Title: Create Useful Summaries of the Portal Data
Description: Download and generate summaries for the rodent,
plant, ant, and weather data from the Portal Project. Portal is a
long-term (and ongoing) experimental monitoring site in the Chihuahuan
desert. The raw data files can be found at
<https://github.com/weecology/portaldata>.
Author: Glenda M. Yenni [aut, cre] ,
Hao Ye [aut] ,
Erica M. Christensen [aut] ,
Juniper L. Simonis [aut] ,
Ellen K. Bledsoe [aut] ,
Renata M. Diaz [aut] ,
Shawn D. Taylor [aut] ,
Ethan P, White [aut] ,
S.K. Morgan Ernest [aut] ,
Weecology [cph]
Maintainer: Glenda M. Yenni <glenda@weecology.org>
Diff between portalr versions 0.4.2 dated 2024-08-28 and 0.4.3 dated 2024-09-23
portalr-0.4.2/portalr/R/utils-format-message.R |only portalr-0.4.2/portalr/man/format_code.Rd |only portalr-0.4.2/portalr/man/format_todo.Rd |only portalr-0.4.2/portalr/man/format_value.Rd |only portalr-0.4.3/portalr/DESCRIPTION | 6 portalr-0.4.3/portalr/MD5 | 35 +-- portalr-0.4.3/portalr/NAMESPACE | 4 portalr-0.4.3/portalr/NEWS.md | 13 + portalr-0.4.3/portalr/R/NDVI.R | 7 portalr-0.4.3/portalr/R/load_data.R | 93 ++++++---- portalr-0.4.3/portalr/R/process_data_utils.R | 20 +- portalr-0.4.3/portalr/R/summarize_individual_rodents.R | 25 ++ portalr-0.4.3/portalr/R/summarize_rodents.R | 22 +- portalr-0.4.3/portalr/inst/doc/portal_researcher_examples.html | 76 +++----- portalr-0.4.3/portalr/inst/doc/rodent-abundance-demo.html | 12 - portalr-0.4.3/portalr/man/load_datafile.Rd | 5 portalr-0.4.3/portalr/man/load_rodent_data.Rd | 14 + portalr-0.4.3/portalr/man/print.Rd |only portalr-0.4.3/portalr/man/summarize_plant_data.Rd | 2 portalr-0.4.3/portalr/man/summarize_rodent_data.Rd | 2 portalr-0.4.3/portalr/tests/testthat/test-99-regression.R | 8 21 files changed, 193 insertions(+), 151 deletions(-)
Title: Multilevel B-Spline Approximation
Description: Functions to interpolate irregularly and regularly spaced data using Multilevel B-spline Approximation (MBA). Functions call portions of the SINTEF Multilevel B-spline Library written by Øyvind Hjelle which implements methods developed by Lee, Wolberg and Shin (1997; <doi:10.1109/2945.620490>).
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut],
Oeyvind Hjelle [aut],
Roger Bivand [ctb]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between MBA versions 0.1-1 dated 2024-08-19 and 0.1-2 dated 2024-09-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/UCBsplines.cpp | 4 +++- src/include/GenMatrix.h | 4 +++- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: A 'Shiny' App to Analyze Accelerometer-Measured Daily Physical
Behavior Data
Description: A tool to analyse 'ActiGraph' accelerometer data and to implement
the use of the PROactive Physical Activity in COPD (chronic obstructive pulmonary disease) instruments. Once analysis
is completed, the app allows to export results to .csv files and to generate
a report of the measurement. All the configured inputs relevant for interpreting
the results are recorded in the report. In addition to the existing 'R' packages
that are fully integrated with the app, the app uses some functions from the
'actigraph.sleepr' package developed by Petkova (2021) <https://github.com/dipetkov/actigraph.sleepr/>.
Author: Pierre-Yves de Muellenheim [cre, aut]
Maintainer: Pierre-Yves de Muellenheim <pydemull@uco.fr>
Diff between activAnalyzer versions 2.1.1 dated 2024-05-05 and 2.1.2 dated 2024-09-23
DESCRIPTION | 22 - MD5 | 30 - NEWS.md | 392 +++++++++++++------------- R/app_server.R | 10 R/app_ui.R | 2 R/globals.R | 3 build/vignette.rds |binary inst/doc/activAnalyzer.R | 4 inst/doc/activAnalyzer.Rmd | 36 ++ inst/doc/activAnalyzer.html | 603 +--------------------------------------- inst/report/report_en_long.Rmd | 2 inst/report/report_en_short.Rmd | 2 inst/report/report_fr_long.Rmd | 3 inst/report/report_fr_short.Rmd | 3 tests/testthat/Rplots.pdf |binary vignettes/activAnalyzer.Rmd | 36 ++ 16 files changed, 332 insertions(+), 816 deletions(-)
Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute
distance, correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis
of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad
Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut],
Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between tgstat versions 2.3.27 dated 2024-02-15 and 2.3.28 dated 2024-09-23
DESCRIPTION | 11 + MD5 | 42 ++++--- NEWS.md | 6 + R/dist.R | 2 R/tgstat-package.R | 5 build/partial.rdb |only build/vignette.rds |binary inst/doc/manual.html | 240 ++----------------------------------------- man/tgstat-package.Rd | 23 +++- src/ProgressReporter.cpp | 3 src/corgraph.cpp | 51 ++++----- src/correlation.cpp | 241 ++++++++++++++++++++++--------------------- src/correlation_knn.cpp | 113 ++++++++++---------- src/dist.cpp | 91 ++++++++-------- src/graph2cluster.cpp | 259 +++++++++++++++++++++++------------------------ src/knn.cpp | 59 +++++----- src/matrix_tapply.cpp | 166 +++++++++++++++--------------- src/tgstat-init.cpp | 3 src/tgstat.cpp | 74 ++++++++----- src/tgstat.h | 5 src/utils.cpp | 13 +- tests |only 22 files changed, 641 insertions(+), 766 deletions(-)
Title: A Concentration-Response Modeling Utility
Description: The tcplfit2 R package performs basic concentration-response curve fitting. The original tcplFit() function in the tcpl R package performed basic concentration-response curvefitting to 3 models. With tcplfit2, the core tcpl concentration-response functionality has been expanded to process diverse high-throughput screen (HTS) data generated at the US Environmental Protection Agency, including targeted ToxCast, high-throughput transcriptomics (HTTr) and high-throughput phenotypic profiling (HTPP). tcplfit2 can be used independently to support analysis for diverse chemical screening efforts.
Author: Thomas Sheffield [aut],
Richard S Judson [ctb] ,
Jason Brown [cre] ,
Sarah E. Davidson [ctb] ,
Zhihui Zhao [ctb],
Madison Feshuk [ctb] ,
Katie Paul Friedman [ctb]
Maintainer: Jason Brown <brown.jason@epa.gov>
Diff between tcplfit2 versions 0.1.6 dated 2023-10-10 and 0.1.7 dated 2024-09-23
tcplfit2-0.1.6/tcplfit2/README |only tcplfit2-0.1.7/tcplfit2/DESCRIPTION | 49 tcplfit2-0.1.7/tcplfit2/MD5 | 121 tcplfit2-0.1.7/tcplfit2/NAMESPACE | 10 tcplfit2-0.1.7/tcplfit2/NEWS.md | 9 tcplfit2-0.1.7/tcplfit2/R/acy.R | 15 tcplfit2-0.1.7/tcplfit2/R/bmdbounds.R | 20 tcplfit2-0.1.7/tcplfit2/R/bmdobj.R | 28 tcplfit2-0.1.7/tcplfit2/R/concRespCore.R | 30 tcplfit2-0.1.7/tcplfit2/R/concRespPlot2.R |only tcplfit2-0.1.7/tcplfit2/R/fitcnst.R | 8 tcplfit2-0.1.7/tcplfit2/R/fitexp2.R | 11 tcplfit2-0.1.7/tcplfit2/R/fitexp3.R | 11 tcplfit2-0.1.7/tcplfit2/R/fitexp4.R | 11 tcplfit2-0.1.7/tcplfit2/R/fitexp5.R | 11 tcplfit2-0.1.7/tcplfit2/R/fitgnls.R | 12 tcplfit2-0.1.7/tcplfit2/R/fithill.R | 11 tcplfit2-0.1.7/tcplfit2/R/fitpoly1.R | 11 tcplfit2-0.1.7/tcplfit2/R/fitpoly2.R | 111 tcplfit2-0.1.7/tcplfit2/R/fitpow.R | 12 tcplfit2-0.1.7/tcplfit2/R/get_AUC.R |only tcplfit2-0.1.7/tcplfit2/R/hitcontinner.R | 20 tcplfit2-0.1.7/tcplfit2/R/plot_allcurves.R |only tcplfit2-0.1.7/tcplfit2/R/post_hit_AUC.R |only tcplfit2-0.1.7/tcplfit2/R/sysdata.rda |only tcplfit2-0.1.7/tcplfit2/R/tcplObj.R | 23 tcplfit2-0.1.7/tcplfit2/R/tcplfit2_core.R | 27 tcplfit2-0.1.7/tcplfit2/R/tcplhit2_core.R | 114 tcplfit2-0.1.7/tcplfit2/R/toplikelihood.R | 13 tcplfit2-0.1.7/tcplfit2/README.md |only tcplfit2-0.1.7/tcplfit2/build/partial.rdb |binary tcplfit2-0.1.7/tcplfit2/build/vignette.rds |binary tcplfit2-0.1.7/tcplfit2/inst/doc/tcplfit2-vignette.R | 1207 ++ tcplfit2-0.1.7/tcplfit2/inst/doc/tcplfit2-vignette.Rmd | 1815 +++- tcplfit2-0.1.7/tcplfit2/inst/doc/tcplfit2-vignette.html | 6808 ++++++++++++++-- tcplfit2-0.1.7/tcplfit2/man/acy.Rd | 4 tcplfit2-0.1.7/tcplfit2/man/bmdbounds.Rd | 11 tcplfit2-0.1.7/tcplfit2/man/bmdobj.Rd | 21 tcplfit2-0.1.7/tcplfit2/man/concRespCore.Rd | 24 tcplfit2-0.1.7/tcplfit2/man/concRespPlot2.Rd |only tcplfit2-0.1.7/tcplfit2/man/fitcnst.Rd | 6 tcplfit2-0.1.7/tcplfit2/man/fitexp2.Rd | 13 tcplfit2-0.1.7/tcplfit2/man/fitexp3.Rd | 7 tcplfit2-0.1.7/tcplfit2/man/fitexp4.Rd | 13 tcplfit2-0.1.7/tcplfit2/man/fitexp5.Rd | 7 tcplfit2-0.1.7/tcplfit2/man/fitgnls.Rd | 7 tcplfit2-0.1.7/tcplfit2/man/fithill.Rd | 13 tcplfit2-0.1.7/tcplfit2/man/fitpoly1.Rd | 13 tcplfit2-0.1.7/tcplfit2/man/fitpoly2.Rd | 35 tcplfit2-0.1.7/tcplfit2/man/fitpow.Rd | 7 tcplfit2-0.1.7/tcplfit2/man/get_AUC.Rd |only tcplfit2-0.1.7/tcplfit2/man/hitcontinner.Rd | 17 tcplfit2-0.1.7/tcplfit2/man/plot_allcurves.Rd |only tcplfit2-0.1.7/tcplfit2/man/poly2bmds.Rd |only tcplfit2-0.1.7/tcplfit2/man/post_hit_AUC.Rd |only tcplfit2-0.1.7/tcplfit2/man/tcplObj.Rd | 6 tcplfit2-0.1.7/tcplfit2/man/tcplfit2_core.Rd | 14 tcplfit2-0.1.7/tcplfit2/man/tcplhit2_core.Rd | 20 tcplfit2-0.1.7/tcplfit2/man/toplikelihood.Rd | 6 tcplfit2-0.1.7/tcplfit2/tests |only tcplfit2-0.1.7/tcplfit2/vignettes/css |only tcplfit2-0.1.7/tcplfit2/vignettes/img |only tcplfit2-0.1.7/tcplfit2/vignettes/tcplfit2-vignette.Rmd | 1815 +++- 63 files changed, 11033 insertions(+), 1544 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.0.8 dated 2024-09-20 and 1.0.9 dated 2024-09-23
renv-1.0.8/renv/R/pkgtype.R |only renv-1.0.8/renv/inst/repos/src/contrib/renv_1.0.8.tar.gz |only renv-1.0.9/renv/DESCRIPTION | 6 - renv-1.0.9/renv/MD5 | 45 +++++++------- renv-1.0.9/renv/NEWS.md | 9 ++ renv-1.0.9/renv/R/aaa.R | 5 + renv-1.0.9/renv/R/activate.R | 16 ++--- renv-1.0.9/renv/R/checkout.R | 6 - renv-1.0.9/renv/R/install.R | 8 -- renv-1.0.9/renv/R/load.R | 46 +++++++-------- renv-1.0.9/renv/R/pak.R | 7 +- renv-1.0.9/renv/R/ppm.R | 10 +-- renv-1.0.9/renv/R/sandbox.R | 5 - renv-1.0.9/renv/R/utils.R | 15 +--- renv-1.0.9/renv/README.md | 2 renv-1.0.9/renv/build/vignette.rds |binary renv-1.0.9/renv/inst/doc/docker.html | 2 renv-1.0.9/renv/inst/doc/renv.html | 2 renv-1.0.9/renv/inst/repos/src/contrib/PACKAGES | 4 - renv-1.0.9/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.0.9/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.0.9/renv/inst/repos/src/contrib/renv_1.0.9.tar.gz |only renv-1.0.9/renv/man/checkout.Rd | 6 - renv-1.0.9/renv/tests/testthat/test-lockfile-validate.R | 18 +++++ renv-1.0.9/renv/tests/testthat/test-watchdog.R | 4 - 25 files changed, 116 insertions(+), 100 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <http://www.pcre.org/licence.txt>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.4 dated 2024-02-29 and 0.6.5 dated 2024-09-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 7 ++++++- build/vignette.rds |binary inst/doc/vignette.html | 10 +++++----- src/cwb/cqp/parser.tab.c | 2 +- 6 files changed, 21 insertions(+), 16 deletions(-)
Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al <doi:10.2307/2533043> and the two level random effects model in Beath and Heller <doi:10.1177/1471082X0800900302>. Examples are given for their use in diagnostic testing.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken@kjbeath.id.au>
Diff between randomLCA versions 1.1-3 dated 2023-06-22 and 1.1-4 dated 2024-09-23
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 +- inst/NEWS | 6 ++++++ man/outcomeProbs.Rd | 2 +- 7 files changed, 21 insertions(+), 15 deletions(-)
Title: Graphs and Tables for OMOP Results
Description: Provides methods to transform omop_result objects into
formatted tables and figures, facilitating the visualization of study
results working with the Observational Medical Outcomes Partnership
(OMOP) Common Data Model.
Author: Marti Catala [aut] ,
Nuria Mercade-Besora [aut, cre]
,
Yuchen Guo [aut]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between visOmopResults versions 0.3.0 dated 2024-05-02 and 0.4.0 dated 2024-09-23
visOmopResults-0.3.0/visOmopResults/R/assertions.R |only visOmopResults-0.3.0/visOmopResults/R/filterSettings.R |only visOmopResults-0.3.0/visOmopResults/inst/doc/formatFunctions.R |only visOmopResults-0.3.0/visOmopResults/inst/doc/formatFunctions.Rmd |only visOmopResults-0.3.0/visOmopResults/inst/doc/formatFunctions.html |only visOmopResults-0.3.0/visOmopResults/inst/doc/splitAndUnite.R |only visOmopResults-0.3.0/visOmopResults/inst/doc/splitAndUnite.Rmd |only visOmopResults-0.3.0/visOmopResults/inst/doc/splitAndUnite.html |only visOmopResults-0.3.0/visOmopResults/inst/doc/tidy.R |only visOmopResults-0.3.0/visOmopResults/inst/doc/tidy.Rmd |only visOmopResults-0.3.0/visOmopResults/inst/doc/tidy.html |only visOmopResults-0.3.0/visOmopResults/tests/testthat/test-README.R |only visOmopResults-0.3.0/visOmopResults/tests/testthat/test-utilities.R |only visOmopResults-0.3.0/visOmopResults/vignettes/formatFunctions.Rmd |only visOmopResults-0.3.0/visOmopResults/vignettes/splitAndUnite.Rmd |only visOmopResults-0.3.0/visOmopResults/vignettes/tidy.Rmd |only visOmopResults-0.4.0/visOmopResults/DESCRIPTION | 28 visOmopResults-0.4.0/visOmopResults/MD5 | 170 +- visOmopResults-0.4.0/visOmopResults/NAMESPACE | 20 visOmopResults-0.4.0/visOmopResults/R/addSettings.R | 69 - visOmopResults-0.4.0/visOmopResults/R/columns.R | 186 +-- visOmopResults-0.4.0/visOmopResults/R/filter.R |only visOmopResults-0.4.0/visOmopResults/R/formatEstimateName.R | 377 +++--- visOmopResults-0.4.0/visOmopResults/R/formatEstimateValue.R | 152 +- visOmopResults-0.4.0/visOmopResults/R/formatHeader.R | 237 +-- visOmopResults-0.4.0/visOmopResults/R/formatTable.R |only visOmopResults-0.4.0/visOmopResults/R/fxTable.R | 479 ++++--- visOmopResults-0.4.0/visOmopResults/R/gtTable.R | 223 +-- visOmopResults-0.4.0/visOmopResults/R/helperTableFunctions.R |only visOmopResults-0.4.0/visOmopResults/R/mockResults.R | 356 ++--- visOmopResults-0.4.0/visOmopResults/R/pivotEstimates.R | 139 +- visOmopResults-0.4.0/visOmopResults/R/plot.R |only visOmopResults-0.4.0/visOmopResults/R/reexports.R | 16 visOmopResults-0.4.0/visOmopResults/R/split.R | 497 ++++---- visOmopResults-0.4.0/visOmopResults/R/tidy.R | 166 +- visOmopResults-0.4.0/visOmopResults/R/unite.R | 44 visOmopResults-0.4.0/visOmopResults/R/utilities.R | 336 +++-- visOmopResults-0.4.0/visOmopResults/R/visOmopTable.R | 610 ++-------- visOmopResults-0.4.0/visOmopResults/R/visTable.R |only visOmopResults-0.4.0/visOmopResults/README.md | 390 +++--- visOmopResults-0.4.0/visOmopResults/build/vignette.rds |binary visOmopResults-0.4.0/visOmopResults/inst/doc/filterSummarisedResult.R |only visOmopResults-0.4.0/visOmopResults/inst/doc/filterSummarisedResult.Rmd |only visOmopResults-0.4.0/visOmopResults/inst/doc/filterSummarisedResult.html |only visOmopResults-0.4.0/visOmopResults/inst/doc/plots.R |only visOmopResults-0.4.0/visOmopResults/inst/doc/plots.Rmd |only visOmopResults-0.4.0/visOmopResults/inst/doc/plots.html |only visOmopResults-0.4.0/visOmopResults/inst/doc/tables.R |only visOmopResults-0.4.0/visOmopResults/inst/doc/tables.Rmd |only visOmopResults-0.4.0/visOmopResults/inst/doc/tables.html |only visOmopResults-0.4.0/visOmopResults/inst/doc/tidySummarisedResult.R |only visOmopResults-0.4.0/visOmopResults/inst/doc/tidySummarisedResult.Rmd |only visOmopResults-0.4.0/visOmopResults/inst/doc/tidySummarisedResult.html |only visOmopResults-0.4.0/visOmopResults/inst/doc/utilityFunctions.R |only visOmopResults-0.4.0/visOmopResults/inst/doc/utilityFunctions.Rmd |only visOmopResults-0.4.0/visOmopResults/inst/doc/utilityFunctions.html |only visOmopResults-0.4.0/visOmopResults/man/addSettings.Rd | 25 visOmopResults-0.4.0/visOmopResults/man/additionalColumns.Rd | 4 visOmopResults-0.4.0/visOmopResults/man/barPlot.Rd |only visOmopResults-0.4.0/visOmopResults/man/boxPlot.Rd |only visOmopResults-0.4.0/visOmopResults/man/figures/README-unnamed-chunk-10-1.png |only visOmopResults-0.4.0/visOmopResults/man/figures/README-unnamed-chunk-11-1.png |only visOmopResults-0.4.0/visOmopResults/man/filterAdditional.Rd |only visOmopResults-0.4.0/visOmopResults/man/filterGroup.Rd |only visOmopResults-0.4.0/visOmopResults/man/filterSettings.Rd | 16 visOmopResults-0.4.0/visOmopResults/man/filterStrata.Rd |only visOmopResults-0.4.0/visOmopResults/man/formatEstimateName.Rd | 17 visOmopResults-0.4.0/visOmopResults/man/formatEstimateValue.Rd | 6 visOmopResults-0.4.0/visOmopResults/man/formatHeader.Rd | 12 visOmopResults-0.4.0/visOmopResults/man/formatTable.Rd | 145 +- visOmopResults-0.4.0/visOmopResults/man/fxTable.Rd | 42 visOmopResults-0.4.0/visOmopResults/man/groupColumns.Rd | 4 visOmopResults-0.4.0/visOmopResults/man/gtTable.Rd | 50 visOmopResults-0.4.0/visOmopResults/man/mockSummarisedResult.Rd | 6 visOmopResults-0.4.0/visOmopResults/man/optionsVisOmopTable.Rd | 16 visOmopResults-0.4.0/visOmopResults/man/pivotEstimates.Rd | 3 visOmopResults-0.4.0/visOmopResults/man/reexports.Rd | 6 visOmopResults-0.4.0/visOmopResults/man/scatterPlot.Rd |only visOmopResults-0.4.0/visOmopResults/man/settingsColumns.Rd |only visOmopResults-0.4.0/visOmopResults/man/splitAdditional.Rd | 9 visOmopResults-0.4.0/visOmopResults/man/splitAll.Rd | 26 visOmopResults-0.4.0/visOmopResults/man/splitGroup.Rd | 9 visOmopResults-0.4.0/visOmopResults/man/splitNameLevel.Rd | 15 visOmopResults-0.4.0/visOmopResults/man/splitStrata.Rd | 9 visOmopResults-0.4.0/visOmopResults/man/strataColumns.Rd | 4 visOmopResults-0.4.0/visOmopResults/man/tableOptions.Rd |only visOmopResults-0.4.0/visOmopResults/man/tableStyle.Rd |only visOmopResults-0.4.0/visOmopResults/man/tableType.Rd |only visOmopResults-0.4.0/visOmopResults/man/tidy.summarised_result.Rd | 41 visOmopResults-0.4.0/visOmopResults/man/tidyColumns.Rd |only visOmopResults-0.4.0/visOmopResults/man/uniteNameLevel.Rd | 17 visOmopResults-0.4.0/visOmopResults/man/visOmopResults-package.Rd | 3 visOmopResults-0.4.0/visOmopResults/man/visOmopTable.Rd | 112 + visOmopResults-0.4.0/visOmopResults/man/visTable.Rd |only visOmopResults-0.4.0/visOmopResults/tests/testthat/test-addSettings.R | 35 visOmopResults-0.4.0/visOmopResults/tests/testthat/test-columns.R | 23 visOmopResults-0.4.0/visOmopResults/tests/testthat/test-filter.R |only visOmopResults-0.4.0/visOmopResults/tests/testthat/test-formatEstimateName.R | 52 visOmopResults-0.4.0/visOmopResults/tests/testthat/test-formatHeader.R | 22 visOmopResults-0.4.0/visOmopResults/tests/testthat/test-formatTable.R |only visOmopResults-0.4.0/visOmopResults/tests/testthat/test-fxTable.R | 162 +- visOmopResults-0.4.0/visOmopResults/tests/testthat/test-gtTable.R | 263 ++-- visOmopResults-0.4.0/visOmopResults/tests/testthat/test-helperTableFunctions.R |only visOmopResults-0.4.0/visOmopResults/tests/testthat/test-mockResults.R | 2 visOmopResults-0.4.0/visOmopResults/tests/testthat/test-pivotEstimates.R | 8 visOmopResults-0.4.0/visOmopResults/tests/testthat/test-plot.R |only visOmopResults-0.4.0/visOmopResults/tests/testthat/test-split.R | 45 visOmopResults-0.4.0/visOmopResults/tests/testthat/test-tidy.R | 53 visOmopResults-0.4.0/visOmopResults/tests/testthat/test-unite.R | 19 visOmopResults-0.4.0/visOmopResults/tests/testthat/test-visOmopTable.R | 523 ++++---- visOmopResults-0.4.0/visOmopResults/tests/testthat/test-visTable.R |only visOmopResults-0.4.0/visOmopResults/vignettes/filterSummarisedResult.Rmd |only visOmopResults-0.4.0/visOmopResults/vignettes/plots.Rmd |only visOmopResults-0.4.0/visOmopResults/vignettes/tables.Rmd |only visOmopResults-0.4.0/visOmopResults/vignettes/tidySummarisedResult.Rmd |only visOmopResults-0.4.0/visOmopResults/vignettes/utilityFunctions.Rmd |only 116 files changed, 3318 insertions(+), 2981 deletions(-)
More information about visOmopResults at CRAN
Permanent link
Title: Random Forest Two-Sample Tests
Description: An implementation of Random Forest-based two-sample tests as introduced in Hediger & Michel & Naef (2022).
