Title: Data Access and Analytical Tools for 'VectorSurv' Users
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Diff between vectorsurvR versions 1.5.2 dated 2025-08-21 and 1.6.0 dated 2025-11-03
DESCRIPTION | 10 MD5 | 44 NAMESPACE | 11 R/getAbundance.R | 331 ++- R/getAbundanceAnomaly.R | 9 R/getArthroCollections.R | 138 + R/getPools.R | 12 R/getSites.R | 14 R/getSpeciesTable.R |only R/getVectorIndex.R | 147 - R/globals.R | 7 R/plotInvasiveSums.R |only R/plotVectorAbundance.R |only data/sample_pools.rda |binary inst/doc/vectorsurvR.html | 2557 +++++++++++++++++++++--------- man/getAbundance.Rd | 11 man/getAbundanceAnomaly.Rd | 6 man/getArthroCollections.Rd | 5 man/getSites.Rd | 4 man/getSpeciesTable.Rd |only man/getVectorIndex.Rd | 14 man/plotInvasiveSums.Rd |only man/plotVectorAbundance.Rd |only tests/testthat/test-getAbundance.R | 4 tests/testthat/test-getAbundanceAnomaly.R | 2 tests/testthat/test-getSpeciesTable.R |only tests/testthat/test-plotVectorAbundance.R |only 27 files changed, 2427 insertions(+), 899 deletions(-)
Title: Read-Write Support for 'NumPy' Files via 'Rcpp'
Description: The 'cnpy' library written by Carl Rogers provides read and write
facilities for files created with (or for) the 'NumPy' extension for 'Python'.
Vectors and matrices of numeric types can be read or written to and from
files as well as compressed files. Support for integer files is available if
the package has been built with as C++11 which should be the default on
all platforms since the release of R 3.3.0.
Author: Dirk Eddelbuettel [aut, cre] ,
Wush Wu [aut] ,
Carl Rogers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCNPy versions 0.2.13 dated 2024-09-03 and 0.2.14 dated 2025-11-03
ChangeLog | 17 +++++++++++++++++ DESCRIPTION | 15 ++++++++------- MD5 | 14 +++++++------- README.md | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 10 ++++++++++ inst/doc/RcppCNPy-intro.pdf |binary inst/doc/UsingReticulate.pdf |binary 8 files changed, 43 insertions(+), 15 deletions(-)
Title: Two-Steps Benchmarks for Time Series Disaggregation
Description: The twoStepsBenchmark() and threeRuleSmooth() functions allow you to
disaggregate a low-frequency time series with higher frequency time series,
using the French National Accounts methodology. The aggregated sum of the
resulting time series is strictly equal to the low-frequency time series within the
benchmarking window. Typically, the low-frequency time series is an annual one,
unknown for the last year, and the high frequency one is either quarterly or
monthly. See "Methodology of quarterly national accounts", Insee Méthodes
N°126, by Insee (2012, ISBN:978-2-11-068613-8, <https://www.insee.fr/en/information/2579410>).
Author: Arnaud Feldmann [aut] ,
Pauline Meinzel [cre],
Thomas Laurent [ctb] ,
Franck Arnaud [ctb] ,
Institut national de la statistique et des etudes economiques [cph]
Maintainer: Pauline Meinzel <pauline.meinzel@insee.fr>
This is a re-admission after prior archival of version 1.0.5.3 dated 2024-07-11
Diff between disaggR versions 1.0.5.3 dated 2024-07-11 and 1.0.5.4 dated 2025-11-03
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Title: Create and Format Correlation Matrices
Description: Create correlation (or partial correlation) matrices. Correlation matrices are formatted with significance stars based on user preferences. Matrices of coefficients, p-values, and number of pairwise observations are returned. Send resultant formatted matrices to the clipboard to be pasted into excel and other programs. A plot method allows users to visualize correlation matrices created with 'corx'.
Author: James Conigrave [aut, cre]
Maintainer: James Conigrave <james.conigrave@gmail.com>
Diff between corx versions 1.0.7.2 dated 2023-06-16 and 1.0.7.3 dated 2025-11-03
DESCRIPTION | 17 LICENSE | 4 MD5 | 59 +- NEWS.md | 34 - R/adjust_p.R | 42 - R/cormat_list.R | 172 +++-- R/corx.R | 1072 ++++++++++++++++++++----------------- R/methods.R | 132 ++-- R/plot_mds.R | 200 +++--- R/to_clipboard.r | 32 - R/to_table.R | 256 ++++---- R/utils.R |only README.md | 586 ++++++++++---------- man/adjust_pmat.Rd | 32 - man/apa_table.corx.Rd | 32 - man/check_classes.Rd | 40 - man/cormat_list.Rd | 48 - man/corx.Rd | 192 +++--- man/digits.Rd | 32 - man/partial_n_matrix.Rd | 40 - man/plot.corx.Rd | 32 - man/plot_mds.Rd | 62 +- man/print.corx.Rd | 32 - man/rename_if_needed.Rd | 32 - man/star_matrix.Rd | 32 - man/to_clipboard.Rd | 32 - man/to_table.Rd | 32 - tests/testthat.R | 8 tests/testthat/test_classes.R | 30 - tests/testthat/test_describe.R |only tests/testthat/test_matrix.R | 926 +++++++++++++++---------------- tests/testthat/test_value_labels.R |only 32 files changed, 2179 insertions(+), 2061 deletions(-)
Title: Assessment of Predictions for an Ordinal Response
Description: Produces several metrics to assess the prediction of ordinal
categories based on the estimated probability distribution for each unit of analysis
produced by any model returning a matrix with these probabilities.
Author: Javier Espinosa-Brito [aut, cre]
Maintainer: Javier Espinosa-Brito <javier.espinosa.b@usach.cl>
Diff between apor versions 0.1.0 dated 2025-11-03 and 0.1.1 dated 2025-11-03
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/opdRef.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Generate Tile Maps
Description: Implements an algorithm for generating maps, known as tile maps,
in which each region is represented by a single tile of the same shape and
size. The algorithm was first proposed in "Generating Tile Maps" by Graham
McNeill and Scott Hale (2017) <doi:10.1111/cgf.13200>. Functions allow
users to generate, plot, and compare square or hexagon tile maps.
Author: Kaelyn Rosenberg [aut, cre]
Maintainer: Kaelyn Rosenberg <kaerosenberg@gmail.com>
Diff between tilemaps versions 0.2.1 dated 2025-09-29 and 0.2.2 dated 2025-11-03
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 3 +++ R/generate_map.R | 2 +- R/many_maps.R | 2 +- inst/doc/tilemaps.html | 14 +++++++------- 6 files changed, 20 insertions(+), 17 deletions(-)
Title: Just Another Latent Space Network Clustering Algorithm
Description: Fit latent space network cluster models using an expectation-maximization algorithm. Enables flexible modeling of unweighted or weighted network data (with or without noise edges), supporting both directed and undirected networks (with or without degree and strength heterogeneity). Designed to handle large networks efficiently, it allows users to explore network structure through latent space representations, identify clusters (i.e., community detection) within network data, and simulate networks with varying clustering, connectivity patterns, and noise edges. Methodology for the implementation is described in Arakkal and Sewell (2025) <doi:10.1016/j.csda.2025.108228>.
Author: Alan Arakkal [aut, cre, cph] ,
Daniel Sewell [aut]
Maintainer: Alan Arakkal <alan-arakkal@uiowa.edu>
Diff between JANE versions 2.0.0 dated 2025-07-30 and 2.1.0 dated 2025-11-03
JANE-2.0.0/JANE/R/log_Q_funs.R |only JANE-2.1.0/JANE/DESCRIPTION | 9 JANE-2.1.0/JANE/MD5 | 68 JANE-2.1.0/JANE/NAMESPACE | 2 JANE-2.1.0/JANE/NEWS.md | 16 JANE-2.1.0/JANE/R/BICL.R | 35 JANE-2.1.0/JANE/R/JANE.R | 106 - JANE-2.1.0/JANE/R/RcppExports.R | 92 - JANE-2.1.0/JANE/R/check_priors.R | 95 - JANE-2.1.0/JANE/R/initialize_starting_values.R | 16 JANE-2.1.0/JANE/R/sim_A.R | 39 JANE-2.1.0/JANE/R/specify_priors.R | 24 JANE-2.1.0/JANE/R/zzz.R | 3 JANE-2.1.0/JANE/inst/doc/JANE-User-Guide.R | 2 JANE-2.1.0/JANE/inst/doc/JANE-User-Guide.Rmd | 4 JANE-2.1.0/JANE/inst/doc/JANE-User-Guide.html | 6 JANE-2.1.0/JANE/man/JANE.Rd | 2 JANE-2.1.0/JANE/man/specify_priors.Rd | 24 JANE-2.1.0/JANE/src/BIC_funs.cpp | 83 JANE-2.1.0/JANE/src/Makevars | 4 JANE-2.1.0/JANE/src/Makevars.win | 4 JANE-2.1.0/JANE/src/RcppExports.cpp | 112 - JANE-2.1.0/JANE/src/helper_funs.cpp |only JANE-2.1.0/JANE/src/helper_funs.h |only JANE-2.1.0/JANE/src/initialize_starting_values.cpp | 13 JANE-2.1.0/JANE/src/log_Q_funs.cpp | 10 JANE-2.1.0/JANE/src/sim_A.cpp | 7 JANE-2.1.0/JANE/src/update_U_funs.cpp | 51 JANE-2.1.0/JANE/src/update_beta2.cpp | 13 JANE-2.1.0/JANE/src/update_beta_funs.cpp | 35 JANE-2.1.0/JANE/src/update_mus_omegas.cpp | 9 JANE-2.1.0/JANE/src/update_prob_matrix_W_DA.cpp | 58 JANE-2.1.0/JANE/tests/testthat/test-BIC.R |only JANE-2.1.0/JANE/tests/testthat/test-JANE.R | 1733 ++++++++++++++++++- JANE-2.1.0/JANE/tests/testthat/test-sim_A.R | 173 + JANE-2.1.0/JANE/tests/testthat/test-specify_priors.R | 88 JANE-2.1.0/JANE/vignettes/JANE-User-Guide.Rmd | 4 37 files changed, 2335 insertions(+), 605 deletions(-)
Title: Fast Two Stage Multiple Change Point Detection
Description: A novel and fast two stage method for simultaneous multiple change point detection and variable selection for piecewise stationary autoregressive (PSAR) processes and linear regression model. It also simultaneously performs variable selection for each autoregressive model and hence the order selection.
