Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2016. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods 19(1), 10-52) <doi:10.1177/1094428115584005>.
NCA identifies necessary (but not sufficient) conditions in datasets, where x causes (e.g. precedes) y. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations.
(Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates which level of x (e.g. an effort or [...truncated...]
Author: Jan Dul [aut],
Govert Buijs [cre]
Maintainer: Govert Buijs <buijs@rsm.nl>
Diff between NCA versions 4.0.3 dated 2025-10-14 and 4.0.4 dated 2025-11-14
DESCRIPTION | 8 - MD5 | 18 +- NEWS.md | 5 R/nca.R | 1 R/nca_bottleneck.R | 8 - R/nca_tests.R | 4 R/p_bottleneck.R | 383 +++++++++++++++++++++++++++-------------------------- R/p_nca_ce_fdh.R | 6 build/partial.rdb |binary man/NCA-package.Rd | 4 10 files changed, 233 insertions(+), 204 deletions(-)
Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper; see <doi:10.1177/0962280219842890> and discussed in a tutorial <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre],
Giovanna Cilluffo [aut, ctb],
Vito MR Muggeo [aut, ctb]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between islasso versions 1.6.0 dated 2025-07-31 and 1.6.1 dated 2025-11-14
islasso-1.6.0/islasso/NEWS |only islasso-1.6.1/islasso/DESCRIPTION | 13 - islasso-1.6.1/islasso/MD5 | 40 ++- islasso-1.6.1/islasso/NAMESPACE | 1 islasso-1.6.1/islasso/NEWS.md |only islasso-1.6.1/islasso/R/auxiliary.R | 4 islasso-1.6.1/islasso/R/islasso-package.R | 4 islasso-1.6.1/islasso/R/islasso.R | 87 +++++++ islasso-1.6.1/islasso/R/islasso.path.R | 4 islasso-1.6.1/islasso/README.md |only islasso-1.6.1/islasso/build/vignette.rds |only islasso-1.6.1/islasso/inst/doc |only islasso-1.6.1/islasso/man/aic.islasso.Rd | 2 islasso-1.6.1/islasso/man/figures |only islasso-1.6.1/islasso/man/is.control.Rd | 2 islasso-1.6.1/islasso/man/islasso.Rd | 17 + islasso-1.6.1/islasso/man/islasso.path.Rd | 4 islasso-1.6.1/islasso/man/relax.islasso.Rd |only islasso-1.6.1/islasso/man/simulXy.Rd | 6 islasso-1.6.1/islasso/src/auxiliary.f90 | 107 +++++++-- islasso-1.6.1/islasso/src/family_link.f90 | 297 ++++++++++--------------- islasso-1.6.1/islasso/src/gradient_hessian.f90 | 61 +++-- islasso-1.6.1/islasso/src/islasso.f90 | 86 ++++--- islasso-1.6.1/islasso/vignettes |only 24 files changed, 458 insertions(+), 277 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. Supports checks implied
by an SDMX DSD file as well. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6
and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.
Author: Mark van der Loo [cre, aut] ,
Edwin de Jonge [aut] ,
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 1.1.5 dated 2024-02-14 and 1.1.6 dated 2025-11-14
DESCRIPTION | 13 - MD5 | 38 ++-- NEWS | 7 R/compare.R | 4 R/parse.R | 3 R/retailers.R | 3 R/sdmx.R | 2 R/syntax.R | 3 R/yaml.R | 2 build/vignette.rds |binary inst/doc/JSS_3483.pdf |binary inst/doc/cookbook.R | 158 ++++++++--------- inst/doc/cookbook.Rmd | 28 +-- inst/doc/cookbook.html | 369 ++++++++++++++++++++--------------------- inst/tinytest/test_validator.R | 6 man/cells.Rd | 2 man/compare.Rd | 2 man/nace_rev2.Rd | 4 man/syntax.Rd | 3 vignettes/cookbook.Rmd | 28 +-- 20 files changed, 341 insertions(+), 334 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: <https://sdmx.org>.
Author: Attilio Mattiocco [aut, cre]
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 3.7-0 dated 2025-06-05 and 3.8-0 dated 2025-11-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/SdmxClient.R | 15 +++++++++++++-- R/TSConverter.R | 2 +- R/test_automation/test.sdmx.r | 31 ++++++++++++++++++++++++++++--- inst/java/SDMX.jar |binary man/addProvider.Rd | 5 ++--- 7 files changed, 53 insertions(+), 18 deletions(-)
Title: Solver for Delay Differential Equations
Description: Functions for solving systems of delay differential equations by
interfacing with numerical routines written by Simon N. Wood, including
contributions from Benjamin J. Cairns. These numerical routines first
appeared in Simon Wood's 'solv95' program. This package includes a vignette
and a complete user's guide. 'PBSddesolve' originally appeared on CRAN under
the name 'ddesolve'. That version is no longer supported. The current name
emphasizes a close association with other 'PBS' packages, particularly
'PBSmodelling'.
