Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in
the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing
weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020)
<doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.3.0 dated 2025-03-03 and 0.4.0 dated 2025-06-11
DESCRIPTION | 20 +-- MD5 | 44 +++--- NAMESPACE | 12 + NEWS.md | 14 ++ R/fwb.R | 116 ++++++++++++----- R/fwb.ci.R | 284 +++++++++++++++++++++++-------------------- R/plot.fwb.R | 22 +-- R/summary.fwb.R | 6 R/utils.R | 54 ++++++++ R/vcovFWB.R | 122 ++++++++++++++---- R/weighted-statistics.R |only README.md | 26 +++ build/stage23.rdb |binary build/vignette.rds |binary inst/doc/fwb-rep.Rmd | 38 +++-- inst/doc/fwb-rep.html | 135 ++++++++++---------- man/fwb-package.Rd | 2 man/fwb.Rd | 24 +-- man/fwb.ci.Rd | 6 man/plot.fwb.Rd | 2 man/summary.fwb.Rd | 3 man/w_mean.Rd |only tests/testthat/helpers.R |only tests/testthat/test-w_mean.R |only vignettes/fwb-rep.Rmd | 38 +++-- 25 files changed, 616 insertions(+), 352 deletions(-)
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 1.0.1 dated 2025-03-07 and 1.1.0 dated 2025-06-11
Luminescence-1.0.1/Luminescence/man/get_Quote.Rd |only Luminescence-1.0.1/Luminescence/tests/testthat/_snaps |only Luminescence-1.0.1/Luminescence/tests/testthat/test_plot_Functions.R |only Luminescence-1.1.0/Luminescence/DESCRIPTION | 65 Luminescence-1.1.0/Luminescence/MD5 | 669 +++--- Luminescence-1.1.0/Luminescence/NAMESPACE | 6 Luminescence-1.1.0/Luminescence/NEWS.md | 1028 ++++++---- Luminescence-1.1.0/Luminescence/R/Analyse_SAR.OSLdata.R | 2 Luminescence-1.1.0/Luminescence/R/Luminescence-generics.R | 106 - Luminescence-1.1.0/Luminescence/R/Luminescence-package.R | 55 Luminescence-1.1.0/Luminescence/R/RLum.Analysis-class.R | 254 +- Luminescence-1.1.0/Luminescence/R/RcppExports.R | 20 Luminescence-1.1.0/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 149 - Luminescence-1.1.0/Luminescence/R/analyse_Al2O3C_CrossTalk.R | 5 Luminescence-1.1.0/Luminescence/R/analyse_Al2O3C_ITC.R | 3 Luminescence-1.1.0/Luminescence/R/analyse_FadingMeasurement.R | 94 Luminescence-1.1.0/Luminescence/R/analyse_IRSAR.RF.R | 742 ++----- Luminescence-1.1.0/Luminescence/R/analyse_SAR.CWOSL.R | 971 ++++----- Luminescence-1.1.0/Luminescence/R/analyse_SAR.TL.R | 25 Luminescence-1.1.0/Luminescence/R/analyse_ThermochronometryData.R | 17 Luminescence-1.1.0/Luminescence/R/analyse_baSAR.R | 229 -- Luminescence-1.1.0/Luminescence/R/analyse_pIRIRSequence.R | 125 - Luminescence-1.1.0/Luminescence/R/analyse_portableOSL.R | 485 ++-- Luminescence-1.1.0/Luminescence/R/apply_CosmicRayRemoval.R | 38 Luminescence-1.1.0/Luminescence/R/calc_AliquotSize.R | 327 +-- Luminescence-1.1.0/Luminescence/R/calc_AverageDose.R | 49 Luminescence-1.1.0/Luminescence/R/calc_CentralDose.R | 87 Luminescence-1.1.0/Luminescence/R/calc_CobbleDoseRate.R | 16 Luminescence-1.1.0/Luminescence/R/calc_CommonDose.R | 18 Luminescence-1.1.0/Luminescence/R/calc_CosmicDoseRate.R | 38 Luminescence-1.1.0/Luminescence/R/calc_FadingCorr.R | 9 Luminescence-1.1.0/Luminescence/R/calc_FastRatio.R | 10 Luminescence-1.1.0/Luminescence/R/calc_FiniteMixture.R | 639 ++++-- Luminescence-1.1.0/Luminescence/R/calc_FuchsLang2001.R | 21 Luminescence-1.1.0/Luminescence/R/calc_HomogeneityTest.R | 24 Luminescence-1.1.0/Luminescence/R/calc_Huntley2006.R | 304 +- Luminescence-1.1.0/Luminescence/R/calc_MinDose.R | 95 Luminescence-1.1.0/Luminescence/R/calc_OSLLxTxDecomposed.R | 12 Luminescence-1.1.0/Luminescence/R/calc_OSLLxTxRatio.R | 179 - Luminescence-1.1.0/Luminescence/R/calc_SourceDoseRate.R | 2 Luminescence-1.1.0/Luminescence/R/calc_ThermalLifetime.R | 65 Luminescence-1.1.0/Luminescence/R/calc_gSGC.R | 100 Luminescence-1.1.0/Luminescence/R/calc_gSGC_feldspar.R | 17 Luminescence-1.1.0/Luminescence/R/convert_Activity2Concentration.R | 3 Luminescence-1.1.0/Luminescence/R/convert_Concentration2DoseRate.R | 84 Luminescence-1.1.0/Luminescence/R/convert_RLum2Risoe.BINfileData.R | 50 Luminescence-1.1.0/Luminescence/R/convert_Wavelength2Energy.R | 4 Luminescence-1.1.0/Luminescence/R/extract_IrradiationTimes.R | 220 +- Luminescence-1.1.0/Luminescence/R/fit_CWCurve.R | 33 Luminescence-1.1.0/Luminescence/R/fit_DoseResponseCurve.R | 895 +++++--- Luminescence-1.1.0/Luminescence/R/fit_EmissionSpectra.R | 18 Luminescence-1.1.0/Luminescence/R/fit_IsothermalHolding.R | 72 Luminescence-1.1.0/Luminescence/R/fit_LMCurve.R | 565 ++--- Luminescence-1.1.0/Luminescence/R/fit_OSLLifeTimes.R | 8 Luminescence-1.1.0/Luminescence/R/fit_SurfaceExposure.R | 98 Luminescence-1.1.0/Luminescence/R/fit_ThermalQuenching.R | 176 - Luminescence-1.1.0/Luminescence/R/get_Quote.R | 2 Luminescence-1.1.0/Luminescence/R/import_Data.R | 3 Luminescence-1.1.0/Luminescence/R/install_DevelopmentVersion.R | 4 Luminescence-1.1.0/Luminescence/R/internal_as.latex.table.R | 195 - Luminescence-1.1.0/Luminescence/R/internals_RLum.R | 86 Luminescence-1.1.0/Luminescence/R/internals_Thermochronometry.R | 2 Luminescence-1.1.0/Luminescence/R/merge_RLum.Data.Curve.R | 2 Luminescence-1.1.0/Luminescence/R/merge_RLum.Data.Spectrum.R | 5 Luminescence-1.1.0/Luminescence/R/merge_RLum.R | 10 Luminescence-1.1.0/Luminescence/R/methods_DRAC.R | 10 Luminescence-1.1.0/Luminescence/R/plot_AbanicoPlot.R | 484 +--- Luminescence-1.1.0/Luminescence/R/plot_DRCSummary.R | 42 Luminescence-1.1.0/Luminescence/R/plot_DRTResults.R | 191 + Luminescence-1.1.0/Luminescence/R/plot_DetPlot.R | 48 Luminescence-1.1.0/Luminescence/R/plot_DoseResponseCurve.R | 241 +- Luminescence-1.1.0/Luminescence/R/plot_FilterCombinations.R | 3 Luminescence-1.1.0/Luminescence/R/plot_GrowthCurve.R | 16 Luminescence-1.1.0/Luminescence/R/plot_Histogram.R | 510 +--- Luminescence-1.1.0/Luminescence/R/plot_KDE.R | 367 +-- Luminescence-1.1.0/Luminescence/R/plot_RLum.Analysis.R | 16 Luminescence-1.1.0/Luminescence/R/plot_RLum.Data.Curve.R | 84 Luminescence-1.1.0/Luminescence/R/plot_RLum.Data.Spectrum.R | 86 Luminescence-1.1.0/Luminescence/R/plot_RLum.Results.R | 381 --- Luminescence-1.1.0/Luminescence/R/plot_ROI.R | 65 Luminescence-1.1.0/Luminescence/R/plot_RadialPlot.R | 392 --- Luminescence-1.1.0/Luminescence/R/plot_ViolinPlot.R | 37 Luminescence-1.1.0/Luminescence/R/read_BIN2R.R | 2 Luminescence-1.1.0/Luminescence/R/read_SPE2R.R | 47 Luminescence-1.1.0/Luminescence/R/read_TIFF2R.R | 46 Luminescence-1.1.0/Luminescence/R/read_XSYG2R.R | 206 -- Luminescence-1.1.0/Luminescence/R/remove_SignalBackground.R |only Luminescence-1.1.0/Luminescence/R/report_RLum.R | 40 Luminescence-1.1.0/Luminescence/R/scale_GammaDose.R | 36 Luminescence-1.1.0/Luminescence/R/template_DRAC.R | 6 Luminescence-1.1.0/Luminescence/R/use_DRAC.R | 32 Luminescence-1.1.0/Luminescence/R/utils_DRAC.R | 2 Luminescence-1.1.0/Luminescence/R/verify_SingleGrainData.R | 52 Luminescence-1.1.0/Luminescence/R/write_R2TIFF.R | 24 Luminescence-1.1.0/Luminescence/R/write_RLum2CSV.R | 3 Luminescence-1.1.0/Luminescence/R/zzz.R | 32 Luminescence-1.1.0/Luminescence/README.md | 5 Luminescence-1.1.0/Luminescence/build/partial.rdb |binary Luminescence-1.1.0/Luminescence/build/vignette.rds |binary Luminescence-1.1.0/Luminescence/data/ExampleData.RF70Curves.rda |only Luminescence-1.1.0/Luminescence/data/datalist | 1 Luminescence-1.1.0/Luminescence/inst/WORDLIST | 39 Luminescence-1.1.0/Luminescence/inst/doc/crosstalk.html | 60 Luminescence-1.1.0/Luminescence/man/Analyse_SAR.OSLdata.Rd | 2 Luminescence-1.1.0/Luminescence/man/ExampleData.RF70Curves.Rd |only Luminescence-1.1.0/Luminescence/man/GitHub-API.Rd | 2 Luminescence-1.1.0/Luminescence/man/RLum-class.Rd | 2 Luminescence-1.1.0/Luminescence/man/RLum.Analysis-class.Rd | 62 Luminescence-1.1.0/Luminescence/man/RLum.Data-class.Rd | 2 Luminescence-1.1.0/Luminescence/man/RLum.Data.Curve-class.Rd | 2 Luminescence-1.1.0/Luminescence/man/RLum.Data.Image-class.Rd | 2 Luminescence-1.1.0/Luminescence/man/RLum.Data.Spectrum-class.Rd | 2 Luminescence-1.1.0/Luminescence/man/RLum.Results-class.Rd | 2 Luminescence-1.1.0/Luminescence/man/Risoe.BINfileData-class.Rd | 2 Luminescence-1.1.0/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 16 Luminescence-1.1.0/Luminescence/man/analyse_Al2O3C_CrossTalk.Rd | 2 Luminescence-1.1.0/Luminescence/man/analyse_Al2O3C_ITC.Rd | 2 Luminescence-1.1.0/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 2 Luminescence-1.1.0/Luminescence/man/analyse_FadingMeasurement.Rd | 7 Luminescence-1.1.0/Luminescence/man/analyse_IRSAR.RF.Rd | 113 - Luminescence-1.1.0/Luminescence/man/analyse_SAR.CWOSL.Rd | 31 Luminescence-1.1.0/Luminescence/man/analyse_SAR.TL.Rd | 2 Luminescence-1.1.0/Luminescence/man/analyse_baSAR.Rd | 5 Luminescence-1.1.0/Luminescence/man/analyse_pIRIRSequence.Rd | 5 Luminescence-1.1.0/Luminescence/man/analyse_portableOSL.Rd | 90 Luminescence-1.1.0/Luminescence/man/apply_CosmicRayRemoval.Rd | 20 Luminescence-1.1.0/Luminescence/man/apply_Crosstalk.Rd | 2 Luminescence-1.1.0/Luminescence/man/apply_EfficiencyCorrection.Rd | 2 Luminescence-1.1.0/Luminescence/man/bin_RLum.Data.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_AliquotSize.Rd | 73 Luminescence-1.1.0/Luminescence/man/calc_AverageDose.Rd | 4 Luminescence-1.1.0/Luminescence/man/calc_CentralDose.Rd | 4 Luminescence-1.1.0/Luminescence/man/calc_CobbleDoseRate.Rd | 9 Luminescence-1.1.0/Luminescence/man/calc_CommonDose.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_CosmicDoseRate.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_EED_Model.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_FadingCorr.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_FastRatio.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_FiniteMixture.Rd | 50 Luminescence-1.1.0/Luminescence/man/calc_FuchsLang2001.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_HomogeneityTest.Rd | 6 Luminescence-1.1.0/Luminescence/man/calc_Huntley2006.Rd | 105 - Luminescence-1.1.0/Luminescence/man/calc_IEU.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_Lamothe2003.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_MaxDose.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_MinDose.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_MoransI.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_OSLLxTxRatio.Rd | 8 Luminescence-1.1.0/Luminescence/man/calc_SourceDoseRate.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_Statistics.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_TLLxTxRatio.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_ThermalLifetime.Rd | 4 Luminescence-1.1.0/Luminescence/man/calc_WodaFuchs2008.Rd | 2 Luminescence-1.1.0/Luminescence/man/calc_gSGC.Rd | 23 Luminescence-1.1.0/Luminescence/man/calc_gSGC_feldspar.Rd | 2 Luminescence-1.1.0/Luminescence/man/combine_De_Dr.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_Activity2Concentration.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_BIN2CSV.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_CW2pHMi.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_CW2pLM.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_CW2pLMi.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_CW2pPMi.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_Concentration2DoseRate.Rd | 16 Luminescence-1.1.0/Luminescence/man/convert_Daybreak2CSV.