Author: Simon Hediger [aut, cre],
Loris Michel [aut],
Jeffrey Naef [aut]
Maintainer: Simon Hediger <simon.hediger@uzh.ch>
Diff between hypoRF versions 1.0.0 dated 2021-05-07 and 1.0.1 dated 2024-09-23
DESCRIPTION | 21 +- MD5 | 13 - NAMESPACE | 4 NEWS |only R/hypoRF.R | 448 ++++++++++++++++++++----------------------- man/hypoRF.Rd | 128 ++++++------ tests/testthat.R | 8 tests/testthat/test_hypoRF.R | 62 ++--- 8 files changed, 336 insertions(+), 348 deletions(-)
Title: Dose Rate Estimation from in-Situ Gamma-Ray Spectrometry
Measurements
Description: Process in-situ Gamma-Ray Spectrometry for Luminescence
Dating. This package allows to import, inspect and correct the energy
shifts of gamma-ray spectra. It provides methods for estimating the
gamma dose rate by the use of a calibration curve as described in
Mercier and Falguères (2007). The package only supports Canberra CNF
and TKA and Kromek SPE files.
Author: Nicolas Frerebeau [aut] ,
Brice Lebrun [aut] ,
Guilhem Paradol [aut] ,
Magali Rizza [ctb] ,
Christelle Lahaye [ctb] ,
Sebastian Kreutzer [aut] ,
Archeosciences Bordeaux [cre],
Universite Bordeaux Montaigne [cph, fnd],
CNRS [fnd],
LabEx Sciences arche [...truncated...]
Maintainer: Archeosciences Bordeaux <services-archeosciences@u-bordeaux-montaigne.fr>
Diff between gamma versions 1.0.5 dated 2024-04-08 and 1.1.0 dated 2024-09-23
gamma-1.0.5/gamma/tests/testthat/_snaps/plot/spectrum-peaks.svg |only gamma-1.1.0/gamma/DESCRIPTION | 19 gamma-1.1.0/gamma/MD5 | 131 - gamma-1.1.0/gamma/NAMESPACE | 3 gamma-1.1.0/gamma/NEWS.md | 32 gamma-1.1.0/gamma/R/AllClasses.R | 7 gamma-1.1.0/gamma/R/AllGenerics.R | 154 + gamma-1.1.0/gamma/R/coerce.R | 42 gamma-1.1.0/gamma/R/data.R | 56 gamma-1.1.0/gamma/R/dose_fit.R | 57 gamma-1.1.0/gamma/R/dose_predict.R | 171 + gamma-1.1.0/gamma/R/energy_calibrate.R | 159 + gamma-1.1.0/gamma/R/gamma-package.R | 6 gamma-1.1.0/gamma/R/mutators.R | 49 gamma-1.1.0/gamma/R/plot.R | 8 gamma-1.1.0/gamma/R/read.R | 83 gamma-1.1.0/gamma/R/show.R | 7 gamma-1.1.0/gamma/R/signal_integrate.R | 9 gamma-1.1.0/gamma/R/zzz.R | 4 gamma-1.1.0/gamma/README.md | 50 gamma-1.1.0/gamma/build/partial.rdb |binary gamma-1.1.0/gamma/build/vignette.rds |binary gamma-1.1.0/gamma/data/AIX_NaI_1.rda |binary gamma-1.1.0/gamma/data/BDX_LaBr_1.rda |binary gamma-1.1.0/gamma/data/clermont.rda |binary gamma-1.1.0/gamma/data/clermont_2024.rda |only gamma-1.1.0/gamma/data/datalist |only gamma-1.1.0/gamma/inst/CITATION | 3 gamma-1.1.0/gamma/inst/doc/doserate.R | 94 - gamma-1.1.0/gamma/inst/doc/doserate.Rmd | 254 ++ gamma-1.1.0/gamma/inst/doc/doserate.html | 869 +++++++--- gamma-1.1.0/gamma/inst/doc/gamma.R | 7 gamma-1.1.0/gamma/inst/doc/gamma.Rmd | 26 gamma-1.1.0/gamma/inst/doc/gamma.html | 247 +- gamma-1.1.0/gamma/inst/extdata/Kromek_CZT.spe |only gamma-1.1.0/gamma/man/AIX_NaI_1.Rd | 5 gamma-1.1.0/gamma/man/BDX_LaBr_1.Rd | 5 gamma-1.1.0/gamma/man/GammaSpectrum-class.Rd | 2 gamma-1.1.0/gamma/man/clermont.Rd | 5 gamma-1.1.0/gamma/man/clermont_2024.Rd |only gamma-1.1.0/gamma/man/doserate.Rd | 135 + gamma-1.1.0/gamma/man/energy.Rd | 35 gamma-1.1.0/gamma/man/figures/README-calib-1.png |binary gamma-1.1.0/gamma/man/figures/README-usage-1.png |binary gamma-1.1.0/gamma/man/gamma-package.Rd | 8 gamma-1.1.0/gamma/man/integrate.Rd | 35 gamma-1.1.0/gamma/man/mutator.Rd | 22 gamma-1.1.0/gamma/man/plot.Rd | 3 gamma-1.1.0/gamma/man/read.Rd | 6 gamma-1.1.0/gamma/tests/testthat/_snaps/plot/gg-calib-bar-false.svg | 2 gamma-1.1.0/gamma/tests/testthat/_snaps/plot/gg-calib-bar-true.svg | 2 gamma-1.1.0/gamma/tests/testthat/_snaps/plot/gg-calib-ellipse-false.svg | 2 gamma-1.1.0/gamma/tests/testthat/_snaps/plot/gg-calib-ellipse-true.svg | 2 gamma-1.1.0/gamma/tests/testthat/_snaps/plot/gg-calib-energy-false.svg | 2 gamma-1.1.0/gamma/tests/testthat/_snaps/plot/gg-calib-energy-true.svg | 2 gamma-1.1.0/gamma/tests/testthat/_snaps/plot/spectra-facet-false.svg | 56 gamma-1.1.0/gamma/tests/testthat/_snaps/plot/spectra-facet-true.svg | 121 - gamma-1.1.0/gamma/tests/testthat/_snaps/plot/spectrum-peaks-expected.svg |only gamma-1.1.0/gamma/tests/testthat/_snaps/plot/spectrum-peaks-observed.svg |only gamma-1.1.0/gamma/tests/testthat/test-calibrate.R | 134 + gamma-1.1.0/gamma/tests/testthat/test-coerce.R | 24 gamma-1.1.0/gamma/tests/testthat/test-doserate.R | 156 + gamma-1.1.0/gamma/tests/testthat/test-integrate.R | 19 gamma-1.1.0/gamma/tests/testthat/test-mutator.R | 18 gamma-1.1.0/gamma/tests/testthat/test-plot.R | 9 gamma-1.1.0/gamma/tests/testthat/test-read.R | 13 gamma-1.1.0/gamma/tests/testthat/test-utilities.R | 6 gamma-1.1.0/gamma/vignettes/bibliography.bib | 22 gamma-1.1.0/gamma/vignettes/doserate.Rmd | 254 ++ gamma-1.1.0/gamma/vignettes/gamma.Rmd | 26 70 files changed, 2869 insertions(+), 809 deletions(-)
Title: Multiscale Codependence Analysis
Description: Computation of Multiscale Codependence Analysis and spatial eigenvector maps.
Author: Guillaume Guenard [aut, cre] ,
Pierre Legendre [ctb] ,
Bertrand Pages [ctb]
Maintainer: Guillaume Guenard <guillaume.guenard@umontreal.ca>
Diff between codep versions 1.2-3 dated 2024-04-16 and 1.2-4 dated 2024-09-23
codep-1.2-3/codep/R/codep-package.R |only codep-1.2-3/codep/man/codep-package.Rd |only codep-1.2-4/codep/DESCRIPTION | 36 ++++++++++++++++++++++++++------- codep-1.2-4/codep/MD5 | 14 ++++++------ codep-1.2-4/codep/R/codep_PACKAGE.R |only codep-1.2-4/codep/build/partial.rdb |binary codep-1.2-4/codep/man/codep_PACKAGE.Rd |only codep-1.2-4/codep/src/LGTransforms.c | 4 +-- codep-1.2-4/codep/src/codep.c | 12 +++++------ codep-1.2-4/codep/src/geodists.c | 12 +++++------ 10 files changed, 50 insertions(+), 28 deletions(-)
Title: Calculate Distance Measures for a Given List of Data Frames with
Factors
Description: It provides functions that calculate Mahalanobis distance, Euclidean distance, Manhattan distance and Chebyshev distance between each pair of species in a list of data frames. These metrics are fundamental in various fields, such as cluster analysis, classification, and other applications of machine learning and data mining, where assessing similarity or dissimilarity between data is crucial. The package is designed to be flexible and easily integrated into data analysis workflows, providing reliable tools for evaluating distances in multidimensional contexts.
Author: Flavio Gioia [aut, cre]
Maintainer: Flavio Gioia <flaviogioia.fg@gmail.com>
Diff between cmahalanobis versions 0.4.1 dated 2024-09-21 and 0.4.2 dated 2024-09-23
DESCRIPTION | 6 MD5 | 14 - R/cmahalanobis.R | 201 +++++++++++++++++++----- inst/rmarkdown/template_report_cchebyshev.Rmd | 2 inst/rmarkdown/template_report_ceuclide.Rmd | 2 inst/rmarkdown/template_report_cmahalanobis.Rmd | 2 inst/rmarkdown/template_report_cmanhattan.Rmd | 2 tests/testthat/cmahalanobis.R | 201 +++++++++++++++++++----- 8 files changed, 334 insertions(+), 96 deletions(-)
Title: Case-Cohort Cox Survival Inference
Description: Cox model inference for relative hazard and covariate-specific pure risk estimated
from stratified and unstratified case-cohort data as described in
Etievant, L., Gail, M.H. (Lifetime Data Analysis, 2024) <doi:10.1007/s10985-024-09621-2>.
Author: Lola Etievant [cre, aut],
Mitchell H. Gail [aut],
Bill Wheeler [aut]
Maintainer: Lola Etievant <lola.etievant@gmail.com>
Diff between CaseCohortCoxSurvival versions 0.0.34 dated 2024-01-08 and 0.0.36 dated 2024-09-23
DESCRIPTION | 20 - MD5 | 62 ++-- data/dataexample.missingdata.rda |binary data/dataexample.missingdata.stratified.rda |only data/dataexample.missingdata.unstratified.rda |only data/dataexample.rda |binary data/dataexample.stratified.rda |only data/dataexample.unstratified.rda |only data/datalist |only man/CaseCohortCoxSurvival-package.Rd | 15 - man/auxiliary.construction.Rd | 118 ++++----- man/calibration.Rd | 75 +++-- man/caseCohortCoxSurvival.Rd | 336 +++++++++++++------------- man/dataexample.Rd | 12 man/dataexample.missingdata.Rd | 12 man/dataexample.missingdata.stratified.Rd |only man/dataexample.missingdata.unstratified.Rd |only man/dataexample.stratified.Rd |only man/dataexample.unstratified.Rd |only man/deprecateddata.Rd |only man/estimatePureRisk.Rd | 41 +-- man/estimation.CumBH.Rd | 130 +++++----- man/estimation.PR.Rd | 17 - man/estimation.Rd | 125 +++++---- man/estimation.weights.phase3.Rd | 80 ++---- man/influences.CumBH.Rd | 104 ++------ man/influences.CumBH.missingdata.Rd | 166 +++++++----- man/influences.PR.Rd | 115 +++----- man/influences.PR.missingdata.Rd | 216 +++++++++------- man/influences.RH.Rd | 66 ++--- man/influences.RH.missingdata.Rd | 147 ++++++----- man/influences.Rd | 124 +++------ man/influences.missingdata.Rd | 218 +++++++++------- man/product.covar.weight.Rd | 60 ++-- man/robustvariance.Rd | 67 ++--- man/variance.Rd | 152 ++++------- man/variance.missingdata.Rd | 304 ++++++++++++----------- 37 files changed, 1424 insertions(+), 1358 deletions(-)
More information about CaseCohortCoxSurvival at CRAN
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Title: LUCID with Multiple Omics Data
Description: An implementation of estimating the Latent Unknown Clusters By Integrating Multi-omics Data (LUCID) model (Peng (2019) <doi:10.1093/bioinformatics/btz667>). LUCID conducts integrated clustering using exposures, omics information (and outcome information as an option). This package implements three different integration strategies for multi-omics data analysis within the LUCID framework: LUCID early integration (the original LUCID model), LUCID in parallel (intermediate integration), and LUCID in serial (late integration). Automated model selection for each LUCID model is available to obtain the optimal number of latent clusters, and an integrated imputation approach is implemented to handle sporadic and list-wise missingness in multi-omics data. Lasso-type regularity for exposure and omics features were added. S3 methods for summary and plotting functions were fixed. Fixed minor bugs.
Author: Qiran Jia [aut, cre] ,
Yinqi Zhao [aut] ,
David Conti [ths] ,
Jesse Goodrich [ctb]
Maintainer: Qiran Jia <qiranjia@usc.edu>
Diff between LUCIDus versions 3.0.2 dated 2024-07-08 and 3.0.3 dated 2024-09-23
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/early_mstep.R | 4 +- R/em.R | 3 - R/plot_lucid.R | 106 +++++++++++++++++++++++++++++++++++++++++++++++++++++++- 5 files changed, 115 insertions(+), 14 deletions(-)
Title: Designing Cluster-Randomized Trials with Two Co-Primary Outcomes
Description: Provides methods for powering cluster-randomized trials with two co-primary outcomes using five key design techniques. Includes functions for calculating required sample size and statistical power. For more details on methodology, see Li et al. (2020) <doi:10.1111/biom.13212>, Pocock et al. (1987) <doi:10.2307/2531989>, Vickerstaff et al. (2019) <doi:10.1186/s12874-019-0754-4>, and Yang et al. (2022) <doi:10.1111/biom.13692>.
Author: Melody Owen [aut, cre]
Maintainer: Melody Owen <melody.owen@yale.edu>
Diff between crt2power versions 1.0.0 dated 2024-06-20 and 1.1.0 dated 2024-09-23
DESCRIPTION | 6 +-- MD5 | 14 +++---- R/calc_pwr_comb_outcome.R | 30 ++++++++++++--- R/calc_pwr_pval_adj.R | 82 +++++++++++++++++++++++++++++++---------- R/calc_pwr_single_1dftest.R | 32 +++++++++++++--- man/calc_pwr_comb_outcome.Rd | 3 + man/calc_pwr_pval_adj.Rd | 3 + man/calc_pwr_single_1dftest.Rd | 3 + 8 files changed, 132 insertions(+), 41 deletions(-)
Title: Spatial Regression Models for Large Datasets using Nearest
Neighbor Gaussian Processes
Description: Fits univariate Bayesian spatial regression models for large datasets using Nearest Neighbor Gaussian Processes (NNGP) detailed in Finley, Datta, Banerjee (2022) <doi:10.18637/jss.v103.i05>, Finley, Datta, Cook, Morton, Andersen, and Banerjee (2019) <doi:10.1080/10618600.2018.1537924>, and Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091>.
Author: Andrew Finley [aut, cre],
Abhirup Datta [aut],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spNNGP versions 1.0.0 dated 2022-06-27 and 1.0.1 dated 2024-09-23
DESCRIPTION | 8 +++--- MD5 | 40 +++++++++++++++++----------------- build/partial.rdb |binary src/Makevars | 4 +++ src/PGLogit.cpp | 22 +++++++++++------- src/cNNGP.cpp | 48 ++++++++++++++++++++++------------------- src/cSLGP.cpp | 56 +++++++++++++++++++++++++----------------------- src/init.cpp | 4 +++ src/nn.cpp | 16 ++++++++----- src/nn.h | 4 +++ src/rNNGP.cpp | 34 ++++++++++++++++------------- src/rNNGPPredict.cpp | 20 ++++++++++------- src/rNNGPReplicated.cpp | 20 ++++++++++------- src/rpg.cpp | 4 +++ src/rpg.h | 4 +++ src/sNNGP.cpp | 34 ++++++++++++++++------------- src/sNNGPLogit.cpp | 34 ++++++++++++++++------------- src/sNNGPPredict.cpp | 24 ++++++++++++-------- src/spNNGP.h | 4 +++ src/util.cpp | 12 ++++++---- src/util.h | 6 ++++- 21 files changed, 235 insertions(+), 163 deletions(-)
Title: Univariate and Multivariate Spatial-Temporal Modeling
Description: Fits univariate and multivariate spatio-temporal
random effects models for point-referenced data using Markov chain Monte Carlo (MCMC). Details are given in Finley, Banerjee, and Gelfand (2015) <doi:10.18637/jss.v063.i13> and Finley and Banerjee <doi:10.1016/j.envsoft.2019.104608>.
