Title: Variational Multivariate Spatial Small Area Estimation
Description: Variational Autoencoded Multivariate Spatial Fay-Herriot models are designed to efficiently estimate population parameters in small area estimation. This package implements the variational generalized multivariate spatial Fay-Herriot model (VGMSFH) using 'NumPyro' and 'PyTorch' backends, as demonstrated by Wang, Parker, and Holan (2025) <doi:10.48550/arXiv.2503.14710>. The 'vmsae' package provides utility functions to load weights of the pretrained variational autoencoders (VAEs) as well as tools to train custom VAEs tailored to users specific applications.
Author: Zhenhua Wang [aut, cre],
Paul A. Parker [aut, res],
Scott H. Holan [aut, res]
Maintainer: Zhenhua Wang <zhenhua.wang@missouri.edu>
Diff between vmsae versions 0.1.1 dated 2025-06-20 and 0.1.2 dated 2025-10-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/py/vgmsfh.py | 34 +++++++++++++++++----------------- 3 files changed, 22 insertions(+), 22 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with 'Rscript' to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L. Davis [aut, cre] ,
Allen Day [ctb] ,
Python Software Foundation [ctb] ,
Paul Newell [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 2.2.5 dated 2024-12-20 and 2.3.1 dated 2025-10-08
DESCRIPTION | 11 MD5 | 16 NEWS.md | 37 +- R/argparse.R | 733 +++++++++++++++++++++++------------------ build/vignette.rds |binary exec/display_file.R | 49 +- exec/example.R | 98 +++-- inst/doc/argparse.html | 227 ++++++------ tests/testthat/test-argparse.R | 689 +++++++++++++++++++++----------------- 9 files changed, 1054 insertions(+), 806 deletions(-)
Title: Manipulating External Pointers
Description: There is limited native support for external pointers in the R interface.
This package provides some basic tools to verify, create and modify 'externalptr' objects.
Author: Randy Lai [aut],
Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
This is a re-admission after prior archival of version 1.1.3 dated 2020-04-03
Diff between xptr versions 1.1.3 dated 2020-04-03 and 1.2.0 dated 2025-10-08
ChangeLog |only DESCRIPTION | 30 ++++++------- LICENSE | 4 - MD5 | 41 ++++++++++-------- NAMESPACE | 2 R/xptr.R | 92 +++++++++++++++++++++-------------------- README.md | 52 +++++++++++++++++++---- cleanup |only inst |only man/is_null_xptr.Rd | 4 - man/is_xptr.Rd | 4 - man/new_xptr.Rd | 6 +- man/register_xptr_finalizer.Rd | 11 +++- man/set_xptr_address.Rd | 7 ++- man/set_xptr_protected.Rd | 11 +++- man/set_xptr_tag.Rd | 11 +++- man/xptr.Rd | 9 ++-- man/xptr_address.Rd | 9 ++-- man/xptr_clear.Rd | 5 +- man/xptr_protected.Rd | 4 - man/xptr_tag.Rd | 4 - src/xptr.c | 32 ++++++++------ tests |only 23 files changed, 206 insertions(+), 132 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 13. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood est [...truncated...]
Author: Anthony Hammond [aut, cre],
Environment Agency [ctb],
JBA Consulting [ctb]
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.4.0 dated 2025-02-09 and 1.0.1 dated 2025-10-08
UKFE-0.4.0/UKFE/data/AMSP.csv |only UKFE-0.4.0/UKFE/data/NRFAData.csv |only UKFE-0.4.0/UKFE/data/QMEDData.csv |only UKFE-0.4.0/UKFE/data/ThamesPQ.csv |only UKFE-0.4.0/UKFE/data/UKOutline.csv |only UKFE-1.0.1/UKFE/DESCRIPTION | 25 UKFE-1.0.1/UKFE/MD5 | 289 UKFE-1.0.1/UKFE/NAMESPACE | 16 UKFE-1.0.1/UKFE/NEWS.md |only UKFE-1.0.1/UKFE/R/AMSP.R | 26 UKFE-1.0.1/UKFE/R/All.R |12991 +++++++++++++++++-------------- UKFE-1.0.1/UKFE/R/FlowAnalysis.R | 589 - UKFE-1.0.1/UKFE/R/GISfuncs.R | 209 UKFE-1.0.1/UKFE/R/GetData.R | 1620 ++- UKFE-1.0.1/UKFE/R/NRFAData.R | 18 UKFE-1.0.1/UKFE/R/QMEDData.R | 18 UKFE-1.0.1/UKFE/R/RainfallAnalysis.R | 220 UKFE-1.0.1/UKFE/R/ThamesPQ.R | 28 UKFE-1.0.1/UKFE/R/UKOutline.R | 22 UKFE-1.0.1/UKFE/README.md |only UKFE-1.0.1/UKFE/build |only UKFE-1.0.1/UKFE/data/AMSP.rda |binary UKFE-1.0.1/UKFE/data/NRFAData.rda |binary UKFE-1.0.1/UKFE/data/QMEDData.rda |binary UKFE-1.0.1/UKFE/data/ThamesPQ.rda |binary UKFE-1.0.1/UKFE/data/UKOutline.rda |binary UKFE-1.0.1/UKFE/inst |only UKFE-1.0.1/UKFE/man/AMImport.Rd | 13 UKFE-1.0.1/UKFE/man/AMSP.Rd | 4 UKFE-1.0.1/UKFE/man/AMplot.Rd | 3 UKFE-1.0.1/UKFE/man/ARF.Rd | 3 UKFE-1.0.1/UKFE/man/AddGauge.Rd | 28 UKFE-1.0.1/UKFE/man/AggDayHour.Rd | 26 UKFE-1.0.1/UKFE/man/AnnualStat.Rd | 21 UKFE-1.0.1/UKFE/man/BFI.Rd | 9 UKFE-1.0.1/UKFE/man/Bootstrap.Rd | 21 UKFE-1.0.1/UKFE/man/CDsXML.Rd | 17 UKFE-1.0.1/UKFE/man/ConvertGridRef.Rd | 6 UKFE-1.0.1/UKFE/man/DDF.Rd | 16 UKFE-1.0.1/UKFE/man/DDF99.Rd | 14 UKFE-1.0.1/UKFE/man/DDF99Pars.Rd | 19 UKFE-1.0.1/UKFE/man/DDFExtract.Rd | 16 UKFE-1.0.1/UKFE/man/DDFImport.Rd | 19 UKFE-1.0.1/UKFE/man/DeTrend.Rd | 12 UKFE-1.0.1/UKFE/man/DesHydro.Rd | 9 UKFE-1.0.1/UKFE/man/DiagPlots.Rd | 14 UKFE-1.0.1/UKFE/man/DonAdj.Rd | 19 UKFE-1.0.1/UKFE/man/ERPlot.Rd | 27 UKFE-1.0.1/UKFE/man/EVPlot.Rd | 7 UKFE-1.0.1/UKFE/man/EVPlotAdd.Rd | 39 UKFE-1.0.1/UKFE/man/EVPool.Rd | 42 UKFE-1.0.1/UKFE/man/EncProb.Rd | 10 UKFE-1.0.1/UKFE/man/FlowDurationCurve.Rd | 30 UKFE-1.0.1/UKFE/man/FlowSplit.Rd | 45 UKFE-1.0.1/UKFE/man/GEVAM.Rd | 16 UKFE-1.0.1/UKFE/man/GEVEst.Rd | 24 UKFE-1.0.1/UKFE/man/GEVGF.Rd | 3 UKFE-1.0.1/UKFE/man/GEVPars.Rd | 30 UKFE-1.0.1/UKFE/man/GenLogAM.Rd | 16 UKFE-1.0.1/UKFE/man/GenLogEst.Rd | 23 UKFE-1.0.1/UKFE/man/GenLogGF.Rd | 3 UKFE-1.0.1/UKFE/man/GenLogPars.Rd | 28 UKFE-1.0.1/UKFE/man/GenParetoEst.Rd | 26 UKFE-1.0.1/UKFE/man/GenParetoGF.Rd | 16 UKFE-1.0.1/UKFE/man/GenParetoPOT.Rd | 18 UKFE-1.0.1/UKFE/man/GenParetoPars.Rd | 29 UKFE-1.0.1/UKFE/man/GetAM.Rd | 8 UKFE-1.0.1/UKFE/man/GetCDs.Rd | 7 UKFE-1.0.1/UKFE/man/GetDataEA_QH.Rd | 38 UKFE-1.0.1/UKFE/man/GetDataEA_Rain.Rd | 33 UKFE-1.0.1/UKFE/man/GetDataMetOffice.Rd | 16 UKFE-1.0.1/UKFE/man/GetDataNRFA.Rd | 16 UKFE-1.0.1/UKFE/man/GetDataSEPA_QH.Rd | 33 UKFE-1.0.1/UKFE/man/GetDataSEPA_Rain.Rd | 27 UKFE-1.0.1/UKFE/man/GetQMED.Rd | 5 UKFE-1.0.1/UKFE/man/GoFCompare.Rd | 7 UKFE-1.0.1/UKFE/man/GoFComparePool.Rd | 7 UKFE-1.0.1/UKFE/man/GumbelAM.Rd | 16 UKFE-1.0.1/UKFE/man/GumbelEst.Rd | 16 UKFE-1.0.1/UKFE/man/GumbelGF.Rd | 3 UKFE-1.0.1/UKFE/man/GumbelPars.Rd | 23 UKFE-1.0.1/UKFE/man/H2.Rd | 11 UKFE-1.0.1/UKFE/man/HydroPlot.Rd | 11 UKFE-1.0.1/UKFE/man/Kappa3AM.Rd | 16 UKFE-1.0.1/UKFE/man/Kappa3Est.Rd | 24 UKFE-1.0.1/UKFE/man/Kappa3GF.Rd | 10 UKFE-1.0.1/UKFE/man/Kappa3Pars.Rd | 20 UKFE-1.0.1/UKFE/man/LKurt.Rd | 7 UKFE-1.0.1/UKFE/man/LMoments.Rd | 7 UKFE-1.0.1/UKFE/man/LRatioChange.Rd | 16 UKFE-1.0.1/UKFE/man/LSkew.Rd | 7 UKFE-1.0.1/UKFE/man/LSkewUrb.Rd | 22 UKFE-1.0.1/UKFE/man/Lcv.Rd | 7 UKFE-1.0.1/UKFE/man/LcvUrb.Rd | 20 UKFE-1.0.1/UKFE/man/MonthlyStats.Rd | 14 UKFE-1.0.1/UKFE/man/NGRDist.Rd | 16 UKFE-1.0.1/UKFE/man/NRFAData.Rd | 4 UKFE-1.0.1/UKFE/man/NonFloodAdj.Rd | 13 UKFE-1.0.1/UKFE/man/NonFloodAdjPool.Rd | 18 UKFE-1.0.1/UKFE/man/OptimPars.Rd | 7 UKFE-1.0.1/UKFE/man/POTextract.Rd | 29 UKFE-1.0.1/UKFE/man/POTt.Rd | 18 UKFE-1.0.1/UKFE/man/Pool.Rd | 41 UKFE-1.0.1/UKFE/man/PoolEst.Rd | 26 UKFE-1.0.1/UKFE/man/PoolSmall.Rd | 25 UKFE-1.0.1/UKFE/man/QMED.Rd | 28 UKFE-1.0.1/UKFE/man/QMEDData.Rd | 4 UKFE-1.0.1/UKFE/man/QMEDDonEq.Rd | 35 UKFE-1.0.1/UKFE/man/QMEDLink.Rd | 5 UKFE-1.0.1/UKFE/man/QMEDPOT.Rd | 7 UKFE-1.0.1/UKFE/man/QMEDfseSS.Rd | 7 UKFE-1.0.1/UKFE/man/QuickResults.Rd | 24 UKFE-1.0.1/UKFE/man/Rating.Rd | 23 UKFE-1.0.1/UKFE/man/ReFH.Rd | 19 UKFE-1.0.1/UKFE/man/SCF.Rd | 5 UKFE-1.0.1/UKFE/man/SimData.Rd | 8 UKFE-1.0.1/UKFE/man/TrendTest.Rd | 20 UKFE-1.0.1/UKFE/man/UAF.Rd | 13 UKFE-1.0.1/UKFE/man/UEF.Rd | 3 UKFE-1.0.1/UKFE/man/Uncertainty.Rd | 38 UKFE-1.0.1/UKFE/man/WGaugLSkew.Rd | 9 UKFE-1.0.1/UKFE/man/WGaugLcv.Rd | 9 UKFE-1.0.1/UKFE/man/WeightsGLSkew.Rd | 9 UKFE-1.0.1/UKFE/man/WeightsGLcv.Rd | 9 UKFE-1.0.1/UKFE/man/WeightsUnLSkew.Rd | 9 UKFE-1.0.1/UKFE/man/WeightsUnLcv.Rd | 9 UKFE-1.0.1/UKFE/man/WungLSkew.Rd | 9 UKFE-1.0.1/UKFE/man/WungLcv.Rd | 9 UKFE-1.0.1/UKFE/man/Zdists.Rd | 13 UKFE-1.0.1/UKFE/tests |only UKFE-1.0.1/UKFE/vignettes |only 131 files changed, 10149 insertions(+), 7611 deletions(-)
Title: Fast Library for Number Theory
Description: An R interface to 'FLINT' <https://flintlib.org/>, a C library for
number theory. 'FLINT' extends GNU 'MPFR' <https://www.mpfr.org/>
and GNU 'MP' <https://gmplib.org/> with support for operations on
standard rings (the integers, the integers modulo n, finite
fields, the rational, p-adic, real, and complex numbers) as well
as matrices and polynomials over rings. 'FLINT' implements
midpoint-radius interval arithmetic, also known as ball
arithmetic, in the real and complex numbers, enabling computation
in arbitrary precision with rigorous propagation of rounding and
other errors; see Johansson (2017) <doi:10.1109/TC.2017.2690633>.
Finally, 'FLINT' provides ball arithmetic implementations of many
special mathematical functions, with high coverage of reference
works such as the NIST Digital Library of Mathematical Functions
<https://dlmf.nist.gov/>. The R interface defines S4 classes,
generic functions, and methods for representation and basic
operations as [...truncated...]
Author: Mikael Jagan [aut, cre] ,
Martin Maechler [ctb]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Diff between flint versions 0.1.0 dated 2025-09-21 and 0.1.1 dated 2025-10-08
flint-0.1.0/flint/tests/hypgeom.R |only flint-0.1.1/flint/DESCRIPTION | 38 - flint-0.1.1/flint/MD5 | 58 +- flint-0.1.1/flint/NAMESPACE | 12 flint-0.1.1/flint/R/S3.R | 4 flint-0.1.1/flint/R/flint.R | 112 ++++- flint-0.1.1/flint/R/utils.R | 8 flint-0.1.1/flint/R/zzz.R | 90 ++++ flint-0.1.1/flint/configure | 18 flint-0.1.1/flint/configure.ac | 2 flint-0.1.1/flint/inst/NEWS.Rd | 78 +++ flint-0.1.1/flint/man/arb_hypgeom_bessel_j.Rd | 2 flint-0.1.1/flint/man/flint-class.Rd | 41 +- flint-0.1.1/flint/man/flint-package.Rd | 29 + flint-0.1.1/flint/src/acb.c | 7 flint-0.1.1/flint/src/acf.c | 7 flint-0.1.1/flint/src/arb.c | 7 flint-0.1.1/flint/src/arf.c | 7 flint-0.1.1/flint/src/flint.c | 525 +++++++++++++++++++++----- flint-0.1.1/flint/src/flint.h | 14 flint-0.1.1/flint/src/fmpq.c | 7 flint-0.1.1/flint/src/fmpz.c | 7 flint-0.1.1/flint/src/foreign.c |only flint-0.1.1/flint/src/init.c | 23 + flint-0.1.1/flint/src/mag.c | 7 flint-0.1.1/flint/src/slong.c | 6 flint-0.1.1/flint/src/ulong.c | 6 flint-0.1.1/flint/tests/ambiguity.R | 7 flint-0.1.1/flint/tests/foreign.R |only flint-0.1.1/flint/tests/match.R | 2 flint-0.1.1/flint/tests/reg-tests.R | 45 ++ flint-0.1.1/flint/tests/special.R |only 32 files changed, 955 insertions(+), 214 deletions(-)
Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian
Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O
pacote é baseado em conjuntos de dados espaciais abertos de endereços
brasileiros, utilizando como fonte principal o Cadastro Nacional de Endereços
para Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro
de Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia
do Brasil. (A simple and efficient method for geolocating data in Brazil. The
package is based on open spatial datasets of Brazilian addresses, primarily
using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE),
published by the Instituto Brasileiro de Geografia e Estatística (IBGE),
Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre] ,
Daniel Herszenhut [aut] ,
Arthur Bazolli [ctb],
Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geocodebr versions 0.2.1 dated 2025-07-07 and 0.3.0 dated 2025-10-08
geocodebr-0.2.1/geocodebr/tests/tests_rafa/arrow_distinct.R |only geocodebr-0.2.1/geocodebr/tests/tests_rafa/busca_por_cep_alternativas.R |only geocodebr-0.2.1/geocodebr/tests/tests_rafa/calculate_precision.R |only geocodebr-0.2.1/geocodebr/tests/tests_rafa/geocoding_en.Rmd |only geocodebr-0.2.1/geocodebr/tests/tests_rafa/geocoding_pt.Rmd |only geocodebr-0.3.0/geocodebr/DESCRIPTION | 8 geocodebr-0.3.0/geocodebr/MD5 | 114 +- geocodebr-0.3.0/geocodebr/NEWS.md | 28 geocodebr-0.3.0/geocodebr/R/busca_por_cep.R | 35 geocodebr-0.3.0/geocodebr/R/cache.R | 77 + geocodebr-0.3.0/geocodebr/R/create_geocodebr_db.R | 3 geocodebr-0.3.0/geocodebr/R/download_cnefe.R | 27 geocodebr-0.3.0/geocodebr/R/geocode.R | 40 geocodebr-0.3.0/geocodebr/R/geocode_duckdb.R |only geocodebr-0.3.0/geocodebr/R/geocode_reverso.R | 20 geocodebr-0.3.0/geocodebr/R/match_cases.R | 41 geocodebr-0.3.0/geocodebr/R/match_cases_probabilistic.R | 221 ----- geocodebr-0.3.0/geocodebr/R/match_weighted_cases.R | 67 - geocodebr-0.3.0/geocodebr/R/match_weighted_cases_probabilistic.R | 156 +-- geocodebr-0.3.0/geocodebr/R/trata_empates_geocode.R | 1 geocodebr-0.3.0/geocodebr/R/trata_empates_geocode_duckdb.R |only geocodebr-0.3.0/geocodebr/R/trata_empates_geocode_duckdb2.R |only geocodebr-0.3.0/geocodebr/R/utils.R | 4 geocodebr-0.3.0/geocodebr/README.md | 29 geocodebr-0.3.0/geocodebr/build/vignette.rds |binary geocodebr-0.3.0/geocodebr/inst/doc/geocode.R | 51 - geocodebr-0.3.0/geocodebr/inst/doc/geocode.Rmd | 72 + geocodebr-0.3.0/geocodebr/inst/doc/geocode.html | 146 +-- geocodebr-0.3.0/geocodebr/inst/doc/geocode_reverso.R | 38 geocodebr-0.3.0/geocodebr/inst/doc/geocode_reverso.html | 56 - geocodebr-0.3.0/geocodebr/inst/doc/geocodebr.R | 114 +- geocodebr-0.3.0/geocodebr/inst/doc/geocodebr.Rmd | 12 geocodebr-0.3.0/geocodebr/inst/doc/geocodebr.html | 49 - geocodebr-0.3.0/geocodebr/man/apaga_data_release_antigo.Rd |only geocodebr-0.3.0/geocodebr/man/busca_por_cep.Rd | 108 +- geocodebr-0.3.0/geocodebr/man/create_index.Rd | 24 geocodebr-0.3.0/geocodebr/man/definir_pasta_cache.Rd | 6 geocodebr-0.3.0/geocodebr/man/figures/logo.svg | 412 +++++----- geocodebr-0.3.0/geocodebr/man/geocode.Rd | 68 + geocodebr-0.3.0/geocodebr/man/geocode_reverso.Rd | 132 +-- geocodebr-0.3.0/geocodebr/man/roxygen/templates/h3_res.R |only geocodebr-0.3.0/geocodebr/man/roxygen/templates/precision_section.R | 40 geocodebr-0.3.0/geocodebr/man/roxygen/templates/resultado_sf.R |only geocodebr-0.3.0/geocodebr/man/update_input_db.Rd | 44 - geocodebr-0.3.0/geocodebr/tests/tests_pedro |only geocodebr-0.3.0/geocodebr/tests/tests_rafa/benchmark_LIKE.R | 40 geocodebr-0.3.0/geocodebr/tests/tests_rafa/benchmark_reg_adm.R | 62 + geocodebr-0.3.0/geocodebr/tests/tests_rafa/empate_duck.R |only geocodebr-0.3.0/geocodebr/tests/tests_rafa/meta.R | 2 geocodebr-0.3.0/geocodebr/tests/tests_rafa/munis_bbox.R | 2 geocodebr-0.3.0/geocodebr/tests/tests_rafa/release_v2_v3.R |only geocodebr-0.3.0/geocodebr/tests/tests_rafa/states_bbox.R | 2 geocodebr-0.3.0/geocodebr/tests/tests_rafa/test_rafa.R | 67 - geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/cache.md | 60 - geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/definir_campos.md | 16 geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/download_cnefe.md | 18 geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/error.md | 18 geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/message.md | 14 geocodebr-0.3.0/geocodebr/tests/testthat/test-busca_por_cep.R | 6 geocodebr-0.3.0/geocodebr/tests/testthat/test-download_cnefe.R | 12 geocodebr-0.3.0/geocodebr/tests/testthat/test-geocode.R | 13 geocodebr-0.3.0/geocodebr/tests/testthat/test-geocode_duckdb.R |only geocodebr-0.3.0/geocodebr/tests/testthat/test-geocode_reverso.R | 2 geocodebr-0.3.0/geocodebr/vignettes/geocode.Rmd | 72 + geocodebr-0.3.0/geocodebr/vignettes/geocodebr.Rmd | 12 65 files changed, 1383 insertions(+), 1278 deletions(-)
Title: Maps Bone Densities from CT Scans to Surface Models
Description: Allows local bone density estimates to be derived from CT data and mapped to 3D bone models in a reproducible manner. Processing can be performed at the individual bone or group level. Also includes tools for visualizing the bone density estimates. Example methods are described in Telfer et al., (2021) <doi:10.1002/jor.24792>, Telfer et al., (2021) <doi:10.1016/j.jse.2021.05.011>.
