Title: Soil Organic Carbon and CN Ratio Driven Nitrogen Modelling
Framework
Description: Can be used to model the fate of soil organic carbon and soil organic nitrogen and to calculate N mineralisation rates. Provides a framework that numerically solves differential equations of soil organic carbon models based on first-order kinetics and extends these models to include the nitrogen component. The name 'sorcering' is an acronym for 'Soil ORganic Carbon & CN Ratio drIven Nitrogen modellinG framework'.
Author: Marc Scherstjanoi [aut, cre],
Rene Dechow [aut]
Maintainer: Marc Scherstjanoi <marc.scherstjanoi@thuenen.de>
Diff between sorcering versions 1.0.0.1 dated 2023-12-18 and 1.0.1 dated 2024-04-28
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NEWS.md |only build/partial.rdb |binary build/sorcering.pdf |binary build/stage23.rdb |binary inst/doc/sorcering.pdf |binary man/sorcering.Rd | 2 +- src/sorcering.cpp | 29 +++++++++++++++++++++-------- vignettes/sorcering_vignette.pdf |binary 10 files changed, 35 insertions(+), 21 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. pathfindR is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
pathfindR also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in pathfindR are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 2.3.1 dated 2024-01-19 and 2.4.0 dated 2024-04-28
pathfindR-2.3.1/pathfindR/man/download_KGML_file.Rd |only pathfindR-2.3.1/pathfindR/man/download_kegg_png.Rd |only pathfindR-2.3.1/pathfindR/man/obtain_colored_url.Rd |only pathfindR-2.3.1/pathfindR/man/visualize_hsa_KEGG.Rd |only pathfindR-2.3.1/pathfindR/vignettes/hsaKEGG_diagram.png |only pathfindR-2.4.0/pathfindR/DESCRIPTION | 12 pathfindR-2.4.0/pathfindR/MD5 | 89 pathfindR-2.4.0/pathfindR/NAMESPACE | 2 pathfindR-2.4.0/pathfindR/NEWS.md | 14 pathfindR-2.4.0/pathfindR/R/comparison.R | 2 pathfindR-2.4.0/pathfindR/R/data_generation.R | 94 pathfindR-2.4.0/pathfindR/R/scoring.R | 4 pathfindR-2.4.0/pathfindR/R/visualization.R | 519 +---- pathfindR-2.4.0/pathfindR/build/vignette.rds |binary pathfindR-2.4.0/pathfindR/inst/doc/comparing_results.R | 2 pathfindR-2.4.0/pathfindR/inst/doc/comparing_results.html | 4 pathfindR-2.4.0/pathfindR/inst/doc/intro_vignette.R | 91 pathfindR-2.4.0/pathfindR/inst/doc/intro_vignette.Rmd | 85 pathfindR-2.4.0/pathfindR/inst/doc/intro_vignette.html | 244 +- pathfindR-2.4.0/pathfindR/inst/doc/manual_execution.html | 8 pathfindR-2.4.0/pathfindR/inst/doc/non_hs_analysis.R | 2 pathfindR-2.4.0/pathfindR/inst/doc/non_hs_analysis.html | 4 pathfindR-2.4.0/pathfindR/inst/doc/obtain_data.R | 4 pathfindR-2.4.0/pathfindR/inst/doc/obtain_data.html | 6 pathfindR-2.4.0/pathfindR/inst/doc/visualization_vignette.R | 26 pathfindR-2.4.0/pathfindR/inst/doc/visualization_vignette.Rmd | 34 pathfindR-2.4.0/pathfindR/inst/doc/visualization_vignette.html | 62 pathfindR-2.4.0/pathfindR/inst/extdata/resultActiveSubnetworkSearch.txt | 1020 +++++++++- pathfindR-2.4.0/pathfindR/man/color_kegg_pathway.Rd | 12 pathfindR-2.4.0/pathfindR/man/get_biogrid_pin.Rd | 4 pathfindR-2.4.0/pathfindR/man/pathfindR.Rd | 2 pathfindR-2.4.0/pathfindR/man/visualize_KEGG_diagram.Rd |only pathfindR-2.4.0/pathfindR/man/visualize_term_interactions.Rd | 10 pathfindR-2.4.0/pathfindR/man/visualize_terms.Rd | 35 pathfindR-2.4.0/pathfindR/tests/testthat/test-active_snw_search.R | 4 pathfindR-2.4.0/pathfindR/tests/testthat/test-data_generation.R | 108 - pathfindR-2.4.0/pathfindR/tests/testthat/test-enrichment.R | 2 pathfindR-2.4.0/pathfindR/tests/testthat/test-visualization.R | 159 - pathfindR-2.4.0/pathfindR/vignettes/combined_graph.png |binary pathfindR-2.4.0/pathfindR/vignettes/enrichment_chart.png |binary pathfindR-2.4.0/pathfindR/vignettes/example_interaction_vis.png |binary pathfindR-2.4.0/pathfindR/vignettes/example_kegg_pathway_diagram.png |only pathfindR-2.4.0/pathfindR/vignettes/hmap.png |binary pathfindR-2.4.0/pathfindR/vignettes/intro_vignette.Rmd | 85 pathfindR-2.4.0/pathfindR/vignettes/man_enrichment_chart.png |binary pathfindR-2.4.0/pathfindR/vignettes/score_hmap.png |binary pathfindR-2.4.0/pathfindR/vignettes/term_gene.png |binary pathfindR-2.4.0/pathfindR/vignettes/upset.png |binary pathfindR-2.4.0/pathfindR/vignettes/visualization_vignette.Rmd | 34 49 files changed, 1778 insertions(+), 1005 deletions(-)
Title: Datasets and Code Examples from P. J. Aphalo's "Learn R" Book
Description: Data, scripts and code from chunks used as examples in the book
"Learn R: As a Language" 1ed and 2ed by Pedro J. Aphalo.
ISBN 9780367182533 (pbk 1ed); ISBN 9780367182557 (hbk 1ed); ISBN 9780429060342 (ebk 1ed).
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between learnrbook versions 1.0.2-1 dated 2023-02-15 and 2.0.1 dated 2024-04-28
learnrbook-1.0.2-1/learnrbook/inst/example-chunks/purl-output.zip |only learnrbook-1.0.2-1/learnrbook/man/figures/cover-small.png |only learnrbook-1.0.2-1/learnrbook/man/pkgs_all.Rd |only learnrbook-1.0.2-1/learnrbook/man/pkgs_ch_data.Rd |only learnrbook-1.0.2-1/learnrbook/man/pkgs_ch_data_io.Rd |only learnrbook-1.0.2-1/learnrbook/man/pkgs_ch_graphics.Rd |only learnrbook-1.0.2-1/learnrbook/vignettes/images |only learnrbook-2.0.1/learnrbook/DESCRIPTION | 23 learnrbook-2.0.1/learnrbook/MD5 | 57 learnrbook-2.0.1/learnrbook/NEWS.md | 26 learnrbook-2.0.1/learnrbook/R/learnrbook.R | 5 learnrbook-2.0.1/learnrbook/R/used-packages-data.R | 76 learnrbook-2.0.1/learnrbook/README.md | 79 learnrbook-2.0.1/learnrbook/build/vignette.rds |binary learnrbook-2.0.1/learnrbook/data/pkgs-in-book.rda |binary learnrbook-2.0.1/learnrbook/data/volcano-example.rda |binary learnrbook-2.0.1/learnrbook/data/weather-wk-25-2019-tb.rda |binary learnrbook-2.0.1/learnrbook/data/wind-data.rda |binary learnrbook-2.0.1/learnrbook/inst/doc/user-guide.R | 29 learnrbook-2.0.1/learnrbook/inst/doc/user-guide.Rmd | 244 - learnrbook-2.0.1/learnrbook/inst/doc/user-guide.html | 288 - learnrbook-2.0.1/learnrbook/inst/example-chunks/R-code-from-examples-learnrbook-1ed.zip |only learnrbook-2.0.1/learnrbook/inst/example-chunks/R-code-from-examples-learnrbook-2ed.zip |only learnrbook-2.0.1/learnrbook/inst/extdata/cloudindex.idx | 1121 ------ learnrbook-2.0.1/learnrbook/inst/extdata/rcatsidx.idx | 1121 ------ learnrbook-2.0.1/learnrbook/inst/extdata/rindex.idx | 1121 ------ learnrbook-2.0.1/learnrbook/inst/extdata/using-r-main-crc.idx | 1752 +--------- learnrbook-2.0.1/learnrbook/man/figures/cover-small-1ed.png |only learnrbook-2.0.1/learnrbook/man/figures/cover-small-2ed.jpg |only learnrbook-2.0.1/learnrbook/man/learnrbook-package.Rd | 8 learnrbook-2.0.1/learnrbook/man/pkgs_all_1ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_all_2ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch10_2ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch6_1ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch7_1ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch8_1ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch8_2ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch9_2ed.Rd |only learnrbook-2.0.1/learnrbook/vignettes/user-guide.Rmd | 244 - 39 files changed, 926 insertions(+), 5268 deletions(-)
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and
direct extraction for many archive formats including 'tar', 'ZIP',
'7-zip', 'RAR', 'CAB' and compression formats including 'gzip',
'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] ,
Gabor Csardi [aut, cre],
Ondrej Holy [cph] ,
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between archive versions 1.1.7 dated 2023-12-11 and 1.1.8 dated 2024-04-28
archive-1.1.7/archive/build |only archive-1.1.8/archive/DESCRIPTION | 10 +-- archive-1.1.8/archive/MD5 | 59 ++++++++++++++----- archive-1.1.8/archive/NEWS.md | 6 + archive-1.1.8/archive/R/cpp11.R | 40 ++++++------- archive-1.1.8/archive/cleanup | 5 - archive-1.1.8/archive/configure | 15 +++- archive-1.1.8/archive/man/archive_read.Rd | 6 + archive-1.1.8/archive/man/archive_write.Rd | 6 + archive-1.1.8/archive/man/archive_write_files.Rd | 6 + archive-1.1.8/archive/man/file_connections.Rd | 3 archive-1.1.8/archive/man/macros |only archive-1.1.8/archive/src/Makevars.in | 3 archive-1.1.8/archive/src/Makevars.ucrt | 2 archive-1.1.8/archive/src/Makevars.win | 2 archive-1.1.8/archive/src/archive_extract.cpp | 7 +- archive-1.1.8/archive/src/cpp11 |only archive-1.1.8/archive/src/cpp11.cpp | 70 +++++++++++------------ archive-1.1.8/archive/tools/dynamic-help.R |only 19 files changed, 145 insertions(+), 95 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 1.2.2 dated 2023-07-11 and 1.2.3 dated 2024-04-28
diemr-1.2.2/diemr/inst/extdata/testdata.vcf |only diemr-1.2.2/diemr/tests/testthat/multiallelic-01.txt |only diemr-1.2.2/diemr/tests/testthat/test-01.txt |only diemr-1.2.2/diemr/tests/testthat/test-02.txt |only diemr-1.2.2/diemr/tests/testthat/test-03.txt |only diemr-1.2.3/diemr/DESCRIPTION | 6 diemr-1.2.3/diemr/MD5 | 23 - diemr-1.2.3/diemr/NEWS.md | 8 diemr-1.2.3/diemr/R/vcf2diem.r | 216 +++++----- diemr-1.2.3/diemr/inst/CITATION | 2 diemr-1.2.3/diemr/inst/doc/Importing-data-for-genome-polarisation.html | 4 diemr-1.2.3/diemr/inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 2 diemr-1.2.3/diemr/inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 10 diemr-1.2.3/diemr/man/vcf2diem.Rd | 44 +- diemr-1.2.3/diemr/vignettes/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 2 15 files changed, 185 insertions(+), 132 deletions(-)
Title: Biological Entity Dictionary (BED)
Description: An interface for the 'Neo4j' database providing
mapping between different identifiers of biological entities.
This Biological Entity Dictionary (BED)
has been developed to address three main challenges.
The first one is related to the completeness of identifier mappings.
Indeed, direct mapping information provided by the different systems
are not always complete and can be enriched by mappings provided by other
resources.
More interestingly, direct mappings not identified by any of these
resources can be indirectly inferred by using mappings to a third reference.
For example, many human Ensembl gene ID are not directly mapped to any
Entrez gene ID but such mappings can be inferred using respective mappings
to HGNC ID. The second challenge is related to the mapping of deprecated
identifiers. Indeed, entity identifiers can change from one resource
release to another. The identifier history is provided by some resources,
such as Ensembl or the NCBI, but it is generally not used by mapping [...truncated...]
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between BED versions 1.5.0 dated 2024-01-18 and 1.5.1 dated 2024-04-28
DESCRIPTION | 10 MD5 | 26 R/dumpEnsCore.R | 9 R/dumpUniprotDb.R | 27 R/getUniprot.R | 4 build/vignette.rds |binary inst/Documentation/BED-Model/BED.png |only inst/doc/BED.R | 19 inst/doc/BED.Rmd | 20 inst/doc/BED.html | 9909 +++++++++++++++++++---------------- inst/pkgdown.yml | 4 man/dumpUniprotDb.Rd | 10 man/getUniprot.Rd | 5 vignettes/BED.Rmd | 20 vignettes/img/BED-data-model.png |only 15 files changed, 5530 insertions(+), 4533 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-14 1.0-4
2014-08-14 1.0-3
2014-01-08 1.0-2
2013-02-15 1.0-1
2012-11-17 1.0.0
Title: Create, Read, Write, and Work with 'iCalander' Files, Calendars
and Scheduling Data
Description: Provides function to create, read, write, and work with
'iCalander' files (which typically have '.ics' or '.ical' extensions),
and the scheduling data, calendars and timelines of people,
organisations and other entities that they represent. 'iCalendar' is
an open standard for exchanging calendar and scheduling information
between users and computers, described at <https://icalendar.org/>.
Author: Robin Lovelace [aut, cre] ,
Layik Hama [aut] ,
Ollie Lloyd [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between calendar versions 0.0.1 dated 2019-02-11 and 0.1.0 dated 2024-04-28
DESCRIPTION | 57 ++++--- MD5 | 53 +++--- R/ic_date.R | 13 + R/ic_event.R | 2 R/ic_find.R | 1 R/ic_read.R | 8 - R/ical.R | 11 - README.md | 63 ++++--- build/vignette.rds |binary inst/doc/ical-creating-calendars.R | 8 - inst/doc/ical-creating-calendars.html | 271 ++++++++++++++++++++-------------- man/calendar.Rd | 1 man/formats.Rd | 4 man/holidays.Rd | 4 man/ic_attributes_vec.Rd | 8 - man/ic_char_event.Rd | 6 man/ic_character.Rd | 6 man/ic_event.Rd | 16 +- man/ic_list.Rd | 2 man/ic_spec.Rd | 3 man/ic_write.Rd | 6 man/ical_example.Rd | 6 man/ical_outlook.Rd | 4 man/properties.Rd | 6 man/properties_core.Rd | 4 man/properties_ical.Rd | 4 tests/testthat/test-ic-extract.R |only tests/testthat/test-ic-read.R |only tests/testthat/test-ic-spec.R |only 29 files changed, 346 insertions(+), 221 deletions(-)
Title: Tools for Analyzing Remote Sensing Forest Data
Description: Tools for analyzing remote sensing forest data, including functions for detecting treetops from canopy models, outlining tree crowns, and calculating textural metrics.
Author: Andrew Plowright [aut, cre],
Jean-Romain Roussel [ctb]
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>
Diff between ForestTools versions 1.0.1 dated 2023-10-02 and 1.0.2 dated 2024-04-28
ForestTools-1.0.1/ForestTools/R/ForestTools-package.R |only ForestTools-1.0.1/ForestTools/R/RcppExports.R |only ForestTools-1.0.1/ForestTools/R/glcm_stats.R |only ForestTools-1.0.1/ForestTools/build |only ForestTools-1.0.1/ForestTools/inst/doc |only ForestTools-1.0.1/ForestTools/man/ForestTools-package.Rd |only ForestTools-1.0.1/ForestTools/man/glcm0.Rd |only ForestTools-1.0.1/ForestTools/man/glcm135.Rd |only ForestTools-1.0.1/ForestTools/man/glcm45.Rd |only ForestTools-1.0.1/ForestTools/man/glcm90.Rd |only ForestTools-1.0.1/ForestTools/man/glcm_features.Rd |only ForestTools-1.0.1/ForestTools/src |only ForestTools-1.0.1/ForestTools/tests/testthat/validation_data/glcm_features |only ForestTools-1.0.1/ForestTools/vignettes |only ForestTools-1.0.2/ForestTools/DESCRIPTION | 16 - ForestTools-1.0.2/ForestTools/MD5 | 77 ++--- ForestTools-1.0.2/ForestTools/NAMESPACE | 2 ForestTools-1.0.2/ForestTools/NEWS.md | 55 +++- ForestTools-1.0.2/ForestTools/R/glcm.R | 136 +++------- ForestTools-1.0.2/ForestTools/README.md | 65 +++- ForestTools-1.0.2/ForestTools/inst/guides |only ForestTools-1.0.2/ForestTools/man/glcm.Rd | 11 ForestTools-1.0.2/ForestTools/tests/testthat/test_data/ttops_orphans.Rda |binary ForestTools-1.0.2/ForestTools/tests/testthat/test_data/ttops_test.Rda |binary ForestTools-1.0.2/ForestTools/tests/testthat/test_glcm.R | 12 ForestTools-1.0.2/ForestTools/tests/testthat/test_glcm_internal.R | 123 ++++----- ForestTools-1.0.2/ForestTools/tests/testthat/validation_data/glcm_metrics |only 27 files changed, 264 insertions(+), 233 deletions(-)
Title: Creating and Annotating a Composite Plot in 'ggplot2'
Description: Provides functions for creating and annotating a composite plot in 'ggplot2'. Offers background themes and shortcut plotting functions that produce figures that are appropriate for the format of scientific journals. Some methods are described in Min and Zhou (2021) <doi:10.3389/fgene.2021.802894>.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun (Sam) Min <seung.min@mail.mcgill.ca>
Diff between smplot2 versions 0.2.0 dated 2024-04-14 and 0.2.1 dated 2024-04-27
smplot2-0.2.0/smplot2/R/sm_add_arrow.R |only smplot2-0.2.0/smplot2/R/sm_add_line.R |only smplot2-0.2.0/smplot2/R/sm_add_polygon.R |only smplot2-0.2.0/smplot2/R/sm_add_rect.R |only smplot2-0.2.0/smplot2/man/sm_add_arrow.Rd |only smplot2-0.2.0/smplot2/man/sm_add_line.Rd |only smplot2-0.2.0/smplot2/man/sm_add_polygon.Rd |only smplot2-0.2.0/smplot2/man/sm_add_rect.Rd |only smplot2-0.2.1/smplot2/DESCRIPTION | 12 ++--- smplot2-0.2.1/smplot2/MD5 | 38 ++++++---------- smplot2-0.2.1/smplot2/NAMESPACE | 4 - smplot2-0.2.1/smplot2/NEWS.md | 6 ++ smplot2-0.2.1/smplot2/R/sm_add_legend.R | 2 smplot2-0.2.1/smplot2/R/sm_add_point.R | 10 +--- smplot2-0.2.1/smplot2/R/sm_add_text.R | 8 +-- smplot2-0.2.1/smplot2/R/sm_auc_all.R | 2 smplot2-0.2.1/smplot2/R/sm_common_axis.R | 63 ++++++++++++++++++++------- smplot2-0.2.1/smplot2/R/sm_plot_clean.R | 42 +++++++++++++----- smplot2-0.2.1/smplot2/R/sm_put_together.R | 45 ++++++++++++++++--- smplot2-0.2.1/smplot2/R/sm_slope_all.R | 2 smplot2-0.2.1/smplot2/man/sm_add_point.Rd | 6 -- smplot2-0.2.1/smplot2/man/sm_add_text.Rd | 9 +-- smplot2-0.2.1/smplot2/man/sm_common_axis.Rd | 10 ++-- smplot2-0.2.1/smplot2/man/sm_put_together.Rd | 22 +++++++++ 24 files changed, 188 insertions(+), 93 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>), univariate and multivariate (<doi:10.1186/s12711-022-00730-w>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.7 dated 2024-04-04 and 2.2.8 dated 2024-04-27
bWGR-2.2.7/bWGR/src/RegisteringDynamic.c |only bWGR-2.2.7/bWGR/src/added20230407.cpp |only bWGR-2.2.7/bWGR/src/eigen20220714.cpp |only bWGR-2.2.7/bWGR/src/emm20220213.cpp |only bWGR-2.2.7/bWGR/src/mega20231111.cpp |only bWGR-2.2.7/bWGR/src/mega20240303.cpp |only bWGR-2.2.7/bWGR/src/mrr20220709.cpp |only bWGR-2.2.7/bWGR/src/wgr20210213.cpp |only bWGR-2.2.8/bWGR/DESCRIPTION | 8 bWGR-2.2.8/bWGR/MD5 | 24 bWGR-2.2.8/bWGR/R/RcppExports.R | 276 +++---- bWGR-2.2.8/bWGR/R/mix.R | 77 +- bWGR-2.2.8/bWGR/man/bWGR.Rd | 4 bWGR-2.2.8/bWGR/man/mvr.Rd | 12 bWGR-2.2.8/bWGR/man/xtra.Rd | 9 bWGR-2.2.8/bWGR/src/Rcpp20230423.cpp |only bWGR-2.2.8/bWGR/src/RcppEigen20230423.cpp |only bWGR-2.2.8/bWGR/src/RcppExports.cpp | 1153 +++++++++++++++--------------- 18 files changed, 823 insertions(+), 740 deletions(-)
Title: Easily Create Pretty Popup Messages (Modals) in 'Shiny'
Description: Easily create pretty popup messages (modals) in 'Shiny'. A modal can
contain text, images, OK/Cancel buttons, an input to get a response from the
user, and many more customizable options.
Author: Dean Attali [aut, cre] ,
Tristan Edwards [aut] ,
Zhengjia Wang [ctb]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyalert versions 3.0.0 dated 2021-12-20 and 3.1.0 dated 2024-04-27
shinyalert-3.0.0/shinyalert/inst/www |only shinyalert-3.1.0/shinyalert/DESCRIPTION | 12 +- shinyalert-3.1.0/shinyalert/LICENSE | 2 shinyalert-3.1.0/shinyalert/MD5 | 32 +++-- shinyalert-3.1.0/shinyalert/NEWS.md | 7 + shinyalert-3.1.0/shinyalert/R/shinyalert-package.R |only shinyalert-3.1.0/shinyalert/R/shinyalert.R | 19 --- shinyalert-3.1.0/shinyalert/R/useShinyalert.R | 4 shinyalert-3.1.0/shinyalert/R/utils.R | 57 ++++------ shinyalert-3.1.0/shinyalert/README.md | 64 ++++++----- shinyalert-3.1.0/shinyalert/inst/assets |only shinyalert-3.1.0/shinyalert/man/shinyalert-package.Rd |only shinyalert-3.1.0/shinyalert/man/shinyalert.Rd | 4 shinyalert-3.1.0/shinyalert/man/useShinyalert.Rd | 102 +++++++++--------- 14 files changed, 149 insertions(+), 154 deletions(-)
Title: Convert Addresses to Standard Inputs
Description: Efficient tools for parsing and standardizing Australian
addresses from textual data. It utilizes optimized algorithms to accurately identify and
extract components of addresses, such as street names, types, and postcodes, especially
for large batched data in contexts where sending addresses to internet services may be
slow or inappropriate. The core functionality is built on fast string processing techniques
to handle variations in address formats and abbreviations commonly found in Australian
address data. Designed for data scientists, urban planners, and logistics analysts, the
package facilitates the cleaning and normalization of address information, supporting
better data integration and analysis in urban studies, geography, and related fields.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between healthyAddress versions 0.2.0 dated 2024-02-07 and 0.4.1 dated 2024-04-27
DESCRIPTION | 8 - MD5 | 43 ++++--- NAMESPACE | 10 + NEWS.md | 27 +++- R/download_latlon_data.R |only R/healthyAddress-package.R | 5 R/latlon.R |only R/mutate_latlon.R |only R/postcode2ste.R | 105 +++++++++--------- R/unique_Postcodes.R | 43 +++++-- inst/extdata/POSTCODE-STREET_TYPE_CODE-STREET_NAME.qs |binary inst/tinytest/test_compress_latlon.R |only inst/tinytest/test_healthyAddress.R | 6 + inst/tinytest/test_is_postcode.R | 2 inst/tinytest/test_unique_Postcodes.R | 3 man/compress_latlon.Rd |only man/download_latlon_data.Rd |only man/healthyAddress-package.Rd | 8 + man/mutate_latlon.Rd |only man/unique_Postcodes.Rd | 44 ++++--- src/StandardAddress.c | 95 +++++++++------- src/constants.c |only src/healthyAddress.h | 19 ++- src/init.c | 16 ++ src/latlon.c |only src/postcode2intrnl.c | 7 - src/verifyEquiStr.c | 13 ++ 27 files changed, 303 insertions(+), 151 deletions(-)
More information about healthyAddress at CRAN
Permanent link
Title: 'teal' Modules for Standard Clinical Outputs
Description: Provides user-friendly tools for creating and customizing
clinical trial reports. By leveraging the 'teal' framework, this
package provides 'teal' modules to easily create an interactive panel
that allows for seamless adjustments to data presentation, thereby
streamlining the creation of detailed and accurate reports.
Author: Joe Zhu [aut, cre],
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Mahmoud Hallal [aut],
Dawid Kaledkowski [aut],
Rosemary Li [aut],
Heng Wang [aut],
Pawel Rucki [aut],
Nikolas Burkoff [aut],
Konrad Paga [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between teal.modules.clinical versions 0.9.0 dated 2024-02-23 and 0.9.1 dated 2024-04-27
teal.modules.clinical-0.9.0/teal.modules.clinical/man/teal.modules.clinical.Rd |only teal.modules.clinical-0.9.1/teal.modules.clinical/DESCRIPTION | 45 - teal.modules.clinical-0.9.1/teal.modules.clinical/MD5 | 355 +++++----- teal.modules.clinical-0.9.1/teal.modules.clinical/NAMESPACE | 1 teal.modules.clinical-0.9.1/teal.modules.clinical/NEWS.md | 16 teal.modules.clinical-0.9.1/teal.modules.clinical/R/argument_convention.R | 16 teal.modules.clinical-0.9.1/teal.modules.clinical/R/arm_ref_comp.R | 8 teal.modules.clinical-0.9.1/teal.modules.clinical/R/labels.R | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/R/string_ops.R | 13 teal.modules.clinical-0.9.1/teal.modules.clinical/R/teal.modules.clinical.R | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_a_gee.R | 50 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_a_mmrm.R | 138 +-- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_barchart_simple.R | 71 -- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_ci.R | 34 teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_forest_rsp.R | 155 ++-- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_forest_tte.R | 143 ++-- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_ipp.R | 42 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_km.R | 176 +++- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_lineplot.R | 48 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_pp_adverse_events.R | 46 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_pp_patient_timeline.R | 67 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_pp_therapy.R | 48 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_pp_vitals.R | 54 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_abnormality.R | 43 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_abnormality_by_worst_grade.R | 63 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_ancova.R | 72 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_binary_outcome.R | 130 ++- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_coxreg.R | 82 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_events.R | 50 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_events_by_grade.R | 72 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_events_patyear.R | 46 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_events_summary.R | 53 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_exposure.R | 39 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_logistic.R | 76 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_mult_events.R | 44 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_pp_basic_info.R | 40 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_pp_laboratory.R | 46 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_pp_medical_history.R | 42 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_pp_prior_medication.R | 36 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_shift_by_arm.R | 56 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_shift_by_arm_by_worst.R | 60 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_shift_by_grade.R | 46 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_smq.R | 36 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_summary.R | 64 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_summary_by.R | 66 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_tte.R | 86 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/utils.R | 13 teal.modules.clinical-0.9.1/teal.modules.clinical/R/validate_standard_inputs.R | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/R/zzz.R | 3 teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adae.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adaette.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adcm.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adeg.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adex.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adlb.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_admh.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adqs.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adrs.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adsl.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adtte.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_advs.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/inst/WORDLIST | 1 teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/generate_tmc_test_data.R | 100 +- teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/generate_tmc_test_data.Rmd | 103 +- teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/generate_tmc_test_data.html | 251 +++---- teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/quickstart_substitute.R | 38 - teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/quickstart_substitute.Rmd | 15 teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/quickstart_substitute.html | 25 teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/teal-modules-clinical.Rmd | 14 teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/teal-modules-clinical.html | 18 teal.modules.clinical-0.9.1/teal.modules.clinical/man/add_expr.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/arm_ref_comp_observer.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/column_annotation_label.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/extract_input.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/h_concat_expr.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/make_barchart_simple_call.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/module_arguments.Rd | 10 teal.modules.clinical-0.9.1/teal.modules.clinical/man/teal.modules.clinical-package.Rd |only teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_a_gee.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_abnormality.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_abnormality_by_worst_grade.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_adverse_events.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_ancova.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_arguments.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_binary_outcome.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_coxreg_m.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_coxreg_u.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_events.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_events_by_grade.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_events_col_by_grade.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_events_patyear.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_exposure.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_fit_mmrm.Rd | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_forest_rsp.Rd | 14 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_forest_tte.Rd | 9 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_g_ci.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_g_ipp.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_g_km.Rd | 49 - 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More information about teal.modules.clinical at CRAN
Permanent link
Title: Data Package for 'pathfindR'
Description: This is a data-only package, containing data needed to run the CRAN
package 'pathfindR', a package for enrichment analysis utilizing active
subnetworks. This package contains protein-protein interaction network data,
data related to gene sets and example input/output data.
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR.data versions 2.0.0 dated 2023-04-27 and 2.1.0 dated 2024-04-27
DESCRIPTION | 8 +- MD5 | 86 ++++++++++++++-------------- NEWS.md | 16 +++++ R/data.R | 72 ++++++++++++----------- R/sysdata.rda |binary data/biocarta_descriptions.rda |binary data/biocarta_genes.rda |binary data/cell_markers_descriptions.rda |binary data/cell_markers_gsets.rda |binary data/example_active_snws.rda |binary data/example_comparison_output.rda |binary data/example_custom_genesets_result.rda |binary data/example_mmu_output.rda |binary data/example_pathfindR_output.rda |binary data/example_pathfindR_output_clustered.rda |binary data/go_all_genes.rda |binary data/kegg_descriptions.rda |binary data/kegg_genes.rda |binary data/mmu_kegg_descriptions.rda |binary data/mmu_kegg_genes.rda |binary data/pathfindR.data_updates.rda |binary data/reactome_descriptions.rda |binary data/reactome_genes.rda |binary man/biocarta_descriptions.Rd | 2 man/biocarta_genes.Rd | 2 man/cell_markers_descriptions.Rd | 2 man/cell_markers_gsets.Rd | 2 man/example_active_snws.Rd | 4 - man/example_comparison_output.Rd | 4 - man/example_custom_genesets_result.Rd | 4 - man/example_experiment_matrix.Rd | 2 man/example_mmu_input.Rd | 2 man/example_mmu_output.Rd | 4 - man/example_pathfindR_input.Rd | 2 man/example_pathfindR_output.Rd | 4 - man/example_pathfindR_output_clustered.Rd | 4 - man/go_all_genes.Rd | 4 - man/kegg_descriptions.Rd | 4 - man/kegg_genes.Rd | 4 - man/mmu_kegg_descriptions.Rd | 4 - man/mmu_kegg_genes.Rd | 4 - man/pathfindR.data_updates.Rd | 6 + man/reactome_descriptions.Rd | 4 - man/reactome_genes.Rd | 4 - 44 files changed, 137 insertions(+), 117 deletions(-)
More information about pathfindR.data at CRAN
Permanent link
Title: Collapsed Gibbs Sampling Methods for Topic Models
Description: Implements latent Dirichlet allocation (LDA)
and related models. This includes (but is not limited
to) sLDA, corrLDA, and the mixed-membership stochastic
blockmodel. Inference for all of these models is
implemented via a fast collapsed Gibbs sampler written
in C. Utility functions for reading/writing data
typically used in topic models, as well as tools for
examining posterior distributions are also included.
Author: Jonathan Chang
Maintainer: Santiago Olivella <olivella@unc.edu>
Diff between lda versions 1.4.2 dated 2015-11-22 and 1.5.2 dated 2024-04-27
DESCRIPTION | 17 ++-- MD5 | 63 +++++++++-------- NAMESPACE | 12 ++- R/lda.collapsed.gibbs.sampler.R | 2 R/slda.em.R | 4 - README.md |only build |only data/cora.cites.rda |binary data/cora.documents.rda |binary data/cora.titles.rda |binary data/cora.vocab.rda |binary data/newsgroup.label.map.rda |binary data/newsgroup.test.documents.rda |binary data/newsgroup.test.labels.rda |binary data/newsgroup.train.documents.rda |binary data/newsgroup.train.labels.rda |binary data/newsgroup.vocab.rda |binary data/poliblog.documents.rda |binary data/poliblog.ratings.rda |binary data/poliblog.vocab.rda |binary data/sampson.rda |binary demo/lda.R | 5 - demo/mmsb.R | 9 +- demo/rtm.R | 20 +++-- demo/slda.R | 22 ++---- man/lda-package.Rd | 30 +++----- man/lda.collapsed.gibbs.sampler.Rd | 5 - man/links.as.edgelist.Rd | 14 +-- man/nubbi.collapsed.gibbs.sampler.Rd | 3 man/read.documents.Rd | 4 - man/top.topic.words.Rd | 2 src/cvb0.c | 1 src/gibbs.c | 124 +++++++++++++++++++++++------------ src/lda-init.c |only 34 files changed, 197 insertions(+), 140 deletions(-)
Title: Bayesian Post-Estimation on the Mean Scale
Description: Computes Bayesian posterior distributions of predictions, marginal effects, and differences of marginal effects for various generalized linear models. Importantly, the posteriors are on the mean (response) scale, allowing for more natural interpretation than summaries on the link scale. Also, predictions and marginal effects of the count probabilities for Poisson and negative binomial models can be computed.
