Title: Sparse Time Series Chain Graphical Models
Description: Computes sparse vector autoregressive coefficients and sparse
precision matrices for time series chain graphical models. Methods are
described in Abegaz and Wit (2013)
<doi:10.1093/biostatistics/kxt005>.
Author: Fentaw Abegaz [aut, cre],
Ernst Wit [aut]
Maintainer: Fentaw Abegaz <fentawabegaz@yahoo.com>
This is a re-admission after prior archival of version 4.1 dated 2026-01-09
Diff between SparseTSCGM versions 4.1 dated 2026-01-09 and 5.0 dated 2026-03-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plot.tscgm.R | 4 ++++ man/SparseTSCGM-package.Rd | 4 ++-- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Test Theory Analysis and Biclustering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.8.1 dated 2026-02-17 and 1.10.1 dated 2026-03-19
exametrika-1.10.1/exametrika/DESCRIPTION | 13 exametrika-1.10.1/exametrika/MD5 | 243 ++- exametrika-1.10.1/exametrika/NAMESPACE | 8 exametrika-1.10.1/exametrika/NEWS.md | 228 +++ exametrika-1.10.1/exametrika/R/00_EMclus.R | 238 +++ exametrika-1.10.1/exametrika/R/00_GridSearch.R | 68 - exametrika-1.10.1/exametrika/R/00_IRM_Gibbs_CORE.R |only exametrika-1.10.1/exametrika/R/00_IRPindex.R | 59 exametrika-1.10.1/exametrika/R/00_ModelFitModule.R | 2 exametrika-1.10.1/exametrika/R/00_dataset_explain.R | 18 exametrika-1.10.1/exametrika/R/00_exametrikaPlot.R | 746 ----------- exametrika-1.10.1/exametrika/R/00_exametrikaPrint.R | 4 exametrika-1.10.1/exametrika/R/00_plot_biclustering.R |only exametrika-1.10.1/exametrika/R/00_plot_irt.R |only exametrika-1.10.1/exametrika/R/00_plot_lca_lra.R |only exametrika-1.10.1/exametrika/R/00_plot_network.R |only exametrika-1.10.1/exametrika/R/00_plot_poly_biclustering.R |only exametrika-1.10.1/exametrika/R/01_dataFormat.R | 109 + exametrika-1.10.1/exametrika/R/02B_TestStatistics.R | 3 exametrika-1.10.1/exametrika/R/04C_ParameterEstimation.R | 3 exametrika-1.10.1/exametrika/R/05_LCA.R | 19 exametrika-1.10.1/exametrika/R/06_LRA.R | 120 - exametrika-1.10.1/exametrika/R/07_Biclustering.R | 15 exametrika-1.10.1/exametrika/R/07_IRM.R | 114 + exametrika-1.10.1/exametrika/R/08A_BNM.R | 1 exametrika-1.10.1/exametrika/R/09_LDLRA.R | 2 exametrika-1.10.1/exametrika/R/10_LDB.R | 5 exametrika-1.10.1/exametrika/R/11_BINET.R | 50 exametrika-1.10.1/exametrika/R/12_LRA_ordinal.R | 48 exametrika-1.10.1/exametrika/R/13_LRA_rated.R | 32 exametrika-1.10.1/exametrika/R/14_grm.R |only exametrika-1.10.1/exametrika/R/15_Biclustering_nominal.R | 25 exametrika-1.10.1/exametrika/R/16_Biclustering_ordinal.R | 46 exametrika-1.10.1/exametrika/R/17_Biclustering_nominal_IRM.R |only exametrika-1.10.1/exametrika/R/18_Biclustering_ordinal_IRM.R |only exametrika-1.10.1/exametrika/README.md | 87 + exametrika-1.10.1/exametrika/build |only exametrika-1.10.1/exametrika/data/J20S400.rda |binary exametrika-1.10.1/exametrika/data/J20S600.rda |only exametrika-1.10.1/exametrika/data/J35S500.rda |only exametrika-1.10.1/exametrika/inst |only exametrika-1.10.1/exametrika/man/Biclustering.Rd | 14 exametrika-1.10.1/exametrika/man/Biclustering_IRM.Rd | 142 +- exametrika-1.10.1/exametrika/man/GRM.Rd | 4 exametrika-1.10.1/exametrika/man/GridSearch.Rd | 6 exametrika-1.10.1/exametrika/man/J20S600.Rd |only exametrika-1.10.1/exametrika/man/J35S500.Rd |only exametrika-1.10.1/exametrika/man/LCA.Rd | 9 exametrika-1.10.1/exametrika/man/LRA.Rd | 7 exametrika-1.10.1/exametrika/man/TestStatistics.Rd | 3 exametrika-1.10.1/exametrika/man/dataFormat.Rd | 9 exametrika-1.10.1/exametrika/man/figures/logo.png |only exametrika-1.10.1/exametrika/man/generate_start_values.Rd | 2 exametrika-1.10.1/exametrika/man/grm_cumprob.Rd | 2 exametrika-1.10.1/exametrika/man/grm_iif.Rd | 2 exametrika-1.10.1/exametrika/man/grm_prob.Rd | 2 exametrika-1.10.1/exametrika/man/params_to_target.Rd | 2 exametrika-1.10.1/exametrika/man/plot.exametrika.Rd | 20 exametrika-1.10.1/exametrika/tests |only exametrika-1.10.1/exametrika/vignettes |only exametrika-1.8.1/exametrika/R/14_GRM.R |only 61 files changed, 1484 insertions(+), 1046 deletions(-)
Title: Continuous Time Structural Equation Modelling - Old
'OpenMx'-Based Version
Description: Original 'ctsem' (continuous time structural equation modelling)
functionality, based on the 'OpenMx' software, as described in
Driver, Oud, Voelkle (2017) <doi:10.18637/jss.v077.i05>, with updated details in vignette.
Combines stochastic differential equations representing latent processes with
structural equation measurement models. This package is maintained for consistency with the
original 'ctsem' paper, but for the much newer and more capable 'ctsem' package, see
<https://cran.r-project.org/package=ctsem>.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsemOMX versions 1.0.7 dated 2025-08-19 and 2.0.0 dated 2026-03-19
ctsemOMX-1.0.7/ctsemOMX/vignettes/ctsemOMX-concordance.tex |only ctsemOMX-2.0.0/ctsemOMX/DESCRIPTION | 27 +- ctsemOMX-2.0.0/ctsemOMX/MD5 | 59 +++-- ctsemOMX-2.0.0/ctsemOMX/NAMESPACE | 9 ctsemOMX-2.0.0/ctsemOMX/NEWS | 5 ctsemOMX-2.0.0/ctsemOMX/R/ctCI.R | 4 ctsemOMX-2.0.0/ctsemOMX/R/ctDataHelp.R | 8 ctsemOMX-2.0.0/ctsemOMX/R/ctDeintervalise.R |only ctsemOMX-2.0.0/ctsemOMX/R/ctDiscretiseData.R |only ctsemOMX-2.0.0/ctsemOMX/R/ctFit.R | 4 ctsemOMX-2.0.0/ctsemOMX/R/ctGenerate.R |only ctsemOMX-2.0.0/ctsemOMX/R/ctIntervalise.R |only ctsemOMX-2.0.0/ctsemOMX/R/ctLongtowide.r |only ctsemOMX-2.0.0/ctsemOMX/R/ctModel.R |only ctsemOMX-2.0.0/ctsemOMX/R/ctTransforms.R |only ctsemOMX-2.0.0/ctsemOMX/R/ctWideToLong.R |only ctsemOMX-2.0.0/ctsemOMX/R/ctsemOMX-package.R | 4 ctsemOMX-2.0.0/ctsemOMX/R/ctsemOMXImportedHelpers.R |only ctsemOMX-2.0.0/ctsemOMX/build/vignette.rds |binary ctsemOMX-2.0.0/ctsemOMX/data/ctstantestdat.rda |only ctsemOMX-2.0.0/ctsemOMX/inst/doc/ctsemOMX.R | 6 ctsemOMX-2.0.0/ctsemOMX/inst/doc/ctsemOMX.pdf |binary ctsemOMX-2.0.0/ctsemOMX/inst/doc/ctsemOMX.rnw | 102 +++------- ctsemOMX-2.0.0/ctsemOMX/man/AnomAuth.Rd | 2 ctsemOMX-2.0.0/ctsemOMX/man/ctCI.Rd | 2 ctsemOMX-2.0.0/ctsemOMX/man/ctDeintervalise.Rd |only ctsemOMX-2.0.0/ctsemOMX/man/ctDiscretiseData.Rd |only ctsemOMX-2.0.0/ctsemOMX/man/ctFit.Rd | 4 ctsemOMX-2.0.0/ctsemOMX/man/ctGenerate.Rd |only ctsemOMX-2.0.0/ctsemOMX/man/ctIntervalise.Rd |only ctsemOMX-2.0.0/ctsemOMX/man/ctLongToWide.Rd |only ctsemOMX-2.0.0/ctsemOMX/man/ctModel.Rd |only ctsemOMX-2.0.0/ctsemOMX/man/ctWideToLong.Rd |only ctsemOMX-2.0.0/ctsemOMX/man/ctstantestdat.Rd |only ctsemOMX-2.0.0/ctsemOMX/tests/testthat/test-differenttraits.R | 2 ctsemOMX-2.0.0/ctsemOMX/tests/testthat/test-intervalise.R | 2 ctsemOMX-2.0.0/ctsemOMX/tests/testthat/test-kalmanVram.R | 2 ctsemOMX-2.0.0/ctsemOMX/tests/testthat/test-reshaping.R | 2 ctsemOMX-2.0.0/ctsemOMX/tests/testthat/test-ukfpoptest.R | 23 -- ctsemOMX-2.0.0/ctsemOMX/vignettes/ctsemOMX.rnw | 102 +++------- 40 files changed, 162 insertions(+), 207 deletions(-)
Title: Bootstrapping Helpers for Structural Equation Modelling
Description: A collection of helper functions for forming
bootstrapping confidence intervals and examining bootstrap
estimates in structural equation modelling,
introduced in Yang and Cheung (2026) <doi: 10.3758/s13428-025-02911-z>
The function currently
support models fitted by the 'lavaan' package by
Rosseel (2012) <doi:10.18637/jss.v048.i02>.
