Title: Optimal Adaptive Allocation Using Deep Reinforcement Learning
Description: An implementation to compute an optimal adaptive allocation rule
using deep reinforcement learning in a dose-response study
(Matsuura et al. (2022) <doi:10.1002/sim.9247>).
The adaptive allocation rule can directly optimize a performance metric,
such as power, accuracy of the estimated target dose, or mean absolute error
over the estimated dose-response curve.
Author: Kentaro Matsuura [aut, cre, cph]
,
Koji Makiyama [aut, ctb]
Maintainer: Kentaro Matsuura <matsuurakentaro55@gmail.com>
Diff between RLoptimal versions 1.1.1 dated 2024-11-21 and 1.2.0 dated 2024-12-20
DESCRIPTION | 6 ++-- MD5 | 21 ++++++++-------- NEWS.md | 4 +-- R/generate_setup_code.R | 27 +++++++++++---------- R/learn_allocation_rule.R | 2 - R/simulate_one_trial.R | 8 +++--- README.md | 38 +++++++++++++++--------------- inst/doc/RLoptimal.R | 34 +++++++++++++------------- inst/doc/RLoptimal.Rmd | 34 +++++++++++++------------- inst/doc/RLoptimal.html | 38 +++++++++++++++--------------- tests/testthat/test-generate_setup_code.R |only vignettes/RLoptimal.Rmd | 34 +++++++++++++------------- 12 files changed, 126 insertions(+), 120 deletions(-)
Title: Interactively Visualize Structural Equation Modeling Diagrams
Description: It allows users to perform interactive and reproducible visualizations of path diagrams for structural equation modeling (SEM) and small-to-medium sized networks using the 'ggplot2' engine. Its 'shiny' app provides an interface that allows extensive customization, and creates CSV outputs, which can then be used to recreate the figures either using the 'shiny' app or in a typical 'ggplot2' workflow.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun Min <seung.min@mail.mcgill.ca>
Diff between ggsem versions 0.1.1 dated 2024-11-11 and 0.1.2 dated 2024-12-20
ggsem-0.1.1/ggsem/man/launch.Rd |only ggsem-0.1.2/ggsem/DESCRIPTION | 6 ggsem-0.1.2/ggsem/MD5 | 14 - ggsem-0.1.2/ggsem/NAMESPACE | 48 ++-- ggsem-0.1.2/ggsem/R/launch.R | 2 ggsem-0.1.2/ggsem/README.md | 2 ggsem-0.1.2/ggsem/inst/shiny/app.R | 115 +++++++--- ggsem-0.1.2/ggsem/inst/shiny/rsconnect/shinyapps.io/smin95/ggsem.dcf | 2 ggsem-0.1.2/ggsem/man/ggsem.Rd |only 9 files changed, 127 insertions(+), 62 deletions(-)
Title: Cellular Energetics Analysis Software
Description: Measuring cellular energetics is essential to understanding a
matrix’s (e.g. cell, tissue or biofluid) metabolic state. The Agilent
Seahorse machine is a common method to measure real-time cellular
energetics, but existing analysis tools are highly manual or lack
functionality. The Cellular Energetics Analysis Software (ceas) R package
fills this analytical gap by providing modular and automated Seahorse data
analysis and visualization using the methods described by Mookerjee et al.
(2017) <doi:10.1074/jbc.m116.774471>.
Author: Rachel House [aut, cre] ,
James P. Eapen [aut] ,
Hui Shen [fnd] ,
Carrie R. Graveel [fnd] ,
Matthew R. Steensma [fnd] ,
Van Andel Institute [cph]
Maintainer: Rachel House <rachel.house@vai.org>
Diff between ceas versions 1.0.0 dated 2024-05-07 and 1.3.0 dated 2024-12-20
DESCRIPTION | 38 -- MD5 | 60 +-- NAMESPACE | 14 NEWS.md | 102 +++++ R/atp_plot.R | 89 +++- R/bioscope_plot.R | 52 ++ R/energetics.R | 238 ++++++++++-- R/fit_lme.R |only R/globals.R |only R/normalize.R | 100 ++++- R/rate_plot.R | 239 +++++++++++- R/reader.R | 75 +++ README.md | 39 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/ceas.R | 145 ++++++- inst/doc/ceas.Rmd | 270 +++++++++++--- inst/doc/ceas.html | 738 +++++++++++++++++++++++++++------------ inst/extdata/well_norm.csv |only man/atp_plot.Rd | 53 ++ man/bioscope_plot.Rd | 29 + man/ceas-package.Rd | 8 man/energetics_lme_summary.Rd |only man/energetics_ols_summary.Rd |only man/fit_lme.Rd |only man/get_energetics.Rd | 7 man/get_energetics_summary.Rd | 40 +- man/get_rate_summary.Rd | 50 ++ man/normalize.Rd | 58 ++- man/rate_plot.Rd | 34 + man/rates_lme_summary.Rd |only man/read_data.Rd | 56 ++ tests/testthat/test-energetics.R | 16 vignettes/ceas.Rmd | 270 +++++++++++--- 35 files changed, 2247 insertions(+), 573 deletions(-)
Title: Map Layers and Spatial Utilities for British Columbia
Description: Various layers of B.C., including administrative boundaries,
natural resource management boundaries, census boundaries etc. All
layers are available in BC Albers
(<https://spatialreference.org/ref/epsg/3005/>) equal-area projection,
which is the B.C. government standard. The layers are sourced from the
British Columbia and Canadian government under open licenses,
including B.C. Data Catalogue (<https://data.gov.bc.ca>), the
Government of Canada Open Data Portal
(<https://open.canada.ca/en/using-open-data>), and Statistics Canada
(<https://www.statcan.gc.ca/en/reference/licence>).
Author: Andy Teucher [aut, cre] ,
Sam Albers [aut, ctb] ,
Stephanie Hazlitt [aut, ctb] ,
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gmail.com>
Diff between bcmaps versions 2.2.0 dated 2024-01-24 and 2.2.1 dated 2024-12-20
DESCRIPTION | 24 +-- MD5 | 88 +++++------ NEWS.md | 271 ++++++++++++++++++++++------------- R/bc_bound.R | 2 R/cded.R | 8 - R/utm-convert.R | 21 +- README.md | 2 build/vignette.rds |binary inst/doc/add_points.html | 7 inst/doc/bcmaps.html | 13 - man/airzones.Rd | 2 man/bc_cities.Rd | 2 man/bec.Rd | 2 man/census_dissemination_area.Rd | 2 man/census_division.Rd | 2 man/census_economic.Rd | 2 man/census_metropolitan_area.Rd | 2 man/census_subdivision.Rd | 2 man/census_tract.Rd | 2 man/ecoprovinces.Rd | 2 man/ecoregions.Rd | 2 man/ecosections.Rd | 2 man/fsa.Rd | 2 man/gw_aquifers.Rd | 2 man/health_chsa.Rd | 2 man/health_ha.Rd | 2 man/health_hsda.Rd | 2 man/health_lha.Rd | 2 man/hydrozones.Rd | 2 man/mapsheets_250K.Rd | 2 man/mapsheets_50K.Rd | 2 man/municipalities.Rd | 2 man/nr_areas.Rd | 2 man/nr_districts.Rd | 2 man/nr_regions.Rd | 2 man/regional_districts.Rd | 2 man/tsa.Rd | 2 man/vrt_info.Rd | 2 man/water_districts.Rd | 2 man/water_precincts.Rd | 2 man/watercourses_15M.Rd | 2 man/watercourses_5M.Rd | 2 man/wsc_drainages.Rd | 2 tests/testthat/test-data_functions.R | 9 - tests/testthat/test-utm-convert.R | 88 +++++++++++ 45 files changed, 389 insertions(+), 210 deletions(-)
Title: 'fxl' Single Case Design Charting Package
Description: The 'fxl' Charting package is used to prepare and design single case design figures that are typically prepared in spreadsheet software. With 'fxl', there is no need to leave the R environment to prepare these works and many of the more unique conventions in single case experimental designs can be performed without the need for physically constructing features of plots (e.g., drawing annotations across plots). Support is provided for various different plotting arrangements (e.g., multiple baseline), annotations (e.g., brackets, arrows), and output formats (e.g., svg, rasters).