Author: Yaguang Li [aut, cre],
Baisuo Jin [aut]
Maintainer: Yaguang Li <liyg@mail.ustc.edu.cn>
This is a re-admission after prior archival of version 1.0 dated 2018-11-18
Diff between TSMCP versions 1.0 dated 2018-11-18 and 1.1 dated 2025-11-03
DESCRIPTION | 25 - MD5 | 12 NAMESPACE | 13 R/cpvnts.R | 871 +++++++++++++++++++++--------------------- R/tsmcp.R | 1176 ++++++++++++++++++++++++++++----------------------------- man/cpvnts.Rd | 250 ++++++------ man/tsmcplm.Rd | 162 +++---- 7 files changed, 1252 insertions(+), 1257 deletions(-)
Title: Transfer Function and ARIMA Models
Description: Build customized transfer function and ARIMA models with multiple operators
and parameter restrictions. Provides tools for model identification, estimation
using exact or conditional maximum likelihood, diagnostic checking, automatic outlier
detection, calendar effects, forecasting, and seasonal adjustment. The new version
also supports unobserved component ARIMA model specification and estimation
for structural time series analysis.
Author: Jose L. Gallego [aut, cre]
Maintainer: Jose L. Gallego <jose.gallego@unican.es>
Diff between tfarima versions 0.3.2 dated 2022-05-20 and 0.4.1 dated 2025-11-03
tfarima-0.3.2/tfarima/inst/doc/tfarima.Rnw |only tfarima-0.3.2/tfarima/inst/doc/tfarima.pdf |only tfarima-0.3.2/tfarima/man/bsm.Rd |only tfarima-0.3.2/tfarima/man/fit.stsm.Rd |only tfarima-0.3.2/tfarima/man/fit2autocov.Rd |only tfarima-0.3.2/tfarima/man/output.tf.Rd |only tfarima-0.3.2/tfarima/man/rform.Rd |only tfarima-0.3.2/tfarima/man/roots.lagpol.Rd |only tfarima-0.3.2/tfarima/man/sform.Rd |only tfarima-0.3.2/tfarima/man/stsm.Rd |only tfarima-0.3.2/tfarima/man/sum_um.Rd |only tfarima-0.3.2/tfarima/man/ucomp.Rd |only tfarima-0.3.2/tfarima/vignettes/tfarima-concordance.tex |only tfarima-0.3.2/tfarima/vignettes/tfarima.Rnw |only tfarima-0.3.2/tfarima/vignettes/tfarima0.pdf |only tfarima-0.4.1/tfarima/DESCRIPTION | 32 tfarima-0.4.1/tfarima/MD5 | 228 + tfarima-0.4.1/tfarima/NAMESPACE | 109 tfarima-0.4.1/tfarima/R/RcppExports.R | 68 tfarima-0.4.1/tfarima/R/as_ucarima.R |only tfarima-0.4.1/tfarima/R/data.R | 19 tfarima-0.4.1/tfarima/R/detvar.R | 230 - tfarima-0.4.1/tfarima/R/ide.R | 221 + tfarima-0.4.1/tfarima/R/lagpol.R | 1431 ++++++----- tfarima-0.4.1/tfarima/R/stsm.R | 2074 +++++++++++++--- tfarima-0.4.1/tfarima/R/tf.R | 559 ++-- tfarima-0.4.1/tfarima/R/tfarima-package.R | 87 tfarima-0.4.1/tfarima/R/tfm.R | 1968 ++++++++------- tfarima-0.4.1/tfarima/R/ucarima.R |only tfarima-0.4.1/tfarima/R/um.R | 1375 +++++++--- tfarima-0.4.1/tfarima/R/utils.R | 185 + tfarima-0.4.1/tfarima/README.md | 188 + tfarima-0.4.1/tfarima/build/partial.rdb |only tfarima-0.4.1/tfarima/build/vignette.rds |binary tfarima-0.4.1/tfarima/data/BuildingMat.rda |only tfarima-0.4.1/tfarima/inst/doc/tfarima.R |only tfarima-0.4.1/tfarima/inst/doc/tfarima.Rmd |only tfarima-0.4.1/tfarima/inst/doc/tfarima.html |only tfarima-0.4.1/tfarima/man/AIC.ssm.Rd |only tfarima-0.4.1/tfarima/man/AIC.tfm.Rd |only tfarima-0.4.1/tfarima/man/BuildingMat.Rd |only tfarima-0.4.1/tfarima/man/CalendarVar.Rd | 44 tfarima-0.4.1/tfarima/man/InterventionVar.Rd | 31 tfarima-0.4.1/tfarima/man/S.Rd | 12 tfarima-0.4.1/tfarima/man/add_um.Rd |only tfarima-0.4.1/tfarima/man/airline.Rd |only tfarima-0.4.1/tfarima/man/as.lagpol.Rd | 15 tfarima-0.4.1/tfarima/man/as.ssm.Rd |only tfarima-0.4.1/tfarima/man/as.ucarima.Rd |only tfarima-0.4.1/tfarima/man/as.ucarima.um.Rd |only tfarima-0.4.1/tfarima/man/as.um.Rd | 4 tfarima-0.4.1/tfarima/man/autocorr.Rd | 13 tfarima-0.4.1/tfarima/man/autocov.Rd | 33 tfarima-0.4.1/tfarima/man/autocov2MA.Rd |only tfarima-0.4.1/tfarima/man/calendar.Rd | 32 tfarima-0.4.1/tfarima/man/ccf.tfm.Rd | 13 tfarima-0.4.1/tfarima/man/coef.tfm.Rd | 23 tfarima-0.4.1/tfarima/man/coef.ucm.Rd |only tfarima-0.4.1/tfarima/man/cwfact.Rd |only tfarima-0.4.1/tfarima/man/decomp.Rd |only tfarima-0.4.1/tfarima/man/diagchk.Rd | 50 tfarima-0.4.1/tfarima/man/diagchk.tfm.Rd |only tfarima-0.4.1/tfarima/man/display.Rd | 6 tfarima-0.4.1/tfarima/man/easter.Rd | 4 tfarima-0.4.1/tfarima/man/equation.Rd |only tfarima-0.4.1/tfarima/man/factorize.Rd |only tfarima-0.4.1/tfarima/man/factors.Rd |only 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tfarima-0.4.1/tfarima/man/sincos.Rd | 16 tfarima-0.4.1/tfarima/man/spec.Rd | 6 tfarima-0.4.1/tfarima/man/ssm.Rd |only tfarima-0.4.1/tfarima/man/std.Rd | 6 tfarima-0.4.1/tfarima/man/summary.ssm.Rd |only tfarima-0.4.1/tfarima/man/summary.tfm.Rd | 48 tfarima-0.4.1/tfarima/man/tf.Rd | 43 tfarima-0.4.1/tfarima/man/tfarima-package.Rd | 55 tfarima-0.4.1/tfarima/man/tfest.Rd | 46 tfarima-0.4.1/tfarima/man/tfm.Rd | 63 tfarima-0.4.1/tfarima/man/tsvalue.Rd | 11 tfarima-0.4.1/tfarima/man/uc.Rd |only tfarima-0.4.1/tfarima/man/uc0.Rd |only tfarima-0.4.1/tfarima/man/ucarima.Rd |only tfarima-0.4.1/tfarima/man/ucm.Rd |only tfarima-0.4.1/tfarima/man/um.Rd | 4 tfarima-0.4.1/tfarima/man/unitcircle.Rd |only tfarima-0.4.1/tfarima/man/varsel.Rd | 4 tfarima-0.4.1/tfarima/man/wkfilter.Rd |only tfarima-0.4.1/tfarima/man/wold.pol.Rd |only tfarima-0.4.1/tfarima/src/Makevars | 1 tfarima-0.4.1/tfarima/src/Makevars.win | 1 tfarima-0.4.1/tfarima/src/RcppExports.cpp | 243 + tfarima-0.4.1/tfarima/src/acovtoma.cpp | 43 tfarima-0.4.1/tfarima/src/acovtoma.h | 5 tfarima-0.4.1/tfarima/src/decomp.cpp | 38 tfarima-0.4.1/tfarima/src/filter.cpp | 2 tfarima-0.4.1/tfarima/src/filter.h | 1 tfarima-0.4.1/tfarima/src/loglik.cpp | 1 tfarima-0.4.1/tfarima/src/pol.cpp | 274 -- tfarima-0.4.1/tfarima/src/pol.h | 9 tfarima-0.4.1/tfarima/src/presample.cpp |only tfarima-0.4.1/tfarima/src/presample.h |only tfarima-0.4.1/tfarima/src/res.cpp | 72 tfarima-0.4.1/tfarima/src/res.h | 5 tfarima-0.4.1/tfarima/src/sim.cpp | 37 tfarima-0.4.1/tfarima/src/sim.h | 2 tfarima-0.4.1/tfarima/src/stsm.cpp | 518 +++ tfarima-0.4.1/tfarima/src/stsm.h | 28 tfarima-0.4.1/tfarima/src/tacov.cpp | 2 tfarima-0.4.1/tfarima/vignettes/tfarima.Rmd |only 152 files changed, 7625 insertions(+), 3583 deletions(-)
Title: Markdown-Based Programmable Surveys Using 'Quarto' and 'shiny'
Description: Generate programmable surveys using markdown and R code chunks. Surveys
are composed of two files: a survey.qmd 'Quarto' file defining the
survey content (pages, questions, etc), and an app.R file defining a
'shiny' app with global settings (libraries, database configuration,
etc.) and server configuration options (e.g., conditional skipping /
display, etc.). Survey data collected from respondents is stored in a
'PostgreSQL' database. Features include controls for conditional skip
logic (skip to a page based on an answer to a question), conditional
display logic (display a question based on an answer to a question), a
customizable progress bar, and a wide variety of question types,
including multiple choice (single choice and multiple choices),
select, text, numeric, multiple choice buttons, text area, and dates.
