Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Mollie Brooks [aut, cre] ,
Ben Bolker [aut] ,
Kasper Kristensen [aut],
Martin Maechler [aut] ,
Arni Magnusson [aut] ,
Maeve McGillycuddy [ctb],
Hans Skaug [aut] ,
Anders Nielsen [aut] ,
Casper Berg [aut] ,
Koen van Bentham [aut],
Nafis Sadat [ctb] ,
[...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.10 dated 2024-09-26 and 1.1.11 dated 2025-04-02
glmmTMB-1.1.10/glmmTMB/inst/Matrix-version |only glmmTMB-1.1.10/glmmTMB/inst/TMB-version |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/sherman.R |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/sherman.csv |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/sherman.rda |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/tmbstan_traceplot.png |only glmmTMB-1.1.10/glmmTMB/vignettes/covstruct_files |only glmmTMB-1.1.10/glmmTMB/vignettes/lineno.sty |only glmmTMB-1.1.11/glmmTMB/DESCRIPTION | 13 glmmTMB-1.1.11/glmmTMB/MD5 | 152 ++-- glmmTMB-1.1.11/glmmTMB/NAMESPACE | 1 glmmTMB-1.1.11/glmmTMB/R/VarCorr.R | 2 glmmTMB-1.1.11/glmmTMB/R/diagnose.R | 4 glmmTMB-1.1.11/glmmTMB/R/enum.R | 4 glmmTMB-1.1.11/glmmTMB/R/family.R | 40 - glmmTMB-1.1.11/glmmTMB/R/glmmTMB.R | 141 ++-- glmmTMB-1.1.11/glmmTMB/R/methods.R | 51 + glmmTMB-1.1.11/glmmTMB/R/predict.R | 38 - glmmTMB-1.1.11/glmmTMB/R/profile.R | 2 glmmTMB-1.1.11/glmmTMB/R/utils.R | 100 +- glmmTMB-1.1.11/glmmTMB/build/partial.rdb |binary glmmTMB-1.1.11/glmmTMB/build/vignette.rds |binary glmmTMB-1.1.11/glmmTMB/inst/CITATION | 36 - glmmTMB-1.1.11/glmmTMB/inst/NEWS.Rd | 50 + glmmTMB-1.1.11/glmmTMB/inst/doc/covstruct.R | 352 +++++----- glmmTMB-1.1.11/glmmTMB/inst/doc/covstruct.html | 96 +- glmmTMB-1.1.11/glmmTMB/inst/doc/covstruct.rmd | 49 - glmmTMB-1.1.11/glmmTMB/inst/doc/glmmTMB.R | 92 +- glmmTMB-1.1.11/glmmTMB/inst/doc/glmmTMB.pdf |binary glmmTMB-1.1.11/glmmTMB/inst/doc/hacking.R | 48 - glmmTMB-1.1.11/glmmTMB/inst/doc/hacking.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/mcmc.R | 251 ++++--- glmmTMB-1.1.11/glmmTMB/inst/doc/mcmc.html | 270 ++++++- glmmTMB-1.1.11/glmmTMB/inst/doc/mcmc.rmd | 162 +++- glmmTMB-1.1.11/glmmTMB/inst/doc/miscEx.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/model_evaluation.R | 30 glmmTMB-1.1.11/glmmTMB/inst/doc/model_evaluation.Rnw | 2 glmmTMB-1.1.11/glmmTMB/inst/doc/model_evaluation.pdf |binary glmmTMB-1.1.11/glmmTMB/inst/doc/parallel.R | 58 - glmmTMB-1.1.11/glmmTMB/inst/doc/parallel.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/priors.R | 26 glmmTMB-1.1.11/glmmTMB/inst/doc/priors.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/sim.html | 6 glmmTMB-1.1.11/glmmTMB/inst/doc/troubleshooting.R | 154 ++-- glmmTMB-1.1.11/glmmTMB/inst/doc/troubleshooting.html | 320 ++++++++- glmmTMB-1.1.11/glmmTMB/inst/doc/troubleshooting.rmd | 83 +- glmmTMB-1.1.11/glmmTMB/inst/test_data/models.rda |binary glmmTMB-1.1.11/glmmTMB/inst/test_data/sim_ar1.rds |only glmmTMB-1.1.11/glmmTMB/inst/vignette_data/mcmc.R | 79 +- glmmTMB-1.1.11/glmmTMB/inst/vignette_data/mcmc.rda |binary glmmTMB-1.1.11/glmmTMB/inst/vignette_data/model_evaluation.rda |binary glmmTMB-1.1.11/glmmTMB/inst/vignette_data/sleepstudy_traceplot_bounds_theta3.png |only glmmTMB-1.1.11/glmmTMB/inst/vignette_data/sleepstudy_traceplot_theta3.png |only glmmTMB-1.1.11/glmmTMB/inst/vignette_data/troubleshooting.R | 8 glmmTMB-1.1.11/glmmTMB/inst/vignette_data/troubleshooting.rda |binary glmmTMB-1.1.11/glmmTMB/inst/vignette_data/volcano_data.png |binary glmmTMB-1.1.11/glmmTMB/man/dot-checkRankX.Rd | 2 glmmTMB-1.1.11/glmmTMB/man/get_autopar.Rd |only glmmTMB-1.1.11/glmmTMB/man/get_cor.Rd | 22 glmmTMB-1.1.11/glmmTMB/man/glmmTMB.Rd | 5 glmmTMB-1.1.11/glmmTMB/man/glmmTMBControl.Rd | 2 glmmTMB-1.1.11/glmmTMB/man/mkTMBStruc.Rd | 1 glmmTMB-1.1.11/glmmTMB/man/nbinom2.Rd | 14 glmmTMB-1.1.11/glmmTMB/man/predict.glmmTMB.Rd | 20 glmmTMB-1.1.11/glmmTMB/man/simulate_new.Rd | 42 - glmmTMB-1.1.11/glmmTMB/src/glmmTMB.cpp | 127 ++- glmmTMB-1.1.11/glmmTMB/tests/testthat/test-basics.R | 23 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-control.R | 30 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-diagnose.R | 13 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-downstream.R | 2 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-families.R | 38 + glmmTMB-1.1.11/glmmTMB/tests/testthat/test-mapequal.R | 2 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-methods.R | 46 + glmmTMB-1.1.11/glmmTMB/tests/testthat/test-predict.R | 17 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-priors.R | 17 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-propto.R | 17 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-rr.R | 35 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-varstruc.R | 77 +- glmmTMB-1.1.11/glmmTMB/vignettes/covstruct.rmd | 49 - glmmTMB-1.1.11/glmmTMB/vignettes/glmmTMB.bib | 6 glmmTMB-1.1.11/glmmTMB/vignettes/mcmc.rmd | 162 +++- glmmTMB-1.1.11/glmmTMB/vignettes/model_evaluation.Rnw | 2 glmmTMB-1.1.11/glmmTMB/vignettes/troubleshooting.rmd | 83 +- 83 files changed, 2477 insertions(+), 1113 deletions(-)
Title: Estimating Dynamic Correlation
Description: Implementations for two different Bayesian models of differential co-expression. scdeco.cop() fits the bivariate Gaussian copula model from Zichen Ma, Shannon W. Davis, Yen-Yi Ho (2023) <doi:10.1111/biom.13701>, while scdeco.pg() fits the bivariate Poisson-Gamma model from Zhen Yang, Yen-Yi Ho (2022) <doi:10.1111/biom.13457>.
Author: Anderson Bussing [aut, cre],
Yen-Yi Ho [aut, ths],
Zichen Ma [aut],
Zhen Yang [aut]
Maintainer: Anderson Bussing <abussing@email.sc.edu>
Diff between scDECO versions 0.1.0 dated 2024-06-04 and 0.1.1 dated 2025-04-02
DESCRIPTION | 8 ++-- MD5 | 13 +++--- NEWS.md |only R/scdeco.cop.R | 70 +++++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/scDECO-Copula.html | 28 +++++++------- inst/doc/scDECO-Poisson-Gamma.html | 22 +++++------ man/scdeco.cop.Rd | 16 +++++++- 8 files changed, 110 insertions(+), 47 deletions(-)
Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis,
including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>],
calculation of relatedness coefficients using path-tracing methods
[Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>],
inference of relatedness, pedigree conversion, and simulation of multi-generational family data
[Lyu et al. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview,
see Garrison et al. (2024) <doi:10.21105/joss.06203>.
Author: S. Mason Garrison [aut, cre] ,
Michael D. Hunter [aut] ,
Xuanyu Lyu [aut] ,
Rachel N. Good [ctb],
Jonathan D. Trattner [aut] ,
S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between BGmisc versions 1.3.3 dated 2025-02-19 and 1.3.5 dated 2025-04-02
BGmisc-1.3.3/BGmisc/man/compute_transpose.Rd |only BGmisc-1.3.3/BGmisc/tests/testthat/Rplots.pdf |only BGmisc-1.3.5/BGmisc/DESCRIPTION | 14 BGmisc-1.3.5/BGmisc/MD5 | 109 +- BGmisc-1.3.5/BGmisc/NAMESPACE | 5 BGmisc-1.3.5/BGmisc/NEWS.md | 17 BGmisc-1.3.5/BGmisc/R/calculateFamilySize.R | 3 BGmisc-1.3.5/BGmisc/R/checkPedigree.R |only BGmisc-1.3.5/BGmisc/R/checkSex.R | 20 BGmisc-1.3.5/BGmisc/R/computeRelatedness.R | 2 BGmisc-1.3.5/BGmisc/R/convertPedigree.R | 430 +++++++--- BGmisc-1.3.5/BGmisc/R/documentData.R | 49 + BGmisc-1.3.5/BGmisc/R/makeLinks.R |only BGmisc-1.3.5/BGmisc/R/plotPedigree.R | 55 - BGmisc-1.3.5/BGmisc/R/readPedigree.R | 272 +++++- BGmisc-1.3.5/BGmisc/R/summarizePedigree.R | 24 BGmisc-1.3.5/BGmisc/README.md | 10 BGmisc-1.3.5/BGmisc/build/vignette.rds |binary BGmisc-1.3.5/BGmisc/data/ASOIAF.rda |only BGmisc-1.3.5/BGmisc/data/royal92.rda |only BGmisc-1.3.5/BGmisc/inst/doc/analyticrelatedness.R | 8 BGmisc-1.3.5/BGmisc/inst/doc/analyticrelatedness.Rmd | 46 - BGmisc-1.3.5/BGmisc/inst/doc/analyticrelatedness.html | 118 +- BGmisc-1.3.5/BGmisc/inst/doc/modelingrelatedness.Rmd | 3 BGmisc-1.3.5/BGmisc/inst/doc/modelingrelatedness.html | 12 BGmisc-1.3.5/BGmisc/inst/doc/partial.R |only BGmisc-1.3.5/BGmisc/inst/doc/partial.Rmd |only BGmisc-1.3.5/BGmisc/inst/doc/partial.html |only BGmisc-1.3.5/BGmisc/inst/doc/pedigree.html | 225 ----- BGmisc-1.3.5/BGmisc/inst/doc/validation.R | 21 BGmisc-1.3.5/BGmisc/inst/doc/validation.Rmd | 45 - BGmisc-1.3.5/BGmisc/inst/doc/validation.html | 148 +-- BGmisc-1.3.5/BGmisc/man/ASOIAF.Rd |only BGmisc-1.3.5/BGmisc/man/BGmisc-package.Rd | 2 BGmisc-1.3.5/BGmisc/man/assignParentIDs.Rd | 4 BGmisc-1.3.5/BGmisc/man/checkPedigreeNetwork.Rd |only BGmisc-1.3.5/BGmisc/man/com2links.Rd |only BGmisc-1.3.5/BGmisc/man/compute_parent_adjacency.Rd |only BGmisc-1.3.5/BGmisc/man/createFamilyToParentsMapping.Rd | 2 BGmisc-1.3.5/BGmisc/man/dot-computeTranspose.Rd |only BGmisc-1.3.5/BGmisc/man/extractSummaryText.Rd |only BGmisc-1.3.5/BGmisc/man/inferRelatedness.Rd | 2 BGmisc-1.3.5/BGmisc/man/makeLongTree.Rd |only BGmisc-1.3.5/BGmisc/man/matchMembers.Rd |only BGmisc-1.3.5/BGmisc/man/parseRelationships.Rd |only BGmisc-1.3.5/BGmisc/man/parseTree.Rd |only BGmisc-1.3.5/BGmisc/man/ped2add.Rd | 3 BGmisc-1.3.5/BGmisc/man/ped2cn.Rd | 3 BGmisc-1.3.5/BGmisc/man/ped2com.Rd | 8 BGmisc-1.3.5/BGmisc/man/ped2mit.Rd | 5 BGmisc-1.3.5/BGmisc/man/processParents.Rd | 2 BGmisc-1.3.5/BGmisc/man/readWikifamilytree.Rd |only BGmisc-1.3.5/BGmisc/man/repairSex.Rd | 4 BGmisc-1.3.5/BGmisc/man/royal92.Rd |only BGmisc-1.3.5/BGmisc/man/summarizePedigrees.Rd | 3 BGmisc-1.3.5/BGmisc/tests/testthat/test-calculateFamilySize.R | 22 BGmisc-1.3.5/BGmisc/tests/testthat/test-checkPedigreeNetwork.R |only BGmisc-1.3.5/BGmisc/tests/testthat/test-checkSex.R | 27 BGmisc-1.3.5/BGmisc/tests/testthat/test-convertPedigree.R | 209 ++++ BGmisc-1.3.5/BGmisc/tests/testthat/test-makeLinks.R |only BGmisc-1.3.5/BGmisc/tests/testthat/test-plotPedigree.R |only BGmisc-1.3.5/BGmisc/tests/testthat/test-readPedigrees.R | 33 BGmisc-1.3.5/BGmisc/tests/testthat/test-simulatePedigree.R | 29 BGmisc-1.3.5/BGmisc/tests/testthat/test-tweakPedigree.R | 12 BGmisc-1.3.5/BGmisc/vignettes/analyticrelatedness.Rmd | 46 - BGmisc-1.3.5/BGmisc/vignettes/modelingrelatedness.Rmd | 3 BGmisc-1.3.5/BGmisc/vignettes/partial.Rmd |only BGmisc-1.3.5/BGmisc/vignettes/validation.Rmd | 45 - 68 files changed, 1413 insertions(+), 687 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types
of resampling objects (e.g. bootstrap, cross-validation).
Author: Hannah Frick [aut, cre] ,
Fanny Chow [aut],
Max Kuhn [aut],
Michael Mahoney [aut] ,
Julia Silge [aut] ,
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>
Diff between rsample versions 1.2.1 dated 2024-03-25 and 1.3.0 dated 2025-04-02
rsample-1.2.1/rsample/R/nest.R |only rsample-1.2.1/rsample/tests/testthat/_snaps/initial.md |only rsample-1.2.1/rsample/tests/testthat/_snaps/nesting.md |only rsample-1.2.1/rsample/tests/testthat/_snaps/strata.md |only rsample-1.2.1/rsample/tests/testthat/_snaps/validation.md |only rsample-1.2.1/rsample/tests/testthat/test-for-pred.R |only rsample-1.2.1/rsample/tests/testthat/test-initial.R |only rsample-1.2.1/rsample/tests/testthat/test-make-splits.R |only rsample-1.2.1/rsample/tests/testthat/test-names.R |only rsample-1.2.1/rsample/tests/testthat/test-nesting.R |only rsample-1.2.1/rsample/tests/testthat/test-rolling.R |only rsample-1.2.1/rsample/tests/testthat/test-strata.R |only rsample-1.2.1/rsample/tests/testthat/test-validation.R |only rsample-1.3.0/rsample/DESCRIPTION | 12 rsample-1.3.0/rsample/MD5 | 213 +- rsample-1.3.0/rsample/NAMESPACE | 32 rsample-1.3.0/rsample/NEWS.md | 65 rsample-1.3.0/rsample/R/apparent.R | 5 rsample-1.3.0/rsample/R/boot.R | 8 rsample-1.3.0/rsample/R/bootci.R | 272 ++- rsample-1.3.0/rsample/R/caret.R | 33 rsample-1.3.0/rsample/R/clustering.R | 4 rsample-1.3.0/rsample/R/compat-vctrs-helpers.R | 53 rsample-1.3.0/rsample/R/complement.R | 9 rsample-1.3.0/rsample/R/fingerprint.R |only rsample-1.3.0/rsample/R/form_pred.R | 2 rsample-1.3.0/rsample/R/import-standalone-obj-type.R |only rsample-1.3.0/rsample/R/import-standalone-types-check.R |only rsample-1.3.0/rsample/R/initial_split.R | 52 rsample-1.3.0/rsample/R/initial_validation_split.R | 41 rsample-1.3.0/rsample/R/inner_split.R |only rsample-1.3.0/rsample/R/labels.R | 19 rsample-1.3.0/rsample/R/loo.R | 2 rsample-1.3.0/rsample/R/make_groups.R | 27 rsample-1.3.0/rsample/R/make_strata.R | 36 rsample-1.3.0/rsample/R/mc.R | 12 rsample-1.3.0/rsample/R/misc.R | 248 --- rsample-1.3.0/rsample/R/nested_cv.R |only rsample-1.3.0/rsample/R/permutations.R | 15 rsample-1.3.0/rsample/R/printing.R | 6 rsample-1.3.0/rsample/R/reg_intervals.R | 16 rsample-1.3.0/rsample/R/reshuffle_rset.R |only rsample-1.3.0/rsample/R/reverse_splits.R |only rsample-1.3.0/rsample/R/rolling_origin.R | 16 rsample-1.3.0/rsample/R/rsample-package.R | 11 rsample-1.3.0/rsample/R/rset.R | 14 rsample-1.3.0/rsample/R/rsplit.R | 37 rsample-1.3.0/rsample/R/slide.R | 46 rsample-1.3.0/rsample/R/tidy.R | 16 rsample-1.3.0/rsample/R/validation_set.R | 33 rsample-1.3.0/rsample/R/validation_split.R | 11 rsample-1.3.0/rsample/R/vfold.R | 81 - rsample-1.3.0/rsample/build/vignette.rds |binary rsample-1.3.0/rsample/inst/doc/Common_Patterns.R | 2 rsample-1.3.0/rsample/inst/doc/Common_Patterns.Rmd | 6 rsample-1.3.0/rsample/inst/doc/Common_Patterns.html | 16 rsample-1.3.0/rsample/inst/doc/Working_with_rsets.Rmd | 9 rsample-1.3.0/rsample/inst/doc/Working_with_rsets.html | 734 ++-------- rsample-1.3.0/rsample/inst/doc/rsample.html | 422 ----- rsample-1.3.0/rsample/man/add_resample_id.Rd | 2 rsample-1.3.0/rsample/man/as.data.frame.rsplit.Rd | 6 rsample-1.3.0/rsample/man/bootstraps.Rd | 2 rsample-1.3.0/rsample/man/dot-get_split_args.Rd |only rsample-1.3.0/rsample/man/form_pred.Rd | 2 rsample-1.3.0/rsample/man/get_fingerprint.Rd | 4 rsample-1.3.0/rsample/man/group_bootstraps.Rd | 2 rsample-1.3.0/rsample/man/initial_split.Rd | 11 rsample-1.3.0/rsample/man/initial_validation_split.Rd | 7 rsample-1.3.0/rsample/man/inner_split.Rd |only rsample-1.3.0/rsample/man/int_pctl.Rd | 56 rsample-1.3.0/rsample/man/labels.rset.Rd | 5 rsample-1.3.0/rsample/man/make_groups.Rd | 2 rsample-1.3.0/rsample/man/make_strata.Rd | 1 rsample-1.3.0/rsample/man/nested_cv.Rd | 24 rsample-1.3.0/rsample/man/permutations.Rd | 4 rsample-1.3.0/rsample/man/reg_intervals.Rd | 12 rsample-1.3.0/rsample/man/reshuffle_rset.Rd | 2 rsample-1.3.0/rsample/man/reverse_splits.Rd | 2 rsample-1.3.0/rsample/man/rolling_origin.Rd | 7 rsample-1.3.0/rsample/man/rsample2caret.Rd | 8 rsample-1.3.0/rsample/man/tidy.rsplit.Rd | 12 rsample-1.3.0/rsample/man/validation_set.Rd | 2 rsample-1.3.0/rsample/tests/testthat/_snaps/boot.md | 17 rsample-1.3.0/rsample/tests/testthat/_snaps/bootci.md | 224 ++- rsample-1.3.0/rsample/tests/testthat/_snaps/clustering.md | 48 rsample-1.3.0/rsample/tests/testthat/_snaps/form_pred.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/initial_split.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/initial_validation_split.md | 4 rsample-1.3.0/rsample/tests/testthat/_snaps/labels.md | 34 rsample-1.3.0/rsample/tests/testthat/_snaps/make_strata.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/mc.md | 87 + rsample-1.3.0/rsample/tests/testthat/_snaps/misc.md | 163 -- rsample-1.3.0/rsample/tests/testthat/_snaps/nested_cv.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/permutations.md | 39 rsample-1.3.0/rsample/tests/testthat/_snaps/reg_intervals.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/reshuffle_rset.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/reverse_splits.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/rolling_origin.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/rset.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/rsplit.md | 70 rsample-1.3.0/rsample/tests/testthat/_snaps/slide.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/validation_set.md | 1 rsample-1.3.0/rsample/tests/testthat/_snaps/validation_split.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/vfold.md | 202 ++ rsample-1.3.0/rsample/tests/testthat/test-boot.R | 8 rsample-1.3.0/rsample/tests/testthat/test-bootci.R | 312 ++-- rsample-1.3.0/rsample/tests/testthat/test-caret.R | 405 +++-- rsample-1.3.0/rsample/tests/testthat/test-clustering.R | 31 rsample-1.3.0/rsample/tests/testthat/test-form_pred.R |only rsample-1.3.0/rsample/tests/testthat/test-initial_split.R |only rsample-1.3.0/rsample/tests/testthat/test-inner_split.R |only rsample-1.3.0/rsample/tests/testthat/test-labels.R | 16 rsample-1.3.0/rsample/tests/testthat/test-make_strata.R |only rsample-1.3.0/rsample/tests/testthat/test-mc.R | 44 rsample-1.3.0/rsample/tests/testthat/test-misc.R | 195 -- rsample-1.3.0/rsample/tests/testthat/test-nested_cv.R |only rsample-1.3.0/rsample/tests/testthat/test-permutations.R | 16 rsample-1.3.0/rsample/tests/testthat/test-reg_intervals.R |only rsample-1.3.0/rsample/tests/testthat/test-reshuffle_rset.R |only rsample-1.3.0/rsample/tests/testthat/test-reverse_splits.R |only rsample-1.3.0/rsample/tests/testthat/test-rolling_origin.R |only rsample-1.3.0/rsample/tests/testthat/test-rset.R | 31 rsample-1.3.0/rsample/tests/testthat/test-rsplit.R | 42 rsample-1.3.0/rsample/tests/testthat/test-slide.R | 72 rsample-1.3.0/rsample/tests/testthat/test-validation_split.R |only rsample-1.3.0/rsample/tests/testthat/test-vfold.R | 144 + rsample-1.3.0/rsample/vignettes/Applications/Intervals.Rmd | 2 rsample-1.3.0/rsample/vignettes/Common_Patterns.Rmd | 6 rsample-1.3.0/rsample/vignettes/Working_with_rsets.Rmd | 9 129 files changed, 2657 insertions(+), 2374 deletions(-)
Title: Friendly Input-Output Analysis
Description: Simplifies the process of importing and managing input-output
matrices from 'Microsoft Excel' into R, and provides a suite of functions for
analysis. It leverages the 'R6' class for clean, memory-efficient
object-oriented programming. Furthermore, all linear algebra computations are
implemented in 'Rust' to achieve highly optimized performance.
Author: Alberson da Silva Miranda [aut, cre, cph]
,
Celso Bissoli Sessa [dtc]
Maintainer: Alberson da Silva Miranda <albersonmiranda@hotmail.com>
Diff between fio versions 0.1.2 dated 2024-08-27 and 0.1.5 dated 2025-04-02
fio-0.1.2/fio/src/Makevars |only fio-0.1.2/fio/src/Makevars.ucrt |only fio-0.1.2/fio/src/Makevars.win |only fio-0.1.5/fio/DESCRIPTION | 14 fio-0.1.5/fio/MD5 | 52 +- fio-0.1.5/fio/NEWS.md | 16 fio-0.1.5/fio/R/extendr-wrappers.R | 1 fio-0.1.5/fio/R/import_iom.R | 2 fio-0.1.5/fio/R/r6.R | 91 ++-- fio-0.1.5/fio/README.md | 13 fio-0.1.5/fio/build/partial.rdb |binary fio-0.1.5/fio/build/vignette.rds |binary fio-0.1.5/fio/configure | 2 fio-0.1.5/fio/configure.win | 2 fio-0.1.5/fio/data/br_2020.rda |binary fio-0.1.5/fio/inst/doc/getting_started.html | 40 +- fio-0.1.5/fio/inst/extdata/iom/br/2020.xlsx |binary fio-0.1.5/fio/man/figures/example_leontief_inverse.png |binary fio-0.1.5/fio/man/import_element.Rd | 2 fio-0.1.5/fio/man/iom.Rd | 104 +++-- fio-0.1.5/fio/src/Makevars.in |only fio-0.1.5/fio/src/Makevars.win.in |only fio-0.1.5/fio/src/rust/Cargo.lock | 319 ++++++++++------- fio-0.1.5/fio/src/rust/Cargo.toml | 8 fio-0.1.5/fio/src/rust/src/lib.rs | 3 fio-0.1.5/fio/src/rust/vendor-config.toml | 5 fio-0.1.5/fio/src/rust/vendor.tar.xz |binary fio-0.1.5/fio/tests/testthat/test-computations.R | 13 fio-0.1.5/fio/tools/config.R |only fio-0.1.5/fio/tools/msrv.R | 4 30 files changed, 395 insertions(+), 296 deletions(-)
Title: Allelic Series Test
Description: Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1016/j.ajhg.2023.07.001>.
Author: Zachary McCaw [aut, cre] ,
Christoph Klein [ctb] ,
Thomas Soare [ctb] ,
Jianhui Gao [ctb] ,
insitro [cph]
Maintainer: Zachary McCaw <zmccaw@alumni.harvard.edu>
Diff between AllelicSeries versions 0.1.1.2 dated 2024-11-23 and 0.1.1.5 dated 2025-04-02
DESCRIPTION | 10 - MD5 | 46 +++--- NAMESPACE | 2 NEWS.md | 3 R/allelic_series.R | 13 + R/generate_data.R | 17 ++ R/generate_sumstats.R | 15 +- R/input_checks.R | 1 R/utilities.R | 107 +++++++++++++++ build/vignette.rds |binary inst/doc/coast.R | 33 ++++ inst/doc/coast.Rmd | 48 ++++++ inst/doc/coast.html | 240 +++++++++++++++++++++------------- inst/doc/covariate_inference.R |only inst/doc/covariate_inference.Rmd |only inst/doc/covariate_inference.html |only man/AllelicSeries-package.Rd | 2 man/COAST.Rd | 4 man/CalcSumstats.Rd | 4 man/CollapseGeno.Rd |only man/ContainsInt.Rd |only man/DGP.Rd | 7 tests/testthat/test-allelic_series.R | 78 ++++++++++- tests/testthat/test-data_generation.R | 28 +++ tests/testthat/test-utils.R | 97 +++++++++++++ vignettes/coast.Rmd | 48 ++++++ vignettes/covariate_inference.Rmd |only 27 files changed, 675 insertions(+), 128 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.51 dated 2025-02-19 and 0.52 dated 2025-04-02
xfun-0.51/xfun/man/attr.Rd |only xfun-0.52/xfun/DESCRIPTION | 11 +-- xfun-0.52/xfun/MD5 | 64 ++++++++++---------- xfun-0.52/xfun/NAMESPACE | 3 xfun-0.52/xfun/NEWS.md | 18 +++++ xfun-0.52/xfun/R/algorithm.R |only xfun-0.52/xfun/R/cache.R | 13 +++- xfun-0.52/xfun/R/citation.R | 15 ++++ xfun-0.52/xfun/R/command.R | 11 --- xfun-0.52/xfun/R/data-structure.R | 2 xfun-0.52/xfun/R/image.R | 14 ---- xfun-0.52/xfun/R/io.R | 32 +++++++++- xfun-0.52/xfun/R/knitr.R | 17 ++++- xfun-0.52/xfun/R/markdown.R | 4 - xfun-0.52/xfun/R/packages.R | 2 xfun-0.52/xfun/R/record.R | 6 - xfun-0.52/xfun/R/utils.R | 14 +++- xfun-0.52/xfun/R/yaml.R | 17 +++-- xfun-0.52/xfun/build/vignette.rds |binary xfun-0.52/xfun/inst/doc/xfun.R | 6 - xfun-0.52/xfun/inst/doc/xfun.Rmd | 66 +------------------- xfun-0.52/xfun/inst/doc/xfun.html | 89 ++++++---------------------- xfun-0.52/xfun/man/attr2.Rd |only xfun-0.52/xfun/man/cache_exec.Rd | 4 + xfun-0.52/xfun/man/cache_rds.Rd | 11 +++ xfun-0.52/xfun/man/divide_chunk.Rd | 8 ++ xfun-0.52/xfun/man/pkg_bib.Rd | 10 ++- xfun-0.52/xfun/man/rand_unit.Rd |only xfun-0.52/xfun/man/upload_ftp.Rd | 6 - xfun-0.52/xfun/man/upload_imgur.Rd | 2 xfun-0.52/xfun/man/url_destination.Rd |only xfun-0.52/xfun/src/init.c | 2 xfun-0.52/xfun/src/rand_lcg.c |only xfun-0.52/xfun/tests/test-cran/test-utils.R | 6 - xfun-0.52/xfun/tests/test-cran/test-yaml.R | 4 + xfun-0.52/xfun/vignettes/xfun.Rmd | 66 +------------------- 36 files changed, 230 insertions(+), 293 deletions(-)
Title: Sample Size Calculation for Propensity Score Analysis
Description: Sample size calculations in causal inference with observational data are increasingly desired. This package is a tool to calculate sample size under prespecified power with minimal summary quantities needed.
Author: Bo Liu [aut, cre],
Xiaoxiao Zhou [ctb],
Fan Li [ctb]
Maintainer: Bo Liu <bl226@duke.edu>
Diff between PSpower versions 0.1.0 dated 2025-01-15 and 0.1.1 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 10 +- R/PSpower.R | 229 +++++++++++++++++++++++++--------------------------- R/util.R | 23 +---- man/PSpower.Rd | 29 ++---- man/plot.PSpower.Rd | 3 6 files changed, 143 insertions(+), 157 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 0.10.0 dated 2025-01-29 and 0.11.3 dated 2025-04-02
DESCRIPTION | 12 +- MD5 | 42 +++++---- NAMESPACE | 39 +++++++++ NEWS.md | 37 ++++++++ R/createOctaveLevel.R | 169 ++++++++++++--------------------------- R/evaluateDeployment.R |only R/evaluateRecordings.R |only R/formatEffort.R | 40 +++++++-- R/loadDetectionData.R | 128 ++++++++++++++++------------- R/loadMantaNc.R | 52 +++++++----- R/loadMultiscapeData.R | 13 +-- R/loadSoundscapeData.R | 109 ++++++++++++++++++++----- R/plotDetectionBoxplot.R | 6 + R/plotQAQC.R |only R/runQAQCReview.R |only R/utils.R | 13 ++- man/createOctaveLevel.Rd | 30 +++--- man/evaluateDeployment.Rd |only man/evaluateRecordings.Rd |only man/loadDetectionData.Rd | 11 +- man/loadMultiscapeData.Rd | 12 +- man/loadSoundscapeData.Rd | 7 + man/plotQAQC.Rd |only man/runQAQCReview.Rd |only tests/testthat/test-detection.R | 9 ++ tests/testthat/test-soundscape.R | 28 +++--- 26 files changed, 472 insertions(+), 285 deletions(-)
Title: Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq)
Description: This lightweight R package provides a method for normalizing and denoising protein expression data from droplet based single cell experiments. Raw protein Unique Molecular Index (UMI) counts from sequencing DNA-conjugated antibody derived tags (ADT) in droplets (e.g. 'CITE-seq') have substantial measurement noise. Our experiments and computational modeling revealed two major components of this noise: 1) protein-specific noise originating from ambient, unbound antibody encapsulated in droplets that can be accurately inferred via the expected protein counts detected in empty droplets, and 2) droplet/cell-specific noise revealed via the shared variance component associated with isotype antibody controls and background protein counts in each cell. This package normalizes and removes both of these sources of noise from raw protein data derived from methods such as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' data from the Mission Bio platform, etc. See the vignette for tut [...truncated...]
Author: Matthew Mule [aut, cre] ,
Andrew Martins [aut] ,
John Tsang [pdr]
Maintainer: Matthew Mule <mattmule@gmail.com>
Diff between dsb versions 1.0.4 dated 2024-06-15 and 2.0.0 dated 2025-04-02
DESCRIPTION | 8 MD5 | 48 +- NAMESPACE | 1 NEWS.md | 4 R/ModelNegativeADTnorm.r | 63 ++- R/dsb.r | 143 ++++---- README.md | 284 +++++++++------- build/vignette.rds |binary inst/doc/additional_topics.R | 22 - inst/doc/additional_topics.html | 356 ++++++++++----------- inst/doc/end_to_end_workflow.R | 36 +- inst/doc/end_to_end_workflow.html | 622 ++++++++++++++++++------------------- inst/doc/fastkm.R |only inst/doc/fastkm.Rmd |only inst/doc/fastkm.html |only inst/doc/no_empty_drops.R | 17 - inst/doc/no_empty_drops.Rmd | 12 inst/doc/no_empty_drops.html | 195 +++++------ inst/doc/understanding_dsb.R | 18 - inst/doc/understanding_dsb.html | 408 ++++++++++++------------ man/DSBNormalizeProtein.Rd | 47 +- man/ModelNegativeADTnorm.Rd | 11 man/figures/dsb_arguments.png |only man/figures/timingsfig2.png |only man/figures/vignette/compare.png |only man/figures/vignette/corr.png |only tests/testthat/test_dsb_function.R | 61 ++- vignettes/fastkm.Rmd |only vignettes/no_empty_drops.Rmd | 12 29 files changed, 1238 insertions(+), 1130 deletions(-)
Title: Parallel Numerical Derivatives, Gradients, Jacobians, and
Hessians of Arbitrary Accuracy Order
Description: Numerical derivatives through finite-difference approximations
can be calculated using the 'pnd' package with parallel capabilities and
optimal step-size selection to improve accuracy. These functions facilitate
efficient computation of derivatives, gradients, Jacobians, and Hessians,
allowing for more evaluations to reduce the mathematical and machine errors.
Designed for compatibility with the 'numDeriv' package,
which has not received updates in several years, it introduces advanced features
such as computing derivatives of arbitrary order, improving
the accuracy of Hessian approximations by avoiding repeated differencing,
and parallelising slow functions on Windows, Mac, and Linux.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between pnd versions 0.0.9 dated 2025-03-11 and 0.0.10 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 42 +++++----- NEWS.md | 1 R/gradient.R | 99 +++++++++++++------------ R/step-select.R | 118 +++++++++++++++--------------- R/zzz.R | 2 build/partial.rdb |binary inst/CITATION | 28 +++---- inst/doc/compatibility-with-numDeriv.html | 15 ++- inst/doc/fast-and-accurate.html | 7 + inst/doc/step-size-selection.html | 7 + man/GenD.Rd | 14 +++ man/Grad.Rd | 24 ++++-- man/Jacobian.Rd | 14 +++ man/checkDimensions.Rd | 6 + man/step.DV.Rd | 21 ++--- tests/testthat/Rplots.pdf |binary tests/testthat/test-Grad.R | 14 +++ tests/testthat/test-Jacobian.R | 12 +++ tests/testthat/test-gradstep.R | 4 - tests/testthat/test-step.CR.R | 2 tests/testthat/test-step.DV.R | 9 +- 22 files changed, 262 insertions(+), 183 deletions(-)
Title: Methods for Penetrance Estimation in Family-Based Studies
Description: Implements statistical methods for estimating disease penetrance in
family-based studies. Penetrance refers to the probability of disease§
manifestation in individuals carrying specific genetic variants. The package
provides tools for age-specific penetrance estimation, handling missing data,
and accounting for ascertainment bias in family studies.
Cite as: Kubista, N., Braun, D. & Parmigiani, G. (2024) <doi:10.48550/arXiv.2411.18816>.
Author: Nicolas Kubista [aut, cre],
BayesMendel Lab [aut]
Maintainer: Nicolas Kubista <bmendel@jimmy.harvard.edu>
Diff between penetrance versions 0.1.0 dated 2025-03-03 and 0.1.1 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 14 +- R/helpers.R | 8 - R/mhChain.R | 187 ++++++++++++++++++++++++++--------- R/mhLoglikehood.r | 6 - R/penetranceMain.R | 277 ++++++++++++++++++++++++++++++++++++++++++----------- man/mhChain.Rd | 28 ++--- man/penetrance.Rd | 33 +++--- 8 files changed, 411 insertions(+), 148 deletions(-)
Title: Precipitation R Recipes
Description: An open-access tool/framework to download, validate, visualize, and
analyze multi-source precipitation data. More information and an example of
implementation can be found in Vargas Godoy and Markonis (2023,
<doi:10.1016/j.envsoft.2023.105711>).
Author: Mijael Rodrigo Vargas Godoy [aut, cre]
,
Yannis Markonis [aut, ths]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between pRecipe versions 3.0.2 dated 2024-12-07 and 3.0.3 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++++++-------- NAMESPACE | 4 ---- R/core_functions.R | 12 ------------ R/csi.R |only R/far.R |only R/nse.R |only R/pod.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/case_study.html | 4 ++-- inst/doc/introduction.html | 4 ++-- man/csi.Rd |only man/far.Rd |only man/nse.Rd |only man/pod.Rd |only man/reexports.Rd | 6 +----- 17 files changed, 24 insertions(+), 36 deletions(-)
Title: Nonparametric Bootstrap Test for Regression Monotonicity
Description: Implements nonparametric bootstrap tests for detecting monotonicity
in regression functions from Hall, P. and Heckman, N. (2000) <doi:10.1214/aos/1016120363>
Includes tools for visualizing results using Nadaraya-Watson kernel regression and supports
efficient computation with 'C++'.
Author: Dylan Huynh [aut, cre]
Maintainer: Dylan Huynh <dylanhuynh@utexas.edu>
Diff between MonotonicityTest versions 1.0 dated 2025-01-17 and 1.1 dated 2025-04-02
DESCRIPTION | 7 ++-- MD5 | 13 ++++--- NAMESPACE | 6 ++- R/diabetes.R |only R/main.R | 74 +++++++++++++++++++++++++++++++++++++-------- data |only man/create_kernel_plot.Rd | 14 ++++++-- man/diabetes.Rd |only tests/testthat/test-main.R | 27 +++++++++++++--- 9 files changed, 110 insertions(+), 31 deletions(-)
More information about MonotonicityTest at CRAN
Permanent link
Title: Identification of Periodically Expressed Genes
Description: The GeneCycle package implements the approaches of Wichert
et al. (2004) <doi:10.1093/bioinformatics/btg364>, Ahdesmaki
et al. (2005) <doi:10.1186/1471-2105-6-117> and Ahdesmaki et al.
(2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically
expressed genes from gene expression time series data.
Author: Miika Ahdesmaki [aut, cre],
Konstantinos Fokianos [aut],
Korbinian Strimmer [aut]
Maintainer: Miika Ahdesmaki <miika.ahdesmaki@gmail.com>
Diff between GeneCycle versions 1.1.5 dated 2021-01-05 and 1.1.6 dated 2025-04-02
CHANGES | 3 +++ DESCRIPTION | 26 ++++++++++++++++++++------ MD5 | 16 ++++++++-------- man/avpg.Rd | 2 +- man/dominant.freqs.Rd | 2 +- man/fisher.g.test.Rd | 2 +- man/is.constant.Rd | 2 +- man/periodogram.Rd | 2 +- man/robust.g.test.Rd | 2 +- 9 files changed, 37 insertions(+), 20 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre] ,
Hugh Chipman [aut],
Robert McCulloch [aut],
Armon Dadgar [ctb] ,
R Core Team [ctb] ,
Guido U Draheim [ctb] ,
Maarten Bosmans [ctb] ,
Christophe Tournayre [ctb] ,
Michael Petch [ctb] ,
Rafael de Lucena Valle [ctb] ,
Steven G [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-30 dated 2024-12-03 and 0.9-32 dated 2025-04-02
dbarts-0.9-30/dbarts/tests/testthat |only dbarts-0.9-30/dbarts/tests/testthat.R |only dbarts-0.9-32/dbarts/DESCRIPTION | 10 dbarts-0.9-32/dbarts/MD5 | 139 - dbarts-0.9-32/dbarts/R/A_class.R | 267 +- dbarts-0.9-32/dbarts/R/bart.R | 48 dbarts-0.9-32/dbarts/R/dbarts.R | 1333 +++++----- dbarts-0.9-32/dbarts/R/generics.R | 5 dbarts-0.9-32/dbarts/R/multipleAssignment.R | 1 dbarts-0.9-32/dbarts/R/partialDependence.R | 7 dbarts-0.9-32/dbarts/R/rbart.R | 14 dbarts-0.9-32/dbarts/build/vignette.rds |binary dbarts-0.9-32/dbarts/configure.ac | 2 dbarts-0.9-32/dbarts/inst/NEWS.Rd | 31 dbarts-0.9-32/dbarts/inst/doc/gibbs_sampler_mixture_model.pdf |binary dbarts-0.9-32/dbarts/inst/doc/working_with_saved_trees.pdf |binary dbarts-0.9-32/dbarts/inst/include/dbarts/R_C_interface.hpp | 10 dbarts-0.9-32/dbarts/inst/include/dbarts/bartFit.hpp | 10 dbarts-0.9-32/dbarts/inst/include/dbarts/control.hpp | 99 dbarts-0.9-32/dbarts/inst/tinytest |only dbarts-0.9-32/dbarts/man/bart.Rd | 4 dbarts-0.9-32/dbarts/man/dbartsSampler-class.Rd | 20 dbarts-0.9-32/dbarts/src/R_C_interface.cpp | 31 dbarts-0.9-32/dbarts/src/R_interface.cpp | 12 dbarts-0.9-32/dbarts/src/R_interface_common.cpp | 2 dbarts-0.9-32/dbarts/src/R_interface_sampler.cpp | 50 dbarts-0.9-32/dbarts/src/R_interface_sampler.hpp | 8 dbarts-0.9-32/dbarts/src/crossvalidate.cpp | 4 dbarts-0.9-32/dbarts/src/dbarts/bartFit.cpp | 339 +- dbarts-0.9-32/dbarts/src/dbarts/tree.cpp | 14 dbarts-0.9-32/dbarts/src/dbarts/tree.hpp | 4 dbarts-0.9-32/dbarts/src/external/randomBase.c | 10 dbarts-0.9-32/dbarts/src/include/external/random.h | 2 dbarts-0.9-32/dbarts/src/include/misc/thread.h | 3 dbarts-0.9-32/dbarts/src/misc/hierarchicalThreadManager.c | 4 dbarts-0.9-32/dbarts/src/misc/partition_body.c | 79 dbarts-0.9-32/dbarts/src/misc/partition_neon.c | 39 dbarts-0.9-32/dbarts/src/rc/bounds.c | 71 dbarts-0.9-32/dbarts/tests/tinytest.R |only 39 files changed, 1653 insertions(+), 1019 deletions(-)
Title: Retrieval and Processing of the Spanish National Forest
Inventory
Description: Data sets of the Spanish National Forest Inventory <https://www.miteco.gob.es/es/biodiversidad/servicios/banco-datos-naturaleza/informacion-disponible.html> are processed to compute tree metrics and statistics. Function metrics2Vol() controls most of the routines.
Author: Wilson Lara [aut, cre] ,
Cristobal Ordonez [aut] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between basifoR versions 0.4 dated 2021-09-20 and 0.4.1 dated 2025-04-02
DESCRIPTION | 30 ++++++++++++++++++++++++------ MD5 | 22 +++++++++++----------- NEWS | 14 +++++++++++++- R/nfiMetrics.R | 2 +- R/readNFI.R | 6 +++--- R/urlToTemp.R | 2 +- man/dbhMetric.Rd | 2 +- man/dendroMetrics.Rd | 16 ++++++++-------- man/metrics2Vol.Rd | 2 +- man/nfiMetrics.Rd | 4 ++-- man/readNFI.Rd | 20 ++++++++++---------- man/urlToTemp.Rd | 4 ++-- 12 files changed, 77 insertions(+), 47 deletions(-)
Title: 'shiny' App for National Accounts
Description: Provides a comprehensive suite of tools for analyzing Pakistan's Quarterly National Accounts data. Users can gain detailed insights into Pakistan's economic performance, visualize quarterly trends, and detect patterns and anomalies in key economic indicators. Compare sector contributions—including agriculture, industry, and services—to understand their influence on economic growth or decline. Customize analyses by filtering and manipulating data to focus on specific areas of interest. Ideal for policymakers, researchers, and analysts aiming to make informed, data-driven decisions based on timely and detailed economic insights.
Author: Muhammad Yaseen [aut, cre, cph]
,
Zahid Asghar [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakNAcc versions 0.1.0 dated 2024-11-11 and 0.3.0 dated 2025-04-02
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NEWS.md | 6 ++++ README.md | 17 +++++++++-- inst/shinyapp/GNIConstant.RDS |binary inst/shinyapp/GNICurrent.RDS |binary inst/shinyapp/NAConstant.RDS |binary inst/shinyapp/NACurrent.RDS |binary inst/shinyapp/rsconnect/shinyapps.io/myaseen208/PakNAcc.dcf | 2 - inst/shinyapp/ui.R | 8 ++--- 10 files changed, 37 insertions(+), 20 deletions(-)
Title: Applied Latent Semantic Analysis (LSA) Functions
Description: Provides functions that allow for convenient working with vector space models of semantics/distributional semantic models/word embeddings.
Originally built for LSA models (hence the name), but can be used for all such vector-based models.
For actually building a vector semantic space, use the package 'lsa' or other specialized software.
Downloadable semantic spaces can be found at <https://sites.google.com/site/fritzgntr/software-resources>.
Author: Fritz Guenther [aut, cre]
Maintainer: Fritz Guenther <fritz.guenther@uni-tuebingen.de>
Diff between LSAfun versions 0.7.1 dated 2023-11-17 and 0.8.1 dated 2025-04-02
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 10 ++++++---- NAMESPACE | 2 ++ R/Predication.r | 13 +++++++------ R/centroid_analysis.r |only man/centroid_analysis.Rd |only 7 files changed, 28 insertions(+), 15 deletions(-)
Title: R and C/C++ Wrappers to Run the Leiden find_partition() Function
Description: An R to C/C++ interface that runs the Leiden community
detection algorithm to find a basic partition (). It runs the
equivalent of the 'leidenalg' find_partition() function, which is
given in the 'leidenalg' distribution file
'leiden/src/functions.py'. This package includes the
required source code files from the official 'leidenalg'
distribution and functions from the R 'igraph'
package. The 'leidenalg' distribution is available from
<https://github.com/vtraag/leidenalg/>
and the R 'igraph' package is available from
<https://igraph.org/r/>.
The Leiden algorithm is described in the article by
Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>.
Leidenbase includes code from the packages:
igraph version 0.9.8 with license GPL (>= 2),
leidenalg version 0.8.10 with license GPL 3.
Author: Brent Ewing [aut, cre],
Vincent Traag [ctb],
Gabor Csardi [ctb],
Tamas Nepusz [ctb],
Szabolcs Horvat [ctb],
Fabio Zanini [ctb]
Maintainer: Brent Ewing <bge@uw.edu>
Diff between leidenbase versions 0.1.32 dated 2025-02-05 and 0.1.35 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 8 + build/vignette.rds |binary src/core/isomorphism/foo.c |only src/core/isomorphism/lad.c | 136 ++++++++++++++++---------------- src/core/isomorphism/lad.c.org.20250205 |only 6 files changed, 76 insertions(+), 74 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 there 2014 and 2024 versions are supported.
