Title: Predict and Map Oyster Growth Suitability from Environmental
Data
Description: Predicts spatial suitability for oyster growth from environmental
survey data using rank-reciprocal weighted scoring.
Users supply sensor data from Acoustic Doppler Current Profilers (ADCP),
Conductivity-Temperature-Depth (CTD) sensors, bathymetric sonar, and
sidescan sonar, specify a target species, and receive per-location
suitability scores, a five-band 'GeoTIFF' heatmap for 'QGIS', contour
lines, and a formatted PDF or HTML report. Supports seventeen species across
global aquaculture regions, including Ostrea edulis, Magallana gigas,
Crassostrea virginica, Crassostrea hongkongensis, and thirteen further
species; see list_species(). Includes ocean acidification scoring via
in-house aragonite saturation state (Omega_arag) calculation using
Lueker et al. (2000) <doi:10.1016/S0304-4203(00)00022-0> and Mucci (1983)
<doi:10.1357/002224083788520153> equilibrium constants (no external
dependencies), variable impact diagnostics (variable_impact()), fine-scale
habitat area analys [...truncated...]
Author: T Tucker [aut, cre]
Maintainer: T Tucker <tristantucker48@gmail.com>
Diff between oystermapR versions 1.5.0 dated 2026-08-31 and 1.6.0 dated 2026-10-13
DESCRIPTION | 20 +- MD5 | 88 ++++++---- NAMESPACE | 20 ++ NEWS.md | 173 +++++++++++++++++++ R/area_summary.R | 31 ++- R/bayesian_update.R | 207 +++++++++++++++-------- R/evidence_weights.R |only R/exclusion_check.R | 43 ++-- R/export_geotiff.R | 107 +++++++++++- R/help.R | 144 +++++++++++++++- R/layer_reproducibility.R |only R/lineage_tolerances.R |only R/oystermapR-package.R | 2 R/predict_oyster.R | 244 +++++++++++++++++++++++++++- R/species_tolerances.R | 2 R/summary_pdf.R | 64 +++++-- R/validate.R | 4 R/variable_importance.R | 2 README.md | 67 +++++++ inst/REFERENCES.md | 4 inst/doc/example-bay-survey.R | 47 +++++ inst/doc/example-bay-survey.Rmd | 172 ++++++++++++++++++- inst/doc/example-bay-survey.html | 170 ++++++++++++++++++- inst/rmd/oystermapR_report.Rmd | 2 man/area_summary.Rd | 15 + man/as_lineage_distances.Rd |only man/confidence_score.Rd |only man/dot-apply_evidence_weighting.Rd |only man/dot-evidence_row_support.Rd |only man/dot-fit_suitability.Rd |only man/dot-params_at.Rd |only man/evidence_coverage.Rd |only man/evidence_suitability.Rd |only man/evidence_weights.Rd |only man/export_contours.Rd | 3 man/export_geotiff.Rd | 19 +- man/export_qml_style.Rd | 10 + man/fit_lineages.Rd |only man/layer_reproducibility.Rd |only man/lineage_fits_as_list.Rd |only man/lineage_occurrence.Rd |only man/lineage_signal.Rd |only man/oystermapR-package.Rd | 2 man/oystermapR_help.Rd | 5 man/predict_oyster.Rd | 88 +++++++++- man/rank_source_populations.Rd |only man/reliability_from_perturbation.Rd |only man/reliability_from_replicates.Rd |only man/update_species_tolerances.Rd | 24 ++ man/validate_against_records.Rd | 2 man/weight_table_md.Rd |only tests/testthat/test-bayesian.R | 84 +++++++++ tests/testthat/test-core.R | 65 +++++++ tests/testthat/test-evidence-weights.R |only tests/testthat/test-layer-reproducibility.R |only tests/testthat/test-lineage-tolerances.R |only vignettes/example-bay-survey.Rmd | 172 ++++++++++++++++++- 57 files changed, 1874 insertions(+), 228 deletions(-)
Title: Fitting the Metastatistical Extreme Value Distribution MEVD
Description: Extreme value analysis with the metastatistical extreme value distribution MEVD (Marani and Ignaccolo, 2015, <doi:10.1016/j.advwatres.2015.03.001>) and some of its variants. In particular, analysis can be performed with the simplified metastatistical extreme value distribution SMEV (Marra et al., 2019, <doi:10.1016/j.advwatres.2019.04.002>) and the temporal metastatistical extreme value distribution TMEV (Falkensteiner et al., 2023, <doi:10.1016/j.wace.2023.100601>). Parameters can be estimated with probability weighted moments, maximum likelihood and least squares. The data can also be left-censored prior to a fit. Density, distribution function, quantile function and random generation for the MEVD, SMEV and TMEV are included. In addition, functions for the calculation of return levels including confidence intervals are provided. For a description of use cases please see the provided references.
Author: Harald Schellander [aut, cre] ,
Alexander Lieb [ctb] ,
Marc-Andre Falkensteiner [ctb]
Maintainer: Harald Schellander <harald.schellander@geosphere.at>
Diff between mevr versions 1.1.1 dated 2024-06-30 and 1.3.3 dated 2026-10-13
DESCRIPTION | 18 MD5 | 64 NAMESPACE | 88 - NEWS | 84 - R/mevr.R | 2651 ++++++++++++++++++++++---------- R/weibull_tail_test.R | 263 +-- README.md | 10 build |only man/censored_weibull_fit.Rd | 15 man/dailyrainfall.Rd | 20 man/dmev.Rd | 22 man/dtmev.Rd | 19 man/event_separation.Rd |only man/fmev.Rd | 170 +- man/fsmev.Rd | 209 +- man/ftmev.Rd | 207 +- man/ordinary_events.Rd |only man/plot.mevr.Rd | 24 man/pp.weibull.Rd | 9 man/predict.mevr.Rd | 40 man/return.levels.mev.Rd | 29 man/weibull_tail_test.Rd | 70 tests/testthat/test-dtmev.R | 44 tests/testthat/test-event_separation.R |only tests/testthat/test-fmev.R | 183 +- tests/testthat/test-fsmev.R | 344 ++-- tests/testthat/test-ftmev.R | 147 + tests/testthat/test-left-censoring.R |only tests/testthat/test-ordinary_events.R |only tests/testthat/test-pp-weibull.R | 12 tests/testthat/test-predict-mevr.R | 85 - tests/testthat/test-print-mevr.R | 150 + tests/testthat/test-qtmev.R | 8 tests/testthat/test-return-levels-mev.R | 173 +- tests/testthat/test-return-levels.R | 222 +- tests/testthat/test-weibull-tail-test.R | 119 - 36 files changed, 3618 insertions(+), 1881 deletions(-)
Title: Chinese Text Segmentation, POS Tagging, and Keyword Extraction
Description: Provides fast Chinese text segmentation, keyword extraction
via 'TF-IDF' and 'TextRank', and part-of-speech tagging, powered by a
'Rust' backend ('jieba-rs'). Supports custom dictionaries, user words,
stop words, IDF files, and HMM models, with parallel batch processing
of multiple strings. Serves as a modern, maintained replacement for
the 'jiebaR' package.
Author: Hao Cheng [aut, cre, cph]
Maintainer: Hao Cheng <Yousa-Mirage@foxmail.com>
Diff between jiebaRS versions 0.3.0 dated 2026-08-26 and 0.3.1 dated 2026-10-13
DESCRIPTION | 6 +- MD5 | 14 ++-- NEWS.md | 5 + README.md | 10 +-- inst/WORDLIST | 2 src/rust/Cargo.lock | 147 +------------------------------------------------ src/rust/Cargo.toml | 2 src/rust/vendor.tar.xz |binary 8 files changed, 25 insertions(+), 161 deletions(-)
Title: Geometric Features and Footprint Comparison for 'sf' Objects
Description: Extracts reproducible geometric and urban-morphology descriptors from
polygon and multipart polygon building footprints stored as 'sf' objects,
including area, perimeter, compactness, shape, topology, convexity, orientation,
and optional building-height and floor-area metrics. Compares polygon footprints
across periods using the intersection-over-union (Jaccard) index (Jaccard,
1912) <doi:10.1111/j.1469-8137.1912.tb05611.x> to identify new constructions,
potential demolitions, and footprint changes. Supports vector file formats
readable by 'sf', including Shapefiles and GeoPackage (GPKG) vector files with
named layers, optional boundary clipping, and reprojection to a common coordinate
reference system. Returned 'sf' objects preserve source attributes and geometry
for spatial analysis and downstream workflows, with optional parallel processing
using 'future' for larger feature-extraction jobs.
Author: Jonathan Cohen [aut, cre]
Maintainer: Jonathan Cohen <cohen.jota@gmail.com>
Diff between geomorphR versions 0.1.0 dated 2026-10-04 and 0.2.0 dated 2026-10-13
DESCRIPTION | 21 ++- MD5 | 27 ++++ NAMESPACE | 1 NEWS.md |only R/compare_footprints.R |only README.md | 130 +++++++++++++++++++++-- inst/examples |only inst/extdata/footprint_comparison |only man/compare_footprints.Rd |only tests/testthat/test_compare_footprints.R |only tests/testthat/test_extract_geometric_features.R | 1 11 files changed, 162 insertions(+), 18 deletions(-)
Title: Genotyping Triploids/Tetraploids (or Diploids) from Luminescence
Data
Description: Genotyping of triploid individuals from luminescence data (marker probeset A and B). Works also for diploids and tetraploids.
Three main functions: Create_Dataset_from_file() to build dataset ; Clustering_parallele_from_dir() that regroups individuals with a same genotype based on proximity and
Genotyping_parallele_from_dir() that assigns a genotype to each cluster. For Shiny interface use: launch_GenoShiny().
Author: Julien Roche [aut, cre],
Florence Phocas [aut],
Mathieu Besson [aut],
Pierre Patrice [aut],
Marc Vandeputte [aut],
Francois Allal [aut],
Pierrick Haffray [aut]
Maintainer: Julien Roche <julien.roche@inrae.fr>
Diff between GenoTriplo versions 2.2.1 dated 2026-07-28 and 2.2.2 dated 2026-10-13
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++--------- R/App_GenoTriploShiny.R | 37 +++++++++++++++++++++-------------- R/function_create_dataset.R | 2 - R/function_run_clustering.R | 8 +++++-- R/function_run_genotyping.R | 4 +-- man/Clustering_from_dir.Rd | 8 +++---- man/Create_Dataset_from_file.Rd | 2 - man/Genotyping_from_file.Rd | 2 - man/Genotyping_parallele_from_dir.Rd | 2 - 10 files changed, 51 insertions(+), 38 deletions(-)
Title: Continuous Epidemiological Week Indexing for Time-Series
Analysis
Description: Provides a simple algorithm to generate a continuous epidemiological week index from date variables in a data frame. Weeks are computed as sequential 7-day intervals aligned to Mondays, starting from the earliest observed date or from a user-supplied start date. They do not reset at calendar year boundaries and are not ISO 8601 nor MMWR calendar weeks. Missing or non-convertible dates are returned as NA instead of stopping the computation. The approach is intended for epidemiological modeling and time-series analysis where temporal continuity is required.
