Title: Spatial Regression Analysis
Description: A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep'. These model fitting functions include maximum likelihood methods for cross-sectional models proposed by 'Cliff' and 'Ord' (1973, ISBN:0850860369) and (1981, ISBN:0850860814), fitting methods initially described by 'Ord' (1975) <doi:10.1080/01621459.1975.10480272>. The models are further described by 'Anselin' (1988) <doi:10.1007/978-94-015-7799-1>. Spatial two stage least squares and spatial general method of moment models initially proposed by 'Kelejian' and 'Prucha' (1998) <doi:10.1023/A:1007707430416> and (1999) <doi:10.1111/1468-2354.00027> are provided. Impact methods and MCMC fitting methods proposed by 'LeSage' and 'Pace' (2009) <doi:10.1201/9781420064254> are implemented for the family of cross-sectional spatial regression models. Methods for fitting the log determinant term in maximu [...truncated...]
Author: Roger Bivand [cre, aut] ,
Gianfranco Piras [aut],
Luc Anselin [ctb] ,
Andrew Bernat [ctb],
Eric Blankmeyer [ctb],
Yongwan Chun [ctb] ,
Virgilio Gomez-Rubio [ctb] ,
Daniel Griffith [ctb] ,
Martin Gubri [ctb] ,
Rein Halbersma [ctb],
James LeSage [ctb], [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spatialreg versions 1.4-2 dated 2025-09-06 and 1.4-3 dated 2026-03-20
DESCRIPTION | 47 +++++++++++---------- MD5 | 42 +++++++++---------- NAMESPACE | 7 ++- NEWS.md | 2 R/impacts.R | 15 ++++-- R/kpgm_new.R | 7 +-- R/mess.R | 6 -- R/s2sls.R | 7 +-- R/sarlm_functions.R | 15 ++++++ R/sarlm_tests.R | 7 +-- R/spBreg.R | 9 +--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/SpatialFiltering.html | 4 - inst/doc/nb_igraph.html | 8 +-- inst/doc/sids_models.html | 6 +- man/ML_models.Rd | 7 ++- man/gstsls.Rd | 4 - man/impacts.Rd | 8 +-- man/sarlm_tests.Rd | 6 -- man/stsls.Rd | 5 -- src/ml_sse.c | 88 ++++++++++++++++++++++++++++++++++++----- 22 files changed, 193 insertions(+), 107 deletions(-)
Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Several approaches are described in the review Dray et al (2012)
<doi:10.1890/11-1183.1>.
Author: Stephane Dray [aut] ,
David Bauman [ctb],
Guillaume Blanchet [ctb],
Daniel Borcard [ctb],
Sylvie Clappe [ctb],
Guillaume Guenard [ctb] ,
Thibaut Jombart [ctb],
Guillaume Larocque [ctb],
Pierre Legendre [ctb] ,
Naima Madi [ctb],
Helene H Wagner [ctb], [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adespatial versions 0.3-28 dated 2025-04-16 and 0.3-29 dated 2026-03-20
DESCRIPTION | 17 MD5 | 12 R/TBI.R | 15 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tutorial.html | 1239 +++++++++++++++++++++++++++++++------------------ man/TBI.Rd | 10 7 files changed, 827 insertions(+), 466 deletions(-)
Title: Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stephane Dray [aut] ,
Anne-Beatrice Dufour [aut] ,
Jean Thioulouse [aut] ,
Daniel Chessel [ant],
Thibaut Jombart [ctb],
Sandrine Pavoine [ctb],
Jean R. Lobry [ctb],
Sebastien Ollier [ctb],
Daniel Borcard [ctb],
Pierre Legendre [ctb],
Stephanie Bougea [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-23 dated 2025-02-14 and 1.7-24 dated 2026-03-20
DESCRIPTION | 17 +-- MD5 | 25 ++--- NAMESPACE | 6 + R/dpcaiv.R |only R/loocv.R | 2 R/pcaiv.R | 4 R/varipart.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/faq.html | 185 ++++++++++++++++++++------------------- man/dpcaiv.Rd |only man/loocv.bca.Rd | 3 man/pcaiv.Rd | 7 + man/varipart.Rd | 4 vignettes/ade4_with_ggplot2.html |only 15 files changed, 139 insertions(+), 116 deletions(-)
Title: Collection of Correlation and Association Estimators
Description: Compute correlation and other association matrices from
small to high-dimensional datasets with relative simple functions and
sensible defaults. Includes options for shrinkage and robustness to improve
results in noisy or high-dimensional settings (p >= n), plus convenient
print/plot methods for inspection. Implemented with optimised C++ backends
using BLAS/OpenMP and memory-aware symmetric updates. Works with base
matrices and data frames, returning standard R objects via a consistent S3
interface. Useful across genomics, agriculture, and machine-learning
workflows. Supports Pearson, Spearman, Kendall, distance correlation,
partial correlation, and robust biweight mid-correlation; Bland–Altman
analyses and Lin's concordance correlation coefficient (including
repeated-measures extensions). Methods based on Ledoit and Wolf (2004)
<doi:10.1016/S0047-259X(03)00096-4>; Schäfer and Strimmer (2005)
<doi:10.2202/1544-6115.1175>; Lin (1989) <doi:10.2307/2532051>.
Author: Thiago de Paula Oliveira [aut, cre]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@gmail.com>
Diff between matrixCorr versions 0.8.4 dated 2026-03-03 and 0.8.5 dated 2026-03-20
DESCRIPTION | 6 - MD5 | 10 +- README.md | 12 ++- build/partial.rdb |binary src/kendall_corr.cpp | 185 +++++++++++++++++++++------------------------------ src/pearson.cpp | 114 +++++++++++++++---------------- 6 files changed, 153 insertions(+), 174 deletions(-)
Title: Management Strategy Evaluation for Salmon Species
Description: Simulation tools to evaluate the long-term effects of salmon management strategies, including a combination of habitat, harvest, and
habitat actions. The stochastic age-structured operating model accommodates complex life histories, including freshwater survival across
early life stages, juvenile survival and fishery exploitation in the marine life stage, partial maturity by age class, and fitness impacts of
hatchery programs on natural spawning populations. 'salmonMSE' also provides an age-structured conditioning model to develop operating models
fitted to data.
Author: Quang Huynh [aut, cre]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between salmonMSE versions 0.1.0 dated 2025-09-23 and 1.0.0 dated 2026-03-20
DESCRIPTION | 15 MD5 | 81 ++--- NAMESPACE | 33 ++ NEWS.md |only R/AHA.R | 4 R/CM.R | 652 ++++++++++++++++++++++--------------------- R/CM_int.R | 141 ++++++--- R/CMfun.R | 563 ++++++++++++++++++++++++++++++++----- R/Harvest_MMP.R | 2 R/MMSE2SMSE.R | 13 R/Rel.R | 81 +++-- R/SOM2MOM.R | 189 ++++-------- R/SOM2MOM_int.R | 232 +++++++-------- R/SRR.R | 1 R/compare.R | 65 +++- R/define-SOM.R | 37 -- R/hatchery.R | 62 +++- R/multiHist2SHist.R | 25 - R/plot-SOM.R | 8 R/plot-statevar.R | 160 ++++++++++ R/plot-table.R | 14 R/ref.R | 6 R/rmd_SMSE.R | 352 ++++++++++++++++++++++- R/salmonMSE.R | 85 +++++ data/glossary.rda |binary inst/include/CMreport.Rmd | 572 +++++++++++++++++++------------------ inst/include/SMSEcompare.Rmd |only man/Bio-class.Rd | 12 man/CM2SOM.Rd | 2 man/CMfigures.Rd |only man/Hatchery-class.Rd | 23 - man/Historical-class.Rd | 36 -- man/SHist-class.Rd | 4 man/SMSE-class.Rd | 2 man/SOM-class.Rd | 2 man/compare.Rd |only man/compare_statevar_ts.Rd |only man/fit_CM.Rd | 38 +- man/plot_decision_table.Rd | 80 +++-- man/plot_statevar_ts.Rd | 4 man/plot_tradeoff.Rd | 20 + man/report.Rd | 3 man/report_CM.Rd | 5 man/smolt_func.Rd | 8 44 files changed, 2416 insertions(+), 1216 deletions(-)
Title: Multi-Stock Assessment
Description: Implementation of a next-generation, multi-stock age-structured fisheries assessment model.
'multiSA' is intended for use in mixed fisheries where stock composition can not be readily identified in
fishery data alone, e.g., from catch and age/length composition. Models can be fitted to genetic data,
e.g., stock composition of catches and close-kin pairs, with seasonal stock availability and movement.
Author: Quang Huynh [aut, cre]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between multiSA versions 0.1.0 dated 2026-02-03 and 0.1.1 dated 2026-03-20
multiSA-0.1.0/multiSA/man/residuals.MSAassess.Rd |only multiSA-0.1.1/multiSA/DESCRIPTION | 10 multiSA-0.1.1/multiSA/MD5 | 43 multiSA-0.1.1/multiSA/NAMESPACE | 13 multiSA-0.1.1/multiSA/NEWS.md | 18 multiSA-0.1.1/multiSA/R/define-s4-class.R | 335 +++---- multiSA-0.1.1/multiSA/R/make-parameters.R | 38 multiSA-0.1.1/multiSA/R/misc.R | 7 multiSA-0.1.1/multiSA/R/model.R | 2 multiSA-0.1.1/multiSA/R/model_int.R | 5 multiSA-0.1.1/multiSA/R/profile.R | 507 +++++----- multiSA-0.1.1/multiSA/R/resid.R | 1064 +++++++++++------------ multiSA-0.1.1/multiSA/R/retrospective.R | 572 ++++++------ multiSA-0.1.1/multiSA/R/rtmb-methods.R | 31 multiSA-0.1.1/multiSA/R/simulate.R | 49 - multiSA-0.1.1/multiSA/README.md | 8 multiSA-0.1.1/multiSA/build/partial.rdb |binary multiSA-0.1.1/multiSA/man/MSAassess-class.Rd | 48 - multiSA-0.1.1/multiSA/man/profile.Rd | 6 multiSA-0.1.1/multiSA/man/report.Rd | 5 multiSA-0.1.1/multiSA/man/residuals.Rd |only multiSA-0.1.1/multiSA/man/retrospective.Rd | 6 multiSA-0.1.1/multiSA/man/simulate.Rd | 3 multiSA-0.1.1/multiSA/man/summary.Rd |only 24 files changed, 1417 insertions(+), 1353 deletions(-)
Title: Probabilistic Knowledge Structures
Description: Fitting and testing probabilistic knowledge structures,
especially the basic local independence model (BLIM, Doignon & Flamagne,
1999) and the simple learning model (SLM), using the minimum discrepancy
maximum likelihood (MDML) method (Heller & Wickelmaier, 2013
<doi:10.1016/j.endm.2013.05.145>).
Author: Florian Wickelmaier [aut, cre],
Juergen Heller [aut],
Julian Mollenhauer [aut],
Pasquale Anselmi [ctb],
Debora de Chiusole [ctb],
Andrea Brancaccio [ctb],
Luca Stefanutti [ctb],
Paul Doerrbecker [ctb]
Maintainer: Florian Wickelmaier <wickelmaier@web.de>
Diff between pks versions 0.6-1 dated 2024-09-16 and 0.7-0 dated 2026-03-20
ChangeLog | 10 ++++++ DESCRIPTION | 16 +++++----- MD5 | 36 ++++++++++++---------- NAMESPACE | 1 R/blim.R | 60 ++++++++++++++++++++++---------------- R/blim_predict.R |only R/conversion.R | 6 ++- R/slm.R | 34 ++++++++------------- build/partial.rdb |binary build/vignette.rds |binary data/DoignonFalmagne7.rda |binary data/Taagepera.rda |binary data/endm.rda |binary data/hsgeometry.rda |only inst/doc/EstimationStepByStep.pdf |binary man/blim.Rd | 5 +-- man/conversion.Rd | 2 - man/endm.Rd | 4 +- man/hsgeometry.Rd |only man/predict.blim.Rd |only man/slm.Rd | 2 - 21 files changed, 101 insertions(+), 75 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using the 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre],
John Magnotti [ctb] ,
Xiang Zhang [ctb]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between dipsaus versions 0.3.3 dated 2026-01-09 and 0.3.4 dated 2026-03-20
DESCRIPTION | 6 - MD5 | 17 +-- NEWS.md | 8 + build/vignette.rds |binary inst/doc/r_expr_addons.html | 6 - inst/doc/shiny_customized_widgets.html | 14 +- inst/doc/utility_functions.html | 2 inst/shiny-addons/dipsaus/dipsaus-dipterix-lib.js | 14 +- src/utils.cpp | 108 ++++++++++++++++------ tests/testthat/test-missing-dots.R |only 10 files changed, 121 insertions(+), 54 deletions(-)
Title: Publication-Ready Summary Tables and Forest Plots
Description: A comprehensive framework for descriptive statistics and regression
analysis that produces publication-ready tables and forest plots. Provides a
unified interface from descriptive statistics through multivariable modeling,
with support for linear models, generalized linear models, Cox proportional
hazards, and mixed-effects models. Also includes univariable screening,
multivariate regression, model comparison, and export to multiple formats
including PDF, DOCX, PPTX, 'LaTeX', HTML, and RTF. Built on 'data.table'
for computational efficiency.
Author: Paul Hsin-ti McClelland [aut, cre, cph]
Maintainer: Paul Hsin-ti McClelland <PaulHMcClelland@protonmail.com>
Diff between summata versions 0.11.3 dated 2026-03-08 and 0.11.4 dated 2026-03-20
DESCRIPTION | 6 MD5 | 79 - NEWS.md | 10 R/coxforest.R | 2 R/fit.R | 136 ++ R/forest_utils.R | 33 R/fullfit.R | 65 + R/glmforest.R | 2 R/globals.R | 4 R/lmforest.R | 2 R/m2dt.R | 115 ++ R/multifit.R | 100 +- R/uniscreen.R | 34 README.md | 18 inst/doc/advanced_workflows.html | 130 +- inst/doc/installation_setup.Rmd | 4 inst/doc/installation_setup.html | 6 inst/doc/model_comparison.html | 4 inst/doc/multivariate_regression.html | 58 - inst/doc/regression_modeling.R | 86 + inst/doc/regression_modeling.Rmd | 136 +- inst/doc/regression_modeling.html | 1159 +++++++++++++------------ man/extract_predictor_effects.Rd | 3 man/figures/summata.png |binary man/figures/summata.svg | 40 man/fit.Rd | 103 +- man/fullfit.Rd | 36 man/get_cached_confint.Rd |only man/m2dt.Rd | 34 man/multifit.Rd | 20 man/uniscreen.Rd | 20 tests/benchmarks/benchmarks.R | 77 + tests/testthat/test_fit.R | 133 ++ tests/testthat/test_fullfit.R | 147 +++ tests/testthat/test_m2dt.R | 141 +++ tests/testthat/test_multivariate.R | 89 + vignettes/articles/benchmarks.Rmd | 209 ++-- vignettes/articles/feature_comparison.Rmd | 6 vignettes/articles/statistical_foundations.Rmd | 69 + vignettes/installation_setup.Rmd | 4 vignettes/regression_modeling.Rmd | 136 +- 41 files changed, 2407 insertions(+), 1049 deletions(-)
Title: Docorate (Decorate + Output) Displays
Description: A framework for creating production outputs. Users can frame a table, listing, or figure with headers and footers and save to an output file. Stores an intermediate 'docorator' object for reproducibility and rendering to multiple output types.
Author: Becca Krouse [aut, cre],
Shannon Haughton [aut],
Seongbin Hong [aut],
Dragoș Moldovan-Gruenfeld [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between docorator versions 0.5.2 dated 2026-01-23 and 0.6.0 dated 2026-03-20
docorator-0.5.2/docorator/man/create_chunk.Rd |only docorator-0.6.0/docorator/DESCRIPTION | 9 docorator-0.6.0/docorator/MD5 | 48 - docorator-0.6.0/docorator/NAMESPACE | 7 docorator-0.6.0/docorator/NEWS.md | 10 docorator-0.6.0/docorator/R/docorate.R | 7 docorator-0.6.0/docorator/R/render.R | 8 docorator-0.6.0/docorator/R/utils.R | 44 - docorator-0.6.0/docorator/R/utils_fancyhdr.R | 119 ++ docorator-0.6.0/docorator/R/utils_gt.R | 4 docorator-0.6.0/docorator/README.md | 15 docorator-0.6.0/docorator/inst/doc/display_sizing.html | 440 +++++----- docorator-0.6.0/docorator/inst/doc/headers_footers.Rmd | 4 docorator-0.6.0/docorator/inst/doc/headers_footers.html | 7 docorator-0.6.0/docorator/inst/template/template.Rmd | 14 docorator-0.6.0/docorator/inst/template/template.qmd | 11 docorator-0.6.0/docorator/man/create_chunks_all.Rd |only docorator-0.6.0/docorator/man/render_pdf.Rd | 5 docorator-0.6.0/docorator/tests/testthat/_snaps/prep_obj_tex.md | 2 docorator-0.6.0/docorator/tests/testthat/_snaps/utils.md | 12 docorator-0.6.0/docorator/tests/testthat/_snaps/utils_fancyhdr.md | 10 docorator-0.6.0/docorator/tests/testthat/test-render.R | 41 docorator-0.6.0/docorator/tests/testthat/test-utils.R | 24 docorator-0.6.0/docorator/tests/testthat/test-utils_fancyhdr.R | 152 +++ docorator-0.6.0/docorator/tests/testthat/test_docorate.R | 24 docorator-0.6.0/docorator/vignettes/headers_footers.Rmd | 4 26 files changed, 692 insertions(+), 329 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.56 dated 2026-01-18 and 0.57 dated 2026-03-20
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 2 ++ R/cran.R | 10 +++++++--- R/github.R | 14 ++++++++++++++ R/json.R | 11 +++++++---- R/markdown.R | 29 ++++++++++++++++++++++++----- R/record.R | 5 +++-- build/vignette.rds |binary inst/doc/xfun.Rmd | 2 +- inst/doc/xfun.html | 14 +++++++------- man/submit_cran.Rd | 9 ++++++--- man/tabset.Rd | 19 +++++++++++++++++-- man/tojson.Rd | 10 ++++++---- tests/test-cran/test-json.R | 3 +-- vignettes/xfun.Rmd | 2 +- 16 files changed, 114 insertions(+), 52 deletions(-)
Title: A Calculator for Melting Temperature of Nucleic Acid Sequences
Description: A comprehensive R package for calculating melting temperatures of nucleic acid sequences.