Author: Nicholas Lyon [aut, cre, cph] ,
Tim Schatto-Eckrodt [aut] ,
Humberto Nappo [ctb]
Maintainer: Nicholas Lyon <njlyon@alumni.iastate.edu>
Diff between dndR versions 2.0.0 dated 2024-04-26 and 3.0.0 dated 2025-04-02
DESCRIPTION | 27 +-- MD5 | 164 ++++++++++++---------- NEWS.md | 15 ++ R/ability_scores.R | 121 ++++++++-------- R/class_block.R | 120 ++++++++++------ R/cr_convert.R | 16 -- R/creature_list.R | 89 ++++++------ R/creature_text.R | 16 +- R/data-doc_creatures.R | 2 R/data-doc_monster-table.R | 2 R/data-doc_spells.R | 2 R/encounter_creator.R | 254 ++++++++++++++++++++++------------ R/mod_calc.R | 10 - R/monster_creator.R | 100 ++++++------- R/monster_stats.R | 21 +- R/npc_creator.R | 20 +- R/party_diagram.R | 131 +++++++++-------- R/pc_creator.R | 76 ++++++---- R/pc_level_calc.R | 18 -- R/probability_plot.R | 18 +- R/race_mods.R | 278 +++++++++++++++++++++++++------------- R/reference_functions.R | 6 R/reroll.R | 4 R/roll.R | 36 +++- R/spell_list.R | 19 +- R/spell_text.R | 16 +- R/xp_cost.R | 66 +++++---- R/xp_pool.R | 147 +++++++++++++------- README.md | 108 +------------- build/vignette.rds |binary data/creatures.rda |binary data/spells.rda |binary inst/doc/dndr_00_dice.html | 18 +- inst/doc/dndr_01_characters.html | 39 ++--- inst/doc/dndr_02_creatures.html | 50 ++++-- inst/doc/dndr_03_spells.html | 24 ++- inst/doc/dndr_04_encounters.R | 20 +- inst/doc/dndr_04_encounters.Rmd | 57 +++++-- inst/doc/dndr_04_encounters.html | 163 ++++++++++++++-------- inst/doc/dndr_05_visuals.html | 10 - inst/doc/dndr_99_dmg-vs-dndr.R | 5 inst/doc/dndr_99_dmg-vs-dndr.Rmd | 7 inst/doc/dndr_99_dmg-vs-dndr.html | 14 - man/ability_scores.Rd | 8 - man/class_block.Rd | 19 +- man/creature_list.Rd | 10 - man/creature_text.Rd | 8 - man/creatures.Rd | 2 man/dndR-package.Rd | 6 man/dnd_classes.Rd | 2 man/dnd_damage_types.Rd | 2 man/dnd_races.Rd | 2 man/encounter_creator.Rd | 26 +++ man/mod_calc.Rd | 2 man/monster_creator.Rd | 4 man/monster_stats.Rd | 8 + man/monster_table.Rd | 2 man/npc_creator.Rd | 2 man/party_diagram.Rd | 4 man/pc_creator.Rd | 23 +-- man/pc_level_calc.Rd | 2 man/probability_plot.Rd | 2 man/race_mods.Rd | 4 man/reroll.Rd | 4 man/roll.Rd | 6 man/spell_list.Rd | 9 - man/spell_text.Rd | 8 - man/spells.Rd | 2 man/xp_cost.Rd | 13 + man/xp_pool.Rd | 15 +- tests |only vignettes/dndr_04_encounters.Rmd | 57 +++++-- vignettes/dndr_99_dmg-vs-dndr.Rmd | 7 73 files changed, 1516 insertions(+), 1052 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>),
Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>)
and several simulation functions. It also allows dealing with intermittent demand based on the
iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between smooth versions 4.1.1 dated 2025-02-03 and 4.2.0 dated 2025-04-02
smooth-4.1.1/smooth/man/auto.ces.Rd |only smooth-4.1.1/smooth/man/auto.gum.Rd |only smooth-4.2.0/smooth/DESCRIPTION | 8 smooth-4.2.0/smooth/MD5 | 116 +++--- smooth-4.2.0/smooth/NAMESPACE | 2 smooth-4.2.0/smooth/NEWS | 11 smooth-4.2.0/smooth/R/RcppExports.R | 4 smooth-4.2.0/smooth/R/adam-ces.R |only smooth-4.2.0/smooth/R/adam-gum.R |only smooth-4.2.0/smooth/R/adam-sma.R | 2 smooth-4.2.0/smooth/R/adam.R | 383 +++++++++++++++------- smooth-4.2.0/smooth/R/adamGeneral.R | 43 ++ smooth-4.2.0/smooth/R/autoces.R | 283 +++++++--------- smooth-4.2.0/smooth/R/autogum.R | 288 +++++++--------- smooth-4.2.0/smooth/R/automsarima.R | 1 smooth-4.2.0/smooth/R/ces.R | 145 +------- smooth-4.2.0/smooth/R/es.R | 6 smooth-4.2.0/smooth/R/gum.R | 181 +--------- smooth-4.2.0/smooth/R/methods.R | 14 smooth-4.2.0/smooth/R/oes.R | 48 +- smooth-4.2.0/smooth/R/oesg.R | 79 ++-- smooth-4.2.0/smooth/R/smooth-package.R | 12 smooth-4.2.0/smooth/README.md | 2 smooth-4.2.0/smooth/build/partial.rdb |binary smooth-4.2.0/smooth/build/vignette.rds |binary smooth-4.2.0/smooth/inst/doc/adam.R | 6 smooth-4.2.0/smooth/inst/doc/adam.html | 228 ++++++------- smooth-4.2.0/smooth/inst/doc/ces.R | 11 smooth-4.2.0/smooth/inst/doc/ces.Rmd | 25 - smooth-4.2.0/smooth/inst/doc/ces.html | 137 +++---- smooth-4.2.0/smooth/inst/doc/es.R | 2 smooth-4.2.0/smooth/inst/doc/es.html | 18 - smooth-4.2.0/smooth/inst/doc/gum.R | 2 smooth-4.2.0/smooth/inst/doc/gum.Rmd | 2 smooth-4.2.0/smooth/inst/doc/gum.html | 137 ++----- smooth-4.2.0/smooth/inst/doc/oes.R | 7 smooth-4.2.0/smooth/inst/doc/oes.Rmd | 5 smooth-4.2.0/smooth/inst/doc/oes.html | 129 +++---- smooth-4.2.0/smooth/inst/doc/simulate.R | 2 smooth-4.2.0/smooth/inst/doc/simulate.Rmd | 4 smooth-4.2.0/smooth/inst/doc/simulate.html | 80 ++-- smooth-4.2.0/smooth/inst/doc/sma.html | 18 - smooth-4.2.0/smooth/inst/doc/smooth.html | 4 smooth-4.2.0/smooth/inst/doc/ssarima.R | 2 smooth-4.2.0/smooth/inst/doc/ssarima.html | 46 +- smooth-4.2.0/smooth/man/adam.Rd | 4 smooth-4.2.0/smooth/man/ces.Rd | 351 +++++++++----------- smooth-4.2.0/smooth/man/forecast.smooth.Rd | 7 smooth-4.2.0/smooth/man/gum.Rd | 352 ++++++++------------ smooth-4.2.0/smooth/man/msarima.Rd | 1 smooth-4.2.0/smooth/man/sim.ces.Rd | 8 smooth-4.2.0/smooth/man/smooth.Rd | 20 - smooth-4.2.0/smooth/src/RcppExports.cpp | 7 smooth-4.2.0/smooth/src/adamGeneral.cpp | 10 smooth-4.2.0/smooth/tests/testthat/test_ces.R | 30 - smooth-4.2.0/smooth/tests/testthat/test_gum.R | 28 - smooth-4.2.0/smooth/tests/testthat/test_ssarima.R | 2 smooth-4.2.0/smooth/vignettes/ces.Rmd | 25 - smooth-4.2.0/smooth/vignettes/gum.Rmd | 2 smooth-4.2.0/smooth/vignettes/oes.Rmd | 5 smooth-4.2.0/smooth/vignettes/simulate.Rmd | 4 61 files changed, 1563 insertions(+), 1786 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.20.4 dated 2025-03-15 and 2.21.2 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Consensus Clustering of Omic Data
Description: Procedures to perform consensus clustering starting from a dissimilarity matrix or a data matrix. It's allowed to select if the subsampling has to be by samples or features. In case of computational heavy load, the procedures can run in parallel.
Author: Stefano Maria Pagnotta [aut, cre, cph]
Maintainer: Stefano Maria Pagnotta <pagnotta@unisannio.it>
Diff between yaConsensus versions 1.0 dated 2021-07-01 and 1.1 dated 2025-04-02
DESCRIPTION | 8 ++-- MD5 | 19 ++++++---- NAMESPACE | 7 ++- R/cut_k_leaves.R |only R/get_ecdf.R |only R/monti.R |only R/plot.yaConsensus.R | 78 +++++++++++++++++++++++++++++++++++-------- R/print.yaConsensus.R | 29 ++++++++------- R/reduce_dist.R |only R/summary.yaConsensus_plot.R | 6 +++ man/monti.Rd |only man/plot.yaConsensus.Rd | 15 ++++++-- man/yaConsensus.Rd | 2 - 13 files changed, 118 insertions(+), 46 deletions(-)
Title: Terrestrial Water Cycle
Description: An open-access tool/framework that constitutes the core functions
to analyze terrestrial water cycle data across various spatio-temporal scales.
Author: Mijael Rodrigo Vargas Godoy [aut, cre]
,
Yannis Markonis [aut]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between twc versions 0.0.1 dated 2024-12-02 and 0.0.2 dated 2025-04-02
twc-0.0.1/twc/R/csi.R |only twc-0.0.1/twc/R/far.R |only twc-0.0.1/twc/R/pod.R |only twc-0.0.1/twc/man/csi.Rd |only twc-0.0.1/twc/man/far.Rd |only twc-0.0.1/twc/man/pod.Rd |only twc-0.0.2/twc/DESCRIPTION | 8 ++++---- twc-0.0.2/twc/MD5 | 18 +++++++----------- twc-0.0.2/twc/NAMESPACE | 8 +++++--- twc-0.0.2/twc/R/fldmean.R | 8 ++++++-- twc-0.0.2/twc/R/globals.R | 8 +++++--- twc-0.0.2/twc/R/rank_repres.R |only twc-0.0.2/twc/README.md | 2 +- twc-0.0.2/twc/man/rank_repres.Rd |only 14 files changed, 28 insertions(+), 24 deletions(-)
Title: Time-Based Rolling Functions
Description: Provides rolling statistical functions based
on date and time windows instead of n-lagged observations.
Author: Michael Schramm [aut, cre, cph]
,
Frank Harrell [ctb]
Maintainer: Michael Schramm <mpschramm@gmail.com>
Diff between tbrf versions 0.1.5 dated 2020-04-09 and 0.1.6 dated 2025-04-02
tbrf-0.1.5/tbrf/tests/spelling.R |only tbrf-0.1.6/tbrf/DESCRIPTION | 18 tbrf-0.1.6/tbrf/MD5 | 40 tbrf-0.1.6/tbrf/NEWS.md | 8 tbrf-0.1.6/tbrf/R/tbr_binom.R | 2 tbrf-0.1.6/tbrf/R/tbr_gmean.R | 33 tbrf-0.1.6/tbrf/R/tbr_mean.R | 14 tbrf-0.1.6/tbrf/R/tbr_median.R | 14 tbrf-0.1.6/tbrf/R/tbr_sd.R | 2 tbrf-0.1.6/tbrf/R/tbr_sum.R | 2 tbrf-0.1.6/tbrf/README.md | 149 +-- tbrf-0.1.6/tbrf/build/vignette.rds |binary tbrf-0.1.6/tbrf/inst/CITATION |only tbrf-0.1.6/tbrf/inst/WORDLIST | 4 tbrf-0.1.6/tbrf/inst/doc/intro_to_tbrf.R | 2 tbrf-0.1.6/tbrf/inst/doc/intro_to_tbrf.html | 526 ++++++----- tbrf-0.1.6/tbrf/man/figures/README-tbr_hour-1.png |binary tbrf-0.1.6/tbrf/man/figures/README-tbr_threehour-1.png |binary tbrf-0.1.6/tbrf/man/gm_mean_ci.Rd | 16 tbrf-0.1.6/tbrf/man/mean_ci.Rd | 12 tbrf-0.1.6/tbrf/man/median_ci.Rd | 12 tbrf-0.1.6/tbrf/tests/testthat/test-internalStatsFunctions.R | 28 22 files changed, 510 insertions(+), 372 deletions(-)
Title: Access the City of Toronto Open Data Portal
Description: Access data from the "City of Toronto
Open Data Portal" (<https://open.toronto.ca>) directly from R.
Author: Sharla Gelfand [aut, cre],
City of Toronto [cph, fnd]
Maintainer: Sharla Gelfand <sharla.gelfand@gmail.com>
Diff between opendatatoronto versions 0.1.5 dated 2022-04-13 and 0.1.6 dated 2025-04-02
opendatatoronto-0.1.5/opendatatoronto/vignettes/articles/multiple_resources_purrr.Rmd |only opendatatoronto-0.1.6/opendatatoronto/DESCRIPTION | 8 opendatatoronto-0.1.6/opendatatoronto/LICENSE | 2 opendatatoronto-0.1.6/opendatatoronto/MD5 | 29 - opendatatoronto-0.1.6/opendatatoronto/NEWS.md | 4 opendatatoronto-0.1.6/opendatatoronto/R/utils.R | 2 opendatatoronto-0.1.6/opendatatoronto/README.md | 140 +++--- opendatatoronto-0.1.6/opendatatoronto/build/vignette.rds |binary opendatatoronto-0.1.6/opendatatoronto/inst/doc/intro-opendatatoronto.html | 216 +++++++++- opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-browse.R | 15 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-get_resource.R | 16 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-list_package_resources.R | 20 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-packages.R | 21 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-utils.R | 7 opendatatoronto-0.1.6/opendatatoronto/vignettes/articles/opendatatoronto.Rmd | 4 opendatatoronto-0.1.6/opendatatoronto/vignettes/articles/spatial_data.Rmd | 87 ---- 16 files changed, 355 insertions(+), 216 deletions(-)
More information about opendatatoronto at CRAN
Permanent link
Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar [aut, cre] ,
Felix Andrews [ctb],
Kevin Wright [ctb] ,
Neil Klepeis [ctb],
Johan Larsson [ctb] ,
Zhijian Wen [cph] ,
Paul Murrell [ctb],
Stefan Eng [ctb] ,
Achim Zeileis [ctb] ,
Alexandre Courtiol [ctb]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.22-6 dated 2024-03-20 and 0.22-7 dated 2025-04-02
lattice-0.22-6/lattice/man/foo |only lattice-0.22-7/lattice/ChangeLog | 76 ++++++++++ lattice-0.22-7/lattice/DESCRIPTION | 8 - lattice-0.22-7/lattice/MD5 | 47 +++--- lattice-0.22-7/lattice/build/vignette.rds |binary lattice-0.22-7/lattice/data/barley.rda |binary lattice-0.22-7/lattice/data/environmental.rda |binary lattice-0.22-7/lattice/data/ethanol.rda |binary lattice-0.22-7/lattice/data/melanoma.rda |binary lattice-0.22-7/lattice/data/singer.rda |binary lattice-0.22-7/lattice/inst/doc/grid.pdf |binary lattice-0.22-7/lattice/inst/po/de/LC_MESSAGES/R-lattice.mo |binary lattice-0.22-7/lattice/inst/po/en@quot/LC_MESSAGES/R-lattice.mo |binary lattice-0.22-7/lattice/po/R-de.po | 30 ++- lattice-0.22-7/lattice/po/R-fr.po | 13 + lattice-0.22-7/lattice/po/R-it.po | 13 + lattice-0.22-7/lattice/po/R-ko.po | 13 + lattice-0.22-7/lattice/po/R-lattice.pot | 13 + lattice-0.22-7/lattice/po/R-pl.po | 17 +- lattice-0.22-7/lattice/tests/MASSch04.R | 6 lattice-0.22-7/lattice/tests/call.R | 2 lattice-0.22-7/lattice/tests/dataframe-methods.R | 2 lattice-0.22-7/lattice/tests/scales.R | 2 lattice-0.22-7/lattice/tests/temp.R | 6 lattice-0.22-7/lattice/tests/test.R | 12 - 25 files changed, 179 insertions(+), 81 deletions(-)
Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and (Multiple)
Correspondence Analysis (CA) based on the Singular Value Decomposition
(SVD). This package provides S4 classes and methods to compute,
extract, summarize and visualize results of multivariate data
analysis. It also includes methods for partial bootstrap validation
described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et
al. (2006, ISBN: 978-2-10-049616-7).
Author: Nicolas Frerebeau [aut, cre] ,
Jean-Baptiste Fourvel [ctb] ,
Camille Thabard [ctb] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between dimensio versions 0.12.0 dated 2025-02-25 and 0.13.0 dated 2025-04-02
dimensio-0.12.0/dimensio/inst/examples/ex-envelopes.R |only dimensio-0.12.0/dimensio/inst/examples/ex-wrap.R |only dimensio-0.12.0/dimensio/man/viz_biplot.Rd |only dimensio-0.12.0/dimensio/man/wrap.Rd |only dimensio-0.13.0/dimensio/DESCRIPTION | 9 dimensio-0.13.0/dimensio/MD5 | 107 ++-- dimensio-0.13.0/dimensio/NEWS.md | 11 dimensio-0.13.0/dimensio/R/AllGenerics.R | 144 +++-- dimensio-0.13.0/dimensio/R/biplot.R | 55 +- dimensio-0.13.0/dimensio/R/ca.R | 19 dimensio-0.13.0/dimensio/R/dimensio-package.R | 2 dimensio-0.13.0/dimensio/R/export.R | 29 + dimensio-0.13.0/dimensio/R/pca.R | 4 dimensio-0.13.0/dimensio/R/pcoa.R | 8 dimensio-0.13.0/dimensio/R/plot.R | 33 + dimensio-0.13.0/dimensio/R/viz_ellipse.R | 80 +++ dimensio-0.13.0/dimensio/R/viz_hull.R | 75 ++- dimensio-0.13.0/dimensio/R/wrap_ellipses.R | 90 +++ dimensio-0.13.0/dimensio/R/wrap_hull.R | 38 + dimensio-0.13.0/dimensio/README.md | 4 dimensio-0.13.0/dimensio/inst/doc/pca.R | 20 dimensio-0.13.0/dimensio/inst/doc/pca.Rmd | 21 dimensio-0.13.0/dimensio/inst/doc/pca.html | 247 ++++------ dimensio-0.13.0/dimensio/inst/examples/ex-confidence.R |only dimensio-0.13.0/dimensio/inst/examples/ex-ellipses.R |only dimensio-0.13.0/dimensio/inst/examples/ex-hull.R |only dimensio-0.13.0/dimensio/inst/examples/ex-pcoa.R | 14 dimensio-0.13.0/dimensio/inst/examples/ex-plot.R | 2 dimensio-0.13.0/dimensio/inst/examples/ex-tolerance.R |only dimensio-0.13.0/dimensio/inst/tinytest/_snaps/pca_correlations.rds |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/CA_biplot_contrib.svg | 200 ++++---- dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/CA_biplot_sup_col.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/CA_biplot_sup_row.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_biplot_sup_col.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_biplot_sup_row.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_confidence.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_hull.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_tolerance.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_confidence.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_eig.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_hull.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_quali.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_quanti.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_tolerance.svg |only dimensio-0.13.0/dimensio/inst/tinytest/test_biplot_ca.R | 26 - dimensio-0.13.0/dimensio/inst/tinytest/test_biplot_pca.R | 18 dimensio-0.13.0/dimensio/inst/tinytest/test_ca.R | 1 dimensio-0.13.0/dimensio/inst/tinytest/test_pca.R | 4 dimensio-0.13.0/dimensio/inst/tinytest/test_pcoa.R | 34 + dimensio-0.13.0/dimensio/inst/tinytest/test_plot_ca.R | 2 dimensio-0.13.0/dimensio/inst/tinytest/test_plot_pca.R | 30 - dimensio-0.13.0/dimensio/man/PCOA-class.Rd | 14 dimensio-0.13.0/dimensio/man/biplot.Rd | 39 - dimensio-0.13.0/dimensio/man/ca.Rd | 12 dimensio-0.13.0/dimensio/man/dimensio-package.Rd | 2 dimensio-0.13.0/dimensio/man/export.Rd | 3 dimensio-0.13.0/dimensio/man/pcoa.Rd | 14 dimensio-0.13.0/dimensio/man/plot.Rd | 19 dimensio-0.13.0/dimensio/man/screeplot.Rd | 4 dimensio-0.13.0/dimensio/man/viz_confidence.Rd |only dimensio-0.13.0/dimensio/man/viz_contributions.Rd | 4 dimensio-0.13.0/dimensio/man/viz_ellipses.Rd | 115 ---- dimensio-0.13.0/dimensio/man/viz_hull.Rd |only dimensio-0.13.0/dimensio/man/viz_individuals.Rd | 6 dimensio-0.13.0/dimensio/man/viz_tolerance.Rd |only dimensio-0.13.0/dimensio/man/viz_variables.Rd | 6 dimensio-0.13.0/dimensio/vignettes/pca.Rmd | 21 67 files changed, 984 insertions(+), 602 deletions(-)
Title: Timing, Anatomical, Therapeutic and Chemical Based Medication
Clustering
Description: Agglomerative hierarchical clustering with a bespoke distance
measure based on medication similarities in the Anatomical Therapeutic
Chemical Classification System, medication timing and
medication amount or dosage. Tools for summarizing, illustrating and
manipulating the cluster objects are also available.
Author: Anna Laksafoss [aut, cre]
Maintainer: Anna Laksafoss <adls@ssi.dk>
Diff between tame versions 0.0.1 dated 2023-02-23 and 0.2.0 dated 2025-04-02
tame-0.0.1/tame/R/is.medic.R |only tame-0.0.1/tame/R/medic_helpers.R |only tame-0.0.1/tame/R/summary_helpers.R |only tame-0.0.1/tame/man/amounts.Rd |only tame-0.0.1/tame/man/frequencies.Rd |only tame-0.0.1/tame/man/interactions.Rd |only tame-0.0.1/tame/man/medications.Rd |only tame-0.0.1/tame/man/trajectories.Rd |only tame-0.0.1/tame/tests/testthat/test-medic_helpers.R |only tame-0.0.1/tame/tests/testthat/test-summary_helpers.R |only tame-0.2.0/tame/DESCRIPTION | 16 tame-0.2.0/tame/LICENSE | 4 tame-0.2.0/tame/MD5 | 84 - tame-0.2.0/tame/NAMESPACE | 70 + tame-0.2.0/tame/R/crop.R |only tame-0.2.0/tame/R/documenting_data.R | 6 tame-0.2.0/tame/R/employ.R | 202 ++-- tame-0.2.0/tame/R/enrich.R | 5 tame-0.2.0/tame/R/extractors.R | 37 tame-0.2.0/tame/R/medic-utils.R |only tame-0.2.0/tame/R/medic.R | 223 ++-- tame-0.2.0/tame/R/plot-utils.R |only tame-0.2.0/tame/R/plot.R |only tame-0.2.0/tame/R/summary-utils.R |only tame-0.2.0/tame/R/summary.R | 905 +++++++++++++++--- tame-0.2.0/tame/R/tame_package.R | 6 tame-0.2.0/tame/README.md | 23 tame-0.2.0/tame/man/cluster_frequency.Rd |only tame-0.2.0/tame/man/cluster_selector.Rd | 8 tame-0.2.0/tame/man/comedication_count.Rd |only tame-0.2.0/tame/man/construct_color_scales.Rd |only tame-0.2.0/tame/man/construct_plot_data.Rd |only tame-0.2.0/tame/man/construct_time_scale.Rd |only tame-0.2.0/tame/man/default_atc_groups.Rd |only tame-0.2.0/tame/man/employ.Rd | 2 tame-0.2.0/tame/man/enrich.Rd | 4 tame-0.2.0/tame/man/flatten_trajctories.Rd |only tame-0.2.0/tame/man/is.medic.Rd | 2 tame-0.2.0/tame/man/medic.Rd | 12 tame-0.2.0/tame/man/medication_frequency.Rd |only tame-0.2.0/tame/man/method_selector.Rd | 8 tame-0.2.0/tame/man/parameters_constructor.Rd | 6 tame-0.2.0/tame/man/plot_cluster_frequency.Rd |only tame-0.2.0/tame/man/plot_comedication_count.Rd |only tame-0.2.0/tame/man/plot_medication_frequency.Rd |only tame-0.2.0/tame/man/plot_summary.Rd |only tame-0.2.0/tame/man/plot_timing_atc_group.Rd |only tame-0.2.0/tame/man/plot_timing_trajectory.Rd |only tame-0.2.0/tame/man/print.summary.medic.Rd |only tame-0.2.0/tame/man/str.summary.medic.Rd |only tame-0.2.0/tame/man/summary.medic.Rd | 60 - tame-0.2.0/tame/man/summary_crop.Rd |only tame-0.2.0/tame/man/timing_atc_group.Rd |only tame-0.2.0/tame/man/timing_trajectory.Rd |only tame-0.2.0/tame/tests/testthat/test-RcppExports.R | 30 tame-0.2.0/tame/tests/testthat/test-enrich.R | 6 tame-0.2.0/tame/tests/testthat/test-extractors.R | 18 tame-0.2.0/tame/tests/testthat/test-ismedic.R | 6 tame-0.2.0/tame/tests/testthat/test-medic-utils.R |only tame-0.2.0/tame/tests/testthat/test-summary-utils.R |only tame-0.2.0/tame/tests/testthat/test-summary.R | 6 61 files changed, 1261 insertions(+), 488 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <r.puggaard@phonetik.uni-muenchen.de>
Diff between praatpicture versions 1.4.0 dated 2025-01-14 and 1.4.2 dated 2025-04-02
DESCRIPTION | 9 - MD5 | 36 ++-- NEWS.md | 10 + R/formantplot.R | 50 ++++- R/intensityplot.R | 45 ++++- R/pitchplot.R | 90 +++++++--- R/praatpicture.R | 44 +++- R/specplot.R | 74 ++++++-- R/tgplot.R | 55 +++++- R/waveplot.R | 34 ++- inst/shiny/shiny_praatpicture/rsconnect/shinyapps.io/rpuggaardrode/praatpicture.dcf | 2 inst/shiny/shiny_praatpicture/server.R | 18 +- inst/shiny/shiny_praatpicture/ui.R | 3 man/formantplot.Rd | 3 man/intensityplot.Rd | 3 man/pitchplot.Rd | 3 man/praatpicture.Rd | 25 ++ man/tgplot.Rd | 13 + man/waveplot.Rd | 3 19 files changed, 399 insertions(+), 121 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood [aut, cre]
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.9-1 dated 2023-12-20 and 1.9-2 dated 2025-04-02
ChangeLog | 81 + DESCRIPTION | 14 MD5 | 98 - NAMESPACE | 14 R/bam.r | 692 ++++++++----- R/efam.r | 854 ++++++++++++++-- R/fast-REML.r | 372 +++++-- R/gam.fit3.r | 55 - R/gam.fit4.r | 76 - R/gamlss.r | 207 ++-- R/mgcv.r | 488 ++++++--- R/misc.r | 87 + R/mvam.r | 8 R/plots.r | 24 R/smooth.r | 158 ++- build/partial.rdb |binary inst/CITATION | 18 man/NCV.Rd | 36 man/Sl.setup.Rd | 7 man/XWXd.Rd | 16 man/bam.Rd | 11 man/clog.Rd |only man/cpois.Rd |only man/family.mgcv.Rd | 9 man/gam.Rd | 2 man/gam.side.Rd | 2 man/gammals.Rd | 2 man/gevlss.Rd | 11 man/ldetS.Rd | 12 man/lp.Rd |only man/mchol.Rd |only man/mgcv-package.Rd | 2 man/mgcv-parallel.Rd | 6 man/mroot.Rd | 12 man/pcls.Rd | 3 man/predict.gam.Rd | 22 man/slanczos.Rd | 2 man/smooth.construct.gp.smooth.spec.Rd | 2 man/twlss.Rd | 12 src/Makevars | 3 src/discrete.c | 1697 +++++++++++++++++++++++++++++++-- src/gdi.c | 58 - src/init.c | 13 src/magic.c | 6 src/mat.c | 286 ++++- src/matrix.c | 201 --- src/mgcv.c | 153 -- src/mgcv.h | 59 - src/ncv.c | 16 src/qp.c | 125 ++ src/sparse.c | 1 src/tprs.c | 5 52 files changed, 4611 insertions(+), 1427 deletions(-)
Title: Estimation and Testing for a Lognormal-Pareto Mixture
Description: Estimates a lognormal-Pareto mixture by means of the Expectation-Conditional-Maximization-Either algorithm and by maximizing the profile likelihood function. A likelihood ratio test for discriminating between lognormal and Pareto tail is also implemented. See Bee, M. (2022) <doi:10.1007/s11634-022-00497-4>.
Author: Marco Bee [aut, cre]
Maintainer: Marco Bee <marco.bee@unitn.it>
Diff between LNPar versions 1.1.0 dated 2025-03-24 and 1.1.1 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++-- R/dpareto.r | 42 +++++++++++++++++++++--------------------- build/partial.rdb |binary man/dpareto.Rd | 2 +- 6 files changed, 33 insertions(+), 33 deletions(-)
Title: Boltzmann Entropy for Spatial Data
Description: Calculates several entropy metrics for spatial data
inspired by Boltzmann's entropy formula.
It includes metrics introduced by Cushman for landscape mosaics
(Cushman (2015) <doi:10.1007/s10980-015-0305-2>),
and landscape gradients and point patterns
(Cushman (2021) <doi:10.3390/e23121616>); by Zhao and Zhang for
landscape mosaics (Zhao and Zhang (2019) <doi:10.1007/s10980-019-00876-x>);
and by Gao et al. for landscape gradients
(Gao et al. (2018) <doi:10.1111/tgis.12315>; Gao and Li (2019) <doi:10.1007/s10980-019-00854-3>).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between bespatial versions 0.1.2 dated 2024-06-07 and 0.1.3 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/get_distance.R | 2 +- README.md | 12 +++++++----- build/partial.rdb |binary man/figures/README-unnamed-chunk-3-1.png |binary 6 files changed, 17 insertions(+), 15 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: <https://sdmx.org>.
Author: Attilio Mattiocco [aut, cre]
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 3.5-0 dated 2024-11-07 and 3.6-0 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/java/SDMX.jar |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Kim Lopez-Gueell [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut] ,
Xintong Li [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut]
Maintainer: Kim Lopez-Gueell <kim.lopez@spc.ox.ac.uk>
Diff between CohortSurvival versions 1.0.0 dated 2025-03-19 and 1.0.1 dated 2025-04-02
DESCRIPTION | 14 MD5 | 28 NAMESPACE | 84 R/estimateSurvival.R | 3356 +++++++++++++-------------- R/tableSurvival.R | 843 +++--- README.md | 2 inst/doc/a01_Single_event_of_interest.R | 12 inst/doc/a01_Single_event_of_interest.Rmd | 649 ++--- inst/doc/a01_Single_event_of_interest.html | 1436 +++++------ inst/doc/a02_Competing_risk_survival.html | 220 - inst/doc/a03_Further_survival_analyses.html | 22 man/CohortSurvival-package.Rd | 2 tests/testthat/test-reexports-omopgenerics.R | 32 tests/testthat/test-tableSurvival.R | 237 + vignettes/a01_Single_event_of_interest.Rmd | 649 ++--- 15 files changed, 3871 insertions(+), 3715 deletions(-)
More information about CohortSurvival at CRAN
Permanent link
Title: Tools for Biometry and Applied Statistics in Agricultural
Science
Description: Tools designed to perform and evaluate cluster analysis (including Tocher's algorithm),
discriminant analysis and path analysis (standard and under collinearity), as well as some
useful miscellaneous tools for dealing with sample size and optimum plot size calculations.
A test for seed sample heterogeneity is now available. Mantel's permutation test can be found in this package.
A new approach for calculating its power is implemented. biotools also contains tests for genetic covariance components.
Heuristic approaches for performing non-parametric spatial predictions of generic response variables and
spatial gene diversity are implemented.
Author: Anderson Rodrigo da Silva [aut, cre]
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between biotools versions 4.2 dated 2021-08-07 and 4.3 dated 2025-04-02
DESCRIPTION | 11 MD5 | 55 +- NEWS | 11 README.md |only build/vignette.rds |binary inst/CITATION | 41 -- inst/doc/overview.R | 30 - inst/doc/overview.html | 946 ++++++++++++++++++++++++++++-------------------- man/D2.disc.Rd | 10 man/D2.dist.Rd | 2 man/aer.Rd | 2 man/biotools-package.Rd | 26 - man/confusionmatrix.Rd | 2 man/cov2pcov.Rd | 6 man/distClust.Rd | 2 man/findSubsample.Rd | 4 man/fitplotsize.Rd | 6 man/gencovtest.Rd | 38 - man/mantelPower.Rd | 8 man/mantelTest.Rd | 14 man/multcor.test.Rd | 8 man/mvpaircomp.Rd | 14 man/optimumplotsize.Rd | 6 man/raise.matrix.rd | 2 man/sHe.Rd | 22 - man/samplesize.Rd | 24 - man/singh.Rd | 2 man/spatialpred.Rd | 10 man/tocher.Rd | 18 29 files changed, 750 insertions(+), 570 deletions(-)
Title: Secure and Intuitive Access to 'BigDataPE' 'API' Datasets
Description: Designed to simplify the process of retrieving datasets from the 'Big Data PE' platform using secure token-based authentication. It provides functions for securely storing, retrieving, and managing tokens associated with specific datasets, as well as fetching and processing data using the 'httr2' package.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between BigDataPE versions 0.0.95 dated 2025-02-17 and 0.0.96 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS.md |only R/BigDataPE.R | 47 ++++++++++++++++++++++++++--------------------- README.md | 2 +- man/bdpe_fetch_chunks.Rd | 10 +++++----- man/bdpe_fetch_data.Rd | 12 ++++++------ 7 files changed, 48 insertions(+), 42 deletions(-)
Title: SIMulated Structural Equation Modeling
Description: Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Author: Sunthud Pornprasertmanit [aut],
Patrick Miller [aut],
Alexander M. Schoemann [aut] ,
Terrence D. Jorgensen [aut, cre]
,
Corbin Quick [ctb]
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>
Diff between simsem versions 0.5-16 dated 2021-03-28 and 0.5-17 dated 2025-04-02
DESCRIPTION | 18 +- MD5 | 63 ++++----- NAMESPACE | 4 R/analyze.R | 79 ++++++----- R/anova-methods.R | 312 ++++++++++++++++++++++++++--------------------- R/bind.R | 2 R/drawParam.R | 6 R/find.R | 158 ++++++++++++----------- R/generate.R | 6 R/getPowerCoverage.R | 83 ++++++------ R/imposeMissing.R | 4 R/miss.R | 88 +++++++------ R/model.R | 31 +++- R/openMx.R | 4 R/sim.R | 89 +++++++++---- R/summarySimResult.R | 15 +- inst/CITATION |only man/SimDataDist-class.Rd | 116 ++++++++--------- man/SimMissing-class.Rd | 114 ++++++++--------- man/SimResult-class.Rd | 244 ++++++++++++++++++------------------ man/analyze.Rd | 24 +-- man/createData.Rd | 208 +++++++++++++++---------------- man/exportData.Rd | 60 ++++----- man/findPower.Rd | 10 - man/getExtraOutput.Rd | 8 - man/likRatioFit.Rd | 4 man/miss.Rd | 26 +-- man/model.Rd | 54 ++++---- man/modelLavaan.Rd | 4 man/pValue.Rd | 2 man/pValueNested.Rd | 4 man/pValueNonNested.Rd | 4 man/sim.Rd | 24 +-- 33 files changed, 989 insertions(+), 879 deletions(-)
Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with
nanosecond granularity is provided, with easy transition to and from
the standard 'POSIXct' type. Three additional classes offer interval,
period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel [aut, cre] ,
Leonardo Silvestri [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.3.11 dated 2025-01-10 and 0.3.12 dated 2025-04-02
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/nanotime.R | 2 +- build/vignette.rds |binary inst/doc/nanotime-introduction.pdf |binary 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Wai Wong [ctb]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 1.1-0 dated 2025-01-26 and 1.2-0 dated 2025-04-02
Changelog | 6 + DESCRIPTION | 9 -- MD5 | 38 ++++---- NAMESPACE | 2 R/kmSRdiagram.R |only R/kmbasisdiagram.R | 4 R/kmhasse.R | 4 R/kmsrvalidate.R |only R/kmsurmisefunction.R | 3 R/kmvalidate.R | 2 R/xpl.R | 11 +- build/vignette.rds |binary data/xpl.rda |binary inst/doc/kstMatrix.html | 210 +++++++++++++++++++----------------------------- man/kmSRdiagram.Rd |only man/kmSRvalidate.Rd |only man/kmbasisdiagram.Rd | 5 - man/kmdist.Rd | 1 man/kmhasse.Rd | 5 - man/kmvalidate.Rd | 3 man/xpl.Rd | 11 +- src/basis.c | 2 22 files changed, 144 insertions(+), 172 deletions(-)
Title: Generalized Additive Models for Bivariate Conditional Dependence
Structures and Vine Copulas
Description: Implementation of various inference and simulation tools to
apply generalized additive models to bivariate dependence structures and
non-simplified vine copulas.
Author: Thomas Nagler [aut],
Thibault Vatter [aut, cre]
Maintainer: Thibault Vatter <thibault.vatter@gmail.com>
Diff between gamCopula versions 0.0-7 dated 2020-02-05 and 0.0-8 dated 2025-04-02
DESCRIPTION | 11 - MD5 | 87 ++++---- NEWS.md | 40 ++- R/AllClasses.R | 7 R/gamBiCop.R | 22 +- R/gamBiCopCDF.R | 2 R/gamBiCopFit.R | 6 R/gamBiCopPDF.R | 2 R/gamBiCopPredict.R | 6 R/gamBiCopSelect.R | 8 R/gamBiCopSimulate.R | 2 R/gamCopula-package.R |only R/gamVine.R | 19 - R/gamVineCopSelect.R | 4 R/gamVinePDF.R | 2 R/gamVineSeqFit.R | 2 R/gamVineStructureSelect.R | 2 R/utilsFamilies.R | 3 R/utilsPrivate.R | 4 R/utilsPublic.R | 11 - README.md | 110 +++++----- man/BiCopEta2Par.Rd | 5 man/BiCopPar2Eta.Rd | 6 man/EDF.gamBiCop-methods.Rd | 2 man/RVM2GVC.Rd | 6 man/formula.gamBiCop-methods.Rd | 6 man/gamBiCop-class.Rd | 4 man/gamBiCop.Rd | 4 man/gamBiCopCDF.Rd | 2 man/gamBiCopFit.Rd | 6 man/gamBiCopPDF.Rd | 2 man/gamBiCopPredict.Rd | 6 man/gamBiCopSelect.Rd | 6 man/gamBiCopSimulate.Rd | 2 man/gamCopula-package.Rd | 409 ++++++++++++++++++++-------------------- man/gamVine-class.Rd | 3 man/gamVine.Rd | 2 man/gamVineCopSelect.Rd | 4 man/gamVinePDF.Rd | 2 man/gamVineSeqFit.Rd | 2 man/gamVineStructureSelect.Rd | 2 man/plot.gamBiCop-methods.Rd | 6 man/plot.gamVine-methods.Rd | 6 man/summary.gamBiCop-methods.Rd | 4 man/summary.gamVine-methods.Rd | 4 45 files changed, 433 insertions(+), 418 deletions(-)
Title: Vector Summaries of Persistence Diagrams
Description: Provides tools for computing various vector summaries of persistence diagrams studied in Topological Data Analysis. For improved computational efficiency,
all code for the vector summaries is written in 'C++' using the 'Rcpp' and 'RcppArmadillo' packages.
Author: Umar Islambekov [aut],
Aleksei Luchinsky [aut, cre]
Maintainer: Aleksei Luchinsky <aluchi@bgsu.edu>
Diff between TDAvec versions 0.1.4 dated 2025-02-15 and 0.1.41 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/TDAvec_vignette.html | 7 ++++--- man/computePersistenceLandscape.Rd | 14 ++++++++------ src/PersistenceLandscape.cpp | 30 ++++++++++++++++-------------- 6 files changed, 36 insertions(+), 31 deletions(-)
Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). It allows to easily visualize
count data and statistical thresholds: rank vs abundance plots,
heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Matthew Peeples [ctb] ,
Ben Marwick [ctb] ,
Jean-Baptiste Fourvel [ctb] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 3.2.0 dated 2025-01-10 and 3.2.1 dated 2025-04-02
DESCRIPTION | 35 ++-- MD5 | 44 ++--- NEWS.md | 4 R/AllGenerics.R | 28 ++- R/tabula-package.R | 2 README.md | 13 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/alpha.Rmd | 1 inst/doc/alpha.html | 282 ++++++++++++++++------------------- inst/doc/beta.Rmd | 1 inst/doc/beta.html | 225 ++++++++++++--------------- inst/tinytest/test_index.R | 14 - man/figures/README-sample-size-1.png |binary man/figures/README-sample-size-2.png |binary man/index_bray.Rd | 2 man/index_jaccard.Rd | 4 man/index_sorenson.Rd | 8 man/similarity.Rd | 18 +- man/tabula-package.Rd | 6 vignettes/alpha.Rmd | 1 vignettes/beta.Rmd | 1 23 files changed, 328 insertions(+), 363 deletions(-)
Title: Conditional Process Analysis (CPA) via SEM Approach
Description: Utilizes the Reliability-Adjusted Product Indicator (RAPI) method to
estimate effects among latent variables, thus allowing for more precise definition and analysis of
mediation and moderation models. Our simulation studies reveal that while 'silp' may exhibit
instability with smaller sample sizes and lower reliability scores (e.g., N = 100, 'omega' = 0.7),
implementing nearest positive definite matrix correction and bootstrap confidence interval
estimation can significantly ameliorate this volatility. When these adjustments are applied,
'silp' achieves estimations akin in quality to those derived from LMS. In conclusion, the 'silp'
package is a valuable tool for researchers seeking to explore complex relational structures between
variables without resorting to commercial software.
Cheung et al.(2021)<doi:10.1007/s10869-020-09717-0>
Hsiao et al.(2018)<doi:10.1177/0013164416679877>.
Author: Yi-Hsuan Tseng [aut, cre],
Po-Hsien Huang [aut]
Maintainer: Yi-Hsuan Tseng <r12227115@g.ntu.edu.tw>
Diff between silp versions 1.0.1 dated 2025-03-11 and 1.0.2 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 2 ++ R/resilp.R | 2 ++ R/silp.R | 5 ++--- R/utility.R | 4 ++-- 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct
full and abridge life tables given various input indices. A mortality
law is a parametric function that describes the dying-out process of
individuals in a population during a significant portion of their
life spans. For a comprehensive review of the most important mortality
laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>.
Practical functions for downloading data from various human mortality
databases are provided as well.
Author: Marius D. Pascariu [aut, cre, cph]
,
Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>
Diff between MortalityLaws versions 2.1.0 dated 2024-01-15 and 2.1.2 dated 2025-04-02
DESCRIPTION | 8 MD5 | 276 ++++---- NAMESPACE | 190 ++--- NEWS | 153 ++-- R/LawTable.R | 220 +++--- R/LifeTable.R | 1162 +++++++++++++++++------------------ R/MortalityLaw_S3.R | 342 +++++----- R/MortalityLaw_check.R | 98 +- R/MortalityLaw_main.R | 824 ++++++++++++------------ R/MortalityLaw_models.R | 1094 ++++++++++++++++---------------- R/MortalityLaws-data.R | 92 +- R/MortalityLaws-package.R | 48 - R/availableHMD.R | 155 ++-- R/availableLF.R | 120 +-- R/availableLaws.R | 428 ++++++------ R/convertFx.R | 172 ++--- R/graphics.R | 336 +++++----- R/readAHMD.R | 393 +++++------ R/readCHMD.R | 502 +++++++-------- R/readHMD.R | 800 ++++++++++++------------ R/readJMD.R | 550 ++++++++-------- R/utils.R | 98 +- R/zzz.R | 18 README.md | 98 +- THANKS | 28 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Installation.R | 24 inst/doc/Installation.Rmd | 122 +-- inst/doc/Installation.pdf |binary inst/doc/Intro.R | 236 +++---- inst/doc/Intro.Rmd | 486 +++++++------- inst/doc/Intro.pdf |binary man/AHMD_sample.Rd | 42 - man/AIC.MortalityLaw.Rd | 36 - man/AUSregions.Rd | 30 man/CANregions.Rd | 30 man/CHMD_sample.Rd | 42 - man/HMD_sample.Rd | 42 - man/HMDcountries.Rd | 30 man/HMDindices.Rd | 30 man/HP.Rd | 48 - man/HP2.Rd | 48 - man/HP3.Rd | 48 - man/HP4.Rd | 48 - man/JMD_sample.Rd | 42 - man/JPNregions.Rd | 30 man/LawTable.Rd | 234 +++---- man/LifeTable.check.Rd | 36 - man/LifeTable.core.Rd | 92 +- man/MortalityLaw.Rd | 314 ++++----- man/MortalityLaws.Rd | 62 - man/ReadAHMD.Rd | 249 +++---- man/ReadCHMD.Rd | 250 +++---- man/ReadHMD.Rd | 274 ++++---- man/ReadHMD.core.Rd | 114 +-- man/ReadJMD.Rd | 262 +++---- man/addDetails.Rd | 58 - man/ageMsg.Rd | 36 - man/ahmd.Rd | 62 - man/availableHMD.Rd | 60 - man/availableLF.Rd | 52 - man/availableLaws.Rd | 227 +++--- man/beard.Rd | 48 - man/beard_makeham.Rd | 48 - man/bring_parameters.Rd | 46 - man/carriere1.Rd | 48 - man/carriere2.Rd | 48 - man/check.MortalityLaw.Rd | 36 - man/check_input_ReadAHMD.Rd | 36 - man/check_input_ReadCHMD.Rd | 36 - man/check_input_ReadHMD.Rd | 36 - man/check_input_ReadJMD.Rd | 36 - man/choose_optim.Rd | 36 - man/coale.demeny.ax.Rd | 70 +- man/compute.ax.Rd | 46 - man/convertFx.Rd | 126 +-- man/data_format.Rd | 30 man/deviance.MortalityLaw.Rd | 36 - man/df.residual.MortalityLaw.Rd | 36 - man/dx_lx.Rd | 40 - man/find.my.case.Rd | 62 - man/ggompertz.Rd | 48 - man/gompertz.Rd | 48 - man/gompertz0.Rd | 48 - man/head_tail.Rd | 60 - man/invgompertz.Rd | 50 - man/invweibull.Rd | 54 - man/kannisto.Rd | 48 - man/kannisto_makeham.Rd | 48 - man/kostaki.Rd | 48 - man/logLik.MortalityLaw.Rd | 36 - man/make_http_request.Rd | 36 - man/makeham.Rd | 48 - man/makeham0.Rd | 48 - man/martinelle.Rd | 48 - man/mx_qx.Rd | 50 - man/objective_fun.Rd | 82 +- man/opperman.Rd | 48 - man/perks.Rd | 48 - man/plot.MortalityLaw.Rd | 58 - man/predict.MortalityLaw.Rd | 76 +- man/print.MortalityLaw.Rd | 40 - man/print.ReadAHMD.Rd | 40 - man/print.ReadCHMD.Rd | 40 - man/print.ReadHMD.Rd | 40 - man/print.ReadJMD.Rd | 40 - man/print.availableLF.Rd | 40 - man/print.availableLaws.Rd | 40 - man/print.summary.MortalityLaw.Rd | 40 - man/quadratic.Rd | 48 - man/rogersplanck.Rd | 48 - man/saveMsg.Rd | 30 man/saveOutput.Rd | 42 - man/scale_x.Rd | 36 - man/siler.Rd | 48 - man/strehler_mildvan.Rd | 48 - man/substrRight.Rd | 40 - man/summary.MortalityLaw.Rd | 44 - man/thiele.Rd | 48 - man/uxAbove100.Rd | 54 - man/vandermaen.Rd | 48 - man/vandermaen2.Rd | 48 - man/weibull.Rd | 56 - man/wittstein.Rd | 48 - tests/testthat.R | 20 tests/testthat/test_LawTable.R | 64 - tests/testthat/test_LifeTable.R | 402 ++++++------ tests/testthat/test_MortalityLaws.R | 338 +++++----- tests/testthat/test_MortalityLaws2.R | 478 +++++++------- tests/testthat/test_ReadAHMD.R | 100 +-- tests/testthat/test_ReadCHMD.R | 100 +-- tests/testthat/test_ReadHMD.R | 186 ++--- tests/testthat/test_ReadJMD.R | 108 +-- tests/testthat/test_availableX.R | 56 - tests/testthat/test_convertFx.R | 124 +-- vignettes/Installation.Rmd | 122 +-- vignettes/Intro.Rmd | 486 +++++++------- vignettes/Mlaw_Refrences.bib | 420 ++++++------ 139 files changed, 8974 insertions(+), 8967 deletions(-)
Title: Variable Selection for Gaussian Model-Based Clustering
Description: Variable selection for Gaussian model-based clustering as implemented in the 'mclust' package. The methodology allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting 'mclust' models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean [aut] ,
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between clustvarsel versions 2.3.4 dated 2020-12-16 and 2.3.5 dated 2025-04-02
DESCRIPTION | 14 MD5 | 29 - NEWS.md | 5 R/clvarselgrbkw.R | 12 R/clvarselgrfwd.R | 42 + R/clvarselhlfwd.R | 16 README.md | 4 build/vignette.rds |binary inst/CITATION | 34 - inst/doc/clustvarsel.R | 422 +++++++++---------- inst/doc/clustvarsel.Rmd | 2 inst/doc/clustvarsel.html | 959 +++++++++++++++++++++++++++++---------------- man/clustvarsel.Rd | 6 vignettes/clustvarsel.Rmd | 2 vignettes/vignette.css | 39 - vignettes/vignette_old.css |only 16 files changed, 958 insertions(+), 628 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb],
Roger Bivand [ctb] ,
Andrew Brown [ctb],
Michael Chirico [ctb],
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb],
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-29 dated 2025-02-26 and 1.8-42 dated 2025-04-02
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terra-1.8-42/terra/man/inset.Rd | 194 - terra-1.8-42/terra/man/interpIDW.Rd | 126 terra-1.8-42/terra/man/interpNear.Rd | 124 terra-1.8-42/terra/man/interpolate.Rd | 304 - terra-1.8-42/terra/man/intersect.Rd | 180 - terra-1.8-42/terra/man/is.bool.Rd | 168 terra-1.8-42/terra/man/is.empty.Rd | 80 terra-1.8-42/terra/man/is.flipped.Rd | 82 terra-1.8-42/terra/man/is.lonlat.Rd | 100 terra-1.8-42/terra/man/is.rotated.Rd | 84 terra-1.8-42/terra/man/is.valid.Rd | 112 terra-1.8-42/terra/man/k_means.Rd | 86 terra-1.8-42/terra/man/lapp.Rd | 202 - terra-1.8-42/terra/man/layerCor.Rd | 146 terra-1.8-42/terra/man/legend.Rd | 72 terra-1.8-42/terra/man/linearUnits.Rd | 102 terra-1.8-42/terra/man/lines.Rd | 172 terra-1.8-42/terra/man/makeTiles.Rd | 136 terra-1.8-42/terra/man/makeVRT.Rd | 94 terra-1.8-42/terra/man/map_extent.Rd | 66 terra-1.8-42/terra/man/mappal.Rd | 150 terra-1.8-42/terra/man/mask.Rd | 144 terra-1.8-42/terra/man/match.Rd | 98 terra-1.8-42/terra/man/math-generics.Rd | 206 - terra-1.8-42/terra/man/mem.Rd | 78 terra-1.8-42/terra/man/merge.Rd | 174 terra-1.8-42/terra/man/mergeTime.Rd | 98 terra-1.8-42/terra/man/meta.Rd | 58 terra-1.8-42/terra/man/metags.Rd | 136 terra-1.8-42/terra/man/minmax.Rd | 88 terra-1.8-42/terra/man/modal.Rd | 74 terra-1.8-42/terra/man/mosaic.Rd | 132 terra-1.8-42/terra/man/na.omit.Rd | 84 terra-1.8-42/terra/man/names.Rd | 148 terra-1.8-42/terra/man/nearby.Rd | 92 terra-1.8-42/terra/man/normalize.longitude.Rd | 68 terra-1.8-42/terra/man/north.Rd | 134 terra-1.8-42/terra/man/nseg.Rd | 66 terra-1.8-42/terra/man/origin.Rd | 78 terra-1.8-42/terra/man/pairs.Rd | 94 terra-1.8-42/terra/man/panel.Rd | 104 terra-1.8-42/terra/man/patches.Rd | 156 terra-1.8-42/terra/man/perim.Rd | 74 terra-1.8-42/terra/man/persp.Rd | 74 terra-1.8-42/terra/man/pitfinder.Rd | 162 terra-1.8-42/terra/man/plet.Rd | 256 - terra-1.8-42/terra/man/plot.Rd | 427 +- terra-1.8-42/terra/man/plotRGB.Rd | 118 terra-1.8-42/terra/man/plot_extent.Rd | 74 terra-1.8-42/terra/man/plot_graticule.Rd | 120 terra-1.8-42/terra/man/prcomp.Rd | 98 terra-1.8-42/terra/man/predict.Rd | 310 - terra-1.8-42/terra/man/princomp.Rd | 116 terra-1.8-42/terra/man/project.Rd | 248 - terra-1.8-42/terra/man/quantile.Rd | 114 terra-1.8-42/terra/man/query.Rd | 121 terra-1.8-42/terra/man/rangeFill.Rd | 96 terra-1.8-42/terra/man/rapp.Rd | 128 terra-1.8-42/terra/man/rast.Rd | 279 - terra-1.8-42/terra/man/rasterize.Rd | 175 - terra-1.8-42/terra/man/rasterizeGeom.Rd | 116 terra-1.8-42/terra/man/rasterizeWin.Rd | 144 terra-1.8-42/terra/man/rcl.Rd | 108 terra-1.8-42/terra/man/readwrite.Rd | 174 terra-1.8-42/terra/man/rectify.Rd | 74 terra-1.8-42/terra/man/regress.Rd | 88 terra-1.8-42/terra/man/rep.Rd | 78 terra-1.8-42/terra/man/replace_dollar.Rd | 98 terra-1.8-42/terra/man/replace_layers.Rd | 110 terra-1.8-42/terra/man/replace_values.Rd | 122 terra-1.8-42/terra/man/resample.Rd | 152 terra-1.8-42/terra/man/rescale.Rd | 88 terra-1.8-42/terra/man/roll.Rd | 124 terra-1.8-42/terra/man/rotate.Rd | 128 terra-1.8-42/terra/man/rowSums.Rd | 100 terra-1.8-42/terra/man/same.crs.Rd | 66 terra-1.8-42/terra/man/sample.Rd | 4 terra-1.8-42/terra/man/sapp.Rd | 104 terra-1.8-42/terra/man/sbar.Rd | 122 terra-1.8-42/terra/man/scale.Rd | 86 terra-1.8-42/terra/man/scale_linear.Rd | 78 terra-1.8-42/terra/man/scatter.Rd | 90 terra-1.8-42/terra/man/scoff.Rd | 104 terra-1.8-42/terra/man/sds.Rd | 145 terra-1.8-42/terra/man/segregate.Rd | 84 terra-1.8-42/terra/man/select.Rd | 138 terra-1.8-42/terra/man/selectRange.Rd | 102 terra-1.8-42/terra/man/serialize.Rd | 146 terra-1.8-42/terra/man/setValues.Rd | 144 terra-1.8-42/terra/man/shade.Rd | 118 terra-1.8-42/terra/man/sharedPaths.Rd | 106 terra-1.8-42/terra/man/shift.Rd | 94 terra-1.8-42/terra/man/simplify.Rd | 98 terra-1.8-42/terra/man/sort.Rd | 106 terra-1.8-42/terra/man/spin.Rd | 86 terra-1.8-42/terra/man/split.Rd | 111 terra-1.8-42/terra/man/sprc.Rd | 127 terra-1.8-42/terra/man/stretch.Rd | 106 terra-1.8-42/terra/man/subset.Rd | 152 terra-1.8-42/terra/man/subset_dollar.Rd | 130 terra-1.8-42/terra/man/subset_double.Rd | 160 terra-1.8-42/terra/man/subset_single.Rd | 228 - terra-1.8-42/terra/man/subst.Rd | 102 terra-1.8-42/terra/man/summarize-generics.Rd | 338 - terra-1.8-42/terra/man/summary.Rd | 96 terra-1.8-42/terra/man/surfArea.Rd | 82 terra-1.8-42/terra/man/svc.Rd | 137 terra-1.8-42/terra/man/symdif.Rd | 84 terra-1.8-42/terra/man/tapp.Rd | 120 terra-1.8-42/terra/man/terra-package.Rd | 1363 +++---- terra-1.8-42/terra/man/terrain.Rd | 166 terra-1.8-42/terra/man/text.Rd | 106 terra-1.8-42/terra/man/time.Rd | 156 terra-1.8-42/terra/man/tmpFile.Rd | 76 terra-1.8-42/terra/man/topology.Rd | 146 terra-1.8-42/terra/man/transpose.Rd | 94 terra-1.8-42/terra/man/trim.Rd | 78 terra-1.8-42/terra/man/unique.Rd | 124 terra-1.8-42/terra/man/units.Rd | 102 terra-1.8-42/terra/man/update.Rd | 78 terra-1.8-42/terra/man/values.Rd | 150 terra-1.8-42/terra/man/varnames.Rd | 142 terra-1.8-42/terra/man/vect.Rd | 5 terra-1.8-42/terra/man/vector_layers.Rd | 50 terra-1.8-42/terra/man/viewshed.Rd | 84 terra-1.8-42/terra/man/voronoi.Rd | 104 terra-1.8-42/terra/man/vrt.Rd | 128 terra-1.8-42/terra/man/vrt_tiles.Rd | 60 terra-1.8-42/terra/man/watershed.Rd | 82 terra-1.8-42/terra/man/weighted.mean.Rd | 120 terra-1.8-42/terra/man/where.Rd | 86 terra-1.8-42/terra/man/which.Rd | 72 terra-1.8-42/terra/man/width.Rd | 109 terra-1.8-42/terra/man/window.Rd | 126 terra-1.8-42/terra/man/wrap.Rd | 120 terra-1.8-42/terra/man/wrapCache.Rd | 92 terra-1.8-42/terra/man/writeCDF.Rd | 179 - terra-1.8-42/terra/man/writeRaster.Rd | 198 - terra-1.8-42/terra/man/writeVector.Rd | 96 terra-1.8-42/terra/man/xapp.Rd | 92 terra-1.8-42/terra/man/xmin.Rd | 198 - terra-1.8-42/terra/man/xyCellFrom.Rd | 266 - terra-1.8-42/terra/man/zonal.Rd | 218 - terra-1.8-42/terra/man/zoom.Rd | 80 terra-1.8-42/terra/src/Makevars.ucrt | 6 terra-1.8-42/terra/src/RcppExports.cpp | 11 terra-1.8-42/terra/src/RcppFunctions.cpp | 26 terra-1.8-42/terra/src/RcppModule.cpp | 35 terra-1.8-42/terra/src/arith.cpp | 85 terra-1.8-42/terra/src/crs.cpp | 2 terra-1.8-42/terra/src/distRaster.cpp | 59 terra-1.8-42/terra/src/distValueRaster.cpp | 6 terra-1.8-42/terra/src/distVector.cpp | 299 + terra-1.8-42/terra/src/distance.cpp | 2 terra-1.8-42/terra/src/extract.cpp | 66 terra-1.8-42/terra/src/focal.cpp | 2 terra-1.8-42/terra/src/gdal_algs.cpp | 50 terra-1.8-42/terra/src/gdalio.cpp | 4 terra-1.8-42/terra/src/geodesic.c | 66 terra-1.8-42/terra/src/geos_methods.cpp | 67 terra-1.8-42/terra/src/geos_spat.h | 20 terra-1.8-42/terra/src/math_utils.h | 34 terra-1.8-42/terra/src/memory.cpp | 3 terra-1.8-42/terra/src/raster_methods.cpp | 22 terra-1.8-42/terra/src/raster_stats.cpp | 63 terra-1.8-42/terra/src/rasterize.cpp | 4 terra-1.8-42/terra/src/read.cpp | 4 terra-1.8-42/terra/src/read_gdal.cpp | 142 terra-1.8-42/terra/src/read_ogr.cpp | 30 terra-1.8-42/terra/src/recycle.h | 8 terra-1.8-42/terra/src/sample.cpp | 278 + terra-1.8-42/terra/src/spatBase.cpp | 2 terra-1.8-42/terra/src/spatBase.h | 3 terra-1.8-42/terra/src/spatDataframe.cpp | 114 terra-1.8-42/terra/src/spatDataframe.h | 50 terra-1.8-42/terra/src/spatFactor.cpp | 14 terra-1.8-42/terra/src/spatFactor.h | 18 terra-1.8-42/terra/src/spatRaster.cpp | 106 terra-1.8-42/terra/src/spatRaster.h | 49 terra-1.8-42/terra/src/spatRasterMultiple.cpp | 124 terra-1.8-42/terra/src/spatRasterMultiple.h | 49 terra-1.8-42/terra/src/spatSources.cpp | 49 terra-1.8-42/terra/src/spatTime.cpp | 9 terra-1.8-42/terra/src/spatVector.cpp | 102 terra-1.8-42/terra/src/spatVector.h | 68 terra-1.8-42/terra/src/table_utils.cpp |only terra-1.8-42/terra/src/table_utils.h |only terra-1.8-42/terra/src/vecmath.h | 10 terra-1.8-42/terra/src/vector_methods.cpp | 4 terra-1.8-42/terra/src/write.cpp | 18 terra-1.8-42/terra/src/write_gdal.cpp | 78 terra-1.8-42/terra/tests/tinytest.R | 8 451 files changed, 44361 insertions(+), 42999 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Detecting spatial associations via spatial stratified heterogeneity, accounting for spatial dependencies, interpretability, complex interactions, and robust stratification. In addition, it supports the spatial stratified heterogeneity family described in Lv et al. (2025)<doi:10.1111/tgis.70032>.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.3-2 dated 2025-02-17 and 1.3-3 dated 2025-04-02
DESCRIPTION | 8 +- MD5 | 75 ++++++++++----------- NEWS.md | 6 + README.md | 42 ++++++++++-- build/vignette.rds |binary inst/CITATION |only inst/doc/consistency.Rmd | 46 +++++++------ inst/doc/consistency.html | 76 +++++++++++---------- inst/doc/gd.Rmd | 18 ----- inst/doc/gd.html | 142 +++++++++++++++++------------------------ inst/doc/idsa.Rmd | 22 ------ inst/doc/idsa.html | 78 ++++++++-------------- inst/doc/opgd.Rmd | 4 - inst/doc/opgd.html | 28 +++----- inst/doc/rgdrid.Rmd | 2 inst/doc/rgdrid.html | 6 - inst/doc/sesu.Rmd | 20 ----- inst/doc/sesu.html | 48 ++++--------- inst/doc/shegd.Rmd | 12 --- inst/doc/shegd.html | 38 +++------- inst/doc/spade.Rmd | 20 ----- inst/doc/spade.html | 76 ++++++++------------- vignettes/consistency.Rmd | 46 +++++++------ vignettes/consistency.Rmd.orig | 21 +++--- vignettes/gd.Rmd | 18 ----- vignettes/gd.Rmd.orig | 1 vignettes/idsa.Rmd | 22 ------ vignettes/idsa.Rmd.orig | 1 vignettes/opgd.Rmd | 4 - vignettes/opgd.Rmd.orig | 1 vignettes/precompile.R | 2 vignettes/rgdrid.Rmd | 2 vignettes/rgdrid.Rmd.orig | 1 vignettes/sesu.Rmd | 20 ----- vignettes/sesu.Rmd.orig | 7 +- vignettes/shegd.Rmd | 12 --- vignettes/shegd.Rmd.orig | 1 vignettes/spade.Rmd | 20 ----- vignettes/spade.Rmd.orig | 1 39 files changed, 372 insertions(+), 575 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.0.6 dated 2025-02-28 and 5.1 dated 2025-04-02
ChangeLog | 4 DESCRIPTION | 8 MD5 | 16 - R/ETSvalidate.R | 30 + R/TETSvalidate.R | 30 + src/ETSmodel.h | 149 --------- src/TETSmodel.h | 873 ++++++++++++++++++++++++++++++++++++++++++++++--------- src/optim.h | 3 src/stats.h | 6 9 files changed, 812 insertions(+), 307 deletions(-)
Title: Plot and Analyse Time-Intensity Data
Description: Plots and analyzes time-intensity curve data, such as data from
(contrast-enhanced) ultrasound. Values such as peak intensity, time to
peak and area under the curve are calculated.
