Title: Get Executing Script's Path, from 'RStudio', 'Rgui', 'VSCode',
'Rscript' (Shells Including Windows Command-Line / / Unix
Terminal), and 'source'
Description: Determine the full path of the executing script. Works when
running a line or selection from a script in 'RStudio', 'Rgui', and
'VSCode', when using 'source', 'sys.source', 'debugSource' in 'RStudio',
and 'testthat::source_file', and when running from a shell.
Author: Andrew Simmons
Maintainer: Andrew Simmons <akwsimmo@gmail.com>
Diff between this.path versions 0.11.0 dated 2022-09-03 and 1.0.0 dated 2022-09-21
this.path-0.11.0/this.path/tests/main.R |only this.path-1.0.0/this.path/DESCRIPTION | 8 this.path-1.0.0/this.path/MD5 | 38 ++- this.path-1.0.0/this.path/NAMESPACE | 15 + this.path-1.0.0/this.path/NEWS | 16 + this.path-1.0.0/this.path/R/Args.R | 2 this.path-1.0.0/this.path/R/as.relative.path.R | 4 this.path-1.0.0/this.path/R/basename2.R |only this.path-1.0.0/this.path/R/check.path.R | 2 this.path-1.0.0/this.path/R/hooks-for-namespace-events.R | 6 this.path-1.0.0/this.path/R/path.join.R |only this.path-1.0.0/this.path/R/rprojroot.R | 2 this.path-1.0.0/this.path/R/this.path.R | 144 +++++---------- this.path-1.0.0/this.path/R/tryCatch2.R | 4 this.path-1.0.0/this.path/R/utils.R | 3 this.path-1.0.0/this.path/build/partial.rdb |binary this.path-1.0.0/this.path/inst/NEWS.Rd | 19 + this.path-1.0.0/this.path/man/basename2.Rd |only this.path-1.0.0/this.path/man/path.join.Rd |only this.path-1.0.0/this.path/src |only this.path-1.0.0/this.path/tests/basename2.tests.R |only this.path-1.0.0/this.path/tests/path.join.tests.R |only this.path-1.0.0/this.path/tests/this.path.tests.R |only 23 files changed, 150 insertions(+), 113 deletions(-)
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes
details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is
useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out.
Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre],
Carly Levitz [ctb],
Dario Mavec [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 1.0.1 dated 2022-05-31 and 2.0 dated 2022-09-21
survivoR-1.0.1/survivoR/R/helpers.R |only survivoR-1.0.1/survivoR/data/boot-mapping.rda |only survivoR-1.0.1/survivoR/data/hidden-idols.rda |only survivoR-1.0.1/survivoR/data/jury-votes.rda |only survivoR-1.0.1/survivoR/data/season-palettes.rda |only survivoR-1.0.1/survivoR/data/season-summary.rda |only survivoR-1.0.1/survivoR/data/tribe-colours.rda |only survivoR-1.0.1/survivoR/data/tribe-mapping.rda |only survivoR-1.0.1/survivoR/data/vote-history.rda |only survivoR-1.0.1/survivoR/man/clean_votes.Rd |only survivoR-1.0.1/survivoR/man/hidden_idols.Rd |only survivoR-2.0/survivoR/DESCRIPTION | 21 survivoR-2.0/survivoR/MD5 | 74 - survivoR-2.0/survivoR/NAMESPACE | 3 survivoR-2.0/survivoR/NEWS.md | 31 survivoR-2.0/survivoR/R/datasets.R | 136 ++ survivoR-2.0/survivoR/R/scales.R | 8 survivoR-2.0/survivoR/README.md | 774 ++++++++-------- survivoR-2.0/survivoR/data/advantage_details.rda |binary survivoR-2.0/survivoR/data/advantage_movement.rda |binary survivoR-2.0/survivoR/data/boot_mapping.rda |only survivoR-2.0/survivoR/data/castaway_details.rda |binary survivoR-2.0/survivoR/data/castaways.rda |binary survivoR-2.0/survivoR/data/challenge_description.rda |binary survivoR-2.0/survivoR/data/challenge_results.rda |binary survivoR-2.0/survivoR/data/challenge_results_dep.rda |only survivoR-2.0/survivoR/data/confessionals.rda |binary survivoR-2.0/survivoR/data/jury_votes.rda |only survivoR-2.0/survivoR/data/screen_time.rda |only survivoR-2.0/survivoR/data/season_palettes.rda |only survivoR-2.0/survivoR/data/season_summary.rda |only survivoR-2.0/survivoR/data/survivor_auction.rda |only survivoR-2.0/survivoR/data/tribe_colours.rda |only survivoR-2.0/survivoR/data/tribe_mapping.rda |only survivoR-2.0/survivoR/data/viewers.rda |binary survivoR-2.0/survivoR/data/vote_history.rda |only survivoR-2.0/survivoR/man/boot_mapping.Rd | 2 survivoR-2.0/survivoR/man/castaway_details.Rd | 4 survivoR-2.0/survivoR/man/castaways.Rd | 1 survivoR-2.0/survivoR/man/challenge_results.Rd | 111 -- survivoR-2.0/survivoR/man/challenge_results_dep.Rd |only survivoR-2.0/survivoR/man/scales_survivor.Rd | 4 survivoR-2.0/survivoR/man/scales_tribes.Rd | 4 survivoR-2.0/survivoR/man/screen_time.Rd |only survivoR-2.0/survivoR/man/season_palettes.Rd | 2 survivoR-2.0/survivoR/man/survivor_auction.Rd |only survivoR-2.0/survivoR/man/viewers.Rd | 2 survivoR-2.0/survivoR/tests/testthat/test-advantages.R | 2 survivoR-2.0/survivoR/tests/testthat/test-challenges.R | 24 survivoR-2.0/survivoR/tests/testthat/test-general.R |only survivoR-2.0/survivoR/tests/testthat/test-screen-time.R |only 51 files changed, 679 insertions(+), 524 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the location
of the species (as a point pattern) is needed together with environmental conditions
(as a categorical raster). To test for significance habitat associations, one of
the two components is randomized. Methods are mainly based on Plotkin et al. (2000)
<doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximillian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Zeke Marshall [ctb] ,
Thomas Etherington [ctb]
Maintainer: Maximillian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between shar versions 1.3.2 dated 2022-03-08 and 2.0.0 dated 2022-09-21
DESCRIPTION | 18 MD5 | 99 +- NAMESPACE | 2 NEWS.md | 15 R/classify_habitats.R | 22 R/data.R | 2 R/extract_points.R | 8 R/list_to_randomized.R | 4 R/onLoad.R |only R/pack_randomized.R |only R/plot.rd_pat.R | 2 R/plot.rd_ras.R | 10 R/print.rd_ras.R | 20 R/randomize_raster.R | 18 R/results_habitat_association.R | 35 R/sysdata.rda |only R/translate_raster.R | 53 - R/unpack_randomized.R |only build/vignette.rds |binary data/gamma_test.rda |binary data/landscape.rda |binary data/random_walk.rda |binary data/reconstruction.rda |binary data/species_a.rda |binary data/species_b.rda |binary data/torus_trans.rda |binary inst/Hesselbarth_2021_Journal_of_Open_Source_Software_6_68.pdf |only inst/doc/get_started.R | 13 inst/doc/get_started.Rmd | 16 inst/doc/get_started.html | 452 +++++++--- man/classify_habitats.Rd | 10 man/extract_points.Rd | 4 man/figures/README-plot-random_pattern-1.png |binary man/landscape.Rd | 2 man/pack_randomized.Rd |only man/plot.rd_pat.Rd | 2 man/plot.rd_ras.Rd | 2 man/print.rd_ras.Rd | 2 man/randomize_raster.Rd | 8 man/results_habitat_association.Rd | 6 man/translate_raster.Rd | 6 man/unpack_randomized.Rd |only tests/testthat.R | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-calculate_energy.R | 1 tests/testthat/test-classify_habitats.R | 8 tests/testthat/test-extract_points.R | 2 tests/testthat/test-list_to_randomized.R | 33 tests/testthat/test-plot_rd_ras.R | 4 tests/testthat/test-print.R | 2 tests/testthat/test-randomize_raster.R | 8 tests/testthat/test-results_habitat_association.R | 12 tests/testthat/test-translate_raster.R | 11 vignettes/get_started.Rmd | 16 54 files changed, 614 insertions(+), 315 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Paul Hoffman [aut, cre] ,
Jaison Jain [ctb] ,
Efthymia Papalexi [ctb] ,
Patrick Roelli [ctb],
Rahul Satija [ctb] [...truncated...]
