Title: Tools for Gaussian Process Modeling in Uncertainty
Quantification
Description: Gaussian processes ('GPs') have been widely used to model spatial data, 'spatio'-temporal data, and computer experiments in diverse areas of statistics including spatial statistics, 'spatio'-temporal statistics, uncertainty quantification, and machine learning. This package creates basic tools for fitting and prediction based on 'GPs' with spatial data, 'spatio'-temporal data, and computer experiments. Key characteristics for this GP tool include: (1) the comprehensive implementation of various covariance functions including the 'Matérn' family and the Confluent 'Hypergeometric' family with isotropic form, tensor form, and automatic relevance determination form, where the isotropic form is widely used in spatial statistics, the tensor form is widely used in design and analysis of computer experiments and uncertainty quantification, and the automatic relevance determination form is widely used in machine learning; (2) implementations via Markov chain Monte Carlo ('MCMC') algorithms and [...truncated...]
Author: Pulong Ma [aut, cre]
Maintainer: Pulong Ma <mpulong@gmail.com>
Diff between GPBayes versions 0.1.0-5.1 dated 2023-02-01 and 0.1.0-6 dated 2024-04-24
DESCRIPTION | 10 +- MD5 | 64 ++++++------- NAMESPACE | 1 R/AllClass.R | 4 R/GaSPUtils.R | 166 ++++++++++++++++++++++++++++++---- R/RcppExports.R | 19 ++- R/utils.R | 4 build |only configure | 18 +-- configure.ac | 2 inst/CITATION | 6 - inst/NEWS.Rd | 9 + man/CH.Rd | 7 - man/GPBayes-package.Rd | 4 man/GaSP.Rd | 2 man/cor.to.par.Rd | 4 man/deriv_kernel.Rd | 2 man/gp-class.Rd | 4 man/gp.Rd | 2 man/gp.condsim.Rd |only man/gp.fisher.Rd | 21 ++-- man/gp.model.adequacy.Rd | 2 man/gp.predict.Rd | 2 man/gp.sim.Rd | 2 man/ikernel.Rd | 2 man/kernel.Rd | 2 man/loglik.Rd | 2 src/RcppExports.cpp | 25 +++++ src/SPtool.cpp | 123 +++++++++++++++++++++++++ src/SPtool.h | 7 + src/UQtool.cpp | 226 ++++++++++++++++++++++++++++++++++++++++++++++- src/UQtool.h | 11 ++ src/utils.cpp | 7 - src/wrapper.cpp | 88 +++++++++++++++++- 34 files changed, 733 insertions(+), 115 deletions(-)
Title: Standard TLGs for Clinical Trials Reporting
Description: Provide standard tables, listings, and graphs (TLGs)
libraries used in clinical trials. This package implements a structure
to reformat the data with 'dunlin', create reporting tables using
'rtables' and 'tern' with standardized input arguments to enable quick
generation of standard outputs. In addition, it also provides
comprehensive data checks and script generation functionality.
Author: Liming Li [aut, cre],
Benoit Falquet [aut],
Xiaoli Duan [aut],
Adrian Waddell [ctb],
Chenkai Lv [ctb],
Pawel Rucki [ctb],
Tim Barnett [ctb],
Tian Fang [ctb],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Liming Li <liming.li@roche.com>
Diff between chevron versions 0.2.5 dated 2024-02-01 and 0.2.6 dated 2024-04-24
DESCRIPTION | 25 MD5 | 75 NEWS.md | 7 R/ael01_nollt.R | 18 R/dmt01.R | 1 R/fstg01.R | 5 R/fstg02.R | 5 R/kmg01.R | 26 R/mng01.R | 7 R/ttet01.R | 2 R/utils.R | 54 build/vignette.rds |binary data/syn_data.rda |binary inst/WORDLIST | 4 inst/doc/chevron.html | 423 - inst/doc/chevron_catalog.R | 60 inst/doc/chevron_catalog.html | 7394 ++++++++++++--------------- inst/doc/chevron_catalog.rmd | 65 inst/doc/script_generator.html | 237 man/ael01_nollt.Rd | 4 man/gg_list.Rd | 2 man/grob_list.Rd | 2 man/kmg01.Rd | 18 man/mng01.Rd | 2 tests/testthat/_snaps/ael01_nollt.md | 47 tests/testthat/_snaps/chevron_tlg-methods.md | 275 - tests/testthat/_snaps/lbt14.md | 551 -- tests/testthat/_snaps/rspt01.md | 533 - tests/testthat/setup-options.R |only tests/testthat/test-ael01_nollt.R | 33 tests/testthat/test-chevron_tlg-methods.R | 23 tests/testthat/test-dmt01.R | 14 tests/testthat/test-fstg01.R | 14 tests/testthat/test-fstg02.R | 16 tests/testthat/test-kmg01.R | 85 tests/testthat/test-lbt14.R | 40 tests/testthat/test-mng01.R | 188 tests/testthat/test-utils.R | 46 vignettes/chevron_catalog.rmd | 65 39 files changed, 4619 insertions(+), 5747 deletions(-)
Title: A Compilation of Applicability Domain Methods
Description: A modeling package compiling applicability domain methods in
R. It combines different methods to measure the amount of
extrapolation new samples can have from the training set. See Gadaleta
et al (2016) <doi:10.4018/IJQSPR.2016010102> for an overview of
applicability domains.
Author: Marly Gotti [aut, cre],
Max Kuhn [aut],
RStudio [cph]
Maintainer: Marly Gotti <marlygotti@gmail.com>
Diff between applicable versions 0.1.0 dated 2022-08-20 and 0.1.1 dated 2024-04-24
applicable-0.1.0/applicable/build/vignette.rds |only applicable-0.1.0/applicable/inst/doc |only applicable-0.1.0/applicable/vignettes |only applicable-0.1.1/applicable/DESCRIPTION | 27 +++--- applicable-0.1.1/applicable/MD5 | 39 +++------ applicable-0.1.1/applicable/R/data.R | 2 applicable-0.1.1/applicable/README.md | 40 +++------- applicable-0.1.1/applicable/build/partial.rdb |binary applicable-0.1.1/applicable/man/okc_binary.Rd | 2 applicable-0.1.1/applicable/tests/testthat/_snaps/hat_values-fit.md | 20 +++-- applicable-0.1.1/applicable/tests/testthat/_snaps/hat_values-score.md | 15 ++- applicable-0.1.1/applicable/tests/testthat/_snaps/isolation-fit.md | 4 - applicable-0.1.1/applicable/tests/testthat/_snaps/misc.md | 5 - applicable-0.1.1/applicable/tests/testthat/_snaps/pca-fit.md | 10 +- applicable-0.1.1/applicable/tests/testthat/_snaps/pca-score.md | 15 ++- applicable-0.1.1/applicable/tests/testthat/_snaps/similarity.md | 38 +++++---- applicable-0.1.1/applicable/tests/testthat/test-hat_values-fit.R | 1 applicable-0.1.1/applicable/tests/testthat/test-isolation-fit.R | 4 - applicable-0.1.1/applicable/tests/testthat/test-pca-fit.R | 1 19 files changed, 112 insertions(+), 111 deletions(-)
Title: Fast, Easy, and Visual Bayesian Inference
Description: Accelerate Bayesian analytics workflows in 'R' through interactive modelling,
visualization, and inference. Define probabilistic graphical models using directed
acyclic graphs (DAGs) as a unifying language for business stakeholders, statisticians,
and programmers. This package relies on interfacing with the 'numpyro' python package.
Author: Adam Fleischhacker [aut, cre, cph],
Daniela Dapena [ctb],
Rose Nguyen [ctb],
Jared Sharpe [ctb]
Maintainer: Adam Fleischhacker <ajf@udel.edu>
Diff between causact versions 0.5.4 dated 2024-02-24 and 0.5.5 dated 2024-04-24
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 3 +++ R/causact-package.R | 2 +- R/data.R | 6 +++--- R/install_causact_deps.R | 6 +++++- README.md | 20 ++++++++++---------- build/vignette.rds |binary man/figures/chimpsGraphPost-1.png |binary man/figures/gretaPost-1.png |binary man/houseDF.Rd | 2 +- man/houseDFDescr.Rd | 6 +++--- 12 files changed, 40 insertions(+), 33 deletions(-)
Title: Tools for 'CRAN'-Like Repositories
Description: A set of functions to manage 'CRAN'-like repositories
efficiently.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between cranlike versions 1.0.2 dated 2018-11-26 and 1.0.3 dated 2024-04-24
DESCRIPTION | 9 ++++----- MD5 | 31 ++++++++++++++++--------------- NEWS.md | 13 ++++++++++--- R/cranlike.R | 31 ++++++++++++++++++++++--------- R/db.R | 34 ++++++++++++---------------------- R/parse.R | 3 +++ README.md | 15 ++++++++------- man/add_PACKAGES.Rd | 11 ++++++++--- man/cranlike.Rd | 10 +++++++++- man/create_empty_PACKAGES.Rd | 6 +++++- man/remove_PACKAGES.Rd | 5 +++-- man/update_PACKAGES.Rd | 21 +++++++++++++++------ tests/testthat/test-cranlike.R | 21 +++++++++++++-------- tests/testthat/test-db.R | 30 +++--------------------------- tests/testthat/test-edge-cases.R | 3 ++- tests/testthat/test-extra-cols.R |only tests/testthat/test-old.R | 4 ++-- 17 files changed, 135 insertions(+), 112 deletions(-)
Title: Clinical Data Review Tool
Description: Creation of interactive tables, listings and figures ('TLFs')
and associated report for exploratory analysis of data in a clinical trial,
e.g. for clinical oversight activities.
Interactive figures include sunburst, treemap, scatterplot, line plot and
barplot of counts data.
Interactive tables include table of summary statistics
(as counts of adverse events, enrollment table) and listings.
Possibility to compare data (summary table or listing) across two data batches/sets.
