Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous posterior
distributions with a customizable trajectory length termination criterion.
See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for the original
Discontinuous Hamiltonian Monte Carlo; Hoffman et al. (2014)
<doi:10.48550/arXiv.1111.4246> and Betancourt (2016) <doi:10.48550/arXiv.1601.00225>
for the definition of possible Hamiltonian Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@phd.unipd.it>
Diff between XDNUTS versions 1.6.1 dated 2025-08-24 and 1.6.3 dated 2025-09-07
DESCRIPTION | 34 +++--- MD5 | 52 ++++----- R/interface.R | 7 + build/partial.rdb |binary inst/doc/Tutorial_for_main_functions.R | 8 - inst/doc/Tutorial_for_main_functions.Rmd | 8 - inst/doc/Tutorial_for_main_functions.html | 14 +- src/Makevars | 1 src/Makevars.win | 2 src/dnuts.cpp | 69 ++++++------ src/epsilon_adapt.cpp | 103 +++++++++---------- src/epsilon_adapt.h | 11 ++ src/epsilon_init.cpp | 45 ++++---- src/epsilon_init.h | 3 src/globals_functions.cpp | 6 + src/globals_functions.h | 6 + src/globals_interact.h | 2 src/leapfrog.cpp | 43 ++++---- src/leapfrog.h | 5 src/mcmc.h | 8 + src/recursive_tree.cpp | 161 +++++++++++++++--------------- src/recursive_tree.h | 5 src/single_hmc.cpp | 36 +++--- src/single_hmc.h | 5 src/single_nuts.cpp | 48 ++++---- src/single_nuts.h | 5 vignettes/Tutorial_for_main_functions.Rmd | 8 - 27 files changed, 380 insertions(+), 315 deletions(-)
Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data
Analysis
Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between wnl versions 0.8.3 dated 2025-03-22 and 0.8.4 dated 2025-09-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/nComp.R | 2 +- R/nlr.R | 4 +++- inst/NEWS.Rd | 6 ++++++ 5 files changed, 17 insertions(+), 9 deletions(-)
Title: Articulatory Data Processing in R
Description: A tool for processing Articulate
Assistant Advanced™ (AAA) ultrasound tongue imaging data and Carstens AG500/1 electro-magnetic articulographic data.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between rticulate versions 2.0.1 dated 2025-02-20 and 2.2.0 dated 2025-09-07
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 12 ++++++++++++ R/transform.R | 14 +++++++++++--- build/vignette.rds |binary inst/doc/filter-signals.html | 4 ++-- inst/doc/overview.html | 4 ++-- inst/doc/polar-gams.html | 34 +++++++++++++++++----------------- inst/doc/tongue-imaging.html | 4 ++-- inst/doc/transform-coord.R | 22 +++++++++++++--------- inst/doc/transform-coord.Rmd | 24 ++++++++++++++---------- inst/doc/transform-coord.html | 37 +++++++++++++++++++------------------ vignettes/transform-coord.Rmd | 24 ++++++++++++++---------- 13 files changed, 122 insertions(+), 89 deletions(-)
Title: Use Time Series to Generate and Compare Power Spectral Density
Description: Functions that allow you to generate and compare power spectral density (PSD)
plots given time series data. Fast Fourier Transform (FFT) is used to take a time series
data, analyze the oscillations, and then output the frequencies of these oscillations
in the time series in the form of a PSD plot.Thus given a time series, the dominant
frequencies in the time series can be identified. Additional functions in this package
allow the dominant frequencies of multiple groups of time series to be compared with each other.
To see example usage with the main functions of this package, please visit
this site: <https://yhhc2.github.io/psdr/articles/Introduction.html>.
The mathematical operations used to generate the PSDs are described in these sites:
<https://www.mathworks.com/help/matlab/ref/fft.html>.
<https://www.mathworks.com/help/signal/ug/power-spectral-density-estimates-using-fft.html>.
Author: Yong-Han Hank Cheng [aut, cre]
Maintainer: Yong-Han Hank Cheng <yhhc@uw.edu>
Diff between psdr versions 1.0.1 dated 2021-06-04 and 1.0.3 dated 2025-09-07
DESCRIPTION | 16 LICENSE | 4 MD5 | 24 NEWS.md | 10 README.md | 1 build/vignette.rds |binary inst/doc/Examples.R | 8 inst/doc/Examples.html | 1889 ++++++++++++++++++++++----------------------- inst/doc/Introduction.R | 38 inst/doc/Introduction.html | 600 +++++++------- man/GenerateExampleData.Rd | 28 tests/testthat.R | 8 tests/testthat/test-PSD.R | 145 +-- 13 files changed, 1408 insertions(+), 1363 deletions(-)
Title: Compute Neural Fragility for Ictal iEEG Time Series
Description: Provides tools to compute the neural fragility matrix from intracranial electrocorticographic (iEEG) recordings, enabling the analysis of brain dynamics during seizures. The package implements the method described by Li et al. (2017) <doi:10.23919/ACC.2017.7963378> and includes functions for data preprocessing ('Epoch'), fragility computation ('calcAdjFrag'), and visualization.
Author: Jiefei Wang [aut, cre] ,
Patrick Karas [aut],
Anne-Cecile Lesage [aut] ,
Ioannis Malagaris [aut] ,
Oliver Zhou [aut],
Liliana Camarillo Rodriguez [aut] ,
Sean O'Leary [aut] ,
Yuanyi Zhang [aut]
Maintainer: Jiefei Wang <szwjf08@gmail.com>
Diff between EZFragility versions 1.0.3 dated 2025-04-10 and 2.0.1 dated 2025-09-07
EZFragility-1.0.3/EZFragility/R/class_Epoch.r |only EZFragility-1.0.3/EZFragility/man/Epoch-class.Rd |only EZFragility-1.0.3/EZFragility/man/Epoch-method.Rd |only EZFragility-1.0.3/EZFragility/man/Epoch.Rd |only EZFragility-1.0.3/EZFragility/man/visuIEEGData.Rd |only EZFragility-1.0.3/EZFragility/tests/testthat/test-Epoch.R |only EZFragility-1.0.3/EZFragility/tests/testthat/test-truncateTime.R |only EZFragility-2.0.1/EZFragility/DESCRIPTION | 51 +- EZFragility-2.0.1/EZFragility/MD5 | 65 +- EZFragility-2.0.1/EZFragility/NAMESPACE | 32 - EZFragility-2.0.1/EZFragility/R/class_AAA.r | 6 EZFragility-2.0.1/EZFragility/R/class_FragStat.r | 11 EZFragility-2.0.1/EZFragility/R/class_Fragility.r | 8 EZFragility-2.0.1/EZFragility/R/fragStat.r | 83 ++- EZFragility-2.0.1/EZFragility/R/main.r | 31 - EZFragility-2.0.1/EZFragility/R/sysdata.rda |binary EZFragility-2.0.1/EZFragility/R/utils.r | 23 EZFragility-2.0.1/EZFragility/R/visualization.R | 255 ++++------ EZFragility-2.0.1/EZFragility/R/zzz.R | 8 EZFragility-2.0.1/EZFragility/README.md | 7 EZFragility-2.0.1/EZFragility/build/vignette.rds |binary EZFragility-2.0.1/EZFragility/data/pt01EcoG.rda |binary EZFragility-2.0.1/EZFragility/data/pt01Frag.rda |binary EZFragility-2.0.1/EZFragility/inst/doc/Intro_to_EZFragility.R | 36 - EZFragility-2.0.1/EZFragility/inst/doc/Intro_to_EZFragility.Rmd | 58 +- EZFragility-2.0.1/EZFragility/inst/doc/Intro_to_EZFragility.html | 207 ++++---- EZFragility-2.0.1/EZFragility/inst/doc/manuscript_reproducible.R |only EZFragility-2.0.1/EZFragility/inst/doc/manuscript_reproducible.Rmd |only EZFragility-2.0.1/EZFragility/inst/doc/manuscript_reproducible.html |only EZFragility-2.0.1/EZFragility/man/calcAdjFrag.Rd | 7 EZFragility-2.0.1/EZFragility/man/estimateSOZ.Rd | 9 EZFragility-2.0.1/EZFragility/man/fragStat.Rd | 21 EZFragility-2.0.1/EZFragility/man/plotFragHeatmap.Rd | 57 +- EZFragility-2.0.1/EZFragility/man/show-FragStat-method.Rd | 34 - EZFragility-2.0.1/EZFragility/man/show-Fragility-method.Rd | 34 - EZFragility-2.0.1/EZFragility/tests/testthat/test-fragStat.R | 2 EZFragility-2.0.1/EZFragility/tests/testthat/test-visualization.R | 4 EZFragility-2.0.1/EZFragility/vignettes/Intro_to_EZFragility.Rmd | 58 +- EZFragility-2.0.1/EZFragility/vignettes/manuscript_reproducible.Rmd |only 39 files changed, 604 insertions(+), 503 deletions(-)
Title: Crosstables for Descriptive Analyses
Description: Create descriptive tables for continuous and categorical variables.
Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'.
You can also compute effect sizes and statistical tests if needed.
Author: Dan Chaltiel [aut, cre] ,
David Hajage [ccp]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between crosstable versions 0.8.1 dated 2024-11-01 and 0.8.2 dated 2025-09-07
DESCRIPTION | 17 ++-- MD5 | 54 ++++++------- NAMESPACE | 2 NEWS.md | 12 +++ R/cross_numeric.R | 5 - R/labels.R | 45 ++++++++--- R/officer.R | 7 - R/options.R | 2 R/utils.R | 37 +++++---- README.md | 24 +----- inst/doc/crosstable-report.R | 2 inst/doc/crosstable-report.html | 9 +- inst/doc/crosstable-selection.html | 48 +++++++----- inst/doc/crosstable.R | 2 inst/doc/crosstable.Rmd | 2 inst/doc/crosstable.html | 44 +++++++---- inst/doc/percent_pattern.html | 28 +++++-- man/apply_labels.Rd | 9 +- tests/testthat/_snaps/by_numeric.md | 141 ++++++++++++++++++++++++++++-------- tests/testthat/_snaps/options.md | 73 +++++++++++++++--- tests/testthat/_snaps/pivot.md | 27 +++++- tests/testthat/_snaps/tests.md | 55 +++++++------- tests/testthat/test-by_factor.R | 1 tests/testthat/test-by_numeric.R | 64 +++++++--------- tests/testthat/test-effects.R | 3 tests/testthat/test-options.R | 24 +++++- tests/testthat/test-tests.R | 25 +++++- vignettes/crosstable.Rmd | 2 28 files changed, 507 insertions(+), 257 deletions(-)
Title: Survey Analysis with Auxiliary Discretized Variables
Description: Probability surveys often use auxiliary continuous data from administrative records, but the utility of this data is diminished when it is discretized for confidentiality. We provide a set of survey estimators to make full use of information from the discretized variables. See Williams, S.Z., Zou, J., Liu, Y., Si, Y., Galea, S. and Chen, Q. (2024), Improving Survey Inference Using Administrative Records Without Releasing Individual-Level Continuous Data. Statistics in Medicine, 43: 5803-5813. <doi:10.1002/sim.10270> for details.
Author: Jungang Zou [aut, cre],
Yutao Liu [aut],
Sharifa Williams [aut],
Qixuan Chen [aut]
Maintainer: Jungang Zou <jungang.zou@gmail.com>
Diff between AuxSurvey versions 1.0 dated 2024-12-20 and 1.1 dated 2025-09-07
DESCRIPTION | 8 ++--- MD5 | 18 +++++------ R/AuxSurvey.R | 45 +++++++++------------------- inst/doc/introduction.html | 6 +-- man/auxsurvey.Rd | 72 +++++++++++++++++++-------------------------- man/postStr_wt.Rd | 20 ++++++------ man/rake_wt.Rd | 20 ++++++------ man/simulate.Rd | 16 ++++------ man/svyBayesmod.Rd | 35 +++++++++------------ man/uwt.Rd | 24 +++++++-------- 10 files changed, 116 insertions(+), 148 deletions(-)
Title: Statistical Tools for Immune Correlates Analysis of Vaccine
Clinical Trial Data
Description: Various semiparametric and nonparametric statistical tools for
immune correlates analysis of vaccine clinical trial data. This includes
calculation of summary statistics and estimation of risk, vaccine efficacy,
controlled effects (controlled risk and controlled vaccine efficacy), and
mediation effects (natural direct effect, natural indirect effect,
proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022)
<doi:10.1093/biostatistics/kxac024> and Fay MP and Follmann DA (2023)
<doi:10.48550/arXiv.2208.06465>.
Author: Avi Kenny [aut, cre]
Maintainer: Avi Kenny <avi.kenny@gmail.com>
Diff between vaccine versions 1.3.0 dated 2025-01-07 and 1.3.1 dated 2025-09-07
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 9 +++++++++ R/load_data.R | 1 + R/plots.R | 21 ++++++++++++++------- R/vaccine-package.R | 7 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/vaccine.html | 10 +++++----- man/hvtn505.Rd | 7 +++++-- man/plot_ce.Rd | 10 +++++++++- tests/testthat/test-test-core-functions.R | 2 +- 12 files changed, 63 insertions(+), 32 deletions(-)
Title: Tools for Causal Inference with Possibly Invalid Instrumental
Variables
Description: Two stage curvature identification with machine learning for causal
inference in settings when instrumental variable regression is not suitable
because of potentially invalid instrumental variables. Based on Guo and
Buehlmann (2022) "Two Stage Curvature Identification with Machine Learning:
Causal Inference with Possibly Invalid Instrumental Variables"
<doi:10.48550/arXiv.2203.12808>. The vignette is available in Carl, Emmenegger, Bühlmann and Guo (2025)
"TSCI: Two Stage Curvature Identification for Causal Inference with Invalid Instruments in R" <doi:10.18637/jss.v114.i07>.
Author: David Carl [aut, cre] ,
Corinne Emmenegger [aut] ,
Wei Yuan [aut],
Mengchu Zheng [aut],
Zijian Guo [aut]
Maintainer: David Carl <david.carl@phd.unibocconi.it>
Diff between TSCI versions 3.0.4 dated 2023-10-09 and 3.0.5 dated 2025-09-07
DESCRIPTION | 18 +++++++++--------- MD5 | 20 ++++++++++---------- R/tsci_boosting.R | 6 +++--- R/tsci_forest.R | 6 +++--- R/tsci_poly.R | 6 +++--- R/tsci_secondstage.R | 6 +++--- inst/CITATION | 43 +++++++++++++++++++++---------------------- man/tsci_boosting.Rd | 6 +++--- man/tsci_forest.Rd | 6 +++--- man/tsci_poly.Rd | 6 +++--- man/tsci_secondstage.Rd | 6 +++--- 11 files changed, 64 insertions(+), 65 deletions(-)
Title: Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng [aut, cre]
Maintainer: Riyan Cheng <riyancheng@hotmail.com>
Diff between QTLRel versions 1.14 dated 2023-08-08 and 1.15 dated 2025-09-07
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/pedRecode.R | 40 ++++++++++++++++++++++++++++------------ data/miscEx.RData |binary inst/doc/QTLRel_Tutorial.pdf |binary man/ibs.Rd | 2 +- 7 files changed, 40 insertions(+), 23 deletions(-)
Title: A Comprehensive Collection of Neuroscience and Brain-Related
Datasets
Description: Offers a rich and diverse collection of datasets focused on the brain, nervous system, and related disorders.
The package includes clinical, experimental, neuroimaging, behavioral, cognitive, and simulated data on conditions such as Parkinson's disease, Alzheimer's, epilepsy, schizophrenia, gliomas, and mental health.
Datasets cover structural and functional brain data, neurotransmission, gene expression, cognitive performance, and treatment outcomes.