Author: Wendie Yang [aut, cre] ,
Shu Fai Cheung [aut]
Maintainer: Wendie Yang <1581075494q@gmail.com>
Diff between semboottools versions 0.1.1 dated 2025-09-17 and 0.1.2 dated 2026-03-19
semboottools-0.1.1/semboottools/inst/doc/hist_qq_boot_and_scatter_boot.R |only semboottools-0.1.1/semboottools/inst/doc/hist_qq_boot_and_scatter_boot.Rmd |only semboottools-0.1.1/semboottools/inst/doc/hist_qq_boot_and_scatter_boot.html |only semboottools-0.1.1/semboottools/vignettes/hist_qq_boot_and_scatter_boot.Rmd |only semboottools-0.1.2/semboottools/DESCRIPTION | 19 semboottools-0.1.2/semboottools/MD5 | 69 - semboottools-0.1.2/semboottools/NAMESPACE | 28 semboottools-0.1.2/semboottools/NEWS.md | 83 - semboottools-0.1.2/semboottools/R/gg_hist_qq_boot.R |only semboottools-0.1.2/semboottools/R/jab_after_boot.R |only semboottools-0.1.2/semboottools/R/plot_boot.R | 229 ++--- semboottools-0.1.2/semboottools/README.md | 33 semboottools-0.1.2/semboottools/build/vignette.rds |binary semboottools-0.1.2/semboottools/inst/CITATION |only semboottools-0.1.2/semboottools/inst/doc/gg_hist_qq_boot_and_gg_scatter_boot.R |only semboottools-0.1.2/semboottools/inst/doc/gg_hist_qq_boot_and_gg_scatter_boot.Rmd |only semboottools-0.1.2/semboottools/inst/doc/gg_hist_qq_boot_and_gg_scatter_boot.html |only semboottools-0.1.2/semboottools/inst/doc/jab_after_boot.R |only semboottools-0.1.2/semboottools/inst/doc/jab_after_boot.Rmd |only semboottools-0.1.2/semboottools/inst/doc/jab_after_boot.html |only semboottools-0.1.2/semboottools/inst/doc/parameterEstimates_boot.R | 45 - semboottools-0.1.2/semboottools/inst/doc/parameterEstimates_boot.Rmd | 79 + semboottools-0.1.2/semboottools/inst/doc/parameterEstimates_boot.html | 208 +++-- semboottools-0.1.2/semboottools/inst/doc/semboottools.R | 36 semboottools-0.1.2/semboottools/inst/doc/semboottools.Rmd | 74 + semboottools-0.1.2/semboottools/inst/doc/semboottools.html | 391 +++++---- semboottools-0.1.2/semboottools/inst/doc/standardizedSolution_boot.R | 67 + semboottools-0.1.2/semboottools/inst/doc/standardizedSolution_boot.Rmd | 121 ++ semboottools-0.1.2/semboottools/inst/doc/standardizedSolution_boot.html | 340 +++++--- semboottools-0.1.2/semboottools/man/gg_hist_qq_boot.Rd |only semboottools-0.1.2/semboottools/man/gg_scatter_boot.Rd |only semboottools-0.1.2/semboottools/man/jab_after_boot.Rd |only semboottools-0.1.2/semboottools/man/parameterEstimates_boot.Rd | 348 ++++---- semboottools-0.1.2/semboottools/man/print.sbt_std_boot.Rd | 260 +++--- semboottools-0.1.2/semboottools/man/print.sbt_ustd_boot.Rd | 214 ++--- semboottools-0.1.2/semboottools/man/semboottools-package.Rd | 2 semboottools-0.1.2/semboottools/man/standardizedSolution_boot.Rd | 396 ++++----- semboottools-0.1.2/semboottools/man/store_boot.Rd | 416 +++++----- semboottools-0.1.2/semboottools/tests/testthat/test-jab_after_boot.R |only semboottools-0.1.2/semboottools/vignettes/apa.csl |only semboottools-0.1.2/semboottools/vignettes/gg_hist_qq_boot_and_gg_scatter_boot.Rmd |only semboottools-0.1.2/semboottools/vignettes/jab_after_boot.Rmd |only semboottools-0.1.2/semboottools/vignettes/parameterEstimates_boot.Rmd | 79 + semboottools-0.1.2/semboottools/vignettes/references.bib |only semboottools-0.1.2/semboottools/vignettes/semboottools.Rmd | 74 + semboottools-0.1.2/semboottools/vignettes/standardizedSolution_boot.Rmd | 121 ++ 46 files changed, 2207 insertions(+), 1525 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon-related timescales (cal BP, cal BC/AD, C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). Supporting publication: Blaauw, M., Reimer, P.J., in press. An open-source toolkit for radiocarbon dating and calibration. Radiocarbon. The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package uses the calibration curves from the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre] ,
Paula Reimer [ctb] ,
Vegard Martinsen [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 1.6.2 dated 2026-01-22 and 2.0.1 dated 2026-03-19
DESCRIPTION | 10 +- MD5 | 59 +++++++------- NAMESPACE | 1 NEWS.md | 13 +++ R/calibrate.R | 163 ++++++++++++++++++++++++++--------------- R/plots.R | 146 ++++++++++++++++++++++-------------- R/sets.R | 60 +++++++++++++++ R/sources.R | 4 - R/timescales.R | 70 ++++------------- build/partial.rdb |binary build/vignette.rds |binary data/shells.rda |binary inst/CITATION | 13 +-- inst/doc/rice.R | 22 +++-- inst/doc/rice.Rmd | 22 ++++- inst/doc/rice.html | 178 ++++++++++++++++++++++----------------------- man/F14C.age.Rd | 21 +---- man/age.F14C.Rd | 21 +---- man/age.pMC.Rd | 23 +---- man/caldist.Rd | 16 ++-- man/calibratable.Rd | 3 man/calibrate.Rd | 25 +++--- man/coverage.Rd |only man/draw.ccurve.Rd | 6 - man/draw.dates.Rd | 40 ++++++---- man/pMC.age.Rd | 23 +---- man/r.calib.Rd | 3 man/rice-package.Rd | 2 man/rice.Rd | 2 tests/testthat/test-rice.R | 8 +- vignettes/rice.Rmd | 22 ++++- 31 files changed, 542 insertions(+), 434 deletions(-)
Title: Dimension Reduction and Estimation Methods
Description: We provide linear and nonlinear dimension reduction techniques.
Intrinsic dimension estimation methods for exploratory analysis are also provided.
For more details on the package, see the paper by You and Shung (2022) <doi:10.1016/j.simpa.2022.100414>.
Author: Kisung You [aut, cre] ,
Changhee Suh [ctb],
Dennis Shung [ctb]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between Rdimtools versions 1.1.3 dated 2025-09-22 and 1.1.4 dated 2026-03-19
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 10 +++++++++- NEWS.md | 4 ++++ R/Rdimtools-package.R | 2 +- R/linear_DSPP.R | 6 ++---- R/linear_SPP.R | 4 ++-- R/nonlinear_MVE.R | 4 ++-- README.md | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary vignettes/quick-start.html | 8 ++++---- 12 files changed, 41 insertions(+), 31 deletions(-)
Title: Comparison of Phylogenetic Trees Using Quartet and Split
Measures
Description: Calculates the number of four-taxon subtrees consistent with a pair
of cladograms, calculating the symmetric quartet distance of Bandelt & Dress
(1986), Reconstructing the shape of a tree from observed dissimilarity data,
Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>,
and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for
computing the quartet and triplet distances between binary or general trees,
Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157>
for pairs of binary trees.
