Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE)
Solvers
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
Author: Satyaprakash Nayak [aut, cre, cph] ,
Lawrence Livermore National Security [cph],
Southern Methodist University [cph],
University of Maryland Baltimore County [cph]
Maintainer: Satyaprakash Nayak <satyaprakash.nayak@gmail.com>
Diff between sundialr versions 0.2.0 dated 2026-08-07 and 0.2.1 dated 2026-10-17
sundialr-0.2.0/sundialr/src/sundials-mod-7.8.0.tar.gz |only sundialr-0.2.1/sundialr/DESCRIPTION | 10 sundialr-0.2.1/sundialr/MD5 | 90 - sundialr-0.2.1/sundialr/NEWS.md | 11 sundialr-0.2.1/sundialr/R/RcppExports.R | 56 - sundialr-0.2.1/sundialr/README.md | 6 sundialr-0.2.1/sundialr/cleanup | 6 sundialr-0.2.1/sundialr/configure | 34 sundialr-0.2.1/sundialr/configure.ac | 18 sundialr-0.2.1/sundialr/inst/COPYRIGHTS | 2 sundialr-0.2.1/sundialr/inst/doc/my-vignette.R | 18 sundialr-0.2.1/sundialr/inst/doc/my-vignette.Rmd | 128 ++ sundialr-0.2.1/sundialr/inst/doc/my-vignette.html | 208 +++ sundialr-0.2.1/sundialr/inst/examples/cv_Roberts_dns.r | 44 sundialr-0.2.1/sundialr/inst/examples/cvs_Roberts_dns.r | 56 - sundialr-0.2.1/sundialr/inst/examples/ida_Roberts_dns.r | 56 - sundialr-0.2.1/sundialr/inst/include/arkode/arkode.hpp | 20 sundialr-0.2.1/sundialr/inst/include/arkode/arkode_arkstep.h | 6 sundialr-0.2.1/sundialr/inst/include/arkode/arkode_butcher_dirk.h | 10 sundialr-0.2.1/sundialr/inst/include/arkode/arkode_butcher_erk.h | 12 sundialr-0.2.1/sundialr/inst/include/arkode/arkode_mristep.h | 20 sundialr-0.2.1/sundialr/inst/include/cvode/cvode.h | 6 sundialr-0.2.1/sundialr/inst/include/cvodes/cvodes.h | 6 sundialr-0.2.1/sundialr/inst/include/sundialr_capi.h | 195 +++ sundialr-0.2.1/sundialr/inst/include/sundials/sundials_config.h | 5 sundialr-0.2.1/sundialr/inst/include/sundials/sundials_export.h | 13 sundialr-0.2.1/sundialr/inst/include/sundials/sundials_nvector.h | 3 sundialr-0.2.1/sundialr/inst/include/sundomeigest/sundomeigest_power.h | 15 sundialr-0.2.1/sundialr/man/cvode.Rd | 44 sundialr-0.2.1/sundialr/man/cvodes.Rd | 62 - sundialr-0.2.1/sundialr/man/cvsolve.Rd | 2 sundialr-0.2.1/sundialr/man/ida.Rd | 58 - sundialr-0.2.1/sundialr/src/RcppExports.cpp | 165 ++- sundialr-0.2.1/sundialr/src/capi_internal.h |only sundialr-0.2.1/sundialr/src/capi_register.cpp | 20 sundialr-0.2.1/sundialr/src/capi_test.cpp | 549 +++++++++- sundialr-0.2.1/sundialr/src/cvsolve.cpp | 2 sundialr-0.2.1/sundialr/src/ida.cpp | 2 sundialr-0.2.1/sundialr/src/scripts/cran_patches.sh | 57 - sundialr-0.2.1/sundialr/src/scripts/dedupe_static_libs.sh |only sundialr-0.2.1/sundialr/src/scripts/sundials_download.sh | 16 sundialr-0.2.1/sundialr/src/sundialr_capi.cpp | 122 +- sundialr-0.2.1/sundialr/src/sundialr_capi_arkode.cpp |only sundialr-0.2.1/sundialr/src/sundials-mod-7.9.0.tar.gz |only sundialr-0.2.1/sundialr/tests/testthat/test-capi-arkode.r |only sundialr-0.2.1/sundialr/tests/testthat/test-capi.r | 48 sundialr-0.2.1/sundialr/tools/cmake_call.sh | 57 - sundialr-0.2.1/sundialr/tools/strip_sundials_tarball.sh | 4 sundialr-0.2.1/sundialr/vignettes/my-vignette.Rmd | 128 ++ 49 files changed, 1953 insertions(+), 437 deletions(-)
Title: Optimal Stratification of Univariate Populations
Description: Determines Optimum Strata Boundaries (OSB) and Optimum Sample
Sizes (OSS) for univariate stratified sampling designs under Neyman
allocation. The stratification variable is described by a best-fitting
parametric distribution, selected automatically by AIC from a set of
continuous families (normal, log-normal, gamma, Weibull, exponential,
Cauchy, uniform, Pareto, triangular and right-triangular), and the
optimum boundaries are obtained by minimising the Neyman objective.
Version 2.0 keeps the Dynamic Programming (DP) solver of Reddy and Khan
(2020), which is globally optimal for the fitted distribution, as the
default. It adds two fast derivative-free solvers, a multi-start
'COBYLA' solver and a two-phase global solver that couples 'DIRECT-L'
with 'BOBYQA' refinement, and an exact solver that runs dynamic
programming on the sorted data and returns the partition with the
smallest empirical Neyman cost. It also provides cost-constrained
allocation with unequal per-stratum costs, a desi [...truncated...]
Author: Karuna G. Reddy [aut, cre] ,
M. G. M. Khan [aut]
Maintainer: Karuna G. Reddy <karuna.reddy@auckland.ac.nz>
Diff between stratifyR versions 2.0-2 dated 2026-10-14 and 2.0-3 dated 2026-10-17
DESCRIPTION | 8 MD5 | 36 NEWS.md | 112 ++ R/cobyla.optim.R | 239 +++- R/data.root.R | 102 + R/distr.alloc.R | 16 R/distr.root.R | 62 - R/exact.optim.R | 15 R/get.dist.R | 82 + R/plot.strata.R | 4 R/strata.data.R | 88 + R/strata.distr.R | 27 R/summary.strata.R | 21 inst/app/app.R | 6 inst/doc/stratifyR-vignette.R | 8 inst/doc/stratifyR-vignette.Rmd | 38 inst/doc/stratifyR-vignette.html | 2064 +++++++++++++++++++++++++-------------- tests/testthat/test-solvers.R | 47 vignettes/stratifyR-vignette.Rmd | 38 19 files changed, 2021 insertions(+), 992 deletions(-)
Title: High Performance Tools for Combinatorics and Computational
Mathematics
Description: Provides optimized functions and flexible iterators implemented in
C++ for solving problems in combinatorics and computational mathematics.
Handles various combinatorial objects including combinations, permutations,
integer partitions and compositions, Cartesian products, unordered
Cartesian products, and partition of groups. Utilizes the RMatrix class
from 'RcppParallel' for thread safety. The combination and permutation
functions contain constraint parameters that allow for generation of all
results of a vector meeting specific criteria (e.g. finding all
combinations such that the sum is between two bounds). Capable of
ranking/unranking combinatorial objects efficiently (e.g. retrieve only the
nth lexicographical result) which sets up nicely for parallelization as
well as random sampling. Gmp support permits exploration where the total
number of results is large (e.g. comboSample(10000, 500, n = 4)).
Additionally, there are several high performance number theoretic
functions that are [...truncated...]
Author: Joseph Wood [aut, cre],
Joseph J. Allaire [ctb]
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 2.10.1 dated 2026-06-08 and 2.10.2 dated 2026-10-17
DESCRIPTION | 16 MD5 | 266 ++-- NAMESPACE | 5 NEWS.md | 35 R/compositionsCount.R | 25 R/partitionsCount.R | 24 R/testEnumCoverage.R |only build/vignette.rds |binary inst/CITATION | 4 inst/NEWS.Rd | 50 inst/doc/CombPermConstraints.Rmd | 30 inst/doc/CombPermConstraints.html | 32 inst/doc/CombinatorialSampling.Rmd | 31 inst/doc/CombinatorialSampling.html | 71 - inst/doc/CombinatoricsIterators.Rmd | 156 +- inst/doc/CombinatoricsIterators.html | 186 +-- inst/doc/ComputationalMathematics.Rmd | 36 inst/doc/ComputationalMathematics.html | 38 inst/doc/GeneralCombinatorics.Rmd | 32 inst/doc/GeneralCombinatorics.html | 34 inst/doc/HighPerformanceBenchmarks.Rmd | 124 +- inst/doc/HighPerformanceBenchmarks.html | 126 +- inst/doc/IntegerCompositions.Rmd | 27 inst/doc/IntegerCompositions.html | 57 - inst/doc/IntegerPartitions.Rmd | 25 inst/doc/IntegerPartitions.html | 29 inst/doc/OtherCombinatorics.Rmd | 24 inst/doc/OtherCombinatorics.html | 26 inst/doc/SubsetSum.Rmd | 40 inst/doc/SubsetSum.html | 42 inst/include/ClassUtils/ComboResClass.h | 5 inst/include/Constraints/CnstrntsSpecialClass.h | 1 inst/include/Constraints/CnstrntsToRClass.h | 1 inst/include/Constraints/ConstraintsSpecial.h | 18 inst/include/Constraints/ConstraintsUtils.h | 8 inst/include/Constraints/GetContraints.h | 2 inst/include/Partitions/BigPartsCountDistinct.h | 4 inst/include/Partitions/BigPartsCountMultiset.h |only inst/include/Partitions/BigPartsCountRep.h | 6 inst/include/Partitions/BrutePartitionsCountMultiset.h |only inst/include/Partitions/CompositionsDistinct.h | 10 inst/include/Partitions/MultisetCountClass.h |only inst/include/Partitions/PartitionsCount.h | 3 inst/include/Partitions/PartitionsCountDistinct.h | 4 inst/include/Partitions/PartitionsCountMultiset.h | 21 inst/include/Partitions/PartitionsCountRep.h | 4 inst/include/Partitions/PartitionsManager.h | 11 inst/include/Partitions/PartitionsMultiset.h | 19 inst/include/Partitions/PartitionsTypes.h | 945 +++++++++++------ inst/include/Partitions/PartitionsUtils.h | 2 inst/include/Partitions/ThreadSafeParts.h | 8 inst/include/Permutations/BigPermuteCount.h | 1 inst/include/Permutations/PermuteCount.h | 4 inst/include/RMatrix.h | 4 inst/include/SetUpUtils.h | 13 man/combinatoricsGeneral.Rd | 5 man/combinatoricsIterator.Rd | 4 man/comboGroupsIterator.Rd | 1 man/expandGridIterator.Rd | 1 man/partitionsIterator.Rd | 1 src/BigPartsCountDistinct.cpp | 4 src/BigPartsCountMultiset.cpp |only src/BigPartsCountRep.cpp | 8 src/BigPermuteCount.cpp | 58 - src/BrutePartitionsCountMultiset.cpp |only src/CartesianClass.cpp | 31 src/CheckReturn.cpp | 2 src/CnstrntsSpecialClass.cpp | 107 + src/CnstrntsToRClass.cpp | 54 src/CombinatoricsApply.cpp | 10 src/CombinatoricsCount.cpp | 197 +++ src/CombinatoricsMain.cpp | 13 src/ComboApplyClass.cpp | 18 src/ComboClass.cpp | 4 src/ComboGroups.cpp | 10 src/ComboGroupsClass.cpp | 10 src/ComboGroupsTemplate.cpp | 2 src/ComboResClass.cpp | 37 src/CompositionsDistinct.cpp | 52 src/ConstraintsMain.cpp | 73 - src/ConstraintsSpecial.cpp | 76 - src/ConstraintsUtils.cpp | 18 src/ExposeClass.cpp | 31 src/FunAssign.cpp | 3 src/GetClassVals.cpp | 2 src/GetCombPermApply.cpp | 15 src/GetConstraints.cpp | 46 src/GmpConvert.cpp | 89 - src/NextPartition.cpp | 62 - src/NthPartition.cpp | 100 - src/PartitionsClass.cpp | 55 src/PartitionsCount.cpp | 298 +++-- src/PartitionsCountDistinct.cpp | 4 src/PartitionsCountMultiset.cpp | 182 ++- src/PartitionsCountRep.cpp | 6 src/PartitionsDesign.cpp | 98 + src/PartitionsManager.cpp | 156 +- src/PartitionsMultiset.cpp | 108 + src/PartitionsUtils.cpp | 198 ++- src/PermuteCount.cpp | 85 - src/PollardRhoContainer.cpp | 5 src/ProductCartesian.cpp | 13 src/RankCombPermMain.cpp | 3 src/RankPartition.cpp | 104 - src/RankPartitionMain.cpp | 16 src/SampleCombPerm.cpp | 2 src/SamplePartitions.cpp | 28 src/SetUpUtils.cpp | 143 +- src/StdConvert.cpp | 46 src/TestEnumCoverage.cpp |only src/ThreadSafeParts.cpp | 52 src/cpp11.cpp | 102 + src/version.cpp | 2 tests/testthat/testCartesianClass.R | 78 + tests/testthat/testComboClass.R | 153 ++ tests/testthat/testComboGeneral.R | 243 ++++ tests/testthat/testComboGroupsClass.R | 55 tests/testthat/testConstraintsClass.R | 29 tests/testthat/testErrors.R | 37 tests/testthat/testParallelIterators.R |only tests/testthat/testPartitionTypeRefactor.R |only tests/testthat/testPartitionsClass.R | 162 ++ tests/testthat/testPartitionsDesign.R | 18 tests/testthat/testPartitionsGmp.R | 58 - tests/testthat/testPartitionsMultisetCount.R |only tests/testthat/testPartitionsParallel.R | 68 - tests/testthat/testPartitionsSampleRank.R | 34 tests/testthat/testPermuteGeneral.R | 13 tests/testthat/testSpecialSubsetSum.R | 4 vignettes/CombPermConstraints.Rmd | 30 vignettes/CombinatorialSampling.Rmd | 31 vignettes/CombinatoricsIterators.Rmd | 156 +- vignettes/ComputationalMathematics.Rmd | 36 vignettes/GeneralCombinatorics.Rmd | 32 vignettes/HighPerformanceBenchmarks.Rmd | 124 +- vignettes/IntegerCompositions.Rmd | 27 vignettes/IntegerPartitions.Rmd | 25 vignettes/OtherCombinatorics.Rmd | 24 vignettes/SubsetSum.Rmd | 40 139 files changed, 4399 insertions(+), 2613 deletions(-)
Title: Water Quality Assessment and Environmental Compliance in Brazil
Description: Tools to import, clean, validate, and analyze freshwater quality data
in Brazil. Implements water quality indices including the Water Quality Index
('WQI'/'IQA') using the weighted geometric mean following 'CETESB' methodology,
an independent engine reproducing the 'IQA' of the Minas Gerais water agency
'IGAM' (a documented reproduction, not endorsed by the agency), paired
comparison of 'IQA' engines with compare_iqa(), the Trophic State Index ('TSI'/'IET') after Carlson (1977)
<doi:10.4319/lo.1977.22.2.0361> and Lamparelli (2004)
<https://teses.usp.br/teses/disponiveis/41/41134/tde-20032006-075813/publico/TeseLamparelli2004.pdf>,
and the National Sanitation Foundation Water Quality Index ('NSF WQI', Brown
(1970)). The package also checks compliance with Brazilian standard 'CONAMA'
Resolution 357/2005
<https://conama.mma.gov.br/?id=450&option=com_sisconama&task=arquivo.download>
including the legal frequency rule (Art. 15, 80% conformity over six or more
sampl [...truncated...]
Author: Vinicius Saraiva Santos [aut, cre] ,
Fabricio Berton Zanchi [ctb]
Maintainer: Vinicius Saraiva Santos <vinisaraiva@gmail.com>
Diff between tikatuwq versions 0.10.0 dated 2026-08-31 and 0.11.0 dated 2026-10-17
tikatuwq-0.10.0/tikatuwq/R/testando.R |only tikatuwq-0.10.0/tikatuwq/inst/ANALISE_TECNICA_TIKATUWQ.md |only tikatuwq-0.10.0/tikatuwq/inst/CRAN-SUBMISSION |only tikatuwq-0.10.0/tikatuwq/inst/run_check_cran.R |only tikatuwq-0.11.0/tikatuwq/DESCRIPTION | 10 tikatuwq-0.11.0/tikatuwq/LICENSE | 2 tikatuwq-0.11.0/tikatuwq/MD5 | 295 +- tikatuwq-0.11.0/tikatuwq/NAMESPACE | 232 +- tikatuwq-0.11.0/tikatuwq/NEWS.md | 573 +++-- tikatuwq-0.11.0/tikatuwq/R/analysis_text.R | 399 +-- tikatuwq-0.11.0/tikatuwq/R/balnear.R | 410 +-- tikatuwq-0.11.0/tikatuwq/R/compare_iqa.R |only tikatuwq-0.11.0/tikatuwq/R/conama.R | 846 +++---- tikatuwq-0.11.0/tikatuwq/R/conama_freq.R | 324 +- tikatuwq-0.11.0/tikatuwq/R/data_wq_demo.R | 92 tikatuwq-0.11.0/tikatuwq/R/iet.R | 389 +-- tikatuwq-0.11.0/tikatuwq/R/iet_lamparelli.R | 360 +-- tikatuwq-0.11.0/tikatuwq/R/io_clean.R | 910 ++++---- tikatuwq-0.11.0/tikatuwq/R/iqa.R | 939 +++++--- tikatuwq-0.11.0/tikatuwq/R/iqa_curves.R | 192 - tikatuwq-0.11.0/tikatuwq/R/iqa_equations.R | 1115 +++++----- tikatuwq-0.11.0/tikatuwq/R/iqa_igam.R |only tikatuwq-0.11.0/tikatuwq/R/load_exceedance.R | 376 +-- tikatuwq-0.11.0/tikatuwq/R/mk_seasonal.R | 490 ++-- tikatuwq-0.11.0/tikatuwq/R/nsfwqi.R | 358 +-- tikatuwq-0.11.0/tikatuwq/R/param_analysis.R | 500 ++-- tikatuwq-0.11.0/tikatuwq/R/param_analysis_multi.R | 346 +-- tikatuwq-0.11.0/tikatuwq/R/plot_iet.R | 306 +- tikatuwq-0.11.0/tikatuwq/R/plot_map.R | 304 +- tikatuwq-0.11.0/tikatuwq/R/plot_map_quality.R | 479 ++-- tikatuwq-0.11.0/tikatuwq/R/plot_trend.R | 378 +-- tikatuwq-0.11.0/tikatuwq/R/report.R | 194 - tikatuwq-0.11.0/tikatuwq/R/seasonal.R | 634 ++--- tikatuwq-0.11.0/tikatuwq/R/summaries.R | 132 - tikatuwq-0.11.0/tikatuwq/R/tikatuwq-package.R | 138 - tikatuwq-0.11.0/tikatuwq/R/trend_param.R | 310 +- tikatuwq-0.11.0/tikatuwq/R/utils_sanitize.R | 549 ++-- tikatuwq-0.11.0/tikatuwq/R/viz.R | 302 +- tikatuwq-0.11.0/tikatuwq/R/wq_buranhem.R | 40 tikatuwq-0.11.0/tikatuwq/R/wq_pca.R | 480 ++-- tikatuwq-0.11.0/tikatuwq/README.md | 558 ++--- tikatuwq-0.11.0/tikatuwq/inst/CITATION | 46 tikatuwq-0.11.0/tikatuwq/inst/README_install.md | 28 tikatuwq-0.11.0/tikatuwq/inst/WORDLIST | 392 +-- tikatuwq-0.11.0/tikatuwq/inst/audit |only tikatuwq-0.11.0/tikatuwq/inst/doc/tikatuwq-methods.R | 10 tikatuwq-0.11.0/tikatuwq/inst/doc/tikatuwq-methods.Rmd | 610 ++--- tikatuwq-0.11.0/tikatuwq/inst/doc/tikatuwq-methods.html | 34 tikatuwq-0.11.0/tikatuwq/inst/doc/tikatuwq-workflow.R | 2 tikatuwq-0.11.0/tikatuwq/inst/doc/tikatuwq-workflow.Rmd | 576 ++--- tikatuwq-0.11.0/tikatuwq/inst/doc/tikatuwq-workflow.html | 14 tikatuwq-0.11.0/tikatuwq/inst/doc/tikatuwq.R | 2 tikatuwq-0.11.0/tikatuwq/inst/doc/tikatuwq.Rmd | 304 +- tikatuwq-0.11.0/tikatuwq/inst/doc/tikatuwq.html | 4 tikatuwq-0.11.0/tikatuwq/inst/extdata/conama_limits.csv | 232 +- tikatuwq-0.11.0/tikatuwq/inst/extdata/exemplo_chamagunga.csv | 12 tikatuwq-0.11.0/tikatuwq/inst/extdata/wq_demo_README.txt | 12 tikatuwq-0.11.0/tikatuwq/inst/methodology |only tikatuwq-0.11.0/tikatuwq/inst/templates/report_rmd.Rmd | 112 - tikatuwq-0.11.0/tikatuwq/man/assign_season.Rd | 166 - tikatuwq-0.11.0/tikatuwq/man/balnear_check.Rd | 200 - tikatuwq-0.11.0/tikatuwq/man/classify_iqa.Rd | 106 tikatuwq-0.11.0/tikatuwq/man/classify_tsi_carlson.Rd | 52 tikatuwq-0.11.0/tikatuwq/man/classify_tsi_lamparelli.Rd | 52 tikatuwq-0.11.0/tikatuwq/man/clean_units.Rd | 78 tikatuwq-0.11.0/tikatuwq/man/compare_iqa.Rd |only tikatuwq-0.11.0/tikatuwq/man/compare_seasons.Rd | 160 - tikatuwq-0.11.0/tikatuwq/man/compute_load.Rd | 136 - tikatuwq-0.11.0/tikatuwq/man/conama_check.Rd | 86 tikatuwq-0.11.0/tikatuwq/man/conama_freq_check.Rd | 158 - tikatuwq-0.11.0/tikatuwq/man/conama_limits.Rd | 62 tikatuwq-0.11.0/tikatuwq/man/conama_report.Rd | 96 tikatuwq-0.11.0/tikatuwq/man/conama_summary.Rd | 62 tikatuwq-0.11.0/tikatuwq/man/conama_text.Rd | 82 tikatuwq-0.11.0/tikatuwq/man/exceedance_prob.Rd | 148 - tikatuwq-0.11.0/tikatuwq/man/fix_coords.Rd | 60 tikatuwq-0.11.0/tikatuwq/man/generate_analysis.Rd | 118 - tikatuwq-0.11.0/tikatuwq/man/iet_carlson.Rd | 185 - tikatuwq-0.11.0/tikatuwq/man/iet_lamparelli.Rd | 169 - tikatuwq-0.11.0/tikatuwq/man/iqa.Rd | 318 ++ tikatuwq-0.11.0/tikatuwq/man/iqa_components.Rd | 103 tikatuwq-0.11.0/tikatuwq/man/iqa_methods.Rd |only tikatuwq-0.11.0/tikatuwq/man/mk_seasonal.Rd | 212 - tikatuwq-0.11.0/tikatuwq/man/normalize_param_names.Rd | 44 tikatuwq-0.11.0/tikatuwq/man/nsfwqi.Rd | 161 - tikatuwq-0.11.0/tikatuwq/man/param_analysis.Rd | 20 tikatuwq-0.11.0/tikatuwq/man/param_analysis_multi.Rd | 20 tikatuwq-0.11.0/tikatuwq/man/param_plot.Rd | 106 tikatuwq-0.11.0/tikatuwq/man/param_plot_multi.Rd | 110 tikatuwq-0.11.0/tikatuwq/man/param_summary.Rd | 110 tikatuwq-0.11.0/tikatuwq/man/param_summary_multi.Rd | 102 tikatuwq-0.11.0/tikatuwq/man/param_trend.Rd | 88 tikatuwq-0.11.0/tikatuwq/man/param_trend_multi.Rd | 84 tikatuwq-0.11.0/tikatuwq/man/plot_box.Rd | 62 tikatuwq-0.11.0/tikatuwq/man/plot_heatmap.Rd | 64 tikatuwq-0.11.0/tikatuwq/man/plot_iet.Rd | 144 - tikatuwq-0.11.0/tikatuwq/man/plot_iqa.Rd | 56 tikatuwq-0.11.0/tikatuwq/man/plot_map.Rd | 130 - tikatuwq-0.11.0/tikatuwq/man/plot_map_quality.Rd | 166 - tikatuwq-0.11.0/tikatuwq/man/plot_series.Rd | 70 tikatuwq-0.11.0/tikatuwq/man/plot_trend.Rd | 158 - tikatuwq-0.11.0/tikatuwq/man/read_wq.Rd | 152 - tikatuwq-0.11.0/tikatuwq/man/render_report.Rd | 136 - tikatuwq-0.11.0/tikatuwq/man/resume_wq.Rd | 98 tikatuwq-0.11.0/tikatuwq/man/tikatuwq-package.Rd | 132 - tikatuwq-0.11.0/tikatuwq/man/trend_param.Rd | 96 tikatuwq-0.11.0/tikatuwq/man/validate_wq.Rd | 92 tikatuwq-0.11.0/tikatuwq/man/wq_demo.Rd | 138 - tikatuwq-0.11.0/tikatuwq/man/wq_pca.Rd | 144 - tikatuwq-0.11.0/tikatuwq/tests/testthat.R | 6 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-balnear.R | 130 - tikatuwq-0.11.0/tikatuwq/tests/testthat/test-clean_units.R | 100 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-conama-db.R | 10 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-conama.R | 20 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-conama_freq.R | 90 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-conama_text.R | 70 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-fix_coords.R | 94 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-generate_analysis.R | 188 - tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iet-values.R |only tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-audit-validation.R |only tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-cetesb-formulas.R | 258 +- tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-components.R | 100 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-curves.R | 30 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-geometric.R | 92 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-igam-api.R |only tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-igam-compare.R |only tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-igam-engine.R |only tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-inema-benchmark.R | 61 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-solids-tds.R | 58 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa-temperature.R | 136 - tikatuwq-0.11.0/tikatuwq/tests/testthat/test-iqa.R | 36 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-load_exceedance.R | 86 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-mk_seasonal.R | 115 - tikatuwq-0.11.0/tikatuwq/tests/testthat/test-nd-ld-policy.R | 226 +- tikatuwq-0.11.0/tikatuwq/tests/testthat/test-nsfwqi.R |only tikatuwq-0.11.0/tikatuwq/tests/testthat/test-param_analysis.R | 174 - tikatuwq-0.11.0/tikatuwq/tests/testthat/test-param_analysis_multi.R | 212 - tikatuwq-0.11.0/tikatuwq/tests/testthat/test-plot_functions.R | 138 - tikatuwq-0.11.0/tikatuwq/tests/testthat/test-plot_iet.R | 66 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-plot_map.R | 84 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-plot_map_quality.R | 89 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-plot_trend.R | 46 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-render_report.R | 188 - tikatuwq-0.11.0/tikatuwq/tests/testthat/test-seasonal.R | 90 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-trend_param.R | 26 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-wq-demo.R | 48 tikatuwq-0.11.0/tikatuwq/tests/testthat/test-wq_pca.R | 92 tikatuwq-0.11.0/tikatuwq/vignettes/tikatuwq-methods.Rmd | 610 ++--- tikatuwq-0.11.0/tikatuwq/vignettes/tikatuwq-workflow.Rmd | 576 ++--- tikatuwq-0.11.0/tikatuwq/vignettes/tikatuwq.Rmd | 304 +- 150 files changed, 13833 insertions(+), 12660 deletions(-)
Title: Simulation-Based Power Evaluation for Stepped-Wedge Cluster
Randomized Trials
Description: Provides simulation-based power, type I error, and operating-
characteristic evaluation for stepped-wedge cluster randomized trials.