Designed for researchers, neuroscientists, clinicians, psychologists, data scientists, and students, this package facilitates exploratory data analysis, statistical modeling, and hypothesis testing in neuroscience and neuroepidemiology.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between NeuroDataSets versions 0.1.0 dated 2025-05-27 and 0.2.0 dated 2025-09-07
NeuroDataSets-0.1.0/NeuroDataSets/R/view_datasets_neuro.R |only NeuroDataSets-0.1.0/NeuroDataSets/man/view_datasets_neuro.Rd |only NeuroDataSets-0.2.0/NeuroDataSets/DESCRIPTION | 12 NeuroDataSets-0.2.0/NeuroDataSets/MD5 | 96 +++--- NeuroDataSets-0.2.0/NeuroDataSets/NAMESPACE | 2 NeuroDataSets-0.2.0/NeuroDataSets/NEWS.md |only NeuroDataSets-0.2.0/NeuroDataSets/R/data-documentation.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/R/neurodatasets-package.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/R/view_datasets_NeuroDataSets.R |only NeuroDataSets-0.2.0/NeuroDataSets/README.md | 2 NeuroDataSets-0.2.0/NeuroDataSets/build/vignette.rds |binary NeuroDataSets-0.2.0/NeuroDataSets/inst/CITATION | 10 NeuroDataSets-0.2.0/NeuroDataSets/inst/doc/introduction_to_neurodatasets.R | 7 NeuroDataSets-0.2.0/NeuroDataSets/inst/doc/introduction_to_neurodatasets.Rmd | 17 - NeuroDataSets-0.2.0/NeuroDataSets/inst/doc/introduction_to_neurodatasets.html | 156 +++++----- NeuroDataSets-0.2.0/NeuroDataSets/inst/licenses/LICENSE | 2 NeuroDataSets-0.2.0/NeuroDataSets/man/view_datasets_NeuroDataSets.Rd |only NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-aba_phenotype_data_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-ability_intelligence_list.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-adolescent_mental_health_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-alzheimer_smoking_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-alzheimers_biomarkers_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-bilingual_brains_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-blood_brain_barrier_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-brain_litter_mammals_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-brain_size_iq_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-brain_string_players_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-brains_cognitive_matrix.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-cocaine_dopamine_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-dopamine_schizophrenia_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-epilepsy_RCT_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-epilepsy_drug_qol_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-epilepsy_drug_trial_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-gm_expected_patterns_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-guineapig_neurotransmission_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-hippocampus_lesions_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-mammals_brain_body_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-markers_brain_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-markers_human_brain_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-markers_mouse_brain_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-migraine_treatment_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-neanderthal_brains_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-neuro_pointprocess_matrix.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-neurocognitive_psychiatric_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-oasis_dementia_mri_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-parkinsons_dopamine_list.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-pediatric_glioma_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-sleep_performance_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-subcortical_patterns_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-view_datasets_NeuroDataSets.R |only NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-white_matter_patterns_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/vignettes/introduction_to_neurodatasets.Rmd | 17 - 52 files changed, 226 insertions(+), 165 deletions(-)
Title: Ecological Indices Calculator for Nematode Communities
Description: Provides a computational toolkit for analyzing nematode communities in ecological studies.
Includes methods to quantify nematode-based ecological indicators such as metabolic footprints,
energy flow metrics, and community structure. These tools support assessments of soil health,
ecosystem functioning, and trophic interactions, standardizing the use of nematodes as
bioindicators.
Author: Yuxuan He [aut, cre, cph] ,
Dong Wang [ths, cph]
Maintainer: Yuxuan He <heyuxuan@henu.edu.cn>
Diff between Nematode versions 0.2.0 dated 2025-08-20 and 0.2.1 dated 2025-09-07
DESCRIPTION | 17 ++++++------- MD5 | 9 ++++--- NEWS.md |only R/ecological_indices.R | 57 +++++++++++----------------------------------- man/Ecological.Indices.Rd | 41 ++++----------------------------- man/cal.SRI.Rd | 16 ++++-------- 6 files changed, 37 insertions(+), 103 deletions(-)
Title: Correction of Preprocessed MS Data
Description: An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) <doi:10.1021/acs.analchem.2c04632>). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.
Author: Allison Mason [aut] ,
Gregory Johnson [aut] ,
Patrick Schloss [aut, cre, cph]
Maintainer: Patrick Schloss <pschloss@umich.edu>
Diff between mpactr versions 0.2.1 dated 2025-03-28 and 0.3.0 dated 2025-09-07
DESCRIPTION | 14 - MD5 | 80 +++++---- NEWS.md | 8 R/RcppExports.R | 4 R/data.R | 2 R/filter_pactr-accessors.R | 1 R/filter_pactr-methods.R | 50 +++--- R/filters.R | 21 -- R/import_data.R | 7 R/peak_table_formatter.R | 35 ++-- R/quality_control.R | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/downstream_analyses.R | 2 inst/doc/downstream_analyses.Rmd | 8 inst/doc/downstream_analyses.html | 223 +++++++++++++-------------- inst/doc/mpactr.R | 12 - inst/doc/mpactr.Rmd | 26 +-- inst/doc/mpactr.html | 108 ++++++------- inst/doc/reference_semantics.html | 5 man/cultures_data.Rd | 2 man/filter_cv.Rd | 13 - man/filter_group.Rd | 2 man/filter_mispicked_ions.Rd | 2 man/get_cv_data.Rd | 1 man/import_data.Rd | 6 man/qc_summary.Rd | 8 src/CvFilter.cpp |only src/CvFilter.h |only src/FeatureData.h |only src/IntensityPeaks.h |only src/Makevars |only src/Math.h |only src/RcppExports.cpp | 15 + src/main.cpp | 13 + tests/testthat/test-filter_pactr-accessors.R | 4 tests/testthat/test-filter_pactr-class.R | 4 tests/testthat/test-filter_pactr-methods.R | 13 - tests/testthat/test-filters.R | 65 +++---- tests/testthat/test-import_data.R | 85 ++++++++++ tests/testthat/test-peak_table_formatter.R | 2 tests/testthat/test-quality_control.R | 2 vignettes/downstream_analyses.Rmd | 8 vignettes/mpactr.Rmd | 26 +-- 44 files changed, 489 insertions(+), 396 deletions(-)
Title: Learning from Black-Box Models by Maximum Interpretation
Decomposition
Description: The goal of 'midr' is to provide a model-agnostic method for interpreting and explaining black-box predictive models by creating a globally interpretable surrogate model. The package implements 'Maximum Interpretation Decomposition' (MID), a functional decomposition technique that finds an optimal additive approximation of the original model. This approximation is achieved by minimizing the squared error between the predictions of the black-box model and the surrogate model. The theoretical foundations of MID are described in Iwasawa & Matsumori (2025) [Forthcoming], and the package itself is detailed in Asashiba et al. (2025) <doi:10.48550/arXiv.2506.08338>.