Author: Scott Telfer [aut, cre, cph] ,
Lucas Lacambra [aut]
Maintainer: Scott Telfer <scott.telfer@gmail.com>
Diff between BoneDensityMapping versions 0.1.3 dated 2025-08-26 and 0.1.4 dated 2025-10-08
DESCRIPTION | 6 MD5 | 18 +- NEWS.md | 4 R/BoneDensityFunctions.R | 4 build/vignette.rds |binary inst/doc/example-workflow-vignette.R | 43 +++-- inst/doc/example-workflow-vignette.Rmd | 47 +++--- inst/doc/example-workflow-vignette.html | 245 +++++++++++++++----------------- man/plot_mesh.Rd | 4 vignettes/example-workflow-vignette.Rmd | 47 +++--- 10 files changed, 220 insertions(+), 198 deletions(-)
More information about BoneDensityMapping at CRAN
Permanent link
Title: Agricultural Datasets
Description: Datasets from books, papers, and websites related to
agriculture. Example graphics and analyses are included. Data come
from small-plot trials, multi-environment trials, uniformity trials,
yield monitors, and more.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between agridat versions 1.24 dated 2024-10-27 and 1.25 dated 2025-10-08
agridat-1.24/agridat/data/arankacami.groundnut.uniformity.txt |only agridat-1.24/agridat/man/arankacami.groundnut.uniformity.Rd |only agridat-1.25/agridat/DESCRIPTION | 17 agridat-1.25/agridat/LICENSE | 2 agridat-1.25/agridat/MD5 | 148 +- agridat-1.25/agridat/NEWS.md | 383 ++++- agridat-1.25/agridat/R/libs.R | 18 agridat-1.25/agridat/build/vignette.rds |binary agridat-1.25/agridat/data/beckett.maize.uniformity.txt |only agridat-1.25/agridat/data/gorski.oats.uniformity.txt |only agridat-1.25/agridat/data/kotowski.potato.uniformity.txt |only agridat-1.25/agridat/data/larsen.timothy.uniformity.txt |only agridat-1.25/agridat/data/lehmann.rice.uniformity.txt |only agridat-1.25/agridat/data/love.sugarcane.uniformity.txt |only agridat-1.25/agridat/data/oliveira.lupin.uniformity.txt |only agridat-1.25/agridat/data/oliveira.potato.uniformity.txt |only agridat-1.25/agridat/data/rangaswamy.groundnut.uniformity.txt |only agridat-1.25/agridat/data/rau.coffee.uniformity.txt |only agridat-1.25/agridat/data/usda.gmoadoption.txt |only agridat-1.25/agridat/inst/doc/agridat_data.Rmd | 5 agridat-1.25/agridat/inst/doc/agridat_data.html | 5 agridat-1.25/agridat/inst/doc/agridat_graphical_gems.R | 18 agridat-1.25/agridat/inst/doc/agridat_graphical_gems.html | 18 agridat-1.25/agridat/inst/doc/agridat_mixed_model_example.R | 448 +++--- agridat-1.25/agridat/inst/doc/agridat_mixed_model_example.html | 5 agridat-1.25/agridat/inst/doc/agridat_uniformity_data.Rmd | 626 +++++--- agridat-1.25/agridat/inst/doc/agridat_uniformity_data.html | 728 ++++++---- agridat-1.25/agridat/man/agridat.Rd | 21 agridat-1.25/agridat/man/bailey.cotton.uniformity.Rd | 6 agridat-1.25/agridat/man/baker.barley.uniformity.Rd | 10 agridat-1.25/agridat/man/baker.wheat.uniformity.Rd | 22 agridat-1.25/agridat/man/barrero.maize.Rd | 4 agridat-1.25/agridat/man/batchelor.uniformity.Rd | 5 agridat-1.25/agridat/man/beckett.maize.uniformity.Rd |only agridat-1.25/agridat/man/bradley.multi.uniformity.Rd | 2 agridat-1.25/agridat/man/connolly.potato.Rd | 8 agridat-1.25/agridat/man/davies.pasture.uniformity.Rd | 2 agridat-1.25/agridat/man/draper.safflower.uniformity.Rd | 3 agridat-1.25/agridat/man/ducker.groundnut.uniformity.Rd | 3 agridat-1.25/agridat/man/eden.tea.uniformity.Rd | 17 agridat-1.25/agridat/man/evans.sugarcane.uniformity.Rd | 16 agridat-1.25/agridat/man/forster.wheat.uniformity.Rd | 13 agridat-1.25/agridat/man/garber.multi.uniformity.Rd | 14 agridat-1.25/agridat/man/gomez.rice.uniformity.Rd | 18 agridat-1.25/agridat/man/gorski.oats.uniformity.Rd |only agridat-1.25/agridat/man/hansen.multi.uniformity.Rd | 6 agridat-1.25/agridat/man/haritonenko.sugarbeet.uniformity.Rd | 3 agridat-1.25/agridat/man/harris.multi.uniformity.Rd | 2 agridat-1.25/agridat/man/hartman.tomato.uniformity.Rd | 2 agridat-1.25/agridat/man/heath.cabbage.uniformity.Rd | 7 agridat-1.25/agridat/man/heath.raddish.uniformity.Rd | 5 agridat-1.25/agridat/man/holtsmark.timothy.uniformity.Rd | 31 agridat-1.25/agridat/man/hutchinson.cotton.uniformity.Rd | 4 agridat-1.25/agridat/man/jegorow.oats.uniformity.Rd | 3 agridat-1.25/agridat/man/jurowski.wheat.uniformity.Rd | 3 agridat-1.25/agridat/man/kerr.sugarcane.uniformity.Rd | 3 agridat-1.25/agridat/man/khin.rice.uniformity.Rd | 2 agridat-1.25/agridat/man/kotowski.potato.uniformity.Rd |only agridat-1.25/agridat/man/larsen.timothy.uniformity.Rd |only agridat-1.25/agridat/man/lehmann.millet.uniformity.Rd | 20 agridat-1.25/agridat/man/lehmann.rice.uniformity.Rd |only agridat-1.25/agridat/man/love.sugarcane.uniformity.Rd |only agridat-1.25/agridat/man/mercer.mangold.uniformity.Rd | 21 agridat-1.25/agridat/man/mercer.wheat.uniformity.Rd | 27 agridat-1.25/agridat/man/minnesota.barley.yield.Rd | 1 agridat-1.25/agridat/man/montgomery.wheat.uniformity.Rd | 4 agridat-1.25/agridat/man/nonnecke.peas.uniformity.Rd | 1 agridat-1.25/agridat/man/nonnecke.sweetcorn.uniformity.Rd | 1 agridat-1.25/agridat/man/oliveira.lupin.uniformity.Rd |only agridat-1.25/agridat/man/oliveira.potato.uniformity.Rd |only agridat-1.25/agridat/man/paez.coffee.uniformity.Rd | 10 agridat-1.25/agridat/man/panse.cotton.uniformity.Rd | 4 agridat-1.25/agridat/man/rangaswamy.groundnut.uniformity.Rd |only agridat-1.25/agridat/man/rau.coffee.uniformity.Rd |only agridat-1.25/agridat/man/roemer.sugarbeet.uniformity.Rd | 3 agridat-1.25/agridat/man/saunders.maize.uniformity.Rd | 9 agridat-1.25/agridat/man/shafii.rapeseed.Rd | 24 agridat-1.25/agridat/man/siao.cotton.uniformity.Rd | 16 agridat-1.25/agridat/man/stroup.nin.Rd | 16 agridat-1.25/agridat/man/summerby.multi.uniformity.Rd | 5 agridat-1.25/agridat/man/talbot.potato.Rd | 1 agridat-1.25/agridat/man/tulaikow.wheat.uniformity.Rd | 4 agridat-1.25/agridat/man/usda.gmoadoption.Rd |only agridat-1.25/agridat/man/usgs.herbicides.Rd | 75 - agridat-1.25/agridat/man/wiedemann.safflower.uniformity.Rd | 4 agridat-1.25/agridat/vignettes/agridat_data.Rmd | 5 agridat-1.25/agridat/vignettes/agridat_uniformity_data.Rmd | 626 +++++--- 87 files changed, 2350 insertions(+), 1183 deletions(-)
Title: Interpretable Neural Network Based on Generalized Additive
Models
Description: Neural Additive Model framework based on Generalized Additive Models from Hastie & Tibshirani (1990, ISBN:9780412343902), which trains a different neural network to estimate the contribution of each feature to the response variable. The networks are trained independently leveraging the local scoring and backfitting algorithms to ensure that the Generalized Additive Model converges and it is additive. The resultant Neural Network is a highly accurate and interpretable deep learning model, which can be used for high-risk AI practices where decision-making should be based on accountable and interpretable algorithms.
Author: Ines Ortega-Fernandez [aut, cre, cph] ,
Marta Sestelo [aut, cph]
Maintainer: Ines Ortega-Fernandez <iortega@gradiant.org>
Diff between neuralGAM versions 1.1.1 dated 2024-04-19 and 2.0.0 dated 2025-10-08
neuralGAM-1.1.1/neuralGAM/man/neuralGAM.Rd |only neuralGAM-1.1.1/neuralGAM/man/plot.neuralGAM.Rd |only neuralGAM-1.1.1/neuralGAM/man/predict.neuralGAM.Rd |only neuralGAM-1.1.1/neuralGAM/man/print.neuralGAM.Rd |only neuralGAM-1.1.1/neuralGAM/man/summary.neuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/DESCRIPTION | 22 neuralGAM-2.0.0/neuralGAM/MD5 | 110 +- neuralGAM-2.0.0/neuralGAM/NAMESPACE | 41 neuralGAM-2.0.0/neuralGAM/NEWS.md | 18 neuralGAM-2.0.0/neuralGAM/R/NeuralGAM.R | 517 ++++++---- neuralGAM-2.0.0/neuralGAM/R/autoplot.neuralGAM.R | 337 ++++-- neuralGAM-2.0.0/neuralGAM/R/build_feature_NN.R | 294 ++++- neuralGAM-2.0.0/neuralGAM/R/dev.R | 82 + neuralGAM-2.0.0/neuralGAM/R/diagnose.R |only neuralGAM-2.0.0/neuralGAM/R/diriv.R | 9 neuralGAM-2.0.0/neuralGAM/R/formula.R | 292 ++++- neuralGAM-2.0.0/neuralGAM/R/install.R | 59 + neuralGAM-2.0.0/neuralGAM/R/inv_link.R | 19 neuralGAM-2.0.0/neuralGAM/R/link.R | 20 neuralGAM-2.0.0/neuralGAM/R/mu_eta.R |only neuralGAM-2.0.0/neuralGAM/R/neuralGAM-package.R | 1 neuralGAM-2.0.0/neuralGAM/R/plot.NeuralGAM.R | 184 +-- neuralGAM-2.0.0/neuralGAM/R/plot_history.NeuralGAM.R |only neuralGAM-2.0.0/neuralGAM/R/predict.NeuralGAM.R | 475 ++++++--- neuralGAM-2.0.0/neuralGAM/R/print.NeuralGAM.R | 106 -- neuralGAM-2.0.0/neuralGAM/R/sim_neuralGAM_data.R |only neuralGAM-2.0.0/neuralGAM/R/summary.NeuralGAM.R | 330 +++++- neuralGAM-2.0.0/neuralGAM/R/uncertainty_estimation.R |only neuralGAM-2.0.0/neuralGAM/R/weight.R | 16 neuralGAM-2.0.0/neuralGAM/README.md | 223 +++- neuralGAM-2.0.0/neuralGAM/man/NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/autoplot.neuralGAM.Rd | 118 +- neuralGAM-2.0.0/neuralGAM/man/build_feature_NN.Rd | 129 +- neuralGAM-2.0.0/neuralGAM/man/dev.Rd | 6 neuralGAM-2.0.0/neuralGAM/man/diagnose.Rd |only neuralGAM-2.0.0/neuralGAM/man/diriv.Rd | 2 neuralGAM-2.0.0/neuralGAM/man/dot-combine_uncertainties_sampling.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-combine_uncertainties_variance.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-compute_uncertainty.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-joint_pi_both_variance.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-joint_se_eta_mcdropout.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-mc_dropout_forward.Rd |only neuralGAM-2.0.0/neuralGAM/man/get_formula_elements.Rd | 80 + neuralGAM-2.0.0/neuralGAM/man/inv_link.Rd | 2 neuralGAM-2.0.0/neuralGAM/man/link.Rd | 4 neuralGAM-2.0.0/neuralGAM/man/mu_eta.Rd |only neuralGAM-2.0.0/neuralGAM/man/neuralGAM-package.Rd | 3 neuralGAM-2.0.0/neuralGAM/man/plot.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/plot_history.Rd |only neuralGAM-2.0.0/neuralGAM/man/predict.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/print.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/sim_neuralGAM_data.Rd |only neuralGAM-2.0.0/neuralGAM/man/summary.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/validate_activation.Rd |only neuralGAM-2.0.0/neuralGAM/man/validate_loss.Rd |only neuralGAM-2.0.0/neuralGAM/man/weight.Rd | 4 neuralGAM-2.0.0/neuralGAM/tests/testthat/setup.R | 1 neuralGAM-2.0.0/neuralGAM/tests/testthat/test-NeuralGAM.R | 486 ++++++++- neuralGAM-2.0.0/neuralGAM/tests/testthat/test-autoplot.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-build_feature_NN.R | 183 +++ neuralGAM-2.0.0/neuralGAM/tests/testthat/test-dev.R | 142 +- neuralGAM-2.0.0/neuralGAM/tests/testthat/test-diagnose.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-diriv.R | 2 neuralGAM-2.0.0/neuralGAM/tests/testthat/test-epistemic-pi.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-formula.R | 152 ++ neuralGAM-2.0.0/neuralGAM/tests/testthat/test-inv_link.R | 32 neuralGAM-2.0.0/neuralGAM/tests/testthat/test-link.R | 49 neuralGAM-2.0.0/neuralGAM/tests/testthat/test-mu_eta.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-plot.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-plot_history.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-predict.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-print.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-summary.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-weight.R | 16 74 files changed, 3399 insertions(+), 1167 deletions(-)
Title: Constrained Multivariate Least Squares
Description: Solves multivariate least squares (MLS) problems subject to constraints on the coefficients, e.g., non-negativity, orthogonality, equality, inequality, monotonicity, unimodality, smoothness, etc. Includes flexible functions for solving MLS problems subject to user-specified equality and/or inequality constraints, as well as a wrapper function that implements 24 common constraint options. Also does k-fold or generalized cross-validation to tune constraint options for MLS problems. See ten Berge (1993, ISBN:9789066950832) for an overview of MLS problems, and see Goldfarb and Idnani (1983) <doi:10.1007/BF02591962> for a discussion of the underlying quadratic programming algorithm.
