Title: Network Reverse Engineering with Approximate Bayesian
Computation
Description: We developed an inference tool based on approximate Bayesian computation to decipher network data and assess the strength of the inferred links between network's actors. It is a new multi-level approximate Bayesian computation (ABC) approach. At the first level, the method captures the global properties of the network, such as a scale-free structure and clustering coefficients, whereas the second level is targeted to capture local properties, including the probability of each couple of genes being linked. Up to now, Approximate Bayesian Computation (ABC) algorithms have been scarcely used in that setting and, due to the computational overhead, their application was limited to a small number of genes. On the contrary, our algorithm was made to cope with that issue and has low computational cost. It can be used, for instance, for elucidating gene regulatory network, which is an important step towards understanding the normal cell physiology and complex pathological phenotype. Reverse-eng [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Khadija Musayeva [ctb],
Nicolas Jung [ctb],
Universite de Strasbourg [cph],
CNRS [cph]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between networkABC versions 0.9-0 dated 2025-08-28 and 0.9-1 dated 2025-09-19
DESCRIPTION | 16 ++++++++-------- MD5 | 42 +++++++++++++++++++++--------------------- NEWS.md | 5 +++++ README.md | 5 ++++- inst/CITATION | 4 +++- inst/doc/vignette.html | 8 ++++---- man/networkABC-package.Rd | 4 ++-- src/R_init_networkABC.c | 2 +- src/abc_R.c | 2 +- src/abc_R.h | 2 +- src/graph.c | 2 +- src/graph.h | 2 +- src/graph_adjacency_list.h | 2 +- src/motif.c | 2 +- src/motif.h | 2 +- src/network.h | 2 +- src/network_random_R.c | 2 +- src/network_random_R.h | 2 +- src/pool.c | 2 +- src/pool.h | 2 +- src/utils.c | 2 +- src/utils.h | 2 +- 22 files changed, 62 insertions(+), 52 deletions(-)
Title: Classification Models with Copula Functions
Description: Provides several classifiers based on probabilistic models. These classifiers allow to model the dependence structure of continuous features through bivariate copula functions and graphical models, see Salinas-Gutiérrez et al. (2014) <doi:10.1007/s00180-013-0457-y>.
Author: Rogelio Salinas Gutierrez [aut, cre, cph] ,
Angelica Hernandez Quintero [aut, cph] ,
Pedro Abraham Montoya Calzada [aut, cph] ,
Carlos Alberto Lopez Hernandez [aut, cph] ,
Juan Manuel Marquez Romero [aut, cph]
Maintainer: Rogelio Salinas Gutierrez <rsalinas@correo.uaa.mx>
This is a re-admission after prior archival of version 1.0.1 dated 2024-10-23
Diff between MLCOPULA versions 1.0.1 dated 2024-10-23 and 1.1.0 dated 2025-09-19
DESCRIPTION | 28 +++---- MD5 | 42 +++++----- NAMESPACE | 22 +++-- R/aux_mi_report.R | 20 ++--- R/classification_report.R | 24 +++--- R/copulaClassifier.R | 5 + R/copulaPredict.R | 13 --- R/density_estimation.R | 24 ++++-- R/f_aux2.R | 32 ++++---- R/faux.R | 44 +++++------ R/join_marginal.R |only R/kernel_estimation.R | 18 +--- R/mi_gaussian.R | 10 +- R/mi_report.R | 20 ++--- R/norm_test.R |only R/normal_estimation.R | 7 - R/sfmx.R | 8 +- R/train_independent.R | 28 +++---- README.md | 166 +++++++++++++++++++++---------------------- build/partial.rdb |binary man/classification_report.Rd | 94 ++++++++++++------------ man/copulaClassifier.Rd | 154 +++++++++++++++++++-------------------- man/copulaPredict.Rd | 78 ++++++++++---------- 23 files changed, 420 insertions(+), 417 deletions(-)
Title: Multiple Imputation for Proteomics
Description: A framework for multiple imputation for proteomics is proposed by Marie Chion, Christine Carapito and Frederic Bertrand (2021) <doi:10.1371/journal.pcbi.1010420>. It is dedicated to dealing with multiple imputation for proteomics.
Author: Marie Chion [aut] ,
Christine Carapito [aut] ,
Frederic Bertrand [cre, aut] ,
Gordon Smyth [ctb],
Davis McCarthy [ctb],
Helene Borges [ctb],
Thomas Burger [ctb],
Quentin Giai-Gianetto [ctb],
Samuel Wieczorek [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between mi4p versions 1.2 dated 2024-10-02 and 1.3 dated 2025-09-19
DESCRIPTION | 28 ++++++++++++++++------------ MD5 | 27 +++++++++++++++++---------- NEWS.md | 6 ++++++ README.md | 37 ++++++++++--------------------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 +++++- inst/_pkgdown.yml |only inst/doc/Intromi4p.Rmd | 2 +- inst/doc/Intromi4p.html | 8 ++++---- man/mi4p-package.Rd | 2 +- tests |only vignettes/Intromi4p.Rmd | 2 +- 13 files changed, 61 insertions(+), 57 deletions(-)
Title: Database Queries Using 'data.table' Syntax
Description: Query database tables over a 'DBI' connection using 'data.table' syntax.
Attach database schemas to the search path. Automatically merge using foreign
key constraints.
Author: Kjell P. Konis [aut, cre],
Luis Rocha [ctb]
Maintainer: Kjell P. Konis <kjellk@gmail.com>
Diff between dbi.table versions 1.0.4 dated 2025-06-28 and 1.0.5 dated 2025-09-19
dbi.table-1.0.4/dbi.table/vignettes/introduction_to_dbi_table.md |only dbi.table-1.0.5/dbi.table/DESCRIPTION | 8 dbi.table-1.0.5/dbi.table/MD5 | 163 dbi.table-1.0.5/dbi.table/NAMESPACE | 186 dbi.table-1.0.5/dbi.table/NEWS.md | 60 dbi.table-1.0.5/dbi.table/R/DBI_methods.R | 1848 - dbi.table-1.0.5/dbi.table/R/as.data.table.R | 24 dbi.table-1.0.5/dbi.table/R/attach.R | 244 dbi.table-1.0.5/dbi.table/R/calls.R | 390 dbi.table-1.0.5/dbi.table/R/catalog.R | 354 dbi.table-1.0.5/dbi.table/R/connection.R | 118 dbi.table-1.0.5/dbi.table/R/cte.R | 158 dbi.table-1.0.5/dbi.table/R/dbi.table.R | 1612 dbi.table-1.0.5/dbi.table/R/examples.R | 162 dbi.table-1.0.5/dbi.table/R/extract.R | 710 dbi.table-1.0.5/dbi.table/R/merge.R | 848 dbi.table-1.0.5/dbi.table/R/onLoad.R | 74 dbi.table-1.0.5/dbi.table/R/reference.test.R | 176 dbi.table-1.0.5/dbi.table/R/relational.R | 266 dbi.table-1.0.5/dbi.table/R/s3_methods_duckdb.R | 144 dbi.table-1.0.5/dbi.table/R/s3_methods_mariadb.R | 102 dbi.table-1.0.5/dbi.table/R/s3_methods_postgres.R | 50 dbi.table-1.0.5/dbi.table/R/s3_methods_sql_server.R | 204 dbi.table-1.0.5/dbi.table/R/s3_methods_sqlite.R | 56 dbi.table-1.0.5/dbi.table/R/specials.R | 216 dbi.table-1.0.5/dbi.table/R/sql.join.R | 450 dbi.table-1.0.5/dbi.table/R/sql_statement.R | 10 dbi.table-1.0.5/dbi.table/R/sql_translation.R | 42 dbi.table-1.0.5/dbi.table/R/tables_schema.R | 146 dbi.table-1.0.5/dbi.table/R/utilities.R | 370 dbi.table-1.0.5/dbi.table/R/write_sql.R | 372 dbi.table-1.0.5/dbi.table/build/vignette.rds |binary dbi.table-1.0.5/dbi.table/inst/doc/introduction_to_dbi_table.R | 252 dbi.table-1.0.5/dbi.table/inst/doc/introduction_to_dbi_table.Rmd | 756 dbi.table-1.0.5/dbi.table/inst/doc/introduction_to_dbi_table.html | 1703 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/LICENSE | 40 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/album.csv | 696 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/artist.csv | 552 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/customer.csv | 120 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/employee.csv | 18 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/genre.csv | 52 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/invoice.csv | 826 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/invoiceline.csv | 4482 +- dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/mediatype.csv | 12 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/playlist.csv | 38 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/playlisttrack.csv |17432 +++++----- dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/schema.sql | 56 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/track.csv | 7008 ++-- dbi.table-1.0.5/dbi.table/inst/sql_statements/foreign_keys_postgres.sql | 106 dbi.table-1.0.5/dbi.table/inst/sql_statements/foreign_keys_sqlite.sql | 4 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_Microsoft_SQL_Server.sql | 64 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_default.sql | 4 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_duckdb.sql | 44 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_mariadb.sql | 52 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_postgres.sql | 60 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_sqlite.sql | 24 dbi.table-1.0.5/dbi.table/man/DBI-methods.Rd | 454 dbi.table-1.0.5/dbi.table/man/as.data.frame.Rd | 114 dbi.table-1.0.5/dbi.table/man/as.dbi.table.Rd | 102 dbi.table-1.0.5/dbi.table/man/csql.Rd | 46 dbi.table-1.0.5/dbi.table/man/dbi.attach.Rd | 94 dbi.table-1.0.5/dbi.table/man/dbi.catalog.Rd | 66 dbi.table-1.0.5/dbi.table/man/dbi.table-package.Rd | 386 dbi.table-1.0.5/dbi.table/man/example_databases.Rd | 40 dbi.table-1.0.5/dbi.table/man/merge.Rd | 240 dbi.table-1.0.5/dbi.table/man/reference.test.Rd | 120 dbi.table-1.0.5/dbi.table/man/sql.join.Rd | 92 dbi.table-1.0.5/dbi.table/tests/testthat.R | 24 dbi.table-1.0.5/dbi.table/tests/testthat/setup.R | 68 dbi.table-1.0.5/dbi.table/tests/testthat/test-DBI-methods.R | 560 dbi.table-1.0.5/dbi.table/tests/testthat/test-as.dbi.table.R | 94 dbi.table-1.0.5/dbi.table/tests/testthat/test-assumptions.R | 42 dbi.table-1.0.5/dbi.table/tests/testthat/test-attach.R | 98 dbi.table-1.0.5/dbi.table/tests/testthat/test-data.table-examples.R | 684 dbi.table-1.0.5/dbi.table/tests/testthat/test-data.table-set-functions.R | 42 dbi.table-1.0.5/dbi.table/tests/testthat/test-dbi.catalog.R | 30 dbi.table-1.0.5/dbi.table/tests/testthat/test-dbi.table.R | 352 dbi.table-1.0.5/dbi.table/tests/testthat/test-mariadb.R | 74 dbi.table-1.0.5/dbi.table/tests/testthat/test-merge.R | 478 dbi.table-1.0.5/dbi.table/tests/testthat/test-postgres.R | 34 dbi.table-1.0.5/dbi.table/tests/testthat/test-relational.R | 180 dbi.table-1.0.5/dbi.table/tests/testthat/test-sql.join.R | 128 dbi.table-1.0.5/dbi.table/vignettes/introduction_to_dbi_table.Rmd | 756 83 files changed, 24686 insertions(+), 24676 deletions(-)
Title: Simulation-Based Inference for Regression Models
Description: Performs simulation-based inference as an alternative to the delta method for obtaining valid confidence intervals and p-values for regression post-estimation quantities, such as average marginal effects and predictions at representative values. This framework for simulation-based inference is especially useful when the resulting quantity is not normally distributed and the delta method approximation fails. The methodology is described in Greifer, et al. (2025) <doi:10.32614/RJ-2024-015>. 'clarify' is meant to replace some of the functionality of the archived package 'Zelig'; see the vignette "Translating Zelig to clarify" for replicating this functionality.