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spBayes versions 0.4-7 dated 2023-12-11 and 0.4-8 dated 2024-09-23
DESCRIPTION | 8 +-- MD5 | 90 +++++++++++++++++++++---------------------- src/Makevars | 4 + src/adaptMetropGibbs.cpp | 36 +++++++++-------- src/idist.cpp | 4 + src/init.cpp | 4 + src/mkSpCov.cpp | 8 ++- src/nonSpGLM_AMCMC.cpp | 26 +++++++----- src/ptsInPoly.cpp | 4 + src/spBayes.h | 8 +++ src/spDynLM.cpp | 90 ++++++++++++++++++++++--------------------- src/spGLM.cpp | 28 +++++++------ src/spGLM_AMCMC.cpp | 46 +++++++++++---------- src/spLM.cpp | 32 ++++++++------- src/spLMPredict.cpp | 16 ++++--- src/spLMRecover.cpp | 46 +++++++++++---------- src/spMPPMvDIC.cpp | 16 ++++--- src/spMisalign.cpp | 34 +++++++++------- src/spMisalignGLM.cpp | 52 +++++++++++++----------- src/spMisalignGLMPredict.cpp | 26 +++++++----- src/spMisalignPredict.cpp | 20 +++++---- src/spMisalignRecover.cpp | 42 ++++++++++---------- src/spMvGLM.cpp | 30 ++++++++------ src/spMvGLMPredict.cpp | 28 +++++++------ src/spMvGLM_AMCMC.cpp | 50 ++++++++++++----------- src/spMvLM.cpp | 36 +++++++++-------- src/spMvLMPredict.cpp | 20 +++++---- src/spMvLMRecover.cpp | 54 +++++++++++++------------ src/spPPDynLM.cpp | 88 +++++++++++++++++++++--------------------- src/spPPGLM.cpp | 32 ++++++++------- src/spPPGLM_AMCMC.cpp | 50 ++++++++++++----------- src/spPPLM.cpp | 44 +++++++++++---------- src/spPPLMPredict.cpp | 16 ++++--- src/spPPLMRecover.cpp | 28 +++++++------ src/spPPMvGLM.cpp | 34 +++++++++------- src/spPPMvGLMPredict.cpp | 26 +++++++----- src/spPPMvGLM_AMCMC.cpp | 54 +++++++++++++------------ src/spPPMvLM.cpp | 56 ++++++++++++++------------ src/spPPMvLMPredict.cpp | 28 +++++++------ src/spPPMvLMRecover.cpp | 38 ++++++++++-------- src/spSVC.cpp | 36 +++++++++-------- src/spSVCPredictJoint.cpp | 24 ++++++----- src/spSVCPredictMarg.cpp | 24 ++++++----- src/spSVCRecover.cpp | 44 +++++++++++---------- src/util.cpp | 40 ++++++++++--------- src/util.h | 8 ++- 46 files changed, 854 insertions(+), 674 deletions(-)
Title: Estimation Statistics with Confidence Intervals
Description: A collection of functions and 'jamovi' module for the estimation approach to inferential statistics, the approach which emphasizes effect sizes, interval estimates, and meta-analysis. Nearly all functions are based on 'statpsych' and 'metafor'. This package is still under active development, and breaking changes are likely, especially with the plot and hypothesis test functions. Data sets are included for all examples from Cumming & Calin-Jageman (2024) <ISBN:9780367531508>.
Author: Robert Calin-Jageman [aut, cre, cph]
Maintainer: Robert Calin-Jageman <rcalinjageman@dom.edu>
Diff between esci versions 1.0.4 dated 2024-09-12 and 1.0.5 dated 2024-09-23
DESCRIPTION | 6 MD5 | 112 +++++----- NEWS.md | 9 R/statpsych_wrapper.R | 20 + build/stage23.rdb |binary man/data_altruism_happiness.Rd | 76 +++--- man/data_anchor_estimate_ma.Rd | 86 +++---- man/data_basol_badnews.Rd | 96 ++++---- man/data_bem_psychic.Rd | 96 ++++---- man/data_bodywellf.Rd | 48 ++-- man/data_bodywellfm.Rd | 48 ++-- man/data_bodywellm.Rd | 48 ++-- man/data_campus_involvement.Rd | 66 ++--- man/data_chap_8_paired_ex_8.18.Rd | 54 ++-- man/data_clean_moral.Rd | 78 +++---- man/data_college_survey_1.Rd | 90 ++++---- man/data_college_survey_2.Rd | 76 +++--- man/data_damischrcj.Rd | 52 ++-- man/data_effronraj_fakenews.Rd | 90 ++++---- man/data_emotion_heartrate.Rd | 64 ++--- man/data_exam_scores.Rd | 58 ++--- man/data_flag_priming_ma.Rd | 76 +++--- man/data_gender_math_iat.Rd | 78 +++---- man/data_gender_math_iat_ma.Rd | 84 +++---- man/data_halagappa.Rd | 82 +++---- man/data_home_prices.Rd | 66 ++--- man/data_kardas_expt_3.Rd | 86 +++---- man/data_kardas_expt_4.Rd | 94 ++++---- man/data_labels_flavor.Rd | 78 +++---- man/data_latimier_3groups.Rd | 84 +++---- man/data_latimier_prequiz.Rd | 56 ++--- man/data_latimier_quiz.Rd | 56 ++--- man/data_latimier_quiz_prequiz.Rd | 56 ++--- man/data_latimier_reread.Rd | 56 ++--- man/data_latimier_reread_prequiz.Rd | 56 ++--- man/data_latimier_reread_quiz.Rd | 56 ++--- man/data_macnamara_r_ma.Rd | 86 +++---- man/data_mccabemichael_brain.Rd | 130 +++++------ man/data_mccabemichael_brain2.Rd | 68 +++--- man/data_meditationbrain.Rd | 92 ++++---- man/data_organicmoral.Rd | 92 ++++---- man/data_penlaptop1.Rd | 52 ++-- man/data_powerperformance_ma.Rd | 94 ++++---- man/data_rattanmotivation.Rd | 82 +++---- man/data_religionsharing.Rd | 72 +++--- man/data_religious_belief.Rd | 54 ++-- man/data_selfexplain.Rd | 78 +++---- man/data_simmonscredibility.Rd | 120 +++++----- man/data_sleep_beauty.Rd | 58 ++--- man/data_smithrecall.Rd | 54 ++-- man/data_stickgold.Rd | 74 +++--- man/data_studystrategies.Rd | 82 +++---- man/data_thomason_1.Rd | 60 ++--- man/data_videogameaggression.Rd | 74 +++--- man/estimate_r.Rd | 312 ++++++++++++++-------------- tests/testthat/test_estimate_mdiff_paired.R | 19 + tests/testthat/test_estimate_mdiff_two.R | 34 +++ 57 files changed, 2096 insertions(+), 2028 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.7.1 dated 2024-02-06 and 3.7.2 dated 2024-09-23
MSEtool-3.7.1/MSEtool/man/expandHerm.Rd |only MSEtool-3.7.2/MSEtool/DESCRIPTION | 9 MSEtool-3.7.2/MSEtool/MD5 | 103 ++--- MSEtool-3.7.2/MSEtool/NAMESPACE | 5 MSEtool-3.7.2/MSEtool/NEWS.md | 26 + MSEtool-3.7.2/MSEtool/R/BAM2OM.R |only MSEtool-3.7.2/MSEtool/R/Class_definitions.R | 2 MSEtool-3.7.2/MSEtool/R/Data_Functions.R | 12 MSEtool-3.7.2/MSEtool/R/Data_make_update.R | 104 ++++- MSEtool-3.7.2/MSEtool/R/MOM_object.r | 4 MSEtool-3.7.2/MSEtool/R/MP_tuning.R |only MSEtool-3.7.2/MSEtool/R/MSE_functions.R | 4 MSEtool-3.7.2/MSEtool/R/Misc_Exported.R | 23 + MSEtool-3.7.2/MSEtool/R/Misc_Internal.R | 18 MSEtool-3.7.2/MSEtool/R/OM_init_doc.R | 2 MSEtool-3.7.2/MSEtool/R/PMobjects.R | 16 MSEtool-3.7.2/MSEtool/R/SS2MOM.R | 6 MSEtool-3.7.2/MSEtool/R/SS2MOM_plots.R | 34 + MSEtool-3.7.2/MSEtool/R/SS2OM.R | 11 MSEtool-3.7.2/MSEtool/R/SSinternal.R | 17 MSEtool-3.7.2/MSEtool/R/SampleOM.R | 30 + MSEtool-3.7.2/MSEtool/R/WHAM2OM.R | 14 MSEtool-3.7.2/MSEtool/R/applyMMP.R | 11 MSEtool-3.7.2/MSEtool/R/iSCAM2OM.R | 41 -- MSEtool-3.7.2/MSEtool/R/multiMSE.R | 441 ++++++++++++++-------- MSEtool-3.7.2/MSEtool/R/multiMSE_internal.R | 86 +++- MSEtool-3.7.2/MSEtool/R/multi_q_estimation.R | 21 - MSEtool-3.7.2/MSEtool/R/popdyn.R | 474 ++++++++++++------------ MSEtool-3.7.2/MSEtool/R/popdyn_MICE.R | 376 ++++++++++++++----- MSEtool-3.7.2/MSEtool/R/runMSE.R | 49 +- MSEtool-3.7.2/MSEtool/R/spatial_targ_opt.R |only MSEtool-3.7.2/MSEtool/R/sysdata.rda |binary MSEtool-3.7.2/MSEtool/build/partial.rdb |binary MSEtool-3.7.2/MSEtool/man/BAM2MOM.Rd |only MSEtool-3.7.2/MSEtool/man/CalcAsymptoticDist.Rd | 54 +- MSEtool-3.7.2/MSEtool/man/Herm-int.Rd |only MSEtool-3.7.2/MSEtool/man/MOM-class.Rd | 4 MSEtool-3.7.2/MSEtool/man/OM-class.Rd | 2 MSEtool-3.7.2/MSEtool/man/PerformanceMetric.Rd | 3 MSEtool-3.7.2/MSEtool/man/ResFromRel.Rd | 6 MSEtool-3.7.2/MSEtool/man/WHAM2OM.Rd | 6 MSEtool-3.7.2/MSEtool/man/applyMMP.Rd | 2 MSEtool-3.7.2/MSEtool/man/checkMSE.Rd | 2 MSEtool-3.7.2/MSEtool/man/getMP.Rd |only MSEtool-3.7.2/MSEtool/man/getq_multi_MICE.Rd | 7 MSEtool-3.7.2/MSEtool/man/iSCAM2OM.Rd | 10 MSEtool-3.7.2/MSEtool/man/makemov2.Rd | 72 +-- MSEtool-3.7.2/MSEtool/man/multiMSE.Rd | 6 MSEtool-3.7.2/MSEtool/man/popdynMICE.Rd | 6 MSEtool-3.7.2/MSEtool/man/popdynOneMICE.Rd | 5 MSEtool-3.7.2/MSEtool/man/qestMICE.Rd | 4 MSEtool-3.7.2/MSEtool/man/runMSE.Rd | 11 MSEtool-3.7.2/MSEtool/man/select_MP.Rd |only MSEtool-3.7.2/MSEtool/man/simmov2.Rd | 136 +++--- MSEtool-3.7.2/MSEtool/man/tune_MP.Rd |only MSEtool-3.7.2/MSEtool/man/validcpars.Rd | 27 + MSEtool-3.7.2/MSEtool/src/genLenComp.cpp | 69 ++- 57 files changed, 1547 insertions(+), 824 deletions(-)
Title: IMAGing engINEs, Tools for Application of Image Filters to Data
Matrices
Description: Provides fast application of image filters to data matrices,
using R and C++ algorithms.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between imagine versions 2.1.0 dated 2024-01-09 and 2.1.1 dated 2024-09-23
DESCRIPTION | 10 +++--- MD5 | 28 +++++++++--------- NEWS.md | 4 ++ R/RcppExports.R | 16 +++++----- R/imagine-main.R | 56 +++++++++++++++++++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/imagine-intro.html | 2 - man/basic2DFilter.Rd | 13 ++++++-- man/convolutions.Rd | 20 +++++++++++-- src/2D-convolution.cpp | 9 +++++ src/RcppExports.cpp | 36 +++++++++++++---------- src/convolution-with-quantiles.cpp | 9 +++++ src/mean-filter.cpp | 9 +++++ src/quantile-filter.cpp | 9 +++++ 15 files changed, 155 insertions(+), 66 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-10 0.1.30
2023-12-01 0.1.27
2023-07-19 0.1.25
2023-07-16 0.1.23
2023-04-15 0.1.18
2023-04-12 0.1.17
2022-12-14 0.1.14
2022-09-29 0.1.12
2022-03-28 0.1.11
2022-03-10 0.1.9
2022-02-22 0.1.8
Title: ODE Generation and Integration
Description: Generate systems of ordinary differential equations
(ODE) and integrate them, using a domain specific language
(DSL). The DSL uses R's syntax, but compiles to C in order to
efficiently solve the system. A solver is not provided, but
instead interfaces to the packages 'deSolve' and 'dde' are
generated. With these, while solving the differential equations,
no allocations are done and the calculations remain entirely in
compiled code. Alternatively, a model can be transpiled to R for
use in contexts where a C compiler is not present. After
compilation, models can be inspected to return information about
parameters and outputs, or intermediate values after calculations.
'odin' is not targeted at any particular domain and is suitable
for any system that can be expressed primarily as mathematical
expressions. Additional support is provided for working with
delays (delay differential equations, DDE), using interpolated
functions during interpolation, and for integrating quantities
that [...truncated...]
Author: Rich FitzJohn [aut, cre],
Thibaut Jombart [ctb],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between odin versions 1.2.5 dated 2023-10-02 and 1.2.6 dated 2024-09-23
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/utils.R | 3 +-- build/vignette.rds |binary inst/doc/discrete.html | 22 +++++++++++----------- inst/doc/functions.html | 4 ++-- inst/doc/odin.R | 3 --- inst/doc/odin.Rmd | 2 +- inst/doc/odin.html | 8 ++++---- tests/testthat/test-package.R | 1 + tests/testthat/test-run-examples.R | 4 ++++ vignettes/odin.Rmd | 2 +- 12 files changed, 39 insertions(+), 38 deletions(-)
Title: 'BLAS' and 'LAPACK' Routines for Native R Matrices and
'big.matrix' Objects
Description: Provides arithmetic functions for R matrix and 'big.matrix' objects as well as functions for QR factorization, Cholesky factorization, General eigenvalue, and Singular value decomposition (SVD). A method matrix multiplication and an arithmetic method -for matrix addition, matrix difference- allows for mixed type operation -a matrix class object and a big.matrix class object- and pure type operation for two big.matrix class objects.
Author: Frederic Bertrand [cre, ctb] ,
Michael J. Kane [aut],
Bryan Lewis [aut],
John W. Emerson [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between bigalgebra versions 1.1.1 dated 2023-12-09 and 1.1.2 dated 2024-09-23
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 6 +++--- src/bigalgebra.cpp | 19 ++++++++++--------- 5 files changed, 26 insertions(+), 21 deletions(-)
Title: Low-Level Browser Automation Interface
Description: An implementation of 'W3C WebDriver 2.0'
(<https://w3c.github.io/webdriver/>), allowing interaction
with a 'Selenium Server' (<https://www.selenium.dev/documentation/grid/>)
instance from 'R'. Allows a web browser to be automated from 'R'.
Author: Ashby Thorpe [aut, cre, cph]
Maintainer: Ashby Thorpe <ashbythorpe@gmail.com>
Diff between selenium versions 0.1.3 dated 2023-11-28 and 0.1.4 dated 2024-09-23
selenium-0.1.3/selenium/man/selenium_server_available.Rd |only selenium-0.1.4/selenium/DESCRIPTION | 12 - selenium-0.1.4/selenium/MD5 | 24 +-- selenium-0.1.4/selenium/NAMESPACE | 4 selenium-0.1.4/selenium/NEWS.md | 33 +++- selenium-0.1.4/selenium/R/capabilities.R |only selenium-0.1.4/selenium/R/commands.R | 5 selenium-0.1.4/selenium/R/server.R | 41 +++-- selenium-0.1.4/selenium/R/session.R | 19 +- selenium-0.1.4/selenium/R/status.R | 110 ++++++++++++--- selenium-0.1.4/selenium/README.md | 38 +++-- selenium-0.1.4/selenium/man/SeleniumSession.Rd | 3 selenium-0.1.4/selenium/man/chrome_options.Rd |only selenium-0.1.4/selenium/man/selenium_server.Rd | 19 ++ selenium-0.1.4/selenium/man/wait_for_server.Rd |only 15 files changed, 226 insertions(+), 82 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.2.0 dated 2024-08-27 and 0.3.0 dated 2024-09-23
maestro-0.2.0/maestro/R/check_pipelines.R |only maestro-0.2.0/maestro/R/example_schedule.R |only maestro-0.2.0/maestro/R/run_schedule_entry.R |only maestro-0.2.0/maestro/data/example_schedule.rda |only maestro-0.2.0/maestro/man/check_pipelines.Rd |only maestro-0.2.0/maestro/man/example_schedule.Rd |only maestro-0.2.0/maestro/man/run_schedule_entry.Rd |only maestro-0.2.0/maestro/man/schedule_validity_check.Rd |only maestro-0.2.0/maestro/tests/testthat/_snaps/build_schedule.md |only maestro-0.2.0/maestro/tests/testthat/_snaps/build_schedule_entry.md |only maestro-0.3.0/maestro/DESCRIPTION | 12 maestro-0.3.0/maestro/MD5 | 125 +-- maestro-0.3.0/maestro/NAMESPACE | 12 maestro-0.3.0/maestro/NEWS.md | 30 maestro-0.3.0/maestro/R/MaestroPipeline.R |only maestro-0.3.0/maestro/R/MaestroPipelineList.R |only maestro-0.3.0/maestro/R/MaestroSchedule.R |only maestro-0.3.0/maestro/R/build_schedule.R | 71 - maestro-0.3.0/maestro/R/build_schedule_entry.R | 198 +++-- maestro-0.3.0/maestro/R/get_artifacts.R |only maestro-0.3.0/maestro/R/get_schedule.R |only maestro-0.3.0/maestro/R/get_status.R |only maestro-0.3.0/maestro/R/invoke.R |only maestro-0.3.0/maestro/R/maestro.R | 2 maestro-0.3.0/maestro/R/roxy_maestro.R | 33 maestro-0.3.0/maestro/R/run_schedule.R | 362 +--------- maestro-0.3.0/maestro/R/suggest_orch_frequency.R | 92 -- maestro-0.3.0/maestro/R/utils.R | 114 --- maestro-0.3.0/maestro/R/utils_cli.R | 1 maestro-0.3.0/maestro/README.md | 6 maestro-0.3.0/maestro/inst/doc/maestro-1-quick-start.R | 4 maestro-0.3.0/maestro/inst/doc/maestro-1-quick-start.Rmd | 6 maestro-0.3.0/maestro/inst/doc/maestro-1-quick-start.html | 17 maestro-0.3.0/maestro/inst/doc/maestro-2-motivation-concepts.R | 4 maestro-0.3.0/maestro/inst/doc/maestro-2-motivation-concepts.Rmd | 4 maestro-0.3.0/maestro/inst/doc/maestro-2-motivation-concepts.html | 4 maestro-0.3.0/maestro/inst/doc/maestro-4-advanced-scheduling.Rmd | 2 maestro-0.3.0/maestro/inst/doc/maestro-4-advanced-scheduling.html | 117 +-- maestro-0.3.0/maestro/man/MaestroPipeline.Rd |only maestro-0.3.0/maestro/man/MaestroPipelineList.Rd |only maestro-0.3.0/maestro/man/MaestroSchedule.Rd |only maestro-0.3.0/maestro/man/build_schedule.Rd | 2 maestro-0.3.0/maestro/man/build_schedule_entry.Rd | 7 maestro-0.3.0/maestro/man/convert_to_seconds.Rd | 1 maestro-0.3.0/maestro/man/figures/README-/unnamed-chunk-3-dark.svg | 2 maestro-0.3.0/maestro/man/figures/README-/unnamed-chunk-3.svg | 2 maestro-0.3.0/maestro/man/get_artifacts.Rd |only maestro-0.3.0/maestro/man/get_pipeline_run_sequence.Rd | 1 maestro-0.3.0/maestro/man/get_schedule.Rd |only maestro-0.3.0/maestro/man/get_status.Rd |only maestro-0.3.0/maestro/man/invoke.Rd |only maestro-0.3.0/maestro/man/maestro.Rd | 1 maestro-0.3.0/maestro/man/maestro_parse_cli.Rd | 1 maestro-0.3.0/maestro/man/parse_rounding_unit.Rd | 1 maestro-0.3.0/maestro/man/run_schedule.Rd | 42 - maestro-0.3.0/maestro/man/suggest_orch_frequency.Rd | 9 maestro-0.3.0/maestro/tests/testthat/_snaps/MaestroPipeline.md |only maestro-0.3.0/maestro/tests/testthat/_snaps/MaestroPipelineList.md |only maestro-0.3.0/maestro/tests/testthat/_snaps/get_schedule.md |only maestro-0.3.0/maestro/tests/testthat/_snaps/run_schedule.md | 38 - maestro-0.3.0/maestro/tests/testthat/test-MaestroPipeline.R |only maestro-0.3.0/maestro/tests/testthat/test-MaestroPipelineList.R |only maestro-0.3.0/maestro/tests/testthat/test-MaestroSchedule.R |only maestro-0.3.0/maestro/tests/testthat/test-build_schedule.R | 33 maestro-0.3.0/maestro/tests/testthat/test-build_schedule_entry.R | 39 - maestro-0.3.0/maestro/tests/testthat/test-get_artifacts.R |only maestro-0.3.0/maestro/tests/testthat/test-get_schedule.R |only maestro-0.3.0/maestro/tests/testthat/test-get_status.R |only maestro-0.3.0/maestro/tests/testthat/test-invoke.R |only maestro-0.3.0/maestro/tests/testthat/test-roclets.R | 10 maestro-0.3.0/maestro/tests/testthat/test-run_schedule.R | 250 ------ maestro-0.3.0/maestro/tests/testthat/test-suggest_orch_frequency.R | 113 --- maestro-0.3.0/maestro/tests/testthat/test_pipelines/test_pipeline_inputs.R |only maestro-0.3.0/maestro/tests/testthat/test_pipelines_dags_bad |only maestro-0.3.0/maestro/tests/testthat/test_pipelines_dags_good |only maestro-0.3.0/maestro/tests/testthat/test_pipelines_dup_names |only maestro-0.3.0/maestro/tests/testthat/test_pipelines_parse_all_bad/dags.R |only maestro-0.3.0/maestro/tests/testthat/test_pipelines_parse_all_good/pipe1.R | 2 maestro-0.3.0/maestro/tests/testthat/test_pipelines_run_all_good/chatty.R | 2 maestro-0.3.0/maestro/tests/testthat/test_pipelines_run_some_errors/pipe2.R | 2 maestro-0.3.0/maestro/vignettes/maestro-1-quick-start.Rmd | 6 maestro-0.3.0/maestro/vignettes/maestro-2-motivation-concepts.Rmd | 4 maestro-0.3.0/maestro/vignettes/maestro-4-advanced-scheduling.Rmd | 2 83 files changed, 601 insertions(+), 1185 deletions(-)
Title: End-to-End Automated Machine Learning and Model Evaluation
Description: Single unified interface for end-to-end modelling of regression,
categorical and time-to-event (survival) outcomes. Models created using
familiar are self-containing, and their use does not require additional
information such as baseline survival, feature clustering, or feature
transformation and normalisation parameters. Model performance,
calibration, risk group stratification, (permutation) variable importance,
individual conditional expectation, partial dependence, and more, are
assessed automatically as part of the evaluation process and exported in
tabular format and plotted, and may also be computed manually using export
and plot functions. Where possible, metrics and values obtained during the
evaluation process come with confidence intervals.