Because the surveys render into a 'shiny' app, designers can also
leverage the reactive capabilities of 'shiny' to create dynamic and
interactive surveys.
Author: John Paul Helveston [aut, cre, cph] ,
Pingfan Hu [aut, cph] ,
Bogdan Bunea [aut, cph] ,
Stefan Munnes [ctb]
Maintainer: John Paul Helveston <john.helveston@gmail.com>
Diff between surveydown versions 0.13.3 dated 2025-09-30 and 0.14.0 dated 2025-11-03
DESCRIPTION | 6 - MD5 | 14 ++-- NEWS.md | 13 +++- R/db.R | 8 -- R/ui.R | 12 ++- R/util.R | 31 ++++++---- README.md | 6 + inst/lua/include-resources.lua | 127 +++++++++++++++++++++++++++++++++++++++++ 8 files changed, 182 insertions(+), 35 deletions(-)
Title: Mathematical Modelling of (Dynamic) Microbial Inactivation
Description: Functions for modelling microbial inactivation under
isothermal or dynamic conditions. The calculations are based on several mathematical models broadly
used by the scientific community and industry. Functions enable to make predictions for cases where the
kinetic parameters are known. It also implements functions for parameter estimation for isothermal and
dynamic conditions. The model fitting capabilities include an Adaptive Monte Carlo method for a Bayesian
approach to parameter estimation.
Author: Alberto Garre [aut, cre],
Pablo S. Fernandez [aut],
Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between bioinactivation versions 1.3.0 dated 2025-04-06 and 1.3.1 dated 2025-11-03
DESCRIPTION | 6 MD5 | 129 +++--- NAMESPACE | 131 +++--- NEWS.md | 3 R/AIC_functions.R | 314 +++++++------- R/arrhenius_model.R | 128 ++--- R/bigelow_model.R | 228 +++++----- R/doc_examples.R | 144 +++--- R/geeraerd_model.R | 138 +++--- R/methods_s3_others.R | 270 ++++++------ R/methods_s3_plot.R | 726 +++++++++++++++++----------------- R/metselaar_model.R | 136 +++--- R/temperature_interpolation.R | 86 ++-- R/time_to_reduction.R | 119 ++--- R/weibull-mafart_model.R | 246 +++++------ R/weibull-peleg_model.R | 260 ++++++------ README.md |only inst/doc/inactivation.html | 95 +++- man/Arrhenius_iso.Rd | 58 +- man/Bigelow_iso.Rd | 54 +- man/Geeraerd_iso.Rd | 50 +- man/Metselaar_iso.Rd | 64 +- man/WeibullMafart_iso.Rd | 60 +- man/WeibullPeleg_iso.Rd | 56 +- man/build_temperature_interpolator.Rd | 58 +- man/check_model_params.Rd | 74 +-- man/dArrhenius_model.Rd | 104 ++-- man/dBigelow_model.Rd | 108 ++--- man/dGeeraerd_model.Rd | 140 +++--- man/dMafart_model.Rd | 128 ++--- man/dMetselaar_model.Rd | 130 +++--- man/dPeleg_model.Rd | 128 ++--- man/dynamic_inactivation.Rd | 48 +- man/fit_dynamic_inactivation.Rd | 200 ++++----- man/fit_inactivation_MCMC.Rd | 200 ++++----- man/fit_isothermal_inactivation.Rd | 166 +++---- man/get_isothermal_model_data.Rd | 52 +- man/get_model_data.Rd | 90 ++-- man/get_prediction_cost.Rd | 80 +-- man/goodness_MCMC.Rd | 28 - man/goodness_dyna.Rd | 28 - man/goodness_iso.Rd | 28 - man/goodness_of_fit.Rd | 52 +- man/is.FitInactivation.Rd | 36 - man/is.FitInactivationMCMC.Rd | 36 - man/is.IsoFitInactivation.Rd | 36 - man/is.PredInactivationMCMC.Rd | 36 - man/is.SimulInactivation.Rd | 36 - man/isothermal_inactivation.Rd | 48 +- man/laterosporus_dyna.Rd | 48 +- man/laterosporus_iso.Rd | 48 +- man/plot.FitInactivation.Rd | 94 ++-- man/plot.FitInactivationMCMC.Rd | 94 ++-- man/plot.IsoFitInactivation.Rd | 48 +- man/plot.PredInactivationMCMC.Rd | 74 +-- man/plot.SimulInactivation.Rd | 92 ++-- man/predict_inactivation.Rd | 204 ++++----- man/predict_inactivation_MCMC.Rd | 104 ++-- man/sample_IsoFit.Rd | 76 +-- man/sample_MCMCfit.Rd | 66 +-- man/sample_dynaFit.Rd | 80 +-- man/summary.FitInactivation.Rd | 32 - man/summary.FitInactivationMCMC.Rd | 32 - man/summary.IsoFitInactivation.Rd | 32 - man/time_to_logreduction.Rd | 40 - tests/testthat.R | 120 ++--- 66 files changed, 3449 insertions(+), 3406 deletions(-)
More information about bioinactivation at CRAN
Permanent link
Title: Seasonal to Decadal Verification
Description: An advanced version of package 's2dverification'. Intended for
seasonal to decadal (s2d) climate forecast verification, but also applicable
to other types of forecasts or general climate analysis. This package is
specifically designed for comparing experimental and observational datasets.
It provides functionality for data retrieval, post-processing, skill score
computation against observations, and visualization. Compared to
's2dverification', 's2dv' is more compatible with the package 'startR', able
to use multiple cores for computation and handle multi-dimensional arrays
with a higher flexibility. The Climate Data Operators (CDO) version used in
development is 1.9.8. Implements methods described in Wilks (2011)
<doi:10.1016/B978-0-12-385022-5.00008-7>, DelSole and Tippett
(2016) <doi:10.1175/MWR-D-15-0218.1>, Kharin et al. (2012)
<doi:10.1029/2012GL052647>, Doblas-Reyes et al. (2003)
<doi:10.1007/s00382-003-0350-4>.
Author: BSC-CNS [aut, cph],
An-Chi Ho [aut],
Nuria Perez-Zanon [aut],
Roberto Bilbao [ctb],
Josep Cos [ctb],
Carlos Delgado [ctb],
Llorenc Lledo [ctb],
Andrea Manrique [ctb],
Deborah Verfaillie [ctb],
Eva Rifa [ctb],
Victoria Agudetse [ctb],
Nadia Milders [c [...truncated...]
