Title: EBGM Disproportionality Scores for Adverse Event Data Mining
Description: An implementation of DuMouchel's (1999) <doi:10.1080/00031305.1999.10474456>
Bayesian data mining method for the market basket problem.
Calculates Empirical Bayes Geometric Mean (EBGM) and posterior quantile scores
using the Gamma-Poisson Shrinker (GPS) model to find unusually large cell
counts in large, sparse contingency tables. Can be used to find unusually high
reporting rates of adverse events associated with products. In general, can be
used to mine any database where the co-occurrence of two variables or items is
of interest. Also calculates relative and proportional reporting ratios.
Builds on the work of the 'PhViD' package, from which much of the code is
derived. Some of the added features include stratification to adjust for
confounding variables and data squashing to improve computational efficiency.
Includes an implementation of the EM algorithm for hyperparameter estimation
loosely derived from the 'mederrRank' package.
Author: John Ihrie [cre, aut],
Travis Canida [aut],
Ismail Ahmed [ctb] ),
Antoine Poncet [ctb] ,
Sergio Venturini [ctb] ),
Jessica Myers [ctb]
Maintainer: John Ihrie <John.Ihrie@fda.hhs.gov>
Diff between openEBGM versions 0.10.0 dated 2026-09-03 and 0.11.0 dated 2026-10-22
DESCRIPTION | 6 MD5 | 40 ++-- NEWS.md | 5 R/f_EM_helpers.R | 8 R/f_EM_hyperEstimation.R | 20 +- R/f_EM_scoreFunctions.R | 51 +++-- R/f_EM_updateTheta.R | 15 + R/f_createObject.R | 11 - R/f_hyperConfIntervals.R | 64 +++++- R/f_hyperEstimation.R | 12 - R/f_likelihoodEqs.R | 44 ++-- inst/doc/vignette01-introAndDataPrep.html | 4 inst/doc/vignette02-rawDataProcessing.html | 4 inst/doc/vignette03-hyperparameterEstimation.R | 2 inst/doc/vignette03-hyperparameterEstimation.Rmd | 5 inst/doc/vignette03-hyperparameterEstimation.html | 148 ++++++--------- inst/doc/vignette04-posteriorCalculation.html | 4 inst/doc/vignette05-openEBGMObject.html | 4 man/hyperEM.Rd | 10 - tests/testthat/testHypers.R | 214 ++++++++++------------ vignettes/vignette03-hyperparameterEstimation.Rmd | 5 21 files changed, 367 insertions(+), 309 deletions(-)
Title: Bias Diagnostic for Linear Mixed Models
Description: Provides a function to perform bias diagnostics on linear mixed models fitted with lmer() from the 'lme4' package. Compares an internal random-effects alignment diagnostic with a fitted permutation reference distribution, following Karl and Zimmerman (2021) <doi:10.1016/j.jspi.2020.06.004>. Conditional response-refit simulations separately record random-effects alignment and residual-weight contributions to estimation error. Karl and Zimmerman (2020) <doi:10.17632/tmynggddfm.1> provide R code for implementing the test using 'mvglmmRank' output. Development and review were assisted by 'GPT o1-preview', 'GPT 5 Pro', and 'GPT6 Astra'; the author is responsible for the code and its interpretation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mixedbiastest versions 1.0.3 dated 2026-09-18 and 1.1.0 dated 2026-10-22
DESCRIPTION | 12 MD5 | 26 + NAMESPACE | 2 NEWS.md | 72 +++- R/mixedbiastest-package.R | 17 - R/mixedbiastest.R | 496 +++++++++++++--------------------- R/model_components.R |only R/plot.R | 4 R/print-simulation.R |only R/print.R | 2 R/simulate_bias.R |only man/mixedbiastest-package.Rd | 17 - man/mixedbiastest.Rd | 32 +- man/plot.mixedbiastest.Rd | 2 man/print.mixedbiastest_simulation.Rd |only man/simulate_bias.Rd |only tests/testthat/test-simulate-bias.R |only 17 files changed, 321 insertions(+), 361 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>,
estimates generalized, reduced generalized, variable, complete, and zero
persistence models by maximum likelihood or restricted maximum likelihood
(the default). These are multiple-membership linear mixed models with
teachers modeled as "G-side" effects and students modeled with either
"G-side" or "R-side" effects; see Mariano et al. (2010)
<doi:10.3102/1076998609346967>.
Author: Andrew Karl [cre, aut] ,
Yan Yang [aut],
Sharon Lohr [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.3-0 dated 2026-09-18 and 3.4-0 dated 2026-10-22
DESCRIPTION | 10 +- MD5 | 25 ++++--- NAMESPACE | 2 NEWS | 30 ++++++++ R/GPvam-package.R | 8 +- R/GPvam.R | 11 +++ R/bias.test.custom.R | 100 ++++++++++++++++++++++++----- R/simulate_bias.R |only man/GPvam-package.Rd | 8 +- man/GPvam.Rd | 3 man/bias.test.custom.Rd | 81 ++++++++++++++++++++--- man/print.GPvam_simulation.Rd |only man/simulate_bias.Rd |only tests/testthat/helper-simulation-fixture.R |only tests/testthat/test-diagnostics.R | 36 ++++++++++ tests/testthat/test-simulate-bias.R |only 16 files changed, 271 insertions(+), 43 deletions(-)
Title: Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have
Accompanying Setup Files (.sps or .sas)
Description: Lets you open a fixed-width ASCII file (.txt or
.dat) that has an accompanying setup file (.sps or .sas). These file
combinations are sometimes referred to as .txt+.sps, .txt+.sas,
.dat+.sps, or .dat+.sas. This will only run in a txt-sps or txt-sas
pair in which the setup file contains instructions to open that text
file. It will NOT open other text files, .sav, .sas, or .por data
files. Fixed-width ASCII files with setup files are common in older
(pre-2000) government data.
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between asciiSetupReader versions 2.6.0 dated 2026-10-17 and 3.0.0 dated 2026-10-22
asciiSetupReader-2.6.0/asciiSetupReader/inst/testdata |only asciiSetupReader-2.6.0/asciiSetupReader/man/figures/asciiSetupReader_badge.png |only asciiSetupReader-3.0.0/asciiSetupReader/DESCRIPTION | 14 asciiSetupReader-3.0.0/asciiSetupReader/MD5 | 365 +- asciiSetupReader-3.0.0/asciiSetupReader/NEWS.md | 241 + asciiSetupReader-3.0.0/asciiSetupReader/R/helper.R | 332 -- asciiSetupReader-3.0.0/asciiSetupReader/R/make_sps_setup.R | 4 asciiSetupReader-3.0.0/asciiSetupReader/R/messages.R |only asciiSetupReader-3.0.0/asciiSetupReader/R/parse_setup.R | 1496 ++++++++-- asciiSetupReader-3.0.0/asciiSetupReader/R/read_ascii_setup.R | 233 + asciiSetupReader-3.0.0/asciiSetupReader/R/sas.R | 8 asciiSetupReader-3.0.0/asciiSetupReader/R/spss.R | 12 asciiSetupReader-3.0.0/asciiSetupReader/R/utils.R | 412 ++ asciiSetupReader-3.0.0/asciiSetupReader/R/value_labels.R |only asciiSetupReader-3.0.0/asciiSetupReader/README.md | 11 asciiSetupReader-3.0.0/asciiSetupReader/inst/doc/Introduction_to_asciiSetupReader.R | 2 asciiSetupReader-3.0.0/asciiSetupReader/inst/doc/Introduction_to_asciiSetupReader.Rmd | 12 asciiSetupReader-3.0.0/asciiSetupReader/inst/doc/Introduction_to_asciiSetupReader.html | 31 asciiSetupReader-3.0.0/asciiSetupReader/inst/doc/making-an-sps-file.html | 4 asciiSetupReader-3.0.0/asciiSetupReader/inst/doc/parsing-an-sps-or-sas-file.Rmd | 4 asciiSetupReader-3.0.0/asciiSetupReader/inst/doc/parsing-an-sps-or-sas-file.html | 43 asciiSetupReader-3.0.0/asciiSetupReader/man/figures/logo.png |only asciiSetupReader-3.0.0/asciiSetupReader/man/parse_setup.Rd | 34 asciiSetupReader-3.0.0/asciiSetupReader/man/read_ascii_setup.Rd | 114 asciiSetupReader-3.0.0/asciiSetupReader/man/sas_ascii_reader.Rd | 27 asciiSetupReader-3.0.0/asciiSetupReader/man/spss_ascii_reader.Rd | 27 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/fixtures |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/helper-files.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/helper-messages.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/setup.R | 982 ++---- asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-all-value-labels-assigned.R | 2 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-column-labels.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-column-names.R | 10 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-column-type.R | 226 - asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-column-widths.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-data-list.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-dimensions-missing.R | 11 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-edge-cases.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-error.R | 3 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-implied-decimals.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-messages.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-missing-ranges.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-missing-values-argument.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-missing-values.R | 80 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-parse-value-labels-sas.R | 78 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-parse-value-labels-sps.R | 88 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-parser-missing-sas.R | 2 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-parser-missing-sps.R | 6 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-parser-sas.R | 74 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-parser-sps.R | 58 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-psid-test.R | 129 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-reading-values.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-sas-formats.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-sas-statements.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-setup-files.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-silent.R | 28 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-unique-names.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-value-labels-lists.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-value-labels-quoting.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-value-labels-real-files.R |only asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/test-value-labels.R | 2 asciiSetupReader-3.0.0/asciiSetupReader/tests/testthat/testdata |only asciiSetupReader-3.0.0/asciiSetupReader/vignettes/Introduction_to_asciiSetupReader.Rmd | 12 asciiSetupReader-3.0.0/asciiSetupReader/vignettes/parsing-an-sps-or-sas-file.Rmd | 4 64 files changed, 3394 insertions(+), 1827 deletions(-)
More information about asciiSetupReader at CRAN
Permanent link
Title: Differential Item Functioning for AI-Scored Assessments
Description: Detects and quantifies differential item functioning (DIF) in
AI-scored educational and psychological assessments. Provides a fully
self-contained robust DIF engine (M-estimation via iteratively
re-weighted least squares with the bi-square loss), cross-checked
against the reference implementation in 'robustDIF', alongside the
Differential AI Scoring Bias (DASB) test, which detects item-level
scoring shifts that differ across subgroups when comparing human and AI
scoring conditions. Supports independent and paired scoring designs,
including a bootstrap estimator of the cross-condition covariance that
paired designs require, a one-call workflow from raw item scores
through 'mirt' calibration, robust linking of the cross-condition
contrast, bootstrap standard errors, multiplicity control, simulation
of paired human and AI item scores, anchor weight diagnostics, and an
AI-effect classification framework. Methods follow Halpin (2024)
<doi:10.1007/s11336-024-09957-6>.
Author: Subir Hait [aut, cre]
Maintainer: Subir Hait <haitsubi@msu.edu>
Diff between aiDIF versions 0.2.0 dated 2026-09-05 and 0.3.0 dated 2026-10-22
DESCRIPTION | 30 +- MD5 | 35 +- NAMESPACE | 40 +-- NEWS.md | 53 ++++ R/adapters.R | 56 ++++ R/aidif_core.R | 5 R/responses.R |only R/scoring_bias.R | 14 - R/validate_inputs.R | 4 README.md | 32 ++ build/partial.rdb |only inst/doc/introduction.R | 15 + inst/doc/introduction.Rmd | 69 ++++- inst/doc/introduction.html | 524 ++++++++++++++++++++++------------------ man/compare_robustdif.Rd |only man/fit_aidif.Rd | 3 man/fit_aidif_responses.Rd |only man/paired_cross_cov.Rd |only man/scoring_bias_test.Rd | 6 man/simulate_aidif_responses.Rd |only tests/testthat/test-responses.R |only vignettes/introduction.Rmd | 69 ++++- 22 files changed, 659 insertions(+), 296 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] ,
Devin J. Johnson [aut] ,
Peter Mueller [aut],
Andres Felipe Barrientos [aut],
Garritt Page [aut],
David Dunson [aut],
Authors of the dependency Rust crates [ctb]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.3.79 dated 2026-09-24 and 0.3.80 dated 2026-10-22
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 8 ++++++++ inst/AUTHORS | 35 ++++++++++++----------------------- src/rust/Cargo.lock | 27 +++++++++++++++------------ src/rust/Cargo.toml | 11 +++-------- src/rust/src/lib.rs | 45 +++++++++++++++++++++++++++++++++------------ src/rust/vendor.tar.xz |binary 8 files changed, 81 insertions(+), 65 deletions(-)
Title: Terrains and Routes Directed in Spacetime
Description: Implements classes and methods for constructing and analysing graph representations of complex geographic spaces at local to global scales, particularly where accessible spaces are discontinuously distributed but retain connectivity (e.g., island systems where isolation is prevalent but not necessarily absolute), and where that distribution also changes through time (e.g., habitat patch fragmentation or plate tectonic drift). The package (originally named TARDIS) was first described and published in: Flannery-Sutherland, J., Elsler, A., Farnsworth, A., Lunt, D., Benton, M. (2025) <doi:10.1038/s41559-025-02739-y>.
Author: Joe Flannery-Sutherland [aut, cre]
Maintainer: Joe Flannery-Sutherland <josephflannerysutherland@gmail.com>
Diff between rTARDIS versions 2.1.1 dated 2026-10-21 and 2.1.2 dated 2026-10-22
DESCRIPTION | 10 MD5 | 88 +-- NAMESPACE | 61 +- R/build_tardis.R | 9 R/cell_to_coords.R | 47 +- R/click_iso.R | 4 R/click_lcp.R | 4 R/click_msa.R | 5 R/click_optim.R | 5 R/click_points.R | 4 R/click_to_link.R | 4 R/click_to_snip.R | 4 R/cumulative_cost.R | 2 R/domains.R | 134 ++--- R/get_cost.R | 4 R/instantiate_tardis.R | 68 +- R/isochrone.R | 2 R/least_cost.R | 8 R/link_islands.R | 27 - R/min_span.R | 321 +++++++------ R/optim_route.R | 281 ++++++------ R/plot.geoglist.R | 464 ++++++++++---------- R/plot_globe.R | 1 R/point_check.R | 199 +++++--- R/rand_walk.R | 2 R/read_geoglist.R |only R/save_geoglist.R |only R/slice_geoglist.R | 2 R/slice_tardis.R | 13 README.md | 14 build/vignette.rds |binary inst/doc/building-landscapes.R | 8 inst/doc/building-landscapes.Rmd | 2 inst/doc/building-landscapes.html | 284 ++++++------ inst/doc/geographic-distances-and-re-weighting.html | 48 -- inst/doc/package-overview.html | 13 inst/doc/palaeogeography-quick-guide.R | 58 +- inst/doc/palaeogeography-quick-guide.html | 4 man/cell_to_coords.Rd | 34 + man/min_span.Rd | 36 + man/optim_route.Rd | 26 - man/plot.Rd | 15 man/point_check.Rd | 21 man/read_geoglist.Rd |only man/save_geoglist.Rd |only man/slice_tardis.Rd | 4 vignettes/building-landscapes.Rmd | 2 47 files changed, 1284 insertions(+), 1058 deletions(-)
Title: Map Quantiles for Physical Activity from 'NHANES'
Description: Maps physical activity from the National Health and Nutrition
Examination Survey ('NHANES') study into population-based quantiles,
using the NHANES 2011-2014 step count and physical activity summaries
described in Koffman, Crainiceanu, and Muschelli (2025)
<doi:10.1249/MSS.0000000000003616>, with minute-level data from
Koffman and Muschelli (2025) <doi:10.13026/9n0r-tv02>.
Author: John Muschelli [aut, cre] ,
Lily Koffman [aut]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between mapnhanespa versions 0.2.0 dated 2026-08-21 and 0.3.0 dated 2026-10-22
DESCRIPTION | 23 ++- MD5 | 27 ++-- NAMESPACE | 2 NEWS.md | 22 +++ R/map-quantiles.R | 76 +---------- R/measure-map.R |only README.md | 171 ++++++++++++++++++++++---- inst/doc/mapnhanespa.R | 24 +++ inst/doc/mapnhanespa.Rmd | 38 +++++ inst/doc/mapnhanespa.html | 231 ++++++++++++++++++++++++++---------- man/map_nhanes_pa_quantiles.Rd | 10 + man/nhanes_pa_measure_cdf.Rd |only man/nhanes_pa_measure_map.Rd |only man/nhanes_pa_quantile.Rd | 7 - tests/testthat/test-map-quantiles.R | 50 +++++++ vignettes/mapnhanespa.Rmd | 38 +++++ 16 files changed, 526 insertions(+), 193 deletions(-)
Title: 'GGML' Tensor Operations for Machine Learning
Description: Provides 'R' bindings to the 'GGML' tensor library for machine
learning, optimized for 'Vulkan' GPU acceleration with a transparent CPU
fallback. The package features a 'Keras'-like sequential API and a
'PyTorch'-style 'autograd' engine for building, training, and deploying
neural networks. Key capabilities include high-performance 5D tensor
operations, 'f16' precision, and efficient quantization. It supports
native 'ONNX' model import (50+ operators) and 'GGUF' weight loading
from the 'llama.cpp' and 'Hugging Face' ecosystems. Designed for
zero-overhead inference via dedicated weight buffering, it integrates
seamlessly as a 'parsnip' engine for 'tidymodels' and provides
first-class learners for the 'mlr3' framework.
See <https://github.com/ggml-org/ggml> for more information about the
underlying library.
Author: Yuri Baramykov [aut, cre] ,
Georgi Gerganov [ctb, cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
Mozilla Foundation [ctb, cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between ggmlR versions 0.8.8 dated 2026-10-20 and 0.8.8.1 dated 2026-10-22
DESCRIPTION | 6 MD5 | 75 +- NEWS.md | 6 R/ag_device.R | 106 ++- R/ag_tape_memory.R | 12 R/autograd.R | 56 + README.md | 31 inst/doc/autograd-engine.R | 30 inst/doc/autograd-engine.Rmd | 61 + inst/doc/autograd-engine.html | 411 +++++++------ inst/doc/gpu-vulkan.R | 6 inst/doc/gpu-vulkan.Rmd | 55 + inst/doc/gpu-vulkan.html | 97 ++- inst/doc/keras-like-api.R | 113 +++ inst/doc/keras-like-api.Rmd | 208 ++++++ inst/doc/keras-like-api.html | 817 ++++++++++++++++---------- inst/doc/onnx-import.R | 26 inst/doc/onnx-import.Rmd | 159 +++-- inst/doc/onnx-import.html | 487 +++++++++++++-- man/optimizer_adam.Rd | 8 src/ggml-core.c | 161 +++-- src/ggml-cpu/ggml-cpu-backend.c | 35 - src/ggml-cpu/vec.cpp | 4 src/ggml-cpu/vec.h | 4 src/ggml-vulkan/ggml-vulkan-umap.cpp | 14 src/ggml-vulkan/vulkan-shaders/roi_align.comp | 11 src/onnx/onnx_ggml.c | 16 src/onnx/onnx_ops_internal.h | 8 src/onnx/onnx_ops_nn.c | 18 src/onnx/onnx_ops_tensor.c | 12 src/onnx/roi_align.c | 30 src/r_interface.c | 13 src/r_interface_graph.c | 19 tests/testthat/test-ag-adam-f16-master.R |only tests/testthat/test-ag-adam-fused.R | 6 vignettes/autograd-engine.Rmd | 61 + vignettes/gpu-vulkan.Rmd | 55 + vignettes/keras-like-api.Rmd | 208 ++++++ vignettes/onnx-import.Rmd | 159 +++-- 39 files changed, 2741 insertions(+), 863 deletions(-)
Title: Maps of the Provinces, Cantons and Parishes of Ecuador (Mapas de
Provincias, Cantones y Parroquias del Ecuador)
Description: Provides the boundaries of the provinces, cantons and parishes
of Ecuador as 'sf' objects, identified by the codes of the national
political-administrative division (DPA, "División Político-Administrativa"),
ready to be mapped and joined with health, epidemiological surveillance or
other data. The three levels nest exactly and are offered in two
resolutions: a light one for maps and dashboards and a detailed one for
spatial analysis. The layers are derived from the open data of the
Territorial Organization of the State published by the National Committee
of Internal Boundaries (CONALI, Ministry of Government of Ecuador) under a
CC BY licence <https://www.datosabiertos.gob.ec/>, and are downloaded on
first use as 'GeoPackage' files, verified and cached locally. Includes a
catalogue of DPA codes, a table to update codes from earlier versions,
helpers to clean codes and place names, and tools to relocate the
Galapagos Islands in national maps. Documentation is in Spanish.
Author: Ronald Fabricio Salas Guerrero [aut, cre, cph]
Maintainer: Ronald Fabricio Salas Guerrero <fabriciosalasguerrero@gmail.com>
Diff between geoecu versions 0.3.0 dated 2026-10-22 and 0.4.0 dated 2026-10-22
DESCRIPTION | 24 +++++--- MD5 | 58 +++++++++++---------- NAMESPACE | 1 NEWS.md | 46 ++++++++++++++++ R/archivos.R | 12 ++++ R/datos.R | 59 +++++++++++++++++++-- R/galapagos.R | 2 R/geoecu-package.R | 10 ++- R/leer.R | 63 ++++++++++++++++++----- R/utilidades.R | 50 ++++++++++++++++++ R/zzz.R | 8 ++ README.md | 98 ++++++++++++++++++++++++++++-------- data/dpa.rda |binary data/dpa_equivalencias.rda |only inst |only man/actualizar_codigo.Rd |only man/dpa.Rd | 25 ++++++--- man/dpa_equivalencias.Rd |only man/figures/README-loja.png |binary man/figures/README-nacional.png |binary man/figures/README-niveles.png |binary man/figures/logo.png |binary man/geoecu-package.Rd | 16 +++++ man/geoecu_cache_dir.Rd | 2 man/geoecu_limpiar_cache.Rd | 2 man/geoecu_unir.Rd | 2 man/marco_galapagos.Rd | 2 man/read_dpa.Rd | 46 ++++++++++++---- man/reubicar_galapagos.Rd | 2 tests/testthat/test-dpa.R | 26 ++++++--- tests/testthat/test-equivalencias.R |only tests/testthat/test-leer.R | 35 +++++++++--- 32 files changed, 467 insertions(+), 122 deletions(-)
Title: Retrieve Data on European Union Law
Description: Access to data on European Union laws and court decisions made easy with pre-defined 'SPARQL' queries and 'GET' requests. See Ovadek (2021) <doi:10.1080/2474736X.2020.1870150> .
Author: Michal Ovadek [aut, cre, cph]
Maintainer: Michal Ovadek <michal.ovadek@gmail.com>
Diff between eurlex versions 0.5.0 dated 2026-07-08 and 0.5.1 dated 2026-10-22
eurlex-0.5.0/eurlex/R/elx_council_votes.R |only eurlex-0.5.1/eurlex/DESCRIPTION | 6 eurlex-0.5.1/eurlex/MD5 | 23 + eurlex-0.5.1/eurlex/NEWS.md | 17 + eurlex-0.5.1/eurlex/R/elx_make_query.R | 192 +++++++++------ eurlex-0.5.1/eurlex/R/elx_make_query_new.R |only eurlex-0.5.1/eurlex/R/elx_query_helpers.R |only eurlex-0.5.1/eurlex/R/test_byte_identical.R |only eurlex-0.5.1/eurlex/inst/doc/sparql-queries.Rmd | 2 eurlex-0.5.1/eurlex/inst/doc/sparql-queries.html | 8 eurlex-0.5.1/eurlex/man/elx_make_query.Rd | 24 + eurlex-0.5.1/eurlex/tests/testthat/test-download-xml.R |only eurlex-0.5.1/eurlex/tests/testthat/test-eurovoc.R |only eurlex-0.5.1/eurlex/tests/testthat/test-make-query-new.R |only eurlex-0.5.1/eurlex/tests/testthat/test-query.R | 166 ++++++++++++ eurlex-0.5.1/eurlex/vignettes/sparql-queries.Rmd | 2 16 files changed, 344 insertions(+), 96 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Benedikt Sommer [ctb],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.9.3 dated 2026-08-20 and 1.10 dated 2026-10-22
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Title: Missing Morphometric Data Simulation and Estimation
Description: Functions for simulating missing morphometric
data randomly, with taxonomic bias and with anatomical bias. LOST also
includes functions for estimating linear and geometric morphometric data.
Author: J. Arbour [aut, cre],
C. Brown [aut]
Maintainer: J. Arbour <jessica.arbour@mtsu.edu>
Diff between LOST versions 2.1.4 dated 2026-07-14 and 2.1.5 dated 2026-10-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/bilat.align.R | 35 +++++++++++++++++++++++++---------- R/unbend.spine.R | 25 ++++++++++++++++++++----- R/unbend.tps.poly.R | 18 +++++++++++++++--- man/bilat.align.Rd | 2 +- man/unbend.spine.Rd | 7 +++++-- man/unbend.tps.poly.Rd | 2 +- 8 files changed, 78 insertions(+), 33 deletions(-)
Title: Import, Inspect, Analyse, and Report Gazepoint GP3 Exports
Description: Tools for importing, inspecting, cleaning, summarising,
modelling, and reporting Gazepoint GP3 and Gazepoint Analysis CSV
exports. The package supports offline workflows for all-gaze,
fixation, pupil, area-of-interest, transition, time-course, quality-audit, and
manuscript-reporting analyses.
The package methodology is described in the peer-reviewed
software paper <doi:10.3390/jemr19040076>.