Author: Samuel James Tingle [aut, cre]
Maintainer: Samuel James Tingle <samjamestingle@gmail.com>
Diff between tican versions 1.0.1 dated 2024-08-28 and 1.0.2 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- NEWS.md |only build/vignette.rds |binary inst/CITATION |only 5 files changed, 7 insertions(+), 5 deletions(-)
Title: Semi-Automatic Grading of R and Rmd Scripts
Description: A customisable set of tools for assessing and grading
R or R-markdown scripts from students. It allows for checking correctness
of code output, runtime statistics and static code analysis. The latter
feature is made possible by representing R expressions using a tree
structure.
Author: Vik Gopal [aut, cre],
Samuel Seah [aut],
Viknesh Jeya Kumar [aut],
Gabriel Ang [aut],
Ruofan Liu [ctb],
National University of Singapore [cph]
Maintainer: Vik Gopal <vik.gopal@nus.edu.sg>
Diff between autoharp versions 0.0.10 dated 2021-11-12 and 0.0.12 dated 2025-04-02
autoharp-0.0.10/autoharp/R/examplify_to_r.R |only autoharp-0.0.10/autoharp/R/lum_local_match.R |only autoharp-0.0.10/autoharp/man/examplify_to_r.Rd |only autoharp-0.0.10/autoharp/man/lum_local_match.Rd |only autoharp-0.0.12/autoharp/DESCRIPTION | 26 ++++++------ autoharp-0.0.12/autoharp/MD5 | 40 +++++++++---------- autoharp-0.0.12/autoharp/NAMESPACE | 4 - autoharp-0.0.12/autoharp/NEWS | 9 ++++ autoharp-0.0.12/autoharp/R/autoharp.R | 3 - autoharp-0.0.12/autoharp/R/extracton_section_text.R |only autoharp-0.0.12/autoharp/R/forestharp.R | 10 ++-- autoharp-0.0.12/autoharp/R/join_treeharp.R | 5 +- autoharp-0.0.12/autoharp/R/populate_soln_env.R | 37 +---------------- autoharp-0.0.12/autoharp/R/tree_routines.R | 19 +++++---- autoharp-0.0.12/autoharp/man/TreeHarp-class.Rd | 12 ++--- autoharp-0.0.12/autoharp/man/autoharp.Rd | 25 +++++++++++ autoharp-0.0.12/autoharp/man/extract_section_text.Rd |only autoharp-0.0.12/autoharp/man/forestharp-helpers.Rd | 30 +++++++------- autoharp-0.0.12/autoharp/man/get_adj_list.Rd | 4 - autoharp-0.0.12/autoharp/man/get_child_ids.Rd | 6 +- autoharp-0.0.12/autoharp/man/get_node_types.Rd | 4 - autoharp-0.0.12/autoharp/man/get_parent_id.Rd | 6 +- autoharp-0.0.12/autoharp/man/populate_soln_env.Rd | 10 +--- autoharp-0.0.12/autoharp/man/rmd_to_forestharp.Rd | 2 24 files changed, 128 insertions(+), 124 deletions(-)
Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Kamil Zyla [aut, cre],
Jakub Nowicki [aut],
Leszek Sieminski [aut],
Marek Rogala [aut],
Recle Vibal [aut],
Tymoteusz Makowski [aut],
Rodrigo Basa [aut],
Eduardo Almeida [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Kamil Zyla <opensource+kamil@appsilon.com>
Diff between rhino versions 1.10.1 dated 2024-09-20 and 1.11.0 dated 2025-04-02
DESCRIPTION | 17 + MD5 | 29 ++- NAMESPACE | 3 NEWS.md | 14 + R/destructure.R |only R/node.R | 12 - R/tools.R | 175 +++++++++++++++++++- inst/WORDLIST | 6 inst/templates/app_structure/app/static/favicon.ico |binary man/auto_test_r.Rd |only man/devmode.Rd |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/format_r.Rd | 4 man/grapes-set-grapes.Rd |only man/test_r.Rd | 5 tests/testthat/test-destructure.R |only tests/testthat/test-tools.R | 6 20 files changed, 237 insertions(+), 34 deletions(-)
Title: The Double-Gap Life Expectancy Forecasting Model
Description: Life expectancy is highly correlated over time among countries and
between males and females. These associations can be used to improve forecasts.
Here we have implemented a method for forecasting female life expectancy based on
analysis of the gap between female life expectancy in a country compared with
the record level of female life expectancy in the world. Second, to forecast
male life expectancy, the gap between male life expectancy and female life
expectancy in a country is analysed. We named this method the Double-Gap model.
For a detailed description of the method see Pascariu et al. (2018).
<doi:10.1016/j.insmatheco.2017.09.011>.
Author: Marius D. Pascariu [aut, cre]
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>
Diff between MortalityGaps versions 1.0.0 dated 2018-07-20 and 1.0.7 dated 2025-04-02
MortalityGaps-1.0.0/MortalityGaps/R/Utils.R |only MortalityGaps-1.0.0/MortalityGaps/R/data_and_imports.R |only MortalityGaps-1.0.0/MortalityGaps/man/onAttach.Rd |only MortalityGaps-1.0.7/MortalityGaps/DESCRIPTION | 28 MortalityGaps-1.0.7/MortalityGaps/MD5 | 75 MortalityGaps-1.0.7/MortalityGaps/NAMESPACE | 70 MortalityGaps-1.0.7/MortalityGaps/NEWS | 7 MortalityGaps-1.0.7/MortalityGaps/R/DGM_fit.R | 779 +++++----- MortalityGaps-1.0.7/MortalityGaps/R/DGM_predict.R | 310 +-- MortalityGaps-1.0.7/MortalityGaps/R/Graphics.R | 184 +- MortalityGaps-1.0.7/MortalityGaps/R/MortalityGaps-data.R |only MortalityGaps-1.0.7/MortalityGaps/R/MortalityGaps-package.R |only MortalityGaps-1.0.7/MortalityGaps/README.md | 115 - MortalityGaps-1.0.7/MortalityGaps/THANKS | 24 MortalityGaps-1.0.7/MortalityGaps/build/partial.rdb |only MortalityGaps-1.0.7/MortalityGaps/build/vignette.rds |binary MortalityGaps-1.0.7/MortalityGaps/inst/REFERENCES.bib |only MortalityGaps-1.0.7/MortalityGaps/inst/doc/Manual.R | 56 MortalityGaps-1.0.7/MortalityGaps/inst/doc/Manual.Rmd | 208 +- MortalityGaps-1.0.7/MortalityGaps/inst/doc/Manual.pdf |binary MortalityGaps-1.0.7/MortalityGaps/inst/figures |only MortalityGaps-1.0.7/MortalityGaps/man/DoubleGap.Rd | 283 +-- MortalityGaps-1.0.7/MortalityGaps/man/MortalityGaps.Rd |only MortalityGaps-1.0.7/MortalityGaps/man/MortalityGaps.data.Rd | 64 MortalityGaps-1.0.7/MortalityGaps/man/bp_gap.model.Rd | 56 MortalityGaps-1.0.7/MortalityGaps/man/compute_CI.Rd | 58 MortalityGaps-1.0.7/MortalityGaps/man/find_fitted_values.Rd | 38 MortalityGaps-1.0.7/MortalityGaps/man/find_observed_values.Rd | 30 MortalityGaps-1.0.7/MortalityGaps/man/find_record_ex.Rd | 30 MortalityGaps-1.0.7/MortalityGaps/man/find_tau.Rd | 46 MortalityGaps-1.0.7/MortalityGaps/man/plot.predict.DoubleGap.Rd | 79 - MortalityGaps-1.0.7/MortalityGaps/man/predict.DoubleGap.Rd | 72 MortalityGaps-1.0.7/MortalityGaps/man/prepare_data.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/prepare_data_for_prediction.Rd | 42 MortalityGaps-1.0.7/MortalityGaps/man/print.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/print.MortalityGaps.data.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/print.predict.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/print.summary.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/sex_gap.model.Rd | 52 MortalityGaps-1.0.7/MortalityGaps/man/summary.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/tests/testthat.R | 8 MortalityGaps-1.0.7/MortalityGaps/tests/testthat/testDGM.R | 208 +- MortalityGaps-1.0.7/MortalityGaps/vignettes/Manual.Rmd | 208 +- 43 files changed, 1690 insertions(+), 1644 deletions(-)
Title: Testing for Spatial Independence of Cross-Sectional Qualitative
Data
Description: Testing for Spatial Dependence of Qualitative Data in Cross Section. The list of functions includes join-count tests, Q test, spatial scan test, similarity test and spatial runs test. The methodology of these models can be found in <doi:10.1007/s10109-009-0100-1> and <doi:10.1080/13658816.2011.586327>.
Author: Fernando Lopez [aut, cre] ,
Roman Minguez [aut] ,
Antonio Paez [aut] ,
Manuel Ruiz [aut]
Maintainer: Fernando Lopez <fernando.lopez@upct.es>
Diff between spqdep versions 0.1.3.5 dated 2025-01-08 and 0.1.3.6 dated 2025-04-02
DESCRIPTION | 13 +- MD5 | 28 +++--- NAMESPACE | 2 R/m.surround.R | 3 R/methods_qmap.R | 5 - R/plot.sprunstest.R | 69 ++++++++------ R/summary.spjctest.R | 20 ++-- R/summary.spqtest.R | 14 +-- R/utils-pipe.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/user-guide.R | 7 - inst/doc/user-guide.Rmd | 11 +- inst/doc/user-guide.html | 217 +++++++++++++++++++++++------------------------ man/pipe.Rd |only vignettes/user-guide.Rmd | 11 +- 16 files changed, 204 insertions(+), 196 deletions(-)
Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform
reproducible parallel foreach loops, using independent
random streams as generated by L'Ecuyer's combined
multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>].
It enables to easily convert standard '%dopar%' loops into
fully reproducible loops, independently of the number
of workers, the task scheduling strategy, or the chosen
parallel environment and associated foreach backend.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between doRNG versions 1.8.6.1 dated 2025-01-13 and 1.8.6.2 dated 2025-04-02
doRNG-1.8.6.1/doRNG/build |only doRNG-1.8.6.1/doRNG/inst/doc |only doRNG-1.8.6.1/doRNG/vignettes |only doRNG-1.8.6.2/doRNG/DESCRIPTION | 9 ++++----- doRNG-1.8.6.2/doRNG/MD5 | 11 +++-------- doRNG-1.8.6.2/doRNG/man/doRNG-package.Rd | 2 +- doRNG-1.8.6.2/doRNG/man/grapes-dorng-grapes.Rd | 8 +++++--- 7 files changed, 13 insertions(+), 17 deletions(-)
Title: Scopus Database 'API' Interface
Description: Uses Elsevier 'Scopus' API
<https://dev.elsevier.com/sc_apis.html> to download
information about authors and their citations.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between rscopus versions 0.6.6 dated 2019-09-17 and 0.8.1 dated 2025-04-02
rscopus-0.6.6/rscopus/R/read_cto.R |only rscopus-0.8.1/rscopus/DESCRIPTION | 15 rscopus-0.8.1/rscopus/MD5 | 106 +- rscopus-0.8.1/rscopus/NAMESPACE | 5 rscopus-0.8.1/rscopus/NEWS.md | 8 rscopus-0.8.1/rscopus/R/author_df.R | 12 rscopus-0.8.1/rscopus/R/author_retrieval.R | 8 rscopus-0.8.1/rscopus/R/author_search.R | 8 rscopus-0.8.1/rscopus/R/bibtex_core_data.R | 118 +- rscopus-0.8.1/rscopus/R/citation_retrieval.R | 48 rscopus-0.8.1/rscopus/R/elsevier_authenticate.R | 23 rscopus-0.8.1/rscopus/R/generic_elsevier_search.R | 6 rscopus-0.8.1/rscopus/R/get_affiliation_info.R | 4 rscopus-0.8.1/rscopus/R/get_all_coauthors.R |only rscopus-0.8.1/rscopus/R/get_author_info.R | 8 rscopus-0.8.1/rscopus/R/get_next.R | 2 rscopus-0.8.1/rscopus/R/object_retrieval.R | 11 rscopus-0.8.1/rscopus/R/read_cto.r |only rscopus-0.8.1/rscopus/R/scopus_search.R | 39 rscopus-0.8.1/rscopus/R/utils-pipe.R |only rscopus-0.8.1/rscopus/build/vignette.rds |binary rscopus-0.8.1/rscopus/inst/doc/api_key.R | 40 rscopus-0.8.1/rscopus/inst/doc/api_key.Rmd | 36 rscopus-0.8.1/rscopus/inst/doc/api_key.html | 285 +++-- rscopus-0.8.1/rscopus/inst/doc/multi_author.R | 32 rscopus-0.8.1/rscopus/inst/doc/multi_author.Rmd | 13 rscopus-0.8.1/rscopus/inst/doc/multi_author.html | 824 ++++++++-------- rscopus-0.8.1/rscopus/man/abstract_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/affil_df.Rd | 22 rscopus-0.8.1/rscopus/man/affil_search.Rd | 9 rscopus-0.8.1/rscopus/man/affiliation_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/article_retrieval.Rd | 10 rscopus-0.8.1/rscopus/man/author_df.Rd | 51 rscopus-0.8.1/rscopus/man/author_retrieval.Rd | 42 rscopus-0.8.1/rscopus/man/author_search.Rd | 27 rscopus-0.8.1/rscopus/man/author_search_by_affil.Rd | 2 rscopus-0.8.1/rscopus/man/bibtex_core_data.Rd | 2 rscopus-0.8.1/rscopus/man/citation_retrieval.Rd | 27 rscopus-0.8.1/rscopus/man/complete_multi_author_info.Rd | 3 rscopus-0.8.1/rscopus/man/elsevier_authenticate.Rd | 22 rscopus-0.8.1/rscopus/man/embase_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/entitlement_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/generic_elsevier_api.Rd | 32 rscopus-0.8.1/rscopus/man/get_affiliation_info.Rd | 13 rscopus-0.8.1/rscopus/man/get_all_coauthors.Rd |only rscopus-0.8.1/rscopus/man/get_complete_author_info.Rd | 26 rscopus-0.8.1/rscopus/man/get_links.Rd | 5 rscopus-0.8.1/rscopus/man/object_retrieval.Rd | 30 rscopus-0.8.1/rscopus/man/pipe.Rd |only rscopus-0.8.1/rscopus/man/process_affiliation_name.Rd | 8 rscopus-0.8.1/rscopus/man/process_author_name.Rd | 16 rscopus-0.8.1/rscopus/man/read_cto.Rd | 2 rscopus-0.8.1/rscopus/man/recommendation_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/scopus_search.Rd | 47 rscopus-0.8.1/rscopus/tests/testthat/test_author_df.R | 11 rscopus-0.8.1/rscopus/vignettes/api_key.Rmd | 36 rscopus-0.8.1/rscopus/vignettes/multi_author.Rmd | 13 57 files changed, 1285 insertions(+), 862 deletions(-)
Title: Quadratic Programming with Absolute Value Constraints
Description: Extends the quadprog package to solve quadratic programs with
absolute value constraints and absolute values in the objective function.
Author: Bob Harlow [aut, cre],
Brian Koch [ctb]
Maintainer: Bob Harlow <rharlow86@gmail.com>
Diff between quadprogXT versions 0.0.5 dated 2020-01-15 and 0.0.6 dated 2025-04-02
DESCRIPTION | 18 +++++---- MD5 | 10 ++--- R/convertToCompactQP.R | 68 +++++++++++++++++++++------------- inst/tinytest/test-convertToCompact.R | 17 ++++++-- man/convertToCompact.Rd | 9 ++-- man/solveQPXT.Rd | 23 +++++++++-- 6 files changed, 93 insertions(+), 52 deletions(-)
Title: Person Fit
Description: Several person-fit statistics
(PFSs; Meijer and Sijtsma, 2001, <doi:10.1177/01466210122031957>)
are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro [aut, cre]
Maintainer: Jorge N. Tendeiro <tendeiro@hiroshima-u.ac.jp>
Diff between PerFit versions 1.4.6 dated 2021-10-15 and 1.4.7 dated 2025-04-02
DESCRIPTION | 17 +-- MD5 | 12 +- R/PerFitPFS.R | 180 ++++++++++++++++----------------- R/SanityChecks.R | 272 +++++++++++++++++++++++++------------------------- build/partial.rdb |binary man/PerFit-package.Rd | 1 man/lz.Rd | 2 7 files changed, 244 insertions(+), 240 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.8 dated 2024-11-21 and 1.3.9 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 12 ++--- R/addBagPlot.R | 8 +-- R/plotPCAw.R | 25 +++++++---- build/vignette.rds |binary inst/doc/wrGraphVignette1.html | 93 ++++++++++++++++++----------------------- man/addBagPlot.Rd | 2 7 files changed, 73 insertions(+), 73 deletions(-)
Title: Utilities for Interacting with the 'CTX' APIs
Description: Access chemical, hazard, bioactivity, and exposure data from the
Computational Toxicology and Exposure ('CTX') APIs
<https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>.
'ctxR' was developed to streamline the process of accessing the information
available through the 'CTX' APIs without requiring prior knowledge of how to
use APIs. Most data is also available on the CompTox Chemical Dashboard
('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the
EPA Computational Toxicology and Exposure Online Resources
<https://www.epa.gov/comptox-tools>.
Author: Paul Kruse [aut] ,
Caroline Ring [aut] ,
Madison Feshuk [ctb] ,
Carter Thunes [ctb],
Jason Brown [cre]
Maintainer: Jason Brown <brown.jason@epa.gov>
Diff between ctxR versions 1.1.0 dated 2025-01-08 and 1.1.1 dated 2025-04-01
DESCRIPTION | 16 MD5 | 172 NEWS.md | 6 build/vignette.rds |binary inst/doc/Bioactivity.html | 2 inst/doc/Chemical.html | 2 inst/doc/Exposure.html | 2 inst/doc/Hazard.html | 2 inst/doc/Introduction.html | 2 tests/testthat/bioactivity/bioactivity/data/search/by-aeid/1.json | 6 tests/testthat/chemical-batch/chemical/detail/search/by-dtxcid/DTXCID30182-9e51f1.json | 78 tests/testthat/chemical-batch/chemical/detail/search/by-dtxsid-9e51f1-ddb193-POST.json | 6 tests/testthat/chemical-batch/chemical/fate/search/by-dtxsid-cd40e5-POST.json | 862 tests/testthat/chemical-batch/chemical/fate/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/chemical-batch/chemical/file/mol/search/by-dtxcid/DTXCID30182.txt | 94 tests/testthat/chemical-batch/chemical/file/mol/search/by-dtxsid/DTXSID7020182.txt | 94 tests/testthat/chemical-batch/chemical/ghslink/to-dtxsid-cd40e5-POST.json | 14 tests/testthat/chemical-batch/chemical/list/chemicals/search/contain/Biosolids2021/Bis.json | 126 tests/testthat/chemical-batch/chemical/list/chemicals/search/equal/Biosolids2021/Bis.json | 6 tests/testthat/chemical-batch/chemical/list/chemicals/search/start-with/Biosolids2021/Bis.json | 60 tests/testthat/chemical-batch/chemical/list/search/by-dtxsid/DTXSID7020182.json | 3700 +- tests/testthat/chemical-batch/chemical/list/search/by-name/BIOSOLIDS2021.json | 24 tests/testthat/chemical-batch/chemical/list/search/by-type/federal.json | 3964 +- tests/testthat/chemical-batch/chemical/msready/search/by-dtxcid/DTXCID30182.json | 52 tests/testthat/chemical-batch/chemical/msready/search/by-formula/8x.json | 6 tests/testthat/chemical-batch/chemical/msready/search/by-formula/CH4.json | 406 tests/testthat/chemical-batch/chemical/msready/search/by-mass-8e72d4-POST.json | 16 tests/testthat/chemical-batch/chemical/msready/search/by-mass/1/1.json | 6 tests/testthat/chemical-batch/chemical/msready/search/by-mass/16.0313/16.0314.json | 406 tests/testthat/chemical-batch/chemical/msready/search/by-mass/16.0314/16.0314.json | 6 tests/testthat/chemical-batch/chemical/property/search/by-dtxsid-cd40e5-POST.json | 1036 tests/testthat/chemical-batch/chemical/property/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/chemical-batch/chemical/search/equal-a5c27e-POST.json | 34 tests/testthat/chemical-batch/chemical/search/equal-b2fb80-POST.json | 42 tests/testthat/chemical-batch/chemical/synonym/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/chemical/chemical/file/mol/search/by-dtxcid/DTXCID30182.txt | 94 tests/testthat/chemical/chemical/file/mol/search/by-dtxsid/DTXSID7020182.txt | 94 tests/testthat/chemical/chemical/ghslink/to-dtxsid/DTXSID7020182.json | 10 tests/testthat/chemical/chemical/list/chemicals/search/equal/Biosolids2021/Bisphenol%20A.json | 6 tests/testthat/chemical/chemical/list/chemicals/search/equal/Biosolids2021/zy.json | 6 tests/testthat/chemical/chemical/list/chemicals/search/start-with/CCL4/Bi.json | 22 tests/testthat/chemical/chemical/list/chemicals/search/start-with/CCL4/zy.json | 6 tests/testthat/chemical/chemical/list/search/by-name/Biosolids2021.json | 24 tests/testthat/chemical/chemical/msready/search/by-dtxcid/DTXCID30182.json | 52 tests/testthat/chemical/chemical/msready/search/by-formula/8x.json | 6 tests/testthat/chemical/chemical/msready/search/by-formula/CH4.json | 406 tests/testthat/chemical/chemical/msready/search/by-mass/1/4.json | 6 tests/testthat/chemical/chemical/msready/search/by-mass/16.0313/16.0314.json | 406 tests/testthat/chemical/chemical/msready/search/by-mass/16.0314/16.0314.json | 6 tests/testthat/chemical/chemical/property/search/by-dtxsid/DTXSID.json | 6 tests/testthat/chemical/chemical/property/search/by-dtxsid/DTXSID7020182-f7c7b7.json | 772 tests/testthat/exposure-batch/exposure/fun-use/probability/search/by-dtxsid/DTXSID7020182.json | 100 tests/testthat/exposure-batch/exposure/fun-use/search/by-dtxsid/DTXSID7020182.json | 724 tests/testthat/exposure-batch/exposure/list-presence/search/by-dtxsid/DTXSID7020182.json | 1278 tests/testthat/exposure-batch/exposure/product-data/search/by-dtxsid/DTXSID7020182.json |12394 +++--- tests/testthat/exposure/exposure/fun-use/category.json | 1284 tests/testthat/exposure/exposure/fun-use/probability/search/by-dtxsid/DTXSID7020182.json | 100 tests/testthat/exposure/exposure/fun-use/search/by-dtxsid/DTXSID7020182.json | 724 tests/testthat/exposure/exposure/list-presence/search/by-dtxsid/DTXSID7020182.json | 1278 tests/testthat/exposure/exposure/list-presence/tags.json | 1876 - tests/testthat/exposure/exposure/product-data/puc.json | 7028 +-- tests/testthat/exposure/exposure/product-data/search/by-dtxsid/DTXSID7020182.json |12394 +++--- tests/testthat/hazard-batch/hazard/cancer-summary/search/by-dtxsid-cd40e5-POST.json | 6 tests/testthat/hazard-batch/hazard/cancer-summary/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/eco/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/genetox/details/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/genetox/summary/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/human/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/skin-eye/search/by-dtxsid-ddb193-POST.json | 6 vignettes/4/0/bioactivity/assay/search/by-aeid/700.json | 156 vignettes/4/0/bioactivity/assay/search/by-aeid/891.json | 162 vignettes/4/0/bioactivity/data/search/by-aeid/704.json |18414 +++++----- vignettes/4/0/bioactivity/data/search/by-dtxsid/DTXSID30944145.json | 2128 - vignettes/4/0/bioactivity/data/search/by-m4id/739695.json | 430 vignettes/4/0/bioactivity/data/search/by-spid/TP0000904H05.json | 3430 - vignettes/4/0/bioactivity/data/summary/search/by-aeid/700.json | 14 vignettes/4/0/bioactivity/data/summary/search/by-aeid/759.json | 14 vignettes/4/0/bioactivity/data/summary/search/by-aeid/891.json | 14 vignettes/5/0/exposure/fun-use/category.json | 1284 vignettes/5/0/exposure/fun-use/probability/search/by-dtxsid/DTXSID0020232.json | 36 vignettes/5/0/exposure/fun-use/probability/search/by-dtxsid/DTXSID7020182.json | 100 vignettes/5/0/exposure/fun-use/search/by-dtxsid/DTXSID7020182.json | 724 vignettes/5/0/exposure/list-presence/search/by-dtxsid/DTXSID7020182.json | 1278 vignettes/5/0/exposure/list-presence/tags.json | 1876 - vignettes/5/0/exposure/product-data/puc.json | 7028 +-- vignettes/5/0/exposure/product-data/search/by-dtxsid/DTXSID7020182.json |12394 +++--- 87 files changed, 50952 insertions(+), 50946 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.13.0 dated 2024-11-18 and 1.13.1 dated 2025-04-01
DESCRIPTION | 6 MD5 | 32 - R/getUPS1acc.R | 4 R/readAlphaPeptFile.R | 9 R/readMaxQuantFile.R | 2 R/readProteomeDiscovererFile.R | 48 + R/readProteomeDiscovererPeptides.R | 7 build/vignette.rds |binary inst/doc/wrProteoVignette1.R | 22 inst/doc/wrProteoVignette1.Rmd | 6 inst/doc/wrProteoVignette1.html | 245 +++----- inst/doc/wrProteoVignetteUPS1.R | 32 - inst/doc/wrProteoVignetteUPS1.Rmd | 2 inst/doc/wrProteoVignetteUPS1.html | 1130 ++++++++++++++++++------------------- man/getUPS1acc.Rd | 4 vignettes/wrProteoVignette1.Rmd | 6 vignettes/wrProteoVignetteUPS1.Rmd | 2 17 files changed, 767 insertions(+), 790 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between mongolite versions 3.1.2 dated 2025-03-17 and 4.0.0 dated 2025-04-01
DESCRIPTION | 6 ++-- MD5 | 13 +++++----- NEWS | 3 ++ src/Makevars.in | 2 - src/Makevars.win | 56 ++++++++++++++++++++++++++++---------------- src/mongoc/mongoc-openssl.c | 2 - src/osx/Makevars | 2 - tools |only 8 files changed, 52 insertions(+), 32 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.5.2 dated 2025-03-14 and 0.5.3 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 15 ++--- NEWS.md | 6 ++ R/MaestroPipeline.R | 8 ++ inst/doc/maestro-1-quick-start.html | 20 ++----- inst/doc/maestro-4-advanced-scheduling.html | 12 ++-- inst/doc/maestro-5-directed-acyclic-graphs.html | 22 ++++---- inst/doc/maestro-6-logging.html | 66 ++++++++++++------------ vignettes/maestro-8-tag-reference.html |only 9 files changed, 80 insertions(+), 75 deletions(-)
Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method
which can be called to terminate the background job. Also provides timeouts
and other mechanisms for automatically terminating a background job. The
result of the expression is available synchronously via $result or
asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between jobqueue versions 1.5.1 dated 2025-02-28 and 1.6.0 dated 2025-04-01
DESCRIPTION | 8 - MD5 | 16 +-- NAMESPACE | 2 NEWS.md | 6 + R/process.r | 201 +++++++++++++++++++++++------------------- R/utils.r | 2 R/validate.r | 7 + build/vignette.rds |binary tests/testthat/test-process.r | 60 ++++++++++-- 9 files changed, 187 insertions(+), 115 deletions(-)
Title: Interface to 'Glassdoor' API
Description: Interacts with the 'Glassdoor' API
<https://www.glassdoor.com/developer/index.htm>. Allows the user to
search job statistics, employer statistics, and job progression,
where 'Glassdoor' provides a breakdown of other jobs a person did
after their current one.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between glassdoor versions 0.8.1 dated 2018-11-21 and 0.9.0 dated 2025-04-01
glassdoor-0.8.1/glassdoor/R/glassdoor_job_prog.R |only glassdoor-0.8.1/glassdoor/man/gd_job_prog.Rd |only glassdoor-0.9.0/glassdoor/DESCRIPTION | 11 glassdoor-0.9.0/glassdoor/MD5 | 34 - glassdoor-0.9.0/glassdoor/NAMESPACE | 1 glassdoor-0.9.0/glassdoor/NEWS.md | 5 glassdoor-0.9.0/glassdoor/R/gdoor.R | 2 glassdoor-0.9.0/glassdoor/R/results.R | 2 glassdoor-0.9.0/glassdoor/README.md | 24 - glassdoor-0.9.0/glassdoor/build/vignette.rds |binary glassdoor-0.9.0/glassdoor/inst/doc/running-glassdoor.R | 22 glassdoor-0.9.0/glassdoor/inst/doc/running-glassdoor.Rmd | 20 glassdoor-0.9.0/glassdoor/inst/doc/running-glassdoor.html | 322 +++++++------- glassdoor-0.9.0/glassdoor/man/gd_api.Rd | 18 glassdoor-0.9.0/glassdoor/man/gd_company.Rd | 26 - glassdoor-0.9.0/glassdoor/man/gd_job_stats.Rd | 26 - glassdoor-0.9.0/glassdoor/man/gd_review.Rd | 3 glassdoor-0.9.0/glassdoor/man/results.Rd | 2 glassdoor-0.9.0/glassdoor/vignettes/running-glassdoor.Rmd | 20 19 files changed, 284 insertions(+), 254 deletions(-)
Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.modules.general versions 0.4.0 dated 2025-02-28 and 0.4.1 dated 2025-04-01
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/tm_a_pca.R | 6 ++++-- R/tm_a_regression.R | 7 +++---- R/tm_g_association.R | 7 +++---- R/tm_g_bivariate.R | 7 +++---- R/tm_g_distribution.R | 7 +++---- R/tm_g_response.R | 7 +++---- R/tm_g_scatterplot.R | 6 ++++-- R/tm_t_crosstable.R | 6 ++++-- build/vignette.rds |binary 12 files changed, 47 insertions(+), 41 deletions(-)
More information about teal.modules.general at CRAN
Permanent link
Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Cole C. Monnahan [ctb, cph] ,
Mollie Brooks [ct [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 0.6.0 dated 2024-05-29 and 0.7.0 dated 2025-04-01
sdmTMB-0.6.0/sdmTMB/man/figures/logo-sdmTMB.png |only sdmTMB-0.7.0/sdmTMB/DESCRIPTION | 20 sdmTMB-0.7.0/sdmTMB/MD5 | 126 + sdmTMB-0.7.0/sdmTMB/NAMESPACE | 8 sdmTMB-0.7.0/sdmTMB/NEWS.md | 109 + sdmTMB-0.7.0/sdmTMB/R/caic.R |only sdmTMB-0.7.0/sdmTMB/R/check.R | 5 sdmTMB-0.7.0/sdmTMB/R/cross-val.R | 40 sdmTMB-0.7.0/sdmTMB/R/dharma.R | 2 sdmTMB-0.7.0/sdmTMB/R/families.R | 26 sdmTMB-0.7.0/sdmTMB/R/fit.R | 690 +++++----- sdmTMB-0.7.0/sdmTMB/R/index.R | 234 ++- sdmTMB-0.7.0/sdmTMB/R/mesh.R | 39 sdmTMB-0.7.0/sdmTMB/R/methods.R | 46 sdmTMB-0.7.0/sdmTMB/R/parsing.R |only sdmTMB-0.7.0/sdmTMB/R/plot.R | 1 sdmTMB-0.7.0/sdmTMB/R/predict.R | 119 + sdmTMB-0.7.0/sdmTMB/R/print.R | 106 + sdmTMB-0.7.0/sdmTMB/R/priors.R | 53 sdmTMB-0.7.0/sdmTMB/R/project.R |only sdmTMB-0.7.0/sdmTMB/R/smoothers.R | 9 sdmTMB-0.7.0/sdmTMB/R/tidy.R | 284 +++- sdmTMB-0.7.0/sdmTMB/R/tmb-sim.R | 117 + sdmTMB-0.7.0/sdmTMB/R/utils.R | 9 sdmTMB-0.7.0/sdmTMB/build/partial.rdb |binary sdmTMB-0.7.0/sdmTMB/build/vignette.rds |binary sdmTMB-0.7.0/sdmTMB/inst/WORDLIST | 32 sdmTMB-0.7.0/sdmTMB/inst/doc/model-description.Rmd | 4 sdmTMB-0.7.0/sdmTMB/inst/doc/model-description.html | 11 sdmTMB-0.7.0/sdmTMB/man/cAIC.Rd |only sdmTMB-0.7.0/sdmTMB/man/coef.sdmTMB.Rd |only sdmTMB-0.7.0/sdmTMB/man/dharma_residuals.Rd | 2 sdmTMB-0.7.0/sdmTMB/man/figures/logo.png |only sdmTMB-0.7.0/sdmTMB/man/get_index.Rd | 103 + sdmTMB-0.7.0/sdmTMB/man/make_mesh.Rd | 6 sdmTMB-0.7.0/sdmTMB/man/plot_anisotropy.Rd | 1 sdmTMB-0.7.0/sdmTMB/man/predict.sdmTMB.Rd | 2 sdmTMB-0.7.0/sdmTMB/man/priors.Rd | 32 sdmTMB-0.7.0/sdmTMB/man/project.Rd |only sdmTMB-0.7.0/sdmTMB/man/sdmTMB.Rd | 17 sdmTMB-0.7.0/sdmTMB/man/sdmTMB_cv.Rd | 2 sdmTMB-0.7.0/sdmTMB/man/sdmTMBcontrol.Rd | 4 sdmTMB-0.7.0/sdmTMB/man/simulate.sdmTMB.Rd | 19 sdmTMB-0.7.0/sdmTMB/man/tidy.sdmTMB.Rd | 15 sdmTMB-0.7.0/sdmTMB/src/sdmTMB.cpp | 314 +++- sdmTMB-0.7.0/sdmTMB/tests/testthat/Rplots.pdf |binary sdmTMB-0.7.0/sdmTMB/tests/testthat/test-1-fit-basic.R | 2 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-1-visreg.R | 2 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-4-index-calculation.R | 29 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-6-tmb-simulation.R | 66 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-8-delta2.R | 27 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-cAIC.R |only sdmTMB-0.7.0/sdmTMB/tests/testthat/test-cross-validation.R | 1 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-index.R | 94 + sdmTMB-0.7.0/sdmTMB/tests/testthat/test-mesh.R |only sdmTMB-0.7.0/sdmTMB/tests/testthat/test-methods.R | 14 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-offset.R | 40 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-poisson-link.R |only sdmTMB-0.7.0/sdmTMB/tests/testthat/test-priors.R | 162 +- sdmTMB-0.7.0/sdmTMB/tests/testthat/test-projection.R |only sdmTMB-0.7.0/sdmTMB/tests/testthat/test-random-effects.R |only sdmTMB-0.7.0/sdmTMB/tests/testthat/test-random-intercepts.R | 93 - sdmTMB-0.7.0/sdmTMB/tests/testthat/test-reml.R | 18 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-smooths.R | 20 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-threshold-models.R | 3 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-tidy.R | 69 + sdmTMB-0.7.0/sdmTMB/tests/testthat/test-time-varying.R | 73 + sdmTMB-0.7.0/sdmTMB/tests/testthat/test-tinyVAST.R | 259 +-- sdmTMB-0.7.0/sdmTMB/tests/testthat/test-tmb-simulation.R | 25 sdmTMB-0.7.0/sdmTMB/tests/testthat/test-truncated-dists.R |only sdmTMB-0.7.0/sdmTMB/vignettes/model-description.Rmd | 4 71 files changed, 2617 insertions(+), 991 deletions(-)
Title: Client for the YouTube API
Description: Get comments posted on YouTube videos, information on how
many times a video has been liked, search for videos with particular
content, and much more. You can also scrape captions from a few
videos. To learn more about the YouTube API, see
<https://developers.google.com/youtube/v3/>.
