Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is
a C++ library for translating between absolute and civil times using the rules
of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License,
is included in this package. See <https://github.com/google/cctz> for more
details.
Author: Dirk Eddelbuettel [aut, cre] ,
Bradley White [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.2.12 dated 2022-11-06 and 0.2.13 dated 2024-12-11
ChangeLog | 29 +++++++++++++++++++++++++++++ DESCRIPTION | 16 ++++++++++------ MD5 | 16 ++++++++-------- README.md | 2 +- inst/NEWS.Rd | 25 +++++++++++++++++++++---- src/Makevars | 4 ---- src/Makevars.ucrt | 3 --- src/Makevars.win | 4 ---- src/examples.cpp | 2 +- 9 files changed, 70 insertions(+), 31 deletions(-)
Title: Search and Retrieve Data from the BC Data Catalogue
Description: Search, query, and download tabular and
'geospatial' data from the British Columbia Data Catalogue
(<https://catalogue.data.gov.bc.ca/>). Search catalogue data records
based on keywords, data licence, sector, data format, and B.C.
government organization. View metadata directly in R, download many
data formats, and query 'geospatial' data available via the B.C.
government Web Feature Service ('WFS') using 'dplyr' syntax.
Author: Andy Teucher [aut, cre] ,
Sam Albers [aut, ctb] ,
Stephanie Hazlitt [aut, ctb] ,
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gmail.com>
Diff between bcdata versions 0.4.1 dated 2023-03-18 and 0.5.0 dated 2024-12-11
DESCRIPTION | 13 MD5 | 122 ++--- NEWS.md | 181 +++++-- R/bcdata-package.R | 7 R/bcdc-get-citation.R | 4 R/bcdc-web-services.R | 5 R/bcdc_options.R | 124 +++-- R/bcdc_search.R | 4 R/describe-feature.R | 6 R/utils-classes.R | 21 R/utils.R | 66 +- R/zzz.R | 2 README.md | 12 build/vignette.rds |binary inst/doc/bcdata.Rmd | 227 +++++---- inst/doc/bcdata.html | 228 +++++----- inst/doc/efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd | 181 ++++--- inst/doc/efficiently-query-spatial-data-in-the-bc-data-catalogue.html | 162 +++---- inst/doc/explore-silviculture-data-using-bcdata.Rmd | 68 +- inst/doc/explore-silviculture-data-using-bcdata.html | 69 +-- inst/doc/local-filter.Rmd | 41 - inst/doc/local-filter.html | 38 - man/bcdc_options.Rd | 48 +- man/bcdc_preview.Rd | 2 man/bcdc_query_geodata.Rd | 3 man/bcdc_search_facets.Rd | 6 man/filter.Rd | 2 tests/testthat.R | 25 - tests/testthat/helper-bcdata.R | 7 tests/testthat/test-bcdc-get-citation.R | 5 tests/testthat/test-browse.R | 2 tests/testthat/test-cql-string.R | 3 tests/testthat/test-describe-feature.R | 5 tests/testthat/test-edge-cases.R | 6 tests/testthat/test-geom-operators.R | 33 - tests/testthat/test-get-data.R | 201 ++++++-- tests/testthat/test-get_record.R | 76 ++- tests/testthat/test-options.R | 24 - tests/testthat/test-print-methods.R | 6 tests/testthat/test-query-geodata-base-methods.R | 7 tests/testthat/test-query-geodata-collect.R | 83 ++- tests/testthat/test-query-geodata-filter.R | 36 - tests/testthat/test-query-geodata-mutate.R | 2 tests/testthat/test-query-geodata-select.R | 18 tests/testthat/test-query-geodata.R | 16 tests/testthat/test-search.R | 21 tests/testthat/test-utils.R | 9 vignettes/bcdata.Rmd | 227 +++++---- vignettes/bcdata.Rmd.orig | 2 vignettes/efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd | 181 ++++--- vignettes/efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd.orig | 2 vignettes/explore-silviculture-data-using-bcdata.Rmd | 68 +- vignettes/local-filter.Rmd | 41 - vignettes/vignette-fig-air_zones-1.png |binary vignettes/vignette-fig-bbox-1.png |binary vignettes/vignette-fig-district_parks-1.png |binary vignettes/vignette-fig-dp_join-1.png |binary vignettes/vignette-fig-map-larch-plantations-dpg-1.png |binary vignettes/vignette-fig-plot-dpg-1.png |binary vignettes/vignette-fig-regional_districts-1.png |binary vignettes/vignette-fig-unnamed-chunk-1-1.png |binary vignettes/vignette-fig-unnamed-chunk-3-1.png |binary 62 files changed, 1550 insertions(+), 1198 deletions(-)
Title: Exposes the 'Uber' 'H3' Library to R Packages
Description: 'H3' is a hexagonal hierarchical spatial index developed by 'Uber' <https://h3geo.org/>.
This package exposes the source code of 'H3' (written in 'C') to routines that are callable through 'R'.
Author: David Cooley [aut, cre],
Ray Shao [ctb]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between h3lib versions 0.1.3 dated 2024-01-30 and 0.1.4 dated 2024-12-11
DESCRIPTION | 8 +- MD5 | 42 ++++++----- NEWS.md | 4 + inst/include/h3libapi.h | 1 src/algos.c | 19 +++-- src/bbox.c | 138 +++++++++++++++++++++++++++++++++++++ src/bbox.h | 10 ++ src/constants.h | 29 +++++-- src/coordijk.c | 56 +++++++-------- src/faceijk.c | 19 ++--- src/h3Index.c | 132 +++++++++++++++++++++++------------- src/h3Index.h | 27 +++---- src/h3api.h | 33 +++++++-- src/iterators.c | 26 ++++--- src/iterators.h | 1 src/latLng.c | 41 ++++++++--- src/latLng.h | 8 ++ src/localij.c | 16 +--- src/mathExtensions.h | 19 ++++- src/polyfill.c |only src/polyfill.h |only src/polygon.c | 175 ++++++++++++++++++++++++++++++++++++++++++++++++ src/polygon.h | 29 +++++++ 23 files changed, 651 insertions(+), 182 deletions(-)
Title: Miscellaneous Functions for Passive Acoustic Analysis
Description: A collection of miscellaneous functions for passive acoustics.
Much of the content here is adapted to R from code written by other people.
If you have any ideas of functions to add, please contact Taiki Sakai.
Author: Taiki Sakai [aut, cre],
Jay Barlow [ctb],
Julie Oswald [ctb],
Val Schmidt [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMmisc versions 1.12.1 dated 2024-06-10 and 1.12.3 dated 2024-12-11
DESCRIPTION | 15 ++++----- MD5 | 46 +++++++++++++++++------------ NAMESPACE | 11 ++++++ NEWS.md | 18 ++++++++++- R/PAMmisc-package.R |only R/decimateWavFiles.R | 8 +---- R/erddapToEdinfo.R | 49 ++++++++++++++++++++++++++++--- R/fastReadWave.R |only R/matchEnvData.R | 24 +++++++++++---- R/ncToData.R | 7 +++- R/ncUtils.R | 14 +++++--- R/peakTrough.R | 1 R/plotPresBar.R | 2 - R/plotPresGrid.R | 24 ++++++++++----- R/pwelch.R |only R/soundtrapQAQC.R | 74 +++++++++++++++++++++++++++++++++-------------- R/writeAMWave.R | 2 - R/writeClickWave.R | 2 - inst/extdata/testWav.wav |only man/decimateWavFiles.Rd | 8 +---- man/fastReadWave.Rd |only man/plotPresBar.Rd | 2 - man/pwelch.Rd |only man/soundtrapQAQC.Rd | 3 + man/writeAMWave.Rd | 2 - man/writeClickWave.Rd | 2 - src |only 27 files changed, 222 insertions(+), 92 deletions(-)
Title: Design on-Farm Precision Field Agronomic Trials
Description: A comprehensive system for designing and implementing on-farm precision field agronomic trials. You provide field data, tell 'ofpetrial' how to design a trial, and get readily-usable trial design files and a report checks the validity and reliability of the trial design.
Author: Taro Mieno [aut, cre, cph] ,
Brittani Edge [aut, ctb]
Maintainer: Taro Mieno <tmieno2@unl.edu>
Diff between ofpetrial versions 0.1.1 dated 2024-05-15 and 0.1.2 dated 2024-12-11
DESCRIPTION | 13 - MD5 | 45 +-- NAMESPACE | 1 NEWS.md | 5 R/assign_rates.R | 348 ++++++++++++++++++--------- R/diagnose.R | 4 R/make_exp_plots.R | 11 R/make_trial_report.R | 226 ++++++++++-------- R/prepare_plot_info.R | 76 +++--- R/prepare_rate_info.R | 152 ++++++++---- R/utility.R | 6 R/utility_spatial.R | 51 +--- README.md | 39 ++- build/vignette.rds |binary data/exp_data.rda |binary data/rate_info.rda |binary data/td_curved.rda |binary data/td_single_input.rda |binary data/td_two_input.rda |binary inst/doc/basic-work-flow.html | 389 +++++++++++++++---------------- man/assign_rates_conditional.Rd |only man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/ofpetrial-package.Rd | 4 24 files changed, 814 insertions(+), 556 deletions(-)
Title: Robust Score Testing in GLMs, by Sign-Flip Contributions
Description: Provides robust tests for testing in GLMs, by sign-flipping score contributions. The tests are robust against overdispersion, heteroscedasticity and, in some cases, ignored nuisance variables. See Hemerik, Goeman and Finos (2020) <doi:10.1111/rssb.12369>.
Author: Livio Finos [cre, aut] ,
Jelle J. Goeman [ctb],
Jesse Hemerik [ctb],
Riccardo De Santis [ctb]
Maintainer: Livio Finos <livio.finos@unipd.it>
Diff between flipscores versions 1.3.1 dated 2024-11-22 and 1.3.2 dated 2024-12-11
DESCRIPTION | 8 +- MD5 | 14 ++-- R/compute_flips.R | 22 +++--- R/compute_scores.R | 77 +++++++++++----------- R/flipscores.R | 109 ++++++++++++++++--------------- R/utiliy_score_functions.R | 71 ++++++++++---------- man/compute_scores.Rd | 4 - man/flipscores.Rd | 156 ++++++++++++++++++++++----------------------- 8 files changed, 235 insertions(+), 226 deletions(-)
Title: 2D and 3D Movement-Based Kernel Density Estimates (MKDEs)
Description: Provides functions to compute and visualize movement-based kernel density estimates (MKDEs) for animal utilization distributions in 2 or 3 spatial dimensions.
Author: Jeff A. Tracey [aut],
James Sheppard [aut],
Jun Zhu [aut],
Amit Chourasia [aut],
Glenn Lockwood [aut],
Matthew Wang [aut],
Robert N. Fisher [aut],
Robert Sinkovits [aut, cre]
Maintainer: Robert Sinkovits <sinkovit@sdsc.edu>
Diff between mkde versions 0.3 dated 2024-07-02 and 0.4 dated 2024-12-11
mkde-0.3/mkde/man/mkdeToRaster.Rd |only mkde-0.3/mkde/man/readdem_example.Rd |only mkde-0.4/mkde/DESCRIPTION | 44 ++++++++++++++++++++++++++++++----- mkde-0.4/mkde/MD5 | 13 ++++++---- mkde-0.4/mkde/NAMESPACE | 3 -- mkde-0.4/mkde/R/mkdeFunctions.R | 19 ++++----------- mkde-0.4/mkde/man/condordem.Rd |only mkde-0.4/mkde/man/condordem120.Rd |only mkde-0.4/mkde/man/dugongdem.Rd |only mkde-0.4/mkde/man/mkdeToTerra.Rd |only mkde-0.4/mkde/man/pandadem.Rd |only 11 files changed, 53 insertions(+), 26 deletions(-)
Title: Markov Chain Monte Carlo Small Area Estimation
Description: Fit multi-level models with possibly correlated
random effects using Markov Chain Monte Carlo simulation.
Such models allow smoothing over space and time and are useful in,
for example, small area estimation.
