++--------------------- man/MPGE.Rd | 22 +- man/SST.Rd | 4 man/WHT.Rd | 4 man/genotype_data.Rd | 4 man/mv_G_GE.Rd | 4 man/phenotype_data.Rd | 2 tests/spelling.R |only tests/testthat.R | 8 tests/testthat/test-mv_G_GE.R | 2 tests/testthat/test-sst.R | 2 tests/testthat/test-whmt.R | 2 vignettes/mpge.Rmd | 4 27 files changed, 350 insertions(+), 307 deletions(-)
More information about INCVCommunityDetection at CRAN
Permanent link
Title: Quantifying and Monetizing Health Impacts Attributable to
Exposure
Description: This R package has been developed with a focus on air pollution and noise but can be applied to other exposures. The initial development has been funded by the European Union project BEST-COST. Disclaimer: It is work in progress and the developers are not liable for any calculation errors or inaccuracies resulting from the use of this package.
Selection of relevant references (in chronological order):
WHO (2003) <https://www.who.int/publications/i/item/9241546204>,
Murray et al. (2003) <doi:10.1186/1478-7954-1-1>,
Miller & Hurley (2003) <doi:10.1136/jech.57.3.200>,
Steenland & Armstrong (2006) <doi:10.1097/01.ede.0000229155.05644.43>,
WHO (2011) <https://iris.who.int/items/723ab97c-5c33-4e3b-8df1-744aa5bc1c27>,
GBD 2019 Risk Factors Collaborators (2020) <doi:10.1016/S0140-6736(20)30752-2>.
Author: Alberto Castro [cre, aut] ,
Axel Luyten [aut] ,
Arno Pauwels [ctb] ,
Liliana Vazquez Fernandez [ctb] ,
Gianni Ardielli [ctb] ,
Iracy Pimenta [ctb] ,
Susanne Breitner [ctb] ,
Carl Baravelli [ctb] ,
Vanessa Gorasso [ctb] ,
Maria Lepnurm [ctb] ,
Andreia [...truncated...]
Maintainer: Alberto Castro <alberto.castrofernandez@swisstph.ch>
Diff between healthiar versions 0.2.3 dated 2026-02-19 and 0.2.4 dated 2026-03-12
DESCRIPTION | 8 +-- MD5 | 82 +++++++++++++++---------------- NEWS.md | 20 ++++++- R/attribute_health.R | 2 R/cba.R | 17 ++++-- R/compare.R | 6 +- R/data.R | 7 +- R/discount.R | 27 +++++----- R/get_discount_factor.R | 34 ++---------- R/get_inflation_factor.R | 13 ++++ R/get_paf.R | 2 R/monetize.R | 103 ++++++++++++++++++++++++++------------- R/socialize.R | 2 R/summarize_uncertainty.R | 7 +- R/zzz_global_variables.R | 2 README.md | 2 build/partial.rdb |binary data/exdat_cantons.rda |binary data/exdat_lifetable.rda |binary data/exdat_noise.rda |binary data/exdat_ozone.rda |binary data/exdat_pm.rda |binary data/exdat_socialize.rda |binary inst/CITATION | 3 - inst/REFERENCES.bib | 24 +++++++-- inst/doc/intro_to_healthiar.Rmd | 52 +++++++++++++------ inst/doc/intro_to_healthiar.html | 87 +++++++++++++++++++++----------- man/attribute_health.Rd | 2 man/cba.Rd | 14 ++++- man/compare.Rd | 6 +- man/discount.Rd | 28 +++++----- man/exdat_pm.Rd | 7 +- man/get_discount_factor.Rd | 13 +--- man/get_inflation_factor.Rd | 11 +++- man/get_paf.Rd | 2 man/healthiar-package.Rd | 2 man/monetize.Rd | 26 ++++++++- man/socialize.Rd | 2 man/summarize_uncertainty.Rd | 7 +- tests/testthat/test-cba.R | 36 ++++++++++--- tests/testthat/test-monetize.R | 101 +++++++++++++++++++++++++++++++++----- vignettes/intro_to_healthiar.Rmd | 52 +++++++++++++------ 42 files changed, 540 insertions(+), 269 deletions(-)
Title: Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Description: Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
su [...truncated...]