A clinical data review report is created via study-specific configuration
files and template 'R Markdown' reports contained in the package.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Lennart Tuijnder [aut],
Adriaan Blommaert [aut],
Arne De Roeck [ctb, rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between clinDataReview versions 1.5.0 dated 2023-12-11 and 1.5.1 dated 2024-04-24
clinDataReview-1.5.0/clinDataReview/inst/skeleton/config/config-adverseEvents-all-countsVisualization.yml |only clinDataReview-1.5.1/clinDataReview/DESCRIPTION | 10 - clinDataReview-1.5.1/clinDataReview/MD5 | 65 +++---- clinDataReview-1.5.1/clinDataReview/R/reporting-render-html.R | 4 clinDataReview-1.5.1/clinDataReview/R/reporting-skeleton.R | 11 - clinDataReview-1.5.1/clinDataReview/build/vignette.rds |binary clinDataReview-1.5.1/clinDataReview/inst/NEWS | 11 + clinDataReview-1.5.1/clinDataReview/inst/doc/clinDataReview-dataPreprocessing.html | 20 +- clinDataReview-1.5.1/clinDataReview/inst/doc/clinDataReview-dataVisualization.html | 92 ++++------ clinDataReview-1.5.1/clinDataReview/inst/doc/clinDataReview-reporting.html | 36 +-- clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-adverseEvents-countsVisualization.yml |only clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-adverseEvents-listing-comparison.yml | 9 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-adverseEvents-summaryTable-comparison.yml | 8 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-adverseEvents-summaryTable.yml | 8 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-adverseEvents-timeProfiles.yml | 10 - clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-alert-death.yml | 5 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-concomitantMedications-listing.yml | 4 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-cumulativeEnrollment.yml | 9 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-demographics-summaryTable.yml | 9 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-discontinuation-listing.yml |only clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-efficacy-division.yml |only clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-efficacy-errorBar.yml |only clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-enrollment-countsVisualization.yml | 3 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-laboratory-division.yml | 2 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-laboratory-eDISH-ALT.yml | 6 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-laboratory-errorBar.yml |only clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-laboratory-shiftPlot.yml |only clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-laboratory-spaghettiPlot-byVisit.yml | 22 +- clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-laboratory-spaghettiPlot.yml | 18 + clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-laboratory-summaryBarplot.yml | 14 + clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-patientProfiles.yml | 2 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-subjectDisposition-division.yml | 2 clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-subjectVisits-summaryBarplot.yml |only clinDataReview-1.5.1/clinDataReview/inst/skeleton/config/config-summaryDisposition.yml |only clinDataReview-1.5.1/clinDataReview/inst/skeleton/index.Rmd | 2 clinDataReview-1.5.1/clinDataReview/inst/template/patientProfilesTemplate.Rmd | 2 clinDataReview-1.5.1/clinDataReview/tests/testthat/test_render_clinDataReviewReport.R | 8 clinDataReview-1.5.1/clinDataReview/tests/testthat/test_skeleton.R | 47 ++++- 38 files changed, 271 insertions(+), 168 deletions(-)
More information about clinDataReview at CRAN
Permanent link
Title: Create Rich Command Line Applications
Description: Create rich command line applications, with colors, headings,
lists, alerts, progress bars, etc. It uses CSS for custom themes.
This package is now superseded by the 'cli' package. Please use 'cli'
instead in new projects.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between cliapp versions 0.1.1 dated 2020-10-07 and 0.1.2 dated 2024-04-24
cliapp-0.1.1/cliapp/man/cliapp.Rd |only cliapp-0.1.2/cliapp/DESCRIPTION | 21 ++++++++++++++------- cliapp-0.1.2/cliapp/LICENSE | 4 ++-- cliapp-0.1.2/cliapp/MD5 | 21 +++++++++++---------- cliapp-0.1.2/cliapp/NEWS.md | 3 +++ cliapp-0.1.2/cliapp/R/cliapp-package.R |only cliapp-0.1.2/cliapp/R/package.R | 23 ++--------------------- cliapp-0.1.2/cliapp/README.md | 29 ++++++++++++++++++++++++----- cliapp-0.1.2/cliapp/man/cliapp-package.Rd |only cliapp-0.1.2/cliapp/man/inline-markup.Rd | 18 ++++++++++++------ cliapp-0.1.2/cliapp/man/simple_theme.Rd | 10 ++++++---- cliapp-0.1.2/cliapp/man/start_app.Rd | 4 ++-- cliapp-0.1.2/cliapp/man/themes.Rd | 12 ++++++++---- 13 files changed, 84 insertions(+), 61 deletions(-)
Title: Optimized Integer Risk Score Models
Description: Implements an optimized approach to learning risk score models, where sparsity and integer constraints are integrated into the model-fitting process.
Author: Hannah Eglinton [aut, cre],
Alice Paul [aut, cph],
Oscar Yan [aut],
R Core Team [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Ross Ihaka [ctb, cph] ,
Simon Davies [ctb] ),
Thomas Lumley [ctb] )
Maintainer: Hannah Eglinton <eglintonh@gmail.com>
Diff between riskscores versions 1.1.0 dated 2024-04-16 and 1.1.1 dated 2024-04-24
riskscores-1.1.0/riskscores/src |only riskscores-1.1.1/riskscores/DESCRIPTION | 8 ++-- riskscores-1.1.1/riskscores/MD5 | 16 ++------ riskscores-1.1.1/riskscores/NAMESPACE | 1 riskscores-1.1.1/riskscores/R/risk_mod.R | 3 - riskscores-1.1.1/riskscores/R/utils.R | 35 ++++--------------- riskscores-1.1.1/riskscores/inst/doc/riskscores.html | 6 +-- 7 files changed, 21 insertions(+), 48 deletions(-)
Title: Basic R Input Output
Description: Functions to handle basic input output, these functions
always read and write UTF-8 (8-bit Unicode Transformation Format)
files and provide more explicit control over line endings.
Author: Jim Hester [aut] ,
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between brio versions 1.1.4 dated 2023-12-10 and 1.1.5 dated 2024-04-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/read_lines.c | 19 ++++++++++++++----- 4 files changed, 24 insertions(+), 11 deletions(-)
Title: Statistical Inference in High Dimensional Regression
Description: The goal of SIHR is to provide inference procedures in the high-dimensional generalized linear regression setting for:
(1) linear functionals <doi:10.48550/arXiv.1904.12891> <doi:10.48550/arXiv.2012.07133>,
(2) conditional average treatment effects,
(3) quadratic functionals <doi:10.48550/arXiv.1909.01503>,
(4) inner product,
(5) distance.
Author: Zhenyu Wang [aut],
Prabrisha Rakshit [aut],
Tony Cai [aut],
Zijian Guo [aut, cre]
Maintainer: Zijian Guo <zijguo@stat.rutgers.edu>
Diff between SIHR versions 2.0.1 dated 2023-04-09 and 2.1.0 dated 2024-04-24
DESCRIPTION | 38 +- MD5 | 70 +++-- R/CATE.R | 104 +++---- R/Dist.R | 263 +++++++++---------- R/InnProd.R | 258 +++++++++--------- R/LF.R | 310 ++++++++-------------- R/Methods.R | 529 ++++++++++++++++++++------------------ R/QF.R | 312 ++++++++-------------- R/check.R | 251 ++++++++---------- R/helpers.R | 350 ++++++++++++++++--------- README.md | 593 ++++--------------------------------------- build |only inst |only man/CATE.Rd | 37 +- man/Dist.Rd | 86 +++--- man/InnProd.Rd | 82 +++-- man/LF.Rd | 28 -- man/QF.Rd | 26 - man/ci.CATE.Rd | 22 - man/ci.Dist.Rd | 13 man/ci.InnProd.Rd | 13 man/ci.LF.Rd | 22 - man/ci.QF.Rd | 22 - man/ci.Rd | 10 man/figures |only man/print.summary.Dist.Rd | 3 man/print.summary.InnProd.Rd | 3 man/summary.CATE.Rd | 7 man/summary.Dist.Rd | 7 man/summary.InnProd.Rd | 7 man/summary.LF.Rd | 7 man/summary.QF.Rd | 7 vignettes |only 33 files changed, 1514 insertions(+), 1966 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between mongolite versions 2.7.3 dated 2023-12-04 and 2.8.0 dated 2024-04-24