Maintainer: Ariadna Batalla <ariadna.batalla@bsc.es>
Diff between s2dv versions 2.2.0 dated 2025-09-25 and 2.2.1 dated 2025-11-03
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 5 +++++ R/AnimateMap.R | 6 ++++-- R/ColorBar.R | 5 ++--- R/Plot2VarsVsLTime.R | 3 ++- R/PlotACC.R | 3 ++- R/PlotAno.R | 4 ++-- R/PlotBoxWhisker.R | 2 +- R/PlotClim.R | 3 ++- R/PlotEquiMap.R | 2 +- R/PlotLayout.R | 2 +- R/PlotMatrix.R | 2 +- R/PlotSection.R | 2 +- R/PlotStereoMap.R | 2 +- R/PlotVsLTime.R | 3 ++- man/s2dv-package.Rd | 6 +++--- 17 files changed, 51 insertions(+), 41 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 0.2.5 dated 2025-09-05 and 0.2.6 dated 2025-11-03
NMsim-0.2.5/NMsim/R/NMreadSizes.R |only NMsim-0.2.5/NMsim/R/addBlocks.R |only NMsim-0.2.5/NMsim/R/dcastSe.R |only NMsim-0.2.5/NMsim/R/message_dt.R |only NMsim-0.2.5/NMsim/man/NMreadSizes.Rd |only NMsim-0.2.5/NMsim/man/addBlocks.Rd |only NMsim-0.2.5/NMsim/man/dcastSe.Rd |only NMsim-0.2.5/NMsim/man/message_dt.Rd |only NMsim-0.2.6/NMsim/DESCRIPTION | 10 NMsim-0.2.6/NMsim/MD5 | 120 +++++---- NMsim-0.2.6/NMsim/NAMESPACE | 9 NMsim-0.2.6/NMsim/NEWS.md | 36 ++ NMsim-0.2.6/NMsim/R/NMaddSamples.R | 3 NMsim-0.2.6/NMsim/R/NMctl.R | 32 +- NMsim-0.2.6/NMsim/R/NMextractText.R | 2 NMsim-0.2.6/NMsim/R/NMreadFilters.R |only NMsim-0.2.6/NMsim/R/NMreadInits.R | 124 ++++++++-- NMsim-0.2.6/NMsim/R/NMreadSimModTab.R | 26 +- NMsim-0.2.6/NMsim/R/NMsim.R | 2 NMsim-0.2.6/NMsim/R/NMsim_EBE.R | 93 ++++--- NMsim-0.2.6/NMsim/R/NMsim_NWPRI.R | 103 ++++++-- NMsim-0.2.6/NMsim/R/NMsim_VarCov.R | 65 +++-- NMsim-0.2.6/NMsim/R/NMsim_helpers.R | 11 NMsim-0.2.6/NMsim/R/NMwriteInits.R | 2 NMsim-0.2.6/NMsim/R/addParType.R | 6 NMsim-0.2.6/NMsim/R/deleteTmpDirs.R | 2 NMsim-0.2.6/NMsim/R/fnAppend.R | 8 NMsim-0.2.6/NMsim/R/forestSummarize.R | 24 - NMsim-0.2.6/NMsim/R/sampleCovs.R | 15 - NMsim-0.2.6/NMsim/R/samplePars_mvrnorm.R | 2 NMsim-0.2.6/NMsim/R/summary_NMsimRes.R | 6 NMsim-0.2.6/NMsim/README.md | 10 NMsim-0.2.6/NMsim/man/NMaddSamples.Rd | 3 NMsim-0.2.6/NMsim/man/NMreadFilters.Rd |only NMsim-0.2.6/NMsim/man/NMsim.Rd | 2 NMsim-0.2.6/NMsim/man/NMsim_NWPRI.Rd | 32 +- NMsim-0.2.6/NMsim/man/addSameBlocks.Rd |only NMsim-0.2.6/NMsim/man/as.NMctl.Rd | 1 NMsim-0.2.6/NMsim/man/readCtl.Rd | 1 NMsim-0.2.6/NMsim/man/sampleCovs.Rd | 13 - NMsim-0.2.6/NMsim/tests/simres |only NMsim-0.2.6/NMsim/tests/testOutput2 |only NMsim-0.2.6/NMsim/tests/testthat/simres/xgxr021_sd1_NMreadSim_MetaData.rds |only NMsim-0.2.6/NMsim/tests/testthat/simres/xgxr021_sd1_NMreadSim_ResultsData.fst |only NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd3_NWPRI |only NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd3_NWPRI_MetaData.rds |only NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail.lst | 2 NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |binary NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr032_VarCov_1/xgxr032_VarCov_1_1.mod | 34 +- NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr032_VarCov_1/xgxr032_VarCov_1_2.mod | 34 +- NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr032_VarCov_1_MetaData.rds |binary NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr057_NWPRI_04 |only NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr057_NWPRI_04_MetaData.rds |only NMsim-0.2.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr057_NWPRI_04_ResultsData.fst |only NMsim-0.2.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_01.rds |binary NMsim-0.2.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_01_OMEGAP.rds |binary NMsim-0.2.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_03.rds |binary NMsim-0.2.6/NMsim/tests/testthat/testReference/NMsim_VarCov_01a.rds |binary NMsim-0.2.6/NMsim/tests/testthat/testReference/NMsim_VarCov_01b.rds |binary NMsim-0.2.6/NMsim/tests/testthat/testReference/NMwriteFilters_01.rds |binary NMsim-0.2.6/NMsim/tests/testthat/testReference/sampleCovs_01.rds |only NMsim-0.2.6/NMsim/tests/testthat/test_NMreadSim.R | 42 +++ NMsim-0.2.6/NMsim/tests/testthat/test_NMsim_NWPRI.R | 1 NMsim-0.2.6/NMsim/tests/testthat/test_NMsim_VarCov.R | 24 + NMsim-0.2.6/NMsim/tests/testthat/test_NMwriteFilters.R | 5 NMsim-0.2.6/NMsim/tests/testthat/test_sampleCovs.R |only NMsim-0.2.6/NMsim/tests/testthat/test_sampleParsSimpar.R | 2 NMsim-0.2.6/NMsim/tests/testthat/test_simplePath.R | 3 68 files changed, 623 insertions(+), 287 deletions(-)
Title: 'DataSHIELD' Interface
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This package defines the API that is to be implemented by 'DataSHIELD' compliant
data repositories.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
Tim Cadman [ctb] ,
Paul Burton [ctb]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between DSI versions 1.7.1 dated 2024-11-03 and 1.8.0 dated 2025-11-03
DESCRIPTION | 24 +++---- MD5 | 76 ++++++++++++----------- NAMESPACE | 6 + R/DSConnection.R | 73 ++++++++++++++++++---- R/DSSession.R |only R/datashield.aggregate.R | 1 R/datashield.assign.R | 3 R/datashield.login.R | 147 +++++---------------------------------------- R/datashield.sessions.R |only R/datashield.symbol.R | 1 R/datashield.workspace.R | 2 README.md | 2 man/DSConnection-class.Rd | 7 +- man/DSDriver-class.Rd | 3 man/DSObject-class.Rd | 3 man/DSResult-class.Rd | 3 man/DSSession-class.Rd |only man/datashield.sessions.Rd |only man/dsAggregate.Rd | 7 +- man/dsAssignExpr.Rd | 7 +- man/dsAssignResource.Rd | 7 +- man/dsAssignTable.Rd | 7 +- man/dsDisconnect.Rd | 4 - man/dsGetInfo.Rd | 4 - man/dsHasResource.Rd | 7 +- man/dsHasSession.Rd |only man/dsHasTable.Rd | 7 +- man/dsIsAsync.Rd | 9 ++ man/dsIsReady.Rd |only man/dsKeepAlive.Rd | 4 - man/dsListMethods.Rd | 4 - man/dsListPackages.Rd | 4 - man/dsListProfiles.Rd | 7 +- man/dsListResources.Rd | 7 +- man/dsListSymbols.Rd | 7 +- man/dsListTables.Rd | 4 - man/dsListWorkspaces.Rd | 4 - man/dsRestoreWorkspace.Rd | 4 - man/dsRmSymbol.Rd | 4 - man/dsRmWorkspace.Rd | 4 - man/dsSaveWorkspace.Rd | 4 - man/dsSession.Rd |only man/dsStateMessage.Rd |only 43 files changed, 255 insertions(+), 212 deletions(-)
Title: Convert Rd to 'Roxygen' Documentation
Description: Functions to convert Rd to 'roxygen' documentation. It can parse an
Rd file to a list, create the 'roxygen' documentation and update the original
R script (e.g. the one containing the definition of the function)
accordingly. This package also provides utilities that can help developers
build packages using 'roxygen' more easily. The 'formatR' package can be used
to reformat the R code in the examples sections so that the code will be
more readable.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between Rd2roxygen versions 1.16 dated 2024-04-15 and 1.17 dated 2025-11-03
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/Rd2roxygen-package.R | 2 +- R/utils.R | 3 +++ build/vignette.rds |binary inst/doc/Rd2roxygen.R | 30 +++++++++++++++--------------- inst/doc/Rd2roxygen.html | 28 +++++++++++++++------------- 8 files changed, 50 insertions(+), 41 deletions(-)
Title: Genomic Prediction of Hybrid Performance with Graphical User
Interface
Description: Performs genomic prediction of hybrid performance using eight GS methods including GBLUP, BayesB, RKHS, PLS, LASSO, Elastic net, XGBoost and LightGBM.
GBLUP: genomic best liner unbiased prediction, RKHS: reproducing kernel Hilbert space, PLS: partial least squares regression, LASSO: least absolute shrinkage and selection operator, XGBoost: extreme gradient boosting, LightGBM: light gradient boosting machine.
It also provides fast cross-validation and mating design scheme for training population (Xu S et al (2016) <doi:10.1111/tpj.13242>; Xu S (2017) <doi:10.1534/g3.116.038059>).