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Diana Robledo-Ruiz [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Emily Stringer [ctb],
Floriaan Devloo-Delva [ctb],
Eric Archer [c [...truncated...]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.base versions 1.0.7 dated 2025-10-01 and 1.2.2 dated 2026-03-12
DESCRIPTION | 25 MD5 | 613 ++++++++-------- NAMESPACE | 39 - R/gi2gl.R | 1 R/gl.He.r | 4 R/gl.Ho.r | 4 R/gl.add.indmetrics.r | 4 R/gl.alf.r | 6 R/gl.allele.freq.r | 2 R/gl.amova.r | 6 R/gl.define.pop.r | 1 R/gl.diagnostics.hwe.r | 45 - R/gl.dist.ind.r | 548 +++++++------- R/gl.dist.phylo.r | 317 +++++--- R/gl.dist.pop.r | 1 R/gl.document.R |only R/gl.drop.ind.r | 1 R/gl.drop.loc.r | 5 R/gl.drop.pop.r | 17 R/gl.drop.sexlinked.r |only R/gl.edit.recode.ind.r | 1 R/gl.edit.recode.pop.r | 1 R/gl.fbm2gen.r |only R/gl.fdsim.r | 1 R/gl.filter.allna.r | 1 R/gl.filter.callrate.r | 21 R/gl.filter.excess.het.r | 1 R/gl.filter.factorloadings.r | 1 R/gl.filter.hamming.r | 498 ++++++------- R/gl.filter.heterozygosity.r | 1 R/gl.filter.hwe.r | 1 R/gl.filter.ld.r | 30 R/gl.filter.locmetric.r | 1 R/gl.filter.maf.r | 25 R/gl.filter.monomorphs.r | 1 R/gl.filter.overshoot.r | 62 - R/gl.filter.pa.r | 1 R/gl.filter.rdepth.r | 9 R/gl.filter.replicates.r |only R/gl.filter.reproducibility.r | 5 R/gl.filter.secondaries.r | 5 R/gl.filter.sexlinked.r |only R/gl.filter.taglength.r | 1 R/gl.fixed.diff.r | 1 R/gl.fst.pop.r | 6 R/gl.gen2fbm.r |only R/gl.hwe.pop.r | 1 R/gl.impute.r | 262 +++++-- R/gl.join.r | 837 +++++++++++----------- R/gl.keep.ind.r | 1 R/gl.keep.loc.r | 1 R/gl.keep.pop.r | 34 R/gl.load.r | 10 R/gl.make.recode.ind.r | 1 R/gl.make.recode.pop.r | 1 R/gl.map.interactive.r | 41 - R/gl.merge.pop.r | 1 R/gl.pcoa.plot.r | 3 R/gl.pcoa.r | 40 - R/gl.plot.heatmap.r | 302 ++++++-- R/gl.plot.snp.density.r |only R/gl.print.history.r | 1 R/gl.propShared.r | 5 R/gl.random.snp.r | 1 R/gl.randomize.snps.r | 1 R/gl.read.PLINK.r | 524 +++++++------- R/gl.read.csv.r | 54 - R/gl.read.dart.r | 22 R/gl.read.fasta.r | 33 R/gl.read.silicodart.r | 25 R/gl.read.vcf.r | 21 R/gl.reassign.ind.r |only R/gl.reassign.pop.r | 3 R/gl.recalc.metrics.r | 1 R/gl.recode.ind.r | 1 R/gl.recode.pop.r | 3 R/gl.rename.pop.r | 1 R/gl.report.allelerich.r | 740 +++++++++++++++---- R/gl.report.allna.r | 1 R/gl.report.bases.r | 1 R/gl.report.basics.r | 1 R/gl.report.callrate.r | 1 R/gl.report.diversity.r | 6 R/gl.report.excess.het.r | 1 R/gl.report.factorloadings.r | 1 R/gl.report.fstat.r | 9 R/gl.report.hamming.r | 7 R/gl.report.heterozygosity.r | 30 R/gl.report.hwe.r | 22 R/gl.report.ld.map.r | 1 R/gl.report.locmetric.r | 1 R/gl.report.maf.r | 1 R/gl.report.monomorphs.r | 3 R/gl.report.overshoot.r | 17 R/gl.report.pa.r | 1 R/gl.report.polyploid_heterozygosity.r | 6 R/gl.report.rdepth.r | 1 R/gl.report.replicates.r | 369 +++++---- R/gl.report.reproducibility.r | 3 R/gl.report.secondaries.r | 1 R/gl.report.sexlinked.r |only R/gl.report.shannon.r | 3 R/gl.report.taglength.r | 1 R/gl.sample.r | 1 R/gl.save.r | 7 R/gl.select.colors.r | 7 R/gl.select.shapes.r | 1 R/gl.smearplot.r | 85 ++ R/gl.sort.r | 56 + R/gl.subsample.ind.r | 8 R/gl.subsample.loc.r | 1 R/gl.subsample.loci.r | 1 R/gl.test.heterozygosity.r | 25 R/gl.tree.fitch.r | 1 R/gl.tree.nj.r | 3 R/gl.write.csv.r | 1 R/gl2bayesAss.R | 1 R/gl2bayescan.r | 1 R/gl2bpp.r | 5 R/gl2demerelate.r | 1 R/gl2eigenstrat.r | 1 R/gl2fasta.r | 17 R/gl2gapit.r | 5 R/gl2gds.r | 1 R/gl2genalex.r | 1 R/gl2genepop.r | 7 R/gl2gi.r | 3 R/gl2hapmap.r | 257 +++++- R/gl2hiphop.r | 1 R/gl2paup.parsimony.r | 1 R/gl2paup.svdquartets.r | 1 R/gl2phylip.r | 1 R/gl2plink.r | 18 R/gl2related.r | 3 R/gl2sa.r | 150 +--- R/gl2snapper.r | 7 R/gl2structure.r | 1 R/gl2treemix.r | 1 R/gl2vcf.r | 334 ++++---- R/theme_dartR.r | 6 R/utils.allelic.richness.r |only R/utils.basic.stats.r | 1 R/utils.check.datatype.R | 1 R/utils.collapse.matrix.r | 1 R/utils.dart2genlight.r | 32 R/utils.dartR.class.def.r | 1120 ++++++++++++++++++++++++------ R/utils.dist.binary.r | 178 +++- R/utils.dist.ind.snp.r | 322 ++++++-- R/utils.heatmap.r |only R/utils.het.report.r | 2 R/utils.plink.run.r | 2 R/utils.recalc.callrate.r | 2 R/utils.recalc.maf.r | 3 R/utils.stats.r | 2 R/zzz.r | 13 man/cbind.dartR.Rd | 18 man/gl.He.Rd | 45 - man/gl.Ho.Rd | 45 - man/gl.add.indmetrics.Rd | 4 man/gl.alf.Rd | 6 man/gl.allele.freq.Rd | 3 man/gl.amova.Rd | 1 man/gl.define.pop.Rd | 2 man/gl.diagnostics.hwe.Rd | 13 man/gl.dist.ind.Rd | 20 man/gl.dist.phylo.Rd | 163 ++-- man/gl.dist.pop.Rd | 1 man/gl.document.Rd |only man/gl.drop.ind.Rd | 2 man/gl.drop.loc.Rd | 2 man/gl.drop.pop.Rd | 2 man/gl.drop.sexlinked.Rd |only man/gl.edit.recode.ind.Rd | 1 man/gl.edit.recode.pop.Rd | 2 man/gl.fbm2gen.Rd |only man/gl.fdsim.Rd | 1 man/gl.filter.allna.Rd | 1 man/gl.filter.callrate.Rd | 10 man/gl.filter.excess.het.Rd | 1 man/gl.filter.factorloadings.Rd | 1 man/gl.filter.hamming.Rd | 110 +- man/gl.filter.heterozygosity.Rd | 1 man/gl.filter.hwe.Rd | 1 man/gl.filter.ld.Rd | 16 man/gl.filter.locmetric.Rd | 2 man/gl.filter.maf.Rd | 2 man/gl.filter.monomorphs.Rd | 2 man/gl.filter.overshoot.Rd | 2 man/gl.filter.pa.Rd | 2 man/gl.filter.rdepth.Rd | 1 man/gl.filter.replicates.Rd |only man/gl.filter.reproducibility.Rd | 1 man/gl.filter.secondaries.Rd | 8 man/gl.filter.sexlinked.Rd |only man/gl.filter.taglength.Rd | 1 man/gl.fixed.diff.Rd | 1 man/gl.fst.pop.Rd | 1 man/gl.gen2fbm.Rd |only man/gl.hwe.pop.Rd | 1 man/gl.impute.Rd | 48 + man/gl.join.Rd | 55 - man/gl.keep.ind.Rd | 2 man/gl.keep.loc.Rd | 2 man/gl.keep.pop.Rd | 2 man/gl.load.Rd | 5 man/gl.make.recode.ind.Rd | 2 man/gl.make.recode.pop.Rd | 1 man/gl.map.interactive.Rd | 5 man/gl.merge.pop.Rd | 2 man/gl.pcoa.Rd | 5 man/gl.pcoa.plot.Rd | 3 man/gl.plot.heatmap.Rd | 118 +++ man/gl.plot.snp.density.Rd |only man/gl.print.history.Rd | 1 man/gl.prop.shared.Rd | 1 man/gl.randomize.snps.Rd | 2 man/gl.read.PLINK.Rd | 22 man/gl.read.csv.Rd | 15 man/gl.read.dart.Rd | 12 man/gl.read.fasta.Rd | 25 man/gl.read.vcf.Rd | 19 man/gl.reassign.ind.Rd |only man/gl.reassign.pop.Rd | 4 man/gl.recalc.metrics.Rd | 1 man/gl.recode.ind.Rd | 2 man/gl.recode.pop.Rd | 4 man/gl.rename.pop.Rd | 2 man/gl.report.allelerich.Rd | 257 ++++++ man/gl.report.allna.Rd | 1 man/gl.report.bases.Rd | 1 man/gl.report.basics.Rd | 2 man/gl.report.callrate.Rd | 1 man/gl.report.diversity.Rd | 2 man/gl.report.excess.het.Rd | 2 man/gl.report.factorloadings.Rd | 1 man/gl.report.fstat.Rd | 9 man/gl.report.hamming.Rd | 3 man/gl.report.heterozygosity.Rd | 8 man/gl.report.ld.map.Rd | 1 man/gl.report.locmetric.Rd | 1 man/gl.report.maf.Rd | 1 man/gl.report.monomorphs.Rd | 1 man/gl.report.overshoot.Rd | 1 man/gl.report.pa.Rd | 1 man/gl.report.polyploid_heterozygosity.Rd | 7 man/gl.report.rdepth.Rd | 1 man/gl.report.replicates.Rd | 75 +- man/gl.report.reproducibility.Rd | 3 man/gl.report.secondaries.Rd | 1 man/gl.report.sexlinked.Rd |only man/gl.report.shannon.Rd | 3 man/gl.report.taglength.Rd | 1 man/gl.sample.Rd | 2 man/gl.select.colors.Rd | 7 man/gl.select.shapes.Rd | 1 man/gl.sim.genotypes.Rd | 1 man/gl.smearplot.Rd | 18 man/gl.sort.Rd | 44 - man/gl.subsample.ind.Rd | 3 man/gl.subsample.loc.Rd | 2 man/gl.subsample.loci.Rd | 1 man/gl.test.heterozygosity.Rd | 1 man/gl.tree.fitch.Rd | 1 man/gl.tree.nj.Rd | 3 man/gl.write.csv.Rd | 1 man/gl2bayesAss.Rd | 3 man/gl2bayescan.Rd | 3 man/gl2bpp.Rd | 7 man/gl2demerelate.Rd | 3 man/gl2eigenstrat.Rd | 3 man/gl2fasta.Rd | 10 man/gl2faststructure.Rd | 2 man/gl2gds.Rd | 3 man/gl2genalex.Rd | 3 man/gl2genepop.Rd | 4 man/gl2geno.Rd | 5 man/gl2gi.Rd | 8 man/gl2hapmap.Rd |only man/gl2hiphop.Rd | 3 man/gl2paup.parsimony.Rd | 1 man/gl2paup.svdquartets.Rd | 1 man/gl2phylip.Rd | 3 man/gl2plink.Rd | 13 man/gl2related.Rd | 5 man/gl2sa.Rd | 32 man/gl2snapper.Rd | 32 man/gl2structure.Rd | 3 man/gl2treemix.Rd | 3 man/gl2vcf.Rd | 19 man/glMean.Rd |only man/glSum.Rd |only man/rbind.dartR.Rd | 20 man/sub-dartR-ANY-ANY-ANY-method.Rd | 3 man/utils.allelic.richness.Rd |only man/utils.basic.stats.Rd | 1 man/utils.check.datatype.Rd | 2 man/utils.collapse.matrix.Rd | 1 man/utils.dart2genlight.Rd | 1 man/utils.dist.binary.Rd | 1 man/utils.dist.ind.snp.Rd | 15 man/utils.flag.start.Rd | 1 man/utils.hamming.Rd | 1 man/utils.heatmap.Rd |only man/utils.het.pop.Rd | 1 man/utils.impute.Rd | 1 man/utils.is.fixed.Rd | 1 man/utils.jackknife.Rd | 1 man/utils.n.var.invariant.Rd | 1 man/utils.plot.save.Rd | 1 man/utils.read.fasta.Rd | 1 man/utils.read.ped.Rd | 1 man/utils.recalc.avgpic.Rd | 1 man/utils.recalc.callrate.Rd | 1 man/utils.recalc.freqhets.Rd | 1 man/utils.recalc.freqhomref.Rd | 1 man/utils.recalc.freqhomsnp.Rd | 1 man/utils.recalc.maf.Rd | 1 man/utils.reset.flags.Rd | 1 man/utils.transpose.Rd | 1 man/utils.vcfr2genlight.polyploid.Rd | 1 320 files changed, 6734 insertions(+), 3295 deletions(-)