Maintainer: Paul Hoffman <seurat@nygenome.org>
Diff between Seurat versions 4.1.1 dated 2022-05-02 and 4.2.0 dated 2022-09-21
DESCRIPTION | 16 ++-- MD5 | 60 ++++++++-------- NAMESPACE | 1 NEWS.md | 13 +++ R/clustering.R | 6 - R/differential_expression.R | 57 +++++++++------ R/dimensional_reduction.R | 6 + R/integration.R | 94 ++++++++------------------ R/mixscape.R | 25 +----- R/objects.R | 7 + R/preprocessing.R | 35 ++++----- R/utilities.R | 40 ++--------- R/visualization.R | 32 +++++++- build/partial.rdb |binary man/FeaturePlot.Rd | 8 +- man/FindAllMarkers.Rd | 4 - man/FindMarkers.Rd | 5 + man/FoldChange.Rd | 10 +- man/IntegrateData.Rd | 6 + man/IntegrateEmbeddings.Rd | 6 + man/PolyFeaturePlot.Rd | 5 - man/PrepSCTIntegration.Rd | 2 man/RidgePlot.Rd | 2 man/Seurat-package.Rd | 2 man/SingleExIPlot.Rd | 5 + man/VlnPlot.Rd | 5 + man/reexports.Rd | 2 tests/testthat/test_data_manipulation.R | 6 - tests/testthat/test_differential_expression.R | 92 +++++++++++++++++++++++++ tests/testthat/test_preprocessing.R | 2 tests/testthat/test_utilities.R | 2 31 files changed, 318 insertions(+), 238 deletions(-)
Title: Applied Statistics for Economics and Management with R
Description: Datasets and functions for the book "Statistiques pour l’économie et la gestion", "Théorie et applications en entreprise", F. Bertrand, Ch. Derquenne, G. Dufrénot, F. Jawadi and M. Maumy, C. Borsenberger editor, (2021, ISBN:9782807319448, De Boeck Supérieur, Louvain-la-Neuve).
The first chapter of the book is dedicated to an introduction to statistics and their world.
The second chapter deals with univariate exploratory statistics and graphics.
The third chapter deals with bivariate and multivariate exploratory statistics and graphics.
The fourth chapter is dedicated to data exploration with Principal Component Analysis.
The fifth chapter is dedicated to data exploration with Correspondance Analysis.
The sixth chapter is dedicated to data exploration with Multiple Correspondance Analysis.
The seventh chapter is dedicated to data exploration with automatic clustering.
The eighth chapter is dedicated to an introduction to probability theory and classical probability distributions.
The ni [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Claire Borsenberger [ctb],
Christian Derquenne [ctb],
Gilles Dufrenot [ctb],
Fredj Jawadi [ctb],
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between sageR versions 0.3.0 dated 2021-07-20 and 0.6.0 dated 2022-09-21
DESCRIPTION | 15 - MD5 | 74 +++--- NAMESPACE | 5 NEWS.md | 16 + R/datasets.R | 453 ++++++++++++++++++++++++++++++++++++- R/functions.R | 176 ++++++++++++++ R/sageR-package.R | 3 README.md | 56 ++-- build/partial.rdb |binary build/vignette.rds |binary data/AgevsProter_Canada_full.RData |binary data/AgevsSexe_Canada_full.RData |binary data/Emploi_Etude_Age.RData |only data/Europe.RData |binary data/HospitFull.RData |binary data/Proter_Canada.RData |only data/ProtervsSexe_Canada.RData |binary data/ReaFull.RData |binary data/Richesse.RData |binary data/Sieges_Voix.RData |binary data/Total_Pays.RData |binary data/Total_Secteur.RData |binary data/air_pollution.RData |only data/bilan.RData |only data/bitcoin.RData |only data/champignons.RData |only data/conso_temp.RData |only data/presid_2012.RData |only inst/doc/AllLinksExtVignettes.Rmd | 53 ++-- inst/doc/AllLinksExtVignettes.html | 131 ++++++++-- man/AgevsProter_Canada_full.Rd | 4 man/AgevsSexe_Canada_full.Rd | 4 man/Emploi_Etude_Age.Rd |only man/Proter_Canada.Rd |only man/ProtervsSexe_Canada.Rd | 2 man/Resistance.Rd | 4 man/air_pollution.Rd |only man/att_rep_ind.Rd |only man/bilan.Rd |only man/bitcoin.Rd |only man/champignons.Rd |only man/conso_temp.Rd |only man/moments.grouped.Rd |only man/presid_2012.Rd |only man/sageR-package.Rd | 17 - man/sheppardCorrection.Rd |only tests/testthat/Rplots.pdf |only vignettes/AllLinksExtVignettes.Rmd | 53 ++-- 48 files changed, 895 insertions(+), 171 deletions(-)
Title: Processing of Accelerometry Data with 'GGIR' in mMARCH
Description: Mobile Motor Activity Research Consortium for Health (mMARCH) is a collaborative network of studies of clinical and community samples that employ common clinical, biological, and digital mobile measures across involved studies. One of the main scientific goals of mMARCH sites is developing a better understanding of the inter-relationships between accelerometry-measured physical activity (PA), sleep (SL), and circadian rhythmicity (CR) and mental and physical health in children, adolescents, and adults. Currently, there is no consensus on a standard procedure for a data processing pipeline of raw accelerometry data, and few open-source tools to facilitate their development. The R package 'GGIR' is the most prominent open-source software package that offers great functionality and tremendous user flexibility to process raw accelerometry data. However, even with 'GGIR', processing done in a harmonized and reproducible fashion requires a non-trivial amount of expertise combined with a care [...truncated...]