A complete manual for this package is provided in the manual folder of the package installation directory.
You can locate the manual by running the following command in R: system.file("manual", package = "predhy.GUI").
Author: Yang Xu [aut],
Guangning Yu [aut],
Yuxiang Zhang [aut, cre],
Yanru Cui [ctb],
Shizhong Xu [ctb],
Chenwu Xu [ctb]
Maintainer: Yuxiang Zhang <yuxiangzhang_99@foxmail.com>
Diff between predhy.GUI versions 2.1 dated 2025-04-14 and 2.1.1 dated 2025-11-03
DESCRIPTION | 8 +++++--- MD5 | 6 +++--- R/predhy.GUI.R | 17 ++++++++++++++++- inst/manual/Introduction.pdf |binary 4 files changed, 24 insertions(+), 7 deletions(-)
Title: Get Data from the Swiss Federal Statistical Office
Description: Search and download data from the Swiss Federal Statistical Office (BFS) APIs <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre, cph] ,
Marius Hodel [ctb] ,
Janosch Brenzel-Weiss [ctb],
Joao Martins [ctb],
Philipp Baumann [ctb]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between BFS versions 0.6.0 dated 2025-06-09 and 0.7.0 dated 2025-11-03
DESCRIPTION | 13 - MD5 | 22 +- NAMESPACE | 3 R/BFS-package.R |only R/bfs_get_sse_data.R |only R/bfs_get_sse_metadata.R |only R/bfs_search_catalog-DESKTOP-1S038UM.R |only R/bfs_sse_helpers.R |only R/globals.R | 3 README.md | 142 +++++++++++---- man/BFS-package.Rd |only man/bfs_get_sse_data.Rd |only man/bfs_get_sse_metadata.Rd |only man/bfs_get_sse_url.Rd |only man/get_xml_name.Rd |only tests/testthat/test-bfs_get_sse_data.R |only tests/testthat/test-bfs_get_sse_metadata.R |only tests/testthat/test-bfs_get_sse_url.R |only tests/testthat/test-bfs_search_catalog-DESKTOP-1S038UM.R |only 19 files changed, 143 insertions(+), 40 deletions(-)
Title: Conduct a Prospective or Retrospective Design Analysis
Description: An implementation of the "Design Analysis" proposed by
Gelman and Carlin (2014) <doi:10.1177/1745691614551642>. It combines
the evaluation of Power-Analysis with other inferential-risks as
Type-M error (i.e. Magnitude) and Type-S error (i.e. Sign). See also
Altoè et al. (2020) <doi:10.3389/fpsyg.2019.02893> and
Bertoldo et al. (2020) <doi:10.31234/osf.io/q9f86>.
Author: Claudio Zandonella Callegher [aut, cre] ,
Massimiliano Pastore [aut] ,
Angela Andreella [aut] ,
Anna Vesely [aut] ,
Enrico Toffalini [aut] ,
Giulia Bertoldo [aut] ,
Gianmarco Altoe [aut]
Maintainer: Claudio Zandonella Callegher <claudiozandonella@gmail.com>
Diff between PRDA versions 1.0.0 dated 2020-12-08 and 1.0.2 dated 2025-11-03
PRDA-1.0.0/PRDA/man/PRDA.Rd |only PRDA-1.0.2/PRDA/DESCRIPTION | 78 +-- PRDA-1.0.2/PRDA/MD5 | 44 - PRDA-1.0.2/PRDA/NEWS.md |only PRDA-1.0.2/PRDA/R/PRDA-package.R | 17 PRDA-1.0.2/PRDA/R/prospective.R | 6 PRDA-1.0.2/PRDA/R/retrospective.R | 6 PRDA-1.0.2/PRDA/README.md | 38 - PRDA-1.0.2/PRDA/build/partial.rdb |only PRDA-1.0.2/PRDA/build/vignette.rds |binary PRDA-1.0.2/PRDA/inst/CITATION | 2 PRDA-1.0.2/PRDA/inst/doc/PRDA.R | 16 PRDA-1.0.2/PRDA/inst/doc/PRDA.Rmd | 8 PRDA-1.0.2/PRDA/inst/doc/PRDA.html | 498 ++++++++++++++------ PRDA-1.0.2/PRDA/inst/doc/prospective.R | 34 - PRDA-1.0.2/PRDA/inst/doc/prospective.html | 627 ++++++++++++++++---------- PRDA-1.0.2/PRDA/inst/doc/retrospective.R | 36 - PRDA-1.0.2/PRDA/inst/doc/retrospective.html | 665 ++++++++++++++++++---------- PRDA-1.0.2/PRDA/man/PRDA-package.Rd |only PRDA-1.0.2/PRDA/man/prospective.Rd | 6 PRDA-1.0.2/PRDA/man/retrospective.Rd | 6 PRDA-1.0.2/PRDA/src/Makevars | 6 PRDA-1.0.2/PRDA/src/Makevars.win | 14 PRDA-1.0.2/PRDA/src/RcppExports.cpp | 5 PRDA-1.0.2/PRDA/vignettes/PRDA.Rmd | 8 25 files changed, 1347 insertions(+), 773 deletions(-)
Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative
maps. The package is a dependency for mvp-type
packages that use the STL map class: it traps
plausible idiom that is ill-defined (implementation-specific) and
returns an informative error, rather than returning a possibly
incorrect result. To cite the package in publications please use
Hankin (2022) <doi:10.48550/ARXIV.2210.03856>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between disordR versions 0.9-8-4 dated 2024-11-13 and 0.9-8-5 dated 2025-11-03
DESCRIPTION | 14 - MD5 | 18 - NAMESPACE | 60 ++++-- R/disordR.R | 426 +++++++++++++++++++++++++--------------------- R/experimental_disindex.R | 17 + build/vignette.rds |binary inst/doc/disindex.html | 17 - inst/doc/disordR.R | 6 inst/doc/disordR.html | 34 +-- man/misc.Rd | 1 10 files changed, 344 insertions(+), 249 deletions(-)
Title: Methods and Measures for Semantic Network Analysis
Description: Implements several functions for the analysis of semantic networks including different network estimation algorithms, partial node bootstrapping (Kenett, Anaki, & Faust, 2014 <doi:10.3389/fnhum.2014.00407>), random walk simulation (Kenett & Austerweil, 2016 <http://alab.psych.wisc.edu/papers/files/Kenett16CreativityRW.pdf>), and a function to compute global network measures. Significance tests and plotting features are also implemented.
Author: Alexander P. Christensen [aut, cre] ,
Yoed N. Kenett [aut, ctb]
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNeT versions 1.4.4 dated 2023-08-12 and 1.4.5 dated 2025-11-03
DESCRIPTION | 23 MD5 | 82 R/NRW.R | 296 +- R/SemNeTShiny.R | 102 - R/bootSemNeT.R | 985 ++++----- R/compare_nets.R | 455 ++-- R/convert2igraph.R | 76 R/response.analysis.R | 304 +-- R/test.bootSemNeT.R | 1002 +++++----- R/utils-SemNeT.R | 3708 ++++++++++++++++++------------------- R/utils-SemNeTShiny.R | 4669 +++++++++++++++++++++++------------------------ man/ASPL.Rd | 74 man/CC.Rd | 74 man/CN.Rd | 122 - man/NRW.Rd | 124 - man/PF.Rd | 78 man/Q.Rd | 72 man/SemNeT-package.Rd | 76 man/SemNeTShiny.Rd | 108 - man/TMFG.Rd | 142 - man/bootSemNeT.Rd | 285 +- man/compare_nets.Rd | 212 +- man/convert2cytoscape.Rd | 96 man/convert2igraph.Rd | 4 man/equate.Rd | 88 man/finalize.Rd | 68 man/net.high.Rd | 48 man/net.low.Rd | 48 man/open.binary.Rd | 50 man/open.clean.Rd | 50 man/open.group.Rd | 50 man/plot.animateShiny.Rd | 88 man/plot.bootSemNeT.Rd | 78 man/plot.compareShiny.Rd | 141 - man/randnet.test.Rd | 110 - man/randwalk.Rd | 134 - man/response.analysis.Rd | 94 man/semnetmeas.Rd | 92 man/sim.fluency.Rd | 82 man/similarity.Rd | 150 - man/test.bootSemNeT.Rd | 304 +-- man/vignette.plots.Rd | 48 42 files changed, 7439 insertions(+), 7453 deletions(-)
Title: Detection and Control of Tree-Ring Widths on Scanned Image
Sections
Description: Identification of ring borders on scanned image sections from dendrochronological samples. Processing of image reflectances to produce gray matrices and time series of smoothed gray values. Luminance data is plotted on segmented images for users to perform both: visual identification of ring borders or control of automatic detection. Routines to visually include/exclude ring borders on the R graphical devices, or automatically detect ring borders using a linear detection algorithm. This algorithm detects ring borders according to positive/negative extreme values in the smoothed time-series of gray values. Most of the in-package routines can be recursively implemented using the multiDetect() function.
