Title: Permutations of Treatment Labels and TITAN2 Analysis
Description: Permute treatment labels for taxa and environmental gradients to
generate an empirical distribution of change points. This is an extension
for the 'TITAN2' package <https://cran.r-project.org/package=TITAN2>.
Author: Peter DeWitt [aut, cre] (<https://orcid.org/0000-0002-6391-0795>),
Stephanie Figary [aut] (<https://orcid.org/0000-0002-4876-9850>),
Naomi Detenbeck [aut] (<https://orcid.org/0000-0002-9868-0475>)
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between pTITAN2 versions 1.0.0 dated 2021-11-17 and 1.0.1 dated 2021-12-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 7 +++++++ README.md | 2 ++ build/vignette.rds |binary inst/doc/pTITAN2.html | 18 +++++++++--------- 6 files changed, 27 insertions(+), 18 deletions(-)
Title: Interpretable Matching for Causal Inference
Description: Efficient implementations of the algorithms in the
Almost-Matching-Exactly framework for interpretable matching in causal
inference. These algorithms match units via a learned, weighted Hamming
distance that determines which covariates are more important to match on.
For more information and examples, see the Almost-Matching-Exactly website.
Author: Vittorio Orlandi [aut, cre],
Sudeepa Roy [aut],
Cynthia Rudin [aut],
Alexander Volfovsky [aut]
Maintainer: Vittorio Orlandi <almost.matching.exactly@gmail.com>
Diff between FLAME versions 2.1.0 dated 2021-07-07 and 2.1.1 dated 2021-12-07
DESCRIPTION | 8 MD5 | 27 - R/PE_functions.R | 14 R/algos.R | 19 - R/arg_checker.R | 29 + R/post_matching.R | 4 build/vignette.rds |binary inst/doc/intro_to_AME.Rmd | 6 inst/doc/intro_to_AME.html | 789 ++++++++++++++++-------------------------- man/AME.Rd | 21 - man/ATE.Rd | 8 tests/testthat/test_PE.R | 2 tests/testthat/test_user_PE.R | 8 vignettes/intro_to_AME.Rmd | 6 vignettes/intro_to_AME.md |only 15 files changed, 398 insertions(+), 543 deletions(-)
Title: Work with 'YouTube API'
Description: Provide function for get data from 'YouTube Data API'
<https://developers.google.com/youtube/v3/docs/>, 'YouTube Analytics API'
<https://developers.google.com/youtube/analytics/reference/> and
'YouTube Reporting API' <https://developers.google.com/youtube/reporting/v1/reports>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>),
Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rytstat versions 0.1.0 dated 2021-10-27 and 0.2.1 dated 2021-12-07
rytstat-0.1.0/rytstat/R/ryt_get_video_list.R |only rytstat-0.1.0/rytstat/man/ryt_get_video_list.Rd |only rytstat-0.2.1/rytstat/DESCRIPTION | 10 rytstat-0.2.1/rytstat/LICENSE | 4 rytstat-0.2.1/rytstat/MD5 | 64 - rytstat-0.2.1/rytstat/NAMESPACE | 73 - rytstat-0.2.1/rytstat/NEWS.md | 33 rytstat-0.2.1/rytstat/R/ryoutube-package.R | 22 rytstat-0.2.1/rytstat/R/ryt_auth.R | 11 rytstat-0.2.1/rytstat/R/ryt_get_analytics.R | 214 ++--- rytstat-0.2.1/rytstat/R/ryt_get_channel_activities.R |only rytstat-0.2.1/rytstat/R/ryt_get_channels.R |only rytstat-0.2.1/rytstat/R/ryt_get_comments.R |only rytstat-0.2.1/rytstat/R/ryt_get_playlist_items.R |only rytstat-0.2.1/rytstat/R/ryt_get_playlist_items_helper.R |only rytstat-0.2.1/rytstat/R/ryt_get_playlists.R | 132 +-- rytstat-0.2.1/rytstat/R/ryt_get_report.R | 654 ++++++++-------- rytstat-0.2.1/rytstat/R/ryt_get_video_details.R | 100 +- rytstat-0.2.1/rytstat/R/ryt_get_videos.R |only rytstat-0.2.1/rytstat/R/ryt_get_videos_details_helper.R | 142 +-- rytstat-0.2.1/rytstat/R/zzz.R | 138 +-- rytstat-0.2.1/rytstat/README.md | 132 ++- rytstat-0.2.1/rytstat/man/figures/auth_process.png |only rytstat-0.2.1/rytstat/man/figures/logo.png |binary rytstat-0.2.1/rytstat/man/reporting_api.Rd | 234 ++--- rytstat-0.2.1/rytstat/man/ryt_auth.Rd | 204 ++-- rytstat-0.2.1/rytstat/man/ryt_auth_configure.Rd | 192 ++-- rytstat-0.2.1/rytstat/man/ryt_deauth.Rd | 56 - rytstat-0.2.1/rytstat/man/ryt_get_analytics.Rd | 140 +-- rytstat-0.2.1/rytstat/man/ryt_get_channel_activities.Rd |only rytstat-0.2.1/rytstat/man/ryt_get_channels.Rd |only rytstat-0.2.1/rytstat/man/ryt_get_comments.Rd |only rytstat-0.2.1/rytstat/man/ryt_get_playlist_items.Rd |only rytstat-0.2.1/rytstat/man/ryt_get_playlists.Rd | 38 rytstat-0.2.1/rytstat/man/ryt_get_video_details.Rd | 66 - rytstat-0.2.1/rytstat/man/ryt_get_videos.Rd |only rytstat-0.2.1/rytstat/man/ryt_has_token.Rd | 40 rytstat-0.2.1/rytstat/man/ryt_token.Rd | 52 - rytstat-0.2.1/rytstat/man/ryt_user.Rd | 38 rytstat-0.2.1/rytstat/man/rytstat-package.Rd | 53 - 40 files changed, 1476 insertions(+), 1366 deletions(-)
Title: Authentication, User Administration, and Hosting for 'shiny'
Apps
Description: Easily add modern authentication and user administration to your 'shiny' apps.
Customize user sign in and registration pages to match your brand. Control who can
access one or more of your 'shiny' apps.