Author: Wei Guo [aut, cre],
Andrew Leroux [aut],
Vadim Zipunnikov [aut],
Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>
Diff between mMARCH.AC versions 2.4.0.0 dated 2022-08-22 and 2.4.0.1 dated 2022-09-21
DESCRIPTION | 12 +-- MD5 | 42 ++++++------ R/module0_maincall.R | 27 ++++--- R/module1_csv_data_transform.R | 2 R/module2_summary.pipeline.R | 9 +- R/module3_data_shrink.R | 15 ++-- R/module4_data_imputation.R | 34 +++++++-- R/phenotype.plot.R | 2 inst/doc/mMARCH.AC.R | 2 inst/doc/mMARCH.AC.Rmd | 9 +- inst/doc/mMARCH.AC.html | 23 ++++-- inst/doc/mMARCH.AC.output.description.xlsx |binary inst/extdata/example/afterGGIR/Example_module0.maincall.R | 2 inst/extdata/example/afterGGIR/STUDYNAME_module0.maincall.R | 2 inst/template/STUDYNAME_module0.maincall.txt | 2 inst/template/module7c_runJIVE.Rmd | 4 - inst/template/module7d_calculate_WD_WE_avg_features.Rmd | 15 +++- man/DataShrink.Rd | 5 - man/data.imputation.Rd | 4 - man/mMARCH.AC.maincall.Rd | 6 - vignettes/mMARCH.AC.Rmd | 9 +- vignettes/mMARCH.AC.output.description.xlsx |binary 22 files changed, 137 insertions(+), 89 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut, cre],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between geoknife versions 1.6.7 dated 2022-07-20 and 1.6.8 dated 2022-09-21
geoknife-1.6.7/geoknife/inst/draw.xsd |only geoknife-1.6.8/geoknife/DESCRIPTION | 8 geoknife-1.6.8/geoknife/MD5 | 56 +- geoknife-1.6.8/geoknife/R/00-gconfig.R | 15 geoknife-1.6.8/geoknife/R/02-webgeom-obj.R | 2 geoknife-1.6.8/geoknife/R/06-simplegeom-obj.R | 4 geoknife-1.6.8/geoknife/R/query.R | 2 geoknife-1.6.8/geoknife/build/vignette.rds |binary geoknife-1.6.8/geoknife/inst/doc/custom_data_sources.html | 18 geoknife-1.6.8/geoknife/inst/doc/geoknife.R | 6 geoknife-1.6.8/geoknife/inst/doc/geoknife.Rmd | 16 geoknife-1.6.8/geoknife/inst/doc/geoknife.html | 257 +++++----- geoknife-1.6.8/geoknife/inst/doc/plot_geotiff.html | 20 geoknife-1.6.8/geoknife/inst/extdata/completed_request.xml | 4 geoknife-1.6.8/geoknife/inst/extdata/draw.xsd |only geoknife-1.6.8/geoknife/inst/extdata/get_attribute_values.xml | 2 geoknife-1.6.8/geoknife/inst/extdata/multi_poly_post.xml | 4 geoknife-1.6.8/geoknife/inst/extdata/state_webgeom_post.xml | 2 geoknife-1.6.8/geoknife/inst/extdata/testjob.xml | 2 geoknife-1.6.8/geoknife/man/webdata-methods.Rd | 3 geoknife-1.6.8/geoknife/tests/testthat/00_create_test_data.R | 4 geoknife-1.6.8/geoknife/tests/testthat/data/test_XML_sg_xml.xml | 2 geoknife-1.6.8/geoknife/tests/testthat/data/test_XML_wg_xml.xml | 2 geoknife-1.6.8/geoknife/tests/testthat/data/test_keeptimes.xml |only geoknife-1.6.8/geoknife/tests/testthat/data/test_notimesjob.xml |only geoknife-1.6.8/geoknife/tests/testthat/data/test_webgeom_WI.rds |binary geoknife-1.6.8/geoknife/tests/testthat/test-download_result.R | 2 geoknife-1.6.8/geoknife/tests/testthat/test-query_webgeom.R | 1 geoknife-1.6.8/geoknife/tests/testthat/test-webdata_object.R | 4 geoknife-1.6.8/geoknife/tests/testthat/test-webprocess_object.R | 4 geoknife-1.6.8/geoknife/vignettes/geoknife.Rmd | 16 31 files changed, 240 insertions(+), 216 deletions(-)
Title: A Collection of Functions for Graphing Correlation Matrices
Description: Routines for the graphical representation of correlation matrices by means of correlograms, biplots and MDS maps.
Author: Jan Graffelman
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between Correlplot versions 1.0.3 dated 2022-09-20 and 1.0.4 dated 2022-09-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/Correlplot.Rnw | 10 +++------- inst/doc/Correlplot.pdf |binary vignettes/Correlplot.Rnw | 10 +++------- 5 files changed, 14 insertions(+), 22 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and inference.
This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC,
Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu
Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete,
Gaussian and conditional Gaussian networks, along with many score functions and
conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented.
Some utility functions (model comparison and manipulation, random data generation, arc
orientation testing, simple and advanced plots) are included, as well as support for
parameter estimation (maximum likelihood and Bayesian) and inference, conditional
probability queries, cross-validation, bootstrap and model averaging.
Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre], Tomi Silander [ctb], Robert Ness [ctb]
Maintainer: Marco Scutari <scutari@bnlearn.com>
Diff between bnlearn versions 4.8 dated 2022-09-19 and 4.8.1 dated 2022-09-21
Changelog | 4 ++ DESCRIPTION | 8 ++-- MD5 | 40 +++++++++++------------ src/Makevars | 2 - src/bnlearn/cpdag.c | 4 +- src/core/math.functions.c | 7 ++++ src/core/math.functions.h | 1 src/core/sampling.c | 4 +- src/core/sets.c | 10 +++-- src/graphs/path.c | 2 - src/include/graph.h | 2 - src/include/rcore.h | 2 + src/include/register.h | 4 +- src/math/conditional.least.squares.c | 13 ++++--- src/minimal/table.c | 5 +- src/parameters/discrete/hierarchical_dirichlet.c | 4 +- src/preprocessing/discretize.c | 4 +- src/sanitization/covariance.c | 2 - src/tests/patterns/allsubs.test.c | 29 +++++++++------- src/tests/patterns/roundrobin.test.c | 12 +++--- src/tests/permutation/discrete.monte.carlo.c | 6 ++- 21 files changed, 93 insertions(+), 72 deletions(-)
Title: List, String, and Meta Programming Utility Functions
Description: Includes functions for mapping named lists to function arguments, random strings,
pasting and combining rows together across columns, etc.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Diff between toolbox versions 0.1.0 dated 2022-06-23 and 0.1.1 dated 2022-09-21
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NAMESPACE | 2 +- R/toolbox.R | 15 ++++++++++++++- man/pastePaths.Rd |only 5 files changed, 23 insertions(+), 9 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.8.4 dated 2022-04-01 and 2.9.0 dated 2022-09-21
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++++----- NAMESPACE | 3 +++ NEWS | 13 ++++++++----- R/labkey.setCurlOptions.R | 2 +- R/labkey.storage.R |only man/Rlabkey-package.Rd | 4 ++-- man/labkey.storage.create.Rd |only man/labkey.storage.delete.Rd |only man/labkey.storage.update.Rd |only 10 files changed, 27 insertions(+), 17 deletions(-)
Title: Heatmap for Categorical Data using 'plotly'
Description: Methods and plotting functions for displaying categorical data on an
interactive heatmap using 'plotly'. Provides functionality for strictly
categorical heatmaps, heatmaps illustrating categorized continuous data
and annotated heatmaps. Also, there are various options to interact with the x-axis
to prevent overlapping axis labels, e.g. via simple sliders or range sliders.
Besides the viewer pane, resulting plots can be saved as a standalone HTML file,
embedded in 'R Markdown' documents or in a 'Shiny' app.
Author: Yves Mauron [aut, cre],
Trivadis AG [cph]
Maintainer: Yves Mauron <ypmauron@gmail.com>
Diff between catmaply versions 0.9.0 dated 2020-09-07 and 0.9.2 dated 2022-09-21
DESCRIPTION | 17 - MD5 | 16 - NEWS.md | 9 README.md | 17 + build/vignette.rds |binary inst/doc/catmaply.Rmd | 20 + inst/doc/catmaply.html | 529 ++++++++++++++++++++++++++++++------------------ man/catmaply-package.Rd | 12 - vignettes/catmaply.Rmd | 20 + 9 files changed, 399 insertions(+), 241 deletions(-)
Title: 'RStudio' Addin for Network Analysis and Visualization
Description: 'RStudio' addin which provides a GUI to visualize and analyse networks.
After finishing a session, the code to produce the plot is inserted in the current script.
Alternatively, the function SNAhelperGadget() can be used directly from the console.
Additional addins include the Netreader() for reading network files, Netbuilder() to create
small networks via point and click, and the Componentlayouter() to layout networks with many components manually.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between snahelper versions 1.4.0 dated 2021-12-17 and 1.4.1 dated 2022-09-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/Netreader.R | 2 +- R/SNAhelper.R | 4 ++-- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Assesses the Quality of Estimates Made by Complex Sample Designs
Description: Assesses the quality of estimates made by complex sample designs,
following the methodology developed by the National Institute of Statistics Chile (2020, <https://www.ine.cl/docs/default-source/institucionalidad/buenas-pr%C3%A1cticas/clasificaciones-y-estandares/est%C3%A1ndar-evaluaci%C3%B3n-de-calidad-de-estimaciones-publicaci%C3%B3n-27022020.pdf>)
and by Economic Commission for Latin America and
Caribbean (2020, <https://repositorio.cepal.org/bitstream/handle/11362/45681/1/S2000293_es.pdf>).