Author: Martin R. Smith [aut, cre, cph] ,
Andreas Sand [ant],
Gerth Stoelting Brodal [ant],
Rolf Fagerberg [ant],
Thomas Mailund [ant],
Christian N. S. Pedersen [ant] ,
Jens Johansen [ant],
Morten K. Holt [ant]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Quartet versions 1.2.7 dated 2024-10-31 and 1.3.0 dated 2026-03-19
Quartet-1.2.7/Quartet/inst/doc/Quartet-Distance.pdf |only Quartet-1.3.0/Quartet/DESCRIPTION | 16 Quartet-1.3.0/Quartet/MD5 | 105 Quartet-1.3.0/Quartet/NEWS.md | 9 Quartet-1.3.0/Quartet/R/CompareQuartets.R | 640 +- Quartet-1.3.0/Quartet/R/QuartetDistance.R | 232 Quartet-1.3.0/Quartet/R/RcppExports.R | 4 Quartet-1.3.0/Quartet/R/ResolvedQuartets.R | 186 Quartet-1.3.0/Quartet/R/TernaryPoints.R | 220 Quartet-1.3.0/Quartet/R/VisualizeQuartets.R | 292 Quartet-1.3.0/Quartet/R/tqDist.r | 58 Quartet-1.3.0/Quartet/build/partial.rdb |binary Quartet-1.3.0/Quartet/build/vignette.rds |binary Quartet-1.3.0/Quartet/inst/WORDLIST | 2 Quartet-1.3.0/Quartet/inst/apa-old-doi-prefix.csl | 3174 ++++++---- Quartet-1.3.0/Quartet/inst/benchmarks |only Quartet-1.3.0/Quartet/inst/doc/Quartet-Distance.R | 2 Quartet-1.3.0/Quartet/inst/doc/Quartet-Distance.Rmd | 428 - Quartet-1.3.0/Quartet/inst/doc/Quartet-Distance.html |only Quartet-1.3.0/Quartet/inst/doc/Using-Quartet.R | 10 Quartet-1.3.0/Quartet/inst/doc/Using-Quartet.Rmd | 379 - Quartet-1.3.0/Quartet/inst/doc/Using-Quartet.html | 29 Quartet-1.3.0/Quartet/man/AllQuartets.Rd | 96 Quartet-1.3.0/Quartet/man/CompareQuartets.Rd | 130 Quartet-1.3.0/Quartet/man/CompareQuartetsMulti.Rd | 170 Quartet-1.3.0/Quartet/man/CompareSplits.Rd | 136 Quartet-1.3.0/Quartet/man/Distances.Rd | 208 Quartet-1.3.0/Quartet/man/PairSharedQuartetStatus.Rd | 88 Quartet-1.3.0/Quartet/man/PlotQuartet.Rd | 94 Quartet-1.3.0/Quartet/man/QuartetPoints.Rd | 144 Quartet-1.3.0/Quartet/man/QuartetState.Rd | 188 Quartet-1.3.0/Quartet/man/QuartetStatus.Rd | 306 Quartet-1.3.0/Quartet/man/ResolvedQuartets.Rd | 126 Quartet-1.3.0/Quartet/man/SplitStatus.Rd | 204 Quartet-1.3.0/Quartet/man/SymmetricDifferenceLineEnds.Rd | 70 Quartet-1.3.0/Quartet/man/TQDist.Rd | 106 Quartet-1.3.0/Quartet/man/VisualizeQuartets.Rd | 208 Quartet-1.3.0/Quartet/src/AllQuartets.cpp | 4 Quartet-1.3.0/Quartet/src/HDTFactory.cpp | 5 Quartet-1.3.0/Quartet/src/Makevars |only Quartet-1.3.0/Quartet/src/QuartetDistanceCalculator.cpp | 507 - Quartet-1.3.0/Quartet/src/QuartetDistanceCalculator.h | 7 Quartet-1.3.0/Quartet/src/RcppExports.cpp | 13 Quartet-1.3.0/Quartet/src/TripletDistanceCalculator.cpp | 81 Quartet-1.3.0/Quartet/src/counting_linked_list.h | 7 Quartet-1.3.0/Quartet/src/counting_linked_list_num_only.h | 7 Quartet-1.3.0/Quartet/src/rQuartetDist.cpp | 85 Quartet-1.3.0/Quartet/src/unrooted_tree.h | 19 Quartet-1.3.0/Quartet/tests/testthat/test-1-tqdist.R | 430 - Quartet-1.3.0/Quartet/tests/testthat/test-AllQuartets.cpp.R | 60 Quartet-1.3.0/Quartet/tests/testthat/test-CompareQuartets.R | 273 Quartet-1.3.0/Quartet/tests/testthat/test-VisualizeQuartet.R | 62 Quartet-1.3.0/Quartet/tests/testthat/test-ZZZ-Metrics.R | 396 - Quartet-1.3.0/Quartet/tests/testthat/test-regression-correctness.R |only Quartet-1.3.0/Quartet/vignettes/Quartet-Distance.Rmd | 428 - Quartet-1.3.0/Quartet/vignettes/Using-Quartet.Rmd | 379 - 56 files changed, 5868 insertions(+), 4955 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb],
Boris Grinshpun [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.2.6 dated 2025-11-03 and 0.2.7 dated 2026-03-19
NMsim-0.2.6/NMsim/R/NMctl.R |only NMsim-0.2.6/NMsim/R/NMextractText.R |only NMsim-0.2.6/NMsim/R/NMreadFilters.R |only NMsim-0.2.6/NMsim/R/NMreadInits.R |only NMsim-0.2.6/NMsim/R/NMreadSection.R |only NMsim-0.2.6/NMsim/R/addParType.R |only NMsim-0.2.6/NMsim/R/fnAppend.R |only NMsim-0.2.6/NMsim/man/NMextractText.Rd |only NMsim-0.2.6/NMsim/man/NMreadFilters.Rd |only NMsim-0.2.6/NMsim/man/NMreadInits.Rd |only NMsim-0.2.6/NMsim/man/NMreadSection.Rd |only NMsim-0.2.6/NMsim/man/addParType.Rd |only NMsim-0.2.6/NMsim/man/addParameter.Rd |only NMsim-0.2.6/NMsim/man/addSameBlocks.Rd |only NMsim-0.2.6/NMsim/man/as.NMctl.Rd |only NMsim-0.2.6/NMsim/man/count_ij.Rd |only NMsim-0.2.6/NMsim/man/fnAppend.Rd |only NMsim-0.2.6/NMsim/man/initsToExt.Rd |only NMsim-0.2.6/NMsim/man/itriag.Rd |only NMsim-0.2.6/NMsim/man/jtriag.Rd |only NMsim-0.2.6/NMsim/man/readCtl.Rd |only NMsim-0.2.6/NMsim/man/triagSize.Rd |only NMsim-0.2.7/NMsim/DESCRIPTION | 8 - NMsim-0.2.7/NMsim/MD5 | 70 +++------- NMsim-0.2.7/NMsim/NAMESPACE | 1 NMsim-0.2.7/NMsim/NEWS.md | 18 ++ NMsim-0.2.7/NMsim/R/NMcreateMatLines.R | 8 - NMsim-0.2.7/NMsim/R/NMsim.R | 9 + NMsim-0.2.7/NMsim/R/NMsim_EBE.R | 9 + NMsim-0.2.7/NMsim/R/NMsim_NWPRI.R | 2 NMsim-0.2.7/NMsim/R/NMupdateFn.R | 7 - NMsim-0.2.7/NMsim/R/NMwriteInits.R | 27 +-- NMsim-0.2.7/NMsim/R/addResVar.R | 7 - NMsim-0.2.7/NMsim/R/deleteTmpDirs.R | 17 +- NMsim-0.2.7/NMsim/R/forestSummarize.R | 5 NMsim-0.2.7/NMsim/R/prioritizePaths.R | 9 + NMsim-0.2.7/NMsim/R/samplePars_simpar.R | 6 NMsim-0.2.7/NMsim/R/typicalize.R | 6 NMsim-0.2.7/NMsim/man/deleteTmpDirs.Rd | 7 - NMsim-0.2.7/NMsim/man/prioritizePaths.Rd | 9 + NMsim-0.2.7/NMsim/tests/testthat/test-addResVar.R |only NMsim-0.2.7/NMsim/tests/testthat/test-deleteTmpDirs.R |only NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail.lst | 2 NMsim-0.2.7/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |binary NMsim-0.2.7/NMsim/tests/testthat/testReference/NMsim_NWPRI_03.rds |binary NMsim-0.2.7/NMsim/tests/testthat/testReference/NMsim_NWPRI_03_OMEGAP.rds |binary NMsim-0.2.7/NMsim/tests/testthat/test_NMcreateMatLines.R | 4 NMsim-0.2.7/NMsim/tests/testthat/test_nameMultipleFiles.R | 1 48 files changed, 134 insertions(+), 98 deletions(-)
Title: Ecological Indices Calculator for Nematode Communities
Description: Provides a computational toolkit for analyzing nematode communities in ecological studies.