Author: Noah Greifer [aut, cre] ,
Steven Worthington [aut] ,
Stefano Iacus [aut] ,
Gary King [aut]
Maintainer: Noah Greifer <ngreifer@iq.harvard.edu>
Diff between clarify versions 0.2.1 dated 2024-05-30 and 0.2.2 dated 2025-09-19
clarify-0.2.1/clarify/inst/doc/Zelig.R |only clarify-0.2.1/clarify/inst/doc/clarify.R |only clarify-0.2.1/clarify/tests/testthat/helper.R |only clarify-0.2.2/clarify/DESCRIPTION | 35 clarify-0.2.2/clarify/MD5 | 100 clarify-0.2.2/clarify/NAMESPACE | 2 clarify-0.2.2/clarify/NEWS.md | 23 clarify-0.2.2/clarify/R/checks.R | 163 - clarify-0.2.2/clarify/R/clarify-package.R | 5 clarify-0.2.2/clarify/R/clarify_est_methods.R | 80 clarify-0.2.2/clarify/R/clarify_predict.R | 70 clarify-0.2.2/clarify/R/get_model_components.R | 38 clarify-0.2.2/clarify/R/misim.R | 88 clarify-0.2.2/clarify/R/plot.clarify_adrf.R | 75 clarify-0.2.2/clarify/R/plot.clarify_est.R | 42 clarify-0.2.2/clarify/R/plot.clarify_setx.R | 157 - clarify-0.2.2/clarify/R/sim.R | 116 clarify-0.2.2/clarify/R/sim_adrf.R | 144 - clarify-0.2.2/clarify/R/sim_ame.R | 264 + clarify-0.2.2/clarify/R/sim_apply.R | 113 clarify-0.2.2/clarify/R/sim_setx.R | 171 - clarify-0.2.2/clarify/R/summary.clarify_est.R | 144 - clarify-0.2.2/clarify/R/transform.clarify_est.R | 78 clarify-0.2.2/clarify/R/utils.R | 401 ++ clarify-0.2.2/clarify/README.md | 204 - clarify-0.2.2/clarify/build/partial.rdb |binary clarify-0.2.2/clarify/build/vignette.rds |binary clarify-0.2.2/clarify/inst/CITATION |only clarify-0.2.2/clarify/inst/doc/Zelig.Rmd | 2 clarify-0.2.2/clarify/inst/doc/Zelig.html | 49 clarify-0.2.2/clarify/inst/doc/clarify.Rmd | 397 +- clarify-0.2.2/clarify/inst/doc/clarify.html | 1380 ++++++---- clarify-0.2.2/clarify/man/clarify-package.Rd | 5 clarify-0.2.2/clarify/man/figures/README-example-1.png |binary clarify-0.2.2/clarify/man/figures/README-example2-1.png |binary clarify-0.2.2/clarify/man/figures/README-unnamed-chunk-6-1.png |binary clarify-0.2.2/clarify/man/misim.Rd | 2 clarify-0.2.2/clarify/man/plot.clarify_adrf.Rd | 8 clarify-0.2.2/clarify/man/plot.clarify_setx.Rd | 4 clarify-0.2.2/clarify/man/sim.Rd | 11 clarify-0.2.2/clarify/man/sim_adrf.Rd | 26 clarify-0.2.2/clarify/man/sim_ame.Rd | 42 clarify-0.2.2/clarify/man/sim_apply.Rd | 42 clarify-0.2.2/clarify/man/sim_setx.Rd | 38 clarify-0.2.2/clarify/man/summary.clarify_est.Rd | 31 clarify-0.2.2/clarify/man/transform.clarify_est.Rd | 6 clarify-0.2.2/clarify/tests/testthat/helpers.R |only clarify-0.2.2/clarify/tests/testthat/setup.R |only clarify-0.2.2/clarify/tests/testthat/test-misim.R | 14 clarify-0.2.2/clarify/tests/testthat/test-sim.R | 5 clarify-0.2.2/clarify/tests/testthat/test-sim_ame.R | 569 +++- clarify-0.2.2/clarify/vignettes/Zelig.Rmd | 2 clarify-0.2.2/clarify/vignettes/clarify.Rmd | 397 +- clarify-0.2.2/clarify/vignettes/references.bib | 303 ++ 54 files changed, 3701 insertions(+), 2145 deletions(-)
Title: A Cepstral Model for Covariate-Dependent Time Series
Description: Modeling associations between covariates and power spectra of replicated time series using a cepstral-based semiparametric framework. Implements a fast two-stage estimation procedure via Whittle likelihood and multivariate regression.The methodology is based on Li and Dong (2025) <doi:10.1080/10618600.2025.2473936>.
Author: Qi Xia [aut, cre],
Zeda Li [aut, ctb]
Maintainer: Qi Xia <xiaqi1010@gmail.com>
Diff between CepReg versions 0.1.0 dated 2025-09-10 and 0.1.2 dated 2025-09-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/cepstral.R | 30 ++++++++++++++++-------------- man/CepReg.Rd | 14 ++++++-------- man/boot_effect.Rd | 12 ++++++++---- man/env_get.Rd | 4 ++-- 6 files changed, 40 insertions(+), 36 deletions(-)
Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2021) <doi:10.1016/j.insmatheco.2020.11.010> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] ,
Sander Devriendt [aut],
Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens.r@gmail.com>
Diff between smurf versions 1.1.7 dated 2025-02-23 and 1.1.8 dated 2025-09-19
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/smurf.html | 4 ++-- src/Makevars | 2 +- src/Makevars.win | 2 +- 8 files changed, 25 insertions(+), 17 deletions(-)
Title: Motion Trajectory Analysis
Description: Methods for analyzing (cell) motion in two or three dimensions.
Available measures include displacement, confinement ratio, autocorrelation,
straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks,
steps, or subtracks with varying length. While the methodology has been developed for
cell trajectory analysis, it is applicable to anything that moves including animals,
people, or vehicles.
Some of the methodology implemented in this packages was described by:
Beauchemin, Dixit, and Perelson (2007) <doi:10.4049/jimmunol.178.9.5505>,
Beltman, Maree, and de Boer (2009) <doi:10.1038/nri2638>,
Gneiting and Schlather (2004) <doi:10.1137/S0036144501394387>,
Mokhtari, Mech, Zitzmann, Hasenberg, Gunzer, and Figge (2013) <doi:10.1371/journal.pone.0080808>,
Moreau, Lemaitre, Terriac, Azar, Piel, Lennon-Dumenil, and Bousso (2012) <doi:10.1016/j.immuni.2012.05.014>,
Textor, Peixoto, Henrickson, Sinn, von Andrian, and Westermann (2011) [...truncated...]
Author: Johannes Textor [aut, cre],
Katharina Dannenberg [aut],
Jeffrey Berry [aut],
Gerhard Burger [aut],
Annie Liu [aut],
Mark Miller [aut],
Inge Wortel [aut]
Maintainer: Johannes Textor <johannes.textor@gmx.de>
Diff between celltrackR versions 1.2.1 dated 2024-08-26 and 1.2.2 dated 2025-09-19
DESCRIPTION | 8 ++-- MD5 | 26 +++++++-------- NEWS.md | 6 +++ build/vignette.rds |binary inst/doc/QC.Rmd | 2 - inst/doc/QC.html | 11 +++--- inst/doc/ana-methods.R | 2 - inst/doc/ana-methods.html | 9 +++-- inst/doc/clustering.html | 11 +++--- inst/doc/data-QC.R | 56 +++++++++++++++++----------------- inst/doc/data-QC.html | 9 +++-- inst/doc/reading-converting-data.html | 9 +++-- inst/doc/simulation.html | 9 +++-- vignettes/QC.Rmd | 2 - 14 files changed, 86 insertions(+), 74 deletions(-)
Title: Iterative Extrapolation of Species' Haplotype Accumulation
Curves for Genetic Diversity Assessment
Description: Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide [...truncated...]
Author: Jarrett D. Phillips [aut, cre],
Steven H. French [ctb],
Navdeep Singh [ctb]
Maintainer: Jarrett D. Phillips <phillipsjarrett1@gmail.com>
Diff between HACSim versions 1.0.6-1 dated 2022-06-13 and 1.0.7-1 dated 2025-09-19
HACSim-1.0.6-1/HACSim/R/launchApp.R |only HACSim-1.0.6-1/HACSim/inst |only HACSim-1.0.6-1/HACSim/man/launchApp.Rd |only HACSim-1.0.7-1/HACSim/DESCRIPTION | 25 ++++++++++++++------ HACSim-1.0.7-1/HACSim/MD5 | 38 +++++++------------------------ HACSim-1.0.7-1/HACSim/NAMESPACE | 6 +++- HACSim-1.0.7-1/HACSim/R/HAC.sim.R | 3 +- HACSim-1.0.7-1/HACSim/R/sim.seqs.R | 2 - HACSim-1.0.7-1/HACSim/R/zzz.R | 2 - HACSim-1.0.7-1/HACSim/build/partial.rdb |binary HACSim-1.0.7-1/HACSim/src/Makevars | 4 --- HACSim-1.0.7-1/HACSim/src/Makevars.win | 1 HACSim-1.0.7-1/HACSim/src/accumulate.cpp | 21 +++++++++-------- 13 files changed, 48 insertions(+), 54 deletions(-)
Title: Import and Process Data from the 'Lattes' Curriculum Platform
Description: Tool for import and process data from 'Lattes' curriculum platform (<http://lattes.cnpq.br/>). The Brazilian government keeps an extensive base of curricula for academics from all over the country, with over 5 million registrations. The academic life of the Brazilian researcher, or related to Brazilian universities, is documented in 'Lattes'. Some information that can be obtained: professional formation, research area, publications, academics advisories, projects, etc. 'getLattes' package allows work with 'Lattes' data exported to XML format.
Author: Roney Fraga Souza [aut, cre, cph] ,
Winicius Sabino [aut],
Luis Felipe de Souza Rodrigues [aut]
Maintainer: Roney Fraga Souza <roneyfraga@gmail.com>
Diff between getLattes versions 0.2.0 dated 2021-06-11 and 1.0.0 dated 2025-09-19
getLattes-0.2.0/getLattes/man/figures/README-pressure-1.png |only getLattes-1.0.0/getLattes/DESCRIPTION | 38 getLattes-1.0.0/getLattes/MD5 | 28 getLattes-1.0.0/getLattes/NAMESPACE | 3 getLattes-1.0.0/getLattes/NEWS.md | 6 getLattes-1.0.0/getLattes/R/getArtigosAceitos.R |only getLattes-1.0.0/getLattes/R/getTrabalhoEmEventos.R |only getLattes-1.0.0/getLattes/R/writePublicationsRis.R |only getLattes-1.0.0/getLattes/README.md | 56 getLattes-1.0.0/getLattes/build/vignette.rds |binary getLattes-1.0.0/getLattes/inst/CITATION | 35 getLattes-1.0.0/getLattes/inst/doc/introduction_getLattes.R | 127 - getLattes-1.0.0/getLattes/inst/doc/introduction_getLattes.Rmd | 84 - getLattes-1.0.0/getLattes/inst/doc/introduction_getLattes.html | 819 ++++++---- getLattes-1.0.0/getLattes/man/figures/logo.png |only getLattes-1.0.0/getLattes/man/getArtigosAceitos.Rd |only getLattes-1.0.0/getLattes/man/getTrabalhosEmEventos.Rd |only getLattes-1.0.0/getLattes/man/writePublicationsRis.Rd |only getLattes-1.0.0/getLattes/vignettes/introduction_getLattes.Rmd | 84 - 19 files changed, 873 insertions(+), 407 deletions(-)
Title: Tables of Descriptive Statistics in HTML
Description: Create HTML tables of descriptive statistics, as one would expect
to see as the first table (i.e. "Table 1") in a medical/epidemiological journal
article.
Author: Benjamin Rich [aut, cre, cph]
Maintainer: Benjamin Rich <mail@benjaminrich.net>
Diff between table1 versions 1.5.0 dated 2025-09-12 and 1.5.1 dated 2025-09-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/table1.R | 2 +- inst/doc/table1-examples.html | 4 ++-- inst/doc/table1-latex.pdf |binary inst/doc/table1-weighted.html | 4 ++-- 7 files changed, 19 insertions(+), 15 deletions(-)
Title: User-Friendly 'shiny' App for Bayesian Species Distribution
Models
Description: A user-friendly 'shiny' application for Bayesian machine
learning analysis of marine species distributions. GLOSSA (Global
Ocean Species Spatio-temporal Analysis) uses Bayesian Additive
Regression Trees (BART; Chipman, George, and McCulloch (2010)
<doi:10.1214/09-AOAS285>) to model species distributions with
intuitive workflows for data upload, processing, model fitting, and
result visualization. It supports presence-absence and presence-only
data (with pseudo-absence generation), spatial thinning,
cross-validation, and scenario-based projections. GLOSSA is designed
to facilitate ecological research by providing easy-to-use tools for
analyzing and visualizing marine species distributions across
different spatial and temporal scales. Optionally, pseudo-absences can
be generated within the environmental space using the external package
'flexsdm' (not on CRAN), which can be downloaded from
<https://github.com/sjevelazco/flexsdm>; this functionality is used
conditionally when a [...truncated...]
Author: Jorge Mestre-Tomas [aut, cre] ,
Alba Fuster-Alonso [aut]
Maintainer: Jorge Mestre-Tomas <jorge.mestre.tomas@csic.es>
Diff between glossa versions 1.2.3 dated 2025-08-27 and 1.2.4 dated 2025-09-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/glossa_analysis.R | 5 +++-- R/read_validate_files.R | 34 ++++++++++++++++++++++++---------- man/read_layers_zip.Rd | 5 ++++- 6 files changed, 47 insertions(+), 21 deletions(-)
Title: R Wrapper for 'pikchr' (PIC) Diagram Language
Description: An 'R' interface to 'pikchr' (<https://pikchr.org>, pronounced “picture”), a 'PIC'-like markup language for creating diagrams within technical documentation. Originally developed by Brian Kernighan, 'PIC' has been adapted into 'pikchr' by D. Richard Hipp, the creator of 'SQLite'. 'pikchr' is designed to be embedded in fenced code blocks of Markdown or other documentation markup languages, making it ideal for generating diagrams in text-based formats. This package allows R users to seamlessly integrate the descriptive syntax of 'pikchr' for diagram creation directly within the 'R' environment.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Richard Hipp [ctb],
Brian Kernighan [ctb]
Maintainer: Andre Leite <leite@castlab.org>
Diff between pikchr versions 1.0.1 dated 2025-03-31 and 1.0.3 dated 2025-09-19
DESCRIPTION | 10 +-- MD5 | 14 ++-- NEWS.md | 12 +++ R/engine.R | 108 +++++++++++++++++++++++++++------- R/pikchrWrappers.R | 34 ++++++---- build/vignette.rds |binary inst/doc/Examples.html | 152 +------------------------------------------------ src/pikchr.c | 10 +-- 8 files changed, 141 insertions(+), 199 deletions(-)
Title: Multivariable Fractional Polynomials
Description: Multivariable Fractional Polynomial algorithm for model-building. Fractional polynomials are used to represent curvature in regression models. A key reference is Royston and Altman, 1994.
