Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the
Web Service methods provided by the National 'Phenology' Network
(<https://usanpn.org/>), which includes data on various life history
events that occur at specific times.
Author: Jeff Switzer [aut, cre],
Scott Chamberlain [aut],
Lee Marsh [aut],
Kevin Wong [aut],
David LeBauer [ctb],
Eric R Scott [ctb]
Maintainer: Jeff Switzer <jeff@usanpn.org>
Diff between rnpn versions 1.2.6 dated 2023-08-30 and 1.2.7.0 dated 2024-01-24
rnpn-1.2.6/rnpn/tests/fixtures |only rnpn-1.2.7.0/rnpn/DESCRIPTION | 9 - rnpn-1.2.7.0/rnpn/MD5 | 79 ++---------- rnpn-1.2.7.0/rnpn/NEWS.md | 11 + rnpn-1.2.7.0/rnpn/R/npn_geoserver.R | 8 - rnpn-1.2.7.0/rnpn/R/zzz.R | 8 - rnpn-1.2.7.0/rnpn/build/vignette.rds |binary rnpn-1.2.7.0/rnpn/inst/doc/III_individual_phenometrics.R | 2 rnpn-1.2.7.0/rnpn/inst/doc/III_individual_phenometrics.html | 8 - rnpn-1.2.7.0/rnpn/inst/doc/II_status_intensity.html | 8 - rnpn-1.2.7.0/rnpn/inst/doc/IV_site_phenometrics.R | 2 rnpn-1.2.7.0/rnpn/inst/doc/IV_site_phenometrics.html | 8 - rnpn-1.2.7.0/rnpn/inst/doc/I_introduction.html | 8 - rnpn-1.2.7.0/rnpn/inst/doc/VIII_data_cleaning.R | 10 - rnpn-1.2.7.0/rnpn/inst/doc/VIII_data_cleaning.html | 8 - rnpn-1.2.7.0/rnpn/inst/doc/VII_combine_raster_point.R | 2 rnpn-1.2.7.0/rnpn/inst/doc/VII_combine_raster_point.html | 8 - rnpn-1.2.7.0/rnpn/inst/doc/VI_geospatial.html | 25 --- rnpn-1.2.7.0/rnpn/inst/doc/V_magnitude_phenometrics.R | 2 rnpn-1.2.7.0/rnpn/inst/doc/V_magnitude_phenometrics.html | 8 - rnpn-1.2.7.0/rnpn/tests/testthat/test-npn-stations.R | 24 +-- 21 files changed, 80 insertions(+), 158 deletions(-)
Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10918-6, Nankodo, ISBN: 978-4-524-26158-1, Ohmsha, ISBN: 978-4-274-22632-8), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below. This report has been cited in more than 10,000 scientific articles.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda <ycanda-tky@umin.ac.jp>
Diff between RcmdrPlugin.EZR versions 1.63 dated 2023-12-03 and 1.64 dated 2024-01-24
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 6 ++++++ R/EZR.R | 24 +++++++++++++++--------- inst/CHANGES | 6 ++++++ inst/doc/EZR.htm | 4 ++-- inst/doc/EZR.pdf |binary inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.EZR.mo |binary man/EZR.Rd | 4 ++-- po/R-RcmdrPlugin.EZR.po | 5 ++++- 10 files changed, 48 insertions(+), 27 deletions(-)
More information about RcmdrPlugin.EZR at CRAN
Permanent link
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.10.0 dated 2023-11-19 and 0.10.1 dated 2024-01-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/est.R | 21 +++++++++++---------- inst/NEWS.Rd | 6 ++++++ inst/doc/sasLM-manual.pdf |binary man/T3test.Rd | 2 +- 6 files changed, 26 insertions(+), 19 deletions(-)
Title: Access Formula 1 Data
Description: Obtain Formula 1 data via the 'Ergast API' <https://ergast.com/mrd/> and the unofficial API <https://www.formula1.com/en/f1-live.html> via the 'fastf1' 'Python' library <https://docs.fastf1.dev/>.
Author: Santiago Casanova [aut, cre, cph],
Philip Bulsink [aut]
Maintainer: Santiago Casanova <santiago.casanova@yahoo.com>
Diff between f1dataR versions 1.4.1 dated 2023-11-13 and 1.5.0 dated 2024-01-24
DESCRIPTION | 6 +-- MD5 | 23 +++++++----- NAMESPACE | 1 NEWS.md | 6 ++- R/circuit_details.R |only R/clear_f1_cache.R | 1 R/load_session_laps.R | 2 - R/utils.R | 1 R/zzz.R | 5 ++ README.md | 50 ++++++---------------------- man/load_circuit_details.Rd |only tests/testthat/test-load_circuit_details.R |only tests/testthat/test-load_driver_telemetry.R | 2 - tests/testthat/test-load_session_laps.R | 2 + 14 files changed, 45 insertions(+), 54 deletions(-)
Title: UK Biobank COVID-19 Data Processing and Risk Factor Association
Tests
Description: Process UK Biobank COVID-19 test result data for susceptibility, severity and mortality analyses, perform potential non-genetic COVID-19 risk factor and co-morbidity association tests. Wang et al. (2021) <doi:10.5281/zenodo.5174381>.
Author: Longfei Wang [aut, cre]
Maintainer: Longfei Wang <wang.lo@wehi.edu.au>
Diff between UKB.COVID19 versions 0.1.3 dated 2022-01-04 and 0.1.4 dated 2024-01-24
UKB.COVID19-0.1.3/UKB.COVID19/tests/testthat/test_asso_test.R |only UKB.COVID19-0.1.3/UKB.COVID19/tests/testthat/test_comorbidity_asso.R |only UKB.COVID19-0.1.3/UKB.COVID19/tests/testthat/test_makePhenotypes.R |only UKB.COVID19-0.1.3/UKB.COVID19/tests/testthat/test_risk_factor.R |only UKB.COVID19-0.1.4/UKB.COVID19/DESCRIPTION | 9 +++++---- UKB.COVID19-0.1.4/UKB.COVID19/MD5 | 6 +----- 6 files changed, 6 insertions(+), 9 deletions(-)
Title: Process NEON Plant Data for Ecological Analysis
Description: Downloading and organizing plant presence and percent cover data from the National Ecological Observatory Network <https://www.neonscience.org>.
Author: Adam Mahood [aut, cre],
Jacob Macdonald [ctb],
Ranjan Muthukrishnan [ctb]
Maintainer: Adam Mahood <admahood@gmail.com>
Diff between neonPlantEcology versions 1.3.5 dated 2024-01-16 and 1.4.0 dated 2024-01-24
DESCRIPTION | 6 LICENSE | 4 MD5 | 56 NAMESPACE | 34 R/data.R | 114 - R/diversity_data_prep.R | 3410 ++++++++++++++++++++-------------------- R/pkg_housekeeping.R | 48 README.md | 178 +- build/vignette.rds |binary data/site_polygons.rda |binary inst/doc/using_npe.R | 276 +-- inst/doc/using_npe.Rmd | 394 ++-- inst/doc/using_npe.html | 1084 ++++++------ man/D14.Rd | 44 man/npe_change_native_status.Rd | 68 man/npe_cm_metadata.Rd | 50 man/npe_community_matrix.Rd | 112 - man/npe_download.Rd | 97 - man/npe_eventID_fixer.Rd | 52 man/npe_groundcover.Rd | 79 man/npe_heights.Rd | 74 man/npe_longform.Rd | 97 - man/npe_plot_centroids.Rd | 66 man/npe_site_ids.Rd | 72 man/npe_summary.Rd | 110 - man/npe_update_subplots.Rd | 48 man/site_polygons.Rd | 62 man/sites.Rd | 68 vignettes/using_npe.Rmd | 394 ++-- 29 files changed, 3605 insertions(+), 3492 deletions(-)
More information about neonPlantEcology at CRAN
Permanent link
Title: R-Client for Interacting with the 'UCSF Data Library'
Description: A client for interacting with 'magma', the data warehouse of the
'UCSF Data Library'. 'magmaR' includes functions for querying and
downloading data from 'magma', in order to enable working with such data in
R, as well as for uploading local data to 'magma'.