Implements three calculation methods:
1. Wallace rule (Thein & Wallace, 1986)
2. Empirical formulas based on GC content (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991;
Untergasser, 2012; von Ahsen, 2001)
3. Nearest neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998;
SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010;
Sugimoto, 1995; Allawi, 1997; Santalucia, 2005)
Includes corrections for:
- Salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008)
- Chemical compounds (dimethyl sulfoxide, formamide)
Supports both direct sequence input and FASTA file input.
Author: Junhui Li [cre, aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between TmCalculator versions 1.0.3 dated 2022-02-20 and 1.0.4 dated 2026-03-20
TmCalculator-1.0.3/TmCalculator/R/GC.R |only TmCalculator-1.0.3/TmCalculator/R/Tm_GC.R |only TmCalculator-1.0.3/TmCalculator/R/Tm_NN.R |only TmCalculator-1.0.3/TmCalculator/R/Tm_Wallace.R |only TmCalculator-1.0.3/TmCalculator/R/c2s.R |only TmCalculator-1.0.3/TmCalculator/R/check_filter.R |only TmCalculator-1.0.3/TmCalculator/R/chem_correction.R |only TmCalculator-1.0.3/TmCalculator/R/complement.R |only TmCalculator-1.0.3/TmCalculator/R/s2c.R |only TmCalculator-1.0.3/TmCalculator/man/GC.Rd |only TmCalculator-1.0.3/TmCalculator/man/Tm_GC.Rd |only TmCalculator-1.0.3/TmCalculator/man/Tm_NN.Rd |only TmCalculator-1.0.3/TmCalculator/man/Tm_Wallace.Rd |only TmCalculator-1.0.3/TmCalculator/man/check_filter.Rd |only TmCalculator-1.0.3/TmCalculator/man/chem_correction.Rd |only TmCalculator-1.0.3/TmCalculator/man/complement.Rd |only TmCalculator-1.0.4/TmCalculator/DESCRIPTION | 45 + TmCalculator-1.0.4/TmCalculator/LICENSE |only TmCalculator-1.0.4/TmCalculator/MD5 | 82 ++ TmCalculator-1.0.4/TmCalculator/NAMESPACE | 83 ++- TmCalculator-1.0.4/TmCalculator/R/TmCalculator-package.R |only TmCalculator-1.0.4/TmCalculator/R/chem_correct.R |only TmCalculator-1.0.4/TmCalculator/R/gc.R |only TmCalculator-1.0.4/TmCalculator/R/generate_complement.R |only TmCalculator-1.0.4/TmCalculator/R/plot_tm_genome_tracks.R |only TmCalculator-1.0.4/TmCalculator/R/plot_tm_heatmap.R |only TmCalculator-1.0.4/TmCalculator/R/plot_tm_interactive.R |only TmCalculator-1.0.4/TmCalculator/R/plot_tm_karyotype.R |only TmCalculator-1.0.4/TmCalculator/R/print.TmCalculator.R | 2 TmCalculator-1.0.4/TmCalculator/R/salt_correction.R | 275 +++++----- TmCalculator-1.0.4/TmCalculator/R/thermodynamic_gc_params.R |only TmCalculator-1.0.4/TmCalculator/R/thermodynamic_nn_params.R |only TmCalculator-1.0.4/TmCalculator/R/tm_calculate.R |only TmCalculator-1.0.4/TmCalculator/R/tm_gc.R |only TmCalculator-1.0.4/TmCalculator/R/tm_nn.R |only TmCalculator-1.0.4/TmCalculator/R/tm_wallace.R |only TmCalculator-1.0.4/TmCalculator/R/to_genomic_ranges.R |only TmCalculator-1.0.4/TmCalculator/R/utils.R |only TmCalculator-1.0.4/TmCalculator/README.md |only TmCalculator-1.0.4/TmCalculator/build |only TmCalculator-1.0.4/TmCalculator/data |only TmCalculator-1.0.4/TmCalculator/inst |only TmCalculator-1.0.4/TmCalculator/man/TmCalculator-package.Rd |only TmCalculator-1.0.4/TmCalculator/man/c2s.Rd | 8 TmCalculator-1.0.4/TmCalculator/man/check_filter_seq.Rd |only TmCalculator-1.0.4/TmCalculator/man/chem_correct.Rd |only TmCalculator-1.0.4/TmCalculator/man/coor_to_genomic_ranges.Rd |only TmCalculator-1.0.4/TmCalculator/man/fa_to_genomic_ranges.Rd |only TmCalculator-1.0.4/TmCalculator/man/figures |only TmCalculator-1.0.4/TmCalculator/man/gc.Rd |only TmCalculator-1.0.4/TmCalculator/man/generate_complement.Rd |only TmCalculator-1.0.4/TmCalculator/man/plot_tm_genome_tracks.Rd |only TmCalculator-1.0.4/TmCalculator/man/plot_tm_heatmap.Rd |only TmCalculator-1.0.4/TmCalculator/man/plot_tm_interactive.Rd |only TmCalculator-1.0.4/TmCalculator/man/plot_tm_karyotype.Rd |only TmCalculator-1.0.4/TmCalculator/man/s2c.Rd | 8 TmCalculator-1.0.4/TmCalculator/man/salt_correction.Rd | 91 +-- TmCalculator-1.0.4/TmCalculator/man/thermodynamic_gc_params.Rd |only TmCalculator-1.0.4/TmCalculator/man/thermodynamic_nn_params.Rd |only TmCalculator-1.0.4/TmCalculator/man/tm_calculate.Rd |only TmCalculator-1.0.4/TmCalculator/man/tm_gc.Rd |only TmCalculator-1.0.4/TmCalculator/man/tm_nn.Rd |only TmCalculator-1.0.4/TmCalculator/man/tm_wallace.Rd |only TmCalculator-1.0.4/TmCalculator/man/to_genomic_ranges.Rd |only TmCalculator-1.0.4/TmCalculator/man/vec_to_genomic_ranges.Rd |only TmCalculator-1.0.4/TmCalculator/tests |only TmCalculator-1.0.4/TmCalculator/vignettes |only 67 files changed, 357 insertions(+), 237 deletions(-)
Title: 'R' Bindings for 'TMB'
Description: Native 'R' interface to 'TMB' (Template Model Builder) so models can be written entirely in 'R' rather than 'C++'. Automatic differentiation, to any order, is available for a rich subset of 'R' features, including linear algebra for dense and sparse matrices, complex arithmetic, Fast Fourier Transform, probability distributions and special functions. 'RTMB' provides easy access to model fitting and validation following the principles of Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. M. (2016) <DOI:10.18637/jss.v070.i05> and Thygesen, U.H., Albertsen, C.M., Berg, C.W. et al. (2017) <DOI:10.1007/s10651-017-0372-4>.
Author: Kasper Kristensen [aut, cre]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between RTMB versions 1.8 dated 2025-10-14 and 1.9 dated 2026-03-20
DESCRIPTION | 11 - MD5 | 85 +++++++----- NAMESPACE | 10 + NEWS |only R/00roxygen.R | 3 R/RcppExports.R | 44 +++++- R/adcomplex.R | 2 R/adjoint.R | 8 + R/advector.R | 69 +++++++--- R/branching.R |only R/distributions.R | 17 -- R/integrate.R |only R/methods.R | 190 +++++++++++++++++++++++++-- R/poshess.R | 2 R/uniroot.R |only build/vignette.rds |binary inst/doc/RTMB-advanced.R | 25 +++ inst/doc/RTMB-advanced.html | 255 +++++++++++++++++++++---------------- inst/doc/RTMB-advanced.rmd | 75 +++++++--- inst/doc/RTMB-introduction.html | 6 inst/doc/RTMB-tips.R |only inst/doc/RTMB-tips.html |only inst/doc/RTMB-tips.rmd |only inst/include/CallRTMB.hpp | 21 +-- inst/include/config.h | 3 inst/tinytest/test-distributions.R | 42 ++++++ inst/tinytest/test-factorize.R | 18 +- inst/tinytest/test-integrate.R |only inst/tinytest/test-pnorm.R |only inst/tinytest/test-ridge_correct.R |only man/ADapply.Rd | 22 +-- man/ADconstruct.Rd | 12 - man/ADintegrate.Rd |only man/ADoverload.Rd | 12 + man/ADuniroot.Rd |only man/ADvector.Rd | 34 ++++ man/Distributions.Rd | 84 ++++++++++-- man/TMB-interface.Rd | 14 -- src/RTMB.cpp | 28 ++++ src/RTMB.h | 8 + src/RTMB_tape.cpp | 62 ++++++++ src/RcppExports.cpp | 143 ++++++++++++++++++-- src/branching.cpp |only src/config.h | 3 src/distributions.cpp | 47 ++++-- src/integrate.cpp |only src/math.cpp | 53 +++++-- src/math_complex.cpp | 1 src/pnorm.cpp |only src/uniroot.cpp |only vignettes/RTMB-advanced.rmd | 75 +++++++--- vignettes/RTMB-tips.rmd |only 52 files changed, 1107 insertions(+), 377 deletions(-)
Title: Tidy Presentation of Clinical Reporting
Description: Streamlined statistical reporting in 'Rmarkdown' environments.
Facilitates the automated reporting of descriptive statistics, multiple
univariate models, multivariable models and tables combining these outputs.
Plotting functions include customisable survival curves, forest plots from
logistic and ordinal regression and bivariate comparison plots.
Author: Lisa Avery [cre, aut] ,
Ryan Del Bel [aut],
Osvaldo Espin-Garcia [aut],
Katherine Lajkosz [aut] ,
Clarina Ong [aut],
Tyler Pittman [aut] ,
Anna Santiago [aut] ,
Yanning Wang [ctr],
Jessica Weiss [aut],
Wei Xu [aut]
Maintainer: Lisa Avery <lisa.avery@uhn.ca>
Diff between reportRmd versions 0.1.1 dated 2025-01-24 and 0.1.3 dated 2026-03-20
reportRmd-0.1.1/reportRmd/data/uvmodels.rda |only reportRmd-0.1.1/reportRmd/man/addspace.Rd |only reportRmd-0.1.1/reportRmd/man/cap.Rd |only reportRmd-0.1.1/reportRmd/man/formatp.Rd |only reportRmd-0.1.1/reportRmd/man/lbld.Rd |only reportRmd-0.1.1/reportRmd/man/lpvalue.Rd |only reportRmd-0.1.1/reportRmd/man/niceNum.Rd |only reportRmd-0.1.1/reportRmd/man/nicename.Rd |only reportRmd-0.1.1/reportRmd/man/pvalue.Rd |only reportRmd-0.1.1/reportRmd/man/rmds.Rd |only reportRmd-0.1.1/reportRmd/man/sanitizestr.Rd |only reportRmd-0.1.1/reportRmd/man/uvmodels.Rd |only reportRmd-0.1.1/reportRmd/man/uvsum.Rd |only reportRmd-0.1.1/reportRmd/man/xvar_function.default.Rd |only reportRmd-0.1.1/reportRmd/vignettes/i1.png |only reportRmd-0.1.1/reportRmd/vignettes/i2.png |only reportRmd-0.1.1/reportRmd/vignettes/libs |only reportRmd-0.1.1/reportRmd/vignettes/overview.qmd |only reportRmd-0.1.1/reportRmd/vignettes/some_SPSS_data.rda |only reportRmd-0.1.1/reportRmd/vignettes/usingLabels.docx |only 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Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.2.0 dated 2026-03-20 and 1.2.1 dated 2026-03-20
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 11 +++++++++++ R/morph_pixel.R | 6 ++++++ inst/doc/matching-workflows.html | 8 ++++---- inst/doc/troubleshooting.html | 2 +- tests/testthat/test-morph-coverage-boost.R | 2 ++ tests/testthat/test-morph-pixel.R | 3 +++ 8 files changed, 37 insertions(+), 15 deletions(-)
Title: A Package for Biometrics and Modelling
Description: A system of functions and datasets to carry out quantitative analyses in the biological
sciences. The package facilitates data management, exploratory analyses, and model assessment.
Although it currently focuses on forest ecology, silviculture and decision-making, most of
the package functions are applicable across several disciplines, including economics,
environmental science, and healthcare.
Author: Christian Salas-Eljatib [aut, cre] ,
Nicolas Campos [ctb] ,
Marcos Marivil [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Diff between biometrics versions 1.0.3 dated 2026-03-03 and 1.0.4 dated 2026-03-20
biometrics-1.0.3/biometrics/R/data-densidadcanelo2.r |only biometrics-1.0.3/biometrics/data/densidadcanelo2.rda |only biometrics-1.0.3/biometrics/man/densidadcanelo2.Rd |only biometrics-1.0.4/biometrics/DESCRIPTION | 6 biometrics-1.0.4/biometrics/MD5 | 129 ++++++++++--------- biometrics-1.0.4/biometrics/NAMESPACE | 3 biometrics-1.0.4/biometrics/R/asymregfx.r | 21 +-- biometrics-1.0.4/biometrics/R/bertarich.r | 20 +- biometrics-1.0.4/biometrics/R/curtis.r | 17 +- biometrics-1.0.4/biometrics/R/curtisori.r | 17 +- biometrics-1.0.4/biometrics/R/data-thinningtrial.r |only biometrics-1.0.4/biometrics/R/data-thinningtrial2.r |only biometrics-1.0.4/biometrics/R/data-treevolruca2.r | 2 biometrics-1.0.4/biometrics/R/expogral.r |only biometrics-1.0.4/biometrics/R/expogralfull.r |only biometrics-1.0.4/biometrics/R/gompertz.r | 19 +- biometrics-1.0.4/biometrics/R/gompertzm.r | 19 +- biometrics-1.0.4/biometrics/R/hossfeld.r | 19 +- biometrics-1.0.4/biometrics/R/invfx.r | 19 +- biometrics-1.0.4/biometrics/R/lang.r | 17 +- biometrics-1.0.4/biometrics/R/logistic.r | 19 +- biometrics-1.0.4/biometrics/R/logisticm.r | 19 +- biometrics-1.0.4/biometrics/R/meyer.r | 17 +- biometrics-1.0.4/biometrics/R/mmenten.r | 17 +- biometrics-1.0.4/biometrics/R/naslund.r | 17 +- biometrics-1.0.4/biometrics/R/ogawa.r | 17 +- biometrics-1.0.4/biometrics/R/power.r | 17 +- biometrics-1.0.4/biometrics/R/prodan.r | 19 +- biometrics-1.0.4/biometrics/R/ratkow.r | 19 +- biometrics-1.0.4/biometrics/R/schnute.r | 19 +- biometrics-1.0.4/biometrics/R/schuma.r | 17 +- biometrics-1.0.4/biometrics/R/sibbesen.r | 19 +- biometrics-1.0.4/biometrics/R/stage.r | 19 +- biometrics-1.0.4/biometrics/R/standtab.r |only biometrics-1.0.4/biometrics/R/strand.r | 17 +- biometrics-1.0.4/biometrics/R/strandg.r | 19 +- biometrics-1.0.4/biometrics/R/weibfx.r | 19 +- biometrics-1.0.4/biometrics/R/wykoff.r | 17 +- biometrics-1.0.4/biometrics/data/thinningtrial.rda |only biometrics-1.0.4/biometrics/data/thinningtrial2.rda |only biometrics-1.0.4/biometrics/inst/CITATION | 4 biometrics-1.0.4/biometrics/man/asymreg.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/bertarich.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/curtis.fx.Rd | 14 +- biometrics-1.0.4/biometrics/man/curtisori.fx.Rd | 14 +- biometrics-1.0.4/biometrics/man/expogral.fx.Rd |only biometrics-1.0.4/biometrics/man/expogralfull.fx.Rd |only biometrics-1.0.4/biometrics/man/gompertz.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/gompertzm.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/hossfeld.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/inv.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/lang.fx.Rd | 14 +- biometrics-1.0.4/biometrics/man/logist.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/logistm.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/meyer.fx.Rd | 14 +- biometrics-1.0.4/biometrics/man/mmenten.fx.Rd | 14 +- biometrics-1.0.4/biometrics/man/naslund.fx.Rd | 14 +- biometrics-1.0.4/biometrics/man/ogawa.fx.Rd | 12 - biometrics-1.0.4/biometrics/man/power.fx.Rd | 14 +- biometrics-1.0.4/biometrics/man/prodan.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/ratkow.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/schnute.fx.Rd | 24 +-- biometrics-1.0.4/biometrics/man/schum.fx.Rd | 14 +- biometrics-1.0.4/biometrics/man/sibbesen.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/stage.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/standtab.Rd |only biometrics-1.0.4/biometrics/man/strand.fx.Rd | 14 +- biometrics-1.0.4/biometrics/man/strandg.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/thinningtrial.Rd |only biometrics-1.0.4/biometrics/man/thinningtrial2.Rd |only biometrics-1.0.4/biometrics/man/treevolruca2.Rd | 2 biometrics-1.0.4/biometrics/man/weib.fx.Rd | 16 +- biometrics-1.0.4/biometrics/man/wykoff.fx.Rd | 14 +- 73 files changed, 501 insertions(+), 520 deletions(-)
Title: Interface to the Global Biodiversity Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility (GBIF;
<https://www.gbif.org/developer/summary>). GBIF is a database
of species occurrence records from sources all over the globe.
rgbif includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the GBIF
tile map service to make rasters summarizing huge amounts of data.