Author: Alex Zwanenburg [aut, cre] ,
Steffen Loeck [aut],
Stefan Leger [ctb],
Iram Shahzadi [ctb],
Asier Rabasco Meneghetti [ctb],
Sebastian Starke [ctb],
Technische Universitaet Dresden [cph],
German Cancer Research Center [cph]
Maintainer: Alex Zwanenburg <alexander.zwanenburg@nct-dresden.de>
Diff between familiar versions 1.4.8 dated 2024-05-24 and 1.5.0 dated 2024-09-23
familiar-1.4.8/familiar/R/ProcessTimeUtilites.R |only familiar-1.4.8/familiar/man/plotting.check_data_handling.Rd |only familiar-1.4.8/familiar/man/plotting.check_input_args.Rd |only familiar-1.5.0/familiar/DESCRIPTION | 62 familiar-1.5.0/familiar/MD5 | 807 familiar-1.5.0/familiar/NEWS.md | 26 familiar-1.5.0/familiar/R/BatchNormalisation.R | 651 familiar-1.5.0/familiar/R/BootstrapConfidenceInterval.R | 101 familiar-1.5.0/familiar/R/CheckArguments.R | 336 familiar-1.5.0/familiar/R/CheckHyperparameters.R | 367 familiar-1.5.0/familiar/R/CheckPackages.R | 376 familiar-1.5.0/familiar/R/ClassBalance.R | 226 familiar-1.5.0/familiar/R/ClusterRepresentation.R | 402 familiar-1.5.0/familiar/R/Clustering.R | 577 familiar-1.5.0/familiar/R/ClusteringMethod.R | 2915 +- familiar-1.5.0/familiar/R/CombatNormalisation.R | 515 familiar-1.5.0/familiar/R/DataObject.R | 3720 +-- familiar-1.5.0/familiar/R/DataParameterChecks.R | 1500 - familiar-1.5.0/familiar/R/DataPreProcessing.R | 917 familiar-1.5.0/familiar/R/DataProcessing.R | 93 familiar-1.5.0/familiar/R/DataServerBackend.R | 555 familiar-1.5.0/familiar/R/ErrorMessages.R | 329 familiar-1.5.0/familiar/R/Evaluation.R | 723 familiar-1.5.0/familiar/R/ExperimentData.R | 198 familiar-1.5.0/familiar/R/ExperimentSetup.R | 519 familiar-1.5.0/familiar/R/Familiar.R | 750 familiar-1.5.0/familiar/R/FamiliarCollection.R | 969 familiar-1.5.0/familiar/R/FamiliarCollectionExport.R | 1029 familiar-1.5.0/familiar/R/FamiliarData.R | 362 familiar-1.5.0/familiar/R/FamiliarDataComputation.R | 1036 familiar-1.5.0/familiar/R/FamiliarDataComputationAUCCurves.R | 733 familiar-1.5.0/familiar/R/FamiliarDataComputationCalibrationData.R | 1099 - familiar-1.5.0/familiar/R/FamiliarDataComputationCalibrationInfo.R | 482 familiar-1.5.0/familiar/R/FamiliarDataComputationConfusionMatrix.R | 347 familiar-1.5.0/familiar/R/FamiliarDataComputationDecisionCurveAnalysis.R | 849 familiar-1.5.0/familiar/R/FamiliarDataComputationFeatureExpression.R | 456 familiar-1.5.0/familiar/R/FamiliarDataComputationFeatureSimilarity.R | 1011 familiar-1.5.0/familiar/R/FamiliarDataComputationHyperparameters.R | 510 familiar-1.5.0/familiar/R/FamiliarDataComputationICE.R | 1572 - familiar-1.5.0/familiar/R/FamiliarDataComputationModelPerformance.R | 573 familiar-1.5.0/familiar/R/FamiliarDataComputationPermutationVimp.R | 1199 - familiar-1.5.0/familiar/R/FamiliarDataComputationPredictionData.R | 1031 familiar-1.5.0/familiar/R/FamiliarDataComputationRiskStratificationData.R | 972 familiar-1.5.0/familiar/R/FamiliarDataComputationRiskStratificationInfo.R | 271 familiar-1.5.0/familiar/R/FamiliarDataComputationSampleSimilarity.R | 727 familiar-1.5.0/familiar/R/FamiliarDataComputationUnivariateAnalysis.R | 585 familiar-1.5.0/familiar/R/FamiliarDataComputationVimp.R | 1036 familiar-1.5.0/familiar/R/FamiliarDataElement.R | 2401 +- familiar-1.5.0/familiar/R/FamiliarEnsemble.R | 1650 - familiar-1.5.0/familiar/R/FamiliarHyperparameterLearner.R | 731 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616 familiar-1.5.0/familiar/tests/testthat/test-learner_rfsrc_s4.R | 602 familiar-1.5.0/familiar/tests/testthat/test-learner_survival_regression_S4.R | 98 familiar-1.5.0/familiar/tests/testthat/test-learner_svm_S4.R | 558 familiar-1.5.0/familiar/tests/testthat/test-learner_xgboost_dart_S4.R | 786 familiar-1.5.0/familiar/tests/testthat/test-learner_xgboost_lm_S4.R | 551 familiar-1.5.0/familiar/tests/testthat/test-learner_xgboost_tree_S4.R | 705 familiar-1.5.0/familiar/tests/testthat/test-metric_auc_roc_S4.R | 173 familiar-1.5.0/familiar/tests/testthat/test-metric_brier_S4.R | 167 familiar-1.5.0/familiar/tests/testthat/test-metric_concordance_index_S4.R | 310 familiar-1.5.0/familiar/tests/testthat/test-metric_confusion_matrix_metrics_S4.R | 528 familiar-1.5.0/familiar/tests/testthat/test-metric_regression_S4.R | 429 familiar-1.5.0/familiar/tests/testthat/test-naive_model.R | 15 familiar-1.5.0/familiar/tests/testthat/test-novelty_isolation_forest_S4.R | 9 familiar-1.5.0/familiar/tests/testthat/test-novelty_none_S4.R | 15 familiar-1.5.0/familiar/tests/testthat/test-object_conversion.R | 201 familiar-1.5.0/familiar/tests/testthat/test-parallel_backend.R | 62 familiar-1.5.0/familiar/tests/testthat/test-plot_auc_curves.R | 177 familiar-1.5.0/familiar/tests/testthat/test-plot_confusion_matrix.R | 93 familiar-1.5.0/familiar/tests/testthat/test-plot_decision_curve.R | 120 familiar-1.5.0/familiar/tests/testthat/test-plot_feature_similarity.R | 55 familiar-1.5.0/familiar/tests/testthat/test-plot_kaplan_meier_curve.R | 102 familiar-1.5.0/familiar/tests/testthat/test-plot_model_performance.R | 615 familiar-1.5.0/familiar/tests/testthat/test-plot_model_ranks.R | 83 familiar-1.5.0/familiar/tests/testthat/test-plot_permutation_variable_importance.R | 135 familiar-1.5.0/familiar/tests/testthat/test-plot_univariate_importance.R | 96 familiar-1.5.0/familiar/tests/testthat/test-predict.R | 490 familiar-1.5.0/familiar/tests/testthat/test-process_time.R | 16 familiar-1.5.0/familiar/tests/testthat/test-rank_aggregation_methods.R | 316 familiar-1.5.0/familiar/tests/testthat/test-sample_weights.R | 127 familiar-1.5.0/familiar/tests/testthat/test-stratification.R | 231 familiar-1.5.0/familiar/tests/testthat/test-subsampling_functions.R | 2507 +- familiar-1.5.0/familiar/tests/testthat/test-train_familiar.R | 299 familiar-1.5.0/familiar/tests/testthat/test-transformation.R | 633 familiar-1.5.0/familiar/tests/testthat/test-update_object.R | 257 familiar-1.5.0/familiar/tests/testthat/test-vimp_concordance_S4.R | 157 familiar-1.5.0/familiar/tests/testthat/test-vimp_corelearn_S4.R | 376 familiar-1.5.0/familiar/tests/testthat/test-vimp_correlation_S4.R | 105 familiar-1.5.0/familiar/tests/testthat/test-vimp_glmnet_S4.R | 84 familiar-1.5.0/familiar/tests/testthat/test-vimp_mutual_information_S4.R | 398 familiar-1.5.0/familiar/tests/testthat/test-vimp_ranger_S4.R | 866 familiar-1.5.0/familiar/tests/testthat/test-vimp_regression_S4.R | 188 familiar-1.5.0/familiar/tests/testthat/test-vimp_table.R | 349 familiar-1.5.0/familiar/vignettes/eval_and_explain/auc-pr-curve-bci-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/auc-pr-curve-point-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/auc-roc-curve-bci-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/auc-roc-curve-point-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/calibration-data-bci-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/calibration-data-point-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/decision-curve-bci-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/feature-similarity-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/ice-2d-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/ice-2d-anchored-1.png |binary familiar-1.5.0/familiar/vignettes/eval_and_explain/ice-2d-survival-1.png |binary 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familiar-1.5.0/familiar/vignettes/introduction_precompiled.Rmd | 180 familiar-1.5.0/familiar/vignettes/learners_precompiled.Rmd | 2 familiar-1.5.0/familiar/vignettes/performance_metrics_precompiled.Rmd | 2 familiar-1.5.0/familiar/vignettes/prospective_use/prospective-auc_roc-plot-1.png |binary familiar-1.5.0/familiar/vignettes/prospective_use/prospective-auc_roc-plot-from-exported-collection-1.png |binary familiar-1.5.0/familiar/vignettes/prospective_use/prospective-model-performance-plot-1.png |binary familiar-1.5.0/familiar/vignettes/prospective_use/prospective-model-performance-plot-ensemble-1.png |binary familiar-1.5.0/familiar/vignettes/prospective_use/prospective-model-performance-plot-implicit-1.png |binary familiar-1.5.0/familiar/vignettes/prospective_use/prospective-model-performance-plot-new-directory-1.png |binary familiar-1.5.0/familiar/vignettes/prospective_use_precompiled.Rmd | 335 408 files changed, 100932 insertions(+), 84081 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 0.1.2 dated 2024-07-26 and 0.1.3 dated 2024-09-23
CohortSymmetry-0.1.2/CohortSymmetry/man/figures/CSHex.png |only CohortSymmetry-0.1.3/CohortSymmetry/DESCRIPTION | 10 CohortSymmetry-0.1.3/CohortSymmetry/MD5 | 92 CohortSymmetry-0.1.3/CohortSymmetry/R/crudeSequenceRatio.R | 26 CohortSymmetry-0.1.3/CohortSymmetry/R/displayTables.R | 496 +- CohortSymmetry-0.1.3/CohortSymmetry/R/generateSequenceCohortSet.R | 112 CohortSymmetry-0.1.3/CohortSymmetry/R/getConfidenceInterval.R | 92 CohortSymmetry-0.1.3/CohortSymmetry/R/getSummarisedResult.R | 132 CohortSymmetry-0.1.3/CohortSymmetry/R/inputValidation.R | 16 CohortSymmetry-0.1.3/CohortSymmetry/R/mockCohortSymmetry.R | 188 CohortSymmetry-0.1.3/CohortSymmetry/R/nullSequenceRatio.R | 298 - CohortSymmetry-0.1.3/CohortSymmetry/R/plotSequenceRatios.R | 26 CohortSymmetry-0.1.3/CohortSymmetry/R/plotTemporalSymmetry.R | 28 CohortSymmetry-0.1.3/CohortSymmetry/R/summariseSequenceRatios.R | 402 - CohortSymmetry-0.1.3/CohortSymmetry/R/summariseTemporalSymmetry.R | 51 CohortSymmetry-0.1.3/CohortSymmetry/README.md | 11 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a01_Introduction.R | 20 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a01_Introduction.Rmd | 20 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a01_Introduction.html | 200 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort_set.R | 84 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort_set.Rmd | 84 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort_set.html | 165 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.R | 30 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.Rmd | 30 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.html | 10 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.R | 19 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.Rmd | 19 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.html | 428 +- CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.R | 29 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.Rmd | 29 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.html | 26 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.R | 19 CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.Rmd | 19 CohortSymmetry-0.1.3/CohortSymmetry/man/CohortSymmetry-package.Rd | 2 CohortSymmetry-0.1.3/CohortSymmetry/man/figures/logo.png |only CohortSymmetry-0.1.3/CohortSymmetry/man/summariseTemporalSymmetry.Rd | 87 CohortSymmetry-0.1.3/CohortSymmetry/tests/testthat/test-attrition.R | 1833 ++++---- CohortSymmetry-0.1.3/CohortSymmetry/tests/testthat/test-displayTable.R | 10 CohortSymmetry-0.1.3/CohortSymmetry/tests/testthat/test-generateSequenceCohortSet.R | 2040 +++++----- CohortSymmetry-0.1.3/CohortSymmetry/tests/testthat/test-plotSequenceRatio.R | 8 CohortSymmetry-0.1.3/CohortSymmetry/tests/testthat/test-plotTemporalSymmetry.R | 274 - CohortSymmetry-0.1.3/CohortSymmetry/tests/testthat/test-summariseSequenceRatios.R | 68 CohortSymmetry-0.1.3/CohortSymmetry/vignettes/a01_Introduction.Rmd | 20 CohortSymmetry-0.1.3/CohortSymmetry/vignettes/a02_Generate_a_sequence_cohort_set.Rmd | 84 CohortSymmetry-0.1.3/CohortSymmetry/vignettes/a03_Summarise_sequence_ratios.Rmd | 30 CohortSymmetry-0.1.3/CohortSymmetry/vignettes/a04_Visualise_sequence_ratios.Rmd | 19 CohortSymmetry-0.1.3/CohortSymmetry/vignettes/a05_Summarise_temporal_symmetry.Rmd | 29 CohortSymmetry-0.1.3/CohortSymmetry/vignettes/a06_Visualise_temporal_symmetry.Rmd | 19 48 files changed, 3830 insertions(+), 3904 deletions(-)
More information about CohortSymmetry at CRAN
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Title: Data Analysis Tools Customized for TNTP
Description: An assortment of functions and templates customized to meet
the needs of data analysts at the non-profit organization TNTP.
Includes functions for branded colors and plots, credentials management,
repository set-up, and other common analytic tasks.
Author: Dustin Pashouwer [aut, cre],
Sam Firke [aut],
Shane Orr [aut],
Sam Talcott [aut]
Maintainer: Dustin Pashouwer <dustin.pashouwer@tntp.org>
Diff between tntpr versions 1.0.3 dated 2024-05-28 and 1.1.0 dated 2024-09-23
DESCRIPTION | 16 ++--- MD5 | 31 ++++++----- NAMESPACE | 3 + NEWS.md | 12 ++++ R/position_diverge.R |only R/theme_tntp_2018.R | 2 R/tntp_colors.R | 80 ++++++++++++++++++++++++++--- R/tntp_style.R | 6 +- inst/doc/visualization-cookbook.R | 31 ++++++++--- inst/doc/visualization-cookbook.Rmd | 39 +++++++++++--- inst/doc/visualization-cookbook.html | 90 +++++++++++++++++++-------------- man/choose_text_color.Rd | 38 ++++++++++++- man/position_diverge.Rd |only man/theme_tntp_2018.Rd | 2 man/tntp_style.Rd | 4 - tests/testthat/test-position_diverge.R |only tests/testthat/test-tntp_colors.R | 24 ++++++++ vignettes/visualization-cookbook.Rmd | 39 +++++++++++--- 18 files changed, 314 insertions(+), 103 deletions(-)
Title: Templated Reporting Workflows in Word and PowerPoint
Description: Automated reporting in Word and PowerPoint can require customization for each organizational template. This package works around this by adding standard reporting functions and an abstraction layer to facilitate automated reporting workflows that can be replicated across different organizational templates.
Author: John Harrold [aut, cre] ,
Bryan Smith [aut]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between onbrand versions 1.0.5 dated 2024-02-05 and 1.0.6 dated 2024-09-23
DESCRIPTION | 8 MD5 | 31 - NAMESPACE | 1 NEWS.md | 9 R/mk_lg_tbl.R |only build/vignette.rds |binary inst/doc/Creating_Templated_Office_Workflows.html | 638 +++++++++++----------- inst/doc/Custom_Office_Templates.Rmd | 2 inst/doc/Custom_Office_Templates.html | 62 +- inst/templates/report.pptx |binary inst/templates/report.yaml | 20 inst/test_scripts/mk_multipage_table.R |only inst/test_scripts/span_table.R | 106 --- man/build_span.Rd | 106 --- man/mk_lg_tbl.Rd |only man/onbrand.Rd | 4 man/span_table.Rd | 106 --- vignettes/Custom_Office_Templates.Rmd | 2 18 files changed, 412 insertions(+), 683 deletions(-)
Title: Estimation for MVN and Student-t Data with Monotone Missingness
Description: Estimation of multivariate normal (MVN) and student-t data of
arbitrary dimension where the pattern of missing data is monotone.
See Pantaleo and Gramacy (2010) <doi:10.48550/arXiv.0907.2135>.
Through the use of parsimonious/shrinkage regressions
(plsr, pcr, lasso, ridge, etc.), where standard regressions fail,
the package can handle a nearly arbitrary amount of missing data.
The current version supports maximum likelihood inference and
a full Bayesian approach employing scale-mixtures for Gibbs sampling.
Monotone data augmentation extends this Bayesian approach to arbitrary
missingness patterns. A fully functional standalone interface to the
Bayesian lasso (from Park & Casella), Normal-Gamma (from Griffin & Brown),
Horseshoe (from Carvalho, Polson, & Scott), and ridge regression
with model selection via Reversible Jump, and student-t errors
(from Geweke) is also provided.
Author: Robert B. Gramacy [aut, cre] as updated by Berwin A. Turlach
)
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between monomvn versions 1.9-20 dated 2024-01-11 and 1.9-21 dated 2024-09-23
ChangeLog | 6 ++++++ DESCRIPTION | 19 +++++++++++++------ MD5 | 20 ++++++++++---------- build/partial.rdb |binary data/cement.rda |binary src/blasso.cc | 28 ++++++++++++++-------------- src/bmonomvn.cc | 4 ++-- src/matrix.c | 10 +++++----- src/nu.c | 5 +++-- src/rhelp.h | 2 +- src/ustructs.cc | 2 +- 11 files changed, 55 insertions(+), 41 deletions(-)
Title: Power Analysis and Sample Size Calculation
Description: Power analysis and sample size calculation for Welch and Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) t-tests including Monte-Carlo simulations of empirical power and type-I-error. Power and sample size calculation for Wilcoxon rank sum and signed rank tests via Monte-Carlo simulations. Power and sample size required for the evaluation of a diagnostic test(-system) (Flahault et al. (2005), <doi:10.1016/j.jclinepi.2004.12.009>; Dobbin and Simon (2007), <doi:10.1093/biostatistics/kxj036>) as well as for a single proportion (Fleiss et al. (2003), ISBN:978-0-471-52629-2; Piegorsch (2004), <doi:10.1016/j.csda.2003.10.002>; Thulin (2014), <doi:10.1214/14-ejs909>), comparing two negative binomial rates (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>), ANCOVA (Shieh (2020), <doi:10.1007/s11336-019-09692-3>), reference ranges (Jennen-Steinmetz and Wellek (2005), <doi:10.1002/sim.2177>), multiple primary endpoints (Sozu et al. (2015), ISBN:978 [...truncated...]