General binary-outcome designs support arbitrary crossover schedules,
unequal clusters per sequence, secular trends, flexible cluster-period
sizes, reproducible parallel execution, sensitivity grids, and mixed-model
diagnostics. A component-based engine supports the four treatment states
Control, A, B, and A+B under arbitrary asynchronous schedules, including
structurally unobserved cluster-periods, withdrawal, reintroduction,
wash-in delays, user-defined carryover decay, component main effects, an
A-by-B interaction, estimability audits, multiplicity adjustment,
conditional and failure-aware power, and explicit classification of hard
model errors, nonconvergence, non-finite contrasts, singular fits, and
successful fits. A batch-aware interface represents classic and batched
stepped-wedge designs with delayed cluster initiation, structurally
unobserved cl [...truncated...]
Author: Lin Li [aut, cre],
Florin Vaida [aut]
Maintainer: Lin (Amanda) Li <amandali14124277@gmail.com>
Diff between stepwedgepower versions 0.1.3 dated 2026-07-13 and 0.4.1 dated 2026-10-17
stepwedgepower-0.1.3/stepwedgepower/inst/WORDLIST |only stepwedgepower-0.1.3/stepwedgepower/inst/scripts/Lpa_analysis_FV_20260217_original.R |only stepwedgepower-0.4.1/stepwedgepower/DESCRIPTION | 61 stepwedgepower-0.4.1/stepwedgepower/MD5 | 166 ++ stepwedgepower-0.4.1/stepwedgepower/NAMESPACE | 76 - stepwedgepower-0.4.1/stepwedgepower/NEWS.md | 278 +++ stepwedgepower-0.4.1/stepwedgepower/R/analyze.R |only stepwedgepower-0.4.1/stepwedgepower/R/assumptions.R |only stepwedgepower-0.4.1/stepwedgepower/R/batched_analyze.R |only stepwedgepower-0.4.1/stepwedgepower/R/batched_assumptions.R |only stepwedgepower-0.4.1/stepwedgepower/R/batched_audit.R |only stepwedgepower-0.4.1/stepwedgepower/R/batched_compare.R |only stepwedgepower-0.4.1/stepwedgepower/R/batched_design.R |only stepwedgepower-0.4.1/stepwedgepower/R/batched_power.R |only stepwedgepower-0.4.1/stepwedgepower/R/batched_simulate.R |only stepwedgepower-0.4.1/stepwedgepower/R/batched_utils.R |only stepwedgepower-0.4.1/stepwedgepower/R/component_analyze.R |only stepwedgepower-0.4.1/stepwedgepower/R/component_assumptions.R |only stepwedgepower-0.4.1/stepwedgepower/R/component_audit.R |only stepwedgepower-0.4.1/stepwedgepower/R/component_compare.R |only stepwedgepower-0.4.1/stepwedgepower/R/component_design.R |only stepwedgepower-0.4.1/stepwedgepower/R/component_power.R |only stepwedgepower-0.4.1/stepwedgepower/R/component_resources.R |only stepwedgepower-0.4.1/stepwedgepower/R/component_simulate.R |only stepwedgepower-0.4.1/stepwedgepower/R/component_utils.R |only stepwedgepower-0.4.1/stepwedgepower/R/data_tools.R | 203 +- stepwedgepower-0.4.1/stepwedgepower/R/deprecate.R |only stepwedgepower-0.4.1/stepwedgepower/R/design.R |only stepwedgepower-0.4.1/stepwedgepower/R/fit_diagnostics.R |only stepwedgepower-0.4.1/stepwedgepower/R/grid.R |only stepwedgepower-0.4.1/stepwedgepower/R/icc.R |only stepwedgepower-0.4.1/stepwedgepower/R/models.R | 321 ++-- stepwedgepower-0.4.1/stepwedgepower/R/multistage_analyze.R |only stepwedgepower-0.4.1/stepwedgepower/R/multistage_assumptions.R |only stepwedgepower-0.4.1/stepwedgepower/R/multistage_audit.R |only stepwedgepower-0.4.1/stepwedgepower/R/multistage_compare.R |only stepwedgepower-0.4.1/stepwedgepower/R/multistage_design.R |only stepwedgepower-0.4.1/stepwedgepower/R/multistage_power.R |only stepwedgepower-0.4.1/stepwedgepower/R/multistage_simulate.R |only stepwedgepower-0.4.1/stepwedgepower/R/parallel_utils.R |only stepwedgepower-0.4.1/stepwedgepower/R/power.R | 738 ++-------- stepwedgepower-0.4.1/stepwedgepower/R/power_engine.R |only stepwedgepower-0.4.1/stepwedgepower/R/simulate.R |only stepwedgepower-0.4.1/stepwedgepower/R/stepwedgepower-package.R |only stepwedgepower-0.4.1/stepwedgepower/R/validate.R |only stepwedgepower-0.4.1/stepwedgepower/README.md | 369 +++-- stepwedgepower-0.4.1/stepwedgepower/build |only stepwedgepower-0.4.1/stepwedgepower/inst/CITATION |only stepwedgepower-0.4.1/stepwedgepower/inst/benchmarks |only stepwedgepower-0.4.1/stepwedgepower/inst/doc |only stepwedgepower-0.4.1/stepwedgepower/inst/examples |only stepwedgepower-0.4.1/stepwedgepower/inst/extdata/example_physicians.csv | 34 stepwedgepower-0.4.1/stepwedgepower/man/analyze_aggregated_outcomes.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/analyze_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/as_component_design.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/audit_batched_design.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/audit_component_design.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/audit_multistage_design.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/cluster_sd_to_icc.Rd | 10 stepwedgepower-0.4.1/stepwedgepower/man/compare_batched_designs.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/compare_component_designs.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/compare_multistage_designs.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/compare_with_swdpwr.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/component_resource_summary.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/estimate_group_rates.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/estimate_power.Rd | 77 - stepwedgepower-0.4.1/stepwedgepower/man/estimate_type1_error.Rd | 69 stepwedgepower-0.4.1/stepwedgepower/man/fit_batched_model.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/fit_component_model.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/fit_grouped_rate_model.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/fit_multistage_model.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/fit_stepwedge_model.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/icc_to_cluster_sd.Rd | 13 stepwedgepower-0.4.1/stepwedgepower/man/power_batched_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/power_component_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/power_grid.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/power_multistage_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/power_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/prepare_cluster_data.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/run_stepwedge_analysis.Rd | 29 stepwedgepower-0.4.1/stepwedgepower/man/simulate_batched_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/simulate_component_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/simulate_multistage_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/simulate_stepwedge_trial.Rd | 75 - stepwedgepower-0.4.1/stepwedgepower/man/simulate_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/stepwedgepower-package.Rd | 41 stepwedgepower-0.4.1/stepwedgepower/man/summarize_by_group.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_assumptions.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_batched_assumptions.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_batched_design.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_component_assumptions.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_component_design.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_component_power.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_design.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_incomplete_component_design.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_multistage_assumptions.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_multistage_design.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_multistage_power.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/sw_power.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/type1_component_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/type1_multistage_swcrt.Rd |only stepwedgepower-0.4.1/stepwedgepower/man/validate_engine.Rd |only stepwedgepower-0.4.1/stepwedgepower/tests/testthat/test-batched.R |only stepwedgepower-0.4.1/stepwedgepower/tests/testthat/test-benchmark-module.R |only stepwedgepower-0.4.1/stepwedgepower/tests/testthat/test-component.R |only stepwedgepower-0.4.1/stepwedgepower/tests/testthat/test-core.R | 113 - stepwedgepower-0.4.1/stepwedgepower/tests/testthat/test-generic-tools.R |only stepwedgepower-0.4.1/stepwedgepower/tests/testthat/test-grid.R |only stepwedgepower-0.4.1/stepwedgepower/tests/testthat/test-multistage.R |only stepwedgepower-0.4.1/stepwedgepower/tests/testthat/test-swcrt.R |only stepwedgepower-0.4.1/stepwedgepower/tests/testthat/test-validate.R |only stepwedgepower-0.4.1/stepwedgepower/vignettes |only 112 files changed, 1515 insertions(+), 1158 deletions(-)
More information about stepwedgepower at CRAN
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Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Synthesize Bio [aut],
Alex David [aut, cre]
Maintainer: Alex David <alex@synthesize.bio>
Diff between rsynthbio versions 4.2.2 dated 2026-10-14 and 4.2.3 dated 2026-10-17
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++-------- NEWS.md | 8 ++++++ R/call_model_api.R | 3 +- R/gem2-output-transformers.R |only README.md | 41 +++++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/baseline.html | 3 +- inst/doc/getting-started.html | 3 +- inst/doc/metadata-prediction.html | 3 +- inst/doc/reference-conditioning.html | 3 +- inst/doc/self-hosted.html | 3 +- tests/testthat/test-gem2-hosted.R |only 13 files changed, 76 insertions(+), 19 deletions(-)
Title: Creates Statistical Reports
Description: Contains functions to create regulatory-style statistical reports.
Originally designed to create tables, listings, and figures for the
pharmaceutical, biotechnology, and medical device industries, these
reports are generalized enough that they could be used in any industry.
Generates text, rich-text, PDF, HTML, and Microsoft Word file formats.
The package specializes
in printing wide and long tables with automatic page wrapping and splitting.
Reports can be produced with a minimum of function calls, and without
relying on other table packages. The package supports titles, footnotes,
page header, page footers, spanning headers, page by variables,
and automatic page numbering.
Author: David Bosak [aut, cre],
Bill Huang [aut],
Kevin Kramer [ctb],
Duong Tran [ctb],
Raphael Huang [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between reporter versions 1.4.9 dated 2026-09-12 and 1.5.0 dated 2026-10-17
DESCRIPTION | 6 MD5 | 71 +- NEWS.md | 38 - R/create_style.R | 523 ++++++++++++++- R/create_table_docx.R | 45 + R/create_table_html.R | 70 +- R/create_table_pdf.R | 1049 ++++++++++++++++++++++++++++---- R/create_table_rtf.R | 127 +-- R/page_template_docx.R | 2 R/page_template_html.R | 18 R/page_template_rtf.R | 8 R/reporter.R | 3 R/sizing_functions.R | 175 +++++ R/table_spec.r | 36 - R/utilities.R | 187 +++-- R/write_docx.R | 32 R/write_pdf.R | 124 +++ README.md | 2 inst/doc/reporter-styles.R | 31 inst/doc/reporter-styles.Rmd | 77 +- inst/doc/reporter-styles.html | 118 ++- man/cell_style.Rd | 244 +++++-- man/column_defaults.Rd | 3 man/define.Rd | 7 man/images/example12k.png |binary man/reporter.Rd | 3 man/stub.Rd | 3 tests/testthat/test-create_style.R |only tests/testthat/test-docx.R | 282 ++++++++ tests/testthat/test-html.R | 348 ++++++++++ tests/testthat/test-page_template_rtf.R | 9 tests/testthat/test-pdf2.R | 882 ++++++++++++++++++++++++++ tests/testthat/test-rtf2.R | 278 ++++++++ tests/testthat/test-sizing_functions.R | 237 +++++++ tests/testthat/test-utilities.R | 35 + tests/testthat/test-write_pdf.R | 16 vignettes/reporter-styles.Rmd | 77 +- 37 files changed, 4567 insertions(+), 599 deletions(-)
Title: Progress Reporting of Common Functions via One Magic Function
Description: The progressify() function rewrites (transpiles) calls to sequential and parallel map-reduce functions such as base::lapply(), purrr::map(), foreach::foreach(), and plyr::llply() to signal progress updates. By combining this function with R's native pipe operator, you have a straightforward way to report progress on iterative computations with minimal refactoring, e.g. 'lapply(x, fcn) |> progressify()' and 'purrr::map(x, fcn) |> progressify()'. It is compatible with the parallel-processing map-reduce packages 'future.apply', 'furrr', 'crossmap', 'foreach', 'doFuture', and 'futurize'. It also supports domain-specific packages including 'boot', 'fwb', 'lme4', 'partykit', 'sandwich', and 'SimDesign', e.g. 'boot::boot(data, stat, R) |> progressify()'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressify versions 0.2.0 dated 2026-05-31 and 0.4.0 dated 2026-10-17
DESCRIPTION | 8 MD5 | 96 ++++---- NAMESPACE | 13 - NEWS.md | 71 ++++++ R/000.bquote.R | 5 R/000.import-progressr.R |only R/000.import.R | 13 - R/builtin-base.R | 241 +++++++++++++++++++++ R/builtin-common-templates.R | 45 +++ R/builtin-crossmap.R | 8 R/builtin-foreach.R | 24 +- R/builtin-future.apply.R | 20 + R/builtin-fwb.R | 10 R/builtin-stats.R | 7 R/find_s3_method.R | 132 +++++++++++ R/find_s4_method.R | 20 + R/is_s3_generic.R | 3 R/parse_call.R | 15 + R/progressify.R | 26 ++ R/transpile.R | 168 ++++++++++++-- R/transpiler-hooks.R |only R/transpiler-unwrap.R | 7 R/utils-debug.R | 54 +++- R/utils.R | 3 R/vignette_engine.R | 9 R/zzz.R | 2 build/vignette.rds |binary inst/doc/progressify-11-base.html | 4 inst/doc/progressify-11-base.md | 4 inst/testme/run.R | 15 - inst/testme/test-progressify-SimDesign.R | 7 inst/testme/test-progressify-base-apply.R |only inst/testme/test-progressify-base-mapply.R |only inst/testme/test-progressify-base-tapply.R |only inst/testme/test-progressify-base.R | 135 +++++++++++ inst/testme/test-progressify-crossmap-future.R | 70 ++++++ inst/testme/test-progressify-crossmap.R | 70 ++++++ inst/testme/test-progressify-foreach-doFuture.R | 40 +++ inst/testme/test-progressify-foreach.R | 66 +++++ inst/testme/test-progressify-furrr.R | 9 inst/testme/test-progressify-future.apply-apply.R |only inst/testme/test-progressify-future.apply-mapply.R |only inst/testme/test-progressify-future.apply-tapply.R |only inst/testme/test-progressify-future.apply.R | 118 ++++++++++ inst/testme/test-progressify-fwb.R | 3 inst/testme/test-progressify-generic.R |only inst/testme/test-progressify-plyr.R | 37 +++ inst/testme/test-progressify-purrr.R | 8 inst/testme/test-progressify-stats.R | 35 +++ inst/testme/test-progressify-unwrap.R |only man/progressify.Rd | 24 ++ man/transpile.Rd | 2 tests/test-progressify-generic.R |only tests/test-progressify-unwrap.R |only vignettes/progressify-11-base.md | 4 55 files changed, 1510 insertions(+), 141 deletions(-)
Title: Web Interface to 'IsoplotR'
Description: Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Author: Pieter Vermeesch [aut, cre],
Tim Band [ctb]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotRgui versions 7.0 dated 2026-08-21 and 7.1 dated 2026-10-17
DESCRIPTION | 10 ++-- MD5 | 60 ++++++++++++------------- R/IsoplotR.R | 24 +++++++++- R/server.R | 2 inst/www/help/ages.html | 10 ++-- inst/www/help/unmix.html |only inst/www/home/news.html | 53 +++++++++++----------- inst/www/js/IsoplotR.js | 44 ++++++++++-------- inst/www/js/examples.js | 74 +++++++++++++------------------ inst/www/js/js2R.js | 2 inst/www/js/settings.json | 10 +++- inst/www/locales/en/contextual_help.json | 9 ++- inst/www/locales/en/dictionary_id.json | 9 ++- inst/www/locales/en/home_id.json | 2 inst/www/options/Ar-Ar.html | 4 - inst/www/options/K-Ca.html | 10 ++-- inst/www/options/Lu-Hf.html | 14 ++--- inst/www/options/Pb-Pb.html | 10 ++-- inst/www/options/Rb-Sr.html | 10 ++-- inst/www/options/Re-Os.html | 16 +++--- inst/www/options/Sm-Nd.html | 26 +++++----- inst/www/options/Th-Pb.html | 4 - inst/www/options/Th-U.html | 12 ++--- inst/www/options/U-Pb.html | 35 +++++++------- inst/www/options/U-Th-He.html | 12 ++--- inst/www/options/ages.html | 1 inst/www/options/detritals.html | 4 + inst/www/options/evolution.html | 2 inst/www/options/fissiontracks.html | 6 +- inst/www/options/isochron.html | 2 inst/www/options/unmix.html |only inst/www/version.txt | 2 32 files changed, 254 insertions(+), 225 deletions(-)
Title: Wrangle and Analyze Growth Curve Data
Description: Easy importing, wrangling, and model-free analysis of microbial
growth curve data, as commonly output by plate readers. Tools for flexibly
importing all the common data formats output by plate readers and reshaping
them into 'tidy' formats for analyses. Tools for importing experimental
designs from files or generating them in R and merging design information
with density data, making it easy to analyze with 'gcplyr' and 'tidyverse'
or 'dplyr' functions, and to plot with 'ggplot2'. Streamlines extracting
parameters like growth rate/doubling time, maximum density (carrying capacity),
lag time, area under the curve, diauxic shifts, extinction, and more without
fitting an equation for growth to your data. Has several methods to deal with
noise in growth curve data. See methods at
<https://mikeblazanin.github.io/gcplyr/>.