Author: David M. Dalenberg [aut, cre]
Maintainer: David M. Dalenberg <dalenbe2@gmail.com>
Diff between bayesMeanScale versions 0.1.0 dated 2024-04-23 and 0.1.1 dated 2024-04-27
DESCRIPTION | 13 +-- MD5 | 17 ++-- NEWS.md |only R/bayes-count-marg-effects.R | 8 +- R/bayes-count-preds.R | 6 + R/bayes-marg-effects.R | 8 +- R/bayes-preds.R | 8 +- R/mean-count-pred.R | 13 +-- R/mean-pred.R | 11 +- inst/doc/introduction.html | 172 +++++++++++++++++++++---------------------- 10 files changed, 134 insertions(+), 122 deletions(-)
More information about bayesMeanScale at CRAN
Permanent link
Title: Estimation, Variable Selection and Prediction for Functional
Semiparametric Models
Description: Routines for the estimation or simultaneous estimation and variable selection in several functional semiparametric models with scalar responses are provided. These models include the functional single-index model, the semi-functional partial linear model, and the semi-functional partial linear single-index model. Additionally, the package offers algorithms for handling scalar covariates with linear effects that originate from the discretization of a curve. This functionality is applicable in the context of the linear model, the multi-functional partial linear model, and the multi-functional partial linear single-index model.
Author: German Aneiros [aut],
Silvia Novo [aut, cre]
Maintainer: Silvia Novo <snovo@est-econ.uc3m.es>
Diff between fsemipar versions 1.0.1 dated 2024-02-21 and 1.1.0 dated 2024-04-27
fsemipar-1.0.1/fsemipar/R/normaliza.R |only fsemipar-1.1.0/fsemipar/DESCRIPTION | 15 - fsemipar-1.1.0/fsemipar/MD5 | 177 ++++++------- fsemipar-1.1.0/fsemipar/NAMESPACE | 16 - fsemipar-1.1.0/fsemipar/R/FASSMR.kNN.R | 70 ++++- fsemipar-1.1.0/fsemipar/R/FASSMR.kNN.fit.R | 47 +-- fsemipar-1.1.0/fsemipar/R/FASSMR.kernel.R | 68 +++- fsemipar-1.1.0/fsemipar/R/FASSMR.kernel.fit.R | 63 ++-- fsemipar-1.1.0/fsemipar/R/H.fsim.kernel.R | 2 fsemipar-1.1.0/fsemipar/R/IASSMR.kNN.R | 76 ++++- fsemipar-1.1.0/fsemipar/R/IASSMR.kNN.fit.R | 40 +- fsemipar-1.1.0/fsemipar/R/IASSMR.kernel.R | 68 +++- fsemipar-1.1.0/fsemipar/R/IASSMR.kernel.fit.R | 47 +-- fsemipar-1.1.0/fsemipar/R/LASSOmia.R |only fsemipar-1.1.0/fsemipar/R/PVS.R | 52 +++ fsemipar-1.1.0/fsemipar/R/PVS.fit.R | 8 fsemipar-1.1.0/fsemipar/R/PVS.kNN.R | 51 +++ fsemipar-1.1.0/fsemipar/R/PVS.kNN.fit.R | 7 fsemipar-1.1.0/fsemipar/R/PVS.kernel.R | 51 +++ fsemipar-1.1.0/fsemipar/R/PVS.kernel.fit.R | 7 fsemipar-1.1.0/fsemipar/R/fnp.kNN.GCV.R | 8 fsemipar-1.1.0/fsemipar/R/fnp.kNN.fit.R | 4 fsemipar-1.1.0/fsemipar/R/fnp.kNN.fit.test.loc.R | 2 fsemipar-1.1.0/fsemipar/R/fnp.kernel.fit.R | 37 +- fsemipar-1.1.0/fsemipar/R/fnp.kernel.test.R | 2 fsemipar-1.1.0/fsemipar/R/fsim.kNN.R | 34 +- fsemipar-1.1.0/fsemipar/R/fsim.kNN.fit.R | 149 +++++++--- fsemipar-1.1.0/fsemipar/R/fsim.kNN.fit.fixedtheta.R | 56 ++-- fsemipar-1.1.0/fsemipar/R/fsim.kNN.fit.fixedtheta.com.R |only fsemipar-1.1.0/fsemipar/R/fsim.kNN.fit.optim.R |only fsemipar-1.1.0/fsemipar/R/fsim.kNN.test.R | 2 fsemipar-1.1.0/fsemipar/R/fsim.kernel.R | 32 +- fsemipar-1.1.0/fsemipar/R/fsim.kernel.fit.R | 128 ++++++--- fsemipar-1.1.0/fsemipar/R/fsim.kernel.fit.fixedtheta.R | 25 - fsemipar-1.1.0/fsemipar/R/fsim.kernel.fit.fixedtheta.com.R |only fsemipar-1.1.0/fsemipar/R/fsim.kernel.fit.optim.R |only fsemipar-1.1.0/fsemipar/R/fsim.kernel.test.R | 6 fsemipar-1.1.0/fsemipar/R/fun.kNN.R | 2 fsemipar-1.1.0/fsemipar/R/fun.kNN.fixedtheta.R | 31 -- fsemipar-1.1.0/fsemipar/R/fun.kernel.R | 8 fsemipar-1.1.0/fsemipar/R/fun.kernel.fixedtheta.R | 43 +-- fsemipar-1.1.0/fsemipar/R/funopare.kNN.R | 8 fsemipar-1.1.0/fsemipar/R/globals.R |only fsemipar-1.1.0/fsemipar/R/lm.pels.R | 30 +- fsemipar-1.1.0/fsemipar/R/lm.pels.fit.R | 16 - fsemipar-1.1.0/fsemipar/R/projec.R | 4 fsemipar-1.1.0/fsemipar/R/sfpl.kNN.R | 30 +- fsemipar-1.1.0/fsemipar/R/sfpl.kNN.fit.R | 24 - fsemipar-1.1.0/fsemipar/R/sfpl.kernel.R | 30 +- fsemipar-1.1.0/fsemipar/R/sfpl.kernel.fit.R | 22 - fsemipar-1.1.0/fsemipar/R/sfplsim.kNN.R | 43 ++- fsemipar-1.1.0/fsemipar/R/sfplsim.kNN.fit.R | 146 ++++++++-- fsemipar-1.1.0/fsemipar/R/sfplsim.kNN.fit.fixedtheta.R | 33 +- fsemipar-1.1.0/fsemipar/R/sfplsim.kernel.R | 45 ++- fsemipar-1.1.0/fsemipar/R/sfplsim.kernel.fit.R | 160 ++++++++--- fsemipar-1.1.0/fsemipar/R/sfplsim.kernel.fit.fixedtheta.R | 69 ++--- fsemipar-1.1.0/fsemipar/build/partial.rdb |binary fsemipar-1.1.0/fsemipar/man/FASSMR.kNN.fit.Rd | 120 ++++---- fsemipar-1.1.0/fsemipar/man/FASSMR.kernel.fit.Rd | 113 +++----- fsemipar-1.1.0/fsemipar/man/IASSMR.kNN.fit.Rd | 159 +++++------ fsemipar-1.1.0/fsemipar/man/IASSMR.kernel.fit.Rd | 158 +++++------ fsemipar-1.1.0/fsemipar/man/PVS.fit.Rd | 105 +++---- fsemipar-1.1.0/fsemipar/man/PVS.kNN.fit.Rd | 151 +++++------ fsemipar-1.1.0/fsemipar/man/PVS.kernel.fit.Rd | 146 +++++----- fsemipar-1.1.0/fsemipar/man/Sugar.Rd | 8 fsemipar-1.1.0/fsemipar/man/Tecator.Rd | 12 fsemipar-1.1.0/fsemipar/man/fsemipar-package.Rd | 46 +-- fsemipar-1.1.0/fsemipar/man/fsemipar.internal.Rd | 5 fsemipar-1.1.0/fsemipar/man/fsim.kNN.fit.Rd | 96 +++---- fsemipar-1.1.0/fsemipar/man/fsim.kNN.fit.optim.Rd |only fsemipar-1.1.0/fsemipar/man/fsim.kNN.test.Rd | 62 ++-- fsemipar-1.1.0/fsemipar/man/fsim.kernel.fit.Rd | 70 ++--- fsemipar-1.1.0/fsemipar/man/fsim.kernel.fit.optim.Rd |only fsemipar-1.1.0/fsemipar/man/fsim.kernel.test.Rd | 61 ++-- fsemipar-1.1.0/fsemipar/man/lm.pels.fit.Rd | 95 +++--- fsemipar-1.1.0/fsemipar/man/plot.classes.Rd | 92 ++++-- fsemipar-1.1.0/fsemipar/man/predict.IASSMR.Rd | 39 +- fsemipar-1.1.0/fsemipar/man/predict.fsim.Rd | 11 fsemipar-1.1.0/fsemipar/man/predict.lm.Rd | 14 - fsemipar-1.1.0/fsemipar/man/predict.mfplm.Rd | 47 +-- fsemipar-1.1.0/fsemipar/man/predict.sfpl.Rd | 25 - fsemipar-1.1.0/fsemipar/man/predict.sfplsim.FASSMR.Rd | 35 +- fsemipar-1.1.0/fsemipar/man/print.summary.fsim.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.lm.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.mfpl.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.mfplsim.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.sfpl.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.sfplsim.Rd | 8 fsemipar-1.1.0/fsemipar/man/projec.Rd | 10 fsemipar-1.1.0/fsemipar/man/semimetric.projec.Rd | 16 - fsemipar-1.1.0/fsemipar/man/sfpl.kNN.fit.Rd | 126 ++++----- fsemipar-1.1.0/fsemipar/man/sfpl.kernel.fit.Rd | 126 ++++----- fsemipar-1.1.0/fsemipar/man/sfplsim.kNN.fit.Rd | 134 ++++----- fsemipar-1.1.0/fsemipar/man/sfplsim.kernel.fit.Rd | 123 +++------ 94 files changed, 2435 insertions(+), 1912 deletions(-)
Title: Interpretable Machine Learning
Description: Interpretability methods to analyze the behavior and
predictions of any machine learning model. Implemented methods are:
Feature importance described by Fisher et al. (2018)
<doi:10.48550/arxiv.1801.01489>, accumulated local effects plots described by Apley
(2018) <doi:10.48550/arxiv.1612.08468>, partial dependence plots described by
Friedman (2001) <www.jstor.org/stable/2699986>, individual conditional
expectation ('ice') plots described by Goldstein et al. (2013)
<doi:10.1080/10618600.2014.907095>, local models (variant of 'lime')
described by Ribeiro et. al (2016) <doi:10.48550/arXiv.1602.04938>, the Shapley
Value described by Strumbelj et. al (2014)
<doi:10.1007/s10115-013-0679-x>, feature interactions described by
Friedman et. al <doi:10.1214/07-AOAS148> and tree surrogate models.
Author: Giuseppe Casalicchio [aut, cre],
Christoph Molnar [aut],
Patrick Schratz [aut]
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@lmu.de>
Diff between iml versions 0.11.2 dated 2024-03-29 and 0.11.3 dated 2024-04-27
DESCRIPTION | 18 MD5 | 20 NEWS.md | 288 ++++----- R/FeatureEffect.R | 1536 ++++++++++++++++++++++++------------------------- R/LocalModel.R | 658 ++++++++++---------- R/Predictor.R | 377 ++++++------ R/create_predict_fun.R | 314 +++++----- R/utils.R | 658 ++++++++++---------- inst/doc/parallel.html | 20 man/FeatureEffect.Rd | 2 man/Predictor.Rd | 8 11 files changed, 1956 insertions(+), 1943 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.10 dated 2024-01-24 and 0.0.11 dated 2024-04-27
ChangeLog | 22 ++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- build/partial.rdb |binary inst/NEWS.Rd | 13 +++++++++++-- src/ql/time/calendar.cpp | 12 +++++++++--- src/ql/time/calendars/brazil.cpp | 2 +- src/ql/time/calendars/brazil.hpp | 2 +- src/ql/time/calendars/india.cpp | 30 ++++++++++++++++++------------ src/ql/time/calendars/singapore.cpp | 18 ++++++++++++++++++ src/ql/time/calendars/singapore.hpp | 3 ++- src/ql/time/calendars/southafrica.cpp | 4 +++- src/ql/time/calendars/thailand.cpp | 3 ++- src/ql/time/calendars/unitedstates.cpp | 11 +++++++++-- 14 files changed, 113 insertions(+), 41 deletions(-)
Title: Factor and Autoregressive Models for Tensor Time Series
Description: Factor and autoregressive models for matrix and tensor valued time series. We provide functions for estimation, simulation and prediction. The models are discussed in
Li et al (2021) <doi:10.48550/arXiv.2110.00928>, Chen et al (2020) <DOI:10.1080/01621459.2021.1912757>,
Chen et al (2020) <DOI:10.1016/j.jeconom.2020.07.015>, and Xiao et al (2020) <doi:10.48550/arXiv.2006.02611>.
Author: Zebang Li [aut, cre],
Ruofan Yu [aut],
Rong Chen [aut],
Yuefeng Han [aut],
Han Xiao [aut],
Dan Yang [aut]
Maintainer: Zebang Li <zl326@stat.rutgers.edu>
Diff between tensorTS versions 1.0.1 dated 2023-05-07 and 1.0.2 dated 2024-04-27
DESCRIPTION | 10 +-- MD5 | 10 +-- R/tenFM.R | 164 +++++++++++++---------------------------------------- man/taxi.sim.FM.Rd | 15 ---- man/tenFM.est.Rd | 2 man/tenFM.rank.Rd | 32 +++++----- 6 files changed, 74 insertions(+), 159 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.73 dated 2024-04-09 and 2.0.74 dated 2024-04-27
DESCRIPTION | 8 +-- MD5 | 34 +++++++------- NEWS | 10 +++- R/epi.betabuster.R | 24 +++++++-- inst/doc/epiR_descriptive.R | 2 inst/doc/epiR_descriptive.html | 47 +++++++------------ inst/doc/epiR_measures_of_association.R | 34 +++++++------- inst/doc/epiR_measures_of_association.html | 12 ++-- inst/doc/epiR_sample_size.R | 2 inst/doc/epiR_sample_size.html | 4 - inst/doc/epiR_surveillance.R | 2 inst/doc/epiR_surveillance.html | 14 ++--- man/epi.2by2.Rd | 20 ++++---- man/epi.betabuster.Rd | 22 ++++----- man/epi.ccc.Rd | 30 +++++++----- man/epi.edr.Rd | 70 ++++++++++++++--------------- man/epi.empbayes.Rd | 15 +++--- man/epi.psi.Rd | 1 18 files changed, 185 insertions(+), 166 deletions(-)
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for
k-centroids cluster analysis supporting arbitrary distance measures
and centroid computation. Further cluster methods include hard
competitive learning, neural gas, and QT clustering. There are
numerous visualization methods for cluster results (neighborhood
graphs, convex cluster hulls, barcharts of centroids, ...), and
bootstrap methods for the analysis of cluster stability.
Author: Friedrich Leisch [aut] ,
Evgenia Dimitriadou [ctb],
Bettina Gruen [ctb, cre]
Maintainer: Bettina Gruen <Bettina.Gruen@R-project.org>
Diff between flexclust versions 1.4-1 dated 2022-04-08 and 1.4-2 dated 2024-04-27
DESCRIPTION | 28 ++++++------- MD5 | 16 +++---- NEWS | 4 + R/histogram.R | 2 inst/CITATION | 101 ++++++++++++++--------------------------------- man/cclust.Rd | 4 - man/histogram-methods.Rd | 5 +- man/randIndex.Rd | 4 - man/vacmot.Rd | 4 - 9 files changed, 68 insertions(+), 100 deletions(-)
Title: Japanese Text Processing Tools
Description: A collection of Japanese text processing tools for filling
Japanese iteration marks, Japanese character type conversions,
segmentation by phrase, and text normalization which is based on rules
for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism
dictionary for 'MeCab'). These features are specific to Japanese and
are not implemented in 'ICU' (International Components for Unicode).
Author: Akiru Kato [cre, aut],
Koki Takahashi [cph] ,
Shuhei Iitsuka [cph] ,
Taku Kudo [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>
Diff between audubon versions 0.5.1 dated 2023-05-02 and 0.5.2 dated 2024-04-26
DESCRIPTION | 8 +- MD5 | 62 ++++++++++----------- NEWS.md | 8 ++ R/audubon-package.R | 1 R/bind_lr.R | 7 +- R/bind_tf_idf2.R | 85 +++++++++++++++++------------- R/collapse_tokens.R | 7 +- R/lexical_density.R | 2 R/mute_tokens.R | 5 + R/pack.R | 53 ++++++------------ R/prettify.R | 19 +++--- R/strj-fill.R | 2 R/strj-japanese.R | 16 ++--- R/strj-normalize.R | 2 R/strj-rewrite.R | 2 R/strj-tokenize.R | 6 +- R/tokenize-impl.R | 4 - R/zzz.R | 3 + README.md | 8 +- build/partial.rdb |binary inst/packer/audubon.bundle.js | 2 inst/packer/audubon.bundle.js.LICENSE.txt | 18 ++++++ inst/testdata/testdata.rda |binary man/bind_lr.Rd | 5 + man/bind_tf_idf2.Rd | 32 ++++++----- man/collapse_tokens.Rd | 5 + man/mute_tokens.Rd | 5 + man/ngram_tokenizer.Rd | 2 man/pack.Rd | 5 + man/prettify.Rd | 5 + tests/testthat/test-bind_tf_idf2.R | 41 ++++++++++++-- tests/testthat/test-other-utils.R | 2 32 files changed, 245 insertions(+), 177 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 2.0.2 dated 2024-01-08 and 2.1.0 dated 2024-04-26
DESCRIPTION | 28 - MD5 | 66 ++-- NEWS.md | 8 R/app_ui.R | 2 R/compute_intensity_distri_metrics.R | 12 R/compute_mx.R |only R/compute_peak_step_acc.R |only R/create_fig_mvpa.R | 94 +++++ R/create_fig_pal.R | 50 +++ R/create_fig_ratio_mvpa_sed.R | 87 +++++ R/create_fig_res_by_day.R | 292 ++++++++++++++++++ R/create_fig_sed.R | 85 +++++ R/create_fig_steps.R | 100 ++++++ R/get_pal_status.R | 15 R/recap_by_day.R | 24 - README.md | 22 - build/vignette.rds |binary inst/doc/activAnalyzer.html | 24 - inst/guide/user_guide_en.Rmd | 12 inst/guide/user_guide_en.aux | 100 ++---- inst/guide/user_guide_en.log | 542 +++++++++++++++++---------------- inst/guide/user_guide_en.pdf |binary inst/guide/user_guide_fr.Rmd | 12 inst/guide/user_guide_fr.log | 560 +++++++++++++++++------------------ inst/guide/user_guide_fr.pdf |binary inst/report/report_en_long.Rmd | 2 inst/report/report_en_short.Rmd | 2 man/compute_mx.Rd |only man/compute_peak_step_acc.Rd |only man/create_fig_mvpa.Rd | 2 man/create_fig_pal.Rd | 2 man/create_fig_ratio_mvpa_sed.Rd | 2 man/create_fig_res_by_day.Rd | 2 man/create_fig_sed.Rd | 2 man/create_fig_steps.Rd | 2 man/get_pal_status.Rd | 2 36 files changed, 1426 insertions(+), 727 deletions(-)
Title: Dungeons & Dragons Functions for Players and Dungeon Masters
Description: The goal of 'dndR' is to provide a suite of Dungeons & Dragons related functions.
This package is meant to be useful both to players and Dungeon Masters (DMs).
All functions currently focus on Fifth Edition (a.k.a. "5e") but once the next edition is published functions will likely be expanded to include any rule changes.
Author: Nicholas Lyon [aut, cre, cph] ,
Tim Schatto-Eckrodt [aut] ,
Humberto Nappo [ctb]
Maintainer: Nicholas Lyon <njlyon@alumni.iastate.edu>
Diff between dndR versions 1.3.1 dated 2023-08-07 and 2.0.0 dated 2024-04-26
dndR-1.3.1/dndR/inst/doc/dndR_Vignette.R |only dndR-1.3.1/dndR/inst/doc/dndR_Vignette.Rmd |only dndR-1.3.1/dndR/inst/doc/dndR_Vignette.html |only dndR-1.3.1/dndR/vignettes/dndR_Vignette.Rmd |only dndR-2.0.0/dndR/DESCRIPTION | 22 ++-- dndR-2.0.0/dndR/MD5 | 65 ++++++++++---- dndR-2.0.0/dndR/NAMESPACE | 5 + dndR-2.0.0/dndR/NEWS.md | 12 ++ dndR-2.0.0/dndR/R/creature_list.R |only dndR-2.0.0/dndR/R/creature_text.R |only dndR-2.0.0/dndR/R/data-doc_creatures.R |only dndR-2.0.0/dndR/R/encounter_creator.R |only dndR-2.0.0/dndR/R/reroll.R |only dndR-2.0.0/dndR/R/roll.R | 92 ++++--------------- dndR-2.0.0/dndR/R/spell_list.R | 1 dndR-2.0.0/dndR/README.md | 102 ++++++++++++---------- dndR-2.0.0/dndR/build/vignette.rds |binary dndR-2.0.0/dndR/data/creatures.rda |only dndR-2.0.0/dndR/data/spells.rda |binary dndR-2.0.0/dndR/inst/doc/dndr_00_dice.R |only dndR-2.0.0/dndR/inst/doc/dndr_00_dice.Rmd |only dndR-2.0.0/dndR/inst/doc/dndr_00_dice.html |only dndR-2.0.0/dndR/inst/doc/dndr_01_characters.R |only dndR-2.0.0/dndR/inst/doc/dndr_01_characters.Rmd |only dndR-2.0.0/dndR/inst/doc/dndr_01_characters.html |only dndR-2.0.0/dndR/inst/doc/dndr_02_creatures.R |only dndR-2.0.0/dndR/inst/doc/dndr_02_creatures.Rmd |only dndR-2.0.0/dndR/inst/doc/dndr_02_creatures.html |only dndR-2.0.0/dndR/inst/doc/dndr_03_spells.R |only dndR-2.0.0/dndR/inst/doc/dndr_03_spells.Rmd |only dndR-2.0.0/dndR/inst/doc/dndr_03_spells.html |only dndR-2.0.0/dndR/inst/doc/dndr_04_encounters.R |only dndR-2.0.0/dndR/inst/doc/dndr_04_encounters.Rmd |only dndR-2.0.0/dndR/inst/doc/dndr_04_encounters.html |only dndR-2.0.0/dndR/inst/doc/dndr_05_visuals.R |only dndR-2.0.0/dndR/inst/doc/dndr_05_visuals.Rmd |only dndR-2.0.0/dndR/inst/doc/dndr_05_visuals.html |only dndR-2.0.0/dndR/inst/doc/dndr_99_dmg-vs-dndr.R |only dndR-2.0.0/dndR/inst/doc/dndr_99_dmg-vs-dndr.Rmd |only dndR-2.0.0/dndR/inst/doc/dndr_99_dmg-vs-dndr.html |only dndR-2.0.0/dndR/man/creature_list.Rd |only dndR-2.0.0/dndR/man/creature_text.Rd |only dndR-2.0.0/dndR/man/creatures.Rd |only dndR-2.0.0/dndR/man/dndR-package.Rd | 14 ++- dndR-2.0.0/dndR/man/encounter_creator.Rd |only dndR-2.0.0/dndR/man/reroll.Rd |only dndR-2.0.0/dndR/man/roll.Rd | 16 ++- dndR-2.0.0/dndR/man/spell_list.Rd | 1 dndR-2.0.0/dndR/vignettes/dndr_00_dice.Rmd |only dndR-2.0.0/dndR/vignettes/dndr_01_characters.Rmd |only dndR-2.0.0/dndR/vignettes/dndr_02_creatures.Rmd |only dndR-2.0.0/dndR/vignettes/dndr_03_spells.Rmd |only dndR-2.0.0/dndR/vignettes/dndr_04_encounters.Rmd |only dndR-2.0.0/dndR/vignettes/dndr_05_visuals.Rmd |only dndR-2.0.0/dndR/vignettes/dndr_99_dmg-vs-dndr.Rmd |only 55 files changed, 177 insertions(+), 153 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to a three-way or four-way data array. See Harshman and Lundy (1994): <doi:10.1016/0167-9473(94)90132-5>. Uses component weights from one mode of a Parafac or Parafac2 model as features to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Allows for constraints on different tensor modes. Supports penalized logistic regression, support vector machine, random forest, feed-forward neural network, regularized discriminant analysis, and gradient boosting machine. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Implements parallel computing via the 'parallel' and 'doParallel' packages.
Author: Matthew A. Snodgress <snodg031@umn.edu>
Maintainer: Matthew A. Snodgress <snodg031@umn.edu>
Diff between cpfa versions 1.1-3 dated 2024-04-06 and 1.1-4 dated 2024-04-26
cpfa-1.1-3/cpfa/R/predict.cpfa.R |only cpfa-1.1-3/cpfa/R/print.cpfa.R |only cpfa-1.1-3/cpfa/R/tune.cpfa.R |only cpfa-1.1-3/cpfa/man/predict.cpfa.Rd |only cpfa-1.1-3/cpfa/man/print.cpfa.Rd |only cpfa-1.1-3/cpfa/man/tune.cpfa.Rd |only cpfa-1.1-4/cpfa/DESCRIPTION | 8 ++++---- cpfa-1.1-4/cpfa/MD5 | 18 ++++++------------ cpfa-1.1-4/cpfa/NAMESPACE | 2 -- cpfa-1.1-4/cpfa/R/kcv.gbm.R | 5 ++--- cpfa-1.1-4/cpfa/inst/ChangeLog.txt | 8 ++++++++ cpfa-1.1-4/cpfa/man/cpfa.Rd | 6 +++--- cpfa-1.1-4/cpfa/man/cpm.Rd | 4 ++-- 13 files changed, 25 insertions(+), 26 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.6.3 dated 2023-09-09 and 0.6.4 dated 2024-04-26
DESCRIPTION | 6 MD5 | 104 ++++--- NAMESPACE | 3 NEWS.md | 291 ++++++++------------- R/add_inactive_replicates.R |only R/as_bootstrap_design.R | 48 +-- R/as_jackknife_design.R | 80 ++++- R/calibrate_to_sample.R | 6 R/fays_generalized_replication.R | 63 ++-- R/generalized_bootstrap.R | 235 ++-------------- R/libraries_data.R | 58 ++-- R/lou_vax_data.R | 30 +- R/make_bootstrap_weights.R | 18 - R/quadratic_forms.R | 83 ++--- R/quadratic_forms_of_survey_design_objects.R | 46 +-- R/rescale_reps.R |only R/shuffle_replicates.R |only R/stack_replicate_designs.R | 44 ++- R/subsample_replicates.R |only R/summarize_rep_weights.R | 34 +- R/variance-estimators.R | 8 README.md | 190 +++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/bootstrap-replicates.R | 8 inst/doc/nonresponse-adjustments.R | 6 inst/doc/sample-based-calibration.R | 10 inst/doc/sample-based-calibration.html | 78 ++--- inst/doc/two-phase-sampling.R | 6 man/add_inactive_replicates.Rd |only man/as_bootstrap_design.Rd | 48 +-- man/as_fays_gen_rep_design.Rd | 55 ++- man/as_gen_boot_design.Rd | 47 +-- man/as_random_group_jackknife_design.Rd | 19 - man/calibrate_to_sample.Rd | 6 man/get_design_quad_form.Rd | 46 +-- man/libraries.Rd | 58 ++-- man/lou_pums_microdata.Rd | 22 - man/lou_vax_survey_control_totals.Rd | 8 man/make_ppswor_approx_matrix.Rd | 12 man/make_quad_form_matrix.Rd | 35 +- man/make_rwyb_bootstrap_weights.Rd | 18 - man/rescale_reps.Rd | 56 ++-- man/shift_weight.Rd | 46 +-- man/shuffle_replicates.Rd |only man/stack_replicate_designs.Rd | 140 +++++----- man/subsample_replicates.Rd |only man/summarize_rep_weights.Rd | 34 +- man/variance-estimators.Rd | 8 tests/testthat/test-add_inactive_replicates.R |only tests/testthat/test-calibrate_to_estimate.R | 4 tests/testthat/test-database-backed-designs.R | 12 tests/testthat/test-fays-generalized-replication.R | 16 + tests/testthat/test-generalized-bootstrap.R | 4 tests/testthat/test-random-group-jackknife.R | 37 ++ tests/testthat/test-shuffle_replicates.R |only tests/testthat/test-stack_replicate_designs.R | 31 ++ tests/testthat/test-subsample_replicates.R |only 58 files changed, 1078 insertions(+), 1139 deletions(-)
Title: TeX-to-HTML/MathML Translators TtH/TtM
Description: C source code and R wrappers for the tth/ttm TeX-to-HTML/MathML translators.
Author: Ian H. Hutchinson [aut] ,
Friedrich Leisch [aut] ,
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between tth versions 4.12-0-1 dated 2022-03-30 and 4.16-0 dated 2024-04-26
tth-4.12-0-1/tth/NEWS |only tth-4.12-0-1/tth/README |only tth-4.16-0/tth/DESCRIPTION | 25 tth-4.16-0/tth/MD5 | 20 tth-4.16-0/tth/NEWS.md |only tth-4.16-0/tth/R/tex2html.R | 4 tth-4.16-0/tth/README.md |only tth-4.16-0/tth/man/figures |only tth-4.16-0/tth/man/tth-package.Rd | 8 tth-4.16-0/tth/man/tth.Rd | 13 tth-4.16-0/tth/src/tth.c | 2690 ++++++++++++++++++------------------ tth-4.16-0/tth/src/ttm.c | 2822 +++++++++++++++++++------------------- 12 files changed, 2801 insertions(+), 2781 deletions(-)
Title: Generation of Artificial Binary Data
Description: Generation of correlated artificial binary data.
Author: Friedrich Leisch [aut] ,
Andreas Weingessel [aut],
Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between bindata versions 0.9-20 dated 2021-01-29 and 0.9-21 dated 2024-04-26
DESCRIPTION | 25 +++++++++++++++---------- MD5 | 6 +++--- R/sysdata.rda |binary inst/doc/artdatagen.pdf |binary 4 files changed, 18 insertions(+), 13 deletions(-)
Title: Analysing Convergent Evolution using the Wheatsheaf Index
Description: Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other unrelated but perhaps useful functions.
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle <kevin.arbuckle@swansea.ac.uk>
Diff between windex versions 2.0.7 dated 2023-12-14 and 2.0.8 dated 2024-04-26
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- R/mark.dist.R | 8 ++++---- R/nodeDist.R | 10 ++++++++-- R/test.windex.R | 4 ++-- R/treedatacheck.R | 35 ++++++++++++++++++++++++++++++----- R/windex.sim.test.R | 4 ++-- man/mark.dist.Rd | 5 ++++- man/test.windex.Rd | 8 +++++++- man/windex.sim.test.Rd | 8 +++++++- 11 files changed, 79 insertions(+), 33 deletions(-)
Title: Deconvolution of Spatial Transcriptomics Data Based on Neural
Networks
Description: Deconvolution of spatial transcriptomics data based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using deep learning and the meaningful information provided by single-cell RNA-seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2024) <doi:10.1093/bioinformatics/btae072> to get an overview of the method and see some examples of its performance.
Author: Diego Mananes [aut, cre] ,
Carlos Torroja [aut] ,
Fatima Sanchez-Cabo [aut]
Maintainer: Diego Mananes <dmananesc@cnic.es>
Diff between SpatialDDLS versions 1.0.1 dated 2024-03-15 and 1.0.2 dated 2024-04-26
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 6 ++++++ R/utils.R | 38 +++++++++++++++++++++++++++----------- inst/CITATION |only man/installTFpython.Rd | 15 ++++++++++++++- 6 files changed, 55 insertions(+), 19 deletions(-)
Title: A Wrapper of the JavaScript Library 'jsTree'
Description: Creates interactive trees that can be included in 'Shiny'
apps and R markdown documents. A tree allows to represent hierarchical
data (e.g. the contents of a directory). Similar to the 'shinyTree'
package but offers more features and options, such as the grid
extension, restricting the drag-and-drop behavior, and settings for
the search functionality. It is possible to attach some data to the
nodes of a tree and then to get these data in 'Shiny' when a node is
selected. Also provides a 'Shiny' gadget allowing to manipulate one or
more folders, and a 'Shiny' module allowing to navigate in the server
side file system.
Author: Stephane Laurent [aut, cre],
jQuery contributors [ctb, cph] ,
Ivan Bozhanov [ctb, cph] ,
Vedran Opacic [ctb, cph] ,
Avi Deitcher [ctb, cph] ,
Philip Hutchison [ctb, cph] ,
Terence Eden [ctb, cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between jsTreeR versions 2.5.0 dated 2023-12-19 and 2.6.0 dated 2024-04-26
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 12 ++++++++++++ R/jstree.R | 8 ++++++-- README.md | 21 +++++++++++++++++++++ inst/htmlwidgets/jstreer.js | 14 +++++++++++--- inst/htmlwidgets/lib/jstreegrid/jstreegrid.min.js | 2 +- man/jstree.Rd | 5 ++++- 8 files changed, 66 insertions(+), 18 deletions(-)
Title: Structural Data for Norway
Description: Datasets relating to population in municipalities, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2024.