Author: Stefanos Balaskas [aut, cre]
Maintainer: Stefanos Balaskas <s.balaskas@ac.upatras.gr>
Diff between gp3tools versions 2.3.0 dated 2026-08-21 and 2.4.2 dated 2026-10-22
DESCRIPTION | 15 MD5 | 1086 +- NAMESPACE | 585 - NEWS.md | 1168 +- R/advanced_aoi_assignment.R | 2830 +++--- R/aoi_entropy.R | 388 R/aoi_sequence_helpers.R | 396 R/aoi_sequence_metrics.R | 260 R/aoi_uncertainty_eyeprocess_adapter.R |only R/as_gazepoint_master.R | 828 - R/audit_gazepoint_aoi_coding_matrix.R | 1576 +-- R/audit_gazepoint_aoi_geometry.R | 1318 +-- R/audit_gazepoint_aoi_margin_sensitivity.R | 1496 +-- R/audit_gazepoint_aoi_overlap.R | 968 +- R/audit_gazepoint_aoi_window_denominators.R | 836 - R/audit_gazepoint_condition_quality_imbalance.R | 1008 +- R/audit_gazepoint_design_balance.R | 968 +- R/audit_gazepoint_event_sync.R | 1148 +- R/audit_gazepoint_exclusion_flow.R | 1368 +-- R/audit_gazepoint_gaze_signal_quality.R | 1394 +-- R/audit_gazepoint_master.R | 668 - R/audit_gazepoint_post_exclusion_balance.R | 1720 ++-- R/audit_gazepoint_pupil_baseline.R | 940 +- R/audit_gazepoint_pupil_drift.R | 1024 +- R/audit_gazepoint_pupil_gaps.R | 686 - R/audit_gazepoint_pupil_imbalance.R | 822 - R/audit_gazepoint_pupil_overlap_risk.R | 926 +- R/audit_gazepoint_pupil_reliability.R | 1312 +-- R/audit_gazepoint_stimulus_luminance.R | 1048 +- R/baseline_correct_gazepoint_pupil.R | 854 +- R/bayesian_planning_helpers.R | 1626 +-- R/binocular_pupil_reconstruction.R | 2240 ++--- R/binocular_pupil_validation.R | 1968 ++-- R/binocular_trackloss_simulation_extensions.R | 802 - R/check_gazepoint_file_pairs.R | 292 R/check_gazepoint_model_convergence.R | 418 R/check_gazepoint_model_overdispersion.R | 426 - R/check_gazepoint_model_singularity.R | 284 R/check_gazepoint_real_data_readiness.R | 2086 ++-- R/cluster_permutation_extensions.R | 2614 +++--- R/compare_gazepoint_nested_models.R | 844 - R/compute_gazepoint_aoi_transition_matrix.R | 834 - R/compute_gazepoint_time_varying_transition_matrix.R | 1052 +- R/create_gazepoint_analysis_decision_audit.R | 1550 +-- R/create_gazepoint_markovchain_object.R | 1162 +- R/create_gazepoint_master.R | 724 - R/create_gazepoint_preprocessing_multiverse.R | 908 +- R/create_gazepoint_preprocessing_registry.R | 464 - R/create_gazepoint_report.R | 570 - R/create_gazepoint_reporting_checklist.R | 2220 ++--- R/data.R | 216 R/diagnose_gazepoint_gamm.R | 908 +- R/diagnose_gazepoint_glmm.R | 1198 +- R/estimate_gazepoint_divergence_point.R | 1398 +-- R/event_detection_extensions.R | 1424 +-- R/event_detector_benchmarking.R | 3278 +++---- R/event_detector_comparison.R | 3876 ++++----- R/experimental_bayesian_bridges.R | 1118 +- R/export_gazepoint_master_audit.R | 452 - R/export_gazepoint_model_tables.R | 718 - R/export_gazepoint_tables.R | 240 R/face_export_import.R | 1158 +- R/face_quality_audit.R | 1552 +-- R/face_reporting.R | 1590 +-- R/face_sync.R | 1826 ++-- R/face_window_summaries.R | 2194 ++--- R/final_statistical_extensions.R | 744 - R/fit_gazepoint_aoi_gamm.R | 850 - R/fit_gazepoint_aoi_model_sensitivity.R | 1118 +- R/fit_gazepoint_aoi_window_glmm.R | 844 - R/fit_gazepoint_gca.R | 1004 +- R/fit_gazepoint_pupil_gamm.R | 756 - R/fit_gazepoint_pupil_pfe_gamm.R | 1078 +- R/fit_gazepoint_pupil_window_lmm.R | 1182 +- R/fit_gazepoint_pupil_window_sensitivity.R | 744 - R/fit_gazepoint_transition_count_nb_sensitivity.R | 1258 +- R/fixation_reliability.R | 610 - R/flag_gazepoint_pupil.R | 624 - R/flag_gazepoint_pupil_artifacts.R | 1636 +-- R/flag_gazepoint_pupil_hampel.R | 830 - R/flag_tracking_quality.R | 264 R/gaze-survival-adapter.R |only R/gazepoint_spatial_quality.R |only R/gpbiometrics_bridge.R | 1938 ++-- R/heatmap_spatial_visualisation.R | 1296 +-- R/high_priority_signal_helpers.R | 580 - R/interpolate_gazepoint_pupil.R | 754 - R/interpolate_gazepoint_pupil_pchip.R | 952 +- R/markov_semimarkov_summaries.R | 698 - R/missingness_coverage_extensions.R | 636 - R/model_reporting_extensions.R | 622 - R/multimodal_modelling.R | 1280 +-- R/naming_compatibility_aliases.R | 96 R/naming_policy.R | 382 R/package-globals.R | 106 R/performance_benchmarking.R | 1782 ++-- R/phase_segmentation_extensions.R | 998 +- R/plot_aoi_timeline.R | 328 R/plot_diagnostics.R | 452 - R/plot_gazepoint_aoi_gamm.R | 1118 +- R/plot_gazepoint_aoi_transition_matrix.R | 778 - R/plot_gazepoint_aoi_verification.R | 742 - R/plot_gazepoint_binocular_diagnostics.R | 672 - R/plot_gazepoint_cluster_results.R | 870 +- R/plot_gazepoint_gca.R | 748 - R/plot_gazepoint_model_predictions.R | 1324 +-- R/plot_gazepoint_multiverse_results.R | 716 - R/plot_gazepoint_pupil_preprocessing.R | 1052 +- R/plot_gazepoint_pupil_status.R | 906 +- R/plot_gazepoint_pupil_timecourse.R | 682 - R/prepare_gazepoint_aoi_gamm_data.R | 1094 +- R/prepare_gazepoint_aoi_glmm_data.R | 650 - R/prepare_gazepoint_aoi_sequences.R | 590 - R/prepare_gazepoint_cluster_data.R | 920 +- R/prepare_gazepoint_eyetools_data.R | 1350 +-- R/prepare_gazepoint_eyetrackingr_data.R | 1114 +- R/prepare_gazepoint_fixation_aligned_data.R | 982 +- R/prepare_gazepoint_gazer_data.R | 1104 +- R/prepare_gazepoint_gca_data.R | 728 - R/prepare_gazepoint_hmm_data.R | 1922 ++-- R/prepare_gazepoint_pupil_gamm_data.R | 1122 +- R/prepare_gazepoint_pupil_window_model_data.R | 746 - R/prepare_gazepoint_pupillometryr_data.R | 1048 +- R/prepare_gazepoint_semimarkov_data.R | 1420 +-- R/pupil-latency-sensitivity.R |only R/pupil_signal_extensions.R | 946 +- R/qc_reporting_bundle.R | 1276 +- R/recalibrate_gazepoint_gaze.R | 1030 +- R/recommend_gazepoint_exclusions.R | 1078 +- R/run_gazepoint_aoi_multiverse.R | 764 - R/run_gazepoint_cluster_permutation.R | 1144 +- R/run_gazepoint_eyetools_fixation_detection.R | 1446 +-- R/run_gazepoint_gazer_crosscheck.R | 1968 ++-- R/run_gazepoint_model_leave_one_out.R | 1202 +- R/run_gazepoint_pupil_multiverse.R | 826 - R/run_gazepoint_workflow.R | 428 - R/saccade_scanpath.R | 456 - R/save_gazepoint_plots.R | 176 R/scanpath_cluster_stability.R | 3020 +++---- R/scanpath_clustering.R | 944 +- R/scanpath_clustering_workflow.R | 1592 +-- R/scanpath_qc_plot_extensions.R | 524 - R/scanpath_similarity.R | 158 R/screen_coordinate_qc_extensions.R | 426 - R/sequence_anomalies.R | 180 R/sequence_complexity.R | 158 R/sequence_distance.R | 190 R/signal_preprocessing_workflow.R | 2300 ++--- R/simulation_bids_brms.R | 772 - R/smooth_gazepoint_pupil.R | 604 - R/statistical_extension_helpers.R | 200 R/stimulus_layout_qc_extensions.R | 894 +- R/summarise_gazepoint_aoi_entries.R | 550 - R/summarise_gazepoint_aoi_transitions.R | 852 +- R/summarise_gazepoint_aoi_trial_features.R | 1214 +- R/summarise_gazepoint_aoi_windows.R | 986 +- R/summarise_gazepoint_clusters.R | 750 - R/summarise_gazepoint_emmeans.R | 1402 +-- R/summarise_gazepoint_fixation_trials.R | 1824 ++-- R/summarise_gazepoint_fixed_effects.R | 636 - R/summarise_gazepoint_multiverse_results.R | 492 - R/summarise_gazepoint_pupil.R | 722 - R/summarise_gazepoint_pupil_trial_features.R | 1084 +- R/summarise_gazepoint_pupil_windows.R | 1086 +- R/summarise_gazepoint_workflow.R | 242 R/tidy_gazepoint_model_summary.R | 900 +- R/timecourse_bootstrap.R | 368 R/transform_gazepoint_aoi_empirical_logit.R | 594 - R/validate_gazepoint_master.R | 1148 +- R/window_aoi_extensions.R | 806 - README.md | 4257 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 58 inst/WORDLIST | 212 inst/benchmarks/gp3tools-performance-limits.csv | 12 inst/benchmarks/run-large-export-performance.R | 96 inst/case-studies/gp3tools_realistic_showcase.Rmd | 4198 ++++----- inst/doc/aoi-boundary-stability-october-2026.R |only inst/doc/aoi-boundary-stability-october-2026.Rmd |only inst/doc/aoi-boundary-stability-october-2026.html |only inst/doc/aoi_workflow.R | 924 +- inst/doc/aoi_workflow.Rmd | 1258 +- inst/doc/aoi_workflow.html | 1744 ++-- inst/doc/dabest-estimation-designs.R |only inst/doc/dabest-estimation-designs.Rmd |only inst/doc/dabest-estimation-designs.html |only inst/doc/ecosystem-update-2026-09.Rmd |only inst/doc/ecosystem-update-2026-09.html |only inst/doc/pupil_workflow.R | 758 - inst/doc/pupil_workflow.Rmd | 986 +- inst/doc/pupil_workflow.html | 1578 +-- inst/examples |only inst/extdata/gazepoint_realistic_demo_exports/Data_Summary_export_synthetic_demo.csv | 14 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_00_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_00_fixations.csv | 122 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_01_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_01_fixations.csv | 128 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_02_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_02_fixations.csv | 108 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_03_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_03_fixations.csv | 116 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_04_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_04_fixations.csv | 124 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_05_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_05_fixations.csv | 116 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_06_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_06_fixations.csv | 120 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_07_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_07_fixations.csv | 118 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_08_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_08_fixations.csv | 126 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_09_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_09_fixations.csv | 124 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_10_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_10_fixations.csv | 132 inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_11_all_gaze.csv | 2442 ++--- inst/extdata/gazepoint_realistic_demo_exports/synthetic_user_11_fixations.csv | 110 inst/research |only man/add_gazepoint_aoi.Rd | 126 man/add_gazepoint_dynamic_aoi.Rd | 180 man/add_gazepoint_polygon_aoi.Rd | 154 man/analyse_gazepoint_binocular_sensitivity.Rd | 126 man/analyze_gazepoint_window.Rd | 134 man/as_gazepoint_master.Rd | 158 man/audit_gazepoint_aoi_screen_coverage.Rd | 98 man/audit_gazepoint_binocular_reconstruction.Rd | 114 man/audit_gazepoint_dynamic_aoi_coverage.Rd | 88 man/audit_gazepoint_face_quality.Rd | 132 man/audit_gazepoint_face_sync.Rd | 128 man/audit_gazepoint_fixation_reliability.Rd | 158 man/audit_gazepoint_master.Rd | 102 man/audit_gazepoint_naming_consistency.Rd | 38 man/audit_gazepoint_screen_bounds.Rd | 90 man/audit_gazepoint_timecourse_grid.Rd | 70 man/audit_gp3_pupil_latency_resolution.Rd |only man/baseline_correct_gazepoint_pupil.Rd | 158 man/benchmark_gazepoint_event_detectors.Rd | 174 man/benchmark_gazepoint_export_performance.Rd | 100 man/bootstrap_gazepoint_scanpath_clusters.Rd | 188 man/bootstrap_gazepoint_timecourse.Rd | 108 man/check_gazepoint_bayesian_readiness.Rd | 98 man/check_gazepoint_performance_regression.Rd | 66 man/classify_gazepoint_events_hmm.Rd | 82 man/clean_gazepoint_by_trackloss.Rd | 130 man/cluster_gazepoint_scanpaths.Rd | 210 man/collect_gazepoint_qc_summaries.Rd | 86 man/combine_gazepoint_eyes.Rd | 84 man/compare_gazepoint_event_detectors.Rd | 184 man/compute_gazepoint_aoi_entropy.Rd | 124 man/compute_gazepoint_aoi_sequence_metrics.Rd | 114 man/compute_gazepoint_saccade_metrics.Rd | 100 man/compute_gazepoint_scanpath_geometry.Rd | 76 man/compute_gazepoint_scanpath_similarity.Rd | 90 man/compute_gazepoint_sequence_complexity.Rd | 90 man/compute_gazepoint_sequence_distance.Rd | 104 man/compute_gazepoint_sequence_recurrence.Rd | 84 man/compute_gazepoint_transition_network_metrics.Rd | 78 man/construct_gazepoint_combined_pupil.Rd | 116 man/create_gazepoint_bayesian_sap.Rd | 82 man/create_gazepoint_brms_template.Rd | 74 man/create_gazepoint_cross_package_report.Rd | 38 man/create_gazepoint_event_review_template.Rd | 120 man/create_gazepoint_face_reporting_checklist.Rd | 128 man/create_gazepoint_hddm_fit_script.Rd | 80 man/detect_gazepoint_blinks.Rd | 128 man/detect_gazepoint_fixations_ivt.Rd | 94 man/detect_gazepoint_fixations_velocity.Rd | 150 man/diagnose_gazepoint_binocular_pupil.Rd | 148 man/diagnose_gazepoint_cluster_design.Rd | 64 man/downsample_gazepoint_pupil.Rd | 102 man/estimate_gazepoint_cluster_offset.Rd | 36 man/estimate_gazepoint_cluster_onset.Rd | 36 man/export_gazepoint_cluster_results.Rd | 46 man/export_gazepoint_heatmap_png.Rd | 112 man/export_gazepoint_master_audit.Rd | 152 man/export_gazepoint_mne_cluster_input.Rd | 80 man/export_gazepoint_permuco_cluster_input.Rd | 78 man/export_gazepoint_permutes_cluster_input.Rd | 78 man/export_gazepoint_to_bids.Rd | 110 man/extract_gazepoint_representative_scanpaths.Rd | 76 man/filter_gazepoint_cnn_uncertainty.Rd | 78 man/fit_gazepoint_aoi_brms.Rd | 86 man/fit_gazepoint_binocular_calibration.Rd | 156 man/fit_gazepoint_brms_model.Rd | 94 man/fit_gazepoint_face_window_lmm.Rd | 110 man/fit_gazepoint_multimodal_response_model.Rd | 130 man/flag_gazepoint_pupil.Rd | 132 man/flag_gazepoint_pupil_artifacts.Rd | 246 man/flag_gazepoint_sequence_anomalies.Rd | 92 man/gaze-survival-adapter.Rd |only man/gazepoint_aoi_uncertainty.Rd |only man/gazepoint_spatial_quality.Rd |only man/gp3tools_naming_policy.Rd | 32 man/gp3tools_performance_limits.Rd | 32 man/harmonize_gazepoint_screen_coordinates.Rd | 108 man/impute_gazepoint_pupil_gp.Rd | 96 man/interpolate_gazepoint_blinks.Rd | 134 man/interpolate_gazepoint_pupil.Rd | 138 man/launch_gazepoint_qc_dashboard.Rd | 54 man/mean_gazepoint_pupil.Rd | 72 man/plot_gazepoint_aoi_timeline.Rd | 156 man/plot_gazepoint_binocular_diagnostics.Rd | 126 man/plot_gazepoint_cluster_null_distribution.Rd | 56 man/plot_gazepoint_cluster_permutation.Rd | 48 man/plot_gazepoint_event_detector_agreement.Rd | 62 man/plot_gazepoint_event_detector_benchmark.Rd | 64 man/plot_gazepoint_face_quality.Rd | 96 man/plot_gazepoint_heatmap.Rd | 142 man/plot_gazepoint_heatmap_overlay.Rd | 150 man/plot_gazepoint_missingness_profile.Rd | 90 man/plot_gazepoint_model_residuals.Rd | 72 man/plot_gazepoint_phase_timeline.Rd | 88 man/plot_gazepoint_qc_overview.Rd | 74 man/plot_gazepoint_scanpath.Rd | 116 man/plot_gazepoint_scanpath_cluster_stability.Rd | 126 man/plot_gazepoint_scanpath_clusters.Rd | 126 man/plot_gazepoint_scanpaths.Rd | 146 man/plot_gazepoint_stimulus_layout_qc.Rd | 164 man/plot_gazepoint_time_series.Rd | 122 man/plot_gazepoint_time_varying_effect.Rd | 98 man/prepare_gazepoint_gpbiometrics_bridge.Rd | 76 man/prepare_gazepoint_hddm_export.Rd | 82 man/prepare_gazepoint_heatmap_data.Rd | 120 man/prepare_gazepoint_multimodal_data.Rd | 176 man/prepare_gazepoint_timecourse_test_data.Rd | 128 man/prepare_gazepoint_traminer_data.Rd | 94 man/preprocess_gazepoint_signals.Rd | 224 man/read_gazepoint_face_export.Rd | 142 man/recommend_gazepoint_model_family.Rd | 42 man/reconstruct_gazepoint_binocular_pupil.Rd | 234 man/regress_gazepoint_pupils.Rd | 108 man/report_gazepoint_cluster_permutation.Rd | 44 man/report_gazepoint_face_qc.Rd | 138 man/report_gazepoint_missingness.Rd | 84 man/report_gazepoint_multiverse.Rd | 78 man/report_gazepoint_phase_coverage.Rd | 76 man/report_gazepoint_qc_overview.Rd | 54 man/run_gazepoint_cluster_permutation_anova.Rd | 40 man/run_gazepoint_cluster_permutation_covariate_adjusted.Rd | 36 man/run_gazepoint_cluster_permutation_lmer.Rd | 36 man/run_gazepoint_cluster_permutation_parallel.Rd | 36 man/run_gazepoint_cluster_threshold_sensitivity.Rd | 52 man/run_gazepoint_gpbiometrics_workflow.Rd | 110 man/run_gazepoint_multidimensional_cluster_permutation.Rd | 36 man/run_gazepoint_tfce.Rd | 36 man/segment_gazepoint_task_phases.Rd | 116 man/select_gazepoint_adaptive_trial.Rd | 82 man/select_gazepoint_scanpath_clusters.Rd | 166 man/simulate_gazepoint_cluster_timecourse_data.Rd | 90 man/simulate_gazepoint_data.Rd | 102 man/simulate_gazepoint_fixations.Rd | 102 man/simulate_gazepoint_pupil_data.Rd | 110 man/smooth_gazepoint_coordinate.Rd | 106 man/smooth_gazepoint_pupil.Rd | 144 man/standardize_gazepoint_face_columns.Rd | 132 man/stress_test_gazepoint_binocular_reconstruction.Rd | 130 man/summarise_gazepoint_binocular_reporting.Rd | 96 man/summarise_gazepoint_coordinate_coverage.Rd | 34 man/summarise_gazepoint_event_detector_agreement.Rd | 50 man/summarise_gazepoint_event_detector_benchmark.Rd | 52 man/summarise_gazepoint_face_reactivity.Rd | 34 man/summarise_gazepoint_face_windows.Rd | 34 man/summarise_gazepoint_markovchain.Rd | 86 man/summarise_gazepoint_pupil.Rd | 134 man/summarise_gazepoint_pupil_response_features.Rd | 34 man/summarise_gazepoint_pupil_windows.Rd | 142 man/summarise_gazepoint_scanpath_cluster_stability.Rd | 102 man/summarise_gazepoint_semimarkov.Rd | 82 man/summarise_gazepoint_time_clusters.Rd | 34 man/summarise_gazepoint_workflow.Rd | 68 man/summarize_gazepoint_coordinate_coverage.Rd | 104 man/summarize_gazepoint_face_quality.Rd | 72 man/summarize_gazepoint_face_reactivity.Rd | 150 man/summarize_gazepoint_face_windows.Rd | 178 man/summarize_gazepoint_missingness.Rd | 98 man/summarize_gazepoint_phase_coverage.Rd | 100 man/summarize_gazepoint_pupil_response_features.Rd | 86 man/summarize_gazepoint_qc_status.Rd | 52 man/summarize_gazepoint_time_clusters.Rd | 52 man/sync_gazepoint_face_data.Rd | 188 man/validate_gazepoint_binocular_reconstruction.Rd | 196 man/validate_gazepoint_master.Rd | 146 man/write_gazepoint_naming_audit.Rd | 38 man/write_gazepoint_performance_benchmark.Rd | 50 tests/testthat/helper-binocular.R | 30 tests/testthat/helper-source-contract-root.R |only tests/testthat/test-advanced-aoi-assignment.R | 498 - tests/testthat/test-aoi_entropy.R | 90 tests/testthat/test-aoi_sequence_metrics.R | 86 tests/testthat/test-aoi_uncertainty_eyeprocess_adapter.R |only tests/testthat/test-as_gazepoint_master.R | 446 - tests/testthat/test-audit_gazepoint_aoi_coding_matrix.R | 1312 +-- tests/testthat/test-audit_gazepoint_aoi_geometry.R | 950 +- tests/testthat/test-audit_gazepoint_aoi_margin_sensitivity.R | 1290 +-- tests/testthat/test-audit_gazepoint_aoi_overlap.R | 756 - tests/testthat/test-audit_gazepoint_aoi_window_denominators.R | 916 +- tests/testthat/test-audit_gazepoint_condition_quality_imbalance.R | 750 - tests/testthat/test-audit_gazepoint_design_balance.R | 648 - tests/testthat/test-audit_gazepoint_event_sync.R | 614 - tests/testthat/test-audit_gazepoint_exclusion_flow.R | 798 - tests/testthat/test-audit_gazepoint_gaze_signal_quality.R | 844 - tests/testthat/test-audit_gazepoint_master.R | 434 - tests/testthat/test-audit_gazepoint_post_exclusion_balance.R | 1120 +- tests/testthat/test-audit_gazepoint_pupil_baseline.R | 564 - tests/testthat/test-audit_gazepoint_pupil_drift.R | 652 - tests/testthat/test-audit_gazepoint_pupil_gaps.R | 490 - tests/testthat/test-audit_gazepoint_pupil_imbalance.R | 512 - tests/testthat/test-audit_gazepoint_pupil_overlap_risk.R | 632 - tests/testthat/test-audit_gazepoint_pupil_reliability.R | 776 - tests/testthat/test-audit_gazepoint_stimulus_luminance.R | 604 - tests/testthat/test-baseline_correct_gazepoint_pupil.R | 848 - tests/testthat/test-bayesian_planning_helpers.R | 264 tests/testthat/test-binocular-pupil-plots.R | 102 tests/testthat/test-binocular-pupil-reconstruction.R | 786 - tests/testthat/test-binocular-pupil-validation.R | 216 tests/testthat/test-binocular_trackloss_simulation_extensions.R | 320 tests/testthat/test-check_gazepoint_file_pairs.R | 152 tests/testthat/test-check_gazepoint_model_convergence.R | 340 tests/testthat/test-check_gazepoint_model_overdispersion.R | 576 - tests/testthat/test-check_gazepoint_model_singularity.R | 434 - tests/testthat/test-check_gazepoint_real_data_readiness.R | 1042 +- tests/testthat/test-cluster_permutation_batch_b.R | 382 tests/testthat/test-cluster_permutation_extensions.R | 290 tests/testthat/test-cluster_permutation_external_exports.R | 208 tests/testthat/test-cluster_permutation_guardrails.R | 74 tests/testthat/test-compare_gazepoint_nested_models.R | 774 - tests/testthat/test-compute_gazepoint_aoi_transition_matrix.R | 564 - tests/testthat/test-compute_gazepoint_time_varying_transition_matrix.R | 892 +- tests/testthat/test-create_gazepoint_analysis_decision_audit.R | 650 - tests/testthat/test-create_gazepoint_markovchain_object.R | 904 +- tests/testthat/test-create_gazepoint_master.R | 292 tests/testthat/test-create_gazepoint_preprocessing_multiverse.R | 630 - tests/testthat/test-create_gazepoint_preprocessing_registry.R | 332 tests/testthat/test-create_gazepoint_report.R | 130 tests/testthat/test-create_gazepoint_reporting_checklist.R | 828 - tests/testthat/test-diagnose_gazepoint_gamm.R | 610 - tests/testthat/test-diagnose_gazepoint_glmm.R | 608 - tests/testthat/test-estimate_gazepoint_divergence_point.R | 1366 +-- tests/testthat/test-event-detector-benchmarking.R | 562 - tests/testthat/test-event-detector-comparison.R | 442 - tests/testthat/test-experimental_bayesian_bridges.R | 250 tests/testthat/test-export_gazepoint_master_audit.R | 456 - tests/testthat/test-export_gazepoint_model_tables.R | 518 - tests/testthat/test-export_gazepoint_tables.R | 136 tests/testthat/test-face_export_import.R | 306 tests/testthat/test-face_quality_audit.R | 518 - tests/testthat/test-face_reporting.R | 368 tests/testthat/test-face_sync.R | 760 - tests/testthat/test-face_window_summaries.R | 570 - tests/testthat/test-final_statistical_extensions.R | 106 tests/testthat/test-fit_gazepoint_aoi_gamm.R | 546 - tests/testthat/test-fit_gazepoint_aoi_model_sensitivity.R | 1228 +- tests/testthat/test-fit_gazepoint_aoi_window_glmm.R | 972 +- tests/testthat/test-fit_gazepoint_gca.R | 1002 +- tests/testthat/test-fit_gazepoint_pupil_gamm.R | 820 - tests/testthat/test-fit_gazepoint_pupil_pfe_gamm.R | 994 +- tests/testthat/test-fit_gazepoint_pupil_window_lmm.R | 542 - tests/testthat/test-fit_gazepoint_pupil_window_sensitivity.R | 566 - tests/testthat/test-fit_gazepoint_transition_count_nb_sensitivity.R | 916 +- tests/testthat/test-fixation_reliability.R | 92 tests/testthat/test-flag_gazepoint_pupil.R | 672 - tests/testthat/test-flag_gazepoint_pupil_artifacts.R | 892 +- tests/testthat/test-flag_gazepoint_pupil_hampel.R | 752 - tests/testthat/test-gaze-survival-adapter.R |only 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| 462 - tests/testthat/test-plot_aoi_timeline.R | 44 tests/testthat/test-plot_diagnostics.R | 100 tests/testthat/test-plot_gazepoint_aoi_gamm.R | 772 - tests/testthat/test-plot_gazepoint_aoi_transition_matrix.R | 612 - tests/testthat/test-plot_gazepoint_aoi_verification.R | 774 - tests/testthat/test-plot_gazepoint_cluster_results.R | 568 - tests/testthat/test-plot_gazepoint_gca.R | 750 - tests/testthat/test-plot_gazepoint_model_predictions.R | 1052 +- tests/testthat/test-plot_gazepoint_multiverse_results.R | 750 - tests/testthat/test-plot_gazepoint_pupil_preprocessing.R | 550 - tests/testthat/test-plot_gazepoint_pupil_status.R | 512 - tests/testthat/test-plot_gazepoint_pupil_timecourse.R | 566 - tests/testthat/test-prepare_gazepoint_aoi_gamm_data.R | 902 +- tests/testthat/test-prepare_gazepoint_aoi_glmm_data.R | 886 +- tests/testthat/test-prepare_gazepoint_aoi_sequences.R | 496 - tests/testthat/test-prepare_gazepoint_cluster_data.R | 766 - tests/testthat/test-prepare_gazepoint_eyetools_data.R | 1238 +- tests/testthat/test-prepare_gazepoint_eyetrackingr_data.R | 938 +- tests/testthat/test-prepare_gazepoint_fixation_aligned_data.R | 1142 +- tests/testthat/test-prepare_gazepoint_gazer_data.R | 1070 +- tests/testthat/test-prepare_gazepoint_gca_data.R | 850 - tests/testthat/test-prepare_gazepoint_hmm_data.R | 1106 +- tests/testthat/test-prepare_gazepoint_pupil_gamm_data.R | 698 - tests/testthat/test-prepare_gazepoint_pupil_window_model_data.R | 544 - tests/testthat/test-prepare_gazepoint_pupillometryr_data.R | 908 +- tests/testthat/test-prepare_gazepoint_semimarkov_data.R | 792 - tests/testthat/test-pupil-latency-sensitivity.R |only tests/testthat/test-qc_reporting_bundle.R | 414 tests/testthat/test-recalibrate_gazepoint_gaze.R | 1158 +- tests/testthat/test-recommend_gazepoint_exclusions.R | 1006 +- tests/testthat/test-run_gazepoint_aoi_multiverse.R | 792 - tests/testthat/test-run_gazepoint_cluster_permutation.R | 638 - tests/testthat/test-run_gazepoint_eyetools_fixation_detection.R | 1060 +- tests/testthat/test-run_gazepoint_gazer_crosscheck.R | 876 +- tests/testthat/test-run_gazepoint_model_leave_one_out.R | 916 +- tests/testthat/test-run_gazepoint_pupil_multiverse.R | 566 - tests/testthat/test-run_gazepoint_workflow.R | 604 - tests/testthat/test-saccade_scanpath.R | 112 tests/testthat/test-save_gazepoint_plots.R | 92 tests/testthat/test-scanpath-cluster-stability.R | 504 - tests/testthat/test-scanpath-clustering-workflow.R | 488 - tests/testthat/test-scanpath-clustering.R | 308 tests/testthat/test-scanpath_qc_plot_extensions.R | 206 tests/testthat/test-scanpath_similarity.R | 42 tests/testthat/test-screen_coordinate_qc_extensions.R | 348 tests/testthat/test-sequence_anomalies.R | 28 tests/testthat/test-sequence_complexity.R | 34 tests/testthat/test-sequence_distance.R | 64 tests/testthat/test-signal-preprocessing-workflow.R | 458 - tests/testthat/test-simulation_bids_brms.R | 112 tests/testthat/test-smooth_gazepoint_pupil.R | 828 - tests/testthat/test-stimulus_layout_qc_extensions.R | 444 - tests/testthat/test-summarise_gazepoint_aoi_entries.R | 440 - tests/testthat/test-summarise_gazepoint_aoi_transitions.R | 626 - tests/testthat/test-summarise_gazepoint_aoi_trial_features.R | 638 - tests/testthat/test-summarise_gazepoint_aoi_windows.R | 1060 +- tests/testthat/test-summarise_gazepoint_clusters.R | 550 - tests/testthat/test-summarise_gazepoint_emmeans.R | 470 - tests/testthat/test-summarise_gazepoint_fixation_trials.R | 824 - tests/testthat/test-summarise_gazepoint_fixed_effects.R | 632 - tests/testthat/test-summarise_gazepoint_multiverse_results.R | 526 - tests/testthat/test-summarise_gazepoint_pupil.R | 594 - tests/testthat/test-summarise_gazepoint_pupil_trial_features.R | 612 - tests/testthat/test-summarise_gazepoint_pupil_windows.R | 908 +- tests/testthat/test-summarise_gazepoint_workflow.R | 230 tests/testthat/test-tidy_gazepoint_model_summary.R | 538 - tests/testthat/test-timecourse_bootstrap.R | 60 tests/testthat/test-transform_gazepoint_aoi_empirical_logit.R | 742 - tests/testthat/test-validate_gazepoint_master.R | 456 - tests/testthat/test-workflow_stress.R | 130 vignettes/aoi-boundary-stability-october-2026.Rmd |only vignettes/aoi_workflow.Rmd | 1258 +- vignettes/dabest-estimation-designs.Rmd |only vignettes/ecosystem-update-2026-09.Rmd |only vignettes/pupil_workflow.Rmd | 986 +- 558 files changed, 162134 insertions(+), 161991 deletions(-)
Title: A Library for using 'Pathling'
Description: R API for 'Pathling', a tool for querying and transforming electronic health record data that is represented using the 'Fast Healthcare Interoperability Resources' (FHIR) standard - see <https://pathling.csiro.au/docs>.
Author: Australian e-Health Research Centre, CSIRO [cph, cre],
Piotr Szul [aut],
John Grimes [aut]
Maintainer: "Australian e-Health Research Centre, CSIRO" <pathling@csiro.au>
Diff between pathling versions 9.9.0 dated 2026-09-02 and 10.0.0 dated 2026-10-22
DESCRIPTION | 10 +++++----- MD5 | 27 ++++++++++++++++----------- NAMESPACE | 4 ++++ R/context.R | 4 ++-- R/datasource.R | 9 ++++++--- R/terminology_import.R | 28 +++++++++++++++++++++++++--- R/terminology_relations.R |only R/udfs.R | 9 +++++---- man/ds_write_ndjson.Rd | 5 +++-- man/ds_write_parquet.Rd | 4 +++- man/pathling_concept_map.Rd |only man/pathling_concept_map_from_json.Rd |only man/pathling_connect.Rd | 4 ++-- man/pathling_import_fhir_terminology.Rd | 20 +++++++++++++++++++- man/pathling_value_set.Rd |only man/pathling_value_set_from_json.Rd |only man/tx_member_of.Rd | 9 +++++---- 17 files changed, 95 insertions(+), 38 deletions(-)
Title: Heterogeneous Methods for Shape and Other Multidimensional Data
Description: Tools for geometric morphometric analyses and multidimensional
data. Implements methods for morphological disparity analysis using
bootstrap and rarefaction,
as reviewed in Foote (1997) <doi:10.1146/annurev.ecolsys.28.1.129>.
Includes integration and modularity testing,
following Fruciano et al. (2013) <doi:10.1371/journal.pone.0069376>,
using Escoufier's RV coefficient as test statistic as well as
two-block partial least squares -
PLS, Rohlf and Corti (2000) <doi:10.1080/106351500750049806>.
Also includes vector angle comparisons,
orthogonal projection for data correction
(Burnaby (1966) <doi:10.2307/2528217>; Fruciano (2016) <doi:10.1007/s00427-016-0537-4>),
and parallel analysis for dimensionality reduction (Buja and Eyuboglu (1992)
<doi:10.1207/s15327906mbr2704_2>).
Author: Carmelo Fruciano [aut, cre]
Maintainer: Carmelo Fruciano <carmelo.fruciano@unict.it>
Diff between GeometricMorphometricsMix versions 0.6.1.1 dated 2026-04-17 and 0.6.1.3 dated 2026-10-22
DESCRIPTION | 12 - MD5 | 32 ++-- NEWS.md | 5 R/Kmultparallel.R | 190 ++++++++++++------------- R/disparity_resample.R | 30 +++ R/repeated_measures_test.R | 2 R/scaled_variance_of_eigenvalues.R | 5 README.md | 2 inst/doc/disparity_analysis.html | 44 ++--- inst/doc/pls_analysis_use_case.html | 4 man/GeometricMorphometricsMix-deprecated.Rd | 20 +- man/disparity_resample.Rd | 9 + man/plot.disparity_resample.Rd | 11 + tests/README.md | 146 ++++--------------- tests/testthat/test-ancillary-calculations.R |only tests/testthat/test-disparity_resample.R | 3 tests/testthat/test-geometry-transformations.R |only tests/testthat/test-resampling-comparisons.R |only tests/testthat/test-statistical-calculations.R |only 19 files changed, 244 insertions(+), 271 deletions(-)
More information about GeometricMorphometricsMix at CRAN
Permanent link
Title: Doubly Robust Difference-in-Differences Estimators
Description: Implements the locally efficient doubly robust difference-in-differences (DiD)
estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020)
<doi:10.1016/j.jeconom.2020.06.003>. The estimator combines inverse probability weighting and outcome
regression estimators (also implemented in the package) to form estimators with
more attractive statistical properties. Two different estimation methods can be used
to estimate the nuisance functions.
Author: Pedro H. C. Sant'Anna [aut, cre, cph],
Jun Zhao [aut]
Maintainer: Pedro H. C. Sant'Anna <pedrohcgs@gmail.com>
Diff between DRDID versions 1.3.0 dated 2026-06-10 and 1.4.0 dated 2026-10-22
DESCRIPTION | 10 - MD5 | 119 ++++++++----- NEWS.md | 110 ++++++++++++ R/bootstrap_inference.R |only R/drdid.R | 18 +- R/drdid_imp_panel.R | 58 ++++-- R/drdid_imp_rc.R | 49 +++-- R/drdid_imp_rc1.R | 49 +++-- R/drdid_panel.R | 35 +--- R/drdid_rc.R | 40 ++-- R/drdid_rc1.R | 40 ++-- R/fastglm_fit.R | 3 R/ipt.loss.aggregate.R |only R/ipt.valid.R |only R/ipw_did_panel.R | 35 +--- R/ipw_did_rc.R | 37 ++-- R/ipwdid.R | 2 R/loss.ps.IPT.R | 106 +++++++++--- R/loss.ps.cal.R | 86 ++++++--- R/ordid.R | 2 R/pre_process_drdid.R | 140 +++++++++------- R/pscore.cal.R | 101 +++++------ R/reg_did_panel.R | 35 +--- R/reg_did_rc.R | 35 +--- R/std_ipw_did_panel.R | 35 +--- R/std_ipw_did_rc.R | 35 +--- R/twfe_did_panel.R | 77 +++++--- R/twfe_did_rc.R | 37 ++-- R/validate_bootstrap_count.R |only R/validate_sampling_weights.R |only R/validate_treatment_indicator.R |only R/wboot.dr.imp.panel.R | 9 - R/wboot_drdid_imp_rc.R | 2 R/wboot_drdid_imp_rc1.R | 2 R/wboot_ipw_rc.R | 22 +- inst/WORDLIST | 7 man/drdid.Rd | 18 +- man/drdid_imp_panel.Rd | 29 ++- man/drdid_imp_rc.Rd | 20 +- man/drdid_imp_rc1.Rd | 20 +- man/drdid_panel.Rd | 6 man/drdid_rc.Rd | 6 man/drdid_rc1.Rd | 6 man/ipw_did_panel.Rd | 6 man/ipw_did_rc.Rd | 6 man/ipwdid.Rd | 2 man/ordid.Rd | 2 man/reg_did_panel.Rd | 6 man/reg_did_rc.Rd | 6 man/std_ipw_did_panel.Rd | 6 man/std_ipw_did_rc.Rd | 6 man/twfe_did_panel.Rd | 20 +- man/twfe_did_rc.Rd | 6 tests/testthat/test_bootstrap_count.R |only tests/testthat/test_bootstrap_scale.R |only tests/testthat/test_fastglm_undersized_design.R |only tests/testthat/test_improved_panel_weighted_bootstrap.R |only tests/testthat/test_ipt_fallback_objective.R |only tests/testthat/test_ipt_optimized_guards.R |only tests/testthat/test_ipt_weighted_arithmetic.R |only tests/testthat/test_ipt_zero_weight_arithmetic.R |only tests/testthat/test_ipw_rc_weight_normalization.R |only tests/testthat/test_ipw_rc_weighted_bootstrap.R |only tests/testthat/test_panel_missing_covariates_weights.R |only tests/testthat/test_panel_missing_outcomes.R |only tests/testthat/test_preprocess_column_names.R |only tests/testthat/test_rc_inffunc.R |only tests/testthat/test_regression_lock.R | 4 tests/testthat/test_required_ipt_fit.R |only tests/testthat/test_sampling_weight_validation.R |only tests/testthat/test_treatment_indicator_validation.R |only tests/testthat/test_twfe_covariate_dimensions.R |only tests/testthat/test_twfe_panel_inference.R |only 73 files changed, 947 insertions(+), 564 deletions(-)
Title: Spatial Phylogenetic Analysis
Description: Analyze spatial phylogenetic diversity patterns.