Author: Andy Merlino [aut, cre],
Patrick Howard [aut],
Jimmy Briggs [aut]
Maintainer: Andy Merlino <andy.merlino@tychobra.com>
Diff between polished versions 0.4.0 dated 2021-09-16 and 0.5.0 dated 2021-12-07
polished-0.4.0/polished/inst/assets/js/set_password_module.js |only polished-0.4.0/polished/inst/examples/test_app |only polished-0.5.0/polished/DESCRIPTION | 8 polished-0.5.0/polished/MD5 | 96 ++++------ polished-0.5.0/polished/NAMESPACE | 1 polished-0.5.0/polished/NEWS.md | 13 + polished-0.5.0/polished/R/Sessions.R | 2 polished-0.5.0/polished/R/api_00.R | 2 polished-0.5.0/polished/R/api_03_app_users.R | 2 polished-0.5.0/polished/R/deploy_app.R | 40 +++- polished-0.5.0/polished/R/global_sessions_config.R | 22 +- polished-0.5.0/polished/R/package_deps.R | 6 polished-0.5.0/polished/R/profile_module.R | 2 polished-0.5.0/polished/R/secure_server.R | 40 ---- polished-0.5.0/polished/R/secure_ui.R | 51 +---- polished-0.5.0/polished/R/sign_in_components.R | 8 polished-0.5.0/polished/R/sign_in_module.R | 7 polished-0.5.0/polished/R/user_access_module.R | 2 polished-0.5.0/polished/R/utils.R | 6 polished-0.5.0/polished/R/verify_email_module.R | 2 polished-0.5.0/polished/README.md | 2 polished-0.5.0/polished/build/vignette.rds |binary polished-0.5.0/polished/inst/assets/images/add_user_1.png |binary polished-0.5.0/polished/inst/assets/images/add_user_2.png |binary polished-0.5.0/polished/inst/assets/images/add_web_app.png |binary polished-0.5.0/polished/inst/assets/images/default_sign_in.png |binary polished-0.5.0/polished/inst/assets/images/placeholder_company_logo.jpg |binary polished-0.5.0/polished/inst/assets/images/polished_icon.png |binary polished-0.5.0/polished/inst/assets/images/polished_logo_transparent.png |binary polished-0.5.0/polished/inst/assets/images/polished_logo_transparent_text.png |binary polished-0.5.0/polished/inst/assets/images/polished_logo_transparent_text_2.png |binary polished-0.5.0/polished/inst/assets/images/polished_logo_transparent_white.png |binary polished-0.5.0/polished/inst/assets/images/tychobra-icon-blue.png |binary polished-0.5.0/polished/inst/assets/images/tychobra_logo_blue_co_name.png |binary polished-0.5.0/polished/inst/assets/images/tychobra_logo_white.svg | 81 -------- polished-0.5.0/polished/inst/assets/js/auth_firebase.js | 6 polished-0.5.0/polished/inst/assets/js/auth_main.js | 11 - polished-0.5.0/polished/inst/assets/js/toast_options.js | 6 polished-0.5.0/polished/inst/examples/polished_example_01/global.R | 3 polished-0.5.0/polished/inst/examples/polished_example_01/server.R | 7 polished-0.5.0/polished/inst/examples/polished_example_01/ui.R | 3 polished-0.5.0/polished/man/add_app_user.Rd | 2 polished-0.5.0/polished/man/deploy_app.Rd | 20 +- polished-0.5.0/polished/man/get_package_deps.Rd | 6 polished-0.5.0/polished/man/global_sessions_config.Rd | 8 polished-0.5.0/polished/man/secure_server.Rd | 8 polished-0.5.0/polished/man/secure_ui.Rd | 8 polished-0.5.0/polished/tests/testthat/setup-api-options.R | 2 polished-0.5.0/polished/tests/testthat/test-api-01-apps.R | 2 49 files changed, 196 insertions(+), 289 deletions(-)
Title: Network-Based Gene Set Analysis
Description: Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.
Author: Michael Hellstern [aut, cre],
Ali Shojaie [aut],
Jing Ma [aut],
Kun Yue [aut]
Maintainer: Michael Hellstern <mikeh1@uw.edu>
Diff between netgsa versions 4.0.2 dated 2021-11-17 and 4.0.3 dated 2021-12-07
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- R/obtainEdgeList.R | 2 +- build/partial.rdb |binary inst/doc/netgsa.R | 2 +- inst/doc/netgsa.Rmd | 2 +- inst/doc/netgsa.html | 9 ++++----- vignettes/netgsa.Rmd | 2 +- 8 files changed, 22 insertions(+), 23 deletions(-)
Title: Visualising Single-Cell Trajectories
Description: Visualise a single-cell trajectory as a graph or dendrogram,
as a dimensionality reduction or heatmap of the expression data,
or a comparison between two trajectories as a pairwise scatterplot
or dimensionality reduction projection. Saelens and Cannoodt et
al. (2019) <doi:10.1038/s41587-019-0071-9>.
Author: Robrecht Cannoodt [aut, cre, cph]
(<https://orcid.org/0000-0003-3641-729X>),
Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynplot versions 1.1.1 dated 2021-06-28 and 1.1.2 dated 2021-12-07
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/plot_onedim.R | 7 +++---- inst/doc/plotting-a-toy.html | 12 ++++++------ man/figures/dendro-1.png |binary man/figures/scatterplot-1.png |binary 6 files changed, 17 insertions(+), 18 deletions(-)
Title: Easily Create Production-Ready Rich Text Format (RTF) Table and
Figure
Description: Create production-ready Rich Text Format (RTF) table and figure with flexible format.
Author: Yilong Zhang [aut, cre],
Siruo Wang [aut],
Simiao Ye [aut],
Fansen Kong [aut],
Nan Xiao [ctb],
Madhusudhan Ginnaram [ctb],
Ruchitbhai Patel [ctb],
Huei-Ling Chen [ctb],
Peikun Wu [ctb],
Uday Preetham Palukuru [ctb],
Daniel Woodie [ctb],
Sarad Nepal [ctb],
Jane Liao [ctb],
Benjamin Wang [ctb],
Jeff Cheng [ctb],
Yirong Cao [ctb],
Amin Shirazi [ctb],
Merck Sharp & Dohme Corp [cph]
Maintainer: Yilong Zhang <yilong.zhang@merck.com>
Diff between r2rtf versions 0.3.1 dated 2021-09-09 and 0.3.2 dated 2021-12-07
r2rtf-0.3.1/r2rtf/R/rtf_read_png.R |only r2rtf-0.3.1/r2rtf/tests/testthat/test-independent-testing-rtf_read_png.R |only r2rtf-0.3.2/r2rtf/DESCRIPTION | 10 - r2rtf-0.3.2/r2rtf/MD5 | 66 +++--- r2rtf-0.3.2/r2rtf/NAMESPACE | 1 r2rtf-0.3.2/r2rtf/NEWS.md | 9 r2rtf-0.3.2/r2rtf/R/check_args.R | 2 r2rtf-0.3.2/r2rtf/R/dictionary.R | 25 ++ r2rtf-0.3.2/r2rtf/R/rtf_convert_format.R | 95 ++++++++-- r2rtf-0.3.2/r2rtf/R/rtf_encode.R | 2 r2rtf-0.3.2/r2rtf/R/rtf_encode_figure.R | 5 r2rtf-0.3.2/r2rtf/R/rtf_figure.R | 11 - r2rtf-0.3.2/r2rtf/R/rtf_footnote.R | 6 r2rtf-0.3.2/r2rtf/R/rtf_paragraph.R | 6 r2rtf-0.3.2/r2rtf/R/rtf_read.R |only r2rtf-0.3.2/r2rtf/README.md | 2 r2rtf-0.3.2/r2rtf/man/fig_format.Rd |only r2rtf-0.3.2/r2rtf/man/obj_rtf_text.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_body.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_colheader.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_convert_format.Rd | 4 r2rtf-0.3.2/r2rtf/man/rtf_encode.Rd | 2 r2rtf-0.3.2/r2rtf/man/rtf_figure.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_footnote.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_page_footer.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_page_header.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_paragraph.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_read_figure.Rd |only r2rtf-0.3.2/r2rtf/man/rtf_read_png.Rd | 16 - r2rtf-0.3.2/r2rtf/man/rtf_source.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_subline.Rd | 6 r2rtf-0.3.2/r2rtf/man/rtf_title.Rd | 6 r2rtf-0.3.2/r2rtf/man/update_cellx.Rd |only r2rtf-0.3.2/r2rtf/tests/testthat/test-independent-testing-rtf_encode.R | 2 r2rtf-0.3.2/r2rtf/tests/testthat/test-independent-testing-rtf_encode_figure.R | 2 r2rtf-0.3.2/r2rtf/tests/testthat/test-independent-testing-rtf_figure.R | 2 r2rtf-0.3.2/r2rtf/tests/testthat/test-independent-testing-rtf_read.R |only r2rtf-0.3.2/r2rtf/tests/testthat/test-independent-testing-update_cellx.R |only 38 files changed, 222 insertions(+), 112 deletions(-)
Title: Minimal Protein Set Explaining Peptide Spectrum Matches
Description: Determine minimal protein set explaining
peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants.
Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein
level. Computing dynamic swath window sizes based on MS1 or MS2 signal distributions.
Author: Witold Wolski [aut, cre] (<https://orcid.org/0000-0002-6468-120X>)
Maintainer: Witold Wolski <wewolski@gmail.com>
Diff between prozor versions 0.2.11 dated 2018-07-26 and 0.3.1 dated 2021-12-07
prozor-0.2.11/prozor/R/DeprecatedAnnotatePeptides.R |only prozor-0.2.11/prozor/data/fdrSample.tab |only prozor-0.2.11/prozor/data/pepprot.tab |only prozor-0.2.11/prozor/data/protpepmetashort.tab |only prozor-0.2.11/prozor/inst/extdata/Annotation_allSeq.fasta.gz |only prozor-0.2.11/prozor/inst/extdata/Annotation_canSeq.fasta.gz |only prozor-0.2.11/prozor/inst/extdata/UnimodMappings.txt |only prozor-0.2.11/prozor/inst/extdata/fgcz_ContaminantsWithAnnotation.fasta.gz |only prozor-0.2.11/prozor/inst/extdata/fgcz_ContaminantsWithAnnotationNoHuman.fasta.gz |only prozor-0.2.11/prozor/inst/extdata/fgcz_contaminants_20130115_patchedWithRespectiveUniprot2.fasta.gz |only prozor-0.2.11/prozor/inst/extdata/fgcz_contaminants_20150123.fasta.gz |only prozor-0.2.11/prozor/inst/extdata/shortfasta.fasta.gz |only prozor-0.2.11/prozor/inst/p1000_db1_example/shortfasta.fasta.gz |only prozor-0.2.11/prozor/inst/p1000_db1_example/uniprot_taxonomy_Oryctolagus_cuniculus.fasta.gz |only prozor-0.2.11/prozor/man/annotateVec.Rd |only prozor-0.2.11/prozor/man/filterSequences.Rd |only prozor-0.2.11/prozor/man/loadContaminantsFasta.Rd |only prozor-0.2.11/prozor/man/loadContaminantsNoHumanFasta.Rd |only prozor-0.2.11/prozor/vignettes/spectraAnnotationwithProzor.R |only prozor-0.2.11/prozor/vignettes/spectraAnnotationwithProzor_files |only prozor-0.3.1/prozor/DESCRIPTION | 31 prozor-0.3.1/prozor/MD5 | 145 - prozor-0.3.1/prozor/NAMESPACE | 19 prozor-0.3.1/prozor/NEWS.md |only prozor-0.3.1/prozor/R/annotatePeptides.R | 183 + prozor-0.3.1/prozor/R/cdsw.R |only prozor-0.3.1/prozor/R/computeFDR.R | 126 - prozor-0.3.1/prozor/R/createDecoyDB.R | 17 prozor-0.3.1/prozor/R/create_fgcz_fasta_db.R |only prozor-0.3.1/prozor/R/greedy.R | 42 prozor-0.3.1/prozor/R/hello.R | 37 prozor-0.3.1/prozor/R/loadContaminantsFasta.R | 49 prozor-0.3.1/prozor/R/prepareMatrix.R | 18 prozor-0.3.1/prozor/R/readFasta.R | 8 prozor-0.3.1/prozor/R/readjustWindow.R |only prozor-0.3.1/prozor/R/removeSignalPeptides.R | 27 prozor-0.3.1/prozor/R/reverseSeq.R | 27 prozor-0.3.1/prozor/R/writeFasta.R | 16 prozor-0.3.1/prozor/R/zzz.R | 15 prozor-0.3.1/prozor/README.md | 40 prozor-0.3.1/prozor/build/vignette.rds |binary prozor-0.3.1/prozor/data/datalist | 1 prozor-0.3.1/prozor/data/fdrSample.rda |only prozor-0.3.1/prozor/data/masses.rda |only prozor-0.3.1/prozor/data/pepprot.rda |only prozor-0.3.1/prozor/data/protpepmetashort.tab.gz |only prozor-0.3.1/prozor/inst/creatingDBs/CreateDB.Rmd | 951 +++++++++- prozor-0.3.1/prozor/inst/creatingDBs/fixCont.Rmd | 79 prozor-0.3.1/prozor/inst/creatingDBs/specAnnotationMilena.Rmd | 6 prozor-0.3.1/prozor/inst/doc/CreatingDecoyDB.R | 47 prozor-0.3.1/prozor/inst/doc/CreatingDecoyDB.Rmd | 53 prozor-0.3.1/prozor/inst/doc/CreatingDecoyDB.html | 495 ++++- prozor-0.3.1/prozor/inst/doc/PeptideAnnotationwithProzor.R | 134 - prozor-0.3.1/prozor/inst/doc/PeptideAnnotationwithProzor.Rmd | 150 - prozor-0.3.1/prozor/inst/doc/PeptideAnnotationwithProzor.html | 674 ++++--- prozor-0.3.1/prozor/inst/doc/TargetDecoyFDR_Example.R | 54 prozor-0.3.1/prozor/inst/doc/TargetDecoyFDR_Example.Rmd | 105 - prozor-0.3.1/prozor/inst/doc/TargetDecoyFDR_Example.html | 619 ++++-- prozor-0.3.1/prozor/inst/doc/cdsw.R |only prozor-0.3.1/prozor/inst/doc/cdsw.Rmd |only prozor-0.3.1/prozor/inst/doc/cdsw.html |only prozor-0.3.1/prozor/inst/extdata/fgcz_contaminants2019_20190708.fasta.gz |only prozor-0.3.1/prozor/inst/extdata/fgcz_contaminants2021_20210929.fasta.gz |only prozor-0.3.1/prozor/inst/p1000_db1_example/Annotation_allSeq.fasta.gz |only prozor-0.3.1/prozor/inst/p1000_db1_example/Annotation_canSeq.fasta.gz |only prozor-0.3.1/prozor/inst/script |only prozor-0.3.1/prozor/man/Cdsw-class.Rd |only prozor-0.3.1/prozor/man/annotateAHO.Rd | 23 prozor-0.3.1/prozor/man/annotatePeptides.Rd | 34 prozor-0.3.1/prozor/man/computeFDR.Rd | 7 prozor-0.3.1/prozor/man/computeFDRwithID.Rd | 8 prozor-0.3.1/prozor/man/createDecoyDB.Rd | 17 prozor-0.3.1/prozor/man/create_fgcz_fasta_db.Rd |only prozor-0.3.1/prozor/man/fdrSample.Rd | 2 prozor-0.3.1/prozor/man/greedy.Rd | 4 prozor-0.3.1/prozor/man/hardconstrain.Rd |only prozor-0.3.1/prozor/man/loadContaminantsFasta2019.Rd |only prozor-0.3.1/prozor/man/loadContaminantsFasta2021.Rd |only prozor-0.3.1/prozor/man/makeID.Rd | 17 prozor-0.3.1/prozor/man/makeIDUnip.Rd | 17 prozor-0.3.1/prozor/man/masses.Rd |only prozor-0.3.1/prozor/man/objectiveMS1Function.Rd |only prozor-0.3.1/prozor/man/plotFDR.Rd | 6 prozor-0.3.1/prozor/man/predictScoreFDR.Rd | 5 prozor-0.3.1/prozor/man/prepareMatrix.Rd | 11 prozor-0.3.1/prozor/man/prozor.Rd | 8 prozor-0.3.1/prozor/man/readPeptideFasta.Rd | 10 prozor-0.3.1/prozor/man/readjustWindows.Rd |only prozor-0.3.1/prozor/man/removeSignalPeptide.Rd | 3 prozor-0.3.1/prozor/man/reverseSeq.Rd | 10 prozor-0.3.1/prozor/man/writeFasta.Rd | 8 prozor-0.3.1/prozor/vignettes/CreatingDecoyDB.Rmd | 53 prozor-0.3.1/prozor/vignettes/PeptideAnnotationwithProzor.Rmd | 150 - prozor-0.3.1/prozor/vignettes/TargetDecoyFDR_Example.Rmd | 105 - prozor-0.3.1/prozor/vignettes/bibliography.bib | 860 ++++----- prozor-0.3.1/prozor/vignettes/cdsw.Rmd |only 96 files changed, 3784 insertions(+), 1742 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-22 2.3.5
2021-05-15 2.3.4
2021-05-02 2.3.3
2021-04-29 2.3.2
2020-05-18 2.0.7
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Hothorn, 2019, <arxiv:1910.09219>).