Author: Scott Chamberlain [aut] ,
Damiano Oldoni [aut] ,
Vijay Barve [ctb] ,
Peter Desmet [ctb] ,
Laurens Geffert [ctb],
Dan Mcglinn [ctb] ,
Karthik Ram [ctb] ,
rOpenSci [fnd] ,
John Waller [aut, cre]
Maintainer: John Waller <jwaller@gbif.org>
Diff between rgbif versions 3.8.4 dated 2025-11-13 and 3.8.5 dated 2026-03-20
DESCRIPTION | 9 MD5 | 94 ++++---- NAMESPACE | 7 NEWS.md | 30 ++ R/bbox.R | 50 ++++ R/check_wkt.r | 78 ++++++ R/download_predicate_dsl.R | 58 ++++- R/name_backbone.r | 16 + R/name_backbone_checklist.R | 2 R/occ_data.R | 2 R/occ_download.R | 31 ++ R/occ_download_stats.R |only man/download_predicate_dsl.Rd | 16 + man/occ_data.Rd | 2 man/occ_download.Rd | 12 + man/occ_download_cached.Rd | 6 man/occ_download_cancel.Rd | 6 man/occ_download_dataset_activity.Rd | 6 man/occ_download_datasets.Rd | 6 man/occ_download_get.Rd | 6 man/occ_download_import.Rd | 6 man/occ_download_list.Rd | 6 man/occ_download_meta.Rd | 6 man/occ_download_queue.Rd | 6 man/occ_download_stats.Rd |only man/occ_download_stats_dataset.Rd |only man/occ_download_stats_dataset_records.Rd |only man/occ_download_stats_export.Rd |only man/occ_download_stats_source.Rd |only man/occ_download_stats_user_country.Rd |only man/occ_download_wait.Rd | 6 man/occ_search.Rd | 2 tests/fixtures/name_backbone.yml | 40 +-- tests/fixtures/name_backbone_acceptedUsageKey.yml |only tests/fixtures/name_backbone_verbose_true.yml | 10 tests/fixtures/occ_download_1.yml | 10 tests/fixtures/occ_download_10.yml |only tests/fixtures/occ_download_2.yml | 12 - tests/fixtures/occ_download_3.yml | 10 tests/fixtures/occ_download_4.yml | 10 tests/fixtures/occ_download_5.yml | 10 tests/fixtures/occ_download_6.yml | 10 tests/fixtures/occ_download_7.yml | 10 tests/fixtures/occ_download_8.yml | 10 tests/fixtures/occ_download_9.yml |only tests/fixtures/occ_download_stats.yml |only tests/fixtures/occ_download_stats_dataset.yml |only tests/fixtures/occ_download_stats_dataset_records.yml |only tests/fixtures/occ_download_stats_source.yml |only tests/fixtures/occ_download_stats_user_country.yml |only tests/testthat/test-check_wkt.r | 67 +++++ tests/testthat/test-download_parsing.R | 203 ++++++++++-------- tests/testthat/test-name_backbone.r | 11 tests/testthat/test-name_backbone_checklist.R | 68 ++++-- tests/testthat/test-occ_download.R | 42 +++ tests/testthat/test-occ_download_stats.R |only 56 files changed, 743 insertions(+), 249 deletions(-)
Title: Geocoding with the 'ArcGIS' REST API Service
Description: Lite interface for finding locations of addresses or
businesses around the world using the 'ArcGIS' REST API service
<https://developers.arcgis.com/rest/geocode/api-reference/overview-world-geocoding-service.htm>.
Address text can be converted to location candidates and a location
can be converted into an address. No API key required.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between arcgeocoder versions 0.3.0 dated 2026-01-15 and 0.4.0 dated 2026-03-20
arcgeocoder-0.3.0/arcgeocoder/inst/doc/arcgeocoder.Rmd |only arcgeocoder-0.3.0/arcgeocoder/inst/doc/feature-types.Rmd |only arcgeocoder-0.3.0/arcgeocoder/vignettes/arcgeocoder.Rmd |only arcgeocoder-0.3.0/arcgeocoder/vignettes/feature-types.Rmd |only arcgeocoder-0.4.0/arcgeocoder/DESCRIPTION | 12 arcgeocoder-0.4.0/arcgeocoder/MD5 | 58 arcgeocoder-0.4.0/arcgeocoder/NEWS.md | 4 arcgeocoder-0.4.0/arcgeocoder/R/arc_geo.R | 40 arcgeocoder-0.4.0/arcgeocoder/R/arc_geo_categories.R | 606 ++++----- arcgeocoder-0.4.0/arcgeocoder/R/arc_geo_multi.R | 541 ++++---- arcgeocoder-0.4.0/arcgeocoder/R/arc_reverse_geo.R | 22 arcgeocoder-0.4.0/arcgeocoder/R/arcgeocoder_check_access.R | 1 arcgeocoder-0.4.0/arcgeocoder/R/data.R | 343 ++--- arcgeocoder-0.4.0/arcgeocoder/README.md | 109 - arcgeocoder-0.4.0/arcgeocoder/build/vignette.rds |binary arcgeocoder-0.4.0/arcgeocoder/data/arc_categories.rda |binary arcgeocoder-0.4.0/arcgeocoder/data/arc_spatial_references.rda |binary arcgeocoder-0.4.0/arcgeocoder/inst/REFERENCES.bib | 10 arcgeocoder-0.4.0/arcgeocoder/inst/WORDLIST | 4 arcgeocoder-0.4.0/arcgeocoder/inst/doc/arcgeocoder.html | 619 +++------ arcgeocoder-0.4.0/arcgeocoder/inst/doc/arcgeocoder.qmd |only arcgeocoder-0.4.0/arcgeocoder/inst/doc/feature-types.html | 626 +++------- arcgeocoder-0.4.0/arcgeocoder/inst/doc/feature-types.qmd |only arcgeocoder-0.4.0/arcgeocoder/inst/schemaorg.json | 4 arcgeocoder-0.4.0/arcgeocoder/man/arc_categories.Rd | 1 arcgeocoder-0.4.0/arcgeocoder/man/arc_geo.Rd | 49 arcgeocoder-0.4.0/arcgeocoder/man/arc_geo_categories.Rd | 395 +++--- arcgeocoder-0.4.0/arcgeocoder/man/arc_geo_multi.Rd | 39 arcgeocoder-0.4.0/arcgeocoder/man/arc_reverse_geo.Rd | 18 arcgeocoder-0.4.0/arcgeocoder/man/chunks/out1.Rmd | 18 arcgeocoder-0.4.0/arcgeocoder/tests/testthat/test-arc_geo_multi.R | 524 ++++---- arcgeocoder-0.4.0/arcgeocoder/vignettes/REFERENCES.bib | 10 arcgeocoder-0.4.0/arcgeocoder/vignettes/arcgeocoder.qmd |only arcgeocoder-0.4.0/arcgeocoder/vignettes/feature-types.qmd |only 34 files changed, 1852 insertions(+), 2201 deletions(-)
Title: MCMC Sampling from 'TMB' Model Object using 'Stan'
Description: Enables all 'rstan' functionality for a 'TMB' model object, in particular MCMC sampling and chain visualization. Sampling can be performed with or without Laplace approximation for the random effects. This is demonstrated in Monnahan & Kristensen (2018) <DOI:10.1371/journal.pone.0197954>.
Author: Kasper Kristensen [aut, cre]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between tmbstan versions 1.0.91 dated 2023-08-26 and 1.1.0 dated 2026-03-20
tmbstan-1.0.91/tmbstan/inst/model.hpp |only tmbstan-1.0.91/tmbstan/src/include/model.hpp |only tmbstan-1.1.0/tmbstan/DESCRIPTION | 19 +++++++++------ tmbstan-1.1.0/tmbstan/MD5 | 10 +++----- tmbstan-1.1.0/tmbstan/R/tmbstan.R | 33 ++++++++++++++++++--------- tmbstan-1.1.0/tmbstan/man/tmbstan.Rd | 22 +++++++++--------- tmbstan-1.1.0/tmbstan/tools/autogen.R | 4 +-- 7 files changed, 52 insertions(+), 36 deletions(-)
Title: Multidimensional Penalized Splines for (Excess) Hazard Models,
Relative Mortality Ratio Models and Marginal Intensity Models
Description: Fits (excess) hazard, relative mortality ratio or marginal intensity models with multidimensional penalized splines allowing for
time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (than [...truncated...]
Author: Mathieu Fauvernier [aut, cre],
Laurent Roche [aut],
Laurent Remontet [aut],
Zoe Uhry [ctb],
Nadine Bossard [ctb],
Elsa Coz [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>
Diff between survPen versions 2.0.2 dated 2025-03-08 and 2.0.3 dated 2026-03-20
survPen-2.0.2/survPen/R/survPenV2_02.r |only survPen-2.0.3/survPen/DESCRIPTION | 6 - survPen-2.0.3/survPen/MD5 | 10 - survPen-2.0.3/survPen/NEWS | 7 + survPen-2.0.3/survPen/R/survPenV2_03.r |only survPen-2.0.3/survPen/build/vignette.rds |binary survPen-2.0.3/survPen/inst/doc/survival_analysis_with_survPen.html | 57 ++++------ 7 files changed, 40 insertions(+), 40 deletions(-)
Title: Seamless Access to World Bank International Debt Statistics
(IDS)
Description: Access and analyze the World Bank's International Debt Statistics
(IDS) <https://www.worldbank.org/en/programs/debt-statistics/ids>.
IDS provides creditor-debtor relationships between countries, regions, and
institutions. 'wbids' enables users to download, process and work with IDS
series across multiple geographies, counterparts, and time periods.
Author: Teal Emery [aut, cre],
Teal Insights [cph],
Christoph Scheuch [aut] ,
Christopher Smith [ctb]
Maintainer: Teal Emery <lte@tealinsights.com>
Diff between wbids versions 1.1.4 dated 2026-03-10 and 1.1.5 dated 2026-03-20
DESCRIPTION | 14 MD5 | 39 NEWS.md | 80 - R/ids_bulk.R | 50 - R/ids_bulk_files.R | 1 man/ids_bulk.Rd | 2 man/ids_bulk_files.Rd | 2 man/ids_bulk_series.Rd | 2 man/ids_get_ed.Rd | 2 tests/testthat/helper.R |only tests/testthat/test-ids_bulk.R | 689 +++++++------ tests/testthat/test-ids_bulk_files.R | 24 tests/testthat/test-ids_bulk_series.R | 30 tests/testthat/test-ids_get.R | 1336 ++++++++++++++------------- tests/testthat/test-ids_get_ed.R | 20 tests/testthat/test-ids_list_counterparts.R | 20 tests/testthat/test-ids_list_entities.R | 48 tests/testthat/test-ids_list_series.R | 18 tests/testthat/test-ids_list_series_topics.R | 16 tests/testthat/test-perform_request.R | 161 +-- tests/testthat/test-read_bulk_info.R | 24 21 files changed, 1370 insertions(+), 1208 deletions(-)
Title: Compact Inline Widgets for 'shiny' Apps
Description: Provides a basic set of compact widgets for 'shiny' apps which
occupy less space and can appear inline with surrounding text.
Author: Nick Davies [aut, cre]
Maintainer: Nick Davies <nicholas.davies@lshtm.ac.uk>
Diff between inshiny versions 0.1.2 dated 2026-02-14 and 0.1.3 dated 2026-03-20
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 13 +++++++++++++ R/number.R | 25 ++++++++++++++++--------- inst/www/inshiny/inshiny.css | 13 ++++++++++++- man/inline_number.Rd | 7 ++++++- tests/testthat/_snaps/shiny-1.12.0/action.md | 13 ------------- tests/testthat/_snaps/shiny-1.13.0 |only tests/testthat/test-action.R | 14 ++++++++++++-- 9 files changed, 70 insertions(+), 36 deletions(-)
Title: Information-Theoretic Measure of Causality
Description: Methods for quantifying temporal and spatial causality through information flow, and decomposing it into unique, redundant, and synergistic components, following the framework described in Martinez-Sanchez et al. (2024) <doi:10.1038/s41467-024-53373-4>.
Author: Wenbo Lyu [aut, cre, cph]
Maintainer: Wenbo Lyu <lyu.geosocial@gmail.com>
Diff between infocausality versions 1.0 dated 2025-11-03 and 1.1 dated 2026-03-20
infocausality-1.0/infocausality/inst/python/__pycache__ |only infocausality-1.1/infocausality/DESCRIPTION | 15 infocausality-1.1/infocausality/MD5 | 30 infocausality-1.1/infocausality/NAMESPACE | 8 infocausality-1.1/infocausality/NEWS.md | 6 infocausality-1.1/infocausality/R/Agenerics.R | 24 infocausality-1.1/infocausality/R/RcppExports.R | 62 - infocausality-1.1/infocausality/R/infocausality-package.R | 8 infocausality-1.1/infocausality/R/surd.R | 166 +-- infocausality-1.1/infocausality/R/utils.R | 24 infocausality-1.1/infocausality/R/zzz.R | 15 infocausality-1.1/infocausality/README.md | 16 infocausality-1.1/infocausality/build/vignette.rds |binary infocausality-1.1/infocausality/inst/CITATION |only infocausality-1.1/infocausality/inst/doc/surd.html | 5 infocausality-1.1/infocausality/inst/python/InfoCausality.py | 530 +++++------ infocausality-1.1/infocausality/man/surd.Rd | 174 +-- 17 files changed, 552 insertions(+), 531 deletions(-)
Title: Feature Stores for the 'diseasy' Framework
Description: Simple feature stores and tools for creating personalised feature stores.
'diseasystore' powers feature stores which can automatically link and aggregate features to a given stratification
level. These feature stores are automatically time-versioned (powered by the 'SCDB' package) and allows you to easily
and dynamically compute features as part of your continuous integration.
Author: Rasmus Skytte Randloev [aut, cre] ,
Kaare Graesboell [rev] ,
Kasper Schou Telkamp [rev] ,
Lasse Engbo Christiansen [rev] ,
Marcus Munch Gruenewald [rev] ,
Sofia Myrup Otero [rev],
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between diseasystore versions 0.3.2 dated 2025-10-17 and 0.3.3 dated 2026-03-20
DESCRIPTION | 13 MD5 | 59 +-- NEWS.md | 368 ++++++++++---------- R/0_linters.R | 10 R/0_miscellaneous.R | 4 R/DiseasystoreBase.R | 216 ++++++----- R/age_helpers.R | 2 R/test_diseasystore.R | 35 + inst/WORDLIST | 48 ++ inst/doc/benchmarks.html | 2 inst/doc/diseasystore-ecdc-respiratory-viruses.html | 4 inst/doc/diseasystore-google-covid-19.R | 2 inst/doc/diseasystore-google-covid-19.Rmd | 2 inst/doc/diseasystore-google-covid-19.html | 6 inst/doc/diseasystore.html | 18 inst/doc/extending-diseasystore-example.Rmd | 34 - inst/doc/extending-diseasystore-example.html | 42 +- inst/doc/extending-diseasystore.Rmd | 15 inst/extdata/benchmarks.rds |binary man/DiseasystoreBase.Rd | 38 ++ man/DiseasystoreEcdcRespiratoryViruses.Rd | 1 man/DiseasystoreGoogleCovid19.Rd | 1 man/DiseasystoreSimulist.Rd | 1 tests/testthat/test-DiseasystoreBase.R | 280 ++++++++++----- tests/testthat/test-age_helpers.R | 5 vignettes/diseasystore-google-covid-19.Rmd | 2 vignettes/extending-diseasystore-example.Rmd | 34 - vignettes/extending-diseasystore.Rmd | 15 vignettes/vignette_data |only 29 files changed, 771 insertions(+), 486 deletions(-)
Title: Causal Graph Interface
Description: Create, query, and modify causal graphs. 'caugi' (Causal Graph
Interface) is a causality-first, high performance graph package that
provides a simple interface to build, structure, and examine causal
relationships.
Author: Frederik Fabricius-Bjerre [aut, cre, cph],
Johan Larsson [aut] ,
Michael Sachs [aut] ,
Bjarke Hautop Kristensen [aut]
Maintainer: Frederik Fabricius-Bjerre <frederik@fabriciusbjerre.dk>
Diff between caugi versions 1.0.0 dated 2026-01-22 and 1.1.0 dated 2026-03-20
caugi-1.0.0/caugi/R/plot.R |only caugi-1.0.0/caugi/inst/doc/get_started.R |only caugi-1.0.0/caugi/inst/doc/get_started.Rmd |only caugi-1.0.0/caugi/inst/doc/get_started.html |only caugi-1.0.0/caugi/man/dot-cg_state.Rd |only caugi-1.0.0/caugi/man/dot-mark_not_built.Rd |only caugi-1.0.0/caugi/man/dot-view_to_caugi.Rd |only caugi-1.0.0/caugi/vignettes/get_started.Rmd |only caugi-1.1.0/caugi/DESCRIPTION | 23 caugi-1.1.0/caugi/MD5 | 350 - caugi-1.1.0/caugi/NAMESPACE | 9 caugi-1.1.0/caugi/NEWS.md | 57 caugi-1.1.0/caugi/R/adjustment.R | 244 - caugi-1.1.0/caugi/R/all-classes.R | 21 caugi-1.1.0/caugi/R/as_caugi.R | 26 caugi-1.1.0/caugi/R/caugi.R | 421 -- caugi-1.1.0/caugi/R/extendr-wrappers.R | 152 caugi-1.1.0/caugi/R/format-caugi.R | 58 caugi-1.1.0/caugi/R/format-dot.R | 3 caugi-1.1.0/caugi/R/format-graphml.R | 11 caugi-1.1.0/caugi/R/format-mermaid.R | 3 caugi-1.1.0/caugi/R/layout.R |only caugi-1.1.0/caugi/R/methods.R | 176 caugi-1.1.0/caugi/R/metrics.R | 31 caugi-1.1.0/caugi/R/operations.R | 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Title: The Ultimate Tool for Reading Data in Bulk
Description: Designed to simplify and streamline the process of reading
and processing large volumes of data in R, this package offers a
collection of functions tailored for bulk data operations. It enables
users to efficiently read multiple sheets from Microsoft Excel and
Google Sheets workbooks, as well as various CSV files from a
directory. The data is returned as organized data frames, facilitating
further analysis and manipulation. Ideal for handling extensive data
sets or batch processing tasks, bulkreadr empowers users to manage
data in bulk effortlessly, saving time and effort in data preparation
workflows. Additionally, the package seamlessly works with labelled
data from SPSS and Stata.