Author: Daniel Bunis [aut, cre]
Maintainer: Daniel Bunis <daniel.bunis@ucsf.edu>
Diff between magmaR versions 1.0.2 dated 2021-10-02 and 1.0.3 dated 2024-01-24
DESCRIPTION | 18 MD5 | 45 NEWS.md | 5 R/retrieve.R | 9 R/update-special.R | 8 R/update.R | 19 R/url-adjust.R | 10 build/vignette.rds |binary inst/doc/Download.Rmd | 10 inst/doc/Download.html | 1932 ++++++++++++++++++++++++++++++--- inst/doc/Upload.Rmd | 8 inst/doc/Upload.html | 1928 ++++++++++++++++++++++++++++++-- man/authentication-and-environments.Rd | 10 man/retrieve.Rd | 5 man/retrieveJSON.Rd | 5 man/retrieve_SpecialCases.Rd | 10 man/updateFromDF.Rd | 11 man/updateMatrix.Rd | 11 man/updateValues.Rd | 13 tests/fixtures/update_6.yml |only tests/testthat/test-retrieve.R | 27 tests/testthat/test-update.R | 66 + vignettes/Download.Rmd | 10 vignettes/Upload.Rmd | 8 24 files changed, 3779 insertions(+), 389 deletions(-)
Title: 'OpenAI' API R Interface
Description: A comprehensive set of helpers that streamline data transmission
and processing, making it effortless to interact with the 'OpenAI' API.
Author: Cezary Kuran [aut, cre]
Maintainer: Cezary Kuran <cezary.kuran@gmail.com>
Diff between oaii versions 0.3.0 dated 2024-01-21 and 0.4.0 dated 2024-01-24
oaii-0.3.0/oaii/R/api_fine-tunes.R |only oaii-0.3.0/oaii/man/fine_tunes_create_request.Rd |only oaii-0.3.0/oaii/man/fine_tunes_fetch_list.Rd |only oaii-0.3.0/oaii/man/fine_tunes_list_request.Rd |only oaii-0.3.0/oaii/man/images_roxygen_tpl.Rd |only oaii-0.3.0/oaii/man/moderations_object_request.Rd |only oaii-0.3.0/oaii/man/print.oaiiFilesDF.Rd |only oaii-0.3.0/oaii/man/print.oaiiFineTunesDF.Rd |only oaii-0.3.0/oaii/man/print.oaiiModelsDF.Rd |only oaii-0.3.0/oaii/man/print.oaiiResSE.Rd |only oaii-0.4.0/oaii/DESCRIPTION | 6 oaii-0.4.0/oaii/MD5 | 89 ++++--- oaii-0.4.0/oaii/NAMESPACE | 25 +- oaii-0.4.0/oaii/R/api.R | 16 - oaii-0.4.0/oaii/R/api_audio.R | 19 + oaii-0.4.0/oaii/R/api_chat.R | 157 +++++++++++--- oaii-0.4.0/oaii/R/api_embeddings.R | 27 -- oaii-0.4.0/oaii/R/api_files.R | 106 +++++---- oaii-0.4.0/oaii/R/api_fine-tuning.R |only oaii-0.4.0/oaii/R/api_images.R | 179 +++++++++------- oaii-0.4.0/oaii/R/api_models.R | 39 ++- oaii-0.4.0/oaii/R/api_moderations.R | 54 ---- oaii-0.4.0/oaii/R/api_utils.R | 4 oaii-0.4.0/oaii/R/df.R | 25 -- oaii-0.4.0/oaii/R/utils.R |only oaii-0.4.0/oaii/man/audio_transcription_request.Rd | 14 - oaii-0.4.0/oaii/man/chat_fetch_messages.Rd | 3 oaii-0.4.0/oaii/man/chat_request.Rd | 127 +++++++++-- oaii-0.4.0/oaii/man/df_col_dt_format.Rd | 17 - oaii-0.4.0/oaii/man/embeddings_create_request.Rd | 23 -- oaii-0.4.0/oaii/man/embeddings_object_request.Rd | 4 oaii-0.4.0/oaii/man/files_delete_request.Rd | 4 oaii-0.4.0/oaii/man/files_list_request.Rd | 7 oaii-0.4.0/oaii/man/files_retrieve_content_request.Rd | 12 + oaii-0.4.0/oaii/man/files_retrieve_request.Rd | 5 oaii-0.4.0/oaii/man/files_upload_request.Rd | 15 - oaii-0.4.0/oaii/man/fine_tuning_cancel_job_request.Rd |only oaii-0.4.0/oaii/man/fine_tuning_create_job_request.Rd |only oaii-0.4.0/oaii/man/fine_tuning_events_list_request.Rd |only oaii-0.4.0/oaii/man/fine_tuning_fetch_events_list.Rd |only oaii-0.4.0/oaii/man/fine_tuning_fetch_jobs_list.Rd |only oaii-0.4.0/oaii/man/fine_tuning_fetch_retrived_job.Rd |only oaii-0.4.0/oaii/man/fine_tuning_jobs_list_request.Rd |only oaii-0.4.0/oaii/man/fine_tuning_retrive_job_request.Rd |only oaii-0.4.0/oaii/man/images_edit_request.Rd | 35 +-- oaii-0.4.0/oaii/man/images_fech_set.Rd | 6 oaii-0.4.0/oaii/man/images_generator_request.Rd | 31 +- oaii-0.4.0/oaii/man/images_variation_request.Rd |only oaii-0.4.0/oaii/man/models_delete_request.Rd | 6 oaii-0.4.0/oaii/man/models_list_request.Rd | 4 oaii-0.4.0/oaii/man/models_retrieve_request.Rd |only oaii-0.4.0/oaii/man/moderation_create_request.Rd | 17 - oaii-0.4.0/oaii/man/print.oaii_files_df.Rd |only oaii-0.4.0/oaii/man/print.oaii_fine_tuning_events_df.Rd |only oaii-0.4.0/oaii/man/print.oaii_fine_tuning_job.Rd |only oaii-0.4.0/oaii/man/print.oaii_fine_tuning_jobs_df.Rd |only oaii-0.4.0/oaii/man/print.oaii_models_df.Rd |only oaii-0.4.0/oaii/man/print.oaii_res_se.Rd |only oaii-0.4.0/oaii/man/request.Rd | 11 oaii-0.4.0/oaii/man/timestap_dt_str.Rd |only 60 files changed, 678 insertions(+), 409 deletions(-)
Title: Many Ways to Make, Modify, Mark, and Map Myriad Networks
Description: A set of tools for making, modifying, marking, and mapping many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing and visualizing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 0.3.0 dated 2023-12-15 and 0.4.1 dated 2024-01-24
manynet-0.3.0/manynet/R/make_as.R |only manynet-0.3.0/manynet/R/manip_add.R |only manynet-0.3.0/manynet/R/manip_tidy.R |only manynet-0.3.0/manynet/R/manip_transform.R |only manynet-0.3.0/manynet/R/map_is.R |only manynet-0.3.0/manynet/data/ison_konigsberg.rda |only manynet-0.3.0/manynet/man/add.Rd |only manynet-0.3.0/manynet/man/ison_konigsberg.Rd |only manynet-0.3.0/manynet/man/tidy.Rd |only manynet-0.3.0/manynet/man/transform.Rd |only manynet-0.3.0/manynet/tests/testthat/test-map_is.R |only manynet-0.3.0/manynet/tests/testthat/test_plots.R |only manynet-0.4.1/manynet/DESCRIPTION | 27 manynet-0.4.1/manynet/MD5 | 170 +- manynet-0.4.1/manynet/NAMESPACE | 96 + manynet-0.4.1/manynet/NEWS.md | 106 + manynet-0.4.1/manynet/R/class_diff_model.R |only manynet-0.4.1/manynet/R/class_marks.R |only manynet-0.4.1/manynet/R/data_ison.R | 195 ++- manynet-0.4.1/manynet/R/make_create.R | 93 - manynet-0.4.1/manynet/R/make_generate.R | 51 manynet-0.4.1/manynet/R/make_play.R |only manynet-0.4.1/manynet/R/make_read.R | 757 ++++++------ manynet-0.4.1/manynet/R/manip_as.R |only manynet-0.4.1/manynet/R/manip_from.R | 72 - manynet-0.4.1/manynet/R/manip_miss.R | 22 manynet-0.4.1/manynet/R/manip_nodes.R |only manynet-0.4.1/manynet/R/manip_reformat.R | 237 ++- manynet-0.4.1/manynet/R/manip_reformed.R |only manynet-0.4.1/manynet/R/manip_split.R | 100 + manynet-0.4.1/manynet/R/manip_ties.R |only manynet-0.4.1/manynet/R/map_attributes.R | 51 manynet-0.4.1/manynet/R/map_autographr.R | 319 +++-- manynet-0.4.1/manynet/R/map_layout_partition.R | 42 manynet-0.4.1/manynet/R/map_properties.R | 28 manynet-0.4.1/manynet/R/map_theme.R | 154 +- manynet-0.4.1/manynet/R/mark_is.R |only manynet-0.4.1/manynet/R/mark_nodes.R |only manynet-0.4.1/manynet/R/mark_ties.R |only manynet-0.4.1/manynet/R/pkg_tutorials.R | 73 + manynet-0.4.1/manynet/R/reexports_classes.R | 16 manynet-0.4.1/manynet/README.md | 105 + manynet-0.4.1/manynet/build/partial.rdb |binary manynet-0.4.1/manynet/data/ison_algebra.rda |binary manynet-0.4.1/manynet/data/ison_hightech.rda |only manynet-0.4.1/manynet/data/ison_karateka.rda |binary manynet-0.4.1/manynet/data/ison_koenigsberg.rda |only manynet-0.4.1/manynet/data/ison_lawfirm.rda |binary manynet-0.4.1/manynet/data/ison_monastery_esteem.rda |only manynet-0.4.1/manynet/data/ison_monastery_influence.rda |only manynet-0.4.1/manynet/data/ison_monastery_like.rda |only manynet-0.4.1/manynet/data/ison_monastery_praise.rda |only manynet-0.4.1/manynet/data/ison_potter.rda |only manynet-0.4.1/manynet/data/ison_southern_women.rda |binary manynet-0.4.1/manynet/data/ison_usstates.rda |only manynet-0.4.1/manynet/inst/tutorials/tutorial7 |only manynet-0.4.1/manynet/man/add_nodes.Rd |only manynet-0.4.1/manynet/man/add_ties.Rd |only manynet-0.4.1/manynet/man/as.Rd | 87 - manynet-0.4.1/manynet/man/attributes.Rd | 43 manynet-0.4.1/manynet/man/autographing.Rd | 82 - manynet-0.4.1/manynet/man/configuration_layouts.Rd | 3 manynet-0.4.1/manynet/man/create.Rd | 69 - manynet-0.4.1/manynet/man/features.Rd |only manynet-0.4.1/manynet/man/from.Rd | 65 - manynet-0.4.1/manynet/man/generate.Rd | 57 manynet-0.4.1/manynet/man/is.Rd | 146 -- manynet-0.4.1/manynet/man/is_format.Rd |only manynet-0.4.1/manynet/man/ison_algebra.Rd | 22 manynet-0.4.1/manynet/man/ison_hightech.Rd |only manynet-0.4.1/manynet/man/ison_karateka.Rd | 36 manynet-0.4.1/manynet/man/ison_koenigsberg.Rd |only manynet-0.4.1/manynet/man/ison_lawfirm.Rd | 45 manynet-0.4.1/manynet/man/ison_marvel.Rd | 6 manynet-0.4.1/manynet/man/ison_monastery.Rd |only manynet-0.4.1/manynet/man/ison_potter.Rd |only manynet-0.4.1/manynet/man/ison_southern_women.Rd | 12 manynet-0.4.1/manynet/man/ison_usstates.Rd |only manynet-0.4.1/manynet/man/learning.Rd |only manynet-0.4.1/manynet/man/mark_diff.Rd |only manynet-0.4.1/manynet/man/mark_nodes.Rd |only manynet-0.4.1/manynet/man/mark_select.Rd |only manynet-0.4.1/manynet/man/mark_tie_select.Rd |only manynet-0.4.1/manynet/man/mark_ties.Rd |only manynet-0.4.1/manynet/man/miss.Rd | 35 manynet-0.4.1/manynet/man/partition_layouts.Rd | 21 manynet-0.4.1/manynet/man/play.Rd |only manynet-0.4.1/manynet/man/properties.Rd | 26 manynet-0.4.1/manynet/man/read.Rd | 104 - manynet-0.4.1/manynet/man/reexports.Rd | 9 manynet-0.4.1/manynet/man/reformat.Rd | 94 - manynet-0.4.1/manynet/man/scales.Rd | 38 manynet-0.4.1/manynet/man/split.Rd | 26 manynet-0.4.1/manynet/man/themes.Rd | 4 manynet-0.4.1/manynet/man/to_levels.Rd |only manynet-0.4.1/manynet/man/to_paths.Rd |only manynet-0.4.1/manynet/man/to_project.Rd |only manynet-0.4.1/manynet/man/to_scope.Rd |only manynet-0.4.1/manynet/man/tutorials.Rd | 29 manynet-0.4.1/manynet/man/write.Rd |only manynet-0.4.1/manynet/tests/testthat/helper-manynet.R |only manynet-0.4.1/manynet/tests/testthat/test-make_create.R | 5 manynet-0.4.1/manynet/tests/testthat/test-make_read.R | 4 manynet-0.4.1/manynet/tests/testthat/test-manip_add.R | 2 manynet-0.4.1/manynet/tests/testthat/test-manip_as.R | 2 manynet-0.4.1/manynet/tests/testthat/test-manip_reformat.R | 14 manynet-0.4.1/manynet/tests/testthat/test-manip_split.R | 15 manynet-0.4.1/manynet/tests/testthat/test-manip_transform.R | 13 manynet-0.4.1/manynet/tests/testthat/test-map_autographr.R | 16 manynet-0.4.1/manynet/tests/testthat/test-map_theme.R | 14 manynet-0.4.1/manynet/tests/testthat/test-mark_is.R |only manynet-0.4.1/manynet/tests/testthat/test-mark_nodes.R |only manynet-0.4.1/manynet/tests/testthat/test-mark_ties.R |only manynet-0.4.1/manynet/tests/testthat/test-model_play.R |only 114 files changed, 2296 insertions(+), 1562 deletions(-)
Title: Generalized Linear Density Ratio Models
Description: Fits a generalized linear density ratio model (GLDRM).
A GLDRM is a semiparametric generalized linear model.
In contrast to a GLM, which assumes a particular exponential family distribution,
the GLDRM uses a semiparametric likelihood to estimate the reference distribution.
The reference distribution may be any discrete, continuous, or mixed exponential
family distribution. The model parameters, which include both the regression
coefficients and the cdf of the unspecified reference distribution, are estimated
by maximizing a semiparametric likelihood. Regression coefficients are estimated
with no loss of efficiency, i.e. the asymptotic variance is the same as if the
true exponential family distribution were known.
Huang (2014) <doi:10.1080/01621459.2013.824892>.
Huang and Rathouz (2012) <doi:10.1093/biomet/asr075>.
Rathouz and Gao (2008) <doi:10.1093/biostatistics/kxn030>.
Author: Michael Wurm [aut, cre],
Paul Rathouz [aut]
Maintainer: Michael Wurm <wurm@uwalumni.com>
Diff between gldrm versions 1.5 dated 2018-04-13 and 1.6 dated 2024-01-24
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 38 +++++++++++++++++++------------------- R/getBeta.R | 6 +++--- R/getTheta.R | 2 +- R/getf0.R | 2 +- R/gldrmCI.R | 2 +- R/gldrmFit.R | 2 +- R/gldrmLRT.R | 4 ++-- R/gldrmPIT.R | 2 +- man/getBeta.Rd | 23 ++++++++++++++++++----- man/getTheta.Rd | 11 +++++++++-- man/getf0.Rd | 16 ++++++++++++++-- man/gldrm.Rd | 15 +++++++++++---- man/gldrm.control.Rd | 12 +++++++++--- man/gldrmCI.Rd | 11 +++++++++-- man/gldrmFit.Rd | 18 ++++++++++++++---- man/gldrmPIT.Rd | 9 +++++++-- man/predict.gldrm.Rd | 10 ++++++++-- man/theta.control.Rd | 10 ++++++++-- 20 files changed, 142 insertions(+), 63 deletions(-)
Title: Partial Datetime Handling
Description: Datetimes and timestamps are invariably an imprecise notation, with any
partial representation implying some amount of uncertainty. To handle this,
'parttime' provides classes for embedding partial missingness as a central
part of its datetime classes. This central feature allows for more ergonomic
use of datetimes for challenging datetime computation, including
calculations of overlapping date ranges, imputations, and more thoughtful
handling of ambiguity that arises from uncertain time zones. This package was
developed first and foremost with pharmaceutical applications in mind, but
aims to be agnostic to application to accommodate general use cases just as
conveniently.