Author: Harm Jan Boonstra [aut, cre],
Grzegorz Baltissen [ctb]
Maintainer: Harm Jan Boonstra <hjboonstra@gmail.com>
Diff between mcmcsae versions 0.7.7 dated 2024-02-26 and 0.7.8 dated 2024-12-11
mcmcsae-0.7.7/mcmcsae/man/compute_GMRF_matrices.Rd |only mcmcsae-0.7.7/mcmcsae/man/nchains-ndraws-nvars.Rd |only mcmcsae-0.7.7/mcmcsae/tests/testthat/test_linalg_closures.R |only mcmcsae-0.7.8/mcmcsae/DESCRIPTION | 27 mcmcsae-0.7.8/mcmcsae/MD5 | 180 +- mcmcsae-0.7.8/mcmcsae/NAMESPACE | 15 mcmcsae-0.7.8/mcmcsae/NEWS | 19 mcmcsae-0.7.8/mcmcsae/R/AR1_sampler.R |only mcmcsae-0.7.8/mcmcsae/R/GMRF_extension.R |only mcmcsae-0.7.8/mcmcsae/R/MCMCsim.R | 170 +- mcmcsae-0.7.8/mcmcsae/R/MH.R | 169 +- mcmcsae-0.7.8/mcmcsae/R/MatrixUtils.R | 114 - mcmcsae-0.7.8/mcmcsae/R/RcppExports.R | 4 mcmcsae-0.7.8/mcmcsae/R/TMVN_methods.R | 30 mcmcsae-0.7.8/mcmcsae/R/TMVN_sampler.R | 979 +++++------- mcmcsae-0.7.8/mcmcsae/R/aux_closures.R | 463 ++--- mcmcsae-0.7.8/mcmcsae/R/cMVN_sampler.R | 184 +- mcmcsae-0.7.8/mcmcsae/R/cholesky.R | 80 mcmcsae-0.7.8/mcmcsae/R/conjugate_gradients.R | 40 mcmcsae-0.7.8/mcmcsae/R/f_gamma.R |only mcmcsae-0.7.8/mcmcsae/R/f_poisson.R |only mcmcsae-0.7.8/mcmcsae/R/family.R | 294 --- mcmcsae-0.7.8/mcmcsae/R/formulas.R | 106 - mcmcsae-0.7.8/mcmcsae/R/kronprod.R | 64 mcmcsae-0.7.8/mcmcsae/R/mc_bart.R | 63 mcmcsae-0.7.8/mcmcsae/R/mc_block.R | 110 - mcmcsae-0.7.8/mcmcsae/R/mc_gen.R | 448 +++-- mcmcsae-0.7.8/mcmcsae/R/mc_gl.R | 22 mcmcsae-0.7.8/mcmcsae/R/mc_mec.R | 104 - mcmcsae-0.7.8/mcmcsae/R/mc_offset.R |only mcmcsae-0.7.8/mcmcsae/R/mc_reg.R | 135 - mcmcsae-0.7.8/mcmcsae/R/mc_vfac.R | 9 mcmcsae-0.7.8/mcmcsae/R/mc_vreg.R | 9 mcmcsae-0.7.8/mcmcsae/R/mcmcsae.R | 21 mcmcsae-0.7.8/mcmcsae/R/model_eval.R | 80 mcmcsae-0.7.8/mcmcsae/R/modelmatrix.R | 54 mcmcsae-0.7.8/mcmcsae/R/models.R | 529 ++++-- mcmcsae-0.7.8/mcmcsae/R/opts.R | 4 mcmcsae-0.7.8/mcmcsae/R/parallel.R | 29 mcmcsae-0.7.8/mcmcsae/R/plots.R | 27 mcmcsae-0.7.8/mcmcsae/R/prediction.R | 35 mcmcsae-0.7.8/mcmcsae/R/priors.R | 93 + mcmcsae-0.7.8/mcmcsae/R/projection.R |only mcmcsae-0.7.8/mcmcsae/R/random.R | 4 mcmcsae-0.7.8/mcmcsae/R/samplers.R | 290 +-- mcmcsae-0.7.8/mcmcsae/R/sbc.R | 10 mcmcsae-0.7.8/mcmcsae/R/sparse_template.R | 93 - mcmcsae-0.7.8/mcmcsae/R/tabMatrix.R | 11 mcmcsae-0.7.8/mcmcsae/R/utils.R | 20 mcmcsae-0.7.8/mcmcsae/build/vignette.rds |binary mcmcsae-0.7.8/mcmcsae/inst/doc/area_level.html | 73 mcmcsae-0.7.8/mcmcsae/inst/doc/linear_weighting.html | 51 mcmcsae-0.7.8/mcmcsae/inst/doc/unit_level.html | 325 +-- mcmcsae-0.7.8/mcmcsae/man/GMRF_structure.Rd |only mcmcsae-0.7.8/mcmcsae/man/SBC_test.Rd | 8 mcmcsae-0.7.8/mcmcsae/man/TMVN-methods.Rd | 28 mcmcsae-0.7.8/mcmcsae/man/brt.Rd | 2 mcmcsae-0.7.8/mcmcsae/man/correlation.Rd | 72 mcmcsae-0.7.8/mcmcsae/man/create_TMVN_sampler.Rd | 12 mcmcsae-0.7.8/mcmcsae/man/create_block_cMVN_sampler.Rd |only mcmcsae-0.7.8/mcmcsae/man/create_cMVN_sampler.Rd | 29 mcmcsae-0.7.8/mcmcsae/man/create_sampler.Rd | 9 mcmcsae-0.7.8/mcmcsae/man/gen.Rd | 30 mcmcsae-0.7.8/mcmcsae/man/gen_control.Rd | 4 mcmcsae-0.7.8/mcmcsae/man/generate_data.Rd | 3 mcmcsae-0.7.8/mcmcsae/man/mc_offset.Rd |only mcmcsae-0.7.8/mcmcsae/man/mcmcsae-family.Rd | 60 mcmcsae-0.7.8/mcmcsae/man/model_matrix.Rd | 5 mcmcsae-0.7.8/mcmcsae/man/n_chains-n_draws-n_vars.Rd |only mcmcsae-0.7.8/mcmcsae/man/plot_coef.Rd | 4 mcmcsae-0.7.8/mcmcsae/man/pr_beta.Rd |only mcmcsae-0.7.8/mcmcsae/man/pr_truncnormal.Rd |only mcmcsae-0.7.8/mcmcsae/man/pr_unif.Rd |only mcmcsae-0.7.8/mcmcsae/man/residuals-fitted-values.Rd | 8 mcmcsae-0.7.8/mcmcsae/man/sampler_control.Rd | 2 mcmcsae-0.7.8/mcmcsae/man/set_MH.Rd |only mcmcsae-0.7.8/mcmcsae/man/sim_marg_var.Rd |only mcmcsae-0.7.8/mcmcsae/man/subset.dc.Rd | 10 mcmcsae-0.7.8/mcmcsae/src/RcppExports.cpp | 13 mcmcsae-0.7.8/mcmcsae/src/TN.cpp | 2 mcmcsae-0.7.8/mcmcsae/src/mcmcsae_init.c | 5 mcmcsae-0.7.8/mcmcsae/src/speed_ups.cpp | 28 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_AR1.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_Cholesky.R | 16 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_GMRF_extensions.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_GMRF_matrices.R | 16 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_Poisson.R | 34 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_TMVN.R | 107 + mcmcsae-0.7.8/mcmcsae/tests/testthat/test_bart.R | 10 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_cMVNsampler.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_checks.R | 7 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_gammareg.R | 15 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_gen.R | 22 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_grouplevel.R | 6 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_linalg.R | 26 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_linreg.R | 23 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_mat_sum.R | 76 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_modelmatrix.R | 11 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_offset.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_output.R | 2 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_predict.R | 14 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_sim.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_spatial.R |only 103 files changed, 3379 insertions(+), 2927 deletions(-)
Title: Causal Modeling in Epidemiology
Description: Create causal models for use in epidemiological studies,
including sufficient-component cause models as introduced by
Rothman (1976) <doi:10.1093/oxfordjournals.aje.a112335>.
Author: Felix Forster [aut, cre, cph]
Maintainer: Felix Forster <felix.forster@med.uni-muenchen.de>
Diff between epicmodel versions 0.1.1 dated 2024-11-08 and 0.2.0 dated 2024-12-11
epicmodel-0.1.1/epicmodel/R/server_utils.R |only epicmodel-0.2.0/epicmodel/DESCRIPTION | 13 - epicmodel-0.2.0/epicmodel/MD5 | 93 +++---- epicmodel-0.2.0/epicmodel/NAMESPACE | 3 epicmodel-0.2.0/epicmodel/NEWS.md | 12 epicmodel-0.2.0/epicmodel/R/check_steplist.R | 2 epicmodel-0.2.0/epicmodel/R/create_scc.R | 78 +++++- epicmodel-0.2.0/epicmodel/R/intervention.R | 26 +- epicmodel-0.2.0/epicmodel/R/launch_steplist_creator.R | 2 epicmodel-0.2.0/epicmodel/R/mechanism.R | 2 epicmodel-0.2.0/epicmodel/R/prevent.R |only epicmodel-0.2.0/epicmodel/R/process_steplist.R | 2 epicmodel-0.2.0/epicmodel/R/process_steplist_user.R | 7 epicmodel-0.2.0/epicmodel/R/scc_utils.R | 10 epicmodel-0.2.0/epicmodel/README.md | 13 - epicmodel-0.2.0/epicmodel/build/partial.rdb |binary epicmodel-0.2.0/epicmodel/build/vignette.rds |binary epicmodel-0.2.0/epicmodel/inst/CITATION | 2 epicmodel-0.2.0/epicmodel/inst/doc/epicmodel.R | 17 - epicmodel-0.2.0/epicmodel/inst/doc/epicmodel.Rmd | 22 + epicmodel-0.2.0/epicmodel/inst/doc/epicmodel.html | 127 ++++++---- epicmodel-0.2.0/epicmodel/inst/doc/glossary.Rmd | 5 epicmodel-0.2.0/epicmodel/inst/doc/glossary.html | 14 - epicmodel-0.2.0/epicmodel/inst/doc/modules.R | 7 epicmodel-0.2.0/epicmodel/inst/doc/modules.Rmd | 1 epicmodel-0.2.0/epicmodel/inst/doc/modules.html | 3 epicmodel-0.2.0/epicmodel/inst/doc/scc.R | 12 epicmodel-0.2.0/epicmodel/inst/doc/scc.Rmd | 14 - epicmodel-0.2.0/epicmodel/inst/doc/scc.html | 16 - epicmodel-0.2.0/epicmodel/inst/doc/steplist.R | 124 ++++----- epicmodel-0.2.0/epicmodel/inst/doc/steplist.Rmd | 2 epicmodel-0.2.0/epicmodel/inst/doc/steplist.html | 2 epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/R/icc.R | 2 epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/R/server_utils.R |only epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/R/ui_utils.R | 92 ++++--- epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/R/upload.R | 2 epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/server.R | 93 +++++-- epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/ui.R | 3 epicmodel-0.2.0/epicmodel/man/mechanism.Rd | 2 epicmodel-0.2.0/epicmodel/man/necessary_causes.Rd |only epicmodel-0.2.0/epicmodel/man/prevent.Rd |only epicmodel-0.2.0/epicmodel/man/uncheck_steplist.Rd |only epicmodel-0.2.0/epicmodel/tests/testthat/test-create_scc.R | 28 ++ epicmodel-0.2.0/epicmodel/tests/testthat/test-intervention.R | 13 + epicmodel-0.2.0/epicmodel/tests/testthat/test-prevent.R |only epicmodel-0.2.0/epicmodel/tests/testthat/test-server_utils.R | 2 epicmodel-0.2.0/epicmodel/vignettes/epicmodel.Rmd | 22 + epicmodel-0.2.0/epicmodel/vignettes/glossary.Rmd | 5 epicmodel-0.2.0/epicmodel/vignettes/modules.Rmd | 1 epicmodel-0.2.0/epicmodel/vignettes/scc.Rmd | 14 - epicmodel-0.2.0/epicmodel/vignettes/steplist.Rmd | 2 51 files changed, 618 insertions(+), 294 deletions(-)
Title: Effect Plots
Description: High-performance implementation of various effect plots
useful for regression and probabilistic classification tasks. The
package includes partial dependence plots (Friedman, 2021,
<doi:10.1214/aos/1013203451>), accumulated local effect plots and
M-plots (both from Apley and Zhu, 2016, <doi:10.1111/rssb.12377>), as
well as plots that describe the statistical associations between model
response and features. It supports visualizations with either
'ggplot2' or 'plotly', and is compatible with most models, including
'Tidymodels', models wrapped in 'DALEX' explainers, or models with
case weights.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between effectplots versions 0.1.0 dated 2024-11-18 and 0.2.0 dated 2024-12-11
effectplots-0.1.0/effectplots/src/clamp2.cpp |only effectplots-0.2.0/effectplots/DESCRIPTION | 7 effectplots-0.2.0/effectplots/MD5 | 86 - effectplots-0.2.0/effectplots/NAMESPACE | 4 effectplots-0.2.0/effectplots/NEWS.md | 47 effectplots-0.2.0/effectplots/R/RcppExports.R | 31 effectplots-0.2.0/effectplots/R/ale.R | 131 + effectplots-0.2.0/effectplots/R/average_observed.R | 25 effectplots-0.2.0/effectplots/R/average_predicted.R | 13 effectplots-0.2.0/effectplots/R/bias.R | 9 effectplots-0.2.0/effectplots/R/crunch.R | 197 +- effectplots-0.2.0/effectplots/R/feature_effects.R | 262 ++- effectplots-0.2.0/effectplots/R/importance.R | 10 effectplots-0.2.0/effectplots/R/input.R | 7 effectplots-0.2.0/effectplots/R/partial_dependence.R | 71 effectplots-0.2.0/effectplots/R/plot.R | 144 +- effectplots-0.2.0/effectplots/R/update.R | 79 - effectplots-0.2.0/effectplots/R/utils.R | 70 effectplots-0.2.0/effectplots/README.md | 107 + effectplots-0.2.0/effectplots/man/ale.Rd | 120 + effectplots-0.2.0/effectplots/man/average_observed.Rd | 65 effectplots-0.2.0/effectplots/man/average_predicted.Rd | 168 +- effectplots-0.2.0/effectplots/man/bias.Rd | 155 +- effectplots-0.2.0/effectplots/man/dot-ale.Rd | 155 +- effectplots-0.2.0/effectplots/man/dot-pd.Rd | 126 - effectplots-0.2.0/effectplots/man/effect_importance.Rd | 80 - effectplots-0.2.0/effectplots/man/fcut.Rd |only effectplots-0.2.0/effectplots/man/feature_effects.Rd | 470 +++--- effectplots-0.2.0/effectplots/man/figures/avg_obs.svg | 594 ++++---- effectplots-0.2.0/effectplots/man/figures/bias.svg | 716 +++++----- effectplots-0.2.0/effectplots/man/figures/classification.svg |only effectplots-0.2.0/effectplots/man/figures/dalex.svg | 450 +++--- effectplots-0.2.0/effectplots/man/figures/feature_effects.svg | 469 +++--- effectplots-0.2.0/effectplots/man/figures/tidymodels.svg |only effectplots-0.2.0/effectplots/man/figures/train_test.svg | 472 +++--- effectplots-0.2.0/effectplots/man/partial_dependence.Rd | 98 - effectplots-0.2.0/effectplots/man/plot.EffectData.Rd | 262 +-- effectplots-0.2.0/effectplots/man/update.EffectData.Rd | 144 +- effectplots-0.2.0/effectplots/src/RcppExports.cpp | 25 effectplots-0.2.0/effectplots/src/findInterval_equi.cpp | 57 effectplots-0.2.0/effectplots/tests/testthat/test-ale.R | 1 effectplots-0.2.0/effectplots/tests/testthat/test-bias.R | 4 effectplots-0.2.0/effectplots/tests/testthat/test-crunch.R | 244 ++- effectplots-0.2.0/effectplots/tests/testthat/test-feature_effects.R | 20 effectplots-0.2.0/effectplots/tests/testthat/test-partial_dependence.R | 40 effectplots-0.2.0/effectplots/tests/testthat/test-update.R |only effectplots-0.2.0/effectplots/tests/testthat/test-utils.R |only 47 files changed, 3584 insertions(+), 2651 deletions(-)
Title: High-Level Functions for Tabulating, Charting and Reporting
Survey Data
Description: Craft polished tables and plots in Markdown reports.