Use your data on an evolutionary tree and geographic distributions of the
terminal taxa to compute diversity and endemism metrics, test significance
with null model randomization, analyze community turnover and biotic
regionalization, and perform spatial conservation prioritizations. All
functions support quantitative community data in addition to binary data.
Author: Matthew Kling [aut, cre, cph]
Maintainer: Matthew Kling <mattkling@berkeley.edu>
Diff between phylospatial versions 1.5.0 dated 2026-10-01 and 1.6.0 dated 2026-10-22
phylospatial-1.5.0/phylospatial/tests/testthat/Rplots.pdf |only phylospatial-1.6.0/phylospatial/DESCRIPTION | 6 phylospatial-1.6.0/phylospatial/MD5 | 92 phylospatial-1.6.0/phylospatial/NAMESPACE | 1 phylospatial-1.6.0/phylospatial/NEWS.md | 16 phylospatial-1.6.0/phylospatial/R/moss.R | 50 phylospatial-1.6.0/phylospatial/R/phylospatial-methods.R | 45 phylospatial-1.6.0/phylospatial/R/phylospatial.R | 57 phylospatial-1.6.0/phylospatial/R/ps_area.R |only phylospatial-1.6.0/phylospatial/R/ps_canape.R | 4 phylospatial-1.6.0/phylospatial/R/ps_dissim.R | 9 phylospatial-1.6.0/phylospatial/R/ps_diversity.R | 11 phylospatial-1.6.0/phylospatial/R/ps_grid.R | 4 phylospatial-1.6.0/phylospatial/R/ps_performance.R | 3 phylospatial-1.6.0/phylospatial/R/ps_prioritize.R | 34 phylospatial-1.6.0/phylospatial/R/ps_prioritizr.R | 2 phylospatial-1.6.0/phylospatial/R/ps_rand.R | 9 phylospatial-1.6.0/phylospatial/R/ps_regions.R | 8 phylospatial-1.6.0/phylospatial/R/utils.R | 16 phylospatial-1.6.0/phylospatial/inst/doc/beta-diversity.html | 5 phylospatial-1.6.0/phylospatial/inst/doc/phylospatial-data.Rmd | 4 phylospatial-1.6.0/phylospatial/inst/doc/phylospatial-data.html | 44 phylospatial-1.6.0/phylospatial/inst/doc/prioritization.R | 15 phylospatial-1.6.0/phylospatial/inst/doc/prioritization.Rmd | 21 phylospatial-1.6.0/phylospatial/inst/doc/prioritization.html | 88 phylospatial-1.6.0/phylospatial/inst/extdata/moss_popdens.tif |only phylospatial-1.6.0/phylospatial/inst/extdata/moss_protection.tif |only phylospatial-1.6.0/phylospatial/inst/extdata/priority-performance.csv | 1052 +++++----- phylospatial-1.6.0/phylospatial/inst/extdata/priority-prioritizr.tif |binary phylospatial-1.6.0/phylospatial/inst/extdata/priority-prob.tif |binary phylospatial-1.6.0/phylospatial/inst/extdata/priority.tif |binary phylospatial-1.6.0/phylospatial/man/moss.Rd | 34 phylospatial-1.6.0/phylospatial/man/phylospatial.Rd | 40 phylospatial-1.6.0/phylospatial/man/plot.phylospatial.Rd | 15 phylospatial-1.6.0/phylospatial/man/ps_area.Rd |only phylospatial-1.6.0/phylospatial/man/ps_canape.Rd | 2 phylospatial-1.6.0/phylospatial/man/ps_dissim.Rd | 5 phylospatial-1.6.0/phylospatial/man/ps_diversity.Rd | 9 phylospatial-1.6.0/phylospatial/man/ps_grid.Rd | 4 phylospatial-1.6.0/phylospatial/man/ps_performance.Rd | 3 phylospatial-1.6.0/phylospatial/man/ps_prioritize.Rd | 4 phylospatial-1.6.0/phylospatial/man/ps_prioritizr.Rd | 2 phylospatial-1.6.0/phylospatial/man/ps_rand.Rd | 8 phylospatial-1.6.0/phylospatial/man/ps_regions.Rd | 4 phylospatial-1.6.0/phylospatial/tests/testthat/test-moss.R | 25 phylospatial-1.6.0/phylospatial/tests/testthat/test-phylospatial-methods.R | 33 phylospatial-1.6.0/phylospatial/tests/testthat/test-ps_area.R |only phylospatial-1.6.0/phylospatial/tests/testthat/test-ps_prioritize.R | 18 phylospatial-1.6.0/phylospatial/vignettes/phylospatial-data.Rmd | 4 phylospatial-1.6.0/phylospatial/vignettes/prioritization.Rmd | 21 50 files changed, 1080 insertions(+), 747 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] ,
Heidi Seibold [ctb] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.3-0 dated 2026-08-22 and 1.3-1 dated 2026-10-22
DESCRIPTION | 6 +- MD5 | 39 +++++++++--------- R/cforest.R | 100 ++++++++++++++++++++++++++++++++--------------- R/modelparty.R | 2 R/party.R | 2 R/varimp.R | 13 +----- build/partial.rdb |binary inst/NEWS.Rd | 41 ++++++++++++++++++- inst/doc/constparty.pdf |binary inst/doc/ctree.pdf |binary inst/doc/mob.R | 4 - inst/doc/mob.Rnw | 13 ------ inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary man/cforest.Rd | 6 +- src/rfweights.c | 18 ++++++-- tests/Rplots.pdf |only tests/bugfixes.R | 12 +++++ tests/bugfixes.Rout.save | 19 +++++++- tests/regtest-honesty.R | 13 +++--- vignettes/mob.Rnw | 13 ------ 21 files changed, 192 insertions(+), 109 deletions(-)
Title: Tools for Two-Dimensional Monte-Carlo Simulations
Description: A complete framework to build and study Two-Dimensional Monte-Carlo simulations, aka Second-Order Monte-Carlo simulations. Also includes various distributions (pert, triangular, Bernoulli, empirical discrete and continuous).
Author: Regis Pouillot [aut, cre] ,
Marie-Laure Delignette-Muller [ctb] ,
Jean-Baptiste Denis [ctb],
Yu Chen [ctb],
Arie Havelaar [ctb]
Maintainer: Regis Pouillot <rpouillot@yahoo.fr>
Diff between mc2d versions 0.2.2 dated 2026-06-01 and 0.3.0 dated 2026-10-22
mc2d-0.2.2/mc2d/vignettes/figs |only mc2d-0.3.0/mc2d/DESCRIPTION | 16 mc2d-0.3.0/mc2d/MD5 | 131 - mc2d-0.3.0/mc2d/NAMESPACE | 1 mc2d-0.3.0/mc2d/R/Ops.mcnode.R | 88 mc2d-0.3.0/mc2d/R/betagen.R | 30 mc2d-0.3.0/mc2d/R/betasubjective.R | 1 mc2d-0.3.0/mc2d/R/converg.R | 272 +- mc2d-0.3.0/mc2d/R/cornode.R | 357 +-- mc2d-0.3.0/mc2d/R/empiricalC.R | 179 + mc2d-0.3.0/mc2d/R/empiricalD.R | 590 +++-- mc2d-0.3.0/mc2d/R/evalmccut.R | 521 ++--- mc2d-0.3.0/mc2d/R/gghist.R | 418 ++-- mc2d-0.3.0/mc2d/R/ggplotmc.R | 610 +++--- mc2d-0.3.0/mc2d/R/ggspaghetti.R | 411 ++-- mc2d-0.3.0/mc2d/R/ggtornado.R | 284 +- mc2d-0.3.0/mc2d/R/hist.mc.R | 11 mc2d-0.3.0/mc2d/R/internal.R |only mc2d-0.3.0/mc2d/R/is.mc.R | 6 mc2d-0.3.0/mc2d/R/lhs.R | 16 mc2d-0.3.0/mc2d/R/lognormalb.R | 4 mc2d-0.3.0/mc2d/R/mc.R | 197 + mc2d-0.3.0/mc2d/R/mc2d-package.R | 1 mc2d-0.3.0/mc2d/R/mcapply.R | 4 mc2d-0.3.0/mc2d/R/mcdata.R | 227 +- mc2d-0.3.0/mc2d/R/mcdatanocontrol.R | 37 mc2d-0.3.0/mc2d/R/mcprobtree.R | 18 mc2d-0.3.0/mc2d/R/mcratio.R | 189 - mc2d-0.3.0/mc2d/R/mcstoc.R | 36 mc2d-0.3.0/mc2d/R/minimuminfo.R | 9 mc2d-0.3.0/mc2d/R/outm.R | 66 mc2d-0.3.0/mc2d/R/pert.R | 420 ++-- mc2d-0.3.0/mc2d/R/plot.mc.R | 280 +- mc2d-0.3.0/mc2d/R/plot.mccut.R | 108 - mc2d-0.3.0/mc2d/R/plot.tornado.R | 10 mc2d-0.3.0/mc2d/R/pmin.R | 213 -- mc2d-0.3.0/mc2d/R/print.mc.R | 4 mc2d-0.3.0/mc2d/R/quantile.mc.R | 213 +- mc2d-0.3.0/mc2d/R/rdirichlet.R | 151 - mc2d-0.3.0/mc2d/R/rmultinomial.R | 200 -- mc2d-0.3.0/mc2d/R/rtrunc.R | 140 - mc2d-0.3.0/mc2d/R/spaghetti.R | 231 +- mc2d-0.3.0/mc2d/R/summary.mc.R | 277 +- mc2d-0.3.0/mc2d/R/tornado.R | 333 +-- mc2d-0.3.0/mc2d/R/tornadounc.mc.R | 330 +-- mc2d-0.3.0/mc2d/R/tornadounc.mccut.R | 158 - mc2d-0.3.0/mc2d/R/triang.R | 392 ++- mc2d-0.3.0/mc2d/R/unmc.R | 70 mc2d-0.3.0/mc2d/README.md | 2 mc2d-0.3.0/mc2d/inst/NEWS | 546 +++-- mc2d-0.3.0/mc2d/inst/doc/docmcEnglish.R | 2 mc2d-0.3.0/mc2d/inst/doc/docmcEnglish.Rmd | 1590 ++++++++-------- mc2d-0.3.0/mc2d/inst/doc/docmcEnglish.pdf |binary mc2d-0.3.0/mc2d/inst/doc/mc2dLmEnglish.pdf |binary mc2d-0.3.0/mc2d/man/figures |only mc2d-0.3.0/mc2d/man/ggspaghetti.Rd | 13 mc2d-0.3.0/mc2d/man/lhs.Rd | 3 mc2d-0.3.0/mc2d/man/mc.Rd | 9 mc2d-0.3.0/mc2d/man/mc2d-package.Rd | 2 mc2d-0.3.0/mc2d/tests/testthat/helper-ref.R |only mc2d-0.3.0/mc2d/tests/testthat/test-bugfixes.R |only mc2d-0.3.0/mc2d/tests/testthat/test-ref-core.R |only mc2d-0.3.0/mc2d/tests/testthat/test-ref-distributions.R |only mc2d-0.3.0/mc2d/tests/testthat/test-ref-plots.R |only mc2d-0.3.0/mc2d/tests/testthat/test-ref-summaries.R |only mc2d-0.3.0/mc2d/vignettes/docmcEnglish.Rmd | 1590 ++++++++-------- 66 files changed, 6191 insertions(+), 5826 deletions(-)
Title: Toolbox for Regression Discontinuity Design ('RDD')
Description: Set of functions for Regression Discontinuity Design ('RDD'), for
data visualisation, estimation and testing.
Author: Matthieu Stigler [aut, cre] ,
Bastiaan Quast [aut]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
Diff between rddtools versions 2.0.2 dated 2025-10-29 and 2.0.3 dated 2026-10-22
DESCRIPTION | 10 ++++----- MD5 | 32 +++++++++++++++--------------- NAMESPACE | 43 ++++++++++++++++++++++++++++------------- NEWS.md | 5 ++++ R/as.npreg.R | 5 +--- R/clusterInf.R | 2 + R/get_methods.R | 9 ++++++-- R/rddtools.R | 10 ++++----- R/waldci.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 - inst/devtools_internal_tests.R | 4 +-- inst/doc/morocco.html | 10 ++++----- inst/doc/rddtools.html | 17 ++++++++-------- man/house.Rd | 10 ++++----- man/rddtools-package.Rd | 1 17 files changed, 96 insertions(+), 66 deletions(-)
More information about MultipleSystemsEstimation at CRAN
Permanent link
Title: Distance and Travel Time Between Two Points from Google Maps
Description: Get distance and travel time between two points from Google Maps.
Supports both the legacy 'Distance Matrix API' (XML endpoint) and the
newer 'Routes API' (REST).
Author: Rodrigo Azuero Melo [aut],
David Zarruk [aut],
Jindra Lacko [cre]
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between gmapsdistance versions 4.0.5 dated 2025-01-11 and 4.1.0 dated 2026-10-22
gmapsdistance-4.0.5/gmapsdistance/tests/testthat/test-1-sanity.R |only gmapsdistance-4.0.5/gmapsdistance/tests/testthat/test-2-input.R |only gmapsdistance-4.0.5/gmapsdistance/tests/testthat/test-3-matrix.R |only gmapsdistance-4.0.5/gmapsdistance/tests/testthat/test-4-invalid-input.R |only gmapsdistance-4.0.5/gmapsdistance/tests/testthat/test-5-vignette.R |only gmapsdistance-4.0.5/gmapsdistance/tests/testthat/test-6-graceful-fail.R |only gmapsdistance-4.0.5/gmapsdistance/tests/testthat/test-7-arrival-time.R |only gmapsdistance-4.1.0/gmapsdistance/DESCRIPTION | 19 gmapsdistance-4.1.0/gmapsdistance/MD5 | 38 gmapsdistance-4.1.0/gmapsdistance/NAMESPACE | 6 gmapsdistance-4.1.0/gmapsdistance/NEWS.md | 6 gmapsdistance-4.1.0/gmapsdistance/R/distance_routes.R |only gmapsdistance-4.1.0/gmapsdistance/README.md | 83 - gmapsdistance-4.1.0/gmapsdistance/build/vignette.rds |binary gmapsdistance-4.1.0/gmapsdistance/inst/doc/vignette.Rmd | 390 +++++--- gmapsdistance-4.1.0/gmapsdistance/inst/doc/vignette.html | 440 +++++----- gmapsdistance-4.1.0/gmapsdistance/man/distance_routes.Rd |only gmapsdistance-4.1.0/gmapsdistance/man/pkg.env.Rd | 4 gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v1-1-sanity.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v1-2-input.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v1-3-matrix.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v1-4-invalid-input.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v1-5-vignette.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v1-6-graceful-fail.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v1-7-arrival-time.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v2-1-sanity.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v2-2-errors.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v2-3-pairwise.R |only gmapsdistance-4.1.0/gmapsdistance/tests/testthat/test-v2-4-graceful-fail.R |only gmapsdistance-4.1.0/gmapsdistance/vignettes/vignette.Rmd | 390 +++++--- 30 files changed, 783 insertions(+), 593 deletions(-)
Title: Flexible Odds Ratio Curves
Description: Provides flexible odds ratio curves that enable modeling non-linear relationships between continuous predictors and binary outcomes.
Facilitates a deeper understanding of the impact of each continuous predictor on the outcome by presenting results in terms of odds ratio (OR) curves based on splines.
These curves allow for comparison against a specified reference value, aiding in the interpretation of the predictor's effect.
Methods are described in Azevedo et al. (2024) <doi:10.3390/app14093897>.
Author: Marta Azevedo [aut] ,
Luis Meira-Machado [aut] ,
Artur Araujo [aut, cre]
Maintainer: Artur Araujo <artur.stat@gmail.com>
This is a re-admission after prior archival of version 1.0.0 dated 2024-04-16
Diff between flexOR versions 1.0.0 dated 2024-04-16 and 1.0.3 dated 2026-10-22
DESCRIPTION | 36 +++-- MD5 | 51 ++++--- NAMESPACE | 28 ++-- R/AICc.R | 17 +- R/PimaIndiansDiabetes2.R |only R/dfgam.R | 48 +++--- R/flexOR-package.R | 69 +++++----- R/flexOR.R | 14 +- R/floor_to.R | 12 + R/plot.OR.R | 77 +++++------ R/predict.OR.R | 34 ++-- README.md | 30 ++-- build/partial.rdb |binary build/vignette.rds |binary data |only inst/CITATION |only inst/NEWS.md |only inst/doc/main_vignette.R | 3 inst/doc/main_vignette.Rmd | 35 ++--- inst/doc/main_vignette.html | 303 +++++++++++++++++++------------------------- man/AICc.Rd | 11 + man/PimaIndiansDiabetes2.Rd |only man/dfgam.Rd | 11 + man/flexOR-package.Rd | 80 ++++++----- man/flexOR.Rd | 10 + man/floor_to.Rd | 6 man/plot.OR.Rd | 22 ++- man/predict.OR.Rd | 10 + vignettes/main_vignette.Rmd | 35 ++--- 29 files changed, 507 insertions(+), 435 deletions(-)
Title: Read and Write CDISC Dataset JSON Files
Description: Read, construct and write CDISC (Clinical Data Interchange Standards Consortium) Dataset JSON (JavaScript Object Notation) files, while validating per the Dataset JSON schema file, as described in CDISC (2023) <https://www.cdisc.org/standards/data-exchange/dataset-json>.
Author: Mike Stackhouse [aut, cre] ,
Nicholas Masel [aut],
Atorus Research, Inc. [cph],
Yao Yuan [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between datasetjson versions 0.4.0 dated 2026-09-03 and 0.4.1 dated 2026-10-22
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ NEWS.md | 9 +++++++++ README.md | 6 +++--- build/vignette.rds |binary inst/doc/datasetjson.html | 4 ++-- inst/doc/date_time_datetime.Rmd | 2 +- inst/doc/precision.Rmd | 2 +- inst/doc/precision.html | 2 +- tests/testthat/helper-datetime.R |only tests/testthat/test-dsjc.R | 8 ++++++-- tests/testthat/test-write_dataset_json.R | 2 ++ vignettes/date_time_datetime.Rmd | 2 +- vignettes/precision.Rmd | 2 +- 14 files changed, 44 insertions(+), 28 deletions(-)
More information about CoxRMSTSimpson at CRAN
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Title: Reproducible Data Capsules with Provenance and Fallback
Description: For analyzing published and unpublished tables, from open-data
portals and statistical agencies to a researcher's own data, so that a
result can be traced to the exact data behind it and checked again
afterwards. A 'capsule' records where each source came from, its Secure
Hash Algorithm 256 ('SHA-256') hash, the schema it should have and an
archived copy in the Internet Archive 'Wayback Machine'
('web.archive.org'); sources are found through the Comprehensive
Knowledge Archive Network ('CKAN', 'ckan.org'). Run again, a capsule
says whether each source still matches and, if it does not, how its
distribution moved (Kolmogorov-Smirnov, chi-square, population stability
index and 'Benford' first-digit screens), and when a source cannot be
reached it runs on schema-driven synthetic data that is marked as such.
Capsules can be signed with keyed hashes ('HMAC-SHA-256', RFC 2104) or
with the post-quantum signature standards 'ML-DSA' (FIPS 204), 'SLH-DSA'
(FIPS 205) and 'XMSS' (RFC 8391), implem [...truncated...]
Author: Vansh Singh Ruhela [aut, cre]
Maintainer: Vansh Singh Ruhela <vsruhela@proton.me>
Diff between rmoriebricklayer versions 1.0.0 dated 2026-10-21 and 1.0.2 dated 2026-10-22
DESCRIPTION | 49 - MD5 | 60 - NAMESPACE | 3 NEWS.md | 19 R/archive_capture.R | 109 ++ R/archive_rmorie.R |only R/archive_warc.R |only R/capsule_check.R | 37 R/capsule_cli.R | 15 R/cli.R | 72 + R/fetch_verified.R | 39 R/srr-stats-standards.R | 2 R/wayback_save.R | 27 README.md | 21 inst/CITATION | 3 inst/doc/applied-analyses.html | 70 - inst/doc/capsules-and-provenance.R | 11 inst/doc/capsules-and-provenance.html | 1137 +++++++++++++++-------------- inst/doc/describing-data-and-tables.html | 40 - inst/doc/integrity-and-cryptography.html | 8 inst/doc/statistical-methods.html | 8 inst/smoke/smoke.R | 14 man/arccap.Rd | 42 - man/arcfind.Rd |only man/arcget.Rd |only man/cpschk.Rd | 11 man/fetchvrf.Rd | 22 man/wbsave.Rd | 12 tests/testthat/test-archive-rmorie.R |only tests/testthat/test-archive-warc.R |only tests/testthat/test-coverage-1_0_0-audit.R | 6 tests/testthat/test-patch-pr56.R | 6 tests/testthat/test-wayback-save.R | 9 vignettes/parts/_provenance.Rmd | 49 + 34 files changed, 1200 insertions(+), 701 deletions(-)
More information about rmoriebricklayer at CRAN
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Title: Classifying DNA Sequences to Taxonomic Groupings
Description: Classification based analysis of DNA sequences to taxonomic groupings. This package primarily implements Naive Bayesian Classifier from the Ribosomal Database Project. This approach has traditionally been used to classify 16S rRNA gene sequences to bacterial taxonomic outlines; however, it can be used for any type of gene sequence. The method was originally described by Wang, Garrity, Tiedje, and Cole in Applied and Environmental Microbiology 73(16):5261-7 <doi:10.1128/AEM.00062-07>. The package also provides functions to read in 'FASTA'-formatted sequence data.
Author: Pat Schloss [aut, cre, cph]
Maintainer: Pat Schloss <pschloss@umich.edu>
Diff between phylotypr versions 0.1.1 dated 2025-02-21 and 0.2.0 dated 2026-10-22
phylotypr-0.1.1/phylotypr/data/trainset9_pds.rda |only phylotypr-0.1.1/phylotypr/data/trainset9_rdp.rda |only phylotypr-0.1.1/phylotypr/man/trainset9_rdp.Rd |only phylotypr-0.2.0/phylotypr/DESCRIPTION | 18 phylotypr-0.2.0/phylotypr/MD5 | 89 phylotypr-0.2.0/phylotypr/NAMESPACE | 44 phylotypr-0.2.0/phylotypr/NEWS.md | 37 phylotypr-0.2.0/phylotypr/R/RcppExports.R | 16 phylotypr-0.2.0/phylotypr/R/classify_sequences.R |only phylotypr-0.2.0/phylotypr/R/create_database.R |only phylotypr-0.2.0/phylotypr/R/data.R | 29 phylotypr-0.2.0/phylotypr/R/filter_taxonomy.R | 74 phylotypr-0.2.0/phylotypr/R/kmers.R | 266 phylotypr-0.2.0/phylotypr/R/print_taxonomy.R | 128 phylotypr-0.2.0/phylotypr/R/read_fasta.R | 27 phylotypr-0.2.0/phylotypr/R/read_taxonomy.R | 10 phylotypr-0.2.0/phylotypr/R/write_fasta.R | 18 phylotypr-0.2.0/phylotypr/README.md | 6 phylotypr-0.2.0/phylotypr/build/partial.rdb |only phylotypr-0.2.0/phylotypr/build/vignette.rds |binary phylotypr-0.2.0/phylotypr/data/rdp_trainset9.rda |only phylotypr-0.2.0/phylotypr/data/rdp_trainset9_pds.rda |only phylotypr-0.2.0/phylotypr/inst/WORDLIST | 52 phylotypr-0.2.0/phylotypr/inst/doc/phylotypr.R | 121 phylotypr-0.2.0/phylotypr/inst/doc/phylotypr.Rmd | 141 phylotypr-0.2.0/phylotypr/inst/doc/phylotypr.html |10264 ---------- phylotypr-0.2.0/phylotypr/man/build_kmer_database.Rd | 29 phylotypr-0.2.0/phylotypr/man/classify_sequence.Rd | 33 phylotypr-0.2.0/phylotypr/man/classify_sequences.Rd |only phylotypr-0.2.0/phylotypr/man/create_database.Rd |only phylotypr-0.2.0/phylotypr/man/filter_taxonomy.Rd | 32 phylotypr-0.2.0/phylotypr/man/print_taxonomy.Rd | 48 phylotypr-0.2.0/phylotypr/man/rdp_trainset9.Rd |only phylotypr-0.2.0/phylotypr/man/read_fasta.Rd | 8 phylotypr-0.2.0/phylotypr/man/read_taxonomy.Rd | 8 phylotypr-0.2.0/phylotypr/man/write_fasta.Rd | 16 phylotypr-0.2.0/phylotypr/src/RcppExports.cpp | 61 phylotypr-0.2.0/phylotypr/src/classify_bs.cpp |only phylotypr-0.2.0/phylotypr/src/classify_bs.h |only phylotypr-0.2.0/phylotypr/src/detect_kmers.cpp |only phylotypr-0.2.0/phylotypr/src/detect_kmers.h |only phylotypr-0.2.0/phylotypr/src/do_classify.cpp |only phylotypr-0.2.0/phylotypr/src/do_classify.h |only phylotypr-0.2.0/phylotypr/src/kmers.cpp | 47 phylotypr-0.2.0/phylotypr/src/rng.cpp |only phylotypr-0.2.0/phylotypr/src/rng.h |only phylotypr-0.2.0/phylotypr/src/utils.cpp |only phylotypr-0.2.0/phylotypr/src/utils.h |only phylotypr-0.2.0/phylotypr/tests/testthat/test-classify_sequences.R |only phylotypr-0.2.0/phylotypr/tests/testthat/test-create_database.R |only phylotypr-0.2.0/phylotypr/tests/testthat/test-filter_taxonomy.R | 78 phylotypr-0.2.0/phylotypr/tests/testthat/test-kmers.R | 268 phylotypr-0.2.0/phylotypr/tests/testthat/test-print_taxonomy.R | 185 phylotypr-0.2.0/phylotypr/tests/testthat/test-read_fasta.R | 10 phylotypr-0.2.0/phylotypr/tests/testthat/test-read_taxonomy.R | 2 phylotypr-0.2.0/phylotypr/tests/testthat/test-write_fasta.R | 8 phylotypr-0.2.0/phylotypr/vignettes/phylotypr.Rmd | 141 57 files changed, 1435 insertions(+), 10879 deletions(-)
Title: Extract Muscle Synergies from Electromyography
Description: Provides a framework to factorise electromyography (EMG) data.
Tools are provided for raw data pre-processing, non negative matrix factorisation,
classification of factorised data and plotting of obtained outcomes.
In particular, reading from ASCII files is supported, along with wide-used
filtering approaches to process EMG data. All steps include one or more sensible
defaults that aim at simplifying the workflow. Yet, all functions are largely
tunable at need. Example data sets are included.
Author: Alessandro Santuz [aut, cre]
Maintainer: Alessandro Santuz <alessandro.santuz@gmail.com>
Diff between musclesyneRgies versions 1.3.1 dated 2026-08-26 and 1.4.0 dated 2026-10-22
DESCRIPTION | 12 MD5 | 55 ++- NEWS.md | 16 + R/classify_kmeans.R | 118 ++++---- R/data.R | 271 +++++++++---------- R/plot_classified_syns.R | 98 ++++-- R/plot_classified_syns_UMAP.R | 276 +++++++++---------- R/plot_meanEMG.R | 248 ++++++++--------- R/plot_rawEMG.R | 280 +++++++++---------- R/plot_syn_trials.R | 399 ++++++++++++++-------------- R/synsNMF.R | 56 ++- R/utils-weights.R |only README.md | 276 ++++++++++++------- data/SYNS.RData |binary inst/doc/analysis.R | 70 ++++ inst/doc/analysis.Rmd | 70 ++++ inst/doc/analysis.html | 82 ++++- inst/doc/plots.R | 4 inst/doc/plots.Rmd | 198 ++++++------- inst/doc/plots.html | 25 - man/RAW_DATA.Rd | 26 - man/SYNS.Rd | 3 man/classify_kmeans.Rd | 5 man/plot_classified_syns.Rd | 16 - man/synsNMF.Rd | 5 tests/testthat/test-classify_kmeans.R | 6 tests/testthat/test-weights-compatibility.R |only tests/testthat/test-weights-lifecycle.R |only vignettes/analysis.Rmd | 70 ++++ vignettes/plots.Rmd | 198 ++++++------- 30 files changed, 1617 insertions(+), 1266 deletions(-)
More information about musclesyneRgies at CRAN
Permanent link
Title: Representation for Glycan Compositions and Structures
Description: Computational representations of glycan compositions and structures,
including details such as linkages, anomers, and substituents. Supports varying
levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages.
Provides robust parsing and generation of IUPAC-condensed structure strings.
Optimized for vectorized operations on glycan structures, with efficient handling
of duplications. As the cornerstone of the glycoverse ecosystem, this package
delivers the foundational data structures that power glycomics and glycoproteomics
analysis workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyrepr versions 1.1.0 dated 2026-09-22 and 1.2.0 dated 2026-10-22
DESCRIPTION | 13 - MD5 | 101 ++++---- NAMESPACE | 1 NEWS.md | 17 + R/RcppExports.R | 48 +++- R/canonicalize-graphs.R | 11 R/compact-graphs.R |only R/compact-iupac.R | 152 ++++++++++-- R/composition.R | 15 + R/count-mono.R | 8 R/fill-anomer-pos.R | 5 R/floating-localization.R | 35 ++ R/linkage.R | 5 R/mono-type.R | 5 R/native-counts.R |only R/reorder-graph.R | 7 R/smap.R | 11 R/structure-arrays.R | 205 +++++++++++++++-- R/structure-graph-low-level.R | 26 ++ R/structure-progress.R |only R/structure-tables.R | 46 +++ R/structure-to-iupac.R | 4 R/structure.R | 270 ++++++++++++++++++++-- R/substituent.R | 5 inst/doc/glycan-graph.html | 13 - inst/doc/glyrepr.html | 13 - inst/doc/smap.html | 62 ++--- man/as_glycan_structure.Rd | 21 + man/canonicalize_glycan_graph.Rd | 9 man/enumerate_floating_graph_localizations.Rd | 9 man/graph_to_iupac.Rd | 9 man/new_glycan_structure.Rd | 9 man/structure_from_arrays.Rd | 22 + man/validate_glycan_graph.Rd | 9 man/validate_glycan_graph_vector.Rd | 9 src/Makevars | 5 src/Makevars.win | 5 src/RcppExports.cpp | 183 ++++++++++++++- src/array-validation.cpp |only src/compact-arrays.cpp | 308 ++++++++++++++++++++++++-- src/compact-core.h | 206 +++++++++++++---- src/compact-igraph.cpp |only src/compact-iupac.cpp | 98 +++++--- src/compact-progress.h |only src/graph-counts.cpp |only tests/testthat/_snaps/compact-iupac.md | 9 tests/testthat/_snaps/structure-arrays.md | 10 tests/testthat/test-canonicalize-graphs.R | 16 + tests/testthat/test-compact-graphs.R |only tests/testthat/test-compact-igraph.R |only tests/testthat/test-compact-iupac.R | 37 +++ tests/testthat/test-native-counts.R |only tests/testthat/test-smap.R | 8 tests/testthat/test-structure-arrays.R | 60 +++++ tests/testthat/test-structure-progress.R |only tests/testthat/test-structure-to-iupac.R | 46 ++- tests/testthat/test-structure.R | 56 ++-- 57 files changed, 1887 insertions(+), 335 deletions(-)
Title: Equating of Multiple Forms
Description: Equating of multiple forms using Item Response Theory (IRT) methods. See Battauz (2025) <doi:10.18637/jss.v115.i11> for a detailed description of the package. See Battauz M. (2017) <doi:10.1007/s11336-016-9517-x>, Battauz and 'Leoncio' (2023) <doi:10.1177/01466216231151702> and Haberman S. J. (2009) <doi:10.1002/j.2333-8504.2009.tb02197.x>) for the methods to link multiple test forms. See <doi:10.1111/bmsp.70023> for DIF detection across multiple groups.