Author: Nathaniel E. Helwig [aut, cre]
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between CMLS versions 1.0-1 dated 2023-03-31 and 1.1 dated 2025-10-08
ChangeLog | 10 ++++++++++ DESCRIPTION | 16 ++++++++++------ MD5 | 10 +++++----- build/partial.rdb |binary man/mlsei.Rd | 2 +- man/mlsun.Rd | 2 +- 6 files changed, 27 insertions(+), 13 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen [aut, cre],
Gavin L. Simpson [aut],
F. Guillaume Blanchet [aut],
Roeland Kindt [aut],
Pierre Legendre [aut],
Peter R. Minchin [aut],
R.B. O'Hara [aut],
Peter Solymos [aut],
M. Henry H. Stevens [aut],
Eduard Szoecs [aut],
Helene Wagner [a [...truncated...]
Maintainer: Jari Oksanen <jhoksane@gmail.com>
Diff between vegan versions 2.7-1 dated 2025-06-05 and 2.7-2 dated 2025-10-08
vegan-2.7-1/vegan/inst/doc/FAQ-vegan.R |only vegan-2.7-2/vegan/DESCRIPTION | 6 vegan-2.7-2/vegan/MD5 | 163 +++--- vegan-2.7-2/vegan/NEWS.md | 67 ++ vegan-2.7-2/vegan/R/CCorA.R | 4 vegan-2.7-2/vegan/R/MDSaddpoints.R | 3 vegan-2.7-2/vegan/R/add1.cca.R | 18 vegan-2.7-2/vegan/R/anova.ccabyterm.R | 21 vegan-2.7-2/vegan/R/beals.R | 4 vegan-2.7-2/vegan/R/biplot.rda.R | 54 -- vegan-2.7-2/vegan/R/capscale.R | 3 vegan-2.7-2/vegan/R/cca.default.R | 2 vegan-2.7-2/vegan/R/cca.formula.R | 3 vegan-2.7-2/vegan/R/dbrda.R | 3 vegan-2.7-2/vegan/R/decorana.R | 4 vegan-2.7-2/vegan/R/decostand.R | 23 vegan-2.7-2/vegan/R/designdist.R | 10 vegan-2.7-2/vegan/R/distconnected.R | 2 vegan-2.7-2/vegan/R/diversity.R | 2 vegan-2.7-2/vegan/R/downweight.R | 2 vegan-2.7-2/vegan/R/factorfit.R | 6 vegan-2.7-2/vegan/R/fisher.alpha.R | 4 vegan-2.7-2/vegan/R/influence.cca.R | 5 vegan-2.7-2/vegan/R/make.commsim.R | 32 - vegan-2.7-2/vegan/R/mantel.R | 19 vegan-2.7-2/vegan/R/mantel.partial.R | 27 - vegan-2.7-2/vegan/R/monoMDS.R | 2 vegan-2.7-2/vegan/R/no.shared.R | 4 vegan-2.7-2/vegan/R/nullmodel.R | 2 vegan-2.7-2/vegan/R/ordConstrained.R | 2 vegan-2.7-2/vegan/R/orderingKM.R | 20 vegan-2.7-2/vegan/R/ordiParseFormula.R | 16 vegan-2.7-2/vegan/R/ordilabel.R | 19 vegan-2.7-2/vegan/R/ordipointlabel.R | 2 vegan-2.7-2/vegan/R/ordisurf.R | 3 vegan-2.7-2/vegan/R/permatfull.R | 2 vegan-2.7-2/vegan/R/permatswap.R | 2 vegan-2.7-2/vegan/R/permustats.R | 8 vegan-2.7-2/vegan/R/permutest.cca.R | 5 vegan-2.7-2/vegan/R/plot.varpart234.R | 6 vegan-2.7-2/vegan/R/poolaccum.R | 2 vegan-2.7-2/vegan/R/predict.cca.R | 5 vegan-2.7-2/vegan/R/predict.rda.R | 5 vegan-2.7-2/vegan/R/print.monoMDS.R | 3 vegan-2.7-2/vegan/R/rarecurve.R | 2 vegan-2.7-2/vegan/R/rarefy.R | 2 vegan-2.7-2/vegan/R/raupcrick.R | 2 vegan-2.7-2/vegan/R/rda.default.R | 2 vegan-2.7-2/vegan/R/rda.formula.R | 3 vegan-2.7-2/vegan/R/rrarefy.R | 4 vegan-2.7-2/vegan/R/scores.default.R | 4 vegan-2.7-2/vegan/R/simpleRDA2.R | 2 vegan-2.7-2/vegan/R/spantree.R | 2 vegan-2.7-2/vegan/R/specaccum.R | 3 vegan-2.7-2/vegan/R/stepacross.R | 5 vegan-2.7-2/vegan/R/taxondive.R | 2 vegan-2.7-2/vegan/R/treedist.R | 2 vegan-2.7-2/vegan/R/treedive.R | 2 vegan-2.7-2/vegan/R/vectorfit.R | 6 vegan-2.7-2/vegan/R/vegdist.R | 4 vegan-2.7-2/vegan/R/wascores.R | 4 vegan-2.7-2/vegan/R/wcmdscale.R | 4 vegan-2.7-2/vegan/build/partial.rdb |binary vegan-2.7-2/vegan/build/vignette.rds |binary vegan-2.7-2/vegan/inst/doc/FAQ-vegan.Rmd | 356 +++++--------- vegan-2.7-2/vegan/inst/doc/FAQ-vegan.html | 323 ++++--------- vegan-2.7-2/vegan/inst/doc/decision-vegan.pdf |binary vegan-2.7-2/vegan/inst/doc/diversity-vegan.pdf |binary vegan-2.7-2/vegan/inst/doc/intro-vegan.R | 86 +-- vegan-2.7-2/vegan/inst/doc/intro-vegan.Rnw | 203 ++++---- vegan-2.7-2/vegan/inst/doc/intro-vegan.pdf |binary vegan-2.7-2/vegan/inst/doc/partitioning.Rnw | 4 vegan-2.7-2/vegan/inst/doc/partitioning.pdf |binary vegan-2.7-2/vegan/man/biplot.rda.Rd | 20 vegan-2.7-2/vegan/man/cascadeKM.Rd | 8 vegan-2.7-2/vegan/man/mantel.Rd | 15 vegan-2.7-2/vegan/man/ordilabel.Rd | 4 vegan-2.7-2/vegan/src/getF.c | 55 +- vegan-2.7-2/vegan/tests/cca-object-tests.Rout.save | 502 +++++++++------------ vegan-2.7-2/vegan/tests/vegan-tests.Rout.save | 64 +- vegan-2.7-2/vegan/vignettes/FAQ-vegan.Rmd | 356 +++++--------- vegan-2.7-2/vegan/vignettes/intro-vegan.Rnw | 203 ++++---- vegan-2.7-2/vegan/vignettes/partitioning.Rnw | 4 83 files changed, 1286 insertions(+), 1567 deletions(-)
Title: Time Series Analysis Tools
Description: A system contains easy-to-use tools as a support for time series analysis courses. In particular, it incorporates a technique called Generalized Method of Wavelet Moments (GMWM) as well as its robust implementation for fast and robust parameter estimation of time series models which is described, for example, in Guerrier et al. (2013) <doi: 10.1080/01621459.2013.799920>. More details can also be found in the paper linked to via the URL below.
Author: Stephane Guerrier [aut, cre, cph],
James Balamuta [aut, cph],
Roberto Molinari [aut, cph],
Justin Lee [aut],
Lionel Voirol [aut],
Yuming Zhang [aut],
Wenchao Yang [ctb],
Nathanael Claussen [ctb],
Yunxiang Zhang [ctb],
Christian Gunning [cph],
Romain [...truncated...]
Maintainer: Stephane Guerrier <stef.guerrier@gmail.com>
Diff between simts versions 0.2.2 dated 2023-08-31 and 0.2.3 dated 2025-10-08
DESCRIPTION | 9 +-- MD5 | 100 ++++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS.md | 5 ++ R/RcppExports.R | 58 ------------------------- R/gmwm.r | 8 --- R/model_selection.R | 2 R/ts.model.R | 2 README.md | 47 ++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignettes.R | 52 +++++++++++----------- inst/doc/vignettes.html | 62 ++++++++++++++------------- man/batch_modwt_wvar_cpp.Rd | 2 man/bl14_filter.Rd | 2 man/bl20_filter.Rd | 2 man/ci_eta3.Rd | 2 man/ci_eta3_robust.Rd | 2 man/ci_wave_variance.Rd | 2 man/d16_filter.Rd | 2 man/d4_filter.Rd | 2 man/d6_filter.Rd | 2 man/d8_filter.Rd | 2 man/fk14_filter.Rd | 2 man/fk22_filter.Rd | 2 man/fk4_filter.Rd | 2 man/fk6_filter.Rd | 2 man/fk8_filter.Rd | 2 man/gmwm_engine.Rd | 4 - man/gmwm_imu.Rd | 2 man/haar_filter.Rd | 2 man/la16_filter.Rd | 2 man/la20_filter.Rd | 2 man/la8_filter.Rd | 2 man/mb16_filter.Rd | 2 man/mb24_filter.Rd | 2 man/mb4_filter.Rd | 2 man/mb8_filter.Rd | 2 man/modwt_wvar_cpp.Rd | 2 man/plus-.ts.model.Rd | 2 man/predict.gmwm.Rd | 2 man/select_filter.Rd | 2 man/simts-package.Rd | 1 man/summary.gmwm.Rd | 2 man/update.gmwm.Rd | 2 man/w4_filter.Rd | 2 man/wvar_cpp.Rd | 2 src/gmwm_logic.cpp | 4 - src/rtoarmadillo.cpp | 4 - src/wave_variance.cpp | 12 ----- src/wv_filters.cpp | 42 ------------------ 51 files changed, 156 insertions(+), 321 deletions(-)
Title: R Interface to the Pushbullet Messaging Service
Description: An R interface to the Pushbullet messaging service which
provides fast and efficient notifications (and file transfer) between
computers, phones and tablets. An account has to be registered at the
site <https://www.pushbullet.com> site to obtain a (free) API key.
Author: Dirk Eddelbuettel [aut, cre] ,
Bill Evans [ctb],
Mike Birdgeneau [ctb],
Henrik Bengtsson [ctb],
Seth Wenchel [ctb],
Colin Gillespie [ctb],
Chan-Yub Park [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RPushbullet versions 0.3.4 dated 2021-03-01 and 0.3.5 dated 2025-10-08
ChangeLog | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 31 ++++++++++++++++++++++------- MD5 | 12 +++++------ R/isValid.R | 10 ++++----- R/pushes.R | 2 - README.md | 8 +++---- inst/NEWS.Rd | 13 ++++++++++++ 7 files changed, 115 insertions(+), 23 deletions(-)
Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Oeyvind Langsrud [aut, cre],
Jan Bruusgaard [aut],
Solveig Bjoerkholt [ctb],
Susie Jentoft [ctb]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between PxWebApiData versions 1.0.0 dated 2024-11-01 and 1.1.0 dated 2025-10-08
DESCRIPTION | 10 - MD5 | 25 ++-- NAMESPACE | 1 NEWS.md | 10 + R/ApiData.R | 61 ++++++---- build/vignette.rds |binary inst/doc/Introduction.R | 17 ++ inst/doc/Introduction.Rmd | 43 +++++-- inst/doc/Introduction.html | 246 ++++++++++++++++++++++++------------------ man/ApiData.Rd | 25 +++- man/MakeUrl.Rd | 6 - man/figures |only tests/testthat/test-ApiData.R | 25 ---- vignettes/Introduction.Rmd | 43 +++++-- 14 files changed, 310 insertions(+), 202 deletions(-)
Title: Converting Transport Data from GTFS Format to GPS-Like Records
Description: Convert general transit feed specification (GTFS) data to global positioning system (GPS) records in 'data.table' format. It also has some functions to subset GTFS data in time and space and to convert both representations to simple feature format.
Author: Rafael H. M. Pereira [aut] ,
Pedro R. Andrade [aut, cre] ,
Joao Bazzo [aut] ,
Daniel Herszenhut [ctb] ,
Marcin Stepniak [ctb],
Marcus Saraiva [ctb] ,
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro R. Andrade <pedro.andrade@inpe.br>
Diff between gtfs2gps versions 2.1-2 dated 2024-10-08 and 2.1-3 dated 2025-10-08
DESCRIPTION | 23 +++++----- MD5 | 25 ++++++++--- R/zzz.R | 4 - build/vignette.rds |binary inst/doc/intro_to_gtfs2gps.R | 2 inst/doc/intro_to_gtfs2gps.html | 71 +++++++++++++++----------------- tests/testthat/agency.txt |only tests/testthat/calendar.txt |only tests/testthat/poa.zip |only tests/testthat/routes.txt |only tests/testthat/shapes.txt |only tests/testthat/stop_times.txt |only tests/testthat/stops.txt |only tests/testthat/test_gtfs2gps.R | 2 tests/testthat/test_simplify_shapes.R | 5 -- tests/testthat/trips.txt |only vignettes/poa_small.zip |only vignettes/sao_small-DESKTOP-V07AVEN.zip |only vignettes/sao_small.zip |only 19 files changed, 71 insertions(+), 61 deletions(-)
Title: Power Calculation for Two-Way Factorial Designs
Description: The basic use of this package is with 3 sequential functions. One to generate expected cell means and standard deviations, along with correlation and covariance matrices in the case of repeated measurements. This is followed by experiment simulation i number of times. Finally, power is calculated from the simulated data. Features that may be considered in the model are interaction, measure correlation and non-normal distributions.
Author: Louis Macias [aut, cre, cph] ,
Silke Szymczak [aut]
Maintainer: Louis Macias <louis.macias@uni-luebeck.de>
Diff between extraSuperpower versions 1.5.4 dated 2025-08-25 and 1.5.5 dated 2025-10-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/repeated_twoway_generation.R | 2 +- inst/doc/eSp_balanced_design_powertest.html | 8 ++++---- 5 files changed, 17 insertions(+), 13 deletions(-)
More information about extraSuperpower at CRAN
Permanent link
Title: Electric Vehicle Charging Sessions Simulation
Description: Simulation of Electric Vehicles charging sessions using Gaussian models, together with time-series power demand calculations.
Author: Marc Canigueral [aut, cre, cph]
Maintainer: Marc Canigueral <marccanyigueral@gmail.com>
Diff between evsim versions 1.6.1 dated 2025-05-07 and 1.7.0 dated 2025-10-08
evsim-1.6.1/evsim/R/parallel-processing.R |only evsim-1.6.1/evsim/man/mclapply.windows.Rd |only evsim-1.7.0/evsim/DESCRIPTION | 12 evsim-1.7.0/evsim/MD5 | 24 - evsim-1.7.0/evsim/NAMESPACE | 6 evsim-1.7.0/evsim/NEWS.md | 7 evsim-1.7.0/evsim/R/charging_infrastructure.R | 9 evsim-1.7.0/evsim/R/demand.R | 197 ++++------ evsim-1.7.0/evsim/R/simulation.R | 31 + evsim-1.7.0/evsim/man/adapt_charging_features.Rd | 9 evsim-1.7.0/evsim/man/get_demand.Rd | 11 evsim-1.7.0/evsim/man/get_occupancy.Rd | 11 evsim-1.7.0/evsim/man/plot_occupancy_duration_curve.Rd | 6 evsim-1.7.0/evsim/tests/testthat/test-charging_infrastructure.R | 2 14 files changed, 166 insertions(+), 159 deletions(-)
Title: A Modular Approach to Dose-Finding Clinical Trials
Description: Methods for working with dose-finding clinical trials. We provide
implementations of many dose-finding clinical trial designs, including the
continual reassessment method (CRM) by O'Quigley et al. (1990)
<doi:10.2307/2531628>, the toxicity probability interval (TPI) design by Ji
et al. (2007) <doi:10.1177/1740774507079442>, the modified TPI (mTPI) design
by Ji et al. (2010) <doi:10.1177/1740774510382799>, the Bayesian optimal
interval design (BOIN) by Liu & Yuan (2015) <doi:10.1111/rssc.12089>, EffTox
by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the design of
Wages & Tait (2015) <doi:10.1080/10543406.2014.920873>, and the 3+3
described by Korn et al. (1994) <doi:10.1002/sim.4780131802>. All designs
are implemented with a common interface. We also offer optional additional
classes to tailor the behaviour of all designs, including avoiding skipping
doses, stopping after n patients have been treated at the recommended [...truncated...]