Title: Modelling Continuous Report Visual Short-Term Memory Studies
Description: A set of utility functions for analysing and modelling data from
continuous report short-term memory experiments using either the 2-component
mixture model of Zhang and Luck (2008) <doi:10.1038/nature06860> or the
3-component mixture model of Bays et al. (2009) <doi:10.1167/9.10.7>. Users
are also able to simulate from these models.
Author: Jim Grange [aut, cre] ,
Stuart B. Moore [aut] ,
Ed D. J. Berry [ctb],
Vencislav Popov [ctb]
Maintainer: Jim Grange <grange.jim@gmail.com>
Diff between mixtur versions 1.2.2 dated 2025-07-21 and 1.2.3 dated 2026-03-12
DESCRIPTION | 10 ++-- MD5 | 10 ++-- NAMESPACE | 1 NEWS.md | 5 +- R/plotting.R | 140 ++++++++++++++++++++++++++++++++++++----------------------- README.md | 4 - 6 files changed, 104 insertions(+), 66 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 10.1.4 dated 2026-02-23 and 10.1.5 dated 2026-03-12
rswipl-10.1.4/rswipl/src/swipl-devel/cmake/TestSignalType.c |only rswipl-10.1.4/rswipl/src/swipl-devel/cmake/TestSignalType.cmake |only rswipl-10.1.4/rswipl/src/swipl-devel/src/pl-trie.c.save |only rswipl-10.1.5/rswipl/DESCRIPTION | 10 rswipl-10.1.5/rswipl/MD5 | 127 +- rswipl-10.1.5/rswipl/NEWS.md | 6 rswipl-10.1.5/rswipl/inst/patch/03-cpp.patch | 2 rswipl-10.1.5/rswipl/inst/patch/04-cpp.patch | 4 rswipl-10.1.5/rswipl/src/install.libs.R | 2 rswipl-10.1.5/rswipl/src/swipl-devel/VERSION | 2 rswipl-10.1.5/rswipl/src/swipl-devel/boot/init.pl | 3 rswipl-10.1.5/rswipl/src/swipl-devel/boot/messages.pl | 60 - rswipl-10.1.5/rswipl/src/swipl-devel/boot/toplevel.pl | 11 rswipl-10.1.5/rswipl/src/swipl-devel/cmake/BuildType.cmake | 22 rswipl-10.1.5/rswipl/src/swipl-devel/cmake/PGO.cmake | 29 rswipl-10.1.5/rswipl/src/swipl-devel/library/console_input.pl | 94 + rswipl-10.1.5/rswipl/src/swipl-devel/library/csv.pl | 53 rswipl-10.1.5/rswipl/src/swipl-devel/library/dialect/swi/syspred_options.pl | 1 rswipl-10.1.5/rswipl/src/swipl-devel/library/prolog_code.pl | 2 rswipl-10.1.5/rswipl/src/swipl-devel/library/prolog_debug.pl | 41 rswipl-10.1.5/rswipl/src/swipl-devel/library/tableutil.pl |only rswipl-10.1.5/rswipl/src/swipl-devel/library/threadutil.pl | 249 ++-- rswipl-10.1.5/rswipl/src/swipl-devel/packages/clib/process.c.rej |only rswipl-10.1.5/rswipl/src/swipl-devel/packages/cpp/test_cpp.cpp.rej |only rswipl-10.1.5/rswipl/src/swipl-devel/packages/cpp/test_cpp.pl.rej |only rswipl-10.1.5/rswipl/src/swipl-devel/packages/http/thread_httpd.pl | 13 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/config.h.cmake | 1 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/prolog_mode.pl | 11 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/epilog.pl | 37 