Author: Gaurav Sood [aut, cre],
Kate Lyons [ctb],
John Muschelli [ctb]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 0.9.9 dated 2020-06-11 and 1.0.1 dated 2025-04-01
tuber-0.9.9/tuber/tests/testthat/test-pkg-style.R |only tuber-0.9.9/tuber/tests/testthat/token_file.rds |only tuber-0.9.9/tuber/vignettes/tuber-ex.md |only tuber-1.0.1/tuber/DESCRIPTION | 38 tuber-1.0.1/tuber/LICENSE | 2 tuber-1.0.1/tuber/MD5 | 217 + tuber-1.0.1/tuber/NAMESPACE | 148 - tuber-1.0.1/tuber/NEWS.md | 243 +- tuber-1.0.1/tuber/R/add_video_to_playlist.R |only tuber-1.0.1/tuber/R/change_playlist_title.R |only tuber-1.0.1/tuber/R/create_playlist.R |only tuber-1.0.1/tuber/R/delete_captions.R | 58 tuber-1.0.1/tuber/R/delete_channel_sections.R | 60 tuber-1.0.1/tuber/R/delete_comments.R | 58 tuber-1.0.1/tuber/R/delete_playlist_items.R | 58 tuber-1.0.1/tuber/R/delete_playlists.R | 58 tuber-1.0.1/tuber/R/delete_videos.R | 57 tuber-1.0.1/tuber/R/get_all_channel_video_stats.R | 143 - tuber-1.0.1/tuber/R/get_all_comments.R | 183 - tuber-1.0.1/tuber/R/get_captions.R | 84 tuber-1.0.1/tuber/R/get_channel_stats.R | 163 - tuber-1.0.1/tuber/R/get_comment_threads.R | 234 +- tuber-1.0.1/tuber/R/get_comments.R | 180 - tuber-1.0.1/tuber/R/get_playlist_item_ids.R |only tuber-1.0.1/tuber/R/get_playlist_item_videoids.R |only tuber-1.0.1/tuber/R/get_playlist_items.R | 186 - tuber-1.0.1/tuber/R/get_playlists.R | 151 - tuber-1.0.1/tuber/R/get_related_videos.R | 137 - tuber-1.0.1/tuber/R/get_stats.R | 77 tuber-1.0.1/tuber/R/get_subscriptions.R | 120 - tuber-1.0.1/tuber/R/get_video_details.R | 176 + tuber-1.0.1/tuber/R/list_abuse_report_reasons.R | 115 - tuber-1.0.1/tuber/R/list_caption_tracks.R | 107 tuber-1.0.1/tuber/R/list_captions.R | 82 tuber-1.0.1/tuber/R/list_channel_activities.R | 201 - tuber-1.0.1/tuber/R/list_channel_resources.R | 155 - tuber-1.0.1/tuber/R/list_channel_sections.R | 85 tuber-1.0.1/tuber/R/list_channel_videos.R | 88 tuber-1.0.1/tuber/R/list_guidecats.R | 135 - tuber-1.0.1/tuber/R/list_langs.R | 78 tuber-1.0.1/tuber/R/list_my_videos.R | 34 tuber-1.0.1/tuber/R/list_regions.R | 81 tuber-1.0.1/tuber/R/list_videocats.R | 132 - tuber-1.0.1/tuber/R/list_videos.R | 94 tuber-1.0.1/tuber/R/read_sbv.R | 78 tuber-1.0.1/tuber/R/tuber.R | 399 ++- tuber-1.0.1/tuber/R/update_video_metadata.R |only tuber-1.0.1/tuber/R/upload_caption.R | 170 - tuber-1.0.1/tuber/R/upload_video.R | 257 +- tuber-1.0.1/tuber/R/utils-pipe.R |only tuber-1.0.1/tuber/R/yt_oauth.R | 152 - tuber-1.0.1/tuber/R/yt_search.R | 457 ++-- tuber-1.0.1/tuber/R/yt_topic_search.R | 78 tuber-1.0.1/tuber/R/zzz.R |only tuber-1.0.1/tuber/README.md | 169 - tuber-1.0.1/tuber/build/vignette.rds |binary tuber-1.0.1/tuber/inst/CITATION | 31 tuber-1.0.1/tuber/inst/doc/tuber-ex.R | 139 - tuber-1.0.1/tuber/inst/doc/tuber-ex.Rmd | 523 ++-- tuber-1.0.1/tuber/inst/doc/tuber-ex.html | 1087 +++++----- tuber-1.0.1/tuber/man/add_video_to_playlist.Rd |only tuber-1.0.1/tuber/man/change_playlist_title.Rd |only tuber-1.0.1/tuber/man/create_playlist.Rd |only tuber-1.0.1/tuber/man/delete_captions.Rd | 54 tuber-1.0.1/tuber/man/delete_channel_sections.Rd | 56 tuber-1.0.1/tuber/man/delete_comments.Rd | 54 tuber-1.0.1/tuber/man/delete_playlist_items.Rd | 54 tuber-1.0.1/tuber/man/delete_playlists.Rd | 54 tuber-1.0.1/tuber/man/delete_videos.Rd | 54 tuber-1.0.1/tuber/man/get_all_channel_video_stats.Rd | 74 tuber-1.0.1/tuber/man/get_all_comments.Rd | 68 tuber-1.0.1/tuber/man/get_captions.Rd | 76 tuber-1.0.1/tuber/man/get_channel_stats.Rd | 79 tuber-1.0.1/tuber/man/get_comment_threads.Rd | 137 - tuber-1.0.1/tuber/man/get_comments.Rd | 138 - tuber-1.0.1/tuber/man/get_playlist_item_ids.Rd |only tuber-1.0.1/tuber/man/get_playlist_item_videoids.Rd |only tuber-1.0.1/tuber/man/get_playlist_items.Rd | 119 - tuber-1.0.1/tuber/man/get_playlists.Rd | 119 - tuber-1.0.1/tuber/man/get_related_videos.Rd | 89 tuber-1.0.1/tuber/man/get_stats.Rd | 61 tuber-1.0.1/tuber/man/get_subscriptions.Rd | 112 - tuber-1.0.1/tuber/man/get_video_details.Rd | 94 tuber-1.0.1/tuber/man/list_abuse_report_reasons.Rd | 79 tuber-1.0.1/tuber/man/list_caption_tracks.Rd | 103 tuber-1.0.1/tuber/man/list_captions.Rd | 58 tuber-1.0.1/tuber/man/list_channel_activities.Rd | 143 - tuber-1.0.1/tuber/man/list_channel_resources.Rd | 121 - tuber-1.0.1/tuber/man/list_channel_sections.Rd | 81 tuber-1.0.1/tuber/man/list_channel_videos.Rd | 96 tuber-1.0.1/tuber/man/list_guidecats.Rd | 75 tuber-1.0.1/tuber/man/list_langs.Rd | 62 tuber-1.0.1/tuber/man/list_my_videos.Rd | 48 tuber-1.0.1/tuber/man/list_regions.Rd | 63 tuber-1.0.1/tuber/man/list_videocats.Rd | 71 tuber-1.0.1/tuber/man/list_videos.Rd | 108 tuber-1.0.1/tuber/man/pipe.Rd |only tuber-1.0.1/tuber/man/read_sbv.Rd | 62 tuber-1.0.1/tuber/man/tuber-package.Rd |only tuber-1.0.1/tuber/man/tuber.Rd | 19 tuber-1.0.1/tuber/man/tuber_DELETE.Rd | 42 tuber-1.0.1/tuber/man/tuber_GET.Rd | 44 tuber-1.0.1/tuber/man/tuber_POST.Rd | 46 tuber-1.0.1/tuber/man/tuber_POST_json.Rd |only tuber-1.0.1/tuber/man/tuber_check.Rd | 34 tuber-1.0.1/tuber/man/update_video_metadata.Rd |only tuber-1.0.1/tuber/man/upload_caption.Rd | 110 - tuber-1.0.1/tuber/man/upload_video.Rd | 120 - tuber-1.0.1/tuber/man/yt_key.Rd |only tuber-1.0.1/tuber/man/yt_oauth.Rd | 104 tuber-1.0.1/tuber/man/yt_search.Rd | 264 +- tuber-1.0.1/tuber/man/yt_token.Rd | 40 tuber-1.0.1/tuber/man/yt_topic_search.Rd | 58 tuber-1.0.1/tuber/tests/testthat.R | 8 tuber-1.0.1/tuber/tests/testthat/test-captions.R | 26 tuber-1.0.1/tuber/tests/testthat/test-get-details.R | 39 tuber-1.0.1/tuber/tests/testthat/test-get-related-videos.R | 24 tuber-1.0.1/tuber/tests/testthat/test-list-channel-activities.R | 26 tuber-1.0.1/tuber/tests/testthat/test-list-channel-sections.R | 52 tuber-1.0.1/tuber/vignettes/tuber-ex.Rmd | 523 ++-- 120 files changed, 6399 insertions(+), 5600 deletions(-)
Title: Grammar of Graphics for Linear Model Diagnostic Plots
Description: Allows for easy creation of diagnostic plots for a variety of model objects using the Grammar of Graphics.
Provides functionality for both individual diagnostic plots and an array of four standard diagnostic plots.
Author: Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between gglm versions 1.0.3 dated 2024-01-16 and 1.0.4 dated 2025-04-01
DESCRIPTION | 14 ++++++++------ MD5 | 2 +- 2 files changed, 9 insertions(+), 7 deletions(-)
Title: Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Description: Articles in the 'R Journal' were first authored in 'LaTeX', which performs
admirably for 'PDF' files but is less than ideal for modern online interfaces.
The 'texor' package does all the transitional chores and conversions necessary
to move to the online versions.
Author: Abhishek Ulayil [aut, cre, cph]
,
Heather Turner [ctb] ,
Christophe Dervieux [ctb] ,
Mitchell O'Hara-Wild [ctb] ,
Dianne Cook [ctb] ,
Yinxiang Huang [ctb]
Maintainer: Abhishek Ulayil <perricoq@outlook.com>
Diff between texor versions 1.5.3 dated 2024-12-13 and 1.5.6 dated 2025-04-01
DESCRIPTION | 6 ++--- LICENSE | 2 - MD5 | 26 +++++++++++----------- NEWS.md | 9 +++++++ R/article-tools.R | 2 + R/automation-tools.R | 10 +++++--- R/table-tools.R | 33 +++++++++++++++++++++++++++- build/vignette.rds |binary inst/bookdown_ref.lua | 28 +++++++++++++++++++----- inst/doc/environment-handling.html | 18 +++++++-------- inst/fig_code_chunk.lua | 39 +++++++++++++++++++++++++++++++-- inst/table_caption.lua | 43 ++++++++++++++++++++++++++++++++----- inst/table_code_chunk.lua | 8 ++++-- man/latex_to_web.Rd | 8 +++--- 14 files changed, 182 insertions(+), 50 deletions(-)
Title: XML Generation from Tables
Description: Converting structured data from tables into XML format using
predefined templates ensures consistency and flexibility, making it
ideal for data exchange, reporting, and automated workflows.
Author: Jose Samos [aut, cre] ,
Universidad de Granada [cph]
Maintainer: Jose Samos <jsamos@ugr.es>
Diff between tab2xml versions 1.0.0 dated 2025-02-21 and 1.1.0 dated 2025-04-01
DESCRIPTION | 6 - LICENSE | 4 MD5 | 37 ++++--- NAMESPACE | 7 - NEWS.md | 14 +- R/check.R |only R/keys.R |only R/new.R | 87 +++++++++++------ R/sheet2xml.R | 10 +- R/utils.R | 39 ++++++++ README.md | 208 +++++++++++++++++++++++------------------- inst/doc/tab2xml.R | 10 +- inst/doc/tab2xml.Rmd | 36 ++++++- inst/doc/tab2xml.html | 213 +++++++++++++++++++++++++------------------- man/check_tab.Rd |only man/is_cell_empty.Rd |only man/remove_empty_nodes.Rd |only man/sheet2xml.Rd | 78 ++++++++-------- man/validate_fk.Rd |only man/validate_pk.Rd |only tests/testthat/test-check.R |only tests/testthat/test-keys.R |only tests/testthat/test-utils.R | 45 +++++++++ vignettes/tab2xml.Rmd | 36 ++++++- 24 files changed, 542 insertions(+), 288 deletions(-)
Title: Create Custom 'Rstudio' Keyboard Shortcuts
Description: Create custom keyboard shortcuts to examine code selected in the 'Rstudio' editor.
F3 can for example yield 'str(selection)' and F7 open the source
code of CRAN and base package functions on 'github'.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rskey versions 0.4.4 dated 2020-06-05 and 0.4.19 dated 2025-04-01
DESCRIPTION | 12 +- MD5 | 28 +++--- NAMESPACE | 7 + R/addins.R | 32 ++++++- R/href.R |only R/selectobject.R | 2 R/setKeyboardBindings.R | 184 +++++++++++++++++++++------------------------ R/umlaut2ascii.R |only README.md | 15 ++- inst/keyboardRlabels.ods |binary inst/rstudio/addins.dcf | 26 ++++++ man/addins.Rd | 14 +++ man/bdoc.Rd | 40 ++++----- man/href.Rd |only man/selectobject.Rd | 2 man/setKeyboardBindings.Rd | 12 ++ man/umlaut2ascii.Rd |only 17 files changed, 226 insertions(+), 148 deletions(-)
Title: Human 'Connectome' Project Interface
Description: Downloads and reads data from Human 'Connectome' Project
<https://db.humanconnectome.org> using Amazon Web Services ('AWS')
'S3' buckets.
Author: John Muschelli [aut, cre],
Adi Gherman [ctb]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurohcp versions 0.9.0 dated 2020-10-14 and 0.11.0 dated 2025-04-01
DESCRIPTION | 12 MD5 | 32 NEWS.md | 9 R/bucketlist.R | 14 R/download_hcp_file.R | 13 R/get_hcp_file.R | 4 R/hcp_list_files.R | 87 - R/make_aws_call.R | 8 R/parse_list_files.R | 11 README.md | 4102 +++++++++++++++++++++++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/hcp.R | 32 inst/doc/hcp.html | 303 +-- man/bucketlist.Rd | 2 man/get_hcp_file.Rd | 4 man/hcp_list_files.Rd | 28 man/make_aws_call.Rd | 8 17 files changed, 4441 insertions(+), 228 deletions(-)
Title: Simultaneous Truth and Performance Level Estimation
Description: An implementation of Simultaneous Truth and
Performance Level Estimation (STAPLE) <doi:10.1109/TMI.2004.828354>. This
method is used when there are multiple raters for an object, typically an
image, and this method fuses these ratings into one rating. It uses an
expectation-maximization method to estimate this rating and the individual
specificity/sensitivity for each rater.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between stapler versions 0.7.1 dated 2020-01-09 and 0.8.0 dated 2025-04-01
DESCRIPTION | 9 - MD5 | 30 ++-- NEWS.md | 8 + R/staple.R | 59 ++++++++ R/staple_binimg.R | 9 + R/staple_binmat.R | 3 R/staple_multi_mat.R | 55 +++++++- README.md | 11 - build/vignette.rds |binary inst/doc/staple_example.R | 8 - inst/doc/staple_example.html | 260 ++++++++++++++++++++++----------------- man/staple.Rd | 59 ++++++++ man/staple_bin_img.Rd | 8 + man/staple_multi_mat.Rd | 6 tests/testthat/test-binmat-bad.R | 6 tests/testthat/test-binmat.R | 4 16 files changed, 383 insertions(+), 152 deletions(-)
Title: Multi-Model Inference
Description: Tools for model selection and model averaging with support for a
wide range of statistical models. Automated model selection through
subsets of the maximum model, with optional constraints for model
inclusion. Averaging of model parameters and predictions based on
model weights derived from information criteria (AICc and alike)
or custom model weighting schemes.
Author: Kamil Barton [aut, cre]
Maintainer: Kamil Barton <kamil.barton@go2.pl>
Diff between MuMIn versions 1.48.4 dated 2024-06-22 and 1.48.11 dated 2025-04-01
DESCRIPTION | 18 ++--- MD5 | 130 +++++++++++++++++++++------------------- NAMESPACE | 15 +++- NEWS | 39 ++++++++++-- R/class-fitdistr.R |only R/class-glmmTMB.R | 3 R/class-unmarkedFit.R | 53 +++++++--------- R/coefTable.R | 2 R/dredge.R | 41 ++++++------ R/frmsplit.R |only R/getAllTerms.R | 4 - R/getspecs.R |only R/methods-averaging.R | 2 R/model.names.R | 2 R/model.sel.R | 15 ++-- R/model.selection.R | 7 -- R/modelspecs.R |only R/modify.model.selection.R | 3 R/pdredge.R | 2 R/plot.model.selection.R | 19 ----- R/predict.R | 2 R/r.squaredLR.R | 39 ++++++++---- R/rbind.model.selection.R | 8 ++ R/substitution.R | 9 +- R/umf_specs.R | 34 +++++----- R/unfckme.R | 28 +++++--- R/utils-misc.R | 89 ++++++++++++++++++++------- R/utils-models.R | 4 - data/Beetle.rda |binary data/Cement.rda |binary data/GPA.rda |binary demo/pdredge.pcount.R | 5 - man/AICc.Rd | 18 ++--- man/BGweights.Rd | 20 +++--- man/ICs.Rd | 21 +++--- man/MuMIn-package.Rd | 30 ++++----- man/QAIC.Rd | 12 +-- man/QIC.Rd | 25 ++++--- man/Weights.Rd | 56 +++++++++++------ man/arm.glm.Rd | 26 ++++---- man/bootWeights.Rd | 10 +-- man/coefplot.Rd | 8 +- man/cos2weights.Rd | 6 - man/dredge.Rd | 134 +++++++++++++++++++++--------------------- man/exprApply.Rd | 10 +-- man/get.models.Rd | 12 +-- man/jackknifeWeights.Rd | 16 ++--- man/macros/macros.Rd | 24 ++++++- man/manip-formula.Rd | 6 - man/merge.model.selection.Rd | 6 - man/model-utils.Rd | 20 ++++-- man/model.avg.Rd | 28 ++++---- man/model.sel.Rd | 16 ++--- man/model.selection.object.Rd | 12 ++- man/nested.Rd | 6 - man/par.avg.Rd | 2 man/pdredge.Rd | 4 - man/plot.model.selection.Rd | 28 ++++---- man/predict.averaging.Rd | 12 +-- man/r.squaredGLMM.Rd | 25 ++++--- man/r.squaredLR.Rd | 4 - man/stackingWeights.Rd | 6 - man/std.coef.Rd | 6 - man/stdize.Rd | 16 ++--- man/subset.model.selection.Rd | 6 - man/sumofweights.Rd | 4 - man/supported-classes.Rd | 28 +++++--- man/updateable.Rd | 76 ++++++++++++++--------- 68 files changed, 732 insertions(+), 580 deletions(-)
Title: Survival Trees to Fit Left-Truncated and Right-Censored and
Interval-Censored Survival Data
Description: Recursive partition algorithms designed for fitting survival trees with left-truncated and right-censored (LTRC) data, as well as interval-censored data.
The LTRC trees can also be used to fit survival trees with time-varying covariates.
Author: Wei Fu [aut],
Jeffrey Simonoff [aut],
Wenbo Jing [aut, cre]
Maintainer: Wenbo Jing <wj2093@stern.nyu.edu>
Diff between LTRCtrees versions 1.1.1 dated 2021-01-13 and 1.1.2 dated 2025-04-01
DESCRIPTION | 33 - MD5 | 12 R/LTRCART.R | 436 +++++++-------- build/vignette.rds |binary inst/doc/LTRCtrees.R | 278 ++++----- inst/doc/LTRCtrees.html | 1350 ++++++++++++++++++++++++++---------------------- man/LTRCART.Rd | 258 ++++----- 7 files changed, 1255 insertions(+), 1112 deletions(-)
Title: 'Leanpub' API Interface
Description: Provides access to the 'Leanpub' API
<https://leanpub.com/help/api> for gathering information about
publications and submissions to the 'Leanpub' platform.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between leanpubr versions 0.3.1 dated 2018-08-16 and 0.4.0 dated 2025-04-01
DESCRIPTION | 18 +- MD5 | 55 +++--- NAMESPACE | 4 NEWS.md | 8 R/aaa_utils.R | 16 + R/lp_book.R | 2 R/lp_coupons.R | 2 R/lp_download.R | 6 R/lp_get_wrapper.R | 35 ++-- R/lp_job_status.R | 2 R/lp_preview.R | 4 R/lp_publish.R | 5 R/lp_quiz_responses.R |only R/lp_sales.R | 49 +++++ README.md |only build/vignette.rds |binary inst/doc/getting_data_leanpub.R | 7 inst/doc/getting_data_leanpub.Rmd | 6 inst/doc/getting_data_leanpub.html | 312 +++++++++++++++++++------------------ man/lp_book_info.Rd | 7 man/lp_coupons.Rd | 4 man/lp_download.Rd | 16 + man/lp_get_wrapper.Rd | 26 ++- man/lp_job_status.Rd | 7 man/lp_links.Rd | 2 man/lp_preview.Rd | 6 man/lp_publish.Rd | 4 man/lp_quiz_responses.Rd |only man/lp_sales.Rd | 32 +++ vignettes/getting_data_leanpub.Rmd | 6 30 files changed, 387 insertions(+), 254 deletions(-)
Title: File-Backed Array for Out-of-Memory Computation
Description: Stores large arrays in files to avoid occupying large
memories. Implemented with super fast gigabyte-level multi-threaded
reading/writing via 'OpenMP'. Supports multiple non-character data
types (double, float, complex, integer, logical, and raw).
Author: Zhengjia Wang [aut, cre, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between filearray versions 0.1.9 dated 2024-11-08 and 0.2.0 dated 2025-04-01
DESCRIPTION | 6 MD5 | 22 +- NEWS.md | 4 R/load.R | 15 - build/vignette.rds |binary inst/doc/performance.R | 428 +++++++++++++++++++-------------------- inst/doc/performance.Rmd | 6 inst/doc/performance.html | 22 +- man/filearray.Rd | 6 tests/testthat/test-method_add.R | 8 tests/testthat/test-method_sub.R | 8 vignettes/performance.Rmd | 6 12 files changed, 276 insertions(+), 255 deletions(-)
Title: Forward Selection using Concordance/C-Index
Description: Performs forward model selection, using the C-index/concordance
in survival analysis models.
Author: John Muschelli [aut, cre] ,
Andrew Leroux [aut]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between cforward versions 0.1.0 dated 2021-03-29 and 0.2.0 dated 2025-04-01
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/cforward.R | 16 ++++++++-------- README.md | 2 ++ man/cforward.Rd | 8 ++++---- man/estimate_concordance.Rd | 8 ++++---- man/figures/README-pressure-1.png |binary 8 files changed, 33 insertions(+), 27 deletions(-)
Title: A Toolbox for Writing Pretty Papers and Reports
Description: A toolbox for writing 'knitr', 'Sweave' or other 'LaTeX'- or 'markdown'-based
reports and to prettify the output of various estimated models.
Author: Benjamin Hofner [aut, cre] ,
Romain Francois [ctb],
Kurt Hornik [ctb],
Martin Maechler [ctb],
David Dahl [ctb]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between papeR versions 1.0-5 dated 2021-03-22 and 1.0-6 dated 2025-04-01
ChangeLog | 32 +++ DESCRIPTION | 22 +- MD5 | 34 +-- NAMESPACE | 2 R/helpers.R | 4 R/summarize.R | 38 +-- README.md | 1 build/vignette.rds |binary inst/CITATION | 6 inst/NEWS.Rd | 19 + inst/doc/papeR_introduction.R | 14 - inst/doc/papeR_introduction.html | 403 ++++++++++++++++++++++++--------------- inst/doc/papeR_with_latex.pdf |binary man/Anova.lme.Rd | 4 man/confint.Rd | 4 man/labels.data.frame.Rd | 4 man/papeR-package.Rd | 4 man/prettify.Rd | 12 - 18 files changed, 387 insertions(+), 216 deletions(-)
Title: Example T1 Structural Data from the Multi-Modal MRI
'Reproducibility' Resource
Description: Structural T1 magnetic resonance imaging ('MRI')
data from the 'Kirby21' 'reproducibility' study
<doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.t1 versions 1.7.0 dated 2018-08-13 and 1.8.0 dated 2025-04-01
DESCRIPTION | 21 +++++++++++++-------- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/delete_t1_data.R | 2 +- R/download_t1_data.R | 15 ++++++++++++--- R/get_t1_filenames.R | 9 ++++++++- README.md | 8 +++++--- man/delete_t1_data.Rd | 2 +- man/download_t1_data.Rd | 5 ++++- man/get_t1_filenames.Rd | 5 ++++- 11 files changed, 63 insertions(+), 29 deletions(-)
Title: Example Functional Imaging Data from the Multi-Modal MRI
'Reproducibility' Resource
Description: Functional magnetic resonance imaging ('fMRI')
data from the 'Kirby21' 'reproducibility' study
<doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.fmri versions 1.7.0 dated 2018-08-13 and 1.8.0 dated 2025-04-01
DESCRIPTION | 19 ++++++++++++------- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/delete_fmri_data.R | 2 +- R/download_fmri_data.R | 2 +- R/get_fmri_filenames.R | 2 +- README.md | 7 ++++--- man/delete_fmri_data.Rd | 2 +- man/download_fmri_data.Rd | 2 +- man/get_fmri_filenames.Rd | 2 +- 10 files changed, 35 insertions(+), 25 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 0.11.2 dated 2024-12-12 and 1.0.0 dated 2025-04-01
glmmrBase-0.11.2/glmmrBase/src/heckman.cpp |only glmmrBase-1.0.0/glmmrBase/DESCRIPTION | 8 glmmrBase-1.0.0/glmmrBase/MD5 | 45 +- glmmrBase-1.0.0/glmmrBase/R/R6Model.R | 42 + glmmrBase-1.0.0/glmmrBase/R/RcppExports.R | 44 +- glmmrBase-1.0.0/glmmrBase/R/extrafunctions.R | 8 glmmrBase-1.0.0/glmmrBase/build/partial.rdb |binary glmmrBase-1.0.0/glmmrBase/inst/cmdstan/mcml.stan | 12 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/covariance.hpp | 36 + glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/general.h | 6 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/hsgpcovariance.hpp | 9 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/linearpredictor.hpp | 3 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/maths.h | 36 - glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/matrixfield.h | 4 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 59 +- glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/modelmcmc.hpp | 35 - glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/modeloptim.hpp | 219 ++++++---- glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/nngpcovariance.hpp | 17 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/optim/lbfgs/Param.h | 12 glmmrBase-1.0.0/glmmrBase/inst/stan/mcml.stan | 12 glmmrBase-1.0.0/glmmrBase/man/Model.Rd | 2 glmmrBase-1.0.0/glmmrBase/src/RcppExports.cpp | 12 glmmrBase-1.0.0/glmmrBase/src/model_module.cpp | 164 +++---- glmmrBase-1.0.0/glmmrBase/src/stanExports_mcml.h | 12 24 files changed, 487 insertions(+), 310 deletions(-)
Title: Google Citation Parser
Description: Scrapes Google Citation pages and creates data frames of
citations over time.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between gcite versions 0.10.1 dated 2019-03-06 and 0.11.0 dated 2025-04-01
DESCRIPTION | 11 ++----- MD5 | 64 ++++++++++++++++++++++---------------------- NEWS.md | 5 +++ R/author_cloud.R | 2 - R/gcite.R | 2 - R/gcite_author_info.R | 8 ++--- R/gcite_citation_index.R | 2 - R/gcite_citation_page.R | 22 ++++++++++----- R/gcite_cite_over_time.R | 2 - R/gcite_graph.R | 5 ++- R/gcite_main_graph.R | 2 - R/gcite_paper_df.R | 2 - R/gcite_papers.R | 2 - R/gcite_user_info.R | 2 - R/gcite_username.R | 21 ++++++++------ R/gcite_wordcloud_spec.R | 4 +- R/set_cookies_txt.R | 4 +- README.md | 11 ++----- man/author_cloud.Rd | 25 ++++++++++++----- man/gcite.Rd | 16 ++++++++--- man/gcite_author_info.Rd | 22 ++++++++++----- man/gcite_citation_index.Rd | 2 - man/gcite_citation_page.Rd | 19 ++++--------- man/gcite_cite_over_time.Rd | 2 - man/gcite_graph.Rd | 2 - man/gcite_main_graph.Rd | 2 - man/gcite_paper_df.Rd | 5 +-- man/gcite_papers.Rd | 2 - man/gcite_user_info.Rd | 14 +++++++-- man/gcite_username.Rd | 5 +-- man/gcite_wordcloud.Rd | 8 ++++- man/gcite_wordcloud_spec.Rd | 17 ++++++++--- man/set_cookies_txt.Rd | 4 +- 33 files changed, 184 insertions(+), 132 deletions(-)
Title: Display Differences Between Two Files using Codediff Library
Description: An R interface to the 'codediff' JavaScript library (a copy of which is included in the package,
see <https://github.com/danvk/codediff.js> for information).
Allows for visualization of the difference between 2 files, usually text files or R scripts, in a browser.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between diffr versions 0.1 dated 2017-02-27 and 0.3.0 dated 2025-04-01
DESCRIPTION | 9 ++++----- MD5 | 12 +++++++----- NEWS.md |only R/diffr.R | 4 ++-- inst/htmlwidgets/lib/codediff/codediff.css | 2 +- man/diffr.Rd | 21 +++++++++++++++------ man/diffrOutput.Rd | 4 ++-- man/img |only 8 files changed, 31 insertions(+), 21 deletions(-)
Title: Helper Functions to 'misc3d' and 'rgl' Packages for Brain
Imaging
Description: This includes functions for creating 3D and 4D images using
'WebGL', 'rgl', and 'JavaScript' commands.
This package relies on the X toolkit ('XTK',
<https://github.com/xtk/X#readme>).
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between brainR versions 1.6.0 dated 2019-12-05 and 1.7.0 dated 2025-04-01
DESCRIPTION | 10 ++++------ MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/brainR-package.R | 5 ++--- R/makeScene.R | 4 ++-- R/scene4d.R | 1 + R/write4D.R | 16 ++++++++-------- R/write4D.file.R | 6 +++--- R/writeTrianglesSTL.R | 2 +- README.md | 15 +++++++-------- man/brainR-package.Rd | 2 +- man/makeScene.Rd | 4 ++-- man/write4D.Rd | 6 +++--- man/write4D.file.Rd | 4 ++-- man/writeTrianglesSTL.Rd | 2 +- 15 files changed, 55 insertions(+), 54 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM)
for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of larg [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 1.15.2 dated 2024-08-20 and 1.15.3.1 dated 2025-04-01
DESCRIPTION | 6 MD5 | 41 +++-- NAMESPACE | 2 R/checkFilePath.R | 296 +++++++++++++++++++++--------------------- R/matchMatrixLinesToRef.R | 22 +-- R/moderTest2grp.R | 14 - R/nonAmbiguousNum.R | 20 +- R/normalizeThis.R | 33 ++-- R/summarizeCols.R | 1 R/top3mean.R |only R/trimRedundText.R | 1 R/trimmedMean.R | 3 build/vignette.rds |binary inst/doc/wrMiscVignette1.R | 28 +-- inst/doc/wrMiscVignette1.html | 73 ++++------ man/checkFilePath.Rd | 14 - man/dot-doubleExt.Rd |only man/dot-normalize.Rd | 4 man/moderTest2grp.Rd | 14 - man/nonAmbiguousNum.Rd | 14 + man/normalizeThis.Rd | 13 - man/top3mean.Rd |only man/trimmedMean.Rd | 1 23 files changed, 316 insertions(+), 284 deletions(-)
Title: Mutation Models for Pedigree Likelihood Computations
Description: A collection of functions for modelling mutations in
pedigrees with marker data, as used e.g. in likelihood computations
with microsatellite data. Implemented models include equal,
proportional and stepwise models, as well as random models for
experimental work, and custom models allowing the user to apply any
valid mutation matrix. Allele lumping is done following the
lumpability criteria of Kemeny and Snell (1976), ISBN:0387901922.
Author: Magnus Dehli Vigeland [aut, cre]
,
Thore Egeland [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedmut versions 0.7.1 dated 2023-11-04 and 0.8.0 dated 2025-04-01
DESCRIPTION | 8 MD5 | 38 +- NAMESPACE | 2 NEWS.md | 29 + R/adjustRate.R |only R/makeReversible.R |only R/mutRate.R | 24 - R/mutationMatrix.R | 561 ++++++++++++++++++++++++----------- R/mutationModel.R | 14 R/stepwiseReversible.R | 26 + R/utils.R | 31 - README.md | 69 ++-- man/adjustRate.Rd |only man/makeReversible.Rd |only man/mutRate.Rd | 12 man/mutationMatrix.Rd | 60 ++- man/mutationModel.Rd | 4 man/pedmut-package.Rd | 54 +-- man/stepwiseReversible.Rd | 7 tests/testthat/test-mutationMatrix.R | 30 + tests/testthat/test-mutationModel.R | 6 tests/testthat/test-properties.R | 11 22 files changed, 641 insertions(+), 345 deletions(-)
Title: Data Integration with Two-Way Orthogonal Partial Least Squares
Description: Performs the O2PLS data integration method for two datasets, yielding joint and data-specific parts for each dataset.
The algorithm automatically switches to a memory-efficient approach to fit O2PLS to high dimensional data.
It provides a rigorous and a faster alternative cross-validation method to select the number of components,
as well as functions to report proportions of explained variation and to construct plots of the results.
See the software article by el Bouhaddani et al (2018) <doi:10.1186/s12859-018-2371-3>,
and Trygg and Wold (2003) <doi:10.1002/cem.775>.
It also performs Sparse Group (Penalized) O2PLS, see Gu et al (2020) <doi:10.1186/s12859-021-03958-3> and cross-validation for the degree of sparsity.
Author: Said el Bouhaddani [aut, cre],
Zander Gu [aut],
Jeanine Houwing-Duistermaat [aut],
Geurt Jongbloed [aut],
Szymon Kielbasa [aut],
Hae-Won Uh [aut]
Maintainer: Said el Bouhaddani <s.elbouhaddani@umcutrecht.nl>
Diff between OmicsPLS versions 2.0.2 dated 2021-05-19 and 2.1.0 dated 2025-04-01
OmicsPLS-2.0.2/OmicsPLS/man/OmicsPLS.Rd |only OmicsPLS-2.1.0/OmicsPLS/DESCRIPTION | 40 + OmicsPLS-2.1.0/OmicsPLS/MD5 | 42 - OmicsPLS-2.1.0/OmicsPLS/NAMESPACE | 2 OmicsPLS-2.1.0/OmicsPLS/R/Crossval_OmicsPLS.R | 25 OmicsPLS-2.1.0/OmicsPLS/R/OmicsPLS.R | 75 +- OmicsPLS-2.1.0/OmicsPLS/R/OmicsPLS_o2m.R | 32 - OmicsPLS-2.1.0/OmicsPLS/build/partial.rdb |binary OmicsPLS-2.1.0/OmicsPLS/build/vignette.rds |binary OmicsPLS-2.1.0/OmicsPLS/inst/CITATION | 26 OmicsPLS-2.1.0/OmicsPLS/inst/doc/OmicsPLS_vignette.html | 489 ++++++++++++---- OmicsPLS-2.1.0/OmicsPLS/man/OmicsPLS-package.Rd |only OmicsPLS-2.1.0/OmicsPLS/man/adjR2.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/man/crossval_o2m.Rd | 11 OmicsPLS-2.1.0/OmicsPLS/man/crossval_o2m_adjR2.Rd | 5 OmicsPLS-2.1.0/OmicsPLS/man/impute_matrix.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/man/loadings.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/man/loocv.Rd | 5 OmicsPLS-2.1.0/OmicsPLS/man/loocv_combi.Rd | 5 OmicsPLS-2.1.0/OmicsPLS/man/plot.o2m.Rd | 4 OmicsPLS-2.1.0/OmicsPLS/man/scores.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/man/summary.o2m.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/tests/testthat/Rplots.pdf |binary 23 files changed, 538 insertions(+), 233 deletions(-)
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Penalized and non-penalized maximum likelihood estimation of smooth
transition vector autoregressive models with various types of transition weight
functions, conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, and calculation of impulse
response functions, generalized impulse response functions, and generalized
forecast error variance decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2025) <doi:10.48550/arXiv.2403.14216>,
Savi Virolainen (2025) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.1.4 dated 2025-02-27 and 1.1.5 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 114 ++++++++++++++++++++--------------------- NEWS.md | 7 ++ R/LSest.R | 22 +++---- R/STVARconstruction.R | 2 R/data.R | 2 R/geneticAlgorithm.R | 14 ++--- R/loglikelihood.R | 12 ++-- R/miscellaneous.R | 6 +- R/parameterReforms.R | 6 +- R/pickParams.R | 18 +++--- inst/doc/sstvars-vignette.Rnw | 114 ++++++++++++++++++++--------------------- inst/doc/sstvars-vignette.pdf |binary man/GAfit.Rd | 16 ++--- man/STVAR.Rd | 14 ++--- man/alt_stvar.Rd | 2 man/change_parametrization.Rd | 10 +-- man/change_regime.Rd | 14 ++--- man/check_constraints.Rd | 2 man/check_params.Rd | 12 ++-- man/estim_LS.Rd | 6 +- man/estim_NLS.Rd | 6 +- man/filter_estimates.Rd | 2 man/fitSSTVAR.Rd | 2 man/fitSTVAR.Rd | 4 - man/fitbsSSTVAR.Rd | 14 ++--- man/get_boldA_eigens_par.Rd | 12 ++-- man/get_omega_eigens_par.Rd | 12 ++-- man/get_regime_autocovs.Rd | 10 +-- man/get_regime_means.Rd | 12 ++-- man/get_residuals.Rd | 12 ++-- man/in_paramspace.Rd | 10 +-- man/iterate_more.Rd | 2 man/loglikelihood.Rd | 12 ++-- man/pick_Am.Rd | 8 +- man/pick_Ami.Rd | 8 +- man/pick_Omegas.Rd | 8 +- man/pick_W.Rd | 10 +-- man/pick_allA.Rd | 8 +- man/pick_distpars.Rd | 8 +- man/pick_lambdas.Rd | 10 +-- man/pick_phi0.Rd | 12 ++-- man/pick_regime.Rd | 14 ++--- man/pick_weightpars.Rd | 8 +- man/random_ind.Rd | 4 - man/reform_constrained_pars.Rd | 10 +-- man/regime_distance.Rd | 6 +- man/reorder_B_columns.Rd | 2 man/smart_ind.Rd | 14 ++--- man/sort_impactmats.Rd | 10 +-- man/sort_regimes.Rd | 10 +-- man/stab_conds_satisfied.Rd | 8 +- man/standard_errors.Rd | 12 ++-- man/swap_B_signs.Rd | 2 man/swap_parametrization.Rd | 2 man/usacpu.Rd | 2 vignettes/refs.bib | 10 +++ vignettes/sstvars-vignette.Rnw | 114 ++++++++++++++++++++--------------------- 58 files changed, 415 insertions(+), 394 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code
ported from S-PLUS. A modern 'MySQL' client written in 'C++' is available
from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] ,
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between RMySQL versions 0.11.0 dated 2025-02-08 and 0.11.1 dated 2025-04-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars.in | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Implicit Association Test Scores Using Robust Statistics
Description: Compute several variations of the Implicit Association Test (IAT) scores, including the D scores (Greenwald, Nosek, Banaji, 2003, <doi:10.1037/0022-3514.85.2.197>) and the new scores that were developed using robust statistics (Richetin, Costantini, Perugini, and Schonbrodt, 2015, <doi:10.1371/journal.pone.0129601>).
Author: Giulio Costantini [aut, cre]
Maintainer: Giulio Costantini <costantinigiulio@gmail.com>
Diff between IATscores versions 0.2.7 dated 2020-05-09 and 0.2.8 dated 2025-04-01
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NEWS.md | 5 +++-- inst/CITATION | 35 ++++++++++++----------------------- man/Tgraph.Rd | 5 ++++- 5 files changed, 29 insertions(+), 35 deletions(-)
Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <rpackages@fredriksavje.com>
Diff between distances versions 0.1.11 dated 2024-07-31 and 0.1.12 dated 2025-04-01
DESCRIPTION | 10 +++--- MD5 | 20 ++++++------ NEWS.md | 5 +++ R/distances-package.R | 5 +-- man/distances-package.Rd | 13 ++++++++ src/Makevars | 2 - src/libann/Makefile | 2 - src/libann/include/ANN/ANNperf.h | 2 - src/libann/src/ANN.cpp | 6 +-- src/libann/src/kd_dump.cpp | 2 - src/libann/src/perf.cpp | 61 +++++++++++++++++++-------------------- 11 files changed, 73 insertions(+), 55 deletions(-)
Title: Spanish version of orloca package. Modelos de localizacion en
investigacion operativa
Description: Help and demo in Spanish of the orloca package. Ayuda y demo en espanol del paquete orloca. Objetos y metodos para manejar y resolver el problema de localizacion de suma minima, tambien conocido como problema de Fermat-Weber. El problema de localizacion de suma minima busca un punto tal que la suma ponderada de las distancias a los puntos de demanda se minimice. Vease "The Fermat-Weber location problem revisited" por Brimberg, Mathematical Programming, 1, pag. 71-76, 1995. <DOI: 10.1007/BF01592245>.
Se usan algoritmos generales de optimizacion global para resolver el problema, junto con el metodo especifico Weiszfeld, vease "Sur le point pour lequel la Somme des distance de n points donnes est minimum", por Weiszfeld, Tohoku Mathematical Journal, First Series, 43, pag. 355-386, 1937 o "On the point for which the sum of the distances to n given points is minimum", por E. Weiszfeld y F. Plastria, Annals of Operations Research, 167, pg. 7-41, 2009. <DOI:10.1007/s10479-008-0352-z& [...truncated...]
Author: Manuel Munoz-Marquez [aut, cre]
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between orloca.es versions 4.9 dated 2020-03-06 and 5.5 dated 2025-04-01
DESCRIPTION | 28 ++++++++++++------------ MD5 | 51 ++++++++++++++++++++++---------------------- NAMESPACE | 2 + build |only man/andalucia.Rd | 2 - man/as-methods.Rd | 6 ----- man/as.data.frame.loca.p.Rd | 11 ++++----- man/as.loca.p.Rd | 2 - man/as.loca.p.data.frame.Rd | 2 - man/as.loca.p.matrix.Rd | 2 - man/as.matrix.loca.p.Rd | 2 - man/contour.loca.p.Rd | 2 - man/distsum.Rd | 2 - man/distsumgra.Rd | 2 - man/distsuml2.Rd | 2 - man/distsuml2min.Rd | 2 - man/distsumlp.Rd | 2 - man/distsumlpmin.Rd | 2 - man/distsummin.Rd | 2 - man/loca.p.Rd | 4 +-- man/orloca.es-package.Rd | 14 ++++++++---- man/persp.loca.p.Rd | 2 - man/plot.Rd | 4 +-- man/rloca.p.Rd | 2 - man/zsum.Rd | 2 - man/zsumgra.Rd | 2 - man/zsummin.Rd | 2 - 27 files changed, 80 insertions(+), 76 deletions(-)
Title: Optimising Random Forest Stability by Determining the Optimal
Number of Trees
Description: Calculating the stability of random forest with certain numbers of trees. The non-linear relationship between stability and numbers of trees is described using a logistic regression model and used to estimate the optimal number of trees.
Author: Thomas Martin Lange [cre, aut]
,
Felix Heinrich [ctb]
Maintainer: Thomas Martin Lange <thomas.lange@uni-goettingen.de>
Diff between optRF versions 1.1.0 dated 2025-02-03 and 1.2.0 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 56 +++++++++++--------- NAMESPACE | 1 NEWS.md | 14 +++++ R/measure_stability.R |only R/opt_importance.R | 37 ++++++++----- R/opt_prediction.R | 42 +++++++++------ R/plot_stability.R | 10 +-- R/utils.R | 31 ++++++++--- README.md | 4 - build/vignette.rds |binary inst/CITATION | 9 +-- inst/doc/optRF.R | 17 ++++++ inst/doc/optRF.Rmd | 31 +++++++++++ inst/doc/optRF.html | 31 +++++++++++ inst/doc/opt_importance.R | 19 ++++++ inst/doc/opt_importance.Rmd | 36 +++++++++++- inst/doc/opt_importance.html | 40 +++++++++++++- inst/doc/opt_prediction.R | 17 ++++++ inst/doc/opt_prediction.Rmd | 32 ++++++++++- inst/doc/opt_prediction.html | 37 ++++++++++++- man/figures |only man/measure_stability.Rd |only man/opt_importance.Rd | 12 ++-- man/opt_prediction.Rd | 12 ++-- man/plot_stability.Rd | 8 +- vignettes/optRF.Rmd | 31 +++++++++++ vignettes/optRF_vignette_stabilityData.Rda |only vignettes/opt_importance.Rmd | 36 +++++++++++- vignettes/opt_importance_vignette_stabilityData.Rda |only vignettes/opt_prediction.Rmd | 32 ++++++++++- vignettes/opt_prediction_vignette_stabilityData.Rda |only 32 files changed, 495 insertions(+), 106 deletions(-)
Title: Compound Annual Growth Rate
Description: A time series usually does not have a uniform growth rate. Compound Annual Growth Rate measures the average annual growth over a given period. More details can be found in Bardhan et al. (2022) <DOI:10.18805/ag.D-5418>.
Author: Debopam Rakshit [aut, cre],
Dwaipayan Bardhan [aut]
Maintainer: Debopam Rakshit <rakshitdebopam@yahoo.com>
Diff between CAGR versions 1.1.0 dated 2024-03-02 and 1.1.1 dated 2025-04-01
DESCRIPTION | 9 +++++---- MD5 | 15 ++++++++------- NAMESPACE | 2 ++ R/CAGR.R | 51 ++++++++++++++++++++++++++++++++++++++++----------- man/CAGR.Rd | 6 +++--- man/LLTM.Rd |only man/data.first.Rd | 4 ++-- man/data.last.Rd | 4 ++-- man/n.years.Rd | 4 ++-- 9 files changed, 64 insertions(+), 31 deletions(-)
Title: In-Code Documentation for 'GAMS'
Description: A collection of tools which extract a model documentation from 'GAMS' code and comments.
In order to use the package you need to install 'pandoc' and 'pandoc-citeproc'
first (<https://pandoc.org/>).
Author: Jan Philipp Dietrich [aut, cre],
Kristine Karstens [aut],
David Klein [aut],
Lavinia Baumstark [aut],
Falk Benke [aut]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between goxygen versions 1.0.3 dated 2020-08-16 and 1.4.5 dated 2025-04-01
goxygen-1.0.3/goxygen/inst/templates/ming.css |only goxygen-1.0.3/goxygen/inst/templates/template.latex |only goxygen-1.0.3/goxygen/tests/testthat/test-travisCI.R |only goxygen-1.4.5/goxygen/DESCRIPTION | 22 goxygen-1.4.5/goxygen/MD5 | 72 +- goxygen-1.4.5/goxygen/NAMESPACE | 1 goxygen-1.4.5/goxygen/R/appendExtraPageBlocks.R |only goxygen-1.4.5/goxygen/R/buildHTML.R | 169 ++--- goxygen-1.4.5/goxygen/R/buildTEX.R | 23 goxygen-1.4.5/goxygen/R/chooseTemplate.R |only goxygen-1.4.5/goxygen/R/createListModularCode.R | 301 +++++---- goxygen-1.4.5/goxygen/R/createListSimpleCode.R | 46 - goxygen-1.4.5/goxygen/R/createModulePage.R | 95 +- goxygen-1.4.5/goxygen/R/extractDocumentation.R | 165 ++-- goxygen-1.4.5/goxygen/R/flattenPageBlockList.R |only goxygen-1.4.5/goxygen/R/goxygen.R | 140 ++-- goxygen-1.4.5/goxygen/R/helper_functions.R | 108 +-- goxygen-1.4.5/goxygen/R/mergeDocumentation.R | 10 goxygen-1.4.5/goxygen/R/oldBuildHTML.R | 2 goxygen-1.4.5/goxygen/README.md | 19 goxygen-1.4.5/goxygen/build/vignette.rds |binary goxygen-1.4.5/goxygen/inst/doc/goxygen.R | 4 goxygen-1.4.5/goxygen/inst/doc/goxygen.Rmd | 26 goxygen-1.4.5/goxygen/inst/doc/goxygen.html | 332 +++++++--- goxygen-1.4.5/goxygen/inst/templates/classic.latex |only goxygen-1.4.5/goxygen/inst/templates/ming |only goxygen-1.4.5/goxygen/inst/templates/ming.html5 | 10 goxygen-1.4.5/goxygen/man/appendExtraPageBlocks.Rd |only goxygen-1.4.5/goxygen/man/buildHTML.Rd | 13 goxygen-1.4.5/goxygen/man/buildTEX.Rd | 12 goxygen-1.4.5/goxygen/man/chooseTemplate.Rd |only goxygen-1.4.5/goxygen/man/createListModularCode.Rd | 10 goxygen-1.4.5/goxygen/man/createListSimpleCode.Rd | 2 goxygen-1.4.5/goxygen/man/createModulePage.Rd | 2 goxygen-1.4.5/goxygen/man/dot-section.Rd |only goxygen-1.4.5/goxygen/man/extractDocumentation.Rd | 14 goxygen-1.4.5/goxygen/man/flattenPageBlockList.Rd |only goxygen-1.4.5/goxygen/man/goxygen.Rd | 43 - goxygen-1.4.5/goxygen/tests/testthat/test-appendExtraPageBlocks.R |only goxygen-1.4.5/goxygen/tests/testthat/test-flattenPageBlockList.R |only goxygen-1.4.5/goxygen/tests/testthat/test-goxygen.R | 75 +- goxygen-1.4.5/goxygen/vignettes/goxygen.Rmd | 26 42 files changed, 1060 insertions(+), 682 deletions(-)
Title: Generalized Order-Restricted Information Criterion
Description: Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate linear models and generalised linear models.
Author: Daniel Gerhard [aut, cre],
Rebecca M. Kuiper [aut]
Maintainer: Daniel Gerhard <00gerhard@gmail.com>
Diff between goric versions 1.1-2 dated 2021-04-19 and 1.1-3 dated 2025-04-01
DESCRIPTION | 8 - MD5 | 18 +-- build/vignette.rds |binary inst/doc/goric.R | 4 inst/doc/goric.Rmd | 4 inst/doc/goric.html | 285 +++++++++++++++++++++++++++++----------------------- man/orgls.Rd | 6 - man/orglsSet.Rd | 4 man/orlm.Rd | 2 vignettes/goric.Rmd | 4 10 files changed, 187 insertions(+), 148 deletions(-)
Title: Simple Animated Plots for R
Description: Simple animated versions of basic R plots, using the 'animation'
package. Includes animated versions of plot, barplot, persp, contour,
filled.contour, hist, curve, points, lines, text, symbols, segments, and
arrows.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between anim.plots versions 0.2.2 dated 2021-04-30 and 0.2.3 dated 2025-04-01
DESCRIPTION | 15 + MD5 | 18 +- NEWS.md | 8 - R/anim.plots.R | 3 R/postprocessing.R | 4 build/vignette.rds |binary inst/doc/anim.plots-stub.R | 8 - inst/doc/anim.plots-stub.html | 331 ++++++++++++++++++++++++++++++++---------- man/anim.plots-package.Rd | 13 + man/anim.save.Rd | 4 10 files changed, 307 insertions(+), 97 deletions(-)
Title: Strategy Estimation
Description: Variants of strategy estimation (Dal Bo & Frechette, 2011, <doi:10.1257/aer.101.1.411>), including the model with parameters for the choice probabilities of the strategies (Breitmoser, 2015, <doi:10.1257/aer.20130675>), and the model with individual level covariates for the selection of strategies by individuals (Dvorak & Fehrler, 2018, <doi:10.2139/ssrn.2986445>).
Author: Fabian Dvorak [aut, cre]
Maintainer: Fabian Dvorak <fabian.dvorak@uni.kn>
Diff between stratEst versions 1.1.6 dated 2022-11-29 and 1.1.7 dated 2025-04-01
DESCRIPTION | 19 ++++++++++++------- MD5 | 36 ++++++++++++++++++------------------ R/is_stratEst_check.R | 2 +- R/is_stratEst_data.R | 2 +- R/is_stratEst_model.R | 2 +- R/is_stratEst_strategy.R | 2 +- R/summary_stratEst_data.R | 2 +- R/summary_stratEst_model.R | 2 +- README.md | 5 +++++ configure | 4 ++-- configure.ac | 6 +++--- inst/WORDLIST | 34 +++++++++++++++++++--------------- man/is.stratEst.check.Rd | 2 +- man/is.stratEst.data.Rd | 2 +- man/is.stratEst.model.Rd | 2 +- man/is.stratEst.strategy.Rd | 2 +- man/summary.stratEst.data.Rd | 2 +- man/summary.stratEst.model.Rd | 2 +- src/Makevars.win | 2 +- 19 files changed, 72 insertions(+), 58 deletions(-)
Title: Multiblock Data Fusion in Statistics and Machine Learning
Description: Functions and datasets to support Smilde, Næs and Liland (2021, ISBN: 978-1-119-60096-1)
"Multiblock Data Fusion in Statistics and Machine Learning - Applications in the Natural and Life Sciences".
This implements and imports a large collection of methods for multiblock data analysis with common interfaces, result- and plotting
functions, several real data sets and six vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
,
Solve Saeboe [ctb],
Stefan Schrunner [rev]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between multiblock versions 0.8.9.0 dated 2025-01-20 and 0.8.10 dated 2025-04-01
DESCRIPTION | 12 +++--- MD5 | 17 +++++--- NAMESPACE | 2 - R/datasets.R | 27 ++++++++++++++ R/direct_export.R | 6 +-- R/sopls.R | 87 ++++++++++++++++++++++++++++++++++++---------- R/sopls_crossvalidation.R | 4 +- data/mobile.rda |only man/figures/mobile.png |only man/mobile.Rd |only man/reexports.Rd | 3 - 11 files changed, 118 insertions(+), 40 deletions(-)
Title: Analyze Two Choice Reaction Time Data with the D*M Method
Description: A collection of functions to estimate parameters of a diffusion model via a D*M analysis. Build in models are: the Ratcliff diffusion model, the RWiener diffusion model, and Linear Ballistic Accumulator models. Custom models functions can be specified as long as they have a density function.
Author: Don van den Bergh [aut, cre] ,
Stijn Verdonck [aut] ,
Francis Tuerlinckx [aut]
Maintainer: Don van den Bergh <donvdbergh@hotmail.com>
Diff between DstarM versions 0.4.0 dated 2020-08-28 and 0.5.0 dated 2025-04-01
DstarM-0.4.0/DstarM/R/DstarMmethodsDeprecated.R |only DstarM-0.5.0/DstarM/DESCRIPTION | 22 ++++++++++++++++------ DstarM-0.5.0/DstarM/MD5 | 21 ++++++++++----------- DstarM-0.5.0/DstarM/NAMESPACE | 1 + DstarM-0.5.0/DstarM/NEWS.md | 6 ++++++ DstarM-0.5.0/DstarM/R/Densities.R | 9 +++++---- DstarM-0.5.0/DstarM/R/estDstarM.R | 6 +++--- DstarM-0.5.0/DstarM/R/estND.R | 4 ++-- DstarM-0.5.0/DstarM/man/Voss.density.Rd | 8 ++++---- DstarM-0.5.0/DstarM/man/estDstarM.Rd | 6 +++--- DstarM-0.5.0/DstarM/man/estND.Rd | 4 ++-- DstarM-0.5.0/DstarM/src/RcppExports.cpp | 5 +++++ 12 files changed, 57 insertions(+), 35 deletions(-)
Title: CAESAR: a Cross-Technology and Cross-Resolution Framework for
Spatial Omics Annotation
Description: Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. [...truncated...]