Author: Klaus Lehmann [aut, cre],
Ricardo Pizarro [aut],
Ignacio Agloni [ctb]
Maintainer: Klaus Lehmann <klehmann@fen.uchile.cl>
Diff between calidad versions 0.1.0 dated 2022-08-23 and 0.2.0 dated 2022-09-21
calidad-0.1.0/calidad/man/calcular_estrato.Rd |only calidad-0.1.0/calidad/man/calcular_gl_total.Rd |only calidad-0.1.0/calidad/man/calcular_tabla.Rd |only calidad-0.1.0/calidad/man/calcular_tabla_ratio.Rd |only calidad-0.1.0/calidad/man/calcular_upm.Rd |only calidad-0.1.0/calidad/man/check_input_var.Rd |only calidad-0.1.0/calidad/man/check_subpop_var.Rd |only calidad-0.1.0/calidad/man/chequear_var_disenio.Rd |only calidad-0.1.0/calidad/man/concat_domains.Rd |only calidad-0.1.0/calidad/man/convert_to_formula.Rd |only calidad-0.1.0/calidad/man/create_groupby_vars.Rd |only calidad-0.1.0/calidad/man/get_ci.Rd |only calidad-0.1.0/calidad/man/get_sample_size.Rd |only calidad-0.1.0/calidad/man/unificar_variables_estrato.Rd |only calidad-0.1.0/calidad/man/unificar_variables_factExp.Rd |only calidad-0.1.0/calidad/man/unificar_variables_upm.Rd |only calidad-0.2.0/calidad/DESCRIPTION | 14 calidad-0.2.0/calidad/MD5 | 64 -- calidad-0.2.0/calidad/NEWS.md |only calidad-0.2.0/calidad/R/create_external.R | 160 +++-- calidad-0.2.0/calidad/R/create_internal.R | 313 ++++------ calidad-0.2.0/calidad/R/data.R | 116 +-- calidad-0.2.0/calidad/R/evaluate_external.R | 12 calidad-0.2.0/calidad/R/evaluate_internal.R | 11 calidad-0.2.0/calidad/R/report.R | 8 calidad-0.2.0/calidad/inst/doc/tutorial.R | 4 calidad-0.2.0/calidad/inst/doc/tutorial.Rmd | 9 calidad-0.2.0/calidad/inst/doc/tutorial.html | 43 - calidad-0.2.0/calidad/man/casen.Rd | 22 calidad-0.2.0/calidad/man/create_html.Rd | 9 calidad-0.2.0/calidad/man/ene.Rd | 26 calidad-0.2.0/calidad/man/enusc.Rd | 46 - calidad-0.2.0/calidad/man/epf_personas.Rd | 22 calidad-0.2.0/calidad/man/get_cv.Rd | 12 calidad-0.2.0/calidad/man/get_df.Rd | 8 calidad-0.2.0/calidad/man/get_survey_table.Rd |only calidad-0.2.0/calidad/man/standardize_columns.Rd | 10 calidad-0.2.0/calidad/man/standardize_design_variables.Rd | 8 calidad-0.2.0/calidad/tests/testthat/test-create_prop.R | 26 calidad-0.2.0/calidad/tests/testthat/test-create_size.R | 7 calidad-0.2.0/calidad/tests/testthat/test-evaluate_external.R | 13 calidad-0.2.0/calidad/vignettes/tutorial.Rmd | 9 42 files changed, 517 insertions(+), 455 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Author: Tim Stuart [aut, cre] ,
Avi Srivastava [aut] ,
Paul Hoffman [ctb] ,
Rahul Satija [ctb]
Maintainer: Tim Stuart <tstuart@nygenome.org>
Diff between Signac versions 1.7.0 dated 2022-06-01 and 1.8.0 dated 2022-09-21
DESCRIPTION | 14 +-- MD5 | 69 +++++++-------- NAMESPACE | 1 NEWS.md | 154 ++++++++++++++++++---------------- R/differential_accessibility.R | 7 - R/generics.R | 1 R/motifs.R | 9 + R/objects.R | 63 ++++++++++--- R/preprocessing.R | 32 +++++-- R/quantification.R | 8 + R/utilities.R | 24 ++--- R/visualization.R | 84 +++++++++++++++--- R/zzz.R | 1 README.md | 14 +-- build/partial.rdb |binary man/AnnotationPlot.Rd | 20 ++++ man/Cells-set.Rd | 1 man/LinkPlot.Rd | 20 ++++ man/MotifCounts.Rd | 1 man/PeakPlot.Rd | 13 ++ man/SetMotifData.Rd | 4 man/Signac-package.Rd | 9 + man/coverage-ChromatinAssay-method.Rd | 6 - man/findOverlaps-methods.Rd | 24 ++--- man/granges-methods.Rd | 4 man/inter-range-methods.Rd | 24 ++--- man/nearest-methods.Rd | 60 ++++++------- man/seqinfo-methods.Rd | 48 +++++----- man/subset.Fragment.Rd |only man/subset.Motif.Rd | 1 src/filter.cpp | 15 +++ src/group.cpp | 16 +++ src/split.cpp | 12 ++ src/validate.cpp | 19 +++- tests/testdata/featurematrix.rds |binary tests/testthat/test_fragments.R | 46 ++++++++++ 36 files changed, 560 insertions(+), 264 deletions(-)
Title: Global Sensitivity Analysis in Physiologically Based Kinetic
Modeling
Description: Applying the global sensitivity analysis workflow to investigate
the parameter uncertainty and sensitivity in physiologically based
kinetic (PK) models, especially the physiologically based
pharmacokinetic/toxicokinetic model with multivariate outputs.
The package also provides some functions to check the convergence
and sensitivity of model parameters. The workflow was first mentioned
in Hsieh et al., (2018) <doi:10.3389/fphar.2018.00588>, then further
refined (Hsieh et al., 2020 <doi:10.1016/j.softx.2020.100609>).
Author: Nan-Hung Hsieh [aut, cre] ,
Brad Reisfeld [ctb] ,
Weihsueh A. Chiu [ctb]
Maintainer: Nan-Hung Hsieh <d99622005@ntu.edu.tw>
Diff between pksensi versions 1.2.2 dated 2021-07-04 and 1.2.3 dated 2022-09-21
DESCRIPTION | 15 MD5 | 54 +-- NAMESPACE | 97 ++--- NEWS.md | 291 +++++++++-------- R/check.R | 773 ++++++++++++++++++++++++----------------------- R/compile.R | 362 ++++++++++++++-------- R/install.R | 507 +++++++++++++++++-------------- R/models.R | 110 +++--- R/package.R | 5 R/rfast99.R | 4 R/solve_mcsim.R | 716 +++++++++++++++++++++++-------------------- R/tell2.R | 4 build/vignette.rds |binary inst/CITATION | 2 inst/doc/pbpk_apap.R | 355 ++++++++++----------- inst/doc/pbpk_apap.Rmd | 510 +++++++++++++++---------------- inst/doc/pbpk_apap.html | 634 +++++++++++++++++++------------------- inst/doc/pbtk1cpt.R | 372 +++++++++++----------- inst/doc/pbtk1cpt.Rmd | 662 ++++++++++++++++++++-------------------- inst/doc/pbtk1cpt.html | 784 ++++++++++++++++++++++++------------------------ man/about-pksensi.Rd | 5 man/check.Rd | 18 - man/compile_model.Rd | 12 man/mcsim.Rd | 27 - man/models.Rd | 12 man/solve_mcsim.Rd | 17 - vignettes/pbpk_apap.Rmd | 510 +++++++++++++++---------------- vignettes/pbtk1cpt.Rmd | 662 ++++++++++++++++++++-------------------- 28 files changed, 3897 insertions(+), 3623 deletions(-)
Title: Standardized Moderation Effect and Its Confidence Interval
Description: Functions for computing a standardized moderation effect
in moderated regression and forming its confidence interval
by nonparametric bootstrapping as proposed in
Cheung, Cheung, Lau, Hui, and Vong (2022)
<doi:10.1037/hea0001188>. Also includes simple-to-use
functions for computing conditional effects (unstandardized
or standardized) and plotting moderation effects.
