Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 9.3.12 dated 2024-09-29 and 9.3.16 dated 2024-12-04
rswipl-9.3.12/rswipl/src/swipl-devel/packages/cpp/pl2cpp2.doc |only rswipl-9.3.16/rswipl/DESCRIPTION | 14 rswipl-9.3.16/rswipl/MD5 | 254 rswipl-9.3.16/rswipl/NEWS.md | 14 rswipl-9.3.16/rswipl/R/rswipl.R | 1 rswipl-9.3.16/rswipl/inst/include/linkingto.txt | 2 rswipl-9.3.16/rswipl/src/Makevars | 6 rswipl-9.3.16/rswipl/src/install.libs.R | 2 rswipl-9.3.16/rswipl/src/swipl-devel/VERSION | 2 rswipl-9.3.16/rswipl/src/swipl-devel/bench/port/sicstus.pl | 10 rswipl-9.3.16/rswipl/src/swipl-devel/bench/port/swi.pl | 169 rswipl-9.3.16/rswipl/src/swipl-devel/bench/port/yap.pl | 10 rswipl-9.3.16/rswipl/src/swipl-devel/bench/run.pl | 154 rswipl-9.3.16/rswipl/src/swipl-devel/boot/autoload.pl | 24 rswipl-9.3.16/rswipl/src/swipl-devel/boot/dcg.pl | 33 rswipl-9.3.16/rswipl/src/swipl-devel/boot/expand.pl | 16 rswipl-9.3.16/rswipl/src/swipl-devel/boot/history.pl | 9 rswipl-9.3.16/rswipl/src/swipl-devel/boot/init.pl | 10 rswipl-9.3.16/rswipl/src/swipl-devel/boot/load.pl | 5 rswipl-9.3.16/rswipl/src/swipl-devel/boot/messages.pl | 33 rswipl-9.3.16/rswipl/src/swipl-devel/boot/threads.pl |only rswipl-9.3.16/rswipl/src/swipl-devel/boot/toplevel.pl | 3 rswipl-9.3.16/rswipl/src/swipl-devel/cmake/EmscriptenTargets.cmake | 2 rswipl-9.3.16/rswipl/src/swipl-devel/cmake/LocationsPostPorts.cmake | 1 rswipl-9.3.16/rswipl/src/swipl-devel/cmake/PackageSelection.cmake | 1 rswipl-9.3.16/rswipl/src/swipl-devel/cmake/QLF.cmake | 3 rswipl-9.3.16/rswipl/src/swipl-devel/cmake/TestSignalType.c | 6 rswipl-9.3.16/rswipl/src/swipl-devel/library/date.pl | 203 rswipl-9.3.16/rswipl/src/swipl-devel/library/debug.pl | 13 rswipl-9.3.16/rswipl/src/swipl-devel/library/dialect/sicstus/block.pl | 366 rswipl-9.3.16/rswipl/src/swipl-devel/library/dicts.pl | 81 rswipl-9.3.16/rswipl/src/swipl-devel/library/error.pl | 31 rswipl-9.3.16/rswipl/src/swipl-devel/library/exceptions.pl |only rswipl-9.3.16/rswipl/src/swipl-devel/library/explain.pl | 8 rswipl-9.3.16/rswipl/src/swipl-devel/library/main.pl | 3 rswipl-9.3.16/rswipl/src/swipl-devel/library/nb_set.pl | 180 rswipl-9.3.16/rswipl/src/swipl-devel/library/option.pl | 172 rswipl-9.3.16/rswipl/src/swipl-devel/library/pprint.pl | 5 rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_clause.pl | 18 rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_colour.pl | 22 rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_deps.pl | 22 rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_locale.pl |only rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_pack.pl | 25 rswipl-9.3.16/rswipl/src/swipl-devel/library/shlib.pl | 93 rswipl-9.3.16/rswipl/src/swipl-devel/library/solution_sequences.pl | 80 rswipl-9.3.16/rswipl/src/swipl-devel/library/theme/dark.pl | 4 rswipl-9.3.16/rswipl/src/swipl-devel/library/ugraphs.pl | 26 rswipl-9.3.16/rswipl/src/swipl-devel/library/wasm.pl | 4 rswipl-9.3.16/rswipl/src/swipl-devel/packages/clib/udp_broadcast.pl | 4 rswipl-9.3.16/rswipl/src/swipl-devel/packages/cpp/CMakeLists.txt | 2 rswipl-9.3.16/rswipl/src/swipl-devel/packages/cpp/SWI-cpp.h | 4 rswipl-9.3.16/rswipl/src/swipl-devel/packages/cpp/SWI-cpp2.cpp | 12 rswipl-9.3.16/rswipl/src/swipl-devel/packages/cpp/SWI-cpp2.h | 9 rswipl-9.3.16/rswipl/src/swipl-devel/packages/cpp/pl2cpp.doc | 4106 +++++++++- rswipl-9.3.16/rswipl/src/swipl-devel/packages/cpp/test_cpp.cpp | 21 rswipl-9.3.16/rswipl/src/swipl-devel/packages/cpp/test_cpp.pl | 9 rswipl-9.3.16/rswipl/src/swipl-devel/packages/http/http.doc | 86 rswipl-9.3.16/rswipl/src/swipl-devel/packages/http/http_dispatch.pl | 3 rswipl-9.3.16/rswipl/src/swipl-devel/packages/http/http_header.pl | 39 rswipl-9.3.16/rswipl/src/swipl-devel/packages/http/thread_httpd.pl | 5 rswipl-9.3.16/rswipl/src/swipl-devel/packages/plunit/plunit.pl | 25 rswipl-9.3.16/rswipl/src/swipl-devel/packages/ssl/cryptolib.c | 9 rswipl-9.3.16/rswipl/src/swipl-devel/packages/ssl/test_ssl.pl | 11 rswipl-9.3.16/rswipl/src/swipl-devel/scripts/configure | 10 rswipl-9.3.16/rswipl/src/swipl-devel/src/ATOMS | 14 rswipl-9.3.16/rswipl/src/swipl-devel/src/CMakeLists.txt | 16 rswipl-9.3.16/rswipl/src/swipl-devel/src/SWI-Prolog.h | 17 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/GC/test_ch_shift.pl | 1 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/core/test_call.pl | 16 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/core/test_dict.pl | 21 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/core/test_locale.pl | 6 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/core/test_scan_options.pl | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/core/test_syntax.pl | 32 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/core/test_time.pl | 4 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/library/test_date.pl | 8 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/library/test_pio.pl | 206 rswipl-9.3.16/rswipl/src/swipl-devel/src/Tests/thread/test_rwlocks.pl |only rswipl-9.3.16/rswipl/src/swipl-devel/src/os/SWI-Stream.h | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-file.c | 38 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-fmt.c | 220 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-fmt.h |only rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-option.c | 51 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-prologflag.c | 55 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-prologflag.h | 9 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-stream.c | 14 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-string.c | 12 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-string.h | 29 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-tai.c | 64 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-text.c | 48 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-text.h | 19 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-alloc.c | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-arith.c | 6 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-arith.h | 20 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-attvar.c | 12 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-attvar.h | 8 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-debug.c | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-debug.h | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-dict.c | 433 - rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-error.c | 61 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-error.h | 23 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-ext.c | 236 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-ext.h | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-fli.c | 160 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-gc.h | 21 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-global.h | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-gmp.c | 14 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-gmp.h | 8 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-incl.h | 18 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-init.c | 374 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-op.c | 1 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-prims.c | 13 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-prims.h | 1 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-pro.c | 82 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-pro.h | 15 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-proc.c | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-prof.c | 3 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-read.c | 94 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-ressymbol.c | 12 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-setup.c | 27 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-thread.c | 126 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-thread.h | 4 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-trace.c | 66 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-trace.h | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-vmi.c | 29 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-wam.c | 166 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-wam.h | 10 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-write.c | 301 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-write.h | 11 rswipl-9.3.16/rswipl/src/swipl-devel/src/wasm/prolog.js | 21 rswipl-9.3.16/rswipl/src/swipl-devel/src/wasm/runtime_exports.json | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/wasm/server.pl | 25 131 files changed, 7428 insertions(+), 2388 deletions(-)
Title: Analyzing Gastric Emptying from MRI or Scintigraphy
Description: Fits gastric emptying time series from MRI or 'scintigraphic' measurements
using nonlinear mixed-model population fits with 'nlme' and Bayesian methods with
Stan; computes derived parameters such as t50 and AUC.
Author: Dieter Menne [aut, cre]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between gastempt versions 0.6.1 dated 2024-09-27 and 0.6.2 dated 2024-12-04
gastempt-0.6.1/gastempt/tests/testthat/_snaps |only gastempt-0.6.2/gastempt/DESCRIPTION | 6 gastempt-0.6.2/gastempt/MD5 | 36 +- gastempt-0.6.2/gastempt/README.md | 2 gastempt-0.6.2/gastempt/build/vignette.rds |binary gastempt-0.6.2/gastempt/inst/doc/gastempt.Rmd | 4 gastempt-0.6.2/gastempt/inst/doc/gastempt.html | 9 gastempt-0.6.2/gastempt/man/coef.nlme_gastempt.Rd | 38 +- gastempt-0.6.2/gastempt/man/coef.stan_gastempt.Rd | 38 +- gastempt-0.6.2/gastempt/man/gastemptfunc.Rd | 184 +++++------ gastempt-0.6.2/gastempt/man/nlme_gastempt.Rd | 184 +++++------ gastempt-0.6.2/gastempt/man/plot.nlme_gastempt.Rd | 38 +- gastempt-0.6.2/gastempt/man/plot.stan_gastempt.Rd | 40 +- gastempt-0.6.2/gastempt/man/run_shiny.Rd | 28 - gastempt-0.6.2/gastempt/man/simulate_gastempt.Rd | 182 +++++----- gastempt-0.6.2/gastempt/man/stan_gastempt.Rd | 158 ++++----- gastempt-0.6.2/gastempt/man/stan_model_names.Rd | 46 +- gastempt-0.6.2/gastempt/man/t50.Rd | 40 +- gastempt-0.6.2/gastempt/tests/testthat/testthat-problems.rds |only gastempt-0.6.2/gastempt/vignettes/gastempt.Rmd | 4 20 files changed, 518 insertions(+), 519 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-04 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-16 1.0.0
2015-07-07 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-06 1.1
2017-08-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-02 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-16 0.0.2-1
2017-12-11 0.0.1-5
Title: Metabolomics Data Analysis Functions
Description: A collection of functions for processing and analyzing metabolite data.
The namesake function mrbin() converts 1D
or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and
performs basic processing steps in a reproducible way. Negative values, a
common issue in such data, can be replaced by positive values (<doi:10.1021/acs.jproteome.0c00684>). All used
parameters are stored in a readable text file and can be restored from that
file to enable exact reproduction of the data at a later time. The function fia() ranks features according
to their impact on classifier models, especially artificial neural network models.
Author: Matthias Klein [aut, cre]
Maintainer: Matthias Klein <matthias.s.klein@gmx.net>
Diff between mrbin versions 1.7.5 dated 2024-06-12 and 1.8.0 dated 2024-12-04
DESCRIPTION | 6 MD5 | 76 - NEWS.md | 13 R/mrbin.R | 2266 ++++++++++++++++++++++++++------------- inst/doc/mrbin.R | 94 - inst/doc/mrbin.Rnw | 64 - inst/doc/mrbin.pdf |binary inst/extdata/1/10/pdata/10/title | 3 inst/extdata/1/12/pdata/10/title | 3 inst/extdata/2/10/pdata/10/title | 3 inst/extdata/2/12/pdata/10/title | 3 inst/extdata/3/10/pdata/10/title | 3 inst/extdata/3/12/pdata/10/title | 3 man/PQNScaling.Rd | 4 man/addToPlot.Rd | 5 man/annotatemrbin.Rd | 8 man/atnv.Rd | 6 man/cropNMR.Rd | 2 man/dilutionCorrection.Rd | 4 man/editmetabolitesmrbin.Rd | 6 man/logTrafo.Rd | 4 man/metadatamrbin.Rd | 8 man/mrbin.Rd | 14 man/mrbinrun.Rd | 17 man/mrplot.Rd | 29 man/plotMultiNMR.Rd | 34 man/plotNMR.Rd | 33 man/plotPCA.Rd | 4 man/plotResults.Rd | 4 man/recreatemrbin.Rd | 4 man/removeNoise.Rd | 4 man/removeSpectrum.Rd | 9 man/setCurrentSpectrum.Rd | 4 man/setDilutionFactors.Rd | 9 man/setNoiseLevels.Rd | 9 man/trimZeros.Rd | 4 man/unitVarianceScaling.Rd | 4 man/zoom.Rd | 13 vignettes/mrbin.Rnw | 64 - 39 files changed, 1950 insertions(+), 893 deletions(-)
Title: Structured Learning in Time-Dependent Cox Models
Description: Efficient procedures for fitting and cross-validating the structurally-regularized time-dependent Cox models.
Author: Yi Lian [aut, cre],
Guanbo Wang [aut],
Archer Y. Yang [aut],
Mireille E. Schnitzer [aut],
Robert W. Platt [aut],
Rui Wang [aut],
Marc Dorais [aut],
Sylvie Perreault [aut],
Julien Mairal [ctb],
Yuansi Chen [ctb]
Maintainer: Yi Lian <yi.lian@mail.mcgill.ca>
Diff between sox versions 1.2 dated 2024-07-15 and 1.2.1 dated 2024-12-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- R/auxiliary_functions.R | 2 +- tests/testthat/Rplots.pdf |binary 5 files changed, 10 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-18 1.0.1
2024-10-10 1.0.0
Title: Data Wrangling and Automated Reports from 'SIVIGILA' Source
Description: Data wrangling, pre-processing, and generating automated reports
from Colombia's epidemiological surveillance system,
'SIVIGILA' <https://portalsivigila.ins.gov.co/>. It provides a
customizable R Markdown template for analysis and automatic
generation of epidemiological reports that can be adapted to local,
regional, and national contexts. This tool offers a standardized and
reproducible workflow that helps to reduce manual labor and potential
errors in report generation, improving their efficiency and consistency.
Author: Geraldine Gomez-Millan [aut, cre, ctb]
,
Zulma M. Cucunuba [aut, ctb] ,
Jennifer A. Mendez-Romero [aut, ctb]
,
Claudia Huguett-Aragon [aut, ctb]
,
Hugo Gruson [ctb] ,
Juanita Romero-Garces [ctb] ,
Jaime Pavlich-Mariscal [ctb] ,
Laura Gomez Bermeo [ct [...truncated...]
Maintainer: Geraldine Gomez-Millan <geralidine.gomez@javeriana.edu.co>
Diff between sivirep versions 1.0.0 dated 2024-11-14 and 1.0.1 dated 2024-12-03
sivirep-1.0.0/sivirep/inst/video |only sivirep-1.0.0/sivirep/tests/report_example.Rmd |only sivirep-1.0.1/sivirep/DESCRIPTION | 13 sivirep-1.0.1/sivirep/MD5 | 47 -- sivirep-1.0.1/sivirep/NEWS.md | 15 sivirep-1.0.1/sivirep/R/checking_data.R | 46 +- sivirep-1.0.1/sivirep/R/import_data.R | 12 sivirep-1.0.1/sivirep/R/plotting.R | 38 + sivirep-1.0.1/sivirep/README.md | 92 ---- sivirep-1.0.1/sivirep/inst/doc/sivirep.Rmd | 14 sivirep-1.0.1/sivirep/inst/doc/sivirep.html | 15 sivirep-1.0.1/sivirep/inst/rmarkdown/templates/reports/template.yaml | 2 sivirep-1.0.1/sivirep/man/calcular_incidencia.Rd | 194 ++++---- sivirep-1.0.1/sivirep/man/calcular_incidencia_geo.Rd | 140 +++--- sivirep-1.0.1/sivirep/man/calcular_incidencia_sex.Rd | 170 +++---- sivirep-1.0.1/sivirep/man/import_data_event.Rd | 94 ++-- sivirep-1.0.1/sivirep/man/import_pob_incidencia.Rd | 110 ++-- sivirep-1.0.1/sivirep/man/import_pob_proyecciones.Rd | 67 +-- sivirep-1.0.1/sivirep/man/import_pob_riesgo.Rd | 73 +-- sivirep-1.0.1/sivirep/man/plot_map.Rd | 222 +++++----- sivirep-1.0.1/sivirep/man/plot_mpios.Rd | 2 sivirep-1.0.1/sivirep/man/plot_sex_semanaepi.Rd | 2 sivirep-1.0.1/sivirep/man/plot_tipo_caso.Rd | 2 sivirep-1.0.1/sivirep/man/plot_years.Rd | 2 sivirep-1.0.1/sivirep/vignettes/sivirep.Rmd | 14 25 files changed, 679 insertions(+), 707 deletions(-)
Title: Generate Simulated Datasets
Description: Generate simulated datasets from an initial underlying
distribution and apply transformations to obtain realistic data. Implements
the 'NORTA' (Normal-to-anything) approach from Cario and Nelson (1997)
and other data generating mechanisms. Simple network visualization tools
are provided to facilitate communicating the simulation setup.
Author: Michael Kammer [aut, cre]
Maintainer: Michael Kammer <michael.kammer@meduniwien.ac.at>
Diff between simdata versions 0.4.0 dated 2024-07-01 and 0.4.1 dated 2024-12-03
DESCRIPTION | 10 - MD5 | 18 +-- NEWS.md | 4 R/utilities.R | 4 inst/doc/Demo.html | 40 +++---- inst/doc/NORTA_demo.R | 48 ++++---- inst/doc/NORTA_demo.Rmd | 67 ++++++------ inst/doc/NORTA_demo.html | 189 +++++++++++++++++----------------- inst/doc/Technical_documentation.html | 151 +++++++++++++-------------- vignettes/NORTA_demo.Rmd | 67 ++++++------ 10 files changed, 308 insertions(+), 290 deletions(-)
Title: Import, Recompute and Analyze Data from Portable Gas Analyzers
Description: The gasanalyzer R package offers methods for importing, preprocessing,
and analyzing data related to photosynthetic characteristics (gas exchange,
chlorophyll fluorescence and isotope ratios). It translates variable names
into a standard format, and can recalculate derived, physiological
quantities using imported or predefined equations. The package also allows
users to assess the sensitivity of their results to different assumptions
used in the calculations.
See also Tholen (2024) <doi:10.1093/aobpla/plae035>.
Author: Danny Tholen [aut, cre]
Maintainer: Danny Tholen <thalecress+p@gmail.com>
Diff between gasanalyzer versions 0.4.1 dated 2024-06-21 and 0.4.2 dated 2024-12-03
DESCRIPTION | 10 MD5 | 19 - NEWS.md | 6 R/equations.R | 3 R/read_6800.R | 13 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/gasanalyzer.R | 6 inst/doc/gasanalyzer.html | 648 ++++++++++++++++++++-------------------- inst/extdata/lowo2recalc.xlsx |only tests/testthat/test-equations.R | 7 11 files changed, 364 insertions(+), 349 deletions(-)
Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension
that allows for the creation of time aware tibbles. Some immediate
advantages of this include: the ability to perform time-based subsetting
on tibbles, quickly summarising and aggregating results by time periods,
and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between tibbletime versions 0.1.8 dated 2023-01-24 and 0.1.9 dated 2024-12-03
DESCRIPTION | 12 - MD5 | 38 ++-- NAMESPACE | 42 ++++ NEWS.md | 4 R/index-based-generics.R | 28 ++ R/seq.R | 3 R/to_posixct_numeric.R | 11 + build/vignette.rds |binary inst/doc/TT-01-time-based-filtering.R | 2 inst/doc/TT-01-time-based-filtering.html | 112 +++++------ inst/doc/TT-02-changing-time-periods.R | 2 inst/doc/TT-02-changing-time-periods.html | 72 +++---- inst/doc/TT-03-rollify-for-rolling-analysis.R | 2 inst/doc/TT-03-rollify-for-rolling-analysis.html | 216 +++++++++++------------ inst/doc/TT-04-use-with-dplyr.R | 2 inst/doc/TT-04-use-with-dplyr.html | 194 ++++++++++---------- man/ceiling_index.Rd | 9 man/floor_index.Rd | 9 man/tibbletime.Rd | 4 tests/testthat/test_create_series.R | 4 20 files changed, 430 insertions(+), 336 deletions(-)
Title: Causal Inference with Spatio-Temporal Data
Description: Spatio-temporal causal inference based on point process data.
You provide the raw data of locations and timings of treatment and
outcome events, specify counterfactual scenarios, and the package
estimates causal effects over specified spatial and temporal windows.
See Papadogeorgou, et al. (2022) <doi:10.1111/rssb.12548> and
Mukaigawara, et al. (2024) <doi:10.31219/osf.io/5kc6f>.
Author: Mitsuru Mukaigawara [cre, aut]
,
Lingxiao Zhou [aut],
Georgia Papadogeorgou [aut] ,
Jason Lyall [aut] ,
Kosuke Imai [aut]
Maintainer: Mitsuru Mukaigawara <mitsuru_mukaigawara@g.harvard.edu>
Diff between geocausal versions 0.3.2 dated 2024-07-19 and 0.3.3 dated 2024-12-03
DESCRIPTION | 12 +- MD5 | 60 ++++++++------ NAMESPACE | 65 ++++++++++++--- NEWS.md | 5 + R/get_cate.R | 23 +---- R/get_distexp.R | 154 ++++-------------------------------- R/get_estimates.R | 2 R/get_obs_dens.R | 2 R/get_var_bound.R | 33 +------ R/get_weighted_surf.R | 15 +++ R/plot.cflist.R |only R/plot.distlist.R |only R/plot.est.R | 13 ++- R/plot.hyperframe.R | 21 ++-- R/plot.imlist.R |only R/plot.obs.R | 207 +++++++++++++++++++++++++++---------------------- R/plot.powerlist.R |only R/plot.ppplist.R |only R/print.cate.R |only R/print.est.R |only R/sim_cf_dens.R | 94 +++------------------- R/sim_power_dens.R | 80 +----------------- README.md | 18 ++-- man/get_cate.Rd | 3 man/get_distexp.Rd | 8 - man/get_var_bound.Rd | 12 -- man/plot.cflist.Rd |only man/plot.distlist.Rd |only man/plot.est.Rd | 4 man/plot.hyperframe.Rd | 7 + man/plot.imlist.Rd |only man/plot.obs.Rd | 13 ++- man/plot.powerlist.Rd |only man/plot.ppplist.Rd |only man/print.cate.Rd |only man/print.est.Rd |only man/sim_cf_dens.Rd | 15 --- man/sim_power_dens.Rd | 16 --- 38 files changed, 354 insertions(+), 528 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine and for various extensions in a recent version is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 2.3.8 dated 2024-11-17 and 2.3.9 dated 2024-12-03
DESCRIPTION | 8 +- MD5 | 18 ++-- NEWS.md | 13 +++ build/vignette.rds |binary src/import-file.c | 18 ++++ src/vendor/extensions/regexp.c | 3 src/vendor/extensions/series.c | 8 +- src/vendor/sqlite3/sqlite3.c | 118 ++++++++++++++++++++++--------- src/vendor/sqlite3/sqlite3.h | 15 +++ tests/testthat/test-regularExpressions.R | 1 10 files changed, 148 insertions(+), 54 deletions(-)
Title: A Unified Time Series Event Detection Framework
Description: By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Antonio Castro [aut],
Antonio Mello [aut],
Ellen Paixao [aut],
Fernando Fraga [aut],
Heraldo Borges [aut],
Janio Lima [aut],
Jessica Souza [aut],
Lais Baroni [aut],
Lucas Tavares [aut],
Rebecca Salles [aut],
Diego [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between harbinger versions 1.0.787 dated 2024-05-13 and 1.1.707 dated 2024-12-03
harbinger-1.0.787/harbinger/R/hmo_discord.R |only harbinger-1.0.787/harbinger/man/hmo_discord.Rd |only harbinger-1.1.707/harbinger/DESCRIPTION | 8 - harbinger-1.1.707/harbinger/MD5 | 64 +++++++------- harbinger-1.1.707/harbinger/NAMESPACE | 7 - harbinger-1.1.707/harbinger/R/han_autoencoder.R | 19 ++-- harbinger-1.1.707/harbinger/R/hanc_ml.R | 15 ++- harbinger-1.1.707/harbinger/R/hanct_dtw.R | 8 - harbinger-1.1.707/harbinger/R/hanct_kmeans.R | 8 - harbinger-1.1.707/harbinger/R/hanr_arima.R | 8 - harbinger-1.1.707/harbinger/R/hanr_emd.R | 25 ----- harbinger-1.1.707/harbinger/R/hanr_fbiad.R | 19 ++-- harbinger-1.1.707/harbinger/R/hanr_fft.R | 11 +- harbinger-1.1.707/harbinger/R/hanr_garch.R | 8 - harbinger-1.1.707/harbinger/R/hanr_ml.R | 8 - harbinger-1.1.707/harbinger/R/hanr_red.R | 4 harbinger-1.1.707/harbinger/R/hanr_remd.R | 14 ++- harbinger-1.1.707/harbinger/R/hanr_wavelet.R | 8 - harbinger-1.1.707/harbinger/R/har_ensemble.R |only harbinger-1.1.707/harbinger/R/har_eval_soft.R | 5 + harbinger-1.1.707/harbinger/R/harbinger.R | 93 +++------------------ harbinger-1.1.707/harbinger/R/harbinger_utils.R |only harbinger-1.1.707/harbinger/R/hcp_cf_arima.R | 15 +-- harbinger-1.1.707/harbinger/R/hcp_cf_ets.R | 15 +-- harbinger-1.1.707/harbinger/R/hcp_cf_lr.R | 15 +-- harbinger-1.1.707/harbinger/R/hcp_garch.R | 6 - harbinger-1.1.707/harbinger/R/hcp_red.R | 24 +++-- harbinger-1.1.707/harbinger/R/hcp_scp.R | 13 ++ harbinger-1.1.707/harbinger/R/hmo_xsax.R | 52 +++++++---- harbinger-1.1.707/harbinger/R/hmu_pca.R | 22 +--- harbinger-1.1.707/harbinger/README.md | 10 -- harbinger-1.1.707/harbinger/man/detect.Rd | 15 --- harbinger-1.1.707/harbinger/man/han_autoencoder.Rd | 11 ++ harbinger-1.1.707/harbinger/man/har_ensemble.Rd |only harbinger-1.1.707/harbinger/man/harbinger.Rd | 15 --- harbinger-1.1.707/harbinger/man/harutils.Rd |only 36 files changed, 250 insertions(+), 295 deletions(-)
Title: Inference on Predicted Data
Description: Performs valid statistical inference on predicted data (IPD) using recent methods, where for a subset of the data, the outcomes have been predicted by an algorithm. Provides a wrapper function with specified defaults for the type of model and method to be used for estimation and inference. Further provides methods for tidying and summarizing results. Salerno et al., (2024) <doi:10.48550/arXiv.2410.09665>.
Author: Stephen Salerno [aut, cre, cph]
,
Jiacheng Miao [aut],
Awan Afiaz [aut],
Kentaro Hoffman [aut],
Anna Neufeld [aut],
Qiongshi Lu [aut],
Tyler H McCormick [aut],
Jeffrey T Leek [aut]
Maintainer: Stephen Salerno <ssalerno@fredhutch.org>
Diff between ipd versions 0.1.2 dated 2024-10-24 and 0.1.3 dated 2024-12-03
DESCRIPTION | 8 MD5 | 9 NEWS.md |only R/ipd.R | 999 ++++++++++++++++++++++++++++++--------------------------- inst/doc/ipd.R | 16 man/ipd.Rd | 10 6 files changed, 567 insertions(+), 475 deletions(-)
Title: Fitting Deep Conditional Transformation Models
Description: Allows for the specification of deep conditional transformation
models (DCTMs) and ordinal neural network transformation models, as
described in Baumann et al (2021) <doi:10.1007/978-3-030-86523-8_1> and
Kook et al (2022) <doi:10.1016/j.patcog.2021.108263>. Extensions such as
autoregressive DCTMs (Ruegamer et al, 2023, <doi:10.1007/s11222-023-10212-8>)
and transformation ensembles (Kook et al, 2022, <doi:10.48550/arXiv.2205.12729>)
are implemented. The software package is described in Kook et al (2024,
<doi:10.18637/jss.v111.i10>).
Author: Lucas Kook [aut, cre],
Philipp Baumann [aut],
David Ruegamer [aut]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between deeptrafo versions 0.1-1 dated 2022-11-22 and 1.0-0 dated 2024-12-03
deeptrafo-0.1-1/deeptrafo/R/callbacks.R |only deeptrafo-0.1-1/deeptrafo/inst/python/distributions/__pycache__ |only deeptrafo-0.1-1/deeptrafo/inst/python/layers |only deeptrafo-0.1-1/deeptrafo/tests/testthat/Rplots.pdf |only deeptrafo-1.0-0/deeptrafo/DESCRIPTION | 22 deeptrafo-1.0-0/deeptrafo/MD5 | 87 - deeptrafo-1.0-0/deeptrafo/NAMESPACE | 19 deeptrafo-1.0-0/deeptrafo/R/alias-deeptrafo.R | 100 +- deeptrafo-1.0-0/deeptrafo/R/controls.R | 56 - deeptrafo-1.0-0/deeptrafo/R/ensembles.R | 115 ++ deeptrafo-1.0-0/deeptrafo/R/helperfuns.R | 88 + deeptrafo-1.0-0/deeptrafo/R/main.R | 297 +++-- deeptrafo-1.0-0/deeptrafo/R/methods.R | 353 ++++--- deeptrafo-1.0-0/deeptrafo/R/processor.R | 23 deeptrafo-1.0-0/deeptrafo/R/trafo_ensembles.R |only deeptrafo-1.0-0/deeptrafo/build |only deeptrafo-1.0-0/deeptrafo/inst/CITATION |only deeptrafo-1.0-0/deeptrafo/inst/python/dtlayers |only deeptrafo-1.0-0/deeptrafo/man/BoxCoxNN.Rd | 8 deeptrafo-1.0-0/deeptrafo/man/ColrNN.Rd | 8 deeptrafo-1.0-0/deeptrafo/man/CoxphNN.Rd | 8 deeptrafo-1.0-0/deeptrafo/man/LehmanNN.Rd | 8 deeptrafo-1.0-0/deeptrafo/man/LmNN.Rd | 10 deeptrafo-1.0-0/deeptrafo/man/PolrNN.Rd | 10 deeptrafo-1.0-0/deeptrafo/man/SurvregNN.Rd | 10 deeptrafo-1.0-0/deeptrafo/man/cotramNN.Rd | 10 deeptrafo-1.0-0/deeptrafo/man/dctm.Rd | 8 deeptrafo-1.0-0/deeptrafo/man/deeptrafo.Rd | 75 + deeptrafo-1.0-0/deeptrafo/man/ensemble.deeptrafo.Rd | 4 deeptrafo-1.0-0/deeptrafo/man/from_preds_to_trafo.Rd | 5 deeptrafo-1.0-0/deeptrafo/man/methodTrafo.Rd | 61 - deeptrafo-1.0-0/deeptrafo/man/nll.Rd | 4 deeptrafo-1.0-0/deeptrafo/man/ontram.Rd | 10 deeptrafo-1.0-0/deeptrafo/man/plot.deeptrafo.Rd |only deeptrafo-1.0-0/deeptrafo/man/trafo_control.Rd | 6 deeptrafo-1.0-0/deeptrafo/man/trafoensemble.Rd |only deeptrafo-1.0-0/deeptrafo/man/weighted_logLik.Rd |only deeptrafo-1.0-0/deeptrafo/tests/testthat.R | 8 deeptrafo-1.0-0/deeptrafo/tests/testthat/test-funs.R | 21 deeptrafo-1.0-0/deeptrafo/tests/testthat/test_alias.R | 363 +++---- deeptrafo-1.0-0/deeptrafo/tests/testthat/test_ensembles.R | 416 ++++++-- deeptrafo-1.0-0/deeptrafo/tests/testthat/test_helper.R | 180 +-- deeptrafo-1.0-0/deeptrafo/tests/testthat/test_main.R | 496 ++++------ deeptrafo-1.0-0/deeptrafo/tests/testthat/test_residuals.R |only 44 files changed, 1710 insertions(+), 1179 deletions(-)
Title: Fast Spatial and Spatio-Temporal Regression using Moran
Eigenvectors
Description: A collection of functions for estimating spatial and spatio-temporal regression models. Moran eigenvectors are used as spatial basis functions to efficiently approximate spatially dependent Gaussian processes (i.e., random effects eigenvector spatial filtering; see Murakami and Griffith 2015 <doi: 10.1007/s10109-015-0213-7>). The implemented models include linear regression with residual spatial dependence, spatially/spatio-temporally varying coefficient models (Murakami et al., 2017, 2024; <doi:10.1016/j.spasta.2016.12.001>,<doi:10.48550/arXiv.2410.07229>), spatially filtered unconditional quantile regression (Murakami and Seya, 2019 <doi:10.1002/env.2556>), Gaussian and non-Gaussian spatial mixed models through compositionally-warping (Murakami et al. 2021, <doi:10.1016/j.spasta.2021.100520>).
Author: Daisuke Murakami [aut, cre]
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spmoran versions 0.3.1 dated 2024-10-12 and 0.3.2 dated 2024-12-03
DESCRIPTION | 10 MD5 | 14 R/addlearn_local.R | 4582 +++++++++++++++++++++++++------------------------- R/predict0.R | 3275 +++++++++++++++++------------------ R/resf.R | 398 ++-- R/resf_vc.R | 30 man/addlearn_local.Rd | 16 man/weigen.Rd | 5 8 files changed, 4215 insertions(+), 4115 deletions(-)
Title: Tools for Approximate Bayesian Computation (ABC)
Description: Implements several ABC algorithms for
performing parameter estimation, model selection, and goodness-of-fit.
Cross-validation tools are also available for measuring the
accuracy of ABC estimates, and to calculate the
misclassification probabilities of different models.
Author: Csillery Katalin [aut],
Lemaire Louisiane [aut],
Francois Olivier [aut],
Blum Michael [aut, cre]
Maintainer: Blum Michael <michael.blum.temp@gmail.com>
Diff between abc versions 2.2.1 dated 2022-05-19 and 2.2.2 dated 2024-12-03
CHANGES | 7 ++++ DESCRIPTION | 8 ++--- MD5 | 26 ++++++++--------- build/vignette.rds |binary inst/CITATION | 22 ++++++++------ inst/doc/abcvignette.R | 68 +++++++++++++++++++++++++--------------------- inst/doc/abcvignette.Rnw | 16 +++++----- inst/doc/abcvignette.pdf |binary man/abc.Rd | 24 ++++++++-------- man/cv4abc.Rd | 10 +++--- man/cv4postpr.Rd | 10 +++--- man/plot.abc.Rd | 4 +- man/postpr.Rd | 12 ++++---- vignettes/abcvignette.Rnw | 16 +++++----- 14 files changed, 120 insertions(+), 103 deletions(-)
Title: Stan-Based Fit to Gastric Emptying Curves
Description: Stan-based curve-fitting function
for use with package 'breathtestcore' by the same author.