Author: Georg Heinze [cre],
Gareth Ambler [aut],
Axel Benner [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>
Diff between mfp versions 1.5.4.1 dated 2024-05-14 and 1.5.5.1 dated 2025-09-19
DESCRIPTION | 12 MD5 | 23 NEWS.md | 4 R/predict.mfp.R | 10 build/vignette.rds |binary data/GBSG.rda |binary data/bodyfat.rda |binary inst/doc/mfp_vignette.R | 94 +- inst/doc/mfp_vignette.html | 1655 ++++++++++++++++++++++----------------------- man/bodyfat.Rd | 2 man/mfp.Rd | 2 man/predict.mfp.Rd | 11 vignettes/jointfp_model.R |only 13 files changed, 908 insertions(+), 905 deletions(-)
Title: Event Classification, Visualization and Analysis of Eye Tracking
Data
Description: Functions for analysing eye tracking data, including event detection, visualizations and area of interest (AOI) based analyses.
The package includes implementations of the IV-T, I-DT, adaptive velocity threshold, and Identification by two means clustering (I2MC) algorithms.
See separate documentation for each function. The principles underlying I-VT and I-DT algorithms are described in Salvucci & Goldberg (2000,\doi{10.1145/355017.355028}).
Two-means clustering is described in Hessels et al. (2017, \doi{10.3758/s13428-016-0822-1}).
The adaptive velocity threshold algorithm is described in Nyström & Holmqvist (2010,\doi{10.3758/BRM.42.1.188}).
See a demonstration in the URL.
Author: Johan Lundin Kleberg [aut, cre]
Maintainer: Johan Lundin Kleberg <johan.lundin.kleberg@su.se>
Diff between kollaR versions 1.1.0 dated 2025-05-07 and 1.1.2 dated 2025-09-19
DESCRIPTION | 6 +-- MD5 | 24 ++++++++------- R/FixationFilterFunctions.R | 32 ++++++++++++++------ R/PreprocessingFunctions.R | 68 +++++++++++++++++++++++++++++++++++++++++--- R/VisualizationFunctions.R | 7 ++-- man/algorithm_adaptive.Rd | 3 + man/algorithm_ivt.Rd | 6 +++ man/calculate_rms.Rd |only man/ivt_filter.Rd | 3 + man/kollaR-package.Rd | 2 - man/movmean.filter.Rd |only man/plot_sample_velocity.Rd | 3 + man/preprocess_gaze.Rd | 5 ++- man/trim_fixations.Rd | 2 - 14 files changed, 127 insertions(+), 34 deletions(-)
Title: Analysis of Visual Meteor Data
Description: Provides a suite of analytical functionalities to process and analyze
visual meteor observations from the Visual Meteor Database
of the International Meteor Organization <https://www.imo.net/>.
Author: Janko Richter [aut, cre]
Maintainer: Janko Richter <janko@richtej.de>
Diff between vismeteor versions 2.0.0 dated 2025-09-07 and 2.0.1 dated 2025-09-19
DESCRIPTION | 8 - MD5 | 61 ++++++------ NEWS.md | 11 ++ R/data.R | 4 R/freq.R | 85 +++++++++-------- R/perception.R | 2 R/vmgeom.R | 13 +- R/vmgeom_vst.R | 36 ++++--- R/vmideal.R | 10 +- R/vmideal_vst.R | 55 ++++++----- README.md | 16 +++ inst/derivation/vmgeom_vst.R | 94 +++++++++++++++++++ inst/derivation/vmideal_vst.R | 116 ++++++++++++++++++++++- inst/derivation/vmperceptions.R | 94 +++++++++++++++++-- inst/doc/vismeteor.R | 10 ++ inst/doc/vismeteor.Rmd | 24 +++- inst/doc/vismeteor.html | 196 ++++++++++++++++++++-------------------- inst/doc/vmgeom.R | 2 inst/doc/vmgeom.Rmd | 2 inst/doc/vmgeom.html | 15 +-- inst/doc/vmideal.html | 11 +- man/PER_2015_magn.Rd | 3 man/PER_2015_rates.Rd | 5 - man/vmgeom.Rd | 3 man/vmgeomVst.Rd | 16 +++ man/vmideal.Rd | 10 +- man/vmidealVst.Rd | 18 +++ man/vmperception.Rd | 2 man/vmtable.Rd | 14 ++ tests/testthat/test_load_vmdb.R |only vignettes/vismeteor.Rmd | 24 +++- vignettes/vmgeom.Rmd | 2 32 files changed, 690 insertions(+), 272 deletions(-)
Title: Transmodal Analysis (TMA)
Description: A robust computational framework for analyzing complex multimodal data. Extends existing state-dependent models to account for diverse data streams, addressing challenges such as varying temporal scales and learner characteristics to improve the robustness and interpretability of findings. For methodological details, see Shaffer, Wang, and Ruis (2025) "Transmodal Analysis" <doi:10.18608/jla.2025.8423>.
Author: Cody L Marquart [aut, cre] ,
Muhammad Hasnat Ashiq [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between tma versions 0.3.0 dated 2025-08-25 and 0.3.1 dated 2025-09-19
DESCRIPTION | 10 +- MD5 | 41 ++++++---- NAMESPACE | 12 ++ NEWS.md | 11 ++ R/accum_multidim_c.R | 8 + R/qedata_classes.R |only R/temp_accum_multidim.R | 8 + R/utils.R | 14 +-- R/view.R | 5 + R/zzz.R | 15 +++ man/ATTR_NAMES.Rd |only man/accumulate.Rd | 4 man/adjacency_key.Rd |only man/as.qe.code.Rd |only man/as.qe.data.Rd |only man/as.qe.horizon.Rd |only man/as.qe.metadata.Rd |only man/as.qe.unit.Rd |only man/is.qe.code.Rd |only man/is.qe.data.Rd |only man/is.qe.horizon.Rd |only man/is.qe.metadata.Rd |only man/is.qe.unit.Rd |only src/Makevars | 2 src/code.cpp | 78 ++++++++++--------- tests/testthat/test-accum-multidim.R | 117 +++++++++++++++------------- tests/testthat/test-multidim-cpp.R | 123 ++++++++++++++++-------------- tests/testthat/test-simple-conversation.R | 33 ++++++-- 28 files changed, 297 insertions(+), 184 deletions(-)
Title: Robust and User-Friendly Analysis of Growth and Fluorescence
Curves
Description: High-throughput analysis of growth curves and fluorescence
data using three methods: linear regression, growth model fitting, and
smooth spline fit. Analysis of dose-response relationships via
smoothing splines or dose-response models. Complete data analysis
workflows can be executed in a single step via user-friendly wrapper
functions. The results of these workflows are summarized in detailed
reports as well as intuitively navigable 'R' data containers. A 'shiny'
application provides access to all features without
requiring any programming knowledge. The package is described in further
detail in Wirth et al. (2023) <doi:10.1038/s41596-023-00850-7>.
Author: Nicolas T. Wirth [aut, cre, cph] ,
Jonathan Funk [aut] ,
Matthias Kahm [ctb] ,
Maik Kschischo [ctb] ,
Thomas Petzoldt [ctb] ,
Andrew Stein [ctb] ,
Michael W. Kearney [ctb] ,
Santiago I. Hurtado [ctb] ,
Mark Heckmann [ctb] ,
Nicholas Hamilton [ctb] ,
[...truncated...]
Maintainer: Nicolas T. Wirth <mail.nicowirth@gmail.com>
Diff between QurvE versions 1.1.1 dated 2024-01-26 and 1.1.2 dated 2025-09-19
DESCRIPTION | 69 ++-- MD5 | 52 +-- NAMESPACE | 2 NEWS.md | 21 + R/data_parsers.R | 70 ++++ R/dose-response-analysis.R | 2 R/fluorescence_plots.R | 122 +++++-- R/fluorescence_workflows.R | 31 + R/group_tables.R | 24 + R/growth_plots.R | 600 ++++++++++++++++++++++-------------- R/growth_workflows.R | 36 +- R/utils.R | 10 build/partial.rdb |binary build/vignette.rds |binary inst/doc/shiny_app_manual.html | 14 inst/doc/vignette_fluorescence.html | 23 - inst/doc/vignette_growth.html | 31 + inst/shiny_app/app.R | 119 +++++-- man/big_palette.Rd |only man/fl.drFitModel.Rd | 2 man/flBootSpline.Rd | 4 man/growth.drFit.Rd | 2 man/growth.gcBootSpline.Rd | 2 man/growth.gcFitLinear.Rd | 2 man/growth.gcFitModel.Rd | 2 man/growth.gcFitSpline.Rd | 2 man/growth.workflow.Rd | 4 man/single_hue_palettes.Rd |only 28 files changed, 848 insertions(+), 398 deletions(-)
Title: Conducts Analyses Informing Ecosystem Restoration Decisions
Description: Three sets of data and functions for informing ecosystem restoration
decisions, particularly in the context of the U.S. Army Corps of Engineers.
First, model parameters are compiled as a data set and associated metadata
for over 300 habitat suitability models developed by the U.S. Fish and
Wildlife Service (USFWS 1980, <https://www.fws.gov/policy-library/870fw1>).
Second, functions for conducting habitat suitability analyses both for the
models described above as well as generic user-specified model parameterizations.
Third, a suite of decision support tools for conducting cost-effectiveness and
incremental cost analyses (Robinson et al. 1995, IWR Report 95-R-1, U.S.
Army Corps of Engineers).
Author: S. Kyle McKay [aut, cre] ,
Darixa D. Hernandez-Abrams [aut],
Kiara C. Cushway [aut]
Maintainer: S. Kyle McKay <skmckay@gmail.com>
Diff between ecorest versions 2.0.0 dated 2024-09-12 and 2.0.1 dated 2025-09-19
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- data/HSImetadata.RData |binary data/HSImodels.RData |binary man/HSImodels.Rd | 2 +- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Dynamic Models for Confidence and Response Time Distributions
Description: Provides density functions for the joint distribution of
choice, response time and confidence for discrete confidence judgments
as well as functions for parameter fitting, prediction and simulation
for various dynamical models of decision confidence. All models are
explained in detail by Hellmann et al. (2023;
Preprint available at <https://osf.io/9jfqr/>, published version: <doi:10.1037/rev0000411>). Implemented models are the dynaViTE model,
dynWEV model, the 2DSD model (Pleskac & Busemeyer, 2010, <doi:10.1037/a0019737>),
and various race models. C++ code for dynWEV and 2DSD is based on the
'rtdists' package by Henrik Singmann.
Author: Sebastian Hellmann [aut, cre] ,
Manuel Rausch [aut, fnd]
Maintainer: Sebastian Hellmann <sebastian.hellmann@tum.de>
Diff between dynConfiR versions 1.0.0 dated 2025-05-08 and 1.1.0 dated 2025-09-19
DESCRIPTION | 12 - MD5 | 85 ++++++----- NAMESPACE | 7 NEWS.md | 4 R/RaceModels.R | 11 - R/RcppExports.R | 8 + R/d2DSD.R | 2 R/dDDConf.R | 8 - R/dMTLNR.R |only R/dWEV.R | 10 - R/ddynaViTE.R | 10 - R/fitRTConf.R | 32 +++- R/fitRTConfModels.R | 14 + R/int_fill_thresholds.R | 2 R/int_find_start_thetas_MTLNR_simulation.R |only R/int_fitting_MTLNR.R |only R/int_fitting_RMs_simulate_start_thetas.R | 2 R/likelihood_MTLNR.R |only R/predictRTConf.R | 18 +- R/predictRTConfModels.R | 25 +-- R/predictratingdist_DDConf.R | 2 R/predictratingdist_MTLNR.R |only R/predictratingdist_RM.R | 2 R/predictratingdist_WEV.R | 2 R/rLCA.R | 11 - R/simulateConfModel.R | 15 + R/simulateMTLNR.R |only inst/doc/dynConfiR.html | 5 man/LogLikMTLNR.Rd |only man/MTLNR.Rd |only man/RaceModels.Rd | 11 - man/d2DSD.Rd | 2 man/dDDConf.Rd | 8 - man/dynaViTE.Rd | 20 +- man/fitRTConf.Rd | 20 ++ man/fitRTConfModels.Rd | 4 man/predictDDConf.Rd | 2 man/predictMTLNR.Rd |only man/predictRM.Rd | 2 man/predictRTConf.Rd | 14 - man/predictRTConfModels.Rd | 17 +- man/predictWEV.Rd | 2 man/rLCA.Rd | 11 - man/simulateMTLNR.Rd |only man/simulateRTConf.Rd | 13 - src/Density_MTLNR.h |only src/RcppExports.cpp | 31 ++++ src/SeqSampConf.cpp | 220 +++++++++++++++++++++++++++++ src/SeqSampConf.h | 1 49 files changed, 497 insertions(+), 168 deletions(-)
Title: Display Idiomatic Code to Construct Most R Objects
Description: Prints code that can be used to recreate R objects. In a
sense it is similar to 'base::dput()' or 'base::deparse()' but
'constructive' strives to use idiomatic constructors.