Author: Shu Fai Cheung [aut, cre] ,
David Weng Ngai Vong [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between stdmod versions 0.1.7.4 dated 2022-08-07 and 0.2.0.0 dated 2022-09-21
DESCRIPTION | 8 - MD5 | 82 +++++++++---------- NEWS.md | 16 +++ R/confint_stdmod.R | 33 +++++-- R/std_selected.R | 2 R/stdmod.R | 2 R/stdmod_lavaan.R | 2 R/vcov_stdmod.R | 26 ++++-- README.md | 23 ++++- inst/CITATION | 6 - inst/doc/cond_effect.Rmd | 2 inst/doc/cond_effect.html | 19 +++- inst/doc/moderation.Rmd | 10 +- inst/doc/moderation.html | 19 +++- inst/doc/plotmod.Rmd | 10 +- inst/doc/plotmod.html | 19 +++- inst/doc/std_selected.Rmd | 8 - inst/doc/std_selected.html | 19 +++- inst/doc/stdmod.Rmd | 8 - inst/doc/stdmod.html | 25 +++-- inst/doc/stdmod_lavaan.Rmd | 2 inst/doc/stdmod_lavaan.html | 19 +++- man/cond_effect.Rd | 4 man/confint.std_selected.Rd | 19 ++-- man/std_selected.Rd | 8 - man/stdmod.Rd | 8 - man/stdmod_lavaan.Rd | 2 man/test_mod1.Rd | 6 - man/test_mod2.Rd | 6 - man/test_mod3_miss.Rd | 66 +++++++-------- man/vcov.std_selected.Rd | 16 ++- tests/testthat/test_plotmod.R | 17 ++- tests/testthat/test_plotmod_percentile_more_levels.R | 3 tests/testthat/test_plotmod_tumble.R | 19 ++-- tests/testthat/test_stdmod_selected_confint.R | 4 tests/testthat/test_stdmod_selected_vcov.R | 4 vignettes/cond_effect.Rmd | 2 vignettes/moderation.Rmd | 10 +- vignettes/plotmod.Rmd | 10 +- vignettes/std_selected.Rmd | 8 - vignettes/stdmod.Rmd | 8 - vignettes/stdmod_lavaan.Rmd | 2 42 files changed, 351 insertions(+), 231 deletions(-)
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija (2019)
<doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9>
for more details.
Author: Christoph Hafemeister [aut] ,
Saket Choudhary [aut, cre] ,
Rahul Satija [ctb]
Maintainer: Saket Choudhary <schoudhary@nygenome.org>
Diff between sctransform versions 0.3.4 dated 2022-08-20 and 0.3.5 dated 2022-09-21
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- NEWS.md | 5 +++++ inst/CITATION | 13 +++++++++++++ 4 files changed, 28 insertions(+), 9 deletions(-)
Title: Kalman Filter
Description: 'Rcpp' implementation of the multivariate Kalman filter for state space models that can handle missing values and exogenous data in the observation and state equations.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between kalmanfilter versions 1.0.0 dated 2022-09-02 and 2.0.0 dated 2022-09-21
kalmanfilter-1.0.0/kalmanfilter/R/kalmanfilter.R |only kalmanfilter-1.0.0/kalmanfilter/man/filter.Rd |only kalmanfilter-1.0.0/kalmanfilter/man/kalman_lik.Rd |only kalmanfilter-1.0.0/kalmanfilter/man/likelihood.Rd |only kalmanfilter-2.0.0/kalmanfilter/DESCRIPTION | 10 kalmanfilter-2.0.0/kalmanfilter/MD5 | 39 kalmanfilter-2.0.0/kalmanfilter/NAMESPACE | 4 kalmanfilter-2.0.0/kalmanfilter/NEWS.md | 13 kalmanfilter-2.0.0/kalmanfilter/R/RcppExports.R | 72 - kalmanfilter-2.0.0/kalmanfilter/R/data.R | 12 kalmanfilter-2.0.0/kalmanfilter/R/zzz.R | 3 kalmanfilter-2.0.0/kalmanfilter/data/sw_dcf.RData |only kalmanfilter-2.0.0/kalmanfilter/inst/doc/kalmanfilter_vignette.R | 287 +++- kalmanfilter-2.0.0/kalmanfilter/inst/doc/kalmanfilter_vignette.Rmd | 360 +++-- kalmanfilter-2.0.0/kalmanfilter/inst/doc/kalmanfilter_vignette.html | 700 ++++++---- kalmanfilter-2.0.0/kalmanfilter/man/Rginv.Rd | 3 kalmanfilter-2.0.0/kalmanfilter/man/contains.Rd |only kalmanfilter-2.0.0/kalmanfilter/man/gen_inv.Rd | 3 kalmanfilter-2.0.0/kalmanfilter/man/kalman_filter.Rd | 60 kalmanfilter-2.0.0/kalmanfilter/man/sw_dcf.Rd |only kalmanfilter-2.0.0/kalmanfilter/src/RcppExports.cpp | 34 kalmanfilter-2.0.0/kalmanfilter/src/kalmanfilter.cpp | 254 +-- kalmanfilter-2.0.0/kalmanfilter/tests/testthat/test.R | 45 kalmanfilter-2.0.0/kalmanfilter/vignettes/kalmanfilter_vignette.Rmd | 360 +++-- 24 files changed, 1554 insertions(+), 705 deletions(-)
Title: Miscellaneous Functions for Environmental Analyses
Description: Small toolbox for data analyses in environmental chemistry and
ecotoxicology. Provides, for example, calibration() to calculate calibration
curves and corresponding limits of detection (LODs) and limits of
quantification (LOQs) according to German DIN 32645 (2008). texture() makes
it easy to estimate soil particle size distributions from hydrometer
measurements (ASTM D422-63, 2007).
Author: Zacharias Steinmetz [aut, cre]
,
Julius Albert [ctb] ,
Kilian Kenngott [ctb]
Maintainer: Zacharias Steinmetz <steinmetz-z@uni-landau.de>
Diff between envalysis versions 0.5.1 dated 2021-03-05 and 0.5.3 dated 2022-09-21
envalysis-0.5.1/envalysis/NEWS |only envalysis-0.5.1/envalysis/R/pkgname.R |only envalysis-0.5.1/envalysis/man/envalysis.Rd |only envalysis-0.5.3/envalysis/DESCRIPTION | 22 envalysis-0.5.3/envalysis/MD5 | 41 - envalysis-0.5.3/envalysis/NEWS.md |only envalysis-0.5.3/envalysis/R/clayloam.R | 2 envalysis-0.5.3/envalysis/R/envalysis-package.R |only envalysis-0.5.3/envalysis/R/signifig.R | 54 + envalysis-0.5.3/envalysis/R/sorption.R | 30 envalysis-0.5.3/envalysis/R/texture.R | 17 envalysis-0.5.3/envalysis/README.md | 5 envalysis-0.5.3/envalysis/build/partial.rdb |binary envalysis-0.5.3/envalysis/build/vignette.rds |binary envalysis-0.5.3/envalysis/inst/doc/texture.html | 345 ++++++++-- envalysis-0.5.3/envalysis/inst/doc/theme_publish.html | 270 ++++++- envalysis-0.5.3/envalysis/man/clayloam.Rd | 2 envalysis-0.5.3/envalysis/man/envalysis-package.Rd |only envalysis-0.5.3/envalysis/man/signifig.Rd | 13 envalysis-0.5.3/envalysis/man/sorption.Rd | 14 envalysis-0.5.3/envalysis/man/texture.Rd | 9 envalysis-0.5.3/envalysis/tests/testthat/Rplots.pdf |only envalysis-0.5.3/envalysis/tests/testthat/_snaps/weight_select.md | 2 envalysis-0.5.3/envalysis/tests/testthat/test-signifig.R | 21 envalysis-0.5.3/envalysis/tests/testthat/test-theme_publish.R | 3 25 files changed, 636 insertions(+), 214 deletions(-)
Title: R2 Statistic
Description: R2 statistic for significance test. Variance and covariance of R2 values used to assess the 95% CI and p-value of the R2 difference.
Author: Hong Lee [aut, cph],
Moksedul Momin [aut, cre, cph]
Maintainer: Moksedul Momin <cvasu.momin@gmail.com>
Diff between r2redux versions 1.0.10 dated 2022-08-08 and 1.0.11 dated 2022-09-21
DESCRIPTION | 8 +++++--- MD5 | 4 +++- tests |only 3 files changed, 8 insertions(+), 4 deletions(-)
Title: Fitting Deep Distributional Regression
Description: Allows for the specification of semi-structured deep distributional regression models which are fitted in a neural network as
proposed by Ruegamer et al. (2021) <arXiv:2104.02705>.
Predictors can be modeled using structured (penalized) linear effects, structured non-linear effects or using an unstructured deep network model.