Author: Richard Aubrey White [aut, cre]
,
Chi Zhang [aut] ,
CSIDS [cph]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between csdata versions 2024.1.17 dated 2024-01-18 and 2024.4.26 dated 2024-04-26
DESCRIPTION | 6 MD5 | 14 NEWS.md | 8 R/nor_population_by_age_cats.R | 7 R/sysdata.rda |binary inst/doc/csdata.html | 318 ++++++++-------- inst/doc/locations_norway.html | 106 ++--- inst/doc/population_norway.html | 764 ++++++++++++++++++++-------------------- 8 files changed, 628 insertions(+), 595 deletions(-)
Title: Black Marble Data and Statistics
Description: Geographically referenced data and statistics of nighttime lights from NASA Black Marble <https://blackmarble.gsfc.nasa.gov/>.
Author: Robert Marty [aut, cre] ,
Gabriel Stefanini Vicente [aut]
Maintainer: Robert Marty <rmarty@worldbank.org>
Diff between blackmarbler versions 0.1.2 dated 2024-01-10 and 0.2.0 dated 2024-04-26
DESCRIPTION | 13 +- MD5 | 15 +-- NAMESPACE | 4 R/blackmarbler.R | 259 ++++++++++++++++++++++++++++++++++-------------------- README.md | 47 ++++----- man/bm_extract.Rd | 12 +- man/bm_raster.Rd | 12 +- tests |only 8 files changed, 226 insertions(+), 136 deletions(-)
Title: Fit Hill Dose Response Models
Description: Evaluate, fit, and analyze Hill dose response models (Goutelle et
al., 2008 <doi:10.1111/j.1472-8206.2008.00633.x>), also sometimes referred
to as four-parameter log-logistic models. Includes tools to invert Hill
models, select models based on the Akaike information criterion
(Akaike, 1974 <doi:10.1109/TAC.1974.1100705>) or Bayesian information
criterion (Schwarz, 1978 <https://www.jstor.org/stable/2958889>), and
construct bootstrapped confidence intervals both
on the Hill model parameters and values derived from the Hill model
parameters.
Author: Anang Shelat [aut],
Nathaniel Twarog [aut, cre]
Maintainer: Nathaniel Twarog <nathaniel.twarog@stjude.org>
Diff between basicdrm versions 0.1.0 dated 2024-02-16 and 0.3.0 dated 2024-04-26
DESCRIPTION | 6 - MD5 | 18 +-- NAMESPACE | 4 R/bestHillModel.R | 57 ++++++++- R/bootHillModel.R | 2 R/boundedOptimize.R | 6 - R/fitHillModel.R | 112 ++++++++++++++---- R/hillModel.R | 278 +++++++++++++++++++++++------------------------ man/findBestHillModel.Rd | 24 +++- man/fitHillModel.Rd | 27 +++- 10 files changed, 330 insertions(+), 204 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 2.3 dated 2022-10-18 and 2.4 dated 2024-04-26
breakfast-2.3/breakfast/man/dup.merge.Rd |only breakfast-2.4/breakfast/DESCRIPTION | 15 breakfast-2.4/breakfast/MD5 | 88 breakfast-2.4/breakfast/NAMESPACE | 6 breakfast-2.4/breakfast/R/IDETECT.R | 1018 ++ breakfast-2.4/breakfast/R/IDETECT_seq.R | 191 breakfast-2.4/breakfast/R/NOT.R | 39 breakfast-2.4/breakfast/R/RcppExports.R | 66 breakfast-2.4/breakfast/R/TGUH.R | 349 - breakfast-2.4/breakfast/R/WBS.R | 48 breakfast-2.4/breakfast/R/WBS2.R | 34 breakfast-2.4/breakfast/R/breakfast-package.R | 20 breakfast-2.4/breakfast/R/fixednum.R |only breakfast-2.4/breakfast/R/ic.R | 56 breakfast-2.4/breakfast/R/local_prune.R | 44 breakfast-2.4/breakfast/R/main.R | 228 breakfast-2.4/breakfast/R/misc.R | 268 breakfast-2.4/breakfast/R/sdll.R | 107 breakfast-2.4/breakfast/R/thresholding.R | 154 breakfast-2.4/breakfast/R/tools.R | 6 breakfast-2.4/breakfast/R/wemgsc.R |only breakfast-2.4/breakfast/R/zzz.R | 2 breakfast-2.4/breakfast/build/vignette.rds |binary breakfast-2.4/breakfast/inst/doc/breakfast-vignette.R | 12 breakfast-2.4/breakfast/inst/doc/breakfast-vignette.Rmd | 5162 ++++++++------- breakfast-2.4/breakfast/inst/doc/breakfast-vignette.html | 4667 +++++++++++-- breakfast-2.4/breakfast/man/breakfast-package.Rd | 18 breakfast-2.4/breakfast/man/breakfast.Rd | 84 breakfast-2.4/breakfast/man/model.fixednum.Rd |only breakfast-2.4/breakfast/man/model.gsa.Rd |only breakfast-2.4/breakfast/man/model.ic.Rd | 17 breakfast-2.4/breakfast/man/model.lp.Rd | 14 breakfast-2.4/breakfast/man/model.sdll.Rd | 31 breakfast-2.4/breakfast/man/model.thresh.Rd | 30 breakfast-2.4/breakfast/man/plot.breakfast.cpts.Rd | 2 breakfast-2.4/breakfast/man/print.breakfast.cpts.Rd | 2 breakfast-2.4/breakfast/man/sol.idetect.Rd | 24 breakfast-2.4/breakfast/man/sol.idetect_seq.Rd | 20 breakfast-2.4/breakfast/man/sol.not.Rd | 10 breakfast-2.4/breakfast/man/sol.tguh.Rd | 7 breakfast-2.4/breakfast/man/sol.wbs.Rd | 13 breakfast-2.4/breakfast/man/sol.wbs2.Rd | 9 breakfast-2.4/breakfast/man/sol.wcm.Rd |only breakfast-2.4/breakfast/src/RcppExports.cpp | 95 breakfast-2.4/breakfast/src/contrasts.c | 4 breakfast-2.4/breakfast/src/exhaust_bic.cpp | 17 breakfast-2.4/breakfast/src/not_wrapper.cpp | 1 breakfast-2.4/breakfast/vignettes/breakfast-vignette.Rmd | 5162 ++++++++------- 48 files changed, 11699 insertions(+), 6441 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-16 2.3.2
2023-06-29 2.3.1
Title: Functions for Tidy Analysis and Generation of Random Data
Description: To make it easy to generate random numbers based upon the underlying stats
distribution functions. All data is returned in a tidy and structured
format making working with the data simple and straight forward. Given that the
data is returned in a tidy 'tibble' it lends itself to working with the rest of the
'tidyverse'.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between TidyDensity versions 1.3.0 dated 2024-01-09 and 1.4.0 dated 2024-04-26
DESCRIPTION | 12 MD5 | 182 +++-- NAMESPACE | 19 NEWS.md | 21 R/00_global_variables.R | 2 R/autoplot-combined-dist.R | 2 R/autoplot-four-graphs.R | 2 R/autoplot-multi-dist.R | 2 R/combine-multi-single-dist-tbl.R | 31 R/est-param-chisq.R |only R/utils-aic-beta.R |only R/utils-aic-binomial.R |only R/utils-aic-cauchy.R |only R/utils-aic-chisq.R |only R/utils-aic-exponential.R |only R/utils-aic-gamma.R |only R/utils-aic-geometric.R |only R/utils-aic-hypergeometric.R |only R/utils-aic-logistic.R |only R/utils-aic-lognormal.R |only R/utils-aic-normal.R |only R/utils-aic-pareto.R |only R/utils-aic-poisson.R |only R/utils-aic-uniform.R |only R/utils-aic-weibull.R |only R/utils-check-dupe-rows.R |only R/utils-distribution-comparison.R | 698 +++++++++++--------- R/utils-mcmc-sampling.R |only R/utils-quantile-normalize.R |only README.md | 24 inst/doc/getting-started.html | 40 - man/check_duplicate_rows.Rd |only man/convert_to_ts.Rd | 21 man/figures/README-more_than_nine_simulations-1.png |binary man/figures/README-more_than_nine_simulations-2.png |binary man/figures/README-more_than_nine_simulations-3.png |binary man/figures/README-more_than_nine_simulations-4.png |binary man/figures/README-plot_density-1.png |binary man/figures/README-plot_density-2.png |binary man/figures/README-plot_density-3.png |binary man/figures/README-plot_density-4.png |binary man/quantile_normalize.Rd |only man/tidy_beta.Rd | 4 man/tidy_burr.Rd | 4 man/tidy_cauchy.Rd | 4 man/tidy_chisquare.Rd | 5 man/tidy_combined_autoplot.Rd | 2 man/tidy_distribution_comparison.Rd | 5 man/tidy_exponential.Rd | 4 man/tidy_f.Rd | 4 man/tidy_four_autoplot.Rd | 2 man/tidy_gamma.Rd | 4 man/tidy_generalized_beta.Rd | 4 man/tidy_generalized_pareto.Rd | 6 man/tidy_geometric.Rd | 4 man/tidy_inverse_burr.Rd | 4 man/tidy_inverse_exponential.Rd | 4 man/tidy_inverse_gamma.Rd | 4 man/tidy_inverse_normal.Rd | 4 man/tidy_inverse_pareto.Rd | 6 man/tidy_inverse_weibull.Rd | 4 man/tidy_logistic.Rd | 4 man/tidy_lognormal.Rd | 4 man/tidy_mcmc_sampling.Rd |only man/tidy_multi_dist_autoplot.Rd | 2 man/tidy_multi_single_dist.Rd | 12 man/tidy_normal.Rd | 4 man/tidy_paralogistic.Rd | 4 man/tidy_pareto.Rd | 2 man/tidy_pareto1.Rd | 2 man/tidy_t.Rd | 2 man/tidy_triangular.Rd | 2 man/tidy_uniform.Rd | 4 man/tidy_weibull.Rd | 4 man/tidy_zero_truncated_geometric.Rd | 4 man/util_bernoulli_param_estimate.Rd | 1 man/util_beta_aic.Rd |only man/util_beta_param_estimate.Rd | 1 man/util_binomial_aic.Rd |only man/util_binomial_param_estimate.Rd | 1 man/util_burr_param_estimate.Rd | 1 man/util_cauchy_aic.Rd |only man/util_cauchy_param_estimate.Rd | 1 man/util_chisq_aic.Rd |only man/util_chisquare_param_estimate.Rd |only man/util_chisquare_stats_tbl.Rd | 3 man/util_exponential_aic.Rd |only man/util_exponential_param_estimate.Rd | 1 man/util_gamma_aic.Rd |only man/util_gamma_param_estimate.Rd | 1 man/util_geometric_aic.Rd |only man/util_geometric_param_estimate.Rd | 1 man/util_hypergeometric_aic.Rd |only man/util_hypergeometric_param_estimate.Rd | 1 man/util_logistic_aic.Rd |only man/util_logistic_param_estimate.Rd | 1 man/util_lognormal_aic.Rd |only man/util_lognormal_param_estimate.Rd | 1 man/util_negative_binomial_param_estimate.Rd | 1 man/util_normal_aic.Rd |only man/util_normal_param_estimate.Rd | 1 man/util_pareto_aic.Rd |only man/util_pareto_param_estimate.Rd | 3 man/util_pareto_stats_tbl.Rd | 2 man/util_poisson_aic.Rd |only man/util_poisson_param_estimate.Rd | 1 man/util_triangular_param_estimate.Rd | 1 man/util_uniform_aic.Rd |only man/util_uniform_param_estimate.Rd | 1 man/util_weibull_aic.Rd |only man/util_weibull_param_estimate.Rd | 1 111 files changed, 727 insertions(+), 482 deletions(-)
Title: Test Helpers for 'httr2'
Description: Testing and documenting code that communicates with remote servers
can be painful. This package helps with writing tests for packages that
use 'httr2'. It enables testing all of the logic
on the R sides of the API without requiring access to the
remote service, and it also allows recording real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables writing vignettes and other dynamic documents that can be
distributed without access to a live server.
Author: Neal Richardson [aut, cre] ,
Jonathan Keane [ctb],
Maelle Salmon [ctb]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest2 versions 1.0.0 dated 2023-11-07 and 1.1.0 dated 2024-04-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/capture-requests.R | 13 +++++++++---- man/httptest2.Rd | 2 +- tests/testthat/test-capture-requests.R | 7 +++++++ 6 files changed, 31 insertions(+), 14 deletions(-)
Title: Helper Functions for Structural Equation Modeling
Description: An assortment of helper functions for doing structural equation
modeling, mainly by 'lavaan' for now. Most of them are time-saving functions
for common tasks in doing structural equation modeling and reading the
output. This package is not for functions that implement advanced statistical
procedures. It is a light-weight package for simple functions that do simple
tasks conveniently, with as few dependencies as possible.
Author: Shu Fai Cheung [aut, cre]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semhelpinghands versions 0.1.10 dated 2024-03-12 and 0.1.11 dated 2024-04-26
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 13 +++++++++++++ R/ptable_to_syntax.R | 2 +- R/standardizedSolution_boot_ci.R | 4 +--- README.md | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/semhelpinghands.html | 11 ++++++++--- man/ptable_to_syntax.Rd | 2 +- tests/testthat/test-ptable_to_syntax.R | 4 ++-- tests/testthat/test-ptable_to_syntax_incomplete.R | 4 ++-- 12 files changed, 43 insertions(+), 27 deletions(-)
More information about semhelpinghands at CRAN
Permanent link
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 1.4.0 dated 2024-02-02 and 1.4.5 dated 2024-04-26
DESCRIPTION | 8 MD5 | 26 NEWS.md | 52 R/common.r | 4 R/lsa.bench.r | 4 R/lsa.bin.log.reg.r | 1250 +-- R/lsa.convert.data.r | 3 R/lsa.convert.data2.r | 3 R/lsa.crosstabs.r | 2 R/lsa.lin.reg.r | 1238 +-- R/lsa.pcts.means.r | 2 R/lsa.prctls.r | 4 inst/shiny/GUI/server.r |17333 ++++++++++++++++++++++++------------------------ inst/shiny/GUI/ui.r | 1344 ++- 14 files changed, 10787 insertions(+), 10486 deletions(-)
Title: Partitioning the Drivers of Stability of Ecological Communities
Description: Contains the basic functions to apply the unified framework
for partitioning the drivers of stability of ecological communities.
Segrestin et al. (2024) <doi:10.1111/geb.13828>.
Author: Jules Segrestin [aut, cre, cph]
Maintainer: Jules Segrestin <jsegrestin@gmail.com>
Diff between comstab versions 0.0.2 dated 2024-03-14 and 0.0.3 dated 2024-04-26
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 6 ++++++ R/partitionR.R | 36 ++++++++++++++++++++++++------------ inst |only man/partitionR.Rd | 2 +- 6 files changed, 39 insertions(+), 20 deletions(-)
Title: Affinity Propagation Clustering
Description: Implements Affinity Propagation clustering introduced by Frey and
Dueck (2007) <DOI:10.1126/science.1136800>. The algorithms are largely
analogous to the 'Matlab' code published by Frey and Dueck.
The package further provides leveraged affinity propagation and an
algorithm for exemplar-based agglomerative clustering that can also be
used to join clusters obtained from affinity propagation. Various
plotting functions are available for analyzing clustering results.
Author: Ulrich Bodenhofer [aut, cre],
Johannes Palme [ctb],
Chrats Melkonian [ctb],
Andreas Kothmeier [aut],
Nikola Kostic [ctb]
Maintainer: Ulrich Bodenhofer <ulrich@bodenhofer.com>
Diff between apcluster versions 1.4.12 dated 2024-04-19 and 1.4.13 dated 2024-04-26
DESCRIPTION | 8 +++--- MD5 | 52 +++++++++++++++++++++-------------------- README.md |only TODO |only inst/CITATION | 4 +-- inst/NEWS | 3 ++ inst/doc/apcluster.Rnw | 2 - inst/doc/apcluster.pdf |binary man/APResult-class.Rd | 7 ++--- man/AggExResult-class.Rd | 5 +-- man/ExClust-class.Rd | 5 +-- man/aggExCluster-methods.Rd | 5 +-- man/apcluster-methods.Rd | 7 ++--- man/apcluster-package.Rd | 5 +-- man/apclusterDemo.Rd | 5 +-- man/apclusterK-methods.Rd | 5 +-- man/apclusterL-methods.Rd | 5 +-- man/coerce-methods.Rd | 5 +-- man/conversions.Rd | 5 +-- man/cutree-methods.Rd | 5 +-- man/heatmap-methods.Rd | 5 +-- man/labels-methods.Rd | 5 +-- man/plot-methods.Rd | 5 +-- man/preferenceRange-methods.Rd | 5 +-- man/show-methods.Rd | 5 +-- man/similarities.Rd | 5 +-- man/sort-methods.Rd | 5 +-- vignettes/apcluster.Rnw | 2 - 28 files changed, 78 insertions(+), 92 deletions(-)
Title: Robust Rank Correlation Coefficient and Test
Description: Provides the robust gamma rank correlation coefficient as introduced by
Bodenhofer, Krone, and Klawonn (2013) <DOI:10.1016/j.ins.2012.11.026>
along with a permutation-based rank correlation test.
The rank correlation coefficient and the test are explicitly
designed for dealing with noisy numerical data.
Author: Martin Krone [aut], Ulrich Bodenhofer [aut,cre]
Maintainer: Ulrich Bodenhofer <ulrich@bodenhofer.com>
Diff between rococo versions 1.1.8 dated 2024-04-22 and 1.1.9 dated 2024-04-26
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- build/partial.rdb |only inst/NEWS | 3 +++ inst/doc/rococo.pdf |binary man/RococoTestResult-class.Rd | 10 +++++----- man/gauss.cor.Rd | 11 ++++++----- man/gauss.cor.test-methods.Rd | 11 ++++++----- man/rococo.Rd | 10 +++++----- man/rococo.test-methods.Rd | 8 ++++---- 10 files changed, 42 insertions(+), 36 deletions(-)
Title: QTL Mapping and Hotspots Detection
Description: For QTL mapping, this package comprises several functions designed to execute diverse
tasks, such as simulating or analyzing data, calculating significance thresholds, and
visualizing QTL mapping results. The single-QTL or multiple-QTL method, which enables
the fitting and comparison of various statistical models, is employed to analyze the
data for estimating QTL parameters. The models encompass linear regression, permutation
tests, normal mixture models, and truncated normal mixture models. The Gaussian stochastic
process is utilized to compute significance thresholds for QTL detection on a genetic
linkage map within experimental populations. Two types of data, complete genotyping, and
selective genotyping data from various experimental populations, including backcross, F2,
recombinant inbred (RI) populations, and advanced intercrossed (AI) populations, are
considered in the QTL mapping analysis. For QTL hotspot detection, statistical methods can
be developed based on either utilizin [...truncated...]
Author: Ping-Yuan Chung [cre],
Chen-Hung Kao [aut],
Y.-T. Guo [aut],
H.-N. Ho [aut],
H.-I. Lee [aut],
P.-Y. Wu [aut],
M.-H. Yang [aut],
M.-H. Zeng [aut]
Maintainer: Ping-Yuan Chung <pychung@webmail.stat.sinica.edu.tw>
Diff between QTLEMM versions 1.5.2 dated 2024-03-13 and 1.5.3 dated 2024-04-26
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/EQF.permu.R | 8 ++++---- R/EQF.plot.R | 6 +++--- R/LOD.QTLdetect.R | 5 ++--- R/Qhot.R | 2 +- inst/extdata/LODexample.RDATA |binary man/EQF.permu.Rd | 2 +- man/LOD.QTLdetect.Rd | 2 +- 9 files changed, 24 insertions(+), 25 deletions(-)
Title: Fast Change Point Detection via Sequential Gradient Descent
Description: Implements fast change point detection algorithm based on the
paper "Sequential Gradient Descent and Quasi-Newton's Method for
Change-Point Analysis" by Xianyang Zhang, Trisha Dawn
<https://proceedings.mlr.press/v206/zhang23b.html>. The algorithm is
based on dynamic programming with pruning and sequential gradient
descent. It is able to detect change points a magnitude faster than
the vanilla Pruned Exact Linear Time(PELT). The package includes
examples of linear regression, logistic regression, Poisson
regression, penalized linear regression data, and whole lot more
examples with custom cost function in case the user wants to use their
own cost function.
Author: Xingchi Li [aut, cre, cph] ,
Xianyang Zhang [aut, cph]
Maintainer: Xingchi Li <anthony.li@stat.tamu.edu>
Diff between fastcpd versions 0.14.1 dated 2024-04-18 and 0.14.3 dated 2024-04-26
DESCRIPTION | 9 MD5 | 123 +++--- NEWS.md | 8 R/fastcpd.R | 2 R/fastcpd_class.R | 13 inst/doc/comparison-packages.html | 30 + inst/doc/comparison-pelt.R | 4 inst/doc/comparison-pelt.Rmd | 2 inst/doc/comparison-pelt.html | 108 ++--- man/bitcoin.Rd | 73 +-- man/fastcpd.Rd | 211 +++++----- man/fastcpd_binomial.Rd | 26 - man/fastcpd_lasso.Rd | 107 ++--- man/fastcpd_lm.Rd | 54 +- man/fastcpd_mean.Rd | 20 man/fastcpd_meanvariance.Rd | 53 +- man/fastcpd_poisson.Rd | 32 - man/fastcpd_variance.Rd | 26 - man/plot.Rd | 32 - man/transcriptome.Rd | 58 +- man/uk_seatbelts.Rd | 76 ++- man/variance_lm.Rd | 53 +- man/variance_mean.Rd | 18 man/well_log.Rd | 47 +- src/fastcpd_class_cost.cc | 6 src/fastcpd_class_nll.cc |only src/fastcpd_class_private.cc | 238 ----------- src/fastcpd_class_public.cc | 265 ------------- src/fastcpd_classes.h | 112 ++++- src/fastcpd_types.h | 9 src/test-functions.cc | 14 tests/testthat/examples/data-bitcoin.txt | 73 +-- tests/testthat/examples/data-transcriptome.txt | 58 +- tests/testthat/examples/data-uk_seatbelts.R | 76 ++- tests/testthat/examples/data-well_log-quantile.txt | 47 +- tests/testthat/examples/fastcpd_1.R | 32 - tests/testthat/examples/fastcpd_2.R | 107 ++--- tests/testthat/examples/fastcpd_4.txt | 70 +-- tests/testthat/examples/fastcpd_binomial.R | 26 - tests/testthat/examples/fastcpd_lasso.txt | 107 ++--- tests/testthat/examples/fastcpd_lm.R | 54 +- tests/testthat/examples/fastcpd_mean.R | 20 tests/testthat/examples/fastcpd_meanvariance_1.R | 27 - tests/testthat/examples/fastcpd_meanvariance_2.R | 26 - tests/testthat/examples/fastcpd_poisson.txt | 32 - tests/testthat/examples/fastcpd_variance_2.R | 26 - tests/testthat/examples/plot.R | 32 - tests/testthat/examples/variance_lm.R | 53 +- tests/testthat/examples/variance_mean.R | 18 tests/testthat/test-examples-fastcpd_1.R | 1 tests/testthat/test-examples-fastcpd_2.R | 2 tests/testthat/test-examples-fastcpd_3.R | 3 tests/testthat/test-examples-fastcpd_binomial.R | 1 tests/testthat/test-examples-fastcpd_mean-time_1.R | 2 tests/testthat/test-examples-fastcpd_mean-time_2.R | 2 tests/testthat/test-examples-fastcpd_mean-time_3.R | 2 tests/testthat/test-examples-fastcpd_meanvariance-time_1.R | 2 tests/testthat/test-examples-fastcpd_meanvariance-time_2.R | 2 tests/testthat/test-examples-fastcpd_variance-time_1.R | 2 tests/testthat/test-examples-fastcpd_variance-time_2.R | 2 tests/testthat/test-fastcpd-class.R | 4 tests/testthat/test-vignettes-comparison-pelt.R | 10 vignettes/comparison-pelt.Rmd | 2 63 files changed, 1271 insertions(+), 1479 deletions(-)
Title: Yatchew (1997), De Chaisemartin & D'Haultfoeuille (2024)
Linearity Test
Description: Test of linearity originally proposed by Yatchew (1997) <doi:10.1016/S0165-1765(97)00218-8> and improved by de Chaisemartin & D'Haultfoeuille (2024) <doi:10.2139/ssrn.4284811> to be robust under heteroskedasticity.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut],
Xavier D'Haultfoeuille [aut]
Maintainer: Diego Ciccia <diego.ciccia@sciencespo.fr>
Diff between YatchewTest versions 1.0.0 dated 2024-04-04 and 1.0.2 dated 2024-04-26
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/print.R | 16 ++++++++-------- R/yatchew_test.R | 20 +++++++++++++------- man/yatchew_test.Rd | 2 +- man/yatchew_test.data.frame.Rd | 16 +++++++++++----- 6 files changed, 44 insertions(+), 32 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb],
Shota Ochi [ctb],
Aaron Robotham [cre],
Rodrigo Tobar [ctb]
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between imager versions 0.45.8 dated 2024-02-20 and 1.0.1 dated 2024-04-26
DESCRIPTION | 18 MD5 | 18 R/datasets.R | 2 inst/doc/gettingstarted.html | 6 inst/doc/pixsets.html | 4 inst/include/CImg.h |17950 +++++++++++++++++++++++++++--------------- man/boats.Rd | 2 src/Makevars.in | 1 src/Makevars.ucrt | 14 tests/testthat/test_cpp_api.R | 2 10 files changed, 11629 insertions(+), 6388 deletions(-)
Title: Linear and Nonlinear Methods for Analyzing Daily and Monthly
Dendroclimatological Data
Description: Provides novel dendroclimatological methods, primarily used by the
Tree-ring research community. There are four core functions. The first one is
daily_response(), which finds the optimal sequence of days that are related
to one or more tree-ring proxy records. Similar function is daily_response_seascorr(),
which implements partial correlations in the analysis of daily response functions.
For the enthusiast of monthly data, there is monthly_response() function.
The last core function is compare_methods(), which effectively compares several
linear and nonlinear regression algorithms on the task of climate reconstruction.
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between dendroTools versions 1.2.11 dated 2024-01-25 and 1.2.13 dated 2024-04-26
dendroTools-1.2.11/dendroTools/R/plot_specific.R |only dendroTools-1.2.11/dendroTools/man/plot_specific.Rd |only dendroTools-1.2.13/dendroTools/DESCRIPTION | 6 dendroTools-1.2.13/dendroTools/MD5 | 68 - dendroTools-1.2.13/dendroTools/NAMESPACE | 1 dendroTools-1.2.13/dendroTools/NEWS.md | 11 dendroTools-1.2.13/dendroTools/R/calculate_metrics.R | 2 dendroTools-1.2.13/dendroTools/R/compare_methods.R | 120 +- dendroTools-1.2.13/dendroTools/R/count_ones.R | 2 dendroTools-1.2.13/dendroTools/R/daily_response.R | 550 +++++----- dendroTools-1.2.13/dendroTools/R/daily_response_seascorr.R | 359 +++--- dendroTools-1.2.13/dendroTools/R/generics.R | 6 dendroTools-1.2.13/dendroTools/R/generics2.R | 8 dendroTools-1.2.13/dendroTools/R/glimpse_daily_data.R | 8 dendroTools-1.2.13/dendroTools/R/monthly_response.R | 457 ++++---- dendroTools-1.2.13/dendroTools/R/monthly_response_seascorr.R | 283 ++--- dendroTools-1.2.13/dendroTools/R/plot_extreme.R | 76 + dendroTools-1.2.13/dendroTools/R/plot_heatmap.R | 6 dendroTools-1.2.13/dendroTools/R/round_df.R | 2 dendroTools-1.2.13/dendroTools/inst/doc/Compare_different_regression_methods.html | 4 dendroTools-1.2.13/dendroTools/inst/doc/Examples_with_daily_climate_data.R | 57 - dendroTools-1.2.13/dendroTools/inst/doc/Examples_with_daily_climate_data.Rmd | 78 - dendroTools-1.2.13/dendroTools/inst/doc/Examples_with_daily_climate_data.html | 135 -- dendroTools-1.2.13/dendroTools/man/calculate_metrics.Rd | 2 dendroTools-1.2.13/dendroTools/man/compare_methods.Rd | 82 - dendroTools-1.2.13/dendroTools/man/count_ones.Rd | 2 dendroTools-1.2.13/dendroTools/man/daily_response.Rd | 203 +-- dendroTools-1.2.13/dendroTools/man/daily_response_seascorr.Rd | 153 +- dendroTools-1.2.13/dendroTools/man/glimpse_daily_data.Rd | 8 dendroTools-1.2.13/dendroTools/man/monthly_response.Rd | 132 -- dendroTools-1.2.13/dendroTools/man/monthly_response_seascorr.Rd | 95 - dendroTools-1.2.13/dendroTools/man/plot_extreme.Rd | 8 dendroTools-1.2.13/dendroTools/man/plot_heatmap.Rd | 6 dendroTools-1.2.13/dendroTools/man/round_df.Rd | 2 dendroTools-1.2.13/dendroTools/tests/testthat/test_general.R | 62 - dendroTools-1.2.13/dendroTools/vignettes/Examples_with_daily_climate_data.Rmd | 78 - 36 files changed, 1324 insertions(+), 1748 deletions(-)
Title: Tools to Visualize CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafvis' R-package provides a collection of R-operators for the analysis and
visualization of CM SAF NetCDF data.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafvis versions 1.2.3 dated 2024-01-26 and 1.2.6 dated 2024-04-26
cmsafvis-1.2.3/cmsafvis/R/cmsafvis-package.R |only cmsafvis-1.2.6/cmsafvis/DESCRIPTION | 8 cmsafvis-1.2.6/cmsafvis/MD5 | 15 cmsafvis-1.2.6/cmsafvis/NEWS.md | 13 cmsafvis-1.2.6/cmsafvis/R/quicklook.R | 233 ++++++++++---- cmsafvis-1.2.6/cmsafvis/inst/WORDLIST | 101 ++---- cmsafvis-1.2.6/cmsafvis/inst/extdata/quicklook_config.yml | 185 ++++------- cmsafvis-1.2.6/cmsafvis/man/cmsafvis-package.Rd | 13 cmsafvis-1.2.6/cmsafvis/man/quicklook.Rd | 1 9 files changed, 324 insertions(+), 245 deletions(-)
Title: Fast and Exact Computation of Gaussian Stochastic Process
Description: Implements fast and exact computation of Gaussian stochastic process with the Matern kernel using forward filtering and backward smoothing algorithm. It allows for the cases with or without a noise. See the reference: Mengyang Gu and Yanxun Xu, 2020, Journal of Computational and Graphical Statistics.
Author: Mengyang Gu [aut, cre]
Maintainer: Mengyang Gu <mengyang@pstat.ucsb.edu>
Diff between FastGaSP versions 0.5.2 dated 2021-09-02 and 0.5.3 dated 2024-04-26
CHANGELOG | 6 ++++++ DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 1 - build/partial.rdb |binary man/Get_C_R_K_Q.Rd | 1 - man/Sample_KF_post.Rd | 3 --- man/show.fgasp.Rd | 2 +- src/RcppExports.cpp | 5 +++++ 9 files changed, 26 insertions(+), 20 deletions(-)
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafops' R-package provides a collection of R-operators for the analysis and
manipulation of CM SAF NetCDF formatted data. Other CF conform NetCDF data with time,
longitude and latitude dimension should be applicable, but there is no guarantee for
an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox& [...truncated...]
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafops versions 1.3.0 dated 2023-09-18 and 1.4.0 dated 2024-04-26
DESCRIPTION | 8 - MD5 | 136 ++++++++++----------- NAMESPACE | 2 NEWS.md | 6 R/add_grid_info.R | 33 +++-- R/cmsaf.cat.R | 19 ++ R/map_regular.R |only R/remap.R | 12 + R/ymonmedian.R |only R/ymonx_wrapper.R | 7 - inst/WORDLIST | 200 ++++++++++++++----------------- man/acsaf_box_mergetime.Rd | 1 man/add_grid_info.Rd | 1 man/box_mergetime.Rd | 1 man/cmsaf.abs.Rd | 8 - man/cmsaf.add.Rd | 6 man/cmsaf.addc.Rd | 6 man/cmsaf.detrend.Rd | 4 man/cmsaf.div.Rd | 6 man/cmsaf.divc.Rd | 6 man/cmsaf.mk.test.Rd | 4 man/cmsaf.mul.Rd | 6 man/cmsaf.mulc.Rd | 6 man/cmsaf.regres.Rd | 4 man/cmsaf.sub.Rd | 6 man/cmsaf.subc.Rd | 6 man/cmsaf.transform.coordinate.system.Rd | 1 man/divdpm.Rd | 8 - man/extract.level.Rd | 2 man/extract.period.Rd | 2 man/levbox_mergetime.Rd | 1 man/map_regular.Rd |only man/mon.anomaly.Rd | 1 man/mon_num_above.Rd | 1 man/mon_num_below.Rd | 1 man/mon_num_equal.Rd | 1 man/monavg.Rd | 1 man/mondaymean.Rd | 1 man/monmax.Rd | 1 man/monmean.Rd | 1 man/monmin.Rd | 1 man/monpctl.Rd | 1 man/monsd.Rd | 1 man/monsum.Rd | 1 man/monvar.Rd | 1 man/muldpm.Rd | 8 - man/multimonmean.Rd | 1 man/multimonsum.Rd | 1 man/num_above.Rd | 4 man/num_below.Rd | 4 man/num_equal.Rd | 4 man/remap.Rd | 7 - man/sellonlatbox.Rd | 2 man/selmon.Rd | 2 man/selperiod.Rd | 2 man/seltime.Rd | 2 man/selyear.Rd | 2 man/timavg.Rd | 4 man/timmax.Rd | 4 man/timmean.Rd | 4 man/timmin.Rd | 4 man/timpctl.Rd | 4 man/timsd.Rd | 4 man/timsum.Rd | 4 man/ymonmax.Rd | 1 man/ymonmean.Rd | 1 man/ymonmedian.Rd |only man/ymonmin.Rd | 1 man/ymonsd.Rd | 1 man/ymonsum.Rd | 1 tests/testthat/test_cmsaf.cat.R | 8 - 71 files changed, 335 insertions(+), 266 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package 'arules' with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration. Michael Hahsler (2017) <doi:10.32614/RJ-2017-047>.
