Title: Map Quantiles for Physical Activity from 'NHANES'
Description: Maps physical activity from the National Health and Nutrition
Examination Survey ('NHANES') study into population-based quantiles,
using the NHANES 2011-2014 step count and physical activity summaries
described in Koffman, Crainiceanu, and Muschelli (2025)
<doi:10.1249/MSS.0000000000003616>, with minute-level data from
Koffman and Muschelli (2025) <doi:10.13026/9n0r-tv02>.
Author: John Muschelli [aut, cre] ,
Lily Koffman [aut]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between mapnhanespa versions 0.3.0 dated 2026-10-22 and 0.4.0 dated 2026-11-09
DESCRIPTION | 8 - MD5 | 40 +++--- NAMESPACE | 1 NEWS.md | 16 ++ R/data.R | 73 ++++++++++- R/map-quantiles.R | 105 ++++++++++++--- R/measure-map.R | 13 + R/wear-criteria.R |only README.md | 138 ++++++++++++++------ build/partial.rdb |only data/nhanes_measure_data_wear_criteria.rda |only inst/doc/mapnhanespa.R | 17 ++ inst/doc/mapnhanespa.Rmd | 39 +++++ inst/doc/mapnhanespa.html | 192 +++++++++++++++++++---------- man/map_nhanes_pa_quantiles.Rd | 18 ++ man/nhanes_measure_data.Rd | 16 ++ man/nhanes_measure_data_wear_criteria.Rd |only man/nhanes_pa_measure_cdf.Rd | 17 ++ man/nhanes_pa_quantile.Rd | 24 +++ man/nhanes_pa_wear_criteria.Rd |only man/precompute_nhanes_pa_cdfs.Rd | 16 ++ tests/testthat/test-map-quantiles.R | 4 tests/testthat/test-wear-criteria.R |only vignettes/mapnhanespa.Rmd | 39 +++++ 24 files changed, 614 insertions(+), 162 deletions(-)
Title: Project Scaffolding for R and 'Quarto'
Description: Creates structured R and 'Quarto' projects with a consistent directory layout: scripts in R/, analysis documents in analysis/, and web assets in www/. The primary entry point, init(), downloads the latest template from a companion 'GitHub' repository so that project structure evolves independently of package releases. Supports persistent author metadata and 'Quarto' brand configuration that carry across projects automatically.
Author: Kyle Grealis [aut, cre]
Maintainer: Kyle Grealis <kyleGrealis@proton.me>
Diff between froggeR versions 1.0.1 dated 2026-03-17 and 1.1.0 dated 2026-11-09
DESCRIPTION | 8 +-- MD5 | 24 ++++----- NEWS.md | 15 ++++++ R/write_variables.R | 4 - README.md | 16 ++++-- build/vignette.rds |binary inst/CITATION | 4 - inst/doc/every-file-in-its-place.Rmd | 22 ++++----- inst/doc/every-file-in-its-place.html | 54 +++++++++++----------- inst/doc/from-zero-to-project.Rmd | 48 ++++--------------- inst/doc/from-zero-to-project.html | 82 ++++++++++++---------------------- vignettes/every-file-in-its-place.Rmd | 22 ++++----- vignettes/from-zero-to-project.Rmd | 48 ++++--------------- 13 files changed, 146 insertions(+), 201 deletions(-)
Title: R Client for the ZENTRA Cloud V5 API
Description: Downloads environmental sensor data from the ZENTRA Cloud V5 API
(<https://api.zentracloud.io>) into tidy data frames. Provides device
discovery, reading retrieval with automatic pagination and rate-limit
handling, tidy long output with a wide-format helper, and an incremental
'sync' engine with pluggable local storage (RDS files, CSV files, or
return-only) so that new readings can be fetched on a schedule and
appended to a growing local record.
Author: Travis Bates [aut, cre],
METER Group, Inc. [cph, fnd]
Maintainer: Travis Bates <travis@metergroup.com>
Diff between zentraR versions 0.1.3 dated 2026-08-07 and 0.1.4 dated 2026-11-09
DESCRIPTION | 6 MD5 | 44 - NEWS.md | 15 R/auth.R | 8 R/readings.R | 27 R/sync-parallel.R | 4 R/sync.R | 4 R/utils-time.R | 71 ++ README.md | 42 + build/vignette.rds |binary inst/doc/getting-started.R | 183 +++--- inst/doc/getting-started.Rmd | 11 inst/doc/getting-started.html | 1056 ++++++++++++++++++------------------ inst/doc/scheduling.R | 130 ++-- inst/doc/scheduling.html | 974 ++++++++++++++++----------------- inst/doc/working-with-data.R | 148 ++--- inst/doc/working-with-data.html | 962 ++++++++++++++++---------------- man/zc_get_readings.Rd | 20 man/zc_set_key.Rd | 8 tests/testthat/helper-live.R |only tests/testthat/test-api.R | 36 + tests/testthat/test-live-contract.R |only tests/testthat/test-time.R | 62 ++ vignettes/getting-started.Rmd | 11 24 files changed, 2034 insertions(+), 1788 deletions(-)
Title: Operationalizing Social Determinants of Health Data for
Researchers
Description: Accesses raw data via API and calculates social
determinants of health measures for user-specified locations in the
US, returning them in tidyverse- and sf-compatible data frames.
Author: Nik Krieger [aut, cre],
Jarrod Dalton [aut],
Cindy Wang [aut],
Adam Perzynski [aut],
National Institutes of Health/National Institute on Aging [fnd] . All of its contents
are solely the responsibility of the authors and do not necessarily
represent t [...truncated...]
Maintainer: Nik Krieger <nikkrieger@gmail.com>
Diff between sociome versions 3.0.1 dated 2026-06-03 and 3.1.1 dated 2026-11-09
DESCRIPTION | 8 LICENSE | 2 MD5 | 86 - NEWS.md | 391 ++++--- R/calculate_adi.R | 1348 +++++++++++++-------------- R/census_api_key.R | 14 R/centers.R | 956 +++++++++---------- R/data_documentation.R | 304 +++--- R/dissimilarity.R | 294 ++--- R/get_adi.R | 576 +++++------ R/get_geoids.R | 244 ++-- R/get_tidycensus.R | 840 ++++++++-------- R/ref_area.R | 600 ++++++------ R/setup.R | 2 R/synthetic_population.R | 688 ++++++------- R/utils-pipe.R | 24 R/validation.R | 858 ++++++++--------- data/dataset_year_geography_availability.rda |binary man/acs_age_sex_race_ethnicity_vars.Rd | 64 - man/acs_vars.Rd | 102 +- man/append_dissimilarities.Rd | 178 +-- man/calculate_adi.Rd | 144 +- man/census_api_key.Rd | 16 man/dataset_year_geography_availability.Rd | 54 - man/decennial_age_sex_race_ethnicity_vars.Rd | 66 - man/decennial_vars.Rd | 54 - man/get_areas_near_coordinates.Rd | 322 +++--- man/get_geoids.Rd | 250 ++--- man/lon_lat_from_area.Rd | 122 +- man/pipe.Rd | 24 man/state_geoids.Rd | 48 man/synthetic_population.Rd | 360 +++---- tests/testthat.R | 24 tests/testthat/_snaps/get_adi.md | 36 tests/testthat/_snaps/get_geoids.md | 59 - tests/testthat/helper-setup.R | 2 tests/testthat/test-dissimilarity.R | 52 - tests/testthat/test-get_adi.R | 282 ++--- tests/testthat/test-get_geoids.R | 517 +++++----- tests/testthat/test-get_tidycensus.R | 14 tests/testthat/test-ref_area.R | 900 +++++++++--------- tests/testthat/test-synthetic_population.R | 94 - tests/testthat/test-validators.R | 244 ++-- tests/testthat/test_area_population.R | 114 +- 44 files changed, 5719 insertions(+), 5658 deletions(-)
Title: Local Large Language Models as Base-R Objects
Description: Load and run local large language models (through a vendored,
patched 'llama.cpp') from R and work with them as plain data frames and
matrices in base-R idiom. Provides model loading and tokenization (llm(),
llm_tokens()), text generation (llm_generate()), next-token distributions
(llm_logits()), embeddings (llm_embed()), and mechanistic
interpretability tools -- activation tracing (llm_trace()), activation
steering (llm_steer()), neuron ablation (llm_ablate()), and grouped statistical
probes (llm_probe()). Vision-language
models loaded with their projector take image input in generation and
embeddings. A checksum-verified downloader (llm_download()) fetches pinned
models.
Author: Alessandro Vadala [aut, cre, cph],
ggml authors [ctb, cph] ),
Authors of the bundled Rust and native dependencies [ctb, cph]
Maintainer: Alessandro Vadala <vadale93@gmail.com>
Diff between relm versions 0.6.2 dated 2026-11-02 and 0.6.3 dated 2026-11-09
DESCRIPTION | 6 MD5 | 36 - NEWS.md | 9 build/vignette.rds |binary inst/doc/anatomy-lab.R | 390 +++++++------- inst/doc/anatomy-lab.html | 860 ++++++++++++++++---------------- inst/doc/contrast-directions.R | 210 +++---- inst/doc/contrast-directions.html | 832 +++++++++++++++---------------- inst/doc/model-interventions.R | 170 +++--- inst/doc/model-interventions.html | 648 ++++++++++++------------ inst/doc/token-streaming.R | 114 ++-- inst/doc/token-streaming.html | 568 ++++++++++----------- inst/doc/topics-without-python.R | 384 +++++++------- inst/doc/topics-without-python.html | 896 +++++++++++++++++----------------- inst/doc/vision.R | 362 ++++++------- inst/doc/vision.html | 798 +++++++++++++++--------------- src/llama-sources.tar.xz |binary src/rust/rebirth-llm/src/async_job.rs | 10 tools/bundled-sources.json | 15 19 files changed, 3162 insertions(+), 3146 deletions(-)
Title: Core File Structures and Workflows for 'RAVE'
Description: Defines storage standard for Read, process, and analyze
intracranial electroencephalography and deep-brain stimulation in 'RAVE',
a reproducible framework for analysis and visualization of iEEG
by Magnotti, Wang, and Beauchamp, (2020,
<doi:10.1016/j.neuroimage.2020.117341>).
Supports brain imaging data structure (BIDS)
<https://bids.neuroimaging.io> and native file structure to
ingest signals from 'Matlab' data files, hierarchical data format 5 (HDF5),
European data format (EDF), BrainVision core data format (BVCDF), or
BlackRock Microsystem (NEV/NSx); process images in
Neuroimaging informatics technology initiative (NIfTI) and
'FreeSurfer' formats, providing brain imaging normalization to template
brain, facilitating 'threeBrain' package for comprehensive electrode
localization via 'YAEL' (your advanced electrode localizer) by Wang,
Magnotti, Zhang, and Beauchamp
(2023, <doi:10.1523/ENEURO.0328-23.2023>).
Author: Zhengjia Wang [aut, cre] ,
Xiang Zhang [aut],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravecore versions 0.1.1 dated 2026-04-02 and 1.0.0 dated 2026-11-09
DESCRIPTION | 18 MD5 | 160 +-- NAMESPACE | 16 NEWS.md | 56 + R/aaa-constants.R | 7 R/class002-project.R | 2 R/class004-epoch.R | 326 +++++- R/class005-subject.R | 243 ++++ R/class006-rawsubject.R | 2 R/class011-YAEL_native_process.R |only R/class011-YAEL_process.R | 343 +++++- R/class012-rave_brain.R | 14 R/class100-base_repository.R | 60 + R/import-h5_matlab_per_channel.R | 2 R/import-nev.R | 2 R/math-baseline_power.R | 17 R/utils-package.R | 1 R/utils-realign_trials.R |only R/utils-spikeinterface.R | 6 R/validator-condition_groups.R |only R/validator-nev.R | 22 R/validator-subject.R | 142 +- R/workflow-YBA_atlas.R |only R/workflow-dcm2niix.R | 29 R/workflow-freesurfer_macaque.R |only R/workflow-freesurfer_recon_all.R | 49 R/workflow-reg3d.R |only R/workflow-template_mapping.R | 13 R/workflow-volumetric_atlases.R | 76 - R/workflow-yael_brain_extract.R |only R/workflow-yael_native_helpers.R |only R/workflow-yael_preprocess.R | 75 + R/workflow-yael_preprocess_native.R |only build/partial.rdb |binary inst/reports/atlas-overlay.rmd |only inst/shell-templates/rave-reg3d-rigid.R |only inst/shell-templates/yael-preprocess-native.R |only inst/shell-templates/yael-preprocess.R | 24 inst/tech-details |only man/Auxiliary_electrode.Rd | 455 ++++----- man/LFP_electrode.Rd | 557 +++++------ man/LFP_reference.Rd | 503 +++++----- man/RAVEAbstarctElectrode.Rd | 441 ++++---- man/RAVEEpoch.Rd | 431 +++++--- man/RAVEPreprocessSettings.Rd | 488 +++++---- man/RAVEProject.Rd | 342 +++--- man/RAVESubject.Rd | 759 +++++++-------- man/RAVESubjectBaseRepository.Rd | 309 +++--- man/RAVESubjectEpochPhaseRepository.Rd | 190 +-- man/RAVESubjectEpochPowerRepository.Rd | 190 +-- man/RAVESubjectEpochRawVoltageRepository.Rd | 230 ++-- man/RAVESubjectEpochRepository.Rd | 345 +++--- man/RAVESubjectEpochTimeFreqBaseRepository.Rd | 239 ++-- man/RAVESubjectEpochTimeFreqCoefRepository.Rd | 192 +-- man/RAVESubjectEpochVoltageRepository.Rd | 228 ++-- man/RAVESubjectRecordingBlockPhaseRepository.Rd | 182 +-- man/RAVESubjectRecordingBlockPowerRepository.Rd | 182 +-- man/RAVESubjectRecordingBlockRawVoltageRepository.Rd | 231 ++-- man/RAVESubjectRecordingBlockRepository.Rd | 256 ++--- man/RAVESubjectRecordingBlockTimeFreqBaseRepository.Rd | 222 ++-- man/RAVESubjectRecordingBlockTimeFreqCoefRepository.Rd | 182 +-- man/RAVESubjectRecordingBlockVoltageRepository.Rd | 223 ++-- man/Spike_electrode.Rd | 455 ++++----- man/YAELNativeProcess.Rd |only man/YAELProcess.Rd | 853 +++++++++-------- man/as_rave_project.Rd | 2 man/as_yael_process.Rd | 16 man/cmd_run_yael_preprocess.Rd | 24 man/cmd_run_yael_preprocess_native.Rd |only man/generate_atlas_YBA.Rd |only man/generate_atlases_from_template.Rd | 12 man/get_available_morph_to_template.Rd | 9 man/import-signals.Rd | 4 man/power_baseline.Rd | 12 man/rave_brain.Rd | 6 man/ravecore-constants.Rd | 13 man/ravecore-package.Rd | 4 man/realign_trials.Rd |only man/reg3d_rigid.Rd |only man/validate_condition_groupings.Rd |only man/validate_subject.Rd | 16 man/yael_brain_extract.Rd |only man/yael_macaque.Rd |only tests/testthat/helper-yael-native.R |only tests/testthat/test-atlas-surface.R |only tests/testthat/test-class004-epoch.R |only tests/testthat/test-class005-subject.R |only tests/testthat/test-class011-YAEL_native_process.R |only tests/testthat/test-class011-YAEL_process.R | 26 tests/testthat/test-class011-YAEL_talairach.R |only tests/testthat/test-namespace_call_signatures.R |only tests/testthat/test-validator-nev.R |only tests/testthat/test-workflow-dcm2niix.R |only tests/testthat/test-workflow-reg3d.R |only tests/testthat/test-workflow-yael_brain_extract.R |only tests/testthat/test-workflow-yael_preprocess_native.R |only tests/testthat/test-workflow-yael_readers_native.R |only tests/testthat/test-yael-engine-consistency.R |only 98 files changed, 6005 insertions(+), 4529 deletions(-)
Title: Mobility Oriented-Parity Metric
Description: A set of tools to perform multiple versions of the Mobility
Oriented-Parity metric. This multivariate analysis helps to characterize
levels of dissimilarity between a set of conditions of reference and another
set of conditions of interest. If predictive models are transferred to
conditions different from those over which models were calibrated (trained),
this metric helps to identify transfer conditions that differ
substantially from those of calibration. These tools are implemented
following principles proposed in Owens et al. (2013)
<doi:10.1016/j.ecolmodel.2013.04.011>, and expanded to obtain more detailed
results that aid in interpretation as in Cobos et al. (2024)
<doi:10.21425/fob.17.132916>.