Author: David Ruegamer [aut, cre],
Florian Pfisterer [ctb],
Philipp Baumann [ctb],
Chris Kolb [ctb],
Lucas Kook [ctb]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between deepregression versions 0.1 dated 2021-10-04 and 0.2 dated 2022-09-21
deepregression-0.1/deepregression/inst/python/layers/__pycache__/keras_generators.cpython-36.pyc |only deepregression-0.1/deepregression/inst/python/layers/__pycache__/orthog.cpython-36.pyc |only deepregression-0.1/deepregression/inst/python/layers/__pycache__/rlayer.cpython-36.pyc |only deepregression-0.1/deepregression/man/extractval.Rd |only deepregression-0.1/deepregression/man/fit.Rd |only deepregression-0.1/deepregression/man/processor.Rd |only deepregression-0.2/deepregression/DESCRIPTION | 30 deepregression-0.2/deepregression/MD5 | 188 ++- deepregression-0.2/deepregression/NAMESPACE | 62 + deepregression-0.2/deepregression/R/aaa.R |only deepregression-0.2/deepregression/R/controls.R | 125 ++ deepregression-0.2/deepregression/R/cross-validation.R | 42 deepregression-0.2/deepregression/R/data_handler.R | 40 deepregression-0.2/deepregression/R/deep-ensembles.R |only deepregression-0.2/deepregression/R/deepregression.R | 351 +++--- deepregression-0.2/deepregression/R/families.R | 95 + deepregression-0.2/deepregression/R/formula_helpers.R |only deepregression-0.2/deepregression/R/generator.R | 35 deepregression-0.2/deepregression/R/helperfuns.R | 340 +++-- deepregression-0.2/deepregression/R/layers.R |only deepregression-0.2/deepregression/R/methods.R | 225 ++- deepregression-0.2/deepregression/R/models.R | 20 deepregression-0.2/deepregression/R/orthogonalization.R | 38 deepregression-0.2/deepregression/R/psplinelayer.R | 550 ++++++++- deepregression-0.2/deepregression/R/special_processing.R | 571 +++++++--- deepregression-0.2/deepregression/R/subnetwork_init.R | 132 +- deepregression-0.2/deepregression/R/tf_helpers.R |only deepregression-0.2/deepregression/R/zzz.R | 34 deepregression-0.2/deepregression/inst/python/distributions |only deepregression-0.2/deepregression/inst/python/generators/__pycache__/__init__.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/generators/__pycache__/keras_generators.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/generators/keras_generators.py | 6 deepregression-0.2/deepregression/inst/python/layers/__init__.py | 1 deepregression-0.2/deepregression/inst/python/layers/__pycache__/__init__.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/layers/__pycache__/__init__.cpython-36.pyc |binary deepregression-0.2/deepregression/inst/python/layers/__pycache__/convlasso.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/layers/__pycache__/convlasso.cpython-36.pyc |only deepregression-0.2/deepregression/inst/python/layers/__pycache__/lasso.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/layers/__pycache__/lasso.cpython-36.pyc |binary deepregression-0.2/deepregression/inst/python/layers/convlasso.py |only deepregression-0.2/deepregression/inst/python/layers/lasso.py | 340 +++++ deepregression-0.2/deepregression/inst/python/misc |only deepregression-0.2/deepregression/inst/python/models/__init__.py | 1 deepregression-0.2/deepregression/inst/python/models/__pycache__/__init__.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/models/__pycache__/__init__.cpython-36.pyc |binary deepregression-0.2/deepregression/inst/python/models/__pycache__/custom_train_step.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/models/__pycache__/custom_train_step.cpython-36.pyc |binary deepregression-0.2/deepregression/inst/python/models/__pycache__/model_trainable_para.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/models/__pycache__/model_trainable_para.cpython-36.pyc |only deepregression-0.2/deepregression/inst/python/models/custom_train_step.py | 62 - deepregression-0.2/deepregression/inst/python/models/model_trainable_para.py |only deepregression-0.2/deepregression/inst/python/optimizers |only deepregression-0.2/deepregression/inst/python/psplines/__pycache__/__init__.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/psplines/__pycache__/__init__.cpython-36.pyc |binary deepregression-0.2/deepregression/inst/python/psplines/__pycache__/psplines.cpython-310.pyc |only deepregression-0.2/deepregression/inst/python/psplines/__pycache__/psplines.cpython-36.pyc |binary deepregression-0.2/deepregression/inst/python/psplines/native_bsplines.py |only deepregression-0.2/deepregression/inst/python/psplines/psplines.py | 10 deepregression-0.2/deepregression/man/check_and_install.Rd | 6 deepregression-0.2/deepregression/man/coef.drEnsemble.Rd |only deepregression-0.2/deepregression/man/combine_penalties.Rd |only deepregression-0.2/deepregression/man/create_penalty.Rd |only deepregression-0.2/deepregression/man/deepregression.Rd | 22 deepregression-0.2/deepregression/man/dr_families.Rd | 6 deepregression-0.2/deepregression/man/ensemble.Rd |only deepregression-0.2/deepregression/man/ensemble.deepregression.Rd |only deepregression-0.2/deepregression/man/extract_S.Rd |only deepregression-0.2/deepregression/man/extract_pure_gam_part.Rd |only deepregression-0.2/deepregression/man/extractvar.Rd |only deepregression-0.2/deepregression/man/fitted.drEnsemble.Rd |only deepregression-0.2/deepregression/man/form_control.Rd |only deepregression-0.2/deepregression/man/formulaHelpers.Rd |only deepregression-0.2/deepregression/man/from_preds_to_dist.Rd | 12 deepregression-0.2/deepregression/man/gam_plot_data.Rd |only deepregression-0.2/deepregression/man/get_ensemble_distribution.Rd |only deepregression-0.2/deepregression/man/get_gam_part.Rd |only deepregression-0.2/deepregression/man/get_gamdata.Rd |only deepregression-0.2/deepregression/man/get_gamdata_reduced_nr.Rd |only deepregression-0.2/deepregression/man/get_layer_by_opname.Rd |only deepregression-0.2/deepregression/man/get_layernr_by_opname.Rd |only deepregression-0.2/deepregression/man/get_layernr_trainable.Rd |only deepregression-0.2/deepregression/man/get_partial_effect.Rd | 9 deepregression-0.2/deepregression/man/get_processor_name.Rd |only deepregression-0.2/deepregression/man/get_special.Rd |only deepregression-0.2/deepregression/man/get_weight_by_name.Rd | 4 deepregression-0.2/deepregression/man/get_weight_by_opname.Rd |only deepregression-0.2/deepregression/man/hadamard_layers.Rd |only deepregression-0.2/deepregression/man/keras_dr.Rd | 24 deepregression-0.2/deepregression/man/layer_sparse_conv_2d.Rd |only deepregression-0.2/deepregression/man/layer_spline.Rd |only deepregression-0.2/deepregression/man/log_score.Rd | 2 deepregression-0.2/deepregression/man/makelayername.Rd |only deepregression-0.2/deepregression/man/methodDR.Rd | 10 deepregression-0.2/deepregression/man/multioptimizer.Rd |only deepregression-0.2/deepregression/man/orthog_P.Rd |only deepregression-0.2/deepregression/man/orthog_structured_smooths_Z.Rd |only deepregression-0.2/deepregression/man/penalty_control.Rd | 9 deepregression-0.2/deepregression/man/precalc_gam.Rd |only deepregression-0.2/deepregression/man/prepare_data.Rd | 4 deepregression-0.2/deepregression/man/prepare_newdata.Rd | 4 deepregression-0.2/deepregression/man/process_terms.Rd |only deepregression-0.2/deepregression/man/processors.Rd |only deepregression-0.2/deepregression/man/reinit_weights.Rd |only deepregression-0.2/deepregression/man/reinit_weights.deepregression.Rd |only deepregression-0.2/deepregression/man/separate_define_relation.Rd | 5 deepregression-0.2/deepregression/man/subnetwork_init.Rd | 19 deepregression-0.2/deepregression/man/tf_repeat.Rd |only deepregression-0.2/deepregression/man/tf_row_tensor.Rd |only deepregression-0.2/deepregression/man/tf_split_multiple.Rd |only deepregression-0.2/deepregression/man/tf_stride_cols.Rd | 2 deepregression-0.2/deepregression/man/tf_stride_last_dim_tensor.Rd |only deepregression-0.2/deepregression/man/tfd_mse.Rd |only deepregression-0.2/deepregression/man/weight_control.Rd |only deepregression-0.2/deepregression/tests/testthat/test_controls.R | 7 deepregression-0.2/deepregression/tests/testthat/test_customtraining.R |only deepregression-0.2/deepregression/tests/testthat/test_data_handler.R | 44 deepregression-0.2/deepregression/tests/testthat/test_deepregression.R | 157 ++ deepregression-0.2/deepregression/tests/testthat/test_ensemble.R |only deepregression-0.2/deepregression/tests/testthat/test_families.R | 33 deepregression-0.2/deepregression/tests/testthat/test_layers.R |only deepregression-0.2/deepregression/tests/testthat/test_special_processing.R | 97 + deepregression-0.2/deepregression/tests/testthat/test_subnetwork_init.R | 68 - deepregression-0.2/deepregression/tests/testthat/test_unstructured.R | 2 123 files changed, 2951 insertions(+), 893 deletions(-)
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Title: Precipitation R Recipe
Description: An open-access tool/framework to download, validate, visualize, and analyze multi-source precipitation data across various spatio-temporal scales. Ultimately providing the hydrology science community with the tools for consistent and reproducible analysis regarding precipitation.