mongolite-2.7.3/mongolite/src/mongoc/mongoc-write-command-legacy-private.h |only mongolite-2.7.3/mongolite/src/mongoc/mongoc-write-command-legacy.c |only mongolite-2.7.3/mongolite/src/mongoc/op-compressed.def |only mongolite-2.7.3/mongolite/src/mongoc/op-delete.def |only mongolite-2.7.3/mongolite/src/mongoc/op-get-more.def |only mongolite-2.7.3/mongolite/src/mongoc/op-header.def |only mongolite-2.7.3/mongolite/src/mongoc/op-insert.def |only mongolite-2.7.3/mongolite/src/mongoc/op-kill-cursors.def |only mongolite-2.7.3/mongolite/src/mongoc/op-msg.def |only mongolite-2.7.3/mongolite/src/mongoc/op-query.def |only mongolite-2.7.3/mongolite/src/mongoc/op-reply-header.def |only mongolite-2.7.3/mongolite/src/mongoc/op-reply.def |only mongolite-2.7.3/mongolite/src/mongoc/op-update.def |only mongolite-2.8.0/mongolite/DESCRIPTION | 13 mongolite-2.8.0/mongolite/MD5 | 455 +- mongolite-2.8.0/mongolite/NEWS | 3 mongolite-2.8.0/mongolite/configure | 2 mongolite-2.8.0/mongolite/src/Makevars.in | 9 mongolite-2.8.0/mongolite/src/Makevars.win | 14 mongolite-2.8.0/mongolite/src/bson/bcon.c | 2 mongolite-2.8.0/mongolite/src/bson/bcon.h | 2 mongolite-2.8.0/mongolite/src/bson/bson-atomic.c | 6 mongolite-2.8.0/mongolite/src/bson/bson-atomic.h | 16 mongolite-2.8.0/mongolite/src/bson/bson-clock.c | 29 mongolite-2.8.0/mongolite/src/bson/bson-clock.h | 8 mongolite-2.8.0/mongolite/src/bson/bson-cmp.h | 6 mongolite-2.8.0/mongolite/src/bson/bson-compat.h | 140 mongolite-2.8.0/mongolite/src/bson/bson-context-private.h | 4 mongolite-2.8.0/mongolite/src/bson/bson-context.c | 16 mongolite-2.8.0/mongolite/src/bson/bson-context.h | 6 mongolite-2.8.0/mongolite/src/bson/bson-decimal128.c | 42 mongolite-2.8.0/mongolite/src/bson/bson-decimal128.h | 8 mongolite-2.8.0/mongolite/src/bson/bson-endian.h | 8 mongolite-2.8.0/mongolite/src/bson/bson-error.c | 85 mongolite-2.8.0/mongolite/src/bson/bson-error.h | 8 mongolite-2.8.0/mongolite/src/bson/bson-iso8601-private.h | 8 mongolite-2.8.0/mongolite/src/bson/bson-iso8601.c | 12 mongolite-2.8.0/mongolite/src/bson/bson-iter.c | 15 mongolite-2.8.0/mongolite/src/bson/bson-iter.h | 50 mongolite-2.8.0/mongolite/src/bson/bson-json-private.h | 3 mongolite-2.8.0/mongolite/src/bson/bson-json.c | 73 mongolite-2.8.0/mongolite/src/bson/bson-json.h | 6 mongolite-2.8.0/mongolite/src/bson/bson-keys.c | 9 mongolite-2.8.0/mongolite/src/bson/bson-keys.h | 6 mongolite-2.8.0/mongolite/src/bson/bson-macros.h | 35 mongolite-2.8.0/mongolite/src/bson/bson-md5.c | 4 mongolite-2.8.0/mongolite/src/bson/bson-md5.h | 4 mongolite-2.8.0/mongolite/src/bson/bson-memory.c | 13 mongolite-2.8.0/mongolite/src/bson/bson-memory.h | 6 mongolite-2.8.0/mongolite/src/bson/bson-oid.c | 10 mongolite-2.8.0/mongolite/src/bson/bson-oid.h | 14 mongolite-2.8.0/mongolite/src/bson/bson-private.h | 8 mongolite-2.8.0/mongolite/src/bson/bson-reader.c | 4 mongolite-2.8.0/mongolite/src/bson/bson-reader.h | 8 mongolite-2.8.0/mongolite/src/bson/bson-string.c | 23 mongolite-2.8.0/mongolite/src/bson/bson-string.h | 6 mongolite-2.8.0/mongolite/src/bson/bson-timegm-private.h | 6 mongolite-2.8.0/mongolite/src/bson/bson-timegm.c | 172 - mongolite-2.8.0/mongolite/src/bson/bson-types.h | 13 mongolite-2.8.0/mongolite/src/bson/bson-utf8.c | 10 mongolite-2.8.0/mongolite/src/bson/bson-utf8.h | 6 mongolite-2.8.0/mongolite/src/bson/bson-value.c | 11 mongolite-2.8.0/mongolite/src/bson/bson-value.h | 6 mongolite-2.8.0/mongolite/src/bson/bson-version-functions.c | 4 mongolite-2.8.0/mongolite/src/bson/bson-version-functions.h | 4 mongolite-2.8.0/mongolite/src/bson/bson-version.h | 13 mongolite-2.8.0/mongolite/src/bson/bson-writer.c | 4 mongolite-2.8.0/mongolite/src/bson/bson-writer.h | 2 mongolite-2.8.0/mongolite/src/bson/bson.c | 469 ++ mongolite-2.8.0/mongolite/src/bson/bson.h | 273 + mongolite-2.8.0/mongolite/src/common/bson-dsl.h |only mongolite-2.8.0/mongolite/src/common/common-prelude.h | 3 mongolite-2.8.0/mongolite/src/common/common-thread-private.h | 81 mongolite-2.8.0/mongolite/src/common/common-thread.c | 11 mongolite-2.8.0/mongolite/src/kms/hexlify.c | 28 mongolite-2.8.0/mongolite/src/kms/hexlify.h | 3 mongolite-2.8.0/mongolite/src/kms/kms_azure_request.c |only mongolite-2.8.0/mongolite/src/kms/kms_b64.c | 189 + mongolite-2.8.0/mongolite/src/kms/kms_caller_identity_request.c | 5 mongolite-2.8.0/mongolite/src/kms/kms_crypto.h | 16 mongolite-2.8.0/mongolite/src/kms/kms_crypto_apple.c | 102 mongolite-2.8.0/mongolite/src/kms/kms_crypto_libcrypto.c | 50 mongolite-2.8.0/mongolite/src/kms/kms_crypto_none.c | 15 mongolite-2.8.0/mongolite/src/kms/kms_crypto_windows.c | 136 mongolite-2.8.0/mongolite/src/kms/kms_decrypt_request.c | 5 mongolite-2.8.0/mongolite/src/kms/kms_encrypt_request.c | 5 mongolite-2.8.0/mongolite/src/kms/kms_endian_private.h |only mongolite-2.8.0/mongolite/src/kms/kms_gcp_request.c |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_item_type_private.h |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_reader_writer.c |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_reader_writer_private.h |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_request.c |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_response.c |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_response_parser.c |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_response_parser_private.h |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_result_reason_private.h |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_result_status_private.h |only mongolite-2.8.0/mongolite/src/kms/kms_kmip_tag_type_private.h |only mongolite-2.8.0/mongolite/src/kms/kms_message/kms_azure_request.h |only mongolite-2.8.0/mongolite/src/kms/kms_message/kms_b64.h | 25 mongolite-2.8.0/mongolite/src/kms/kms_message/kms_caller_identity_request.h | 4 mongolite-2.8.0/mongolite/src/kms/kms_message/kms_decrypt_request.h | 4 mongolite-2.8.0/mongolite/src/kms/kms_message/kms_encrypt_request.h | 4 mongolite-2.8.0/mongolite/src/kms/kms_message/kms_gcp_request.h |only mongolite-2.8.0/mongolite/src/kms/kms_message/kms_kmip_request.h |only mongolite-2.8.0/mongolite/src/kms/kms_message/kms_kmip_response.h |only mongolite-2.8.0/mongolite/src/kms/kms_message/kms_kmip_response_parser.h |only mongolite-2.8.0/mongolite/src/kms/kms_message/kms_message.h | 3 mongolite-2.8.0/mongolite/src/kms/kms_message/kms_message_defines.h | 6 mongolite-2.8.0/mongolite/src/kms/kms_message/kms_request.h | 21 mongolite-2.8.0/mongolite/src/kms/kms_message/kms_request_opt.h | 24 mongolite-2.8.0/mongolite/src/kms/kms_message/kms_response.h | 13 mongolite-2.8.0/mongolite/src/kms/kms_message/kms_response_parser.h | 10 mongolite-2.8.0/mongolite/src/kms/kms_message_private.h | 63 mongolite-2.8.0/mongolite/src/kms/kms_port.c | 4 mongolite-2.8.0/mongolite/src/kms/kms_port.h | 2 mongolite-2.8.0/mongolite/src/kms/kms_request.c | 190 + mongolite-2.8.0/mongolite/src/kms/kms_request_opt.c | 29 mongolite-2.8.0/mongolite/src/kms/kms_request_opt_private.h | 1 mongolite-2.8.0/mongolite/src/kms/kms_request_str.c | 22 mongolite-2.8.0/mongolite/src/kms/kms_request_str.h | 2 mongolite-2.8.0/mongolite/src/kms/kms_response.c | 14 mongolite-2.8.0/mongolite/src/kms/kms_response_parser.c | 111 mongolite-2.8.0/mongolite/src/mongoc/mcd-azure.c |only mongolite-2.8.0/mongolite/src/mongoc/mcd-azure.h |only mongolite-2.8.0/mongolite/src/mongoc/mcd-integer.h |only mongolite-2.8.0/mongolite/src/mongoc/mcd-rpc.c |only mongolite-2.8.0/mongolite/src/mongoc/mcd-rpc.h |only mongolite-2.8.0/mongolite/src/mongoc/mcd-time.h |only mongolite-2.8.0/mongolite/src/mongoc/mongoc-aggregate.c | 127 mongolite-2.8.0/mongolite/src/mongoc/mongoc-apm.c | 43 mongolite-2.8.0/mongolite/src/mongoc/mongoc-apm.h | 19 mongolite-2.8.0/mongolite/src/mongoc/mongoc-async-cmd-private.h | 8 mongolite-2.8.0/mongolite/src/mongoc/mongoc-async-cmd.c | 135 mongolite-2.8.0/mongolite/src/mongoc/mongoc-buffer-private.h | 6 mongolite-2.8.0/mongolite/src/mongoc/mongoc-buffer.c | 116 mongolite-2.8.0/mongolite/src/mongoc/mongoc-bulk-operation.c | 8 mongolite-2.8.0/mongolite/src/mongoc/mongoc-change-stream-private.h | 1 mongolite-2.8.0/mongolite/src/mongoc/mongoc-change-stream.c | 39 mongolite-2.8.0/mongolite/src/mongoc/mongoc-client-pool.c | 33 mongolite-2.8.0/mongolite/src/mongoc/mongoc-client-private.h | 57 mongolite-2.8.0/mongolite/src/mongoc/mongoc-client-session.c | 22 mongolite-2.8.0/mongolite/src/mongoc/mongoc-client-side-encryption-private.h | 44 mongolite-2.8.0/mongolite/src/mongoc/mongoc-client-side-encryption.c | 548 +++ mongolite-2.8.0/mongolite/src/mongoc/mongoc-client-side-encryption.h | 59 mongolite-2.8.0/mongolite/src/mongoc/mongoc-client.c | 374 +- mongolite-2.8.0/mongolite/src/mongoc/mongoc-cluster-aws-private.h | 92 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cluster-aws.c | 606 +++ mongolite-2.8.0/mongolite/src/mongoc/mongoc-cluster-private.h | 64 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cluster-sspi.c | 6 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cluster.c | 1608 ++++++---- mongolite-2.8.0/mongolite/src/mongoc/mongoc-cmd-private.h | 7 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cmd.c | 101 mongolite-2.8.0/mongolite/src/mongoc/mongoc-collection.c | 448 +- mongolite-2.8.0/mongolite/src/mongoc/mongoc-collection.h | 17 mongolite-2.8.0/mongolite/src/mongoc/mongoc-compression.c | 26 mongolite-2.8.0/mongolite/src/mongoc/mongoc-config.h | 19 mongolite-2.8.0/mongolite/src/mongoc/mongoc-counters-private.h | 25 mongolite-2.8.0/mongolite/src/mongoc/mongoc-counters.c | 18 mongolite-2.8.0/mongolite/src/mongoc/mongoc-crypt-private.h | 47 mongolite-2.8.0/mongolite/src/mongoc/mongoc-crypt.c | 580 +++ mongolite-2.8.0/mongolite/src/mongoc/mongoc-cursor-array.c | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cursor-change-stream.c | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cursor-cmd-deprecated.c | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cursor-cmd.c | 35 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cursor-find.c | 11 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cursor-legacy.c | 351 +- mongolite-2.8.0/mongolite/src/mongoc/mongoc-cursor-private.h | 6 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cursor.c | 269 - mongolite-2.8.0/mongolite/src/mongoc/mongoc-cyrus-private.h | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-cyrus.c | 148 mongolite-2.8.0/mongolite/src/mongoc/mongoc-database-private.h | 33 mongolite-2.8.0/mongolite/src/mongoc/mongoc-database.c | 174 - mongolite-2.8.0/mongolite/src/mongoc/mongoc-deprioritized-servers-private.h |only mongolite-2.8.0/mongolite/src/mongoc/mongoc-deprioritized-servers.c |only mongolite-2.8.0/mongolite/src/mongoc/mongoc-error-private.h | 14 mongolite-2.8.0/mongolite/src/mongoc/mongoc-error.c | 78 mongolite-2.8.0/mongolite/src/mongoc/mongoc-error.h | 9 mongolite-2.8.0/mongolite/src/mongoc/mongoc-flags.c |only mongolite-2.8.0/mongolite/src/mongoc/mongoc-gridfs-bucket-file-private.h | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-gridfs-bucket-file.c | 89 mongolite-2.8.0/mongolite/src/mongoc/mongoc-gridfs-bucket.c | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-gridfs-file.c | 73 mongolite-2.8.0/mongolite/src/mongoc/mongoc-gridfs.c | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-handshake-private.h | 93 mongolite-2.8.0/mongolite/src/mongoc/mongoc-handshake.c | 375 +- mongolite-2.8.0/mongolite/src/mongoc/mongoc-host-list-private.h | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-host-list.c | 47 mongolite-2.8.0/mongolite/src/mongoc/mongoc-http-private.h | 47 mongolite-2.8.0/mongolite/src/mongoc/mongoc-http.c | 181 - mongolite-2.8.0/mongolite/src/mongoc/mongoc-init.c | 13 mongolite-2.8.0/mongolite/src/mongoc/mongoc-linux-distro-scanner.c | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-log.c | 29 mongolite-2.8.0/mongolite/src/mongoc/mongoc-macros.h | 9 mongolite-2.8.0/mongolite/src/mongoc/mongoc-matcher-op.c | 21 mongolite-2.8.0/mongolite/src/mongoc/mongoc-matcher.c | 4 mongolite-2.8.0/mongolite/src/mongoc/mongoc-opcode.c |only mongolite-2.8.0/mongolite/src/mongoc/mongoc-openssl.c | 3 mongolite-2.8.0/mongolite/src/mongoc/mongoc-opts-helpers.c | 4 mongolite-2.8.0/mongolite/src/mongoc/mongoc-opts-private.h | 24 mongolite-2.8.0/mongolite/src/mongoc/mongoc-opts.c | 199 + mongolite-2.8.0/mongolite/src/mongoc/mongoc-rand-openssl.c | 1 mongolite-2.8.0/mongolite/src/mongoc/mongoc-read-prefs-private.h | 4 mongolite-2.8.0/mongolite/src/mongoc/mongoc-read-prefs.c | 6 mongolite-2.8.0/mongolite/src/mongoc/mongoc-rpc-private.h | 164 - mongolite-2.8.0/mongolite/src/mongoc/mongoc-rpc.c | 1281 +------ mongolite-2.8.0/mongolite/src/mongoc/mongoc-scram-private.h | 352 ++ mongolite-2.8.0/mongolite/src/mongoc/mongoc-scram.c | 797 +++- mongolite-2.8.0/mongolite/src/mongoc/mongoc-secure-channel-private.h | 11 mongolite-2.8.0/mongolite/src/mongoc/mongoc-secure-channel.c | 43 mongolite-2.8.0/mongolite/src/mongoc/mongoc-secure-transport.c | 4 mongolite-2.8.0/mongolite/src/mongoc/mongoc-server-description-private.h | 6 mongolite-2.8.0/mongolite/src/mongoc/mongoc-server-description.c | 87 mongolite-2.8.0/mongolite/src/mongoc/mongoc-server-monitor.c | 495 +-- mongolite-2.8.0/mongolite/src/mongoc/mongoc-server-stream-private.h | 14 mongolite-2.8.0/mongolite/src/mongoc/mongoc-server-stream.c | 1 mongolite-2.8.0/mongolite/src/mongoc/mongoc-set-private.h | 10 mongolite-2.8.0/mongolite/src/mongoc/mongoc-set.c | 35 mongolite-2.8.0/mongolite/src/mongoc/mongoc-shared.c | 30 mongolite-2.8.0/mongolite/src/mongoc/mongoc-sleep.h |only mongolite-2.8.0/mongolite/src/mongoc/mongoc-socket.c | 33 mongolite-2.8.0/mongolite/src/mongoc/mongoc-sspi.c | 44 mongolite-2.8.0/mongolite/src/mongoc/mongoc-stream-file.c | 22 mongolite-2.8.0/mongolite/src/mongoc/mongoc-stream-private.h | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-stream-socket.c | 5 mongolite-2.8.0/mongolite/src/mongoc/mongoc-stream-tls-openssl-bio.c | 50 mongolite-2.8.0/mongolite/src/mongoc/mongoc-stream-tls-openssl.c | 28 mongolite-2.8.0/mongolite/src/mongoc/mongoc-stream-tls-private.h | 2 mongolite-2.8.0/mongolite/src/mongoc/mongoc-stream-tls-secure-channel.c | 16 mongolite-2.8.0/mongolite/src/mongoc/mongoc-stream-tls.c | 14 mongolite-2.8.0/mongolite/src/mongoc/mongoc-stream.c | 32 mongolite-2.8.0/mongolite/src/mongoc/mongoc-topology-background-monitoring.c | 38 mongolite-2.8.0/mongolite/src/mongoc/mongoc-topology-description-apm.c | 5 mongolite-2.8.0/mongolite/src/mongoc/mongoc-topology-description-private.h | 11 mongolite-2.8.0/mongolite/src/mongoc/mongoc-topology-description.c | 314 + mongolite-2.8.0/mongolite/src/mongoc/mongoc-topology-private.h | 17 mongolite-2.8.0/mongolite/src/mongoc/mongoc-topology-scanner-private.h | 8 mongolite-2.8.0/mongolite/src/mongoc/mongoc-topology-scanner.c | 103 mongolite-2.8.0/mongolite/src/mongoc/mongoc-topology.c | 250 - mongolite-2.8.0/mongolite/src/mongoc/mongoc-uri.c | 247 - mongolite-2.8.0/mongolite/src/mongoc/mongoc-util-private.h | 40 mongolite-2.8.0/mongolite/src/mongoc/mongoc-util.c | 221 + mongolite-2.8.0/mongolite/src/mongoc/mongoc-version.h | 13 mongolite-2.8.0/mongolite/src/mongoc/mongoc-write-command-private.h | 30 mongolite-2.8.0/mongolite/src/mongoc/mongoc-write-command.c | 845 +---- mongolite-2.8.0/mongolite/src/mongoc/mongoc.h | 1 mongolite-2.8.0/mongolite/src/mongoc/service-gcp.c |only mongolite-2.8.0/mongolite/src/mongoc/service-gcp.h |only mongolite-2.8.0/mongolite/src/osx/Makevars | 12 mongolite-2.8.0/mongolite/src/utf8proc |only 250 files changed, 10882 insertions(+), 5915 deletions(-)
Title: Extensible Style-Sheet Language Transformations
Description: An extension for the 'xml2' package to transform XML documents
by applying an 'xslt' style-sheet.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between xslt versions 1.4.4 dated 2023-02-21 and 1.4.5 dated 2024-04-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/xslt_init.cpp | 6 +++++- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: GSL Multi-Start Nonlinear Least-Squares Fitting
Description: An R interface to nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.2.0 dated 2023-12-11 and 1.3.0 dated 2024-04-24
gslnls-1.2.0/gslnls/src/Makevars.ucrt |only gslnls-1.2.0/gslnls/src/Makevars.win |only gslnls-1.2.0/gslnls/tools |only gslnls-1.3.0/gslnls/DESCRIPTION | 13 gslnls-1.3.0/gslnls/MD5 | 77 gslnls-1.3.0/gslnls/NEWS.md | 12 gslnls-1.3.0/gslnls/R/nls.R | 439 ++- gslnls-1.3.0/gslnls/R/nls_large.R | 12 gslnls-1.3.0/gslnls/R/nls_methods.R | 39 gslnls-1.3.0/gslnls/R/nls_test.R | 229 + gslnls-1.3.0/gslnls/cleanup.win |only gslnls-1.3.0/gslnls/configure | 2073 +++++++++++----- gslnls-1.3.0/gslnls/configure.ac | 21 gslnls-1.3.0/gslnls/configure.win |only gslnls-1.3.0/gslnls/inst/unit_tests/unit_tests_gslnls.R | 271 +- gslnls-1.3.0/gslnls/man/anova.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/coef.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/confint.gsl_nls.Rd | 4 gslnls-1.3.0/gslnls/man/confintd.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/deviance.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/df.residual.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/fitted.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/formula.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/gsl_nls.Rd | 108 gslnls-1.3.0/gslnls/man/gsl_nls_control.Rd | 38 gslnls-1.3.0/gslnls/man/gsl_nls_large.Rd | 12 gslnls-1.3.0/gslnls/man/logLik.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/nls_test_list.Rd | 6 gslnls-1.3.0/gslnls/man/nls_test_problem.Rd | 5 gslnls-1.3.0/gslnls/man/nobs.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/predict.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/residuals.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/sigma.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/summary.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/man/vcov.gsl_nls.Rd | 2 gslnls-1.3.0/gslnls/src/Makevars.win.in |only gslnls-1.3.0/gslnls/src/gsl_nls.h | 96 gslnls-1.3.0/gslnls/src/init.c | 4 gslnls-1.3.0/gslnls/src/nls.c | 531 +++- gslnls-1.3.0/gslnls/src/nls_large.c | 139 + gslnls-1.3.0/gslnls/src/nls_test.c | 6 gslnls-1.3.0/gslnls/src/test_nls.f90 | 6 gslnls-1.3.0/gslnls/src/trust.c |only 43 files changed, 3008 insertions(+), 1161 deletions(-)
Title: Geometrically Designed Spline Regression
Description: Spline Regression, Generalized Additive Models, and Component-wise Gradient
Boosting, utilizing Geometrically Designed (GeD) Splines. GeDS regression is a
non-parametric method inspired by geometric principles, for fitting spline regression
models with variable knots in one or two independent variables. It efficiently estimates
the number of knots and their positions, as well as the spline order, assuming the
response variable follows a distribution from the exponential family. GeDS models
integrate the broader category of Generalized (Non-)Linear Models, offering a flexible
approach to modeling complex relationships. A description of the method can be found in
Kaishev et al. (2016) <doi:10.1007/s00180-015-0621-7> and Dimitrova et al. (2023)
<doi:10.1016/j.amc.2022.127493>. Further extending its capabilities, GeDS's implementation
includes Generalized Additive Models (GAM) and Functional Gradient Boosting (FGB),
enabling versatile multivariate predictor modeling, as discuss [...truncated...]