Author: Ryoichi Asashiba [aut, cre],
Hirokazu Iwasawa [aut],
Reiji Kozuma [ctb]
Maintainer: Ryoichi Asashiba <ryoichi.asashiba@gmail.com>
This is a re-admission after prior archival of version 0.5.1 dated 2025-08-27
Diff between midr versions 0.5.1 dated 2025-08-27 and 0.5.2 dated 2025-09-07
DESCRIPTION | 12 +++---- MD5 | 68 +++++++++++++++++++++---------------------- NEWS.md | 10 ++++++ R/color_theme.R | 2 - R/color_theme_info.R | 2 - R/ggmid_mid_breakdown.R | 8 ++--- R/ggmid_mid_conditional.R | 4 +- R/ggmid_mid_importance.R | 12 +++---- R/interpret.R | 4 +- R/mid_conditional.R | 12 +++---- R/mid_effect.R | 2 - R/mid_plots.R | 10 +++--- R/plot_mid_breakdown.R | 6 +-- R/plot_mid_importance.R | 10 +++--- R/scale_color_theme.R | 2 - R/summary_mid.R | 2 - R/weighted_quantile.R | 4 +- R/zzz.R | 1 README.md | 5 +-- man/color.theme.Rd | 2 - man/color.theme.info.Rd | 2 - man/ggmid.mid.breakdown.Rd | 6 +-- man/ggmid.mid.conditional.Rd | 4 +- man/ggmid.mid.importance.Rd | 6 +-- man/interpret.Rd | 4 +- man/mid.conditional.Rd | 8 ++--- man/mid.effect.Rd | 2 - man/mid.plots.Rd | 6 +-- man/midr-package.Rd | 2 - man/plot.mid.breakdown.Rd | 4 +- man/plot.mid.importance.Rd | 6 +-- man/scale_color_theme.Rd | 2 - man/summary.mid.Rd | 2 - man/weighted.quantile.Rd | 2 - man/weighted.tabulate.Rd | 2 - 35 files changed, 123 insertions(+), 113 deletions(-)
Title: Foundations Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver," symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.20 dated 2025-08-21 and 1.21 dated 2025-09-07
DESCRIPTION | 10 +++---- MD5 | 40 +++++++++++++++---------------- NEWS.md | 11 -------- README.md | 2 - man/adult.Rd | 8 ++---- man/advertising.Rd | 4 +-- man/bank.Rd | 4 +-- man/caravan.Rd | 2 - man/cereal.Rd | 8 +++--- man/churn.Rd | 13 ++++++++-- man/churnCredit.Rd | 2 - man/churnTel.Rd | 2 - man/corona.Rd | 7 +++-- man/house.Rd | 4 +-- man/housePrice.Rd | 64 +++++++++++++++++++++++++-------------------------- man/insurance.Rd | 4 +-- man/liver-package.Rd | 2 - man/marketing.Rd | 4 +-- man/redWines.Rd | 4 +-- man/risk.Rd | 4 +++ man/whiteWines.Rd | 4 +-- 21 files changed, 103 insertions(+), 100 deletions(-)
Title: Guillem Hurault Functions' Library
Description: Contains various functions for data analysis, notably helpers and diagnostics for Bayesian modelling using Stan.
Author: Guillem Hurault [aut, cre]
Maintainer: Guillem Hurault <ghurault.dev@outlook.com>
Diff between HuraultMisc versions 1.1.1 dated 2021-09-06 and 1.2.1 dated 2025-09-07
HuraultMisc-1.1.1/HuraultMisc/R/illustrations.R |only HuraultMisc-1.1.1/HuraultMisc/man/illustrate_RPS.Rd |only HuraultMisc-1.1.1/HuraultMisc/man/illustrate_forward_chaining.Rd |only HuraultMisc-1.1.1/HuraultMisc/tests/testthat/test-illustrations.R |only HuraultMisc-1.2.1/HuraultMisc/DESCRIPTION | 25 - HuraultMisc-1.2.1/HuraultMisc/MD5 | 115 +++-- HuraultMisc-1.2.1/HuraultMisc/NAMESPACE | 3 HuraultMisc-1.2.1/HuraultMisc/NEWS.md | 16 HuraultMisc-1.2.1/HuraultMisc/R/HuraultMisc-package.R | 2 HuraultMisc-1.2.1/HuraultMisc/R/calibration.R | 66 +-- HuraultMisc-1.2.1/HuraultMisc/R/coverage.R | 64 +-- HuraultMisc-1.2.1/HuraultMisc/R/data.R | 19 HuraultMisc-1.2.1/HuraultMisc/R/deprec-stan.R | 34 - HuraultMisc-1.2.1/HuraultMisc/R/deprec-utils.R |only HuraultMisc-1.2.1/HuraultMisc/R/distribution.R | 103 +++-- HuraultMisc-1.2.1/HuraultMisc/R/draws.R | 38 + HuraultMisc-1.2.1/HuraultMisc/R/misc.R | 26 - HuraultMisc-1.2.1/HuraultMisc/R/predicates.R | 8 HuraultMisc-1.2.1/HuraultMisc/R/prior_post.R | 156 +++++-- HuraultMisc-1.2.1/HuraultMisc/R/pval.R | 34 - HuraultMisc-1.2.1/HuraultMisc/R/stan_misc.R | 63 ++- HuraultMisc-1.2.1/HuraultMisc/R/utility_functions.R | 92 +--- HuraultMisc-1.2.1/HuraultMisc/README.md | 22 - HuraultMisc-1.2.1/HuraultMisc/build |only HuraultMisc-1.2.1/HuraultMisc/inst/WORDLIST |only HuraultMisc-1.2.1/HuraultMisc/inst/testdata/stanmodel_config.rds |only HuraultMisc-1.2.1/HuraultMisc/inst/testdata/stanmodel_post |only HuraultMisc-1.2.1/HuraultMisc/inst/testdata/stanmodel_prior |only HuraultMisc-1.2.1/HuraultMisc/man/HuraultMisc-package.Rd | 47 +- HuraultMisc-1.2.1/HuraultMisc/man/PPC_group_distribution.Rd | 2 HuraultMisc-1.2.1/HuraultMisc/man/approx_equal.Rd | 58 +- HuraultMisc-1.2.1/HuraultMisc/man/cbbPalette.Rd | 53 +- HuraultMisc-1.2.1/HuraultMisc/man/change_colnames.Rd | 5 HuraultMisc-1.2.1/HuraultMisc/man/compute_calibration.Rd | 27 - HuraultMisc-1.2.1/HuraultMisc/man/compute_rsquared.Rd |only HuraultMisc-1.2.1/HuraultMisc/man/coverage.Rd | 4 HuraultMisc-1.2.1/HuraultMisc/man/extract_ci.Rd | 52 +- HuraultMisc-1.2.1/HuraultMisc/man/extract_distribution.Rd | 13 HuraultMisc-1.2.1/HuraultMisc/man/extract_draws.Rd | 6 HuraultMisc-1.2.1/HuraultMisc/man/extract_index_nd.Rd | 58 +- HuraultMisc-1.2.1/HuraultMisc/man/extract_parameters_from_draw.Rd | 1 HuraultMisc-1.2.1/HuraultMisc/man/extract_pdf.Rd | 48 +- HuraultMisc-1.2.1/HuraultMisc/man/extract_pmf.Rd | 44 +- HuraultMisc-1.2.1/HuraultMisc/man/factor_to_numeric.Rd | 2 HuraultMisc-1.2.1/HuraultMisc/man/is_scalar.Rd | 44 +- HuraultMisc-1.2.1/HuraultMisc/man/is_stanfit.Rd | 34 - HuraultMisc-1.2.1/HuraultMisc/man/is_wholenumber.Rd | 78 +-- HuraultMisc-1.2.1/HuraultMisc/man/logit.Rd | 48 +- HuraultMisc-1.2.1/HuraultMisc/man/pipe.Rd | 24 - HuraultMisc-1.2.1/HuraultMisc/man/post_pred_pval.Rd | 10 HuraultMisc-1.2.1/HuraultMisc/man/prior_posterior.Rd | 206 +++++----- HuraultMisc-1.2.1/HuraultMisc/man/process_replications.Rd | 1 HuraultMisc-1.2.1/HuraultMisc/man/summary_statistics.Rd | 4 HuraultMisc-1.2.1/HuraultMisc/tests/spelling.R |only HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-compute_calibration.R | 3 HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-coverage.R | 12 HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-draws.R | 48 +- HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-extract_distribution.R | 47 +- HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-misc.R | 4 HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-pval.R | 6 HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-stan.R |only HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-utility.R | 15 62 files changed, 1094 insertions(+), 796 deletions(-)
Title: Goodness-of-Fit for Zero-Inflated Univariate Hidden Markov
Models
Description: Inference, goodness-of-fit tests, and predictions for continuous and discrete univariate Hidden Markov Models (HMM), including zero-inflated distributions. The goodness-of-fit test is based on a Cramer-von Mises statistic and uses parametric bootstrap to estimate the p-value. The description of the methodology is taken from Nasri et al (2020) <doi:10.1029/2019WR025122>.
Author: Bouchra R. Nasri [aut, cre, cph],
Mamadou Yamar Thioub [aut, cph],
Bruno N. Remillard [aut, cph]
Maintainer: Bouchra R. Nasri <bouchra.nasri@umontreal.ca>
Diff between GenHMM1d versions 0.2.1 dated 2025-03-13 and 0.2.6 dated 2025-09-07
DESCRIPTION | 6 MD5 | 18 R/EstHMMGen.R | 1963 +++++++++++++++++++++++++++---------------------------- R/GofHMMGen.R | 9 R/PDF.R | 5 R/PDF_unc.R | 378 +++++----- R/bfun.R | 13 man/EstHMMGen.Rd | 6 man/GofHMMGen.Rd | 9 man/bfun.Rd | 14 10 files changed, 1227 insertions(+), 1194 deletions(-)
Title: A Curated Collection of Digestive System and Gastrointestinal
Disease Datasets
Description: Provides an extensive and curated collection of datasets related to the digestive system, stomach, intestines, liver, pancreas, and associated diseases.