Includes methods to quantify nematode-based ecological indicators such as metabolic footprints,
energy flow metrics, and community structure. These tools support assessments of soil health,
ecosystem functioning, and trophic interactions, standardizing the use of nematodes as
bioindicators.
Author: Yuxuan He [aut, cre] ,
Dong Wang [ths],
Yuan Miao [ths]
Maintainer: Yuxuan He <heyuxuan0525@outlook.com>
Diff between Nematode versions 0.2.1 dated 2025-09-07 and 0.2.2 dated 2026-03-19
DESCRIPTION | 23 ++-- MD5 | 21 ++- NAMESPACE | 240 ++++++++++++++++++++++----------------------- NEWS.md | 15 ++ R/data.R | 8 - R/ecological_indices.R | 36 +++--- R/zzz.R | 2 data/nematode.ave.mass.rda |binary data/nematode.info.rda |binary inst |only man/nematode.ave.mass.Rd | 4 man/nematode.info.Rd | 4 12 files changed, 186 insertions(+), 167 deletions(-)
Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The
base classes and methods are inspired by the python code found in
the 'ObsPy' python toolbox <https://github.com/obspy/obspy>. Additional classes and
methods support data returned by web services provided by the EarthScope Consortium.
<https://service.earthscope.org/>.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Gillian Sharer [aut, cre],
Mary Templeton [aut],
Chad Trabant [ctb]
Maintainer: Gillian Sharer <gillian.sharer@earthscope.org>
Diff between IRISSeismic versions 1.7.0 dated 2025-04-25 and 1.8.0 dated 2026-03-19
DESCRIPTION | 10 MD5 | 182 + NAMESPACE | 1 R/Class-IrisClient.R | 4182 ++++++++++++++++++++++++++-------------- R/Class-Stream.R | 1230 +++++++---- R/Class-Trace.R | 786 ++++--- R/Utils.R | 428 ++-- R/mseedWrappers.R | 4 R/spectralUtils.R | 1055 +++++----- R/zzz.R | 20 build/vignette.rds |binary inst/doc/IRISSeismic-intro.R | 189 - inst/doc/IRISSeismic-intro.Rmd | 189 - inst/doc/IRISSeismic-intro.html | 168 - man/IRISSeismic-package.Rd | 12 man/IrisClient-class.Rd | 13 man/Stream-class.Rd | 54 man/Trace-class.Rd | 43 man/assignQuality.Rd |only man/getDataAvailability.Rd | 4 man/miniseed2Stream.Rd | 54 src/libmseed/example |only src/libmseed/test |only src/libmseed2 |only vignettes/IRISSeismic-intro.Rmd | 189 - 25 files changed, 5494 insertions(+), 3319 deletions(-)
Title: Genome and Transcriptome Wide Association Study
Description: Quantitative trait loci mapping and genome wide association analysis are used to find candidate molecular marker or region associated with phenotype based on linkage analysis and linkage disequilibrium. Gene expression quantitative trait loci mapping is used to find candidate molecular marker or region associated with gene expression. In this package, we applied the method in Liu W. (2011) <doi:10.1007/s00122-011-1631-7> and Gusev A. (2016) <doi:10.1038/ng.3506> to genome and transcriptome wide association study, which is aimed at revealing the association relationship between phenotype and molecular markers, expression levels, molecular markers nested within different related expression effect and expression effect nested within different related molecular marker effect. F test based on full and reduced model are performed to obtain p value or likelihood ratio statistic. The best linear model can be obtained by stepwise regression analysis.
Author: Junhui Li [aut, cre]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between gtWAS versions 1.1.0 dated 2019-06-01 and 1.1.1 dated 2026-03-19
DESCRIPTION | 17 +++++++++++------ MD5 | 4 ++-- R/stp.R | 4 ++-- 3 files changed, 15 insertions(+), 10 deletions(-)
Title: Icon-Based Population Charts and Plots for 'ggplot2'
Description: Create engaging population and point plots charts in R. 'ggpop' allows users to represent population data and points proportionally using customizable icons, facilitating the creation of circular representative population charts as well as any point-plots.
Author: Jorge A. Roa-Contreras [aut, cre] ,
Ralitza Soultanova [aut] ,
Fernando Alarid-Escudero [aut] ,
Carlos Pineda-Antunez [aut]
Maintainer: Jorge A. Roa-Contreras <jorgeroa@stanford.edu>
Diff between ggpop versions 1.7.0 dated 2026-03-17 and 1.7.1 dated 2026-03-19
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/fetch_df_coordinates.R | 8 ++++++-- inst/doc/v-geom-pop.html | 6 +++--- inst/doc/v-ggpop.html | 2 +- inst/doc/v-process-data.html | 4 ++-- inst/doc/v-themes.html | 6 +++--- 8 files changed, 35 insertions(+), 24 deletions(-)
Title: Scrubbing and Other Data Cleaning Routines for fMRI
Description: Data-driven fMRI denoising with projection scrubbing (Pham et al
(2022) <doi:10.1016/j.neuroimage.2023.119972>). Also includes routines for
DVARS (Derivatives VARianceS) (Afyouni and Nichols (2018)
<doi:10.1016/j.neuroimage.2017.12.098>), motion scrubbing (Power et al
(2012) <doi:10.1016/j.neuroimage.2011.10.018>), aCompCor (anatomical
Components Correction) (Muschelli et al (2014)
<doi:10.1016/j.neuroimage.2014.03.028>), detrending, and nuisance
regression. Projection scrubbing is also applicable to other
outlier detection tasks involving high-dimensional data.
Author: Amanda Mejia [aut, cre],
John Muschelli [aut] ,
Damon Pham [aut] ,
Daniel McDonald [ctb],
Fatma Parlak [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between fMRIscrub versions 0.14.5 dated 2023-10-25 and 0.15.0 dated 2026-03-19
fMRIscrub-0.14.5/fMRIscrub/R/SHASH.R |only fMRIscrub-0.14.5/fMRIscrub/R/flags_to_nuis_spikes.R |only fMRIscrub-0.14.5/fMRIscrub/R/robdist.R |only fMRIscrub-0.14.5/fMRIscrub/R/scrub.R |only fMRIscrub-0.14.5/fMRIscrub/man/RD_impData.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/RD_meas.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/RD_univOut.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/SHASH_out.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/SHASH_to_normal.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/emprule_rob.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/flags_to_nuis_spikes.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/plot.scrub_DVARS.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/plot.scrub_FD.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/plot.scrub_projection.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/plot.scrub_projection_multi.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/plot_scrub_wrapper.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/robdist.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/scrub.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/scrub_plot.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/scrub_xifti.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/summary.scrub_DVARS.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/summary.scrub_FD.Rd |only fMRIscrub-0.14.5/fMRIscrub/man/summary.scrub_projection.Rd |only fMRIscrub-0.15.0/fMRIscrub/DESCRIPTION | 21 +- fMRIscrub-0.15.0/fMRIscrub/MD5 | 78 ++++----- fMRIscrub-0.15.0/fMRIscrub/NAMESPACE | 35 +--- fMRIscrub-0.15.0/fMRIscrub/NEWS.md | 5 fMRIscrub-0.15.0/fMRIscrub/R/DVARS.R | 2 fMRIscrub-0.15.0/fMRIscrub/R/FD.R | 77 +++++++-- fMRIscrub-0.15.0/fMRIscrub/R/IDvols.R |only fMRIscrub-0.15.0/fMRIscrub/R/artifact_images.R | 2 fMRIscrub-0.15.0/fMRIscrub/R/deprecated.R |only fMRIscrub-0.15.0/fMRIscrub/R/fMRIscrub-package.R | 4 fMRIscrub-0.15.0/fMRIscrub/R/flags2spikes.R |only fMRIscrub-0.15.0/fMRIscrub/R/high_kurtosis.R | 6 fMRIscrub-0.15.0/fMRIscrub/R/plot.R | 56 +++--- fMRIscrub-0.15.0/fMRIscrub/R/pscrub_from_multi.R | 2 fMRIscrub-0.15.0/fMRIscrub/R/pscrub_multi.R | 27 ++- fMRIscrub-0.15.0/fMRIscrub/R/utils_scrub.R | 84 +++++----- fMRIscrub-0.15.0/fMRIscrub/README.md | 29 ++- fMRIscrub-0.15.0/fMRIscrub/man/FD.Rd | 41 +++- fMRIscrub-0.15.0/fMRIscrub/man/IDvols.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/IDvols_plot.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/IDvols_xifti.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/artifact_images.Rd | 2 fMRIscrub-0.15.0/fMRIscrub/man/fMRIscrub.Rd | 25 ++ fMRIscrub-0.15.0/fMRIscrub/man/flags2spikes.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/high_kurtosis.Rd | 4 fMRIscrub-0.15.0/fMRIscrub/man/plot.IDvols_DVARS.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/plot.IDvols_FD.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/plot.IDvols_projection.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/plot.IDvols_projection_multi.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/plot_IDvols_wrapper.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/pscrub_multi.Rd | 6 fMRIscrub-0.15.0/fMRIscrub/man/summary.IDvols_DVARS.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/summary.IDvols_FD.Rd |only fMRIscrub-0.15.0/fMRIscrub/man/summary.IDvols_projection.Rd |only fMRIscrub-0.15.0/fMRIscrub/tests/testthat/test-test_all_methods.R | 4 fMRIscrub-0.15.0/fMRIscrub/tests/testthat/test-test_scrubbing.R | 6 59 files changed, 316 insertions(+), 200 deletions(-)
Title: Mathematical Modeling of Infectious Disease Dynamics
Description: Tools for simulating mathematical models of infectious disease dynamics.