Author: Daniel Degina [aut, cre],
Joel Mbuyi [ctb]
Maintainer: Daniel Degina <deginadan@gmail.com>
Diff between cepiweek versions 0.1.2 dated 2026-02-19 and 0.2.0 dated 2026-10-13
DESCRIPTION | 14 +-- LICENSE | 4 MD5 | 16 +-- NAMESPACE | 6 - R/cepiweek.R | 165 +++++++++++++++++++++++++++-------------- README.md | 124 +++++++++++++++--------------- man/cepiweek.Rd | 141 +++++++++++++++++++---------------- tests/testthat.R | 107 +++++++++++++++++++++++--- tests/testthat/test-cepiweek.R | 118 +++++++++++++++++++++-------- 9 files changed, 456 insertions(+), 239 deletions(-)
Title: Time Series Forecasting Using GRNN
Description: A general regression neural network (GRNN) is a variant of a
Radial Basis Function Network characterized by a fast single-pass learning.
'tsfgrnn' allows you to forecast time series using a GRNN model Francisco
Martinez et al. (2019) <doi:10.1007/978-3-030-20521-8_17> and Francisco
Martinez et al. (2022) <doi:10.1016/j.neucom.2021.12.028>. When the forecasting
horizon is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is autoregressive, that is, it is only based on the
observations of the time series. You can consult and plot how the
prediction was done. It is also possible to assess the forecasting accuracy
of the model using rolling origin evaluation.
Author: Maria Pilar Frias-Bustamante [aut],
Ana Maria Martinez-Rodriguez [aut],
Antonio Conde-Sanchez [aut],
Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfgrnn versions 1.0.5 dated 2024-02-15 and 1.0.6 dated 2026-10-13
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/tsfgrnn.html | 48 +++++++++++++++++++++++++++++------------------- src/code.cpp | 6 +++--- 6 files changed, 46 insertions(+), 32 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 vendored 'SUNDIALS'
'CVODE' sources and headers are released under the BSD-3-Clause license.
The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Aaron Collier [ctb] ,
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Ashley Crawford [ctb] ,
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Brian Ripley [ctb],
Cleve Moler [ctb],
Cody J. Balos [ctb] ,
Dan [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.1.7.1 dated 2026-09-29 and 5.1.8 dated 2026-10-13
rxode2-5.1.7.1/rxode2/src/linCmt.cpp |only rxode2-5.1.7.1/rxode2/src/linCmt.h |only rxode2-5.1.7.1/rxode2/src/linCmtDualN.h |only rxode2-5.1.7.1/rxode2/src/macros2micros.cpp |only rxode2-5.1.7.1/rxode2/src/macros2micros.h |only rxode2-5.1.7.1/rxode2/src/rxDerived.cpp |only rxode2-5.1.7.1/rxode2/src/rxode2_sundials_stan_compat.h |only rxode2-5.1.7.1/rxode2/src/solComp.cpp |only rxode2-5.1.7.1/rxode2/src/solComp.h |only rxode2-5.1.7.1/rxode2/tests/testthat/test-lincmt-modeldouble-senstype.R |only rxode2-5.1.8/rxode2/DESCRIPTION | 38 rxode2-5.1.8/rxode2/MD5 | 1156 rxode2-5.1.8/rxode2/NAMESPACE | 49 rxode2-5.1.8/rxode2/NEWS.md | 729 rxode2-5.1.8/rxode2/R/000.R | 6 rxode2-5.1.8/rxode2/R/CTS.R | 21 rxode2-5.1.8/rxode2/R/RcppExports.R | 89 rxode2-5.1.8/rxode2/R/adjoint.R | 995 rxode2-5.1.8/rxode2/R/adjointDiscrete.R | 536 rxode2-5.1.8/rxode2/R/asFunction.R | 16 rxode2-5.1.8/rxode2/R/asIni.R | 21 rxode2-5.1.8/rxode2/R/asModel.R | 33 rxode2-5.1.8/rxode2/R/asRxui.R | 18 rxode2-5.1.8/rxode2/R/assert.R | 697 rxode2-5.1.8/rxode2/R/build.R | 269 rxode2-5.1.8/rxode2/R/collectWarnings.R | 9 rxode2-5.1.8/rxode2/R/confint.R | 46 rxode2-5.1.8/rxode2/R/confintSummary.R | 89 rxode2-5.1.8/rxode2/R/d.R | 614 rxode2-5.1.8/rxode2/R/dde.R | 1166 rxode2-5.1.8/rxode2/R/dfIni.R | 222 rxode2-5.1.8/rxode2/R/dfWishart.R | 42 rxode2-5.1.8/rxode2/R/dsl.R | 317 rxode2-5.1.8/rxode2/R/elu.R | 48 rxode2-5.1.8/rxode2/R/err-foceiBase.R | 405 rxode2-5.1.8/rxode2/R/err-sim.R | 486 rxode2-5.1.8/rxode2/R/err.R | 1506 rxode2-5.1.8/rxode2/R/et-helpers.R | 475 rxode2-5.1.8/rxode2/R/et-methods.R | 263 rxode2-5.1.8/rxode2/R/et.R | 972 rxode2-5.1.8/rxode2/R/etNew.R | 499 rxode2-5.1.8/rxode2/R/etTran.R | 164 rxode2-5.1.8/rxode2/R/etVctrs.R | 37 rxode2-5.1.8/rxode2/R/etaDist.R |only rxode2-5.1.8/rxode2/R/eventSens.R | 633 rxode2-5.1.8/rxode2/R/evidPush.R | 89 rxode2-5.1.8/rxode2/R/fixef.R | 8 rxode2-5.1.8/rxode2/R/forder.R | 40 rxode2-5.1.8/rxode2/R/format.R | 18 rxode2-5.1.8/rxode2/R/gelu.R | 11 rxode2-5.1.8/rxode2/R/genShinyApp.template.R | 61 rxode2-5.1.8/rxode2/R/geom-amt.R | 17 rxode2-5.1.8/rxode2/R/geom-cens.R | 49 rxode2-5.1.8/rxode2/R/getBaseSim.R | 45 rxode2-5.1.8/rxode2/R/indLin.R | 146 rxode2-5.1.8/rxode2/R/intern.R | 47 rxode2-5.1.8/rxode2/R/linCmt.R | 160 rxode2-5.1.8/rxode2/R/linMod.R | 215 rxode2-5.1.8/rxode2/R/llik.R | 222 rxode2-5.1.8/rxode2/R/lotriCompat.R | 22 rxode2-5.1.8/rxode2/R/lrelu.R | 4 rxode2-5.1.8/rxode2/R/mix.R | 136 rxode2-5.1.8/rxode2/R/mlogit.R | 82 rxode2-5.1.8/rxode2/R/modelExtract.R | 198 rxode2-5.1.8/rxode2/R/modlib.R | 147 rxode2-5.1.8/rxode2/R/mu-cov-downgrade.R | 97 rxode2-5.1.8/rxode2/R/mu.R | 1011 rxode2-5.1.8/rxode2/R/normui.R |only rxode2-5.1.8/rxode2/R/odeToLin.R | 546 rxode2-5.1.8/rxode2/R/parseFuns.R | 64 rxode2-5.1.8/rxode2/R/piping-ini.R | 687 rxode2-5.1.8/rxode2/R/piping-model.R | 600 rxode2-5.1.8/rxode2/R/piping-update.R | 12 rxode2-5.1.8/rxode2/R/piping.R | 327 rxode2-5.1.8/rxode2/R/plogis.R | 12 rxode2-5.1.8/rxode2/R/plot.R | 201 rxode2-5.1.8/rxode2/R/prelu.R | 32 rxode2-5.1.8/rxode2/R/print.R | 234 rxode2-5.1.8/rxode2/R/prior-density-families.R |only rxode2-5.1.8/rxode2/R/prior-density-kernels-cdf.R |only rxode2-5.1.8/rxode2/R/prior-density-kernels.R |only rxode2-5.1.8/rxode2/R/prior-sim.R | 509 rxode2-5.1.8/rxode2/R/priorDensity.R | 447 rxode2-5.1.8/rxode2/R/progress.R | 2 rxode2-5.1.8/rxode2/R/rbind.R | 46 rxode2-5.1.8/rxode2/R/reexport.R | 1 rxode2-5.1.8/rxode2/R/relu.R | 4 rxode2-5.1.8/rxode2/R/rstudio.R | 12 rxode2-5.1.8/rxode2/R/rudf.R | 557 rxode2-5.1.8/rxode2/R/rudfModelC.R |only rxode2-5.1.8/rxode2/R/rudfModelFind.R |only rxode2-5.1.8/rxode2/R/rudfModelLookup.R |only rxode2-5.1.8/rxode2/R/rudfModelReg.R |only rxode2-5.1.8/rxode2/R/rudfModelScope.R |only rxode2-5.1.8/rxode2/R/rudfui.R | 455 rxode2-5.1.8/rxode2/R/rxEvent.R |only rxode2-5.1.8/rxode2/R/rxEventEmit.R |only rxode2-5.1.8/rxode2/R/rxFormat.R | 22 rxode2-5.1.8/rxode2/R/rxIndLin.R | 21 rxode2-5.1.8/rxode2/R/rxJacobian.R | 164 rxode2-5.1.8/rxode2/R/rxLinCmt.R | 407 rxode2-5.1.8/rxode2/R/rxMemoryEstimate.R | 450 rxode2-5.1.8/rxode2/R/rxOom.R | 627 rxode2-5.1.8/rxode2/R/rxOptExpr.R | 428 rxode2-5.1.8/rxode2/R/rxParams.R | 166 rxode2-5.1.8/rxode2/R/rxPrune.R | 175 rxode2-5.1.8/rxode2/R/rxRaw.R | 102 rxode2-5.1.8/rxode2/R/rxReq.R | 5 rxode2-5.1.8/rxode2/R/rxResidualError.R | 3 rxode2-5.1.8/rxode2/R/rxSerialize.R | 20 rxode2-5.1.8/rxode2/R/rxShiny.R | 57 rxode2-5.1.8/rxode2/R/rxStack.R | 113 rxode2-5.1.8/rxode2/R/rxSymInv.R | 250 rxode2-5.1.8/rxode2/R/rxSyntaxFunctions.R | 2 rxode2-5.1.8/rxode2/R/rxUiGet.R | 443 rxode2-5.1.8/rxode2/R/rxValidate.R | 19 rxode2-5.1.8/rxode2/R/rxode-options.R | 89 rxode2-5.1.8/rxode2/R/rxode2.R | 1001 rxode2-5.1.8/rxode2/R/rxode2_md5.R | 3 rxode2-5.1.8/rxode2/R/rxrandom.R | 148 rxode2-5.1.8/rxode2/R/rxsolve.R | 4008 +- rxode2-5.1.8/rxode2/R/selu.R | 4 rxode2-5.1.8/rxode2/R/softplus.R | 10 rxode2-5.1.8/rxode2/R/splitBolus.R | 143 rxode2-5.1.8/rxode2/R/str.R | 49 rxode2-5.1.8/rxode2/R/summary.R | 22 rxode2-5.1.8/rxode2/R/swish.R | 4 