Stan functions are refactored here for easier testing.
Author: Dieter Menne [aut, cre],
Menne Biomed Consulting Tuebingen [cph],
Benjamin Misselwitz [fnd],
Mark Fox [fnd],
University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between breathteststan versions 0.8.5 dated 2024-01-13 and 0.8.8 dated 2024-12-03
breathteststan-0.8.5/breathteststan/src/Makevars |only breathteststan-0.8.5/breathteststan/src/Makevars.win |only breathteststan-0.8.8/breathteststan/DESCRIPTION | 16 breathteststan-0.8.8/breathteststan/MD5 | 22 breathteststan-0.8.8/breathteststan/NAMESPACE | 2 breathteststan-0.8.8/breathteststan/R/breathteststan-package.R | 4 breathteststan-0.8.8/breathteststan/R/stan_fit.R | 8 breathteststan-0.8.8/breathteststan/README.md | 6 breathteststan-0.8.8/breathteststan/man/figures |only breathteststan-0.8.8/breathteststan/man/stan_fit.Rd | 2 breathteststan-0.8.8/breathteststan/src/stanExports_breath_test_1.h | 1791 +++++----- breathteststan-0.8.8/breathteststan/tests/testthat.R | 5 breathteststan-0.8.8/breathteststan/tools |only 13 files changed, 956 insertions(+), 900 deletions(-)
More information about breathteststan at CRAN
Permanent link
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre] ,
Hugh Chipman [aut],
Robert McCulloch [aut],
Armon Dadgar [ctb] ,
R Core Team [ctb] ,
Guido U Draheim [ctb] ,
Maarten Bosmans [ctb] ,
Christophe Tournayre [ctb] ,
Michael Petch [ctb] ,
Rafael de Lucena Valle [ctb] ,
Steven G [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-28 dated 2024-05-01 and 0.9-30 dated 2024-12-03
DESCRIPTION | 8 MD5 | 24 R/dbarts.R | 9 R/utility.R | 4 build/vignette.rds |binary configure | 2078 ++++++++++++++++++------------- configure.ac | 3 inst/NEWS.Rd | 11 inst/doc/gibbs_sampler_mixture_model.pdf |binary inst/doc/working_with_saved_trees.pdf |binary src/config.hpp.in | 28 src/guessNumCores.cpp | 4 src/include/external/stats.h | 22 13 files changed, 1327 insertions(+), 864 deletions(-)
Title: Core Functions to Read and Fit 13c Time Series from Breath Tests
Description: Reads several formats of 13C data (IRIS/Wagner,
BreathID) and CSV. Creates artificial sample data for testing. Fits
Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'.
Methods to fit breath test curves with Bayesian Stan methods are
refactored to package 'breathteststan'. For a Shiny GUI, see package
'dmenne/breathtestshiny' on github.
Author: Dieter Menne [aut, cre],
Menne Biomed Consulting Tuebingen [cph],
Benjamin Misselwitz [fnd],
Mark Fox [fnd],
Andreas Steingoetter [dtc],
University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between breathtestcore versions 0.8.7 dated 2024-01-24 and 0.8.8 dated 2024-12-03
DESCRIPTION | 17 ++++------ MD5 | 45 +++++++++++++------------- R/breathtestcore-package.R |only R/coef_diff_by_group.R | 13 +++---- R/exp_beta.R | 2 - R/nlme_fit.R | 2 - R/plot_breathtestfit.R | 8 ++-- R/read_iris.R | 2 - R/read_iris_csv.R | 2 - build/vignette.rds |binary inst/doc/data_formats.Rmd | 4 -- inst/doc/data_formats.html | 43 ++++++++++--------------- inst/doc/methods_and_concepts.R | 24 +++++++------- inst/doc/methods_and_concepts.Rmd | 20 +++++------ inst/doc/methods_and_concepts.html | 52 +++++++++++++------------------ man/exp_beta.Rd | 2 - man/nlme_fit.Rd | 2 - man/plot.breathtestfit.Rd | 4 +- man/read_iris.Rd | 2 - man/read_iris_csv.Rd | 2 - tests/test-all.R | 4 +- tests/testthat/test_coef_diff_by_group.R | 3 + vignettes/data_formats.Rmd | 4 -- vignettes/methods_and_concepts.Rmd | 20 +++++------ 24 files changed, 132 insertions(+), 145 deletions(-)
More information about breathtestcore at CRAN
Permanent link
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.5.35 dated 2024-08-29 and 1.5.36 dated 2024-12-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/CDCabove.R | 4 ++-- R/CDCbelow.R | 4 ++-- R/RobustCDCabove.R | 4 ++-- R/RobustCDCbelow.R | 2 +- 6 files changed, 16 insertions(+), 16 deletions(-)
Title: Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library
(by the 'MLPACK' team) that provides a simple set of abstractions for writing an
objective function to optimize. Provided within are various standard and
cutting-edge optimizers that include full-batch gradient descent techniques,
small-batch techniques, gradient-free optimizers, and constrained optimization.
The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library
and pairs the appropriate header files from 'armadillo' through the
'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor
'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under
3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2,
'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under
the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
similar terms. Note that 'Ensmallen' requires a compiler that supports
'C++14 [...truncated...]
Author: James Joseph Balamuta [aut, cre, cph]
,
Dirk Eddelbuettel [aut, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between RcppEnsmallen versions 0.2.21.1.1 dated 2024-02-16 and 0.2.22.1.1 dated 2024-12-03
ChangeLog | 25 ++++++ DESCRIPTION | 12 +-- MD5 | 58 ++++++++++------ NEWS.md | 23 ++++++ build/vignette.rds |binary inst/doc/package-usage.html | 2 inst/doc/using-rcppensmallen.R | 4 - inst/doc/using-rcppensmallen.html | 22 +++--- inst/include/ensmallen.hpp | 30 +++++--- inst/include/ensmallen_bits/agemoea |only inst/include/ensmallen_bits/cmaes/cmaes.hpp | 6 + inst/include/ensmallen_bits/cmaes/cmaes_impl.hpp | 3 inst/include/ensmallen_bits/cmaes/pop_cmaes.hpp |only inst/include/ensmallen_bits/cmaes/pop_cmaes_impl.hpp |only inst/include/ensmallen_bits/config.hpp | 16 ---- inst/include/ensmallen_bits/ens_version.hpp | 8 +- inst/include/ensmallen_bits/function/arma_traits.hpp | 8 -- inst/include/ensmallen_bits/function/sfinae_utility.hpp | 8 +- inst/include/ensmallen_bits/fw/atoms.hpp | 3 inst/include/ensmallen_bits/fw/constr_lpball.hpp | 4 - inst/include/ensmallen_bits/nsga2/nsga2.hpp | 2 inst/include/ensmallen_bits/problems/dtlz |only inst/include/ensmallen_bits/problems/maf |only inst/include/ensmallen_bits/problems/problems.hpp | 13 +++ inst/include/ensmallen_bits/utility/arma_traits.hpp | 29 ++------ inst/include/ensmallen_bits/utility/indicators/igd.hpp |only man/RcppEnsmallen-package.Rd | 2 27 files changed, 170 insertions(+), 108 deletions(-)
Title: Classes and Methods for Fast Memory-Efficient Boolean Selections
Description: Provided are classes for boolean and skewed boolean vectors,
fast boolean methods, fast unique and non-unique integer sorting,
fast set operations on sorted and unsorted sets of integers, and
foundations for ff (range index, compression, chunked processing).
Author: Jens Oehlschlaegel [aut, cre],
Brian Ripley [ctb]
Maintainer: Jens Oehlschlaegel <Jens.Oehlschlaegel@truecluster.com>
Diff between bit versions 4.5.0 dated 2024-09-20 and 4.5.0.1 dated 2024-12-03
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/bit.c | 24 ++++++++++++------------ 3 files changed, 17 insertions(+), 17 deletions(-)
Title: Construct Process Maps Using Event Data
Description: Visualize event logs using directed graphs, i.e. process maps. Part of the 'bupaR' framework.
Author: Gert Janssenswillen [aut, cre],
Gerard van Hulzen [ctb],
Benoît Depaire [ctb],
Felix Mannhardt [ctb],
Thijs Beuving [ctb],
urvikalia [ctb],
Hasselt University [cph]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between processmapR versions 0.5.5 dated 2024-08-30 and 0.5.6 dated 2024-12-03
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/precedence_matrix.plot.R | 6 +++--- R/processmapR.R | 2 +- build/vignette.rds |binary inst/doc/processmapr.html | 4 ++-- man/export_graph.Rd | 21 ++++++++++++--------- man/processmapR.Rd | 1 - tests/testthat/test_dotted_chart_helpers.R | 2 ++ 10 files changed, 34 insertions(+), 29 deletions(-)
Title: Reading and Writing Open Data Format Files
Description: The Open Data Format (ODF) is a new, non-proprietary, multilingual, metadata enriched, and zip-compressed data format with metadata structured in the Data Documentation Initiative (DDI) Codebook standard. This package allows reading and writing of data files in the Open Data Format (ODF) in R, and displaying metadata in different languages. For further information on the Open Data Format, see <https://opendataformat.github.io/>.
Author: Tom Hartl [aut, cre] ,
Claudia Saalbach [ctb]
Maintainer: Tom Hartl <thartl@diw.de>
Diff between opendataformat versions 2.0.0 dated 2024-11-19 and 2.1.0 dated 2024-12-03
DESCRIPTION | 6 +- MD5 | 7 +- R/docu_odf.R | 18 ++++++- inst/doc/opendataformat.html | 74 ++++++++++++++++--------------- vignettes/opendataformat-tom-D15S-2.html |only 5 files changed, 62 insertions(+), 43 deletions(-)
More information about opendataformat at CRAN
Permanent link
Title: Classifications and Codelists for Statistics Norway
Description: Functions to search, retrieve, apply and update classifications
and codelists using Statistics Norway's API <https://www.ssb.no/klass>
from the system 'KLASS'. Retrieves classifications by date with options
to choose language, hierarchical level and formatting.
Author: Susie Jentoft [aut, cre],
Diana-Cristina Iancu [aut],
Lisa Li [aut],
Oeyvind I. Berntsen [aut],
Statistics Norway [cph]
Maintainer: Susie Jentoft <susie.jentoft@ssb.no>
Diff between klassR versions 1.0.0 dated 2024-11-15 and 1.0.1 dated 2024-12-03
DESCRIPTION | 8 +- MD5 | 74 +++++++++++++------------- NAMESPACE | 7 -- R/Hent_data.R | 4 - R/KLASS.R | 59 +++++++++++--------- R/Klass_list.R | 17 +----- R/UpdateKlass-graph-build.R | 14 ++++ R/UpdateKlass-graph-navigate.R | 9 ++- R/UpdateKlass.R | 1 data/klass_131_1964_graph.RData |binary data/klass_131_2020_graph.RData |binary data/klass_131_graph.RData |binary man/apply_klass.Rd | 14 ++-- man/correspond_list.Rd | 3 - man/count_neighbors.Rd | 1 man/find_dates.Rd | 1 man/find_name.Rd | 1 man/find_variant_from.Rd | 1 man/find_variant_to.Rd | 1 man/get_family.Rd | 3 - man/get_klass.Rd | 3 - man/get_klass_changes.Rd | 1 man/get_name.Rd | 1 man/get_version.Rd | 3 - man/is_combined.Rd | 1 man/is_split.Rd | 1 man/klass_131_1964_graph.Rd | 32 +++++------ man/klass_131_2020_graph.Rd | 32 +++++------ man/klass_131_graph.Rd | 32 +++++------ man/klass_graph.Rd | 76 +++++++++++++------------- man/klass_node.Rd | 80 ++++++++++++++-------------- man/list_family.Rd | 1 man/list_klass.Rd | 1 man/search_klass.Rd | 1 man/update_code.Rd | 1 man/update_klass_node.Rd | 71 ++++++++++++------------- tests/testthat/test_ApplyKlass.R | 110 ++++++++++++++++++++++----------------- tests/testthat/test_GetKlass.R | 18 ++++-- 38 files changed, 360 insertions(+), 323 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-03 0.32.10
2023-02-14 0.32.8
2023-01-11 0.32.7
Title: Miscellaneous Functions for 'ggplot2'
Description: Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).
Author: Guangchuang Yu [aut, cre, cph]
,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.1.7 dated 2024-10-23 and 0.1.8 dated 2024-12-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/utilities.R | 11 ++++++++++- build/vignette.rds |binary inst/doc/ggfun.R | 8 ++++---- inst/doc/ggfun.html | 14 +++++++------- 7 files changed, 34 insertions(+), 21 deletions(-)
Title: Bayesian Analysis of the Network Autocorrelation Model
Description: The network autocorrelation model (NAM) can be used for studying the degree of social influence
regarding an outcome variable based on one or more known networks.
The degree of social influence is quantified via the network autocorrelation parameters. In case of a single
network, the Bayesian methods of Dittrich, Leenders, and Mulder
(2017) <DOI:10.1016/j.socnet.2016.09.002> and Dittrich, Leenders, and Mulder (2019)
<DOI:10.1177/0049124117729712> are implemented using a normal, flat, or independence
Jeffreys prior for the network autocorrelation. In the case of multiple
networks, the Bayesian methods of Dittrich, Leenders, and Mulder (2020)
<DOI:10.1177/0081175020913899> are implemented using a multivariate normal prior for
the network autocorrelation parameters. Flat priors are implemented
for estimating the coefficients. For Bayesian testing of equality and order-constrained
hypotheses, the default Bayes factor of Gu, Mulder, and Hoijtink, (2018)
<DOI:10.1111/bms [...truncated...]
Author: Joris Mulder [aut, cre],
Dino Dittrich [aut, ctb],
Roger Leenders [aut, ctb]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between BANAM versions 0.2.1 dated 2024-06-20 and 0.2.2 dated 2024-12-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test_banam.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: A Graph Based Particle Simulator Based on D3-Force
Description: Simulating particle movement in 2D space has many
application. The 'particles' package implements a particle simulator
based on the ideas behind the 'd3-force' 'JavaScript' library.
'particles' implements all forces defined in 'd3-force' as well as
others such as vector fields, traps, and attractors.
Author: Thomas Lin Pedersen [aut, cre]
,
Andrei Kashcha [ctb]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between particles versions 0.2.3 dated 2022-08-19 and 0.2.4 dated 2024-12-03
DESCRIPTION | 48 ++-- MD5 | 26 +- NAMESPACE | 12 + NEWS.md | 6 R/constraint.R | 6 R/force.R | 6 README.md | 41 ++-- build/vignette.rds |binary inst/doc/intro.R | 10 - inst/doc/intro.html | 306 ++++++++++++++++--------------- man/figures/README-unnamed-chunk-3-1.png |binary man/particles-package.Rd | 3 src/collision.cpp | 8 src/quadTree.h | 1 14 files changed, 258 insertions(+), 215 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-21 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-07 0.3-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-08 1.0.0
2022-12-15 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-16 1.0
2022-10-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-28 0.5.0
2021-01-30 0.4.1
2021-01-13 0.4.0
2020-09-10 0.3.0
2020-05-02 0.2.0
2020-02-06 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-17 0.0.2
2020-11-18 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-03 1.4-3
Title: Nonparametric Tests for Incomplete Clustered Data
Description: Nonparametric tests for clustered data in pre-post intervention design documented in Cui and Harrar (2021) <doi:10.1002/bimj.201900310> and Harrar and Cui (2022) <doi:10.1016/j.jspi.2022.05.009>. Other than the main test results mentioned in the reference paper, this package also provides a function to calculate the sample size allocations for the input long format data set, and also a function for adjusted/unadjusted confidence intervals calculations. There are also functions to visualize the distribution of data across different intervention groups over time, and also the adjusted/unadjusted confidence intervals.
Author: Yue Cui [aut, cre] ,
Solomon W. Harrar [aut]
Maintainer: Yue Cui <YueCui@MissouriState.edu>
Diff between npclust versions 0.1.0 dated 2023-04-12 and 0.1.1 dated 2024-12-03
DESCRIPTION | 13 +++++++------ MD5 | 4 ++-- R/ncda.R | 4 ++-- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: Analysis of Korean National Forest Inventory Database
Description: Understanding the current status of forest resources is essential for monitoring changes
in forest ecosystems and generating related statistics. In South Korea, the National Forest
Inventory (NFI) surveys over 4,500 sample plots nationwide every five years and records 70 items,
including forest stand, forest resource, and forest vegetation surveys. Many researchers use NFI
as the primary data for research, such as biomass estimation or analyzing the importance value of
each species over time and space, depending on the research purpose. However, the large volume
of accumulated forest survey data from across the country can make it challenging to manage and
utilize such a vast dataset. To address this issue, we developed an R package that efficiently
handles large-scale NFI data across time and space. The package offers a comprehensive
workflow for NFI data analysis. It starts with data processing, where read_nfi() function
reconstructs NFI data according to the researcher's needs while [...truncated...]
Author: Sinyoung Park [aut, cre] ,
Wonhee Cho [aut, ctb] ,
Inyoo Kim [aut, ctb] ,
Wontaek Lim [aut, ctb] ,
Dongwook W. Ko [aut, ths]
Maintainer: Sinyoung Park <youngsin0306@kookmin.ac.kr>
Diff between knfi versions 1.0.1 dated 2024-11-20 and 1.0.1.9 dated 2024-12-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/biomass_nfi.R | 20 +++++++++++--------- 4 files changed, 21 insertions(+), 15 deletions(-)
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
It offers additional options for protein quantification using
the N most intense fragment ions, using all fragment ions, and
a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
In general, the tool can be used to integrate multiple
proportional observations into a single quantitative value.
Author: Thang Pham [aut, cre, cph, ctb]
,
Alex Henneman [ctb]
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 1.9.12 dated 2023-12-06 and 1.10 dated 2024-12-03
iq-1.10/iq/DESCRIPTION | 6 iq-1.10/iq/LICENSE | 2 iq-1.10/iq/MD5 | 28 iq-1.10/iq/R/iq-fast.R | 128 ++++ iq-1.10/iq/R/iq.R | 26 iq-1.10/iq/build/vignette.rds |binary iq-1.10/iq/inst/doc/iq-fast.Rmd | 340 ++++++++++- iq-1.10/iq/inst/doc/iq-fast.html | 1031 +++++++++++++++++----------------- iq-1.10/iq/inst/doc/iq.Rmd | 108 ++- iq-1.10/iq/inst/doc/iq.html | 766 +++++++++++++++---------- iq-1.10/iq/man/preprocess.Rd | 4 iq-1.10/iq/man/process_long_format.Rd | 9 iq-1.10/iq/vignettes/iq-fast.Rmd | 340 ++++++++++- iq-1.10/iq/vignettes/iq.Rmd | 108 ++- iq-1.9.12/iq/inst/doc/iq-fast.R |only iq-1.9.12/iq/inst/doc/iq.R |only 16 files changed, 1931 insertions(+), 965 deletions(-)
Title: Flexible Bayes Factor Testing of Scientific Expectations
Description: Implementation of default Bayes factors
for testing statistical hypotheses under various statistical models. The package is
intended for applied quantitative researchers in the
social and behavioral sciences, medical research,
and related fields. The Bayes factor tests can be
executed for statistical models such as
univariate and multivariate normal linear models,
correlation analysis, generalized linear models, special cases of
linear mixed models, survival models, relational
event models. Parameters that can be tested are
location parameters (e.g., group means, regression coefficients),
variances (e.g., group variances), and measures of
association (e.g,. polychoric/polyserial/biserial/tetrachoric/product
moments correlations), among others.
The statistical underpinnings are
described in
Mulder and Xin (2022) <DOI:10.1080/00273171.2021.1904809>,
Mulder and Gelissen (2019) <DOI:10.1080/02664763.2021.1992360>,
Mulder (2016) <DOI:10.1016/j.jmp.2014.09.004>,
Mulder and [...truncated...]
Author: Joris Mulder [aut, cre],
Caspar van Lissa [aut, ctb],
Donald R. Williams [aut, ctb],
Xin Gu [aut, ctb],
Anton Olsson-Collentine [aut, ctb],
Florian Boeing-Messing [aut, ctb],
Jean-Paul Fox [aut, ctb],
Janosch Menke [ctb],
Robbie van Aert [ctb],
Barry [...truncated...]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between BFpack versions 1.3.0 dated 2024-06-19 and 1.4.0 dated 2024-12-03
BFpack-1.3.0/BFpack/R/mvt_test.R |only BFpack-1.4.0/BFpack/DESCRIPTION | 20 BFpack-1.4.0/BFpack/MD5 | 98 BFpack-1.4.0/BFpack/NAMESPACE | 8 BFpack-1.4.0/BFpack/R/BF.coeftest.R | 3 BFpack-1.4.0/BFpack/R/BF.cortest.R | 321 +- BFpack-1.4.0/BFpack/R/BF.coxph.R | 2 BFpack-1.4.0/BFpack/R/BF.ergm.R | 11 BFpack-1.4.0/BFpack/R/BF.gaussian.R | 16 BFpack-1.4.0/BFpack/R/BF.glm.R | 3 BFpack-1.4.0/BFpack/R/BF.hetcor.R | 9 BFpack-1.4.0/BFpack/R/BF.icc.R | 14 BFpack-1.4.0/BFpack/R/BF.lm.R | 199 - BFpack-1.4.0/BFpack/R/BF.meta.R | 1289 ++++++---- BFpack-1.4.0/BFpack/R/BF.methods.R | 55 BFpack-1.4.0/BFpack/R/BF.mvt_test.R |only BFpack-1.4.0/BFpack/R/BF.polr.R | 2 BFpack-1.4.0/BFpack/R/BF.print.R | 4 BFpack-1.4.0/BFpack/R/BF.summary.R | 4 BFpack-1.4.0/BFpack/R/BF.survreg.R | 2 BFpack-1.4.0/BFpack/R/BF.ttest.R | 145 - BFpack-1.4.0/BFpack/R/BF.var.R | 15 BFpack-1.4.0/BFpack/R/cor_test.print.R | 32 BFpack-1.4.0/BFpack/R/get_estimates_unique_to_BFpack.R | 8 BFpack-1.4.0/BFpack/R/helper_functions.R | 12 BFpack-1.4.0/BFpack/R/zzz.R |only BFpack-1.4.0/BFpack/inst/doc/vignette_BFpack.Rmd | 242 + BFpack-1.4.0/BFpack/inst/doc/vignette_BFpack.html | 416 ++- BFpack-1.4.0/BFpack/man/BF.Rd | 90 BFpack-1.4.0/BFpack/man/cor_test.Rd | 38 BFpack-1.4.0/BFpack/man/mvt_test.Rd | 2 BFpack-1.4.0/BFpack/src/BFpack_init.c | 4 BFpack-1.4.0/BFpack/src/bct_mixedordinal.f90 | 36 BFpack-1.4.0/BFpack/tests/testthat/test_BFcortest.R | 43 BFpack-1.4.0/BFpack/tests/testthat/test_BFcoxph.R | 4 BFpack-1.4.0/BFpack/tests/testthat/test_BFergm.R | 6 BFpack-1.4.0/BFpack/tests/testthat/test_BFglm.R | 2 BFpack-1.4.0/BFpack/tests/testthat/test_BFmeta.R | 25 BFpack-1.4.0/BFpack/tests/testthat/test_BFmlm.R | 12 BFpack-1.4.0/BFpack/tests/testthat/test_BFregression.R | 20 BFpack-1.4.0/BFpack/tests/testthat/test_BFzeroinfl.R | 2 BFpack-1.4.0/BFpack/tests/testthat/test_anova_manova.R | 2 BFpack-1.4.0/BFpack/tests/testthat/test_application1_BF.bain_ttest.R | 6 BFpack-1.4.0/BFpack/tests/testthat/test_application2_BF.lm.R | 4 BFpack-1.4.0/BFpack/tests/testthat/test_application4_BF.mlm_regression.R | 32 BFpack-1.4.0/BFpack/tests/testthat/test_application5_BF.glm_BF_Gaussian.R | 2 BFpack-1.4.0/BFpack/tests/testthat/test_application6_BF.mlm_correlations.R | 34 BFpack-1.4.0/BFpack/tests/testthat/test_hetcor.R | 2 BFpack-1.4.0/BFpack/tests/testthat/test_metafor.R | 11 BFpack-1.4.0/BFpack/tests/testthat/test_ttest.R | 40 BFpack-1.4.0/BFpack/vignettes/rsconnect |only BFpack-1.4.0/BFpack/vignettes/vignette_BFpack.Rmd | 242 + 52 files changed, 2189 insertions(+), 1400 deletions(-)
Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly
needed for production level projects such as logging, error handling,
cache management and date-time parsing. Functions for date-time parsing and
formatting require that time zones be specified explicitly, avoiding a common
source of error when working with environmental time series.
Author: Jonathan Callahan [aut, cre],
Eli Grosman [ctb],
Spencer Pease [ctb],
Thomas Bergamaschi [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaCoreUtils versions 0.5.2 dated 2024-02-08 and 0.5.3 dated 2024-12-03
MazamaCoreUtils-0.5.2/MazamaCoreUtils/R/MazamaCoreUtils.R |only MazamaCoreUtils-0.5.2/MazamaCoreUtils/man/MazamaCoreUtils.Rd |only MazamaCoreUtils-0.5.3/MazamaCoreUtils/DESCRIPTION | 8 MazamaCoreUtils-0.5.3/MazamaCoreUtils/MD5 | 64 +-- MazamaCoreUtils-0.5.3/MazamaCoreUtils/NEWS.md | 6 MazamaCoreUtils-0.5.3/MazamaCoreUtils/R/MazamaCoreUtils-package.R |only MazamaCoreUtils-0.5.3/MazamaCoreUtils/R/createLocationID.R | 1 MazamaCoreUtils-0.5.3/MazamaCoreUtils/R/functionArgument_lintRules.R | 36 ++ MazamaCoreUtils-0.5.3/MazamaCoreUtils/R/loadDataFile.R | 164 +++++++--- MazamaCoreUtils-0.5.3/MazamaCoreUtils/R/parseDatetime.R | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/R/timeStamp.R | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/R/utils-location.R | 4 MazamaCoreUtils-0.5.3/MazamaCoreUtils/README.md | 12 MazamaCoreUtils-0.5.3/MazamaCoreUtils/inst/doc/cache-management.R | 3 MazamaCoreUtils-0.5.3/MazamaCoreUtils/inst/doc/cache-management.Rmd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/inst/doc/cache-management.html | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/inst/doc/date-parsing.Rmd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/inst/doc/date-parsing.html | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/inst/doc/error-handling.html | 12 MazamaCoreUtils-0.5.3/MazamaCoreUtils/inst/doc/logging.R | 6 MazamaCoreUtils-0.5.3/MazamaCoreUtils/inst/doc/logging.Rmd | 6 MazamaCoreUtils-0.5.3/MazamaCoreUtils/inst/doc/logging.html | 47 +- MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/APIKeys.Rd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/MazamaCoreUtils-package.Rd |only MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/createLocationID.Rd | 1 MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/getAPIKey.Rd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/loadDataFile.Rd | 46 ++ MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/parseDatetime.Rd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/setAPIKey.Rd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/showAPIKeys.Rd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/timeStamp.Rd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/man/timezoneLintRules.Rd | 37 ++ MazamaCoreUtils-0.5.3/MazamaCoreUtils/vignettes/cache-management.Rmd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/vignettes/date-parsing.Rmd | 2 MazamaCoreUtils-0.5.3/MazamaCoreUtils/vignettes/logging.Rmd | 6 35 files changed, 346 insertions(+), 141 deletions(-)
More information about MazamaCoreUtils at CRAN
Permanent link
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
,
Mike Cheng [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.39.0 dated 2024-11-07 and 1.40.0 dated 2024-12-02
parallelly-1.39.0/parallelly/README.md |only parallelly-1.40.0/parallelly/DESCRIPTION | 12 parallelly-1.40.0/parallelly/MD5 | 72 ++ parallelly-1.40.0/parallelly/NAMESPACE | 3 parallelly-1.40.0/parallelly/NEWS.md | 27 parallelly-1.40.0/parallelly/R/availableCores.R | 55 -- parallelly-1.40.0/parallelly/R/availableWorkers.R | 4 parallelly-1.40.0/parallelly/R/cgroups.R | 490 +++++++++++++++--- parallelly-1.40.0/parallelly/R/makeClusterPSOCK.R | 77 ++ parallelly-1.40.0/parallelly/R/utils,cluster.R | 2 parallelly-1.40.0/parallelly/R/vignette_engine.R |only parallelly-1.40.0/parallelly/R/zzz.R | 3 parallelly-1.40.0/parallelly/build |only parallelly-1.40.0/parallelly/inst/doc |only parallelly-1.40.0/parallelly/inst/test-data |only parallelly-1.40.0/parallelly/man/makeClusterPSOCK.Rd | 38 - parallelly-1.40.0/parallelly/tests/cgroups.R | 21 parallelly-1.40.0/parallelly/tests/makeClusterPSOCK.R | 2 parallelly-1.40.0/parallelly/vignettes |only 19 files changed, 627 insertions(+), 179 deletions(-)
Title: Centered Isotonic Regression and Dose-Response Utilities
Description: Isotonic regression (IR) and its improvement: centered isotonic regression (CIR). CIR is recommended in particular with small samples. Also, interval estimates for both, and additional utilities such as plotting dose-response data. For dev version and change history, see GitHub assaforon/cir.
Author: Assaf P. Oron [cre, aut]
Maintainer: Assaf P. Oron <assaf.oron@gmail.com>
Diff between cir versions 2.3.1 dated 2023-04-27 and 2.5.0 dated 2024-12-02
cir-2.3.1/cir/R/iterative.r |only cir-2.3.1/cir/man/iterCIR.Rd |only cir-2.5.0/cir/DESCRIPTION | 10 cir-2.5.0/cir/MD5 | 65 ++--- cir-2.5.0/cir/NAMESPACE | 1 cir-2.5.0/cir/R/analIntervals.r | 55 +++- cir-2.5.0/cir/R/cir.R | 35 +- cir-2.5.0/cir/R/classes.r | 2 cir-2.5.0/cir/R/invCIR.r | 61 +++- cir-2.5.0/cir/R/methods.r | 4 cir-2.5.0/cir/R/morrisCI.r | 4 cir-2.5.0/cir/R/pava.r | 11 cir-2.5.0/cir/R/utilities.r | 8 cir-2.5.0/cir/build/vignette.rds |binary cir-2.5.0/cir/inst/doc/BenHamou03.R | 2 cir-2.5.0/cir/inst/doc/BenHamou03.html | 340 +++++++++++++-------------- cir-2.5.0/cir/inst/doc/BenHamou03.rmd | 30 +- cir-2.5.0/cir/inst/examples/classExamples.r | 10 cir-2.5.0/cir/inst/examples/invCiExamples.r | 4 cir-2.5.0/cir/inst/examples/shrinkExamples.r |only cir-2.5.0/cir/man/DRshrink.Rd | 92 ++++--- cir-2.5.0/cir/man/DRtrace.Rd | 140 +++++------ cir-2.5.0/cir/man/cir-package.Rd | 5 cir-2.5.0/cir/man/cirPAVA.Rd | 214 ++++++++-------- cir-2.5.0/cir/man/deltaInverse.Rd | 213 ++++++++-------- cir-2.5.0/cir/man/doseFind.Rd | 164 ++++++------- cir-2.5.0/cir/man/isotInterval.Rd | 176 ++++++------- cir-2.5.0/cir/man/morrisCI.Rd | 190 +++++++-------- cir-2.5.0/cir/man/oldPAVA.Rd | 111 ++++---- cir-2.5.0/cir/man/plot.DRtrace.Rd | 188 +++++++------- cir-2.5.0/cir/man/quickInverse.Rd | 210 ++++++++-------- cir-2.5.0/cir/man/quickIsotone.Rd | 218 ++++++++--------- cir-2.5.0/cir/man/slope.Rd | 90 +++---- cir-2.5.0/cir/man/wilsonCI.Rd | 160 ++++++------ cir-2.5.0/cir/vignettes/BenHamou03.rmd | 30 +- 35 files changed, 1456 insertions(+), 1387 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between mongolite versions 2.8.1 dated 2024-10-04 and 2.8.2 dated 2024-12-02
DESCRIPTION | 10 +++++----- MD5 | 22 ++++++++++++---------- NAMESPACE | 2 ++ NEWS | 3 +++ R/mongo.R | 6 +++--- R/reader.R |only inst/WORDLIST | 4 ++-- man/gridfs.Rd | 2 +- man/mongo.Rd | 6 +++--- man/read_bson.Rd |only src/mongolite.h | 2 +- src/reader.c | 43 +++++++++++++++++++++++++++++++++++++++++++ src/utils.c | 2 +- 13 files changed, 76 insertions(+), 26 deletions(-)
Title: R Interface for Apache Sedona
Description: R interface for 'Apache Sedona' based on 'sparklyr'
(<https://sedona.apache.org>).