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_PSL2CSV.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_PSL2Risoe.BINfileData.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_SG2MG.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_Second2Gray.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_Wavelength2Energy.Rd | 2 Luminescence-1.1.0/Luminescence/man/convert_XSYG2CSV.Rd | 2 Luminescence-1.1.0/Luminescence/man/dot-as.latex.table.Rd |only Luminescence-1.1.0/Luminescence/man/extdata.Rd | 8 Luminescence-1.1.0/Luminescence/man/extract_IrradiationTimes.Rd | 82 Luminescence-1.1.0/Luminescence/man/extract_ROI.Rd | 2 Luminescence-1.1.0/Luminescence/man/fit_CWCurve.Rd | 2 Luminescence-1.1.0/Luminescence/man/fit_DoseResponseCurve.Rd | 135 - Luminescence-1.1.0/Luminescence/man/fit_EmissionSpectra.Rd | 17 Luminescence-1.1.0/Luminescence/man/fit_LMCurve.Rd | 78 Luminescence-1.1.0/Luminescence/man/fit_OSLLifeTimes.Rd | 2 Luminescence-1.1.0/Luminescence/man/fit_SurfaceExposure.Rd | 21 Luminescence-1.1.0/Luminescence/man/fit_ThermalQuenching.Rd | 32 Luminescence-1.1.0/Luminescence/man/get_Layout.Rd | 2 Luminescence-1.1.0/Luminescence/man/get_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/get_Risoe.BINfileData.Rd | 2 Luminescence-1.1.0/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-1.1.0/Luminescence/man/import_Data.Rd | 2 Luminescence-1.1.0/Luminescence/man/length_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/melt_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/merge_RLum.Analysis.Rd | 2 Luminescence-1.1.0/Luminescence/man/merge_RLum.Data.Curve.Rd | 2 Luminescence-1.1.0/Luminescence/man/merge_RLum.Data.Spectrum.Rd | 2 Luminescence-1.1.0/Luminescence/man/merge_RLum.Rd | 12 Luminescence-1.1.0/Luminescence/man/merge_RLum.Results.Rd | 2 Luminescence-1.1.0/Luminescence/man/merge_Risoe.BINfileData.Rd | 2 Luminescence-1.1.0/Luminescence/man/metadata.Rd | 2 Luminescence-1.1.0/Luminescence/man/names_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_AbanicoPlot.Rd | 12 Luminescence-1.1.0/Luminescence/man/plot_DRCSummary.Rd | 7 Luminescence-1.1.0/Luminescence/man/plot_DRTResults.Rd | 33 Luminescence-1.1.0/Luminescence/man/plot_DetPlot.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_DoseResponseCurve.Rd | 8 Luminescence-1.1.0/Luminescence/man/plot_FilterCombinations.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_GrowthCurve.Rd | 15 Luminescence-1.1.0/Luminescence/man/plot_Histogram.Rd | 42 Luminescence-1.1.0/Luminescence/man/plot_KDE.Rd | 35 Luminescence-1.1.0/Luminescence/man/plot_MoranScatterplot.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_NRt.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_OSLAgeSummary.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_RLum.Analysis.Rd | 6 Luminescence-1.1.0/Luminescence/man/plot_RLum.Data.Curve.Rd | 11 Luminescence-1.1.0/Luminescence/man/plot_RLum.Data.Image.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 24 Luminescence-1.1.0/Luminescence/man/plot_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_RLum.Results.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_ROI.Rd | 15 Luminescence-1.1.0/Luminescence/man/plot_RadialPlot.Rd | 10 Luminescence-1.1.0/Luminescence/man/plot_Risoe.BINfileData.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_SingleGrainDisc.Rd | 2 Luminescence-1.1.0/Luminescence/man/plot_ViolinPlot.Rd | 6 Luminescence-1.1.0/Luminescence/man/read_BIN2R.Rd | 2 Luminescence-1.1.0/Luminescence/man/read_Daybreak2R.Rd | 2 Luminescence-1.1.0/Luminescence/man/read_HeliosOSL2R.Rd | 2 Luminescence-1.1.0/Luminescence/man/read_PSL2R.Rd | 2 Luminescence-1.1.0/Luminescence/man/read_RF2R.Rd | 2 Luminescence-1.1.0/Luminescence/man/read_SPE2R.Rd | 22 Luminescence-1.1.0/Luminescence/man/read_TIFF2R.Rd | 23 Luminescence-1.1.0/Luminescence/man/read_XSYG2R.Rd | 9 Luminescence-1.1.0/Luminescence/man/remove_RLum.Rd |only Luminescence-1.1.0/Luminescence/man/remove_SignalBackground.Rd |only Luminescence-1.1.0/Luminescence/man/replicate_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/report_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/sTeve.Rd | 2 Luminescence-1.1.0/Luminescence/man/scale_GammaDose.Rd | 4 Luminescence-1.1.0/Luminescence/man/set_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/set_Risoe.BINfileData.Rd | 2 Luminescence-1.1.0/Luminescence/man/smooth_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/sort_RLum.Rd | 10 Luminescence-1.1.0/Luminescence/man/structure_RLum.Rd | 2 Luminescence-1.1.0/Luminescence/man/subset_SingleGrainData.Rd | 2 Luminescence-1.1.0/Luminescence/man/template_DRAC.Rd | 6 Luminescence-1.1.0/Luminescence/man/trim_RLum.Data.Rd | 2 Luminescence-1.1.0/Luminescence/man/tune_Data.Rd | 2 Luminescence-1.1.0/Luminescence/man/use_DRAC.Rd | 18 Luminescence-1.1.0/Luminescence/man/verify_SingleGrainData.Rd | 2 Luminescence-1.1.0/Luminescence/man/view.Rd | 2 Luminescence-1.1.0/Luminescence/man/write_R2BIN.Rd | 2 Luminescence-1.1.0/Luminescence/man/write_R2TIFF.Rd | 4 Luminescence-1.1.0/Luminescence/man/write_RLum2CSV.Rd | 2 Luminescence-1.1.0/Luminescence/src/RcppExports.cpp | 83 Luminescence-1.1.0/Luminescence/src/create_UID.cpp | 33 Luminescence-1.1.0/Luminescence/src/src_ThermoChronometry.cpp |only Luminescence-1.1.0/Luminescence/src/src_fit_functions.cpp |only Luminescence-1.1.0/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 99 Luminescence-1.1.0/Luminescence/tests/testthat/test_Risoe.BINfileData2RLum.Analysis.R | 9 Luminescence-1.1.0/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 2 Luminescence-1.1.0/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 54 Luminescence-1.1.0/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R | 45 Luminescence-1.1.0/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 75 Luminescence-1.1.0/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 20 Luminescence-1.1.0/Luminescence/tests/testthat/test_analyse_ThermochronometryData.R | 4 Luminescence-1.1.0/Luminescence/tests/testthat/test_analyse_baSAR.R | 74 Luminescence-1.1.0/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 51 Luminescence-1.1.0/Luminescence/tests/testthat/test_analyse_portableOSL.R | 93 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_AliquotSize.R | 38 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_AverageDose.R | 13 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_CentralDose.R | 12 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_CobbleDoseRate.R | 2 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_FastRatio.R | 11 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_FiniteMixture.R | 42 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_FuchsLang2001.R | 11 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_Huntley2006.R | 79 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_MaxDose.R | 29 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_MinDose.R | 36 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_OSLLxTxDecomposed.R | 5 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_OSLLxTxRatio.R | 20 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_SourceDoseRate.R | 68 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_ThermalLifetime.R | 100 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_gSGC.R | 37 Luminescence-1.1.0/Luminescence/tests/testthat/test_calc_gSGC_feldspar.R | 24 Luminescence-1.1.0/Luminescence/tests/testthat/test_convert_Activity2Concentration.R | 46 Luminescence-1.1.0/Luminescence/tests/testthat/test_convert_Concentration2DoseRate.R | 63 Luminescence-1.1.0/Luminescence/tests/testthat/test_convert_RLum2Risoe.BINfileData.R | 6 Luminescence-1.1.0/Luminescence/tests/testthat/test_extract_IrradiationTimes.R | 14 Luminescence-1.1.0/Luminescence/tests/testthat/test_fit_DoseResponseCurve.R | 167 + Luminescence-1.1.0/Luminescence/tests/testthat/test_fit_EmissionSpectra.R | 19 Luminescence-1.1.0/Luminescence/tests/testthat/test_fit_IsothermalHolding.R | 18 Luminescence-1.1.0/Luminescence/tests/testthat/test_fit_LMCurve.R | 58 Luminescence-1.1.0/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 5 Luminescence-1.1.0/Luminescence/tests/testthat/test_fit_SurfaceExposure.R | 35 Luminescence-1.1.0/Luminescence/tests/testthat/test_fit_ThermalQuenching.R | 40 Luminescence-1.1.0/Luminescence/tests/testthat/test_internals.R | 31 Luminescence-1.1.0/Luminescence/tests/testthat/test_merge_RLum.Data.Curve.R | 5 Luminescence-1.1.0/Luminescence/tests/testthat/test_methods_DRAC.R | 8 Luminescence-1.1.0/Luminescence/tests/testthat/test_methods_S3.R | 4 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 50 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_DRCSummary.R | 35 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_DRTResults.R | 65 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_DetPlot.R | 22 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_DoseResponseCurve.R | 41 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_FilterCombinations.R | 24 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_GrowthCurve.R | 9 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_Histogram.R | 54 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_KDE.R | 37 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_MoranScatterplot.R | 17 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_RLum.Analysis.R | 34 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_RLum.Data.Curve.R | 3 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 65 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_RLum.R | 6 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_RLum.Results.R | 1 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_ROI.R | 30 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_RadialPlot.R | 63 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_SingleGrainDisc.R | 18 Luminescence-1.1.0/Luminescence/tests/testthat/test_plot_ViolinPlot.R | 27 Luminescence-1.1.0/Luminescence/tests/testthat/test_read_BIN2R.R | 2 Luminescence-1.1.0/Luminescence/tests/testthat/test_read_HeliosOSL2R.R | 4 Luminescence-1.1.0/Luminescence/tests/testthat/test_read_TIFF2R.R | 11 Luminescence-1.1.0/Luminescence/tests/testthat/test_remove_SignalBackground.R |only Luminescence-1.1.0/Luminescence/tests/testthat/test_report_RLum.R | 15 Luminescence-1.1.0/Luminescence/tests/testthat/test_scale_GammaDose.R | 102 Luminescence-1.1.0/Luminescence/tests/testthat/test_use_DRAC.R | 10 Luminescence-1.1.0/Luminescence/tests/testthat/test_utils_DRAC.R | 9 Luminescence-1.1.0/Luminescence/tests/testthat/test_verify_SingleGrainData.R | 46 Luminescence-1.1.0/Luminescence/tests/testthat/test_write_R2TIFF.R | 7 325 files changed, 9149 insertions(+), 8131 deletions(-)
Title: Audiogram Scattergrams
Description: Creates pre- and post- intervention scattergrams based on audiometric data. These scattergrams are formatted for publication in Otology & Neurotology and other otolaryngology journals. For more details, see Gurgel et al (2012) <doi:10.1177/0194599812458401>, Oghalai and Jackler (2016) <doi:10.1177/0194599816638314>.