Author: Antoine Fabri [aut, cre],
Kirill Mueller [ctb] ,
Jacob Scott [ctb],
cynkra GmbH [fnd]
Maintainer: Antoine Fabri <antoine.fabri@gmail.com>
Diff between constructive versions 1.2.0 dated 2025-08-28 and 1.3.0 dated 2025-09-19
DESCRIPTION | 10 +++--- MD5 | 48 ++++++++++++++++--------------- NAMESPACE | 3 + NEWS.md | 14 ++++++++- R/C_wrappers.R | 6 +++ R/construct_idiomatic.R | 9 ++++- R/s3-externalptr.R | 8 ++++- R/s3-ggplot2-CoordCartesian.R | 5 +-- R/s3-xml_document.R |only R/templates.R | 2 + R/zzz.R | 2 + inst/doc/extend-constructive.html | 10 +++--- man/construct.Rd | 1 man/constructive-package.Rd | 2 - man/opts_xml_document.Rd |only src/constructive.cpp | 46 +++++++++-------------------- tests/testthat/_snaps/s3-data.table.md | 47 ++++++++++++++++-------------- tests/testthat/_snaps/s3-externalptr.md | 10 +----- tests/testthat/_snaps/s3-xml_document.md |only tests/testthat/_snaps/s3-xts.md | 13 +++----- tests/testthat/test-construct_diff.R | 2 - tests/testthat/test-s3-data.table.R | 44 ++++++++++++++-------------- tests/testthat/test-s3-externalptr.R | 4 +- tests/testthat/test-s3-xml_document.R |only tests/testthat/test-s7-S7_S3_class.R | 2 - tests/testthat/test-s7-S7_generic.R | 2 - tests/testthat/test-s7-S7_union.R | 2 - 27 files changed, 155 insertions(+), 137 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-24 0.0.9
Title: Tools to Use and Explore the 'BioTIME' Database
Description: The 'BioTIME' database was first published in
2018 and inspired ideas, questions, project and research
article. To make it even more accessible, an R package
was created.
The 'BioTIMEr' package provides tools designed to interact with the
'BioTIME' database. The functions provided include the 'BioTIME' recommended
methods for preparing (gridding and rarefaction) time series data, a
selection of standard biodiversity metrics (including species richness,
numerical abundance and exponential Shannon) alongside examples on how to
display change over time. It also includes a sample subset of both the query
and meta data, the full versions of which are freely available on the 'BioTIME'
website <https://biotime.st-andrews.ac.uk/home.php>.
Author: Alban Sagouis [aut, cre] ,
Faye Moyes [aut] ,
Ines S. Martins [aut, rev] ,
Shane A. Blowes [ctb] ,
Viviana Brambilla [ctb] ,
Cher F. Y. Chow [ctb] ,
Ada Fontrodona-Eslava [ctb] ,
Laura Antao [ctb, rev] ,
Jonathan M. Chase [fnd] ,
Maria Dornelas [fnd, [...truncated...]
Maintainer: Alban Sagouis <alban.sagouis@idiv.de>
Diff between BioTIMEr versions 0.2.4 dated 2025-06-06 and 0.2.5 dated 2025-09-19
DESCRIPTION | 8 MD5 | 24 NEWS.md | 4 README.md | 5 inst/doc/vignette1.html | 4 tests/testthat/_snaps/runResampling.md |32652 ++++++++++++++++++++++++++++++++- tests/testthat/test-gridding.R | 3 tests/testthat/test-metrics.R | 10 tests/testthat/test-runResampling.R | 80 tests/testthat/test-scales.R | 3 tests/testthat/test-slopes.R | 2 tests/testthat/test-workflow_alpha.R | 1 tests/testthat/test-workflow_beta.R | 1 13 files changed, 32719 insertions(+), 78 deletions(-)
Title: Manipulate ACLED Data
Description: Tools working with data from ACLED (Armed Conflict Location and Event Data). Functions include simplified access to ACLED's API (<https://apidocs.acleddata.com/>), methods for keeping local versions of ACLED data up-to-date, and functions for common ACLED data transformations.
Author: Armed Conflict Location and Event Data ACLED [cph],
Trey Billing [aut, cre],
Lucas Fagliano [aut],
Katayoun Kishi [ctb]
Maintainer: Trey Billing <t.billing@acleddata.com>
Diff between acledR versions 1.0.0 dated 2025-09-04 and 1.0.1 dated 2025-09-19
acledR-1.0.0/acledR/R/acled_access.R |only acledR-1.0.0/acledR/man/acled_access.Rd |only acledR-1.0.0/acledR/tests/testthat/setup-acled_access.R |only acledR-1.0.0/acledR/tests/testthat/test-acled_access.R |only acledR-1.0.1/acledR/DESCRIPTION | 6 acledR-1.0.1/acledR/MD5 | 34 - acledR-1.0.1/acledR/NAMESPACE | 1 acledR-1.0.1/acledR/NEWS.md | 5 acledR-1.0.1/acledR/R/acled_api.R | 209 +--------- acledR-1.0.1/acledR/R/acled_deletions_api.R | 162 ------- acledR-1.0.1/acledR/R/acled_update.R | 88 ---- acledR-1.0.1/acledR/man/acled_api.Rd | 15 acledR-1.0.1/acledR/man/acled_auth.Rd | 1 acledR-1.0.1/acledR/man/acled_deletions_api.Rd | 18 acledR-1.0.1/acledR/man/acled_update.Rd | 12 acledR-1.0.1/acledR/tests/testthat/setup-acled_api.R | 10 acledR-1.0.1/acledR/tests/testthat/setup-acled_deletions_api.R | 6 acledR-1.0.1/acledR/tests/testthat/test-acled_api.R | 59 +- acledR-1.0.1/acledR/tests/testthat/test-acled_deletions_api.R | 6 acledR-1.0.1/acledR/tests/testthat/test-acled_update.R | 12 20 files changed, 136 insertions(+), 508 deletions(-)
Title: Information Bottleneck Methods for Clustering Mixed-Type Data
Description: Implements multiple variants of the Information Bottleneck ('IB') method
for clustering datasets containing continuous, categorical (nominal/ordinal) and mixed-type variables.
The package provides deterministic, agglomerative, generalized,
and standard 'IB' clustering algorithms that preserve relevant information while
forming interpretable clusters. The Deterministic Information Bottleneck is described in
Costa et al. (2024) <doi:10.48550/arXiv.2407.03389>. The standard 'IB' method
originates from Tishby et al. (2000) <doi:10.48550/arXiv.physics/0004057>,
the agglomerative variant from Slonim and Tishby (1999) <https://papers.nips.cc/paper/1651-agglomerative-information-bottleneck>,
and the generalized 'IB' from Strouse and Schwab (2017) <doi:10.1162/NECO_a_00961>.
Author: Efthymios Costa [aut],
Ioanna Papatsouma [aut],
Angelos Markos [aut, cre]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between IBclust versions 1.2 dated 2025-07-10 and 1.2.1 dated 2025-09-19
IBclust-1.2.1/IBclust/DESCRIPTION | 15 + IBclust-1.2.1/IBclust/MD5 | 70 +++----- IBclust-1.2.1/IBclust/NAMESPACE | 13 + IBclust-1.2.1/IBclust/R/AIB.R | 8 - IBclust-1.2.1/IBclust/R/AIBmix.R | 137 +++++++++-------- IBclust-1.2.1/IBclust/R/DIBmix.R | 123 +++++++-------- IBclust-1.2.1/IBclust/R/DIBmix_iterate.R | 188 +++++++++++++++--------- IBclust-1.2.1/IBclust/R/GIBmix.R | 161 +++++++++----------- IBclust-1.2.1/IBclust/R/GIBmix_iterate.R | 192 +++++++++++++++--------- IBclust-1.2.1/IBclust/R/IBmix.R | 130 +++++++--------- IBclust-1.2.1/IBclust/R/IBmix_iterate.R | 186 +++++++++++++++-------- IBclust-1.2.1/IBclust/R/aibclust-class.R |only IBclust-1.2.1/IBclust/R/aibclust-methods.R |only IBclust-1.2.1/IBclust/R/bw_select.R | 147 ++++++++++++------ IBclust-1.2.1/IBclust/R/calc_metrics.R | 3 IBclust-1.2.1/IBclust/R/coord_to_pxy_R.R | 20 +- IBclust-1.2.1/IBclust/R/gibclust-class.R |only IBclust-1.2.1/IBclust/R/gibclust-methods.R |only IBclust-1.2.1/IBclust/R/input_checks.R |only IBclust-1.2.1/IBclust/README.md | 12 - IBclust-1.2.1/IBclust/build/partial.rdb |binary IBclust-1.2.1/IBclust/inst/CITATION | 4 IBclust-1.2.1/IBclust/inst/REFERENCES.bib | 30 +++ IBclust-1.2.1/IBclust/man/AIBmix.Rd | 167 +++++++++++++++++---- IBclust-1.2.1/IBclust/man/DIBmix.Rd | 226 ++++++++++++++++++++++------- IBclust-1.2.1/IBclust/man/GIBmix.Rd | 203 ++++++++++++++++++-------- IBclust-1.2.1/IBclust/man/IBmix.Rd | 192 ++++++++++++++++++------ IBclust-1.2.1/IBclust/man/figures/logo.png |binary IBclust-1.2.1/IBclust/src/Makevars.win | 4 IBclust-1.2.1/IBclust/src/qt_x_step.cpp | 5 IBclust-1.2/IBclust/LICENSE |only IBclust-1.2/IBclust/R/AIBcat.R |only IBclust-1.2/IBclust/R/AIBcont.R |only IBclust-1.2/IBclust/R/DIBcat.R |only IBclust-1.2/IBclust/R/DIBcont.R |only IBclust-1.2/IBclust/R/GIBcat.R |only IBclust-1.2/IBclust/R/GIBcont.R |only IBclust-1.2/IBclust/R/IBcat.R |only IBclust-1.2/IBclust/R/IBcont.R |only IBclust-1.2/IBclust/man/AIBcat.Rd |only IBclust-1.2/IBclust/man/AIBcont.Rd |only IBclust-1.2/IBclust/man/DIBcat.Rd |only IBclust-1.2/IBclust/man/DIBcont.Rd |only IBclust-1.2/IBclust/man/GIBcat.Rd |only IBclust-1.2/IBclust/man/GIBcont.Rd |only IBclust-1.2/IBclust/man/IBcat.Rd |only IBclust-1.2/IBclust/man/IBcont.Rd |only 47 files changed, 1435 insertions(+), 801 deletions(-)
Title: Dynamic Model Averaging
Description: Dynamic model averaging for binary and continuous
outcomes.
Author: Tyler H. McCormick [aut],
Adrian Raftery [aut],
David Madigan [aut],
Sevvandi Kandanaarachchi [ctb, aut],
Hana Sevcikova [ctb, aut, cre]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between dma versions 1.4-1 dated 2025-07-29 and 1.4-2 dated 2025-09-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test-logistic-dma.R | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: Choice models are a widely used technique across numerous scientific disciplines. The Apollo package is a very flexible tool for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<https://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and [...truncated...]