Author: Alex Couture-Beil [aut],
Jon T. Schnute [aut],
Rowan Haigh [aut],
Simon N. Wood [aut],
Benjamin J. Cairns [aut],
Nicholas Boers [ctb],
Nick Fisch [cre]
Maintainer: Nick Fisch <nick.fisch@dfo-mpo.gc.ca>
Diff between PBSddesolve versions 1.13.4 dated 2024-01-09 and 1.13.7 dated 2025-11-14
PBSddesolve-1.13.4/PBSddesolve/inst/doc/ChangeLog.txt |only PBSddesolve-1.13.4/PBSddesolve/inst/doc/License.txt |only PBSddesolve-1.13.4/PBSddesolve/inst/doc/PBSddesolve-UG.pdf |only PBSddesolve-1.13.4/PBSddesolve/inst/doc/index.html |only PBSddesolve-1.13.4/PBSddesolve/inst/doc/solv95.pdf |only PBSddesolve-1.13.7/PBSddesolve/DESCRIPTION | 24 ++++---- PBSddesolve-1.13.7/PBSddesolve/MD5 | 23 +++---- PBSddesolve-1.13.7/PBSddesolve/build |only PBSddesolve-1.13.7/PBSddesolve/inst/doc/PBSddesolveIntro.Rnw |only PBSddesolve-1.13.7/PBSddesolve/inst/doc/PBSddesolveIntro.pdf |binary PBSddesolve-1.13.7/PBSddesolve/man/PBSddesolve.Rd | 19 ++++-- PBSddesolve-1.13.7/PBSddesolve/man/dde.Rd | 29 +++++----- PBSddesolve-1.13.7/PBSddesolve/man/dot-PBSddeEnv.Rd | 10 ++- PBSddesolve-1.13.7/PBSddesolve/man/dot-onClosePBSddeExamples.Rd | 6 +- PBSddesolve-1.13.7/PBSddesolve/man/pastvalue.Rd | 12 ++-- PBSddesolve-1.13.7/PBSddesolve/src/PBSddesolve.c | 5 + 16 files changed, 68 insertions(+), 60 deletions(-)
Title: Kernel Local Polynomial Regression
Description: Computes local polynomial estimators for
the regression and also density. It comprises several
different utilities to handle kernel estimators.
Author: Jorge Luis Ojeda Cabrera [aut],
Bastiaan Quast [cre, ctb]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between locpol versions 0.8.0 dated 2022-11-29 and 0.9.0 dated 2025-11-14
DESCRIPTION | 17 ++++++++--------- MD5 | 8 ++++---- man/PRDenEstC.Rd | 4 ++-- man/locpol.Rd | 2 +- man/locpolSmoothers.Rd | 6 +----- 5 files changed, 16 insertions(+), 21 deletions(-)
Title: Visualize R Data Structures with Trees
Description: A set of tools for inspecting and understanding R data
structures inspired by str(). Includes ast() for visualizing abstract
syntax trees, ref() for showing shared references, cst() for showing
call stack trees, and obj_size() for computing object sizes.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between lobstr versions 1.1.2 dated 2022-06-22 and 1.1.3 dated 2025-11-14
DESCRIPTION | 20 ++++----- LICENSE | 2 MD5 | 46 +++++++++++---------- NEWS.md | 6 ++ R/ast.R | 23 ++++------ R/cst.R | 2 R/lobstr-package.R |only R/ref.R | 40 +++++++++++++----- R/size.R | 2 R/sxp.R | 65 ++++++++++++++++++++++-------- R/tree.R | 91 ++++++++++++++++++++++++++---------------- R/utils.R | 26 ++++++------ README.md | 28 ++++++------ man/figures/logo.png |binary man/lobstr-package.Rd |only src/address.cpp | 9 ++-- src/inspect.cpp | 43 +++++++++++-------- src/size.cpp | 45 +++++++++++++++----- src/utils.h | 7 +++ tests/testthat/_snaps/sxp.md | 10 ++++ tests/testthat/_snaps/tree.md | 4 - tests/testthat/test-ast.R | 1 tests/testthat/test-size.R | 8 +++ tests/testthat/test-sxp.R | 20 ++------- tests/testthat/test-tree.R | 19 +++----- 25 files changed, 318 insertions(+), 199 deletions(-)
Title: Solving Complex Game Problems using Gaussian Processes
Description: Sequential strategies for finding a game equilibrium are proposed in a black-box setting (expensive pay-off evaluations, no derivatives). The algorithm handles noiseless or noisy evaluations. Two acquisition functions are available. Graphical outputs can be generated automatically. V. Picheny, M. Binois, A. Habbal (2018) <doi:10.1007/s10898-018-0688-0>. M. Binois, V. Picheny, P. Taillandier, A. Habbal (2020) <doi:10.48550/arXiv.1902.06565>.
Author: Victor Picheny [aut] ,
Mickael Binois [aut, cre]
Maintainer: Mickael Binois <mickael.binois@inria.fr>
This is a re-admission after prior archival of version 1.2.0 dated 2022-01-23
Diff between GPGame versions 1.2.0 dated 2022-01-23 and 1.2.1 dated 2025-11-14
DESCRIPTION | 25 ++++++++++++++----------- MD5 | 9 +++++---- NEWS | 5 +++++ R/solve_game.R | 10 +++++----- man/solve_game.Rd | 10 +++++----- tests/testthat/Rplots.pdf |only 6 files changed, 34 insertions(+), 25 deletions(-)
Title: A Grammar of Graphics for Comparative Genomics
Description: An extension of 'ggplot2' for creating complex genomic
maps. It builds on the power of 'ggplot2' and 'tidyverse' adding new 'ggplot2'-style
geoms & positions and 'dplyr'-style verbs to manipulate the underlying data. It
implements a layout concept inspired by 'ggraph' and introduces tracks to bring
tidiness to the mess that is genomics data.