Author: Dorothy W. Pan [aut, cre],
John S. Oghalai [aut]
Maintainer: Dorothy W. Pan <dorothy.pan@med.usc.edu>
Diff between AudioScatter versions 0.1.0 dated 2025-06-05 and 1.1.0 dated 2025-06-11
AudioScatter-0.1.0/AudioScatter/R/AudioScatterV5.R |only AudioScatter-1.1.0/AudioScatter/DESCRIPTION | 8 +++--- AudioScatter-1.1.0/AudioScatter/MD5 | 20 +++++++++-------- AudioScatter-1.1.0/AudioScatter/NAMESPACE | 17 +++++++++++--- AudioScatter-1.1.0/AudioScatter/R/AudioScatterV6.R |only AudioScatter-1.1.0/AudioScatter/R/utils-pipe.R |only AudioScatter-1.1.0/AudioScatter/man/AudioData.Rd | 2 - AudioScatter-1.1.0/AudioScatter/man/CalcChange.Rd | 12 ++++------ AudioScatter-1.1.0/AudioScatter/man/SavePostScatter.Rd | 2 - AudioScatter-1.1.0/AudioScatter/man/SavePreScatter.Rd | 3 -- AudioScatter-1.1.0/AudioScatter/man/dTable.Rd | 6 ++--- AudioScatter-1.1.0/AudioScatter/man/dTablePost.Rd | 2 - AudioScatter-1.1.0/AudioScatter/man/pipe.Rd |only 13 files changed, 40 insertions(+), 32 deletions(-)
Title: High-Dimensional Mediation Analysis
Description: Allows to estimate and test high-dimensional mediation effects based on advanced mediator screening and penalized regression techniques. Methods used in the package refer to Zhang H, Zheng Y, Zhang Z, Gao T, Joyce B, Yoon G, Zhang W, Schwartz J, Just A, Colicino E, Vokonas P, Zhao L, Lv J, Baccarelli A, Hou L, Liu L. Estimating and Testing High-dimensional Mediation Effects in Epigenetic Studies. Bioinformatics. (2016) <doi:10.1093/bioinformatics/btw351>. PMID: 27357171.
Author: Yinan Zheng [aut, cre] ,
Haixiang Zhang [aut],
Lifang Hou [aut],
Lei Liu [aut, cph]
Maintainer: Yinan Zheng <y-zheng@northwestern.edu>
Diff between HIMA versions 2.3.1 dated 2025-01-27 and 2.3.2 dated 2025-06-11
DESCRIPTION | 12 +-- MD5 | 46 +++++------ NEWS.md | 4 + R/HIMA-package.R | 7 + R/hima.R | 113 ++++++++++++++++++----------- R/hima_classic.R | 49 ++++++------ R/hima_dblasso.R | 59 +++++++-------- R/hima_efficient.R | 106 +++++++++++++-------------- R/hima_microbiome.R | 61 +++++++++------ R/hima_quantile.R | 51 ++++++++----- R/hima_survival.R | 83 +++++++++++---------- README.md | 2 inst/doc/hima-vignette.R | 46 ++++++++--- inst/doc/hima-vignette.Rmd | 57 ++++++++++---- inst/doc/hima-vignette.html | 171 ++++++++++++++++++++++++++------------------ man/HIMA-package.Rd | 2 man/hima.Rd | 58 +++++++++----- man/hima_classic.Rd | 37 +++++---- man/hima_dblasso.Rd | 20 +++-- man/hima_efficient.Rd | 20 +++-- man/hima_microbiome.Rd | 27 +++++- man/hima_quantile.Rd | 18 +++- man/hima_survival.Rd | 22 +++-- vignettes/hima-vignette.Rmd | 57 ++++++++++---- 24 files changed, 691 insertions(+), 437 deletions(-)
Title: Spatio-Temporal Estimation and Prediction for Censored/Missing
Responses
Description: It estimates the parameters of spatio-temporal models with censored or missing data using the SAEM algorithm (Delyon et al., 1999). This algorithm is a stochastic approximation of the widely used EM algorithm and is particularly valuable for models in which the E-step lacks a closed-form expression. It also provides a function to compute the observed information matrix using the method developed by Louis (1982). To assess the performance of the fitted model, case-deletion diagnostics are provided.
Author: Larissa A. Matos [aut, cre] ,
Katherine L. Valeriano [aut] ,
Victor H. Lachos [ctb]
Maintainer: Larissa A. Matos <larissa.amatos@gmail.com>
Diff between StempCens versions 1.1.0 dated 2020-10-21 and 1.2.0 dated 2025-06-11
DESCRIPTION | 20 - MD5 | 51 +- NAMESPACE | 3 NEWS.md | 16 R/CovarianceM.R | 34 - R/CrossStempCens.R | 87 +---- R/DiagStempCens.R | 340 +++++++++---------- R/EffectiveRange.R | 2 R/EstStempCens.R | 723 ++++++++++++++++++++---------------------- R/PredStempCens.R | 118 ++---- R/RcppExports.R | 8 R/rStempCens.R |only R/utils_SpatioTemporal_Rcpp.R | 94 ++++- README.md | 185 +++++----- build/partial.rdb |binary inst/CITATION | 16 inst/REFERENCES.bib | 108 +++--- man/CovarianceM.Rd | 27 - man/CrossStempCens.Rd | 83 +--- man/DiagStempCens.Rd | 59 +-- man/EstStempCens.Rd | 81 +--- man/PredStempCens.Rd | 87 +---- man/figures |only man/rnStempCens.Rd |only src/Functions_Rcpp.cpp | 89 +++-- src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 29 + 28 files changed, 1109 insertions(+), 1153 deletions(-)
Title: Multiverse Analyses for Conditioning Data
Description: A suite of functions for performing analyses, based on a multiverse approach, for conditioning data. Specifically, given the appropriate data, the functions are able to perform t-tests, analyses of variance, and mixed models for the provided data and return summary statistics and plots. The function is also able to return for all those tests p-values, confidence intervals, and Bayes factors. The methods are described in Lonsdorf, Gerlicher, Klingelhofer-Jens, & Krypotos (2022) <doi:10.1016/j.brat.2022.104072>.
Author: Angelos-Miltiadis Krypotos [aut, cre, cph]
Maintainer: Angelos-Miltiadis Krypotos <amkrypotos@gmail.com>
Diff between multifear versions 0.1.3 dated 2023-09-23 and 0.1.4 dated 2025-06-11
DESCRIPTION | 21 ++++++++------- MD5 | 40 ++++++++++++++++++------------ NEWS.md | 6 ++++ R/bt_test_mf.R | 8 +++--- R/chop_cs.R | 4 +-- R/chop_css.R | 2 - R/combine_cs.R | 4 +-- R/internal.R | 38 ++++++++++++++-------------- R/t_test_mf.R | 19 +++++++------- R/utils.R | 1 README.md | 37 ++++++++++++++------------- build/vignette.rds |binary inst/WORDLIST |only inst/doc/internals.R | 4 +-- inst/doc/internals.Rmd | 2 - inst/doc/internals.html | 4 +-- man/figures/README |only man/figures/README-unnamed-chunk-14-1.png |only man/figures/README-unnamed-chunk-15-1.png |only man/figures/README-unnamed-chunk-17-1.png |only man/figures/README-unnamed-chunk-18-1.png |only man/figures/README-unnamed-chunk-8-1.png |only tests/spelling.R |only tests/testthat/test.output.R | 31 ++++++++++------------- vignettes/internals.Rmd | 2 - 25 files changed, 119 insertions(+), 104 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to a three-way or four-way data array. See Harshman and Lundy (1994): <doi:10.1016/0167-9473(94)90132-5>. Uses component weights from one mode of a Parafac or Parafac2 model as features to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Allows for constraints on different tensor modes. Supports penalized logistic regression, support vector machine, random forest, feed-forward neural network, regularized discriminant analysis, and gradient boosting machine. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Implements parallel computing via the 'parallel' and 'doParallel' packages.
Author: Matthew A. Snodgress [aut, cre]
Maintainer: Matthew A. Snodgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.1-9 dated 2025-05-23 and 1.2-0 dated 2025-06-11
ChangeLog | 20 ++++++++++++++++---- DESCRIPTION | 10 ++++++---- MD5 | 15 ++++++++++----- R/cpfa.R | 8 ++++---- R/predict.tunecpfa.R | 2 +- R/print.tunecpfa.R | 11 ++++------- build |only inst |only vignettes |only 9 files changed, 41 insertions(+), 25 deletions(-)
Title: Clinical Trial Simulation
Description: Provides some basic routines for simulating a
clinical trial. The primary intent is to provide some tools to
generate trial simulations for trials with time to event outcomes.
Piecewise exponential failure rates and piecewise constant
enrollment rates are the underlying mechanism used to simulate
a broad range of scenarios such as those presented in
Lin et al. (2020) <doi:10.1080/19466315.2019.1697738>.
However, the basic generation of data is done using pipes to allow
maximum flexibility for users to meet different needs.
Author: Keaven Anderson [aut],
Yujie Zhao [aut, cre],
John Blischak [aut],
Nan Xiao [ctb],
Yilong Zhang [aut],
Jianxiao Yang [ctb],
Lili Ling [ctb],
Xintong Li [ctb],
Ruixue Wang [ctb],
Yi Cui [ctb],
Ping Yang [ctb],
Yalin Zhu [ctb],
Heng Zhou [ctb],
Amin Sh [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between simtrial versions 0.4.2 dated 2024-11-18 and 1.0.0 dated 2025-06-11
DESCRIPTION | 24 - MD5 | 140 ++++---- NAMESPACE | 4 NEWS.md | 26 + R/as_gt.R | 2 R/check_args.R | 2 R/counting_process.R | 21 - R/cut_data_by_date.R | 7 R/cut_data_by_event.R | 9 R/early_zero_weight.R | 2 R/ex1_delayed_effect.R | 2 R/ex2_delayed_effect.R | 2 R/ex3_cure_with_ph.R | 2 R/ex4_belly.R | 2 R/ex5_widening.R | 2 R/ex6_crossing.R | 2 R/fh_weight.R | 2 R/fit_pwexp.R | 2 R/get_analysis_date.R | 2 R/get_cut_date_by_event.R | 2 R/global.R | 2 R/input_checking.R | 2 R/maxcombo.R | 2 R/mb_delayed_effect.R | 2 R/mb_weight.R | 2 R/milestone.R | 2 R/pvalue_maxcombo.R | 2 R/randomize_by_fixed_block.R | 2 R/rmst.R | 5 R/rpwexp.R | 2 R/rpwexp_enroll.R | 2 R/rpwexp_naive.R | 2 R/sim_fixed_n.R | 9 R/sim_gs_n.R | 123 +++++++ R/sim_pw_surv.R | 16 - R/simtrial-package.R | 2 R/summary.R | 2 R/to_sim_pw_surv.R | 2 R/wlr.R | 59 +++ R/wlr_weight.R | 2 build/vignette.rds |binary inst/doc/arbitrary-hazard.html | 10 inst/doc/discrepancy-between-simtrial-and-survival.R |only inst/doc/discrepancy-between-simtrial-and-survival.Rmd |only inst/doc/discrepancy-between-simtrial-and-survival.html |only inst/doc/maxcombo.html | 251 ++++++++-------- inst/doc/modest-wlrt.html | 11 inst/doc/parallel.R | 47 +- inst/doc/parallel.Rmd | 70 +++- inst/doc/parallel.html | 232 ++++++++------ inst/doc/rmst.html | 7 inst/doc/routines.html | 6 inst/doc/sim_fixed_design_custom.R |only inst/doc/sim_fixed_design_custom.Rmd |only inst/doc/sim_fixed_design_custom.html |only inst/doc/sim_fixed_design_simple.R |only inst/doc/sim_fixed_design_simple.Rmd |only inst/doc/sim_fixed_design_simple.html |only inst/doc/sim_gs_design_simple.R |only inst/doc/sim_gs_design_simple.Rmd |only inst/doc/sim_gs_design_simple.html |only inst/doc/workflow.html | 2 man/counting_process.Rd | 17 - man/cut_data_by_date.Rd | 5 man/cut_data_by_event.Rd | 6 man/sim_gs_n.Rd | 57 +++ man/sim_pw_surv.Rd | 14 man/simtrial-package.Rd | 5 man/wlr.Rd | 33 +- tests/testthat/test-independent_test_fh_weight.R | 6 tests/testthat/test-independent_test_pvalue_maxcombo.R | 4 tests/testthat/test-unvalidated-sim_gs_n.R | 99 ++++++ tests/testthat/test-unvalidated-summary.R | 4 tests/testthat/test-unvalidated-wlr.R | 140 ++++++++ vignettes/discrepancy-between-simtrial-and-survival.Rmd |only vignettes/parallel.Rmd | 70 +++- vignettes/sim_fixed_design_custom.Rmd |only vignettes/sim_fixed_design_simple.Rmd |only vignettes/sim_gs_design_simple.Rmd |only 79 files changed, 1121 insertions(+), 474 deletions(-)
Title: Create Tibbles and Lists of 'ggplot' Figures for Reporting
Description: Create tibbles and lists of 'ggplot' figures that can be modified as easily as
regular 'ggplot' figures. Typical use cases are for creating reports or web
pages where many figures are needed with different data and similar
formatting.