Author: Doug Kelkhoff [aut, cre],
Bill Denney [ctb]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Diff between parttime versions 0.1.1 dated 2023-03-08 and 0.1.2 dated 2024-01-24
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/class_partial_time_coercion.R | 10 ++++++---- R/class_partial_time_utils.R | 14 +++++++------- R/class_timespan_coercion.R | 11 ++++++----- R/includes.R | 1 + R/parse_iso8601.R | 2 +- README.md | 39 +++++++++++++++++++-------------------- man/parse_iso8601_matrix.Rd | 2 +- man/vec_cast.partial_time.Rd | 2 +- man/vec_cast.timespan.Rd | 2 +- 13 files changed, 63 insertions(+), 55 deletions(-)
Title: Diversity-Interactions (DI) Models
Description: The 'DImodels' package is suitable for analysing data from biodiversity and ecosystem function studies using the Diversity-Interactions (DI) modelling approach introduced by Kirwan et al. (2009) <doi:10.1890/08-1684.1>. Suitable data will contain proportions for each species and a community-level response variable, and may also include additional factors, such as blocks or treatments. The package can perform data manipulation tasks, such as computing pairwise interactions (the DI_data() function), can perform an automated model selection process (the autoDI() function) and has the flexibility to fit a wide range of user-defined DI models (the DI() function).
Author: Rafael de Andrade Moral [aut, cre],
John Connolly [aut],
Rishabh Vishwakarma [ctb],
Caroline Brophy [aut]
Maintainer: Rafael de Andrade Moral <rafael.deandrademoral@mu.ie>
Diff between DImodels versions 1.3 dated 2023-11-22 and 1.3.1 dated 2024-01-24
DESCRIPTION | 14 - MD5 | 35 ++-- NAMESPACE | 3 R/DI.R | 71 +++++++-- R/autoDI.R | 25 +-- R/dataDI.R | 6 R/predictDI.R | 78 +++++++++ README.md | 29 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/DImodels.R | 50 +++--- inst/doc/DImodels.Rmd | 5 inst/doc/DImodels.html | 314 +++++++++++++++++++--------------------- man/DI_methods.Rd | 6 man/describe_model.Rd |only man/sim4.Rd | 6 tests/testthat/test-DI.R | 43 +++++ tests/testthat/test-predictDI.R | 36 ++++ vignettes/DImodels.Rmd | 5 19 files changed, 455 insertions(+), 271 deletions(-)
Title: Solves a Generic Stochastic Growth Model with a Representative
Agent
Description: It computes the solutions to a generic stochastic growth model for a given set of user supplied parameters. It includes
the solutions to the model, plots of the solution,
a summary of the features of the model, a function that covers different types of consumption preferences,
and a function that computes the moments of a Markov process.
Merton, Robert C (1971) <doi:10.1016/0022-0531(71)90038-X>,
Tauchen, George (1986) <doi:10.1016/0165-1765(86)90168-0>,
Wickham, Hadley (2009, ISBN:978-0-387-98140-6 ).
Author: Thomas Vigie <vigiethomas@gmail.com>
Maintainer: Thomas Vigie <vigiethomas@gmail.com>
Diff between sgmodel versions 0.1.1 dated 2020-02-27 and 0.1.2 dated 2024-01-24
DESCRIPTION | 7 +- MD5 | 16 ++--- NEWS.md | 5 + R/stochastic_growth_model.R | 7 +- build/vignette.rds |binary inst/doc/sgmodel_vignette.html | 123 +++++++++++++++++++++++++++++++++-------- man/package_sgmodel.Rd | 3 - man/sgmodel.Rd | 2 man/util.Rd | 2 9 files changed, 120 insertions(+), 45 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2023.3.31 dated 2023-04-03 and 2024.1.24 dated 2024-01-24
atime-2023.3.31/atime/vignettes/ci.html |only atime-2024.1.24/atime/DESCRIPTION | 6 atime-2024.1.24/atime/MD5 | 79 atime-2024.1.24/atime/NAMESPACE | 35 atime-2024.1.24/atime/NEWS | 137 atime-2024.1.24/atime/R/atime.R | 369 +- atime-2024.1.24/atime/R/predict.R |only atime-2024.1.24/atime/R/references.R | 358 +- atime-2024.1.24/atime/R/versions.R | 681 ++-- atime-2024.1.24/atime/build/vignette.rds |binary atime-2024.1.24/atime/inst/doc/Custom_Plots.R | 144 atime-2024.1.24/atime/inst/doc/Custom_Plots.Rmd | 204 - atime-2024.1.24/atime/inst/doc/Custom_Plots.html | 472 +-- atime-2024.1.24/atime/inst/doc/Custom_References.R | 109 atime-2024.1.24/atime/inst/doc/Custom_References.Rmd | 242 - atime-2024.1.24/atime/inst/doc/Custom_References.html | 506 +-- atime-2024.1.24/atime/inst/doc/Custom_Units.R | 108 atime-2024.1.24/atime/inst/doc/Custom_Units.Rmd | 220 - atime-2024.1.24/atime/inst/doc/Custom_Units.html | 488 +-- atime-2024.1.24/atime/inst/doc/cum_median.R | 62 atime-2024.1.24/atime/inst/doc/cum_median.Rmd | 108 atime-2024.1.24/atime/inst/doc/cum_median.html | 376 +- atime-2024.1.24/atime/inst/doc/regex.R | 121 atime-2024.1.24/atime/inst/doc/regex.Rmd | 181 - atime-2024.1.24/atime/inst/doc/regex.html | 468 +-- atime-2024.1.24/atime/man/atime.Rd | 129 atime-2024.1.24/atime/man/atime_grid.Rd | 132 atime-2024.1.24/atime/man/atime_pkg.Rd | 75 atime-2024.1.24/atime/man/atime_versions.Rd | 153 - atime-2024.1.24/atime/man/atime_versions_exprs.Rd | 157 - atime-2024.1.24/atime/man/atime_versions_remove.Rd | 26 atime-2024.1.24/atime/man/glob_find_replace.Rd | 38 atime-2024.1.24/atime/man/references_best.Rd | 102 atime-2024.1.24/atime/tests/testthat.R | 2 atime-2024.1.24/atime/tests/testthat/test-CRAN.R | 492 ++- atime-2024.1.24/atime/vignettes/Custom_Plots.Rmd | 204 - atime-2024.1.24/atime/vignettes/Custom_References.Rmd | 242 - atime-2024.1.24/atime/vignettes/Custom_Units.Rmd | 220 - atime-2024.1.24/atime/vignettes/binseg.html |only atime-2024.1.24/atime/vignettes/compare-data.table-tidyverse.html | 1453 ++++------ atime-2024.1.24/atime/vignettes/cum_median.Rmd | 108 atime-2024.1.24/atime/vignettes/regex.Rmd | 181 - 42 files changed, 4811 insertions(+), 4377 deletions(-)
Title: Animated Interactive Grammar of Graphics
Description: Functions are provided for defining animated,
interactive data visualizations in R code, and rendering
on a web page. The 2018 Journal of Computational and
Graphical Statistics paper,
<doi:10.1080/10618600.2018.1513367>
describes the concepts implemented.
Author: Toby Hocking [aut, cre] ,
Hadley Wickham [aut] ,
Winston Chang [aut] ,
RStudio [cph] ,
Nicholas Lewin-Koh [aut] ,
Martin Maechler [aut] ,
Randall Prium [aut] ,
Susan VanderPlas [aut] ,
Carson Sievert [aut] ,
Kevin Ferris [aut] ,
Jun Cai [aut] ,
Faiza [...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between animint2 versions 2023.11.21 dated 2023-11-21 and 2024.1.24 dated 2024-01-24
DESCRIPTION | 20 ++++++------- MD5 | 14 ++++----- NEWS.md | 5 +++ R/z_animint.R | 9 +----- R/z_facets.R | 15 ++++++---- build/partial.rdb |binary man/animint2dir.Rd | 3 -- tests/testthat/test-renderer1-facet-space.R | 42 ++++++++++++++++++++++------ 8 files changed, 67 insertions(+), 41 deletions(-)
Title: Download 'Qualtrics' Survey Data
Description: Provides functions to access survey results directly into R
using the 'Qualtrics' API. 'Qualtrics'
<https://www.qualtrics.com/about/> is an online survey and data
collection software platform. See <https://api.qualtrics.com/> for
more information about the 'Qualtrics' API. This package is
community-maintained and is not officially supported by 'Qualtrics'.