Author: Michael Hahsler [aut, cre, cph]
,
Giallanza Tyler [ctb],
Sudheer Chelluboina [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.5-2 dated 2023-03-07 and 1.5.3 dated 2024-04-26
arulesViz-1.5-2/arulesViz/R/groupedmatrix.R |only arulesViz-1.5-2/arulesViz/R/matrix.R |only arulesViz-1.5-2/arulesViz/man/plot.Rd |only arulesViz-1.5.3/arulesViz/DESCRIPTION | 24 arulesViz-1.5.3/arulesViz/MD5 | 82 - arulesViz-1.5.3/arulesViz/NAMESPACE | 65 - arulesViz-1.5.3/arulesViz/NEWS.md | 7 arulesViz-1.5.3/arulesViz/R/AAA_arulesViz-package.R |only arulesViz-1.5.3/arulesViz/R/check_installed.R | 36 arulesViz-1.5.3/arulesViz/R/colors.R | 12 arulesViz-1.5.3/arulesViz/R/doubledecker.R | 53 arulesViz-1.5.3/arulesViz/R/gInteraction.R | 236 ++- arulesViz-1.5.3/arulesViz/R/gPlots.R | 244 ++-- arulesViz-1.5.3/arulesViz/R/ggplot2.R | 187 +-- arulesViz-1.5.3/arulesViz/R/ggraph.R | 195 +-- arulesViz-1.5.3/arulesViz/R/graph.R | 105 + arulesViz-1.5.3/arulesViz/R/igraph.R | 211 +-- arulesViz-1.5.3/arulesViz/R/inspectDT.R | 87 + arulesViz-1.5.3/arulesViz/R/limit_associations.R | 20 arulesViz-1.5.3/arulesViz/R/map.R | 39 arulesViz-1.5.3/arulesViz/R/paracoord.R | 183 +-- arulesViz-1.5.3/arulesViz/R/parameters.R | 61 - arulesViz-1.5.3/arulesViz/R/plot.R | 596 ++++++++-- arulesViz-1.5.3/arulesViz/R/plotly.R | 228 ++- arulesViz-1.5.3/arulesViz/R/ruleExplorer.R | 414 +++--- arulesViz-1.5.3/arulesViz/R/rules2groupedmatrix.R |only arulesViz-1.5.3/arulesViz/R/rules2matrix.R |only arulesViz-1.5.3/arulesViz/R/saveAsGraph.R | 62 - arulesViz-1.5.3/arulesViz/R/scatterplot.R | 293 ++-- arulesViz-1.5.3/arulesViz/R/visNetwork.R | 84 - arulesViz-1.5.3/arulesViz/README.md | 60 - arulesViz-1.5.3/arulesViz/build/partial.rdb |binary arulesViz-1.5.3/arulesViz/build/vignette.rds |binary arulesViz-1.5.3/arulesViz/inst/README_files/graph-1.png |binary arulesViz-1.5.3/arulesViz/inst/README_files/scatterplot-1.png |binary arulesViz-1.5.3/arulesViz/inst/doc/arulesViz.R | 22 arulesViz-1.5.3/arulesViz/inst/doc/arulesViz.Rnw | 10 arulesViz-1.5.3/arulesViz/inst/doc/arulesViz.pdf |binary arulesViz-1.5.3/arulesViz/man/arulesViz-package.Rd |only arulesViz-1.5.3/arulesViz/man/inspectDT.Rd | 66 - arulesViz-1.5.3/arulesViz/man/plot_arulesViz.Rd |only arulesViz-1.5.3/arulesViz/man/ruleExplorer.Rd | 56 arulesViz-1.5.3/arulesViz/man/rules2matrix.Rd | 85 - arulesViz-1.5.3/arulesViz/man/saveAsGraph.Rd | 62 - arulesViz-1.5.3/arulesViz/tests |only arulesViz-1.5.3/arulesViz/vignettes/arulesViz.Rnw | 10 46 files changed, 2398 insertions(+), 1497 deletions(-)
Title: Simulate and Conduct Dose-Escalation Phase I Studies
Description: Two Phase I designs are implemented in the package: the classical 3+3 and the Continual Reassessment Method (<doi:10.2307/2531628>). Simulations tools are also available to estimate the operating characteristics of the methods with several user-dependent options.
Author: Benjamin Esterni with contribution from Baboukar Mane
Maintainer: Christophe Zemmour <christophe.zemmour@gmail.com>
Diff between UBCRM versions 1.0.2 dated 2022-05-16 and 1.0.3 dated 2024-04-26
DESCRIPTION | 13 ++++++------- MD5 | 30 +++++++++++++++--------------- inst/NEWS | 12 +++++++++++- man/CreData.Rd | 8 ++++---- man/Crm.Rd | 8 ++++---- man/Lp.Rd | 33 ++++----------------------------- man/UBCRM-package.Rd | 17 ++++------------- man/aip.Rd | 8 ++++---- man/fp.Rd | 8 ++++---- man/psip.Rd | 8 ++++---- man/sim3p3.Rd | 8 ++++---- man/simCrm.Rd | 8 ++++---- man/ssim3p3.Rd | 8 ++++---- man/ssimCrm.Rd | 8 ++++---- man/troisPtrois.Rd | 8 ++++---- man/updata.Rd | 8 ++++---- 16 files changed, 84 insertions(+), 109 deletions(-)
Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial
transport data and non-motorized modes.
The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool
(Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been
extended to support public transport routing and accessibility analysis
(Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and
routing with locally hosted routing engines such as 'OSRM'
(Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>.
The main functions are for creating and manipulating geographic "desire
lines" from origin-destination (OD) data (building on the 'od'
package); calculating routes on the transport network locally and via
interfaces to routing services such as <https://cyclestreets.net/>
(Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>;
and calculating route segment attributes such as bearing. The package
imp [...truncated...]
Author: Robin Lovelace [aut, cre] ,
Richard Ellison [aut],
Malcolm Morgan [aut] ,
Barry Rowlingson [ctb],
Nick Bearman [ctb],
Nikolai Berkoff [ctb],
Scott Chamberlain [rev] ,
Mark Padgham [ctb],
Zhao Wang [ctb] ,
Andrea Gilardi [ctb] ,
Josiah Parry [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 1.1.2 dated 2023-09-15 and 1.2.0 dated 2024-04-26
DESCRIPTION | 50 +++- MD5 | 115 +++++----- NAMESPACE | 6 NEWS.md | 9 R/data.R | 6 R/geo_projected.R | 25 +- R/line_via.R | 20 + R/linefuns.R | 337 +++++++++++++++++++++++++------ R/rnet_boundary_points.R | 22 -- R/rnet_join.R | 226 +++++++++++--------- R/toptail.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/flowlines_sf.rda |binary data/routes_fast_sf.rda |binary data/routes_slow_sf.rda |binary inst/doc/merging-route-networks.R | 81 ++++++- inst/doc/merging-route-networks.Rmd | 88 +++++++- inst/doc/merging-route-networks.html | 214 +++++++++++++++++++ inst/doc/stplanr-od.R | 46 ++-- inst/doc/stplanr-paper.R | 38 +-- inst/doc/stplanr-paper.Rmd | 2 inst/doc/stplanr-paper.html | 5 inst/doc/stplanr-parallel.R | 2 inst/doc/stplanr-route-nets.R | 62 ++--- inst/doc/stplanr-route-nets.html | 14 + inst/doc/stplanr-routing.R | 24 +- inst/doc/stplanr-routing.html | 6 inst/doc/stplanr.R | 84 +++---- inst/doc/stplanr.html | 131 ++++++++---- man/angle_diff.Rd | 2 man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/flowlines_sf.Rd | 2 man/geo_toptail.Rd | 4 man/is_linepoint.Rd | 2 man/line2df.Rd | 2 man/line2points.Rd | 2 man/line_bearing.Rd | 17 - man/line_breakup.Rd | 2 man/line_midpoint.Rd | 9 man/line_segment.Rd | 60 ++++- man/line_segment1.Rd |only man/line_via.Rd | 2 man/mats2line.Rd | 2 man/n_segments.Rd |only man/n_vertices.Rd | 4 man/onewaygeo.Rd | 2 man/points2line.Rd | 2 man/rnet_group.Rd | 2 man/rnet_join.Rd | 31 +- man/rnet_merge.Rd | 41 +++ man/rnet_subset.Rd | 6 man/routes_fast_sf.Rd | 2 man/routes_slow_sf.Rd | 2 man/toptail_buff.Rd | 2 tests/testthat/test-mats2line.R |only vignettes/merging-route-networks.Rmd | 88 +++++++- vignettes/stplanr-paper.Rmd | 2 60 files changed, 1384 insertions(+), 523 deletions(-)
Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides
many desirable features. This package bundles these header files for easy use by R packages
from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also
see the 'spdl' package which enhanced this package with a consistent R and C++ interface.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSpdlog versions 0.0.16 dated 2024-01-12 and 0.0.17 dated 2024-04-26
ChangeLog | 13 DESCRIPTION | 8 MD5 | 69 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 13 inst/include/spdlog/async_logger-inl.h | 12 inst/include/spdlog/common.h | 2 inst/include/spdlog/details/circular_q.h | 2 inst/include/spdlog/details/os-inl.h | 10 inst/include/spdlog/details/periodic_worker.h | 1 inst/include/spdlog/details/registry-inl.h | 31 inst/include/spdlog/details/registry.h | 16 inst/include/spdlog/details/thread_pool-inl.h | 11 inst/include/spdlog/details/thread_pool.h | 19 inst/include/spdlog/fmt/bundled/args.h | 13 inst/include/spdlog/fmt/bundled/chrono.h | 999 ++++++----- inst/include/spdlog/fmt/bundled/color.h | 132 - inst/include/spdlog/fmt/bundled/compile.h | 146 - inst/include/spdlog/fmt/bundled/core.h | 1926 +++++++++------------- inst/include/spdlog/fmt/bundled/format-inl.h | 367 +--- inst/include/spdlog/fmt/bundled/format.h | 2200 ++++++++++++++------------ inst/include/spdlog/fmt/bundled/os.h | 157 - inst/include/spdlog/fmt/bundled/ostream.h | 146 - inst/include/spdlog/fmt/bundled/printf.h | 385 ++-- inst/include/spdlog/fmt/bundled/ranges.h | 332 ++- inst/include/spdlog/fmt/bundled/std.h | 470 ++++- inst/include/spdlog/fmt/bundled/xchar.h | 106 - inst/include/spdlog/fmt/fmt.h | 6 inst/include/spdlog/mdc.h |only inst/include/spdlog/pattern_formatter-inl.h | 60 inst/include/spdlog/sinks/qt_sinks.h | 6 inst/include/spdlog/spdlog-inl.h | 10 inst/include/spdlog/spdlog.h | 8 inst/include/spdlog/stopwatch.h | 4 inst/include/spdlog/version.h | 2 36 files changed, 4142 insertions(+), 3540 deletions(-)
Title: Functions, Data Sets and Vignettes to Aid in Learning Principal
Components Analysis (PCA)
Description: Principal component analysis (PCA) is one of the most widely used data analysis techniques. This package provides a series of vignettes explaining PCA starting from basic concepts. The primary purpose is to serve as a self-study resource for anyone wishing to understand PCA better. A few convenience functions are provided as well.
Author: Bryan A. Hanson [aut, cre] ,
David T. Harvey [aut]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between LearnPCA versions 0.2.0 dated 2022-05-01 and 0.3.4 dated 2024-04-26
DESCRIPTION | 11 + MD5 | 64 ++++++----- NAMESPACE | 4 NEWS.md | 14 ++ R/LearnPCA-package.R | 10 - R/PCsearch.R | 2 R/demo_PC_search.R | 1 build/vignette.rds |binary inst/doc/Vig_01_Start_Here.R | 6 - inst/doc/Vig_01_Start_Here.pdf |binary inst/doc/Vig_02_Conceptual_Intro_PCA.R | 6 - inst/doc/Vig_02_Conceptual_Intro_PCA.pdf |binary inst/doc/Vig_03_Step_By_Step_PCA.R | 6 - inst/doc/Vig_03_Step_By_Step_PCA.pdf |binary inst/doc/Vig_04_Scores_Loadings.R | 6 - inst/doc/Vig_04_Scores_Loadings.Rmd | 2 inst/doc/Vig_04_Scores_Loadings.pdf |binary inst/doc/Vig_05_Visualizing_PCA_3D.R | 2 inst/doc/Vig_05_Visualizing_PCA_3D.pdf |binary inst/doc/Vig_06_Math_Behind_PCA.R | 73 +++++++++---- inst/doc/Vig_06_Math_Behind_PCA.Rmd | 173 ++++++++++++++++++++++--------- inst/doc/Vig_06_Math_Behind_PCA.pdf |binary inst/doc/Vig_07_Functions_PCA.R | 8 - inst/doc/Vig_07_Functions_PCA.pdf |binary inst/doc/Vig_08_Notes.R |only inst/doc/Vig_08_Notes.Rmd |only inst/doc/Vig_08_Notes.pdf |only man/LearnPCA-package.Rd | 9 + vignettes/PCA.bib | 7 + vignettes/Vig_04_Scores_Loadings.Rmd | 2 vignettes/Vig_06_Math_Behind_PCA.Rmd | 173 ++++++++++++++++++++++--------- vignettes/Vig_08_Notes.Rmd |only vignettes/refer_to_works_consulted.md | 2 vignettes/top_matter.md | 15 +- vignettes/works_consulted.md | 1 35 files changed, 410 insertions(+), 187 deletions(-)
Title: Make, Update, and Query Binary Causal Models
Description: Users can declare binary causal models, update beliefs about causal types given data and calculate arbitrary estimands. Model definition makes use of 'dagitty' functionality. Updating is implemented in 'stan'. The approach used in 'CausalQueries' is a generalization of the 'biqq' models described in "Mixing Methods: A Bayesian Approach" (Humphreys and Jacobs, 2015, <DOI:10.1017/S0003055415000453>). The conceptual extension makes use of work on probabilistic causal models described in Pearl's Causality (Pearl, 2009, <DOI:10.1017/CBO9780511803161>).
Author: Clara Bicalho [ctb],
Jasper Cooper [ctb],
Macartan Humphreys [aut] ,
Till Tietz [aut, cre] ,
Alan Jacobs [aut],
Merlin Heidemanns [ctb],
Lily Medina [aut] ,
Julio Solis [ctb],
Georgiy Syunyaev [aut]
Maintainer: Till Tietz <ttietz2014@gmail.com>
Diff between CausalQueries versions 1.1.0 dated 2024-04-10 and 1.1.1 dated 2024-04-26
CausalQueries-1.1.0/CausalQueries/man/print.type_posterior.Rd |only CausalQueries-1.1.1/CausalQueries/DESCRIPTION | 6 CausalQueries-1.1.1/CausalQueries/MD5 | 33 +- CausalQueries-1.1.1/CausalQueries/NAMESPACE | 3 CausalQueries-1.1.1/CausalQueries/NEWS.md | 5 CausalQueries-1.1.1/CausalQueries/R/grab.R | 23 + CausalQueries-1.1.1/CausalQueries/R/methods.R | 59 ++- CausalQueries-1.1.1/CausalQueries/R/parmap.R | 3 CausalQueries-1.1.1/CausalQueries/R/set_parameter_matrix.R | 17 - CausalQueries-1.1.1/CausalQueries/R/update_model.R | 2 CausalQueries-1.1.1/CausalQueries/inst/doc/front-door.html | 28 - CausalQueries-1.1.1/CausalQueries/inst/doc/getting-started.html | 152 +++++----- CausalQueries-1.1.1/CausalQueries/inst/doc/inspecting-posteriors.html | 90 ++--- CausalQueries-1.1.1/CausalQueries/man/grab.Rd | 10 CausalQueries-1.1.1/CausalQueries/man/print.nodes.Rd | 2 CausalQueries-1.1.1/CausalQueries/man/print.parameter_mapping.Rd |only CausalQueries-1.1.1/CausalQueries/man/print.type_distribution.Rd |only CausalQueries-1.1.1/CausalQueries/tests/testthat/test_grab.R | 23 - CausalQueries-1.1.1/CausalQueries/tests/testthat/test_methods.R | 4 19 files changed, 255 insertions(+), 205 deletions(-)
Title: Core Utilities for Developing and Running Spatially Explicit
Discrete Event Models
Description: Provides the core framework for a discrete event system to
implement a complete data-to-decisions, reproducible workflow.
The core components facilitate the development of modular pieces,
and enable the user to include additional functionality by running user-built modules.
Includes conditional scheduling, restart after interruption, packaging of
reusable modules, tools for developing arbitrary automated workflows,
automated interweaving of modules of different temporal resolution,
and tools for visualizing and understanding the within-project dependencies.
The suggested package 'NLMR' can be installed from the repository
(<https://PredictiveEcology.r-universe.dev>).
Author: Alex M Chubaty [aut] ,
Eliot J B McIntire [aut, cre] ,
Yong Luo [ctb],
Steve Cumming [ctb],
Ceres Barros [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between SpaDES.core versions 2.0.4 dated 2024-04-16 and 2.0.5 dated 2024-04-25
DESCRIPTION | 8 - MD5 | 22 +-- NEWS.md | 4 build/vignette.rds |binary inst/doc/i-introduction.html | 2 inst/doc/ii-modules.html | 58 ++++----- inst/doc/iii-cache.html | 240 +++++++++++++++++++------------------- inst/doc/iv-advanced.html | 2 inst/doc/v-automated-testing.html | 2 tests/testthat/test-cache.R | 14 +- tests/testthat/test-checkpoint.R | 1 tests/testthat/test-save.R | 4 12 files changed, 184 insertions(+), 173 deletions(-)
Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models. Methods are described in Meyer et al. (2018) <doi:10.1016/j.envsoft.2017.12.001>; Meyer et al. (2019) <doi:10.1016/j.ecolmodel.2019.108815>; Meyer and Pebesma (2021) <doi:10.1111/2041-210X.13650>; Milà et al. (2022) <doi:10.1111/2041-210X.13851>; Meyer and Pebesma (2022) <doi:10.1038/s41467-022-29838-9>; L [...truncated...]
Author: Hanna Meyer [cre, aut],
Carles Mila [aut],
Marvin Ludwig [aut],
Jan Linnenbrink [aut],
Fabian Schumacher [aut],
Philipp Otto [ctb],
Chris Reudenbach [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>
Diff between CAST versions 1.0.0 dated 2024-04-08 and 1.0.1 dated 2024-04-25
DESCRIPTION | 8 +- MD5 | 44 +++++------ NEWS.md | 3 R/CAST-package.R | 2 README.md | 4 + inst/doc/cast01-CAST-intro.R | 2 inst/doc/cast01-CAST-intro.Rmd | 4 - inst/doc/cast01-CAST-intro.html | 43 +++++------ inst/doc/cast02-plotgeodist.R | 25 ------ inst/doc/cast02-plotgeodist.Rmd | 34 +------- inst/doc/cast02-plotgeodist.html | 102 ++++++++++---------------- inst/doc/cast03-CV.html | 4 - inst/doc/cast04-AOA-tutorial.R | 2 inst/doc/cast04-AOA-tutorial.Rmd | 2 inst/doc/cast04-AOA-tutorial.html | 6 - inst/doc/cast05-parallel.html | 4 - man/CAST.Rd | 2 tests/testthat/test-errorProfiles.R | 13 ++- tests/testthat/test-fss.R | 124 +++++++++++++++++--------------- tests/testthat/test-global_validation.R | 11 +- vignettes/cast01-CAST-intro.Rmd | 4 - vignettes/cast02-plotgeodist.Rmd | 34 +------- vignettes/cast04-AOA-tutorial.Rmd | 2 23 files changed, 212 insertions(+), 267 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes eaxis(), an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] ,
Werner Stahel [ctb] , f.robftest, last,
p.scales, p.dnorm),
Andreas Ruckstuhl [ctb] , p.profileTraces,
p.res.2x),
Christian Keller [ctb] , p.tachoPlot),
Kjetil Halvorsen [ctb] , ecdf.ksCI),
Alain Hauser [ctb] , is.whole,
[...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-17 dated 2024-02-01 and 1.1-18 dated 2024-04-25
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/misc-goodies.R | 10 +++++++--- R/p.goodies.R | 1 - R/sessionInfo-ext.R | 5 +++++ build/partial.rdb |binary inst/NEWS.Rd | 14 ++++++++++++++ man/f.robftest.Rd | 2 +- man/integrate.xy.Rd | 2 +- man/polyn.eval.Rd | 6 ++++++ man/sessionInfoX.Rd | 1 + man/xy.grid.Rd | 2 +- 12 files changed, 52 insertions(+), 23 deletions(-)
Title: Estimation of the Weights Attached to the Two-Way Fixed Effects
Regressions
Description: Estimates the weights and measure of robustness to treatment effect heterogeneity attached to two-way fixed effects regressions.
Clément de Chaisemartin, Xavier D'Haultfœuille (2020) <DOI: 10.1257/aer.20181169>.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Shuo Zhang [aut],
Clement de Chaisemartin [aut],
Grant McDermott [ctb]
Maintainer: Diego Ciccia <diego.ciccia@sciencespo.fr>
Diff between TwoWayFEWeights versions 2.0.2 dated 2024-04-15 and 2.0.3 dated 2024-04-25
DESCRIPTION | 6 ++-- MD5 | 10 +++---- R/print.R | 55 +++++++++++++----------------------------- R/twowayfeweights_calculate.R | 3 -- R/twowayfeweights_result.R | 11 ++++++++ R/utils.R | 2 - 6 files changed, 39 insertions(+), 48 deletions(-)
More information about TwoWayFEWeights at CRAN
Permanent link
Title: Runs Monte Carlo Markov Chain - With Either 'JAGS', 'nimble' or
'greta' - While Adjusting Burn-in and Thinning Parameters
Description: The function runMCMC_btadjust() returns a mcmc.list object which is the output of a
Markov Chain Monte Carlo obtained - from either 'JAGS', 'nimble' or 'greta' - after adjusting burn-in and thinning parameters to meet
pre-specified criteria in terms of convergence & effective sample size.
Author: Frederic Gosselin [cre, aut] ,
Institut national de recherche pour l'agriculture, l'alimentation et
l'environnement [cph]
Maintainer: Frederic Gosselin <frederic.gosselin@inrae.fr>
Diff between runMCMCbtadjust versions 1.0.5 dated 2023-12-13 and 1.1.0 dated 2024-04-25
DESCRIPTION | 9 MD5 | 31 NAMESPACE | 1 NEWS.md | 47 R/findMCMC_strong_corrs.R |only R/runMCMC_btadjust.r | 3884 +++++++++++++++++++---------- build/vignette.rds |binary inst/doc/runMCMCbtadjust_Presentation.R | 69 inst/doc/runMCMCbtadjust_Presentation.Rmd | 7 inst/doc/runMCMCbtadjust_Presentation.html | 1198 ++++++-- man/findMCMC_strong_corrs.Rd |only man/fragments/Greta_fragment.Rmd | 20 man/fragments/Jags_fragment.Rmd | 12 man/fragments/Nimble&Jags2_fragment.rmd |only man/fragments/Nimble1_alone_fragment.Rmd | 91 man/runMCMC_btadjust.Rd | 150 - tests/testthat/test-runMCMC_btadjust.R | 7 vignettes/runMCMCbtadjust_Presentation.Rmd | 7 18 files changed, 3810 insertions(+), 1723 deletions(-)
More information about runMCMCbtadjust at CRAN
Permanent link
Title: Graph/Network Analysis Based on L1 Centrality
Description: Analyze graph/network data using L1 centrality and prestige. Functions for deriving global and local L1 centrality/prestige and L1 centrality/prestige-based neighborhoods of vertices are provided. Routines for visual inspection of a graph/network are also provided. Details are in Kang and Oh (2024) <doi:10.48550/arXiv.2404.13233>.
Author: Seungwoo Kang [aut, cre] ,
Hee-Seok Oh [aut]
Maintainer: Seungwoo Kang <kangsw0401@snu.ac.kr>
Diff between L1centrality versions 0.0.3 dated 2024-01-09 and 0.1.1 dated 2024-04-25
DESCRIPTION | 10 +- MD5 | 40 +++++------ NEWS.md | 18 +++++ R/L1cent.R | 150 ++++++++++++++++++++++++++++++-------------- R/L1centEDGE.R | 5 + R/L1centLOC.R | 66 +++++++++++-------- R/L1centMDS.R | 14 ++-- R/L1centNB.R | 63 +++++++++++++----- R/L1centrality-package.R | 35 ++++++++-- R/MCUmovie.R | 6 - R/rokassembly21.R | 4 - R/validate.R | 10 +- man/L1cent.Rd | 121 ++++++++++++++++++++++++----------- man/L1centEDGE.Rd | 4 - man/L1centLOC.Rd | 66 +++++++++++++------ man/L1centMDS.Rd | 10 +- man/L1centNB.Rd | 64 ++++++++++++++---- man/L1centrality-package.Rd | 36 ++++++++-- man/Lorenz_plot.Rd | 2 man/MCUmovie.Rd | 6 - man/rokassembly21.Rd | 4 - 21 files changed, 509 insertions(+), 225 deletions(-)
Title: Methods for High-Dimensional Repeated Measures Data
Description: A toolkit for the analysis of high-dimensional repeated measurements, providing functions
for outlier detection, differential expression analysis, gene-set tests, and binary random data generation.
Author: Klaus Jung [aut, cre],
Jochen Kruppa [aut],
Sergej Ruff [aut]
Maintainer: Klaus Jung <klaus.jung@tiho-hannover.de>
Diff between RepeatedHighDim versions 2.2.0 dated 2023-06-29 and 2.3.0 dated 2024-04-25
DESCRIPTION | 15 - MD5 | 96 +++++------ NAMESPACE | 107 ++++++------ R/GA_diagplot.R | 128 +++++++-------- R/GlobTestMissing.R | 148 ++++++++--------- R/RepeatedHighDim-package.R | 220 +++++++++++++------------- R/RepeatedHighDim.R | 84 +++++----- R/TestStatSP.R | 134 ++++++++-------- R/TestStatSimple.R | 58 +++--- R/bag.R | 367 ++++++++++++++++++++++---------------------- R/check_limma.R | 50 +++-- R/depmed.R | 139 ++++++++-------- R/fc_ci.R | 172 ++++++++++---------- R/fc_plot.R | 196 +++++++++++------------ R/gem.R | 229 +++++++++++++-------------- R/gridfun.R | 92 +++++------ R/hldepth.R | 177 ++++++++++----------- R/iter_matrix.R | 172 ++++++++++---------- R/loop.R | 241 ++++++++++++++-------------- R/netRNA.R |only R/rho_bounds.R | 96 +++++------ R/rmvbinary_EP.R | 116 +++++++------ R/rmvbinary_QA.R | 100 ++++++----- R/sequence_probs.R | 80 ++++----- R/start_matrix.R | 70 ++++---- R/summary_RHD.R | 62 +++---- build/partial.rdb |binary man/GA_diagplot.Rd | 5 man/GlobTestMissing.Rd | 3 man/RHighDim.Rd | 3 man/RepeatedHighDim.Rd | 9 - man/TestStatSP.Rd | 3 man/TestStatSimple.Rd | 3 man/bag.Rd | 114 +++++++------ man/check_limma.Rd | 3 man/depmed.Rd | 28 +-- man/fc_ci.Rd | 3 man/fc_plot.Rd | 3 man/gem.Rd | 158 +++++++++--------- man/gridfun.Rd | 3 man/hldepth.Rd | 26 +-- man/iter_matrix.Rd | 3 man/loop.Rd | 116 +++++++------ man/netRNA.Rd |only man/rho_bounds.Rd | 3 man/rmvbinary_EP.Rd | 3 man/rmvbinary_QA.Rd | 3 man/sequence_probs.Rd | 3 man/start_matrix.Rd | 3 man/summary_RHD.Rd | 3 50 files changed, 1991 insertions(+), 1859 deletions(-)
More information about RepeatedHighDim at CRAN
Permanent link
Title: Mobility Network Analysis
Description: Implements the method to analyse weighted mobility networks or distribution networks as outlined in:
Block, P., Stadtfeld, C., & Robins, G. (2022) <doi:10.1016/j.socnet.2021.08.003>.
The purpose of the model is to analyse the structure of mobility,
incorporating exogenous predictors pertaining to individuals and locations
known from classical mobility analyses, as well as modelling emergent mobility
patterns akin to structural patterns known from the statistical analysis of social networks.
Author: Per Block [cre, aut, cph] ,
Christoph Stadtfeld [aut] ,
Nico Keiser [aut],
Marion Hoffman [aut]
Maintainer: Per Block <block@soziologie.uzh.ch>
Diff between MoNAn versions 0.1.3 dated 2024-02-05 and 1.0.0 dated 2024-04-25
MoNAn-0.1.3/MoNAn/data/myCache.rda |only MoNAn-1.0.0/MoNAn/DESCRIPTION | 10 MoNAn-1.0.0/MoNAn/MD5 | 99 +-- MoNAn-1.0.0/MoNAn/NAMESPACE | 38 - MoNAn-1.0.0/MoNAn/NEWS.md | 51 + MoNAn-1.0.0/MoNAn/R/1_hiddenFunctions.R | 160 ++++ MoNAn-1.0.0/MoNAn/R/2_effectFunctions.R | 214 ------ MoNAn-1.0.0/MoNAn/R/2c_effectFunctions_concentration.R | 198 +++++- MoNAn-1.0.0/MoNAn/R/2f_effectFunctions_endogenousCovariateBased.R |only MoNAn-1.0.0/MoNAn/R/2x_effects_test.R | 40 - MoNAn-1.0.0/MoNAn/R/3_coreFunctions.R | 298 +++++---- MoNAn-1.0.0/MoNAn/R/3b_wrapperFunctions.R |only MoNAn-1.0.0/MoNAn/R/4_auxiliaryFunctions.R | 276 +++++++- MoNAn-1.0.0/MoNAn/R/myOutcomeObjects.R | 10 MoNAn-1.0.0/MoNAn/R/sysdata.rda |binary MoNAn-1.0.0/MoNAn/R/zzz.R |only MoNAn-1.0.0/MoNAn/README.md | 327 +++++++--- MoNAn-1.0.0/MoNAn/data/myAlg.rda |binary MoNAn-1.0.0/MoNAn/data/myEffects.rda |binary MoNAn-1.0.0/MoNAn/data/myResDN.rda |binary MoNAn-1.0.0/MoNAn/data/mySimDN.rda |binary MoNAn-1.0.0/MoNAn/data/myState.rda |binary MoNAn-1.0.0/MoNAn/man/addEffect.Rd |only MoNAn-1.0.0/MoNAn/man/avoiding_dissimilar_covar_bin.Rd |only MoNAn-1.0.0/MoNAn/man/avoiding_dissimilar_covar_cont.Rd |only MoNAn-1.0.0/MoNAn/man/concentration_GW_resource_covar_bin.Rd |only MoNAn-1.0.0/MoNAn/man/concentration_basic_squared.Rd |only MoNAn-1.0.0/MoNAn/man/concentration_norm.Rd |only MoNAn-1.0.0/MoNAn/man/concentration_norm_squared.Rd |only MoNAn-1.0.0/MoNAn/man/createAlgorithm.Rd | 20 MoNAn-1.0.0/MoNAn/man/createEdgelist.Rd | 11 MoNAn-1.0.0/MoNAn/man/createEffects.Rd |only MoNAn-1.0.0/MoNAn/man/createNetwork.Rd | 15 MoNAn-1.0.0/MoNAn/man/createNodeSet.Rd | 6 MoNAn-1.0.0/MoNAn/man/createNodeVariable.Rd | 25 MoNAn-1.0.0/MoNAn/man/createWeightedCache.Rd | 21 MoNAn-1.0.0/MoNAn/man/crowding_out_prop_covar_bin.Rd | 2 MoNAn-1.0.0/MoNAn/man/estimateMobilityNetwork.Rd | 55 + MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-18-1.png |binary MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-18-2.png |binary MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-18-3.png |binary MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-19-1.png |binary MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-19-2.png |binary MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-19-3.png |binary MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-20-1.png |binary MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-20-2.png |binary MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-21-1.png |binary MoNAn-1.0.0/MoNAn/man/figures/README-unnamed-chunk-21-2.png |binary MoNAn-1.0.0/MoNAn/man/getMultinomialStatistics.Rd | 10 MoNAn-1.0.0/MoNAn/man/gofMobilityNetwork.Rd | 30 MoNAn-1.0.0/MoNAn/man/joining_similar_avoiding_dissimilar_covar_bin.Rd |only MoNAn-1.0.0/MoNAn/man/joining_similar_avoiding_dissimilar_covar_cont.Rd |only MoNAn-1.0.0/MoNAn/man/monanDataCreate.Rd |only MoNAn-1.0.0/MoNAn/man/myOutcomeObjects.Rd | 7 MoNAn-1.0.0/MoNAn/man/print.effectsList.monan.Rd |only MoNAn-1.0.0/MoNAn/man/print.processState.monan.Rd |only MoNAn-1.0.0/MoNAn/man/scoreTest.Rd | 14 MoNAn-1.0.0/MoNAn/man/simulateMobilityNetworks.Rd | 26 MoNAn-1.0.0/MoNAn/man/staying_by_prop_bin_inflow.Rd | 2 59 files changed, 1327 insertions(+), 638 deletions(-)
Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built
on top of the 'libuv' C library.