Simply choose whether to treat your data as counts or metrics,
and the package will automatically generate well-designed default tables and plots for you.
Boiled down to the basics, with labeling features and simple interactive reports.
All functions are 'tidyverse' compatible.
Author: Jakob Juenger [aut, cre, cph] ,
Henrieke Kotthoff [aut, ctb],
Chantal Gaertner [ctb]
Maintainer: Jakob Juenger <jakob.juenger@uni-muenster.de>
Diff between volker versions 2.1.0 dated 2024-09-10 and 3.0.0 dated 2024-12-11
volker-2.1.0/volker/man/idx_alpha.Rd |only volker-3.0.0/volker/DESCRIPTION | 8 volker-3.0.0/volker/LICENSE | 4 volker-3.0.0/volker/MD5 | 443 volker-3.0.0/volker/NAMESPACE | 187 volker-3.0.0/volker/NEWS.md | 66 volker-3.0.0/volker/R/checks.R | 198 volker-3.0.0/volker/R/clean.R | 757 - volker-3.0.0/volker/R/cluster.R |only volker-3.0.0/volker/R/config.R | 241 volker-3.0.0/volker/R/data.R | 42 volker-3.0.0/volker/R/effects.R | 2516 ++--- volker-3.0.0/volker/R/factor.R |only volker-3.0.0/volker/R/idx.R | 223 volker-3.0.0/volker/R/import-standalone-purrr.R | 488 volker-3.0.0/volker/R/imports.R | 204 volker-3.0.0/volker/R/labels.R | 1876 +-- volker-3.0.0/volker/R/plots.R | 4898 +++++----- volker-3.0.0/volker/R/report.R | 1110 +- volker-3.0.0/volker/R/skim.R | 222 volker-3.0.0/volker/R/tables.R | 3814 +++---- volker-3.0.0/volker/R/utils.R | 158 volker-3.0.0/volker/R/volker-package.R | 16 volker-3.0.0/volker/README.md | 43 volker-3.0.0/volker/inst/doc/introduction.R | 39 volker-3.0.0/volker/inst/doc/introduction.Rmd | 801 - volker-3.0.0/volker/inst/doc/introduction.html | 2300 ++++ volker-3.0.0/volker/inst/extdata/header.tex | 14 volker-3.0.0/volker/inst/extdata/styles.css | 96 volker-3.0.0/volker/inst/rmarkdown/templates/volker-report/skeleton/skeleton.Rmd | 100 volker-3.0.0/volker/inst/rmarkdown/templates/volker-report/template.yaml | 8 volker-3.0.0/volker/man/VLKR_FIG_SETTINGS.Rd | 36 volker-3.0.0/volker/man/VLKR_FILLDISCRETE.Rd | 32 volker-3.0.0/volker/man/VLKR_FILLGRADIENT.Rd | 32 volker-3.0.0/volker/man/VLKR_FILLPOLARIZED.Rd | 32 volker-3.0.0/volker/man/VLKR_NA_LEVELS.Rd | 32 volker-3.0.0/volker/man/VLKR_NA_NUMBERS.Rd | 32 volker-3.0.0/volker/man/VLKR_NORMAL_DIGITS.Rd | 32 volker-3.0.0/volker/man/VLKR_PLOT_LABELWRAP.Rd | 36 volker-3.0.0/volker/man/VLKR_POINT_ALPHA.Rd | 32 volker-3.0.0/volker/man/VLKR_POINT_MEAN_SHAPE.Rd | 32 volker-3.0.0/volker/man/VLKR_POINT_SIZE.Rd | 32 volker-3.0.0/volker/man/VLKR_WRAP_SEPARATOR.Rd | 32 volker-3.0.0/volker/man/add_clusters.Rd |only volker-3.0.0/volker/man/add_factors.Rd |only volker-3.0.0/volker/man/add_index.Rd |only volker-3.0.0/volker/man/cfg_get_na_numbers.Rd | 46 volker-3.0.0/volker/man/chatgpt.Rd | 72 volker-3.0.0/volker/man/check_has_column.Rd | 44 volker-3.0.0/volker/man/check_is_dataframe.Rd | 44 volker-3.0.0/volker/man/check_is_param.Rd | 48 volker-3.0.0/volker/man/cluster_plot.Rd |only volker-3.0.0/volker/man/cluster_tab.Rd |only volker-3.0.0/volker/man/codebook.Rd | 60 volker-3.0.0/volker/man/data_clean.Rd | 62 volker-3.0.0/volker/man/data_clean_sosci.Rd | 84 volker-3.0.0/volker/man/data_prepare.Rd | 60 volker-3.0.0/volker/man/data_rev.Rd |only volker-3.0.0/volker/man/data_rm_missings.Rd | 40 volker-3.0.0/volker/man/data_rm_na_levels.Rd | 46 volker-3.0.0/volker/man/data_rm_na_numbers.Rd | 48 volker-3.0.0/volker/man/data_rm_negatives.Rd | 40 volker-3.0.0/volker/man/data_rm_zeros.Rd | 40 volker-3.0.0/volker/man/dot-add_to_vlkr_rprt.Rd | 44 volker-3.0.0/volker/man/dot-attr_insert.Rd | 48 volker-3.0.0/volker/man/dot-attr_transfer.Rd | 44 volker-3.0.0/volker/man/dot-density_mode.Rd | 40 volker-3.0.0/volker/man/dot-effect_correlations.Rd | 54 volker-3.0.0/volker/man/dot-effect_npmi.Rd | 62 volker-3.0.0/volker/man/dot-factor_with_attr.Rd | 40 volker-3.0.0/volker/man/dot-get_fig_settings.Rd | 30 volker-3.0.0/volker/man/dot-iqr.Rd | 36 volker-3.0.0/volker/man/dot-knit_plot.Rd | 64 volker-3.0.0/volker/man/dot-knit_prepare.Rd | 40 volker-3.0.0/volker/man/dot-knit_table.Rd | 36 volker-3.0.0/volker/man/dot-outliers.Rd | 36 volker-3.0.0/volker/man/dot-plot_bars.Rd | 80 volker-3.0.0/volker/man/dot-plot_cor.Rd | 72 volker-3.0.0/volker/man/dot-plot_lines.Rd | 52 volker-3.0.0/volker/man/dot-plot_scree.Rd |only volker-3.0.0/volker/man/dot-plot_summary.Rd | 72 volker-3.0.0/volker/man/dot-report_cls.Rd |only volker-3.0.0/volker/man/dot-report_fct.Rd |only volker-3.0.0/volker/man/dot-report_idx.Rd | 80 volker-3.0.0/volker/man/dot-tab_split.Rd | 48 volker-3.0.0/volker/man/dot-to_vlkr_df.Rd | 36 volker-3.0.0/volker/man/dot-to_vlkr_list.Rd | 42 volker-3.0.0/volker/man/dot-to_vlkr_plot.Rd | 72 volker-3.0.0/volker/man/dot-to_vlkr_rprt.Rd | 40 volker-3.0.0/volker/man/dot-to_vlkr_tab.Rd | 48 volker-3.0.0/volker/man/dot-whisker_lower.Rd | 36 volker-3.0.0/volker/man/dot-whisker_upper.Rd | 36 volker-3.0.0/volker/man/effect_counts.Rd | 118 volker-3.0.0/volker/man/effect_counts_items.Rd | 68 volker-3.0.0/volker/man/effect_counts_items_cor.Rd | 52 volker-3.0.0/volker/man/effect_counts_items_cor_items.Rd | 52 volker-3.0.0/volker/man/effect_counts_items_grouped.Rd | 52 volker-3.0.0/volker/man/effect_counts_items_grouped_items.Rd | 52 volker-3.0.0/volker/man/effect_counts_one.Rd | 66 volker-3.0.0/volker/man/effect_counts_one_cor.Rd | 52 volker-3.0.0/volker/man/effect_counts_one_grouped.Rd | 76 volker-3.0.0/volker/man/effect_metrics.Rd | 118 volker-3.0.0/volker/man/effect_metrics_items.Rd | 68 volker-3.0.0/volker/man/effect_metrics_items_cor.Rd | 94 volker-3.0.0/volker/man/effect_metrics_items_cor_items.Rd | 100 volker-3.0.0/volker/man/effect_metrics_items_grouped.Rd | 90 volker-3.0.0/volker/man/effect_metrics_items_grouped_items.Rd | 52 volker-3.0.0/volker/man/effect_metrics_one.Rd | 66 volker-3.0.0/volker/man/effect_metrics_one_cor.Rd | 90 volker-3.0.0/volker/man/effect_metrics_one_grouped.Rd | 104 volker-3.0.0/volker/man/ends_with.Rd | 18 volker-3.0.0/volker/man/factor_plot.Rd |only volker-3.0.0/volker/man/factor_tab.Rd |only volker-3.0.0/volker/man/figures/lifecycle-archived.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-defunct.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-deprecated.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-experimental.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-maturing.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-questioning.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-soft-deprecated.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-stable.svg | 58 volker-3.0.0/volker/man/figures/lifecycle-superseded.svg | 42 volker-3.0.0/volker/man/filter.Rd | 18 volker-3.0.0/volker/man/get_alpha.Rd |only volker-3.0.0/volker/man/get_angle.Rd | 48 volker-3.0.0/volker/man/get_baseline.Rd | 40 volker-3.0.0/volker/man/get_ci.Rd | 40 volker-3.0.0/volker/man/get_direction.Rd | 50 volker-3.0.0/volker/man/get_gini.Rd | 36 volker-3.0.0/volker/man/get_limits.Rd | 60 volker-3.0.0/volker/man/get_prefix.Rd | 64 volker-3.0.0/volker/man/get_stars.Rd | 36 volker-3.0.0/volker/man/get_title.Rd | 44 volker-3.0.0/volker/man/html_report.Rd | 64 volker-3.0.0/volker/man/idx_add.Rd | 52 volker-3.0.0/volker/man/knit_print.vlkr_plt.Rd | 56 volker-3.0.0/volker/man/label_scale.Rd | 42 volker-3.0.0/volker/man/labs_apply.Rd | 176 volker-3.0.0/volker/man/labs_clear.Rd | 52 volker-3.0.0/volker/man/labs_impute.Rd | 36 volker-3.0.0/volker/man/labs_replace.Rd | 82 volker-3.0.0/volker/man/labs_restore.Rd | 66 volker-3.0.0/volker/man/labs_store.Rd | 62 volker-3.0.0/volker/man/mutate.Rd | 18 volker-3.0.0/volker/man/pdf_report.Rd | 62 volker-3.0.0/volker/man/pipe.Rd | 40 volker-3.0.0/volker/man/plot_counts.Rd | 156 volker-3.0.0/volker/man/plot_counts_items.Rd | 130 volker-3.0.0/volker/man/plot_counts_items_cor.Rd | 120 volker-3.0.0/volker/man/plot_counts_items_cor_items.Rd | 78 volker-3.0.0/volker/man/plot_counts_items_grouped.Rd | 118 volker-3.0.0/volker/man/plot_counts_items_grouped_items.Rd | 78 volker-3.0.0/volker/man/plot_counts_one.Rd | 118 volker-3.0.0/volker/man/plot_counts_one_cor.Rd | 142 volker-3.0.0/volker/man/plot_counts_one_grouped.Rd | 142 volker-3.0.0/volker/man/plot_metrics.Rd | 154 volker-3.0.0/volker/man/plot_metrics_items.Rd | 104 volker-3.0.0/volker/man/plot_metrics_items_cor.Rd | 104 volker-3.0.0/volker/man/plot_metrics_items_cor_items.Rd | 104 volker-3.0.0/volker/man/plot_metrics_items_grouped.Rd | 98 volker-3.0.0/volker/man/plot_metrics_items_grouped_items.Rd | 78 volker-3.0.0/volker/man/plot_metrics_one.Rd | 104 volker-3.0.0/volker/man/plot_metrics_one_cor.Rd | 106 volker-3.0.0/volker/man/plot_metrics_one_grouped.Rd | 110 volker-3.0.0/volker/man/prepare_scale.Rd | 36 volker-3.0.0/volker/man/print.vlkr_list.Rd | 56 volker-3.0.0/volker/man/print.vlkr_plt.Rd | 62 volker-3.0.0/volker/man/print.vlkr_rprt.Rd | 56 volker-3.0.0/volker/man/print.vlkr_tbl.Rd | 56 volker-3.0.0/volker/man/report_counts.Rd | 150 volker-3.0.0/volker/man/report_metrics.Rd | 158 volker-3.0.0/volker/man/select.Rd | 18 volker-3.0.0/volker/man/skim_boxplot.Rd | 28 volker-3.0.0/volker/man/skim_metrics.Rd | 48 volker-3.0.0/volker/man/starts_with.Rd | 18 volker-3.0.0/volker/man/tab_counts.Rd | 142 volker-3.0.0/volker/man/tab_counts_items.Rd | 96 volker-3.0.0/volker/man/tab_counts_items_cor.Rd | 126 volker-3.0.0/volker/man/tab_counts_items_cor_items.Rd | 78 volker-3.0.0/volker/man/tab_counts_items_grouped.Rd | 120 volker-3.0.0/volker/man/tab_counts_items_grouped_items.Rd | 78 volker-3.0.0/volker/man/tab_counts_one.Rd | 90 volker-3.0.0/volker/man/tab_counts_one_cor.Rd | 102 volker-3.0.0/volker/man/tab_counts_one_grouped.Rd | 102 volker-3.0.0/volker/man/tab_metrics.Rd | 142 volker-3.0.0/volker/man/tab_metrics_items.Rd | 90 volker-3.0.0/volker/man/tab_metrics_items_cor.Rd | 106 volker-3.0.0/volker/man/tab_metrics_items_cor_items.Rd | 112 volker-3.0.0/volker/man/tab_metrics_items_grouped.Rd | 96 volker-3.0.0/volker/man/tab_metrics_items_grouped_items.Rd | 78 volker-3.0.0/volker/man/tab_metrics_one.Rd | 90 volker-3.0.0/volker/man/tab_metrics_one_cor.Rd | 102 volker-3.0.0/volker/man/tab_metrics_one_grouped.Rd | 96 volker-3.0.0/volker/man/theme_set.Rd | 18 volker-3.0.0/volker/man/theme_vlkr.Rd | 88 volker-3.0.0/volker/man/tibble.Rd | 18 volker-3.0.0/volker/man/tidy_lm_levels.Rd | 42 volker-3.0.0/volker/man/tribble.Rd | 18 volker-3.0.0/volker/man/trim_label.Rd | 44 volker-3.0.0/volker/man/trim_prefix.Rd | 47 volker-3.0.0/volker/man/trunc_labels.Rd | 40 volker-3.0.0/volker/man/vlkr_colors_discrete.Rd | 48 volker-3.0.0/volker/man/vlkr_colors_polarized.Rd | 36 volker-3.0.0/volker/man/vlkr_colors_sequential.Rd | 36 volker-3.0.0/volker/man/volker-package.Rd | 72 volker-3.0.0/volker/man/wrap_label.Rd | 40 volker-3.0.0/volker/man/zip_tables.Rd | 56 volker-3.0.0/volker/tests/testthat.R | 24 volker-3.0.0/volker/tests/testthat/_markdown/plots.Rmd | 332 volker-3.0.0/volker/tests/testthat/_markdown/reports.Rmd | 173 volker-3.0.0/volker/tests/testthat/_markdown/tables.Rmd | 292 volker-3.0.0/volker/tests/testthat/_snaps/clean.md | 26 volker-3.0.0/volker/tests/testthat/_snaps/clusters.md |only volker-3.0.0/volker/tests/testthat/_snaps/effects.md | 858 - volker-3.0.0/volker/tests/testthat/_snaps/factors.md |only volker-3.0.0/volker/tests/testthat/_snaps/idx.md |only volker-3.0.0/volker/tests/testthat/_snaps/labels.md | 15 volker-3.0.0/volker/tests/testthat/_snaps/skim.md | 94 volker-3.0.0/volker/tests/testthat/_snaps/tables.md | 451 volker-3.0.0/volker/tests/testthat/test-checks.R | 142 volker-3.0.0/volker/tests/testthat/test-clean.R | 207 volker-3.0.0/volker/tests/testthat/test-clusters.R |only volker-3.0.0/volker/tests/testthat/test-effects.R | 228 volker-3.0.0/volker/tests/testthat/test-factors.R |only volker-3.0.0/volker/tests/testthat/test-idx.R |only volker-3.0.0/volker/tests/testthat/test-labels.R | 453 volker-3.0.0/volker/tests/testthat/test-markdown.R | 54 volker-3.0.0/volker/tests/testthat/test-plots.R | 164 volker-3.0.0/volker/tests/testthat/test-tables.R | 495 - volker-3.0.0/volker/tests/testthat/test-theme.R | 106 volker-3.0.0/volker/tests/testthat/test-utils.R | 62 volker-3.0.0/volker/tests/testthat/test_skim.R | 50 volker-3.0.0/volker/vignettes/introduction.Rmd | 801 - 233 files changed, 19794 insertions(+), 16724 deletions(-)
Title: Interact with Simile Models
Description: Allows a Simile model saved as a compiled binary to be
loaded, parameterized, executed and interrogated. This version works
with Simile v6 on.
Author: Simulistics Ltd [cph],
Jasper Taylor [aut, cre]
Maintainer: Jasper Taylor <support@simulistics.com>
Diff between Simile versions 1.3.3 dated 2015-02-19 and 1.3.4 dated 2024-12-11
DESCRIPTION | 22 +++++++++++++++------- MD5 | 12 ++++++------ NAMESPACE | 14 +++++--------- man/Simile-package.Rd | 10 +++++----- man/get.model.property.Rd | 4 ++-- man/list.objects.Rd | 4 ++-- man/load.model.Rd | 4 ++-- 7 files changed, 37 insertions(+), 33 deletions(-)
More information about SaturnCoefficient at CRAN
Permanent link
Title: General Purpose Client for 'ERDDAP™' Servers
Description: General purpose R client for 'ERDDAP™' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP™' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut],
Ben Tupper [ctb],
Salvador Jesus Fernandez Bejarano [ctb],
Roy Mendelssohn [cre, ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddap versions 1.1.0 dated 2024-01-12 and 1.2.0 dated 2024-12-11
DESCRIPTION | 19 MD5 | 82 +-- NEWS.md | 7 R/browse.R | 20 R/convert_time.R | 6 R/default-url.R | 2 R/fipscounty.R | 2 R/global_search.R | 6 R/grid.R | 12 R/info.R | 6 R/keywords.R | 4 R/rerddap-package.r | 10 R/search.R | 6 R/search_adv.R | 4 R/servers.R | 6 R/table.R | 113 +++- R/utils.R | 2 R/version.R | 4 R/zzz.r | 19 build/vignette.rds |binary inst/doc/Using_rerddap.R | 825 ++++++++++++++++++---------------- inst/doc/Using_rerddap.Rmd | 130 ++++- inst/doc/Using_rerddap.html | 1039 +++++++++++++++++++++++--------------------- inst/doc/rerddap.Rmd | 10 inst/doc/rerddap.html | 24 - man/browse.Rd | 5 man/convert_time.Rd | 6 man/disk.Rd | 4 man/ed_search.Rd | 8 man/ed_search_adv.Rd | 6 man/eurl.Rd | 4 man/fipscounty.Rd | 2 man/global_search.Rd | 6 man/griddap.Rd | 4 man/info.Rd | 8 man/key_words.Rd | 4 man/rerddap.Rd | 12 man/servers.Rd | 8 man/tabledap.Rd | 21 man/version.Rd | 6 vignettes/Using_rerddap.Rmd | 130 ++++- vignettes/rerddap.Rmd | 10 42 files changed, 1482 insertions(+), 1120 deletions(-)
Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre] ,
Peter Rousseeuw [aut] ,
Anja Struyf [aut] ,
Mia Hubert [aut] ,
Kurt Hornik [trl, ctb] ,
<https://orcid.org/0000-0003-4198-9911>),
Matthias Studer [ctb],
Pierre Roudier [ctb],
Juan Gonzalez [ctb],
Kamil Kozlowski [ctb],
Er [...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.1.7 dated 2024-12-08 and 2.1.8 dated 2024-12-11
DESCRIPTION | 11 ++++---- MD5 | 12 ++++----- R/agnes.q | 41 ++++++++++++++++---------------- R/daisy.q | 27 +++++++++++---------- R/diana.q | 24 ++++++++++--------- inst/NEWS.Rd | 17 +++++++++---- src/daisy.c | 74 +++++++++++++++++++++++++++-------------------------------- 7 files changed, 108 insertions(+), 98 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.
Author: Marcelo Araya-Salas [aut, cre]
,
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between warbleR versions 1.1.32 dated 2024-08-19 and 1.1.33 dated 2024-12-11
warbleR-1.1.32/warbleR/inst/doc/annotation_data_format.R |only warbleR-1.1.32/warbleR/inst/doc/annotation_data_format.Rmd |only warbleR-1.1.32/warbleR/inst/doc/annotation_data_format.html |only warbleR-1.1.32/warbleR/inst/doc/warbleR.R |only warbleR-1.1.32/warbleR/inst/doc/warbleR.Rmd |only warbleR-1.1.32/warbleR/inst/doc/warbleR.html |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_01.R |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_01.Rmd |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_01.html |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_02.R |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_02.Rmd |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_02.html |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_03.R |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_03.Rmd |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_03.html |only warbleR-1.1.32/warbleR/vignettes/annotation_data_format.Rmd |only warbleR-1.1.32/warbleR/vignettes/warbleR.Rmd |only warbleR-1.1.32/warbleR/vignettes/warbleR_workflow_01.Rmd |only warbleR-1.1.32/warbleR/vignettes/warbleR_workflow_02.Rmd |only warbleR-1.1.32/warbleR/vignettes/warbleR_workflow_03.Rmd |only warbleR-1.1.33/warbleR/DESCRIPTION | 10 warbleR-1.1.33/warbleR/MD5 | 100 ++--- warbleR-1.1.33/warbleR/NAMESPACE | 2 warbleR-1.1.33/warbleR/NEWS.md | 16 warbleR-1.1.33/warbleR/R/compare_methods.R | 2 warbleR-1.1.33/warbleR/R/freq_ts.R | 2 warbleR-1.1.33/warbleR/R/internal_functions.R | 9 warbleR-1.1.33/warbleR/R/move_images.R | 4 warbleR-1.1.33/warbleR/R/open_wd.R | 2 warbleR-1.1.33/warbleR/R/overlapping_sels.R | 2 warbleR-1.1.33/warbleR/R/phylo_spectro.R | 8 warbleR-1.1.33/warbleR/R/plot_coordination.R | 2 warbleR-1.1.33/warbleR/R/read_sound_file.R | 19 - warbleR-1.1.33/warbleR/R/read_wave.R | 169 ---------- warbleR-1.1.33/warbleR/R/selection_table.R | 2 warbleR-1.1.33/warbleR/R/spectro_analysis.R | 5 warbleR-1.1.33/warbleR/R/sth_annotations-data.R | 2 warbleR-1.1.33/warbleR/R/test_coordination.R | 19 - warbleR-1.1.33/warbleR/R/warbleR-package.R | 2 warbleR-1.1.33/warbleR/README.md | 13 warbleR-1.1.33/warbleR/build/vignette.rds |binary warbleR-1.1.33/warbleR/data/comp_matrix.rda |binary warbleR-1.1.33/warbleR/data/lbh_selec_table.rda |binary warbleR-1.1.33/warbleR/data/sim_coor_sing.rda |binary warbleR-1.1.33/warbleR/data/sth_annotations.rda |binary warbleR-1.1.33/warbleR/inst/doc/a_warbleR.R |only warbleR-1.1.33/warbleR/inst/doc/a_warbleR.Rmd |only warbleR-1.1.33/warbleR/inst/doc/a_warbleR.html |only warbleR-1.1.33/warbleR/inst/doc/b_annotation_data_format.R |only warbleR-1.1.33/warbleR/inst/doc/b_annotation_data_format.Rmd |only warbleR-1.1.33/warbleR/inst/doc/b_annotation_data_format.html |only warbleR-1.1.33/warbleR/inst/doc/c_warbleR_workflow_02.R |only warbleR-1.1.33/warbleR/inst/doc/c_warbleR_workflow_02.Rmd |only warbleR-1.1.33/warbleR/inst/doc/c_warbleR_workflow_02.html |only warbleR-1.1.33/warbleR/inst/doc/d_warbleR_workflow_03.R |only warbleR-1.1.33/warbleR/inst/doc/d_warbleR_workflow_03.Rmd |only warbleR-1.1.33/warbleR/inst/doc/d_warbleR_workflow_03.html |only warbleR-1.1.33/warbleR/man/move_images.Rd | 4 warbleR-1.1.33/warbleR/man/open_wd.Rd | 2 warbleR-1.1.33/warbleR/man/phylo_spectro.Rd | 6 warbleR-1.1.33/warbleR/man/plot_coordination.Rd | 2 warbleR-1.1.33/warbleR/man/read_wave.Rd | 31 - warbleR-1.1.33/warbleR/man/selection_table.Rd | 2 warbleR-1.1.33/warbleR/man/spectro_analysis.Rd | 3 warbleR-1.1.33/warbleR/man/test_coordination.Rd | 2 warbleR-1.1.33/warbleR/vignettes/a_warbleR.Rmd |only warbleR-1.1.33/warbleR/vignettes/b_annotation_data_format.Rmd |only warbleR-1.1.33/warbleR/vignettes/c_warbleR_workflow_02.Rmd |only warbleR-1.1.33/warbleR/vignettes/d_warbleR_workflow_03.Rmd |only 69 files changed, 157 insertions(+), 285 deletions(-)
Title: Analyzing the Orientation of Maximum Horizontal Stress
Description: Models the direction of the maximum horizontal stress using
relative plate motion parameters. Statistical algorithms to evaluate
the modeling results compared with the observed data. Provides plots
to visualize the results. Methods described in Stephan et al. (2023)
<doi:10.1038/s41598-023-42433-2> and Wdowinski (1998)
<doi:10.1016/S0079-1946(98)00091-3>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between tectonicr versions 0.4.0 dated 2024-08-21 and 0.4.4 dated 2024-12-11