Multivariate conditional transformation models (<arxiv:1906.03151>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Luisa Barbanti [aut],
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 0.6-1 dated 2021-09-16 and 0.6-2 dated 2021-12-07
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/methods.R | 27 +++++++++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 12 +++++++++++- inst/doc/mtram.Rnw | 5 +---- inst/doc/mtram.pdf |binary inst/doc/tram.Rnw | 8 +++++++- inst/doc/tram.pdf |binary man/Coxph.Rd | 2 +- vignettes/mtram.Rnw | 5 +---- vignettes/tram.Rnw | 8 +++++++- 13 files changed, 63 insertions(+), 36 deletions(-)
Title: R Interface to 'Bloomberg'
Description: An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Author: Whit Armstrong, Dirk Eddelbuettel and John Laing
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.11 dated 2021-04-20 and 0.3.12 dated 2021-12-07
Rblpapi-0.3.11/Rblpapi/inst/doc/rblpapi-intro.R |only Rblpapi-0.3.11/Rblpapi/inst/doc/rblpapi-intro.Rmd |only Rblpapi-0.3.11/Rblpapi/vignettes/rblpapi-intro.Rmd |only Rblpapi-0.3.12/Rblpapi/ChangeLog | 51 ++ Rblpapi-0.3.12/Rblpapi/DESCRIPTION | 13 Rblpapi-0.3.12/Rblpapi/MD5 | 28 - Rblpapi-0.3.12/Rblpapi/R/bdh.R | 26 + Rblpapi-0.3.12/Rblpapi/build/vignette.rds |binary Rblpapi-0.3.12/Rblpapi/inst/NEWS.Rd | 13 Rblpapi-0.3.12/Rblpapi/inst/doc/rblpapi-intro.html | 361 ++++++++++----------- Rblpapi-0.3.12/Rblpapi/inst/doc/rblpapi-intro.md |only Rblpapi-0.3.12/Rblpapi/inst/tinytest/test_bdh.R | 18 + Rblpapi-0.3.12/Rblpapi/man/bdh.Rd | 18 - Rblpapi-0.3.12/Rblpapi/src/Rblpapi_types.h | 4 Rblpapi-0.3.12/Rblpapi/src/bdh.cpp | 14 Rblpapi-0.3.12/Rblpapi/src/bds.cpp | 10 Rblpapi-0.3.12/Rblpapi/vignettes/rblpapi-intro.md |only Rblpapi-0.3.12/Rblpapi/vignettes/water.css |only 18 files changed, 338 insertions(+), 218 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-0 dated 2021-03-11 and 1.1-1 dated 2021-12-07
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/mlt.Rnw | 8 +++++++- inst/doc/mlt.pdf |binary tests/truncreg-Ex.R | 2 ++ tests/truncreg-Ex.Rout.save | 18 +++++++++--------- vignettes/mlt.Rnw | 8 +++++++- 9 files changed, 45 insertions(+), 23 deletions(-)
Title: Variance Components Testing for Linear and Nonlinear Mixed
Effects Models
Description: An implementation of the Likelihood ratio Test (LRT) for testing that,
in a (non)linear mixed effects model, the variances of a subset of the random
effects are equal to zero. There is no restriction on the subset of variances
that can be tested: for example, it is possible to test that all the variances
are equal to zero. Note that the implemented test is asymptotic.
This package should be used on model fits from packages 'nlme', 'lmer', and 'saemix'.
Charlotte Baey, Paul-Henry Cournède and Estelle Kuhn (2019) <doi:10.1016/j.csda.2019.01.014>.
Author: Charlotte Baey [aut, cre] (<https://orcid.org/0000-0002-1413-1058>),
Estelle Kuhn [aut]
Maintainer: Charlotte Baey <charlotte.baey@univ-lille.fr>
Diff between varTestnlme versions 1.1.1 dated 2021-10-22 and 1.2.0 dated 2021-12-07
varTestnlme-1.1.1/varTestnlme/R/varCompTest.saemix.R |only varTestnlme-1.1.1/varTestnlme/man/bootinvFIM.saemix.Rd |only varTestnlme-1.1.1/varTestnlme/man/extractStruct.saemix.Rd |only varTestnlme-1.2.0/varTestnlme/DESCRIPTION | 8 +-- varTestnlme-1.2.0/varTestnlme/MD5 | 24 +++++----- varTestnlme-1.2.0/varTestnlme/NAMESPACE | 8 +-- varTestnlme-1.2.0/varTestnlme/NEWS.md | 5 ++ varTestnlme-1.2.0/varTestnlme/R/methods.R | 4 - varTestnlme-1.2.0/varTestnlme/R/saemix_utilities.R | 14 ++--- varTestnlme-1.2.0/varTestnlme/R/varCompTest.lme.R | 2 varTestnlme-1.2.0/varTestnlme/R/varCompTest.merMod.R | 11 ++-- varTestnlme-1.2.0/varTestnlme/R/varCompTest.saemixObject.R |only varTestnlme-1.2.0/varTestnlme/inst/doc/varTestnlme.html | 9 +++ varTestnlme-1.2.0/varTestnlme/man/bootinvFIM.SaemixObject.Rd |only varTestnlme-1.2.0/varTestnlme/man/extractStruct.SaemixObject.Rd |only varTestnlme-1.2.0/varTestnlme/man/varCompTest.Rd | 5 +- 16 files changed, 53 insertions(+), 37 deletions(-)
Title: Meta-Analyses for Simultaneously Estimating Individual Means
Description: Implement meta-analyses for simultaneously estimating individual means with shrinkage,
isotonic regression and pretests. Include our original implementation of the isotonic regression via the pool-adjacent-violators algorithm (PAVA) algorithm.
This methodology is published in Taketomi et al.(2021) <doi:10.3390/axioms10040267>.
Author: Nanami Taketomi, Takeshi Emura
Maintainer: Nanami Taketomi <nanamitaketomitommy@gmail.com>
Diff between meta.shrinkage versions 0.1.0 dated 2021-11-19 and 0.1.1 dated 2021-12-07
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/gpt.R | 6 +++--- R/js.R | 20 +++----------------- R/rjs.R | 33 +++++++-------------------------- R/rml.R | 17 +++++++---------- man/gpt.Rd | 19 +++++++++---------- man/js.Rd | 26 +++++++++++--------------- man/rjs.Rd | 34 +++++++++++++++++----------------- man/rml.Rd | 49 ++++++++++++++++++++++++++++++------------------- 10 files changed, 99 insertions(+), 129 deletions(-)
More information about meta.shrinkage at CRAN
Permanent link
Title: Categorical Functional Data Analysis
Description: Package for the analysis of categorical functional data.
The main purpose is to compute an encoding (real functional variable) for each state <doi:10.3390/math9233074>.
It also provides functions to perform basic statistical analysis on categorical functional data.
