Title: All-Cause and Excess Mortality Calculator
Description: An interactive 'shiny' application that estimates all-cause
mortality and excess mortality from country-level weekly or monthly death
counts. Users supply observed deaths and an event calendar (for example
COVID-19 waves or typhoons); the app fits one or more statistical
baseline models (historical average, negative binomial regression,
quasi-Poisson regression, zero-inflated Poisson regression, ARIMA
(autoregressive integrated moving average) and SARIMA (seasonal ARIMA)
models, GAM (generalized additive model) splines, and the model of
Karlinsky and Kobak (2021) <doi:10.7554/eLife.69336>) using periods outside
the supplied events, estimates expected deaths across the observed
series, and reports excess deaths, P-scores (excess deaths as a
percentage of expected deaths) and confidence limits with tables, plots
and downloadable reports. Launch the application with run_app().
Author: Shanlong Ding [aut, cre],
World Health Organization Regional Office for the Western Pacific [cph,
fnd]
Maintainer: Shanlong Ding <dings@who.int>
Diff between exmort versions 0.1.0 dated 2026-07-30 and 0.1.1 dated 2026-10-05
DESCRIPTION | 18 MD5 | 24 - NEWS.md | 11 README.md | 36 + build |only inst/app/app.R | 730 ++++++++++++++++---------------- inst/app/www/style.css | 1106 ++++++++++++++++++++++++------------------------- inst/doc |only man/figures |only vignettes |only 10 files changed, 989 insertions(+), 936 deletions(-)
Title: Interactive Training App for Data Science and AI Skills
Description: An interactive 'shiny' training companion for people who are
new to data, developed for World Health Organization data trainings.
Bundles hands-on modules for importing data, missing values, outliers,
text cleaning, merging, visualization, and basic statistics, plus a set
of AI-skills pages (prompting levels, a prompt gallery, AI safety rules,
and a methodology case study) and an interactive quiz with per-session
topic filters. Launch the app with run_cata().
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
Diff between cataScience versions 2.1.3 dated 2026-08-28 and 2.1.4 dated 2026-10-05
DESCRIPTION | 12 MD5 | 58 +- NEWS.md | 11 README.md | 150 +++--- build |only inst/app/R/app-function.R | 466 ++++++++++---------- inst/app/R/server-merging.R | 2 inst/app/app.R | 28 - inst/app/markdown/background-import-issues.md | 82 +-- inst/app/markdown/background-import.md | 138 ++--- inst/app/markdown/background-merging-methodology.md | 126 ++--- inst/app/markdown/background-merging.md | 38 - inst/app/markdown/background-missing-methodology.md | 114 ++-- inst/app/markdown/background-missing-type.md | 78 +-- inst/app/markdown/background-missing.md | 70 +-- inst/app/markdown/background-outlier-detect.md | 46 - inst/app/markdown/background-outlier-handle.md | 100 ++-- inst/app/markdown/background-outlier.md | 54 +- inst/app/markdown/background-text.md | 52 +- inst/app/markdown/background-vis-principles.md | 140 +++--- inst/app/markdown/background-vis-type.md | 192 ++++---- inst/app/markdown/background-vis.md | 74 +-- inst/app/markdown/principle-bar.md | 170 +++---- inst/doc |only man/figures |only vignettes |only 26 files changed, 1126 insertions(+), 1075 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Roenkkoe [aut],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.27 dated 2026-08-30 and 2.28 dated 2026-10-05
DESCRIPTION | 6 - MD5 | 45 ++++++------- NEWS.md | 15 ++++ R/SimCheck.R | 4 - R/SimCollect.R | 85 +++++++++++++++++++++---- R/SimExtract.R | 6 + R/descript.R | 60 ++++++++++++----- R/rejectionSampling.R | 28 +++++--- R/runArraySimulation.R | 15 ++-- R/runSimulation.R | 8 +- inst/doc/Catch_errors.html | 10 +- inst/doc/Fixed_obj_fun.html | 10 +- inst/doc/HPC-computing.html | 4 - inst/doc/MultipleAnalyses.html | 4 - inst/doc/Parallel-computing.html | 4 - inst/doc/Saving-results.html | 4 - inst/doc/SimDesign-intro.html | 131 +++++++++++++++++++-------------------- man/SimCollect.Rd | 6 + man/SimExtract.Rd | 2 man/descript.Rd | 28 ++++++-- man/rejectionSampling.Rd | 28 +++++--- man/runArraySimulation.Rd | 11 ++- man/runSimulation.Rd | 5 - tests/tests/test-05-extras.R |only 24 files changed, 337 insertions(+), 182 deletions(-)
Title: Mechanistic Functional Response Analysis
Description: Implements the mechanistic functional response
model proposed by Okuyama (2012) <doi:10.1016/j.biocontrol.2011.10.008> for
host-parasitoid systems. Provides tools for model fitting, likelihood
profiling, stochastic simulation, and visualization of parasitism
distributions.
The stochastic simulation engine is implemented in C++ via 'Rcpp'.
Includes an interactive 'shiny' application for complete analysis workflows,
built with 'plotly' for interactive graphics and 'rmarkdown' for
reproducible reports.
Author: Segundo Nunez-Campero [aut, cre]
Maintainer: Segundo Nunez-Campero <segundo.nc@conicet.gov.ar>
Diff between funresMech versions 1.0.4 dated 2026-09-24 and 1.1.0 dated 2026-10-05
funresMech-1.0.4/funresMech/R/fit_full.R |only funresMech-1.1.0/funresMech/DESCRIPTION | 12 funresMech-1.1.0/funresMech/MD5 | 36 funresMech-1.1.0/funresMech/NAMESPACE | 9 funresMech-1.1.0/funresMech/NEWS.md |only funresMech-1.1.0/funresMech/R/RcppExports.R |only funresMech-1.1.0/funresMech/R/fit_profile.R |only funresMech-1.1.0/funresMech/R/funresMech-package.R |only funresMech-1.1.0/funresMech/R/negloglik_fixed_z.R | 72 - funresMech-1.1.0/funresMech/R/profile_ci.R |only funresMech-1.1.0/funresMech/R/reparam.R |only funresMech-1.1.0/funresMech/R/run_app.R | 20 funresMech-1.1.0/funresMech/R/screening.R |only funresMech-1.1.0/funresMech/R/server.R | 245 ++-- funresMech-1.1.0/funresMech/R/simulate_distribution.R | 42 funresMech-1.1.0/funresMech/R/simulate_trial.R | 81 - funresMech-1.1.0/funresMech/R/ui.R | 40 funresMech-1.1.0/funresMech/README.md | 253 ++-- funresMech-1.1.0/funresMech/build |only funresMech-1.1.0/funresMech/inst/app/report_template.Rmd | 735 +++++++------- funresMech-1.1.0/funresMech/man/funresMech-package.Rd |only funresMech-1.1.0/funresMech/man/run_app.Rd | 20 funresMech-1.1.0/funresMech/src |only funresMech-1.1.0/funresMech/tests/testthat/test-modelos.R | 318 +++++- 24 files changed, 1099 insertions(+), 784 deletions(-)
Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Description: Raman and (FT)IR spectral analysis tool for plastic particles and
other environmental samples (Cowger et al. 2025,
<doi:10.1021/acs.analchem.5c00962>). With read_any(), Open Specy provides a
single function for reading individual, batch, or map spectral data files
like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies
processing spectra, including smoothing, baseline correction,
range restriction and flattening, intensity conversions, wavenumber
alignment, and min-max normalization. Spectra can be identified in batch
using an onboard reference library using match_spec(). A bundled Shiny app
is available via run_app() or online at
<https://www.openanalysis.org/OpenSpecyV2/>.
Author: Win Cowger [cre, aut, dtc] ,
Zacharias Steinmetz [aut] ,
Hazel Vaquero [aut] ,
Nick Leong [aut] ,
Andrea Faltynkova [aut, dtc] ,
Hannah Sherrod [aut] ,
Andrew B Gray [ctb] ,
Hannah Hapich [ctb] ,
Jennifer Lynch [ctb, dtc] ,
Hannah De Frond [ctb, dtc] [...truncated...]
Maintainer: Win Cowger <wincowger@gmail.com>
This is a re-admission after prior archival of version 1.5.3 dated 2025-04-26
Diff between OpenSpecy versions 1.5.3 dated 2025-04-26 and 2.0.1 dated 2026-10-05
OpenSpecy-1.5.3/OpenSpecy/inst/extdata/raman_hdpe.yml |only OpenSpecy-1.5.3/OpenSpecy/tests/testthat/Rplots.pdf |only OpenSpecy-2.0.1/OpenSpecy/DESCRIPTION | 98 OpenSpecy-2.0.1/OpenSpecy/MD5 | 297 OpenSpecy-2.0.1/OpenSpecy/NAMESPACE | 118 OpenSpecy-2.0.1/OpenSpecy/NEWS.md | 1451 +++- OpenSpecy-2.0.1/OpenSpecy/R/OpenSpecy-package.R | 86 OpenSpecy-2.0.1/OpenSpecy/R/Specs.R |only OpenSpecy-2.0.1/OpenSpecy/R/Specs_compact.R |only OpenSpecy-2.0.1/OpenSpecy/R/Specs_file.R |only OpenSpecy-2.0.1/OpenSpecy/R/Specs_methods.R |only OpenSpecy-2.0.1/OpenSpecy/R/adj_intens.R | 44 OpenSpecy-2.0.1/OpenSpecy/R/adj_range.R | 624 + OpenSpecy-2.0.1/OpenSpecy/R/adj_wave.R | 9 OpenSpecy-2.0.1/OpenSpecy/R/area_under_band.R |only OpenSpecy-2.0.1/OpenSpecy/R/as_OpenSpecy.R | 245 OpenSpecy-2.0.1/OpenSpecy/R/assess_spec.R |only OpenSpecy-2.0.1/OpenSpecy/R/automate_particle_analysis.R |only OpenSpecy-2.0.1/OpenSpecy/R/automate_particle_filespecs.R |only OpenSpecy-2.0.1/OpenSpecy/R/build_lib.R |only OpenSpecy-2.0.1/OpenSpecy/R/conform_spec.R | 171 OpenSpecy-2.0.1/OpenSpecy/R/correct_spike.R |only OpenSpecy-2.0.1/OpenSpecy/R/data_norm.R | 23 OpenSpecy-2.0.1/OpenSpecy/R/def_features.R | 383 - OpenSpecy-2.0.1/OpenSpecy/R/gen_OpenSpecy.R | 48 OpenSpecy-2.0.1/OpenSpecy/R/interactive_plots.R | 211 OpenSpecy-2.0.1/OpenSpecy/R/io_spec.R | 177 OpenSpecy-2.0.1/OpenSpecy/R/make_rel.R | 62 OpenSpecy-2.0.1/OpenSpecy/R/manage_lib.R | 230 OpenSpecy-2.0.1/OpenSpecy/R/manage_na.R | 240 OpenSpecy-2.0.1/OpenSpecy/R/manage_spec.R | 176 OpenSpecy-2.0.1/OpenSpecy/R/match_spec.R | 768 +- OpenSpecy-2.0.1/OpenSpecy/R/material_percentage_uncertainty.R |only OpenSpecy-2.0.1/OpenSpecy/R/particle_image.R |only OpenSpecy-2.0.1/OpenSpecy/R/peak_ratio.R |only OpenSpecy-2.0.1/OpenSpecy/R/point_intensity.R |only OpenSpecy-2.0.1/OpenSpecy/R/process_spec.R | 182 OpenSpecy-2.0.1/OpenSpecy/R/raman_hdpe.R | 69 OpenSpecy-2.0.1/OpenSpecy/R/read_envi.R | 534 + OpenSpecy-2.0.1/OpenSpecy/R/read_ext.R | 654 + OpenSpecy-2.0.1/OpenSpecy/R/read_multi.R | 131 OpenSpecy-2.0.1/OpenSpecy/R/read_opus.R | 2 OpenSpecy-2.0.1/OpenSpecy/R/read_opus_raw.R | 15 OpenSpecy-2.0.1/OpenSpecy/R/run_app.R | 197 OpenSpecy-2.0.1/OpenSpecy/R/sig_noise.R | 303 OpenSpecy-2.0.1/OpenSpecy/R/smooth_intens.R | 206 OpenSpecy-2.0.1/OpenSpecy/R/spatial_calibration.R |only OpenSpecy-2.0.1/OpenSpecy/R/spatial_smooth.R | 120 OpenSpecy-2.0.1/OpenSpecy/R/split_h5.R |only OpenSpecy-2.0.1/OpenSpecy/R/split_spec.R | 51 OpenSpecy-2.0.1/OpenSpecy/R/subtr_baseline.R | 430 + OpenSpecy-2.0.1/OpenSpecy/R/temperature_emissivity.R |only OpenSpecy-2.0.1/OpenSpecy/R/validation_metrics.R |only OpenSpecy-2.0.1/OpenSpecy/R/visual_image.R |only OpenSpecy-2.0.1/OpenSpecy/R/zzz.R | 53 OpenSpecy-2.0.1/OpenSpecy/README.md | 71 OpenSpecy-2.0.1/OpenSpecy/build/vignette.rds |binary OpenSpecy-2.0.1/OpenSpecy/data/raman_hdpe.RData |binary OpenSpecy-2.0.1/OpenSpecy/data/test_lib.RData |binary OpenSpecy-2.0.1/OpenSpecy/inst/CITATION |only OpenSpecy-2.0.1/OpenSpecy/inst/doc/library-builder.R |only OpenSpecy-2.0.1/OpenSpecy/inst/doc/library-builder.Rmd |only OpenSpecy-2.0.1/OpenSpecy/inst/doc/library-builder.html |only OpenSpecy-2.0.1/OpenSpecy/inst/doc/sop.R | 515 - OpenSpecy-2.0.1/OpenSpecy/inst/doc/sop.Rmd | 456 + OpenSpecy-2.0.1/OpenSpecy/inst/doc/sop.html | 1295 ++- OpenSpecy-2.0.1/OpenSpecy/inst/extdata/raman_hdpe.json | 2 OpenSpecy-2.0.1/OpenSpecy/inst/extdata/raman_hdpe.rds |binary OpenSpecy-2.0.1/OpenSpecy/inst/extdata/raman_hdpe_os.csv | 2 OpenSpecy-2.0.1/OpenSpecy/inst/shiny |only OpenSpecy-2.0.1/OpenSpecy/man/OpenSpecy-package.Rd | 193 OpenSpecy-2.0.1/OpenSpecy/man/Specs.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/adj_range.Rd | 66 OpenSpecy-2.0.1/OpenSpecy/man/area_under_band.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/as_OpenSpecy.Rd | 34 OpenSpecy-2.0.1/OpenSpecy/man/assess_spec.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/automate_particle_analysis.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/build_lib.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/calculate_emissivity.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/conform_spec.Rd | 10 OpenSpecy-2.0.1/OpenSpecy/man/correct_spike.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/data_norm.Rd | 10 OpenSpecy-2.0.1/OpenSpecy/man/def_features.Rd | 5 OpenSpecy-2.0.1/OpenSpecy/man/estimate_temperature.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/interactive_plots.Rd | 35 OpenSpecy-2.0.1/OpenSpecy/man/io_spec.Rd | 34 OpenSpecy-2.0.1/OpenSpecy/man/lib_metadata_name_lookup.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/make_rel.Rd | 8 OpenSpecy-2.0.1/OpenSpecy/man/manage_lib.Rd | 27 OpenSpecy-2.0.1/OpenSpecy/man/manage_na.Rd | 7 OpenSpecy-2.0.1/OpenSpecy/man/manage_spec.Rd | 19 OpenSpecy-2.0.1/OpenSpecy/man/match_spec.Rd | 44 OpenSpecy-2.0.1/OpenSpecy/man/material_percentage_uncertainty.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/open_specs.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/particle_image.Rd |only OpenSpecy-2.0.1/OpenSpecy/man/peak_ratio.Rd |only 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OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-FileSpecs-particle.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-FileSpecs.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-Specs.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-adj_intens.R | 21 OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-adj_range.R | 341 OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-app-in-memory-helpers.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-app-onboarding.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-area_under_band.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-as_OpenSpecy.R | 22 OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-assess_spec.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-automate_particle_analysis.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-build_lib.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-conform_spec.R | 31 OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-correct_spike.R |only 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OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-validation_metrics.R |only OpenSpecy-2.0.1/OpenSpecy/tests/testthat/test-visual_image.R |only OpenSpecy-2.0.1/OpenSpecy/tests/validation/test-augmented.R | 6 OpenSpecy-2.0.1/OpenSpecy/tools |only OpenSpecy-2.0.1/OpenSpecy/vignettes/library-builder.Rmd |only OpenSpecy-2.0.1/OpenSpecy/vignettes/sop.Rmd | 456 + 162 files changed, 14733 insertions(+), 3054 deletions(-)
Title: Learning Hybrid Bayesian Networks using Mixtures of Truncated
Basis Functions
Description: Learning, manipulation and evaluation of mixtures of truncated basis functions
(MoTBFs), which include mixtures of polynomials (MOPs) and mixtures of truncated
exponentials (MTEs). MoTBFs are a flexible framework for modelling hybrid Bayesian
networks (I. Pérez-Bernabé, A. Salmerón, H. Langseth (2015) <doi:10.1007/978-3-319-20807-7_36>; H. Langseth, T.D. Nielsen, I. Pérez-Bernabé, A. Salmerón (2014) <doi:10.1016/j.ijar.2013.09.012>; I. Pérez-Bernabé, A. Fernández, R. Rumí, A. Salmerón (2016) <doi:10.1007/s10618-015-0429-7>). The package provides functionality for learning univariate, multivariate and conditional densities, with the possibility of incorporating prior knowledge. Structural learning of hybrid Bayesian networks is also provided. A set of useful tools is provided, including plotting, printing and likelihood evaluation. This package makes use of S3 objects, with two new classes called 'motbf' and 'jointmotbf'.
Author: Inmaculada Perez-Bernabe [aut],
Antonio Salmeron [aut],
Thomas D. Nielsen [aut],
Angel T. Saez-Ruiz [aut],
Ana D. Maldonado [aut, cre]
Maintainer: Ana D. Maldonado <ana.d.maldonado@ual.es>
Diff between MoTBFs versions 2.0 dated 2026-08-21 and 2.0.1 dated 2026-10-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/LearningBN.R | 18 +++++++++++++----- R/MI_MoP_TAN.R | 14 ++++---------- R/conditional.R | 24 ++++++++++++++++-------- R/functions.R | 2 +- inst/doc/packageUsage.html | 16 ++++++++-------- man/conditionalmotbf.learning.Rd | 3 ++- 8 files changed, 54 insertions(+), 43 deletions(-)
Title: Recalibration Methods for Improved Clinical Utility of Risk
Scores
Description: Recalibrate risk scores (predicting binary outcomes) to improve clinical utility of risk score using weighted logistic or constrained logistic recalibration methods. Additionally, produces plots to assess the potential for recalibration to improve the clinical utility of a risk model. Methods are described in detail in Mishra, A. (2019) "Methods for Risk Markers that Incorporate Clinical Utility" <http://hdl.handle.net/1773/44068>.
Author: Anu Mishra [aut, cre]
Maintainer: Anu Mishra <anupam.roth@gmail.com>
Diff between ClinicalUtilityRecal versions 0.1.0 dated 2020-04-15 and 0.1.1 dated 2026-10-05
DESCRIPTION | 13 ++++++++----- MD5 | 9 +++++---- NEWS.md |only man/RAWgrid.Rd | 4 +++- man/cvReptWtTuning.Rd | 2 +- man/cvWtTuning.Rd | 2 +- 6 files changed, 18 insertions(+), 12 deletions(-)
More information about ClinicalUtilityRecal at CRAN
Permanent link
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070> for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre <DOI:10.1177/0146621613479818> for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided. For tutorials, please check Ma and de la Torre (2020) <DOI:10.18637/jss.v093.i14>, Ma and de la Torre (2019) <DOI:10.1111/emip.12262>, Ma (2019) <DOI:10.1007/978-3-030-05584-4_29> and de la Torre and Akbay (2019).
Author: Wenchao Ma [aut, cre, cph],
Jimmy de la Torre [aut, cph],
Samuel Huang [ctb],
Miguel Sorrel [ctb],
Zhehan Jiang [ctb],
Pablo Najera [ctb]
Maintainer: Wenchao Ma <wma@umn.edu>
Diff between GDINA versions 2.13.1 dated 2026-09-16 and 2.13.2 dated 2026-10-05
GDINA-2.13.1/GDINA/man/check_em_convergence.Rd |only GDINA-2.13.1/GDINA/man/init_constraint_matrices.Rd |only GDINA-2.13.1/GDINA/man/init_control.Rd |only GDINA-2.13.1/GDINA/man/init_design_matrices.Rd |only GDINA-2.13.1/GDINA/man/init_solver.Rd |only GDINA-2.13.1/GDINA/man/init_solver_args.Rd |only GDINA-2.13.1/GDINA/man/print_em_progress.Rd |only GDINA-2.13.2/GDINA/DESCRIPTION | 13 ++-- GDINA-2.13.2/GDINA/MD5 | 45 ++++++--------- GDINA-2.13.2/GDINA/NAMESPACE | 61 ++++++++++++--------- GDINA-2.13.2/GDINA/NEWS.md | 3 - GDINA-2.13.2/GDINA/R/estimation_utils.R | 20 ++---- GDINA-2.13.2/GDINA/R/plotIRF.GDINA.R | 7 +- GDINA-2.13.2/GDINA/inst/doc/GDINA.html | 4 - GDINA-2.13.2/GDINA/man/plot.Qval.Rd | 2 GDINA-2.13.2/GDINA/man/realdata_ECPE.Rd | 2 GDINA-2.13.2/GDINA/man/realdata_Tatsuoka1990.Rd | 2 GDINA-2.13.2/GDINA/man/sim10GDINA.Rd | 2 GDINA-2.13.2/GDINA/man/sim10MCDINA.Rd | 2 GDINA-2.13.2/GDINA/man/sim10MCDINA2.Rd | 2 GDINA-2.13.2/GDINA/man/sim20seqGDINA.Rd | 2 GDINA-2.13.2/GDINA/man/sim21seqDINA.Rd | 2 GDINA-2.13.2/GDINA/man/sim30DINA.Rd | 2 GDINA-2.13.2/GDINA/man/sim30GDINA.Rd | 2 GDINA-2.13.2/GDINA/man/sim30pGDINA.Rd | 2 GDINA-2.13.2/GDINA/tests/testthat/Rplots.pdf |binary GDINA-2.13.2/GDINA/tests/testthat/test-Qval.R | 4 + 27 files changed, 94 insertions(+), 85 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general
engine for big data processing, see <https://spark.apache.org/>. This
package supports connecting to local and remote Apache Spark clusters,
provides a 'dplyr' compatible back-end, and provides an interface to
Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut],
Kevin Kuo [aut] ,
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
Hossein Falaki [aut],
Lu Wang [aut],
Andy Zhang [aut],
Yitao Li [aut] ,
Jozef Hajnala [ctb],
Maciej Szymkiewicz [ctb] ,
Wil Davis [ctb],
Edgar Ruiz [au [...truncated...]