Author: Thomas Hackl [aut, cre],
Markus J. Ankenbrand [aut],
Bart van Adrichem [aut],
Kristina Haslinger [ctb, sad]
Maintainer: Thomas Hackl <t.hackl@rug.nl>
This is a re-admission after prior archival of version 1.0.1 dated 2024-08-30
Diff between gggenomes versions 1.0.1 dated 2024-08-30 and 1.1.2 dated 2025-11-14
gggenomes-1.0.1/gggenomes/man/figures/logo-slack.pdf |only gggenomes-1.0.1/gggenomes/man/figures/logo-slack.png |only gggenomes-1.0.1/gggenomes/man/figures/logo-smaller.png |only gggenomes-1.0.1/gggenomes/man/ggplot.gggenomes_layout.Rd |only gggenomes-1.1.2/gggenomes/DESCRIPTION | 20 gggenomes-1.1.2/gggenomes/MD5 | 150 gggenomes-1.1.2/gggenomes/NAMESPACE | 4 gggenomes-1.1.2/gggenomes/NEWS.md |only gggenomes-1.1.2/gggenomes/R/aaa.R | 23 gggenomes-1.1.2/gggenomes/R/align.R |only gggenomes-1.1.2/gggenomes/R/clusters.R | 4 gggenomes-1.1.2/gggenomes/R/data.R | 2 gggenomes-1.1.2/gggenomes/R/feats.R | 12 gggenomes-1.1.2/gggenomes/R/flip.R | 10 gggenomes-1.1.2/gggenomes/R/focus.R | 18 gggenomes-1.1.2/gggenomes/R/geom.R | 15 gggenomes-1.1.2/gggenomes/R/geom_gene.R | 14 gggenomes-1.1.2/gggenomes/R/geom_link.R | 108 gggenomes-1.1.2/gggenomes/R/geom_variant.R | 2 gggenomes-1.1.2/gggenomes/R/geom_wiggle.R | 6 gggenomes-1.1.2/gggenomes/R/gggenomes.R | 44 gggenomes-1.1.2/gggenomes/R/global.R | 4 gggenomes-1.1.2/gggenomes/R/links.R | 26 gggenomes-1.1.2/gggenomes/R/pick.R | 36 gggenomes-1.1.2/gggenomes/R/position_strandpile.R | 8 gggenomes-1.1.2/gggenomes/R/pull_tracks.R | 2 gggenomes-1.1.2/gggenomes/R/ranges.R | 4 gggenomes-1.1.2/gggenomes/R/read_alitv.R | 8 gggenomes-1.1.2/gggenomes/R/read_feats.R | 10 gggenomes-1.1.2/gggenomes/R/read_gff3.R | 39 gggenomes-1.1.2/gggenomes/R/read_paf.R | 2 gggenomes-1.1.2/gggenomes/R/read_seqs.R | 9 gggenomes-1.1.2/gggenomes/R/seqs.R | 10 gggenomes-1.1.2/gggenomes/R/set_class.R | 2 gggenomes-1.1.2/gggenomes/R/shift.R | 2 gggenomes-1.1.2/gggenomes/R/subfeats.R | 12 gggenomes-1.1.2/gggenomes/R/sublinks.R | 26 gggenomes-1.1.2/gggenomes/R/synteny_to_link.R | 2 gggenomes-1.1.2/gggenomes/R/tracks.R | 11 gggenomes-1.1.2/gggenomes/R/zzz.R |only gggenomes-1.1.2/gggenomes/README.md | 20 gggenomes-1.1.2/gggenomes/build/partial.rdb |binary gggenomes-1.1.2/gggenomes/build/vignette.rds |binary gggenomes-1.1.2/gggenomes/inst/CITATION |only gggenomes-1.1.2/gggenomes/inst/doc/emales.R | 248 - gggenomes-1.1.2/gggenomes/inst/doc/emales.Rmd | 2 gggenomes-1.1.2/gggenomes/inst/doc/emales.html | 6 gggenomes-1.1.2/gggenomes/inst/doc/flip.R | 2 gggenomes-1.1.2/gggenomes/inst/doc/flip.Rmd | 2 gggenomes-1.1.2/gggenomes/inst/doc/flip.html | 32 gggenomes-1.1.2/gggenomes/inst/doc/gggenomes.Rmd | 2 gggenomes-1.1.2/gggenomes/inst/doc/gggenomes.pdf |binary gggenomes-1.1.2/gggenomes/man/add_seqs.Rd | 2 gggenomes-1.1.2/gggenomes/man/add_tracks.Rd | 2 gggenomes-1.1.2/gggenomes/man/align.Rd |only gggenomes-1.1.2/gggenomes/man/def_formats.Rd | 22 gggenomes-1.1.2/gggenomes/man/emale_cogs.Rd | 2 gggenomes-1.1.2/gggenomes/man/figures/logo.png |binary gggenomes-1.1.2/gggenomes/man/figures/logo.svg | 2995 ++++++++++++--- gggenomes-1.1.2/gggenomes/man/geom_feat.Rd | 8 gggenomes-1.1.2/gggenomes/man/geom_feat_text.Rd | 14 gggenomes-1.1.2/gggenomes/man/geom_gene.Rd | 38 gggenomes-1.1.2/gggenomes/man/geom_link.Rd | 50 gggenomes-1.1.2/gggenomes/man/geom_seq_break.Rd | 8 gggenomes-1.1.2/gggenomes/man/geom_variant.Rd | 8 gggenomes-1.1.2/gggenomes/man/geom_wiggle.Rd | 14 gggenomes-1.1.2/gggenomes/man/get_seqs.Rd | 2 gggenomes-1.1.2/gggenomes/man/gggenomes.Rd | 8 gggenomes-1.1.2/gggenomes/man/in_range.Rd | 2 gggenomes-1.1.2/gggenomes/man/layout_seqs.Rd | 2 gggenomes-1.1.2/gggenomes/man/pick.Rd | 26 gggenomes-1.1.2/gggenomes/man/pull_track.Rd | 2 gggenomes-1.1.2/gggenomes/man/qw.Rd | 4 gggenomes-1.1.2/gggenomes/man/read_tracks.Rd | 4 gggenomes-1.1.2/gggenomes/man/set_class.Rd | 2 gggenomes-1.1.2/gggenomes/man/split_by.Rd | 2 gggenomes-1.1.2/gggenomes/man/swap_if.Rd | 2 gggenomes-1.1.2/gggenomes/tests/testthat/test_strand.R |only gggenomes-1.1.2/gggenomes/vignettes/emales.Rmd | 2 gggenomes-1.1.2/gggenomes/vignettes/flip.Rmd | 2 gggenomes-1.1.2/gggenomes/vignettes/gggenomes.Rmd | 2 81 files changed, 3202 insertions(+), 982 deletions(-)
Title: Distributed Laplace Factor Model
Description: Distributed estimation method is based on a Laplace factor model to solve the estimates of load and specific variance. The philosophy of the package is described in Guangbao Guo. (2022). <doi:10.1007/s00180-022-01270-z>.