Author: Apache Sedona [aut, cre],
Jia Yu [ctb, cph],
Yitao Li [aut, cph] ,
The Apache Software Foundation [cph],
RStudio [cph]
Maintainer: Apache Sedona <private@sedona.apache.org>
Diff between apache.sedona versions 1.6.1 dated 2024-08-25 and 1.7.0 dated 2024-12-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/dependencies.R | 12 ++++++------ README.md | 2 +- man/figures/logo.png |binary 5 files changed, 14 insertions(+), 14 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library implementing 'Scalability Protocols', a reliable,
high-performance standard for common communications patterns including
publish/subscribe, request/reply and service discovery, over in-process,
IPC, TCP, WebSocket and secure TLS transports. As its own threaded
concurrency framework, provides a toolkit for asynchronous programming and
distributed computing, with intuitive 'aio' objects which resolve
automatically upon completion of asynchronous operations, and
synchronisation primitives allowing R to wait upon events signalled by
concurrent threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 1.3.2 dated 2024-11-14 and 1.4.0 dated 2024-12-02
nanonext-1.3.2/nanonext/man/collect_pipe.Rd |only nanonext-1.4.0/nanonext/DESCRIPTION | 6 nanonext-1.4.0/nanonext/MD5 | 57 ++++----- nanonext-1.4.0/nanonext/NAMESPACE | 7 - nanonext-1.4.0/nanonext/NEWS.md | 16 ++ nanonext-1.4.0/nanonext/R/aio.R | 10 - nanonext-1.4.0/nanonext/R/nano.R | 4 nanonext-1.4.0/nanonext/R/sendrecv.R | 6 nanonext-1.4.0/nanonext/R/socket.R | 88 +++++++------- nanonext-1.4.0/nanonext/R/sync.R | 7 - nanonext-1.4.0/nanonext/R/utils.R | 20 +++ nanonext-1.4.0/nanonext/inst/doc/nanonext.html | 2 nanonext-1.4.0/nanonext/man/close.Rd | 9 - nanonext-1.4.0/nanonext/man/dot-dispatcher.Rd | 3 nanonext-1.4.0/nanonext/man/dot-interrupt.Rd |only nanonext-1.4.0/nanonext/man/dot-online.Rd | 4 nanonext-1.4.0/nanonext/man/is_aio.Rd | 2 nanonext-1.4.0/nanonext/man/monitor.Rd |only nanonext-1.4.0/nanonext/man/send.Rd | 5 nanonext-1.4.0/nanonext/man/send_aio.Rd | 7 - nanonext-1.4.0/nanonext/src/aio.c | 78 +++++------- nanonext-1.4.0/nanonext/src/comms.c | 59 +++------ nanonext-1.4.0/nanonext/src/core.c | 39 +++++- nanonext-1.4.0/nanonext/src/init.c | 14 +- nanonext-1.4.0/nanonext/src/nanonext.h | 23 ++- nanonext-1.4.0/nanonext/src/nng-190.tar.xz |binary nanonext-1.4.0/nanonext/src/proto.c | 73 ------------ nanonext-1.4.0/nanonext/src/sync.c | 128 +++++++++++++++++++-- nanonext-1.4.0/nanonext/src/thread.c | 152 ++++++++++++------------- nanonext-1.4.0/nanonext/src/utils.c | 13 +- nanonext-1.4.0/nanonext/tests/tests.R | 49 ++++---- 31 files changed, 492 insertions(+), 389 deletions(-)
Title: Tools for Customer Lifetime Value Estimation
Description: A set of state-of-the-art probabilistic modeling approaches to derive estimates of individual customer lifetime values (CLV).
Commonly, probabilistic approaches focus on modelling 3 processes, i.e. individuals' attrition, transaction, and spending process.
Latent customer attrition models, which are also known as "buy-'til-you-die models", model the attrition as well as the transaction process.
They are used to make inferences and predictions about transactional patterns of individual customers such as their future purchase behavior.
Moreover, these models have also been used to predict individuals’ long-term engagement in activities such as playing an online game or
posting to a social media platform. The spending process is usually modelled by a separate probabilistic model. Combining these results yields in
lifetime values estimates for individual customers.
This package includes fast and accurate implementations of various probabilistic models for non-contractual settings
(e.g., gr [...truncated...]
Author: Patrick Bachmann [cre, aut],
Niels Kuebler [aut],
Markus Meierer [aut],
Jeffrey Naef [aut],
E. Shin Oblander [aut],
Patrik Schilter [aut]
Maintainer: Patrick Bachmann <pbachma@ethz.ch>
Diff between CLVTools versions 0.11.1 dated 2024-10-13 and 0.11.2 dated 2024-12-02
DESCRIPTION | 8 +- MD5 | 54 ++++++++-------- NAMESPACE | 1 NEWS.md | 8 ++ R/all_generics.R | 8 +- R/class_clv_model_bgnbd.R | 6 - R/class_clv_model_bgnbd_staticcov.R | 6 - R/class_clv_model_gg.R | 12 +++ R/class_clv_model_ggomnbd_nocov.R | 6 - R/class_clv_model_ggomnbd_staticcov.R | 6 - R/class_clv_model_pnbd.R | 6 - R/class_clv_model_pnbd_dynamiccov.R | 8 +- R/class_clv_model_pnbd_staticcov.R | 6 - R/f_clvfitted_inputchecks.R | 2 R/f_generics_clvfittedspending.R | 17 +++++ R/f_generics_clvfittedtransactions.R | 7 -- R/f_generics_clvfittedtransactionsdyncov.R | 3 R/f_generics_clvfittedtransactionsstaticcov.R | 5 - R/f_interface_newcustomer.R | 83 ++++++++++++++++++++----- R/f_interface_predict_clvfittedspending.R | 50 +++++++++++++-- R/f_interface_predict_clvfittedtransactions.R | 51 ++++++--------- inst/doc/CLVTools.pdf |binary man/newcustomer.Rd | 39 +++++++++-- man/predict.clv.fitted.spending.Rd | 51 ++++++++++++++- man/predict.clv.fitted.transactions.Rd | 8 +- tests/testthat/test_inputchecks_newcustomer.R | 33 ++++++++- tests/testthat/test_runability_bootstrapping.R | 56 +++++++++++++++- tests/testthat/test_runability_newcustomer.R | 10 +++ 28 files changed, 409 insertions(+), 141 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The functions
are pipe-friendly and provide a consistent syntax to work with tidy
data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'. References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 1.6.1 dated 2024-10-30 and 1.6.2 dated 2024-12-02
DESCRIPTION | 15 MD5 | 44 - NAMESPACE | 5 NEWS.md | 5 R/add-expression-col.R | 359 +++++------ R/centrality-description.R | 155 ++-- R/contingency-table.R | 307 ++++----- R/corr-test.R | 115 +-- R/long-to-wide-converter.R | 191 +++--- R/meta-analysis.R | 193 +++--- R/one-sample-test.R | 207 +++--- R/oneway-anova.R | 575 +++++++++--------- R/pairwise-comparisons.R | 617 +++++++++---------- R/reexports.R | 8 R/statsExpressions-package.R | 1 R/tidy-model-expressions.R | 233 +++---- R/two-sample-test.R | 273 ++++---- build/vignette.rds |binary man/reexports.Rd | 4 man/tidy_model_parameters.Rd | 26 tests/testthat/_snaps/tidy-model-expressions.md | 23 tests/testthat/helper.R | 6 tests/testthat/test-pairwise-comparisons.R | 747 +++++++++++------------- 23 files changed, 2067 insertions(+), 2042 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Principal Components Analysis using NIPALS or Weighted EMPCA,
with Gram-Schmidt Orthogonalization
Description: Principal Components Analysis of a matrix using Non-linear
Iterative Partial Least Squares or weighted Expectation Maximization
PCA with Gram-Schmidt orthogonalization of the scores and loadings.
Optimized for speed. See Andrecut (2009) <doi:10.1089/cmb.2008.0221>.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between nipals versions 0.8 dated 2021-09-15 and 1.0 dated 2024-12-02
DESCRIPTION | 30 - LICENSE |only MD5 | 56 +-- NAMESPACE | 1 NEWS.md | 33 + R/nipals.R | 68 +++ build/vignette.rds |binary inst/doc/empca_notes.R | 78 ++-- inst/doc/empca_notes.Rmd | 19 - inst/doc/empca_notes.html | 477 +++++++++++++++++++------- inst/doc/nipals_algorithm.Rmd | 1 inst/doc/nipals_algorithm.html | 501 +++++++++++++++++++++------- inst/doc/nipals_comparisons.R | 294 ++++++++-------- inst/doc/nipals_comparisons.Rmd | 1 inst/doc/nipals_comparisons.html | 629 ++++++++++++++++++++++++----------- inst/doc/nipals_optimization.R | 235 ++++++------- inst/doc/nipals_optimization.Rmd | 6 inst/doc/nipals_optimization.html | 639 +++++++++++++++++++++++++----------- man/avg_angular_distance.Rd |only man/empca.Rd | 180 +++++----- man/nipals.Rd | 223 ++++++------ man/uscrime.Rd | 118 +++--- tests/testthat/setup-expectations.R | 24 - tests/testthat/test-empca.R | 24 - tests/testthat/test-nipals.R | 152 +++++--- tests/testthat/test-uscrime.R | 81 ++-- vignettes/empca_notes.Rmd | 19 - vignettes/nipals_algorithm.Rmd | 1 vignettes/nipals_comparisons.Rmd | 1 vignettes/nipals_optimization.Rmd | 6 30 files changed, 2471 insertions(+), 1426 deletions(-)
Title: Tools to Analyze Repertory Grid Data
Description: Analyze repertory grids, a qualitative-quantitative
data collection technique devised by George A. Kelly in the 1950s. Today, grids are used across
various domains ranging from clinical psychology to marketing. The package contains functions
to quantitatively analyze and visualize repertory grid data (e.g. 'Fransella', 'Bell', & 'Bannister',
2004, ISBN: 978-0-470-09080-0). The package is part of the The package is part of the
<https://openrepgrid.org/> project.
Author: Mark Heckmann [aut, cre, cph] ,
Alejandro Garcia Gutierrez [ctb],
Diego Vitali [ctb]
Maintainer: Mark Heckmann <heckmann.mark@gmail.com>
Diff between OpenRepGrid versions 0.1.15 dated 2024-07-20 and 0.1.16 dated 2024-12-02
DESCRIPTION | 10 +- MD5 | 19 ++-- NEWS.md | 6 + R/data-openrepgrid.r | 9 +- R/import.r | 176 +++++++++++++++++++++++--------------------- inst/extdata/boeker.xlsx |only inst/extdata/grid_01.txt |only inst/extdata/grid_02.txt |only man/data-bellmcgorry1992.Rd | 1 man/data-boeker.Rd | 4 + man/importTxt.Rd | 94 ++++++++++++----------- man/importTxtInternal.Rd | 58 +++++++------- 12 files changed, 202 insertions(+), 175 deletions(-)
Title: Fitting Deep Distributional Regression
Description: Allows for the specification of semi-structured deep distributional regression models which are fitted in a neural network as
proposed by Ruegamer et al. (2023) <doi:10.18637/jss.v105.i02>.
Predictors can be modeled using structured (penalized) linear effects, structured non-linear effects or using an unstructured deep network model.
Author: David Ruegamer [aut, cre],
Christopher Marquardt [ctb],
Laetitia Frost [ctb],
Florian Pfisterer [ctb],
Philipp Baumann [ctb],
Chris Kolb [ctb],
Lucas Kook [ctb]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between deepregression versions 1.0.0 dated 2023-01-17 and 2.2.0 dated 2024-12-02
deepregression-1.0.0/deepregression/R/aaa.R |only deepregression-1.0.0/deepregression/R/rstudio |only deepregression-1.0.0/deepregression/inst/python/distributions/__pycache__/__init__.cpython-36.pyc |only deepregression-1.0.0/deepregression/inst/python/distributions/__pycache__/convlasso.cpython-310.pyc |only deepregression-1.0.0/deepregression/inst/python/distributions/__pycache__/convlasso.cpython-36.pyc |only deepregression-1.0.0/deepregression/inst/python/distributions/__pycache__/lasso.cpython-310.pyc |only deepregression-1.0.0/deepregression/inst/python/distributions/__pycache__/lasso.cpython-36.pyc |only deepregression-1.0.0/deepregression/inst/python/generators/__pycache__/__init__.cpython-36.pyc |only deepregression-1.0.0/deepregression/inst/python/generators/__pycache__/keras_generators.cpython-36.pyc |only deepregression-1.0.0/deepregression/inst/python/layers/__pycache__/__init__.cpython-36.pyc |only 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deepregression-2.2.0/deepregression/R/nodelayer.R |only deepregression-2.2.0/deepregression/R/orthogonalization.R | 124 + deepregression-2.2.0/deepregression/R/psplinelayer.R | 52 deepregression-2.2.0/deepregression/R/psplinelayer_torch.R |only deepregression-2.2.0/deepregression/R/special_processing.R | 716 ++++++---- deepregression-2.2.0/deepregression/R/subnetwork_init_torch.R |only deepregression-2.2.0/deepregression/R/torch_helpers.R |only deepregression-2.2.0/deepregression/R/zzz.R | 72 - deepregression-2.2.0/deepregression/build/partial.rdb |binary deepregression-2.2.0/deepregression/inst/python/activations |only deepregression-2.2.0/deepregression/inst/python/distributions/__init__.py | 1 deepregression-2.2.0/deepregression/inst/python/distributions/__pycache__/__init__.cpython-310.pyc |binary deepregression-2.2.0/deepregression/inst/python/distributions/__pycache__/__init__.cpython-39.pyc |only 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More information about deepregression at CRAN
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Title: Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models. Mokany K, Ware C, Woolley SNC, Ferrier S, Fitzpatrick MC (2022) <doi:10.1111/geb.13459> Ferrier S, Manion G, Elith J, Richardson K (2007) <doi:10.1111/j.1472-4642.2007.00341.x>.
Author: Matt Fitzpatrick [aut, cre] ,
Karel Mokany [aut] ,
Glenn Manion [aut],
Diego Nieto-Lugilde [aut] ,
Simon Ferrier [aut] ,
Roozbeh Valavi [ctb],
Matthew Lisk [ctb],
Chris Ware [ctb],
Skip Woolley [ctb],
Tom Harwood [ctb]
Maintainer: Matt Fitzpatrick <mfitzpatrick@umces.edu>
Diff between gdm versions 1.6.0-3 dated 2024-11-01 and 1.6.0-4 dated 2024-12-02
gdm-1.6.0-3/gdm/inst/extdata/test_data/gdm_trans_vars.grd.aux.xml |only gdm-1.6.0-4/gdm/DESCRIPTION | 8 - gdm-1.6.0-4/gdm/MD5 | 21 +-- gdm-1.6.0-4/gdm/R/gdm.fit.R | 4 gdm-1.6.0-4/gdm/R/gdm.formatsitepair.R | 4 gdm-1.6.0-4/gdm/R/gdm.partition.deviance.R | 4 gdm-1.6.0-4/gdm/R/gdm.plot.R | 4 gdm-1.6.0-4/gdm/R/gdm.plot.uncertainty.R | 4 gdm-1.6.0-4/gdm/R/gdm.subsample.sitepair.R | 4 gdm-1.6.0-4/gdm/R/gdm.variable.importance.R | 4 gdm-1.6.0-4/gdm/README.md | 6 gdm-1.6.0-4/gdm/inst/tinytest/test_gdm.R | 62 +++++----- 12 files changed, 61 insertions(+), 64 deletions(-)
Title: Interact with Data Type Registries and Create Machine-Readable
Data
Description: You can load a schema from a DTR (data type registry) as an R
object. Use this schema to write your data in JSON-LD (JavaScript
Object Notation for Linked Data) format to make it machine readable.
Author: Olga Lezhnina [aut, cre] ,
Manuel Prinz [aut] ,
Markus Stocker [aut] ,
Open Research Knowledge Graph Project and Contributors [cph]
Maintainer: Olga Lezhnina <olga.lezhnina@tib.eu>
Diff between dtreg versions 1.0.0 dated 2024-09-16 and 1.1.0 dated 2024-12-02
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Title: Extending Base 'R' Lists
Description: Extends the functionality of base 'R' lists and
provides specialized data structures 'deque',
'set', 'dict', and 'dict.table', the latter to extend the 'data.table'
package.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between container versions 1.0.4 dated 2022-12-11 and 1.0.5 dated 2024-12-02
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Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 10.9.3 dated 2024-10-14 and 10.9.4 dated 2024-12-02
DESCRIPTION | 8 - MD5 | 27 ++--- R/NNS_MC.R | 19 ++- R/NNS_meboot.R | 138 +++++++++++++++++----------- R/Normalization.R | 2 README.md | 4 inst/doc/NNSvignette_Sampling.R | 37 ++++--- inst/doc/NNSvignette_Sampling.Rmd | 47 ++++++--- inst/doc/NNSvignette_Sampling.html | 159 +++++++++++++++++---------------- man/NNS.MC.Rd | 5 - man/NNS.meboot.Rd | 33 +++++- man/NNS.norm.Rd | 2 vignettes/NNSvignette_Sampling.Rmd | 47 ++++++--- vignettes/images/NNSmc_1.png |binary vignettes/images/NNSmc_1_tgt_drift.png |only 15 files changed, 315 insertions(+), 213 deletions(-)
Title: Group-Based Multivariate Trajectory Modeling
Description: Estimation and analysis of group-based multivariate trajectory models (Nagin, 2018 <doi:10.1177/0962280216673085>; Magrini, 2022 <doi:10.1007/s10182-022-00437-9>). The package implements an Expectation-Maximization (EM) algorithm allowing unbalanced panel and missing values, and provides several functionalities for prediction and graphical representation.
Author: Alessandro Magrini [aut, cre]
Maintainer: Alessandro Magrini <alessandro.magrini@unifi.it>
Diff between gbmt versions 0.1.3 dated 2022-03-05 and 0.1.4 dated 2024-12-02
Changelog | 8 +- DESCRIPTION | 11 +- MD5 | 21 +++-- NAMESPACE | 2 R/gbmt.R | 190 ++++++++++++++++++++++++++++----------------------- data/achievement.rda |only inst |only man/achievement.Rd |only man/agrisus.Rd | 2 man/agrisus2.Rd | 2 man/gbmt-package.Rd | 14 +-- man/gbmt.Rd | 57 ++++++++------- man/plot.gbmt.Rd | 13 +-- 13 files changed, 182 insertions(+), 138 deletions(-)
Title: Adds Subtotals to Data Reports
Description: Adds subtotal rows / sections (a la the 'SAS' 'Proc Tabulate' All option) to a Group By output by running a series of Group By functions with partial sets of the same variables and combining the results with the original. Can be used to add comprehensive information to a data report or to quickly aggregate Group By outputs used to gain a greater understanding of data.
Author: Yoni Aboody [aut, cre, cph]
Maintainer: Yoni Aboody <yoniaboody@gmail.com>
Diff between ReportSubtotal versions 0.1 dated 2024-11-15 and 0.1.2 dated 2024-12-02
DESCRIPTION | 8 - MD5 | 18 +- NAMESPACE | 1 NEWS.md | 11 - R/ReportSubtotal-package.R | 47 +++--- R/subtotal_dupe_removal.R | 33 ++-- R/subtotal_row.R | 3 R/subtotal_section.R | 319 +++++++++++++++++++++--------------------- man/ReportSubtotal-package.Rd | 2 man/subtotal_dupe_removal.Rd | 4 10 files changed, 230 insertions(+), 216 deletions(-)
More information about ReportSubtotal at CRAN
Permanent link
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] ,
Heidi Seibold [ctb] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-22 dated 2024-08-17 and 1.2-23 dated 2024-12-02
partykit-1.2-22/partykit/tests/Rplots.pdf |only partykit-1.2-23/partykit/DESCRIPTION | 8 +- partykit-1.2-23/partykit/MD5 | 25 ++++---- partykit-1.2-23/partykit/R/extree.R | 2 partykit-1.2-23/partykit/R/party.R | 5 + partykit-1.2-23/partykit/build/partial.rdb |binary partykit-1.2-23/partykit/build/vignette.rds |binary partykit-1.2-23/partykit/inst/NEWS.Rd | 8 ++ partykit-1.2-23/partykit/inst/doc/constparty.pdf |binary partykit-1.2-23/partykit/inst/doc/ctree.pdf |binary partykit-1.2-23/partykit/inst/doc/mob.pdf |binary partykit-1.2-23/partykit/inst/doc/partykit.pdf |binary partykit-1.2-23/partykit/tests/bugfixes.R | 10 +++ partykit-1.2-23/partykit/tests/bugfixes.Rout.save | 62 ++++++++++++++++++++-- 14 files changed, 97 insertions(+), 23 deletions(-)
Title: Multimodal Automated Phenotyping
Description: Electronic health records (EHR) linked with biorepositories are
a powerful platform for translational studies. A major bottleneck exists
in the ability to phenotype patients accurately and efficiently.
Towards that end, we developed an automated high-throughput
phenotyping method integrating International
Classification of Diseases (ICD) codes and narrative data extracted
using natural language processing (NLP). Specifically, our proposed method,
called MAP (Map Automated Phenotyping algorithm), fits an ensemble of latent
mixture models on aggregated ICD and NLP counts along with healthcare
utilization. The MAP algorithm yields a predicted probability of phenotype
for each patient and a threshold for classifying subjects with phenotype
yes/no (See Katherine P. Liao, et al. (2019) <doi:10.1093/jamia/ocz066>.).
Author: Thomas Charlon [aut, cre] ,
Chuan Hong [aut],
Jiehuan Sun [aut],
Katherine Liao [aut],
Sheng Yu [aut],
Tianxi Cai [aut],
PARSE Health [aut] ,
CELEHS [aut]
Maintainer: Thomas Charlon <charlon@protonmail.com>
Diff between MAP versions 0.1.3 dated 2019-04-01 and 1.0.0 dated 2024-12-02
DESCRIPTION | 41 ++++- MD5 | 27 ++- NAMESPACE | 22 ++ R/MAP.R | 373 +++++++++++++++++++++++++++-------------------- R/MAP_project.R |only R/package.R |only README.md |only build |only data |only inst |only man/MAP.Rd | 33 +++- man/compound.Rd |only man/exposition.Rd |only man/phecode.cuis.list.Rd |only man/pipe.Rd |only tests |only vignettes |only 17 files changed, 316 insertions(+), 180 deletions(-)
Title: Flexible and General Mediation Analysis Using Riesz Representers
Description: Implements a modern, unified estimation strategy for common
mediation estimands (natural effects, organic effects, interventional effects,
and recanting twins) in combination with modified treatment policies as
described in Liu, Williams, Rudolph, and Díaz (2024)
<doi:10.48550/arXiv.2408.14620>. Estimation makes use of recent advancements
in Riesz-learning to estimate a set of required nuisance parameters with
deep learning. The result is the capability to estimate mediation effects with
binary, categorical, continuous, or multivariate exposures with
high-dimensional mediators and mediator-outcome confounders using machine
learning.
Author: Nicholas Williams [aut, cre, cph]
,
Richard Liu [ctb],
Ivan Diaz [aut, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between crumble versions 0.1.1 dated 2024-11-14 and 0.1.2 dated 2024-12-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/crumble_data.R | 4 ++-- README.md | 3 +++ 5 files changed, 18 insertions(+), 9 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.3.9 dated 2020-08-27 and 0.3.10 dated 2024-12-02
anytime-0.3.10/anytime/ChangeLog | 157 +++++++++++++++ anytime-0.3.10/anytime/DESCRIPTION | 17 - anytime-0.3.10/anytime/MD5 | 35 +-- anytime-0.3.10/anytime/R/anytime.R | 12 - anytime-0.3.10/anytime/R/formats.R | 6 anytime-0.3.10/anytime/README.md | 27 ++ anytime-0.3.10/anytime/build/partial.rdb |binary anytime-0.3.10/anytime/build/vignette.rds |binary anytime-0.3.10/anytime/cleanup | 1 anytime-0.3.10/anytime/inst/NEWS.Rd | 18 + anytime-0.3.10/anytime/inst/doc/anytime-introduction.pdf |binary anytime-0.3.10/anytime/inst/tinytest/test_all_formats.R | 21 +- anytime-0.3.10/anytime/inst/tinytest/test_gh_issue_129.R |only anytime-0.3.10/anytime/inst/tinytest/test_simple.R | 38 +-- anytime-0.3.10/anytime/man/anytime.Rd | 12 + anytime-0.3.10/anytime/man/iso8601.Rd | 4 anytime-0.3.10/anytime/src/anytime.cpp | 35 ++- anytime-0.3.10/anytime/tests/tinytest.R | 9 anytime-0.3.9/anytime/src/Makevars |only anytime-0.3.9/anytime/src/Makevars.win |only 20 files changed, 306 insertions(+), 86 deletions(-)
Title: Process Stream Temperature, Intermittency, and Conductivity
(STIC) Sensor Data
Description: A collection of functions for processing raw data from Stream Temperature, Intermittency, and Conductivity (STIC) loggers. 'STICr' (pronounced "sticker") includes functions for tidying, calibrating, classifying, and doing quality checks on data from STIC sensors. Some package functionality is described in Wheeler/Zipper et al. (2023) <doi:10.31223/X5636K>.
Author: Sam Zipper [aut, cre, cph] ,
Christopher T. Wheeler [aut] ,
Stephen Cook [ctb] ,
Delaney Peterson [ctb] ,
Sarah Godsey [ctb]
Maintainer: Sam Zipper <samzipper@ku.edu>
Diff between STICr versions 1.0 dated 2024-09-30 and 1.1 dated 2024-12-02
DESCRIPTION | 6 - MD5 | 27 +++---- NEWS.md | 8 +- R/apply_calibration.R | 2 R/qaqc_stic_data.R | 71 ++++++++++--------- R/validate_stic_data.R | 109 ++++++++++++++++++----------- README.md | 48 +++++++++++- inst/doc/intro-to-STICr.R | 44 ++++++++++- inst/doc/intro-to-STICr.Rmd | 57 ++++++++++++--- inst/doc/intro-to-STICr.html | 122 ++++++++++++++++++++++++--------- man/apply_calibration.Rd | 2 man/figures/README-validate-data-1.png |only man/qaqc_stic_data.Rd | 26 ++----- man/validate_stic_data.Rd | 31 ++++++-- vignettes/intro-to-STICr.Rmd | 57 ++++++++++++--- 15 files changed, 433 insertions(+), 177 deletions(-)
Title: Generate Samples with a Variety of Probability Distributions
Description: Simplifies the process of generating samples from a variety of probability distributions, allowing users to quickly create data frames for demonstrations, troubleshooting, or teaching purposes. Data is available in multiple sizes—small, medium, and large. For more information, refer to the package documentation.
Author: Nicholas Vietto [aut, cre, cph]
Maintainer: Nicholas Vietto <nicholasvietto@gmail.com>
Diff between samplezoo versions 1.1.0 dated 2024-11-28 and 1.1.1 dated 2024-12-02
DESCRIPTION | 8 ++-- MD5 | 14 +++---- NEWS.md | 6 +++ README.md | 22 ++++++++---- inst/doc/Example.Rmd | 2 - inst/doc/Example.html | 84 +++++++++++++++++++++++------------------------ man/samplezoo-package.Rd | 2 - vignettes/Example.Rmd | 2 - 8 files changed, 77 insertions(+), 63 deletions(-)
Title: Rational Approximations of Fractional Stochastic Partial
Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main references for rSPDE are Bolin, Simas and Xiong (2023) <doi:10.1080/10618600.2023.2231051> for the covariance-based method and Bolin and Kirchner (2020) <doi:10.1080/10618600.2019.1665537> for the operator-based rational approximation. These can be generated by the citation function in R.
Author: David Bolin [cre, aut],
Alexandre Simas [aut],
Finn Lindgren [ctb]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between rSPDE versions 2.3.3 dated 2023-11-05 and 2.4.0 dated 2024-12-02
rSPDE-2.3.3/rSPDE/R/rSPDE.R |only rSPDE-2.3.3/rSPDE/man/rSPDE.Rd |only rSPDE-2.4.0/rSPDE/DESCRIPTION | 18 rSPDE-2.4.0/rSPDE/MD5 | 163 rSPDE-2.4.0/rSPDE/NAMESPACE | 64 rSPDE-2.4.0/rSPDE/NEWS.md | 15 rSPDE-2.4.0/rSPDE/R/covariance.functions.R |only rSPDE-2.4.0/rSPDE/R/fractional.computations.R | 2521 ++++--- rSPDE-2.4.0/rSPDE/R/fractional.operators.R | 1057 ++- rSPDE-2.4.0/rSPDE/R/inla_rspde.R | 3215 +++++----- rSPDE-2.4.0/rSPDE/R/inla_rspde_1d.R |only rSPDE-2.4.0/rSPDE/R/inla_rspde_anisotropic.R |only rSPDE-2.4.0/rSPDE/R/inla_rspde_intrinsic.R |only rSPDE-2.4.0/rSPDE/R/inla_rspde_spacetime.R |only rSPDE-2.4.0/rSPDE/R/inlabru_rspde.R | 2699 +++++--- rSPDE-2.4.0/rSPDE/R/intrinsic.R | 645 +- rSPDE-2.4.0/rSPDE/R/markov.approx.R | 54 rSPDE-2.4.0/rSPDE/R/operator.operations.R | 36 rSPDE-2.4.0/rSPDE/R/print.summary.R |only rSPDE-2.4.0/rSPDE/R/rSPDE-package.R |only rSPDE-2.4.0/rSPDE/R/rspde_lme.R | 2339 ++++--- rSPDE-2.4.0/rSPDE/R/spacetime.R |only rSPDE-2.4.0/rSPDE/R/stationary1d.R |only rSPDE-2.4.0/rSPDE/R/sysdata.rda |binary rSPDE-2.4.0/rSPDE/R/util.R | 2528 ++++--- rSPDE-2.4.0/rSPDE/build/vignette.rds |binary rSPDE-2.4.0/rSPDE/inst/CITATION | 10 rSPDE-2.4.0/rSPDE/inst/doc/rSPDE_package.Rmd | 105 rSPDE-2.4.0/rSPDE/inst/doc/rSPDE_package.html | 27 rSPDE-2.4.0/rSPDE/man/augment.rspde_lme.Rd | 11 rSPDE-2.4.0/rSPDE/man/bru_get_mapper.inla_rspde.Rd | 95 rSPDE-2.4.0/rSPDE/man/bru_get_mapper.inla_rspde_anisotropic2d.Rd |only rSPDE-2.4.0/rSPDE/man/bru_get_mapper.inla_rspde_matern1d.Rd |only rSPDE-2.4.0/rSPDE/man/bru_get_mapper.inla_rspde_spacetime.Rd |only rSPDE-2.4.0/rSPDE/man/construct.spde.matern.loglike.Rd | 32 rSPDE-2.4.0/rSPDE/man/create_train_test_indices.Rd |only rSPDE-2.4.0/rSPDE/man/cross_validation.Rd | 10 rSPDE-2.4.0/rSPDE/man/folded.matern.covariance.1d.Rd | 7 rSPDE-2.4.0/rSPDE/man/folded.matern.covariance.2d.Rd | 2 rSPDE-2.4.0/rSPDE/man/graph_data_rspde.Rd | 16 rSPDE-2.4.0/rSPDE/man/group_predict.Rd |only rSPDE-2.4.0/rSPDE/man/intrinsic.matern.operators.Rd | 37 rSPDE-2.4.0/rSPDE/man/matern.covariance.Rd | 2 rSPDE-2.4.0/rSPDE/man/matern.operators.Rd | 20 rSPDE-2.4.0/rSPDE/man/matern.rational.Rd |only rSPDE-2.4.0/rSPDE/man/matern.rational.cov.Rd |only rSPDE-2.4.0/rSPDE/man/matern2d.operators.Rd |only rSPDE-2.4.0/rSPDE/man/precision.CBrSPDEobj.Rd | 26 rSPDE-2.4.0/rSPDE/man/precision.CBrSPDEobj2d.Rd |only rSPDE-2.4.0/rSPDE/man/precision.rSPDEobj1d.Rd |only rSPDE-2.4.0/rSPDE/man/precision.spacetimeobj.Rd |only rSPDE-2.4.0/rSPDE/man/predict.CBrSPDEobj.Rd | 2 rSPDE-2.4.0/rSPDE/man/predict.CBrSPDEobj2d.Rd |only rSPDE-2.4.0/rSPDE/man/predict.inla_rspde_matern1d.Rd |only rSPDE-2.4.0/rSPDE/man/predict.rSPDEobj.Rd | 2 rSPDE-2.4.0/rSPDE/man/predict.rspde_lme.Rd | 42 rSPDE-2.4.0/rSPDE/man/predict.spacetimeobj.Rd |only rSPDE-2.4.0/rSPDE/man/rSPDE-package.Rd |only rSPDE-2.4.0/rSPDE/man/rSPDE.Ast.Rd |only rSPDE-2.4.0/rSPDE/man/rSPDE.construct.matern.loglike.Rd | 35 rSPDE-2.4.0/rSPDE/man/rSPDE.fem1d.Rd | 6 rSPDE-2.4.0/rSPDE/man/rSPDE.fem2d.Rd | 8 rSPDE-2.4.0/rSPDE/man/rSPDE.loglike.Rd | 3 rSPDE-2.4.0/rSPDE/man/rSPDE.matern.loglike.Rd | 35 rSPDE-2.4.0/rSPDE/man/rspde.anistropic2d.Rd |only rSPDE-2.4.0/rSPDE/man/rspde.make.A.Rd | 22 rSPDE-2.4.0/rSPDE/man/rspde.make.index.Rd | 94 rSPDE-2.4.0/rSPDE/man/rspde.matern.Rd | 8 rSPDE-2.4.0/rSPDE/man/rspde.matern.intrinsic.Rd |only rSPDE-2.4.0/rSPDE/man/rspde.matern.precision.Rd | 4 rSPDE-2.4.0/rSPDE/man/rspde.matern.precision.integer.Rd | 4 rSPDE-2.4.0/rSPDE/man/rspde.matern1d.Rd |only rSPDE-2.4.0/rSPDE/man/rspde.mesh.project.Rd | 6 rSPDE-2.4.0/rSPDE/man/rspde.metric_graph.Rd | 4 rSPDE-2.4.0/rSPDE/man/rspde.result.Rd | 92 rSPDE-2.4.0/rSPDE/man/rspde.spacetime.Rd |only rSPDE-2.4.0/rSPDE/man/rspde_lme.Rd | 93 rSPDE-2.4.0/rSPDE/man/simulate.CBrSPDEobj.Rd | 32 rSPDE-2.4.0/rSPDE/man/simulate.CBrSPDEobj2d.Rd |only rSPDE-2.4.0/rSPDE/man/simulate.intrinsicCBrSPDEobj.Rd |only rSPDE-2.4.0/rSPDE/man/simulate.rSPDEobj.Rd | 2 rSPDE-2.4.0/rSPDE/man/simulate.rSPDEobj1d.Rd |only rSPDE-2.4.0/rSPDE/man/simulate.spacetimeobj.Rd |only rSPDE-2.4.0/rSPDE/man/spacetime.operators.Rd |only rSPDE-2.4.0/rSPDE/man/spde.make.A.Rd | 20 rSPDE-2.4.0/rSPDE/man/spde.matern.loglike.Rd | 32 rSPDE-2.4.0/rSPDE/man/spde.matern.operators.Rd | 2 rSPDE-2.4.0/rSPDE/man/summary.CBrSPDEobj.Rd | 6 rSPDE-2.4.0/rSPDE/man/summary.CBrSPDEobj2d.Rd |only rSPDE-2.4.0/rSPDE/man/summary.rSPDEobj.Rd | 2 rSPDE-2.4.0/rSPDE/man/summary.rSPDEobj1d.Rd |only rSPDE-2.4.0/rSPDE/man/summary.rspde_result.Rd | 92 rSPDE-2.4.0/rSPDE/man/summary.spacetimeobj.Rd |only rSPDE-2.4.0/rSPDE/man/transform_parameters_anisotropic.Rd |only rSPDE-2.4.0/rSPDE/man/transform_parameters_spacetime.Rd |only rSPDE-2.4.0/rSPDE/man/update.CBrSPDEobj.Rd | 36 rSPDE-2.4.0/rSPDE/man/update.CBrSPDEobj2d.Rd |only rSPDE-2.4.0/rSPDE/man/update.rSPDEobj.Rd | 36 rSPDE-2.4.0/rSPDE/man/update.rSPDEobj1d.Rd |only rSPDE-2.4.0/rSPDE/man/update.spacetimeobj.Rd |only rSPDE-2.4.0/rSPDE/man/variogram.intrinsic.spde.Rd | 37 rSPDE-2.4.0/rSPDE/tests/testthat/test.CBrSPDE.R | 6 rSPDE-2.4.0/rSPDE/tests/testthat/test.fractional.operators.R | 4 rSPDE-2.4.0/rSPDE/tests/testthat/test.rational.R |only rSPDE-2.4.0/rSPDE/vignettes/rSPDE_package.Rmd | 105 105 files changed, 9491 insertions(+), 7135 deletions(-)
Title: Fitting Periodic Coefficients Linear Regression Models
Description: Provides tools for fitting periodic coefficients regression models to data where periodicity plays a crucial role. It allows users to model and analyze relationships between variables that exhibit cyclical or seasonal patterns, offering functions for estimating parameters and testing the periodicity of coefficients in linear regression models. For simple periodic coefficient regression model see Regui et al. (2024) <doi:10.1080/03610918.2024.2314662>.