Author: Kristian Brock [aut, cre] ,
Daniel Slade [aut] ,
Michael Sweeting [aut] ,
Conor Norris [ctb] ,
Bharat Bhushan [ctb]
Maintainer: Kristian Brock <kristian.brock@gmail.com>
Diff between escalation versions 0.1.10 dated 2024-06-27 and 0.2.3 dated 2025-10-08
DESCRIPTION | 32 MD5 | 271 +- NAMESPACE | 77 NEWS.md | 20 R/boin12_rds.R |only R/boin_comb_selector.R |only R/boin_selector.R | 44 R/check_simulations_consistency.R |only R/combo_selector.R |only R/combo_selector_factory.R |only R/convergence_plot.R | 25 R/demand_n_at_dose.R | 41 R/derived_dose_selector.R | 36 R/dfcrm_selector.R | 36 R/dont_skip_doses.R | 3 R/dose_escalation_table.R |only R/dose_selector_summary_methods.R | 120 - R/escalation-package.R | 4 R/expand_last_dose_to_cohort.R |only R/follow_path.R | 53 R/helpers.R | 146 + R/interface.R | 22 R/mtpi2_selector.R | 28 R/mtpi_selector.R | 37 R/outcomes_to_arrays.R |only R/parse_phase1_2_outcomes.R | 44 R/parse_phase1_outcomes.R | 42 R/phase1_2_comb_sim.R |only R/phase1_2_dose_paths.R | 12 R/phase1_2_outcomes_to_cohorts.R | 24 R/phase1_2_sim.R | 6 R/phase1_dose_paths.R | 12 R/phase1_outcomes_to_cohorts.R | 30 R/phase1_sim.R | 4 R/phase1_tite_sim.R | 45 R/select_boin12_obd.R | 39 R/select_boin_comb_mtd.R |only R/select_boin_mtd.R | 30 R/select_dose_by_cibp.R | 1 R/select_mtpi2_mtd.R | 94 R/select_mtpi_mtd.R | 75 R/select_tpi_mtd.R | 86 R/selector.R | 57 R/simulations.R | 396 ++- R/stack_sims_vert.R | 46 R/stick_on_num_tox.R |only R/stop_when_n_at_dose_selector.R | 31 R/stop_when_too_toxic.R | 66 R/stop_when_tox_ci_covered.R | 50 R/tpi_selector.R | 17 R/try_rescue_dose.R | 53 R/unadmit_untested.R |only README.md | 46 build/vignette.rds |binary inst/doc/A100-DoseSelectors.R | 5 inst/doc/A100-DoseSelectors.Rmd | 11 inst/doc/A100-DoseSelectors.html | 197 - inst/doc/A205-CRM.R | 8 inst/doc/A205-CRM.Rmd | 4 inst/doc/A205-CRM.html | 76 inst/doc/A207-NBG.R | 6 inst/doc/A207-NBG.Rmd | 4 inst/doc/A207-NBG.html | 77 inst/doc/A210-TPI.R | 15 inst/doc/A210-TPI.Rmd | 22 inst/doc/A210-TPI.html | 183 - inst/doc/A220-mTPI.R | 15 inst/doc/A220-mTPI.Rmd | 22 inst/doc/A220-mTPI.html | 184 - inst/doc/A230-BOIN.R | 12 inst/doc/A230-BOIN.Rmd | 22 inst/doc/A230-BOIN.html | 89 inst/doc/A280-TITE.R |only inst/doc/A280-TITE.Rmd |only inst/doc/A280-TITE.html |only inst/doc/A310-EfficacyToxicity.R |only inst/doc/A310-EfficacyToxicity.Rmd |only inst/doc/A310-EfficacyToxicity.html |only inst/doc/A360-Combinations.R |only inst/doc/A360-Combinations.Rmd |only inst/doc/A360-Combinations.html |only inst/doc/A600-DosePaths.R | 20 inst/doc/A600-DosePaths.html | 60 inst/doc/A700-Simulation.R | 16 inst/doc/A700-Simulation.html | 6 inst/doc/A710-SimulationComparison.R | 6 inst/doc/A710-SimulationComparison.html | 8 man/boin12_rds.Rd |only man/check_simulations_consistency.Rd |only man/combo_selector.Rd |only man/convergence_plot.Rd | 25 man/dose_escalation_table.Rd |only man/dose_string_to_vector.Rd |only man/dose_strings.Rd |only man/dose_vector_to_string.Rd |only man/doses_given.Rd | 15 man/escalation-package.Rd | 26 man/expand_last_dose_to_cohort.Rd |only man/get_boin.Rd | 19 man/get_boin_comb.Rd |only man/get_dose_combo_indices.Rd |only man/get_mtpi.Rd | 8 man/get_mtpi2.Rd | 8 man/get_tpi.Rd | 8 man/median_prob_tox.Rd | 11 man/prob_tox_exceeds.Rd | 11 man/prob_tox_quantile.Rd | 11 man/recommended_dose.Rd | 11 man/select_boin12_obd.Rd | 32 man/select_boin_comb_mtd.Rd |only man/select_boin_mtd.Rd | 28 man/select_mtpi2_mtd.Rd | 39 man/select_mtpi_mtd.Rd | 40 man/select_tpi_mtd.Rd | 42 man/selector.Rd | 2 man/simulations.Rd | 3 man/stick_on_num_tox.Rd |only man/try_rescue_dose.Rd | 2 man/unadmit_untested.Rd |only tests/testthat/test_boin.R | 54 tests/testthat/test_boin12_rds.R |only tests/testthat/test_boin_comb.R |only tests/testthat/test_demand_n_at_dose.R | 8 tests/testthat/test_dfcrm.R | 8 tests/testthat/test_dont_skip_doses.R | 8 tests/testthat/test_expand_last_dose_to_cohort.R |only tests/testthat/test_follow_path.R | 15 tests/testthat/test_helpers.R |only tests/testthat/test_mtpi.R | 2700 +++++++++++------------ tests/testthat/test_mtpi2.R | 716 +++--- tests/testthat/test_outcomes_to_arrays.R |only tests/testthat/test_select_boin_mtd.R | 24 tests/testthat/test_select_dose_by_cibp.R | 11 tests/testthat/test_select_mtpi2_mtd.R | 24 tests/testthat/test_select_mtpi_mtd.R | 24 tests/testthat/test_select_tpi_mtd.R | 24 tests/testthat/test_simulate_trials.R | 39 tests/testthat/test_spruce_outcomes_df.R |only tests/testthat/test_stick_on_num_tox.R |only tests/testthat/test_stop_at_n.R | 8 tests/testthat/test_stop_when_n_at_dose.R | 8 tests/testthat/test_stop_when_too_toxic.R | 8 tests/testthat/test_stop_when_tox_ci_covered.R | 8 tests/testthat/test_three_plus_three.R | 16 tests/testthat/test_tpi.R | 835 +++---- tests/testthat/test_trialr_crm.R | 24 tests/testthat/test_trialr_nbg.R | 8 tests/testthat/test_try_rescue_dose.R | 8 tests/testthat/test_unadmit_untested.R |only vignettes/A100-DoseSelectors.Rmd | 11 vignettes/A205-CRM.Rmd | 4 vignettes/A207-NBG.Rmd | 4 vignettes/A210-TPI.Rmd | 22 vignettes/A220-mTPI.Rmd | 22 vignettes/A230-BOIN.Rmd | 22 vignettes/A280-TITE.Rmd |only vignettes/A310-EfficacyToxicity.Rmd |only vignettes/A360-Combinations.Rmd |only vignettes/library.bib | 54 159 files changed, 5159 insertions(+), 3268 deletions(-)
Title: Forest Estimations and Dendrometric Computations
Description: Computation of dendrometric and structural parameters from forest inventory data. The objective is to provide a user-friendly R package for researchers, ecologists, foresters, statisticians, loggers and other persons who deal with forest inventory data. The package includes advanced distribution fitting capabilities with multiple estimation methods (Maximum Likelihood, Maximum Product Spacing with ties correction methods following Cheng & Amin (1983), and Method of Moments) for probability distributions commonly used in forestry. Visualization tools with confidence bands using delta method and parametric bootstrap are provided for three-parameter Weibull distribution fitting to diameter data. Useful conversion of angle value from degree to radian, conversion from angle to slope (in percentage) and their reciprocals as well as principal angle determination are also included. Position and dispersion parameters usually found in forest studies are implemented. The package contains Fibo [...truncated...]
Author: Narcisse Yehouenou [aut, cre],
Information and Communication Technology for you ONG [fnd]
Maintainer: Narcisse Yehouenou <narcisstar211@gmail.com>
Diff between dendrometry versions 0.0.3 dated 2025-04-24 and 0.0.4 dated 2025-10-08
dendrometry-0.0.3/dendrometry/man/adjWeibull.Rd |only dendrometry-0.0.3/dendrometry/man/param_i.Rd |only dendrometry-0.0.4/dendrometry/DESCRIPTION | 27 dendrometry-0.0.4/dendrometry/MD5 | 63 dendrometry-0.0.4/dendrometry/NAMESPACE | 17 dendrometry-0.0.4/dendrometry/NEWS.md | 26 dendrometry-0.0.4/dendrometry/R/dendrometry.R | 1308 ++++++++++----- dendrometry-0.0.4/dendrometry/R/fit_distributions.R |only dendrometry-0.0.4/dendrometry/build/partial.rdb |binary dendrometry-0.0.4/dendrometry/build/vignette.rds |binary dendrometry-0.0.4/dendrometry/inst/doc/dendrometry.R | 4 dendrometry-0.0.4/dendrometry/inst/doc/dendrometry.Rmd | 155 + dendrometry-0.0.4/dendrometry/inst/doc/dendrometry.html | 17 dendrometry-0.0.4/dendrometry/man/AIC.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/BIC.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/Tree.Rd | 6 dendrometry-0.0.4/dendrometry/man/basal.Rd | 15 dendrometry-0.0.4/dendrometry/man/basal_i.Rd | 2 dendrometry-0.0.4/dendrometry/man/baseFunction.Rd |only dendrometry-0.0.4/dendrometry/man/ci_bands_bootstrap.Rd |only dendrometry-0.0.4/dendrometry/man/ci_bands_delta.Rd |only dendrometry-0.0.4/dendrometry/man/coef.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/confint.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/create_objective.Rd |only dendrometry-0.0.4/dendrometry/man/dendrometry-package.Rd | 9 dendrometry-0.0.4/dendrometry/man/densityRegen.Rd | 7 dendrometry-0.0.4/dendrometry/man/dweibull3.Rd |only dendrometry-0.0.4/dendrometry/man/fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/fit_lmoments.Rd |only dendrometry-0.0.4/dendrometry/man/fit_moments.Rd |only dendrometry-0.0.4/dendrometry/man/fit_optimization.Rd |only dendrometry-0.0.4/dendrometry/man/fit_weibull_plot.Rd |only dendrometry-0.0.4/dendrometry/man/format_ci.Rd |only dendrometry-0.0.4/dendrometry/man/format_ci_inline.Rd |only dendrometry-0.0.4/dendrometry/man/get_cdf.Rd |only dendrometry-0.0.4/dendrometry/man/get_default_bounds.Rd |only dendrometry-0.0.4/dendrometry/man/get_param_names.Rd |only dendrometry-0.0.4/dendrometry/man/get_pdf.Rd |only dendrometry-0.0.4/dendrometry/man/get_start_values.Rd |only dendrometry-0.0.4/dendrometry/man/logLik.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/makedata.Rd | 39 dendrometry-0.0.4/dendrometry/man/nestedFunBuilder.Rd |only dendrometry-0.0.4/dendrometry/man/optimize_params.Rd |only dendrometry-0.0.4/dendrometry/man/param.Rd |only dendrometry-0.0.4/dendrometry/man/print.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/summary.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/vcov.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/vignettes/dendrometry.Rmd | 155 + 48 files changed, 1252 insertions(+), 598 deletions(-)
Title: Utilities for Interacting with the 'CTX' APIs
Description: Access chemical, hazard, bioactivity, and exposure data from the
Computational Toxicology and Exposure ('CTX') APIs
<https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>.
'ctxR' was developed to streamline the process of accessing the information
available through the 'CTX' APIs without requiring prior knowledge of how to
use APIs. Most data is also available on the CompTox Chemical Dashboard
('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the
EPA Computational Toxicology and Exposure Online Resources
<https://www.epa.gov/comptox-tools>.
Author: Paul Kruse [aut] ,
Caroline Ring [aut] ,
Madison Feshuk [ctb, cre] ,
Brianna Dirks [ctb] ,
Carter Thunes [ctb],
Jason Brown [ctb]
Maintainer: Madison Feshuk <feshuk.madison@epa.gov>
Diff between ctxR versions 1.1.2 dated 2025-04-07 and 1.1.3 dated 2025-10-08
ctxR-1.1.2/ctxR/inst/doc/Bioactivity.R |only ctxR-1.1.2/ctxR/inst/doc/Bioactivity.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Bioactivity.html |only ctxR-1.1.2/ctxR/inst/doc/Chemical.R |only ctxR-1.1.2/ctxR/inst/doc/Chemical.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Chemical.html |only ctxR-1.1.2/ctxR/inst/doc/Exposure.R |only ctxR-1.1.2/ctxR/inst/doc/Exposure.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Exposure.html |only ctxR-1.1.2/ctxR/inst/doc/Hazard.R |only ctxR-1.1.2/ctxR/inst/doc/Hazard.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Hazard.html |only ctxR-1.1.2/ctxR/inst/doc/Introduction.R |only ctxR-1.1.2/ctxR/inst/doc/Introduction.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Introduction.html |only ctxR-1.1.2/ctxR/tests/testthat/chemical/chemical |only ctxR-1.1.2/ctxR/tests/testthat/exposure-batch/expo-demo |only ctxR-1.1.2/ctxR/tests/testthat/exposure-batch/expo-gen |only ctxR-1.1.2/ctxR/tests/testthat/exposure-batch/exposure |only ctxR-1.1.2/ctxR/tests/testthat/exposure/expo-demo |only ctxR-1.1.2/ctxR/tests/testthat/exposure/expo-gen |only ctxR-1.1.2/ctxR/tests/testthat/exposure/exposure |only ctxR-1.1.2/ctxR/vignettes/1/0/chemical |only ctxR-1.1.2/ctxR/vignettes/1/0/hazard |only ctxR-1.1.2/ctxR/vignettes/5/0/expo-demo |only ctxR-1.1.2/ctxR/vignettes/5/0/expo-gen |only ctxR-1.1.2/ctxR/vignettes/5/0/exposure |only ctxR-1.1.2/ctxR/vignettes/Bioactivity.Rmd |only ctxR-1.1.2/ctxR/vignettes/Chemical.Rmd |only ctxR-1.1.2/ctxR/vignettes/Exposure.Rmd |only ctxR-1.1.2/ctxR/vignettes/Hazard.Rmd |only ctxR-1.1.2/ctxR/vignettes/Introduction.Rmd |only ctxR-1.1.3/ctxR/DESCRIPTION | 42 ctxR-1.1.3/ctxR/MD5 | 641 +++++--- ctxR-1.1.3/ctxR/NAMESPACE | 27 ctxR-1.1.3/ctxR/NEWS.md | 27 ctxR-1.1.3/ctxR/R/chemical-APIs-batch.R | 329 +++- ctxR-1.1.3/ctxR/R/chemical-APIs.R | 295 +++- ctxR-1.1.3/ctxR/R/exposure-APIs-batch.R | 722 ++++++++++ ctxR-1.1.3/ctxR/R/exposure-APIs.R | 515 +++++++ ctxR-1.1.3/ctxR/R/hazard-APIs-batch.R | 31 ctxR-1.1.3/ctxR/R/hazard-APIs.R | 34 ctxR-1.1.3/ctxR/README.md | 33 ctxR-1.1.3/ctxR/build/vignette.rds |binary ctxR-1.1.3/ctxR/data/bioactivity_api_server.rda |binary ctxR-1.1.3/ctxR/data/chemical_api_server.rda |binary ctxR-1.1.3/ctxR/data/exposure_api_server.rda |binary ctxR-1.1.3/ctxR/data/hazard_api_server.rda |binary ctxR-1.1.3/ctxR/inst/CITATION |only ctxR-1.1.3/ctxR/inst/doc/ctxR_01_Introduction.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_01_Introduction.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_01_Introduction.html |only ctxR-1.1.3/ctxR/inst/doc/ctxR_02_Chemical.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_02_Chemical.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_02_Chemical.html |only ctxR-1.1.3/ctxR/inst/doc/ctxR_03_Bioactivity.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_03_Bioactivity.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_03_Bioactivity.html |only ctxR-1.1.3/ctxR/inst/doc/ctxR_04_Exposure.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_04_Exposure.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_04_Exposure.html |only ctxR-1.1.3/ctxR/inst/doc/ctxR_05_Hazard.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_05_Hazard.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_05_Hazard.html |only ctxR-1.1.3/ctxR/inst/httptest/request.R | 8 ctxR-1.1.3/ctxR/man/check_existence_by_dtxsid.Rd | 2 ctxR-1.1.3/ctxR/man/check_existence_by_dtxsid_batch.Rd | 2 ctxR-1.1.3/ctxR/man/chemical_contains.Rd | 6 ctxR-1.1.3/ctxR/man/chemical_contains_batch.Rd | 2 ctxR-1.1.3/ctxR/man/chemical_equal.Rd | 6 ctxR-1.1.3/ctxR/man/chemical_equal_batch.Rd | 2 ctxR-1.1.3/ctxR/man/chemical_starts_with.Rd | 6 ctxR-1.1.3/ctxR/man/chemical_starts_with_batch.Rd | 2 ctxR-1.1.3/ctxR/man/create_hazard_data.table.Rd | 2 ctxR-1.1.3/ctxR/man/ctxR_options.Rd | 6 ctxR-1.1.3/ctxR/man/get_aggregate_records_by_dtxsid.Rd |only ctxR-1.1.3/ctxR/man/get_aggregate_records_by_dtxsid_batch.Rd |only ctxR-1.1.3/ctxR/man/get_aggregate_records_by_medium.Rd |only ctxR-1.1.3/ctxR/man/get_aggregate_records_by_medium_batch.Rd |only ctxR-1.1.3/ctxR/man/get_all_assays.Rd | 2 ctxR-1.1.3/ctxR/man/get_all_list_types.Rd | 2 ctxR-1.1.3/ctxR/man/get_all_public_chemical_lists.Rd | 2 ctxR-1.1.3/ctxR/man/get_annotation_by_aeid.Rd | 2 ctxR-1.1.3/ctxR/man/get_annotation_by_aeid_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_bioactivity_details.Rd | 2 ctxR-1.1.3/ctxR/man/get_bioactivity_details_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_bioactivity_endpoint_status.Rd | 2 ctxR-1.1.3/ctxR/man/get_bioactivity_summary.Rd | 2 ctxR-1.1.3/ctxR/man/get_bioactivity_summary_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_biomonitoring_data.Rd |only ctxR-1.1.3/ctxR/man/get_biomonitoring_data_batch.Rd |only ctxR-1.1.3/ctxR/man/get_cancer_hazard.Rd | 2 ctxR-1.1.3/ctxR/man/get_cancer_hazard_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chem_info.Rd | 2 ctxR-1.1.3/ctxR/man/get_chem_info_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chem_props_exp.Rd |only ctxR-1.1.3/ctxR/man/get_chem_props_exp_batch.Rd |only ctxR-1.1.3/ctxR/man/get_chem_props_pred.Rd |only ctxR-1.1.3/ctxR/man/get_chem_props_pred_batch.Rd |only ctxR-1.1.3/ctxR/man/get_chem_props_summary.Rd |only ctxR-1.1.3/ctxR/man/get_chemical_by_property_range.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_by_property_range_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_details.Rd | 4 ctxR-1.1.3/ctxR/man/get_chemical_details_batch.Rd | 4 ctxR-1.1.3/ctxR/man/get_chemical_endpoint_status.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_image.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_image_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_lists_by_type.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_lists_by_type_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_mol.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_mol_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_mrv.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_mrv_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_synonym.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_synonym_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemical_weight_fraction.Rd |only ctxR-1.1.3/ctxR/man/get_chemical_weight_fraction_batch.Rd |only ctxR-1.1.3/ctxR/man/get_chemicals_in_list.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemicals_in_list_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemicals_in_list_contain.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemicals_in_list_contain_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemicals_in_list_exact.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemicals_in_list_exact_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemicals_in_list_start.Rd | 2 ctxR-1.1.3/ctxR/man/get_chemicals_in_list_start_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_demographic_exposure_prediction.Rd | 2 ctxR-1.1.3/ctxR/man/get_demographic_exposure_prediction_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_ecotox_hazard_by_dtxsid.Rd | 7 ctxR-1.1.3/ctxR/man/get_ecotox_hazard_by_dtxsid_batch.Rd | 7 ctxR-1.1.3/ctxR/man/get_exposure_endpoint_status.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_functional_use.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_functional_use_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_functional_use_category.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_functional_use_probability.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_functional_use_probability_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_list_presence_tags.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_list_presence_tags_by_dtxsid.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_list_presence_tags_by_dtxsid_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_product_data.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_product_data_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_exposure_product_data_puc.Rd | 2 ctxR-1.1.3/ctxR/man/get_fate_by_dtxsid.Rd | 2 ctxR-1.1.3/ctxR/man/get_fate_by_dtxsid_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_general_exposure_prediction.Rd | 2 ctxR-1.1.3/ctxR/man/get_general_exposure_prediction_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_general_use_keywords.Rd |only ctxR-1.1.3/ctxR/man/get_general_use_keywords_batch.Rd |only ctxR-1.1.3/ctxR/man/get_genetox_details.Rd | 2 ctxR-1.1.3/ctxR/man/get_genetox_details_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_genetox_summary.Rd | 2 ctxR-1.1.3/ctxR/man/get_genetox_summary_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_hazard_by_dtxsid.Rd | 4 ctxR-1.1.3/ctxR/man/get_hazard_by_dtxsid_batch.Rd | 4 ctxR-1.1.3/ctxR/man/get_hazard_endpoint_status.Rd | 2 ctxR-1.1.3/ctxR/man/get_httk_data.Rd | 2 ctxR-1.1.3/ctxR/man/get_httk_data_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_human_hazard_by_dtxsid.Rd | 7 ctxR-1.1.3/ctxR/man/get_human_hazard_by_dtxsid_batch.Rd | 7 ctxR-1.1.3/ctxR/man/get_inchi.Rd | 2 ctxR-1.1.3/ctxR/man/get_inchikey.Rd | 2 ctxR-1.1.3/ctxR/man/get_lists_containing_chemical.Rd | 2 ctxR-1.1.3/ctxR/man/get_lists_containing_chemical_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_medium_categories.Rd |only ctxR-1.1.3/ctxR/man/get_msready_by_dtxcid.Rd | 2 ctxR-1.1.3/ctxR/man/get_msready_by_dtxcid_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_msready_by_formula.Rd | 2 ctxR-1.1.3/ctxR/man/get_msready_by_formula_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_msready_by_mass.Rd | 2 ctxR-1.1.3/ctxR/man/get_msready_by_mass_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_msready_by_mass_with_error_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_product_use_categories_batch.Rd |only ctxR-1.1.3/ctxR/man/get_product_use_category.Rd |only ctxR-1.1.3/ctxR/man/get_production_volume.Rd |only ctxR-1.1.3/ctxR/man/get_production_volume_batch.Rd |only ctxR-1.1.3/ctxR/man/get_public_chemical_list_by_name.Rd | 2 ctxR-1.1.3/ctxR/man/get_public_chemical_list_by_name_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_reported_functional_use.Rd |only ctxR-1.1.3/ctxR/man/get_reported_functional_use_batch.Rd |only ctxR-1.1.3/ctxR/man/get_single_sample_records_by_dtxsid.Rd |only ctxR-1.1.3/ctxR/man/get_single_sample_records_by_dtxsid_batch.Rd |only ctxR-1.1.3/ctxR/man/get_single_sample_records_by_medium.Rd |only ctxR-1.1.3/ctxR/man/get_single_sample_records_by_medium_batch.Rd |only ctxR-1.1.3/ctxR/man/get_skin_eye_hazard.Rd | 2 ctxR-1.1.3/ctxR/man/get_skin_eye_hazard_batch.Rd | 2 ctxR-1.1.3/ctxR/man/get_smiles.Rd | 2 ctxR-1.1.3/ctxR/man/register_ctx_api_key.Rd | 14 ctxR-1.1.3/ctxR/tests/testthat/bioactivity-batch/ctx |only ctxR-1.1.3/ctxR/tests/testthat/bioactivity/ctx |only ctxR-1.1.3/ctxR/tests/testthat/chemical-batch/ctx |only ctxR-1.1.3/ctxR/tests/testthat/chemical/ctx |only ctxR-1.1.3/ctxR/tests/testthat/exposure-batch/ctx |only ctxR-1.1.3/ctxR/tests/testthat/exposure/ctx |only ctxR-1.1.3/ctxR/tests/testthat/hazard-batch/ctx |only ctxR-1.1.3/ctxR/tests/testthat/hazard/ctx |only ctxR-1.1.3/ctxR/tests/testthat/test-chemical-APIs-batch.R | 8 ctxR-1.1.3/ctxR/tests/testthat/test-chemical-APIs.R | 27 ctxR-1.1.3/ctxR/tests/testthat/test-exposure-APIs-batch.R | 50 ctxR-1.1.3/ctxR/tests/testthat/test-exposure-APIs.R | 29 ctxR-1.1.3/ctxR/tests/testthat/test-hazard-APIs-batch.R | 40 ctxR-1.1.3/ctxR/tests/testthat/test-hazard-APIs.R | 14 ctxR-1.1.3/ctxR/vignettes/1/0/ctx |only ctxR-1.1.3/ctxR/vignettes/3/0/ctx |only ctxR-1.1.3/ctxR/vignettes/4/0/ctx |only ctxR-1.1.3/ctxR/vignettes/5/0/ctx |only ctxR-1.1.3/ctxR/vignettes/ctxR_01_Introduction.Rmd |only ctxR-1.1.3/ctxR/vignettes/ctxR_02_Chemical.Rmd |only ctxR-1.1.3/ctxR/vignettes/ctxR_03_Bioactivity.Rmd |only ctxR-1.1.3/ctxR/vignettes/ctxR_04_Exposure.Rmd |only ctxR-1.1.3/ctxR/vignettes/ctxR_05_Hazard.Rmd |only 209 files changed, 2580 insertions(+), 538 deletions(-)
Title: Draw Venn Diagram by 'ggplot2'
Description: An easy-to-use way to draw pretty Venn diagrams using 'ggplot2'.