Author: Bill Denney [aut, cre]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between ggtibble versions 1.0.1 dated 2024-06-19 and 1.0.2 dated 2025-06-11
DESCRIPTION | 18 +++--- MD5 | 32 +++++++---- NAMESPACE | 10 +++ NEWS.md | 13 ++++ R/extract_glue_expr.R |only R/gglist.R | 17 +++++- R/ggsave.R |only R/ggtibble.R | 15 +++++ R/percent_plus.R |only README.md | 6 +- build/vignette.rds |binary inst/WORDLIST | 11 +++- inst/doc/v01-introduction.html | 71 +++++++++++++------------- man/extract_glue_expr.Rd |only man/ggsave.Rd |only man/grapes-plus-grapes.Rd |only man/knit_print.gg.Rd | 87 ++++++++++++++++---------------- tests/testthat/test-extract_glue_expr.R |only tests/testthat/test-gglist.R | 12 ++++ tests/testthat/test-ggsave.R |only tests/testthat/test-ggtibble.R | 50 +++++++++++++++++- 21 files changed, 238 insertions(+), 104 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: The standard linear regression theory whether frequentist or Bayesian is based on an 'assumed (revealed?) truth' (John Tukey) attitude to models. This is reflected in the language of statistical inference which involves a concept of truth, for example confidence intervals, hypothesis testing and consistency. The motivation behind this package was to remove the word true from the theory and practice of linear regression and to replace it by approximation. The approximations considered are the least squares approximations. An approximation is called valid if it contains no irrelevant covariates. This is operationalized using the concept of a Gaussian P-value which is the probability that pure Gaussian noise is better in term of least squares than the covariate. The precise definition given in the paper "An Approximation Based Theory of Linear Regression". Only four simple equations are required. Moreover the Gaussian P-values can be simply derived from standard F P-values. Furthermore [...truncated...]
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <pldavies44@cantab.net>
Diff between gausscov versions 1.1.5 dated 2025-02-23 and 1.1.6 dated 2025-06-11
gausscov-1.1.5/gausscov/R/simgpval.R |only gausscov-1.1.5/gausscov/man/simgpval.Rd |only gausscov-1.1.6/gausscov/DESCRIPTION | 10 - gausscov-1.1.6/gausscov/MD5 | 26 +++-- gausscov-1.1.6/gausscov/R/f1bsf.R |only gausscov-1.1.6/gausscov/R/f1st.R | 42 +------- gausscov-1.1.6/gausscov/R/fasb.R | 18 +-- gausscov-1.1.6/gausscov/R/fgenbsf.R |only gausscov-1.1.6/gausscov/R/fgr1st.R | 2 gausscov-1.1.6/gausscov/R/fpval.R | 2 gausscov-1.1.6/gausscov/data/lymphoma.rda |only gausscov-1.1.6/gausscov/data/m15005m.rda |only gausscov-1.1.6/gausscov/man/f1bsf.Rd |only gausscov-1.1.6/gausscov/man/f1st.Rd | 1 gausscov-1.1.6/gausscov/man/fgenbsf.Rd |only gausscov-1.1.6/gausscov/man/lymphoma.Rd |only gausscov-1.1.6/gausscov/man/m15005m.Rd |only gausscov-1.1.6/gausscov/src/gaucov.f | 155 +++++++++++++++++++++++++++++- gausscov-1.1.6/gausscov/src/init.c | 12 +- 19 files changed, 200 insertions(+), 68 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385>, Wilson (2025) <DOI:10.1002/mrm.30462> and
spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 3.3.0 dated 2025-03-28 and 3.4.0 dated 2025-06-11
DESCRIPTION | 15 ++-- MD5 | 31 +++++---- NAMESPACE | 2 NEWS.md | 4 + R/fit_svs.R | 12 +-- R/mrs_data_proc.R | 35 ++++++++++- R/mrs_read_ima.R | 13 +++- R/rats.R | 19 ++++-- R/utils.R | 46 ++++++++++++++ inst/CITATION | 16 ++++- inst/doc/spant-intro.html | 120 +++++++++++++++++++------------------- inst/doc/spant-preprocessing.html | 4 - inst/rmd/svs_edited_report.Rmd | 8 +- inst/rmd/svs_report.Rmd | 8 +- man/rats.Rd | 5 + man/read_dkd_moco_log.Rd |only man/sd.Rd | 5 + 17 files changed, 238 insertions(+), 105 deletions(-)
Title: Multivariate ANalysis of VAriance with Ridge Regularization for
Semicontinuous High-Dimensional Data
Description: Implements Multivariate ANalysis Of VAriance (MANOVA) parameters' inference and test with regularization for semicontinuous high-dimensional data. The method can be applied also in presence of low-dimensional data. The p-value can be obtained through asymptotic distribution or using a permutation procedure. The package gives also the possibility to simulate this type of data. Method is described in Elena Sabbioni, Claudio Agostinelli and Alessio Farcomeni (2025) A regularized MANOVA test for semicontinuous high-dimensional data. Biometrical Journal, 67:e70054. DOI <doi:10.1002/bimj.70054>, arXiv DOI <doi:10.48550/arXiv.2401.04036>.
Author: Elena Sabbioni [aut, cre] ,
Claudio Agostinelli [aut] ,
Alessio Farcomeni [aut]
Maintainer: Elena Sabbioni <elena.sabbioni@stats.ox.ac.uk>
Diff between semicontMANOVA versions 0.1-8 dated 2024-01-10 and 0.2 dated 2025-06-11
DESCRIPTION | 23 +++-- MD5 | 18 ++-- R/scMANOVA.R | 17 ++-- R/scMANOVA_H1.R | 177 ++++++++++++++++++++++++++++++---------------- R/scMANOVAestimation.R | 9 +- R/scMANOVApermTest.R | 36 ++------- man/scMANOVA.Rd | 15 ++- man/scMANOVAestimation.Rd | 6 + man/scMANOVApermTest.Rd | 6 + man/scMANOVAsimulation.Rd | 6 + 10 files changed, 190 insertions(+), 123 deletions(-)
More information about semicontMANOVA at CRAN
Permanent link
Title: Causal Inference with Super Learner and Deep Neural Networks
Description: Functions to estimate Conditional Average Treatment Effects (CATE)
and Population Average Treatment Effects on the Treated (PATT) from
experimental or observational data using the Super Learner (SL) ensemble
method and Deep neural networks. The package first provides functions to
implement meta-learners such as the Single-learner (S-learner) and
Two-learner (T-learner) described in KC<nzel et al. (2019)
<doi:10.1073/pnas.1804597116> for estimating the CATE. The S- and T-learner
are each estimated using the SL ensemble method and deep neural networks. It
then provides functions to implement the Ottoboni and Poulos (2020)
<doi:10.1515/jci-2018-0035> PATT-C estimator to obtain the PATT from
experimental data with noncompliance by using the SL ensemble method and
deep neural networks.
Author: Nguyen K. Huynh [aut, cre] ,
Bumba Mukherjee [aut] ,
Yang Yang [aut]
Maintainer: Nguyen K. Huynh <khoinguyen.huynh@r.hit-u.ac.jp>
Diff between DeepLearningCausal versions 0.0.104 dated 2024-07-29 and 0.0.106 dated 2025-06-11
DESCRIPTION | 32 - MD5 | 19 - NAMESPACE | 73 ++-- R/global.R |only R/meta_learners.R | 645 +++++++++++++++++++++++++++---------- R/neural_meta_learners.R | 538 +++++++++++++++++++++++------- R/plots.R |only man/hte_plot.Rd |only man/metalearner_deepneural.Rd | 208 ++++++----- man/metalearner_ensemble.Rd | 178 +++++----- man/plot.metalearner_deepneural.Rd |only man/plot.metalearner_ensemble.Rd |only man/plot.pattc_deepneural.Rd |only man/plot.pattc_ensemble.Rd |only 14 files changed, 1174 insertions(+), 519 deletions(-)
More information about DeepLearningCausal at CRAN
Permanent link
Title: Clustering of Datasets
Description: Hierarchical and partitioning algorithms to cluster blocks of variables. The partitioning algorithm includes an option called noise cluster to set aside atypical blocks of variables. Different thresholds per cluster can be sets. The CLUSTATIS method (for quantitative blocks) (Llobell, Cariou, Vigneau, Labenne & Qannari (2020) <doi:10.1016/j.foodqual.2018.05.013>, Llobell, Vigneau & Qannari (2019) <doi:10.1016/j.foodqual.2019.02.017>) and the CLUSCATA method (for Check-All-That-Apply data) (Llobell, Cariou, Vigneau, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2018.09.006>, Llobell, Giacalone, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2019.05.017>) are the core of this package. The CATATIS methods allows to compute some indices and tests to control the quality of CATA data. Multivariate analysis and clustering of subjects for quantitative multiblock data, CATA, RATA, Free Sorting and JAR experiments are available. Clustering of rows in [...truncated...]