Epidemic model classes include deterministic compartmental models, stochastic
individual-contact models, and stochastic network models. Network models use the
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features an API for
extending these templates to address novel scientific research aims. Full
methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Adrien Le Guillou [aut],
Chad Klumb [aut],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between EpiModel versions 2.5.0 dated 2024-10-11 and 2.6.0 dated 2026-03-19
EpiModel-2.5.0/EpiModel/R/comp_plot.R |only EpiModel-2.5.0/EpiModel/R/net.accessor.R |only EpiModel-2.5.0/EpiModel/R/net.end.horizon.R |only EpiModel-2.5.0/EpiModel/R/net.record.R |only EpiModel-2.5.0/EpiModel/R/net.scenarios.R |only EpiModel-2.5.0/EpiModel/R/net.utils.R |only EpiModel-2.5.0/EpiModel/R/netsim_checkpoint.R |only EpiModel-2.5.0/EpiModel/R/param_df.R |only EpiModel-2.5.0/EpiModel/R/plot_stat_table.R |only EpiModel-2.5.0/EpiModel/inst/shiny/epinet |only EpiModel-2.5.0/EpiModel/inst/web |only EpiModel-2.5.0/EpiModel/tests/testthat/Rplots.pdf |only EpiModel-2.5.0/EpiModel/tests/testthat/test-attr-copy.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-dcm-dede.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-extremal-targets.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-netoffset.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-netrestart.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-netsim-checkpoint.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-netsim-end-horizon.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-netvary.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-newdcm.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-newicm.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-parameters_df.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-random-params.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-record.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-scenarios.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-shiny.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-stergm.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-term-fuzzynodematch.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-trackers.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-trim_netest.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-update.R |only EpiModel-2.5.0/EpiModel/tests/testthat/test-updater.R |only EpiModel-2.6.0/EpiModel/DESCRIPTION | 23 EpiModel-2.6.0/EpiModel/MD5 | 509 ++---- EpiModel-2.6.0/EpiModel/NAMESPACE | 9 EpiModel-2.6.0/EpiModel/NEWS.md | 708 ++++---- EpiModel-2.6.0/EpiModel/R/EpiModel-package.R | 105 - EpiModel-2.6.0/EpiModel/R/ErgmTerms.R | 46 EpiModel-2.6.0/EpiModel/R/as.data.frame.R | 199 +- EpiModel-2.6.0/EpiModel/R/dcm.R | 91 - EpiModel-2.6.0/EpiModel/R/dcm.inputs.R | 179 +- EpiModel-2.6.0/EpiModel/R/dcm.mods.R | 18 EpiModel-2.6.0/EpiModel/R/dendo.R | 65 EpiModel-2.6.0/EpiModel/R/edgelists.R | 63 EpiModel-2.6.0/EpiModel/R/geom_bands.R | 8 EpiModel-2.6.0/EpiModel/R/get.R | 229 +- EpiModel-2.6.0/EpiModel/R/icm.R | 34 EpiModel-2.6.0/EpiModel/R/icm.inputs.R | 114 - EpiModel-2.6.0/EpiModel/R/icm.mod.init.R | 10 EpiModel-2.6.0/EpiModel/R/icm.mod.status.R | 6 EpiModel-2.6.0/EpiModel/R/icm.mod.vital.R | 16 EpiModel-2.6.0/EpiModel/R/icm.utils.R | 2 EpiModel-2.6.0/EpiModel/R/merge.R | 64 EpiModel-2.6.0/EpiModel/R/modules.icm.R | 42 EpiModel-2.6.0/EpiModel/R/modules.net.R | 62 EpiModel-2.6.0/EpiModel/R/net.fn.accessor.R |only EpiModel-2.6.0/EpiModel/R/net.fn.checkpoint.R |only EpiModel-2.6.0/EpiModel/R/net.fn.end.horizon.R |only EpiModel-2.6.0/EpiModel/R/net.fn.logs.R |only EpiModel-2.6.0/EpiModel/R/net.fn.modules.R | 2 EpiModel-2.6.0/EpiModel/R/net.fn.param_df.R |only EpiModel-2.6.0/EpiModel/R/net.fn.record.R |only EpiModel-2.6.0/EpiModel/R/net.fn.scenarios.R |only EpiModel-2.6.0/EpiModel/R/net.fn.utils.R |only EpiModel-2.6.0/EpiModel/R/net.helpers.R | 42 EpiModel-2.6.0/EpiModel/R/net.inputs.R | 237 +- EpiModel-2.6.0/EpiModel/R/net.mod.infection.R | 105 - EpiModel-2.6.0/EpiModel/R/net.mod.init.R | 38 EpiModel-2.6.0/EpiModel/R/net.mod.nwupdate.R | 2 EpiModel-2.6.0/EpiModel/R/net.mod.prevalence.R | 2 EpiModel-2.6.0/EpiModel/R/net.mod.recovery.R | 10 EpiModel-2.6.0/EpiModel/R/net.mod.simnet.R | 32 EpiModel-2.6.0/EpiModel/R/net.mod.summary.R | 14 EpiModel-2.6.0/EpiModel/R/net.mod.trackers.R | 12 EpiModel-2.6.0/EpiModel/R/net.mod.updater.R | 22 EpiModel-2.6.0/EpiModel/R/net.mod.vital.R | 16 EpiModel-2.6.0/EpiModel/R/netdx.R | 136 + EpiModel-2.6.0/EpiModel/R/netest.R | 111 + EpiModel-2.6.0/EpiModel/R/netsim.R | 193 +- EpiModel-2.6.0/EpiModel/R/network.R | 47 EpiModel-2.6.0/EpiModel/R/plot.R | 14 EpiModel-2.6.0/EpiModel/R/plot.comp_plot.R |only EpiModel-2.6.0/EpiModel/R/plot.dcm.R | 69 EpiModel-2.6.0/EpiModel/R/plot.epi.data.frame.R | 2 EpiModel-2.6.0/EpiModel/R/plot.icm.R | 53 EpiModel-2.6.0/EpiModel/R/plot.netdx.R | 46 EpiModel-2.6.0/EpiModel/R/plot.netsim.R | 177 +- EpiModel-2.6.0/EpiModel/R/plot.stat_table.R |only EpiModel-2.6.0/EpiModel/R/print.R | 156 + EpiModel-2.6.0/EpiModel/R/reachable.R | 10 EpiModel-2.6.0/EpiModel/R/saveout.R | 104 - EpiModel-2.6.0/EpiModel/R/shiny.R | 124 + EpiModel-2.6.0/EpiModel/R/summary.R | 50 EpiModel-2.6.0/EpiModel/R/test.R | 6 EpiModel-2.6.0/EpiModel/R/update.R | 40 EpiModel-2.6.0/EpiModel/R/utils.R | 200 -- EpiModel-2.6.0/EpiModel/R/verbose.R | 22 EpiModel-2.6.0/EpiModel/build/partial.rdb |binary EpiModel-2.6.0/EpiModel/build/vignette.rds |binary EpiModel-2.6.0/EpiModel/inst/doc/Intro.R | 2 EpiModel-2.6.0/EpiModel/inst/doc/Intro.html | 6 EpiModel-2.6.0/EpiModel/inst/doc/attributes-and-summary-statistics.R | 202 +- EpiModel-2.6.0/EpiModel/inst/doc/attributes-and-summary-statistics.html | 149 - EpiModel-2.6.0/EpiModel/inst/doc/model-parameters.html | 21 EpiModel-2.6.0/EpiModel/inst/doc/network-objects.R | 26 EpiModel-2.6.0/EpiModel/inst/doc/network-objects.html | 8 EpiModel-2.6.0/EpiModel/inst/shiny/epidcm/server.R | 715 +++++++- EpiModel-2.6.0/EpiModel/inst/shiny/epidcm/ui.R | 608 +++++-- EpiModel-2.6.0/EpiModel/inst/shiny/epiicm/server.R | 821 ++++++++-- EpiModel-2.6.0/EpiModel/inst/shiny/epiicm/ui.R | 670 +++++--- EpiModel-2.6.0/EpiModel/man/EpiModel-package.Rd | 29 EpiModel-2.6.0/EpiModel/man/arrivals.2g.net.Rd | 6 EpiModel-2.6.0/EpiModel/man/arrivals.icm.Rd | 4 EpiModel-2.6.0/EpiModel/man/arrivals.icm.bip.Rd | 4 EpiModel-2.6.0/EpiModel/man/arrivals.net.Rd | 6 EpiModel-2.6.0/EpiModel/man/as.data.frame.dcm.Rd | 14 EpiModel-2.6.0/EpiModel/man/as.data.frame.icm.Rd | 14 EpiModel-2.6.0/EpiModel/man/as.data.frame.netdx.Rd | 10 EpiModel-2.6.0/EpiModel/man/as.phylo.transmat.Rd | 10 EpiModel-2.6.0/EpiModel/man/auto_update_attr.Rd | 10 EpiModel-2.6.0/EpiModel/man/check_attr_lengths.Rd | 4 EpiModel-2.6.0/EpiModel/man/check_degdist_bal.Rd | 2 EpiModel-2.6.0/EpiModel/man/check_end_horizon_control.Rd | 4 EpiModel-2.6.0/EpiModel/man/color_tea.Rd | 16 EpiModel-2.6.0/EpiModel/man/common_updater.Rd | 2 EpiModel-2.6.0/EpiModel/man/comp_plot.Rd | 2 EpiModel-2.6.0/EpiModel/man/control.dcm.Rd | 39 EpiModel-2.6.0/EpiModel/man/control.icm.Rd | 24 EpiModel-2.6.0/EpiModel/man/control.net.Rd | 12 EpiModel-2.6.0/EpiModel/man/copy_datattr_to_nwattr.Rd | 10 EpiModel-2.6.0/EpiModel/man/copy_nwattr_to_datattr.Rd | 10 EpiModel-2.6.0/EpiModel/man/create_dat_object.Rd | 8 EpiModel-2.6.0/EpiModel/man/create_scenario_list.Rd | 2 EpiModel-2.6.0/EpiModel/man/crosscheck.dcm.Rd | 10 EpiModel-2.6.0/EpiModel/man/crosscheck.icm.Rd | 10 EpiModel-2.6.0/EpiModel/man/crosscheck.net.Rd | 14 EpiModel-2.6.0/EpiModel/man/dcm.Rd | 24 EpiModel-2.6.0/EpiModel/man/dcm.mods.Rd | 18 EpiModel-2.6.0/EpiModel/man/departures.2g.net.Rd | 4 EpiModel-2.6.0/EpiModel/man/departures.icm.Rd | 4 EpiModel-2.6.0/EpiModel/man/departures.icm.bip.Rd | 4 EpiModel-2.6.0/EpiModel/man/departures.net.Rd | 4 EpiModel-2.6.0/EpiModel/man/discord_edgelist.Rd | 7 EpiModel-2.6.0/EpiModel/man/dissolution_coefs.Rd | 8 EpiModel-2.6.0/EpiModel/man/edgelist_censor.Rd | 2 EpiModel-2.6.0/EpiModel/man/edges_correct.Rd | 6 EpiModel-2.6.0/EpiModel/man/epi_trackers.Rd | 4 EpiModel-2.6.0/EpiModel/man/epiweb.Rd | 91 - EpiModel-2.6.0/EpiModel/man/generate_random_params.Rd | 2 EpiModel-2.6.0/EpiModel/man/geom_bands.Rd | 2 EpiModel-2.6.0/EpiModel/man/get_attr_prop.Rd | 12 EpiModel-2.6.0/EpiModel/man/get_cumulative_degree.Rd | 2 EpiModel-2.6.0/EpiModel/man/get_cumulative_edgelist.Rd | 2 EpiModel-2.6.0/EpiModel/man/get_cumulative_edgelists_df.Rd | 2 EpiModel-2.6.0/EpiModel/man/get_current_timestep.Rd | 2 EpiModel-2.6.0/EpiModel/man/get_degree.Rd | 2 EpiModel-2.6.0/EpiModel/man/get_discordant_edgelist.Rd | 4 EpiModel-2.6.0/EpiModel/man/get_edgelist.Rd | 2 EpiModel-2.6.0/EpiModel/man/get_edgelists_df.Rd | 2 EpiModel-2.6.0/EpiModel/man/get_formula_term_attr.Rd | 4 EpiModel-2.6.0/EpiModel/man/get_modules.Rd | 2 EpiModel-2.6.0/EpiModel/man/get_network.Rd | 14 EpiModel-2.6.0/EpiModel/man/get_network_term_attr.Rd | 4 EpiModel-2.6.0/EpiModel/man/get_nwstats.Rd | 9 EpiModel-2.6.0/EpiModel/man/get_partners.Rd | 6 EpiModel-2.6.0/EpiModel/man/get_sims.Rd | 4 EpiModel-2.6.0/EpiModel/man/get_transmat.Rd | 4 EpiModel-2.6.0/EpiModel/man/get_vertex_attribute.Rd | 7 EpiModel-2.6.0/EpiModel/man/icm.Rd | 16 EpiModel-2.6.0/EpiModel/man/idgroup.Rd | 6 EpiModel-2.6.0/EpiModel/man/increment_timestep.Rd | 2 EpiModel-2.6.0/EpiModel/man/infection.2g.net.Rd | 8 EpiModel-2.6.0/EpiModel/man/infection.net.Rd | 6 EpiModel-2.6.0/EpiModel/man/init.dcm.Rd | 25 EpiModel-2.6.0/EpiModel/man/init.icm.Rd | 8 EpiModel-2.6.0/EpiModel/man/init.net.Rd | 8 EpiModel-2.6.0/EpiModel/man/init_nets.Rd | 2 EpiModel-2.6.0/EpiModel/man/init_status.icm.Rd | 2 EpiModel-2.6.0/EpiModel/man/init_status.net.Rd | 6 EpiModel-2.6.0/EpiModel/man/initialize.icm.Rd | 6 EpiModel-2.6.0/EpiModel/man/initialize.net.Rd | 6 EpiModel-2.6.0/EpiModel/man/is_active_posit_ids.Rd | 4 EpiModel-2.6.0/EpiModel/man/is_active_unique_ids.Rd | 4 EpiModel-2.6.0/EpiModel/man/make_module_list.Rd | 2 EpiModel-2.6.0/EpiModel/man/make_restart_point.Rd |only EpiModel-2.6.0/EpiModel/man/merge.icm.Rd | 10 EpiModel-2.6.0/EpiModel/man/merge.netsim.Rd | 16 EpiModel-2.6.0/EpiModel/man/modules.icm.Rd | 22 EpiModel-2.6.0/EpiModel/man/modules.net.Rd | 36 EpiModel-2.6.0/EpiModel/man/multilayer.Rd | 4 EpiModel-2.6.0/EpiModel/man/net-accessor.Rd | 19 EpiModel-2.6.0/EpiModel/man/netdx.Rd | 110 + EpiModel-2.6.0/EpiModel/man/netest.Rd | 92 - EpiModel-2.6.0/EpiModel/man/netsim.Rd | 139 + EpiModel-2.6.0/EpiModel/man/netsim_cond_msg.Rd | 2 EpiModel-2.6.0/EpiModel/man/netsim_error_logger.Rd | 4 EpiModel-2.6.0/EpiModel/man/nwupdate.net.Rd | 2 EpiModel-2.6.0/EpiModel/man/overwrite_attrs.Rd | 2 EpiModel-2.6.0/EpiModel/man/padded_vector.Rd | 4 EpiModel-2.6.0/EpiModel/man/param.dcm.Rd | 19 EpiModel-2.6.0/EpiModel/man/param.icm.Rd | 12 EpiModel-2.6.0/EpiModel/man/param.net.Rd | 20 EpiModel-2.6.0/EpiModel/man/param.net_from_table.Rd | 6 EpiModel-2.6.0/EpiModel/man/param.net_to_table.Rd | 2 EpiModel-2.6.0/EpiModel/man/param_random.Rd | 4 EpiModel-2.6.0/EpiModel/man/plot.dcm.Rd | 14 EpiModel-2.6.0/EpiModel/man/plot.epi.data.frame.Rd | 2 EpiModel-2.6.0/EpiModel/man/plot.icm.Rd | 8 EpiModel-2.6.0/EpiModel/man/plot.netdx.Rd | 12 EpiModel-2.6.0/EpiModel/man/plot.netsim.Rd | 28 EpiModel-2.6.0/EpiModel/man/plot.transmat.Rd | 6 EpiModel-2.6.0/EpiModel/man/prevalence.net.Rd | 4 EpiModel-2.6.0/EpiModel/man/print.dcm.Rd |only EpiModel-2.6.0/EpiModel/man/print.icm.Rd |only EpiModel-2.6.0/EpiModel/man/print.netdx.Rd | 14 EpiModel-2.6.0/EpiModel/man/print.netsim.Rd |only EpiModel-2.6.0/EpiModel/man/process_out.net.Rd | 4 EpiModel-2.6.0/EpiModel/man/reachable-nodes.Rd | 4 EpiModel-2.6.0/EpiModel/man/record_attr_history.Rd | 4 EpiModel-2.6.0/EpiModel/man/record_raw_object.Rd | 4 EpiModel-2.6.0/EpiModel/man/recovery.2g.net.Rd | 4 EpiModel-2.6.0/EpiModel/man/recovery.icm.Rd | 2 EpiModel-2.6.0/EpiModel/man/recovery.icm.bip.Rd | 2 EpiModel-2.6.0/EpiModel/man/recovery.net.Rd | 4 EpiModel-2.6.0/EpiModel/man/remove_modules.Rd | 2 EpiModel-2.6.0/EpiModel/man/resim_nets.Rd | 4 EpiModel-2.6.0/EpiModel/man/saveout.dcm.Rd | 12 EpiModel-2.6.0/EpiModel/man/saveout.icm.Rd | 6 EpiModel-2.6.0/EpiModel/man/saveout.net.Rd | 8 EpiModel-2.6.0/EpiModel/man/set_current_timestep.Rd | 2 EpiModel-2.6.0/EpiModel/man/set_modules.Rd | 2 EpiModel-2.6.0/EpiModel/man/set_transmat.Rd | 8 EpiModel-2.6.0/EpiModel/man/set_vertex_attribute.Rd | 4 EpiModel-2.6.0/EpiModel/man/sim_nets_t1.Rd | 6 EpiModel-2.6.0/EpiModel/man/simulate_dat.Rd | 