Author: Cristian Preda [aut],
Quentin Grimonprez [aut, cre],
Vincent Vandewalle [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between cfda versions 0.9.10 dated 2021-12-06 and 0.9.11 dated 2021-12-07
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/CITATION | 2 +- inst/doc/cfda.html | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression
model 'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel D. Sjoberg [aut] (<https://orcid.org/0000-0003-0862-2018>)
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.4.0 dated 2021-09-30 and 1.5.0 dated 2021-12-07
DESCRIPTION | 6 MD5 | 69 +++--- NAMESPACE | 4 NEWS.md | 320 +++++++++++++++-------------- R/assert_package.R |only R/model_get_coefficients_type.R | 12 + R/model_get_model_matrix.R | 7 R/model_get_n.R | 3 R/model_get_xlevels.R | 21 + R/model_list_variables.R | 16 - R/select_utilities.R | 74 ++++++ R/tidiers.R | 17 - R/tidy_add_estimate_to_reference_rows.R | 40 +-- R/tidy_add_header_rows.R | 30 +- R/tidy_add_reference_rows.R | 29 +- R/tidy_disambiguate_terms.R | 9 R/tidy_plus_plus.R | 27 +- README.md | 8 inst/doc/tidy.R | 13 - inst/doc/tidy.Rmd | 17 - inst/doc/tidy.html | 236 ++++++++++----------- man/assert_package.Rd |only man/dot-formula_list_to_named_list.Rd | 28 ++ man/model_get_coefficients_type.Rd | 6 man/model_get_n.Rd | 3 man/model_list_variables.Rd | 16 - man/tidy_add_estimate_to_reference_rows.Rd | 30 +- man/tidy_add_header_rows.Rd | 30 +- man/tidy_add_reference_rows.Rd | 28 +- man/tidy_disambiguate_terms.Rd | 8 man/tidy_parameters.Rd | 8 man/tidy_plus_plus.Rd | 27 +- tests/testthat/test-assert_package.R |only tests/testthat/test-identify_variables.R | 22 + tests/testthat/test-select_helpers.R | 44 +++ tests/testthat/test-tidy_plus_plus.R | 13 + vignettes/tidy.Rmd | 17 - 37 files changed, 725 insertions(+), 513 deletions(-)
Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd,
lz4 and xxHash code),
Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled
zstd code),
Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd
bundled code),
Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Romain Francois [ctb, cph] (Derived example/tutorials for ALTREP
structures),
Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc
library),
Bryce Chamberlain [ctb] (qsavem and qload functions),
Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>,
documentation)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.25.1.1 dated 2021-11-05 and 0.25.2 dated 2021-12-07
qs-0.25.1.1/qs/R/help_files.R |only qs-0.25.1.1/qs/man/convertToAlt.Rd |only qs-0.25.1.1/qs/man/randomStrings.Rd |only qs-0.25.2/qs/ChangeLog | 6 qs-0.25.2/qs/DESCRIPTION | 20 qs-0.25.2/qs/MD5 | 114 ++-- qs-0.25.2/qs/NAMESPACE | 63 +- qs-0.25.2/qs/R/RcppExports.R | 16 qs-0.25.2/qs/R/ascii_encoding.R |only qs-0.25.2/qs/R/qcache.R | 94 +-- qs-0.25.2/qs/R/qs-package.R |only qs-0.25.2/qs/R/qsavem-load.R | 86 +-- qs-0.25.2/qs/R/zz_help_files.R |only qs-0.25.2/qs/R/zzz.R | 2 qs-0.25.2/qs/README.md | 48 - qs-0.25.2/qs/configure | 718 +++++++++++++---------------- qs-0.25.2/qs/data/starnames.rda |binary qs-0.25.2/qs/inst/doc/vignette.R | 20 qs-0.25.2/qs/inst/doc/vignette.html | 153 ++---- qs-0.25.2/qs/inst/doc/vignette.rmd | 41 + qs-0.25.2/qs/inst/extra_tests |only qs-0.25.2/qs/inst/include/qs_RcppExports.h | 65 -- qs-0.25.2/qs/man/base85_decode.Rd | 7 qs-0.25.2/qs/man/base85_encode.Rd | 11 qs-0.25.2/qs/man/base91_decode.Rd | 7 qs-0.25.2/qs/man/base91_encode.Rd | 21 qs-0.25.2/qs/man/blosc_shuffle_raw.Rd | 8 qs-0.25.2/qs/man/blosc_unshuffle_raw.Rd | 10 qs-0.25.2/qs/man/catquo.Rd | 6 qs-0.25.2/qs/man/decode_source.Rd |only qs-0.25.2/qs/man/encode_source.Rd |only qs-0.25.2/qs/man/is_big_endian.Rd | 8 qs-0.25.2/qs/man/lz4_compress_bound.Rd | 8 qs-0.25.2/qs/man/lz4_compress_raw.Rd | 10 qs-0.25.2/qs/man/lz4_decompress_raw.Rd | 8 qs-0.25.2/qs/man/qcache.Rd | 51 +- qs-0.25.2/qs/man/qdeserialize.Rd | 14 qs-0.25.2/qs/man/qdump.Rd | 15 qs-0.25.2/qs/man/qread.Rd | 21 qs-0.25.2/qs/man/qread_fd.Rd | 14 qs-0.25.2/qs/man/qread_handle.Rd | 14 qs-0.25.2/qs/man/qread_ptr.Rd | 14 qs-0.25.2/qs/man/qreadm.Rd | 26 - qs-0.25.2/qs/man/qs-package.Rd |only qs-0.25.2/qs/man/qsave.Rd | 74 +- qs-0.25.2/qs/man/qsave_fd.Rd | 55 +- qs-0.25.2/qs/man/qsave_handle.Rd | 55 +- qs-0.25.2/qs/man/qsavem.Rd | 18 qs-0.25.2/qs/man/qserialize.Rd | 54 +- qs-0.25.2/qs/man/starnames.Rd | 6 qs-0.25.2/qs/man/zstd_compress_bound.Rd | 4 qs-0.25.2/qs/man/zstd_compress_raw.Rd | 11 qs-0.25.2/qs/man/zstd_decompress_raw.Rd | 8 qs-0.25.2/qs/src/Makevars.in | 2 qs-0.25.2/qs/src/Makevars.win | 2 qs-0.25.2/qs/src/RcppExports.cpp | 93 +-- qs-0.25.2/qs/src/extra_functions.h | 97 --- qs-0.25.2/qs/src/qs_common.h | 1 qs-0.25.2/qs/src/qs_functions.cpp | 7 qs-0.25.2/qs/tests |only qs-0.25.2/qs/vignettes/vignette.rmd | 41 + 61 files changed, 1112 insertions(+), 1135 deletions(-)
Title: Biological Risk Assessment
Description: A spatio-temporal exposure-hazard model for assessing biological
risk and impact. The model is based on stochastic geometry for describing
the landscape and the exposed individuals, a dispersal kernel for the
dissemination of contaminants, a set of tools to handle spatio-temporal dataframe
and ecotoxicological equations.
Walker E, Leclerc M, Rey JF, Beaudouin R, Soubeyrand S, and Messean A, (2017),
A Spatio-Temporal Exposure-Hazard Model for Assessing Biological Risk and Impact,
Risk Analysis, <doi:10.1111/risa.12941>.
Leclerc M, Walker E, Messean A, Soubeyrand S (2018),
Spatial exposure-hazard and landscape models for assessing the impact of GM crops on non-target organisms,
Science of the Total Environment, 624, 470-479.