Author: Fabien Llobell [aut, cre] ,
Evelyne Vigneau [ctb] ,
Veronique Cariou [ctb] ,
El Mostafa Qannari [ctb]
Maintainer: Fabien Llobell <fabienllobellresearch@gmail.com>
Diff between ClustBlock versions 4.1.0 dated 2025-05-13 and 4.1.1 dated 2025-06-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 8 ++------ R/cluscata.R | 7 +------ R/clustatis.R | 7 +------ inst/CITATION | 4 ++-- man/ClustBlock-package.Rd | 4 ++-- 7 files changed, 18 insertions(+), 32 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007) (temporarily unavailable)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8. [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.8 dated 2025-04-30 and 1.0.9 dated 2025-06-11
modsem-1.0.8/modsem/R/est_h0_da.R |only modsem-1.0.9/modsem/DESCRIPTION | 15 modsem-1.0.9/modsem/MD5 | 143 ++-- modsem-1.0.9/modsem/NAMESPACE | 7 modsem-1.0.9/modsem/R/calc_se_da.R | 62 + modsem-1.0.9/modsem/R/check_model_da.R | 27 modsem-1.0.9/modsem/R/compare_fit.R |only modsem-1.0.9/modsem/R/equations_lms.R | 78 +- modsem-1.0.9/modsem/R/est_h0.R |only modsem-1.0.9/modsem/R/est_lms.R | 316 +++++++-- modsem-1.0.9/modsem/R/est_qml.R | 4 modsem-1.0.9/modsem/R/generics.R | 90 +- modsem-1.0.9/modsem/R/generics_modsem_da.R | 382 +++++++++--- modsem-1.0.9/modsem/R/generics_modsem_mplus.R | 7 modsem-1.0.9/modsem/R/generics_modsem_pi.R | 173 +++++ modsem-1.0.9/modsem/R/inspect_da.R | 2 modsem-1.0.9/modsem/R/labelled_params_da.R | 38 + modsem-1.0.9/modsem/R/lms_observed_ll.R |only modsem-1.0.9/modsem/R/method_settings_da.R | 28 modsem-1.0.9/modsem/R/model_da.R | 25 modsem-1.0.9/modsem/R/model_parameters_da.R | 14 modsem-1.0.9/modsem/R/modsem_da.R | 78 +- modsem-1.0.9/modsem/R/modsem_mplus.R | 31 modsem-1.0.9/modsem/R/modsem_pi.R | 201 +++++- modsem-1.0.9/modsem/R/plot_interaction.R | 24 modsem-1.0.9/modsem/R/print_partable.R | 2 modsem-1.0.9/modsem/R/quadrature.R | 277 ++++++++ modsem-1.0.9/modsem/R/simple_slopes.R | 221 +++++- modsem-1.0.9/modsem/R/standardize_model.R |only modsem-1.0.9/modsem/R/tokenizer.R | 10 modsem-1.0.9/modsem/R/trace_paths_wright.R | 53 + modsem-1.0.9/modsem/R/utils.R | 81 ++ modsem-1.0.9/modsem/R/utils_da.R | 70 ++ modsem-1.0.9/modsem/build/vignette.rds |binary modsem-1.0.9/modsem/inst/doc/customizing.R | 13 modsem-1.0.9/modsem/inst/doc/customizing.Rmd | 18 modsem-1.0.9/modsem/inst/doc/customizing.html | 12 modsem-1.0.9/modsem/inst/doc/estimation_lms.R |only modsem-1.0.9/modsem/inst/doc/estimation_lms.Rmd |only modsem-1.0.9/modsem/inst/doc/estimation_lms.html |only modsem-1.0.9/modsem/inst/doc/fit_measures_da.R | 2 modsem-1.0.9/modsem/inst/doc/fit_measures_da.Rmd | 10 modsem-1.0.9/modsem/inst/doc/fit_measures_da.html | 10 modsem-1.0.9/modsem/inst/doc/lms_qml.R | 9 modsem-1.0.9/modsem/inst/doc/lms_qml.Rmd | 13 modsem-1.0.9/modsem/inst/doc/lms_qml.html | 25 modsem-1.0.9/modsem/inst/doc/observed_lms_qml.html | 308 ++++----- modsem-1.0.9/modsem/inst/doc/plot_interactions.html | 2 modsem-1.0.9/modsem/inst/doc/quadratic.Rmd | 2 modsem-1.0.9/modsem/inst/doc/quadratic.html | 2 modsem-1.0.9/modsem/inst/doc/simple_slopes.R | 4 modsem-1.0.9/modsem/inst/doc/simple_slopes.Rmd | 22 modsem-1.0.9/modsem/inst/doc/simple_slopes.html | 8 modsem-1.0.9/modsem/man/compare_fit.Rd | 41 - modsem-1.0.9/modsem/man/estimate_h0.Rd | 21 modsem-1.0.9/modsem/man/modsem_da.Rd | 42 + modsem-1.0.9/modsem/man/modsem_mplus.Rd | 21 modsem-1.0.9/modsem/man/modsem_pi.Rd | 11 modsem-1.0.9/modsem/man/plot_interaction.Rd | 3 modsem-1.0.9/modsem/man/plot_jn.Rd | 3 modsem-1.0.9/modsem/man/plot_surface.Rd | 3 modsem-1.0.9/modsem/man/simple_slopes.Rd | 3 modsem-1.0.9/modsem/man/standardize_model.Rd |only modsem-1.0.9/modsem/man/standardized_estimates.modsem_da.Rd |only modsem-1.0.9/modsem/man/summary.Rd | 19 modsem-1.0.9/modsem/man/trace_path.Rd | 3 modsem-1.0.9/modsem/tests/testthat/test_adaptive_quad.R |only modsem-1.0.9/modsem/tests/testthat/test_cluster.R |only modsem-1.0.9/modsem/tests/testthat/test_h0.R | 16 modsem-1.0.9/modsem/tests/testthat/test_lav_models.R | 8 modsem-1.0.9/modsem/tests/testthat/test_lms.R | 57 + modsem-1.0.9/modsem/tests/testthat/test_qml.R | 44 - modsem-1.0.9/modsem/tests/testthat/test_quadratic_effects.R | 6 modsem-1.0.9/modsem/vignettes/customizing.Rmd | 18 modsem-1.0.9/modsem/vignettes/estimation_lms.Rmd |only modsem-1.0.9/modsem/vignettes/fit_measures_da.Rmd | 10 modsem-1.0.9/modsem/vignettes/lms_qml.Rmd | 13 modsem-1.0.9/modsem/vignettes/quadratic.Rmd | 2 modsem-1.0.9/modsem/vignettes/simple_slopes.Rmd | 22 79 files changed, 2512 insertions(+), 773 deletions(-)
Title: Dungeons & Dragons Functions for Players and Dungeon Masters
Description: The goal of 'dndR' is to provide a suite of Dungeons & Dragons related functions.
This package is meant to be useful both to players and Dungeon Masters (DMs).
Some functions apply to many tabletop role-playing games (e.g., dice rolling), but others are focused on Fifth Edition (a.k.a. "5e") and where possible both the 2014 and 2024 versions are supported.
Author: Nicholas Lyon [aut, cre, cph] ,
Tim Schatto-Eckrodt [aut] ,
Humberto Nappo [aut] ,
Billy Mitchell [aut]
Maintainer: Nicholas Lyon <njlyon@alumni.iastate.edu>
Diff between dndR versions 3.0.0 dated 2025-04-02 and 3.1.0 dated 2025-06-11
DESCRIPTION | 26 +- MD5 | 63 ++--- NAMESPACE | 3 NEWS.md | 7 R/data-doc_creatures.R | 2 R/encounter_creator.R | 26 +- R/npc_creator.R | 64 ++++- R/reference_functions.R | 367 ++++++++++++++++++++++++++++++++- R/xp_pool.R | 2 README.md | 22 - inst/doc/dndr_00_dice.html | 13 - inst/doc/dndr_01_characters.Rmd | 4 inst/doc/dndr_01_characters.html | 42 +-- inst/doc/dndr_02_creatures.html | 32 +- inst/doc/dndr_04_encounters.R | 11 inst/doc/dndr_04_encounters.Rmd | 11 inst/doc/dndr_04_encounters.html | 27 +- inst/doc/dndr_05_visuals.html | 6 inst/doc/dndr_99_dmg-vs-dndr.R | 2 inst/doc/dndr_99_dmg-vs-dndr.Rmd | 2 inst/doc/dndr_99_dmg-vs-dndr.html | 4 man/creatures.Rd | 2 man/dndR-package.Rd | 9 man/encounter_creator.Rd | 4 man/first_names_fem.Rd |only man/first_names_masc.Rd |only man/npc_creator.Rd | 6 man/surnames.Rd |only man/xp_pool.Rd | 2 tests/testthat/test-party_diagram.R | 2 tests/testthat/test-probability_plot.R | 2 vignettes/dndr_01_characters.Rmd | 4 vignettes/dndr_04_encounters.Rmd | 11 vignettes/dndr_99_dmg-vs-dndr.Rmd | 2 34 files changed, 587 insertions(+), 193 deletions(-)
Title: Spatial Constrained Clusterwise Regression
Description: A collection of functions for estimating spatial regimes, aggregations of neighboring spatial units that are homogeneous in functional terms. The term spatial regime, therefore, should not be understood as a synonym for cluster. More precisely, the term cluster does not presuppose any functional relationship between the variables considered, while the term regime is linked to a regressive relationship underlying the spatial process.
Author: Francesco Vidoli [aut, cre],
Roberto Benedetti [aut]
Maintainer: Francesco Vidoli <fvidoli@gmail.com>
Diff between SpatialRegimes versions 1.1 dated 2022-09-30 and 1.2 dated 2025-06-11
DESCRIPTION | 18 +++++++++++++----- MD5 | 10 +++++----- NEWS | 7 +++++++ R/sswf.R | 7 +++++++ build/vignette.rds |binary man/SkaterF.Rd | 6 ++++-- 6 files changed, 36 insertions(+), 12 deletions(-)
More information about SpatialRegimes at CRAN
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Title: Functional Profile Chain Ladder for Claims Reserving
Description: Functional claims reserving methods based on aggregated chain-ladder data, also known as the run-off triangle (functional) development profiles, implemented in three nonparametric algorithms (PARALLAX, REACT, and MACRAME) proposed in Maciak, Mizera, and Pešta (2022) <doi:10.1017/asb.2022.4>.
Author: Matus Maciak [aut, cre],
Rastislav Matus [ctb],
Ivan Mizera [aut],
Michal Pesta [aut]
Maintainer: Matus Maciak <maciak@karlin.mff.cuni.cz>
Diff between ProfileLadder versions 0.1.1 dated 2025-04-30 and 0.1.2 dated 2025-06-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/summary.profileLadder.R | 5 +++++ README.md | 18 ++++++++++++++++-- 4 files changed, 28 insertions(+), 9 deletions(-)
Title: Detection of Multiple Changes in Slope in Univariate Time-Series
Description: Detects multiple changes in slope using the CPOP dynamic programming approach of Fearnhead, Maidstone, and Letchford (2019) <doi:10.1080/10618600.2018.1512868>. This method finds the best continuous piecewise linear fit to data under a criterion that measures fit to data using the residual sum of squares, but penalizes complexity based on an L0 penalty on changes in slope. Further information regarding the use of this package with detailed examples can be found in Fearnhead and Grose (2024) <doi:10.18637/jss.v109.i07>.
Author: Daniel Grose [aut, cre],
Paul Fearnhead [aut]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between cpop versions 1.0.7 dated 2024-05-28 and 1.0.8 dated 2025-06-11
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/cpop.R | 7 +++++++ build/cpop.pdf |binary build/partial.rdb |binary build/stage23.rdb |binary 7 files changed, 23 insertions(+), 11 deletions(-)
Title: Draw Flows (Migration, Goods, Money, Information) on 'ggplot2'
Plots
Description: Adds flow maps to 'ggplot2' plots. The flow maps consist of 'ggplot2' layers which visualize the nodes as circles and the bilateral flows between the nodes as bidirectional half-arrows.
Author: Johannes Mast [aut, cre]
Maintainer: Johannes Mast <johannes.mast@dlr.de>
Diff between flowmapper versions 0.1.3 dated 2024-11-15 and 0.1.4 dated 2025-06-11
DESCRIPTION | 16 +- MD5 | 20 ++ NAMESPACE | 5 NEWS.md | 6 R/add_flowmap.R | 319 ++++------------------------------------------ R/add_flowmap_list.R |only R/flowmap_sf.R |only R/flowmapper-package.R |only R/hca_flowdat.R | 12 + R/prep_flowmap.R |only man/add_flowmap_list.Rd |only man/flowmap_sf.Rd |only man/flowmapper-package.Rd |only man/hca_flowdat.Rd | 4 man/prep_flowmap.Rd |only 15 files changed, 73 insertions(+), 309 deletions(-)
More information about alternativeROC at CRAN
Permanent link
Title: Compensation Analysis Tool for Instructor Overload Pay
Description: Calculates equitable overload compensation for college instructors
based on institutional policies, enrollment thresholds, and regular teaching load limits.
Compensation is awarded only for credit hours that exceed the regular load and meet
minimum enrollment criteria. When enrollment is below a specified threshold, pay is
prorated accordingly. The package prioritizes compensation from high-enrollment courses,
or optionally from low-enrollment courses for fairness, depending on user-defined strategy.
Includes tools for flexible policy settings, instructor filtering, and produces
clean, audit-ready summary tables suitable for payroll and administrative reporting.
Author: Dawit Aberra [aut, cre]
Maintainer: Dawit Aberra <dawit3000@hotmail.com>
Diff between catool versions 1.0.0 dated 2025-06-06 and 1.0.1 dated 2025-06-11
DESCRIPTION | 7 - MD5 | 24 ++-- R/filter_schedule.R | 164 ++++++++++++++++--------------- R/get_unique_instructors.R | 40 +++---- R/globals.R | 24 +--- R/ol_comp.R | 49 +++------ R/ol_comp_byindex.R | 120 +++++++++++----------- R/ol_comp_summary.R | 19 +-- README.md | 38 +++---- inst/doc/catool-walkthrough.Rmd | 35 +++++- inst/doc/catool-walkthrough.html | 73 ++++++++++++- tests/testthat/test-calculate_overload.R | 6 - vignettes/catool-walkthrough.Rmd | 35 +++++- 13 files changed, 368 insertions(+), 266 deletions(-)
Title: Read and Manipulate Camera Trap Data Packages
Description: Read and manipulate Camera Trap Data Packages ('Camtrap DP').