Author: Stephane Hess [aut, cre],
David Palma [aut],
Thomas Hancock [ctb]
Maintainer: Stephane Hess <S.Hess@leeds.ac.uk>
Diff between apollo versions 0.3.5 dated 2025-03-12 and 0.3.6 dated 2025-09-19
DESCRIPTION | 14 +- MD5 | 176 ++++++++++++++------------- NAMESPACE | 2 R/apollo_avgInterDraws.R | 4 R/apollo_avgIntraDraws.R | 4 R/apollo_classAlloc.R | 9 + R/apollo_cnl.R | 10 + R/apollo_cnl2.R | 10 + R/apollo_combineModels.R | 4 R/apollo_dft.R | 2 R/apollo_drugChoiceData.R | 2 R/apollo_el.R | 10 + R/apollo_emdc.R | 2 R/apollo_emdc1.R | 8 - R/apollo_emdc2.R | 13 -- R/apollo_estimate.R | 125 +++++++++++++++++-- R/apollo_estimateHB.R | 3 R/apollo_expandLoop.R | 28 +++- R/apollo_fmnl.R | 10 + R/apollo_fnl.R | 10 + R/apollo_initialise.R | 2 R/apollo_lc.R | 13 +- R/apollo_lcEM_new.R |only R/apollo_makeCluster.R | 76 +++++------ R/apollo_makeGrad.R | 4 R/apollo_makeHessian.R | 2 R/apollo_mixUnconditionals.R | 14 +- R/apollo_mnl.R | 12 + R/apollo_modeChoiceData.R | 2 R/apollo_modelOutput.R | 49 ++++++- R/apollo_modifyUserDefFunc.R | 2 R/apollo_nl.R | 17 ++ R/apollo_normalDensity.R | 10 + R/apollo_ol.R | 13 +- R/apollo_op.R | 13 +- R/apollo_panelProd.R | 4 R/apollo_preEstimate.R |only R/apollo_prediction.R | 59 ++++++++- R/apollo_prepareProb.R | 6 R/apollo_preprocess.R | 2 R/apollo_print.R | 4 R/apollo_rrm.R | 12 + R/apollo_saveOutput.R | 14 +- R/apollo_sharesTest.R | 18 ++ R/apollo_swissRouteChoiceData.R | 14 +- R/apollo_timeUseData.R | 2 R/apollo_tobit.R | 10 + R/apollo_unconditionals.R | 5 R/apollo_validateInputs.R | 2 R/apollo_varcov.R | 12 - R/onAttach.R | 2 build/vignette.rds |binary inst/CITATION | 2 inst/doc/apollofirstexample.html | 237 ++++++++++++++++++------------------- man/apollo_avgInterDraws.Rd | 2 man/apollo_avgIntraDraws.Rd | 2 man/apollo_classAlloc.Rd | 1 man/apollo_cnl.Rd | 2 man/apollo_cnl2.Rd | 2 man/apollo_combineModels.Rd | 2 man/apollo_dft.Rd | 2 man/apollo_drugChoiceData.Rd | 2 man/apollo_el.Rd | 2 man/apollo_emdc.Rd | 2 man/apollo_emdc1.Rd | 2 man/apollo_emdc2.Rd | 11 - man/apollo_estimate.Rd | 2 man/apollo_fmnl.Rd | 2 man/apollo_fnl.Rd | 2 man/apollo_lc.Rd | 2 man/apollo_lcEM_new.Rd |only man/apollo_mixUnconditionals.Rd | 9 + man/apollo_mnl.Rd | 2 man/apollo_modeChoiceData.Rd | 2 man/apollo_modelOutput.Rd | 1 man/apollo_nl.Rd | 2 man/apollo_normalDensity.Rd | 2 man/apollo_ol.Rd | 5 man/apollo_op.Rd | 4 man/apollo_panelProd.Rd | 2 man/apollo_preEstimate.Rd |only man/apollo_prediction.Rd | 2 man/apollo_prepareProb.Rd | 2 man/apollo_rrm.Rd | 2 man/apollo_saveOutput.Rd | 2 man/apollo_swissRouteChoiceData.Rd | 14 +- man/apollo_timeUseData.Rd | 2 man/apollo_tobit.Rd | 2 man/apollo_unconditionals.Rd | 9 + man/apollo_validateInputs.Rd | 2 man/apollo_varcov.Rd | 2 91 files changed, 811 insertions(+), 377 deletions(-)
Title: Package Documentation Websites with 'Quarto', 'Docsify',
'Docute', or 'MkDocs'
Description: This is a simple and powerful package to create, render, preview,
and deploy documentation websites for 'R' packages. It is a lightweight and
flexible alternative to 'pkgdown', with support for many documentation
generators, including 'Quarto', 'Docute', 'Docsify', and 'MkDocs'.
Author: Etienne Bacher [aut, cre, cph],
Vincent Arel-Bundock [aut]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between altdoc versions 0.5.0 dated 2025-01-23 and 0.6.0 dated 2025-09-19
DESCRIPTION | 9 LICENSE | 4 MD5 | 207 + NAMESPACE | 12 NEWS.md | 357 +-- R/altdoc_variables.R | 136 - R/check.R | 117 - R/freeze.R | 130 - R/import_man.R | 479 ++-- R/import_misc.R | 354 +-- R/import_readme.R | 169 - R/import_vignettes.R | 496 ++-- R/preview_docs.R | 60 R/qmd2md.R | 113 R/rd2qmd.R | 249 +- R/render_docs.R | 286 +- R/settings.R | 134 - R/settings_docsify.R | 196 - R/settings_docute.R | 195 - R/settings_mkdocs.R | 352 +-- R/settings_quarto_website.R | 264 +- R/setup_docs.R | 391 +-- R/setup_github_actions.R | 92 R/utils.R | 436 ++- README.md | 488 ++-- build/vignette.rds |binary inst/WORDLIST | 75 inst/doc/get-started.R | 6 inst/doc/get-started.Rmd | 390 +-- inst/doc/get-started.html | 1133 +++++----- inst/docsify/docsify.html | 90 inst/docsify/docsify.md | 18 inst/docute/docute.html | 104 inst/gha/altdoc.yaml | 146 - inst/mkdocs/mkdocs.yml | 80 inst/preamble/preamble_man_qmd.yml | 12 inst/preamble/preamble_vignettes_qmd.yml | 12 inst/preamble/preamble_vignettes_rmd.yml | 8 inst/quarto_website/quarto_website.yml | 84 man/preview_docs.Rd | 62 man/render_docs.Rd | 244 +- man/setup_docs.Rd | 168 - man/setup_github_actions.Rd | 50 tests/spelling.R | 13 tests/testthat.R | 8 tests/testthat/_snaps/docsify/render_docs.md | 373 +-- tests/testthat/_snaps/docute/render_docs.md | 284 +- tests/testthat/_snaps/mkdocs/render_docs.md | 498 ++-- tests/testthat/_snaps/rd2qmd.md |only tests/testthat/examples/examples-man/between.Rd | 36 tests/testthat/examples/examples-man/between.md | 80 tests/testthat/examples/examples-man/is-internal.Rd | 36 tests/testthat/examples/examples-man/long_title.Rd |only tests/testthat/examples/examples-man/should-fail.Rd | 34 tests/testthat/examples/examples-qmd/with-preamble.qmd | 26 tests/testthat/examples/examples-qmd/without-preamble.qmd | 16 tests/testthat/examples/examples-vignettes/basic.Rmd | 36 tests/testthat/examples/examples-vignettes/several-outputs.Rmd | 48 tests/testthat/examples/examples-vignettes/with-figure.Rmd | 50 tests/testthat/examples/examples-yaml/basic.Rmd | 20 tests/testthat/examples/examples-yaml/options.Rmd | 28 tests/testthat/examples/examples-yaml/several-outputs.Rmd | 32 tests/testthat/examples/testpkg.altdoc.noURL |only tests/testthat/examples/testpkg.altdoc.nonGithubURL |only tests/testthat/examples/testpkg.altdoc/DESCRIPTION | 32 tests/testthat/examples/testpkg.altdoc/NAMESPACE | 14 tests/testthat/examples/testpkg.altdoc/NEWS.md | 18 tests/testthat/examples/testpkg.altdoc/R/examplesIf_false.R | 24 tests/testthat/examples/testpkg.altdoc/R/examplesIf_true.R | 24 tests/testthat/examples/testpkg.altdoc/R/hello_base.R | 56 tests/testthat/examples/testpkg.altdoc/R/hello_r6.R | 59 tests/testthat/examples/testpkg.altdoc/README.Rmd | 82 tests/testthat/examples/testpkg.altdoc/README.md | 72 tests/testthat/examples/testpkg.altdoc/man/examplesIf_false.Rd | 44 tests/testthat/examples/testpkg.altdoc/man/examplesIf_true.Rd | 44 tests/testthat/examples/testpkg.altdoc/man/hello_base.Rd | 74 tests/testthat/examples/testpkg.altdoc/man/hello_r6.Rd | 178 - tests/testthat/examples/testpkg.altdoc/vignettes/test.Rmd | 42 tests/testthat/examples/testpkg.lifecycle |only tests/testthat/helper.R | 183 - tests/testthat/test-check_md_structure.R | 62 tests/testthat/test-freeze.R | 46 tests/testthat/test-import_man.R | 141 - tests/testthat/test-parallel.R | 19 tests/testthat/test-preview_docs.R | 26 tests/testthat/test-qmd2md.R | 89 tests/testthat/test-rd2qmd.R | 81 tests/testthat/test-render_docs.R | 517 ++-- tests/testthat/test-settings.R | 38 tests/testthat/test-setup_docs.R | 130 - tests/testthat/test-setup_github_actions.R | 62 tests/testthat/test-update.R | 247 +- tests/testthat/test-utils.R | 116 - vignettes/customize.qmd | 546 ++-- vignettes/deploy.qmd | 176 - vignettes/get-started.Rmd | 390 +-- 96 files changed, 7142 insertions(+), 6516 deletions(-)
Title: Simulate Non-Proportional Hazards
Description: A toolkit for simulation studies concerning time-to-event endpoints
with non-proportional hazards. 'SimNPH' encompasses functions for simulating
time-to-event data in various scenarios, simulating different trial designs
like fixed-followup, event-driven, and group sequential designs. The package
provides functions to calculate the true values of common summary statistics
for the implemented scenarios and offers common analysis methods for
time-to-event data. Helper functions for running simulations with the
'SimDesign' package and for aggregating and presenting the results are also
included. Results of the conducted simulation study are available in the
paper: "A Comparison of Statistical Methods for Time-To-Event Analyses in
Randomized Controlled Trials Under Non-Proportional Hazards",
Klinglmüller et al. (2025) <doi:10.1002/sim.70019>.
Author: Tobias Fellinger [aut, cre] ,
Florian Klinglmueller [aut]
Maintainer: Tobias Fellinger <tobias.fellinger@ages.at>
Diff between SimNPH versions 0.5.7 dated 2025-04-08 and 0.5.8 dated 2025-09-19
DESCRIPTION | 16 +- MD5 | 32 +++-- NEWS.md | 7 + R/report_plots.R | 2 R/shhr_gg.R | 25 +--- build/vignette.rds |binary inst/doc/simple_example.Rmd | 81 ++++++++------ inst/doc/simple_example.html | 180 +++++++++++++++++---------------- man/results_pivot_longer.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-analyse_describe.R | 28 ++--- tests/testthat/test-report_plots.R | 72 ++----------- tests/testthat/test-shhr_gg.R | 9 - tests/testthat/test-summarise.R | 35 +++--- vignettes/simple_example.Rmd | 81 ++++++++------ 15 files changed, 280 insertions(+), 290 deletions(-)
Title: Visualization of Viral Protein Sequence Diversity Dynamics
Description: To ease the visualization of outputs from Diversity Motif Analyser ('DiMA';
<https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity
motifs (index and its variants – major, minor and unique) for elucidation of
the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/>
for more information.
Author: Pendy Tok [aut, cre],
Li Chuin Chong [aut],
Evgenia Chikina [aut],
Yin Cheng Chen [aut],
Mohammad Asif Khan [aut]
Maintainer: Pendy Tok <pendytok0518@gmail.com>
Diff between vDiveR versions 2.0.1 dated 2024-11-22 and 2.1.0 dated 2025-09-19
DESCRIPTION | 8 LICENSE | 4 MD5 | 75 NAMESPACE | 197 NEWS.md | 16 R/DiveR-package.R | 12 R/concat_conserved_kmer.R | 8 R/metadata_extraction.R | 316 R/plot_conservation_level.R | 435 R/plot_correlation.R | 96 R/plot_dynamics_protein.R | 402 R/plot_dynamics_proteome.R | 380 R/plot_entropy.R | 390 R/plot_time.R | 116 R/plot_world_map.R | 272 R/sample_data.R | 146 README.md | 66 inst/extdata/GISAID_EpiCoV.faa | 230 inst/extdata/NCBI_Protein.faa | 114 inst/extdata/city_mapper.csv |84914 +++++++++++++++++++-------------------- man/JSON_sample.Rd | 32 man/concat_conserved_kmer.Rd | 72 man/extract_from_GISAID.Rd | 28 man/extract_from_NCBI.Rd | 28 man/json2csv.Rd | 58 man/match_region_to_target.Rd |only man/metadata.Rd | 42 man/metadata_extraction.Rd | 52 man/plot_correlation.Rd | 96 man/plot_dynamics_protein.Rd | 88 man/plot_dynamics_proteome.Rd | 82 man/plot_entropy.Rd | 98 man/plot_time.Rd | 74 man/protein_2hosts.Rd | 70 man/proteins_1host.Rd | 70 man/vDiveR-package.Rd | 46 tests/testthat.R | 24 tests/testthat/test-concat-seq.R | 154 tests/testthat/test-json2csv.R | 108 39 files changed, 44716 insertions(+), 44703 deletions(-)
Title: Variable Selection for Model-Based Clustering of Mixed-Type Data
Set with Missing Values
Description: Full model selection (detection of the relevant features and estimation of the number of clusters) for model-based clustering (see reference here <doi:10.1007/s11222-016-9670-1>). Data to analyze can be continuous, categorical, integer or mixed. Moreover, missing values can occur and do not necessitate any pre-processing. Shiny application permits an easy interpretation of the results.