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKpower versions 0.9 dated 2024-04-07 and 1.0 dated 2024-09-23
DESCRIPTION | 10 MD5 | 30 - NAMESPACE | 4 NEWS | 10 R/powerDiagnosticTest.R | 18 R/ssizeAUCCI.R |only R/ssizePropCI.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/MKpower.R | 13 inst/doc/MKpower.Rmd | 21 inst/doc/MKpower.html | 965 ++++++++++++++++++++++++------------------- man/0MKpower-package.Rd | 5 man/power.diagnostic.test.Rd | 14 man/ssize.auc.ci.Rd |only man/ssize.propCI.Rd | 3 vignettes/MKpower.Rmd | 21 17 files changed, 669 insertions(+), 450 deletions(-)
Title: Change Point Tests for Joint Distributions and Copulas
Description: Change point tests for joint distributions and copulas using pseudo-observations with multipliers or bootstrap. The processes used here have been defined in Bucher, Kojadinovic, Rohmer & Segers <doi:10.1016/j.jmva.2014.07.012> and Nasri & Remillard <doi:10.1016/j.jmva.2019.03.002>.
Author: Bouchra R Nasri [aut],
Bruno N Remillard [aut, cre, cph]
Maintainer: Bruno N Remillard <bruno.remillard@hec.ca>
Diff between changepointTests versions 0.1.5 dated 2024-02-12 and 0.1.7 dated 2024-09-23
DESCRIPTION | 8 +-- MD5 | 14 +++--- R/cpCopMultStatsBKRSNonSeq.R | 1 R/cpCopMultStatsBKRSSeq.R | 1 R/cpCopStats.R | 1 R/cpCopStatsBKRS.R | 1 R/emp.cdf.R | 1 src/changepointCopR.c | 96 +++++++++++++++++++++---------------------- 8 files changed, 59 insertions(+), 64 deletions(-)
More information about changepointTests at CRAN
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Title: Seasonal Adjustment of Weekly Data
Description: Perform seasonal adjustment of weekly data. The package provides a user-friendly interface for computing seasonally adjusted estimates of weekly data and includes functions for the creation of country-specific prior adjustment variables, as well as diagnostic tools to assess the quality of the adjustments. The method is described in more detail in Ginker (2023) <doi:10.13140/RG.2.2.12221.44000>.
Author: Tim Ginker [aut, cre, cph]
Maintainer: Tim Ginker <tim.ginker@gmail.com>
Diff between boiwsa versions 1.1.1 dated 2024-06-05 and 1.1.2 dated 2024-09-23
DESCRIPTION | 11 +-- MD5 | 22 ++++--- NAMESPACE | 7 ++ NEWS.md | 4 + R/boiwsa.R | 94 ++++++++++++------------------- R/data.R | 2 R/generic_functions.R |only README.md | 33 ++++------ man/figures/README-unnamed-chunk-5-1.png |binary man/gasoline.data.Rd | 2 man/plot.boiwsa.Rd |only man/print.Rd |only man/print.boiwsa.Rd |only man/summary.Rd |only man/summary.boiwsa.Rd |only 15 files changed, 87 insertions(+), 88 deletions(-)
More information about shinycroneditor at CRAN
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Title: Narrowest-Over-Threshold Change-Point Detection
Description: Provides efficient implementation of the Narrowest-Over-Threshold methodology for detecting an unknown number of change-points occurring at unknown locations in one-dimensional data following 'deterministic signal + noise' model. Currently implemented scenarios are: piecewise-constant signal, piecewise-constant signal with a heavy-tailed noise, piecewise-linear signal, piecewise-quadratic signal, piecewise-constant signal and with piecewise-constant variance of the noise. For details, see Baranowski, Chen and Fryzlewicz (2019) <doi:10.1111/rssb.12322>.
Author: Rafal Baranowski [aut],
Yining Chen [aut, cre],
Piotr Fryzlewicz [aut]
Maintainer: Yining Chen <y.chen101@lse.ac.uk>
Diff between not versions 1.5 dated 2023-02-01 and 1.6 dated 2024-09-23
DESCRIPTION | 17 +++++-- MD5 | 10 ++-- R/not.R | 2 src/changepoints_tree.c | 44 ++++++++++---------- src/contrasts.c | 104 ++++++++++++++++++++++++------------------------ src/not.c | 4 - 6 files changed, 93 insertions(+), 88 deletions(-)
Title: Simulating and Analyzing Time to Event Data in the Presence of
Population Mortality
Description: Implements two methods: a nonparametric risk adjustment and a
data imputation method that use general population mortality tables to allow a
correct analysis of time to disease recurrence. Also includes a powerful set of
object oriented survival data simulation functions.
Author: Tomaz Stupnik [aut, cre],
Maja Pohar Perme [ctb]
Maintainer: Tomaz Stupnik <tomaz.stupnik@guest.arnes.si>
Diff between missDeaths versions 2.7 dated 2020-10-17 and 2.8 dated 2024-09-23
DESCRIPTION | 8 MD5 | 13 NAMESPACE | 83 +++--- R/exports.R | 686 +++++++++++++++++++++++++-------------------------- R/init.R | 22 - man/md.binom.Rd | 54 ++-- man/md.survdump.Rd |only src/survexpcache.cpp | 44 +-- 8 files changed, 449 insertions(+), 461 deletions(-)
Title: Identifying Interactions Between Binary Predictors
Description: A statistical learning method that tries to find the best set
of predictors and interactions between predictors for modeling binary or
quantitative response data in a decision tree. Several search algorithms
and ensembling techniques are implemented allowing for finetuning the
method to the specific problem. Interactions with quantitative
covariables can be properly taken into account by fitting local
regression models. Moreover, a variable importance measure for assessing
marginal and interaction effects is provided. Implements the
procedures proposed by Lau et al. (2024, <doi:10.1007/s10994-023-06488-6>).
Author: Michael Lau [aut, cre]
Maintainer: Michael Lau <michael.lau@hhu.de>
Diff between logicDT versions 1.0.4 dated 2024-01-19 and 1.0.5 dated 2024-09-23
DESCRIPTION | 6 MD5 | 84 ++--- build/partial.rdb |binary man/bestBoostingIter.Rd | 88 ++--- man/calcAUC.Rd | 52 +-- man/calcBrier.Rd | 42 +- man/calcDev.Rd | 42 +- man/calcMSE.Rd | 38 +- man/calcMis.Rd | 48 +- man/calcNCE.Rd | 88 ++--- man/calcNRMSE.Rd | 44 +- man/cooling.schedule.Rd | 286 ++++++++--------- man/cv.prune.Rd | 166 +++++----- man/figures |only man/fit4plModel.Rd | 58 +-- man/fitLinearBoostingModel.Rd | 86 ++--- man/fitLinearLogicModel.Rd | 170 +++++----- man/fitLinearModel.Rd | 62 +-- man/get.ideal.penalty.Rd | 94 ++--- man/getDesignMatrix.Rd | 44 +- man/gxe.test.Rd | 210 ++++++------ man/gxe.test.boosting.Rd | 76 ++-- man/importance.test.boosting.Rd | 100 +++--- man/logicDT.Rd | 656 ++++++++++++++++++++-------------------- man/logicDT.bagging.Rd | 98 ++--- man/logicDT.boosting.Rd | 180 +++++----- man/partial.predict.Rd | 72 ++-- man/plot.logicDT.Rd | 136 ++++---- man/plot.vim.Rd | 46 +- man/predict.4pl.Rd | 48 +- man/predict.linear.Rd | 56 +-- man/predict.linear.logic.Rd | 64 +-- man/predict.logicDT.Rd | 160 ++++----- man/prune.Rd | 72 ++-- man/prune.path.Rd | 78 ++-- man/refitTrees.Rd | 52 +-- man/splitSNPs.Rd | 46 +- man/tree.control.Rd | 206 ++++++------ man/vim.Rd | 478 ++++++++++++++--------------- src/gxe-test.c | 46 +- src/logicDT.c | 252 +++++++-------- src/pruning.c | 18 - src/sa-greedy.c | 156 ++++----- 43 files changed, 2403 insertions(+), 2401 deletions(-)
Title: Load and Wrangle IDMC Displacement Data
Description: Utilities to work with data from the Internal Displacement
Monitoring Centre (IDMC) (<https://www.internal-displacement.org/>),
with convenient functions for loading events data from the IDMC API
and transforming events data to daily displacement estimates.
Author: Seth Caldwell [aut, cre, cph]
Maintainer: Seth Caldwell <caldwellst@gmail.com>
Diff between idmc versions 0.3.0 dated 2023-08-28 and 0.3.1 dated 2024-09-23
DESCRIPTION | 12 +++++------ MD5 | 20 +++++++++---------- NEWS.md | 7 ++++++ R/idmc_get_data.R | 4 +-- R/idmc_transform_daily.R | 35 +++++++++++++-------------------- build/vignette.rds |binary inst/doc/idmc-usage.R | 2 - inst/doc/idmc-usage.html | 46 ++++++++++++++++++++++---------------------- man/idmc-package.Rd | 2 - man/idmc_get_data.Rd | 2 - man/idmc_transform_daily.Rd | 14 +++++++++---- 11 files changed, 75 insertions(+), 69 deletions(-)
Title: HDX Theme, Scales, and Other Conveniences for 'ggplot2'
Description: A Humanitarian Data Exchange (HDX) theme, color palettes, and
scales for 'ggplot2' to allow users to easily follow the HDX visual design
guide, including convenience functions for for loading and using the
Source Sans 3 font.
Author: Seth Caldwell [aut, cre, cph]
Maintainer: Seth Caldwell <caldwellst@gmail.com>
Diff between gghdx versions 0.1.3 dated 2024-05-14 and 0.1.4 dated 2024-09-23
gghdx-0.1.3/gghdx/man/format_number_hdx.Rd |only gghdx-0.1.3/gghdx/man/label_number_hdx.Rd |only gghdx-0.1.4/gghdx/DESCRIPTION | 8 +-- gghdx-0.1.4/gghdx/MD5 | 17 +++---- gghdx-0.1.4/gghdx/NAMESPACE | 1 gghdx-0.1.4/gghdx/NEWS.md | 7 ++- gghdx-0.1.4/gghdx/R/label_number_hdx.R | 62 ++++++++++++++++++----------- gghdx-0.1.4/gghdx/README.md | 5 +- gghdx-0.1.4/gghdx/build/vignette.rds |binary gghdx-0.1.4/gghdx/inst/doc/gghdx.R | 2 gghdx-0.1.4/gghdx/man/number_hdx.Rd |only 11 files changed, 62 insertions(+), 40 deletions(-)
Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using 'Stan' for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include both theory-driven and
data-driven non-linear terms, auto-correlation structures, censoring and
truncation, meta-analytic standard errors, and quite a few more.
In addition, all parameters of the response distribution can be predicted
in order to perform distributional regression. Prior specifications are
flexible and explicitly encourage users to apply prior distributions that
actually reflect their prior knowledge. Models can easily be evaluated and
compared using several methods assessing posterior or prior predictions.
References: Bürkner (2017) <doi:10.18637/jss.v080.i01>;
B [...truncated...]
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [ctb],
Sebastian Weber [ctb],
Andrew Johnson [ctb],
Martin Modrak [ctb],
Hamada S. Badr [ctb],
Frank Weber [ctb],
Aki Vehtari [ctb],
Mattan S. Ben-Shachar [ctb],
Hayden Rabel [ctb],
Simon C. Mills [ctb], [...truncated...]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 2.21.0 dated 2024-03-20 and 2.22.0 dated 2024-09-23
brms-2.21.0/brms/inst/chunks/fun_gaussian_process.stan |only brms-2.21.0/brms/inst/chunks/fun_gaussian_process_approx.stan |only brms-2.21.0/brms/inst/chunks/fun_von_mises.stan |only brms-2.22.0/brms/DESCRIPTION | 28 brms-2.22.0/brms/MD5 | 258 +- brms-2.22.0/brms/NAMESPACE | 88 brms-2.22.0/brms/NEWS.md | 34 brms-2.22.0/brms/R/autocor.R | 10 brms-2.22.0/brms/R/backends.R | 90 brms-2.22.0/brms/R/brm.R | 30 brms-2.22.0/brms/R/brm_multiple.R | 38 brms-2.22.0/brms/R/brmsfit-class.R | 15 brms-2.22.0/brms/R/brmsfit-helpers.R | 10 brms-2.22.0/brms/R/brmsfit-methods.R | 34 brms-2.22.0/brms/R/brmsformula.R | 18 brms-2.22.0/brms/R/brmsframe.R |only brms-2.22.0/brms/R/brmsterms.R | 39 brms-2.22.0/brms/R/conditional_effects.R | 48 brms-2.22.0/brms/R/conditional_smooths.R | 14 brms-2.22.0/brms/R/data-helpers.R | 25 brms-2.22.0/brms/R/data-predictor.R | 336 +- brms-2.22.0/brms/R/data-response.R | 101 brms-2.22.0/brms/R/distributions.R | 10 brms-2.22.0/brms/R/exclude_pars.R | 124 - brms-2.22.0/brms/R/families.R | 77 brms-2.22.0/brms/R/family-lists.R | 13 brms-2.22.0/brms/R/formula-ac.R | 85 brms-2.22.0/brms/R/formula-ad.R | 49 brms-2.22.0/brms/R/formula-gp.R | 175 + brms-2.22.0/brms/R/formula-re.R | 240 -- brms-2.22.0/brms/R/formula-sm.R | 23 brms-2.22.0/brms/R/formula-sp.R | 71 brms-2.22.0/brms/R/log_lik.R | 2 brms-2.22.0/brms/R/loo.R | 27 brms-2.22.0/brms/R/loo_moment_match.R | 28 brms-2.22.0/brms/R/loo_predict.R | 102 brms-2.22.0/brms/R/misc.R | 28 brms-2.22.0/brms/R/model_weights.R | 2 brms-2.22.0/brms/R/numeric-helpers.R | 23 brms-2.22.0/brms/R/posterior_smooths.R | 16 brms-2.22.0/brms/R/pp_check.R | 43 brms-2.22.0/brms/R/pp_mixture.R | 10 brms-2.22.0/brms/R/predictor.R | 29 brms-2.22.0/brms/R/prepare_predictions.R | 417 +-- brms-2.22.0/brms/R/priors.R | 366 +-- brms-2.22.0/brms/R/priorsense.R |only brms-2.22.0/brms/R/reloo.R | 17 brms-2.22.0/brms/R/rename_pars.R | 322 +- brms-2.22.0/brms/R/restructure.R | 47 brms-2.22.0/brms/R/stan-helpers.R | 166 - brms-2.22.0/brms/R/stan-likelihood.R | 1176 ++++++---- brms-2.22.0/brms/R/stan-predictor.R | 605 ++--- brms-2.22.0/brms/R/stan-prior.R | 8 brms-2.22.0/brms/R/stan-response.R | 467 +-- brms-2.22.0/brms/R/stancode.R | 89 brms-2.22.0/brms/R/standata.R | 184 - brms-2.22.0/brms/R/summary.R | 20 brms-2.22.0/brms/R/update.R | 12 brms-2.22.0/brms/R/zzz.R | 5 brms-2.22.0/brms/README.md | 4 brms-2.22.0/brms/build/vignette.rds |binary brms-2.22.0/brms/inst/chunks/fun_add_int.stan |only brms-2.22.0/brms/inst/chunks/fun_cox.stan | 34 brms-2.22.0/brms/inst/chunks/fun_gp_exp_quad.stan |only brms-2.22.0/brms/inst/chunks/fun_gp_exponential.stan |only brms-2.22.0/brms/inst/chunks/fun_gp_matern32.stan |only brms-2.22.0/brms/inst/chunks/fun_gp_matern52.stan |only brms-2.22.0/brms/inst/chunks/fun_scale_time_err.stan | 42 brms-2.22.0/brms/inst/chunks/fun_scale_time_err_flex.stan |only brms-2.22.0/brms/inst/chunks/fun_spd_gp_exp_quad.stan |only brms-2.22.0/brms/inst/chunks/fun_spd_gp_matern32.stan |only brms-2.22.0/brms/inst/chunks/fun_spd_gp_matern52.stan |only brms-2.22.0/brms/inst/doc/brms_customfamilies.R | 2 brms-2.22.0/brms/inst/doc/brms_customfamilies.html | 62 brms-2.22.0/brms/inst/doc/brms_distreg.R | 12 brms-2.22.0/brms/inst/doc/brms_distreg.html | 92 brms-2.22.0/brms/inst/doc/brms_families.html | 12 brms-2.22.0/brms/inst/doc/brms_missings.R | 20 brms-2.22.0/brms/inst/doc/brms_missings.Rmd | 16 brms-2.22.0/brms/inst/doc/brms_missings.html | 122 - brms-2.22.0/brms/inst/doc/brms_monotonic.R | 14 brms-2.22.0/brms/inst/doc/brms_monotonic.html | 142 - brms-2.22.0/brms/inst/doc/brms_multilevel.pdf |binary brms-2.22.0/brms/inst/doc/brms_multivariate.R | 2 brms-2.22.0/brms/inst/doc/brms_multivariate.Rmd | 4 brms-2.22.0/brms/inst/doc/brms_multivariate.html | 180 - brms-2.22.0/brms/inst/doc/brms_nonlinear.R | 14 brms-2.22.0/brms/inst/doc/brms_nonlinear.html | 100 brms-2.22.0/brms/inst/doc/brms_overview.pdf |binary brms-2.22.0/brms/inst/doc/brms_phylogenetics.R | 14 brms-2.22.0/brms/inst/doc/brms_phylogenetics.html | 100 brms-2.22.0/brms/inst/doc/brms_threading.R | 28 brms-2.22.0/brms/inst/doc/brms_threading.html | 96 brms-2.22.0/brms/man/R2D2.Rd | 21 brms-2.22.0/brms/man/addition-terms.Rd | 15 brms-2.22.0/brms/man/brm.Rd | 4 brms-2.22.0/brms/man/brm_multiple.Rd | 27 brms-2.22.0/brms/man/brmsfamily.Rd | 7 brms-2.22.0/brms/man/brmsfit-class.Rd | 4 brms-2.22.0/brms/man/car.Rd | 6 brms-2.22.0/brms/man/conditional_effects.brmsfit.Rd | 45 brms-2.22.0/brms/man/create_priorsense_data.brmsfit.Rd |only brms-2.22.0/brms/man/fitted.brmsfit.Rd | 11 brms-2.22.0/brms/man/get_refmodel.brmsfit.Rd | 9 brms-2.22.0/brms/man/gp.Rd | 34 brms-2.22.0/brms/man/horseshoe.Rd | 13 brms-2.22.0/brms/man/log_lik.brmsfit.Rd | 11 brms-2.22.0/brms/man/loo.brmsfit.Rd | 9 brms-2.22.0/brms/man/loo_moment_match.brmsfit.Rd | 25 brms-2.22.0/brms/man/loo_predict.brmsfit.Rd | 33 brms-2.22.0/brms/man/model_weights.brmsfit.Rd | 2 brms-2.22.0/brms/man/posterior_average.brmsfit.Rd | 2 brms-2.22.0/brms/man/posterior_epred.brmsfit.Rd | 11 brms-2.22.0/brms/man/posterior_linpred.brmsfit.Rd | 11 brms-2.22.0/brms/man/posterior_predict.brmsfit.Rd | 11 brms-2.22.0/brms/man/pp_average.brmsfit.Rd | 2 brms-2.22.0/brms/man/pp_check.brmsfit.Rd | 11 brms-2.22.0/brms/man/pp_mixture.brmsfit.Rd | 21 brms-2.22.0/brms/man/predict.brmsfit.Rd | 11 brms-2.22.0/brms/man/predictive_error.brmsfit.Rd | 11 brms-2.22.0/brms/man/prepare_predictions.Rd | 11 brms-2.22.0/brms/man/psis.brmsfit.Rd | 18 brms-2.22.0/brms/man/reloo.brmsfit.Rd | 18 brms-2.22.0/brms/man/residuals.brmsfit.Rd | 11 brms-2.22.0/brms/man/standata.brmsfit.Rd | 11 brms-2.22.0/brms/man/threading.Rd | 7 brms-2.22.0/brms/man/validate_newdata.Rd | 2 brms-2.22.0/brms/tests/testthat/tests.brm.R | 9 brms-2.22.0/brms/tests/testthat/tests.brmsfit-methods.R | 40 brms-2.22.0/brms/tests/testthat/tests.distributions.R | 16 brms-2.22.0/brms/tests/testthat/tests.misc.R | 9 brms-2.22.0/brms/tests/testthat/tests.priors.R | 8 brms-2.22.0/brms/tests/testthat/tests.priorsense.R |only brms-2.22.0/brms/tests/testthat/tests.restructure.R | 2 brms-2.22.0/brms/tests/testthat/tests.stancode.R | 104 brms-2.22.0/brms/tests/testthat/tests.standata.R | 16 brms-2.22.0/brms/vignettes/brms_missings.Rmd | 16 brms-2.22.0/brms/vignettes/brms_multivariate.Rmd | 4 138 files changed, 4393 insertions(+), 3682 deletions(-)
Title: An Implementation of Sensitivity Analysis in Bayesian Networks
Description: An implementation of sensitivity and robustness methods in Bayesian networks in R. It includes methods to perform parameter variations via a variety of co-variation schemes, to compute sensitivity functions and to quantify the dissimilarity of two Bayesian networks via distances and divergences. It further includes diagnostic methods to assess the goodness of fit of a Bayesian networks to data, including global, node and parent-child monitors. Reference: M. Leonelli, R. Ramanathan, R.L. Wilkerson (2022) <doi:10.1016/j.knosys.2023.110882>.