Author: Wilson Lara [aut, cre] ,
Carlos Sierra [aut] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between measuRing versions 0.5.1 dated 2025-03-27 and 0.5.2 dated 2025-11-03
DESCRIPTION | 14 +++++++------- MD5 | 38 +++++++++++++++++++------------------- NEWS | 6 ++++++ R/dataSegments.R | 9 ++++++++- build/partial.rdb |binary man/colNarrow.Rd | 2 +- man/crossRings.Rd | 2 +- man/dataSegments.Rd | 2 +- man/grayDarker.Rd | 2 +- man/graySmoothed.Rd | 2 +- man/imageTogray.Rd | 2 +- man/lagIngray.Rd | 2 +- man/linearDetect.Rd | 2 +- man/multiDetect.Rd | 2 +- man/plotSegments.Rd | 2 +- man/reduceList.Rd | 2 +- man/ringBorders.Rd | 2 +- man/ringDetect.Rd | 2 +- man/ringSelect.Rd | 2 +- man/ringWidths.Rd | 2 +- 20 files changed, 55 insertions(+), 42 deletions(-)
Title: Lipid Annotation for LC-MS/MS DDA or DIA Data
Description: Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.
Author: M Isabel Alcoriza-Balaguer [aut, cre],
Celia Regal-Marques [aut]
Maintainer: M Isabel Alcoriza-Balaguer <maribel_alcoriza@iislafe.es>
Diff between LipidMS versions 3.1.0 dated 2025-10-27 and 3.1.1 dated 2025-11-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/LipidMS.R | 6 +----- README.md | 10 ++-------- 4 files changed, 9 insertions(+), 19 deletions(-)
Title: 'Schwab API' Interface
Description: Use R to interface with the 'Charles Schwab Trade API' <https://developer.schwab.com/>.
Functions include authentication, trading, price requests, account information, and option
chains. A user will need a Schwab brokerage account and Schwab Individual Developer app. See README
for authentication process and examples.
Author: Anthony Trevisan [aut, cre]
Maintainer: Anthony Trevisan <anthonytrevisan@gmail.com>
Diff between schwabr versions 0.1.3 dated 2025-02-24 and 0.1.4 dated 2025-11-03
DESCRIPTION | 6 - MD5 | 19 ++--- NAMESPACE | 1 NEWS.md | 7 + R/orders.R | 142 ++++++++++++++++++++++++++++++++++---- R/other.R | 22 ++++- README.md | 2 man/schwab_optionChain.Rd | 12 ++- man/schwab_placeOrder.Rd | 12 +++ man/schwab_replaceOrder.Rd |only tests/testthat/test-testOutputs.R | 3 11 files changed, 191 insertions(+), 35 deletions(-)
Title: Graph Community Detection Methods into Systematic Conservation
Planning
Description: An innovative tool-set that incorporates graph community detection
methods into systematic conservation planning. It is designed to
enhance spatial prioritization by focusing on the protection of
areas with high ecological connectivity. Unlike traditional
approaches that prioritize individual planning units, 'priorCON'
focuses on clusters of features that exhibit strong ecological
linkages. The 'priorCON' package is built upon the 'prioritizr'
package <doi:10.32614/CRAN.package.prioritizr>, using commercial
and open-source exact algorithm solvers that ensure optimal
solutions to prioritization problems.
Author: Christos Adam [aut, cre] ,
Aggeliki Doxa [aut] ,
Nikolaos Nagkoulis [aut] ,
Maria Papazekou [aut] ,
Antonios D. Mazaris [aut] ,
Stelios Katsanevakis [aut]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between priorCON versions 0.1.6 dated 2025-08-19 and 0.1.7 dated 2025-11-03
DESCRIPTION | 6 +- MD5 | 24 ++++----- NAMESPACE | 2 NEWS.md | 8 +++ R/functions_connect.R | 112 +++++++++++++++++++++++++++++++------------ README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.html | 5 + man/basic_scenario.Rd | 2 man/connectivity_scenario.Rd | 2 man/get_outputs.Rd | 13 +++- man/preprocess_graphs.Rd | 11 ++-- 13 files changed, 126 insertions(+), 61 deletions(-)
Title: Similarity and Distance Quantification Between Probability
Functions
Description: Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.
Author: Hajk-Georg Drost [aut, cre] ,
Jakub Nowosad [ctb] ,
Andrew Brown [ctb]
Maintainer: Hajk-Georg Drost <hajk-georg.drost@tuebingen.mpg.de>
Diff between philentropy versions 0.9.0 dated 2024-11-12 and 0.10.0 dated 2025-11-03
DESCRIPTION | 33 MD5 | 148 NAMESPACE | 1 NEWS.md | 14 R/RcppExports.R | 151 R/distance.R | 798 -- R/lin.cor.R | 23 R/utils.R | 3 README.md | 569 - build/vignette.rds |binary inst/doc/Distances.html | 5 inst/doc/Information_Theory.html | 5 inst/doc/Introduction.Rmd | 2 inst/doc/Introduction.html | 4 inst/doc/Many_Distances.R | 12 inst/doc/Many_Distances.Rmd | 24 inst/doc/Many_Distances.html |10323 ++++++++++++++++++++++++++++++++++- man/additive_symm_chi_sq.Rd | 2 man/avg.Rd | 2 man/bhattacharyya.Rd | 2 man/canberra.Rd | 2 man/chebyshev.Rd | 2 man/clark_sq.Rd | 2 man/cosine_dist.Rd | 2 man/czekanowski.Rd | 2 man/dice_dist.Rd | 2 man/dist_many_many.Rd | 15 man/dist_one_many.Rd | 23 man/dist_one_one.Rd | 2 man/distance.Rd | 11 man/divergence_sq.Rd | 2 man/euclidean.Rd | 2 man/fidelity.Rd | 2 man/gower.Rd | 2 man/harmonic_mean_dist.Rd | 2 man/hellinger.Rd | 2 man/inner_product.Rd | 2 man/intersection_dist.Rd | 2 man/jaccard.Rd | 2 man/jeffreys.Rd | 2 man/jensen_difference.Rd | 2 man/jensen_shannon.Rd | 2 man/k_divergence.Rd | 2 man/kulczynski_d.Rd | 2 man/kullback_leibler_distance.Rd | 2 man/kumar_hassebrook.Rd | 2 man/kumar_johnson.Rd | 2 man/lin.cor.Rd | 15 man/lorentzian.Rd | 2 man/manhattan.Rd | 2 man/matusita.Rd | 2 man/minkowski.Rd | 2 man/motyka.Rd | 2 man/neyman_chi_sq.Rd | 2 man/pearson_chi_sq.Rd | 2 man/prob_symm_chi_sq.Rd | 2 man/ruzicka.Rd | 2 man/soergel.Rd | 2 man/sorensen.Rd | 2 man/squared_chi_sq.Rd | 2 man/squared_chord.Rd | 2 man/squared_euclidean.Rd | 2 man/taneja.Rd | 2 man/tanimoto.Rd | 2 man/topsoe.Rd | 2 man/wave_hedges.Rd | 2 src/RcppExports.cpp | 124 src/dist_dispatch.h |only src/dist_matrix.cpp | 523 - src/distances.h | 2075 ------- src/distances_internal.h |only src/utils.h | 31 tests/testthat/test-dist-euclidean.R | 2 tests/testthat/test-distances.R | 81 vignettes/Introduction.Rmd | 2 vignettes/Many_Distances.Rmd | 24 76 files changed, 11430 insertions(+), 3701 deletions(-)
Title: Data Simulation Based on Latent Factors
Description: Generates data based on latent factor models. Data can be continuous, polytomous, dichotomous, or mixed. Skews, cross-loadings, wording effects, population errors, and local dependencies can be added. All parameters can be manipulated. Data categorization is based on Garrido, Abad, and Ponsoda (2011) <doi:10.1177/0013164410389489>.
Author: Alexander Christensen [aut, cre] ,
Luis Eduardo Garrido [aut] ,
Maria Dolores Nieto Canaveras [aut],
Hudson Golino [aut] ,
Marcos Jimenez [aut],
Francisco Abad [ctb],
Eduardo Garcia-Garzon [ctb],
Vithor Franco [aut]
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Diff between latentFactoR versions 0.0.6 dated 2024-04-18 and 0.0.7 dated 2025-11-03
DESCRIPTION | 21 MD5 | 18 NEWS | 57 +- R/ESEM.R | 4 R/NEST.R | 137 ++--- R/add_population_error.R | 56 +- R/simulation_helpers.R | 178 +++--- R/utils-latentFactoR.R | 1199 +++++++++++++++++++++++--------------------- man/ESEM.Rd | 2 man/add_population_error.Rd | 4 10 files changed, 900 insertions(+), 776 deletions(-)
More information about vaccinationimpact at CRAN
Permanent link
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
NNG is a socket library for reliable, high-performance messaging over
in-process, IPC, TCP, WebSocket and secure TLS transports. Implements
'Scalability Protocols', a standard for common communications patterns
including publish/subscribe, request/reply and service discovery. As
its own threaded concurrency framework, provides a toolkit for
asynchronous programming and distributed computing. Intuitive 'aio'
objects resolve automatically when asynchronous operations complete,
and synchronisation primitives allow R to wait upon events signalled
by concurrent threads.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.7.1 dated 2025-10-01 and 1.7.2 dated 2025-11-03
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 7 +++++++ R/aio.R | 2 +- R/sync.R | 4 +++- R/utils.R | 10 +++------- README.md | 9 ++++----- inst/doc/nanonext.html | 2 +- man/parse_url.Rd | 10 +++------- man/pipe_notify.Rd | 4 +++- man/unresolved.Rd | 2 +- src/comms.c | 18 ++++++++---------- src/nanonext.h | 1 + src/sync.c | 47 ++++++++++++++++++++--------------------------- src/thread.c | 12 ++++++++---- src/utils.c | 21 +++++++++------------ tests/tests.R | 2 +- 17 files changed, 92 insertions(+), 97 deletions(-)
Title: Lightweight Framework for Orchestrating Multi-Agent Large
Language Models
Description: Provides tools for creating agents with persistent state using
R6 classes <https://cran.r-project.org/package=R6> and the 'ellmer'
package <https://cran.r-project.org/package=ellmer>. Tracks prompts,
messages, and agent metadata for reproducible, multi-turn large language
model sessions.