4 EpiModel-2.6.0/EpiModel/man/summary.dcm.Rd | 2 EpiModel-2.6.0/EpiModel/man/summary.icm.Rd | 2 EpiModel-2.6.0/EpiModel/man/summary.netsim.Rd | 2 EpiModel-2.6.0/EpiModel/man/summary_nets.Rd | 2 EpiModel-2.6.0/EpiModel/man/toggles_to_diss_stats.Rd | 2 EpiModel-2.6.0/EpiModel/man/trigger_end_horizon.Rd | 4 EpiModel-2.6.0/EpiModel/man/trim_netest.Rd | 8 EpiModel-2.6.0/EpiModel/man/truncate_sim.Rd | 57 EpiModel-2.6.0/EpiModel/man/unique_id-tools.Rd | 4 EpiModel-2.6.0/EpiModel/man/update_cumulative_edgelist.Rd | 2 EpiModel-2.6.0/EpiModel/man/update_dissolution.Rd | 8 EpiModel-2.6.0/EpiModel/man/update_params.Rd | 8 EpiModel-2.6.0/EpiModel/man/update_unique_ids.Rd | 6 EpiModel-2.6.0/EpiModel/man/use_scenario.Rd | 4 EpiModel-2.6.0/EpiModel/man/verbose.dcm.Rd | 2 EpiModel-2.6.0/EpiModel/man/verbose.icm.Rd | 2 EpiModel-2.6.0/EpiModel/man/verbose.net.Rd | 4 EpiModel-2.6.0/EpiModel/tests/testthat/test-accessors.R | 46 EpiModel-2.6.0/EpiModel/tests/testthat/test-cumulative_edgelist.R | 2 EpiModel-2.6.0/EpiModel/tests/testthat/test-dcm-long.R | 4 EpiModel-2.6.0/EpiModel/tests/testthat/test-dcm.R | 331 +++- EpiModel-2.6.0/EpiModel/tests/testthat/test-get.R | 2 EpiModel-2.6.0/EpiModel/tests/testthat/test-icm-long.R | 2 EpiModel-2.6.0/EpiModel/tests/testthat/test-icm.R | 94 + EpiModel-2.6.0/EpiModel/tests/testthat/test-merge.R | 2 EpiModel-2.6.0/EpiModel/tests/testthat/test-multinets.R | 12 EpiModel-2.6.0/EpiModel/tests/testthat/test-mutate.R | 2 EpiModel-2.6.0/EpiModel/tests/testthat/test-net-long.R | 2 EpiModel-2.6.0/EpiModel/tests/testthat/test-net-tergmLite.R | 4 EpiModel-2.6.0/EpiModel/tests/testthat/test-netattr.R | 163 + EpiModel-2.6.0/EpiModel/tests/testthat/test-netdx.R | 7 EpiModel-2.6.0/EpiModel/tests/testthat/test-netest.R | 165 +- EpiModel-2.6.0/EpiModel/tests/testthat/test-netsim-parallel.R | 26 EpiModel-2.6.0/EpiModel/tests/testthat/test-netsim.R | 200 ++ EpiModel-2.6.0/EpiModel/tests/testthat/test-newmodules.R | 414 +++++ EpiModel-2.6.0/EpiModel/tests/testthat/test-print.R | 4 EpiModel-2.6.0/EpiModel/tests/testthat/test-terms.R | 73 EpiModel-2.6.0/EpiModel/tests/testthat/test-transmat-dendo.R | 2 EpiModel-2.6.0/EpiModel/tests/testthat/test-utils.R | 84 - 275 files changed, 7376 insertions(+), 3658 deletions(-)
Title: T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
Description: A "pure R" implementation of the t-SNE algorithm.
Author: Justin Donaldson [aut, cre]
Maintainer: Justin Donaldson <jdonaldson@gmail.com>
Diff between tsne versions 0.1-3.1 dated 2022-03-28 and 0.2-0 dated 2026-03-19
DESCRIPTION | 16 ++++++++++------ MD5 | 8 ++++---- NEWS | 1 + R/tsne-internal.R | 26 ++++++-------------------- R/tsne.R | 11 ++++++----- 5 files changed, 27 insertions(+), 35 deletions(-)
Title: Summarise and Explore Continuous, Categorical and Date Variables
Description: Explore continuous, date and categorical variables with summary
statistics, visualisations, and frequency tables. Brings the ease and
simplicity of the sum and tab commands from 'Stata' to 'R', including
support for two-way cross-tabulations, hypothesis tests, duplicate and
missing data exploration, and automated HTML or PDF exploratory reports.
Author: Alexander Stockdale [aut, cre, cph]
Maintainer: Alexander Stockdale <a.stockdale@liverpool.ac.uk>
Diff between sumvar versions 0.1 dated 2025-06-13 and 0.2.0 dated 2026-03-19
DESCRIPTION | 27 + LICENSE | 4 MD5 | 44 +-- NAMESPACE | 16 - NEWS.md |only R/dist_date.R | 11 R/dist_sum.R | 140 +++++++--- R/dup.R | 16 - R/explorer.R |only R/global_var.R | 2 R/tab.R | 427 ++++++++++++++++++++++++++----- R/tab1.R | 21 + README.md | 45 ++- build/vignette.rds |binary inst/doc/exploring-data-with-sumvar.R | 18 + inst/doc/exploring-data-with-sumvar.Rmd | 29 ++ inst/doc/exploring-data-with-sumvar.html | 114 ++++++-- man/dist_date.Rd | 1 man/dist_sum.Rd | 56 +++- man/explorer.Rd |only man/sumvar.Rd | 2 man/tab.Rd | 67 +++- man/tab1.Rd | 7 tests |only vignettes/exploring-data-with-sumvar.Rmd | 29 ++ 25 files changed, 832 insertions(+), 244 deletions(-)
Title: Robust Estimation in Very Small Samples
Description: Implements and enhances the estimation techniques described in
Rousseeuw & Verboven (2002) <doi:10.1016/S0167-9473(02)00078-6> for the
location and scale of very small samples.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between revss versions 3.0.0 dated 2026-03-18 and 3.1.0 dated 2026-03-19
revss-3.0.0/revss/inst/tinytest/test_robLocScale.R |only revss-3.0.0/revss/man/revss-internal.Rd |only revss-3.1.0/revss/DESCRIPTION | 6 - revss-3.1.0/revss/MD5 | 36 ++++---- revss-3.1.0/revss/R/adm.R | 20 ---- revss-3.1.0/revss/R/madn.R | 28 ------ revss-3.1.0/revss/R/robLoc.R | 29 ++++--- revss-3.1.0/revss/R/robScale.R | 62 ++++++++++----- revss-3.1.0/revss/build/partial.rdb |binary revss-3.1.0/revss/inst/CITATION | 2 revss-3.1.0/revss/inst/NEWS.Rd | 31 +++++++ revss-3.1.0/revss/inst/tinytest/test_adm.R | 11 -- revss-3.1.0/revss/inst/tinytest/test_mad.R | 7 - revss-3.1.0/revss/inst/tinytest/test_robLoc.R |only revss-3.1.0/revss/inst/tinytest/test_robScale.R |only revss-3.1.0/revss/inst/tinytest/test_sort.R | 8 - revss-3.1.0/revss/man/adm.Rd | 16 ++- revss-3.1.0/revss/man/admn.Rd | 42 ++++++---- revss-3.1.0/revss/man/madn.Rd | 61 ++++++--------- revss-3.1.0/revss/man/robLoc.Rd | 53 +++++++------ revss-3.1.0/revss/man/robScale.Rd | 85 +++++++++++---------- 21 files changed, 260 insertions(+), 237 deletions(-)
Title: Ordered Panel
Description: The ordered panel methodology (Zezulinski et al 2025 <doi:10.1159/000545366>) provides a structured framework for identifying and organizing sets of biomarkers, such as genetic variants, that distinguish between positive and negative subjects in a study when only a training cohort is available. This approach is particularly useful in situations where an independent validation cohort does not yet exist, rendering conventional performance metrics such as the receiver operating characteristic (ROC) curve and area under the ROC curve (AUC) inappropriate or potentially misleading. The methodology emphasizes transparent construction and evaluation of ordered signatures of biomarkers, allowing investigators to examine operating characteristics without establishing predictive performance.