Author: Michela Battauz [aut, cre],
Waldir Leoncio [ctb]
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between equateMultiple versions 1.1.3 dated 2026-01-15 and 1.2.0 dated 2026-10-22
DESCRIPTION | 8 MD5 | 39 NAMESPACE | 5 R/EqMult.r | 1335 +++++++++++++++++++++++----------- R/RcppExports.R | 32 build/vignette.rds |binary data/timss19.rda |only inst/doc/DIF_tutorial.R |only inst/doc/DIF_tutorial.Rmd |only inst/doc/DIF_tutorial.html |only inst/doc/equateMultiple_tutorial.R | 9 inst/doc/equateMultiple_tutorial.Rmd | 11 inst/doc/equateMultiple_tutorial.html | 68 - man/equateMultiple-package.Rd | 27 man/logLik.mltDIF.Rd |only man/logLik.mlteqc.Rd |only man/multiDIF.Rd |only man/multiec.Rd | 22 man/summary.mltDIF.Rd |only man/timss19.Rd |only src/EqMult.cpp | 442 +++++++++++ src/Makevars | 1 src/RcppExports.cpp | 144 +++ vignettes/DIF_tutorial.Rmd |only vignettes/equateMultiple_tutorial.Rmd | 11 vignettes/references.bib |only 26 files changed, 1645 insertions(+), 509 deletions(-)
More information about equateMultiple at CRAN
Permanent link
Title: Fetch Data from the Federal Reserve Economic Database
Description: Interact with the FRED API, <https://fred.stlouisfed.org/docs/api/fred/>,
to fetch observations across economic series;
find information about different economic sources, releases, series, etc.;
conduct searches by series name, attributes, or tags; and determine the
latest updates. Includes functions for creating panels of related variables
with minimal effort and datasets containing data sources, releases, and
popular FRED tags.
Author: Chris Mann [aut, cre]
Maintainer: Chris Mann <cmann3@unl.edu>
Diff between eFRED versions 0.1.0 dated 2021-01-15 and 0.2.0 dated 2026-10-22
DESCRIPTION | 17 + MD5 | 74 ++++---- NAMESPACE | 1 R/fred.R | 34 +++ R/fred_category.R | 3 R/fred_release.R | 3 R/fred_search.R | 3 R/fred_series.R | 3 R/fred_sources.R | 3 R/fred_tags.R | 3 R/fred_updates.R | 4 R/internal.R | 76 +++++++- R/internal_other.R | 5 R/internal_series.R | 67 ++++++- R/register.R | 10 + build/vignette.rds |binary inst/doc/FetchingDataFromFRED.R | 23 +- inst/doc/FetchingDataFromFRED.Rmd | 53 +++++- inst/doc/FetchingDataFromFRED.html | 316 ++++++++++++++++++++----------------- man/countries.Rd | 4 man/country2.Rd | 4 man/country3.Rd | 4 man/fred.Rd | 13 + man/fred_category.Rd | 17 + man/fred_group.Rd | 7 man/fred_releases.Rd | 23 +- man/fred_search.Rd | 11 - man/fred_series.Rd | 17 + man/fred_sources.Rd | 11 - man/fred_tags.Rd | 11 - man/fred_updates.Rd | 3 man/releases.Rd | 6 man/set_fred_key.Rd | 10 + man/sources.Rd | 6 man/states.Rd | 4 man/states_extended.Rd | 4 man/tags.Rd | 6 vignettes/FetchingDataFromFRED.Rmd | 53 +++++- 38 files changed, 607 insertions(+), 305 deletions(-)
Title: 'CppAD' C++ Header Files for Automatic Differentiation
Description: Provides the 'CppAD' C++ header library for automatic
differentiation, for use by R packages via LinkingTo. Headers are
vendored with CRAN-safe defaults and R-safe error handling that does not call std::cerr or
std::exit. The two final components of the version number are the 'CppAD' release number.
Author: Patrick Brown [aut, cre, cph],
Bradley M. Bell [aut, cph] ,
COIN-OR Foundation [cph]
Maintainer: Patrick Brown <patrick.borgnine@gmail.com>
Diff between RCppAD versions 1.20260000.0-1 dated 2026-09-11 and 1.20260000.0-2 dated 2026-10-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ inst/include/cppad/README.RCppAD.md | 2 ++ inst/include/cppad/core/fun_construct.hpp | 4 +++- tests/compile-smoke.R | 22 ++++++++++++++++++---- 6 files changed, 38 insertions(+), 14 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information on accumulation rates and their variability. See Blaauw & Christen (2011).
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [aut, ctb, cph] ,
Marco A. Aquino Lopez [aut] ,
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 4.0.0 dated 2026-09-16 and 4.0.2 dated 2026-10-22
DESCRIPTION | 8 +- MD5 | 46 ++++++------ NAMESPACE | 1 NEWS.md | 11 +++ R/MCMC.R | 17 +++- R/accrate.R | 7 + R/agedepth.R | 162 +++++++++++++++++++++++++++++++++++++++------ R/calc.R | 88 ++++++++++++++++++++++++ R/forplum.R | 12 --- R/internal_plots.R | 115 ++++++++++++++++++++----------- R/rbacon-package.R | 3 R/rbacon.R | 19 +++-- R/read_write.R | 128 +++++------------------------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/rbacon.html | 54 +++++++-------- man/Bacon.Rd | 7 + man/accrate.age.ghost.Rd | 2 man/accrate.depth.ghost.Rd | 2 man/agedepth.Rd | 46 +++++++++--- man/ageranges.Rd | 2 src/bacon.cpp | 4 - src/events.cpp | 1 src/hists.cpp | 2 24 files changed, 466 insertions(+), 271 deletions(-)
Title: Various Methods for the Two Sample Problem in D>1 Dimensions
Description: The routine twosample_test() in this package runs the
two-sample test using various test statistic for multivariate data.
The user can also run several tests and then find a p value adjusted for simultaneous inference.
The p values are found via permutation or via the parametric bootstrap.
The routine twosample_power() allows the estimation of the power of the tests.
The routine run.studies() allows a user to quickly study the power of a new method and
how it compares to those included in the package.
For details of the methods and references see the included vignettes.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between MD2sample versions 1.4.1 dated 2026-10-14 and 1.4.2 dated 2026-10-22
DESCRIPTION | 6 ++-- MD5 | 10 +++--- NEWS.md | 3 ++ inst/doc/CaseStudies.html | 68 +++++++++++++++++++++++----------------------- inst/doc/MD2sample.html | 52 +++++++++++++++++------------------ src/TS_cont.cpp | 2 - 6 files changed, 72 insertions(+), 69 deletions(-)
Title: Infinitesimal Jackknife Standard Errors for 'brms' Models
Description: Computes infinitesimal jackknife standard errors and covariance
matrices for posterior expectations from 'brms' models or matched posterior
draws and pointwise log likelihoods. Supports independent and clustered
sampling units, transformed quantities, blockwise likelihood evaluation,
and chain stability diagnostics. References: Ji et al. (2026)
<doi:10.3102/10769986251379738>; Giordano and Broderick (2024)
<doi:10.48550/arXiv.2305.06466>.
Author: Feng Ji [aut, cre] ,
JoonHo Lee [aut],
Sophia Rabe-Hesketh [aut]
Maintainer: Feng Ji <f.ji@utoronto.ca>
Diff between IJSE versions 0.1.2 dated 2025-07-18 and 0.3.4 dated 2026-10-22
IJSE-0.1.2/IJSE/R/IJSE.R |only IJSE-0.1.2/IJSE/man/IJ_se.Rd |only IJSE-0.1.2/IJSE/tests/testthat/test-IJ_se.R |only IJSE-0.3.4/IJSE/DESCRIPTION | 25 ++- IJSE-0.3.4/IJSE/MD5 | 100 +++++++++++++- IJSE-0.3.4/IJSE/NAMESPACE | 21 ++ IJSE-0.3.4/IJSE/NEWS.md | 85 +++++++++++ IJSE-0.3.4/IJSE/R/IJSE-package.R |only IJSE-0.3.4/IJSE/R/brms.R |only IJSE-0.3.4/IJSE/R/core.R |only IJSE-0.3.4/IJSE/R/methods.R |only IJSE-0.3.4/IJSE/README.md |only IJSE-0.3.4/IJSE/build |only IJSE-0.3.4/IJSE/inst |only IJSE-0.3.4/IJSE/man/IJSE-package.Rd |only IJSE-0.3.4/IJSE/man/ijse.Rd |only IJSE-0.3.4/IJSE/man/ijse_draws.Rd |only IJSE-0.3.4/IJSE/man/summary.ijse.Rd |only IJSE-0.3.4/IJSE/tests/testthat/fixtures |only IJSE-0.3.4/IJSE/tests/testthat/helper-inputs.R |only IJSE-0.3.4/IJSE/tests/testthat/test-brms-deep.R |only IJSE-0.3.4/IJSE/tests/testthat/test-brms.R |only IJSE-0.3.4/IJSE/tests/testthat/test-bugs-032.R |only IJSE-0.3.4/IJSE/tests/testthat/test-bugs-033.R |only IJSE-0.3.4/IJSE/tests/testthat/test-bugs-034.R |only IJSE-0.3.4/IJSE/tests/testthat/test-core.R |only IJSE-0.3.4/IJSE/tests/testthat/test-methods-diagnostics.R |only IJSE-0.3.4/IJSE/tests/testthat/test-study.R |only IJSE-0.3.4/IJSE/tests/testthat/test-tutorials.R |only IJSE-0.3.4/IJSE/tests/testthat/test-v03.R |only IJSE-0.3.4/IJSE/tests/testthat/test-validation.R |only IJSE-0.3.4/IJSE/tools |only IJSE-0.3.4/IJSE/vignettes |only 33 files changed, 210 insertions(+), 21 deletions(-)
Title: Sample Size and Simulation for Negative Binomial Outcomes
Description: Provides tools for planning and simulating recurrent event trials
with overdispersed count endpoints analyzed using negative binomial (or
Poisson) rate models. Implements sample size and power calculations for
fixed designs with variable accrual, dropout, maximum follow-up, and event
gaps, including methods of Zhu and Lakkis (2014) <doi:10.1002/sim.5947> and
Friede and Schmidli (2010) <doi:10.3414/ME09-02-0060> as well as
extensions for score-test sizing and gaps between events. Supports group
sequential monitoring by building on the 'gsDesign' package.
Includes recurrent-event simulation utilities (including seasonal rates),
interim data truncation, Wald and score-test inference for rate ratios,
and information estimation and sample size re-estimation with or without
treatment-group labels.
Author: Keaven Anderson [aut, cre],
Hongtao Zhang [aut],
Andrea Maes [aut],
Nan Xiao [ctb],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesignNB versions 0.3.2 dated 2026-07-06 and 0.4.0 dated 2026-10-22
gsDesignNB-0.3.2/gsDesignNB/R/preview_pkgdown_site.R |only gsDesignNB-0.3.2/gsDesignNB/man/preview_pkgdown_site.Rd |only gsDesignNB-0.3.2/gsDesignNB/vignettes/completers_interim_example.html |only gsDesignNB-0.3.2/gsDesignNB/vignettes/group_sequential_simulation.html |only gsDesignNB-0.4.0/gsDesignNB/DESCRIPTION | 10 gsDesignNB-0.4.0/gsDesignNB/MD5 | 78 gsDesignNB-0.4.0/gsDesignNB/NAMESPACE | 1 gsDesignNB-0.4.0/gsDesignNB/NEWS.md | 218 gsDesignNB-0.4.0/gsDesignNB/R/gsNBCalendar.R | 12 gsDesignNB-0.4.0/gsDesignNB/build/vignette.rds |binary gsDesignNB-0.4.0/gsDesignNB/inst/doc/blinded-info-diagnostics.html | 85 gsDesignNB-0.4.0/gsDesignNB/inst/doc/completers-interim-example.R | 1 gsDesignNB-0.4.0/gsDesignNB/inst/doc/completers-interim-example.Rmd | 1 gsDesignNB-0.4.0/gsDesignNB/inst/doc/completers-interim-example.html | 5 gsDesignNB-0.4.0/gsDesignNB/inst/doc/group-sequential-simulation.R | 34 gsDesignNB-0.4.0/gsDesignNB/inst/doc/group-sequential-simulation.Rmd | 34 gsDesignNB-0.4.0/gsDesignNB/inst/doc/group-sequential-simulation.html | 2372 ++---- gsDesignNB-0.4.0/gsDesignNB/inst/doc/multiple-imputation-nb.html | 80 gsDesignNB-0.4.0/gsDesignNB/inst/doc/sample-size-nbinom.html | 4 gsDesignNB-0.4.0/gsDesignNB/inst/doc/sample-size-skills-example.html | 2 gsDesignNB-0.4.0/gsDesignNB/inst/doc/score-vs-wald-simulation.html | 6 gsDesignNB-0.4.0/gsDesignNB/inst/doc/seasonal-simulation.html | 4 gsDesignNB-0.4.0/gsDesignNB/inst/doc/simulation-example.R | 12 gsDesignNB-0.4.0/gsDesignNB/inst/doc/simulation-example.Rmd | 14 gsDesignNB-0.4.0/gsDesignNB/inst/doc/simulation-example.html | 1344 ++- gsDesignNB-0.4.0/gsDesignNB/inst/doc/ssr-example.R | 14 gsDesignNB-0.4.0/gsDesignNB/inst/doc/ssr-example.Rmd | 14 gsDesignNB-0.4.0/gsDesignNB/inst/doc/ssr-example.html | 2382 ++---- gsDesignNB-0.4.0/gsDesignNB/inst/doc/ssr-simulation-study.R | 41 gsDesignNB-0.4.0/gsDesignNB/inst/doc/ssr-simulation-study.Rmd | 41 gsDesignNB-0.4.0/gsDesignNB/inst/doc/ssr-simulation-study.html | 3750 ++-------- gsDesignNB-0.4.0/gsDesignNB/inst/doc/verification-simulation.R | 90 gsDesignNB-0.4.0/gsDesignNB/inst/doc/verification-simulation.Rmd | 90 gsDesignNB-0.4.0/gsDesignNB/inst/doc/verification-simulation.html | 2879 ++----- gsDesignNB-0.4.0/gsDesignNB/man/gsNBCalendar.Rd | 12 gsDesignNB-0.4.0/gsDesignNB/tests/testthat/test-gsNBCalendar.R | 93 gsDesignNB-0.4.0/gsDesignNB/vignettes/completers-interim-example.Rmd | 1 gsDesignNB-0.4.0/gsDesignNB/vignettes/group-sequential-simulation.Rmd | 34 gsDesignNB-0.4.0/gsDesignNB/vignettes/simulation-example.Rmd | 14 gsDesignNB-0.4.0/gsDesignNB/vignettes/ssr-example.Rmd | 14 gsDesignNB-0.4.0/gsDesignNB/vignettes/ssr-simulation-study.Rmd | 41 gsDesignNB-0.4.0/gsDesignNB/vignettes/verification-simulation.Rmd | 90 42 files changed, 5480 insertions(+), 8437 deletions(-)
Title: Extracts Knowledge from 'Git' Repositories
Description: Scan multiple 'Git' repositories, pull specified files content and process it with large language models. You can summarize the content in specific way, extract information and data, or find answers to your questions about the repositories. The output can be stored in vector database and used for semantic search or as a part of a RAG (Retrieval Augmented Generation) prompt.
Author: Kamil Wais [aut, cre],
Krystian Igras [aut],
Maciej Banas [aut]
Maintainer: Kamil Wais <kamil.wais@gmail.com>
Diff between GitAI versions 0.1.3 dated 2025-12-03 and 0.1.4 dated 2026-10-22
DESCRIPTION | 6 ++--- MD5 | 15 ++++++------ NEWS.md | 5 ++++ R/zzz.R |only tests/testthat/setup.R | 40 +++++++++++++++++++++++++++++++--- tests/testthat/test-process_content.R | 2 + tests/testthat/test-process_repos.R | 2 + tests/testthat/test-set_llm.R | 2 - tests/testthat/test-set_repos.R | 1 9 files changed, 59 insertions(+), 14 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
References: Patil (2021) <doi:10.21105/joss.03167>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 1.1.3 dated 2026-10-17 and 1.1.4 dated 2026-10-22
ggstatsplot-1.1.3/ggstatsplot/tests/testthat/_snaps/ggwithinstats/defaults-plots-more-than-two-groups.svg |only ggstatsplot-1.1.3/ggstatsplot/tests/testthat/_snaps/ggwithinstats/defaults-plots-two-groups.svg |only ggstatsplot-1.1.4/ggstatsplot/DESCRIPTION | 8 ggstatsplot-1.1.4/ggstatsplot/MD5 | 175 - ggstatsplot-1.1.4/ggstatsplot/NEWS.md | 36 ggstatsplot-1.1.4/ggstatsplot/R/0-utils.R | 13 ggstatsplot-1.1.4/ggstatsplot/R/combine-plots.R | 19 ggstatsplot-1.1.4/ggstatsplot/R/data.R | 4 ggstatsplot-1.1.4/ggstatsplot/R/extract-stats.R | 18 ggstatsplot-1.1.4/ggstatsplot/R/ggbarstats.R | 26 ggstatsplot-1.1.4/ggstatsplot/R/ggbetweenstats-helpers.R | 6 ggstatsplot-1.1.4/ggstatsplot/R/ggbetweenstats.R | 111 - ggstatsplot-1.1.4/ggstatsplot/R/ggcoefstats.R | 140 - ggstatsplot-1.1.4/ggstatsplot/R/ggcorrmat.R | 43 ggstatsplot-1.1.4/ggstatsplot/R/ggdotplotstats.R | 28 ggstatsplot-1.1.4/ggstatsplot/R/gghistostats-helpers.R | 1 ggstatsplot-1.1.4/ggstatsplot/R/gghistostats.R | 56 ggstatsplot-1.1.4/ggstatsplot/R/ggpiestats-ggbarstats-helpers.R | 20 ggstatsplot-1.1.4/ggstatsplot/R/ggpiestats.R | 69 ggstatsplot-1.1.4/ggstatsplot/R/ggscatterstats.R | 75 ggstatsplot-1.1.4/ggstatsplot/R/ggstatsplot-package.R | 66 ggstatsplot-1.1.4/ggstatsplot/R/ggwithinstats.R | 57 ggstatsplot-1.1.4/ggstatsplot/R/theme-ggstatsplot.R | 9 ggstatsplot-1.1.4/ggstatsplot/README.md | 148 - ggstatsplot-1.1.4/ggstatsplot/inst/doc/ggstatsplot.R | 1 ggstatsplot-1.1.4/ggstatsplot/inst/doc/ggstatsplot.Rmd | 8 ggstatsplot-1.1.4/ggstatsplot/inst/doc/ggstatsplot.html | 9 ggstatsplot-1.1.4/ggstatsplot/man/combine_plots.Rd | 19 ggstatsplot-1.1.4/ggstatsplot/man/dot-grouped_list.Rd | 5 ggstatsplot-1.1.4/ggstatsplot/man/extract_stats.Rd | 2 ggstatsplot-1.1.4/ggstatsplot/man/ggbarstats.Rd | 101 - ggstatsplot-1.1.4/ggstatsplot/man/ggbetweenstats.Rd | 133 - ggstatsplot-1.1.4/ggstatsplot/man/ggcoefstats.Rd | 130 - ggstatsplot-1.1.4/ggstatsplot/man/ggcorrmat.Rd | 56 ggstatsplot-1.1.4/ggstatsplot/man/ggdotplotstats.Rd | 88 ggstatsplot-1.1.4/ggstatsplot/man/gghistostats.Rd | 87 ggstatsplot-1.1.4/ggstatsplot/man/ggpiestats.Rd | 100 - ggstatsplot-1.1.4/ggstatsplot/man/ggscatterstats.Rd | 89 ggstatsplot-1.1.4/ggstatsplot/man/ggstatsplot-package.Rd | 57 ggstatsplot-1.1.4/ggstatsplot/man/ggwithinstats.Rd | 173 - ggstatsplot-1.1.4/ggstatsplot/man/grouped_ggbarstats.Rd | 83 ggstatsplot-1.1.4/ggstatsplot/man/grouped_ggbetweenstats.Rd | 105 - ggstatsplot-1.1.4/ggstatsplot/man/grouped_ggcorrmat.Rd | 54 ggstatsplot-1.1.4/ggstatsplot/man/grouped_ggdotplotstats.Rd | 83 ggstatsplot-1.1.4/ggstatsplot/man/grouped_gghistostats.Rd | 79 ggstatsplot-1.1.4/ggstatsplot/man/grouped_ggpiestats.Rd | 84 ggstatsplot-1.1.4/ggstatsplot/man/grouped_ggscatterstats.Rd | 102 - ggstatsplot-1.1.4/ggstatsplot/man/grouped_ggwithinstats.Rd | 134 - ggstatsplot-1.1.4/ggstatsplot/man/iris_long.Rd | 2 ggstatsplot-1.1.4/ggstatsplot/man/movies_long.Rd | 2 ggstatsplot-1.1.4/ggstatsplot/man/rmd-fragments/ggbarstats_graphics.Rmd | 2 ggstatsplot-1.1.4/ggstatsplot/man/theme_ggstatsplot.Rd | 9 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/extract-stats.md | 29 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/ggbarstats/prop-test-fails-with-dropped-levels.svg | 113 - ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/ggdotplotstats/parametric-without-na.svg | 199 +- ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/ggdotplotstats/robust-with-na.svg | 213 +- ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/gghistostats/aesthetic-modifications-work.svg | 2 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/gghistostats/all-values-identical-and-large.svg |only ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/gghistostats/all-values-identical.svg |only ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/gghistostats/defaults-as-expected.svg | 969 +++++----- ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/gghistostats/modification-with-ggplot2-works.svg | 511 ++--- ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/ggwithinstats/default-plots-more-than-two-groups.svg |only ggstatsplot-1.1.4/ggstatsplot/tests/testthat/_snaps/ggwithinstats/default-plots-two-groups.svg |only ggstatsplot-1.1.4/ggstatsplot/tests/testthat/helper-combine-plots.R | 8 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/helper-extract-stats.R |only ggstatsplot-1.1.4/ggstatsplot/tests/testthat/helper-ggpiestats-ggbarstats.R | 72 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-extract-stats.R | 86 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-ggbarstats.R | 94 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-ggbetweenstats.R | 2 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-ggcoefstats.R | 40 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-ggcorrmat.R | 27 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-ggdotplotstats.R | 5 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-gghistostats.R | 59 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-ggpiestats.R | 84 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-ggscatterstats.R | 8 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-ggwithinstats.R | 37 ggstatsplot-1.1.4/ggstatsplot/tests/testthat/test-pairwise-ggsignif.R | 9 ggstatsplot-1.1.4/ggstatsplot/vignettes/ggstatsplot.Rmd | 8 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/faq.Rmd | 9 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/ggbarstats.Rmd | 38 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/ggbetweenstats.Rmd | 19 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/ggcoefstats.Rmd | 42 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/ggcorrmat.Rmd | 5 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/ggdotplotstats.Rmd | 8 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/gghistostats.Rmd | 4 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/ggpiestats.Rmd | 2 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/ggscatterstats.Rmd | 2 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/ggwithinstats.Rmd | 29 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/interpretation.Rmd | 2 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/pairwise.Rmd | 23 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/principles.Rmd | 13 ggstatsplot-1.1.4/ggstatsplot/vignettes/web_only/purrr_examples.Rmd | 54 92 files changed, 2671 insertions(+), 3079 deletions(-)
Title: Pre-Processing of 'GENEActiv' Data
Description: Analytics to read in and segment raw 'GENEActiv' accelerometer data into epochs and events.
For more details on the 'GENEActiv' device, see <https://activinsights.com/resources/geneactiv-support-1-2/>.
Author: Joss Langford [aut],
Ian Long [aut],
Jia Ying Chua [aut, cre],
Activinsights Ltd [cph]
Maintainer: Jia Ying Chua <jiayingc@activinsights.com>
Diff between GENEAcore versions 1.2.0 dated 2026-04-02 and 1.3.9 dated 2026-10-22
GENEAcore-1.2.0/GENEAcore/inst/extdata/GENEAcore_Data_Dictionary_2Apr26.pdf |only GENEAcore-1.2.0/GENEAcore/man/apply_updown.Rd |only GENEAcore-1.3.9/GENEAcore/DESCRIPTION | 10 GENEAcore-1.3.9/GENEAcore/MD5 | 124 GENEAcore-1.3.9/GENEAcore/NAMESPACE | 139 GENEAcore-1.3.9/GENEAcore/NEWS.md | 191 - GENEAcore-1.3.9/GENEAcore/R/MPI_calibrate.R | 6 GENEAcore-1.3.9/GENEAcore/R/MPI_create.R | 1892 +++++----- GENEAcore-1.3.9/GENEAcore/R/MPI_detect.R | 674 +-- GENEAcore-1.3.9/GENEAcore/R/aggregate_periods.R | 51 GENEAcore-1.3.9/GENEAcore/R/apply_measures.R | 66 GENEAcore-1.3.9/GENEAcore/R/coel_json_builder.R | 1176 +++--- GENEAcore-1.3.9/GENEAcore/R/coel_json_create.R | 270 - GENEAcore-1.3.9/GENEAcore/R/daily_measures.R | 1281 +++--- GENEAcore-1.3.9/GENEAcore/R/geneabout.R | 259 - GENEAcore-1.3.9/GENEAcore/R/geneabout_functions.R | 693 ++- GENEAcore-1.3.9/GENEAcore/R/geneacore.R | 134 GENEAcore-1.3.9/GENEAcore/R/geneacore_part1.R | 234 - GENEAcore-1.3.9/GENEAcore/R/geneacore_part2.R | 246 - GENEAcore-1.3.9/GENEAcore/R/geneacore_part3.R | 554 +- GENEAcore-1.3.9/GENEAcore/R/geneacore_part4.R | 11 GENEAcore-1.3.9/GENEAcore/R/math.R | 459 +- GENEAcore-1.3.9/GENEAcore/R/sample_binfile.R | 67 GENEAcore-1.3.9/GENEAcore/R/step_counter.R | 92 GENEAcore-1.3.9/GENEAcore/R/utils.R | 948 ++--- GENEAcore-1.3.9/GENEAcore/inst/doc/GENEAcore.R | 24 GENEAcore-1.3.9/GENEAcore/inst/doc/GENEAcore.Rmd | 64 GENEAcore-1.3.9/GENEAcore/inst/doc/GENEAcore.html | 106 GENEAcore-1.3.9/GENEAcore/inst/doc/breaking-changes.R | 71 GENEAcore-1.3.9/GENEAcore/inst/doc/breaking-changes.Rmd | 84 GENEAcore-1.3.9/GENEAcore/inst/doc/breaking-changes.html | 104 GENEAcore-1.3.9/GENEAcore/inst/documents |only GENEAcore-1.3.9/GENEAcore/inst/extdata/math_example_13Mar26.R | 4 GENEAcore-1.3.9/GENEAcore/man/CirSD.Rd |only GENEAcore-1.3.9/GENEAcore/man/MeanDir.Rd |only GENEAcore-1.3.9/GENEAcore/man/apply_all.Rd | 2 GENEAcore-1.3.9/GENEAcore/man/apply_calibration.Rd | 2 GENEAcore-1.3.9/GENEAcore/man/apply_elevation.Rd |only GENEAcore-1.3.9/GENEAcore/man/apply_jerk.Rd |only GENEAcore-1.3.9/GENEAcore/man/bouts_decision_tree.Rd | 6 GENEAcore-1.3.9/GENEAcore/man/calculate_daily_activity_measures.Rd | 8 GENEAcore-1.3.9/GENEAcore/man/calculate_daily_sleep_measures.Rd | 8 GENEAcore-1.3.9/GENEAcore/man/cx_percentile.Rd | 4 GENEAcore-1.3.9/GENEAcore/man/find_rest_intervals.Rd | 7 GENEAcore-1.3.9/GENEAcore/man/folder_measures.Rd | 68 GENEAcore-1.3.9/GENEAcore/man/fx_count.Rd | 21 GENEAcore-1.3.9/GENEAcore/man/geneabout.Rd | 2 GENEAcore-1.3.9/GENEAcore/man/geneacore.Rd | 12 GENEAcore-1.3.9/GENEAcore/man/geneacore_part1.Rd | 4 GENEAcore-1.3.9/GENEAcore/man/geneacore_part2.Rd | 2 GENEAcore-1.3.9/GENEAcore/man/geneacore_part3.Rd | 13 GENEAcore-1.3.9/GENEAcore/man/geneacore_part4.Rd | 4 GENEAcore-1.3.9/GENEAcore/man/identifier_mapping.Rd | 38 GENEAcore-1.3.9/GENEAcore/man/merge_control.Rd |only GENEAcore-1.3.9/GENEAcore/man/mx_lx_window.Rd | 17 GENEAcore-1.3.9/GENEAcore/man/radian_fun.Rd |only GENEAcore-1.3.9/GENEAcore/man/return_milliseconds_ISO.Rd |only GENEAcore-1.3.9/GENEAcore/man/single_file_measures.Rd | 76 GENEAcore-1.3.9/GENEAcore/tests/testthat/test-MPI_create.R | 8 GENEAcore-1.3.9/GENEAcore/tests/testthat/test-apply_measures.R | 165 GENEAcore-1.3.9/GENEAcore/tests/testthat/test-daily_measures.R | 353 + GENEAcore-1.3.9/GENEAcore/tests/testthat/test-geneabout_functions.R | 314 + GENEAcore-1.3.9/GENEAcore/tests/testthat/test-geneacore.R | 558 +- GENEAcore-1.3.9/GENEAcore/tests/testthat/test-math.R | 109 GENEAcore-1.3.9/GENEAcore/tests/testthat/test-step_counter.R | 103 GENEAcore-1.3.9/GENEAcore/tests/testthat/test_aggregate_periods.R | 1065 ++--- GENEAcore-1.3.9/GENEAcore/vignettes/GENEAcore.Rmd | 64 GENEAcore-1.3.9/GENEAcore/vignettes/breaking-changes.Rmd | 84 68 files changed, 7165 insertions(+), 5986 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph] ,
Finnish Biodiversity Information Facility [cph] ,
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.10.0 dated 2026-07-02 and 0.10.1 dated 2026-10-22
DESCRIPTION | 8 MD5 | 75 NAMESPACE | 32 NEWS.md | 17 R/api_get.R | 6 R/finbif_occurrence.R | 401 + R/finbif_records.R | 28 R/finbif_request_token.R | 5 R/sysdata.rda |binary R/variables.R | 5 README.md | 2 man/finbif_occurrence.Rd | 2 man/variables.Rd | 5 tests/fixtures/finbif_cache_db_timeout.yml | 20 tests/fixtures/finbif_cache_file_timeout.yml | 30 tests/fixtures/finbif_cache_timeout.yml | 30 tests/fixtures/finbif_check_taxa.yml | 14 tests/fixtures/finbif_collections.yml | 1600 +++--- tests/fixtures/finbif_informal_groups.yml | 4 tests/fixtures/finbif_last_mod1.yml | 6 tests/fixtures/finbif_last_mod2.yml | 6 tests/fixtures/finbif_last_mod3.yml | 6 tests/fixtures/finbif_metadata.yml | 782 +-- tests/fixtures/finbif_occurrence.yml | 2439 +++++----- tests/fixtures/finbif_occurrence_aggregate.yml | 1632 +++--- tests/fixtures/finbif_occurrence_api_error.yml | 4 tests/fixtures/finbif_occurrence_compute_var_from_id_zero_rows.yml | 1636 +++--- tests/fixtures/finbif_occurrence_dates.yml | 1648 +++--- tests/fixtures/finbif_occurrence_load.yml | 60 tests/fixtures/finbif_occurrence_print.yml | 18 tests/fixtures/finbif_occurrence_select_local_area.yml | 6 tests/fixtures/finbif_taxa.yml | 20 tests/testthat/_snaps/caching.md | 6 tests/testthat/_snaps/finbif_collections.md | 64 tests/testthat/_snaps/finbif_metadata.md | 3 tests/testthat/_snaps/finbif_occurrence.md | 45 tests/testthat/_snaps/finbif_occurrence_load.md | 10 tests/testthat/test-finbif_occurrence.R | 50 tests/testthat/test-iso8061.R |only 39 files changed, 6150 insertions(+), 4575 deletions(-)
Title: Data and Code for Empirical Research in Accounting
Description: Data sets and functions for empirical accounting research,
including event-return calculations, panel-data simulations, classification
performance measures, and 'Parquet' file workflows using 'DuckDB'. Supports
methods described in "Empirical Research in Accounting: Tools and Methods"
(2024) <doi:10.1201/9781003456230>. The online companion is
available at <https://iangow.github.io/far_book/>.
Author: Ian Gow [aut, cre]
Maintainer: Ian Gow <iandgow@gmail.com>
Diff between farr versions 1.1.0 dated 2026-10-15 and 1.1.1 dated 2026-10-22
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ NEWS.md | 6 +++++ R/get_event_cum_rets.R | 6 ++--- R/get_event_cum_rets_mth.R | 6 ++--- R/gross_return_sql.R | 16 +++++++++++--- tests/testthat/helper-cumulative-returns.R | 9 +++++++- tests/testthat/test-get_event_cum_rets.R | 32 +++++++++++++++++++---------- 8 files changed, 65 insertions(+), 30 deletions(-)
Title: A 'DuckDB'-Backed Version of 'dplyr'
Description: A drop-in replacement for 'dplyr', powered by 'DuckDB' for
performance. Offers convenient utilities for working with in-memory and
larger-than-memory data while retaining full 'dplyr' compatibility.