Maintainer: Edgar Ruiz <edgar@rstudio.com>
Diff between sparklyr versions 1.9.5 dated 2026-06-20 and 1.9.6 dated 2026-10-05
sparklyr-1.9.5/sparklyr/R/arrow_data.R |only sparklyr-1.9.5/sparklyr/R/avro_utils.R |only sparklyr-1.9.5/sparklyr/R/browse_url.R |only sparklyr-1.9.5/sparklyr/R/config_settings.R |only sparklyr-1.9.5/sparklyr/R/config_spark.R |only sparklyr-1.9.5/sparklyr/R/connection_instances.R |only sparklyr-1.9.5/sparklyr/R/connection_shinyapp.R |only sparklyr-1.9.5/sparklyr/R/core_arrow.R |only sparklyr-1.9.5/sparklyr/R/core_config.R |only sparklyr-1.9.5/sparklyr/R/core_connection.R |only sparklyr-1.9.5/sparklyr/R/core_deserialize.R |only sparklyr-1.9.5/sparklyr/R/core_worker_config.R |only sparklyr-1.9.5/sparklyr/R/data_csv.R |only sparklyr-1.9.5/sparklyr/R/data_interface.R |only sparklyr-1.9.5/sparklyr/R/databricks_connection.R |only sparklyr-1.9.5/sparklyr/R/dbi_spark_connection.R |only sparklyr-1.9.5/sparklyr/R/dbi_spark_result.R |only sparklyr-1.9.5/sparklyr/R/dbi_spark_table.R |only sparklyr-1.9.5/sparklyr/R/do_spark.R |only sparklyr-1.9.5/sparklyr/R/dplyr_do.R |only sparklyr-1.9.5/sparklyr/R/dplyr_join.R |only sparklyr-1.9.5/sparklyr/R/dplyr_spark_data.R |only sparklyr-1.9.5/sparklyr/R/dplyr_spark_table.R |only sparklyr-1.9.5/sparklyr/R/java.R |only sparklyr-1.9.5/sparklyr/R/kubernetes_config.R |only sparklyr-1.9.5/sparklyr/R/livy_connection.R |only sparklyr-1.9.5/sparklyr/R/livy_install.R |only sparklyr-1.9.5/sparklyr/R/livy_invoke.R |only sparklyr-1.9.5/sparklyr/R/livy_service.R |only sparklyr-1.9.5/sparklyr/R/ml_classification_decision_tree_classifier.R |only sparklyr-1.9.5/sparklyr/R/ml_classification_gbt_classifier.R |only sparklyr-1.9.5/sparklyr/R/ml_classification_linear_svc.R |only sparklyr-1.9.5/sparklyr/R/ml_classification_logistic_regression.R |only sparklyr-1.9.5/sparklyr/R/ml_classification_multilayer_perceptron_classifier.R |only sparklyr-1.9.5/sparklyr/R/ml_classification_naive_bayes.R |only sparklyr-1.9.5/sparklyr/R/ml_classification_one_vs_rest.R |only sparklyr-1.9.5/sparklyr/R/ml_classification_random_forest_classifier.R |only 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sparklyr-1.9.5/sparklyr/R/ml_feature_dplyr_transformer.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_elementwise_product.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_feature_hasher.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_hashing_tf.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_idf.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_index_to_string.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_interaction.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_lsh_utils.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_max_abs_scaler.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_min_max_scaler.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_minhash_lsh.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_ngram.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_normalizer.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_one_hot_encoder.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_one_hot_encoder_estimator.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_pca.R |only sparklyr-1.9.5/sparklyr/R/ml_feature_polynomial_expansion.R |only 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| 33 sparklyr-1.9.6/sparklyr/R/connection_qubole.R |only sparklyr-1.9.6/sparklyr/R/connection_shell.R |only sparklyr-1.9.6/sparklyr/R/connection_spark.R | 799 +-- sparklyr-1.9.6/sparklyr/R/connection_test.R |only sparklyr-1.9.6/sparklyr/R/connection_yarn.R |only sparklyr-1.9.6/sparklyr/R/core_gateway.R | 149 sparklyr-1.9.6/sparklyr/R/core_invoke.R | 133 sparklyr-1.9.6/sparklyr/R/core_serialize.R | 309 + sparklyr-1.9.6/sparklyr/R/core_utils.R | 281 + sparklyr-1.9.6/sparklyr/R/data_copy.R | 4 sparklyr-1.9.6/sparklyr/R/data_read.R |only sparklyr-1.9.6/sparklyr/R/data_write.R |only sparklyr-1.9.6/sparklyr/R/dbi.R |only sparklyr-1.9.6/sparklyr/R/dplyr_hof.R | 69 sparklyr-1.9.6/sparklyr/R/dplyr_spark.R | 160 sparklyr-1.9.6/sparklyr/R/dplyr_sql.R | 29 sparklyr-1.9.6/sparklyr/R/dplyr_verbs.R | 722 +++ sparklyr-1.9.6/sparklyr/R/imports.R | 175 sparklyr-1.9.6/sparklyr/R/ml_aft_survival_regression.R |only sparklyr-1.9.6/sparklyr/R/ml_als.R |only sparklyr-1.9.6/sparklyr/R/ml_bisecting_kmeans.R |only sparklyr-1.9.6/sparklyr/R/ml_decision_tree.R |only sparklyr-1.9.6/sparklyr/R/ml_evaluation.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_encoders.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_lsh.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_math.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_normalizers.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_scalers.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_selectors.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_sql.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_string_indexer.R | 237 + sparklyr-1.9.6/sparklyr/R/ml_feature_text_vectorizers.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_tokenizers.R |only sparklyr-1.9.6/sparklyr/R/ml_feature_vectors.R |only sparklyr-1.9.6/sparklyr/R/ml_fpm.R |only sparklyr-1.9.6/sparklyr/R/ml_gaussian_mixture.R |only sparklyr-1.9.6/sparklyr/R/ml_gbt.R |only sparklyr-1.9.6/sparklyr/R/ml_generalized_linear_regression.R |only sparklyr-1.9.6/sparklyr/R/ml_isotonic_regression.R |only sparklyr-1.9.6/sparklyr/R/ml_kmeans.R |only sparklyr-1.9.6/sparklyr/R/ml_lda.R |only sparklyr-1.9.6/sparklyr/R/ml_linear_regression.R |only sparklyr-1.9.6/sparklyr/R/ml_linear_svc.R |only sparklyr-1.9.6/sparklyr/R/ml_logistic_regression.R |only sparklyr-1.9.6/sparklyr/R/ml_metrics.R | 39 sparklyr-1.9.6/sparklyr/R/ml_model_constructors.R | 149 sparklyr-1.9.6/sparklyr/R/ml_multilayer_perceptron.R |only sparklyr-1.9.6/sparklyr/R/ml_naive_bayes.R |only sparklyr-1.9.6/sparklyr/R/ml_one_vs_rest.R |only sparklyr-1.9.6/sparklyr/R/ml_param_utils.R | 203 sparklyr-1.9.6/sparklyr/R/ml_pipeline.R | 331 + sparklyr-1.9.6/sparklyr/R/ml_power_iteration.R |only sparklyr-1.9.6/sparklyr/R/ml_random_forest.R |only sparklyr-1.9.6/sparklyr/R/ml_transformer.R |only sparklyr-1.9.6/sparklyr/R/ml_tuning.R | 369 + sparklyr-1.9.6/sparklyr/R/ml_utils.R | 82 sparklyr-1.9.6/sparklyr/R/precondition.R | 165 sparklyr-1.9.6/sparklyr/R/sdf_interface.R | 47 sparklyr-1.9.6/sparklyr/R/sdf_io.R |only sparklyr-1.9.6/sparklyr/R/sdf_stat.R | 167 sparklyr-1.9.6/sparklyr/R/sdf_unnest.R |only sparklyr-1.9.6/sparklyr/R/sdf_utils.R | 11 sparklyr-1.9.6/sparklyr/R/sdf_wrapper.R | 119 sparklyr-1.9.6/sparklyr/R/spark_apply.R | 160 sparklyr-1.9.6/sparklyr/R/spark_compat.R |only sparklyr-1.9.6/sparklyr/R/spark_compile.R | 124 sparklyr-1.9.6/sparklyr/R/spark_context.R |only sparklyr-1.9.6/sparklyr/R/spark_data.R |only sparklyr-1.9.6/sparklyr/R/spark_ide.R | 28 sparklyr-1.9.6/sparklyr/R/spark_sql.R | 23 sparklyr-1.9.6/sparklyr/R/spark_submit.R | 287 + sparklyr-1.9.6/sparklyr/R/stream.R |only sparklyr-1.9.6/sparklyr/R/stream_data.R | 2 sparklyr-1.9.6/sparklyr/R/stream_ui.R |only sparklyr-1.9.6/sparklyr/R/tbl_spark.R | 114 sparklyr-1.9.6/sparklyr/R/tidiers_ml_classification.R |only sparklyr-1.9.6/sparklyr/R/tidiers_ml_other.R |only sparklyr-1.9.6/sparklyr/R/tidiers_ml_regression.R |only sparklyr-1.9.6/sparklyr/R/tidyr_nest.R | 150 sparklyr-1.9.6/sparklyr/R/tidyr_pivot_longer.R | 2 sparklyr-1.9.6/sparklyr/R/tidyr_pivot_wider.R | 2 sparklyr-1.9.6/sparklyr/R/tidyr_reshape.R |only sparklyr-1.9.6/sparklyr/R/tidyr_utils.R | 6 sparklyr-1.9.6/sparklyr/R/utils.R | 261 - sparklyr-1.9.6/sparklyr/R/utils_cast.R |only sparklyr-1.9.6/sparklyr/R/worker.R |only sparklyr-1.9.6/sparklyr/build/partial.rdb |binary sparklyr-1.9.6/sparklyr/inst/extdata/versions-next.json | 9 sparklyr-1.9.6/sparklyr/inst/extdata/versions.json | 24 sparklyr-1.9.6/sparklyr/inst/java/sparklyr-2.4-2.11.jar |binary sparklyr-1.9.6/sparklyr/inst/java/sparklyr-3.0-2.12.jar |binary sparklyr-1.9.6/sparklyr/inst/java/sparklyr-3.5-2.12.jar |binary sparklyr-1.9.6/sparklyr/inst/java/sparklyr-master-2.13.jar |binary sparklyr-1.9.6/sparklyr/inst/rstudio/connections/Livy.R | 14 sparklyr-1.9.6/sparklyr/inst/rstudio/shinycon/app.R | 201 sparklyr-1.9.6/sparklyr/inst/sparkml/class_mapping.json | 2 sparklyr-1.9.6/sparklyr/java/embedded_sources.R | 2043 ++++++---- sparklyr-1.9.6/sparklyr/java/spark-4.0.0/serializer.scala | 13 sparklyr-1.9.6/sparklyr/man/DBISparkResult-class.Rd | 2 sparklyr-1.9.6/sparklyr/man/arrow_enabled_object.Rd | 2 sparklyr-1.9.6/sparklyr/man/collect.Rd | 2 sparklyr-1.9.6/sparklyr/man/connection_config.Rd | 2 sparklyr-1.9.6/sparklyr/man/connection_is_open.Rd | 2 sparklyr-1.9.6/sparklyr/man/connection_spark_shinyapp.Rd | 2 sparklyr-1.9.6/sparklyr/man/copy_to.Rd | 2 sparklyr-1.9.6/sparklyr/man/distinct.Rd | 2 sparklyr-1.9.6/sparklyr/man/download_scalac.Rd | 12 sparklyr-1.9.6/sparklyr/man/fill.Rd | 2 sparklyr-1.9.6/sparklyr/man/filter.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_binarizer.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_bucketizer.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_chisq_selector.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_count_vectorizer.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_dct.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_elementwise_product.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_feature_hasher.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_hashing_tf.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_idf.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_index_to_string.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_interaction.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_lsh.Rd | 3 sparklyr-1.9.6/sparklyr/man/ft_lsh_utils.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_max_abs_scaler.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_min_max_scaler.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_ngram.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_normalizer.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_one_hot_encoder.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_one_hot_encoder_estimator.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_pca.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_polynomial_expansion.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_quantile_discretizer.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_r_formula.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_regex_tokenizer.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_robust_scaler.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_standard_scaler.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_stop_words_remover.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_string_indexer.Rd | 3 sparklyr-1.9.6/sparklyr/man/ft_tokenizer.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_vector_assembler.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_vector_indexer.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_vector_slicer.Rd | 2 sparklyr-1.9.6/sparklyr/man/ft_word2vec.Rd | 2 sparklyr-1.9.6/sparklyr/man/full_join.Rd | 2 sparklyr-1.9.6/sparklyr/man/get_spark_sql_catalog_implementation.Rd | 2 sparklyr-1.9.6/sparklyr/man/hive_context_config.Rd | 2 sparklyr-1.9.6/sparklyr/man/inner_join.Rd | 2 sparklyr-1.9.6/sparklyr/man/invoke.Rd | 2 sparklyr-1.9.6/sparklyr/man/invoke_method.Rd | 2 sparklyr-1.9.6/sparklyr/man/j_invoke.Rd | 2 sparklyr-1.9.6/sparklyr/man/j_invoke_method.Rd | 2 sparklyr-1.9.6/sparklyr/man/jobj_set_param.Rd | 2 sparklyr-1.9.6/sparklyr/man/join.tbl_spark.Rd | 28 sparklyr-1.9.6/sparklyr/man/left_join.Rd | 2 sparklyr-1.9.6/sparklyr/man/livy_config.Rd | 2 sparklyr-1.9.6/sparklyr/man/livy_install.Rd | 2 sparklyr-1.9.6/sparklyr/man/livy_service.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml-constructors.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml-model-constructors.Rd | 72 sparklyr-1.9.6/sparklyr/man/ml-transform-methods.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml-tuning.Rd | 3 sparklyr-1.9.6/sparklyr/man/ml_add_stage.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_aft_survival_regression.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_als.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_als_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_bisecting_kmeans.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_call_constructor.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_clustering_evaluator.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_decision_tree.Rd | 49 sparklyr-1.9.6/sparklyr/man/ml_default_stop_words.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_evaluate.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_evaluator.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_feature_importances.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_fpgrowth.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_gaussian_mixture.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_generalized_linear_regression.Rd | 4 sparklyr-1.9.6/sparklyr/man/ml_glm_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_gradient_boosted_trees.Rd | 51 sparklyr-1.9.6/sparklyr/man/ml_isotonic_regression.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_isotonic_regression_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_kmeans.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_lda.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_lda_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_linear_regression.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_linear_svc.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_linear_svc_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_logistic_regression.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_logistic_regression_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_multilayer_perceptron_classifier.Rd | 3 sparklyr-1.9.6/sparklyr/man/ml_multilayer_perceptron_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_naive_bayes.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_naive_bayes_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_one_vs_rest.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_pca_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_power_iteration.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_prefixspan.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_random_forest.Rd | 49 sparklyr-1.9.6/sparklyr/man/ml_stage.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_standardize_formula.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_summary.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_survival_regression_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_tree_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_uid.Rd | 2 sparklyr-1.9.6/sparklyr/man/ml_unsupervised_tidiers.Rd | 2 sparklyr-1.9.6/sparklyr/man/mutate.Rd | 2 sparklyr-1.9.6/sparklyr/man/na.replace.Rd | 2 sparklyr-1.9.6/sparklyr/man/nest.Rd | 2 sparklyr-1.9.6/sparklyr/man/pipe.Rd | 2 sparklyr-1.9.6/sparklyr/man/pivot_longer.Rd | 2 sparklyr-1.9.6/sparklyr/man/pivot_wider.Rd | 2 sparklyr-1.9.6/sparklyr/man/quote_sql_name.Rd | 2 sparklyr-1.9.6/sparklyr/man/reactiveSpark.Rd | 2 sparklyr-1.9.6/sparklyr/man/registerDoSpark.Rd | 2 sparklyr-1.9.6/sparklyr/man/register_extension.Rd | 2 sparklyr-1.9.6/sparklyr/man/replace_na.Rd | 2 sparklyr-1.9.6/sparklyr/man/right_join.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf-saveload.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf-transform-methods.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_along.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_bind.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_dim.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_distinct.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_is_streaming.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_len.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_project.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_random_split.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_residuals.Rd | 4 sparklyr-1.9.6/sparklyr/man/sdf_seq.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_sql.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_unnest_longer.Rd | 2 sparklyr-1.9.6/sparklyr/man/sdf_unnest_wider.Rd | 2 sparklyr-1.9.6/sparklyr/man/select.Rd | 2 sparklyr-1.9.6/sparklyr/man/separate.Rd | 2 sparklyr-1.9.6/sparklyr/man/slice_.tbl_spark.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark-api.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark-connections.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_adaptive_query_execution.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_advisory_shuffle_partition_size.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_apply_bundle.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_auto_broadcast_join_threshold.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_coalesce_initial_num_partitions.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_coalesce_min_num_partitions.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_coalesce_shuffle_partitions.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_config.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_config_exists.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_config_kubernetes.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_config_packages.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_config_settings.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_config_value.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_configuration.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_connect_method.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_connection-class.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_connection.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_connection_find.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_context_config.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_dataframe.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_dependency.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_dependency_fallback.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_get_java.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_home_dir.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_home_set.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_insert_table.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_jobj-class.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_load_table.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_log.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_pipeline_stage.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_avro.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_binary.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_csv.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_delta.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_image.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_jdbc.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_json.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_libsvm.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_orc.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_parquet.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_source.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_table.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_read_text.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_save_table.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_version.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_version_from_home.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_web.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_avro.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_csv.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_delta.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_jdbc.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_json.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_orc.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_parquet.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_rds.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_source.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_table.Rd | 2 sparklyr-1.9.6/sparklyr/man/spark_write_text.Rd | 2 sparklyr-1.9.6/sparklyr/man/sparklyr_get_backend_port.Rd | 2 sparklyr-1.9.6/sparklyr/man/sql-transformer.Rd | 3 sparklyr-1.9.6/sparklyr/man/src_databases.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_find.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_generate_test.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_id.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_lag.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_name.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_render.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_stats.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_stop.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_trigger_continuous.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_trigger_interval.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_view.Rd | 2 sparklyr-1.9.6/sparklyr/man/stream_watermark.Rd | 2 sparklyr-1.9.6/sparklyr/man/tbl_cache.Rd | 2 sparklyr-1.9.6/sparklyr/man/tbl_change_db.Rd | 2 sparklyr-1.9.6/sparklyr/man/tbl_uncache.Rd | 2 sparklyr-1.9.6/sparklyr/man/unite.Rd | 2 sparklyr-1.9.6/sparklyr/man/unnest.Rd | 2 514 files changed, 7278 insertions(+), 2680 deletions(-)
Title: Lightweight Framework for Orchestrating Multi-Agent Large
Language Models
Description: Provides tools for creating agents with persistent state using
R6 classes <https://cran.r-project.org/package=R6> and the 'ellmer'
package <https://cran.r-project.org/package=ellmer>. Tracks prompts,
messages, and agent metadata for reproducible, multi-turn large language
model sessions.
Author: Mohamed El Fodil Ihaddaden [aut, cre]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between mini007 versions 0.4.0 dated 2026-05-27 and 0.5.0 dated 2026-10-05
DESCRIPTION | 10 MD5 | 26 + NAMESPACE | 4 NEWS.md | 93 ++++++ R/Agent.R | 87 ++++-- R/LeadAgent.R | 270 ++++++++++++++++--- R/Workflow.R | 568 +++++++++++++++++++++++++++++++++++----- R/pending.R |only man/LeadAgent.Rd | 120 ++++++++ man/Workflow.Rd | 152 ++++++++++ man/WorkflowAgent.Rd | 8 man/is_pending.Rd |only man/mini007_pending.Rd |only tests/testthat/test-agent.R | 66 ++++ tests/testthat/test-leadagent.R |only tests/testthat/test-workflow.R | 426 ++++++++++++++++++++++++++++++ 16 files changed, 1685 insertions(+), 145 deletions(-)
Title: Functions Related to ICES Advice
Description: A collection of functions that facilitate computational steps
related to advice for fisheries management, according to ICES guidelines.
These include methods for calculating reference points and model diagnostics.
Author: Arni Magnusson [aut],
Colin Millar [aut, cre],
Anne Cooper [aut],
Ruben Verkempynck [ctb],
Raphael Girardin [ctb]
Maintainer: Colin Millar <colin.millar@ices.dk>
Diff between icesAdvice versions 2.1.1 dated 2022-02-18 and 2.1.2 dated 2026-10-05
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 4 ++++ R/Bpa.R | 7 ++++--- R/DLS3.2.R | 9 +++++---- R/Fpa.R | 7 ++++--- R/icesAdvice-package.R | 4 +--- R/icesRound.R | 7 ++++--- R/mohn.R | 30 ++++++++++++++++++------------ R/shake.R | 7 ++++--- build/partial.rdb |binary man/Bpa.Rd | 7 ++++--- man/DLS3.2.Rd | 9 +++++---- man/Fpa.Rd | 7 ++++--- man/icesAdvice-package.Rd | 9 +++++++++ man/icesRound.Rd | 7 ++++--- man/mohn.Rd | 30 ++++++++++++++++++------------ man/shake.Rd | 7 ++++--- 18 files changed, 113 insertions(+), 80 deletions(-)
Title: Interface to 'TA-Lib' for Technical Analysis and Candlestick
Patterns
Description: Interface to the 'TA-Lib' (Technical Analysis Library) 'C'
library, providing access to 150+ indicators (e.g. Average Directional
Movement Index (ADX), Moving Average Convergence Divergence (MACD),
Relative Strength Index (RSI), Stochastic Oscillator, Bollinger Bands),
candlestick pattern recognition, and rolling-window utilities. Core
computations are implemented in 'C' for fast Open-High-Low-Close-Volume
(OHLCV) time-series feature engineering and rule-based signal
generation, with optional interactive visualization via 'plotly'.
Author: Serkan Korkmaz [cre, aut, cph] ,
Mario Fortier [cph] )
Maintainer: Serkan Korkmaz <serkor1@duck.com>
Diff between talib versions 0.9-3 dated 2026-09-27 and 0.9-4 dated 2026-10-05
talib-0.9-3/talib/src/ta-lib/aclocal.m4 |only talib-0.9-3/talib/src/ta-lib/ar-lib |only talib-0.9-3/talib/src/ta-lib/compile |only talib-0.9-3/talib/src/ta-lib/config.guess |only talib-0.9-3/talib/src/ta-lib/config.log |only talib-0.9-3/talib/src/ta-lib/config.status |only talib-0.9-3/talib/src/ta-lib/config.sub |only talib-0.9-3/talib/src/ta-lib/configure |only talib-0.9-3/talib/src/ta-lib/depcomp |only talib-0.9-3/talib/src/ta-lib/include/stamp-h1 |only talib-0.9-3/talib/src/ta-lib/include/ta_config.h.in |only talib-0.9-3/talib/src/ta-lib/install-sh |only talib-0.9-3/talib/src/ta-lib/libtool |only talib-0.9-3/talib/src/ta-lib/ltmain.sh |only talib-0.9-3/talib/src/ta-lib/missing |only talib-0.9-3/talib/src/ta-lib/ta-lib.dpkg |only talib-0.9-3/talib/src/ta-lib/ta-lib.pc |only talib-0.9-3/talib/src/ta-lib/ta-lib.spec |only talib-0.9-4/talib/DESCRIPTION | 6 - talib-0.9-4/talib/MD5 | 39 ++------ talib-0.9-4/talib/NEWS.md | 7 + talib-0.9-4/talib/R/zzz.R | 2 talib-0.9-4/talib/inst/doc/candlestick.html | 8 - talib-0.9-4/talib/inst/doc/charting.html | 92 ++++++++++---------- talib-0.9-4/talib/inst/doc/talib.html | 6 - talib-0.9-4/talib/src/TA-Lib.c | 1 talib-0.9-4/talib/src/data-frame.c | 1 talib-0.9-4/talib/src/init.c | 19 ---- talib-0.9-4/talib/src/routines.h |only talib-0.9-4/talib/src/volume.c | 1 30 files changed, 81 insertions(+), 101 deletions(-)
Title: Automated Item Removal Strategies for Exploratory Factor
Analysis
Description: Identifies candidate item sets through threshold-driven iterative
removal searches in exploratory factor analysis. Provides a no-removal
baseline, numerical diagnostics, factor reliability, holdout evaluation,
and bootstrap search stability to support transparent screening and
documented content review rather than automatic measurement decisions.
The loading criteria are
based on best practices and established heuristics (e.g., Costello &
Osborne (2005) <doi:10.7275/jyj1-4868>, Howard (2016)
<doi:10.1080/10447318.2015.1087664>). Includes flexible thresholds for
factor loadings (min_loading) and cross-loading differences (loading_diff).
Author: Ahmet Caliskan [aut, cre],
Abdullah Faruk Kilic [aut]
Maintainer: Ahmet Caliskan <ahmetcaliskan1987@gmail.com>
Diff between ItemRest versions 0.2.5 dated 2026-04-14 and 1.0.0 dated 2026-10-05
ItemRest-0.2.5/ItemRest/man/get_combinations.Rd |only ItemRest-0.2.5/ItemRest/man/sort_item_ids.Rd |only ItemRest-1.0.0/ItemRest/DESCRIPTION | 23 ItemRest-1.0.0/ItemRest/MD5 | 58 ItemRest-1.0.0/ItemRest/NAMESPACE | 14 ItemRest-1.0.0/ItemRest/NEWS.md | 70 ItemRest-1.0.0/ItemRest/R/ItemRest-package.R | 3 ItemRest-1.0.0/ItemRest/R/bootstrap.R |only ItemRest-1.0.0/ItemRest/R/efa_diagnostics.R |only ItemRest-1.0.0/ItemRest/R/input_helpers.R |only ItemRest-1.0.0/ItemRest/R/itemrest_core.R | 776 +++---- ItemRest-1.0.0/ItemRest/R/validation.R |only ItemRest-1.0.0/ItemRest/README.md | 225 +- ItemRest-1.0.0/ItemRest/build/vignette.rds |binary ItemRest-1.0.0/ItemRest/inst/doc/ItemRest_Demonstration.R | 98 ItemRest-1.0.0/ItemRest/inst/doc/ItemRest_Demonstration.Rmd | 234 +- ItemRest-1.0.0/ItemRest/inst/doc/ItemRest_Demonstration.html | 1197 ++++++----- ItemRest-1.0.0/ItemRest/inst/examples |only ItemRest-1.0.0/ItemRest/man/cor_matrix_custom.Rd | 9 ItemRest-1.0.0/ItemRest/man/descriptive_stats.Rd | 4 ItemRest-1.0.0/ItemRest/man/determine_n_factors.Rd | 12 ItemRest-1.0.0/ItemRest/man/efa_custom.Rd | 12 ItemRest-1.0.0/ItemRest/man/howard.Rd | 4 ItemRest-1.0.0/ItemRest/man/identify_problem_items.Rd | 4 ItemRest-1.0.0/ItemRest/man/itemrest.Rd | 165 + ItemRest-1.0.0/ItemRest/man/itemrest_bootstrap.Rd |only ItemRest-1.0.0/ItemRest/man/itemrest_split.Rd |only ItemRest-1.0.0/ItemRest/man/itemrest_validate.Rd |only ItemRest-1.0.0/ItemRest/man/print.itemrest_result.Rd | 30 ItemRest-1.0.0/ItemRest/man/test_removals.Rd | 12 ItemRest-1.0.0/ItemRest/tests |only ItemRest-1.0.0/ItemRest/vignettes/ItemRest_Demonstration.Rmd | 234 +- 32 files changed, 1874 insertions(+), 1310 deletions(-)
Title: High Dimensional Bayesian Omnibus Sampler
Description: Enables high dimensional statistical modeling using Bayesian
inference and provides a probabilistic programming language for high
dimensional problems. See Kleinsasser (2026)
<doi:10.5281/zenodo.22309216>.
Author: Mike Kleinsasser [aut, cre]
Maintainer: Mike Kleinsasser <mjkleinsa@gmail.com>
Diff between hobbs versions 0.4.4 dated 2026-09-30 and 0.4.5 dated 2026-10-05
hobbs-0.4.4/hobbs/man/hobbs_check_toolchain.Rd |only hobbs-0.4.4/hobbs/man/hobbs_install_sampler.Rd |only hobbs-0.4.5/hobbs/DESCRIPTION | 6 hobbs-0.4.5/hobbs/MD5 | 23 - hobbs-0.4.5/hobbs/NAMESPACE | 2 hobbs-0.4.5/hobbs/R/hobbs.R | 270 ++++---------- hobbs-0.4.5/hobbs/README.md | 10 hobbs-0.4.5/hobbs/inst/hobbs/Cargo.lock | 2 hobbs-0.4.5/hobbs/inst/hobbs/Cargo.toml | 2 hobbs-0.4.5/hobbs/man/hobbs.Rd | 16 hobbs-0.4.5/hobbs/man/hobbs_build_sampler.Rd | 5 hobbs-0.4.5/hobbs/man/hobbs_check_sampler.Rd | 9 hobbs-0.4.5/hobbs/tests/testthat/helper-distributions.R | 3 hobbs-0.4.5/hobbs/tests/testthat/test-installed-sampler.R |only 14 files changed, 130 insertions(+), 218 deletions(-)
Title: Bootstrap-Based Methods for the Study of Fish Stocks and Aquatic
Populations
Description: A suite of bootstrap-based models and tools for analyzing fish
stocks and aquatic populations. Designed for ecologists and fisheries
scientists, it supports data from length-frequency distributions,
tag-and-recapture studies, and hard structure readings (e.g., otoliths). See
Schwamborn et al., 2019 <doi:10.1016/j.ecolmodel.2018.12.001> for background.
The package includes functions for bootstrapped fitting of growth curves and
plotting.
Author: Ralf Schwamborn [aut] ,
Tobias K. Mildenberger [aut],
Marc H. Taylor [aut],
Margit Wilhelm [aut] ,
Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between fishboot versions 1.0.3 dated 2026-09-28 and 1.0.4 dated 2026-10-05
DESCRIPTION | 17 ++++--- MD5 | 27 ++++++------ NAMESPACE | 6 ++ NEWS.md |only R/ELEFAN_GA_boot.R | 2 R/ELEFAN_SA_boot.R | 4 - R/LinfK_scatterhist.R | 12 +++-- R/fishboot-package.R | 42 ++++++++++-------- R/grolenage_boot.R | 12 ++++- R/grotag_boot.R | 112 ++++++++++++++++++++++++++++---------------------- R/vbgfCI_time.R | 20 +++++--- man/ELEFAN_GA_boot.Rd | 2 man/ELEFAN_SA_boot.Rd | 2 man/grolenage_boot.Rd | 2 man/grotag_boot.Rd | 48 ++++++++++++--------- 15 files changed, 177 insertions(+), 131 deletions(-)
Title: Weighted Meta-Analysis with Pseudo-Populations
Description: Implementation of integrative weighting approaches for multiple observational studies and causal inferences. The package features three weighting approaches, each representing a special case of the unified weighting framework, introduced by Guha and Li (2024) <doi:10.1093/biomtc/ujae070>, which includes an extension of inverse probability weights for data integration settings.
Author: Subharup Guha [aut, cre],
Mengqi Xu [aut],
Chayce Reed [aut],
Kashish Priyam [aut],
Yi Li [aut]
Maintainer: Subharup Guha <Subharup.Guha@dartmouth.edu>
Diff between WMAP versions 1.3.1 dated 2026-06-09 and 1.3.2 dated 2026-10-05
DESCRIPTION | 9 ++-- MD5 | 29 ++++++++------ R/other-functions.R | 80 ++++++++++++++++++++++++++++++++++++----- R/stage-1-functions.R | 10 ++++- R/stage-1.R | 13 +++++- R/stage-2-functions.R | 34 +++++++++++++---- inst/doc/WMAP.Rmd | 2 + inst/doc/WMAP.html | 39 ++++++++++--------- man/balancing.weights.Rd | 9 ++++ man/checkSample.Rd | 4 +- man/fn.Estimate_mgPS.Rd | 5 ++ man/fn.RF_ZFirst.Rd | 11 ++++- man/fn.Weights.Rd | 8 +++- man/fn.folds_by_observation.Rd |only tests |only vignettes/WMAP.Rmd | 2 + 16 files changed, 193 insertions(+), 62 deletions(-)
Title: Tidy Finance Helper Functions
Description: Helper functions for empirical research in financial
economics, addressing a variety of topics covered in Scheuch, Voigt,
and Weiss (2023) <doi:10.1201/b23237>. The package is designed to
provide shortcuts for issues extensively discussed in the book,
facilitating easier application of its concepts. For more information
and resources related to the book, visit
<https://www.tidy-finance.org/index.html>.