This package includes clinical trials, observational studies, experimental datasets, cohort data, and case series involving gastrointestinal disorders such as gastritis, ulcers, pancreatitis, liver cirrhosis, colon cancer, colorectal conditions, Helicobacter pylori infection, irritable bowel syndrome, intestinal infections, and post-surgical outcomes.
The datasets support educational, clinical, and research applications in gastroenterology, public health, epidemiology, and biomedical sciences.
Designed for researchers, clinicians, data scientists, students, and educators interested in digestive diseases, the package facilitates reproducible analysis, modeling, and hypothesis testing using real-world and historical data.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between DigestiveDataSets versions 0.1.0 dated 2025-06-03 and 0.2.0 dated 2025-09-07
DigestiveDataSets-0.1.0/DigestiveDataSets/R/view_datasets_digestive.R |only DigestiveDataSets-0.1.0/DigestiveDataSets/man/view_datasets_digestive.Rd |only DigestiveDataSets-0.1.0/DigestiveDataSets/tests/testthat/test-view_datasets_digestive.R |only DigestiveDataSets-0.2.0/DigestiveDataSets/DESCRIPTION | 12 - DigestiveDataSets-0.2.0/DigestiveDataSets/MD5 | 79 +++--- DigestiveDataSets-0.2.0/DigestiveDataSets/NAMESPACE | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/NEWS.md |only DigestiveDataSets-0.2.0/DigestiveDataSets/R/data-documentation.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/R/digestivedatasets-package.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/R/view_datasets_DigestiveDataSets.R |only DigestiveDataSets-0.2.0/DigestiveDataSets/README.md | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/build/vignette.rds |binary DigestiveDataSets-0.2.0/DigestiveDataSets/inst/CITATION | 9 DigestiveDataSets-0.2.0/DigestiveDataSets/inst/doc/introduction_to_digestivedatasets.R | 7 DigestiveDataSets-0.2.0/DigestiveDataSets/inst/doc/introduction_to_digestivedatasets.Rmd | 15 + DigestiveDataSets-0.2.0/DigestiveDataSets/inst/doc/introduction_to_digestivedatasets.html | 116 +++++----- DigestiveDataSets-0.2.0/DigestiveDataSets/man/view_datasets_DigestiveDataSets.Rd |only DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-anorexia_weight_change_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-bleeding_ulcers_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-campylobacter_infections_ts.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-cholera_deaths_1849_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-colon_stageBC_chemo_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-colonoscopy_features_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-crc_mirnas_pubmed_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-cystic_fibrosis_snps_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-digestive_cancer_survival_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-ecoli_infections_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-gastric_cancer_trial_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-gi_damage_prevention_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-helicobacter_children_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-horse_colic_surgery_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-ibs_cam_trials_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-intestinal_smartpill_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-intestinal_surgery_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-liver_cirrhosis_prednisone_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-lynch_ontario_families_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-norovirus_derbyshire_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-pancreatic_cancer_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-pbc_mayo_survival_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-post_ercp_pancreatitis_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-ugi_bleeding_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-view_datasets_DigestiveDataSets.R |only DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-weight_loss_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/vignettes/introduction_to_digestivedatasets.Rmd | 15 + 44 files changed, 183 insertions(+), 128 deletions(-)
More information about DigestiveDataSets at CRAN
Permanent link
Title: Multivariate Random Forest with Compositional Responses
Description: Multivariate random forests with compositional responses and Euclidean predictors is performed. The compositional data are first transformed using the additive log-ratio transformation, or the alpha-transformation of Tsagris, Preston and Wood (2011), <doi:10.48550/arXiv.1106.1451>, and then the multivariate random forest of Rahman R., Otridge J. and Pal R. (2017), <doi:10.1093/bioinformatics/btw765>, is applied.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalRF versions 1.3 dated 2025-07-10 and 1.4 dated 2025-09-07
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ man/CompositionalRF-package.Rd | 9 +++++++-- man/comp.rf.Rd | 5 ++--- man/cv.alfacomprf.Rd | 5 +++++ man/cv.comprf.Rd | 2 +- man/mrf.Rd | 3 +-- 7 files changed, 27 insertions(+), 19 deletions(-)
More information about CompositionalRF at CRAN
Permanent link
Title: Extract, Format, and Print Statistical Output
Description: Provides functions that format statistical output in a way that
can be inserted into R Markdown documents. This is analogous to the
apa_print() functions in the 'papaja' package but prints Markdown
or LaTeX syntax.
Author: Jeffrey R. Stevens [aut, cre, cph]
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@protonmail.com>
Diff between cocoon versions 0.2.0 dated 2025-01-29 and 0.2.1 dated 2025-09-07
DESCRIPTION | 10 ++--- MD5 | 36 ++++++++++----------- NEWS.md | 8 +++- R/format_stats.R | 5 +- R/format_stats_BFBayesFactor.R | 17 ++++----- R/format_stats_easycorrelation.R | 32 +++++++++--------- R/import-standalone-types-check.R | 1 README.md | 2 - build/vignette.rds |binary inst/CITATION | 2 - inst/doc/cocoon.html | 6 +-- tests/testthat/helper.R | 18 +++++----- tests/testthat/test-format_stats.R | 1 tests/testthat/test-format_stats_BFBayesFactor.R | 1 tests/testthat/test-format_stats_aov.R | 1 tests/testthat/test-format_stats_easycorrelation.R | 1 tests/testthat/test-format_stats_htest.R | 1 tests/testthat/test-format_stats_lm.R | 1 tests/testthat/test-format_stats_lmerModLmerTest.R | 1 19 files changed, 71 insertions(+), 73 deletions(-)
Title: Behavioral Insight Design: A Toolkit for Integrating Behavioral
Science in UI/UX Design
Description: Provides a framework and toolkit to guide 'shiny' developers in
implementing the Behavioral Insight Design (BID) framework. The package offers
functions for documenting each of the five stages (Notice, Interpret,
Structure, Anticipate, and Validate), along with a comprehensive concept
dictionary.