rxode2-5.1.8/rxode2/R/symengine.R | 2738 - rxode2-5.1.8/rxode2/R/tran.R | 214 rxode2-5.1.8/rxode2/R/tranTranslation.R |only rxode2-5.1.8/rxode2/R/ui-assign-parts.R | 85 rxode2-5.1.8/rxode2/R/ui-bind.R | 79 rxode2-5.1.8/rxode2/R/ui-fix.R | 152 rxode2-5.1.8/rxode2/R/ui-getControl.R | 30 rxode2-5.1.8/rxode2/R/ui-modelName.R | 113 rxode2-5.1.8/rxode2/R/ui-rename.R | 276 rxode2-5.1.8/rxode2/R/ui.R | 386 rxode2-5.1.8/rxode2/R/utils.R | 498 rxode2-5.1.8/rxode2/README.md | 16 rxode2-5.1.8/rxode2/build/buildLinCmt.R | 18 rxode2-5.1.8/rxode2/build/linCmtTest.R | 16 rxode2-5.1.8/rxode2/build/partial.rdb |binary rxode2-5.1.8/rxode2/build/test.R | 59 rxode2-5.1.8/rxode2/build/vendor-sundials.R | 245 rxode2-5.1.8/rxode2/data/rxSyntaxFunctions.rda |binary rxode2-5.1.8/rxode2/demo/demo1.R | 27 rxode2-5.1.8/rxode2/inst/doc/rxode2-syntax.html | 364 rxode2-5.1.8/rxode2/inst/include/rxode2.h | 2 rxode2-5.1.8/rxode2/inst/include/rxode2EventTranslate.h | 27 rxode2-5.1.8/rxode2/inst/include/rxode2_control.h | 1 rxode2-5.1.8/rxode2/inst/include/rxode2_model_shared.c | 64 rxode2-5.1.8/rxode2/inst/include/rxode2_model_shared.h | 18 rxode2-5.1.8/rxode2/inst/include/rxode2parseGetTime.h | 5 rxode2-5.1.8/rxode2/inst/include/rxode2parseHandleEvid.h | 775 rxode2-5.1.8/rxode2/inst/include/rxode2parseStruct.h | 39 rxode2-5.1.8/rxode2/inst/include/rxode2parseVer.h | 4 rxode2-5.1.8/rxode2/inst/include/rxode2parse_control.h | 5 rxode2-5.1.8/rxode2/inst/include/rxode2prior.h | 30 rxode2-5.1.8/rxode2/inst/tools/fflags.R | 84 rxode2-5.1.8/rxode2/inst/tools/genOptExprFixture.R | 38 rxode2-5.1.8/rxode2/inst/tools/genSymengineFixture.R | 130 rxode2-5.1.8/rxode2/inst/tools/optExprFixtureCorpus.R | 145 rxode2-5.1.8/rxode2/inst/tools/symengineFixtureCapture.R | 13 rxode2-5.1.8/rxode2/inst/tools/symengineFixtureCorpus.R | 309 rxode2-5.1.8/rxode2/inst/tools/workaround.R | 513 rxode2-5.1.8/rxode2/inst/tran.g | 53 rxode2-5.1.8/rxode2/man/as.rxUi.Rd | 4 rxode2-5.1.8/rxode2/man/assertRxUi.Rd | 65 rxode2-5.1.8/rxode2/man/dot-extraC.Rd | 5 rxode2-5.1.8/rxode2/man/dot-rxEtaDistAnchors.Rd |only rxode2-5.1.8/rxode2/man/dot-rxEtaDistDerivLines.Rd |only rxode2-5.1.8/rxode2/man/dot-rxSymInvBlockZeroFreeCallback.Rd |only rxode2-5.1.8/rxode2/man/dot-udfEnvSet.Rd | 4 rxode2-5.1.8/rxode2/man/genShinyApp.template.Rd | 3 rxode2-5.1.8/rxode2/man/linCmtCarryFastStats.Rd | 2 rxode2-5.1.8/rxode2/man/linCmtCarrySentinelMax.Rd | 2 rxode2-5.1.8/rxode2/man/linCmtCarrySetFast.Rd | 2 rxode2-5.1.8/rxode2/man/linCmtDeltaMemo.Rd | 2 rxode2-5.1.8/rxode2/man/linCmtMicro.Rd |only rxode2-5.1.8/rxode2/man/linCmtSeqStats.Rd | 2 rxode2-5.1.8/rxode2/man/llikGamma.Rd | 2 rxode2-5.1.8/rxode2/man/llikGeom.Rd | 2 rxode2-5.1.8/rxode2/man/llikNorm.Rd | 2 rxode2-5.1.8/rxode2/man/llikUnif.Rd | 2 rxode2-5.1.8/rxode2/man/llikWeibull.Rd | 2 rxode2-5.1.8/rxode2/man/mexpit.Rd | 3 rxode2-5.1.8/rxode2/man/phiU.Rd |only rxode2-5.1.8/rxode2/man/rmdhunks/rxode2-syntax-hunk.Rmd | 106 rxode2-5.1.8/rxode2/man/rxCombineErrorLines.Rd | 4 rxode2-5.1.8/rxode2/man/rxDerived.Rd | 3 rxode2-5.1.8/rxode2/man/rxEtaDistExpand.Rd |only rxode2-5.1.8/rxode2/man/rxEtaDistMuRef.Rd |only rxode2-5.1.8/rxode2/man/rxEventListen.Rd |only rxode2-5.1.8/rxode2/man/rxModels_.Rd | 3 rxode2-5.1.8/rxode2/man/rxPriorBuildSpec.Rd | 6 rxode2-5.1.8/rxode2/man/rxPriorLogDensity.Rd | 6 rxode2-5.1.8/rxode2/man/rxResidualError.Rd | 3 rxode2-5.1.8/rxode2/man/rxRmvn.Rd | 3 rxode2-5.1.8/rxode2/man/rxS.Rd | 14 rxode2-5.1.8/rxode2/man/rxSimThetaOmega.Rd | 6 rxode2-5.1.8/rxode2/man/rxSolve.Rd | 36 rxode2-5.1.8/rxode2/man/rxSyntaxFunctions.Rd | 2 rxode2-5.1.8/rxode2/man/rxTrans.Rd | 4 rxode2-5.1.8/rxode2/man/rxUdfUiLhs.Rd |only rxode2-5.1.8/rxode2/man/rxUdfUiLhs.dist.Rd |only rxode2-5.1.8/rxode2/man/rxUiEtaDistAnchors.Rd |only rxode2-5.1.8/rxode2/man/rxUiEtaDists.Rd |only rxode2-5.1.8/rxode2/man/rxUiGet.Rd | 18 rxode2-5.1.8/rxode2/man/rxode2.Rd | 126 rxode2-5.1.8/rxode2/man/rxode2parseAssignPackagesToLoad.Rd | 2 rxode2-5.1.8/rxode2/man/rxode2parseAssignPointerTranslation.Rd | 2 rxode2-5.1.8/rxode2/man/rxode2parseAssignTranslation.Rd | 2 rxode2-5.1.8/rxode2/man/rxode2parseGetPointerAssignment.Rd | 2 rxode2-5.1.8/rxode2/man/rxode2parseGetTranslation.Rd | 2 rxode2-5.1.8/rxode2/man/splitBolusInfusion-directive.Rd |only rxode2-5.1.8/rxode2/man/splitInfusion.Rd |only rxode2-5.1.8/rxode2/man/splitInfusionBolus-directive.Rd |only rxode2-5.1.8/rxode2/src/Makevars.in | 36 rxode2-5.1.8/rxode2/src/RcppExports.cpp | 143 rxode2-5.1.8/rxode2/src/approx.cpp | 205 rxode2-5.1.8/rxode2/src/boost.cpp | 345 rxode2-5.1.8/rxode2/src/codegen.c | 74 rxode2-5.1.8/rxode2/src/codegen.h | 51 rxode2-5.1.8/rxode2/src/codegen2.h | 55 rxode2-5.1.8/rxode2/src/etTran.cpp | 500 rxode2-5.1.8/rxode2/src/genModelVars.c | 53 rxode2-5.1.8/rxode2/src/genModelVars.h | 11 rxode2-5.1.8/rxode2/src/handle_evid.cpp | 18 rxode2-5.1.8/rxode2/src/init.c | 125 rxode2-5.1.8/rxode2/src/install.libs.R | 8 rxode2-5.1.8/rxode2/src/invCdfMemo.h |only rxode2-5.1.8/rxode2/src/linCmtSensType.h | 2 rxode2-5.1.8/rxode2/src/par_solve.cpp | 496 rxode2-5.1.8/rxode2/src/par_solve.h | 19 rxode2-5.1.8/rxode2/src/parseAssignStr.h | 5 rxode2-5.1.8/rxode2/src/parseDdt.h | 8 rxode2-5.1.8/rxode2/src/parseDfdy.h | 11 rxode2-5.1.8/rxode2/src/parseFuns.h | 216 rxode2-5.1.8/rxode2/src/parseFunsDiff.h | 39 rxode2-5.1.8/rxode2/src/parseFunsRandom.h | 57 rxode2-5.1.8/rxode2/src/parseLogical.h | 36 rxode2-5.1.8/rxode2/src/parseSyntaxErrors.h | 1 rxode2-5.1.8/rxode2/src/parseVars.h | 43 rxode2-5.1.8/rxode2/src/pkTime.h |only rxode2-5.1.8/rxode2/src/print_node.c | 90 rxode2-5.1.8/rxode2/src/print_node.h | 18 rxode2-5.1.8/rxode2/src/priorDensity.cpp | 276 rxode2-5.1.8/rxode2/src/rk4s.cpp | 5 rxode2-5.1.8/rxode2/src/ros4.cpp | 7 rxode2-5.1.8/rxode2/src/rxCse.cpp | 5 rxode2-5.1.8/rxode2/src/rxCseRun.h | 10 rxode2-5.1.8/rxode2/src/rxCseSel.h | 22 rxode2-5.1.8/rxode2/src/rxData.cpp | 122 rxode2-5.1.8/rxode2/src/rxGlobals.h | 2 rxode2-5.1.8/rxode2/src/rxMemoryComponents.cpp | 8 rxode2-5.1.8/rxode2/src/rxSerialize.cpp | 73 rxode2-5.1.8/rxode2/src/rxode2_df.cpp | 77 rxode2-5.1.8/rxode2/src/rxode2lincmtLink.cpp |only rxode2-5.1.8/rxode2/src/rxode2lincmtLink.h |only rxode2-5.1.8/rxode2/src/rxomp.h | 14 rxode2-5.1.8/rxode2/src/rxthreefry.cpp | 201 rxode2-5.1.8/rxode2/src/rxthreefry.h | 1 rxode2-5.1.8/rxode2/src/seBatch.h | 11 rxode2-5.1.8/rxode2/src/seed.cpp | 8 rxode2-5.1.8/rxode2/src/tran.c | 62 rxode2-5.1.8/rxode2/src/tran.g.d_parser.h |19138 ++++++---- rxode2-5.1.8/rxode2/src/tran.h | 16 rxode2-5.1.8/rxode2/src/utilc.cpp | 111 rxode2-5.1.8/rxode2/tests/testthat.R | 4 rxode2-5.1.8/rxode2/tests/testthat/helper-etTrans-golden-corpus.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-etTrans-golden-grid.R |only rxode2-5.1.8/rxode2/tests/testthat/helper-etTrans-golden.R | 335 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rxode2-5.1.8/rxode2/tests/testthat/test-capture-adaptive-dosing.R | 34 rxode2-5.1.8/rxode2/tests/testthat/test-cbind-study-individual.R | 32 rxode2-5.1.8/rxode2/tests/testthat/test-ceiling.