Author: Slimane Regui [aut, cre] ,
Abdelhadi Akharif [aut],
Amal Mellouk [aut]
Maintainer: Slimane Regui <slimaneregui111997@gmail.com>
Diff between PerRegMod versions 4.4.2 dated 2024-11-26 and 4.4.3 dated 2024-12-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/PerRegMod.R | 4 +++- tests/test.R | 7 ++++--- 4 files changed, 13 insertions(+), 10 deletions(-)
Title: Analysis and Visualisation of Benchmark Experiments
Description: Implements methods for post-hoc analysis and
visualisation of benchmark experiments, for 'mlr3' and beyond.
Author: Sonabend Raphael [aut] ,
Florian Pfisterer [aut] ,
Michel Lang [ctb] ,
Bernd Bischl [ctb] ,
Sebastian Fischer [cre, ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3benchmark versions 0.1.6 dated 2023-05-30 and 0.1.7 dated 2024-12-02
DESCRIPTION | 8 ++-- MD5 | 20 +++++----- NEWS.md | 5 ++ R/BenchmarkAggr.R | 22 +++++------ R/autoplot.BenchmarkAggr.R | 11 +++-- R/plots_cd.R | 70 ++++++++++++++++++++++-------------- man/BenchmarkAggr.Rd | 13 ++++-- man/as.BenchmarkAggr.Rd | 6 +-- man/as_benchmark_aggr.Rd | 6 +-- man/autoplot.BenchmarkAggr.Rd | 3 + tests/testthat/test_BenchmarkAggr.R | 10 ++--- 11 files changed, 100 insertions(+), 74 deletions(-)
Title: Fast Alternatives to 'tidyverse' Functions
Description: A full set of fast data manipulation tools with a tidy
front-end and a fast back-end using 'collapse' and 'cheapr'.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between fastplyr versions 0.4.0 dated 2024-11-15 and 0.5.0 dated 2024-12-02
DESCRIPTION | 8 - MD5 | 86 ++++++------ NAMESPACE | 4 NEWS.md | 28 ++++ R/GRP_utils.R | 2 R/abc.R | 63 ++++----- R/add_id.R | 29 ---- R/cpp11.R | 4 R/df_utils.R | 77 +++++------ R/f_arrange.R | 9 - R/f_bind.R | 20 +- R/f_count.R | 40 +---- R/f_distinct.R | 21 --- R/f_duplicates.R | 12 - R/f_expand.R | 75 ++++++----- R/f_fill.R | 4 R/f_group_by.R | 10 - R/f_nest_by.R | 134 +++++++++---------- R/f_select.R | 16 ++ R/f_slice.R | 37 ----- R/f_summarise.R | 97 ++++++++------ R/f_tibble.R | 212 ++++++++++++++++--------------- R/fastplyr.R | 55 ++++---- R/group_collapse.R | 18 +- R/list_tidy.R |only R/remove_na.R |only R/tidy_quantiles.R | 6 R/tidy_utils.R | 259 +++++++++++++++++++++++++++++--------- man/add_id.Rd | 7 - man/duplicate_rows.Rd | 3 man/f_arrange.Rd | 78 ++++++----- man/f_count.Rd | 4 man/f_distinct.Rd | 8 - man/f_expand.Rd | 20 -- man/f_group_by.Rd | 3 man/f_select.Rd | 5 man/f_slice.Rd | 6 man/list_tidy.Rd |only man/new_tbl.Rd | 99 +++++++------- man/remove_na.Rd |only src/cpp11.cpp | 8 - src/fastplyr.cpp | 72 ---------- tests/testthat/test-f_arrange.R | 54 +++---- tests/testthat/test-f_bind.R |only tests/testthat/test-f_slice.R | 63 ++------- tests/testthat/test-f_summarise.R | 51 +++++++ tests/testthat/test-list_tidy.R |only 47 files changed, 926 insertions(+), 881 deletions(-)
Title: A Toolbox for Clinical Significance Analyses in Intervention
Studies
Description: A clinical significance analysis can be used to determine if an
intervention has a meaningful or practical effect for patients. You provide
a tidy data set plus a few more metrics and this package will take care of
it to make your results publication ready. Accompanying package to
Claus et al. <doi:10.18637/jss.v111.i01>.
Author: Benedikt Claus [aut, cre]
Maintainer: Benedikt Claus <b.claus@pedscience.de>
Diff between clinicalsignificance versions 2.0.0 dated 2023-11-16 and 2.1.0 dated 2024-12-02
DESCRIPTION | 11 MD5 | 25 - NEWS.md | 3 build/vignette.rds |binary inst/CITATION |only inst/doc/anchor-based-approach.html | 30 - inst/doc/combined-approach.html | 16 inst/doc/distribution-based-approach.html | 18 inst/doc/percentage-change-approach.html | 14 inst/doc/statistical-approach.html | 12 tests/testthat/_snaps/cs_combined.md | 362 +++++++++---------- tests/testthat/_snaps/cs_distribution.md | 314 ++++++++-------- tests/testthat/_snaps/cs_percentage.md | 80 ++-- tests/testthat/_snaps/plot/distribution-hlm-plot.svg | 2 14 files changed, 448 insertions(+), 439 deletions(-)
More information about clinicalsignificance at CRAN
Permanent link
Title: Generate Visual Predictive Checks (VPC) Using 'shiny'
Description: Utilize the 'shiny' interface to parameterize a Visual Predictive Check (VPC),
including selecting from different binning or binless methods and performing stratification,
censoring, and prediction correction. Generate the underlying 'tidyvpc' and 'ggplot2' code
directly from the user interface and download R or Rmd scripts to reproduce the VPCs in R.
Author: James Craig [aut, cre],
Mike Talley [aut],
Certara USA, Inc [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Diff between Certara.VPCResults versions 3.0.1 dated 2024-10-10 and 3.0.2 dated 2024-12-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/create_rmd.R | 6 +++++- 3 files changed, 10 insertions(+), 6 deletions(-)
More information about Certara.VPCResults at CRAN
Permanent link
Title: Generalized Ridge Trace Plots for Ridge Regression
Description: The genridge package introduces generalizations of the standard univariate
ridge trace plot used in ridge regression and related methods. These graphical methods
show both bias (actually, shrinkage) and precision, by plotting the covariance ellipsoids of the estimated
coefficients, rather than just the estimates themselves. 2D and 3D plotting methods are provided,
both in the space of the predictor variables and in the transformed space of the PCA/SVD of the
predictors.
Author: Michael Friendly [aut, cre]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between genridge versions 0.7.1 dated 2024-11-13 and 0.8.0 dated 2024-12-02
DESCRIPTION | 10 - MD5 | 36 +++--- NAMESPACE | 3 NEWS.md | 14 ++ R/data.R | 51 +++++++++ R/plot.precision.R | 2 R/plot.ridge.R | 9 + R/precision.R | 56 ++++++++-- R/ridge.R | 45 ++++++++ R/traceplot.R | 4 R/vif.ridge.R | 162 +++++++++++++++++++++++-------- data/diab.RData |only man/diab.Rd |only man/figures/README-plot-vif-1.png |only man/figures/README-precision-plot2-1.png |only man/plot.precision.Rd | 2 man/plot.ridge.Rd | 9 + man/precision.Rd | 29 ++++- man/ridge.Rd | 23 ++++ man/traceplot.Rd | 2 man/vif.ridge.Rd | 111 ++++++++++++++------- 21 files changed, 449 insertions(+), 119 deletions(-)
Title: Multidimensional Penalized Splines for (Excess) Hazard Models,
Relative Mortality Ratio Models and Marginal Intensity Models
Description: Fits (excess) hazard, relative mortality ratio or marginal intensity models with multidimensional penalized splines allowing for
time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (than [...truncated...]
Author: Mathieu Fauvernier [aut, cre],
Laurent Roche [aut],
Laurent Remontet [aut],
Zoe Uhry [ctb],
Nadine Bossard [ctb],
Elsa Coz [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>
Diff between survPen versions 1.6.0 dated 2023-09-13 and 2.0.0 dated 2024-12-02
survPen-1.6.0/survPen/R/survPenV1_60.r |only survPen-2.0.0/survPen/DESCRIPTION | 46 survPen-2.0.0/survPen/MD5 | 102 survPen-2.0.0/survPen/NAMESPACE | 7 survPen-2.0.0/survPen/NEWS | 19 survPen-2.0.0/survPen/R/RcppExports.R | 120 + survPen-2.0.0/survPen/R/survPenV2_00.r |only survPen-2.0.0/survPen/build/vignette.rds |binary survPen-2.0.0/survPen/data/HeartFailure.RData |only survPen-2.0.0/survPen/data/expected.table.RData |only survPen-2.0.0/survPen/data/list.wicss.rdata |only survPen-2.0.0/survPen/inst/doc/survival_analysis_with_survPen.R | 237 +- survPen-2.0.0/survPen/inst/doc/survival_analysis_with_survPen.Rmd | 202 + survPen-2.0.0/survPen/inst/doc/survival_analysis_with_survPen.html | 1135 +++------- survPen-2.0.0/survPen/man/CumulHazard.Rd |only survPen-2.0.0/survPen/man/DerivCumulHazard.Rd |only survPen-2.0.0/survPen/man/HazGL.Rd |only survPen-2.0.0/survPen/man/HeartFailure.Rd |only survPen-2.0.0/survPen/man/Hess_rho_mult.Rd |only survPen-2.0.0/survPen/man/NR.beta.Rd | 5 survPen-2.0.0/survPen/man/NR.rho.Rd | 2 survPen-2.0.0/survPen/man/constraint.Rd | 2 survPen-2.0.0/survPen/man/cor.var.Rd | 2 survPen-2.0.0/survPen/man/crs.FP.Rd | 2 survPen-2.0.0/survPen/man/crs.Rd | 2 survPen-2.0.0/survPen/man/datCancer.Rd | 2 survPen-2.0.0/survPen/man/design.matrix.Rd | 4 survPen-2.0.0/survPen/man/expected.table.Rd |only survPen-2.0.0/survPen/man/grad_rho_mult.Rd |only survPen-2.0.0/survPen/man/instr.Rd | 2 survPen-2.0.0/survPen/man/inv.repam.Rd | 2 survPen-2.0.0/survPen/man/list.wicss.Rd |only survPen-2.0.0/survPen/man/model.cons.Rd | 6 survPen-2.0.0/survPen/man/predSNS.Rd |only survPen-2.0.0/survPen/man/predict.survPen.Rd | 40 survPen-2.0.0/survPen/man/print.summary.survPen.Rd | 2 survPen-2.0.0/survPen/man/pwcst.Rd | 2 survPen-2.0.0/survPen/man/rd.Rd | 2 survPen-2.0.0/survPen/man/repam.Rd | 4 survPen-2.0.0/survPen/man/robust.var.Rd |only survPen-2.0.0/survPen/man/smf.Rd | 2 survPen-2.0.0/survPen/man/smooth.cons.Rd | 2 survPen-2.0.0/survPen/man/smooth.cons.integral.Rd | 2 survPen-2.0.0/survPen/man/smooth.spec.Rd | 2 survPen-2.0.0/survPen/man/splitmult.Rd |only survPen-2.0.0/survPen/man/summary.survPen.Rd | 3 survPen-2.0.0/survPen/man/survPen.Rd | 94 survPen-2.0.0/survPen/man/survPen.fit.Rd | 4 survPen-2.0.0/survPen/man/survPenObject.Rd | 5 survPen-2.0.0/survPen/man/tensor.in.Rd | 2 survPen-2.0.0/survPen/man/tensor.prod.S.Rd | 2 survPen-2.0.0/survPen/man/tensor.prod.X.Rd | 2 survPen-2.0.0/survPen/src/RcppExports.cpp | 129 + survPen-2.0.0/survPen/src/rcpp_survPen.cpp | 422 +++ survPen-2.0.0/survPen/tests/testthat/test_error.R | 2 survPen-2.0.0/survPen/tests/testthat/test_marginal_intensity.R |only survPen-2.0.0/survPen/tests/testthat/test_relative_mortality_ratio.R |only survPen-2.0.0/survPen/vignettes/survival_analysis_with_survPen.Rmd | 202 + survPen-2.0.0/survPen/vignettes/survival_analysis_with_survPen_files/figure-html/unnamed-chunk-10-1.png |binary survPen-2.0.0/survPen/vignettes/survival_analysis_with_survPen_files/figure-html/unnamed-chunk-51-1.png |binary survPen-2.0.0/survPen/vignettes/survival_analysis_with_survPen_files/figure-html/unnamed-chunk-52-1.png |only survPen-2.0.0/survPen/vignettes/survival_analysis_with_survPen_files/figure-html/unnamed-chunk-53-1.png |only 62 files changed, 1946 insertions(+), 878 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
< [...truncated...]
Author: Roger Bivand [cre, aut] ,
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assuncao [ctb],
Anil Bera [ctb],
Olaf Berke [ctb],
F. Guillaume Blanchet [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Steph [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.3-7 dated 2024-11-25 and 1.3-8 dated 2024-12-02
DESCRIPTION | 11 +++++++---- MD5 | 20 ++++++++++---------- NEWS.md | 5 ++++- inst/doc/CO69.html | 6 +++--- inst/doc/nb_sf.html | 28 ++++++++++++++-------------- inst/doc/sids.R | 5 +---- inst/doc/sids.Rmd | 8 ++------ inst/doc/sids.html | 32 +++++++++++++++++++++++++------- inst/doc/subgraphs.html | 6 +++--- man/moran.plot.Rd | 2 +- vignettes/sids.Rmd | 8 ++------ 11 files changed, 72 insertions(+), 59 deletions(-)
Title: Double Constrained Correspondence Analysis for Trait-Environment
Analysis in Ecology
Description: Double constrained correspondence analysis (dc-CA) analyzes
(multi-)trait (multi-)environment ecological data by using the 'vegan'
package and native R code. Throughout the two step algorithm of ter Braak
et al. (2018) is used. This algorithm combines and extends community-
(sample-) and species-level analyses, i.e. the usual community weighted
means (CWM)-based regression analysis and the species-level analysis of
species-niche centroids (SNC)-based regression analysis. The two steps use
canonical correspondence analysis to regress the abundance data on to the
traits and (weighted) redundancy analysis to regress the CWM of the
orthonormalized traits on to the environmental predictors. The function
dc_CA() has an option to divide the abundance data of a site by the site
total, giving equal site weights. This division has the advantage that the
multivariate analysis corresponds with an unweighted (multi-trait)
community-level analysis, instead of being weighted. The first step of
the al [...truncated...]
Author: Cajo J.F ter Braak [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between douconca versions 1.2.1 dated 2024-09-25 and 1.2.2 dated 2024-12-02
douconca-1.2.1/douconca/inst/tinytest/anova_dcca |only douconca-1.2.1/douconca/inst/tinytest/predict_env_dcca |only douconca-1.2.1/douconca/inst/tinytest/predict_regEnv_dcca |only douconca-1.2.1/douconca/inst/tinytest/predict_regTraits_dcca |only douconca-1.2.1/douconca/inst/tinytest/predict_response_dcca |only douconca-1.2.1/douconca/inst/tinytest/predict_traits_dcca |only douconca-1.2.1/douconca/inst/tinytest/scores_dcca |only douconca-1.2.2/douconca/DESCRIPTION | 11 douconca-1.2.2/douconca/MD5 | 166 ++-- douconca-1.2.2/douconca/NAMESPACE | 2 douconca-1.2.2/douconca/NEWS.md | 10 douconca-1.2.2/douconca/R/anova.dcca.R | 24 douconca-1.2.2/douconca/R/anova.wrda.R | 44 - douconca-1.2.2/douconca/R/anova_sites.R | 68 - douconca-1.2.2/douconca/R/anova_species.R | 275 +++++-- douconca-1.2.2/douconca/R/coef.dcca.R |only douconca-1.2.2/douconca/R/dc_CA.R | 137 --- douconca-1.2.2/douconca/R/fCWM_SNC.R | 388 +++++----- douconca-1.2.2/douconca/R/f_dc_CA.R | 18 douconca-1.2.2/douconca/R/f_env_axes.R | 6 douconca-1.2.2/douconca/R/f_trait_axes.R | 4 douconca-1.2.2/douconca/R/fitted.dcca.R |only douconca-1.2.2/douconca/R/functions_using_cca_object_internals.R | 29 douconca-1.2.2/douconca/R/getPlotdata.R | 31 douconca-1.2.2/douconca/R/get_Z_X_XZ_formula.R | 14 douconca-1.2.2/douconca/R/plot.dcCA.R | 34 douconca-1.2.2/douconca/R/plot_dcCA_CWM_SNC.R | 22 douconca-1.2.2/douconca/R/plot_species_scores_bk.R | 2 douconca-1.2.2/douconca/R/predict.dcca.R | 122 ++- douconca-1.2.2/douconca/R/predict_functions.R | 292 +++++-- douconca-1.2.2/douconca/R/print.dcca.R | 2 douconca-1.2.2/douconca/R/print.wrda.R | 2 douconca-1.2.2/douconca/R/scores.dcca.R | 10 douconca-1.2.2/douconca/R/scores.wrda.R | 10 douconca-1.2.2/douconca/R/scores_dcca.R | 98 +- douconca-1.2.2/douconca/R/wrda.R | 2 douconca-1.2.2/douconca/README.md | 9 douconca-1.2.2/douconca/build/partial.rdb |binary douconca-1.2.2/douconca/build/vignette.rds |binary douconca-1.2.2/douconca/demo/00Index | 2 douconca-1.2.2/douconca/demo/dune_dcCA.R | 10 douconca-1.2.2/douconca/demo/dune_dcCA_coef.R |only douconca-1.2.2/douconca/demo/dune_dcCA_fitted.R |only douconca-1.2.2/douconca/demo/dune_dcCA_predict.R | 43 - douconca-1.2.2/douconca/demo/dune_test.R | 2 douconca-1.2.2/douconca/inst/doc/douconca.html | 106 +- douconca-1.2.2/douconca/inst/tinytest/anova_byaxis_wrda |only douconca-1.2.2/douconca/inst/tinytest/anova_dccaDivF |only douconca-1.2.2/douconca/inst/tinytest/anova_dccaDivT |only douconca-1.2.2/douconca/inst/tinytest/anova_wrda |only douconca-1.2.2/douconca/inst/tinytest/modDivF1a_an |only douconca-1.2.2/douconca/inst/tinytest/modDivFq11_an |only douconca-1.2.2/douconca/inst/tinytest/modDivT1a_an |only douconca-1.2.2/douconca/inst/tinytest/modDivTq11_an |only douconca-1.2.2/douconca/inst/tinytest/modq11_predDivFenv |only douconca-1.2.2/douconca/inst/tinytest/modq11_predDivFtraits |only douconca-1.2.2/douconca/inst/tinytest/modq11_predDivTenv |only douconca-1.2.2/douconca/inst/tinytest/modq11_predDivTtraits |only douconca-1.2.2/douconca/inst/tinytest/plotdat_dcca |binary douconca-1.2.2/douconca/inst/tinytest/predDivF1a_env |only douconca-1.2.2/douconca/inst/tinytest/predDivF1a_env1 |only douconca-1.2.2/douconca/inst/tinytest/predDivF1a_reg |only douconca-1.2.2/douconca/inst/tinytest/predDivF1a_reg1 |only douconca-1.2.2/douconca/inst/tinytest/predDivF1a_reg_traits |only douconca-1.2.2/douconca/inst/tinytest/predDivF1a_reg_traits1 |only douconca-1.2.2/douconca/inst/tinytest/predDivF1a_response |only douconca-1.2.2/douconca/inst/tinytest/predDivF1a_response1 |only douconca-1.2.2/douconca/inst/tinytest/predDivF1a_traits |only douconca-1.2.2/douconca/inst/tinytest/predDivF1a_traits1 |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_env |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_env1 |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_reg |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_reg1 |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_reg_traits |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_reg_traits1 |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_response |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_response1 |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_traits |only douconca-1.2.2/douconca/inst/tinytest/predDivT1a_traits1 |only douconca-1.2.2/douconca/inst/tinytest/scores_dccaA11DivF_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_dccav_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_mod_DivF1a_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_mod_DivF_fact_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_mod_DivFc_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_mod_DivFq11_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_mod_DivT1a_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_mod_DivT_fact_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_mod_DivTc_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_mod_DivTq11_abs |only douconca-1.2.2/douconca/inst/tinytest/scores_wrda_abs |binary douconca-1.2.2/douconca/inst/tinytest/test_anova.dcca.R |only douconca-1.2.2/douconca/inst/tinytest/test_anova.dccav.R |only douconca-1.2.2/douconca/inst/tinytest/test_dcca.R | 329 +++++++- douconca-1.2.2/douconca/inst/tinytest/test_dccav.R |only douconca-1.2.2/douconca/inst/tinytest/test_fCWMSNC.R | 228 ++++- douconca-1.2.2/douconca/inst/tinytest/test_fCWMSNCv.R |only douconca-1.2.2/douconca/inst/tinytest/test_plot.dcca.R | 121 +-- douconca-1.2.2/douconca/inst/tinytest/test_predict.dcca.R | 374 +++++++-- douconca-1.2.2/douconca/inst/tinytest/test_predict.dccav.R |only douconca-1.2.2/douconca/inst/tinytest/test_wrda.R | 14 douconca-1.2.2/douconca/man/anova.dcca.Rd | 4 douconca-1.2.2/douconca/man/anova_sites.Rd | 2 douconca-1.2.2/douconca/man/anova_species.Rd | 2 douconca-1.2.2/douconca/man/coef.dcca.Rd |only douconca-1.2.2/douconca/man/dc_CA.Rd | 45 - douconca-1.2.2/douconca/man/fCWM_SNC.Rd | 7 douconca-1.2.2/douconca/man/fitted.dcca.Rd |only douconca-1.2.2/douconca/man/getPlotdata.Rd | 8 douconca-1.2.2/douconca/man/plot.dcca.Rd | 273 +++---- douconca-1.2.2/douconca/man/plot_dcCA_CWM_SNC.Rd | 18 douconca-1.2.2/douconca/man/predict.dcca.Rd | 109 +- douconca-1.2.2/douconca/man/print.dcca.Rd | 10 douconca-1.2.2/douconca/man/scores.dcca.Rd | 15 douconca-1.2.2/douconca/man/scores.wrda.Rd | 5 114 files changed, 2280 insertions(+), 1279 deletions(-)
Title: R Wrapper for 'pikchr' (PIC) Diagram Language
Description: An 'R' interface to 'pikchr' (<https://pikchr.org>, pronounced “picture”), a 'PIC'-like markup language for creating diagrams within technical documentation. Originally developed by Brian Kernighan, 'PIC' has been adapted into 'pikchr' by D. Richard Hipp, the creator of 'SQLite'. 'pikchr' is designed to be embedded in fenced code blocks of Markdown or other documentation markup languages, making it ideal for generating diagrams in text-based formats. This package allows R users to seamlessly integrate the descriptive syntax of 'pikchr' for diagram creation directly within the 'R' environment.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Richard Hipp [ctb],
Brian Kernighan [ctb]
Maintainer: Andre Leite <leite@castlab.org>
Diff between pikchr versions 0.97 dated 2024-09-30 and 1.0 dated 2024-12-02
DESCRIPTION | 14 MD5 | 38 NAMESPACE | 1 NEWS.md |only R/engine.R | 87 +- R/pikchrWrappers.R | 48 + R/zzz.R | 1 README.md |only build/vignette.rds |binary data |only inst/doc/Examples.R | 4 inst/doc/Examples.Rmd | 226 ++++- inst/doc/Examples.html | 2007 ++++++++++++++++++++++++++++--------------------- inst/doc/userman.R |only inst/doc/userman.Rmd |only inst/doc/userman.html |only man/eng_pikchr.Rd | 3 man/figures |only man/google_fonts.Rd |only man/pikchr.Rd | 8 vignettes/Examples.Rmd | 226 ++++- vignettes/userman.Rmd |only 22 files changed, 1721 insertions(+), 942 deletions(-)
Title: A Simple Interface for Interacting with 'WebDAV' Servers
Description: An easy-to-use interface for interacting with 'WebDAV' servers,
including 'OwnCloud'. It simplifies the use of 'WebDAV' methods such as COPY, MKCOL, MOVE, and others.
With built-in authentication and request handling, it allows for easy
management of files and directories over the 'WebDAV' protocol.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between webdav versions 0.1.1 dated 2024-10-08 and 0.1.2 dated 2024-12-02
DESCRIPTION | 11 - MD5 | 19 ++- NEWS.md |only README.md | 270 +++----------------------------------------- build/vignette.rds |binary inst/doc/env_variables.Rmd | 8 - inst/doc/env_variables.html | 26 ++-- inst/doc/webdav.R |only inst/doc/webdav.Rmd |only inst/doc/webdav.html |only man/figures |only vignettes/env_variables.Rmd | 8 - vignettes/webdav.Rmd |only 13 files changed, 62 insertions(+), 280 deletions(-)
Title: Spatial Regression Analysis
Description: A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep'. These model fitting functions include maximum likelihood methods for cross-sectional models proposed by 'Cliff' and 'Ord' (1973, ISBN:0850860369) and (1981, ISBN:0850860814), fitting methods initially described by 'Ord' (1975) <doi:10.1080/01621459.1975.10480272>. The models are further described by 'Anselin' (1988) <doi:10.1007/978-94-015-7799-1>. Spatial two stage least squares and spatial general method of moment models initially proposed by 'Kelejian' and 'Prucha' (1998) <doi:10.1023/A:1007707430416> and (1999) <doi:10.1111/1468-2354.00027> are provided. Impact methods and MCMC fitting methods proposed by 'LeSage' and 'Pace' (2009) <doi:10.1201/9781420064254> are implemented for the family of cross-sectional spatial regression models. Methods for fitting the log determinant term in maximu [...truncated...]
Author: Roger Bivand [cre, aut] ,
Gianfranco Piras [aut],
Luc Anselin [ctb],
Andrew Bernat [ctb],
Eric Blankmeyer [ctb],
Yongwan Chun [ctb],
Virgilio Gomez-Rubio [ctb],
Daniel Griffith [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
James LeSage [ctb],
Ange [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spatialreg versions 1.3-5 dated 2024-08-19 and 1.3-6 dated 2024-12-02
DESCRIPTION | 12 MD5 | 26 - NAMESPACE | 2 NEWS.md | 8 R/kpgm_new.R | 10 R/s2sls.R | 766 ++++++++++++++++++++------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/SpatialFiltering.html | 57 +- inst/doc/nb_igraph.html | 7 inst/doc/sids_models.html | 5 inst/tinytest/test_TR_20_07_20.R | 3 man/gstsls.Rd | 3 man/stsls.Rd | 17 14 files changed, 481 insertions(+), 435 deletions(-)
Title: REDCap Metadata Casting and Castellated Data Handling
Description: Casting metadata for REDCap database creation and handling of
castellated data using repeated instruments and longitudinal projects in
'REDCap'. Keeps a focused data export approach, by allowing to only export
required data from the database. Also for casting new REDCap databases based
on datasets from other sources.
Originally forked from the R part of 'REDCapRITS' by Paul Egeler.
See <https://github.com/pegeler/REDCapRITS>.
'REDCap' (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for
tracking data manipulation and export procedures; 3) automated export
procedures for seamless data downloads to common statistical packages; and
4) procedures for data integration and interoperability with external
sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>;
Harris et al (2019) <doi:10.1016/j.jbi.2019.103208> [...truncated...]
Author: Andreas Gammelgaard Damsbo [aut, cre]
,
Paul Egeler [aut]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between REDCapCAST versions 24.11.2 dated 2024-11-22 and 24.12.1 dated 2024-12-02
REDCapCAST-24.11.2/REDCapCAST/R/ds2dd.R |only REDCapCAST-24.11.2/REDCapCAST/inst/shiny-examples/casting/server.R |only REDCapCAST-24.11.2/REDCapCAST/inst/shiny-examples/casting/ui.R |only REDCapCAST-24.12.1/REDCapCAST/DESCRIPTION | 14 REDCapCAST-24.12.1/REDCapCAST/MD5 | 104 REDCapCAST-24.12.1/REDCapCAST/NAMESPACE | 11 REDCapCAST-24.12.1/REDCapCAST/NEWS.md | 17 REDCapCAST-24.12.1/REDCapCAST/R/REDCap_split.r | 11 REDCapCAST-24.12.1/REDCapCAST/R/as_factor.R | 136 - REDCapCAST-24.12.1/REDCapCAST/R/ds2dd_detailed.R | 110 - REDCapCAST-24.12.1/REDCapCAST/R/easy_redcap.R | 28 REDCapCAST-24.12.1/REDCapCAST/R/export_redcap_instrument.R | 22 REDCapCAST-24.12.1/REDCapCAST/R/fct_drop.R |only REDCapCAST-24.12.1/REDCapCAST/R/read_redcap_tables.R | 141 + REDCapCAST-24.12.1/REDCapCAST/R/redcap_wider.R | 112 - REDCapCAST-24.12.1/REDCapCAST/R/redcapcast_meta.R | 2 REDCapCAST-24.12.1/REDCapCAST/R/sysdata.rda |binary REDCapCAST-24.12.1/REDCapCAST/R/utils.r | 34 REDCapCAST-24.12.1/REDCapCAST/build/vignette.rds |binary REDCapCAST-24.12.1/REDCapCAST/inst/WORDLIST | 8 REDCapCAST-24.12.1/REDCapCAST/inst/doc/Database-creation.R | 14 REDCapCAST-24.12.1/REDCapCAST/inst/doc/Database-creation.Rmd | 2 REDCapCAST-24.12.1/REDCapCAST/inst/doc/Database-creation.html | 641 ------ REDCapCAST-24.12.1/REDCapCAST/inst/doc/REDCapCAST.R | 39 REDCapCAST-24.12.1/REDCapCAST/inst/doc/REDCapCAST.Rmd | 78 REDCapCAST-24.12.1/REDCapCAST/inst/doc/REDCapCAST.html | 1043 +++++++--- REDCapCAST-24.12.1/REDCapCAST/inst/doc/Shiny-app.R |only REDCapCAST-24.12.1/REDCapCAST/inst/doc/Shiny-app.Rmd |only REDCapCAST-24.12.1/REDCapCAST/inst/doc/Shiny-app.html |only REDCapCAST-24.12.1/REDCapCAST/inst/shiny-examples/casting/app.R |only REDCapCAST-24.12.1/REDCapCAST/inst/shiny-examples/casting/rsconnect |only REDCapCAST-24.12.1/REDCapCAST/man/REDCapCAST-package.Rd | 2 REDCapCAST-24.12.1/REDCapCAST/man/REDCap_split.Rd | 11 REDCapCAST-24.12.1/REDCapCAST/man/all_na.Rd | 2 REDCapCAST-24.12.1/REDCapCAST/man/apply_factor_labels.Rd |only REDCapCAST-24.12.1/REDCapCAST/man/apply_field_label.Rd |only REDCapCAST-24.12.1/REDCapCAST/man/as_factor.Rd | 10 REDCapCAST-24.12.1/REDCapCAST/man/clean_field_label.Rd |only REDCapCAST-24.12.1/REDCapCAST/man/create_instrument_meta.Rd | 8 REDCapCAST-24.12.1/REDCapCAST/man/ds2dd.Rd | 6 REDCapCAST-24.12.1/REDCapCAST/man/ds2dd_detailed.Rd | 5 REDCapCAST-24.12.1/REDCapCAST/man/easy_redcap.Rd | 9 REDCapCAST-24.12.1/REDCapCAST/man/export_redcap_instrument.Rd | 4 REDCapCAST-24.12.1/REDCapCAST/man/fct2num.Rd | 16 REDCapCAST-24.12.1/REDCapCAST/man/fct_drop.Rd |only REDCapCAST-24.12.1/REDCapCAST/man/format_redcap_factor.Rd |only REDCapCAST-24.12.1/REDCapCAST/man/get_api_key.Rd | 8 REDCapCAST-24.12.1/REDCapCAST/man/is.labelled.Rd |only REDCapCAST-24.12.1/REDCapCAST/man/named_levels.Rd | 18 REDCapCAST-24.12.1/REDCapCAST/man/possibly_numeric.Rd |only REDCapCAST-24.12.1/REDCapCAST/man/possibly_roman.Rd | 8 REDCapCAST-24.12.1/REDCapCAST/man/read_redcap_tables.Rd | 25 REDCapCAST-24.12.1/REDCapCAST/man/redcap_wider.Rd | 20 REDCapCAST-24.12.1/REDCapCAST/man/redcapcast_meta.Rd | 2 REDCapCAST-24.12.1/REDCapCAST/man/sanitize_split.Rd | 9 REDCapCAST-24.12.1/REDCapCAST/man/suffix2label.Rd |only REDCapCAST-24.12.1/REDCapCAST/tests/testthat/test-as_factor.R |only REDCapCAST-24.12.1/REDCapCAST/tests/testthat/test-ds2dd.R | 31 REDCapCAST-24.12.1/REDCapCAST/tests/testthat/test-redcap_wider.R | 16 REDCapCAST-24.12.1/REDCapCAST/vignettes/Database-creation.Rmd | 2 REDCapCAST-24.12.1/REDCapCAST/vignettes/REDCapCAST.Rmd | 78 REDCapCAST-24.12.1/REDCapCAST/vignettes/Shiny-app.Rmd |only 62 files changed, 1711 insertions(+), 1146 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@data-intuitive.com>
Diff between laminr versions 0.2.0 dated 2024-11-20 and 0.3.0 dated 2024-12-02
laminr-0.2.0/laminr/tests/testthat/helper-setup_lamindata_instance.R |only laminr-0.2.0/laminr/tests/testthat/test-connect_lamindata.R |only laminr-0.2.0/laminr/vignettes/example_workflow.Rmd |only laminr-0.3.0/laminr/DESCRIPTION | 15 laminr-0.3.0/laminr/MD5 | 52 +- laminr-0.3.0/laminr/R/Artifact.R | 52 +- laminr-0.3.0/laminr/R/Instance.R | 58 +- laminr-0.3.0/laminr/R/InstanceAPI.R | 64 -- laminr-0.3.0/laminr/R/connect.R | 5 laminr-0.3.0/laminr/R/save_active_file.R |only laminr-0.3.0/laminr/R/settings_store.R | 3 laminr-0.3.0/laminr/R/utils.R | 125 ++++ laminr-0.3.0/laminr/README.md | 71 +- laminr-0.3.0/laminr/inst/doc/architecture.R | 1 laminr-0.3.0/laminr/inst/doc/architecture.html | 1 laminr-0.3.0/laminr/inst/doc/architecture.qmd | 1 laminr-0.3.0/laminr/inst/doc/development.html | 20 laminr-0.3.0/laminr/inst/doc/development.qmd | 14 laminr-0.3.0/laminr/inst/rstudio |only laminr-0.3.0/laminr/man/laminr-package.Rd | 2 laminr-0.3.0/laminr/tests/testthat/helper-skip_if_not_logged_in.R |only laminr-0.3.0/laminr/tests/testthat/test-Artifact.R | 8 laminr-0.3.0/laminr/tests/testthat/test-Registry.R | 6 laminr-0.3.0/laminr/tests/testthat/test-RelatedRecords.R | 2 laminr-0.3.0/laminr/tests/testthat/test-connect.R |only laminr-0.3.0/laminr/tests/testthat/test-instance_api.R | 10 laminr-0.3.0/laminr/tests/testthat/test-utils.R | 15 laminr-0.3.0/laminr/vignettes/architecture.qmd | 1 laminr-0.3.0/laminr/vignettes/concepts_features.Rmd |only laminr-0.3.0/laminr/vignettes/development.qmd | 14 laminr-0.3.0/laminr/vignettes/laminr.Rmd | 260 ++++++---- 31 files changed, 530 insertions(+), 270 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, simulation, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX and html code,
recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.