Author: Hannes Muehleisen [aut] ,
Kirill Mueller [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckplyr versions 1.2.1 dated 2026-03-10 and 1.2.2 dated 2026-10-22
duckplyr-1.2.1/duckplyr/R/construct_constant.R |only duckplyr-1.2.1/duckplyr/R/construct_function.R |only duckplyr-1.2.1/duckplyr/R/construct_reference.R |only duckplyr-1.2.1/duckplyr/R/construct_window.R |only duckplyr-1.2.2/duckplyr/DESCRIPTION | 17 - duckplyr-1.2.2/duckplyr/MD5 | 41 +-- duckplyr-1.2.2/duckplyr/NAMESPACE | 4 duckplyr-1.2.2/duckplyr/NEWS.md | 7 duckplyr-1.2.2/duckplyr/R/zzz.R | 6 duckplyr-1.2.2/duckplyr/build/vignette.rds |binary duckplyr-1.2.2/duckplyr/inst/doc/developers.html | 20 + duckplyr-1.2.2/duckplyr/inst/doc/duckdb.html | 16 - duckplyr-1.2.2/duckplyr/inst/doc/extend.html | 2 duckplyr-1.2.2/duckplyr/inst/doc/fallback.html | 10 duckplyr-1.2.2/duckplyr/inst/doc/large.html | 135 +++++----- duckplyr-1.2.2/duckplyr/inst/doc/limits.html | 95 ++----- duckplyr-1.2.2/duckplyr/inst/doc/prudence.html | 23 - duckplyr-1.2.2/duckplyr/inst/doc/telemetry.html | 10 duckplyr-1.2.2/duckplyr/tests/testthat/_snaps/dplyr-all-equal.md | 10 duckplyr-1.2.2/duckplyr/tests/testthat/_snaps/dplyr-bind-rows.md | 2 duckplyr-1.2.2/duckplyr/tests/testthat/_snaps/dplyr-case-when.md | 4 duckplyr-1.2.2/duckplyr/tests/testthat/helper-snapshot.R |only duckplyr-1.2.2/duckplyr/tests/testthat/test-compute.R | 2 duckplyr-1.2.2/duckplyr/tests/testthat/test-relational-duckdb.R | 2 24 files changed, 200 insertions(+), 206 deletions(-)
Title: Scalable Bayesian Inference for Discrete Markov Random Fields
Description: Estimation of discrete Markov random fields through the pseudo-likelihood, for both Ising models
(Ising (1925) <doi:10.1007/BF02980577>) and ordinal Markov random fields (Marsman et al. (2025)
<doi:10.1017/psy.2024.4>). Point estimates, either maximum pseudo-likelihood or maximum a posteriori, are
obtained through a trust region optimization algorithm, with robust standard errors from the
Godambe-Huber-White (GHW, or sandwich) estimator, for both full and constrained network structures. Bayesian
inference corrects the pseudo-posterior through coordinate rescaling (Arena and Marsman (2026)
<doi:10.48550/arXiv.2601.17205>), which matches its covariance to the GHW covariance, and samples from it with the Fisher adaptive Metropolis-adjusted Langevin algorithm (Titsias (2024)
<doi:10.48550/arXiv.2305.14442>). For comparison, the posterior based on the full likelihood can also be
sampled, exactly for small networks or with the double Metropolis-Hastings algorithm (Lia [...truncated...]
Author: Giuseppe Arena [aut, cre]
Maintainer: Giuseppe Arena <g.arena@uva.nl>
Diff between dmrfit versions 0.1.0 dated 2026-10-18 and 0.1.1 dated 2026-10-22
DESCRIPTION | 8 MD5 | 37 +-- NEWS.md |only R/dmrfit.R | 47 ++-- R/dmrfit_bayes.R | 94 +++++--- inst/doc/dmrfit.Rmd | 380 ++++++++++++++++---------------- inst/doc/dmrfit.html | 397 +++++++++++++++++----------------- inst/tinytest/test_dmrfit.R | 26 +- inst/tinytest/test_dmrfit_bayes.R | 15 + man/dmrfit.Rd | 13 - man/dmrfit_bayes.Rd | 6 src/optimize.cpp | 27 +- src/priors.cpp | 4 src/sampler-exact.cpp | 2 vignettes/dmrfit-bf-network-1.png |binary vignettes/dmrfit-centrality-1.png |binary vignettes/dmrfit-density-1.png |binary vignettes/dmrfit-network-within-1.png |binary vignettes/dmrfit-trace-1.png |binary vignettes/dmrfit.Rmd | 380 ++++++++++++++++---------------- 20 files changed, 764 insertions(+), 672 deletions(-)
Title: Display Idiomatic Code to Construct Most R Objects
Description: Prints code that can be used to recreate R objects. In a
sense it is similar to 'base::dput()' or 'base::deparse()' but
'constructive' strives to use idiomatic constructors.
Author: Antoine Fabri [aut, cre],
Kirill Mueller [ctb] ,
Jacob Scott [ctb],
cynkra GmbH [fnd]
Maintainer: Antoine Fabri <antoine.fabri@gmail.com>
This is a re-admission after prior archival of version 1.3.0 dated 2025-09-19
Diff between constructive versions 1.3.0 dated 2025-09-19 and 1.4.0 dated 2026-10-22
DESCRIPTION | 22 MD5 | 542 +++++++++++++------ NAMESPACE | 237 +++++++- NEWS.md | 71 ++ R/bypass.R | 39 + R/character-helpers.R | 43 + R/clock-helpers.R |only R/construct-helpers.R | 97 +++ R/construct_serialize.R |only R/constructive-package.R | 1 R/repair_attributes.R | 16 R/s3-IDate.R |only R/s3-ITime.R |only R/s3-POSIXct.R | 5 R/s3-POSIXlt.R | 14 R/s3-R6.R | 3 R/s3-R6ClassGenerator.R | 7 R/s3-Surv.R |only R/s3-array.R | 10 R/s3-bbox.R |only R/s3-blob.R | 4 R/s3-character.R | 16 R/s3-clock_duration.R |only R/s3-clock_iso_year_week_day.R |only R/s3-clock_naive_time.R |only R/s3-clock_sys_time.R |only R/s3-clock_weekday.R |only R/s3-clock_year_day.R |only R/s3-clock_year_month_day.R |only R/s3-clock_year_month_weekday.R |only R/s3-clock_year_quarter_day.R |only R/s3-clock_year_week_day.R |only R/s3-clock_zoned_time.R |only R/s3-col_spec.R |only R/s3-collector.R |only R/s3-constructive_options.R | 3 R/s3-crs.R |only R/s3-data.frame.R | 2 R/s3-data.table.R | 4 R/s3-date_names.R |only R/s3-dist.R |only R/s3-dm.R | 9 R/s3-ecdf.R |only R/s3-environment.R | 99 +++ R/s3-factor.R | 11 R/s3-formula.R | 4 R/s3-fs_bytes.R |only R/s3-fs_path.R |only R/s3-fs_perms.R |only R/s3-ftable.R |only R/s3-function.R | 2 R/s3-ggplot2-CoordCartesian.R | 10 R/s3-ggplot2-CoordFixed.R | 7 R/s3-ggplot2-CoordFlip.R | 6 R/s3-ggplot2-CoordMap.R | 7 R/s3-ggplot2-CoordMunch.R | 7 R/s3-ggplot2-CoordPolar.R | 7 R/s3-ggplot2-CoordQuickmap.R | 6 R/s3-ggplot2-CoordRadial.R | 15 R/s3-ggplot2-CoordSf.R | 18 R/s3-ggplot2-CoordTrans.R | 8 R/s3-ggplot2-CoordTransform.R | 8 R/s3-ggplot2-FacetGrid.R | 11 R/s3-ggplot2-FacetNull.R | 3 R/s3-ggplot2-FacetWrap.R | 11 R/s3-ggplot2-Guide.R | 5 R/s3-ggplot2-GuideNone.R | 3 R/s3-ggplot2-Guides.R | 2 R/s3-ggplot2-Layer.R | 18 R/s3-ggplot2-Scale.R | 3 R/s3-ggplot2-ScalesList.R | 4 R/s3-ggplot2-element_blank.R | 3 R/s3-ggplot2-ggplot.R | 17 R/s3-ggplot2-ggplot2-element_blank.R | 6 R/s3-ggplot2-ggplot2-element_geom.R | 6 R/s3-ggplot2-ggplot2-element_line.R | 6 R/s3-ggplot2-ggplot2-element_point.R | 6 R/s3-ggplot2-ggplot2-element_polygon.R | 6 R/s3-ggplot2-ggplot2-element_rect.R | 6 R/s3-ggplot2-ggplot2-element_text.R | 6 R/s3-ggplot2-ggplot2-ggplot.R | 4 R/s3-ggplot2-ggplot2-labels.R | 4 R/s3-ggplot2-ggplot2-mapping.R | 5 R/s3-ggplot2-ggplot2-margin.R | 7 R/s3-ggplot2-ggplot2-theme.R | 29 - R/s3-ggplot2-ggproto.R | 2 R/s3-ggplot2-labels.R | 3 R/s3-ggplot2-theme.R | 43 - R/s3-ggplot2-waiver.R | 3 R/s3-glue.R |only R/s3-grouped_df.R | 5 R/s3-grouped_ts.R |only R/s3-haven_labelled.R |only R/s3-haven_labelled_spss.R |only R/s3-hms.R |only R/s3-html.R |only R/s3-html_dependency.R |only R/s3-integer64.R | 8 R/s3-locale.R |only R/s3-matrix.R | 20 R/s3-mixed_units.R |only R/s3-mts.R | 7 R/s3-ordered.R | 15 R/s3-quosure.R | 5 R/s3-quosures.R | 3 R/s3-raster.R |only R/s3-roman.R |only R/s3-rowwise_df.R | 5 R/s3-sf.R |only R/s3-sfc.R |only R/s3-sfg.R |only R/s3-shiny.tag.R |only R/s3-shiny.tag.function.R |only R/s3-shiny.tag.list.R |only R/s3-stepfun.R |only R/s3-table.R |only R/s3-tbl_ts.R |only R/s3-ts.R | 6 R/s3-units.R |only R/s3-vctrs_list_of.R | 5 R/s3-vctrs_rcrd.R |only R/s3-vctrs_unspecified.R |only R/s3-vctrs_vctr.R |only R/s3-xml_document.R | 3 R/s3-xts.R | 46 - R/s3-yearmonth.R |only R/s3-yearquarter.R |only R/s3-yearweek.R |only R/s3-zooreg.R | 3 R/s4-Duration.R |only R/s4-Interval.R |only R/s4-Period.R |only R/s4-denseMatrix.R |only R/s4-diagonalMatrix.R |only R/s4-indMatrix.R |only R/s4-sparseMatrix.R |only R/s4-sparseVector.R |only R/s4.R | 21 R/s7-S7-object.R | 52 + R/s7-S7_any.R | 2 R/s7-S7_base_class.R | 2 R/s7-S7_class.R | 31 - R/s7-S7_class_ref.R |only R/s7-S7_generic.R | 4 R/s7-ellmer_TypeArray.R | 6 R/s7-elmer_TypeBasic.R | 6 R/s7-elmer_TypeEnum.R | 6 R/s7-elmer_TypeJsonSchema.R | 6 R/s7-elmer_TypeObject.R | 19 R/serialize_data.R |only R/serialize_header.R |only R/utils.R | 25 README.md | 18 build/vignette.rds |binary inst/doc/extend-constructive.html | 13 man/construct.Rd | 73 ++ man/construct_serialize.Rd |only man/constructive-package.Rd | 5 man/opts_Duration.Rd |only man/opts_IDate.Rd |only man/opts_ITime.Rd |only man/opts_Interval.Rd |only man/opts_Period.Rd |only man/opts_S7_class_ref.Rd |only man/opts_S7_object.Rd | 8 man/opts_Surv.Rd |only man/opts_bbox.Rd |only man/opts_character.Rd | 8 man/opts_clock_duration.Rd |only man/opts_clock_iso_year_week_day.Rd |only man/opts_clock_naive_time.Rd |only man/opts_clock_sys_time.Rd |only man/opts_clock_weekday.Rd |only man/opts_clock_year_day.Rd |only man/opts_clock_year_month_day.Rd |only man/opts_clock_year_month_weekday.Rd |only man/opts_clock_year_quarter_day.Rd |only man/opts_clock_year_week_day.Rd |only man/opts_clock_zoned_time.Rd |only man/opts_col_spec.Rd |only man/opts_collector.Rd |only man/opts_crs.Rd |only man/opts_date_names.Rd |only man/opts_denseMatrix.Rd |only man/opts_diagonalMatrix.Rd |only man/opts_dist.Rd |only man/opts_dm.Rd | 3 man/opts_ecdf.Rd |only man/opts_environment.Rd | 32 + man/opts_fs_bytes.Rd |only man/opts_fs_path.Rd |only man/opts_fs_perms.Rd |only man/opts_ftable.Rd |only man/opts_glue.Rd |only man/opts_grouped_ts.Rd |only man/opts_haven_labelled.Rd |only man/opts_haven_labelled_spss.Rd |only man/opts_hms.Rd |only man/opts_html.Rd |only man/opts_html_dependency.Rd |only man/opts_indMatrix.Rd |only man/opts_locale.Rd |only man/opts_matrix.Rd | 9 man/opts_mixed_units.Rd |only man/opts_raster.Rd |only man/opts_roman.Rd |only man/opts_sf.Rd |only man/opts_sfc.Rd |only man/opts_sfg.Rd |only man/opts_shiny.tag.Rd |only man/opts_shiny.tag.function.Rd |only man/opts_shiny.tag.list.Rd |only man/opts_sparseMatrix.Rd |only man/opts_sparseVector.Rd |only man/opts_stepfun.Rd |only man/opts_table.Rd |only man/opts_tbl_ts.Rd |only man/opts_units.Rd |only man/opts_vctrs_rcrd.Rd |only man/opts_vctrs_unspecified.Rd |only man/opts_vctrs_vctr.Rd |only man/opts_xts.Rd | 12 man/opts_yearmonth.Rd |only man/opts_yearquarter.Rd |only man/opts_yearweek.Rd |only man/other-opts.Rd | 35 - tests/testthat/_snaps/s3-IDate.md |only tests/testthat/_snaps/s3-ITime.md |only tests/testthat/_snaps/s3-POSIXct.md | 107 +++ tests/testthat/_snaps/s3-POSIXlt.md | 35 + tests/testthat/_snaps/s3-R6.md | 24 tests/testthat/_snaps/s3-R6ClassGenerator.md | 86 ++- tests/testthat/_snaps/s3-Surv.md |only tests/testthat/_snaps/s3-array.md | 4 tests/testthat/_snaps/s3-atomic.md | 56 + tests/testthat/_snaps/s3-bbox.md |only tests/testthat/_snaps/s3-citationHeader.md | 2 tests/testthat/_snaps/s3-clock_duration.md |only tests/testthat/_snaps/s3-clock_iso_year_week_day.md |only tests/testthat/_snaps/s3-clock_naive_time.md |only tests/testthat/_snaps/s3-clock_sys_time.md |only tests/testthat/_snaps/s3-clock_weekday.md |only tests/testthat/_snaps/s3-clock_year_day.md |only tests/testthat/_snaps/s3-clock_year_month_day.md |only tests/testthat/_snaps/s3-clock_year_month_weekday.md |only tests/testthat/_snaps/s3-clock_year_quarter_day.md |only tests/testthat/_snaps/s3-clock_year_week_day.md |only tests/testthat/_snaps/s3-clock_zoned_time.md |only tests/testthat/_snaps/s3-col_spec.md |only tests/testthat/_snaps/s3-collector.md |only tests/testthat/_snaps/s3-crs.md |only tests/testthat/_snaps/s3-date_names.md |only tests/testthat/_snaps/s3-dist.md |only tests/testthat/_snaps/s3-dm.md | 49 + tests/testthat/_snaps/s3-ecdf.md |only tests/testthat/_snaps/s3-environment.md | 39 + tests/testthat/_snaps/s3-fs_bytes.md |only tests/testthat/_snaps/s3-fs_path.md |only tests/testthat/_snaps/s3-fs_perms.md |only tests/testthat/_snaps/s3-ftable.md |only tests/testthat/_snaps/s3-glue.md |only tests/testthat/_snaps/s3-grouped_ts.md |only tests/testthat/_snaps/s3-haven_labelled.md |only tests/testthat/_snaps/s3-haven_labelled_spss.md |only tests/testthat/_snaps/s3-hms.md |only tests/testthat/_snaps/s3-html.md |only tests/testthat/_snaps/s3-html_dependency.md |only tests/testthat/_snaps/s3-integer64.md | 12 tests/testthat/_snaps/s3-locale.md |only tests/testthat/_snaps/s3-matrix.md | 26 tests/testthat/_snaps/s3-mixed_units.md |only tests/testthat/_snaps/s3-quosure.md | 16 tests/testthat/_snaps/s3-raster.md |only tests/testthat/_snaps/s3-roman.md |only tests/testthat/_snaps/s3-sf.md |only tests/testthat/_snaps/s3-sfc.md |only tests/testthat/_snaps/s3-sfg.md |only tests/testthat/_snaps/s3-shiny.tag.function.md |only tests/testthat/_snaps/s3-shiny.tag.list.md |only tests/testthat/_snaps/s3-shiny.tag.md |only tests/testthat/_snaps/s3-stepfun.md |only tests/testthat/_snaps/s3-table.md |only tests/testthat/_snaps/s3-tbl_df.md | 13 tests/testthat/_snaps/s3-tbl_ts.md |only tests/testthat/_snaps/s3-units.md |only tests/testthat/_snaps/s3-vctrs_rcrd.md |only tests/testthat/_snaps/s3-vctrs_unspecified.md |only tests/testthat/_snaps/s3-vctrs_vctr.md |only tests/testthat/_snaps/s3-xts.md | 25 tests/testthat/_snaps/s3-yearmonth.md |only tests/testthat/_snaps/s3-yearquarter.md |only tests/testthat/_snaps/s3-yearweek.md |only tests/testthat/_snaps/s4-Duration.md |only tests/testthat/_snaps/s4-Interval.md |only tests/testthat/_snaps/s4-Period.md |only tests/testthat/_snaps/s4-denseMatrix.md |only tests/testthat/_snaps/s4-diagonalMatrix.md |only tests/testthat/_snaps/s4-indMatrix.md |only tests/testthat/_snaps/s4-sparseMatrix.md |only tests/testthat/_snaps/s4-sparseVector.md |only tests/testthat/_snaps/s7-S7-object.md | 24 tests/testthat/_snaps/s7-S7_class.md | 32 + tests/testthat/_snaps/s7-S7_class_ref.md |only tests/testthat/_snaps/s7-S7_generic.md | 51 + tests/testthat/_snaps/s7-S7_union.md | 95 +++ tests/testthat/helper-timezone.R |only tests/testthat/helper-valgrind.R |only tests/testthat/setup.R | 18 tests/testthat/test-construct_serialize.R |only tests/testthat/test-others.R | 18 tests/testthat/test-s3-IDate.R |only tests/testthat/test-s3-ITime.R |only tests/testthat/test-s3-POSIXct.R | 35 - tests/testthat/test-s3-POSIXlt.R | 16 tests/testthat/test-s3-R6.R | 10 tests/testthat/test-s3-R6ClassGenerator.R | 57 + tests/testthat/test-s3-Surv.R |only tests/testthat/test-s3-array.R | 1 tests/testthat/test-s3-atomic.R | 22 tests/testthat/test-s3-bbox.R |only tests/testthat/test-s3-citationHeader.R | 2 tests/testthat/test-s3-clock_duration.R |only tests/testthat/test-s3-clock_iso_year_week_day.R |only tests/testthat/test-s3-clock_naive_time.R |only tests/testthat/test-s3-clock_sys_time.R |only tests/testthat/test-s3-clock_weekday.R |only tests/testthat/test-s3-clock_year_day.R |only tests/testthat/test-s3-clock_year_month_day.R |only tests/testthat/test-s3-clock_year_month_weekday.R |only tests/testthat/test-s3-clock_year_quarter_day.R |only tests/testthat/test-s3-clock_year_week_day.R |only tests/testthat/test-s3-clock_zoned_time.R |only tests/testthat/test-s3-col_spec.R |only tests/testthat/test-s3-collector.R |only tests/testthat/test-s3-crs.R |only tests/testthat/test-s3-date_names.R |only tests/testthat/test-s3-dist.R |only tests/testthat/test-s3-dm.R | 102 +++ tests/testthat/test-s3-ecdf.R |only tests/testthat/test-s3-environment.R | 47 + tests/testthat/test-s3-fs_bytes.R |only tests/testthat/test-s3-fs_path.R |only tests/testthat/test-s3-fs_perms.R |only tests/testthat/test-s3-ftable.R |only tests/testthat/test-s3-ggplot2-Coord.R | 2 tests/testthat/test-s3-ggplot2-FacetGrid.R | 2 tests/testthat/test-s3-ggplot2-GuideBins.R | 1 tests/testthat/test-s3-ggplot2-GuideLegend.R | 1 tests/testthat/test-s3-ggplot2-Scale.R | 1 tests/testthat/test-s3-ggplot2-ggplot.R | 17 tests/testthat/test-s3-ggplot2-theme.R | 17 tests/testthat/test-s3-glue.R |only tests/testthat/test-s3-grouped_ts.R |only tests/testthat/test-s3-haven_labelled.R |only tests/testthat/test-s3-haven_labelled_spss.R |only tests/testthat/test-s3-hms.R |only tests/testthat/test-s3-html.R |only tests/testthat/test-s3-html_dependency.R |only tests/testthat/test-s3-integer64.R | 5 tests/testthat/test-s3-locale.R |only tests/testthat/test-s3-matrix.R | 9 tests/testthat/test-s3-mixed_units.R |only tests/testthat/test-s3-quosure.R | 15 tests/testthat/test-s3-raster.R |only tests/testthat/test-s3-roman.R |only tests/testthat/test-s3-sf.R |only tests/testthat/test-s3-sfc.R |only tests/testthat/test-s3-sfg.R |only tests/testthat/test-s3-shiny.tag.R |only tests/testthat/test-s3-shiny.tag.function.R |only tests/testthat/test-s3-shiny.tag.list.R |only tests/testthat/test-s3-stepfun.R |only tests/testthat/test-s3-table.R |only tests/testthat/test-s3-tbl_df.R | 18 tests/testthat/test-s3-tbl_ts.R |only tests/testthat/test-s3-units.R |only tests/testthat/test-s3-vctrs_rcrd.R |only tests/testthat/test-s3-vctrs_unspecified.R |only tests/testthat/test-s3-vctrs_vctr.R |only tests/testthat/test-s3-xml_document.R | 1 tests/testthat/test-s3-xts.R | 3 tests/testthat/test-s3-yearmonth.R |only tests/testthat/test-s3-yearquarter.R |only tests/testthat/test-s3-yearweek.R |only tests/testthat/test-s4-Duration.R |only tests/testthat/test-s4-Interval.R |only tests/testthat/test-s4-Period.R |only tests/testthat/test-s4-denseMatrix.R |only tests/testthat/test-s4-diagonalMatrix.R |only tests/testthat/test-s4-indMatrix.R |only tests/testthat/test-s4-sparseMatrix.R |only tests/testthat/test-s4-sparseVector.R |only tests/testthat/test-s7-S7-object.R | 24 tests/testthat/test-s7-S7_class.R | 45 + tests/testthat/test-s7-S7_class_ref.R |only tests/testthat/test-s7-S7_generic.R | 20 tests/testthat/test-s7-S7_union.R | 16 tests/testthat/test-s7-elmer_TypeBasic.R | 6 398 files changed, 2857 insertions(+), 479 deletions(-)
Title: Longitudinal EHR Analysis with Informative Visits and Recording
Description: Longitudinal outcomes in electronic health records (EHR) are seen
only when a patient visits and the outcome is recorded at that visit, and
both processes can depend on the patient's latent health. The package fits
the CIMEHR estimator for this setting, a three-stage procedure linked by a
shared latent factor: a frailty partial likelihood for the visiting process,
a pairwise likelihood for the recording (observation) process, and an
estimating equation for the outcome. Spline and higher-order Laplace
variants are included, together with comparison methods (summary
statistics, linear mixed models, Lin-Ying, Liang, pairwise likelihood,
joint models, inverse intensity rate ratio weighting and balancing,
multiple imputation, linear increments and EHRJoint) behind one common
interface. Methods are described in Yang, Shi, and Mukherjee (2026)
<doi:10.48550/arXiv.2602.15374>.
Author: Cheng-Han Yang [aut, cre] ,
Yiren Hou [aut]
Maintainer: Cheng-Han Yang <chenghanyang728@gmail.com>
Diff between CIMEHR versions 0.1.0 dated 2026-06-08 and 0.2.0 dated 2026-10-22
CIMEHR-0.1.0/CIMEHR/R/CIMEHR.R |only CIMEHR-0.1.0/CIMEHR/R/CIMEHR_timevarying_integral.R |only CIMEHR-0.1.0/CIMEHR/R/CIMEHR_timevarying_ou.R |only CIMEHR-0.1.0/CIMEHR/R/EHRJoint.R |only CIMEHR-0.1.0/CIMEHR/R/Inverse_intensity_rate_ratio_balancing.R |only CIMEHR-0.1.0/CIMEHR/R/Inverse_intensity_rate_ratio_weighting.R |only CIMEHR-0.1.0/CIMEHR/R/Joint_modeling_visiting_and_longitudinal_Liang.R |only CIMEHR-0.1.0/CIMEHR/R/Linear_increment_IP.R |only CIMEHR-0.1.0/CIMEHR/R/Linear_mixed_model.R |only CIMEHR-0.1.0/CIMEHR/R/Multiple_imputation_IP.R |only CIMEHR-0.1.0/CIMEHR/R/Pairwise_likelihood.R |only CIMEHR-0.1.0/CIMEHR/R/Summary_stat.R |only CIMEHR-0.1.0/CIMEHR/R/bootstrap.R |only CIMEHR-0.1.0/CIMEHR/R/data-generation.R |only CIMEHR-0.1.0/CIMEHR/R/data.R |only CIMEHR-0.1.0/CIMEHR/R/forRcpp.R |only CIMEHR-0.1.0/CIMEHR/R/main-comparison-function.R |only CIMEHR-0.1.0/CIMEHR/R/print-summary-CIMEHR.R |only CIMEHR-0.1.0/CIMEHR/R/print-summary-other-methods.R |only CIMEHR-0.1.0/CIMEHR/R/stage-summary-extract.R |only CIMEHR-0.1.0/CIMEHR/R/utils.R |only CIMEHR-0.1.0/CIMEHR/data/sim_ehr_data.rda |only CIMEHR-0.1.0/CIMEHR/inst/doc/getting-started.R |only CIMEHR-0.1.0/CIMEHR/inst/doc/getting-started.Rmd |only CIMEHR-0.1.0/CIMEHR/inst/doc/getting-started.html |only CIMEHR-0.1.0/CIMEHR/man/CIMEHR_timevarying_integral.Rd |only CIMEHR-0.1.0/CIMEHR/man/CIMEHR_timevarying_ou.Rd |only CIMEHR-0.1.0/CIMEHR/man/EHRJoint.Rd |only CIMEHR-0.1.0/CIMEHR/man/Inverse_intensity_rate_ratio_balancing.Rd |only CIMEHR-0.1.0/CIMEHR/man/Inverse_intensity_rate_ratio_weighting.Rd |only CIMEHR-0.1.0/CIMEHR/man/Joint_modeling_visiting_and_longitudinal_Liang.Rd |only CIMEHR-0.1.0/CIMEHR/man/Linear_increment_IP.Rd |only CIMEHR-0.1.0/CIMEHR/man/Linear_mixed_model.Rd |only CIMEHR-0.1.0/CIMEHR/man/Multiple_imputation_IP.Rd |only CIMEHR-0.1.0/CIMEHR/man/Pairwise_likelihood.Rd |only CIMEHR-0.1.0/CIMEHR/man/Summary_stat.Rd |only CIMEHR-0.1.0/CIMEHR/man/available_comparison_methods.Rd |only CIMEHR-0.1.0/CIMEHR/man/bootstrap.Rd |only CIMEHR-0.1.0/CIMEHR/man/coef.CIMEHR.Rd |only CIMEHR-0.1.0/CIMEHR/man/confint.CIMEHR.Rd |only CIMEHR-0.1.0/CIMEHR/man/extract_coefficient.Rd |only CIMEHR-0.1.0/CIMEHR/man/method_comparisons.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.CIMEHR.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.CIMEHR_timevarying_integral.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.CIMEHR_timevarying_ou.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.EHRJoint.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.Inverse_intensity_rate_ratio_balancing.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.Inverse_intensity_rate_ratio_weighting.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.Joint_modeling_visiting_and_longitudinal_Liang.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.Linear_increment_IP_result.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.Linear_mixed_model_result.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.Multiple_imputation_IP_result.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.Pairwise_likelihood.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.Summary_stat_result.Rd |only CIMEHR-0.1.0/CIMEHR/man/print.cimehr_bootstrap.Rd |only CIMEHR-0.1.0/CIMEHR/man/sim_data_gen.Rd |only CIMEHR-0.1.0/CIMEHR/man/sim_ehr_data.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.CIMEHR.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.CIMEHR_timevarying_integral.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.CIMEHR_timevarying_ou.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.EHRJoint.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.Inverse_intensity_rate_ratio_balancing.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.Inverse_intensity_rate_ratio_weighting.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.Joint_modeling_visiting_and_longitudinal_Liang.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.Linear_increment_IP_result.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.Linear_mixed_model_result.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.Multiple_imputation_IP_result.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.Pairwise_likelihood.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.Summary_stat_result.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary.cimehr_bootstrap.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary_observation.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary_outcome.Rd |only CIMEHR-0.1.0/CIMEHR/man/summary_visiting.Rd |only CIMEHR-0.1.0/CIMEHR/man/vcov.CIMEHR.Rd |only CIMEHR-0.1.0/CIMEHR/src/pairwise_glm_fit.cpp |only CIMEHR-0.1.0/CIMEHR/vignettes/getting-started.Rmd |only CIMEHR-0.2.0/CIMEHR/DESCRIPTION | 73 CIMEHR-0.2.0/CIMEHR/MD5 | 196 +- CIMEHR-0.2.0/CIMEHR/NAMESPACE | 146 - 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Title: Beta Regression for Interval-Censored Scale-Derived Outcomes
Description: Maximum-likelihood estimation of beta regression models for
responses derived from bounded rating scales. Observations are treated
as interval-censored on (0, 1) after a scale-to-unit transformation,
and the likelihood is built from the difference of the beta CDF at the
interval endpoints. The complete likelihood supports mixed censoring
types: uncensored, left-censored, right-censored, and
interval-censored observations. Both fixed- and
variable-dispersion submodels are supported, with flexible link
functions for the mean and precision components. A compiled C++ backend
(via 'Rcpp' and 'RcppArmadillo') provides numerically stable,
high-performance log-likelihood evaluation. Standard S3 methods
(print(), summary(), coef(), fitted(), residuals(), predict(),
plot(), confint(), vcov(), logLik(), AIC(), BIC(), simulate()) are
available for fitted objects.
Author: Jose Evandeilton Lopes [aut, cre] ,
Wagner Hugo Bonat [aut]
Maintainer: Jose Evandeilton Lopes <evandeilton@gmail.com>
Diff between betaregscale versions 2.7.4 dated 2026-08-23 and 3.1.1 dated 2026-10-22
betaregscale-2.7.4/betaregscale/src/loglik_mixed_eigen.cpp |only betaregscale-2.7.4/betaregscale/tests/testthat/test-backlog-tools.R |only betaregscale-2.7.4/betaregscale/tests/testthat/test-re-and-autoplot-improvements.R |only betaregscale-2.7.4/betaregscale/tests/testthat/test-regression-fixes.R |only betaregscale-3.1.1/betaregscale/DESCRIPTION | 16 betaregscale-3.1.1/betaregscale/MD5 | 239 betaregscale-3.1.1/betaregscale/NAMESPACE | 131 betaregscale-3.1.1/betaregscale/NEWS.md | 398 + betaregscale-3.1.1/betaregscale/R/RcppExports.R | 125 betaregscale-3.1.1/betaregscale/R/anova-methods.R | 238 betaregscale-3.1.1/betaregscale/R/autoplot-brsmm.R | 8 betaregscale-3.1.1/betaregscale/R/autoplot.R | 56 betaregscale-3.1.1/betaregscale/R/betaregscale-package.R | 133 betaregscale-3.1.1/betaregscale/R/bootstrap.R | 398 + betaregscale-3.1.1/betaregscale/R/brsmm-methods.R | 460 + betaregscale-3.1.1/betaregscale/R/brsmm-random-effects-study.R | 105 betaregscale-3.1.1/betaregscale/R/brsmm.R | 466 + betaregscale-3.1.1/betaregscale/R/censoring-summary.R | 13 betaregscale-3.1.1/betaregscale/R/check-response.R | 635 +- betaregscale-3.1.1/betaregscale/R/cutpoints.R |only betaregscale-3.1.1/betaregscale/R/cv.R | 344 + betaregscale-3.1.1/betaregscale/R/diagnostics.R |only betaregscale-3.1.1/betaregscale/R/fit.R | 820 ++- betaregscale-3.1.1/betaregscale/R/links.R | 327 + betaregscale-3.1.1/betaregscale/R/loglik-contrib.R |only betaregscale-3.1.1/betaregscale/R/loglik.R | 151 betaregscale-3.1.1/betaregscale/R/marginal.R |only betaregscale-3.1.1/betaregscale/R/marginaleffects.R | 91 betaregscale-3.1.1/betaregscale/R/methods.R | 605 +- betaregscale-3.1.1/betaregscale/R/plot-brsmm.R | 59 betaregscale-3.1.1/betaregscale/R/prepare.R | 679 +- betaregscale-3.1.1/betaregscale/R/residuals-score.R |only betaregscale-3.1.1/betaregscale/R/scoreprob.R | 43 betaregscale-3.1.1/betaregscale/R/simulate-brsmm.R |only betaregscale-3.1.1/betaregscale/R/simulate.R | 436 - 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Title: Survival Model-Based Imputation for Laboratory Non-Detect Data
Description: Implements survival-model-based imputation for censored
laboratory measurements, including Tobit-type models with several
distribution options. Suitable for data with values below detection
or quantification limits, the package identifies the best-fitting
distribution and produces realistic imputations that respect the
censoring thresholds.