Author: Marlon E. Cobos [aut, cre] ,
Hannah L. Owens [aut] ,
Jorge Soberon [aut] ,
A. Townsend Peterson [aut]
Maintainer: Marlon E. Cobos <manubio13@gmail.com>
Diff between mop versions 0.1.4 dated 2026-04-22 and 0.1.5 dated 2026-11-09
DESCRIPTION | 14 ++-- MD5 | 28 ++++---- NAMESPACE | 10 +-- NEWS.md | 5 + R/methods.R | 2 R/mop_distance.R | 49 +++++++-------- README.md | 129 +++++++++++++++++++++-------------------- man/figures/README-load-1.png |binary man/figures/README-load-2.png |binary man/figures/README-plots-1.png |binary man/figures/README-plots-2.png |binary man/figures/README-plots-3.png |binary man/figures/README-plots-4.png |binary man/figures/README-plots-5.png |binary man/mop-package.Rd | 1 15 files changed, 125 insertions(+), 113 deletions(-)
Title: Fast Masked K-Nearest Neighbor Imputation
Description: Fast masked k-nearest neighbor imputation for mixed-type
tabular data. Distances are computed only on the variables jointly observed
by the receiver and the donor, and missing values are filled by local
regression (numeric) or weighted vote (categorical) over the nearest donors.
Returns completed data for single imputation or a list of completed data
sets for multiple imputation.
Author: Imad El Badisy [aut, cre]
Maintainer: Imad El Badisy <elbadisyimad@gmail.com>
Diff between missknn versions 1.1.2 dated 2026-08-21 and 1.2.0 dated 2026-11-09
missknn-1.1.2/missknn/R/complete.R |only missknn-1.1.2/missknn/R/print_summary.R |only missknn-1.1.2/missknn/man/complete.Rd |only missknn-1.2.0/missknn/DESCRIPTION | 15 missknn-1.2.0/missknn/MD5 | 107 missknn-1.2.0/missknn/NAMESPACE | 6 missknn-1.2.0/missknn/NEWS.md |only missknn-1.2.0/missknn/R/internal.R | 50 missknn-1.2.0/missknn/R/missknn.R | 51 missknn-1.2.0/missknn/README.md | 381 +- missknn-1.2.0/missknn/inst/CITATION |only missknn-1.2.0/missknn/inst/benchmark/benchmark_30.R | 7 missknn-1.2.0/missknn/inst/benchmark/benchmark_bigdata.R | 100 missknn-1.2.0/missknn/inst/benchmark/benchmark_bio.R | 5 missknn-1.2.0/missknn/inst/benchmark/benchmark_biobench.R |only missknn-1.2.0/missknn/inst/benchmark/benchmark_mixed.R | 9 missknn-1.2.0/missknn/inst/benchmark/benchmark_real.R | 70 missknn-1.2.0/missknn/inst/benchmark/benchmark_real_bign.R |only missknn-1.2.0/missknn/inst/benchmark/benchmark_speed_mixgb.R | 2 missknn-1.2.0/missknn/inst/benchmark/output/benchmark_report.md | 8 missknn-1.2.0/missknn/inst/benchmark/output/bigdata_benchmark_report.md | 57 missknn-1.2.0/missknn/inst/benchmark/output/bigdata_cells |only missknn-1.2.0/missknn/inst/benchmark/output/bigdata_mse_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/bigdata_results.csv | 30 missknn-1.2.0/missknn/inst/benchmark/output/bigdata_runtime_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/bign_cells |only missknn-1.2.0/missknn/inst/benchmark/output/bio_data_benchmark_report.md | 24 missknn-1.2.0/missknn/inst/benchmark/output/bio_data_results.csv | 24 missknn-1.2.0/missknn/inst/benchmark/output/bio_data_speed_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/biobench |only missknn-1.2.0/missknn/inst/benchmark/output/coefficient_results.csv | 1296 +++++----- missknn-1.2.0/missknn/inst/benchmark/output/mixed_categorical_results.csv | 8 missknn-1.2.0/missknn/inst/benchmark/output/mixed_correlated_results.csv | 4 missknn-1.2.0/missknn/inst/benchmark/output/mixed_validation_report.md | 12 missknn-1.2.0/missknn/inst/benchmark/output/real_data_benchmark_report.md | 54 missknn-1.2.0/missknn/inst/benchmark/output/real_data_nrmse_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/real_data_results.csv | 32 missknn-1.2.0/missknn/inst/benchmark/output/real_data_speed_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/runtime_plot.png |binary missknn-1.2.0/missknn/inst/benchmark/output/runtime_results.csv | 240 - missknn-1.2.0/missknn/inst/doc/missknn.R | 19 missknn-1.2.0/missknn/inst/doc/missknn.Rmd | 35 missknn-1.2.0/missknn/inst/doc/missknn.html | 55 missknn-1.2.0/missknn/man/missknn-package.Rd | 2 missknn-1.2.0/missknn/man/missknn.Rd | 43 missknn-1.2.0/missknn/tests/testthat/test-missknn.R | 115 missknn-1.2.0/missknn/vignettes/missknn.Rmd | 35 47 files changed, 1573 insertions(+), 1323 deletions(-)
Title: Balancing Confounder Distributions with Forest Energy Balancing
Description: Estimates average treatment effects using kernel energy balancing
with random forest similarity kernels. A multivariate random forest jointly
models covariates, outcome, and treatment to build a similarity kernel
between observations. This kernel is then used for energy balancing to create
weights that control for confounding. The method is described in
De and Huling (2025) <doi:10.48550/arXiv.2512.18069>.
Author: Jared Huling [aut, cre],
Simion De [aut]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between forestBalance versions 0.1.0 dated 2026-04-07 and 0.1.1 dated 2026-11-09
DESCRIPTION | 6 MD5 | 56 ++--- NEWS.md |only R/RcppExports.R | 4 R/forest_balance.R | 193 ++++++++++++++----- R/kernel_balance.R | 287 ++++++++++++++++++++++++----- R/summary.R | 5 inst/doc/augmented.Rmd | 24 +- inst/doc/augmented.html | 60 +++--- inst/doc/crossfitting.Rmd | 43 ++-- inst/doc/crossfitting.html | 113 +++++------ inst/doc/guide.Rmd | 61 +++--- inst/doc/guide.html | 85 ++++---- inst/doc/performance.Rmd | 71 +++---- inst/doc/performance.html | 134 ++++++------- man/forest_balance.Rd | 23 ++ man/kernel_balance.Rd | 13 + src/RcppExports.cpp | 9 src/cg_solve.cpp | 16 + tests/testthat/test-forest_balance.R | 37 +++ tests/testthat/test-kernel_balance.R | 70 +++++++ tests/testthat/test-production-guards.R |only vignettes/augmented.Rmd | 24 +- vignettes/crossfitting.Rmd | 43 ++-- vignettes/guide-sim-plot-1.png |binary vignettes/guide.Rmd | 61 +++--- vignettes/performance-breakdown-plot-1.png |binary vignettes/performance-timing-plot-1.png |binary vignettes/performance-tree-plot-1.png |binary vignettes/performance.Rmd | 71 +++---- 30 files changed, 987 insertions(+), 522 deletions(-)
Title: Nonparametric Sobol Estimator with Bootstrap Bandwidth
Description: Algorithm to estimate the Sobol indices using a non-parametric
fit of the regression curve. The bandwidth is estimated using bootstrap
to reduce the finite-sample bias. The package is based on the paper
Solís, M. (2021) <doi:10.1080/03610918.2019.1655575>.
Author: Maikol Solis [aut, cre]
Maintainer: Maikol Solis <maikol.solis@ucr.ac.cr>
Diff between sobolnp versions 0.1.0 dated 2019-04-29 and 0.2.0 dated 2026-11-09
sobolnp-0.1.0/sobolnp/man/plot.Rd |only sobolnp-0.1.0/sobolnp/man/print.Rd |only sobolnp-0.1.0/sobolnp/tests/tests.R |only sobolnp-0.2.0/sobolnp/DESCRIPTION | 26 + sobolnp-0.2.0/sobolnp/MD5 | 25 + sobolnp-0.2.0/sobolnp/NAMESPACE | 26 + sobolnp-0.2.0/sobolnp/NEWS.md | 37 ++ sobolnp-0.2.0/sobolnp/R/plot.sobolnp.R | 111 +++---- sobolnp-0.2.0/sobolnp/R/print.sobolnp.R | 35 +- sobolnp-0.2.0/sobolnp/R/sobolnp.R | 411 +++++++++++------------------ sobolnp-0.2.0/sobolnp/README.md |only sobolnp-0.2.0/sobolnp/build |only sobolnp-0.2.0/sobolnp/inst |only sobolnp-0.2.0/sobolnp/man/figures |only sobolnp-0.2.0/sobolnp/man/plot.sobolnp.Rd |only sobolnp-0.2.0/sobolnp/man/print.sobolnp.Rd |only sobolnp-0.2.0/sobolnp/man/sobolnp.Rd | 52 +++ sobolnp-0.2.0/sobolnp/tests/testthat |only sobolnp-0.2.0/sobolnp/tests/testthat.R |only 19 files changed, 349 insertions(+), 374 deletions(-)
Title: Statistical Inference on Lineup Fairness
Description: Computes statistical measures for laboratory and police lineups in
forensic psychology, including lineup bias, functional and effective size,
diagnosticity, confidence-accuracy curves, signal detection models, and
simulation tools. Optional face-similarity functions use numeric face
representations computed by Python's 'deepface' library; optional
lineup-memory model fitting uses a separately installed, pinned
'pyWitness' engine.
Author: Colin Tredoux [aut, cre] ,
Tamsyn Naylor [aut]
Maintainer: Colin Tredoux <colin.tredoux@uct.ac.za>
Diff between r4lineups versions 2.3.0 dated 2026-11-02 and 2.3.1 dated 2026-11-09
DESCRIPTION | 6 MD5 | 374 ++-- NEWS.md | 147 + R/anri_functions.R | 29 R/bayes_curves_functions.R | 121 + R/bias_effective_distributions.R | 18 R/cac_functions.R | 6 R/calibration_bayes.R | 12 R/calibration_functions.R | 139 + R/classify_choices.R | 22 R/data_standardization.R | 12 R/datacheck1.R | 8 R/datacheck2.R | 12 R/datacheck3.R | 12 R/diag_ratio_T.R | 4 R/diag_ratio_T_bayes.R | 9 R/diag_ratio_W.R | 4 R/eff_size_per_foils.R | 11 R/effsize_compare.R | 23 R/eig_functions.R | 8 R/embeddings.R | 4 R/esize_T_bayes.R | 5 R/esize_T_ci_n.R | 6 R/esize_m.R | 5 R/fullroc_functions.R | 55 R/func_size.R | 5 R/func_size_bayes.R | 11 R/func_size_report.R | 5 R/gen_lineup_prop.R | 9 R/homog_diag.R | 17 R/line73.R | 12 R/lineup_boot_allprop.R | 2 R/lineup_models_pywitness.R | 20 R/lineup_prop_tab.R | 12 R/make_roc.R | 7 R/max_sdt_fit.R | 16 R/mockdata.R | 1 R/model_comparison.R | 21 R/multid_functions.R | 10 R/nortje2012.R | 1 R/pauc_comparison.R | 33 R/ppv_range_functions.R | 17 R/ppv_range_plots.R | 15 R/rac_functions.R | 11 R/roc_functions.R | 6 R/sdt_compare.R | 26 R/sdt_glm.R | 7 R/sdt_summary_compare.R | 47 R/setup.R | 13 R/similarity.R | 8 R/simulate_lineup_data.R | 92 - R/utility_functions.R | 26 R/var_d.R | 4 R/visualization_faces.R | 8 R/winter_2ht_boot.R | 2 R/zroc_sdt.R | 32 inst/doc/Vignette.R | 8 inst/doc/Vignette.Rmd | 72 inst/doc/Vignette.html | 109 - inst/doc/bayesian_inference.R | 2 inst/doc/bayesian_inference.Rmd | 7 inst/doc/bayesian_inference.html | 27 inst/doc/calibration_decision_analysis.R | 13 inst/doc/calibration_decision_analysis.Rmd | 189 +- inst/doc/calibration_decision_analysis.html | 1208 +++++++-------- inst/doc/face_similarity.Rmd | 19 inst/doc/face_similarity.html | 25 inst/doc/fullroc_analysis.Rmd | 52 inst/doc/fullroc_analysis.html | 106 - inst/doc/information_error_rate_analysis.R | 2 inst/doc/information_error_rate_analysis.Rmd | 46 inst/doc/information_error_rate_analysis.html | 63 inst/doc/lineup_memory_models.Rmd | 12 inst/doc/lineup_memory_models.html | 17 inst/doc/model_comparison.R | 2 inst/doc/model_comparison.Rmd | 72 inst/doc/model_comparison.html | 151 + inst/doc/msdt_model.html | 4 inst/doc/multid_model.Rmd | 16 inst/doc/multid_model.html | 20 inst/doc/pauc_statistical_comparison.Rmd | 19 inst/doc/pauc_statistical_comparison.html | 37 inst/doc/rac_analysis.Rmd | 45 inst/doc/rac_analysis.html | 64 inst/doc/sdt_glm_analysis.R | 45 inst/doc/sdt_glm_analysis.Rmd | 95 - inst/doc/sdt_glm_analysis.html | 256 +-- inst/doc/sdt_summary_comparisons.Rmd | 25 inst/doc/sdt_summary_comparisons.html | 31 inst/doc/simulation_power_analysis.R | 6 inst/doc/simulation_power_analysis.Rmd | 88 - inst/doc/simulation_power_analysis.html | 123 + inst/doc/winter_2ht_model.Rmd | 50 inst/doc/winter_2ht_model.html | 67 inst/shiny/r4lineups_app/R/mod_bayes.R | 2 inst/shiny/r4lineups_app/R/mod_calibration.R | 6 inst/shiny/r4lineups_app/R/mod_roc.R | 2 man/available_detectors.Rd | 5 man/available_models.Rd | 2 man/bootstrap_anri.Rd | 8 man/calibration_bayes.Rd | 5 man/check_pywitness_deps.Rd | 3 man/classify_lineup_choices.Rd | 4 man/compare_anri.Rd | 5 man/compare_models.Rd | 11 man/compare_pauc.Rd | 20 man/compare_sdt_summary.Rd | 6 man/compute_anri.Rd | 11 man/compute_eig.Rd | 3 man/create_example_lineup_data.Rd | 10 man/datacheck1.Rd | 8 man/datacheck2.Rd | 12 man/datacheck3.Rd | 12 man/diag_ratio_T.Rd | 4 man/diag_ratio_W.Rd | 4 man/eff_size_per_foils.Rd | 6 man/esize_T_ci_n.Rd | 8 man/face_similarity.Rd | 4 man/fit_lineup_models.Rd | 3 man/fit_sdt_glm.Rd | 5 man/fit_sdt_roc.Rd | 6 man/get_embedding.Rd | 4 man/innocent_id_rate_nominal.Rd | 4 man/install_pywitness.Rd | 4 man/install_r4lineups_python.Rd | 4 man/line73.Rd | 12 man/lineup_boot_allprop.Rd | 2 man/lineup_prop_tab.Rd | 3 man/lineup_similarity.Rd | 4 man/make_bayes_curves.Rd | 48 man/make_cacdata.Rd | 6 man/make_calibration.Rd | 21 man/make_calibration_by_condition.Rd | 5 man/make_calibration_data.Rd | 48 man/make_eig_data.Rd | 5 man/make_fullroc.Rd | 4 man/make_fullroc_data.Rd | 18 man/make_multid.Rd | 6 man/make_racdata.Rd | 11 man/make_roc.Rd | 7 man/make_rocdata.Rd | 6 man/make_utility_curves.Rd | 6 man/make_utility_difference.Rd | 8 man/mockdata.Rd | 3 man/nortje2012.Rd | 3 man/plot_bayes_information_gain.Rd | 19 man/plot_effective_size_conf.Rd | 6 man/plot_embedding_space.Rd | 8 man/plot_error_rate_conf.Rd | 9 man/plot_fullroc.Rd | 6 man/ppv_range_by_confidence.Rd | 13 man/sdt_compare.Rd | 16 man/sdt_summary_from_counts.Rd | 12 man/simulate_lineup_data.Rd | 19 man/simulate_power_analysis.Rd | 53 man/validate_lineup_data.Rd | 2 man/var_diag_ratio.Rd | 4 tests/testthat/test-calibration-population.R |only tests/testthat/test-classify-choices.R | 6 tests/testthat/test-decision-rules.R | 3 tests/testthat/test-eig-ppv.R | 33 tests/testthat/test-export-contracts.R | 3 tests/testthat/test-fullroc.R | 19 tests/testthat/test-homog-diag-boundary.R |only tests/testthat/test-homog-diag-heterogeneity.R | 1 tests/testthat/test-innocent-suspect.R | 1 tests/testthat/test-max-sdt-fit.R | 8 tests/testthat/test-multid.R | 6 tests/testthat/test-pauc-comparison.R | 6 tests/testthat/test-published-bayes-bree.R |only tests/testthat/test-published-core-fairness.R |only tests/testthat/test-published-eig-ppv.R |only tests/testthat/test-published-process-sdt.R |only tests/testthat/test-published-roc-calibration-decision.R |only tests/testthat/test-sdt-none-correction.R |only tests/testthat/test-simulation.R | 7 tests/testthat/test-zroc-sdt.R | 1 vignettes/Vignette.Rmd | 72 vignettes/bayesian_inference.Rmd | 7 vignettes/calibration_decision_analysis.Rmd | 189 +- vignettes/face_similarity.Rmd | 19 vignettes/fullroc_analysis.Rmd | 52 vignettes/information_error_rate_analysis.Rmd | 46 vignettes/lineup_memory_models.Rmd | 12 vignettes/model_comparison.Rmd | 72 vignettes/multid_model.Rmd | 16 vignettes/pauc_statistical_comparison.Rmd | 19 vignettes/rac_analysis.Rmd | 45 vignettes/sdt_glm_analysis.Rmd | 95 - vignettes/sdt_summary_comparisons.Rmd | 25 vignettes/simulation_power_analysis.Rmd | 88 - vignettes/winter_2ht_model.Rmd | 50 192 files changed, 4021 insertions(+), 2205 deletions(-)
Title: Algorithm Portfolio Selection with Machine Learning
Description: A wrapper for machine learning (ML) methods to select among a portfolio of algorithms based on the value of a key performance indicator (KPI). A number of features is used to adjust a model to predict the value of the KPI for each algorithm, then, for a new value of the features the KPI is estimated and the algorithm with the best one is chosen. To learn it can use the regression methods in 'caret' package or a custom function defined by the user. Several graphics available to analyze the results obtained. This library has been used in Ghaddar et al. (2023) <doi:10.1287/ijoc.2022.0090>).