Author: Christoph Scheuch [aut, cre, cph] ,
Stefan Voigt [aut, cph] ,
Patrick Weiss [aut, cph] ,
Maximilian Muecke [ctb]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between tidyfinance versions 0.8.0 dated 2026-07-02 and 0.9.0 dated 2026-10-05
DESCRIPTION | 8 MD5 | 178 ++++----- NAMESPACE | 51 +- NEWS.md | 94 ++++ R/download_data.R | 52 ++ R/download_data_constituents.R | 386 +++++++++++-------- R/download_data_factors.R | 21 - R/download_data_fred.R | 446 +++++++++++++++++++++++ R/download_data_huggingface.R | 262 ++++++------- R/download_data_macro_predictors.R | 11 R/download_data_pastor_stambaugh.R | 6 R/download_data_stambaugh_yuan.R | 5 R/download_data_stock_prices.R | 39 +- R/download_data_wrds.R | 11 R/download_data_wrds_compustat.R | 11 R/download_data_wrds_crsp.R | 11 R/estimate_fama_macbeth.R | 11 R/list_supported_datasets.R | 6 R/list_supported_indexes.R | 133 +++--- README.md | 112 +++-- build/partial.rdb |binary build/vignette.rds |binary man/add_lagged_columns.Rd | 6 man/assign_portfolio.Rd | 20 - man/breakpoint_options.Rd | 20 - man/compute_breakpoints.Rd | 20 - man/compute_long_short_returns.Rd | 20 - man/compute_portfolio_returns.Rd | 20 - man/compute_rolling_value.Rd | 6 man/create_summary_statistics.Rd | 32 - man/data_options.Rd | 20 - man/disconnect_connection.Rd | 18 man/download_data.Rd | 36 + man/download_data_constituents.Rd | 47 +- man/download_data_factors_ff.Rd | 31 - man/download_data_factors_q.Rd | 31 - man/download_data_fred.Rd | 31 - man/download_data_fred_md.Rd |only man/download_data_huggingface.Rd | 72 ++- man/download_data_jkp.Rd | 31 - man/download_data_macro_predictors.Rd | 31 - man/download_data_osap.Rd | 31 - man/download_data_pastor_stambaugh.Rd | 37 + man/download_data_pseudo_ccm_links.Rd | 6 man/download_data_pseudo_compustat.Rd | 6 man/download_data_pseudo_crsp.Rd | 6 man/download_data_risk_free.Rd | 31 - man/download_data_stambaugh_yuan.Rd | 36 - man/download_data_stock_prices.Rd | 36 + man/download_data_wrds.Rd | 18 man/download_data_wrds_ccm_links.Rd | 18 man/download_data_wrds_compustat.Rd | 18 man/download_data_wrds_crsp.Rd | 18 man/download_data_wrds_fisd.Rd | 18 man/download_data_wrds_trace_enhanced.Rd | 18 man/download_factor_library_grid.Rd | 42 +- man/download_factor_library_ids.Rd | 53 +- man/estimate_betas.Rd | 8 man/estimate_fama_macbeth.Rd | 14 man/estimate_model.Rd | 6 man/filter_options.Rd | 20 - man/filter_sorting_data.Rd | 20 - man/get_available_huggingface_files.Rd | 32 - man/get_wrds_connection.Rd | 18 man/implement_portfolio_sort.Rd | 20 - man/join_lagged_values.Rd | 6 man/list_supported_datasets.Rd | 32 - man/list_supported_datasets_ff.Rd | 32 - man/list_supported_datasets_ff_legacy.Rd | 32 - man/list_supported_datasets_macro_predictors.Rd | 32 - man/list_supported_datasets_other.Rd | 32 - man/list_supported_datasets_pseudo.Rd | 32 - man/list_supported_datasets_wrds.Rd | 32 - man/list_supported_indexes.Rd | 39 +- man/list_supported_jkp_factors.Rd | 32 - man/list_tidy_finance_chapters.Rd | 32 - man/open_tidy_finance_website.Rd | 32 - man/portfolio_sort_options.Rd | 20 - man/set_wrds_credentials.Rd | 18 man/tidyfinance-package.Rd | 1 man/trim.Rd | 32 - man/validate_dates.Rd | 32 - man/winsorize.Rd | 32 - tests/testthat/_snaps/list_supported_datasets.md | 30 - tests/testthat/_snaps/list_supported_indexes.md | 24 - tests/testthat/test-download_data_constituents.R | 152 +++++++ tests/testthat/test-download_data_factors.R | 27 + tests/testthat/test-download_data_fred_md.R |only tests/testthat/test-download_data_huggingface.R | 273 +++++++++++--- tests/testthat/test-download_data_stock_prices.R | 155 +++++++ tests/testthat/test-estimate_fama_macbeth.R | 62 +++ 91 files changed, 2692 insertions(+), 1407 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 4.0.0 dated 2026-09-13 and 4.0.1 dated 2026-10-05
Rgof-4.0.0/Rgof/R/case_studies.R |only Rgof-4.0.0/Rgof/R/gof_power_adaptive.R |only Rgof-4.0.0/Rgof/man/as.data.frame.Rgof_power_adaptive.Rd |only Rgof-4.0.0/Rgof/man/case_studies.Rd |only Rgof-4.0.0/Rgof/man/gof_power_adaptive.Rd |only Rgof-4.0.0/Rgof/man/print.Rgof_power_adaptive.Rd |only Rgof-4.0.0/Rgof/tests/testthat/test-gof-power-adaptive.R |only Rgof-4.0.1/Rgof/DESCRIPTION | 6 Rgof-4.0.1/Rgof/MD5 | 59 - Rgof-4.0.1/Rgof/NAMESPACE | 6 Rgof-4.0.1/Rgof/NEWS.md | 2 Rgof-4.0.1/Rgof/R/case.studies.R |only Rgof-4.0.1/Rgof/R/chi_power_cont.R | 4 Rgof-4.0.1/Rgof/R/chi_power_disc.R | 4 Rgof-4.0.1/Rgof/R/chi_test_cont.R | 57 + Rgof-4.0.1/Rgof/R/chi_test_disc.R | 29 Rgof-4.0.1/Rgof/R/gof_power.R | 44 Rgof-4.0.1/Rgof/R/gof_test.R | 683 +++++++-------- Rgof-4.0.1/Rgof/R/gof_test_adjusted_pvalue.R | 37 Rgof-4.0.1/Rgof/R/helper_functions.R | 61 + Rgof-4.0.1/Rgof/R/mle.R | 4 Rgof-4.0.1/Rgof/R/plot_power.R | 86 - Rgof-4.0.1/Rgof/R/run.studies.R | 10 Rgof-4.0.1/Rgof/inst/doc/Rgof.html | 252 ++--- Rgof-4.0.1/Rgof/man/case.studies.Rd |only Rgof-4.0.1/Rgof/man/chi_power_cont.Rd | 4 Rgof-4.0.1/Rgof/man/chi_power_disc.Rd | 4 Rgof-4.0.1/Rgof/man/chi_test_cont.Rd | 4 Rgof-4.0.1/Rgof/man/chi_test_disc.Rd | 4 Rgof-4.0.1/Rgof/man/gof_power.Rd | 12 Rgof-4.0.1/Rgof/man/gof_test.Rd | 10 Rgof-4.0.1/Rgof/man/gof_test_adjusted_pvalue.Rd | 10 Rgof-4.0.1/Rgof/man/makemaxProcessor.Rd |only Rgof-4.0.1/Rgof/man/run.studies.Rd | 2 Rgof-4.0.1/Rgof/man/validate_integer_scalar.Rd |only Rgof-4.0.1/Rgof/tests/testthat/test-case-studies.R | 18 36 files changed, 757 insertions(+), 655 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The 'HistData' package provides a collection of small data sets
that are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available, both for
instructional use and for historical research. Some of these present interesting
challenges for graphics or analysis in R.
Author: Michael Friendly [aut, cre] ,
Stephane Dray [aut] ,
Peter Li [aut] ,
David Bellhouse [aut],
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb],
Luiz Droubi [ctb],
James Riley [ctb],
Antoine de Falguerolles [ctb],
Monique Graf [ctb],
Nevill [...truncated...]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 1.1.0 dated 2026-08-30 and 1.1.1 dated 2026-10-05
DESCRIPTION | 10 - MD5 | 39 +++--- NEWS.md | 9 + R/Handwashing.R |only R/HistData-package.R | 14 +- R/Perozzo.R | 41 ++++-- R/data-concepts.R | 133 +++++++++------------ data/Handwashing.clinics.RData |only data/Handwashing.hospital.RData |only data/Handwashing.monthly.RData |only inst/doc/HistData-Challenge.Rmd | 2 inst/doc/HistData-Challenge.html | 7 - inst/doc/Snow_deaths-duplicates.html | 4 man/Breslau.Rd | 4 man/GaltonFamilies.Rd | 6 man/Handwashing.Rd |only man/HistData-package.Rd | 14 +- man/Mayer.Rd | 14 +- man/Minard.Rd | 4 man/Nightingale.Rd | 84 +++++-------- man/PearsonLee.Rd | 17 -- man/Perozzo.Rd | 219 ++++++++++++++++++----------------- vignettes/HistData-Challenge.Rmd | 2 23 files changed, 317 insertions(+), 306 deletions(-)
Title: Interface to the 'Hawkin Dynamics' Force Platform API
Description: Provides a secure and configurable interface to the 'Hawkin Dynamics' API for accessing athlete performance data, tests, and metadata.
The package supports profile-based authentication with secure credential storage via the operating system keychain, automatic access token refresh, and region-aware API routing.
Designed for reproducible analysis, data synchronization workflows, and production deployment.
Author: Lauren Green [aut, cre]
Maintainer: Lauren Green <lauren@hawkindynamics.com>
Diff between hawkinR versions 2.0.1 dated 2026-07-21 and 2.2.0 dated 2026-10-05
DESCRIPTION | 16 - MD5 | 40 +-- NAMESPACE | 1 NEWS.md | 32 ++ R/auth_system.R | 2 R/create_athletes.R | 38 +++ R/get_athletes.R | 2 R/get_cop.R | 2 R/get_forcetime.R | 2 R/get_groups.R | 2 R/get_tags.R | 2 R/get_teams.R | 2 R/get_tests.R | 110 ++++++++- R/update_athletes.R | 52 ++++ R/utils.R | 419 +++++++++++++++++++++++++++++++++---- README.md | 97 ++------ man/create_athletes.Rd | 37 +++ man/get_tests.Rd | 35 ++- man/update_athletes.Rd | 48 +++- tests/testthat/test-athlete_json.R | 400 +++++++++++++++++++++++++++++++++++ tests/testthat/test-get_tests.R | 232 ++++++++++++++++++++ 21 files changed, 1396 insertions(+), 175 deletions(-)
Title: Data Mining and R Programming for Beginners
Description: Contains functions to simplify the use of data mining methods (classification, regression, clustering, etc.), for students and beginners in R programming. Various R packages are used and wrappers are built around the main functions, to standardize the use of data mining methods (input/output): it brings a certain loss of flexibility, but also a gain of simplicity. The package name came from the French "Fouille de Données en Master 2 Informatique Décisionnelle".
Author: Alexandre Blansche [aut, cre]
Maintainer: Alexandre Blansche <alexandre.blansche@univ-lorraine.fr>
Diff between fdm2id versions 1.0.1 dated 2026-09-04 and 1.0.2 dated 2026-10-05
DESCRIPTION | 6 MD5 | 145 ++++++++++++----- NAMESPACE | 10 + NEWS.md | 77 +++++++++ R/classification.R | 61 +++++-- R/clustering.R | 162 +++++++++++++++----- R/factorial.R | 19 +- R/feature.R | 16 + R/imports.R | 2 R/misc.R | 136 ++++++++++++++++ R/regression.R | 111 +++++++++++-- R/text.R | 4 R/visualization.R | 71 ++++---- inst/doc/v01-pca-breast-tumours.html | 8 inst/doc/v02-discriminant-analysis-spine.html | 8 inst/doc/v03-linear-regression-hill-races.Rmd | 4 inst/doc/v03-linear-regression-hill-races.html | 14 - inst/doc/v04-clustering-wheat-varieties.html | 8 inst/doc/v05-visualisation-cars.html | 16 - inst/doc/v06-ensemble-methods-ionosphere.Rmd | 8 inst/doc/v06-ensemble-methods-ionosphere.html | 8 inst/doc/v07-clustering-earthquakes.Rmd | 24 +- inst/doc/v07-clustering-earthquakes.html | 24 +- inst/doc/v08-feature-selection-crabs.Rmd | 4 inst/doc/v08-feature-selection-crabs.html | 4 man/ADABOOST.Rd | 8 man/BAGGING.Rd | 8 man/LINREG.Rd | 6 man/boxclus.Rd | 7 man/model-methods.Rd |only man/performance.Rd | 14 + man/plot.cda.Rd | 2 man/plot.factorial.Rd | 8 man/plot.hca.Rd |only man/plot.selection.Rd | 7 man/plotdata.Rd | 21 +- man/resplot.Rd | 28 ++- man/scatterplot.Rd | 8 man/treeplot.Rd | 13 + tests/testthat/test-classification.R | 17 ++ tests/testthat/test-clustering.R | 43 +++++ tests/testthat/test-feature.R | 9 + tests/testthat/test-misc.R | 34 ++++ tests/testthat/test-regression.R | 26 +++ tests/testthat/test-visualization.R | 10 + vignettes/fig |only vignettes/v01-pca-breast-tumours.Rmd.orig |only vignettes/v02-discriminant-analysis-spine.Rmd.orig |only vignettes/v03-linear-regression-hill-races.Rmd | 4 vignettes/v03-linear-regression-hill-races.Rmd.orig |only vignettes/v04-clustering-wheat-varieties.Rmd.orig |only vignettes/v05-visualisation-cars.Rmd.orig |only vignettes/v06-ensemble-methods-ionosphere.Rmd | 8 vignettes/v06-ensemble-methods-ionosphere.Rmd.orig |only vignettes/v07-clustering-earthquakes.Rmd | 24 +- vignettes/v07-clustering-earthquakes.Rmd.orig |only vignettes/v08-feature-selection-crabs.Rmd | 4 vignettes/v08-feature-selection-crabs.Rmd.orig |only 58 files changed, 986 insertions(+), 273 deletions(-)
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration
Description: Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome-wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes four input sources: sequence strings, a FASTA file, an installed 'BSgenome' package named by string, or a 'GRanges' carrying sequences. A 'regions' argument selects what to cover and 'window' and 'slide' set the resolution at which it is tiled. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC-content formulas (Marmur, 1962; Schildkraut, 1965; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest-neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1997, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugim [...truncated...]
Author: Junhui Li [cre, aut] ,
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between TmCalculator versions 1.1.1 dated 2026-09-21 and 1.1.2 dated 2026-10-05
DESCRIPTION | 10 MD5 | 71 +-- NEWS.md | 395 +++++++++++++++++++ R/chem_correct.R | 18 R/coor_to_genomic_ranges.R | 6 R/generate_complement.R | 45 +- R/salt_correction.R | 140 ++++-- R/sysdata.rda |binary R/thermodynamic_nn_params.R | 45 +- R/tm_calculate.R | 106 ++++- R/tm_gc.R | 129 ++++-- R/tm_nn.R | 532 ++++++++++++++++++-------- R/tm_source.R | 11 R/tm_wallace.R | 11 R/to_genomic_ranges.R | 106 +++++ R/zzz.R | 85 ++-- README.md | 14 data/thermodynamic_nn_params.RData |binary inst/doc/genome_wide_tm_ecoli.html | 44 +- inst/doc/hg38_performance_parallel.html | 6 inst/doc/window_size_sensitivity.html | 116 ++--- inst/extdata/nn_params_provenance_v1.1.1.md | 37 - inst/extdata/terminal_core_reconstruction.tsv |only inst/extdata/terminal_initiation_evidence.md |only inst/extdata/tm_nn_parameter_sources.tsv |only inst/extdata/tm_nn_reference_audit.md |only man/TmCalculator-package.Rd | 2 man/chem_correct.Rd | 18 man/generate_complement.Rd | 25 + man/salt_correct.Rd | 30 + man/thermodynamic_nn_params.Rd | 24 - man/tm_calculate.Rd | 44 +- man/tm_gc.Rd | 49 +- man/tm_nn.Rd | 162 +++++-- man/tm_wallace.Rd | 10 man/to_genomic_ranges.Rd | 22 + src/tm_nn_core.cpp | 137 +++++- tests/testthat/test_regressions_1_1_2.R |only tests/testthat/test_tm_nn_rcpp.R | 28 + 39 files changed, 1909 insertions(+), 569 deletions(-)
Title: Coarse-to-Fine Spatial and Spatio-Temporal Modeling
Description: Provides functions for coarse-to-fine spatial and spatio-temporal modeling, enabling fast prediction, regression, and uncertainty quantification for moderate to large datasets. For methodological details, see Murakami et al. (2026) <doi:10.1111/gean.70034> and related work on generalized linear, downscaling, and dynamic spatio-temporal extensions.
Author: Daisuke Murakami [aut, cre],
Alexis Comber [aut],
Takahiro Yoshida [aut],
Narumasa Tsutsumida [aut],
Chris Brunsdon [aut],
Tomoki Nakaya [aut],
Jose Luis Blanco-Claraco [ctb, cph] ),
Marius Muja [cph] ,
David G. Lowe [cph]
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spCF versions 0.2.1 dated 2026-08-28 and 0.2.2 dated 2026-10-05
DESCRIPTION | 8 - MD5 | 98 +++++++------ NAMESPACE | 10 + NEWS.md |only R/RcppExports.R | 16 +- R/cf_dglm.R | 251 +++++++++++++++++++++++++++-------- R/cf_dglm_hv.R | 51 ++++++- R/cf_downscale.R | 2 R/cf_downscale_hv.R | 2 R/cf_glm.R | 149 +++++++++++++++++---- R/cf_glm_hv.R | 23 +++ R/cf_lm.R | 159 +++++++++++++++++----- R/cf_quantile.R |only R/internal_family.R |only R/internal_prediction_se.R | 267 ++++++++++++++++++++++++++++++++------ R/internal_stage_var.R |only R/internal_utils_dglm.R | 46 +++++- R/internal_utils_ds.R | 8 - R/internal_utils_glm.R | 44 +++++- R/internal_utils_lm.R | 28 +++ R/predict.R |only R/sp_map_core.R | 101 +++++++++++--- R/sp_scalewise.R | 3 README.md |only inst/doc/spCF_dglm.R | 23 +++ inst/doc/spCF_dglm.Rmd | 43 +++++- inst/doc/spCF_dglm.html | 121 ++++++++++++----- inst/doc/spCF_downscale.html | 10 - inst/doc/spCF_glm.R | 10 + inst/doc/spCF_glm.Rmd | 18 ++ inst/doc/spCF_glm.html | 50 +++++-- inst/doc/spCF_lm.R | 9 + inst/doc/spCF_lm.Rmd | 19 ++ inst/doc/spCF_lm.html | 78 ++++++++--- man/cf_dglm.Rd | 131 +++++++++++++----- man/cf_dglm_hv.Rd | 9 - man/cf_downscale.Rd | 2 man/cf_downscale_hv.Rd | 2 man/cf_glm.Rd | 48 +++++- man/cf_glm_hv.Rd | 7 man/cf_lm.Rd | 47 +++++- man/negbin.Rd |only man/spCF-predict.Rd |only src/RcppExports.cpp | 60 +++++++- src/dglm_chunk.cpp | 129 ++++++++++++++++-- src/lwr_chunk_glm_fused.cpp | 99 +++++++++++++- tests/testthat/test-cf_dglm.R | 29 ++++ tests/testthat/test-cf_glm.R | 60 ++++++++ tests/testthat/test-mapping.R | 18 ++ tests/testthat/test-predict.R |only tests/testthat/test-print.R |only tests/testthat/test-quantile.R |only tests/testthat/test-stage_bound.R |only vignettes/spCF_dglm.Rmd | 43 +++++- vignettes/spCF_glm.Rmd | 18 ++ vignettes/spCF_lm.Rmd | 19 ++ 56 files changed, 1965 insertions(+), 403 deletions(-)
More information about rapsimng.decide.sowing at CRAN
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More information about rapsimng.decide.nitrogen at CRAN
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More information about rapsimng.decide.cultivar at CRAN
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Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.8.10 dated 2026-06-17 and 0.9.0 dated 2026-10-05
DESCRIPTION | 37 ++++++------ MD5 | 56 ++++++++++-------- NAMESPACE | 24 +++++--- NEWS.md | 10 +++ R/client.R | 16 ++++- R/config.R | 48 +++++++++++++++- R/credential_providers.R | 1 R/custom_checksum.R |only R/custom_s3.R | 92 +++++++++++++++++++++++++----- R/handlers_query.R | 4 + R/jsonutil.R | 11 ++- R/request.R | 25 +++++++- R/service.R | 7 ++ R/service_parameter_helper.R | 76 +++++++++++++++++-------- R/signer_bearer.R | 2 R/signer_v1.R | 7 -- R/signer_v4.R | 23 +++++-- build |only inst |only man/new_operation.Rd | 5 + man/set_service_parameter.Rd | 5 + src/url_parse.cpp | 84 +++++++++++++--------------- tests/testthat/test_client.R | 41 +++++++++++++ tests/testthat/test_config.R | 102 +++++++++++++++++++++++++++++++++- tests/testthat/test_custom_checksum.R |only tests/testthat/test_custom_s3.R | 50 ++++++++++++++++ tests/testthat/test_request.R | 28 +++++++++ tests/testthat/test_signer_query.R | 49 ++++++++++++++++ tests/testthat/test_signer_v4.R | 36 ++++++++++++ tests/testthat/test_url.R | 17 +++++ vignettes |only 31 files changed, 690 insertions(+), 166 deletions(-)
Title: Many Marks, Measures, Memberships, and Motifs for Networks
Description: Many tools for calculating network, node, or tie
marks, measures, motifs and memberships of many different types of networks.
Marks identify structural positions, measures quantify network properties,
memberships classify nodes into groups, and motifs tabulate substructure participation.
All functions operate with all classes of network data covered in 'manynet',
and on directed, undirected, multiplex, multimodal, signed, and other networks.