Author: Ezekiel Ogundepo [aut, cre] ,
Ernest Fokoue [ctb] ,
Golibe Ezeechesi [ctb],
Fatimo Adebanjo [ctb],
Isaac Ajao [ctb]
Maintainer: Ezekiel Ogundepo <gbganalyst@gmail.com>
Diff between bulkreadr versions 1.2.1 dated 2025-07-28 and 1.2.2 dated 2026-03-20
DESCRIPTION | 14 - MD5 | 32 +-- NAMESPACE | 1 NEWS.md | 173 ++++++++++--------- R/bulkreadr-package.R | 2 R/inspect_na.R | 132 +++++++++----- README.md | 2 build/vignette.rds |binary inst/doc/intro-to-bulkreadr.html | 15 - inst/doc/labelled-data.Rmd | 256 ++++++++++++++-------------- inst/doc/labelled-data.html | 5 inst/doc/other-functions.R | 1 inst/doc/other-functions.Rmd | 351 +++++++++++++++++++-------------------- inst/doc/other-functions.html | 49 ++--- man/inspect_na.Rd | 33 +-- vignettes/labelled-data.Rmd | 256 ++++++++++++++-------------- vignettes/other-functions.Rmd | 351 +++++++++++++++++++-------------------- 17 files changed, 860 insertions(+), 813 deletions(-)
Title: Calibration of Computer-Coded Verbal Autopsy Algorithm
Description: Calibrates population-level cause-specific mortality fractions (CSMFs) that are derived using computer-coded verbal autopsy (CCVA) algorithms. Leveraging the data collected in the Child Health and Mortality Prevention Surveillance (CHAMPS;<https://champshealth.org/>) project, the package stores misclassification matrix estimates of three CCVA algorithms (EAVA, InSilicoVA, and InterVA) and two age groups (neonates aged 0-27 days, and children aged 1-59 months) across countries (specific estimates for Bangladesh, Ethiopia, Kenya, Mali, Mozambique, Sierra Leone, and South Africa, and a combined estimate for all other countries), enabling global calibration. These estimates are obtained using the framework proposed in Pramanik et al. (2025;<doi:10.1214/24-AOAS2006>) and are analyzed in Pramanik et al. (2026;<doi:10.1136/bmjgh-2025-021747>). Given VA-only data for an age group, CCVA algorithm, and country, the package utilizes the corresponding misclassification matrix est [...truncated...]
Author: Sandipan Pramanik [aut, cre] ,
Emily Wilson [aut],
Jacob Fiksel [aut],
Brian Gilbert [aut],
Abhirup Datta [aut]
Maintainer: Sandipan Pramanik <sandy.pramanik@gmail.com>
Diff between vacalibration versions 2.0 dated 2025-07-24 and 2.2 dated 2026-03-20
vacalibration-2.0/vacalibration/R/Mmat_champs.R |only vacalibration-2.0/vacalibration/R/comsamoz_public_broad.R |only vacalibration-2.0/vacalibration/R/comsamoz_public_openVAout.R |only vacalibration-2.0/vacalibration/R/modular_vacalib.R |only vacalibration-2.0/vacalibration/data/Mmat_champs.rda |only vacalibration-2.0/vacalibration/data/comsamoz_public_broad.rda |only vacalibration-2.0/vacalibration/data/comsamoz_public_openVAout.rda |only vacalibration-2.0/vacalibration/inst/stan/seqcalib_mmat.rds |only vacalibration-2.0/vacalibration/man/Mmat_champs.Rd |only vacalibration-2.0/vacalibration/man/comsamoz_public_broad.Rd |only vacalibration-2.0/vacalibration/man/comsamoz_public_openVAout.Rd |only vacalibration-2.0/vacalibration/man/modular.vacalib.Rd |only vacalibration-2.2/vacalibration/DESCRIPTION | 20 vacalibration-2.2/vacalibration/LICENSE |only vacalibration-2.2/vacalibration/MD5 | 68 vacalibration-2.2/vacalibration/NAMESPACE | 8 vacalibration-2.2/vacalibration/R/CCVA_missmat.R |only vacalibration-2.2/vacalibration/R/cause_map.R | 64 vacalibration-2.2/vacalibration/R/comsamoz_CCVAoutput.R |only vacalibration-2.2/vacalibration/R/model_utils.R |only vacalibration-2.2/vacalibration/R/modular_vacalib_fixed.R |only vacalibration-2.2/vacalibration/R/modular_vacalib_prior.R |only vacalibration-2.2/vacalibration/R/plot_vacalib.R |only vacalibration-2.2/vacalibration/R/plot_vacalib_fixed.R |only vacalibration-2.2/vacalibration/R/plot_vacalib_prior.R |only vacalibration-2.2/vacalibration/R/smart_round.R |only vacalibration-2.2/vacalibration/R/vacalibration.R | 1331 ++++- vacalibration-2.2/vacalibration/R/zzz.R | 19 vacalibration-2.2/vacalibration/README.md |only vacalibration-2.2/vacalibration/build/partial.rdb |only vacalibration-2.2/vacalibration/build/vignette.rds |binary vacalibration-2.2/vacalibration/data/CCVA_missmat.rda |only vacalibration-2.2/vacalibration/data/comsamoz_CCVAoutput.rda |only vacalibration-2.2/vacalibration/inst/doc/intro_to_vacalibration.R | 199 vacalibration-2.2/vacalibration/inst/doc/intro_to_vacalibration.Rmd | 359 - vacalibration-2.2/vacalibration/inst/doc/intro_to_vacalibration.html | 2366 +++++++--- vacalibration-2.2/vacalibration/inst/stan/seqcalib.rds |binary vacalibration-2.2/vacalibration/inst/stan/seqcalib.stan | 70 vacalibration-2.2/vacalibration/inst/stan/seqcalib_mmat.stan | 60 vacalibration-2.2/vacalibration/man/CCVA_missmat.Rd |only vacalibration-2.2/vacalibration/man/cause_map.Rd | 30 vacalibration-2.2/vacalibration/man/comsamoz_CCVAoutput.Rd |only vacalibration-2.2/vacalibration/man/figures |only vacalibration-2.2/vacalibration/man/modular_vacalib_fixed.Rd |only vacalibration-2.2/vacalibration/man/modular_vacalib_prior.Rd |only vacalibration-2.2/vacalibration/man/plot_vacalib.Rd |only vacalibration-2.2/vacalibration/man/plot_vacalib_fixed.Rd |only vacalibration-2.2/vacalibration/man/plot_vacalib_prior.Rd |only vacalibration-2.2/vacalibration/man/smart_round.Rd |only vacalibration-2.2/vacalibration/man/vacalibration.Rd | 367 - vacalibration-2.2/vacalibration/vignettes/custom.css |only vacalibration-2.2/vacalibration/vignettes/figures |only vacalibration-2.2/vacalibration/vignettes/intro_to_vacalibration.Rmd | 359 - 53 files changed, 3619 insertions(+), 1701 deletions(-)
Title: Construct Process Maps Using Event Data
Description: Visualize event logs using directed graphs, i.e. process maps. Part of the 'bupaR' framework.
Author: Gert Janssenswillen [aut],
Gerard van Hulzen [ctb],
Benoît Depaire [cre],
Felix Mannhardt [ctb],
Thijs Beuving [ctb],
urvikalia [ctb],
Hasselt University [cph]
Maintainer: Benoît Depaire <benoit.depaire@uhasselt.be>
This is a re-admission after prior archival of version 0.5.7 dated 2025-07-09
Diff between processmapR versions 0.5.7 dated 2025-07-09 and 0.5.8 dated 2026-03-20
DESCRIPTION | 26 ++++++++-------- MD5 | 21 ++++++------- NAMESPACE | 1 R/dotted_chart.R | 2 - R/groupby_helpers.R |only R/processmapR.R | 4 +- R/resource_map.R | 2 - R/trace_explorer.R | 61 ++++++++++++++++++++++++++++---------- R/utils.R | 8 ++++ README.md | 3 - inst/doc/processmapr.html | 4 +- man/figures/README-example2-1.png |binary 12 files changed, 84 insertions(+), 48 deletions(-)
Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2016. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods 19(1), 10-52) <doi:10.1177/1094428115584005>.
NCA identifies necessary (but not sufficient) conditions in datasets, where x causes (e.g. precedes) y. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations.
(Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates which level of x (e.g., an effort, [...truncated...]
Author: Jan Dul [aut],
Govert Buijs [cre]
Maintainer: Govert Buijs <buijs@rsm.nl>
Diff between NCA versions 4.0.5 dated 2025-12-21 and 5.0.0 dated 2026-03-20
NCA-4.0.5/NCA/R/p_above.R |only NCA-4.0.5/NCA/R/p_fit.R |only NCA-4.0.5/NCA/R/p_nca_ce_cm.R |only NCA-4.0.5/NCA/R/p_nca_ce_cm_conf.R |only NCA-4.0.5/NCA/R/p_nca_ce_fdhi.R |only NCA-4.0.5/NCA/R/p_nca_ce_lfdh.R |only NCA-4.0.5/NCA/R/p_nca_cr_cm.R |only NCA-4.0.5/NCA/R/p_nca_cr_cm_conf.R |only NCA-4.0.5/NCA/R/p_nca_cr_fdhi.R |only NCA-4.0.5/NCA/R/p_nca_ct_fdh.R |only NCA-4.0.5/NCA/R/p_nca_lh.R |only NCA-4.0.5/NCA/R/p_nca_sfa.R |only NCA-5.0.0/NCA/DESCRIPTION | 15 - NCA-5.0.0/NCA/MD5 | 112 +++---- NCA-5.0.0/NCA/NAMESPACE | 15 - NCA-5.0.0/NCA/NEWS.md | 28 + NCA-5.0.0/NCA/R/nca.R | 45 +-- NCA-5.0.0/NCA/R/nca_bottleneck.R | 139 +++++++-- NCA-5.0.0/NCA/R/nca_difference.R |only NCA-5.0.0/NCA/R/nca_extract.R |only NCA-5.0.0/NCA/R/nca_normalize.R |only NCA-5.0.0/NCA/R/nca_outliers.R | 110 ++++--- NCA-5.0.0/NCA/R/nca_output.R | 100 ++++++ NCA-5.0.0/NCA/R/nca_plotly.R | 248 ++++++++-------- NCA-5.0.0/NCA/R/nca_plots.R | 381 ++++++++++++-------------- NCA-5.0.0/NCA/R/nca_power.R | 288 +++++++++++++------ NCA-5.0.0/NCA/R/nca_random.R | 6 NCA-5.0.0/NCA/R/nca_summary.R | 367 +++++++++++++------------ NCA-5.0.0/NCA/R/nca_tests.R | 32 -- NCA-5.0.0/NCA/R/onAttach.R | 57 --- NCA-5.0.0/NCA/R/p_bottleneck.R | 4 NCA-5.0.0/NCA/R/p_ceiling.R | 33 -- NCA-5.0.0/NCA/R/p_confidence.R | 6 NCA-5.0.0/NCA/R/p_constants.R | 58 +-- NCA-5.0.0/NCA/R/p_graphics.R | 2 NCA-5.0.0/NCA/R/p_line_to_points.R |only NCA-5.0.0/NCA/R/p_loop_data.R | 4 NCA-5.0.0/NCA/R/p_metrics.R |only NCA-5.0.0/NCA/R/p_nca_c_lp.R | 102 ++++-- NCA-5.0.0/NCA/R/p_nca_ce_fdh.R | 95 ++++-- NCA-5.0.0/NCA/R/p_nca_ce_vrs.R | 78 +++-- NCA-5.0.0/NCA/R/p_nca_cols.R | 82 +++-- NCA-5.0.0/NCA/R/p_nca_cr_fdh.R | 100 ++++-- NCA-5.0.0/NCA/R/p_nca_cr_vrs.R | 84 +++-- NCA-5.0.0/NCA/R/p_nca_custom.R |only NCA-5.0.0/NCA/R/p_nca_ols.R | 50 ++- NCA-5.0.0/NCA/R/p_nca_qr.R | 78 +++-- NCA-5.0.0/NCA/R/p_peers.R | 11 NCA-5.0.0/NCA/R/p_purity_helpers.R |only NCA-5.0.0/NCA/R/p_purity_metrics.R |only NCA-5.0.0/NCA/R/p_purity_sql.R |only NCA-5.0.0/NCA/R/p_scope.R | 84 ++--- NCA-5.0.0/NCA/R/p_utils.R | 133 +++++---- NCA-5.0.0/NCA/R/p_validate.R | 169 +++++++---- NCA-5.0.0/NCA/build/partial.rdb |binary NCA-5.0.0/NCA/man/NCA-package.Rd | 27 - NCA-5.0.0/NCA/man/nca.Rd | 6 NCA-5.0.0/NCA/man/nca.example.Rd | 6 NCA-5.0.0/NCA/man/nca.example2.Rd | 4 NCA-5.0.0/NCA/man/nca_analysis.Rd | 55 ++- NCA-5.0.0/NCA/man/nca_difference.Rd |only NCA-5.0.0/NCA/man/nca_extract.Rd |only NCA-5.0.0/NCA/man/nca_normalize.Rd |only NCA-5.0.0/NCA/man/nca_outliers.Rd | 16 - NCA-5.0.0/NCA/man/nca_output.Rd | 29 + NCA-5.0.0/NCA/man/nca_power.Rd | 20 - NCA-5.0.0/NCA/man/nca_powerplot.Rd |only NCA-5.0.0/NCA/man/nca_random.Rd | 4 NCA-5.0.0/NCA/tests/testthat/test-intercept.R |only NCA-5.0.0/NCA/tests/testthat/test.p_ceiling.R | 7 70 files changed, 1910 insertions(+), 1380 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data. Has functions for extracting
and manipulating parameter estimates and predicted values (ci.lin
and its cousins), as well as a number of epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.61 dated 2025-10-07 and 2.63 dated 2026-03-20
CHANGES | 23 DESCRIPTION | 8 MD5 | 154 NAMESPACE | 4 R/LexisScarf.R |only R/cutLexis.R | 20 R/lexis.R | 15 R/overlap.Lexis.R |only R/paths.Lexis.R | 10 R/xcutLexis.R | 2 inst/doc/01flup.R | 94 inst/doc/01flup.pdf |binary inst/doc/02addLexis.pdf |binary inst/doc/03crisk.pdf |binary inst/doc/04simLexis.pdf |binary inst/doc/05yll.pdf |binary man/Icens.Rd | 72 man/LexisScarf.Rd |only man/ci.lin.Rd | 38 man/cutLexis.Rd | 2 man/mcutLexis.Rd | 2 man/overlap.Lexis.Rd |only man/paths.Lexis.Rd | 12 man/time.scales.Rd | 8 man/xcutLexis.Rd | 40 vignettes/01flup-Ieff.pdf |binary vignettes/01flup-IeffR.pdf |binary vignettes/01flup-box1.pdf |binary vignettes/01flup-box4.pdf |binary vignettes/01flup-dmL1.pdf |binary vignettes/01flup-dmL2.pdf |binary vignettes/01flup-dur-int-RR.pdf |binary vignettes/01flup-dur-int.pdf |binary vignettes/01flup-ins-time.pdf |binary vignettes/01flup-mbox.pdf |binary vignettes/01flup-mboxr.pdf |binary vignettes/01flup-pr-a.pdf |binary vignettes/01flup-sep-HR.pdf |binary vignettes/01flup-sep-mort.pdf |binary vignettes/01flup.R | 94 vignettes/01flup.pdf | 6380 +++++++++++++++----------------------- vignettes/01flup.rnw | 68 vignettes/01flup.tex | 140 vignettes/02addLexis.pdf | 1772 +++++----- vignettes/02addLexis.rnw | 4 vignettes/02addLexis.tex | 20 vignettes/03crisk-Sr1.pdf |binary vignettes/03crisk-Sr2.pdf |binary vignettes/03crisk-boxes.pdf |binary vignettes/03crisk-boxes4.pdf |binary vignettes/03crisk-boxes5.pdf |binary vignettes/03crisk-cR.pdf |binary vignettes/03crisk-crates.pdf |binary vignettes/03crisk-difrat.pdf |binary vignettes/03crisk-difratx.pdf |binary vignettes/03crisk-rates-ci.pdf |binary vignettes/03crisk-rates-l.pdf |binary vignettes/03crisk-rates.pdf |binary vignettes/03crisk-stack-ci.pdf |binary vignettes/03crisk-stack.pdf |binary vignettes/03crisk.pdf | 2900 ++++++++--------- vignettes/03crisk.rnw | 4 vignettes/03crisk.tex | 12 vignettes/04simLexis-boxes.pdf |binary vignettes/04simLexis-comp-0.pdf |binary vignettes/04simLexis-mort-int.pdf |binary vignettes/04simLexis-pstate0.pdf |binary vignettes/04simLexis-pstatex.pdf |binary vignettes/04simLexis-pstatey.pdf |binary vignettes/04simLexis.pdf | 6342 ++++++++++++++++++------------------- vignettes/04simLexis.rnw | 10 vignettes/04simLexis.tex | 44 vignettes/05yll-imm.pdf |binary vignettes/05yll-states.pdf |binary vignettes/05yll-sus.pdf |binary vignettes/05yll-tot.pdf |binary vignettes/05yll.pdf |binary vignettes/05yll.rnw | 4 vignettes/05yll.tex | 12 vignettes/fixall.bat | 12 80 files changed, 8608 insertions(+), 9714 deletions(-)
Title: Create Spreadsheet Publications Following Best Practice
Description: Generate spreadsheet publications that follow best practice
guidance from the UK government's Analysis Function, available at
<https://analysisfunction.civilservice.gov.uk/policy-store/releasing-statistics-in-spreadsheets/>,
with a focus on accessibility. See also the 'Python' package 'gptables'.