Author: Mike Blazanin [aut, cre]
Maintainer: Mike Blazanin <mikeblazanin@gmail.com>
Diff between gcplyr versions 1.12.0 dated 2025-07-29 and 1.13.1 dated 2026-10-17
DESCRIPTION | 30 MD5 | 164 +- NEWS.md | 22 R/data.R | 52 R/example_functions.R | 2 R/functions.R | 1877 ++++++++++++++++---------------- R/utility_functions.R | 392 +++--- README.md | 24 build/vignette.rds |binary inst/doc/gc01_gcplyr.R | 5 inst/doc/gc01_gcplyr.Rmd | 5 inst/doc/gc01_gcplyr.pdf |binary inst/doc/gc02_import_reshape.pdf |binary inst/doc/gc03_incorporate_designs.pdf |binary inst/doc/gc04_preprocess_plot.pdf |binary inst/doc/gc05_process.Rmd | 34 inst/doc/gc05_process.pdf |binary inst/doc/gc06_analyze.R | 45 inst/doc/gc06_analyze.Rmd | 73 - inst/doc/gc06_analyze.pdf |binary inst/doc/gc07_noise.pdf |binary inst/doc/gc08_conclusion.pdf |binary inst/doc/gc09_multiple_plates.pdf |binary inst/doc/gc10_using_make_design.pdf |binary man/CentroidFunctions.Rd | 44 man/ExtremaFunctions.Rd | 74 - man/MinMaxGC.Rd | 26 man/MovingWindowFunctions.Rd | 30 man/ThresholdFunctions.Rd | 66 - man/WhichMinMaxGC.Rd | 28 man/auc.Rd | 30 man/block_tidydesign.Rd | 18 man/calc_deriv.Rd | 128 +- man/doubling_time.Rd | 18 man/example_design_tidy.Rd | 25 man/example_widedata.Rd | 24 man/example_widedata_noiseless.Rd | 24 man/extr_val.Rd | 47 man/first_peak.Rd | 55 man/from_excel.Rd | 4 man/gc_smooth.spline.Rd | 22 man/import_blockdesigns.Rd | 112 - man/import_blockmeasures.Rd | 46 man/lag_time.Rd | 76 - man/make_design.Rd | 95 - man/make_designpattern.Rd | 12 man/make_tidydesign.Rd | 74 - man/makemethod_train_smooth_data.Rd | 30 man/merge_dfs.Rd | 61 - man/paste_blocks.Rd | 30 man/predict_interpolation.Rd | 16 man/print_df.Rd | 2 man/read_blocks.Rd | 152 +- man/read_tidys.Rd | 80 - man/read_wides.Rd | 78 - man/separate_tidy.Rd | 38 man/smooth_data.Rd | 130 +- man/solve_linear.Rd | 50 man/to_excel.Rd | 4 man/train_smooth_data.Rd | 92 - man/trans_block_to_wide.Rd | 14 man/trans_wide_to_tidy.Rd | 46 man/uninterleave.Rd | 20 man/write_blocks.Rd | 88 - tests/testthat/test_utilityfunctions.R | 19 vignettes/gc01_gcplyr.Rmd | 5 vignettes/gc01_gcplyr.docx |only vignettes/gc01_gcplyr.html | 75 - vignettes/gc02_import_reshape.docx |only vignettes/gc02_import_reshape.html | 19 vignettes/gc03_incorporate_designs.docx |only vignettes/gc03_incorporate_designs.html | 5 vignettes/gc04_preprocess_plot.docx |only vignettes/gc04_preprocess_plot.html | 5 vignettes/gc05_process.Rmd | 34 vignettes/gc05_process.docx |only vignettes/gc05_process.html | 67 - vignettes/gc06_analyze.Rmd | 73 - vignettes/gc06_analyze.docx |only vignettes/gc06_analyze.html | 859 ++++++++------ vignettes/gc07_noise.docx |only vignettes/gc07_noise.html | 61 - vignettes/gc08_conclusion.docx |only vignettes/gc08_conclusion.html | 13 vignettes/gc09_multiple_plates.docx |only vignettes/gc09_multiple_plates.html | 41 vignettes/gc10_using_make_design.docx |only vignettes/gc10_using_make_design.html | 5 88 files changed, 3215 insertions(+), 2800 deletions(-)
Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to assist in key steps involved in any data
analysis workflow: (1) wrangling the raw data to get it in the needed form,
(2) applying preprocessing steps and statistical transformations, and
(3) compute statistical summaries of data properties and distributions.
It is also the data wrangling backend for packages in 'easystats' ecosystem.
References: Patil et al. (2022) <doi:10.21105/joss.04684>.
Author: Jeffrey Girard [aut, cre] ,
Indrajeet Patil [aut] ,
Etienne Bacher [aut] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [ctb] ,
Elin Waring [ctb],
Thomas J. Faulkenberry [re [...truncated...]
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between datawizard versions 1.4.0 dated 2026-09-10 and 1.4.1 dated 2026-10-17
DESCRIPTION | 21 MD5 | 474 ++--- NAMESPACE | 708 +++---- NEWS.md | 2255 ++++++++++++------------ R/adjust.R | 472 ++--- R/assign_labels.R | 362 +-- R/categorize.R | 986 +++++----- R/center.R | 708 +++---- R/contrs.R | 206 +- R/convert_na_to.R | 434 ++-- R/convert_to_na.R | 438 ++-- R/data.R | 42 R/data_addprefix.R | 148 - R/data_arrange.R | 308 +-- R/data_codebook.R | 1144 ++++++------ R/data_duplicated.R | 210 +- R/data_extract.R | 310 +-- R/data_group.R | 158 - R/data_match.R | 824 ++++---- R/data_merge.R | 860 ++++----- R/data_modify.R | 1354 +++++++------- R/data_partition.R | 326 +-- R/data_peek.R | 304 +-- R/data_read.R | 1180 ++++++------ R/data_relocate.R | 354 +-- R/data_remove.R | 76 R/data_rename.R | 582 +++--- R/data_replicate.R | 252 +- R/data_rescale.R | 718 +++---- R/data_restoretype.R | 100 - R/data_reverse.R | 624 +++--- R/data_rotate.R | 206 +- R/data_seek.R | 380 ++-- R/data_select.R | 88 R/data_separate.R | 876 ++++----- R/data_summary.R | 836 ++++---- R/data_tabulate.R | 2594 +++++++++++++-------------- R/data_to_long.R | 764 ++++---- R/data_to_wide.R | 930 ++++----- R/data_unique.R | 308 +-- R/data_unite.R | 238 +- R/data_write.R | 834 ++++---- R/data_xtabulate.R | 1164 ++++++------ R/datawizard-package.R | 42 R/demean.R | 1156 ++++++------ R/describe_distribution.R | 1640 ++++++++--------- R/descriptives.R | 452 ++-- R/extract_column_names.R | 360 +-- R/format.R | 214 +- R/labels_to_levels.R | 216 +- R/makepredictcall.R | 166 - R/mean_sd.R | 192 +- R/means_by_group.R | 684 +++---- R/normalize.R | 622 +++--- R/ranktransform.R | 404 ++-- R/recode_into.R | 606 +++--- R/recode_values.R | 1136 ++++++------ R/remove_empty.R | 254 +- R/replace_nan_inf.R | 126 - R/rescale_weights.R | 950 +++++----- R/reshape_ci.R | 274 +- R/row_count.R | 266 +- R/row_means.R | 428 ++-- R/select_nse.R | 1516 ++++++++-------- R/skewness_kurtosis.R | 994 +++++----- R/slide.R | 210 +- R/smoothness.R | 270 +- R/standardize.R | 874 ++++----- R/standardize.models.R | 1186 ++++++------ R/text_format.R | 334 +-- R/to_factor.R | 284 +-- R/to_numeric.R | 674 +++---- R/unnormalize.R | 332 +-- R/unstandardize.R | 686 +++---- R/utils-cols.R | 188 +- R/utils-rows.R | 302 +-- R/utils.R | 524 ++--- R/utils_labels.R | 190 +- R/utils_standardize_center.R | 1056 +++++------ R/visualisation_recipe.R | 184 - R/weighted_mean_median_sd_mad.R | 328 +-- R/winsorize.R | 298 +-- README.md | 1242 ++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 236 +- man/adjust.Rd | 328 +-- man/as.prop.table.Rd | 206 +- man/assign_labels.Rd | 296 +-- man/categorize.Rd | 528 ++--- man/center.Rd | 400 ++-- man/coef_var.Rd | 186 - man/coerce_to_numeric.Rd | 44 man/colnames.Rd | 100 - man/contr.deviation.Rd | 206 +- man/convert_na_to.Rd | 344 +-- man/convert_to_na.Rd | 252 +- man/data_arrange.Rd | 70 man/data_codebook.Rd | 344 +-- man/data_duplicated.Rd | 218 +- man/data_extract.Rd | 294 +-- man/data_group.Rd | 212 +- man/data_match.Rd | 268 +- man/data_merge.Rd | 412 ++-- man/data_modify.Rd | 368 +-- man/data_partition.Rd | 168 - man/data_peek.Rd | 210 +- man/data_prefix_suffix.Rd | 214 +- man/data_read.Rd | 326 +-- man/data_relocate.Rd | 310 +-- man/data_rename.Rd | 286 +-- man/data_replicate.Rd | 200 +- man/data_restoretype.Rd | 70 man/data_rotate.Rd | 136 - man/data_seek.Rd | 136 - man/data_separate.Rd | 454 ++-- man/data_summary.Rd | 258 +- man/data_tabulate.Rd | 532 ++--- man/data_to_long.Rd | 486 ++--- man/data_to_wide.Rd | 512 ++--- man/data_unique.Rd | 214 +- man/data_unite.Rd | 232 +- man/datawizard-package.Rd | 105 - man/demean.Rd | 702 +++---- man/describe_distribution.Rd | 370 +-- man/distribution_mode.Rd | 76 man/efc.Rd | 24 man/extract_column_names.Rd | 398 ++-- man/labels_to_levels.Rd | 240 +- man/makepredictcall.dw_transformer.Rd | 106 - man/mean_sd.Rd | 98 - man/means_by_group.Rd | 272 +- man/nhanes_sample.Rd | 28 man/normalize.Rd | 372 +-- man/ranktransform.Rd | 288 +-- man/recode_into.Rd | 252 +- man/recode_values.Rd | 600 +++--- man/reexports.Rd | 36 man/remove_empty.Rd | 150 - man/replace_nan_inf.Rd | 64 man/rescale.Rd | 390 ++-- man/rescale_weights.Rd | 354 +-- man/reshape_ci.Rd | 76 man/reverse.Rd | 300 +-- man/row_count.Rd | 274 +- man/row_means.Rd | 336 +-- man/rownames.Rd | 110 - man/skewness.Rd | 296 +-- man/slide.Rd | 288 +-- man/smoothness.Rd | 74 man/standardize.Rd | 584 +++--- man/standardize.default.Rd | 200 +- man/text_format.Rd | 162 - man/to_factor.Rd | 268 +- man/to_numeric.Rd | 290 +-- man/visualisation_recipe.Rd | 60 man/weighted_mean.Rd | 112 - man/winsorize.Rd | 196 +- tests/testthat/_snaps/data_tabulate.md | 2016 ++++++++++----------- tests/testthat/test-adjust.R | 98 - tests/testthat/test-assign_labels.R | 138 - tests/testthat/test-attributes-grouped-df.R | 132 - tests/testthat/test-attributes.R | 360 +-- tests/testthat/test-categorize.R | 1388 +++++++------- tests/testthat/test-center.R | 396 ++-- tests/testthat/test-coef_var.R | 80 tests/testthat/test-contr.deviation.R | 68 tests/testthat/test-convert_na_to.R | 934 ++++----- tests/testthat/test-convert_to_na.R | 380 ++-- tests/testthat/test-data_addprefix.R | 114 - tests/testthat/test-data_arrange.R | 310 +-- tests/testthat/test-data_codebook.R | 514 ++--- tests/testthat/test-data_duplicated.R | 224 +- tests/testthat/test-data_extract.R | 336 +-- tests/testthat/test-data_group.R | 266 +- tests/testthat/test-data_match.R | 746 +++---- tests/testthat/test-data_merge.R | 634 +++--- tests/testthat/test-data_modify.R | 2022 ++++++++++----------- tests/testthat/test-data_partition.R | 318 +-- tests/testthat/test-data_peek.R | 70 tests/testthat/test-data_read.R | 1254 ++++++------- tests/testthat/test-data_recode.R | 1010 +++++----- tests/testthat/test-data_relocate.R | 274 +- tests/testthat/test-data_remove.R | 262 +- tests/testthat/test-data_rename.R | 498 ++--- tests/testthat/test-data_reorder.R | 58 tests/testthat/test-data_replicate.R | 210 +- tests/testthat/test-data_rescale.R | 484 ++--- tests/testthat/test-data_restoretype.R | 68 tests/testthat/test-data_reverse.R | 1058 +++++------ tests/testthat/test-data_rotate.R | 182 - tests/testthat/test-data_seek.R | 176 - tests/testthat/test-data_select.R | 864 ++++----- tests/testthat/test-data_separate.R | 838 ++++---- tests/testthat/test-data_shift.R | 78 tests/testthat/test-data_summary.R | 1118 +++++------ tests/testthat/test-data_tabulate.R | 2626 ++++++++++++++-------------- tests/testthat/test-data_to_factor.R | 436 ++-- tests/testthat/test-data_to_long.R | 1062 +++++------ tests/testthat/test-data_to_numeric.R | 528 ++--- tests/testthat/test-data_to_wide.R | 1305 +++++++------ tests/testthat/test-data_unique.R | 338 +-- tests/testthat/test-data_unite.R | 428 ++-- tests/testthat/test-data_write.R | 548 ++--- tests/testthat/test-demean.R | 724 +++---- tests/testthat/test-describe_distribution.R | 1112 +++++------ tests/testthat/test-discovr.R | 26 tests/testthat/test-distributions.R | 24 tests/testthat/test-empty-dataframe.R | 148 - tests/testthat/test-extract_column_names.R | 388 ++-- tests/testthat/test-labelled_data.R | 794 ++++---- tests/testthat/test-labels_to_levels.R | 310 +-- tests/testthat/test-makepredictcall.R | 134 - tests/testthat/test-mean_sd.R | 60 tests/testthat/test-means_by_group.R | 74 tests/testthat/test-normalize.R | 496 ++--- tests/testthat/test-print.dw_transformer.R | 14 tests/testthat/test-ranktransform.R | 284 +-- tests/testthat/test-recode_into.R | 970 +++++----- tests/testthat/test-replace_nan_inf.R | 78 tests/testthat/test-rescale_weights.R | 332 +-- tests/testthat/test-reshape_ci.R | 54 tests/testthat/test-row_count.R | 198 +- tests/testthat/test-row_means.R | 162 - tests/testthat/test-select_nse.R | 346 +-- tests/testthat/test-skewness-kurtosis.R | 204 +- tests/testthat/test-smoothness.R | 74 tests/testthat/test-standardize-data.R | 856 ++++----- tests/testthat/test-standardize_datagrid.R | 40 tests/testthat/test-std_center.R | 492 ++--- tests/testthat/test-std_center_scale_args.R | 158 - tests/testthat/test-text_format.R | 174 - tests/testthat/test-unnormalize.R | 306 +-- tests/testthat/test-utils.R | 92 tests/testthat/test-utils_cols.R | 232 +- tests/testthat/test-utils_rows.R | 460 ++-- tests/testthat/test-weighted-stats.R | 86 tests/testthat/test-winsorization.R | 106 - 238 files changed, 51948 insertions(+), 51930 deletions(-)
Title: A Common Interface for Visualizing and Reporting Sensitivity
Analyses for Unmeasured Confounding
Description: A common interface to established sensitivity analyses for
unmeasured confounding in observational studies. Results of impact
threshold and robustness of inference to replacement analysis (Frank,
2000, <doi:10.1177/0049124100029002001>; Frank et al., 2013,
<doi:10.3102/0162373713493129>), partial R-squared omitted-variable bias
analysis (Cinelli and Hazlett, 2020, <doi:10.1111/rssb.12348>), E-values
(VanderWeele and Ding, 2017, <doi:10.7326/M16-2607>), and Rosenbaum
bounds for matched pairs (Rosenbaum, 2002,
<doi:10.1007/978-1-4757-3692-2>) are stored in one object that keeps
each framework's own parameter. Robustness curves, summary tables,
and plain-language reports are available for every framework;
two-parameter surfaces, the exact correlation contour, and
observed-covariate benchmarks are provided where the corresponding
framework defines them. Results
can be computed from fitted models or matched-pair differences, or
converted from the 'sensemakr', ' [...truncated...]