Author: James Hollway [cre, aut, ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between netrics versions 1.0.3 dated 2026-09-09 and 1.1.0 dated 2026-10-05
netrics-1.0.3/netrics/man/member_community_non.Rd |only netrics-1.1.0/netrics/DESCRIPTION | 8 netrics-1.1.0/netrics/MD5 | 239 +++--- netrics-1.1.0/netrics/NAMESPACE | 7 netrics-1.1.0/netrics/NEWS.md | 104 ++ netrics-1.1.0/netrics/R/class_metrics.R | 60 + netrics-1.1.0/netrics/R/mark_nodes.R | 24 netrics-1.1.0/netrics/R/mark_ties.R | 90 ++ netrics-1.1.0/netrics/R/measure_centrality_between.R | 118 ++- netrics-1.1.0/netrics/R/measure_centrality_closeness.R | 67 + netrics-1.1.0/netrics/R/measure_centrality_degree.R | 19 netrics-1.1.0/netrics/R/measure_centrality_eigen.R | 57 + netrics-1.1.0/netrics/R/measure_change.R | 70 + netrics-1.1.0/netrics/R/measure_closure.R | 165 ++++ netrics-1.1.0/netrics/R/measure_cohesion.R | 56 + netrics-1.1.0/netrics/R/measure_diffusion.R | 2 netrics-1.1.0/netrics/R/measure_features.R | 300 ++++++++ netrics-1.1.0/netrics/R/measure_heterogeneity.R | 61 + netrics-1.1.0/netrics/R/measure_hierarchy.R | 11 netrics-1.1.0/netrics/R/measure_holes.R | 17 netrics-1.1.0/netrics/R/member_cliques.R | 195 ++++- netrics-1.1.0/netrics/R/member_community.R | 292 +++++++- netrics-1.1.0/netrics/R/member_components.R | 1 netrics-1.1.0/netrics/R/member_core.R | 11 netrics-1.1.0/netrics/R/member_equivalence.R | 159 ++-- netrics-1.1.0/netrics/R/member_ties.R |only netrics-1.1.0/netrics/R/method_cluster.R | 113 ++- netrics-1.1.0/netrics/R/method_coreness.R | 2 netrics-1.1.0/netrics/R/method_regularity.R | 7 netrics-1.1.0/netrics/R/method_search.R |only netrics-1.1.0/netrics/R/motif_brokerage.R | 11 netrics-1.1.0/netrics/R/motif_census.R | 36 netrics-1.1.0/netrics/R/motif_cliques.R | 71 + netrics-1.1.0/netrics/R/motif_composition.R | 127 ++- netrics-1.1.0/netrics/R/netrics-utils.R | 191 +++-- netrics-1.1.0/netrics/inst/tutorials/netrics1/centrality.Rmd | 9 netrics-1.1.0/netrics/inst/tutorials/netrics3/position.Rmd | 86 +- netrics-1.1.0/netrics/inst/tutorials/netrics3/position.html | 361 +++++----- netrics-1.1.0/netrics/man/mark_core.Rd | 33 netrics-1.1.0/netrics/man/mark_degree.Rd | 33 netrics-1.1.0/netrics/man/mark_diff.Rd | 33 netrics-1.1.0/netrics/man/mark_dyads.Rd | 53 + netrics-1.1.0/netrics/man/mark_nodes.Rd | 33 netrics-1.1.0/netrics/man/mark_select_node.Rd | 6 netrics-1.1.0/netrics/man/mark_select_tie.Rd | 5 netrics-1.1.0/netrics/man/mark_ties.Rd | 32 netrics-1.1.0/netrics/man/mark_triangles.Rd | 32 netrics-1.1.0/netrics/man/measure_assort_net.Rd | 27 netrics-1.1.0/netrics/man/measure_assort_node.Rd | 33 netrics-1.1.0/netrics/man/measure_breadth.Rd | 27 netrics-1.1.0/netrics/man/measure_broker_node.Rd | 33 netrics-1.1.0/netrics/man/measure_broker_tie.Rd | 32 netrics-1.1.0/netrics/man/measure_brokerage.Rd | 31 netrics-1.1.0/netrics/man/measure_central_between.Rd | 83 ++ netrics-1.1.0/netrics/man/measure_central_close.Rd | 36 netrics-1.1.0/netrics/man/measure_central_degree.Rd | 33 netrics-1.1.0/netrics/man/measure_central_eigen.Rd | 33 netrics-1.1.0/netrics/man/measure_central_tie_between.Rd | 32 netrics-1.1.0/netrics/man/measure_central_tie_close.Rd | 32 netrics-1.1.0/netrics/man/measure_central_tie_degree.Rd | 32 netrics-1.1.0/netrics/man/measure_central_tie_eigen.Rd | 32 netrics-1.1.0/netrics/man/measure_centralisation_between.Rd | 29 netrics-1.1.0/netrics/man/measure_centralisation_close.Rd | 29 netrics-1.1.0/netrics/man/measure_centralisation_degree.Rd | 29 netrics-1.1.0/netrics/man/measure_centralisation_eigen.Rd | 31 netrics-1.1.0/netrics/man/measure_closure.Rd | 29 netrics-1.1.0/netrics/man/measure_closure_node.Rd | 133 +++ netrics-1.1.0/netrics/man/measure_cohesion.Rd | 27 netrics-1.1.0/netrics/man/measure_core.Rd | 33 netrics-1.1.0/netrics/man/measure_diffusion_node.Rd | 31 netrics-1.1.0/netrics/man/measure_diverse_net.Rd | 15 netrics-1.1.0/netrics/man/measure_diverse_node.Rd | 36 netrics-1.1.0/netrics/man/measure_features.Rd | 29 netrics-1.1.0/netrics/man/measure_fit.Rd | 161 ++++ netrics-1.1.0/netrics/man/measure_fragmentation.Rd | 54 + netrics-1.1.0/netrics/man/measure_hierarchy.Rd | 27 netrics-1.1.0/netrics/man/member_brokerage.Rd | 36 netrics-1.1.0/netrics/man/member_cliques.Rd | 109 ++- netrics-1.1.0/netrics/man/member_community.Rd | 58 + netrics-1.1.0/netrics/man/member_community_hier.Rd | 54 + netrics-1.1.0/netrics/man/member_community_link.Rd |only netrics-1.1.0/netrics/man/member_community_modular.Rd |only netrics-1.1.0/netrics/man/member_community_partition.Rd |only netrics-1.1.0/netrics/man/member_community_spread.Rd |only netrics-1.1.0/netrics/man/member_components.Rd | 9 netrics-1.1.0/netrics/man/member_core.Rd | 36 netrics-1.1.0/netrics/man/member_diffusion.Rd | 9 netrics-1.1.0/netrics/man/member_equivalence.Rd | 128 ++- netrics-1.1.0/netrics/man/method_cluster.Rd | 80 +- netrics-1.1.0/netrics/man/method_regularity.Rd | 27 netrics-1.1.0/netrics/man/method_search.Rd |only netrics-1.1.0/netrics/man/motif_brokerage_net.Rd | 27 netrics-1.1.0/netrics/man/motif_brokerage_node.Rd | 33 netrics-1.1.0/netrics/man/motif_clique.Rd | 60 + netrics-1.1.0/netrics/man/motif_composition.Rd | 89 ++ netrics-1.1.0/netrics/man/motif_exposure.Rd | 6 netrics-1.1.0/netrics/man/motif_hierarchy.Rd | 27 netrics-1.1.0/netrics/man/motif_homophily.Rd | 27 netrics-1.1.0/netrics/man/motif_net.Rd | 27 netrics-1.1.0/netrics/man/motif_node.Rd | 38 - netrics-1.1.0/netrics/man/motif_path.Rd | 38 - netrics-1.1.0/netrics/man/motif_periods.Rd | 4 netrics-1.1.0/netrics/tests/testthat/Rplots.pdf |binary netrics-1.1.0/netrics/tests/testthat/helper-contract.R | 85 ++ netrics-1.1.0/netrics/tests/testthat/helper-netrics.R | 32 netrics-1.1.0/netrics/tests/testthat/test-mark_ties.R | 2 netrics-1.1.0/netrics/tests/testthat/test-measure_centrality.R | 71 + netrics-1.1.0/netrics/tests/testthat/test-measure_closure.R | 42 + netrics-1.1.0/netrics/tests/testthat/test-measure_closure_contract.R | 5 netrics-1.1.0/netrics/tests/testthat/test-measure_cognitive_contract.R |only netrics-1.1.0/netrics/tests/testthat/test-measure_cohesion.R | 28 netrics-1.1.0/netrics/tests/testthat/test-measure_fit.R | 95 ++ netrics-1.1.0/netrics/tests/testthat/test-measure_heterogeneity.R | 25 netrics-1.1.0/netrics/tests/testthat/test-measure_nodes.R | 2 netrics-1.1.0/netrics/tests/testthat/test-member_cliques.R | 77 ++ netrics-1.1.0/netrics/tests/testthat/test-member_community.R | 50 + netrics-1.1.0/netrics/tests/testthat/test-member_equivalence.R | 82 ++ netrics-1.1.0/netrics/tests/testthat/test-member_nodes.R | 6 netrics-1.1.0/netrics/tests/testthat/test-member_ties.R |only netrics-1.1.0/netrics/tests/testthat/test-method_search.R |only netrics-1.1.0/netrics/tests/testthat/test-model_cluster.R | 39 - netrics-1.1.0/netrics/tests/testthat/test-motif_cliques.R | 31 netrics-1.1.0/netrics/tests/testthat/test-motif_composition.R | 60 + netrics-1.1.0/netrics/tests/testthat/test-motif_net.R | 22 netrics-1.1.0/netrics/tests/testthat/test-motif_nodes.R | 1 netrics-1.1.0/netrics/tests/testthat/test-shapes.R | 136 ++- 126 files changed, 5424 insertions(+), 985 deletions(-)
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 0.1.3 dated 2026-06-20 and 0.2.0 dated 2026-10-05
mintyr-0.1.3/mintyr/inst/doc/get-started.R |only mintyr-0.1.3/mintyr/inst/doc/get-started.Rmd |only mintyr-0.1.3/mintyr/inst/doc/get-started.html |only mintyr-0.1.3/mintyr/vignettes/get-started.Rmd |only mintyr-0.2.0/mintyr/DESCRIPTION | 34 mintyr-0.2.0/mintyr/LICENSE | 4 mintyr-0.2.0/mintyr/MD5 | 141 +- mintyr-0.2.0/mintyr/NAMESPACE | 64 - mintyr-0.2.0/mintyr/NEWS.md | 81 + mintyr-0.2.0/mintyr/R/c2p_nest.R | 234 +--- mintyr-0.2.0/mintyr/R/desc_stats.R |only mintyr-0.2.0/mintyr/R/export_list.R | 225 +--- mintyr-0.2.0/mintyr/R/export_nest.R | 374 ++---- mintyr-0.2.0/mintyr/R/export_xlsx.R | 533 ++++++--- mintyr-0.2.0/mintyr/R/format_digits.R | 145 -- mintyr-0.2.0/mintyr/R/get_path_info.R | 170 +-- mintyr-0.2.0/mintyr/R/import_csv.R | 142 -- mintyr-0.2.0/mintyr/R/import_xlsx.R | 543 ++++++---- mintyr-0.2.0/mintyr/R/mintyr_example.R | 2 mintyr-0.2.0/mintyr/R/mintyr_examples.R | 2 mintyr-0.2.0/mintyr/R/nest_cv.R | 298 +---- mintyr-0.2.0/mintyr/R/r2p_nest.R | 205 ++- mintyr-0.2.0/mintyr/R/resolve_cols.R |only mintyr-0.2.0/mintyr/R/split_cv.R | 308 ++--- mintyr-0.2.0/mintyr/R/top_perc.R | 239 +--- mintyr-0.2.0/mintyr/R/w2l_nest.R | 249 +--- mintyr-0.2.0/mintyr/R/w2l_split.R | 223 +--- mintyr-0.2.0/mintyr/R/zzz.R | 41 mintyr-0.2.0/mintyr/README.md | 164 ++- mintyr-0.2.0/mintyr/build/vignette.rds |binary mintyr-0.2.0/mintyr/inst/doc/cross-validation.R |only mintyr-0.2.0/mintyr/inst/doc/cross-validation.Rmd |only mintyr-0.2.0/mintyr/inst/doc/cross-validation.html |only mintyr-0.2.0/mintyr/inst/doc/descriptive-statistics.R |only mintyr-0.2.0/mintyr/inst/doc/descriptive-statistics.Rmd |only mintyr-0.2.0/mintyr/inst/doc/descriptive-statistics.html |only mintyr-0.2.0/mintyr/inst/doc/import-and-export.R |only mintyr-0.2.0/mintyr/inst/doc/import-and-export.Rmd |only mintyr-0.2.0/mintyr/inst/doc/import-and-export.html |only mintyr-0.2.0/mintyr/inst/doc/mintyr.R |only mintyr-0.2.0/mintyr/inst/doc/mintyr.Rmd |only mintyr-0.2.0/mintyr/inst/doc/mintyr.html |only mintyr-0.2.0/mintyr/inst/doc/reshape-and-nest.R |only mintyr-0.2.0/mintyr/inst/doc/reshape-and-nest.Rmd |only mintyr-0.2.0/mintyr/inst/doc/reshape-and-nest.html |only mintyr-0.2.0/mintyr/inst/doc/utilities.R |only mintyr-0.2.0/mintyr/inst/doc/utilities.Rmd |only mintyr-0.2.0/mintyr/inst/doc/utilities.html |only mintyr-0.2.0/mintyr/inst/extdata/multiheader_test.xlsx |only mintyr-0.2.0/mintyr/man/c2p_nest.Rd | 51 mintyr-0.2.0/mintyr/man/desc_stats.Rd |only mintyr-0.2.0/mintyr/man/export_list.Rd | 68 - mintyr-0.2.0/mintyr/man/export_nest.Rd | 108 + mintyr-0.2.0/mintyr/man/export_xlsx.Rd | 210 ++- mintyr-0.2.0/mintyr/man/figures/cheatsheet.svg | 6 mintyr-0.2.0/mintyr/man/figures/lifecycle-archived.svg | 42 mintyr-0.2.0/mintyr/man/figures/lifecycle-defunct.svg | 42 mintyr-0.2.0/mintyr/man/figures/lifecycle-deprecated.svg | 42 mintyr-0.2.0/mintyr/man/figures/lifecycle-experimental.svg | 42 mintyr-0.2.0/mintyr/man/figures/lifecycle-maturing.svg | 42 mintyr-0.2.0/mintyr/man/figures/lifecycle-questioning.svg | 42 mintyr-0.2.0/mintyr/man/figures/lifecycle-soft-deprecated.svg | 42 mintyr-0.2.0/mintyr/man/figures/lifecycle-stable.svg | 58 - mintyr-0.2.0/mintyr/man/figures/lifecycle-superseded.svg | 42 mintyr-0.2.0/mintyr/man/get_path_info.Rd | 15 mintyr-0.2.0/mintyr/man/import_csv.Rd | 32 mintyr-0.2.0/mintyr/man/import_xlsx.Rd | 152 ++ mintyr-0.2.0/mintyr/man/nest_cv.Rd | 141 +- mintyr-0.2.0/mintyr/man/r2p_nest.Rd | 75 - mintyr-0.2.0/mintyr/man/split_cv.Rd | 165 +-- mintyr-0.2.0/mintyr/man/top_perc.Rd | 41 mintyr-0.2.0/mintyr/man/w2l_nest.Rd | 47 mintyr-0.2.0/mintyr/man/w2l_split.Rd | 45 mintyr-0.2.0/mintyr/tests |only mintyr-0.2.0/mintyr/vignettes/cross-validation.Rmd |only mintyr-0.2.0/mintyr/vignettes/descriptive-statistics.Rmd |only mintyr-0.2.0/mintyr/vignettes/import-and-export.Rmd |only mintyr-0.2.0/mintyr/vignettes/mintyr.Rmd |only mintyr-0.2.0/mintyr/vignettes/reshape-and-nest.Rmd |only mintyr-0.2.0/mintyr/vignettes/utilities.Rmd |only 80 files changed, 3011 insertions(+), 2960 deletions(-)
Title: Unidimensional Item Response Theory Modeling
Description: Fit unidimensional item response theory (IRT) models to test
data, which includes both dichotomous and polytomous items, calibrate
pretest item parameters, estimate examinees' abilities, and examine
the IRT model-data fit on item-level in different ways as well as provide
useful functions related to IRT analyses such as differential item
functioning analysis.
In addition, the package provides a set of classical test theory functions
for computing item- and test-level statistics (e.g., item difficulty, item-total
correlation, and coefficient alpha) and for scoring and analyzing selected-response
item data.
The bring.flexmirt() and write.flexmirt() functions were written by modifying
the read.flexmirt() function (Pritikin & Falk (2020) <doi:10.1177/0146621620929431>).
The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog()
and read.parscale() functions, respectively (Weeks (2010) <doi:10.18637/jss.v035.i12>).
The bisection() function wa [...truncated...]
Author: Hwanggyu Lim [aut, cre],
Craig S. Wells [ctb],
James Howard [ctb],
Joshua Pritikin [ctb],
Jonathan P Weeks [ctb],
Jorge Gonzalez [ctb],
David Magis [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Diff between irtQ versions 1.2.0 dated 2026-07-27 and 1.3.0 dated 2026-10-05
DESCRIPTION | 26 MD5 | 206 ++-- NAMESPACE | 7 NEWS.md | 72 + R/EM.R | 24 R/LSAT6.R | 7 R/SimCAT_DC.R | 23 R/SimCAT_MX.R | 29 R/bring_output.R | 68 - R/cac_lee.R | 6 R/cac_rud.R | 12 R/catsib.R | 27 R/collapse_ftable.R | 5 R/covirt.R | 8 R/crdif.R | 19 R/ctt.R |only R/ctt_alpha.R |only R/ctt_distr.R |only R/ctt_item.R |only R/est_irt.R | 112 +- R/est_item.R | 65 - R/est_mg.R | 115 +- R/est_score.R | 103 +- R/estimation.R | 10 R/expFreq.R | 2 R/find_cut.R | 12 R/freq_score.R |only R/getirt.R | 28 R/gradient.R | 11 R/grdif.R | 9 R/hessian.R | 11 R/info.R | 6 R/info_xpd.R | 23 R/irtQ-package.R | 242 +++-- R/irtfit.R | 1586 +++++++++++++++++------------------ R/loglike_item.R | 10 R/lwrc.R | 12 R/optim_fns.R | 22 R/panel_info.R | 247 ++--- R/pcd2.R | 16 R/plot_irtfit.R | 14 R/posterior.R | 3 R/print.R | 152 +++ R/rdif.R | 31 R/reval_mst.R | 12 R/ripd.R | 26 R/run_flexmirt.R | 2 R/run_mst.R | 59 - R/score_resp.R |only R/shape_df_fipc.R | 12 R/simIPD.R | 12 R/simMG.R | 22 R/simMST.R | 21 R/summary.R | 50 + R/util.R | 11 R/write_flexmirt.R | 3 README.md | 435 ++++----- build/vignette.rds |only inst/doc |only man/LSAT6.Rd | 58 - man/bring.flexmirt.Rd | 327 +++---- man/cac_lee.Rd | 300 +++--- man/cac_rud.Rd | 318 +++---- man/catsib.Rd | 811 +++++++++--------- man/covirt.Rd | 250 ++--- man/crdif.Rd | 832 +++++++++--------- man/ctt.Rd |only man/ctt_alpha.Rd |only man/ctt_distr.Rd |only man/ctt_item.Rd |only man/est_irt.Rd | 1620 ++++++++++++++++++------------------ man/est_item.Rd | 616 ++++++------- man/est_mg.Rd | 1574 +++++++++++++++++----------------- man/est_score.Rd | 772 ++++++++--------- man/figures/README-example-1.png |binary man/find_cut.Rd | 425 ++++----- man/freq_score.Rd |only man/getirt.Rd | 444 +++++---- man/grdif.Rd | 904 ++++++++++---------- man/info.Rd | 330 +++---- man/irtQ-package.Rd | 240 +++-- man/irtfit.Rd | 668 +++++++------- man/lwrc.Rd | 10 man/panel_info.Rd | 141 +-- man/pcd2.Rd | 15 man/plot.find_cut.Rd | 151 +-- man/plot.irtfit.Rd | 424 ++++----- man/print.ctt.Rd |only man/print.summary.ctt.Rd |only man/rdif.Rd | 31 man/reval_mst.Rd | 580 ++++++------ man/ripd.Rd | 995 +++++++++++----------- man/run_flexmirt.Rd | 210 ++-- man/run_mst.Rd | 1000 +++++++++++----------- man/score_resp.Rd |only man/simCAT_DC.Rd | 80 + man/simCAT_MX.Rd | 88 + man/simIPD.Rd | 228 ++--- man/simMG.Rd | 93 +- man/simMST.Rd | 126 +- man/summary.ctt.Rd |only man/write.flexmirt.Rd | 205 ++-- tests/testthat.R | 44 tests/testthat/test-bring_mirt.R |only tests/testthat/test-ctt.R |only tests/testthat/test-ctt_distr.R |only tests/testthat/test-dif.R | 22 tests/testthat/test-est_irt.R | 116 ++ tests/testthat/test-est_item.R | 51 - tests/testthat/test-est_mg.R | 58 + tests/testthat/test-find_cut.R | 454 +++++----- tests/testthat/test-freq_score.R |only tests/testthat/test-score_resp.R |only tests/testthat/test-shape_df_fipc.R |only vignettes |only 115 files changed, 10234 insertions(+), 9423 deletions(-)
Title: Mixed-Effects Models Enhancing Functions
Description: Special functions that enhance other mixed effect model packages by creating overlayed, reduced rank, and reduced model matrices together with multiple data sets to practice the use of these models. For more details see Covarrubias-Pazaran (2016) <doi:10.1371/journal.pone.0156744>.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between enhancer versions 1.1.1 dated 2026-04-12 and 1.1.2 dated 2026-10-05
enhancer-1.1.1/enhancer/man/rrm.Rd |only enhancer-1.1.2/enhancer/DESCRIPTION | 8 ++--- enhancer-1.1.2/enhancer/MD5 | 38 ++++++++++++------------ enhancer-1.1.2/enhancer/NAMESPACE | 2 - enhancer-1.1.2/enhancer/R/AllClass.R | 2 - enhancer-1.1.2/enhancer/man/DT_augment.Rd | 5 +++ enhancer-1.1.2/enhancer/man/DT_big.Rd | 15 +++++++++ enhancer-1.1.2/enhancer/man/DT_btdata.Rd | 5 +++ enhancer-1.1.2/enhancer/man/DT_cornhybrids.Rd | 10 +++--- enhancer-1.1.2/enhancer/man/DT_cpdata.Rd | 17 +++++----- enhancer-1.1.2/enhancer/man/DT_example.Rd | 5 +++ enhancer-1.1.2/enhancer/man/DT_expdesigns.Rd | 5 +++ enhancer-1.1.2/enhancer/man/DT_fulldiallel.Rd | 7 +++- enhancer-1.1.2/enhancer/man/DT_gryphon.Rd | 17 ++++++---- enhancer-1.1.2/enhancer/man/DT_halfdiallel.Rd | 18 +++++++---- enhancer-1.1.2/enhancer/man/DT_polyploid.Rd | 13 +++++--- enhancer-1.1.2/enhancer/man/DT_rice.Rd | 16 ++++------ enhancer-1.1.2/enhancer/man/DT_technow.Rd | 16 ++++++---- enhancer-1.1.2/enhancer/man/DT_wheat.Rd | 11 +++--- enhancer-1.1.2/enhancer/man/enhancer-package.Rd | 2 - enhancer-1.1.2/enhancer/man/rrmat.Rd |only 21 files changed, 135 insertions(+), 77 deletions(-)
Title: Pedigree Validation Genetic Composition of Diploids & Polyploids
Description: Tools for pedigree quality control and genomic breed/line
composition estimation in diploid and polyploid breeding populations.
'BIGpopA' provides functions to check and correct common pedigree
errors, assign parentage from SNP genotype data using Mendelian error
rates, validate parent-offspring trios, and estimate genome-wide
breed or line composition using quadratic programming. Pedigree
validation and parentage assignment support any ploidy, using a
polysomic Mendelian test for even ploidy and a homozygosity-based
check for odd ploidy. Genotypes can be supplied as dosage tables, VCF
files, or 'PLINK' .ped files. For more details about the included
'breedTools' functions, see Funkhouser et al. (2017)
<doi:10.2527/tas2016.0003>.
Author: Josue Chinchilla-Vargas [cre, aut],
Alexander Sandercock [aut],
University of Florida [cph]
Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>
Diff between BIGpopA versions 2.0.0 dated 2026-08-21 and 2.1.0 dated 2026-10-05
BIGpopA-2.0.0/BIGpopA/tests/testthat/Rplots.pdf |only BIGpopA-2.1.0/BIGpopA/DESCRIPTION | 18 - BIGpopA-2.1.0/BIGpopA/MD5 | 49 ++- BIGpopA-2.1.0/BIGpopA/NAMESPACE | 81 +++--- BIGpopA-2.1.0/BIGpopA/NEWS.md | 11 BIGpopA-2.1.0/BIGpopA/R/allele_freq_poly.R | 26 +- BIGpopA-2.1.0/BIGpopA/R/check_ped.R | 3 BIGpopA-2.1.0/BIGpopA/R/find_parentage.R | 18 + BIGpopA-2.1.0/BIGpopA/R/ped_to_dosage.R |only BIGpopA-2.1.0/BIGpopA/R/solve_composition_poly.R | 84 +----- BIGpopA-2.1.0/BIGpopA/R/utils.R | 155 +++++++++++- BIGpopA-2.1.0/BIGpopA/R/validate_pedigree.R | 17 - BIGpopA-2.1.0/BIGpopA/R/vcf_to_dosage.R |only BIGpopA-2.1.0/BIGpopA/README.md | 43 +++ BIGpopA-2.1.0/BIGpopA/inst/CITATION | 2 BIGpopA-2.1.0/BIGpopA/inst/WORDLIST | 17 + BIGpopA-2.1.0/BIGpopA/inst/doc/BIGpopA.Rmd | 8 BIGpopA-2.1.0/BIGpopA/inst/doc/BIGpopA.html | 55 ++-- BIGpopA-2.1.0/BIGpopA/man/allele_freq_poly.Rd | 15 - BIGpopA-2.1.0/BIGpopA/man/find_parentage.Rd | 8 BIGpopA-2.1.0/BIGpopA/man/ped_to_dosage.Rd |only BIGpopA-2.1.0/BIGpopA/man/solve_composition_poly.Rd | 45 +-- BIGpopA-2.1.0/BIGpopA/man/validate_pedigree.Rd | 9 BIGpopA-2.1.0/BIGpopA/man/vcf_to_dosage.Rd |only BIGpopA-2.1.0/BIGpopA/tests/testthat/setup-tempfiles.R |only BIGpopA-2.1.0/BIGpopA/tests/testthat/test-breedtools_poly.R | 72 ----- BIGpopA-2.1.0/BIGpopA/tests/testthat/test-column_names.R |only BIGpopA-2.1.0/BIGpopA/tests/testthat/test-genotype_input.R |only BIGpopA-2.1.0/BIGpopA/tests/testthat/test-vcf_to_dosage.R |only BIGpopA-2.1.0/BIGpopA/vignettes/BIGpopA.Rmd | 8 30 files changed, 467 insertions(+), 277 deletions(-)
More information about AgroMetIndices at CRAN
Permanent link
Title: Model Based Clustering for Spherical Data Using Elliptically
Symmetric Distributions
Description: Model based clustering with spherical data using mixtures of elliptically symmetric distributions, namely mixtures of spherical elliptically symmetric projected Cauchy (SESPC) or mixtures of elliptically symmetric angular Gaussian (ESAG) distributions. The relevant paper is: Perdikis T., Alharbi N. and Tsagris M. (2026). <doi:10.48550/arXiv.2605.27496>.
Author: Michail Tsagris [aut, cre],
Theodoros Perdikis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between sphereclust versions 1.1 dated 2026-09-02 and 1.2 dated 2026-10-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/mixkent.mle.R | 6 +++++- man/sphereclust-package.Rd | 4 ++-- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: 3D Segmentation of Voxels into Morphologic Classes
Description: Automatically segments a 3D array that represents a volume of binary voxels into mutually exclusive morphological elements. This package extends existing work for segmenting 2D binary raster data. A paper documenting this approach has been published in the journal Landscape Ecology: Remmel, T.K. (2022) <doi:10.1007/s10980-021-01384-7>. The output is a cartridge (list object) that maintains the input array, the segmentation results in array format, and a summary table. Plotting functionality is provided to produce interactive visual outputs from the produced results cartridge, allowing custom plotting to be performed separately from the segmentation, which speeds-up processing. While the old functions persist, they are being phased out and will eventually be replaced with the new runmorph3d() and plotmorph3d() functions.
Author: Tarmo K. Remmel [aut, cre]
Maintainer: Tarmo K. Remmel <remmelt@yorku.ca>
Diff between morph versions 1.1.0 dated 2023-02-14 and 2.0.0 dated 2026-10-05
DESCRIPTION | 13 +-- MD5 | 28 +++--- NAMESPACE | 6 - NEWS.md | 23 +++++ R/arraytrim.R | 4 R/morph3d.R | 210 ++++++++++++++++++++++++++++++++------------------- R/morph3dlinks.R | 27 +++--- R/morph3dplot.R | 9 +- R/morph3dprep.R | 5 - R/plotmorph3d.R |only R/runmoprh3d.R |only build/partial.rdb |binary man/morph-package.Rd | 4 man/morph3d.Rd | 5 - man/morph3dplot.Rd | 19 +++- man/plotmorph3d.Rd |only man/runmorph3d.Rd |only 17 files changed, 224 insertions(+), 129 deletions(-)
Title: Reproducible Occurrence-to-Biome Classification Using 31 Global
Biome Schemes
Description: Reproducibly classifies occurrence records into biomes using
31 published global biome schemes compiled by Fischer and colleagues
(2022) <doi:10.1111/geb.13574>, provided as harmonised raster layers at 10x10 km
resolution globally. Includes functions to choose the most suitable biome scheme
for a dataset by a data-driven ranking, to classify occurrence records, and to
tabulate and visualise the result. Works with user-provided occurrences or a
taxon name, in which case occurrences are downloaded from GBIF
(<https://www.gbif.org>) and
cleaned automatically.
Author: Hans Christian Gross [cre, aut],
Jan-Christopher Fischer [aut],
Anna Walentowitz [aut],
Alexander Zizka [aut, fnd]
Maintainer: Hans Christian Gross <grossha@uni-marburg.de>
Diff between biomes versions 0.9.4 dated 2026-08-31 and 0.9.5 dated 2026-10-05
biomes-0.9.4/biomes/data/biomes_example.rda |only biomes-0.9.4/biomes/inst/doc/step1-occurrence-records-and-biome-schemes.R |only biomes-0.9.4/biomes/inst/doc/step1-occurrence-records-and-biome-schemes.Rmd |only biomes-0.9.4/biomes/inst/doc/step1-occurrence-records-and-biome-schemes.html |only biomes-0.9.4/biomes/inst/doc/step2-choosing-a-biome-scheme.R |only biomes-0.9.4/biomes/inst/doc/step2-choosing-a-biome-scheme.Rmd |only biomes-0.9.4/biomes/inst/doc/step2-choosing-a-biome-scheme.html |only biomes-0.9.4/biomes/inst/extdata |only biomes-0.9.4/biomes/man/biomes_example.Rd |only biomes-0.9.4/biomes/vignettes/step1-occurrence-records-and-biome-schemes.Rmd |only biomes-0.9.4/biomes/vignettes/step2-choosing-a-biome-scheme.Rmd |only biomes-0.9.5/biomes/DESCRIPTION | 22 biomes-0.9.5/biomes/MD5 | 84 - biomes-0.9.5/biomes/NEWS.md | 38 biomes-0.9.5/biomes/R/biomes_classify.R | 638 +++++----- biomes-0.9.5/biomes/R/biomes_full.R | 32 biomes-0.9.5/biomes/R/biomes_info.R | 104 - biomes-0.9.5/biomes/R/biomes_rank.R | 301 ++-- biomes-0.9.5/biomes/R/biomes_tab.R | 168 +- biomes-0.9.5/biomes/R/biomes_visualise.R | 535 +++++--- biomes-0.9.5/biomes/R/data.R | 191 +- biomes-0.9.5/biomes/R/internal.R | 78 - biomes-0.9.5/biomes/README.md | 65 - biomes-0.9.5/biomes/build/vignette.rds |binary biomes-0.9.5/biomes/data/biomes_information.rda |binary biomes-0.9.5/biomes/data/bombacoideae_occurrences.rda |only biomes-0.9.5/biomes/inst/CITATION | 20 biomes-0.9.5/biomes/inst/doc/step1-assembly-of-occurrence-records-and-biome-schemes.R |only biomes-0.9.5/biomes/inst/doc/step1-assembly-of-occurrence-records-and-biome-schemes.Rmd |only biomes-0.9.5/biomes/inst/doc/step1-assembly-of-occurrence-records-and-biome-schemes.html |only biomes-0.9.5/biomes/inst/doc/step2-choice-of-a-biome-scheme.R |only biomes-0.9.5/biomes/inst/doc/step2-choice-of-a-biome-scheme.Rmd |only biomes-0.9.5/biomes/inst/doc/step2-choice-of-a-biome-scheme.html |only biomes-0.9.5/biomes/inst/doc/step3-occurrence-to-biome-classification.R | 14 biomes-0.9.5/biomes/inst/doc/step3-occurrence-to-biome-classification.Rmd | 30 biomes-0.9.5/biomes/inst/doc/step3-occurrence-to-biome-classification.html | 48 biomes-0.9.5/biomes/inst/doc/step4-output-and-visualisation.R | 18 biomes-0.9.5/biomes/inst/doc/step4-output-and-visualisation.Rmd | 38 biomes-0.9.5/biomes/inst/doc/step4-output-and-visualisation.html | 48 biomes-0.9.5/biomes/man/biomes_classify.Rd | 10 biomes-0.9.5/biomes/man/biomes_full.Rd | 14 biomes-0.9.5/biomes/man/biomes_globals.Rd | 6 biomes-0.9.5/biomes/man/biomes_info.Rd | 6 biomes-0.9.5/biomes/man/biomes_information.Rd | 22 biomes-0.9.5/biomes/man/biomes_legend.Rd | 12 biomes-0.9.5/biomes/man/biomes_rank.Rd | 127 + biomes-0.9.5/biomes/man/biomes_tab.Rd | 12 biomes-0.9.5/biomes/man/biomes_visualise.Rd | 75 - biomes-0.9.5/biomes/man/bombacoideae_occurrences.Rd |only biomes-0.9.5/biomes/tests/testthat/test-biomes_rank.R |only biomes-0.9.5/biomes/vignettes/step1-assembly-of-occurrence-records-and-biome-schemes.Rmd |only biomes-0.9.5/biomes/vignettes/step2-choice-of-a-biome-scheme.Rmd |only biomes-0.9.5/biomes/vignettes/step3-occurrence-to-biome-classification.Rmd | 30 biomes-0.9.5/biomes/vignettes/step4-output-and-visualisation.Rmd | 38 54 files changed, 1552 insertions(+), 1272 deletions(-)
Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'OpenAI', 'Gemini', 'Mistral', and local models via 'Ollama' into R workflows. The package supports text, image, audio, video, and document interactions; a unified media interface for attaching inline files or uploading to provider file stores; batch request APIs for cost-efficient large-scale processing; and a pipeline-oriented interface for seamless integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://aistudio.google.com/>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre],
Jia Zhang [ctb]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between tidyllm versions 0.6.0 dated 2026-09-08 and 0.7.0 dated 2026-10-05
DESCRIPTION | 25 +- MD5 | 115 +++++----- NAMESPACE | 6 NEWS.md | 203 +++++++++++++++++ R/APIProvider.R | 34 +++ R/api_azure_openai.R | 3 R/api_chat_completions.R | 20 + R/api_claude.R | 24 -- R/api_claude_cli.R |only R/api_deepseek.R | 3 R/api_ellmer.R | 3 R/api_gemini.R | 17 - R/api_groq.R | 5 R/api_llamacpp.R | 3 R/api_mistral.R | 81 ++++++- R/api_ollama.R | 3 R/api_openai.R | 41 +-- R/api_openrouter.R | 7 R/api_perplexity.R | 43 +++ R/api_voyage.R | 7 R/async_chat.R | 16 - R/llm_message.R | 17 - R/llm_verbs.R | 42 ++- R/provider_capabilities.R |only R/stream_pump.R | 59 ++++- R/tools.R | 50 ++++ R/utilites.R | 25 ++ R/websearch.R |only README.md | 44 +-- inst/doc/tidyllm.R | 31 +- inst/doc/tidyllm.Rmd | 66 ++++- inst/doc/tidyllm.html | 316 ++++++++++++++++------------ man/claude_chat.Rd | 4 man/claude_cli.Rd |only man/claude_cli_chat.Rd |only man/gemini_chat.Rd | 4 man/groq_transcribe.Rd | 2 man/llm_message.Rd | 2 man/mistral_chat.Rd | 4 man/openai_chat.Rd | 4 man/openai_deep_research.Rd | 13 - man/openrouter_chat.Rd | 2 man/perplexity.Rd | 7 man/perplexity_chat.Rd | 7 man/perplexity_check_research.Rd | 7 man/perplexity_deep_research.Rd | 7 man/perplexity_fetch_research.Rd | 7 man/provider_capabilities.Rd |only man/send_claude_batch.Rd | 4 man/send_gemini_batch.Rd | 2 man/send_openai_batch.Rd | 4 man/voyage_rerank.Rd | 4 man/websearch.Rd |only man/websearch_tool.Rd |only tests/testthat/test_api_gemini.R | 4 tests/testthat/test_api_mistral.R | 24 ++ tests/testthat/test_api_openai.R | 2 tests/testthat/test_api_perplexity.R | 8 tests/testthat/test_chat_pipeline.R | 2 tests/testthat/test_provider_capabilities.R |only tests/testthat/test_tooldef.R | 36 +++ tests/testthat/test_tools.R |only tests/testthat/test_websearch.R |only vignettes/tidyllm.Rmd | 66 ++++- 64 files changed, 1127 insertions(+), 408 deletions(-)
Title: Patient Reported Outcomes Regression Analysis
Description: It offers a wide variety of techniques, such as graphics, recoding, or regression models, for a comprehensive analysis of patient-reported outcomes (PRO). Especially novel is the broad range of regression models based on the beta-binomial distribution useful for analyzing binomial data with over-dispersion in cross-sectional, longitudinal, or multidimensional response studies (see Najera-Zuloaga J., Lee D.-J. and Arostegui I. (2019) <doi:10.1002/bimj.201700251>).