tectonicr-0.4.0/tectonicr/man/compact_grid.Rd |only tectonicr-0.4.0/tectonicr/man/figures/Figure_07_san_andreas_data.png |only tectonicr-0.4.4/tectonicr/DESCRIPTION | 8 tectonicr-0.4.4/tectonicr/MD5 | 143 tectonicr-0.4.4/tectonicr/NAMESPACE | 5 tectonicr-0.4.4/tectonicr/NEWS.md | 263 - tectonicr-0.4.4/tectonicr/R/coordinates.R | 921 ++-- tectonicr-0.4.4/tectonicr/R/interpolation.R | 371 + tectonicr-0.4.4/tectonicr/R/plotting.R | 127 tectonicr-0.4.4/tectonicr/R/stat_tests.R | 17 tectonicr-0.4.4/tectonicr/R/statistics.R | 2282 +++++----- tectonicr-0.4.4/tectonicr/R/trigonometry_degrees.R | 722 +-- tectonicr-0.4.4/tectonicr/R/various.R | 51 tectonicr-0.4.4/tectonicr/README.md | 117 tectonicr-0.4.4/tectonicr/build/vignette.rds |binary tectonicr-0.4.4/tectonicr/data/iceland.rda |binary tectonicr-0.4.4/tectonicr/data/san_andreas.rda |binary tectonicr-0.4.4/tectonicr/data/tibet.rda |binary tectonicr-0.4.4/tectonicr/inst/doc/A_tectonicr.Rmd | 453 - tectonicr-0.4.4/tectonicr/inst/doc/A_tectonicr.html | 22 tectonicr-0.4.4/tectonicr/inst/doc/B_datasets.html | 44 tectonicr-0.4.4/tectonicr/inst/doc/C_stress_trajectories.html | 4 tectonicr-0.4.4/tectonicr/inst/doc/D_statistics.R | 11 tectonicr-0.4.4/tectonicr/inst/doc/D_statistics.Rmd | 380 - tectonicr-0.4.4/tectonicr/inst/doc/D_statistics.html | 140 tectonicr-0.4.4/tectonicr/inst/doc/E_interpolation.R | 22 tectonicr-0.4.4/tectonicr/inst/doc/E_interpolation.Rmd | 340 - tectonicr-0.4.4/tectonicr/inst/doc/E_interpolation.html | 44 tectonicr-0.4.4/tectonicr/inst/doc/F_spatial.R |only tectonicr-0.4.4/tectonicr/inst/doc/F_spatial.Rmd |only tectonicr-0.4.4/tectonicr/inst/doc/F_spatial.html |only tectonicr-0.4.4/tectonicr/man/PoR_coordinates.Rd | 66 tectonicr-0.4.4/tectonicr/man/PoR_distance.Rd |only tectonicr-0.4.4/tectonicr/man/PoR_map.Rd | 4 tectonicr-0.4.4/tectonicr/man/PoR_stress2grid.Rd | 20 tectonicr-0.4.4/tectonicr/man/circle_stats.Rd | 3 tectonicr-0.4.4/tectonicr/man/circular_dispersion_boot.Rd | 2 tectonicr-0.4.4/tectonicr/man/circular_mode.Rd |only tectonicr-0.4.4/tectonicr/man/circular_qqplot.Rd | 102 tectonicr-0.4.4/tectonicr/man/circular_summary.Rd | 14 tectonicr-0.4.4/tectonicr/man/compact-grid.Rd |only tectonicr-0.4.4/tectonicr/man/dispersion.Rd | 2 tectonicr-0.4.4/tectonicr/man/figures/Figure_07_san_andreas_data_low.jpg |only tectonicr-0.4.4/tectonicr/man/figures/logo.png |only tectonicr-0.4.4/tectonicr/man/figures/logo_hi.png |only tectonicr-0.4.4/tectonicr/man/figures/logo_lo.png |only tectonicr-0.4.4/tectonicr/man/figures/logo_med.png |only tectonicr-0.4.4/tectonicr/man/figures/logo_orig.svg |only tectonicr-0.4.4/tectonicr/man/import_WSM2016.Rd | 7 tectonicr-0.4.4/tectonicr/man/kernel_dispersion.Rd | 12 tectonicr-0.4.4/tectonicr/man/line_azimuth.Rd | 8 tectonicr-0.4.4/tectonicr/man/mean_SC.Rd | 4 tectonicr-0.4.4/tectonicr/man/plot_density.Rd | 21 tectonicr-0.4.4/tectonicr/man/prd_err.Rd | 7 tectonicr-0.4.4/tectonicr/man/quick_plot.Rd | 8 tectonicr-0.4.4/tectonicr/man/rose.Rd | 11 tectonicr-0.4.4/tectonicr/man/rose_stats.Rd | 7 tectonicr-0.4.4/tectonicr/man/sample_median.Rd | 2 tectonicr-0.4.4/tectonicr/man/spherical_angle.Rd | 4 tectonicr-0.4.4/tectonicr/man/stress2grid.Rd | 42 tectonicr-0.4.4/tectonicr/man/stress_data.Rd | 6 tectonicr-0.4.4/tectonicr/man/vm_qqplot.Rd | 106 tectonicr-0.4.4/tectonicr/tests/testthat/Rplots.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots1.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots10.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots11.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots12.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots13.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots14.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots15.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots16.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots17.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots18.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots19.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots2.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots20.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots21.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots22.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots23.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots24.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots25.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots26.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots27.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots3.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots4.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots5.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots6.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots7.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots8.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots9.pdf |only tectonicr-0.4.4/tectonicr/vignettes/A_tectonicr.Rmd | 453 - tectonicr-0.4.4/tectonicr/vignettes/D_statistics.Rmd | 380 - tectonicr-0.4.4/tectonicr/vignettes/E_interpolation.Rmd | 340 - tectonicr-0.4.4/tectonicr/vignettes/F_spatial.Rmd |only 94 files changed, 4361 insertions(+), 3757 deletions(-)
Title: Spatial Data Science Complementary Features
Description: Wrapping and supplementing commonly used functions in the R ecosystem related to spatial data science,
while serving as a basis for other packages maintained by Wenbo Lv.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between sdsfun versions 0.5.0 dated 2024-11-25 and 0.6.0 dated 2024-12-11
DESCRIPTION | 6 - MD5 | 25 +++--- NAMESPACE | 2 NEWS.md | 10 ++ R/RcppExports.R | 12 ++ R/linear_regression.R |only R/spvar.R | 3 R/stratification.R | 177 +++++++++++++++++++++--------------------- R/utils.R | 195 +++++++++++++++++++++++++++-------------------- man/hclustgeo_disc.Rd | 96 +++++++++++++---------- man/rm_lineartrend.Rd |only man/spvar.Rd | 2 man/tbl_xyz2mat.Rd |only src/LinearRegression.cpp |only src/RcppExports.cpp | 39 +++++++++ src/Tbl2Mat.cpp |only 16 files changed, 342 insertions(+), 225 deletions(-)
Title: Functional Control Charts
Description: Provides functional control charts
for statistical process monitoring of functional data,
using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507>,
Centofanti et al. (2021) <doi:10.1080/00401706.2020.1753581>,
Capezza et al. (2024) <doi:10.1080/00401706.2024.2327346>,
Capezza et al. (2024) <doi:10.1080/00224065.2024.2383674>,
Centofanti et al. (2022) <doi:10.48550/arXiv.2205.06256>.
The package is thoroughly illustrated in the paper of
Capezza et al (2023) <doi:10.1080/00224065.2023.2219012>.
Author: Christian Capezza [cre, aut],
Fabio Centofanti [aut],
Antonio Lepore [aut],
Biagio Palumbo [aut],
Alessandra Menafoglio [ctb],
Simone Vantini [ctb]
Maintainer: Christian Capezza <christian.capezza@unina.it>
Diff between funcharts versions 1.5.0 dated 2024-07-19 and 1.6.0 dated 2024-12-11
DESCRIPTION | 25 +- MD5 | 109 ++++++----- NAMESPACE | 15 + NEWS.md | 18 + R/00_mfd.R | 134 +++++++++++++ R/02_fof_pc.R | 3 R/02_sof_pc.R | 3 R/04_phaseII.R | 4 R/05_fault_detection.R | 6 R/FRTM.R |only R/FRTM_plot_functions.R |only R/FRTM_scamfunctions.R |only R/FRTM_util.R |only R/RcppExports.R | 20 ++ R/amfewma.R | 7 R/funcharts-package.R | 48 +++- R/real_time_01_pca.mfd.R | 1 R/real_time_02_fof_pc.R | 1 R/real_time_02_sof_pc.R | 1 R/rmfcc.R | 22 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/capezza2020.html | 8 inst/doc/centofanti2021.html | 10 - inst/doc/colosimo2010.html | 12 - inst/doc/mfd.html | 6 man/AMFEWMA_PhaseI.Rd | 411 +++++++++++++++++++++--------------------- man/AMFEWMA_PhaseII.Rd | 6 man/FRTM_PhaseI.Rd |only man/FRTM_PhaseII.Rd |only man/OEBFDTW.Rd |only man/RoMFCC_PhaseI.Rd | 6 man/RoMFCC_PhaseII.Rd | 6 man/RoMFDI.Rd | 185 +++++++++--------- man/control_charts_pca.Rd | 1 man/control_charts_sof_pc.Rd | 3 man/cor_mfd.Rd |only man/cov_mfd.Rd |only man/fof_pc.Rd | 3 man/fof_pc_real_time.Rd | 3 man/funcharts-package.Rd | 35 +++ man/functional_filter.Rd | 5 man/mFPCA.Rd |only man/mean_mfd.Rd |only man/par.FDTW.Rd |only man/par.mFPCA.Rd |only man/par.rtr.Rd |only man/pca_mfd_real_time.Rd | 3 man/plot.FRTM_PhaseI.Rd |only man/plot.mFPCA.Rd |only man/plot_bootstrap_sof_pc.Rd | 3 man/predict_fof_pc.Rd | 4 man/predict_sof_pc.Rd | 3 man/regr_cc_fof.Rd | 3 man/regr_cc_sof.Rd | 3 man/rpca_mfd.Rd | 6 man/simulate_data_FRTM.Rd |only man/sof_pc.Rd | 3 man/sof_pc_real_time.Rd | 3 src/RcppExports.cpp | 99 ++++++++++ src/src.cpp | 357 ++++++++++++++++++++++++++++++++++++ tests/testthat/Rplots.pdf |only tests/testthat/test_FRTM.R |only tests/testthat/test_OEBFDTW.R |only tests/testthat/test_mFPCA.R |only tests/testthat/test_mfd.R | 12 + 66 files changed, 1214 insertions(+), 402 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 5.0.4 dated 2024-07-26 and 5.0.5 dated 2024-12-11