Author: Jasper Ginn [aut],
Jackson Curtis [ctb],
Shaun Jackson [ctb],
Samuel Kaminsky [ctb],
Eric Knudsen [ctb],
Joseph O'Brien [aut],
Daniel Seneca [ctb],
Julia Silge [aut, cre] ,
Phoebe Wong [ctb]
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between qualtRics versions 3.1.7 dated 2022-11-18 and 3.2.0 dated 2024-01-24
qualtRics-3.1.7/qualtRics/man/checkarg_save_dir.Rd |only qualtRics-3.2.0/qualtRics/DESCRIPTION | 16 qualtRics-3.2.0/qualtRics/MD5 | 77 +- qualtRics-3.2.0/qualtRics/NAMESPACE | 11 qualtRics-3.2.0/qualtRics/NEWS.md | 8 qualtRics-3.2.0/qualtRics/R/all_mailinglists.R | 2 qualtRics-3.2.0/qualtRics/R/checks.R | 33 qualtRics-3.2.0/qualtRics/R/fetch_mailinglist.R | 85 +- qualtRics-3.2.0/qualtRics/R/fetch_survey.R | 337 +++++++-- qualtRics-3.2.0/qualtRics/R/globals.R | 3 qualtRics-3.2.0/qualtRics/R/read_survey.R | 372 +++++----- qualtRics-3.2.0/qualtRics/R/utils.R | 260 ------ qualtRics-3.2.0/qualtRics/build/vignette.rds |binary qualtRics-3.2.0/qualtRics/inst/doc/qualtRics.R | 16 qualtRics-3.2.0/qualtRics/inst/doc/qualtRics.html | 115 +-- qualtRics-3.2.0/qualtRics/man/checkarg_tempdir.Rd |only qualtRics-3.2.0/qualtRics/man/export_responses_filedownload.Rd | 14 qualtRics-3.2.0/qualtRics/man/export_responses_init.Rd | 2 qualtRics-3.2.0/qualtRics/man/export_responses_progress.Rd | 2 qualtRics-3.2.0/qualtRics/man/export_responses_request.Rd | 8 qualtRics-3.2.0/qualtRics/man/fetch_survey.Rd | 49 - qualtRics-3.2.0/qualtRics/man/qualtrics_api_request.Rd | 3 qualtRics-3.2.0/qualtRics/man/read_survey.Rd | 48 - qualtRics-3.2.0/qualtRics/tests/testthat.R | 8 qualtRics-3.2.0/qualtRics/tests/testthat/_snaps |only qualtRics-3.2.0/qualtRics/tests/testthat/test-all-surveys.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-api-credentials.R | 3 qualtRics-3.2.0/qualtRics/tests/testthat/test-check-params.R | 10 qualtRics-3.2.0/qualtRics/tests/testthat/test-column_map.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-extract-colmap.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-fetch-description.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-fetch-distribution-history.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-fetch-distributions.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-fetch-id.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-fetch-mailinglist.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-fetch-survey.R | 52 - qualtRics-3.2.0/qualtRics/tests/testthat/test-generate-url.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-list-distribution-links.R | 2 qualtRics-3.2.0/qualtRics/tests/testthat/test-metadata.R | 4 qualtRics-3.2.0/qualtRics/tests/testthat/test-qualtrics-api-request.R | 4 qualtRics-3.2.0/qualtRics/tests/testthat/test-survey-questions.R | 2 41 files changed, 822 insertions(+), 742 deletions(-)
Title: Easy, Fast, and Pretty Specification Curve Analysis
Description: Making specification curve analysis easy, fast, and pretty. It
improves upon existing offerings with additional features and 'tidyverse'
integration. Users can easily visualize and evaluate how their models behave
under different specifications with a high degree of customization. For a
description and applications of specification curve analysis see Simonsohn,
Simmons, and Nelson (2020) <doi:10.1038/s41562-020-0912-z>.
Author: Zayne Sember [aut, cre, cph]
Maintainer: Zayne Sember <zsember@ucsd.edu>
Diff between speccurvieR versions 0.1.0 dated 2023-10-05 and 0.3.0 dated 2024-01-24
DESCRIPTION | 10 +- MD5 | 28 +++---- NAMESPACE | 2 NEWS.md | 5 + R/functions.R | 166 ++++++++++++++++++++++++++++----------------- R/globals.R | 3 R/helpers.R | 30 +++++--- R/speccurvieR-package.R | 2 build/partial.rdb |binary man/controlExtractor.Rd | 8 +- man/plotCurve.Rd | 6 + man/plotR2Adj.Rd | 4 - man/sca.Rd | 2 man/scp.Rd | 4 - man/speccurvieR-package.Rd | 8 ++ 15 files changed, 177 insertions(+), 101 deletions(-)
Title: Optimal Segmentation Subject to Up-Down Constraints
Description: Computes optimal changepoint models using the
Poisson likelihood for non-negative count data,
subject to the PeakSeg constraint:
the first change must be up, second change down, third change up, etc.
For more info about the models and algorithms,
read "A log-linear time algorithm for constrained changepoint detection"
<arXiv:1703.03352> by TD Hocking et al.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between PeakSegOptimal versions 2018.05.25 dated 2018-05-25 and 2024.1.24 dated 2024-01-24
PeakSegOptimal-2018.05.25/PeakSegOptimal/src/Makevars |only PeakSegOptimal-2018.05.25/PeakSegOptimal/tests/test |only PeakSegOptimal-2018.05.25/PeakSegOptimal/tests/testthat/test-PeakSegFPOP.R |only PeakSegOptimal-2018.05.25/PeakSegOptimal/tests/testthat/test-PeakSegPDPA.R |only PeakSegOptimal-2018.05.25/PeakSegOptimal/tests/testthat/test-PeakSegPDPAInf.R |only PeakSegOptimal-2018.05.25/PeakSegOptimal/tests/testthat/test-simulation.R |only PeakSegOptimal-2024.1.24/PeakSegOptimal/DESCRIPTION | 8 PeakSegOptimal-2024.1.24/PeakSegOptimal/MD5 | 55 PeakSegOptimal-2024.1.24/PeakSegOptimal/NAMESPACE | 8 PeakSegOptimal-2024.1.24/PeakSegOptimal/NEWS | 252 +-- PeakSegOptimal-2024.1.24/PeakSegOptimal/R/PeakSegFPOP.R | 460 +++--- PeakSegOptimal-2024.1.24/PeakSegOptimal/R/PeakSegPDPA.R | 748 +++++----- PeakSegOptimal-2024.1.24/PeakSegOptimal/R/PoissonLoss.R | 78 - PeakSegOptimal-2024.1.24/PeakSegOptimal/R/oracle.R | 20 PeakSegOptimal-2024.1.24/PeakSegOptimal/man/H3K4me3_PGP_immune_chunk24.Rd | 36 PeakSegOptimal-2024.1.24/PeakSegOptimal/man/H3K4me3_XJ_immune_chunk1.Rd | 30 PeakSegOptimal-2024.1.24/PeakSegOptimal/man/PeakSegFPOP.Rd | 34 PeakSegOptimal-2024.1.24/PeakSegOptimal/man/PeakSegFPOPchrom.Rd | 9 PeakSegOptimal-2024.1.24/PeakSegOptimal/man/PeakSegPDPA.Rd | 42 PeakSegOptimal-2024.1.24/PeakSegOptimal/man/PeakSegPDPAInf.Rd | 10 PeakSegOptimal-2024.1.24/PeakSegOptimal/man/PeakSegPDPAchrom.Rd | 7 PeakSegOptimal-2024.1.24/PeakSegOptimal/man/PoissonLoss.Rd | 16 PeakSegOptimal-2024.1.24/PeakSegOptimal/man/oracleModelComplexity.Rd | 9 PeakSegOptimal-2024.1.24/PeakSegOptimal/src/PeakSegFPOPLog.cpp | 6 PeakSegOptimal-2024.1.24/PeakSegOptimal/src/PeakSegFPOPLog.h | 12 PeakSegOptimal-2024.1.24/PeakSegOptimal/src/PeakSegPDPALog.cpp | 6 PeakSegOptimal-2024.1.24/PeakSegOptimal/src/PeakSegPDPALog.h | 2 PeakSegOptimal-2024.1.24/PeakSegOptimal/src/funPieceListLog.h | 1 PeakSegOptimal-2024.1.24/PeakSegOptimal/src/interface.cpp | 19 PeakSegOptimal-2024.1.24/PeakSegOptimal/tests/testthat.R | 4 PeakSegOptimal-2024.1.24/PeakSegOptimal/tests/testthat/test-CRAN-PeakSegFPOP.R |only PeakSegOptimal-2024.1.24/PeakSegOptimal/tests/testthat/test-CRAN-PeakSegPDPA.R |only PeakSegOptimal-2024.1.24/PeakSegOptimal/tests/testthat/test-CRAN-PeakSegPDPAInf.R |only 33 files changed, 915 insertions(+), 957 deletions(-)
More information about PeakSegOptimal at CRAN
Permanent link
Title: Agglomerative Partitioning Framework for Dimension Reduction
Description: A fast and flexible framework for agglomerative partitioning.