Author: Luis Pereira [aut, cre] ,
Paulo Infante [aut] ,
Teresa Ferreira [ths] ,
Paulo Quaresma [ths]
Maintainer: Luis Pereira <d57177@alunos.uevora.pt>
Diff between survlab versions 0.1.0 dated 2025-12-11 and 0.2.0 dated 2026-10-22
DESCRIPTION | 8 +- MD5 | 21 ++--- NAMESPACE | 34 ++++---- NEWS.md | 19 ++++ R/impute_nondetect.R | 155 +++++++++++++++++++++++++++++++-------- README.md | 11 ++ build/vignette.rds |binary inst/CITATION | 9 +- inst/doc/package_vignette.html | 12 +-- man/impute_nondetect.Rd | 37 +++++++++ tests/testthat/test-imputation.r | 66 ++++++++++++++++ vignettes/authors.md |only 12 files changed, 300 insertions(+), 72 deletions(-)
Title: Nonparametric Quantile Density Estimation and Structural
Analysis of First-Price Auctions
Description: Nonparametric estimators of the quantile density function
(the derivative of the quantile function): kernel, boundary-corrected
kernel, Poisson-weight and Bernstein-polynomial smoothers, indirect
estimators (Jones (1992)
<https://www.ism.ac.jp/editsec/aism/pdf/044_4_0721.pdf>; Soni, Dewan and
Jain (2012) <doi:10.1016/j.csda.2012.04.014>; Chaubey, Dewan and Li (2024)
<doi:10.1080/03610926.2023.2222922>), and linear, hard-thresholded and
block-thresholded wavelet estimators (Chesneau, Dewan and Doosti (2016)
<doi:10.1016/j.csda.2015.08.006>; Shirazi and Doosti (2022)
<doi:10.1080/03610918.2019.1656250>), with smoothing parameters chosen by
biased, robust likelihood (Wu (2019) <doi:10.1080/07350015.2018.1424633>)
or least-squares cross-validation. The estimators are applied to the
structural analysis of first-price sealed-bid auctions: recovery of
private values for independent or affiliated values and risk-neutral or
risk-averse bidders (Doosti, Dewan [...truncated...]
Author: Hassan Doosti [aut, cre, cph] ,
Yogendra P. Chaubey [ctb, cph] ,
Isha Dewan [ctb, cph] ,
Jun Li [ctb, cph] ,
Brent R. Hickman [ctb, cph] ),
Timothy P. Hubbard [ctb, cph] ),
Brani Vidakovic [ctb, cph] , phi_jk,
dwt_periodic, idwt_periodic and loclin_s [...truncated...]
Maintainer: Hassan Doosti <Hassan.doosti@mq.edu.au>
Diff between qdfauction versions 0.1.0 dated 2026-10-20 and 0.2.0 dated 2026-10-22
DESCRIPTION | 10 - MD5 | 79 +++++---- NAMESPACE | 5 NEWS.md | 115 ++++++++++++++ R/bandwidth.R | 125 +++++++++++++-- R/copula.R | 27 ++- R/data.R | 52 ++++-- R/estimators.R | 56 ++++++- R/evaluate.R | 8 - R/fpa_density.R | 3 R/fpa_density_ci.R | 7 R/fpa_revenue.R | 302 +++++++++++++++++++++++++++++++++++--- R/fpa_values.R | 7 R/qdf.R | 46 ++++- R/wavelet.R | 2 R/wavelet_nl.R | 7 inst/benchmarks/scaling.R | 25 +++ inst/doc/timber.R | 3 inst/doc/timber.Rmd | 17 +- inst/doc/timber.html | 62 +++++-- man/bcv_criterion.Rd | 21 ++ man/fpa_corner_test.Rd |only man/fpa_density.Rd | 3 man/fpa_density_ci.Rd | 7 man/fpa_montecarlo.Rd | 7 man/fpa_revenue.Rd | 6 man/fpa_revenue_boot.Rd | 27 ++- man/fpa_revenue_model.Rd | 2 man/fpa_revenue_qd.Rd | 3 man/fpa_values.Rd | 4 man/fpa_virtual_value_model.Rd |only man/qdf.Rd | 24 +-- man/qdf_poisson.Rd | 28 +++ man/qdf_wavelet_nl.Rd | 7 man/select_bandwidth.Rd | 44 ++++- man/select_wavelet.Rd | 2 man/timber.Rd | 52 ++++-- tests/testthat/test-fpa-revenue.R | 4 tests/testthat/test-fpa-values.R | 17 +- tests/testthat/test-merge-020.R |only tests/testthat/test-qdf.R | 12 + vignettes/timber.Rmd | 17 +- 42 files changed, 1019 insertions(+), 226 deletions(-)
Title: Topographic Position Index-Based Landform Classification
Description: Classifies a landscape into slope-position and landform classes on the
basis of the Topographic Position Index (TPI) and slope, following
Weiss (2001) and Jenness (2006). Two classifications are offered: a
six-class Slope Position Classification, based on one TPI scale, and a
ten-class Landform Classification, based on a small and a large TPI
scale. The TPI can be computed over square, circular or annular
neighbourhoods, sized in cells or in map units, and standardised
either over the whole grid (as in the original method) or locally.
Results are returned as an object holding the classified raster, the
TPI and slope surfaces, and per-class descriptive statistics, with
methods for printing, summarising and plotting.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between landform versions 0.2 dated 2023-10-04 and 0.3.0 dated 2026-10-22
DESCRIPTION | 31 + MD5 | 31 + NAMESPACE | 13 NEWS.md | 90 ++++- R/data.R |only R/landform-package.R |only R/landform.R | 859 ++++++++++++++++++++++++++++++------------------ R/tpi.R |only README.md | 46 ++ build |only inst |only man/class_layers.Rd |only man/landform-package.Rd |only man/landform.Rd | 278 ++++++++++----- man/malta_dtm.Rd |only man/plot.landform.Rd |only man/tpi.Rd |only tests |only vignettes |only 19 files changed, 909 insertions(+), 439 deletions(-)
Title: Process and Report Gazepoint Biometrics Data
Description: Gazepoint-native tools for reproducible analysis and reporting of Gazepoint
Biometrics and GP3-derived physiological, gaze, pupil, fixation, AOI,
marker, and event-level exports. The package supports import, validation,
preprocessing, missing-value imputation, EDA/GSR, SCR epoching, IBI/RR/HRV,
PPG/pulse workflows, pupil blink detection and cleaning, gaze filtering,
fixation summaries, engagement-dial indices, multimodal trial regressors,
quality reports, exclusion and QC recommendations, synthetic eye-data
generation, and interoperability or workflow-inspired helpers for common
psychophysiology toolchains. The package is designed for transparent,
CRAN-safe, scriptable analysis rather than as a full clone of external
commercial or open-source toolboxes.
Author: Stefanos Balaskas [aut, cre]
Maintainer: Stefanos Balaskas <s.balaskas@ac.upatras.gr>
Diff between gpbiometrics versions 0.1.0 dated 2026-07-04 and 2.1.1 dated 2026-10-22
DESCRIPTION | 34 MD5 | 502 + NAMESPACE | 289 NEWS.md | 154 R/alignment-aoi-eventlocked-dashboard.R |only R/analysis-decision-log.R |only R/aoi-assignment.R |only R/audit-trail-summary.R |only R/beat-correction-audit.R |only R/bids-export.R |only R/bids-layout-audit.R |only R/biometrics-report.R | 1642 ++-- R/biosppy-input.R |only R/biosppy-style.R |only R/cluster-permutation-advanced-guardrails.R |only R/cluster-permutation-diagnostics.R |only R/cluster-permutation.R |only R/condition-bootstrap.R |only R/data-io-cleaning.R |only R/dataset-structure-audit.R |only R/design-event-audit.R |only R/downsample.R |only R/event-physiology-indices.R |only R/export-folder-profile.R |only R/eyetrackingr-input.R |only R/frontdoor-audit-missingness.R |only R/gaze-event-detection.R |only R/gazer-input.R |only R/heartpy-bridge.R |only R/heartpy-extended.R |only R/interoperability-version-testing.R |only R/measurement-accountability-2026-09.R |only R/mne-eeg-lsl-interoperability.R |only R/physiology-qc-refinements.R |only R/pipeline-comparison-dashboard.R |only R/pipeline-visualization.R |only R/preregistration-readiness.R |only R/pspm-style.R |only R/pupil-gaze-cleaning.R |only R/pupil-qc-reporting.R |only R/pupillometryr-input.R |only R/pyhrv-input.R |only R/pyhrv-style.R |only R/real-data-smoke-harness.R |only R/release-readiness-audit.R |only R/reproducibility-simulation.R |only R/reviewer-report-templates.R |only R/roadmap-compatibility-aliases.R |only R/roadmap-exact-backlog-helpers.R |only R/roadmap-final-gaps.R |only R/roadmap-remaining-helpers.R |only R/session-quality-audit.R |only R/signal-dropout-preprocessing.R |only R/signal-quality-reporting.R |only R/simulate-gazepoint-eye-data.R |only R/ttl-alignment.R | 1372 +-- R/workflow-reporting-pipeline.R |only README.md | 461 - build/vignette.rds |binary inst/CITATION | 42 inst/doc/dabest-estimation-gallery.R |only inst/doc/dabest-estimation-gallery.Rmd |only inst/doc/dabest-estimation-gallery.html |only 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inst/extdata/gazepoint_biometrics_kiosk_demo_exports/synthetic_kiosk_p031_all_gaze.csv | 3842 +++++----- inst/extdata/gazepoint_biometrics_kiosk_demo_exports/synthetic_kiosk_p032_all_gaze.csv | 3842 +++++----- inst/extdata/gazepoint_biometrics_kiosk_demo_exports/synthetic_kiosk_p033_all_gaze.csv | 3842 +++++----- inst/extdata/gazepoint_biometrics_kiosk_demo_exports/synthetic_kiosk_p034_all_gaze.csv | 3842 +++++----- inst/extdata/gazepoint_biometrics_kiosk_demo_exports/synthetic_kiosk_p035_all_gaze.csv | 3842 +++++----- inst/extdata/gazepoint_biometrics_kiosk_demo_exports/synthetic_kiosk_p036_all_gaze.csv | 3842 +++++----- inst/extdata/gazepoint_biometrics_kiosk_demo_exports/synthetic_kiosk_trial_design.csv | 290 inst/scripts |only man/add_gazepoint_decision.Rd |only man/align_gazepoint_streams_by_events.Rd |only man/align_gazepoint_to_eeg.Rd |only man/anonymize_gazepoint_data.Rd |only man/assert_gazepoint_columns.Rd |only man/assess_gazepoint_sampling_irregularity.Rd |only man/assign_gazepoint_aoi.Rd |only man/audit_gazepoint_beats.Rd |only man/audit_gazepoint_biometrics_file.Rd |only man/audit_gazepoint_condition_balance.Rd |only man/audit_gazepoint_dataset_structure.Rd |only man/audit_gazepoint_event_coverage.Rd |only man/audit_gazepoint_experiment_design.Rd |only man/audit_gazepoint_export_schema.Rd |only man/audit_gazepoint_interoperability_versions.Rd |only man/audit_gazepoint_pipeline_steps.Rd |only man/audit_gazepoint_preregistration_consistency.Rd |only man/audit_gazepoint_pupil_luminance.Rd |only man/audit_gazepoint_release_readiness.Rd |only man/audit_gazepoint_session_comparability.Rd |only man/audit_gazepoint_smoke_privacy.Rd |only man/audit_gazepoint_timecourse_grid.Rd |only man/build_gazepoint_aoi_timecourse.Rd |only man/check_gazepoint_bids.Rd |only man/check_gazepoint_ppg_binary_quality.Rd |only man/check_gazepoint_pyhrv_interval.Rd |only man/classify_gazepoint_signal_quality.Rd |only man/clean_gazepoint_pupil.Rd |only man/clean_gazepoint_pupil_signal.Rd |only man/clean_gazepoint_rr_intervals.Rd |only man/combine_gazepoint_marker_channels_pspm_style.Rd |only man/compare_gazepoint_conditions_bootstrap.Rd |only man/compare_gazepoint_export_profiles.Rd |only man/compare_gazepoint_pyhrv_psd_methods.Rd |only man/compare_hrv_prv_devices.Rd |only man/compute_gazepoint_engagement_index.Rd |only man/compute_gazepoint_hrv_wavelet_psd.Rd |only man/compute_gazepoint_ppg_frequency_measures.Rd |only man/compute_gazepoint_ppg_measures.Rd |only man/compute_gazepoint_ppg_template_similarity.Rd |only man/compute_gazepoint_pyhrv_ar_psd.Rd |only man/compute_gazepoint_pyhrv_dfa.Rd |only man/compute_gazepoint_pyhrv_frequency_domain.Rd |only man/compute_gazepoint_pyhrv_heart_rate.Rd |only man/compute_gazepoint_pyhrv_hr_parameters.Rd |only man/compute_gazepoint_pyhrv_lomb_psd.Rd |only man/compute_gazepoint_pyhrv_nn20.Rd |only man/compute_gazepoint_pyhrv_nn50.Rd |only man/compute_gazepoint_pyhrv_nn_diff.Rd |only man/compute_gazepoint_pyhrv_nni_differences_parameters.Rd |only man/compute_gazepoint_pyhrv_nni_parameters.Rd |only man/compute_gazepoint_pyhrv_nnxx.Rd |only man/compute_gazepoint_pyhrv_nonlinear.Rd |only man/compute_gazepoint_pyhrv_poincare.Rd |only man/compute_gazepoint_pyhrv_psd_waterfall.Rd |only man/compute_gazepoint_pyhrv_rmssd.Rd |only man/compute_gazepoint_pyhrv_sample_entropy.Rd |only man/compute_gazepoint_pyhrv_sdann.Rd |only man/compute_gazepoint_pyhrv_sdnn.Rd |only man/compute_gazepoint_pyhrv_sdnn_index.Rd |only man/compute_gazepoint_pyhrv_sdsd.Rd |only man/compute_gazepoint_pyhrv_time_domain.Rd |only man/compute_gazepoint_pyhrv_tinn.Rd |only man/compute_gazepoint_pyhrv_triangular_index.Rd |only man/compute_gazepoint_pyhrv_welch_psd.Rd |only man/compute_gazepoint_quality_index.Rd |only man/compute_gazepoint_scr_habituation.Rd |only man/compute_gazepoint_scr_latency.Rd |only man/compute_gazepoint_signal_band_power.Rd |only man/compute_gazepoint_signal_correlation.Rd |only man/compute_gazepoint_signal_lag_matrix.Rd |only man/compute_gazepoint_signal_phase_locking.Rd |only man/compute_gazepoint_signal_power_spectrum.Rd |only man/compute_gazepoint_signal_quality.Rd |only man/correct_gazepoint_beats.Rd |only man/correct_gazepoint_ppg_hampel.Rd |only man/correct_gazepoint_rri_artifacts_local.Rd |only man/create_gazepoint_analysis_decision_log.Rd |only man/create_gazepoint_analysis_manifest.Rd |only man/create_gazepoint_audit_index.Rd |only man/create_gazepoint_audit_report_section.Rd |only man/create_gazepoint_dictionary.Rd |only man/create_gazepoint_eye_methods_text.Rd |only man/create_gazepoint_heartpy_report.Rd |only man/create_gazepoint_methods_section.Rd |only man/create_gazepoint_pipeline_map.Rd |only man/create_gazepoint_preregistration_checklist.Rd |only man/create_gazepoint_pspm_glm_design.Rd |only man/create_gazepoint_pyhrv_time_vector.Rd |only man/create_gazepoint_qc_supplement.Rd |only man/create_gazepoint_quality_dashboard.Rd |only man/create_gazepoint_release_checklist.Rd |only man/create_gazepoint_reproducibility_statement.Rd |only man/create_gazepoint_sidecar_template.Rd |only man/create_gazepoint_trial_regressors.Rd |only man/detect_gazepoint_blinks.Rd |only man/detect_gazepoint_fixations.Rd |only man/detect_gazepoint_nonwear.Rd |only man/detect_gazepoint_ppg_onsets.Rd |only man/detect_gazepoint_ppg_peaks.Rd |only man/detect_gazepoint_pupil_blinks.Rd |only man/detect_gazepoint_saccades.Rd |only man/detrend_gazepoint_rri_window.Rd |only man/detrend_gazepoint_signal.Rd |only man/diagnose_gazepoint_cluster_design.Rd |only man/diagnose_gazepoint_sync_drift.Rd |only man/downsample_gazepoint_data.Rd |only man/enhance_gazepoint_ppg_peaks.Rd |only man/epoch_gazepoint_scr.Rd |only man/estimate_gazepoint_breathing_rate_from_ibi.Rd |only man/estimate_gazepoint_cluster_offset.Rd |only man/estimate_gazepoint_cluster_onset.Rd |only man/estimate_gazepoint_eda_recovery_times.Rd |only man/estimate_gazepoint_lsl_clock_offsets.Rd |only man/estimate_gazepoint_respiration_from_ppg.Rd |only man/estimate_gazepoint_samplerate_datetime.Rd |only man/estimate_gazepoint_samplerate_mstimer.Rd |only man/export_gazepoint_audit_trail_markdown.Rd |only man/export_gazepoint_cluster_results.Rd |only man/export_gazepoint_heartpy_input.Rd |only man/export_gazepoint_mne_cluster_input.Rd |only man/export_gazepoint_permuco_cluster_input.Rd |only man/export_gazepoint_permutes_cluster_input.Rd |only man/export_gazepoint_pipeline_dot.Rd |only man/export_gazepoint_pspm_model_estimates.Rd |only man/export_gazepoint_pyhrv_results.Rd |only man/export_gazepoint_to_bids.Rd |only man/extract_gazepoint_eda_events_biosppy_style.Rd |only man/extract_gazepoint_markerinfo_pspm_style.Rd |only man/extract_gazepoint_ppg_morphology.Rd |only man/extract_gazepoint_ppg_templates.Rd |only man/extract_gazepoint_pyhrv_nn_intervals.Rd |only man/extract_gazepoint_segments_pspm_style.Rd |only man/figures |only man/filter_gazepoint_gaze.Rd |only man/filter_gazepoint_ppg_butterworth.Rd |only man/filter_gazepoint_ppg_signal.Rd |only man/filter_gazepoint_signal.Rd |only man/fit_gazepoint_convolution_glm.Rd |only man/flag_gazepoint_hrv_segments.Rd |only man/flag_gazepoint_ppg_quality.Rd |only man/flag_gazepoint_rr_outliers.Rd |only man/flip_gazepoint_ppg_signal.Rd |only man/gazepoint_interoperability_manifest.Rd |only man/generate_gazepoint_manifest.Rd |only man/gpbiometrics-package.Rd | 9 man/gpbiometrics_info.Rd |only man/import_gazepoint_data.Rd |only man/import_gazepoint_event_log.Rd |only man/import_gazepoint_pyhrv_results.Rd |only man/impute_gazepoint_missing.Rd |only man/interpolate_gazepoint_pupil_blinks.Rd |only man/match_gazepoint_events_to_biometrics.Rd |only man/merge_gazepoint_recordings_pspm_style.Rd |only man/normalize_gazepoint_scr.Rd |only man/physiology_validation_ladder.Rd |only man/pipeline_comparison_dashboard.Rd |only man/plot_gazepoint_cluster_null_distribution.Rd |only man/plot_gazepoint_cluster_permutation.Rd |only man/plot_gazepoint_design_coverage.Rd |only man/plot_gazepoint_export_profile.Rd |only man/plot_gazepoint_missingness.Rd |only man/plot_gazepoint_ppg_breathing.Rd |only man/plot_gazepoint_ppg_peak_detection.Rd |only man/plot_gazepoint_ppg_poincare.Rd |only man/plot_gazepoint_ppg_segmentwise.Rd |only man/plot_gazepoint_pyhrv_hr_heatplot.Rd |only man/plot_gazepoint_pyhrv_radar_chart.Rd |only man/plot_gazepoint_pyhrv_tachogram.Rd |only man/plot_gazepoint_signal_quality.Rd |only man/ppg_topology_features.Rd |only man/prepare_gazepoint_bids_eye.Rd |only man/prepare_gazepoint_bids_physio.Rd |only man/prepare_gazepoint_biosppy_input.Rd |only man/prepare_gazepoint_eyetrackingr_input.Rd |only man/prepare_gazepoint_gazer_input.Rd |only man/prepare_gazepoint_heartpy_input.Rd |only man/prepare_gazepoint_mixed_model_data.Rd |only man/prepare_gazepoint_mne_events.Rd |only man/prepare_gazepoint_mne_input.Rd |only man/prepare_gazepoint_pupillometryr_input.Rd |only man/prepare_gazepoint_pyhrv_input.Rd |only man/prepare_gazepoint_timecourse_test_data.Rd |only man/preprocess_gazepoint_all.Rd |only man/preprocess_gazepoint_scr_pspm_style.Rd |only man/process_gazepoint_ppg_heartpy_style.Rd |only man/process_gazepoint_ppg_segmentwise.Rd |only man/profile_gazepoint_export_folder.Rd |only man/reconstruct_gazepoint_ppg_clipping.Rd |only man/reject_gazepoint_ppg_peaks.Rd |only man/remove_gazepoint_ppg_baseline_wander.Rd |only man/report_gazepoint_cluster_permutation.Rd |only man/report_gazepoint_data_quality.Rd |only man/respiration_from_ppg.Rd |only man/run_gazepoint_biosppy_eda.Rd |only man/run_gazepoint_biosppy_ppg.Rd |only man/run_gazepoint_cluster_permutation.Rd |only man/run_gazepoint_cluster_permutation_anova.Rd |only man/run_gazepoint_cluster_permutation_covariate_adjusted.Rd |only man/run_gazepoint_cluster_permutation_lmer.Rd |only man/run_gazepoint_cluster_permutation_parallel.Rd |only man/run_gazepoint_cluster_threshold_sensitivity.Rd |only man/run_gazepoint_heartpy_crosscheck.Rd |only man/run_gazepoint_multidimensional_cluster_permutation.Rd |only man/run_gazepoint_pyhrv_style.Rd |only man/run_gazepoint_real_data_smoke.Rd |only man/run_gazepoint_tfce.Rd |only man/scale_gazepoint_ppg_sections.Rd |only man/scale_gazepoint_ppg_signal.Rd |only man/scr_responsivity_sensitivity.Rd |only man/segment_gazepoint_pyhrv_nni.Rd |only man/session_info_gazepoint.Rd |only man/simulate_gazepoint_artifact.Rd |only man/simulate_gazepoint_cluster_timecourse_data.Rd |only man/simulate_gazepoint_eye_data.Rd |only man/simulate_gazepoint_multimodal_data.Rd |only man/smooth_gazepoint_ppg_signal.Rd |only man/smooth_gazepoint_pupil.Rd |only man/split_gazepoint_sessions_pspm_style.Rd |only man/standardize_gazepoint_column_names.Rd |only man/standardize_gazepoint_columns.Rd |only man/summarise_gazepoint_decision_log.Rd |only man/summarise_gazepoint_fixations_by_aoi.Rd |only man/summarize_gazepoint_aoi_dwell.Rd |only man/summarize_gazepoint_audit_trail.Rd |only man/summarize_gazepoint_beat_corrections.Rd |only man/summarize_gazepoint_eventlocked_multimodal.Rd |only man/summarize_gazepoint_export_inventory.Rd |only man/summarize_gazepoint_feature_coverage.Rd |only man/summarize_gazepoint_fixations.Rd |only man/summarize_gazepoint_fixations_by_aoi.Rd |only man/summarize_gazepoint_missingness.Rd |only man/summarize_gazepoint_nonwear.Rd |only man/summarize_gazepoint_preregistration_readiness.Rd |only man/summarize_gazepoint_pupil_events.Rd |only man/summarize_gazepoint_qc_overview.Rd |only man/summarize_gazepoint_scanpath_metrics.Rd |only man/summarize_gazepoint_scr_recovery.Rd |only man/summarize_gazepoint_signal_quality.Rd |only man/summarize_gazepoint_time_clusters.Rd |only man/summarize_gazepoint_tracking.Rd |only man/sync_gazepoint_signals_via_lsl.Rd |only man/trim_gazepoint_biometrics_pspm_style.Rd |only man/upsample_gazepoint_data.Rd |only man/validate_gazepoint_format.Rd |only man/validate_gazepoint_gaze.Rd |only man/validate_gazepoint_metadata.Rd |only man/write_gazepoint_decision_log.Rd |only man/write_gazepoint_export_profile.Rd |only man/write_gazepoint_interoperability_audit.Rd |only man/write_gazepoint_mne_fif.Rd |only man/write_gazepoint_real_data_smoke.Rd |only tests/testthat/test-alignment-aoi-eventlocked-dashboard.R |only tests/testthat/test-analysis-decision-log.R |only tests/testthat/test-aoi-assignment.R |only tests/testthat/test-aoi-biometrics.R | 1 tests/testthat/test-audit-trail-summary.R |only tests/testthat/test-beat-correction-audit.R |only tests/testthat/test-bids-export.R |only tests/testthat/test-bids-layout-audit.R |only tests/testthat/test-biosppy-input.R |only tests/testthat/test-biosppy-style.R |only tests/testthat/test-cluster-permutation-advanced-guardrails.R |only tests/testthat/test-cluster-permutation-diagnostics.R |only tests/testthat/test-cluster-permutation.R |only tests/testthat/test-condition-bootstrap.R |only tests/testthat/test-data-io-cleaning.R |only tests/testthat/test-dataset-structure-audit.R |only tests/testthat/test-design-event-audit.R |only tests/testthat/test-downsample.R |only tests/testthat/test-event-physiology-indices.R |only tests/testthat/test-export-folder-profile.R |only tests/testthat/test-eyetrackingr-input.R |only tests/testthat/test-frontdoor-audit-missingness.R |only tests/testthat/test-gaze-event-detection.R |only tests/testthat/test-gazer-input.R |only tests/testthat/test-heartpy-bridge.R |only tests/testthat/test-heartpy-extended.R |only tests/testthat/test-interoperability-version-testing.R |only tests/testthat/test-measurement-accountability-2026-09.R |only tests/testthat/test-mne-eeg-lsl-interoperability.R |only tests/testthat/test-physiology-qc-refinements.R |only tests/testthat/test-pipeline-comparison-dashboard.R |only tests/testthat/test-pipeline-visualization.R |only tests/testthat/test-preregistration-readiness.R |only tests/testthat/test-pspm-style.R |only tests/testthat/test-pupil-gaze-cleaning.R |only tests/testthat/test-pupil-qc-reporting.R |only tests/testthat/test-pupillometryr-input.R |only tests/testthat/test-pyhrv-input.R |only tests/testthat/test-pyhrv-style.R |only tests/testthat/test-real-data-smoke-harness.R |only tests/testthat/test-release-readiness-audit.R |only tests/testthat/test-reproducibility-simulation.R |only tests/testthat/test-reviewer-report-templates.R |only tests/testthat/test-roadmap-compatibility-aliases.R |only tests/testthat/test-roadmap-exact-backlog-helpers.R |only tests/testthat/test-roadmap-final-gaps.R |only tests/testthat/test-roadmap-remaining-helpers.R |only tests/testthat/test-session-quality-audit.R |only tests/testthat/test-signal-dropout-preprocessing.R |only tests/testthat/test-signal-quality-reporting.R |only tests/testthat/test-simulate-gazepoint-eye-data.R |only tests/testthat/test-workflow-reporting-pipeline.R |only tools |only vignettes/articles |only vignettes/dabest-estimation-gallery.Rmd |only vignettes/ecosystem-update-2026-09.Rmd |only vignettes/gpbiometrics-workflow.Rmd | 560 - vignettes/measurement-accountability.Rmd |only vignettes/october-2026-acquisition-availability.Rmd |only 424 files changed, 73246 insertions(+), 72576 deletions(-)
Title: Contract-First Bayesian Workflows for Hierarchical Behavioural
Data
Description: Provides transparent, contract-first infrastructure for Bayesian
analysis of repeated-measures and hierarchical behavioural data. It
supports approved Bernoulli-logit, positive lognormal duration, and
governed Gaussian dynamic-pupillometry workflows with strict readiness
auditing, deterministic simulation, explicit preparation and
transformation replay, inspectable scale-aware priors, prior and posterior
predictive checks, restricted optional fitting through 'brms' with either
'rstan' or 'cmdstanr', sampling and temporal diagnostics, explicit
posterior estimands, sensitivity analysis, target-specific predictive
validation, simulation-based calibration, and conservative reporting.
Core contracts and validation remain backend-independent.
Version 0.5 adds governed robust and distributional dynamic pupillometry, bounded ARMA residual structures, Gaussian-process trajectories, explicit measurement uncertainty and missing-data models, joint binocular analysis, predictive model comparison, f [...truncated...]