Author: Virgile Baudrot [aut],
Emily Walker [aut],
Jean-Francois Rey [aut, cre],
Melen Leclerc [aut],
Samuel Soubeyrand [ctb],
Marc Bourotte [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between briskaR versions 1.0.3 dated 2021-11-18 and 1.0.4 dated 2021-12-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/brk_dispersal.R | 2 +- R/brk_exposure.R | 14 +++++++++++--- inst/doc/demonstrations.html | 14 +++++++------- man/brk_exposure.Rd | 5 ++++- 6 files changed, 32 insertions(+), 21 deletions(-)
Title: Generic Machine Learning Inference
Description: Generic Machine Learning Inference on heterogeneous treatment effects in randomized experiments as proposed in Chernozhukov, Demirer, Duflo and Fernández-Val (2020) <arXiv:1712.04802>. This package's workhorse is the 'mlr3' framework of Lang et al. (2019) <doi:10.21105/joss.01903>, which enables the specification of a wide variety of machine learners. The main functionality, GenericML(), runs Algorithm 1 in Chernozhukov, Demirer, Duflo and Fernández-Val (2020) <arXiv:1712.04802> for a suite of user-specified machine learners. All steps in the algorithm are customizable via setup functions. Methods for printing and plotting are available for objects returned by GenericML(). Parallel computing is supported.
Author: Max Welz [aut, cre] (<https://orcid.org/0000-0003-2945-1860>),
Andreas Alfons [aut] (<https://orcid.org/0000-0002-2513-3788>),
Mert Demirer [aut],
Victor Chernozhukov [aut]
Maintainer: Max Welz <welz@ese.eur.nl>
Diff between GenericML versions 0.1.0 dated 2021-11-24 and 0.1.1 dated 2021-12-07
DESCRIPTION | 8 ++-- MD5 | 41 +++++++++++----------- NEWS.md |only R/GenericML.R | 3 + R/accessors.R | 30 ++++++++-------- R/gates.R | 4 +- R/misc.R | 4 +- R/plot.R | 6 +-- R/print.R | 4 +- README.md | 24 +++++++++--- build/partial.rdb |binary inst/CITATION | 50 +++++++++++++-------------- man/GATES.Rd | 4 +- man/GenericML.Rd | 3 + man/GenericML_single.Rd | 2 + man/Med.Rd | 2 - man/get_BLP.Rd | 2 - man/get_CLAN.Rd | 14 +++---- man/get_GATES.Rd | 14 +++---- man/plot.GenericML.Rd | 6 +-- man/print.GenericML.Rd | 4 +- tests/testthat/test_GenericML-input-checks.R | 4 +- 22 files changed, 124 insertions(+), 105 deletions(-)
Title: Research Assessment Tools
Description: Includes algorithms to assess research productivity and patterns, such as the h-index and i-index. Cardoso et al. (subm.) Quantifying the international collaboration of researchers and research institutions.
Author: Pedro Cardoso [aut, cre],
Stefano Mammola [aut]
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between RAT versions 0.1.0 dated 2021-12-02 and 0.1.1 dated 2021-12-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/RAT.R | 33 +++++++++++++++------------------ man/h.index.Rd | 2 +- man/i.index.Rd | 6 ++---- man/i.map.Rd | 2 +- man/wos.Rd | 2 +- 7 files changed, 30 insertions(+), 35 deletions(-)
Title: Quadratic Programming Solver using the 'OSQP' Library
Description: Provides bindings to the 'OSQP' solver. The 'OSQP' solver is a numerical optimization package or solving convex quadratic programs written in 'C' and based on the alternating direction method of multipliers. See <arXiv:1711.08013> for details.
Author: Bartolomeo Stellato [aut, ctb, cph],
Goran Banjac [aut, ctb, cph],
Paul Goulart [aut, ctb, cph],
Stephen Boyd [aut, ctb, cph],
Eric Anderson [ctb],
Vineet Bansal [cre]
Maintainer: Vineet Bansal <vineetb@princeton.edu>
Diff between osqp versions 0.6.0.4 dated 2021-12-06 and 0.6.0.5 dated 2021-12-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/osqp_sources/configure/cmake/FindR.cmake | 7 +------ 3 files changed, 7 insertions(+), 12 deletions(-)
Title: Bayesian Estimation of (Sparse) Latent Factor Stochastic
Volatility Models
Description: Markov chain Monte Carlo (MCMC) sampler for fully Bayesian estimation of latent factor stochastic volatility models with interweaving <doi:10.1080/10618600.2017.1322091>. Sparsity can be achieved through the usage of Normal-Gamma priors on the factor loading matrix <doi:10.1016/j.jeconom.2018.11.007>.
Author: Gregor Kastner [aut, cre] (<https://orcid.org/0000-0002-8237-8271>),
Darjus Hosszejni [ctb] (<https://orcid.org/0000-0002-3803-691X>),
Luis Gruber [ctb] (<https://orcid.org/0000-0002-2399-738X>)
Maintainer: Gregor Kastner <gregor.kastner@aau.at>
Diff between factorstochvol versions 1.0.0 dated 2021-11-29 and 1.0.1 dated 2021-12-07
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 5 +++++ build/partial.rdb |binary inst/CITATION | 2 +- inst/doc/paper.pdf |binary src/sampler.cpp | 4 ++-- 7 files changed, 17 insertions(+), 12 deletions(-)
More information about factorstochvol at CRAN
Permanent link
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
low similarity of the different 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 function anticlustering() implements exact and
heuristic anticlustering algorithms as described in Papenberg and Klau
(2021; <doi:10.1037/met0000301>). The exact algorithms require that
the GNU linear programming kit
(<https://www.gnu.org/software/glpk/glpk.html>) is available and the R
package 'Rglpk' (<https://cran.R-project.org/package=Rglpk>) is
installed. A bicriterion anticlustering method proposed by Brusco et al.
(2020; <doi:10.1111/bmsp.12186>) is available through the function
bicriterion_anticlustering(). Some other functions are available to
solve classical clustering problems. The function
balanced_clustering() applies a cluster analysis under size
constraints, i.e., creates equal-sized clusters. The function
matching() can be used for (unrestricted, bipartite, or K-partite)
matching. The function wce() can be used optimally solve the
(weighted) cluster editing problem, also known as correlation
clustering, clique partitioning problem or transitivity clustering.
Author: Martin Papenberg [aut, cre] (<https://orcid.org/0000-0002-9900-4268>),
Meik Michalke [ctb] (centroid based clustering algorithm),
Gunnar W. Klau [ths],
Juliane V. Tkotz [ctb] (package logo),
Martin Breuer [ctb] (Bicriterion algorithm by Brusco et al.)
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.6.0 dated 2021-12-01 and 0.6.1 dated 2021-12-07
DESCRIPTION | 6 +-- MD5 | 6 +-- inst/doc/stimulus-selection.html | 42 +++++++++++++-------------- src/bicriterion_iterated_local_search_call.c | 4 +- 4 files changed, 29 insertions(+), 29 deletions(-)
Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography
formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and
'Bibentry'. Includes a port of the 'bibutils' utilities by Chris
Putnam <https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and
modifications to bibutils' C code, conversion to Bibentry (R and C
code)),
Chris Putman [aut] (src/*, author of the bibutils libraries,
https://sourceforge.net/projects/bibutils/),
Richard Mathar [ctb] (src/addsout.c),
Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c)
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 2.2.5 dated 2021-12-04 and 2.2.7 dated 2021-12-07
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 12 +++++++++++- build/partial.rdb |binary src/adsout.c | 3 ++- src/isiout.c | 22 ++++++++++++++++++++-- src/name.c | 1 + src/nbibout.c | 3 ++- src/str_conv.c | 8 ++++++++ tests/testthat/xampl_bib2isi.rds |binary 10 files changed, 57 insertions(+), 18 deletions(-)
Title: Multivariate Morphometric Analysis
Description: Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package will be described in Šlenker et al. (in prep).