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/gui_tracer.pl | 23 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/prolog_predicate.pl | 28 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/swi/thread_monitor.pl | 162 ++ rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/trace/trace.pl | 9 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/evt/event.c | 21 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/ker/conversion.c | 4 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/md/md-windows.h | 3 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdlevent.c | 24 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdlimage.c | 2 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/txt/editor.c | 43 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/swipl/swipl-rc | 1 rswipl-10.1.5/rswipl/src/swipl-devel/scripts/make-distribution | 9 rswipl-10.1.5/rswipl/src/swipl-devel/scripts/make-ppa | 8 rswipl-10.1.5/rswipl/src/swipl-devel/src/ATOMS | 2 rswipl-10.1.5/rswipl/src/swipl-devel/src/CMakeLists.txt | 3 rswipl-10.1.5/rswipl/src/swipl-devel/src/SWI-Prolog.h | 19 rswipl-10.1.5/rswipl/src/swipl-devel/src/config.h.cmake | 2 rswipl-10.1.5/rswipl/src/swipl-devel/src/config/wincfg.h | 9 rswipl-10.1.5/rswipl/src/swipl-devel/src/libbf/bf_gmp.c | 21 rswipl-10.1.5/rswipl/src/swipl-devel/src/os/pl-prologflag.c | 592 +++++----- rswipl-10.1.5/rswipl/src/swipl-devel/src/os/pl-prologflag.h | 17 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-arith.c | 41 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-arith.h | 5 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-fli.c | 4 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-global.h | 1 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-gmp.c | 11 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-incl.h | 16 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-init.c | 14 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-init.h | 7 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-pro.c | 10 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-qlf.c | 33 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-thread.c | 243 +++- rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-thread.h | 8 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-trace.c | 96 - rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-trace.h | 6 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-vmi.c | 6 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-wam.c | 49 rswipl-10.1.5/rswipl/src/swipl-devel/tests/core/test_bips.pl | 193 +-- rswipl-10.1.5/rswipl/src/swipl-devel/tests/core/test_prolog_flag.pl | 88 + 68 files changed, 1712 insertions(+), 901 deletions(-)
Title: Simple Interactive Controls for R using the 'tcltk' Package
Description: A set of functions to build simple
GUI controls for R functions. These are built on the 'tcltk' package.