Author: Stefanos Balaskas [aut, cre, cph]
Maintainer: Stefanos Balaskas <s.balaskas@ac.upatras.gr>
Diff between gp3bayes versions 0.5.0 dated 2026-08-23 and 0.6.1 dated 2026-10-22
DESCRIPTION | 11 MD5 | 1440 +- NAMESPACE | 1406 +- NEWS.md | 568 R/advanced-optional-workflows.R | 4336 +++---- R/advanced-predictive-graphics.R | 672 - R/analysis-bundle.R | 634 - R/analysis-manifest.R | 1330 +- R/backend-reliability.R | 1682 +- R/binary-model-fitting.R | 1362 +- R/binary-posterior-validation.R | 3936 +++--- R/binary-workflow-foundation.R | 3442 ++--- R/design-support-diagnostics.R | 1670 +- R/duration-model-fitting.R | 1236 +- R/duration-posterior-validation.R | 3426 ++--- R/duration-workflow-foundation.R | 3884 +++--- R/evidence-graphics-gg.R | 614 R/global-variables.R | 192 R/gp3bayes-package.R | 84 R/hierarchical-effects-advanced.R | 788 - R/internal-scope.R | 8 R/loo-group-influence.R | 222 R/loo-influence-atlas.R | 454 R/model-card.R | 520 R/model-contract.R | 1244 +- R/model-readiness-audit.R | 3682 ++--- R/model-specification.R | 2508 ++-- R/multilevel-gaze-mediation.R |only R/posterior-validation-core.R | 1880 +-- R/postfit-exploration.R | 1592 +- 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| 68 man/predictive_residuals.Rd | 46 man/preflight_model_specification.Rd | 40 man/prepare_hierarchical_binary_data.Rd | 178 man/prepare_hierarchical_duration_data.Rd | 100 man/prepare_pupil_timecourse.Rd | 144 man/print.gp3bayes_model_contract.Rd | 42 man/print.gp3bayes_model_specification.Rd | 40 man/print.gp3bayes_prior_specification.Rd | 40 man/print.gp3bayes_readiness_audit.Rd | 44 man/prior_posterior_bridge.Rd | 70 man/prior_posterior_distance_table.Rd | 34 man/prior_posterior_draws_long.Rd | 42 man/prior_posterior_summary_table.Rd | 34 man/prior_sensitivity_scenario_table.Rd | 34 man/prior_sensitivity_table.Rd | 34 man/prior_specification_table.Rd | 34 man/publication_registry_table.Rd | 34 man/pupil_condition_contrast.Rd | 80 man/pupil_measurement_audit_table.Rd | 40 man/pupil_ppc_table.Rd | 56 man/pupil_readiness_table.Rd | 50 man/pupil_residual_acf.Rd | 48 man/pupil_sensitivity_table.Rd | 40 man/pupil_specification_table.Rd | 40 man/pupil_trajectory_table.Rd | 40 man/pupil_validation_table.Rd | 40 man/random_intercept_variance_partition.Rd | 42 man/random_intercept_variance_partition_table.Rd | 34 man/random_slope_sensitivity_table.Rd | 34 man/read_analysis_manifest.Rd | 34 man/read_gp3bayes_schema.Rd | 34 man/recovery_estimate_table.Rd | 34 man/recovery_fit_status_table.Rd | 34 man/recovery_parameter_table.Rd | 34 man/register_publication_figure.Rd | 62 man/register_publication_table.Rd | 62 man/review_duration_extremes.Rd | 50 man/run_binary_recovery.Rd | 144 man/run_duration_recovery.Rd | 152 man/run_group_deletion_sensitivity.Rd | 80 man/run_random_slope_sensitivity.Rd | 76 man/run_sbc_plan.Rd | 68 man/run_sensitivity_suite.Rd | 64 man/sampler_diagnostic_table.Rd | 34 man/save_figure_set.Rd | 70 man/save_publication_registry_figures.Rd | 70 man/sbc_overview_table.Rd | 34 man/sbc_stats_table.Rd | 34 man/schema_comparison_table.Rd | 34 man/sensitivity_suite_table.Rd | 34 man/simulate_binary_pathology.Rd | 48 man/simulate_declared_prior_draws.Rd | 64 man/simulate_duration_pathology.Rd | 48 man/simulate_hierarchical_binary_data.Rd | 178 man/simulate_hierarchical_duration_data.Rd | 170 man/simulate_pupil_timecourse.Rd | 200 man/specify_binary_model.Rd | 152 man/specify_binary_model_with_interaction_prior.Rd | 86 man/specify_duration_model.Rd | 82 man/specify_duration_model_with_interaction_prior.Rd | 90 man/specify_pupil_timecourse_model.Rd | 158 man/summarise_binary_group_variation.Rd | 52 man/summarise_binary_posterior.Rd | 56 man/summarise_condition_balance.Rd | 64 man/summarise_duration_posterior.Rd | 54 man/summarise_estimand_draws.Rd | 42 man/summarise_mcmc_quality.Rd | 40 man/summarise_model_posterior.Rd | 40 man/summarise_pupil_posterior.Rd | 46 man/summarise_sbc_result.Rd | 34 man/summarise_sensitivity_suite.Rd | 34 man/theme_gp3bayes.Rd | 44 man/translate_binary_model_to_brms.Rd | 122 man/translate_binary_model_with_interaction_prior.Rd | 34 man/translate_duration_model_to_brms.Rd | 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tests/testthat/test-recovery-sensitivity-publication.R | 124 tests/testthat/test-sbc-publication-adapters.R | 44 tests/testthat/test-scr-responsivity.R |only tests/testthat/test-sensitivity-evidence-suite.R | 182 tests/testthat/test-specification-closure.R | 680 - tests/testthat/test-unified-workflow-api.R | 254 vignettes/advanced-optional-workflows.Rmd | 286 vignettes/advanced-predictive-diagnostics.Rmd | 120 vignettes/backend-portability.Rmd | 128 vignettes/backend-reliability.Rmd | 210 vignettes/bayesian-dynamic-pupillometry.Rmd | 220 vignettes/bayesian-multilevel-gaze-mediation.Rmd |only vignettes/binary-end-to-end.Rmd | 456 vignettes/declared-prior-versus-posterior.Rmd | 62 vignettes/duration-end-to-end.Rmd | 458 vignettes/ecosystem-update-2026-09.Rmd |only vignettes/end-to-end-evidence-showcase.Rmd | 118 vignettes/estimands-and-sensitivity.Rmd | 302 vignettes/evidence-graphics-and-governance.Rmd | 86 vignettes/fitting-pupil-timecourse-models.Rmd | 240 vignettes/gazepoint-pupil-interoperability.Rmd | 130 vignettes/grouped-loo-influence.Rmd | 56 vignettes/hierarchical-effect-atlas.Rmd | 80 vignettes/hierarchical-effects-and-uncertainty.Rmd | 112 vignettes/loo-influence-and-model-comparison.Rmd | 90 vignettes/loo-influence-atlas.Rmd | 62 vignettes/mediation-estimation-graphics-gallery.Rmd |only vignettes/model-cards-and-reporting-inventories.Rmd | 102 vignettes/october-2026-conjugate-prior-sensitivity.Rmd |only vignettes/optional-backend-installation.Rmd | 388 vignettes/pathological-simulation-scenarios.Rmd | 212 vignettes/posterior-diagnostics.Rmd | 252 vignettes/posterior-exploration-and-graphics.Rmd | 128 vignettes/pre-fit-design-diagnostics.Rmd | 226 vignettes/prediction-calibration-and-scoring.Rmd | 170 vignettes/prediction-contrasts-ranking-and-groups.Rmd | 94 vignettes/prediction-profiles-surfaces-and-contrasts.Rmd | 100 vignettes/predictive-distribution-and-calibration-uncertainty.Rmd | 106 vignettes/public-api-map.Rmd | 776 - vignettes/publication-analysis-bundles.Rmd | 106 vignettes/publication-registries-and-dashboards.Rmd | 106 vignettes/pupil-baseline-gaze-luminance-sensitivity.Rmd | 178 vignettes/pupil-ppc-and-temporal-diagnostics.Rmd | 112 vignettes/pupil-preparation-and-auditing.Rmd | 200 vignettes/pupil-temporal-validation.Rmd | 178 vignettes/pupil-trajectories-and-estimands.Rmd | 150 vignettes/quality-hardening-and-failure-contracts.Rmd | 144 vignettes/recovery-diagnostics-for-publication.Rmd | 60 vignettes/release-case-study.Rmd | 346 vignettes/reproducible-analysis-manifests.Rmd | 220 vignettes/sbc-publication-diagnostics.Rmd | 56 vignettes/scr-responsivity-sensitivity.Rmd |only vignettes/sensitivity-and-recovery.Rmd | 254 vignettes/sensitivity-atlas.Rmd | 70 vignettes/sensitivity-evidence-workflow.Rmd | 196 vignettes/specification-closure.Rmd | 298 vignettes/stable-unified-workflow.Rmd | 234 vignettes/synthetic-gazepoint-pupillometry-case-study.Rmd | 282 vignettes/transformation-replay-and-detailed-ppc.Rmd | 248 733 files changed, 100269 insertions(+), 100433 deletions(-)
Title: 'Constrained Quantile Regression with B-Splines'
Description: Quantile regression with B-splines under shape constraints.
The initial version with cubic splines, augmented with splines of
degree 1 to 4, is now able to handle all degrees (degree >= 6
without any constraint).
Constraints for degrees 3 (monotone), 4 (monotone and convex) and 5
(convex) use the Karlin-Studden SOCP characterization for the sign
of the polynomial (Karlin and Studden, 1966; Papp and Alizadeh, 2014),
while other constraints are added as linear problems. The method for
monotone constraints of cubic splines is described in Abbes (2025)
<doi:10.5281/zenodo.17427913>. For quartic splines, see other
references given in the README. All B-spline and polynomial functions
have been rewritten for consistency. This package provides a fully
independent original B-spline library for conversion between PP-form
and B-spline representation, evaluation, differentiation, callable
and non-callable objects, human-readable PP forms, and basis
visualization, all based on De Boor's th [...truncated...]
Author: Alexandre Abbes [aut, cre]
Maintainer: Alexandre Abbes <alexandre.abbes@proton.me>
Diff between BsplineQuantReg versions 0.2.5 dated 2026-08-20 and 0.2.6 dated 2026-10-22
DESCRIPTION | 48 MD5 | 74 - NAMESPACE | 2 NEWS | 17 R/bspline-eval.R | 46 R/constant-regression.R |only R/deriv-coeffs.R | 85 + R/general-regression.R |only R/polynomial-utils.R | 224 +--- R/quantile-regression.R | 28 R/quartic-regression.R | 77 + README.md | 10 demo/00Index | 2 demo/shock.R |only demo/shock_basis.R |only demo/temperature2.R | 45 inst/References.bib | 2 inst/doc/bspline_basis_manipulation.R | 2 inst/doc/bspline_basis_manipulation.Rmd | 31 inst/doc/bspline_basis_manipulation.html | 1542 +++++++++++++------------------ inst/doc/introduction.R | 93 + inst/doc/introduction.Rmd | 177 +++ inst/doc/introduction.html | 206 ++++ inst/doc/polynomial_library.R | 173 +-- inst/doc/polynomial_library.Rmd | 386 +++---- inst/doc/polynomial_library.html | 694 +++++++------ inst/doc/shape_constraints.R | 25 inst/doc/shape_constraints.Rmd | 149 +- inst/doc/shape_constraints.html | 1436 ++++++++-------------------- inst/doc/theoretical_background.R | 20 inst/doc/theoretical_background.Rmd | 29 inst/doc/theoretical_background.html | 135 ++ man/SplineConstantQuant.Rd |only man/SplinePolynQuant.Rd |only man/evalpp.Rd | 1 man/makpp.Rd | 4 vignettes/bspline_basis_manipulation.Rmd | 31 vignettes/introduction.Rmd | 177 +++ vignettes/polynomial_library.Rmd | 386 +++---- vignettes/shape_constraints.Rmd | 149 +- vignettes/theoretical_background.Rmd | 29 41 files changed, 3304 insertions(+), 3231 deletions(-)
More information about BsplineQuantReg at CRAN
Permanent link
Title: Automated Reproducibility Checks for R Markdown Documents
Description: Provide reproducible R chunks in R Markdown document that automatically check computational results for reproducibility. This is achieved by creating json files storing metadata about computational results. A comprehensive tutorial to the package is available as preprint by Brandmaier & Peikert (2024, <doi:10.31234/osf.io/3zjvf>).
Author: Andreas M. Brandmaier [aut, cre],
Aaron Peikert [ctb]
Maintainer: Andreas M. Brandmaier <andreas.brandmaier@medicalschool-berlin.de>
Diff between reproducibleRchunks versions 1.2.0 dated 2025-07-23 and 1.2.1 dated 2026-10-22
DESCRIPTION | 10 - MD5 | 65 +++++++----- NAMESPACE | 1 NEWS.md | 80 +++++++++------ R/hash.R | 26 ++++- R/isReproducible.R | 34 +++++- R/load_repro_data.R | 2 R/normalize_for_hash.R |only R/reproducibleR.R | 65 ++++++++++-- R/reset.R | 8 + R/save_repro_data.R | 6 - R/symbols.R | 48 ++++----- R/use_github_action.R | 9 + R/zzz.R | 128 ++++++++++++------------ build/vignette.rds |binary inst/doc/custom_reports.html | 16 +-- inst/doc/html_styling.R |only inst/doc/html_styling.Rmd |only inst/doc/html_styling.html |only inst/doc/minimal_example.html | 10 - inst/doc/object_identity.R |only inst/doc/object_identity.Rmd |only inst/doc/object_identity.html |only inst/doc/plots.html | 12 +- inst/doc/regression_example.html | 20 +-- inst/doc/renv_example.html | 130 ++++++++++++------------- inst/doc/use_case_simulation.Rmd | 2 inst/doc/use_case_simulation.html | 11 +- inst/rmarkdown |only man/hash.Rd |only man/isReproducible.Rd | 2 tests/testthat/test-canonical-representation.R |only tests/testthat/testdata/test2.pdf | 4 tests/testthat/testdata/test3.html | 2 tests/testthat/testdata/test_json.html | 2 tests/testthat/testdata/test_json.knit.md | 2 vignettes/html_styling.Rmd |only vignettes/object_identity.Rmd |only vignettes/use_case_simulation.Rmd | 2 39 files changed, 414 insertions(+), 283 deletions(-)
More information about reproducibleRchunks at CRAN
Permanent link
Title: Transparent Analysis of Ordered Categorical Sequences
Description: Provides transparent, reproducible, and auditable tools for validating,
preparing, encoding, summarising, comparing, modelling, and diagnosing
ordered categorical sequence data. Supports explicit preprocessing
policies, contiguous motifs and bounded subsequences, consensus and group
comparisons, edit and transition distances, clustering and stability
diagnostics, transition networks, higher-order models, categorical,
mixture, multichannel, and covariate hidden Markov models, longitudinal
panel workflows, time-varying models, design-aware inference, analysis
contracts and provenance audits, and guarded adapters to specialist
sequence-analysis packages.
Author: Stefanos Balaskas [aut, cre]
Maintainer: Stefanos Balaskas <s.balaskas@ac.upatras.gr>
Diff between gp3sequences versions 0.3.0 dated 2026-08-23 and 0.3.2 dated 2026-10-22
DESCRIPTION | 6 MD5 | 81 NEWS.md | 113 README.md | 718 ++-- build/vignette.rds |binary inst/doc/choosing-a-sequence-analysis-method.R | 88 inst/doc/choosing-a-sequence-analysis-method.html | 1088 +++---- inst/doc/consensus-and-group-comparisons.R | 98 inst/doc/consensus-and-group-comparisons.html | 1052 +++---- inst/doc/contiguous-motif-workflow.R | 264 - inst/doc/contiguous-motif-workflow.html | 1362 ++++----- inst/doc/distances-clustering-and-stability.R | 154 - inst/doc/distances-clustering-and-stability.html | 966 +++--- inst/doc/ecosystem-update-2026-09.Rmd |only inst/doc/ecosystem-update-2026-09.html |only inst/doc/estimation-visualization-boundaries.R |only inst/doc/estimation-visualization-boundaries.Rmd |only inst/doc/estimation-visualization-boundaries.html |only inst/doc/extended-sequence-visualisations.R | 72 inst/doc/extended-sequence-visualisations.html | 810 ++--- inst/doc/getting-started-with-gp3sequences.R | 408 +- inst/doc/getting-started-with-gp3sequences.html | 1906 ++++++------ inst/doc/latent-models-and-optional-adapters.R | 166 - inst/doc/latent-models-and-optional-adapters.html | 1106 +++---- inst/doc/longitudinal-panel-sequences.R | 90 inst/doc/longitudinal-panel-sequences.html | 942 +++--- inst/doc/multichannel-and-covariate-hmms.R | 110 inst/doc/multichannel-and-covariate-hmms.html | 954 +++--- inst/doc/noncontiguous-subsequence-mining.R | 112 inst/doc/noncontiguous-subsequence-mining.html | 1172 +++---- inst/doc/reproducible-sequence-analysis-case-study.R | 482 +-- inst/doc/reproducible-sequence-analysis-case-study.html | 2102 +++++++------- inst/doc/sequence-data-validation-and-preparation.R | 180 - inst/doc/sequence-data-validation-and-preparation.html | 1334 ++++---- inst/doc/sequence-inference-and-randomization.R | 94 inst/doc/sequence-inference-and-randomization.html | 898 ++--- inst/doc/time-varying-condition-models.R | 124 inst/doc/time-varying-condition-models.html | 908 +++--- inst/doc/transition-networks-and-higher-order-models.R | 92 inst/doc/transition-networks-and-higher-order-models.html | 958 +++--- inst/doc/transition-unit-audit-october-2026.R |only inst/doc/transition-unit-audit-october-2026.Rmd |only inst/doc/transition-unit-audit-october-2026.html |only inst/research |only tests/testthat/test-october-2026-transition-unit-audit.R |only vignettes/ecosystem-update-2026-09.Rmd |only vignettes/estimation-visualization-boundaries.Rmd |only vignettes/transition-unit-audit-october-2026.Rmd |only 48 files changed, 10522 insertions(+), 10488 deletions(-)
Title: Governance-First Predictive Modelling for 'Gazepoint' Research
Description: Provides governance-first infrastructure for leakage-resistant
predictive modelling and validation using 'Gazepoint'-derived research
data. Supports explicit task and role declarations, feature-provenance
manifests, group-aware holdout splitting and repeated resampling,
repository-aware fold evaluation, explicit governed tuning, nested grouped
resampling, fold-local preprocessing, discrimination and calibration
metrics, target-aligned uncertainty, external-validation and
transportability reports, prediction-to-decision governance, target-aware
conformal prediction, dataset-shift auditing, locked analysis plans,
portable model artifacts, robustness diagnostics, environment provenance,
research-object export, model cards, and reproducibility evidence.
Intended only for explicitly observed, non-sensitive outcomes and declared
scientific purposes. Use is prohibited for person identification,
biometric authentication, health or protected-attribute inference, and
direct or indirect inference [...truncated...]
Author: Stefanos Balaskas [aut, cre]
Maintainer: Stefanos Balaskas <s.balaskas@ac.upatras.gr>
Diff between gp3ml versions 0.3.0 dated 2026-08-23 and 0.3.2 dated 2026-10-22
DESCRIPTION | 6 MD5 | 101 - NEWS.md | 16 build/vignette.rds |binary inst/doc/analysis-plan-governance.R | 60 inst/doc/analysis-plan-governance.html | 784 ++++++------ inst/doc/api-stability-contracts.R | 86 - inst/doc/api-stability-contracts.html | 918 +++++++------- inst/doc/assigned-condition-discrimination.R | 64 - inst/doc/assigned-condition-discrimination.html | 898 +++++++------- inst/doc/contaminated-manifest-leakage.R | 58 inst/doc/contaminated-manifest-leakage.html | 814 ++++++------ inst/doc/cross-package-interoperability.R | 56 inst/doc/cross-package-interoperability.html | 922 +++++++------- inst/doc/dataset-shift-and-robustness.R | 58 inst/doc/dataset-shift-and-robustness.html | 818 ++++++------ inst/doc/decision-governance.R | 54 inst/doc/decision-governance.html | 820 ++++++------ inst/doc/ecosystem-update-2026-09.Rmd |only inst/doc/ecosystem-update-2026-09.html |only inst/doc/external-validation-reporting.R | 112 - inst/doc/external-validation-reporting.html | 988 +++++++-------- inst/doc/governance-standards-profile.R | 34 inst/doc/governance-standards-profile.html | 768 ++++++------ inst/doc/group-aware-conformal-prediction.R | 54 inst/doc/group-aware-conformal-prediction.html | 844 ++++++------- inst/doc/integrated-research-workflow.R | 212 +-- inst/doc/integrated-research-workflow.html | 1082 ++++++++--------- inst/doc/nested-grouped-resampling.R | 84 - inst/doc/nested-grouped-resampling.html | 896 +++++++------- inst/doc/observed-behavioral-endpoint.R | 78 - inst/doc/observed-behavioral-endpoint.html | 834 ++++++------- inst/doc/optional-engine-portability.R | 32 inst/doc/optional-engine-portability.html | 814 ++++++------ inst/doc/participant-generalization.R | 44 inst/doc/participant-generalization.html | 830 ++++++------- inst/doc/participant-identity-leakage-synthetic.R |only inst/doc/participant-identity-leakage-synthetic.Rmd |only inst/doc/participant-identity-leakage-synthetic.html |only inst/doc/participant-stimulus-generalization.R | 50 inst/doc/participant-stimulus-generalization.html | 968 +++++++-------- inst/doc/portable-research-artifacts.R | 20 inst/doc/portable-research-artifacts.html | 752 +++++------ inst/doc/recording-quality-review.R | 84 - inst/doc/recording-quality-review.html | 920 +++++++------- inst/doc/reproducibility-hardening.R | 66 - inst/doc/reproducibility-hardening.html | 802 ++++++------ inst/doc/stimulus-generalization.R | 42 inst/doc/stimulus-generalization.html | 828 ++++++------- inst/governance/GOVERNANCE.md | 84 - inst/governance/PROHIBITED-USE.md | 52 inst/research |only tests/testthat.R | 8 tests/testthat/test-october-2026-participant-leakage.R |only vignettes/ecosystem-update-2026-09.Rmd |only vignettes/participant-identity-leakage-synthetic.Rmd |only 56 files changed, 9470 insertions(+), 9445 deletions(-)
Title: Harmonize Eye-Tracking, Pupillometry, Biometrics, and
Psychometric Process Data
Description: Provides an extensible, vendor-neutral framework for importing, validating, harmonizing, transforming,
visualizing, and modelling eye-tracking, pupillometry, behavioural, and biometric process data. The package uses
explicit timebase and coordinate-space registries, preserves native fields and provenance, and offers first-class
adapters for Gazepoint Analysis and Gazepoint Biometrics exports alongside generic and vendor-specific importers.
Downstream tools support trial and area of interest reconstruction, signal-quality auditing, feature derivation,
scanpath analysis, response-time and item-response workflows, and optional psychometric modelling engines. An
integrated Gazepoint workflow produces quality-control evidence, media-trial reconstruction, plots, analysis-ready
process tables, item response theory (IRT)-ready response structures, and reproducible reports. Brain Imaging Data
Structure (BIDS) interoperability for eye-tracking and validation-release infrastructure support disk-b [...truncated...]
Author: Stefanos Balaskas [aut, cre]
Maintainer: Stefanos Balaskas <s.balaskas@ac.upatras.gr>
Diff between eyeprocess versions 0.11.1 dated 2026-09-28 and 0.12.1 dated 2026-10-22
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Title: Analysis of Antimicrobial Minimum Inhibitory Concentration Data
Description: Analyse, plot, and tabulate antimicrobial minimum inhibitory concentration (MIC) data.
Validate the results of an MIC experiment by comparing observed MIC values to
a gold standard assay, in line with standards from the International Organization for
Standardization (2021) <https://www.iso.org/standard/79377.html>.
Author: Alessandro Gerada [aut, cre, cph]
Maintainer: Alessandro Gerada <alessandro.gerada2@liverpool.ac.uk>
Diff between MIC versions 2.0.1 dated 2026-07-21 and 2.0.2 dated 2026-10-22
MIC-2.0.1/MIC/man/as.sir_vectorised.Rd |only MIC-2.0.2/MIC/DESCRIPTION | 10 +- MIC-2.0.2/MIC/MD5 | 30 +++---- MIC-2.0.2/MIC/NAMESPACE | 2 MIC-2.0.2/MIC/NEWS.md | 6 + MIC-2.0.2/MIC/R/mic_manipulation.R | 65 ++++------------- MIC-2.0.2/MIC/R/plotting.R | 4 - MIC-2.0.2/MIC/R/validation.R | 30 +++++++ MIC-2.0.2/MIC/README.md | 62 ++++------------ MIC-2.0.2/MIC/man/as.sir_fallback_ecoff.Rd |only MIC-2.0.2/MIC/man/figures/README-fig-val-ea-1.png |binary MIC-2.0.2/MIC/man/figures/README-unnamed-chunk-8-1.png |binary MIC-2.0.2/MIC/man/mic_r_breakpoint.Rd | 2 MIC-2.0.2/MIC/man/mic_s_breakpoint.Rd | 2 MIC-2.0.2/MIC/man/summary.mic_validation.Rd | 4 - MIC-2.0.2/MIC/man/table.Rd | 2 MIC-2.0.2/MIC/tests/testthat/test-validation.R | 34 +++++++- 17 files changed, 128 insertions(+), 125 deletions(-)
Title: Nicely Formatted Contingency Tables and Frequency Tables
Description: Nicely formatted frequency tables and contingency tables (1-way, 2-way, 3-way and 4-way tables), that can easily be exported to HTML or 'Office' documents. Designed to work with pipes.
Author: Mans Thulin [aut, cre],
Kajsa Grind [aut],
Stefan Furne [aut]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Diff between ivo.table versions 0.7.1 dated 2025-11-25 and 0.8.0 dated 2026-10-22
DESCRIPTION | 8 MD5 | 22 +- NEWS.md | 3 R/ivo_tables.R | 108 ++++++---- build/vignette.rds |binary inst/doc/ivo_table.R | 29 ++ inst/doc/ivo_table.Rmd | 43 ++++ inst/doc/ivo_table.html | 83 ++++++-- inst/doc/ivo_table_gt.html | 444 ++++++++++++++++++++++----------------------- man/ivo_flextable_theme.Rd | 10 - man/ivo_table.Rd | 8 vignettes/ivo_table.Rmd | 43 ++++ 12 files changed, 490 insertions(+), 311 deletions(-)
Title: Handling and Analysing 'EQ-5D' Data
Description: The EQ-5D is a widely-used standardised instrument for measuring Health Related Quality Of Life (HRQOL),
developed by the EuroQol group <https://euroqol.org/>. It assesses five dimensions; mobility, self-care,
usual activities, pain/discomfort, and anxiety/depression, using either a three-level (EQ-5D-3L) or five-level (EQ-5D-5L) scale.
Scores from these dimensions are commonly converted into a single utility index using country-specific value sets,
which are critical in clinical and economic evaluations of healthcare and in population health surveys.
The eq5dsuite package enables users to calculate utility index values for the EQ-5D instruments,
including crosswalk utilities using the original crosswalk developed by van Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008>
(mapping EQ-5D-5L responses to EQ-5D-3L index values), or the recently developed reverse crosswalk
by van Hout et al. (2021) <doi:10.1016/j.jval.2021.03.009> (mapping EQ-5D-3L responses
to EQ-5D-5L i [...truncated...]
Author: Kim Rand [aut, cre] ,
Oliver Rivero-Arias [aut] ,
Iryna Schlackow [aut] ,
Anabel Estevez-Carrillo [aut]
Maintainer: Kim Rand <krand@mathsinhealth.com>
Diff between eq5dsuite versions 2.0.0 dated 2026-05-14 and 2.1.0 dated 2026-10-22
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Title: Document Conversion to 'PDF', Thumbnails and Visual Testing
Description: Provides the ability to generate images from documents of
different types. Three main features are provided: generating document
thumbnails, performing visual tests of documents, and updating fields
and tables of contents of a 'Microsoft Word' or 'RTF' document.
'Microsoft Office' ('Word', 'PowerPoint', 'Excel') and/or
'LibreOffice' must be installed on the machine. If 'Microsoft Office'
is available, it can produce PDF documents or images identical to the
originals; otherwise 'LibreOffice' is used and the rendering may
sometimes differ from the original documents.
Author: David Gohel [aut, cre],
ArData [cph],
David Hajage [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between doconv versions 0.4.0 dated 2026-02-14 and 0.4.2 dated 2026-10-22
DESCRIPTION | 27 +-- MD5 | 50 ++++-- NAMESPACE | 24 ++- NEWS.md | 88 +++++++++++ R/docx2pdf.R | 192 +++++++++++++++++++++---- R/expect_snapshot_doc.R | 81 ++++++---- R/run_in_shiny_app.R | 59 ++++++- R/to_miniature.R | 66 +++++++- R/to_pdf.R | 85 +++++++---- R/utils.R | 117 ++++++++++++++- inst/doc-examples/example.xlsx |only inst/scripts/applescripts/docx2pdf.applescript | 5 inst/scripts/applescripts/xlsx2pdf.applescript |only inst/scripts/powershell/docx2pdf.ps1 | 9 + inst/scripts/powershell/xlsx2pdf.ps1 |only man/docx2pdf.Rd | 11 + man/docx_update.Rd | 2 man/expect_snapshot_doc.Rd | 9 - man/pptx2pdf.Rd | 5 man/to_miniature.Rd | 17 +- man/to_pdf.Rd | 46 +++-- man/xlsx2pdf.Rd |only tests |only 23 files changed, 731 insertions(+), 162 deletions(-)
Title: Visualise the Anatomical Therapeutic Chemical (ATC) Hierarchy
Description: Visualisation and subsetting of the World Health Organisation Anatomical Therapeutic Chemical (ATC) classification system.
Author: J Matthews [aut, cre, cph]
Maintainer: J Matthews <jnmatt212@gmail.com>
Diff between visATC versions 1.0.0 dated 2026-09-22 and 1.1.0 dated 2026-10-22
visATC-1.0.0/visATC/man/parents.Rd |only visATC-1.1.0/visATC/DESCRIPTION | 9 visATC-1.1.0/visATC/MD5 | 38 - visATC-1.1.0/visATC/NAMESPACE | 6 visATC-1.1.0/visATC/NEWS.md | 32 + visATC-1.1.0/visATC/R/atctree.r | 10 visATC-1.1.0/visATC/R/atctree_class.r | 433 ++++++++++++---- visATC-1.1.0/visATC/R/atctree_helpers.r | 45 + visATC-1.1.0/visATC/R/make_ATC_df.r | 3 visATC-1.1.0/visATC/R/node_helpers.r | 37 - visATC-1.1.0/visATC/R/sysdata.rda |only visATC-1.1.0/visATC/R/visATC-package.R | 4 visATC-1.1.0/visATC/man/atctree-class.Rd | 2 visATC-1.1.0/visATC/man/cutting-atctree-method.Rd | 4 visATC-1.1.0/visATC/man/drugnames.Rd | 5 visATC-1.1.0/visATC/man/graft-atctree-atctree-method.Rd |only visATC-1.1.0/visATC/man/helpers.Rd | 28 + visATC-1.1.0/visATC/man/look-atctree-method.Rd |only visATC-1.1.0/visATC/man/parents-atctree-method.Rd |only visATC-1.1.0/visATC/man/parents-character-method.Rd |only visATC-1.1.0/visATC/man/plot-atctree-method.Rd | 12 visATC-1.1.0/visATC/man/pruning-atctree-method.Rd | 2 visATC-1.1.0/visATC/man/sub-atctree-method.Rd | 13 23 files changed, 508 insertions(+), 175 deletions(-)
Title: Estimation of the ROC Curve and the AUC for Complex Survey Data
Description: Estimate the receiver operating characteristic (ROC) curve, area under the curve (AUC) and optimal cut-off points for individual classification taking into account complex sampling designs when working with complex survey data. Methods implemented in this package are described in: A. Iparragirre, I. Barrio, I. Arostegui (2024) <doi:10.1002/sta4.635>; A. Iparragirre, I. Barrio, J. Aramendi, I. Arostegui (2022) <doi:10.2436/20.8080.02.121>; A. Iparragirre, I. Barrio (2024) <doi:10.1007/978-3-031-65723-8_7>.
Author: Amaia Iparragirre [aut, cre, cph] ,
Irantzu Barrio [aut],
Inmaculada Arostegui [aut]
Maintainer: Amaia Iparragirre <amaia.iparragirre@ehu.eus>
Diff between svyROC versions 1.1.0 dated 2026-04-14 and 1.2.0 dated 2026-10-22
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------- NAMESPACE | 21 +++++++++----- NEWS.md | 5 +++ R/ci.wauc.R | 79 +++++++++++++++++++++++++++++++++++++++---------------- R/ht.indep.R | 59 ++++++++++++++++++++++++++++++++--------- R/ht.paired.R | 47 ++++++++++++++++++++++++++------ README.md | 4 ++ man/ci.wauc.Rd | 27 +++++++++++++----- man/ht.indep.Rd | 10 ++++++ man/ht.paired.Rd | 12 ++++++-- 11 files changed, 216 insertions(+), 76 deletions(-)
Title: An Open-Source Loader for Bruker's timsTOF Data Files
Description: Reads raw data from Bruker's timsTOF mass spectrometers,
stored in analysis.tdf and analysis.tdf_bin files inside .d folders.
Frames can be selected by number or by retention time, and each peak is
reported with its scan, time-of-flight index, intensity, mass-to-charge
ratio and inverse ion mobility. Mass-to-charge ratios and ion mobilities
are computed with built-in open-source calibration, or optionally with
Bruker's proprietary library.
See Łącki et al. (2021) <doi:10.1021/acs.jproteome.0c00962>.