Author: Matt Dray [aut],
Tim Taylor [ctb],
Matt Kerlogue [ctb],
Crown Copyright [cph],
Olivia Box Power [cre, ctb],
Zachary Gleisner [ctb]
Maintainer: Olivia Box Power <Olivia.BoxPower@dhsc.gov.uk>
Diff between aftables versions 1.0.1 dated 2025-02-19 and 2.0.0 dated 2026-03-20
DESCRIPTION | 28 - MD5 | 117 +++--- NAMESPACE | 19 NEWS.md | 12 R/addin.R | 16 R/aftable.R | 46 -- R/aftables-package.R | 18 R/config_utils.R |only R/data.R | 10 R/sysdata.rda |only R/utils-aftable.R | 36 - R/utils-workbook-style.R | 385 ++++++++++--------- R/utils-workbook.R | 641 ++++++++++++++++++++++++--------- R/utils.R | 3 R/workbook.R | 121 +++++- README.md | 34 - build/vignette.rds |binary data/demo_workbook.rda |binary inst/doc/aftables.R | 7 inst/doc/aftables.Rmd | 517 +++++++++++++------------- inst/doc/aftables.html | 137 ++----- inst/doc/checklist.Rmd | 194 ++++----- inst/doc/checklist.html | 17 inst/doc/configfiles.R |only inst/doc/configfiles.Rmd |only inst/doc/configfiles.html |only inst/doc/structure.Rmd | 349 +++++++++-------- inst/doc/structure.html | 73 +-- inst/doc/terminology.Rmd | 124 +++--- inst/doc/terminology.html | 2 inst/ext-data |only inst/rstudio/addins.dcf | 11 man/aftables-package.Rd | 3 man/at_template_aftable.Rd | 4 man/at_template_workflow.Rd | 2 man/create_aftable.Rd | 22 - man/create_config_yaml.Rd |only man/demo_aftable.Rd | 4 man/demo_df.Rd | 2 man/demo_workbook.Rd | 4 man/figures/vignette-workbook.gif |binary man/generate_workbook.Rd | 81 +++- tests/testthat/configs |only tests/testthat/test-addins.R | 1 tests/testthat/test-aftable.R | 385 ++++++++++--------- tests/testthat/test-apply-config.R |only tests/testthat/test-read-config-yaml.R |only tests/testthat/test-utils.R | 168 ++++++++ tests/testthat/test-workbook.R | 56 ++ vignettes/aftables.Rmd | 517 +++++++++++++------------- vignettes/checklist.Rmd | 194 ++++----- vignettes/configfiles.Rmd |only vignettes/structure.Rmd | 349 +++++++++-------- vignettes/terminology.Rmd | 124 +++--- 54 files changed, 2742 insertions(+), 2091 deletions(-)
Title: Analysing Prognostic Studies
Description: Functions that help with analysis of prognostic study data. This allows users with little experience of developing models to develop models and assess the performance of the prognostic models. This also summarises the information, so the performance of multiple models can be displayed simultaneously. This minor update fixes issues related to memory requirements with large number of simulations and deals with situations when there is overfitting of data. Gurusamy, K (2026)<https://github.com/kurinchi2k/EQUALPrognosis>.
Author: Kurinchi Gurusamy [aut, cre]
Maintainer: Kurinchi Gurusamy <k.gurusamy@ucl.ac.uk>
Diff between EQUALPrognosis versions 0.1.2 dated 2026-02-04 and 0.1.3 dated 2026-03-20
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/calculate_actual_predicted.R | 2 +- R/compile_results.R | 26 +++++++++++++------------- 4 files changed, 22 insertions(+), 22 deletions(-)
More information about EQUALPrognosis at CRAN
Permanent link
Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Exploratory and descriptive analysis of event based data. Provides methods for describing and selecting process data, and for preparing event log data for process mining. Builds on the S3-class for event logs implemented in the package 'bupaR'.
Author: Benoît Depaire [cre],
Gert Janssenswillen [aut],
Gerard van Hulzen [ctb],
Marijke Swennen [ctb],
Ivan Esin [ctb],
Felix Mannhardt [ctb],
Hasselt University [cph]
Maintainer: Benoît Depaire <benoit.depaire@uhasselt.be>
Diff between edeaR versions 1.0.0 dated 2025-11-29 and 1.0.1 dated 2026-03-20
edeaR-1.0.0/edeaR/R/ifilter.R |only edeaR-1.0.0/edeaR/man/ifilter.Rd |only edeaR-1.0.1/edeaR/DESCRIPTION | 6 edeaR-1.0.1/edeaR/MD5 | 144 ++--- edeaR-1.0.1/edeaR/R/activity_frequency.R | 222 ++++---- edeaR-1.0.1/edeaR/R/activity_presence.R | 198 +++---- edeaR-1.0.1/edeaR/R/calculate_queuing_times.R | 114 ++-- edeaR-1.0.1/edeaR/R/edeaR.R | 70 +- edeaR-1.0.1/edeaR/R/end_activities.R | 228 ++++---- edeaR-1.0.1/edeaR/R/filter_activity.R | 146 ++--- edeaR-1.0.1/edeaR/R/filter_activity_frequency.R | 318 ++++++------ edeaR-1.0.1/edeaR/R/filter_activity_instance.R | 150 ++--- edeaR-1.0.1/edeaR/R/filter_activity_presence.R | 320 ++++++------ edeaR-1.0.1/edeaR/R/filter_case.R | 148 ++--- edeaR-1.0.1/edeaR/R/filter_case_condition.R | 76 +- edeaR-1.0.1/edeaR/R/filter_endpoints.R | 234 ++++----- edeaR-1.0.1/edeaR/R/filter_endpoints_condition.R | 270 +++++----- edeaR-1.0.1/edeaR/R/filter_lifecycle.R | 146 ++--- edeaR-1.0.1/edeaR/R/filter_lifecycle_presence.R | 268 +++++----- edeaR-1.0.1/edeaR/R/filter_precedence.R | 390 +++++++-------- edeaR-1.0.1/edeaR/R/filter_precedence_condition.R | 268 +++++----- edeaR-1.0.1/edeaR/R/filter_precedence_resource.R | 434 ++++++++--------- edeaR-1.0.1/edeaR/R/filter_processing_time.R | 294 +++++------ edeaR-1.0.1/edeaR/R/filter_resource.R | 140 ++--- edeaR-1.0.1/edeaR/R/filter_resource_frequency.R | 320 ++++++------ edeaR-1.0.1/edeaR/R/filter_throughput_time.R | 242 ++++----- edeaR-1.0.1/edeaR/R/filter_time_period.R | 404 +++++++-------- edeaR-1.0.1/edeaR/R/filter_trace_frequency.R | 238 ++++----- edeaR-1.0.1/edeaR/R/filter_trace_length.R | 252 ++++----- edeaR-1.0.1/edeaR/R/filter_trim.R | 316 ++++++------ edeaR-1.0.1/edeaR/R/filter_trim_lifecycle.R | 258 +++++----- edeaR-1.0.1/edeaR/R/groupby_helpers.R | 158 +++--- edeaR-1.0.1/edeaR/R/idle_time.R | 270 +++++----- edeaR-1.0.1/edeaR/R/idle_time_case.R | 114 ++-- edeaR-1.0.1/edeaR/R/idle_time_resource.R | 112 ++-- edeaR-1.0.1/edeaR/R/idle_time_trace.R | 42 - edeaR-1.0.1/edeaR/R/number_of_repetitions.R | 414 ++++++++-------- edeaR-1.0.1/edeaR/R/number_of_selfloops.R | 416 ++++++++-------- edeaR-1.0.1/edeaR/R/number_of_traces.R | 106 ++-- edeaR-1.0.1/edeaR/R/plot.activity_frequency.R | 102 +-- edeaR-1.0.1/edeaR/R/plot.activity_presence.R | 40 - edeaR-1.0.1/edeaR/R/plot.end_activity.R | 138 ++--- edeaR-1.0.1/edeaR/R/plot.idle_time.R | 90 +-- edeaR-1.0.1/edeaR/R/plot.number_of_repetitions.R | 188 +++---- edeaR-1.0.1/edeaR/R/plot.number_of_selfloops.R | 188 +++---- edeaR-1.0.1/edeaR/R/plot.processing_time.R | 130 ++--- edeaR-1.0.1/edeaR/R/plot.referral_matrix.R | 38 - edeaR-1.0.1/edeaR/R/plot.resource_frequency.R | 130 ++--- edeaR-1.0.1/edeaR/R/plot.resource_involvement.R | 94 +-- edeaR-1.0.1/edeaR/R/plot.resource_specialisation.R | 96 +-- edeaR-1.0.1/edeaR/R/plot.start_activities.R | 136 ++--- edeaR-1.0.1/edeaR/R/plot.throughput_time.R | 106 ++-- edeaR-1.0.1/edeaR/R/plot.trace_coverage.R | 114 ++-- edeaR-1.0.1/edeaR/R/plot.trace_length.R | 94 +-- edeaR-1.0.1/edeaR/R/processing_time.R | 354 ++++++------- edeaR-1.0.1/edeaR/R/processing_time_case.R | 56 +- edeaR-1.0.1/edeaR/R/processing_time_trace.R | 54 +- edeaR-1.0.1/edeaR/R/redo_repetitions_referral_matrix.R | 98 +-- edeaR-1.0.1/edeaR/R/redo_selfloops_referral_matrix.R | 92 +-- edeaR-1.0.1/edeaR/R/resource_frequency.R | 250 ++++----- edeaR-1.0.1/edeaR/R/resource_involvement.R | 178 +++--- edeaR-1.0.1/edeaR/R/resource_specialisation.R | 200 +++---- edeaR-1.0.1/edeaR/R/size_of_repetitions.R | 268 +++++----- edeaR-1.0.1/edeaR/R/size_of_selfloops.R | 278 +++++----- edeaR-1.0.1/edeaR/R/start_activities.R | 228 ++++---- edeaR-1.0.1/edeaR/R/throughput_time.R | 312 ++++++------ edeaR-1.0.1/edeaR/R/throughput_time_activity.R | 50 - edeaR-1.0.1/edeaR/R/throughput_time_trace.R | 48 - edeaR-1.0.1/edeaR/R/trace_coverage.R | 150 ++--- edeaR-1.0.1/edeaR/R/trace_length.R | 224 ++++---- edeaR-1.0.1/edeaR/inst/doc/filters.html | 4 edeaR-1.0.1/edeaR/inst/doc/metrics.html | 66 +- edeaR-1.0.1/edeaR/inst/doc/queue.html | 19 edeaR-1.0.1/edeaR/inst/doc/work_schedules.html | 4 74 files changed, 6435 insertions(+), 6428 deletions(-)
Title: Analysing SNP Data to Identify Sex-Linked Markers
Description: Identifies, filters and exports sex linked markers using 'SNP'
(single nucleotide polymorphism) data. To install the other packages, we
recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'.
If you want understand the applied rational to identify sexlinked markers
and/or want to cite 'dartR.sexlinked', you find the information by typing
citation('dartR.sexlinked') in the console.
Author: Diana Robledo-Ruiz [aut, cre],
Floriaan Devloo-Delva [aut],
Bernd Gruber [aut],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb]
Maintainer: Diana Robledo-Ruiz <diana.robledoruiz1@monash.edu>
Diff between dartR.sexlinked versions 1.0.5 dated 2024-06-24 and 1.2.2 dated 2026-03-20
DESCRIPTION | 17 - MD5 | 24 - NAMESPACE | 3 R/gl.drop.sexlinked.r | 660 ------------------------------------------- R/gl.filter.sexlinked.r |only R/gl.infer.sex.r | 288 +++++++++++-------- R/gl.keep.sexlinked.r | 678 +++++++++++++++++++++++++-------------------- R/gl.report.sexlinked.r | 565 +++++++++++++++++++++---------------- R/zzz.r | 2 man/gl.drop.sexlinked.Rd | 80 ----- man/gl.filter.sexlinked.Rd |only man/gl.infer.sex.Rd | 69 ++-- man/gl.keep.sexlinked.Rd | 55 +-- man/gl.report.sexlinked.Rd | 71 ++-- 14 files changed, 1033 insertions(+), 1479 deletions(-)
More information about dartR.sexlinked at CRAN
Permanent link
Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.1.0 dated 2026-03-03 and 1.2.0 dated 2026-03-20
DESCRIPTION | 9 MD5 | 139 ++++-- NAMESPACE | 26 + NEWS.md | 126 +++++ R/RcppExports.R | 4 R/matching_cem.R |only R/matching_core.R | 60 +- R/matching_diagnostics.R | 210 +++++++++ R/matching_distance.R | 52 +- R/matching_full.R |only R/matching_interop.R |only R/matching_join.R | 57 ++ R/matching_output.R |only R/matching_parallel.R | 6 R/matching_plots.R | 10 R/matching_subclass.R |only R/utils.R | 3 R/zzz.R | 19 README.md | 64 ++ inst/WORDLIST | 2 inst/doc/algorithms.html | 4 inst/doc/comparison.R | 139 +++--- inst/doc/comparison.Rmd | 52 +- inst/doc/comparison.html | 134 ++++-- inst/doc/getting-started.R | 12 inst/doc/getting-started.Rmd | 44 +- inst/doc/getting-started.html | 393 ++++++++++-------- inst/doc/matching-workflows.R | 205 +++++++++ inst/doc/matching-workflows.Rmd | 312 ++++++++++++++ inst/doc/matching-workflows.html | 495 ++++++++++++++++++++++- inst/doc/pixel-morphing.html | 4 inst/doc/troubleshooting.html | 6 inst/extdata/icons/circleA_40.png |only inst/extdata/icons/circleA_80.png |only inst/extdata/icons/circleB_40.png |only inst/extdata/icons/circleB_80.png |only inst/extdata/icons/circle_color_walk.png |only inst/extdata/icons/circle_exact.png |only inst/extdata/icons/circle_recursive.png |only inst/extdata/morphs/image_color_walk.png |only inst/extdata/morphs/image_exact.png |only inst/extdata/morphs/image_recursive.png |only inst/extdata/work |only man/as_matchit.Rd |only man/bal.tab.matching_result.Rd |only man/balance_diagnostics.Rd | 43 + man/build_cost_matrix.Rd | 3 man/cem_match.Rd |only man/compute_distance_matrix.Rd | 17 man/dot-auto_breaks.Rd |only man/dot-blocks_parallel.Rd | 3 man/dot-couples_blocked.Rd | 3 man/dot-couples_single.Rd | 3 man/full_match.Rd |only man/greedy_couples.Rd | 7 man/greedy_couples_blocked.Rd | 3 man/greedy_couples_single.Rd | 3 man/join_matched.Rd | 25 - man/match_couples.Rd | 7 man/match_couples_blocked.Rd | 3 man/match_couples_single.Rd | 3 man/match_data.Rd |only man/print.cem_result.Rd |only man/print.full_matching_result.Rd |only man/print.subclass_result.Rd |only man/subclass_match.Rd |only src/Makevars | 4 src/Makevars.win | 4 src/RcppExports.cpp | 14 src/rcpp_interface.cpp | 6 src/solvers/solve_full_matching.cpp |only src/solvers/solve_full_matching.h |only src/solvers/solve_full_matching_rcpp.cpp |only tests/testthat/test-lap-solve-batch-coverage-3.R | 6 tests/testthat/test-lap-solve-batch-coverage.R | 17 tests/testthat/test-matching-cem.R |only tests/testthat/test-matching-full-optimal.R |only tests/testthat/test-matching-full.R |only tests/testthat/test-matching-interop.R |only tests/testthat/test-matching-mahalanobis.R |only tests/testthat/test-matching-output.R |only tests/testthat/test-matching-subclass.R |only vignettes/comparison.Rmd | 52 +- vignettes/getting-started.Rmd | 44 +- vignettes/images/ImageA_80.png |only vignettes/images/ImageB_80.png |only vignettes/images/circleA_80.png |only vignettes/images/circleB_80.png |only vignettes/matching-workflows.Rmd | 312 ++++++++++++++ 89 files changed, 2698 insertions(+), 471 deletions(-)
Title: Create Publication-Ready Regression Tables with Panels
Description: Create an automated regression table that is well-suited for models that are estimated with multiple dependent variables. 'panelsummary' extends 'modelsummary' (Arel-Bundock, V. (2022) <doi:10.18637/jss.v103.i01>) by allowing regression tables to be split into multiple sections with a simple function call. Utilize familiar arguments such as fmt, estimate, statistic, vcov, conf_level, stars, coef_map, coef_omit, coef_rename, gof_map, and gof_omit from 'modelsummary' to clean the table, and additionally, add a row for the mean of the dependent variable without external manipulation.
Author: Michael Topper [aut, cre],
Vincent Arel-Bundock [cph]
Maintainer: Michael Topper <miketopper123@gmail.com>
Diff between panelsummary versions 0.1.2.1 dated 2023-08-16 and 0.1.3 dated 2026-03-20
DESCRIPTION | 9 - MD5 | 46 +++---- NEWS.md | 5 R/clean_raw.R | 9 + R/helper_functions.R | 2 R/panelsummary_raw.R | 34 +++++ README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/adding_rows.R | 2 inst/doc/adding_rows.html | 4 inst/doc/panelsummary.R | 2 inst/doc/panelsummary.Rmd | 4 inst/doc/panelsummary.html | 237 +++++++++++++++++++++++++++++++++---- inst/doc/with_fixest.R | 2 inst/doc/with_fixest.Rmd | 2 inst/doc/with_fixest.html | 151 ++++++++++++----------- man/clean_raw.Rd | 8 + man/panelsummary-package.Rd | 1 man/panelsummary.Rd | 41 +++--- man/panelsummary_raw.Rd | 45 ++++--- tests/testthat/test-create_means.R | 26 ++-- vignettes/panelsummary.Rmd | 4 vignettes/with_fixest.Rmd | 2 24 files changed, 454 insertions(+), 184 deletions(-)
Title: Integrated Interface of Bayesian Single Index Models using
'nimble'
Description: Provides tools for fitting Bayesian single index models with
flexible choices of priors for both the index and the link function.