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-cholperm.R | 16 rxode2-5.1.8/rxode2/tests/testthat/test-cmt-directive-order.R |only rxode2-5.1.8/rxode2/tests/testthat/test-cmt-order.R | 325 rxode2-5.1.8/rxode2/tests/testthat/test-codegen-md5.R |only rxode2-5.1.8/rxode2/tests/testthat/test-compile-env.R | 29 rxode2-5.1.8/rxode2/tests/testthat/test-compile-error.R | 73 rxode2-5.1.8/rxode2/tests/testthat/test-compile-olevel.R | 23 rxode2-5.1.8/rxode2/tests/testthat/test-confint.R | 96 rxode2-5.1.8/rxode2/tests/testthat/test-convertId.R | 44 rxode2-5.1.8/rxode2/tests/testthat/test-cov.R | 483 rxode2-5.1.8/rxode2/tests/testthat/test-cvode.R | 23 rxode2-5.1.8/rxode2/tests/testthat/test-cvpost-separation-bound.R | 40 rxode2-5.1.8/rxode2/tests/testthat/test-cvpost.R | 24 rxode2-5.1.8/rxode2/tests/testthat/test-data-frame.R | 18 rxode2-5.1.8/rxode2/tests/testthat/test-data-table.R | 79 rxode2-5.1.8/rxode2/tests/testthat/test-dde-ini.R |only rxode2-5.1.8/rxode2/tests/testthat/test-dde-past.R | 183 rxode2-5.1.8/rxode2/tests/testthat/test-dde-sens.R | 81 rxode2-5.1.8/rxode2/tests/testthat/test-dde-ss.R |only rxode2-5.1.8/rxode2/tests/testthat/test-dde.R | 98 rxode2-5.1.8/rxode2/tests/testthat/test-demo.R | 9 rxode2-5.1.8/rxode2/tests/testthat/test-derived.R | 205 rxode2-5.1.8/rxode2/tests/testthat/test-dfRep.R | 18 rxode2-5.1.8/rxode2/tests/testthat/test-dfdy.R | 60 rxode2-5.1.8/rxode2/tests/testthat/test-dnorm.R |only rxode2-5.1.8/rxode2/tests/testthat/test-dollar-names.R | 366 rxode2-5.1.8/rxode2/tests/testthat/test-dplyr.R | 46 rxode2-5.1.8/rxode2/tests/testthat/test-drop.R | 77 rxode2-5.1.8/rxode2/tests/testthat/test-dsl.R | 991 rxode2-5.1.8/rxode2/tests/testthat/test-dur-0.R | 100 rxode2-5.1.8/rxode2/tests/testthat/test-et-r.R | 136 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rxode2-5.1.8/rxode2/tests/testthat/test-expand-grid.R | 22 rxode2-5.1.8/rxode2/tests/testthat/test-fixef.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-focei-variances.R | 1 rxode2-5.1.8/rxode2/tests/testthat/test-forced-pars.R | 230 rxode2-5.1.8/rxode2/tests/testthat/test-fun.R | 53 rxode2-5.1.8/rxode2/tests/testthat/test-gammap.R | 4 rxode2-5.1.8/rxode2/tests/testthat/test-geom-cens.R | 6 rxode2-5.1.8/rxode2/tests/testthat/test-getdur-1322-forward.R |only rxode2-5.1.8/rxode2/tests/testthat/test-getdur-1322.R | 183 rxode2-5.1.8/rxode2/tests/testthat/test-hmax.R | 12 rxode2-5.1.8/rxode2/tests/testthat/test-iCov.R | 134 rxode2-5.1.8/rxode2/tests/testthat/test-ifelse.R | 78 rxode2-5.1.8/rxode2/tests/testthat/test-ignore-state.R | 5 rxode2-5.1.8/rxode2/tests/testthat/test-implicit-time.R | 17 rxode2-5.1.8/rxode2/tests/testthat/test-ind-alloc.R | 4 rxode2-5.1.8/rxode2/tests/testthat/test-ind-lin-1298-expand.R | 50 rxode2-5.1.8/rxode2/tests/testthat/test-ind-lin-1298.R | 94 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Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level". Messages are signalled as classed R conditions, so that calling code can decide how serious a situation is, rather than the function which detects it having to be told in advance.
Author: Jon Clayden [aut, cre]
Maintainer: Jon Clayden <code@clayden.org>
Diff between reportr versions 1.3.1 dated 2025-03-29 and 2.0.0 dated 2026-10-13
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Title: Data Envelopment Analysis for Pollution-Generating Technologies
Description: Nonparametric efficiency analysis for pollution-generating
technologies under the materials-balance principle. Implements the
weak-G-disposability technology of Hampf and Rodseth (2015)
<doi:10.1016/j.eneco.2015.04.001>, scored by the minimal-emission
programme of Rodseth (2025) <doi:10.1007/s11123-025-00768-0> with
its directional representation and five-component decomposition,
the by-production intersection
technology of Murty, Russell and Levkoff (2012)
<doi:10.1016/j.jeem.2012.02.005>, the materials-balance cost model of
Coelli, Lauwers and Van Huylenbroeck (2007)
<doi:10.1007/s11123-007-0052-8> and a weak-disposability reference
model, with a pre-estimation audit of every materials-balance
account, metafrontier decompositions, bad-output shadow prices,
marginal abatement cost curves, a cross-axiom comparison harness, a
global Malmquist-Luenberger productivity index and subsampling
sensitivity intervals. Estimators are solved with 'lpSolveAPI'.
Author: Erik Enstad [aut, cre]
Maintainer: Erik Enstad <erik.enstad@nhh.no>
Diff between pgt versions 0.7.0 dated 2026-09-22 and 0.7.1 dated 2026-10-13
DESCRIPTION | 16 +- MD5 | 84 +++++----- NEWS.md | 155 +++++++++++++++++++ R/boot.R | 29 ++- R/compare_models.R | 31 +++ R/data.R | 17 +- R/decompose.R | 24 ++- R/lp_solvers.R | 251 +++++++++++++++++++++++++------ R/ml_index.R | 52 ++++-- R/pgt.R | 121 ++++++++++----- README.md | 14 + inst/doc/comparing-axioms.Rmd | 16 +- inst/doc/comparing-axioms.html | 26 +-- inst/doc/introduction.Rmd | 19 +- inst/doc/introduction.html | 63 ++++--- inst/doc/models.Rmd | 83 +++++++--- inst/doc/models.html | 100 +++++++++--- inst/doc/productivity.R | 13 + inst/doc/productivity.Rmd | 87 +++++++---- inst/doc/productivity.html | 142 ++++++++++++------ inst/doc/replication.R | 35 ++-- inst/doc/replication.Rmd | 108 +++++++------ inst/doc/replication.html | 268 ++++++++++++++++++---------------- inst/simulations/coverage-reps.csv |only inst/simulations/coverage-results.csv | 16 +- inst/simulations/coverage.R | 156 ++++++++++++++----- man/boot_pgt.Rd | 29 ++- man/compare_models.Rd | 9 + man/pgt.Rd | 112 +++++++++----- man/pgt_decompose.Rd | 24 ++- man/pgt_ml.Rd | 45 +++-- man/pigfarms.Rd | 13 + man/uscoal.Rd | 4 tests/testthat/test-byprod.R | 6 tests/testthat/test-compare.R | 17 ++ tests/testthat/test-fdmo.R | 46 +++++ tests/testthat/test-pigfarms.R | 59 +++++-- tests/testthat/test-scaling.R |only tests/testthat/test-wgd.R | 15 + vignettes/comparing-axioms.Rmd | 16 +- vignettes/introduction.Rmd | 19 +- vignettes/models.Rmd | 83 +++++++--- vignettes/productivity.Rmd | 87 +++++++---- vignettes/replication.Rmd | 108 +++++++------ 44 files changed, 1823 insertions(+), 795 deletions(-)
Title: Identifies Parameters in a Tree-Shaped SCM
Description: Implements the algorithm by Briefs and Bläser (2025) <https://openreview.net/forum?id=8PHOPPH35D>, based on the approach of Gupta and Bläser (2024) <doi:10.1609/aaai.v38i18.30023>. It determines, for a structural causal model (SCM) whose directed edges form a tree, whether each parameter is unidentifiable, 1-identifiable or 2-identifiable (other cases cannot occur), using a randomized algorithm with provable running time O(n^3 log^2 n).
Author: Yasmine Briefs [aut, cre],
Markus Blaeser [aut]
Maintainer: Yasmine Briefs <ybriefs@mpi-inf.mpg.de>
Diff between fasttreeid versions 1.0.2 dated 2026-08-31 and 1.1.0 dated 2026-10-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- src/algebra.cpp | 3 +++ src/identification.cpp | 16 ++++++++++++---- src/identification.h | 2 ++ src/random.cpp | 16 +++++++++++++--- src/random.h | 1 + tests/testthat/test-one-option.R | 2 +- 8 files changed, 42 insertions(+), 18 deletions(-)
Title: Inequality Measures for Weighted Data
Description: Computes inequality measures of a given variable taking into account weights. Suitable for ratio, interval and ordered scale. Includes measures developed by Gini, Theil, Leti, Palma ratio, 20:20 ratio, Allison and Foster, Jenkins, Cowell and Flechaire, Abul Naga and Yalcin, Apouey, Blair and Lacy. Bootstrap provides distribution of inequality measures enabling significance tests.