Author: Guangbao Guo [aut, cre],
Siqi Liu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between DLFM versions 0.1.0 dated 2025-10-30 and 0.1.1 dated 2025-11-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++++-- NAMESPACE | 10 ++++++++++ R/DIPC.R |only R/factor.tests.R |only man/DIPC.Rd |only man/factor.tests.Rd |only 7 files changed, 19 insertions(+), 5 deletions(-)
Title: Assessing Skill of Climate Forecasts on Seasonal-to-Decadal
Timescales
Description: Exploits dynamical seasonal forecasts in order to provide
information relevant to stakeholders at the seasonal timescale. The package
contains process-based methods for forecast calibration, bias correction,
statistical and stochastic downscaling, optimal forecast combination and
multivariate verification, as well as basic and advanced tools to obtain
tailored products. This package was developed in the context of the ERA4CS
project MEDSCOPE and the H2020 S2S4E project and includes contributions from
ArticXchange project founded by EU-PolarNet 2. Implements methods described in
Pérez-Zanón et al. (2022) <doi:10.5194/gmd-15-6115-2022>,
Doblas-Reyes et al. (2005) <doi:10.1111/j.1600-0870.2005.00104.x>,
Mishra et al. (2018) <doi:10.1007/s00382-018-4404-z>,
Sanchez-Garcia et al. (2019) <doi:10.5194/asr-16-165-2019>,
Straus et al. (2007) <doi:10.1175/JCLI4070.1>,
Terzago et al. (2018) <doi:10.5194/nhess-18-2825-2018>,
Torralba et al. (2017) <doi:10.117 [...truncated...]
Author: Nuria Perez-Zanon [aut] ,
Louis-Philippe Caron [aut] ,
Carmen Alvarez-Castro [aut] ,
Lauriane Batte [aut],
Carlos Delgado [aut],
Jost von Hardenberg [aut] ,
Llorenc LLedo [aut],
Nicolau Manubens [aut],
Lluis Palma [aut],
Eroteida Sanchez-Garcia [aut] [...truncated...]
Maintainer: Theertha Kariyathan <theertha.kariyathan@bsc.es>
This is a re-admission after prior archival of version 5.2.0 dated 2024-01-25
Diff between CSTools versions 5.2.0 dated 2024-01-25 and 5.3.0 dated 2025-11-14
DESCRIPTION | 56 +-- MD5 | 150 ++++---- NAMESPACE | 8 NEWS.md | 21 + R/AreaWeighted.R |only R/BEI_PDFBest.R | 2 R/CST_Analogs.R | 2 R/CST_BindDim.R |only R/CST_Calibration.R | 122 +++--- R/CST_CategoricalEnsCombination.R | 51 +- R/CST_DynBiasCorrection.R | 4 R/CST_EnsClustering.R | 26 - R/CST_MergeDims.R | 14 R/CST_MultiEOF.R | 6 R/CST_QuantileMapping.R | 215 +++++++----- R/CST_SaveExp.R | 16 R/CST_SplitDim.R | 29 + R/CST_Start.R | 24 + R/CST_Subset.R | 3 R/CST_Summary.R |only R/EvalTrainIndices.R |only R/PlotCombinedMap.R | 33 + R/PlotForecastPDF.R | 28 - R/PlotMostLikelyQuantileMap.R | 18 - R/PlotTriangles4Categories.R | 19 - R/as.s2dv_cube.R | 11 R/print.s2dv_cube.R | 4 R/sample_data.R | 3 R/sample_data_st.R | 3 R/zzz.R | 8 README.md | 10 build/partial.rdb |binary build/vignette.rds |binary data/lonlat_prec.rda |binary data/lonlat_prec_st.rda |binary data/lonlat_temp.rda |binary data/lonlat_temp_st.rda |binary inst/doc/Analogs_vignette.R | 2 inst/doc/Analogs_vignette.html | 553 +++++++++++-------------------- inst/doc/BestEstimateIndex_vignette.html | 304 +++++------------ inst/doc/Data_Considerations.Rmd | 2 inst/doc/Data_Considerations.html | 448 ++++++++++--------------- inst/doc/ENSclustering_vignette.html | 478 ++++++++++---------------- inst/doc/MostLikelyTercile_vignette.html | 473 ++++++++++---------------- inst/doc/MultiModelSkill_vignette.html | 476 ++++++++++---------------- inst/doc/MultivarRMSE_vignette.html | 462 ++++++++++--------------- inst/doc/PlotForecastPDF.html | 392 ++++++++------------- inst/doc/RainFARM_vignette.R | 2 inst/doc/RainFARM_vignette.html | 445 +++++++++--------------- inst/doc/WeatherRegimes_vignette.Rmd | 2 inst/doc/WeatherRegimes_vignette.html | 456 ++++++++++--------------- man/AreaWeighted.Rd |only man/BindDim.Rd |only man/CST_AreaWeighted.Rd |only man/CST_BindDim.Rd |only man/CST_Calibration.Rd | 22 - man/CST_CategoricalEnsCombination.Rd | 17 man/CST_EnsClustering.Rd | 2 man/CST_MergeDims.Rd | 4 man/CST_QuantileMapping.Rd | 26 + man/CST_SaveExp.Rd | 4 man/CST_SplitDim.Rd | 5 man/CST_Start.Rd | 17 man/CST_Summary.Rd |only man/Calibration.Rd | 27 + man/CategoricalEnsCombination.Rd | 24 + man/EnsClustering.Rd | 2 man/EvalTrainIndices.Rd |only man/MergeDims.Rd | 3 man/PlotCombinedMap.Rd | 26 + man/PlotMostLikelyQuantileMap.Rd | 20 - man/QuantileMapping.Rd | 41 +- man/SaveExp.Rd | 5 man/SplitDim.Rd | 6 man/lonlat_prec.Rd | 32 - man/lonlat_prec_st.Rd | 32 - man/lonlat_temp.Rd | 29 - man/lonlat_temp_st.Rd | 35 + man/print.s2dv_cube.Rd | 4 vignettes/Data_Considerations.Rmd | 2 vignettes/WeatherRegimes_vignette.Rmd | 2 81 files changed, 2565 insertions(+), 3203 deletions(-)