Author: Jim Hester [aut],
Hadley Wickham [aut],
Gabor Csardi [aut, cre],
libuv project contributors [cph] ,
Joyent, Inc. and other Node contributors [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between fs versions 1.6.3 dated 2023-07-20 and 1.6.4 dated 2024-04-25
DESCRIPTION | 18 ++++++------- LICENSE | 2 - MD5 | 27 ++++++++++--------- NEWS.md | 4 ++ R/file.R | 2 - R/path.R | 2 - R/tree.R | 2 - README.md | 71 ++++++++++++++++++++++++---------------------------- build/vignette.rds |binary inst/WORDLIST | 2 - man/figures |only man/file_info.Rd | 2 - man/fs-package.Rd | 6 ++-- src/CollectorList.h | 12 +++++++- src/Makevars | 2 - 15 files changed, 81 insertions(+), 71 deletions(-)
Title: Continuous Time Meta-Analysis ('CoTiMA')
Description: The 'CoTiMA' package performs meta-analyses of correlation matrices of repeatedly measured variables taken from
studies that used different time intervals. Different time intervals between measurement occasions impose problems for
meta-analyses because the effects (e.g. cross-lagged effects) cannot be simply aggregated, for example, by means of common
fixed or random effects analysis. However, continuous time math, which is applied in 'CoTiMA', can be used to extrapolate or
intrapolate the results from all studies to any desired time lag. By this, effects obtained in studies that used different
time intervals can be meta-analyzed. 'CoTiMA' fits models to empirical data using the structural equation model (SEM) package
'ctsem', the effects specified in a SEM are related to parameters that are not directly included in the model (i.e.,
continuous time parameters; together, they represent the continuous time structural equation model, CTSEM). Statistical
model comparisons and significance [...truncated...]
Author: Christian Dormann [aut, cph],
Markus Homberg [aut, com, cre],
Olga Diener [ctb],
Christina Guthier [ctb],
Manuel Voelkle [ctb]
Maintainer: Markus Homberg <cotima@uni-mainz.de>
Diff between CoTiMA versions 0.7.0 dated 2023-12-16 and 0.8.0 dated 2024-04-25
CoTiMA-0.7.0/CoTiMA/data/CoTiMAStanctArgs.rda |only CoTiMA-0.7.0/CoTiMA/data/CoTiMAoptimFit313.rda |only CoTiMA-0.7.0/CoTiMA/data/addedByResearcher2.rda |only CoTiMA-0.7.0/CoTiMA/data/addedByResearcher3.rda |only CoTiMA-0.7.0/CoTiMA/data/addedByResearcher313.rda |only CoTiMA-0.7.0/CoTiMA/data/ageM2.rda |only CoTiMA-0.7.0/CoTiMA/data/ageM3.rda |only CoTiMA-0.7.0/CoTiMA/data/ageSD2.rda |only CoTiMA-0.7.0/CoTiMA/data/ageSD3.rda |only CoTiMA-0.7.0/CoTiMA/data/burnout2.rda |only CoTiMA-0.7.0/CoTiMA/data/burnout3.rda |only CoTiMA-0.7.0/CoTiMA/data/country2.rda |only CoTiMA-0.7.0/CoTiMA/data/country3.rda |only CoTiMA-0.7.0/CoTiMA/data/delta_t2.rda |only CoTiMA-0.7.0/CoTiMA/data/delta_t3.rda |only CoTiMA-0.7.0/CoTiMA/data/demands2.rda |only CoTiMA-0.7.0/CoTiMA/data/demands3.rda |only CoTiMA-0.7.0/CoTiMA/data/empcov2.rda |only CoTiMA-0.7.0/CoTiMA/data/empcov3.rda |only CoTiMA-0.7.0/CoTiMA/data/malePercent2.rda |only CoTiMA-0.7.0/CoTiMA/data/malePercent3.rda |only CoTiMA-0.7.0/CoTiMA/data/moderator2.rda |only CoTiMA-0.7.0/CoTiMA/data/moderator3.rda |only CoTiMA-0.7.0/CoTiMA/data/occupation2.rda |only CoTiMA-0.7.0/CoTiMA/data/occupation3.rda |only CoTiMA-0.7.0/CoTiMA/data/rawdata128.rda |only CoTiMA-0.7.0/CoTiMA/data/rawdata128.txt |only CoTiMA-0.7.0/CoTiMA/data/sampleSize2.rda |only CoTiMA-0.7.0/CoTiMA/data/sampleSize3.rda |only CoTiMA-0.7.0/CoTiMA/data/source2.rda |only CoTiMA-0.7.0/CoTiMA/data/source3.rda |only CoTiMA-0.7.0/CoTiMA/data/targetVariables2.rda |only CoTiMA-0.7.0/CoTiMA/data/targetVariables3.rda |only CoTiMA-0.7.0/CoTiMA/man/CoTiMAoptimFit313.Rd |only CoTiMA-0.7.0/CoTiMA/man/addedByResearcher2.Rd |only CoTiMA-0.7.0/CoTiMA/man/addedByResearcher3.Rd |only CoTiMA-0.7.0/CoTiMA/man/addedByResearcher313.Rd |only CoTiMA-0.7.0/CoTiMA/man/ageM2.Rd |only CoTiMA-0.7.0/CoTiMA/man/ageM3.Rd |only CoTiMA-0.7.0/CoTiMA/man/ageSD2.Rd |only CoTiMA-0.7.0/CoTiMA/man/ageSD3.Rd |only CoTiMA-0.7.0/CoTiMA/man/burnout2.Rd |only CoTiMA-0.7.0/CoTiMA/man/burnout3.Rd |only CoTiMA-0.7.0/CoTiMA/man/country2.Rd |only CoTiMA-0.7.0/CoTiMA/man/country3.Rd |only CoTiMA-0.7.0/CoTiMA/man/delta_t2.Rd |only CoTiMA-0.7.0/CoTiMA/man/delta_t3.Rd |only CoTiMA-0.7.0/CoTiMA/man/demands2.Rd |only CoTiMA-0.7.0/CoTiMA/man/demands3.Rd |only CoTiMA-0.7.0/CoTiMA/man/empcov2.Rd |only CoTiMA-0.7.0/CoTiMA/man/empcov3.Rd |only CoTiMA-0.7.0/CoTiMA/man/malePercent2.Rd |only CoTiMA-0.7.0/CoTiMA/man/malePercent3.Rd |only CoTiMA-0.7.0/CoTiMA/man/moderator2.Rd |only CoTiMA-0.7.0/CoTiMA/man/moderator3.Rd |only CoTiMA-0.7.0/CoTiMA/man/occupation2.Rd |only CoTiMA-0.7.0/CoTiMA/man/occupation3.Rd |only CoTiMA-0.7.0/CoTiMA/man/rawData128.Rd |only CoTiMA-0.7.0/CoTiMA/man/sampleSize2.Rd |only CoTiMA-0.7.0/CoTiMA/man/sampleSize3.Rd |only CoTiMA-0.7.0/CoTiMA/man/source2.Rd |only CoTiMA-0.7.0/CoTiMA/man/source3.Rd |only CoTiMA-0.7.0/CoTiMA/man/targetVariables2.Rd |only CoTiMA-0.7.0/CoTiMA/man/targetVariables3.Rd |only CoTiMA-0.8.0/CoTiMA/DESCRIPTION | 21 CoTiMA-0.8.0/CoTiMA/MD5 | 416 +-- CoTiMA-0.8.0/CoTiMA/R/ctmaAllInvFit.R | 53 CoTiMA-0.8.0/CoTiMA/R/ctmaBiG.R | 1 CoTiMA-0.8.0/CoTiMA/R/ctmaEmpCov.R | 12 CoTiMA-0.8.0/CoTiMA/R/ctmaEqual.R | 19 CoTiMA-0.8.0/CoTiMA/R/ctmaFit.R | 1406 ++++++---- CoTiMA-0.8.0/CoTiMA/R/ctmaFitToPrep.R | 2 CoTiMA-0.8.0/CoTiMA/R/ctmaInit.R | 1477 ++++++----- CoTiMA-0.8.0/CoTiMA/R/ctmaLabels.R | 18 CoTiMA-0.8.0/CoTiMA/R/ctmaOptimizeFit.R | 486 ++- CoTiMA-0.8.0/CoTiMA/R/ctmaPlotCtsemMod.R | 131 CoTiMA-0.8.0/CoTiMA/R/ctmaPower.R | 8 CoTiMA-0.8.0/CoTiMA/R/ctmaPrep.R | 762 +++-- CoTiMA-0.8.0/CoTiMA/R/ctmaPub.R | 2 CoTiMA-0.8.0/CoTiMA/R/ctmaRedHet.R | 1861 +++++--------- CoTiMA-0.8.0/CoTiMA/R/ctmaShapeRawData.R | 10 CoTiMA-0.8.0/CoTiMA/R/ctmaStanctArgs.R | 38 CoTiMA-0.8.0/CoTiMA/R/data.R | 236 - CoTiMA-0.8.0/CoTiMA/build/vignette.rds |binary CoTiMA-0.8.0/CoTiMA/data/A128.rda |binary CoTiMA-0.8.0/CoTiMA/data/A313.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMABiG_D_BO.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAFullFit_3.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAFullFit_6.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAFullFit_6_new.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAFullInv23Fit_6.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAFullInvEq23Fit_6.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAInitFit_3.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAInitFit_6.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAInitFit_6_NUTS.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAInitFit_6_new.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAInitFit_D_BO.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAMod1onFullFit_6.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAMod1onFullFit_6_cats12.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAMod2on23Fit_6.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAPart134Inv3Fit_6.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAPower_D_BO.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAstudyList_3.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAstudyList_6.rda |binary CoTiMA-0.8.0/CoTiMA/data/CoTiMAstudyList_6_new.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageM1.rda |only CoTiMA-0.8.0/CoTiMA/data/ageM128.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageM18.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageM201.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageM313.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageM32.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageM4.rda |only CoTiMA-0.8.0/CoTiMA/data/ageSD1.rda |only CoTiMA-0.8.0/CoTiMA/data/ageSD128.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageSD18.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageSD201.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageSD313.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageSD32.rda |binary CoTiMA-0.8.0/CoTiMA/data/ageSD4.rda |only CoTiMA-0.8.0/CoTiMA/data/alphas128.rda |binary CoTiMA-0.8.0/CoTiMA/data/alphas313.rda |binary CoTiMA-0.8.0/CoTiMA/data/burnout1.rda |only CoTiMA-0.8.0/CoTiMA/data/burnout128.rda |binary CoTiMA-0.8.0/CoTiMA/data/burnout18.rda |binary CoTiMA-0.8.0/CoTiMA/data/burnout201.rda |binary CoTiMA-0.8.0/CoTiMA/data/burnout313.rda |binary CoTiMA-0.8.0/CoTiMA/data/burnout32.rda |binary CoTiMA-0.8.0/CoTiMA/data/burnout4.rda |only CoTiMA-0.8.0/CoTiMA/data/combineVariables128.rda |binary CoTiMA-0.8.0/CoTiMA/data/combineVariablesNames128.rda |binary CoTiMA-0.8.0/CoTiMA/data/country1.rda |only CoTiMA-0.8.0/CoTiMA/data/country128.rda |binary CoTiMA-0.8.0/CoTiMA/data/country18.rda |binary CoTiMA-0.8.0/CoTiMA/data/country201.rda |binary CoTiMA-0.8.0/CoTiMA/data/country313.rda |binary CoTiMA-0.8.0/CoTiMA/data/country32.rda |binary CoTiMA-0.8.0/CoTiMA/data/country4.rda |only CoTiMA-0.8.0/CoTiMA/data/delta_t1.rda |only CoTiMA-0.8.0/CoTiMA/data/delta_t128.rda |binary CoTiMA-0.8.0/CoTiMA/data/delta_t18.rda |binary CoTiMA-0.8.0/CoTiMA/data/delta_t201.rda |binary CoTiMA-0.8.0/CoTiMA/data/delta_t228.rda |only CoTiMA-0.8.0/CoTiMA/data/delta_t313.rda |binary CoTiMA-0.8.0/CoTiMA/data/delta_t32.rda |binary CoTiMA-0.8.0/CoTiMA/data/delta_t4.rda |only CoTiMA-0.8.0/CoTiMA/data/demands1.rda |only CoTiMA-0.8.0/CoTiMA/data/demands128.rda |binary CoTiMA-0.8.0/CoTiMA/data/demands18.rda |binary CoTiMA-0.8.0/CoTiMA/data/demands201.rda |binary CoTiMA-0.8.0/CoTiMA/data/demands313.rda |binary CoTiMA-0.8.0/CoTiMA/data/demands32.rda |binary CoTiMA-0.8.0/CoTiMA/data/demands4.rda |only CoTiMA-0.8.0/CoTiMA/data/dl_link.rda |binary CoTiMA-0.8.0/CoTiMA/data/empcov1.rda |only CoTiMA-0.8.0/CoTiMA/data/empcov128.rda |binary CoTiMA-0.8.0/CoTiMA/data/empcov18.rda |binary CoTiMA-0.8.0/CoTiMA/data/empcov201.rda |binary CoTiMA-0.8.0/CoTiMA/data/empcov313.rda |binary CoTiMA-0.8.0/CoTiMA/data/empcov32.rda |binary CoTiMA-0.8.0/CoTiMA/data/empcov4.rda |only CoTiMA-0.8.0/CoTiMA/data/malePercent1.rda |only CoTiMA-0.8.0/CoTiMA/data/malePercent128.rda |binary CoTiMA-0.8.0/CoTiMA/data/malePercent18.rda |binary CoTiMA-0.8.0/CoTiMA/data/malePercent201.rda |binary CoTiMA-0.8.0/CoTiMA/data/malePercent313.rda |binary CoTiMA-0.8.0/CoTiMA/data/malePercent32.rda |binary CoTiMA-0.8.0/CoTiMA/data/malePercent4.rda |only CoTiMA-0.8.0/CoTiMA/data/moderator1.rda |only CoTiMA-0.8.0/CoTiMA/data/moderator128.rda |binary CoTiMA-0.8.0/CoTiMA/data/moderator18.rda |binary CoTiMA-0.8.0/CoTiMA/data/moderator201.rda |binary CoTiMA-0.8.0/CoTiMA/data/moderator313.rda |binary CoTiMA-0.8.0/CoTiMA/data/moderator32.rda |binary CoTiMA-0.8.0/CoTiMA/data/moderator4.rda |only CoTiMA-0.8.0/CoTiMA/data/moderatorLabels.rda |binary CoTiMA-0.8.0/CoTiMA/data/moderatorValues.rda |binary CoTiMA-0.8.0/CoTiMA/data/occupation1.rda |only CoTiMA-0.8.0/CoTiMA/data/occupation128.rda |binary CoTiMA-0.8.0/CoTiMA/data/occupation18.rda |binary CoTiMA-0.8.0/CoTiMA/data/occupation201.rda |binary CoTiMA-0.8.0/CoTiMA/data/occupation313.rda |binary CoTiMA-0.8.0/CoTiMA/data/occupation32.rda |binary CoTiMA-0.8.0/CoTiMA/data/occupation4.rda |only CoTiMA-0.8.0/CoTiMA/data/pairwiseN128.rda |binary CoTiMA-0.8.0/CoTiMA/data/pubList_8.rda |binary CoTiMA-0.8.0/CoTiMA/data/rawData228.rda |only CoTiMA-0.8.0/CoTiMA/data/recodeVariables128.rda |binary CoTiMA-0.8.0/CoTiMA/data/results128.rda |binary CoTiMA-0.8.0/CoTiMA/data/sampleSize1.rda |only CoTiMA-0.8.0/CoTiMA/data/sampleSize128.rda |binary CoTiMA-0.8.0/CoTiMA/data/sampleSize18.rda |binary CoTiMA-0.8.0/CoTiMA/data/sampleSize201.rda |binary CoTiMA-0.8.0/CoTiMA/data/sampleSize313.rda |binary CoTiMA-0.8.0/CoTiMA/data/sampleSize32.rda |binary CoTiMA-0.8.0/CoTiMA/data/sampleSize4.rda |only CoTiMA-0.8.0/CoTiMA/data/source1.rda |only CoTiMA-0.8.0/CoTiMA/data/source128.rda |binary CoTiMA-0.8.0/CoTiMA/data/source18.rda |only CoTiMA-0.8.0/CoTiMA/data/source201.rda |binary CoTiMA-0.8.0/CoTiMA/data/source313.rda |binary CoTiMA-0.8.0/CoTiMA/data/source4.rda |only CoTiMA-0.8.0/CoTiMA/data/targetVariables1.rda |only CoTiMA-0.8.0/CoTiMA/data/targetVariables128.rda |binary CoTiMA-0.8.0/CoTiMA/data/targetVariables313.rda |binary CoTiMA-0.8.0/CoTiMA/data/targetVariables4.rda |only CoTiMA-0.8.0/CoTiMA/data/variableNames128.rda |binary CoTiMA-0.8.0/CoTiMA/data/variableNames18.rda |only CoTiMA-0.8.0/CoTiMA/data/variableNames201.rda |only CoTiMA-0.8.0/CoTiMA/data/variableNames32.rda |only CoTiMA-0.8.0/CoTiMA/inst/doc/CoTiMA_User_Guide.pdf |binary CoTiMA-0.8.0/CoTiMA/man/CoTiMAFullFit_3.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAFullFit_6.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAFullFit_6_new.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAFullInv23Fit_6.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAFullInvEq23Fit_6.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAInitFit_3.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAInitFit_6.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAInitFit_6_NUTS.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAInitFit_6_new.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAMod1onFullFit_6.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAMod1onFullFit_6_cats12.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAMod2on23Fit_6.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAPart134Inv3Fit_6.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAStanctArgs.Rd | 4 CoTiMA-0.8.0/CoTiMA/man/CoTiMAstudyList_6.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/CoTiMAstudyList_6_new.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/ageM1.Rd |only CoTiMA-0.8.0/CoTiMA/man/ageM4.Rd |only CoTiMA-0.8.0/CoTiMA/man/ageSD1.Rd |only CoTiMA-0.8.0/CoTiMA/man/ageSD4.Rd |only CoTiMA-0.8.0/CoTiMA/man/burnout1.Rd |only CoTiMA-0.8.0/CoTiMA/man/burnout4.Rd |only CoTiMA-0.8.0/CoTiMA/man/country1.Rd |only CoTiMA-0.8.0/CoTiMA/man/country4.Rd |only CoTiMA-0.8.0/CoTiMA/man/ctmaAllInvFit.Rd | 9 CoTiMA-0.8.0/CoTiMA/man/ctmaEmpCov.Rd | 6 CoTiMA-0.8.0/CoTiMA/man/ctmaFit.Rd | 19 CoTiMA-0.8.0/CoTiMA/man/ctmaInit.Rd | 22 CoTiMA-0.8.0/CoTiMA/man/ctmaOptimizeFit.Rd | 55 CoTiMA-0.8.0/CoTiMA/man/ctmaPlotCtsemMod.Rd | 14 CoTiMA-0.8.0/CoTiMA/man/ctmaPower.Rd | 4 CoTiMA-0.8.0/CoTiMA/man/ctmaPrep.Rd | 13 CoTiMA-0.8.0/CoTiMA/man/ctmaPub.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/ctmaRedHet.Rd | 6 CoTiMA-0.8.0/CoTiMA/man/ctmaShapeRawData.Rd | 10 CoTiMA-0.8.0/CoTiMA/man/delta_t1.Rd |only CoTiMA-0.8.0/CoTiMA/man/delta_t228.Rd |only CoTiMA-0.8.0/CoTiMA/man/delta_t4.Rd |only CoTiMA-0.8.0/CoTiMA/man/demands1.Rd |only CoTiMA-0.8.0/CoTiMA/man/demands4.Rd |only CoTiMA-0.8.0/CoTiMA/man/empcov1.Rd |only CoTiMA-0.8.0/CoTiMA/man/empcov128.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/empcov4.Rd |only CoTiMA-0.8.0/CoTiMA/man/malePercent1.Rd |only CoTiMA-0.8.0/CoTiMA/man/malePercent4.Rd |only CoTiMA-0.8.0/CoTiMA/man/moderator1.Rd |only CoTiMA-0.8.0/CoTiMA/man/moderator4.Rd |only CoTiMA-0.8.0/CoTiMA/man/occupation1.Rd |only CoTiMA-0.8.0/CoTiMA/man/occupation4.Rd |only CoTiMA-0.8.0/CoTiMA/man/pairwiseN128.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/rawData228.Rd |only CoTiMA-0.8.0/CoTiMA/man/results128.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/sampleSize1.Rd |only CoTiMA-0.8.0/CoTiMA/man/sampleSize128.Rd | 2 CoTiMA-0.8.0/CoTiMA/man/sampleSize4.Rd |only CoTiMA-0.8.0/CoTiMA/man/source1.Rd |only CoTiMA-0.8.0/CoTiMA/man/source18.Rd |only CoTiMA-0.8.0/CoTiMA/man/source4.Rd |only CoTiMA-0.8.0/CoTiMA/man/targetVariables1.Rd |only CoTiMA-0.8.0/CoTiMA/man/targetVariables4.Rd |only CoTiMA-0.8.0/CoTiMA/man/variableNames18.Rd |only CoTiMA-0.8.0/CoTiMA/man/variableNames201.Rd |only CoTiMA-0.8.0/CoTiMA/man/variableNames32.Rd |only 273 files changed, 3748 insertions(+), 3413 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel, Khanh Nguyen , Terry Leitch
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.21 dated 2024-02-01 and 0.4.22 dated 2024-04-25
ChangeLog | 30 ++++++++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/asian.R | 20 -------------------- R/zzz.R | 4 ++-- configure | 18 +++++++++--------- configure.ac | 2 +- data/tsQuotes.RData |binary data/vcube.RData |binary inst/NEWS.Rd | 11 ++++++++++- inst/tinytest/test_schedule.R | 4 ++-- src/Makevars.in | 2 +- src/bonds.cpp | 18 ++++++++++++++++-- src/zero.cpp | 8 ++++++-- 14 files changed, 94 insertions(+), 57 deletions(-)
Title: A Tool for Creating Custom Neural Networks in C++ and using Them
in R
Description: Contains a module to define neural networks from custom components and versions of Autoencoder, BP, LVQ, MAM NN.
Author: Vasilis Nikolaidis [aut, cph, cre]
Maintainer: Vasilis Nikolaidis <v.nikolaidis@uop.gr>
Diff between nnlib2Rcpp versions 0.2.5 dated 2024-03-09 and 0.2.6 dated 2024-04-25
DESCRIPTION | 6 MD5 | 24 +-- inst/doc/intro.ltx | 1 inst/doc/intro.pdf |binary man/LVQs-class.Rd | 267 ++++++++++++++++++++++++++----------- src/Rcpp_LVQ_supervised_module.cpp | 128 +++++++++++++++-- src/Rcpp_NN_module.cpp | 7 src/nn_lvq.cpp | 188 ++++++++++++++++++++------ src/nn_lvq.h | 150 ++++++++++++-------- src/nnlib2.h | 2 src/nnlib2_error.cpp | 5 src/nnlib2_error.h | 1 vignettes/intro.ltx | 1 13 files changed, 573 insertions(+), 207 deletions(-)
Title: Functions for Calculating Fit-Robustness of CNA-Solutions
Description: Functions for automatically performing
a reanalysis series
on a data set using CNA, and for calculating the fit-robustness
of the resulting models, as described in
Parkkinen and Baumgartner (2021) <doi:10.1177/0049124120986200>.
Author: Veli-Pekka Parkkinen [aut, cre, cph],
Michael Baumgartner [aut, cph],
Mathias Ambuehl [aut, cph]
Maintainer: Veli-Pekka Parkkinen <parkkinenv@gmail.com>
Diff between frscore versions 0.3.1 dated 2023-04-28 and 0.4.0 dated 2024-04-25
DESCRIPTION | 10 - MD5 | 28 +-- NEWS.md | 39 +++- R/causal_submodel.R | 2 R/frscore.R | 311 ++++++++++++++++++++-------------- R/frscored_cna.R | 22 +- README.md | 56 ------ build/partial.rdb |binary man/frscore-package.Rd | 1 man/frscored_cna.Rd | 7 man/rean_cna.Rd | 8 tests/testthat/_snaps/frscore.md | 95 ++++++++++ tests/testthat/_snaps/frscored_cna.md | 51 +++++ tests/testthat/test_frscore.R | 17 + tests/testthat/test_frscored_cna.R | 37 ++++ 15 files changed, 459 insertions(+), 225 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description: Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights; see Kolenikov, 2010;
Pfefferman & Rao, 2009a, 2009b, <doi:10.1016/S0169-7161(09)70003-3>,
<doi:10.1016/S0169-7161(09)70037-9>); Shao, 1996,
<doi:10.1080/02331889708802523>).
Descriptive statistics, linear and logistic regression,
path models for manifest variables with measurement error
correction and two-level hierarchical regressions for weighted
samples are included. Statistical inference can be conducted for
multiply imputed datasets and nested multiply imputed datasets
and is in particularly suited for the analysis of plausible values
(for details see George, Oberwimmer & Itzlinger-Bruneforth, 2016;
Bruneforth, Oberwimmer & Robitzsch, 2016; Robitzsch, Pham &
Yanagida, 2016). The package development was supported by BIFIE
(Federal Institute for Educational Research, Innovation and Development
of [...truncated...]
Author: BIFIE [aut], Alexander Robitzsch [aut, cre],
Konrad Oberwimmer [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between BIFIEsurvey versions 3.5-19 dated 2024-02-18 and 3.6-6 dated 2024-04-25
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/RcppExports.R | 2 +- build/partial.rdb |binary inst/NEWS | 9 +++++++++ src/RcppExports.cpp | 2 +- src/bifiesurvey_rcpp_logistreg.cpp | 8 +++++--- 7 files changed, 26 insertions(+), 15 deletions(-)
Title: Character String Operations and Interpolation, Magic Edition
Description: Performs complex string operations compactly and efficiently. Supports string interpolation jointly with over 50 string operations. Also enhances regular string functions (like grep() and co). See an introduction at <https://lrberge.github.io/stringmagic/>.
Author: Laurent R Berge [aut, cre] ,
Morgan Jacob [ctb]
Maintainer: Laurent R Berge <laurent.berge@u-bordeaux.fr>
Diff between stringmagic versions 1.1.0 dated 2024-03-06 and 1.1.1 dated 2024-04-25
DESCRIPTION | 6 - MD5 | 28 ++++---- NEWS.md | 6 + R/check.R | 7 +- R/string_magic_main.R | 8 ++ R/test_funs.R | 73 +++++++++++++--------- build/vignette.rds |binary inst/doc/guide_customization.R | 4 - inst/doc/guide_customization.html | 10 +-- inst/doc/guide_string_magic.html | 4 - inst/doc/guide_string_tools.html | 4 - inst/doc/ref_operations.html | 10 +-- inst/doc/ref_regex_flags.html | 4 - inst/doc/ref_regex_logic.html | 4 - inst/doc/ref_string_magic_special_operations.html | 26 +++---- 15 files changed, 113 insertions(+), 81 deletions(-)
Title: Policy Learning
Description: Framework for evaluating user-specified finite stage policies and learning realistic policies via doubly robust loss functions. Policy learning methods include doubly robust Q-learning, sequential policy tree learning, and outcome weighted learning. See Nordland and Holst (2022) <doi:10.48550/arXiv.2212.02335> for documentation and references.
Author: Andreas Nordland [aut, cre],
Klaus Holst [aut]
Maintainer: Andreas Nordland <andreasnordland@gmail.com>
Diff between polle versions 1.3 dated 2023-07-06 and 1.4 dated 2024-04-25
DESCRIPTION | 15 +++++---- MD5 | 70 ++++++++++++++++++++++++++------------------ NAMESPACE | 17 ++++++++++ NEWS.md | 15 +++++---- R/Q_function.R | 1 R/blip.R | 3 - R/drql.R | 2 - R/g_function.R | 3 + R/g_models.R | 18 +++++++---- R/nuisance_functions.R | 2 - R/policy_data.R | 22 ++++++------- R/policy_data_functions.R | 1 R/policy_def.R | 2 - R/policy_eval.R | 12 +++---- R/policy_learn.R | 48 +++++++++++++++--------------- R/policy_object_functions.R | 12 ++++++- R/polle-package.R | 16 ++-------- R/q_models.R | 20 ++++++------ R/sl_models.R | 4 +- build/partial.rdb |binary build/vignette.rds |only inst/doc |only man/g_model.Rd | 4 +- man/get_policy_functions.Rd | 2 + man/nuisance_functions.Rd | 2 - man/policy.Rd | 2 - man/policy_data.Rd | 22 ++++++------- man/policy_eval.Rd | 12 +++---- man/policy_learn.Rd | 46 ++++++++++++++-------------- man/polle-package.Rd | 27 +++++++++++----- man/q_model.Rd | 4 +- vignettes |only 32 files changed, 229 insertions(+), 175 deletions(-)
Title: Open System Files, 'URLs', Anything
Description: Cross platform solution to open files, directories or 'URLs'
with their associated programs.
Author: Gabor Csardi [aut, cre],
Fathi Boudra [aut],
Rex Dieter [aut],
Kevin Krammer [aut],
Jeremy White [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between xopen versions 1.0.0 dated 2018-09-17 and 1.0.1 dated 2024-04-25
DESCRIPTION | 27 ++++++++++++++++----------- LICENSE | 4 ++-- MD5 | 16 +++++++++------- NEWS.md | 5 ++++- R/xopen-package.R |only README.md | 18 +++++++++++++----- man/xopen-package.Rd |only man/xopen.Rd | 6 ++++-- tests/testthat.R | 8 ++++++++ tests/testthat/test.R | 3 --- 10 files changed, 56 insertions(+), 31 deletions(-)
Title: Visualization of Structures in High-Dimensional Data
Description: By gaining the property of emergence through self-organization, the enhancement of SOMs(self organizing maps) is called Emergent SOM (ESOM). The result of the projection by ESOM is a grid of neurons which can be visualised as a three dimensional landscape in form of the Umatrix. Further details can be found in the referenced publications (see url). This package offers tools for calculating and visualising the ESOM as well as Umatrix, Pmatrix and UStarMatrix. All the functionality is also available through graphical user interfaces implemented in 'shiny'. Based on the recognized data structures, the method can be used to generate new data.
Author: Florian Lerch[aut,cre], Michael Thrun[aut], Felix Pape[ctb], Jorn Lotsch[aut], Raphael Paebst[ctb], Alfred Ultsch[aut]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Diff between Umatrix versions 3.4.1 dated 2023-11-25 and 4.0 dated 2024-04-25
DESCRIPTION | 12 +- MD5 | 26 +++- NAMESPACE | 2 R/calculate_Delauny_radius.R |only R/esomInit.R | 4 R/esomTrain.R | 10 + R/esomTrainOnline.R | 212 +++++++++++++++++++++------------------- R/generate_data.R |only R/iEsomTrain.R | 7 - data/BMUHepta.rda |only man/BMUHepta.Rd |only man/Hepta.Rd | 4 man/Umatrix-package.Rd | 6 - man/calculate_Delauny_radius.Rd |only man/esomTrain.Rd | 3 man/generate_data.Rd |only man/iEsomTrain.Rd | 1 17 files changed, 160 insertions(+), 127 deletions(-)
Title: Models of Decision Confidence and Metacognition
Description: Provides fitting functions and other tools for decision confidence
and metacognition researchers, including meta-d'/d', often considered to be
the gold standard to measure metacognitive efficiency.
Also allows to fit several static models of decision making and confidence
to test the assumptions underlying meta-d'/d' and which may serve as an
alternative when the assumptions of meta-d'/d' do not hold. See also Rausch
et al. (2023) <doi:10.1037/met0000634>.
Author: Manuel Rausch [aut, cre] ,
Sebastian Hellmann [aut]
Maintainer: Manuel Rausch <manuel.rausch@hochschule-rhein-waal.de>
Diff between statConfR versions 0.0.1 dated 2023-09-22 and 0.1.1 dated 2024-04-25
statConfR-0.0.1/statConfR/R/int_fitSDTvarS.R |only statConfR-0.0.1/statConfR/R/int_rCEV.R |only statConfR-0.1.1/statConfR/DESCRIPTION | 22 +- statConfR-0.1.1/statConfR/MD5 | 51 +++-- statConfR-0.1.1/statConfR/NAMESPACE | 4 statConfR-0.1.1/statConfR/R/MaskOri-data.R | 12 - statConfR-0.1.1/statConfR/R/fitConf.R | 217 +++++++++++++++-------- statConfR-0.1.1/statConfR/R/fitConfModels.R | 223 ++++++++++++++++-------- statConfR-0.1.1/statConfR/R/fitMetaDprime.R | 20 +- statConfR-0.1.1/statConfR/R/int_fit2Chan.R | 80 +++----- statConfR-0.1.1/statConfR/R/int_fitCEV.R | 65 ++---- statConfR-0.1.1/statConfR/R/int_fitITG.R | 136 ++++++-------- statConfR-0.1.1/statConfR/R/int_fitLogWEV.R |only statConfR-0.1.1/statConfR/R/int_fitLognorm.R |only statConfR-0.1.1/statConfR/R/int_fitMetaDprime.R | 53 +++-- statConfR-0.1.1/statConfR/R/int_fitNoisy.R | 72 +++---- statConfR-0.1.1/statConfR/R/int_fitPDA.R | 73 +++---- statConfR-0.1.1/statConfR/R/int_fitSDT.R | 68 +++---- statConfR-0.1.1/statConfR/R/int_ll2Chan.R | 2 statConfR-0.1.1/statConfR/R/int_llITG.R | 2 statConfR-0.1.1/statConfR/R/int_llLogWEV.R |only statConfR-0.1.1/statConfR/R/int_llLognorm.R |only statConfR-0.1.1/statConfR/R/int_simulateConf.R |only statConfR-0.1.1/statConfR/R/simulateConf.R |only statConfR-0.1.1/statConfR/README.md | 165 ++++++++--------- statConfR-0.1.1/statConfR/data/MaskOri.RData |binary statConfR-0.1.1/statConfR/man/MaskOri.Rd | 8 statConfR-0.1.1/statConfR/man/fitConf.Rd | 164 +++++++++++------ statConfR-0.1.1/statConfR/man/fitConfModels.Rd | 177 ++++++++++++------- statConfR-0.1.1/statConfR/man/fitMetaDprime.Rd | 168 +++++++++--------- statConfR-0.1.1/statConfR/man/simConf.Rd |only 31 files changed, 998 insertions(+), 784 deletions(-)
Title: Package Admix for Admixture (aka Contamination) Models
Description: Implements techniques to estimate the unknown quantities related
to two-component admixture models, where the two components can belong to any
distribution (note that in the case of multinomial mixtures, the two components
must belong to the same family). Estimation methods depend on the assumptions
made on the unknown component density (see Bordes and Vandekerkhove (2010) <doi:10.3103/S1066530710010023>;
Patra and Sen (2016) <doi:10.1111/rssb.12148>); Milhaud, Pommeret, Salhi and Vandekerkhove
(2022) <doi:10.1016/j.jspi.2021.05.010>). In practice, one can estimate both the
mixture weight and the unknown component density in a wide variety of frameworks.