Author: Mijael Rodrigo Vargas Godoy [aut, cre],
Yannis Markonis [aut, ths]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between pRecipe versions 0.2.0 dated 2022-04-22 and 0.3.0 dated 2022-09-21
pRecipe-0.2.0/pRecipe/R/aux_functions.R |only pRecipe-0.2.0/pRecipe/R/downloaders.R |only pRecipe-0.2.0/pRecipe/R/graphics.R |only pRecipe-0.2.0/pRecipe/R/integrator.R |only pRecipe-0.2.0/pRecipe/R/reformatters.R |only pRecipe-0.2.0/pRecipe/man/display_data.Rd |only pRecipe-0.2.0/pRecipe/man/download_gpm_imergm.Rd |only pRecipe-0.2.0/pRecipe/man/dt_aggregate.Rd |only pRecipe-0.2.0/pRecipe/man/dt_parallel.Rd |only pRecipe-0.2.0/pRecipe/man/import_full_data.Rd |only pRecipe-0.2.0/pRecipe/man/import_subset_data.Rd |only pRecipe-0.2.0/pRecipe/man/merge_1836_1890.Rd |only pRecipe-0.2.0/pRecipe/man/merge_1891_2020.Rd |only pRecipe-0.2.0/pRecipe/man/merge_time.Rd |only pRecipe-0.2.0/pRecipe/man/plot_bar.Rd |only pRecipe-0.2.0/pRecipe/man/plot_matrix.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_20cr.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_all.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_cmap.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_cpc.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_cru_ts.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_data.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_ghcn.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_gpcc.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_gpcp.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_gpm_imergm.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_ncep_doe.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_ncep_ncar.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_precl.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_trmm_3b43.Rd |only pRecipe-0.2.0/pRecipe/man/reformat_udel.Rd |only pRecipe-0.2.0/pRecipe/man/resample_data.Rd |only pRecipe-0.2.0/pRecipe/man/sd_20cr.Rd |only pRecipe-0.2.0/pRecipe/vignettes/CZ_P_2000_2020.png |only pRecipe-0.3.0/pRecipe/DESCRIPTION | 27 pRecipe-0.3.0/pRecipe/MD5 | 169 +-- pRecipe-0.3.0/pRecipe/NAMESPACE | 96 - pRecipe-0.3.0/pRecipe/NEWS.md | 7 pRecipe-0.3.0/pRecipe/R/create_folders.R |only pRecipe-0.3.0/pRecipe/R/crop_data.R |only pRecipe-0.3.0/pRecipe/R/download_20cr.R |only pRecipe-0.3.0/pRecipe/R/download_all.R |only pRecipe-0.3.0/pRecipe/R/download_chirps.R |only pRecipe-0.3.0/pRecipe/R/download_cmap.R |only pRecipe-0.3.0/pRecipe/R/download_cmorph.R |only pRecipe-0.3.0/pRecipe/R/download_cpc.R |only pRecipe-0.3.0/pRecipe/R/download_cru_ts.R |only pRecipe-0.3.0/pRecipe/R/download_data.R |only pRecipe-0.3.0/pRecipe/R/download_em_earth.R |only pRecipe-0.3.0/pRecipe/R/download_era20c.R |only pRecipe-0.3.0/pRecipe/R/download_era5.R |only pRecipe-0.3.0/pRecipe/R/download_ghcn.R |only pRecipe-0.3.0/pRecipe/R/download_gldas_clsm.R |only pRecipe-0.3.0/pRecipe/R/download_gldas_noah.R |only pRecipe-0.3.0/pRecipe/R/download_gldas_vic.R |only pRecipe-0.3.0/pRecipe/R/download_gpcc.R |only pRecipe-0.3.0/pRecipe/R/download_gpcp.R |only pRecipe-0.3.0/pRecipe/R/download_gpm_imerg.R |only pRecipe-0.3.0/pRecipe/R/download_mswep.R |only pRecipe-0.3.0/pRecipe/R/download_ncep_doe.R |only pRecipe-0.3.0/pRecipe/R/download_ncep_ncar.R |only pRecipe-0.3.0/pRecipe/R/download_persiann.R |only pRecipe-0.3.0/pRecipe/R/download_precl.R |only pRecipe-0.3.0/pRecipe/R/download_terraclimate.R |only pRecipe-0.3.0/pRecipe/R/download_trmm_3b43.R |only pRecipe-0.3.0/pRecipe/R/download_udel.R |only pRecipe-0.3.0/pRecipe/R/globals.R | 2 pRecipe-0.3.0/pRecipe/R/make_ts.R |only pRecipe-0.3.0/pRecipe/R/mon_to_year.R |only pRecipe-0.3.0/pRecipe/R/pRecipe.R | 325 ----- pRecipe-0.3.0/pRecipe/R/plot_box.R |only pRecipe-0.3.0/pRecipe/R/plot_density.R |only pRecipe-0.3.0/pRecipe/R/plot_heatmap.R |only pRecipe-0.3.0/pRecipe/R/plot_line.R |only pRecipe-0.3.0/pRecipe/R/plot_map.R |only pRecipe-0.3.0/pRecipe/R/plot_summary.R |only pRecipe-0.3.0/pRecipe/R/rescale_data.R |only pRecipe-0.3.0/pRecipe/R/show_info.R |only pRecipe-0.3.0/pRecipe/R/subset_space.R |only pRecipe-0.3.0/pRecipe/R/subset_spacetime.R |only pRecipe-0.3.0/pRecipe/R/subset_time.R |only pRecipe-0.3.0/pRecipe/build/vignette.rds |binary pRecipe-0.3.0/pRecipe/inst/WORDLIST | 42 pRecipe-0.3.0/pRecipe/inst/doc/pRecipe.R | 70 + pRecipe-0.3.0/pRecipe/inst/doc/pRecipe.Rmd | 386 ++++++- pRecipe-0.3.0/pRecipe/inst/doc/pRecipe.html | 1094 +++++++++++++++++++- pRecipe-0.3.0/pRecipe/man/create_folders.Rd | 10 pRecipe-0.3.0/pRecipe/man/crop_data.Rd | 19 pRecipe-0.3.0/pRecipe/man/download_20cr.Rd | 7 pRecipe-0.3.0/pRecipe/man/download_all.Rd | 7 pRecipe-0.3.0/pRecipe/man/download_chirps.Rd |only pRecipe-0.3.0/pRecipe/man/download_cmap.Rd | 7 pRecipe-0.3.0/pRecipe/man/download_cmorph.Rd |only pRecipe-0.3.0/pRecipe/man/download_cpc.Rd | 11 pRecipe-0.3.0/pRecipe/man/download_cru_ts.Rd | 9 pRecipe-0.3.0/pRecipe/man/download_data.Rd | 39 pRecipe-0.3.0/pRecipe/man/download_em_earth.Rd |only pRecipe-0.3.0/pRecipe/man/download_era20c.Rd |only pRecipe-0.3.0/pRecipe/man/download_era5.Rd |only pRecipe-0.3.0/pRecipe/man/download_ghcn.Rd | 9 pRecipe-0.3.0/pRecipe/man/download_gldas_clsm.Rd |only pRecipe-0.3.0/pRecipe/man/download_gldas_noah.Rd |only pRecipe-0.3.0/pRecipe/man/download_gldas_vic.Rd |only