Author: Sebastian Wojcik [aut, cre] ,
Agnieszka Giemza [aut],
Jaroslaw Napora [aut]
Maintainer: Sebastian Wojcik <S.Wojcik@stat.gov.pl>
Diff between wINEQ versions 1.2.2 dated 2026-04-23 and 1.2.3 dated 2026-10-13
DESCRIPTION | 10 MD5 | 47 +-- NAMESPACE | 7 NEWS.md | 237 ++++++++------- R/inequalityMeasure.R | 660 ++++++++++++++++++++++++++++++++++---------- R/inequalityMeasureBoot.R | 574 ++++++++++++++++++++------------------ data/Tourism.rda |binary man/Abul_Naga_and_Yalcin.Rd | 17 - man/Allison_and_Foster.Rd | 21 - man/Apouey.Rd | 13 man/Atkinson.Rd | 8 man/Blair_Lacy.Rd | 17 - man/Bonferroni.Rd |only man/Gini.Rd | 6 man/Hoover.Rd | 1 man/Jenkins.Rd | 1 man/Kakwani.Rd |only man/Leti.Rd | 14 man/LowerSum.Rd | 1 man/Rosenbluth.Rd |only man/SST.Rd |only man/Theil_T.Rd | 2 man/Wolfson.Rd |only man/Zenga.Rd |only man/figures |only man/ineq_weighted.Rd | 20 + man/ineq_weighted_boot.Rd | 18 + man/medianf.Rd | 2 28 files changed, 1067 insertions(+), 609 deletions(-)
Title: Time Series Forecasting Using Nearest Neighbors
Description: Allows forecasting time series using nearest neighbors regression
Francisco Martinez, Maria P. Frias, Maria D. Perez-Godoy and Antonio J.
Rivera (2019) <doi:10.1007/s10462-017-9593-z>. When the forecasting horizon
is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is univariate and autoregressive, that is, it is only based
on the observations of the time series. The nearest neighbors used in a
prediction can be consulted and plotted.
Author: Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfknn versions 0.6.0 dated 2023-12-20 and 0.7.1 dated 2026-10-13
DESCRIPTION | 14 ++++++------ MD5 | 28 ++++++++++++------------- NEWS.md | 5 +++- R/forecasting.R | 37 +++++++++++++++++----------------- R/knn.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tsfknn.html | 26 +++++++++++------------ man/knn_examples.Rd | 17 +++++++-------- man/knn_forecasting.Rd | 2 - man/n_training_examples.Rd | 4 +-- man/nearest_neighbors.Rd | 4 +-- man/tsfknn-package.Rd | 7 +++++- src/code.cpp | 6 ++--- tests/testthat/test_knn_forecasting.R | 14 ++++++++++++ 15 files changed, 93 insertions(+), 72 deletions(-)
Title: Estimating Trend, Velocity, and Acceleration from Sea Level
Records
Description: Provides tools for analysing annual average ocean water level time series,
estimating mean sea level trends, velocities, and accelerations using Singular
Spectrum Analysis (SSA). The detailed methodology for resolving mean sea level
with improved temporal resolution follows Watson (2018)
"Improved Techniques to Estimate Mean Sea Level, Velocity and Acceleration from
Long Ocean Water Level Time Series to Augment Sea Level (and Climate Change)
Research" <https://unsworks.unsw.edu.au/entities/publication/5e835c87-aa0a-4457-807e-29d354e91d45>.
Additional methodological developments and applications are described in Watson (2020)
"Status of Mean Sea Level Rise around the USA" <doi:10.3390/geohazards2020005>
and Watson and Lim (2020) "An Update on the Status of Mean Sea Level Rise around
the Korean Peninsula" <doi:10.3390/atmos11111153>. Includes multiple gap-filling
methods for incomplete records, diagnostic tools for inspecting SSA components,
and plotting functions for g [...truncated...]
Author: Phil Watson [aut, cre]
Maintainer: Phil Watson <philwatson.slr@gmail.com>
This is a re-admission after prior archival of version 1.0 dated 2019-08-07
Diff between TrendSLR versions 1.0 dated 2019-08-07 and 2.0.0 dated 2026-10-13
DESCRIPTION | 55 +++++++++++++---------- MD5 | 40 ++++++++--------- NAMESPACE | 1 R/balt-data.R | 4 - R/check.decomp.R | 42 +++++++++-------- R/custom.trend.R | 34 ++++++-------- R/msl-name.R | 4 + R/msl.fileplot.R | 29 ++++++------ R/msl.screenplot.R | 16 ++++-- R/msltrend.R | 40 ++++++++--------- man/Balt.Rd | 10 ++-- man/TrendSLR.Rd | 104 +++++++++++++++++++++++--------------------- man/check.decomp.Rd | 93 ++++++++++++++++++++++----------------- man/custom.trend.Rd | 115 ++++++++++++++++++++++++++----------------------- man/gap.fillview.Rd | 37 +++++++-------- man/msl.fileplot.Rd | 35 +++++++++----- man/msl.screenplot.Rd | 23 +++++---- man/msl.trend.Rd | 117 ++++++++++++++++++++++++++------------------------ man/s.Rd | 4 + man/summary.Rd | 5 ++ man/t.Rd | 4 + 21 files changed, 445 insertions(+), 367 deletions(-)
Title: ROC-Based Methods for Comparing Survival Distributions with
Right, Left, and Doubly Censored Data
Description: Implements nonparametric and semiparametric methods for comparing two survival distributions under non-proportional hazards (non-PH) with right, left, or doubly censored data. The methods are based on the Receiver Operating Characteristic (ROC) curve length and its kernel-based estimate (Bantis et al. (2021) <doi:10.1002/sim.8869>) and the overlap coefficient (OVL) and its kernel-based estimate (Schmid and Schmidt (2006) <doi:10.1016/j.csda.2005.01.014>), as well as a new joint inference approach involving both the kernel-based ROC length and the kernel-based OVL. These methods do not require prior knowledge of the underlying non-PH pattern. The methods also accommodate the "last is censored" phenomenon for right-censored data by using flexible parametric approaches only for the portion of the tail of the distribution that corresponds to time values beyond the last observed event (see also Bantis et al. (2017) <doi:10.1002/sim.7394>). The analogous "first is censored" [...truncated...]
Author: Mohammod Mahmudur Rahman [aut, cre],
Leonidas Bantis [aut]
Maintainer: Mohammod Mahmudur Rahman <mahmudur.asif13@gmail.com>
Diff between ROCsurvcomp versions 0.1.2 dated 2026-05-11 and 0.1.3 dated 2026-10-13
DESCRIPTION | 12 ++--- MD5 | 12 ++--- NAMESPACE | 50 ++++++++++++---------- NEWS.md | 6 ++ inst/doc/ROCsurvcomp.Rmd | 2 inst/doc/ROCsurvcomp.html | 101 ++++++++++++++++++++++------------------------ vignettes/ROCsurvcomp.Rmd | 2 7 files changed, 97 insertions(+), 88 deletions(-)
Title: Interface to the ITALIC Database of Lichen Biodiversity
Description: A programmatic interface to the Web Service methods provided by ITALIC (<https://italic.units.it>).
ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information
about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys.
More information about the data is available at <https://italic.units.it/?procedure=base&t=59&c=60>.
The API documentation is available at <https://italic.units.it/?procedure=api>.
Author: Matteo Conti [aut, cre] ,
Luana Francesconi [aut],
Alice Musina [aut],
Luca Di Nuzzo [aut],
Gabriele Gheza [aut],
Chiara Pistocchi [aut],
Juri Nascimbene [aut],
Pier Luigi Nimis [aut],
Stefano Martellos [aut]
Maintainer: Matteo Conti <matt.ciao@gmail.com>
Diff between ritalic versions 0.13.0 dated 2026-10-12 and 0.13.1 dated 2026-10-13
DESCRIPTION | 6 +-- MD5 | 4 +- tests/testthat/test_api_utils.R | 66 ++++++++++++++++++++++++---------------- 3 files changed, 45 insertions(+), 31 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently. Polynomial mean coefficients are handled conditionally within the Kalman recursion, reducing the dimension of numerical maximum likelihood optimization and permitting exact Gaussian conditional updates during Bayesian posterior sampling. Maximum likelihood estimation is computationally efficient and suitable for large-scale data analysis, while Bayesian posterior sampling is better suited to small-scale analyses requiring more careful uncertainty qua [...truncated...]
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.5 dated 2026-10-13 and 1.0.6 dated 2026-10-13
DESCRIPTION | 6 ++-- MD5 | 6 ++-- R/drw.R | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++++------- man/drw.Rd | 61 +++++++++++++++++++++++++++++++++++++++++++----- 4 files changed, 127 insertions(+), 21 deletions(-)
Title: Restricted Bridge Estimation
Description: Implements bridge regression with linear coefficient restrictions
using the local quadratic approximation described by Yuzbasi, Arashi and
Akdeniz (2021) <doi:10.1007/s00500-021-05763-9>. Provides coefficient paths,
cross-validation, prediction and coefficient extraction for restricted and
unrestricted linear models.
Author: Bahadir Yuzbasi [aut, cre],
Mohammad Arashi [aut],
Fikri Akdeniz [aut],
Jerome Friedman [ctb] ,
Trevor Hastie [ctb] ,
Robert Tibshirani [ctb]
Maintainer: Bahadir Yuzbasi <b.yzb@hotmail.com>
Diff between rbridge versions 1.0.3 dated 2026-10-11 and 1.0.4 dated 2026-10-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 11 ++++++++++- README.md | 18 ++++++++++++------ inst/doc/getting-started.html | 2 +- src/Main_functions.cpp | 1 - src/Makevars | 2 ++ src/Makevars.win | 2 ++ 8 files changed, 38 insertions(+), 20 deletions(-)
Title: Multilevel Unanchored Meta-Regression for Indirect Treatment
Comparisons
Description: Bayesian multilevel unanchored meta-regression (ML-UMR) for
indirect treatment comparisons using individual patient data (IPD) and
aggregate data (AgD). Implements shared prognostic factor assumption
(SPFA) and relaxed SPFA models for binary, continuous, count, and
time-to-event (survival) outcomes via 'Stan', including parametric and
flexible M-spline survival baselines. Also provides a one-arm simulated
treatment comparison (STC) via comparator-population G-computation and
naive unadjusted benchmarks. ML-UMR is an adaptation of the ML-NMR
methodology (Phillippo et al. 2020,
<doi:10.1111/rssa.12579>) implemented in the 'multinma' package
(GPL-3) to the unanchored two-trial case. The public API uses familiar
names for data setup, integration and effect summaries, but ML-NMR and
ML-UMR specifications and fitted objects are not interchangeable because
their evidence structures and models differ.