Author: Shawn Gilroy [aut, cre, cph]
Maintainer: Shawn Gilroy <sgilroy1@lsu.edu>
Diff between fxl versions 1.7.1 dated 2024-06-05 and 1.7.2 dated 2024-12-20
COPYING | 1352 DESCRIPTION | 6 MD5 | 324 NAMESPACE | 146 R/data.R | 406 R/element-anno-arrows-draw.R | 106 R/element-anno-arrows.R | 122 R/element-anno-brackets-draw.R | 128 R/element-anno-brackets.R | 116 R/element-anno-guide-line-draw.R | 176 R/element-anno-guide-line.R | 86 R/element-anno-rect-draw.R | 82 R/element-anno-rect.R | 72 R/element-axis-x.R | 186 R/element-axis-y.R | 137 R/element-criterion-draw.R | 174 R/element-criterion-line.R | 74 R/element-label-facet-draw.R | 114 R/element-label-facet.R | 110 R/element-label-phase-draw.R | 288 R/element-label-phase.R | 124 R/element-label-title.R | 80 R/element-label-xlabel.R | 98 R/element-label-ylabel.R | 98 R/element-legend-draw.R | 104 R/element-legend.R | 132 R/element-line-cumsum-line-draw.R | 116 R/element-line-cumsum-line.R | 84 R/element-line-draw.R | 140 R/element-line.R | 78 R/element-phasechange-draw.R | 214 R/element-phasechange-multiple.R | 54 R/element-phasechange-single.R | 74 R/element-point-cumsum-point-draw.R | 168 R/element-point-cumsum-point.R | 90 R/element-point-draw.R | 242 R/element-point.R | 112 R/element-support-bar-draw.R | 280 R/element-support-bar.R | 148 R/fxl-debugging.R | 488 R/fxl-map.R | 28 R/fxl-print-semilog.R | 1051 R/fxl-print.R | 1122 R/fxl-save.R | 116 R/fxl-utilities.R | 198 R/fxl.R | 392 README.md | 460 build/vignette.rds |binary demo/00Index | 46 demo/annotatedplot.R | 814 demo/atd_concurrentoperant.R | 320 demo/beezdemandInd.R | 158 demo/challenge_1.R | 602 demo/challenge_2.R | 680 demo/challenge_3.R | 644 demo/challenge_4.R | 1150 demo/changing_criterion.R | 386 demo/cigarettepolicy.R | 388 demo/concurrentplot.R | 498 demo/cumulativeplot.R | 570 demo/faplot.R | 210 demo/faplotintegrity.R | 414 demo/greyed_training.R | 632 demo/multiplebaselineplot.R | 302 demo/reports_academic.R | 386 demo/reports_academic_celeration_classes.R | 564 demo/reports_academic_celeration_classes_local_norms.R | 616 demo/reports_academic_rti.R | 536 demo/run_all_demos.R | 44 demo/run_coverage.R | 56 demo/semilogplot.R | 391 demo/silvermanplot.R | 338 inst/CITATION | 24 inst/doc/fxl.R | 4292 +-- inst/doc/fxl.Rmd | 5092 +-- inst/doc/fxl.html | 4206 +- man/Challenge1Data.Rd | 58 man/Challenge2Data.Rd | 46 man/Challenge4Data.Rd | 58 man/GelinoEtAl2022.Rd | 60 man/Gilroyetal2015.Rd | 54 man/Gilroyetal2019.Rd | 60 man/Gilroyetal2019Tx.Rd | 58 man/Gilroyetal2021.Rd | 56 man/KoffarnusEtAl2011.Rd | 48 man/LozyEtAl2020.Rd | 52 man/SimulatedAcademicFluency.Rd | 50 man/assert_input_type.Rd | 42 man/cnvrt_coords.Rd | 54 man/draw_arrows.Rd | 48 man/draw_bar_support.Rd | 52 man/draw_brackets.Rd | 48 man/draw_cumsum_lines.Rd | 48 man/draw_cumsum_points.Rd | 48 man/draw_guide_line.Rd | 48 man/draw_label_facet.Rd | 48 man/draw_label_phase.Rd | 48 man/draw_legend.Rd | 40 man/draw_lines.Rd | 48 man/draw_points.Rd | 52 man/draw_rect.Rd | 52 man/draw_scr_criterion.Rd | 48 man/draw_scr_plines.Rd | 48 man/figures/dragon-cairo.ps.xml | 8504 ++--- man/figures/like-cairo-mod.ps.xml | 614 man/figures/scorpion-cairo.ps.xml |12826 ++++----- man/figures/skinner-cairo.ps.xml |24178 ++++++++--------- man/figures/star-cairo-mod.ps.xml | 1138 man/isValidAXSCharacter.Rd | 38 man/isValidAestheticMapping.Rd | 38 man/isValidCharacterVector.Rd | 42 man/isValidDataFrame.Rd | 38 man/isValidLogicalVector.Rd | 42 man/isValidNumericVector.Rd | 42 man/print.fxl.Rd | 46 man/print.fxlsemilog.Rd | 46 man/scr_anno_arrows.Rd | 98 man/scr_anno_brackets.Rd | 92 man/scr_anno_guide_line.Rd | 74 man/scr_anno_rect.Rd | 52 man/scr_bar_support.Rd | 104 man/scr_criterion_lines.Rd | 68 man/scr_cumsum_lines.Rd | 56 man/scr_cumsum_points.Rd | 74 man/scr_label_facet.Rd | 86 man/scr_label_phase.Rd | 92 man/scr_legend.Rd | 140 man/scr_lines.Rd | 56 man/scr_plines.Rd | 56 man/scr_plines_mbd.Rd | 48 man/scr_plot.Rd | 140 man/scr_points.Rd | 86 man/scr_save.Rd | 80 man/scr_title.Rd | 60 man/scr_xlabel.Rd | 80 man/scr_xoverride.Rd | 98 man/scr_ylabel.Rd | 80 man/scr_yoverride.Rd | 77 man/var_map.Rd | 34 tests/testthat.R | 10 tests/testthat/Rplots.pdf |binary tests/testthat/test-demo-annotatedplot.R | 742 tests/testthat/test-demo-changingcriterion.R | 626 tests/testthat/test-demo-cigarettepolicy.R | 382 tests/testthat/test-demo-concurrentplot.R | 516 tests/testthat/test-demo-cumulativeplot.R | 536 tests/testthat/test-demo-cumulativeplot_single.R | 192 tests/testthat/test-demo-faplot.R | 156 tests/testthat/test-demo-faplotintegrity.R | 208 tests/testthat/test-demo-faplotintegrity_extra.R | 380 tests/testthat/test-demo-multiplebaseline_greyed.R | 1008 tests/testthat/test-demo-multiplebaselineplot.R | 256 tests/testthat/test-demo-semilogplot.R | 368 tests/testthat/test-demo-semilogplot_multi.R | 528 tests/testthat/test-demo-silvermanplot.R | 302 tests/testthat/test-element-bar.R | 390 tests/testthat/test-element-label-facet.R | 190 tests/testthat/test-element-label-phase.R | 190 tests/testthat/test-element-scr_arrows.R | 462 tests/testthat/test-element-scr_xoverride.R | 1252 tests/testthat/test-element-scr_yoverride.R | 640 tests/testthat/test-fxl.R | 800 vignettes/fxl.Rmd | 5092 +-- 163 files changed, 50447 insertions(+), 50429 deletions(-)
Title: Survey Analysis with Auxiliary Discretized Variables
Description: Probability surveys often use auxiliary continuous data from administrative records, but the utility of this data is diminished when it is discretized for confidentiality. We provide a set of survey estimators to make full use of information from the discretized variables. See Williams, S.Z., Zou, J., Liu, Y., Si, Y., Galea, S. and Chen, Q. (2024), Improving Survey Inference Using Administrative Records Without Releasing Individual-Level Continuous Data. Statistics in Medicine, 43: 5803-5813. <doi:10.1002/sim.10270> for details.
Author: Jungang Zou [aut, cre],
Yutao Liu [aut],
Sharifa Williams [aut],
Qixuan Chen [aut]
Maintainer: Jungang Zou <jungang.zou@gmail.com>
Diff between AuxSurvey versions 0.9 dated 2024-12-09 and 1.0 dated 2024-12-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- README.md | 6 +++++- 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>. Functio [...truncated...]