Author: Manuele Leonelli [aut, cre],
Ramsiya Ramanathan [aut],
Rachel Wilkerson [aut]
Maintainer: Manuele Leonelli <manuele.leonelli@ie.edu>
Diff between bnmonitor versions 0.2.1 dated 2024-09-20 and 0.2.2 dated 2024-09-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/aux_node.R | 6 +++++- 3 files changed, 10 insertions(+), 6 deletions(-)
More information about AnimalSequences at CRAN
Permanent link
Title: Statistical Package for Species Richness Estimation
Description: Implementation of various methods in estimation of species richness or diversity in Wang (2011)<doi:10.18637/jss.v040.i09>.
Author: Ji-Ping Wang [aut, cre]
Maintainer: Ji-Ping Wang <jzwang@northwestern.edu>
Diff between SPECIES versions 1.1.4 dated 2023-08-20 and 1.2.0 dated 2024-09-23
DESCRIPTION | 12 +++++++----- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 4 ++-- src/PPCG.f90 | 4 +++- src/norrispollock.f90 | 4 ++-- src/shared.f90 | 26 +++++++++++++------------- 7 files changed, 34 insertions(+), 29 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) 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 0.6.4 dated 2023-10-06 and 1.0.0 dated 2024-09-23
rintcal-0.6.4/rintcal/R/calc.R |only rintcal-0.6.4/rintcal/R/calibrate.R |only rintcal-0.6.4/rintcal/R/plots.R |only rintcal-0.6.4/rintcal/man/D14C.F14C.Rd |only rintcal-0.6.4/rintcal/man/F14C.D14C.Rd |only rintcal-0.6.4/rintcal/man/F14C.age.Rd |only rintcal-0.6.4/rintcal/man/age.F14C.Rd |only rintcal-0.6.4/rintcal/man/age.pMC.Rd |only rintcal-0.6.4/rintcal/man/calBP.14C.Rd |only rintcal-0.6.4/rintcal/man/caldist.Rd |only rintcal-0.6.4/rintcal/man/calibrate.Rd |only rintcal-0.6.4/rintcal/man/contaminate.Rd |only rintcal-0.6.4/rintcal/man/draw.D14C.Rd |only rintcal-0.6.4/rintcal/man/draw.ccurve.Rd |only rintcal-0.6.4/rintcal/man/draw.contamination.Rd |only rintcal-0.6.4/rintcal/man/draw.dates.Rd |only rintcal-0.6.4/rintcal/man/hpd.Rd |only rintcal-0.6.4/rintcal/man/l.calib.Rd |only rintcal-0.6.4/rintcal/man/pMC.age.Rd |only rintcal-0.6.4/rintcal/man/point.estimates.Rd |only rintcal-1.0.0/rintcal/DESCRIPTION | 10 rintcal-1.0.0/rintcal/MD5 | 50 +-- rintcal-1.0.0/rintcal/NAMESPACE | 17 - rintcal-1.0.0/rintcal/NEWS.md | 5 rintcal-1.0.0/rintcal/R/data.R | 61 ++++ rintcal-1.0.0/rintcal/R/rintcal.R | 31 ++ rintcal-1.0.0/rintcal/README | 4 rintcal-1.0.0/rintcal/build/partial.rdb |binary rintcal-1.0.0/rintcal/build/vignette.rds |binary rintcal-1.0.0/rintcal/inst/doc/rintcal.R | 114 -------- rintcal-1.0.0/rintcal/inst/doc/rintcal.Rmd | 217 +--------------- rintcal-1.0.0/rintcal/inst/doc/rintcal.html | 310 ++++++------------------ rintcal-1.0.0/rintcal/man/intcal.data.Rd | 5 rintcal-1.0.0/rintcal/man/mix.ccurves.Rd | 2 rintcal-1.0.0/rintcal/man/rintcal-package.Rd | 2 rintcal-1.0.0/rintcal/vignettes/rintcal.Rmd | 217 +--------------- 36 files changed, 259 insertions(+), 786 deletions(-)
Title: Landscape Epidemiology and Evolution
Description: A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution
of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies.
It is based on a spatial geometry for describing the landscape and allocation of different cultivars,
a dispersal kernel for the dissemination of the pathogen, and a SEIR
('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step.
It provides a useful tool to assess the performance of a wide range of deployment options with
respect to their epidemiological, evolutionary and economic outcomes.
Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett,
Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Author: Loup Rimbaud [aut] ,
Marta Zaffaroni [aut] ,
Jean-Francois Rey [aut, cre] ,
Julien Papaix [aut],
Jean-Loup Gaussen [ctb],
Manon Couty [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between landsepi versions 1.5.0 dated 2024-09-03 and 1.5.1 dated 2024-09-23
DESCRIPTION | 8 MD5 | 42 NEWS.md | 6 R/landsepi-package.R | 4 configure | 18 configure.ac | 3 inst/doc/O1-run_simple_simul.R | 2 inst/doc/O1-run_simple_simul.Rmd | 2 inst/doc/O1-run_simple_simul.html | 2976 +++++++++++++++++++---------------- inst/doc/O2-run_exp_design.html | 602 +++---- inst/doc/O3-landscape_dispersal.html | 489 +++-- inst/doc/O4-run_sex_repro.R | 2 inst/doc/O4-run_sex_repro.Rmd | 2 inst/doc/O4-run_sex_repro.html | 636 ++++--- inst/doc/O5-bibliography.html | 147 + inst/doc/landsepi_poster.pdf |binary inst/doc/list_of_parameters.pdf |binary inst/shiny-landsepi/server.R | 28 man/landsepi-package.Rd | 4 vignettes/O1-run_simple_simul.Rmd | 2 vignettes/O4-run_sex_repro.Rmd | 2 vignettes/listofparameters.pdf |binary 22 files changed, 2784 insertions(+), 2191 deletions(-)
Title: Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan'
Description: Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte
Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological
positions of survey respondents and political actors on a common scale using positional survey
data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform
other versions both in terms of yielding meaningful posterior distributions for respondent
positions and in terms of recovering true respondent positions in simulations. The package
contains functions for preparing data, fitting models, extracting estimates, plotting key
results, and comparing models using cross-validation. The original version of the default
model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Author: Joergen Boelstad [aut, cre]
Maintainer: Joergen Boelstad <jorgen.bolstad@stv.uio.no>
Diff between hbamr versions 2.3.1 dated 2024-06-04 and 2.3.2 dated 2024-09-23
DESCRIPTION | 6 MD5 | 44 ++-- NEWS.md | 6 R/get_est.R | 6 R/get_plot_data.R | 2 R/hbam.R | 2 R/prep_data.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 3 inst/stan/BAM.stan | 3 inst/stan/HBAM.stan | 3 inst/stan/HBAM_MULTI.stan | 3 inst/stan/HBAM_MULTI_NF.stan | 3 inst/stan/HBAM_NF.stan | 3 man/get_plot_data.Rd | 2 man/hbam.Rd | 2 man/prep_data.Rd | 4 src/stanExports_BAM.h | 269 +++++++++++++++++------------- src/stanExports_HBAM.h | 303 +++++++++++++++++++--------------- src/stanExports_HBAM_MULTI.h | 353 ++++++++++++++++++++++------------------ src/stanExports_HBAM_MULTI_NF.h | 325 ++++++++++++++++++++---------------- src/stanExports_HBAM_NF.h | 275 ++++++++++++++++++------------- 23 files changed, 935 insertions(+), 686 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 dated 2024-07-16 and 1.4.1 dated 2024-09-23
DESCRIPTION | 8 MD5 | 82 +++++----- NAMESPACE | 3 NEWS.md | 18 +- R/CheckDiemFormat.r | 39 ++-- R/diem.r | 39 ++-- R/emPolarise.r | 6 R/extdata.r | 6 R/importPolarized.r | 8 R/internal.r | 43 +++++ R/pHetErrOnStateCount.r | 2 R/plotDeFinetti.r | 39 ++-- R/plotMarkerAxis.r | 8 R/plotPolarized.r | 8 R/rank2map.r |only R/sStateCount.r | 2 R/smoothPolarizedGenotypes.r |only R/vcf2diem.r | 8 inst/doc/Importing-data-for-genome-polarisation.Rmd | 4 inst/doc/Importing-data-for-genome-polarisation.html | 15 - inst/doc/Understanding-genome-polarisation-output-files.Rmd | 2 inst/doc/Understanding-genome-polarisation-output-files.html | 8 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 2 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 8 man/CheckDiemFormat.Rd | 7 man/ModelOfDiagnostic.Rd | 4 man/brenthis.Rd | 2 man/diem.Rd | 22 +- man/emPolarise.Rd | 6 man/importPolarized.Rd | 17 -- man/myotis.Rd | 2 man/pHetErrOnStateCount.Rd | 2 man/plotDeFinetti.Rd | 16 - man/plotMarkerAxis.Rd | 8 man/plotPolarized.Rd | 8 man/rank2map.Rd |only man/sStateCount.Rd | 2 man/smoothPolarizedGenotypes.Rd |only man/testdata.Rd | 2 man/vcf2diem.Rd | 8 tests/testthat/test_CheckDiemFormat.r | 26 +++ vignettes/Importing-data-for-genome-polarisation.Rmd | 4 vignettes/Understanding-genome-polarisation-output-files.Rmd | 2 vignettes/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 2 44 files changed, 295 insertions(+), 203 deletions(-)
Title: Methods for Fast Multiple Change-Point/Break-Point Detection and
Estimation
Description: A developing software suite for multiple change-point and change-point-type feature detection/estimation (data segmentation) in data sequences.
Author: Andreas Anastasiou [aut],
Yining Chen [aut, cre],
Haeran Cho [aut],
Piotr Fryzlewicz [aut]
Maintainer: Yining Chen <y.chen101@lse.ac.uk>
Diff between breakfast versions 2.4 dated 2024-04-26 and 2.5 dated 2024-09-23
DESCRIPTION | 6 +- MD5 | 12 ++-- build/vignette.rds |binary inst/doc/breakfast-vignette.R | 6 +- src/changepoints_tree.c | 50 ++++++++++---------- src/contrasts.c | 104 +++++++++++++++++++++--------------------- src/not.c | 4 - 7 files changed, 91 insertions(+), 91 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-13 1.2-2
2018-08-28 1.2-1
2018-08-20 1.2
2018-06-22 1.1
2017-09-21 0.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-25 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-25 0.5.0
2018-10-01 0.4.0
2018-03-28 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-09 1.03
2017-01-09 1.02
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-01 1.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-25 2.0.19
2024-01-29 2.0.18
2023-12-10 2.0.17
2023-03-28 2.0.16
2023-03-19 2.0.15
2023-03-17 2.0.14
2022-11-10 2.0.13
2022-10-29 2.0.12
2022-10-09 2.0.11
2022-10-05 2.0.9
2022-10-05 2.0.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-16 1.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-13 0.1.6
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.7-2 dated 2023-12-11 and 0.7-2.1 dated 2024-09-23
DESCRIPTION | 6 +- MD5 | 4 - src/Rmpi.c | 132 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 71 insertions(+), 71 deletions(-)
Title: Nonlinear Time Series Analysis
Description: Functions for nonlinear time series analysis. This package permits
the computation of the most-used nonlinear statistics/algorithms
including generalized correlation dimension, information dimension,
largest Lyapunov exponent, sample entropy and Recurrence
Quantification Analysis (RQA), among others. Basic routines
for surrogate data testing are also included. Part of this work
was based on the book "Nonlinear time series analysis" by
Holger Kantz and Thomas Schreiber (ISBN: 9780521529020).
Author: Constantino A. Garcia [aut, cre],
Gunther Sawitzki [ctb]
Maintainer: Constantino A. Garcia <constantino.garciama@ceu.es>
Diff between nonlinearTseries versions 0.3.0 dated 2024-04-01 and 0.3.1 dated 2024-09-23
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/nonlinearTseries_quickstart.html | 18 +++++++++--------- src/ANN.cpp | 4 ++-- tests/testthat/test_minimum_embedding.R | 5 ++++- 6 files changed, 25 insertions(+), 22 deletions(-)
More information about nonlinearTseries at CRAN
Permanent link
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007) (temporarily unavailable)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via by modsem it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8 [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.2 dated 2024-08-17 and 1.0.3 dated 2024-09-23
modsem-1.0.2/modsem/tests/testthat/mplusResults.inp |only modsem-1.0.2/modsem/tests/testthat/mplusResults.out |only modsem-1.0.2/modsem/tests/testthat/mplusResults_2f55eb38256759e6ebc9b0699ecf1d13.dat |only modsem-1.0.2/modsem/vignettes/set_eval_false.bash |only modsem-1.0.2/modsem/vignettes/set_eval_true.bash |only modsem-1.0.3/modsem/DESCRIPTION | 9 modsem-1.0.3/modsem/MD5 | 152 +- modsem-1.0.3/modsem/NAMESPACE | 34 modsem-1.0.3/modsem/R/calc_se_da.R | 45 modsem-1.0.3/modsem/R/constraints_pi_ca.R | 4 modsem-1.0.3/modsem/R/construct_matrices_da.R | 509 ++++----- modsem-1.0.3/modsem/R/cov_model.R | 63 - modsem-1.0.3/modsem/R/equations_lms.R | 41 modsem-1.0.3/modsem/R/equations_qml.R | 104 + modsem-1.0.3/modsem/R/est_lms.R | 97 - modsem-1.0.3/modsem/R/est_qml.R | 67 - modsem-1.0.3/modsem/R/fit_modsem_da.R | 81 - modsem-1.0.3/modsem/R/generics.R | 69 - modsem-1.0.3/modsem/R/generics_modsem_da.R | 406 ++----- modsem-1.0.3/modsem/R/generics_modsem_pi.R | 7 modsem-1.0.3/modsem/R/inspect_da.R | 56 - modsem-1.0.3/modsem/R/labelled_params_da.R | 66 + modsem-1.0.3/modsem/R/lavaan_labels.R |only modsem-1.0.3/modsem/R/lexer.R | 38 modsem-1.0.3/modsem/R/method_settings_da.R | 2 modsem-1.0.3/modsem/R/method_settings_pi.R | 2 modsem-1.0.3/modsem/R/model_da.R | 535 +++------- modsem-1.0.3/modsem/R/model_parameters_da.R |only modsem-1.0.3/modsem/R/model_pi.R | 56 - modsem-1.0.3/modsem/R/modsem.R | 63 - modsem-1.0.3/modsem/R/modsem_da.R | 149 +- modsem-1.0.3/modsem/R/modsem_pi.R | 273 ++--- modsem-1.0.3/modsem/R/optimize_da.R | 55 - modsem-1.0.3/modsem/R/parser.R | 34 modsem-1.0.3/modsem/R/plot_interaction.R | 14 modsem-1.0.3/modsem/R/print_partable.R | 77 - modsem-1.0.3/modsem/R/quadrature.R |only modsem-1.0.3/modsem/R/run_multiple_models.R | 2 modsem-1.0.3/modsem/R/simulate_partable.R | 9 modsem-1.0.3/modsem/R/tokenizer.R | 42 modsem-1.0.3/modsem/R/trace_paths_wright.R | 258 ++-- modsem-1.0.3/modsem/R/utils.R | 110 +- modsem-1.0.3/modsem/R/utils_da.R | 62 - modsem-1.0.3/modsem/R/utils_pi.R | 10 modsem-1.0.3/modsem/README.md | 6 modsem-1.0.3/modsem/build/partial.rdb |binary modsem-1.0.3/modsem/build/vignette.rds |binary modsem-1.0.3/modsem/inst/doc/customizing.html | 257 ++-- modsem-1.0.3/modsem/inst/doc/interaction_two_etas.html | 179 +-- modsem-1.0.3/modsem/inst/doc/lavaan.html | 147 +- modsem-1.0.3/modsem/inst/doc/lms_qml.Rmd | 2 modsem-1.0.3/modsem/inst/doc/lms_qml.html | 201 +-- modsem-1.0.3/modsem/inst/doc/methods.html | 153 +- modsem-1.0.3/modsem/inst/doc/modsem.html | 261 ++-- modsem-1.0.3/modsem/inst/doc/observed_lms_qml.R | 15 modsem-1.0.3/modsem/inst/doc/observed_lms_qml.Rmd | 29 modsem-1.0.3/modsem/inst/doc/observed_lms_qml.html | 233 +--- modsem-1.0.3/modsem/inst/doc/plot_interactions.html | 185 +-- modsem-1.0.3/modsem/inst/doc/quadratic.html | 163 +-- modsem-1.0.3/modsem/man/coef_modsem_da.Rd |only modsem-1.0.3/modsem/man/compare_fit.Rd | 4 modsem-1.0.3/modsem/man/default_settings_da.Rd | 2 modsem-1.0.3/modsem/man/default_settings_pi.Rd | 2 modsem-1.0.3/modsem/man/get_pi_data.Rd | 22 modsem-1.0.3/modsem/man/get_pi_syntax.Rd | 26 modsem-1.0.3/modsem/man/modsem.Rd | 56 - modsem-1.0.3/modsem/man/modsem_da.Rd | 138 +- modsem-1.0.3/modsem/man/modsem_inspect.Rd | 4 modsem-1.0.3/modsem/man/modsem_pi.Rd | 61 - modsem-1.0.3/modsem/man/modsemify.Rd | 6 modsem-1.0.3/modsem/man/parameter_estimates.Rd | 2 modsem-1.0.3/modsem/man/plot_interaction.Rd | 12 modsem-1.0.3/modsem/man/standardized_estimates.Rd | 16 modsem-1.0.3/modsem/man/summary.Rd | 44 modsem-1.0.3/modsem/man/trace_path.Rd | 29 modsem-1.0.3/modsem/man/var_interactions.Rd | 4 modsem-1.0.3/modsem/man/vcov_modsem_da.Rd |only modsem-1.0.3/modsem/tests/testthat/test_lms.R | 18 modsem-1.0.3/modsem/tests/testthat/test_pathtracer.R | 20 modsem-1.0.3/modsem/tests/testthat/test_qml.R | 10 modsem-1.0.3/modsem/vignettes/lms_qml.Rmd | 2 modsem-1.0.3/modsem/vignettes/observed_lms_qml.Rmd | 29 82 files changed, 2756 insertions(+), 3183 deletions(-)
Title: Method Comparison Regression
Description: Regression methods to quantify the relation between two measurement
methods are provided by this package. In particular it addresses regression
problems with errors in both variables and without repeated measurements. It
implements the CLSI recommendations (see J. A. Budd et al.
(2018, <https://clsi.org/standards/products/method-evaluation/documents/ep09/>)
for analytical method comparison and bias estimation using patient samples.
Furthermore, algorithms for Theil-Sen and equivariant Passing-Bablok estimators
are implemented, see F. Dufey (2020, <doi:10.1515/ijb-2019-0157>) and
J. Raymaekers and F. Dufey (2022, <arXiv:2202:08060>).
A comprehensive overview over the implemented methods and references can be found
in the manual pages "mcr-package" and "mcreg".
Author: Sergej Potapov [aut, cre] ,
Fabian Model [aut],
Andre Schuetzenmeister [aut] ,
Ekaterina Manuilova [aut],
Florian Dufey [aut] ,
Jakob Raymaekers [aut] ,
Venkatraman E. Seshan [ctb],
Roche [cph, fnd]
Maintainer: Sergej Potapov <sergej.potapov@roche.com>
Diff between mcr versions 1.3.3 dated 2023-10-11 and 1.3.3.1 dated 2024-09-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/PaBaAlgorithm.c | 26 +++++++++++++------------- src/calcRegression.c | 8 ++++---- 4 files changed, 23 insertions(+), 23 deletions(-)
Title: Manly Mixture Modeling and Model-Based Clustering
Description: The utility of this package includes finite mixture modeling and model-based clustering through Manly mixture models by Zhu and Melnykov (2016) <DOI:10.1016/j.csda.2016.01.015>. It also provides capabilities for forward and backward model selection procedures.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Michael Hutt [ctb, cph] ,
Stephen Moshier [ctb, cph] ,
Rouben Rostamian [ctb, cph]
Maintainer: Xuwen Zhu <xzhu20@cba.ua.edu>
Diff between ManlyMix versions 0.1.15 dated 2023-04-29 and 0.1.15.1 dated 2024-09-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/libManly.c | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta
Log-Normal Models
Description: Fits models to catch and effort data. Single-species models are 1) delta log-normal, 2) Tweedie, or 3) Poisson-gamma (G)LMs.