'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a data exchange format
for camera trap data. With 'camtrapdp' you can read, filter and
transform data (including to Darwin Core) before further analysis in
e.g. 'camtraptor' or 'camtrapR'.
Author: Peter Desmet [aut, cre] ),
Sanne Govaert [aut] ),
Pieter Huybrechts [aut] ),
Damiano Oldoni [aut] ),
Research Institute for Nature and Forest [cph] ,
Research Foundation - Flanders [fnd]
Maintainer: Peter Desmet <peter.desmet@inbo.be>
Diff between camtrapdp versions 0.3.1 dated 2024-07-05 and 0.4.0 dated 2025-06-11
camtrapdp-0.3.1/camtrapdp/R/build_taxonomy.R |only camtrapdp-0.3.1/camtrapdp/R/convert.R |only camtrapdp-0.3.1/camtrapdp/tests/testthat/test-build_taxonomy.R |only camtrapdp-0.4.0/camtrapdp/DESCRIPTION | 38 +- camtrapdp-0.4.0/camtrapdp/MD5 | 146 +++++---- camtrapdp-0.4.0/camtrapdp/NAMESPACE | 10 camtrapdp-0.4.0/camtrapdp/NEWS.md | 34 ++ camtrapdp-0.4.0/camtrapdp/R/camtrapdp-package.R | 1 camtrapdp-0.4.0/camtrapdp/R/check_camtrapdp.R | 5 camtrapdp-0.4.0/camtrapdp/R/contributors.R |only camtrapdp-0.4.0/camtrapdp/R/deployments.R | 19 - camtrapdp-0.4.0/camtrapdp/R/events.R | 4 camtrapdp-0.4.0/camtrapdp/R/example_dataset.R | 2 camtrapdp-0.4.0/camtrapdp/R/filter_deployments.R | 5 camtrapdp-0.4.0/camtrapdp/R/filter_media.R | 4 camtrapdp-0.4.0/camtrapdp/R/filter_observations.R | 14 camtrapdp-0.4.0/camtrapdp/R/individuals.R |only camtrapdp-0.4.0/camtrapdp/R/locations.R | 4 camtrapdp-0.4.0/camtrapdp/R/media.R | 8 camtrapdp-0.4.0/camtrapdp/R/merge_camtrapdp.R |only camtrapdp-0.4.0/camtrapdp/R/observations.R | 16 - camtrapdp-0.4.0/camtrapdp/R/print.R | 21 - camtrapdp-0.4.0/camtrapdp/R/read_camtrapdp.R | 114 +++++-- camtrapdp-0.4.0/camtrapdp/R/round_coordinates.R |only camtrapdp-0.4.0/camtrapdp/R/shift_time.R |only camtrapdp-0.4.0/camtrapdp/R/taxa.R | 50 +++ camtrapdp-0.4.0/camtrapdp/R/taxonomic.R |only camtrapdp-0.4.0/camtrapdp/R/update_metadata.R |only camtrapdp-0.4.0/camtrapdp/R/update_taxon.R |only camtrapdp-0.4.0/camtrapdp/R/upgrade.R |only camtrapdp-0.4.0/camtrapdp/R/utils-merge.R |only camtrapdp-0.4.0/camtrapdp/R/utils.R |only camtrapdp-0.4.0/camtrapdp/R/version.R | 33 +- camtrapdp-0.4.0/camtrapdp/R/write_camtrapdp.R |only camtrapdp-0.4.0/camtrapdp/R/write_dwc.R | 151 ++++++---- camtrapdp-0.4.0/camtrapdp/R/write_eml.R |only camtrapdp-0.4.0/camtrapdp/README.md | 19 - camtrapdp-0.4.0/camtrapdp/build/partial.rdb |binary camtrapdp-0.4.0/camtrapdp/inst/extdata/meta.xml | 9 camtrapdp-0.4.0/camtrapdp/man/camtrapdp-package.Rd | 4 camtrapdp-0.4.0/camtrapdp/man/check_camtrapdp.Rd | 5 camtrapdp-0.4.0/camtrapdp/man/contributors.Rd |only camtrapdp-0.4.0/camtrapdp/man/deployments.Rd | 14 camtrapdp-0.4.0/camtrapdp/man/events.Rd | 8 camtrapdp-0.4.0/camtrapdp/man/filter_deployments.Rd | 6 camtrapdp-0.4.0/camtrapdp/man/filter_media.Rd | 5 camtrapdp-0.4.0/camtrapdp/man/filter_observations.Rd | 15 camtrapdp-0.4.0/camtrapdp/man/individuals.Rd |only camtrapdp-0.4.0/camtrapdp/man/locations.Rd | 8 camtrapdp-0.4.0/camtrapdp/man/media.Rd | 12 camtrapdp-0.4.0/camtrapdp/man/merge_camtrapdp.Rd |only camtrapdp-0.4.0/camtrapdp/man/observations.Rd | 15 camtrapdp-0.4.0/camtrapdp/man/print.camtrapdp.Rd | 2 camtrapdp-0.4.0/camtrapdp/man/read_camtrapdp.Rd | 71 +++- camtrapdp-0.4.0/camtrapdp/man/round_coordinates.Rd |only camtrapdp-0.4.0/camtrapdp/man/shift_time.Rd |only camtrapdp-0.4.0/camtrapdp/man/taxa.Rd | 11 camtrapdp-0.4.0/camtrapdp/man/update_taxon.Rd |only camtrapdp-0.4.0/camtrapdp/man/version.Rd | 4 camtrapdp-0.4.0/camtrapdp/man/write_camtrapdp.Rd |only camtrapdp-0.4.0/camtrapdp/man/write_dwc.Rd | 41 +- camtrapdp-0.4.0/camtrapdp/man/write_eml.Rd |only camtrapdp-0.4.0/camtrapdp/tests/testthat.R | 2 camtrapdp-0.4.0/camtrapdp/tests/testthat/_snaps/merge_camtrapdp |only camtrapdp-0.4.0/camtrapdp/tests/testthat/_snaps/write_dwc/meta.xml | 9 camtrapdp-0.4.0/camtrapdp/tests/testthat/_snaps/write_dwc/multimedia.csv | 20 - camtrapdp-0.4.0/camtrapdp/tests/testthat/_snaps/write_dwc/multimedia_media_based.csv |only camtrapdp-0.4.0/camtrapdp/tests/testthat/_snaps/write_dwc/occurrence.csv | 60 +-- camtrapdp-0.4.0/camtrapdp/tests/testthat/_snaps/write_dwc/occurrence_media_based.csv |only camtrapdp-0.4.0/camtrapdp/tests/testthat/_snaps/write_eml |only camtrapdp-0.4.0/camtrapdp/tests/testthat/helper.R | 25 + camtrapdp-0.4.0/camtrapdp/tests/testthat/test-contributors.R |only camtrapdp-0.4.0/camtrapdp/tests/testthat/test-deployments.R | 38 ++ camtrapdp-0.4.0/camtrapdp/tests/testthat/test-example_dataset.R | 8 camtrapdp-0.4.0/camtrapdp/tests/testthat/test-filter_deployments.R | 44 ++ camtrapdp-0.4.0/camtrapdp/tests/testthat/test-filter_media.R | 49 +++ camtrapdp-0.4.0/camtrapdp/tests/testthat/test-filter_observations.R | 59 +++ camtrapdp-0.4.0/camtrapdp/tests/testthat/test-individuals.R |only camtrapdp-0.4.0/camtrapdp/tests/testthat/test-media.R | 4 camtrapdp-0.4.0/camtrapdp/tests/testthat/test-merge_camtrapdp.R |only camtrapdp-0.4.0/camtrapdp/tests/testthat/test-observations.R | 27 + camtrapdp-0.4.0/camtrapdp/tests/testthat/test-print.R | 12 camtrapdp-0.4.0/camtrapdp/tests/testthat/test-read_camtrapdp.R | 30 + camtrapdp-0.4.0/camtrapdp/tests/testthat/test-round_coordinates.R |only camtrapdp-0.4.0/camtrapdp/tests/testthat/test-shift_time.R |only camtrapdp-0.4.0/camtrapdp/tests/testthat/test-taxa.R | 99 ++++++ camtrapdp-0.4.0/camtrapdp/tests/testthat/test-taxonomic.R |only camtrapdp-0.4.0/camtrapdp/tests/testthat/test-update_taxon.R |only camtrapdp-0.4.0/camtrapdp/tests/testthat/test-version.R | 27 + camtrapdp-0.4.0/camtrapdp/tests/testthat/test-write_camtrapdp.R |only camtrapdp-0.4.0/camtrapdp/tests/testthat/test-write_dwc.R | 43 ++ camtrapdp-0.4.0/camtrapdp/tests/testthat/test-write_eml.R |only 92 files changed, 1124 insertions(+), 360 deletions(-)
Title: 'Entrez' in R
Description: Provides an R interface to the NCBI's 'EUtils' API,
allowing users to search databases like 'GenBank'
<https://www.ncbi.nlm.nih.gov/genbank/> and 'PubMed'
<https://pubmed.ncbi.nlm.nih.gov/>, process the
results of those searches and pull data into their R sessions.
Author: David Winter [aut, cre] ,
Scott Chamberlain [ctb] ,
Han Guangchun [ctb]
Maintainer: David Winter <david.winter@gmail.com>
Diff between rentrez versions 1.2.3 dated 2020-11-10 and 1.2.4 dated 2025-06-11
rentrez-1.2.3/rentrez/NEWS |only rentrez-1.2.3/rentrez/R/help.r |only rentrez-1.2.3/rentrez/man/rentrez.Rd |only rentrez-1.2.4/rentrez/DESCRIPTION | 21 rentrez-1.2.4/rentrez/MD5 | 30 rentrez-1.2.4/rentrez/NAMESPACE | 4 rentrez-1.2.4/rentrez/NEWS.md |only rentrez-1.2.4/rentrez/R/entrez_link.r | 2 rentrez-1.2.4/rentrez/R/entrez_search.r | 4 rentrez-1.2.4/rentrez/R/entrez_summary.r | 4 rentrez-1.2.4/rentrez/R/rentrez-package.R |only rentrez-1.2.4/rentrez/build/vignette.rds |binary rentrez-1.2.4/rentrez/inst/doc/rentrez_tutorial.R | 308 ++--- rentrez-1.2.4/rentrez/inst/doc/rentrez_tutorial.Rmd | 8 rentrez-1.2.4/rentrez/inst/doc/rentrez_tutorial.html | 1051 +++++++------------ rentrez-1.2.4/rentrez/man/entrez_link.Rd | 2 rentrez-1.2.4/rentrez/man/rentrez-package.Rd |only rentrez-1.2.4/rentrez/tests/testthat/test_docs.r | 2 rentrez-1.2.4/rentrez/vignettes/rentrez_tutorial.Rmd | 8 19 files changed, 621 insertions(+), 823 deletions(-)
Title: Nucleic Acid Melting Curve Analysis
Description: Lightweight utilities for nucleic acid melting curve analysis are
important in life sciences and diagnostics. This software can be used for
the analysis and presentation of melting curve data from microbead-based
assays (surface melting curve analysis) and reactions in solution (e.g.,
quantitative PCR (qPCR), real-time isothermal Amplification). Further
information are described in detail in two publications in The R Journal [
<https://journal.r-project.org/archive/2013-2/roediger-bohm-schimke.pdf>;
<https://journal.r-project.org/archive/2015-1/RJ-2015-1.pdf>].
Author: Stefan Roediger [aut] ,
Michal Burdukiewicz [aut] ,
Andrej-Nikolai Spiess [cre, aut]
Maintainer: Andrej-Nikolai Spiess <draspiess@gmail.com>
Diff between MBmca versions 1.0.1-3 dated 2021-09-03 and 1.1-0 dated 2025-06-11
MBmca-1.0.1-3/MBmca/tests |only MBmca-1.1-0/MBmca/DESCRIPTION | 25 MBmca-1.1-0/MBmca/MD5 | 15 MBmca-1.1-0/MBmca/R/diffQ.R | 1007 +++++++++++++++++------------------ MBmca-1.1-0/MBmca/R/mcaSmoother.R | 626 ++++++++++----------- MBmca-1.1-0/MBmca/build/vignette.rds |binary MBmca-1.1-0/MBmca/inst/CITATION | 23 MBmca-1.1-0/MBmca/inst/doc/MBmca.pdf |binary MBmca-1.1-0/MBmca/man/mcaSmoother.Rd | 503 ++++++++--------- 9 files changed, 1099 insertions(+), 1100 deletions(-)
Title: An R Interface to Open-Access Malaria Data, Hosted by the
'Malaria Atlas Project'
Description: A suite of tools to allow you to download all
publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from
the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting
the downloaded data.