Author: Tingting Zhan [aut, cre] ,
Aejaz Sayeed [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between ordPanel versions 0.1.0 dated 2026-03-08 and 0.1.1 dated 2026-03-19
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Title: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
Description: CIFTI files contain brain imaging data in "grayordinates," which
represent the gray matter as cortical surface vertices (left and right) and
subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).
'ciftiTools' provides a unified environment for reading, writing,
visualizing and manipulating CIFTI-format data. It supports the "dscalar,"
"dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti"
object, which is structured for convenient access to the data and metadata,
and includes support for surface geometry files to enable
spatially-dependent functionality such as static or interactive
visualizations and smoothing.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
John Muschelli [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between ciftiTools versions 0.18.0 dated 2025-12-20 and 0.19.0 dated 2026-03-19
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++-------- NEWS.md | 6 +++++ R/parc_utils.R | 10 ++++---- R/wb_cmd.R | 6 ++++- R/write_cifti.R | 2 + README.md | 13 ++++++++++- inst/doc/ciftiTools_vignette_mini.html | 37 ++++++++++++++++----------------- man/apply_parc.Rd | 10 ++++---- tests/testthat/test-misc.R | 2 - 10 files changed, 67 insertions(+), 43 deletions(-)
Title: Pattern Causality Algorithm
Description: A comprehensive package for detecting and analyzing causal relationships in complex systems using pattern-based approaches. Key features include state space reconstruction, pattern identification, and causality strength evaluation.
Author: Stavros Stavroglou [aut, cre] ,
Athanasios Pantelous [aut] ,
Hui Wang [aut]
Maintainer: Stavros Stavroglou <stavros.k.stavroglou@gmail.com>
Diff between patterncausality versions 0.2.3 dated 2025-10-01 and 0.2.4 dated 2026-03-19
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patterncausality-0.2.4/patterncausality/R/pcAccuracy.R | 38 - patterncausality-0.2.4/patterncausality/R/pcCV.R | 98 +- patterncausality-0.2.4/patterncausality/R/pcCrossMatrix.R | 60 - patterncausality-0.2.4/patterncausality/R/pcEffect.R | 28 patterncausality-0.2.4/patterncausality/R/pcMatrix.R | 94 +- patterncausality-0.2.4/patterncausality/R/pc_accuracy_methods.R | 18 patterncausality-0.2.4/patterncausality/R/pc_check.R | 5 patterncausality-0.2.4/patterncausality/R/pc_full_details_utils.R | 259 ++++--- patterncausality-0.2.4/patterncausality/R/pc_lightweight_utils.R | 30 patterncausality-0.2.4/patterncausality/R/pc_nature.R | 9 patterncausality-0.2.4/patterncausality/R/pc_neighbors.R | 43 - patterncausality-0.2.4/patterncausality/R/pc_params.R | 101 --- patterncausality-0.2.4/patterncausality/R/pc_point.R | 2 patterncausality-0.2.4/patterncausality/R/pc_strength.R | 17 patterncausality-0.2.4/patterncausality/R/predictionY.R | 14 patterncausality-0.2.4/patterncausality/R/projectedNNsInfo.R | 16 patterncausality-0.2.4/patterncausality/R/signatureSpace.R | 34 - 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More information about patterncausality at CRAN
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Title: Optimization-Based Stable Balancing Weights
Description: Use optimization to estimate weights that balance covariates for binary, multi-category, continuous, and multivariate treatments in the spirit of Zubizarreta (2015) <doi:10.1080/01621459.2015.1023805>. The degree of balance can be specified for each covariate. In addition, sampling weights can be estimated that allow a sample to generalize to a population specified with given target moments of covariates, as in matching-adjusted indirect comparison (MAIC).
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between optweight versions 2.0.0 dated 2026-01-23 and 2.0.1 dated 2026-03-19
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 6 R/opt_prep.R | 20 +- README.md | 4 build/stage23.rdb |binary inst/doc/optweight.html | 32 +-- tests/testthat/test-optweight.R | 321 +++++++++++++++++++++++----------------- 8 files changed, 232 insertions(+), 171 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-21 0.7.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-23 4.5.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-02 1.6.13
2024-06-02 1.6.12
2023-12-14 1.6.10
2022-10-25 1.6.7
2018-10-01 1.5.5
2018-03-05 1.5.1
2018-01-23 1.5.0
2017-05-09 1.3.1
2017-03-12 1.2.2
2016-11-23 1.2.0
2016-06-13 1.1.0
2015-11-24 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-13 1.0.3
2022-05-10 1.0.2
2022-05-02 1.0.1
2021-07-14 1.0.0
Title: Likelihood-Based Statistical Inference in the Fisherian
Tradition
Description: Facilitates building likelihood models in the Fisherian tradition
following Richard Royall (1997, ISBN:978-0412044113) "Statistical Evidence: A
Likelihood Paradigm". Defines generic methods for working with likelihoods
(loglik(), score(), hess_loglik(), fim()) and provides functions for pure
likelihood-based inference (support(), relative_likelihood(),
likelihood_interval(), profile_loglik()).
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between likelihood.model versions 0.9.1 dated 2026-02-11 and 1.0.0 dated 2026-03-19
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More information about likelihood.model at CRAN
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Title: Dynamic Failure Rate Distributions for Survival Analysis
Description: Flexible framework for specifying survival distributions through
their hazard (failure rate) functions. Define arbitrary time-varying
hazard functions to model complex failure patterns including bathtub
curves, proportional hazards with covariates, and other non-standard
hazard behaviors. Provides automatic computation of survival, CDF, PDF,
quantiles, and sampling. Implements the likelihood model interface for
maximum likelihood estimation with right-censored and left-censored
survival data.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <queelius@gmail.com>
Diff between flexhaz versions 0.5.0 dated 2026-03-02 and 0.5.1 dated 2026-03-19
DESCRIPTION | 6 - MD5 | 20 ++-- NEWS.md | 7 + README.md | 159 +++++++++++++++++++-------------- inst/doc/custom_distributions.html | 6 - inst/doc/failure_rate.html | 4 inst/doc/flexhaz-package.html | 4 man/figures/README-bathtub-1.png |binary man/figures/README-diagnostics-1.png |binary tests/testthat/Rplots.pdf |binary tests/testthat/test-likelihood_model.R | 4 11 files changed, 123 insertions(+), 87 deletions(-)
Title: Compositional Maximum Likelihood Estimation
Description: Provides composable optimization strategies for maximum likelihood
estimation (MLE). Solvers are first-class functions that combine via
sequential chaining, parallel racing, and random restarts. Implements
gradient ascent, Newton-Raphson, quasi-Newton (BFGS), and derivative-free
methods with support for constrained optimization and tracing. Returns
'mle' objects compatible with 'algebraic.mle' for downstream analysis.
Methods based on Nocedal J, Wright SJ (2006) "Numerical Optimization"
<doi:10.1007/978-0-387-40065-5>.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <queelius@gmail.com>
Diff between compositional.mle versions 1.0.2 dated 2026-02-09 and 2.0.0 dated 2026-03-19
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Title: Algebraic Maximum Likelihood Estimators
Description: The maximum likelihood estimator (MLE) is a technology: under
regularity conditions, any MLE is asymptotically normal with variance given
by the inverse Fisher information. This package exploits that structure by
defining an algebra over MLEs. Compose independent estimators into joint
MLEs via block-diagonal covariance ('joint'), optimally combine repeated
estimates via inverse-variance weighting ('combine'), propagate
transformations via the delta method ('rmap'), and bridge to distribution
algebra via conversion to normal or multivariate normal objects ('as_dist').
Supports asymptotic ('mle', 'mle_numerical') and bootstrap ('mle_boot')
estimators with a unified interface for inference: confidence intervals,
standard errors, AIC, Fisher information, and predictive intervals.
For background on maximum likelihood estimation, see Casella and Berger
(2002, ISBN:978-0534243128). For the delta method and variance estimation,
see Lehmann and Casella (1998, ISBN:978-0387985022).
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between algebraic.mle versions 0.9.0 dated 2026-01-09 and 2.0.2 dated 2026-03-19
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