Title: Interface to the arXiv API
Description: An interface to the API for 'arXiv',
a repository of electronic preprints for
computer science, mathematics, physics, quantitative biology,
quantitative finance, and statistics.
Author: Karthik Ram [aut] ,
Karl Broman [aut, cre]
Maintainer: Karl Broman <broman@wisc.edu>
Diff between aRxiv versions 0.12 dated 2025-07-29 and 0.14 dated 2025-11-14
DESCRIPTION | 10 MD5 | 36 +- NEWS.md | 20 + R/arxiv_count.R | 4 R/arxiv_search.R | 10 R/can_arxiv_connect.R | 2 build/vignette.rds |binary data/arxiv_cats.RData |binary data/query_terms.RData |binary inst/doc/aRxiv.R | 20 + inst/doc/aRxiv.Rmd | 50 ++-- inst/doc/aRxiv.html | 484 ++++++++++++++++++++++++--------------- man/arxiv_count.Rd | 2 man/arxiv_search.Rd | 4 tests/testthat/test-clean.R | 268 ++++++++++----------- tests/testthat/test-date_range.R | 13 - tests/testthat/test-search.R | 23 - tests/testthat/test-sort.R | 2 vignettes/aRxiv.Rmd | 50 ++-- 19 files changed, 576 insertions(+), 422 deletions(-)
Title: Penalized Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects is a general model for longitudinal data. Here we proposed to solve it by several methods. The estimation methods include three loss functions as check, asymmetric least square and asymmetric Huber functions; and three structures as simple regression, fixed effects and fixed effects with penalized intercepts by LASSO.
Author: Ian Meneghel Danilevicz [aut, cre] ,
Valderio A Reisen [aut],
Pascal Bondon [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Diff between pqrfe versions 1.1 dated 2022-12-01 and 1.2 dated 2025-11-14
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- build/partial.rdb |binary src/Makevars | 1 - src/Makevars.win | 1 - 5 files changed, 10 insertions(+), 12 deletions(-)
Title: SDTM Datacut
Description: Supports the process of applying a cut to Standard Data Tabulation Model (SDTM),
as part of the analysis of specific points in time of the data, normally as part of
investigation into clinical trials. The functions support different approaches of
cutting to the different domains of SDTM normally observed.
Author: Tim Barnett [cph, aut, cre],
Nathan Rees [aut],
Alana Harris [aut],
Cara Andrews [aut]
Maintainer: Tim Barnett <timothy.barnett@roche.com>
Diff between datacutr versions 0.2.3 dated 2025-02-03 and 0.2.4 dated 2025-11-14
DESCRIPTION | 13 +-- MD5 | 60 +++++++-------- NAMESPACE | 4 + NEWS.md | 80 +++++++++++++------- R/apply_cut.R | 69 +++++++++--------- R/create_dcut.R | 70 +++++++++++++----- R/datcutr-package.R | 4 - R/date_cut.R | 41 ++++++---- R/impute_dcutdtc.R | 2 R/impute_sdtm.R | 2 R/pt_cut.R | 27 ++++--- R/read_out.R | 29 +++++++ R/special_dm_cut.R | 60 ++++++++------- build/vignette.rds |binary data/datacutr_dm.rda |binary inst/WORDLIST | 1 inst/doc/examplemodular.html | 2 inst/doc/examplewrapped.html | 2 inst/doc/modular.html | 10 +- inst/doc/variable_cut.html | 26 +++--- inst/doc/wrapper.html | 2 inst/read-out/read_out.Rmd | 2 man/apply_cut.Rd | 4 - man/create_dcut.Rd | 20 ++--- man/date_cut.Rd | 2 tests/testthat/test-apply_cut.R | 40 +++++++++- tests/testthat/test-create_dcut.R | 77 +++++++++++++++++++- tests/testthat/test-date_cut.R | 23 ++++++ tests/testthat/test-process_cut.R | 134 ++++++++++++++++++++++++++++++++++- tests/testthat/test-pt_cut.R | 20 +++++ tests/testthat/test-special_dm_cut.R | 26 ++++++ 31 files changed, 640 insertions(+), 212 deletions(-)
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Description: A system for 'declaratively' creating graphics, based on "The
Grammar of Graphics". You provide the data, tell 'ggplot2' how to map
variables to aesthetics, what graphical primitives to use, and it
takes care of the details.