Author: Matthieu Marbac [aut],
Mohammed Sedki [aut, cre]
Maintainer: Mohammed Sedki <mohammed.sedki@u-psud.fr>
Diff between VarSelLCM versions 2.1.3.1 dated 2020-10-14 and 2.1.3.2 dated 2025-09-19
VarSelLCM-2.1.3.1/VarSelLCM/inst/doc/VarSelLCM.pdf |only VarSelLCM-2.1.3.2/VarSelLCM/DESCRIPTION | 23 ++++++++---- VarSelLCM-2.1.3.2/VarSelLCM/MD5 | 36 +++++++++---------- VarSelLCM-2.1.3.2/VarSelLCM/R/Plot.R | 31 +++++++++------- VarSelLCM-2.1.3.2/VarSelLCM/R/VarSelLCM.R | 10 ++--- VarSelLCM-2.1.3.2/VarSelLCM/R/model.R | 2 - VarSelLCM-2.1.3.2/VarSelLCM/build/vignette.rds |binary VarSelLCM-2.1.3.2/VarSelLCM/inst/CITATION | 10 ++--- VarSelLCM-2.1.3.2/VarSelLCM/inst/doc/VarSelLCM.R | 34 ++++++++--------- VarSelLCM-2.1.3.2/VarSelLCM/inst/doc/VarSelLCM.Rmd | 2 - VarSelLCM-2.1.3.2/VarSelLCM/inst/doc/VarSelLCM.html |only VarSelLCM-2.1.3.2/VarSelLCM/man/VarSelCluster.Rd | 17 +++++++- VarSelLCM-2.1.3.2/VarSelLCM/man/VarSelLCM-package.Rd | 13 +++++- VarSelLCM-2.1.3.2/VarSelLCM/man/plot-methods.Rd | 3 - VarSelLCM-2.1.3.2/VarSelLCM/src/Makevars | 2 - VarSelLCM-2.1.3.2/VarSelLCM/src/Makevars.win | 2 - VarSelLCM-2.1.3.2/VarSelLCM/src/RcppExports.cpp | 5 ++ VarSelLCM-2.1.3.2/VarSelLCM/src/XEM.cpp | 6 +-- VarSelLCM-2.1.3.2/VarSelLCM/src/XEMPen.cpp | 6 ++- VarSelLCM-2.1.3.2/VarSelLCM/vignettes/VarSelLCM.Rmd | 2 - 20 files changed, 121 insertions(+), 83 deletions(-)
Title: Algorithms and Tools for Tabular Statistics and Hierarchical
Computations
Description: Includes general data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Bjoern-Helge Mevik [ctb],
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.8.1 dated 2025-08-18 and 1.8.2 dated 2025-09-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- NAMESPACE | 3 +++ NEWS.md | 8 ++++++++ R/DummyDuplicated.R | 23 ----------------------- R/get_colnames.R |only R/zero_col.R |only man/get_colnames.Rd |only man/zero_col.Rd |only 9 files changed, 23 insertions(+), 31 deletions(-)
Title: Monte-Carlo Methods for Simulating Luminescence Phenomena
Description: A collection of functions to simulate luminescence production in
dosimetric materials using Monte Carlo methods. Implemented are models for
delocalised transitions (e.g., Chen and McKeever (1997) <doi:10.1142/2781>),
localised transitions (e.g., Pagonis et al. (2019) <doi:10.1016/j.jlumin.2018.11.024>)
and tunnelling transitions (Jain et al. (2012) <doi:10.1088/0953-8984/24/38/385402>
and Pagonis et al. (2019) <doi:10.1016/j.jlumin.2018.11.024>).
Supported stimulation methods are thermal luminescence (TL),
continuous-wave optically stimulated luminescence (CW-OSL),
linearly-modulated optically stimulated luminescence (LM-OSL),
linearly-modulated infrared stimulated luminescence (LM-IRSL),
and isothermal luminescence (ITL or ISO-TL).
Author: Johannes Friedrich [aut, trl] ,
Sebastian Kreutzer [aut, trl, cre] ,
Vasilis Pagonis [aut] ,
Christoph Schmidt [aut] ,
Christian Laag [ctb] ,
Ena Rajovic [ctb],
Alex Roy Duncan [ctb]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@uni-heidelberg.de>
Diff between RLumCarlo versions 0.1.9 dated 2022-08-08 and 0.1.10 dated 2025-09-19
DESCRIPTION | 43 ++++---- MD5 | 78 +++++++-------- NEWS.md | 5 R/RLumCarlo-package.R | 10 + README.md | 60 +++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/RLumCarlo_-_Getting_started_with_RLumCarlo.pdf |binary man/RLumCarlo-package.Rd | 14 ++ man/create_ClusterSystem.Rd | 2 man/figures/README-unnamed-chunk-2-1.png |binary man/methods_RLumCarlo.Rd | 2 man/plot_RLumCarlo.Rd | 2 man/run_MC_CW_IRSL_LOC.Rd | 2 man/run_MC_CW_IRSL_TUN.Rd | 2 man/run_MC_CW_OSL_DELOC.Rd | 2 man/run_MC_ISO_DELOC.Rd | 2 man/run_MC_ISO_LOC.Rd | 2 man/run_MC_ISO_TUN.Rd | 2 man/run_MC_LM_OSL_DELOC.Rd | 2 man/run_MC_LM_OSL_LOC.Rd | 2 man/run_MC_LM_OSL_TUN.Rd | 2 man/run_MC_TL_DELOC.Rd | 2 man/run_MC_TL_LOC.Rd | 2 man/run_MC_TL_TUN.Rd | 2 src/Makevars | 4 src/Makevars.win | 4 tests/testthat/test_run_MC_CW_IRSL_LOC.R | 9 + tests/testthat/test_run_MC_CW_IRSL_TUN.R | 3 tests/testthat/test_run_MC_CW_OSL_DELOC.R | 3 tests/testthat/test_run_MC_ISO_DELOC.R | 3 tests/testthat/test_run_MC_ISO_LOC.R | 3 tests/testthat/test_run_MC_ISO_TUN.R | 4 tests/testthat/test_run_MC_LM_OSL_DELOC.R | 3 tests/testthat/test_run_MC_LM_OSL_LOC.R | 3 tests/testthat/test_run_MC_LM_OSL_TUN.R | 3 tests/testthat/test_run_MC_TL_DELOC.R | 3 tests/testthat/test_run_MC_TL_LOC.R | 3 tests/testthat/test_run_MC_TL_TUN.R | 1 vignettes/RLumCarlo_-_Getting_started_with_RLumCarlo.Rmd | 2 40 files changed, 159 insertions(+), 132 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like 'csv',
'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut] ,
Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Shelby Bearrows [ctb],
https://github.com/mandreyel/ [cph] ,
Jukka Jylaenki [cph] ,
Mikkel Joergensen [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between vroom versions 1.6.5 dated 2023-12-05 and 1.6.6 dated 2025-09-19
vroom-1.6.5/vroom/build/vroom.pdf |only vroom-1.6.6/vroom/DESCRIPTION | 17 +++++++++-------- vroom-1.6.6/vroom/MD5 | 21 ++++++++++----------- vroom-1.6.6/vroom/NEWS.md | 4 ++++ vroom-1.6.6/vroom/README.md | 4 +++- vroom-1.6.6/vroom/build/stage23.rdb |binary vroom-1.6.6/vroom/build/vignette.rds |binary vroom-1.6.6/vroom/inst/doc/benchmarks.html | 16 ++++++++-------- vroom-1.6.6/vroom/inst/doc/vroom.R | 18 +++++++++--------- vroom-1.6.6/vroom/inst/doc/vroom.html | 11 ++++++----- vroom-1.6.6/vroom/man/vroom_fwf.Rd | 8 +++++--- vroom-1.6.6/vroom/src/iconv_file.cc | 5 +++-- 12 files changed, 57 insertions(+), 47 deletions(-)
Title: A GUI for Dual and Bulk RNA-Sequencing Analysis
Description: A 'shiny' app that supports both dual and bulk RNA-seq, with the dual
RNA-seq functionality offering the flexibility to perform either a
sequential approach (where reads are mapped separately to each genome)
or a combined approach (where reads are aligned to a single merged
genome). The user-friendly interface automates the analysis process,
providing step-by-step guidance, making it easy for users to navigate
between different analysis steps, and download intermediate results
and publication-ready plots.
Author: Carmine Fruggiero [aut, cre],
Gaetano Aufiero [aut]
Maintainer: Carmine Fruggiero <fruggierocarmine3@gmail.com>
Diff between inDAGO versions 1.0.1 dated 2025-09-13 and 1.0.2 dated 2025-09-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/CombinedAlignment.R | 48 +++++++++++++++++++++++++++++++++++++++++++++--- 3 files changed, 50 insertions(+), 8 deletions(-)
Title: A Fast and Scalable Exhaustive Feature Selection Framework
Description: The goal of this package is to provide an easy to use, fast and
scalable exhaustive search framework. Exhaustive feature selections
typically require a very large number of models to be fitted and evaluated.
Execution speed and memory management are crucial factors here. This package
provides solutions for both. Execution speed is optimized by using a
multi-threaded C++ backend, and memory issues are solved by by only storing
the best results during execution and thus keeping memory usage constant.
Author: Rudolf Jagdhuber [aut, cre],
Jorge Nocedal [cph] ,
Naoaki Okazaki [cph]
Maintainer: Rudolf Jagdhuber <r.jagdhuber@gmail.com>
Diff between ExhaustiveSearch versions 1.0.1 dated 2021-01-18 and 1.0.2 dated 2025-09-19
DESCRIPTION | 8 MD5 | 32 +- NAMESPACE | 22 - NEWS.md | 22 - R/ExhaustiveSearch-package.R | 10 R/ExhaustiveSearch.R | 600 +++++++++++++++++++++--------------------- R/RcppExports.R | 14 R/print.R | 104 +++---- R/resultFunctions.R | 176 ++++++------ README.md | 298 ++++++++++---------- man/ExhaustiveSearch.Rd | 362 ++++++++++++------------- man/getFeatures.Rd | 82 ++--- man/print.ExhaustiveSearch.Rd | 52 +-- man/resultTable.Rd | 112 +++---- src/Makevars | 3 src/Makevars.win | 3 src/RcppExports.cpp | 5 17 files changed, 958 insertions(+), 947 deletions(-)
More information about ExhaustiveSearch at CRAN
Permanent link
Title: Compute Energy Landscapes
Description: Compute energy landscapes using a digital elevation model
and body mass of animals.
Author: Emilio Berti [aut, cre],
Marco Davoli [ctb],
Robert Buitenwerf [ctb],
Alexander Dyer [ctb],
Oskar L.P. Hansen [ctb],
Myriam Hirt [ctb],
Jens-Christian Svenning [ctb],
Joerdis F. Terlau [ctb],
Ulrich Brose [ctb],
Fritz Vollrath [ctb]
Maintainer: Emilio Berti <emilio.berti@idiv.de>
Diff between enerscape versions 1.1.0 dated 2024-01-29 and 1.2.0 dated 2025-09-19
DESCRIPTION | 23 ++- MD5 | 48 +++--- R/RcppExports.R | 44 +++++- R/enerscape.R | 23 +-- R/humanscape.R |only README.md | 263 +++++++++++++++++++++++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/enerscape.R | 119 +++++++++++----- inst/doc/enerscape.Rmd | 71 +++++++++ inst/doc/enerscape.html | 84 ++++++----- man/energy.Rd | 6 man/energyHuman.Rd |only man/energyscape.Rd | 6 man/energyscapeHuman.Rd |only man/enerscape.Rd | 12 - man/humanscape.Rd |only man/slopeRadiant.Rd |only src/RcppExports.cpp | 62 +++++++- src/distance.cpp |only src/distance.h | 34 ---- src/enerscape.cpp | 20 +- src/humanscape.cpp |only src/neighbours.cpp |only src/neighbours.h | 44 ------ src/slope.cpp |only src/slope.h | 36 ---- tests/testthat/test-cpp-functions.R | 2 vignettes/enerscape.Rmd | 71 +++++++++ 30 files changed, 677 insertions(+), 291 deletions(-)
Title: Two-Stage Difference-in-Differences Following Gardner (2021)
Description: Estimates Two-way Fixed Effects difference-in-differences/event-study models using the approach proposed by Gardner (2021) <doi:10.48550/arXiv.2207.05943>. To avoid the problems caused by OLS estimation of the Two-way Fixed Effects model, this function first estimates the fixed effects and covariates using untreated observations and then in a second stage, estimates the treatment effects.