Author: Ahmad Sofi-Mahmudi [aut, cre] ,
Conor Chandler [aut]
Maintainer: Ahmad Sofi-Mahmudi <a.sofimahmudi@gmail.com>
Diff between mlumr versions 0.1.0 dated 2026-05-20 and 0.2.0 dated 2026-10-13
mlumr-0.1.0/mlumr/inst/doc/mlumr-models.Rmd |only mlumr-0.1.0/mlumr/inst/doc/mlumr-models.html |only mlumr-0.1.0/mlumr/inst/doc/model-comparison.Rmd |only mlumr-0.1.0/mlumr/inst/doc/model-comparison.html |only mlumr-0.1.0/mlumr/inst/doc/stc-and-naive.Rmd |only mlumr-0.1.0/mlumr/inst/doc/stc-and-naive.html |only mlumr-0.1.0/mlumr/inst/doc/worked-example.Rmd |only mlumr-0.1.0/mlumr/inst/doc/worked-example.html |only mlumr-0.1.0/mlumr/man/binomial_link_variance.Rd |only mlumr-0.1.0/mlumr/man/bound_probability.Rd |only mlumr-0.1.0/mlumr/man/check_link.Rd |only mlumr-0.1.0/mlumr/man/cor_adjust_pearson.Rd |only mlumr-0.1.0/mlumr/man/cor_adjust_spearman.Rd |only mlumr-0.1.0/mlumr/man/dot-adjust_integration_cor.Rd |only mlumr-0.1.0/mlumr/man/dot-agd_cov_info.Rd |only mlumr-0.1.0/mlumr/man/dot-agd_covariate_spec.Rd |only mlumr-0.1.0/mlumr/man/dot-agd_outcome_summary.Rd |only mlumr-0.1.0/mlumr/man/dot-agd_required_columns.Rd |only mlumr-0.1.0/mlumr/man/dot-attach_integration_points.Rd |only mlumr-0.1.0/mlumr/man/dot-bound_unit_interval.Rd |only mlumr-0.1.0/mlumr/man/dot-bounded_wald_interval.Rd |only mlumr-0.1.0/mlumr/man/dot-check_required_columns.Rd |only mlumr-0.1.0/mlumr/man/dot-cmdstan_available.Rd |only mlumr-0.1.0/mlumr/man/dot-cmdstanr_cache_root.Rd |only mlumr-0.1.0/mlumr/man/dot-cmdstanr_compile_dir.Rd |only mlumr-0.1.0/mlumr/man/dot-comparison_names.Rd |only mlumr-0.1.0/mlumr/man/dot-compute_mean_lp.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_effect_choices.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_eta.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_parameters.Rd |only mlumr-0.1.0/mlumr/man/dot-conditional_profiles.Rd |only mlumr-0.1.0/mlumr/man/dot-diagnostic_count.Rd |only mlumr-0.1.0/mlumr/man/dot-diagnostic_value.Rd |only mlumr-0.1.0/mlumr/man/dot-drop_missing_rows.Rd |only mlumr-0.1.0/mlumr/man/dot-ensure_positive_definite_cor.Rd |only mlumr-0.1.0/mlumr/man/dot-finite_numeric_values.Rd |only mlumr-0.1.0/mlumr/man/dot-generate_copula_uniforms.Rd |only mlumr-0.1.0/mlumr/man/dot-int_cor_stats.Rd |only mlumr-0.1.0/mlumr/man/dot-int_stats.Rd |only mlumr-0.1.0/mlumr/man/dot-ipd_outcome_summary.Rd |only mlumr-0.1.0/mlumr/man/dot-ipd_required_columns.Rd |only mlumr-0.1.0/mlumr/man/dot-is_whole_number_count.Rd |only mlumr-0.1.0/mlumr/man/dot-log_lik_column_index.Rd |only mlumr-0.1.0/mlumr/man/dot-message_engine_unchanged.Rd |only mlumr-0.1.0/mlumr/man/dot-mlumr_build_stan_data.Rd |only mlumr-0.1.0/mlumr/man/dot-mlumr_fit_backend.Rd |only mlumr-0.1.0/mlumr/man/dot-mlumr_log_fit_start.Rd |only mlumr-0.1.0/mlumr/man/dot-mlumr_model_label.Rd |only mlumr-0.1.0/mlumr/man/dot-mlumr_prior_metadata.Rd |only mlumr-0.1.0/mlumr/man/dot-naive_binomial.Rd |only mlumr-0.1.0/mlumr/man/dot-naive_normal.Rd |only mlumr-0.1.0/mlumr/man/dot-naive_poisson.Rd |only mlumr-0.1.0/mlumr/man/dot-nonnegative_variance.Rd |only mlumr-0.1.0/mlumr/man/dot-ordered_log_lik_columns.Rd |only mlumr-0.1.0/mlumr/man/dot-relative_eff_from_log_lik.Rd |only mlumr-0.1.0/mlumr/man/dot-require_draw_columns.Rd |only mlumr-0.1.0/mlumr/man/dot-rescale_prior_beta.Rd |only mlumr-0.1.0/mlumr/man/dot-resolve_integration_cor.Rd |only mlumr-0.1.0/mlumr/man/dot-resolve_mlumr_engine.Rd |only mlumr-0.1.0/mlumr/man/dot-resolved_prior_broadcast_label.Rd |only mlumr-0.1.0/mlumr/man/dot-resolved_prior_family_label.Rd |only mlumr-0.1.0/mlumr/man/dot-safe_positive_ratio.Rd |only mlumr-0.1.0/mlumr/man/dot-sqrt_variance.Rd |only mlumr-0.1.0/mlumr/man/dot-standardize_agd_data.Rd |only mlumr-0.1.0/mlumr/man/dot-standardize_ipd_data.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_agd_mean_newdata.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_binomial.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_binomial_comparator_delta.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_binomial_index_delta.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_comparator_data.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_formula.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_glm_parameters.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_model_matrix.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_normal.Rd |only mlumr-0.1.0/mlumr/man/dot-stc_poisson.Rd |only mlumr-0.1.0/mlumr/man/dot-strip_agd_cov_suffix.Rd |only mlumr-0.1.0/mlumr/man/dot-summarize_draw_matrix.Rd |only mlumr-0.1.0/mlumr/man/dot-summarize_draw_vector.Rd |only mlumr-0.1.0/mlumr/man/dot-summarize_sensitivity.Rd |only mlumr-0.1.0/mlumr/man/dot-supported_engines.Rd |only mlumr-0.1.0/mlumr/man/dot-transform_integration_points.Rd |only mlumr-0.1.0/mlumr/man/dot-validate_agd_binary_covariates.Rd |only mlumr-0.1.0/mlumr/man/dot-validate_agd_binomial_outcomes.Rd |only mlumr-0.1.0/mlumr/man/dot-validate_agd_cov_types.Rd |only mlumr-0.1.0/mlumr/man/dot-validate_agd_covariate_names.Rd |only mlumr-0.1.0/mlumr/man/dot-validate_agd_covariates.Rd |only mlumr-0.1.0/mlumr/man/dot-validate_agd_normal_outcomes.Rd |only mlumr-0.1.0/mlumr/man/dot-validate_agd_outcome_args.Rd |only mlumr-0.1.0/mlumr/man/dot-validate_agd_outcomes.Rd |only mlumr-0.1.0/mlumr/man/dot-validate_agd_poisson_outcomes.Rd 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Title: Hierarchical Risk Clustering Portfolio Allocation Strategies
Description: Machine learning hierarchical risk clustering portfolio allocation strategies.
The implemented methods are:
Hierarchical risk parity (De Prado, 2016) <DOI: 10.3905/jpm.2016.42.4.059>.
Hierarchical clustering-based asset allocation (Raffinot, 2017)
<DOI: 10.3905/jpm.2018.44.2.089>.
Hierarchical equal risk contribution portfolio (Raffinot, 2018)
<DOI: 10.2139/ssrn.3237540>.
A Constrained Hierarchical Risk Parity Algorithm with Cluster-based Capital Allocation (Pfitzingera and Katzke, 2019)
<https://www.ekon.sun.ac.za/wpapers/2019/wp142019/wp142019.pdf>.
Hierarchical Risk Budgeting (Koumou, 2024) <DOI: 10.3905/jfds.2024.1.156>.
Author: Carlos Trucios [aut, cre] ,
Moon Jun Kwon [aut],
Sao Paulo Research Foundation , grants 2022/09122-0,
2025/06131-7 and 2025/08502-2 [fnd],
Programa de Incentivo a Novos Docentes da UNICAMP , grant 2525/23
[fnd]
Maintainer: Carlos Trucios <ctrucios@unicamp.br>
Diff between HierPortfolios versions 1.0.2 dated 2025-09-12 and 1.1.0 dated 2026-10-13
DESCRIPTION | 16 +++++++++------- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + R/DHRP_Portfolio.R | 4 ++-- R/HCAA_Portfolio.R | 4 ++-- R/HERC_Portfolio.R | 18 +++++++----------- R/HRB_Portfolio.R |only R/HRP_Portfolio.R | 4 ++-- man/DHRP_Portfolio.Rd | 4 ++-- man/HCAA_Portfolio.Rd | 4 ++-- man/HERC_Portfolio.Rd | 4 ++-- man/HRB_Portfolio.Rd |only man/HRP_Portfolio.Rd | 4 ++-- 13 files changed, 43 insertions(+), 42 deletions(-)
More information about HierPortfolios at CRAN
Permanent link
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue (202 [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.5.5 dated 2026-09-25 and 1.5.6 dated 2026-10-13
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS | 4 ++++ R/scraping_games_acb.R | 2 +- inst/doc/BAwiR.html | 4 ++-- inst/doc/BAwiR_pbp.html | 4 ++-- inst/doc/BAwiR_sc.html | 4 ++-- 7 files changed, 23 insertions(+), 19 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.4.9 dated 2026-08-28 and 0.5.0 dated 2026-10-13
DESCRIPTION | 11 MD5 | 34 - NAMESPACE | 10 NEWS.md | 390 ++++++------ R/cms_download_native.R | 9 R/cms_download_subset.r | 983 +++++++++++++++---------------- R/import.r | 2 README.md | 6 build/vignette.rds |binary inst/doc/blosc.html | 5 inst/doc/glossary.html | 4 inst/doc/product-info.html | 7 inst/doc/proxy.html | 11 inst/doc/translate.html | 7 man/cms_native_s3.Rd | 1 man/figures/README-download-subset-1.png |binary tests/testthat/test_login.r | 2 tests/testthat/test_subset.r | 442 +++++++------ 18 files changed, 981 insertions(+), 943 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Citations are:
* Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
* Luis F.S. Castro-de-Araujo, Nathan A. Gillespie, Michael C. Neale, and Timothy Charles Bates (2026). umx version 4.5: Extending Twin and Path-Based SEM in R with CLPM, MR-DoC, Definition Variables, Onyx Integration, and Censored Distributions. Twin Research and Human Genetics, 1-6. <doi:10.1017/thg.2026.10056>.