The package implements model estimation and posterior inference using
efficient MCMC algorithms built on the 'nimble' framework, allowing
users to specify, extend, and simulate models in a unified and
reproducible manner. The following methods are implemented in the
package: Antoniadis et al. (2004)
<https://www.jstor.org/stable/24307224>, Wang (2009)
<doi:10.1016/j.csda.2008.12.010>, Choi et al. (2011)
<doi:10.1080/10485251003768019>, Dhara et al. (2019)
<doi:10.1214/19-BA1170>, McGee et al. (2023) <doi:10.1111/biom.13569>.
Author: Seowoo Jung [aut, cre],
Eun-kyung Lee [aut]
Maintainer: Seowoo Jung <jsw1347@ewha.ac.kr>
Diff between BayesSIM versions 1.0.1 dated 2026-01-08 and 1.0.2 dated 2026-03-20
BayesSIM-1.0.1/BayesSIM/man/predict.bsim.Rd |only BayesSIM-1.0.2/BayesSIM/DESCRIPTION | 6 BayesSIM-1.0.2/BayesSIM/MD5 | 90 ++--- BayesSIM-1.0.2/BayesSIM/NAMESPACE | 8 BayesSIM-1.0.2/BayesSIM/R/bayesSIM.R | 2 BayesSIM-1.0.2/BayesSIM/R/bsFisher-sampler.R | 33 ++ BayesSIM-1.0.2/BayesSIM/R/bsFisher.R | 58 ++- BayesSIM-1.0.2/BayesSIM/R/bsPolar.R | 48 ++- BayesSIM-1.0.2/BayesSIM/R/bsSphere-functions.R | 14 BayesSIM-1.0.2/BayesSIM/R/bsSphere-sampler.R | 17 - BayesSIM-1.0.2/BayesSIM/R/bsSphere.R | 48 ++- BayesSIM-1.0.2/BayesSIM/R/bsSpike.R | 48 ++- BayesSIM-1.0.2/BayesSIM/R/generics.R | 262 +++++++++++++---- BayesSIM-1.0.2/BayesSIM/R/gpFisher.R | 49 ++- BayesSIM-1.0.2/BayesSIM/R/gpPolar-functions.R | 160 ++++++---- BayesSIM-1.0.2/BayesSIM/R/gpPolar-sampler.R | 158 +++++++--- BayesSIM-1.0.2/BayesSIM/R/gpPolar.R | 80 +++-- BayesSIM-1.0.2/BayesSIM/R/gpPolarTemp.R | 45 ++ BayesSIM-1.0.2/BayesSIM/R/gpSphere-united.R | 46 ++ BayesSIM-1.0.2/BayesSIM/R/gpspike-functions.R | 1 BayesSIM-1.0.2/BayesSIM/R/gpspike-sampler.R | 8 BayesSIM-1.0.2/BayesSIM/R/gpspike.R | 88 ++++- BayesSIM-1.0.2/BayesSIM/R/initial-params.R | 6 BayesSIM-1.0.2/BayesSIM/man/BayesSIM.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/as.data.frame.bsimPred.Rd |only BayesSIM-1.0.2/BayesSIM/man/as_bsim.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/bsFisher.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/bsPolar.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/bsSphere.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/bsSpike.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/coef.bsim.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/compileModelAndMCMC.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/fitted.bsim.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/genBasic.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/getFunction.Rd | 14 BayesSIM-1.0.2/BayesSIM/man/getInit.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/gof.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/gpFisher.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/gpPolar.Rd | 22 - BayesSIM-1.0.2/BayesSIM/man/gpSphere.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/gpSpike.Rd | 4 BayesSIM-1.0.2/BayesSIM/man/nimTraceplot.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/plot.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/predict.Rd |only BayesSIM-1.0.2/BayesSIM/man/summary.bsim.Rd | 4 BayesSIM-1.0.2/BayesSIM/man/summary.bsimPred.Rd |only BayesSIM-1.0.2/BayesSIM/tests/testthat/test-BayesSIM.R | 2 BayesSIM-1.0.2/BayesSIM/tests/testthat/test-generic.R | 14 48 files changed, 951 insertions(+), 416 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-24 0.0.2
2019-08-27 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-05 0.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-22 2.1.2
2018-10-02 2.1.1
2018-07-05 2.1.0
2017-08-30 2.0.3
2017-04-13 2.0.1
2017-01-10 2.0.0
2016-08-29 1.1.0
2016-08-13 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-12 0.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-04 0.8-3
2015-07-05 0.7-6
2015-05-25 0.6-16
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-29 0.1.3
2025-11-25 0.1.2
2025-11-19 0.1.1
2025-11-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-05 0.3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-10 1.3.4.1
2022-11-10 1.3.4
2021-10-28 1.3.3
2020-02-13 1.3.2
2018-09-14 1.3.1
2015-01-06 1.3.0
2014-11-16 1.2.11
2014-01-08 1.2.10
2013-07-27 1.2.9
2013-07-16 1.2.8
2013-05-23 1.2.7
2013-02-12 1.2.6
2012-11-15 1.2.5
2012-07-06 1.2.4
2012-04-20 1.2.3
2012-03-15 1.2.1
2012-02-15 1.2.0
2012-02-13 1.1.9
2012-02-08 1.1.8
2012-01-10 1.1.7
2011-07-28 1.1.5
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: CRAN Team [ctb] ,
Duncan Temple Lang [aut] ,
Tomas Kalibera [ctb],
Ivan Krylov [cre]
Maintainer: Ivan Krylov <ikrylov@disroot.org>
Diff between XML versions 3.99-0.22 dated 2026-02-10 and 3.99-0.23 dated 2026-03-20
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/Utils.c | 2 +- src/XMLEventParse.c | 5 +++-- src/schema.c | 8 +++++--- 6 files changed, 21 insertions(+), 14 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] ,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 2.1.0 dated 2026-02-11 and 2.2.0 dated 2026-03-20
DESCRIPTION | 12 MD5 | 574 +- NAMESPACE | 1026 +-- NEWS.md | 1244 ++-- R/AddTip.R | 550 +- R/ArtificialExtinction.R | 242 R/Cherries.R | 5 R/ClusterTable.R | 254 R/Combinatorics.R | 696 +- R/Consensus.R | 300 - R/ConsistentSplits.R | 84 R/Decompose.R | 330 - R/DropTip.R | 12 R/EdgeRatio.R |only R/ImposeConstraint.R | 278 - R/Information.R | 502 - R/KeptPaths.R | 94 R/KeptVerts.R | 126 R/LongBranchScore.R | 150 R/MatchNodes.R | 216 R/MatchStrings.R | 66 R/PathLengths.R | 96 R/PhyToString.R | 286 - R/RUtreebalance.R | 648 +- R/RcppExports-manual.R | 64 R/RcppExports.R | 16 R/ReadMrBayes.R | 180 R/ReadTntTree.R | 580 +- R/Reweight.R | 220 R/RoguePlot.R | 618 +- R/SplitFunctions.R | 912 +-- R/Splits.R | 1294 ++-- R/Stemwardness.R | 218 R/Support.R | 348 - R/TipTimedTree.R | 100 R/TopologyOnly.R | 84 R/TotalCopheneticIndex.R | 316 - R/TreeNumber.R | 1042 ++- R/TreeTools-package.R | 50 R/Treeness.R | 116 R/as.matrix.R | 30 R/as.multiPhylo.R | 152 R/data.R | 180 R/helper_functions.R | 200 R/match.R | 496 - R/mst.R | 158 R/parse_files.R | 1830 +++--- R/phylo.R | 644 +- R/sort.R | 156 R/split_analysis.R | 162 R/tree_ancestors.R | 220 R/tree_comparison.R | 86 R/tree_descendants.R | 274 - R/tree_display.R | 292 - R/tree_generation.R | 998 +-- R/tree_information.R | 206 R/tree_numbering.R | 56 R/tree_properties.R | 1096 +--- R/tree_rearrangement.R | 1294 ++-- R/tree_shape.R | 572 +- R/tree_write.R | 262 R/zzz.R | 68 build/partial.rdb |binary build/vignette.rds |binary data/brewer.R | 40 data/nRootedShapes.R | 114 data/nUnrootedShapes.R | 124 inst/CITATION | 34 inst/REFERENCES.bib | 745 +- inst/WORDLIST | 251 inst/apa-old-doi-prefix.csl | 4541 ++++++++--------- inst/doc/filesystem-navigation.Rmd | 104 inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.Rmd | 428 - inst/doc/load-data.html | 4 inst/doc/load-trees.Rmd | 250 inst/doc/load-trees.html | 4 inst/extdata/input/dataset.nex | 44 inst/extdata/input/notes.nex | 54 inst/extdata/output/named.tre | 6 inst/extdata/output/numbered.tre | 8 inst/extdata/tests/ape-tree.nex | 10 inst/extdata/tests/continuous.nex | 44 inst/extdata/tests/encoding.nex | 48 inst/extdata/tests/parse-nexus.nexus | 510 - inst/extdata/tests/taxon-notes.nex | 48 inst/extdata/tests/tnt-bare-tree.tnt | 2 inst/extdata/tests/tnt-dna.tnt | 42 inst/extdata/tests/tnt-matrix.tnt | 294 - inst/extdata/tests/tnt-namedtree.tre | 8 inst/extdata/tests/tnt-tree.tre | 46 inst/extdata/tests/tnt-trees-and-matrix.tnt | 58 inst/include/TreeTools/SplitList.h | 29 inst/include/TreeTools/tree_number.h |only man/AddTip.Rd | 280 - man/AncestorEdge.Rd | 106 man/ApeTime.Rd | 54 man/ArtificialExtinction.Rd | 216 man/CharacterInformation.Rd | 86 man/Cherries.Rd | 101 man/CladeSizes.Rd | 96 man/CladisticInfo.Rd | 144 man/ClusterTable-methods.Rd | 94 man/ClusterTable.Rd | 160 man/CollapseNode.Rd | 162 man/CompatibleSplits.Rd | 108 man/Consensus.Rd | 104 man/ConsensusWithout.Rd | 211 man/ConstrainedNJ.Rd | 108 man/Decompose.Rd | 166 man/DescendantEdges.Rd | 162 man/DoubleFactorial.Rd | 132 man/DropTip.Rd | 280 - man/EdgeAncestry.Rd | 124 man/EdgeDistances.Rd | 104 man/EdgeRatio.Rd |only man/EndSentence.Rd | 64 man/ExtractTaxa.Rd | 90 man/GenerateTree.Rd | 188 man/Hamming.Rd | 156 man/ImposeConstraint.Rd | 148 man/J1Index.Rd | 190 man/KeptPaths.Rd | 132 man/KeptVerts.Rd | 138 man/LabelSplits.Rd | 172 man/LeafLabelInterchange.Rd | 118 man/ListAncestors.Rd | 218 man/Lobo.data.Rd | 66 man/LongBranch.Rd | 129 man/MRCA.Rd | 134 man/MSTEdges.Rd | 146 man/MakeTreeBinary.Rd | 108 man/MatchEdges.Rd | 137 man/MatchStrings.Rd | 80 man/MatrixToPhyDat.Rd | 156 man/MorphoBankDecode.Rd | 58 man/N1Spr.Rd | 76 man/NDescendants.Rd | 92 man/NJTree.Rd | 82 man/NPartitionPairs.Rd | 102 man/NRooted.Rd | 268 - man/NSplits.Rd | 171 man/NTip.Rd | 139 man/NewickTree.Rd | 54 man/Neworder.Rd | 128 man/NodeDepth.Rd | 126 man/NodeNumbers.Rd | 113 man/NodeOrder.Rd | 108 man/PairwiseDistances.Rd | 82 man/PathLengths.Rd | 117 man/PhyToString.Rd | 212 man/PolarizeSplits.Rd | 70 man/ReadCharacters.Rd | 288 - man/ReadMrBayesTrees.Rd | 110 man/ReadTntTree.Rd | 248 man/Renumber.Rd | 118 man/RenumberTips.Rd | 140 man/Reorder.Rd | 556 +- man/Reweight.Rd | 156 man/RightmostCharacter.Rd | 72 man/RoguePlot.Rd | 240 man/RootNode.Rd | 104 man/RootTree.Rd | 190 man/SampleOne.Rd | 84 man/SortTree.Rd | 184 man/SplitConsistent.Rd | 90 man/SplitFrequency.Rd | 161 man/SplitInformation.Rd | 247 man/SplitMatchProbability.Rd | 94 man/Splits.Rd | 216 man/SplitsInBinaryTree.Rd | 161 man/Stemwardness.Rd | 198 man/Subsplit.Rd | 96 man/Subtree.Rd | 122 man/SupportColour.Rd | 142 man/TipLabels.Rd | 251 man/TipTimedTree.Rd | 140 man/TipsInSplits.Rd | 144 man/TopologyOnly.Rd | 46 man/TotalCopheneticIndex.Rd | 188 man/TreeIsRooted.Rd | 85 man/TreeNumber.Rd | 421 - man/TreeShape.Rd | 318 - man/TreeTools-package.Rd | 80 man/Treeness.Rd | 113 man/TreesMatchingSplit.Rd | 92 man/TreesMatchingTree.Rd | 98 man/TrivialSplits.Rd | 96 man/TrivialTree.Rd | 124 man/Unquote.Rd | 64 man/UnrootedTreesMatchingSplit.Rd | 96 man/UnshiftTree.Rd | 116 man/WriteTntCharacters.Rd | 140 man/as.Newick.Rd | 96 man/as.multiPhylo.Rd | 106 man/brewer.Rd | 66 man/dot-RandomParent.Rd | 54 man/doubleFactorials.Rd | 52 man/edge_to_splits.Rd | 98 man/is.TreeNumber.Rd | 64 man/logDoubleFactorials.Rd | 46 man/match.Splits.Rd | 136 man/match.multiPhylo.Rd | 144 man/nRootedShapes.Rd | 56 man/print.TreeNumber.Rd | 44 man/root_on_node.Rd | 58 man/sapply64.Rd | 164 man/sort.multiPhylo.Rd | 114 man/xor.Rd | 62 src/RcppExports-manual.cpp | 6 src/RcppExports.cpp | 55 src/consensus.cpp | 169 src/int_to_tree.cpp | 168 src/node_depth.cpp |only src/renumber_tips.cpp |only src/splits.cpp | 97 src/tips_in_splits.cpp | 4 tests/figs/rogueplot.svg | 68 tests/spelling.R | 8 tests/testthat.R | 8 tests/testthat/_snaps/RoguePlot/rogueplot-poly.svg | 82 tests/testthat/_snaps/RoguePlot/rogueplot-simple.svg | 94 tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg | 106 tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg | 82 tests/testthat/_snaps/Support/labelsplits-nameless.svg | 172 tests/testthat/_snaps/Support/labelsplits-names.svg | 148 tests/testthat/_snaps/Support/labelsplits.svg | 148 tests/testthat/_snaps/mst/mst-plotting.svg | 142 tests/testthat/_snaps/tree_display/sorted-tree.svg | 270 - tests/testthat/test-AddTip.R | 356 - tests/testthat/test-ArtificialExtinction.R | 94 tests/testthat/test-Cherries.R | 24 tests/testthat/test-ClusterTable.R | 284 - tests/testthat/test-Decompose.R | 152 tests/testthat/test-DropTip.R | 6 tests/testthat/test-EdgeRatio.R |only tests/testthat/test-FirstMatchingSplit.R | 68 tests/testthat/test-ImposeConstraint.R | 275 - tests/testthat/test-KeptPaths.R | 40 tests/testthat/test-KeptVerts.R | 172 tests/testthat/test-LongBranchScore.R | 36 tests/testthat/test-MatchNodes.R | 148 tests/testthat/test-MatchStrings.R | 26 tests/testthat/test-PathLengths.R | 70 tests/testthat/test-PhyToString.R | 150 tests/testthat/test-RUtreebalance.R | 128 tests/testthat/test-ReadMrBayes.R | 8 tests/testthat/test-ReadTntTree.R | 290 - tests/testthat/test-Reweight.R | 92 tests/testthat/test-RoguePlot.R | 362 - tests/testthat/test-SplitConsistent.R | 72 tests/testthat/test-SplitFunctions.R | 452 - tests/testthat/test-Splits.R | 1154 ++-- tests/testthat/test-Stemwardness.R | 28 tests/testthat/test-Support.R | 162 tests/testthat/test-TipTimedTree.R | 28 tests/testthat/test-TopologyOnly.R | 54 tests/testthat/test-TotalCopheneticIndex.R | 152 tests/testthat/test-TreeNumber.R | 293 - tests/testthat/test-Treeness.R | 38 tests/testthat/test-as.matrix.R | 14 tests/testthat/test-as.multiPhylo.R | 70 tests/testthat/test-combinatorics.R | 178 tests/testthat/test-consensus.R | 236 tests/testthat/test-helper_functions.R | 22 tests/testthat/test-information.R | 76 tests/testthat/test-int_to_tree.cpp.R | 129 tests/testthat/test-match.R | 58 tests/testthat/test-mst.R | 84 tests/testthat/test-parsers.R | 442 - tests/testthat/test-phylo.R | 112 tests/testthat/test-root_tree.h.R | 226 tests/testthat/test-sort.R | 44 tests/testthat/test-split_analysis.R | 22 tests/testthat/test-splits.cpp.R | 74 tests/testthat/test-tree_ancestors.R | 40 tests/testthat/test-tree_comparison.R | 48 tests/testthat/test-tree_descendants.R | 168 tests/testthat/test-tree_display.R | 128 tests/testthat/test-tree_generation-random.R | 90 tests/testthat/test-tree_generation.R | 438 - tests/testthat/test-tree_information.R | 38 tests/testthat/test-tree_numbering.R | 102 tests/testthat/test-tree_properties.R | 364 - tests/testthat/test-tree_rearrange.R | 830 +-- tests/testthat/test-tree_shape.R | 318 - tests/testthat/test-tree_write.R | 98 tests/testthat/testdata/nonPreCons.nex | 48 vignettes/filesystem-navigation.Rmd | 104 vignettes/load-data.Rmd | 428 - vignettes/load-trees.Rmd | 250 291 files changed, 30003 insertions(+), 29147 deletions(-)
Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute
distance, correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis
of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad
Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut],
Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between tgstat versions 2.3.29 dated 2025-11-12 and 2.3.32 dated 2026-03-20
DESCRIPTION | 8 ++-- MD5 | 14 ++++---- NEWS.md | 11 ++++++ R/knn.R | 3 - R/zzz.R | 3 - src/tgstat.cpp | 69 +++++++++++++++++++++++++++++++++++++++--- src/tgstat.h | 1 tests/testthat/test-cor-knn.R |only tests/testthat/test-tmpdir.R |only 9 files changed, 90 insertions(+), 19 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.0.1 dated 2025-12-09 and 5.0.2 dated 2026-03-20