Author: Kyle Butts [aut, cre] ,
John Gardner [aut] ,
Grant McDermott [ctb] ,
Laurent Berge [ctb]
Maintainer: Kyle Butts <buttskyle96@gmail.com>
Diff between did2s versions 1.0.2 dated 2023-04-07 and 1.2.0 dated 2025-09-19
did2s-1.0.2/did2s/R/utils.R |only did2s-1.0.2/did2s/man/figures/es.png |only did2s-1.0.2/did2s/man/figures/resid.png |only did2s-1.0.2/did2s/man/figures/twfe.png |only did2s-1.0.2/did2s/man/figures/twfe_count.png |only did2s-1.0.2/did2s/man/figures/unnamed-chunk-1-1.png |only did2s-1.2.0/did2s/DESCRIPTION | 26 did2s-1.2.0/did2s/MD5 | 64 did2s-1.2.0/did2s/NAMESPACE | 2 did2s-1.2.0/did2s/NEWS.md | 4 did2s-1.2.0/did2s/R/data.R | 2 did2s-1.2.0/did2s/R/did2s.R | 303 ++-- did2s-1.2.0/did2s/R/event_study.R | 752 +++++----- did2s-1.2.0/did2s/R/gen_data.R | 153 +- did2s-1.2.0/did2s/R/honest_did.R |only did2s-1.2.0/did2s/R/zzz.R | 13 did2s-1.2.0/did2s/README.md | 247 ++- did2s-1.2.0/did2s/build/vignette.rds |binary did2s-1.2.0/did2s/data/castle.rda |binary did2s-1.2.0/did2s/data/df_het.rda |binary did2s-1.2.0/did2s/data/df_hom.rda |binary did2s-1.2.0/did2s/inst/CITATION | 15 did2s-1.2.0/did2s/inst/doc/Two-Stage-Difference-in-Differences.R | 81 - did2s-1.2.0/did2s/inst/doc/Two-Stage-Difference-in-Differences.Rmd | 77 - did2s-1.2.0/did2s/inst/doc/Two-Stage-Difference-in-Differences.html | 223 +- did2s-1.2.0/did2s/man/did2s.Rd | 33 did2s-1.2.0/did2s/man/event_study.Rd | 10 did2s-1.2.0/did2s/man/figures/README-ehec-data-est-1.png |only did2s-1.2.0/did2s/man/figures/README-plot-compare-1.png |binary did2s-1.2.0/did2s/man/figures/README-plot-df-het-1.png |binary did2s-1.2.0/did2s/man/figures/README-plot-es-1.png |binary did2s-1.2.0/did2s/man/figures/README-sensitivity-1.png |only did2s-1.2.0/did2s/man/figures/README-unnamed-chunk-3-1.png |only did2s-1.2.0/did2s/man/get_honestdid_obj_did2s.Rd |only did2s-1.2.0/did2s/man/honest_did_did2s.Rd |only did2s-1.2.0/did2s/man/robust_solve_XtX.Rd |only did2s-1.2.0/did2s/tests/testthat/test-did2s.R | 129 + did2s-1.2.0/did2s/tests/testthat/test-event-study.R | 74 did2s-1.2.0/did2s/tests/testthat/test-robust-solve.R |only did2s-1.2.0/did2s/vignettes/Two-Stage-Difference-in-Differences.Rmd | 77 - 40 files changed, 1396 insertions(+), 889 deletions(-)
Title: Extended Inference for Lasso and Elastic-Net Regularized Cox and
Generalized Linear Models
Description: The c060 package provides additional functions to perform stability selection, model validation and parameter tuning for glmnet models.
Author: Martin Sill [aut],
Thomas Hielscher [aut],
Manuela Zucknick [aut],
Natalia Becker [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between c060 versions 0.3-1 dated 2025-08-18 and 0.4-0 dated 2025-09-19
c060-0.3-1/c060/build |only c060-0.3-1/c060/man/coef.intsearch.Rd |only c060-0.3-1/c060/man/figures/logo.png |only c060-0.3-1/c060/man/plot.summary.int.Rd |only c060-0.3-1/c060/man/predictProb.glmnet.Rd |only c060-0.4-0/c060/DESCRIPTION | 25 c060-0.4-0/c060/MD5 | 86 - c060-0.4-0/c060/NAMESPACE | 77 - c060-0.4-0/c060/NEWS.md | 8 c060-0.4-0/c060/R/EPSGO.R | 190 ++ c060-0.4-0/c060/R/balancedFolds.R | 49 c060-0.4-0/c060/R/c060-package.R |only c060-0.4-0/c060/R/coef_intsearch.R | 19 c060-0.4-0/c060/R/peperr_glmnet.R | 299 +++ c060-0.4-0/c060/R/plot_coef_glmnet.R | 45 c060-0.4-0/c060/R/plot_summary_inter_search.R | 58 c060-0.4-0/c060/R/stabilityselection.R | 215 ++ c060-0.4-0/c060/R/summary_inter_search.R | 33 c060-0.4-0/c060/R/tune_glmnet_interval.R | 183 +- c060-0.4-0/c060/README.md | 1071 +++++++++++++- c060-0.4-0/c060/inst/CITATION | 28 c060-0.4-0/c060/inst/_pkgdown.yml |only c060-0.4-0/c060/man/EPSGO.Rd | 221 +- c060-0.4-0/c060/man/PLL.coxnet.Rd | 53 c060-0.4-0/c060/man/Plot.coef.glmnet.Rd | 60 c060-0.4-0/c060/man/Plot.peperr.curves.Rd | 68 c060-0.4-0/c060/man/aggregation.auc.Rd | 63 c060-0.4-0/c060/man/balancedFolds.Rd | 74 c060-0.4-0/c060/man/c060-package.Rd |only c060-0.4-0/c060/man/coef.sum.intsearch.Rd |only c060-0.4-0/c060/man/complexity.glmnet.Rd | 87 - c060-0.4-0/c060/man/figures/README-unnamed-chunk-13-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-42-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-43-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-44-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-45-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-46-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-5-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-50-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-6-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-7-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-8-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-9-1.png |only c060-0.4-0/c060/man/fit.glmnet.Rd | 75 c060-0.4-0/c060/man/plot.stabpath.Rd | 133 - c060-0.4-0/c060/man/plot.sum.intsearc.Rd |only c060-0.4-0/c060/man/predictProb.coxnet.Rd | 70 c060-0.4-0/c060/man/stabpath.Rd | 141 - c060-0.4-0/c060/man/stabsel.Rd | 101 - c060-0.4-0/c060/man/summary.intsearch.Rd | 76 c060-0.4-0/c060/man/tune.glmnet.interval.Rd | 169 +- c060-0.4-0/c060/tests |only 52 files changed, 3003 insertions(+), 774 deletions(-)
Title: A Family of Beta Mixture Models for Clustering Beta-Valued DNA
Methylation Data
Description: A family of novel beta mixture models (BMMs) has been developed by Majumdar et al. (2022) <doi:10.48550/arXiv.2211.01938> to appositely model the beta-valued cytosine-guanine dinucleotide (CpG) sites, to objectively identify methylation state thresholds and to identify the differentially methylated CpG (DMC) sites using a model-based clustering approach. The family of beta mixture models employs different parameter constraints applicable to different study settings. The EM algorithm is used for parameter estimation, with a novel approximation during the M-step providing tractability and ensuring computational feasibility.
Author: Koyel Majumdar [aut, cre] ,
Romina Silva [aut],
Antoinette Sabrina Perry [aut],
Ronald William Watson [aut],
Andrea Rau [aut] ,
Florence Jaffrezic [aut],
Thomas Brendan Murphy [aut] ,
Isobel Claire Gormley [aut]
Maintainer: Koyel Majumdar <koyelmajumdar.phdresearch@gmail.com>
Diff between betaclust versions 1.0.4 dated 2024-09-24 and 1.0.5 dated 2025-09-19
DESCRIPTION | 23 ++- MD5 | 8 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignettes.html | 294 +++++++++++++++++++++++------------------------- 5 files changed, 159 insertions(+), 166 deletions(-)
Title: An API Client for Australian Weather and Climate Data Resources
Description: Provides automated downloading, parsing and formatting of
weather data for Australia through API endpoints provided by the
Department of Primary Industries and Regional Development (DPIRD) of
Western Australia and by the Science and Technology Division of the
Queensland Government's Department of Environment and Science (DES).
As well as the Bureau of Meteorology (BOM) of the Australian
government precis and coastal forecasts,
and downloading and importing radar and satellite imagery files.
DPIRD weather data are accessed through public APIs provided by
DPIRD, <https://www.dpird.wa.gov.au/online-tools/apis/>, providing
access to weather station data from the DPIRD weather station
network. Australia-wide weather data are based on data from the
Australian Bureau of Meteorology (BOM) data and accessed through
SILO (Scientific Information for Land Owners) Jeffrey et al. (2001)
<doi:10.1016/S1364-8152(01)00008-1>. DPIRD data are made available
under a Creative Commons Attribut [...truncated...]
Author: Rodrigo Pires [aut, cre] ,
Anna Hepworth [aut] ,
Rebecca O'Leary [aut],
Jonathan Carroll [aut] ,
James Goldie [aut] ,
Dean Marchiori [aut] ,
Paul Melloy [aut] ,
Mark Padgham [aut] ,
Hugh Parsonage [aut] ,
Keith Pembleton [ctb] ,
Maelle Salmon [ctb] . [...truncated...]
Maintainer: Rodrigo Pires <rodrigo.pires@dpird.wa.gov.au>
This is a re-admission after prior archival of version 2.0.1 dated 2025-04-16
Diff between weatherOz versions 2.0.1 dated 2025-04-16 and 2.0.2 dated 2025-09-19
DESCRIPTION | 108 ++++++++++++++-------------- MD5 | 88 +++++++++++----------- NAMESPACE | 4 + NEWS.md | 28 +++++++ R/data.R | 6 - R/find_nearby_stations.R | 6 - R/find_stations_in.R | 2 R/get_ag_bulletin.R | 4 - R/get_dpird_apsim.R | 2 R/get_dpird_availability.R | 2 R/get_dpird_extremes.R | 2 R/get_dpird_minute.R | 2 R/get_dpird_summaries.R | 2 R/get_key.R | 2 R/get_radar_imagery.R | 1 R/get_satellite_imagery.R | 1 R/get_stations_metadata.R | 2 R/internal_functions.R | 1 R/query_dpird_api.R | 2 README.md | 14 +-- inst/doc/use_case.Rmd | 2 inst/doc/use_case.html | 14 +-- inst/doc/weatherOz.Rmd | 2 inst/doc/weatherOz.html | 15 ++- inst/doc/weatherOz_for_BOM.html | 5 - inst/doc/weatherOz_for_DPIRD.html | 5 - inst/doc/weatherOz_for_SILO.html | 5 - man/dpird_extreme_weather_values.Rd | 2 man/dpird_minute_values.Rd | 2 man/dpird_summary_values.Rd | 2 man/find_nearby_stations.Rd | 4 - man/find_stations_in.Rd | 2 man/get_ag_bulletin.Rd | 6 - man/get_dpird_apsim.Rd | 2 man/get_dpird_availability.Rd | 2 man/get_dpird_extremes.Rd | 2 man/get_dpird_minute.Rd | 2 man/get_dpird_summaries.Rd | 2 man/get_stations_metadata.Rd | 2 man/weatherOz-package.Rd | 2 tests/testthat/test-find_stations_in.R | 6 + tests/testthat/test-get_stations_metadata.R | 3 vignettes/use_case.Rmd | 2 vignettes/weatherOz.Rmd | 2 vignettes/weatherOz.Rmd.orig | 2 45 files changed, 203 insertions(+), 171 deletions(-)
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 0.15.1 dated 2024-11-22 and 0.16.0 dated 2025-09-19
progressr-0.15.1/progressr/inst/doc/progressr-intro.html |only progressr-0.15.1/progressr/inst/doc/progressr-intro.md |only progressr-0.15.1/progressr/vignettes/progressr-intro.md |only progressr-0.16.0/progressr/DESCRIPTION | 14 - progressr-0.16.0/progressr/MD5 | 116 ++++++---- progressr-0.16.0/progressr/NAMESPACE | 2 progressr-0.16.0/progressr/NEWS.md | 31 ++ progressr-0.16.0/progressr/R/delays.R | 28 ++ progressr-0.16.0/progressr/R/global_progression_handler.R | 2 progressr-0.16.0/progressr/R/handler_cli.R | 3 progressr-0.16.0/progressr/R/handler_pbmcapply.R | 3 progressr-0.16.0/progressr/R/handler_progress.R | 3 progressr-0.16.0/progressr/R/handler_slowdown.R |only progressr-0.16.0/progressr/R/handler_tkprogressbar.R | 5 progressr-0.16.0/progressr/R/handler_txtprogressbar.R | 3 progressr-0.16.0/progressr/R/handler_winprogressbar.R | 8 progressr-0.16.0/progressr/R/handlers.R | 2 progressr-0.16.0/progressr/R/make_progression_handler.R | 5 progressr-0.16.0/progressr/R/progressr-package.R | 57 ++-- progressr-0.16.0/progressr/R/rstudio-console.R |only progressr-0.16.0/progressr/R/vignette_engine.R | 1 progressr-0.16.0/progressr/R/zzz.R | 6 progressr-0.16.0/progressr/build/vignette.rds |binary progressr-0.16.0/progressr/inst/WORDLIST | 27 +- progressr-0.16.0/progressr/inst/doc/progressr-01-intro.html |only progressr-0.16.0/progressr/inst/doc/progressr-01-intro.md |only progressr-0.16.0/progressr/inst/doc/progressr-11-handlers.html |only progressr-0.16.0/progressr/inst/doc/progressr-11-handlers.md |only progressr-0.16.0/progressr/inst/doc/progressr-21-map-reduce.html |only progressr-0.16.0/progressr/inst/doc/progressr-21-map-reduce.md |only progressr-0.16.0/progressr/inst/doc/progressr-22-parallel-processing.html |only progressr-0.16.0/progressr/inst/doc/progressr-22-parallel-processing.md |only progressr-0.16.0/progressr/inst/doc/progressr-25-replace-cli-with-progressr.html |only progressr-0.16.0/progressr/inst/doc/progressr-25-replace-cli-with-progressr.md |only progressr-0.16.0/progressr/inst/doc/progressr-29-debug.html |only progressr-0.16.0/progressr/inst/doc/progressr-29-debug.md |only progressr-0.16.0/progressr/inst/doc/progressr-31-knitr.html |only progressr-0.16.0/progressr/inst/doc/progressr-31-knitr.md |only progressr-0.16.0/progressr/inst/doc/progressr-91-appendix.html |only progressr-0.16.0/progressr/inst/doc/progressr-91-appendix.md |only progressr-0.16.0/progressr/man/figures/handler_cli-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_cli-format-1.svg | 2 progressr-0.16.0/progressr/man/figures/handler_pbcol-adjust-mid.svg | 2 progressr-0.16.0/progressr/man/figures/handler_pbcol-adjust-right-complete.svg | 2 progressr-0.16.0/progressr/man/figures/handler_pbcol-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_pbmcapply-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_progress-complete.svg | 2 progressr-0.16.0/progressr/man/figures/handler_progress-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_progress-format-1.svg | 2 progressr-0.16.0/progressr/man/figures/handler_progress-format-2.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-char-ansi.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-char-width-2.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-char.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-style-1.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-style-3.svg | 2 progressr-0.16.0/progressr/man/handler_cli.Rd | 3 progressr-0.16.0/progressr/man/handler_pbmcapply.Rd | 3 progressr-0.16.0/progressr/man/handler_progress.Rd | 3 progressr-0.16.0/progressr/man/handler_slowdown.Rd |only progressr-0.16.0/progressr/man/handler_tkprogressbar.Rd | 3 progressr-0.16.0/progressr/man/handler_txtprogressbar.Rd | 3 progressr-0.16.0/progressr/man/handler_winprogressbar.Rd | 3 progressr-0.16.0/progressr/man/handlers.Rd | 10 progressr-0.16.0/progressr/man/make_progression_handler.Rd | 3 progressr-0.16.0/progressr/man/progressr.Rd | 59 ++--- progressr-0.16.0/progressr/vignettes/progressr-01-intro.md |only progressr-0.16.0/progressr/vignettes/progressr-11-handlers.md |only progressr-0.16.0/progressr/vignettes/progressr-21-map-reduce.md |only progressr-0.16.0/progressr/vignettes/progressr-22-parallel-processing.md |only progressr-0.16.0/progressr/vignettes/progressr-25-replace-cli-with-progressr.md |only progressr-0.16.0/progressr/vignettes/progressr-29-debug.md |only progressr-0.16.0/progressr/vignettes/progressr-31-knitr.md |only progressr-0.16.0/progressr/vignettes/progressr-91-appendix.md |only 74 files changed, 280 insertions(+), 158 deletions(-)
Title: Experimental Data of Cascade Experiments in Genomics
Description: These experimental expression data (5 leukemic 'CLL' B-lymphocyte of aggressive form from 'GSE39411', <doi:10.1073/pnas.1211130110>), after B-cell receptor stimulation, are used as examples by packages such as the 'Cascade' one, a modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between CascadeData versions 1.5 dated 2025-08-21 and 1.6 dated 2025-09-19
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/CascadeData-package.R | 2 +- README.md | 4 +++- inst/CITATION | 4 +++- man/CascadeData-package.Rd | 2 +- tests/testthat.R | 1 - 8 files changed, 28 insertions(+), 20 deletions(-)
Title: Selection, Reverse-Engineering and Prediction in Cascade
Networks
Description: A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between Cascade versions 2.2 dated 2025-08-20 and 2.3 dated 2025-09-19
DESCRIPTION | 16 ++--- MD5 | 14 ++--- NEWS.md | 10 +++ R/Cascade-package.R | 2 README.md | 137 +++++++++++++++++++++---------------------------- inst/CITATION | 19 ++++++ inst/_pkgdown.yml | 3 + man/Cascade-package.Rd | 2 8 files changed, 108 insertions(+), 95 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library aiming towards
a good balance between speed and ease of use. It provides high-level syntax and
functionality deliberately similar to Matlab. It is useful for algorithm development
directly in C++, or quick conversion of research code into production environments.