Author: Frank E Harrell Jr [aut, cre] ,
Charles Dupont [ctb]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between Hmisc versions 5.2-0 dated 2024-10-28 and 5.2-1 dated 2024-12-02
DESCRIPTION | 8 +-- MD5 | 18 ++++--- NAMESPACE | 2 NEWS | 6 ++ R/label.s | 8 +-- R/qrxcenter.r |only R/rcorr.s | 2 man/qrxcenter.Rd |only man/rcorr.Rd | 2 man/varclus.Rd | 5 ++ src/rcorr.f90 | 125 ++++++++++++++----------------------------------------- 11 files changed, 65 insertions(+), 111 deletions(-)
Title: Efficient Serialization of R Objects
Description: Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Francesc Alted [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs2 versions 0.1.2 dated 2024-11-24 and 0.1.3 dated 2024-12-02
ChangeLog | 5 ++++- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/qs_unwind_protect.h | 12 ++++++++++-- src/qx_file_headers.h | 1 + src/qx_functions.cpp | 29 ++++++++++++++--------------- 6 files changed, 38 insertions(+), 27 deletions(-)
Title: A Way to Perform Code Review or QA on Other Packages
Description: Reviews other packages during code review by looking at their
dependencies, code style, code complexity, and how internally defined
functions interact with one another.
Author: Maarten van Kessel [aut, cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
Diff between PaRe versions 0.1.14 dated 2024-11-29 and 0.1.15 dated 2024-12-02
PaRe-0.1.14/PaRe/tests/testthat/helper-makeRepo.R |only PaRe-0.1.15/PaRe/DESCRIPTION | 8 - PaRe-0.1.15/PaRe/MD5 | 28 ++-- PaRe-0.1.15/PaRe/build/vignette.rds |binary PaRe-0.1.15/PaRe/inst/doc/Documentation.R | 84 +++++++------- PaRe-0.1.15/PaRe/inst/doc/Documentation.html | 26 ++-- PaRe-0.1.15/PaRe/tests/testthat/helper-checkSuggests.R | 3 PaRe-0.1.15/PaRe/tests/testthat/setup.R |only PaRe-0.1.15/PaRe/tests/testthat/test-addPareArticle.R | 6 - PaRe-0.1.15/PaRe/tests/testthat/test-checkDependencies.R | 17 +- PaRe-0.1.15/PaRe/tests/testthat/test-getApplyCall.R | 11 - PaRe-0.1.15/PaRe/tests/testthat/test-getDlplyCall.R | 11 - PaRe-0.1.15/PaRe/tests/testthat/test-getDoCall.R | 11 - PaRe-0.1.15/PaRe/tests/testthat/test-getDoCallFromLines.R | 3 PaRe-0.1.15/PaRe/tests/testthat/test-getFunCall.R | 8 - PaRe-0.1.15/PaRe/tests/testthat/test-getMultiLineFun.R | 8 - 16 files changed, 111 insertions(+), 113 deletions(-)
Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T
in various applications. A 100(1-alpha)% global envelope is a band bounded by two
vectors such that the probability that T falls outside this envelope in any of the d
points is equal to alpha. Global means that the probability is controlled simultaneously
for all the d elements of the vectors. The global envelopes can be used for graphical
Monte Carlo and permutation tests where the test statistic is a multivariate vector or
function (e.g. goodness-of-fit testing for point patterns and random sets, functional
analysis of variance, functional general linear model, n-sample test of correspondence
of distribution functions), for central regions of functional or multivariate data (e.g.
outlier detection, functional boxplot) and for global confidence and prediction bands
(e.g. confidence band in polynomial regression, Bayesian posterior prediction). See
Myllymäki and Mrkvička (2024) <doi:10.18637/jss.v111.i03 [...truncated...]
Author: Mari Myllymaeki [aut, cre],
Tomas Mrkvicka [aut],
Mikko Kuronen [ctb],
Jiri Dvorak [ctb],
Pavel Grabarnik [ctb],
Ute Hahn [ctb],
Michael Rost [ctb],
Henri Seijo [ctb]
Maintainer: Mari Myllymaeki <mari.myllymaki@luke.fi>
Diff between GET versions 1.0-3 dated 2024-08-19 and 1.0-4 dated 2024-12-02
DESCRIPTION | 12 +- MD5 | 58 +++++----- NEWS | 4 R/GET-package.r | 10 + R/adjusted_envelopes.r | 4 R/combined_envelope_tests.R | 4 R/deviation.r | 17 ++- R/deviation_test.r | 35 ++++-- R/envelopes.r | 17 +-- R/forder.r | 8 + R/glm.R | 4 R/graphfanova.r | 2 R/rq.R | 2 README.md | 7 - inst/CITATION | 169 +++++++++++-------------------- inst/doc/FDRenvelopes.pdf |binary inst/doc/GET.pdf |binary inst/doc/HotSpots.pdf |binary inst/doc/QuantileRegression.pdf |binary inst/doc/pointpatterns.pdf |binary man/GET-package.Rd | 10 + man/GET.composite.Rd | 4 man/central_region.Rd | 2 man/combined_scaled_MAD_envelope_test.Rd | 4 man/deviation_test.Rd | 25 +++- man/global_envelope_test.Rd | 4 man/global_rq.Rd | 2 man/graph.fanova.Rd | 2 man/graph.flm.Rd | 4 tests/testthat/test-MAD.R | 7 + 30 files changed, 221 insertions(+), 196 deletions(-)
Title: Diagnostic Index Expectation Maximisation in R
Description: Likelihood-based genome polarisation finds which alleles of genomic markers
belong to which side of the barrier.
Co-estimates which individuals belong to either side of the barrier and barrier strength.
Uses expectation maximisation in likelihood framework. The method is described in
Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.4.1 dated 2024-09-23 and 1.4.2 dated 2024-12-02
DESCRIPTION | 6 MD5 | 34 +- NAMESPACE | 1 NEWS.md | 8 R/internal.r | 122 +++++++--- R/rank2map.r | 11 R/smoothPolarizedGenotypes.r | 64 +++-- R/vcf2diem.r | 11 inst/doc/Importing-data-for-genome-polarisation.html | 4 inst/doc/Understanding-genome-polarisation-output-files.html | 4 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.R | 2 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 2 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 6 man/rank2map.Rd | 7 man/smoothPolarizedGenotypes.Rd | 39 ++- man/truncatedLaplace.Rd |only man/unbiasedWeightedStateChoice.Rd |only tests/testthat/test_internal.r | 59 ++++ vignettes/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 2 19 files changed, 281 insertions(+), 101 deletions(-)
Title: Bayesian partial least squares regression
Description: Fits the Bayesian partial least squares regression model
introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable
for univariate and multivariate regression with high-dimensional data.
Author: Szymon Urbas [aut, cre],
Pierre Lovera [ctb],
Robert Daly [ctb],
Alan O'Riordan [ctb],
Donagh Berry [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Szymon Urbas <szymon.urbas@mu.ie>
Diff between bplsr versions 1.0.0 dated 2024-11-12 and 1.0.1 dated 2024-12-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/BPLSR.R | 4 ++-- README.md | 8 ++++++++ man/bplsr.Rd | 6 +++--- 5 files changed, 21 insertions(+), 13 deletions(-)
Title: Tidy Finance Helper Functions
Description: Helper functions for empirical research in financial
economics, addressing a variety of topics covered in Scheuch, Voigt,
and Weiss (2023) <doi:10.1201/b23237>. The package is designed to
provide shortcuts for issues extensively discussed in the book,
facilitating easier application of its concepts. For more information
and resources related to the book, visit
<https://www.tidy-finance.org/r/index.html>.
Author: Christoph Scheuch [aut, cre, cph]
,
Stefan Voigt [aut, cph] ,
Patrick Weiss [aut, cph] ,
Maximilian Muecke [ctb]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between tidyfinance versions 0.4.1 dated 2024-09-04 and 0.4.2 dated 2024-12-02
DESCRIPTION | 23 - MD5 | 59 ++-- NAMESPACE | 4 NEWS.md | 16 + R/add_lag_columns.R |only R/compute_long_short_returns.R | 2 R/data_options.R | 8 R/download_data_factors.R | 29 ++ R/download_data_macro_predictors.R | 30 ++ R/download_data_osap.R | 13 - R/download_data_wrds_ccm_links.R | 23 - R/global_variables.R | 2 R/handle_download_error.R |only R/lag_column.R | 2 R/tidyfinance-package.R | 2 R/winsorize.R | 7 README.md | 14 - inst/doc/dates-in-tidyfinance.R | 92 +++---- inst/doc/dates-in-tidyfinance.html | 230 +++++++++---------- inst/doc/using-tidyfinance.R | 16 - inst/doc/using-tidyfinance.Rmd | 3 inst/doc/using-tidyfinance.html | 35 -- man/add_lag_columns.Rd |only man/data_options.Rd | 3 man/download_data_factors_q.Rd | 1 man/download_data_macro_predictors.Rd | 2 man/download_data_wrds_ccm_links.Rd | 17 - man/lag_column.Rd | 2 man/tidyfinance-package.Rd | 6 tests/testthat/test-add_lag_columns.R |only tests/testthat/test-download_data_factors.R |only tests/testthat/test-download_data_macro_predictors.R |only tests/testthat/test-download_data_osap.R |only vignettes/using-tidyfinance.Rmd | 3 34 files changed, 360 insertions(+), 284 deletions(-)
Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2021) <doi:10.1016/j.insmatheco.2020.11.010> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] ,
Sander Devriendt [aut],
Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens.r@gmail.com>
Diff between smurf versions 1.1.5 dated 2023-03-22 and 1.1.6 dated 2024-12-02
DESCRIPTION | 14 ++--- MD5 | 14 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 9 +++ inst/doc/smurf.R | 124 +++++++++++++++++++++++++-------------------------- inst/doc/smurf.html | 15 +++--- man/smurf-package.Rd | 2 8 files changed, 94 insertions(+), 84 deletions(-)
Title: Robust Sparse PCA using the ROSPCA Algorithm
Description: Implementation of robust sparse PCA using the ROSPCA algorithm
of Hubert et al. (2016) <DOI:10.1080/00401706.2015.1093962>.
Author: Tom Reynkens [aut, cre] ,
Valentin Todorov [ctb] ,
Mia Hubert [ctb],
Eric Schmitt [ctb],
Tim Verdonck [ctb]
Maintainer: Tom Reynkens <tomreynkens.r@gmail.com>
Diff between rospca versions 1.1.0 dated 2024-03-31 and 1.1.1 dated 2024-12-02
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/Robpca.R | 2 +- R/Rospca.R | 2 +- inst/NEWS.Rd | 10 +++++++++- 5 files changed, 21 insertions(+), 13 deletions(-)
Title: Functions from "Reinsurance: Actuarial and Statistical Aspects"
Description: Functions from the book "Reinsurance: Actuarial and Statistical Aspects" (2017) by Hansjoerg Albrecher, Jan Beirlant and Jef Teugels <https://www.wiley.com/en-us/Reinsurance%3A+Actuarial+and+Statistical+Aspects-p-9780470772683>.
Author: Tom Reynkens [aut, cre] ,
Roel Verbelen [aut] ,
Anastasios Bardoutsos [ctb] ,
Dries Cornilly [ctb] ,
Yuri Goegebeur [ctb] ,
Klaus Herrmann [ctb]
Maintainer: Tom Reynkens <tomreynkens.r@gmail.com>
Diff between ReIns versions 1.0.14 dated 2023-11-03 and 1.0.15 dated 2024-12-02
DESCRIPTION | 12 ++++---- MD5 | 10 +++--- build/vignette.rds |binary inst/NEWS.Rd | 9 ++++-- inst/doc/ReIns.R | 8 ++--- inst/doc/ReIns.html | 77 ++++++++++++++++++++++++++-------------------------- 6 files changed, 61 insertions(+), 55 deletions(-)
Title: Professional Comprehensive Omics Data Analysis
Description: Provides a comprehensive suite of tools for analyzing omics data. It includes functionalities for alpha diversity analysis, beta
diversity analysis, differential abundance analysis, community assembly analysis, visualization of phylogenetic tree, and
functional enrichment analysis. With a progressive approach, the package offers a range of analysis methods to explore and
understand the complex communities. It is designed to support researchers and practitioners in conducting in-depth and
professional omics data analysis.
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Diff between pctax versions 0.1.1 dated 2024-04-10 and 0.1.3 dated 2024-12-02
pctax-0.1.1/pctax/vignettes/pctax_cache/html/lib_bec07e0751cc99eaa0386bda0f0304cb.rdb |only pctax-0.1.1/pctax/vignettes/pctax_cache/html/lib_bec07e0751cc99eaa0386bda0f0304cb.rdx |only pctax-0.1.1/pctax/vignettes/pctax_cache/html/setup_a4314fb22343ed0d94f461570354dd3f.rdb |only pctax-0.1.1/pctax/vignettes/pctax_cache/html/setup_a4314fb22343ed0d94f461570354dd3f.rdx |only pctax-0.1.1/pctax/vignettes/pctax_cache/html/unnamed-chunk-2_41a4a46e9455db91e15ad66260bed593.rdb |only pctax-0.1.1/pctax/vignettes/pctax_cache/html/unnamed-chunk-2_41a4a46e9455db91e15ad66260bed593.rdx |only pctax-0.1.3/pctax/DESCRIPTION | 28 pctax-0.1.3/pctax/MD5 | 87 +- pctax-0.1.3/pctax/NAMESPACE | 3 pctax-0.1.3/pctax/NEWS.md | 17 pctax-0.1.3/pctax/R/Rtaxonkit.R | 50 - pctax-0.1.3/pctax/R/a_diversity.R | 4 pctax-0.1.3/pctax/R/b_analyse.R | 14 pctax-0.1.3/pctax/R/data.R | 12 pctax-0.1.3/pctax/R/diff_analyse.R | 8 pctax-0.1.3/pctax/R/eco_micro.R | 11 pctax-0.1.3/pctax/R/functional.R | 27 pctax-0.1.3/pctax/R/other_software.R | 60 + pctax-0.1.3/pctax/R/pctax-package.R | 2 pctax-0.1.3/pctax/R/phylogenetic.R | 434 +++++++++- pctax-0.1.3/pctax/README.md | 27 pctax-0.1.3/pctax/data/all_ec_info.rda |binary pctax-0.1.3/pctax/data/all_sp_la_zh_name.rda |only pctax-0.1.3/pctax/inst/doc/pctax.html | 2 pctax-0.1.3/pctax/man/all_sp_la_zh_name.Rd |only pctax-0.1.3/pctax/man/ann_tree.Rd | 3 pctax-0.1.3/pctax/man/b_analyse.Rd | 2 pctax-0.1.3/pctax/man/check_taxonkit.Rd | 13 pctax-0.1.3/pctax/man/convert_taxon_name.Rd |only pctax-0.1.3/pctax/man/download_taxonkit_dataset.Rd | 13 pctax-0.1.3/pctax/man/figures/README-unnamed-chunk-2-1.png |binary pctax-0.1.3/pctax/man/figures/README-unnamed-chunk-3-1.png |only pctax-0.1.3/pctax/man/geo_sim.Rd | 3 pctax-0.1.3/pctax/man/get_all_sp_la_zh_name.Rd |only pctax-0.1.3/pctax/man/install_taxonkit.Rd | 13 pctax-0.1.3/pctax/man/name_or_id2df.Rd | 13 pctax-0.1.3/pctax/man/ncm.Rd | 3 pctax-0.1.3/pctax/man/plot.a_res.Rd | 2 pctax-0.1.3/pctax/man/plot_element_cycle.Rd | 3 pctax-0.1.3/pctax/man/plot_two_tree.Rd |only pctax-0.1.3/pctax/man/tax_lca.Rd |only pctax-0.1.3/pctax/man/taxonkit_filter.Rd | 13 pctax-0.1.3/pctax/man/taxonkit_lca.Rd | 13 pctax-0.1.3/pctax/man/taxonkit_lineage.Rd | 13 pctax-0.1.3/pctax/man/taxonkit_list.Rd | 13 pctax-0.1.3/pctax/man/taxonkit_name2taxid.Rd | 13 pctax-0.1.3/pctax/man/taxonkit_reformat.Rd | 13 pctax-0.1.3/pctax/man/z_diversity.Rd | 2 pctax-0.1.3/pctax/vignettes/pctax_cache/html/lib_edaa109a9155baa43419851f33b3cf81.rdb |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/lib_edaa109a9155baa43419851f33b3cf81.rdx |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/setup_8ae11416e5c5639c1c730c1286b53fc5.rdb |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/setup_8ae11416e5c5639c1c730c1286b53fc5.rdx |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/unnamed-chunk-2_a4c6eae63fe4b35c079f4cfe25d48d88.rdb |only pctax-0.1.3/pctax/vignettes/pctax_cache/html/unnamed-chunk-2_a4c6eae63fe4b35c079f4cfe25d48d88.rdx |only 54 files changed, 810 insertions(+), 124 deletions(-)
Title: Multiple Imputation Through 'XGBoost'
Description: Multiple imputation using 'XGBoost', subsampling, and predictive mean
matching as described in Deng and Lumley (2023)
<doi:10.1080/10618600.2023.2252501>. The package supports various types of
variables, offers flexible settings, and enables saving an imputation model to impute
new data. Data processing and memory usage have been optimised to speed up
the imputation process.
Author: Yongshi Deng [aut, cre] ,
Thomas Lumley [ths]
Maintainer: Yongshi Deng <agnes.yongshideng@gmail.com>
Diff between mixgb versions 1.0.2 dated 2023-02-16 and 1.5.2 dated 2024-12-02
mixgb-1.0.2/mixgb/R/plot_1var.R |only mixgb-1.0.2/mixgb/R/plot_2vars.R |only mixgb-1.0.2/mixgb/R/plot_3vars.R |only mixgb-1.0.2/mixgb/man/plot_1num1fac.Rd |only mixgb-1.0.2/mixgb/man/plot_1num2fac.Rd |only mixgb-1.0.2/mixgb/man/plot_2fac.Rd |only mixgb-1.0.2/mixgb/man/plot_2num.Rd |only mixgb-1.0.2/mixgb/man/plot_2num1fac.Rd |only mixgb-1.0.2/mixgb/man/plot_bar.Rd |only mixgb-1.0.2/mixgb/man/plot_box.Rd |only mixgb-1.0.2/mixgb/man/plot_hist.Rd |only mixgb-1.0.2/mixgb/vignettes/web |only mixgb-1.5.2/mixgb/DESCRIPTION | 39 mixgb-1.5.2/mixgb/MD5 | 131 - mixgb-1.5.2/mixgb/NAMESPACE | 99 - mixgb-1.5.2/mixgb/NEWS.md |only mixgb-1.5.2/mixgb/R/RcppExports.R |only mixgb-1.5.2/mixgb/R/createNA.R | 140 - mixgb-1.5.2/mixgb/R/data_clean.R | 308 +-- mixgb-1.5.2/mixgb/R/data_preprocess.R | 194 +- mixgb-1.5.2/mixgb/R/globals.R | 14 mixgb-1.5.2/mixgb/R/impute_new.R | 438 ++-- mixgb-1.5.2/mixgb/R/initial_imp.R | 492 ++--- mixgb-1.5.2/mixgb/R/initial_impnew.R | 508 ++--- mixgb-1.5.2/mixgb/R/mixgb-package.R | 61 mixgb-1.5.2/mixgb/R/mixgb.R | 921 ++++++---- mixgb-1.5.2/mixgb/R/mixgb_boot.R | 382 ++-- mixgb-1.5.2/mixgb/R/mixgb_boot_xgb_save.R |only mixgb-1.5.2/mixgb/R/mixgb_bootsave.R | 624 +++--- mixgb-1.5.2/mixgb/R/mixgb_cv.R | 203 +- mixgb-1.5.2/mixgb/R/mixgb_load_use.R |only mixgb-1.5.2/mixgb/R/mixgb_null.R | 426 +++- mixgb-1.5.2/mixgb/R/mixgb_save.R | 783 ++++++-- mixgb-1.5.2/mixgb/R/mixgb_use.R | 256 +- mixgb-1.5.2/mixgb/R/mixgb_xgb_save.R |only mixgb-1.5.2/mixgb/R/nhanes3.R | 48 mixgb-1.5.2/mixgb/R/nhanes3_newborn.R | 68 mixgb-1.5.2/mixgb/R/pmm.R | 82 mixgb-1.5.2/mixgb/R/save_vars.R | 98 - mixgb-1.5.2/mixgb/R/save_yhatobs.R | 687 +++++-- mixgb-1.5.2/mixgb/R/show_var.R | 55 mixgb-1.5.2/mixgb/R/utils-pipe.R |only mixgb-1.5.2/mixgb/R/validation.R | 149 - mixgb-1.5.2/mixgb/build/partial.rdb |only mixgb-1.5.2/mixgb/build/vignette.rds |binary mixgb-1.5.2/mixgb/inst/CITATION |only mixgb-1.5.2/mixgb/inst/doc/Imputing-newdata.R | 67 mixgb-1.5.2/mixgb/inst/doc/Imputing-newdata.Rmd | 152 - mixgb-1.5.2/mixgb/inst/doc/Imputing-newdata.html | 885 ++++----- mixgb-1.5.2/mixgb/inst/doc/Using-mixgb.R | 108 - mixgb-1.5.2/mixgb/inst/doc/Using-mixgb.Rmd | 313 +-- mixgb-1.5.2/mixgb/inst/doc/Using-mixgb.html | 1098 ++++++------ mixgb-1.5.2/mixgb/man/createNA.Rd | 70 mixgb-1.5.2/mixgb/man/data_clean.Rd | 56 mixgb-1.5.2/mixgb/man/default_params.Rd |only mixgb-1.5.2/mixgb/man/default_params_cran.Rd |only mixgb-1.5.2/mixgb/man/figures/README-unnamed-chunk-14-1.png |binary mixgb-1.5.2/mixgb/man/figures/README-unnamed-chunk-14-2.png |binary mixgb-1.5.2/mixgb/man/figures/README-unnamed-chunk-14-3.png |binary mixgb-1.5.2/mixgb/man/figures/README-unnamed-chunk-14-4.png |binary mixgb-1.5.2/mixgb/man/figures/README-unnamed-chunk-16-1.png |only mixgb-1.5.2/mixgb/man/figures/README-unnamed-chunk-16-2.png |only mixgb-1.5.2/mixgb/man/figures/README-unnamed-chunk-16-3.png |only mixgb-1.5.2/mixgb/man/figures/README-unnamed-chunk-16-4.png |only mixgb-1.5.2/mixgb/man/impute_new.Rd | 105 - mixgb-1.5.2/mixgb/man/mixgb-package.Rd | 55 mixgb-1.5.2/mixgb/man/mixgb.Rd | 223 +- mixgb-1.5.2/mixgb/man/mixgb_cv.Rd | 109 - mixgb-1.5.2/mixgb/man/nhanes3.Rd | 72 mixgb-1.5.2/mixgb/man/nhanes3_newborn.Rd | 92 - mixgb-1.5.2/mixgb/man/pipe.Rd |only mixgb-1.5.2/mixgb/man/pmm.Rd | 48 mixgb-1.5.2/mixgb/man/pmm.multiclass.Rd | 48 mixgb-1.5.2/mixgb/man/show_var.Rd | 65 mixgb-1.5.2/mixgb/man/sortNA.Rd | 24 mixgb-1.5.2/mixgb/src |only mixgb-1.5.2/mixgb/vignettes/Imputing-newdata.Rmd | 152 - mixgb-1.5.2/mixgb/vignettes/Using-mixgb.Rmd | 313 +-- 78 files changed, 6242 insertions(+), 5019 deletions(-)
Title: Univariate and Multivariate Tests for Multimodal and Other
Networks
Description: A set of tools for testing networks.
It includes functions for univariate and multivariate
conditional uniform graph and quadratic assignment procedure testing,
and network regression.
The package is a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Built on the 'manynet' package, all functions operate with matrices,
edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode and two-mode (bipartite) networks.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Bernhard Bieri [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 1.4.3 dated 2024-11-06 and 1.4.5 dated 2024-12-02
DESCRIPTION | 14 ++++++------ MD5 | 14 ++++++------ NAMESPACE | 2 + NEWS.md | 25 ++++++++++++++++++++++ R/class_models.R | 16 ++++++++++++++ R/data_mpn.R | 2 - R/model_regression.R | 56 ++++++++++++++++++++++++++++++++++++++------------- man/mpn_elite_usa.Rd | 2 - 8 files changed, 101 insertions(+), 30 deletions(-)
Title: Kirill's Miscellaneous Functions
Description: A collection of useful functions not found anywhere else,
mainly for programming: Pretty intervals, generalized lagged
differences, checking containment in an interval, and an alternative
interface to assign().
Author: Kirill Mueller [aut, cre]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between kimisc versions 0.4 dated 2017-12-18 and 1.0.0 dated 2024-12-02
kimisc-0.4/kimisc/tests/testthat/test-kimisc.R |only kimisc-1.0.0/kimisc/DESCRIPTION | 36 ++--- kimisc-1.0.0/kimisc/LICENSE |only kimisc-1.0.0/kimisc/MD5 | 91 +++++++------- kimisc-1.0.0/kimisc/NEWS.md | 11 + kimisc-1.0.0/kimisc/R/coalesce_na.R | 8 - kimisc-1.0.0/kimisc/R/cut.R | 11 + kimisc-1.0.0/kimisc/R/export.R | 16 +- kimisc-1.0.0/kimisc/R/gdiff.R | 27 ++-- kimisc-1.0.0/kimisc/R/hms_to_seconds.R | 4 kimisc-1.0.0/kimisc/R/in_interval.R | 20 +-- kimisc-1.0.0/kimisc/R/kimisc-package.R | 6 kimisc-1.0.0/kimisc/R/list_to_df.R | 10 + kimisc-1.0.0/kimisc/R/nlist.R | 29 ++-- kimisc-1.0.0/kimisc/R/ofactor.R | 12 + kimisc-1.0.0/kimisc/R/sample_data_frame.R | 9 + kimisc-1.0.0/kimisc/R/seconds_to_hms.R | 4 kimisc-1.0.0/kimisc/R/thisfile.R | 55 +++++--- kimisc-1.0.0/kimisc/R/tll.R | 13 +- kimisc-1.0.0/kimisc/R/vswitch.R | 4 kimisc-1.0.0/kimisc/man/coalesce.na-deprecated.Rd | 31 ++-- kimisc-1.0.0/kimisc/man/cut_format.Rd | 24 ++- kimisc-1.0.0/kimisc/man/df_to_list-deprecated.Rd | 29 ++-- kimisc-1.0.0/kimisc/man/export.Rd | 4 kimisc-1.0.0/kimisc/man/export.list.Rd | 6 kimisc-1.0.0/kimisc/man/hms.to.seconds-deprecated.Rd | 27 ++-- kimisc-1.0.0/kimisc/man/in.interval.lo.Rd | 4 kimisc-1.0.0/kimisc/man/in.interval.ro.Rd | 4 kimisc-1.0.0/kimisc/man/kimisc-deprecated.Rd | 26 ++-- kimisc-1.0.0/kimisc/man/kimisc-package.Rd | 12 - kimisc-1.0.0/kimisc/man/list_to_df-deprecated.Rd | 27 ++-- kimisc-1.0.0/kimisc/man/nc-deprecated.Rd | 38 +++-- kimisc-1.0.0/kimisc/man/nin.interval.lo.Rd | 4 kimisc-1.0.0/kimisc/man/nin.interval.ro.Rd | 4 kimisc-1.0.0/kimisc/man/nlist-deprecated.Rd | 38 +++-- kimisc-1.0.0/kimisc/man/ofactor-deprecated.Rd | 31 ++-- kimisc-1.0.0/kimisc/man/sample.rows-deprecated.Rd | 33 +++-- kimisc-1.0.0/kimisc/man/seconds.to.hms-deprecated.Rd | 29 ++-- kimisc-1.0.0/kimisc/man/thisfile-deprecated.Rd | 33 ++--- kimisc-1.0.0/kimisc/man/tll-deprecated.Rd | 31 ++-- kimisc-1.0.0/kimisc/man/vswitch-deprecated.Rd | 27 ++-- kimisc-1.0.0/kimisc/tests/testthat.R |only kimisc-1.0.0/kimisc/tests/testthat/scripts/thisfile-cat.R | 2 kimisc-1.0.0/kimisc/tests/testthat/test-cut.R | 28 ++-- kimisc-1.0.0/kimisc/tests/testthat/test-gdiff.R | 20 +-- kimisc-1.0.0/kimisc/tests/testthat/test-list_to_df.R | 2 kimisc-1.0.0/kimisc/tests/testthat/test-thisfile.R | 2 kimisc-1.0.0/kimisc/tests/testthat/test-vswitch.R | 24 ++- 48 files changed, 519 insertions(+), 387 deletions(-)
Title: High Dimensional Time Series Analysis Tools
Description: An implementation for high-dimensional time series analysis methods, including factor model for vector time series
proposed by Lam and Yao (2012) <doi:10.1214/12-AOS970> and Chang, Guo and Yao (2015)
<doi:10.1016/j.jeconom.2015.03.024>, martingale difference test proposed by
Chang, Jiang and Shao (2023) <doi:10.1016/j.jeconom.2022.09.001>, principal
component analysis for vector time series proposed by Chang, Guo and Yao (2018) <doi:10.1214/17-AOS1613>,
cointegration analysis proposed by Zhang, Robinson and Yao (2019)
<doi:10.1080/01621459.2018.1458620>, unit root test proposed by Chang, Cheng and Yao (2022)
<doi:10.1093/biomet/asab034>, white noise test proposed by Chang, Yao and Zhou (2017)
<doi:10.1093/biomet/asw066>, CP-decomposition for matrix time
series proposed by Chang et al. (2023) <doi:10.1093/jrsssb/qkac011> and
Chang et al. (2024) <doi:10.48550/arXiv.2410.05634>, and statistical inference for
spectral density matrix pro [...truncated...]
Author: Jinyuan Chang [aut],
Jing He [aut],
Chen Lin [aut, cre],
Qiwei Yao [aut]
Maintainer: Chen Lin <linchen@smail.swufe.edu.cn>
Diff between HDTSA versions 1.0.4 dated 2024-09-03 and 1.0.5 dated 2024-12-02
DESCRIPTION | 47 +- MD5 | 88 ++- NAMESPACE | 8 R/CP_functions_unified.R | 718 ++++++++++++++++++++------------ R/HDSreg.R | 134 +++-- R/HDTSA-package.R |only R/PCA4_TS.R | 327 ++++++-------- R/RcppExports.R | 24 - R/Tools_SpecTest.R | 395 ++++++----------- R/Tools_martingale.R | 169 ++++--- R/coint.R | 232 +++++----- R/data.R |only R/factors.R | 124 +++-- R/permutationFDR.R | 33 - R/permutationMax.R | 24 - R/predict.R |only R/print.R | 148 ++++-- R/segmentTS.R | 123 +---- R/tools_wntest.R | 143 +++--- R/urtest.R | 80 +-- build |only data |only man/CP_MTS.Rd | 209 +++++++-- man/Coint.Rd | 124 +++-- man/DGP.CP.Rd | 72 +-- man/Factors.Rd | 82 ++- man/Fama-French-data.Rd |only man/HDSReg.Rd | 129 +++-- man/HDTSA-package.Rd |only man/MartG_test.Rd | 115 ++--- man/PCA_TS.Rd | 276 +++++------- man/QWIdata.Rd |only man/SpecMulTest.Rd | 52 +- man/SpecTest.Rd | 60 +- man/UR_test.Rd | 74 +-- man/US-Industrial-Production-indices.Rd |only man/WN_test.Rd | 116 ++--- man/predict.factors.Rd |only man/predict.mtscp.Rd |only man/predict.tspca.Rd |only src/Makevars | 22 src/Makevars.win | 22 src/Martingale.cpp | 4 src/PCAtools.cpp | 25 - src/RcppExports.cpp | 98 +++- src/WNtest.cpp | 16 src/testtools.cpp | 28 - src/testtools.h | 2 src/tool4specTest.cpp | 121 +++++ src/tools4cp.cpp | 5 50 files changed, 2505 insertions(+), 1964 deletions(-)
Title: FAIR Data - Workflow Management
Description: Tools, methods and processes for the management
of analysis workflows. These lightweight solutions facilitate
structuring R&D activities. These solutions were developed to comply
with Good Documentation Practice (GDP),
with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>,
and with ALCOA+ principles as proposed by the U.S. FDA.