Author: Subir Hait [aut, cre]
Maintainer: Subir Hait <haitsubi@msu.edu>
Diff between confoundvis versions 0.2.0 dated 2026-09-30 and 0.3.0 dated 2026-10-17
confoundvis-0.2.0/confoundvis/R/fit_local_quadratic.R |only confoundvis-0.2.0/confoundvis/R/plot_local_taylor.R |only confoundvis-0.2.0/confoundvis/R/plot_reversal_cone.R |only confoundvis-0.2.0/confoundvis/R/plot_taylor_panels.R |only confoundvis-0.2.0/confoundvis/R/simulate_taylor_demo.R |only confoundvis-0.2.0/confoundvis/inst/doc/confoundvis-intro.R |only confoundvis-0.2.0/confoundvis/inst/doc/confoundvis-intro.Rmd |only confoundvis-0.2.0/confoundvis/inst/doc/confoundvis-intro.html |only confoundvis-0.2.0/confoundvis/man/fit_local_quadratic.Rd |only confoundvis-0.2.0/confoundvis/man/plot_cone_comparison.Rd |only confoundvis-0.2.0/confoundvis/man/plot_local_taylor.Rd |only confoundvis-0.2.0/confoundvis/man/plot_reversal_cone.Rd |only confoundvis-0.2.0/confoundvis/man/plot_taylor_panels.Rd |only confoundvis-0.2.0/confoundvis/man/simulate_taylor_demo.Rd |only confoundvis-0.2.0/confoundvis/tests/testthat/test-fit_local_quadratic.R |only confoundvis-0.2.0/confoundvis/tests/testthat/test-geometry_plots.R |only confoundvis-0.2.0/confoundvis/tests/testthat/test-plot_local_taylor.R |only confoundvis-0.2.0/confoundvis/tests/testthat/test-simulate_taylor_demo.R |only confoundvis-0.2.0/confoundvis/vignettes/confoundvis-intro.Rmd |only confoundvis-0.3.0/confoundvis/DESCRIPTION | 46 confoundvis-0.3.0/confoundvis/MD5 | 136 - confoundvis-0.3.0/confoundvis/NAMESPACE | 92 - confoundvis-0.3.0/confoundvis/NEWS.md | 201 +- confoundvis-0.3.0/confoundvis/R/adapters.R | 330 ++-- confoundvis-0.3.0/confoundvis/R/as_confoundsens.R | 224 +- confoundvis-0.3.0/confoundvis/R/as_data_frame_confoundsens.R | 64 confoundvis-0.3.0/confoundvis/R/new_confoundsens.R | 112 - confoundvis-0.3.0/confoundvis/R/plot_robustness_curve.R | 218 +- confoundvis-0.3.0/confoundvis/R/plot_sensitivity_contour.R | 342 ++-- confoundvis-0.3.0/confoundvis/R/plot_sensitivity_love.R | 188 +- confoundvis-0.3.0/confoundvis/R/print_confoundsens.R | 98 - confoundvis-0.3.0/confoundvis/R/report.R | 411 ++-- confoundvis-0.3.0/confoundvis/R/rir.R |only confoundvis-0.3.0/confoundvis/R/sens_lm.R | 823 +++++----- confoundvis-0.3.0/confoundvis/R/sens_pairs.R |only confoundvis-0.3.0/confoundvis/R/sens_table.R |only confoundvis-0.3.0/confoundvis/R/summary_confoundsens.R | 132 - confoundvis-0.3.0/confoundvis/R/surface.R |only confoundvis-0.3.0/confoundvis/R/validate_confoundsens.R | 154 - confoundvis-0.3.0/confoundvis/R/zzz-globals.R | 20 confoundvis-0.3.0/confoundvis/R/zzz.R | 82 confoundvis-0.3.0/confoundvis/README.md | 168 -- confoundvis-0.3.0/confoundvis/build/vignette.rds |binary confoundvis-0.3.0/confoundvis/inst/doc/confoundvis-workflow.R | 27 confoundvis-0.3.0/confoundvis/inst/doc/confoundvis-workflow.Rmd | 497 +++--- confoundvis-0.3.0/confoundvis/inst/doc/confoundvis-workflow.html | 114 + confoundvis-0.3.0/confoundvis/man/as.data.frame.confoundsens.Rd | 56 confoundvis-0.3.0/confoundvis/man/as_confoundsens.Rd | 156 - confoundvis-0.3.0/confoundvis/man/confoundvis-package.Rd | 114 - confoundvis-0.3.0/confoundvis/man/covariate_impacts.Rd | 151 - confoundvis-0.3.0/confoundvis/man/from_evalue.Rd | 78 confoundvis-0.3.0/confoundvis/man/from_konfound.Rd | 106 - confoundvis-0.3.0/confoundvis/man/from_sensemakr.Rd | 80 confoundvis-0.3.0/confoundvis/man/itcv_lm.Rd | 134 - confoundvis-0.3.0/confoundvis/man/new_confoundsens.Rd | 106 - confoundvis-0.3.0/confoundvis/man/plot_robustness_curve.Rd | 106 - confoundvis-0.3.0/confoundvis/man/plot_sensitivity_contour.Rd | 122 + confoundvis-0.3.0/confoundvis/man/plot_sensitivity_love.Rd | 106 - confoundvis-0.3.0/confoundvis/man/plot_sensitivity_surface.Rd |only confoundvis-0.3.0/confoundvis/man/print.confoundsens.Rd | 52 confoundvis-0.3.0/confoundvis/man/rir_lm.Rd |only confoundvis-0.3.0/confoundvis/man/robustness_points.Rd | 76 confoundvis-0.3.0/confoundvis/man/sens_path_lm.Rd | 106 - confoundvis-0.3.0/confoundvis/man/sens_path_pairs.Rd |only confoundvis-0.3.0/confoundvis/man/sens_report.Rd | 62 confoundvis-0.3.0/confoundvis/man/sens_surface.Rd |only confoundvis-0.3.0/confoundvis/man/sens_table.Rd |only confoundvis-0.3.0/confoundvis/man/summary.confoundsens.Rd | 60 confoundvis-0.3.0/confoundvis/man/validate_confoundsens.Rd | 42 confoundvis-0.3.0/confoundvis/tests/testthat.R | 24 confoundvis-0.3.0/confoundvis/tests/testthat/test-adapters.R | 122 - confoundvis-0.3.0/confoundvis/tests/testthat/test-as_confoundsens.R | 50 confoundvis-0.3.0/confoundvis/tests/testthat/test-as_data_frame_confoundsens.R | 46 confoundvis-0.3.0/confoundvis/tests/testthat/test-new_confoundsens.R | 90 - confoundvis-0.3.0/confoundvis/tests/testthat/test-plot_robustness_curve.R | 58 confoundvis-0.3.0/confoundvis/tests/testthat/test-plot_sensitivity_contour.R | 88 - confoundvis-0.3.0/confoundvis/tests/testthat/test-plot_sensitivity_love.R | 60 confoundvis-0.3.0/confoundvis/tests/testthat/test-print_summary.R | 54 confoundvis-0.3.0/confoundvis/tests/testthat/test-report.R | 110 - confoundvis-0.3.0/confoundvis/tests/testthat/test-rir.R |only confoundvis-0.3.0/confoundvis/tests/testthat/test-sens_lm.R | 280 +-- confoundvis-0.3.0/confoundvis/tests/testthat/test-sens_pairs.R |only confoundvis-0.3.0/confoundvis/tests/testthat/test-sens_table.R |only confoundvis-0.3.0/confoundvis/tests/testthat/test-surface.R |only confoundvis-0.3.0/confoundvis/vignettes/confoundvis-workflow.Rmd | 497 +++--- 85 files changed, 4229 insertions(+), 3442 deletions(-)
Title: Augmented Modelling of Relational Events
Description: An integrated workflow for relational event models, in which
timestamped interactions among actors arrive in continuous time and the
event rate depends on the history of the network itself. Event streams are
simulated by an exact Gillespie kernel or an approximate tau-leap kernel;
non-events are drawn by case-control sampling in the manner of Lerner and
Lomi (2020) <doi:10.1017/nws.2019.57>, or from a time-shifted copy of the
process so that covariates shared by all dyads at a given time remain
estimable (Lembo et al. 2025, <doi:10.1093/jrsssc/qlaf058>); the
timing- and closure-based
endogenous statistics of Juozaitiene and Wit (2024)
<doi:10.1093/jrsssa/qnae132> are computed from that history; and one
front-end fits the resulting case-control data by conditional-logistic
partial likelihood, by penalised regression on its degenerate
one-control binomial form (which admits smooth, time-varying and actor
random effects), or by stochastic gradient descent, including the
[...truncated...]
Author: Francisco Richter [aut, cre, cph],
Martina Boschi [aut],
Ernst C. Wit [aut],
Melania Lembo [aut]
Maintainer: Francisco Richter <richtf@usi.ch>
Diff between amorem versions 1.0.0 dated 2026-06-29 and 1.1.0 dated 2026-10-17
DESCRIPTION | 39 +- MD5 | 60 +-- NAMESPACE | 1 NEWS.md | 158 +++++++- R/compare_models.R | 8 R/compare_models_global.R | 86 ++-- R/data.R | 43 ++ R/preprocess.R | 381 +++++++++++++++----- R/rem.R | 159 +++++++- R/widen_case_control.R | 7 README.md | 56 ++ data/enso_nino34.rda |only inst/doc/model-comparison.R | 2 inst/doc/model-comparison.Rmd | 11 inst/doc/model-comparison.html | 34 - inst/doc/species-invasion.R | 115 +++--- inst/doc/species-invasion.Rmd | 250 ++++++++----- inst/doc/species-invasion.html | 275 ++++++++------ inst/extdata/enso_nino34 |only man/amorem-package.Rd | 5 man/compare_models_global.Rd | 26 - man/endogenous_features.Rd | 11 man/enso_nino34.Rd |only man/rem.Rd | 46 ++ man/sample_non_events.Rd | 86 ++++ man/widen_case_control.Rd | 6 tests/testthat/test-case-control-history.R |only tests/testthat/test-compare-models-stratification.R |only tests/testthat/test-enso-nino34.R |only tests/testthat/test-preprocess.R | 9 tests/testthat/test-rem-shifted-time.R |only tests/testthat/test-rem-term-args.R |only tests/testthat/test-sample-non-events-issue102.R |only tests/testthat/test-sample-non-events-shift.R |only vignettes/model-comparison.Rmd | 11 vignettes/species-invasion.Rmd | 250 ++++++++----- 36 files changed, 1535 insertions(+), 600 deletions(-)
Title: Trade and Environment Equilibrium Modeling System
Description: Equilibrium models are frequently employed to examine the
potential impacts of economic, energy, and trade policies as well as
form the foundation of most integrated assessment models. The 'teems'
package handles all aspects of running equilibrium models while
facilitating transparent and reproducible workflows.
Author: Matthew Cantele [aut, cre, cph] ,
Tom Kompas [ctb, ths] ,
Ha Van Pham [ctb] ,
Martin Ingram [ctb]
Maintainer: Matthew Cantele <matthew.cantele@protonmail.com>
Diff between teems versions 0.1.1 dated 2026-06-17 and 1.0.0 dated 2026-10-17
teems-0.1.1/teems/R/agginput_inject.R |only teems-0.1.1/teems/R/array_slice.R |only teems-0.1.1/teems/R/char_inject_v.R |only teems-0.1.1/teems/R/chk_closure.R |only teems-0.1.1/teems/R/chk_nmed_dots.R |only teems-0.1.1/teems/R/chk_sets_consistency.R |only teems-0.1.1/teems/R/chk_shock.R |only teems-0.1.1/teems/R/cls_entry_exp_ele.R |only teems-0.1.1/teems/R/cls_entry_exp_mixed.R |only teems-0.1.1/teems/R/cls_entry_exp_subset.R |only teems-0.1.1/teems/R/coeff_block_parse.R |only teems-0.1.1/teems/R/coeff_compose.R |only teems-0.1.1/teems/R/df_inject_v.R |only teems-0.1.1/teems/R/get_element.R |only teems-0.1.1/teems/R/get_output_paths.R |only teems-0.1.1/teems/R/get_solver_paths.R |only teems-0.1.1/teems/R/get_timesteps.R |only teems-0.1.1/teems/R/infer_set_mappings.R |only teems-0.1.1/teems/R/info_diagnostics.R |only teems-0.1.1/teems/R/input_mod.R |only teems-0.1.1/teems/R/inputs_data.R |only teems-0.1.1/teems/R/int_set_cnvrt.R |only teems-0.1.1/teems/R/invest_convert_e.R |only teems-0.1.1/teems/R/invest_convert_v.R |only teems-0.1.1/teems/R/mkdir_out.R |only teems-0.1.1/teems/R/mod_coeff.R |only teems-0.1.1/teems/R/mod_tab.R |only teems-0.1.1/teems/R/output_diagnostic.R |only teems-0.1.1/teems/R/parse_solution.R |only teems-0.1.1/teems/R/parse_solution_bins.R |only teems-0.1.1/teems/R/rename_names.R |only teems-0.1.1/teems/R/script_injection.R |only teems-0.1.1/teems/R/set_reduction_default.R |only teems-0.1.1/teems/R/shock_construct.R |only teems-0.1.1/teems/R/shock_construct_cst.R |only teems-0.1.1/teems/R/shock_construct_scn.R |only teems-0.1.1/teems/R/shock_construct_uni.R |only teems-0.1.1/teems/R/shock_finalize.R |only teems-0.1.1/teems/R/shock_implement.R |only teems-0.1.1/teems/R/shock_load.R |only teems-0.1.1/teems/R/shock_preload.R |only teems-0.1.1/teems/R/shock_reduce.R |only teems-0.1.1/teems/R/shock_usr.R |only teems-0.1.1/teems/R/shock_write.R |only teems-0.1.1/teems/R/shock_write_order.R |only teems-0.1.1/teems/R/swap_out_full.R |only teems-0.1.1/teems/R/tabcomp_retrieve.R |only teems-0.1.1/teems/R/val_closure.R |only teems-0.1.1/teems/R/val_shock_args.R |only teems-0.1.1/teems/R/value_injection.R |only teems-0.1.1/teems/R/var_omit.R |only teems-0.1.1/teems/R/write_ragged.R |only teems-0.1.1/teems/R/write_ragged_shk.R |only teems-0.1.1/teems/inst/models/GTAP-INT |only teems-0.1.1/teems/inst/models/GTAP-RE/GTAP-RE.tab |only teems-0.1.1/teems/inst/models/GTAPv6/GTAPv6.tab |only teems-0.1.1/teems/inst/models/GTAPv7/GTAPv7.tab |only teems-0.1.1/teems/inst/scripts/GTAP-INT |only teems-0.1.1/teems/tests/testthat/_snaps/Linux |only teems-0.1.1/teems/tests/testthat/_snaps/Windows |only teems-0.1.1/teems/tests/testthat/test-GTAP-INT.R |only teems-0.1.1/teems/tests/testthat/test-GTAP-RE.R |only teems-0.1.1/teems/tests/testthat/test-GTAPv6.R |only teems-0.1.1/teems/tests/testthat/test-GTAPv7.R |only teems-1.0.0/teems/DESCRIPTION | 12 teems-1.0.0/teems/MD5 | 973 ++++--- teems-1.0.0/teems/NAMESPACE | 81 teems-1.0.0/teems/NEWS.md | 53 teems-1.0.0/teems/R/GTAP_convert.R | 33 teems-1.0.0/teems/R/GTAPv7_header.R | 3 teems-1.0.0/teems/R/R6_options_class.R | 274 +- teems-1.0.0/teems/R/RK_implement.R |only teems-1.0.0/teems/R/abind.R | 6 teems-1.0.0/teems/R/aez_prepare.R |only teems-1.0.0/teems/R/agg_input_inject.R |only teems-1.0.0/teems/R/arr_aggregate.R |only teems-1.0.0/teems/R/arr_codes.R |only teems-1.0.0/teems/R/arr_create.R | 9 teems-1.0.0/teems/R/arr_expand_cols.R |only teems-1.0.0/teems/R/arr_reduce.R |only teems-1.0.0/teems/R/arr_slice.R |only teems-1.0.0/teems/R/array2DT.R | 8 teems-1.0.0/teems/R/auto_evidence.R |only teems-1.0.0/teems/R/auto_lu_ceiling.R |only teems-1.0.0/teems/R/auto_memory_gb.R |only teems-1.0.0/teems/R/auto_method.R |only teems-1.0.0/teems/R/auto_partition.R |only teems-1.0.0/teems/R/auto_thresholds.R |only teems-1.0.0/teems/R/backsolve_all.R |only teems-1.0.0/teems/R/backsolves_resolve.R |only teems-1.0.0/teems/R/chk_arg_class.R | 11 teems-1.0.0/teems/R/chk_backsolve_rules.R |only teems-1.0.0/teems/R/chk_cls.R |only teems-1.0.0/teems/R/chk_cst_scen.R | 18 teems-1.0.0/teems/R/chk_docker.R | 17 teems-1.0.0/teems/R/chk_file.R | 2 teems-1.0.0/teems/R/chk_index_domains.R |only teems-1.0.0/teems/R/chk_input.R | 3 teems-1.0.0/teems/R/chk_memory_fit.R |only teems-1.0.0/teems/R/chk_named_dots.R |only teems-1.0.0/teems/R/chk_orig_level.R |only teems-1.0.0/teems/R/chk_raw_reads.R |only teems-1.0.0/teems/R/chk_raw_statements.R |only teems-1.0.0/teems/R/chk_scen_coverage.R |only teems-1.0.0/teems/R/chk_set_consistency.R |only teems-1.0.0/teems/R/chk_set_map.R | 103 teems-1.0.0/teems/R/chk_sets.R | 12 teems-1.0.0/teems/R/chk_shk.R |only teems-1.0.0/teems/R/chk_shk_repeat.R |only teems-1.0.0/teems/R/chk_shk_value.R |only teems-1.0.0/teems/R/chk_solver_log.R | 138 - teems-1.0.0/teems/R/chk_solver_version.R |only teems-1.0.0/teems/R/chk_statements.R | 116 teems-1.0.0/teems/R/chk_subset_containment.R |only teems-1.0.0/teems/R/chk_swap.R | 51 teems-1.0.0/teems/R/chk_system_square.R |only teems-1.0.0/teems/R/chk_tab_comp.R |only teems-1.0.0/teems/R/chk_tab_defaults.R |only teems-1.0.0/teems/R/chk_tab_file.R | 19 teems-1.0.0/teems/R/chk_tab_names.R |only teems-1.0.0/teems/R/chk_tab_parens.R |only teems-1.0.0/teems/R/chk_tab_postsim.R |only teems-1.0.0/teems/R/chk_tab_preflight.R |only teems-1.0.0/teems/R/chk_tab_qualifiers.R |only teems-1.0.0/teems/R/chk_tab_quantifiers.R |only teems-1.0.0/teems/R/chk_tab_reads.R |only teems-1.0.0/teems/R/chk_tab_ref_indices.R |only teems-1.0.0/teems/R/chk_tab_setbuilders.R |only teems-1.0.0/teems/R/chk_tab_stmt_length.R |only teems-1.0.0/teems/R/chk_time_steps.R | 5 teems-1.0.0/teems/R/class_ems_data.R | 4 teems-1.0.0/teems/R/cli_cmds.R | 18 teems-1.0.0/teems/R/cls_classify.R | 27 teems-1.0.0/teems/R/cls_entry_exp.R | 162 + teems-1.0.0/teems/R/cls_finalize.R | 334 +- teems-1.0.0/teems/R/cls_format.R | 5 teems-1.0.0/teems/R/cls_load.R | 13 teems-1.0.0/teems/R/cls_omit.R |only teems-1.0.0/teems/R/cmd_construct.R | 122 teems-1.0.0/teems/R/cmf_core.R | 28 teems-1.0.0/teems/R/cmf_finalize.R | 14 teems-1.0.0/teems/R/cmf_in_situ.R | 61 teems-1.0.0/teems/R/cmf_retrieve.R | 9 teems-1.0.0/teems/R/cndns.R |only teems-1.0.0/teems/R/cndns_abort.R |only teems-1.0.0/teems/R/cndns_advise.R |only teems-1.0.0/teems/R/cndns_binding_used.R |only teems-1.0.0/teems/R/cndns_csub_new.R |only teems-1.0.0/teems/R/cndns_csub_ref.R |only teems-1.0.0/teems/R/cndns_eq_entry.R |only teems-1.0.0/teems/R/cndns_eq_idents.R |only teems-1.0.0/teems/R/cndns_intab_parse.R |only teems-1.0.0/teems/R/cndns_metadata_compute.R |only teems-1.0.0/teems/R/cndns_share.R |only teems-1.0.0/teems/R/cndns_term_hoist.R |only teems-1.0.0/teems/R/cndns_vars_canonical.R |only teems-1.0.0/teems/R/cntnr_resources.R |only teems-1.0.0/teems/R/cntnr_resources_parse.R |only teems-1.0.0/teems/R/coeff_bin_compose.R |only teems-1.0.0/teems/R/coeff_bins_parse.R |only teems-1.0.0/teems/R/coeff_mod.R |only teems-1.0.0/teems/R/comp_active_count.R |only teems-1.0.0/teems/R/comp_cli_flags.R |only teems-1.0.0/teems/R/comp_stmt_parse.R |only teems-1.0.0/teems/R/compose_implement.R | 102 teems-1.0.0/teems/R/cond_logic_split.R |only teems-1.0.0/teems/R/cond_unwrap.R |only teems-1.0.0/teems/R/convert_implement.R | 56 teems-1.0.0/teems/R/cpp11.R | 32 teems-1.0.0/teems/R/data_aggregate.R | 72 teems-1.0.0/teems/R/data_convert.R | 15 teems-1.0.0/teems/R/data_finalize.R | 36 teems-1.0.0/teems/R/data_headers_canonical.R |only teems-1.0.0/teems/R/data_implement.R | 42 teems-1.0.0/teems/R/data_inputs.R |only teems-1.0.0/teems/R/data_map.R | 21 teems-1.0.0/teems/R/data_messages.R | 4 teems-1.0.0/teems/R/data_positional_dim.R |only teems-1.0.0/teems/R/data_process.R | 83 teems-1.0.0/teems/R/data_set_order.R |only teems-1.0.0/teems/R/declared_arg_sets.R |only teems-1.0.0/teems/R/defining_eq_rearrange.R |only teems-1.0.0/teems/R/deploy_metadata.R |only teems-1.0.0/teems/R/diagnostic_output.R |only teems-1.0.0/teems/R/diagnostics_inform.R |only teems-1.0.0/teems/R/docker_image_present.R |only teems-1.0.0/teems/R/docker_run_preamble.R |only teems-1.0.0/teems/R/docker_user_flag.R |only teems-1.0.0/teems/R/e_prepare.R |only teems-1.0.0/teems/R/ele_canonical.R |only teems-1.0.0/teems/R/ele_expand.R | 10 teems-1.0.0/teems/R/element_get.R |only teems-1.0.0/teems/R/ems_RK.R |only teems-1.0.0/teems/R/ems_compose.R | 71 teems-1.0.0/teems/R/ems_data.R | 90 teems-1.0.0/teems/R/ems_deploy.R | 31 teems-1.0.0/teems/R/ems_example.R | 78 teems-1.0.0/teems/R/ems_model.R | 45 teems-1.0.0/teems/R/ems_options.R | 257 + teems-1.0.0/teems/R/ems_probe.R |only teems-1.0.0/teems/R/ems_shock_cstm.R | 14 teems-1.0.0/teems/R/ems_shock_scen.R | 72 teems-1.0.0/teems/R/ems_shock_uni.R | 17 teems-1.0.0/teems/R/ems_solve.R | 343 ++ teems-1.0.0/teems/R/ems_swap.R | 18 teems-1.0.0/teems/R/ep_load_split.R |only teems-1.0.0/teems/R/ep_prepare.R |only teems-1.0.0/teems/R/eq_assemble.R |only teems-1.0.0/teems/R/eq_header_parse.R |only teems-1.0.0/teems/R/eq_quant_sides.R |only teems-1.0.0/teems/R/eq_quants_parse.R |only teems-1.0.0/teems/R/eq_split_chunks.R |only teems-1.0.0/teems/R/eq_statement_serialize.R |only teems-1.0.0/teems/R/eq_substitute.R |only teems-1.0.0/teems/R/equation_if_rewrite.R |only teems-1.0.0/teems/R/excluded_headers_drop.R |only teems-1.0.0/teems/R/extra_cli_flags.R |only teems-1.0.0/teems/R/extracts_generate.R | 3 teems-1.0.0/teems/R/finalize.R | 94 teems-1.0.0/teems/R/formula_if_rewrite.R |only teems-1.0.0/teems/R/formula_lhs_rows.R |only teems-1.0.0/teems/R/har_bytes.R |only teems-1.0.0/teems/R/har_char_read.R |only teems-1.0.0/teems/R/har_header_fields.R |only teems-1.0.0/teems/R/har_headers_class.R |only teems-1.0.0/teems/R/har_headers_split.R |only teems-1.0.0/teems/R/har_int_read.R |only teems-1.0.0/teems/R/har_meta.R | 12 teems-1.0.0/teems/R/har_metadata.R |only teems-1.0.0/teems/R/har_real_read.R |only teems-1.0.0/teems/R/har_set_names.R |only teems-1.0.0/teems/R/har_sparse_read.R |only teems-1.0.0/teems/R/header2GTAPv6.R | 14 teems-1.0.0/teems/R/header2GTAPv7.R | 5 teems-1.0.0/teems/R/homotopy_declare.R |only teems-1.0.0/teems/R/idle_sums_invert.R |only teems-1.0.0/teems/R/if_coeff_name_synth.R |only teems-1.0.0/teems/R/if_comparison_split.R |only teems-1.0.0/teems/R/if_compound_indicator.R |only teems-1.0.0/teems/R/if_cond_classify.R |only teems-1.0.0/teems/R/if_copy_name_synth.R |only teems-1.0.0/teems/R/if_eq_names_synth.R |only teems-1.0.0/teems/R/if_expr_helper.R |only teems-1.0.0/teems/R/if_expr_name_synth.R |only