UComp-5.0.4/UComp/R/PTSS3functions.R |only UComp-5.0.4/UComp/R/PTSfunctions.R |only UComp-5.0.4/UComp/man/ARIMAmodel.Rd |only UComp-5.0.4/UComp/man/ETSmodel.Rd |only UComp-5.0.4/UComp/man/PTS.Rd |only UComp-5.0.4/UComp/man/PTS2modelUC.Rd |only UComp-5.0.4/UComp/man/PTScomponents.Rd |only UComp-5.0.4/UComp/man/PTSestim.Rd |only UComp-5.0.4/UComp/man/PTSmodel.Rd |only UComp-5.0.4/UComp/man/PTSsetup.Rd |only UComp-5.0.4/UComp/man/PTSvalidate.Rd |only UComp-5.0.4/UComp/man/TETSmodel.Rd |only UComp-5.0.4/UComp/man/UCmodel.Rd |only UComp-5.0.4/UComp/man/modelUC2PTS.Rd |only UComp-5.0.4/UComp/man/modelUC2arma.Rd |only UComp-5.0.4/UComp/man/summary.PTS.Rd |only UComp-5.0.5/UComp/ChangeLog | 4 UComp-5.0.5/UComp/DESCRIPTION | 10 +- UComp-5.0.5/UComp/MD5 | 146 ++++++++++++++------------------ UComp-5.0.5/UComp/NAMESPACE | 24 +---- UComp-5.0.5/UComp/R/ARIMAS3functions.R | 14 +-- UComp-5.0.5/UComp/R/ARIMAestim.R | 4 UComp-5.0.5/UComp/R/ARIMAmodel.R | 29 +++--- UComp-5.0.5/UComp/R/ARIMAvalidate.R | 7 - UComp-5.0.5/UComp/R/ETSS3functions.R | 20 ++-- UComp-5.0.5/UComp/R/ETScomponents.R | 4 UComp-5.0.5/UComp/R/ETSestim.R | 4 UComp-5.0.5/UComp/R/ETSmodel.R | 30 +++--- UComp-5.0.5/UComp/R/ETSvalidate.R | 68 ++++++++++---- UComp-5.0.5/UComp/R/TETSS3functions.R | 20 ++-- UComp-5.0.5/UComp/R/TETScomponents.R | 4 UComp-5.0.5/UComp/R/TETSestim.R | 4 UComp-5.0.5/UComp/R/TETSmodel.R | 27 +++-- UComp-5.0.5/UComp/R/TETSvalidate.R | 68 ++++++++++---- UComp-5.0.5/UComp/R/UCS3functions.R | 50 +++++----- UComp-5.0.5/UComp/R/UCcomponents.R | 4 UComp-5.0.5/UComp/R/UCestim.R | 2 UComp-5.0.5/UComp/R/UCfilter.R | 8 - UComp-5.0.5/UComp/R/UCmodel.R | 20 ++-- UComp-5.0.5/UComp/R/UCvalidate.R | 2 UComp-5.0.5/UComp/R/onAttach.R | 2 UComp-5.0.5/UComp/R/tools.R | 4 UComp-5.0.5/UComp/man/AIC.UComp.Rd | 4 UComp-5.0.5/UComp/man/ARIMA.Rd | 6 - UComp-5.0.5/UComp/man/ARIMAestim.Rd | 4 UComp-5.0.5/UComp/man/ARIMAforecast.Rd |only UComp-5.0.5/UComp/man/ARIMAsetup.Rd | 6 - UComp-5.0.5/UComp/man/ARIMAvalidate.Rd | 6 - UComp-5.0.5/UComp/man/BIC.UComp.Rd | 4 UComp-5.0.5/UComp/man/ETS.Rd | 6 - UComp-5.0.5/UComp/man/ETScomponents.Rd | 4 UComp-5.0.5/UComp/man/ETSestim.Rd | 4 UComp-5.0.5/UComp/man/ETSforecast.Rd |only UComp-5.0.5/UComp/man/ETSsetup.Rd | 6 - UComp-5.0.5/UComp/man/ETSvalidate.Rd | 6 - UComp-5.0.5/UComp/man/TETS.Rd | 6 - UComp-5.0.5/UComp/man/TETScomponents.Rd | 4 UComp-5.0.5/UComp/man/TETSestim.Rd | 4 UComp-5.0.5/UComp/man/TETSforecast.Rd |only UComp-5.0.5/UComp/man/TETSsetup.Rd | 6 - UComp-5.0.5/UComp/man/TETSvalidate.Rd | 6 - UComp-5.0.5/UComp/man/UC.Rd | 2 UComp-5.0.5/UComp/man/UCcomponents.Rd | 4 UComp-5.0.5/UComp/man/UCdisturb.Rd | 2 UComp-5.0.5/UComp/man/UCestim.Rd | 2 UComp-5.0.5/UComp/man/UCfilter.Rd | 2 UComp-5.0.5/UComp/man/UCforecast.Rd |only UComp-5.0.5/UComp/man/UChp.Rd | 2 UComp-5.0.5/UComp/man/UCsetup.Rd | 4 UComp-5.0.5/UComp/man/UCsmooth.Rd | 2 UComp-5.0.5/UComp/man/UCvalidate.Rd | 2 UComp-5.0.5/UComp/man/box.cox.Rd | 2 UComp-5.0.5/UComp/man/fitted.Rd | 25 +---- UComp-5.0.5/UComp/man/getp0.Rd | 6 - UComp-5.0.5/UComp/man/inv.box.cox.Rd | 2 UComp-5.0.5/UComp/man/plot.ARIMA.Rd | 4 UComp-5.0.5/UComp/man/plot.Rd | 25 +---- UComp-5.0.5/UComp/man/predict.UComp.Rd | 4 UComp-5.0.5/UComp/man/print.Rd | 28 +----- UComp-5.0.5/UComp/man/residuals.Rd | 25 +---- UComp-5.0.5/UComp/man/summary.ARIMA.Rd | 4 UComp-5.0.5/UComp/man/summary.ETS.Rd | 4 UComp-5.0.5/UComp/man/summary.TETS.Rd | 4 UComp-5.0.5/UComp/src/UCompC.cpp | 38 ++------ 84 files changed, 406 insertions(+), 448 deletions(-)
Title: Feature Stores for the 'diseasy' Framework
Description: Simple feature stores and tools for creating personalised feature stores.
'diseasystore' powers feature stores which can automatically link and aggregate features to a given stratification
level. These feature stores are automatically time-versioned (powered by the 'SCDB' package) and allows you to easily
and dynamically compute features as part of your continuous integration.
Author: Rasmus Skytte Randloev [aut, cre]
,
Kaare Graesboell [rev] ,
Kasper Schou Telkamp [rev] ,
Lasse Engbo Christiansen [rev]
,
Marcus Munch Gruenewald [rev] ,
Sofia Myrup Otero [rev],
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between diseasystore versions 0.2.2 dated 2024-07-15 and 0.3.0 dated 2024-12-11
diseasystore-0.2.2/diseasystore/R/0_locks.R |only diseasystore-0.3.0/diseasystore/DESCRIPTION | 26 diseasystore-0.3.0/diseasystore/MD5 | 118 diseasystore-0.3.0/diseasystore/NAMESPACE | 12 diseasystore-0.3.0/diseasystore/NEWS.md | 240 - diseasystore-0.3.0/diseasystore/R/0_R6_utils.R | 116 diseasystore-0.3.0/diseasystore/R/0_documentation.R | 76 diseasystore-0.3.0/diseasystore/R/0_linters.R | 8 diseasystore-0.3.0/diseasystore/R/0_miscellaneous.R |only diseasystore-0.3.0/diseasystore/R/2_FeatureHandler.R | 9 diseasystore-0.3.0/diseasystore/R/3_feature_store_helpers.R | 23 diseasystore-0.3.0/diseasystore/R/DiseasystoreBase.R | 200 diseasystore-0.3.0/diseasystore/R/DiseasystoreEcdcRespiratoryViruses.R | 28 diseasystore-0.3.0/diseasystore/R/DiseasystoreGoogleCovid19.R | 73 diseasystore-0.3.0/diseasystore/R/DiseasystoreSimulist.R |only diseasystore-0.3.0/diseasystore/R/age_helpers.R |only diseasystore-0.3.0/diseasystore/R/data.R |only diseasystore-0.3.0/diseasystore/R/drop_diseasystore.R | 17 diseasystore-0.3.0/diseasystore/R/test_diseasystore.R | 285 + diseasystore-0.3.0/diseasystore/README.md | 12 diseasystore-0.3.0/diseasystore/build/partial.rdb |only diseasystore-0.3.0/diseasystore/build/vignette.rds |binary diseasystore-0.3.0/diseasystore/data |only diseasystore-0.3.0/diseasystore/inst/WORDLIST | 12 diseasystore-0.3.0/diseasystore/inst/doc/benchmarks.R |only diseasystore-0.3.0/diseasystore/inst/doc/benchmarks.Rmd |only diseasystore-0.3.0/diseasystore/inst/doc/benchmarks.html |only diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.R | 8 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.Rmd | 8 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.html | 25 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-google-covid-19.R | 8 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-google-covid-19.Rmd | 10 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-google-covid-19.html | 20 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore.R | 20 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore.Rmd | 43 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore.html | 339 - diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore-example.R |only diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore-example.Rmd |only diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore-example.html |only diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore.Rmd | 97 diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore.html | 142 diseasystore-0.3.0/diseasystore/inst/extdata |only diseasystore-0.3.0/diseasystore/man/DiseasystoreBase.Rd | 34 diseasystore-0.3.0/diseasystore/man/DiseasystoreEcdcRespiratoryViruses.Rd | 23 diseasystore-0.3.0/diseasystore/man/DiseasystoreGoogleCovid19.Rd | 1 diseasystore-0.3.0/diseasystore/man/DiseasystoreSimulist.Rd |only diseasystore-0.3.0/diseasystore/man/FeatureHandler.Rd | 7 diseasystore-0.3.0/diseasystore/man/add_years.Rd |only diseasystore-0.3.0/diseasystore/man/age_labels.Rd | 10 diseasystore-0.3.0/diseasystore/man/age_on_date.Rd |only diseasystore-0.3.0/diseasystore/man/diseasyoption.Rd | 10 diseasystore-0.3.0/diseasystore/man/diseasystore-package.Rd | 2 diseasystore-0.3.0/diseasystore/man/drop_diseasystore.Rd | 4 diseasystore-0.3.0/diseasystore/man/simulist_data.Rd |only diseasystore-0.3.0/diseasystore/man/test_diseasystore.Rd | 17 diseasystore-0.3.0/diseasystore/tests/spelling.R | 10 diseasystore-0.3.0/diseasystore/tests/testthat/helper-setup.R | 45 diseasystore-0.3.0/diseasystore/tests/testthat/test-0_R6_utils.R | 36 diseasystore-0.3.0/diseasystore/tests/testthat/test-DiseasystoreBase.R | 195 diseasystore-0.3.0/diseasystore/tests/testthat/test-DiseasystoreSimulist.R |only diseasystore-0.3.0/diseasystore/tests/testthat/test-FeatureHandler.R | 4 diseasystore-0.3.0/diseasystore/tests/testthat/test-age_helpers.R |only diseasystore-0.3.0/diseasystore/tests/testthat/test-drop_diseasystore.R | 155 diseasystore-0.3.0/diseasystore/tests/testthat/test-truncate_interlace.R | 20 diseasystore-0.3.0/diseasystore/tests/testthat/test_data/data/snapshots/2023-11-24_ILIARIRates.csv | 2002 +++++----- diseasystore-0.3.0/diseasystore/vignettes/benchmarks.Rmd |only diseasystore-0.3.0/diseasystore/vignettes/diseasystore-ecdc-respiratory-viruses.Rmd | 8 diseasystore-0.3.0/diseasystore/vignettes/diseasystore-google-covid-19.Rmd | 10 diseasystore-0.3.0/diseasystore/vignettes/diseasystore.Rmd | 43 diseasystore-0.3.0/diseasystore/vignettes/extending-diseasystore-example.Rmd |only diseasystore-0.3.0/diseasystore/vignettes/extending-diseasystore.Rmd | 97 71 files changed, 2718 insertions(+), 1990 deletions(-)
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between tree versions 1.0-43 dated 2023-02-05 and 1.0-44 dated 2024-12-11
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- src/grow.c | 12 ++++++------ 3 files changed, 14 insertions(+), 14 deletions(-)
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table',
giving users the speed of 'data.table' while using tidyverse-like syntax.
Author: Mark Fairbanks [aut, cre],
Abdessabour Moutik [ctb],
Matt Carlson [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb],
Robert On [ctb],
Alexander Sevostianov [ctb],
Koen ter Berg [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.11.1 dated 2024-07-18 and 0.11.2 dated 2024-12-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/case.R | 8 +------- R/dt.R | 10 +++++----- R/utils-general.R | 6 ++---- tests/testthat/test-dt.R | 6 ++++++ 7 files changed, 29 insertions(+), 26 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between RODBC versions 1.3-23 dated 2023-11-25 and 1.3-25.1 dated 2024-12-11
ChangeLog | 4 DESCRIPTION | 14 +- MD5 | 10 +- build/vignette.rds |binary inst/doc/RODBC.pdf |binary src/RODBC.c | 253 ++++++++++++++++++++++++++--------------------------- 6 files changed, 143 insertions(+), 138 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Author: Craig Gower-Page [aut, cre],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Isaac Gravestock [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Craig Gower-Page <craig.gower-page@roche.com>
Diff between rbmi versions 1.3.0 dated 2024-10-16 and 1.3.1 dated 2024-12-11
DESCRIPTION | 8 +++++--- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/utilities.R | 36 +++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/advanced.html | 2 +- inst/doc/quickstart.html | 40 ++++++++++++++++++++-------------------- man/get_session_hash.Rd |only man/rbmi-package.Rd | 1 + tests/testthat/test-longData.R | 33 +++++++++++++++++++++++++++++++++ tests/testthat/test-utilities.R | 19 +++++++++++++++++++ 12 files changed, 126 insertions(+), 39 deletions(-)
Title: Statistical Tools for Quantitative Genetic Analyses
Description: Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses.
Rohde et al. (2019) <doi:10.1101/503631>.