Author: Gregoire Thomas [aut, cre]
Maintainer: Gregoire Thomas <gregoire.thomas@SQU4RE.com>
Diff between D4TAlink.light versions 2.1.14 dated 2023-10-04 and 2.1.17 dated 2024-12-02
DESCRIPTION | 23 + MD5 | 103 ++++---- NAMESPACE | 155 +++++++------ NEWS | 20 + R/D4TAlink-common-args-doc.R | 56 ++-- R/D4TAlink-doc.R | 6 R/createTask.R | 66 ++--- R/init.R | 58 ++-- R/initTask.R | 76 +++--- R/listTasks.R | 138 +++++------ R/loadTask.R | 16 - R/pathGenerators.R | 156 ++++++------- R/pythonio.R |only R/taskArchive.R | 186 +++++++-------- R/taskFiles.R | 17 - R/taskGlobals.R | 2 R/taskID.R | 14 - R/taskPaths.R | 298 ++++++++++++------------- R/taskRmarkdown.R | 16 - R/taskRscript.R | 66 ++--- build/vignette.rds |binary inst/doc/D4TAlink_basics.R | 388 ++++++++++++++++----------------- inst/doc/D4TAlink_basics.Rmd | 9 inst/doc/D4TAlink_basics.html | 24 +- inst/doc/D4TAlink_quickstart.R | 110 ++++----- inst/doc/D4TAlink_quickstart.Rmd | 194 ++++++++-------- inst/doc/D4TAlink_quickstart.html | 6 inst/template/SQU4REtemplate.Rmd | 4 inst/template/template.R | 88 +++---- inst/template/template.Rmd | 444 +++++++++++++++++++------------------- man/D4TAlink-common-args.Rd | 82 +++---- man/D4TAlinkTask.Rd | 154 ++++++------- man/catReport.Rd | 3 man/createTask.Rd | 64 ++--- man/initTask.Rd | 98 ++++---- man/jpegReport.Rd | 16 - man/loadTask.Rd | 68 ++--- man/pdfReport.Rd | 44 ++- man/pngReport.Rd | 14 - man/readFeather.Rd |only man/readPickle.Rd |only man/readReportTable.Rd | 109 +++++++++ man/renderTaskRmd.Rd | 1 man/saveFeather.Rd |only man/savePickle.Rd |only man/saveReportJSON.Rd | 12 - man/saveReportTable.Rd | 40 +++ man/saveReportXls.Rd | 3 man/scanReport.Rd | 14 - tests/testthat.R | 5 tests/testthat/test01.R | 10 vignettes/D4TAlink_basics.Rmd | 9 vignettes/D4TAlink_basics.md | 10 vignettes/D4TAlink_quickstart.Rmd | 194 ++++++++-------- vignettes/D4TAlink_quickstart.md | 206 ++++++++--------- 55 files changed, 2039 insertions(+), 1856 deletions(-)
More information about D4TAlink.light at CRAN
Permanent link
Title: 'cpt-city' Colour Gradients
Description: Incorporates colour gradients from the 'cpt-city' web archive available at <http://seaviewsensing.com/pub/cpt-city/>.
Author: Sergio Ibarra-Espinosa [aut, cre]
Maintainer: Sergio Ibarra-Espinosa <zergioibarra@gmail.com>
Diff between cptcity versions 1.0.6 dated 2020-10-02 and 1.1.1 dated 2024-12-02
DESCRIPTION | 17 +++--- MD5 | 24 +++++---- NAMESPACE | 4 + NEWS.md | 93 +++++++++++++++++++------------------ R/cpt.R | 115 ++++++++++++++++++++-------------------------- R/cpt_names.R | 4 - R/show_cpt.R |only data/cpt_names.rda |binary inst/CITATION | 10 ++-- man/cpt.Rd | 7 -- man/cpt_names.Rd | 4 - man/cptcity.Rd | 13 +++++ man/show_cpt.Rd |only tests/testthat/test-cpt.R | 40 +++++++--------- 14 files changed, 167 insertions(+), 164 deletions(-)
Title: Client for the Deutsche Bundesbank and European Central Bank
APIs
Description: Download data and metadata from the 'Bundesbank SDMX Web
Service API' found at
<https://www.bundesbank.de/en/statistics/time-series-databases/help-for-sdmx-web-service/web-service-interface-data>
and the 'ECB Data Portal API' found at
<https://data.ecb.europa.eu/help/api/overview>.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between bbk versions 0.4.0 dated 2024-07-08 and 0.5.0 dated 2024-12-02
DESCRIPTION | 16 ++++++++-------- MD5 | 25 ++++++++++++++----------- NAMESPACE | 2 ++ NEWS.md | 5 +++++ R/bbk-package.R | 3 +++ R/bbk.R | 17 ++++++++++------- R/ecb-euro-rates.R |only R/ecb.R | 6 +++--- R/utils.R | 6 +----- README.md | 4 ++-- man/bbk-package.Rd | 2 +- man/ecb_euro_rates.Rd |only man/figures/README-plotting-1.png |binary tests/testthat/test-bbk.R | 1 + tests/testthat/test-ecb-euro-rates.R |only 15 files changed, 50 insertions(+), 37 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-26 2024.11.19
2024-11-18 2024.11.15
2024-10-11 2024.10.5
2024-10-04 2024.10.3
2024-09-27 2024.9.25
2024-04-29 2024.4.23
2024-04-22 2024.4.17
2024-04-13 2024.4.12
2024-03-08 2024.3.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-19 0.9.2
Title: Simultaneous Multi-Bias Adjustment
Description: Quantify the causal effect of a binary exposure on a binary
outcome with adjustment for multiple biases. The functions can
simultaneously adjust for any combination of uncontrolled confounding,
exposure/outcome misclassification, and selection bias.
The underlying method generalizes the concept of combining inverse
probability of selection weighting with predictive value weighting.
Simultaneous multi-bias analysis can be used to enhance the validity
and transparency of real-world evidence obtained from observational,
longitudinal studies. Based on the work from Paul Brendel, Aracelis Torres,
and Onyebuchi Arah (2023) <doi:10.1093/ije/dyad001>.
Author: Paul Brendel [aut, cre, cph]
Maintainer: Paul Brendel <pcbrendel@gmail.com>
Diff between multibias versions 1.6 dated 2024-10-26 and 1.6.1 dated 2024-12-02
DESCRIPTION | 6 MD5 | 36 +-- NEWS.md | 9 R/adjust_em.R | 65 +++--- R/adjust_em_om.R | 240 ++++++++++++++++++------ R/adjust_em_sel.R | 360 +++++++++++++++++++++++++++--------- R/adjust_om.R | 66 +++--- R/adjust_sel.R | 51 ++--- R/adjust_uc.R | 55 +++-- R/causal_data.R | 37 ++- R/utils.R | 42 ++++ man/adjust_em.Rd | 5 man/adjust_em_om.Rd | 43 +++- man/adjust_em_sel.Rd | 42 +++- man/adjust_om.Rd | 5 man/adjust_sel.Rd | 5 man/adjust_uc.Rd | 5 tests/testthat/test-adjust_em_om.R | 24 ++ tests/testthat/test-adjust_em_sel.R | 24 ++ 19 files changed, 830 insertions(+), 290 deletions(-)
Title: A Finer Way to Render 3D Illustrated Objects in 'grid' Using
Affine Transformations
Description: Dilate, permute, project, reflect, rotate, shear, and translate 2D and 3D points. Supports parallel projections including oblique projections such as the cabinet projection as well as axonometric projections such as the isometric projection. Use 'grid's "affine transformation" feature to render illustrated flat surfaces.
Author: Trevor L. Davis [aut, cre]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between affiner versions 0.1.1 dated 2024-10-14 and 0.1.3 dated 2024-12-02
DESCRIPTION | 11 ++- MD5 | 30 +++++----- NEWS.md | 6 ++ R/affineGrob.r | 7 ++ R/isocubeGrob.r | 27 ++++++++- README.md | 33 ++++++----- build/vignette.rds |binary inst/doc/affiner.R | 18 ++++-- inst/doc/affiner.Rmd | 25 +++++--- inst/doc/affiner.html | 111 +++++++++++++++++++------------------ man/affineGrob.Rd | 11 +++ man/figures/README-hex-logo2-1.png |binary man/isocubeGrob.Rd | 31 ++++++++++ tests/testthat/test-affineGrob.r | 2 tests/testthat/test-isocubeGrob.r | 4 - vignettes/affiner.Rmd | 25 +++++--- 16 files changed, 224 insertions(+), 117 deletions(-)
Title: Quick and Essential 'R' Tricks for Better Scripts
Description: The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.
Author: Obinna Obianom [aut, cre],
Brice Richard [aut]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between quickcode versions 1.0.2 dated 2024-11-06 and 1.0.3 dated 2024-12-01
DESCRIPTION | 8 +- MD5 | 20 +++---- NEWS.md | 4 + R/OR.R | 26 +++++++-- R/pairDist.R | 17 ++++-- inst/doc/add_today_date_to_filenames_quickcode.html | 54 ++++++++++---------- inst/doc/nullish_coalescing_operator_r.html | 4 - inst/doc/quickcode_r_introduction.html | 4 - inst/doc/track_function_usage_r.html | 4 - man/machine_learning.Rd | 17 ++++-- man/orsign.Rd | 21 +++++-- 11 files changed, 112 insertions(+), 67 deletions(-)
Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Description: This model fitting tool incorporates cyclic coordinate descent and
majorization-minimization approaches to fit a variety of regression models
found in large-scale observational healthcare data. Implementations focus
on computational optimization and fine-scale parallelization to yield
efficient inference in massive datasets. Please see:
Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.
Author: Marc A. Suchard [aut, cre],
Martijn J. Schuemie [aut],
Trevor R. Shaddox [aut],
Yuxi Tian [aut],
Jianxiao Yang [aut],
Eric Kawaguchi [aut],
Sushil Mittal [ctb],
Observational Health Data Sciences and Informatics [cph],
Marcus Geelnard [cph, ctb] ,
Ru [...truncated...]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between Cyclops versions 3.4.1 dated 2024-06-06 and 3.5.0 dated 2024-12-01
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NEWS.md | 7 +++++++ R/DataManagement.R | 6 +++--- R/ModelFit.R | 22 +++++++++++++++++----- R/cyclops.R | 3 +-- man/createCyclopsData.Rd | 6 +++--- man/cyclops.Rd | 30 ++++++++++++++++++++++++++++++ man/getCyclopsProfileLogLikelihood.Rd | 9 ++++++++- tests/testthat/save.R |only tests/testthat/test-recenter.R |only 11 files changed, 83 insertions(+), 26 deletions(-)
Title: Forest Mensuration and Management
Description: Processing forest inventory data with methods such as simple random sampling, stratified random sampling and systematic sampling. There are also functions for yield and growth predictions and model fitting, linear and nonlinear grouped data fitting, and statistical tests. References: Kershaw Jr., Ducey, Beers and Husch (2016). <doi:10.1002/9781118902028>.
Author: Sollano Rabelo Braga [aut, cre, cph],
Marcio Leles Romarco de Oliveira [aut],
Eric Bastos Gorgens [aut]
Maintainer: Sollano Rabelo Braga <sollanorb@gmail.com>
Diff between forestmangr versions 0.9.7 dated 2024-09-14 and 0.9.8 dated 2024-12-01
forestmangr-0.9.7/forestmangr/R/Graybill_F.R |only forestmangr-0.9.7/forestmangr/man/Graybill_F.Rd |only forestmangr-0.9.8/forestmangr/DESCRIPTION | 10 +- forestmangr-0.9.8/forestmangr/MD5 | 36 +++++----- forestmangr-0.9.8/forestmangr/NEWS.md | 3 forestmangr-0.9.8/forestmangr/R/graybill_f.R |only forestmangr-0.9.8/forestmangr/R/na_to_0.R | 13 +-- forestmangr-0.9.8/forestmangr/inst/doc/eq_group_fit_en.html | 8 +- forestmangr-0.9.8/forestmangr/inst/doc/eq_group_fit_ptbr.html | 8 +- forestmangr-0.9.8/forestmangr/inst/doc/invent_vol_plot_en.html | 4 - forestmangr-0.9.8/forestmangr/inst/doc/invent_vol_plot_ptbr.html | 4 - forestmangr-0.9.8/forestmangr/inst/doc/phyto_ana_en.html | 4 - forestmangr-0.9.8/forestmangr/inst/doc/phyto_ana_ptbr.html | 4 - forestmangr-0.9.8/forestmangr/inst/doc/sampling_en.html | 2 forestmangr-0.9.8/forestmangr/inst/doc/sampling_ptbr.html | 2 forestmangr-0.9.8/forestmangr/inst/doc/volume_est_en.html | 6 - forestmangr-0.9.8/forestmangr/inst/doc/volume_est_ptbr.html | 6 - forestmangr-0.9.8/forestmangr/inst/doc/yield_growth_en.html | 4 - forestmangr-0.9.8/forestmangr/inst/doc/yield_growth_ptbr.html | 4 - forestmangr-0.9.8/forestmangr/man/graybill_f.Rd |only forestmangr-0.9.8/forestmangr/man/na_to_0.Rd | 7 - 21 files changed, 61 insertions(+), 64 deletions(-)
Title: Fast Time Series Modeling for Seasonal Series with Exogenous
Variables
Description: An implementation of sparsity-ranked lasso and related methods
for time series data. This methodology is especially useful for
large time series with exogenous features and/or complex
seasonality. Originally described in Peterson and Cavanaugh
(2022) <doi:10.1007/s10182-021-00431-7> in the context of variable
selection with interactions and/or polynomials, ranked sparsity is
a philosophy with methods useful for variable selection in the
presence of prior informational asymmetry. This situation exists for time
series data with complex seasonality, as shown in Peterson and Cavanaugh
(2024) <doi:10.1177/1471082X231225307>, which also describes this package
in greater detail. The sparsity-ranked penalization methods for time series
implemented in 'fastTS' can fit large/complex/high-frequency time series
quickly, even with a high-dimensional exogenous feature set. The method is
considerably faster than its competitors, while often producing more
accurate predictions. Also includ [...truncated...]
Author: Ryan Andrew Peterson [aut, cre, cph]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>
Diff between fastTS versions 1.0.1 dated 2024-03-28 and 1.0.2 dated 2024-12-01
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 5 build/vignette.rds |binary inst/doc/case_studies.html | 430 +++++++++++++++++++------------------- inst/doc/forecasting.html | 86 +++---- inst/doc/hourly_er_visits.html | 166 +++++++------- tests/testthat/test-predictions.R | 4 8 files changed, 359 insertions(+), 354 deletions(-)
Title: Customisable Ranking of Numerical and Categorical Data
Description: Provides a flexible alternative to the built-in rank() function called smartrank().
Optionally rank categorical variables by frequency (instead of in alphabetical order), and control whether ranking is based on descending/ascending order.
smartrank() is suitable for both numerical and categorical data.
Author: Sam El-Kamand [aut, cre, cph]
Maintainer: Sam El-Kamand <sam.elkamand@gmail.com>
Diff between rank versions 0.1.0 dated 2024-07-09 and 0.1.1 dated 2024-12-01
DESCRIPTION | 11 +-- MD5 | 17 +++- NEWS.md | 15 ++++ R/smartrank.R | 80 +++++++++++++-------- README.md | 104 +++++++++++++++++++++------- build |only inst |only man/smartrank.Rd | 40 ++++++++-- tests/testthat/test-smartrank.R | 146 +++++++++++++++++++++++++++++++++++++--- vignettes |only 10 files changed, 329 insertions(+), 84 deletions(-)
Title: Read Spectrometric Data and Metadata
Description: Parse various reflectance/transmittance/absorbance spectra file
formats to extract spectral data and metadata, as described in Gruson, White
& Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import
files from 'Avantes' <https://www.avantes.com/>, 'CRAIC'
<https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight'
<https://www.oceanoptics.com/> brands.
Author: Hugo Gruson [cre, aut, cph] ,
Rafael Maia [aut, cph] ,
Thomas White [aut, cph] ,
Kotya Karapetyan [ctb, cph] )
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Diff between lightr versions 1.7.1 dated 2024-03-21 and 1.8.0 dated 2024-12-01
DESCRIPTION | 18 ++++++------ MD5 | 60 ++++++++++++++++++++-------------------- NEWS.md | 16 +++++++++- R/convert_tocsv.R | 4 +- R/get_metadata.R | 4 +- R/get_spec.R | 26 +++++++++-------- R/parse_avantes_binary.R | 14 ++++----- R/parse_avantes_converted.R | 12 ++++---- R/parse_generic.R | 14 ++++----- R/parse_jdx.R | 8 ++--- R/parse_oceanoptics_converted.R | 21 ++++++++------ R/parse_procspec.R | 10 +++--- R/parse_spc.R | 10 +++--- R/utils.R | 15 ++++++++++ README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 4 ++ inst/doc/batch_import.R | 2 - inst/doc/batch_import.html | 10 +++--- inst/doc/renormalise.Rmd | 13 ++------ inst/doc/renormalise.html | 18 ++++++------ inst/doc/true_example.Rmd | 4 +- inst/doc/true_example.html | 21 +++++++------- man/lightr-package.Rd | 2 - man/lr_parse_jaz.Rd | 6 ++-- man/lr_parse_jdx.Rd | 6 ++-- man/lr_parse_procspec.Rd | 8 ++--- man/lr_parse_spc.Rd | 2 - vignettes/renormalise.Rmd | 13 ++------ vignettes/true_example.Rmd | 4 +- 31 files changed, 184 insertions(+), 163 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii)
Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v)
Matrix functions, (vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions. There is a vignette describing how to use the
design functions for randomizing and assessing designs available as a
vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of
information when the 'Error' function has been used in the call to 'aov'.
The package 'dae' can also be installed from
<http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between dae versions 3.2.28 dated 2024-06-12 and 3.2.30 dated 2024-12-01
dae-3.2.28/dae/tests/testthat/testthat-problems.rds |only dae-3.2.30/dae/DESCRIPTION | 8 - dae-3.2.30/dae/MD5 | 48 ++++--- dae-3.2.30/dae/NAMESPACE | 2 dae-3.2.30/dae/R/fac.functions.r | 65 +++++++++- dae-3.2.30/dae/build/partial.rdb |binary dae-3.2.30/dae/build/vignette.rds |binary dae-3.2.30/dae/inst/NEWS.Rd | 10 + dae-3.2.30/dae/inst/doc/DesignNotes.pdf |binary dae-3.2.30/dae/inst/doc/dae-manual.pdf |binary dae-3.2.30/dae/man/as.numfac.Rd | 41 +++++- dae-3.2.30/dae/man/dae-package.Rd | 23 +-- dae-3.2.30/dae/man/designBlocksGGPlot.Rd | 2 dae-3.2.30/dae/man/designGGPlot.Rd | 11 - dae-3.2.30/dae/man/designPlotlabels.Rd | 8 - dae-3.2.30/dae/man/fac.multinested.Rd | 2 dae-3.2.30/dae/man/interaction.ABC.plot.Rd | 6 dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/colfacets-bottom-switch-placement.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/colfacets-bottom.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/colfacets-placement.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/rowfacets-switch-placement.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/rowfacets-switch.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/rows-and-columns-indexed-by-2-factors.new.svg |only dae-3.2.30/dae/tests/testthat/_snaps/testDesignGGPlot/using-facetstrips-place-from-designblocksggplot.new.svg |only dae-3.2.30/dae/tests/testthat/testCanon.r | 6 dae-3.2.30/dae/tests/testthat/testFac.r | 49 +++++++ dae-3.2.30/dae/tests/testthat/testInteractionABCplot.r | 6 dae-3.2.30/dae/tests/testthat/testOneStructure.r | 2 dae-3.2.30/dae/tests/testthat/testSources.r | 14 -- 29 files changed, 224 insertions(+), 79 deletions(-)
Title: A Collection of Scoring Functions for Assessing Point Forecasts
Description: Implements multiple consistent scoring functions
(Gneiting T (2011) <doi:10.1198/jasa.2011.r10138>) for assessing point
forecasts and point predictions. Detailed documentation of scoring
functions' properties is included for facilitating interpretation of
results.
Author: Hristos Tyralis [aut, cre] ,
Georgia Papacharalampous [aut]
Maintainer: Hristos Tyralis <montchrister@gmail.com>
Diff between scoringfunctions versions 0.0.7 dated 2024-11-10 and 1.0 dated 2024-12-01
DESCRIPTION | 8 +- MD5 | 140 +++++++++++++++++++++++--------------- NAMESPACE | 17 ++++ R/aerr_sf.R | 20 ----- R/aperr_sf.R | 20 ----- R/bmedian_sf.R | 21 ----- R/bregman1_sf.R | 26 ------- R/bregman2_sf.R | 30 -------- R/bregman3_sf.R | 28 ------- R/bregman4_sf.R | 28 ------- R/capping_function.R | 17 ---- R/errorspread_sf.R |only R/expectile_rs.R |only R/expectile_sf.R | 24 ------ R/ghuber_sf.R | 24 ------ R/gpl1_sf.R | 28 ------- R/gpl2_sf.R | 26 ------- R/huber_rs.R |only R/huber_sf.R | 20 ----- R/hubermean_if.R |only R/huberquantile_if.R |only R/linex_sf.R |only R/lqmean_sf.R |only R/lqquantile_sf.R |only R/mae.R |only R/maelog_sf.R | 19 ----- R/maesd_sf.R | 19 ----- R/mape.R |only R/mre.R |only R/mse.R |only R/mspe.R |only R/msre.R |only R/nse.R |only R/obsweighted_sf.R | 20 ----- R/quantile_if.R | 2 R/quantile_level.R |only R/quantile_rs.R |only R/quantile_sf.R | 24 ------ R/relerr_sf.R | 20 ----- R/serr_sf.R | 19 ----- R/sperr_sf.R | 21 ----- R/srelerr_sf.R | 20 ----- man/aerr_sf.Rd | 4 - man/aperr_sf.Rd | 4 - man/bmedian_sf.Rd | 4 - man/bregman1_sf.Rd | 4 - man/bregman2_sf.Rd | 4 - man/bregman3_sf.Rd | 4 - man/bregman4_sf.Rd | 4 - man/errorspread_sf.Rd |only man/expectile_if.Rd | 4 - man/expectile_rs.Rd |only man/expectile_sf.Rd | 4 - man/ghuber_sf.Rd | 4 - man/gpl1_sf.Rd | 4 - man/gpl2_sf.Rd | 4 - man/huber_rs.Rd |only man/huber_sf.Rd | 4 - man/hubermean_if.Rd |only man/huberquantile_if.Rd |only man/interval_sf.Rd | 4 - man/linex_sf.Rd |only man/lqmean_sf.Rd |only man/lqquantile_sf.Rd |only man/mae.Rd |only man/maelog_sf.Rd | 4 - man/maesd_sf.Rd | 4 - man/mape.Rd |only man/mean_if.Rd | 4 - man/mre.Rd |only man/mse.Rd |only man/mspe.Rd |only man/msre.Rd |only man/mv_if.Rd | 6 - man/mv_sf.Rd | 6 - man/nmoment_if.Rd | 4 - man/nmoment_sf.Rd | 4 - man/nse.Rd |only man/obsweighted_sf.Rd | 4 - man/quantile_if.Rd | 4 - man/quantile_level.Rd |only man/quantile_rs.Rd |only man/quantile_sf.Rd | 4 - man/relerr_sf.Rd | 4 - man/scoringfunctions-package.Rd | 147 ++++++++++++++++++++++++++++++++++------ man/serr_sf.Rd | 4 - man/sperr_sf.Rd | 4 - man/srelerr_sf.Rd | 4 - 88 files changed, 293 insertions(+), 611 deletions(-)
More information about scoringfunctions at CRAN
Permanent link
Title: Fast Machine Learning Model Training and Evaluation
Description: Streamlines the training, evaluation, and comparison of multiple machine learning models with minimal code by providing
comprehensive data preprocessing and support for a wide range of algorithms with hyperparameter tuning.
It offers performance metrics and visualization tools to facilitate efficient and effective machine learning workflows.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.1.0 dated 2024-11-12 and 0.2.0 dated 2024-11-30
fastml-0.1.0/fastml/R/prepare_data.R |only fastml-0.1.0/fastml/R/validate_tuneGrid.R |only fastml-0.1.0/fastml/man/prepare_data.Rd |only fastml-0.1.0/fastml/man/validate_tuneGrid.Rd |only fastml-0.2.0/fastml/DESCRIPTION | 16 fastml-0.2.0/fastml/MD5 | 51 fastml-0.2.0/fastml/NAMESPACE | 90 fastml-0.2.0/fastml/R/evaluate_models.R | 221 - fastml-0.2.0/fastml/R/fastml.R | 470 +-- fastml-0.2.0/fastml/R/plot.fastml_model.R | 64 fastml-0.2.0/fastml/R/predict.fastml_model.R | 51 fastml-0.2.0/fastml/R/summary.fastml_model.R | 101 fastml-0.2.0/fastml/R/train_models.R | 1545 ++++++---- fastml-0.2.0/fastml/man/define_bagging_spec.Rd |only fastml-0.2.0/fastml/man/define_bayes_glm_spec.Rd |only fastml-0.2.0/fastml/man/define_c5_0_spec.Rd |only fastml-0.2.0/fastml/man/define_decision_tree_spec.Rd |only fastml-0.2.0/fastml/man/define_deep_learning_spec.Rd |only fastml-0.2.0/fastml/man/define_elastic_net_spec.Rd |only fastml-0.2.0/fastml/man/define_knn_spec.Rd |only fastml-0.2.0/fastml/man/define_lasso_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_lda_spec.Rd |only fastml-0.2.0/fastml/man/define_lightgbm_spec.Rd |only fastml-0.2.0/fastml/man/define_linear_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_logistic_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_naive_bayes_spec.Rd |only fastml-0.2.0/fastml/man/define_neural_network_spec.Rd |only fastml-0.2.0/fastml/man/define_penalized_logistic_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_pls_spec.Rd |only fastml-0.2.0/fastml/man/define_qda_spec.Rd |only fastml-0.2.0/fastml/man/define_random_forest_spec.Rd |only fastml-0.2.0/fastml/man/define_ranger_spec.Rd |only fastml-0.2.0/fastml/man/define_ridge_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_svm_linear_spec.Rd |only fastml-0.2.0/fastml/man/define_svm_radial_spec.Rd |only fastml-0.2.0/fastml/man/define_xgboost_spec.Rd |only fastml-0.2.0/fastml/man/evaluate_models.Rd | 8 fastml-0.2.0/fastml/man/fastml.Rd | 132 fastml-0.2.0/fastml/man/predict.fastml_model.Rd | 7 fastml-0.2.0/fastml/man/train_models.Rd | 15 40 files changed, 1769 insertions(+), 1002 deletions(-)
Title: Unpivot Complex and Irregular Data Layouts
Description: Tools for converting data from complex or irregular layouts to a
columnar structure. For example, tables with multilevel column or row
headers, or spreadsheets. Header and data cells are selected by their
contents and position, as well as formatting and comments where available,
and are associated with one other by their proximity in given directions.
Functions for data frames and HTML tables are provided.
Author: Duncan Garmonsway [aut, cre]
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>
Diff between unpivotr versions 0.6.3 dated 2023-01-22 and 0.6.4 dated 2024-11-30
DESCRIPTION | 8 MD5 | 26 NEWS.md | 4 R/purpose.R | 5 README.md | 38 - build/vignette.rds |binary inst/doc/html.R | 12 inst/doc/html.html | 180 +++--- inst/doc/introduction.R | 2 inst/doc/introduction.html | 1137 ++++++++++++++++++-------------------- inst/doc/small-multiples.R | 6 inst/doc/small-multiples.html | 726 ++++++++++++------------ man/purpose.Rd | 5 tests/testthat/test-concatenate.R | 2 14 files changed, 1076 insertions(+), 1075 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets,
regression models, and more. The code to create the tables is concise
and highly customizable. Data frames can be summarized with any
function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] ,
Joseph Larmarange [aut] ,
Michael Curry [aut] ,
Jessica Lavery [aut] ,
Karissa Whiting [aut] ,
Emily C. Zabor [aut] ,
Xing Bai [ctb],
Esther Drill [ctb] ,
Jessica Flynn [ctb] ,
Margie Hannum [ctb] ,
Stephanie Lobaugh [c [...truncated...]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 2.0.3 dated 2024-10-04 and 2.0.4 dated 2024-11-30
gtsummary-2.0.3/gtsummary/build/gtsummary.pdf |only gtsummary-2.0.4/gtsummary/DESCRIPTION | 12 gtsummary-2.0.4/gtsummary/MD5 | 365 +-- gtsummary-2.0.4/gtsummary/NAMESPACE | 5 gtsummary-2.0.4/gtsummary/NEWS.md | 30 gtsummary-2.0.4/gtsummary/R/add_ci.R | 13 gtsummary-2.0.4/gtsummary/R/add_ci.tbl_svysummary.R | 2 gtsummary-2.0.4/gtsummary/R/add_difference.R | 2 gtsummary-2.0.4/gtsummary/R/add_difference.tbl_svysummary.R | 2 gtsummary-2.0.4/gtsummary/R/add_glance.R | 17 gtsummary-2.0.4/gtsummary/R/add_global_p.R | 2 gtsummary-2.0.4/gtsummary/R/add_n.R | 2 gtsummary-2.0.4/gtsummary/R/add_n.tbl_survfit.R | 2 gtsummary-2.0.4/gtsummary/R/add_nevent.R | 2 gtsummary-2.0.4/gtsummary/R/add_nevent.tbl_survfit.R | 4 gtsummary-2.0.4/gtsummary/R/add_overall.R | 20 gtsummary-2.0.4/gtsummary/R/add_p.R | 6 gtsummary-2.0.4/gtsummary/R/add_p.tbl_continuous.R | 10 gtsummary-2.0.4/gtsummary/R/add_p.tbl_cross.R | 9 gtsummary-2.0.4/gtsummary/R/add_p.tbl_survfit.R | 2 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gtsummary-2.0.4/gtsummary/R/tbl_regression.R | 4 gtsummary-2.0.4/gtsummary/R/tbl_regression_methods.R | 4 gtsummary-2.0.4/gtsummary/R/tbl_stack.R | 2 gtsummary-2.0.4/gtsummary/R/tbl_strata.R | 3 gtsummary-2.0.4/gtsummary/R/tbl_summary.R | 16 gtsummary-2.0.4/gtsummary/R/tbl_survfit.R | 6 gtsummary-2.0.4/gtsummary/R/tbl_svysummary.R | 7 gtsummary-2.0.4/gtsummary/R/tbl_uvregression.R | 4 gtsummary-2.0.4/gtsummary/R/theme_gtsummary.R | 13 gtsummary-2.0.4/gtsummary/R/utils-add_p_tests.R | 62 gtsummary-2.0.4/gtsummary/R/utils-as.R | 5 gtsummary-2.0.4/gtsummary/R/utils-gtsummary_core.R | 7 gtsummary-2.0.4/gtsummary/build/stage23.rdb |binary gtsummary-2.0.4/gtsummary/build/vignette.rds |binary gtsummary-2.0.4/gtsummary/inst/WORDLIST | 4 gtsummary-2.0.4/gtsummary/inst/doc/gtsummary_definition.R | 42 gtsummary-2.0.4/gtsummary/inst/doc/gtsummary_definition.Rmd | 24 gtsummary-2.0.4/gtsummary/inst/doc/gtsummary_definition.html | 1188 ++++++---- gtsummary-2.0.4/gtsummary/man/add_ci.Rd | 2 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gtsummary-2.0.4/gtsummary/man/as_hux_table.Rd | 2 gtsummary-2.0.4/gtsummary/man/as_kable_extra.Rd | 2 gtsummary-2.0.4/gtsummary/man/brdg_hierarchical.Rd | 4 gtsummary-2.0.4/gtsummary/man/custom_tidiers.Rd | 11 gtsummary-2.0.4/gtsummary/man/gather_ard.Rd | 2 gtsummary-2.0.4/gtsummary/man/glance_fun_s3.Rd | 2 gtsummary-2.0.4/gtsummary/man/global_pvalue_fun.Rd | 5 gtsummary-2.0.4/gtsummary/man/inline_text.tbl_regression.Rd | 2 gtsummary-2.0.4/gtsummary/man/inline_text.tbl_survfit.Rd | 2 gtsummary-2.0.4/gtsummary/man/inline_text.tbl_uvregression.Rd | 2 gtsummary-2.0.4/gtsummary/man/modify_column_merge.Rd | 2 gtsummary-2.0.4/gtsummary/man/modify_source_note.Rd |only gtsummary-2.0.4/gtsummary/man/plot.Rd | 2 gtsummary-2.0.4/gtsummary/man/tbl_ard_hierarchical.Rd | 10 gtsummary-2.0.4/gtsummary/man/tbl_ard_summary.Rd | 15 gtsummary-2.0.4/gtsummary/man/tbl_hierarchical.Rd | 48 gtsummary-2.0.4/gtsummary/man/tbl_merge.Rd | 2 gtsummary-2.0.4/gtsummary/man/tbl_regression.Rd | 2 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Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use
in photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse ratios and
other derived quantities from spectral data. Local maxima and minima: peaks,
valleys and spikes. Conversion between energy-and photon-based units.