teems-1.0.0/teems/R/if_factor_distribute.R |only teems-1.0.0/teems/R/if_in_rebind.R |only teems-1.0.0/teems/R/if_index_cond.R |only teems-1.0.0/teems/R/if_indicator.R |only teems-1.0.0/teems/R/if_indicator_scalar.R |only teems-1.0.0/teems/R/if_intersect_set_synth.R |only teems-1.0.0/teems/R/if_membership_domains.R |only teems-1.0.0/teems/R/if_native.R |only teems-1.0.0/teems/R/if_rewrite_elements.R |only teems-1.0.0/teems/R/if_scalar_frame.R |only teems-1.0.0/teems/R/if_self_copy.R |only teems-1.0.0/teems/R/if_set_name_synth.R |only teems-1.0.0/teems/R/if_term_parse.R |only teems-1.0.0/teems/R/if_terms_rewrite.R |only teems-1.0.0/teems/R/indicator_eval.R |only teems-1.0.0/teems/R/indicator_formulas.R |only teems-1.0.0/teems/R/input_data_load.R | 18 teems-1.0.0/teems/R/input_generic_split.R |only teems-1.0.0/teems/R/input_read.R | 446 --- teems-1.0.0/teems/R/int_sets_convert.R |only teems-1.0.0/teems/R/invest_e_convert.R |only teems-1.0.0/teems/R/invest_v_convert.R |only teems-1.0.0/teems/R/la_args_resolve.R |only teems-1.0.0/teems/R/layer_cde.R |only teems-1.0.0/teems/R/layer_detect.R |only teems-1.0.0/teems/R/layer_par.R |only teems-1.0.0/teems/R/layer_prepare.R |only teems-1.0.0/teems/R/layer_reclass_blocs.R |only teems-1.0.0/teems/R/layer_rename.R |only teems-1.0.0/teems/R/layer_require.R |only teems-1.0.0/teems/R/layer_set.R |only teems-1.0.0/teems/R/layer_sets.R |only teems-1.0.0/teems/R/levels_linear_alias.R |only teems-1.0.0/teems/R/levels_linear_expand.R |only teems-1.0.0/teems/R/levels_linear_names.R |only teems-1.0.0/teems/R/map_data_finalize.R |only teems-1.0.0/teems/R/map_values_compose.R |only teems-1.0.0/teems/R/mappings_load.R | 34 teems-1.0.0/teems/R/mixed_canonical.R |only teems-1.0.0/teems/R/model_get.R | 29 teems-1.0.0/teems/R/model_implement.R | 15 teems-1.0.0/teems/R/model_summary.R |only teems-1.0.0/teems/R/names_rename.R |only teems-1.0.0/teems/R/occurrence_expand.R |only teems-1.0.0/teems/R/opt_wrappers.R | 92 teems-1.0.0/teems/R/out_mkdir.R |only teems-1.0.0/teems/R/output_paths_get.R |only teems-1.0.0/teems/R/output_retrieve.R | 14 teems-1.0.0/teems/R/par_weights.R |only teems-1.0.0/teems/R/param_weight.R | 263 + teems-1.0.0/teems/R/passes_accuracy.R |only teems-1.0.0/teems/R/pid_alive.R |only teems-1.0.0/teems/R/postsim_decl_names.R |only teems-1.0.0/teems/R/probe_agg_tbl.R |only teems-1.0.0/teems/R/probe_class.R |only teems-1.0.0/teems/R/probe_cmd_construct.R |only teems-1.0.0/teems/R/probe_cndns.R |only teems-1.0.0/teems/R/probe_collect.R |only teems-1.0.0/teems/R/probe_components.R |only teems-1.0.0/teems/R/probe_defects.R |only teems-1.0.0/teems/R/probe_element_tbl.R |only teems-1.0.0/teems/R/probe_implement.R |only teems-1.0.0/teems/R/probe_incidence.R |only teems-1.0.0/teems/R/probe_object.R |only teems-1.0.0/teems/R/probe_paths.R |only teems-1.0.0/teems/R/probe_pattern.R |only teems-1.0.0/teems/R/probe_plot_components.R |only teems-1.0.0/teems/R/probe_plot_dm.R |only teems-1.0.0/teems/R/probe_plot_incidence.R |only teems-1.0.0/teems/R/probe_print_cndns.R |only teems-1.0.0/teems/R/probe_print_detail.R |only teems-1.0.0/teems/R/probe_print_recommendation.R |only teems-1.0.0/teems/R/probe_recommend.R |only teems-1.0.0/teems/R/probe_run_inform.R |only teems-1.0.0/teems/R/probe_statements.R |only teems-1.0.0/teems/R/probe_stats.R |only teems-1.0.0/teems/R/ragged_write.R |only teems-1.0.0/teems/R/read_targets_parse.R |only teems-1.0.0/teems/R/refine_decide.R |only teems-1.0.0/teems/R/remainder_advance.R | 7 teems-1.0.0/teems/R/resources_record_lines.R |only teems-1.0.0/teems/R/resources_resolve.R |only teems-1.0.0/teems/R/round_digits.R |only teems-1.0.0/teems/R/sb_operand_values.R |only teems-1.0.0/teems/R/sbx_coef.R |only teems-1.0.0/teems/R/sbx_eval.R |only teems-1.0.0/teems/R/sbx_parse.R |only teems-1.0.0/teems/R/script_inject.R |only teems-1.0.0/teems/R/scripts_get.R | 12 teems-1.0.0/teems/R/set_builder_eval.R |only teems-1.0.0/teems/R/set_builder_formula_eval.R |only teems-1.0.0/teems/R/set_builder_mapsum_eval.R |only teems-1.0.0/teems/R/set_builder_parse.R |only teems-1.0.0/teems/R/set_builders_parse.R |only teems-1.0.0/teems/R/set_builders_rewrite.R |only teems-1.0.0/teems/R/set_defs_normalize.R |only teems-1.0.0/teems/R/set_ele_lists_chk.R |only teems-1.0.0/teems/R/set_ele_match.R | 13 teems-1.0.0/teems/R/set_equalities_parse.R |only teems-1.0.0/teems/R/set_expr_components.R |only teems-1.0.0/teems/R/set_expr_eval.R |only teems-1.0.0/teems/R/set_expr_info.R |only teems-1.0.0/teems/R/set_expr_refs_chk.R |only teems-1.0.0/teems/R/set_expr_tokens.R |only teems-1.0.0/teems/R/set_fields_parse.R |only teems-1.0.0/teems/R/set_mappings_infer.R |only teems-1.0.0/teems/R/set_product_names.R |only teems-1.0.0/teems/R/set_ranges_expand.R |only teems-1.0.0/teems/R/set_reduction.R | 117 teems-1.0.0/teems/R/set_stmt_row.R |only teems-1.0.0/teems/R/set_subsets_close.R |only teems-1.0.0/teems/R/set_subsets_parse.R |only teems-1.0.0/teems/R/set_superset_cls.R |only teems-1.0.0/teems/R/sets_finalize.R | 117 teems-1.0.0/teems/R/shk_construct.R |only teems-1.0.0/teems/R/shk_finalize.R |only teems-1.0.0/teems/R/shk_implement.R |only teems-1.0.0/teems/R/shk_load.R |only teems-1.0.0/teems/R/shk_preload.R |only teems-1.0.0/teems/R/shk_ragged_write.R |only teems-1.0.0/teems/R/shk_reduce.R |only teems-1.0.0/teems/R/shk_usr.R |only teems-1.0.0/teems/R/shk_write.R |only teems-1.0.0/teems/R/shk_write_order.R |only teems-1.0.0/teems/R/size_metadata_compute.R |only teems-1.0.0/teems/R/solution_bins_parse.R |only teems-1.0.0/teems/R/solution_cols_parse.R |only teems-1.0.0/teems/R/solution_files_clear.R |only teems-1.0.0/teems/R/solution_jac_parse.R |only teems-1.0.0/teems/R/solution_meta_parse.R |only teems-1.0.0/teems/R/solution_xac_parse.R |only teems-1.0.0/teems/R/solve_implement.R | 91 teems-1.0.0/teems/R/solve_in_situ.R | 72 teems-1.0.0/teems/R/solve_in_situ_implement.R | 54 teems-1.0.0/teems/R/solve_lock_acquire.R |only teems-1.0.0/teems/R/solve_lock_release.R |only teems-1.0.0/teems/R/solver_arg_checklist.R |only teems-1.0.0/teems/R/solver_cmd_run.R |only teems-1.0.0/teems/R/solver_dots_resolve.R |only teems-1.0.0/teems/R/solver_enable_time.R |only teems-1.0.0/teems/R/solver_extra_args.R |only teems-1.0.0/teems/R/solver_extra_checklist.R |only teems-1.0.0/teems/R/solver_is_rk.R |only teems-1.0.0/teems/R/solver_method_codes.R |only teems-1.0.0/teems/R/solver_paths_get.R |only teems-1.0.0/teems/R/solver_resources_record.R |only teems-1.0.0/teems/R/solver_uses_random.R |only teems-1.0.0/teems/R/solver_version_core.R |only teems-1.0.0/teems/R/solver_version_query.R |only teems-1.0.0/teems/R/square_candidates.R |only teems-1.0.0/teems/R/stmt_index_sets.R |only teems-1.0.0/teems/R/strip_strong_comments.R |only teems-1.0.0/teems/R/swap_out.R | 52 teems-1.0.0/teems/R/sysdata.rda |binary teems-1.0.0/teems/R/tab_assemble.R |only teems-1.0.0/teems/R/tab_bracket_match.R |only teems-1.0.0/teems/R/tab_cndns_flag.R |only teems-1.0.0/teems/R/tab_coef_is_param.R |only teems-1.0.0/teems/R/tab_coeff_decl.R |only teems-1.0.0/teems/R/tab_comp_retrieve.R |only teems-1.0.0/teems/R/tab_declared_names.R |only teems-1.0.0/teems/R/tab_defaults_expand.R |only teems-1.0.0/teems/R/tab_elements_lower.R |only teems-1.0.0/teems/R/tab_finalize.R | 91 teems-1.0.0/teems/R/tab_if_rewrite.R |only teems-1.0.0/teems/R/tab_is_subset.R |only teems-1.0.0/teems/R/tab_keywords_canonical.R |only teems-1.0.0/teems/R/tab_linear_args.R |only teems-1.0.0/teems/R/tab_linear_expect.R |only teems-1.0.0/teems/R/tab_linear_expr.R |only teems-1.0.0/teems/R/tab_linear_fac_text.R |only teems-1.0.0/teems/R/tab_linear_factor.R |only teems-1.0.0/teems/R/tab_linear_idents.R |only teems-1.0.0/teems/R/tab_linear_if_cond.R |only teems-1.0.0/teems/R/tab_linear_parse.R |only teems-1.0.0/teems/R/tab_linear_peek.R |only teems-1.0.0/teems/R/tab_linear_serialize.R |only teems-1.0.0/teems/R/tab_linear_sum_cond.R |only teems-1.0.0/teems/R/tab_linear_term.R |only teems-1.0.0/teems/R/tab_linear_term_new.R |only teems-1.0.0/teems/R/tab_linear_term_rename.R |only teems-1.0.0/teems/R/tab_linear_term_serialize.R |only teems-1.0.0/teems/R/tab_linear_terms_coerce.R |only teems-1.0.0/teems/R/tab_linear_terms_negate.R |only teems-1.0.0/teems/R/tab_linear_tokenize.R |only teems-1.0.0/teems/R/tab_linear_tokens_rename.R |only teems-1.0.0/teems/R/tab_linear_variable_names.R |only teems-1.0.0/teems/R/tab_mapping_parse.R |only teems-1.0.0/teems/R/tab_mappings.R |only teems-1.0.0/teems/R/tab_maths_parse.R | 168 - teems-1.0.0/teems/R/tab_mod.R |only teems-1.0.0/teems/R/tab_names_canonical.R |only teems-1.0.0/teems/R/tab_number.R |only teems-1.0.0/teems/R/tab_obj_index.R |only teems-1.0.0/teems/R/tab_obj_label.R |only teems-1.0.0/teems/R/tab_obj_name.R |only teems-1.0.0/teems/R/tab_obj_parse.R | 199 - teems-1.0.0/teems/R/tab_obj_read_bind.R |only teems-1.0.0/teems/R/tab_postsim_flag.R |only teems-1.0.0/teems/R/tab_qualifier_groups.R |only teems-1.0.0/teems/R/tab_qualifier_split.R |only teems-1.0.0/teems/R/tab_read_parse.R | 74 teems-1.0.0/teems/R/tab_scan.R |only teems-1.0.0/teems/R/tab_set_parse.R | 329 -- teems-1.0.0/teems/R/tab_stmt_normalize.R |only teems-1.0.0/teems/R/tab_subset_cls.R |only teems-1.0.0/teems/R/tab_sum_cond_rewrite.R |only teems-1.0.0/teems/R/tab_terms_split.R |only teems-1.0.0/teems/R/tab_vpqtype.R |only teems-1.0.0/teems/R/tablo_process.R | 200 - teems-1.0.0/teems/R/tail_dock.R | 9 teems-1.0.0/teems/R/teems_operators.R | 10 teems-1.0.0/teems/R/timesteps_get.R |only teems-1.0.0/teems/R/typed_values.R |only teems-1.0.0/teems/R/v_char_inject.R |only teems-1.0.0/teems/R/v_df_inject.R |only teems-1.0.0/teems/R/vaen_fossil.R |only teems-1.0.0/teems/R/val_RK_args.R |only teems-1.0.0/teems/R/val_cls.R |only teems-1.0.0/teems/R/val_compose_args.R | 16 teems-1.0.0/teems/R/val_convert_args.R | 5 teems-1.0.0/teems/R/val_data_args.R | 37 teems-1.0.0/teems/R/val_deploy_args.R | 34 teems-1.0.0/teems/R/val_exp_args.R | 33 teems-1.0.0/teems/R/val_in_situ_args.R |only teems-1.0.0/teems/R/val_model_args.R | 17 teems-1.0.0/teems/R/val_probe_args.R |only teems-1.0.0/teems/R/val_shk_args.R |only teems-1.0.0/teems/R/val_solver_accuracy_vars.R |only teems-1.0.0/teems/R/val_solver_args.R | 141 - teems-1.0.0/teems/R/val_solver_extras.R |only teems-1.0.0/teems/R/val_solver_methods.R |only teems-1.0.0/teems/R/val_solver_scalars.R |only teems-1.0.0/teems/R/val_solver_steps.R |only teems-1.0.0/teems/R/val_solver_tasks.R |only teems-1.0.0/teems/R/value_inject.R |only teems-1.0.0/teems/R/var_compose.R | 82 teems-1.0.0/teems/R/var_elements_count.R |only teems-1.0.0/teems/R/var_levels.R |only teems-1.0.0/teems/R/write_ems.R | 6 teems-1.0.0/teems/R/writeout.R | 10 teems-1.0.0/teems/R/year2timeset.R | 5 teems-1.0.0/teems/R/year_match.R | 21 teems-1.0.0/teems/build |only teems-1.0.0/teems/inst/CITATION |only teems-1.0.0/teems/inst/WORDLIST |only teems-1.0.0/teems/inst/models/GTAP-AEZ |only teems-1.0.0/teems/inst/models/GTAP-E |only teems-1.0.0/teems/inst/models/GTAP-EP |only teems-1.0.0/teems/inst/models/GTAP-RE/GTAP-RE.cls | 4 teems-1.0.0/teems/inst/models/GTAP-RE/GTAP-RE.tab.gz |only teems-1.0.0/teems/inst/models/GTAPv6/GTAPv6.tab.gz |only teems-1.0.0/teems/inst/models/GTAPv7/GTAPv7.tab.gz |only teems-1.0.0/teems/inst/scripts/GTAP-AEZ |only teems-1.0.0/teems/inst/scripts/GTAP-E |only teems-1.0.0/teems/inst/scripts/GTAP-EP |only teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_full.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_full_csv.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_full_year.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_2d_1fixed.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_3d_1fixed.R | 7 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_3d_2fixed.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_4d_1fixed.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_4d_2fixed.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_4d_3fixed.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_5d_1fixed.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_5d_2fixed.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_5d_3fixed.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/custom_partial_5d_k4.R | 5 teems-1.0.0/teems/inst/scripts/GTAP-RE/full_uniform.R | 8 teems-1.0.0/teems/inst/scripts/GTAP-RE/null.R | 14 teems-1.0.0/teems/inst/scripts/GTAP-RE/numeraire.R | 8 teems-1.0.0/teems/inst/scripts/GTAP-RE/part_uniform.R | 10 teems-1.0.0/teems/inst/scripts/GTAP-RE/part_uniform_full_swap.R | 12 teems-1.0.0/teems/inst/scripts/GTAP-RE/part_uniform_part_swap.R | 12 teems-1.0.0/teems/inst/scripts/GTAP-RE/part_uniform_part_swap_mixed.R | 12 teems-1.0.0/teems/inst/scripts/GTAP-RE/part_uniform_subset_swap.R | 10 teems-1.0.0/teems/inst/scripts/GTAP-RE/part_uniform_year.R | 10 teems-1.0.0/teems/inst/scripts/GTAP-RE/scenario.R | 3 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_full.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_full_csv.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_partial.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_partial_2d_1fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_partial_3d_1fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_partial_3d_2fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_partial_4d_1fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_partial_4d_2fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_partial_4d_3fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/custom_partial_4d_k3.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv6/full_uniform.R | 5 teems-1.0.0/teems/inst/scripts/GTAPv6/null.R | 8 teems-1.0.0/teems/inst/scripts/GTAPv6/numeraire.R | 5 teems-1.0.0/teems/inst/scripts/GTAPv6/part_uniform.R | 7 teems-1.0.0/teems/inst/scripts/GTAPv6/part_uniform_full_swap.R | 9 teems-1.0.0/teems/inst/scripts/GTAPv6/part_uniform_part_swap.R | 9 teems-1.0.0/teems/inst/scripts/GTAPv6/part_uniform_part_swap_mixed.R | 9 teems-1.0.0/teems/inst/scripts/GTAPv6/part_uniform_subset_swap.R | 9 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_full.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_full_csv.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_partial.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_partial_2d_1fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_partial_3d_1fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_partial_3d_2fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_partial_4d_1fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_partial_4d_2fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_partial_4d_3fixed.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/custom_partial_4d_k3.R | 2 teems-1.0.0/teems/inst/scripts/GTAPv7/full_uniform.R | 5 teems-1.0.0/teems/inst/scripts/GTAPv7/null.R | 11 teems-1.0.0/teems/inst/scripts/GTAPv7/numeraire.R | 5 teems-1.0.0/teems/inst/scripts/GTAPv7/part_uniform.R | 7 teems-1.0.0/teems/inst/scripts/GTAPv7/part_uniform_full_swap.R | 35 teems-1.0.0/teems/inst/scripts/GTAPv7/part_uniform_part_swap.R | 14 teems-1.0.0/teems/inst/scripts/GTAPv7/part_uniform_part_swap_mixed.R | 14 teems-1.0.0/teems/inst/scripts/GTAPv7/part_uniform_subset_swap.R | 12 teems-1.0.0/teems/man/GTAP_convert.Rd | 35 teems-1.0.0/teems/man/ems_RK.Rd |only teems-1.0.0/teems/man/ems_compose.Rd | 75 teems-1.0.0/teems/man/ems_custom_shock.Rd | 12 teems-1.0.0/teems/man/ems_data.Rd | 91 teems-1.0.0/teems/man/ems_deploy.Rd | 28 teems-1.0.0/teems/man/ems_example.Rd | 74 teems-1.0.0/teems/man/ems_model.Rd | 51 teems-1.0.0/teems/man/ems_option_get.Rd | 55 teems-1.0.0/teems/man/ems_option_set.Rd | 137 - teems-1.0.0/teems/man/ems_probe.Rd |only teems-1.0.0/teems/man/ems_scenario_shock.Rd | 71 teems-1.0.0/teems/man/ems_solve.Rd | 357 ++ teems-1.0.0/teems/man/ems_swap.Rd | 18 teems-1.0.0/teems/man/ems_uniform_shock.Rd | 15 teems-1.0.0/teems/man/plot.teems_probe.Rd |only teems-1.0.0/teems/man/solve_in_situ.Rd | 172 - teems-1.0.0/teems/src/agg_array.cpp |only teems-1.0.0/teems/src/cpp11.cpp | 68 teems-1.0.0/teems/src/har_read.cpp |only teems-1.0.0/teems/src/parse_solution.cpp | 356 ++ teems-1.0.0/teems/tests/testthat/_snaps/GTAP_convert.md | 27 teems-1.0.0/teems/tests/testthat/_snaps/auto_method.md |only teems-1.0.0/teems/tests/testthat/_snaps/chk_closure.md |only teems-1.0.0/teems/tests/testthat/_snaps/chk_orig_level.md |only teems-1.0.0/teems/tests/testthat/_snaps/chk_statements.md |only teems-1.0.0/teems/tests/testthat/_snaps/chk_subset_containment.md |only teems-1.0.0/teems/tests/testthat/_snaps/chk_tab_preflight.md |only teems-1.0.0/teems/tests/testthat/_snaps/cli_cmds.md |only teems-1.0.0/teems/tests/testthat/_snaps/compose_checks.md |only teems-1.0.0/teems/tests/testthat/_snaps/ems_RK.md |only teems-1.0.0/teems/tests/testthat/_snaps/ems_calculate.md |only teems-1.0.0/teems/tests/testthat/_snaps/ems_complementarity.md |only teems-1.0.0/teems/tests/testthat/_snaps/ems_compose.md | 39 teems-1.0.0/teems/tests/testthat/_snaps/ems_custom_shock.md | 37 teems-1.0.0/teems/tests/testthat/_snaps/ems_data.md | 34 teems-1.0.0/teems/tests/testthat/_snaps/ems_deploy.md | 13 teems-1.0.0/teems/tests/testthat/_snaps/ems_example.md | 19 teems-1.0.0/teems/tests/testthat/_snaps/ems_homogeneity.md |only teems-1.0.0/teems/tests/testthat/_snaps/ems_model.md | 235 + teems-1.0.0/teems/tests/testthat/_snaps/ems_options.md | 78 teems-1.0.0/teems/tests/testthat/_snaps/ems_probe.md |only teems-1.0.0/teems/tests/testthat/_snaps/ems_scenario_shock.md | 44 teems-1.0.0/teems/tests/testthat/_snaps/ems_solve.md | 199 + teems-1.0.0/teems/tests/testthat/_snaps/ems_swap.md | 25 teems-1.0.0/teems/tests/testthat/_snaps/ems_uniform_shock.md | 31 teems-1.0.0/teems/tests/testthat/_snaps/inform_messages.md |only teems-1.0.0/teems/tests/testthat/_snaps/int_sets.md |only teems-1.0.0/teems/tests/testthat/_snaps/layer_prepare.md |only teems-1.0.0/teems/tests/testthat/_snaps/param_weight.md |only teems-1.0.0/teems/tests/testthat/_snaps/postsim.md |only teems-1.0.0/teems/tests/testthat/_snaps/set_builder_eval.md |only teems-1.0.0/teems/tests/testthat/_snaps/set_expr.md |only teems-1.0.0/teems/tests/testthat/_snaps/solve_in_situ.md | 32 teems-1.0.0/teems/tests/testthat/_snaps/solve_lock_acquire.md |only teems-1.0.0/teems/tests/testthat/_snaps/solver_dots.md |only teems-1.0.0/teems/tests/testthat/_snaps/solver_switches.md |only teems-1.0.0/teems/tests/testthat/_snaps/tab_complementarity.md |only teems-1.0.0/teems/tests/testthat/_snaps/tab_fuzz_corpus.md |only teems-1.0.0/teems/tests/testthat/_snaps/tab_levels.md |only teems-1.0.0/teems/tests/testthat/_snaps/tab_mapping.md |only teems-1.0.0/teems/tests/testthat/_snaps/tab_vpqtype.md |only teems-1.0.0/teems/tests/testthat/_snaps/val_solver_steps.md |only teems-1.0.0/teems/tests/testthat/fixtures |only teems-1.0.0/teems/tests/testthat/helper-data_program.R |only teems-1.0.0/teems/tests/testthat/helper-examples.R |only teems-1.0.0/teems/tests/testthat/helper-script_run.R | 111 teems-1.0.0/teems/tests/testthat/test-GTAP_convert.R | 236 + teems-1.0.0/teems/tests/testthat/test-auto_method.R |only teems-1.0.0/teems/tests/testthat/test-chk_closure.R |only teems-1.0.0/teems/tests/testthat/test-chk_orig_level.R |only teems-1.0.0/teems/tests/testthat/test-chk_solver_log.R |only teems-1.0.0/teems/tests/testthat/test-chk_solver_version.R |only teems-1.0.0/teems/tests/testthat/test-chk_statements.R |only teems-1.0.0/teems/tests/testthat/test-chk_subset_containment.R |only teems-1.0.0/teems/tests/testthat/test-chk_tab_preflight.R |only teems-1.0.0/teems/tests/testthat/test-cli_cmds.R |only teems-1.0.0/teems/tests/testthat/test-cmd_construct.R |only teems-1.0.0/teems/tests/testthat/test-compose_checks.R |only teems-1.0.0/teems/tests/testthat/test-ems_RK.R |only teems-1.0.0/teems/tests/testthat/test-ems_compose.R | 205 + teems-1.0.0/teems/tests/testthat/test-ems_custom_shock.R | 82 teems-1.0.0/teems/tests/testthat/test-ems_data.R | 452 +++ teems-1.0.0/teems/tests/testthat/test-ems_deploy.R | 230 + teems-1.0.0/teems/tests/testthat/test-ems_example.R | 298 -- teems-1.0.0/teems/tests/testthat/test-ems_model.R | 1361 +++++++++- teems-1.0.0/teems/tests/testthat/test-ems_options.R | 144 - teems-1.0.0/teems/tests/testthat/test-ems_probe.R |only teems-1.0.0/teems/tests/testthat/test-ems_scenario_shock.R | 190 + teems-1.0.0/teems/tests/testthat/test-ems_solve.R | 1250 ++++++++- teems-1.0.0/teems/tests/testthat/test-ems_swap.R | 212 + teems-1.0.0/teems/tests/testthat/test-ems_uniform_shock.R | 97 teems-1.0.0/teems/tests/testthat/test-examples.R |only teems-1.0.0/teems/tests/testthat/test-host_resources.R |only teems-1.0.0/teems/tests/testthat/test-inform_messages.R |only teems-1.0.0/teems/tests/testthat/test-input_generic_split.R |only teems-1.0.0/teems/tests/testthat/test-input_read.R |only teems-1.0.0/teems/tests/testthat/test-int_sets.R |only teems-1.0.0/teems/tests/testthat/test-layer_prepare.R |only teems-1.0.0/teems/tests/testthat/test-param_weight.R |only teems-1.0.0/teems/tests/testthat/test-postsim.R |only teems-1.0.0/teems/tests/testthat/test-precision.R |only teems-1.0.0/teems/tests/testthat/test-refine_decide.R |only teems-1.0.0/teems/tests/testthat/test-scripts.R |only teems-1.0.0/teems/tests/testthat/test-set_builder_eval.R |only teems-1.0.0/teems/tests/testthat/test-set_expr.R |only teems-1.0.0/teems/tests/testthat/test-solution_bins_parse.R |only teems-1.0.0/teems/tests/testthat/test-solution_cols_parse.R |only teems-1.0.0/teems/tests/testthat/test-solution_files_clear.R |only teems-1.0.0/teems/tests/testthat/test-solution_jac_parse.R |only teems-1.0.0/teems/tests/testthat/test-solution_xac_parse.R |only teems-1.0.0/teems/tests/testthat/test-solve_in_situ.R | 127 teems-1.0.0/teems/tests/testthat/test-solve_lock_acquire.R |only teems-1.0.0/teems/tests/testthat/test-solver_dots.R |only teems-1.0.0/teems/tests/testthat/test-solver_err_e2e.R |only teems-1.0.0/teems/tests/testthat/test-solver_switches.R |only teems-1.0.0/teems/tests/testthat/test-tab_complementarity.R |only teems-1.0.0/teems/tests/testthat/test-tab_fuzz_corpus.R |only teems-1.0.0/teems/tests/testthat/test-tab_levels.R |only teems-1.0.0/teems/tests/testthat/test-tab_linear_parse.R |only teems-1.0.0/teems/tests/testthat/test-tab_mapping.R |only teems-1.0.0/teems/tests/testthat/test-tab_vpqtype.R |only teems-1.0.0/teems/tests/testthat/test-typed_values.R |only teems-1.0.0/teems/tests/testthat/test-vaen_fossil.R |only teems-1.0.0/teems/tests/testthat/test-val_solver_steps.R |only teems-1.0.0/teems/tests/testthat/test-var_levels.R |only teems-1.0.0/teems/tests/testthat/test-year_match.R |only 687 files changed, 11422 insertions(+), 3694 deletions(-)
Title: Execute and View Data Quality Checks on OMOP CDM Database
Description: Assesses data quality in Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) databases. Executes data quality checks and provides an R 'shiny' application to view the results.
Author: Katy Sadowski [aut, cre],
Clair Blacketer [aut],
Maxim Moinat [aut],
Ajit Londhe [aut],
Anthony Sena [aut],
Anthony Molinaro [aut],
Frank DeFalco [aut],
Pavel Grafkin [aut]
Maintainer: Katy Sadowski <sadowski@ohdsi.org>
Diff between DataQualityDashboard versions 2.9.0 dated 2026-10-06 and 2.9.1 dated 2026-10-17
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 3 +++ inst/doc/AddNewCheck.html | 2 +- inst/doc/CheckStatusDefinitions.html | 2 +- inst/doc/DataQualityDashboard.html | 2 +- inst/doc/DqdForCohorts.html | 2 +- inst/doc/SqlOnly.html | 2 +- inst/doc/Thresholds.html | 2 +- tests/testthat/setup.R | 22 ++++++++++++++++++---- tests/testthat/test-executeDqChecks.R | 6 ++++-- tests/testthat/test-writeDBResultsTo.R | 2 +- 12 files changed, 47 insertions(+), 28 deletions(-)
More information about DataQualityDashboard at CRAN
Permanent link
Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Maximilian Muecke [aut, cre] ,
Damir Pulatov [aut],
Michel Lang [aut] ,
Marc Becker [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3cluster versions 0.6.0 dated 2026-09-17 and 0.7.0 dated 2026-10-17
mlr3cluster-0.6.0/mlr3cluster/R/TaskGeneratorMoons.R |only mlr3cluster-0.6.0/mlr3cluster/man/mlr_task_generators_moons.Rd |only mlr3cluster-0.7.0/mlr3cluster/DESCRIPTION | 31 - mlr3cluster-0.7.0/mlr3cluster/MD5 | 233 ++++------ mlr3cluster-0.7.0/mlr3cluster/NAMESPACE | 3 mlr3cluster-0.7.0/mlr3cluster/NEWS.md | 41 + mlr3cluster-0.7.0/mlr3cluster/R/LearnerClust.R | 21 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustAffinityPropagation.R | 49 +- mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustAgnes.R | 8 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustCLARA.R | 11 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustCMeans.R | 10 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustCobweb.R | 7 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustDBSCAN.R | 14 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustDBSCANfpc.R | 23 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustDiana.R | 13 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustEM.R | 6 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustFanny.R | 8 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustFarthestFirst.R | 7 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustFeatureless.R | 8 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustFlexmix.R | 26 - mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustGenie.R | 4 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustHDBSCAN.R | 19 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustHclust.R | 4 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustKCCA.R | 4 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustKKMeans.R | 12 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustKMeans.R | 6 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustKMeansRcpp.R | 14 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustKModes.R | 15 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustKProto.R | 20 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustMclust.R | 6 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustMeanShift.R | 31 - mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustMiniBatchKMeans.R | 14 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustMovMF.R | 6 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustOPTICS.R | 18 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustPAM.R | 11 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustProtoclust.R | 22 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustSKMeans.R | 8 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustSOM.R | 4 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustSTDBSCAN.R | 16 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustSimpleKMeans.R | 7 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustSpectral.R | 7 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustTclust.R | 17 mlr3cluster-0.7.0/mlr3cluster/R/LearnerClustXMeans.R | 8 mlr3cluster-0.7.0/mlr3cluster/R/MeasureClustSimple.R | 2 mlr3cluster-0.7.0/mlr3cluster/R/PredictionDataClust.R | 6 mlr3cluster-0.7.0/mlr3cluster/R/TaskGeneratorBlobs.R | 9 mlr3cluster-0.7.0/mlr3cluster/R/as_task_clust.R | 27 + mlr3cluster-0.7.0/mlr3cluster/R/cluster_stats.R | 5 mlr3cluster-0.7.0/mlr3cluster/R/helper.R | 67 +- mlr3cluster-0.7.0/mlr3cluster/R/zzz.R | 9 mlr3cluster-0.7.0/mlr3cluster/man/LearnerClust.Rd | 7 mlr3cluster-0.7.0/mlr3cluster/man/as_task_clust.Rd | 14 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.MBatchKMeans.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.SimpleKMeans.Rd | 4 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.agnes.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.ap.Rd | 10 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.bico.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.clara.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.cmeans.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.cobweb.Rd | 4 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.dbscan.Rd | 8 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.dbscan_fpc.Rd | 10 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.diana.Rd | 3 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.em.Rd | 4 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.fanny.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.featureless.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.ff.Rd | 4 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.flexmix.Rd | 8 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.genie.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.gmeans.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.hclust.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.hdbscan.Rd | 10 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.kcca.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.kkmeans.Rd | 6 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.kmeans.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.kmeans_rcpp.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.kmodes.Rd | 1 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.kproto.Rd | 3 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.mclust.Rd | 6 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.meanshift.Rd | 10 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.movMF.Rd | 4 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.optics.Rd | 12 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.pam.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.protoclust.Rd | 11 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.skmeans.Rd | 6 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.som.Rd | 2 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.specc.Rd | 3 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.stdbscan.Rd | 10 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.tclust.Rd | 7 mlr3cluster-0.7.0/mlr3cluster/man/mlr_learners_clust.xmeans.Rd | 14 mlr3cluster-0.7.0/mlr3cluster/man/mlr_task_generators_blobs.Rd | 3 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/_snaps/mlr_learners_clust_kmodes.md | 2 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_LearnerClust.R | 6 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_as_task_clust.R | 43 + mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_cluster_stats.R | 5 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_helper.R |only mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_ap.R | 9 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_clara.R | 23 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_cmeans.R | 10 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_cobweb.R | 7 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan.R | 1 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan_fpc.R | 19 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_em.R | 7 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_ff.R | 7 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_flexmix.R | 18 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_hdbscan.R | 1 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_kmeans.R | 6 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_kmodes.R | 8 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_kproto.R | 16 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_mbatchkmeans.R | 13 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_meanshift.R | 8 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_optics.R | 1 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_pam.R | 13 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_simplekmeans.R | 7 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_spectral.R | 7 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_stdbscan.R | 1 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_tclust.R | 4 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_xmeans.R | 6 mlr3cluster-0.7.0/mlr3cluster/tests/testthat/test_mlr_task_generators.R | 40 - 119 files changed, 920 insertions(+), 497 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 0.8.1 dated 2026-07-20 and 0.8.2 dated 2026-10-17
mcmcsae-0.8.1/mcmcsae/man/CG.Rd |only mcmcsae-0.8.1/mcmcsae/man/ac_fft.Rd |only mcmcsae-0.8.1/mcmcsae/man/create_block_cMVN_sampler.Rd |only mcmcsae-0.8.1/mcmcsae/man/create_cMVN_sampler.Rd |only mcmcsae-0.8.1/mcmcsae/man/setup_CG_sampler.Rd |only mcmcsae-0.8.1/mcmcsae/man/sim_marg_var.Rd |only mcmcsae-0.8.2/mcmcsae/DESCRIPTION | 16 mcmcsae-0.8.2/mcmcsae/MD5 | 162 +- mcmcsae-0.8.2/mcmcsae/NAMESPACE | 210 +- mcmcsae-0.8.2/mcmcsae/NEWS | 10 mcmcsae-0.8.2/mcmcsae/R/AR1_sampler.R | 2 mcmcsae-0.8.2/mcmcsae/R/GMRF_extension.R | 14 mcmcsae-0.8.2/mcmcsae/R/MCMCsim.R | 93 - mcmcsae-0.8.2/mcmcsae/R/MH.R | 4 mcmcsae-0.8.2/mcmcsae/R/MatrixUtils.R | 174 -- mcmcsae-0.8.2/mcmcsae/R/RcppExports.R | 568 ++++++- mcmcsae-0.8.2/mcmcsae/R/TMVN_methods.R | 3 mcmcsae-0.8.2/mcmcsae/R/TMVN_sampler.R | 106 - mcmcsae-0.8.2/mcmcsae/R/aux_closures.R | 2 mcmcsae-0.8.2/mcmcsae/R/cMVN_sampler.R | 18 mcmcsae-0.8.2/mcmcsae/R/cholesky.R | 27 mcmcsae-0.8.2/mcmcsae/R/conjugate_gradients.R | 33 mcmcsae-0.8.2/mcmcsae/R/f_binomial.R | 33 mcmcsae-0.8.2/mcmcsae/R/f_gamma.R | 230 ++- mcmcsae-0.8.2/mcmcsae/R/f_gaussian.R | 60 mcmcsae-0.8.2/mcmcsae/R/f_multinomial.R | 21 mcmcsae-0.8.2/mcmcsae/R/f_negbinomial.R | 25 mcmcsae-0.8.2/mcmcsae/R/f_poisson.R | 10 mcmcsae-0.8.2/mcmcsae/R/f_student_t.R | 52 mcmcsae-0.8.2/mcmcsae/R/formulas.R | 20 mcmcsae-0.8.2/mcmcsae/R/mc_bart.R | 35 mcmcsae-0.8.2/mcmcsae/R/mc_block.R | 69 mcmcsae-0.8.2/mcmcsae/R/mc_gen.R | 332 ++-- mcmcsae-0.8.2/mcmcsae/R/mc_gl.R | 16 mcmcsae-0.8.2/mcmcsae/R/mc_mec.R | 79 - mcmcsae-0.8.2/mcmcsae/R/mc_offset.R | 14 mcmcsae-0.8.2/mcmcsae/R/mc_reg.R | 129 - mcmcsae-0.8.2/mcmcsae/R/mc_s.R | 14 mcmcsae-0.8.2/mcmcsae/R/mc_vfac.R | 40 mcmcsae-0.8.2/mcmcsae/R/mc_vreg.R | 36 mcmcsae-0.8.2/mcmcsae/R/mcmcsae.R | 4 mcmcsae-0.8.2/mcmcsae/R/model_eval.R | 13 mcmcsae-0.8.2/mcmcsae/R/modelmatrix.R | 3 mcmcsae-0.8.2/mcmcsae/R/models.R | 59 mcmcsae-0.8.2/mcmcsae/R/parallel.R | 6 mcmcsae-0.8.2/mcmcsae/R/plots.R | 2 mcmcsae-0.8.2/mcmcsae/R/prediction.R | 23 mcmcsae-0.8.2/mcmcsae/R/priors.R | 30 mcmcsae-0.8.2/mcmcsae/R/projection.R | 35 mcmcsae-0.8.2/mcmcsae/R/random.R | 152 +- mcmcsae-0.8.2/mcmcsae/R/samplers.R | 20 mcmcsae-0.8.2/mcmcsae/R/set_constraints.R | 6 mcmcsae-0.8.2/mcmcsae/R/sparse_template.R | 23 mcmcsae-0.8.2/mcmcsae/R/tabMatrix.R | 8 mcmcsae-0.8.2/mcmcsae/inst/doc/area_level.html | 64 mcmcsae-0.8.2/mcmcsae/inst/doc/linear_weighting.html | 4 mcmcsae-0.8.2/mcmcsae/inst/doc/unit_level.html | 6 mcmcsae-0.8.2/mcmcsae/man/MCMCsim.Rd | 5 mcmcsae-0.8.2/mcmcsae/man/TMVN-methods.Rd | 2 mcmcsae-0.8.2/mcmcsae/man/create_TMVN_sampler.Rd | 3 mcmcsae-0.8.2/mcmcsae/man/f_gamma.Rd | 13 mcmcsae-0.8.2/mcmcsae/man/gamma_control.Rd |only mcmcsae-0.8.2/mcmcsae/man/gen.Rd | 8 mcmcsae-0.8.2/mcmcsae/man/generate_data.Rd | 26 mcmcsae-0.8.2/mcmcsae/man/glreg.Rd | 8 mcmcsae-0.8.2/mcmcsae/man/matrix-vector.Rd | 43 mcmcsae-0.8.2/mcmcsae/man/mec.Rd | 13 mcmcsae-0.8.2/mcmcsae/man/model-information-criteria.Rd | 5 mcmcsae-0.8.2/mcmcsae/man/reg.Rd | 13 mcmcsae-0.8.2/mcmcsae/man/sampler_control.Rd | 3 mcmcsae-0.8.2/mcmcsae/man/set_rng.Rd |only mcmcsae-0.8.2/mcmcsae/man/setup_cluster.Rd | 2 mcmcsae-0.8.2/mcmcsae/man/tabMatrix-indexing.Rd | 4 mcmcsae-0.8.2/mcmcsae/man/vreg.Rd | 11 mcmcsae-0.8.2/mcmcsae/src/RcppExports.cpp | 366 +--- mcmcsae-0.8.2/mcmcsae/src/TN.cpp | 155 +- mcmcsae-0.8.2/mcmcsae/src/chMatrix.c | 3 mcmcsae-0.8.2/mcmcsae/src/matvec.cpp |only mcmcsae-0.8.2/mcmcsae/src/mcmcsae_init.c | 50 mcmcsae-0.8.2/mcmcsae/src/random.cpp | 71 mcmcsae-0.8.2/mcmcsae/src/speed_ups.cpp | 743 +++------- mcmcsae-0.8.2/mcmcsae/src/tabMatrix.cpp | 217 -- mcmcsae-0.8.2/mcmcsae/src/transcendental.cpp |only mcmcsae-0.8.2/mcmcsae/tests/testthat/test_binreg.R | 5 mcmcsae-0.8.2/mcmcsae/tests/testthat/test_conjugate_gradient.R | 11 mcmcsae-0.8.2/mcmcsae/tests/testthat/test_multinom.R | 14 mcmcsae-0.8.2/mcmcsae/tests/testthat/test_prior_sampling.R | 4 87 files changed, 2455 insertions(+), 2458 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
References: Patil (2021) <doi:10.21105/joss.03167>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 1.1.2 dated 2026-10-09 and 1.1.3 dated 2026-10-17
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ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-ggbetweenstats.R | 57 ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-ggcoefstats.R | 160 - ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-ggcorrmat.R | 20 ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-ggdotplotstats.R | 13 ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-gghistostats.R | 8 ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-ggpiestats.R | 145 - ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-ggscatterstats.R | 60 ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-ggwithinstats.R | 211 +- ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-pairwise-ggsignif.R | 380 --- ggstatsplot-1.1.3/ggstatsplot/tests/testthat/test-utils.R | 9 ggstatsplot-1.1.3/ggstatsplot/vignettes/ggstatsplot.Rmd | 20 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/faq.Rmd | 954 ++------- ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/ggbarstats.Rmd | 44 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/ggbetweenstats.Rmd | 59 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/ggcoefstats.Rmd | 37 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/ggcorrmat.Rmd | 38 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/ggdotplotstats.Rmd | 56 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/gghistostats.Rmd | 60 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/ggpiestats.Rmd | 210 -- ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/ggscatterstats.Rmd | 55 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/ggwithinstats.Rmd | 61 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/interpretation.Rmd | 36 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/pairwise.Rmd | 38 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/principles.Rmd | 67 ggstatsplot-1.1.3/ggstatsplot/vignettes/web_only/purrr_examples.Rmd | 45 107 files changed, 5891 insertions(+), 7255 deletions(-)
Title: Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Description: Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inverse and determinant of a symmetric and positive-definite Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010).