This package provides functions to create Venn diagrams with customizable
colors, labels, and styling options.
Author: Linlin Yan [aut, cre]
Maintainer: Linlin Yan <yanlinlin82@gmail.com>
Diff between ggvenn versions 0.1.18 dated 2025-10-08 and 0.1.19 dated 2025-10-08
DESCRIPTION | 6 - MD5 | 30 +++--- NEWS.md | 69 +++++++------ R/data_preparation.R | 2 R/geom_venn.R | 21 ++-- R/ggvenn.R | 2 README.md | 164 +++++++++++++++++++++++---------- man/geom_venn.Rd | 2 man/ggvenn.Rd | 2 tests/testthat/_snaps/color_size.md | 8 - tests/testthat/_snaps/geom_venn.md | 32 +++--- tests/testthat/_snaps/ggvenn.md | 70 +++++++------- tests/testthat/_snaps/percentages.md | 24 ++-- tests/testthat/_snaps/set-totals.md | 56 +++++------ tests/testthat/_snaps/show_elements.md | 16 +-- tests/testthat/_snaps/stats.md | 126 ++++++++++++------------- 16 files changed, 352 insertions(+), 278 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] ,
David Bard [ctb] ,
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb] ,
Benjamin Nutter [ctb],
Andrew Peters [ctb] ,
Hao Zhu [ctb] ,
Janosch Linkersdoerfer [ctb] ,
Jonathan Mang [ctb] ,
Felix Torres [ctb],
Philip [...truncated...]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 1.5.0 dated 2025-07-28 and 1.6.0 dated 2025-10-08
DESCRIPTION | 10 LICENSE | 4 MD5 | 770 +- NAMESPACE | 110 NEWS.md | 70 R/REDCapR-package.R | 132 R/constant.R | 462 - R/create-batch-glossary.R | 208 R/helpers-testing.R | 264 R/kernel-api.R | 239 R/metadata-utilities.R | 270 R/project-dag-write.R | 364 - R/project-delete-multiple-arm.R | 220 R/project-delete-single-arm.R | 224 R/project-simple.R | 332 - R/redcap-arm-export.R | 372 - R/redcap-column-sanitize.R | 128 R/redcap-dag-read.R | 335 - R/redcap-delete.R | 432 - R/redcap-event-instruments.R | 366 - R/redcap-event-read.R | 368 - R/redcap-file-download-oneshot.R | 521 - R/redcap-file-repo-list.R | 389 - R/redcap-file-upload-oneshot.R | 401 - R/redcap-instrument-download.R | 465 - R/redcap-instruments.R | 333 - R/redcap-log-read.R | 446 - R/redcap-metadata-coltypes.R | 1014 +-- R/redcap-metadata-read.R | 438 - R/redcap-metadata-write.R | 316 - R/redcap-next-free-record-name.R | 288 R/redcap-project-info-read.R | 604 - R/redcap-project.R | 267 R/redcap-read-eav-oneshot.R | 708 +- R/redcap-read-oneshot-eav.R | 818 +- R/redcap-read-oneshot.R | 808 +- R/redcap-read.R | 1232 ++-- R/redcap-report.R | 499 - R/redcap-survey-link-export-oneshot.R | 343 - R/redcap-users-export.R | 451 - R/redcap-variables.R | 347 - R/redcap-version.R | 221 R/redcap-write-oneshot.R | 406 - R/redcap-write.R | 424 - R/retrieve-credential.R | 794 +- R/sanitize-token.R | 196 R/skippers.R | 38 R/utilities.R | 236 R/validate.R | 830 +- README.md | 190 build/vignette.rds |binary inst/WORDLIST | 316 - inst/doc/BasicREDCapROperations.R | 186 inst/doc/BasicREDCapROperations.Rmd | 344 - inst/doc/BasicREDCapROperations.html | 1044 +-- inst/doc/SecurityDatabase.Rmd | 694 +- inst/doc/SecurityDatabase.html | 1438 ++-- inst/doc/TroubleshootingApiCalls.R | 38 inst/doc/TroubleshootingApiCalls.Rmd | 1068 +-- inst/doc/TroubleshootingApiCalls.html | 2114 +++--- inst/doc/advanced-redcapr-operations.R | 282 inst/doc/advanced-redcapr-operations.Rmd | 540 - inst/doc/advanced-redcapr-operations.html | 1192 +-- inst/doc/longitudinal-and-repeating.R | 254 inst/doc/longitudinal-and-repeating.Rmd | 852 +- inst/doc/longitudinal-and-repeating.html | 3080 +++++----- inst/doc/workflow-read.R | 212 inst/doc/workflow-read.Rmd | 866 +- inst/doc/workflow-read.html | 1422 ++-- inst/doc/workflow-write.R | 34 inst/doc/workflow-write.Rmd | 838 +- inst/doc/workflow-write.html | 1512 ++-- inst/misc/bad.credentials | 16 inst/misc/conflicting-rows.credentials | 16 inst/misc/coph.credentials | 77 inst/misc/dev-2.credentials | 77 inst/misc/example.credentials | 77 inst/misc/out-of-order.credentials | 16 inst/misc/plugin-redirection.yml | 46 inst/misc/project-redirection.yml | 206 inst/misc/skeleton.credentials | 38 inst/misc/validation-transformation.yml | 280 inst/misc/vignette.css | 72 inst/misc/zero-rows.credentials | 12 inst/test-data/project-color-boxes/Readme.md | 106 inst/test-data/project-color-boxes/data.csv | 8 inst/test-data/project-color-boxes/dictionary.csv | 6 inst/test-data/projects/README.md | 54 inst/test-data/projects/arm-multiple-delete/README.md | 14 inst/test-data/projects/arm-multiple-delete/arm.csv | 8 inst/test-data/projects/arm-multiple-delete/data-old.csv | 114 inst/test-data/projects/arm-multiple-delete/data.csv | 122 inst/test-data/projects/arm-multiple-delete/dictionary.csv | 8 inst/test-data/projects/arm-multiple-delete/event.csv | 6 inst/test-data/projects/arm-single-delete/README.md | 14 inst/test-data/projects/arm-single-delete/data-old.csv | 34 inst/test-data/projects/arm-single-delete/data.csv | 42 inst/test-data/projects/arm-single-delete/dictionary.csv | 8 inst/test-data/projects/arm-single-longitudinal/arm.csv | 2 inst/test-data/projects/arm-single-longitudinal/data.csv | 20 inst/test-data/projects/arm-single-longitudinal/dictionary.csv | 10 inst/test-data/projects/arm-single-longitudinal/event.csv | 6 inst/test-data/projects/blank-for-gray-status/README.md | 48 inst/test-data/projects/blank-for-gray-status/data.csv | 14 inst/test-data/projects/blank-for-gray-status/dictionary.csv | 36 inst/test-data/projects/checkboxes-1/data.csv | 10 inst/test-data/projects/checkboxes-1/dictionary.csv | 10 inst/test-data/projects/clinical-trial-1/README.md | 12 inst/test-data/projects/dag-write/README.md | 24 inst/test-data/projects/dag-write/data.csv | 8 inst/test-data/projects/dag-write/dictionary.csv | 32 inst/test-data/projects/dag/README.md | 16 inst/test-data/projects/decimal-comma-and-dot/data.csv | 10 inst/test-data/projects/decimal-comma-and-dot/dictionary.csv | 18 inst/test-data/projects/decimal-comma-and-dot/metadata.csv | 18 inst/test-data/projects/decimal-comma-and-dot/redcapr-specific/default-mismatched.R | 12 inst/test-data/projects/decimal-comma/data.csv | 10 inst/test-data/projects/decimal-comma/dictionay.csv | 12 inst/test-data/projects/decimal-comma/redcapr-specific/default-mismatched.R | 12 inst/test-data/projects/decimal-comma/redcapr-specific/set-locale.R | 10 inst/test-data/projects/decimal-dot/data.csv | 10 inst/test-data/projects/decimal-dot/dictionary.csv | 12 inst/test-data/projects/decimal-dot/redcapr-specific/set-locale.R | 10 inst/test-data/projects/file-repo/README.md | 32 inst/test-data/projects/file-repo/data.csv | 6 inst/test-data/projects/file-repo/dictionary.csv | 12 inst/test-data/projects/longitudinal/arm.csv | 4 inst/test-data/projects/longitudinal/data.csv | 38 inst/test-data/projects/longitudinal/dictionary.csv | 192 inst/test-data/projects/longitudinal/event.csv | 26 inst/test-data/projects/longitudinal/expected/default.R | 398 - inst/test-data/projects/longitudinal/expected/dummy.R | 4 inst/test-data/projects/longitudinal/expected/filter-character.R | 68 inst/test-data/projects/longitudinal/expected/filter-numeric.R | 98 inst/test-data/projects/longitudinal/expected/so-example-data-frame-retrieval.R | 4 inst/test-data/projects/metadata-write/data.csv | 12 inst/test-data/projects/metadata-write/dictionary.csv | 34 inst/test-data/projects/multilevel-model-1 |only inst/test-data/projects/repeating-instruments-sparse/data.csv | 20 inst/test-data/projects/repeating-instruments-sparse/dictionary.csv | 24 inst/test-data/projects/russian/data.csv | 8 inst/test-data/projects/simple-write/README.md | 10 inst/test-data/projects/simple/README.md | 64 inst/test-data/projects/simple/data.csv | 32 inst/test-data/projects/simple/dictionary.csv | 34 inst/test-data/projects/simple/metadata.csv | 34 inst/test-data/projects/simple/project-old.xml | 1082 +-- inst/test-data/projects/super-wide-3/README.md | 44 inst/test-data/projects/super-wide-3/generate-project.R | 212 inst/test-data/projects/survey/README.md | 42 inst/test-data/projects/survey/expected/default.R | 30 inst/test-data/projects/survey/expected/so-example-data-frame-retrieval.R | 4 inst/test-data/projects/validation-types-1/data.csv | 4 inst/test-data/projects/validation-types-1/dictionary.csv | 102 inst/test-data/projects/vignette-repeating/data.csv | 36 inst/test-data/projects/vignette-repeating/dictionary.csv | 20 inst/test-data/specific-redcapr/delete/multiple-arm-four-records.R | 70 inst/test-data/specific-redcapr/delete/single-arm-four-records.R | 14 inst/test-data/specific-redcapr/event-instruments/1-arm.R | 16 inst/test-data/specific-redcapr/event-instruments/2-arms-retrieve-both-arms.R | 48 inst/test-data/specific-redcapr/event-instruments/2-arms-retrieve-only-arm-1.R | 34 inst/test-data/specific-redcapr/event-instruments/2-arms-retrieve-only-arm-2.R | 28 inst/test-data/specific-redcapr/event-instruments/no-arms.R | 2 inst/test-data/specific-redcapr/file-repo-list-oneshot/bad-folder-id.R | 2 inst/test-data/specific-redcapr/file-repo-list-oneshot/default.R | 20 inst/test-data/specific-redcapr/file-repo-list-oneshot/first-subdirectory.R | 14 inst/test-data/specific-redcapr/instruments/default.R | 12 inst/test-data/specific-redcapr/log-read/2024-10-11.R | 62 inst/test-data/specific-redcapr/metadata-coltypes/longitudinal.R | 254 inst/test-data/specific-redcapr/metadata-coltypes/problematic-dictionary.R | 18 inst/test-data/specific-redcapr/metadata-coltypes/repeating-instruments.R | 34 inst/test-data/specific-redcapr/metadata-coltypes/simple.R | 54 inst/test-data/specific-redcapr/metadata-coltypes/validation-types.R | 108 inst/test-data/specific-redcapr/metadata-read/normal-filter-form-all-three.R | 96 inst/test-data/specific-redcapr/metadata-read/normal-filter-form-demographics.R | 64 inst/test-data/specific-redcapr/metadata-read/normal-filter-form-health.R | 50 inst/test-data/specific-redcapr/metadata-read/normal-filter-form-race_and_ethnicity.R | 42 inst/test-data/specific-redcapr/metadata-read/normal.R | 120 inst/test-data/specific-redcapr/metadata-read/super-wide-3-subset.R | 96 inst/test-data/specific-redcapr/project-info-read/all-test-projects.R | 277 inst/test-data/specific-redcapr/project-info-read/chicago.R | 86 inst/test-data/specific-redcapr/project-info-read/simple.R | 84 inst/test-data/specific-redcapr/read-batch-plumbing/longitudinal.R | 72 inst/test-data/specific-redcapr/read-batch-plumbing/repeated.R | 50 inst/test-data/specific-redcapr/read-batch-plumbing/simple.R | 14 inst/test-data/specific-redcapr/read-batch-repeating-sparse/default.R | 28 inst/test-data/specific-redcapr/read-batch-simple/blank-for-gray-false.R | 50 inst/test-data/specific-redcapr/read-batch-simple/blank-for-gray-true.R | 52 inst/test-data/specific-redcapr/read-batch-simple/col_types.R | 48 inst/test-data/specific-redcapr/read-batch-simple/default.R | 46 inst/test-data/specific-redcapr/read-batch-simple/error-bad-token.R | 104 inst/test-data/specific-redcapr/read-batch-simple/export_checkbox_label.R | 62 inst/test-data/specific-redcapr/read-batch-simple/filter-character.R | 18 inst/test-data/specific-redcapr/read-batch-simple/filter-numeric.R | 26 inst/test-data/specific-redcapr/read-batch-simple/label-and-dag-one-single-batch.R | 64 inst/test-data/specific-redcapr/read-batch-simple/label-and-dag-three-tiny-batches.R | 64 inst/test-data/specific-redcapr/read-batch-simple/label-header.R | 54 inst/test-data/specific-redcapr/read-batch-simple/label.R | 62 inst/test-data/specific-redcapr/read-batch-simple/na.R | 104 inst/test-data/specific-redcapr/read-batch-simple/raw-and-dag.R | 48 inst/test-data/specific-redcapr/read-batch-simple/raw.R | 46 inst/test-data/specific-redcapr/read-batch-simple/specify-fields-without-record-id.R | 12 inst/test-data/specific-redcapr/read-batch-simple/specify-fields-zero-length.R | 46 inst/test-data/specific-redcapr/read-batch-simple/specify-fields.R | 8 inst/test-data/specific-redcapr/read-batch-simple/specify-forms-only-1st.R | 24 inst/test-data/specific-redcapr/read-batch-simple/specify-forms-without-record-id.R | 18 inst/test-data/specific-redcapr/read-batch-simple/specify-forms.R | 32 inst/test-data/specific-redcapr/read-batch-simple/specify-records-zero-length.R | 46 inst/test-data/specific-redcapr/read-batch-simple/specify-records.R | 34 inst/test-data/specific-redcapr/read-clinical-trial/default.R | 1998 +++--- inst/test-data/specific-redcapr/read-dag/assigned-to-dag-a.R | 22 inst/test-data/specific-redcapr/read-dag/no-assignment.R | 22 inst/test-data/specific-redcapr/read-eav-oneshot/blank-for-gray-false.R | 94 inst/test-data/specific-redcapr/read-eav-oneshot/blank-for-gray-true.R | 94 inst/test-data/specific-redcapr/read-eav-oneshot/default.R | 90 inst/test-data/specific-redcapr/read-eav-oneshot/filter-character.R | 22 inst/test-data/specific-redcapr/read-eav-oneshot/filter-numeric.R | 38 inst/test-data/specific-redcapr/read-eav-oneshot/specify-fields-zero-length.R | 90 inst/test-data/specific-redcapr/read-eav-oneshot/specify-fields.R | 20 inst/test-data/specific-redcapr/read-eav-oneshot/specify-forms.R | 66 inst/test-data/specific-redcapr/read-eav-oneshot/specify-records-zero-length.R | 90 inst/test-data/specific-redcapr/read-eav-oneshot/specify-records.R | 56 inst/test-data/specific-redcapr/read-oneshot-eav/blank-for-gray-false.R | 44 inst/test-data/specific-redcapr/read-oneshot-eav/blank-for-gray-true.R | 44 inst/test-data/specific-redcapr/read-oneshot-eav/default.R | 42 inst/test-data/specific-redcapr/read-oneshot-eav/filter-character.R | 14 inst/test-data/specific-redcapr/read-oneshot-eav/filter-numeric.R | 24 inst/test-data/specific-redcapr/read-oneshot-eav/label-and-dag.R | 56 inst/test-data/specific-redcapr/read-oneshot-eav/label-header.R | 42 inst/test-data/specific-redcapr/read-oneshot-eav/raw-and-dag.R | 50 inst/test-data/specific-redcapr/read-oneshot-eav/raw.R | 42 inst/test-data/specific-redcapr/read-oneshot-eav/specify-forms.R | 30 inst/test-data/specific-redcapr/read-oneshot/blank-for-gray-false.R | 50 inst/test-data/specific-redcapr/read-oneshot/blank-for-gray-true.R | 106 inst/test-data/specific-redcapr/read-oneshot/col_types.R | 102 inst/test-data/specific-redcapr/read-oneshot/default.R | 100 inst/test-data/specific-redcapr/read-oneshot/export_checkbox_label.R | 114 inst/test-data/specific-redcapr/read-oneshot/filter-character.R | 70 inst/test-data/specific-redcapr/read-oneshot/filter-numeric.R | 80 inst/test-data/specific-redcapr/read-oneshot/force-character-type.R | 102 inst/test-data/specific-redcapr/read-oneshot/label-and-dag.R | 118 inst/test-data/specific-redcapr/read-oneshot/label-header.R | 106 inst/test-data/specific-redcapr/read-oneshot/label.R | 114 inst/test-data/specific-redcapr/read-oneshot/na.R | 104 inst/test-data/specific-redcapr/read-oneshot/raw-and-dag.R | 104 inst/test-data/specific-redcapr/read-oneshot/raw.R | 100 inst/test-data/specific-redcapr/read-oneshot/specify-fields-without-record-id.R | 22 inst/test-data/specific-redcapr/read-oneshot/specify-fields-zero-length.R | 46 inst/test-data/specific-redcapr/read-oneshot/specify-fields.R | 8 inst/test-data/specific-redcapr/read-oneshot/specify-forms-only-1st.R | 48 inst/test-data/specific-redcapr/read-oneshot/specify-forms-only-2nd.R | 34 inst/test-data/specific-redcapr/read-oneshot/specify-forms-without-record-id.R | 32 inst/test-data/specific-redcapr/read-oneshot/specify-forms.R | 74 inst/test-data/specific-redcapr/read-oneshot/specify-records-zero-length.R | 46 inst/test-data/specific-redcapr/read-oneshot/specify-records.R | 34 inst/test-data/specific-redcapr/report/col_types.R | 24 inst/test-data/specific-redcapr/report/default.R | 26 inst/test-data/specific-redcapr/report/export_checkbox_label.R | 30 inst/test-data/specific-redcapr/report/force-character-type.R | 26 inst/test-data/specific-redcapr/report/label-header.R | 106 inst/test-data/specific-redcapr/report/raw.R | 24 inst/test-data/specific-redcapr/test-project/read-insert-and-update.R | 40 inst/test-data/specific-redcapr/users-export/with-dags--user.R | 26 inst/test-data/specific-redcapr/users-export/with-dags--user_form.R | 8 inst/test-data/specific-redcapr/users-export/without-dags--user.R | 28 inst/test-data/specific-redcapr/users-export/without-dags--user_form.R | 12 inst/test-data/specific-redcapr/variables/default.R | 36 inst/test-data/specific-redcapr/write-batch/default.R | 96 inst/test-data/specific-redcapr/write-batch/update-one-field.R | 92 inst/test-data/specific-redcapr/write-batch/update-two-fields.R | 92 inst/test-data/specific-redcapr/write-dag/after.R | 16 inst/test-data/specific-redcapr/write-dag/before.R | 14 inst/test-data/specific-redcapr/write-oneshot/default.R | 96 inst/test-data/specific-redcapr/write-oneshot/one-field.R | 92 inst/test-data/specific-redcapr/write-oneshot/overwrite-true.R | 90 inst/test-data/specific-redcapr/write-oneshot/two-fields.R | 92 man/REDCapR-package.Rd | 212 man/collapse_vector.Rd | 60 man/constant.Rd | 232 man/create_batch_glossary.Rd | 122 man/figures/logo.svg | 278 man/kernel_api.Rd | 151 man/metadata_utilities.Rd | 188 man/redcap_arm_export.Rd | 178 man/redcap_column_sanitize.Rd | 112 man/redcap_dag_read.Rd | 169 man/redcap_delete.Rd | 226 man/redcap_event_instruments.Rd | 204 man/redcap_event_read.Rd | 182 man/redcap_file_download_oneshot.Rd | 291 man/redcap_file_repo_list_oneshot.Rd | 213 man/redcap_file_upload_oneshot.Rd | 265 man/redcap_instrument_download.Rd | 275 man/redcap_instruments.Rd | 173 man/redcap_log_read.Rd | 260 man/redcap_metadata_coltypes.Rd | 346 - man/redcap_metadata_read.Rd | 194 man/redcap_metadata_write.Rd | 200 man/redcap_next_free_record_name.Rd | 172 man/redcap_project.Rd | 169 man/redcap_project_info_read.Rd | 318 - man/redcap_read.Rd | 640 +- man/redcap_read_eav_oneshot.Rd | 350 - man/redcap_read_oneshot.Rd | 502 - man/redcap_read_oneshot_eav.Rd | 360 - man/redcap_report.Rd | 307 man/redcap_survey_link_export_oneshot.Rd | 219 man/redcap_users_export.Rd | 155 man/redcap_variables.Rd | 165 man/redcap_version.Rd | 113 man/redcap_write.Rd | 290 man/redcap_write_oneshot.Rd | 250 man/replace_nas_with_explicit.Rd | 98 man/retrieve_credential.Rd | 288 man/sanitize_token.Rd | 146 man/to_api_array.Rd | 52 man/validate.Rd | 310 - tests/manual/README.md | 8 tests/manual/test-could-not-connect-rate.R | 114 tests/manual/test-stress-test-serial.R | 248 tests/spelling.R | 14 tests/test-all.R | 32 tests/testthat/test-arm-export.R | 260 tests/testthat/test-column-sanitize.R | 70 tests/testthat/test-constant.R | 196 tests/testthat/test-create-batch-glossary.R | 198 tests/testthat/test-create-credential-local.R | 74 tests/testthat/test-dag-read.R | 162 tests/testthat/test-delete.R | 406 - tests/testthat/test-event-instruments.R | 372 - tests/testthat/test-event-read.R | 356 - tests/testthat/test-file-oneshot.R | 1166 +-- tests/testthat/test-file-repo-list-oneshot.R | 330 - tests/testthat/test-instruments-metadata.R | 164 tests/testthat/test-instruments.R | 188 tests/testthat/test-log-read.R | 100 tests/testthat/test-metadata-coltypes.R | 460 - tests/testthat/test-metadata-read.R | 642 +- tests/testthat/test-metadata-utilities.R | 380 - tests/testthat/test-metadata-write.R | 110 tests/testthat/test-next-free-record-name.R | 188 tests/testthat/test-project-info-read.R | 236 tests/testthat/test-project.R | 158 tests/testthat/test-read-batch-longitudinal.R | 390 - tests/testthat/test-read-batch-plumbing.R | 190 tests/testthat/test-read-batch-repeating-sparse.R | 246 tests/testthat/test-read-batch-simple.R | 1800 ++--- tests/testthat/test-read-batch-survey.R | 228 tests/testthat/test-read-clinical-trial.R | 86 tests/testthat/test-read-dag.R | 90 tests/testthat/test-read-decimal-comma.R | 232 tests/testthat/test-read-decimal-dot.R | 176 tests/testthat/test-read-eav-oneshot.R | 706 +- tests/testthat/test-read-errors.R | 184 tests/testthat/test-read-oneshot-eav.R | 698 +- tests/testthat/test-read-oneshot.R | 1542 ++--- tests/testthat/test-read-russian.R | 88 tests/testthat/test-read-superwide.R | 294 tests/testthat/test-report.R | 346 - tests/testthat/test-retrieve-credential-local.R | 346 - tests/testthat/test-retrieve-credential-mssql.R | 332 - tests/testthat/test-sanitize.R | 146 tests/testthat/test-skippers.R | 22 tests/testthat/test-survey-link-export-oneshot.R | 134 tests/testthat/test-users-export.R | 286 tests/testthat/test-utilities-collapse_vector.R | 40 tests/testthat/test-utilities-replace_nas_with_explicit.R | 160 tests/testthat/test-validate-field-names.R | 106 tests/testthat/test-validate-no-logical.R | 160 tests/testthat/test-validate-record-id-name.R | 78 tests/testthat/test-validate-repeat.R | 66 tests/testthat/test-validate-uniqueness.R | 220 tests/testthat/test-validate.R | 182 tests/testthat/test-variables.R | 186 tests/testthat/test-version.R | 90 tests/testthat/test-write-batch.R | 416 - tests/testthat/test-write-dag.R | 428 - tests/testthat/test-write-error.R | 298 tests/testthat/test-write-oneshot.R | 564 - vignettes/BasicREDCapROperations.Rmd | 344 - vignettes/SecurityDatabase.Rmd | 694 +- vignettes/TroubleshootingApiCalls.Rmd | 1068 +-- vignettes/advanced-redcapr-operations.Rmd | 540 - vignettes/longitudinal-and-repeating.Rmd | 852 +- vignettes/workflow-read.Rmd | 866 +- vignettes/workflow-write.Rmd | 838 +- 386 files changed, 42136 insertions(+), 42114 deletions(-)
Title: Machine Learning-Assisted, Marker-Based Tool for Single-Cell and
Spatial Transcriptomics Annotation
Description: Annotates single-cell and spatial-transcriptomic (ST) data using marker datasets. Supports unified markers list ('Markers_list') creation from built-in databases (e.g., 'Cellmarker2', 'PanglaoDB', 'scIBD', 'TCellSI'), Seurat objects, or user-supplied Excel files. SlimR can predict calculate parameters by machine learning algorithms (e.g., 'Random Forest', 'Gradient Boosting', 'Support Vector Machine', 'Ensemble Learning'), and based on Markers_list, calculate gene expression of different cell types and predict annotation information and calculate corresponding AUC and annotate it, then verify it. At the same time, it can calculate gene expression corresponding to the cell type to generate a reference map for manual annotation (e.g., 'Heat Map', 'Feature Plots', 'Combined Plots'). For more details see Kabacoff (2020, ISBN:9787115420572).
Author: Zhaoqing Wang [aut, cre]
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>
Diff between SlimR versions 1.0.7 dated 2025-08-18 and 1.0.8 dated 2025-10-08
DESCRIPTION | 32 +++--- MD5 | 118 ++++++++++++----------- NAMESPACE | 6 + NEWS.md | 8 + R/Celltype_Annotation.R | 2 R/Celltype_Annotation_Combined.R | 4 R/Celltype_Annotation_Features.R | 6 - R/Celltype_Annotation_Heatmap.R | 2 R/Celltype_Calculate.R | 11 +- R/Celltype_Verification.R | 6 - R/Celltype_annotation_Cellmarker2.R | 8 - R/Celltype_annotation_Excel.R | 8 - R/Celltype_annotation_PanglaoDB.R | 8 - R/Celltype_annotation_Seurat.R | 10 +- R/Database_Cellmarker2.R | 2 R/Database_Cellmarker2_raw.R | 2 R/Database_Cellmarker2_table.R | 2 R/Database_Markers_list_TCellSI.R | 2 R/Database_Markers_list_scIBD.R | 6 - R/Database_PanglaoDB.R | 2 R/Database_PanglaoDB_raw.R | 2 R/Database_PanglaoDB_table.R | 2 R/Expression_calculate.R | 2 R/Markers_filter_Cellmarker2.R | 2 R/Markers_filter_PanglaoDB.R | 2 R/Probability_calculate.R | 2 R/Probability_parameter.R |only R/Read_excel_markers.R | 2 R/Read_seurat_markers.R | 14 +- R/onattach.R | 12 +- README.md | 164 ++++++++++++++++++++------------- data/Markers_list_scIBD.rda |binary man/Cellmarker2.Rd | 4 man/Cellmarker2_raw.Rd | 4 man/Cellmarker2_table.Rd | 4 man/Celltype_Annotation.Rd | 7 - man/Celltype_Annotation_Combined.Rd | 6 - man/Celltype_Annotation_Features.Rd | 8 - man/Celltype_Annotation_Heatmap.Rd | 4 man/Celltype_Calculate.Rd | 7 - man/Celltype_Verification.Rd | 9 + man/Celltype_annotation_Cellmarker2.Rd | 8 - man/Celltype_annotation_Excel.Rd | 8 - man/Celltype_annotation_PanglaoDB.Rd | 8 - man/Celltype_annotation_Seurat.Rd | 8 - man/Markers_filter_Cellmarker2.Rd | 4 man/Markers_filter_PanglaoDB.Rd | 4 man/Markers_list_TCellSI.Rd | 4 man/Markers_list_scIBD.Rd | 8 + man/PanglaoDB.Rd | 4 man/PanglaoDB_raw.Rd | 4 man/PanglaoDB_table.Rd | 4 man/Parameter_Calculate.Rd |only man/Read_excel_markers.Rd | 4 man/Read_seurat_markers.Rd | 10 +- man/calculate_cluster_variability.Rd |only man/calculate_expression.Rd | 14 ++ man/calculate_expression_skewness.Rd |only man/calculate_probability.Rd | 14 ++ man/estimate_batch_effect.Rd |only man/extract_dataset_features.Rd |only man/generate_training_data.Rd |only man/postprocess_parameters.Rd |only man/predict_optimal_parameters.Rd |only man/train_parameter_model.Rd |only 65 files changed, 355 insertions(+), 253 deletions(-)
Title: Rapid Asynchronous and Distributed Computing
Description: Package to tackle large-scale problems asynchronously across
a distributed network. Employing a database centric model, rush
enables workers to communicate tasks and their results over a shared
'Redis' database. Key features include low task overhead, efficient
caching, and robust error handling. The package powers the
asynchronous optimization algorithms in the 'bbotk' and 'mlr3tuning'
packages.
Author: Marc Becker [cre, aut, cph]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between rush versions 0.3.1 dated 2025-09-16 and 0.4.0 dated 2025-10-08
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ NEWS.md | 7 ++++++ R/Rush.R | 44 ++++++++++++++++++++++++++++++++++++--- man/Rush.Rd | 28 +++++++++++++++++++++++- man/RushWorker.Rd | 1 tests/testthat/test-Rush.R | 32 ++++++++++++++++++++++++++++ tests/testthat/test-RushWorker.R | 38 +++++++++++++++++++++++++++++++++ 8 files changed, 155 insertions(+), 15 deletions(-)
Title: Patient-Reported Outcome Data Analysis with Stan
Description: Algorithms and subroutines for patient-reported outcome data analysis.
Author: Bin Wang [aut, cre]
Maintainer: Bin Wang <bwang831@gmail.com>
Diff between prome versions 2.0.1.4 dated 2025-10-02 and 2.0.1.9 dated 2025-10-08
DESCRIPTION | 13 ++++++------- MD5 | 6 +++--- R/blindinglogit.R | 5 +++-- man/lslogit.Rd | 6 +++--- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Acquiring and Processing Data from Japan Institute for Health
Security
Description: Download and post process the infectious disease case data
from Japan Institute for Health Security. Also the package included
ready-to-analyse datasets. See the data source website for further details
<https://id-info.jihs.go.jp/>.
Author: Tomonori Hoshi [aut, cre],
Erina Ishigaki [aut],
Satoshi Kaneko [aut]
Maintainer: Tomonori Hoshi <tomonori.hoshi.japan@gmail.com>
Diff between jpinfect versions 0.1.4 dated 2025-10-07 and 0.1.5 dated 2025-10-08
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/jpinfect_read_confirmed.R | 8 ++++++-- inst/doc/jpinfect.html | 4 ++-- 4 files changed, 17 insertions(+), 13 deletions(-)
Title: Simplify Survival Data Analysis and Model Fitting
Description: Inspect survival data, plot Kaplan-Meier curves, assess the
proportional hazards assumption, fit parametric survival models,
predict and plot survival and hazards, and export the outputs to
'Excel'. A simple interface for fitting survival models using
flexsurv::flexsurvreg(), flexsurv::flexsurvspline(),
flexsurvcure::flexsurvcure(), and survival::survreg().