Author: Brais Gonzalez-Rodriguez [aut, cre] ,
Ignacio Gomez-Casares [aut] ,
Beatriz Pateiro-Lopez [aut] ,
Julio Gonzalez-Diaz [aut] ,
Maria Caseiro-Arias [ctb],
Antonio Farina-Elorza [ctb],
Manuel Timiraos-Lopez [ctb],
MICIU/AEI/10.13039/501100011033 [fnd]
Maintainer: Brais Gonzalez-Rodriguez <brais.gonzalez.rodriguez@uvigo.gal>
Diff between ASML versions 1.1.0 dated 2025-09-29 and 1.1.1 dated 2026-11-09
DESCRIPTION | 22 ++++++++++++++++------ MD5 | 6 +++++- NEWS.md |only R/ASML-package.R |only build |only man/ASML-package.Rd |only 6 files changed, 21 insertions(+), 7 deletions(-)
Title: Browse Microdata Catalogs Using 'NADA' REST API
Description: Provides a unified, programmatic interface for searching,
browsing, and retrieving metadata from data repositories that use the
National Data Archive ('NADA') software, such as the World Bank, 'FAO',
the International Household Survey Network ('IHSN'), 'UNHCR', the World
Health Organization, and the statistics offices of Kenya and Zambia.
Functions discover available data collections, country codes, and access
types, search by keyword, country, and year, and retrieve study metadata,
file lists, and variable-level data dictionaries.
Author: Gutama Girja Urago [aut, cre, cph]
Maintainer: Gutama Girja Urago <girjagutama@gmail.com>
Diff between nadaverse versions 0.1.0 dated 2025-12-11 and 0.2.0 dated 2026-11-09
nadaverse-0.1.0/nadaverse/tests/testthat/_search_auto/microdata.fao.org/2606 |only nadaverse-0.2.0/nadaverse/DESCRIPTION | 33 nadaverse-0.2.0/nadaverse/MD5 | 115 nadaverse-0.2.0/nadaverse/NAMESPACE | 23 nadaverse-0.2.0/nadaverse/NEWS.md | 20 nadaverse-0.2.0/nadaverse/R/data_files.R | 25 nadaverse-0.2.0/nadaverse/R/http_helpers.R.R | 122 nadaverse-0.2.0/nadaverse/R/metadata_helpers.R | 88 nadaverse-0.2.0/nadaverse/R/nadaverse-package.R |only nadaverse-0.2.0/nadaverse/R/search_catalog.R | 47 nadaverse-0.2.0/nadaverse/README.md | 53 nadaverse-0.2.0/nadaverse/build |only nadaverse-0.2.0/nadaverse/inst/doc |only nadaverse-0.2.0/nadaverse/man/catalogs.Rd | 276 nadaverse-0.2.0/nadaverse/man/data_files.Rd | 163 nadaverse-0.2.0/nadaverse/man/nadaverse-package.Rd |only nadaverse-0.2.0/nadaverse/man/search_catalog.Rd | 288 nadaverse-0.2.0/nadaverse/man/set_user_agent.Rd |only nadaverse-0.2.0/nadaverse/tests/testthat/_collections/microdata.worldbank.org/collections.json | 420 nadaverse-0.2.0/nadaverse/tests/testthat/_country_codes/microdata.fao.org/country_codes.json | 2510 nadaverse-0.2.0/nadaverse/tests/testthat/_latest_entries/microdata.worldbank.org/latest-00819a.json | 48 nadaverse-0.2.0/nadaverse/tests/testthat/_metadata/microdata.worldbank.org/8098-b6ace8.json | 436 nadaverse-0.2.0/nadaverse/tests/testthat/_metadata/microdata.worldbank.org/ALB_2012_LSMS_v01_M_v01_A_PUF.json | 284 nadaverse-0.2.0/nadaverse/tests/testthat/_nc |only nadaverse-0.2.0/nadaverse/tests/testthat/_search_all/microdata.fao.org/search-2bc657.json | 788 nadaverse-0.2.0/nadaverse/tests/testthat/_search_all/microdata.fao.org/search-3ad53d.json | 70 nadaverse-0.2.0/nadaverse/tests/testthat/_search_all/microdata.worldbank.org/search-13f018.json | 317 nadaverse-0.2.0/nadaverse/tests/testthat/_search_auto/microdata.fao.org/2905 |only nadaverse-0.2.0/nadaverse/tests/testthat/_search_auto/microdata.fao.org/search-7315b4.json | 788 nadaverse-0.2.0/nadaverse/tests/testthat/_search_auto/microdata.worldbank.org/ETH_2015_ESS_v03_M/data_files.json | 2052 nadaverse-0.2.0/nadaverse/tests/testthat/_search_auto/microdata.worldbank.org/ETH_2015_ESS_v03_M/variables.json |25294 ---------- nadaverse-0.2.0/nadaverse/tests/testthat/_snaps/nadaverse.md | 115 nadaverse-0.2.0/nadaverse/tests/testthat/test-nadaverse.R | 336 nadaverse-0.2.0/nadaverse/vignettes |only 34 files changed, 5701 insertions(+), 29010 deletions(-)
Title: Fast Numerical Maximum Likelihood Estimation for Latent Markov
Models
Description: A variety of latent Markov models, including hidden Markov models, hidden semi-Markov models,
state-space models and continuous-time variants can be formulated and estimated within the same framework via directly maximising the likelihood function using the so-called forward algorithm.
Applied researchers often need custom models that standard software does not easily support.
Writing tailored 'R' code offers flexibility but suffers from slow estimation speeds.
We address these issues by providing easy-to-use functions (written in 'C++' for speed) for common tasks like the forward algorithm.
These functions can be combined into custom models in a Lego-type approach, offering up to 10-20 times faster estimation via standard numerical optimisers.
To aid in building fully custom likelihood functions, several vignettes are included that show how to simulate data from and estimate all the above model classes.
Author: Jan-Ole Fischer [aut, cre]
Maintainer: Jan-Ole Fischer <jan-ole.fischer@mailbox.org>
Diff between LaMa versions 3.0.0 dated 2026-10-28 and 3.1.0 dated 2026-11-09
DESCRIPTION | 8 - MD5 | 143 ++++++++++--------- NAMESPACE | 7 NEWS.md | 266 +++++++++++++++++++++--------------- R/data.R | 2 R/decoding_functions.R | 24 +-- R/distribution_functions.R | 4 R/forward_algorithms.R | 47 +++--- R/helper_functions.R | 27 +++ R/hsmm_functions_old.R | 40 ++--- R/lama.R | 69 +++++++++ R/mcreport.R | 38 ++++- R/model_matrix_functions.R | 4 R/penalty_functions.R | 36 ++-- R/qreml_functions.R | 267 +++++++++++++++++++++++++++++-------- R/residual_functions.R | 22 ++- R/stationary_functions.R | 22 +-- R/summary_functions.R | 15 +- R/tpm_functions.R | 179 +++++++++++++++++------- inst/doc/Continuous_time_HMMs.html | 4 inst/doc/Extensions.html | 2 inst/doc/HSMMs.html | 4 inst/doc/Intro_to_LaMa.html | 4 inst/doc/Longitudinal_data.html | 6 inst/doc/MMMPPs.html | 4 inst/doc/Penalised_splines.html | 83 +++++------ inst/doc/State_space_models.html | 4 man/MCreport.Rd | 17 +- man/coef.LaMaModel.Rd |only man/ddwell.Rd | 2 man/dgmrf2.Rd | 2 man/forward.Rd | 7 man/forward_hsmm.Rd | 10 - man/forward_ihsmm.Rd | 16 +- man/forward_p.Rd | 2 man/forward_phsmm.Rd | 12 - man/forward_s.Rd | 6 man/forward_sp.Rd | 8 - man/generator.Rd | 20 ++ man/generator_g.Rd | 6 man/grapes-sp-grapes.Rd | 6 man/nessi.Rd | 2 man/penalty.Rd | 2 man/penalty2.Rd | 4 man/penalty_uni.Rd | 6 man/pred_matrix.Rd | 2 man/process_hid_formulas.Rd | 2 man/pseudo_res.Rd | 6 man/qreml.Rd | 26 ++- man/residuals.LaMaModel.Rd |only man/sdreport_outer.Rd | 6 man/stateprobs_p.Rd | 12 - man/stationary.Rd | 6 man/stationary_ct.Rd | 4 man/stationary_p.Rd | 4 man/stationary_p_sparse.Rd | 4 man/stationary_sparse.Rd | 4 man/tpm.Rd | 4 man/tpm_ct.Rd | 32 ++++ man/tpm_g.Rd | 10 - man/tpm_g2.Rd | 16 +- man/tpm_hsmm.Rd | 4 man/tpm_hsmm2.Rd | 8 - man/tpm_ihsmm.Rd | 14 - man/tpm_p.Rd | 2 man/tpm_phsmm.Rd | 16 +- man/tpm_phsmm2.Rd | 18 +- man/tpm_thinned.Rd | 8 - man/vcov.LaMaModel.Rd |only man/viterbi_p.Rd | 12 - tests/testthat/test-lama.R | 81 +++++++++++ tests/testthat/test-residuals.R | 1 tests/testthat/test-tpm.R | 68 +++++++++ vignettes/refs.bib | 4 74 files changed, 1241 insertions(+), 592 deletions(-)
Title: Extension to 'ggplot2'
Description: The R package 'ggplot2' is a plotting system based on the
grammar of graphics. 'GGally' extends 'ggplot2' by adding several
functions to reduce the complexity of combining geometric objects with
transformed data. Some of these functions include a pairwise plot
matrix, a two group pairwise plot matrix, a parallel coordinates plot,
a survival plot, and several functions to plot networks.