Author: Timothy C. Bates [aut, cre] ,
Luis De Araujo [ctb],
Nathan Gillespie [wit],
Hermine Maes [ctb],
Michael C. Neale [ctb],
Joshua N. Pritikin [ctb],
Brenton Wiernik [ctb],
Michael Zakharin [wit]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
Diff between umx versions 4.80.0 dated 2026-10-11 and 4.80.1 dated 2026-10-13
umx-4.80.0/umx/man/figures/ACEcovOnMeans.pdf |only umx-4.80.0/umx/man/figures/ACEcovVarianceModel.pdf |only umx-4.80.0/umx/man/figures/ACEmatrix.pdf |only umx-4.80.0/umx/man/figures/ACEunivariate.pdf |only umx-4.80.0/umx/man/figures/ACEv.pdf |only umx-4.80.0/umx/man/figures/DiffMZRainMud.pdf |only umx-4.80.0/umx/man/figures/DiffMZexample.pdf |only umx-4.80.0/umx/man/figures/DiscTwinsExample.pdf |only umx-4.80.0/umx/man/figures/DoC.pdf |only umx-4.80.0/umx/man/figures/Duncan.pdf |only umx-4.80.0/umx/man/figures/GxE.pdf |only umx-4.80.0/umx/man/figures/GxEbiv.pdf |only umx-4.80.0/umx/man/figures/TSLS.pdf |only umx-4.80.0/umx/man/figures/discordantCausalPatterns.pdf |only umx-4.80.0/umx/man/figures/formative.pdf |only umx-4.80.0/umx/man/figures/power.pdf |only umx-4.80.0/umx/man/figures/reflective.pdf |only umx-4.80.0/umx/man/figures/simplex.pdf |only umx-4.80.0/umx/man/figures/sketch.pdf |only umx-4.80.0/umx/man/figures/umxEFA.pdf |only umx-4.80.0/umx/man/umx_ICA_report.Rd |only umx-4.80.0/umx/tests/testthat/Rplots.pdf |only umx-4.80.1/umx/DESCRIPTION | 14 umx-4.80.1/umx/MD5 | 234 - umx-4.80.1/umx/NAMESPACE | 2 umx-4.80.1/umx/NEWS.md | 1 umx-4.80.1/umx/R/build_run_modify.R | 2 umx-4.80.1/umx/R/fit_and_reporting.R | 49 umx-4.80.1/umx/R/get_and_set.R |only umx-4.80.1/umx/R/ggplot_stuff.R |only umx-4.80.1/umx/R/help_tutorials.R |only umx-4.80.1/umx/R/misc_and_utility.R | 2273 ---------- umx-4.80.1/umx/R/prolific.R |only umx-4.80.1/umx/R/standardization_helpers.R |only umx-4.80.1/umx/R/stats_helpers.R |only umx-4.80.1/umx/R/umxAPA.R | 10 umx-4.80.1/umx/R/umxCompare.R | 2 umx-4.80.1/umx/R/umxDoC.R | 10 umx-4.80.1/umx/R/umxPlotFun.R |only umx-4.80.1/umx/R/umxPower.R | 4 umx-4.80.1/umx/R/umxRAM.R | 2 umx-4.80.1/umx/R/umxSummary.MxModel.R | 2 umx-4.80.1/umx/R/umx_ICA_report.R | 6 umx-4.80.1/umx/R/umx_build_high_level_models.R | 4 umx-4.80.1/umx/R/umx_build_umxACE.R | 6 umx-4.80.1/umx/R/umx_build_umxACEv.R | 2 umx-4.80.1/umx/R/umx_build_umxGxE.R | 2 umx-4.80.1/umx/R/umx_build_umxSimplex.R | 2 umx-4.80.1/umx/inst/doc/SEs_robustSEs_and_ProfileCIs.html | 4 umx-4.80.1/umx/inst/doc/WLS_in_umx.html | 4 umx-4.80.1/umx/inst/doc/fit_indices_browne_satorra_bentler_savalei.html | 4 umx-4.80.1/umx/inst/doc/modification_indices.html | 4 umx-4.80.1/umx/inst/doc/umx.html | 4 umx-4.80.1/umx/inst/doc/umxGSEM_Psych_LDSC.html | 6 umx-4.80.1/umx/man/aic_weights.Rd | 6 umx-4.80.1/umx/man/dl_from_dropbox.Rd | 3 umx-4.80.1/umx/man/ggAddR.Rd | 2 umx-4.80.1/umx/man/install.OpenMx.Rd | 2 umx-4.80.1/umx/man/libs.Rd | 2 umx-4.80.1/umx/man/oddsratio.Rd | 3 umx-4.80.1/umx/man/power.ACE.test.Rd | 2 umx-4.80.1/umx/man/prolific_anonymize.Rd | 2 umx-4.80.1/umx/man/prolific_check_ID.Rd | 2 umx-4.80.1/umx/man/prolific_read_demog.Rd | 2 umx-4.80.1/umx/man/prolific_scoring_stub.Rd | 2 umx-4.80.1/umx/man/qm.Rd | 2 umx-4.80.1/umx/man/umx.Rd | 2 umx-4.80.1/umx/man/umxACE.Rd | 4 umx-4.80.1/umx/man/umxACEcov.Rd | 2 umx-4.80.1/umx/man/umxACEv.Rd | 2 umx-4.80.1/umx/man/umxAPA.Rd | 3 umx-4.80.1/umx/man/umxDiffMZ.Rd | 4 umx-4.80.1/umx/man/umxDiscTwin.Rd | 4 umx-4.80.1/umx/man/umxDoC.Rd | 2 umx-4.80.1/umx/man/umxEFA.Rd | 2 umx-4.80.1/umx/man/umxGxE.Rd | 2 umx-4.80.1/umx/man/umxLav2RAM.Rd | 2 umx-4.80.1/umx/man/umxModelNames.Rd | 2 umx-4.80.1/umx/man/umxPlotFun.Rd | 35 umx-4.80.1/umx/man/umxPower.Rd | 2 umx-4.80.1/umx/man/umxRAM.Rd | 2 umx-4.80.1/umx/man/umxRAM2Lav.Rd | 2 umx-4.80.1/umx/man/umxSimplex.Rd | 2 umx-4.80.1/umx/man/umxSummary.MxModel.Rd | 2 umx-4.80.1/umx/man/umxTwoStage.Rd | 2 umx-4.80.1/umx/man/umxVersion.Rd | 2 umx-4.80.1/umx/man/umxWeightedAIC.Rd | 6 umx-4.80.1/umx/man/umx_array_shift.Rd | 2 umx-4.80.1/umx/man/umx_complete_dollar.Rd | 2 umx-4.80.1/umx/man/umx_data.Rd | 2 umx-4.80.1/umx/man/umx_detect_cores.Rd | 18 umx-4.80.1/umx/man/umx_find_object.Rd | 2 umx-4.80.1/umx/man/umx_get_bracket_addresses.Rd | 2 umx-4.80.1/umx/man/umx_get_checkpoint.Rd | 2 umx-4.80.1/umx/man/umx_get_options.Rd | 2 umx-4.80.1/umx/man/umx_lower.tri.Rd | 2 umx-4.80.1/umx/man/umx_msg.Rd | 2 umx-4.80.1/umx/man/umx_open_CRAN_page.Rd | 2 umx-4.80.1/umx/man/umx_pad.Rd | 2 umx-4.80.1/umx/man/umx_print.Rd | 2 umx-4.80.1/umx/man/umx_scale_reliabilities.Rd | 2 umx-4.80.1/umx/man/umx_scholastica_report.Rd |only umx-4.80.1/umx/man/umx_set_auto_plot.Rd | 2 umx-4.80.1/umx/man/umx_set_auto_run.Rd | 2 umx-4.80.1/umx/man/umx_set_checkpoint.Rd | 2 umx-4.80.1/umx/man/umx_set_condensed_slots.Rd | 2 umx-4.80.1/umx/man/umx_set_cores.Rd | 17 umx-4.80.1/umx/man/umx_set_data_variance_check.Rd | 2 umx-4.80.1/umx/man/umx_set_optimization_options.Rd | 2 umx-4.80.1/umx/man/umx_set_optimizer.Rd | 2 umx-4.80.1/umx/man/umx_set_plot_file_suffix.Rd | 2 umx-4.80.1/umx/man/umx_set_plot_format.Rd | 2 umx-4.80.1/umx/man/umx_set_separator.Rd | 2 umx-4.80.1/umx/man/umx_set_silent.Rd | 2 umx-4.80.1/umx/man/umx_set_table_format.Rd | 2 umx-4.80.1/umx/man/umx_standardize.Rd | 2 umx-4.80.1/umx/man/umx_tail.Rd | 2 umx-4.80.1/umx/man/umx_tutorials.Rd | 2 umx-4.80.1/umx/man/umx_wide2long.Rd | 4 umx-4.80.1/umx/man/umx_wide4lmer.Rd | 2 umx-4.80.1/umx/man/xmu_custom_completer.Rd | 2 umx-4.80.1/umx/man/xmu_parse_completion_context.Rd | 2 umx-4.80.1/umx/man/xmu_standardize_ACE.Rd | 2 umx-4.80.1/umx/man/xmu_standardize_ACEcov.Rd | 2 umx-4.80.1/umx/man/xmu_standardize_CP.Rd | 2 umx-4.80.1/umx/man/xmu_standardize_IP.Rd | 2 umx-4.80.1/umx/man/xmu_standardize_LISREL.Rd | 2 umx-4.80.1/umx/man/xmu_standardize_RAM.Rd | 2 umx-4.80.1/umx/man/xmu_standardize_SexLim.Rd | 2 umx-4.80.1/umx/man/xmu_utils_completeToken.Rd | 2 umx-4.80.1/umx/tests/testthat/test_fin_.r | 3 umx-4.80.1/umx/tests/testthat/test_umx_make.R | 8 umx-4.80.1/umx/tests/testthat/test_umx_misc.r | 73 133 files changed, 408 insertions(+), 2562 deletions(-)
Title: Post-Linkage Data Analysis
Description: Provides a suite of statistical tools for post-linkage data analysis (PLDA), designed to account for record linkage errors in downstream modeling. The package implements a familiar, formula-based regression interface that adjusts for linkage uncertainty, accommodating workflows where direct access to unlinked primary files is restricted. It consolidates diverse adjustment methodologies, all of which support generalized linear models (linear, logistic, Poisson, and Gamma). These methodologies include weighting approaches (Chambers (2009) <https://hdl.handle.net/10779/uow.27788247>; Chambers et al. (2023) <doi:10.1002/wics.1596>), mixture modeling (Slawski et al. (2025) <doi:10.1093/jrsssa/qnae083>), and Bayesian mixture modeling (Gutman et al. (2016) <doi:10.1002/sim.6586>). For time-to-event data, both the weighting (Vo et al. (2024) <doi:10.1002/sim.9960>) and mixture modeling approaches accommodate Cox proportional hazards models, while the Bayesian appr [...truncated...]