Author: Jeremy Winget [aut, cre]
Maintainer: Jeremy Winget <contact@jrwinget.com>
Diff between bidux versions 0.3.0 dated 2025-08-29 and 0.3.1 dated 2025-09-07
DESCRIPTION | 14 MD5 | 165 ++-- NAMESPACE | 10 NEWS.md | 95 ++ R/bid-concepts.R | 3 R/bid_anticipate.R | 102 +- R/bid_interpret.R | 111 +- R/bid_notice.R | 77 +- R/bid_structure.R | 60 + R/bid_validate.R | 108 +- R/mappings.R | 51 + R/structure_suggest.R | 610 +++++++++++++++- R/suggest_rules.R |only R/telemetry.R | 691 +++++++++++++++++- R/utils.R | 269 +++---- README.md | 229 ++++-- build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/advanced-workflows.R |only inst/doc/advanced-workflows.Rmd |only inst/doc/advanced-workflows.html |only inst/doc/behavioral-science-primer.R |only inst/doc/behavioral-science-primer.Rmd |only inst/doc/behavioral-science-primer.html |only inst/doc/concepts-reference.Rmd | 2 inst/doc/concepts-reference.html | 2 inst/doc/getting-started.R | 71 + inst/doc/getting-started.Rmd | 103 +- inst/doc/getting-started.html | 138 ++- inst/doc/introduction-to-bid.Rmd | 6 inst/doc/introduction-to-bid.html | 6 inst/doc/practical-examples.R |only inst/doc/practical-examples.Rmd |only inst/doc/practical-examples.html |only inst/doc/telemetry-integration.R | 385 +++++++++- inst/doc/telemetry-integration.Rmd | 447 +++++++++++ inst/doc/telemetry-integration.html | 835 ++++++++++++++++------ man/adjust_suggestion_score.Rd | 6 man/apply_suggestion_rules.Rd |only man/as_tibble.bid_issues.Rd |only man/bid_address.Rd |only man/bid_anticipate.Rd | 46 - man/bid_concept.Rd | 3 man/bid_flags.Rd |only man/bid_ingest_telemetry.Rd | 19 man/bid_interpret.Rd | 43 - man/bid_notice.Rd | 43 - man/bid_notice_issue.Rd |only man/bid_notices.Rd |only man/bid_pipeline.Rd |only man/bid_structure.Rd | 35 man/bid_telemetry.Rd |only man/bid_validate.Rd | 60 - man/bidux-package.Rd | 4 man/build_concept_group.Rd | 8 man/build_groups_with_suggestions.Rd | 8 man/deduplicate_warnings_suggestions.Rd |only man/dot-calculate_severity_metrics.Rd |only man/dot-classify_issue_type.Rd |only man/dot-create_issues_tibble.Rd |only man/dot-flags_from_issues.Rd |only man/dot-suggest_theory_from_text.Rd |only man/extract_stage1_theory.Rd | 8 man/figures/logo.png |binary man/get_cognitive_load_suggestions.Rd | 6 man/get_consolidated_suggestion_rules.Rd |only man/get_dual_processing_suggestions.Rd | 6 man/get_fallback_suggestion.Rd |only man/get_generic_suggestions.Rd | 6 man/get_information_scent_suggestions.Rd | 6 man/get_onboarding_suggestions.Rd | 6 man/get_progressive_disclosure_suggestions.Rd | 6 man/get_proximity_suggestions.Rd | 6 man/get_visual_hierarchy_suggestions.Rd | 6 man/infer_concepts_from_story.Rd | 8 man/print.bid_issues.Rd |only man/rank_and_sort_suggestions.Rd | 8 man/structure_suggestions.Rd | 26 man/suggest_layout_from_previous.Rd | 5 tests/testthat/test-bid_anticipate.R | 985 ++++++++++++++++++++++---- tests/testthat/test-bid_concepts.R | 227 +++++ tests/testthat/test-bid_ingest_telemetry.R | 13 tests/testthat/test-bid_interpret.R | 377 ++++++++- tests/testthat/test-bid_issues.R |only tests/testthat/test-bid_notice.R | 171 +++- tests/testthat/test-bid_report.R | 65 - tests/testthat/test-bid_structure.R | 16 tests/testthat/test-bid_suggest_components.R | 82 +- tests/testthat/test-bid_validate.R | 430 +++++++---- tests/testthat/test-bridges.R |only tests/testthat/test-structure_suggest.R |only tests/testthat/test-suggest_rules.R |only tests/testthat/test-telemetry_helpers.R |only tests/testthat/test-utils.R | 561 ++++++++++++++ vignettes/advanced-workflows.Rmd |only vignettes/behavioral-science-primer.Rmd |only vignettes/concepts-reference.Rmd | 2 vignettes/getting-started.Rmd | 103 +- vignettes/introduction-to-bid.Rmd | 6 vignettes/practical-examples.Rmd |only vignettes/telemetry-integration.Rmd | 447 +++++++++++ 101 files changed, 6971 insertions(+), 1486 deletions(-)
Title: Datasets from the Survival TV Series Alone
Description: A collection of datasets on the Alone survival TV series in tidy format.
Included in the package are 4 datasets detailing the survivors, their loadouts,
episode details and season information.
Author: Daniel Oehm [aut, cre],
Carly Levitz [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between alone versions 0.6 dated 2025-06-12 and 0.7 dated 2025-09-07
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ data/episodes.rda |binary data/loadouts.rda |binary data/seasons.rda |binary data/survivalists.rda |binary 7 files changed, 15 insertions(+), 9 deletions(-)
Title: Analysis of Visual Meteor Data
Description: Provides a suite of analytical functionalities to process and analyze
visual meteor observations from the Visual Meteor Database
of the International Meteor Organization <https://www.imo.net/>.
Author: Janko Richter [aut, cre]
Maintainer: Janko Richter <janko@richtej.de>
Diff between vismeteor versions 1.8.5 dated 2024-01-16 and 2.0.0 dated 2025-09-07
vismeteor-1.8.5/vismeteor/man/vmperception.l.Rd |only vismeteor-1.8.5/vismeteor/tests/testthat/test_vmperception.l.R |only vismeteor-2.0.0/vismeteor/DESCRIPTION | 10 vismeteor-2.0.0/vismeteor/LICENSE | 2 vismeteor-2.0.0/vismeteor/MD5 | 64 + vismeteor-2.0.0/vismeteor/NAMESPACE | 5 vismeteor-2.0.0/vismeteor/NEWS.md |only vismeteor-2.0.0/vismeteor/R/mideal.R | 14 vismeteor-2.0.0/vismeteor/R/perception.R | 134 --- vismeteor-2.0.0/vismeteor/R/vmgeom.R | 59 - vismeteor-2.0.0/vismeteor/R/vmgeom_vst.R |only vismeteor-2.0.0/vismeteor/R/vmideal.R | 61 - vismeteor-2.0.0/vismeteor/R/vmideal_vst.R |only vismeteor-2.0.0/vismeteor/build/vignette.rds |binary vismeteor-2.0.0/vismeteor/inst/derivation |only vismeteor-2.0.0/vismeteor/inst/doc/vismeteor.Rmd | 50 - vismeteor-2.0.0/vismeteor/inst/doc/vismeteor.html | 82 +- vismeteor-2.0.0/vismeteor/inst/doc/vmgeom.R | 135 ++- vismeteor-2.0.0/vismeteor/inst/doc/vmgeom.Rmd | 207 ++++- vismeteor-2.0.0/vismeteor/inst/doc/vmgeom.html | 354 ++++++---- vismeteor-2.0.0/vismeteor/inst/doc/vmideal.R | 84 ++ vismeteor-2.0.0/vismeteor/inst/doc/vmideal.Rmd | 181 ++++- vismeteor-2.0.0/vismeteor/inst/doc/vmideal.html | 312 ++++++-- vismeteor-2.0.0/vismeteor/man/mideal.Rd | 14 vismeteor-2.0.0/vismeteor/man/vmgeom.Rd | 56 - vismeteor-2.0.0/vismeteor/man/vmgeomVst.Rd |only vismeteor-2.0.0/vismeteor/man/vmideal.Rd | 59 - vismeteor-2.0.0/vismeteor/man/vmidealVst.Rd |only vismeteor-2.0.0/vismeteor/man/vmperception.Rd | 25 vismeteor-2.0.0/vismeteor/tests/testthat/test_dvmgeom.R | 12 vismeteor-2.0.0/vismeteor/tests/testthat/test_pvmideal.R | 2 vismeteor-2.0.0/vismeteor/tests/testthat/test_vmgeomVst.R |only vismeteor-2.0.0/vismeteor/tests/testthat/test_vmidealVst.R |only vismeteor-2.0.0/vismeteor/tests/testthat/test_vmperception.R | 325 --------- vismeteor-2.0.0/vismeteor/vignettes/vismeteor.Rmd | 50 - vismeteor-2.0.0/vismeteor/vignettes/vmgeom.Rmd | 207 ++++- vismeteor-2.0.0/vismeteor/vignettes/vmideal.Rmd | 181 ++++- 37 files changed, 1570 insertions(+), 1115 deletions(-)
Title: Extraction and Management of Clinical Practice Research Datalink
Data
Description: Simplify the process of extracting and processing Clinical Practice
Research Datalink (CPRD) data in order to build datasets ready for statistical
analysis. This process is difficult in 'R', as the raw data is very large and
cannot be read into the R workspace. 'rcprd' utilises 'RSQLite' to create
'SQLite' databases which are stored on the hard disk. These are then queried
to extract the required information for a cohort of interest, and create
datasets ready for statistical analysis. The processes follow closely that
from the 'rEHR' package, see Springate et al., (2017)
<doi:10.1371/journal.pone.0171784>.