Author: Barret Schloerke [aut, cre] ,
Di Cook [aut, ths] ,
Joseph Larmarange [aut] ,
Francois Briatte [aut],
Moritz Marbach [aut],
Edwin Thoen [aut],
Amos Elberg [aut],
Ott Toomet [ctb],
Jason Crowley [aut],
Heike Hofmann [ths] ,
Hadley Wickham [ths]
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between GGally versions 2.4.0 dated 2025-08-23 and 2.5.0 dated 2026-11-09
GGally-2.4.0/GGally/R/ggaly_trends.R |only GGally-2.4.0/GGally/R/ggmatrix_legend.R |only GGally-2.4.0/GGally/R/ggpairs_add.R |only GGally-2.4.0/GGally/R/ggpairs_getput.R |only GGally-2.4.0/GGally/R/ggpairs_internal_plots.R |only GGally-2.4.0/GGally/tests/testthat/data |only GGally-2.5.0/GGally/DESCRIPTION | 32 GGally-2.5.0/GGally/MD5 | 356 ++++++- GGally-2.5.0/GGally/NAMESPACE | 146 +-- GGally-2.5.0/GGally/NEWS.md | 27 GGally-2.5.0/GGally/R/crosstalk.R |only GGally-2.5.0/GGally/R/gg-plots.R | 50 - GGally-2.5.0/GGally/R/ggally_trends.R |only GGally-2.5.0/GGally/R/ggcoef.R | 25 GGally-2.5.0/GGally/R/gglegend.R |only GGally-2.5.0/GGally/R/gglyph.R | 7 GGally-2.5.0/GGally/R/ggmatrix.R | 2 GGally-2.5.0/GGally/R/ggmatrix_add.R |only GGally-2.5.0/GGally/R/ggmatrix_getput.R |only GGally-2.5.0/GGally/R/ggmatrix_internal_plots.R |only GGally-2.5.0/GGally/R/ggmatrix_location.R |only GGally-2.5.0/GGally/R/ggmatrix_print.R | 4 GGally-2.5.0/GGally/R/ggnet.R | 237 ++--- GGally-2.5.0/GGally/R/ggnet2.R | 432 ++++----- GGally-2.5.0/GGally/R/ggnetworkmap.R | 10 GGally-2.5.0/GGally/R/ggnostic.R | 103 +- GGally-2.5.0/GGally/R/ggpairs.R | 90 -- GGally-2.5.0/GGally/R/ggsurv.R | 4 GGally-2.5.0/GGally/R/ggtable.R | 36 GGally-2.5.0/GGally/R/reexports.R | 4 GGally-2.5.0/GGally/R/utils.R | 8 GGally-2.5.0/GGally/R/wrap.R |only GGally-2.5.0/GGally/R/zzz.R | 16 GGally-2.5.0/GGally/README.md | 6 GGally-2.5.0/GGally/build/stage23.rdb |binary GGally-2.5.0/GGally/man/GGally-package.Rd | 1 GGally-2.5.0/GGally/man/add_ref_boxes.Rd | 2 GGally-2.5.0/GGally/man/add_ref_lines.Rd | 2 GGally-2.5.0/GGally/man/add_to_ggmatrix.Rd | 2 GGally-2.5.0/GGally/man/broomify.Rd | 8 GGally-2.5.0/GGally/man/getPlot.Rd | 2 GGally-2.5.0/GGally/man/ggally_autopoint.Rd | 26 GGally-2.5.0/GGally/man/ggally_blank.Rd | 2 GGally-2.5.0/GGally/man/ggally_count.Rd | 2 GGally-2.5.0/GGally/man/ggally_cross.Rd | 2 GGally-2.5.0/GGally/man/ggally_density.Rd | 20 GGally-2.5.0/GGally/man/ggally_nostic_cooksd.Rd | 10 GGally-2.5.0/GGally/man/ggally_nostic_hat.Rd | 14 GGally-2.5.0/GGally/man/ggally_nostic_line.Rd | 2 GGally-2.5.0/GGally/man/ggally_nostic_resid.Rd | 8 GGally-2.5.0/GGally/man/ggally_nostic_se_fit.Rd | 8 GGally-2.5.0/GGally/man/ggally_nostic_sigma.Rd | 12 GGally-2.5.0/GGally/man/ggally_nostic_std_resid.Rd | 8 GGally-2.5.0/GGally/man/ggally_trends.Rd | 4 GGally-2.5.0/GGally/man/ggcoef.Rd | 31 GGally-2.5.0/GGally/man/gglegend.Rd | 2 GGally-2.5.0/GGally/man/ggmatrix_location.Rd | 4 GGally-2.5.0/GGally/man/ggnet.Rd | 52 - GGally-2.5.0/GGally/man/ggnet2.Rd | 106 +- GGally-2.5.0/GGally/man/ggnetworkmap.Rd | 12 GGally-2.5.0/GGally/man/ggnostic.Rd | 69 - GGally-2.5.0/GGally/man/ggpairs.Rd | 56 - GGally-2.5.0/GGally/man/ggtable.Rd | 36 GGally-2.5.0/GGally/man/grab_legend.Rd | 2 GGally-2.5.0/GGally/man/is_ggmatrix.Rd | 2 GGally-2.5.0/GGally/man/print.ggmatrix.Rd | 3 GGally-2.5.0/GGally/man/putPlot.Rd | 2 GGally-2.5.0/GGally/man/reexports.Rd | 3 GGally-2.5.0/GGally/man/str.ggmatrix.Rd | 5 GGally-2.5.0/GGally/man/wrap.Rd | 2 GGally-2.5.0/GGally/tests/testthat/_snaps |only GGally-2.5.0/GGally/tests/testthat/helper-doppelganger.R | 84 + GGally-2.5.0/GGally/tests/testthat/test-crosstalk.R | 54 - GGally-2.5.0/GGally/tests/testthat/test-deprecated.R | 14 GGally-2.5.0/GGally/tests/testthat/test-find-combo.R |only GGally-2.5.0/GGally/tests/testthat/test-gg-plots.R | 21 GGally-2.5.0/GGally/tests/testthat/test-ggbivariate.R | 5 GGally-2.5.0/GGally/tests/testthat/test-ggcoef.R | 1 GGally-2.5.0/GGally/tests/testthat/test-ggcorr.R | 4 GGally-2.5.0/GGally/tests/testthat/test-gglyph.R | 28 GGally-2.5.0/GGally/tests/testthat/test-ggmatrix.R | 57 - GGally-2.5.0/GGally/tests/testthat/test-ggmatrix_add.R | 2 GGally-2.5.0/GGally/tests/testthat/test-ggmatrix_getput.R | 23 GGally-2.5.0/GGally/tests/testthat/test-ggmatrix_location.R | 70 - GGally-2.5.0/GGally/tests/testthat/test-ggmatrix_progress.R |only GGally-2.5.0/GGally/tests/testthat/test-ggnet.R | 71 - GGally-2.5.0/GGally/tests/testthat/test-ggnet2.R | 126 +- GGally-2.5.0/GGally/tests/testthat/test-ggnetworkmap.R | 49 - GGally-2.5.0/GGally/tests/testthat/test-ggnostic.R | 10 GGally-2.5.0/GGally/tests/testthat/test-ggparcoord.R | 80 - GGally-2.5.0/GGally/tests/testthat/test-ggscatmat.R | 15 GGally-2.5.0/GGally/tests/testthat/test-ggsurv.R | 20 GGally-2.5.0/GGally/tests/testthat/test-ggtable.R | 1 GGally-2.5.0/GGally/tests/testthat/test-wrap.R | 14 GGally-2.5.0/GGally/tests/testthat/test-zzz_ggpairs.R | 540 +----------- GGally-2.5.0/GGally/tests/testthat/test-zzzz_ggmatrix.R |only 96 files changed, 1662 insertions(+), 1744 deletions(-)
Title: Objective Bayesian Distribution Fitting and AFT Regression
Description: Fits common univariate distributions using registered objective
Bayesian priors, including Jeffreys, reference, and maximal data information
priors, and supports user-defined distributions and priors through an
extensible model specification. Model-specific posterior propriety and
moment conditions are checked before computation when registered or supplied.
Exact simulation, marginalization, slice sampling, adaptive Metropolis, and
user-supplied posterior samplers share a common interface for summaries,
diagnostics, prediction, and pointwise log-likelihood evaluation.
A separate interface fits independently right-censored observations using
the registered complete-data priors, observed-data likelihood sampling or
data augmentation, with sufficient posterior-propriety checks. Optional
post-processing provides WAIC, PSIS-LOO, and DIC for observed-data likelihoods.
Formula-based accelerated failure time regression is available for nine
lifetime families with complete or right-censored dat [...truncated...]
Author: Pedro Luiz Ramos [aut, cre, cph]
Maintainer: Pedro Luiz Ramos <pedro.ramos@uc.cl>
Diff between fitdistrBayes versions 0.6.0 dated 2026-10-19 and 0.8.0 dated 2026-11-09
DESCRIPTION | 14 ++- MD5 | 31 +++++++- NAMESPACE | 15 ++++ NEWS.md | 69 +++++++++++++++++++ R/aft-families.R |only R/aft-gg.R |only R/aft-loglik-factory.R |only R/aft-precision.R |only R/aft-sampling.R |only R/aft-standard-fit.R |only R/criteria.R | 128 +++++++++++++++++++++++++++--------- R/fitAFTBayes-methods.R |only R/fitAFTBayes.R |only README.md | 56 ++++++++++++++- inst/doc/aft-models-theory.txt |only inst/doc/gg-aft-theory.txt |only inst/examples/tutorial_aft_gg.R |only inst/examples/tutorial_aft_models.R |only man/criteria.Rd | 21 +++++ man/fitAFTBayes-methods.Rd |only man/fitAFTBayes.Rd |only man/fitAFTBayes_models.Rd |only tests/tests_aft.R |only tests/tests_aft_models.R |only tests/tests_aft_sampling.R |only tests/tests_loo_roundoff.R |only 26 files changed, 289 insertions(+), 45 deletions(-)
Title: Comprehensive, User-Friendly Toolkit for Probing Interactions
Description: A suite of functions for conducting and interpreting analysis
of statistical interaction in regression models that was formerly part of the
'jtools' package. Functionality includes visualization of two- and three-way
interactions among continuous and/or categorical variables as well as
calculation of "simple slopes" and Johnson-Neyman intervals (see e.g.,
Bauer & Curran, 2005 <doi:10.1207/s15327906mbr4003_5>). These
capabilities are implemented for generalized linear models in addition to the
standard linear regression context.
Author: Jacob A. Long [aut, cre]
Maintainer: Jacob A. Long <jacob.long@sc.edu>
Diff between interactions versions 1.2.0 dated 2024-07-29 and 1.3.0 dated 2026-11-09
DESCRIPTION | 13 MD5 | 179 NAMESPACE | 7 NEWS.md | 29 R/cat_plot.R | 73 R/contrast_jn.R |only R/int_utils.R | 170 R/interact_plot.R | 70 R/johnson_neyman.R | 33 R/panel_slopes.R |only R/simple_slopes.R | 121 R/slopes_refit.R |only R/utils.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/categorical.html | 27 inst/doc/interactions.html | 171 man/cat_plot.Rd | 25 man/interact_plot.Rd | 25 man/johnson_neyman.Rd | 24 man/sim_slopes.Rd | 70 tests/testthat/_snaps/cat_plot/p0bar.svg | 102 tests/testthat/_snaps/cat_plot/p0bari.svg | 102 tests/testthat/_snaps/cat_plot/p0barpp.svg | 4102 ++-- tests/testthat/_snaps/cat_plot/p0pt.svg | 102 tests/testthat/_snaps/cat_plot/p0pti.svg | 102 tests/testthat/_snaps/cat_plot/p0ptpp.svg | 4102 ++-- tests/testthat/_snaps/cat_plot/p0ptps.svg | 4102 ++-- tests/testthat/_snaps/cat_plot/p3bar.svg | 202 tests/testthat/_snaps/cat_plot/p3bari.svg | 202 tests/testthat/_snaps/cat_plot/p3barpp.svg | 656 tests/testthat/_snaps/cat_plot/p3barps.svg | 656 tests/testthat/_snaps/cat_plot/p3line.svg | 202 tests/testthat/_snaps/cat_plot/p3linei.svg | 202 tests/testthat/_snaps/cat_plot/p3linelty.svg | 680 tests/testthat/_snaps/cat_plot/p3linepp.svg | 680 tests/testthat/_snaps/cat_plot/p3lineps.svg | 680 tests/testthat/_snaps/cat_plot/p3pt.svg | 190 tests/testthat/_snaps/cat_plot/p3pti.svg | 190 tests/testthat/_snaps/cat_plot/p3ptpp.svg | 668 tests/testthat/_snaps/cat_plot/p3ptps.svg | 668 tests/testthat/_snaps/cat_plot/pcatbfit.svg | 54 tests/testthat/_snaps/cat_plot/pglmcatoff.svg | 54 tests/testthat/_snaps/cat_plot/plmbar-interact-plot.svg | 166 tests/testthat/_snaps/cat_plot/plmbar.svg | 326 tests/testthat/_snaps/cat_plot/plmbari.svg | 326 tests/testthat/_snaps/cat_plot/plmbarpp.svg | 4326 ++--- tests/testthat/_snaps/cat_plot/plme4cat.svg | 66 tests/testthat/_snaps/cat_plot/plmline.svg | 346 tests/testthat/_snaps/cat_plot/plmlinei-interact-plot.svg | 346 tests/testthat/_snaps/cat_plot/plmlinei.svg | 346 tests/testthat/_snaps/cat_plot/plmlinelt.svg | 4346 ++--- tests/testthat/_snaps/cat_plot/plmlinepp.svg | 4346 ++--- tests/testthat/_snaps/cat_plot/plmlineps.svg | 8588 +++++----- tests/testthat/_snaps/cat_plot/plmpt.svg | 326 tests/testthat/_snaps/cat_plot/plmpti.svg | 326 tests/testthat/_snaps/cat_plot/plmptpp.svg | 4326 ++--- tests/testthat/_snaps/cat_plot/plmptps-interact-plot.svg | 8568 ++++----- tests/testthat/_snaps/cat_plot/plmptps.svg | 8568 ++++----- tests/testthat/_snaps/cat_plot/psvycat.svg | 54 tests/testthat/_snaps/interact_plot/pbfcat.svg | 54 tests/testthat/_snaps/interact_plot/pbfcont.svg | 72 tests/testthat/_snaps/interact_plot/pglmoff.svg | 72 tests/testthat/_snaps/interact_plot/pglmrob.svg | 72 tests/testthat/_snaps/interact_plot/plm0.svg | 162 tests/testthat/_snaps/interact_plot/plm1.svg | 170 tests/testthat/_snaps/interact_plot/plma.svg | 170 tests/testthat/_snaps/interact_plot/plme4-interact-plot-to-cat-plot.svg | 74 tests/testthat/_snaps/interact_plot/plme4.svg | 62 tests/testthat/_snaps/interact_plot/plme4i.svg | 64 tests/testthat/_snaps/interact_plot/plmlabelsc.svg | 170 tests/testthat/_snaps/interact_plot/plmlabelsc2.svg | 170 tests/testthat/_snaps/interact_plot/plmlabelscpred-interact-plot-to-cat-plot.svg | 78 tests/testthat/_snaps/interact_plot/plmlabelscpred.svg | 60 tests/testthat/_snaps/interact_plot/plmlabelscs.svg | 170 tests/testthat/_snaps/interact_plot/plmlinearchnp.svg | 136 tests/testthat/_snaps/interact_plot/plmlinearchp.svg | 300 tests/testthat/_snaps/interact_plot/plmm.svg | 162 tests/testthat/_snaps/interact_plot/plmnfchar.svg | 72 tests/testthat/_snaps/interact_plot/plmrob.svg | 170 tests/testthat/_snaps/interact_plot/plmrugb.svg | 332 tests/testthat/_snaps/interact_plot/plmruglb.svg | 432 tests/testthat/_snaps/interact_plot/plmtercs.svg | 154 tests/testthat/_snaps/interact_plot/plmtf.svg | 64 tests/testthat/_snaps/interact_plot/plmw.svg | 154 tests/testthat/_snaps/interact_plot/prsacont.svg | 96 tests/testthat/_snaps/interact_plot/psvy1.svg | 140 tests/testthat/_snaps/interact_plot/psvya.svg | 140 tests/testthat/test-contrast-slopes.R |only tests/testthat/test-panelr-plots.R |only tests/testthat/test-panelr-slopes.R |only tests/testthat/test-slopes-refits.R |only tests/testthat/test_cat_plot.R | 10 tests/testthat/test_interact_plot.R | 54 94 files changed, 35053 insertions(+), 34421 deletions(-)
Title: Decision-Theoretic Causal Diagnostics via Experiment Deficiency
Description: Implements a deficiency-theoretic framework for causal inference,
grounded in the classical theory of statistical experiment comparison,
as described in Akdemir (2026) <doi:10.5281/zenodo.18367346>. Provides
theorem-backed bounds together with computable proxy diagnostics for
information loss from confounding, selection bias, and distributional
shift. Supports continuous, binary, count, survival, and competing risks
outcomes. Key features include propensity-score total-variation deficiency
proxies, negative control diagnostics, policy regret bounds, and
sensitivity analysis via confounding frontiers.
Author: Deniz Akdemir [aut, cre]
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between causaldef versions 0.2.1 dated 2026-08-23 and 0.3.0 dated 2026-11-09
DESCRIPTION | 8 MD5 | 108 +-- NEWS.md | 35 + R/api.R | 16 R/causaldef-package.R | 2 R/confounding_frontier.R | 8 R/data_auditor.R | 2 R/methods-plot.R | 10 R/methods-print.R | 10 R/negative_controls.R | 2 R/policy_bounds.R | 73 +- R/theorem_bounds.R | 90 ++- README.md | 10 build/vignette.rds |binary inst/CITATION | 6 inst/doc/advanced_analysis.Rmd | 2 inst/doc/advanced_analysis.html | 551 +++++++----------- inst/doc/causaldef_methodology.R | 50 - inst/doc/causaldef_methodology.Rmd | 14 inst/doc/causaldef_methodology.html | 675 +++++++++------------- inst/doc/classical_benchmarks.html | 484 +++++++--------- inst/doc/complete_workflow.R | 138 ++-- inst/doc/complete_workflow.Rmd | 6 inst/doc/complete_workflow.html | 1035 +++++++++++++++-------------------- inst/doc/data_auditing.html | 582 ++++++++----------- inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 580 ++++++++----------- inst/doc/negative_controls.Rmd | 2 inst/doc/negative_controls.html | 477 ++++++---------- inst/doc/policy_and_transport.Rmd | 5 inst/doc/policy_and_transport.html | 520 +++++++---------- inst/doc/policy_learning.R | 9 inst/doc/policy_learning.Rmd | 44 - inst/doc/policy_learning.html | 643 ++++++++++----------- inst/doc/sensitivity_analysis.Rmd | 23 inst/doc/sensitivity_analysis.html | 600 +++++++++----------- inst/doc/survival_analysis.R | 16 inst/doc/survival_analysis.html | 614 +++++++++----------- man/audit_data.Rd | 2 man/causaldef-package.Rd | 2 man/confounding_frontier.Rd | 8 man/nc_diagnostic.Rd | 2 man/policy_regret_bound.Rd | 55 + man/policy_regret_bound_vc.Rd | 29 man/rkhs_rate_bound.Rd | 20 tests/testthat/test-policy_bounds.R | 42 + tests/testthat/test-theorem_bounds.R | 27 vignettes/advanced_analysis.Rmd | 2 vignettes/causaldef_methodology.Rmd | 14 vignettes/complete_workflow.Rmd | 6 vignettes/introduction.Rmd | 4 vignettes/negative_controls.Rmd | 2 vignettes/policy_and_transport.Rmd | 5 vignettes/policy_learning.Rmd | 44 - vignettes/sensitivity_analysis.Rmd | 23 55 files changed, 3605 insertions(+), 4136 deletions(-)
Title: Vehicle Routing Problem Solver Built on 'PyVRP'
Description: A 'tidyverse'-style interface to high-performance vehicle routing
problem (VRP) solving. Vendors the C++ core of the 'PyVRP' solver
(<https://github.com/PyVRP/PyVRP>) and rewires it through 'cpp11', with no
'Python' runtime dependency. Supports the capacitated VRP, time windows,
multiple depots, heterogeneous fleets, prize-collecting and multi-trip
variants, driven by an iterated local search metaheuristic.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut] ,
Niels Wouda [ctb, cph] ,
Thibaut Vidal [cph] ,
ORTEC [cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between vrpr versions 0.2.2 dated 2026-10-06 and 0.2.3 dated 2026-11-09
DESCRIPTION | 6 MD5 | 26 ++-- NEWS.md | 16 ++ R/problem_data.R | 80 +++++++++++- R/solve.R | 34 +++++ README.md | 19 ++ inst/doc/vrpr.R | 21 +++ inst/doc/vrpr.Rmd | 53 ++++++++ inst/doc/vrpr.html | 236 ++++++++++++++++++++++++------------- man/vrp_problem_data.Rd | 35 ++++- man/vrp_solve.Rd | 32 ++++- tests/testthat/test-problem-data.R | 30 ++++ tests/testthat/test-solve.R | 33 +++++ vignettes/vrpr.Rmd | 53 ++++++++ 14 files changed, 569 insertions(+), 105 deletions(-)
Title: Tests and Checks Characteristics of R Objects
Description: Allows users to test characteristics of common R objects.