Author: Marek Šlenker [aut, cre] (https://orcid.org/0000-0002-5919-890X)
Petr Koutecký [ctb] (https://orcid.org/0000-0002-3455-850X)
Karol Marhold [ctb] (https://orcid.org/0000-0002-7658-0844)
Maintainer: Marek Šlenker <marek.slenker@savba.sk>
Diff between MorphoTools2 versions 0.9.1 dated 2021-12-02 and 0.9.1.1 dated 2021-12-07
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/pcoa.calc.R | 25 ++++++++++++++++--------- R/zzz.R | 2 +- README.md | 10 ++++++---- inst/doc/MorphoTools2_tutorial.pdf |binary 6 files changed, 31 insertions(+), 22 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological
analyses. Specializes on the construction of historical matrices,
which are 2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices. Methodology based on Ehrlen
(2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2> and
deVries and Caswell (2018) <doi:10.1007/s12080-017-0353-0>.
Author: Richard P. Shefferson [aut, cre]
(<https://orcid.org/0000-0002-5234-3131>),
Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 4.1.0 dated 2021-12-06 and 4.1.1 dated 2021-12-07
DESCRIPTION | 8 +-- MD5 | 6 +- NEWS | 6 ++ src/DataManagement.cpp | 122 ++++++++++++++++++++++++------------------------- 4 files changed, 74 insertions(+), 68 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party package, but on core R
only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 2.4.0 dated 2021-11-15 and 2.5.0 dated 2021-12-07
DESCRIPTION | 6 MD5 | 340 ++++++++++++++++--------- NAMESPACE | 5 NEWS.md | 11 R/batch.R | 10 R/boolean.R | 6 R/call.R | 4 R/compare_vectors.R | 9 R/convert_umlauts_to_ascii.R | 2 R/convert_umlauts_to_tex.R | 2 R/csv.R | 12 R/file_modified_last.R | 4 R/find_files.R | 4 R/find_missing_doc.R |only R/fromto.R |only R/get_package_version.R | 4 R/get_unique_string.R | 2 R/golden_ratio.R | 2 R/installed.R | 12 R/is_cran.R | 4 R/is_difftime_less.R | 2 R/is_files_current.R | 1 R/is_of_length_zero.R | 2 R/is_path.R |only R/is_r_cmd_check.R | 4 R/is_success.R | 4 R/is_valid_primary_key.R | 3 R/is_version_sufficient.R | 6 R/is_windows.R | 4 R/load_internal_functions.R | 2 R/memory_hogs.R | 2 R/options.R | 8 R/paths.R | 36 ++ R/r.R | 1 R/search_files.R | 6 R/search_rows.R | 2 R/split_code_file.R | 2 R/strip_off_attributes.R | 2 R/subsets.R | 4 R/tapply.R | 2 R/test_helpers.R | 22 - R/throw.R | 1 R/touch.R | 2 R/weighted_variance.R | 2 R/wipe_clean.R | 2 R/with_dir.R | 2 inst/NEWS.rd | 13 inst/doc/An_Introduction_to_fritools.html | 29 ++ inst/runit_tests/runit-csv.R | 57 ++-- inst/runit_tests/runit-find_files.R | 22 + inst/runit_tests/runit-find_missing_see_also.R |only inst/runit_tests/runit-fromto.R |only inst/runit_tests/runit-is_path.R |only inst/runit_tests/runit-paths.R | 12 inst/source |only inst/tinytest/test_fritools.R | 4 man/bulk_read_csv.Rd | 4 man/bulk_write_csv.Rd | 4 man/call_conditionally.Rd | 4 man/call_safe.Rd | 4 man/compare_vectors.Rd | 10 man/convert_umlauts_to_ascii.Rd | 4 man/convert_umlauts_to_tex.Rd | 4 man/csv.Rd | 4 man/csv2csv.Rd | 4 man/file_modified_last.Rd | 14 - man/find_files.Rd | 14 - man/fromto.Rd |only man/get_boolean_envvar.Rd | 8 man/get_mtime.Rd |only man/get_options.Rd | 4 man/get_package_version.Rd | 8 man/get_r_cmd_batch_script_path.Rd | 4 man/get_rscript_script_path.Rd | 4 man/get_run_r_tests.Rd | 12 man/get_script_name.Rd | 4 man/get_script_path.Rd | 4 man/get_unique_string.Rd | 8 man/golden_ratio.Rd | 8 man/index_groups.Rd | 4 man/is_batch.Rd | 4 man/is_cran.Rd | 8 man/is_difftime_less.Rd | 18 - man/is_false.Rd | 4 man/is_files_current.Rd | 13 man/is_force.Rd | 8 man/is_installed.Rd | 8 man/is_not_false.Rd | 4 man/is_null_or_true.Rd | 4 man/is_of_length_zero.Rd | 4 man/is_path.Rd |only man/is_r_cmd_check.Rd | 8 man/is_r_package_installed.Rd | 16 - man/is_running_on_fvafrcu_machines.Rd | 8 man/is_running_on_gitlab_com.Rd | 8 man/is_success.Rd | 8 man/is_valid_primary_key.Rd | 13 man/is_version_sufficient.Rd | 12 man/is_windows.Rd | 8 man/load_internal_functions.Rd | 4 man/memory_hogs.Rd | 4 man/missing_docs.Rd |only man/paths.Rd | 8 man/r_cmd_install.Rd | 11 man/run_r_tests_for_known_hosts.Rd | 4 man/search_files.Rd | 14 - man/search_rows.Rd | 6 man/set_hash.Rd | 4 man/set_options.Rd | 4 man/set_run_r_tests.Rd | 4 man/split_code_file.Rd | 8 man/strip_off_attributes.Rd | 8 man/subset_sizes.Rd | 4 man/summary.filesearch.Rd | 6 man/tapply.Rd | 8 man/throw.Rd | 11 man/touch.Rd | 8 man/un_hash.Rd | 4 man/weighted_variance.Rd | 10 man/wipe_clean.Rd | 4 man/with_dir.Rd | 4 tests/testthat/test-csv.R | 5 122 files changed, 743 insertions(+), 394 deletions(-)
Title: Sequential Design for Deep Gaussian Processes using MCMC
Description: Performs model fitting and sequential design for deep Gaussian
processes following Sauer, Gramacy, and Higdon (2020) <arXiv:2012.08015>.
Models extend up to three layers deep; a one layer model is equivalent
to typical Gaussian process regression. Covariance kernel options are
Matern (default) and squared exponential. Sequential design criteria
include integrated mean-squared error (IMSE), active learning Cohn (ALC),
and expected improvement (EI). Applicable to both noisy and
deterministic functions. Incorporates SNOW parallelization and
utilizes C and C++ under the hood.
Author: Annie Sauer <anniees@vt.edu>
Maintainer: Annie Sauer <anniees@vt.edu>
Diff between deepgp versions 0.3.0 dated 2021-11-23 and 0.3.1 dated 2021-12-07
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/cov.cpp | 4 +++- 3 files changed, 8 insertions(+), 6 deletions(-)
Title: Interface to 'D4Science' 'StorageHub' API
Description: Provides an interface to 'D4Science' 'StorageHub' API (<https://dev.d4science.org/>). Allows to get user profile, and perform
actions over the 'StorageHub' (workspace) including creation of folders, files management (upload/update/deletion/sharing), and listing of
stored resources.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between d4storagehub4R versions 0.1 dated 2021-11-30 and 0.2 dated 2021-12-07
DESCRIPTION | 8 +- MD5 | 12 ++-- R/StoragehubManager.R | 128 ++++++++++++++++++++++++++++++++++++----------- R/d4storagehub4R.R | 4 - README.md | 10 +++ man/StoragehubManager.Rd | 24 +++++++- man/d4storagehub4R.Rd | 4 - 7 files changed, 143 insertions(+), 47 deletions(-)
More information about d4storagehub4R at CRAN
Permanent link
Title: Spatial Multivariate Trees
Description: Fits multivariate Bayesian spatial regression models for large datasets using Spatial Multivariate Trees (SpamTrees).