Author: Beata Nowok [aut, cre],
Gillian M Raab [aut],
Chris Dibben [ctb],
Joshua Snoke [ctb],
Caspar van Lissa [ctb],
Lotte Pater [ctb]
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.8-0 dated 2022-08-31 and 1.9-0 dated 2024-12-20
synthpop-1.8-0/synthpop/R/utility.tables.r |only synthpop-1.9-0/synthpop/DESCRIPTION | 48 synthpop-1.9-0/synthpop/MD5 | 162 - synthpop-1.9-0/synthpop/NAMESPACE | 42 synthpop-1.9-0/synthpop/NEWS | 1031 ++++---- synthpop-1.9-0/synthpop/R/IO.r | 984 ++++--- synthpop-1.9-0/synthpop/R/codebook.syn.r | 102 synthpop-1.9-0/synthpop/R/compare.syn.r | 1364 +++++----- synthpop-1.9-0/synthpop/R/disclosure.R |only synthpop-1.9-0/synthpop/R/functions.syn.r | 2583 ++++++++++---------- synthpop-1.9-0/synthpop/R/methods.syn.r | 1654 ++++++------- synthpop-1.9-0/synthpop/R/multi.compare.syn.r | 226 - synthpop-1.9-0/synthpop/R/multi.disclosure.R |only synthpop-1.9-0/synthpop/R/numtocat.syn.r | 286 +- synthpop-1.9-0/synthpop/R/padMis.syn.r | 250 - synthpop-1.9-0/synthpop/R/padModel.syn.r | 218 - synthpop-1.9-0/synthpop/R/sampler.syn.r | 675 ++--- synthpop-1.9-0/synthpop/R/syn.r | 2796 +++++++++++----------- synthpop-1.9-0/synthpop/R/syn.strata.r | 382 +-- synthpop-1.9-0/synthpop/R/synorig.compare.R |only synthpop-1.9-0/synthpop/R/utility.syn.r | 1724 ++++++------- synthpop-1.9-0/synthpop/R/utility.tables.R |only synthpop-1.9-0/synthpop/R/zzz.r | 10 synthpop-1.9-0/synthpop/build/partial.rdb |binary synthpop-1.9-0/synthpop/build/vignette.rds |binary synthpop-1.9-0/synthpop/inst/CITATION | 48 synthpop-1.9-0/synthpop/inst/doc/disclosure.R |only synthpop-1.9-0/synthpop/inst/doc/disclosure.Rnw |only synthpop-1.9-0/synthpop/inst/doc/disclosure.pdf |only synthpop-1.9-0/synthpop/inst/doc/inference.Rnw | 1494 +++++------ synthpop-1.9-0/synthpop/inst/doc/inference.pdf |binary synthpop-1.9-0/synthpop/inst/doc/synthpop.Rnw | 1328 +++++----- synthpop-1.9-0/synthpop/inst/doc/synthpop.pdf |binary synthpop-1.9-0/synthpop/inst/doc/utility.Rnw | 1100 ++++---- synthpop-1.9-0/synthpop/inst/doc/utility.pdf |binary synthpop-1.9-0/synthpop/inst/logo.png |only synthpop-1.9-0/synthpop/man/SD2011.Rd | 132 - synthpop-1.9-0/synthpop/man/codebook.syn.Rd | 68 synthpop-1.9-0/synthpop/man/compare.Rd | 64 synthpop-1.9-0/synthpop/man/compare.fit.synds.Rd | 300 +- synthpop-1.9-0/synthpop/man/compare.synds.Rd | 263 +- synthpop-1.9-0/synthpop/man/disclosure.Rd |only synthpop-1.9-0/synthpop/man/glm.synds.Rd | 166 - synthpop-1.9-0/synthpop/man/mergelevels.syn.Rd |only synthpop-1.9-0/synthpop/man/multi.compare.Rd | 128 - synthpop-1.9-0/synthpop/man/multi.disclosure.Rd |only synthpop-1.9-0/synthpop/man/multinom.synds.Rd | 130 - synthpop-1.9-0/synthpop/man/numtocat.syn.Rd | 108 synthpop-1.9-0/synthpop/man/polr.synds.Rd | 128 - synthpop-1.9-0/synthpop/man/read.obs.Rd | 62 synthpop-1.9-0/synthpop/man/replicated.uniques.Rd | 100 synthpop-1.9-0/synthpop/man/sdc.Rd | 118 synthpop-1.9-0/synthpop/man/summary.fit.synds.Rd | 250 - synthpop-1.9-0/synthpop/man/summary.synds.Rd | 106 synthpop-1.9-0/synthpop/man/syn.Rd | 768 +++--- synthpop-1.9-0/synthpop/man/syn.bag.Rd | 74 synthpop-1.9-0/synthpop/man/syn.cart.Rd | 158 - synthpop-1.9-0/synthpop/man/syn.catall.Rd | 193 - synthpop-1.9-0/synthpop/man/syn.ipf.Rd | 234 - synthpop-1.9-0/synthpop/man/syn.lognorm.Rd | 82 synthpop-1.9-0/synthpop/man/syn.logreg.Rd | 96 synthpop-1.9-0/synthpop/man/syn.nested.Rd | 72 synthpop-1.9-0/synthpop/man/syn.norm.Rd | 66 synthpop-1.9-0/synthpop/man/syn.normrank.Rd | 90 synthpop-1.9-0/synthpop/man/syn.passive.Rd | 166 - synthpop-1.9-0/synthpop/man/syn.pmm.Rd | 92 synthpop-1.9-0/synthpop/man/syn.polr.Rd | 118 synthpop-1.9-0/synthpop/man/syn.polyreg.Rd | 124 synthpop-1.9-0/synthpop/man/syn.ranger.Rd | 74 synthpop-1.9-0/synthpop/man/syn.rf.Rd | 76 synthpop-1.9-0/synthpop/man/syn.sample.Rd | 72 synthpop-1.9-0/synthpop/man/syn.satcat.Rd | 95 synthpop-1.9-0/synthpop/man/syn.smooth.Rd | 78 synthpop-1.9-0/synthpop/man/syn.survctree.Rd | 192 - synthpop-1.9-0/synthpop/man/synorig.compare.Rd |only synthpop-1.9-0/synthpop/man/synthpop-package.Rd | 89 synthpop-1.9-0/synthpop/man/utility.gen.Rd | 498 +-- synthpop-1.9-0/synthpop/man/utility.tab.Rd | 436 +-- synthpop-1.9-0/synthpop/man/utility.tables.Rd | 437 +-- synthpop-1.9-0/synthpop/man/write.syn.Rd | 99 synthpop-1.9-0/synthpop/vignettes/disclosure.Rnw |only synthpop-1.9-0/synthpop/vignettes/disclosure.bib |only synthpop-1.9-0/synthpop/vignettes/fig1dis.png |only synthpop-1.9-0/synthpop/vignettes/fig2dis.png |only synthpop-1.9-0/synthpop/vignettes/fig3dis.png |only synthpop-1.9-0/synthpop/vignettes/inference.Rnw | 1494 +++++------ synthpop-1.9-0/synthpop/vignettes/inference.bib | 152 - synthpop-1.9-0/synthpop/vignettes/synthpop.Rnw | 1328 +++++----- synthpop-1.9-0/synthpop/vignettes/synthpop.bib | 730 ++--- synthpop-1.9-0/synthpop/vignettes/utility.Rnw | 1100 ++++---- synthpop-1.9-0/synthpop/vignettes/utility.bib | 6 91 files changed, 15219 insertions(+), 14700 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.5.4 dated 2024-11-15 and 1.5.5 dated 2024-12-20
DESCRIPTION | 8 MD5 | 94 R/GPModel.R | 109 R/gpb.Booster.R | 12 R/gpb.cv.R | 80 R/gpboost.R | 2 configure | 8 configure.ac | 25 configure.win | 25 demo/GPBoost_algorithm.R | 8 man/GPModel.Rd | 39 man/GPModel_shared_params.Rd | 50 man/fit.GPModel.Rd | 14 man/fit.Rd | 14 man/fitGPModel.Rd | 45 man/gpb.cv.Rd | 17 man/gpb.grid.search.tune.parameters.Rd | 13 man/gpboost.Rd | 15 man/predict.GPModel.Rd | 40 man/set_optim_params.GPModel.Rd | 14 man/set_optim_params.Rd | 14 man/set_prediction_data.GPModel.Rd | 20 man/set_prediction_data.Rd | 20 src/CG_utils.cpp | 229 src/GP_utils.cpp | 2 src/Vecchia_utils.cpp | 11 src/c_api.cpp | 5 src/gpboost_R.cpp | 13 src/gpboost_R.h | 11 src/include/GPBoost/CG_utils.h | 140 src/include/GPBoost/GP_utils.h | 4 src/include/GPBoost/cov_fcts.h | 74 src/include/GPBoost/likelihoods.h | 1249 +++- src/include/GPBoost/re_comp.h | 42 src/include/GPBoost/re_model.h | 6 src/include/GPBoost/re_model_template.h | 808 ++- src/include/LightGBM/bin.h | 1 src/include/LightGBM/c_api.h | 2 src/include/LightGBM/dataset.h | 1 src/include/LightGBM/feature_group.h | 1 src/include/LightGBM/train_share_states.h | 1 src/include/LightGBM/tree.h | 1 src/include/LightGBM/utils/log.h | 7 src/io/json11.cpp | 1 src/re_model.cpp | 104 tests/testthat/_snaps |only tests/testthat/test_GPModel_gaussian_process.R | 264 tests/testthat/test_GPModel_non_Gaussian_data.R | 6440 ++++++++++++------------ tests/testthat/test_z_GPBoost_algorithm.R | 43 49 files changed, 5951 insertions(+), 4195 deletions(-)
Title: Constrained Ordinary Least Squares
Description: Constrained ordinary least squares is performed. One constraint is that all beta coefficients (including the constant) cannot be negative. They can be either 0 or strictly positive. Another constraint is that the sum of the beta coefficients equals a constant. References: Hansen, B. E. (2022). Econometrics, Princeton University Press. <ISBN:9780691235899>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between cols versions 1.3 dated 2024-11-19 and 1.5 dated 2024-12-20
DESCRIPTION | 8 ++++---- MD5 | 29 +++++++++++++++-------------- NAMESPACE | 2 +- R/int.cls.R | 9 +++++---- R/int.mcls.R |only R/mpcls.R | 8 ++++---- R/mpls.R | 8 ++++---- R/mvpls.R | 8 ++++---- R/pcls.R | 6 +++--- R/pls.R | 6 +++--- man/cls.Rd | 2 +- man/cols-package.Rd | 4 ++-- man/int.cls.Rd | 8 +++++--- man/mvpls.Rd | 3 ++- man/pcls.Rd | 3 ++- man/pls.Rd | 3 ++- 16 files changed, 57 insertions(+), 50 deletions(-)
Title: Working with ISO8601 Dates and Times
Description: Functions to parse strings with ISO8601 dates, times, and
date-times into R-objects. Additionally, there are functions to determine
the type of ISO8601 string and to standardise ISO8601 strings.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between iso8601 versions 0.1.1 dated 2024-12-18 and 0.1.2 dated 2024-12-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 7 +++++++ src/parsedatetime.cpp | 3 ++- 4 files changed, 15 insertions(+), 7 deletions(-)
Title: Parametric and Non-Parametric Copula-Based Imputation Methods
Description: Copula-based imputation methods: parametric and non-parametric algorithms for missing multivariate data through conditional copulas.