Author: Frederic Bertrand [cre] ,
Gaston Sanchez [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between tester versions 0.3.0 dated 2025-09-22 and 0.3.1 dated 2026-11-09
DESCRIPTION | 12 ++++----- MD5 | 50 +++++++++++++++++++------------------- NEWS.md | 4 +++ R/is-dataframe.r | 6 ++++ R/is-matrix.r | 6 ++++ R/is-scalar.r | 5 +++ R/is-tabular.r | 5 +++ R/is-triangular.r | 4 +++ R/is-vector.r | 6 ++++ R/list-of-vectors.r | 5 +++ R/list-with-vectors.r | 4 +++ R/true-false.r | 6 ++++ build/vignette.rds |binary inst/doc/tester_introduction.Rnw | 2 - inst/doc/tester_introduction.pdf |binary man/is_TRUE.Rd | 7 +++++ man/is_dataframe.Rd | 7 +++++ man/is_matrix.Rd | 7 +++++ man/is_scalar.Rd | 6 ++++ man/is_tabular.Rd | 6 ++++ man/is_triangular_matrix.Rd | 5 +++ man/is_vector.Rd | 7 +++++ man/list_of_vectors.Rd | 6 ++++ man/list_with_vectors.Rd | 5 +++ tests/testthat/test-Rd.R | 15 +++++++---- vignettes/tester_introduction.Rnw | 2 - 26 files changed, 150 insertions(+), 38 deletions(-)
Title: Partial Least Squares Regression for Cox Models and Related
Techniques
Description: Provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models in high dimensional settings <doi:10.1093/bioinformatics/btu660>, Bastien, P., Bertrand, F., Meyer N., Maumy-Bertrand, M. (2015), Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data, Bioinformatics, 31(3):397-404. Cross validation criteria were studied in <doi:10.48550/arXiv.1810.02962>, Bertrand, F., Bastien, Ph. and Maumy-Bertrand, M. (2018), Cross validating extensions of kernel, sparse or regular partial least squares regression models to censored data.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between plsRcox versions 1.8.2 dated 2026-03-24 and 1.8.3 dated 2026-11-09
DESCRIPTION | 10 MD5 | 25 - NAMESPACE | 46 +- NEWS.md |only R/internal-plsRcox.R | 3 R/plsRcox-package.R | 10 README.md | 485 ++++++++++++++++++++++------ build/partial.rdb |binary man/figures/README-cvcoxDKsplsDR-1.png |binary man/figures/README-cvcoxsplsDR-1.png |binary man/figures/README-cvplsRcox-1.png |binary man/figures/README-devianceresiduals-1.png |binary man/figures/README-devianceresiduals2-1.png |binary man/figures/README-devianceresiduals3-1.png |binary 14 files changed, 436 insertions(+), 143 deletions(-)
Title: Orthogonal Nonlinear Least-Squares Regression
Description: Fits n-dimensional data by means of orthogonal nonlinear least-squares using Levenberg-Marquardt minimization, with a solver that exploits the block structure of the problem as 'ODRPACK' does, so that its cost grows linearly with the number of observations, and provides functionality for fit diagnostics and plotting. Delivers the same results as the 'ODRPACK' Fortran implementation described in Boggs et al. (1989) <doi:10.1145/76909.76913>, but is implemented in pure R.
Author: Andrej-Nikolai Spiess [aut, cre]
Maintainer: Andrej-Nikolai Spiess <draspiess@gmail.com>
Diff between onls versions 0.2 dated 2026-09-21 and 0.3 dated 2026-11-09
onls-0.2/onls/R/NIST.R |only onls-0.2/onls/man/NIST.Rd |only onls-0.3/onls/DESCRIPTION | 15 onls-0.3/onls/MD5 | 50 onls-0.3/onls/NAMESPACE | 21 onls-0.3/onls/NEWS | 39 onls-0.3/onls/R/S3_functions.R | 526 +--- onls-0.3/onls/R/doGauge.R |only onls-0.3/onls/R/fit_functions.R | 216 - onls-0.3/onls/R/inference.R |only onls-0.3/onls/R/onls.R | 605 +++- onls-0.3/onls/build/partial.rdb |binary onls-0.3/onls/build/vignette.rds |binary onls-0.3/onls/demo |only onls-0.3/onls/inst/doc/onls-vignette.R | 706 ++--- onls-0.3/onls/inst/doc/onls-vignette.Rmd | 160 - onls-0.3/onls/inst/doc/onls-vignette.html | 3912 +++++++++++++++--------------- onls-0.3/onls/man/anova.onls.Rd |only onls-0.3/onls/man/check_o.Rd | 58 onls-0.3/onls/man/confint.onls.Rd | 45 onls-0.3/onls/man/doGauge.Rd |only onls-0.3/onls/man/logLik_o.Rd | 53 onls-0.3/onls/man/onls.Rd | 295 -- onls-0.3/onls/man/plot.onls.Rd | 16 onls-0.3/onls/man/predict.onls.Rd |only onls-0.3/onls/man/print.onls.Rd | 2 onls-0.3/onls/man/profile.onls.Rd |only onls-0.3/onls/man/summary.onls.Rd | 12 onls-0.3/onls/man/x0.Rd | 8 onls-0.3/onls/vignettes/onls-vignette.Rmd | 160 - 30 files changed, 3534 insertions(+), 3365 deletions(-)
Title: Testing for Population Trends Using Low-Cost Ecological Count
Data
Description: A Bayesian tool to test for population trends and changes in trends under arbitrary designs, including before-after (BA), control-intervention (CI) and before-after-control-intervention (BACI) designs commonly used to assess conservation impact. It infers changes in trends jointly from data obtained with multiple survey methods, as well as from limited and noisy data not necessarily collected in standardized ecological surveys. Observed counts can be modeled as following either a Poisson or a negative binomial model, and both deterministic and stochastic trend models are available. For more details on the model see Singer et al. (2025) <doi:10.1101/2025.01.08.631844>, and the file 'AUTHORS' for a list of copyright holders and contributors.
Author: Madleina Caduff [aut],
Andreas Fueglistaler [aut, cre],
Daniel Wegmann [aut],
Liam Singer [aut],
Raphael Eckel [ctb],
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Daniel Lemire [cph] ,
Joao Paulo Magalhaes [cph] ,
Rene Brun [cph] ),
Fons Rademakers [c [...truncated...]
Maintainer: Andreas Fueglistaler <andreas.fueglistaler@unifr.ch>
Diff between birp versions 0.9.1 dated 2026-11-02 and 0.9.2 dated 2026-11-09
DESCRIPTION | 8 +- MD5 | 12 ++-- NEWS.md | 3 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/birp-introduction.html | 114 ++++++++++++++++++++-------------------- src/Makevars.in | 28 ++++++++- 7 files changed, 95 insertions(+), 70 deletions(-)
Title: The Skellam Distribution: Densities, Sampling, Estimation and
Regression
Description: Density, distribution function, quantile function and random
generation for the Skellam distribution, the distribution of the
difference of two independent Poisson variables (Skellam, 1946), with
saddlepoint approximations, maximum likelihood estimation, and a
regression model in which both rates depend on covariates. The
distribution functions remain accurate for very large rates and far
into the tails, on the natural and the log scale.
Author: Jerry W. Lewis [aut],
Patrick E. Brown [aut],
Michail Tsagris [aut],
Montasser Ghachem [aut, cre],
Oguz Ersan [aut]
Maintainer: Montasser Ghachem <mg@pinstimation.com>
Diff between skellam versions 0.2.4 dated 2025-04-07 and 0.2.5 dated 2026-11-09
skellam-0.2.4/skellam/tests/skellam.R |only skellam-0.2.5/skellam/DESCRIPTION | 38 +- skellam-0.2.5/skellam/MD5 | 53 +-- skellam-0.2.5/skellam/NAMESPACE | 20 - skellam-0.2.5/skellam/NEWS.md | 45 ++ skellam-0.2.5/skellam/R/bessel.R |only skellam-0.2.5/skellam/R/dskellam.r | 249 +++++++------- skellam-0.2.5/skellam/R/dskellam.sp.r | 35 +- skellam-0.2.5/skellam/R/pskellam.r | 189 +++++++++- skellam-0.2.5/skellam/R/pskellam.sp.r | 17 skellam-0.2.5/skellam/R/qskellam.r | 97 +++-- skellam-0.2.5/skellam/R/rskellam.r | 19 - skellam-0.2.5/skellam/R/skellam.mle.R | 88 +++-- skellam-0.2.5/skellam/R/skellam.reg.R | 122 +++++-- skellam-0.2.5/skellam/R/utils.R |only skellam-0.2.5/skellam/README.md | 210 ++++-------- skellam-0.2.5/skellam/build/vignette.rds |binary skellam-0.2.5/skellam/inst/CITATION | 31 - skellam-0.2.5/skellam/inst/doc/validate_skellam.R | 140 ++++---- skellam-0.2.5/skellam/inst/doc/validate_skellam.Rmd | 231 ++++++------- skellam-0.2.5/skellam/inst/doc/validate_skellam.html | 331 ++++++++++--------- skellam-0.2.5/skellam/man/skellam.Rd | 277 ++++++++------- skellam-0.2.5/skellam/man/skellam.mle.Rd | 159 ++++----- skellam-0.2.5/skellam/man/skellam.reg.Rd | 144 ++++---- skellam-0.2.5/skellam/tests/testthat |only skellam-0.2.5/skellam/tests/testthat.R |only skellam-0.2.5/skellam/vignettes/validate_skellam.Rmd | 231 ++++++------- 27 files changed, 1570 insertions(+), 1156 deletions(-)
Title: 1d Goodness of Fit Tests
Description: Routines that allow the user to run a large number of goodness-of-fit tests.
It allows for data to be continuous or discrete. It includes routines to estimate
the power of the tests and display them as a power graph.
The routine run.studies allows a user to quickly study the power of a new method and
how it compares to some of the standard ones.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between Rgof versions 4.0.1 dated 2026-10-05 and 4.1.0 dated 2026-11-09
Rgof-4.0.1/Rgof/man/Cpporder.Rd |only Rgof-4.0.1/Rgof/man/TS_cont.Rd |only Rgof-4.0.1/Rgof/man/TS_disc.Rd |only Rgof-4.0.1/Rgof/man/TSw_cont.Rd |only Rgof-4.0.1/Rgof/man/TSw_disc.Rd |only Rgof-4.0.1/Rgof/man/bincounter.Rd |only Rgof-4.0.1/Rgof/man/calcTS.Rd |only Rgof-4.0.1/Rgof/man/check.functions.Rd |only Rgof-4.0.1/Rgof/man/chi_power_cont.Rd |only Rgof-4.0.1/Rgof/man/chi_power_disc.Rd |only Rgof-4.0.1/Rgof/man/chi_test_cont.Rd |only Rgof-4.0.1/Rgof/man/chi_test_disc.Rd |only Rgof-4.0.1/Rgof/man/gof_adj_C1.Rd |only Rgof-4.0.1/Rgof/man/gof_adj_C2.Rd |only Rgof-4.0.1/Rgof/man/gof_power_C.Rd |only Rgof-4.0.1/Rgof/man/gof_test_C.Rd |only Rgof-4.0.1/Rgof/man/makeTSextra.Rd |only Rgof-4.0.1/Rgof/man/make_bins_cont.Rd |only Rgof-4.0.1/Rgof/man/make_bins_disc.Rd |only Rgof-4.0.1/Rgof/man/makemaxProcessor.Rd |only Rgof-4.0.1/Rgof/man/maketypeTS.Rd |only Rgof-4.0.1/Rgof/man/power_newtest.Rd |only Rgof-4.0.1/Rgof/man/signif_digits.Rd |only Rgof-4.0.1/Rgof/man/validate_integer_scalar.Rd |only Rgof-4.0.1/Rgof/man/wbincounter.Rd |only Rgof-4.1.0/Rgof/DESCRIPTION | 9 Rgof-4.1.0/Rgof/MD5 | 130 Rgof-4.1.0/Rgof/NAMESPACE | 9 Rgof-4.1.0/Rgof/NEWS.md | 6 Rgof-4.1.0/Rgof/R/RcppExports.R | 25 Rgof-4.1.0/Rgof/R/case.studies.R | 2721 +++++------ Rgof-4.1.0/Rgof/R/check.functions.R | 1 Rgof-4.1.0/Rgof/R/chi_power_cont.R | 1 Rgof-4.1.0/Rgof/R/chi_power_disc.R | 1 Rgof-4.1.0/Rgof/R/chi_test_cont.R | 83 Rgof-4.1.0/Rgof/R/chi_test_disc.R | 140 Rgof-4.1.0/Rgof/R/data.R | 86 Rgof-4.1.0/Rgof/R/gof_power.R | 814 +-- Rgof-4.1.0/Rgof/R/gof_test.R | 704 +- Rgof-4.1.0/Rgof/R/gof_test_adjusted_pvalue.R | 363 - Rgof-4.1.0/Rgof/R/helper_functions.R | 18 Rgof-4.1.0/Rgof/R/hybrid_power.R |only Rgof-4.1.0/Rgof/R/hybrid_test.R |only Rgof-4.1.0/Rgof/R/make_bins_cont.R | 60 Rgof-4.1.0/Rgof/R/make_bins_disc.R | 1 Rgof-4.1.0/Rgof/R/myTS.R | 5 Rgof-4.1.0/Rgof/R/plot_power.R | 92 Rgof-4.1.0/Rgof/R/power_newtest.R | 1 Rgof-4.1.0/Rgof/R/run.studies.R | 270 - Rgof-4.1.0/Rgof/R/signif_digits.R | 1 Rgof-4.1.0/Rgof/R/test_methods.R | 117 Rgof-4.1.0/Rgof/data/power_study.rda |binary Rgof-4.1.0/Rgof/data/power_study_hybrid.rda |only Rgof-4.1.0/Rgof/data/power_study_hybrid_nMC5.rda |only Rgof-4.1.0/Rgof/inst/doc/Rgof.R | 85 Rgof-4.1.0/Rgof/inst/doc/Rgof.Rmd | 113 Rgof-4.1.0/Rgof/inst/doc/Rgof.html | 664 +- Rgof-4.1.0/Rgof/man/gof_power.Rd | 17 Rgof-4.1.0/Rgof/man/gof_test.Rd | 9 Rgof-4.1.0/Rgof/man/gof_test_adjusted_pvalue.Rd | 13 Rgof-4.1.0/Rgof/man/hybrid_power.Rd |only Rgof-4.1.0/Rgof/man/hybrid_test.Rd |only Rgof-4.1.0/Rgof/man/plot_power.Rd | 10 Rgof-4.1.0/Rgof/man/power_study.Rd | 4 Rgof-4.1.0/Rgof/man/power_study_hybrid.Rd |only Rgof-4.1.0/Rgof/man/power_study_hybrid_nMC5.Rd |only Rgof-4.1.0/Rgof/man/run.studies.Rd | 32 Rgof-4.1.0/Rgof/man/summary.Rgof_power_values.Rd |only Rgof-4.1.0/Rgof/src/Cpporder.cpp | 1 Rgof-4.1.0/Rgof/src/TS_cont.cpp | 92 Rgof-4.1.0/Rgof/src/TS_disc.cpp | 235 Rgof-4.1.0/Rgof/src/TSw_cont.cpp | 22 Rgof-4.1.0/Rgof/src/TSw_disc.cpp | 29 Rgof-4.1.0/Rgof/src/bincounter.cpp | 1 Rgof-4.1.0/Rgof/src/calcTS.cpp | 1 Rgof-4.1.0/Rgof/src/gof_adj_C.cpp | 12 Rgof-4.1.0/Rgof/src/gof_power_C.cpp | 1 Rgof-4.1.0/Rgof/src/gof_test_C.cpp | 6 Rgof-4.1.0/Rgof/src/wbincounter.cpp | 1 Rgof-4.1.0/Rgof/tests/testthat/test-gof-power-ci.R | 34 Rgof-4.1.0/Rgof/tests/testthat/test-hybrid.R |only Rgof-4.1.0/Rgof/tests/testthat/test-statistics-definitions.R |only Rgof-4.1.0/Rgof/vignettes/Rgof.Rmd | 113 Rgof-4.1.0/Rgof/vignettes/Rgof.bib | 36 84 files changed, 3983 insertions(+), 3206 deletions(-)
Title: Fill in Missing Species Traits Using a Phylogenetic Tree
Description: Imputes missing species trait data for comparative analyses
by combining three sources of information: phylogenetic similarity
(closely related species share similar traits), cross-trait
correlations (observed traits inform missing ones), and optional
environmental covariates (climate, habitat, geography). Handles
continuous measurements, counts, binary variables, ordered categories,
unordered categories, bounded proportions, zero-inflated counts, and
compositional multi-proportion data in a single call. The default
method is a phylogenetic baseline calibrated on held-out data; an
optional graph neural network prediction is blended in through a
per-trait gate that retains a baseline fallback. Covariates can inform
the network and selected baseline paths. Provides conformal
prediction intervals for continuous, count, ordinal, and proportion
traits and an experimental analysis-aware multiple-imputation workflow
for one missing continuous covariate in Gaussian linear, binomial-logit,
and [...truncated...]