It provides efficient classes for vectors, matrices and cubes where dense and sparse
matrices are supported. Integer, floating point and complex numbers are supported.
A sophisticated expression evaluator (based on template meta-programming) automatically
combines several operations to increase speed and efficiency. Dynamic evaluation
automatically chooses optimal code paths based on detected matrix structures.
Matrix decompositions are provided through integration with LAPACK, or one of its
high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can
automatically use 'OpenMP' multi-threading (parallelisation) to speed up
computationally expensive operations [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 15.0.2-1 dated 2025-09-08 and 15.0.2-2 dated 2025-09-19
RcppArmadillo-15.0.2-1/RcppArmadillo/man/armadillo_set_seed_random.Rd |only RcppArmadillo-15.0.2-2/RcppArmadillo/ChangeLog | 30 +++ RcppArmadillo-15.0.2-2/RcppArmadillo/DESCRIPTION | 8 - RcppArmadillo-15.0.2-2/RcppArmadillo/MD5 | 39 ++-- RcppArmadillo-15.0.2-2/RcppArmadillo/R/RcppExports.R | 33 +--- RcppArmadillo-15.0.2-2/RcppArmadillo/README.md | 5 RcppArmadillo-15.0.2-2/RcppArmadillo/configure | 18 +- RcppArmadillo-15.0.2-2/RcppArmadillo/configure.ac | 2 RcppArmadillo-15.0.2-2/RcppArmadillo/inst/NEWS.Rd | 11 + RcppArmadillo-15.0.2-2/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-15.0.2-2/RcppArmadillo/inst/doc/RcppArmadillo-sparseMatrix.pdf |binary RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/RcppArmadillo/interface/RcppArmadilloForward.h | 2 RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/RcppArmadillo/version/arma.h | 14 + RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/current/armadillo_bits/diskio_bones.hpp | 3 RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/current/armadillo_bits/diskio_meat.hpp | 79 ++++++---- RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/current/armadillo_bits/glue_hist_meat.hpp | 2 RcppArmadillo-15.0.2-2/RcppArmadillo/inst/skeleton/Makevars | 16 -- RcppArmadillo-15.0.2-2/RcppArmadillo/inst/skeleton/Makevars.win | 16 -- RcppArmadillo-15.0.2-2/RcppArmadillo/man/armadillo_set_seed.Rd | 42 ++--- RcppArmadillo-15.0.2-2/RcppArmadillo/man/armadillo_version.Rd | 19 +- RcppArmadillo-15.0.2-2/RcppArmadillo/src/RcppArmadillo.cpp | 36 +--- 21 files changed, 191 insertions(+), 184 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, [...truncated...]
Author: Liam J. Revell [aut, cre]
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 2.4-4 dated 2025-01-07 and 2.5-2 dated 2025-09-19
DESCRIPTION | 8 - MD5 | 49 ++++++----- NAMESPACE | 20 +++- R/bounded_bm.R | 19 +++- R/cladebox.R |only R/ctt.R | 10 +- R/fitMk.parallel.R | 4 R/fitPagel.R | 17 +++- R/fitThresh.R | 199 ++++++++++++++++++++++++++++++++++++++++-------- R/fitcontMk.R |only R/fitgammaMk.R | 85 ++++++++++++++++++++ R/fitmultiBM.R | 37 ++++++-- R/fitmultiTrend.R |only R/phenogram.R | 17 ---- R/sim_absorbing.R |only R/utilities.R | 17 ---- man/bmPlot.Rd | 40 ++++++--- man/bounded_bm.Rd | 4 man/cladelabels.Rd | 7 + man/fitMk.Rd | 4 man/fitThresh.Rd | 11 +- man/fitcontMk.Rd |only man/fitmultiBM.Rd | 12 +- man/genSeq.Rd | 2 man/phytools-package.Rd | 2 man/plotSimmap.Rd | 2 man/reorderSimmap.Rd | 2 man/setMap.Rd | 2 28 files changed, 426 insertions(+), 144 deletions(-)
Title: Multiple Geometric Shape Point Layer for 'ggplot2'
Description: To create the multiple polygonal point layer for easily discernible shapes,
we developed the package, it is like the 'geom_point' of 'ggplot2'.
It can be used to draw the scatter plot.
Author: Shuangbin Xu [aut, cre]
Maintainer: Shuangbin Xu <xshuangbin@163.com>
Diff between ggstar versions 1.0.4 dated 2022-11-08 and 1.0.6 dated 2025-09-19
DESCRIPTION | 16 MD5 | 42 - NAMESPACE | 11 NEWS.md | 15 R/draw-key.R | 4 R/geom-star.R | 14 R/geom_star_interactive.R |only R/import.R |only R/primitive.R | 25 R/scale-identity.R | 2 R/scale-interactive.R |only R/scale-manual.R | 74 ++ R/scale-starshape.R | 5 build/vignette.rds |binary inst/doc/ggstar.R | 41 + inst/doc/ggstar.Rmd | 33 + inst/doc/ggstar.html | 1038 ++++++++++++++++++++++++++++++++++++- man/GeomInteractiveStar.Rd |only man/geom_star.Rd | 66 +- man/geom_star_interactive.Rd |only man/scale_manual.Rd | 44 + man/scale_starshape.Rd | 23 man/scale_starshape_identity.Rd | 33 - man/scale_starshape_interactive.Rd |only vignettes/ggstar.Rmd | 33 + 25 files changed, 1388 insertions(+), 131 deletions(-)
Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in
the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing
weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020)
<doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.5.0 dated 2025-07-08 and 0.5.1 dated 2025-09-19
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 4 ++++ R/compute.ci.R | 7 ++++++- R/fwb.R | 2 +- R/set_fwb_wtype.R | 2 +- R/utils.R | 8 ++------ R/vcovFWB.R | 6 +++--- R/weighted-statistics.R | 2 +- README.md | 1 + build/stage23.rdb |binary build/vignette.rds |binary inst/doc/fwb-rep.html | 5 +++-- man/fwb.Rd | 2 +- man/set_fwb_wtype.Rd | 2 +- man/vcovFWB.Rd | 6 +++--- man/w_mean.Rd | 2 +- 17 files changed, 49 insertions(+), 42 deletions(-)
Title: Harness ArcGIS Data Services
Description: Enables users of 'ArcGIS Enterprise', 'ArcGIS Online', or
'ArcGIS Platform' to read, write, publish, or manage vector and raster
data via ArcGIS location services REST API endpoints
<https://developers.arcgis.com/rest/>.
Author: Josiah Parry [aut, cre] ,
Eli Pousson [ctb] ,
Kenneth Vernon [ctb] ,
Martha Bass [ctb] ,
Antony Barja [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgislayers versions 0.4.0 dated 2025-04-15 and 0.5.0 dated 2025-09-19
arcgislayers-0.4.0/arcgislayers/R/arc-add-update-delete.R |only arcgislayers-0.4.0/arcgislayers/man/list_service_raster_fns.Rd |only arcgislayers-0.5.0/arcgislayers/DESCRIPTION | 40 arcgislayers-0.5.0/arcgislayers/MD5 | 81 - arcgislayers-0.5.0/arcgislayers/NAMESPACE | 5 arcgislayers-0.5.0/arcgislayers/NEWS.md | 34 arcgislayers-0.5.0/arcgislayers/R/add_item.R | 11 arcgislayers-0.5.0/arcgislayers/R/arc-add-delete.R |only arcgislayers-0.5.0/arcgislayers/R/arc-definition.R |only arcgislayers-0.5.0/arcgislayers/R/arc-open.R | 190 ++-- arcgislayers-0.5.0/arcgislayers/R/arc-raster.R | 2 arcgislayers-0.5.0/arcgislayers/R/arc-read.R | 24 arcgislayers-0.5.0/arcgislayers/R/arc-select.R | 180 +-- arcgislayers-0.5.0/arcgislayers/R/attachments.R | 7 arcgislayers-0.5.0/arcgislayers/R/print-methods.R | 8 arcgislayers-0.5.0/arcgislayers/R/raster-fns.R | 26 arcgislayers-0.5.0/arcgislayers/R/update-attachments.R |only arcgislayers-0.5.0/arcgislayers/R/update-features.R |only arcgislayers-0.5.0/arcgislayers/R/utils-feature-server.R | 8 arcgislayers-0.5.0/arcgislayers/R/utils-validation.R |only arcgislayers-0.5.0/arcgislayers/R/utils.R | 52 - arcgislayers-0.5.0/arcgislayers/man/arc_open.Rd | 30 arcgislayers-0.5.0/arcgislayers/man/arc_raster.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/arc_read.Rd | 4 arcgislayers-0.5.0/arcgislayers/man/arc_select.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/attachments.Rd | 5 arcgislayers-0.5.0/arcgislayers/man/definition.Rd |only arcgislayers-0.5.0/arcgislayers/man/encode_field_values.Rd | 7 arcgislayers-0.5.0/arcgislayers/man/figures/README-unnamed-chunk-7-1.png |only arcgislayers-0.5.0/arcgislayers/man/get_layer.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/get_layer_estimates.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/modify.Rd | 35 arcgislayers-0.5.0/arcgislayers/man/raster_fns.Rd |only arcgislayers-0.5.0/arcgislayers/man/truncate_layer.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/update_attachments.Rd |only arcgislayers-0.5.0/arcgislayers/tests/testthat.R | 8 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-adding-features.R | 22 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-arc_open.R | 97 ++ arcgislayers-0.5.0/arcgislayers/tests/testthat/test-arc_read.R | 1 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-arc_select.R | 8 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-attachments.R | 4 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-definition.R |only arcgislayers-0.5.0/arcgislayers/tests/testthat/test-delete-feats.R |only arcgislayers-0.5.0/arcgislayers/tests/testthat/test-encode-field-values.R | 459 +++++++++- arcgislayers-0.5.0/arcgislayers/tests/testthat/test-page-size.R | 4 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-raster-fns.R | 5 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-return-geometry.R | 2 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-returned-fields.R | 5 48 files changed, 972 insertions(+), 402 deletions(-)