Author: Alexander Pate [aut, cre, cph]
Maintainer: Alexander Pate <alexander.pate@manchester.ac.uk>
Diff between rcprd versions 0.0.1 dated 2024-11-13 and 0.0.2 dated 2025-09-07
DESCRIPTION | 14 MD5 | 128 - NAMESPACE | 1 NEWS.md | 4 R/extract_bmi.R | 23 R/extract_cholhdl_ratio.R | 23 R/extract_diabetes.R | 17 R/extract_ho.R | 23 R/extract_impotence.R | 17 R/extract_smoking.R | 67 R/extract_test_data.R | 41 R/extract_test_data_var.R | 18 R/extract_test_recent.R | 38 R/extract_time_until.R | 43 R/functions_read_txt.R | 553 ++-- R/misc_functions.R | 279 +- R/rcprd-misc.R | 6 README.md | 16 inst/aurum_data/aurum_allpatid_extract_practice_001.txt |only inst/aurum_data/aurum_allpatid_extract_practice_002.txt |only inst/aurum_data/aurum_allpatid_set1_extract_drugissue_001.txt | 202 - inst/aurum_data/aurum_allpatid_set1_extract_drugissue_002.txt | 202 - inst/aurum_data/aurum_allpatid_set1_extract_drugissue_003.txt | 202 - inst/doc/Details-on-algorithms-for-extracting-specific-variables.R | 2 inst/doc/Details-on-algorithms-for-extracting-specific-variables.Rmd | 294 +- inst/doc/Details-on-algorithms-for-extracting-specific-variables.html | 325 ++ inst/doc/rcprd.R | 82 inst/doc/rcprd.Rmd | 1058 ++++----- inst/doc/rcprd.html | 1116 +++++----- man/add_to_database.Rd | 9 man/combine_query.aurum.Rd | 2 man/cprd_extract.Rd | 9 man/db_query.Rd | 27 man/extract_bmi.Rd | 15 man/extract_cholhdl_ratio.Rd | 15 man/extract_cohort.Rd | 2 man/extract_diabetes.Rd | 12 man/extract_ho.Rd | 19 man/extract_practices.Rd |only man/extract_smoking.Rd | 21 man/extract_test_data.Rd | 23 man/extract_test_data_var.Rd | 13 man/extract_test_recent.Rd | 22 man/extract_time_until.Rd | 19 man/extract_txt_char.Rd | 2 man/extract_txt_cons.Rd | 2 man/extract_txt_death.Rd | 2 man/extract_txt_drug.Rd | 2 man/extract_txt_hes_primary.Rd | 2 man/extract_txt_linkage.Rd | 2 man/extract_txt_obs.Rd | 2 man/extract_txt_pat.Rd | 2 man/extract_txt_prac.Rd |only man/extract_txt_prob.Rd | 2 man/extract_txt_ref.Rd | 2 tests/testthat/test-extract_vars.R | 38 tests/testthat/test-misc_functions.R | 6 vignettes/Details-on-algorithms-for-extracting-specific-variables.Rmd | 294 +- vignettes/identify_numunits_bmi.csv | 18 vignettes/identify_numunits_chol.csv | 6 vignettes/identify_numunits_cholhdl_ratio.csv | 34 vignettes/identify_numunits_hdl.csv | 8 vignettes/identify_numunits_height.csv | 9 vignettes/identify_numunits_sbp.csv | 11 vignettes/identify_numunits_weight.csv | 7 vignettes/rcprd.Rmd | 1058 ++++----- vignettes/refs.bib | 62 67 files changed, 3774 insertions(+), 2799 deletions(-)
Title: Interactive Overlays on 'shiny' Plots
Description: Provides rectangular elements that can be dragged and resized over
plots in 'shiny' apps. This may be useful in applications where users need
to mark regions on the plot for further input or processing.
Author: Nick Davies [aut, cre, cph]
Maintainer: Nick Davies <nicholas.davies@lshtm.ac.uk>
Diff between overshiny versions 0.1.1 dated 2025-08-28 and 0.2.0 dated 2025-09-07
overshiny-0.1.1/overshiny/tests/testthat/Rplots.pdf |only overshiny-0.2.0/overshiny/DESCRIPTION | 18 overshiny-0.2.0/overshiny/MD5 | 46 - overshiny-0.2.0/overshiny/NAMESPACE | 3 overshiny-0.2.0/overshiny/NEWS.md | 10 overshiny-0.2.0/overshiny/R/bounds.R |only overshiny-0.2.0/overshiny/R/heading.R |only overshiny-0.2.0/overshiny/R/script.R | 41 - overshiny-0.2.0/overshiny/R/server.R | 488 +++++++------ overshiny-0.2.0/overshiny/R/snap.R |only overshiny-0.2.0/overshiny/R/ui.R | 11 overshiny-0.2.0/overshiny/README.md | 64 - overshiny-0.2.0/overshiny/build/vignette.rds |binary overshiny-0.2.0/overshiny/inst/doc/epidemics.R |only overshiny-0.2.0/overshiny/inst/doc/epidemics.Rmd |only overshiny-0.2.0/overshiny/inst/doc/epidemics.html |only overshiny-0.2.0/overshiny/inst/doc/overshiny.R | 59 - overshiny-0.2.0/overshiny/inst/doc/overshiny.Rmd | 156 +--- overshiny-0.2.0/overshiny/inst/doc/overshiny.html | 237 +++--- overshiny-0.2.0/overshiny/inst/www/overshiny/overshiny.css | 3 overshiny-0.2.0/overshiny/man/overlayBounds.Rd | 2 overshiny-0.2.0/overshiny/man/overlayPlotOutput.Rd | 1 overshiny-0.2.0/overshiny/man/overlayServer.Rd | 171 +++- overshiny-0.2.0/overshiny/man/overlayToken.Rd | 8 overshiny-0.2.0/overshiny/man/rangeHeading.Rd |only overshiny-0.2.0/overshiny/man/snapGrid.Rd |only overshiny-0.2.0/overshiny/tests/testthat/test-panel.R | 3 overshiny-0.2.0/overshiny/vignettes/epidemics.Rmd |only overshiny-0.2.0/overshiny/vignettes/overshiny.Rmd | 156 +--- 29 files changed, 730 insertions(+), 747 deletions(-)
Title: Multilevel and Mixed Effects Model Diagnostics and Effect Sizes
Description: Effect sizes, diagnostics and performance metrics for
multilevel and mixed effects models.
Includes marginal and conditional 'R2' estimates for linear mixed effects models
based on Johnson (2014) <doi:10.1111/2041-210X.12225>.
Author: Joshua F. Wiley [aut, cre]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between multilevelTools versions 0.2.0 dated 2025-04-13 and 0.2.1 dated 2025-09-07
DESCRIPTION | 11 MD5 | 60 NAMESPACE | 4 NEWS.md | 5 R/descriptives.R | 10 R/diagnostics.R | 23 R/models.R | 58 R/plotting.R | 352 +- R/ranef.r | 614 +-- R/styler.R | 4 build/vignette.rds |binary inst/doc/lmer-vignette.R | 502 +- inst/doc/lmer-vignette.html | 6316 ++++++++++++++++++------------------ man/APAStyler.modelTest.merMod.Rd | 4 man/acfByID.Rd | 4 man/evaluateLags.Rd | 2 man/meanDecompose.Rd | 74 man/modelCompare.merMod.Rd | 4 man/modelDiagnostics.lme.Rd | 4 man/modelDiagnostics.merMod.Rd | 8 man/modelPerformance.merMod.Rd | 28 man/modelTest.merMod.Rd | 18 man/nEffective.Rd | 2 man/omegaSEM.Rd | 3 man/plot.modelDiagnostics.lme.Rd | 6 man/plot.modelDiagnostics.merMod.Rd | 8 man/ranef2long.Rd | 56 man/ranefdata.Rd | 184 - man/residualDiagnostics.lme.Rd | 6 man/residualDiagnostics.merMod.Rd | 6 man/weighted.sma.Rd | 2 31 files changed, 4189 insertions(+), 4189 deletions(-)
More information about multilevelTools at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-27 0.5.1
2025-06-23 0.5.0
Title: Translation of Logit Regression Coefficients into Percentages
Description: Translation of logit models coefficients into percentages, following Deauvieau (2010) <doi:10.1177/0759106309352586>.