Author: Shinichi Nakagawa [aut, cre, cph],
Daniel Noble [ctb]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>
Diff between pigauto versions 0.11.0 dated 2026-10-18 and 0.11.1 dated 2026-11-09
pigauto-0.11.0/pigauto/tests/testthat/fixtures/gbif_plants_300.rds |only pigauto-0.11.0/pigauto/tests/testthat/fixtures/worldclim_plants_300.rds |only pigauto-0.11.1/pigauto/DESCRIPTION | 25 pigauto-0.11.1/pigauto/MD5 | 267 +- pigauto-0.11.1/pigauto/NAMESPACE | 2 pigauto-0.11.1/pigauto/NEWS.md | 108 pigauto-0.11.1/pigauto/R/active_impute.R | 211 + pigauto-0.11.1/pigauto/R/bm_internal.R | 79 pigauto-0.11.1/pigauto/R/build_phylo_graph.R | 49 pigauto-0.11.1/pigauto/R/check_pigauto.R | 70 pigauto-0.11.1/pigauto/R/cross_validate.R | 56 pigauto-0.11.1/pigauto/R/data.R | 38 pigauto-0.11.1/pigauto/R/evaluate.R | 65 pigauto-0.11.1/pigauto/R/evaluate_imputation.R | 50 pigauto-0.11.1/pigauto/R/fit_baseline.R | 290 +- pigauto-0.11.1/pigauto/R/fit_pigauto.R | 277 +- pigauto-0.11.1/pigauto/R/gbif_centroids.R | 77 pigauto-0.11.1/pigauto/R/impute.R | 431 +-- pigauto-0.11.1/pigauto/R/mask_missing.R | 49 pigauto-0.11.1/pigauto/R/multi_impute.R | 383 ++- pigauto-0.11.1/pigauto/R/multi_impute_analysis.R | 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pigauto-0.11.1/pigauto/tests/testthat/test-community-surface.R | 69 pigauto-0.11.1/pigauto/tests/testthat/test-coverage-workflow.R |only pigauto-0.11.1/pigauto/tests/testthat/test-cran-audit-defaults.R | 6 pigauto-0.11.1/pigauto/tests/testthat/test-docs-phytools-warning.R | 11 pigauto-0.11.1/pigauto/tests/testthat/test-draws-auto.R | 2 pigauto-0.11.1/pigauto/tests/testthat/test-evaluation-gnn.R |only pigauto-0.11.1/pigauto/tests/testthat/test-evaluation-mode.R |only pigauto-0.11.1/pigauto/tests/testthat/test-gbif-centroids.R | 109 pigauto-0.11.1/pigauto/tests/testthat/test-gnn-off.R | 49 pigauto-0.11.1/pigauto/tests/testthat/test-honesty-warnings.R | 95 pigauto-0.11.1/pigauto/tests/testthat/test-issue-input-clarity.R |only pigauto-0.11.1/pigauto/tests/testthat/test-issue-visuals.R |only pigauto-0.11.1/pigauto/tests/testthat/test-joint-lambda.R | 6 pigauto-0.11.1/pigauto/tests/testthat/test-lambda-covariates.R | 77 pigauto-0.11.1/pigauto/tests/testthat/test-lambda-default.R | 13 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Title: Programmatic Access to the European Central Bank's Data Portal
Description: Provides an interface to the European Central Bank's Data
Portal API, allowing for programmatic retrieval of a vast quantity
of statistical data.
Author: Eric Persson [aut, cre],
Franz X. Mohr [ctb]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between ecb versions 0.4.3 dated 2025-03-19 and 0.4.4 dated 2026-11-09
DESCRIPTION | 10 +- MD5 | 28 ++++---- NEWS.md |only R/main.R | 118 +++++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/ecb_edp.R | 104 ++++++++++++++++-------------- inst/doc/ecb_edp.Rmd | 19 ++++- inst/doc/ecb_edp.html | 141 ++++++++++++++++++------------------------ man/convert_dates.Rd | 11 ++- man/get_data.Rd | 7 +- man/get_dataflows.Rd | 5 + man/get_description.Rd | 9 ++ man/get_dimensions.Rd | 8 +- tests/testthat/tests.R | 69 +++++++++++++++++--- vignettes/ecb_edp.Rmd | 19 ++++- vignettes/phillips_plot-1.png |only 16 files changed, 343 insertions(+), 205 deletions(-)
Title: A Tool for Semi-Automating the Statistical Disclosure Control of
Research Outputs
Description: A Tool for Semi-Automating the Statistical Disclosure Control
of Research Outputs.
Author: Jim Smith [aut, ctb] ,
Maha Albashir [cre, ctb],
Richard John Preen [aut, ctb]
Maintainer: Maha Albashir <Maha.Albashir@uwe.ac.uk>
Diff between acro versions 1.0.0 dated 2026-09-09 and 1.1.1 dated 2026-11-09
acro-1.0.0/acro/man/create_factors.Rd |only acro-1.0.0/acro/man/is_excluded.Rd |only acro-1.0.0/acro/man/is_invalid.Rd |only acro-1.0.0/acro/man/to_pandas_categorical.Rd |only acro-1.0.0/acro/tests/testthat/Rplots.pdf |only acro-1.1.1/acro/DESCRIPTION | 20 acro-1.1.1/acro/LICENSE | 4 acro-1.1.1/acro/MD5 | 175 - acro-1.1.1/acro/NAMESPACE | 57 acro-1.1.1/acro/NEWS.md | 6 acro-1.1.1/acro/R/acro-package.R | 10 acro-1.1.1/acro/R/acro_init.R | 2 acro-1.1.1/acro/R/acro_regression.R | 192 + acro-1.1.1/acro/R/acro_tables.R | 910 ++++---- acro-1.1.1/acro/R/lung.R | 44 acro-1.1.1/acro/R/nursery_data.R | 48 acro-1.1.1/acro/R/output_commands.R | 302 +- acro-1.1.1/acro/R/utils.R | 277 +- acro-1.1.1/acro/R/zzz.R | 9 acro-1.1.1/acro/README.md | 130 - acro-1.1.1/acro/build/vignette.rds |binary acro-1.1.1/acro/inst/AI_POLICY.md | 168 - acro-1.1.1/acro/inst/INSTALL.md | 286 +- acro-1.1.1/acro/inst/Images/UK_Research_and_Innovation_logo.svg | 376 +-- acro-1.1.1/acro/inst/WORDLIST | 99 acro-1.1.1/acro/inst/doc/example-notebook.R | 18 acro-1.1.1/acro/inst/doc/example-notebook.Rmd | 38 acro-1.1.1/acro/inst/doc/example-notebook.html | 724 +++---- acro-1.1.1/acro/inst/doc/examples.Rmd | 98 acro-1.1.1/acro/inst/doc/examples.html | 794 +++---- acro-1.1.1/acro/inst/doc/installation.Rmd | 124 - acro-1.1.1/acro/inst/doc/installation.html | 810 +++---- acro-1.1.1/acro/inst/doc/supports.Rmd | 211 +- acro-1.1.1/acro/inst/doc/supports.html | 746 +++---- acro-1.1.1/acro/inst/doc/welcome.html | 850 ++++---- acro-1.1.1/acro/inst/index.md | 98 acro-1.1.1/acro/inst/notebooks/acro_demo_2026.R | 623 +++++- acro-1.1.1/acro/inst/notebooks/acro_demo_2026.Rmd | 1024 +++++----- acro-1.1.1/acro/inst/notebooks/acro_in_tidyverse_demo.Rmd | 182 - acro-1.1.1/acro/inst/notebooks/example-notebook-old.Rmd | 392 +-- acro-1.1.1/acro/man/acro_add_comments.Rd | 38 acro-1.1.1/acro/man/acro_add_exception.Rd | 38 acro-1.1.1/acro/man/acro_coxph.Rd |only acro-1.1.1/acro/man/acro_crosstab.Rd | 98 acro-1.1.1/acro/man/acro_custom_output.Rd | 38 acro-1.1.1/acro/man/acro_disable_rounding.Rd | 28 acro-1.1.1/acro/man/acro_disable_suppression.Rd | 28 acro-1.1.1/acro/man/acro_enable_rounding.Rd | 34 acro-1.1.1/acro/man/acro_enable_suppression.Rd | 28 acro-1.1.1/acro/man/acro_finalise.Rd | 38 acro-1.1.1/acro/man/acro_glm.Rd | 42 acro-1.1.1/acro/man/acro_hist.Rd | 68 acro-1.1.1/acro/man/acro_init.Rd | 78 acro-1.1.1/acro/man/acro_lm.Rd | 38 acro-1.1.1/acro/man/acro_pie.Rd | 92 acro-1.1.1/acro/man/acro_pivot_table.Rd | 62 acro-1.1.1/acro/man/acro_print_outputs.Rd | 28 acro-1.1.1/acro/man/acro_remove_output.Rd | 34 acro-1.1.1/acro/man/acro_rename_output.Rd | 38 acro-1.1.1/acro/man/acro_summarise.Rd | 46 acro-1.1.1/acro/man/acro_surv_func.Rd | 46 acro-1.1.1/acro/man/acro_table.Rd | 74 acro-1.1.1/acro/man/lung.Rd | 62 acro-1.1.1/acro/man/nursery_data.Rd | 70 acro-1.1.1/acro/tests/spelling.R | 12 acro-1.1.1/acro/tests/testthat.R | 24 acro-1.1.1/acro/tests/testthat/test-acro_add_comments.R | 44 acro-1.1.1/acro/tests/testthat/test-acro_add_exception.R | 40 acro-1.1.1/acro/tests/testthat/test-acro_coxph.R |only acro-1.1.1/acro/tests/testthat/test-acro_crosstab.R | 148 - acro-1.1.1/acro/tests/testthat/test-acro_custom_output.R | 32 acro-1.1.1/acro/tests/testthat/test-acro_disable_suppression.R | 28 acro-1.1.1/acro/tests/testthat/test-acro_enable_suppression.R | 28 acro-1.1.1/acro/tests/testthat/test-acro_finalise.R | 30 acro-1.1.1/acro/tests/testthat/test-acro_glm.R | 86 acro-1.1.1/acro/tests/testthat/test-acro_hist.R | 188 - acro-1.1.1/acro/tests/testthat/test-acro_init.R | 16 acro-1.1.1/acro/tests/testthat/test-acro_lm.R | 52 acro-1.1.1/acro/tests/testthat/test-acro_pie.R | 114 - acro-1.1.1/acro/tests/testthat/test-acro_pivot_table.R | 70 acro-1.1.1/acro/tests/testthat/test-acro_print_outputs.R | 26 acro-1.1.1/acro/tests/testthat/test-acro_remove_output.R | 34 acro-1.1.1/acro/tests/testthat/test-acro_rename_output.R | 34 acro-1.1.1/acro/tests/testthat/test-acro_rounding.R | 52 acro-1.1.1/acro/tests/testthat/test-acro_summarise.R | 598 ++--- acro-1.1.1/acro/tests/testthat/test-acro_surv_func.R | 46 acro-1.1.1/acro/tests/testthat/test-acro_table.R | 612 ++--- acro-1.1.1/acro/tests/testthat/test-install_acro.R | 22 acro-1.1.1/acro/vignettes/example-notebook.Rmd | 38 acro-1.1.1/acro/vignettes/examples.Rmd | 98 acro-1.1.1/acro/vignettes/installation.Rmd | 124 - acro-1.1.1/acro/vignettes/supports.Rmd | 211 +- 92 files changed, 7201 insertions(+), 6599 deletions(-)
Title: Facilitate Citation of R Packages
Description: Facilitates the citation of R packages used in analysis
projects. Scans project for packages used, gets their citations, and
produces a document with citations in the preferred bibliography
format, ready to be pasted into reports or manuscripts. Alternatively,
'grateful' can be used directly within an 'R Markdown' or 'Quarto' document.
Author: Francisco Rodriguez-Sanchez [aut, cre, cph] ,
Connor P. Jackson [aut] ,
Shaurita D. Hutchins [ctb],
James M. Clawson [ctb]
Maintainer: Francisco Rodriguez-Sanchez <f.rodriguez.sanc@gmail.com>
Diff between grateful versions 0.3.0 dated 2025-09-04 and 0.3.1 dated 2026-11-09
DESCRIPTION | 8 ++--- MD5 | 40 +++++++++++++-------------- NEWS.md | 9 ++++++ R/cite_packages.R | 2 - R/create_rmd.R | 2 - R/get_citations.R | 3 +- R/render_citations.R | 4 +- R/scan_packages.R | 3 +- R/utils_citations.R | 7 ++++ R/write_citation_paragraph.R | 17 ++++++++--- README.md | 53 ++++++++++++++++++++++-------------- man/cite_packages.Rd | 4 +- man/get_citations.Rd | 2 - man/get_csl.Rd | 2 - man/get_pkgs_info.Rd | 2 - man/grateful-package.Rd | 1 man/nocite_references.Rd | 2 - man/scan_packages.Rd | 2 - tests/testthat/test-cite_packages.R | 47 ++++++++++++++++++++++++++++++- tests/testthat/test-get_citations.R | 10 ++++++ tests/testthat/test-scan_packages.R | 7 ++-- 21 files changed, 159 insertions(+), 68 deletions(-)
Title: Read 'SAS' Data in Chunks and Convert to 'Parquet'
Description: Reads 'SAS' 'sas7bdat' files through a persistent native reader.