Author: Xiao Zhang [aut, cre],
Wei Liu [aut],
Jin Liu [aut]
Maintainer: Xiao Zhang <zhangxiao1994@cuhk.edu.cn>
Diff between CAESAR.Suite versions 0.2.1 dated 2025-03-25 and 0.2.2 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 8 +-- inst/doc/STMOB.html | 10 ++-- inst/doc/XeniumBC.html | 106 ++++++++++++++++++++++++------------------------- src/imfactor.cpp | 2 5 files changed, 67 insertions(+), 65 deletions(-)
Title: Interact with Peak Flow Data in the United Kingdom
Description: Obtain information on peak flow data from the National River Flow Archive (NRFA) in the United Kingdom, either from the Peak Flow Dataset files <https://nrfa.ceh.ac.uk/data/peak-flow-dataset> once these have been downloaded to the user's computer or using the NRFA's API. These files are in a format suitable for direct use in the 'WINFAP' software, hence the name of the package.
Author: Ilaria Prosdocimi [aut, cre] ,
Luke Shaw [aut]
Maintainer: Ilaria Prosdocimi <prosdocimi.ilaria@gmail.com>
Diff between winfapReader versions 0.1-5.1 dated 2024-06-19 and 0.1-6 dated 2025-04-01
DESCRIPTION | 10 - MD5 | 28 ++-- NAMESPACE | 1 NEWS.md | 4 R/dateManupulations.R | 312 ++++++++++++++++++++++----------------------- R/get_winfapapi.R | 2 R/readerFuncs.R | 9 - build/vignette.rds |binary inst/doc/winfapReader.R | 98 +++++++------- inst/doc/winfapReader.Rmd | 10 - inst/doc/winfapReader.html | 129 +++++++++++------- man/get_pot.Rd | 2 man/read_cd3.Rd | 2 tests/testthat/testthat.R | 4 vignettes/winfapReader.Rmd | 10 - 15 files changed, 337 insertions(+), 284 deletions(-)
Title: Utilities for Handling Strings and Text
Description: Utilities for handling character vectors
that store human-readable text (either plain or with
markup, such as HTML or LaTeX). The package provides,
in particular, functions that help with the
preparation of plain-text reports, e.g. for expanding
and aligning strings that form the lines of such
reports. The package also provides generic functions for
transforming R objects to HTML and to plain text.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between textutils versions 0.4-1 dated 2024-04-01 and 0.4-2 dated 2025-04-01
DESCRIPTION | 10 +++--- MD5 | 26 ++++++++-------- NAMESPACE | 1 NEWS | 18 ++++++++++- R/functions.R | 69 +++++++++++++++++++++++++++++++++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/btable.pdf |binary inst/tinytest/test_HTMLrm.R | 10 +++--- inst/tinytest/test_insert.R | 5 ++- inst/tinytest/test_toHTML.R | 47 +++++++++++++++++++++++++++++ man/HTMLdecode.Rd | 9 +++-- man/insert.Rd | 4 +- man/toHTML.Rd | 18 +++++++---- 14 files changed, 174 insertions(+), 43 deletions(-)
Title: Grouped Hyper Data Frame: An Extension of Hyper Data Frame
Object
Description: An S3 class 'groupedHyperframe' that inherits from
hyper data frame. Batch processes on point-pattern hyper
column. Aggregation of function-value-table hyper
column(s) and numeric hyper column(s) over a nested
grouping structure.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [aut]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.1.0 dated 2025-03-25 and 0.2.1 dated 2025-04-01
groupedHyperframe-0.1.0/groupedHyperframe/R/fv_S3.R |only groupedHyperframe-0.1.0/groupedHyperframe/R/key1nonfinite.fv.R |only groupedHyperframe-0.1.0/groupedHyperframe/R/nncross_.R |only groupedHyperframe-0.1.0/groupedHyperframe/man/fvlist.Rd |only groupedHyperframe-0.1.0/groupedHyperframe/man/groupedHyperframe.Rd |only groupedHyperframe-0.1.0/groupedHyperframe/man/is.finite.fv.Rd |only groupedHyperframe-0.1.0/groupedHyperframe/man/key1nonfinite-set.Rd |only groupedHyperframe-0.1.0/groupedHyperframe/man/op_fv.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/DESCRIPTION | 12 groupedHyperframe-0.2.1/groupedHyperframe/MD5 | 81 groupedHyperframe-0.2.1/groupedHyperframe/NAMESPACE | 18 groupedHyperframe-0.2.1/groupedHyperframe/R/0PACKAGE.R | 8 groupedHyperframe-0.2.1/groupedHyperframe/R/aggregate_fv.R | 52 groupedHyperframe-0.2.1/groupedHyperframe/R/aggregate_num.R | 100 - groupedHyperframe-0.2.1/groupedHyperframe/R/as.groupedHyperframe.R | 66 groupedHyperframe-0.2.1/groupedHyperframe/R/data_doc.R | 13 groupedHyperframe-0.2.1/groupedHyperframe/R/fvlist.R | 135 - groupedHyperframe-0.2.1/groupedHyperframe/R/groupedHyperframe.R | 48 groupedHyperframe-0.2.1/groupedHyperframe/R/grouped_ppp.R | 60 groupedHyperframe-0.2.1/groupedHyperframe/R/key1.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/mc_identical_by.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/nncross.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/op_hyperframe.R | 30 groupedHyperframe-0.2.1/groupedHyperframe/R/op_ppp.R | 22 groupedHyperframe-0.2.1/groupedHyperframe/R/op_ppplist.R | 26 groupedHyperframe-0.2.1/groupedHyperframe/R/pmean.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/slice.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/user_hyperframe.R | 25 groupedHyperframe-0.2.1/groupedHyperframe/data/Ki67.rda |binary groupedHyperframe-0.2.1/groupedHyperframe/inst/doc/intro.R | 114 - groupedHyperframe-0.2.1/groupedHyperframe/inst/doc/intro.Rmd | 232 +- groupedHyperframe-0.2.1/groupedHyperframe/inst/doc/intro.html | 968 ++++++---- groupedHyperframe-0.2.1/groupedHyperframe/man/Ki67.Rd | 15 groupedHyperframe-0.2.1/groupedHyperframe/man/aggregate_by_.Rd | 12 groupedHyperframe-0.2.1/groupedHyperframe/man/aggregate_fv.Rd | 17 groupedHyperframe-0.2.1/groupedHyperframe/man/aggregate_num.Rd | 7 groupedHyperframe-0.2.1/groupedHyperframe/man/as.groupedHyperframe.Rd | 26 groupedHyperframe-0.2.1/groupedHyperframe/man/check_fvlist.Rd | 8 groupedHyperframe-0.2.1/groupedHyperframe/man/dot-nncross.Rd | 3 groupedHyperframe-0.2.1/groupedHyperframe/man/dot-slice.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/man/groupedHyperframe-package.Rd | 8 groupedHyperframe-0.2.1/groupedHyperframe/man/grouped_ppp.Rd | 13 groupedHyperframe-0.2.1/groupedHyperframe/man/key1.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/man/mc_identical_by.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/man/op_hyperframe.Rd | 23 groupedHyperframe-0.2.1/groupedHyperframe/man/op_ppp.Rd | 4 groupedHyperframe-0.2.1/groupedHyperframe/man/op_ppplist.Rd | 11 groupedHyperframe-0.2.1/groupedHyperframe/man/pmean.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/man/user_hyperframe.Rd | 7 groupedHyperframe-0.2.1/groupedHyperframe/vignettes/intro.Rmd | 232 +- 50 files changed, 1263 insertions(+), 1133 deletions(-)
More information about groupedHyperframe at CRAN
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Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm).
Estimation is performed using either the Laplace method, variational approximations, or extended variational approximations, implemented via TMB (Kristensen et al. (2016), <doi:10.18637/jss.v070.i05>).
Author: Jenni Niku [aut, cre],
Wesley Brooks [aut],
Riki Herliansyah [aut],
Francis K.C. Hui [aut],
Pekka Korhonen [aut],
Sara Taskinen [aut],
Bert van der Veen [aut],
David I. Warton [aut]
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>
Diff between gllvm versions 2.0 dated 2024-11-26 and 2.0.1 dated 2025-04-01
gllvm-2.0.1/gllvm/DESCRIPTION | 10 gllvm-2.0.1/gllvm/MD5 | 98 +-- gllvm-2.0.1/gllvm/NAMESPACE | 9 gllvm-2.0.1/gllvm/NEWS.md | 29 + gllvm-2.0.1/gllvm/R/TMBtrait.R | 159 +++--- gllvm-2.0.1/gllvm/R/VP.gllvm.R | 94 ++- gllvm-2.0.1/gllvm/R/coefplot.gllvm.R | 2 gllvm-2.0.1/gllvm/R/getEnvironCov.gllvm.R | 129 ++-- gllvm-2.0.1/gllvm/R/gllvm.R | 87 +-- gllvm-2.0.1/gllvm/R/gllvm.TMB.R | 138 +++-- gllvm-2.0.1/gllvm/R/gllvm.auxiliary.R | 178 ++++-- gllvm-2.0.1/gllvm/R/gllvm.iter.R | 9 gllvm-2.0.1/gllvm/R/gllvm.makeform.R | 2 gllvm-2.0.1/gllvm/R/goodnessOfFit.gllvm.R |only gllvm-2.0.1/gllvm/R/logLik.gllvm.R | 7 gllvm-2.0.1/gllvm/R/phyloplot.gllvm.R | 8 gllvm-2.0.1/gllvm/R/plotVP.gllvm.R | 40 - gllvm-2.0.1/gllvm/R/predict.gllvm.R | 2 gllvm-2.0.1/gllvm/R/randomCoefplot.R | 16 gllvm-2.0.1/gllvm/R/residuals.gllvm.R | 117 ++-- gllvm-2.0.1/gllvm/R/se.gllvm.R | 71 +- gllvm-2.0.1/gllvm/R/summary.gllvm.R | 29 + gllvm-2.0.1/gllvm/README.md | 12 gllvm-2.0.1/gllvm/inst/doc/vignette1.Rmd | 6 gllvm-2.0.1/gllvm/inst/doc/vignette1.html | 53 +- gllvm-2.0.1/gllvm/inst/doc/vignette2.R | 3 gllvm-2.0.1/gllvm/inst/doc/vignette2.html | 15 gllvm-2.0.1/gllvm/inst/doc/vignette2.rmd | 5 gllvm-2.0.1/gllvm/inst/doc/vignette3.html | 606 +++++++++++------------ gllvm-2.0.1/gllvm/inst/doc/vignette4.html | 146 ++--- gllvm-2.0.1/gllvm/inst/doc/vignette5.html | 4 gllvm-2.0.1/gllvm/inst/doc/vignette6.Rmd | 27 - gllvm-2.0.1/gllvm/inst/doc/vignette6.html | 39 - gllvm-2.0.1/gllvm/inst/doc/vignette8.html | 218 ++++---- gllvm-2.0.1/gllvm/inst/doc/vignette9.Rmd | 12 gllvm-2.0.1/gllvm/inst/doc/vignette9.html | 12 gllvm-2.0.1/gllvm/man/AICc.Rd | 48 - gllvm-2.0.1/gllvm/man/VP.gllvm.Rd |only gllvm-2.0.1/gllvm/man/coefplot.gllvm.Rd | 2 gllvm-2.0.1/gllvm/man/getEnvironCov.gllvm.Rd | 6 gllvm-2.0.1/gllvm/man/gllvm.Rd | 20 gllvm-2.0.1/gllvm/man/goodnessOfFit.Rd |only gllvm-2.0.1/gllvm/man/phyloplot.gllvm.Rd | 3 gllvm-2.0.1/gllvm/src/gllvm.cpp | 210 ++++++- gllvm-2.0.1/gllvm/tests/testthat/test-fitgllvm.R | 14 gllvm-2.0.1/gllvm/vignettes/fit_4th.Rdata |only gllvm-2.0.1/gllvm/vignettes/rcoefs-1.png |binary gllvm-2.0.1/gllvm/vignettes/vignette1.Rmd | 6 gllvm-2.0.1/gllvm/vignettes/vignette2.rmd | 5 gllvm-2.0.1/gllvm/vignettes/vignette6.Rmd | 27 - gllvm-2.0.1/gllvm/vignettes/vignette9.Rmd | 12 gllvm-2.0/gllvm/man/varPartitioning.gllvm.Rd |only gllvm-2.0/gllvm/vignettes/fit_4th.RData |only 53 files changed, 1609 insertions(+), 1136 deletions(-)
Title: Utilities for Dates and Times
Description: Utilities for handling dates and times, such
as selecting particular days of the week or month,
formatting timestamps as required by RSS feeds, or
converting timestamp representations of other software
(such as 'MATLAB' and 'Excel') to R. The package is
lightweight (no dependencies, pure R implementations) and
relies only on R's standard classes to represent dates
and times ('Date' and 'POSIXt'); it aims to provide
efficient implementations, through vectorisation and the
use of R's native numeric representations of timestamps
where possible.
Author: Enrico Schumann [aut, cre] ,
Unicode, Inc. [dtc, cph]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between datetimeutils versions 0.6-4 dated 2024-04-01 and 0.6-5 dated 2025-04-01
DESCRIPTION | 10 +++++----- MD5 | 25 +++++++++++++------------ NAMESPACE | 1 + NEWS | 8 ++++++++ R/data.R | 34 +++++++++++++++++++++++++++++++++- README.md | 20 +++++++++----------- build/partial.rdb |binary build/vignette.rds |binary data/tznames.RData |binary inst/doc/datetimeutils_examples.pdf |binary man/Easter.Rd |only man/date1904.Rd | 3 +-- man/rfc822t.Rd | 2 +- man/tznames.Rd | 2 +- 14 files changed, 72 insertions(+), 33 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), geeglm() (from package 'geepack'), ivreg() (from package 'AER'), ivreg() (from package 'ivreg' when
estimated by ordinary least squares), [...truncated...]
Author: James E. Pustejovsky [aut, cre]
,
Samuel Pekofsky [ctb],
Jingru Zhang [ctb]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.5.11 dated 2024-06-20 and 0.6.0 dated 2025-04-01
DESCRIPTION | 21 + MD5 | 51 ++- NEWS.md | 8 R/Wald_test.R | 138 +++++++++- R/coef_test.R | 96 +++++-- R/conf_int.R | 34 ++ R/geeglm.R | 3 R/rma-mv.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Wald-tests-in-clubSandwich.html | 167 ++++++------- inst/doc/meta-analysis-with-CRVE.html | 53 ++-- inst/doc/panel-data-CRVE.Rmd | 10 inst/doc/panel-data-CRVE.html | 95 ++++--- man/Wald_test.Rd | 53 +++- man/coef_test.Rd | 30 +- man/conf_int.Rd | 2 man/linear_contrast.Rd | 13 - tests/testthat/test_Wald.R | 126 +++++++++ tests/testthat/test_Wald_multiple_comparisons.R |only tests/testthat/test_coef.R | 69 +++++ tests/testthat/test_geeglm.R | 92 ++++++- tests/testthat/test_gls.R | 8 tests/testthat/test_impute_covariance_matrix.R | 6 tests/testthat/test_linear_contrast_multiple_comparisons.R |only tests/testthat/test_lm_robust.R |only tests/testthat/test_rma-mv.R | 62 ++-- vignettes/panel-data-CRVE.Rmd | 10 28 files changed, 841 insertions(+), 310 deletions(-)
Title: Small Area Estimation for Key Health and Demographic Indicators
from Household Surveys
Description: Enables small area estimation (SAE) of health and demographic indicators in low- and middle-income countries (LMICs). It powers an R 'shiny' application that helps public health analysts, policymakers, and researchers generate subnational estimates and prevalence maps for 150+ binary indicators from Demographic and Health Surveys (DHS). Basing its core SAE analysis workflow on the 'surveyPrev' package, the app ensures methodological rigor through guided model selection, automated fitting, and interactive visualization. For more details, visit <https://sae4health.stat.uw.edu/>.
Author: Yunhan Wu [cre, aut],
Qianyu Dong [aut],
Zehang R Li [aut],
Jon Wakefield [aut]
Maintainer: Yunhan Wu <wu-thomas@outlook.com>
Diff between sae4health versions 1.2.0 dated 2025-03-28 and 1.2.1 dated 2025-04-01
DESCRIPTION | 6 MD5 | 22 R/app_ui.R | 382 +++--- R/fct_analysis_helpers.R | 13 R/fct_helpers.R | 637 +++++----- R/fct_results_visual_helpers.R | 6 R/mod_country_specify.R | 2360 +++++++++++++++++++------------------- R/mod_landing_page.R | 760 ++++++------ R/mod_model_selection.R | 214 ++- R/prepare_preload_dat.R | 8 README.md | 11 tests/testthat/test-app-loading.R | 102 - 12 files changed, 2319 insertions(+), 2202 deletions(-)
Title: Machine Learning for Merging Satellite and Ground Precipitation
Data
Description: A machine learning algorithm that merges satellite and ground precipitation data using Random Forest for spatial prediction, residual modeling for bias correction, and quantile mapping for adjustment, ensuring accurate estimates across temporal scales and regions.
Author: Jonnathan Augusto Landi Bermeo [aut, cre, cph]
,
Alex Aviles [aut] ,
Dario Zhina [aut] ,
Marco Mogro [aut] ,
Anthony Guaman [aut]
Maintainer: Jonnathan Augusto Landi Bermeo <jonnathan.landi@outlook.com>
Diff between RFplus versions 1.4-0 dated 2025-03-10 and 1.5-4 dated 2025-03-31
DESCRIPTION | 8 - MD5 | 38 +++--- NEWS.md | 32 ++++- R/RFplus.R | 164 ++++++++++++++++------------ build/vignette.rds |binary data/BD_Insitu.RData |binary data/Cords_Insitu.RData |binary inst/NEWS | 13 ++ inst/doc/RFplus.Rmd | 224 +++++++++++++++++++------------------- inst/doc/RFplus.html | 91 +++++++-------- inst/extdata/BD_Insitu.csv | 242 +++++++++++++++++++++--------------------- inst/extdata/CHIRPS.nc |binary inst/extdata/Cords_Insitu.csv | 24 +--- inst/extdata/DEM.nc |binary inst/extdata/MSWEP.nc |binary man/BD_Insitu.Rd | 2 man/Cords_Insitu.Rd | 8 + man/RFplus.Rd | 24 +++- tests/testthat/test-RFplus.R | 2 vignettes/RFplus.Rmd | 224 +++++++++++++++++++------------------- 20 files changed, 581 insertions(+), 515 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing sparse priors to
impose exact sparsity leads to efficient Bayesian shrinkage estimation, variable
selection and statistical inference. In this package, we have implemented robust
Bayesian variable selection with spike-and-slab priors under high-dimensional
linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and
Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying
coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular,
valid robust Bayesian inferences under both models in the presence of heavy-tailed errors
can be validated on finite samples. Additional models including robust Bayesian
group LASSO are also included. The Markov Chain Monte Carlo (MCMC) algorithms
of the proposed and alternative models are implemented in C++.
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Xiaoxi Li [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.1.1 dated 2025-02-23 and 1.1.2 dated 2025-03-31
DESCRIPTION | 15 - MD5 | 73 +++---- NAMESPACE | 24 +- NEWS.md | 88 ++++---- R/NonRobust.R | 150 +++++++------- R/NonRobust_vc.R | 150 +++++++------- R/Robust_vc.R | 164 ++++++++-------- R/coverage.R | 75 +++---- R/coverage_lin.R | 22 +- R/coverage_vc.R | 88 ++++---- R/data.R | 104 +++++----- R/estimation.R | 81 ++++---- R/estimation_lin.R | 24 +- R/estimation_vc.R | 126 ++++++------ R/nonrobust_g.R |only R/nonrobust_lin.R | 75 +++---- R/pqrBayes-package.R | 120 +++++------ R/pqrBayes.R | 54 +++-- R/pqrBayes_g.R |only R/pqrBayes_lin.R | 38 +-- R/pqrBayes_vc.R | 38 +-- R/predict.pqrBayes.R | 99 +++++---- R/predict_lin.R | 114 +++++------ R/predict_vc.R | 148 +++++++------- R/print.pqrBayes.R | 106 +++++----- R/robust_g.R |only R/robust_lin.R | 84 ++++---- R/select.pqrBayes.R | 151 +++++++------- R/select_lin.R | 78 +++---- R/select_vc.R | 88 ++++---- README.md | 455 +++++++++++++++++++++++++-------------------- data/data.rda |binary man/coverage.Rd | 8 man/data.Rd | 18 + man/estimation.pqrBayes.Rd | 6 man/pqrBayes-package.Rd | 10 man/pqrBayes.Rd | 46 +++- man/predict_pqrBayes.Rd | 10 man/select.pqrBayes.Rd | 8 39 files changed, 1548 insertions(+), 1390 deletions(-)
Title: Tools for Analyzing Time Series Data of Just Finance and
Econometrics
Description: Offers procedures to support financial-economic time series modelling and enhanced procedures for computing the investment performance indices of Bacon (2004) <DOI:10.1002/9781119206309>.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between JFE versions 2.5.8 dated 2025-01-24 and 2.5.9 dated 2025-03-31
JFE-2.5.8/JFE/man/getBIS.Rd |only JFE-2.5.9/JFE/DESCRIPTION | 8 ++-- JFE-2.5.9/JFE/MD5 | 8 ++-- JFE-2.5.9/JFE/R/dataDownload.R | 81 ++++++++++++++++++++++++++++------------- JFE-2.5.9/JFE/man/getEER.Rd |only JFE-2.5.9/JFE/man/getFed.Rd | 20 +++------- 6 files changed, 70 insertions(+), 47 deletions(-)
Title: Analyze Results Generated by the 'SqueezeMeta' Pipeline
Description: 'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.
Author: Fernando Puente-Sanchez [aut, cre],
Natalia Garcia-Garcia [aut]
Maintainer: Fernando Puente-Sanchez <fernando.puente.sanchez@slu.se>
Diff between SQMtools versions 1.6.3 dated 2023-09-18 and 1.7.0 dated 2025-03-31
DESCRIPTION | 10 - MD5 | 90 ++++++---- NAMESPACE | 15 + R/CheckMProkaryote.R |only R/USiCGs.R | 4 R/aggregate_methods.R | 3 R/bin_methods.R |only R/combineSQM.R | 224 +++++++++++++-------------- R/combineSQMlite.R | 4 R/copy_number.R |only R/exportKrona.R | 6 R/exportPathway.R | 48 +++-- R/exportSeqs.R |only R/exportTable.R | 11 - R/extra_methods.R | 57 +++--- R/figures.R | 30 ++- R/genericTable.R | 9 - R/loadSQM.R | 194 +++++++++++++---------- R/loadSQMlite.R | 2 R/seqvec2fasta.R | 6 R/subset_methods.R | 340 ++++++++++++++++++++++++++++------------- R/summary_bunch.R |only R/summary_lite.R | 2 data/CheckMProkaryote.RData |only data/Hadza.RData |binary data/MGKOs.RData |binary data/MGOGs.RData |binary data/RecA.RData |binary data/USiCGs.RData |binary man/CheckMProkaryote.Rd |only man/USiCGs.Rd | 4 man/combineSQM.Rd | 19 +- man/create_bin.Rd |only man/exportBins.Rd |only man/exportContigs.Rd |only man/exportKrona.Rd | 4 man/exportORFs.Rd |only man/exportPathway.Rd | 19 +- man/exportTable.Rd | 11 - man/find_redundant_contigs.Rd |only man/loadSQM.Rd | 20 +- man/loadSQMlite.Rd | 2 man/plotBins.Rd | 4 man/plotFunctions.Rd | 7 man/plotTaxonomy.Rd | 2 man/remove_contigs_from_bin.Rd |only man/seqvec2fasta.Rd | 7 man/subsetBins.Rd | 5 man/subsetContigs.Rd | 8 man/subsetFun.Rd | 14 + man/subsetORFs.Rd | 10 - man/subsetTax.Rd | 14 + man/summary.SQMbunch.Rd |only 53 files changed, 729 insertions(+), 476 deletions(-)
Title: Kidney-Related Functions for Clinical and Epidemiological
Research
Description: Contains kidney care oriented functions.
Current version contains functions for calculation of:
- Estimated glomerular filtration rate by CKD-EPI (2021 and 2009), MDRD, CKiD, FAS, EKFC, etc.
- Kidney Donor Risk Index and Kidney Donor Profile Index for kidney transplant donors.
- Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, <https://Scientific-Tools.Org>. <doi:10.32614/CRAN.package.kidney.epi>.
Author: Boris Bikbov [aut, cre]
Maintainer: Boris Bikbov <boris.bikbov@scientific-tools.org>
Diff between kidney.epi versions 1.2.0 dated 2020-03-04 and 1.3.0 dated 2025-03-31
kidney.epi-1.2.0/kidney.epi/R/egfr.R |only kidney.epi-1.2.0/kidney.epi/data/ktx.RData |only kidney.epi-1.2.0/kidney.epi/man/egfr.ckdepi.Rd |only kidney.epi-1.2.0/kidney.epi/man/kidney.epi.Rd |only kidney.epi-1.2.0/kidney.epi/man/ktx.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_obligatory_params.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_param_arguments.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_param_number.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_params_numeric.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_plausibility.age.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_plausibility.creatinine.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.count_greater_threshhold.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.count_lowerequal_threshhold.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.is.param_possible.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.is_numeric.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.output_message.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.singular_or_plural.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.strict_to_numeric_threshhold_greater.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.strict_to_numeric_threshhold_lower.Rd |only kidney.epi-1.3.0/kidney.epi/DESCRIPTION | 26 kidney.epi-1.3.0/kidney.epi/MD5 | 107 +- kidney.epi-1.3.0/kidney.epi/NAMESPACE | 34 kidney.epi-1.3.0/kidney.epi/NEWS | 17 kidney.epi-1.3.0/kidney.epi/R/ckd_classify.R |only kidney.epi-1.3.0/kidney.epi/R/data.R | 31 kidney.epi-1.3.0/kidney.epi/R/egfr_ckdepi2009.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_ckdepi2021.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_ckid.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_ekfc.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_fas.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_mdrd.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_other_adults.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_other_children.R |only kidney.epi-1.3.0/kidney.epi/R/kidney.epi.R | 19 kidney.epi-1.3.0/kidney.epi/R/ktx.kdpi.optn.R | 142 +-- kidney.epi-1.3.0/kidney.epi/R/matrix.R |only kidney.epi-1.3.0/kidney.epi/R/service.check_plausibility.R | 153 ++- kidney.epi-1.3.0/kidney.epi/R/service.general.R | 195 ++-- kidney.epi-1.3.0/kidney.epi/R/sysdata.rda |binary kidney.epi-1.3.0/kidney.epi/README.md | 55 - kidney.epi-1.3.0/kidney.epi/build/vignette.rds |binary kidney.epi-1.3.0/kidney.epi/data/ckd.data.rda |only kidney.epi-1.3.0/kidney.epi/data/ktx.data.rda |only kidney.epi-1.3.0/kidney.epi/inst/CITATION | 20 kidney.epi-1.3.0/kidney.epi/inst/doc/gfr.R | 60 + kidney.epi-1.3.0/kidney.epi/inst/doc/gfr.Rmd | 121 ++ kidney.epi-1.3.0/kidney.epi/inst/doc/gfr.html | 450 +++++++--- kidney.epi-1.3.0/kidney.epi/inst/doc/ktx.R | 31 kidney.epi-1.3.0/kidney.epi/inst/doc/ktx.Rmd | 53 - kidney.epi-1.3.0/kidney.epi/inst/doc/ktx.html | 399 +++++--- kidney.epi-1.3.0/kidney.epi/inst/doc/services.Rmd |only kidney.epi-1.3.0/kidney.epi/inst/doc/services.html |only kidney.epi-1.3.0/kidney.epi/inst/figures |only kidney.epi-1.3.0/kidney.epi/man/ckd.data.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckdepi.cr.2009.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckdepi.cr.2021.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckdepi.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckdepi.cr_cys.2021.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckid_u25.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckid_u25.cys.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ekfc.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ekfc.cys.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.fas.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.fas.cr_cys.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.fas.cys.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.lm.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.mdrd4.Rd | 37 kidney.epi-1.3.0/kidney.epi/man/egfr.schwartz.Rd | 37 kidney.epi-1.3.0/kidney.epi/man/figures |only kidney.epi-1.3.0/kidney.epi/man/ktx.data.Rd |only kidney.epi-1.3.0/kidney.epi/man/ktx.kdpi.optn.Rd | 43 kidney.epi-1.3.0/kidney.epi/man/matrix.cross_table.Rd |only kidney.epi-1.3.0/kidney.epi/man/matrix.get_named_matrix_value.Rd |only kidney.epi-1.3.0/kidney.epi/man/matrix.read_excel_to_named_matrix.Rd |only kidney.epi-1.3.0/kidney.epi/man/matrix.save_named_matrix_to_excel.Rd |only kidney.epi-1.3.0/kidney.epi/man/nephro.albuminuria_category.Rd |only kidney.epi-1.3.0/kidney.epi/man/nephro.gfr_category.Rd |only kidney.epi-1.3.0/kidney.epi/man/nephro.kdigo_risk_category.Rd |only kidney.epi-1.3.0/kidney.epi/man/nephro.proteinuria_category.Rd |only kidney.epi-1.3.0/kidney.epi/man/service.convert_creatinine.Rd | 20 kidney.epi-1.3.0/kidney.epi/man/service.convert_cystatin.Rd |only kidney.epi-1.3.0/kidney.epi/vignettes/gfr.Rmd | 121 ++ kidney.epi-1.3.0/kidney.epi/vignettes/ktx.Rmd | 53 - kidney.epi-1.3.0/kidney.epi/vignettes/services.Rmd |only 84 files changed, 1472 insertions(+), 752 deletions(-)
Title: Companion Tools for Open-Source Tools for Training Resources
(OTTR)
Description: Tools for converting Open-Source Tools for Training Resources
(OTTR) courses into Leanpub or Coursera courses. 'ottrpal' is for use
with the OTTR Template repository to create courses.
Author: Candace Savonen [aut, cre] ,
Carrie Wright [ctb],
Howard Baek [ctb],
Kate Isaac [ctb]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between ottrpal versions 1.2.1 dated 2024-01-09 and 2.0.0 dated 2025-03-31
ottrpal-1.2.1/ottrpal/R/aaa_utils.R |only ottrpal-1.2.1/ottrpal/R/bookdown_to_leanpub.R |only ottrpal-1.2.1/ottrpal/R/coursera.R |only ottrpal-1.2.1/ottrpal/R/data.R |only ottrpal-1.2.1/ottrpal/R/example_data.R |only ottrpal-1.2.1/ottrpal/R/footnotes.R |only ottrpal-1.2.1/ottrpal/R/gs_png.R |only ottrpal-1.2.1/ottrpal/R/leanpub_checks.R |only ottrpal-1.2.1/ottrpal/R/quiz.R |only ottrpal-1.2.1/ottrpal/R/remove_yaml.R |only ottrpal-1.2.1/ottrpal/R/replace_html.R |only ottrpal-1.2.1/ottrpal/R/set_knitr_image_path.R |only ottrpal-1.2.1/ottrpal/R/set_up.R |only ottrpal-1.2.1/ottrpal/R/simple_references.R |only ottrpal-1.2.1/ottrpal/R/utils-pipe.R |only ottrpal-1.2.1/ottrpal/R/zzz.R |only ottrpal-1.2.1/ottrpal/inst/extdata/01-intro.Rmd |only ottrpal-1.2.1/ottrpal/inst/extdata/02-example-chapter.Rmd |only ottrpal-1.2.1/ottrpal/inst/extdata/Book.txt |only ottrpal-1.2.1/ottrpal/inst/extdata/_bookdown.yml |only ottrpal-1.2.1/ottrpal/inst/extdata/index.Rmd |only ottrpal-1.2.1/ottrpal/inst/extdata/references.bib |only ottrpal-1.2.1/ottrpal/inst/extdata/resources/chapt_screen_images |only ottrpal-1.2.1/ottrpal/inst/extdata/resources/chapter_urls.tsv |only ottrpal-1.2.1/ottrpal/inst/extdata/tmp |only ottrpal-1.2.1/ottrpal/inst/extdata/toc_close.css |only ottrpal-1.2.1/ottrpal/man/bookdown_destination.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_file.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_path.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_rmd_files.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_to_book_txt.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_to_embed_leanpub.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_to_leanpub.Rd |only ottrpal-1.2.1/ottrpal/man/convert_utube_link.Rd |only ottrpal-1.2.1/ottrpal/man/example_repo_cleanup.Rd |only ottrpal-1.2.1/ottrpal/man/example_repo_setup.Rd |only ottrpal-1.2.1/ottrpal/man/figures |only ottrpal-1.2.1/ottrpal/man/footnotes.Rd |only ottrpal-1.2.1/ottrpal/man/get_bookdown_spec.Rd |only ottrpal-1.2.1/ottrpal/man/leanpub_check.Rd |only ottrpal-1.2.1/ottrpal/man/remove_yaml_header.Rd |only ottrpal-1.2.1/ottrpal/man/replace_html.Rd |only ottrpal-1.2.1/ottrpal/man/set_up_leanpub.Rd |only ottrpal-1.2.1/ottrpal/man/simple_references.Rd |only ottrpal-1.2.1/ottrpal/vignettes/manuscript |only ottrpal-2.0.0/ottrpal/DESCRIPTION | 27 ottrpal-2.0.0/ottrpal/MD5 | 191 +++--- ottrpal-2.0.0/ottrpal/NAMESPACE | 66 +- ottrpal-2.0.0/ottrpal/NEWS.md | 9 ottrpal-2.0.0/ottrpal/R/auth.R | 286 +++++++--- ottrpal-2.0.0/ottrpal/R/book_txt.R |only ottrpal-2.0.0/ottrpal/R/borrow_chapter.R |only ottrpal-2.0.0/ottrpal/R/get_data.R |only ottrpal-2.0.0/ottrpal/R/github_handling.R |only ottrpal-2.0.0/ottrpal/R/google_slides.R |only ottrpal-2.0.0/ottrpal/R/leanpub.R |only ottrpal-2.0.0/ottrpal/R/notes_to_fig_alt.R | 33 - ottrpal-2.0.0/ottrpal/R/ottrfy.R |only ottrpal-2.0.0/ottrpal/R/quiz_formatting.R |only ottrpal-2.0.0/ottrpal/R/render_without_toc.R |only ottrpal-2.0.0/ottrpal/R/spell_check.R |only ottrpal-2.0.0/ottrpal/R/token_handlers.R |only ottrpal-2.0.0/ottrpal/R/url_check.R |only ottrpal-2.0.0/ottrpal/R/utils.R |only ottrpal-2.0.0/ottrpal/README.md | 88 --- ottrpal-2.0.0/ottrpal/build/vignette.rds |binary ottrpal-2.0.0/ottrpal/inst/doc/getting-started.html | 22 ottrpal-2.0.0/ottrpal/inst/extdata/_child_doc.Rmd |only ottrpal-2.0.0/ottrpal/inst/extdata/dictionary.txt |only ottrpal-2.0.0/ottrpal/inst/extdata/exclude_files.txt |only ottrpal-2.0.0/ottrpal/inst/extdata/ignore-urls.txt |only ottrpal-2.0.0/ottrpal/inst/extdata/parent_doc.Rmd |only ottrpal-2.0.0/ottrpal/inst/extdata/parent_doc.html |only ottrpal-2.0.0/ottrpal/inst/extdata/resources/other_chapters |only ottrpal-2.0.0/ottrpal/man/app_set_up.Rd |only ottrpal-2.0.0/ottrpal/man/auth_from_secret.Rd | 39 + ottrpal-2.0.0/ottrpal/man/authorize.Rd | 22 ottrpal-2.0.0/ottrpal/man/bad_quiz_path.Rd | 2 ottrpal-2.0.0/ottrpal/man/borrow_chapter.Rd |only ottrpal-2.0.0/ottrpal/man/cache_secrets_folder.Rd |only ottrpal-2.0.0/ottrpal/man/check_all_questions.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_git_repo.Rd |only ottrpal-2.0.0/ottrpal/man/check_question.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_quiz.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_quiz_attributes.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_quiz_dir.Rd |only ottrpal-2.0.0/ottrpal/man/check_quiz_question_attributes.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_quizzes.Rd | 5 ottrpal-2.0.0/ottrpal/man/check_spelling.Rd |only ottrpal-2.0.0/ottrpal/man/check_urls.Rd |only ottrpal-2.0.0/ottrpal/man/clean_up.Rd |only ottrpal-2.0.0/ottrpal/man/convert_coursera_quizzes.Rd | 2 ottrpal-2.0.0/ottrpal/man/convert_quiz.Rd | 2 ottrpal-2.0.0/ottrpal/man/course_path.Rd |only ottrpal-2.0.0/ottrpal/man/course_to_book_txt.Rd |only ottrpal-2.0.0/ottrpal/man/coursera.Rd | 10 ottrpal-2.0.0/ottrpal/man/delete_creds.Rd |only ottrpal-2.0.0/ottrpal/man/encrypt_creds_path.Rd | 2 ottrpal-2.0.0/ottrpal/man/encrypt_creds_user_path.Rd | 2 ottrpal-2.0.0/ottrpal/man/extract_meta.Rd | 2 ottrpal-2.0.0/ottrpal/man/find_issue.Rd |only ottrpal-2.0.0/ottrpal/man/get_chapters.Rd | 12 ottrpal-2.0.0/ottrpal/man/get_github.Rd |only ottrpal-2.0.0/ottrpal/man/get_object_id_notes.Rd | 2 ottrpal-2.0.0/ottrpal/man/get_pages_url.Rd |only ottrpal-2.0.0/ottrpal/man/get_repo_info.Rd |only ottrpal-2.0.0/ottrpal/man/get_slide_id.Rd | 2 ottrpal-2.0.0/ottrpal/man/get_urls.Rd |only ottrpal-2.0.0/ottrpal/man/good_quiz_path.Rd | 9 ottrpal-2.0.0/ottrpal/man/gs_helpers.Rd | 2 ottrpal-2.0.0/ottrpal/man/gs_png_url.Rd | 2 ottrpal-2.0.0/ottrpal/man/key_encrypt_creds_path.Rd | 2 ottrpal-2.0.0/ottrpal/man/make_embed_markdown.Rd | 25 ottrpal-2.0.0/ottrpal/man/make_screenshots.Rd |only ottrpal-2.0.0/ottrpal/man/ottr_check.Rd |only ottrpal-2.0.0/ottrpal/man/ottrfy.Rd |only ottrpal-2.0.0/ottrpal/man/parse_q_tag.Rd | 2 ottrpal-2.0.0/ottrpal/man/parse_quiz.Rd | 2 ottrpal-2.0.0/ottrpal/man/parse_quiz_df.Rd | 2 ottrpal-2.0.0/ottrpal/man/pipe.Rd | 8 ottrpal-2.0.0/ottrpal/man/qrmd_files.Rd |only ottrpal-2.0.0/ottrpal/man/set_knitr_image_path.Rd | 13 ottrpal-2.0.0/ottrpal/man/setup_ottr_template.Rd |only ottrpal-2.0.0/ottrpal/man/supported_endpoints.Rd |only ottrpal-2.0.0/ottrpal/man/test_url.Rd |only ottrpal-2.0.0/ottrpal/man/website_to_embed_leanpub.Rd |only ottrpal-2.0.0/ottrpal/tests |only 127 files changed, 511 insertions(+), 392 deletions(-)
Title: Climate Services' Indicators Based on Sub-Seasonal to Decadal
Predictions
Description: Set of generalised tools for the flexible computation of climate
related indicators defined by the user. Each method represents a specific
mathematical approach which is combined with the possibility to select an
arbitrary time period to define the indicator. This enables a wide range of
possibilities to tailor the most suitable indicator for each particular climate
service application (agriculture, food security, energy, water management, ...).
This package is intended for sub-seasonal, seasonal and decadal climate
predictions, but its methods are also applicable to other time-scales,
provided the dimensional structure of the input is maintained. Additionally,
the outputs of the functions in this package are compatible with 'CSTools'.
This package is described in 'Pérez-Zanón et al. (2023)
<doi:10.1016/j.cliser.2023.100393>' and it was developed in the context of
'H2020 MED-GOLD' (776467) and 'S2S4E' (776787) projects. See 'Lledó et al. (2019)
<doi:10.1016/j.renene.2019.04.13 [...truncated...]
Author: Theertha Kariyathan [cre],
Victoria Agudetse [ctb],
Eva Rifa [ctb],
Nuria Perez-Zanon [aut] ,
Chou Chihchung [aut],
Llorenc Lledo [aut],
Gonzalez-Reviriego Nube [ctb],
Marcos Rauel [ctb],
Palma Lluis [ctb],
An-Chi Ho [ctb],
BSC-CNS [cph]
Maintainer: Theertha Kariyathan <theertha.kariyathan@bsc.es>
Diff between CSIndicators versions 1.1.1 dated 2024-01-24 and 1.1.2 dated 2025-03-31
DESCRIPTION | 14 +++++++----- MD5 | 38 +++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 19 +++++++++++++++++ R/AccumulationExceedingThreshold.R | 10 +++++---- R/MergeRefToExp.R | 9 +++++--- R/PeriodAccumulation.R | 15 ++++++++----- R/PeriodMax.R | 14 +++++++----- R/PeriodMean.R | 9 +++++--- R/PeriodMin.R | 11 ++++++---- R/PeriodPET.R | 8 +++++-- R/PeriodStandardization.R | 27 +++++++++++++++--------- R/PeriodVariance.R | 8 ++++--- R/SelectPeriodOnData.R | 2 - R/SelectPeriodOnDates.R | 2 - R/TotalSpellTimeExceedingThreshold.R | 10 +++++---- R/TotalTimeExceedingThreshold.R | 10 +++++---- build/partial.rdb |binary inst/CITATION | 2 - man/CST_PeriodStandardization.Rd | 8 +++---- 20 files changed, 136 insertions(+), 81 deletions(-)
Title: Convert Country Names and Country Codes
Description: Standardize country names, convert them into one of 40
different coding schemes, convert between coding schemes, and assign
region descriptors.
Author: Vincent Arel-Bundock [aut, cre]
,
CJ Yetman [ctb] ,
Nils Enevoldsen [ctb] ,
Etienne Bacher [ctb] ,
Samuel Meichtry [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between countrycode versions 1.6.0 dated 2024-03-22 and 1.6.1 dated 2025-03-31
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/codelist.R | 4 ++-- R/countrycode.R | 8 +++++++- data/codelist.rda |binary data/codelist_panel.rda |binary man/codelist.Rd | 4 ++-- 8 files changed, 27 insertions(+), 16 deletions(-)
Title: Chromatographic File Converter
Description: Reads chromatograms from binary formats into R objects. Currently supports
conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions',
'ThermoRaw', and 'Varian Workstation' files as well as various text-based formats.
In addition to its internal parsers, chromConverter contains bindings to parsers in
external libraries, such as 'Aston' <https://github.com/bovee/aston>,
'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>,
and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.
Author: Ethan Bass [aut, cre] ,
James Dillon [ctb, cph] ,
Evan Shi [ctb, cph]
Maintainer: Ethan Bass <ethanbass@gmail.com>
Diff between chromConverter versions 0.2.1 dated 2022-07-11 and 0.7.5 dated 2025-03-31
chromConverter-0.2.1/chromConverter/R/parsers.R |only chromConverter-0.2.1/chromConverter/man/attach_metadata.Rd |only chromConverter-0.2.1/chromConverter/man/configure_aston.Rd |only chromConverter-0.2.1/chromConverter/tests/testthat/testdata/DAD1.CSV |only chromConverter-0.7.5/chromConverter/DESCRIPTION | 58 chromConverter-0.7.5/chromConverter/MD5 | 115 - chromConverter-0.7.5/chromConverter/NAMESPACE | 42 chromConverter-0.7.5/chromConverter/NEWS.md | 262 +++ chromConverter-0.7.5/chromConverter/R/attach_metadata.R | 855 ++++++++-- chromConverter-0.7.5/chromConverter/R/call_aston.R |only chromConverter-0.7.5/chromConverter/R/call_entab.R |only chromConverter-0.7.5/chromConverter/R/call_openchrom.R | 283 ++- chromConverter-0.7.5/chromConverter/R/call_rainbow.R |only chromConverter-0.7.5/chromConverter/R/olefile_utilities.R |only chromConverter-0.7.5/chromConverter/R/read_agilent_d.R |only chromConverter-0.7.5/chromConverter/R/read_asm.R |only chromConverter-0.7.5/chromConverter/R/read_cdf.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_ch.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_csv.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_ms.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_report.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_uv.R |only chromConverter-0.7.5/chromConverter/R/read_chromeleon.R |only chromConverter-0.7.5/chromConverter/R/read_chroms.R | 474 ++++- chromConverter-0.7.5/chromConverter/R/read_mdf.R |only chromConverter-0.7.5/chromConverter/R/read_mzml.R |only chromConverter-0.7.5/chromConverter/R/read_peaklist.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_ascii.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_gcd.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_lcd.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_peaktable.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_qgd.R |only chromConverter-0.7.5/chromConverter/R/read_thermoraw.R | 163 - chromConverter-0.7.5/chromConverter/R/read_varian_peaklist.R |only chromConverter-0.7.5/chromConverter/R/read_varian_sms.R |only chromConverter-0.7.5/chromConverter/R/read_waters_arw.R |only chromConverter-0.7.5/chromConverter/R/read_waters_raw.R |only chromConverter-0.7.5/chromConverter/R/reshape_chroms.R |only chromConverter-0.7.5/chromConverter/R/utils.R | 422 ++++ chromConverter-0.7.5/chromConverter/R/write_andi_ms.R |only chromConverter-0.7.5/chromConverter/R/write_chroms.R |only chromConverter-0.7.5/chromConverter/R/write_mzml.R |only chromConverter-0.7.5/chromConverter/R/zzz.R | 17 chromConverter-0.7.5/chromConverter/README.md | 147 + chromConverter-0.7.5/chromConverter/build/partial.rdb |binary chromConverter-0.7.5/chromConverter/inst/CITATION | 19 chromConverter-0.7.5/chromConverter/inst/shell/path_to_openchrom_commandline.txt | 2 chromConverter-0.7.5/chromConverter/man/call_entab.Rd | 36 chromConverter-0.7.5/chromConverter/man/call_openchrom.Rd | 85 chromConverter-0.7.5/chromConverter/man/call_rainbow.Rd |only chromConverter-0.7.5/chromConverter/man/configure_openchrom.Rd |only chromConverter-0.7.5/chromConverter/man/configure_python_environment.Rd |only chromConverter-0.7.5/chromConverter/man/extract_metadata.Rd |only chromConverter-0.7.5/chromConverter/man/read_agilent_d.Rd |only chromConverter-0.7.5/chromConverter/man/read_agilent_dx.Rd |only chromConverter-0.7.5/chromConverter/man/read_asm.Rd |only chromConverter-0.7.5/chromConverter/man/read_cdf.Rd |only chromConverter-0.7.5/chromConverter/man/read_chemstation_ch.Rd |only chromConverter-0.7.5/chromConverter/man/read_chemstation_csv.Rd | 34 chromConverter-0.7.5/chromConverter/man/read_chemstation_ms.Rd |only chromConverter-0.7.5/chromConverter/man/read_chemstation_reports.Rd |only chromConverter-0.7.5/chromConverter/man/read_chemstation_uv.Rd |only chromConverter-0.7.5/chromConverter/man/read_chromeleon.Rd | 31 chromConverter-0.7.5/chromConverter/man/read_chroms.Rd | 128 + chromConverter-0.7.5/chromConverter/man/read_mdf.Rd |only chromConverter-0.7.5/chromConverter/man/read_mzml.Rd | 42 chromConverter-0.7.5/chromConverter/man/read_peaklist.Rd |only chromConverter-0.7.5/chromConverter/man/read_shimadzu.Rd | 74 chromConverter-0.7.5/chromConverter/man/read_shimadzu_gcd.Rd |only chromConverter-0.7.5/chromConverter/man/read_shimadzu_lcd.Rd |only chromConverter-0.7.5/chromConverter/man/read_shimadzu_qgd.Rd |only chromConverter-0.7.5/chromConverter/man/read_sz_lcd_2d.Rd |only chromConverter-0.7.5/chromConverter/man/read_sz_lcd_3d.Rd |only chromConverter-0.7.5/chromConverter/man/read_thermoraw.Rd | 39 chromConverter-0.7.5/chromConverter/man/read_varian_peaklist.Rd |only chromConverter-0.7.5/chromConverter/man/read_varian_sms.Rd |only chromConverter-0.7.5/chromConverter/man/read_waters_arw.Rd | 31 chromConverter-0.7.5/chromConverter/man/read_waters_raw.Rd |only chromConverter-0.7.5/chromConverter/man/sp_converter.Rd | 35 chromConverter-0.7.5/chromConverter/man/uv_converter.Rd | 34 chromConverter-0.7.5/chromConverter/man/write_andi_chrom.Rd |only chromConverter-0.7.5/chromConverter/man/write_chroms.Rd |only chromConverter-0.7.5/chromConverter/man/write_mzml.Rd |only chromConverter-0.7.5/chromConverter/tests/testthat/helpers.R | 32 chromConverter-0.7.5/chromConverter/tests/testthat/test-extra.R |only chromConverter-0.7.5/chromConverter/tests/testthat/test-read_chroms.R | 334 +++ chromConverter-0.7.5/chromConverter/tests/testthat/test_utils.R |only chromConverter-0.7.5/chromConverter/tests/testthat/testdata/RUTIN2.D |only chromConverter-0.7.5/chromConverter/tests/testthat/testdata/chemstation_130.ch |only chromConverter-0.7.5/chromConverter/tests/testthat/testdata/dad1.csv |only 90 files changed, 3065 insertions(+), 729 deletions(-)
More information about chromConverter at CRAN
Permanent link
Title: Biological Analysis and Visualization of Weather Radar Data
Description: Extract, visualize and summarize aerial movements of birds and
insects from weather radar data. See Dokter, A. M. et al. (2018)
"bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028>
for a software paper describing package and methodologies.
Author: Adriaan M. Dokter [aut, cre] ,
Peter Desmet [aut] ,
Bart Kranstauber [aut] ,
Cecilia Nilsson [aut] ,
Stijn Van Hoey [aut] ,
Bart Hoekstra [ctb] ,
Pieter Huybrechts [ctb] ,
Hidde Leijnse [ctb] ,
Nicolas Noe [ctb] ,
Raphael Nussbaumer [ctb] ,
Jurriaan [...truncated...]