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@csiro.au>
Diff between fishMod versions 0.29 dated 2016-09-22 and 0.29.1 dated 2024-09-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/Tweedie.cc | 8 ++++---- src/TweedieDeriv.cc | 4 ++-- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Modeling Earthquake Data Using 'ETAS' Model
Description: Fits the space-time Epidemic Type Aftershock Sequence
('ETAS') model to earthquake catalogs using a stochastic 'declustering'
approach. The 'ETAS' model is a 'spatio-temporal' marked point process
model and a special case of the 'Hawkes' process. The package is based
on a Fortran program by 'Jiancang Zhuang'
(available at <http://bemlar.ism.ac.jp/zhuang/software.html>),
which is modified and translated into C++ and C such that it
can be called from R. Parallel computing with 'OpenMP' is possible
on supported platforms.
Author: Abdollah Jalilian [aut, cre] ,
Jiancang Zhuang [ctb]
Maintainer: Abdollah Jalilian <stat4aj@gmail.com>
Diff between ETAS versions 0.6.1 dated 2024-03-03 and 0.6.1.1 dated 2024-09-23
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ build/partial.rdb |binary src/declust.c | 4 ++-- src/fitMP.cpp | 6 +++--- src/funcs.h | 16 ++++++++-------- src/lambda.c | 14 +++++++------- 7 files changed, 29 insertions(+), 29 deletions(-)
Title: Cholesky Decomposition of the Wishart Distribution
Description: Sampling from the Cholesky factorization of a Wishart random
variable, sampling from the inverse Wishart distribution, sampling from
the Cholesky factorization of an inverse Wishart random variable, sampling
from the pseudo Wishart distribution, sampling from the generalized
inverse Wishart distribution, computing densities for the Wishart
and inverse Wishart distributions, and computing the multivariate gamma
and digamma functions. Provides a header file so the C functions can be
called directly from other programs.
Author: Geoffrey Thompson [aut, cre] ,
R Core Team [ctb]
Maintainer: Geoffrey Thompson <gzthompson@gmail.com>
Diff between CholWishart versions 1.1.2 dated 2021-10-08 and 1.1.2.1 dated 2024-09-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary src/rCholWishart.c | 26 +++++++++++++------------- 4 files changed, 20 insertions(+), 20 deletions(-)
Title: Time Series Analysis and Computational Finance
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre] ,
Blake LeBaron [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tseries versions 0.10-57 dated 2024-08-13 and 0.10-58 dated 2024-09-23
ChangeLog | 10 + DESCRIPTION | 6 MD5 | 8 - src/dsumsl.f | 404 ++++++++++++++++++++++++++++++++++------------------------- src/garch.c | 12 - 5 files changed, 262 insertions(+), 178 deletions(-)
Title: R Analyzer for Large-Scale Assessments
Description: Prepare and analyze data from large-scale assessments and surveys with
complex sampling and assessment design (see 'Rutkowski', 2010
<doi:10.3102/0013189X10363170>). Such studies are, for example,
international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical
interface is available for the non-technical user.The package includes
functions to covert the original data from 'SPSS' into 'R' data sets
keeping the user-defined missing values, merge data from different
respondents and/or countries, generate variable dictionaries, modify
data, produce descriptive statistics (percentages, means, percentiles,
benchmarks) and multivariate statistics (correlations, linear
regression, binary logistic regression). The number of supported
studies and analysis types will increase in future. For a general
presentation of the package, see 'Mirazchiyski', 2021a
(<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of the
package, see 'Mirazchiyski', 2021b (<doi:10.339 [...truncated...]
Author: Plamen V. Mirazchiyski [aut, cre],
INERI [aut]
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>
Diff between RALSA versions 1.4.7 dated 2024-07-25 and 1.5.0 dated 2024-09-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 12 ++++++++++++ R/lsa.data.diag.r | 14 +++++++------- 4 files changed, 26 insertions(+), 14 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.5-2 dated 2024-08-24 and 1.6-0 dated 2024-09-23
DESCRIPTION | 16 - MD5 | 33 +-- NAMESPACE | 23 +- R/R.R | 73 ++++++ R/loglik.R | 8 R/methods.R | 34 ++- R/mlt.R | 499 ++++++++++++++++++++++++++-------------------- R/mmlt.R |only R/utils.R | 4 inst/NEWS.Rd | 27 ++ man/ctm.Rd | 26 +- man/mlt-methods.Rd | 6 man/mlt-package.Rd | 16 + man/mlt.Rd | 4 man/mmlt-methods.Rd |only man/mmlt.Rd |only tests/bugfixes.R | 24 ++ tests/bugfixes.Rout.save | 33 ++- tests/missing-responses.R |only tests/mmlt_ll_sc.R |only 20 files changed, 543 insertions(+), 283 deletions(-)
Title: Extract and Analyze Rivers from Elevation Data
Description: Seamless extraction of river networks from digital
elevation models data. The package allows analysis of digital
elevation models that can be either externally provided or
downloaded from open source repositories (thus interfacing
with the 'elevatr' package). Extraction is performed via the
'D8' flow direction algorithm of TauDEM (Terrain Analysis Using
Digital Elevation Models), thus interfacing with the 'traudem'
package. Resulting river networks are compatible with functions
from the 'OCNet' package. See Carraro (2023)
<doi:10.5194/hess-27-3733-2023> for a presentation of the package.
Author: Luca Carraro [cre, aut],
University of Zurich [cph, fnd]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between rivnet versions 0.4.2 dated 2024-05-08 and 0.5.0 dated 2024-09-23
DESCRIPTION | 9 +++++---- MD5 | 42 +++++++++++++++++++++++------------------- NAMESPACE | 3 +++ NEWS.md | 12 ++++++++++++ R/contour_to_shapefile.R |only R/extract_river.R | 7 +++++++ R/locate_site.R | 7 +++---- R/river_to_shapefile.R |only build/vignette.rds |binary inst/doc/rivnet.html | 2 +- man/aggregate_river.Rd | 2 +- man/contour_to_shapefile.Rd |only man/covariate_river.Rd | 2 +- man/extract_river.Rd | 4 ++-- man/hydro_river.Rd | 4 ++-- man/locate_site.Rd | 9 ++++----- man/path_velocities_river.Rd | 2 +- man/paths_river.Rd | 2 +- man/plot.Rd | 5 +++-- man/river-class.Rd | 4 ++-- man/river_to_AEM.Rd | 2 +- man/river_to_SSN.Rd | 2 +- man/river_to_igraph.Rd | 2 +- man/river_to_shapefile.Rd |only 24 files changed, 74 insertions(+), 48 deletions(-)
Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses. See e.g. Halekoh and Højsgaard, (2005,
<doi:10.18637/jss.v015.i02>), for details.
Author: Soeren Hoejsgaard [aut, cre, cph],
Ulrich Halekoh [aut, cph],
Jun Yan [aut, cph],
Claus Thorn Ekstroem [ctb]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between geepack versions 1.3.11.1 dated 2024-09-09 and 1.3.12 dated 2024-09-23
DESCRIPTION | 16 +++++++--------- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/qic-ce.R | 2 +- build/vignette.rds |binary inst/doc/geepack-manual.pdf |binary man/geeglm.Rd | 18 ++++++++++++++++++ 7 files changed, 37 insertions(+), 16 deletions(-)
Title: Solve Delay Differential Equations
Description: Solves ordinary and delay differential equations, where
the objective function is written in either R or C. Suitable only
for non-stiff equations, the solver uses a 'Dormand-Prince' method
that allows interpolation of the solution at any point. This
approach is as described by Hairer, Norsett and Wanner (1993)
<ISBN:3540604529>. Support is also included for iterating
difference equations.
Author: Rich FitzJohn [aut, cre],
Wes Hinsley [aut],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between dde versions 1.0.5 dated 2024-01-13 and 1.0.7 dated 2024-09-23
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- build/vignette.rds |binary inst/doc/dde.html | 22 ++++++------ src/dopri.c | 11 +++--- src/r_difeq.c | 60 ++++++++++++++++----------------- src/r_dopri.c | 81 ++++++++++++++++++++++----------------------- src/util.c | 6 +-- tests/testthat/logistic2.c | 6 +-- tests/testthat/lorenz3.c | 6 +-- 10 files changed, 110 insertions(+), 108 deletions(-)
Title: Algorithm Driven Statistical Analysis for Researchers without
Coding Skills
Description: Support functions for R-based 'EQUAL-STATS' software which automatically classifies the data and performs appropriate statistical tests. 'EQUAL-STATS' software is a shiny application with an user-friendly interface to perform complex statistical analysis. Gurusamy,K (2024)<doi:10.5281/zenodo.13354162>.
Author: Kurinchi Gurusamy [aut, cre]
Maintainer: Kurinchi Gurusamy <k.gurusamy@ucl.ac.uk>
Diff between EQUALSTATS versions 0.4.0 dated 2024-09-06 and 0.5.0 dated 2024-09-23
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- R/function.Create_Plots.R | 2 +- R/function.Diagnostic_Accuracy_Tables.R | 2 +- R/function.Sample_Size_Calculations_Primary.R | 14 +++++++------- 5 files changed, 21 insertions(+), 21 deletions(-)
Title: Use 'nlmixr2' to Interact with Open Source and Commercial
Software
Description: Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019)
<doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can
get/install the 'lixoftConnectors' package in the 'Monolix' installation, as
described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When
'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up
command line usage.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [aut] ,
Nook Fulloption [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between babelmixr2 versions 0.1.2 dated 2023-12-12 and 0.1.4 dated 2024-09-23
DESCRIPTION | 18 +-- MD5 | 94 +++++++++++----- NAMESPACE | 54 +++++++++ NEWS.md | 19 +++ R/RcppExports.R | 152 +++++++++++++++++++++++++++ R/as.nlmixr2.R | 6 - R/as.nlmixr2monolixr2rx.R |only R/as.nlmixr2nonmem2rx.R | 6 - R/monolixControl.R | 18 +++ R/monolixNlmixr2est.R | 23 +++- R/monolixReadData.R | 75 +++++++++---- R/monolixRxUiGet.R | 10 + R/nonmemControl.R | 29 +++-- R/nonmemNlmixr2est.R | 12 +- R/nonmemReadData.R | 8 - R/nonmemRxUiGetPk.R | 20 ++- R/pknca.R | 7 + R/poped.R |only R/reexport.R | 27 ++++ R/zzz.R | 26 ++++ README.md | 41 ++++--- build/vignette.rds |binary inst/CITATION | 7 - inst/WORDLIST | 66 +++++++++-- inst/doc/running-pknca.html | 130 +++++++++++------------ inst/poped |only man/as.nlmixr2.Rd | 9 + man/babel.poped.database.Rd |only man/dot-popedF.Rd |only man/dot-popedFree.Rd |only man/dot-popedRxRunSetup.Rd |only man/dot-popedSetup.Rd |only man/dot-popedSolveIdME.Rd |only man/dot-popedW.Rd |only man/dot-setupPopEDdatabase.Rd |only man/monolixControl.Rd | 6 + man/nonmemControl.Rd | 16 +- man/popedControl.Rd |only man/popedGetMultipleEndpointModelingTimes.Rd |only man/popedMultipleEndpointParam.Rd |only man/popedMultipleEndpointResetTimeIndex.Rd |only man/reexports.Rd | 11 + src/RcppExports.cpp | 105 ++++++++++++++++++ src/init.c | 23 +++- src/poped.cpp |only src/timeIndexer.h |only src/timsort.h |only tests/testthat/test-as-nlmixr2.R | 16 ++ tests/testthat/test-monolix.R | 46 +++++++- tests/testthat/test-nonmem.R | 63 ++++++++++- tests/testthat/test-poped.R |only 51 files changed, 940 insertions(+), 203 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-06 0.1.2
Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications.
Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
David Granjon [aut],
Ian Fellows [ctb] ,
Wil Davis [ctb] ,
Spencer Matthews [ctb] ,
JavaScript and CSS libraries authors [ctb, cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.8.6 dated 2024-04-24 and 0.8.7 dated 2024-09-23
DESCRIPTION | 12 MD5 | 89 NAMESPACE | 3 NEWS.md | 1017 ++++---- R/WinBox.R | 408 +-- R/bootstrap-utils.R | 264 +- R/input-airDatepicker.R | 52 R/input-checkboxgroupbuttons.R | 507 ++-- R/input-radiogroupbuttons.R | 543 ++-- R/input-sliderText.R | 498 ++- R/input-switch.R | 682 ++--- R/module-pickerGroup.R | 606 ++-- R/onLoad.R | 45 R/slim-select.R |only R/sw-dropdown.R | 572 ++-- R/sweetalert.R | 1246 +++++----- R/utils.R | 2 R/virtual-select.R | 2 README.md | 4 inst/assets/bootstrap-select/picker-bindings.js | 220 - inst/assets/numericRange/js/numericRange-bindings.js | 124 inst/assets/shinyWidgets-bindings.min.js | 2 inst/assets/sweetalert2/sweetalert-bindings.js | 238 - inst/assets/utils.js | 32 inst/assets/vertical-tab-panel/vertical-tab-panel-bindings.js | 204 - inst/examples/WinBox/apply-method.R | 110 inst/examples/WinBox/htmlwidgets.R | 76 inst/examples/airDatepicker/datepicker/app.R | 4 inst/examples/airDatepicker/timepicker/app.R | 15 inst/examples/checkboxGroupButtons/server.R | 98 inst/examples/radioGroupButtons/server.R | 98 inst/examples/slim-select |only inst/examples/virtual-select/bslib-theming/app.R | 112 inst/packer/air-datepicker.js | 2 inst/packer/slim-select.js |only inst/packer/virtual-select.js | 2 inst/packer/virtual-select.js.LICENSE.txt | 2 man/airDatepicker.Rd | 3 man/prepare_slim_choices.Rd |only man/slimSelectInput.Rd |only man/switchInput.Rd | 4 man/updateAirDateInput.Rd | 3 man/updateSliderTextInput.Rd | 2 man/updateSlimSelect.Rd |only tests/testthat/test-checkboxGroupButtons.R | 398 +-- tests/testthat/test-radioGroupButtons.R | 398 +-- tests/testthat/test-updateCheckboxGroupButtons.R | 90 tests/testthat/test-updateRadioGroupButtons.R | 90 48 files changed, 4475 insertions(+), 4404 deletions(-)
Title: Calibration, Validation, and Simulation of TKTD Models
Description: Eases the use of ecotoxicological effect models. Can simulate
common toxicokinetic-toxicodynamic (TK/TD) models such as
General Unified Threshold models of Survival (GUTS) and Lemna. It can
derive effects and effect profiles (EPx) from scenarios. It supports the
use of 'tidyr' workflows employing the pipe symbol. Time-consuming
tasks can be parallelized.
Author: Nils Kehrein [aut, cre],
Dirk Nickisch [aut],
Peter Vermeiren [aut],
Torben Wittwer [ctb],
Johannes Witt [ctb],
Andre Gergs [ctb]
Maintainer: Nils Kehrein <nils.kehrein@gmail.com>
Diff between cvasi versions 1.1.3 dated 2024-07-25 and 1.2.0 dated 2024-09-23
cvasi-1.1.3/cvasi/R/utils-stats.R |only cvasi-1.1.3/cvasi/man/DEB_Daphnia.Rd |only cvasi-1.1.3/cvasi/src/debtox_daphnia.c |only cvasi-1.1.3/cvasi/tests/testthat/test-GUTS_ring_test.R |only cvasi-1.1.3/cvasi/tests/testthat/test-simulate_Daphnia.R |only cvasi-1.2.0/cvasi/DESCRIPTION | 25 cvasi-1.2.0/cvasi/MD5 | 148 +- cvasi-1.2.0/cvasi/NAMESPACE | 235 ++-- cvasi-1.2.0/cvasi/NEWS.md | 28 cvasi-1.2.0/cvasi/R/calibrate.R | 78 - cvasi-1.2.0/cvasi/R/class-Algae.R | 91 - cvasi-1.2.0/cvasi/R/class-CalibrationSet.R | 53 cvasi-1.2.0/cvasi/R/class-Deb.R | 125 -- cvasi-1.2.0/cvasi/R/class-EffectScenario.R | 2 cvasi-1.2.0/cvasi/R/class-GutsRed.R | 17 cvasi-1.2.0/cvasi/R/class-Lemna.R | 78 - cvasi-1.2.0/cvasi/R/class-Myriophyllum.R | 33 cvasi-1.2.0/cvasi/R/data.R | 6 cvasi-1.2.0/cvasi/R/effect.R | 98 - cvasi-1.2.0/cvasi/R/explore_space.R |only cvasi-1.2.0/cvasi/R/fx.R |only cvasi-1.2.0/cvasi/R/globals.R | 5 cvasi-1.2.0/cvasi/R/lik_profile.R |only cvasi-1.2.0/cvasi/R/model-deb_daphnia.R |only cvasi-1.2.0/cvasi/R/model-debtox.R |only cvasi-1.2.0/cvasi/R/set_bounds.R |only cvasi-1.2.0/cvasi/R/set_param.R | 4 cvasi-1.2.0/cvasi/R/simulate.R | 30 cvasi-1.2.0/cvasi/R/solver.R | 113 -- cvasi-1.2.0/cvasi/R/survival.R | 25 cvasi-1.2.0/cvasi/data/Rsubcapitata.rda |binary cvasi-1.2.0/cvasi/data/dmagna.rda |binary cvasi-1.2.0/cvasi/data/focusd1.rda |binary cvasi-1.2.0/cvasi/data/metsulfuron.rda |binary cvasi-1.2.0/cvasi/data/minnow_it.rda |binary cvasi-1.2.0/cvasi/data/minnow_sd.rda |binary cvasi-1.2.0/cvasi/inst/debtox_license.txt |only cvasi-1.2.0/cvasi/inst/doc/cvasi-1-manual.Rmd | 2 cvasi-1.2.0/cvasi/inst/doc/cvasi-1-manual.html | 18 cvasi-1.2.0/cvasi/inst/doc/cvasi-2-howto.R | 46 cvasi-1.2.0/cvasi/inst/doc/cvasi-2-howto.Rmd | 72 + cvasi-1.2.0/cvasi/inst/doc/cvasi-2-howto.html | 771 +++++++------- cvasi-1.2.0/cvasi/man/Algae-models.Rd | 5 cvasi-1.2.0/cvasi/man/Algae_Simple.Rd | 10 cvasi-1.2.0/cvasi/man/Algae_TKTD.Rd | 14 cvasi-1.2.0/cvasi/man/Algae_Weber.Rd | 24 cvasi-1.2.0/cvasi/man/CalibrationSet.Rd | 18 cvasi-1.2.0/cvasi/man/DEB-models.Rd | 6 cvasi-1.2.0/cvasi/man/DEB_abj.Rd | 2 cvasi-1.2.0/cvasi/man/DEBtox.Rd |only cvasi-1.2.0/cvasi/man/GUTS-RED-models.Rd | 3 cvasi-1.2.0/cvasi/man/GUTS_RED_IT.Rd | 12 cvasi-1.2.0/cvasi/man/GUTS_RED_SD.Rd | 12 cvasi-1.2.0/cvasi/man/Lemna_Schmitt.Rd | 73 - cvasi-1.2.0/cvasi/man/Myrio.Rd | 10 cvasi-1.2.0/cvasi/man/Myrio_log.Rd | 8 cvasi-1.2.0/cvasi/man/Scenarios.Rd | 2 cvasi-1.2.0/cvasi/man/calibrate.Rd | 37 cvasi-1.2.0/cvasi/man/dmagna.Rd | 8 cvasi-1.2.0/cvasi/man/explore_space.Rd |only cvasi-1.2.0/cvasi/man/fx.Rd | 2 cvasi-1.2.0/cvasi/man/lik_profile.Rd |only cvasi-1.2.0/cvasi/man/log_lik.Rd |only cvasi-1.2.0/cvasi/man/minnow_it.Rd | 82 - cvasi-1.2.0/cvasi/man/minnow_sd.Rd | 82 - cvasi-1.2.0/cvasi/man/plot_lik_profile.Rd |only cvasi-1.2.0/cvasi/man/plot_param_space.Rd |only cvasi-1.2.0/cvasi/man/set_bounds.Rd |only cvasi-1.2.0/cvasi/man/set_param.Rd | 2 cvasi-1.2.0/cvasi/man/simulate.Rd | 18 cvasi-1.2.0/cvasi/man/solver.Rd | 43 cvasi-1.2.0/cvasi/man/survival.Rd | 3 cvasi-1.2.0/cvasi/src/debtox.c |only cvasi-1.2.0/cvasi/tests/data/EFSA_propiconazole |only cvasi-1.2.0/cvasi/tests/testthat/_snaps |only cvasi-1.2.0/cvasi/tests/testthat/init-simulate_Daphnia.R | 1 cvasi-1.2.0/cvasi/tests/testthat/morse_guts-red.R |only cvasi-1.2.0/cvasi/tests/testthat/test-calibrate.R | 26 cvasi-1.2.0/cvasi/tests/testthat/test-explore_space.R |only cvasi-1.2.0/cvasi/tests/testthat/test-lik_profile.R |only cvasi-1.2.0/cvasi/tests/testthat/test-log_lik.R |only cvasi-1.2.0/cvasi/tests/testthat/test-set_bounds.R |only cvasi-1.2.0/cvasi/tests/testthat/test-simulate_DEBtox.R |only cvasi-1.2.0/cvasi/tests/testthat/test-simulate_Weber.R | 2 cvasi-1.2.0/cvasi/tests/testthat/test-simulate_transfer.R | 11 cvasi-1.2.0/cvasi/tests/testthat/test-survival.R | 367 ------ cvasi-1.2.0/cvasi/tests/testthat/test-verify_guts.R |only cvasi-1.2.0/cvasi/vignettes/cvasi-1-manual.Rmd | 2 cvasi-1.2.0/cvasi/vignettes/cvasi-2-howto.Rmd | 72 + 89 files changed, 1496 insertions(+), 1564 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-09 3.10.4
2023-12-20 3.10.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-22 0.78
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-04 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-20 1.1.4.1
2024-09-12 1.1.3.1
2024-09-06 1.1.3
2024-04-30 1.1.1
2024-04-03 1.1.0
2024-02-26 1.0.1
2024-02-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-26 0.1-1
2016-01-14 0.0-2
Title: Mixed Models for Repeated Measures
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see Cnaan, Laird and Slasor (1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>
for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso
(2008) <doi:10.1177/009286150804200402> for a review. This package
implements MMRM based on the marginal linear model without random
effects using Template Model Builder ('TMB') which enables fast and
robust model fitting. Users can specify a variety of covariance
matrices, weight observations, fit models with restricted or standard
maximum likelihood inference, perform hypothesis testing with
Satterthwaite or Kenward-Roger adjustment, and extract least square
means estimates by using 'emmeans'.