On top of that, hypothesis tests can be performed in one and two-sample contexts
to test the unknown component density (see Milhaud, Pommeret, Salhi, Vandekerkhove (2023)).
Finally, clustering of unknown mixture components is also feasible in a K-samples setting.
Author: Xavier Milhaud [aut, cre],
Pierre Vandekerkhove [ctb],
Denys Pommeret [ctb],
Yahia Salhi [ctb]
Maintainer: Xavier Milhaud <xavier.milhaud.research@gmail.com>
Diff between admix versions 2.1-2 dated 2023-07-12 and 2.1-3 dated 2024-04-25
DESCRIPTION | 8 - MD5 | 45 ++++--- R/IBM_2samples_test.R | 6 - R/IBM_estimProp.R | 8 - R/IBM_k_samples_test.R | 27 +++- R/IBM_tabul_stochasticInteg.R | 2 R/admix_clustering.R | 45 ++++--- R/admix_estim.R | 8 + R/admix_test.R | 7 - R/mortality_sample.R |only R/orthoBasis_test_H0.R | 8 - build/partial.rdb |binary build/vignette.rds |binary data/mortality_sample.rda |only inst/WORDLIST | 6 - inst/doc/admixture-clustering.R | 2 inst/doc/admixture-clustering.html | 142 +++++++++++-------------- inst/doc/admixture-weight-estimation.R | 2 inst/doc/admixture-weight-estimation.html | 170 +++++++++++++++--------------- inst/doc/test-hypothesis.R | 2 inst/doc/test-hypothesis.html | 124 ++++++++++----------- man/admix_clustering.Rd | 26 +++- man/admix_test.Rd | 5 man/mortality_sample.Rd |only man/orthoBasis_test_H0.Rd | 6 - 25 files changed, 347 insertions(+), 302 deletions(-)
Title: Fake Web Apps for HTTP Testing
Description: Create a web app that makes it easier to test web clients
without using the internet. It includes a web app framework with path
matching, parameters and templates. Can parse various 'HTTP' request
bodies. Can send 'JSON' data or files from the disk. Includes a web
app that implements the 'httpbin.org' web service.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd],
Civetweb contributors [ctb] ,
Redoc contributors [ctb] ,
L. Peter Deutsch [ctb] ,
Martin Purschke [ctb] ,
Aladdin Enterprises [cph] ,
Maelle Salmon [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between webfakes versions 1.3.0 dated 2023-12-10 and 1.3.1 dated 2024-04-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 +++++- src/rweb.c | 4 ++++ 4 files changed, 15 insertions(+), 7 deletions(-)
Title: Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indexes, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [aut] ,
Ned Horning [aut],
Jakob Schwalb-Willmann [aut] ,
Robert J. Hijmans [ctb] ,
Konstantin Mueller [aut, cre]
Maintainer: Konstantin Mueller <konstantinfinn.mueller@gmx.de>
Diff between RStoolbox versions 0.4.0 dated 2024-01-17 and 1.0.0 dated 2024-04-25
RStoolbox-0.4.0/RStoolbox/R/RStoolbox.R |only RStoolbox-0.4.0/RStoolbox/inst/external/srtm.rds |only RStoolbox-0.4.0/RStoolbox/inst/external/trainingPoints.rds |only RStoolbox-0.4.0/RStoolbox/inst/external/trainingPolygons.rds |only RStoolbox-1.0.0/RStoolbox/DESCRIPTION | 20 RStoolbox-1.0.0/RStoolbox/MD5 | 141 +++--- RStoolbox-1.0.0/RStoolbox/NAMESPACE | 4 RStoolbox-1.0.0/RStoolbox/NEWS.md | 22 RStoolbox-1.0.0/RStoolbox/R/RStoolbox-package.R |only RStoolbox-1.0.0/RStoolbox/R/classifyQA.R | 2 RStoolbox-1.0.0/RStoolbox/R/cloudMask.R | 2 RStoolbox-1.0.0/RStoolbox/R/coregisterImages.R | 4 RStoolbox-1.0.0/RStoolbox/R/estimateHaze.R | 2 RStoolbox-1.0.0/RStoolbox/R/fCover.R | 4 RStoolbox-1.0.0/RStoolbox/R/getValidation.R | 2 RStoolbox-1.0.0/RStoolbox/R/ggR.R | 16 RStoolbox-1.0.0/RStoolbox/R/ggRGB.R | 6 RStoolbox-1.0.0/RStoolbox/R/histMatch.R | 4 RStoolbox-1.0.0/RStoolbox/R/internalFunctions.R | 2 RStoolbox-1.0.0/RStoolbox/R/mesma.R | 149 +++++- RStoolbox-1.0.0/RStoolbox/R/oneHotEncode.R | 2 RStoolbox-1.0.0/RStoolbox/R/panSharpen.R | 4 RStoolbox-1.0.0/RStoolbox/R/pifMatch.R | 4 RStoolbox-1.0.0/RStoolbox/R/radCor.R | 3 RStoolbox-1.0.0/RStoolbox/R/rasterCVA.R | 4 RStoolbox-1.0.0/RStoolbox/R/rasterEntropy.R | 2 RStoolbox-1.0.0/RStoolbox/R/rasterPCA.R | 4 RStoolbox-1.0.0/RStoolbox/R/rescaleImage.R | 2 RStoolbox-1.0.0/RStoolbox/R/sam.R | 2 RStoolbox-1.0.0/RStoolbox/R/spectralIndices.R | 2 RStoolbox-1.0.0/RStoolbox/R/superClass.R | 39 - RStoolbox-1.0.0/RStoolbox/R/tasseledCap.R | 2 RStoolbox-1.0.0/RStoolbox/R/unsuperClass.R | 3 RStoolbox-1.0.0/RStoolbox/R/validateMap.R | 4 RStoolbox-1.0.0/RStoolbox/R/zzz.R | 18 RStoolbox-1.0.0/RStoolbox/README.md | 222 +++++++++- RStoolbox-1.0.0/RStoolbox/inst/external/sen2.rds |only RStoolbox-1.0.0/RStoolbox/inst/external/srtm_lsat.rds |only RStoolbox-1.0.0/RStoolbox/inst/external/srtm_sen2.rds |only RStoolbox-1.0.0/RStoolbox/inst/external/trainingPoints_rlogo.rds |only RStoolbox-1.0.0/RStoolbox/inst/external/trainingPolygons_lsat.rds |only RStoolbox-1.0.0/RStoolbox/inst/external/trainingPolygons_sen2.rds |only RStoolbox-1.0.0/RStoolbox/man/RStoolbox.Rd | 20 RStoolbox-1.0.0/RStoolbox/man/classifyQA.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/cloudMask.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/coregisterImages.Rd | 4 RStoolbox-1.0.0/RStoolbox/man/estimateHaze.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/fCover.Rd | 4 RStoolbox-1.0.0/RStoolbox/man/getValidation.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/ggR.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/ggRGB.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/histMatch.Rd | 4 RStoolbox-1.0.0/RStoolbox/man/lsat.Rd | 4 RStoolbox-1.0.0/RStoolbox/man/mesma.Rd | 83 ++- RStoolbox-1.0.0/RStoolbox/man/oneHotEncode.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/panSharpen.Rd | 4 RStoolbox-1.0.0/RStoolbox/man/pifMatch.Rd | 4 RStoolbox-1.0.0/RStoolbox/man/radCor.Rd | 1 RStoolbox-1.0.0/RStoolbox/man/rasterCVA.Rd | 4 RStoolbox-1.0.0/RStoolbox/man/rasterEntropy.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/rasterPCA.Rd | 4 RStoolbox-1.0.0/RStoolbox/man/rescaleImage.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/rlogo.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/sam.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/sen2.Rd |only RStoolbox-1.0.0/RStoolbox/man/spectralIndices.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/srtm.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/srtm_sen2.Rd |only RStoolbox-1.0.0/RStoolbox/man/superClass.Rd | 3 RStoolbox-1.0.0/RStoolbox/man/tasseledCap.Rd | 2 RStoolbox-1.0.0/RStoolbox/man/validateMap.Rd | 4 RStoolbox-1.0.0/RStoolbox/tests/testthat/test-getValidation.R | 2 RStoolbox-1.0.0/RStoolbox/tests/testthat/test-ggplot.R | 8 RStoolbox-1.0.0/RStoolbox/tests/testthat/test-internalFunctions.R | 2 RStoolbox-1.0.0/RStoolbox/tests/testthat/test-mesma.R | 63 ++ RStoolbox-1.0.0/RStoolbox/tests/testthat/test-saveReadRSTBX.R | 2 RStoolbox-1.0.0/RStoolbox/tests/testthat/test-superClass.R | 16 RStoolbox-1.0.0/RStoolbox/tests/testthat/test-validateMap.R | 2 78 files changed, 662 insertions(+), 301 deletions(-)
Title: Cryptographic Hash and Extendable-Output Functions
Description: Fast and memory-efficient streaming hash functions. Performs direct
hashing of strings, raw bytes, and files potentially larger than memory, as
well as hashing in-memory objects through R's serialization mechanism,
without requiring allocation of the serialized object. Implementations
include the SHA-256, SHA-3 and 'Keccak' cryptographic hash functions,
SHAKE256 extendable-output function (XOF), and 'SipHash' pseudo-random
function. The SHA-3 Secure Hash Standard was published by the National
Institute of Standards and Technology (NIST) in 2015 at
<doi:10.6028/NIST.FIPS.202>. The SHA-256 Secure Hash Standard was published
by NIST in 2002 at
<https://csrc.nist.gov/publications/fips/fips180-2/fips180-2.pdf>.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between secretbase versions 0.4.0 dated 2024-04-04 and 0.5.0 dated 2024-04-25
DESCRIPTION | 17 +++-- MD5 | 32 +++++----- NAMESPACE | 2 NEWS.md | 6 ++ R/base.R | 135 ++++++++++++++++++++++++++++++++++++++-------- README.md | 33 ++++++----- man/keccak.Rd |only man/secretbase-package.Rd | 2 man/sha256.Rd | 29 +++++---- man/sha3.Rd | 47 +++++++--------- man/shake256.Rd |only man/siphash13.Rd | 35 ++++++----- src/init.c | 4 + src/secret.c | 84 ++++++++++++++++++++++++---- src/secret.h | 31 +++------- src/secret2.c | 4 - src/secret3.c | 4 - tests/tests.R | 23 +++++++ 18 files changed, 335 insertions(+), 153 deletions(-)
Title: Debug R Packages
Description: Specify debug messages as special string constants, and
control debugging of packages via environment variables.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between debugme versions 1.1.0 dated 2017-10-22 and 1.2.0 dated 2024-04-25
debugme-1.1.0/debugme/inst |only debugme-1.2.0/debugme/DESCRIPTION | 26 ++++-- debugme-1.2.0/debugme/LICENSE | 4 debugme-1.2.0/debugme/MD5 | 39 +++++---- debugme-1.2.0/debugme/NEWS.md | 33 +++++++- debugme-1.2.0/debugme/R/colors.R | 40 +++++++++ debugme-1.2.0/debugme/R/compat-defer.R |only debugme-1.2.0/debugme/R/debug.R | 69 +++++++++++++---- debugme-1.2.0/debugme/R/debugme-package.R |only debugme-1.2.0/debugme/R/instrument.R | 37 ++++++--- debugme-1.2.0/debugme/R/package.R | 61 +++++++++++---- debugme-1.2.0/debugme/R/rematch.R |only debugme-1.2.0/debugme/README.md |only debugme-1.2.0/debugme/man/debug.Rd | 6 - debugme-1.2.0/debugme/man/debugme-package.Rd |only debugme-1.2.0/debugme/man/debugme.Rd | 54 +++++++++---- debugme-1.2.0/debugme/tests/testthat.R | 8 + debugme-1.2.0/debugme/tests/testthat/test-colors.R | 3 debugme-1.2.0/debugme/tests/testthat/test-debug.R | 12 -- debugme-1.2.0/debugme/tests/testthat/test-dynamic.R | 3 debugme-1.2.0/debugme/tests/testthat/test-instrument.R | 17 +++- debugme-1.2.0/debugme/tests/testthat/test-levels.R |only debugme-1.2.0/debugme/tests/testthat/test-package.R | 15 ++- 23 files changed, 315 insertions(+), 112 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.9.5 dated 2024-03-15 and 0.9.6 dated 2024-04-25
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 12 ++++++++++++ R/finbif_occurrence.R | 8 +++++++- R/finbif_occurrence_load.R | 24 +++++++++++++++--------- R/finbif_records.R | 4 ++-- R/sysdata.rda |binary README.md | 2 +- inst/NEWS.Rd | 15 +++++++++++++++ tests/testthat/test-metadata.R | 2 +- 10 files changed, 65 insertions(+), 26 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The [...truncated...]
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.32.6 dated 2024-03-01 and 2.32.7 dated 2024-04-25
DESCRIPTION | 10 MD5 | 35 - inst/doc/stanmath.html | 6 inst/include/stan/math/memory/stack_alloc.hpp | 3 inst/include/stan/math/prim/fun/max.hpp | 2 inst/include/stan/math/prim/fun/min.hpp | 2 inst/include/stan/math/prim/fun/value_of.hpp | 24 - inst/include/stan/math/prim/meta/is_eigen_dense_base.hpp | 16 inst/include/stan/math/prim/meta/promote_scalar_type.hpp | 14 inst/include/stan/math/rev/core/arena_matrix.hpp | 308 ++++++++++++- inst/include/stan/math/rev/core/var.hpp | 12 inst/include/stan/math/rev/core/var_value_fwd_declare.hpp | 10 inst/include/stan/math/rev/core/vari.hpp | 48 +- inst/include/stan/math/rev/fun.hpp | 1 inst/include/stan/math/rev/fun/csr_matrix_times_vector.hpp | 104 ++-- inst/include/stan/math/rev/fun/to_soa_sparse_matrix.hpp |only inst/include/stan/math/rev/fun/to_var_value.hpp | 7 inst/include/stan/math/rev/meta/arena_type.hpp | 6 inst/include/stan/math/rev/meta/conditional_var_value.hpp | 2 19 files changed, 484 insertions(+), 126 deletions(-)
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:
2023-10-02 0.1.4
2023-08-18 0.1.1
2023-07-08 0.0.7
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
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 - 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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(-)
Title: Computation and Visualization of Package Download Counts and
Percentiles
Description: Compute and visualize the cross-sectional and longitudinal number
and rank percentile of package downloads from Posit/RStudio's CRAN mirror.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>
Diff between packageRank versions 0.8.3 dated 2023-11-09 and 0.9.0 dated 2024-04-23
packageRank-0.8.3/packageRank/man/archivePackages.Rd |only packageRank-0.8.3/packageRank/man/cranPackages.Rd |only packageRank-0.8.3/packageRank/man/extractArchiveDate.Rd |only packageRank-0.8.3/packageRank/man/fetchCranLog.Rd |only packageRank-0.8.3/packageRank/man/fetchRLog.Rd |only packageRank-0.8.3/packageRank/man/ipFilter.Rd |only packageRank-0.8.3/packageRank/man/packageArchive.Rd |only packageRank-0.8.3/packageRank/man/packageCRAN.Rd |only packageRank-0.8.3/packageRank/man/packages_in_Archive.Rd |only packageRank-0.8.3/packageRank/man/packages_observed_in_logs.Rd |only packageRank-0.8.3/packageRank/man/packages_on_CRAN.Rd |only packageRank-0.8.3/packageRank/man/packages_partitioned.Rd |only packageRank-0.8.3/packageRank/man/sequenceFilter.Rd |only packageRank-0.8.3/packageRank/man/sizeFilter.Rd |only packageRank-0.8.3/packageRank/man/smallFilter.Rd |only packageRank-0.8.3/packageRank/man/tripletFilter.Rd |only packageRank-0.9.0/packageRank/DESCRIPTION | 13 packageRank-0.9.0/packageRank/MD5 | 155 - 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Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition
Examination Survey (NHANES) website <https://www.cdc.gov/nchs/nhanes/index.htm>.
Author: Christopher Endres [aut, cre],
Laha Ale [aut] ,
Robert Gentleman [aut],
Deepayan Sarkar [aut]
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 1.0 dated 2024-01-09 and 1.1 dated 2024-04-23
DESCRIPTION | 10 ++--- MD5 | 23 ++++++----- R/nhanes.R | 10 ++--- R/nhanes_codebook.R | 4 +- R/nhanes_constants.R | 1 R/nhanes_search.R | 33 +++------------- R/nhanes_tables.R | 75 +++++++++++++++++++++++++++++++++++--- R/nhanes_translate.R | 15 +++++++ build/vignette.rds |binary inst/CITATION |only inst/doc/Introducing_nhanesA.html | 4 +- inst/doc/UsingSurveyWeights.html | 8 ++-- man/nhanesManifest.Rd | 5 ++ 13 files changed, 127 insertions(+), 61 deletions(-)
Title: Causal Moderated Mediation Analysis
Description: Causal moderated mediation analysis using the methods proposed by Qin and Wang (2023) <doi:10.3758/s13428-023-02095-4>. Causal moderated mediation analysis is crucial for investigating how, for whom, and where a treatment is effective by assessing the heterogeneity of mediation mechanism across individuals and contexts. This package enables researchers to estimate and test the conditional and moderated mediation effects, assess their sensitivity to unmeasured pre-treatment confounding, and visualize the results. The package is built based on the quasi-Bayesian Monte Carlo method, because it has relatively better performance at small sample sizes, and its running speed is the fastest. The package is applicable to a treatment of any scale, a binary or continuous mediator, a binary or continuous outcome, and one or more moderators of any scale.
Author: Xu Qin [aut, cre, cph],
Lijuan Wang [ctb]
Maintainer: Xu Qin <xuqin@pitt.edu>
Diff between moderate.mediation versions 0.0.8 dated 2024-02-29 and 0.0.9 dated 2024-04-23
DESCRIPTION | 8 +++---- MD5 | 8 +++---- R/moderate.mediation.R | 54 +++++++++++++++++++++++++++++++++++++------------ man/modmed.Rd | 2 - man/modmed.sens.Rd | 2 - 5 files changed, 51 insertions(+), 23 deletions(-)
More information about moderate.mediation at CRAN
Permanent link
Title: Experimental Statistics and Graphics for Agricultural Sciences
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootech [...truncated...]
Author: Gabriel Danilo Shimizu [aut, cre]
,
Rodrigo Yudi Palhaci Marubayashi [aut, ctb]
,
Leandro Simoes Azeredo Goncalves [aut, ctb]
Maintainer: Gabriel Danilo Shimizu <gabrield.shimizu@gmail.com>
Diff between AgroR versions 1.3.5 dated 2023-09-13 and 1.3.6 dated 2024-04-23
DESCRIPTION | 8 MD5 | 84 +++++----- NAMESPACE | 3 NEWS.md | 14 + R/DBCglm_function.R | 4 R/DICglm_function.R | 4 R/FAT2DBC_function.R | 18 +- R/FAT2DBCad_function.R | 25 +-- R/FAT2DIC_function.R | 18 +- R/FAT2DICad_function.R | 25 +-- R/FAT3DBC_function.R | 8 R/FAT3DBCad_function.R | 10 - R/FAT3DIC_function.R | 8 R/FAT3DICad_function.R | 10 - R/PSUBDBC_function.R | 25 +-- R/PSUBDIC_function.R | 27 +-- R/bargraph_function.R | 10 - R/conjdbc_function.R | 9 - R/conjdic_function.R | 33 ++-- R/correlation_function.R | 34 ++-- R/dbc_function.R | 12 - R/dic_function.R | 16 + R/dql_function.R | 12 - R/dunnet_function.R | 11 - R/fat2_table.R |only R/grid_onefactor.R |only R/polynomial2color_function.R | 2 R/seggraph2_function.R | 6 R/seggraph_function.R | 8 R/sk_graph_function.R | 56 +++--- R/summarise_conj.R |only R/summarise_function.R | 337 +++++++++++++++++++++++++++++++++++------- R/tabledesc_function.R | 2 README.md | 4 build/partial.rdb |binary man/DBC.Rd | 3 man/DIC.Rd | 3 man/DQL.Rd | 3 man/bar_graph.Rd | 10 + man/corgraph.Rd | 20 ++ man/fat2_table.Rd |only man/grid.onefactor.Rd |only man/polynomial2_color.Rd | 2 man/sk_graph.Rd | 4 man/summarise_anova.Rd | 3 man/summarise_conj.Rd |only 46 files changed, 628 insertions(+), 263 deletions(-)
Title: Pediatric Blood Pressure
Description: Data and utilities for estimating pediatric blood pressure
percentiles by sex, age, and optionally height (stature) as described in
Martin et.al. (2022) <doi:10.1001/jamanetworkopen.2022.36918>.
Blood pressure percentiles for children under one year of age come from Gemelli
et.al. (1990) <doi:10.1007/BF02171556>. Estimates of blood pressure
percentiles for children at least one year of age are informed by
data from the National Heart, Lung, and Blood Institute (NHLBI) and the
Centers for Disease Control and Prevention (CDC)
<doi:10.1542/peds.2009-2107C> or from Lo et.al. (2013)
<doi:10.1542/peds.2012-1292>. The flowchart for selecting the informing
data source comes from Martin et.al. (2022)
<doi:10.1542/hpeds.2021-005998>.
Author: Peter DeWitt [aut, cre] ,
Blake Martin [ctb] ,
David Albers [ctb] ,
Tell Bennett [ctb]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between pedbp versions 1.0.2 dated 2022-11-23 and 2.0.0 dated 2024-04-23
pedbp-1.0.2/pedbp/man/pediatric_vital_sign_distributions.Rd |only pedbp-1.0.2/pedbp/tests/test-head_circ_for_age.R |only pedbp-1.0.2/pedbp/tests/test-length_for_age_inf.R |only pedbp-1.0.2/pedbp/tests/test-stature_for_age.R |only pedbp-1.0.2/pedbp/tests/test-weight_for_age_inf.R |only pedbp-1.0.2/pedbp/tests/test-weight_for_length_inf.R |only pedbp-1.0.2/pedbp/tests/test-weight_for_stature.R |only pedbp-2.0.0/pedbp/DESCRIPTION | 21 pedbp-2.0.0/pedbp/MD5 | 143 + pedbp-2.0.0/pedbp/NAMESPACE | 37 pedbp-2.0.0/pedbp/NEWS.md | 52 pedbp-2.0.0/pedbp/R/RcppExports.R |only pedbp-2.0.0/pedbp/R/bmi_for_age.R |only pedbp-2.0.0/pedbp/R/bp_cdf_plot.R | 137 + pedbp-2.0.0/pedbp/R/bp_charts.R |only pedbp-2.0.0/pedbp/R/bp_distribution.R | 282 +-- pedbp-2.0.0/pedbp/R/datasets.R | 12 pedbp-2.0.0/pedbp/R/est_norm.R | 35 pedbp-2.0.0/pedbp/R/growth-standard-charts.R |only pedbp-2.0.0/pedbp/R/growth-standards.R |only pedbp-2.0.0/pedbp/R/gs_cdf.R |only pedbp-2.0.0/pedbp/R/head_circumference_for_age.R |only pedbp-2.0.0/pedbp/R/lms.R | 532 +------ pedbp-2.0.0/pedbp/R/pedbp-defunct.R |only pedbp-2.0.0/pedbp/R/pedbp-package.R |only pedbp-2.0.0/pedbp/R/stature_for_age.R |only pedbp-2.0.0/pedbp/R/sysdata.rda |binary pedbp-2.0.0/pedbp/R/weight_for_age.R |only pedbp-2.0.0/pedbp/R/weight_for_stature.R |only pedbp-2.0.0/pedbp/R/zzz.R |only pedbp-2.0.0/pedbp/README.md | 177 +- pedbp-2.0.0/pedbp/build/partial.rdb |only pedbp-2.0.0/pedbp/build/vignette.rds |binary pedbp-2.0.0/pedbp/data/bp_parameters.rda |binary pedbp-2.0.0/pedbp/data/flynn2017.rda |only pedbp-2.0.0/pedbp/data/gemelli1990.rda |binary pedbp-2.0.0/pedbp/data/lo2013.rda |binary pedbp-2.0.0/pedbp/data/nhlbi_bp_norms.rda |binary pedbp-2.0.0/pedbp/inst/CITATION | 11 pedbp-2.0.0/pedbp/inst/WORDLIST | 36 pedbp-2.0.0/pedbp/inst/doc/bp-distributions.R | 365 ---- pedbp-2.0.0/pedbp/inst/doc/bp-distributions.Rmd | 731 +--------- pedbp-2.0.0/pedbp/inst/doc/bp-distributions.html | 693 ++------- pedbp-2.0.0/pedbp/inst/doc/growth-standards.R |only pedbp-2.0.0/pedbp/inst/doc/growth-standards.Rmd |only pedbp-2.0.0/pedbp/inst/doc/growth-standards.html |only pedbp-2.0.0/pedbp/inst/images/bp_cdf_example-1.png |binary pedbp-2.0.0/pedbp/inst/shinyapps/pedbp/overview.md | 33 pedbp-2.0.0/pedbp/inst/shinyapps/pedbp/server.R | 731 +++++++++- pedbp-2.0.0/pedbp/inst/shinyapps/pedbp/ui.R | 656 +++++++- pedbp-2.0.0/pedbp/man/bmi_for_age.Rd |only pedbp-2.0.0/pedbp/man/bp_cdf.Rd | 60 pedbp-2.0.0/pedbp/man/bp_chart.Rd |only pedbp-2.0.0/pedbp/man/bp_distribution.Rd | 176 ++ pedbp-2.0.0/pedbp/man/bpdata.Rd | 17 pedbp-2.0.0/pedbp/man/cppBP.Rd |only pedbp-2.0.0/pedbp/man/cppPGSF.Rd |only pedbp-2.0.0/pedbp/man/distribution-quantile-zscores-by-lms.Rd |only pedbp-2.0.0/pedbp/man/est_norm.Rd | 19 pedbp-2.0.0/pedbp/man/figures |only pedbp-2.0.0/pedbp/man/growth-standards.Rd |only pedbp-2.0.0/pedbp/man/gs_cdf.Rd |only pedbp-2.0.0/pedbp/man/gs_chart.Rd |only pedbp-2.0.0/pedbp/man/head_circumference_for_age.Rd |only pedbp-2.0.0/pedbp/man/pedbp-defunct.Rd |only pedbp-2.0.0/pedbp/man/pedbp-package.Rd |only pedbp-2.0.0/pedbp/man/stature_for_age.Rd |only pedbp-2.0.0/pedbp/man/weight_for_age.Rd |only pedbp-2.0.0/pedbp/man/weight_for_stature.Rd |only pedbp-2.0.0/pedbp/src |only pedbp-2.0.0/pedbp/tests/test-bmi_for_age.R | 350 +--- pedbp-2.0.0/pedbp/tests/test-bp-by-source.R |only pedbp-2.0.0/pedbp/tests/test-bp_cdf.R |only pedbp-2.0.0/pedbp/tests/test-bp_chart.R |only pedbp-2.0.0/pedbp/tests/test-bp_distributions.R | 453 ++++-- pedbp-2.0.0/pedbp/tests/test-bp_parameters.R | 28 pedbp-2.0.0/pedbp/tests/test-cppBP.R |only pedbp-2.0.0/pedbp/tests/test-cppPGSF.R |only pedbp-2.0.0/pedbp/tests/test-est_norm.R | 93 + pedbp-2.0.0/pedbp/tests/test-gemelli1990.R | 13 pedbp-2.0.0/pedbp/tests/test-gs_chart.R |only pedbp-2.0.0/pedbp/tests/test-head_circumference_for_age.R |only pedbp-2.0.0/pedbp/tests/test-height_for_age.R |only pedbp-2.0.0/pedbp/tests/test-internal-data.R |only pedbp-2.0.0/pedbp/tests/test-length_for_age.R |only pedbp-2.0.0/pedbp/tests/test-lms.R |only pedbp-2.0.0/pedbp/tests/test-lo2013.R | 16 pedbp-2.0.0/pedbp/tests/test-nhlbi_bp_norms.R | 12 pedbp-2.0.0/pedbp/tests/test-weight_for_age.R | 353 +--- pedbp-2.0.0/pedbp/tests/test-weight_for_height.R |only pedbp-2.0.0/pedbp/tests/test-weight_for_length.R |only pedbp-2.0.0/pedbp/vignettes/bp-distributions.Rmd | 731 +--------- pedbp-2.0.0/pedbp/vignettes/growth-standards.Rmd |only pedbp-2.0.0/pedbp/vignettes/references.bib | 41 94 files changed, 3328 insertions(+), 3718 deletions(-)
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>. The package also provides
function [...truncated...]
Author: Stefan Widgren [aut, cre] ,
Robin Eriksson [aut] ,
Stefan Engblom [aut] ,
Pavol Bauer [aut] ,
Thomas Rosendal [ctb] ,
Ivana Rodriguez Ewerloef [ctb] ,
Attractive Chaos [cph]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 9.6.0 dated 2023-12-20 and 9.7.0 dated 2024-04-23
DESCRIPTION | 8 MD5 | 93 ++--- NAMESPACE | 2 NEWS.md | 23 + R/C-generator.R | 144 +++++++- R/SimInf.R | 6 R/SimInf_indiv_events.R | 396 +++++++++++++++++++++-- R/check_arguments.R | 57 +++ R/distance.R | 15 R/mparse.R | 453 ++++++++++++++++++++------ R/prevalence.R | 26 + R/u0.R | 115 ++++-- R/v0.R | 15 README.md | 22 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/SimInf.pdf |binary inst/doc/post-process-data.R |only inst/doc/post-process-data.Rmd |only inst/doc/post-process-data.html |only inst/doc/scheduled-events.R | 39 ++ inst/doc/scheduled-events.Rmd | 96 +++++ inst/doc/scheduled-events.html | 102 +++++- man/SEIR.Rd | 8 man/SIR.Rd | 8 man/SIS.Rd | 8 man/SISe.Rd | 8 man/SISe3.Rd | 8 man/SISe3_sp.Rd | 8 man/SISe_sp.Rd | 8 man/SimInf.Rd | 28 + man/distance_matrix.Rd | 11 man/events.Rd | 22 - man/figures |only man/individual_events.Rd | 3 man/mparse.Rd | 89 +++-- man/node_events.Rd |only man/prevalence-SimInf_pfilter-method.Rd |only man/u0.Rd | 24 - man/v0-set.Rd | 13 src/init.c | 6 src/misc/SimInf_clean_indiv_events.c | 38 +- src/misc/SimInf_distance_matrix.c | 37 +- tests/SimInf_model.R | 4 tests/indiv_events.R | 540 +++++++++++++++++++++++++++++++- tests/ldata_sp.R | 23 + tests/mparse.R | 167 +++++++++ tests/pfilter.R | 12 tests/v0.R | 9 vignettes/post-process-data.Rmd |only vignettes/scheduled-events.Rmd | 96 +++++ 51 files changed, 2368 insertions(+), 422 deletions(-)
Title: Get Silhouettes of Organisms from PhyloPic
Description: Work with the PhyloPic Web Service (<http://api-docs.phylopic.org/v2/>)
to fetch silhouette images of organisms. Includes functions for adding
silhouettes to both base R plots and ggplot2 plots.