Author: Mauricio van den Berg [aut, cre],
Daniel Pfeffer [aut] ,
Tim Lucas [aut] ,
Daniel May [aut] ,
Suzanne Keddie [aut] ,
Jen Rozier [aut] ,
Oliver Watson [aut] ,
Harry Gibson [aut] ,
Nick Golding [ctb],
David Smith [ctb]
Maintainer: Mauricio van den Berg <mauricio.vandenberg@thekids.org.au>
Diff between malariaAtlas versions 1.6.3 dated 2024-08-26 and 1.6.4 dated 2025-06-11
DESCRIPTION | 26 +++----- MD5 | 26 ++++---- NEWS.md | 10 --- R/autoplot.MAPraster.R | 6 - R/autoplot.pr.points.R | 6 - R/autoplot.vector.points.R | 2 R/getRaster.R | 30 +++++---- R/ows4r_utils.R | 2 build/vignette.rds |binary inst/doc/overview.html | 131 ++++++++++++++++++++--------------------- tests/testthat/test_getPR.R | 5 - tests/testthat/test_getShp.R | 2 tests/testthat/test_listData.R | 3 tests/testthat/test_plots.R | 6 + 14 files changed, 131 insertions(+), 124 deletions(-)
Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker [aut, cph],
Jonathon Love [aut, cre, cph],
Damian Dropmann [aut, cph],
Victor Moreno [ctb, cph],
Maurizio Agosti [ctb, cph],
Sebastian Jentschke [ctb, cph]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 2.5.6 dated 2024-06-20 and 2.7.0 dated 2025-06-11
jmv-2.5.6/jmv/tests/testthat/testdescriptives.R |only jmv-2.7.0/jmv/DESCRIPTION | 16 jmv-2.7.0/jmv/MD5 | 143 jmv-2.7.0/jmv/R/00jmv.R | 32 jmv-2.7.0/jmv/R/ancova.b.R | 2 jmv-2.7.0/jmv/R/anovanp.b.R | 166 - jmv-2.7.0/jmv/R/anovanp.h.R | 61 jmv-2.7.0/jmv/R/anovarm.b.R | 819 +++-- jmv-2.7.0/jmv/R/conttables.b.R | 289 + jmv-2.7.0/jmv/R/conttables.h.R | 100 jmv-2.7.0/jmv/R/descriptives.b.R | 528 ++- jmv-2.7.0/jmv/R/descriptives.h.R | 2 jmv-2.7.0/jmv/R/linreg.b.R | 153 + jmv-2.7.0/jmv/R/linreg.h.R | 95 jmv-2.7.0/jmv/R/loglinear.b.R | 21 jmv-2.7.0/jmv/R/logregbin.b.R | 23 jmv-2.7.0/jmv/R/logregbin.h.R | 6 jmv-2.7.0/jmv/R/logregmulti.b.R | 27 jmv-2.7.0/jmv/R/logregord.b.R | 22 jmv-2.7.0/jmv/R/utils.R | 17 jmv-2.7.0/jmv/R/utilsanova.R |only jmv-2.7.0/jmv/R/utilsreg.R |only jmv-2.7.0/jmv/inst/i18n/ar.json | 1065 ------- jmv-2.7.0/jmv/inst/i18n/ca.json | 1060 ------- jmv-2.7.0/jmv/inst/i18n/cs.json | 1044 ------- jmv-2.7.0/jmv/inst/i18n/da.json | 3072 +++++++-------------- jmv-2.7.0/jmv/inst/i18n/de.json | 1050 ------- jmv-2.7.0/jmv/inst/i18n/el.json | 1066 ------- jmv-2.7.0/jmv/inst/i18n/en.json | 1044 ------- jmv-2.7.0/jmv/inst/i18n/es.json | 1080 ------- jmv-2.7.0/jmv/inst/i18n/fa.json |only jmv-2.7.0/jmv/inst/i18n/fi.json |only jmv-2.7.0/jmv/inst/i18n/fr.json | 1060 ------- jmv-2.7.0/jmv/inst/i18n/he.json | 2808 ++++++------------- jmv-2.7.0/jmv/inst/i18n/hr.json | 1164 +------ jmv-2.7.0/jmv/inst/i18n/hu.json | 1047 ------- jmv-2.7.0/jmv/inst/i18n/id.json | 1064 ------- jmv-2.7.0/jmv/inst/i18n/it.json | 1064 ------- jmv-2.7.0/jmv/inst/i18n/ja.json | 1072 ------- jmv-2.7.0/jmv/inst/i18n/kk.json | 1084 ------- jmv-2.7.0/jmv/inst/i18n/ko.json | 1080 ------- jmv-2.7.0/jmv/inst/i18n/ml.json | 1052 ------- jmv-2.7.0/jmv/inst/i18n/nl.json | 1050 ------- jmv-2.7.0/jmv/inst/i18n/nn.json | 1268 +------- jmv-2.7.0/jmv/inst/i18n/no.json | 1048 ------- jmv-2.7.0/jmv/inst/i18n/pl.json | 1084 ------- jmv-2.7.0/jmv/inst/i18n/pt.json | 1058 ------- jmv-2.7.0/jmv/inst/i18n/ro.json | 1044 ------- jmv-2.7.0/jmv/inst/i18n/ru.json | 1068 ------- jmv-2.7.0/jmv/inst/i18n/sl.json | 1044 ------- jmv-2.7.0/jmv/inst/i18n/sv.json | 3072 +++++++-------------- jmv-2.7.0/jmv/inst/i18n/ta.json |only jmv-2.7.0/jmv/inst/i18n/tr.json | 1118 ------- jmv-2.7.0/jmv/inst/i18n/uk.json | 1048 ------- jmv-2.7.0/jmv/inst/i18n/zh-cn.json | 1044 ------- jmv-2.7.0/jmv/inst/i18n/zh-tw.json | 1596 ++-------- jmv-2.7.0/jmv/man/anovaNP.Rd | 7 jmv-2.7.0/jmv/man/calcGG.Rd |only jmv-2.7.0/jmv/man/calcHF.Rd |only jmv-2.7.0/jmv/man/calcMauchlyTest.Rd |only jmv-2.7.0/jmv/man/calcUnivariateTests.Rd |only jmv-2.7.0/jmv/man/contTables.Rd | 26 jmv-2.7.0/jmv/man/descriptives.Rd | 11 jmv-2.7.0/jmv/man/getReferenceLevels.Rd |only jmv-2.7.0/jmv/man/linReg.Rd | 13 jmv-2.7.0/jmv/man/logRegBin.Rd | 4 jmv-2.7.0/jmv/man/setAnalysisNotice.Rd |only jmv-2.7.0/jmv/man/setRefLevelWarning.Rd |only jmv-2.7.0/jmv/man/setSingularityWarning.Rd |only jmv-2.7.0/jmv/man/summarizeAnovaModel.Rd |only jmv-2.7.0/jmv/tests/testthat/Rplots.pdf |binary jmv-2.7.0/jmv/tests/testthat/testanovanp.R | 36 jmv-2.7.0/jmv/tests/testthat/testanovarm.R | 162 + jmv-2.7.0/jmv/tests/testthat/testconttables.R | 35 jmv-2.7.0/jmv/tests/testthat/testlinreg.R | 111 jmv-2.7.0/jmv/tests/testthat/testloglinear.R | 32 jmv-2.7.0/jmv/tests/testthat/testlogregbin.R | 36 jmv-2.7.0/jmv/tests/testthat/testlogregmulti.R | 58 jmv-2.7.0/jmv/tests/testthat/testlogregord.R | 55 jmv-2.7.0/jmv/tests/testthat/testregutils.R |only jmv-2.7.0/jmv/tests/testthat/testthat-problems.rds |only 81 files changed, 8919 insertions(+), 33707 deletions(-)
Title: Functions to Assist Design and Analysis of Agronomic Experiments
Description: Provides functions to aid in the design and analysis of
agronomic and agricultural experiments through easy access to
documentation and helper functions, especially for users who are
learning these concepts. While not required for most functionality,
this package enhances the `asreml` package which provides a
computationally efficient algorithm for fitting mixed models
using Residual Maximum Likelihood. It is a commercial package
that can be purchased as 'asreml-R' from 'VSNi'
<https://vsni.co.uk/>, who will supply a zip file for local
installation/updating (see <https://asreml.kb.vsni.co.uk/>).
Author: Sharon Nielsen [aut],
Sam Rogers [aut, cre],
Annie Conway [aut],
University of Adelaide [cph, fnd] ,
Grains Research and Development Corporation [cph, fnd]
Maintainer: Sam Rogers <biometrytraining@adelaide.edu.au>
Diff between biometryassist versions 1.2.2 dated 2025-04-23 and 1.3.0 dated 2025-06-11
biometryassist-1.2.2/biometryassist/R/normalitycheck.R |only biometryassist-1.2.2/biometryassist/man/compare_version.Rd |only biometryassist-1.2.2/biometryassist/man/get_predictions.Rd |only biometryassist-1.2.2/biometryassist/man/get_predictions.asreml.Rd |only biometryassist-1.2.2/biometryassist/man/get_predictions.lm.Rd |only biometryassist-1.2.2/biometryassist/man/get_predictions.lmerMod.Rd |only biometryassist-1.2.2/biometryassist/tests/testthat/data/complex_model.rds |only biometryassist-1.2.2/biometryassist/tests/testthat/testthat-problems.rds |only biometryassist-1.3.0/biometryassist/DESCRIPTION | 14 biometryassist-1.3.0/biometryassist/LICENSE | 4 biometryassist-1.3.0/biometryassist/MD5 | 482 +++-- biometryassist-1.3.0/biometryassist/NAMESPACE | 14 biometryassist-1.3.0/biometryassist/NEWS.md | 24 biometryassist-1.3.0/biometryassist/R/autoplot.R | 305 ++- biometryassist-1.3.0/biometryassist/R/create_buffers.R | 18 biometryassist-1.3.0/biometryassist/R/des_info.R | 8 biometryassist-1.3.0/biometryassist/R/design.R | 13 biometryassist-1.3.0/biometryassist/R/export_excel.R |only biometryassist-1.3.0/biometryassist/R/heatmap.R | 2 biometryassist-1.3.0/biometryassist/R/install_asreml.R | 539 ++++-- biometryassist-1.3.0/biometryassist/R/logltest.R | 246 +-- biometryassist-1.3.0/biometryassist/R/mct.R | 208 +- biometryassist-1.3.0/biometryassist/R/prediction_methods.R | 78 biometryassist-1.3.0/biometryassist/R/resplot.R | 360 ++-- biometryassist-1.3.0/biometryassist/R/resplot_methods.R |only biometryassist-1.3.0/biometryassist/R/use_template.R |only biometryassist-1.3.0/biometryassist/R/utils.R | 42 biometryassist-1.3.0/biometryassist/R/variogram.r | 62 biometryassist-1.3.0/biometryassist/inst/analysis_template.R |only biometryassist-1.3.0/biometryassist/inst/analysis_template_aov.R |only biometryassist-1.3.0/biometryassist/inst/templates |only biometryassist-1.3.0/biometryassist/man/add_buffers.Rd |only biometryassist-1.3.0/biometryassist/man/autoplot.Rd 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More information about biometryassist at CRAN
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Title: Workflows for Health Technology Assessments in R using Discrete
EveNts
Description: Toolkit to support and perform discrete event simulations without
resource constraints in the context of health technology assessments (HTA).
The package focuses on cost-effectiveness modelling and aims to be submission-ready
to relevant HTA bodies in alignment with 'NICE TSD 15'
<https://www.sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>.