Maintainer: Adriaan M. Dokter <biorad@cornell.edu>
Diff between bioRad versions 0.8.1 dated 2024-07-30 and 0.9.0 dated 2025-03-31
DESCRIPTION | 8 MD5 | 84 ++- NAMESPACE | 6 NEWS.md | 40 + R/apply_mistnet.R | 10 R/as.vp.R |only R/as.vpts.R | 63 ++ R/calculate_param.R | 26 - R/calculate_vp.R | 18 R/clean_mixture.R |only R/filter_precip.R |only R/filter_vpts.R | 5 R/integrate_to_ppi.R | 19 R/map.R | 93 ++-- R/nexrad_odim.R | 2 R/nyquist_velocity.R | 1 R/plot.vpi.R | 10 R/read_vpfiles.R | 5 R/regularize_vpts.R | 17 R/utils.R | 17 README.md | 19 build/partial.rdb |binary build/vignette.rds |binary data/example_vp.rda |binary inst/doc/bioRad.html | 21 inst/doc/rad_aero_22.R | 782 +++++++++++++++++----------------- inst/doc/rad_aero_22.Rmd | 2 inst/doc/rad_aero_22.html | 445 +++++++++---------- inst/doc/range_correction.html | 124 ++--- man/apply_mistnet.Rd | 10 man/as.vp.Rd |only man/calculate_param.Rd | 23 - man/calculate_vp.Rd | 2 man/clean_mixture.Rd |only man/filter_precip.Rd |only man/filter_vpts.Rd | 8 man/map.Rd | 5 man/nexrad_to_odim.Rd | 2 man/nyquist_velocity.Rd | 1 man/regularize_vpts.Rd | 17 tests/testthat/test-as.vp.R |only tests/testthat/test-as.vpts.R | 33 + tests/testthat/test-calculate_param.R | 12 tests/testthat/test-clean_mixture.R |only tests/testthat/test-list_vpts_aloft.R | 6 tests/testthat/test-read_vpts.R | 1 vignettes/rad_aero_22.Rmd | 2 47 files changed, 1074 insertions(+), 865 deletions(-)
Title: 'SAS' Interface
Description: Provides a 'SAS' interface, through
'SASPy'(<https://sassoftware.github.io/saspy/>) and
'reticulate'(<https://rstudio.github.io/reticulate/>). This package
helps you create 'SAS' sessions, execute 'SAS' code in remote 'SAS'
servers, retrieve execution results and log, and exchange datasets
between 'SAS' and 'R'. It also helps you to install 'SASPy' and
create a configuration file for the connection. Please review the
'SASPy' license file as instructed so that you comply with its
separate and independent license.
Author: Liming Li [aut, cre],
Daniel Sabanes Bove [aut],
Isaac Gravestock [aut],
F. Hoffmann-La Roche AG [cph, fnd],
AstraZeneca plc [cph, fnd]
Maintainer: Liming Li <liming.li1@astrazeneca.com>
Diff between sasr versions 0.1.4 dated 2025-02-26 and 0.1.5 dated 2025-03-31
DESCRIPTION | 18 ++++++++++-------- MD5 | 8 ++++---- NEWS.md | 4 ++++ man/sasr-package.Rd | 3 ++- tests/testthat/test-rmarkdown.R | 1 + 5 files changed, 21 insertions(+), 13 deletions(-)
Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our 'JSS'
paper (2016, <doi:10.18637/jss.v071.i02>. A sufficiently recent version of
'Protocol Buffers' library is required; currently version 3.3.0 from 2017
is the stated minimum.
Author: Romain Francois [aut] ,
Dirk Eddelbuettel [aut, cre] ,
Murray Stokely [aut] ,
Jeroen Ooms [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.23 dated 2025-01-14 and 0.4.24 dated 2025-03-31
ChangeLog | 19 +++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/00classes.R | 2 +- build/vignette.rds |binary configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS.Rd | 12 ++++++++++-- inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-paper.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary src/init.c | 2 ++ src/mutators.cpp | 3 +-- src/rprotobuf.cpp | 4 ++-- src/rprotobuf.h | 28 ++++++++++++---------------- 15 files changed, 75 insertions(+), 51 deletions(-)
Title: R Interface to 'Bloomberg'
Description: An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Author: Whit Armstrong [aut],
Dirk Eddelbuettel [aut, cre] ,
John Laing [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.15 dated 2024-09-18 and 0.3.16 dated 2025-03-31
ChangeLog | 109 +++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 13 +++-- MD5 | 60 +++++++++++++------------- R/RcppExports.R | 13 ++++- R/blpConnect.R | 7 ++- R/init.R | 45 ++++++++++---------- build/vignette.rds |binary configure | 47 +++++++++++---------- inst/NEWS.Rd | 12 +++++ man/blpAuthenticate.Rd | 12 +---- man/blpConnect.Rd | 6 ++ man/getTicks.Rd | 2 man/haveBlp.Rd |only src/Makevars.in | 15 ++++-- src/Makevars.no_blp |only src/Makevars.win | 5 -- src/RcppExports.cpp | 24 ++++++++-- src/authenticate.cpp | 21 ++++++--- src/bdh.cpp | 24 +++++++--- src/bdp.cpp | 41 +++++++++++++----- src/bds.cpp | 31 +++++++++---- src/beqs.cpp | 37 ++++++++-------- src/blpConnect.cpp | 21 +++++++-- src/blpVersion.cpp | 30 ++++++++++++- src/blpapi_utils.cpp | 50 ++++++++++++---------- src/bsrch.cpp | 29 ++++++------- src/fieldsearch.cpp | 14 ++++-- src/getBars.cpp | 13 ++++- src/getFieldInfo.cpp | 44 ++++++++++--------- src/getTicks.cpp | 17 ++++--- src/lookup.cpp | 18 ++++---- src/subscribe.cpp | 22 +++++---- 32 files changed, 531 insertions(+), 251 deletions(-)
Title: Decision Trees with Structural Equation Models Fit in 'Mplus'
Description: Uses recursive partitioning to create homogeneous subgroups based on structural equation models
fit in 'Mplus', a stand-alone program developed by Muthen and Muthen.
Author: Sarfaraz Serang [aut, cre],
Ross Jacobucci [aut],
Kevin J. Grimm [ctb],
Gabriela Stegmann [ctb],
Andreas M. Brandmaier [ctb]
Maintainer: Sarfaraz Serang <sserang@mailbox.sc.edu>
Diff between MplusTrees versions 0.2.2 dated 2022-10-11 and 0.2.3 dated 2025-03-31
DESCRIPTION | 35 ++++++++++++++++++++++++++--------- MD5 | 2 +- 2 files changed, 27 insertions(+), 10 deletions(-)
Title: Sparsed Sliced Inverse Regression via Lasso
Description: Estimate the sufficient dimension reduction space using sparsed sliced inverse regression via Lasso (Lasso-SIR) introduced in Lin, Zhao, and Liu (2019) <doi:10.1080/01621459.2018.1520115>. The Lasso-SIR is consistent and achieve the optimal convergence rate under certain sparsity conditions for the multiple index models.
Author: Zhigen Zhao [aut, cre],
Qian Lin [aut],
Jun Liu [aut]
Maintainer: Zhigen Zhao <zhigen.zhao@gmail.com>
Diff between LassoSIR versions 0.1.1 dated 2017-12-06 and 1.0 dated 2025-03-31
DESCRIPTION | 24 ++++++++++--- MD5 | 12 ++++-- R/LassoSIR.R | 81 +++++++++++++++++++++++++++-------------------- R/predict_Lasso_SIR.R |only build/partial.rdb |binary man/LassoSIR-package.Rd | 14 ++++---- man/LassoSIR.Rd | 40 ++++++++++++----------- man/predict_Lasso_SIR.Rd |only 8 files changed, 101 insertions(+), 70 deletions(-)
Title: Model-Based Clustering for Functional Data with Covariates
Description: Routines for model-based functional cluster analysis for functional data with optional covariates. The idea is to cluster functional subjects (often called functional objects) into homogenous groups by using spline smoothers (for functional data) together with scalar covariates. The spline coefficients and the covariates are modelled as a multivariate Gaussian mixture model, where the number of mixtures corresponds to the number of clusters. The parameters of the model are estimated by maximizing the observed mixture likelihood via an EM algorithm (Arnqvist and Sjöstedt de Luna, 2019) <doi:10.48550/arXiv.1904.10265>. The clustering method is used to analyze annual lake sediment from lake Kassjön (Northern Sweden) which cover more than 6400 years and can be seen as historical records of weather and climate.
Author: Natalya Pya [aut, cre],
Per Arnqvist [aut],
Sara Sjoestedt de Luna [aut]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between fdaMocca versions 0.1-1 dated 2022-07-21 and 0.1-2 dated 2025-03-31
DESCRIPTION | 24 ++++++++++++++---------- MD5 | 2 +- 2 files changed, 15 insertions(+), 11 deletions(-)
Title: Fast and Scalable Single Cell Differential Expression Analysis
using Mixed-Effects Models
Description: A fast and scalable linear mixed-effects model (LMM) estimation algorithm
for analysis of single-cell differential expression. The algorithm uses
summary-level statistics and requires less computer memory to fit the LMM.
Author: Changjiang Xu [aut, cre],
Gary Bader [aut]
Maintainer: Changjiang Xu <changjiang.xu@utoronto.ca>
Diff between FLASHMM versions 1.1.0 dated 2025-03-11 and 1.2.0 dated 2025-03-31
DESCRIPTION | 9 MD5 | 22 NEWS.md | 6 R/lmm.R | 64 +- R/lmmfit.R | 17 README.md | 39 - inst/doc/FLASHMM-vignette.R | 223 +++----- inst/doc/FLASHMM-vignette.Rmd | 355 +++++-------- inst/doc/FLASHMM-vignette.html | 1114 +++++++++++++++++++++-------------------- man/lmm.Rd | 6 man/lmmfit.Rd | 4 vignettes/FLASHMM-vignette.Rmd | 355 +++++-------- 12 files changed, 1091 insertions(+), 1123 deletions(-)
Title: Bayesian Modeling of Spatio-Temporal Data with R
Description: Fits, validates and compares a number of Bayesian models for
spatial and space time point referenced and areal unit data. Model fitting
is done using several packages: 'rstan', 'INLA', 'spBayes', 'spTimer',
'spTDyn', 'CARBayes' and 'CARBayesST'. Model comparison is performed using
the DIC and WAIC, and K-fold cross-validation where the user is free
to select their own subset of data rows for validation. Sahu (2022)
<doi:10.1201/9780429318443> describes the methods in detail.
Author: Sujit K. Sahu [aut, cre] ,
Duncan P. Lee [aut],
K. Shuvo Bakar [aut]
Maintainer: Sujit K. Sahu <S.K.Sahu@soton.ac.uk>
Diff between bmstdr versions 0.7.9 dated 2023-12-18 and 0.8.2 dated 2025-03-31
DESCRIPTION | 8 MD5 | 37 NAMESPACE | 1 R/Bspatial.R | 2 R/Bsptime.R | 8 R/methods.R | 25 build/partial.rdb |binary build/vignette.rds |binary inst/doc/vigverysmall.R | 308 ++--- inst/doc/vigverysmall.html | 1354 ++++++++++++++++++------- inst/stan/gp_marginal.stan | 16 inst/stan/ind_gpp_marginal.stan | 26 inst/stan/normal.stan | 2 man/Bspatial.Rd | 2 man/Bsptime.Rd | 8 man/resid.bmstdr.Rd |only src/stanExports_gp_marginal.h | 1426 ++++++++++++-------------- src/stanExports_ind_gpp_marginal.h | 1958 +++++++++++++++++-------------------- src/stanExports_normal.h | 639 +++++------- src/stanExports_spatial_model.h | 1082 +++++++++----------- 20 files changed, 3606 insertions(+), 3296 deletions(-)
Title: Tools for Wikidata and Wikipedia
Description: A set of wrappers intended to check, read and download information from the Wikimedia sources. It is specifically created to work with names of celebrities, in which case their information and statistics can be downloaded. Additionally, it also builds links and snippets to use in combination with the function gallery() in netCoin package.
Author: Modesto Escobar [aut, cph, cre]
,
Angel Zazo [aut],
Carlos Prieto [aut] ,
David Barrios [aut],
Cristina Calvo [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between wikiTools versions 1.2.7 dated 2024-07-27 and 1.2.8 dated 2025-03-31
DESCRIPTION | 10 - MD5 | 18 +- R/wiki_utils.R | 74 ++++----- inst/doc/wiki_utils.R | 18 +- inst/doc/wiki_utils.Rmd | 2 inst/doc/wiki_utils.html | 375 ++++------------------------------------------- man/v_AutoSuggest.Rd | 2 man/v_GetRecord.Rd | 2 man/v_Search.Rd | 2 vignettes/wiki_utils.Rmd | 2 10 files changed, 96 insertions(+), 409 deletions(-)
Title: Data Collection from the Central Bank of Brazil
Description: Provides tools to facilitate the access and processing of data
from the Central Bank of Brazil API. The package allows users
to retrieve economic and financial data, transforming them into usable
tabular formats for further analysis. The data is obtained from the
Central Bank of Brazil API: <https://api.bcb.gov.br/dados/serie/bcdata.sgs.{series_code}/dados?formato=json&dataInicial={start_date}&dataFinal={end_date}>.
Author: Paulo Icaro [aut],
Lissandro Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Sousa <lisandrosousa54@gmail.com>
Diff between BacenAPI versions 0.1.1 dated 2025-03-17 and 0.2.0 dated 2025-03-31
DESCRIPTION | 7 ++++--- MD5 | 9 +++++++-- NAMESPACE | 2 ++ R/bacen_search.R |only R/dataset.R |only data |only man/bacen_search.Rd |only man/dataset.Rd |only 8 files changed, 13 insertions(+), 5 deletions(-)
Title: Fast and Vectorized Base 64 Engine
Description: Provides a fast, lightweight, and vectorized base 64 engine
to encode and decode character and raw vectors as well as files stored
on disk. Common base 64 alphabets are supported out of the box
including the standard, URL-safe, bcrypt, crypt, 'BinHex', and
IMAP-modified UTF-7 alphabets. Custom engines can be created to
support unique base 64 encoding and decoding needs.
Author: Josiah Parry [aut, cre] ,
Etienne Bacher [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between b64 versions 0.1.3 dated 2024-09-26 and 0.1.4 dated 2025-03-31
b64-0.1.3/b64/src/Makevars |only b64-0.1.3/b64/src/Makevars.win |only b64-0.1.4/b64/DESCRIPTION | 13 +++++---- b64-0.1.4/b64/MD5 | 29 ++++++++++---------- b64-0.1.4/b64/NEWS.md | 3 +- b64-0.1.4/b64/R/extendr-wrappers.R | 1 b64-0.1.4/b64/README.md | 42 ++++++++++++++---------------- b64-0.1.4/b64/configure | 2 - b64-0.1.4/b64/configure.win | 2 - b64-0.1.4/b64/man/b64-package.Rd | 12 +++++++- b64-0.1.4/b64/src/Makevars.in |only b64-0.1.4/b64/src/Makevars.win.in |only b64-0.1.4/b64/src/rust/Cargo.lock | 34 ++++++++++++++---------- b64-0.1.4/b64/src/rust/Cargo.toml | 5 ++- b64-0.1.4/b64/src/rust/vendor-config.toml | 4 ++ b64-0.1.4/b64/src/rust/vendor.tar.xz |binary b64-0.1.4/b64/tools/config.R |only b64-0.1.4/b64/tools/msrv.R | 4 +- 18 files changed, 86 insertions(+), 65 deletions(-)
Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Several approaches are described in the review Dray et al (2012)
<doi:10.1890/11-1183.1>.
Author: Stephane Dray [aut] ,
David Bauman [ctb],
Guillaume Blanchet [ctb],
Daniel Borcard [ctb],
Sylvie Clappe [ctb],
Guillaume Guenard [ctb] ,
Thibaut Jombart [ctb],
Guillaume Larocque [ctb],
Pierre Legendre [ctb] ,
Naima Madi [ctb],
Helene H Wagner [ctb], [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adespatial versions 0.3-26 dated 2025-03-21 and 0.3-27 dated 2025-03-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/tutorial.html | 4 ++-- src/constr.hclust.c | 1 + src/constr.hclust.h | 4 ++-- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Compare Human Performance to Sampling Algorithms
Description: Understand human performance from the perspective of sampling, both looking at how people generate samples and how people use the samples they have generated. A longer overview and other resources can be found at <https://sampling.warwick.ac.uk>.
Author: Lucas Castillo [aut, cre, cph]
,
Yun-Xiao Li [aut, cph] ,
Adam N Sanborn [aut, cph] ,
European Research Council [fnd]
Maintainer: Lucas Castillo <lucas.castillo-marti@warwick.ac.uk>
Diff between samplr versions 1.0.1 dated 2024-08-19 and 1.1.0 dated 2025-03-31
DESCRIPTION | 10 ++-- MD5 | 52 ++++++++++++------------ NEWS.md | 11 +++++ R/ABSClass.R | 6 +- R/Z_identities.R | 62 ++++++++++++++++++++++++----- R/calc_functions.R | 26 +++++++++--- build/partial.rdb |binary inst/REFERENCES.bib | 20 ++++++++- inst/doc/abs-simulations.Rmd | 2 inst/doc/abs-simulations.html | 66 +++++++++++++++++++++++-------- inst/doc/custom-density-functions.html | 20 ++++----- inst/doc/how-to-sample.html | 6 +- inst/doc/multivariate-mixtures.html | 10 ++-- inst/doc/supported-distributions.html | 6 +- inst/doc/time-comparisons.html | 26 ++++++------ man/Bayesian_Sampler.Rd | 22 +++++++++- man/Mean_Variance.Rd | 6 ++ man/Z_identities.Rd | 3 + man/Zhu23ABS.Rd | 5 +- man/calc_PSD.Rd | 8 +++ man/calc_all.Rd | 11 ++++- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/samplr-package.Rd | 2 tests/testthat/test-Z_identities.R | 58 ++++++++++++++++++++++++++- tests/testthat/test-calc_functions.R | 16 +++++-- vignettes/abs-simulations.Rmd | 2 27 files changed, 340 insertions(+), 116 deletions(-)
Title: Plot FTIR Spectra
Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions.
L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Author: Philip Bulsink [aut, cre] ,
Ulrich Makanda [trl] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources [cph]
Maintainer: Philip Bulsink <philip.bulsink@nrcan-rncan.gc.ca>
Diff between PlotFTIR versions 1.1.0 dated 2025-02-05 and 1.2.0 dated 2025-03-31
PlotFTIR-1.1.0/PlotFTIR/vignettes/peak_fitting.Rbak |only PlotFTIR-1.2.0/PlotFTIR/DESCRIPTION | 8 PlotFTIR-1.2.0/PlotFTIR/MD5 | 41 PlotFTIR-1.2.0/PlotFTIR/NAMESPACE | 1 PlotFTIR-1.2.0/PlotFTIR/NEWS.md | 5 PlotFTIR-1.2.0/PlotFTIR/R/io.R | 376 ++- PlotFTIR-1.2.0/PlotFTIR/R/manipulations.R | 304 +- PlotFTIR-1.2.0/PlotFTIR/R/maths.R | 440 ++- PlotFTIR-1.2.0/PlotFTIR/R/plot_ftir.R | 117 PlotFTIR-1.2.0/PlotFTIR/R/utils.R | 104 PlotFTIR-1.2.0/PlotFTIR/R/zzz.R | 5 PlotFTIR-1.2.0/PlotFTIR/README.md | 26 PlotFTIR-1.2.0/PlotFTIR/build/vignette.rds |binary PlotFTIR-1.2.0/PlotFTIR/inst/doc/plotting_ftir_spectra.html | 5 PlotFTIR-1.2.0/PlotFTIR/man/check_ftir_data.Rd | 32 PlotFTIR-1.2.0/PlotFTIR/man/intensity_type.Rd | 3 PlotFTIR-1.2.0/PlotFTIR/tests/testthat.R | 24 PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-io.R | 449 +++ PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-manipulations.R | 206 + PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-maths.R | 1441 +++++++++--- PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-plot_ftir.R | 54 PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-utils.R | 14 22 files changed, 2907 insertions(+), 748 deletions(-)
Title: R Wrapper for 'pikchr' (PIC) Diagram Language
Description: An 'R' interface to 'pikchr' (<https://pikchr.org>, pronounced “picture”), a 'PIC'-like markup language for creating diagrams within technical documentation. Originally developed by Brian Kernighan, 'PIC' has been adapted into 'pikchr' by D. Richard Hipp, the creator of 'SQLite'. 'pikchr' is designed to be embedded in fenced code blocks of Markdown or other documentation markup languages, making it ideal for generating diagrams in text-based formats. This package allows R users to seamlessly integrate the descriptive syntax of 'pikchr' for diagram creation directly within the 'R' environment.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Richard Hipp [ctb],
Brian Kernighan [ctb]
Maintainer: Andre Leite <leite@castlab.org>
Diff between pikchr versions 1.0 dated 2024-12-02 and 1.0.1 dated 2025-03-31
DESCRIPTION | 8 MD5 | 10 NEWS.md | 4 inst/doc/Examples.html | 43 inst/doc/userman.html | 109 +- src/pikchr.c | 2320 ++++++++++++++++++++++++++----------------------- 6 files changed, 1345 insertions(+), 1149 deletions(-)
Title: Geocoding Made Easy
Description: An intuitive interface for getting data from geocoding services.
Author: Jesse Cambon [aut, cre] ,
Diego Hernangomez [aut] ,
Christopher Belanger [aut] ,
Daniel Possenriede [aut] ,
Otto Hansen [ctb]
Maintainer: Jesse Cambon <jesse.cambon@gmail.com>
Diff between tidygeocoder versions 1.0.5 dated 2021-11-02 and 1.0.6 dated 2025-03-31
tidygeocoder-1.0.5/tidygeocoder/R/geo_methods.R |only tidygeocoder-1.0.5/tidygeocoder/man/geo_census.Rd |only tidygeocoder-1.0.6/tidygeocoder/DESCRIPTION | 26 tidygeocoder-1.0.6/tidygeocoder/MD5 | 99 tidygeocoder-1.0.6/tidygeocoder/NAMESPACE | 13 tidygeocoder-1.0.6/tidygeocoder/NEWS.md | 25 tidygeocoder-1.0.6/tidygeocoder/R/api_url.R | 92 tidygeocoder-1.0.6/tidygeocoder/R/batch_geocoding.R | 962 ++++---- tidygeocoder-1.0.6/tidygeocoder/R/data.R | 63 tidygeocoder-1.0.6/tidygeocoder/R/documentation.R | 187 - tidygeocoder-1.0.6/tidygeocoder/R/geo.R | 802 +++--- tidygeocoder-1.0.6/tidygeocoder/R/geocode.R | 222 + tidygeocoder-1.0.6/tidygeocoder/R/geocode_combine.R | 521 ++-- tidygeocoder-1.0.6/tidygeocoder/R/global_variables.R | 31 tidygeocoder-1.0.6/tidygeocoder/R/input_handling.R | 96 tidygeocoder-1.0.6/tidygeocoder/R/query_factory.R | 232 +- tidygeocoder-1.0.6/tidygeocoder/R/results_processing.R | 342 +- tidygeocoder-1.0.6/tidygeocoder/R/reverse_batch_geocoding.R | 736 +++--- tidygeocoder-1.0.6/tidygeocoder/R/reverse_geo.R | 611 ++--- tidygeocoder-1.0.6/tidygeocoder/R/reverse_geocode.R | 161 - tidygeocoder-1.0.6/tidygeocoder/R/tidygeocoder.R | 2 tidygeocoder-1.0.6/tidygeocoder/R/utils.R | 346 +-- tidygeocoder-1.0.6/tidygeocoder/R/zzz.R | 4 tidygeocoder-1.0.6/tidygeocoder/README.md | 107 tidygeocoder-1.0.6/tidygeocoder/build/vignette.rds |binary tidygeocoder-1.0.6/tidygeocoder/data/api_info_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/data/api_key_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/data/api_parameter_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/data/batch_limit_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/data/min_time_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/inst/CITATION | 33 tidygeocoder-1.0.6/tidygeocoder/inst/WORDLIST |only tidygeocoder-1.0.6/tidygeocoder/inst/doc/tidygeocoder.Rmd | 278 +- tidygeocoder-1.0.6/tidygeocoder/inst/doc/tidygeocoder.html | 1149 ++++++---- tidygeocoder-1.0.6/tidygeocoder/man/api_parameter_reference.Rd | 10 tidygeocoder-1.0.6/tidygeocoder/man/figures/README-usamap-1.png |binary tidygeocoder-1.0.6/tidygeocoder/man/geo.Rd | 128 - tidygeocoder-1.0.6/tidygeocoder/man/geo_combine.Rd | 47 tidygeocoder-1.0.6/tidygeocoder/man/geocode.Rd | 53 tidygeocoder-1.0.6/tidygeocoder/man/geocode_combine.Rd | 76 tidygeocoder-1.0.6/tidygeocoder/man/get_api_query.Rd | 12 tidygeocoder-1.0.6/tidygeocoder/man/louisville.Rd | 3 tidygeocoder-1.0.6/tidygeocoder/man/min_time_reference.Rd | 10 tidygeocoder-1.0.6/tidygeocoder/man/query_api.Rd | 30 tidygeocoder-1.0.6/tidygeocoder/man/reverse_geo.Rd | 90 tidygeocoder-1.0.6/tidygeocoder/man/reverse_geocode.Rd | 36 tidygeocoder-1.0.6/tidygeocoder/man/tidygeocoder-package.Rd | 5 tidygeocoder-1.0.6/tidygeocoder/tests/testthat/test-geocode-combine.R | 106 tidygeocoder-1.0.6/tidygeocoder/tests/testthat/test-geocode.R | 243 +- tidygeocoder-1.0.6/tidygeocoder/tests/testthat/test-utils.R | 131 - tidygeocoder-1.0.6/tidygeocoder/vignettes/tidygeocoder.Rmd | 278 +- tidygeocoder-1.0.6/tidygeocoder/vignettes/tidygeocoder.Rmd.orig | 4 52 files changed, 4516 insertions(+), 3886 deletions(-)
Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following
the method described in Kang et al. (2010), <doi:10.1038/ng.548>.
One of a series of statistical genetic packages for streamlining the
analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre]
,
Willem Kruijer [aut] ,
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb] ,
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zh [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGWAS versions 1.0.10 dated 2024-11-15 and 1.0.11 dated 2025-03-31
DESCRIPTION | 8 ++-- MD5 | 42 ++++++++++----------- NEWS.md | 7 +++ R/EMMA.R | 2 - R/GWASHelp.R | 14 ++++--- R/RcppExports.R | 2 - R/codeMarkers.R | 7 ++- R/createGData.R | 6 +-- R/createGWAS.R | 6 +-- R/fastGLS.R | 94 ++++++++++++++++++++++++------------------------- R/kinship.R | 2 - R/manhattanPlot.R | 2 - R/qtlPlot.R | 2 - R/readPlink.R | 2 - R/runSingleTraitGwas.R | 2 - build/partial.rdb |binary build/vignette.rds |binary configure | 4 +- configure.ac | 4 +- inst/doc/GWAS.html | 38 +++++++++---------- src/utils.cpp | 2 - tests/tinytest.R | 10 ++--- 22 files changed, 133 insertions(+), 123 deletions(-)
Title: Interface for the 'QuickJS' Lightweight 'JavaScript' Engine
Description: An 'R' interface to the 'QuickJS' portable 'JavaScript'
engine. The engine and all 'R' to 'JavaScript' interoperability is bundled
within the package, requiring no dependencies beyond a 'C' compiler.
Author: Andrew R. Johnson [aut, cre] ,
QuickJS Authors [cph] ,
QuickJS-NG Authors [cph]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between QuickJSR versions 1.6.0 dated 2025-02-26 and 1.7.0 dated 2025-03-31
QuickJSR-1.6.0/QuickJSR/R/flags.R |only QuickJSR-1.6.0/QuickJSR/inst/include/quickjs |only QuickJSR-1.6.0/QuickJSR/man/cxxflags.Rd |only QuickJSR-1.6.0/QuickJSR/man/ldflags.Rd |only QuickJSR-1.7.0/QuickJSR/DESCRIPTION | 8 QuickJSR-1.7.0/QuickJSR/LICENSE | 4 QuickJSR-1.7.0/QuickJSR/MD5 | 133 QuickJSR-1.7.0/QuickJSR/NAMESPACE | 18 QuickJSR-1.7.0/QuickJSR/NEWS.md | 160 QuickJSR-1.7.0/QuickJSR/R/JSContext.R | 336 QuickJSR-1.7.0/QuickJSR/R/qjs.R | 158 QuickJSR-1.7.0/QuickJSR/R/quickjsr-package.R | 20 QuickJSR-1.7.0/QuickJSR/R/utils.R | 6 QuickJSR-1.7.0/QuickJSR/R/zzz.R | 8 QuickJSR-1.7.0/QuickJSR/README.md | 284 QuickJSR-1.7.0/QuickJSR/build/vignette.rds |binary QuickJSR-1.7.0/QuickJSR/inst/doc/working_with_js_types.R | 80 QuickJSR-1.7.0/QuickJSR/inst/doc/working_with_js_types.Rmd | 224 QuickJSR-1.7.0/QuickJSR/inst/doc/working_with_js_types.html | 1043 +- QuickJSR-1.7.0/QuickJSR/inst/include/quickjsr/JSCommonType.hpp | 2 QuickJSR-1.7.0/QuickJSR/inst/include/quickjsr/JSValue_to_SEXP.hpp | 2 QuickJSR-1.7.0/QuickJSR/inst/tinytest/test_JSContext.R | 94 QuickJSR-1.7.0/QuickJSR/inst/tinytest/test_data_conversion.R | 144 QuickJSR-1.7.0/QuickJSR/inst/tinytest/test_qjs_eval.R | 16 QuickJSR-1.7.0/QuickJSR/inst/tinytest/test_to_json_asis.R | 20 QuickJSR-1.7.0/QuickJSR/inst/tinytest/test_to_json_dataframe.R | 32 QuickJSR-1.7.0/QuickJSR/inst/tinytest/test_to_json_date.R | 28 QuickJSR-1.7.0/QuickJSR/inst/tinytest/test_to_json_factor.R | 12 QuickJSR-1.7.0/QuickJSR/inst/tinytest/test_to_json_matrix.R | 22 QuickJSR-1.7.0/QuickJSR/man/JSContext-method-assign.Rd | 64 QuickJSR-1.7.0/QuickJSR/man/JSContext-method-call.Rd | 66 QuickJSR-1.7.0/QuickJSR/man/JSContext-method-get.Rd | 60 QuickJSR-1.7.0/QuickJSR/man/JSContext-method-source.Rd | 70 QuickJSR-1.7.0/QuickJSR/man/JSContext-method-validate.Rd | 58 QuickJSR-1.7.0/QuickJSR/man/JSContext.Rd | 42 QuickJSR-1.7.0/QuickJSR/man/QuickJSR-package.Rd | 58 QuickJSR-1.7.0/QuickJSR/man/from_json.Rd | 34 QuickJSR-1.7.0/QuickJSR/man/qjs_eval.Rd | 56 QuickJSR-1.7.0/QuickJSR/man/quickjs_version.Rd | 28 QuickJSR-1.7.0/QuickJSR/man/to_json.Rd | 38 QuickJSR-1.7.0/QuickJSR/src/Makevars | 14 QuickJSR-1.7.0/QuickJSR/src/libquickjs.c | 14 QuickJSR-1.7.0/QuickJSR/src/quickjs/CMakeLists.txt | 843 +- QuickJSR-1.7.0/QuickJSR/src/quickjs/LICENSE | 48 QuickJSR-1.7.0/QuickJSR/src/quickjs/README.md | 48 QuickJSR-1.7.0/QuickJSR/src/quickjs/amalgam.js |only QuickJSR-1.7.0/QuickJSR/src/quickjs/api-test.c | 100 QuickJSR-1.7.0/QuickJSR/src/quickjs/meson.build |only QuickJSR-1.7.0/QuickJSR/src/quickjs/meson_options.txt |only QuickJSR-1.7.0/QuickJSR/src/quickjs/qjs.c | 12 QuickJSR-1.7.0/QuickJSR/src/quickjs/quickjs-libc.c | 487 - QuickJSR-1.7.0/QuickJSR/src/quickjs/quickjs-libc.h | 6 QuickJSR-1.7.0/QuickJSR/src/quickjs/quickjs.c | 3009 ++++--- QuickJSR-1.7.0/QuickJSR/src/quickjs/quickjs.h | 378 QuickJSR-1.7.0/QuickJSR/src/quickjs/repl.js | 3782 +++++----- QuickJSR-1.7.0/QuickJSR/src/quickjs/run-test262.c | 66 QuickJSR-1.7.0/QuickJSR/src/quickjs/standalone.js | 258 QuickJSR-1.7.0/QuickJSR/src/quickjs/test262-fast.conf | 264 QuickJSR-1.7.0/QuickJSR/src/quickjs/test262.conf | 789 +- QuickJSR-1.7.0/QuickJSR/src/quickjs/test262_errors.txt | 166 QuickJSR-1.7.0/QuickJSR/src/quickjs/tests.conf | 20 QuickJSR-1.7.0/QuickJSR/src/quickjs/unicode_download.sh | 38 QuickJSR-1.7.0/QuickJSR/tests/tinytest.R | 10 QuickJSR-1.7.0/QuickJSR/vignettes/working_with_js_types.Rmd | 224 64 files changed, 7174 insertions(+), 6830 deletions(-)
Title: Lemna Ecotox Effect Model
Description: The reference implementation of model equations and default
parameters for the toxicokinetic-toxicodynamic (TKTD) model of the Lemna
(duckweed) aquatic plant. Lemna is a standard test macrophyte used in ecotox
effect studies. The model was described and published by the SETAC Europe
Interest Group Effect Modeling. It is a refined description of the Lemna
TKTD model published by Schmitt et al. (2013)
<doi:10.1016/j.ecolmodel.2013.01.017>.
Author: Nils Kehrein [aut, cre],
SETAC Europe IG Effect Modeling [ccp]
Maintainer: Nils Kehrein <nils.kehrein@gmail.com>
Diff between lemna versions 1.0.1 dated 2023-04-22 and 1.0.2 dated 2025-03-31
lemna-1.0.1/lemna/vignettes/mmc2.r |only lemna-1.0.1/lemna/vignettes/mmc3.r |only lemna-1.0.2/lemna/DESCRIPTION | 10 lemna-1.0.2/lemna/LICENSE | 2 lemna-1.0.2/lemna/MD5 | 108 - lemna-1.0.2/lemna/NAMESPACE | 38 lemna-1.0.2/lemna/NEWS.md | 24 lemna-1.0.2/lemna/R/data.R | 292 +- lemna-1.0.2/lemna/R/effect.R | 22 lemna-1.0.2/lemna/R/lemna-package.R | 14 lemna-1.0.2/lemna/R/lemna.R | 13 lemna-1.0.2/lemna/R/lemna_ode.R | 262 +- lemna-1.0.2/lemna/R/lemna_scenario.R | 50 lemna-1.0.2/lemna/R/param.R | 10 lemna-1.0.2/lemna/R/plot.R | 184 - lemna-1.0.2/lemna/README.md | 192 - lemna-1.0.2/lemna/build/partial.rdb |binary lemna-1.0.2/lemna/build/vignette.rds |binary lemna-1.0.2/lemna/data/focusd1.rda |binary lemna-1.0.2/lemna/data/focusd2.rda |binary lemna-1.0.2/lemna/data/focusr3.rda |binary lemna-1.0.2/lemna/data/metsulfuron.rda |binary lemna-1.0.2/lemna/inst/doc/lemna-introduction.Rmd | 2 lemna-1.0.2/lemna/inst/doc/lemna-introduction.html | 630 +++--- lemna-1.0.2/lemna/inst/doc/lemna-verification.Rmd | 1558 ++++++++------- lemna-1.0.2/lemna/inst/doc/lemna-verification.html | 1086 +++++----- lemna-1.0.2/lemna/man/effect.Rd | 122 - lemna-1.0.2/lemna/man/figures/README-example-1.png |binary lemna-1.0.2/lemna/man/focusd1.Rd | 76 lemna-1.0.2/lemna/man/focusd2.Rd | 76 lemna-1.0.2/lemna/man/focusr3.Rd | 76 lemna-1.0.2/lemna/man/hommen212.Rd | 58 lemna-1.0.2/lemna/man/lemna.Rd | 524 ++--- lemna-1.0.2/lemna/man/lemna_desolve.Rd | 38 lemna-1.0.2/lemna/man/metsulfuron.Rd | 94 lemna-1.0.2/lemna/man/new_lemna_scenario.Rd | 58 lemna-1.0.2/lemna/man/param_defaults.Rd | 248 +- lemna-1.0.2/lemna/man/plot.lemna_result.Rd | 92 lemna-1.0.2/lemna/man/schmitt77.Rd | 56 lemna-1.0.2/lemna/tests/testthat.R | 8 lemna-1.0.2/lemna/tests/testthat/mmc2.r | 346 +-- lemna-1.0.2/lemna/tests/testthat/mmc3.r | 798 +++---- lemna-1.0.2/lemna/tests/testthat/test-effect.R | 90 lemna-1.0.2/lemna/tests/testthat/test-lemna.R | 80 lemna-1.0.2/lemna/tests/testthat/test-param.R | 6 lemna-1.0.2/lemna/tests/testthat/test-verify-unlimited.R | 18 lemna-1.0.2/lemna/tests/testthat/test-verify-variable.R | 154 - lemna-1.0.2/lemna/vignettes/lemna-introduction.Rmd | 2 lemna-1.0.2/lemna/vignettes/lemna-verification.Rmd | 1558 ++++++++------- lemna-1.0.2/lemna/vignettes/verify_2d12d-klein-1.png |only lemna-1.0.2/lemna/vignettes/verify_2d5d-klein-1.png |only lemna-1.0.2/lemna/vignettes/verify_4d3d-klein-1.png |only lemna-1.0.2/lemna/vignettes/verify_7d7d-dev-1.png |only lemna-1.0.2/lemna/vignettes/verify_7d7d-klein-1.png |only lemna-1.0.2/lemna/vignettes/verify_7d7d-relative-1.png |only lemna-1.0.2/lemna/vignettes/verify_7d7d-schmitt-1.png |only lemna-1.0.2/lemna/vignettes/verify_D1_rainbow-1.png |only lemna-1.0.2/lemna/vignettes/verify_D1_rainbow-2.png |only lemna-1.0.2/lemna/vignettes/verify_D2_rainbow-1.png |only lemna-1.0.2/lemna/vignettes/verify_D2_rainbow-2.png |only lemna-1.0.2/lemna/vignettes/verify_R3_rainbow-1.png |only lemna-1.0.2/lemna/vignettes/verify_R3_rainbow-2.png |only lemna-1.0.2/lemna/vignettes/verify_complex-1.png |only 63 files changed, 4740 insertions(+), 4335 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Further, it has functions for reading text files with epoch level aggregates from 'Actical', 'Fitbit', 'Actiwatch', 'ActiGraph', and 'PhilipsHealthBand'. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
Medical Research Council UK [cph, fnd],
Accelting [cph, fnd]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 1.0.3 dated 2025-03-07 and 1.0.4 dated 2025-03-31
DESCRIPTION | 10 +++---- MD5 | 36 ++++++++++++++++--------- NAMESPACE | 2 - NEWS.md | 6 ++++ R/RcppExports.R | 4 ++ R/mergeFitbitData.R | 43 ++++++++++++++++++++++++++----- R/readActiwatchCount.R | 4 +- R/readFitbit.R | 39 +++++++++++----------------- R/readParmayMatrix.R |only README.md | 1 inst/testfiles/mtx_100Hz_acc_HR_temp.BIN |only inst/testfiles/mtx_12.5Hz_acc.BIN |only inst/testfiles/mtx_12.5Hz_acc_gyro.BIN |only inst/testfiles/mtx_25Hz_acc_HR.BIN |only inst/testfiles/mtx_corrupted.bin |only inst/testfiles/mtx_corrupted_full.bin |only man/GGIRread-package.Rd | 4 +- man/readParmayMatrix.Rd |only src/RcppExports.cpp | 13 +++++++++ src/find_matrix_packet_start.cpp |only src/init.c | 2 + tests/testthat/test_mergeFitbitData.R | 8 +++-- tests/testthat/test_readFitbit.R | 12 ++++---- tests/testthat/test_readParmayMatrix.R |only 24 files changed, 123 insertions(+), 61 deletions(-)
Title: Synthetic Likelihood Methods for Intractable Likelihoods
Description: Framework to perform synthetic likelihood inference
for models where the likelihood function is unavailable or
intractable.
Author: Matteo Fasiolo [aut, cre],
Simon Wood [aut]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between synlik versions 0.1.6 dated 2023-03-02 and 0.1.7 dated 2025-03-31
synlik-0.1.6/synlik/NEWS |only synlik-0.1.6/synlik/README.md |only synlik-0.1.6/synlik/TODO |only synlik-0.1.7/synlik/DESCRIPTION | 21 + synlik-0.1.7/synlik/MD5 | 27 +- synlik-0.1.7/synlik/R/slice_synlik.R | 2 synlik-0.1.7/synlik/build/vignette.rds |binary synlik-0.1.7/synlik/inst/doc/synlik.R | 2 synlik-0.1.7/synlik/inst/doc/synlik.html | 349 +++++++++++++------------------ synlik-0.1.7/synlik/man/robCov.Rd | 8 synlik-0.1.7/synlik/man/slice.Rd | 2 synlik-0.1.7/synlik/src/acf.c | 5 synlik-0.1.7/synlik/src/blowfly.c | 6 synlik-0.1.7/synlik/src/mat.c | 5 synlik-0.1.7/synlik/src/nlar.c | 5 synlik-0.1.7/synlik/src/summ_stats.h | 19 + 16 files changed, 206 insertions(+), 245 deletions(-)
Title: API Client for the 'ClimMob' Platform
Description: API client for 'ClimMob', an open source software for decentralized
large-N trials with the 'tricot' approach <https://climmob.net/>.
Developed by van Etten et al. (2019) <doi:10.1017/S0014479716000739>, it turns the
research paradigm on its head; instead of a few researchers designing complicated
trials to compare several technologies in search of the best solutions for the
target environment, it enables many participants to carry out reasonably simple
experiments that taken together can offer even more information. 'ClimMobTools'
enables project managers to deep explore and analyse their 'ClimMob' data in R.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [aut] ,
Brandon Madriz [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between ClimMobTools versions 1.4 dated 2025-01-16 and 1.5 dated 2025-03-31
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 9 ++++++++- R/AAA-getDataCM.R | 2 ++ R/as.data.frame-climmob_list.R | 12 ++++++------ R/getProjectsCM.R | 7 ++++--- R/internal_functions.R | 1 + man/getProjectsCM.Rd | 3 ++- 8 files changed, 35 insertions(+), 23 deletions(-)
Title: Formal Psychological Models of Categorization and Learning
Description: Formal psychological models of categorization and learning, independently-replicated data sets against which to test them, and simulation archives.
Author: Andy Wills [aut, cre],
Lenard Dome [aut],
Charlotte Edmunds [aut],
Garrett Honke [aut],
Angus Inkster [aut],
Rene Schlegelmilch [aut],
Stuart Spicer [aut]
Maintainer: Andy Wills <andy@willslab.co.uk>
Diff between catlearn versions 1.0 dated 2023-04-04 and 1.1 dated 2025-03-31
DESCRIPTION | 40 +++++++++++++++++++++++++++++++++++----- MD5 | 7 ++++--- man/catlearn-package.Rd | 2 +- man/slpDGCM.Rd | 4 ++-- src/Makevars |only 5 files changed, 42 insertions(+), 11 deletions(-)
Title: Bindings to 'OpenCV' Computer Vision Library
Description: Exposes some of the available 'OpenCV' <https://opencv.org/> algorithms,
such as a QR code scanner, and edge, body or face detection. These can either be
applied to analyze static images, or to filter live video footage from a camera device.
Author: Jeroen Ooms [aut, cre] ,
Jan Wijffels [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between opencv versions 0.5.0 dated 2025-03-06 and 0.5.1 dated 2025-03-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/Makevars.in | 5 +++++ src/Makevars.win | 12 ++++++------ tools/winlibs.R | 10 +++++----- 5 files changed, 23 insertions(+), 18 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: Jose Pinheiro [aut] ,
Douglas Bates [aut] ,
Saikat DebRoy [ctb] ,
Deepayan Sarkar [ctb] ,
EISPACK authors [ctb] ,
Siem Heisterkamp [ctb] ,
Bert Van Willigen [ctb] ,
Johannes Ranke [ctb] ),
R Core Team [aut, cre]
Maintainer: R Core Team <R-core@R-project.org>
Diff between nlme versions 3.1-167 dated 2025-01-27 and 3.1-168 dated 2025-03-31
ChangeLog | 9 ++++ DESCRIPTION | 8 ++-- MD5 | 96 ++++++++++++++++++++++++------------------------- data/Alfalfa.rda |binary data/Assay.rda |binary data/BodyWeight.rda |binary data/Cefamandole.rda |binary data/Dialyzer.rda |binary data/Earthquake.rda |binary data/Fatigue.rda |binary data/Gasoline.rda |binary data/Glucose.rda |binary data/Glucose2.rda |binary data/Gun.rda |binary data/IGF.rda |binary data/Machines.rda |binary data/MathAchSchool.rda |binary data/MathAchieve.rda |binary data/Meat.rda |binary data/Milk.rda |binary data/Muscle.rda |binary data/Nitrendipene.rda |binary data/Oats.rda |binary data/Orthodont.rda |binary data/Ovary.rda |binary data/Oxboys.rda |binary data/Oxide.rda |binary data/PBG.rda |binary data/Phenobarb.rda |binary data/Pixel.rda |binary data/Quinidine.rda |binary data/Rail.rda |binary data/RatPupWeight.rda |binary data/Relaxin.rda |binary data/Remifentanil.rda |binary data/Soybean.rda |binary data/Spruce.rda |binary data/Tetracycline1.rda |binary data/Tetracycline2.rda |binary data/Wafer.rda |binary data/Wheat.rda |binary data/Wheat2.rda |binary data/bdf.rda |binary data/ergoStool.rda |binary po/R-de.po | 28 ++++++++------ po/R-fr.po | 10 ++++- po/R-ko.po | 9 +++- po/R-nlme.pot | 9 +++- po/R-pl.po | 10 ++++- 49 files changed, 106 insertions(+), 73 deletions(-)
Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata',
'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of
'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka',
and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre] ,
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Swetlana Herbrandt [ctb],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Michael [...truncated...]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-89 dated 2025-03-25 and 0.8-90 dated 2025-03-31
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- po/de.po | 36 ++++++++++++++++++------------------ 4 files changed, 30 insertions(+), 25 deletions(-)
Title: 'DT' Extension for CRUD (Create, Read, Update, Delete)
Applications in 'shiny'
Description: The core of this package is a function eDT() which enhances DT::datatable() such that it can be used to interactively modify data in 'shiny'. By the use of generic 'dplyr' methods it supports many types of data storage, with relational databases ('dbplyr') being the main use case.
Author: Jasper Schelfhout [aut, cre],
Maxim Nazarov [rev],
Daan Seynaeve [rev],
Lennart Tuijnder [rev],
Saar Junius [ctb]
Maintainer: Jasper Schelfhout <jasper.schelfhout@openanalytics.eu>
Diff between editbl versions 1.1.0 dated 2025-01-31 and 1.2.0 dated 2025-03-31
DESCRIPTION | 17 ++++++++++------- MD5 | 24 ++++++++++++------------ R/eDT.R | 26 +++++++++++++++++++++++++- build/vignette.rds |binary inst/NEWS | 3 +++ inst/doc/howto_relational_db.html | 19 ++++++++++--------- inst/doc/howto_relational_db_dm.html | 13 +++++++------ inst/doc/howto_row_level_access.html | 24 +++++++++++++----------- inst/doc/howto_row_level_access.rmd | 6 +++--- inst/doc/howto_switch_from_DT.html | 13 +++++++------ man/eDT.Rd | 3 +++ tests/testthat/test-eDT.R | 10 ++++++---- vignettes/howto_row_level_access.rmd | 6 +++--- 13 files changed, 102 insertions(+), 62 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.7.1 dated 2024-12-26 and 0.7.6 dated 2025-03-31
vcfppR-0.7.1/vcfppR/src/Makevars |only vcfppR-0.7.6/vcfppR/DESCRIPTION | 10 vcfppR-0.7.6/vcfppR/MD5 | 117 +++++--- vcfppR-0.7.6/vcfppR/NEWS.md | 15 + vcfppR-0.7.6/vcfppR/R/common.R | 80 ++--- vcfppR-0.7.6/vcfppR/R/vcf-compare.R | 5 vcfppR-0.7.6/vcfppR/cleanup | 5 vcfppR-0.7.6/vcfppR/cleanup.win | 5 vcfppR-0.7.6/vcfppR/configure | 27 + vcfppR-0.7.6/vcfppR/configure.win | 2 vcfppR-0.7.6/vcfppR/inst/doc/concordance-of-two-vcf-files.R | 20 - vcfppR-0.7.6/vcfppR/inst/extdata/test.bcf |only vcfppR-0.7.6/vcfppR/inst/extdata/test.bcf.csi |only vcfppR-0.7.6/vcfppR/inst/include/htslib |only vcfppR-0.7.6/vcfppR/inst/include/vcfpp.h | 12 vcfppR-0.7.6/vcfppR/man/vcfcomp.Rd | 1 vcfppR-0.7.6/vcfppR/src/Makevars.win | 2 vcfppR-0.7.6/vcfppR/src/htslib-1.21/annot-tsv.c | 4 vcfppR-0.7.6/vcfppR/src/htslib-1.21/bcf_sr_sort.c | 59 ---- vcfppR-0.7.6/vcfppR/src/htslib-1.21/bgzf.c | 8 vcfppR-0.7.6/vcfppR/src/htslib-1.21/config.log | 142 +++++----- vcfppR-0.7.6/vcfppR/src/htslib-1.21/config.mk | 2 vcfppR-0.7.6/vcfppR/src/htslib-1.21/config.status | 8 vcfppR-0.7.6/vcfppR/src/htslib-1.21/cram/cram_codecs.c | 22 - vcfppR-0.7.6/vcfppR/src/htslib-1.21/cram/mFILE.c | 32 -- vcfppR-0.7.6/vcfppR/src/htslib-1.21/cram/mFILE.h | 2 vcfppR-0.7.6/vcfppR/src/htslib-1.21/faidx.c | 2 vcfppR-0.7.6/vcfppR/src/htslib-1.21/hfile_gcs.c | 8 vcfppR-0.7.6/vcfppR/src/htslib-1.21/hfile_libcurl.c | 2 vcfppR-0.7.6/vcfppR/src/htslib-1.21/hfile_s3_write.c | 12 vcfppR-0.7.6/vcfppR/src/htslib-1.21/hts.c | 107 ++----- vcfppR-0.7.6/vcfppR/src/htslib-1.21/hts_expr.c | 8 vcfppR-0.7.6/vcfppR/src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr.c | 4 vcfppR-0.7.6/vcfppR/src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr_neon.c | 2 vcfppR-0.7.6/vcfppR/src/htslib-1.21/htscodecs/htscodecs/rANS_static4x16pr.c | 12 vcfppR-0.7.6/vcfppR/src/htslib-1.21/htscodecs/htscodecs/tokenise_name3.c | 77 ----- vcfppR-0.7.6/vcfppR/src/htslib-1.21/htscodecs/htscodecs/utils.c | 36 -- vcfppR-0.7.6/vcfppR/src/htslib-1.21/htscodecs/htscodecs/varint2.h | 10 vcfppR-0.7.6/vcfppR/src/htslib-1.21/htsfile.c | 109 ------- vcfppR-0.7.6/vcfppR/src/htslib-1.21/sam.c | 5 vcfppR-0.7.6/vcfppR/src/htslib-1.21/synced_bcf_reader.c | 16 - vcfppR-0.7.6/vcfppR/src/htslib-1.21/tabix.c | 4 vcfppR-0.7.6/vcfppR/src/htslib-1.21/thread_pool.c | 4 vcfppR-0.7.6/vcfppR/src/htslib-1.21/vcf.c | 52 +-- vcfppR-0.7.6/vcfppR/src/htslib-1.21/vcfutils.c | 10 vcfppR-0.7.6/vcfppR/tests/testthat/test-vcf-comp.R | 2 vcfppR-0.7.6/vcfppR/tests/testthat/test-vcf-reader.R | 13 vcfppR-0.7.6/vcfppR/tests/testthat/test-vcf-table.R | 7 48 files changed, 411 insertions(+), 671 deletions(-)
Title: 'Canvas' LMS API Integration
Description: Allow R users to interact with the 'Canvas' Learning Management System (LMS) API (see
<https://canvas.instructure.com/doc/api/all_resources.html> for details).