Author: Josu Najera-Zuloaga [aut, cre],
Dae-Jin Lee [aut],
Inmaculada Arostegui [aut]
Maintainer: Josu Najera-Zuloaga <josu.najera@ehu.eus>
Diff between PROreg versions 1.3.2 dated 2025-10-29 and 1.3.3 dated 2026-10-05
DESCRIPTION | 6 +- MD5 | 6 +- R/SF36rec.R | 152 ++++++++++++++++++++++++++++----------------------------- man/SF36rec.Rd | 146 +++++++++++++++++++++++++++--------------------------- 4 files changed, 155 insertions(+), 155 deletions(-)
Title: Tidy Access to Spanish INE Demographic Data
Description: Provides tidy, harmonized access to demographic data from the
Spanish National Statistics Institute (INE) fenomenos demograficos
domain, including population, births, and deaths, retrieved live via
the official 'ineapir' API wrapper, with optional spatial integration at
municipality and province level via 'mapSpain'. Mortality indicators
follow the Human Mortality Database Methods Protocol, including the
average age at death in infancy method of Andreev and Kingkade (2015)
<doi:10.4054/DemRes.2015.33.13>.
Author: J. R. Caro-Barrera [aut, cre, cph]
Maintainer: J. R. Caro-Barrera <jrcaro@uco.es>
Diff between inedemogR versions 0.1.0 dated 2026-08-23 and 0.2.0 dated 2026-10-05
DESCRIPTION | 6 MD5 | 81 ++-- NEWS.md | 71 +++ R/abridged_life_tables.R | 215 +++++------ R/births.R | 20 - R/death_rates.R | 176 +++++---- R/deaths.R | 14 R/decomposition.R | 50 +- R/exposure.R | 50 +- R/helpers.R | 25 + R/indicators.R | 191 +++++----- R/life_tables.R | 534 +++++++++++++++++------------ R/population.R | 10 README.md | 72 +++ inst/doc/inedemogR-tutorial.pdf |binary inst/doc/inedemogR-tutorial.tex | 417 +++++++++++----------- man/age_specific_fertility_rate.Rd | 51 +- man/andreev_kingkade_a0.Rd | 26 + man/build_abridged_life_table.Rd | 19 - man/build_life_table.Rd | 26 - man/build_life_tables.Rd | 77 +++- man/compute_death_rates.Rd | 26 + man/compute_exposure.Rd | 22 - man/decompose_life_expectancy.Rd | 19 - man/get_ine_births.Rd | 10 man/get_ine_births_by_age.Rd | 10 man/get_ine_deaths.Rd | 10 man/get_ine_population.Rd | 10 man/gross_reproduction_rate.Rd | 17 man/life_expectancy.Rd | 19 - man/mean_age_at_childbearing.Rd | 9 man/net_reproduction_rate.Rd | 20 - man/total_fertility_rate.Rd | 15 man/validate_abridged_life_table.Rd | 7 man/validate_death_rates.Rd | 5 man/validate_life_table.Rd | 15 tests/testthat/test-abridged_life_tables.R | 27 - tests/testthat/test-corrections.R |only tests/testthat/test-death_rates.R | 9 tests/testthat/test-indicators.R | 44 +- tests/testthat/test-live-integration.R |only tests/testthat/test-parsing.R |only vignettes/inedemogR-tutorial.tex | 417 +++++++++++----------- 43 files changed, 1671 insertions(+), 1171 deletions(-)
Title: Query the Attentional Control Data Collection or the Truth
Effect Database
Description: Interact with the Attentional Control Data Collection (ACDC) or the Truth Effect Database (TED).
Download the databases using download_acdc() or download_ted(), connect to the database via connect_to_db(), set filter arguments via add_argument()
and query the database via query_db().
Author: Sven Lesche [aut, cre, cph],
Julia M. Haaf [ctb, ths],
Madlen Hoffstadt [ctb]
Maintainer: Sven Lesche <sven.lesche@psychologie.uni-heidelberg.de>
Diff between acdcquery versions 1.2.3 dated 2026-02-19 and 1.2.4 dated 2026-10-05
DESCRIPTION | 6 - MD5 | 10 +- NEWS.md | 4 R/check_operator.R | 6 - R/make_valid_sql.R | 25 +++++ README.md | 242 ++++++++++++++++++++++++++--------------------------- 6 files changed, 162 insertions(+), 131 deletions(-)
Title: Insect Ecology Data Analysis Toolkit
Description: A collection of analytical tools for insect ecology research,
currently covering age-stage, two-sex life table analysis,
dose-response bioassays, temperature-dependent development and insect
phenology prediction. The life table module follows the age-stage,
two-sex life table theory of Chi (1988) <doi:10.1093/ee/17.1.26> and
Chi et al. (2020) <doi:10.1127/entomologia/2020/0936>. It supports
fast batch processing of multi-group datasets, validates raw 'csv'
data, computes cohort size, mean fecundity, age-stage survival rates,
age-specific survival, age-specific fecundity, life expectancy, and
derived population parameters (net reproductive rate, intrinsic and
finite rates of increase, mean generation time), simultaneously
generates age-stage survival curves for all groups, and exports all
tabular results and plots to 'Excel' in a single run. The bioassay
module estimates lethal concentrations by the traditional and the
weighted (improved) linear regression methods and by pro [...truncated...]
Author: Wangyao Li [aut, cre, cph],
Yongsheng Zhang [aut],
Huan Yu [aut]
Maintainer: Wangyao Li <1561941342@qq.com>
Diff between insectecol versions 1.0.1 dated 2026-09-27 and 1.1.1 dated 2026-10-05
insectecol-1.0.1/insectecol/R/lc50_auto.R |only insectecol-1.0.1/insectecol/R/lc50_save.R |only insectecol-1.0.1/insectecol/R/lifetable_save.R |only insectecol-1.0.1/insectecol/inst/extdata/Example.csv |only insectecol-1.0.1/insectecol/inst/extdata/bioassay.csv |only insectecol-1.0.1/insectecol/man/build_life_table.Rd |only insectecol-1.0.1/insectecol/man/check_life_table.Rd |only insectecol-1.0.1/insectecol/man/plot_lc50.Rd |only insectecol-1.0.1/insectecol/man/plot_sxj.Rd |only insectecol-1.0.1/insectecol/man/read_lc50.Rd |only insectecol-1.0.1/insectecol/man/read_life_table.Rd |only insectecol-1.0.1/insectecol/man/save_lc50.Rd |only insectecol-1.0.1/insectecol/man/save_lc50_auto.Rd |only insectecol-1.0.1/insectecol/man/save_lc50_plot.Rd |only insectecol-1.0.1/insectecol/man/save_lc50_plot_auto.Rd |only insectecol-1.0.1/insectecol/man/save_results.Rd |only insectecol-1.1.1/insectecol/DESCRIPTION | 75 insectecol-1.1.1/insectecol/MD5 | 162 + insectecol-1.1.1/insectecol/NAMESPACE | 68 insectecol-1.1.1/insectecol/R/check_data.R | 2 insectecol-1.1.1/insectecol/R/check_path_type.R | 132 - insectecol-1.1.1/insectecol/R/emergence_calc.R |only insectecol-1.1.1/insectecol/R/emergence_export.R |only insectecol-1.1.1/insectecol/R/emergence_main.R |only insectecol-1.1.1/insectecol/R/emergence_methods.R |only insectecol-1.1.1/insectecol/R/emergence_plot.R |only insectecol-1.1.1/insectecol/R/emergence_read.R |only insectecol-1.1.1/insectecol/R/gdd_calc.R |only insectecol-1.1.1/insectecol/R/gdd_check.R |only insectecol-1.1.1/insectecol/R/gdd_compare.R |only insectecol-1.1.1/insectecol/R/gdd_daily.R |only insectecol-1.1.1/insectecol/R/gdd_export.R |only insectecol-1.1.1/insectecol/R/gdd_fit.R |only insectecol-1.1.1/insectecol/R/gdd_main.R |only insectecol-1.1.1/insectecol/R/gdd_methods.R |only insectecol-1.1.1/insectecol/R/gdd_models.R |only insectecol-1.1.1/insectecol/R/gdd_plot.R |only insectecol-1.1.1/insectecol/R/gdd_predict.R |only insectecol-1.1.1/insectecol/R/gdd_read.R |only insectecol-1.1.1/insectecol/R/lc50_calculate.R | 14 insectecol-1.1.1/insectecol/R/lc50_data.R | 10 insectecol-1.1.1/insectecol/R/lc50_export.R |only insectecol-1.1.1/insectecol/R/lc50_export_auto.R |only insectecol-1.1.1/insectecol/R/lc50_main.R | 70 insectecol-1.1.1/insectecol/R/lc50_methods.R | 2 insectecol-1.1.1/insectecol/R/lc50_plot.R | 186 + insectecol-1.1.1/insectecol/R/lifetable_bootstrap.R |only insectecol-1.1.1/insectecol/R/lifetable_calculate.R | 66 insectecol-1.1.1/insectecol/R/lifetable_data.R | 30 insectecol-1.1.1/insectecol/R/lifetable_export.R |only insectecol-1.1.1/insectecol/R/lifetable_indicators.R | 1020 ++++----- insectecol-1.1.1/insectecol/R/lifetable_main.R | 110 - insectecol-1.1.1/insectecol/R/lifetable_plot.R | 16 insectecol-1.1.1/insectecol/R/utils.R | 8 insectecol-1.1.1/insectecol/README.md | 1036 ++++++---- insectecol-1.1.1/insectecol/inst/CITATION | 20 insectecol-1.1.1/insectecol/inst/WORDLIST | 5 insectecol-1.1.1/insectecol/inst/extdata/emergence_example.csv |only insectecol-1.1.1/insectecol/inst/extdata/gdd_batch |only insectecol-1.1.1/insectecol/inst/extdata/lc50_example.csv |only insectecol-1.1.1/insectecol/inst/extdata/lifetable_example.csv |only insectecol-1.1.1/insectecol/man/calc_F.Rd | 6 insectecol-1.1.1/insectecol/man/calc_N.Rd | 6 insectecol-1.1.1/insectecol/man/calc_R0.Rd | 6 insectecol-1.1.1/insectecol/man/calc_T.Rd | 6 insectecol-1.1.1/insectecol/man/calc_ex.Rd | 6 insectecol-1.1.1/insectecol/man/calc_fxj.Rd | 6 insectecol-1.1.1/insectecol/man/calc_lambda.Rd | 6 insectecol-1.1.1/insectecol/man/calc_lx.Rd | 6 insectecol-1.1.1/insectecol/man/calc_mx.Rd | 6 insectecol-1.1.1/insectecol/man/calc_r.Rd | 6 insectecol-1.1.1/insectecol/man/calc_sxj.Rd | 8 insectecol-1.1.1/insectecol/man/check_path_type.Rd | 8 insectecol-1.1.1/insectecol/man/emergence_analyze.Rd |only insectecol-1.1.1/insectecol/man/emergence_calc.Rd |only insectecol-1.1.1/insectecol/man/emergence_export.Rd |only insectecol-1.1.1/insectecol/man/emergence_export_plot.Rd |only insectecol-1.1.1/insectecol/man/emergence_read.Rd |only insectecol-1.1.1/insectecol/man/figures |only insectecol-1.1.1/insectecol/man/gdd_analyze.Rd |only insectecol-1.1.1/insectecol/man/gdd_calc.Rd |only insectecol-1.1.1/insectecol/man/gdd_check.Rd |only insectecol-1.1.1/insectecol/man/gdd_compare.Rd |only insectecol-1.1.1/insectecol/man/gdd_daily.Rd |only insectecol-1.1.1/insectecol/man/gdd_export.Rd |only insectecol-1.1.1/insectecol/man/gdd_export_plot.Rd |only insectecol-1.1.1/insectecol/man/gdd_plot.Rd |only insectecol-1.1.1/insectecol/man/gdd_predict.Rd |only insectecol-1.1.1/insectecol/man/gdd_read.Rd |only insectecol-1.1.1/insectecol/man/get_stage_names.Rd | 10 insectecol-1.1.1/insectecol/man/lc50_analyze.Rd | 45 insectecol-1.1.1/insectecol/man/lc50_calculate.Rd | 14 insectecol-1.1.1/insectecol/man/lc50_export.Rd |only insectecol-1.1.1/insectecol/man/lc50_export_auto.Rd |only insectecol-1.1.1/insectecol/man/lc50_export_plot.Rd |only insectecol-1.1.1/insectecol/man/lc50_export_plot_auto.Rd |only insectecol-1.1.1/insectecol/man/lc50_plot.Rd |only insectecol-1.1.1/insectecol/man/lc50_read.Rd |only insectecol-1.1.1/insectecol/man/lc50_traditional.Rd | 2 insectecol-1.1.1/insectecol/man/lifeTable_analyze.Rd | 72 insectecol-1.1.1/insectecol/man/lifeTable_boot_test.Rd |only insectecol-1.1.1/insectecol/man/lifeTable_bootstrap.Rd |only insectecol-1.1.1/insectecol/man/lifeTable_build.Rd |only insectecol-1.1.1/insectecol/man/lifeTable_calculate.Rd | 36 insectecol-1.1.1/insectecol/man/lifeTable_calculate_all.Rd | 6 insectecol-1.1.1/insectecol/man/lifeTable_check.Rd |only insectecol-1.1.1/insectecol/man/lifeTable_export.Rd |only insectecol-1.1.1/insectecol/man/lifeTable_plot.Rd |only insectecol-1.1.1/insectecol/man/lifeTable_read.Rd |only insectecol-1.1.1/insectecol/man/plot.emergence.Rd |only insectecol-1.1.1/insectecol/man/predict.emergence.Rd |only insectecol-1.1.1/insectecol/man/print.emergence.Rd |only insectecol-1.1.1/insectecol/man/summary.emergence.Rd |only insectecol-1.1.1/insectecol/tests/testthat/test-emergence.R |only insectecol-1.1.1/insectecol/tests/testthat/test-gdd.R |only insectecol-1.1.1/insectecol/tests/testthat/test-lc50.R |only insectecol-1.1.1/insectecol/tests/testthat/test-life_table.R | 133 - 117 files changed, 2126 insertions(+), 1300 deletions(-)
Title: Historical, Relational, and Tail Anomaly-Detection Algorithms
Description: The presence of outliers in a dataset can substantially bias the
results of statistical analyses. To correct for outliers, micro edits are
manually performed on all records. A set of constraints and decision rules
is typically used to aid the editing process. However, straightforward
decision rules might overlook anomalies arising from disruption of linear
relationships. Computationally efficient methods are provided to
identify historical, tail, and relational anomalies at the data-entry
level (Sartore et al., 2024; <doi:10.6339/24-JDS1136>). A score statistic
is developed for each anomaly type, using a distribution-free approach
motivated by the Bienaymé-Chebyshev's inequality, and fuzzy logic is used
to detect cellwise outliers resulting from different types of anomalies.
Each data entry is individually scored and individual scores are combined
into a final score to determine anomalous entries. In contrast to fuzzy
logic, Bayesian bootstrap and a Bayesian test based on empiric [...truncated...]
Author: Luca Sartore [aut] ,
Luca Sartore [cre] ,
Lu Chen [aut] ,
Justin van Wart [aut],
Andrew Dau [aut] ,
Valbona Bejleri [aut]
Maintainer: Luca Sartore <drwolf85@gmail.com>
This is a re-admission after prior archival of version 25.11.22 dated 2025-11-25
Diff between HRTnomaly versions 25.11.22 dated 2025-11-25 and 26.9.19 dated 2026-10-05
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Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include:
a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 7.8 dated 2026-09-02 and 7.9 dated 2026-10-05
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/kent.logcon.R | 6 ++++-- man/Directional-package.Rd | 6 ++++-- man/kent.logcon.Rd | 5 +---- 5 files changed, 18 insertions(+), 17 deletions(-)
Title: Composable Runtime Contracts
Description: Build reusable validators from small building blocks using the
base pipe operator. Define runtime contracts once with restrict() and
enforce them anywhere in code. Validators compose naturally, support
dependent rules via formulas, and produce clear, path-aware error
messages. No domain-specific language, no operator overloading, just
idiomatic R.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between restrictR versions 0.1.0 dated 2026-03-09 and 0.3.0 dated 2026-10-05
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Title: Methods for Optimizing Scales of Effect
Description: A tool for optimizing scales of effect when modeling ecological processes in space. Specifically, the scale parameter of a distance-weighted kernel distribution is identified for all environmental layers included in the model. Includes functions to assist in model selection, model evaluation, efficient transformation of raster surfaces using fast Fourier transformation, and projecting models. For more details see Peterman (2026) <doi:10.1007/s10980-025-02267-x>.
Author: Bill Peterman [aut, cre]
Maintainer: Bill Peterman <Peterman.73@osu.edu>
Diff between multiScaleR versions 0.7.0 dated 2026-07-01 and 0.7.2 dated 2026-10-05
DESCRIPTION | 6 MD5 | 137 ++- NAMESPACE | 2 NEWS | 91 +- R/aic_tab.R | 33 R/data_files.R | 2 R/diagnostics.R | 22 R/kernel_dist.R | 183 +++-- R/kernel_prep.R | 106 +-- R/kernel_prep_by_group.R |only R/kernel_scale.raster.R | 78 +- R/kernel_scale_fn.R | 164 +++- R/landscape_metrics.R | 18 R/marginal_effects.R | 14 R/multiScale_optim.R | 89 ++ R/plot_kernel.R | 17 R/plot_method.R | 7 R/print_methods.R | 122 +++ R/profile_scale_ci.R | 19 R/profile_sigma.R | 21 R/scale_vars.R | 38 - R/sim_dat.R | 6 R/sim_dat_unmarked.R | 5 R/surface_metrics.R | 4 R/validation_helpers.R | 32 README.md | 28 build/partial.rdb |binary build/vignette.rds |binary inst/doc/landscape_metric_covariates.Rmd | 2 inst/doc/landscape_metric_covariates.html | 85 +- inst/doc/multiScaleR_Guide.R | 24 inst/doc/multiScaleR_Guide.Rmd | 322 +++++---- inst/doc/multiScaleR_Guide.html | 875 ++++++++++++++----------- inst/doc/quickstart.Rmd | 12 inst/doc/quickstart.html | 135 ++- inst/doc/spatial_projection_clamping.html | 167 ++-- inst/doc/surface_metric_covariates.Rmd | 57 - inst/doc/surface_metric_covariates.html | 101 +- inst/doc/year-specific-rasters.R |only inst/doc/year-specific-rasters.Rmd |only inst/doc/year-specific-rasters.html |only inst/examples |only man/aic_tab.Rd | 8 man/bic_tab.Rd | 5 man/diagnostics.Rd | 17 man/k_dist.Rd | 67 + man/kernel_dist.Rd | 264 ++++--- man/kernel_prep.Rd | 11 man/kernel_prep_by_group.Rd |only man/kernel_scale.raster.Rd | 28 man/kernel_scale_fn.Rd | 3 man/landscape.Rd | 2 man/msr_vars.Rd | 3 man/multiScale_optim.Rd | 44 - man/plot.multiScaleR.Rd | 7 man/plot_kernel.Rd | 17 man/plot_marginal_effects.Rd | 3 man/profile_sigma.Rd | 4 man/sim_dat.Rd | 6 man/sim_dat_unmarked.Rd | 5 man/summary.multiScaleR.Rd | 17 tests/testthat/test-0-7-issues.R |only tests/testthat/test-extract-batches.R |only tests/testthat/test-internals-and-helpers.R | 80 +- tests/testthat/test-kernel-dist-2d.R |only tests/testthat/test-kernel-prep.R | 39 - tests/testthat/test-marginal-offset.R |only tests/testthat/test-optimization-workflow.R | 31 tests/testthat/test-simulation-and-selection.R | 1 tests/testthat/test-unmarked-alignment.R |only tests/testthat/test-year-specific-example.R |only vignettes/landscape_metric_covariates.Rmd | 2 vignettes/multiScaleR_Guide.Rmd | 322 +++++---- vignettes/quickstart.Rmd | 12 vignettes/surface_metric_covariates.Rmd | 57 - vignettes/year-specific-rasters.Rmd |only 76 files changed, 2575 insertions(+), 1504 deletions(-)
Title: Retrieval and Processing of the Spanish National Forest
Inventory
Description: Fetches, harmonizes, and analyses data from the Spanish National
Forest Inventory for reproducible, design-aware forest inventory workflows.
Computes tree- and stand-level metrics, applies sampling-based expansion
factors, estimates volume, and supports extensible processing for external
inventory designs with custom sampling schemes and volume equations. Spatial
extensions can attach plot geometries, preserve geometry sidecars through
metric workflows, and return georeferenced sf outputs for mapping and
remote-sensing integration.
Author: Wilson Lara [aut, cre] ,
Cristobal Ordonez [aut] ,
Aitor Vazquez-Veloso [aut] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between basifoR versions 0.7.9 dated 2026-08-26 and 0.8.0 dated 2026-10-05
DESCRIPTION | 6 - MD5 | 25 ++++---- NEWS | 71 +++++++++++++++++++++++ R/dendroMetrics.R | 26 ++++++++ R/externalMetrics2Vol.R | 20 +++++- R/external_dendroMetrics.R | 18 +++++ R/internal.R | 47 ++++++++++----- R/metrics2Vol.R | 127 +++++++++++++++++++++++++++++++++--------- R/sysdata.rda |binary man/dendroMetrics.Rd | 7 +- man/externalMetrics2Vol.Rd | 2 man/external_dendroMetrics.Rd | 2 man/metrics2Vol.Rd | 15 +++- tests |only 14 files changed, 296 insertions(+), 70 deletions(-)
Title: Imports Datasets from BCB (Central Bank of Brazil) using Its
Official API
Description: Downloads and organizes datasets using BCB's API <https://www.bcb.gov.br/>. Offers options for caching with the 'memoise' package and
, multicore/multisession with 'furrr' and format of output data (long/wide).
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetBCBData versions 0.9.1 dated 2026-02-02 and 0.9.5 dated 2026-10-05
GetBCBData-0.9.1/GetBCBData/build |only GetBCBData-0.9.1/GetBCBData/inst |only GetBCBData-0.9.1/GetBCBData/vignettes |only GetBCBData-0.9.5/GetBCBData/DESCRIPTION | 11 GetBCBData-0.9.5/GetBCBData/MD5 | 26 GetBCBData-0.9.5/GetBCBData/NAMESPACE | 1 GetBCBData-0.9.5/GetBCBData/NEWS.md | 31 + GetBCBData-0.9.5/GetBCBData/R/api.R | 76 +- GetBCBData-0.9.5/GetBCBData/R/gbcbd_get_series.R | 272 ++++++---- GetBCBData-0.9.5/GetBCBData/R/gbcbd_search_series.R |only GetBCBData-0.9.5/GetBCBData/R/gbcbd_utils.R | 31 - GetBCBData-0.9.5/GetBCBData/README.md | 47 + GetBCBData-0.9.5/GetBCBData/man/gbcbd_get_series.Rd | 55 +- GetBCBData-0.9.5/GetBCBData/man/gbcbd_search_series.Rd |only GetBCBData-0.9.5/GetBCBData/tests/testthat/test-get_series.R | 115 ++-- GetBCBData-0.9.5/GetBCBData/tests/testthat/test-search_series.R |only 16 files changed, 425 insertions(+), 240 deletions(-)
Title: Interface to the Spanish 'Catastro' Web Services
Description: Access public spatial data from the Spanish 'Catastro'
through its Infrastructure for Spatial Information in Europe
('INSPIRE') and related web services. Retrieve parcel, building,
address and map image data and convert between property reference
codes and coordinates.