Processes configurable chunks without reopening the input or restarting
the parser between chunks. Supports uncompressed, run-length encoded,
and Ross Data Compression data through the bundled 'ReadStat' library.
Also streams native decoded batches directly to 'Parquet' through the
'Arrow' C Data Interface and the optional 'arrow' package, without
constructing R data frames.
Author: Jianyun Wu [aut, cre],
Evan Miller [aut, cph]
Maintainer: Jianyun Wu <jianyun.fred.wu@hotmail.com>
Diff between anotherSAS7bdat versions 0.0.7 dated 2026-10-21 and 0.0.9 dated 2026-11-09
anotherSAS7bdat-0.0.7/anotherSAS7bdat/R/anotherSAS7bdat-package.R |only anotherSAS7bdat-0.0.7/anotherSAS7bdat/man/anotherSAS7bdat-package.Rd |only anotherSAS7bdat-0.0.9/anotherSAS7bdat/DESCRIPTION | 12 anotherSAS7bdat-0.0.9/anotherSAS7bdat/MD5 | 31 anotherSAS7bdat-0.0.9/anotherSAS7bdat/NEWS.md |only anotherSAS7bdat-0.0.9/anotherSAS7bdat/R/AnotherSAS7bdat-package.R |only anotherSAS7bdat-0.0.9/anotherSAS7bdat/R/RcppExports.R | 54 - anotherSAS7bdat-0.0.9/anotherSAS7bdat/R/parquet.R | 380 +++---- anotherSAS7bdat-0.0.9/anotherSAS7bdat/README.md | 11 anotherSAS7bdat-0.0.9/anotherSAS7bdat/configure | 2 anotherSAS7bdat-0.0.9/anotherSAS7bdat/inst/LICENSE.ReadStat | 38 anotherSAS7bdat-0.0.9/anotherSAS7bdat/man/AnotherSAS7bdat-package.Rd |only anotherSAS7bdat-0.0.9/anotherSAS7bdat/man/sas7bdat_to_parquet.Rd | 234 ++-- anotherSAS7bdat-0.0.9/anotherSAS7bdat/src/reader.cpp | 57 - anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-adaptive-buffers.R | 12 anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-parquet.R | 506 +++++----- anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-read-ahead.R | 21 anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-reader.R | 2 anotherSAS7bdat-0.0.9/anotherSAS7bdat/tests/testthat/test-time-conversion.R | 6 19 files changed, 760 insertions(+), 606 deletions(-)
More information about anotherSAS7bdat at CRAN
Permanent link
Title: Grouped and Nested Data Pipelines Built on 'data.table'
Description: A toolkit for grouped and nested data pipelines built on
'data.table': import many Excel / CSV files (including multi-row
headers) into one table, reshape and nest data by trait and group, run
reproducible (stratified) k-fold cross-validation inside every group,
summarise groups with report-ready descriptive statistics, and write
each piece back to its own file or sheet. Developed for animal
breeding, where it prepares phenotypic files for 'ASReml-R', 'HIBLUP'
or 'DMU', but useful for any multi-group, multi-variable analysis.
Author: Guo Meng [aut, cre],
Guo Meng [cph]
Maintainer: Guo Meng <tony2015116@163.com>
Diff between mintyr versions 0.2.0 dated 2026-10-05 and 0.2.1 dated 2026-11-09
mintyr-0.2.0/mintyr/man/figures/cheatsheet.svg |only mintyr-0.2.1/mintyr/DESCRIPTION | 6 - mintyr-0.2.1/mintyr/MD5 | 37 +++--- mintyr-0.2.1/mintyr/NAMESPACE | 2 mintyr-0.2.1/mintyr/NEWS.md | 28 ++++ mintyr-0.2.1/mintyr/R/import_csv.R | 34 +++++ mintyr-0.2.1/mintyr/R/import_xlsx.R | 99 ++++++++++++++--- mintyr-0.2.1/mintyr/R/resolve_cols.R | 78 +++++++++++++ mintyr-0.2.1/mintyr/README.md | 9 + mintyr-0.2.1/mintyr/inst/doc/import-and-export.R | 16 ++ mintyr-0.2.1/mintyr/inst/doc/import-and-export.Rmd | 16 ++ mintyr-0.2.1/mintyr/inst/doc/import-and-export.html | 81 +++++++++---- mintyr-0.2.1/mintyr/inst/doc/mintyr.html | 2 mintyr-0.2.1/mintyr/inst/doc/utilities.html | 2 mintyr-0.2.1/mintyr/man/import_csv.Rd | 11 + mintyr-0.2.1/mintyr/man/import_xlsx.Rd | 48 ++++++++ mintyr-0.2.1/mintyr/tests/testthat/test-import_csv.R | 26 ++++ mintyr-0.2.1/mintyr/tests/testthat/test-import_xlsx.R | 73 ++++++++++++ mintyr-0.2.1/mintyr/tests/testthat/test-resolve_cols.R | 20 +++ mintyr-0.2.1/mintyr/vignettes/import-and-export.Rmd | 16 ++ 20 files changed, 534 insertions(+), 70 deletions(-)
Title: Fast and Stable Fitting of Generalized Linear Models using
'RcppEigen'
Description: Fits generalized linear models efficiently using 'RcppEigen'. The iteratively reweighted least squares
implementation utilizes the step-halving approach of Marschner (2011) <doi:10.32614/RJ-2011-012> to help safeguard
against convergence issues. Provides formula and matrix interfaces for count and
cumulative-link ordinal models, mean bias reduction, and fitting from data read in blocks of rows for supported
model classes.
Author: Jared Huling [aut, cre],
Douglas Bates [cph],
Dirk Eddelbuettel [cph],
Romain Francois [cph],
Yixuan Qiu [cph],
Noah Greifer [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between fastglm versions 0.1.2 dated 2026-08-27 and 0.1.3 dated 2026-11-09
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Title: Latent and Stochastic Block Model Estimation by a 'V-EM'
Algorithm
Description: Latent and Stochastic Block Model estimation by a Variational EM algorithm.
Various probability distribution are provided (Bernoulli,
Poisson...), with or without covariates. See Leger (2016)
<doi:10.48550/arXiv.1602.07587>.
Author: Jean-Benoist Leger [aut] ,
Julien Chiquet [aut, cre] ,
Pierre Barbillon [aut] ,
Louis Lacoste [aut]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between blockmodels versions 1.1.5 dated 2021-12-01 and 1.2.1 dated 2026-11-09
DESCRIPTION | 35 +- MD5 | 107 ++++-- NEWS.md |only R/membership_LBM.R | 199 +++++++----- R/membership_SBM.R | 48 ++ R/membership_SBM_sym.R | 48 ++ R/misc.R | 62 +++ R/model.R | 21 - R/multivariate_model.R | 55 +++ R/parallel_lapply.R | 2 R/scalar_model.R | 78 +++- R/scalar_model_with_covariates.R | 5 R/zbernoulli_covariates.R | 26 - R/zbernoulli_covariates_fast.R | 26 - R/zgaussian_covariates.R | 2 R/zpoisson_covariates.R | 2 README.md |only inst |only man/BM_bernoulli.Rd | 7 man/BM_bernoulli_covariates.Rd | 9 man/BM_bernoulli_covariates_fast.Rd | 9 man/BM_bernoulli_multiplex.Rd | 7 man/BM_gaussian.Rd | 7 man/BM_gaussian_covariates.Rd | 9 man/BM_gaussian_multivariate.Rd | 7 man/BM_gaussian_multivariate_independent.Rd | 7 man/BM_gaussian_multivariate_independent_homoscedastic.Rd | 7 man/BM_poisson.Rd | 7 man/BM_poisson_covariates.Rd | 9 src/Makevars | 7 src/Makevars.win | 2 src/conf.h | 5 src/dispatcher.cc | 4 src/dispatcher.h | 1 src/memberships/lbm.h | 230 +++++++++----- src/memberships/sbm.h | 83 ++++- src/misc_functions.h | 58 +++ src/models/bernoulli.h | 65 +-- src/models/bernoulli_covariates.h | 9 src/models/bernoulli_covariates_fast.h | 15 src/models/gaussian.h | 49 ++ src/models/gaussian_covariates.h | 68 ++-- src/models/naive_bernoulli.h | 6 src/models/poisson.h | 15 src/models/poisson_covariates.h | 9 src/nodes_covariates.h |only tests/testthat |only tests/testthat.R |only 48 files changed, 1015 insertions(+), 412 deletions(-)
Title: Import Surface Meteorological Data from NOAA
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic
and Atmospheric Administration (NOAA) Global Historical Climate
Network (GHCN) and Integrated Surface Database (ISD).
Author: David Carslaw [aut, cre] ,
Jack Davison [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 1.1.0 dated 2026-05-18 and 1.2.0 dated 2026-11-09
DESCRIPTION | 10 MD5 | 52 - NAMESPACE | 6 NEWS.md | 56 + R/deprecated.R | 27 R/import_ghcn_daily.R | 27 R/import_ghcn_hourly.R | 175 ++- R/import_ghcn_monthly.R | 32 R/import_ghcn_stations.R | 1063 +++++++++++---------- R/import_isd_hourly.R | 2127 ++++++++++++++++++++++---------------------- R/import_isd_lite.R | 36 R/import_isd_stations.R | 15 R/utils.R | 273 +---- R/weatherCodes.R | 24 R/write_adms.R | 8 R/write_met.R | 15 inst |only man/deprecated-isd.Rd | 6 man/import_ghcn_daily.Rd | 2 man/import_ghcn_hourly.Rd | 2 man/import_ghcn_monthly.Rd | 2 man/import_ghcn_stations.Rd | 4 man/import_isd_hourly.Rd | 8 man/import_isd_lite.Rd | 26 man/import_isd_stations.Rd | 17 man/weatherCodes.Rd | 2 man/worldmet-package.Rd | 2 tests |only 28 files changed, 2032 insertions(+), 1985 deletions(-)
Title: Water-Energy-Food-Nutrient-Carbon Nexus Analysis for Agronomic
Systems
Description: Provides functions for analysing
Water-Energy-Food-Nutrient-Carbon (WEFNC) nexus interactions in
agricultural production systems. Includes functions for
computing water use efficiency (WUE), water productivity (WP),
and water footprint (WF) including green, blue, and grey
components following the methodology of Hoekstra et al. (2011,
ISBN:9781849712798). Includes energy budgeting tools for energy
use efficiency (EUE), energy return on investment (EROI), net
energy (NE), and energy productivity (EP). Computes nutrient
use efficiency (NUE) metrics including agronomic efficiency
(AE), physiological efficiency (PE), recovery efficiency (RE),
and partial factor productivity (PFP) as defined by Dobermann
(2007) <https://digitalcommons.unl.edu/agronomyfacpub/316/> and
Congreves et al. (2021) <doi:10.3389/fpls.2021.637108>.
Estimates carbon footprint (CF), greenhouse gas (GHG)
emissions, soil organic carbon (SOC) stocks, and global warming
potential (GWP) using Intergovernmental Pa [...truncated...]
Author: Lalit Kumar Rolaniya [aut, cre] ,
Hemant Poonia [aut] ,
Ram Lal Jat [aut] ,
Monika Punia [aut] ,
Raja Ram Choudhary [aut]
Maintainer: Lalit Kumar Rolaniya <lalitrolaniya@gmail.com>
Diff between wefnexus versions 1.0.0 dated 2026-03-10 and 1.1.0 dated 2026-11-09
DESCRIPTION | 84 +++-- MD5 | 181 ++++++----- NAMESPACE | 18 + NEWS.md | 131 ++++++++ R/analysis.R |only R/anova.R |only R/carbon.R | 253 +++++++++++----- R/classes.R | 5 R/data.R | 32 ++ R/energy.R | 60 ++- R/energy_budget.R |only R/food.R | 56 ++- R/nexus.R | 254 +++++++++++++--- R/nexus_advanced.R | 232 +++++++++----- R/nutrient.R | 85 +++-- R/plots.R |only R/robustness.R |only R/utils.R | 3 R/water.R | 55 ++- R/wefnexus-package.R | 12 R/weights.R |only README.md | 244 +++++++++++++-- build/partial.rdb |binary build/vignette.rds |binary data/arid_pulse_trial.rda |only data/energy_coefficients.rda |only inst/CITATION | 5 inst/doc/wefnexus-intro.R | 93 +++++ inst/doc/wefnexus-intro.Rmd | 176 +++++++++++ inst/doc/wefnexus-intro.html | 515 ++++++++++++++++++++++----------- man/agronomic_efficiency.Rd | 5 man/arid_pulse_trial.Rd |only man/caloric_yield.Rd | 9 man/carbon_efficiency.Rd | 9 man/carbon_footprint.Rd | 36 +- man/carbon_sequestration_rate.Rd | 10 man/carbon_sustainability_index.Rd | 9 man/crop_water_productivity.Rd | 9 man/crop_water_stress_index.Rd | 19 - man/crop_yield_index.Rd | 12 man/depleted_fraction.Rd | 9 man/energy_budget.Rd |only man/energy_coefficients.Rd |only man/energy_input.Rd | 5 man/energy_intensity.Rd | 9 man/energy_output.Rd | 5 man/energy_productivity.Rd | 9 man/energy_profitability.Rd | 14 man/energy_use_efficiency.Rd | 9 man/eroi.Rd | 7 man/figures/README-anova.png |only man/figures/README-radar.png |only man/figures/README-ranks.png |only man/food_productivity_index.Rd | 14 man/ghg_emission.Rd | 66 +++- man/global_warming_potential.Rd | 15 man/harvest_index.Rd | 9 man/human_energy_profitability.Rd | 9 man/internal_utilization_efficiency.Rd | 9 man/irrigation_efficiency.Rd | 5 man/land_equivalent_ratio.Rd | 5 man/net_energy.Rd | 9 man/nexus_analysis.Rd |only man/nexus_anova.Rd |only man/nexus_heatmap.Rd | 3 man/nexus_heatmap_gg.Rd | 8 man/nexus_index.Rd | 5 man/nexus_radar.Rd | 3 man/nexus_radar_gg.Rd | 24 + man/nexus_rank_compare.Rd |only man/nexus_sensitivity.Rd | 5 man/nexus_summary.Rd | 74 +++- man/nexus_sustainability_score.Rd | 9 man/nexus_topsis.Rd |only man/nexus_tradeoff.Rd | 19 - man/nexus_weights.Rd |only man/nutrient_balance.Rd | 14 man/nutrient_harvest_index.Rd | 9 man/nutrient_use_efficiency.Rd | 25 + man/partial_factor_productivity.Rd | 9 man/physiological_efficiency.Rd | 5 man/plot.energy_budget.Rd |only man/plot.nexus_analysis.Rd |only man/plot.nexus_anova.Rd |only man/plot.rank_compare.Rd |only man/plot.topsis_result.Rd |only man/plot.tradeoff_matrix.Rd |only man/plot_tradeoff.Rd |only man/print.energy_budget.Rd |only man/print.nexus_analysis.Rd |only man/print.nexus_anova.Rd |only man/print.rank_compare.Rd |only man/print.tradeoff_matrix.Rd |only man/production_efficiency_index.Rd | 13 man/protein_yield.Rd | 9 man/recovery_efficiency.Rd | 5 man/soil_carbon_stock.Rd | 18 - man/specific_energy.Rd | 17 - man/system_productivity_index.Rd | 10 man/water_footprint.Rd | 9 man/water_productivity.Rd | 5 man/water_use_efficiency.Rd | 9 man/wefnexus-package.Rd | 18 + tests/testthat/test-additional.R | 6 tests/testthat/test-all-modules.R | 14 tests/testthat/test-plots-robustness.R |only tests/testthat/test-v110.R |only vignettes/wefnexus-intro.Rmd | 176 +++++++++++ 108 files changed, 2577 insertions(+), 764 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>;
Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>;
Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank mo [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Waldir Leoncio [aut],
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 2.2.7 dated 2026-01-20 and 2.3.0 dated 2026-11-09
DESCRIPTION | 6 +++--- MD5 | 27 ++++++++++++++------------- NEWS.md | 11 +++++++++++ R/set_priors.R | 11 +++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/BayesMallows.html | 26 ++++++++++++-------------- inst/doc/SMC-Mallows.html | 7 +++---- inst/doc/parallel_chains.html | 3 +-- man/set_priors.Rd | 11 +++++++---- src/distances.cpp | 2 +- src/parameters_class.cpp | 17 +++++++---------- src/rank_proposal.cpp | 27 +++++++++++++++++++-------- tests/testthat/test-bernoulli_error_model.R |only tests/testthat/test-mcmc_correctness.R | 16 ++++++++-------- 15 files changed, 93 insertions(+), 71 deletions(-)
Title: Working with Sets the Tidy Way
Description: Implements a class and methods to work with sets, doing
intersection, union, complementary sets, power sets, cartesian product
and other set operations in a "tidy" way. These set operations are
available for both classical sets and fuzzy sets. Import sets from
several formats or from other several data structures.