DESCRIPTION | 15 MD5 | 338 +++++----- NAMESPACE | 7 NEWS.md | 29 R/CTS.R | 2 R/RcppExports.R | 38 - R/dsl.R | 12 R/err.R | 8 R/et.R | 49 + R/geom-amt.R | 7 R/mix.R | 4 R/mu.R | 2 R/piping-model.R | 6 R/piping.R | 37 + R/print.R | 2 R/reexport.R | 5 R/rudf.R | 14 R/rxParams.R | 6 R/rxRaw.R | 62 + R/rxShiny.R | 4 R/rxUiGet.R | 5 R/rxode-options.R | 71 -- R/rxode2.R | 47 + R/rxode2_md5.R | 2 R/rxrandom.R | 66 +- R/rxsolve.R | 4 R/summary.R | 4 R/symengine.R | 2 R/ui-assign-parts.R | 10 R/ui-bind.R | 3 R/ui-rename.R | 7 R/ui.R | 17 R/utils.R | 13 R/version.R | 7 README.md | 24 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rxode2-syntax.html | 717 +++++++++++++--------- inst/include/rxode2.h | 2 inst/include/rxode2_model_shared.c | 2 inst/include/rxode2parseGetTime.h | 58 + inst/include/rxode2parseHandleEvid.h | 22 inst/include/rxode2parseStruct.h | 10 inst/include/rxode2parseVer.h | 4 inst/tools/workaround.R | 3 inst/tutorials/rxode2-00-syntax/RxODE00syntax.Rmd | 110 +-- inst/tutorials/rxode2-01-events/rxode01events.Rmd | 380 +++++------ man/dot-rxGetSeed.Rd |only man/dot-rxSetSeed.Rd |only man/eventTable.Rd | 10 man/ini.Rd | 14 man/mix.Rd | 4 man/reexports.Rd | 3 man/rmdhunks/rxode2-intro-chunk.Rmd | 24 man/rxAppendModel.Rd | 3 man/rxDemoteAddErr.Rd | 6 man/rxErrTypeCombine.Rd | 2 man/rxFun.Rd | 2 man/rxGetDefaultSerialize.Rd |only man/rxGetSeed.Rd | 2 man/rxGetSerialType_.Rd | 2 man/rxOldQsDes.Rd |only man/rxRawToC.Rd | 6 man/rxRename.Rd | 6 man/rxSetCovariateNamesForPiping.Rd | 4 man/rxSyncOptions.Rd | 3 man/rxVersion.Rd | 8 man/rxode2.Rd | 81 +- man/stat_amt.Rd | 7 src/RcppExports.cpp | 118 +-- src/approx.cpp | 2 src/codegen.c | 47 - src/codegen2.h | 2 src/forder.cpp | 8 src/handle_evid.cpp | 9 src/init.c | 5 src/linCmt.cpp | 2 src/macros2micros.h | 1 src/par_solve.cpp | 340 +++++++++- src/par_solve.h | 55 + src/qs.cpp | 14 src/rxDerived.cpp | 12 src/rxode2_df.cpp | 18 src/seed.cpp | 62 - src/utilc.cpp | 78 +- tests/testthat.R | 4 tests/testthat/_problems |only tests/testthat/test-001-sum.R | 2 tests/testthat/test-100-cmt.R | 6 tests/testthat/test-alag.R | 30 tests/testthat/test-as-ini.R | 18 tests/testthat/test-backward.R | 10 tests/testthat/test-bad-dose.R | 8 tests/testthat/test-cmt-order.R | 10 tests/testthat/test-cov.R | 18 tests/testthat/test-data-table.R | 6 tests/testthat/test-deSolve-events.R | 4 tests/testthat/test-dollar-names.R | 6 tests/testthat/test-dplyr.R | 24 tests/testthat/test-et.R | 137 ++-- tests/testthat/test-etTrans.R | 28 tests/testthat/test-evid2.R | 10 tests/testthat/test-evid3.R | 24 tests/testthat/test-expand-grid.R | 12 tests/testthat/test-focei-variances.R | 126 +-- tests/testthat/test-iCov.R | 12 tests/testthat/test-ind-lin.R | 18 tests/testthat/test-ini.R | 8 tests/testthat/test-interp.R | 4 tests/testthat/test-keep.R | 43 - tests/testthat/test-lag.R | 58 - tests/testthat/test-lhs-ifelse.R | 8 tests/testthat/test-lincmt-solve.R | 434 ++++++------- tests/testthat/test-llik.R | 104 +-- tests/testthat/test-load.R | 1 tests/testthat/test-logit.R | 6 tests/testthat/test-missing-evid.R | 16 tests/testthat/test-mix.R | 36 - tests/testthat/test-model-rate.R | 86 +- tests/testthat/test-mtime.R | 134 ++++ tests/testthat/test-mu2.R | 4 tests/testthat/test-nearpd.R | 6 tests/testthat/test-nesting.R | 10 tests/testthat/test-newind.R | 8 tests/testthat/test-nmtest.R | 4 tests/testthat/test-nopred-ui.R | 2 tests/testthat/test-occ.R | 30 tests/testthat/test-off.R | 16 tests/testthat/test-par-solve.R | 6 tests/testthat/test-parsing.R | 10 tests/testthat/test-pipeline.R | 52 - tests/testthat/test-piping-ini.R | 50 - tests/testthat/test-print.R | 26 tests/testthat/test-rbind.R | 12 tests/testthat/test-resample.R | 28 tests/testthat/test-reset.R | 28 tests/testthat/test-rxIs.R | 24 tests/testthat/test-rxode-issue-005.R | 6 tests/testthat/test-rxode-issue-067.R | 3 tests/testthat/test-rxode-issue-163.R | 8 tests/testthat/test-rxode-issue-272.R | 10 tests/testthat/test-rxode-issue-349.R | 4 tests/testthat/test-rxode-issue-352.R | 12 tests/testthat/test-rxode-issue-375.R | 28 tests/testthat/test-rxode-issue-435.R | 16 tests/testthat/test-rxode-issue-445.R | 32 tests/testthat/test-rxode-issue-450.R | 8 tests/testthat/test-rxui-ctl.R | 8 tests/testthat/test-seq.R | 36 - tests/testthat/test-sim-zeros.R | 20 tests/testthat/test-solComp.R | 34 - tests/testthat/test-state-dep-dur.R |only tests/testthat/test-state-dep-f.R |only tests/testthat/test-state-dep-lag.R |only tests/testthat/test-state-dep-rate.R |only tests/testthat/test-state-dep-sort.R |only tests/testthat/test-steady-state.R | 118 +-- tests/testthat/test-symmetric.R | 2 tests/testthat/test-tad.R | 60 - tests/testthat/test-transit.R | 4 tests/testthat/test-ui-assign-model-parts.R | 10 tests/testthat/test-ui-drop-lines.R | 14 tests/testthat/test-ui-dv.R | 6 tests/testthat/test-ui-fix-unfix.R | 16 tests/testthat/test-ui-ini-lotri.R | 4 tests/testthat/test-ui-ini-str.R | 4 tests/testthat/test-ui-mod-functions.R | 36 - tests/testthat/test-ui-piping-single-endpoint.R | 12 tests/testthat/test-ui-piping.R | 264 ++++---- tests/testthat/test-ui-promote.R | 10 tests/testthat/test-ui-rename.R | 118 +++ tests/testthat/test-ui-simulation.R | 116 +-- tests/testthat/test-utils.R | 4 tests/testthat/test-zzzz-plot.R | 466 +++++++------- tests/testthat/testthat-problems.rds |only 175 files changed, 3706 insertions(+), 2747 deletions(-)
Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides
many desirable features. This package bundles these header files for easy use by R packages
from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also
see the 'spdl' package which enhanced this package with a consistent R and C++ interface.
Author: Dirk Eddelbuettel [aut, cre] ,
Gabi Melman [aut] ,
Victor Zverovic [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSpdlog versions 0.0.27 dated 2026-02-12 and 0.0.28 dated 2026-03-20
ChangeLog | 13 +++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ src/RcppExports.cpp | 32 ++++++++++++++++---------------- 7 files changed, 46 insertions(+), 26 deletions(-)
Title: A Fast and Flexible Pipeline for Text Classification
Description: A high-level pipeline that simplifies text classification into three streamlined steps:
preprocessing, model training, and standardized prediction.
It unifies the interface for multiple algorithms (including 'glmnet', 'ranger',
'xgboost', and 'naivebayes') and memory-efficient sparse matrix vectorization
methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from
raw text to a fully evaluated sentiment model, complete with ROC-optimized
thresholds, in just a few function calls. The resulting model artifact
automatically aligns the vocabulary of new datasets during the prediction phase,
safely appending predicted classes and probability matrices directly to the
user's original dataframe to preserve metadata.
Author: Alabhya Dahal [aut, cre]
Maintainer: Alabhya Dahal <alabhya.dahal@gmail.com>
Diff between quickSentiment versions 0.3.1 dated 2026-03-01 and 0.3.2 dated 2026-03-20
quickSentiment-0.3.1/quickSentiment/R/evaluation.R |only quickSentiment-0.3.1/quickSentiment/man/evaluate_metrics.Rd |only quickSentiment-0.3.2/quickSentiment/DESCRIPTION | 12 - quickSentiment-0.3.2/quickSentiment/LICENSE | 4 quickSentiment-0.3.2/quickSentiment/MD5 | 29 +-- quickSentiment-0.3.2/quickSentiment/NAMESPACE | 11 - quickSentiment-0.3.2/quickSentiment/NEWS.md | 19 -- quickSentiment-0.3.2/quickSentiment/R/evaluate_performance.R |only quickSentiment-0.3.2/quickSentiment/R/pipeline.R | 59 +------ quickSentiment-0.3.2/quickSentiment/R/prediction.R | 22 +- quickSentiment-0.3.2/quickSentiment/R/print.quickSentiment_eval.R |only quickSentiment-0.3.2/quickSentiment/R/route_prediction.R | 8 quickSentiment-0.3.2/quickSentiment/README.md | 30 +-- quickSentiment-0.3.2/quickSentiment/build/vignette.rds |binary quickSentiment-0.3.2/quickSentiment/inst/doc/introduction-to-quickSentiment.html | 82 +++++----- quickSentiment-0.3.2/quickSentiment/man/evaluate_performance.Rd |only quickSentiment-0.3.2/quickSentiment/man/plot.quickSentiment_prc.Rd |only quickSentiment-0.3.2/quickSentiment/man/plot.quickSentiment_roc.Rd |only quickSentiment-0.3.2/quickSentiment/man/predict_sentiment.Rd | 2 19 files changed, 122 insertions(+), 156 deletions(-)
More information about quickSentiment at CRAN
Permanent link
Title: Recreates Some 'SAS®' Procedures in 'R'
Description: Contains functions to simulate the most commonly used
'SAS®' procedures. Specifically, the package aims to
simulate the functionality of 'proc freq', 'proc means', 'proc ttest',
'proc reg', 'proc transpose', 'proc sort', and 'proc print'.
The simulation will include recreating
all statistics with the highest fidelity possible.
Author: David Bosak [aut, cre],
Diyu Yang [aut],
Athenkosi Nkonyeni [aut],
Kevin Kramer [ctb],
Brian Varney [ctb],
Duong Tran [ctb],
Yifei Chen [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between procs versions 1.0.7 dated 2025-07-27 and 1.0.8 dated 2026-03-20
procs-1.0.7/procs/R/plots.R |only procs-1.0.7/procs/R/proc_univariate.R |only procs-1.0.7/procs/tests/testthat/freq/freq10.html |only procs-1.0.7/procs/tests/testthat/freq/freq11.html |only procs-1.0.7/procs/tests/testthat/freq/freq12.html |only procs-1.0.7/procs/tests/testthat/freq/freq2.html |only procs-1.0.7/procs/tests/testthat/freq/freq3.html |only procs-1.0.7/procs/tests/testthat/freq/freq4.html |only procs-1.0.7/procs/tests/testthat/freq/freq5.html |only procs-1.0.7/procs/tests/testthat/freq/freq6.docx |only procs-1.0.7/procs/tests/testthat/freq/freq7.pdf |only procs-1.0.7/procs/tests/testthat/freq/freq8.pdf |only procs-1.0.7/procs/tests/testthat/freq/freq8.rtf |only procs-1.0.7/procs/tests/testthat/freq/freq8.txt |only procs-1.0.7/procs/tests/testthat/log/test.log |only procs-1.0.7/procs/tests/testthat/print/test2.pdf |only procs-1.0.7/procs/tests/testthat/print/test3.docx |only procs-1.0.7/procs/tests/testthat/print/test4.rtf |only procs-1.0.7/procs/tests/testthat/print/test5.html |only procs-1.0.7/procs/tests/testthat/print/test8.html |only procs-1.0.7/procs/tests/testthat/print/test8.rtf |only procs-1.0.7/procs/tests/testthat/utils/test2.html |only procs-1.0.8/procs/DESCRIPTION | 25 procs-1.0.8/procs/MD5 | 196 ++-- procs-1.0.8/procs/NAMESPACE | 6 procs-1.0.8/procs/NEWS.md | 12 procs-1.0.8/procs/R/freqplots.R |only procs-1.0.8/procs/R/proc_freq.R | 388 ++++++++- procs-1.0.8/procs/R/proc_means.R | 534 ++++++++----- procs-1.0.8/procs/R/proc_reg.R | 256 +++++- procs-1.0.8/procs/R/proc_sort.R | 119 ++ procs-1.0.8/procs/R/proc_transpose.R | 82 -- procs-1.0.8/procs/R/proc_ttest.R | 427 ++++++++-- procs-1.0.8/procs/R/regplots.R |only procs-1.0.8/procs/R/statistics.R | 426 ++++++---- procs-1.0.8/procs/R/supplements.R | 50 - procs-1.0.8/procs/R/ttestplots.R |only procs-1.0.8/procs/R/utilities.R | 569 +++++++++++++- procs-1.0.8/procs/README.md | 19 procs-1.0.8/procs/build/vignette.rds |binary procs-1.0.8/procs/inst/doc/procs-dm.R | 90 ++ procs-1.0.8/procs/inst/doc/procs-dm.Rmd | 113 ++ procs-1.0.8/procs/inst/doc/procs-dm.html | 129 ++- procs-1.0.8/procs/inst/doc/procs-example1.R | 93 -- procs-1.0.8/procs/inst/doc/procs-example1.Rmd | 468 +++++------ procs-1.0.8/procs/inst/doc/procs-example1.html | 707 +++++++---------- procs-1.0.8/procs/inst/doc/procs-example2.Rmd | 2 procs-1.0.8/procs/inst/doc/procs-example2.html | 7 procs-1.0.8/procs/inst/doc/procs-example3.Rmd | 2 procs-1.0.8/procs/inst/doc/procs-example3.html | 7 procs-1.0.8/procs/inst/doc/procs-faq.Rmd | 20 procs-1.0.8/procs/inst/doc/procs-faq.html | 25 procs-1.0.8/procs/inst/doc/procs-freq.R | 13 procs-1.0.8/procs/inst/doc/procs-freq.Rmd | 138 +++ procs-1.0.8/procs/inst/doc/procs-freq.html | 318 +++++-- procs-1.0.8/procs/inst/doc/procs-globals.R |only procs-1.0.8/procs/inst/doc/procs-globals.Rmd |only procs-1.0.8/procs/inst/doc/procs-globals.html |only procs-1.0.8/procs/inst/doc/procs-means.R | 75 + procs-1.0.8/procs/inst/doc/procs-means.Rmd | 119 ++ procs-1.0.8/procs/inst/doc/procs-means.html | 190 +++- procs-1.0.8/procs/inst/doc/procs-reg.R | 7 procs-1.0.8/procs/inst/doc/procs-reg.Rmd | 46 - procs-1.0.8/procs/inst/doc/procs-reg.html | 49 + procs-1.0.8/procs/inst/doc/procs-ttest.R | 8 procs-1.0.8/procs/inst/doc/procs-ttest.Rmd | 51 + procs-1.0.8/procs/inst/doc/procs-ttest.html | 56 + procs-1.0.8/procs/inst/doc/procs.R | 3 procs-1.0.8/procs/inst/doc/procs.Rmd | 28 procs-1.0.8/procs/inst/doc/procs.html | 66 - procs-1.0.8/procs/man/freqplot.Rd |only procs-1.0.8/procs/man/images/demog.png |binary procs-1.0.8/procs/man/images/freqtut11.png |only procs-1.0.8/procs/man/images/freqtut12.png |only procs-1.0.8/procs/man/images/freqtut13.png |only procs-1.0.8/procs/man/images/meanstut3.png |binary procs-1.0.8/procs/man/images/meanstut4.png |binary procs-1.0.8/procs/man/images/meanstut5.png |binary procs-1.0.8/procs/man/images/meanstut6.png |binary procs-1.0.8/procs/man/images/meanstut7.png |binary procs-1.0.8/procs/man/images/reg7a.png |only procs-1.0.8/procs/man/images/reg7b.png |only procs-1.0.8/procs/man/images/reg7c.png |only procs-1.0.8/procs/man/images/reg7d.png |only procs-1.0.8/procs/man/images/ttest5a.png |only procs-1.0.8/procs/man/images/ttest5b.png |only procs-1.0.8/procs/man/images/ttest5c.png |only procs-1.0.8/procs/man/images/ttesta.png |only procs-1.0.8/procs/man/images/ttestb.png |only procs-1.0.8/procs/man/images/ttestc.png |only procs-1.0.8/procs/man/images/ttestd.png |only procs-1.0.8/procs/man/proc_freq.Rd | 139 +++ procs-1.0.8/procs/man/proc_means.Rd | 742 +++++++++--------- procs-1.0.8/procs/man/proc_reg.Rd | 123 ++- procs-1.0.8/procs/man/proc_sort.Rd | 41 - procs-1.0.8/procs/man/proc_ttest.Rd | 121 ++ procs-1.0.8/procs/man/procs.Rd | 6 procs-1.0.8/procs/man/regplot.Rd |only procs-1.0.8/procs/man/ttestplot.Rd |only procs-1.0.8/procs/tests/testthat/setup-procs.R |only procs-1.0.8/procs/tests/testthat/test-freq.R | 848 ++++++++++++++++++++- procs-1.0.8/procs/tests/testthat/test-freqplots.R |only procs-1.0.8/procs/tests/testthat/test-means.R | 821 ++++++++++++++++++-- procs-1.0.8/procs/tests/testthat/test-print.R | 128 +++ procs-1.0.8/procs/tests/testthat/test-reg.R | 87 +- procs-1.0.8/procs/tests/testthat/test-regplots.R |only procs-1.0.8/procs/tests/testthat/test-sort.R | 207 +++++ procs-1.0.8/procs/tests/testthat/test-statistics.R | 185 +++- procs-1.0.8/procs/tests/testthat/test-transpose.R | 48 + procs-1.0.8/procs/tests/testthat/test-ttest.R | 171 ++++ procs-1.0.8/procs/tests/testthat/test-ttestplots.R |only procs-1.0.8/procs/tests/testthat/test-user.R | 2 procs-1.0.8/procs/tests/testthat/test-utilities.R | 457 +++++++++++ procs-1.0.8/procs/vignettes/procs-dm.Rmd | 113 ++ procs-1.0.8/procs/vignettes/procs-example1.Rmd | 468 +++++------ procs-1.0.8/procs/vignettes/procs-example2.Rmd | 2 procs-1.0.8/procs/vignettes/procs-example3.Rmd | 2 procs-1.0.8/procs/vignettes/procs-faq.Rmd | 20 procs-1.0.8/procs/vignettes/procs-freq.Rmd | 138 +++ procs-1.0.8/procs/vignettes/procs-globals.Rmd |only procs-1.0.8/procs/vignettes/procs-means.Rmd | 119 ++ procs-1.0.8/procs/vignettes/procs-reg.Rmd | 46 - procs-1.0.8/procs/vignettes/procs-ttest.Rmd | 51 + procs-1.0.8/procs/vignettes/procs.Rmd | 28 124 files changed, 8397 insertions(+), 2655 deletions(-)
Title: Gaussian and Student-t Copula Models for Count Time Series
Description: Provides likelihood-based inference for Gaussian and Student-t
copula models for univariate count time series. Supports Poisson,
negative binomial, binomial, beta-binomial, and zero-inflated
marginals with ARMA dependence structures. Includes simulation,
maximum-likelihood estimation, residual diagnostics, and predictive
inference. Implements Time Series Minimax Exponential Tilting (TMET)
<doi:10.1016/j.csda.2026.108344>, an adaptation of minimax exponential
tilting of Botev (2017) <doi:10.1111/rssb.12162>. Also provides a
linear-cost implementation of the Geweke–Hajivassiliou–Keane (GHK)
simulator following Masarotto and Varin (2012) <doi:10.1214/12-EJS721>,
and the Continuous Extension (CE) approximation of Nguyen and
De Oliveira (2025) <doi:10.1080/02664763.2025.2498502>. The package
follows the S3 design philosophy of 'gcmr' but is developed independently.