Author: Hadley Wickham [aut] ,
Winston Chang [aut] ,
Lionel Henry [aut],
Thomas Lin Pedersen [aut, cre] ,
Kohske Takahashi [aut],
Claus Wilke [aut] ,
Kara Woo [aut] ,
Hiroaki Yutani [aut] ,
Dewey Dunnington [aut] ,
Teun van den Brand [aut] ,
Posit, PBC [cph, [...truncated...]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ggplot2 versions 4.0.0 dated 2025-09-11 and 4.0.1 dated 2025-11-14
ggplot2-4.0.0/ggplot2/inst/doc/extending-ggplot2.Rmd |only ggplot2-4.0.0/ggplot2/inst/doc/ggplot2-in-packages.Rmd |only ggplot2-4.0.0/ggplot2/inst/doc/ggplot2-specs.Rmd |only ggplot2-4.0.0/ggplot2/inst/doc/ggplot2.Rmd |only ggplot2-4.0.0/ggplot2/vignettes/extending-ggplot2.Rmd |only ggplot2-4.0.0/ggplot2/vignettes/ggplot2-in-packages.Rmd |only ggplot2-4.0.0/ggplot2/vignettes/ggplot2-specs.Rmd |only ggplot2-4.0.0/ggplot2/vignettes/ggplot2.Rmd |only ggplot2-4.0.1/ggplot2/DESCRIPTION | 14 ggplot2-4.0.1/ggplot2/MD5 | 259 ggplot2-4.0.1/ggplot2/NEWS.md | 43 ggplot2-4.0.1/ggplot2/R/aes-evaluation.R | 20 ggplot2-4.0.1/ggplot2/R/backports.R | 19 ggplot2-4.0.1/ggplot2/R/bin.R | 7 ggplot2-4.0.1/ggplot2/R/facet-.R | 24 ggplot2-4.0.1/ggplot2/R/fortify-map.R | 2 ggplot2-4.0.1/ggplot2/R/fortify-models.R | 10 ggplot2-4.0.1/ggplot2/R/geom-abline.R | 8 ggplot2-4.0.1/ggplot2/R/geom-count.R | 2 ggplot2-4.0.1/ggplot2/R/geom-errorbar.R | 4 ggplot2-4.0.1/ggplot2/R/geom-hline.R | 9 ggplot2-4.0.1/ggplot2/R/geom-label.R | 1 ggplot2-4.0.1/ggplot2/R/geom-path.R | 2 ggplot2-4.0.1/ggplot2/R/geom-polygon.R | 16 ggplot2-4.0.1/ggplot2/R/geom-ribbon.R | 7 ggplot2-4.0.1/ggplot2/R/geom-text.R | 1 ggplot2-4.0.1/ggplot2/R/geom-violin.R | 3 ggplot2-4.0.1/ggplot2/R/geom-vline.R | 9 ggplot2-4.0.1/ggplot2/R/guide-axis.R | 5 ggplot2-4.0.1/ggplot2/R/guide-colorbar.R | 4 ggplot2-4.0.1/ggplot2/R/guides-.R | 13 ggplot2-4.0.1/ggplot2/R/labeller.R | 2 ggplot2-4.0.1/ggplot2/R/labels.R | 30 ggplot2-4.0.1/ggplot2/R/layer.R | 37 ggplot2-4.0.1/ggplot2/R/legend-draw.R | 35 ggplot2-4.0.1/ggplot2/R/plot-construction.R | 9 ggplot2-4.0.1/ggplot2/R/plot.R | 2 ggplot2-4.0.1/ggplot2/R/position-.R | 11 ggplot2-4.0.1/ggplot2/R/position-stack.R | 4 ggplot2-4.0.1/ggplot2/R/reshape-add-margins.R | 2 ggplot2-4.0.1/ggplot2/R/scale-.R | 93 ggplot2-4.0.1/ggplot2/R/scale-alpha.R | 24 ggplot2-4.0.1/ggplot2/R/scale-colour.R | 58 ggplot2-4.0.1/ggplot2/R/scale-discrete-.R | 2 ggplot2-4.0.1/ggplot2/R/scale-expansion.R | 2 ggplot2-4.0.1/ggplot2/R/scale-gradient.R | 2 ggplot2-4.0.1/ggplot2/R/scale-grey.R | 2 ggplot2-4.0.1/ggplot2/R/scale-hue.R | 2 ggplot2-4.0.1/ggplot2/R/scale-linetype.R | 6 ggplot2-4.0.1/ggplot2/R/scale-linewidth.R | 32 ggplot2-4.0.1/ggplot2/R/scale-manual.R | 2 ggplot2-4.0.1/ggplot2/R/scale-shape.R | 14 ggplot2-4.0.1/ggplot2/R/scale-size.R | 38 ggplot2-4.0.1/ggplot2/R/scale-steps.R | 2 ggplot2-4.0.1/ggplot2/R/scales-.R | 2 ggplot2-4.0.1/ggplot2/R/stat-align.R | 7 ggplot2-4.0.1/ggplot2/R/stat-boxplot.R | 15 ggplot2-4.0.1/ggplot2/R/stat-contour.R | 2 ggplot2-4.0.1/ggplot2/R/stat-ydensity.R | 7 ggplot2-4.0.1/ggplot2/R/theme-current.R | 6 ggplot2-4.0.1/ggplot2/R/theme-sub.R | 34 ggplot2-4.0.1/ggplot2/R/theme.R | 7 ggplot2-4.0.1/ggplot2/R/utilities-grid.R | 9 ggplot2-4.0.1/ggplot2/R/utilities-resolution.R | 9 ggplot2-4.0.1/ggplot2/R/utilities.R | 7 ggplot2-4.0.1/ggplot2/R/zzz.R | 2 ggplot2-4.0.1/ggplot2/README.md | 10 ggplot2-4.0.1/ggplot2/build/vignette.rds |binary ggplot2-4.0.1/ggplot2/inst/doc/extending-ggplot2.R | 125 ggplot2-4.0.1/ggplot2/inst/doc/extending-ggplot2.html | 2847 ++++------ ggplot2-4.0.1/ggplot2/inst/doc/extending-ggplot2.qmd |only ggplot2-4.0.1/ggplot2/inst/doc/ggplot2-in-packages.R | 24 ggplot2-4.0.1/ggplot2/inst/doc/ggplot2-in-packages.html | 758 -- ggplot2-4.0.1/ggplot2/inst/doc/ggplot2-in-packages.qmd |only ggplot2-4.0.1/ggplot2/inst/doc/ggplot2-specs.R | 69 ggplot2-4.0.1/ggplot2/inst/doc/ggplot2-specs.html | 838 -- ggplot2-4.0.1/ggplot2/inst/doc/ggplot2-specs.qmd |only ggplot2-4.0.1/ggplot2/inst/doc/ggplot2.R | 55 ggplot2-4.0.1/ggplot2/inst/doc/ggplot2.html | 616 -- ggplot2-4.0.1/ggplot2/inst/doc/ggplot2.qmd |only ggplot2-4.0.1/ggplot2/inst/doc/profiling.R |only ggplot2-4.0.1/ggplot2/inst/doc/profiling.html |only ggplot2-4.0.1/ggplot2/inst/doc/profiling.qmd |only ggplot2-4.0.1/ggplot2/man/binned_scale.Rd | 4 ggplot2-4.0.1/ggplot2/man/continuous_scale.Rd | 4 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ggplot2-4.0.1/ggplot2/vignettes/ggplot2.qmd |only ggplot2-4.0.1/ggplot2/vignettes/profiling.qmd |only 141 files changed, 3142 insertions(+), 3739 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 1.3.24 dated 2025-06-25 and 1.3.31 dated 2025-11-14
DESCRIPTION | 15 +- MD5 | 53 ++++----- NAMESPACE | 5 NEWS.md | 17 +++ R/arrow3d.R | 3 R/latex3d.R |only R/mesh3d.R | 7 - R/persp3d.R | 3 R/plot3d.R | 3 R/plotmath3d.R | 6 - R/ply.R | 4 R/zzz.R | 15 ++ README.md | 17 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/WebGL.html | 31 ++--- inst/doc/demos.html | 93 ++++++++-------- inst/doc/deprecation.html | 9 - inst/doc/pkgdown.html | 11 +- inst/doc/rgl.Rmd | 20 ++- inst/doc/rgl.html | 247 ++++++++++++++++++++++++--------------------- inst/doc/transparency.html | 29 ++--- man/material.Rd | 6 - man/persp3d.tri.Rd | 30 ----- man/plotmath3d.Rd | 65 ++++++++--- man/writeOBJ.Rd | 5 man/writePLY.Rd | 5 vignettes/rgl.Rmd | 20 ++- 28 files changed, 404 insertions(+), 315 deletions(-)
Title: Bayesian Optimization of Hyperparameters
Description: A Pure R implementation of Bayesian Global Optimization with Gaussian Processes.
Author: Yachen Yan [aut, cre]
Maintainer: Yachen Yan <yanyachen21@gmail.com>
Diff between rBayesianOptimization versions 1.2.1 dated 2024-04-13 and 1.2.2 dated 2025-11-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/BayesianOptimization.R | 2 +- man/BayesianOptimization.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
More information about rBayesianOptimization at CRAN
Permanent link
Title: Syntax Highlighting and Automatic Linking
Description: Syntax highlighting of R code, specifically designed for the
needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and
'bookdown'. It includes linking of function calls to their
documentation on the web, and automatic translation of ANSI escapes in
output to the equivalent HTML.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between downlit versions 0.4.4 dated 2024-06-10 and 0.4.5 dated 2025-11-14
DESCRIPTION | 8 +- MD5 | 42 ++++++------ NEWS.md | 4 + R/downlit-html.R | 13 +++ R/downlit-md.R | 72 +++++++++++++++------- R/evaluate.R | 88 +++++++++++++++++++------- R/highlight.R | 121 +++++++++++++++++++++++++++++-------- R/link.R | 42 ++++++++++-- R/metadata.R | 15 +++- R/topic-index.R | 3 R/utils.R | 12 ++- README.md | 2 man/downlit_html_path.Rd | 2 man/downlit_md_path.Rd | 2 tests/testthat/_snaps/evaluate.md | 2 tests/testthat/test-downlit-html.R | 3 tests/testthat/test-evaluate.R | 40 +++++++++--- tests/testthat/test-highlight.R | 18 +++-- tests/testthat/test-link.R | 77 ++++++++++++++++------- tests/testthat/test-metadata.R | 5 + tests/testthat/test-packages.R | 23 +++---- tests/testthat/test-topic-index.R | 5 + 22 files changed, 433 insertions(+), 166 deletions(-)
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] ,
Marcel Ramos [aut, cre]
Maintainer: Marcel Ramos <marcel.ramos@sph.cuny.edu>
Diff between BiocManager versions 1.30.26 dated 2025-06-05 and 1.30.27 dated 2025-11-14