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>,
Emilio S. Guillen <Emilio.Saenz-Guillen@bayes.city.ac.uk>,
Vladimir K. Kaishev <V.Kaishev@city.ac.uk>,
Andrea Lattuada <andrea.lattuada@hotmail.com> and
Richard J. Verrall <R.J.Verrall@city.ac.uk>
Maintainer: Emilio S. Guillen <Emilio.Saenz-Guillen@bayes.city.ac.uk>
Diff between GeDS versions 0.2.1 dated 2024-04-11 and 0.2.2 dated 2024-04-24
DESCRIPTION | 10 +-- MD5 | 34 ++++++----- NAMESPACE | 8 ++ R/BivariateFitter.R | 78 ++++++++++++++++---------- R/GGeDS.R | 9 ++- R/NGeDS.R | 9 ++- R/NGeDSboost.R | 38 ++++++------ R/NGeDSgam.R | 11 ++- R/S3methods_GeDSboost-GeDSgam.R | 93 ++++++++++++++++++------------- R/UnivariateFitter.R | 120 +++++++++++++++++++++++----------------- R/cv_GeDSMethod.R |only R/helpers_NGeDSboost-NGeDSgam.R | 61 +++++++++----------- R/plot_GeDSMethod.R | 11 +++ R/read.formula.R | 20 +++++- man/BivariateFitters.Rd | 10 ++- man/GGeDS.Rd | 7 ++ man/NGeDS.Rd | 7 ++ man/UnivariateFitters.Rd | 10 ++- man/crossv_GeDS.Rd |only 19 files changed, 321 insertions(+), 215 deletions(-)
Title: Use TauDEM
Description: Simple trustworthy utility functions to use TauDEM
(Terrain Analysis Using Digital Elevation Models <https://hydrology.usu.edu/taudem/taudem5/>) command-line interface.
This package provides a guide to installation of TauDEM and its dependencies GDAL (Geopatial Data Abstraction Library)
and MPI (Message Passing Interface) for different operating systems.
Moreover, it checks that TauDEM and its dependencies are correctly installed and included to the PATH,
and it provides wrapper commands for calling TauDEM methods from R.
Author: Luca Carraro [cre, aut],
University of Zurich [cph, fnd],
Maelle Salmon [aut] ,
Wael Sadek [aut],
Kirill Mueller [aut]
Maintainer: Luca Carraro <Luca.Carraro@eawag.ch>
Diff between traudem versions 1.0.2 dated 2024-02-06 and 1.0.3 dated 2024-04-24
DESCRIPTION | 7 - MD5 | 16 +- NEWS.md | 4 R/aread8.R | 190 +++++++++++++++++----------------- R/d8flowdir.R | 130 +++++++++++------------ R/moveoutletstostrm.R | 188 ++++++++++++++++----------------- R/pitremove.R | 134 ++++++++++++------------ R/taudem-exec.R | 277 +++++++++++++++++++++++++------------------------- R/threshold.R | 144 ++++++++++++------------- 9 files changed, 550 insertions(+), 540 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Ronkko [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.15 dated 2024-04-11 and 2.15.1 dated 2024-04-24
DESCRIPTION | 10 - MD5 | 50 +++---- NEWS.md | 13 + R/SimDesign.R | 4 R/analysis.R | 28 ++-- R/runSimulation.R | 126 +++++++++++-------- R/summary_functions.R | 8 + build/vignette.rds |binary inst/doc/Catch_errors.html | 16 +- inst/doc/Fixed_obj_fun.html | 10 - inst/doc/HPC-computing.R | 76 +++++++++-- inst/doc/HPC-computing.Rmd | 206 ++++++++++++++++++++++--------- inst/doc/HPC-computing.html | 257 ++++++++++++++++++++++++++------------- inst/doc/MultipleAnalyses.html | 4 inst/doc/Parallel-computing.R | 9 - inst/doc/Parallel-computing.Rmd | 38 ----- inst/doc/Parallel-computing.html | 28 +--- inst/doc/Saving-results.html | 8 - inst/doc/SimDesign-intro.html | 16 +- man/SimDesign.Rd | 4 man/bias.Rd | 8 + man/runSimulation.Rd | 59 ++++---- tests/tests/mpi/simulation.R | 19 +- tests/tests/test-03-array.R | 25 +++ vignettes/HPC-computing.Rmd | 206 ++++++++++++++++++++++--------- vignettes/Parallel-computing.Rmd | 38 ----- 26 files changed, 795 insertions(+), 471 deletions(-)
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 0.8.5 dated 2024-04-17 and 0.8.6 dated 2024-04-24
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ README.md | 22 ++++++++++++++++++++++ inst/packer/air-datepicker.js | 2 +- inst/packer/virtual-select.js | 2 +- inst/packer/virtual-select.js.LICENSE.txt | 2 +- 7 files changed, 41 insertions(+), 12 deletions(-)
Title: '2bit' 'C' Library
Description: A trimmed down copy of the "kent-core source tree"
turned into a 'C' library for manipulation of '.2bit' files.
See <https://genome.ucsc.edu/FAQ/FAQformat.html#format7>
for a quick overview of the '2bit' format. The "kent-core source tree"
can be found here: <https://github.com/ucscGenomeBrowser/kent-core/>.
Only the '.c' and '.h' files from the source tree that are related
to manipulation of '.2bit' files were kept. Note that the package
is primarily useful to developers of other R packages who wish
to use the '2bit' 'C' library in their own 'C'/'C++' code.
Author: Herve Pages [aut, cre],
UC Regents [cph]
Maintainer: Herve Pages <hpages.on.github@gmail.com>
Diff between Rtwobitlib versions 0.3.5 dated 2024-04-22 and 0.3.6 dated 2024-04-24
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- inst/doc/Rtwobitlib.Rmd | 4 ++-- inst/doc/Rtwobitlib.html | 4 ++-- src/Makevars | 17 +++++++---------- src/Makevars.common | 28 +++++++++++++++------------- src/Makevars.win | 6 +++--- src/kent/Makefile.Rtwobitlib | 33 ++++++++++++++++++++++----------- src/kent/Makefile.Rtwobitlib.win | 28 +++++++++++++++++----------- vignettes/Rtwobitlib.Rmd | 4 ++-- 10 files changed, 82 insertions(+), 66 deletions(-)
Title: 'LuaJIT' Scripting
Description: An interface to 'LuaJIT' <https://luajit.org>, a just-in-time
compiler for the 'Lua' scripting language <https://www.lua.org>. Allows
users to run 'Lua' code from 'R'.
Author: Mike Pall [aut, cph] ,
Lua.org, PUC-Rio [cph] ,
Nicholas Davies [cre, ctb, cph]
Maintainer: Nicholas Davies <nicholas.davies@lshtm.ac.uk>
Diff between luajr versions 0.1.6 dated 2024-02-23 and 0.1.7 dated 2024-04-24
DESCRIPTION | 6 - MD5 | 72 +++++++++---------- NEWS.md | 24 ++++++ R/lua_func.R | 14 ++- inst/doc/luajr.R | 6 - inst/doc/luajr.Rmd | 18 +++- inst/doc/luajr.html | 28 ++++--- inst/include/luajr_luajit.h | 4 - man/lua_func.Rd | 14 ++- src/Makevars.in | 2 src/lua_api.cpp | 14 +-- src/luajit/dynasm/dasm_x86.h | 35 ++------- src/luajit/src/jit/bcsave.lua | 155 ++++++++--------------------------------- src/luajit/src/jit/dump.lua | 7 + src/luajit/src/jit/v.lua | 9 +- src/luajit/src/lib_ffi.c | 20 ----- src/luajit/src/lj_alloc.c | 2 src/luajit/src/lj_api.c | 1 src/luajit/src/lj_arch.h | 2 src/luajit/src/lj_asm_arm64.h | 2 src/luajit/src/lj_cdata.c | 2 src/luajit/src/lj_ctype.c | 12 +++ src/luajit/src/lj_ctype.h | 2 src/luajit/src/lj_ffrecord.c | 23 ++++-- src/luajit/src/lj_gc.c | 38 ++++------ src/luajit/src/lj_obj.h | 3 src/luajit/src/lj_record.c | 12 ++- src/luajit/src/lj_state.c | 3 src/luajit/src/lj_traceerr.h | 2 src/luajit/src/msvcbuild.bat | 20 +++-- src/luajit_build.h | 4 - src/parallel.cpp | 4 - src/push_to.cpp | 47 +++++++++--- src/setup.cpp | 2 tests/testthat/test-lua_func.R | 2 tools/luajit_relver.txt | 2 vignettes/luajr.Rmd | 18 +++- 37 files changed, 323 insertions(+), 308 deletions(-)
Title: Acceptance-Rejection Method for Generating Pseudo-Random
Observations
Description: Provides a function that implements the acceptance-rejection method in an optimized manner to generate pseudo-random observations for discrete or continuous random variables. The function is optimized to work in parallel on Unix-based operating systems and performs well on Windows systems. The acceptance-rejection method implemented optimizes the probability of generating observations from the desired random variable, by simply providing the probability function or probability density function, in the discrete and continuous cases, respectively. Implementation is based on references CASELLA, George at al. (2004) <https://www.jstor.org/stable/4356322>, NEAL, Radford M. (2003) <https://www.jstor.org/stable/3448413> and Bishop, Christopher M. (2006, ISBN: 978-0387310732).
Author: Pedro Rafael D. Marinho [aut, cre]
,
Vera Lucia Damasceno Tomazella [aut]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between AcceptReject versions 0.1.0 dated 2024-04-11 and 0.1.1 dated 2024-04-24
DESCRIPTION | 16 - MD5 | 47 +++- NAMESPACE | 18 + NEWS.md | 22 ++ R/RcppExports.R |only R/accept_reject.r | 209 +++++++++++++-------- R/plot.r | 105 +++++----- R/plot_inspect.r |only R/print.r | 23 +- README.md | 173 +++++++++++++++-- build/vignette.rds |binary inst/doc/accept_reject.R | 50 ++--- inst/doc/accept_reject.Rmd | 50 ++--- inst/doc/accept_reject.html | 307 ++++++++++++++++--------------- inst/doc/inspect.R |only inst/doc/inspect.Rmd |only inst/doc/inspect.html |only man/accept_reject.Rd | 73 +++++-- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |only man/figures/README-unnamed-chunk-5-1.png |only man/inspect.Rd |only man/plot.accept_reject.Rd | 27 +- man/print.accept_reject.Rd | 7 src |only tests |only vignettes/accept_reject.Rmd | 50 ++--- vignettes/inspect.Rmd |only 29 files changed, 758 insertions(+), 419 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and n-grams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph]
,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Paul Nulty [aut] ,
Adam Obeng [aut] ,
Stefan Mueller [aut] ,
Akitaka Matsuo [aut] ,
William Lowe [aut] ,
Christian Mueller [ctb],
Olivier Delmarcelle [ctb] ,
European Research [...truncated...]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 4.0.1 dated 2024-04-08 and 4.0.2 dated 2024-04-24
quanteda-4.0.1/quanteda/inst/include/recompile.h |only quanteda-4.0.1/quanteda/src/tokens_recompile.cpp |only quanteda-4.0.2/quanteda/DESCRIPTION | 6 quanteda-4.0.2/quanteda/MD5 | 51 quanteda-4.0.2/quanteda/NEWS.md | 6 quanteda-4.0.2/quanteda/R/RcppExports.R | 8 quanteda-4.0.2/quanteda/R/casechange-functions.R | 11 quanteda-4.0.2/quanteda/R/quanteda-documentation.R | 10 quanteda-4.0.2/quanteda/R/textstat.R | 2 quanteda-4.0.2/quanteda/R/tokens.R | 46 quanteda-4.0.2/quanteda/README.md | 16 quanteda-4.0.2/quanteda/configure | 874 +++++----- quanteda-4.0.2/quanteda/configure.ac | 85 quanteda-4.0.2/quanteda/inst/WORDLIST | 4 quanteda-4.0.2/quanteda/inst/include/lib.h | 10 quanteda-4.0.2/quanteda/inst/include/tokens.h | 158 - quanteda-4.0.2/quanteda/man/is.collocations.Rd | 2 quanteda-4.0.2/quanteda/man/quanteda-package.Rd | 10 quanteda-4.0.2/quanteda/man/tokens_recompile.Rd | 8 quanteda-4.0.2/quanteda/src/RcppExports.cpp | 23 quanteda-4.0.2/quanteda/src/fcm.cpp | 10 quanteda-4.0.2/quanteda/src/tokens_select.cpp | 1 quanteda-4.0.2/quanteda/src/tokens_xptr.cpp | 60 quanteda-4.0.2/quanteda/tests/testthat/test-fcm.R | 2 quanteda-4.0.2/quanteda/tests/testthat/test-tbb.R |only quanteda-4.0.2/quanteda/tests/testthat/test-tokens_recompile.R | 81 quanteda-4.0.2/quanteda/tests/testthat/test-tokens_xptr.R | 21 quanteda-4.0.2/quanteda/vignettes/fig1.png |only quanteda-4.0.2/quanteda/vignettes/fig2.png |only 29 files changed, 796 insertions(+), 709 deletions(-)
Title: Data for Package 'Qindex'
Description: Example data used in package 'Qindex'.