It provides a set of functions to access and manipulate course data, assignments, grades, users,
and other resources available through the 'Canvas' API.
Author: Tomer Iwan [aut, cre],
Niels Smits [ctb] ,
VU Analytics [cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between vvcanvas versions 0.0.4 dated 2024-04-29 and 0.0.5 dated 2025-03-31
DESCRIPTION | 29 ++++++++++++----- MD5 | 58 +++++++++++++++++++++++++--------- NAMESPACE | 11 ++++++ NEWS.md | 3 + R/create_module.R |only R/create_module_item.R |only R/delete_page.R |only R/get_assignment_groups.R |only R/get_course_announcements.R | 4 +- R/get_course_files.R | 4 +- R/get_course_folders.R | 4 +- R/get_course_media_objects.R |only R/get_course_quizzes.R | 4 +- R/get_course_students.R | 4 +- R/get_course_users.R |only R/get_discussions.R | 4 +- R/get_modules.R | 4 +- R/get_page_content.R | 11 ++++-- R/get_section_students.R |only R/list_all_enrollment_terms.R |only R/update_page.R |only R/update_quiz.R |only R/upload_file.R |only R/upload_qti_file_with_migration.R |only README.md | 10 +++++ build/vignette.rds |binary inst/doc/QTI_quiz.R |only inst/doc/QTI_quiz.Rmd |only inst/doc/QTI_quiz.html |only man/create_module.Rd |only man/create_module_item.Rd |only man/delete_page.Rd |only man/get_assignment_groups.Rd |only man/get_course_media_objects.Rd |only man/get_course_users.Rd |only man/get_page_content.Rd | 6 ++- man/get_roles.Rd | 42 ++++++++++++------------ man/get_section_students.Rd |only man/list_all_enrollment_terms.Rd |only man/update_page.Rd |only man/update_quiz.Rd |only man/upload_file.Rd |only man/upload_qti_file_with_migration.Rd |only vignettes/QTI_quiz.Rmd |only 44 files changed, 141 insertions(+), 57 deletions(-)
Title: Total, Between-, and Within-Cluster Spearman Rank Correlations
for Clustered Data
Description: Estimates the total, between-, and within-cluster Spearman rank correlations for continuous and ordinal clustered data. See Tu et al. (2024) <DOI:10.1002/sim.10326> for details.
Author: Shengxin Tu [aut, cre],
Chun Li [aut],
Bryan Shepherd [aut]
Maintainer: Shengxin Tu <shengxin.tu@vanderbilt.edu>
Diff between rankCorr versions 1.0.1 dated 2023-11-16 and 1.0.2 dated 2025-03-31
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/rankCorrCluster.R | 6 +++--- man/rankCorrCluster.Rd | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Derive a Color Palette from a Particular Location on Earth
Description: Downloads a satellite image via ESRI and maptiles (these are
originally from a variety of aerial photography sources),
translates the image into a perceptually uniform color space,
runs one of a few different clustering algorithms on the colors in the image
searching for a user-supplied number of colors,
and returns the resulting color palette.
Author: Will Cornwell [aut, cre] ,
Mitch Lyons [aut],
Nick Murray [aut]
Maintainer: Will Cornwell <wcornwell@gmail.com>
Diff between earthtones versions 0.1.1 dated 2019-01-13 and 0.2.0 dated 2025-03-31
DESCRIPTION | 30 ++++-- MD5 | 15 +-- NAMESPACE | 2 NEWS.md | 4 R/earth.R | 199 +++++++++++++++++++++++++++++--------------- README.md |only man/get_earthtones.Rd | 56 ++++++++---- man/print.palette.Rd |only tests/testthat/Rplots.pdf |only tests/testthat/test-earth.R | 4 10 files changed, 209 insertions(+), 101 deletions(-)
Title: Test Suite for 'Future API' Backends
Description: Backends implementing the 'Future' API <doi:10.32614/RJ-2021-048>, as defined by the 'future' package, should use the tests provided by this package to validate that they meet the minimal requirements of the 'Future' API. The tests can be performed easily from within R or from outside of R from the command line making it straightforward to include them in package tests and in Continuous Integration (CI) pipelines.
Author: Henrik Bengtsson [aut, cre, cph],
The R Consortium [fnd] grant in 2017)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.tests versions 0.7.0 dated 2023-05-22 and 0.8.0 dated 2025-03-31
DESCRIPTION | 14 ++--- MD5 | 36 +++++++------- NAMESPACE | 1 NEWS.md | 21 +++++++- R/check.R | 4 + R/run_test.R | 3 - R/test_db.R | 4 + build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/future.tests-01-intro.html | 10 ++-- inst/doc/future.tests-01-intro.md | 15 +++--- inst/doc/future.tests-05-ci-github_actions.html | 58 ++++++++++------------- inst/doc/future.tests-05-ci-github_actions.md | 60 ++++++++++-------------- inst/test-db/lazy.R | 10 ++++ inst/test-db/resolve.R | 1 inst/test-db/resolved-lazy.R | 18 ++++--- tests/test_plans.R | 3 - vignettes/future.tests-01-intro.md | 15 +++--- vignettes/future.tests-05-ci-github_actions.md | 60 ++++++++++-------------- 19 files changed, 178 insertions(+), 157 deletions(-)
Title: Phase I/II CRM Based Drug Combination Design
Description: Implements the adaptive designs for integrated phase I/II trials of drug combinations via continual reassessment method (CRM) to evaluate toxicity and efficacy simultaneously for each enrolled patient cohort based on Bayesian inference. It supports patients assignment guidance in a single trial using current enrolled data, as well as conducting extensive simulation studies to evaluate operating characteristics before the trial starts. It includes various link functions such as empiric, one-parameter logistic, two-parameter logistic, and hyperbolic tangent, as well as considering multiple prior distributions of the parameters like normal distribution, gamma distribution and exponential distribution to accommodate diverse clinical scenarios. Method using Bayesian framework with empiric link function is described in: Wages and Conaway (2014) <doi:10.1002/sim.6097>.
Author: Junying Wang [cre, aut],
Song Wu [aut],
Jie Yang [aut]
Maintainer: Junying Wang <junying.wang@stonybrook.edu>
Diff between crm12Comb versions 0.1.10 dated 2025-03-18 and 0.1.11 dated 2025-03-30
DESCRIPTION | 6 +-- MD5 | 18 +++++----- R/SIM_phase_I_II.R | 4 +- R/est.R | 18 ++++++---- data/examples_results.RData |binary inst/doc/crm12Comb.R | 6 +-- inst/doc/crm12Comb.Rmd | 6 +-- inst/doc/crm12Comb.html | 79 +++++++++++++++++++++++--------------------- man/efficacy_est.Rd | 3 + vignettes/crm12Comb.Rmd | 6 +-- 10 files changed, 79 insertions(+), 67 deletions(-)
Title: Dynamically Generate Tabset Panels in 'Quarto' HTML Documents
Description: Dynamically generate tabset panels
<https://quarto.org/docs/output-formats/html-basics.html#tabsets> in
'Quarto' HTML documents using a data frame as input.
Author: Yusuke Sasaki [aut, cre]
Maintainer: Yusuke Sasaki <sayuks.dev@gmail.com>
Diff between quartabs versions 0.1.0 dated 2025-03-14 and 0.1.1 dated 2025-03-30
DESCRIPTION | 7 +- MD5 | 17 ++--- NEWS.md | 19 +++++ R/render_tabset.R | 89 +++++++++++++++++--------- README.md | 10 ++- inst/CITATION |only inst/WORDLIST | 1 man/render_tabset.Rd | 11 +-- tests/testthat/test-get_tabset_master.R | 106 +++++++++++++++++++++----------- tests/testthat/test-prep_data.R | 91 ++++++++++++--------------- 10 files changed, 214 insertions(+), 137 deletions(-)
Title: Machine Learning Time Series Forecasting
Description: Compute onestep and multistep time series forecasts for machine learning models.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between iForecast versions 1.1.0 dated 2025-01-08 and 1.1.1 dated 2025-03-30
DESCRIPTION | 10 ++--- MD5 | 17 +++++--- R/tts_VAR.R |only R/tts_predict.R | 98 +++++++++++++++++++++++++-------------------------- R/tts_utilities.R | 2 - man/data-sets.Rd | 2 - man/iForecast.Rd | 8 ++-- man/iForecast_var.Rd |only man/tts.autoML.Rd | 2 - man/tts.caret.Rd | 4 +- man/tts.var.Rd |only 11 files changed, 73 insertions(+), 70 deletions(-)
Title: Extract Data from NCAA Women's and Men's Volleyball Website
Description: Extracts team records/schedules and player statistics for the
2020-2024 National Collegiate Athletic Association (NCAA) women's and men's
divisions I, II, and III volleyball teams from <https://stats.ncaa.org>.
Functions can aggregate statistics for teams, conferences, divisions, or
custom groups of teams.
Author: Jeffrey R. Stevens [aut, cre, cph]
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@protonmail.com>
Diff between ncaavolleyballr versions 0.4.1 dated 2025-01-23 and 0.4.2 dated 2025-03-30
ncaavolleyballr-0.4.1/ncaavolleyballr/inst/doc/ncaavolleyballr.R |only ncaavolleyballr-0.4.1/ncaavolleyballr/inst/doc/ncaavolleyballr.qmd |only ncaavolleyballr-0.4.1/ncaavolleyballr/inst/logo/logo.svg |only ncaavolleyballr-0.4.1/ncaavolleyballr/inst/logo/ncaavolleyballr2.png |only ncaavolleyballr-0.4.1/ncaavolleyballr/inst/logo/ncaavolleyballr2.svg |only ncaavolleyballr-0.4.1/ncaavolleyballr/vignettes/ncaavolleyballr.qmd |only ncaavolleyballr-0.4.2/ncaavolleyballr/DESCRIPTION | 12 ncaavolleyballr-0.4.2/ncaavolleyballr/MD5 | 83 ncaavolleyballr-0.4.2/ncaavolleyballr/NEWS.md | 16 ncaavolleyballr-0.4.2/ncaavolleyballr/R/conference_stats.R | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/R/division_stats.R | 4 ncaavolleyballr-0.4.2/ncaavolleyballr/R/find_team_contests.R | 10 ncaavolleyballr-0.4.2/ncaavolleyballr/R/find_team_id.R | 6 ncaavolleyballr-0.4.2/ncaavolleyballr/R/find_team_name.R | 6 ncaavolleyballr-0.4.2/ncaavolleyballr/R/get_teams.R | 15 ncaavolleyballr-0.4.2/ncaavolleyballr/R/group_stats.R | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/R/match_pbp.R | 10 ncaavolleyballr-0.4.2/ncaavolleyballr/R/player_match_stats.R | 10 ncaavolleyballr-0.4.2/ncaavolleyballr/R/player_season_stats.R | 28 ncaavolleyballr-0.4.2/ncaavolleyballr/R/team_match_stats.R | 10 ncaavolleyballr-0.4.2/ncaavolleyballr/R/team_season_info.R | 10 ncaavolleyballr-0.4.2/ncaavolleyballr/R/team_season_stats.R | 12 ncaavolleyballr-0.4.2/ncaavolleyballr/R/utils.R | 21 ncaavolleyballr-0.4.2/ncaavolleyballr/README.md | 12 ncaavolleyballr-0.4.2/ncaavolleyballr/build/vignette.rds |binary ncaavolleyballr-0.4.2/ncaavolleyballr/inst/CITATION | 2 ncaavolleyballr-0.4.2/ncaavolleyballr/inst/doc/ncaavolleyballr.Rmd |only ncaavolleyballr-0.4.2/ncaavolleyballr/inst/doc/ncaavolleyballr.html | 5677 +--------- ncaavolleyballr-0.4.2/ncaavolleyballr/man/conference_stats.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/man/division_stats.Rd | 4 ncaavolleyballr-0.4.2/ncaavolleyballr/man/find_team_contests.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/man/find_team_id.Rd | 6 ncaavolleyballr-0.4.2/ncaavolleyballr/man/find_team_name.Rd | 6 ncaavolleyballr-0.4.2/ncaavolleyballr/man/get_teams.Rd | 3 ncaavolleyballr-0.4.2/ncaavolleyballr/man/group_stats.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/man/match_pbp.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/man/player_match_stats.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/man/player_season_stats.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/man/request_url.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/man/team_match_stats.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/man/team_season_info.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/man/team_season_stats.Rd | 8 ncaavolleyballr-0.4.2/ncaavolleyballr/tests/testthat/test-match_pbp.R | 2 ncaavolleyballr-0.4.2/ncaavolleyballr/tests/testthat/test-player_match_stats.R | 11 ncaavolleyballr-0.4.2/ncaavolleyballr/tests/testthat/test-player_season_stats.R | 1 ncaavolleyballr-0.4.2/ncaavolleyballr/vignettes/ncaavolleyballr.Rmd |only ncaavolleyballr-0.4.2/ncaavolleyballr/vignettes/ncaavolleyballr.Rmd.orig |only 47 files changed, 1033 insertions(+), 5040 deletions(-)
More information about ncaavolleyballr at CRAN
Permanent link
Title: Provides a Link Between the 'LSEG Datastream' System and R
Description: Provides a set of functions and a class to connect, extract and
upload information from the 'LSEG Datastream' database. This
package uses the 'DSWS' API and server used by the 'Datastream DFO addin'.
Details of this API are available at <https://www.lseg.com/en/data-analytics>.
Please report issues at <https://github.com/CharlesCara/DatastreamDSWS2R/issues>.
Author: Charles Cara [aut, cre]
Maintainer: Charles Cara <charles.cara@absolute-strategy.com>
Diff between DatastreamDSWS2R versions 1.9.10 dated 2024-09-05 and 1.9.12 dated 2025-03-30
DESCRIPTION | 10 ++-- MD5 | 8 +-- NEWS.md | 101 ++++++++++++++++++++++++------------------------ R/classConstructor.R | 6 +- man/DatastreamDSWS2R.Rd | 8 +++ 5 files changed, 74 insertions(+), 59 deletions(-)
More information about DatastreamDSWS2R at CRAN
Permanent link
Title: An Implementation of Rubin's (1981) Bayesian Bootstrap
Description: Functions for performing the Bayesian bootstrap as introduced by
Rubin (1981) <doi:10.1214/aos/1176345338> and for summarizing the result.
The implementation can handle both summary statistics that works on a
weighted version of the data and summary statistics that works on a
resampled data set.
Author: Rasmus Baath [aut, cre]
Maintainer: Rasmus Baath <rasmus.baath@gmail.com>
Diff between bayesboot versions 0.2.2 dated 2018-06-29 and 0.2.3 dated 2025-03-30
DESCRIPTION | 11 +-- MD5 | 22 +++---- NEWS | 5 + R/bayesboot.R | 6 +- R/plotPost.R | 4 - README.md | 83 ++++++++++++++++++++--------- man/bayesboot.Rd | 18 ++++-- man/figures/README-car_plot-1.png |binary man/figures/README-height_comparison-1.png |binary man/figures/README-president_summary-1.png |binary man/plot.bayesboot.Rd | 3 - man/plotPost.Rd | 14 +++- 12 files changed, 110 insertions(+), 56 deletions(-)
Title: Interface to the ITALIC Database of Lichen Biodiversity
Description: A programmatic interface to the Web Service methods provided by ITALIC (<https://italic.units.it>).
ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information
about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys.
More information about the data is available at <https://italic.units.it/?procedure=base&t=59&c=60>.
The API documentation is available at <https://italic.units.it/?procedure=api>.
Author: Matteo Conti [aut, cre] ,
Luana Francesconi [aut],
Alice Musina [aut],
Luca Di Nuzzo [aut],
Gabriele Gheza [aut],
Chiara Pistocchi [aut],
Juri Nascimbene [aut],
Pier Luigi Nimis [aut],
Stefano Martellos [aut]
Maintainer: Matteo Conti <matt.ciao@gmail.com>
Diff between ritalic versions 0.10.1 dated 2025-01-07 and 0.11.0 dated 2025-03-30
DESCRIPTION | 24 +++++++++--- MD5 | 67 ++++++++++++++++++---------------- NAMESPACE | 14 +++++++ R/api_utils.R | 2 - R/call_api_base.R | 6 +-- R/data-utils.R | 4 +- R/data.R |only R/italic_checklist.R | 25 ++++++++---- R/italic_description.R | 6 ++- R/italic_distribution_map.R |only R/italic_ecology_traits.R | 6 ++- R/italic_ecoregions_distribution.R | 12 ++++-- R/italic_identification_key.R | 8 ++-- R/italic_match.R | 18 ++++----- R/italic_name_usage.R |only R/italic_occurrences.R | 9 +++- R/italic_occurrences_references.R | 6 +-- R/italic_regions_distribution.R | 6 ++- R/italic_taxon_data.R | 17 ++++++-- R/italic_taxonomy.R | 8 ++-- R/italic_traits_pa.R | 14 ++++--- README.md | 15 ++++++- inst |only man/italic_checklist.Rd | 18 ++++++--- man/italic_description.Rd | 10 +++-- man/italic_distribution_map.Rd |only man/italic_ecology_traits.Rd | 10 +++-- man/italic_ecoregions_distribution.Rd | 16 +++++--- man/italic_identification_key.Rd | 10 +++-- man/italic_match.Rd | 18 ++++----- man/italic_name_usage.Rd |only man/italic_occurrences.Rd | 13 ++++-- man/italic_occurrences_references.Rd | 6 +-- man/italic_regions_distribution.Rd | 8 ++-- man/italic_taxon_data.Rd | 17 ++++++-- man/italic_taxonomy.Rd | 12 +++--- man/italic_traits_pa.Rd | 13 ++++-- 37 files changed, 268 insertions(+), 150 deletions(-)
Title: Gamma and Exponential Generalized Linear Models with Elastic Net
Penalty
Description: Implements the fast iterative shrinkage-thresholding algorithm
(FISTA) algorithm to fit a Gamma distribution with an elastic net
penalty as described in Chen, Arakvin and Martin (2018)
<doi:10.48550/arXiv.1804.07780>. An implementation for the case of the
exponential distribution is also available, with details available
in Chen and Martin (2018) <doi:10.2139/ssrn.3085672>.
Author: Anthony Christidis [aut, cre],
Xin Chen [aut],
Daniel Hanson [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPEGLMEN versions 1.1.2 dated 2023-01-28 and 1.1.3 dated 2025-03-30
DESCRIPTION | 23 +++++++++++++---------- MD5 | 14 +++++++------- NAMESPACE | 2 +- NEWS.md | 5 ++++- README.md | 2 +- build/vignette.rds |binary configure | 4 ++-- configure.ac | 4 ++-- 8 files changed, 30 insertions(+), 24 deletions(-)
Title: Command Line Tools to Produce Accessible Documents using 'R
Markdown'
Description: Provides functions to produce accessible 'HTML' slides, 'HTML',
'Word' and 'PDF' documents from input 'R markdown' files. Accessible 'PDF'
files are produced only on a 'Windows' Operating System. One aspect of
accessibility is providing a headings structure that is recognised by a
screen reader, providing a navigational tool for a blind or
partially-sighted person. A key aim is to produce documents of different
formats easily from each of a collection of 'R markdown' source files.
Input 'R markdown' files are rendered using the render() function from the
'rmarkdown' package <https://cran.r-project.org/package=rmarkdown>. A 'zip'
file containing multiple output files can be produced from one function
call. A user-supplied template 'Word' document can be used to determine the
formatting of an output 'Word' document. Accessible 'PDF' files are
produced from 'Word' documents using 'OfficeToPDF'
<https://github.com/cognidox/OfficeToPDF>. A convenience function,
install_otp() is [...truncated...]
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between accessr versions 1.1.2 dated 2025-03-15 and 1.1.3 dated 2025-03-30
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/rmd2many.R | 1 - R/rmd2word.R | 1 - man/rmd2many.Rd | 1 - man/rmd2word.Rd | 1 - tests/testthat/setup.R | 1 - 8 files changed, 17 insertions(+), 16 deletions(-)
Title: Split Regularized Regression
Description: Functions for computing split regularized estimators defined in Christidis, Lakshmanan,
Smucler and Zamar (2019) <doi:10.48550/arXiv.1712.03561>. The approach fits linear regression models that
split the set of covariates into groups. The optimal split of the variables into groups and the
regularized estimation of the regression coefficients are performed by minimizing an objective
function that encourages sparsity within each group and diversity among them.
The estimated coefficients are then pooled together to form the final fit.
Author: Anthony Christidis [aut, cre],
Ezequiel Smucler [aut],
Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between SplitReg versions 1.0.2 dated 2020-02-05 and 1.0.3 dated 2025-03-30
DESCRIPTION | 21 ++++++++++++--------- MD5 | 16 ++++++++-------- NEWS | 5 ++++- README.md | 4 +++- configure | 4 ++-- configure.ac | 4 ++-- src/Makevars.win | 2 +- src/RcppExports.cpp | 5 +++++ tests/testthat/test_glmnet.R | 24 ++++++++++++------------ 9 files changed, 49 insertions(+), 36 deletions(-)
Title: Split Generalized Linear Models
Description: Functions to compute split generalized linear models. The approach fits
generalized linear models that split the covariates into groups. The
optimal split of the variables into groups and the regularized estimation
of the coefficients are performed by minimizing an objective function
that encourages sparsity within each group and diversity among them.
Example applications can be found in Christidis et al. (2021)
<doi:10.48550/arXiv.2102.08591>.
Author: Anthony Christidis [aut, cre],
Stefan Van Aelst [aut],
Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between SplitGLM versions 1.0.5 dated 2022-11-22 and 1.0.6 dated 2025-03-30
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS | 5 ++++- README.md | 2 +- configure | 4 ++-- configure.ac | 4 ++-- src/Makevars.win | 2 +- src/WEN.cpp | 2 +- 8 files changed, 24 insertions(+), 21 deletions(-)
Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides
many desirable features. This package bundles these header files for easy use by R packages
from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also
see the 'spdl' package which enhanced this package with a consistent R and C++ interface.
Author: Dirk Eddelbuettel [aut, cre] ,
Gabi Melman [aut] ,
Victor Zverovic [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSpdlog versions 0.0.20 dated 2025-02-01 and 0.0.21 dated 2025-03-30
ChangeLog | 7 ++++++ DESCRIPTION | 8 +++---- MD5 | 22 +++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 6 +++++ inst/include/spdlog/details/os-inl.h | 3 +- inst/include/spdlog/fmt/bundled/base.h | 21 +++++++++--------- inst/include/spdlog/fmt/bundled/compile.h | 32 ++++++++-------------------- inst/include/spdlog/fmt/bundled/format.h | 26 +++++++++++++++------- inst/include/spdlog/pattern_formatter-inl.h | 8 ++++--- inst/include/spdlog/version.h | 2 - 12 files changed, 75 insertions(+), 60 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code, automated
reporting or use an easy to remember set of tidy functions for low
code exploratory data analysis.
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 1.3.3 dated 2024-11-12 and 1.3.4 dated 2025-03-30
DESCRIPTION | 8 MD5 | 94 +++++----- NEWS.md | 13 + R/abtest.R | 4 R/explore.R | 4 R/tools.R | 4 README.md | 11 - build/vignette.rds |binary inst/doc/abtest.html | 29 ++- inst/doc/clean-drop.html | 39 ++-- inst/doc/data.html | 369 ++++++++++++++++++++--------------------- inst/doc/describe.html | 49 +++-- inst/doc/explain.html | 81 +++++---- inst/doc/explore-mtcars.html | 37 ++-- inst/doc/explore-penguins.html | 27 +-- inst/doc/explore-titanic.html | 35 ++- inst/doc/explore.R | 26 +- inst/doc/explore.html | 63 +++---- inst/doc/predict.html | 103 ++++++----- inst/doc/report-target.R | 2 inst/doc/report-target.html | 25 +- inst/doc/report-targetpct.R | 2 inst/doc/report-targetpct.html | 23 +- inst/doc/report.R | 2 inst/doc/report.html | 25 +- inst/doc/tips-tricks.R | 18 +- inst/doc/tips-tricks.html | 61 +++--- inst/extdata/wordle.rds |binary man/check_vec_low_variance.Rd | 50 ++--- man/create_data_abtest.Rd | 90 +++++----- man/create_data_esoteric.Rd | 72 ++++---- man/cut_vec_num_avg.Rd | 38 ++-- man/drop_obs_if.Rd | 46 ++--- man/drop_obs_with_na.Rd | 44 ++-- man/drop_var_by_names.Rd | 46 ++--- man/drop_var_low_variance.Rd | 46 ++--- man/drop_var_no_variance.Rd | 42 ++-- man/drop_var_not_numeric.Rd | 42 ++-- man/drop_var_with_na.Rd | 42 ++-- man/explore-package.Rd | 1 man/explore_col.Rd | 106 +++++------ man/explore_density.Rd | 2 man/get_color.Rd | 72 ++++---- man/interact.Rd | 54 +++--- man/log_info_if.Rd | 38 ++-- man/show_color.Rd | 42 ++-- man/use_data_wordle.Rd | 42 ++-- man/yyyymm_calc.Rd | 50 ++--- 48 files changed, 1117 insertions(+), 1002 deletions(-)
Title: Competing Proximal Gradients Library
Description: Functions to generate ensembles of generalized linear models using
competing proximal gradients. The optimal sparsity and diversity
tuning parameters are selected via an alternating grid search.
Author: Anthony Christidis [aut, cre],
Stefan Van Aelst [aut],
Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between CPGLIB versions 1.1.1 dated 2022-11-22 and 1.1.2 dated 2025-03-30
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 ++++- README.md | 2 +- configure | 4 ++-- configure.ac | 4 ++-- src/Makevars.win | 2 +- 7 files changed, 20 insertions(+), 17 deletions(-)
Title: Projected Subset Gradient Descent
Description: Functions to generate ensembles of generalized linear models using
a greedy projected subset gradient descent algorithm. The sparsity
and diversity tuning parameters are selected by cross-validation.
Author: Anthony Christidis [aut, cre],
Stefan Van Aelst [aut],
Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between PSGD versions 1.0.4 dated 2024-12-18 and 1.0.6 dated 2025-03-30
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 8 +++++++- configure | 4 ++-- configure.ac | 4 ++-- 5 files changed, 19 insertions(+), 13 deletions(-)
Title: Extract, Convert, and Merge 'pdf' Files from 'zip' Files
Description: Extracts 'zip' files, converts 'Word', 'Excel', and 'html'/'htm' files to 'pdf' format. 'Word' and 'Excel' conversion uses 'VBScript', while 'html'/'htm' conversion uses 'webshot' and 'PhantomJS'. Additionally, the package merges 'pdf' files into a single document. This package is only supported on 'Windows' due to 'VBScript' dependencies.
Author: Lijin Arakkandathil Thekkathil [aut, cre]
Maintainer: Lijin Arakkandathil Thekkathil <lijin5673@gmail.com>
Diff between LJexm versions 1.0.4 dated 2025-03-24 and 1.0.5 dated 2025-03-30
DESCRIPTION | 10 ++-- MD5 | 18 ++++---- NAMESPACE | 1 NEWS.md | 15 +++++++ R/convert_html_htm_to_pdf.R |only R/merge_pdfs.R | 5 +- R/run_app.R | 1 README.md | 86 +++++++++++++++++++++--------------------- inst/excel.vbs | 3 - man/convert_html_to_pdf.Rd |only tests/testthat/test-run_app.R | 4 + 11 files changed, 85 insertions(+), 58 deletions(-)
Title: 'CDsampling': Constraint Sampling in Paid Research Studies
Description: In the context of paid research studies and clinical trials, budget considerations and patient sampling from available populations are subject to inherent constraints. We introduce the 'CDsampling' package, which integrates optimal design theories within the framework of constrained sampling. This package offers the possibility to find both D-optimal approximate and exact allocations for samplings with or without constraints. Additionally, it provides functions to find constrained uniform sampling as a robust sampling strategy with limited model information. Our package offers functions for the computation of the Fisher information matrix under generalized linear models (including regular linear regression model) and multinomial logistic models.To demonstrate the applications, we also provide a simulated dataset and a real dataset embedded in the package. Yifei Huang, Liping Tong, and Jie Yang (2025)<doi:10.5705/ss.202022.0414>.
Author: Yifei Huang [aut, cre],
Liping Tong [aut],
Jie Yang [aut]
Maintainer: Yifei Huang <yhuan39@uic.edu>
Diff between CDsampling versions 0.1.4 dated 2025-01-11 and 0.1.5 dated 2025-03-30
DESCRIPTION | 6 MD5 | 32 - R/approxtoexact_constrained_func.R | 5 R/liftone_GLM.R | 5 R/liftone_MLM.R | 5 R/liftone_constrained_GLM.R | 5 R/liftone_constrained_MLM.R | 5 R/print.list_output.R | 101 ++- inst/doc/Intro_to_CDsampling.R | 42 - inst/doc/Intro_to_CDsampling.Rmd | 260 +++++++- inst/doc/Intro_to_CDsampling.html | 987 ++++++++++++++++++++-------------- man/approxtoexact_constrained_func.Rd | 5 man/liftone_GLM.Rd | 5 man/liftone_MLM.Rd | 5 man/liftone_constrained_GLM.Rd | 3 man/liftone_constrained_MLM.Rd | 3 vignettes/Intro_to_CDsampling.Rmd | 260 +++++++- 17 files changed, 1157 insertions(+), 577 deletions(-)
Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'DDIwR', 'QCA' and 'venn'.
Interprets and translates, factorizes and negates SOP - Sum of Products
expressions, for both binary and multi-value crisp sets, and extracts
information (set names, set values) from those expressions. Other functions
perform various other checks if possibly numeric (even if all numbers reside
in a character vector) and coerce to numeric, or check if the numbers are
whole. It also offers, among many others, a highly versatile recoding
routine and some more flexible alternatives to the base functions 'with()'
and 'within()'.
SOP simplification functions in this package use related minimization from
package 'QCA', which is recommended to be installed despite not being listed
in the Imports field, due to circular dependency issues.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between admisc versions 0.37 dated 2024-12-08 and 0.38 dated 2025-03-30
admisc-0.37/admisc/R/finvert.R |only admisc-0.37/admisc/R/negate.R |only admisc-0.37/admisc/R/writePrimeimp.R |only admisc-0.37/admisc/man/finvert.Rd |only admisc-0.37/admisc/man/negate.Rd |only admisc-0.38/admisc/DESCRIPTION | 6 - admisc-0.38/admisc/MD5 | 140 ++++++++++++++-------------- admisc-0.38/admisc/NAMESPACE | 3 admisc-0.38/admisc/R/asNumeric.R | 2 admisc-0.38/admisc/R/asSOP.R | 2 admisc-0.38/admisc/R/betweenQuotes.R | 2 admisc-0.38/admisc/R/brackets.R | 2 admisc-0.38/admisc/R/change.R | 2 admisc-0.38/admisc/R/checkMV.R | 2 admisc-0.38/admisc/R/checkSubset.R | 2 admisc-0.38/admisc/R/checkValid.R | 11 +- admisc-0.38/admisc/R/classify.R | 6 - admisc-0.38/admisc/R/coerceMode.R | 2 admisc-0.38/admisc/R/combnk.R | 2 admisc-0.38/admisc/R/compute.R | 2 admisc-0.38/admisc/R/dimnames.R | 2 admisc-0.38/admisc/R/equality.R | 2 admisc-0.38/admisc/R/expand.R | 7 + admisc-0.38/admisc/R/export.R | 2 admisc-0.38/admisc/R/factorize.R | 2 admisc-0.38/admisc/R/frelevel.R | 2 admisc-0.38/admisc/R/frev.R |only admisc-0.38/admisc/R/getInfo.R | 2 admisc-0.38/admisc/R/getLevels.R | 2 admisc-0.38/admisc/R/getMatrix.R | 2 admisc-0.38/admisc/R/getName.R | 2 admisc-0.38/admisc/R/hclr.R | 2 admisc-0.38/admisc/R/inside.R | 2 admisc-0.38/admisc/R/intersection.R | 2 admisc-0.38/admisc/R/invert.R | 145 +++++++++++++++++++++--------- admisc-0.38/admisc/R/listRDA.R | 2 admisc-0.38/admisc/R/mvSOP.R | 2 admisc-0.38/admisc/R/numdec.R | 2 admisc-0.38/admisc/R/objRDA.R | 2 admisc-0.38/admisc/R/onLoad.R | 2 admisc-0.38/admisc/R/overwrite.R | 2 admisc-0.38/admisc/R/pad.R | 2 admisc-0.38/admisc/R/permutations.R | 2 admisc-0.38/admisc/R/possibleNumeric.R | 2 admisc-0.38/admisc/R/prettyString.R | 2 admisc-0.38/admisc/R/prettyTable.R | 2 admisc-0.38/admisc/R/print.R | 2 admisc-0.38/admisc/R/recode.R | 6 + admisc-0.38/admisc/R/recreate.R | 2 admisc-0.38/admisc/R/reload.R | 2 admisc-0.38/admisc/R/replaceText.R | 58 +++++++----- admisc-0.38/admisc/R/scan.clipboard.R | 2 admisc-0.38/admisc/R/simplify.R | 2 admisc-0.38/admisc/R/sopos.R |only admisc-0.38/admisc/R/sortExpressions.R | 2 admisc-0.38/admisc/R/stopError.R | 2 admisc-0.38/admisc/R/string.R | 11 -- admisc-0.38/admisc/R/tagged.R | 2 admisc-0.38/admisc/R/tilde.R | 2 admisc-0.38/admisc/R/translate.R | 5 - admisc-0.38/admisc/R/tryCatchWEM.R | 2 admisc-0.38/admisc/R/unicode.R | 2 admisc-0.38/admisc/R/uninstall.R | 2 admisc-0.38/admisc/R/unload.R | 2 admisc-0.38/admisc/R/update.R | 2 admisc-0.38/admisc/R/using.R | 83 +++++++++-------- admisc-0.38/admisc/R/validateNames.R | 2 admisc-0.38/admisc/R/verify.R | 2 admisc-0.38/admisc/R/wholeNumeric.R | 2 admisc-0.38/admisc/R/write.clipboard.R | 2 admisc-0.38/admisc/R/writePIs.R |only admisc-0.38/admisc/inst/ChangeLog | 10 ++ admisc-0.38/admisc/man/admisc_internal.Rd | 1 admisc-0.38/admisc/man/admisc_package.Rd | 4 admisc-0.38/admisc/man/frev.Rd |only admisc-0.38/admisc/man/invert.Rd |only 76 files changed, 353 insertions(+), 245 deletions(-)
Title: Stepwise Split Regularized Regression
Description: Functions to perform stepwise split regularized regression. The approach first
uses a stepwise algorithm to split the variables into the models with a goodness
of fit criterion, and then regularization is applied to each model. The weights
of the models in the ensemble are determined based on a criterion selected by
the user.
Author: Anthony Christidis [aut, cre],
Stefan Van Aelst [aut],
Ruben Zamar [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between stepSplitReg versions 1.0.4 dated 2024-12-18 and 1.0.5 dated 2025-03-30
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 8 +++++++- configure | 4 ++-- configure.ac | 4 ++-- 5 files changed, 19 insertions(+), 13 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.5 dated 2024-09-23 and 0.6.6 dated 2025-03-30
DESCRIPTION | 12 ++-- MD5 | 98 +++++++++++++++++++-------------------- README.md | 4 - inst/doc/vignette.html | 6 +- man/RcppCWB-packge.Rd | 8 +++ src/cwb/CQi/auth.c | 2 src/cwb/CQi/cqpserver.c | 2 src/cwb/CQi/log.c | 6 +- src/cwb/CQi/server.c | 39 ++++++++++++++- src/cwb/cl/cdaccess.c | 8 +-- src/cwb/cl/corpus.c | 7 ++ src/cwb/cl/fileutils.c | 25 +++++++-- src/cwb/cl/globals.h | 5 + src/cwb/cl/lex.creg.c | 17 +++++- src/cwb/cl/macros.c | 16 ++++++ src/cwb/cl/makecomps.c | 21 ++++++++ src/cwb/cl/registry.tab.c | 14 ++--- src/cwb/cl/registry.y | 14 ++--- src/cwb/cl/regopt.c | 5 + src/cwb/cl/ui-helpers.c | 10 +++ src/cwb/cl/windows-mmap.c | 12 ++++ src/cwb/config.mk | 1 src/cwb/cqp/ascii-print.c | 14 ++--- src/cwb/cqp/concordance.c | 4 - src/cwb/cqp/corpmanag.c | 12 ++-- src/cwb/cqp/cqp.c | 39 +++++++++++++-- src/cwb/cqp/eval.c | 2 src/cwb/cqp/groups.c | 2 src/cwb/cqp/lex.yy.c | 20 ++++++- src/cwb/cqp/llquery.c | 14 ++--- src/cwb/cqp/macro.c | 12 +++- src/cwb/cqp/options.c | 32 ++++++++++++ src/cwb/cqp/output.c | 23 ++++++++- src/cwb/cqp/parse_actions.c | 20 ++++--- src/cwb/cqp/parser.tab.c | 6 ++ src/cwb/cqp/parser.y | 4 + src/cwb/cqp/print-modes.c | 2 src/cwb/cqp/ranges.c | 6 +- src/cwb/cqp/regex2dfa.c | 54 ++++++++++++++++++++- src/cwb/cqp/symtab.c | 8 +++ src/cwb/cqp/tree.c | 12 ++-- src/cwb/definitions.mk | 1 src/cwb/utils/cwb-align-encode.c | 4 - src/cwb/utils/cwb-align-show.c | 14 ++--- src/cwb/utils/cwb-compress-rdx.c | 8 +-- src/cwb/utils/cwb-decode.c | 16 +++--- src/cwb/utils/cwb-encode.c | 24 +++++---- src/cwb/utils/cwb-huffcode.c | 12 ++-- src/cwb/utils/cwb-s-encode.c | 6 +- src/cwb/utils/cwb-scan-corpus.c | 2 50 files changed, 510 insertions(+), 195 deletions(-)
Title: Inferring Cell-Specific Gene Regulatory Network
Description: An R package for inferring cell-type specific gene regulatory network from single-cell RNA data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 1.1.6 dated 2025-03-27 and 1.1.7 dated 2025-03-30
inferCSN-1.1.6/inferCSN/src/sparseCovCor.cpp |only inferCSN-1.1.7/inferCSN/DESCRIPTION | 8 +-- inferCSN-1.1.7/inferCSN/MD5 | 12 ++-- inferCSN-1.1.7/inferCSN/R/RcppExports.R | 4 - inferCSN-1.1.7/inferCSN/R/utils.R | 68 ++++++++++++++++++++++---- inferCSN-1.1.7/inferCSN/man/sparse_cor.Rd | 17 +++--- inferCSN-1.1.7/inferCSN/man/sparse_cov_cor.Rd |only inferCSN-1.1.7/inferCSN/src/RcppExports.cpp | 13 ---- 8 files changed, 78 insertions(+), 44 deletions(-)
Title: Statistical Combination of Diagnostic Tests
Description: A system for combining two diagnostic tests using various approaches
that include statistical and machine-learning-based methodologies.
These approaches are divided into four groups: linear combination
methods, non-linear combination methods, mathematical operators,
and machine learning algorithms. See
the <https://biotools.erciyes.edu.tr/dtComb/> website
for more information, documentation, and examples.
Author: Serra Ilayda Yerlitas [aut, ctb],
Serra Bersan Gengec [aut, ctb],
Necla Kochan [aut, ctb],
Gozde Erturk Zararsiz [aut, ctb],
Selcuk Korkmaz [aut, ctb],
Gokmen Zararsiz [aut, ctb, cre]
Maintainer: Gokmen Zararsiz <gokmen.zararsiz@gmail.com>
Diff between dtComb versions 1.0.6 dated 2025-03-27 and 1.0.7 dated 2025-03-30
DESCRIPTION | 6 +-- MD5 | 41 +++++++++++++------------- R/linComb.R | 41 ++++++++++++-------------- R/mathComb.R | 33 +++++++++----------- R/nonlinComb.R | 33 +++++++++----------- R/standardization.R | 37 ++++++++++------------- inst/doc/vignettedtComb.R | 2 - inst/doc/vignettedtComb.Rnw | 18 +++++------ inst/doc/vignettedtComb.pdf |binary man/linComb.Rd | 26 +++++++--------- man/mathComb.Rd | 26 +++++++--------- man/nonlinComb.Rd | 26 +++++++--------- man/std.train.Rd | 23 ++++++-------- tests/testthat/Rplots.pdf |only tests/testthat/result_data/test_std.test.rda |binary tests/testthat/result_data/test_std.train.rda |binary tests/testthat/test-linComb.R | 8 ++--- tests/testthat/test-mathComb.R | 2 - tests/testthat/test-nonlinComb.R | 4 +- tests/testthat/test-predComb.R | 4 +- tests/testthat/test-standardize.R | 12 +++---- vignettes/vignettedtComb.Rnw | 18 +++++------ 22 files changed, 170 insertions(+), 190 deletions(-)
Title: Simulate Data from a DAG and Associated Node Information
Description: Simulate complex data from a given directed acyclic graph and information about each individual node.
Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to
one of many implemented regressions, such as logistic regression, linear
regression, poisson regression and more. Also includes a comprehensive framework for discrete-time
simulation, which can generate even more complex longitudinal data.
Author: Robin Denz [aut, cre],
Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between simDAG versions 0.2.2 dated 2025-02-23 and 0.3.0 dated 2025-03-30
DESCRIPTION | 9 MD5 | 148 +++++++----- NAMESPACE | 8 NEWS.md | 26 ++ R/dag.r | 20 + R/distributions.r | 12 R/find_cycle.r |only R/formula_interface.r | 113 +++++++-- R/input_checks.r | 2 R/node.r | 4 R/node_binomial.r | 43 ++- R/node_cox.r | 32 ++ R/node_gaussian.r | 10 R/node_lmer.r |only R/node_mixture.r |only R/node_poisson.r | 11 R/node_rsurv.r |only R/node_zeroinfl.r |only R/sim_discrete_time.r | 12 R/sim_from_dag.r | 21 + R/sim_n_datasets.r | 5 R/structural_equations.r | 116 +++++++++ README.md | 2 build/vignette.rds |binary inst/doc/v_cookbook.R |only inst/doc/v_cookbook.Rmd |only inst/doc/v_cookbook.html |only inst/doc/v_covid_example.Rmd | 5 inst/doc/v_covid_example.html | 52 ++++ inst/doc/v_sim_discrete_time.R | 2 inst/doc/v_sim_discrete_time.Rmd | 9 inst/doc/v_sim_discrete_time.html | 30 +- inst/doc/v_sim_from_dag.R | 22 - inst/doc/v_sim_from_dag.Rmd | 60 ++-- inst/doc/v_sim_from_dag.html | 123 ++++++---- inst/doc/v_using_formulas.R | 81 ++++++ inst/doc/v_using_formulas.Rmd | 128 ++++++++++ inst/doc/v_using_formulas.html | 246 +++++++++++++++++++- man/as.igraph.DAG.Rd | 9 man/dag2matrix.Rd | 4 man/node.Rd | 21 + man/node_binomial.Rd | 34 ++ man/node_conditional_distr.Rd | 2 man/node_conditional_prob.Rd | 1 man/node_cox.Rd | 11 man/node_custom.Rd | 4 man/node_gaussian.Rd | 33 ++ man/node_mixture.Rd |only man/node_negative_binomial.Rd | 4 man/node_poisson.Rd | 33 ++ man/node_rsurv.Rd |only man/node_zeroinfl.Rd |only man/rbernoulli.Rd | 5 man/rcategorical.Rd | 6 man/simDAG.Rd | 7 man/sim_n_datasets.Rd | 2 tests/testthat/_snaps/dag.md | 2 tests/testthat/test_add_node.r | 22 + tests/testthat/test_as.igraph.DAG.r | 6 tests/testthat/test_dag2matrix.r | 4 tests/testthat/test_extract_mixed_terms.r |only tests/testthat/test_find_cycle.r |only tests/testthat/test_get_formula_for_node_lmer.r |only tests/testthat/test_input_checks_do.r | 2 tests/testthat/test_names_DAG.r | 2 tests/testthat/test_node_cox.r | 19 + tests/testthat/test_node_custom.r |only tests/testthat/test_node_lmer.r |only tests/testthat/test_node_mixture.r |only tests/testthat/test_node_rsurv.r |only tests/testthat/test_node_zeroinfl.r |only tests/testthat/test_parse_formula.r | 33 ++ tests/testthat/test_rbernoulli.r | 7 tests/testthat/test_rcategorical.r | 18 + tests/testthat/test_remove_mistaken_plus.r |only tests/testthat/test_str_eq_mixture.r |only tests/testthat/test_str_eq_rsurv.r |only tests/testthat/test_str_eq_zeroinfl.r |only tests/testthat/test_str_replace_all.r |only tests/testthat/test_supports_mixed_terms.r |only vignettes/images_v_sim_discrete_time/simple_dag.png |binary vignettes/images_v_sim_from_dag/simple_dag.png |binary vignettes/images_v_sim_from_dag/time_dep_dag.png |binary vignettes/v_cookbook.Rmd |only vignettes/v_covid_example.Rmd | 5 vignettes/v_sim_discrete_time.Rmd | 9 vignettes/v_sim_from_dag.Rmd | 60 ++-- vignettes/v_using_formulas.Rmd | 128 ++++++++++ 88 files changed, 1530 insertions(+), 315 deletions(-)
Title: Get the Insights of Your Neural Network
Description: Interpretation methods for analyzing the behavior and individual
predictions of modern neural networks in a three-step procedure: Converting
the model, running the interpretation method, and visualizing the results.
Implemented methods are, e.g., 'Connection Weights' described by Olden et al. (2004)
<doi:10.1016/j.ecolmodel.2004.03.013>, layer-wise relevance
propagation ('LRP') described by Bach et al. (2015)
<doi:10.1371/journal.pone.0130140>, deep learning important features
('DeepLIFT') described by Shrikumar et al. (2017) <doi:10.48550/arXiv.1704.02685>
and gradient-based methods like 'SmoothGrad' described by Smilkov et
al. (2017) <doi:10.48550/arXiv.1706.03825>, 'Gradient x Input'
or 'Vanilla Gradient'.
Details can be found in the accompanying scientific paper: Koenen & Wright
(2024, Journal of Statistical Software, <doi:10.18637/jss.v111.i08>).
Author: Niklas Koenen [aut, cre] ,
Raphael Baudeu [ctb]
Maintainer: Niklas Koenen <niklas.koenen@gmail.com>
Diff between innsight versions 0.3.1 dated 2024-11-26 and 0.3.2 dated 2025-03-30
DESCRIPTION | 6 MD5 | 60 - NEWS.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Example_1_iris.R | 22 inst/doc/Example_1_iris.html | 32 - inst/doc/Example_2_penguin.R | 6 inst/doc/Example_2_penguin.Rmd | 6 inst/doc/Example_2_penguin.html | 29 inst/doc/detailed_overview.R | 1128 ++++++++++++++++++------------------- inst/doc/detailed_overview.Rmd | 82 +- inst/doc/detailed_overview.html | 78 +- inst/doc/innsight.R | 161 ++--- inst/doc/innsight.Rmd | 9 inst/doc/innsight.html | 14 man/ConnectionWeights.Rd | 2 man/Converter.Rd | 2 man/DeepLift.Rd | 2 man/DeepSHAP.Rd | 2 man/ExpectedGradient.Rd | 2 man/Gradient.Rd | 2 man/IntegratedGradient.Rd | 2 man/LIME.Rd | 8 man/LRP.Rd | 2 man/SmoothGrad.Rd | 2 tests/testthat/test_layer_conv1d.R | 6 tests/testthat/test_layer_conv2d.R | 3 vignettes/Example_2_penguin.Rmd | 6 vignettes/detailed_overview.Rmd | 82 +- vignettes/innsight.Rmd | 9 31 files changed, 900 insertions(+), 873 deletions(-)
Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T
in various applications. A 100(1-alpha)% global envelope is a band bounded by two
vectors such that the probability that T falls outside this envelope in any of the d
points is equal to alpha. Global means that the probability is controlled simultaneously
for all the d elements of the vectors. The global envelopes can be used for graphical
Monte Carlo and permutation tests where the test statistic is a multivariate vector or
function (e.g. goodness-of-fit testing for point patterns and random sets, functional
analysis of variance, functional general linear model, n-sample test of correspondence
of distribution functions), for central regions of functional or multivariate data (e.g.
outlier detection, functional boxplot) and for global confidence and prediction bands
(e.g. confidence band in polynomial regression, Bayesian posterior prediction). See
Myllymäki and Mrkvička (2024) <doi:10.18637/jss.v111.i03 [...truncated...]