Author: Quynh Nguyen [aut, cre],
Victor De Oliveira [aut]
Maintainer: Quynh Nguyen <nqnhu2209@gmail.com>
Diff between gctsc versions 0.2.0 dated 2026-03-13 and 0.2.3 dated 2026-03-20
gctsc-0.2.0/gctsc/data/KCWC.csv |only gctsc-0.2.0/gctsc/data/datalist |only gctsc-0.2.0/gctsc/data/rota.csv |only gctsc-0.2.0/gctsc/src/mvphi.f |only gctsc-0.2.3/gctsc/DESCRIPTION | 8 +-- gctsc-0.2.3/gctsc/MD5 | 22 ++++------ gctsc-0.2.3/gctsc/R/residuals.R | 2 gctsc-0.2.3/gctsc/inst/doc/gctsc_vignette.html | 44 ++++++++++----------- gctsc-0.2.3/gctsc/inst/t_copula_examples/Poisson.R | 2 gctsc-0.2.3/gctsc/man/plot.gctsc.Rd | 2 gctsc-0.2.3/gctsc/src/gauss_utils.cpp | 27 ++++++------ gctsc-0.2.3/gctsc/src/gauss_utils.h | 9 ++-- gctsc-0.2.3/gctsc/src/pred_mvn.cpp | 9 +++- gctsc-0.2.3/gctsc/src/pred_mvt.cpp | 5 +- 14 files changed, 68 insertions(+), 62 deletions(-)
Title: Solvers for Initial Value Problems of Differential Equations
('ODE', 'DAE', 'DDE')
Description: Functions that solve initial value problems of a system
of first-order ordinary differential equations ('ODE'), of
partial differential equations ('PDE'), of differential
algebraic equations ('DAE'), and of delay differential
equations. The functions provide an interface to the FORTRAN
functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK'
collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk'
and a C-implementation of solvers of the 'Runge-Kutta' family with
fixed or variable time steps. The package contains routines
designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D
partial differential equations ('PDE') that have been converted
to 'ODEs' by numerical differencing.
Author: Karline Soetaert [aut] ,
Thomas Petzoldt [aut, cre] ,
R. Woodrow Setzer [aut] ,
Peter N. Brown [ctb] ,
George D. Byrne [ctb] ,
Ernst Hairer [ctb] ,
Alan C. Hindmarsh [ctb] ,
Cleve Moler [ctb] ,
Linda R. Petzold [ctb] ,
Youcef Saad [ctb] ,
Clement W. [...truncated...]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between deSolve versions 1.41 dated 2026-02-06 and 1.42 dated 2026-03-20
DESCRIPTION | 6 MD5 | 46 +-- NEWS.md | 581 +++++++++++++++++++++++----------------------- build/partial.rdb |binary build/vignette.rds |binary data/ccl4data.rda |binary inst/doc/compiledCode.pdf |binary inst/doc/deSolve.pdf |binary src/call_daspk.c | 26 +- src/call_lsoda.c | 14 - src/call_radau.c | 8 src/call_zvode.c | 14 - src/deSolve_utils.c | 45 +-- src/ex_Aquaphy.c | 4 src/ex_CCL4model.c | 2 src/ex_ChemicalDAE.c | 2 src/ex_SCOC.c | 2 src/forcings.c | 4 src/lags.c | 30 +- src/rk_auto.c | 6 src/rk_fixed.c | 4 src/rk_implicit.c | 8 src/rk_util.c | 21 + src/twoDmap.c | 6 24 files changed, 418 insertions(+), 411 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre] ,
Hugh Chipman [aut],
Robert McCulloch [aut],
Armon Dadgar [ctb] ,
R Core Team [ctb] ,
Guido U Draheim [ctb] ,
Maarten Bosmans [ctb] ,
Christophe Tournayre [ctb] ,
Michael Petch [ctb] ,
Rafael de Lucena Valle [ctb] ,
Steven G [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-32 dated 2025-04-02 and 0.9-33 dated 2026-03-20
DESCRIPTION | 15 +++++----- MD5 | 24 ++++++++-------- R/dbarts.R | 14 +++++++++ build/vignette.rds |binary inst/doc/gibbs_sampler_mixture_model.pdf |binary inst/doc/working_with_saved_trees.pdf |binary src/R_interface.cpp | 2 + src/R_interface_crossvalidate.cpp | 2 - src/R_interface_sampler.cpp | 45 +++++++++++++++++++++++++++++++ src/R_interface_sampler.hpp | 3 ++ src/external/randomBase.c | 14 ++++----- src/include/rc/util.h | 6 ++++ src/rc/util.c | 2 - 13 files changed, 99 insertions(+), 28 deletions(-)
Title: Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Description: Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
su [...truncated...]
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Diana Robledo-Ruiz [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Emily Stringer [ctb],
Floriaan Devloo-Delva [ctb],
Eric Archer [c [...truncated...]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.base versions 1.2.2 dated 2026-03-12 and 1.2.3 dated 2026-03-20
dartR.base-1.2.2/dartR.base/R/gl.drop.sexlinked.r |only dartR.base-1.2.2/dartR.base/R/gl.filter.sexlinked.r |only dartR.base-1.2.2/dartR.base/R/gl.report.sexlinked.r |only dartR.base-1.2.2/dartR.base/R/gl2sa.r |only dartR.base-1.2.2/dartR.base/man/gl.drop.sexlinked.Rd |only dartR.base-1.2.2/dartR.base/man/gl.filter.sexlinked.Rd |only dartR.base-1.2.2/dartR.base/man/gl.report.sexlinked.Rd |only dartR.base-1.2.2/dartR.base/man/gl2sa.Rd |only dartR.base-1.2.3/dartR.base/DESCRIPTION | 10 - dartR.base-1.2.3/dartR.base/MD5 | 56 ++---- dartR.base-1.2.3/dartR.base/NAMESPACE | 9 - dartR.base-1.2.3/dartR.base/R/gl.filter.excess.het.r | 4 dartR.base-1.2.3/dartR.base/man/gl.document.Rd | 140 ++++++++--------- dartR.base-1.2.3/dartR.base/man/gl2bayesAss.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2bayescan.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2bpp.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2demerelate.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2eigenstrat.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2faststructure.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2gds.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2genalex.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2genepop.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2geno.Rd | 2 dartR.base-1.2.3/dartR.base/man/gl2gi.Rd | 2 dartR.base-1.2.3/dartR.base/man/gl2hapmap.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2hiphop.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2phylip.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2plink.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2related.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2snapper.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2structure.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2treemix.Rd | 1 dartR.base-1.2.3/dartR.base/man/gl2vcf.Rd | 1 33 files changed, 101 insertions(+), 140 deletions(-)
Title: PolyaGamma Sampling
Description: Tools for sampling from the PolyaGamma distribution based on Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Useful for logistic regression.
Author: Nicholas G. Polson [aut, cph],
James G. Scott [aut, cph],
Jesse Windle [aut, cre, cph],
Jari Oksanen [ctb],
James Balamuta [ctb]
Maintainer: Jesse Windle <jesse.windle@gmail.com>
Diff between BayesLogit versions 2.1 dated 2019-09-26 and 2.3 dated 2026-03-20
BayesLogit-2.1/BayesLogit/inst/dev/data |only BayesLogit-2.3/BayesLogit/DESCRIPTION | 8 ++-- BayesLogit-2.3/BayesLogit/MD5 | 15 +++---- BayesLogit-2.3/BayesLogit/NEWS.md | 31 +++++++++++----- BayesLogit-2.3/BayesLogit/R/PolyaGammaApproxAlt.R | 4 +- BayesLogit-2.3/BayesLogit/R/SaddlePointApprox.R | 30 +++++++-------- BayesLogit-2.3/BayesLogit/README.md | 4 -- BayesLogit-2.3/BayesLogit/inst/CITATION | 42 +++++++++++++++------- BayesLogit-2.3/BayesLogit/man/rpg.Rd | 2 - 9 files changed, 81 insertions(+), 55 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre] ,
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb],
Stephen Roecker [aut, ctb],
David Rossiter [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.3 dated 2026-01-17 and 2.3.1 dated 2026-03-20
aqp-2.3.1/aqp/DESCRIPTION | 6 aqp-2.3.1/aqp/MD5 | 138 ++-- aqp-2.3.1/aqp/NAMESPACE | 6 aqp-2.3.1/aqp/NEWS.md | 34 + aqp-2.3.1/aqp/R/Class-SoilProfileCollection.R | 19 aqp-2.3.1/aqp/R/SoilProfileCollection-methods.R | 157 ++++- aqp-2.3.1/aqp/R/SoilProfileCollection-operators.R | 11 aqp-2.3.1/aqp/R/SoilProfileCollection-setters.R | 32 - aqp-2.3.1/aqp/R/SoilProfileCollection-spatial.R | 3 aqp-2.3.1/aqp/R/addBracket.R | 303 ++++++---- aqp-2.3.1/aqp/R/aggregateColor.R | 2 aqp-2.3.1/aqp/R/col2Munsell.R | 4 aqp-2.3.1/aqp/R/colorChart.R | 105 ++- aqp-2.3.1/aqp/R/colorQuantiles.R | 11 aqp-2.3.1/aqp/R/colorVariation.R | 183 ++++-- aqp-2.3.1/aqp/R/data-documentation.R | 16 aqp-2.3.1/aqp/R/estimateSoilColor.R | 218 +++++-- aqp-2.3.1/aqp/R/fillHzGaps.R | 36 - aqp-2.3.1/aqp/R/hzOffset.R | 260 +++++++- aqp-2.3.1/aqp/R/launderMunsell.R |only aqp-2.3.1/aqp/R/mixMunsell.R | 32 - aqp-2.3.1/aqp/R/mutate_profile.R | 9 aqp-2.3.1/aqp/R/parseMunsell.R | 2 aqp-2.3.1/aqp/R/plotSPC.R | 10 aqp-2.3.1/aqp/R/reduceSPC.R |only aqp-2.3.1/aqp/R/repairMissingHzDepths.R | 2 aqp-2.3.1/aqp/R/simulateColor.R | 6 aqp-2.3.1/aqp/R/soilColorSignature.R | 59 + aqp-2.3.1/aqp/R/spc2mpspline.R | 17 aqp-2.3.1/aqp/R/spec2Munsell.R | 2 aqp-2.3.1/aqp/R/validateMunsell.R |only aqp-2.3.1/aqp/R/warpHorizons.R | 4 aqp-2.3.1/aqp/data/Ohz.colors.rda |only aqp-2.3.1/aqp/data/datalist | 1 aqp-2.3.1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.R | 6 aqp-2.3.1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.Rmd | 8 aqp-2.3.1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 112 +-- aqp-2.3.1/aqp/inst/doc/Munsell-color-conversion.R | 53 + aqp-2.3.1/aqp/inst/doc/Munsell-color-conversion.Rmd | 88 ++ aqp-2.3.1/aqp/inst/doc/Munsell-color-conversion.html | 110 +++ aqp-2.3.1/aqp/inst/doc/aqp-overview.Rmd | 4 aqp-2.3.1/aqp/inst/doc/aqp-overview.html | 8 aqp-2.3.1/aqp/man/Ohz.colors.Rd |only aqp-2.3.1/aqp/man/SoilProfileCollection-plotting-methods.Rd | 3 aqp-2.3.1/aqp/man/addBracket.Rd | 148 ++-- aqp-2.3.1/aqp/man/addDiagnosticBracket.Rd | 43 + aqp-2.3.1/aqp/man/colorChart.Rd | 18 aqp-2.3.1/aqp/man/colorVariation.Rd | 68 ++ aqp-2.3.1/aqp/man/dollarsign.Rd | 8 aqp-2.3.1/aqp/man/estimateSoilColor.Rd | 59 + aqp-2.3.1/aqp/man/grepSPC.Rd | 2 aqp-2.3.1/aqp/man/hzOffset.Rd | 180 +++++ aqp-2.3.1/aqp/man/initSpatial.Rd | 4 aqp-2.3.1/aqp/man/launderMunsell.Rd |only aqp-2.3.1/aqp/man/mixMunsell.Rd | 4 aqp-2.3.1/aqp/man/mutate_profile.Rd | 2 aqp-2.3.1/aqp/man/names.Rd | 12 aqp-2.3.1/aqp/man/parseMunsell.Rd | 3 aqp-2.3.1/aqp/man/reduceSPC.Rd | 2 aqp-2.3.1/aqp/man/simulateColor.Rd | 2 aqp-2.3.1/aqp/man/site.Rd | 4 aqp-2.3.1/aqp/man/soilColorSignature.Rd | 2 aqp-2.3.1/aqp/man/subApply.Rd | 2 aqp-2.3.1/aqp/man/validateMunsell.Rd |only aqp-2.3.1/aqp/tests/testthat/Rplots.pdf |binary aqp-2.3.1/aqp/tests/testthat/test-colorVariation.R |only aqp-2.3.1/aqp/tests/testthat/test-estimateSoilColor.R | 96 +++ aqp-2.3.1/aqp/tests/testthat/test-hzOffset.R | 44 + aqp-2.3.1/aqp/tests/testthat/test-plotSPC.R | 5 aqp-2.3.1/aqp/tests/testthat/test-reduceSPC.R | 9 aqp-2.3.1/aqp/tests/testthat/test-validateMunsell.R |only aqp-2.3.1/aqp/vignettes/Introduction-to-SoilProfileCollection-Objects.Rmd | 8 aqp-2.3.1/aqp/vignettes/Munsell-color-conversion.Rmd | 88 ++ aqp-2.3.1/aqp/vignettes/aqp-overview.Rmd | 4 aqp-2.3/aqp/R/reduce.R |only 75 files changed, 2223 insertions(+), 674 deletions(-)
Title: Versatile R Server
Description: Rserve is a versatile, scalable server enabling the
efficient use of R from other applications through
variety of protocols including QAP, WebSockets, HTTP
and HTTPS. It acts as a server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every
connection has a separate workspace and working
directory. Client-side implementations are available
for many popular languages allowing applications
to use facilities of R without the need of linking to
the R binary. Rserve supports remote connections,
user authentication and file transfer. A simple R client
is included in this package as well. It also supports
OCAP mode for secure remote procedure calls,
including support for full event loop, asynchronous
results/graphics and console I/O.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Rserve versions 1.8-17 dated 2026-02-02 and 1.8-18 dated 2026-03-20
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS | 4 ++++ inst/java/REngine.jar |binary inst/java/Rserve.jar |binary src/Rsrv.h | 4 ++-- src/client/cxx/Rsrv.h | 4 ++-- src/client/java/Rserve/Rserve.jar |binary src/oc.h | 1 + src/rcompat.h | 17 +++++++++++++++++ 10 files changed, 38 insertions(+), 16 deletions(-)