Author: Tingting Zhan [aut, cre, cph] ,
Misung Yi [aut, cph] ,
Inna Chervoneva [aut, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between Qindex.data versions 0.1.0 dated 2024-04-05 and 0.1.1 dated 2024-04-24
Qindex.data-0.1.0/Qindex.data/data/pkg_data.rda |only Qindex.data-0.1.1/Qindex.data/DESCRIPTION | 31 ++++++-------- Qindex.data-0.1.1/Qindex.data/MD5 | 11 ++--- Qindex.data-0.1.1/Qindex.data/R/0PACKAGE.R | 32 --------------- Qindex.data-0.1.1/Qindex.data/R/Ki67.R |only Qindex.data-0.1.1/Qindex.data/data/Ki67.rda |only Qindex.data-0.1.1/Qindex.data/man/Qindex.data-package.Rd | 9 +++- Qindex.data-0.1.1/Qindex.data/man/celldata.Rd | 2 8 files changed, 29 insertions(+), 56 deletions(-)
Title: Adaptive Parallel Tempering for 'NIMBLE'
Description: Functions for adaptive parallel tempering (APT) with NIMBLE models. Adapted from 'Lacki' & 'Miasojedow' (2016) <DOI:10.1007/s11222-015-9579-0> and 'Miasojedow, Moulines and Vihola' (2013) <DOI:10.1080/10618600.2013.778779>.
Author: David Pleydell [aut, cre, cph] ,
Daniel Turek [cph] ,
Perry de Valpine [cph] ,
Christopher Paciorek [cph] ,
Nick Michaud [cph]
Maintainer: David Pleydell <david.pleydell@inrae.fr>
Diff between nimbleAPT versions 1.0.5 dated 2024-04-22 and 1.0.6 dated 2024-04-24
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------- R/APT_functions.R | 30 +++++++++++++++++++-------- inst/NEWS | 9 ++++++++ inst/doc/nimbleAPT-vignette.html | 42 +++++++++++++++++++-------------------- man/buildAPT.Rd | 9 ++++++-- man/nimbleAPT.Rd | 2 - man/samplers.Rd | 4 +-- 8 files changed, 71 insertions(+), 45 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [c [...truncated...]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3 versions 0.18.0 dated 2024-03-05 and 0.19.0 dated 2024-04-24
DESCRIPTION | 10 +- MD5 | 75 ++++++++--------- NAMESPACE | 13 ++ NEWS.md | 13 ++ R/BenchmarkResult.R | 14 +++ R/HotstartStack.R | 11 +- R/Learner.R | 42 ++++++++- R/LearnerClassifDebug.R | 88 +++++++++++++++----- R/LearnerRegrDebug.R | 1 R/Measure.R | 4 R/ResampleResult.R | 15 +++ R/ResultData.R | 21 ++++ R/benchmark.R | 15 ++- R/bibentries.R | 1 R/helper_exec.R | 3 R/marshal.R |only R/mlr_reflections.R | 2 R/resample.R | 14 ++- R/worker.R | 69 ++++++++++++++- inst/testthat/helper_expectations.R | 59 +++++++++++++ man/BenchmarkResult.Rd | 38 ++++++++ man/Learner.Rd | 2 man/LearnerClassif.Rd | 2 man/LearnerRegr.Rd | 2 man/ResampleResult.Rd | 38 ++++++++ man/ResultData.Rd | 40 +++++++++ man/benchmark.Rd | 9 +- man/marshaling.Rd |only man/mlr_learners_classif.debug.Rd | 48 ++++++++++ man/mlr_tasks_german_credit.Rd | 1 man/resample.Rd | 9 +- tests/testthat/test_HotstartStack.R | 8 + tests/testthat/test_Learner.R | 24 +++++ tests/testthat/test_Measure.R | 12 ++ tests/testthat/test_benchmark.R | 67 +++++++++++++++ tests/testthat/test_encapsulate.R | 70 +++++++++++++++ tests/testthat/test_marshal.R |only tests/testthat/test_mlr_learners.R | 6 + tests/testthat/test_mlr_learners_classif_debug.R | 12 ++ tests/testthat/test_resample.R | 101 +++++++++++++++++++++++ 40 files changed, 864 insertions(+), 95 deletions(-)
Title: Computing False Positive Rate from Inter-Rater Reliability
Description: Implements a 'Shiny Item Analysis' module and functions for computing false positive rate
and other binary classification metrics from inter-rater reliability based on Bartoš & Martinková (2024)
<doi:10.1111/bmsp.12343>.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between IRR2FPR versions 0.1 dated 2024-04-10 and 0.1.1 dated 2024-04-24
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NEWS.md | 3 +++ R/sm_IRR2FPR.R | 15 ++++++++------- README.md | 14 ++++++++++---- inst/CITATION |only man/IRR2FPR.Rd | 7 ++++--- 7 files changed, 36 insertions(+), 24 deletions(-)
Title: Crew Launcher Plugins for Traditional High-Performance Computing
Clusters
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'crew.cluster' package extends the 'mirai'-powered
'crew' package with worker launcher plugins for traditional
high-performance computing systems.
Inspiration also comes from packages 'mirai' by Gao (2023)
<https://github.com/shikokuchuo/mirai>,
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischl, and Surmann (2017).
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Michael Gilbert Levin [aut] ,
Brendan Furneaux [aut] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew.cluster versions 0.3.0 dated 2024-02-07 and 0.3.1 dated 2024-04-24
DESCRIPTION | 19 ++++++++++++++----- MD5 | 19 ++++++++++++------- NAMESPACE | 3 +++ NEWS.md | 4 ++++ R/crew_monitor_slurm.R |only R/crew_package.R | 1 + man/crew_class_launcher_slurm.Rd | 4 +++- man/crew_class_monitor_slurm.Rd |only man/crew_controller_slurm.Rd | 4 +++- man/crew_launcher_slurm.Rd | 4 +++- man/crew_monitor_slurm.Rd |only tests/slurm/monitor.R |only tests/testthat/test-crew_monitor_slurm.R |only 13 files changed, 43 insertions(+), 15 deletions(-)
Title: A Distributed Worker Launcher Framework
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'NNG'-powered 'mirai' R package by Gao (2023)
<doi:10.5281/zenodo.7912722> is a sleek
and sophisticated scheduler that
efficiently processes these intense workloads.
The 'crew' package extends 'mirai' with a unifying
interface for third-party worker launchers.
Inspiration also comes from packages.
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischel, and Surmann (2017)
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Daniel Woodie [ctb],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew versions 0.9.1 dated 2024-03-25 and 0.9.2 dated 2024-04-24
crew-0.9.1/crew/vignettes/figures/app.png |only crew-0.9.2/crew/DESCRIPTION | 6 crew-0.9.2/crew/MD5 | 51 - crew-0.9.2/crew/NAMESPACE | 4 crew-0.9.2/crew/NEWS.md | 8 crew-0.9.2/crew/R/crew_async.R | 12 crew-0.9.2/crew/R/crew_controller.R | 175 ++++- crew-0.9.2/crew/R/crew_controller_group.R | 108 ++- crew-0.9.2/crew/R/crew_package.R | 2 crew-0.9.2/crew/R/utils_promises.R | 30 crew-0.9.2/crew/inst/doc/plugins.Rmd | 2 crew-0.9.2/crew/inst/doc/plugins.html | 10 crew-0.9.2/crew/inst/doc/promises.Rmd | 7 crew-0.9.2/crew/inst/doc/promises.html | 15 crew-0.9.2/crew/inst/doc/shiny.Rmd | 296 +++++++++ crew-0.9.2/crew/inst/doc/shiny.html | 377 ++++++++++-- crew-0.9.2/crew/man/crew_class_controller.Rd | 122 +++ crew-0.9.2/crew/man/crew_class_controller_group.Rd | 111 ++- crew-0.9.2/crew/tests/interactive/test-promises-groups.R | 11 crew-0.9.2/crew/tests/interactive/test-promises.R | 9 crew-0.9.2/crew/tests/testthat/test-crew_controller.R | 67 ++ crew-0.9.2/crew/tests/testthat/test-crew_controller_group.R | 71 ++ crew-0.9.2/crew/tests/testthat/test-crew_controller_local.R | 4 crew-0.9.2/crew/vignettes/figures/art.png |only crew-0.9.2/crew/vignettes/figures/coins.png |only crew-0.9.2/crew/vignettes/plugins.Rmd | 2 crew-0.9.2/crew/vignettes/promises.Rmd | 7 crew-0.9.2/crew/vignettes/shiny.Rmd | 296 +++++++++ 28 files changed, 1537 insertions(+), 266 deletions(-)
Title: Test and Item Analysis via Shiny
Description: Package including functions and interactive shiny application
for the psychometric analysis of educational tests, psychological
assessments, health-related and other types of multi-item
measurements, or ratings from multiple raters.