Author: Mohamed El Fodil Ihaddaden [aut, cre]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between mini007 versions 0.2.0 dated 2025-10-29 and 0.2.1 dated 2025-11-03
DESCRIPTION | 10 MD5 | 18 NAMESPACE | 1 NEWS.md | 4 R/Agent.R | 12 R/LeadAgent.R | 20 + README.md | 545 +++++++++++++++++++++--------- man/Agent.Rd | 2 man/LeadAgent.Rd | 2 man/figures/README-unnamed-chunk-21-1.png |only tests |only 11 files changed, 447 insertions(+), 167 deletions(-)
Title: Joint Species Distribution Models
Description: Fits joint species distribution models ('jSDM') in a
hierarchical Bayesian framework (Warton and al. 2015
<doi:10.1016/j.tree.2015.09.007>). The Gibbs sampler is written in
'C++'. It uses 'Rcpp', 'Armadillo' and 'GSL' to maximize
computation efficiency.
Author: Ghislain Vieilledent [aut, cre] ,
Jeanne Clement [aut] ,
Frederic Gosselin [ctb] ,
CIRAD [cph, fnd]
Maintainer: Ghislain Vieilledent <ghislain.vieilledent@cirad.fr>
Diff between jSDM versions 0.2.6 dated 2023-07-22 and 0.2.7 dated 2025-11-03
DESCRIPTION | 48 MD5 | 32 NEWS.md | 22 R/get_residual_cor.R | 74 R/jSDM_binomial_probit_long_format.R | 2 README.md | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/jSDM.R | 3 inst/doc/jSDM.Rmd | 7 inst/doc/jSDM.html | 2488 ++++++++++++++++++++++---------- inst/doc/proof.Rmd | 4 inst/doc/proof.html | 2384 +++++++++++++++++++++--------- man/jSDM_binomial_probit_long_format.Rd | 2 src/Rcpp_jSDM_useful.cpp | 16 vignettes/jSDM.Rmd | 7 vignettes/proof.Rmd | 4 17 files changed, 3542 insertions(+), 1556 deletions(-)
Title: Property-Based Testing
Description: Hedgehog will eat all your bugs.
'Hedgehog' is a property-based testing package in the spirit
of 'QuickCheck'. With 'Hedgehog', one can test properties
of their programs against randomly generated input, providing
far superior test coverage compared to unit testing. One of the
key benefits of 'Hedgehog' is integrated shrinking of
counterexamples, which allows one to quickly find the cause of
bugs, given salient examples when incorrect behaviour occurs.
Author: Huw Campbell [aut, cre]
Maintainer: Huw Campbell <huw.campbell@gmail.com>
Diff between hedgehog versions 0.1 dated 2018-08-22 and 0.2 dated 2025-11-03
DESCRIPTION | 12 MD5 | 44 - NAMESPACE | 2 R/gen.R | 6 R/property.R | 2 R/state.R | 2 R/testthat.R | 12 R/tree.R | 50 +- build/vignette.rds |binary inst/doc/hedgehog.R | 22 inst/doc/hedgehog.Rmd | 4 inst/doc/hedgehog.html | 891 ++++++++++++++++++++++++++++++++++++---- inst/doc/state-machines.R | 24 - inst/doc/state-machines.Rmd | 4 inst/doc/state-machines.html | 953 ++++++++++++++++++++++++++++++++++++------- man/command.Rd | 11 man/forall.Rd | 10 man/hedgehog.Rd | 1 man/tree.Rd | 1 man/tree.replicate.Rd | 9 vignettes/hedgehog-logo.png |binary vignettes/hedgehog.Rmd | 4 vignettes/state-machines.Rmd | 4 23 files changed, 1747 insertions(+), 321 deletions(-)
Title: Clustering with Compositional Data
Description: Cluster analysis with compositional data using the alpha--transformation. Relevant papers include: Tsagris M. and Kontemeniotis N. (2025), <doi:10.48550/arXiv.2509.05945>. Tsagris M.T., Preston S. and Wood A.T.A. (2011), <doi:10.48550/arXiv.1106.1451>. Garcia-Escudero Luis A., Gordaliza Alfonso, Matran Carlos, Mayo-Iscar Agustin. (2008), <doi:10.1214/07-AOS515>.
Author: Michail Tsagris [aut, cre],
Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalClust versions 1.1 dated 2025-09-24 and 1.2 dated 2025-11-03
DESCRIPTION | 12 ++++++------ MD5 | 14 ++++++++++---- NAMESPACE | 3 ++- R/alfa.R |only R/alfa.kmeans.R |only R/clust.plot.R |only R/index_max.R | 8 +++++--- man/CompositionalClust-package.Rd | 4 ++-- man/alfa.Rd |only man/alfa.kmeans.Rd |only man/clust.plot.Rd |only 11 files changed, 25 insertions(+), 16 deletions(-)
More information about CompositionalClust at CRAN
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Title: Easily Build, Simulate, and Visualise Stock-and-Flow Models
Description: Stock-and-flow models are a computational method from the field of
system dynamics. They represent how systems change over time and are
mathematically equivalent to ordinary differential equations. 'sdbuildR'
(system dynamics builder) provides an intuitive interface for constructing
stock-and-flow models without requiring extensive domain knowledge. Models
can quickly be simulated and revised, supporting iterative development.
'sdbuildR' simulates models in 'R' and 'Julia', where 'Julia' offers unit
support and large-scale ensemble simulations. Additionally, 'sdbuildR' can
import models created in 'Insight Maker' (<https://insightmaker.com/>).
Author: Kyra Caitlin Evers [aut, cre, cph]
Maintainer: Kyra Caitlin Evers <kyra.c.evers@gmail.com>
Diff between sdbuildR versions 1.0.5 dated 2025-10-29 and 1.0.7 dated 2025-11-03
DESCRIPTION | 6 - MD5 | 24 +++--- NEWS.md | 8 ++ R/assemble_script_julia.R | 42 ++++++----- R/globals.R | 1 R/julia_setup.R | 103 ++++++++-------------------- R/simulate.R | 22 ++--- R/template.R | 4 - README.md | 6 + inst/Project.toml | 54 +++++++------- man/julia_status.Rd | 1 tests/testthat/test-assemble_script_julia.R | 1 tests/testthat/test-use_julia.R | 2 13 files changed, 124 insertions(+), 150 deletions(-)
More information about MannWhitneyCopula at CRAN
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Title: Estimation of Environmental Variables and Genetic Parameters
Description: Performs analyzes and estimates of environmental covariates
and genetic parameters related to selection strategies and development
of superior genotypes. It has two main functionalities, the first being
about prediction models of covariates and environmental processes, while
the second deals with the estimation of genetic parameters and selection
strategies. Designed for researchers and professionals in genetics and
environmental sciences, the package combines statistical methods
for modeling and data analysis. This includes the plastochron estimate
proposed by Porta et al. (2024) <doi:10.1590/1807-1929/agriambi.v28n10e278299>,
Stress indices for genotype selection referenced by Ghazvini et al. (2024)
<doi:10.1007/s10343-024-00981-1>, the Environmental Stress Index described by
Tazzo et al. (2024) <https://revistas.ufg.br/vet/article/view/77035>,
industrial quality indices of wheat genotypes (Szareski et al., 2019),
<doi:10.4238/gmr18223>, Ear Indexes estimation [...truncated...]
Author: Willyan Junior Adorian Bandeira [aut, cre] ,
Ivan Ricardo Carvalho [aut, ctb] ,
Murilo Vieira Loro [aut, ctb] ,
Leonardo Cesar Pradebon [aut, ctb] ,
Jose Antonio Gonzalez da Silva [aut, ctb]
Maintainer: Willyan Junior Adorian Bandeira <bandeira.wjab@gmail.com>
This is a re-admission after prior archival of version 1.0.1 dated 2025-04-17
Diff between EstimateBreed versions 1.0.1 dated 2025-04-17 and 1.0.2 dated 2025-11-03
DESCRIPTION | 33 +++++++++++++++++---------------- MD5 | 14 +++++++------- NAMESPACE | 1 - R/zzz.R | 1 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/EnvironmentalAnalysis.html | 11 ++++++----- inst/doc/SelectionAnalysis.html | 9 +++++---- 8 files changed, 35 insertions(+), 34 deletions(-)
Title: Quality Assessment for Seasonal Adjustment
Description: Add-in to the 'RJDemetra' package on seasonal adjustments.