Author: Lluis Revilla Sancho [aut, cre, cph] ,
Zebulun Arendsee [rev],
Jennifer Chang [rev]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between BaseSet versions 1.0.0 dated 2025-02-17 and 1.0.1 dated 2026-11-09
DESCRIPTION | 12 MD5 | 346 ++++++++++----------- NAMESPACE | 56 +-- NEWS.md | 9 R/AllClasses.R | 14 R/AllGenerics.R | 247 +++++++-------- R/GMT.R | 50 +-- R/GeneSetCollection.R | 128 +++---- R/activate.R | 52 +-- R/add.R | 214 ++++++------- R/add_column.R | 34 +- R/add_relation.R | 54 +-- R/adjacency.R | 43 +- R/arrange.R | 65 +--- R/c.R | 54 +-- R/cardinality.R | 30 - R/cartesian.R | 108 +++--- R/complement.R | 171 +++++----- R/data_frame.R | 82 ++--- R/deactivate.R | 6 R/droplevels.R | 70 ++-- R/elements.R | 46 +- R/extract.R | 552 +++++++++++++++++----------------- R/filter.R | 89 ++--- R/group.R | 48 +- R/group_by.R | 18 - R/head.R | 7 R/incidence.R | 36 +- R/independent.R | 19 - R/intersection.R | 110 +++--- R/length.R | 413 ++++++++++++------------- R/list.R | 37 +- R/move_to.R | 62 +-- R/mutate.R | 83 ++--- R/names.R | 325 ++++++++++---------- R/naming.R | 96 +++-- R/nested.R | 4 R/obo.R | 233 +++++++------- R/operations.R | 9 R/power_set.R | 94 ++--- R/print.R | 12 R/pull.R | 44 +- R/relations.R | 50 +-- R/remove.R | 68 ++-- R/remove_column.R | 22 - R/rename.R | 52 +-- R/select.R | 65 +--- R/set.R | 46 +- R/size.R | 37 +- R/subtract.R | 113 +++--- R/tidy-set.R | 281 ++++++++--------- R/union.R | 54 +-- R/union_closed.R | 70 ++-- R/utils.R | 14 R/validity.R | 43 +- R/zzz.R | 32 - README.md | 50 +-- build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/BaseSet.R | 74 ++-- inst/doc/BaseSet.Rmd | 78 ++-- inst/doc/BaseSet.html | 163 +++++----- inst/doc/advanced.R | 260 ++++++++-------- inst/doc/advanced.Rmd | 266 ++++++++-------- inst/doc/advanced.html | 389 ++++++++++++----------- inst/doc/fuzzy.R | 94 +++-- inst/doc/fuzzy.Rmd | 100 +++--- inst/doc/fuzzy.html | 148 ++++----- man/BaseSet-package.Rd | 5 man/TidySet-class.Rd | 80 ++-- man/activate.Rd | 78 ++-- man/add_column.Rd | 82 ++--- man/add_elements.Rd | 6 man/add_relation.Rd | 78 ++-- man/add_relations.Rd | 6 man/add_sets.Rd | 6 man/arrange_.Rd | 78 ++-- man/cartesian.Rd | 78 ++-- man/complement.Rd | 86 ++--- man/complement_element.Rd | 96 ++--- man/complement_set.Rd | 96 ++--- man/element_size.Rd | 82 ++--- man/elements.Rd | 84 ++--- man/filter_.Rd | 78 ++-- man/getGAF.Rd | 10 man/getGMT.Rd | 6 man/getOBO.Rd | 6 man/group.Rd | 78 ++-- man/group_by_.Rd | 78 ++-- man/incidence.Rd | 78 ++-- man/intersection.Rd | 88 ++--- man/is.fuzzy.Rd | 78 ++-- man/is_nested.Rd | 78 ++-- man/move_to.Rd | 78 ++-- man/mutate_.Rd | 78 ++-- man/nElements.Rd | 84 ++--- man/nRelations.Rd | 84 ++--- man/nSets.Rd | 84 ++--- man/name_elements-set.Rd | 90 ++--- man/name_elements.Rd | 12 man/name_sets-set.Rd | 90 ++--- man/name_sets.Rd | 90 ++--- man/power_set.Rd | 78 ++-- man/pull_.Rd | 78 ++-- man/reexports.Rd | 2 man/relations.Rd | 84 ++--- man/remove_column.Rd | 82 ++--- man/remove_element.Rd | 84 ++--- man/remove_relation.Rd | 84 ++--- man/remove_set.Rd | 84 ++--- man/rename_elements.Rd | 94 ++--- man/rename_set.Rd | 94 ++--- man/select_.Rd | 78 ++-- man/set_size.Rd | 82 ++--- man/set_symbols.Rd | 5 man/sets.Rd | 84 ++--- man/subtract.Rd | 100 +++--- man/union.Rd | 88 ++--- tests/spelling.R | 9 tests/testthat.R | 6 tests/testthat/test-GMT.R | 12 tests/testthat/test-activate.R | 28 - tests/testthat/test-add_column.R | 20 - tests/testthat/test-add_relation.R | 40 +- tests/testthat/test-add_relations.R | 86 ++--- tests/testthat/test-adjacency.R | 42 +- tests/testthat/test-arrange.R | 56 +-- tests/testthat/test-c.R | 24 - tests/testthat/test-cardinality.R | 16 tests/testthat/test-cartesian.R | 20 - tests/testthat/test-complement.R | 158 ++++----- tests/testthat/test-data_frame.R | 32 - tests/testthat/test-df2TS.R | 38 +- tests/testthat/test-droplevels.R | 30 - tests/testthat/test-element_size.R | 62 +-- tests/testthat/test-elements.R | 30 - tests/testthat/test-extract.R | 118 +++---- tests/testthat/test-filter.R | 52 +-- tests/testthat/test-group.R | 36 +- tests/testthat/test-group_by.R | 28 - tests/testthat/test-head.R | 22 - tests/testthat/test-incidence.R | 12 tests/testthat/test-independent.R | 12 tests/testthat/test-intersection.R | 176 +++++----- tests/testthat/test-length.R | 116 +++---- tests/testthat/test-move_to.R | 18 - tests/testthat/test-mutate.R | 108 +++--- tests/testthat/test-name.R | 120 +++---- tests/testthat/test-naming.R | 32 - tests/testthat/test-nested.R | 10 tests/testthat/test-obo.R | 21 - tests/testthat/test-operations.R | 10 tests/testthat/test-power_set.R | 48 +- tests/testthat/test-print.R | 8 tests/testthat/test-pull.R | 110 +++--- tests/testthat/test-relations.R | 48 +- tests/testthat/test-remove_column.R | 22 - tests/testthat/test-remove_element.R | 16 tests/testthat/test-remove_relation.R | 34 +- tests/testthat/test-remove_set.R | 16 tests/testthat/test-rename.R | 36 +- tests/testthat/test-select.R | 52 +-- tests/testthat/test-setAs.R | 44 +- tests/testthat/test-set_size.R | 112 +++--- tests/testthat/test-sets.R | 30 - tests/testthat/test-size.R | 32 - tests/testthat/test-subtract.R | 44 +- tests/testthat/test-tidy.R | 86 ++--- tests/testthat/test-tidyset.R | 440 +++++++++++++-------------- tests/testthat/test-union.R | 218 ++++++------- tests/testthat/test-union_closed.R | 21 - vignettes/BaseSet.Rmd | 78 ++-- vignettes/advanced.Rmd | 266 ++++++++-------- vignettes/fuzzy.Rmd | 100 +++--- 174 files changed, 6928 insertions(+), 6696 deletions(-)
Title: Modified and Fully Modified Hodrick-Prescott Filters
Description: Decomposes macroeconomic time series into trend and cycle with
the Hodrick-Prescott (HP) filter and two data-driven versions of it. The
modified HP filter of McDermott (1997), assessed by Choudhary, Hanif and
Iqbal (2014) <doi:10.1080/00036846.2014.894631>, chooses the smoothing
parameter of every series by generalised cross-validation (as described
in Coe and McDermott (1997) <doi:10.2307/3867497>). The fully modified HP
filter of Hanif, Iqbal and Choudhary (2017, State Bank of Pakistan
Working Paper 88) also reduces the end-point bias of the HP filter: it
raises the smoothing parameter at the first and last observations, with
linear or quadratic weights chosen to minimise the loss of Bloechl (2014,
University of Munich Discussion Paper 2014-1). Every filter is a banded
linear solve, so the searches are fast; batch processing of many series,
comparisons of the filters, the filter weights, gain functions and
end-point loss, simulation of trend-plus-cycle series and the powe [...truncated...]
Author: Muhammad Yaseen [aut, cre, cph] ,
Javed Iqbal [ctb] ,
M. Nadim Hanif [ctb, cph] ,
M. Ali Choudhary [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between mhpfilter versions 0.1.0 dated 2026-02-13 and 1.0.0 dated 2026-11-09
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Title: Divisia Monetary Aggregates Index
Description: Builds monetary aggregates from their components by the methods
of index number theory. The Divisia index of Barnett (1980)
<doi:10.1016/0304-4076(80)90070-6> weights every component (currency,
demand deposits, savings and time deposits, ...) by its share in the
expenditure on monetary services, priced by its user cost (Barnett 1978)
<doi:10.1016/0165-1765(78)90051-4>. Also gives the Fisher ideal index, a
variant with simple growth rates, the simple-sum aggregate, the currency
equivalent index of Rotemberg, Driscoll and Poterba (1995), the dual
user-cost price index and the Divisia second moments of Barnett and
Serletis (1990) <doi:10.1016/0304-4076(90)90104-2>; benchmark rates
given or taken from the components (upper envelope); 'ggplot2'
graphics, a plain-language interpretation of every result and a built-in
'shiny' application.
Author: Muhammad Yaseen [aut, cre, cph] ,
Ahmad Nadeem [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between dmai versions 0.5.0 dated 2024-03-23 and 1.0.0 dated 2026-11-09
dmai-0.5.0/dmai/R/dmaiIntro-package.R |only dmai-0.5.0/dmai/man/dmaiIntro.Rd |only dmai-1.0.0/dmai/DESCRIPTION | 52 ++-- dmai-1.0.0/dmai/MD5 | 107 +++++++- dmai-1.0.0/dmai/NAMESPACE | 46 ++- dmai-1.0.0/dmai/NEWS.md | 91 ++++++- dmai-1.0.0/dmai/R/analyses.R |only dmai-1.0.0/dmai/R/app.R |only dmai-1.0.0/dmai/R/common-notation.R |only dmai-1.0.0/dmai/R/common-objects.R |only dmai-1.0.0/dmai/R/common-plot.R |only dmai-1.0.0/dmai/R/common-reference.R |only dmai-1.0.0/dmai/R/common-validate.R |only dmai-1.0.0/dmai/R/core.R |only dmai-1.0.0/dmai/R/data.R |only dmai-1.0.0/dmai/R/dmai-package.R |only dmai-1.0.0/dmai/R/dmai.R | 355 ++++++++++++++-------------- dmai-1.0.0/dmai/R/interpret.R |only dmai-1.0.0/dmai/R/plots.R |only dmai-1.0.0/dmai/R/references.R |only dmai-1.0.0/dmai/README.md | 183 +++++++++++++- dmai-1.0.0/dmai/build |only dmai-1.0.0/dmai/data |only dmai-1.0.0/dmai/inst |only dmai-1.0.0/dmai/man/autoplot.dmai_result.Rd |only dmai-1.0.0/dmai/man/cpi_ch19.Rd |only dmai-1.0.0/dmai/man/dmai-methods.Rd |only dmai-1.0.0/dmai/man/dmai-package.Rd |only dmai-1.0.0/dmai/man/dmai.Rd | 243 ++++++++++++------- dmai-1.0.0/dmai/man/dmai_app.Rd |only dmai-1.0.0/dmai/man/dmai_cite.Rd |only dmai-1.0.0/dmai/man/dmai_compare.Rd |only dmai-1.0.0/dmai/man/dmai_interpret.Rd |only dmai-1.0.0/dmai/man/dmai_moments.Rd |only dmai-1.0.0/dmai/man/dmai_notation.Rd |only dmai-1.0.0/dmai/man/dmai_reference.Rd |only dmai-1.0.0/dmai/man/dmai_save.Rd |only dmai-1.0.0/dmai/man/dmai_theme.Rd |only dmai-1.0.0/dmai/man/dmai_user_cost.Rd |only dmai-1.0.0/dmai/man/money_sim.Rd |only dmai-1.0.0/dmai/tests |only dmai-1.0.0/dmai/vignettes |only 42 files changed, 754 insertions(+), 323 deletions(-)
Title: Boxplots for Directional Data
Description: Functions for drawing boxplots for data on (the boundary of) a unit circle (i.e., circular and axial data), from Buttarazzi D., Pandolfo G., Porzio G.C. (2018) <doi:10.1111/biom.12889>. The package allows producing also circular violin plots, and includes methods to calculate robust measures of dispersion for circular data.
Author: Davide Buttarazzi [aut, cre]
Maintainer: Davide Buttarazzi <davidebuttarazzi90@gmail.com>
Diff between bpDir versions 0.1.2 dated 2021-04-08 and 0.2.6 dated 2026-11-09
DESCRIPTION | 18 MD5 | 52 + NAMESPACE | 60 + R/AxialBoxplot.R | 1598 ++++++++++++++++++------------------- R/CircMAD.R |only R/CircularBoxplot.R | 1233 ++++++++++++++-------------- R/CircularLMS.R |only R/CircularLTS.R |only R/CircularMAD.R |only R/CircularTukeyDepth.R | 106 +- R/CircularViolinPlot.R |only R/EstimateKappa.R |only R/EstimateKappaKo.R |only R/EstimateSigma.R |only R/add_geom.R |only R/angular_distance.R |only R/arc_ribbon_df.R |only R/as_circular_rad.R |only R/build_geom.R |only R/compute_SF_VM.R |only R/compute_SF_WN.R |only R/generate_results_grid_sigma.R |only R/generate_vonmises_grid.R |only R/global.R |only R/make_beans.R |only R/make_notch_cutout_df.R |only R/make_region_polygons.R |only R/pol2cart_circle.R |only R/to_plot_coords.R |only data |only man/AxialBoxplot.Rd | 188 ++-- man/CircularBoxplot.Rd | 194 ++-- man/CircularLMS.Rd |only man/CircularLTS.Rd |only man/CircularMAD.Rd |only man/CircularViolinPlot.Rd |only man/EstimateKappa.Rd |only man/EstimateKappaKo.Rd |only man/EstimateSigma.Rd |only man/Spring.Rd |only man/Summer.Rd |only man/e_healthy.Rd |only man/e_parkinson.Rd |only man/generate_results_grid_sigma.Rd |only man/generate_vonmises_grid.Rd |only 45 files changed, 1775 insertions(+), 1674 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
obtained in the 1990s by the research group around Cornelia Dowling
through querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [aut],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 3.0-0 dated 2026-09-01 and 3.0-1 dated 2026-11-09
Changelog | 7 ++++++- DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/kmassessbayesian.R | 9 +++++---- R/kmassessmultiplicative.R | 9 +++++---- R/kmsrvalidate.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 5 ++--- 9 files changed, 34 insertions(+), 28 deletions(-)