Author: Daniel Sabanes Bove [aut, cre]
,
Liming Li [aut],
Julia Dedic [aut],
Doug Kelkhoff [aut],
Kevin Kunzmann [aut],
Brian Matthew Lang [aut],
Christian Stock [aut],
Ya Wang [aut],
Craig Gower-Page [ctb],
Dan James [aut],
Jonathan Sidi [aut],
Daniel Leibo [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between mmrm versions 0.3.12 dated 2024-06-26 and 0.3.13 dated 2024-09-23
mmrm-0.3.12/mmrm/man/h_factor_ref.Rd |only mmrm-0.3.12/mmrm/man/h_factor_ref_data.Rd |only mmrm-0.3.13/mmrm/DESCRIPTION | 35 mmrm-0.3.13/mmrm/MD5 | 487 mmrm-0.3.13/mmrm/NAMESPACE | 143 mmrm-0.3.13/mmrm/NEWS.md | 343 mmrm-0.3.13/mmrm/R/between-within.R | 262 mmrm-0.3.13/mmrm/R/catch-routine-registration.R | 16 mmrm-0.3.13/mmrm/R/component.R | 296 mmrm-0.3.13/mmrm/R/cov_struct.R | 922 - mmrm-0.3.13/mmrm/R/data.R | 136 mmrm-0.3.13/mmrm/R/empirical.R | 54 mmrm-0.3.13/mmrm/R/fit.R | 1032 - mmrm-0.3.13/mmrm/R/interop-car.R | 326 mmrm-0.3.13/mmrm/R/interop-emmeans.R | 180 mmrm-0.3.13/mmrm/R/interop-parsnip.R | 166 mmrm-0.3.13/mmrm/R/kenwardroger.R | 382 mmrm-0.3.13/mmrm/R/mmrm-methods.R | 526 - mmrm-0.3.13/mmrm/R/mmrm-package.R | 53 mmrm-0.3.13/mmrm/R/residual.R | 64 mmrm-0.3.13/mmrm/R/satterthwaite.R | 518 mmrm-0.3.13/mmrm/R/skipping.R | 62 mmrm-0.3.13/mmrm/R/testing.R | 316 mmrm-0.3.13/mmrm/R/tidiers.R | 398 mmrm-0.3.13/mmrm/R/tmb-methods.R | 1392 +- mmrm-0.3.13/mmrm/R/tmb.R | 1130 +- mmrm-0.3.13/mmrm/R/utils-formula.R | 188 mmrm-0.3.13/mmrm/R/utils-nse.R | 264 mmrm-0.3.13/mmrm/R/utils.R | 1061 +- mmrm-0.3.13/mmrm/R/zzz.R | 284 mmrm-0.3.13/mmrm/build/partial.rdb |binary mmrm-0.3.13/mmrm/build/vignette.rds |binary mmrm-0.3.13/mmrm/inst/REFERENCES.bib | 446 mmrm-0.3.13/mmrm/inst/WORDLIST | 230 mmrm-0.3.13/mmrm/inst/doc/algorithm.R | 12 mmrm-0.3.13/mmrm/inst/doc/algorithm.Rmd | 708 - mmrm-0.3.13/mmrm/inst/doc/algorithm.html | 1214 +- mmrm-0.3.13/mmrm/inst/doc/between_within.R | 36 mmrm-0.3.13/mmrm/inst/doc/between_within.Rmd | 250 mmrm-0.3.13/mmrm/inst/doc/between_within.html | 1189 +- mmrm-0.3.13/mmrm/inst/doc/coef_vcov.R | 12 mmrm-0.3.13/mmrm/inst/doc/coef_vcov.Rmd | 190 mmrm-0.3.13/mmrm/inst/doc/coef_vcov.html | 761 - mmrm-0.3.13/mmrm/inst/doc/covariance.R | 12 mmrm-0.3.13/mmrm/inst/doc/covariance.Rmd | 484 mmrm-0.3.13/mmrm/inst/doc/covariance.html | 1087 +- mmrm-0.3.13/mmrm/inst/doc/empirical_wls.Rmd | 512 mmrm-0.3.13/mmrm/inst/doc/empirical_wls.html | 1089 +- mmrm-0.3.13/mmrm/inst/doc/hypothesis_testing.R | 34 mmrm-0.3.13/mmrm/inst/doc/hypothesis_testing.Rmd | 566 - mmrm-0.3.13/mmrm/inst/doc/hypothesis_testing.html | 1351 +- mmrm-0.3.13/mmrm/inst/doc/introduction.R | 716 - mmrm-0.3.13/mmrm/inst/doc/introduction.Rmd | 128 mmrm-0.3.13/mmrm/inst/doc/introduction.html | 5202 +++++----- mmrm-0.3.13/mmrm/inst/doc/kenward.R | 12 mmrm-0.3.13/mmrm/inst/doc/kenward.Rmd | 762 - mmrm-0.3.13/mmrm/inst/doc/kenward.html | 1403 +- mmrm-0.3.13/mmrm/inst/doc/methodological_introduction.R | 12 mmrm-0.3.13/mmrm/inst/doc/methodological_introduction.Rmd | 228 mmrm-0.3.13/mmrm/inst/doc/methodological_introduction.html | 987 - mmrm-0.3.13/mmrm/inst/doc/mmrm_review_methods.R | 252 mmrm-0.3.13/mmrm/inst/doc/mmrm_review_methods.Rmd | 1240 +- mmrm-0.3.13/mmrm/inst/doc/mmrm_review_methods.html | 2270 ++-- mmrm-0.3.13/mmrm/inst/doc/package_structure.Rmd | 390 mmrm-0.3.13/mmrm/inst/doc/package_structure.html | 1116 +- mmrm-0.3.13/mmrm/inst/doc/predict.R | 14 mmrm-0.3.13/mmrm/inst/doc/predict.Rmd | 454 mmrm-0.3.13/mmrm/inst/doc/predict.html | 1076 +- mmrm-0.3.13/mmrm/inst/doc/satterthwaite.R | 12 mmrm-0.3.13/mmrm/inst/doc/satterthwaite.Rmd | 480 mmrm-0.3.13/mmrm/inst/doc/satterthwaite.html | 1047 +- mmrm-0.3.13/mmrm/inst/jss.csl | 1166 +- mmrm-0.3.13/mmrm/man/Anova.mmrm.Rd | 62 mmrm-0.3.13/mmrm/man/COV_TYPES.Rd | 74 mmrm-0.3.13/mmrm/man/as.cov_struct.Rd | 140 mmrm-0.3.13/mmrm/man/bcva_data.Rd | 66 mmrm-0.3.13/mmrm/man/cached_mmrm_results.Rd | 68 mmrm-0.3.13/mmrm/man/car_add_mmrm.Rd | 36 mmrm-0.3.13/mmrm/man/check_package_version.Rd | 48 mmrm-0.3.13/mmrm/man/component.Rd | 166 mmrm-0.3.13/mmrm/man/cov_struct.Rd | 98 mmrm-0.3.13/mmrm/man/cov_type_abbr.Rd | 38 mmrm-0.3.13/mmrm/man/cov_type_name.Rd | 38 mmrm-0.3.13/mmrm/man/covariance_types.Rd | 268 mmrm-0.3.13/mmrm/man/df_1d.Rd | 64 mmrm-0.3.13/mmrm/man/df_md.Rd | 68 mmrm-0.3.13/mmrm/man/drop_elements.Rd | 42 mmrm-0.3.13/mmrm/man/emit_tidymodels_register_msg.Rd | 32 mmrm-0.3.13/mmrm/man/emmeans_support.Rd | 50 mmrm-0.3.13/mmrm/man/emp_start.Rd | 76 mmrm-0.3.13/mmrm/man/fev_data.Rd | 72 mmrm-0.3.13/mmrm/man/figures/lifecycle-archived.svg | 2 mmrm-0.3.13/mmrm/man/figures/lifecycle-defunct.svg | 2 mmrm-0.3.13/mmrm/man/figures/lifecycle-deprecated.svg | 2 mmrm-0.3.13/mmrm/man/figures/lifecycle-experimental.svg | 2 mmrm-0.3.13/mmrm/man/figures/lifecycle-maturing.svg | 2 mmrm-0.3.13/mmrm/man/figures/lifecycle-questioning.svg | 2 mmrm-0.3.13/mmrm/man/figures/lifecycle-stable.svg | 2 mmrm-0.3.13/mmrm/man/figures/lifecycle-superseded.svg | 2 mmrm-0.3.13/mmrm/man/figures/logo.svg | 712 - mmrm-0.3.13/mmrm/man/fill_names.Rd | 38 mmrm-0.3.13/mmrm/man/fit_mmrm.Rd | 138 mmrm-0.3.13/mmrm/man/fit_single_optimizer.Rd | 138 mmrm-0.3.13/mmrm/man/flat_expr.Rd | 98 mmrm-0.3.13/mmrm/man/format.cov_struct.Rd | 38 mmrm-0.3.13/mmrm/man/format_symbols.Rd | 38 mmrm-0.3.13/mmrm/man/formula_rhs.Rd | 46 mmrm-0.3.13/mmrm/man/h_add_covariance_terms.Rd | 54 mmrm-0.3.13/mmrm/man/h_add_terms.Rd | 54 mmrm-0.3.13/mmrm/man/h_coef_table.Rd | 38 mmrm-0.3.13/mmrm/man/h_confirm_large_levels.Rd | 38 mmrm-0.3.13/mmrm/man/h_construct_model_frame_inputs.Rd | 85 mmrm-0.3.13/mmrm/man/h_default_value.Rd | 44 mmrm-0.3.13/mmrm/man/h_df_1d_bw.Rd | 44 mmrm-0.3.13/mmrm/man/h_df_1d_kr.Rd | 46 mmrm-0.3.13/mmrm/man/h_df_1d_res.Rd | 46 mmrm-0.3.13/mmrm/man/h_df_1d_sat.Rd | 46 mmrm-0.3.13/mmrm/man/h_df_bw_calc.Rd | 46 mmrm-0.3.13/mmrm/man/h_df_md_bw.Rd | 46 mmrm-0.3.13/mmrm/man/h_df_md_from_1d.Rd | 42 mmrm-0.3.13/mmrm/man/h_df_md_kr.Rd | 46 mmrm-0.3.13/mmrm/man/h_df_md_res.Rd | 46 mmrm-0.3.13/mmrm/man/h_df_md_sat.Rd | 46 mmrm-0.3.13/mmrm/man/h_df_min_bw.Rd | 44 mmrm-0.3.13/mmrm/man/h_df_to_tibble.Rd | 48 mmrm-0.3.13/mmrm/man/h_drop_covariance_terms.Rd | 46 mmrm-0.3.13/mmrm/man/h_drop_levels.Rd |only mmrm-0.3.13/mmrm/man/h_extra_levels.Rd |only mmrm-0.3.13/mmrm/man/h_extract_covariance_terms.Rd | 38 mmrm-0.3.13/mmrm/man/h_first_contain_categorical.Rd |only 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mmrm-0.3.13/mmrm/tests/testthat/_snaps/between-within.md | 36 mmrm-0.3.13/mmrm/tests/testthat/_snaps/car.md | 156 mmrm-0.3.13/mmrm/tests/testthat/_snaps/emmeans.md |only mmrm-0.3.13/mmrm/tests/testthat/_snaps/empirical.md | 30 mmrm-0.3.13/mmrm/tests/testthat/_snaps/fit.md |only mmrm-0.3.13/mmrm/tests/testthat/_snaps/kenwardroger.md | 4128 +++---- mmrm-0.3.13/mmrm/tests/testthat/_snaps/mmrm-methods.md | 430 mmrm-0.3.13/mmrm/tests/testthat/_snaps/testing.md | 18 mmrm-0.3.13/mmrm/tests/testthat/_snaps/tmb-methods.md | 482 mmrm-0.3.13/mmrm/tests/testthat/helper-examples.R | 283 mmrm-0.3.13/mmrm/tests/testthat/helper-skipping.R | 18 mmrm-0.3.13/mmrm/tests/testthat/test-between-within.R | 342 mmrm-0.3.13/mmrm/tests/testthat/test-car.R | 459 mmrm-0.3.13/mmrm/tests/testthat/test-component.R | 209 mmrm-0.3.13/mmrm/tests/testthat/test-cov-struct.R | 304 mmrm-0.3.13/mmrm/tests/testthat/test-cpp-covariance.R | 402 mmrm-0.3.13/mmrm/tests/testthat/test-cpp-utils.R | 92 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mmrm-0.3.13/mmrm/vignettes/algorithm.Rmd | 708 - mmrm-0.3.13/mmrm/vignettes/between_within.Rmd | 250 mmrm-0.3.13/mmrm/vignettes/coef_vcov.Rmd | 190 mmrm-0.3.13/mmrm/vignettes/covariance.Rmd | 484 mmrm-0.3.13/mmrm/vignettes/empirical_wls.Rmd | 512 mmrm-0.3.13/mmrm/vignettes/hypothesis_testing.Rmd | 566 - mmrm-0.3.13/mmrm/vignettes/introduction.Rmd | 128 mmrm-0.3.13/mmrm/vignettes/kenward.Rmd | 762 - mmrm-0.3.13/mmrm/vignettes/methodological_introduction.Rmd | 228 mmrm-0.3.13/mmrm/vignettes/mmrm_review_methods.Rmd | 1240 +- mmrm-0.3.13/mmrm/vignettes/mmrm_review_refs.bib | 542 - mmrm-0.3.13/mmrm/vignettes/package_structure.Rmd | 390 mmrm-0.3.13/mmrm/vignettes/predict.Rmd | 454 mmrm-0.3.13/mmrm/vignettes/satterthwaite.Rmd | 480 mmrm-0.3.13/mmrm/vignettes/subsections/_intro-acknowledgments.Rmd | 18 mmrm-0.3.13/mmrm/vignettes/subsections/_intro-customizations.Rmd | 642 - mmrm-0.3.13/mmrm/vignettes/subsections/_intro-getting_started.Rmd | 60 mmrm-0.3.13/mmrm/vignettes/subsections/_intro-hypothesis_testing.Rmd | 250 mmrm-0.3.13/mmrm/vignettes/subsections/_intro-lower_level.Rmd | 42 mmrm-0.3.13/mmrm/vignettes/subsections/_intro-model_features.Rmd | 256 mmrm-0.3.13/mmrm/vignettes/subsections/_intro-tidymodels.Rmd | 272 250 files changed, 38884 insertions(+), 37976 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial
stratified heterogeneity, and also takes into account local spatial dependencies, spatial
interpretability, potential spatial interactions, and robust spatial stratification. Additionally,
it supports geographical detector models established in academic literature.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut] ,
Jianwu Yan [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.0-1 dated 2024-09-15 and 1.0-2 dated 2024-09-23
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Title: Multivariate Normal Probabilities using Vecchia Approximation
Description: Under a different representation of the multivariate normal (MVN) probability, we can use the Vecchia approximation to sample the integrand at a linear complexity with respect to n. Additionally, both the SOV algorithm from Genz (92) and the exponential-tilting method from Botev (2017) can be adapted to linear complexity. The reference for the method implemented in this package is Jian Cao and Matthias Katzfuss (2024) "Linear-Cost Vecchia Approximation of Multivariate Normal Probabilities" <doi:10.48550/arXiv.2311.09426>. Two major references for the development of our method are Alan Genz (1992) "Numerical Computation of Multivariate Normal Probabilities" <doi:10.1080/10618600.1992.10477010> and Z. I. Botev (2017) "The Normal Law Under Linear Restrictions: Simulation and Estimation via Minimax Tilting" <doi:10.48550/arXiv.1603.04166>.
Author: Jian Cao [aut, cre],
Matthias Katzfuss [aut]
Maintainer: Jian Cao <jcao2416@gmail.com>
Diff between VeccTMVN versions 1.1.1 dated 2024-09-04 and 1.2.0 dated 2024-09-23
DESCRIPTION | 8 ++++---- MD5 | 28 +++++++++++++++------------- NAMESPACE | 3 +++ NEWS.md | 4 ++-- R/RcppExports.R | 13 +++++++++++++ R/pmvn.R | 19 +++++++++++++++++-- R/pmvn_MLMC.R | 19 +++++++++++++++++-- R/pmvt.R | 19 +++++++++++++++++-- R/pmvt_MLMC.R | 19 +++++++++++++++++-- man/pmvn.Rd | 5 +++-- man/pmvn_MLMC.Rd | 5 +++-- man/pmvt.Rd | 5 +++-- man/pmvt_MLMC.Rd | 5 +++-- man/univar_order.Rd |only src/RcppExports.cpp | 14 ++++++++++++++ src/univar_order.cpp |only 16 files changed, 131 insertions(+), 35 deletions(-)
Title: Tables and Graphs for Mixed Models for Repeated Measures (MMRM)
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see for example Cnaan, Laird and Slasor
(1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>.
This package provides an interface for fitting MMRM within the 'tern'
<https://cran.r-project.org/package=tern> framework by Zhu et al.
(2023) and tabulate results easily using 'rtables'
<https://cran.r-project.org/package=rtables> by Becker et al. (2023).
It builds on 'mmrm' <https://cran.r-project.org/package=mmrm> by
Sabanés Bové et al. (2023) for the actual MMRM computations.
Author: Daniel Sabanes Bove [aut],
Joe Zhu [aut, cre],
Godwin Yung [aut],
Francois Collin [aut],
Julia Dedic [aut],
Jana Stoilova [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern.mmrm versions 0.3.1 dated 2024-06-12 and 0.3.2 dated 2024-09-23
DESCRIPTION | 20 +++--- MD5 | 26 ++++---- NEWS.md | 6 ++ R/g_mmrm.R | 7 ++ inst/doc/introduction.R | 22 +++---- inst/doc/introduction.Rmd | 6 +- inst/doc/introduction.html | 99 ++++++++++++++++++++++++++++------ man/g_mmrm_lsmeans.Rd | 6 ++ tests/testthat.R | 25 +++----- tests/testthat/test-g_mmrm.R | 9 +++ tests/testthat/test-lsmeans.R | 15 +---- tests/testthat/test-subgroups.R | 2 tests/testthat/test_covariance_plot.R | 3 + vignettes/introduction.Rmd | 6 +- 14 files changed, 170 insertions(+), 82 deletions(-)
Title: Spatial Data Science Complementary Features
Description: Wrapping and supplementing commonly used functions in the R ecosystem related
to spatial data science, while serving as a basis for other packages maintained
by Wenbo Lv.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between sdsfun versions 0.2.0 dated 2024-09-15 and 0.2.1 dated 2024-09-23
DESCRIPTION | 6 MD5 | 23 +-- NAMESPACE | 1 NEWS.md | 8 + R/sf_helpers.R | 278 ++++++++++++++++++++++++-------------------- R/spdep_helpers.R | 234 ++++++++++++++++++------------------- R/spwt.R | 12 + README.md | 7 - man/sf_distance_matrix.Rd | 48 +++---- man/sf_utm_proj_wgs84.Rd |only man/sf_voronoi_diagram.Rd | 2 man/spdep_contiguity_swm.Rd | 2 man/spdep_distance_swm.Rd | 2 13 files changed, 338 insertions(+), 285 deletions(-)