DESCRIPTION | 6 +- MD5 | 13 +++--- README.md | 36 ++++++++--------- inst/doc/BiocManager.html | 20 ++++----- man/figures |only tests/testthat/test_install.R | 88 ++++++++++++++---------------------------- tests/testthat/test_valid.R | 4 - tests/testthat/test_version.R | 44 ++++++++++----------- 8 files changed, 93 insertions(+), 118 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-17 1.0.5
Title: Fast Agent-Based Epi Models
Description: A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Author: George Vega Yon [aut, cre] ,
Derek Meyer [aut] ,
Andrew Pulsipher [aut] ,
Susan Holmes [rev] ,
Abinash Satapathy [rev] ,
Carinogurjao [rev],
Centers for Disease Control and Prevention [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between epiworldR versions 0.8.3.0 dated 2025-06-12 and 0.10.0.0 dated 2025-11-14
epiworldR-0.10.0.0/epiworldR/DESCRIPTION | 20 epiworldR-0.10.0.0/epiworldR/MD5 | 291 +++---- epiworldR-0.10.0.0/epiworldR/NAMESPACE | 6 epiworldR-0.10.0.0/epiworldR/NEWS.md | 44 + epiworldR-0.10.0.0/epiworldR/R/LFMCMC.R | 7 epiworldR-0.10.0.0/epiworldR/R/ModelDiagram.R | 104 +- epiworldR-0.10.0.0/epiworldR/R/ModelDiffNet.R | 17 epiworldR-0.10.0.0/epiworldR/R/ModelMeaslesMixing.R |only epiworldR-0.10.0.0/epiworldR/R/ModelMeaslesMixingRiskQuarantine.R |only epiworldR-0.10.0.0/epiworldR/R/ModelMeaslesSchool.R |only epiworldR-0.10.0.0/epiworldR/R/ModelSEIR.R | 15 epiworldR-0.10.0.0/epiworldR/R/ModelSEIRCONN.R | 19 epiworldR-0.10.0.0/epiworldR/R/ModelSEIRD.R | 17 epiworldR-0.10.0.0/epiworldR/R/ModelSEIRDCONN.R | 22 epiworldR-0.10.0.0/epiworldR/R/ModelSEIRMixing.R | 24 epiworldR-0.10.0.0/epiworldR/R/ModelSEIRMixingQuarantine.R |only epiworldR-0.10.0.0/epiworldR/R/ModelSIR.R | 13 epiworldR-0.10.0.0/epiworldR/R/ModelSIRCONN.R | 7 epiworldR-0.10.0.0/epiworldR/R/ModelSIRD.R | 7 epiworldR-0.10.0.0/epiworldR/R/ModelSIRDCONN.R | 19 epiworldR-0.10.0.0/epiworldR/R/ModelSIRLogit.R | 24 epiworldR-0.10.0.0/epiworldR/R/ModelSIRMixing.R | 19 epiworldR-0.10.0.0/epiworldR/R/ModelSIS.R | 11 epiworldR-0.10.0.0/epiworldR/R/ModelSISD.R | 13 epiworldR-0.10.0.0/epiworldR/R/ModelSURV.R | 29 epiworldR-0.10.0.0/epiworldR/R/agents-methods.R | 1 epiworldR-0.10.0.0/epiworldR/R/agents.R | 17 epiworldR-0.10.0.0/epiworldR/R/cpp11.R | 16 epiworldR-0.10.0.0/epiworldR/R/data.R | 49 - epiworldR-0.10.0.0/epiworldR/R/entity.R | 41 epiworldR-0.10.0.0/epiworldR/R/epiworldR-package.R | 1 epiworldR-0.10.0.0/epiworldR/R/global-actions.R | 23 epiworldR-0.10.0.0/epiworldR/R/make_saver.R | 137 ++- epiworldR-0.10.0.0/epiworldR/R/model-methods.R | 20 epiworldR-0.10.0.0/epiworldR/R/plot_epi.R | 24 epiworldR-0.10.0.0/epiworldR/R/tool.R | 29 epiworldR-0.10.0.0/epiworldR/R/virus.R | 27 epiworldR-0.10.0.0/epiworldR/README.md | 112 +- epiworldR-0.10.0.0/epiworldR/build/partial.rdb |binary epiworldR-0.10.0.0/epiworldR/build/vignette.rds |binary epiworldR-0.10.0.0/epiworldR/configure | 19 epiworldR-0.10.0.0/epiworldR/configure.ac | 2 epiworldR-0.10.0.0/epiworldR/inst/doc/advanced-modeling.Rmd | 2 epiworldR-0.10.0.0/epiworldR/inst/doc/advanced-modeling.html | 12 epiworldR-0.10.0.0/epiworldR/inst/doc/getting-started.R | 13 epiworldR-0.10.0.0/epiworldR/inst/doc/getting-started.Rmd | 19 epiworldR-0.10.0.0/epiworldR/inst/doc/getting-started.html | 289 +++--- epiworldR-0.10.0.0/epiworldR/inst/doc/likelihood-free-mcmc.R | 8 epiworldR-0.10.0.0/epiworldR/inst/doc/likelihood-free-mcmc.Rmd | 10 epiworldR-0.10.0.0/epiworldR/inst/doc/likelihood-free-mcmc.html | 44 - epiworldR-0.10.0.0/epiworldR/inst/doc/mixing.html | 10 epiworldR-0.10.0.0/epiworldR/inst/doc/run-multiple.html | 4 epiworldR-0.10.0.0/epiworldR/inst/include/epiworld/agent-bones.hpp | 8 epiworldR-0.10.0.0/epiworldR/inst/include/epiworld/agent-events-meat.hpp | 16 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