Author: Francesca Marta Lilja Di Lascio [aut, cre],
Aurora Gatto [aut],
Simone Giannerini [aut]
Maintainer: Francesca Marta Lilja Di Lascio <marta.dilascio@unibz.it>
Diff between CoImp versions 2.0.1 dated 2024-09-09 and 2.0.2 dated 2024-12-20
ChangeLog | 7 + DESCRIPTION | 8 +- MD5 | 12 +-- R/InternalFunction.R | 10 +- R/NPCoImp.R | 186 ++++++++++++++++++++++++++------------------------- man/NPCoImp-class.Rd | 4 - man/NPCoImp.Rd | 21 +++-- 7 files changed, 130 insertions(+), 118 deletions(-)
Title: Bayesian Post-Estimation on the Mean Scale
Description: Computes Bayesian posterior distributions of predictions, marginal effects, and differences of marginal effects for various generalized linear models. Importantly, the posteriors are on the mean (response) scale, allowing for more natural interpretation than summaries on the link scale. Also, predictions and marginal effects of the count probabilities for Poisson and negative binomial models can be computed.
Author: David M. Dalenberg [aut, cre]
Maintainer: David M. Dalenberg <dalenbe2@gmail.com>
Diff between bayesMeanScale versions 0.1.4 dated 2024-05-30 and 0.2.0 dated 2024-12-20
DESCRIPTION | 10 MD5 | 108 ++++--- NAMESPACE | 8 NEWS.md | 11 R/bayes-count-marg-effects.R | 66 +++- R/bayes-count-preds.R | 42 +-- R/bayes-marg-compare.R | 28 +- R/bayes-marg-effects.R | 63 +++- R/bayes-ordinal-marg-effects.R |only R/bayes-ordinal-preds.R |only R/bayes-preds.R | 42 +-- R/combo-check.R |only R/count-marg-table.R | 17 - R/count-mean-diff-continuous.R |only R/count-pred-table.R | 7 R/global-vars.R | 18 + R/levels-prep.R | 6 R/marg-compare-error-check.R | 4 R/marg-model-data-continuous.R |only R/marg-model-data.R | 46 ++- R/marg-table.R | 17 - R/mean-count-pred.R | 2 R/mean-diff-continuous.R |only R/mean-diff.R | 2 R/mean-pred-ordinal.R |only R/mean-pred.R | 2 R/new-value-continuous.R |only R/ordinal-marg-effects-error-check.R |only R/ordinal-marg-table.R |only R/ordinal-mean-diff-continuous.R |only R/ordinal-mean-diff.R |only R/ordinal-pred-table.R |only R/pred-table.R | 19 - R/preds-error-check.R | 10 R/preds-ordinal-error-check.R |only R/print.R | 6 R/sysdata.rda |only README.md | 4 build/vignette.rds |binary inst/doc/introduction.R | 47 ++- inst/doc/introduction.Rmd | 69 +++- inst/doc/introduction.html | 279 +++++++++----------- man/bayesCountMargEffF.Rd | 17 - man/bayesCountPredsF.Rd | 13 man/bayesMargCompareF.Rd | 2 man/bayesMargEffF.Rd | 17 - man/bayesOrdinalMargEffF.Rd |only man/bayesOrdinalPredsF.Rd |only man/bayesPredsF.Rd | 10 tests/testthat/test-bayes-count-marg-effects.R | 4 tests/testthat/test-bayes-count-preds.R | 25 - tests/testthat/test-bayes-ordinal-marg-effects.R |only tests/testthat/test-bayes-ordinal-preds.R |only tests/testthat/test-bayes-preds.R | 2 tests/testthat/test-count-marg-effect-error-check.R | 3 tests/testthat/test-count-preds-error-check.R | 1 tests/testthat/test-levels-prep.R | 4 tests/testthat/test-marg-compare-error-check.R | 4 tests/testthat/test-marg-compare.R | 18 + tests/testthat/test-marg-effects-error-check.R | 5 tests/testthat/test-marg-effects.R | 12 tests/testthat/test-new-value.R | 2 tests/testthat/test-preds-error-check.R | 5 tests/testthat/test-preds-ordinal-error-check.R |only vignettes/introduction.Rmd | 69 +++- 65 files changed, 700 insertions(+), 446 deletions(-)
More information about bayesMeanScale at CRAN
Permanent link
Title: Power and Sample Size for Health Researchers via Shiny
Description: Power and Sample Size for Health Researchers is a Shiny application that brings together a
series of functions related to sample size and power calculations for common analysis in the healthcare
field. There are functionalities to calculate the power, sample size to estimate or test hypotheses for means and
proportions (including test for correlated groups, equivalence, non-inferiority and superiority), association, correlations coefficients,
regression coefficients (linear, logistic, gamma, and Cox), linear mixed model,
Cronbach's alpha, interobserver agreement, intraclass correlation coefficients,
limit of agreement on Bland-Altman plots,
area under the curve, sensitivity and specificity incorporating the prevalence of disease.
You can also use the online version at <https://hcpa-unidade-bioestatistica.shinyapps.io/PSS_Health/>.
Author: Rogerio Boff Borges [aut, cre]
,
Guilherme Serpa Azambuja [aut]
,
Aline Castello Branco Mancuso [aut]
,
Vanessa Bielefeldt Leotti [aut]
,
Vania Naomi Hirakata [aut] ,
Suzi Alves Camey [aut] ,
Stela Maris de Jezus Castro [aut]
,
Gustavo Thomas [aut] , [...truncated...]
Maintainer: Rogerio Boff Borges <roborges@hcpa.edu.br>
Diff between PSS.Health versions 1.0.2 dated 2023-07-14 and 1.1.4 dated 2024-12-20
DESCRIPTION | 20 ++- MD5 | 28 ++-- NAMESPACE | 1 R/PSS_Health.R | 1 build/vignette.rds |binary inst/PSS.Health/R/modulo_1_media.R | 21 ++- inst/PSS.Health/R/modulo_2_medias_independentes.R | 3 inst/PSS.Health/R/modulo_medidas_repetidas.R | 90 ++++++++++++++- inst/PSS.Health/R/modulo_nao_inferioridade.R | 9 + inst/PSS.Health/R/modulo_regressao_linear.R | 126 +++++++++++----------- inst/PSS.Health/R/modulo_regressao_logistica.R | 2 inst/PSS.Health/global.R | 2 inst/PSS.Health/server.R | 15 +- inst/doc/Vignettes.R | 2 inst/doc/Vignettes.html | 14 +- 15 files changed, 215 insertions(+), 119 deletions(-)
Title: Ecological Niche Modeling using Presence-Absence Data
Description: A set of tools to perform Ecological Niche Modeling with
presence-absence data. It includes algorithms for data partitioning,
model fitting, calibration, evaluation, selection, and prediction.