Author: Mari Myllymaeki [aut, cre],
Tomas Mrkvicka [aut],
Mikko Kuronen [ctb],
Jiri Dvorak [ctb],
Pavel Grabarnik [ctb],
Ute Hahn [ctb],
Michael Rost [ctb],
Henri Seijo [ctb]
Maintainer: Mari Myllymaeki <mari.myllymaki@luke.fi>
Diff between GET versions 1.0-4 dated 2024-12-02 and 1.0-5 dated 2025-03-30
DESCRIPTION | 8 MD5 | 47 +- inst/doc/FDRenvelopes.pdf |binary inst/doc/FDRenvelopes.tex.rsp | 3 inst/doc/GET.pdf |binary inst/doc/GET.tex.rsp | 2 inst/doc/HotSpots.pdf |binary inst/doc/HotSpots.tex.rsp | 566 ++++++++++++++----------- inst/doc/QuantileRegression.pdf |binary inst/doc/pointpatterns.pdf |binary vignettes/FDRenvelopes.Rnw.orig | 3 vignettes/FDRenvelopes.tex.rsp | 3 vignettes/GET.Rnw.orig | 4 vignettes/GET.tex.rsp | 2 vignettes/GETbibfile.bib | 11 vignettes/HotSpots-data_MatClust_param_sim.pdf |binary vignettes/HotSpots-data_covariates.pdf |binary vignettes/HotSpots-data_covariates_subwin.pdf |binary vignettes/HotSpots-data_crashes_thin.pdf |binary vignettes/HotSpots-data_density.pdf |binary vignettes/HotSpots-data_poisson_EIP.pdf |binary vignettes/HotSpots-data_poisson_K.pdf |only vignettes/HotSpots-fdrenvelope.pdf |binary vignettes/HotSpots.Rnw.orig | 424 ++++++++++++------ vignettes/HotSpots.tex.rsp | 566 ++++++++++++++----------- 25 files changed, 954 insertions(+), 685 deletions(-)
Title: 'NoSQL' Database Connector
Description: Simplified JSON document database access and manipulation,
providing a common API across supported 'NoSQL' databases
'Elasticsearch', 'CouchDB', 'MongoDB' as well as
'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] ,
Scott Chamberlain [aut] ,
Rich FitzJohn [aut],
Jeroen Ooms [aut],
Ivan Tarbakou [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between nodbi versions 0.11.0 dated 2024-11-10 and 0.12.0 dated 2025-03-30
DESCRIPTION | 13 +- MD5 | 28 ++--- NEWS.md | 6 + R/create.R | 2 R/get.R | 71 +++++++++----- R/query.R | 43 +++++++- R/src.R | 6 - R/src_postgres.R | 46 ++++----- R/src_sqlite.R | 5 - R/update.R | 208 +++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/nodbi-overview.html | 27 ++--- inst/js/update.sh | 1 man/src.Rd | 6 - man/src_postgres.Rd | 1 15 files changed, 258 insertions(+), 205 deletions(-)
Title: Comprehensive and Easy to Use Quality Control of GWAS Results
Description: When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Author: Alireza Ani [aut, cre],
Peter J. van der Most [aut],
Ahmad Vaez [aut],
Ilja M. Nolte [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between GWASinspector versions 1.7.1 dated 2024-05-06 and 1.7.3 dated 2025-03-30
ChangeLog | 5 +++++ DESCRIPTION | 12 ++++++------ MD5 | 32 ++++++++++++++++---------------- NEWS | 5 +++++ R/GWASinspector.R | 4 ++-- R/aaa.R | 2 +- R/headerRelatedFunctions.R | 3 ++- R/pValueFunctions.R | 14 ++++++++++++++ R/processInputFile.R | 5 +++-- R/saveFilesFunctions.R | 5 +++++ R/zzz.R | 1 + inst/CITATION | 4 ++-- inst/doc/GWASinspector.R | 2 +- inst/doc/GWASinspector.Rmd | 10 +++++----- inst/doc/GWASinspector.html | 14 +++++++------- man/GWASinspector.Rd | 20 ++------------------ vignettes/GWASinspector.Rmd | 10 +++++----- 17 files changed, 82 insertions(+), 66 deletions(-)
Title: 'Rcpp' Integration of Different "Ziggurat" Normal RNG
Implementations
Description: The Ziggurat generator for normally distributed random
numbers, originally proposed by Marsaglia and Tsang (2000,
<doi:10.18637/jss.v005.i08>) has been improved upon a few times
starting with Leong et al (2005, <doi:10.18637/jss.v012.i07>).
This package provides an aggregation in order to compare different
implementations in order to provide a 'faster but good enough'
alternative for use with R and C++ code. See the 'zigg' package
for a lighter implementation for much easier use in other packages.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppZiggurat versions 0.1.7 dated 2025-03-22 and 0.1.8 dated 2025-03-30
RcppZiggurat-0.1.7/RcppZiggurat/inst/doc/RcppZiggurat.R |only RcppZiggurat-0.1.7/RcppZiggurat/inst/doc/RcppZiggurat.Rmd |only RcppZiggurat-0.1.7/RcppZiggurat/vignettes/RcppZiggurat.RData |only RcppZiggurat-0.1.7/RcppZiggurat/vignettes/RcppZiggurat.Rmd |only RcppZiggurat-0.1.7/RcppZiggurat/vignettes/RcppZiggurat.bib |only RcppZiggurat-0.1.7/RcppZiggurat/vignettes/figures |only RcppZiggurat-0.1.7/RcppZiggurat/vignettes/header.tex |only RcppZiggurat-0.1.8/RcppZiggurat/ChangeLog | 25 ++++++++ RcppZiggurat-0.1.8/RcppZiggurat/DESCRIPTION | 12 +--- RcppZiggurat-0.1.8/RcppZiggurat/MD5 | 31 +++-------- RcppZiggurat-0.1.8/RcppZiggurat/README.md | 20 ++++--- RcppZiggurat-0.1.8/RcppZiggurat/build/vignette.rds |binary RcppZiggurat-0.1.8/RcppZiggurat/cleanup | 12 ++-- RcppZiggurat-0.1.8/RcppZiggurat/inst/NEWS.Rd | 9 +++ RcppZiggurat-0.1.8/RcppZiggurat/inst/doc/RcppZiggurat.Rnw |only RcppZiggurat-0.1.8/RcppZiggurat/inst/doc/RcppZiggurat.pdf |binary RcppZiggurat-0.1.8/RcppZiggurat/src/Makevars.ucrt | 11 +++ RcppZiggurat-0.1.8/RcppZiggurat/vignettes/RcppZiggurat.Rnw |only RcppZiggurat-0.1.8/RcppZiggurat/vignettes/pdf |only 19 files changed, 77 insertions(+), 43 deletions(-)
Title: Keyword Assisted Topic Models
Description: Fits keyword assisted topic models (keyATM) using collapsed Gibbs samplers. The keyATM combines the latent dirichlet allocation (LDA) models with a small number of keywords selected by researchers in order to improve the interpretability and topic classification of the LDA. The keyATM can also incorporate covariates and directly model time trends. The keyATM is proposed in Eshima, Imai, and Sasaki (2024) <doi:10.1111/ajps.12779>.
Author: Shusei Eshima [aut, cre] ,
Tomoya Sasaki [aut],
Kosuke Imai [aut],
Chung-hong Chan [ctb] ,
Romain Francois [ctb] ,
Martin Feldkircher [ctb] ,
William Lowe [ctb],
Seo-young Silvia Kim [ctb]
Maintainer: Shusei Eshima <shuseieshima@gmail.com>
Diff between keyATM versions 0.5.2 dated 2024-04-24 and 0.5.3 dated 2025-03-30
DESCRIPTION | 8 +++++--- MD5 | 14 +++++++------- NEWS.md | 7 ++++--- R/posterior.R | 4 ++-- R/utils.R | 2 +- man/keyATM-package.Rd | 1 + man/read_keywords.Rd | 2 +- tests/testthat/test-diagnosis.R | 2 +- 8 files changed, 22 insertions(+), 18 deletions(-)
Title: Word Embedding Research Framework for Psychological Science
Description: An integrative toolbox of word embedding research that provides:
(1) a collection of 'pre-trained' static word vectors in the '.RData'
compressed format <https://psychbruce.github.io/WordVector_RData.pdf>;
(2) a group of functions to process, analyze, and visualize word vectors;
(3) a range of tests to examine conceptual associations, including
the Word Embedding Association Test <doi:10.1126/science.aal4230>
and the Relative Norm Distance <doi:10.1073/pnas.1720347115>,
with permutation test of significance; and
(4) a set of training methods to locally train (static) word vectors
from text corpora, including 'Word2Vec' <doi:10.48550/arXiv.1301.3781>,
'GloVe' <doi:10.3115/v1/D14-1162>, and 'FastText' <doi:10.48550/arXiv.1607.04606>.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between PsychWordVec versions 2023.9 dated 2023-09-27 and 2025.3 dated 2025-03-30
PsychWordVec-2023.9/PsychWordVec/R/03-dynamic.R |only PsychWordVec-2023.9/PsychWordVec/man/text_init.Rd |only PsychWordVec-2023.9/PsychWordVec/man/text_model_download.Rd |only PsychWordVec-2023.9/PsychWordVec/man/text_model_remove.Rd |only PsychWordVec-2023.9/PsychWordVec/man/text_to_vec.Rd |only PsychWordVec-2023.9/PsychWordVec/man/text_unmask.Rd |only PsychWordVec-2025.3/PsychWordVec/DESCRIPTION | 25 +++---- PsychWordVec-2025.3/PsychWordVec/MD5 | 14 +--- PsychWordVec-2025.3/PsychWordVec/NAMESPACE | 5 - PsychWordVec-2025.3/PsychWordVec/NEWS.md | 6 + PsychWordVec-2025.3/PsychWordVec/README.md | 39 ++++-------- 11 files changed, 37 insertions(+), 52 deletions(-)
Title: Water and Measurements Quality
Description: The functions proposed in this package allows to evaluate the process of measurement of the chemical components of water numerically or graphically. TSSS(), ICHS and datacheck() functions are useful to control the quality of measurements of chemical components of a sample of water. If one or more measurements include an error, the generated graph will indicate it with a position of the point that represents the sample outside the confidence interval. The function CI allows to evaluate the possibility of contamination of a water sample after being obtained.
Author: Maela Lupo [aut, cre],
Andrea Porpatto [aut],
Rosa Marzullo [aut],
Alfredo Rigalli [aut]
Maintainer: Maela Lupo <maela.lupo@gmail.com>
Diff between AQuality versions 1.2 dated 2025-03-21 and 1.3 dated 2025-03-30
DESCRIPTION | 10 +++++----- MD5 | 16 +++++++++------- NAMESPACE | 4 ++-- R/datacheck.R |only build/partial.rdb |binary man/AQuality-package.Rd | 4 ++-- man/TSSS.Rd | 2 +- man/dataCI.Rd | 4 ++-- man/dataICHS.Rd | 3 +-- man/datacheck.Rd |only 10 files changed, 22 insertions(+), 21 deletions(-)
Title: Penalized Meta-Analysis
Description: Conduct penalized meta-analysis, see Van Lissa, Van Erp, & Clapper
(2023) <doi:10.31234/osf.io/6phs5>. In meta-analysis, there are
often between-study differences. These can be coded as moderator variables,
and controlled for using meta-regression. However, if the number of
moderators is large relative to the number of studies, such an analysis may
be overfit. Penalized meta-regression is useful in these cases, because
it shrinks the regression slopes of irrelevant moderators towards zero.
Author: Caspar J van Lissa [aut, cre] ,
Sara J van Erp [aut]
Maintainer: Caspar J van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between pema versions 0.1.3 dated 2023-03-16 and 0.1.4 dated 2025-03-30
DESCRIPTION | 22 MD5 | 78 - NAMESPACE | 8 R/brma.R | 4 R/check_workshop_data.R |only R/pema-package.R | 3 R/ui.R |only R/webex.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/meta-analysis_tutorial.R |only inst/doc/meta-analysis_tutorial.Rmd |only inst/doc/meta-analysis_tutorial.html |only inst/doc/using-brma.R | 203 +-- inst/doc/using-brma.Rmd | 697 +++++----- inst/doc/using-brma.html | 170 +- inst/stan/horseshoe_MA.stan | 4 inst/stan/horseshoe_MA_ml.stan | 8 inst/stan/horseshoe_MA_ml_noint.stan | 8 inst/stan/horseshoe_MA_noint.stan | 4 inst/stan/lasso_MA.stan | 4 inst/stan/lasso_MA_ml.stan | 8 inst/stan/lasso_MA_ml_noint.stan | 8 inst/stan/lasso_MA_noint.stan | 4 man/check_workshop_data.Rd |only man/pema-package.Rd | 17 src/Makevars.win | 2 src/stanExports_horseshoe_MA.h | 1717 ++++++++++++-------------- src/stanExports_horseshoe_MA_ml.h | 2077 +++++++++++++++----------------- src/stanExports_horseshoe_MA_ml_noint.h | 2054 ++++++++++++++----------------- src/stanExports_horseshoe_MA_noint.h | 1656 +++++++++++-------------- src/stanExports_hs_prior.h | 802 +++++------- src/stanExports_lasso_MA.h | 1346 +++++++++----------- src/stanExports_lasso_MA_ml.h | 1813 +++++++++++++-------------- src/stanExports_lasso_MA_ml_noint.h | 1759 +++++++++++++-------------- src/stanExports_lasso_MA_noint.h | 1290 +++++++++---------- src/stanExports_lasso_prior.h | 584 ++++---- src/stanExports_prior_meff.h | 826 +++++------- tests/testthat/test-multiple_imp.R | 29 vignettes/check_conv.png |only vignettes/check_function.R |only vignettes/include |only vignettes/meta-analysis_tutorial.Rmd |only vignettes/output_pbf.RData |only vignettes/tutorial.bib |only vignettes/using-brma.Rmd | 697 +++++----- 46 files changed, 8543 insertions(+), 9359 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] ,
Devin J. Johnson [aut] ,
Peter Mueller [aut],
Andres Felipe Barrientos [aut],
Garritt Page [aut],
David Dunson [aut],
Alex Crichton [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [c [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.3.42 dated 2024-09-16 and 0.3.51 dated 2025-03-30
salso-0.3.42/salso/inst |only salso-0.3.42/salso/src/rust/roxido.txt |only salso-0.3.42/salso/src/rust/roxido/src/rbindings.rs |only salso-0.3.42/salso/tools/cargo_run.R |only salso-0.3.51/salso/DESCRIPTION | 14 salso-0.3.51/salso/INSTALL | 17 salso-0.3.51/salso/LICENSE | 2 salso-0.3.51/salso/MD5 | 54 - salso-0.3.51/salso/NAMESPACE | 3 salso-0.3.51/salso/NEWS | 6 salso-0.3.51/salso/R/canonicalize_cluster_labels.R |only salso-0.3.51/salso/R/chips.R | 116 ++- salso-0.3.51/salso/R/roxido.R | 3 salso-0.3.51/salso/build/partial.rdb |binary salso-0.3.51/salso/configure | 36 salso-0.3.51/salso/man/canonicalize_cluster_labels.Rd |only salso-0.3.51/salso/man/chips.Rd | 63 + salso-0.3.51/salso/man/salso-package.Rd | 3 salso-0.3.51/salso/man/threshold.Rd |only salso-0.3.51/salso/src/Makevars | 6 salso-0.3.51/salso/src/rust/Cargo.lock | 106 ++ salso-0.3.51/salso/src/rust/Cargo.toml | 12 salso-0.3.51/salso/src/rust/build.rs | 6 salso-0.3.51/salso/src/rust/rbindings |only salso-0.3.51/salso/src/rust/roxido/Cargo.toml | 5 salso-0.3.51/salso/src/rust/roxido/src/lib.rs | 428 +++++++---- salso-0.3.51/salso/src/rust/roxido_macro/Cargo.toml | 2 salso-0.3.51/salso/src/rust/roxido_macro/src/lib.rs | 18 salso-0.3.51/salso/src/rust/src/lib.rs | 691 +++++++++++++++--- salso-0.3.51/salso/src/rust/vendor.tar.gz |binary salso-0.3.51/salso/tools/build_rust_library.R |only 31 files changed, 1202 insertions(+), 389 deletions(-)
Title: Rarefaction-Based Species Richness Estimator
Description: Calculate rarefaction-based alpha- and beta-diversity. Offer parametric extrapolation to estimate the total expected species in a single community and the total expected shared species between two communities. Visualize the curve-fitting for these estimators.
Author: Peng Zhao [aut, cre] ,
Yi Zou [aut]
Maintainer: Peng Zhao <pengzhao20@outlook.com>
Diff between rarestR versions 1.1.0 dated 2024-09-26 and 1.1.1 dated 2025-03-30
DESCRIPTION | 8 ++--- MD5 | 38 ++++++++++++++-------------- R/data.R | 2 - R/es.R | 2 - R/ess.R | 2 - R/tes.R | 2 - R/tess.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 67 ++++++++++++++++---------------------------------- inst/REFERENCES.bib | 45 ++++++++------------------------- inst/doc/rarestR.R | 32 +++++++++++------------ inst/doc/rarestR.Rmd | 9 ++---- inst/doc/rarestR.html | 24 ++++++----------- man/es.Rd | 2 - man/ess.Rd | 2 - man/share.Rd | 2 - man/tes.Rd | 2 - man/tess.Rd | 2 - vignettes/rarestR.Rmd | 9 ++---- 20 files changed, 97 insertions(+), 155 deletions(-)
Title: Cluster Analysis via Random Partition Distributions
Description: Cluster analysis is performed using pairwise distance information and a random partition distribution. The method is
implemented for two random partition distributions. It draws samples and then obtains and plots clustering estimates.
An implementation of a selection algorithm is provided for the mass parameter of the partition distribution. Since
pairwise distances are the principal input to this procedure, it is most comparable to the hierarchical and k-medoids
clustering methods. The method is Dahl, Andros, Carter (2022+) <doi:10.1002/sam.11602>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
J. Brandon Carter [aut] ,
Alex Crichton [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [ctb] ,
Jorge Aparicio [ctb] ,
Josh Stone [ctb] ,
Mikhail Vorotilov [ [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between caviarpd versions 0.3.13 dated 2024-09-06 and 0.3.14 dated 2025-03-30
caviarpd-0.3.13/caviarpd/inst |only caviarpd-0.3.13/caviarpd/src/rust/roxido/src/rbindings.rs |only caviarpd-0.3.13/caviarpd/src/rust/src/registration.rs |only caviarpd-0.3.13/caviarpd/tools/cargo_run.R |only caviarpd-0.3.14/caviarpd/DESCRIPTION | 14 caviarpd-0.3.14/caviarpd/INSTALL | 17 caviarpd-0.3.14/caviarpd/LICENSE | 2 caviarpd-0.3.14/caviarpd/MD5 | 55 - caviarpd-0.3.14/caviarpd/NAMESPACE | 2 caviarpd-0.3.14/caviarpd/NEWS | 5 caviarpd-0.3.14/caviarpd/R/DDCRPPartition.R | 1 caviarpd-0.3.14/caviarpd/R/roxido.R | 4 caviarpd-0.3.14/caviarpd/R/samplePartition.R | 1 caviarpd-0.3.14/caviarpd/build/partial.rdb |binary caviarpd-0.3.14/caviarpd/configure | 36 - caviarpd-0.3.14/caviarpd/man/caviarpd-package.Rd |only caviarpd-0.3.14/caviarpd/src/Makevars | 6 caviarpd-0.3.14/caviarpd/src/rust/Cargo.lock | 92 +-- caviarpd-0.3.14/caviarpd/src/rust/Cargo.toml | 1 caviarpd-0.3.14/caviarpd/src/rust/build.rs | 6 caviarpd-0.3.14/caviarpd/src/rust/epa/Cargo.lock | 70 ++ caviarpd-0.3.14/caviarpd/src/rust/rbindings |only caviarpd-0.3.14/caviarpd/src/rust/roxido/Cargo.lock | 21 caviarpd-0.3.14/caviarpd/src/rust/roxido/Cargo.toml | 5 caviarpd-0.3.14/caviarpd/src/rust/roxido/src/lib.rs | 428 ++++++++------ caviarpd-0.3.14/caviarpd/src/rust/roxido_macro/Cargo.lock | 16 caviarpd-0.3.14/caviarpd/src/rust/roxido_macro/Cargo.toml | 2 caviarpd-0.3.14/caviarpd/src/rust/roxido_macro/src/lib.rs | 18 caviarpd-0.3.14/caviarpd/src/rust/src/lib.rs | 1 caviarpd-0.3.14/caviarpd/src/rust/vendor.tar.gz |binary caviarpd-0.3.14/caviarpd/tools/build_rust_library.R |only 31 files changed, 501 insertions(+), 302 deletions(-)
Title: Feature Allocation Neighborhood Greedy Search Algorithm
Description: A neighborhood-based, greedy search algorithm is performed to estimate a feature allocation by minimizing the expected loss based on posterior samples from the feature allocation distribution. The method is currently under peer review but an earlier draft is available in Dahl, Johnson, and Andros (2022+) <doi:10.48550/arXiv.2207.13824>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
Devin J. Johnson [aut] ,
Alex Crichton [ctb] ,
Andrii Dmytrenko [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [ctb] ,
Josh Stone [ctb] ,
Niko Matsakis [ctb [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between fangs versions 0.2.17 dated 2024-09-06 and 0.2.18 dated 2025-03-29
fangs-0.2.17/fangs/inst/cargo.log |only fangs-0.2.17/fangs/src/rust/roxido/src/rbindings.rs |only fangs-0.2.17/fangs/tools/cargo_run.R |only fangs-0.2.18/fangs/DESCRIPTION | 14 fangs-0.2.18/fangs/INSTALL | 17 fangs-0.2.18/fangs/LICENSE | 2 fangs-0.2.18/fangs/MD5 | 46 +- fangs-0.2.18/fangs/NEWS | 5 fangs-0.2.18/fangs/R/roxido.R | 4 fangs-0.2.18/fangs/build/partial.rdb |binary fangs-0.2.18/fangs/configure | 36 - fangs-0.2.18/fangs/man/fangs-package.Rd |only fangs-0.2.18/fangs/src/Makevars | 6 fangs-0.2.18/fangs/src/rust/Cargo.lock | 88 ++-- fangs-0.2.18/fangs/src/rust/Cargo.toml | 1 fangs-0.2.18/fangs/src/rust/build.rs | 6 fangs-0.2.18/fangs/src/rust/rbindings |only fangs-0.2.18/fangs/src/rust/roxido/Cargo.lock | 21 fangs-0.2.18/fangs/src/rust/roxido/Cargo.toml | 5 fangs-0.2.18/fangs/src/rust/roxido/src/lib.rs | 428 ++++++++++++-------- fangs-0.2.18/fangs/src/rust/roxido_macro/Cargo.lock | 16 fangs-0.2.18/fangs/src/rust/roxido_macro/Cargo.toml | 2 fangs-0.2.18/fangs/src/rust/roxido_macro/src/lib.rs | 18 fangs-0.2.18/fangs/src/rust/src/lib.rs | 1 fangs-0.2.18/fangs/src/rust/vendor.tar.gz |binary fangs-0.2.18/fangs/tools/build_rust_library.R |only 26 files changed, 427 insertions(+), 289 deletions(-)
Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional
polynomial models under the assumption of normally distributed error terms, see
Sabanes Bove, D. and Held, L. (2011) <doi:10.1007/s11222-010-9170-7>.
Author: Daniel Sabanes Bove [aut, cre],
Isaac Gravestock [aut],
Robert Davies [cph],
Stephen Moshier [cph],
Gareth Ambler [cph],
Axel Benner [cph]
Maintainer: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
Diff between bfp versions 0.0-48 dated 2024-03-14 and 0.0-49 dated 2025-03-29
ChangeLog | 4 ++ DESCRIPTION | 8 ++-- MD5 | 12 +++--- src/combinatorics.cpp | 2 - src/newmat/myexcept.cpp | 85 +++++++++++++++++++++++++----------------------- src/newmat/newmatex.cpp | 7 +++ src/newmat/newmatnl.cpp | 18 +++++----- 7 files changed, 76 insertions(+), 60 deletions(-)
Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework
for simulating data in state space models,
particularly when the number of subjects/units (n) exceeds one,
a scenario commonly encountered in social and behavioral sciences.
For an introduction to state space models in social and behavioral sciences,
refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between simStateSpace versions 1.2.9 dated 2025-02-14 and 1.2.10 dated 2025-03-29
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 6 ++++++ R/RcppExports.R | 4 ++++ R/simStateSpace-lin-sde-cov.R | 8 +++++--- build/partial.rdb |binary src/RcppExports.cpp | 13 +++++++++++++ src/source.cpp | 13 +++++++++++++ tests/testthat/Rplots.pdf |only tests/testthat/test-simStateSpace-lin-sde-cov.R | 20 ++++++++++++++++++++ 10 files changed, 73 insertions(+), 14 deletions(-)
Title: Access to the List of Birds Species of Peru
Description: Allows access to the data found in the species list featured in the renowned 'List of the Birds of Peru' Plenge, M. A. (2023) <https://sites.google.com/site/boletinunop/checklist>. This publication stands as one of Peru's most comprehensive reviews of bird diversity. The dataset incorporates detailed species accounts and has been meticulously structured for effortless utilization within the R environment.
Author: Paul E. Santos Andrade [aut, cre]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between avesperu versions 0.0.3 dated 2024-12-05 and 0.0.4 dated 2025-03-29
DESCRIPTION | 8 ++-- MD5 | 13 ++++--- R/aves_peru_2025_v1.R |only R/get_avesperu.R | 6 +-- README.md | 52 +++++++++++++++++-------------- data/aves_peru_2025_v1.rda |only inst/CITATION | 8 ++-- man/aves_peru_2025_v1.Rd |only man/figures/README-unnamed-chunk-2-1.png |binary 9 files changed, 49 insertions(+), 38 deletions(-)
Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level".
Author: Jon Clayden [aut, cre]
Maintainer: Jon Clayden <code@clayden.org>
Diff between reportr versions 1.3.0 dated 2018-10-26 and 1.3.1 dated 2025-03-29
reportr-1.3.0/reportr/tests/testthat |only reportr-1.3.0/reportr/tests/testthat.R |only reportr-1.3.1/reportr/DESCRIPTION | 17 +++++++++-------- reportr-1.3.1/reportr/MD5 | 18 +++++++++--------- reportr-1.3.1/reportr/NEWS | 8 ++++++++ reportr-1.3.1/reportr/R/reportr.R | 12 ++++++------ reportr-1.3.1/reportr/README.md | 2 ++ reportr-1.3.1/reportr/inst |only reportr-1.3.1/reportr/man/reportr.Rd | 8 ++++---- reportr-1.3.1/reportr/tests/tinytest.R |only 10 files changed, 38 insertions(+), 27 deletions(-)
Title: Create Demographic Table
Description: Functions for creating demographic table of simple summary
statistics and comparison(s) over one or more groups.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DemographicTable versions 0.1.11 dated 2025-03-15 and 0.2.0 dated 2025-03-29
DemographicTable-0.1.11/DemographicTable/inst/extR/toCRAN.R |only DemographicTable-0.1.11/DemographicTable/inst/xtable.R |only DemographicTable-0.2.0/DemographicTable/DESCRIPTION | 17 +- DemographicTable-0.2.0/DemographicTable/MD5 | 36 +++-- DemographicTable-0.2.0/DemographicTable/NEWS.md | 2 DemographicTable-0.2.0/DemographicTable/R/0PACKAGE.R | 18 ++ DemographicTable-0.2.0/DemographicTable/R/DemographicTable.R | 61 ++++------ DemographicTable-0.2.0/DemographicTable/R/as_flextable.R | 39 ++++-- DemographicTable-0.2.0/DemographicTable/R/c.R | 8 - DemographicTable-0.2.0/DemographicTable/R/pval_shapiro.R | 4 DemographicTable-0.2.0/DemographicTable/R/sumstat.R | 4 DemographicTable-0.2.0/DemographicTable/build |only DemographicTable-0.2.0/DemographicTable/inst/doc |only DemographicTable-0.2.0/DemographicTable/inst/extR/xtable.R |only DemographicTable-0.2.0/DemographicTable/man/DemographicTable-package.Rd | 11 + DemographicTable-0.2.0/DemographicTable/man/DemographicTable.Rd | 28 ---- DemographicTable-0.2.0/DemographicTable/man/as_flextable.DemographicTable.Rd | 2 DemographicTable-0.2.0/DemographicTable/man/c.DemographicTable.Rd | 2 DemographicTable-0.2.0/DemographicTable/man/pval_shapiro.Rd | 4 DemographicTable-0.2.0/DemographicTable/man/sumstat.Rd | 4 DemographicTable-0.2.0/DemographicTable/vignettes |only 21 files changed, 126 insertions(+), 114 deletions(-)
More information about DemographicTable at CRAN
Permanent link
Title: Simple, Consistent Package Options
Description: Simple mechanisms for defining and interpreting package options. Provides
helpers for interpreting environment variables, global options, defining
default values and more.
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Diff between options versions 0.3.0 dated 2024-12-12 and 0.3.1 dated 2025-03-29
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 14 ++++++++++++++ R/define_option.R | 15 ++++++++------- R/envvars.R | 7 +++++-- README.md | 1 + inst/doc/envvars.html | 4 ++-- tests/testthat/test-envvars.R | 4 ++++ 8 files changed, 44 insertions(+), 21 deletions(-)
Title: Extensible Classes and Methods for Penalized-Regression-Based
Integration of Base Learners
Description: Extending the base classes and methods of EnsembleBase package for Penalized-Regression-based (Ridge and Lasso) integration of base learners. Default implementation uses cross-validation error to choose the optimal lambda (shrinkage parameter) for the final predictor. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. Users and developers can extend the package by extending the generic methods and classes provided in EnsembleBase package as well as this package.
Author: Mansour T.A. Sharabiani [aut],
Alireza S. Mahani [aut, cre]
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>
Diff between EnsemblePenReg versions 0.7 dated 2016-09-14 and 0.8 dated 2025-03-29
ChangeLog | 16 DESCRIPTION | 20 MD5 | 34 - NAMESPACE | 70 +-- R/aaa.R | 20 R/epenreg.R | 356 ++++++++-------- R/integrator.R | 270 ++++++------ man/Regression.Integrator.PenReg.SelMin.Config-class.Rd | 82 +-- man/Regression.Integrator.PenReg.SelMin.FitObj-class.Rd | 76 +-- man/Regression.Sweep.CV.Fit.Rd | 62 +- man/Regression.Sweep.CV.FitObj-class.Rd | 60 +- man/Regression.Sweep.PenReg.Config-class.Rd | 68 +-- man/Regression.Sweep.PenReg.FitObj-class.Rd | 72 +-- man/epenreg.Rd | 132 ++--- man/epenreg.baselearner.control.Rd | 92 ++-- man/epenreg.save.Rd | 116 ++--- man/plot.epenreg.Rd | 50 +- man/predict.epenreg.Rd | 54 +- 18 files changed, 831 insertions(+), 819 deletions(-)
More information about EnsemblePenReg at CRAN
Permanent link
Title: API Wrapper for the Natural Gas Transparency Platforms of Gas
Infrastructure Europe
Description: Providing access to the API for Gas Infrastructure Europe's
natural gas transparency platforms <https://agsi.gie.eu/> and <https://alsi.gie.eu/>. Lets the user
easily download metadata on companies and gas storage units covered by
the API as well as the respective data on regional, country, company
or facility level.
Author: Yannik Buhl [aut, cre]
Maintainer: Yannik Buhl <ybuhl@posteo.de>
Diff between gie versions 0.1.2 dated 2024-06-02 and 0.1.3 dated 2025-03-29
DESCRIPTION | 8 MD5 | 34 NAMESPACE | 1 R/gie_getumm.R |only R/utils.R | 1775 +++++++++++++++++++---------------- README.md | 4 man/getrequest_general.Rd | 86 - man/gie_getumm.Rd |only man/is_valid_date.Rd |only tests/fixtures/test1.1.yml | 348 ++++++ tests/fixtures/test1.13.yml |only tests/fixtures/test1.2.yml | 498 +++++++++ tests/fixtures/test1.3.yml | 696 +++++++++++++ tests/fixtures/test1.4.yml | 358 ++++++- tests/fixtures/test1.5.yml | 368 +++++++ tests/fixtures/test1.6.yml | 726 ++++++++++++++ tests/fixtures/test1.7.yml | 1074 ++++++++++++++++++++- tests/testthat/setup-giedata.R | 10 tests/testthat/test-datadownloads.R | 515 +++++----- tests/testthat/test-regular-errors.R | 234 ++-- 20 files changed, 5455 insertions(+), 1280 deletions(-)
Title: Density and Abundance from Distance-Sampling Surveys
Description: Distance-sampling (<doi:10.1007/978-3-319-19219-2>)
estimates density and abundance of survey targets (e.g., animals) when
detection probability declines with distance.
Distance-sampling is popular in ecology,
especially when survey targets are observed from aerial platforms (e.g.,
airplane or drone), surface vessels (e.g., boat or truck), or along
walking transects.
Distance-sampling includes line-transect studies that measure observation
distances as the closest approach of the sample route (transect) to the target
(i.e., perpendicular off-transect distance), and point-transect studies that
measure observation distances from stationary observers to
the target (i.e., radial distance).
The routines included here fit smooth (parametric) curves to
histograms of observation distances
and use those functions to compute effective sampling distances, density of
targets in the surveyed area, and abundance
of targets in a surrounding study area. Curve shapes include the
half-normal, haza [...truncated...]
Author: Trent McDonald [cre, aut],
Jason Carlisle [aut],
Aidan McDonald [aut] ,
Ryan Nielson [ctb] ,
Ben Augustine [ctb] ,
James Griswald [ctb] ,
Patrick McKann [ctb] ,
Lacey Jeroue [ctb] ,
Hoffman Abigail [ctb] ,
Kleinsausser Michael [ctb] ,
Joel Reynolds [ [...truncated...]
Maintainer: Trent McDonald <trent@mcdonalddatasciences.com>
Diff between Rdistance versions 3.1.4 dated 2025-03-11 and 4.0.3 dated 2025-03-29
Rdistance-3.1.4/Rdistance/R/F.double.obs.prob.r |only Rdistance-3.1.4/Rdistance/R/F.gx.estim.r |only Rdistance-3.1.4/Rdistance/R/F.maximize.g.r |only Rdistance-3.1.4/Rdistance/R/F.nLL.r |only Rdistance-3.1.4/Rdistance/R/F.start.limits.r |only Rdistance-3.1.4/Rdistance/R/Gamma.like.r |only Rdistance-3.1.4/Rdistance/R/Gamma.start.limits.R |only Rdistance-3.1.4/Rdistance/R/dfuncSmu.R |only Rdistance-3.1.4/Rdistance/R/getDfuncModelFrame.r |only Rdistance-3.1.4/Rdistance/R/integration.constant.R |only Rdistance-3.1.4/Rdistance/R/isUnitless.R |only Rdistance-3.1.4/Rdistance/R/logistic.like.R |only Rdistance-3.1.4/Rdistance/R/logistic.start.limits.R |only Rdistance-3.1.4/Rdistance/R/smu.like.r |only Rdistance-3.1.4/Rdistance/R/uniform.like.R |only Rdistance-3.1.4/Rdistance/R/uniform.start.limits.R |only Rdistance-3.1.4/Rdistance/build/vignette.rds |only Rdistance-3.1.4/Rdistance/inst |only Rdistance-3.1.4/Rdistance/man/F.double.obs.prob.Rd |only Rdistance-3.1.4/Rdistance/man/F.gx.estim.Rd |only Rdistance-3.1.4/Rdistance/man/F.maximize.g.Rd |only Rdistance-3.1.4/Rdistance/man/F.nLL.Rd |only Rdistance-3.1.4/Rdistance/man/F.start.limits.Rd |only Rdistance-3.1.4/Rdistance/man/Gamma.like.Rd |only Rdistance-3.1.4/Rdistance/man/Gamma.start.limits.Rd |only Rdistance-3.1.4/Rdistance/man/dfuncSmu.Rd |only Rdistance-3.1.4/Rdistance/man/figures |only Rdistance-3.1.4/Rdistance/man/getDfuncModelFrame.Rd |only Rdistance-3.1.4/Rdistance/man/integration.constant.Rd |only Rdistance-3.1.4/Rdistance/man/isUnitless.Rd |only Rdistance-3.1.4/Rdistance/man/logistic.like.Rd |only Rdistance-3.1.4/Rdistance/man/logistic.start.limits.Rd |only Rdistance-3.1.4/Rdistance/man/smu.like.Rd |only Rdistance-3.1.4/Rdistance/man/uniform.like.Rd |only Rdistance-3.1.4/Rdistance/man/uniform.start.limits.Rd |only Rdistance-3.1.4/Rdistance/vignettes |only Rdistance-4.0.3/Rdistance/DESCRIPTION | 49 Rdistance-4.0.3/Rdistance/MD5 | 258 ++-- Rdistance-4.0.3/Rdistance/NAMESPACE | 63 - Rdistance-4.0.3/Rdistance/NEWS.md | 42 Rdistance-4.0.3/Rdistance/R/AIC.dfunc.R | 36 Rdistance-4.0.3/Rdistance/R/EDR.R | 172 -- Rdistance-4.0.3/Rdistance/R/ESW.r | 161 +- Rdistance-4.0.3/Rdistance/R/RdistDf.R |only Rdistance-4.0.3/Rdistance/R/Rdistance-package.R | 62 - Rdistance-4.0.3/Rdistance/R/RdistanceControls.R | 140 -- Rdistance-4.0.3/Rdistance/R/abundEstim.R | 835 ++++---------- Rdistance-4.0.3/Rdistance/R/autoDistSamp.R | 359 ++---- Rdistance-4.0.3/Rdistance/R/bcCI.R |only Rdistance-4.0.3/Rdistance/R/checkNEvalPts.R |only Rdistance-4.0.3/Rdistance/R/checkUnits.R |only Rdistance-4.0.3/Rdistance/R/coef.dfunc.r | 46 Rdistance-4.0.3/Rdistance/R/colorize.R | 6 Rdistance-4.0.3/Rdistance/R/cosine.expansion.R | 36 Rdistance-4.0.3/Rdistance/R/dE.multi.R |only Rdistance-4.0.3/Rdistance/R/dE.single.R |only Rdistance-4.0.3/Rdistance/R/dfuncEstim.R | 879 +-------------- Rdistance-4.0.3/Rdistance/R/dfuncEstimErrMessage.R |only Rdistance-4.0.3/Rdistance/R/distances.R |only Rdistance-4.0.3/Rdistance/R/effectiveDistance.R | 57 Rdistance-4.0.3/Rdistance/R/effort.R |only Rdistance-4.0.3/Rdistance/R/errDataUnk.R |only Rdistance-4.0.3/Rdistance/R/estimateN.r | 327 +---- Rdistance-4.0.3/Rdistance/R/expansionTerms.R |only Rdistance-4.0.3/Rdistance/R/groupSizes.R |only Rdistance-4.0.3/Rdistance/R/gxEstim.r |only Rdistance-4.0.3/Rdistance/R/halfnorm.like.R | 288 +--- Rdistance-4.0.3/Rdistance/R/halfnorm.start.limits.R |only Rdistance-4.0.3/Rdistance/R/hazrate.like.R | 225 --- Rdistance-4.0.3/Rdistance/R/hazrate.start.limits.R |only Rdistance-4.0.3/Rdistance/R/hermite.expansion.R | 31 Rdistance-4.0.3/Rdistance/R/intercept.only.R |only Rdistance-4.0.3/Rdistance/R/is.RdistDf.R |only Rdistance-4.0.3/Rdistance/R/is.Unitless.R |only Rdistance-4.0.3/Rdistance/R/is.points.R |only Rdistance-4.0.3/Rdistance/R/is.smoothed.R |only Rdistance-4.0.3/Rdistance/R/lines.dfunc.R | 83 - Rdistance-4.0.3/Rdistance/R/maximize.g.r |only Rdistance-4.0.3/Rdistance/R/mlEstimates.R |only Rdistance-4.0.3/Rdistance/R/model.matrix.dfunc.R |only Rdistance-4.0.3/Rdistance/R/nCovars.R |only Rdistance-4.0.3/Rdistance/R/nLL.R |only Rdistance-4.0.3/Rdistance/R/negexp.like.R | 179 --- Rdistance-4.0.3/Rdistance/R/negexp.start.limits.R |only Rdistance-4.0.3/Rdistance/R/observationType.R |only Rdistance-4.0.3/Rdistance/R/oneBsIter.R |only Rdistance-4.0.3/Rdistance/R/parseModel.R |only Rdistance-4.0.3/Rdistance/R/perpDists.R | 2 Rdistance-4.0.3/Rdistance/R/plot.dfunc.para.R |only Rdistance-4.0.3/Rdistance/R/plot.dfunc.r | 477 -------- Rdistance-4.0.3/Rdistance/R/predDensity.R |only Rdistance-4.0.3/Rdistance/R/predDfuncs.R |only Rdistance-4.0.3/Rdistance/R/predLikelihood.R |only Rdistance-4.0.3/Rdistance/R/predict.dfunc.R | 478 +++----- Rdistance-4.0.3/Rdistance/R/print.abund.r | 31 Rdistance-4.0.3/Rdistance/R/print.dfunc.r | 54 Rdistance-4.0.3/Rdistance/R/secondDeriv.r | 6 Rdistance-4.0.3/Rdistance/R/simple.expansion.r | 24 Rdistance-4.0.3/Rdistance/R/sparrowDetectionData.R | 1 Rdistance-4.0.3/Rdistance/R/sparrowDf.R |only Rdistance-4.0.3/Rdistance/R/sparrowDfuncObserver.R |only Rdistance-4.0.3/Rdistance/R/sparrowSiteData.R | 1 Rdistance-4.0.3/Rdistance/R/startLimits.R |only Rdistance-4.0.3/Rdistance/R/summary.abund.R | 117 - Rdistance-4.0.3/Rdistance/R/summary.dfunc.R | 314 ++--- Rdistance-4.0.3/Rdistance/R/summary.rowwise_df.R |only Rdistance-4.0.3/Rdistance/R/thrasherDetectionData.R | 1 Rdistance-4.0.3/Rdistance/R/thrasherDf.R |only Rdistance-4.0.3/Rdistance/R/thrasherSiteData.R | 1 Rdistance-4.0.3/Rdistance/R/transectType.R |only Rdistance-4.0.3/Rdistance/R/unnest.R |only Rdistance-4.0.3/Rdistance/R/zzz.R | 69 + Rdistance-4.0.3/Rdistance/data/sparrowDf.rda |only Rdistance-4.0.3/Rdistance/data/sparrowDfuncObserver.rda |only Rdistance-4.0.3/Rdistance/data/thrasherDetectionData.rda |binary Rdistance-4.0.3/Rdistance/data/thrasherDf.rda |only Rdistance-4.0.3/Rdistance/data/thrasherSiteData.rda |binary Rdistance-4.0.3/Rdistance/man/AIC.dfunc.Rd | 28 Rdistance-4.0.3/Rdistance/man/EDR.Rd | 93 - Rdistance-4.0.3/Rdistance/man/ESW.Rd | 132 +- Rdistance-4.0.3/Rdistance/man/RdistDf.Rd |only Rdistance-4.0.3/Rdistance/man/Rdistance-package.Rd | 64 - Rdistance-4.0.3/Rdistance/man/RdistanceControls.Rd | 143 +- Rdistance-4.0.3/Rdistance/man/abundEstim.Rd | 358 ++---- Rdistance-4.0.3/Rdistance/man/autoDistSamp.Rd | 321 +++-- Rdistance-4.0.3/Rdistance/man/bcCI.Rd |only Rdistance-4.0.3/Rdistance/man/checkNEvalPts.Rd |only Rdistance-4.0.3/Rdistance/man/checkUnits.Rd |only Rdistance-4.0.3/Rdistance/man/coef.dfunc.Rd | 42 Rdistance-4.0.3/Rdistance/man/cosine.expansion.Rd | 22 Rdistance-4.0.3/Rdistance/man/dE.multi.Rd |only Rdistance-4.0.3/Rdistance/man/dE.single.Rd |only Rdistance-4.0.3/Rdistance/man/dfuncEstim.Rd | 451 ++----- Rdistance-4.0.3/Rdistance/man/dfuncEstimErrMessage.Rd |only Rdistance-4.0.3/Rdistance/man/distances.Rd |only Rdistance-4.0.3/Rdistance/man/effectiveDistance.Rd | 50 Rdistance-4.0.3/Rdistance/man/effort.Rd |only Rdistance-4.0.3/Rdistance/man/errDataUnk.Rd |only Rdistance-4.0.3/Rdistance/man/estimateN.Rd | 102 - Rdistance-4.0.3/Rdistance/man/expansionTerms.Rd |only Rdistance-4.0.3/Rdistance/man/groupSizes.Rd |only Rdistance-4.0.3/Rdistance/man/gxEstim.Rd |only Rdistance-4.0.3/Rdistance/man/halfnorm.like.Rd | 200 +-- Rdistance-4.0.3/Rdistance/man/halfnorm.start.limits.Rd |only Rdistance-4.0.3/Rdistance/man/hazrate.like.Rd | 168 +- Rdistance-4.0.3/Rdistance/man/hazrate.start.limits.Rd |only Rdistance-4.0.3/Rdistance/man/hermite.expansion.Rd | 8 Rdistance-4.0.3/Rdistance/man/intercept.only.Rd |only Rdistance-4.0.3/Rdistance/man/is.RdistDf.Rd |only Rdistance-4.0.3/Rdistance/man/is.Unitless.Rd |only Rdistance-4.0.3/Rdistance/man/is.points.Rd |only Rdistance-4.0.3/Rdistance/man/is.smoothed.Rd |only Rdistance-4.0.3/Rdistance/man/lines.dfunc.Rd | 83 - Rdistance-4.0.3/Rdistance/man/maximize.g.Rd |only Rdistance-4.0.3/Rdistance/man/mlEstimates.Rd |only Rdistance-4.0.3/Rdistance/man/model.matrix.dfunc.Rd |only Rdistance-4.0.3/Rdistance/man/nCovars.Rd |only Rdistance-4.0.3/Rdistance/man/nLL.Rd |only Rdistance-4.0.3/Rdistance/man/negexp.like.Rd | 133 -- Rdistance-4.0.3/Rdistance/man/negexp.start.limits.Rd |only Rdistance-4.0.3/Rdistance/man/observationType.Rd |only Rdistance-4.0.3/Rdistance/man/oneBsIter.Rd |only Rdistance-4.0.3/Rdistance/man/parseModel.Rd |only Rdistance-4.0.3/Rdistance/man/perpDists.Rd | 80 - Rdistance-4.0.3/Rdistance/man/plot.dfunc.Rd | 156 +- Rdistance-4.0.3/Rdistance/man/plot.dfunc.para.Rd |only Rdistance-4.0.3/Rdistance/man/predDensity.Rd |only Rdistance-4.0.3/Rdistance/man/predDfuncs.Rd |only Rdistance-4.0.3/Rdistance/man/predLikelihood.Rd |only Rdistance-4.0.3/Rdistance/man/predict.dfunc.Rd | 279 +++- Rdistance-4.0.3/Rdistance/man/print.abund.Rd | 23 Rdistance-4.0.3/Rdistance/man/print.dfunc.Rd | 15 Rdistance-4.0.3/Rdistance/man/simple.expansion.Rd | 18 Rdistance-4.0.3/Rdistance/man/sparrowDetectionData.Rd | 103 - Rdistance-4.0.3/Rdistance/man/sparrowDf.Rd |only Rdistance-4.0.3/Rdistance/man/sparrowDfuncObserver.Rd |only Rdistance-4.0.3/Rdistance/man/sparrowSiteData.Rd | 113 - Rdistance-4.0.3/Rdistance/man/startLimits.Rd |only Rdistance-4.0.3/Rdistance/man/summary.abund.Rd | 54 Rdistance-4.0.3/Rdistance/man/summary.dfunc.Rd | 37 Rdistance-4.0.3/Rdistance/man/summary.rowwise_df.Rd |only Rdistance-4.0.3/Rdistance/man/thrasherDetectionData.Rd | 91 - Rdistance-4.0.3/Rdistance/man/thrasherDf.Rd |only Rdistance-4.0.3/Rdistance/man/thrasherSiteData.Rd | 101 - Rdistance-4.0.3/Rdistance/man/transectType.Rd |only Rdistance-4.0.3/Rdistance/man/unnest.Rd |only 186 files changed, 3584 insertions(+), 5794 deletions(-)
Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis
Tests
Description: Compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 100 classes of statistical and machine learning models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference. Details can be found in Arel-Bundock, Greifer, and Heiss (2024) <doi:10.18637/jss.v111.i09>.
Author: Vincent Arel-Bundock [aut, cre, cph]
,
Noah Greifer [ctb] ,
Etienne Bacher [ctb] ,
Grant McDermott [ctb] ,
Andrew Heiss [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.25.0 dated 2025-02-01 and 0.25.1 dated 2025-03-29
DESCRIPTION | 51 ++++---- MD5 | 96 ++++++++-------- NEWS.md | 20 +++ R/backtransform.R | 5 R/bootstrap_boot.R | 2 R/bootstrap_simulation.R | 4 R/comparisons.R | 107 +++++++----------- R/complete_levels.R | 4 R/conformal.R | 187 ++++++++++++++++--------------- R/construct_call.R |only R/datagrid.R | 28 +--- R/get_dataset.R | 38 ++++-- R/get_vcov.R | 3 R/hypotheses.R | 68 ++++++----- R/hypothesis_formula.R | 12 +- R/imputation.R | 29 +++- R/inferences.R | 78 +++++++------ R/methods_betareg.R | 20 ++- R/methods_mlogit.R | 2 R/methods_tidymodels.R | 14 +- R/multcomp.R | 5 R/plot_comparisons.R | 10 - R/plot_predictions.R | 9 - R/plot_slopes.R | 5 R/predictions.R | 114 +++++++++---------- R/print.R | 2 R/recall.R | 3 R/sanitize_comparison.R | 4 R/sanitize_conf_level.R | 6 - R/sanitize_hypothesis_formula.R | 3 R/sanitize_newdata.R | 27 ++-- R/sanitize_reserved.R |only R/sanitize_variables.R | 23 --- R/sanity_dots.R | 9 - R/slopes.R | 236 +++++++++++++++++++++------------------- R/utils.R | 71 ++++++++---- R/zzz.R | 4 inst/WORDLIST | 1 inst/doc/model_to_meaning.R | 4 inst/doc/model_to_meaning.Rmd | 12 -- inst/doc/model_to_meaning.html | 12 -- man/comparisons.Rd | 8 - man/get_dataset.Rd | 2 man/get_predict.Rd | 2 man/hypotheses.Rd | 9 - man/inferences.Rd | 14 +- man/predictions.Rd | 3 man/sanitize_model_specific.Rd | 23 --- tests/tinytest.R | 8 - vignettes/model_to_meaning.Rmd | 12 -- 50 files changed, 737 insertions(+), 672 deletions(-)
More information about marginaleffects at CRAN
Permanent link
Title: Generates Multiple Data Sets
Description: Generate multiple data sets for educational purposes to demonstrate the importance of multiple regression. The genset function generates a data set from an initial data set to have the same summary statistics (mean, median, and standard deviation) but opposing regression results.
Author: Lori Murray [aut, cre]
Maintainer: Lori Murray <lori.murray@uwo.ca>
Diff between genset versions 0.1.0 dated 2020-09-16 and 0.1.1 dated 2025-03-29
genset-0.1.0/genset/man/genset.Rd |only genset-0.1.1/genset/DESCRIPTION | 21 genset-0.1.1/genset/MD5 | 18 genset-0.1.1/genset/NAMESPACE | 5 genset-0.1.1/genset/R/genset.R | 93 ---- genset-0.1.1/genset/build/vignette.rds |binary genset-0.1.1/genset/inst/doc/Introduction.R | 16 genset-0.1.1/genset/inst/doc/Introduction.Rmd | 34 + genset-0.1.1/genset/inst/doc/Introduction.html | 562 ++++++++++++++----------- genset-0.1.1/genset/man/Genset.Rd |only genset-0.1.1/genset/vignettes/Introduction.Rmd | 34 + 11 files changed, 407 insertions(+), 376 deletions(-)