pRecipe-0.3.0/pRecipe/man/download_gpcc.Rd | 14 pRecipe-0.3.0/pRecipe/man/download_gpcp.Rd | 7 pRecipe-0.3.0/pRecipe/man/download_gpm_imerg.Rd |only pRecipe-0.3.0/pRecipe/man/download_mswep.Rd |only pRecipe-0.3.0/pRecipe/man/download_ncep_doe.Rd | 9 pRecipe-0.3.0/pRecipe/man/download_ncep_ncar.Rd | 9 pRecipe-0.3.0/pRecipe/man/download_persiann.Rd |only pRecipe-0.3.0/pRecipe/man/download_precl.Rd | 14 pRecipe-0.3.0/pRecipe/man/download_terraclimate.Rd |only pRecipe-0.3.0/pRecipe/man/download_trmm_3b43.Rd | 16 pRecipe-0.3.0/pRecipe/man/download_udel.Rd | 7 pRecipe-0.3.0/pRecipe/man/make_ts.Rd |only pRecipe-0.3.0/pRecipe/man/mon_to_year.Rd |only pRecipe-0.3.0/pRecipe/man/pRecipe-package.Rd |only pRecipe-0.3.0/pRecipe/man/plot_box.Rd | 8 pRecipe-0.3.0/pRecipe/man/plot_density.Rd |only pRecipe-0.3.0/pRecipe/man/plot_heatmap.Rd |only pRecipe-0.3.0/pRecipe/man/plot_line.Rd | 8 pRecipe-0.3.0/pRecipe/man/plot_map.Rd | 14 pRecipe-0.3.0/pRecipe/man/plot_summary.Rd |only pRecipe-0.3.0/pRecipe/man/rescale_data.Rd |only pRecipe-0.3.0/pRecipe/man/show_info.Rd |only pRecipe-0.3.0/pRecipe/man/subset_space.Rd |only pRecipe-0.3.0/pRecipe/man/subset_spacetime.Rd |only pRecipe-0.3.0/pRecipe/man/subset_time.Rd |only pRecipe-0.3.0/pRecipe/tests/testthat/test-pRecipe.R | 2 pRecipe-0.3.0/pRecipe/vignettes/pRecipe.Rmd | 386 ++++++- pRecipe-0.3.0/pRecipe/vignettes/pRecipe.bib |only pRecipe-0.3.0/pRecipe/vignettes/plots |only 132 files changed, 2157 insertions(+), 673 deletions(-)
Title: Curve Text Elements in 'Shiny' Using 'CircleType.js'
Description: Enables curving text elements in 'Shiny' apps.
Author: Etienne Bacher [aut, cre, cph]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between circletyper versions 1.0.1 dated 2021-07-17 and 1.0.2 dated 2022-09-21
DESCRIPTION | 6 - LICENSE | 4 MD5 | 38 ++++----- NAMESPACE | 2 NEWS.md | 18 ++-- R/circletype.R | 144 +++++++++++++++++------------------ R/remove_circletype.R | 86 ++++++++++---------- R/use_circletype.R | 64 +++++++-------- R/zzz.R | 20 ++-- README.md | 122 ++++++++++++++--------------- inst/WORDLIST | 8 - inst/circletype/circletype.min.js | 14 +-- inst/custom/destroy.js | 8 - man/circletype.Rd | 70 ++++++++--------- man/remove_circletype.Rd | 94 +++++++++++----------- man/use_circletype.Rd | 56 ++++++------- tests/spelling.R | 6 - tests/testthat.R | 8 - tests/testthat/test-circletype.R | 114 +++++++++++++-------------- tests/testthat/test-use_circletype.R | 6 - 20 files changed, 446 insertions(+), 442 deletions(-)
Title: Compute MSPE Estimates for the Fay Herriot Model and Nested
Error Regression Model
Description: We describe a new R package entitled 'saeMSPE' for the well-known Fay Herriot model and nested error regression model in small area estimation. Based on this package, it is possible to easily compute various common mean squared predictive error (MSPE) estimators, as well as several existing variance component predictors as a byproduct, for these two models.
Author: Peiwen Xiao [aut, cre],
Xiaohui Liu [aut],
Yuzi Liu [aut],
Shaochu Liu [aut],
Jiming Jiang [ths]
Maintainer: Peiwen Xiao <2569613200@qq.com>
Diff between saeMSPE versions 1.0 dated 2022-03-29 and 1.1 dated 2022-09-21
saeMSPE-1.0/saeMSPE/R/mspeFHlnr.R |only saeMSPE-1.0/saeMSPE/R/mspeNERlnr.R |only saeMSPE-1.0/saeMSPE/man/mspeFHlnr.Rd |only saeMSPE-1.0/saeMSPE/man/mspeFHmcjack.Rd |only saeMSPE-1.0/saeMSPE/man/mspeNERlnr.Rd |only saeMSPE-1.0/saeMSPE/man/mspeNERmcjack.Rd |only saeMSPE-1.0/saeMSPE/man/varOBP.Rd |only saeMSPE-1.0/saeMSPE/src/saefunction.cpp |only saeMSPE-1.1/saeMSPE/DESCRIPTION | 14 +- saeMSPE-1.1/saeMSPE/MD5 | 42 +++---- saeMSPE-1.1/saeMSPE/NAMESPACE | 1 saeMSPE-1.1/saeMSPE/R/RcppExports.R | 44 +++---- saeMSPE-1.1/saeMSPE/R/mspeFHlin.R |only saeMSPE-1.1/saeMSPE/R/mspeNERlin.R |only saeMSPE-1.1/saeMSPE/man/mspeFHdb.Rd | 21 ++- saeMSPE-1.1/saeMSPE/man/mspeFHjack.Rd | 25 ++-- saeMSPE-1.1/saeMSPE/man/mspeFHlin.Rd |only saeMSPE-1.1/saeMSPE/man/mspeFHpb.Rd | 23 ++- saeMSPE-1.1/saeMSPE/man/mspeFHsumca.Rd | 19 +-- saeMSPE-1.1/saeMSPE/man/mspeNERdb.Rd | 31 ++--- saeMSPE-1.1/saeMSPE/man/mspeNERjack.Rd | 27 ++-- saeMSPE-1.1/saeMSPE/man/mspeNERlin.Rd |only saeMSPE-1.1/saeMSPE/man/mspeNERpb.Rd | 25 ++-- saeMSPE-1.1/saeMSPE/man/mspeNERsumca.Rd | 20 ++- saeMSPE-1.1/saeMSPE/man/saeMSPE-package.Rd | 38 +++--- saeMSPE-1.1/saeMSPE/man/varfh.Rd |only saeMSPE-1.1/saeMSPE/man/varner.Rd | 24 ++-- saeMSPE-1.1/saeMSPE/src/RcppExports.cpp | 162 ++++++++++++--------------- saeMSPE-1.1/saeMSPE/src/saeMSPE-function.cpp |only 29 files changed, 269 insertions(+), 247 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre] ,
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Siddharth Agrawal [cph] ),
Brendan Frey [cph] ),
Delbert Dueck [cph] ,
Vitalie Spinu [ctb]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.2.6 dated 2022-01-27 and 1.2.7 dated 2022-09-21
DESCRIPTION | 12 +-- MD5 | 24 +++---- NAMESPACE | 3 NEWS.md | 8 ++ R/ClusterR.R | 3 R/clustering_functions.R | 15 +++- README.md | 5 - inst/CITATION | 2 inst/doc/the_clusterR_package.html | 124 +++++++++++++++++++------------------ inst/include/ClusterRHeader.h | 20 +++-- man/Cluster_Medoids.Rd | 2 man/Optimal_Clusters_KMeans.Rd | 2 src/export_inst_folder_headers.cpp | 4 - 13 files changed, 130 insertions(+), 94 deletions(-)