Other functions help to explore signals of ecological niche using univariate
and multivariate analyses, and model features such as variable response
curves and variable importance. Unique characteristics of this package are
the ability to exclude models with concave quadratic responses, and the
option to clamp model predictions to specific variables. These tools are
implemented following principles proposed in
Cobos et al., (2022) <doi:10.17161/bi.v17i.15985>,
Cobos et al., (2019) <doi:10.7717/peerj.6281>,
and Peterson et al., (2008) <doi:10.1016/j.ecolmodel.2007.11.008>.
Author: Luis F. Arias-Giraldo [aut, cre]
,
Marlon E. Cobos [aut] ,
A. Townsend Peterson [ctb]
Maintainer: Luis F. Arias-Giraldo <lfarias.giraldo@gmail.com>
Diff between enmpa versions 0.1.8 dated 2024-06-19 and 0.1.9 dated 2024-12-20
DESCRIPTION | 10 - MD5 | 30 ++- NAMESPACE | 14 + NEWS.md | 12 + R/calibration_glm.R | 6 R/enmpa.R | 3 R/jackknife.R |only R/plot_jk.R |only R/resp2var.R |only README.md | 158 ++++++++++++------- man/enmpa.Rd | 3 man/figures/README-figures-jackk-1.png |binary man/figures/README-figures-jackk-2.png |binary man/figures/README-figures-jackk-3.png |binary man/figures/README-figures-jackk-4.png |binary man/figures/README-figures-prediction_selected-1.png |binary man/jackknife.Rd |only man/plot_jk.Rd |only man/resp2var.Rd |only 19 files changed, 160 insertions(+), 76 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.2.1 dated 2024-10-19 and 1.2.2 dated 2024-12-20
climate-1.2.1/climate/R/hydro_imgw_annual.R |only climate-1.2.1/climate/man/hydro_imgw_annual.Rd |only climate-1.2.2/climate/DESCRIPTION | 6 climate-1.2.2/climate/MD5 | 53 ++++---- climate-1.2.2/climate/NAMESPACE | 1 climate-1.2.2/climate/NEWS.md | 11 + climate-1.2.2/climate/R/clean_metadata_hydro.R | 17 -- climate-1.2.2/climate/R/hydro_imgw.R | 14 -- climate-1.2.2/climate/R/hydro_imgw_daily.R | 137 ++++++++++++---------- climate-1.2.2/climate/R/hydro_imgw_monthly.R | 19 +-- climate-1.2.2/climate/R/hydro_metadata_imgw.R | 8 - climate-1.2.2/climate/R/hydro_shortening_imgw.R | 3 climate-1.2.2/climate/R/imgw_read.R |only climate-1.2.2/climate/R/meteo_imgw_daily.R | 36 +---- climate-1.2.2/climate/R/meteo_imgw_datastore.R | 5 climate-1.2.2/climate/R/meteo_imgw_hourly.R | 24 +-- climate-1.2.2/climate/R/meteo_imgw_monthly.R | 17 -- climate-1.2.2/climate/R/meteo_shortening_imgw.R | 3 climate-1.2.2/climate/R/nearest_stations_imgw.R | 2 climate-1.2.2/climate/R/ogimet_daily.R | 8 - climate-1.2.2/climate/R/ogimet_hourly.R | 26 ++-- climate-1.2.2/climate/README.md | 53 +++----- climate-1.2.2/climate/data/imgw_hydro_abbrev.rda |binary climate-1.2.2/climate/inst/doc/getstarted.Rmd | 2 climate-1.2.2/climate/inst/doc/getstarted.html | 43 +++--- climate-1.2.2/climate/man/hydro_imgw.Rd | 3 climate-1.2.2/climate/man/meteo_imgw_datastore.Rd | 3 climate-1.2.2/climate/man/ogimet_hourly.Rd | 3 climate-1.2.2/climate/vignettes/getstarted.Rmd | 2 29 files changed, 231 insertions(+), 268 deletions(-)
Title: Download Data from Bank of Spain
Description: Tools to download data series from 'Banco de España' ('BdE')
on 'tibble' format. 'Banco de España' is the national central bank
and, within the framework of the Single Supervisory Mechanism ('SSM'),
the supervisor of the Spanish banking system along with the European
Central Bank. This package is in no way sponsored endorsed or
administered by 'Banco de España'.
Author: Diego H. Herrero [aut, cre, cph]
Maintainer: Diego H. Herrero <dev.dieghernan@gmail.com>
Diff between tidyBdE versions 0.3.7 dated 2024-08-26 and 0.3.8 dated 2024-12-20
DESCRIPTION | 12 MD5 | 26 - NEWS.md | 4 R/bde_check_access.R | 121 +++--- R/bde_tidy_palettes.R | 144 ++++---- R/catalogs.R | 772 +++++++++++++++++++++---------------------- R/indicators.R | 298 ++++++++-------- R/series.R | 872 ++++++++++++++++++++++++------------------------- R/superseded.R | 106 ++--- R/utils.R | 577 ++++++++++++++++---------------- README.md | 8 build/vignette.rds |binary inst/schemaorg.json | 4 man/tidyBdE-package.Rd | 2 14 files changed, 1476 insertions(+), 1470 deletions(-)
Title: Download Weather Station Data from GHCN
Description: The goal of 'GHCNr' is to provide a fast and friendly interface with the Global Historical Climatology Network daily (GHCNd) database, which contains daily summaries of weather station data worldwide (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>). GHCNd is accessed through the web API <https://www.ncei.noaa.gov/access/services/data/v1>. 'GHCNr' main functionalities consist of downloading data from GHCNd, filter it, and to aggregate it at monthly and annual scales.
Author: Emilio Berti [aut, cre]
Maintainer: Emilio Berti <emilio.berti@idiv.de>
Diff between GHCNr versions 0.8.0 dated 2024-12-13 and 1.0.0 dated 2024-12-20
DESCRIPTION | 8 MD5 | 66 ++++--- NAMESPACE | 10 - R/annual.R | 18 +- R/coverage.R | 84 +++++++--- R/daily.R | 60 ++++--- R/data.R | 17 +- R/flags.R | 9 - R/get-country-shapefile.R | 34 +++- R/monthly.R | 1 R/plotting.R | 212 +++++++++++++------------ R/s3_classes.R | 10 - R/stations.R | 38 +++- R/utils.R | 25 ++- data/USC00010655.rda |only inst/doc/daily.R | 135 +++++++++------- inst/doc/daily.Rmd | 132 +++++++++------ inst/doc/daily.html | 298 ++++++++++++++++++++---------------- man/CA003076680.Rd | 4 man/USC00010655.Rd |only man/annual.Rd | 13 + man/annual_coverage.Rd | 7 man/as_daily.Rd | 2 man/coverage.Rd | 8 man/dot-api_error.Rd |only man/dot-missing_variables.Rd | 4 man/monthly_coverage.Rd | 9 - man/period_coverage.Rd | 11 - man/plot.ghcn_annual.Rd | 2 man/plot.ghcn_daily.Rd | 2 man/plot.ghcn_monthly.Rd | 2 man/remove_flagged.Rd | 5 man/stations.Rd | 13 + tests/testthat/test-flags.R |only tests/testthat/test-geoboundaries.R |only tests/testthat/test-inventory.R |only vignettes/daily.Rmd | 132 +++++++++------ 37 files changed, 822 insertions(+), 549 deletions(-)
Title: Distance Sampling Simulations
Description: Performs distance sampling simulations. 'dsims' repeatedly generates
instances of a user defined population within a given survey region. It then
generates realisations of a survey design and simulates the detection process.
The data are then analysed so that the results can be compared for accuracy
and precision across all replications. This process allows users to optimise
survey designs for their specific set of survey conditions. The effects of
uncertainty in population distribution or parameters can be investigated
under a number of simulations so that users can be confident that they have
achieved a robust survey design before deploying vessels into the field. The
distance sampling designs used in this package from 'dssd' are detailed in
Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008, ISBN-13:
978-0199225873). General distance sampling methods are detailed in Introduction
to Distance Sampling: Estimating Abundance of Biological Populations, Buckland
et. al. (2004 [...truncated...]