Author: Giri Gopalan [aut, cre],
Luke Bornn [aut]
Maintainer: Giri Gopalan <gopalan88@gmail.com>
Diff between FastGP versions 1.4 dated 2026-09-19 and 1.5 dated 2026-10-17
DESCRIPTION | 9 +++-- MD5 | 28 ++++++++--------- R/RcppExports.R | 16 ++++----- R/gpfuncs.R | 1 R/rcpp_mvn.R | 36 ++++++++-------------- demo/FastGPdemo.R | 58 ++++++++++++++++++++++++++++++++--- man/ess.Rd | 55 +++++++++++++++++++++++++++++++-- man/rcpp_matrix_ops.Rd | 28 +++++++++++++---- man/rcpp_rmvnorm.Rd | 15 ++++++++- src/RcppExports.cpp | 49 +++++++++++++++--------------- src/distance.cpp | 14 ++++---- src/invert_toeplitz.cpp | 3 + src/rcppeigen.cpp | 60 +++++++++++++++++++++++++----------- src/tchol.cpp | 78 ++++++++++++++++++++---------------------------- src/toep_det.cpp | 2 - 15 files changed, 292 insertions(+), 160 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 0.8-91 dated 2026-01-29 and 0.8-92 dated 2026-10-17
ChangeLog | 20 ++++++++++++++++++-- DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/writeForeignSAS.R | 6 +++--- man/lookup.xport.Rd | 2 +- man/read.xport.Rd | 4 ++-- tests/sas.R | 22 +++++++++++++++++----- tests/spss.R | 4 +++- tests/spss.Rout.save | 6 ++++-- 9 files changed, 60 insertions(+), 28 deletions(-)
Title: Soundscape Spectral Metrics
Description: Accessible and flexible implementation of spectral ecoacoustic indices. The functions were design to accommodate a variety of sampling designs. Users can tailor calculations by specifying spectrogram time bin size, amplitude thresholds and normality tests. By simplifying computation and standardizing reproducible methods, the package aims to support ecoacoustics studies.
Author: Arthur Igor da Fonseca-Freire [aut, cre, cph],
Weslley Geremias dos Santos [aut],
Lucas Rodriguez Forti [aut]
Maintainer: Arthur Igor da Fonseca-Freire <arthur.igorr@gmail.com>
Diff between Ruido versions 1.1.1 dated 2026-09-20 and 1.2.0 dated 2026-10-17
Ruido-1.1.1/Ruido/R/ACIspec.R |only Ruido-1.1.1/Ruido/R/ENTspec.R |only Ruido-1.1.1/Ruido/R/activity.R |only Ruido-1.1.1/Ruido/R/bgNoise.R |only Ruido-1.1.1/Ruido/R/multActivity.R |only Ruido-1.1.1/Ruido/R/satBackup.R |only Ruido-1.1.1/Ruido/R/singleSat.R |only Ruido-1.1.1/Ruido/R/soundMat.R |only Ruido-1.1.1/Ruido/R/soundSat.R |only Ruido-1.2.0/Ruido/DESCRIPTION | 12 Ruido-1.2.0/Ruido/MD5 | 47 +- Ruido-1.2.0/Ruido/NAMESPACE | 8 Ruido-1.2.0/Ruido/R/globals.R | 1 Ruido-1.2.0/Ruido/R/indexes.R |only Ruido-1.2.0/Ruido/R/internalFunctions.R | 604 ++++++++++++-------------------- Ruido-1.2.0/Ruido/R/multFileIndexes.R |only Ruido-1.2.0/Ruido/R/noise.matrix.R | 21 - Ruido-1.2.0/Ruido/R/processFunctions.R |only Ruido-1.2.0/Ruido/R/windows.R |only Ruido-1.2.0/Ruido/man/ACIspec.Rd | 6 Ruido-1.2.0/Ruido/man/ENTspec.Rd | 6 Ruido-1.2.0/Ruido/man/EVNspec.Rd |only Ruido-1.2.0/Ruido/man/activity.Rd | 9 Ruido-1.2.0/Ruido/man/bgNoise.Rd | 29 + Ruido-1.2.0/Ruido/man/bgn.Rd |only Ruido-1.2.0/Ruido/man/hamming.Rd |only Ruido-1.2.0/Ruido/man/hanning.Rd |only Ruido-1.2.0/Ruido/man/multActivity.Rd | 9 Ruido-1.2.0/Ruido/man/satBackup.Rd | 106 ++--- Ruido-1.2.0/Ruido/man/singleSat.Rd | 9 Ruido-1.2.0/Ruido/man/soundMat.Rd | 9 Ruido-1.2.0/Ruido/man/soundSat.Rd | 17 Ruido-1.2.0/Ruido/src |only 33 files changed, 409 insertions(+), 484 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington', 'Ludwig' and Omnivariant Generalised Least-Squares ('OGLS') approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isoch [...truncated...]
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 7.0 dated 2026-08-21 and 7.1 dated 2026-10-17
DESCRIPTION | 8 - MD5 | 51 +++--- NAMESPACE | 1 R/LRisochron.R | 415 ++++++++++++++++------------------------------------ R/UPb.R | 92 +++++------ R/age.R | 13 + R/commonPb.R | 212 +++++++++++++++----------- R/concordia.R | 77 ++++----- R/constants.R | 33 ++-- R/discfilter.R | 131 ++++++++-------- R/evolution.R | 39 +--- R/io.R | 8 - R/isochron.R | 20 +- R/mds.R | 2 R/nnls.R |only R/titterington.R | 13 - R/toolbox.R | 24 +-- R/unmix.R |only R/york.R | 9 - man/age.Rd | 6 man/classes.Rd | 2 man/concordia.Rd | 11 + man/discfilter.Rd | 2 man/isochron.Rd | 4 man/mds.Rd | 2 man/read.data.Rd | 6 man/titterington.Rd | 13 - man/unmix.Rd |only 28 files changed, 537 insertions(+), 657 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-30 1.7
2012-05-25 1.4.11
2012-01-17 1.4.9
2011-09-21 1.4.8
Title: An Implementation of the PREVENT and Pooled Cohort Equations
Description: Implements the American Heart Association Predicting
Risk of cardiovascular disease EVENTs (PREVENT) equations from Khan
SS, Matsushita K, Sang Y, and colleagues (2023)
<doi:10.1161/CIRCULATIONAHA.123.067626>, with optional comparison
with their de facto predecessor, the Pooled Cohort Equations from the
American Heart Association and American College of Cardiology (2013)
<doi:10.1161/01.cir.0000437741.48606.98> and the revision to the Pooled
Cohort Equations from Yadlowsky and colleagues (2018)
<doi:10.7326/M17-3011>.
Author: Martin Mayer [aut, cre, cph]
Maintainer: Martin Mayer <mmayer@ebsco.com>
Diff between preventr versions 0.12.0 dated 2026-06-24 and 0.12.1 dated 2026-10-17
DESCRIPTION | 10 MD5 | 157 NAMESPACE | 40 NEWS.md | 24 R/estimate_risk.R | 88 R/prep_data_for_use.R | 2 R/sysdata.rda |binary README.md | 49 build/partial.rdb |only inst/doc/plot-risk.Rmd | 1548 ++-- inst/doc/using-data-frame.html | 3470 ++++------ man/estimate_risk.Rd | 76 tests/testthat/_snaps/estimate_risk.md | 142 tests/testthat/_snaps/helpers_test.md | 10 tests/testthat/_snaps/plot_risk/check-for-id-1-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-1-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-1-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-103-at-row-1-years-from-data-frame-input.svg | 16 tests/testthat/_snaps/plot_risk/check-for-id-103-at-row-1-years-from-plot-column.svg | 16 tests/testthat/_snaps/plot_risk/check-for-id-105-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-105-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-105-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-107-at-row-3-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-107-at-row-3-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-108-at-row-1-years-from-data-frame-input.svg | 12 tests/testthat/_snaps/plot_risk/check-for-id-108-at-row-1-years-from-plot-column.svg | 12 tests/testthat/_snaps/plot_risk/check-for-id-108-at-row-2-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-108-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-109-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-109-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-109-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-109-at-row-3-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-109-at-row-3-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-2-at-row-1-years-from-data-frame-input.svg | 8 tests/testthat/_snaps/plot_risk/check-for-id-2-at-row-1-years-from-plot-column.svg | 8 tests/testthat/_snaps/plot_risk/check-for-id-2-at-row-2-years-from-data-frame-input.svg | 16 tests/testthat/_snaps/plot_risk/check-for-id-2-at-row-2-years-from-plot-column.svg | 16 tests/testthat/_snaps/plot_risk/check-for-id-201-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-201-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-201-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-206-at-row-1-years-from-data-frame-input.svg | 12 tests/testthat/_snaps/plot_risk/check-for-id-206-at-row-1-years-from-plot-column.svg | 12 tests/testthat/_snaps/plot_risk/check-for-id-206-at-row-2-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-206-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-209-at-row-2-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-209-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-3-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-3-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-3-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-301-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-301-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-301-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-301-at-row-3-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-301-at-row-3-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-307-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-307-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-308-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-308-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-309-at-row-2-years-from-data-frame-input.svg | 4 tests/testthat/_snaps/plot_risk/check-for-id-309-at-row-2-years-from-plot-column.svg | 4 tests/testthat/_snaps/plot_risk/check-for-id-402-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-402-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-403-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-403-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-403-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-403-at-row-3-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-403-at-row-3-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-404-at-row-1-years-from-data-frame-input.svg | 12 tests/testthat/_snaps/plot_risk/check-for-id-404-at-row-1-years-from-plot-column.svg | 12 tests/testthat/_snaps/plot_risk/check-for-id-406-at-row-1-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-406-at-row-1-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-410-at-row-1-years-from-data-frame-input.svg | 16 tests/testthat/_snaps/plot_risk/check-for-id-410-at-row-1-years-from-plot-column.svg | 16 tests/testthat/_snaps/plot_risk/check-for-id-5-at-row-2-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-5-at-row-2-years-from-plot-column.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-9-at-row-3-years-from-data-frame-input.svg | 20 tests/testthat/_snaps/plot_risk/check-for-id-9-at-row-3-years-from-plot-column.svg | 20 tests/testthat/test-estimate_risk.R | 84 tests/testthat/test-other_models.R | 42 vignettes/plot-risk.Rmd | 1548 ++-- 80 files changed, 4152 insertions(+), 4270 deletions(-)
Title: Accelerometer Processing Methods for Cycle 7 of the CHMS
Description: 'ActiGraph wGT3X-BT' accelerometer processing methods using
the standardized workflow developed by Statistics Canada for cycle 7
of the Canadian Health Measures Survey (CHMS). The package promotes
transparent and reproducible data processing while supporting the
harmonization of analytical approaches among researchers wishing to
align with Statistics Canada's methods. For general details about the
processing methods, please consult Clarke J, Gribbon A, St-Laurent M,
Ferrao T, Barnes J, Kuzik N, Colley R (2026) <doi:
10.25318/82-003-x202600200001-eng>.
Author: Joel Barnes [aut, cre],
Janine Clarke [ctb],
Rachel Colley [ctb],
His Majesty the King in Right of Canada, as represented by Statistics
Canada [cph]
Maintainer: Joel Barnes <joel.barnes@statcan.gc.ca>
Diff between chms versions 7.1 dated 2026-09-08 and 7.2 dated 2026-10-17
chms-7.1/chms/man/figures/agd-plot.png |only chms-7.2/chms/DESCRIPTION | 12 chms-7.2/chms/MD5 | 93 + chms-7.2/chms/NEWS.md |only chms-7.2/chms/R/agd-worker.R | 187 +++- chms-7.2/chms/R/agd.R | 461 +++++++-- chms-7.2/chms/R/apply-barreira-algo.R | 390 +++++--- chms-7.2/chms/R/apply-general-bout-algo.R | 94 +- chms-7.2/chms/R/apply-non-wear-algo.R | 86 - chms-7.2/chms/R/apply-sadeh-algo.R | 51 - chms-7.2/chms/R/apply-tudor-locke-algo.R | 83 + chms-7.2/chms/R/classify-agd-data.R | 92 + chms-7.2/chms/R/clean-agd-data.R | 21 chms-7.2/chms/R/get-chms-meta.R | 45 chms-7.2/chms/R/helper-get-stc-vars.R |only chms-7.2/chms/R/load-agd-data.R | 51 - chms-7.2/chms/R/load-agd-settings.R | 8 chms-7.2/chms/R/plot.agd.R | 50 - chms-7.2/chms/R/plot.agd_worker.R | 50 - chms-7.2/chms/R/run-agd-job.R | 18 chms-7.2/chms/R/summarize-agd-data.R | 244 +++-- chms-7.2/chms/R/summary.agd.R | 55 - chms-7.2/chms/R/summary.agd_worker.R | 66 + chms-7.2/chms/README.md | 52 - chms-7.2/chms/inst/qmd/sanity-check-report.qmd | 141 +-- chms-7.2/chms/inst/scripts/demo.R | 2 chms-7.2/chms/man/agd.Rd | 333 ++++--- chms-7.2/chms/man/agd_worker.Rd | 288 +++--- chms-7.2/chms/man/apply_barreira_algo.Rd | 54 - chms-7.2/chms/man/apply_general_bout_algo.Rd | 39 chms-7.2/chms/man/apply_non_wear_algo.Rd | 28 chms-7.2/chms/man/apply_sadeh_algo.Rd | 24 chms-7.2/chms/man/apply_tudor_locke_algo.Rd | 47 - chms-7.2/chms/man/clean_agd_data.Rd | 4 chms-7.2/chms/man/figures/unnamed-chunk-13-1.png |binary chms-7.2/chms/man/figures/unnamed-chunk-31-1.png |binary chms-7.2/chms/man/get_chms_meta.Rd | 27 chms-7.2/chms/man/load_agd_data.Rd | 19 chms-7.2/chms/man/load_agd_settings.Rd | 6 chms-7.2/chms/man/plot.agd.Rd | 10 chms-7.2/chms/man/plot.agd_worker.Rd | 15 chms-7.2/chms/man/run_agd_job.Rd | 10 chms-7.2/chms/man/summary.agd.Rd | 9 chms-7.2/chms/man/summary.agd_worker.Rd | 6 chms-7.2/chms/tests/testthat/test-001-get-chms-meta.R | 33 chms-7.2/chms/tests/testthat/test-004-render-sanity-check-report.R | 16 chms-7.2/chms/tests/testthat/test-005-validate-barreira-algo.R | 467 +++++----- chms-7.2/chms/tools/build-package.R | 251 ++--- chms-7.2/chms/tools/readme.qmd | 20 49 files changed, 2590 insertions(+), 1468 deletions(-)
Title: Exponential Multivariate Hawkes Model
Description: Simulate and fit multivariate Hawkes models with exponential
kernels, introduced by Hawkes (1971) <doi:10.2307/2334319>.
Includes marked, state-dependent, and multi-kernel specifications.
Parameter estimation uses maximum likelihood, following Ozaki (1979)
<doi:10.1007/BF02480272>, through the optional 'maxLik' package or
the optimization functions supplied with R.
Author: Kyungsub Lee [aut, cre]
Maintainer: Kyungsub Lee <kyungsub@gmail.com>
Diff between emhawkes versions 0.9.8 dated 2025-08-26 and 1.0.0 dated 2026-10-17
DESCRIPTION | 32 MD5 | 131 ++- NAMESPACE | 50 - NEWS.md | 148 +++- R/RcppExports.R |only R/harrival.R | 579 +++++++++-------- R/hengine.R |only R/hfit.R | 994 +++++++++++++++++++++-------- R/hfitted.R |only R/hgfit.R | 872 +++++++++++++------------- R/hgradient.R |only R/himpact.R |only R/hinterface.R |only R/hllf.R | 1063 +++++++++++++++++-------------- R/hmoment.R | 670 ++++++++++---------- R/hoptimizer.R |only R/hreal.R | 258 ++++--- R/hsim.R | 806 ++++++++++++++---------- R/hspec.R | 953 +++++++++++++++------------- R/huncertainty.R |only R/script.R | 378 +++++------ R/tzexp.R | 359 +++++----- R/utilities.R | 534 ++++++++++------ R/zzz.R | 26 README.md | 59 + build/vignette.rds |binary inst/doc/example.R | 217 +++--- inst/doc/example.Rmd | 611 ++++++++++-------- inst/doc/example.html | 1566 +++++++++++++++++++++++++---------------------- man/expected_tau.Rd | 10 man/fit_diagnostics.Rd |only man/fit_initial_state.Rd |only man/fitted_hspec.Rd |only man/hfit.Rd | 681 +++++++++++++++----- man/hreal.Rd | 95 +- man/hsim.Rd | 85 ++ man/hspec-class.Rd | 165 +++- man/hvol.Rd | 18 man/infer_lambda.Rd | 158 ++-- man/logLik.Rd | 90 ++ man/residual_process.Rd | 142 ++-- man/set_residual.Rd | 28 man/tzexp.Rd | 23 src |only tests |only vignettes/example.Rmd | 611 ++++++++++-------- 46 files changed, 7345 insertions(+), 5067 deletions(-)
Title: Covariance Measure Tests for Conditional Independence
Description: Covariance measure tests for conditional independence testing
against conditional covariance and nonlinear conditional mean alternatives.
The package implements versions of the generalised covariance measure test
(Shah and Peters, 2020, <doi:10.1214/19-aos1857>) and projected covariance
measure test (Lundborg et al., 2023, <doi:10.1214/24-AOS2447>). The
tram-GCM test, for censored responses, is implemented including the Cox
model and survival forests (Kook et al., 2024,
<doi:10.1080/01621459.2024.2395588>). Application examples to variable
significance testing and modality selection can be found in Kook and
Lundborg (2024, <doi:10.1093/bib/bbae475>).
Author: Lucas Kook [aut, cre] ,
Anton Rask Lundborg [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between comets versions 0.2-2 dated 2025-11-05 and 0.2-3 dated 2026-10-17
DESCRIPTION | 11 +-- MD5 | 32 +++++----- NAMESPACE | 16 ++--- R/RcppExports.R | 5 - R/comet.R | 7 +- R/gcm.R | 103 +++++++++++++++++++++++++-------- R/kgcm.R | 48 ++++++++------- R/pcm.R | 24 +++---- R/regressions.R | 163 ++++++++++++++++++++++++++++++++++++++++++----------- R/wgcm.R | 35 +++++------ build/partial.rdb |binary man/gcm.Rd | 26 +++++--- man/kgcm.Rd | 7 -- man/pcm.Rd | 6 - man/regressions.Rd | 55 +++++++++++++---- man/rgcm.Rd | 28 ++++++--- man/wgcm.Rd | 10 +-- 17 files changed, 393 insertions(+), 183 deletions(-)
Title: Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have
Accompanying Setup Files (.sps or .sas)
Description: Lets you open a fixed-width ASCII file (.txt or
.dat) that has an accompanying setup file (.sps or .sas). These file
combinations are sometimes referred to as .txt+.sps, .txt+.sas,
.dat+.sps, or .dat+.sas. This will only run in a txt-sps or txt-sas
pair in which the setup file contains instructions to open that text
file. It will NOT open other text files, .sav, .sas, or .por data
files. Fixed-width ASCII files with setup files are common in older
(pre-2000) government data.
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between asciiSetupReader versions 2.5.3 dated 2025-09-23 and 2.6.0 dated 2026-10-17
DESCRIPTION | 16 +- MD5 | 61 ++++---- NEWS.md | 49 ++++++ R/helper.R | 173 +++++++++++++---------- R/make_sps_setup.R | 95 ++++++------- R/parse_setup.R | 153 +++++++++++---------- R/read_ascii_setup.R | 52 +++---- R/read_ascii_setup_addin.R | 4 R/sas.R | 59 ++------ R/spss.R | 61 ++------ R/utils.R | 181 +++++++++++++------------ README.md | 15 -- build/vignette.rds |binary inst/doc/Introduction_to_asciiSetupReader.Rmd | 2 inst/doc/Introduction_to_asciiSetupReader.html | 6 inst/doc/making-an-sps-file.Rmd | 4 inst/doc/making-an-sps-file.html | 10 - inst/doc/parsing-an-sps-or-sas-file.html | 4 man/make_sps_setup.Rd | 52 +++---- man/parse_setup.Rd | 30 ++-- man/read_ascii_setup.Rd | 23 +-- man/read_ascii_setup_addin.Rd | 4 man/sas_ascii_reader.Rd | 42 ++--- man/spss_ascii_reader.Rd | 37 ++--- tests/testthat/test-fix-missing.R |only tests/testthat/test-make-cols-numeric.R |only tests/testthat/test-make-sps-setup.R |only tests/testthat/test-parse-codebook.R |only tests/testthat/test-psid-test.R | 4 tests/testthat/test-read-data.R |only tests/testthat/test-readers.R |only tests/testthat/test-sas-format-options.R |only tests/testthat/test-silent.R | 4 vignettes/Introduction_to_asciiSetupReader.Rmd | 2 vignettes/making-an-sps-file.Rmd | 4 35 files changed, 601 insertions(+), 546 deletions(-)
More information about asciiSetupReader at CRAN
Permanent link
Title: Model-Based Causal Feature Selection for General Response Types
Description: Extends invariant causal prediction (Peters et al., 2016,
<doi:10.1111/rssb.12167>) to generalized linear and transformation models
(Hothorn et al., 2018, <doi:10.1111/sjos.12291>).