'partition' uses an approach called Direct-Measure-Reduce to create
new variables that maintain the user-specified minimum level of
information. Each reduced variable is also interpretable: the original
variables map to one and only one variable in the reduced data set.
'partition' is flexible, as well: how variables are selected to
reduce, how information loss is measured, and the way data is reduced
can all be customized. 'partition' is based on the Partition
framework discussed in Millstein et al. (2020)
<doi:10.1093/bioinformatics/btz661>.
Author: Joshua Millstein [aut],
Malcolm Barrett [aut, cre] ,
Katelyn Queen [aut]
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Diff between partition versions 0.1.4 dated 2021-10-05 and 0.2.0 dated 2024-01-24
DESCRIPTION | 60 - MD5 | 77 +- NAMESPACE | 1 NEWS.md | 6 R/directors.R | 61 - R/mappings.R | 12 R/metrics.R | 46 - R/partition.R | 61 - R/permutation.R | 8 R/plot.R | 66 - R/print.R | 14 R/reducers.R | 62 + R/simulate_block.R | 34 R/super_partition.R |only R/utils.R | 4 README.md | 15 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 8 inst/WORDLIST | 6 inst/doc/extending-partition.R | 61 - inst/doc/extending-partition.Rmd | 31 inst/doc/extending-partition.html | 835 +++++++++++++++------- inst/doc/introduction-to-partition.R | 8 inst/doc/introduction-to-partition.Rmd | 6 inst/doc/introduction-to-partition.html | 874 ++++++++++++++++-------- man/as_measure.Rd | 9 man/as_partition.Rd | 2 man/figures/README-secret_benchmarks1-1.png |binary man/figures/README-secret_benchmarks2-1.png |binary man/figures/README-stacked_area_chart-1.png |binary man/mapping_helpers.Rd | 4 man/super_partition.Rd |only src/Makevars | 3 src/Makevars.win | 3 tests/spelling.R | 9 tests/testthat/helper-df.R | 472 ++++++------ tests/testthat/test-partitioners-helpers-work.R | 9 tests/testthat/test-super-partition-objects.R |only vignettes/extending-partition.Rmd | 31 vignettes/introduction-to-partition.Rmd | 6 41 files changed, 1789 insertions(+), 1115 deletions(-)
Title: Direct Labels for Multicolor Plots
Description: An extensible framework
for automatically placing direct labels onto multicolor 'lattice' or
'ggplot2' plots.
Label positions are described using Positioning Methods
which can be re-used across several different plots.
There are heuristics for examining "trellis" and "ggplot" objects
and inferring an appropriate Positioning Method.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between directlabels versions 2023.8.25 dated 2023-09-01 and 2024.1.21 dated 2024-01-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 4 ++++ R/ggplot2.R | 16 ++++++++++++++++ build/vignette.rds |binary inst/doc/examples.html | 6 +----- 6 files changed, 29 insertions(+), 13 deletions(-)
Title: Robust Principal Component Analysis Using the Cauchy
Distribution
Description: A new robust principal component analysis algorithm is implemented that relies upon the Cauchy Distribution. The algorithm is suitable for high dimensional data even if the sample size is less than the number of variables. The methodology is described in this paper: Fayomi A., Pantazis Y., Tsagris M. and Wood A.T.A. (2024). "Cauchy robust principal component analysis with applications to high-dimensional data sets". Statistics and Computing, 34: 26. <doi:10.1007/s11222-023-10328-x>.
Author: Michail Tsagris [aut, cre],
Aisha Fayomi [ctb],
Yannis Pantazis [ctb],
Andrew T.A. Wood [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between cauchypca versions 1.2 dated 2023-10-22 and 1.3 dated 2024-01-24
DESCRIPTION | 13 ++++++------- MD5 | 12 +++++++----- NAMESPACE | 3 ++- R/cauchy.mle.R |only R/cauchy.pca.R | 18 ++++++++++++------ man/cauchy.mle.Rd |only man/cauchy.pca.Rd | 9 ++++++--- man/cauchypca-package.Rd | 8 ++++---- 8 files changed, 37 insertions(+), 26 deletions(-)
Title: Bayesian Zero-and-One Inflated Dirichlet Regression Modelling
Description: Fits Dirichlet regression and zero-and-one inflated Dirichlet regression with Bayesian methods implemented in Stan. These models are sometimes referred to as trinomial mixture models; covariates and overdispersion can optionally be included.
Author: Eric J. Ward [aut, cre] ,
Alexander J. Jensen [aut] ,
Ryan P. Kelly [aut] ,
Andrew O. Shelton [aut] ,
William H. Satterthwaite [aut]
,
Eric C. Anderson [aut]
Maintainer: Eric J. Ward <eric.ward@noaa.gov>
Diff between zoid versions 1.2.0 dated 2023-09-11 and 1.3.1 dated 2024-01-24
DESCRIPTION | 14 MD5 | 46 - NAMESPACE | 2 NEWS.md | 8 R/fit_prior.R | 28 R/fitting.R | 97 ++ R/get_pars.R | 49 + inst/CITATION | 2 inst/doc/a01_fitting.R | 6 inst/doc/a01_fitting.Rmd | 9 inst/doc/a01_fitting.html | 41 - inst/doc/a02_simulating.R | 2 inst/doc/a02_simulating.html | 4 inst/doc/a03_beta_priors.R | 2 inst/doc/a03_beta_priors.html | 4 inst/doc/a04_priors.R | 2 inst/doc/a04_priors.html | 4 inst/stan/dirichregmod.stan | 61 + man/fit_dirichlet.Rd |only man/fit_zoid.Rd | 12 man/get_pars.Rd | 4 man/parse_re_formula.Rd |only src/Makevars | 2 src/stanExports_dirichregmod.h | 1375 +++++++++++++++++++++++++++-------------- vignettes/a01_fitting.Rmd | 9 25 files changed, 1265 insertions(+), 518 deletions(-)
Title: 'KorAP' Web Service Client Package
Description: A client package that makes the 'KorAP' web service API accessible from R.
The corpus analysis platform 'KorAP' has been developed as a scientific tool to make
potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo'
or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify
hypotheses and to find interesting patterns in real language use.
The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code,
as a programmatic alternative to the 'KorAP' web user-interface.