Author: William Gearty [aut, cre] ,
Lewis A. Jones [aut] ,
Scott Chamberlain [aut] ,
David Miller [ctb]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between rphylopic versions 1.3.0 dated 2023-12-20 and 1.4.0 dated 2024-04-23
DESCRIPTION | 8 MD5 | 94 ++++----- NAMESPACE | 4 NEWS.md | 5 R/add_phylopic_legend.R |only R/get_attribution.R | 103 +++++++--- R/pick_phylopic.R | 16 + R/zzz.r | 20 + build/vignette.rds |binary inst/doc/a-getting-started.Rmd | 27 +- inst/doc/a-getting-started.html | 27 +- inst/doc/b-advanced-ggplot.Rmd | 36 ++- inst/doc/b-advanced-ggplot.html | 73 +++---- inst/doc/c-advanced-base.Rmd | 2 inst/doc/c-advanced-base.html | 16 - man/add_phylopic_legend.Rd |only man/get_attribution.Rd | 13 + man/pick_phylopic.Rd | 6 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/add_phylopic_base/phylopic-in-background.svg | 11 - tests/testthat/_snaps/add_phylopic_legend |only tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-img.svg | 13 - tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-larger-glyphs.svg | 26 +- tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-uuid.svg | 13 - tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph.svg | 24 +- tests/testthat/test-add_phylopic_legend.R |only tests/testthat/test-get_attribution.R | 11 - tests/testthat/test-pick_phylo.R | 5 tests/testthat/test-resolve_phylopic.R | 6 vignettes/a-getting-started.Rmd | 27 +- vignettes/b-advanced-ggplot.Rmd | 36 ++- vignettes/base-geog-plot-2-1.png |binary vignettes/base-penguin-plot-2-1.png |binary vignettes/base-penguin-plot-3-1.png |binary vignettes/base-penguin-plot-4-1.png |binary vignettes/base-penguin-plot-5-1.png |binary vignettes/base-phylo-plot-3-1.png |binary vignettes/base-phylo-plot-4-1.png |binary vignettes/c-advanced-base.Rmd | 2 vignettes/ggplot-geog-plot-2-1.png |binary vignettes/ggplot-geog-plot-3-1.png |binary vignettes/ggplot-penguin-plot-2-1.png |binary vignettes/ggplot-penguin-plot-3-1.png |binary vignettes/ggplot-penguin-plot-4-1.png |binary vignettes/ggplot-penguin-plot-5-1.png |binary vignettes/ggplot-penguin-plot-6-1.png |binary vignettes/ggplot-phylo-plot-2-1.png |binary vignettes/ggplot-phylo-plot-3-1.png |binary vignettes/ggplot-phylo-plot-4-1.png |binary 49 files changed, 391 insertions(+), 233 deletions(-)
Title: Infrastructure for Partially Observable Markov Decision
Processes (POMDP)
Description: Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Process (POMDP) models. Interfaces for various exact and approximate solution algorithms are available including value iteration, point-based value iteration and SARSOP. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Author: Michael Hahsler [aut, cph, cre]
,
Hossein Kamalzadeh [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between pomdp versions 1.2.1 dated 2024-04-09 and 1.2.2 dated 2024-04-23
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 7 +++++++ R/round_stochchastic.R | 5 ++--- R/simulate_MDP.R | 2 +- R/simulate_POMDP.R | 7 +++++-- inst/doc/gridworlds.html | 46 +++++++++++++++++++++++----------------------- inst/doc/pomdp.Rmd | 2 +- inst/doc/pomdp.html | 14 +++++++------- man/round_stochastic.Rd | 6 ++---- man/simulate_MDP.Rd | 2 +- man/simulate_POMDP.Rd | 1 + src/POMDP.cpp | 20 ++++++++++++++++---- src/math.cpp | 3 --- tests/testthat/test-cpp.R | 1 + vignettes/pomdp.Rmd | 2 +- 16 files changed, 87 insertions(+), 69 deletions(-)
Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse
set of pipelining operators ('PipeOps') that can be composed into graphs.
Operations exist for data preprocessing, model fitting, and ensemble
learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can
therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre],
Florian Pfisterer [aut] ,
Lennart Schneider [aut] ,
Bernd Bischl [aut] ,
Michel Lang [aut] ,
Sebastian Fischer [ctb] ,
Susanne Dandl [aut]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr3pipelines versions 0.5.1 dated 2024-03-26 and 0.5.2 dated 2024-04-23
mlr3pipelines-0.5.1/mlr3pipelines/tests/testthat/helper_compat.R |only mlr3pipelines-0.5.1/mlr3pipelines/tests/testthat/helper_functions.R |only mlr3pipelines-0.5.1/mlr3pipelines/tests/testthat/helper_test_pipeops.R |only mlr3pipelines-0.5.2/mlr3pipelines/DESCRIPTION | 18 mlr3pipelines-0.5.2/mlr3pipelines/MD5 | 320 +++++----- mlr3pipelines-0.5.2/mlr3pipelines/NAMESPACE | 1 mlr3pipelines-0.5.2/mlr3pipelines/NEWS.md | 8 mlr3pipelines-0.5.2/mlr3pipelines/R/GraphLearner.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpBoxCox.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpClassifAvg.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpEncode.R | 14 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpEncodeLmer.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpFilter.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpICA.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpImputeLearner.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpKernelPCA.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpLearner.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpLearnerCV.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpNMF.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpOVR.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpProxy.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpRandomResponse.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpRegrAvg.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpSmote.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpTextVectorizer.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpThreshold.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpTrafo.R | 6 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpTuneThreshold.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpVtreat.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpYeoJohnson.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/mlr_graphs.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/mlr_pipeops.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_bagging.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_convert_types.R |only mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_ovr.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_robustify.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_stacking.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_targettrafo.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/po.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/ppl.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/inst/testthat |only mlr3pipelines-0.5.2/mlr3pipelines/man/Graph.Rd | 8 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOp.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpEnsemble.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpImpute.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpTargetTrafo.Rd | 20 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpTaskPreproc.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpTaskPreprocSimple.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs.Rd | 10 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_bagging.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_convert_types.Rd |only mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_ovr.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_robustify.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_stacking.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_targettrafo.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_learners_graph.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_boxcox.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_branch.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_chunk.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_classbalancing.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_classifavg.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_classweights.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_colapply.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_collapsefactors.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_colroles.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_copy.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_datefeatures.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_encode.Rd | 24 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_encodeimpact.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_encodelmer.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_featureunion.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_filter.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_fixfactors.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_histbin.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_ica.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputeconstant.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputehist.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputelearner.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputemean.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputemedian.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputemode.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputeoor.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputesample.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_kernelpca.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_learner.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_learner_cv.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_missind.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_modelmatrix.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_multiplicityexply.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_multiplicityimply.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_mutate.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_nmf.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_nop.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_ovrsplit.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_ovrunite.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_pca.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_proxy.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_quantilebin.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_randomprojection.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_randomresponse.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_regravg.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_removeconstants.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_renamecolumns.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_replicate.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_scale.Rd | 10 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_scalemaxabs.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_scalerange.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_select.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_smote.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_spatialsign.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_subsample.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_targetinvert.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_targetmutate.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_targettrafoscalerange.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_textvectorizer.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_threshold.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_tunethreshold.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_unbranch.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_updatetarget.Rd | 18 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_vtreat.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_yeojohnson.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/po.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/ppl.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/helper_mlr3pipelines.R |only mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_Graph.R | 5 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_GraphLearner.R | 9 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_conversion.R | 7 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_dictionary.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_learner_weightedaverage.R | 3 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_bagging.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_branching.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_convert_types.R |only mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_ovr.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_robustify.R | 3 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mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_ovr.R | 3 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_proxy.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_randomresponse.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_smote.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_targetmutate.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_targettrafoscalerange.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_textvectorizer.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_threshold.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_tunethreshold.R | 3 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_updatetarget.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_yeojohnson.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_po.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_ppl.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_resample.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_typecheck.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_usecases.R | 11 164 files changed, 912 insertions(+), 615 deletions(-)
Title: Download Flight and Airport Data from Brazil
Description: Download flight and airport data from Brazil’s Civil Aviation Agency
(ANAC) <https://www.gov.br/anac>. The data includes detailed
information on all aircrafts, aerodromes, airports, and airport
movements registered in ANAC, on airfares and on every international
flight to and from Brazil, as well as domestic flights within the country.
Author: Rafael H. M. Pereira [aut, cre]
,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between flightsbr versions 0.4.0 dated 2023-12-04 and 0.4.1 dated 2024-04-23
DESCRIPTION | 8 +- MD5 | 46 ++++++------- NAMESPACE | 36 +++++----- NEWS.md | 8 ++ R/utils.R | 8 +- README.md | 4 - man/download_aircrafts_data.Rd | 64 +++++++++--------- man/download_airfares_data.Rd | 70 ++++++++++---------- man/download_airport_movement_data.Rd | 70 ++++++++++---------- man/download_flightsbr_file.Rd | 76 ++++++++++----------- man/flightsbr.Rd | 75 ++++++++++----------- man/get_aircrafts_dates_available.Rd | 42 ++++++------ man/get_aircrafts_url.Rd | 52 +++++++------- man/get_airfares_dates_available.Rd | 52 +++++++------- man/get_airfares_url.Rd | 60 ++++++++--------- man/get_airport_movement_dates_available.Rd | 52 +++++++------- man/get_airport_movements_url.Rd | 52 +++++++------- man/get_flight_dates_available.Rd | 42 ++++++------ man/get_flights_url.Rd | 60 ++++++++--------- man/latest_flights_date.Rd | 44 ++++++------ man/read_aircrafts.Rd | 74 ++++++++++----------- man/read_airfares.Rd | 98 ++++++++++++++-------------- man/read_airport_movements.Rd | 78 +++++++++++----------- man/read_airports.Rd | 74 ++++++++++----------- 24 files changed, 628 insertions(+), 617 deletions(-)
Title: Collapsed Latent Position Cluster Model for Social Networks
Description: Markov chain Monte Carlo based inference routines for collapsed latent position cluster models or social networks, which includes searches over the model space (number of clusters in the latent position cluster model). The label switching algorithm used is that of Nobile and Fearnside (2007) <doi:10.1007/s11222-006-9014-7> which relies on the algorithm of Carpaneto and Toth (1980) <doi:10.1145/355873.355883>.
Author: Jason Wyse [aut, cre],
Caitriona Ryan [aut],
Nial Friel [ths]
Maintainer: Jason Wyse <wyseja@tcd.ie>
Diff between collpcm versions 1.3 dated 2024-01-09 and 1.4 dated 2024-04-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/collpcm.undo.label.switching.R | 19 +++++++++++-------- build/vignette.rds |binary inst/doc/collpcm.pdf |binary 6 files changed, 26 insertions(+), 17 deletions(-)
Title: General Utility Functions for Analysis of Clinical Data
Description: Utility functions to facilitate the import,
the reporting and analysis of clinical data.
Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains
from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate
the package functionalities.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Arne De Roeck [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between clinUtils versions 0.1.4 dated 2023-01-06 and 0.1.5 dated 2024-04-23
DESCRIPTION | 10 MD5 | 81 R/compareTables.R | 90 R/data.R | 61 R/loadDataADaMSDTM.R | 13 R/plots-palettes.R | 1 R/plots-palettesCDISC.R | 36 R/plots-utility.R | 13 R/roundHalfUp.R | 8 R/table-getClinDT.R | 30 build/vignette.rds |binary data/dataADaMCDISCP01.RData |binary data/dataSDTMCDISCP01.RData |binary inst/NEWS | 6 inst/doc/clinUtils-vignette.html |90262 ++++++++++++++++++------------ inst/extdata/cdiscpilot01/SDTM/ae.xpt |binary inst/extdata/cdiscpilot01/SDTM/cm.xpt |binary inst/extdata/cdiscpilot01/SDTM/dm.xpt |binary inst/extdata/cdiscpilot01/SDTM/ds.xpt |only inst/extdata/cdiscpilot01/SDTM/ex.xpt |binary inst/extdata/cdiscpilot01/SDTM/lb.xpt |binary inst/extdata/cdiscpilot01/SDTM/mh.xpt |binary inst/extdata/cdiscpilot01/SDTM/qs.xpt |only inst/extdata/cdiscpilot01/SDTM/suppdm.xpt |only inst/extdata/cdiscpilot01/SDTM/sv.xpt |binary inst/extdata/cdiscpilot01/SDTM/vs.xpt |binary man/clinColors.Rd | 13 man/colorPaletteNRIND.Rd | 12 man/compareDiff.Rd | 40 man/compareTables.Rd | 38 man/comparisonTables-common-args.Rd | 22 man/dataADaMCDISCP01.Rd | 32 man/dataSDTMCDISCP01.Rd | 29 man/exportDiffData.Rd | 16 man/formatDTBarVar.Rd | 12 man/formatVarForPlotLabel.Rd | 13 man/getClinDT.Rd | 24 man/getClinDTButtons.Rd | 6 man/getLabelVar.Rd | 13 man/getPaletteCDISC.Rd | 12 man/mergeDiffWithData.Rd | 12 man/roundHalfUpTextFormat.Rd | 8 man/shapePaletteNRIND.Rd | 12 43 files changed, 56895 insertions(+), 34030 deletions(-)
Title: A Program for Missing Data
Description: A tool that "multiply imputes" missing data in a single cross-section
(such as a survey), from a time series (like variables collected for
each year in a country), or from a time-series-cross-sectional data
set (such as collected by years for each of several countries).
Amelia II implements our bootstrapping-based algorithm that gives
essentially the same answers as the standard IP or EMis approaches,
is usually considerably faster than existing approaches and can
handle many more variables. Unlike Amelia I and other statistically
rigorous imputation software, it virtually never crashes (but please
let us know if you find to the contrary!). The program also
generalizes existing approaches by allowing for trends in time series
across observations within a cross-sectional unit, as well as priors
that allow experts to incorporate beliefs they have about the values
of missing cells in their data. Amelia II also includes useful
diagnostics of the fit of multiple imputation models. The p [...truncated...]
Author: James Honaker [aut],
Gary King [aut],
Matthew Blackwell [aut, cre]
Maintainer: Matthew Blackwell <mblackwell@gov.harvard.edu>
Diff between Amelia versions 1.8.1 dated 2022-11-19 and 1.8.2 dated 2024-04-23
Amelia-1.8.1/Amelia/man/amelia.package.Rd |only Amelia-1.8.2/Amelia/DESCRIPTION | 10 Amelia-1.8.2/Amelia/MD5 | 37 +- Amelia-1.8.2/Amelia/R/amelia-package.R |only Amelia-1.8.2/Amelia/R/ameliagui.r | 10 Amelia-1.8.2/Amelia/R/diag.r | 8 Amelia-1.8.2/Amelia/R/emb.r | 6 Amelia-1.8.2/Amelia/R/prep.r | 2 Amelia-1.8.2/Amelia/build/partial.rdb |binary Amelia-1.8.2/Amelia/build/vignette.rds |binary Amelia-1.8.2/Amelia/inst/doc/ameliaview.html | 183 +++++------ Amelia-1.8.2/Amelia/inst/doc/diagnostics.html | 175 +++++------ Amelia-1.8.2/Amelia/inst/doc/intro-mi.Rmd | 2 Amelia-1.8.2/Amelia/inst/doc/intro-mi.html | 86 ++--- Amelia-1.8.2/Amelia/inst/doc/using-amelia.Rmd | 4 Amelia-1.8.2/Amelia/inst/doc/using-amelia.html | 387 ++++++++++++------------- Amelia-1.8.2/Amelia/man/Amelia-package.Rd |only Amelia-1.8.2/Amelia/src/Makevars | 1 Amelia-1.8.2/Amelia/src/Makevars.win | 1 Amelia-1.8.2/Amelia/vignettes/intro-mi.Rmd | 2 Amelia-1.8.2/Amelia/vignettes/using-amelia.Rmd | 4 21 files changed, 455 insertions(+), 463 deletions(-)
Title: Dynamic OpenAPI/Swagger Client
Description: Access services specified in OpenAPI (formerly Swagger) format.
It is not a code generator. Client is generated dynamically as a list of R
functions.
Author: Darko Bergant [aut, cre],
Marcel Ramos [ctb],
Sean Davis [ctb],
Martin Morgan [ctb]
Maintainer: Darko Bergant <darko.bergant@gmail.com>
Diff between rapiclient versions 0.1.3 dated 2020-01-17 and 0.1.4 dated 2024-04-23
DESCRIPTION | 25 ++++++++++++++++--------- MD5 | 26 +++++++++++++------------- R/operations.R | 12 +++++++++--- R/print.R | 6 +++--- R/rapiclient.R | 3 +-- man/get_operation_definitions.Rd | 2 +- man/get_operations.Rd | 3 +-- man/get_parameters.Rd | 2 -- man/get_schema_graphviz_dot.Rd | 9 +++++++-- man/print.rapi_api.Rd | 2 +- man/print.rapi_operation.Rd | 2 +- man/print.rapi_schema_function.Rd | 2 +- man/rapiclient-package.Rd | 19 +++++++++++++++++++ man/result_handlers.Rd | 6 +++--- 14 files changed, 76 insertions(+), 43 deletions(-)
Title: Interfaces to Phylogenetic Software in R
Description: Functions that wrap popular phylogenetic software for sequence
alignment, masking of sequence alignments, and estimation of phylogenies and
ancestral character states.
Author: Christoph Heibl [aut, cre],
Natalie Cusimano [aut],
Franz-Sebastian Krah [aut]
Maintainer: Christoph Heibl <christoph.heibl@gmx.net>
Diff between ips versions 0.0.11 dated 2019-07-04 and 0.0.12 dated 2024-04-23
ips-0.0.11/ips/inst/NEWS.Rd |only ips-0.0.11/ips/man/deleteEmptyCells.Rd |only ips-0.0.12/ips/DESCRIPTION | 15 - ips-0.0.12/ips/MD5 | 132 ++++++++------- ips-0.0.12/ips/NAMESPACE | 19 ++ ips-0.0.12/ips/NEWS.md |only ips-0.0.12/ips/R/EmptyCells.R |only ips-0.0.12/ips/R/aliscore.R | 2 ips-0.0.12/ips/R/assembleDataNode.R | 29 ++- ips-0.0.12/ips/R/assembleDistributionNode.R | 115 ------------- ips-0.0.12/ips/R/assembleInitNode.R | 64 +++++-- ips-0.0.12/ips/R/assembleLikelihoodNode.R |only ips-0.0.12/ips/R/assembleLoggers.R | 189 ++++++++++++++++------ ips-0.0.12/ips/R/assembleOperators.R | 237 ++++++++++++++++++---------- ips-0.0.12/ips/R/assemblePriorNode.R |only ips-0.0.12/ips/R/assembleStateNode.R | 160 +++++++++++++++--- ips-0.0.12/ips/R/assembleTaxonSetPrior.R |only ips-0.0.12/ips/R/assembleTreeNode.R |only ips-0.0.12/ips/R/beastLog.R |only ips-0.0.12/ips/R/blastn.R |only ips-0.0.12/ips/R/combMyTree.R |only ips-0.0.12/ips/R/deleteEmptyCells.R | 37 ---- ips-0.0.12/ips/R/descendants.R | 1 ips-0.0.12/ips/R/extractBEASTstats.R | 1 ips-0.0.12/ips/R/gammaPrior.R |only ips-0.0.12/ips/R/gblocks.R | 4 ips-0.0.12/ips/R/identifyEmptyCells.R |only ips-0.0.12/ips/R/mafft.R | 18 +- ips-0.0.12/ips/R/mrbayes.R | 59 ++++++ ips-0.0.12/ips/R/multistateML.R | 6 ips-0.0.12/ips/R/operator.R |only ips-0.0.12/ips/R/parameter.R |only ips-0.0.12/ips/R/phylo2mafft.R | 2 ips-0.0.12/ips/R/pis.R | 30 +++ ips-0.0.12/ips/R/prank.R | 4 ips-0.0.12/ips/R/raxml.R | 6 ips-0.0.12/ips/R/rbeauti.R | 200 +++++++++++++++++++---- ips-0.0.12/ips/R/rbeauti.taxonset.R | 10 - ips-0.0.12/ips/R/rc.R | 90 +++++++--- ips-0.0.12/ips/R/read.beast.R | 176 ++++++++++---------- ips-0.0.12/ips/R/read.beast.table.R | 2 ips-0.0.12/ips/R/read.fas.R | 3 ips-0.0.12/ips/R/sister.R | 2 ips-0.0.12/ips/R/trimEnds.R | 26 ++- ips-0.0.12/ips/R/write.nex.R | 1 ips-0.0.12/ips/README.md | 2 ips-0.0.12/ips/data/log_list.rda |only ips-0.0.12/ips/data/operator_list.rda |only ips-0.0.12/ips/inst/CITATION | 11 - ips-0.0.12/ips/man/EmptyCells.Rd |only ips-0.0.12/ips/man/aliscore.Rd | 2 ips-0.0.12/ips/man/beastLog.Rd |only ips-0.0.12/ips/man/blastn.Rd |only ips-0.0.12/ips/man/combMyTree.Rd |only ips-0.0.12/ips/man/gblocks.Rd | 16 + ips-0.0.12/ips/man/ips-internal.Rd | 6 ips-0.0.12/ips/man/ips-package.Rd | 4 ips-0.0.12/ips/man/ips.16S.Rd | 2 ips-0.0.12/ips/man/ips.28S.Rd | 2 ips-0.0.12/ips/man/ips.cox1.Rd | 2 ips-0.0.12/ips/man/ips.tree.Rd | 2 ips-0.0.12/ips/man/mafft.Rd | 24 ++ ips-0.0.12/ips/man/mafft.merge.Rd | 3 ips-0.0.12/ips/man/mrbayes.Rd | 130 ++++++++------- ips-0.0.12/ips/man/mrbayes.lset.Rd | 4 ips-0.0.12/ips/man/mrbayes.mcmc.Rd | 2 ips-0.0.12/ips/man/mrbayes.prset.Rd | 2 ips-0.0.12/ips/man/multistate.Rd | 6 ips-0.0.12/ips/man/oi.Rd | 3 ips-0.0.12/ips/man/partitionfinder.Rd | 12 + ips-0.0.12/ips/man/phylo2mafft.Rd | 2 ips-0.0.12/ips/man/pis.Rd | 46 ++--- ips-0.0.12/ips/man/prank.Rd | 2 ips-0.0.12/ips/man/raxml.Rd | 24 ++ ips-0.0.12/ips/man/rbeauti.Rd | 112 +++++++------ ips-0.0.12/ips/man/rc.Rd |only ips-0.0.12/ips/man/read.beast.Rd | 12 - ips-0.0.12/ips/man/read.beast.table.Rd | 2 78 files changed, 1310 insertions(+), 765 deletions(-)
Title: 'R' Bindings for 'TMB'
Description: Native 'R' interface to 'TMB' (Template Model Builder) so models can be written entirely in 'R' rather than 'C++'. Automatic differentiation, to any order, is available for a rich subset of 'R' features, including linear algebra for dense and sparse matrices, complex arithmetic, Fast Fourier Transform, probability distributions and special functions. 'RTMB' provides easy access to model fitting and validation following the principles of Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. M. (2016) <DOI:10.18637/jss.v070.i05> and Thygesen, U.H., Albertsen, C.M., Berg, C.W. et al. (2017) <DOI:10.1007/s10651-017-0372-4>.
Author: Kasper Kristensen [aut, cre]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between RTMB versions 1.4 dated 2023-12-01 and 1.5 dated 2024-04-23
DESCRIPTION | 8 MD5 | 64 +++--- NAMESPACE | 5 R/00roxygen.R | 18 + R/RcppExports.R | 36 ++- R/adjoint.R |only R/advector.R | 101 ++++++--- R/methods.R | 75 ++++++- R/mvgauss.R | 15 + build/vignette.rds |binary inst/doc/RTMB-advanced.R | 46 ++++ inst/doc/RTMB-advanced.html | 207 +++++++++++++------- inst/doc/RTMB-advanced.rmd | 92 ++++++++ inst/doc/RTMB-introduction.html | 6 inst/include |only inst/tinytest/test-distributions.R | 27 ++ inst/tinytest/test-tape.R | 50 ++++ man/ADapply.Rd | 6 man/ADconstruct.Rd | 5 man/ADjoint.Rd |only man/ADmatrix.Rd | 7 man/ADvector.Rd | 10 man/Distributions.Rd | 24 ++ man/RTMB-package.Rd | 8 man/TMB-interface.Rd | 3 man/Tape.Rd | 28 ++ src/RTMB.cpp | 382 ------------------------------------- src/RTMB.h | 11 - src/RTMB_tape.cpp |only src/RcppExports.cpp | 103 +++++++-- src/math.cpp | 20 + src/misc.cpp | 76 ++++++- vignettes/RTMB-advanced.rmd | 92 ++++++++ 33 files changed, 940 insertions(+), 585 deletions(-)
Title: Routines for L1 Estimation
Description: L1 estimation for linear regression using Barrodale and Roberts' method
<doi:10.1145/355616.361024> and the EM algorithm <doi:10.1023/A:1020759012226>.
Estimation of mean and covariance matrix using the multivariate Laplace distribution,
density, distribution function, quantile function and random number generation
for univariate and multivariate Laplace distribution <doi:10.1080/03610929808832115>.
Author: Felipe Osorio [aut, cre] ,
Tymoteusz Wolodzko [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between L1pack versions 0.41-24 dated 2023-05-18 and 0.41-245 dated 2024-04-23
ChangeLog | 17 +++++++++++++---- DESCRIPTION | 15 ++++++++------- MD5 | 46 +++++++++++++++++++++++++++------------------- NAMESPACE | 9 +++++---- R/LaplaceFit.R |only R/distn.R | 21 +++++++++++++-------- R/lad.R | 16 +++++++++------- R/wilson_hilferty.R |only data |only inst/CITATION | 8 ++++---- man/Laplace.Rd | 19 ++++++++----------- man/LaplaceFit.Rd |only man/confint.lad.Rd | 4 ++-- man/ereturns.Rd |only man/l1fit.Rd | 4 ++-- man/lad.Rd | 18 +++++++++--------- man/mLaplace.Rd | 16 ++++++++++------ man/vcov.lad.Rd | 2 +- man/wilson.hilferty.Rd |only src/R_init_L1pack.c | 30 ++++++++++++++++++++---------- src/base.h | 5 +++-- src/distn.c | 33 ++++++++++++++++++++++++++++++++- src/interface.c | 46 +++++++++++++++++++++++++++++++++++++++++++++- src/interface.h | 12 +++++++++++- src/lad.h | 6 ++---- src/lad_EM.c | 15 ++++++++++----- src/laplace_fitter.c |only src/wilson-hilferty.c |only 28 files changed, 234 insertions(+), 108 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre, cph],
Matt Dennis [ctb],
Antoine Bichat [ctb] ,
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb],
Swechhya Bista [ctb],
Colin Fay [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>
Diff between emayili versions 0.7.18 dated 2023-08-30 and 0.8.0 dated 2024-04-23
emayili-0.7.18/emayili/inst/shiny/send-message/rsconnect |only emayili-0.8.0/emayili/DESCRIPTION | 8 +-- emayili-0.8.0/emayili/MD5 | 13 ++--- emayili-0.8.0/emayili/NAMESPACE | 3 + emayili-0.8.0/emayili/R/encodable.R | 1 emayili-0.8.0/emayili/R/header.R | 1 emayili-0.8.0/emayili/R/server.R | 39 +++++++++++++-- emayili-0.8.0/emayili/man/server.Rd | 15 +++++ 8 files changed, 64 insertions(+), 16 deletions(-)
Title: Testing Randomness in R
Description: Provides several non parametric randomness tests for numeric sequences.
Author: Frederico Caeiro [aut, cre] ,
Ayana Mateus [aut]
Maintainer: Frederico Caeiro <fac@fct.unl.pt>
Diff between randtests versions 1.0.1 dated 2022-06-20 and 1.0.2 dated 2024-04-23
randtests-1.0.1/randtests/NEWS |only randtests-1.0.2/randtests/Changes |only randtests-1.0.2/randtests/DESCRIPTION | 8 +-- randtests-1.0.2/randtests/MD5 | 6 +- randtests-1.0.2/randtests/man/randtests-package.Rd | 56 ++++++++++----------- 5 files changed, 35 insertions(+), 35 deletions(-)
Title: Support Technical Processes Following 'Maelstrom Research'
Standards
Description: Functions to support rigorous processes in data cleaning,
evaluation, and documentation across datasets from different studies based
on Maelstrom Research guidelines. The package includes the core functions
to evaluate and format the main inputs that define the process, diagnose
errors, and summarize and evaluate datasets and their associated
data dictionaries. The main outputs are clean datasets and associated
metadata, and tabular and visual summary reports. As described in
Maelstrom Research guidelines for rigorous retrospective data
harmonization (Fortier I and al. (2017) <doi:10.1093/ije/dyw075>).
Author: Guillaume Fabre [aut, cre] ,
Maelstrom-research group [cph, fnd]
Maintainer: Guillaume Fabre <guijoseph.fabre@gmail.com>
Diff between madshapR versions 1.0.3 dated 2023-12-19 and 1.1.0 dated 2024-04-23
madshapR-1.0.3/madshapR/R/07-data_summarise.R |only madshapR-1.0.3/madshapR/man/madshapR_help.Rd |only madshapR-1.1.0/madshapR/DESCRIPTION | 6 madshapR-1.1.0/madshapR/MD5 | 78 - madshapR-1.1.0/madshapR/NAMESPACE | 1 madshapR-1.1.0/madshapR/NEWS.md | 516 ++++++----- madshapR-1.1.0/madshapR/R/01-utils.R | 4 madshapR-1.1.0/madshapR/R/02-dictionaries_functions.R | 60 - madshapR-1.1.0/madshapR/R/03-dataset_functions.R | 13 madshapR-1.1.0/madshapR/R/04-catalogue_functions.R | 302 ++++-- madshapR-1.1.0/madshapR/R/05-unit_checks.R | 230 +--- madshapR-1.1.0/madshapR/R/06-data_evaluate.R | 118 +- madshapR-1.1.0/madshapR/R/07-data_summarize.R |only madshapR-1.1.0/madshapR/R/08-data_visualize.R | 199 ++-- madshapR-1.1.0/madshapR/R/deprecated.R | 23 madshapR-1.1.0/madshapR/README.md | 2 madshapR-1.1.0/madshapR/build/partial.rdb |binary madshapR-1.1.0/madshapR/build/vignette.rds |binary madshapR-1.1.0/madshapR/data/madshapR_DEMO.rda |binary madshapR-1.1.0/madshapR/data/valueType_list.rda |binary madshapR-1.1.0/madshapR/inst/WORDLIST | 14 madshapR-1.1.0/madshapR/inst/doc/madshapR-vignette.R | 2 madshapR-1.1.0/madshapR/inst/doc/madshapR-vignette.Rmd | 2 madshapR-1.1.0/madshapR/inst/doc/madshapR-vignette.html | 2 madshapR-1.1.0/madshapR/man/check_dataset_categories.Rd | 13 madshapR-1.1.0/madshapR/man/data_dict_evaluate.Rd | 3 madshapR-1.1.0/madshapR/man/dataset_evaluate.Rd | 19 madshapR-1.1.0/madshapR/man/dataset_preprocess.Rd | 4 madshapR-1.1.0/madshapR/man/dataset_summarize.Rd | 5 madshapR-1.1.0/madshapR/man/dataset_visualize.Rd | 8 madshapR-1.1.0/madshapR/man/deprecated.Rd | 7 madshapR-1.1.0/madshapR/man/dossier_evaluate.Rd | 12 madshapR-1.1.0/madshapR/man/dossier_summarize.Rd | 2 madshapR-1.1.0/madshapR/man/madshapR_website.Rd |only madshapR-1.1.0/madshapR/man/summary_variables.Rd | 12 madshapR-1.1.0/madshapR/man/summary_variables_categorical.Rd | 12 madshapR-1.1.0/madshapR/man/summary_variables_date.Rd | 19 madshapR-1.1.0/madshapR/man/summary_variables_datetime.Rd | 10 madshapR-1.1.0/madshapR/man/summary_variables_numeric.Rd | 12 madshapR-1.1.0/madshapR/man/summary_variables_text.Rd | 12 madshapR-1.1.0/madshapR/man/variable_visualize.Rd | 7 madshapR-1.1.0/madshapR/vignettes/madshapR-vignette.Rmd | 2 42 files changed, 1029 insertions(+), 702 deletions(-)
Title: Nonparametric Change Point Detection for Multivariate Time
Series
Description: Implements the nonparametric moving sum procedure for detecting
changes in the joint characteristic function (NP-MOJO) for multiple change
point detection in multivariate time series. See McGonigle, E. T., Cho, H.
(2023) <doi:10.48550/arXiv.2305.07581> for description of the NP-MOJO methodology.
Author: Euan T. McGonigle [aut, cre],
Haeran Cho [aut]
Maintainer: Euan T. McGonigle <e.t.mcgonigle@soton.ac.uk>
Diff between CptNonPar versions 0.1.1 dated 2023-06-13 and 0.2.1 dated 2024-04-23
DESCRIPTION | 10 - MD5 | 29 ++- NAMESPACE | 1 NEWS.md | 13 + R/multilag.cpts.merge.R | 14 + R/multiscale.np.mojo.R |only R/np.mojo.R | 45 +++-- R/np.mojo.multilag.R | 52 +++--- R/utils.R | 2 man/multilag.cpts.merge.Rd | 8 - man/multiscale.np.mojo.Rd |only man/np.mojo.Rd | 41 ++--- man/np.mojo.multilag.Rd | 46 +++-- tests/testthat/test-multilag.R | 22 +- tests/testthat/test-multiscale.np.mojo.R |only tests/testthat/test-np.R | 240 ++++++++++++++++++------------- tests/testthat/test-np.mojo.R | 28 ++- 17 files changed, 318 insertions(+), 233 deletions(-)
Title: Multiple Data Analysis Tools for Property Listing Tasks
Description: Application to estimate statistical values using properties provided by a group of individuals to describe
concepts using 'shiny'. It estimates the underlying distribution to generate new descriptive words
Canessa et al. (2023) <doi:10.3758/s13428-022-01811-w>, applies a new clustering model, and uses simulations to estimate
the probability that two persons describe the same words based on their descriptions
Canessa et al. (2022) <doi:10.3758/s13428-022-02030-z>.