Author: Niall Davison [aut, cre] ,
Brad Kievit [aut],
Maple Health Group, LLC [cph, fnd]
Maintainer: Niall Davison <niall.davison@maplehealthgroup.com>
Diff between easysurv versions 2.0.1 dated 2024-06-21 and 2.0.2 dated 2025-10-08
DESCRIPTION | 23 - MD5 | 38 - NEWS.md | 19 R/plot.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/easysurv.R | 126 +++--- inst/doc/easysurv.html | 741 +++++++++++++++++++------------------- man/easy_bc.Rd | 54 +- man/easy_lung.Rd | 68 +-- man/easysurv-package.Rd | 2 man/figures/fit-models-a-dark.svg | 2 man/figures/fit-models-a.svg | 2 man/figures/get-KM-r-1.png |binary man/figures/plot-models-r-1.png |binary man/figures/plot-models-r-2.png |binary man/figures/plot-models-r-3.png |binary man/figures/plot-models-r-4.png |binary man/figures/test-PH-r-1.png |binary man/figures/test-PH-r-2.png |binary 20 files changed, 543 insertions(+), 538 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.5 dated 2025-09-08 and 0.1.6 dated 2025-10-08
DESCRIPTION | 10 MD5 | 10 R/xtdml_data.R | 852 +++++++++++++++++++++++++++---------------------------- R/xtdml_plr.R | 2 README.md | 20 + man/xtdml_plr.Rd | 4 6 files changed, 461 insertions(+), 437 deletions(-)
Title: Automatically Retrieve Multidimensional Distributed Data Sets
Description: Automatically fetch, transform and arrange subsets of
multidimensional data sets (collections of files) stored in local and/or
remote file systems or servers, using multicore capabilities where possible.
This tool provides an interface to perceive a collection of data sets as a single
large multidimensional data array, and enables the user to request for automatic
retrieval, processing and arrangement of subsets of the large array. Wrapper
functions to add support for custom file formats can be plugged in/out, making
the tool suitable for any research field where large multidimensional data sets
are involved.
Author: Nicolau Manubens [aut],
An-Chi Ho [aut] ,
Nuria Perez-Zanon [aut] ,
Victoria Agudetse [cre, ctb],
Eva Rifa [ctb],
Bruno de Paula Kinoshita [ctb],
Javier Vegas [ctb],
Pierre-Antoine Bretonniere [ctb],
Roberto Serrano [ctb],
BSC-CNS [aut, cph]
Maintainer: Victoria Agudetse <victoria.agudetse@bsc.es>
This is a re-admission after prior archival of version 2.4.0 dated 2024-09-19
Diff between startR versions 2.4.0 dated 2024-09-19 and 3.0.0 dated 2025-10-08
DESCRIPTION | 25 ++-- MD5 | 30 ++-- NAMESPACE | 3 NEWS.md | 21 +++ R/ByChunks_autosubmit.R | 159 +++++++++++++++++++------- R/ByChunks_ecflow.R | 67 +++++++++- R/Collect.R | 41 +++++- R/Compute.R | 6 R/NcDataReader.R | 11 - R/SelectorChecker.R | 3 R/Start.R | 17 ++ R/Utils.R | 52 +++++++- inst/chunking/Autosubmit/autosubmit.yml | 2 inst/chunking/Autosubmit/platforms.yml | 29 ++++ inst/chunking/Autosubmit/startR_autosubmit.sh | 3 inst/chunking/ecFlow/Chunk.ecf | 1 16 files changed, 365 insertions(+), 105 deletions(-)
Title: Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Description: Tools for the optimization of stratified sampling design. It determines a stratification of a sampling frame that minimizes sample cost while satisfying precision constraints in a multivariate and multidomain context. The approach relies on a genetic algorithm; each candidate partition of the frame is an individual whose fitness is evaluated via the Bethel-Chromy allocation to meet target precisions. Functions support analysis of optimization results, labeling of the frame with new strata, and drawing a sample according to the optimal allocation. Algorithmic components adapt code from the 'genalg' package. See M. Ballin and G. Barcaroli (2020) "R package SamplingStrata: new developments and extension to Spatial Sampling" <doi:10.48550/arXiv.2004.09366>.
Author: Giulio Barcaroli [aut, cre],
Marco Ballin [aut],
Hanjo Odendaal [aut],
Daniela Pagliuca [aut],
Egon Willighagen [aut],
Diego Zardetto [aut]
Maintainer: Giulio Barcaroli <gbarcaroli@gmail.com>
Diff between SamplingStrata versions 1.5-4 dated 2022-11-15 and 1.5-5 dated 2025-10-08
DESCRIPTION | 33 ++- MD5 | 25 +- NEWS | 4 R/optimizeStrata.R | 2 R/optimizeStrata2.R | 3 R/optimizeStrataSpatial.R | 3 build/vignette.rds |binary inst/CITATION | 69 ++++--- inst/doc/SamplingStrata.html | 209 +++++++++++------------ inst/doc/models.R | 26 +- inst/doc/models.html | 4 inst/doc/spatial.R | 24 +- inst/doc/spatial.html | 4 vignettes/spatial_figures/unnamed-chunk-10-1.jpg |only 14 files changed, 219 insertions(+), 187 deletions(-)
More information about SamplingStrata at CRAN
Permanent link
Title: Factor-Augmented Regression Scenarios
Description: Provides a comprehensive framework in R for modeling and forecasting economic scenarios based on multi-level dynamic factor model. The package enables users to: (i) extract global and group-specific factors using a flexible multi-level factor structure; (ii) compute asymptotically valid confidence regions for the estimated factors, accounting for uncertainty in the factor loadings; (iii) obtain estimates of the parameters of the factor-augmented quantile regressions together with their standard deviations; (iv) recover full predictive conditional densities from estimated quantiles; (v) obtain risk measures based on extreme quantiles of the conditional densities; (vi) estimate the conditional density and the corresponding extreme quantiles when the factors are stressed.
Author: Gian Pietro Bellocca [aut, cre],
Ignacio Garron [aut],
Vladimir Rodriguez-Caballero [aut],
Esther Ruiz [aut]
Maintainer: Gian Pietro Bellocca <gbellocc@est-econ.uc3m.es>
Diff between FARS versions 0.6.0 dated 2025-10-07 and 0.6.1 dated 2025-10-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/plot.R | 3 ++- inst/doc/Factor_Augmented_Regression_Scenarios_in_R.pdf |binary 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Dynamic Mode Decomposition Forecasting with Conformal Predictive
Sampling
Description: The DYMO package provides tools for multi-feature time-series forecasting using a Dynamic Mode Decomposition (DMD) model combined with conformal predictive sampling for uncertainty quantification.
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between dymo versions 1.1.0 dated 2022-05-05 and 2.0.0 dated 2025-10-08
DESCRIPTION | 24 - MD5 | 12 NAMESPACE | 35 +- NEWS.md | 17 + R/main.R | 860 ++++++++++++++++++++++++++++++++++++------------------------ man/dymo.Rd | 79 +++-- tests |only 7 files changed, 628 insertions(+), 399 deletions(-)
Title: Visualising and Interpreting Statistical Models Fit to
Compositional Data
Description: Statistical models fit to compositional data are often difficult to interpret due to the sum to 1 constraint on data variables. 'DImodelsVis' provides novel visualisations tools to aid with the interpretation of models fit to compositional data. All visualisations in the package are created using the 'ggplot2' plotting framework and can be extended like every other 'ggplot' object.
Author: Rishabh Vishwakarma [aut, cre] ,
Caroline Brophy [aut],
Laura Byrne [aut],
Catherine Hurley [aut]
Maintainer: Rishabh Vishwakarma <vishwakr@tcd.ie>
Diff between DImodelsVis versions 1.0.3 dated 2025-08-23 and 1.0.4 dated 2025-10-08
DImodelsVis-1.0.3/DImodelsVis/man/add_ID_terms.Rd |only DImodelsVis-1.0.3/DImodelsVis/man/add_interaction_terms.Rd |only DImodelsVis-1.0.4/DImodelsVis/DESCRIPTION | 11 DImodelsVis-1.0.4/DImodelsVis/MD5 | 127 - DImodelsVis-1.0.4/DImodelsVis/NAMESPACE | 1 DImodelsVis-1.0.4/DImodelsVis/NEWS.md | 6 DImodelsVis-1.0.4/DImodelsVis/R/ConditionalTernary.R | 4 DImodelsVis-1.0.4/DImodelsVis/R/GradientChange.R | 6 DImodelsVis-1.0.4/DImodelsVis/R/GroupedTernary.R | 6 DImodelsVis-1.0.4/DImodelsVis/R/ModelDiagnostics.R | 6 DImodelsVis-1.0.4/DImodelsVis/R/ModelSelection.R | 3 DImodelsVis-1.0.4/DImodelsVis/R/PredictionContributions.R | 22 DImodelsVis-1.0.4/DImodelsVis/R/SanityChecks.R | 9 DImodelsVis-1.0.4/DImodelsVis/R/SimplexPath.R | 11 DImodelsVis-1.0.4/DImodelsVis/R/Ternary.R | 2 DImodelsVis-1.0.4/DImodelsVis/R/VisualiseEffects.R | 9 DImodelsVis-1.0.4/DImodelsVis/R/utilities.R | 175 -- DImodelsVis-1.0.4/DImodelsVis/build/vignette.rds |binary DImodelsVis-1.0.4/DImodelsVis/inst/WORDLIST | 5 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-DImodelsMulti-models.Rmd | 6 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-DImodelsMulti-models.html | 12 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-black-box-models.R |only DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-black-box-models.Rmd |only DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-black-box-models.html |only DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-complex-models.R | 2 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-complex-models.Rmd | 14 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-complex-models.html | 49 DImodelsVis-1.0.4/DImodelsVis/man/DI_ID_and_ints.Rd |only DImodelsVis-1.0.4/DImodelsVis/man/add_add_var.Rd | 4 DImodelsVis-1.0.4/DImodelsVis/man/add_prediction.Rd | 3 DImodelsVis-1.0.4/DImodelsVis/man/conditional_ternary.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/conditional_ternary_data.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/custom_filter.Rd | 158 - DImodelsVis-1.0.4/DImodelsVis/man/get_colours.Rd | 70 DImodelsVis-1.0.4/DImodelsVis/man/get_shades.Rd | 58 DImodelsVis-1.0.4/DImodelsVis/man/gradient_change.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/gradient_change_data.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/gradient_change_plot.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/grouped_ternary.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/grouped_ternary_data.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/grouped_ternary_plot.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/model_diagnostics.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/model_diagnostics_data.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/model_diagnostics_plot.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/model_selection.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/prediction_contributions.Rd | 9 DImodelsVis-1.0.4/DImodelsVis/man/prediction_contributions_plot.Rd | 6 DImodelsVis-1.0.4/DImodelsVis/man/simplex_path.Rd | 3 DImodelsVis-1.0.4/DImodelsVis/man/simplex_path_data.Rd | 3 DImodelsVis-1.0.4/DImodelsVis/man/simplex_path_plot.Rd | 3 DImodelsVis-1.0.4/DImodelsVis/man/visualise_effects.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/visualise_effects_data.Rd | 4 DImodelsVis-1.0.4/DImodelsVis/man/visualise_effects_plot.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/ConditionalTernary/ct-dimodels-data-manual.svg | 16 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/GroupedTernary/gt-with-dimodels-data-manual.svg | 9 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-basic-dimodels-and-custom-data.svg | 140 - DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-add-var-in-dimodels.svg | 840 +++++----- DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-add-var-single-and-custom-data.svg | 300 +-- DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-basic-dimodels.svg | 84 - DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-data-manually-prepared.svg | 120 - DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-pie-data.svg | 474 ++--- DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/Ternary/ternary-with-add-var-and-aes.svg | 34 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/test-ConditionalTernary.R | 3 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/test-GroupedTernary.R | 3 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/test-SanityChecks.R | 7 DImodelsVis-1.0.4/DImodelsVis/vignettes/DImodelsVis-with-DImodelsMulti-models.Rmd | 6 DImodelsVis-1.0.4/DImodelsVis/vignettes/DImodelsVis-with-black-box-models.Rmd |only DImodelsVis-1.0.4/DImodelsVis/vignettes/DImodelsVis-with-complex-models.Rmd | 14 68 files changed, 1436 insertions(+), 1449 deletions(-)
Title: Threshold Selection and Uncertainty for Extreme Value Analysis
Description: Provides functions for the selection of thresholds for use in
extreme value models, based mainly on the methodology in
Northrop, Attalides and Jonathan (2017) <doi:10.1111/rssc.12159>.
It also performs predictive inferences about future extreme values,
based either on a single threshold or on a weighted average of inferences
from multiple thresholds, using the 'revdbayes' package
<https://cran.r-project.org/package=revdbayes>.
At the moment only the case where the data can be treated as
independent identically distributed observations is considered.
Author: Paul J. Northrop [aut, cre, cph],
Nicolas Attalides [aut]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between threshr versions 1.0.6 dated 2024-07-17 and 1.0.7 dated 2025-10-08
DESCRIPTION | 10 +++---- MD5 | 16 ++++++------ NEWS.md | 7 +++++ R/ithresh.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/threshr-vignette.html | 44 +++++++++++++++++---------------- man/ithresh.Rd | 2 - tests/testthat/test-plot_and_summary.R | 3 -- 9 files changed, 46 insertions(+), 38 deletions(-)
Title: Multiblock Exploratory and Predictive Data Analysis
Description: Exploratory and predictive methods for the analysis of several blocks of variables measured on the same individuals.
Author: Benjamin Mahieu [aut, cre],
Essomanda Tchandao Mangamana [aut],
Evelyne Vigneau [aut],
Veronique Cariou [aut]
Maintainer: Benjamin Mahieu <benjamin.mahieu@oniris-nantes.fr>
Diff between MBAnalysis versions 2.1.0 dated 2025-07-10 and 2.1.1 dated 2025-10-08
DESCRIPTION | 6 MD5 | 104 +++--- R/ComDim.R | 598 ++++++++++++++++++------------------- R/MBPCA.R | 584 ++++++++++++++++++------------------ R/MBPLS.R | 756 +++++++++++++++++++++++------------------------ R/MBValidation.R | 418 ++++++++++++------------- R/MBWCov.R | 804 +++++++++++++++++++++++++------------------------- R/MBplotBlocks.R | 392 ++++++++++++------------ R/MBplotScores.R | 280 ++++++++--------- R/MBplotVars.R | 444 +++++++++++++-------------- R/coef.MBPLS.R | 78 ++-- R/coef.MBWCov.R | 72 ++-- R/ham-data.R | 2 R/plot.ComDim.R | 2 R/plot.MBPCA.R | 2 R/plot.MBPLS.R | 2 R/plot.MBWCov.R | 2 R/predict.MBPLS.R | 2 R/predict.MBWCov.R | 100 +++--- R/print.ComDim.R | 120 +++---- R/print.MBPCA.R | 120 +++---- R/print.MBPLS.R | 142 ++++---- R/print.MBWCov.R | 142 ++++---- R/summary.ComDim.R | 7 R/summary.MBPCA.R | 7 R/summary.MBPLS.R | 7 R/summary.MBWCov.R | 7 build/partial.rdb |binary man/ComDim.Rd | 2 man/MBPCA.Rd | 2 man/MBPLS.Rd | 2 man/MBValidation.Rd | 2 man/MBWCov.Rd | 2 man/MBplotBlocks.Rd | 2 man/MBplotScores.Rd | 2 man/MBplotVars.Rd | 2 man/coef.MBPLS.Rd | 2 man/coef.MBWCov.Rd | 2 man/ham.Rd | 2 man/plot.ComDim.Rd | 2 man/plot.MBPCA.Rd | 2 man/plot.MBPLS.Rd | 2 man/plot.MBWCov.Rd | 2 man/predict.MBPLS.Rd | 2 man/predict.MBWCov.Rd | 2 man/print.ComDim.Rd | 4 man/print.MBPCA.Rd | 4 man/print.MBPLS.Rd | 4 man/print.MBWCov.Rd | 4 man/summary.ComDim.Rd | 2 man/summary.MBPCA.Rd | 2 man/summary.MBPLS.Rd | 2 man/summary.MBWCov.Rd | 2 53 files changed, 2635 insertions(+), 2623 deletions(-)
Title: Count Transformation Models
Description: Count transformation models featuring
parameters interpretable as discrete hazard ratios, odds ratios,
reverse-time discrete hazard ratios, or transformed expectations.
An appropriate data transformation for a count outcome and
regression coefficients are simultaneously estimated by maximising
the exact discrete log-likelihood using the computational framework
provided in package 'mlt', technical details are given in
Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>.
The package also contains an experimental implementation of
multivariate count transformation models with an application
to multi-species distribution models <DOI:10.48550/arXiv.2201.13095>.
Author: Sandra Siegfried [aut, cre] ,
Luisa Barbanti [aut] ,
Torsten Hothorn [aut]
Maintainer: Sandra Siegfried <sandra.siegfried@alumni.uzh.ch>
Diff between cotram versions 0.5-2 dated 2024-09-18 and 0.5-3 dated 2025-10-08
cotram-0.5-2/cotram/tests/confband-Ex.Rout.save |only cotram-0.5-3/cotram/DESCRIPTION | 15 ++++++++------- cotram-0.5-3/cotram/MD5 | 13 ++++++------- cotram-0.5-3/cotram/R/predict.R | 10 ++++------ cotram-0.5-3/cotram/build/partial.rdb |binary cotram-0.5-3/cotram/build/vignette.rds |binary cotram-0.5-3/cotram/inst/NEWS.Rd | 6 ++++++ cotram-0.5-3/cotram/inst/doc/cotram.pdf |binary 8 files changed, 24 insertions(+), 20 deletions(-)
Title: Wavelet Variance
Description: Provides a series of tools to compute and plot quantities related to classical and robust wavelet variance for time series and regular lattices. More details can be found, for example, in Serroukh, A., Walden, A.T., & Percival, D.B. (2000) <doi:10.2307/2669537> and Guerrier, S. & Molinari, R. (2016) <doi:10.48550/arXiv.1607.05858>.