Author: Angel Delgado Panadero [aut, cph] ,
Inaki Ucar [ctb] ,
Diego Hernangomez [aut, cre] ,
Direccion General del Catastro [dtc]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between CatastRo versions 1.0.2 dated 2026-06-03 and 1.1.0 dated 2026-10-05
DESCRIPTION | 33 + MD5 | 241 +++++++------- NAMESPACE | 84 ++-- NEWS.md | 91 ++--- R/CatastRo-package.R | 1 R/atom-ad-db.R | 44 +- R/atom-ad.R | 37 +- R/atom-bu-db.R | 25 - R/atom-bu.R | 33 + R/atom-cp-db.R | 20 - R/atom-cp.R | 31 - R/atom-search.R | 42 +- R/cache-utils.R | 289 ++++++++++------- R/catr-code-coords.R | 43 +- R/data.R | 23 - R/docs.R | 69 +++- R/ovc-cpmrc.R | 57 +-- R/ovc-munic.R | 69 ++-- R/ovc-provinces.R | 25 - R/ovc-rccoor-dist.R | 69 ++-- R/ovc-rccoor.R | 44 +- R/run-example.R | 25 - R/utils-atom.R | 79 ++-- R/utils-ovc.R | 24 - R/utils-sf.R | 62 ++- R/utils-url.R | 288 ++++++++++++----- R/utils-wfs.R | 103 +++--- R/utils.R | 167 +++++++-- R/wfs-ad.R | 67 ++- R/wfs-bu.R | 43 +- R/wfs-cp.R | 54 +-- R/wms-all.R | 179 +++++----- README.md | 84 ++-- build/vignette.rds |binary data/catr_srs_values.rda |binary inst/COPYRIGHTS | 118 ++----- inst/WORDLIST | 189 +++++------ inst/doc/CatastRo.html | 84 ++-- inst/doc/CatastRo.qmd | 92 ++--- inst/doc/ovcservice.html | 51 +-- inst/doc/ovcservice.qmd | 84 ++-- inst/schemaorg.json | 24 - man/CatastRo-package.Rd | 4 man/catr_atom_get_address.Rd | 66 +-- man/catr_atom_get_address_db.Rd | 69 +--- man/catr_atom_get_buildings.Rd | 81 +--- man/catr_atom_get_buildings_db.Rd | 69 +--- man/catr_atom_get_parcels.Rd | 73 +--- man/catr_atom_get_parcels_db.Rd | 69 +--- man/catr_atom_search_munic.Rd | 60 +-- man/catr_clear_cache.Rd | 28 - man/catr_get_code_from_coords.Rd | 64 ++- man/catr_ovc_get_cod_munic.Rd | 59 +-- man/catr_ovc_get_cod_provinces.Rd | 33 + man/catr_ovc_get_cpmrc.Rd | 49 +- man/catr_ovc_get_rccoor.Rd | 51 +-- man/catr_ovc_get_rccoor_distancia.Rd | 59 ++- man/catr_set_cache_dir.Rd | 77 ++-- man/catr_srs_values.Rd | 40 -- man/catr_wfs_get_address.Rd | 77 +--- man/catr_wfs_get_buildings.Rd | 90 ++--- man/catr_wfs_get_parcels.Rd | 92 ++--- man/catr_wms_get_layer.Rd | 201 +++++------ man/figures/README-atom-1.png |binary man/figures/README-wfs-1.png |binary man/inspire_wfs_get.Rd | 64 +-- man/roxygen/meta.R | 15 man/run_example.Rd | 6 tests/testthat/_snaps/atom-ad-db.md | 30 - tests/testthat/_snaps/atom-ad.md | 18 - tests/testthat/_snaps/atom-bu-db.md | 30 - tests/testthat/_snaps/atom-bu.md | 18 - tests/testthat/_snaps/atom-cp-db.md | 30 - tests/testthat/_snaps/atom-cp.md | 18 - tests/testthat/_snaps/atom-search.md | 21 - tests/testthat/_snaps/cache-utils.md | 55 +++ tests/testthat/_snaps/catr-code-coords.md | 41 +- tests/testthat/_snaps/docs.md |only tests/testthat/_snaps/ovc-cpmrc.md | 33 + tests/testthat/_snaps/ovc-munic.md | 23 - tests/testthat/_snaps/ovc-provinces.md | 18 - tests/testthat/_snaps/ovc-rccoor-dist.md | 40 ++ tests/testthat/_snaps/ovc-rccoor.md | 27 + tests/testthat/_snaps/utils-atom.md |only tests/testthat/_snaps/utils-ovc.md |only tests/testthat/_snaps/utils-sf.md | 24 + tests/testthat/_snaps/utils-url.md | 68 +++- tests/testthat/_snaps/utils-wfs.md | 20 - tests/testthat/_snaps/utils.md | 129 ++++++- tests/testthat/_snaps/wfs-ad.md | 40 -- tests/testthat/_snaps/wfs-cp.md |only tests/testthat/_snaps/wms-all.md |only tests/testthat/setup.R | 2 tests/testthat/test-atom-ad-db.R | 152 ++------- tests/testthat/test-atom-ad.R | 98 +---- tests/testthat/test-atom-bu-db.R | 157 ++------- tests/testthat/test-atom-bu.R | 92 +---- tests/testthat/test-atom-cp-db.R | 154 ++------- tests/testthat/test-atom-cp.R | 92 +---- tests/testthat/test-atom-search.R | 104 ++---- tests/testthat/test-cache-utils.R | 354 +++++++++++++-------- tests/testthat/test-catr-code-coords.R | 166 ++++++--- tests/testthat/test-docs.R |only tests/testthat/test-ovc-cpmrc.R | 131 +++++-- tests/testthat/test-ovc-munic.R | 68 ++-- tests/testthat/test-ovc-provinces.R | 53 +-- tests/testthat/test-ovc-rccoor-dist.R | 257 +++++++++++---- tests/testthat/test-ovc-rccoor.R | 212 +++++++++--- tests/testthat/test-run-example.R | 75 +++- tests/testthat/test-utils-atom.R |only tests/testthat/test-utils-ovc.R | 72 +--- tests/testthat/test-utils-sf.R | 107 ++++-- tests/testthat/test-utils-url.R | 505 +++++++++++++++++++++++++----- tests/testthat/test-utils-wfs.R | 257 +++++++++++---- tests/testthat/test-utils.R | 107 +++++- tests/testthat/test-wfs-ad.R | 126 ++++++- tests/testthat/test-wfs-bu.R | 236 +++++++++----- tests/testthat/test-wfs-cp.R | 133 ++++++- tests/testthat/test-wms-all.R | 72 +++- vignettes/CatastRo.qmd | 92 ++--- vignettes/REFERENCES.bib | 4 vignettes/dviz-1.png |binary vignettes/minimal-1.png |binary vignettes/ovcservice.qmd | 84 ++-- vignettes/santbernabeu-1.png |binary 125 files changed, 5453 insertions(+), 3875 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut],
Martins Liberts [aut],
Janis Jukams [aut],
Liliana Roze [cre]
Maintainer: Liliana Roze <liliana.roze@csp.gov.lv>
Diff between surveyplanning versions 4.0 dated 2020-05-20 and 4.1 dated 2026-10-05
DESCRIPTION | 24 ++++++++++++------------ MD5 | 25 +++++++++++++------------ NEWS.md |only R/MoE_P.R | 2 +- R/dom_optimal_allocation.R | 18 +++++++++--------- R/expvar.R | 10 +++++----- R/optsize.R | 4 ++-- R/prop_dom_optimal_allocation.R | 22 +++++++++++----------- man/MoE_P.Rd | 4 ++-- man/dom_optimal_allocation.Rd | 18 +++++++++--------- man/expvar.Rd | 10 +++++----- man/optsize.Rd | 4 ++-- man/prop_dom_optimal_allocation.Rd | 22 +++++++++++----------- man/surveyplanning-package.Rd | 13 +------------ 14 files changed, 83 insertions(+), 93 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: Single and Multiple Imputation with Automated Machine Learning
Description: Machine learning algorithms have been used for performing
single missing data imputation and most recently, multiple imputations.
However, this is the first attempt for using automated machine learning algorithms
for performing both
single and multiple imputation. Automated machine learning is a procedure for
fine-tuning the model automatic, performing a random search for a model that
results in less error, without overfitting the data. The main idea is
to allow the model to set its own parameters for imputing each variable separately
instead of setting fixed predefined parameters to impute all variables
of the dataset.
Using automated machine learning, the package fine-tunes an Elastic
Net (default) or Gradient Boosting, Random Forest, Deep Learning, Extreme Gradient Boosting,
or Stacked Ensemble machine learning model (from one or a combination of other
supported algorithms) for imputing the missing
observations. This procedure has been implemented for the
first time by this package [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
Diff between mlim versions 0.3.0 dated 2022-12-16 and 0.6.0 dated 2026-10-05
mlim-0.3.0/mlim/R/algoSelector.R |only mlim-0.3.0/mlim/R/h2o.check.R |only mlim-0.3.0/mlim/R/init.R |only mlim-0.3.0/mlim/R/javaServer.R |only mlim-0.3.0/mlim/R/meanmode.R |only mlim-0.3.0/mlim/R/mlim.postimpute.R |only mlim-0.3.0/mlim/R/mlim.shuffle.R |only mlim-0.3.0/mlim/R/server.check.R |only mlim-0.6.0/mlim/DESCRIPTION | 20 mlim-0.6.0/mlim/MD5 | 88 - mlim-0.6.0/mlim/NAMESPACE | 73 - mlim-0.6.0/mlim/R/addNA.R | 24 mlim-0.6.0/mlim/R/charity.R | 19 mlim-0.6.0/mlim/R/checkNconvert.R | 49 mlim-0.6.0/mlim/R/extractMetrics.R | 80 - mlim-0.6.0/mlim/R/factmem.R | 36 mlim-0.6.0/mlim/R/getMetrics.R | 6 mlim-0.6.0/mlim/R/is.imbalanced.R | 2 mlim-0.6.0/mlim/R/is.valid.R | 36 mlim-0.6.0/mlim/R/iterate.R | 1820 ++++++++++++++++------------- mlim-0.6.0/mlim/R/iteration_loop.R | 414 +++--- mlim-0.6.0/mlim/R/manifest.R | 2 mlim-0.6.0/mlim/R/matching.R | 150 +- mlim-0.6.0/mlim/R/medianmode.R |only mlim-0.6.0/mlim/R/mlim.R | 547 +++----- mlim-0.6.0/mlim/R/mlim.error.R | 671 +++++++--- mlim-0.6.0/mlim/R/mlim.mids.R | 128 +- mlim-0.6.0/mlim/R/mlim.multilevel.R |only mlim-0.6.0/mlim/R/mlim.na.R | 6 mlim-0.6.0/mlim/R/mlim.na.multilevel.R |only mlim-0.6.0/mlim/R/mlim.preimpute.R | 73 - mlim-0.6.0/mlim/R/mlim.stata.R |only mlim-0.6.0/mlim/R/mlim.summarize.R | 140 +- mlim-0.6.0/mlim/R/normalize.R | 2 mlim-0.6.0/mlim/R/nrmse.R | 35 mlim-0.6.0/mlim/R/revert.R | 60 mlim-0.6.0/mlim/R/selectVariables.R | 12 mlim-0.6.0/mlim/R/stochasticFactorImpute.R | 29 mlim-0.6.0/mlim/R/stoppingCriteria.R | 43 mlim-0.6.0/mlim/R/syntaxProcessing.R | 294 +++- mlim-0.6.0/mlim/R/zzz.R | 6 mlim-0.6.0/mlim/README.md | 80 - mlim-0.6.0/mlim/man/charity.Rd | 18 mlim-0.6.0/mlim/man/manifest.Rd | 2 mlim-0.6.0/mlim/man/mlim.Rd | 245 +-- mlim-0.6.0/mlim/man/mlim.error.Rd | 100 - mlim-0.6.0/mlim/man/mlim.mids.Rd | 46 mlim-0.6.0/mlim/man/mlim.na.Rd | 4 mlim-0.6.0/mlim/man/mlim.na.multilevel.Rd |only mlim-0.6.0/mlim/man/mlim.preimpute.Rd | 44 mlim-0.6.0/mlim/man/mlim.stata.Rd |only mlim-0.6.0/mlim/man/mlim.summarize.Rd | 27 52 files changed, 3050 insertions(+), 2381 deletions(-)
Title: Resampling-Based Analysis of Multivariate Data and Repeated
Measures Designs
Description: Implemented are various tests for semi-parametric repeated measures
and general MANOVA designs that do neither assume multivariate normality nor
covariance homogeneity, i.e., the procedures are applicable for a wide range
of general multivariate factorial designs. In addition to asymptotic inference
methods, novel bootstrap and permutation approaches are implemented as well. These provide more
accurate results in case of small to moderate sample sizes. Furthermore, post-hoc
comparisons are provided for the multivariate analyses.
Friedrich, S., Konietschke, F. and Pauly, M. (2019) <doi:10.32614/RJ-2019-051>.
Author: Sarah Friedrich [aut, cre],
Frank Konietschke [aut],
Markus Pauly [aut],
Mona Modrzik [aut]
Maintainer: Sarah Friedrich <sarah.friedrich@math.uni-augsburg.de>
Diff between MANOVA.RM versions 0.5.4 dated 2023-08-25 and 0.6.0 dated 2026-10-05
MANOVA.RM-0.5.4/MANOVA.RM/man/MANOVARM.Rd |only MANOVA.RM-0.5.4/MANOVA.RM/vignettes/Introduction_to_MANOVA.RM.md |only MANOVA.RM-0.6.0/MANOVA.RM/DESCRIPTION | 30 + MANOVA.RM-0.6.0/MANOVA.RM/MD5 | 56 +- MANOVA.RM-0.6.0/MANOVA.RM/NAMESPACE | 7 MANOVA.RM-0.6.0/MANOVA.RM/R/Data.R | 15 MANOVA.RM-0.6.0/MANOVA.RM/R/MANOVA-function.R | 43 -- MANOVA.RM-0.6.0/MANOVA.RM/R/MANOVA.RM-package.R | 58 +-- MANOVA.RM-0.6.0/MANOVA.RM/R/MANOVA_Statistics.R | 188 ---------- MANOVA.RM-0.6.0/MANOVA.RM/R/MANOVAwide-function.R | 44 -- MANOVA.RM-0.6.0/MANOVA.RM/R/RM-function.R | 16 MANOVA.RM-0.6.0/MANOVA.RM/R/RM_MCTP.R |only MANOVA.RM-0.6.0/MANOVA.RM/R/RM_Statistics.R | 48 -- MANOVA.RM-0.6.0/MANOVA.RM/R/hypo_matrix.R | 20 - MANOVA.RM-0.6.0/MANOVA.RM/R/hypo_matrix_MANOVA.R | 82 ---- MANOVA.RM-0.6.0/MANOVA.RM/R/multRM-function.R | 11 MANOVA.RM-0.6.0/MANOVA.RM/R/multRM_Statistics.R | 35 - MANOVA.RM-0.6.0/MANOVA.RM/R/prepdata.R | 30 - MANOVA.RM-0.6.0/MANOVA.RM/R/utility_functions.R | 8 MANOVA.RM-0.6.0/MANOVA.RM/build/partial.rdb |only MANOVA.RM-0.6.0/MANOVA.RM/build/vignette.rds |binary MANOVA.RM-0.6.0/MANOVA.RM/inst/NEWS.md | 11 MANOVA.RM-0.6.0/MANOVA.RM/inst/doc/Introduction_to_MANOVA.RM.Rmd | 12 MANOVA.RM-0.6.0/MANOVA.RM/inst/doc/Introduction_to_MANOVA.RM.html | 123 +++--- MANOVA.RM-0.6.0/MANOVA.RM/man/EEGwide.Rd | 14 MANOVA.RM-0.6.0/MANOVA.RM/man/MANOVA.RM-package.Rd |only MANOVA.RM-0.6.0/MANOVA.RM/man/MANOVA.Rd | 4 MANOVA.RM-0.6.0/MANOVA.RM/man/MANOVA.wide.Rd | 4 MANOVA.RM-0.6.0/MANOVA.RM/man/RM.MCTP.Rd |only MANOVA.RM-0.6.0/MANOVA.RM/man/RM.Rd | 4 MANOVA.RM-0.6.0/MANOVA.RM/man/multRM.Rd | 4 MANOVA.RM-0.6.0/MANOVA.RM/vignettes/Introduction_to_MANOVA.RM.Rmd | 12 32 files changed, 314 insertions(+), 565 deletions(-)
Title: Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
Description: Fast and memory efficient methods for truncated singular value
decomposition and principal components analysis of large sparse and dense
matrices.
Author: Jim Baglama [aut, cph],
Lothar Reichel [aut, cph],
B. W. Lewis [aut, cre, cph]
Maintainer: B. W. Lewis <blewis@illposed.net>
Diff between irlba versions 2.3.7 dated 2026-01-30 and 2.4.1 dated 2026-10-05
irlba-2.3.7/irlba/README |only irlba-2.3.7/irlba/src/irlb.h |only irlba-2.3.7/irlba/src/utility.c |only irlba-2.4.1/irlba/DESCRIPTION | 10 irlba-2.4.1/irlba/MD5 | 32 - irlba-2.4.1/irlba/NAMESPACE | 16 irlba-2.4.1/irlba/R/irlba.R | 545 ++++++++++++++--------------- irlba-2.4.1/irlba/R/prcomp.R | 4 irlba-2.4.1/irlba/R/svdr.R | 4 irlba-2.4.1/irlba/R/utility.R | 156 +++++++- irlba-2.4.1/irlba/README.md | 66 --- irlba-2.4.1/irlba/build/vignette.rds |binary irlba-2.4.1/irlba/inst/doc/irlba.pdf |binary irlba-2.4.1/irlba/man/irlba.Rd | 40 -- irlba-2.4.1/irlba/man/svdr.Rd | 4 irlba-2.4.1/irlba/src/irlb.c | 651 +++++------------------------------ irlba-2.4.1/irlba/tests/edge.R | 124 +++--- irlba-2.4.1/irlba/tests/err.R |only irlba-2.4.1/irlba/tests/test.R | 287 ++++----------- 19 files changed, 681 insertions(+), 1258 deletions(-)
Title: Gene Expression Decomposition and Integration
Description: A memory-efficient implementation for integrating gene expression data
from single-cell RNA sequencing experiments. Uses a C++ backend with
thin R wrappers to enable analysis of large-scale single-cell datasets. The
package supports multiple data modalities including count matrices, paired
data (splicing, RNA velocity, CITE-seq), and binary indicators. It implements
a latent variable model with block coordinate descent optimization for
dimensionality reduction and batch effect correction. The method is
described in Mikaeili Namini et al. (2026)
<doi:10.1093/bioinformatics/btag334>, building on the original GEDI model
of Madrigal et al. (2024) <doi:10.1038/s41467-024-50963-0>.
Author: Arsham Mikaeili Namini [aut, cre],
Hamed S.Najafabadi [aut]
Maintainer: Arsham Mikaeili Namini <arsham.mikaeilinamini@mail.mcgill.ca>
Diff between gedi2 versions 2.3.4 dated 2026-05-19 and 2.3.6 dated 2026-10-05
DESCRIPTION | 13 - LICENSE | 4 MD5 | 24 +- NEWS.md | 28 ++ R/RcppExports.R | 4 R/gedi_class.R | 3 R/gedi_plots.R | 249 +++++++++++++++++++------- R/gedi_projections.R | 97 ++++++++++ man/plot_features.Rd | 71 +++++-- src/RcppExports.cpp | 40 +++- src/gedi_differential.cpp | 200 ++++++++++++++++++++ src/matrix_oprations.cpp | 10 - tests/testthat/test-diffexp-projection-math.R |only tests/testthat/test-diffexp-projection.R |only 14 files changed, 629 insertions(+), 114 deletions(-)
Title: Processing and Analyzing AIS Vessel Tracking Data
Description: Processes Automatic Identification
System (AIS) vessel tracking data, including travel estimation,
trajectory correction, interpolation, extraction, and summarising
vessel information. The package is designed to facilitate
reproducible analyses of maritime traffic in ecological,
environmental, and marine spatial planning applications.
For more details see <https://remip48.github.io/AISanalyze/>.
Author: Remi Pigeault [aut, cre]
Maintainer: Remi Pigeault <remi.pigeault@tiho-hannover.de>
Diff between AISanalyze versions 3.1.3 dated 2026-09-30 and 3.1.4 dated 2026-10-05
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 7 R/AISextract.R | 427 ++++++++++++++++----------------- tests/testthat/test-AIScorrect_speed.R | 2 tests/testthat/test-AISextract.R | 259 +++++++++++--------- tests/testthat/test-AISinterpolate.R | 4 tests/testthat/test-AIStravel.R | 2 8 files changed, 387 insertions(+), 334 deletions(-)
Title: Interface to the Global Biodiversity Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility (GBIF;
<https://www.gbif.org/developer/summary>). GBIF is a database
of species occurrence records from sources all over the globe.
rgbif includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the GBIF
tile map service to make rasters summarizing huge amounts of data.
Author: Scott Chamberlain [aut] ,
Damiano Oldoni [aut] ,
Vijay Barve [ctb] ,
Peter Desmet [ctb] ,
Laurens Geffert [ctb],
Dan Mcglinn [ctb] ,
Karthik Ram [ctb] ,
rOpenSci [fnd] ,
John Waller [aut, cre]
Maintainer: John Waller <jwaller@gbif.org>
Diff between rgbif versions 3.8.5 dated 2026-03-20 and 3.9.0 dated 2026-10-05
rgbif-3.8.5/rgbif/tests/fixtures/elevation.yml |only rgbif-3.8.5/rgbif/tests/fixtures/elevation_geonames_conn.yml |only rgbif-3.8.5/rgbif/tests/fixtures/elevation_geonames_conn_unauthorized.yml |only rgbif-3.8.5/rgbif/tests/fixtures/elevation_models.yml |only rgbif-3.8.5/rgbif/tests/fixtures/elevation_unauthorized.yml |only rgbif-3.8.5/rgbif/tests/fixtures/elevation_warning_zero_zero.yml |only rgbif-3.8.5/rgbif/tests/testthat/elevation_test_data.rda |only rgbif-3.8.5/rgbif/tests/testthat/test-elevation.R |only rgbif-3.9.0/rgbif/DESCRIPTION | 39 rgbif-3.9.0/rgbif/MD5 | 528 rgbif-3.9.0/rgbif/NAMESPACE | 7 rgbif-3.9.0/rgbif/NEWS.md | 70 rgbif-3.9.0/rgbif/R/collection_search.R | 44 rgbif-3.9.0/rgbif/R/dataset_export.R | 46 rgbif-3.9.0/rgbif/R/dataset_search.r | 56 rgbif-3.9.0/rgbif/R/dataset_suggest.r | 47 rgbif-3.9.0/rgbif/R/derived_dataset.R | 4 rgbif-3.9.0/rgbif/R/download_predicate_dsl.R | 196 rgbif-3.9.0/rgbif/R/download_queue.R | 402 rgbif-3.9.0/rgbif/R/downloads.R | 154 rgbif-3.9.0/rgbif/R/elevation.r | 7 rgbif-3.9.0/rgbif/R/gbif_issues.R | 2 rgbif-3.9.0/rgbif/R/gbif_to_col.R |only rgbif-3.9.0/rgbif/R/institution_search.R | 51 rgbif-3.9.0/rgbif/R/map_fetch.R | 11 rgbif-3.9.0/rgbif/R/mvt_fetch.R | 22 rgbif-3.9.0/rgbif/R/name_backbone.r | 9 rgbif-3.9.0/rgbif/R/name_backbone_checklist.R | 5 rgbif-3.9.0/rgbif/R/name_issues.R | 121 rgbif-3.9.0/rgbif/R/name_lookup.r | 9 rgbif-3.9.0/rgbif/R/name_suggest.r | 9 rgbif-3.9.0/rgbif/R/name_usage.r | 29 rgbif-3.9.0/rgbif/R/occ_count.r | 20 rgbif-3.9.0/rgbif/R/occ_download.R | 192 rgbif-3.9.0/rgbif/R/occ_download_countries.R |only rgbif-3.9.0/rgbif/R/occ_download_organizations.R |only rgbif-3.9.0/rgbif/R/occ_download_queue.R | 382 rgbif-3.9.0/rgbif/R/occ_download_user_count.R |only rgbif-3.9.0/rgbif/R/occ_search.r | 108 rgbif-3.9.0/rgbif/R/occ_term.r |only rgbif-3.9.0/rgbif/R/organizations.r | 61 rgbif-3.9.0/rgbif/R/zzz.r | 177 rgbif-3.9.0/rgbif/man/GbifQueue.Rd | 10 rgbif-3.9.0/rgbif/man/collection_search.Rd | 25 rgbif-3.9.0/rgbif/man/dataset_search.Rd | 58 rgbif-3.9.0/rgbif/man/derived_dataset.Rd | 4 rgbif-3.9.0/rgbif/man/download_predicate_dsl.Rd | 38 rgbif-3.9.0/rgbif/man/downloads.Rd | 2 rgbif-3.9.0/rgbif/man/elevation.Rd | 7 rgbif-3.9.0/rgbif/man/gbif_to_col.Rd |only rgbif-3.9.0/rgbif/man/institution_search.Rd | 38 rgbif-3.9.0/rgbif/man/map_fetch.Rd | 10 rgbif-3.9.0/rgbif/man/mvt_fetch.Rd | 21 rgbif-3.9.0/rgbif/man/name_backbone.Rd | 9 rgbif-3.9.0/rgbif/man/name_backbone_checklist.Rd | 5 rgbif-3.9.0/rgbif/man/name_issues.Rd | 7 rgbif-3.9.0/rgbif/man/name_lookup.Rd | 7 rgbif-3.9.0/rgbif/man/name_suggest.Rd | 9 rgbif-3.9.0/rgbif/man/name_usage.Rd | 22 rgbif-3.9.0/rgbif/man/occ_count.Rd | 6 rgbif-3.9.0/rgbif/man/occ_download.Rd | 58 rgbif-3.9.0/rgbif/man/occ_download_countries.Rd |only rgbif-3.9.0/rgbif/man/occ_download_organizations.Rd |only rgbif-3.9.0/rgbif/man/occ_download_queue.Rd | 6 rgbif-3.9.0/rgbif/man/occ_download_user_count.Rd |only rgbif-3.9.0/rgbif/man/occ_search.Rd | 96 rgbif-3.9.0/rgbif/man/occ_term.Rd |only rgbif-3.9.0/rgbif/man/organizations.Rd | 46 rgbif-3.9.0/rgbif/tests/fixtures/collection_search.yml | 160 rgbif-3.9.0/rgbif/tests/fixtures/dataset.yml | 2399 rgbif-3.9.0/rgbif/tests/fixtures/dataset_doi.yml | 10 rgbif-3.9.0/rgbif/tests/fixtures/dataset_list_funs.yml | 35 rgbif-3.9.0/rgbif/tests/fixtures/dataset_search.yml | 8157 rgbif-3.9.0/rgbif/tests/fixtures/dataset_search_category.yml |only rgbif-3.9.0/rgbif/tests/fixtures/dataset_search_continent_deprecation.yml |only rgbif-3.9.0/rgbif/tests/fixtures/dataset_search_facet.yml | 56 rgbif-3.9.0/rgbif/tests/fixtures/dataset_search_new_params.yml |only rgbif-3.9.0/rgbif/tests/fixtures/dataset_search_taxonkey_deprecation.yml |only rgbif-3.9.0/rgbif/tests/fixtures/dataset_suggest.yml | 6117 rgbif-3.9.0/rgbif/tests/fixtures/dataset_suggest_category.yml |only rgbif-3.9.0/rgbif/tests/fixtures/dataset_suggest_description.yml | 2243 rgbif-3.9.0/rgbif/tests/fixtures/dataset_suggest_new_params.yml |only rgbif-3.9.0/rgbif/tests/fixtures/dataset_uuid_funs.yml |165450 +++------- rgbif-3.9.0/rgbif/tests/fixtures/derived_dataset_1.yml | 8 rgbif-3.9.0/rgbif/tests/fixtures/derived_dataset_2.yml | 6 rgbif-3.9.0/rgbif/tests/fixtures/enumeration.yml | 56 rgbif-3.9.0/rgbif/tests/fixtures/enumeration_fails_well.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/gbif_citation_downloadkey.yml | 32 rgbif-3.9.0/rgbif/tests/fixtures/gbif_citation_occ_download_meta.yml | 32 rgbif-3.9.0/rgbif/tests/fixtures/gbif_get_wait.yml | 1209 rgbif-3.9.0/rgbif/tests/fixtures/gbif_oai_get_records.yml | 78 rgbif-3.9.0/rgbif/tests/fixtures/gbif_oai_identify.yml | 48 rgbif-3.9.0/rgbif/tests/fixtures/gbif_oai_list_identifiers.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/gbif_oai_list_metadataformats.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/gbif_oai_list_sets.yml | 1449 rgbif-3.9.0/rgbif/tests/fixtures/gbif_to_col_invalid_v2.yml |only rgbif-3.9.0/rgbif/tests/fixtures/gbif_to_col_multiple_v2.yml |only rgbif-3.9.0/rgbif/tests/fixtures/gbif_to_col_print_multiple_v2.yml |only rgbif-3.9.0/rgbif/tests/fixtures/gbif_to_col_print_single_v2.yml |only rgbif-3.9.0/rgbif/tests/fixtures/gbif_to_col_single_v2.yml |only rgbif-3.9.0/rgbif/tests/fixtures/gbif_to_col_structure_v2.yml |only rgbif-3.9.0/rgbif/tests/fixtures/installation_search.yml | 83 rgbif-3.9.0/rgbif/tests/fixtures/installation_uuid_funs.yml | 33 rgbif-3.9.0/rgbif/tests/fixtures/installations.yml | 1747 rgbif-3.9.0/rgbif/tests/fixtures/installations_deleted.yml | 41 rgbif-3.9.0/rgbif/tests/fixtures/installations_uuid.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/installations_uuid_data.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/institution_search.yml | 224 rgbif-3.9.0/rgbif/tests/fixtures/map_fetch_col_taxonkey.yml |only rgbif-3.9.0/rgbif/tests/fixtures/map_fetch_png.yml | 3869 rgbif-3.9.0/rgbif/tests/fixtures/map_fetch_terra.yml |19254 - rgbif-3.9.0/rgbif/tests/fixtures/name_backbone.yml | 582 rgbif-3.9.0/rgbif/tests/fixtures/name_backbone_acceptedUsageKey.yml | 20 rgbif-3.9.0/rgbif/tests/fixtures/name_backbone_animalia.yml |only rgbif-3.9.0/rgbif/tests/fixtures/name_backbone_gbif_backbone.yml |only rgbif-3.9.0/rgbif/tests/fixtures/name_backbone_verbose_true.yml | 531 rgbif-3.9.0/rgbif/tests/fixtures/name_issues.yml | 105 rgbif-3.9.0/rgbif/tests/fixtures/name_issues_deprecation.yml |only rgbif-3.9.0/rgbif/tests/fixtures/name_lookup_constituentKey.yml | 2462 rgbif-3.9.0/rgbif/tests/fixtures/name_lookup_habitat.yml | 8632 rgbif-3.9.0/rgbif/tests/fixtures/name_lookup_no_results.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/name_suggest.yml | 694 rgbif-3.9.0/rgbif/tests/fixtures/name_suggest_many_args.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/name_usage.yml | 265 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_children.yml | 114 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_descriptions.yml | 243 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_distributions.yml | 482 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_iucnRedListCategory.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_media.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_name.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_parents.yml | 144 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_references.yml | 478 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_related.yml | 898 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_speciesProfiles.yml | 36 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_synonyms.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_typeSpecimens.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_data_vernacularNames.yml | 147 rgbif-3.9.0/rgbif/tests/fixtures/name_usage_fails_well.yml | 8 rgbif-3.9.0/rgbif/tests/fixtures/network.yml | 124 rgbif-3.9.0/rgbif/tests/fixtures/network_constituents.yml | 5366 rgbif-3.9.0/rgbif/tests/fixtures/nodes.yml | 2188 rgbif-3.9.0/rgbif/tests/fixtures/occ_count.yml | 58 rgbif-3.9.0/rgbif/tests/fixtures/occ_count_.yml | 30 rgbif-3.9.0/rgbif/tests/fixtures/occ_count_facet.yml | 94 rgbif-3.9.0/rgbif/tests/fixtures/occ_count_legacy_params.yml | 40 rgbif-3.9.0/rgbif/tests/fixtures/occ_count_nucleotideSequence.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_count_nucleotideSequence_facet.