Author: Sebastian Moreno [aut, cre],
Cristobal Heredia [aut],
Enrique Canessa [ths],
Sergio Chaigneau [ths]
Maintainer: Sebastian Moreno <sebastian.moreno.araya@gmail.com>
Diff between WordListsAnalytics versions 0.2.0 dated 2024-04-18 and 0.2.1 dated 2024-04-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/PLT_server.R | 9 +++++---- 3 files changed, 10 insertions(+), 9 deletions(-)
More information about WordListsAnalytics at CRAN
Permanent link
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] ,
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
Francois Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.12.0 dated 2023-06-21 and 2.13.0 dated 2024-04-23
DESCRIPTION | 13 - MD5 | 105 +++++------ NAMESPACE | 5 NEWS.md | 18 + R/copy_labels.R | 49 +++-- R/is_prefixed.R | 3 R/lookfor.R | 115 +++++++----- R/na_values.R | 77 +++++--- R/recode.R | 32 +-- R/recode_if.R | 14 - R/remove_attributes.R | 3 R/remove_labels.R | 30 +-- R/retrocompatibility.R | 12 - R/tagged_na.R | 44 +++- R/to_character.R | 46 ++-- R/to_factor.R | 146 ++++++++------- R/to_labelled.R | 117 +++++++----- R/to_na.R | 6 R/update_with.R |only R/val_labels.R | 347 +++++++++++++++++++++++++------------ R/var_label.R | 35 ++- README.md | 2 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/intro_labelled.R | 46 ++-- inst/doc/intro_labelled.Rmd | 42 ++-- inst/doc/intro_labelled.html | 40 ++-- inst/doc/look_for.R | 2 inst/doc/look_for.html | 292 +++++++++++++------------------ inst/doc/missing_values.R | 2 inst/doc/packed_columns.Rmd | 2 inst/doc/packed_columns.html | 4 man/copy_labels.Rd | 12 - man/look_for.Rd | 4 man/na_values.Rd | 5 man/recode.haven_labelled.Rd | 7 man/recode_if.Rd | 2 man/remove_attributes.Rd | 3 man/sort_val_labels.Rd | 4 man/to_character.Rd | 5 man/to_factor.Rd | 15 - man/to_labelled.Rd | 32 +-- man/update_variable_labels_with.Rd |only man/val_labels.Rd | 51 ++++- man/var_label.Rd | 15 - tests/spelling.R | 3 tests/testthat/test-copy_labels.r | 4 tests/testthat/test-labelled.r | 50 ++++- tests/testthat/test-miscellanous.R | 2 tests/testthat/test-na_values.R | 21 +- tests/testthat/test-to_labelled.r | 35 +-- tests/testthat/test-update_with.r |only tests/testthat/test_lookfor.R | 13 - vignettes/intro_labelled.Rmd | 42 ++-- vignettes/packed_columns.Rmd | 2 55 files changed, 1148 insertions(+), 829 deletions(-)
Title: Inflators for Australian Policy Analysis
Description: Using Australian Bureau of Statistics indices, provides functions
that convert historical, nominal statistics to real, contemporary values
without worrying about date input quality, performance, or the ABS catalogue.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between grattanInflators versions 0.5.1 dated 2024-03-26 and 0.5.3 dated 2024-04-23
grattanInflators-0.5.1/grattanInflators/src/C_fastIDate.c |only grattanInflators-0.5.3/grattanInflators/DESCRIPTION | 6 grattanInflators-0.5.3/grattanInflators/MD5 | 22 - grattanInflators-0.5.3/grattanInflators/NEWS.md | 7 grattanInflators-0.5.3/grattanInflators/R/fast_as_idate.R | 16 grattanInflators-0.5.3/grattanInflators/inst/tinytest/test_cpi_inflator.R | 2 grattanInflators-0.5.3/grattanInflators/inst/tinytest/test_guess_format.R |only grattanInflators-0.5.3/grattanInflators/inst/tinytest/test_lf_inflator.R | 43 +- grattanInflators-0.5.3/grattanInflators/man/fast_as_idate.Rd | 79 ++- grattanInflators-0.5.3/grattanInflators/src/check_input.c | 2 grattanInflators-0.5.3/grattanInflators/src/grattanInflator.h | 1 grattanInflators-0.5.3/grattanInflators/src/idate_YearMonth.c | 203 +++++++++- grattanInflators-0.5.3/grattanInflators/src/init.c | 24 - 13 files changed, 303 insertions(+), 102 deletions(-)
More information about grattanInflators at CRAN
Permanent link
Title: Estimation in Difference-in-Difference Designs with Multiple
Groups and Periods
Description: Estimation of event-study Difference-in-Difference (DID) estimators in designs with multiple groups and periods, and with a potentially non-binary treatment that may increase or decrease multiple times.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut]
Maintainer: Diego Ciccia <diego.ciccia@sciencespo.fr>
Diff between DIDmultiplegtDYN versions 1.0.5 dated 2024-03-01 and 1.0.8 dated 2024-04-23
DESCRIPTION | 8 +- MD5 | 27 +++--- NAMESPACE | 3 NEWS.md | 18 ++++ R/did_multiplegt_bootstrap.R | 13 ++- R/did_multiplegt_by_path.R |only R/did_multiplegt_dyn.R | 89 +++++++++++++++++----- R/did_multiplegt_dyn_core.R | 10 ++ R/did_multiplegt_dyn_design.R | 1 R/did_multiplegt_dyn_graph.R | 60 +++++++++------ R/did_multiplegt_main.R | 155 ++++++++++++++++++++++++++++++++------- R/print.R | 18 +++- R/progressBar.R | 7 + R/rnames.R |only man/did_multiplegt_dyn.Rd | 41 ++++++---- man/rnames.did_multiplegt_dyn.Rd |only 16 files changed, 338 insertions(+), 112 deletions(-)
More information about DIDmultiplegtDYN at CRAN
Permanent link
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-
of-design-space plots and similar graphics for exploring the properties of
experimental designs. The design region is explored via random sampling, which
allows for more flexibility than traditional variance dispersion graphs. A
formula interface is leveraged to provide access to complex model formulae.
Graphics can be constructed simultaneously for multiple experimental designs
and/or multiple model formulae. Instead of using pointwise optimization to
find the minimum and maximum scaled prediction variance curves, which can be
inaccurate and time consuming, this package uses quantile regression as an
alternative.
Author: Pieter Schoonees [aut, cre, cph],
Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between vdg versions 1.2.2 dated 2022-07-07 and 1.2.3 dated 2024-04-23
vdg-1.2.2/vdg/R/vdg-package.R |only vdg-1.2.3/vdg/DESCRIPTION | 14 +++++++------- vdg-1.2.3/vdg/MD5 | 11 +++++------ vdg-1.2.3/vdg/build/partial.rdb |binary vdg-1.2.3/vdg/build/vignette.rds |binary vdg-1.2.3/vdg/inst/doc/vdg.pdf |binary vdg-1.2.3/vdg/man/vdg-package.Rd | 7 +------ 7 files changed, 13 insertions(+), 19 deletions(-)
More information about bayesMeanScale at CRAN
Permanent link
Title: Available Light Within the Water Column and Seafloor of Arctic
Fjords
Description: Satellite data collected between 2003 and 2022,
in conjunction with gridded bathymetric data (50-150 m resolution),
are used to estimate the irradiance reaching the bottom of a series of representative EU Arctic fjords.
An Earth System Science Data (ESSD) manuscript, Schlegel et al. (2023, in review),
that provides a detailed explanation of the methodology is currently in review.
Author: Bernard Gentili [aut],
Jean-Pierre Gattuso [aut] ,
Robert W. Schlegel [aut, cre]
Maintainer: Robert W. Schlegel <robert.schlegel@imev-mer.fr>
Diff between FjordLight versions 0.7.0 dated 2023-12-02 and 0.8 dated 2024-04-23
DESCRIPTION | 16 MD5 | 57 +-- NAMESPACE | 1 NEWS.md | 39 ++ R/fl_DownloadFjord.R | 40 +- R/fl_ListFjords.R | 15 R/fl_LoadFjord.R | 24 + R/flget_KPARMonthlyTS.R |only R/flget_PARbottomMonthlyTS.R | 90 ++-- R/flplot_KPARMonthlyTS.R |only R/flplot_PARbottomMonthlyTS.R | 2 R/flplot_climatology.R | 4 README.md | 11 build/vignette.rds |binary inst/CITATION |only inst/doc/fl_example.R | 114 +++++- inst/doc/fl_example.Rmd | 150 +++++++- inst/doc/fl_example.html | 455 +++++++++++++++++++------ inst/extdata/test_ClimSD.nc |only inst/extdata/test_MonthlyKpar.nc |only inst/extdata/test_YearlySD.nc |only man/fl_DownloadFjord.Rd | 19 - man/fl_ListFjords.Rd | 4 man/fl_LoadFjord.Rd | 16 man/flget_KPARMonthlyTS.Rd |only man/flplot_KPARMonthlyTS.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-fl_DownloadFjord.R | 38 +- tests/testthat/test-fl_LoadFjord.R | 27 + tests/testthat/test-flget_KPARMonthlyTS.R |only tests/testthat/test-flget_PARbottomMonthlyTS.R | 2 tests/testthat/test-flget_Pfunction.R | 2 tests/testthat/test-flget_climatology.R | 2 vignettes/fl_example.Rmd | 150 +++++++- 34 files changed, 1031 insertions(+), 247 deletions(-)
Title: Modules for 'ShinyItemAnalysis'
Description: Package including additional modules for interactive
'ShinyItemAnalysis' 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]
,
Jan Netik [aut]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between SIAmodules versions 0.1.0 dated 2023-03-29 and 0.1.1 dated 2024-04-23
SIAmodules-0.1.0/SIAmodules/inst/modules |only SIAmodules-0.1.1/SIAmodules/DESCRIPTION | 15 +- SIAmodules-0.1.1/SIAmodules/MD5 | 54 +------- SIAmodules-0.1.1/SIAmodules/NAMESPACE | 2 SIAmodules-0.1.1/SIAmodules/NEWS.md |only SIAmodules-0.1.1/SIAmodules/R/sm_cat.R | 115 +++++++++++++----- SIAmodules-0.1.1/SIAmodules/R/sm_dif_c.R | 10 - SIAmodules-0.1.1/SIAmodules/R/sm_irr.R | 6 SIAmodules-0.1.1/SIAmodules/README.md | 5 SIAmodules-0.1.1/SIAmodules/build/partial.rdb |binary SIAmodules-0.1.1/SIAmodules/inst/sc/cat.R |only SIAmodules-0.1.1/SIAmodules/man/SIAmodules-package.Rd | 2 12 files changed, 121 insertions(+), 88 deletions(-)
Title: Marker-Based Cell Type Purification for Single-Cell Sequencing
Data
Description: A common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. 'scGate' automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. Briefly, 'scGate' takes as input: i) a gene expression matrix stored in a 'Seurat' object and ii) a “gating model” (GM), consisting of a set of marker genes that define the cell population of interest. The GM can be as simple as a single marker gene, or a combination of positive and negative markers. More complex GMs can be constructed in a hierarchical fashion, akin to gating strategies employed in flow cytometry. 'scGate' evaluates the strength of signature marker expression in each cell using the rank-based method 'UCell', and then performs k-nearest neighbor (kNN) smoothing by calculating the mean 'UCell' score across neighboring cells. kNN-smoothing aims at compensating for the large degree of s [...truncated...]
Author: Massimo Andreatta [aut, cre] ,
Ariel Berenstein [aut] ,
Josep Garnica [aut],
Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unil.ch>
Diff between scGate versions 1.6.0 dated 2023-11-06 and 1.6.2 dated 2024-04-23
DESCRIPTION | 12 ++-- MD5 | 16 +++--- NAMESPACE | 1 R/main.R | 35 ++++++++++--- R/utils.R | 100 +++++++++++++++++++++++++++++++++++++-- build/vignette.rds |binary inst/NEWS.Rd | 8 +++ man/combine_scGate_multiclass.Rd | 2 man/scGate.Rd | 8 ++- 9 files changed, 153 insertions(+), 29 deletions(-)
Title: Multivariate Polynomials with Rational Coefficients
Description: Symbolic calculation and evaluation of multivariate
polynomials with rational coefficients. This package is strongly
inspired by the 'spray' package. It provides a function to
compute Gröbner bases (reference <doi:10.1007/978-3-319-16721-3>).
The header file of the C++ code can be used by other packages. It
provides the templated class 'Qspray' that can be used to represent and
to deal with multivariate polynomials with another type of coefficients.
Author: Stephane Laurent [aut, cre],
Robin Hankin [ctb, cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between qspray versions 2.1.1 dated 2023-09-07 and 3.0.0 dated 2024-04-23
DESCRIPTION | 24 - MD5 | 113 ++++- NAMESPACE | 45 ++ NEWS.md | 33 + R/RcppExports.R | 20 - R/characteristicPolynomial.R |only R/creation.R |only R/evaluation.R |only R/groebner.R | 266 +++++++------ R/integrateOnSimplex.R |only R/internal.R | 96 ++++ R/qspray.R | 576 ++++++++--------------------- R/qsprayDivision.R |only R/queries.R |only R/show.R |only R/symmetricPolynomials.R |only R/transformation.R |only R/yacas.R | 48 +- README.md | 370 +++++++++++++++++-- configure | 12 inst/include |only man/ESFpoly.Rd | 4 man/HallInnerProduct.Rd |only man/MSFpoly.Rd | 2 man/MSPcombination.Rd |only man/PSFpoly.Rd |only man/PSPexpression.Rd |only man/as.function.qspray.Rd | 17 man/as.qspray.Rd | 3 man/changeVariables.Rd |only man/characteristicPolynomial.Rd |only man/collinearQsprays.Rd |only man/compactSymmetricQspray.Rd |only man/composeQspray.Rd |only man/dQspray.Rd | 9 man/derivQspray.Rd | 9 man/evalQspray.Rd | 6 man/getCoefficient.Rd |only man/getConstantTerm.Rd |only man/integratePolynomialOnSimplex.Rd | 2 man/isConstant.Rd |only man/isPolynomialOf.Rd |only man/isQone.Rd |only man/isQzero.Rd |only man/isSymmetricQspray.Rd |only man/isUnivariate.Rd |only man/numberOfTerms.Rd |only man/numberOfVariables.Rd |only man/orderedQspray.Rd |only man/permuteVariables.Rd |only man/qdivision.Rd | 12 man/qlone.Rd | 11 man/qone.Rd | 6 man/qsprayDivision.Rd |only man/qsprayMaker.Rd | 4 man/qspray_from_list.Rd |only man/qzero.Rd | 6 man/rQspray.Rd |only man/showMonomialOld.Rd |only man/showMonomialX1X2X3.Rd |only man/showMonomialXYZ.Rd |only man/showQspray.Rd |only man/showQsprayOption-set.Rd |only man/showQsprayX1X2X3.Rd |only man/showQsprayXYZ.Rd |only man/substituteQspray.Rd |only man/swapVariables.Rd |only src/Makevars.in | 2 src/Makevars.win | 3 src/RcppExports.cpp | 70 ++- src/division.cpp |only src/evaluation.cpp |only src/qspray.cpp | 577 ++---------------------------- tests/testthat/helper-00.R |only tests/testthat/test-HallInnerProduct.R |only tests/testthat/test-basic.R | 7 tests/testthat/test-collinear.R |only tests/testthat/test-composeQspray.R |only tests/testthat/test-division.R | 3 tests/testthat/test-getCoefficient.R |only tests/testthat/test-groebner.R |only tests/testthat/test-permuteVariables.R |only tests/testthat/test-show.R |only tests/testthat/test-substitute.R |only tests/testthat/test-symmetricPolynomial.R |only 85 files changed, 1119 insertions(+), 1237 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre],
Eric Anderson [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.1.5 dated 2024-02-21 and 0.1.6 dated 2024-04-23
DESCRIPTION | 16 ++-- MD5 | 71 +++++++++++------- NAMESPACE | 5 + NEWS.md | 102 ++++++++++++++++---------- R/NMcheckData.R | 72 ++++++++++-------- R/NMexpandDoses.R | 21 +++-- R/NMextractDataFile.R | 1 R/NMinfo.R | 12 +-- R/NMreadExt.R | 16 ++-- R/NMreadShk.R |only R/NMreadTab.R | 2 R/NMreadTabSlow.R |only R/NMscanData.R | 17 ---- R/NMwriteSection.R | 22 ++--- R/addOmegaCorr.R |only R/addTAPD.R | 45 ++++++----- R/colLabels.R | 1 R/dt2mat.R |only R/flagsAssign.R | 5 - R/fnAppend.R | 12 ++- R/mat2dt.R |only R/uniquePresent.R | 27 +++++- man/NMcheckData.Rd | 59 +++++++-------- man/NMinfo.Rd | 12 +-- man/NMreadExt.Rd | 14 +-- man/NMreadShk.Rd |only man/NMreadTabSlow.Rd |only man/NMwriteSection.Rd | 22 ++--- man/addOmegaCorr.Rd |only man/addTAPD.Rd | 30 +++---- man/colLabels.Rd | 3 man/dt2mat.Rd |only man/fnAppend.Rd | 2 man/mat2dt.Rd |only man/uniquePresent.Rd |only tests/testthat/testReference/NMreadExt_01.rds |only tests/testthat/testReference/NMreadExt_03.rds |only tests/testthat/testReference/NMreadExt_04.rds |only tests/testthat/testReference/NMreadShk_01.rds |only tests/testthat/testReference/addTAPD_04.rds |only tests/testthat/testReference/fnAppend_02.rds |only tests/testthat/test_NMreadShk.R |only tests/testthat/test_NMscanData.R | 11 +- tests/testthat/test_addTAPD.R | 40 +++++++++- tests/testthat/test_fnAppend.R | 14 +++ tests/testthat/test_uniquePresent.R |only 46 files changed, 394 insertions(+), 260 deletions(-)
More information about GregoryQuadrature at CRAN
Permanent link
Title: Functions for Extreme Value Distributions
Description: Extends simulation, distribution, quantile and density
functions to univariate and multivariate parametric extreme
value distributions, and provides fitting functions which
calculate maximum likelihood estimates for univariate and
bivariate maxima models, and for univariate and bivariate
threshold models.
Author: Alec Stephenson. Function fbvpot by Chris Ferro.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between evd versions 2.3-6.1 dated 2022-07-04 and 2.3-7 dated 2024-04-23
DESCRIPTION | 8 +-- MD5 | 14 ++--- R/mvdist.R | 91 ++++++++++++++++++++----------------- build/vignette.rds |binary inst/CHANGES | 16 ++++++ inst/CITATION | 15 ++---- inst/doc/Multivariate_Extremes.pdf |binary man/uccle.Rd | 4 - 8 files changed, 85 insertions(+), 63 deletions(-)
Title: Young Tableaux
Description: Deals with Young tableaux (field of combinatorics). For standard
Young tabeaux, performs enumeration, counting, random generation, the
Robinson-Schensted correspondence, and conversion to and from paths on
the Young lattice. Also performs enumeration and counting of
semistandard Young tableaux, enumeration of skew semistandard Young
tableaux, and computation of Kostka numbers.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between syt versions 0.3.0 dated 2023-12-06 and 0.4.0 dated 2024-04-23
DESCRIPTION | 19 ++++----- MD5 | 51 ++++++++++++++++-------- NAMESPACE | 15 +++++++ NEWS.md | 15 +++++-- R/Kostka.R |only R/ballot.R | 10 ++-- R/dualsyt.R | 2 R/enumeration.R | 3 - R/hooks.R | 2 R/internal.R | 37 ++++++++++++----- R/isSYT.R |only R/skewTableaux.R |only R/ssyt.R | 78 ++++++++++++++----------------------- R/syt2matrix.R | 41 ++++++++++++++++--- R/tableaux.R |only man/KostkaNumber.Rd |only man/all_ssSkewTableaux.Rd |only man/all_ssytx.Rd | 3 - man/all_sytx.Rd | 3 - man/dualSkewTableau.Rd |only man/dualTableau.Rd |only man/isSSYT.Rd |only man/isSYT.Rd |only man/isSemistandardSkewTableau.Rd |only man/isSkewTableau.Rd |only man/isStandardSkewTableau.Rd |only man/prettySkewTableau.Rd |only man/prettyTableau.Rd |only man/syt2matrix.Rd | 4 + man/tableau2matrix.Rd |only man/tableauShape.Rd |only tests/testthat/test-Kostka.R |only tests/testthat/test-dual.R | 10 +++- tests/testthat/test-enumeration.R | 1 tests/testthat/test-skewTableaux.R |only tests/testthat/test-ssyt.R | 10 ++++ 36 files changed, 198 insertions(+), 106 deletions(-)
Title: Some Datetime Pickers for 'Shiny'
Description: Provides three types of datetime pickers for usage in a
'Shiny' UI. A datetime picker is an input field for selecting both a
date and a time.
Author: Stephane Laurent [aut, cre],
Wojciech Maj [cph] ),
Porinn [cph] ),
Dmitriy Kovalenko [cph] )
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between shinyDatetimePickers versions 1.1.0 dated 2023-08-07 and 1.2.0 dated 2024-04-23
DESCRIPTION | 8 MD5 | 19 NAMESPACE | 3 NEWS.md | 5 R/datetimeMaterialPicker.R | 24 - R/datetimePicker.R | 24 - R/datetimeSliderPicker.R | 24 - inst/www/datetimePicker/datetimePicker.js | 573 +++++++++++++++++++++++--- inst/www/datetimePicker/datetimePicker.js.map | 2 man/updateDatetimeMaterialPickerInput.Rd |only man/updateDatetimePickerInput.Rd |only man/updateDatetimeSliderPickerInput.Rd |only 12 files changed, 576 insertions(+), 106 deletions(-)
More information about shinyDatetimePickers at CRAN
Permanent link
Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut],
Han Chen [aut, cre],
Duy Pham [aut],
Kenneth Westerman [ctb],
Cong Pan [aut],
Eric Biggers [ctb, cph] ,
Tino Reichardt [ctb, cph] library),
Meta Platforms, Inc. and affiliates [cph] library)
Maintainer: Han Chen <han.chen.2@uth.tmc.edu>
Diff between MAGEE versions 1.3.2 dated 2023-11-17 and 1.4.0 dated 2024-04-23
DESCRIPTION | 8 - MD5 | 32 ++--- R/glmm.gei.R | 261 +++++++++++++++++++++++------------------ R/glmm.gei.meta.R | 36 ++--- inst/doc/MAGEE.Rnw | 25 +++ inst/doc/MAGEE.pdf |binary inst/extdata/meta1.txt | 2 inst/extdata/meta2.txt | 2 inst/extdata/meta3.txt | 2 inst/extdata/meta4.txt | 2 inst/extdata/meta5.txt | 2 inst/extdata/readme | 2 man/MAGEE-package.Rd | 4 man/glmm.gei.Rd | 22 ++- src/fitglmm.cpp | 257 ++++++++++++++-------------------------- tests/testthat/test_glmm.gei.R | 72 +++++------ vignettes/MAGEE.Rnw | 25 +++ 17 files changed, 380 insertions(+), 374 deletions(-)
Title: Kantorovich Distance Between Probability Measures
Description: Computes the Kantorovich distance between two probability
measures on a finite set. The Kantorovich distance is also known as
the Monge-Kantorovich distance or the first Wasserstein distance.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between kantorovich versions 3.1.0 dated 2023-08-22 and 3.2.0 dated 2024-04-23
DESCRIPTION | 10 ++--- MD5 | 32 +++++++++--------- NEWS.md | 7 ++++ R/kantorovich_CVX.R | 27 +++++++-------- R/kantorovich_glpk.R | 33 +++++++++---------- R/kantorovich_lpsolve.R | 26 +++++++-------- R/kantorovich_ompr.R | 37 ++++++++++----------- inst/doc/kantorovich.R | 6 +-- inst/doc/kantorovich.html | 4 +- man/kantorovich_CVX.Rd | 14 ++++---- man/kantorovich_glpk.Rd | 21 ++++-------- man/kantorovich_lp.Rd | 14 ++++---- man/kantorovich_ompr.Rd | 72 +++++++++++++++++++++--------------------- tests/testthat/test-CVX.R | 2 - tests/testthat/test-glpk.R | 2 - tests/testthat/test-lpSolve.R | 4 +- tests/testthat/test-ompr.R | 2 - 17 files changed, 157 insertions(+), 156 deletions(-)
Title: Sensitivities of Prices of Financial Options and Implied
Volatilities
Description: Methods to calculate sensitivities of financial option prices for
European, geometric and arithmetic Asian, and American options, with various
payoff functions in the Black Scholes model, and in more general jump diffusion
models. A shiny app to interactively plot the results is included. Furthermore,
methods to compute implied volatilities are provided for a wide range of option
types and custom payoff functions. Classical formulas are implemented for
European options in the Black Scholes Model, as is presented in Hull, J. C.
(2017), Options, Futures, and Other Derivatives.
In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see
Hudde, A. & Rüschendorf, L. (2023). European and Asian Greeks for exponential
Lévy processes. <doi:10.1007/s11009-023-10014-5>. For American
options, the Binomial Tree Method is implemented, as is presented in Hull,
J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 1.3.5 dated 2024-03-03 and 1.4.2 dated 2024-04-23
DESCRIPTION | 6 - MD5 | 14 +- NEWS.md | 33 ++++-- R/Malliavin_Geometric_Asian_Greeks.R | 32 ++---- README.md | 2 tests/testthat/test-Binomial_American_Greeks.R | 9 + tests/testthat/test-Malliavin_European_Greeks.R | 29 +++--- tests/testthat/test-Malliavin_Geometric_Asian_Greeks.R | 81 +++++++---------- 8 files changed, 103 insertions(+), 103 deletions(-)
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Description: A system for 'declaratively' creating graphics, based on "The
Grammar of Graphics". You provide the data, tell 'ggplot2' how to map
variables to aesthetics, what graphical primitives to use, and it
takes care of the details.
Author: Hadley Wickham [aut] ,
Winston Chang [aut] ,
Lionel Henry [aut],
Thomas Lin Pedersen [aut, cre]
,
Kohske Takahashi [aut],
Claus Wilke [aut] ,
Kara Woo [aut] ,
Hiroaki Yutani [aut] ,
Dewey Dunnington [aut] ,
Teun van den Brand [aut] ,
Posit, PBC [cph, [...truncated...]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ggplot2 versions 3.5.0 dated 2024-02-23 and 3.5.1 dated 2024-04-23
DESCRIPTION | 32 - MD5 | 432 +++++++++++++------------- NEWS.md | 48 ++ R/aes.R | 2 R/annotation.R | 17 - R/autolayer.R | 2 R/autoplot.R | 114 ++++++ R/axis-secondary.R | 10 R/bin.R | 8 R/coord-.R | 2 R/coord-flip.R | 13 R/coord-map.R | 20 + R/coord-polar.R | 12 R/coord-radial.R | 58 ++- R/coord-transform.R | 2 R/data.R | 2 R/docs_layer.R |only R/facet-.R | 4 R/facet-grid-.R | 6 R/facet-wrap.R | 6 R/fortify.R | 1 R/geom-.R | 2 R/geom-bar.R | 3 R/geom-bin2d.R | 4 R/geom-blank.R | 1 R/geom-boxplot.R | 6 R/geom-count.R | 4 R/geom-density.R | 4 R/geom-density2d.R | 4 R/geom-dotplot.R | 2 R/geom-errorbar.R | 2 R/geom-errorbarh.R | 2 R/geom-function.R | 16 R/geom-hex.R | 7 R/geom-histogram.R | 4 R/geom-path.R | 9 R/geom-point.R | 30 + R/geom-quantile.R | 4 R/geom-raster.R | 4 R/geom-sf.R | 8 R/geom-smooth.R | 4 R/geom-text.R | 15 R/geom-tile.R | 4 R/geom-violin.R | 6 R/ggproto.R | 12 R/guide-axis-logticks.R | 59 ++- R/guide-bins.R | 12 R/guide-colorbar.R | 2 R/guide-colorsteps.R | 55 +-- R/guide-legend.R | 18 + R/labels.R | 3 R/layer.R | 48 ++ R/plot-build.R | 18 - R/plot.R | 2 R/position-.R | 2 R/position-jitter.R | 4 R/position-jitterdodge.R | 2 R/save.R | 3 R/scale-.R | 25 + R/scale-alpha.R | 9 R/scale-binned.R | 2 R/scale-brewer.R | 2 R/scale-colour.R | 2 R/scale-continuous.R | 2 R/scale-date.R | 4 R/scale-discrete-.R | 4 R/scale-gradient.R | 2 R/scale-grey.R | 4 R/scale-hue.R | 6 R/scale-identity.R | 2 R/scale-linetype.R | 4 R/scale-linewidth.R | 2 R/scale-manual.R | 4 R/scale-shape.R | 4 R/scale-size.R | 12 R/scale-steps.R | 11 R/stat-.R | 5 R/stat-boxplot.R | 2 R/stat-contour.R | 8 R/stat-count.R | 2 R/stat-smooth.R | 5 R/stat-summary-bin.R | 2 R/theme-defaults.R | 3 R/theme-elements.R | 5 R/theme.R | 11 R/utilities-help.R | 10 R/utilities-resolution.R | 10 R/utilities.R | 6 README.md | 4 inst/doc/extending-ggplot2.R | 8 inst/doc/extending-ggplot2.Rmd | 8 inst/doc/extending-ggplot2.html | 21 - inst/doc/ggplot2-in-packages.R | 24 - inst/doc/ggplot2-in-packages.Rmd | 24 - inst/doc/ggplot2-in-packages.html | 24 - inst/doc/ggplot2-specs.Rmd | 3 inst/doc/ggplot2-specs.html | 14 man/aes_colour_fill_alpha.Rd | 4 man/aes_group_order.Rd | 4 man/aes_linetype_size_shape.Rd | 4 man/aes_position.Rd | 4 man/annotate.Rd | 34 +- man/autolayer.Rd | 6 man/automatic_plotting.Rd |only man/autoplot.Rd | 6 man/binned_scale.Rd | 10 man/borders.Rd | 32 + man/continuous_scale.Rd | 4 man/coord_flip.Rd | 14 man/coord_map.Rd | 3 man/coord_polar.Rd | 17 - man/coord_trans.Rd | 3 man/discrete_scale.Rd | 6 man/facet_grid.Rd | 3 man/facet_wrap.Rd | 3 man/fortify.Rd | 6 man/geom_abline.Rd | 31 + man/geom_bar.Rd | 52 ++- man/geom_bin_2d.Rd | 53 ++- man/geom_blank.Rd | 63 +++ man/geom_boxplot.Rd | 53 ++- man/geom_contour.Rd | 82 +++- man/geom_count.Rd | 53 ++- man/geom_density.Rd | 53 ++- man/geom_density_2d.Rd | 20 - man/geom_dotplot.Rd | 47 ++ man/geom_errorbarh.Rd | 63 +++ man/geom_function.Rd | 98 ++++- man/geom_hex.Rd | 52 ++- man/geom_histogram.Rd | 53 ++- man/geom_jitter.Rd | 63 +++ man/geom_linerange.Rd | 63 +++ man/geom_map.Rd | 47 ++ man/geom_path.Rd | 63 +++ man/geom_point.Rd | 63 +++ man/geom_polygon.Rd | 63 +++ man/geom_qq.Rd | 62 +++ man/geom_quantile.Rd | 53 ++- man/geom_ribbon.Rd | 82 +++- man/geom_rug.Rd | 63 +++ man/geom_segment.Rd | 63 +++ man/geom_smooth.Rd | 58 ++- man/geom_spoke.Rd | 63 +++ man/geom_text.Rd | 69 +++- man/geom_tile.Rd | 63 +++ man/geom_violin.Rd | 53 ++- man/ggplot.Rd | 3 man/ggplot2-ggproto.Rd | 15 man/ggplot_build.Rd | 2 man/ggplot_gtable.Rd | 2 man/ggproto.Rd | 15 man/ggsave.Rd | 3 man/ggsf.Rd | 82 +++- man/ggtheme.Rd | 3 man/guide_axis_logticks.Rd | 29 + man/guide_colourbar.Rd | 2 man/guide_coloursteps.Rd | 2 man/guide_legend.Rd | 2 man/labs.Rd | 3 man/layer.Rd | 58 ++- man/layer_geoms.Rd |only man/layer_positions.Rd |only man/layer_sf.Rd | 49 ++ man/layer_stats.Rd |only man/position_dodge.Rd | 2 man/position_identity.Rd | 2 man/position_nudge.Rd | 2 man/position_stack.Rd | 2 man/register_theme_elements.Rd | 3 man/resolution.Rd | 5 man/scale_alpha.Rd | 9 man/scale_binned.Rd | 9 man/scale_brewer.Rd | 2 man/scale_colour_continuous.Rd | 2 man/scale_colour_discrete.Rd | 3 man/scale_continuous.Rd | 3 man/scale_date.Rd | 4 man/scale_discrete.Rd | 7 man/scale_gradient.Rd | 9 man/scale_grey.Rd | 15 man/scale_hue.Rd | 15 man/scale_identity.Rd | 2 man/scale_linetype.Rd | 7 man/scale_linewidth.Rd | 3 man/scale_manual.Rd | 10 man/scale_shape.Rd | 7 man/scale_size.Rd | 16 man/scale_steps.Rd | 35 -- man/sec_axis.Rd | 2 man/stat_ecdf.Rd | 62 +++ man/stat_ellipse.Rd | 62 +++ man/stat_identity.Rd | 62 +++ man/stat_sf_coordinates.Rd | 64 +++ man/stat_summary.Rd | 71 +++- man/stat_summary_2d.Rd | 62 +++ man/stat_unique.Rd | 62 +++ man/theme.Rd | 7 man/txhousing.Rd | 2 tests/testthat/_snaps/annotate.md | 4 tests/testthat/_snaps/coord-map.md | 4 tests/testthat/_snaps/coord-polar.md | 4 tests/testthat/_snaps/guides.md | 2 tests/testthat/_snaps/layer.md | 2 tests/testthat/_snaps/prohibited-functions.md |only tests/testthat/_snaps/sec-axis.md | 2 tests/testthat/test-annotate.R | 6 tests/testthat/test-coord-map.R | 6 tests/testthat/test-coord-polar.R | 22 + tests/testthat/test-coord-train.R | 2 tests/testthat/test-coord_sf.R | 2 tests/testthat/test-draw-key.R | 5 tests/testthat/test-guides.R | 51 ++- tests/testthat/test-prohibited-functions.R | 27 + tests/testthat/test-scales.R | 14 tests/testthat/test-stat-bin.R | 7 tests/testthat/test-theme.R | 2 tests/testthat/test-utilities.R | 3 vignettes/extending-ggplot2.Rmd | 8 vignettes/ggplot2-in-packages.Rmd | 24 - vignettes/ggplot2-specs.Rmd | 3 220 files changed, 3395 insertions(+), 1108 deletions(-)