Author: Peter Soerensen [aut, cre],
Palle Duun Rohde [aut],
Izel Fourie Soerensen [aut]
Maintainer: Peter Soerensen <peter.sorensen@r-qgg.org>
Diff between qgg versions 1.1.2 dated 2023-09-07 and 1.1.3 dated 2024-12-11
qgg-1.1.2/qgg/man/qcStat.Rd |only qgg-1.1.3/qgg/DESCRIPTION | 12 qgg-1.1.3/qgg/MD5 | 126 qgg-1.1.3/qgg/NAMESPACE | 22 qgg-1.1.3/qgg/NEWS.md | 2 qgg-1.1.3/qgg/R/RcppExports.R | 28 qgg-1.1.3/qgg/R/genomic_bayes.R | 3292 +++++++++++++++++++------ qgg-1.1.3/qgg/R/genomic_correlation.R | 85 qgg-1.1.3/qgg/R/genomic_matrix.R | 626 +++- qgg-1.1.3/qgg/R/genomic_reml.R | 2 qgg-1.1.3/qgg/R/genomic_score.R | 62 qgg-1.1.3/qgg/R/genomic_simulation.R | 241 + qgg-1.1.3/qgg/R/genomic_statistics.R | 97 qgg-1.1.3/qgg/R/multiple_marker_test.R | 517 +++ qgg-1.1.3/qgg/R/qgg.R | 11 qgg-1.1.3/qgg/README.md | 177 + qgg-1.1.3/qgg/man/acc.Rd | 36 qgg-1.1.3/qgg/man/adjLDStat.Rd | 76 qgg-1.1.3/qgg/man/adjStat.Rd | 106 qgg-1.1.3/qgg/man/adjustB.Rd | 74 qgg-1.1.3/qgg/man/adjustMapLD.Rd | 54 qgg-1.1.3/qgg/man/auc.Rd | 34 qgg-1.1.3/qgg/man/checkStat.Rd |only qgg-1.1.3/qgg/man/computeROC.Rd | 40 qgg-1.1.3/qgg/man/createLDsets.Rd |only qgg-1.1.3/qgg/man/gbayes.Rd | 3 qgg-1.1.3/qgg/man/getG.Rd | 118 qgg-1.1.3/qgg/man/getLD.Rd | 56 qgg-1.1.3/qgg/man/getLDscores.Rd |only qgg-1.1.3/qgg/man/getLDsets.Rd | 38 qgg-1.1.3/qgg/man/getMap.Rd | 44 qgg-1.1.3/qgg/man/getMarkers.Rd | 46 qgg-1.1.3/qgg/man/getPos.Rd | 44 qgg-1.1.3/qgg/man/getSparseLD.Rd | 76 qgg-1.1.3/qgg/man/gfilter.Rd | 126 qgg-1.1.3/qgg/man/glma.Rd | 268 +- qgg-1.1.3/qgg/man/gmap.Rd | 405 +-- qgg-1.1.3/qgg/man/gprep.Rd | 2 qgg-1.1.3/qgg/man/gsea.Rd | 1 qgg-1.1.3/qgg/man/gsim.Rd | 122 qgg-1.1.3/qgg/man/gsimC.Rd |only qgg-1.1.3/qgg/man/gsimR.Rd |only qgg-1.1.3/qgg/man/hwe.Rd | 30 qgg-1.1.3/qgg/man/ldsc.Rd | 245 - qgg-1.1.3/qgg/man/ldscore.Rd | 82 qgg-1.1.3/qgg/man/magma.Rd |only qgg-1.1.3/qgg/man/mapSets.Rd | 52 qgg-1.1.3/qgg/man/mapStat.Rd | 136 - qgg-1.1.3/qgg/man/mtadj.Rd | 194 - qgg-1.1.3/qgg/man/plotBayes.Rd | 42 qgg-1.1.3/qgg/man/plotForest.Rd | 96 qgg-1.1.3/qgg/man/plotLD.Rd | 50 qgg-1.1.3/qgg/man/plotROC.Rd | 40 qgg-1.1.3/qgg/man/pops.Rd |only qgg-1.1.3/qgg/man/predict_auc_mt_cc.Rd | 78 qgg-1.1.3/qgg/man/predict_auc_mt_continuous.Rd | 70 qgg-1.1.3/qgg/man/predict_auc_st.Rd | 56 qgg-1.1.3/qgg/man/predict_r2_mt.Rd | 60 qgg-1.1.3/qgg/man/predict_r2_st.Rd | 48 qgg-1.1.3/qgg/man/rnag.Rd | 34 qgg-1.1.3/qgg/man/splitWithOverlap.Rd | 46 qgg-1.1.3/qgg/man/vegas.Rd |only qgg-1.1.3/qgg/man/writeBED.Rd |only qgg-1.1.3/qgg/src/Makevars.win | 2 qgg-1.1.3/qgg/src/RcppExports.cpp | 124 qgg-1.1.3/qgg/src/bedfunc.cpp | 153 - qgg-1.1.3/qgg/src/gbayes.cpp | 735 ++++- qgg-1.1.3/qgg/src/mtgbayes.cpp | 2289 ++++++++++++++++- qgg-1.1.3/qgg/src/qgg_init.c | 24 69 files changed, 8595 insertions(+), 3160 deletions(-)
Title: Penalized Smoothing Splines
Description: Smoothing splines with penalties on order m derivatives.
Author: S original by Jim Ramsey <ramsay@psych.mcgill.ca>.
R port by Brian Ripley <Brian.Ripley@R-project.org>.
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between pspline versions 1.0-20 dated 2024-05-25 and 1.0-21 dated 2024-12-11
ChangeLog | 2 ++ DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- 3 files changed, 10 insertions(+), 8 deletions(-)
Title: Estimation/Multiple Imputation for Mixed Categorical and
Continuous Data
Description: Estimation/multiple imputation programs for mixed categorical
and continuous data.
Author: Joseph L. Schafer [aut],
Brian Ripley [aut, trl, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between mix versions 1.0-12 dated 2024-05-13 and 1.0-13 dated 2024-12-11
DESCRIPTION | 22 ++++++++++++++++------ MD5 | 4 ++-- data/stlouis.rda |binary 3 files changed, 18 insertions(+), 8 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.6 dated 2024-11-15 and 1.3.8 dated 2024-12-11
DESCRIPTION | 10 MD5 | 34 - NAMESPACE | 3 NEWS.md | 6 R/CreateTableOneJS.R | 159 ++++---- R/forestcox.R | 2 R/forestglm.R | 572 ++++++++++++++++++++++---------- R/svyCreateTableOneJS.R | 164 +++++---- inst/doc/jstable.html | 30 - man/CreateTableOne2.Rd | 5 man/CreateTableOneJS.Rd | 5 man/TableSubgroupGLM.Rd | 2 man/count_event_by.Rd | 2 man/svyCreateTableOne2.Rd | 5 man/svyCreateTableOneJS.Rd | 5 tests/testthat/test-CreateTableOneJS.R | 14 tests/testthat/test-forestglm.R | 4 tests/testthat/test-svyCreateTableOne.R | 9 18 files changed, 672 insertions(+), 359 deletions(-)
Title: Generalized Estimation Equation Solver
Description: Generalized Estimation Equation solver.
Author: Vincent J Carey [aut],
Thomas S Lumley [trl] ,
Cleve Moler [ctb] ,
Brian Ripley [trl, cre, ctb]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between gee versions 4.13-27 dated 2024-05-25 and 4.13-29 dated 2024-12-11
DESCRIPTION | 12 +++++----- MD5 | 4 +-- src/ugee.c | 72 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 44 insertions(+), 44 deletions(-)
Title: Imputation Procedures and Quality Tests for Fuzzy Data
Description: Special procedures for the imputation of missing fuzzy numbers are still underdeveloped. The goal of the package is to provide the new d-imputation method (DIMP for short, Romaniuk, M. and Grzegorzewski, P. (2023) "Fuzzy Data Imputation with DIMP and FGAIN" RB/23/2023) and covert some classical ones applied in R packages ('missForest','miceRanger','knn') for use with fuzzy datasets. Additionally, specially tailored benchmarking tests are provided to check and compare these imputation procedures with fuzzy datasets.
Author: Maciej Romaniuk [cre, aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyImputationTest versions 0.3.4 dated 2024-10-30 and 0.3.6 dated 2024-12-11
DESCRIPTION | 6 +- MD5 | 66 ++++++++++++++-------- R/ApplyStatisticalTests.R | 6 +- R/CalculateFuzzyMeasures.R | 58 +++++++++++++++++++- R/ErrorMatrix.R | 26 ++++++--- R/FuzzifyMatrix.R | 6 +- R/FuzzyNumbersToMatrix.R | 38 ++++++++++++- R/ImputationDimp.R | 2 R/ImputationTests.R | 69 +++++++++++++++++++++--- R/IntroducingNA.R | 11 ++- R/MatrixToFuzzyNumbers.R | 40 +++++++++++++ R/MeasureAHD.R | 45 +++++++++++++++ R/MeasureEuclidean.R | 47 ++++++++++++++++ R/MeasureHSD.R | 46 ++++++++++++++++ R/MethodsComparison.R | 48 ++++++++++++++++ R/RemoveNotFuzzy.R | 4 - R/StatisticalMeasures.R | 57 ++++++++++++++++++- R/utils.R | 15 +++++ man/ErrorMatrix.Rd | 6 +- man/FuzzifyMatrix.Rd | 4 - man/ImputationTests.Rd | 2 tests/testthat/_snaps/ApplyStatisticalTests.md | 36 ++++++++++++ tests/testthat/_snaps/CalculateFuzzyMeasures.md |only tests/testthat/_snaps/FuzzyNumbersToMatrix.md |only tests/testthat/_snaps/ImputationTests.md |only tests/testthat/_snaps/MatrixToFuzzyNumbers.md |only tests/testthat/_snaps/MeasureAHD.md |only tests/testthat/_snaps/MeasureEuclidean.md |only tests/testthat/_snaps/MeasureHSD.md |only tests/testthat/_snaps/MethodsComparison.md |only tests/testthat/_snaps/StatisticalMeasures.md |only tests/testthat/test-ApplyStatisticalTests.R | 30 ++++++++++ tests/testthat/test-CalculateFuzzyMeasures.R |only tests/testthat/test-ErrorMatrix.R | 4 - tests/testthat/test-FuzzyNumbersToMatrix.R |only tests/testthat/test-ImputationTests.R |only tests/testthat/test-IntroducingNA.R | 8 +- tests/testthat/test-MatrixToFuzzyNumbers.R |only tests/testthat/test-MeasureAHD.R |only tests/testthat/test-MeasureEuclidean.R |only tests/testthat/test-MeasureHSD.R |only tests/testthat/test-MethodsComparison.R |only tests/testthat/test-StatisticalMeasures.R |only 43 files changed, 606 insertions(+), 74 deletions(-)
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Title: FastICA Algorithms to Perform ICA and Projection Pursuit
Description: Implementation of FastICA algorithm to perform Independent
Component Analysis (ICA) and Projection Pursuit.
Author: Jonathan L Marchini [aut],
Chris Heaton [aut],
Brian Ripley [aut, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between fastICA versions 1.2-5.1 dated 2024-08-21 and 1.2-7 dated 2024-12-11
DESCRIPTION | 21 +++++---- MD5 | 4 - src/ica.c | 130 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 79 insertions(+), 76 deletions(-)
Title: Species Distribution Modeling and Ecological Niche Modeling
Description: Implements species distribution modeling and ecological niche
modeling, including: bias correction, spatial cross-validation, model
evaluation, raster interpolation, biotic "velocity" (speed and
direction of movement of a "mass" represented by a raster), interpolating
across a time series of rasters, and use of spatially imprecise records.
The heart of the package is a set of "training" functions which
automatically optimize model complexity based number of available
occurrences. These algorithms include MaxEnt, MaxNet, boosted regression
trees/gradient boosting machines, generalized additive models,
generalized linear models, natural splines, and random forests. To enhance
interoperability with other modeling packages, no new classes are created.
The package works with 'PROJ6' geodetic objects and coordinate reference
systems.