Wavelength interpolation. Astronomical calculations related solar angles and
day length. Colours and vision. This package is part of the 'r4photobiology'
suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb],
Agnese Fazio [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.11.3 dated 2024-08-25 and 0.11.4 dated 2024-11-30
DESCRIPTION | 8 MD5 | 158 ++++++++--------- NAMESPACE | 16 + NEWS.md | 19 ++ R/cieillum.data.r | 66 ++++++- R/ciexyz.data.r | 2 R/color.of.R | 14 + R/on-attach.R | 2 R/photobiology.r | 4 R/rbindspct.r | 8 R/spct.metadata.r | 267 +++++++++++++++++------------ R/spct.normalize.r | 11 - R/sun.calc.r | 20 +- R/zmspct.classes.R | 13 - build/partial.rdb |binary build/vignette.rds |binary data/A.illuminant.spct.rda |binary data/D2-FEL-constants.rda |binary data/D50.illuminant.spct.rda |only data/D65.illuminant.spct.rda |binary data/Ler-leaf-spct.rda |binary data/beesxyz.spct.rda |binary data/black_body.spct.rda |binary data/ccd.spct.rda |binary data/ciev10.spct.rda |binary data/ciev2.spct.rda |binary data/ciexyzCC10.spct.rda |binary data/ciexyzCC2.spct.rda |binary data/ciexyzCMF10.spct.rda |binary data/ciexyzCMF2.spct.rda |binary data/clear_body.spct.rda |binary data/cone_fundamentals10.spct.rda |binary data/filter-cps-mspct.rda |binary data/filter-data.rda |binary data/green_leaf.spct.rda |binary data/photodiode.spct.rda |binary data/r4p-pkgs.rda |binary data/solutes.rda |binary data/sun.data.rda |binary data/white-led-spct.rda |binary data/white_body.spct.rda |binary inst/doc/userguide-0-r4p-introduction.html | 4 inst/doc/userguide-1-radiation.R | 26 +- inst/doc/userguide-1-radiation.Rmd | 12 - inst/doc/userguide-1-radiation.html | 20 +- inst/doc/userguide-2-astronomy.R | 40 ++-- inst/doc/userguide-2-astronomy.Rmd | 46 ++-- inst/doc/userguide-2-astronomy.html | 194 ++++++++++----------- man/A.illuminant.spct.Rd | 18 + man/D50.illuminant.spct.Rd |only man/D65.illuminant.spct.Rd | 17 + man/Ler_leaf.spct.Rd | 1 man/add_attr2tb.Rd | 4 man/black_body.spct.Rd | 1 man/ccd.spct.Rd | 1 man/clear.spct.Rd | 1 man/color_of.Rd | 6 man/cone_fundamentals10.spct.Rd | 2 man/day_night.Rd | 20 +- man/filter_cps.mspct.Rd | 1 man/getHowMeasured.Rd | 9 man/getWhatMeasured.Rd | 10 - man/getWhenMeasured.Rd | 12 - man/getWhereMeasured.Rd | 9 man/green_leaf.spct.Rd | 1 man/phenylalanine.spct.Rd | 1 man/photobiology-package.Rd | 4 man/photodiode.spct.Rd | 1 man/setHowMeasured.Rd | 47 ++++- man/setWhatMeasured.Rd | 35 +++ man/setWhenMeasured.Rd | 13 + man/setWhereMeasured.Rd | 8 man/subset2mspct.Rd | 5 man/sun.spct.Rd | 1 man/sun_daily.spct.Rd | 1 man/sun_evening.spct.Rd | 1 man/two_filters.spct.Rd | 1 man/water.spct.Rd | 1 man/white_led.source_spct.Rd | 1 vignettes/userguide-1-radiation.Rmd | 12 - vignettes/userguide-2-astronomy.Rmd | 46 ++-- 81 files changed, 778 insertions(+), 463 deletions(-)
Title: Access to Spanish Household Income Distribution Atlas Data
Description: Provides access to granular socioeconomic indicators from the
Spanish Statistical Office (INE) Household Income Distribution Atlas.
The package downloads and processes data from a companion 'GitHub'
repository (<https://github.com/pablogguz/ineAtlas.data/>) which contains
processed versions of the official INE Atlas data. Functions are
provided to fetch data at multiple geographic levels (municipalities,
districts, and census tracts), including income indicators,
demographic characteristics, and inequality metrics. The data
repository is updated every year when new releases are published by
INE.
Author: Pablo Garcia Guzman [aut, cre, cph]
Maintainer: Pablo Garcia Guzman <garciagp@ebrd.com>
Diff between ineAtlas versions 0.1.2 dated 2024-11-08 and 0.1.3 dated 2024-11-30
DESCRIPTION | 6 +++--- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/get_atlas.r | 11 +++++++---- R/get_census.r |only README.md | 9 ++++++++- inst/doc/ineAtlas-income-voting.Rmd | 1 + inst/doc/ineAtlas-income-voting.html | 11 +++++++---- inst/doc/mapping-with-ineatlas.html | 4 ++-- man/get_atlas.Rd | 6 +++--- man/get_census.Rd |only vignettes/ineAtlas-income-voting.Rmd | 1 + 13 files changed, 49 insertions(+), 27 deletions(-)
Title: Weighted Meta-Analysis with Pseudo-Populations
Description: Implementation of integrative weighting approaches for multiple observational studies and causal inferences. The package features three weighting approaches, each representing a special case of the unified weighting framework, introduced by Guha and Li (2024) <doi:10.1093/biomtc/ujae070>, which includes an extension of inverse probability weights for data integration settings.
Author: Subharup Guha [aut, cre],
Mengqi Xu [aut],
Kashish Priyam [aut],
Yi Li [aut]
Maintainer: Subharup Guha <s.guha@ufl.edu>
Diff between WMAP versions 1.0.0 dated 2024-11-07 and 1.1.0 dated 2024-11-30
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++++++---------- NAMESPACE | 6 ++++++ R/accessor.R |only R/other-functions.R | 9 +++++---- R/plot.R | 25 +++++++++++++++++-------- R/print.R |only R/stage-1-functions.R | 2 +- R/stage-2-functions.R | 4 +--- R/summary.R | 35 ++++++++++++++++++++++++++--------- man/get_weights.Rd |only man/mean_diff.Rd |only man/percentESS.Rd |only man/plot.causal_estimates.Rd | 13 ++++++++++--- man/print.balancing_weights.Rd |only man/print.causal_estimates.Rd |only man/sigma_ratio.Rd |only man/summary.balancing_weights.Rd | 2 +- man/summary.causal_estimates.Rd | 6 ++++-- 19 files changed, 92 insertions(+), 44 deletions(-)
Title: Fast Robust Moments
Description: Fast, numerically robust computation of weighted moments via 'Rcpp'.
Supports computation on vectors and matrices, and Monoidal append of moments.
Moments and cumulants over running fixed length windows can be computed,
as well as over time-based windows.
Moment computations are via a generalization of Welford's method, as described
by Bennett et. (2009) <doi:10.1109/CLUSTR.2009.5289161>.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between fromo versions 0.2.3 dated 2024-11-07 and 0.2.4 dated 2024-11-29
ChangeLog | 5 DESCRIPTION | 8 MD5 | 64 +++--- NAMESPACE | 14 + R/RcppExports.R | 217 +++++++++++++++++++++ R/fromo.r | 6 R/zzz_centsums.R | 11 - README.md | 325 +++++++++++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/fromo.Rnw | 346 ++++++++++++++++++++++++++++++++++- inst/doc/fromo.pdf |binary man/NEWS.Rd | 8 man/as.centsums.Rd | 40 +++- man/firstmoments.Rd | 11 - man/two_runningmoments.Rd |only man/two_t_runningmoments.Rd |only src/RcppExports.cpp | 327 +++++++++++++++++++++++++++++++++ src/common.h | 7 src/fromo.cpp | 11 - src/moment_interp.h | 1 src/running.h | 23 -- src/t_running.h | 35 +-- src/two_moment_interp.h |only src/two_running.cpp |only src/two_running.h |only src/two_t_running.cpp |only src/two_t_running.h |only src/two_welford.h |only src/vec_welford.h |only tests/testthat/test-correctness.r | 84 ++++++++ tests/testthat/test-running.r | 125 ++++++++++++ tests/testthat/test-trunning.r | 162 ++++++++++++++++ tools/figure/toy_zscore-1.png |binary tools/figure/trun_corr_testing-1.png |only tools/figure/trun_testing-1.png |binary vignettes/fromo.Rnw | 346 ++++++++++++++++++++++++++++++++++- vignettes/fromo.bib | 14 + 38 files changed, 1958 insertions(+), 232 deletions(-)
Title: Self-Validated Ensemble Models with Elastic Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM, Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using Elastic Net regression via 'glmnet' (Friedman et al. <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). \\Code for the whole model test was taken from the supplementary material of Karl (2024). Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 1.0.3 dated 2024-11-20 and 1.1.1 dated 2024-11-29
DESCRIPTION | 12 ++++++---- MD5 | 40 +++++++++++++++++++++++++----------- NAMESPACE | 1 NEWS |only R/SVEMnet-package.R | 4 ++- R/SVEMnet.R | 29 +++++++++++++------------- R/plot.svemnet.R | 4 +-- R/predict.svem_lasso.R | 23 +++++++------------- R/print.R |only R/svem_significance_test.R | 33 +++++++++++++++-------------- build/vignette.rds |only inst/doc |only inst/scripts |only man/SVEMnet-package.Rd | 4 ++- man/SVEMnet.Rd | 25 +++++++++++++--------- man/plot.svem_model.Rd | 4 +-- man/predict.svem_model.Rd | 6 ++--- man/print.svem_significance_test.Rd |only man/svem_significance_test.Rd | 27 +++++++++++------------- vignettes |only 20 files changed, 117 insertions(+), 95 deletions(-)
Title: Marginal Modeling for Exposure Data with Values Below the LOD
Description: Functions of marginal mean and quantile regression models are used to analyze environmental exposure and biomonitoring data with repeated measurements and non-detects (i.e., values below the limit of detection (LOD)), as well as longitudinal exposure data that include non-detects and time-dependent covariates.
Author: I-Chen Chen [cre, aut] ,
Philip Westgate [ctb],
Liya Fu [ctb]
Maintainer: I-Chen Chen <okv0@cdc.gov>
Diff between marlod versions 0.1.1 dated 2024-08-27 and 0.1.2 dated 2024-11-29
DESCRIPTION | 8 +-- MD5 | 14 ++--- inst/doc/marlod.R | 10 +-- inst/doc/marlod.Rmd | 14 ++--- inst/doc/marlod.html | 136 +++++++++++++++++++++++++-------------------------- man/Simdata15.Rd | 4 - man/Simdata58.Rd | 2 vignettes/marlod.Rmd | 14 ++--- 8 files changed, 101 insertions(+), 101 deletions(-)
Title: Transformation Models with Mixed Effects
Description: Likelihood-based estimation of mixed-effects transformation models
using the Template Model Builder ('TMB', Kristensen et al., 2016)
<doi:10.18637/jss.v070.i05>. The technical details of transformation models
are given in Hothorn et al. (2018) <doi:10.1111/sjos.12291>. Likelihood
contributions of exact, randomly censored (left, right, interval) and
truncated observations are supported. The random effects are assumed to be
normally distributed on the scale of the transformation function, the
marginal likelihood is evaluated using the Laplace approximation, and the
gradients are calculated with automatic differentiation (Tamasi & Hothorn,
2021) <doi:10.32614/RJ-2021-075>. Penalized smooth shift terms can be
defined using 'mgcv'.
Author: Balint Tamasi [aut, cre] ,
Torsten Hothorn [ctb]
Maintainer: Balint Tamasi <balint.tamasi+tramME@gmail.com>
Diff between tramME versions 1.0.6 dated 2024-07-02 and 1.0.7 dated 2024-11-29
DESCRIPTION | 8 +- MD5 | 18 +++- NEWS.md | 6 + build/vignette.rds |binary inst/doc/RJ-2021-075.R | 44 ++++++------ inst/doc/RJ-2021-075.pdf |binary inst/doc/mixed-effects-additive-models.R | 106 ++++++++++++++--------------- inst/doc/mixed-effects-additive-models.pdf |binary inst/doc/tramME-JSS.Rnw |only inst/doc/tramME-JSS.pdf |only vignettes/tramME-JSS.Rnw |only vignettes/tramME-JSS_orig.pdf |only 12 files changed, 95 insertions(+), 87 deletions(-)
Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and
Debian-derived Linux systems with a powerful system to resolve package
dependencies. This package offers access directly from R. This can
only work on a system with a suitable 'libapt-pkg-dev' installation
so functionality is curtailed if such a library is not found.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAPT versions 0.0.9 dated 2022-05-25 and 0.0.10 dated 2024-11-29
ChangeLog | 35 ++++ DESCRIPTION | 14 + MD5 | 16 +- README.md | 12 - build/vignette.rds |binary inst/NEWS.Rd | 8 + inst/doc/binnmuAfterR340.html | 309 ++++++++++++++++++++++++++---------------- src/Makevars.in | 5 src/Makevars.win | 5 9 files changed, 261 insertions(+), 143 deletions(-)
Title: Causal Analysis of Observational Time-to-Event Data
Description: Implements target trial emulation methods to apply randomized
clinical trial design and analysis in an observational setting. Using
marginal structural models, it can estimate intention-to-treat and
per-protocol effects in emulated trials using electronic health
records. A description and application of the method can be found in
Danaei et al (2013) <doi:10.1177/0962280211403603>.
Author: Isaac Gravestock [aut, cre] ,
Li Su [aut],
Roonak Rezvani [aut] ,
Julia Moesch [aut],
Medical Research Council [fnd],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between TrialEmulation versions 0.0.3.9 dated 2024-09-09 and 0.0.4.0 dated 2024-11-29
TrialEmulation-0.0.3.9/TrialEmulation/man/predict.TE_msm.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/DESCRIPTION | 36 TrialEmulation-0.0.4.0/TrialEmulation/MD5 | 147 ++- TrialEmulation-0.0.4.0/TrialEmulation/NAMESPACE | 39 TrialEmulation-0.0.4.0/TrialEmulation/NEWS.md | 19 TrialEmulation-0.0.4.0/TrialEmulation/R/calculate_weights.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/data.R | 23 TrialEmulation-0.0.4.0/TrialEmulation/R/data_preparation.R | 2 TrialEmulation-0.0.4.0/TrialEmulation/R/data_simulation.R | 2 TrialEmulation-0.0.4.0/TrialEmulation/R/expand_trials.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/generics.R | 437 +++++++++- TrialEmulation-0.0.4.0/TrialEmulation/R/initiators.R | 2 TrialEmulation-0.0.4.0/TrialEmulation/R/modelling.R | 39 TrialEmulation-0.0.4.0/TrialEmulation/R/package.R | 3 TrialEmulation-0.0.4.0/TrialEmulation/R/predict.R | 47 - TrialEmulation-0.0.4.0/TrialEmulation/R/sampling.R | 63 + TrialEmulation-0.0.4.0/TrialEmulation/R/te_data.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_datastore.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_datastore_csv.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_datastore_duckdb.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_expansion.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_model_fitter.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_outcome_model.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_parsnip.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_stats_glm_logit.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_weights.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/trial_sequence.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/utils.R | 33 TrialEmulation-0.0.4.0/TrialEmulation/README.md | 3 TrialEmulation-0.0.4.0/TrialEmulation/build/vignette.rds |binary TrialEmulation-0.0.4.0/TrialEmulation/data/data_censored.rda |only TrialEmulation-0.0.4.0/TrialEmulation/inst/WORDLIST | 33 TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/Extending-TrialEmulation.R |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/Extending-TrialEmulation.Rmd |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/Extending-TrialEmulation.html |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/Getting-Started.html | 194 ++-- TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/new-interface.R |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/new-interface.Rmd |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/new-interface.html |only TrialEmulation-0.0.4.0/TrialEmulation/man/TrialEmulation-package.Rd | 3 TrialEmulation-0.0.4.0/TrialEmulation/man/calculate_weights.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/case_control_sampling_trials.Rd | 3 TrialEmulation-0.0.4.0/TrialEmulation/man/data_censored.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/data_preparation.Rd | 6 TrialEmulation-0.0.4.0/TrialEmulation/man/expand_trials.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/figures |only TrialEmulation-0.0.4.0/TrialEmulation/man/fit_msm.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/fit_outcome_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/fit_weights_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/initiators.Rd | 3 TrialEmulation-0.0.4.0/TrialEmulation/man/internal-methods.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/ipw_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/load_expanded_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/outcome_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/parsnip_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/predict_marginal.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/print_TE.Rd | 2 TrialEmulation-0.0.4.0/TrialEmulation/man/read_expanded_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/sample_expanded_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/save_expanded_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/save_to_csv.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/save_to_datatable.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/save_to_duckdb.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_censor_weight_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_expansion_options.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_outcome_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_switch_weight_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/show_weight_models.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/stats_glm_logit.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/summary_TE.Rd | 1 TrialEmulation-0.0.4.0/TrialEmulation/man/te_data-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_datastore-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_datastore_csv-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_datastore_duckdb-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_model_fitter-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_outcome_data-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_outcome_fitted-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_outcome_model-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_parsnip_model-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_stats_glm_logit-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/trial_msm.Rd | 6 TrialEmulation-0.0.4.0/TrialEmulation/man/trial_sequence-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/trial_sequence.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/weight_model_data_indices.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/generics.md | 34 TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/modelling.md | 80 + TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/predict.md | 252 +++++ TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/te_weights.md |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/trial_sequence.md |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/data/new_pre_weight_func.rds |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-modelling.R | 117 ++ TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-predict.R | 69 + TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-sampling.R | 90 ++ TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_data.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_datastore.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_datastore_csv.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_datastore_duckdb.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_model_fitter.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_parsnip.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_weights.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-trial_sequence.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-utils.R | 6 TrialEmulation-0.0.4.0/TrialEmulation/vignettes/Extending-TrialEmulation.Rmd |only TrialEmulation-0.0.4.0/TrialEmulation/vignettes/img |only TrialEmulation-0.0.4.0/TrialEmulation/vignettes/new-interface.Rmd |only 106 files changed, 1591 insertions(+), 203 deletions(-)
More information about TrialEmulation at CRAN
Permanent link
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Maximum likelihood estimation of smooth transition vector
autoregressive models with various types of transition weight functions,
conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, and calculation of impulse
response functions, generalized impulse response functions, and generalized
forecast error variance decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2024) <doi:10.48550/arXiv.2403.14216>,
Savi Virolainen (2024) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.0.1 dated 2024-05-29 and 1.1.0 dated 2024-11-29
DESCRIPTION | 10 MD5 | 240 +++---- NAMESPACE | 3 NEWS.md | 33 R/GIRFandGFEVD.R | 20 R/MAINest.R | 639 +++++++++++++----- R/RcppExports.R | 22 R/STVARconstruction.R | 363 +++++++++- R/argumentChecks.R | 73 +- R/data.R | 8 R/diagTests.R | 4 R/diagnosticPlot.R | 129 ++- R/distributionFuns.R |only R/eigens.R | 21 R/generateParams.R | 264 +++++-- R/geneticAlgorithm.R | 227 +++++- R/hypoTests.R | 13 R/jointSpectralRadius.R | 2 R/linearIRF.R | 17 R/loglikelihood.R | 175 +++-- R/miscS3methods.R | 5 R/moreEst.R | 1085 ++++++++++++++++++++++++++++---- R/morePlots.R |only R/numericalDifferentiation.R | 38 - R/parameterReforms.R | 95 +- R/pickParams.R | 76 +- R/printMethods.R | 45 + R/profileLogliks.R | 57 + R/residuals.R | 30 R/simulate.R | 52 + R/standardErrors.R | 13 R/uncondMoments.R | 19 README.md | 70 +- build/vignette.rds |binary inst/doc/sstvars-vignette.Rnw | 293 +++++++- inst/doc/sstvars-vignette.pdf |binary man/GAfit.Rd | 91 ++ man/STVAR.Rd | 62 + man/Wald_test.Rd | 4 man/acidata.Rd | 2 man/alt_stvar.Rd | 15 man/bound_JSR.Rd | 2 man/bounding_const_M.Rd |only man/calc_gradient.Rd | 17 man/change_parametrization.Rd | 34 - man/change_regime.Rd | 42 - man/check_constraints.Rd | 12 man/check_params.Rd | 38 - man/check_weightfun_pars.Rd | 7 man/diagnostic_plot.Rd | 10 man/estim_LS.Rd |only man/estim_NLS.Rd |only man/filter_estimates.Rd |only man/fitSSTVAR.Rd | 80 +- man/fitSTVAR.Rd | 174 ++--- man/fitbsSSTVAR.Rd | 59 + man/form_boldA.Rd | 4 man/generate_skewed_t.Rd |only man/get_alpha_mt.Rd | 4 man/get_boldA_eigens_par.Rd | 34 - man/get_hetsked_sstvar.Rd | 2 man/get_omega_eigens_par.Rd | 34 - man/get_regime_autocovs.Rd | 36 - man/get_regime_means.Rd | 36 - man/get_residuals.Rd | 55 + man/in_paramspace.Rd | 26 man/ind_Student_densities_Cpp.Rd | 4 man/ind_skewed_t_densities_Cpp.Rd |only man/iterate_more.Rd | 37 + man/loglikelihood.Rd | 57 + man/n_params.Rd | 19 man/pick_Am.Rd | 38 - man/pick_Ami.Rd | 38 - man/pick_Omegas.Rd | 44 - man/pick_W.Rd | 15 man/pick_allA.Rd | 38 - man/pick_distpars.Rd | 51 + man/pick_lambdas.Rd | 17 man/pick_phi0.Rd | 40 - man/pick_regime.Rd | 45 - man/pick_weightpars.Rd | 45 - man/plot_struct_shocks.Rd |only man/predict.stvar.Rd | 4 man/print.stvarsum.Rd | 6 man/profile_logliks.Rd | 6 man/random_distpars.Rd | 9 man/random_ind.Rd | 43 - man/random_weightpars.Rd | 12 man/reform_constrained_pars.Rd | 34 - man/reform_data.Rd | 9 man/reorder_B_columns.Rd | 3 man/simulate.stvar.Rd | 4 man/simulate_from_regime.Rd | 4 man/skewed_t_dens.Rd |only man/smart_distpars.Rd | 2 man/smart_ind.Rd | 56 + man/smart_weightpars.Rd | 4 man/sort_impactmats.Rd | 51 - man/sort_regimes.Rd | 22 man/stab_conds_satisfied.Rd | 38 - man/stand_t_dens.Rd |only man/standard_errors.Rd | 49 + man/stvar_to_sstvars110.Rd |only man/swap_B_signs.Rd | 3 man/swap_parametrization.Rd | 3 man/usacpu.Rd | 8 man/warn_eigens.Rd | 5 src/RcppExports.cpp | 19 src/get_Bt_Cpp.cpp | 2 src/ind_Student_densities_Cpp.cpp | 12 src/ind_skewed_t_densities_Cpp.cpp |only tests/testthat/test_GIRFandGFEVD.R | 51 + tests/testthat/test_MAINest.R | 7 tests/testthat/test_STVARconstruction.R | 81 ++ tests/testthat/test_argumentChecks.R | 569 ++++++++++++++++ tests/testthat/test_distributionFuns.R |only tests/testthat/test_eigens.R | 44 + tests/testthat/test_loglikelihood.R | 364 ++++++++++ tests/testthat/test_moreEst.R | 174 ++++- tests/testthat/test_parameterReforms.R | 439 ++++++++++++ tests/testthat/test_pickParams.R | 193 +++++ tests/testthat/test_predict.R | 28 tests/testthat/test_residuals.R | 34 + tests/testthat/test_simulate.R | 33 tests/testthat/test_standardErrors.R | 30 tests/testthat/test_uncondMoments.R | 70 ++ vignettes/refs.bib | 18 vignettes/sstvars-vignette.Rnw | 293 +++++++- 128 files changed, 6627 insertions(+), 1718 deletions(-)
Title: Tidy and Geospatial Kernel Smoothing
Description: Extensions of the kernel smoothing functions from the 'ks' package for compatibility with the tidyverse and geospatial ecosystems <doi:10.1007/s00180-024-01543-9>.
Author: Tarn Duong [aut, cre]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between eks versions 1.0.5 dated 2024-05-01 and 1.0.6 dated 2024-11-29
CHANGELOG | 3 DESCRIPTION | 11 - MD5 | 10 build/vignette.rds |binary inst/doc/tidysf_kde.html | 487 ++++++++++++++++++++++++++--------------------- man/eks-package.Rd | 2 6 files changed, 293 insertions(+), 220 deletions(-)
Title: Fertility Models
Description: Four fertility models are fitted using non-linear least squares. These are the Hadwiger, the Gamma, the Model1 and Model2, following the terminology of the following paper: Peristera P. and Kostaki A. (2007). "Modeling fertility in modern populations". Demographic Research, 16(6): 141--194. <doi:10.4054/DemRes.2007.16.6>. Model based averaging is also supported.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between fertilmodel versions 1.1 dated 2023-01-07 and 1.4 dated 2024-11-29
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ R/Gama.R | 18 ++++++++++-------- R/Hadwiger.R | 4 ++-- man/comb.Rd | 4 ++-- man/fertil.plot.Rd | 2 +- man/fertilmodel-package.Rd | 4 ++-- 7 files changed, 28 insertions(+), 25 deletions(-)
Title: Spatiotemporal Resampling Methods for 'mlr3'
Description: Extends the mlr3 machine learning framework with
spatio-temporal resampling methods to account for the presence of
spatiotemporal autocorrelation (STAC) in predictor variables. STAC may
cause highly biased performance estimates in cross-validation if
ignored. A JSS article is available at <doi:10.18637/jss.v111.i07>.
Author: Patrick Schratz [aut, cre] ,
Marc Becker [aut] ,
Jannes Muenchow [ctb] ,
Michel Lang [ctb]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3spatiotempcv versions 2.3.1 dated 2024-04-17 and 2.3.2 dated 2024-11-29
DESCRIPTION | 17 - MD5 | 167 +++++----- NEWS.md | 5 R/ResamplingRepeatedSpCVBlock.R | 2 R/ResamplingRepeatedSpCVCoords.R | 2 R/ResamplingRepeatedSpCVDisc.R | 2 R/ResamplingRepeatedSpCVEnv.R | 2 R/ResamplingRepeatedSpCVTiles.R | 2 R/ResamplingRepeatedSpCVknndm.R | 2 R/ResamplingRepeatedSptCVCstf.R | 2 R/ResamplingSpCVBlock.R | 2 R/ResamplingSpCVBuffer.R | 2 R/ResamplingSpCVCoords.R | 2 R/ResamplingSpCVDisc.R | 2 R/ResamplingSpCVEnv.R | 2 R/ResamplingSpCVKnndm.R | 2 R/ResamplingSpCVTiles.R | 2 R/ResamplingSptCVCstf.R | 2 R/TaskClassifST.R | 2 R/TaskRegrST.R | 2 R/Task_classif_diplodia.R | 2 R/Task_classif_ecuador.R | 2 R/Task_regr_cookfarm_profiles.R | 2 R/as_task_classif_st.R | 4 R/as_task_regr_st.R | 4 R/autoplot.R | 14 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/mlr3spatiotempcv.html | 7 inst/doc/spatiotemp-viz.html | 8 man/TaskClassifST.Rd | 13 man/TaskRegrST.Rd | 13 man/as_task_classif_st.Rd | 4 man/as_task_regr_st.Rd | 4 man/autoplot.ResamplingCV.Rd | 8 man/autoplot.ResamplingCustomCV.Rd | 4 man/autoplot.ResamplingSpCVBlock.Rd | 2 man/mlr3spatiotempcv-package.Rd | 2 man/mlr_resamplings_repeated_spcv_block.Rd | 2 man/mlr_resamplings_repeated_spcv_coords.Rd | 2 man/mlr_resamplings_repeated_spcv_disc.Rd | 2 man/mlr_resamplings_repeated_spcv_env.Rd | 2 man/mlr_resamplings_repeated_spcv_knndm.Rd | 2 man/mlr_resamplings_repeated_spcv_tiles.Rd | 2 man/mlr_resamplings_repeated_sptcv_cstf.Rd | 2 man/mlr_resamplings_spcv_block.Rd | 2 man/mlr_resamplings_spcv_buffer.Rd | 2 man/mlr_resamplings_spcv_coords.Rd | 2 man/mlr_resamplings_spcv_disc.Rd | 2 man/mlr_resamplings_spcv_env.Rd | 2 man/mlr_resamplings_spcv_knndm.Rd | 2 man/mlr_resamplings_spcv_tiles.Rd | 2 man/mlr_resamplings_sptcv_cstf.Rd | 2 man/mlr_tasks_cookfarm_mlr3.Rd | 6 man/mlr_tasks_diplodia.Rd | 6 man/mlr_tasks_ecuador.Rd | 6 tests/testthat/_snaps/1-autoplot/custom-cv-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/custom-cv-fold-1-2.svg | 61 --- tests/testthat/_snaps/1-autoplot/cv-fold-1-2-groups-col-role.svg | 61 --- tests/testthat/_snaps/1-autoplot/cv-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/cv-fold-1-2.svg | 61 --- tests/testthat/_snaps/1-autoplot/repcv-fold-1-2-rep-1.svg | 61 --- tests/testthat/_snaps/1-autoplot/repspcvblock-fold-1-2-rep-1.svg | 61 --- tests/testthat/_snaps/1-autoplot/repspcvcoords-fold-1-2-rep-1.svg | 61 --- tests/testthat/_snaps/1-autoplot/repspcvcoords-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/repspcvenv-fold-1-2-rep-1.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvblock-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvblock-fold-1-2.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvcoords-fold-1-2.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvenv-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvenv-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvdisc-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvknndm-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvtiles-fold-1-2-rep-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvtiles-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvtiles-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/spcvdisc-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/spcvknndm-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-space-var-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1-2.svg | 61 --- tests/testthat/_snaps/autoplot_buffer/spcvbuffer-fold-1-2.svg | 61 --- tests/testthat/test-TaskClassifST.R | 2 85 files changed, 449 insertions(+), 1505 deletions(-)
More information about mlr3spatiotempcv at CRAN
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Title: Draw Network with Data
Description: Extends the 'ggplot2' plotting system to support network visualization. Inspired by 'ggtree', 'ggtangle' is designed to work with network associated data.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggtangle versions 0.0.4 dated 2024-10-30 and 0.0.5 dated 2024-11-29
DESCRIPTION | 10 +-- MD5 | 29 +++++----- NAMESPACE | 2 NEWS.md | 16 +++++ R/AllGenerics.r | 4 - R/cnet.r | 132 +++++++++++++++++++++++++++++++++++++++++------- R/ggtangle-package.R |only R/graph.r | 22 ++++---- R/utilities.r | 5 + build/vignette.rds |binary inst/doc/ggtangle.R | 43 +++++++++++++++ inst/doc/ggtangle.Rmd | 52 ++++++++++++++++++ inst/doc/ggtangle.html | 61 +++++++++++++++++++--- man/cnetplot.Rd | 4 - man/geom_cnet_label.Rd |only man/ggtangle-package.Rd |only vignettes/ggtangle.Rmd | 52 ++++++++++++++++++ 17 files changed, 375 insertions(+), 57 deletions(-)
Title: Sequence Symmetry Analysis Using the Observational Medical
Outcomes Partnership Common Data Model
Description: Calculating crude sequence ratio, adjusted sequence ratio and
confidence intervals using data mapped to the Observational Medical
Outcomes Partnership Common Data Model.
Author: Xihang Chen [aut, cre] ,
Tyman Stanford [aut] ,
Berta Raventos [aut] ,
Nicole Pratt [aut] ,
Ed Burn [aut] ,
Marti Catala [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez [aut] ,
Marta Alcalde-He [...truncated...]