Author: Patricia Martinkova [aut, cre],
Adela Hladka [aut],
Jan Netik [aut],
Ondrej Leder [ctb],
Jakub Houdek [ctb],
Lubomir Stepanek [ctb],
Tomas Jurica [ctb],
Jana Vorlickova [ctb]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between ShinyItemAnalysis versions 1.5.0 dated 2023-05-08 and 1.5.1 dated 2024-04-24
DESCRIPTION | 17 +- MD5 | 54 ++++---- NAMESPACE | 5 NEWS.md | 19 ++ R/blis.R | 2 R/cronbach_alpha.R | 10 - R/package_options.R |only R/startShinyItemAnalysis.R | 69 ++++++++++ README.md | 14 +- build/partial.rdb |binary inst/CITATION | 3 inst/ShinyItemAnalysis/reporthtml.Rmd | 7 - inst/ShinyItemAnalysis/reportpdf.Rmd | 26 ++- inst/ShinyItemAnalysis/server.R | 7 - inst/ShinyItemAnalysis/server/Data.R | 147 ++++++++++------------ inst/ShinyItemAnalysis/server/IRT.R | 61 +++++---- inst/ShinyItemAnalysis/server/IRT/polytomous.R | 4 inst/ShinyItemAnalysis/server/Modules.R | 140 +++++++++++--------- inst/ShinyItemAnalysis/server/Validity.R | 39 ++--- inst/ShinyItemAnalysis/titlepage.sty | 5 inst/ShinyItemAnalysis/ui.R | 6 inst/ShinyItemAnalysis/ui/uiAbout.R | 85 ++++++++++-- inst/ShinyItemAnalysis/ui/uiData.R | 4 inst/ShinyItemAnalysis/ui/uiReferences.R | 10 - inst/ShinyItemAnalysis/ui/uiSetting.R | 10 - inst/ShinyItemAnalysis/ui/uiTraditionalAnalysis.R | 2 man/ShinyItemAnalysis-package.Rd | 3 man/ShinyItemAnalysis_options.Rd |only man/fit_blis.Rd | 13 + 29 files changed, 473 insertions(+), 289 deletions(-)
More information about ShinyItemAnalysis at CRAN
Permanent link
Title: Keyword Assisted Topic Models
Description: Fits keyword assisted topic models (keyATM) using collapsed Gibbs samplers. The keyATM combines the latent dirichlet allocation (LDA) models with a small number of keywords selected by researchers in order to improve the interpretability and topic classification of the LDA. The keyATM can also incorporate covariates and directly model time trends. The keyATM is proposed in Eshima, Imai, and Sasaki (2024) <doi:10.1111/ajps.12779>.
Author: Shusei Eshima [aut, cre] ,
Tomoya Sasaki [aut],
Kosuke Imai [aut],
Chung-hong Chan [ctb] ,
Romain Francois [ctb] ,
William Lowe [ctb],
Seo-young Silvia Kim [ctb]
Maintainer: Shusei Eshima <shuseieshima@gmail.com>
Diff between keyATM versions 0.5.1 dated 2024-02-04 and 0.5.2 dated 2024-04-24
keyATM-0.5.1/keyATM/man/save.keyATM_output.Rd |only keyATM-0.5.2/keyATM/DESCRIPTION | 8 - keyATM-0.5.2/keyATM/MD5 | 25 ++-- keyATM-0.5.2/keyATM/NAMESPACE | 1 keyATM-0.5.2/keyATM/NEWS.md | 5 keyATM-0.5.2/keyATM/R/keyATM.R | 4 keyATM-0.5.2/keyATM/R/posterior.R | 12 -- keyATM-0.5.2/keyATM/inst/CITATION | 9 + keyATM-0.5.2/keyATM/man/keyATM.Rd | 2 keyATM-0.5.2/keyATM/man/weightedLDA.Rd | 2 keyATM-0.5.2/keyATM/tests/testthat/test-diagnosis.R | 22 +--- keyATM-0.5.2/keyATM/tests/testthat/test-keyATMBase.R | 7 + keyATM-0.5.2/keyATM/tests/testthat/test-keyATMCovDirMulti.R | 52 ---------- keyATM-0.5.2/keyATM/tests/testthat/test-keyATMHeterogeneity.R | 8 - 14 files changed, 50 insertions(+), 107 deletions(-)
More information about CalcThemAll.PRM at CRAN
Permanent link
Title: Tools for Handling Indices and Proportions in Small Area
Estimation
Description: It allows for mapping proportions and indicators defined on the unit interval. It implements Beta-based small area methods comprising the classical Beta regression models, the Flexible Beta model and Zero and/or One Inflated extensions (Janicki 2020 <doi:10.1080/03610926.2019.1570266>). Such methods, developed within a Bayesian framework through Stan <https://mc-stan.org/>, come equipped with a set of diagnostics and complementary tools, visualizing and exporting functions. A Shiny application with a user-friendly interface can be launched to further simplify the process. For further details, refer to De Nicolò and Gardini (2024 <doi:10.18637/jss.v108.i01>).
Author: Silvia De Nicolo [aut, cre] ,
Aldo Gardini [aut]
Maintainer: Silvia De Nicolo <silvia.denicolo@unibo.it>
Diff between tipsae versions 1.0.0 dated 2024-03-26 and 1.0.1 dated 2024-04-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/util_fit.R | 6 +++++- build/partial.rdb |binary 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements
into groups (i.e., anticlusters) with the goal of maximizing
between-group similarity or within-group heterogeneity. The
anticlustering approach thereby reverses the logic of cluster analysis
that strives for high within-group homogeneity and clear separation
between groups. Computationally, anticlustering is accomplished by
maximizing instead of minimizing a clustering objective function, such
as the intra-cluster variance (used in k-means clustering) or the sum
of pairwise distances within clusters. The main function
anticlustering() gives access to exact and heuristic anticlustering
methods described in Papenberg and Klau (2021;
<doi:10.1037/met0000301>), Brusco et al. (2020;
<doi:10.1111/bmsp.12186>), and Papenberg (2024;
<doi:10.1111/bmsp.12315>). The exact algorithms require that an
integer linear programming solver is installed, either the GNU linear
programming kit (<https://www.gnu.org/software/g [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.1 dated 2023-10-26 and 0.8.3 dated 2024-04-24
anticlust-0.8.1/anticlust/R/anticlust.R |only anticlust-0.8.1/anticlust/R/exchange-method-kmeans-anticlustering.R |only anticlust-0.8.1/anticlust/man/anticlust.Rd |only anticlust-0.8.3/anticlust/DESCRIPTION | 15 anticlust-0.8.3/anticlust/LICENSE | 4 anticlust-0.8.3/anticlust/MD5 | 89 - anticlust-0.8.3/anticlust/NAMESPACE | 1 anticlust-0.8.3/anticlust/R/Optimal_Dispersion.R | 3 anticlust-0.8.3/anticlust/R/c-anticlustering.R | 20 anticlust-0.8.3/anticlust/R/categories_to_binary.R | 7 anticlust-0.8.3/anticlust/R/fast_anticlustering.R |only anticlust-0.8.3/anticlust/R/objective-kplus.R | 9 anticlust-0.8.3/anticlust/R/wrapper-anticlustering.R | 34 anticlust-0.8.3/anticlust/R/wrapper-k-plus-anticlustering.R | 11 anticlust-0.8.3/anticlust/build/vignette.rds |binary anticlust-0.8.3/anticlust/inst/doc/Best_practices.R | 5 anticlust-0.8.3/anticlust/inst/doc/Best_practices.Rmd | 23 anticlust-0.8.3/anticlust/inst/doc/Best_practices.html | 155 --- anticlust-0.8.3/anticlust/inst/doc/Categorical_vars.R | 2 anticlust-0.8.3/anticlust/inst/doc/Categorical_vars.Rmd | 1 anticlust-0.8.3/anticlust/inst/doc/Categorical_vars.html | 486 ++++------ anticlust-0.8.3/anticlust/inst/doc/Speeding_up_anticlustering.R | 83 - anticlust-0.8.3/anticlust/inst/doc/Speeding_up_anticlustering.Rmd | 152 +-- anticlust-0.8.3/anticlust/inst/doc/Speeding_up_anticlustering.html | 416 ++++---- anticlust-0.8.3/anticlust/inst/doc/stimulus-selection.R | 6 anticlust-0.8.3/anticlust/inst/doc/stimulus-selection.Rmd | 1 anticlust-0.8.3/anticlust/inst/doc/stimulus-selection.html | 370 +++---- anticlust-0.8.3/anticlust/inst/render.sh | 2 anticlust-0.8.3/anticlust/man/anticlustering.Rd | 32 anticlust-0.8.3/anticlust/man/categories_to_binary.Rd | 7 anticlust-0.8.3/anticlust/man/fast_anticlustering.Rd | 225 +++- anticlust-0.8.3/anticlust/man/figures/clustering-1.png |binary anticlust-0.8.3/anticlust/man/figures/matching-1.png |binary anticlust-0.8.3/anticlust/man/generate_exchange_partners.Rd |only anticlust-0.8.3/anticlust/man/kplus_anticlustering.Rd | 11 anticlust-0.8.3/anticlust/man/kplus_moment_variables.Rd | 9 anticlust-0.8.3/anticlust/man/optimal_dispersion.Rd | 3 anticlust-0.8.3/anticlust/src/anticlust_init.c | 2 anticlust-0.8.3/anticlust/src/declarations.h | 22 anticlust-0.8.3/anticlust/src/fast-kmeans-anticlustering.c |only anticlust-0.8.3/anticlust/src/misc-array-methods.c | 9 anticlust-0.8.3/anticlust/tests/testthat/test-equivalent-preclustering.R | 9 anticlust-0.8.3/anticlust/tests/testthat/test-exchange-method.R | 24 anticlust-0.8.3/anticlust/tests/testthat/test-exchange-partner-generation.R | 31 anticlust-0.8.3/anticlust/tests/testthat/test-new-kmeans-c-implementation.R |only anticlust-0.8.3/anticlust/vignettes/Best_practices.Rmd | 23 anticlust-0.8.3/anticlust/vignettes/Categorical_vars.Rmd | 1 anticlust-0.8.3/anticlust/vignettes/Speeding_up_anticlustering.Rmd | 152 +-- anticlust-0.8.3/anticlust/vignettes/stimulus-selection.Rmd | 1 49 files changed, 1186 insertions(+), 1270 deletions(-)
Title: Statistical Process Control -- Calculation of ARL and Other
Control Chart Performance Measures
Description: Evaluation of control charts by means of
the zero-state, steady-state ARL (Average Run Length) and RL quantiles.
Setting up control charts for given in-control ARL. The control charts
under consideration are one- and two-sided EWMA, CUSUM, and
Shiryaev-Roberts schemes for monitoring the mean or variance of normally
distributed independent data. ARL calculation of the same set of schemes under drift (in the mean) are added.