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_data_args_with_many_inputs.yml | 1197 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_catalog_number.yml | 428 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_coordinateUncertaintyInMeters.yml | 615 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_degreeOfEstablishment.yml | 720 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_depth.yml | 126 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_distanceFromCentroidInMeters.yml | 614 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_dropped_fields.yml | 297 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_elevation.yml | 197 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_eventId.yml | 913 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_fails_well.yml | 8 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_gadmGid.yml | 556 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_identifiedBy.yml | 981 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_isInCluster.yml | 563 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_iucnRedListCategory.yml | 1087 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_key_gbifid_character_class.yml | 224 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_lifeStage.yml | 1067 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_networkKey.yml | 979 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_occurrenceId.yml | 955 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_occurrencestatus.yml | 633 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_organismQuantity.yml | 571 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_organismQuantityType.yml | 314 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_relativeOrganismQuantity.yml | 515 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_scientificname.yml | 978 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_speciesKey.yml | 1003 rgbif-3.9.0/rgbif/tests/fixtures/occ_data_verbatimScientificName.yml | 999 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_1.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_10.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_11.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_download_12.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_download_13.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_download_2.yml | 14 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_3.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_4.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_5.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_6.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_7.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_8.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_9.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_cancel.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_cancel_prep.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_countries.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_download_countries_error.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_download_dataset_activity.yml | 44 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_dataset_activity_error.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_datasets.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_datasets_error.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_describe.yml | 19 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_doi.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_list.yml | 64 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_list_unauthorized.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_meta.yml | 6 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_meta_na_results.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_meta_with_results.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_organizations.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_download_organizations_error.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_download_queue.yml | 699 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_sql_1.yml | 14 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_stats.yml | 26 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_stats_dataset.yml | 20 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_stats_dataset_records.yml | 20 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_stats_source.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_stats_user_country.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_user_count.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_download_user_count_status.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_download_wait_character.yml | 4 rgbif-3.9.0/rgbif/tests/fixtures/occ_download_wait_request.yml | 422 rgbif-3.9.0/rgbif/tests/fixtures/occ_get.yml | 737 rgbif-3.9.0/rgbif/tests/fixtures/occ_get_other.yml | 327 rgbif-3.9.0/rgbif/tests/fixtures/occ_metadata.yml | 44 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_catalognumber.yml | 6 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_classifications.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_classifications_columns.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_classifications_empty.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_classifications_names.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_classifications_rows.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_classifications_uuid.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_coordinateUncertaintyInMeters.yml | 620 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_degreeOfEstablishment.yml | 729 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_depth.yml | 130 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_distanceFromCentroidInMeters.yml | 621 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_elevation.yml | 375 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_eventId.yml | 922 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_fails_well.yml | 12 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_gadmGid.yml | 562 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_geoDistance.yml | 162 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_hierarchy_data.yml | 184 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_identifiedBy.yml | 1003 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_isInCluster.yml | 556 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_isSequenced.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_iucnRedListCategory.yml | 1112 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_key_gbifid_character_class.yml | 228 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_lifeStage.yml | 1077 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_many_inputs.yml | 1208 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_networkKey.yml | 995 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_nucleotideSequence_booleans.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_nucleotideSequence_gcContent.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_nucleotideSequence_sequenceLength.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_nucleotideSequence_targetGene.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_numeric_key_backbone.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_numeric_key_warning.yml |only rgbif-3.9.0/rgbif/tests/fixtures/occ_search_occurrenceId.yml | 947 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_occurrencestatus.yml | 645 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_organismQuantity.yml | 577 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_organismQuantityType.yml | 318 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_relativeOrganismQuantity.yml | 535 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_scientificname.yml | 992 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_speciesKey.yml | 1002 rgbif-3.9.0/rgbif/tests/fixtures/occ_search_verbatimScientificName.yml | 1014 rgbif-3.9.0/rgbif/tests/fixtures/occ_term.yml |only rgbif-3.9.0/rgbif/tests/fixtures/organizations_search_country.yml | 2 rgbif-3.9.0/rgbif/tests/fixtures/organizations_search_uuid.yml | 6178 rgbif-3.9.0/rgbif/tests/fixtures/wkt_large_occ_data.yml | 2353 rgbif-3.9.0/rgbif/tests/fixtures/wkt_large_occ_search.yml | 2357 rgbif-3.9.0/rgbif/tests/testthat/test-collection_search.R | 27 rgbif-3.9.0/rgbif/tests/testthat/test-dataset_export.R | 89 rgbif-3.9.0/rgbif/tests/testthat/test-dataset_search.r | 63 rgbif-3.9.0/rgbif/tests/testthat/test-dataset_suggest.r | 61 rgbif-3.9.0/rgbif/tests/testthat/test-dataset_uuid_funs.R | 3 rgbif-3.9.0/rgbif/tests/testthat/test-derived_dataset.R | 2 rgbif-3.9.0/rgbif/tests/testthat/test-download_parsing.R | 43 rgbif-3.9.0/rgbif/tests/testthat/test-downloads.R | 260 rgbif-3.9.0/rgbif/tests/testthat/test-gbif_names.R | 10 rgbif-3.9.0/rgbif/tests/testthat/test-gbif_to_col.R |only rgbif-3.9.0/rgbif/tests/testthat/test-institution_search.R | 64 rgbif-3.9.0/rgbif/tests/testthat/test-lit_search.R | 1 rgbif-3.9.0/rgbif/tests/testthat/test-map_fetch.R | 82 rgbif-3.9.0/rgbif/tests/testthat/test-mvt_fetch.R | 43 rgbif-3.9.0/rgbif/tests/testthat/test-name_backbone.r | 50 rgbif-3.9.0/rgbif/tests/testthat/test-name_backbone_checklist.R | 41 rgbif-3.9.0/rgbif/tests/testthat/test-name_issues.R | 110 rgbif-3.9.0/rgbif/tests/testthat/test-name_lookup.r | 58 rgbif-3.9.0/rgbif/tests/testthat/test-name_suggest.r | 26 rgbif-3.9.0/rgbif/tests/testthat/test-name_usage.r | 93 rgbif-3.9.0/rgbif/tests/testthat/test-occ_count.r | 142 rgbif-3.9.0/rgbif/tests/testthat/test-occ_data.R | 3 rgbif-3.9.0/rgbif/tests/testthat/test-occ_download.R | 70 rgbif-3.9.0/rgbif/tests/testthat/test-occ_download_cached.R | 18 rgbif-3.9.0/rgbif/tests/testthat/test-occ_download_cancel.R | 62 rgbif-3.9.0/rgbif/tests/testthat/test-occ_download_countries.R |only rgbif-3.9.0/rgbif/tests/testthat/test-occ_download_meta.R | 2 rgbif-3.9.0/rgbif/tests/testthat/test-occ_download_organizations.R |only rgbif-3.9.0/rgbif/tests/testthat/test-occ_download_prep.R | 618 rgbif-3.9.0/rgbif/tests/testthat/test-occ_download_queue.R | 3 rgbif-3.9.0/rgbif/tests/testthat/test-occ_download_user_count.R |only rgbif-3.9.0/rgbif/tests/testthat/test-occ_download_wait.R | 4 rgbif-3.9.0/rgbif/tests/testthat/test-occ_search.r | 422 rgbif-3.9.0/rgbif/tests/testthat/test-occ_term.r |only rgbif-3.9.0/rgbif/tests/testthat/test-organizations.r | 13 rgbif-3.9.0/rgbif/tests/testthat/test-predicate_builders.R | 37 rgbif-3.9.0/rgbif/tests/testthat/test-utils.R | 3 297 files changed, 116211 insertions(+), 172761 deletions(-)
Title: Read xlsx Files with a Native Parser
Description: Reads tabular data from xlsx files with a specialized C parser.
Worksheet XML is scanned in a single pass and decoded directly into R
vectors, with no intermediate document model. Bundles the 'miniz' and
'libdeflate' decompressors to read the underlying archive.
Author: Vincent Shields [aut, cre, cph],
Rich Geldreich [ctb, cph] ,
Tenacious Software LLC [cph] ,
RAD Game Tools and Valve Software [cph] ,
Martin Raiber [ctb, cph] ,
Alex Evans [ctb] ,
Alistair Moffat [ctb] ,
Jyrki Katajainen [ctb] ,
Eric Biggers [ctb, cp [...truncated...]
Maintainer: Vincent Shields <vince.shields913@gmail.com>
Diff between rcxl versions 0.1.0 dated 2026-09-17 and 0.1.1 dated 2026-10-05
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md |only README.md | 16 +++++++++++++--- src/read_xlsx.c | 42 ++++++++++++++++++++++-------------------- 5 files changed, 42 insertions(+), 29 deletions(-)
Title: Tools for Scoring and Evaluating Hubverse Model Outputs
Description: Provides tools for scoring and evaluating 'hubverse' model outputs
against observed data, wrapping scoring workflows from the
'scoringutils' package and bridging hubverse model output formats
to 'scoringutils' forecast classes.
Author: Anna Krystalli [aut, cre] ,
Nicholas Reich [aut] ,
Evan Ray [aut],
Nikos Bosse [aut] ,
Kimberlyn Roosa [aut],
Zhian Kamvar [ctb] ,
Li Shandross [ctb] ,
Becky Sweger [ctb],
Lucie Contamin [ctb],
Consortium of Infectious Disease Modeling Hubs [cph]
Maintainer: Anna Krystalli <annakrystalli@googlemail.com>
Diff between hubEvals versions 0.4.0 dated 2026-07-22 and 0.5.0 dated 2026-10-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/score_model_out.R | 25 +------------------------ tests/testthat/test-score_model_out.R | 27 ++++++++++++++++----------- 5 files changed, 29 insertions(+), 43 deletions(-)
Title: Behavior-Driven Development for R
Description: Write executable specifications in a natural language that describes how your code should behave.
Write specifications in feature files using 'Gherkin' language and execute them using functions implemented in R.
Use them as an extension to your 'testthat' tests to provide a high level description of how your code works.
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>
Diff between cucumber versions 2.1.1 dated 2025-07-21 and 2.2.0 dated 2026-10-05
cucumber-2.1.1/cucumber/R/parse_token.R |only cucumber-2.1.1/cucumber/tests/testthat/_snaps/local |only cucumber-2.1.1/cucumber/tests/testthat/test-parse_token.R |only cucumber-2.2.0/cucumber/DESCRIPTION | 15 cucumber-2.2.0/cucumber/MD5 | 103 +- cucumber-2.2.0/cucumber/NAMESPACE | 17 cucumber-2.2.0/cucumber/NEWS.md | 11 cucumber-2.2.0/cucumber/R/detect.R | 52 - cucumber-2.2.0/cucumber/R/doc-opts.R | 14 cucumber-2.2.0/cucumber/R/errors.R |only cucumber-2.2.0/cucumber/R/execute.R | 52 + cucumber-2.2.0/cucumber/R/execute_pickles.R |only cucumber-2.2.0/cucumber/R/match.R |only cucumber-2.2.0/cucumber/R/normalize_feature.R | 54 + cucumber-2.2.0/cucumber/R/pending.R |only cucumber-2.2.0/cucumber/R/pickle.R |only cucumber-2.2.0/cucumber/R/preview.R |only cucumber-2.2.0/cucumber/R/reporter.R |only cucumber-2.2.0/cucumber/R/tag_expression.R |only cucumber-2.2.0/cucumber/R/test.R | 70 + cucumber-2.2.0/cucumber/R/token.R |only cucumber-2.2.0/cucumber/R/tokenize.R | 67 + cucumber-2.2.0/cucumber/R/validate.R | 85 +- cucumber-2.2.0/cucumber/README.md | 217 +++-- cucumber-2.2.0/cucumber/build/vignette.rds |binary cucumber-2.2.0/cucumber/inst/doc/bdd.html | 161 +++- cucumber-2.2.0/cucumber/inst/doc/bdd.qmd | 2 cucumber-2.2.0/cucumber/inst/doc/how-it-works.html | 153 +++ cucumber-2.2.0/cucumber/inst/doc/migration-to-2-0-0.html | 153 +++ cucumber-2.2.0/cucumber/inst/doc/reference-gherkin.html | 331 ++++++++ cucumber-2.2.0/cucumber/inst/doc/reference-gherkin.qmd | 175 ++++ cucumber-2.2.0/cucumber/inst/examples/duplicate_step |only cucumber-2.2.0/cucumber/inst/examples/invalid_feature |only cucumber-2.2.0/cucumber/inst/examples/missing_step |only cucumber-2.2.0/cucumber/inst/examples/no_steps |only cucumber-2.2.0/cucumber/inst/examples/step_error |only cucumber-2.2.0/cucumber/inst/examples/tags |only cucumber-2.2.0/cucumber/man/CucumberProgressReporter.Rd |only cucumber-2.2.0/cucumber/man/CucumberReporter.Rd |only cucumber-2.2.0/cucumber/man/opts.Rd | 12 cucumber-2.2.0/cucumber/man/pending.Rd |only cucumber-2.2.0/cucumber/man/run.Rd | 9 cucumber-2.2.0/cucumber/man/test.Rd | 13 cucumber-2.2.0/cucumber/tests/acceptance/background.feature |only cucumber-2.2.0/cucumber/tests/acceptance/parameter_types.feature |only cucumber-2.2.0/cucumber/tests/acceptance/pending.feature |only cucumber-2.2.0/cucumber/tests/acceptance/scenario_outlines.feature |only cucumber-2.2.0/cucumber/tests/acceptance/setup-steps.R | 52 + cucumber-2.2.0/cucumber/tests/acceptance/snippets.feature |only cucumber-2.2.0/cucumber/tests/acceptance/step_arguments_docstrings.feature |only cucumber-2.2.0/cucumber/tests/acceptance/step_arguments_tables.feature |only cucumber-2.2.0/cucumber/tests/acceptance/tag.feature |only cucumber-2.2.0/cucumber/tests/acceptance/tag_expressions.feature |only cucumber-2.2.0/cucumber/tests/testthat/_snaps/examples-errors.md |only cucumber-2.2.0/cucumber/tests/testthat/_snaps/examples.md |only cucumber-2.2.0/cucumber/tests/testthat/_snaps/preview.md |only cucumber-2.2.0/cucumber/tests/testthat/_snaps/reporter.md |only cucumber-2.2.0/cucumber/tests/testthat/_snaps/snippet.md |only cucumber-2.2.0/cucumber/tests/testthat/_snaps/validate.md | 4 cucumber-2.2.0/cucumber/tests/testthat/setup-examples.R |only cucumber-2.2.0/cucumber/tests/testthat/test-examples-errors.R |only cucumber-2.2.0/cucumber/tests/testthat/test-examples.R | 64 - cucumber-2.2.0/cucumber/tests/testthat/test-normalize_feature.R | 38 cucumber-2.2.0/cucumber/tests/testthat/test-preview.R |only cucumber-2.2.0/cucumber/tests/testthat/test-reporter.R |only cucumber-2.2.0/cucumber/tests/testthat/test-snippet.R |only cucumber-2.2.0/cucumber/tests/testthat/test-tag_expression.R |only cucumber-2.2.0/cucumber/tests/testthat/test-tokenize.R | 401 ++++++---- cucumber-2.2.0/cucumber/tests/testthat/test-validate_tags.R |only cucumber-2.2.0/cucumber/vignettes/bdd.qmd | 2 cucumber-2.2.0/cucumber/vignettes/reference-gherkin.qmd | 175 ++++ 71 files changed, 2071 insertions(+), 431 deletions(-)
Title: Panel Cointegration Tests Based on Westerlund (2007)
Description: Implements a functional approximation of the four panel
cointegration tests developed by Westerlund (2007)
<doi:10.1111/j.1468-0084.2007.00477.x>. The tests are based on structural
rather than residual dynamics and allow for heterogeneity in both the
long-run cointegrating relationship and the short-run dynamics. The package
includes logic for automated lag and lead selection via AIC/BIC, Bartlett
kernel long-run variance estimation, and a bootstrap procedure to handle
cross-sectional dependence. It also includes a bootstrapping distribution
visualization function for diagnostic purposes.
Author: Bosco Hung [aut, cre]
Maintainer: Bosco Hung <bosco.hung@politics.ox.ac.uk>
Diff between Westerlund versions 0.1.3 dated 2026-04-12 and 0.1.4 dated 2026-10-05
DESCRIPTION | 14 MD5 | 33 - NAMESPACE | 2 R/Westerlund.R | 1025 ++++++++++++++--------------------- R/imports.R | 4 README.md | 69 +- inst/doc/my-vignette.R | 13 inst/doc/my-vignette.Rmd | 101 ++- inst/doc/my-vignette.html | 464 ++++++++------- man/DisplayWesterlund.Rd | 4 man/WesterlundBootstrap.Rd | 171 +---- man/plot.westerlund_test.Rd | 126 ---- man/print.summary.westerlund_test.Rd |only man/print.westerlund_test.Rd | 66 -- man/summary.westerlund_test.Rd | 44 - man/westerlund_test.Rd | 212 +++---- man/westerlund_test_reg.Rd | 82 -- vignettes/my-vignette.Rmd | 101 ++- 18 files changed, 1105 insertions(+), 1426 deletions(-)
Title: High-Performance Interactive Mapping
Description: Interactive spatial visualisations are a cornerstone for exploring
and communicating complexity, and are commonly embedded into reports or interactive
dashboards. However, as the amount of data grows, so do the demands on
functionality, especially for technical and scientific data. To bridge this
gap and create a mapping package that is high performing, a modern approach is
needed that draws from best software engineering practices. Toro provides
bindings to 'MapLibre GL JS', an open-source 'JavaScript'/'TypeScript' library for
rendering interactive maps in the browser, built from the ground up for
responsiveness and scale, by the MapLibre Organization (2020) <https://github.com/MapLibre>.
This connection allows users to create interactive maps that can easily be
integrated into both 'Quarto' and the 'R Shiny' dashboard framework. Toro
thereby enables spatial visualisation and exploration of data that might
otherwise be too limited, too slow, or too hard to scale using more tradi [...truncated...]
Author: Epi, NZ [aut, cph, fnd] ),
Uli Muellner [cre],
Poppy Pakinui [ctb],
Kiel Hards [ctb],
Nick Snellgrove [ctb],
Jocelyn Qian [ctb],
Petra Muellner [ctb],
MapLibre contributors [cph] ,
Turf contributors [cph] ,
Mapbox contributors [cph]
Maintainer: Uli Muellner <uli@epi.group>
Diff between toro versions 0.1.0 dated 2026-05-07 and 0.2.0 dated 2026-10-05
DESCRIPTION | 79 ++++-- MD5 | 88 ++++--- NAMESPACE | 11 NEWS.md | 14 + R/animation.R | 44 +++ R/animation_controls.R | 66 ++++- R/control_panel.R | 61 ++++- R/draw_control.R | 108 +++++++++ R/export.R | 41 ++- R/get_map_items.R | 4 R/layer_controls.R | 1 R/layers.R | 16 - R/legends.R |only R/paint_control.R |only R/scale_control.R |only R/sources.R | 74 +++++- R/views.R | 105 ++++++++ README.md | 96 ++++++-- inst/htmlwidgets/lib/map/cluster-utils.js | 88 ++++--- inst/htmlwidgets/lib/map/control-utils.js | 352 +++++++++++++++++++----------- inst/htmlwidgets/lib/map/controls |only inst/htmlwidgets/lib/map/draw-controls.js |only inst/htmlwidgets/lib/map/layer-utils.js | 14 - inst/htmlwidgets/lib/map/legend-utils.js |only inst/htmlwidgets/lib/map/map-utils.js | 19 + inst/htmlwidgets/lib/map/map.css | 77 ++++++ inst/htmlwidgets/lib/map/map.js | 269 ++++++++++++++++++---- inst/htmlwidgets/lib/map/source-utils.js | 31 ++ inst/htmlwidgets/lib/map/view-utils.js | 44 ++- inst/htmlwidgets/map.yaml | 8 man/add_animation_controls.Rd | 21 + man/add_control_group.Rd | 15 + man/add_control_panel.Rd | 15 + man/add_draw_control.Rd | 4 man/add_drawn_shape.Rd |only man/add_layer_selector_control.Rd | 1 man/add_legend.Rd |only man/add_paint_control.Rd |only man/add_scale_control.Rd |only man/add_timeline_control.Rd | 12 - man/check_chrome_available.Rd | 15 - man/export_map_image.Rd | 18 - man/remove_legend.Rd |only man/remove_paint_control.Rd |only man/remove_scale_control.Rd |only man/set_bounds.Rd | 15 + man/set_scale_control_unit.Rd |only man/set_source_data.Rd | 20 + man/toggle_scale_control.Rd |only man/update_drawn_shape.Rd |only man/validate_bounds.Rd |only tests/testthat/test-control-panel.R | 10 tests/testthat/test-tiles.R | 12 - 53 files changed, 1441 insertions(+), 427 deletions(-)
Title: Semantic Factor Analysis of Language Model Embeddings
Description: Performs exploratory factor analysis on language model embeddings
of psychological scale items. Embeds item text with sentence transformers
or other language models, transforms the embeddings into item-by-item
similarity matrices, and extracts latent factor structure via standard
exploratory factor analysis, using several similarity transforms (atomic
reversed, SQuID centering, mean-centered Pearson) and fit diagnostics
tailored to embedding matrices (TEFI, RMSR, CAF, McDonald's omega).
Factor retention spans embedding-adapted parallel analysis, the empirical
Kaiser criterion, Velicer's minimum average partial, a comparison-data
misfit profile, and a calibrated learned rule that reports conformal
intervals. Further tools orient factor axes toward retrieved construct
terms by lexical target rotation, and audit whether a scale's items cover
their construct's semantic region without collecting responses. The
underlying methods are documented with full citations in the
corresponding functi [...truncated...]
Author: Devon Yanitski [aut, cre] ,
Chris Westbury [aut]
Maintainer: Devon Yanitski <dyanitsk@ualberta.ca>
Diff between semanticfa versions 0.5.0 dated 2026-09-01 and 0.5.1 dated 2026-10-05
semanticfa-0.5.0/semanticfa/inst/python/semk/__pycache__ |only semanticfa-0.5.1/semanticfa/DESCRIPTION | 6 semanticfa-0.5.1/semanticfa/MD5 | 36 - semanticfa-0.5.1/semanticfa/NEWS.md | 16 semanticfa-0.5.1/semanticfa/R/dimselect.R | 13 semanticfa-0.5.1/semanticfa/R/sfa.R | 6 semanticfa-0.5.1/semanticfa/R/similarity.R | 10 semanticfa-0.5.1/semanticfa/README.md | 4 semanticfa-0.5.1/semanticfa/inst/doc/introduction.Rmd | 5 semanticfa-0.5.1/semanticfa/inst/doc/introduction.html | 193 +++++----- semanticfa-0.5.1/semanticfa/man/sfa.Rd | 6 semanticfa-0.5.1/semanticfa/man/sfa_dimselect.Rd | 4 semanticfa-0.5.1/semanticfa/man/sfa_similarity.Rd | 10 semanticfa-0.5.1/semanticfa/tests/testthat/test-congruence.R | 9 semanticfa-0.5.1/semanticfa/tests/testthat/test-diagnostics.R | 7 semanticfa-0.5.1/semanticfa/tests/testthat/test-dimselect.R | 5 semanticfa-0.5.1/semanticfa/tests/testthat/test-load.R | 4 semanticfa-0.5.1/semanticfa/tests/testthat/test-sfa.R | 28 - semanticfa-0.5.1/semanticfa/vignettes/introduction.Rmd | 5 19 files changed, 202 insertions(+), 165 deletions(-)
Title: Fast Pixel-by-Pixel Image Comparison Using 'odiff'
Description: R bindings to 'odiff', a fast SIMD pixel-by-pixel image
comparison tool <https://github.com/dmtrKovalenko/odiff>. Compares PNG,
JPEG, WEBP, TIFF and BMP images, plots and PDF pages with configurable
thresholds, antialiasing detection and ignore regions. Provides 'testthat'
expectations and snapshot testing (including for 'shinytest2' screenshots),
batch and directory comparison, HTML, Markdown and JUnit reports, baseline
approval and audit records. Requires the 'odiff' binary, which can be
downloaded with install_odiff().