You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Author: Marc Kupietz [aut, cre],
Nils Diewald [ctb],
Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Diff between RKorAPClient versions 0.7.7 dated 2023-08-08 and 0.8.0 dated 2024-01-24
DESCRIPTION | 10 +-- MD5 | 27 +++++----- NAMESPACE | 2 NEWS.md | 9 +++ R/KorAPCorpusStats.R | 10 ++- R/KorAPQuery.R | 23 +++------ R/collocationAnalysis.R | 74 +++++++++++++++++++++++++++-- R/hc_add_onclick_korap_search.R | 1 R/textMetadata.R |only demo/frequenciesOverDomains.R | 2 demo/regional.R | 2 man/KorAPCorpusStats-class.Rd | 2 man/KorAPQuery-class.Rd | 6 +- man/textMetadata-KorAPConnection-method.Rd |only tests/testthat/test-corpusStats.R | 13 ++++- tests/testthat/test-textMetadata.R |only 16 files changed, 138 insertions(+), 43 deletions(-)
Title: Joint Peak Detection in Several ChIP-Seq Samples
Description: Jointly segment several ChIP-seq samples to find the peaks
which are the same and different across samples. The fast approximate
maximum Poisson likelihood algorithm is described in
"PeakSegJoint: fast supervised peak detection via joint segmentation
of multiple count data samples"
<arXiv:1506.01286> by TD Hocking and G Bourque.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between PeakSegJoint versions 2023.4.24 dated 2023-04-24 and 2024.1.24 dated 2024-01-24
DESCRIPTION | 6 MD5 | 90 - NAMESPACE | 16 NEWS | 318 ++-- R/PeakErrorSamples.R | 72 - R/PeakSegJoint.R | 1514 ++++++++++----------- R/PeakSegJointError.R | 280 +-- R/PoissonLoss.R | 78 - R/binSum.R | 158 +- R/clusterPeaks.R | 92 - R/features.R | 148 +- R/multiClusterPeaks.R | 124 - man/ConvertModelList.Rd | 48 man/H3K27ac.TDH.MMM4.Rd | 42 man/H3K36me3.AM.immune.chunk21.Rd | 38 man/H3K36me3.TDH.other.chunk1.Rd | 44 man/H3K4me3.PGP.immune.chunk2.Rd | 36 man/H3K4me3.TDH.other.chunk8.Rd | 40 man/PeakErrorSamples.Rd | 38 man/PeakSegJointError.Rd | 168 +- man/PeakSegJointFaster.Rd | 112 - man/PeakSegJointFasterOne.Rd | 394 ++--- man/PeakSegJointHeuristic.Rd | 170 +- man/PeakSegJointHeuristicStep1.Rd | 174 +- man/PeakSegJointHeuristicStep2.Rd | 54 man/PeakSegJointSeveral.Rd | 228 +-- man/PoissonLoss.Rd | 61 man/ProfileList.Rd | 40 man/binSum.Rd | 116 - man/chr7.peaks.Rd | 40 man/clusterPeaks.Rd | 84 - man/demo.profiles.Rd | 44 man/featureMatrixJoint.Rd | 53 man/multiClusterPeaks.Rd | 104 - man/overflow.list.Rd | 28 man/peak.at.profile.end.Rd | 30 man/peak1.infeasible.Rd | 28 tests/testthat.R | 8 tests/testthat/test-CRAN-PeakSegJoint.R | 2192 +++++++++++++++---------------- tests/testthat/test-CRAN-binSum.R | 364 ++--- tests/testthat/test-CRAN-converted.R | 36 tests/testthat/test-CRAN-features.R | 30 tests/testthat/test-CRAN-likelihood.R | 320 ++-- tests/testthat/test-CRAN-no-zeros.R | 2248 ++++++++++++++++---------------- tests/testthat/test-CRAN-trivial.R | 122 - tests/testthat/test-CRAN.R | 274 +-- 46 files changed, 5354 insertions(+), 5350 deletions(-)
Title: Dynamic Programming Algorithm for Peak Detection in ChIP-Seq
Data
Description: A quadratic time dynamic programming algorithm
can be used to compute an approximate solution to the problem of
finding the most likely changepoints
with respect to the Poisson likelihood, subject
to a constraint on the number of segments, and the changes which must
alternate: up, down, up, down, etc. For more info read
<http://proceedings.mlr.press/v37/hocking15.html>
"PeakSeg: constrained optimal segmentation and supervised penalty learning
for peak detection in count data" by TD Hocking et al,
proceedings of ICML2015.
Author: Toby Dylan Hocking, Guillem Rigaill
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between PeakSegDP versions 2017.08.15 dated 2017-08-15 and 2024.1.24 dated 2024-01-24
DESCRIPTION | 8 - MD5 | 38 ++-- NAMESPACE | 12 - NEWS | 129 +++++++--------- R/PeakSegDP.R | 226 ++++++++++++++--------------- R/PoissonLoss.R | 78 +++++----- R/cDPA.R | 106 ++++++------- man/H3K36me3.AM.immune.19.Rd | 38 ++-- man/H3K36me3.TDH.other.chunk3.cluster4.Rd | 50 +++--- man/H3K4me3.TDH.immune.chunk12.cluster4.Rd | 36 ++-- man/PeakSegDP.Rd | 5 man/PoissonLoss.Rd | 16 -- man/cDPA.Rd | 5 man/chr11ChIPseq.Rd | 106 ++++++------- man/chr11first.Rd | 130 ++++++++-------- man/getPath.Rd | 5 tests/testthat.R | 4 tests/testthat/test-PoissonLoss.R | 94 ++++++------ tests/testthat/test-small.R | 48 +++--- tests/testthat/test-trivial.R | 132 ++++++++-------- 20 files changed, 631 insertions(+), 635 deletions(-)
Title: Fit a Penalized Continuation Ratio Model for Predicting an
Ordinal Response
Description: Provides a function for fitting a penalized constrained continuation ratio model using the glmpath algorithm and methods for extracting coefficient estimates, predicted class, class probabilities, and plots as described by Archer and Williams (2012) <doi:10.1002/sim.4484>.
Author: Kellie J. Archer [aut, cre] ,
Andre Williams [aut]
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between glmpathcr versions 1.0.9 dated 2023-06-14 and 1.0.10 dated 2024-01-24
DESCRIPTION | 19 ++++++++++++------- MD5 | 12 ++++++------ build/partial.rdb |binary build/vignette.rds |binary data/diabetes.rda |binary inst/doc/glmpathcr.pdf |binary man/glmpathcr-internal.Rd | 3 +-- 7 files changed, 19 insertions(+), 15 deletions(-)
Title: Access Finnish Geospatial Data
Description: Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.
Author: Markus Kainu [aut, cre] ,
Joona Lehtomaki [aut] ,
Juuso Parkkinen [ctb] ,
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Sampo Vesanen [ctb],
Leo Lahti [aut]
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.0.11 dated 2023-12-18 and 1.0.13 dated 2024-01-24
DESCRIPTION | 14 ++--- MD5 | 18 +++---- NEWS.md | 5 ++ inst/doc/geofi_datasets.html | 22 ++++----- inst/doc/geofi_joining_attribute_data.R | 26 +--------- inst/doc/geofi_joining_attribute_data.Rmd | 28 ++--------- inst/doc/geofi_joining_attribute_data.html | 70 ++++++++--------------------- inst/doc/geofi_making_maps.html | 40 ++++++++-------- inst/doc/geofi_spatial_analysis.html | 34 +++++++------- vignettes/geofi_joining_attribute_data.Rmd | 28 ++--------- 10 files changed, 103 insertions(+), 182 deletions(-)
Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Kamil Zyla [aut, cre],
Jakub Nowicki [aut],
Leszek Sieminski [aut],
Marek Rogala [aut],
Recle Vibal [aut],
Tymoteusz Makowski [aut],
Eduardo Almeida [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Kamil Zyla <opensource+kamil@appsilon.com>
Diff between rhino versions 1.5.0 dated 2023-09-06 and 1.6.0 dated 2024-01-24
rhino-1.5.0/rhino/inst/templates/e2e_tests/tests/cypress.json |only rhino-1.5.0/rhino/inst/templates/e2e_tests/tests/cypress/integration |only rhino-1.5.0/rhino/tests/e2e/app-files/hello.spec.js |only rhino-1.6.0/rhino/DESCRIPTION | 6 rhino-1.6.0/rhino/MD5 | 36 rhino-1.6.0/rhino/NEWS.md | 17 rhino-1.6.0/rhino/R/dependencies.R | 37 rhino-1.6.0/rhino/R/node.R | 47 rhino-1.6.0/rhino/R/tools.R | 6 rhino-1.6.0/rhino/inst/WORDLIST | 7 rhino-1.6.0/rhino/inst/templates/e2e_tests/tests/cypress.config.js |only rhino-1.6.0/rhino/inst/templates/e2e_tests/tests/cypress/e2e |only rhino-1.6.0/rhino/inst/templates/github_ci/dot.github/workflows/rhino-test.yml | 44 rhino-1.6.0/rhino/inst/templates/node/dot.stylelintrc.json | 11 rhino-1.6.0/rhino/inst/templates/node/package-lock.json | 9327 +++++----- rhino-1.6.0/rhino/inst/templates/node/package.json | 31 rhino-1.6.0/rhino/man/dependencies.Rd | 12 rhino-1.6.0/rhino/man/test_e2e.Rd | 4 rhino-1.6.0/rhino/tests/e2e/app-files/hello.cy.js |only rhino-1.6.0/rhino/tests/e2e/test-custom-npm.R |only rhino-1.6.0/rhino/tests/e2e/test-dependencies.R | 57 rhino-1.6.0/rhino/tests/e2e/test-lint-sass.R | 4 rhino-1.6.0/rhino/tests/testthat/test-dependencies.R |only 23 files changed, 5164 insertions(+), 4482 deletions(-)
Title: Risk-Adjusted Regression
Description: Perform risk-adjusted regression and sensitivity analysis as
developed in "Mitigating Omitted- and Included-Variable Bias in Estimates of
Disparate Impact" Jung et al. (2024) <arXiv:1809.05651>.