Author: Stephane Guerrier [aut, cre],
James Balamuta [aut],
Justin Lee [aut],
Roberto Molinari [aut],
Yuming Zhang [aut],
Mucyo Karemera [aut],
Nathanael Claussen [ctb],
Haotian Xu [ctb],
Lionel Voirol [ctb]
Maintainer: Stephane Guerrier <stef.guerrier@gmail.com>
Diff between wv versions 0.1.2 dated 2023-08-31 and 0.1.3 dated 2025-10-08
DESCRIPTION | 11 ++++------ MD5 | 32 ++++++++++++++--------------- NEWS.md | 5 ++++ R/RcppExports.R | 34 ++++++++++--------------------- README.md | 16 ++++++-------- man/batch_modwt_wvar_cpp.Rd | 8 ++----- man/ci_eta3.Rd | 10 +++------ man/ci_eta3_robust.Rd | 4 --- man/ci_wave_variance.Rd | 4 --- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/modwt_wvar_cpp.Rd | 4 --- man/wv.Rd | 2 - man/wvar_cpp.Rd | 4 --- src/rtoarmadillo.cpp | 4 +-- src/wave_variance.cpp | 34 ++++++++++--------------------- 17 files changed, 69 insertions(+), 103 deletions(-)
Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models as introduced in <DOI:10.1007/s11222-019-09870-4>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-7 dated 2025-04-09 and 0.3-8 dated 2025-10-08
tbm-0.3-7/tbm/tests/bodyfat.Rout.save |only tbm-0.3-8/tbm/DESCRIPTION | 11 ++++++----- tbm-0.3-8/tbm/MD5 | 9 ++++----- tbm-0.3-8/tbm/build/vignette.rds |binary tbm-0.3-8/tbm/inst/NEWS.Rd | 6 ++++++ tbm-0.3-8/tbm/inst/doc/tbm_supplement.pdf |binary 6 files changed, 16 insertions(+), 10 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-10 dated 2024-11-19 and 1.1-11 dated 2025-10-08
mlt.docreg-1.1-10/mlt.docreg/tests/AFT-Ex.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/KM-Ex.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/faithful.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/orm-Ex.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/timedep_covar.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/truncreg-Ex.Rout.save |only mlt.docreg-1.1-11/mlt.docreg/DESCRIPTION | 11 +++---- mlt.docreg-1.1-11/mlt.docreg/MD5 | 20 ++++--------- mlt.docreg-1.1-11/mlt.docreg/build/vignette.rds |binary mlt.docreg-1.1-11/mlt.docreg/inst/NEWS.Rd | 8 ++++- mlt.docreg-1.1-11/mlt.docreg/inst/doc/mlt.pdf |binary mlt.docreg-1.1-11/mlt.docreg/tests/AFT-Ex.R | 1 mlt.docreg-1.1-11/mlt.docreg/tests/orm-Ex.R | 3 - mlt.docreg-1.1-11/mlt.docreg/vignettes/mlt.bib | 9 +++-- 14 files changed, 28 insertions(+), 24 deletions(-)
Title: Hierarchical Partitioning of Marginal R2 for Generalized
Mixed-Effect Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor (fixed effects) towards marginal R2 for generalized linear mixed-effect model (including lm, glm and glmm) based on output of r.squaredGLMM() in 'MuMIn', applying the algorithm of Lai J.,Zou Y., Zhang S.,Zhang X.,Mao L.(2022)glmm.hp: an R package for computing individual effect of predictors in generalized linear mixed models.Journal of Plant Ecology,15(6)1302-1307<doi:10.1093/jpe/rtac096>.
Author: Jiangshan Lai [aut, cre] ,
Kim Nimon [aut],
Yao Liu [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between glmm.hp versions 0.1-8 dated 2025-03-24 and 1.0-0 dated 2025-10-08
DESCRIPTION | 11 ++++++----- MD5 | 6 ++++-- NAMESPACE | 2 ++ R/detect_glm_family.r |only man/detect_glm_family.Rd |only 5 files changed, 12 insertions(+), 7 deletions(-)
Title: High Dimensional Data Visualization
Description: It provides materials (i.e. 'serial axes' objects, Andrew's plot, various glyphs for scatter plot) to visualize high dimensional data.
Author: Zehao Xu [aut, cre],
R. Wayne Oldford [aut],
Teun van den Brand [ctb]
Maintainer: Zehao Xu <z267xu@gmail.com>
Diff between ggmulti versions 1.0.7 dated 2024-04-09 and 1.0.8 dated 2025-10-08
DESCRIPTION | 16 ++--- MD5 | 88 +++++++++++++-------------- NAMESPACE | 4 - R/coord-serialaxes.R | 9 ++ R/geom-density-.R | 2 R/geom-hist-.R | 2 R/geom-image-glyph.R | 4 - R/geom-polygon-glyph.R | 5 - R/geom-quantiles.R | 2 R/geom-serialaxes-density.R | 4 - R/geom-serialaxes-glyph.R | 4 - R/geom-serialaxes-hist.R | 4 - R/geom-serialaxes-quantile.R | 15 ++-- R/geom-serialaxes.R | 8 +- R/position-dodge-.R | 10 +-- R/position-identity-.R | 4 - R/position-stack-.R | 14 ++-- R/stat-hist-.R | 6 - R/stat-serialaxes-hist.R | 3 R/stat-serialaxes.R | 4 - R/unexported_ggplot2_functions.R | 1 R/utils-geom.R | 2 inst/doc/glyph.R | 4 - inst/doc/glyph.Rmd | 4 - inst/doc/glyph.html | 24 +++---- inst/doc/highDim.html | 12 +-- inst/doc/histogram-density-.Rmd | 2 inst/doc/histogram-density-.html | 12 +-- man/geom_density_.Rd | 64 +++++++++++++++----- man/geom_hist_.Rd | 53 +++++++++++----- man/geom_image_glyph.Rd | 73 ++++++++++++++++++----- man/geom_polygon_glyph.Rd | 73 ++++++++++++++++++----- man/geom_quantiles.Rd | 55 +++++++++++++---- man/geom_serialaxes.Rd | 88 +++++++++++++++++++++------ man/geom_serialaxes_density.Rd | 91 ++++++++++++++++++++++------ man/geom_serialaxes_glyph.Rd | 73 ++++++++++++++++++----- man/geom_serialaxes_hist.Rd | 101 +++++++++++++++++++++++--------- man/geom_serialaxes_quantile.Rd | 88 +++++++++++++++++++++------ man/ggmulti-package.Rd | 7 +- man/position_dodge_.Rd | 26 +++++++- man/position_stack_.Rd | 4 - tests/testthat/test_generalized_geoms.R | 2 tests/testthat/test_glyphs.R | 4 - vignettes/glyph.Rmd | 4 - vignettes/histogram-density-.Rmd | 2 45 files changed, 755 insertions(+), 322 deletions(-)
Title: Penalized Transformation Models
Description: Partially penalized versions of specific transformation models
implemented in package 'mlt'. Available models include a fully parametric version
of the Cox model, other parametric survival models (Weibull, etc.), models for
binary and ordered categorical variables, normal and transformed-normal (Box-Cox type)
linear models, and continuous outcome logistic regression. Hyperparameter tuning
is facilitated through model-based optimization functionalities from package 'mlrMBO'.
The accompanying vignette describes the methodology used in 'tramnet' in detail.
Transformation models and model-based optimization are described in
Hothorn et al. (2019) <doi:10.1111/sjos.12291> and
Bischl et al. (2016) <doi:10.48550/arXiv.1703.03373>, respectively.
Author: Lucas Kook [cre, aut],
Balint Tamasi [ctb],
Sandra Siegfried [ctb],
Samuel Pawel [ctb],
Torsten Hothorn [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between tramnet versions 0.0-8 dated 2023-03-10 and 0.0-9 dated 2025-10-08
tramnet-0.0-8/tramnet/tests/Colr-pen.Rout.save |only tramnet-0.0-9/tramnet/DESCRIPTION | 12 ++++++------ tramnet-0.0-9/tramnet/MD5 | 7 +++---- tramnet-0.0-9/tramnet/build/vignette.rds |binary tramnet-0.0-9/tramnet/inst/doc/tramnet.pdf |binary 5 files changed, 9 insertions(+), 10 deletions(-)
Title: Track 'ggplot2' Calls
Description: Provides a way to log 'ggplot' component calls, which can be
useful for debugging and understanding how 'ggplot' objects are created.
The logged calls can be printed, saved, and re-executed to reproduce the
original 'ggplot' object.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between gglogger versions 0.1.6 dated 2025-06-19 and 0.1.7 dated 2025-10-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/gglogger.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Draw Venn Diagram by 'ggplot2'
Description: An easy-to-use way to draw pretty Venn diagrams using 'ggplot2'.
This package provides functions to create Venn diagrams with customizable
colors, labels, and styling options.
Author: Linlin Yan [aut, cre]
Maintainer: Linlin Yan <yanlinlin82@gmail.com>
Diff between ggvenn versions 0.1.10 dated 2023-03-30 and 0.1.18 dated 2025-10-08
ggvenn-0.1.10/ggvenn/R/data_frame_to_list.R |only ggvenn-0.1.10/ggvenn/R/list_to_data_frame.R |only ggvenn-0.1.10/ggvenn/man/data_frame_to_list.Rd |only ggvenn-0.1.10/ggvenn/man/figures |only ggvenn-0.1.10/ggvenn/man/list_to_data_frame.Rd |only ggvenn-0.1.18/ggvenn/DESCRIPTION | 22 ggvenn-0.1.18/ggvenn/MD5 | 47 + ggvenn-0.1.18/ggvenn/NAMESPACE | 11 ggvenn-0.1.18/ggvenn/NEWS.md |only ggvenn-0.1.18/ggvenn/R/data_preparation.R |only ggvenn-0.1.18/ggvenn/R/geom_venn.R | 396 +++++++++----- ggvenn-0.1.18/ggvenn/R/ggvenn-package.R |only ggvenn-0.1.18/ggvenn/R/ggvenn.R | 676 +++++++------------------ ggvenn-0.1.18/ggvenn/R/globals.R | 31 - ggvenn-0.1.18/ggvenn/R/venn_geometry.R |only ggvenn-0.1.18/ggvenn/README.md | 11 ggvenn-0.1.18/ggvenn/man/data_preparation.Rd |only ggvenn-0.1.18/ggvenn/man/geom_venn.Rd | 118 +++- ggvenn-0.1.18/ggvenn/man/get_venn_table.Rd |only ggvenn-0.1.18/ggvenn/man/ggvenn-package.Rd |only ggvenn-0.1.18/ggvenn/man/ggvenn.Rd | 75 +- ggvenn-0.1.18/ggvenn/tests |only 22 files changed, 676 insertions(+), 711 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.1080/00031305.2023.2203177>) can be fitted as well. The package contains an implementation of
a doubly robust score test, [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.2-4 dated 2025-09-23 and 1.2-5 dated 2025-10-08
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- R/methods.R | 8 ++++++-- cleanup |only inst/NEWS.Rd | 6 ++++++ inst/doc/NAMI.pdf |binary inst/doc/mtram.pdf |binary inst/doc/survtram.pdf |binary inst/doc/tram.pdf |binary 9 files changed, 24 insertions(+), 13 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.9.0 dated 2025-09-20 and 0.9.1 dated 2025-10-08
DESCRIPTION | 6 MD5 | 20 NEWS.md | 418 +-- R/bootstrap_helpers.R | 7 README.md | 2 inst/CITATION | 4 man/estimate_boot_sim_cv.Rd | 4 tests/testthat/test-add_inactive_replicates.R | 294 +- tests/testthat/test-bootstrap-helpers.R | 19 tests/testthat/test-fays-generalized-replication.R | 1134 +++++----- tests/testthat/test-quadratic_forms_of_survey_design_objects.R | 544 ++-- 11 files changed, 1222 insertions(+), 1230 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 4.1.0 dated 2025-08-29 and 4.1.1 dated 2025-10-08
DESCRIPTION | 8 - MD5 | 51 +++++------ NAMESPACE | 2 NEWS.md | 19 ++++ R/err.R | 15 +++ R/mu-cov-downgrade.R | 2 R/mu.R | 8 + R/rxShiny.R | 4 R/rxStack.R | 36 ++++++- R/rxUiGet.R | 2 R/rxode2_md5.R | 2 R/rxsolve.R | 8 - R/symengine.R | 6 - inst/doc/rxode2-syntax.html | 28 +++--- inst/include/rxode2_model_shared.h | 9 + inst/include/rxode2parseVer.h | 4 man/dot-getErrDist.Rd |only man/rxStack.Rd | 6 + src/etTran.cpp | 18 ++- src/par_solve.cpp | 6 - src/parseVars.h | 3 src/tran.c | 4 tests/testthat/test-etTrans.R | 167 ++++++++++++++++++++++++++++++++++++- tests/testthat/test-mix.R | 9 + tests/testthat/test-occ.R | 34 +++++++ tests/testthat/test-ui-assert.R | 10 -- tests/testthat/test-ui-props.R | 43 +++++++++ 27 files changed, 422 insertions(+), 82 deletions(-)
Title: Render Sequence Plots using 'ggplot2'
Description: A set of wrapper functions that mainly re-produces most of the
sequence plots rendered with TraMineR::seqplot(). Whereas 'TraMineR' uses base
R to produce the plots this library draws on 'ggplot2'.
The plots are produced on the basis of a sequence object defined
with TraMineR::seqdef(). The package automates the reshaping and plotting
of sequence data. Resulting plots are of class 'ggplot', i.e. components
can be added and tweaked using '+' and regular 'ggplot2' functions.
Author: Marcel Raab [aut, cre]
Maintainer: Marcel Raab <marcel.raab@gmail.com>
Diff between ggseqplot versions 0.8.7 dated 2025-06-30 and 0.8.8 dated 2025-10-08
ggseqplot-0.8.7/ggseqplot/tests/testthat/test-internal_helper.R |only ggseqplot-0.8.8/ggseqplot/DESCRIPTION | 13 ggseqplot-0.8.8/ggseqplot/MD5 | 41 ggseqplot-0.8.8/ggseqplot/NAMESPACE | 1 ggseqplot-0.8.8/ggseqplot/NEWS.md | 142 - ggseqplot-0.8.8/ggseqplot/R/ggseqdplot.R | 752 ++--- ggseqplot-0.8.8/ggseqplot/R/ggseqeplot.R | 8 ggseqplot-0.8.8/ggseqplot/R/ggseqfplot.R | 17 ggseqplot-0.8.8/ggseqplot/R/ggseqiplot.R | 38 ggseqplot-0.8.8/ggseqplot/R/ggseqmsplot.R | 23 ggseqplot-0.8.8/ggseqplot/R/ggseqmtplot.R | 23 ggseqplot-0.8.8/ggseqplot/R/ggseqrfplot.R | 81 ggseqplot-0.8.8/ggseqplot/R/ggseqrplot.R | 52 ggseqplot-0.8.8/ggseqplot/R/ggseqtrplot.R | 15 ggseqplot-0.8.8/ggseqplot/R/internal_helpers.R | 20 ggseqplot-0.8.8/ggseqplot/build/partial.rdb |binary ggseqplot-0.8.8/ggseqplot/build/vignette.rds |binary ggseqplot-0.8.8/ggseqplot/inst/CITATION | 20 ggseqplot-0.8.8/ggseqplot/inst/doc/ggseqplot.R | 37 ggseqplot-0.8.8/ggseqplot/inst/doc/ggseqplot.Rmd | 1293 +++++----- ggseqplot-0.8.8/ggseqplot/inst/doc/ggseqplot.html | 120 ggseqplot-0.8.8/ggseqplot/vignettes/ggseqplot.Rmd | 1293 +++++----- 22 files changed, 2018 insertions(+), 1971 deletions(-)
Title: Kernel Ridge Regression using 'RcppArmadillo'
Description: Provides core computational operations in C++ via 'RcppArmadillo', enabling faster performance than pure R, improved numerical stability, and parallel execution with OpenMP where available. On systems without OpenMP support, the package automatically falls back to single-threaded execution with no user configuration required. For efficient model selection, it integrates with 'CVST' to provide sequential-testing cross-validation that identifies competitive hyperparameters without exhaustive grid search. The package offers a unified interface for exact kernel ridge regression and three scalable approximations—Nyström, Pivoted Cholesky, and Random Fourier Features—allowing analyses with substantially larger sample sizes than are feasible with exact KRR. It also integrates with the 'tidymodels' ecosystem via the 'parsnip' model specification 'krr_reg', and the S3 method tunable.krr_reg(). To understand the theoretical background, one can refer to Wainwright (2019) <doi:10.1017/978110862 [...truncated...]
Author: Gyeongmin Kim [aut] ,
Seyoung Lee [aut] ,
Miyoung Jang [aut] ,
Kwan-Young Bak [aut, cre, cph]
Maintainer: Kwan-Young Bak <kybak@sungshin.ac.kr>
Diff between FastKRR versions 0.1.0 dated 2025-09-22 and 0.1.1 dated 2025-10-08
FastKRR-0.1.0/FastKRR/R/make_Z.R |only FastKRR-0.1.0/FastKRR/man/fit_krr.Rd |only FastKRR-0.1.0/FastKRR/man/make_Z.Rd |only FastKRR-0.1.0/FastKRR/man/pred_krr.Rd |only FastKRR-0.1.0/FastKRR/man/rff_random.Rd |only FastKRR-0.1.1/FastKRR/DESCRIPTION | 10 FastKRR-0.1.1/FastKRR/MD5 | 49 - FastKRR-0.1.1/FastKRR/NAMESPACE | 12 FastKRR-0.1.1/FastKRR/R/CVST_linkfunction.R | 295 +++++----- FastKRR-0.1.1/FastKRR/R/FastKRR-package.R | 4 FastKRR-0.1.1/FastKRR/R/RcppExports.R | 4 FastKRR-0.1.1/FastKRR/R/approx_kernel.R | 188 +++--- FastKRR-0.1.1/FastKRR/R/link2tidymodels.R | 137 ---- FastKRR-0.1.1/FastKRR/R/make_kernel.R | 25 FastKRR-0.1.1/FastKRR/R/print.R |only FastKRR-0.1.1/FastKRR/R/rff_random.R | 49 - FastKRR-0.1.1/FastKRR/README.md | 79 +- FastKRR-0.1.1/FastKRR/man/FastKRR-package.Rd | 2 FastKRR-0.1.1/FastKRR/man/approx_kernel.Rd | 128 ++-- FastKRR-0.1.1/FastKRR/man/fastkrr.Rd | 75 +- FastKRR-0.1.1/FastKRR/man/figures/README-unnamed-chunk-4-1.png |only FastKRR-0.1.1/FastKRR/man/krr_reg.Rd | 4 FastKRR-0.1.1/FastKRR/man/make_kernel.Rd | 23 FastKRR-0.1.1/FastKRR/man/predict.krr.Rd |only FastKRR-0.1.1/FastKRR/man/print.approx_kernel.Rd |only FastKRR-0.1.1/FastKRR/man/print.kernel_matrix.Rd |only FastKRR-0.1.1/FastKRR/man/print.krr.Rd |only FastKRR-0.1.1/FastKRR/src/RcppExports.cpp | 15 FastKRR-0.1.1/FastKRR/src/kernel.cpp | 8 FastKRR-0.1.1/FastKRR/src/pchol.cpp | 3 FastKRR-0.1.1/FastKRR/src/rff.cpp | 12 31 files changed, 526 insertions(+), 596 deletions(-)