Author: Priyanjali Bukke [aut, cre],
Gauri Kamat [aut],
Jiahao Cui [aut],
Roee Gutman [aut],
Martin Slawski [aut],
Zhenbang Wang [ctb],
Brady T. West [ctb],
Emanuel Ben-David [ctb],
Guoqing Diao [ctb]
Maintainer: Priyanjali Bukke <postlink.group@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2026-09-04
Diff between postlink versions 0.1.1 dated 2026-09-04 and 0.1.2 dated 2026-10-13
DESCRIPTION | 12 - MD5 | 110 ++++++------ NEWS.md | 13 + R/mixture_coxph.R | 33 ++- R/mixture_glm.R | 120 ++++++------- README.md | 16 + configure.win | 3 inst/stan/glmMixBayes_binomial.stan | 4 inst/stan/glmMixBayes_gamma.stan | 2 inst/stan/glmMixBayes_gaussian.stan | 2 inst/stan/glmMixBayes_poisson.stan | 4 inst/stan/survMixBayes_gamma.stan | 4 inst/stan/survMixBayes_weibull.stan | 4 man/adjELE.Rd | 180 ++++++++++---------- man/adjMixture.Rd | 182 ++++++++++---------- man/brfss.Rd | 106 +++++------ man/confint.coxphELE.Rd | 124 ++++++------- man/confint.coxphMixture.Rd | 142 +++++++-------- man/confint.glmELE.Rd | 82 ++++----- man/confint.glmMixture.Rd | 110 ++++++------ man/coxphELE.Rd | 192 ++++++++++----------- man/coxphMixture.Rd | 242 +++++++++++++------------- man/ctableMixture.Rd | 204 +++++++++++----------- man/glmELE.Rd | 166 +++++++++--------- man/glmMixture.Rd | 186 ++++++++++---------- man/predict.coxphELE.Rd | 140 +++++++-------- man/predict.coxphMixture.Rd | 208 +++++++++++------------ man/predict.glmELE.Rd | 132 +++++++------- man/predict.glmMixture.Rd | 160 ++++++++--------- man/print.adjELE.Rd | 78 ++++---- man/print.adjMixture.Rd | 88 ++++----- man/print.coxphELE.Rd | 116 ++++++------ man/print.coxphMixture.Rd | 122 ++++++------- man/print.glmELE.Rd | 74 ++++---- man/print.glmMixture.Rd | 92 +++++----- man/summary.coxphELE.Rd | 132 +++++++------- man/summary.coxphMixture.Rd | 148 ++++++++-------- man/summary.glmELE.Rd | 80 ++++---- man/summary.glmMixture.Rd | 108 ++++++------ man/vcov.coxphELE.Rd | 114 ++++++------ man/vcov.coxphMixture.Rd | 142 +++++++-------- man/vcov.glmELE.Rd | 74 ++++---- man/vcov.glmMixture.Rd | 94 +++++----- src/Makevars.win | 2 src/stanExports_glmMixBayes_binomial.cc | 34 +-- src/stanExports_glmMixBayes_binomial.h | 181 ++++++++++++++------ src/stanExports_glmMixBayes_gamma.cc | 34 +-- src/stanExports_glmMixBayes_gamma.h | 233 ++++++++++++++++++------- src/stanExports_glmMixBayes_gaussian.cc | 34 +-- src/stanExports_glmMixBayes_gaussian.h | 220 +++++++++++++++++------- src/stanExports_glmMixBayes_poisson.cc | 34 +-- src/stanExports_glmMixBayes_poisson.h | 181 ++++++++++++++------ src/stanExports_survMixBayes_gamma.cc | 34 +-- src/stanExports_survMixBayes_gamma.h | 273 +++++++++++++++++++++--------- src/stanExports_survMixBayes_weibull.cc | 34 +-- src/stanExports_survMixBayes_weibull.h | 287 +++++++++++++++++++++++--------- 56 files changed, 3283 insertions(+), 2643 deletions(-)
Title: One-Way Statistical Analyses
Description: Performs one-way tests of assumptions (normality and homoscedasticity),
analysis of variance, robust and nonparametric alternatives, multiple comparison
procedures, effect size estimators, confidence intervals, and descriptive summaries.
Functions are designed with a consistent interface to support reproducible and
user-friendly statistical workflows. For more details see
Howell (2010, ISBN:978-0-495-59784-1),
Zar (2014, ISBN:978-0-13-100846-5),
Hollander et al. (2014, ISBN:978-0-470-38737-5),
Montgomery (2017, ISBN:978-1-119-11347-8),
Lakens (2013) <doi:10.3389/fpsyg.2013.00863>, and
Piepho (2004) <doi:10.1198/1061860043515>.
Author: Joon-Keat Lai [aut, cre, cph]
Maintainer: Joon-Keat Lai <p10911004@gmail.com>
Diff between oneway versions 0.0.2 dated 2026-09-15 and 0.0.3 dated 2026-10-13
DESCRIPTION | 26 +++++++++--------- MD5 | 53 +++++++++++++++++++++---------------- NAMESPACE | 2 + NEWS.md | 16 +++++++++-- R/Dunn_test.R | 2 - R/Games_Howell_test.R | 4 +- R/REGWQ_test.R | 20 ++++++------- R/Scheffe_test.R |only R/Tukey_HSD_test.R | 16 ++++------- R/Tukey_Kramer_test.R | 4 +- R/anova.R | 34 +++++++++++------------ R/compact_letter_display.R | 2 - R/pairwise_comparison.R | 4 +- R/utils.R | 2 - README.md | 10 ++++++ build |only data/O_O_O.rda |binary inst |only man/Kruskal_Wallis_test.Rd | 8 ++++- man/REGWQ_test.Rd | 16 ++++------- man/Scheffe_test.Rd |only man/Tukey_HSD_test.Rd | 12 +++----- man/oneway_anova.Rd | 2 - man/oneway_art.Rd | 2 - man/pairwise_comparison.Rd | 2 - man/pairwise_contrasts.Rd |only man/simulated_data.Rd | 2 - tests/testthat/test-REGWQ_test.R | 9 ++++-- tests/testthat/test-Scheffe_test.R |only vignettes |only 30 files changed, 143 insertions(+), 105 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.2-6 dated 2026-03-06 and 1.2-7 dated 2026-10-13
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/Bernstein.R | 40 ++++++++++++++++++++-------------------- R/formula.R | 6 +++--- R/legendre.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 6 ++++++ tests/bugfixes.R | 12 ++++++++++++ 9 files changed, 56 insertions(+), 38 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently. Polynomial mean coefficients are handled conditionally within the Kalman recursion, reducing the dimension of numerical maximum likelihood optimization and permitting exact Gaussian conditional updates during Bayesian posterior sampling. Maximum likelihood estimation is computationally efficient and suitable for large-scale data analysis, while Bayesian posterior sampling is better suited to small-scale analyses requiring more careful uncertainty qua [...truncated...]
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.4 dated 2026-08-20 and 1.0.5 dated 2026-10-13
DESCRIPTION | 8 - MD5 | 6 R/drw.R | 369 ++++++++++++++++++++++++++++++++++++++++++++++-------------- man/drw.Rd | 36 +++-- 4 files changed, 313 insertions(+), 106 deletions(-)
Title: L1-Norm PCA Methods
Description: Implementations of several methods for principal component analysis
using the L1 norm. The package depends on COIN-OR Clp version >=
1.17.4. The methods implemented are
PCA-L1 (Kwak 2008) <DOI:10.1109/TPAMI.2008.114>,
L1-PCA (Ke and Kanade 2003, 2005) <DOI:10.1109/CVPR.2005.309>,
L1-PCA* (Brooks, Dula, and Boone 2013) <DOI:10.1016/j.csda.2012.11.007>,
L1-PCAhp (Visentin, Prestwich and Armagan 2016)
<DOI:10.1007/978-3-319-46227-1_37>,
wPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
awPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
PCA-Lp (Kwak 2014) <DOI:10.1109/TCYB.2013.2262936>, and
SharpEl1-PCA (Brooks and Dula, submitted).
Author: Sapan Jot [aut],
Paul Brooks [aut, cre],
Andrea Visentin [aut],
Young Woong Park [aut],
and Yi-Hui Zhou [aut]
Maintainer: Paul Brooks <jpbrooks@ou.edu>
Diff between pcaL1 versions 1.5.9 dated 2025-05-03 and 1.5.10 dated 2026-10-13
ChangeLog | 7 ++++++- DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS | 14 ++++++++++++++ configure | 18 +++++++++--------- configure.ac | 2 +- man/pcaL1-package.Rd | 8 ++++---- src/sparsel1pca.c | 2 +- 8 files changed, 48 insertions(+), 29 deletions(-)
Title: Multipurpose Aids for R Kit
Description: Miscellaneous functions and wrappers for development in other
packages created, maintained by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between mark versions 0.8.3 dated 2025-04-22 and 0.9.0 dated 2026-10-13
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Title: Implement Fleming-Viot-Dependent Dirichlet Processes
Description: A Bayesian Nonparametric model for the study of time-evolving frequencies, which has become renowned in the study of population genetics.
The model consists of a Hidden Markov Model (HMM) in which the latent signal is a distribution-valued stochastic process that takes the form of a finite mixture of Dirichlet Processes, indexed by vectors that count how many times each value is observed in the population.
The package implements methodologies presented in Ascolani, Lijoi and Ruggiero (2021) <doi:10.1214/20-BA1206> and Ascolani, Lijoi and Ruggiero (2023) <doi:10.3150/22-BEJ1504> that make it possible to study the process at the time of data collection or to predict its evolution in future or in the past.
The package itself is described in Ascolani, Damato and Ruggiero (2024) <doi:10.1089/cmb.2024.0600>.
Author: Stefano Damato [aut, cre]
Maintainer: Stefano Damato <stefanodamato128@gmail.com>
Diff between FVDDPpkg versions 0.1.2 dated 2024-07-09 and 0.1.3 dated 2026-10-13
DESCRIPTION | 11 - MD5 | 13 - README.md | 58 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/FVDDPpkg.html | 489 +++++++++++++++++++++++++------------------------ src/C++FVDDP.cpp | 2 8 files changed, 290 insertions(+), 283 deletions(-)
Title: An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between configr versions 0.3.5 dated 2020-07-17 and 0.3.6 dated 2026-10-13
ChangeLog | 4 DESCRIPTION | 11 LICENSE | 2 MD5 | 54 - NAMESPACE | 6 NEWS.md | 4 R/configr.R | 1 R/configtype.R | 8 R/parse.R | 16 R/read.R | 14 R/utils.R | 2 README.md | 69 -- build/vignette.rds |binary inst/doc/configr.R | 22 inst/doc/configr.Rmd | 2 inst/doc/configr.html | 1567 ++++++++++++++++++++++++------------------------ inst/doc/filetypes.R | 2 inst/doc/filetypes.Rmd | 2 inst/doc/filetypes.html | 572 +++++++++-------- man/configr.Rd | 1 man/is.ini.file.Rd | 4 man/is.json.file.Rd | 4 man/is.toml.file.Rd | 4 man/is.yaml.file.Rd | 4 man/parse.extra.Rd | 16 man/read.config.Rd | 14 vignettes/configr.Rmd | 2 vignettes/filetypes.Rmd | 2 28 files changed, 1228 insertions(+), 1181 deletions(-)