It allows to produce dashboards to summarise models and quickly check the quality of the seasonal adjustment.
Author: Alain Quartier-la-Tente [aut, cre]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between rjdqa versions 0.1.5 dated 2024-06-15 and 0.1.6 dated 2025-11-03
DESCRIPTION | 18 +- MD5 | 31 ++-- NAMESPACE | 2 NEWS.md | 13 + R/autoplot.R |only R/sc_d_moving_holiday.R | 134 +++---------------- R/sc_d_net_effects.R | 296 ++----------------------------------------- R/sc_d_recent_history.R | 3 R/sc_d_seasonal.R | 28 ++-- R/sc_d_summary_diagnostics.R | 141 +++++--------------- R/sc_d_trading_day.R | 136 ++----------------- R/sc_dashboard.R | 25 --- R/simple_dashboard.R | 107 +++++++++++---- R/simple_dashboard2.R | 130 +----------------- README.md | 10 - man/plot.simple_dashboard.Rd | 12 - man/simple_dashboard.Rd | 15 +- 17 files changed, 269 insertions(+), 832 deletions(-)
Title: Correction Factors for Tree Plot Areas Intersected by Stand
Boundaries
Description: The German national forest inventory uses angle count sampling,
a sampling method first published as `Bitterlich, W.: Die Winkelzählmessung.
Allgemeine Forst- und Holzwirtschaftliche Zeitung, 58. Jahrg., Folge 11/12
vom Juni 1947` and extended by Grosenbaugh
(<https://academic.oup.com/jof/article-abstract/50/1/32/4684174>)
as probability proportional to size sampling.
When plots are located near stand boundaries, their sizes and hence
their probabilities need to be corrected.
Author: Andreas Dominik Cullmann [aut, cre],
Bernhard Boesch [ctb],
Christoph Fischer [ctb],
Gerald Kaendler [ctb]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between treePlotArea versions 2.1.0 dated 2024-04-04 and 3.0.0 dated 2025-11-03
DESCRIPTION | 8 +- MD5 | 16 ++--- NEWS.md | 8 ++ R/plot_tree_plot_area.R | 83 +++++++++++++++------------ build/vignette.rds |binary inst/NEWS.rd | 12 +++ inst/doc/An_Introduction_to_treePlotArea.pdf |binary inst/tinytest/test_plot.R | 4 - man/plot_tree_plot_area.Rd | 26 ++++++-- 9 files changed, 103 insertions(+), 54 deletions(-)
Title: Automated Reporting of Results and Statistical Models
Description: The aim of the 'report' package is to bridge the gap between
R’s output and the formatted results contained in your manuscript.
This package converts statistical models and data frames into textual
reports suited for publication, ensuring standardization and quality
in results reporting.
Author: Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut, cre] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Rudolf Siegel [ctb] ,
Camden Bock [ctb]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Diff between report versions 0.6.1 dated 2025-02-07 and 0.6.2 dated 2025-11-03
DESCRIPTION | 42 - MD5 | 206 ++++--- NEWS.md | 14 R/cite_easystats.R | 161 +++--- R/format_algorithm.R | 32 - R/format_model.R | 69 +- R/report.BFBayesFactor.R | 12 R/report.MixMod.R | 10 R/report.aov.R | 131 ++--- R/report.bayesfactor_models.R | 6 R/report.brmsfit.R | 278 +++++++++- R/report.character.R | 63 +- R/report.compare_performance.R | 52 +- R/report.data.frame.R | 105 ++-- R/report.estimate_contrasts.R | 17 R/report.factor.R | 28 - R/report.glmmTMB.R | 10 R/report.htest.R | 111 ++-- R/report.lavaan.R | 26 - R/report.lm.R | 520 ++++++++++++++------ R/report.lme.R | 10 R/report.lme4.R | 10 R/report.numeric.R | 108 +--- R/report.sessionInfo.R | 44 - R/report.stanreg.R | 66 +- R/report.test_performance.R | 51 + R/report_effectsize.R | 60 +- R/report_htest_chi2.R | 46 - R/report_htest_cor.R | 30 - R/report_htest_fisher.R | 40 - R/report_htest_friedman.R | 96 ++- R/report_htest_kruskal.R | 103 +++ R/report_htest_ttest.R | 26 - R/report_htest_wilcox.R | 16 R/report_info.R | 57 +- R/report_intercept.R | 25 R/report_misc.R | 12 R/report_parameters.R | 148 ++++- R/report_performance.R | 44 - R/report_sample.R | 32 - R/report_table.R | 30 - R/utils_combine_tables.R | 40 - R/utils_grouped_df.R | 23 README.md | 2 build/vignette.rds |binary inst/CITATION | 5 inst/WORDLIST | 8 inst/doc/cite_packages.html | 13 inst/doc/report.R | 12 inst/doc/report.Rmd | 4 inst/doc/report.html | 294 +++++------ inst/doc/report_table.html | 5 man/cite_easystats.Rd | 28 - man/format_formula.Rd | 6 man/report.BFBayesFactor.Rd | 2 man/report.aov.Rd | 9 man/report.bayesfactor_models.Rd | 2 man/report.brmsfit.Rd | 19 man/report.compare.loo.Rd | 2 man/report.compare_performance.Rd | 3 man/report.data.frame.Rd | 2 man/report.estimate_contrasts.Rd | 2 man/report.htest.Rd | 5 man/report.lavaan.Rd | 5 man/report.lm.Rd | 5 man/report.stanreg.Rd | 2 man/report.test_performance.Rd | 3 man/report_effectsize.Rd | 4 man/report_info.Rd | 4 man/report_intercept.Rd | 4 man/report_model.Rd | 4 man/report_parameters.Rd | 4 man/report_performance.Rd | 6 man/report_priors.Rd | 2 man/report_random.Rd | 6 man/report_statistics.Rd | 4 man/report_table.Rd | 6 man/report_text.Rd | 4 tests/testthat/_snaps/windows/report.brmsfit.md |only tests/testthat/_snaps/windows/report.data.frame.md | 12 tests/testthat/_snaps/windows/report.lavaan.md | 2 tests/testthat/_snaps/windows/report.lm.md | 2 tests/testthat/setup-00-toolchain.R |only tests/testthat/test-brms-performance-fix.R |only tests/testthat/test-cite_easystats.R |only tests/testthat/test-coverage-MixMod.R |only tests/testthat/test-coverage-brmsfit.R |only tests/testthat/test-coverage-compare-loo.R |only tests/testthat/test-coverage-glmmTMB.R |only tests/testthat/test-format_algorithm_formula.R |only tests/testthat/test-format_citation.R |only tests/testthat/test-glmmtmb-duplication-fix.R |only tests/testthat/test-issue-481-glmmtmb-duplication.R |only tests/testthat/test-report.BFBayesFactor.R |only tests/testthat/test-report.MixMod.R |only tests/testthat/test-report.bayesfactor_models.R | 47 + tests/testthat/test-report.brmsfit.R | 60 ++ tests/testthat/test-report.compare.loo.R |only tests/testthat/test-report.compare_performance.R |only tests/testthat/test-report.data.frame.R | 5 tests/testthat/test-report.estimate_contrasts.R |only tests/testthat/test-report.glmmTMB.R |only tests/testthat/test-report.htest-correlation.R | 31 - tests/testthat/test-report.lavaan.R | 1 tests/testthat/test-report.lm.R | 20 tests/testthat/test-report.lme.R |only tests/testthat/test-report.lmer.R | 1 tests/testthat/test-report.numeric.R |only tests/testthat/test-report.stanreg.R | 1 tests/testthat/test-report.survreg.R | 5 tests/testthat/test-report.test_performance.R |only tests/testthat/test-report_basic_methods.R |only tests/testthat/test-report_info_misc_text.R |only tests/testthat/test-report_stats_params.R |only tests/testthat/test-report_table.R |only tests/testthat/test-utils_helpers.R |only vignettes/report.Rmd | 4 117 files changed, 2295 insertions(+), 1392 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.9 dated 2025-09-29 and 2.2.11 dated 2025-11-03
copBasic-2.2.11/copBasic/DESCRIPTION | 8 ++++---- copBasic-2.2.11/copBasic/MD5 | 17 +++++++++-------- copBasic-2.2.11/copBasic/NAMESPACE | 3 ++- copBasic-2.2.11/copBasic/NEWS | 12 ++++++++++++ copBasic-2.2.11/copBasic/R/JOMAcop.R |only copBasic-2.2.11/copBasic/R/derCOP.R | 15 +++++++++++++++ copBasic-2.2.11/copBasic/build/partial.rdb |binary copBasic-2.2.11/copBasic/man/JOMAcop.Rd |only copBasic-2.2.11/copBasic/man/copBasic-package.Rd | 3 ++- copBasic-2.2.11/copBasic/man/lcomCOP.Rd | 2 +- copBasic-2.2.9/copBasic/man/LCOMDIA_GHcop.Rd |only 11 files changed, 45 insertions(+), 15 deletions(-)