Author: Laura Marshall [aut, cre],
Thomas Len [ctb]
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Diff between dsims versions 1.0.4 dated 2023-11-29 and 1.0.5 dated 2024-12-20
dsims-1.0.4/dsims/NEWS |only dsims-1.0.4/dsims/build |only dsims-1.0.4/dsims/inst |only dsims-1.0.4/dsims/vignettes |only dsims-1.0.5/dsims/DESCRIPTION | 17 - dsims-1.0.5/dsims/MD5 | 49 +-- dsims-1.0.5/dsims/NEWS.md |only dsims-1.0.5/dsims/R/ClassConstructors.R | 10 dsims-1.0.5/dsims/R/Simulation.R | 37 ++ dsims-1.0.5/dsims/R/Survey.LT.R | 2 dsims-1.0.5/dsims/R/Survey.PT.R | 2 dsims-1.0.5/dsims/R/calculate.scale.param.R | 2 dsims-1.0.5/dsims/R/dsims-package.R | 11 dsims-1.0.5/dsims/R/simulation.consistency.check.R |only dsims-1.0.5/dsims/README.md | 29 -- dsims-1.0.5/dsims/man/Survey.LT-class.Rd | 2 dsims-1.0.5/dsims/man/Survey.PT-class.Rd | 2 dsims-1.0.5/dsims/man/dsims-package.Rd | 11 dsims-1.0.5/dsims/man/make.density.Rd | 2 dsims-1.0.5/dsims/man/make.ds.analysis.Rd | 2 dsims-1.0.5/dsims/man/make.population.description.Rd | 2 dsims-1.0.5/dsims/man/make.simulation.Rd | 4 dsims-1.0.5/dsims/tests/testthat/test-ProblemCases.R | 41 +++ dsims-1.0.5/dsims/tests/testthat/test-check_Constructors.R | 124 ++++++++++ dsims-1.0.5/dsims/tests/testthat/test-check_ExtremeCases.R | 2 dsims-1.0.5/dsims/tests/testthat/test-check_IndividualCovariates.R | 52 ++++ 26 files changed, 313 insertions(+), 90 deletions(-)
Title: Calculate Ecological Information and Diatom Based Indices
Description: Calculate multiple biotic indices using diatoms from environmental samples. Diatom species are recognized by their species' name using a heuristic search, and their ecological data is retrieved from multiple sources.
It includes number/shape of chloroplasts diversity indices, size classes, ecological guilds, and multiple biotic indices.
It outputs both a dataframe with all the results and plots of all the obtained data in a defined output folder.
- Sample data was taken from Nicolosi Gelis, Cochero & Gómez (2020, <doi:10.1016/j.ecolind.2019.105951>).
- The package uses the 'Diat.Barcode' database to calculate morphological and ecological information by Rimet & Couchez (2012, <doi:10.1051/kmae/2012018>),and the combined classification of guilds and size classes established by B-Béres et al. (2017, <doi:10.1016/j.ecolind.2017.07.007>).
- Current diatom-based biotic indices include the DES index by Descy (1979)
- EPID index by Dell'Uomo (1996, ISBN: 3950009002)
- [...truncated...]
Author: Maria Mercedes Nicolosi Gelis [aut]
,
Maria Belen Sathicq [aut] ,
Joaquin Cochero [cre]
Maintainer: Joaquin Cochero <jcochero@ilpla.edu.ar>
Diff between diathor versions 0.1.4 dated 2024-09-20 and 0.1.5 dated 2024-12-20
DESCRIPTION | 36 +++++- MD5 | 115 +++++++++++--------- NAMESPACE | 3 R/data.R | 52 +++++++-- R/diaThor.R | 16 ++ R/diat_cemfgs_rb.R | 196 +++++++++++++---------------------- R/diat_ddi.R |only R/diat_des.R | 14 -- R/diat_disp.R | 12 -- R/diat_diversity.R | 13 -- R/diat_edi.R |only R/diat_epid.R | 13 -- R/diat_getDiatBarcode.R | 7 - R/diat_guilds.R | 13 -- R/diat_idap.R | 13 -- R/diat_idch.R | 12 -- R/diat_idp.R | 12 -- R/diat_ilm.R | 12 -- R/diat_ips.R | 13 -- R/diat_loadData.R | 49 +++----- R/diat_lobo.R | 15 -- R/diat_morpho.R | 13 -- R/diat_pbidw.R | 13 -- R/diat_pdise.R |only R/diat_sla.R | 16 -- R/diat_spear.R | 12 -- R/diat_tdi.R | 13 -- R/diathorAll.R | 53 +++++++-- README.md |only data/ddi.rda |only data/edi.rda |only data/pdise.rda |only man/cemfgs_rb.Rd | 2 man/dbc_offline.Rd | 4 man/ddi.Rd |only man/diaThor.Rd | 252 +++++++++++++++++++++++---------------------- man/diaThorAll.Rd | 153 +++++++++++++-------------- man/diat_cemfgs_rb.Rd | 78 ++++++------- man/diat_checkName.Rd | 42 +++---- man/diat_ddi.Rd |only man/diat_disp.Rd | 88 +++++++-------- man/diat_diversity.Rd | 54 ++++----- man/diat_edi.Rd |only man/diat_getDiatBarcode.Rd | 38 +++--- man/diat_idch.Rd | 88 +++++++-------- man/diat_ips.Rd | 88 +++++++-------- man/diat_loadData.Rd | 10 + man/diat_pdise.Rd |only man/diat_sampleData.Rd | 2 man/diat_sla.Rd | 3 man/diat_spear.Rd | 88 +++++++-------- man/diat_taxaList.Rd | 32 ++--- man/diathor-package.Rd | 40 +++---- man/disp.Rd | 2 man/edi.Rd |only man/idch.Rd | 46 ++++---- man/idp.Rd | 46 ++++---- man/ilm.Rd | 46 ++++---- man/ips.Rd | 43 ++++--- man/lobo.Rd | 40 +++---- man/pbidw.Rd | 46 ++++---- man/pdise.Rd |only man/sla.Rd | 46 ++++---- man/spear.Rd | 2 man/tdi.Rd | 46 ++++---- 65 files changed, 1074 insertions(+), 1087 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with 'Rscript' to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L. Davis [aut, cre] ,
Allen Day [ctb] ,
Python Software Foundation [ctb] ,
Paul Newell [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 2.2.4 dated 2024-11-20 and 2.2.5 dated 2024-12-20
argparse-2.2.4/argparse/R/utils.R |only argparse-2.2.5/argparse/DESCRIPTION | 8 +- argparse-2.2.5/argparse/MD5 | 11 +-- argparse-2.2.5/argparse/NEWS.md | 5 + argparse-2.2.5/argparse/README.md | 2 argparse-2.2.5/argparse/inst/doc/argparse.html | 60 +++++++++++------ argparse-2.2.5/argparse/tests/testthat/test-argparse.R | 26 +++---- 7 files changed, 65 insertions(+), 47 deletions(-)
Title: Outcome Weights of Treatment Effect Estimators
Description: Many treatment effect estimators can be written as weighted outcomes.
These weights have established use cases like checking covariate balancing via packages like 'cobalt'.
This package takes the original estimator objects and outputs these outcome weights.
It builds on the general framework of Knaus (2024) <doi:10.48550/arXiv.2411.11559>.
This version is compatible with the 'grf' package and provides an internal implementation of Double Machine Learning.
Author: Michael C. Knaus [aut, cre] ,
Henri Pfleiderer [ctb]
Maintainer: Michael C. Knaus <michael.knaus@uni-tuebingen.de>
Diff between OutcomeWeights versions 0.1.0 dated 2024-11-21 and 0.1.1 dated 2024-12-20
DESCRIPTION | 6 +-- MD5 | 9 ++-- NEWS.md | 7 +++ R/NuPa_honest_forest.R | 6 +-- README.md | 48 ++++++++++++++++---------- tests/testthat/test-estimator_combinatorics.R |only 6 files changed, 49 insertions(+), 27 deletions(-)
More information about OutcomeWeights at CRAN
Permanent link
More information about Certara.RsNLME.ModelBuilder at CRAN
Permanent link
More information about backtestGraphics at CRAN
Permanent link
Title: Quantile-Frequency Analysis (QFA) of Time Series
Description: Quantile-frequency analysis (QFA) of time series based on trigonometric quantile regression.
References:
[1] Li, T.-H. (2012) "Quantile periodograms", Journal of the American Statistical
Association, 107, 765–776, <doi:10.1080/01621459.2012.682815>.