The methods in this package are detailed in Peruzzi and Dunson (2020) <arXiv:2012.00943>.
Funded by ERC grant 856506 and NIH grant R01ES028804.
Author: Michele Peruzzi
Maintainer: Michele Peruzzi <michele.peruzzi@duke.edu>
Diff between spamtree versions 0.2.1 dated 2021-06-09 and 0.2.2 dated 2021-12-07
DESCRIPTION | 12 +++++++----- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ README.md | 31 ++++++++++++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/spatial_multivariate.html | 26 +++++++++++++------------- src/Makevars | 1 + src/Makevars.win | 1 + src/RcppExports.cpp | 5 +++++ src/mh_adapt.h | 2 +- 11 files changed, 62 insertions(+), 40 deletions(-)
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets. Use all of your data at once, with few limits. Memory mapped data can be shared between multiple R processes. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface or a fast network file system. The data is memory mapped into R and then accessed using usual R list and array subscription operators. Convenience functions are provided for merging, grouping and indexing large vectors and data.frames. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as a standalone C library. libMVL has simple C API making it easy to interchange datasets with outside programs.
Author: Vladimir Dergachev [aut, cre] (<https://orcid.org/0000-0003-4708-6625>)
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 0.0.3.0 dated 2021-09-20 and 0.0.4.1 dated 2021-12-07
DESCRIPTION | 8 MD5 | 48 - NAMESPACE | 9 R/RMVL.R | 504 +++++++++--- man/mvl_compute_repeats.Rd |only man/mvl_extent_index_lapply.Rd |only man/mvl_find_matches.Rd | 4 man/mvl_fused_write_objects.Rd | 2 man/mvl_get_neighbors.Rd | 10 man/mvl_group.Rd | 2 man/mvl_group_lapply.Rd | 2 man/mvl_index_lapply.Rd |only man/mvl_indexed_copy.Rd | 8 man/mvl_inherits.Rd | 2 man/mvl_neighbors_lapply.Rd | 9 man/mvl_object_stats.Rd | 8 man/mvl_remap.Rd | 7 man/mvl_start_write_vector.Rd |only man/mvl_write_extent_index.Rd |only man/mvl_write_spatial_groups.Rd | 15 man/mvl_write_spatial_index1.Rd |only man/mvl_xlength.Rd | 6 man/sub-.MVL.Rd | 4 src/RlibMVL.c | 1511 ++++++++++++++++++++++++++++++++------ src/libMVL.c | 1340 +++++++++++++++++++++++++++++---- src/libMVL.h | 646 ++++++++++++++-- src/libMVL_sort.cc | 105 +- tests/test_extent_index.R |only tests/test_extent_index.Rout.save |only 29 files changed, 3594 insertions(+), 656 deletions(-)
Title: Practical Numerical Math Functions
Description: Provides a large number of functions from numerical analysis and
linear algebra, numerical optimization, differential equations,
time series, plus some well-known special mathematical functions.
Uses 'MATLAB' function names where appropriate to simplify porting.
Author: Hans W. Borchers [aut, cre]
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between pracma versions 2.3.3 dated 2021-01-23 and 2.3.6 dated 2021-12-07
pracma-2.3.3/pracma/data/nile.rda |only pracma-2.3.3/pracma/man/nile.Rd |only pracma-2.3.6/pracma/COPYING | 10 +++++----- pracma-2.3.6/pracma/DESCRIPTION | 12 ++++++------ pracma-2.3.6/pracma/MD5 | 34 ++++++++++++++++------------------ pracma-2.3.6/pracma/NEWS | 17 +++++++++++++++++ pracma-2.3.6/pracma/NEWS.md | 17 +++++++++++++++++ pracma-2.3.6/pracma/R/deval.R | 2 ++ pracma-2.3.6/pracma/R/movavg.R | 3 ++- pracma-2.3.6/pracma/R/pinv.R | 2 +- pracma-2.3.6/pracma/R/randortho.R | 8 +------- pracma-2.3.6/pracma/R/steep_descent.R | 2 +- pracma-2.3.6/pracma/R/subspace.R | 2 +- pracma-2.3.6/pracma/README.md | 2 +- pracma-2.3.6/pracma/data/brown72.rda |binary pracma-2.3.6/pracma/data/titanium.rda |binary pracma-2.3.6/pracma/man/movavg.Rd | 2 +- pracma-2.3.6/pracma/man/pinv.Rd | 2 +- pracma-2.3.6/pracma/man/subspace.Rd | 3 +-- 19 files changed, 73 insertions(+), 45 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.21.0 dated 2021-11-11 and 1.22.0 dated 2021-12-07
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/install.R | 2 +- R/tracking-runs.R | 9 ++++++++- man/install_mlflow.Rd | 2 +- tests/testthat/test-model-mleap.R | 25 ++++++++++++++++++++++++- tests/testthat/test-tracking-runs.R | 7 +++++++ 7 files changed, 50 insertions(+), 13 deletions(-)
Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum
Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Emmanuel Sikali [pdr],
Paul Bailey [aut, cre],
Claire Kelley [aut],
Trang Nguyen [aut],
Huade Huo [aut],
Eric Buehler [ctb],
Christian Kjeldsen [ctb]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between WeMix versions 3.2.0 dated 2021-11-16 and 3.2.1 dated 2021-12-07
DESCRIPTION | 8 MD5 | 16 - R/adaptiveQuad.R | 4 R/analyticSolve.R | 118 +++++----- R/lnl.R | 2 inst/NEWS.Rd | 13 + inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.pdf |binary inst/doc/Weighted_Linear_Mixed_Effects_Models.pdf |binary tests/testthat/test-1-main.R | 127 ++++++++++- 9 files changed, 211 insertions(+), 77 deletions(-)
Title: Blood Pressure Analysis in R
Description: A comprehensive package to aid in the analysis of blood pressure data of all forms by providing both descriptive and visualization tools for researchers.
Author: John Schwenck [aut, cre],
Irina Gaynanova [aut] (<https://orcid.org/0000-0002-4116-0268>)
Maintainer: John Schwenck <jschwenck12@gmail.com>
Diff between bp versions 2.0.0 dated 2021-09-20 and 2.0.1 dated 2021-12-07
DESCRIPTION | 8 MD5 | 54 +- NEWS.md | 9 R/bp_arv.R | 17 R/bp_center.R | 17 R/bp_cv.R | 17 R/bp_mag.R | 17 R/bp_range.R | 8 R/bp_report.R | 518 +++++++++++----------- R/bp_sleep_metrics.R | 491 ++++++++++++--------- R/bp_stages.R | 383 ++++++++-------- R/bp_sv.R | 20 R/bp_visuals_hist.R | 6 R/bp_visuals_scatter.R | 1060 +++++++++++++++++++++++------------------------ R/bp_visuals_ts_plot.R | 1010 ++++++++++++++++++++++---------------------- R/data_process.R | 42 - R/data_process_helpers.R | 618 +++++++++++++++++++++------ R/dip_calc.R | 8 R/dip_class_plot.R | 12 README.md | 49 +- build/partial.rdb |binary inst/doc/bp.html | 148 +++--- man/bp_report.Rd | 2 man/bp_sleep_metrics.Rd | 15 man/bp_stages.Rd | 8 man/bp_ts_plots.Rd | 29 + man/dip_calc.Rd | 6 man/dip_class_plot.Rd | 8 28 files changed, 2568 insertions(+), 2012 deletions(-)