Maintainer: Xihang Chen <xihang.chen@ndorms.ox.ac.uk>
Diff between CohortSymmetry versions 0.1.4 dated 2024-11-15 and 0.2.0 dated 2024-11-29
CohortSymmetry-0.1.4/CohortSymmetry/R/displayTables.R |only CohortSymmetry-0.1.4/CohortSymmetry/R/inputValidation.R |only CohortSymmetry-0.1.4/CohortSymmetry/man/tableSequenceRatiosOptions.Rd |only CohortSymmetry-0.1.4/CohortSymmetry/tests/testthat/test-displayTable.R |only CohortSymmetry-0.1.4/CohortSymmetry/tests/testthat/test-test-dbs.R |only CohortSymmetry-0.2.0/CohortSymmetry/DESCRIPTION | 17 CohortSymmetry-0.2.0/CohortSymmetry/MD5 | 89 CohortSymmetry-0.2.0/CohortSymmetry/NAMESPACE | 2 CohortSymmetry-0.2.0/CohortSymmetry/R/generateSequenceCohortSet.R | 80 CohortSymmetry-0.2.0/CohortSymmetry/R/getConfidenceInterval.R | 82 CohortSymmetry-0.2.0/CohortSymmetry/R/helpers.R | 15 CohortSymmetry-0.2.0/CohortSymmetry/R/plotSequenceRatios.R | 250 - CohortSymmetry-0.2.0/CohortSymmetry/R/plotTemporalSymmetry.R | 168 CohortSymmetry-0.2.0/CohortSymmetry/R/summariseSequenceRatios.R | 17 CohortSymmetry-0.2.0/CohortSymmetry/R/summariseTemporalSymmetry.R | 247 - CohortSymmetry-0.2.0/CohortSymmetry/R/tableSequenceRatios.R |only CohortSymmetry-0.2.0/CohortSymmetry/R/tableTemporalSymmetry.R |only CohortSymmetry-0.2.0/CohortSymmetry/inst/WORDLIST | 133 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a01_Introduction.R | 29 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a01_Introduction.Rmd | 264 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a01_Introduction.html | 508 -- CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort.html | 6 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.R | 16 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.Rmd | 206 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.html | 91 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.R | 34 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.Rmd | 316 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.html | 1812 ---------- CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.R | 5 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.Rmd | 234 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.html | 42 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.R | 20 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.Rmd | 225 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.html | 50 CohortSymmetry-0.2.0/CohortSymmetry/man/plotSequenceRatios.Rd | 15 CohortSymmetry-0.2.0/CohortSymmetry/man/summariseTemporalSymmetry.Rd | 2 CohortSymmetry-0.2.0/CohortSymmetry/man/tableSequenceRatios.Rd | 33 CohortSymmetry-0.2.0/CohortSymmetry/man/tableTemporalSymmetry.Rd |only CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-dbs.R |only CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-generateSequenceCohortSet.R | 10 CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-plotSequenceRatio.R | 16 CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-plotTemporalSymmetry.R | 271 - CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-summariseSequenceRatios.R | 69 CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-summariseTemporalSymmetry.R | 321 - CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-tableSequenceRatios.R |only CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-tableTemporalSymmetry.R |only CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a01_Introduction.Rmd | 264 - CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a03_Summarise_sequence_ratios.Rmd | 206 - CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a04_Visualise_sequence_ratios.Rmd | 316 - CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a05_Summarise_temporal_symmetry.Rmd | 234 - CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a06_Visualise_temporal_symmetry.Rmd | 225 - 51 files changed, 2123 insertions(+), 4817 deletions(-)
More information about CohortSymmetry at CRAN
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Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Luedecke [aut, cre] ,
Alexander Bartel [ctb] ,
Carsten Schwemmer [ctb],
Chuck Powell [ctb] ,
Amir Djalovski [ctb],
Johannes Titz [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.8.16 dated 2024-05-13 and 2.8.17 dated 2024-11-29
DESCRIPTION | 14 ++++----- MD5 | 52 ++++++++++++++++++------------------ NEWS.md | 22 ++++++++++----- R/plot_frq.R | 2 - R/plot_grid.R | 20 ++++++------- R/plot_grpfrq.R | 2 - R/plot_type_eff.R | 12 ++++++-- R/plot_type_int.R | 7 ++++ build/vignette.rds |binary inst/doc/blackwhitefigures.html | 12 ++++---- inst/doc/custplot.R | 4 +- inst/doc/custplot.html | 32 +++++++++++----------- inst/doc/plot_interactions.html | 26 +++++++++--------- inst/doc/plot_likert_scales.html | 20 ++++++------- inst/doc/plot_marginal_effects.R | 2 - inst/doc/plot_marginal_effects.html | 26 +++++++++--------- inst/doc/plot_model_estimates.html | 34 +++++++++++------------ inst/doc/sjtitemanalysis.html | 6 ++-- inst/doc/tab_bayes.R | 46 +++++++++++++++---------------- inst/doc/tab_bayes.html | 30 ++++++++++---------- inst/doc/tab_mixed.R | 2 - inst/doc/tab_mixed.html | 12 ++++---- inst/doc/tab_model_estimates.html | 6 ++-- inst/doc/tab_model_robust.R | 2 - inst/doc/tab_model_robust.html | 2 - inst/doc/table_css.html | 6 ++-- man/plot_grid.Rd | 8 ++--- 27 files changed, 212 insertions(+), 195 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake',
'Azure Synapse Analytics Dedicated', 'Apache Spark', 'SQLite', and 'InterSystems IRIS'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.19.0 dated 2024-10-09 and 1.19.1 dated 2024-11-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ inst/csv/replacementPatterns.csv | 10 +++++++++- inst/doc/UsingSqlRender.pdf |binary tests/testthat/test-translate-iris.R | 7 +++++++ 6 files changed, 33 insertions(+), 10 deletions(-)
More information about greta.censored at CRAN
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Title: Extreme Value Analysis
Description: General functions for performing extreme value analysis. In particular, allows for inclusion of covariates into the parameters of the extreme-value distributions, as well as estimation through MLE, L-moments, generalized (penalized) MLE (GMLE), as well as Bayes. Inference methods include parametric normal approximation, profile-likelihood, Bayes, and bootstrapping. Some bivariate functionality and dependence checking (e.g., auto-tail dependence function plot, extremal index estimation) is also included. For a tutorial, see Gilleland and Katz (2016) <doi: 10.18637/jss.v072.i08> and for bootstrapping, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Author: Eric Gilleland [aut, cre]
Maintainer: Eric Gilleland <eric.gilleland@colostate.edu>
Diff between extRemes versions 2.1-4 dated 2024-02-02 and 2.2 dated 2024-11-29
DESCRIPTION | 18 +++++++++++------- MD5 | 26 +++++++++++++------------- build/partial.rdb |binary inst/CITATION | 2 +- man/Peak.Rd | 2 +- man/Potomac.Rd | 2 +- man/ci.fevd.Rd | 2 +- man/datagrabber.Rd | 2 +- man/decluster.Rd | 2 +- man/distill.fevd.Rd | 2 +- man/fevd.Rd | 4 ++-- man/findpars.Rd | 2 +- man/xbooter.Rd | 2 +- man/xtibber.Rd | 2 +- 14 files changed, 36 insertions(+), 32 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Adam Black [aut, cre] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut]
Maintainer: Adam Black <black@ohdsi.org>
Diff between CDMConnector versions 1.6.0 dated 2024-11-13 and 1.6.1 dated 2024-11-29
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 4 R/cohort_ddl.R | 2 inst/doc/a01_getting-started.html | 34 ++--- inst/doc/a02_cohorts.html | 188 +++++++++++++++++---------------- inst/doc/a06_using_cdm_attributes.html | 4 7 files changed, 130 insertions(+), 120 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous
posterior distributions with customisable trajectory length
termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for
the original Discontinuous Hamiltonian Monte Carlo,
Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016)
<doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian
Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@studenti.unipd.it>
Diff between XDNUTS versions 1.5 dated 2024-10-28 and 1.5.3 dated 2024-11-29
DESCRIPTION | 8 MD5 | 28 R/interface.R | 63 - build/partial.rdb |binary inst/doc/Tutorial_for_main_functions.R | 10 inst/doc/Tutorial_for_main_functions.Rmd | 16 inst/doc/Tutorial_for_main_functions.html | 246 +-- src/dnuts.cpp | 11 src/epsilon_adapt.cpp | 143 ++ src/epsilon_init.cpp | 1852 ++++++++++++++---------------- src/epsilon_init.h | 131 +- src/globals_functions.cpp | 29 src/single_nuts.cpp | 280 ++-- vignettes/REFERENCES.bib | 11 vignettes/Tutorial_for_main_functions.Rmd | 16 15 files changed, 1427 insertions(+), 1417 deletions(-)
Title: Predicted Means for Linear and Semiparametric Models
Description: Providing functions to diagnose and make inferences from various linear models,
such as those obtained from 'aov', 'lm', 'glm', 'gls', 'lme', 'lmer', 'glmmTMB' and 'semireg'.
Inferences include predicted means and standard errors, contrasts, multiple comparisons,
permutation tests, adjusted R-square and graphs.
Author: Dongwen Luo [aut, cre],
Siva Ganesh [ctb],
John Koolaard [ctb]
Maintainer: Dongwen Luo <dongwen.luo@agresearch.co.nz>
Diff between predictmeans versions 1.1.0 dated 2024-02-29 and 1.1.1 dated 2024-11-29
DESCRIPTION | 22 ++- MD5 | 60 ++++----- NAMESPACE | 10 - R/CookD.R | 2 R/Kmatrix.R | 96 +++++++------- R/PMplot.R | 2 R/R2_glmm.R | 41 +++--- R/contrastmeans.R | 6 R/covariatemeans.R | 23 +++ R/misc.R | 214 ++++++++++++++++++++------------- R/mymodelparm.R | 4 R/permanova.lmer.R | 2 R/permlmer.R | 2 R/predictmeans.R | 283 +++++++++++++++++++++++++++----------------- R/residplot.R | 4 R/rsplot.lme.R | 2 R/semipred.R | 28 +++- R/semireg_tmb.R | 24 +-- R/varcomp.R | 41 ++++-- man/CookD.Rd | 4 man/PMplot.Rd | 7 - man/covariatemeans.Rd | 15 +- man/permanova.lmer.Rd | 10 - man/permmodels.Rd | 42 +++--- man/predictmeans-package.Rd | 5 man/predictmeans.Rd | 35 ++--- man/residplot.Rd | 4 man/semipred.Rd | 56 ++++---- man/semireg.Rd | 24 +-- man/semireg_tmb.Rd | 40 +++--- man/varcomp.Rd | 2 31 files changed, 659 insertions(+), 451 deletions(-)
Title: Dynamic Panel Multiple Threshold Model with Fixed Effects
Description: Compute the fixed effects dynamic panel threshold model suggested by Ramírez-Rondán (2020) <doi:10.1080/07474938.2019.1624401>, and dynamic panel linear model suggested by Hsiao et al. (2002) <doi:10.1016/S0304-4076(01)00143-9>, where maximum likelihood type estimators are used. Multiple threshold estimation based on Markov Chain Monte Carlo (MCMC) is allowed, and model selection of linear model, threshold model and multiple threshold model is also allowed.
Author: Bai Hujie [aut, cre, cph]
Maintainer: Bai Hujie <hujiebai@163.com>
Diff between DPTM versions 1.5.0 dated 2024-08-17 and 1.6.0 dated 2024-11-28
DESCRIPTION | 10 MD5 | 15 - NEWS.md | 27 + R/DPM.R | 732 ++++++++++++++++++++++++++------------------------- R/RcppExports.R | 30 +- R/thresholdS.R | 790 ++++++++++++++++++++++++++++---------------------------- README.md |only man/DPML.Rd | 4 man/DPTS.Rd | 6 9 files changed, 823 insertions(+), 791 deletions(-)
Title: Weather Forecast Verification Utilities
Description: Utilities for verifying discrete, continuous and probabilistic forecasts, and forecasts expressed as parametric distributions are included.
Author: Eric Gilleland [aut, cre] ,
Matt Pocernich [ctb],
Sabrina Wahl [ctb],
Ronald Frenette [ctb]
Maintainer: Eric Gilleland <eric.gilleland@colostate.edu>
Diff between verification versions 1.42 dated 2015-07-14 and 1.44 dated 2024-11-28
DESCRIPTION | 19 +++++-- MD5 | 111 +++++++++++++++++++++---------------------- NAMESPACE | 2 R/attribute.R | 8 --- R/attribute.default.R | 8 --- R/attribute.prob.bin.R | 8 --- R/conditional.quantile.R | 8 --- R/crps.r | 8 --- R/discrimination.plot.R | 8 --- R/hgtest.R | 35 +++++++++++-- R/leps.r | 8 --- R/observation.error.R | 8 --- R/plot.cont.cont.R | 8 --- R/plot.prob.bin.R | 8 --- R/predcomptests.R | 4 - R/qrelPlotDefault.R | 8 --- R/ranked.hist.R | 8 --- R/reliability.plot.R | 8 --- R/reliability.plot.default.R | 8 --- R/reliability.plot.verify.R | 8 --- R/roc.plot.R | 8 --- R/roc.plot.prob.bin.R | 8 --- R/summary.bin.bin.R | 8 --- R/summary.cat.cat.R | 8 --- R/summary.cont.cont.R | 8 --- R/summary.norm.dist.cont.R | 8 --- R/summary.prob.bin.R | 8 --- R/table.stats.R | 8 --- R/value.r | 8 +-- R/verify.R | 7 -- man/attribute.Rd | 8 --- man/brier.Rd | 8 --- man/conditional.quantile.Rd | 8 --- man/crps.Rd | 18 +----- man/disc.dat.Rd | 8 --- man/discrimination.plot.Rd | 8 --- man/fss.Rd | 8 --- man/hg.test.Rd |only man/leps.Rd | 8 --- man/lines.verify.Rd | 8 --- man/measurement.error.Rd | 8 --- man/multi.cont.Rd | 8 --- man/observation.error.Rd | 8 --- man/performance.diagram.Rd | 8 --- man/pop.Rd | 10 --- man/precip.ensemble.Rd | 8 --- man/predcomp.test.Rd | 10 +-- man/prob.frcs.dat.Rd | 8 --- man/probcont2disc.Rd | 8 --- man/reliability.plot.Rd | 8 --- man/roc.area.Rd | 8 --- man/roc.plot.Rd | 8 --- man/rps.Rd | 10 --- man/table.stats.Rd | 8 --- man/value.Rd | 12 ---- man/verify-internal.Rd | 9 --- man/verify.Rd | 10 --- 57 files changed, 121 insertions(+), 480 deletions(-)
Title: Two-Dimensional Field Smoothing
Description: Perform two-dimensional smoothing for spatial fields using FFT and the convolution theorem (see Gilleland 2013, <doi:10.5065/D61834G2>).
Author: Eric Gilleland [aut, cre]
Maintainer: Eric Gilleland <eric.gilleland@colostate.edu>
Diff between smoothie versions 1.0-3 dated 2021-05-31 and 1.0-4 dated 2024-11-28
DESCRIPTION | 15 +++++++-------- MD5 | 14 +++++++------- build/partial.rdb |binary inst/CITATION | 7 ++++--- man/hoods2dsmooth.Rd | 2 +- man/kernel2dmeitsjer.Rd | 2 +- man/kernel2dsmooth.Rd | 2 +- man/smoothie-package.Rd | 2 +- 8 files changed, 22 insertions(+), 22 deletions(-)
Title: Converts 'Monolix' Models to 'rxode2'
Description: 'Monolix' is a tool for running mixed effects model using
'saem'. This tool allows you to convert 'Monolix' models to 'rxode2'
(Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) using the
form compatible with 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>).
If available, the 'rxode2' model will
read in the 'Monolix' data and compare the simulation for the
population model individual model and residual
model to immediately show how well the translation is
performing. This saves the model development time for people who are
creating an 'rxode2' model manually. Additionally, this package reads
in all the information to allow simulation with uncertainty (that is the
number of observations, the number of subjects, and the covariance
matrix) with a 'rxode2' model. This is complementary to the
'babelmixr2' package that translates 'nlmixr2' models to 'Monolix' and can
convert the objects converted from 'monolix2rx' to a full 'nlmixr2' fit. While not
required, you c [...truncated...]
Author: Matthew Fidler [aut, cre] ,
Justin Wilkins [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between monolix2rx versions 0.0.3 dated 2024-10-24 and 0.0.4 dated 2024-11-28
DESCRIPTION | 6 MD5 | 26 NEWS.md | 4 R/content.R | 5 R/dataImport.R | 3 R/ind.R | 25 R/monolix2rx.R | 2 R/validate.R | 8 inst/mlxtranContent.g | 5 src/mlxtranContent.c | 13 src/mlxtranContent.g.d_parser.h | 4798 +++++++++++++++++++++------------------- src/mlxtranInd.c | 14 tests/testthat/test-content.R | 55 tests/testthat/test-ind.R | 2 14 files changed, 2772 insertions(+), 2194 deletions(-)
Title: ISO 3166-1 Country Codes
Description: ISO 3166-1 country codes and ISO 4217 currency codes provided
by the International Organization for Standardization.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between isocountry versions 0.2.0 dated 2024-04-09 and 0.3.0 dated 2024-11-28
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NEWS.md | 4 ++++ data/isocountry.rda |binary data/isocurrency.rda |binary 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Client for the Ifo Institute Time Series
Description: Download ifo business survey data and more time series from
ifo institute <https://www.ifo.de/en/ifo-time-series>.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between ifo versions 0.1.0 dated 2024-06-06 and 0.2.0 dated 2024-11-28
DESCRIPTION | 18 +++++++++--------- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/ifo.R | 2 +- README.md | 16 ++++++++++++---- man/figures/README-plotting-1.png |binary man/ifo-package.Rd | 2 +- tests/testthat/test-ifo.R | 4 +--- 8 files changed, 35 insertions(+), 25 deletions(-)
Title: Doubly Robust Average Partial Effects
Description: Doubly robust average partial effect estimation. This implementation contains methods for adding additional smoothness to plug-in regression procedures and for estimating score functions using smoothing splines. Details of the method can be found in Harvey Klyne and Rajen D. Shah (2023) <doi:10.48550/arXiv.2308.09207>.
Author: Harvey Klyne [aut, cre, cph]
Maintainer: Harvey Klyne <hck33@cantab.ac.uk>
Diff between drape versions 0.0.1 dated 2023-09-18 and 0.0.2 dated 2024-11-28
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/simulation_settings.R | 13 ++++++------- man/simulate_data.Rd | 12 +++++------- man/z_correlated_normal.Rd | 4 ++-- 6 files changed, 29 insertions(+), 28 deletions(-)
Title: Method Functions for Confidence Intervals and to Distill
Information from an Object
Description: Some very simple method functions for confidence interval calculation, bootstrap resampling aimed at atmospheric science applications, and to distill pertinent information from a potentially complex object; primarily used in common with packages extRemes and SpatialVx. To reference this package and for a tutorial on the bootstrap functions, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0069.1> and Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Author: Eric Gilleland [aut, cre]
Maintainer: Eric Gilleland <eric.gilleland@colostate.edu>
Diff between distillery versions 1.2-1 dated 2021-05-19 and 1.2-2 dated 2024-11-28
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ R/booter.R | 16 ++++------------ man/booter.Rd | 8 ++------ man/ci.booted.Rd | 2 +- man/pbooter.Rd | 2 +- man/tibber.Rd | 2 +- 7 files changed, 22 insertions(+), 34 deletions(-)
Title: Creates Safety Results Summary in XML to Upload to EudraCT, or
ClinicalTrials.gov
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by Eudr [...truncated...]
Author: Simon Bond [cre],
Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>
Diff between eudract versions 1.0.1 dated 2024-08-23 and 1.0.2 dated 2024-11-28
DESCRIPTION | 8 +-- MD5 | 18 +++---- NEWS.md | 4 + R/safety_summary.R | 4 - inst/doc/eudract.html | 10 +-- tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/dotplot/dotplot-3groups.svg | 56 ++++++++++++++++++---- tests/testthat/_snaps/dotplot/dotplot-ref-rr.svg | 44 +++++++++++++---- tests/testthat/_snaps/dotplot/dotplot-ref.svg | 44 +++++++++++++---- tests/testthat/_snaps/dotplot/dotplot.svg | 44 +++++++++++++---- 10 files changed, 172 insertions(+), 60 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.2.1 dated 2024-10-25 and 1.2.2 dated 2024-11-28
PatientProfiles-1.2.1/PatientProfiles/R/utils-pipe.R |only PatientProfiles-1.2.1/PatientProfiles/man/pipe.Rd |only PatientProfiles-1.2.2/PatientProfiles/DESCRIPTION | 15 PatientProfiles-1.2.2/PatientProfiles/MD5 | 176 ++--- PatientProfiles-1.2.2/PatientProfiles/NAMESPACE | 3 PatientProfiles-1.2.2/PatientProfiles/NEWS.md | 15 PatientProfiles-1.2.2/PatientProfiles/R/PatientProfiles-package.R | 1 PatientProfiles-1.2.2/PatientProfiles/R/addCategories.R | 32 PatientProfiles-1.2.2/PatientProfiles/R/addCohortIntersect.R | 27 PatientProfiles-1.2.2/PatientProfiles/R/addConceptIntersect.R | 44 - PatientProfiles-1.2.2/PatientProfiles/R/addDeath.R | 12 PatientProfiles-1.2.2/PatientProfiles/R/addDemographics.R | 22 PatientProfiles-1.2.2/PatientProfiles/R/addDemographicsQuery.R | 31 PatientProfiles-1.2.2/PatientProfiles/R/addIntersect.R | 122 +-- PatientProfiles-1.2.2/PatientProfiles/R/addObservationPeriodId.R | 9 PatientProfiles-1.2.2/PatientProfiles/R/addTableIntersect.R | 21 PatientProfiles-1.2.2/PatientProfiles/R/checks.R | 24 PatientProfiles-1.2.2/PatientProfiles/R/formats.R | 10 PatientProfiles-1.2.2/PatientProfiles/R/summariseResult.R | 26 PatientProfiles-1.2.2/PatientProfiles/R/utilities.R | 8 PatientProfiles-1.2.2/PatientProfiles/README.md | 324 ++++------ PatientProfiles-1.2.2/PatientProfiles/inst/doc/cohort-intersect.R | 28 PatientProfiles-1.2.2/PatientProfiles/inst/doc/cohort-intersect.Rmd | 28 PatientProfiles-1.2.2/PatientProfiles/inst/doc/cohort-intersect.html | 122 +-- PatientProfiles-1.2.2/PatientProfiles/inst/doc/concept-intersect.R | 24 PatientProfiles-1.2.2/PatientProfiles/inst/doc/concept-intersect.Rmd | 24 PatientProfiles-1.2.2/PatientProfiles/inst/doc/concept-intersect.html | 119 +-- PatientProfiles-1.2.2/PatientProfiles/inst/doc/demographics.R | 68 +- PatientProfiles-1.2.2/PatientProfiles/inst/doc/demographics.html | 318 ++++----- PatientProfiles-1.2.2/PatientProfiles/inst/doc/demographics.rmd | 68 +- PatientProfiles-1.2.2/PatientProfiles/inst/doc/summarise.html | 213 +++--- PatientProfiles-1.2.2/PatientProfiles/inst/doc/table-intersect.R | 2 PatientProfiles-1.2.2/PatientProfiles/inst/doc/table-intersect.Rmd | 2 PatientProfiles-1.2.2/PatientProfiles/inst/doc/table-intersect.html | 88 +- PatientProfiles-1.2.2/PatientProfiles/man/PatientProfiles-package.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addAgeQuery.Rd | 1 PatientProfiles-1.2.2/PatientProfiles/man/addCategories.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addCdmName.Rd | 2 PatientProfiles-1.2.2/PatientProfiles/man/addCohortIntersectCount.Rd | 3 PatientProfiles-1.2.2/PatientProfiles/man/addCohortIntersectDate.Rd | 7 PatientProfiles-1.2.2/PatientProfiles/man/addCohortIntersectDays.Rd | 7 PatientProfiles-1.2.2/PatientProfiles/man/addCohortIntersectFlag.Rd | 2 PatientProfiles-1.2.2/PatientProfiles/man/addCohortName.Rd | 2 PatientProfiles-1.2.2/PatientProfiles/man/addConceptIntersectCount.Rd | 11 PatientProfiles-1.2.2/PatientProfiles/man/addConceptIntersectDate.Rd | 11 PatientProfiles-1.2.2/PatientProfiles/man/addConceptIntersectDays.Rd | 11 PatientProfiles-1.2.2/PatientProfiles/man/addConceptIntersectFlag.Rd | 11 PatientProfiles-1.2.2/PatientProfiles/man/addDateOfBirth.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addDateOfBirthQuery.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addDeathDate.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addDeathDays.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addDeathFlag.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addDemographics.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addDemographicsQuery.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addFutureObservation.Rd | 3 PatientProfiles-1.2.2/PatientProfiles/man/addFutureObservationQuery.Rd | 3 PatientProfiles-1.2.2/PatientProfiles/man/addInObservation.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addInObservationQuery.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addObservationPeriodId.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addObservationPeriodIdQuery.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addPriorObservation.Rd | 3 PatientProfiles-1.2.2/PatientProfiles/man/addPriorObservationQuery.Rd | 3 PatientProfiles-1.2.2/PatientProfiles/man/addSex.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addSexQuery.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/man/addTableIntersectCount.Rd | 2 PatientProfiles-1.2.2/PatientProfiles/man/addTableIntersectDate.Rd | 2 PatientProfiles-1.2.2/PatientProfiles/man/addTableIntersectDays.Rd | 2 PatientProfiles-1.2.2/PatientProfiles/man/addTableIntersectField.Rd | 2 PatientProfiles-1.2.2/PatientProfiles/man/addTableIntersectFlag.Rd | 3 PatientProfiles-1.2.2/PatientProfiles/man/summariseResult.Rd | 4 PatientProfiles-1.2.2/PatientProfiles/tests/manual/test-sqltest.R | 24 PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addAttributes.R | 4 PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addCategories.R | 46 - PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addCohortIntersect.R | 212 +++--- PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addConceptIntersect.R | 24 PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addDemographics.R | 306 ++++----- PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addFutureObservation.R | 36 - PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addInObservation.R | 28 PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addIntersect.R | 232 +++---- PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addObservationPeriodId.R | 76 ++ PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addPriorObservation.R | 24 PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addSex.R | 10 PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-addTableIntersect.R | 192 ++--- PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-checks.R | 24 PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-format.R | 30 PatientProfiles-1.2.2/PatientProfiles/tests/testthat/test-summariseResult.R | 120 +-- PatientProfiles-1.2.2/PatientProfiles/vignettes/cohort-intersect.Rmd | 28 PatientProfiles-1.2.2/PatientProfiles/vignettes/concept-intersect.Rmd | 24 PatientProfiles-1.2.2/PatientProfiles/vignettes/demographics.rmd | 68 +- PatientProfiles-1.2.2/PatientProfiles/vignettes/table-intersect.Rmd | 2 90 files changed, 1904 insertions(+), 1787 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Graphical User Interface for Data Quality Assessment
Description: A graphical user interface (GUI) to the functions implemented
in the R package 'DQAstats'. Publication: Mang et al. (2021)
<doi:10.1186/s12911-022-01961-z>.
Author: Lorenz A. Kapsner [cre, aut] ,
Jonathan M. Mang [aut] ,
Helene Koester [ctb],
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between DQAgui versions 0.2.4 dated 2024-06-06 and 0.2.5 dated 2024-11-28
DESCRIPTION | 11 MD5 | 44 R/app_utils.R | 1811 ++++++++++++------------- R/custom_buttons.R | 234 +-- R/dot_helper.R | 52 R/launch_app.R | 194 +- R/moduleAtempPlausibility.R | 2 R/moduleCompleteness.R | 2 R/moduleConfig.R | 343 ++++ R/moduleDashboard.R | 6 R/moduleDescriptive.R | 2 R/moduleDifferences.R | 2 R/moduleLog.R | 2 R/moduleMDR.R | 2 R/moduleReport.R | 2 R/moduleUniquePlausibility.R | 2 inst/application/global.R | 134 - inst/application/server.R | 795 +++++------ inst/application/ui.R | 344 ++-- tests/testthat/_snaps/shinyapp.md | 2688 +++++++++++++++++++------------------- tests/testthat/apps/dqagui/app.R | 88 - tests/testthat/test-lints.R | 66 tests/testthat/test-shinyapp.R | 230 +-- 23 files changed, 3708 insertions(+), 3348 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98), other curves (e.g., NOTCal04 [van der Plicht et al. 2004], Arnold & Libby 1951) and postbomb curves. Also provided are functions to copy the curves into memory, and to read, query and plot the data underlying the IntCal20 curves.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rintcal versions 1.0.0 dated 2024-09-23 and 1.1.0 dated 2024-11-28
DESCRIPTION | 8 +++---- MD5 | 26 +++++++++++++---------- NEWS.md | 5 ++++ R/rintcal.R | 50 ++++++++++++++++++++++++++++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rintcal.R | 6 ++--- inst/doc/rintcal.html | 28 +++++++++++++------------ inst/extdata/NOTCal04.14C |only inst/extdata/intcal20.14c |only inst/extdata/marine20.14c |only inst/extdata/shcal20.14c |only man/ccurve.Rd | 2 + man/glue.ccurves.Rd | 12 ++++++++++- man/mix.ccurves.Rd | 12 +++++++++++ man/rintcal-package.Rd | 2 - 16 files changed, 108 insertions(+), 43 deletions(-)
Title: Generalized Reporter Score-Based Enrichment Analysis for Omics
Data
Description: Inspired by the classic 'RSA', we developed the improved 'Generalized Reporter
Score-based Analysis (GRSA)' method, implemented in the R package 'ReporterScore', along
with comprehensive visualization methods and pathway databases. 'GRSA' is a threshold-free
method that works well with all types of biomedical features, such as genes, chemical compounds,
and microbial species. Importantly, the 'GRSA' supports multi-group and longitudinal experimental
designs, because of the included multi-group-compatible statistical methods.
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Diff between ReporterScore versions 0.1.8 dated 2024-08-26 and 0.1.9 dated 2024-11-28
DESCRIPTION | 6 ++-- MD5 | 14 +++++----- NEWS.md | 8 +++++ R/calculation.R | 16 ++++++++++- R/check_files.R | 22 ++++++++-------- R/plot.R | 60 ++++++++++++++++++++++++-------------------- inst/doc/ReporterScore.html | 4 +- man/plot_report.Rd | 10 +++++-- 8 files changed, 87 insertions(+), 53 deletions(-)
Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between sgs versions 0.3.1 dated 2024-11-16 and 0.3.2 dated 2024-11-28
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++----------- R/atos.R | 44 ++++++++++++++++++------------------- R/fit_goscar.R | 22 ++++++++++-------- R/fit_gslope.R | 16 ++++++------- R/fit_sgo.R | 23 ++++++++++++++----- R/fit_sgs.R | 25 +++++++++++++++------ R/global_wrapper_code.R | 5 +++- R/utils.R | 8 ++++++ inst/doc/reproducible_example.html | 12 +++++----- man/fit_goscar.Rd | 14 +++++------ man/fit_gslope.Rd | 14 +++++------ man/fit_sgo.Rd | 22 +++++++++++++----- man/fit_sgs.Rd | 22 +++++++++++++----- 14 files changed, 159 insertions(+), 102 deletions(-)
Title: Patient Rule Induction Method (PRIM)
Description: Patient Rule Induction Method (PRIM) for bump hunting in high-dimensional data.
Author: Tarn Duong [aut, cre]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between prim versions 1.0.21 dated 2023-01-06 and 1.0.22 dated 2024-11-28
DESCRIPTION | 8 - MD5 | 16 +- build/vignette.rds |binary inst/doc/prim-2d.R | 8 - inst/doc/prim-2d.html | 303 +++++++++++++++++++++++++++----------------------- inst/doc/prim-3d.R | 6 inst/doc/prim-3d.html | 283 ++++++++++++++++++++++++---------------------- man/prim-package.Rd | 1 man/prim.box.Rd | 8 - 9 files changed, 337 insertions(+), 296 deletions(-)
Title: Group Subset Selection
Description: Provides tools for sparse regression modelling with grouped predictors using the group
subset selection penalty. Uses coordinate descent and local search algorithms to rapidly deliver
near optimal estimates. The group subset penalty can be combined with a group lasso or ridge
penalty for added shrinkage. Linear and logistic regression are supported, as are overlapping
groups.
Author: Ryan Thompson [aut, cre]
Maintainer: Ryan Thompson <ryan.thompson-1@uts.edu.au>
Diff between grpsel versions 1.3.1 dated 2022-09-07 and 1.3.2 dated 2024-11-28
DESCRIPTION | 12 MD5 | 32 +- NEWS.md | 5 R/cv-grpsel.R | 15 - R/grpsel.R | 17 - build/vignette.rds |binary inst/CITATION | 19 - inst/doc/vignette.R | 2 inst/doc/vignette.html | 577 +++++++++++++++++++++++------------------------ man/coef.cv.grpsel.Rd | 2 man/coef.grpsel.Rd | 2 man/cv.grpsel.Rd | 2 man/grpsel.Rd | 7 man/plot.cv.grpsel.Rd | 2 man/plot.grpsel.Rd | 2 man/predict.cv.grpsel.Rd | 2 man/predict.grpsel.Rd | 2 17 files changed, 354 insertions(+), 346 deletions(-)
Title: Cross-Design & Cross-Format Network Meta-Analysis and Regression
Description: Network meta-analysis and meta-regression (allows
including up to three covariates) for individual participant data,
aggregate data, and mixtures of both formats using the three-level
hierarchical model. Each format can come from randomized controlled
trials or non-randomized studies or mixtures of both. Estimates are
generated in a Bayesian framework using JAGS. The implemented models
are described by Hamza et al. 2023 <DOI:10.1002/jrsm.1619>.
Author: Tasnim Hamza [aut] ,
Guido Schwarzer [aut, cre] ,
Georgia Salanti [aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between crossnma versions 1.2.0 dated 2023-09-18 and 1.3.0 dated 2024-11-28
DESCRIPTION | 16 ++++---- MD5 | 70 ++++++++++++++++++------------------ NAMESPACE | 2 - NEWS.md | 20 ++++++++++ R/crossnma-package.R | 30 +++++++++------ R/crossnma.R | 11 ++--- R/crossnma.code.R | 31 +++++++-------- R/crossnma.model.R | 37 +++++++++---------- R/heatplot.crossnma.R | 2 - R/league.crossnma.R | 32 ++++++++-------- R/max_TE.R | 4 +- R/netconnection.crossnma.R | 6 +-- R/netconnection.crossnma.model.R | 6 +-- R/netgraph.crossnma.R | 13 +++--- R/netgraph.crossnma.model.R | 13 +++--- R/plot.crossnma.R | 2 - R/print.crossnma.R | 2 - R/print.summary.crossnma.R | 2 - R/summary.crossnma.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 26 +++++++------ inst/doc/crossnma.pdf |binary man/crossnma-package.Rd | 26 ++++++++++--- man/crossnma.Rd | 11 ++--- man/crossnma.model.Rd | 7 ++- man/heatplot.crossnma.Rd | 2 - man/league.crossnma.Rd | 2 - man/netconnection.crossnma.Rd | 2 - man/netconnection.crossnma.model.Rd | 2 - man/netgraph.crossnma.Rd | 4 +- man/netgraph.crossnma.model.Rd | 4 +- man/plot.crossnma.Rd | 2 - man/print.crossnma.Rd | 2 - man/print.summary.crossnma.Rd | 2 - man/summary.crossnma.Rd | 2 - 36 files changed, 219 insertions(+), 176 deletions(-)
Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Edward Burn [aut, cre] ,
Kim Lopez-Gueell [aut] ,
Marti Catala [aut] ,
Xintong Li [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortSurvival versions 0.6.0 dated 2024-11-10 and 0.6.1 dated 2024-11-28
DESCRIPTION | 15 MD5 | 38 - R/CohortSurvival-package.R | 16 R/asSurvivalResult.R | 7 R/deathDiagnostics.R | 11 R/estimateSurvival.R | 14 R/generateDeathCohort.R | 328 ++++++++-------- R/plotSurvival.R | 3 R/tableSurvival.R | 556 ++++++++++++++-------------- R/utils-pipe.R | 28 - R/utils-tidy-eval.R | 216 +++++----- build/vignette.rds |binary inst/doc/a01_Single_event_of_interest.html | 232 ++++++----- inst/doc/a02_Competing_risk_survival.html | 234 ++++++----- inst/doc/a03_Further_survival_analyses.html | 4 man/pipe.Rd | 40 +- man/tidyeval.Rd | 202 +++++----- tests/testthat.R | 24 - tests/testthat/test-deathDiagnostics.R | 372 +++++++++--------- tests/testthat/test-mockMGUS2cdm.R | 26 - 20 files changed, 1205 insertions(+), 1161 deletions(-)
More information about CohortSurvival at CRAN
Permanent link
Title: Dual Feature Reduction for SGL
Description: Implementation of the Dual Feature Reduction (DFR) approach for the Sparse Group Lasso (SGL) and the Adaptive Sparse Group Lasso (aSGL) (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.17094>). The DFR approach is a feature reduction approach that applies strong screening to reduce the feature space before optimisation, leading to speed-up improvements for fitting SGL (Simon et al. (2013) <doi:10.1080/10618600.2012.681250>) and aSGL (Mendez-Civieta et al. (2020) <doi:10.1007/s11634-020-00413-8> and Poignard (2020) <doi:10.1007/s10463-018-0692-7>) models. DFR is implemented using the Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) algorithm, with linear and logistic SGL models supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between dfr versions 0.1.1 dated 2024-11-16 and 0.1.2 dated 2024-11-28
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/dfr_adap_sgl.R | 21 +++++++++++++++++---- R/dfr_sgl.R | 19 +++++++++++++++---- R/global_wrapper_code.R | 10 ++++++++-- R/utils.R | 8 ++++++++ man/dfr_adap_sgl.Rd | 20 ++++++++++++++++---- man/dfr_sgl.Rd | 18 ++++++++++++++---- 8 files changed, 89 insertions(+), 29 deletions(-)
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