Author: Ben Wolstenholme [aut, cre]
Maintainer: Ben Wolstenholme <odiffr@benwolst.dev>
Diff between odiffr versions 0.5.1 dated 2025-12-09 and 0.6.0 dated 2026-10-05
odiffr-0.5.1/odiffr/tests/testthat/_odiffr |only odiffr-0.6.0/odiffr/DESCRIPTION | 34 odiffr-0.6.0/odiffr/MD5 | 184 +- odiffr-0.6.0/odiffr/NAMESPACE | 16 odiffr-0.6.0/odiffr/NEWS.md | 135 + odiffr-0.6.0/odiffr/R/approve.R |only odiffr-0.6.0/odiffr/R/audit.R |only odiffr-0.6.0/odiffr/R/binary.R | 362 ++++ odiffr-0.6.0/odiffr/R/ci-output.R |only odiffr-0.6.0/odiffr/R/compare_images.R | 445 ++++-- odiffr-0.6.0/odiffr/R/expect.R | 199 ++ odiffr-0.6.0/odiffr/R/magick-support.R | 57 odiffr-0.6.0/odiffr/R/odiff_run.R | 239 ++- odiffr-0.6.0/odiffr/R/odiffr-package.R | 38 odiffr-0.6.0/odiffr/R/pdf.R |only odiffr-0.6.0/odiffr/R/render.R |only odiffr-0.6.0/odiffr/R/report.R | 440 ++++- odiffr-0.6.0/odiffr/R/snapshot-report.R |only odiffr-0.6.0/odiffr/R/snapshot.R |only odiffr-0.6.0/odiffr/R/summary.R | 110 + odiffr-0.6.0/odiffr/R/update.R | 198 ++ odiffr-0.6.0/odiffr/R/use-ci.R |only odiffr-0.6.0/odiffr/R/utils.R | 279 ++- odiffr-0.6.0/odiffr/R/view.R |only odiffr-0.6.0/odiffr/R/zzz.R | 8 odiffr-0.6.0/odiffr/README.md | 338 ++-- odiffr-0.6.0/odiffr/build/vignette.rds |binary odiffr-0.6.0/odiffr/inst/WORDLIST |only odiffr-0.6.0/odiffr/inst/doc/getting-started.R | 111 + odiffr-0.6.0/odiffr/inst/doc/getting-started.Rmd | 290 +++ odiffr-0.6.0/odiffr/inst/doc/getting-started.html | 739 ++++++---- odiffr-0.6.0/odiffr/inst/doc/pdf-outputs.R |only odiffr-0.6.0/odiffr/inst/doc/pdf-outputs.Rmd |only odiffr-0.6.0/odiffr/inst/doc/pdf-outputs.html |only odiffr-0.6.0/odiffr/inst/doc/shinytest2.R |only odiffr-0.6.0/odiffr/inst/doc/shinytest2.Rmd |only odiffr-0.6.0/odiffr/inst/doc/shinytest2.html |only odiffr-0.6.0/odiffr/inst/doc/web-pages.R |only odiffr-0.6.0/odiffr/inst/doc/web-pages.Rmd |only odiffr-0.6.0/odiffr/inst/doc/web-pages.html |only odiffr-0.6.0/odiffr/inst/templates |only odiffr-0.6.0/odiffr/man/approve_changes.Rd |only odiffr-0.6.0/odiffr/man/audit_record.Rd |only odiffr-0.6.0/odiffr/man/batch_junit.Rd |only odiffr-0.6.0/odiffr/man/batch_markdown.Rd |only odiffr-0.6.0/odiffr/man/batch_report.Rd | 36 odiffr-0.6.0/odiffr/man/compare_dirs_report.Rd | 5 odiffr-0.6.0/odiffr/man/compare_file_odiff.Rd |only odiffr-0.6.0/odiffr/man/compare_image_dirs.Rd | 29 odiffr-0.6.0/odiffr/man/compare_images.Rd | 39 odiffr-0.6.0/odiffr/man/compare_images_batch.Rd | 20 odiffr-0.6.0/odiffr/man/compare_pdf_dirs.Rd |only odiffr-0.6.0/odiffr/man/compare_pdfs.Rd |only odiffr-0.6.0/odiffr/man/diff_image.Rd |only odiffr-0.6.0/odiffr/man/expect_images.Rd | 19 odiffr-0.6.0/odiffr/man/expect_snapshot_image.Rd |only odiffr-0.6.0/odiffr/man/find_odiff.Rd | 38 odiffr-0.6.0/odiffr/man/install_odiff.Rd |only odiffr-0.6.0/odiffr/man/odiff_available.Rd | 3 odiffr-0.6.0/odiffr/man/odiff_info.Rd | 3 odiffr-0.6.0/odiffr/man/odiff_preset.Rd |only odiffr-0.6.0/odiffr/man/odiff_run.Rd | 59 odiffr-0.6.0/odiffr/man/odiff_version.Rd | 4 odiffr-0.6.0/odiffr/man/odiffr-package.Rd | 48 odiffr-0.6.0/odiffr/man/odiffr_update.Rd | 19 odiffr-0.6.0/odiffr/man/plot.odiff_result.Rd |only odiffr-0.6.0/odiffr/man/plot_options.Rd |only odiffr-0.6.0/odiffr/man/snapshot_report.Rd |only odiffr-0.6.0/odiffr/man/summary.odiffr_batch.Rd | 9 odiffr-0.6.0/odiffr/man/use_odiffr_ci.Rd |only odiffr-0.6.0/odiffr/tests/testthat/helper-batch.R |only odiffr-0.6.0/odiffr/tests/testthat/test-approve.R |only odiffr-0.6.0/odiffr/tests/testthat/test-audit.R |only odiffr-0.6.0/odiffr/tests/testthat/test-binary.R | 356 ++++ odiffr-0.6.0/odiffr/tests/testthat/test-ci-output.R |only odiffr-0.6.0/odiffr/tests/testthat/test-compare_images-errors.R |only odiffr-0.6.0/odiffr/tests/testthat/test-compare_images.R | 113 + odiffr-0.6.0/odiffr/tests/testthat/test-expect.R | 235 +++ odiffr-0.6.0/odiffr/tests/testthat/test-install.R |only odiffr-0.6.0/odiffr/tests/testthat/test-magick-support.R | 18 odiffr-0.6.0/odiffr/tests/testthat/test-odiff_run.R | 381 +++++ odiffr-0.6.0/odiffr/tests/testthat/test-pdf.R |only odiffr-0.6.0/odiffr/tests/testthat/test-render.R |only odiffr-0.6.0/odiffr/tests/testthat/test-report.R | 398 +++++ odiffr-0.6.0/odiffr/tests/testthat/test-snapshot-report.R |only odiffr-0.6.0/odiffr/tests/testthat/test-snapshot.R |only odiffr-0.6.0/odiffr/tests/testthat/test-summary.R | 92 + odiffr-0.6.0/odiffr/tests/testthat/test-update.R | 247 +++ odiffr-0.6.0/odiffr/tests/testthat/test-use-ci.R |only odiffr-0.6.0/odiffr/tests/testthat/test-utils.R | 331 ++++ odiffr-0.6.0/odiffr/tests/testthat/test-view.R |only odiffr-0.6.0/odiffr/tests/testthat/test-zzz.R | 13 odiffr-0.6.0/odiffr/vignettes/getting-started.Rmd | 290 +++ odiffr-0.6.0/odiffr/vignettes/pdf-outputs.Rmd |only odiffr-0.6.0/odiffr/vignettes/shinytest2.Rmd |only odiffr-0.6.0/odiffr/vignettes/web-pages.Rmd |only 96 files changed, 5911 insertions(+), 1116 deletions(-)
Title: Diagnostics for Soil-Plant-Microbial Redox Recovery
Description: Provides diagnostic functions for integrating longitudinal soil,
plant and microbial observations during redox disturbance and recovery.
Functions calculate stoichiometric potential oxygen demand, accessible
electron capacity from explicitly supplied inventories and kinetic
parameters, recovery signatures, fixed-reference domain scores, and
exploratory multiblock scores with observation-coverage diagnostics.
Memory is represented as a holobiont state accumulating from mineralogical,
plant-acclimation and microbial-community legacies.
An illustrative simulator produces closed Fe and Mn inventories alongside
synthetic observations; its carbon, nitrogen, sulfur and oxygen budgets
are not closed and its parameters are not calibrated to field rates.
Simulation benchmarks assess agreement with a prescribed synthetic target
and do not constitute empirical validation or parameter identification.
Accuracy assessment is cluster-aware: intervals come from resampling whole
trajectories, agreement [...truncated...]
Author: Mitra Ghotbi [aut, cre] ,
Marjan Ghotbi [ctb]
Maintainer: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Diff between HRRI versions 1.0.6 dated 2026-09-23 and 1.0.9 dated 2026-10-05
HRRI-1.0.6/HRRI/vignettes/css |only HRRI-1.0.9/HRRI/DESCRIPTION | 10 HRRI-1.0.9/HRRI/MD5 | 77 - HRRI-1.0.9/HRRI/NAMESPACE | 3 HRRI-1.0.9/HRRI/NEWS.md | 61 + HRRI-1.0.9/HRRI/R/HRRI-package.R |only HRRI-1.0.9/HRRI/R/plot_accuracy_paper.R |only HRRI-1.0.9/HRRI/R/plot_internal.R | 15 HRRI-1.0.9/HRRI/R/plot_rri_accuracy.R | 90 + HRRI-1.0.9/HRRI/R/plot_rri_framework.R |only HRRI-1.0.9/HRRI/R/plot_rri_identifiability.R |only HRRI-1.0.9/HRRI/R/plot_rri_properties.R | 441 ++------- HRRI-1.0.9/HRRI/R/plot_rri_recovery_diagnostics.R |only HRRI-1.0.9/HRRI/R/plot_rri_recovery_landscape.R | 79 - HRRI-1.0.9/HRRI/R/plot_rri_recovery_map.R | 119 +- HRRI-1.0.9/HRRI/R/plot_rri_timeseries.R | 47 HRRI-1.0.9/HRRI/R/rri_internal.R | 5 HRRI-1.0.9/HRRI/R/theme_ems.R | 22 HRRI-1.0.9/HRRI/README.md | 53 + HRRI-1.0.9/HRRI/build/partial.rdb |binary HRRI-1.0.9/HRRI/build/vignette.rds |binary HRRI-1.0.9/HRRI/inst/doc/HRRI_gallery.R | 112 +- HRRI-1.0.9/HRRI/inst/doc/HRRI_gallery.Rmd | 482 +++++++++- HRRI-1.0.9/HRRI/inst/doc/HRRI_gallery.html | 769 +++++++--------- HRRI-1.0.9/HRRI/inst/doc/HRRI_paper_figures.R |only HRRI-1.0.9/HRRI/inst/doc/HRRI_paper_figures.Rmd |only HRRI-1.0.9/HRRI/inst/doc/HRRI_paper_figures.html |only HRRI-1.0.9/HRRI/inst/doc/HRRI_workflow.R | 60 - HRRI-1.0.9/HRRI/inst/doc/HRRI_workflow.Rmd | 444 ++++++++- HRRI-1.0.9/HRRI/inst/doc/HRRI_workflow.html | 694 ++++++-------- HRRI-1.0.9/HRRI/inst/examples |only HRRI-1.0.9/HRRI/inst/scripts/check_model_accuracy.R | 13 HRRI-1.0.9/HRRI/man/HRRI-package.Rd |only HRRI-1.0.9/HRRI/man/figures |only HRRI-1.0.9/HRRI/man/plot_rri_accuracy.Rd | 32 HRRI-1.0.9/HRRI/man/plot_rri_framework.Rd |only HRRI-1.0.9/HRRI/man/plot_rri_identifiability.Rd |only HRRI-1.0.9/HRRI/man/plot_rri_properties.Rd | 30 HRRI-1.0.9/HRRI/man/plot_rri_recovery_diagnostics.Rd |only HRRI-1.0.9/HRRI/man/plot_rri_recovery_landscape.Rd | 17 HRRI-1.0.9/HRRI/man/plot_rri_recovery_map.Rd | 28 HRRI-1.0.9/HRRI/man/plot_rri_timeseries.Rd | 19 HRRI-1.0.9/HRRI/tests/testthat/test-gallery-alignment.R |only HRRI-1.0.9/HRRI/tests/testthat/test-paper-figures.R |only HRRI-1.0.9/HRRI/tests/testthat/test-publication-plots.R |only HRRI-1.0.9/HRRI/vignettes/HRRI_gallery.Rmd | 482 +++++++++- HRRI-1.0.9/HRRI/vignettes/HRRI_paper_figures.Rmd |only HRRI-1.0.9/HRRI/vignettes/HRRI_workflow.Rmd | 444 ++++++++- 48 files changed, 3109 insertions(+), 1539 deletions(-)
Title: Geoadditive Small Area Estimation for Area-Level Model
Description: Fits area-level geoadditive small area estimation (SAE)
models by extending the Fay-Herriot area-level model with linear,
nonlinear, and spatial effects. The Fay-Herriot model is described by
Fay and Herriot (1979) <doi:10.1080/01621459.1979.10482505>.
Geoadditive models combine nonlinear covariate effects and spatial
variation as described by Kammann and Wand (2003)
<doi:10.1111/1467-9876.00385>, while their application to small area
estimation is discussed by Pusponegoro et al. (2019)
<doi:10.21108/JDSA.2019.2.15>. Nonlinear covariate effects are represented
using penalized splines, while spatial effects are represented using a
smooth function of geographic coordinates. Models are estimated using
restricted maximum likelihood (REML), and mean squared error (MSE) is
estimated using a parametric bootstrap. The package also provides
comparisons with the Fay-Herriot and spatial Fay-Herriot (SFH) models.
Author: Amalyah Rizky Khairunnisa Sutarto [aut, cre],
Novi Hidayat Pusponegoro [aut, ths]
Maintainer: Amalyah Rizky Khairunnisa Sutarto <222212489@stis.ac.id>
Diff between geoaddSAE2 versions 0.1.0 dated 2026-09-30 and 0.1.1 dated 2026-10-05
DESCRIPTION | 6 - MD5 | 22 +-- NEWS.md | 6 + R/compare.R | 19 ++- R/geoadditive.R | 143 +++++++++++++++-------- README.md | 2 inst/doc/geoaddSAE2-intro.R | 1 inst/doc/geoaddSAE2-intro.Rmd | 1 inst/doc/geoaddSAE2-intro.html | 246 ++++++++++++++++++++--------------------- man/geosae.Rd | 5 tests/testthat/test-data.R | 1 vignettes/geoaddSAE2-intro.Rmd | 1 12 files changed, 250 insertions(+), 203 deletions(-)
Title: Use Foreach to Parallelize via the Future Framework
Description: The 'future' package provides a unifying parallelization framework for R that supports many parallel and distributed backends <doi:10.32614/RJ-2021-048>. The 'foreach' package provides a powerful API for iterating over an R expression in parallel. The 'doFuture' package brings the best of the two together. There are three ways to use this package. The recommended approach is to use 'y <- foreach(...) %do% { ... } |> futurize()' via the 'futurize' package (<doi:10.48550/arXiv.2601.17578>). The second alternative, which was formerly recommended, is to use 'y <- foreach(...) %dofuture% { ... }', which does not require using 'registerDoFuture()' and has many advantages over '%dopar%'. The third alternative is the traditional 'foreach' approach by registering the 'foreach' adapter 'registerDoFuture()' and so that 'y <- foreach(...) %dopar% { ... }' parallelizes with the 'future' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 1.3.0 dated 2026-08-03 and 1.4.0 dated 2026-10-05
DESCRIPTION | 8 - MD5 | 56 ++++++------- NAMESPACE | 48 ++++++----- NEWS.md | 54 ++++++++++++ R/doFuture.R | 32 ++++--- R/doFuture2.R | 90 ++++++++++++++------- R/dofuture_OP.R | 22 ++++- R/makeChunks.R | 9 +- R/registerDoFuture.R | 41 ++++++++- R/utils-debug.R | 9 +- R/with.DoPar.R | 3 R/withDoRNG.R | 7 - inst/CITATION | 2 inst/doc/doFuture-1-overview.html | 4 inst/doc/doFuture-1-overview.md.rsp | 2 inst/doc/doFuture-2-dopar.html | 2 inst/doc/doFuture-3-dofuture.html | 2 inst/testme/test-foreach_dofuture,errors.R | 22 +++++ inst/testme/test-foreach_dofuture,globals.R | 9 ++ inst/testme/test-foreach_dofuture,rng,disposable.R |only inst/testme/test-foreach_dopar,flavor_dofuture.R | 14 +++ inst/testme/test-labels.R | 16 +++ inst/testme/test-makeChunks.R | 53 ++++++++++++ inst/testme/test-with.DoPar.R | 26 ++++++ inst/testme/test-withDoRNG.R | 13 +++ man/grapes-dofuture-grapes.Rd | 24 ++++- man/makeChunks.Rd | 5 - man/registerDoFuture.Rd | 21 ++++ tests/test-foreach_dofuture,rng,disposable.R |only vignettes/doFuture-1-overview.md.rsp | 2 30 files changed, 469 insertions(+), 127 deletions(-)
Title: Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms
of the DBSCAN family. Includes the clustering algorithms DBSCAN
(density-based spatial clustering of applications with noise) and
HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering
points to identify the clustering structure), shared nearest neighbor
clustering, and the outlier detection algorithms LOF (local outlier
factor) and GLOSH (global-local outlier score from hierarchies). The
implementations use the kd-tree data structure (from library ANN) for
faster k-nearest neighbor search. An R interface to fast kNN and
fixed-radius NN search is also provided. Hahsler, Piekenbrock and
Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph] ,
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph],
Claudia Malzer [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.2.6 dated 2026-08-25 and 1.2.7 dated 2026-10-05
dbscan-1.2.6/dbscan/inst/README_files |only dbscan-1.2.6/dbscan/inst/doc/dbscan.Rnw |only dbscan-1.2.6/dbscan/inst/doc/dbscan.pdf |only dbscan-1.2.6/dbscan/vignettes/dbscan.Rnw |only dbscan-1.2.7/dbscan/DESCRIPTION | 31 - dbscan-1.2.7/dbscan/MD5 | 181 +++--- dbscan-1.2.7/dbscan/NAMESPACE | 54 + dbscan-1.2.7/dbscan/NEWS.md | 13 dbscan-1.2.7/dbscan/R/AAA_definitions.R | 64 ++ dbscan-1.2.7/dbscan/R/DBCV_datasets.R | 3 dbscan-1.2.7/dbscan/R/DS3.R | 4 dbscan-1.2.7/dbscan/R/GLOSH.R | 4 dbscan-1.2.7/dbscan/R/LOF.R | 17 dbscan-1.2.7/dbscan/R/NN.R | 2 dbscan-1.2.7/dbscan/R/comps.R | 2 dbscan-1.2.7/dbscan/R/dbcv.R | 4 dbscan-1.2.7/dbscan/R/dbscan.R | 32 - dbscan-1.2.7/dbscan/R/dendrogram.R | 2 dbscan-1.2.7/dbscan/R/extractFOSC.R | 5 dbscan-1.2.7/dbscan/R/frNN.R | 29 dbscan-1.2.7/dbscan/R/hdbscan.R | 10 dbscan-1.2.7/dbscan/R/hullplot.R | 4 dbscan-1.2.7/dbscan/R/jpclust.R | 2 dbscan-1.2.7/dbscan/R/kNN.R | 28 dbscan-1.2.7/dbscan/R/kNNdist.R | 2 dbscan-1.2.7/dbscan/R/moons.R | 17 dbscan-1.2.7/dbscan/R/ncluster.R | 4 dbscan-1.2.7/dbscan/R/optics.R | 296 ---------- dbscan-1.2.7/dbscan/R/optics_extractXi.R |only dbscan-1.2.7/dbscan/R/pointdensity.R | 9 dbscan-1.2.7/dbscan/R/predict.R | 6 dbscan-1.2.7/dbscan/R/reachability.R | 2 dbscan-1.2.7/dbscan/R/sNN.R | 3 dbscan-1.2.7/dbscan/R/sNNclust.R | 2 dbscan-1.2.7/dbscan/README.md | 167 +---- dbscan-1.2.7/dbscan/build/vignette.rds |binary dbscan-1.2.7/dbscan/inst/CITATION | 2 dbscan-1.2.7/dbscan/inst/doc/dbscan.R | 232 +++---- dbscan-1.2.7/dbscan/inst/doc/dbscan.Rmd |only dbscan-1.2.7/dbscan/inst/doc/dbscan.html |only dbscan-1.2.7/dbscan/inst/doc/dbscan_paper_vignette.R |only dbscan-1.2.7/dbscan/inst/doc/dbscan_paper_vignette.Rnw |only dbscan-1.2.7/dbscan/inst/doc/dbscan_paper_vignette.pdf |only dbscan-1.2.7/dbscan/inst/doc/hdbscan.Rmd | 5 dbscan-1.2.7/dbscan/inst/doc/hdbscan.html | 13 dbscan-1.2.7/dbscan/inst/doc/knn.R |only dbscan-1.2.7/dbscan/inst/doc/knn.Rmd |only dbscan-1.2.7/dbscan/inst/doc/knn.html |only dbscan-1.2.7/dbscan/inst/doc/nnclustering.R |only dbscan-1.2.7/dbscan/inst/doc/nnclustering.Rmd |only dbscan-1.2.7/dbscan/inst/doc/nnclustering.html |only dbscan-1.2.7/dbscan/inst/doc/optics.R |only dbscan-1.2.7/dbscan/inst/doc/optics.Rmd |only dbscan-1.2.7/dbscan/inst/doc/optics.html |only dbscan-1.2.7/dbscan/inst/doc/outlier.R |only dbscan-1.2.7/dbscan/inst/doc/outlier.Rmd |only dbscan-1.2.7/dbscan/inst/doc/outlier.html |only dbscan-1.2.7/dbscan/inst/doc/python.R |only dbscan-1.2.7/dbscan/inst/doc/python.Rmd |only dbscan-1.2.7/dbscan/inst/doc/python.html |only dbscan-1.2.7/dbscan/inst/doc/tidyverse.R |only dbscan-1.2.7/dbscan/inst/doc/tidyverse.Rmd |only dbscan-1.2.7/dbscan/inst/doc/tidyverse.html |only dbscan-1.2.7/dbscan/man/DS3.Rd | 2 dbscan-1.2.7/dbscan/man/dbcv.Rd | 2 dbscan-1.2.7/dbscan/man/dbscan-package.Rd | 1 dbscan-1.2.7/dbscan/man/figures/README-OPTICS_extractDBSCAN-1.png |only dbscan-1.2.7/dbscan/man/figures/README-dbscan-1.png |only dbscan-1.2.7/dbscan/man/figures/README-hdbscan-1.png |only dbscan-1.2.7/dbscan/man/frNN.Rd | 2 dbscan-1.2.7/dbscan/man/moons.Rd | 13 dbscan-1.2.7/dbscan/man/optics.Rd | 12 dbscan-1.2.7/dbscan/src/JP.cpp | 2 dbscan-1.2.7/dbscan/src/UnionFind.cpp | 2 dbscan-1.2.7/dbscan/src/UnionFind.h | 2 dbscan-1.2.7/dbscan/src/cleanup.cpp | 2 dbscan-1.2.7/dbscan/src/connectedComps.cpp | 2 dbscan-1.2.7/dbscan/src/dbcv.cpp | 4 dbscan-1.2.7/dbscan/src/dbscan.cpp | 3 dbscan-1.2.7/dbscan/src/dendrogram.cpp | 4 dbscan-1.2.7/dbscan/src/density.cpp | 3 dbscan-1.2.7/dbscan/src/frNN.cpp | 2 dbscan-1.2.7/dbscan/src/hdbscan.cpp | 3 dbscan-1.2.7/dbscan/src/kNN.cpp | 2 dbscan-1.2.7/dbscan/src/lof.cpp | 2 dbscan-1.2.7/dbscan/src/mrd.cpp | 2 dbscan-1.2.7/dbscan/src/mst.cpp | 2 dbscan-1.2.7/dbscan/src/optics.cpp | 3 dbscan-1.2.7/dbscan/src/regionQuery.cpp | 3 dbscan-1.2.7/dbscan/src/regionQuery.h | 2 dbscan-1.2.7/dbscan/src/utilities.cpp | 3 dbscan-1.2.7/dbscan/src/utilities.h | 2 dbscan-1.2.7/dbscan/tests/testthat/test-coverage-misc.R |only dbscan-1.2.7/dbscan/tests/testthat/test-dbscan.R | 1 dbscan-1.2.7/dbscan/tests/testthat/test-frNN.R | 1 dbscan-1.2.7/dbscan/tests/testthat/test-hdbscan.R | 1 dbscan-1.2.7/dbscan/tests/testthat/test-kNN.R | 3 dbscan-1.2.7/dbscan/tests/testthat/test-optics.R | 8 dbscan-1.2.7/dbscan/tests/testthat/test-predict.R | 11 dbscan-1.2.7/dbscan/tests/testthat/test-sNN.R | 1 dbscan-1.2.7/dbscan/tests/testthat/test-validation.R |only dbscan-1.2.7/dbscan/vignettes/dbscan.Rmd |only dbscan-1.2.7/dbscan/vignettes/dbscan_paper_vignette.Rnw |only dbscan-1.2.7/dbscan/vignettes/hdbscan.Rmd | 5 dbscan-1.2.7/dbscan/vignettes/knn.Rmd |only dbscan-1.2.7/dbscan/vignettes/nnclustering.Rmd |only dbscan-1.2.7/dbscan/vignettes/optics.Rmd |only dbscan-1.2.7/dbscan/vignettes/outlier.Rmd |only dbscan-1.2.7/dbscan/vignettes/python.Rmd |only dbscan-1.2.7/dbscan/vignettes/tidyverse.Rmd |only 110 files changed, 537 insertions(+), 827 deletions(-)
Title: Create Consort Diagram
Description: To make it easy to create CONSORT diagrams for the transparent reporting of participant allocation in randomized, controlled clinical trials. This is done by creating a standardized disposition data, and using this data as the source for the creation a standard CONSORT diagram. Human effort by supplying text labels on the node can also be achieved.
Author: Alim Dayim [aut, cre]
Maintainer: Alim Dayim <ad938@cam.ac.uk>
Diff between consort versions 1.2.3 dated 2026-04-25 and 1.2.4 dated 2026-10-05
DESCRIPTION | 13 MD5 | 119 - NAMESPACE | 2 NEWS.md | 12 R/add_box.R | 270 ++-- R/add_label_box.R | 232 +-- R/add_side_box.R | 10 R/add_split.R | 222 +-- R/build_grid.R | 138 +- R/build_grviz.R | 654 ++++----- R/consort_plot.R | 171 +- R/defaults.R | 28 R/gen_text.R | 101 + R/get_coords.R | 36 R/grid_util.R | 394 +++-- R/grviz_util.R | 669 +++++----- R/markup.R | 51 R/move_box.R | 2 R/textbox.R | 108 - R/utils.R | 8 build/vignette.rds |binary inst/doc/consort_diagram.Rmd | 19 inst/doc/consort_diagram.html | 130 - man/build_grid.Rd | 33 man/build_grviz.Rd | 12 man/consort.Rd | 5 man/consort_plot.Rd | 19 man/gen_text.Rd | 20 man/set_consort_defaults.Rd | 34 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/auto/auto-grviz.gv | 32 tests/testthat/_snaps/auto/auto-last-grviz.gv | 20 tests/testthat/_snaps/auto/auto-nolab-grviz.gv | 20 tests/testthat/_snaps/auto/autogen-last.png |binary tests/testthat/_snaps/auto/autogen-nolab.png |binary tests/testthat/_snaps/auto/autogen.png |binary tests/testthat/_snaps/build_grviz/build-grviz-withopts.png |binary tests/testthat/_snaps/build_grviz/build-grviz.png |binary tests/testthat/_snaps/build_grviz/empty-middle-grviz.gv | 24 tests/testthat/_snaps/build_grviz/end-miss-grviz.gv | 32 tests/testthat/_snaps/build_grviz/end-miss-grviz.png |binary tests/testthat/_snaps/build_grviz/grviz-withopts.gv | 38 tests/testthat/_snaps/build_grviz/grviz.gv | 38 tests/testthat/_snaps/build_grviz/multi-miss-grviz.gv | 36 tests/testthat/_snaps/build_grviz/multi-miss-grviz.png |binary tests/testthat/_snaps/build_grviz/nested-split-grviz.gv |only tests/testthat/_snaps/build_grviz/split-comb-grviz.gv | 60 tests/testthat/_snaps/layout |only tests/testthat/_snaps/manually/manually-gen.png |binary tests/testthat/_snaps/multiple-split/multiple-split-nokick.gv | 68 - tests/testthat/_snaps/multiple-split/multiple-split-nokick.png |binary tests/testthat/_snaps/multiple-split/multiple-split.gv | 88 - tests/testthat/_snaps/multiple-split/multiple-split.png |binary tests/testthat/helper-snapshot.R |only tests/testthat/test-auto.R | 224 +-- tests/testthat/test-build_grviz.R | 368 +++-- tests/testthat/test-gen_text.R | 68 - tests/testthat/test-layout.R |only tests/testthat/test-manually.R | 85 - tests/testthat/test-multiple-split.R | 136 -- tests/testthat/test-textbox.R | 18 vignettes/consort_diagram.Rmd | 19 62 files changed, 2591 insertions(+), 2295 deletions(-)
Title: Get EC2 Instance Metadata
Description: Retrieve Amazon EC2 instance metadata from within the running instance.
Author: Thomas J. Leeper [aut] ,
Jonathan Stott [aut],
Gonzalo Diaz [cre, aut] ,
Michael Condouris [ctb]
Maintainer: Gonzalo Diaz <gonzalomartindiaz22@gmail.com>
This is a re-admission after prior archival of version 0.2.0 dated 2019-07-15
Diff between aws.ec2metadata versions 0.2.0 dated 2019-07-15 and 0.2.2 dated 2026-10-05
DESCRIPTION | 29 +- MD5 | 16 - NAMESPACE | 18 - NEWS.md | 67 +++-- R/aws.ec2metadata-package.R | 517 +++++++++++++++++++++++--------------------- R/onLoad.R | 18 - README.md | 111 +++++---- inst/CITATION | 38 +-- man/ec2metadata.Rd | 180 +++++++-------- 9 files changed, 534 insertions(+), 460 deletions(-)
More information about aws.ec2metadata at CRAN
Permanent link
Title: Translates an R Function to a C++ Function
Description: Enable translation of a tiny subset of R to C++. The user has to define a R function which gets translated. For a full list of possible functions check the documentation. After translation an R function is returned which is a shallow wrapper around the C++ code. Alternatively an external pointer to the C++ function is returned to the user. The intention of the package is to generate fast functions which can be used as ode-system or during optimization.
Author: Kraemer Konrad [aut, cre]
Maintainer: Kraemer Konrad <konrad_kraemer@yahoo.de>
Diff between ast2ast versions 1.0 dated 2026-09-14 and 1.0.2 dated 2026-10-05
DESCRIPTION | 8 ++-- MD5 | 8 ++-- inst/include/etr_bits/Core/Scalars.hpp | 65 +++++++++++++++++++-------------- inst/include/etr_bits/Core/Types.hpp | 6 ++- src/tests_scalar_types.cpp | 13 ++++++ 5 files changed, 64 insertions(+), 36 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-16 1.0.2
2025-07-22 1.0.1