[2] Li, T.-H. (2014) Time Series with Mixed Spectra, CRC Press, <doi:10.1201/b15154>
[3] Li, T.-H. (2022) "Quantile Fourier transform, quantile series, and nonparametric
estimation of quantile spectra", <doi:10.48550/arXiv.2211.05844>.
[4] Li, T.-H. (2024) "Quantile crossing spectrum and spline autoregression
estimation," <doi:10.48550/arXiv.2412.02513>.
Author: Ta-Hsin Li [cre, aut]
Maintainer: Ta-Hsin Li <thl024@outlook.com>
Diff between qfa versions 2.1 dated 2023-08-21 and 3.1 dated 2024-12-20
qfa-2.1/qfa/R/qfa2.1.R |only qfa-2.1/qfa/man/ar2qspec.Rd |only qfa-2.1/qfa/man/qsmooth.qdft.Rd |only qfa-2.1/qfa/man/qsmooth.qper.Rd |only qfa-2.1/qfa/man/qspec.lwqs.Rd |only qfa-2.1/qfa/man/qspec.qslw.Rd |only qfa-2.1/qfa/man/qspec.sqrlw.Rd |only qfa-2.1/qfa/man/sqdft.Rd |only qfa-2.1/qfa/man/tsqr.fit.Rd |only qfa-3.1/qfa/DESCRIPTION | 26 +++++++++----- qfa-3.1/qfa/MD5 | 65 ++++++++++++++++-------------------- qfa-3.1/qfa/NAMESPACE | 11 +----- qfa-3.1/qfa/R/qfa3.1.R |only qfa-3.1/qfa/man/per.Rd |only qfa-3.1/qfa/man/qacf.Rd | 2 - qfa-3.1/qfa/man/qcser.Rd |only qfa-3.1/qfa/man/qdft.Rd | 2 - qfa-3.1/qfa/man/qdft2qacf.Rd | 4 +- qfa-3.1/qfa/man/qdft2qper.Rd | 8 ++-- qfa-3.1/qfa/man/qdft2qser.Rd | 4 +- qfa-3.1/qfa/man/qfa.plot.Rd | 2 - qfa-3.1/qfa/man/qkl.divergence.Rd | 4 +- qfa-3.1/qfa/man/qper.Rd | 8 ++-- qfa-3.1/qfa/man/qper2.Rd | 2 - qfa-3.1/qfa/man/qser.Rd | 2 - qfa-3.1/qfa/man/qser2ar.Rd | 6 ++- qfa-3.1/qfa/man/qser2qacf.Rd |only qfa-3.1/qfa/man/qser2sar.Rd | 4 +- qfa-3.1/qfa/man/qspec.ar.Rd | 24 +++++++++---- qfa-3.1/qfa/man/qspec.lw.Rd | 53 ++++++++++++++++++++--------- qfa-3.1/qfa/man/qspec.sar.Rd | 8 ++-- qfa-3.1/qfa/man/qspec2qcoh.Rd | 8 ++-- qfa-3.1/qfa/man/sar.eq.bootstrap.Rd | 2 - qfa-3.1/qfa/man/sar.eq.test.Rd | 4 +- qfa-3.1/qfa/man/sar.gc.bootstrap.Rd | 2 - qfa-3.1/qfa/man/sar.gc.coef.Rd | 2 - qfa-3.1/qfa/man/sar.gc.test.Rd | 4 +- qfa-3.1/qfa/man/sqr.fit.Rd | 2 - qfa-3.1/qfa/man/tqr.fit.Rd | 2 - qfa-3.1/qfa/src/rqfnb.f | 2 - 40 files changed, 147 insertions(+), 116 deletions(-)
Title: Salary Analysis by the Swiss Federal Office for Gender Equality
Description: Implementation of the Swiss Confederation's standard analysis
model for salary analyses
<https://www.ebg.admin.ch/en/equal-pay-analysis-with-logib> in R. The
analysis is run at company-level and the model is intended for
medium-sized and large companies. It can technically be used with 50
or more employees (apprentices, trainees/interns and expats are not
included in the analysis). Employees with at least 100 employees are
required by the Gender Equality Act to conduct an equal pay analysis.
This package allows users to run the equal salary analysis in R,
providing additional transparency with respect to the methodology and
simple automation possibilities.
Author: Marc Stoeckli [aut, cre],
Jonathan Chassot [aut],
Jeremy Kolly [ctb],
Federal Office for Gender Equality of Switzerland [cph, fnd]
Maintainer: Marc Stoeckli <marc.stoeckli@ebg.admin.ch>
Diff between logib versions 0.1.2 dated 2021-11-21 and 0.2.0 dated 2024-12-20
logib-0.1.2/logib/R/sysdata.rda |only logib-0.1.2/logib/data/datalist_imprimerie.rda |only logib-0.1.2/logib/man/cleanup_errors.Rd |only logib-0.1.2/logib/man/datalist_imprimerie.Rd |only logib-0.1.2/logib/tests/testthat/test_analysis.R |only logib-0.2.0/logib/DESCRIPTION | 48 +- logib-0.2.0/logib/MD5 | 79 ++-- logib-0.2.0/logib/NAMESPACE | 15 logib-0.2.0/logib/NEWS.md | 16 logib-0.2.0/logib/R/analysis.R | 69 +--- logib-0.2.0/logib/R/data.R | 6 logib-0.2.0/logib/R/data_check.R | 158 +++++---- logib-0.2.0/logib/R/data_preparation.R | 166 +++++----- logib-0.2.0/logib/R/data_transformation.R | 21 - logib-0.2.0/logib/R/datalists.R | 73 +++- logib-0.2.0/logib/R/models.R | 17 - logib-0.2.0/logib/README.md | 15 logib-0.2.0/logib/data/all_column_names.rda |only logib-0.2.0/logib/data/datalist_example.rda |only logib-0.2.0/logib/man/all_column_names.Rd | 34 +- logib-0.2.0/logib/man/analysis.Rd | 43 +- logib-0.2.0/logib/man/build_custom_mapping.Rd | 72 ++-- logib-0.2.0/logib/man/build_errors.Rd | 60 +-- logib-0.2.0/logib/man/check_data.Rd | 48 +- logib-0.2.0/logib/man/compute_age.Rd | 54 +-- logib-0.2.0/logib/man/compute_years_of_service.Rd | 72 ++-- logib-0.2.0/logib/man/datalist_example.Rd |only logib-0.2.0/logib/man/download_datalist.Rd | 44 +- logib-0.2.0/logib/man/download_example_datalist.Rd |only logib-0.2.0/logib/man/feb29_between.Rd | 40 +- logib-0.2.0/logib/man/get_kennedy_estimator.Rd | 60 +-- logib-0.2.0/logib/man/prepare_data.Rd | 124 +++---- logib-0.2.0/logib/man/read_data.Rd | 86 ++--- logib-0.2.0/logib/man/read_official_excel.Rd | 38 +- logib-0.2.0/logib/man/run_standard_analysis_model.Rd | 64 +-- logib-0.2.0/logib/man/summary.analysis_model.Rd | 5 logib-0.2.0/logib/man/transform_data.Rd | 86 ++--- logib-0.2.0/logib/man/within_a_year.Rd | 40 +- logib-0.2.0/logib/man/yearfrac.Rd | 44 +- logib-0.2.0/logib/tests/testthat.R | 1 logib-0.2.0/logib/tests/testthat/Beispiel_Datenblatt_M1.xlsx |only logib-0.2.0/logib/tests/testthat/Datalist_d.xlsx |only logib-0.2.0/logib/tests/testthat/Datalist_e.xlsx |only logib-0.2.0/logib/tests/testthat/Datalist_f.xlsx |only logib-0.2.0/logib/tests/testthat/Datalist_i.xlsx |only logib-0.2.0/logib/tests/testthat/Esempio_foglio_di_dati_M1.xlsx |only logib-0.2.0/logib/tests/testthat/Example_data_sheet_M1.xlsx |only logib-0.2.0/logib/tests/testthat/Exemple_feuille_de_donnees_M1.xlsx |only logib-0.2.0/logib/tests/testthat/test-analysis.R |only logib-0.2.0/logib/tests/testthat/test-download.R |only 50 files changed, 921 insertions(+), 777 deletions(-)
Title: Holistic Generalized Linear Models
Description: Holistic generalized linear models (HGLMs) extend generalized linear models (GLMs) by enabling the possibility to add further constraints to the model. The 'holiglm' package simplifies estimating HGLMs using convex optimization. Additional information about the package can be found in the reference manual, the 'README' and the accompanying paper <doi:10.18637/jss.v108.i07>.