Author: Michal Piotr Startek [aut, cph] ,
Mateusz Krzysztof Lacki [aut, cre, cph] ,
mandreyel [ctb, cph] )
Maintainer: Mateusz Krzysztof Lacki <matteo.lacki@gmail.com>
This is a re-admission after prior archival of version 1.0.13 dated 2022-03-29
Diff between opentimsr versions 1.0.13 dated 2022-03-29 and 1.2.0 dated 2026-10-22
opentimsr-1.0.13/opentimsr/src/bruker_api.h |only opentimsr-1.0.13/opentimsr/src/converters.h |only opentimsr-1.0.13/opentimsr/src/opentims.h |only opentimsr-1.0.13/opentimsr/src/scan2inv_ion_mobility_converter.h |only opentimsr-1.0.13/opentimsr/src/so_manager.h |only opentimsr-1.0.13/opentimsr/src/thread_mgr.h |only opentimsr-1.0.13/opentimsr/src/tof2mz_converter.h |only opentimsr-1.0.13/opentimsr/src/zstd |only opentimsr-1.0.13/opentimsr/src/zstddec_cpl.c |only opentimsr-1.2.0/opentimsr/DESCRIPTION | 55 opentimsr-1.2.0/opentimsr/LICENSE |only opentimsr-1.2.0/opentimsr/MD5 | 112 + opentimsr-1.2.0/opentimsr/NAMESPACE | 15 opentimsr-1.2.0/opentimsr/R/RcppExports.R | 20 opentimsr-1.2.0/opentimsr/R/opentimsr.R | 388 +++-- opentimsr-1.2.0/opentimsr/cleanup |only opentimsr-1.2.0/opentimsr/configure |only opentimsr-1.2.0/opentimsr/inst/CITATION | 15 opentimsr-1.2.0/opentimsr/inst/COPYRIGHTS |only opentimsr-1.2.0/opentimsr/inst/extdata |only opentimsr-1.2.0/opentimsr/man/CloseTIMS.Rd | 8 opentimsr-1.2.0/opentimsr/man/MS1.Rd | 9 opentimsr-1.2.0/opentimsr/man/OpenTIMS.Rd | 12 opentimsr-1.2.0/opentimsr/man/download_bruker_proprietary_code.Rd | 15 opentimsr-1.2.0/opentimsr/man/explore.tdf.tables.Rd | 12 opentimsr-1.2.0/opentimsr/man/get_separate_frames.Rd |only opentimsr-1.2.0/opentimsr/man/length-OpenTIMS-method.Rd | 12 opentimsr-1.2.0/opentimsr/man/min_max_measurements.Rd | 9 opentimsr-1.2.0/opentimsr/man/opentims_set_threads.Rd | 10 opentimsr-1.2.0/opentimsr/man/peaks_per_frame_cnts.Rd | 9 opentimsr-1.2.0/opentimsr/man/query.Rd | 11 opentimsr-1.2.0/opentimsr/man/query_slice.Rd | 12 opentimsr-1.2.0/opentimsr/man/range-OpenTIMS-method.Rd | 20 opentimsr-1.2.0/opentimsr/man/retention_times.Rd | 9 opentimsr-1.2.0/opentimsr/man/rt_query.Rd | 9 opentimsr-1.2.0/opentimsr/man/setup_bruker_so.Rd | 19 opentimsr-1.2.0/opentimsr/man/setup_opensource.Rd |only opentimsr-1.2.0/opentimsr/man/sub-OpenTIMS-method.Rd | 14 opentimsr-1.2.0/opentimsr/man/table2df.Rd | 9 opentimsr-1.2.0/opentimsr/man/tables_names.Rd | 9 opentimsr-1.2.0/opentimsr/man/use_inv_ion_mobility_lookup.Rd |only opentimsr-1.2.0/opentimsr/man/use_mz_lookup.Rd |only opentimsr-1.2.0/opentimsr/src/Makevars.in |only opentimsr-1.2.0/opentimsr/src/Makevars.win |only opentimsr-1.2.0/opentimsr/src/RcppExports.cpp | 62 opentimsr-1.2.0/opentimsr/src/Rinterface.cpp | 365 +++-- opentimsr-1.2.0/opentimsr/src/converters.cpp | 37 opentimsr-1.2.0/opentimsr/src/opentims.cpp | 682 ---------- opentimsr-1.2.0/opentimsr/src/opentims_core |only opentimsr-1.2.0/opentimsr/src/opentimsr_types.h | 454 ------ opentimsr-1.2.0/opentimsr/src/platform_os.h | 14 opentimsr-1.2.0/opentimsr/src/scan2inv_ion_mobility_converter.cpp | 158 -- opentimsr-1.2.0/opentimsr/src/so_manager.cpp | 46 opentimsr-1.2.0/opentimsr/src/thread_mgr.cpp | 125 - opentimsr-1.2.0/opentimsr/src/tof2mz_converter.cpp | 150 -- opentimsr-1.2.0/opentimsr/tests |only 56 files changed, 827 insertions(+), 2079 deletions(-)
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modelling, to calibrate, evaluate, and project
species-environment relationships across space and time using multiple modelling algorithms and
ensemble forecasting. It accommodates diverse ecological data types (presence-only, presence-absence,
counts, multi-class abundance, or relative/absolute abundance) within a unified modelling workflow
which includes cross-validation schemes, pseudo-absence selection strategies, expanded model
parametrization options, a dozen of algorithms, and tools for exploring and visualizing outputs.
Author: Maya Gueguen [aut, cre] ,
Helene Blancheteau [aut],
Remi Lemaire-Patin [aut],
Wilfried Thuiller [aut]
Maintainer: Maya Gueguen <maya.gueguen@univ-grenoble-alpes.fr>
Diff between biomod2 versions 4.3-4-7 dated 2026-10-08 and 4.3-4-8 dated 2026-10-22
DESCRIPTION | 8 - MD5 | 30 ++--- R/BIOMOD_EnsembleModeling.R | 4 R/BIOMOD_Modeling.R | 21 +-- R/biomod2_classes_4.R | 7 - R/bm_CrossValidation.R | 8 - R/bm_FindOptimStat.R | 17 +- R/bm_RangeSize.R | 251 ++++++++++++++++++++---------------------- R/bm_RunModelsLoop.R | 4 R/bm_VariablesImportance.R | 20 +-- README.md | 6 - inst/doc/news.Rmd | 20 +++ inst/doc/news.html | 34 +++++ man/bm_RangeSize.Rd | 55 ++++++--- man/bm_VariablesImportance.Rd | 4 vignettes/news.Rmd | 20 +++ 16 files changed, 299 insertions(+), 210 deletions(-)
Title: 'SPSS'-Compatible Statistical Tools for Survey Data
Description: Statistical analysis of survey data with full support
for survey weights, grouped operations, and 'tidyverse' integration. Provides
80 functions for data import/export ('SPSS', 'Stata', 'SAS', 'Excel') with
label roundtripping and tagged NA preservation, label management (variable
labels, value labels, type conversions, missing value declaration), data
transformation (recoding, dummy coding, standardization, centering),
descriptive statistics, codebook generation, hypothesis testing, correlation
analysis, post-hoc comparisons, weighted statistics, scale analysis,
regression, non-parametric tests, exact tests, factorial ANOVA, and ANCOVA.
Every analysis offers compact print() and detailed summary() output with
toggleable sections. Statistical results are checked against reference
output of 'SPSS' version 29 (see the compatibility vignette for the
status of each function). Methods follow the published
algorithms of IBM Corp. (2023, "IBM SPSS Statistics Algorithms"),
the Lilliefors-correc [...truncated...]
Author: Yannick Diehl [aut, cre]
Maintainer: Yannick Diehl <yannick.diehl@gmail.com>
Diff between mariposa versions 0.7.3 dated 2026-09-28 and 0.7.4 dated 2026-10-22
DESCRIPTION | 16 MD5 | 518 +-- NAMESPACE | 87 NEWS.md | 2168 ++++---------- R/ancova.R | 576 ++- R/binomial_test.R | 333 +- R/broom_methods.R | 58 R/chi_square.R | 769 ++-- R/chisq_gof.R | 376 +- R/codebook.R | 130 R/correlation-engine.R | 324 +- R/crosstab.R | 557 ++- R/data.R | 12 R/describe.R | 396 +- R/dunn_test.R | 84 R/efa.R | 1211 ++++++- R/factorial_anova.R | 502 ++- R/find_var.R | 88 R/fisher_test.R | 356 +- R/frequency.R | 605 +-- R/friedman_test.R | 155 - R/globals.R | 2 R/helpers.R | 555 +++ R/imports.R | 1 R/kendall_tau.R | 202 - R/kernels-weighted.R | 220 + R/kruskal_wallis.R | 197 - R/label_conversion.R | 296 + R/label_management.R | 226 + R/label_missing.R | 96 R/levene_test.R | 913 ++--- R/linear_regression.R | 1100 +++++-- R/logistic_regression.R | 701 +++- R/mann_whitney.R | 299 + R/marginal_effects.R | 214 + R/mcnemar_test.R | 331 +- R/multiple_response.R | 150 R/normality_test.R | 142 R/np-helpers.R |only R/oneway_anova.R | 274 + R/pairwise_wilcoxon.R | 133 R/parametric-helpers.R |only R/partial_cor.R | 92 R/pearson_cor.R | 105 R/posthoc-pairwise.R | 226 - R/print_helpers.R | 178 - R/read_sas.R | 11 R/read_spss.R | 473 ++- R/read_stata.R | 2 R/read_xlsx.R | 4 R/recode.R | 612 ++- R/reexports.R |only R/reliability.R | 565 ++- R/result-export.R |only R/row_operations.R | 134 R/scale_helpers.R | 53 R/scheffe_test.R | 12 R/spearman_rho.R | 71 R/standardize.R | 220 - R/summary_helpers.R | 17 R/t_test.R | 592 ++- R/tukey_test.R | 12 R/utils-format.R | 175 - R/w_factory.R | 447 +- R/w_iqr.R | 33 R/w_kurtosis.R | 25 R/w_mean.R | 21 R/w_median.R | 26 R/w_modus.R | 133 R/w_quantile.R | 180 - R/w_range.R | 15 R/w_sd.R | 24 R/w_se.R | 24 R/w_skew.R | 21 R/w_var.R | 21 R/wilcoxon_test.R | 227 - R/write_sas.R | 116 R/write_spss.R | 250 + R/write_stata.R | 7 R/write_xlsx.R | 541 ++- R/zzz.R | 31 README.md | 34 build/vignette.rds |binary inst/CITATION |only inst/doc/correlation-analysis.R | 4 inst/doc/correlation-analysis.Rmd | 8 inst/doc/correlation-analysis.html | 186 - inst/doc/data-transformation.R | 4 inst/doc/data-transformation.Rmd | 6 inst/doc/data-transformation.html | 222 - inst/doc/descriptive-statistics.R | 6 inst/doc/descriptive-statistics.Rmd | 6 inst/doc/descriptive-statistics.html | 612 ++- inst/doc/hypothesis-testing.Rmd | 2 inst/doc/hypothesis-testing.html | 290 + inst/doc/introduction.Rmd | 7 inst/doc/introduction.html | 301 + inst/doc/labels-and-missing-values.R | 14 inst/doc/labels-and-missing-values.Rmd | 14 inst/doc/labels-and-missing-values.html | 22 inst/doc/regression-analysis.html | 508 +-- inst/doc/scale-analysis.R | 11 inst/doc/scale-analysis.Rmd | 5 inst/doc/scale-analysis.html | 537 ++- inst/doc/spss-compatibility.Rmd | 240 - inst/doc/spss-compatibility.html | 710 +--- inst/doc/survey-weights.html | 355 +- man/ancova.Rd | 24 man/as.data.frame.mariposa.Rd |only man/binomial_test.Rd | 42 man/center.Rd | 15 man/chi_square.Rd | 23 man/chisq_gof.Rd | 20 man/codebook.Rd | 21 man/coef.linear_regression.Rd |only man/confint.linear_regression.Rd |only man/confint.logistic_regression.Rd |only man/copy_labels.Rd | 28 man/crosstab.Rd | 26 man/describe.Rd | 36 man/df.residual.linear_regression.Rd |only man/drop_labels.Rd | 25 man/dunn_test.Rd | 14 man/efa.Rd | 68 man/factorial_anova.Rd | 18 man/find_var.Rd | 25 man/fisher_test.Rd | 25 man/fitted.linear_regression.Rd |only man/frequency.Rd | 36 man/friedman_test.Rd | 17 man/kendall_tau.Rd | 20 man/kruskal_wallis.Rd | 17 man/levene_test.Rd | 37 man/linear_regression.Rd | 35 man/logistic_regression-accessors.Rd |only man/logistic_regression.Rd | 46 man/longitudinal_data.Rd | 5 man/longitudinal_data_wide.Rd | 7 man/mann_whitney.Rd | 41 man/marginal_effects.Rd | 23 man/mariposa-package.Rd | 2 man/mcnemar_test.Rd | 4 man/multiple_response.Rd | 26 man/na_frequencies.Rd | 31 man/nobs.linear_regression.Rd |only man/normality_test.Rd | 6 man/oneway_anova.Rd | 4 man/pairwise_wilcoxon.Rd | 35 man/partial_cor.Rd | 15 man/pearson_cor.Rd | 20 man/phi.Rd | 12 man/pomps.Rd | 8 man/print.crosstab.Rd | 23 man/print.fisher_test.Rd | 6 man/print.frequency.Rd | 22 man/print.linear_regression.Rd | 5 man/print.logistic_regression.Rd | 5 man/print.multiple_response.Rd | 10 man/print.normality_test.Rd | 9 man/print.summary.factorial_anova.Rd | 4 man/print.summary.w_quantile.Rd |only man/print.summary.w_statistic.Rd |only man/print.w_quantile.Rd | 6 man/profile.logistic_regression.Rd |only man/read_spss.Rd | 6 man/read_xpt.Rd | 2 man/rec.Rd | 48 man/reexports.Rd |only man/reliability.Rd | 44 man/residuals.linear_regression.Rd |only man/row_count.Rd | 17 man/row_means.Rd | 30 man/row_sums.Rd | 15 man/scheffe_test.Rd | 6 man/set_na.Rd | 4 man/spearman_rho.Rd | 24 man/std.Rd | 17 man/strip_tags.Rd | 16 man/summary.crosstab.Rd | 5 man/summary.efa.Rd | 4 man/summary.fisher_test.Rd | 3 man/summary.frequency.Rd | 2 man/t_test.Rd | 14 man/to_character.Rd | 4 man/to_dummy.Rd | 13 man/to_label.Rd | 20 man/to_labelled.Rd | 8 man/to_numeric.Rd | 26 man/tukey_test.Rd | 6 man/untag_na.Rd | 18 man/update.linear_regression.Rd |only man/update.logistic_regression.Rd |only man/val_labels.Rd | 21 man/var_label.Rd | 18 man/vcov.linear_regression.Rd |only man/w_iqr.Rd | 25 man/w_kurtosis.Rd | 14 man/w_mean.Rd | 14 man/w_median.Rd | 21 man/w_modus.Rd | 21 man/w_quantile.Rd | 23 man/w_range.Rd | 8 man/w_sd.Rd | 14 man/w_se.Rd | 14 man/w_skew.Rd | 14 man/w_var.Rd | 14 man/wilcoxon_test.Rd | 22 man/write_spss.Rd | 20 man/write_xlsx.Rd | 50 man/write_xpt.Rd | 8 tests/testthat/helper-crosstab-cells.R |only tests/testthat/helper-mariposa.R | 14 tests/testthat/helper-validation-tolerances.R | 47 tests/testthat/test-ancova-spss-validation.R | 646 ++++ tests/testthat/test-audit-regressions.R | 614 +++ tests/testthat/test-binomial-test-spss-validation.R | 99 tests/testthat/test-chi-squared-spss-validation.R | 420 ++ tests/testthat/test-chisq-gof-spss-validation.R | 161 - tests/testthat/test-console-discipline.R | 7 tests/testthat/test-crosstab-spss-validation.R | 1234 +++++++ tests/testthat/test-describe-spss-validation.R | 260 + tests/testthat/test-dunn-test-spss-validation.R | 15 tests/testthat/test-edge-cases.R | 9 tests/testthat/test-efa-spss-validation.R | 600 +++ tests/testthat/test-factorial-anova-spss-validation.R | 439 ++ tests/testthat/test-fisher-test-spss-validation.R | 466 ++- tests/testthat/test-frequency-spss-validation.R | 192 - tests/testthat/test-helpers.R | 6 tests/testthat/test-kendall-tau-spss-validation.R | 466 ++- tests/testthat/test-kruskal-wallis-spss-validation.R | 14 tests/testthat/test-label-conversion.R | 2 tests/testthat/test-levene-test-spss-validation.R | 101 tests/testthat/test-linear-regression-spss-validation.R | 410 ++ tests/testthat/test-mann-whitney-spss-validation.R | 32 tests/testthat/test-mcnemar-test-spss-validation.R | 191 + tests/testthat/test-multiple-response-spss-validation.R | 2 tests/testthat/test-normality-test-spss-validation.R | 6 tests/testthat/test-oneway-anova-spss-validation.R | 639 +++- tests/testthat/test-pairwise-wilcoxon-spss-validation.R | 306 + tests/testthat/test-practice-DESC.R |only tests/testthat/test-practice-IO.R |only tests/testthat/test-practice-NP.R |only tests/testthat/test-practice-PAR.R |only tests/testthat/test-practice-REG.R |only tests/testthat/test-practice-SCALE.R |only tests/testthat/test-practice-X1.R |only tests/testthat/test-practice-X2.R |only tests/testthat/test-practice-X3.R |only tests/testthat/test-practice-X4.R |only tests/testthat/test-print-helpers.R | 226 - tests/testthat/test-print-methods.R | 77 tests/testthat/test-read-sas.R | 4 tests/testthat/test-read-spss.R | 20 tests/testthat/test-read-stata.R | 4 tests/testthat/test-reliability-omega.R | 2 tests/testthat/test-reliability-spss-validation.R | 457 ++ tests/testthat/test-scale-helpers.R | 2 tests/testthat/test-scheffe-spss-validation.R | 667 ++++ tests/testthat/test-spearman-rho-spss-validation.R | 417 ++ tests/testthat/test-summary-methods.R | 35 tests/testthat/test-t-test-spss-validation.R | 782 ++--- tests/testthat/test-tukey-test-spss-validation.R | 703 ++++ tests/testthat/test-validation-discipline.R | 15 tests/testthat/test-weighted-statistics-spss-validation.R | 351 +- tests/testthat/test-weights-invariance.R | 10 tests/testthat/test-wilcoxon-test-spss-validation.R | 127 tests/testthat/test-write-spss.R | 4 tests/testthat/test-write-xlsx.R | 4 vignettes/correlation-analysis.Rmd | 8 vignettes/data-transformation.Rmd | 6 vignettes/descriptive-statistics.Rmd | 6 vignettes/hypothesis-testing.Rmd | 2 vignettes/introduction.Rmd | 7 vignettes/labels-and-missing-values.Rmd | 14 vignettes/scale-analysis.Rmd | 5 vignettes/spss-compatibility.Rmd | 240 - 276 files changed, 26677 insertions(+), 11709 deletions(-)
Title: Safe Zig Bindings
Description: Scaffolds packages backed by Zig and generates a safe native
boundary for plain Zig functions. The generated integration converts
objects at the language boundary, registers native routines, propagates
errors, and compiles across platforms without requiring C++. Each step
of the workflow is a function: locating a supported Zig compiler,
scaffolding the package, scanning the Zig source for exported functions,
rendering and writing the bindings, checking the package before
compilation, and building it with the compiler errors reported by file
and line. The scan, the checks and the generated bindings are pure R; a
Zig compiler is needed only to build a package created with the
scaffold.
Author: Marek Deja [aut, cre]
Maintainer: Marek Deja <marek.deja@uj.edu.pl>
Diff between rzig versions 0.2.3 dated 2026-09-12 and 1.0.0 dated 2026-10-22
rzig-0.2.3/rzig/LICENSE |only rzig-0.2.3/rzig/inst/zig/tools/scan.zig |only rzig-1.0.0/rzig/DESCRIPTION | 29 rzig-1.0.0/rzig/MD5 | 208 +- rzig-1.0.0/rzig/NAMESPACE | 32 rzig-1.0.0/rzig/NEWS.md | 855 +++++++++ rzig-1.0.0/rzig/R/build.R |only rzig-1.0.0/rzig/R/checks.R |only rzig-1.0.0/rzig/R/create.R |only rzig-1.0.0/rzig/R/document.R |only rzig-1.0.0/rzig/R/imports.R |only rzig-1.0.0/rzig/R/install-zig.R |only rzig-1.0.0/rzig/R/known-templates.R |only rzig-1.0.0/rzig/R/lapack.R |only rzig-1.0.0/rzig/R/mixed.R |only rzig-1.0.0/rzig/R/rd.R |only rzig-1.0.0/rzig/R/render.R |only rzig-1.0.0/rzig/R/scan.R |only rzig-1.0.0/rzig/R/source.R |only rzig-1.0.0/rzig/R/status.R |only rzig-1.0.0/rzig/R/test-zig.R |only rzig-1.0.0/rzig/R/update-rzig.R |only rzig-1.0.0/rzig/R/use-ci.R |only rzig-1.0.0/rzig/R/use-rzig.R | 517 +---- rzig-1.0.0/rzig/R/utils.R |only rzig-1.0.0/rzig/R/zig.R |only rzig-1.0.0/rzig/R/zzz.R |only rzig-1.0.0/rzig/README.md | 828 ++++++++- rzig-1.0.0/rzig/build/vignette.rds |binary rzig-1.0.0/rzig/inst/doc/distributing.R |only rzig-1.0.0/rzig/inst/doc/distributing.Rmd |only rzig-1.0.0/rzig/inst/doc/distributing.html |only rzig-1.0.0/rzig/inst/doc/exports.R |only rzig-1.0.0/rzig/inst/doc/exports.Rmd |only rzig-1.0.0/rzig/inst/doc/exports.html |only rzig-1.0.0/rzig/inst/doc/numerics.R |only rzig-1.0.0/rzig/inst/doc/numerics.Rmd |only rzig-1.0.0/rzig/inst/doc/numerics.html |only rzig-1.0.0/rzig/inst/doc/parallel.R |only rzig-1.0.0/rzig/inst/doc/parallel.Rmd |only rzig-1.0.0/rzig/inst/doc/parallel.html |only rzig-1.0.0/rzig/inst/doc/porting-rcpp.R | 73 rzig-1.0.0/rzig/inst/doc/porting-rcpp.Rmd | 172 + rzig-1.0.0/rzig/inst/doc/porting-rcpp.html | 249 +- rzig-1.0.0/rzig/inst/doc/rzig.R |only rzig-1.0.0/rzig/inst/doc/rzig.Rmd |only rzig-1.0.0/rzig/inst/doc/rzig.html |only rzig-1.0.0/rzig/inst/doc/sharing.R |only rzig-1.0.0/rzig/inst/doc/sharing.Rmd |only rzig-1.0.0/rzig/inst/doc/sharing.html |only rzig-1.0.0/rzig/inst/doc/updating.R |only 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rzig-1.0.0/rzig/inst/zig/framework/convert.zig | 927 +++++++++- rzig-1.0.0/rzig/inst/zig/framework/error_state.zig | 83 rzig-1.0.0/rzig/inst/zig/framework/external.zig |only rzig-1.0.0/rzig/inst/zig/framework/generated/arity.zig | 1259 ++++++++++++-- rzig-1.0.0/rzig/inst/zig/framework/generated/manifest.zig | 6 rzig-1.0.0/rzig/inst/zig/framework/io.zig |only rzig-1.0.0/rzig/inst/zig/framework/lapack.zig |only rzig-1.0.0/rzig/inst/zig/framework/matrix.zig | 116 + rzig-1.0.0/rzig/inst/zig/framework/na.zig | 62 rzig-1.0.0/rzig/inst/zig/framework/optimize.zig |only rzig-1.0.0/rzig/inst/zig/framework/panic.zig | 55 rzig-1.0.0/rzig/inst/zig/framework/parallel.zig | 235 ++ rzig-1.0.0/rzig/inst/zig/framework/progress.zig |only rzig-1.0.0/rzig/inst/zig/framework/rcall.zig |only rzig-1.0.0/rzig/inst/zig/framework/record.zig |only rzig-1.0.0/rzig/inst/zig/framework/register.zig | 127 + rzig-1.0.0/rzig/inst/zig/framework/rmath.zig | 214 ++ rzig-1.0.0/rzig/inst/zig/framework/rng.zig | 50 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Title: Echo State Networks for Time Series Modeling and Forecasting
Description: Provides a lightweight implementation of functions and methods for
fast and fully automatic time series modeling and forecasting using Echo
State Networks (ESNs).
Author: Alexander Haeusser [aut, cre, cph]
Maintainer: Alexander Haeusser <alexander-haeusser@gmx.de>
Diff between echos versions 1.0.4 dated 2026-06-15 and 1.0.5 dated 2026-10-22
echos-1.0.4/echos/inst/doc/vignette_01_baseR.R |only echos-1.0.4/echos/inst/doc/vignette_01_baseR.Rmd |only echos-1.0.4/echos/inst/doc/vignette_01_baseR.html |only echos-1.0.4/echos/inst/doc/vignette_02_tidyR.R |only echos-1.0.4/echos/inst/doc/vignette_02_tidyR.Rmd |only echos-1.0.4/echos/inst/doc/vignette_02_tidyR.html |only echos-1.0.4/echos/inst/doc/vignette_03_datasets.R |only echos-1.0.4/echos/inst/doc/vignette_03_datasets.Rmd |only echos-1.0.4/echos/inst/doc/vignette_03_datasets.html |only echos-1.0.4/echos/vignettes/vignette_01_baseR.Rmd |only echos-1.0.4/echos/vignettes/vignette_02_tidyR.Rmd |only echos-1.0.4/echos/vignettes/vignette_03_datasets.Rmd |only echos-1.0.5/echos/DESCRIPTION | 11 echos-1.0.5/echos/MD5 | 103 - echos-1.0.5/echos/NAMESPACE | 77 - echos-1.0.5/echos/NEWS.md | 7 echos-1.0.5/echos/R/RcppExports.R | 6 echos-1.0.5/echos/R/echos-package.R | 1 echos-1.0.5/echos/R/forecast_esn.R | 13 echos-1.0.5/echos/R/methods-fable.R | 20 echos-1.0.5/echos/R/train_esn.R | 15 echos-1.0.5/echos/R/tune_esn.R | 13 echos-1.0.5/echos/README.md | 22 echos-1.0.5/echos/build/partial.rdb |only echos-1.0.5/echos/build/vignette.rds |binary echos-1.0.5/echos/inst/doc/vignette_100_base_airpassengers.R |only echos-1.0.5/echos/inst/doc/vignette_100_base_airpassengers.Rmd |only echos-1.0.5/echos/inst/doc/vignette_100_base_airpassengers.html |only echos-1.0.5/echos/inst/doc/vignette_201_tidy_m4_monthly_models.R |only echos-1.0.5/echos/inst/doc/vignette_201_tidy_m4_monthly_models.Rmd |only echos-1.0.5/echos/inst/doc/vignette_201_tidy_m4_monthly_models.html |only echos-1.0.5/echos/inst/doc/vignette_202_tidy_m4_monthly_splits.R |only echos-1.0.5/echos/inst/doc/vignette_202_tidy_m4_monthly_splits.Rmd |only echos-1.0.5/echos/inst/doc/vignette_202_tidy_m4_monthly_splits.html |only echos-1.0.5/echos/inst/doc/vignette_300_datasets.R |only echos-1.0.5/echos/inst/doc/vignette_300_datasets.Rmd |only echos-1.0.5/echos/inst/doc/vignette_300_datasets.html |only echos-1.0.5/echos/man/ESN.Rd | 20 echos-1.0.5/echos/man/figures/README-base-1.svg | 124 +- echos-1.0.5/echos/man/figures/README-tidy-1.svg | 550 +++++----- echos-1.0.5/echos/man/filter_esn.Rd | 20 echos-1.0.5/echos/man/fitted.ESN.Rd | 20 echos-1.0.5/echos/man/forecast.ESN.Rd | 20 echos-1.0.5/echos/man/forecast_esn.Rd | 35 echos-1.0.5/echos/man/glance.ESN.Rd | 20 echos-1.0.5/echos/man/is.esn.Rd | 24 echos-1.0.5/echos/man/is.forecast_esn.Rd | 24 echos-1.0.5/echos/man/is.tune_esn.Rd | 24 echos-1.0.5/echos/man/model_sum.ESN.Rd | 20 echos-1.0.5/echos/man/plot.esn.Rd | 24 echos-1.0.5/echos/man/plot.forecast_esn.Rd | 24 echos-1.0.5/echos/man/plot.tune_esn.Rd | 24 echos-1.0.5/echos/man/print.esn.Rd | 24 echos-1.0.5/echos/man/report.ESN.Rd | 20 echos-1.0.5/echos/man/reservoir.Rd | 20 echos-1.0.5/echos/man/residuals.ESN.Rd | 20 echos-1.0.5/echos/man/run_reservoir.Rd | 7 echos-1.0.5/echos/man/summary.esn.Rd | 24 echos-1.0.5/echos/man/summary.tune_esn.Rd | 24 echos-1.0.5/echos/man/tidy.ESN.Rd | 20 echos-1.0.5/echos/man/train_esn.Rd | 35 echos-1.0.5/echos/man/tune_esn.Rd | 35 echos-1.0.5/echos/src/run_reservoir.cpp | 9 echos-1.0.5/echos/vignettes/vignette_100_base_airpassengers.Rmd |only echos-1.0.5/echos/vignettes/vignette_201_tidy_m4_monthly_models.Rmd |only echos-1.0.5/echos/vignettes/vignette_202_tidy_m4_monthly_splits.Rmd |only echos-1.0.5/echos/vignettes/vignette_300_datasets.Rmd |only 67 files changed, 778 insertions(+), 721 deletions(-)
Title: Your Go-to Motif Accountant
Description: Provides the 'C++' header-only library 'barry' for use in R packages.
'barry' is a 'C++' template library for counting sufficient statistics on binary
arrays and building discrete exponential-family models. It provides tools for
sparse arrays, user-defined count statistics, support set constraints,
power set generation, and includes modules for Discrete Exponential Family Models
(DEFMs) and network statistics. By placing these headers in this package, we
offer an efficient distribution system for CRAN as replication of this code in
the sources of other packages is avoided. This package follows the same
approach as the 'BH' package which provides 'Boost' headers for R packages.
Author: George Vega Yon [aut, cre] ,
U.S. Army Medical Research Acquisition Activity [fnd] ,
National Cancer Institute [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between barry versions 0.2.2 dated 2026-07-22 and 0.3.0 dated 2026-10-22
DESCRIPTION | 6 MD5 | 20 + NEWS.md | 23 ++ R/barry-package.R | 3 R/zzz.R |only README.md | 11 + inst/CITATION |only inst/include/barry/barry.hpp | 4 inst/include/barry/model-bones.hpp | 44 ++++ inst/include/barry/model-meat.hpp | 310 ++++++++++++++++++++++++++++- inst/include/barry/models/defm/formula.hpp | 118 ++++++----- man/barry-package.Rd | 4 12 files changed, 475 insertions(+), 68 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-31 0.1.3
2021-05-24 0.1.2
2020-03-26 0.1.1
2017-06-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-09-30 0.4.1
2026-09-13 0.4.0
2026-06-01 0.3.0
2026-01-12 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-02-13 0.1.1
2024-06-17 0.1.0
Title: Analysis of Diffusion and Contagion Processes on Networks
Description: Empirical statistical analysis, visualization and simulation of
diffusion and contagion processes on networks. The package implements algorithms
for calculating network diffusion statistics such as transmission rate, hazard
rates, exposure models, network threshold levels, infectiousness (contagion),
and susceptibility. The package is inspired by work published in Valente,
et al., (2015) <DOI:10.1016/j.socscimed.2015.10.001>; Valente (1995) <ISBN:
9781881303213>, Myers (2000) <DOI:10.1086/303110>, Iyengar and others (2011)
<DOI:10.1287/mksc.1100.0566>, Burt (1987) <DOI:10.1086/228667>; among others.
Author: George Vega Yon [aut, cre] ,
Thomas Valente [aut, cph] ,
Anibal Olivera Morales [aut, ctb] ,
Stephanie Dyal [ctb] ,
Timothy Hayes [ctb]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between netdiffuseR versions 1.25.0 dated 2026-04-10 and 1.25.1 dated 2026-10-22
DESCRIPTION | 8 MD5 | 45 - NEWS.md | 14 R/diffnet-class.r | 2 R/misc.r | 5 R/zzz.R |only README.md | 11 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 70 +- inst/doc/analyzing-medical-innovation-data.Rmd | 5 inst/doc/analyzing-medical-innovation-data.html | 236 +++++----- inst/doc/introduction-to-netdiffuser.Rmd | 5 inst/doc/introduction-to-netdiffuser.html | 7 inst/doc/not-lost-in-translation-importing-and-exporting-graphs.Rmd | 5 inst/doc/not-lost-in-translation-importing-and-exporting-graphs.html | 7 inst/doc/time_discount_suscep_infect.Rmd | 5 inst/doc/time_discount_suscep_infect.html | 7 tests/testthat/test-rdiffnet.R | 17 tests/testthat/test-struct_equiv.R | 14 vignettes/analyzing-medical-innovation-data.Rmd | 5 vignettes/introduction-to-netdiffuser.Rmd | 5 vignettes/not-lost-in-translation-importing-and-exporting-graphs.Rmd | 5 vignettes/time_discount_suscep_infect.Rmd | 5 24 files changed, 312 insertions(+), 171 deletions(-)
Title: Extract Glycan Motifs from Glycan Structures
Description: Identify, count, and match recurring substructures in glycan structures.
Supports concrete and generic monosaccharide matching, several structural
alignment modes, node-to-node mappings, and batch analysis using subgraph
isomorphism. Includes curated motif annotations derived from the
'GlycoMotif' resource <https://glycomotif.glyomics.org/>. Integrates with
'glyrepr' and 'glyparse' for structural glycomics workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glymotif versions 1.0.0 dated 2026-10-07 and 1.0.1 dated 2026-10-22
DESCRIPTION | 6 MD5 | 16 NEWS.md | 4 README.md | 8 inst/doc/glymotif.html | 683 ++++++++++++++---------------------- inst/doc/motif-matching.html | 527 +++++++++++---------------- src/extract-motifs.cpp | 3 src/structure-matcher.cpp | 2 tests/testthat/test-extract-motif.R | 44 ++ 9 files changed, 562 insertions(+), 731 deletions(-)