More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Author: Javier Sanchez Alvarez [aut, cre],
Gabriel Lemyre [ctb],
Valerie Aponte Ribero [ctb]
Maintainer: Javier Sanchez Alvarez <javiersanchezeco@gmail.com>
Diff between WARDEN versions 1.0 dated 2025-05-28 and 1.2.0 dated 2025-06-11
DESCRIPTION | 8 MD5 | 51 ++-- NAMESPACE | 4 NEWS.md | 16 + R/engine_helper_f.R | 216 ++++++++++++++------ R/input_f.R | 407 ++++++++++++++++++++++++++++++++------ R/run_engine.R | 100 +++++---- R/run_sim.R | 130 +++++++----- R/run_sim_parallel.R | 128 +++++++---- build/vignette.rds |binary inst/doc/example_ssd.R | 65 ++++-- inst/doc/example_ssd.Rmd | 79 +++++-- inst/doc/example_ssd.html | 399 ++++++++++++++++++++----------------- man/add_item.Rd | 4 man/add_item2.Rd |only man/ast_as_list.Rd | 126 +++++------ man/extract_elements_from_list.Rd | 4 man/extract_from_reactions.Rd | 22 +- man/modify_item.Rd | 4 man/modify_item_seq.Rd | 4 man/pick_val_v.Rd | 5 man/qgamma_mse.Rd | 54 ++--- man/random_stream.Rd |only man/run_sim.Rd | 13 - man/run_sim_parallel.Rd | 21 + man/sens_iterator.Rd |only tests/testthat/test-input_f.R | 101 ++++++--- vignettes/example_ssd.Rmd | 79 +++++-- 28 files changed, 1378 insertions(+), 662 deletions(-)
Title: Laplace Factor Model Analysis and Evaluation
Description: Enables the generation of Laplace factor models across diverse Laplace distributions and facilitates the application of Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Perturbation Principal Component (PPC), Stochastic Approximation Principal Component (SAPC), Sparse Principal Component (SPC) and other PC methods and Farm Test methods to these models. Evaluates the efficacy of these methods within the context of Laplace factor models by scrutinizing parameter estimation accuracy, mean square error, and the degree of sparsity.
Author: Guangbao Guo [aut, cre],
Siqi Liu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between LFM versions 0.3.0 dated 2025-04-16 and 0.3.1 dated 2025-06-11
DESCRIPTION | 10 +++++----- MD5 | 32 +++++++++++++++++++++++--------- data/Australian.rda |only data/Breast.rda |only data/Heart.rda |only data/Iris.rda |only data/Sonar.rda |only data/Wine.rda |only data/ionosphere.rda |only man/Australian.Rd |only man/Breast.Rd |only man/Heart.Rd |only man/Iris.Rd |only man/Sonar.Rd |only man/Wine.Rd |only man/concrete.Rd | 12 ------------ man/ionosphere.Rd |only man/protein.Rd | 9 --------- man/review.Rd | 9 --------- man/riboflavin.Rd | 9 --------- man/riboflavinv100.Rd | 9 --------- man/vehicle.Rd | 9 --------- man/wholesale.Rd | 9 --------- man/yacht_hydrodynamics.Rd | 9 --------- 24 files changed, 28 insertions(+), 89 deletions(-)
Title: Hypothesis Tests for Quantiles and Quantile-Based Measures
Description: Functions to conduct hypothesis tests and derive confidence intervals
for quantiles, linear combinations of quantiles,
ratios of dependent linear combinations and differences
and ratios of all of the above for comparisons between independent samples.
Additionally, quantile-based measures of inequality are also considered.
Author: Shenal Dedduwakumara [aut, cre],
Luke Prendergast [aut],
Robert Staudte [aut]
Maintainer: Shenal Dedduwakumara <shenal.dedduwakumara@adelaide.edu.au>
Diff between rquest versions 1.0.4 dated 2025-05-19 and 1.0.5 dated 2025-06-11
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/q.test.R | 4 ++-- R/qcov.R | 3 +-- man/q.test.Rd | 4 ++-- man/qcov.Rd | 3 +-- 7 files changed, 19 insertions(+), 17 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 and 'HippUnfold' hippocampal segmentation 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 1.3.1 dated 2025-04-14 and 1.3.2 dated 2025-06-11
VertexWiseR-1.3.1/VertexWiseR/man/figures/Flowchart.jpg |only VertexWiseR-1.3.2/VertexWiseR/DESCRIPTION | 15 ++++---- VertexWiseR-1.3.2/VertexWiseR/MD5 | 18 +++++----- VertexWiseR-1.3.2/VertexWiseR/NEWS.md | 17 ++++++--- VertexWiseR-1.3.2/VertexWiseR/R/FSLRvextract.R | 12 +++--- VertexWiseR-1.3.2/VertexWiseR/README.md | 9 ++--- VertexWiseR-1.3.2/VertexWiseR/inst/doc/VertexWiseR_surface_extraction.html | 2 - VertexWiseR-1.3.2/VertexWiseR/man/FSLRvextract.Rd | 6 +-- VertexWiseR-1.3.2/VertexWiseR/man/figures/Flowchart.JPG |only VertexWiseR-1.3.2/VertexWiseR/vignettes/SPRENG_tstatmaps.png |binary VertexWiseR-1.3.2/VertexWiseR/vignettes/surfextract.jpg |binary 11 files changed, 42 insertions(+), 37 deletions(-)
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic, meta-regression, and
multilevel models (assuming either presence or absence of the effect, heterogeneity,
publication bias, and moderators). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2022,
<doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022,
<doi:10.1037/met0000405>; Bartoš et al., 2025, <doi:10.1037/met0000737>).
Users can define a wide range of prior distributions for the effect size, heterogeneity,
publication bias (including selection models and PET-PEESE), and moderator components.
The package provides convenient functions for summary, visualizations, and fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBMA versions 3.4.0 dated 2025-02-04 and 3.5.0 dated 2025-06-11
RoBMA-3.4.0/RoBMA/man/contr.independent.Rd |only RoBMA-3.4.0/RoBMA/man/contr.meandif.Rd |only RoBMA-3.4.0/RoBMA/man/contr.orthonormal.Rd |only RoBMA-3.5.0/RoBMA/DESCRIPTION | 28 +-- RoBMA-3.5.0/RoBMA/MD5 | 85 ++++----- RoBMA-3.5.0/RoBMA/NAMESPACE | 2 RoBMA-3.5.0/RoBMA/NEWS.md | 16 + RoBMA-3.5.0/RoBMA/R/BiBMA-reg.R | 11 - RoBMA-3.5.0/RoBMA/R/BiBMA.R | 13 - RoBMA-3.5.0/RoBMA/R/RoBMA-reg.R | 4 RoBMA-3.5.0/RoBMA/R/RoBMA.R | 4 RoBMA-3.5.0/RoBMA/R/check-input-and-settings.R | 8 RoBMA-3.5.0/RoBMA/R/check-priors-and-models.R | 98 ++++++++--- RoBMA-3.5.0/RoBMA/R/fit-and-marglik.R | 175 ++++++++++---------- RoBMA-3.5.0/RoBMA/R/inference-and-model-averaging.R | 31 +-- RoBMA-3.5.0/RoBMA/R/priors.R | 111 +++++------- RoBMA-3.5.0/RoBMA/R/summary-effect.R |only RoBMA-3.5.0/RoBMA/R/summary-heterogeneity.R | 82 ++++++--- RoBMA-3.5.0/RoBMA/R/summary.R | 5 RoBMA-3.5.0/RoBMA/R/tools.R | 10 + RoBMA-3.5.0/RoBMA/R/transformations.R | 39 ++++ RoBMA-3.5.0/RoBMA/R/utilities.R | 7 RoBMA-3.5.0/RoBMA/README.md | 36 ++-- RoBMA-3.5.0/RoBMA/build/partial.rdb |binary RoBMA-3.5.0/RoBMA/inst/REFERENCES.bib | 10 - RoBMA-3.5.0/RoBMA/inst/doc/CustomEnsembles.html | 9 - RoBMA-3.5.0/RoBMA/inst/doc/FastRoBMA.Rmd | 2 RoBMA-3.5.0/RoBMA/inst/doc/FastRoBMA.html | 25 +- RoBMA-3.5.0/RoBMA/inst/doc/HierarchicalBMA.Rmd | 2 RoBMA-3.5.0/RoBMA/inst/doc/HierarchicalBMA.html | 25 ++ RoBMA-3.5.0/RoBMA/inst/doc/MedicineBMA.html | 9 - RoBMA-3.5.0/RoBMA/inst/doc/MedicineBiBMA.html | 9 - RoBMA-3.5.0/RoBMA/inst/doc/MetaRegression.html | 32 +-- RoBMA-3.5.0/RoBMA/inst/doc/ReproducingBMA.html | 9 - RoBMA-3.5.0/RoBMA/inst/doc/Tutorial.html | 10 - RoBMA-3.5.0/RoBMA/man/BiBMA.Rd | 11 + RoBMA-3.5.0/RoBMA/man/BiBMA.reg.Rd | 11 + RoBMA-3.5.0/RoBMA/man/NoBMA.Rd | 3 RoBMA-3.5.0/RoBMA/man/RoBMA.Rd | 3 RoBMA-3.5.0/RoBMA/man/RoBMA_control.Rd | 5 RoBMA-3.5.0/RoBMA/man/adjusted_effect.Rd |only RoBMA-3.5.0/RoBMA/man/combine_data.Rd | 3 RoBMA-3.5.0/RoBMA/man/contr.BayesTools.Rd |only RoBMA-3.5.0/RoBMA/man/pooled_effect.Rd |only RoBMA-3.5.0/RoBMA/man/summary_heterogeneity.Rd | 9 - RoBMA-3.5.0/RoBMA/vignettes/FastRoBMA.Rmd | 2 RoBMA-3.5.0/RoBMA/vignettes/HierarchicalBMA.Rmd | 2 47 files changed, 582 insertions(+), 374 deletions(-)
Title: Tools for Summarising and Analysing Soundscape Data
Description: A variety of tools relevant to the analysis
of marine soundscape data. There are tools for downloading AIS (automatic identification system)
data from Marine Cadastre <https://hub.marinecadastre.gov>,
connecting AIS data to GPS coordinates, plotting summaries of various soundscape
measurements, and downloading relevant environmental variables (wind, swell height) from the
National Center for Atmospheric Research data server <https://rda.ucar.edu/datasets/ds084.1/>.
Most tools were developed to work well with output from 'Triton' software, but can be adapted
to work with any similar measurements.
Author: Taiki Sakai [aut, cre],
Anne Simonis [ctb],
Shannon Rankin [ctb],
Megan McKenna [ctb],
Kaitlin Palmer [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMscapes versions 0.11.3 dated 2025-04-02 and 0.14.0 dated 2025-06-11
DESCRIPTION | 8 ++-- MD5 | 59 +++++++++++++++++++++++------------- NAMESPACE | 19 +++++++++++ NEWS.md | 43 ++++++++++++++++++++++++++ R/binDetectionData.R | 4 +- R/createOctaveLevel.R | 22 +++++++++++++ R/formatEffort.R | 27 +++++++++++++++- R/loadDetectionData.R | 62 ++++++++++++++++++++++++++++++++------ R/matchDetectionData.R |only R/matchGFS.R | 3 + R/plotAcousticScene.R | 45 +++++++++++++++++---------- R/plotDetectionBoxplot.R | 30 ++++++++++++++---- R/plotPSD.R | 3 + R/plotPolarDetections.R |only R/plotQAQC.R | 2 - R/runDailyLTSAReview.R |only R/runDetLoadHelper.R |only R/runDetectionExplorer.R |only R/runQAQCReview.R | 4 ++ R/runSoundscapeExplorer.R | 4 +- README.md | 2 - inst/extdata/detectionExample.csv |only inst/images/boxplot-ex.png |only inst/images/data-loading-blue.png |only inst/images/data-loading.png |only inst/images/freq-scene-ex.png |only inst/images/polar-ex.png |only inst/images/scene-ex.png |only man/binDetectionData.Rd | 4 +- man/formatEffort.Rd | 4 +- man/loadDetectionData.Rd | 13 +++++++ man/matchDetectionData.Rd |only man/plotAcousticScene.Rd | 9 ++++- man/plotDetectionBoxplot.Rd | 7 +++- man/plotPolarDetections.Rd |only man/runDailyLTSAReview.Rd |only man/runDetLoadHelper.Rd |only man/runDetectionExplorer.Rd |only tests/testthat/test-detection.R | 8 ++-- 39 files changed, 306 insertions(+), 76 deletions(-)
Title: Read and Process 'Pamguard' Binary Data
Description: Functions for easily reading and processing binary data files created by
'Pamguard' (<https://www.pamguard.org/>). All functions for directly reading the
binary data files are based on 'MATLAB' code written by Michael Oswald.
Author: Taiki Sakai [aut, cre],
Michael Oswald [aut],
Douglas Gillespie [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PamBinaries versions 1.9.0 dated 2024-05-13 and 1.9.3 dated 2025-06-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/contourToFreq.R | 10 +++++----- R/loadPamguardBinaryFile.R | 15 ++++++++++++++- tests/testthat/test-binaryReading.R | 8 ++++---- 5 files changed, 31 insertions(+), 18 deletions(-)