The methodology is described in Kook et al. (2023,
<doi:10.1080/01621459.2024.2395588>).
Author: Lucas Kook [aut, cre] ,
Sorawit Saengkyongam [ctb],
Anton Rask Lundborg [ctb],
Torsten Hothorn [ctb],
Jonas Peters [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between tramicp versions 0.1-0 dated 2025-01-31 and 0.1-1 dated 2026-10-17
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + R/alias.R | 2 +- R/helpers.R | 7 +++++-- R/invariance-types.R | 2 +- R/tests.R | 2 +- R/tramicp.R | 12 ++++++------ build/partial.rdb |binary man/dicp.Rd | 13 ++++++++----- man/tramicp-alias.Rd | 2 +- tests/testthat/test-bugfixes.R |only 12 files changed, 40 insertions(+), 32 deletions(-)
Title: Optimal Subset Selection for Transformation Models
Description: Greedy optimal subset selection for transformation models
(Hothorn et al., 2018, <doi:10.1111/sjos.12291> ) based on the abess
algorithm (Zhu et al., 2020, <doi:10.1073/pnas.2014241117> ). Applicable to
models from packages 'tram' and 'cotram'. Application to shift-scale
transformation models are described in Siegfried et al. (2024,
<doi:10.1080/00031305.2023.2203177>).
Author: Lucas Kook [aut, cre] ,
Sandra Siegfried [ctb],
Torsten Hothorn [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between tramvs versions 0.0-9 dated 2026-03-10 and 0.0-10 dated 2026-10-17
DESCRIPTION | 10 +-- MD5 | 51 +++++++++---------- NAMESPACE | 60 +++++++++++++--------- R/methods.R | 2 R/mmltvs.R | 65 +++++++++++------------- R/models.R | 32 +++++++++--- R/tramvs.R | 107 ++++++++++++++++++----------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/tramvs.R | 12 ++-- inst/doc/tramvs.Rnw | 9 ++- inst/doc/tramvs.pdf |binary man/BoxCoxVS.Rd | 10 ++- man/ColrVS.Rd | 10 ++- man/CoxphVS.Rd | 10 ++- man/LehmannVS.Rd | 10 ++- man/LmVS.Rd | 10 ++- man/PolrVS.Rd | 10 ++- man/SurvregVS.Rd | 10 ++- man/abess_mmlt.Rd | 10 ++- man/abess_tram.Rd | 10 ++- man/cor_init.stram.Rd | 4 - man/cotramVS.Rd | 10 ++- man/mmltVS.Rd | 23 ++++---- man/tramvs.Rd | 21 ++++---- tests/testthat/test-splicing.R |only vignettes/tramvs.Rnw | 9 ++- 27 files changed, 275 insertions(+), 230 deletions(-)
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of one or more categorical
variables; paired(), a Table-1-like summary of multiple variable types paired across
two time points; modelsum(), which performs simple model fits on one or more endpoints
for many variables (univariate or adjusted for covariates);
freqlist(), a powerful frequency table across many categorical variables;
comparedf(), a function for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb],
[...truncated...]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 3.7.1 dated 2026-07-02 and 3.7.4 dated 2026-10-17
DESCRIPTION | 10 +++---- MD5 | 22 ++++++++--------- NAMESPACE | 6 +++- NEWS.md | 14 +++++++++++ R/arsenal_table.R | 2 - R/defunct.R | 2 - inst/doc/modelsum.html | 2 - inst/doc/tableby.html | 2 - man/arsenal-defunct.Rd | 5 --- man/arsenal_table.Rd | 2 - tests/testthat/test_formulize.R | 12 +-------- tests/testthat/test_lhs_modelsum.R | 47 +++---------------------------------- 12 files changed, 44 insertions(+), 82 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The functions
are pipe-friendly and provide a consistent syntax to work with tidy
data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'. References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 2.1.2 dated 2026-10-09 and 2.2.0 dated 2026-10-17
DESCRIPTION | 11 MD5 | 178 ++++----- NAMESPACE | 1 NEWS.md | 46 ++ R/add-expression-col.R | 81 ++-- R/centrality-description.R | 17 R/complete-subjects.R |only R/contingency-table.R | 80 +--- R/corr-test.R | 6 R/data.R | 22 - R/globals.R | 3 R/helpers-easystats.R | 32 - R/long-to-wide-converter.R | 50 +- R/meta-analysis.R | 17 R/one-sample-test.R | 2 R/oneway-anova.R | 179 ++------- R/pairwise-comparisons.R | 213 ++--------- R/pairwise-contingency-table.R | 22 - R/statsExpressions-package.R | 5 R/switch-functions.R | 3 R/tidy-model-expressions.R | 67 ++- R/two-sample-test.R | 68 +-- README.md | 315 +--------------- inst/doc/statsExpressions.R | 29 - inst/doc/statsExpressions.Rmd | 91 +--- inst/doc/statsExpressions.html | 398 ++++++++++----------- inst/doc/stats_details.R | 2 inst/doc/stats_details.Rmd | 22 - inst/doc/stats_details.html | 265 +++++-------- man/add_expression_col.Rd | 3 man/centrality_description.Rd | 3 man/complete_subjects.Rd |only man/contingency_table.Rd | 15 man/corr_test.Rd | 13 man/examples/examples-oneway-anova.R |only man/examples/examples-pairwise-comparisons.R |only man/iris_long.Rd | 8 man/long_to_wide_converter.Rd | 20 - man/meta_analysis.Rd | 13 man/movies_long.Rd | 14 man/one_sample_test.Rd | 15 man/oneway_anova.Rd | 97 ++--- man/pairwise_comparisons.Rd | 126 +++--- man/pairwise_contingency_table.Rd | 11 man/rmd-fragments/contingency_table.Rmd | 4 man/rmd-fragments/corr_test.Rmd | 2 man/rmd-fragments/functionality.Rmd | 50 -- man/rmd-fragments/meta_analysis.Rmd | 2 man/rmd-fragments/one_sample_test.Rmd | 2 man/rmd-fragments/oneway_anova.Rmd | 10 man/rmd-fragments/pairwise_comparisons.Rmd | 9 man/rmd-fragments/return.Rmd | 12 man/rmd-fragments/return_centrality.Rmd | 3 man/rmd-fragments/two_sample_test.Rmd | 13 man/statsExpressions-package.Rd | 5 man/two_sample_test.Rd | 31 - tests/testthat/_snaps/add-expression-col.md |only tests/testthat/_snaps/complete-subjects.md |only tests/testthat/_snaps/contingency-table.md | 8 tests/testthat/_snaps/long-to-wide-converter.md | 18 tests/testthat/_snaps/one-two-sample-dataframes.md | 2 tests/testthat/_snaps/oneway-anova-robust.md | 14 tests/testthat/_snaps/pairwise-comparisons.md | 150 +++---- tests/testthat/_snaps/tidy-model-expressions.md | 163 +++++++- tests/testthat/_snaps/two-sample-parametric.md | 12 tests/testthat/helper-long-to-wide.R |only tests/testthat/helper-one-sample.R | 8 tests/testthat/helper-subject-id.R |only tests/testthat/helper.R | 9 tests/testthat/test-add-expression-col.R |only tests/testthat/test-centrality-description.R | 32 - tests/testthat/test-complete-subjects.R |only tests/testthat/test-contingency-table.R | 99 +---- tests/testthat/test-corr-test.R | 12 tests/testthat/test-long-to-wide-converter.R | 236 ++++-------- tests/testthat/test-meta-random-bayes.R | 2 tests/testthat/test-meta-random-parametric.R | 2 tests/testthat/test-meta-random-robust.R | 2 tests/testthat/test-one-two-sample-dataframes.R | 65 +-- tests/testthat/test-oneway-anova-bayes.R | 50 -- tests/testthat/test-oneway-anova-nonparametric.R | 27 - tests/testthat/test-oneway-anova-parametric.R | 26 - tests/testthat/test-oneway-anova-robust.R | 8 tests/testthat/test-pairwise-comparisons.R | 269 ++++---------- tests/testthat/test-pairwise-contingency-table.R | 15 tests/testthat/test-print.R | 16 tests/testthat/test-tidy-model-expressions.R | 131 ++++-- tests/testthat/test-two-sample-bayes.R | 38 -- tests/testthat/test-two-sample-nonparametric.R | 33 - tests/testthat/test-two-sample-parametric.R | 71 +-- tests/testthat/test-two-sample-robust.R | 32 - vignettes/statsExpressions.Rmd | 91 +--- vignettes/stats_details.Rmd | 22 - vignettes/web_only/dataframe_outputs.Rmd | 236 ------------ vignettes/web_only/return_value_schema.Rmd | 136 +------ 95 files changed, 1799 insertions(+), 2942 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Randomized Singular Value Decomposition
Description: Low-rank matrix decompositions are fundamental tools and widely used for data
analysis, dimension reduction, and data compression. Classically, highly accurate
deterministic matrix algorithms are used for this task. However, the emergence of
large-scale data has severely challenged our computational ability to analyze big data.
The concept of randomness has been demonstrated as an effective strategy to quickly produce
approximate answers to familiar problems such as the singular value decomposition (SVD).
The rsvd package provides several randomized matrix algorithms such as the randomized
singular value decomposition (rsvd), randomized principal component analysis (rpca),
randomized robust principal component analysis (rrpca), randomized interpolative
decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot
functions are provided.
Author: N. Benjamin Erichson [aut, cre]
Maintainer: N. Benjamin Erichson <erichson@icsi.berkeley.edu>
Diff between rsvd versions 1.0.5 dated 2021-04-16 and 1.0.6 dated 2026-10-17
DESCRIPTION | 12 ++++++------ MD5 | 5 +++-- README.md |only build/partial.rdb |binary 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the embedded
'libxls' C library <https://github.com/libxls/libxls> and '.xlsx' via
the embedded 'RapidXML' C++ library
<https://rapidxml.sourceforge.net/>. Works on Windows, Mac and Linux
without external dependencies. Reading of password-encrypted '.xlsx'
files is supported via the embedded 'tiny-AES-c' C library
<https://github.com/kokke/tiny-AES-c>.
Author: Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Posit, PBC [cph, fnd] ,
Marcin Kalicinski [ctb, cph] ,
Komarov Valery [ctb, cph] ,
Christophe Leitienne [ctb, cph] ,
Bob Colbert [ctb, cph] ,
David Hoerl [ctb, cph] ,
Evan Miller [ctb, cph] ,
kokke [ [...truncated...]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between readxl versions 1.5.0.1 dated 2026-09-16 and 1.6.0 dated 2026-10-17
DESCRIPTION | 27 - LICENSE.note | 30 + MD5 | 98 +++-- NAMESPACE | 10 NEWS.md | 9 R/cpp11.R | 8 R/decrypt.R |only R/excel-sheets.R | 8 R/read_excel.R | 75 +++- build/vignette.rds |binary man/excel_sheets.Rd | 16 man/read_excel.Rd | 27 + man/readxl-package.Rd | 3 src/CellLimits.h | 13 src/Decrypt.cpp |only src/Makevars | 4 src/Makevars.win | 6 src/aes-variant.h |only src/aes128.c |only src/aes192.c |only src/aes256.c |only src/cpp11.cpp | 16 src/cran.c | 4 src/cran.h | 7 src/libxls/brdb.h | 6 src/libxls/endian.c | 2 src/libxls/endian.h | 6 src/libxls/locale.c | 33 - src/libxls/locale.h | 20 - src/libxls/ole.c | 147 +++++++- src/libxls/ole.h | 2 src/libxls/xls.c | 221 +++++++++---- src/libxls/xls.h | 13 src/libxls/xlsstruct.h | 51 --- src/libxls/xlstool.c | 57 ++- src/libxls/xlstool.h | 6 src/libxls/xlstypes.h | 13 src/sha.h |only src/tinyaes |only src/unix/config-macos.h | 8 src/unix/config-unix.h | 8 src/windows/config.h | 8 tests/testthat/_snaps/decrypt.md |only tests/testthat/_snaps/read-excel.md | 30 + tests/testthat/_snaps/sheets.md | 32 + tests/testthat/fixtures |only tests/testthat/sheets/encryptAES.xlsx |only tests/testthat/sheets/encryptSHA1.xlsx |only tests/testthat/sheets/encryptSHA512.xlsx |only tests/testthat/sheets/mtcars-xlsx-encrypted-with-cars.xlsx |only tests/testthat/sheets/mtcars-xlsx.xlsx |only tests/testthat/test-decrypt.R |only tests/testthat/test-empty.R | 100 +++++ tests/testthat/test-missing-values.R | 12 tests/testthat/test-read-excel.R | 25 + tests/testthat/test-sheets.R | 16 tests/testthat/test-skipping.R | 18 - 57 files changed, 912 insertions(+), 283 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library aiming towards
a good balance between speed and ease of use. It provides high-level syntax and
functionality deliberately similar to Matlab. It is useful for algorithm development
directly in C++, or quick conversion of research code into production environments.
It provides efficient classes for vectors, matrices and cubes where dense and sparse
matrices are supported. Integer, floating point and complex numbers are supported.
A sophisticated expression evaluator (based on template meta-programming) automatically
combines several operations to increase speed and efficiency. Dynamic evaluation
automatically chooses optimal code paths based on detected matrix structures.
Matrix decompositions are provided through integration with LAPACK, or one of its
high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can
automatically use 'OpenMP' multi-threading (parallelisation) to speed up
computationally expensive operations [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 15.6.0-1 dated 2026-09-08 and 15.6.2-1 dated 2026-10-17
ChangeLog | 17 ++++ DESCRIPTION | 8 +- MD5 | 28 +++---- README.md | 2 configure | 18 ++-- configure.ac | 2 inst/NEWS.Rd | 19 ++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/Mat_meat.hpp | 48 ++++++++++++ inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/glue_cubemul_bones.hpp | 3 inst/include/armadillo_bits/glue_cubemul_meat.hpp | 81 +++++++++++++++++++++ inst/include/armadillo_bits/op_pinv_meat.hpp | 2 inst/include/armadillo_bits/traits.hpp | 13 +++ 15 files changed, 212 insertions(+), 31 deletions(-)
Title: Robust Image Rendering Support for 'ggplot2'
Description: A 'ggplot2' extension that enables robust image grobs in
panels and theme elements.
Author: Sebastian Carl [aut, cre, cph]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between ggpath versions 1.1.1 dated 2025-10-16 and 1.1.2 dated 2026-10-17
DESCRIPTION | 10 +-- MD5 | 19 +++--- NAMESPACE | 8 +- NEWS.md | 4 + R/theme_element.R | 72 +++++++++---------------- R/zzz.R | 16 +++++ man/element_path.Rd | 22 ++++--- man/geom_from_path.Rd | 2 man/geom_lines.Rd | 2 man/ggpath-package.Rd | 14 ++-- tests/testthat/test-theme-element-properties.R |only 11 files changed, 88 insertions(+), 81 deletions(-)
Title: Branch-Level Inference Framework for Recognizing Optimal Shifts
in Traits
Description: Methods for detecting, visualizing, and evaluating cladogenic shifts in multivariate trait data on phylogenies. Implements penalized-likelihood multivariate generalized least squares models and a greedy step-wise shift search for high-dimensional trait datasets and large trees via searchOptimalConfiguration(). Provides tools for inspecting search trajectories, summarizing branch and lineage rates, analyzing shift timing and magnitudes, estimating post-hoc regime covariance and integration, and running simulation-based calibration and tuning. The search follows approaches developed in Smith et al. (2023) <doi:10.1111/nph.19099> and Berv et al. (2024) <doi:10.1126/sciadv.adp0114>. Methods build on multivariate generalized least squares approaches described in Clavel et al. (2019) <doi:10.1093/sysbio/syy045> and implemented in the mvgls() function from the 'mvMORPH' package. Documentation and worked examples are available at <https://jakeberv.com/bifrost/>.
Author: Jacob S. Berv [aut, cre, cph, fnd] ,
Nathan Fox [aut] ,
Matt J. Thorstensen [aut] ,
Henry Lloyd-Laney [aut] ,
Emily M. Troyer [aut] ,
Rafael A. Rivero-Vega [aut] ,
Stephen A. Smith [aut, fnd] ,
Matt Friedman [aut, fnd] ,
David F. Fouhey [aut, fnd] ,
[...truncated...]
Maintainer: Jacob S. Berv <jacob.berv@gmail.com>
Diff between bifrost versions 0.2.0 dated 2026-09-27 and 0.2.2 dated 2026-10-17
DESCRIPTION | 17 - MD5 | 35 +- NEWS.md | 48 ++ R/bifrost_search-methods.R | 4 R/mvgls-starts.R |only R/searchOptimalConfiguration-helpers.R | 334 ++++++++++++-------- R/searchOptimalConfiguration.R | 64 +++ R/utils.R | 12 README.md | 47 +- inst/CITATION | 69 +--- inst/WORDLIST | 20 - man/searchOptimalConfiguration.Rd | 55 ++- tests/testthat/fixtures/mvgls-starts-historical.rds |only tests/testthat/helper-search-characterization.R | 4 tests/testthat/test-mvgls-starts.R |only tests/testthat/test-print-bifrost_search.R | 37 ++ tests/testthat/test-search-background-history.R |only tests/testthat/test-search-progress-atomic.R |only tests/testthat/test-search-progress-equivalence.R |only tests/testthat/test-search-progress-rng.R |only tests/testthat/test-search-progress.R | 50 ++ tests/testthat/test-search-spinner.R |only tests/testthat/test-search-threading.R |only 23 files changed, 535 insertions(+), 261 deletions(-)
Title: Process Command Line Arguments
Description: Process command line arguments. Processing
includes checking, naming, and coercing to numeric,
date, or logical. By capturing assumptions about
inputs and outputs, the 'command' package can
provide scripts with well defined interfaces,
leading to safer, more modular data analysis pipelines.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between command versions 0.2.0 dated 2026-07-22 and 0.3.0 dated 2026-10-17
DESCRIPTION | 18 MD5 | 53 +- NAMESPACE | 2 NEWS.md | 51 ++ R/check-functions.R | 122 +++++ R/cmd_assign.R | 294 +++++++++++-- R/command-package.R | 6 R/extract_make.R | 28 - R/extract_shell.R | 25 - R/helper-functions.R | 743 ++++++++++++++++++++++++++++----- R/makefile.R | 9 R/shell_script.R | 20 R/use_renv.R | 2 README.md | 2 man/cmd_assign.Rd | 145 ++++-- man/cmd_assign_collect.Rd |only man/command-package.Rd | 6 man/extract_make.Rd | 27 - man/extract_shell.Rd | 25 - man/makefile.Rd | 9 man/shell_script.Rd | 18 man/use_renv.Rd | 2 tests/testthat/test-check-functions.R | 75 +++ tests/testthat/test-cmd_assign.R | 90 +++ tests/testthat/test-extract_make.R | 20 tests/testthat/test-helper-functions.R | 480 +++++++++++++++++++++ tests/testthat/test-shell_script.R | 13 tests/testthat/test-use_renv.R | 104 ++++ 28 files changed, 2103 insertions(+), 286 deletions(-)
Title: Multi-Layer Decomposition of Functional Community Restructuring
Description: Implements the 'ASC-CFD' (Assemblage Shift Characterization -
Community Functional Dynamics) framework for decomposing functional community
restructuring into positional (centroid displacement), dispersive
(functional dispersion), and boundary (convex hull volume) components.
Tests each component against two null models: a sampling null model
(individuals or replicates reassigned between communities) and a
stratified trait-permutation null model, with a single global test when
many communities are compared. Functional entities (species with similar
traits) help detect replacement among similar species, and species-level
leverage identifies the taxa driving functional shifts. Supports both
temporal (paired) and spatial (pairwise) comparisons.
Author: Rogelio R. Munoz-Li [aut, cre],
Flavia Alvarez-Denis [aut]
Maintainer: Rogelio R. Munoz-Li <munozrogelio16@gmail.com>
Diff between ascent versions 0.1.1 dated 2026-07-30 and 0.5.0 dated 2026-10-17
DESCRIPTION | 21 MD5 | 64 +-- NAMESPACE | 55 +- NEWS.md | 80 +++ R/asc_baseline.R | 162 +++---- R/asc_entities.R | 220 +++++++--- R/asc_null.R | 518 +++++++++++++++--------- R/asc_paired.R | 290 +++++++------ R/asc_pairwise.R | 220 +++++----- R/asc_transitions.R | 242 ++++++----- R/ascent-package.R |only R/assess_functional_space.R | 295 +++++++------ R/data.R |only R/print.R | 109 ++--- R/summary.R | 491 ++++++++++++----------- R/utils_topology.R | 319 +++++++++----- README.md | 358 ++++++++-------- build/vignette.rds |binary data |only inst/CITATION | 23 - inst/doc/ascent_tutorial.R | 105 ++-- inst/doc/ascent_tutorial.Rmd | 411 +++++++++---------- inst/doc/ascent_tutorial.html | 810 ++++++++++++++++++++------------------ man/asc_baseline.Rd | 110 ++--- man/asc_entities.Rd | 157 +++++-- man/asc_null.Rd | 193 +++++---- man/asc_paired.Rd | 48 +- man/asc_pairwise.Rd | 38 + man/asc_transitions.Rd | 125 +++-- man/ascent-package.Rd |only man/assess_functional_space.Rd | 151 +++---- man/birds_sim.Rd |only man/summary.ascfcd_transitions.Rd | 45 +- tests/testthat/test-core.R | 31 - tests/testthat/test-v020.R |only vignettes/ascent_tutorial.Rmd | 411 +++++++++---------- 36 files changed, 3457 insertions(+), 2645 deletions(-)