Author: Adam B. Smith [cre, aut]
Maintainer: Adam B. Smith <adam.smith@mobot.org>
Diff between enmSdmX versions 1.1.9 dated 2024-11-03 and 1.2.10 dated 2024-12-11
enmSdmX-1.1.9/enmSdmX/R/trainBRT.r |only enmSdmX-1.1.9/enmSdmX/R/trainGAM.r |only enmSdmX-1.1.9/enmSdmX/R/trainGLM.r |only enmSdmX-1.1.9/enmSdmX/R/trainNS.r |only enmSdmX-1.1.9/enmSdmX/R/trainRF.r |only enmSdmX-1.2.10/enmSdmX/DESCRIPTION | 10 enmSdmX-1.2.10/enmSdmX/MD5 | 116 - enmSdmX-1.2.10/enmSdmX/NAMESPACE | 106 - enmSdmX-1.2.10/enmSdmX/NEWS.md | 6 enmSdmX-1.2.10/enmSdmX/R/aaa.r | 6 enmSdmX-1.2.10/enmSdmX/R/geoFold.r | 2 enmSdmX-1.2.10/enmSdmX/R/predict_maxent.r | 174 - enmSdmX-1.2.10/enmSdmX/R/trainBrt.r |only enmSdmX-1.2.10/enmSdmX/R/trainGam.r |only enmSdmX-1.2.10/enmSdmX/R/trainGlm.r |only enmSdmX-1.2.10/enmSdmX/R/trainNs.r |only enmSdmX-1.2.10/enmSdmX/R/trainRf.r |only enmSdmX-1.2.10/enmSdmX/README.md | 230 +- enmSdmX-1.2.10/enmSdmX/inst/CITATION | 2 enmSdmX-1.2.10/enmSdmX/inst/extdata/canada_level0_gadm41.gpkg |binary enmSdmX-1.2.10/enmSdmX/man/bioticVelocity.Rd | 1016 +++++----- enmSdmX-1.2.10/enmSdmX/man/canada.Rd | 48 enmSdmX-1.2.10/enmSdmX/man/compareResponse.Rd | 178 - enmSdmX-1.2.10/enmSdmX/man/customAlbers.Rd | 182 - enmSdmX-1.2.10/enmSdmX/man/dot-calcWeights.Rd | 48 enmSdmX-1.2.10/enmSdmX/man/dot-cardinalDistance.Rd | 106 - enmSdmX-1.2.10/enmSdmX/man/dot-scalePredictors.Rd | 38 enmSdmX-1.2.10/enmSdmX/man/elimCellDuplicates.Rd | 78 enmSdmX-1.2.10/enmSdmX/man/enmSdmX.Rd | 254 +- enmSdmX-1.2.10/enmSdmX/man/evalAUC.Rd | 118 - enmSdmX-1.2.10/enmSdmX/man/evalContBoyce.Rd | 154 - enmSdmX-1.2.10/enmSdmX/man/evalMultiAUC.Rd | 106 - enmSdmX-1.2.10/enmSdmX/man/evalTSS.Rd | 134 - enmSdmX-1.2.10/enmSdmX/man/evalThreshold.Rd | 148 - enmSdmX-1.2.10/enmSdmX/man/evalThresholdStats.Rd | 160 - enmSdmX-1.2.10/enmSdmX/man/evalTjursR2.Rd | 118 - enmSdmX-1.2.10/enmSdmX/man/examples/customCRS_examples.r | 8 enmSdmX-1.2.10/enmSdmX/man/extentToVect.Rd | 70 enmSdmX-1.2.10/enmSdmX/man/geoFold.Rd | 186 - enmSdmX-1.2.10/enmSdmX/man/geoFoldContrast.Rd | 182 - enmSdmX-1.2.10/enmSdmX/man/geoThin.Rd | 128 - enmSdmX-1.2.10/enmSdmX/man/getCRS.Rd | 86 enmSdmX-1.2.10/enmSdmX/man/globalx.Rd | 78 enmSdmX-1.2.10/enmSdmX/man/interpolateRasts.Rd | 242 +- enmSdmX-1.2.10/enmSdmX/man/mad0.Rd | 54 enmSdmX-1.2.10/enmSdmX/man/mad1.Rd | 54 enmSdmX-1.2.10/enmSdmX/man/nearestEnvPoints.Rd | 392 +-- enmSdmX-1.2.10/enmSdmX/man/nearestGeogPoints.Rd | 500 ++-- enmSdmX-1.2.10/enmSdmX/man/nicheOverlapMetrics.Rd | 124 - enmSdmX-1.2.10/enmSdmX/man/predictEnmSdm.Rd | 532 ++--- enmSdmX-1.2.10/enmSdmX/man/predictMaxEnt.Rd | 560 ++--- enmSdmX-1.2.10/enmSdmX/man/predictMaxNet.Rd | 526 ++--- enmSdmX-1.2.10/enmSdmX/man/summaryByCrossValid.Rd | 440 ++-- enmSdmX-1.2.10/enmSdmX/man/trainBRT.Rd | 2 enmSdmX-1.2.10/enmSdmX/man/trainByCrossValid.Rd | 504 ++-- enmSdmX-1.2.10/enmSdmX/man/trainESM.Rd | 342 +-- enmSdmX-1.2.10/enmSdmX/man/trainGAM.Rd | 2 enmSdmX-1.2.10/enmSdmX/man/trainGLM.Rd | 19 enmSdmX-1.2.10/enmSdmX/man/trainMaxEnt.Rd | 610 +++--- enmSdmX-1.2.10/enmSdmX/man/trainMaxNet.Rd | 584 ++--- enmSdmX-1.2.10/enmSdmX/man/trainNS.Rd | 23 enmSdmX-1.2.10/enmSdmX/man/trainRF.Rd | 2 enmSdmX-1.2.10/enmSdmX/man/troubleshooting_parallel_operations.Rd | 72 enmSdmX-1.2.10/enmSdmX/man/weightByDist.Rd | 90 64 files changed, 4994 insertions(+), 4956 deletions(-)
Title: 'Rcpp' Integration for 'CGAL'
Description: Creates a header only package to link to the 'CGAL'
(Computational Geometry Algorithms Library)
header files in 'Rcpp'. There are a variety of potential uses for
the software such as Hilbert sorting, K-D Tree nearest neighbors,
and convex hull algorithms. For more information about how to use the header files,
see the 'CGAL' documentation at <https://www.cgal.org>. Currently
downloads version 6.0.1 of the 'CGAL' header files.
Author: Eric Dunipace [aut, cre] ,
Tyler Morgan-Wall [ctb],
The CGAL Project [cph]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Diff between RcppCGAL versions 5.6.4 dated 2024-07-04 and 6.0 dated 2024-12-11
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- R/downloader.R | 10 +++++----- README.md | 7 ++++++- build/vignette.rds |binary inst/WORDLIST | 2 ++ inst/doc/Installation.R | 10 +++++----- inst/doc/Installation.html | 4 ++-- inst/include/CGAL_zip.tar.xz |binary man/RcppCGAL-package.Rd | 2 +- tools/config/configure.R | 4 ++-- tools/config/downloader_functions.R | 3 +++ 12 files changed, 43 insertions(+), 33 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut],
Youngsun Park [aut] ,
Hyungwoo Jo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.5.9 dated 2024-10-17 and 1.6.0 dated 2024-12-11
DESCRIPTION | 14 ++++--- MD5 | 22 ++++++------ NAMESPACE | 1 NEWS.md | 9 ++++ R/bar.R | 2 - R/box.R | 3 + R/coxph.R | 89 +++++++++++++++++++++++++++++++++++-------------- R/forestcox.R | 40 +++++++++++++++++++--- R/kaplan.R | 80 +++++++++++++++++++++++++++++++++++++++----- R/line.R | 72 ++++++++++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/jsmodule.html | 4 +- 12 files changed, 271 insertions(+), 65 deletions(-)
Title: Searching Shared HLA Amino Acid Residue Prevalence
Description: Processes amino acid alignments produced by the 'IPD-IMGT/HLA (Immuno Polymorphism-ImMunoGeneTics/Human Leukocyte Antigen) Database' to identify user-defined amino acid residue motifs shared across HLA alleles, HLA alleles, or HLA haplotypes, and calculates frequencies based on HLA allele frequency data. 'SSHAARP' (Searching Shared HLA Amino Acid Residue Prevalence) uses 'Generic Mapping Tools (GMT)' software and the 'GMT' R package to generate global frequency heat maps that illustrate the distribution of each user-defined map around the globe. 'SSHAARP' analyzes the allele frequency data described by Solberg et al. (2008) <doi:10.1016/j.humimm.2008.05.001>, a global set of 497 population samples from 185 published datasets, representing 66,800 individuals total. Users may also specify their own datasets, but file conventions must follow the prebundled Solberg dataset, or the mock haplotype dataset.
Author: Livia Tran [aut, cre],
Steven Mack [aut],
Josh Bredeweg [ctb],
Dale Steinhardt [ctb]
Maintainer: Livia Tran <livia.tran@ucsf.edu>
Diff between SSHAARP versions 1.1.0 dated 2021-09-17 and 2.0.5 dated 2024-12-11
SSHAARP-1.1.0/SSHAARP/R/BLAASD.R |only SSHAARP-1.1.0/SSHAARP/R/checkMotif.R |only SSHAARP-1.1.0/SSHAARP/data/AA_atlas.rda |only SSHAARP-1.1.0/SSHAARP/data/IMGTprotalignments.rda |only SSHAARP-1.1.0/SSHAARP/man/AA_atlas.Rd |only SSHAARP-1.1.0/SSHAARP/man/BLAASD.Rd |only SSHAARP-1.1.0/SSHAARP/man/IMGTprotalignments.Rd |only SSHAARP-1.1.0/SSHAARP/man/checkMotif.Rd |only SSHAARP-1.1.0/SSHAARP/vignettes/basemap_bw.jpg |only SSHAARP-2.0.5/SSHAARP/DESCRIPTION | 15 SSHAARP-2.0.5/SSHAARP/MD5 | 73 +- SSHAARP-2.0.5/SSHAARP/NAMESPACE | 30 SSHAARP-2.0.5/SSHAARP/NEWS | 35 - SSHAARP-2.0.5/SSHAARP/R/PALM.R | 583 +++++++++++------- SSHAARP-2.0.5/SSHAARP/R/checkAlleleSyntax.R |only SSHAARP-2.0.5/SSHAARP/R/checkHaplotypeSyntax.R |only SSHAARP-2.0.5/SSHAARP/R/checkLocusANHIG.R |only SSHAARP-2.0.5/SSHAARP/R/checkLocusDataset.R |only SSHAARP-2.0.5/SSHAARP/R/checkMotifSyntax.R |only SSHAARP-2.0.5/SSHAARP/R/checkPosition.R |only SSHAARP-2.0.5/SSHAARP/R/data.R | 33 - SSHAARP-2.0.5/SSHAARP/R/dataSubset.R | 70 +- SSHAARP-2.0.5/SSHAARP/R/dataSubsetHaplo.R |only SSHAARP-2.0.5/SSHAARP/R/findMotif.R | 59 - SSHAARP-2.0.5/SSHAARP/R/getVariantInfo.R |only SSHAARP-2.0.5/SSHAARP/R/isNamePresent.R |only SSHAARP-2.0.5/SSHAARP/R/readFileName.R |only SSHAARP-2.0.5/SSHAARP/R/verifyAlleleANHIG.R |only SSHAARP-2.0.5/SSHAARP/R/verifyAlleleANHIGHaplo.R |only SSHAARP-2.0.5/SSHAARP/R/verifyAlleleDataset.R |only SSHAARP-2.0.5/SSHAARP/build/vignette.rds |binary SSHAARP-2.0.5/SSHAARP/data/mock_haplotype_dataset.rda |only SSHAARP-2.0.5/SSHAARP/data/solberg_dataset.rda |binary SSHAARP-2.0.5/SSHAARP/inst/doc/vignette.R | 9 SSHAARP-2.0.5/SSHAARP/inst/doc/vignette.Rmd | 145 ++-- SSHAARP-2.0.5/SSHAARP/inst/doc/vignette.html | 257 +++++-- SSHAARP-2.0.5/SSHAARP/man/PALM.Rd | 73 +- SSHAARP-2.0.5/SSHAARP/man/checkAlleleSyntax.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkHaplotypeSyntax.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkLocusANHIG.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkLocusDataset.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkMotifSyntax.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkPosition.Rd |only SSHAARP-2.0.5/SSHAARP/man/dataSubset.Rd | 12 SSHAARP-2.0.5/SSHAARP/man/dataSubsetHaplo.Rd |only SSHAARP-2.0.5/SSHAARP/man/findMotif.Rd | 23 SSHAARP-2.0.5/SSHAARP/man/getVariantInfo.Rd |only SSHAARP-2.0.5/SSHAARP/man/isNamePresent.Rd |only SSHAARP-2.0.5/SSHAARP/man/mock_haplotype_dataset.Rd |only SSHAARP-2.0.5/SSHAARP/man/readFilename.Rd |only SSHAARP-2.0.5/SSHAARP/man/verifyAlleleANHIG.Rd |only SSHAARP-2.0.5/SSHAARP/man/verifyAlleleANHIGHaplo.Rd |only SSHAARP-2.0.5/SSHAARP/man/verifyAlleleDataset.Rd |only SSHAARP-2.0.5/SSHAARP/vignettes/allele_bw.jpg |only SSHAARP-2.0.5/SSHAARP/vignettes/basemap_color.jpg |binary SSHAARP-2.0.5/SSHAARP/vignettes/haplo_color.jpg |only SSHAARP-2.0.5/SSHAARP/vignettes/vignette.Rmd | 145 ++-- 57 files changed, 968 insertions(+), 594 deletions(-)
Title: Sequential Imputation with Bayesian Trees Mixed-Effects Models
for Longitudinal Data
Description: Implements a sequential imputation framework using Bayesian Mixed-Effects Trees ('SBMTrees') for handling missing data in longitudinal studies. The package supports a variety of models, including non-linear relationships and non-normal random effects and residuals, leveraging Dirichlet Process priors for increased flexibility. Key features include handling Missing at Random (MAR) longitudinal data, imputation of both covariates and outcomes, and generating posterior predictive samples for further analysis. The methodology is designed for applications in epidemiology, biostatistics, and other fields requiring robust handling of missing data in longitudinal settings.
Author: Jungang Zou [aut, cre],
Liangyuan Hu [aut],
Robert McCulloch [ctb],
Rodney Sparapani [ctb],
Charles Spanbauer [ctb]
Maintainer: Jungang Zou <jungang.zou@gmail.com>
Diff between SBMTrees versions 1.1 dated 2024-12-09 and 1.2 dated 2024-12-11
DESCRIPTION | 6 - MD5 | 30 ++++---- NEWS.md | 9 ++ R/BMTrees_prediction.R | 10 ++ R/sequential_imputation.R | 10 ++ README.md | 16 ++++ inst/doc/SBMTrees_Introduction.R | 6 - inst/doc/SBMTrees_Introduction.Rmd | 10 +- inst/doc/SBMTrees_Introduction.html | 121 +++++++++++++++++++----------------- man/BMTrees_prediction.Rd | 8 +- man/SBMTrees-package.Rd | 9 +- man/sequential_imputation.Rd | 10 ++ src/BART/bart.h | 9 +- src/DP_lambda.h | 6 + src/sequential_imputation.cpp | 4 - vignettes/SBMTrees_Introduction.Rmd | 10 +- 16 files changed, 165 insertions(+), 109 deletions(-)
More information about IRISMustangMetrics at CRAN
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