Eventually, all ARL measures for the multivariate EWMA (MEWMA) are provided.
Author: Sven Knoth
Maintainer: Sven Knoth <Sven.Knoth@gmx.de>
Diff between spc versions 0.6.7 dated 2022-10-24 and 0.6.8 dated 2024-04-24
DESCRIPTION | 8 - MD5 | 26 ++--- NAMESPACE | 2 R/xewma.arl.R | 26 +++-- R/xewma.crit.R | 42 +++++++- man/dphat.Rd | 9 + man/pois.crit.L0L1.Rd | 3 man/quadrature.nodes.weights.Rd | 2 man/xewma.arl.Rd | 70 +++++++------- man/xewma.crit.Rd | 3 man/xshewhartrunsrules.arl.Rd | 2 src/allspc.c | 187 +++++++++++++++++++++++++++++++++++++++- src/xewma_arl.c | 6 + src/xewma_crit.c | 15 ++- 14 files changed, 316 insertions(+), 85 deletions(-)
Title: Bivariate Segmentation/Clustering Methods and Tools
Description: Provides two methods for segmentation and joint segmentation/clustering of
bivariate time-series. Originally intended for ecological segmentation
(home-range and behavioural modes) but easily applied on other series,
the package also provides tools for analysing outputs from R packages 'moveHMM' and 'marcher'.
The segmentation method is a bivariate extension of Lavielle's method available in 'adehabitatLT'
(Lavielle, 1999 <doi:10.1016/S0304-4149(99)00023-X> and 2005 <doi:10.1016/j.sigpro.2005.01.012>).
This method rely on dynamic programming for efficient segmentation.
The segmentation/clustering method alternates steps of dynamic programming with an Expectation-Maximization algorithm.
This is an extension of Picard et al (2007) <doi:10.1111/j.1541-0420.2006.00729.x> method
(formerly available in 'cghseg' package) to the bivariate case.
The method is fully described in Patin et al (2018) <doi:10.1101/444794>.
Author: Remi Patin [aut, cre],
Marie-Pierre Etienne [aut],
Emilie Lebarbier [aut],
Simon Benhamou [aut]
Maintainer: Remi Patin <remi.patin@normale.fr>
Diff between segclust2d versions 0.3.1 dated 2023-08-21 and 0.3.3 dated 2024-04-24
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 16 ++++++++++++++++ R/prepare_covariates.R | 23 ++++++++++++----------- R/segTraj_Gmixt_simultanee.R | 35 +++++++++++++++++++---------------- R/segclust2d.R | 6 ++---- build/vignette.rds |binary inst/CITATION | 8 ++++---- inst/doc/v01_preparing_data.html | 4 ++-- inst/doc/v02_run_segclust2d.html | 20 ++++++++++---------- inst/doc/v03_explore_outputs.R | 2 +- inst/doc/v03_explore_outputs.html | 14 +++++++------- man/Gmixt_simultanee.Rd | 14 ++++++-------- man/segclust2d.Rd | 23 +++++++++++++++++++++-- 14 files changed, 117 insertions(+), 82 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-01 0.2.0
2024-02-13 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-02 0.1.4
2023-08-18 0.1.1
2023-07-08 0.0.7
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] ,
Atkinson Elizabeth [ctb],
Crowson Cynthia [ctb]
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 3.5-8 dated 2024-02-14 and 3.6-4 dated 2024-04-24
survival-3.5-8/survival/R/residcsum.R |only survival-3.5-8/survival/R/residuals.survfitcoxms.R |only survival-3.5-8/survival/R/survfitCI.R |only survival-3.5-8/survival/inst/NEWS.Rd.orig |only survival-3.5-8/survival/inst/doc/discrim.R |only survival-3.5-8/survival/inst/doc/discrim.Rnw |only survival-3.5-8/survival/inst/doc/discrim.pdf |only survival-3.5-8/survival/noweb/code.nw |only survival-3.5-8/survival/noweb/code.toc |only survival-3.5-8/survival/noweb/concordance.Rnw.orig |only survival-3.5-8/survival/noweb/noweb.sty |only survival-3.5-8/survival/noweb/score.Rnw |only survival-3.5-8/survival/noweb/survfitCI.Rnw |only survival-3.5-8/survival/noweb/survfitKM.Rnw |only survival-3.5-8/survival/src/coxfit7.c |only survival-3.5-8/survival/src/survfitci.c |only survival-3.5-8/survival/tests/plot1.pdf |only survival-3.5-8/survival/vignettes/.install_extras |only survival-3.5-8/survival/vignettes/discrim.Rnw |only survival-3.6-4/survival/DESCRIPTION | 8 survival-3.6-4/survival/MD5 | 194 - survival-3.6-4/survival/R/aeqSurv.R | 1 survival-3.6-4/survival/R/brier.R | 2 survival-3.6-4/survival/R/concordance.R | 2 survival-3.6-4/survival/R/parsecovar.R | 2 survival-3.6-4/survival/R/print.survfit.R | 48 survival-3.6-4/survival/R/pseudo.R | 274 -- survival-3.6-4/survival/R/residuals.survfit.R | 1115 ++--------- survival-3.6-4/survival/R/rsurvpart2.R |only survival-3.6-4/survival/R/survdiff.R | 2 survival-3.6-4/survival/R/survfit.R | 47 survival-3.6-4/survival/R/survfit.coxph.R | 5 survival-3.6-4/survival/R/survfit.coxphms.R | 15 survival-3.6-4/survival/R/survfit0.R | 61 survival-3.6-4/survival/R/survfitAJ.R |only survival-3.6-4/survival/R/survfitKM.R | 186 + survival-3.6-4/survival/R/survfitTurnbull.R | 2 survival-3.6-4/survival/R/survfitms.R | 40 survival-3.6-4/survival/R/xtras.R | 35 survival-3.6-4/survival/build/vignette.rds |binary survival-3.6-4/survival/data/survexp.rda |binary survival-3.6-4/survival/inst/NEWS.Rd | 57 survival-3.6-4/survival/inst/doc/adjcurve.pdf |binary survival-3.6-4/survival/inst/doc/approximate.pdf |binary survival-3.6-4/survival/inst/doc/compete.pdf |binary survival-3.6-4/survival/inst/doc/concordance.pdf |binary survival-3.6-4/survival/inst/doc/matrix.pdf |binary survival-3.6-4/survival/inst/doc/methods.R |only survival-3.6-4/survival/inst/doc/methods.Rnw |only survival-3.6-4/survival/inst/doc/methods.pdf |only survival-3.6-4/survival/inst/doc/multi.pdf |binary survival-3.6-4/survival/inst/doc/other.pdf |binary survival-3.6-4/survival/inst/doc/population.pdf |binary survival-3.6-4/survival/inst/doc/redistribute.pdf |binary survival-3.6-4/survival/inst/doc/splines.pdf |binary survival-3.6-4/survival/inst/doc/survival.pdf |binary survival-3.6-4/survival/inst/doc/tiedtimes.pdf |binary survival-3.6-4/survival/inst/doc/timedep.pdf |binary survival-3.6-4/survival/inst/doc/validate.pdf |binary survival-3.6-4/survival/man/basehaz.Rd | 33 survival-3.6-4/survival/man/pbcseq.Rd | 6 survival-3.6-4/survival/man/pseudo.Rd | 53 survival-3.6-4/survival/man/reliability.Rd | 19 survival-3.6-4/survival/man/residuals.survfit.Rd | 55 survival-3.6-4/survival/man/survcheck.Rd | 11 survival-3.6-4/survival/man/survfit.coxph.Rd | 33 survival-3.6-4/survival/man/survfit.formula.Rd | 145 + survival-3.6-4/survival/man/survfit.object.Rd | 54 survival-3.6-4/survival/man/survfit0.Rd | 64 survival-3.6-4/survival/man/survival-internal.Rd | 12 survival-3.6-4/survival/noweb/Makefile | 14 survival-3.6-4/survival/noweb/concordance.Rnw | 2 survival-3.6-4/survival/noweb/coxsurv.Rnw | 5 survival-3.6-4/survival/noweb/coxsurv3.Rnw | 14 survival-3.6-4/survival/noweb/parse.Rnw | 4 survival-3.6-4/survival/noweb/residuals.survfit.Rnw | 3 survival-3.6-4/survival/noweb/residuals.survfit2.Rnw | 2 survival-3.6-4/survival/src/init.c | 5 survival-3.6-4/survival/src/survfitaj.c |only survival-3.6-4/survival/src/survfitkm.c | 499 ++-- survival-3.6-4/survival/src/survfitresid.c | 27 survival-3.6-4/survival/src/survproto.h | 22 survival-3.6-4/survival/src/twoclust.c |only survival-3.6-4/survival/tests/Examples/survival-Ex.Rout.save | 102 - survival-3.6-4/survival/tests/coxsurv5.R | 6 survival-3.6-4/survival/tests/coxsurv5.Rout.save | 14 survival-3.6-4/survival/tests/coxsurv6.R | 4 survival-3.6-4/survival/tests/coxsurv6.Rout.save | 12 survival-3.6-4/survival/tests/ekm.R |only survival-3.6-4/survival/tests/ekm.Rout.save |only survival-3.6-4/survival/tests/mstate.R | 240 +- survival-3.6-4/survival/tests/mstate.Rout.save | 251 +- survival-3.6-4/survival/tests/mstate2.R |only survival-3.6-4/survival/tests/mstate2.Rout.save |only survival-3.6-4/survival/tests/mstrata.R | 14 survival-3.6-4/survival/tests/mstrata.Rout.save | 22 survival-3.6-4/survival/tests/pseudo.R | 124 - survival-3.6-4/survival/tests/pseudo.Rout.save | 151 - survival-3.6-4/survival/tests/ratetable.Rout.save | 10 survival-3.6-4/survival/tests/residsf.R | 58 survival-3.6-4/survival/tests/residsf.Rout.save | 66 survival-3.6-4/survival/tests/rttright.R | 12 survival-3.6-4/survival/tests/rttright.Rout.save | 20 survival-3.6-4/survival/tests/summary_survfit.R | 9 survival-3.6-4/survival/tests/summary_survfit.Rout.save | 17 survival-3.6-4/survival/tests/survfit1.R | 81 survival-3.6-4/survival/tests/survfit1.Rout.save | 104 - survival-3.6-4/survival/tests/testci.R | 47 survival-3.6-4/survival/tests/testci.Rout.save | 62 survival-3.6-4/survival/tests/testci2.R | 34 survival-3.6-4/survival/tests/testci2.Rout.save | 55 survival-3.6-4/survival/tests/tt2.Rout.save | 6 survival-3.6-4/survival/vignettes/methods.Rnw |only survival-3.6-4/survival/vignettes/refer.bib | 11 114 files changed, 2460 insertions(+), 2250 deletions(-)