Uses could include changing a parameter on a graph by animating it
with a slider or a "doublebutton", up to more sophisticated control
panels.
Some functions for specific graphical tasks, referred to as 'cartoons',
are provided.
Author: Adrian Bowman [aut, cre, cph],
Ewan Crawford [aut],
Gavin Alexander [aut],
Richard Bowman [aut]
Maintainer: Adrian Bowman <adrian.bowman@glasgow.ac.uk>
Diff between rpanel versions 1.1-5.2 dated 2023-02-07 and 1.1-6 dated 2026-03-12
rpanel-1.1-5.2/rpanel/R/rp-ancova.r |only rpanel-1.1-5.2/rpanel/R/rp-anova.R |only rpanel-1.1-5.2/rpanel/R/rp-ci.r |only rpanel-1.1-5.2/rpanel/R/rp-geosim.r |only rpanel-1.1-5.2/rpanel/R/rp-gulls.r |only rpanel-1.1-5.2/rpanel/R/rp-mururoa.r |only rpanel-1.1-5.2/rpanel/R/rp-power.r |only rpanel-1.1-5.2/rpanel/R/rp-regression.r |only rpanel-1.1-5.2/rpanel/R/rp-sample.r |only rpanel-1.1-5.2/rpanel/R/rp-tables.r |only rpanel-1.1-6/rpanel/ChangeLog | 2 rpanel-1.1-6/rpanel/DESCRIPTION | 38 + rpanel-1.1-6/rpanel/MD5 | 188 ++++--- rpanel-1.1-6/rpanel/NAMESPACE | 99 ++- rpanel-1.1-6/rpanel/NEWS.md | 6 rpanel-1.1-6/rpanel/R/image.r | 257 +++++----- rpanel-1.1-6/rpanel/R/rp-colour-key.r | 4 rpanel-1.1-6/rpanel/R/rp-firth.r | 32 - rpanel-1.1-6/rpanel/R/rp-likelihood.r | 296 +++++------ rpanel-1.1-6/rpanel/R/rp-logistic.r | 68 +- rpanel-1.1-6/rpanel/R/rp-normal.r | 24 rpanel-1.1-6/rpanel/R/rp-plot3d.r | 250 +++++----- rpanel-1.1-6/rpanel/R/rp-plot4d.r | 300 +++++++----- rpanel-1.1-6/rpanel/R/rp-rmplot.r | 570 +++++++++++------------ rpanel-1.1-6/rpanel/R/rp-surface.r | 1 rpanel-1.1-6/rpanel/R/rp_ancova.R |only rpanel-1.1-6/rpanel/R/rp_anova.R |only rpanel-1.1-6/rpanel/R/rp_ci.r |only rpanel-1.1-6/rpanel/R/rp_coefficients.R |only rpanel-1.1-6/rpanel/R/rp_colours.R |only rpanel-1.1-6/rpanel/R/rp_contingency.R |only rpanel-1.1-6/rpanel/R/rp_datalink.R |only rpanel-1.1-6/rpanel/R/rp_drop1.R |only rpanel-1.1-6/rpanel/R/rp_geosim.r |only rpanel-1.1-6/rpanel/R/rp_gulls.r |only rpanel-1.1-6/rpanel/R/rp_lm.R |only rpanel-1.1-6/rpanel/R/rp_mururoa.r |only rpanel-1.1-6/rpanel/R/rp_power.r |only rpanel-1.1-6/rpanel/R/rp_regression.r |only rpanel-1.1-6/rpanel/R/rp_regression2.r |only rpanel-1.1-6/rpanel/R/rp_regression2_lm.r |only rpanel-1.1-6/rpanel/R/rp_sample.r |only rpanel-1.1-6/rpanel/R/rp_sample_old.r |only rpanel-1.1-6/rpanel/R/rp_t_test.R |only rpanel-1.1-6/rpanel/R/rp_tables.r |only rpanel-1.1-6/rpanel/R/rp_wrangle.R |only rpanel-1.1-6/rpanel/R/rpanel.r | 7 rpanel-1.1-6/rpanel/R/sysdata.rda |binary rpanel-1.1-6/rpanel/R/tkrplot.r | 264 ++++++---- rpanel-1.1-6/rpanel/R/window.r | 44 - 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Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene
sets typically used with the 'Gene Set Enrichment Analysis' (GSEA)
software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>,
Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al.