Author: Benjamin Schwendinger [aut, cre],
Florian Schwendinger [aut],
Laura Vana [aut]
Maintainer: Benjamin Schwendinger <benjaminschwe@gmail.com>
Diff between holiglm versions 1.0.0 dated 2024-02-15 and 1.0.1 dated 2024-12-20
holiglm-1.0.0/holiglm/inst/doc/extending_holiglm.Rmd |only holiglm-1.0.0/holiglm/inst/doc/extending_holiglm.html |only holiglm-1.0.0/holiglm/vignettes/extending_holiglm.Rmd |only holiglm-1.0.1/holiglm/DESCRIPTION | 12 holiglm-1.0.1/holiglm/MD5 | 41 +-- holiglm-1.0.1/holiglm/NAMESPACE | 2 holiglm-1.0.1/holiglm/R/auxiliary.R | 6 holiglm-1.0.1/holiglm/R/hglm.R | 57 ++-- holiglm-1.0.1/holiglm/R/log-likelihood.R | 199 +++++++++++++++- holiglm-1.0.1/holiglm/R/simulate.R | 4 holiglm-1.0.1/holiglm/build/partial.rdb |binary holiglm-1.0.1/holiglm/build/vignette.rds |binary holiglm-1.0.1/holiglm/inst/doc/conic_representable.html | 130 +++++----- holiglm-1.0.1/holiglm/inst/doc/solver_installation.Rmd | 2 holiglm-1.0.1/holiglm/inst/doc/solver_installation.html | 34 ++ holiglm-1.0.1/holiglm/inst/tinytest/test_binomial.R | 5 holiglm-1.0.1/holiglm/inst/tinytest/test_gaussian.R | 5 holiglm-1.0.1/holiglm/inst/tinytest/test_poisson.R | 5 holiglm-1.0.1/holiglm/man/hglm.Rd | 12 holiglm-1.0.1/holiglm/man/hglm_fit.Rd | 5 holiglm-1.0.1/holiglm/man/hglm_model.Rd | 5 holiglm-1.0.1/holiglm/man/holiglm-package.Rd | 1 holiglm-1.0.1/holiglm/vignettes/solver_installation.Rmd | 2 23 files changed, 376 insertions(+), 151 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-12-13 1.1
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 0.3.3 dated 2024-04-22 and 1.0.0 dated 2024-12-20
aifeducation-0.3.3/aifeducation/R/aif_gui.R |only aifeducation-0.3.3/aifeducation/R/aux_fct.R |only aifeducation-0.3.3/aifeducation/R/aux_gui.R |only aifeducation-0.3.3/aifeducation/R/preparation.R |only aifeducation-0.3.3/aifeducation/R/te_classifier_neuralnet_model.R |only aifeducation-0.3.3/aifeducation/R/text_embedding_model.R |only aifeducation-0.3.3/aifeducation/R/transformer_bert.R |only aifeducation-0.3.3/aifeducation/R/transformer_deberta_v2.R |only aifeducation-0.3.3/aifeducation/R/transformer_funnel.R |only aifeducation-0.3.3/aifeducation/R/transformer_longformer.R |only aifeducation-0.3.3/aifeducation/R/transformer_roberta.R |only aifeducation-0.3.3/aifeducation/data/test_classifier_sustainability.rda |only aifeducation-0.3.3/aifeducation/data/test_metric_mean.rda |only aifeducation-0.3.3/aifeducation/inst/doc/sharing_and_publishing.R |only aifeducation-0.3.3/aifeducation/inst/doc/sharing_and_publishing.Rmd |only aifeducation-0.3.3/aifeducation/inst/doc/sharing_and_publishing.html |only aifeducation-0.3.3/aifeducation/man/AifeducationConfiguration.Rd |only aifeducation-0.3.3/aifeducation/man/TextEmbeddingClassifierNeuralNet.Rd |only aifeducation-0.3.3/aifeducation/man/aifeducation_config.Rd |only aifeducation-0.3.3/aifeducation/man/array_to_matrix.Rd |only aifeducation-0.3.3/aifeducation/man/bow_pp_create_basic_text_rep.Rd |only aifeducation-0.3.3/aifeducation/man/bow_pp_create_vocab_draft.Rd |only aifeducation-0.3.3/aifeducation/man/check_embedding_models.Rd |only aifeducation-0.3.3/aifeducation/man/combine_embeddings.Rd |only aifeducation-0.3.3/aifeducation/man/create_bert_model.Rd |only aifeducation-0.3.3/aifeducation/man/create_deberta_v2_model.Rd |only aifeducation-0.3.3/aifeducation/man/create_funnel_model.Rd |only aifeducation-0.3.3/aifeducation/man/create_iota2_mean_object.Rd |only aifeducation-0.3.3/aifeducation/man/create_longformer_model.Rd |only aifeducation-0.3.3/aifeducation/man/create_roberta_model.Rd |only aifeducation-0.3.3/aifeducation/man/create_synthetic_units.Rd |only aifeducation-0.3.3/aifeducation/man/figures/gui_aife_readme.JPG |only aifeducation-0.3.3/aifeducation/man/get_folds.Rd |only aifeducation-0.3.3/aifeducation/man/get_stratified_train_test_split.Rd |only aifeducation-0.3.3/aifeducation/man/get_synthetic_cases.Rd |only aifeducation-0.3.3/aifeducation/man/get_train_test_split.Rd |only aifeducation-0.3.3/aifeducation/man/load_ai_model.Rd |only aifeducation-0.3.3/aifeducation/man/save_ai_model.Rd |only aifeducation-0.3.3/aifeducation/man/split_labeled_unlabeled.Rd |only aifeducation-0.3.3/aifeducation/man/test_classifier_sustainability.Rd |only aifeducation-0.3.3/aifeducation/man/test_metric_mean.Rd |only aifeducation-0.3.3/aifeducation/man/train_tune_bert_model.Rd |only aifeducation-0.3.3/aifeducation/man/train_tune_deberta_v2_model.Rd |only aifeducation-0.3.3/aifeducation/man/train_tune_funnel_model.Rd |only aifeducation-0.3.3/aifeducation/man/train_tune_longformer_model.Rd |only aifeducation-0.3.3/aifeducation/man/train_tune_roberta_model.Rd |only aifeducation-0.3.3/aifeducation/man/update_aifeducation_progress_bar.Rd |only aifeducation-0.3.3/aifeducation/man/update_aifeducation_progress_bar_epochs.Rd |only aifeducation-0.3.3/aifeducation/man/update_aifeducation_progress_bar_steps.Rd |only aifeducation-0.3.3/aifeducation/tests/testthat/test-01_vocab_draft.R |only aifeducation-0.3.3/aifeducation/tests/testthat/test-02_basic_text_rep.R |only aifeducation-0.3.3/aifeducation/tests/testthat/test-03_text_embedding_model_gvc_lda.R |only aifeducation-0.3.3/aifeducation/tests/testthat/test-04_transformer_models.R |only aifeducation-0.3.3/aifeducation/tests/testthat/test-05_classifier_neural_net.R |only aifeducation-0.3.3/aifeducation/tests/testthat/test-06_install_and_config.R |only aifeducation-0.3.3/aifeducation/tests/testthat/test_data/classifier |only aifeducation-0.3.3/aifeducation/tests/testthat/test_data/gvc_lda |only aifeducation-0.3.3/aifeducation/vignettes/sharing_and_publishing.Rmd |only aifeducation-1.0.0/aifeducation/DESCRIPTION | 70 - 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Title: Analyzing Gastric Emptying from MRI or Scintigraphy
Description: Fits gastric emptying time series from MRI or 'scintigraphic' measurements
using nonlinear mixed-model population fits with 'nlme' and Bayesian methods with
Stan; computes derived parameters such as t50 and AUC.
Author: Dieter Menne [aut, cre]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between gastempt versions 0.6.2 dated 2024-12-04 and 0.7.0 dated 2024-12-20
DESCRIPTION | 16 +-- MD5 | 21 ++-- R/fitfuncs.r | 2 R/fitnlme.R | 7 + R/fitparams.R | 61 +++++++++++--- R/stan_gastempt.R | 16 +-- inst/doc/gastempt.html | 4 inst/shiny/server.R | 6 - man/simulate_gastempt.Rd | 182 +++++++++++++++++++++--------------------- man/stan_gastempt.Rd | 12 +- tests/testthat/_snaps |only tests/testthat/test-fitnlme.R | 7 + 12 files changed, 188 insertions(+), 146 deletions(-)