Author: Nicolas Robette [aut, cre]
Maintainer: Nicolas Robette <nicolas.robette@uvsq.fr>
Diff between translate.logit versions 1.0 dated 2023-02-23 and 1.0.2 dated 2025-09-07
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NEWS.md |only R/translate.logit.R | 3 +++ README.md |only man/translate.logit.Rd | 4 ++-- 6 files changed, 13 insertions(+), 8 deletions(-)
More information about translate.logit at CRAN
Permanent link
Title: Miscellaneous Tools for Sequence Analysis
Description: It provides miscellaneous sequence analysis functions for describing episodes in individual sequences, measuring association between domains in multidimensional sequence analysis (see Piccarreta (2017) <doi:10.1177/0049124115591013>), heat maps of sequence data, Globally Interdependent Multidimensional Sequence Analysis (see Robette et al (2015) <doi:10.1177/0081175015570976>), smoothing sequences for index plots (see Piccarreta (2012) <doi:10.1177/0049124112452394>), coding sequences for Qualitative Harmonic Analysis (see Deville (1982)), measuring stress from multidimensional scaling factors (see Piccarreta and Lior (2010) <doi:10.1111/j.1467-985X.2009.00606.x>), symmetrical (or canonical) Partial Least Squares (see Bry (1996)).
Author: Nicolas Robette [aut, cre]
Maintainer: Nicolas Robette <nicolas.robette@uvsq.fr>
Diff between seqhandbook versions 0.1.1 dated 2023-04-02 and 0.1.2 dated 2025-09-07
seqhandbook-0.1.1/seqhandbook/build |only seqhandbook-0.1.1/seqhandbook/inst |only seqhandbook-0.1.1/seqhandbook/vignettes |only seqhandbook-0.1.2/seqhandbook/DESCRIPTION | 25 +++++++++++++---------- seqhandbook-0.1.2/seqhandbook/MD5 | 23 ++++++++------------- seqhandbook-0.1.2/seqhandbook/NEWS.md | 5 ++++ seqhandbook-0.1.2/seqhandbook/README.md | 19 +++++++++++++++-- seqhandbook-0.1.2/seqhandbook/man/seq2qha.Rd | 2 - seqhandbook-0.1.2/seqhandbook/man/seq_heatmap.Rd | 6 ++--- seqhandbook-0.1.2/seqhandbook/man/seqi1epi.Rd | 4 +-- seqhandbook-0.1.2/seqhandbook/man/seqifpos.Rd | 4 +-- seqhandbook-0.1.2/seqhandbook/man/seqinepi.Rd | 4 +-- seqhandbook-0.1.2/seqhandbook/man/seqsmooth.Rd | 4 +-- 13 files changed, 58 insertions(+), 38 deletions(-)
Title: A Curated Collection of Pulmonary and Respiratory Disease
Datasets
Description: Provides a comprehensive and curated collection of datasets related to the lungs, respiratory system, and associated diseases.
This package includes epidemiological, clinical, experimental, and simulated datasets on conditions such as lung cancer, asthma,
Chronic Obstructive Pulmonary Disease (COPD), tuberculosis, whooping cough, pneumonia, influenza, and other respiratory illnesses.
It is designed to support data exploration, statistical modeling, teaching, and research in pulmonary medicine, public health,
environmental epidemiology, and respiratory disease surveillance.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between PulmoDataSets versions 0.1.0 dated 2025-06-03 and 0.2.0 dated 2025-09-07
PulmoDataSets-0.1.0/PulmoDataSets/R/view_datasets_pulmo.R |only PulmoDataSets-0.1.0/PulmoDataSets/man/view_datasets_pulmo.Rd |only PulmoDataSets-0.1.0/PulmoDataSets/tests/testthat/test-view_datasets_pulmo.R |only PulmoDataSets-0.2.0/PulmoDataSets/DESCRIPTION | 12 PulmoDataSets-0.2.0/PulmoDataSets/MD5 | 101 +++--- PulmoDataSets-0.2.0/PulmoDataSets/NAMESPACE | 2 PulmoDataSets-0.2.0/PulmoDataSets/NEWS.md |only PulmoDataSets-0.2.0/PulmoDataSets/R/data-documentation.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/R/pulmodatasets-package.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/R/view_datasets_PulmoDataSets.R |only PulmoDataSets-0.2.0/PulmoDataSets/README.md | 2 PulmoDataSets-0.2.0/PulmoDataSets/build/vignette.rds |binary PulmoDataSets-0.2.0/PulmoDataSets/inst/CITATION | 8 PulmoDataSets-0.2.0/PulmoDataSets/inst/doc/introduction_to_pulmodatasets.R | 7 PulmoDataSets-0.2.0/PulmoDataSets/inst/doc/introduction_to_pulmodatasets.Rmd | 14 PulmoDataSets-0.2.0/PulmoDataSets/inst/doc/introduction_to_pulmodatasets.html | 147 +++++----- PulmoDataSets-0.2.0/PulmoDataSets/man/view_datasets_PulmoDataSets.Rd |only PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-UK_female_lung_deaths_ts.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-UK_male_lung_deaths_ts.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-USMortality_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-USRegionalMortality_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-ai_ipn_performance_dt.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-air_polution_mortality_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-asthma_patients_tbl_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-bronchitis_Cardiff_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-chicago_pollution_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-child_wheeze_pollution_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-children_respiratory_rates_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-danish_lung_incidence_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-engwales_cancer_mortality_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-influenza_us_1975_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-lung_cancer_survival_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-lung_nodules_detection_dt.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-lungca_cancer_deaths_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-neonatal_intubation_times_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-nicotine_gum_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-ohio_children_wheeze_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-patients_lung_diseases_tbl_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-pneumonia_influenza_ts.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-respiratory_clinical_trial_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-respiratory_infections_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-respiratory_trial_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-respiratory_trial_outcomes_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-smoking_UK_tbl_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-smoking_doctors_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-smoking_lung_cancer_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-smoking_youth_tbl_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-tlc_lung_capacity_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-tuberculosis_vaccine_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-veterans_lung_cancer_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-view_datasets_PulmoDataSets.R |only PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-whooping_cough_dk_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-whooping_cough_phila_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-whooping_cough_ts.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/vignettes/introduction_to_pulmodatasets.Rmd | 14 55 files changed, 251 insertions(+), 162 deletions(-)
Title: Create Pharmacometric Models
Description: Provides a user interface to create or modify pharmacometric
models for various modeling and simulation software platforms.
Author: Sebastien Bihorel [cre, aut]
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between pmxcode versions 0.3.0 dated 2025-04-12 and 0.3.1 dated 2025-09-07
DESCRIPTION | 6 MD5 | 12 NEWS.md | 6 R/utils_nonmem.R | 5 inst/doc/covariates.html | 572 ++++++++++----------------------------------- inst/doc/library.html | 429 +++++++++++---------------------- inst/resources/rv_lib.json | 8 7 files changed, 304 insertions(+), 734 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>. Thong Pham et al. (2020) <doi:10.18637/jss.v092.i03>. Thong Pham et al. (2021) <doi:10.1093/comnet/cnab024>.
Author: Thong Pham [aut, cre],
Paul Sheridan [aut],
Hidetoshi Shimodaira [aut]
Maintainer: Thong Pham <thongphamthe@gmail.com>
Diff between PAFit versions 1.2.10 dated 2024-03-28 and 1.2.11 dated 2025-09-07
DESCRIPTION | 22 +++++++++--- MD5 | 8 ++-- man/PAFit-package.Rd | 4 +- man/plot.PAFit_net.Rd | 2 - man/test_linear_PA.rd | 90 +++++++++++++++++++++++++------------------------- 5 files changed, 69 insertions(+), 57 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-22 0.3.1
2025-07-10 0.3.0
2022-02-16 0.2.1
2020-07-27 0.2.0
2020-05-28 0.1.3
2020-04-05 0.1.2
2020-02-28 0.1.1
2019-08-20 0.1.0