2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package
includes the human genes as listed in MSigDB as well as the
corresponding symbols and IDs for frequently studied model organisms
such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 25.1.1 dated 2025-07-21 and 26.1.0 dated 2026-03-12
DESCRIPTION | 8 - MD5 | 22 ++-- NAMESPACE | 2 NEWS.md | 9 + R/msigdbr-collections.R | 41 ++++---- R/msigdbr.R | 50 ++++------ R/utils.R | 149 +++++++++++++++++++----------- build/partial.rdb |binary man/msigdbr.Rd | 2 man/msigdbr_collections.Rd | 2 tests/testthat/test-msigdbr-collections.R | 3 tests/testthat/test-msigdbr.R | 15 ++- 12 files changed, 186 insertions(+), 117 deletions(-)
Title: Leveraging Experiment Lines to Data Analytics
Description: The natural increase in the complexity of current research experiments and data demands better tools to enhance productivity in Data Analytics. The package is a framework designed to address the modern challenges in data analytics workflows. The package is inspired by Experiment Line concepts. It aims to provide seamless support for users in developing their data mining workflows by offering a uniform data model and method API. It enables the integration of various data mining activities, including data preprocessing, classification, regression, clustering, and time series prediction. It also offers options for hyper-parameter tuning and supports integration with existing libraries and languages. Overall, the package provides researchers with a comprehensive set of functionalities for data science, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_2 [...truncated...]
Author: Eduardo Ogasawara [aut, ths, cre] ,
Ana Carolina Sá [aut],
Antonio Castro [aut],
Caio Santos [aut],
Diego Carvalho [ctb],
Diego Salles [aut],
Eduardo Bezerra [ctb],
Esther Pacitti [ctb],
Fabio Porto [ctb],
Janio Lima [aut],
Lucas Tavares [aut],
Ra [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolbox versions 1.3.717 dated 2026-02-10 and 1.3.727 dated 2026-03-12
DESCRIPTION | 14 +++++----- MD5 | 46 ++++++++++++++++++++++------------ NAMESPACE | 22 ++++++++++++++++ R/cla_xgboost.R | 2 - R/graphics_plot_boxplot.R | 21 ++++++++------- R/graphics_plot_boxplot_class.R | 19 +++++++------- R/pat_apriori.R | 8 ++--- R/pat_cspade.R | 8 ++--- R/pat_eclat.R | 8 ++--- R/pat_pattern_miner.R | 24 +++++++++++++++++ R/trans_feature_selection_corr.R | 41 +++++++++++++++++++++++++++--- R/trans_feature_selection_fss.R |only R/trans_feature_selection_info_gain.R |only R/trans_feature_selection_lasso.R |only R/trans_feature_selection_relief.R |only R/trans_feature_selection_stepwise.R |only R/trans_sample_oversampling.R |only R/trans_sample_subsampling.R |only README.md | 6 +++- man/bal_oversampling.Rd |only man/bal_subsampling.Rd |only man/cla_xgboost.Rd | 2 - man/feature_selection_corr.Rd | 7 ++++- man/feature_selection_fss.Rd |only man/feature_selection_info_gain.Rd |only man/feature_selection_lasso.Rd |only man/feature_selection_relief.Rd |only man/feature_selection_stepwise.Rd |only man/pat_apriori.Rd | 2 - man/pat_cspade.Rd | 2 - man/pat_eclat.Rd | 2 - 31 files changed, 168 insertions(+), 66 deletions(-)