Author: Johann Gaebler [aut, cre, cph]
Maintainer: Johann Gaebler <me@jgaeb.com>
Diff between rar versions 0.0.2 dated 2024-01-18 and 0.0.3 dated 2024-01-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/cpp11.cpp | 2 +- tests/testthat/test-sens.R | 4 ++++ 5 files changed, 16 insertions(+), 8 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.filesets versions 2.15.0 dated 2022-07-21 and 2.15.1 dated 2024-01-24
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- NEWS.md | 7 +++++++ R/ChecksumFile.R | 1 - R/GenericDataFile.R | 9 ++------- R/GenericDataFileSet.PARALLEL.R | 2 +- R/GenericTabularFile.R | 4 ---- man/GenericDataFile.Rd | 2 +- man/compareChecksum.GenericDataFile.Rd | 3 +-- man/dim.GenericTabularFile.Rd | 4 ---- man/dsApplyInPairs.GenericDataFileSet.Rd | 2 +- man/fromFile.GenericDataFile.Rd | 2 -- man/gzip.GenericDataFile.Rd | 1 - man/readChecksum.ChecksumFile.Rd | 1 - man/writeChecksum.GenericDataFile.Rd | 1 - tests/TabularTextFileSet.R | 27 +++++++++++++++++++++++++-- 16 files changed, 56 insertions(+), 46 deletions(-)
Title: Bayesian Meta-Analysis and Network Meta-Analysis
Description: Contains functions performing Bayesian inference for meta-analytic and network meta-analytic models through Markov chain Monte Carlo algorithm. Currently, the package implements Hui Yao, Sungduk Kim, Ming-Hui Chen, Joseph G. Ibrahim, Arvind K. Shah, and Jianxin Lin (2015) <doi:10.1080/01621459.2015.1006065> and Hao Li, Daeyoung Lim, Ming-Hui Chen, Joseph G. Ibrahim, Sungduk Kim, Arvind K. Shah, Jianxin Lin (2021) <doi:10.1002/sim.8983>. For maximal computational efficiency, the Markov chain Monte Carlo samplers for each model, written in C++, are fine-tuned. This software has been developed under the auspices of the National Institutes of Health and Merck & Co., Inc., Kenilworth, NJ, USA.
Author: Daeyoung Lim [aut, cre],
Ming-Hui Chen [ctb],
Sungduk Kim [ctb],
Joseph Ibrahim [ctb],
Arvind Shah [ctb],
Jianxin Lin [ctb]
Maintainer: Daeyoung Lim <Daeyoung.Lim@fda.hhs.gov>
Diff between metapack versions 0.2.0 dated 2022-05-30 and 0.3 dated 2024-01-24
metapack-0.2.0/metapack/README.md |only metapack-0.3/metapack/DESCRIPTION | 14 metapack-0.3/metapack/MD5 | 27 metapack-0.3/metapack/NEWS.md | 14 metapack-0.3/metapack/R/meta_analyze.R | 2 metapack-0.3/metapack/R/zzz.R | 2 metapack-0.3/metapack/build/vignette.rds |binary metapack-0.3/metapack/inst/CITATION | 35 metapack-0.3/metapack/inst/doc/intro-to-metapack.R | 12 metapack-0.3/metapack/inst/doc/intro-to-metapack.html | 825 ++++++++++++++---- metapack-0.3/metapack/src/Makevars | 2 metapack-0.3/metapack/src/Makevars.win | 2 metapack-0.3/metapack/src/fmodel3.cpp | 166 ++- metapack-0.3/metapack/src/fmodel3pp.cpp | 90 + metapack-0.3/metapack/src/loglik_POCov.cpp | 4 15 files changed, 877 insertions(+), 318 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new
approach to the statistical analysis of multi-valued data, we consider
histogram-valued data, i.e., data described by univariate histograms. The
methods and the basic statistics for histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., the Euclidean metric
between quantile functions. The package contains unsupervised classification
techniques, least square regression and tools for histogram-valued data and for
histogram time series. An introducing paper is Irpino A. Verde R. (2015) <doi: 10.1007/s11634-014-0176-4>.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unicampania.it>
Diff between HistDAWass versions 1.0.7 dated 2022-09-26 and 1.0.8 dated 2024-01-24
DESCRIPTION | 12 +++++----- MD5 | 27 +++++++++++----------- NAMESPACE | 1 R/HistDAWass-package.R | 12 +++++----- R/Met_HTS.R | 38 -------------------------------- R/Plotting_with_ggplot.R | 52 +++++++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary data/HData.RData |binary man/China_Month.Rd | 2 - man/China_Seas.Rd | 2 - man/HistDAWass-package.Rd | 6 ++--- man/stations_coordinates.Rd | 2 - man/summaryHTS.Rd |only src/Makevars | 1 src/Makevars.win | 1 15 files changed, 85 insertions(+), 71 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <arXiv:1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.1.2 dated 2023-12-21 and 2.2.0 dated 2024-01-24
DESCRIPTION | 12 - MD5 | 100 +++++++------ NAMESPACE | 5 NEWS.md | 16 +- R/calc_shape_dist.R | 100 ++++++++----- R/curve_depth.R |only R/curve_functions.R | 57 ++++--- R/curve_geodesic.R | 8 - R/curve_karcher_cov.R | 21 +- R/curve_karcher_mean.R | 289 +++++++++++++++++++------------------- R/curve_pair_align.R | 48 +++--- R/curve_principal_directions.R | 14 + R/curve_srvf_align.R | 34 ++-- R/curve_to_q.R | 20 +- R/elastic.depth.R | 25 +-- R/elastic.distance.R | 19 +- R/f_to_srvf.R | 62 +------- R/fdasrvf-package.R | 5 R/horizFPCA.R | 18 +- R/jointfPCA.R | 29 ++- R/kmeans.R | 138 ++++++++++++------ R/multivariate_karcher_mean.R |only R/optimum.reparam.R | 10 - R/predict.hfpca.R |only R/predict.jfpca.R |only R/predict.vfpca.R |only R/q_to_curve.R | 6 R/reparam_curve.R | 24 +-- R/srvf_to_f.R | 82 ++-------- R/vertFPCA.R | 16 +- README.md | 8 - man/calc_shape_dist.Rd | 38 ++++ man/curve_depth.Rd |only man/curve_geodesic.Rd | 8 - man/curve_karcher_cov.Rd | 5 man/curve_karcher_mean.Rd | 23 +-- man/curve_pair_align.Rd | 20 +- man/curve_principal_directions.Rd | 11 - man/curve_srvf_align.Rd | 17 +- man/curve_to_q.Rd | 17 +- man/elastic.depth.Rd | 22 +- man/elastic.distance.Rd | 17 +- man/f_to_srvf.Rd | 27 +-- man/fdasrvf.Rd | 21 ++ man/horizFPCA.Rd | 5 man/jointFPCA.Rd | 8 - man/kmeans_align.Rd | 27 ++- man/multivariate_karcher_mean.Rd |only man/optimum.reparam.Rd | 6 man/predict.hfpca.Rd |only man/predict.jfpca.Rd |only man/predict.vfpca.Rd |only man/q_to_curve.Rd | 6 man/reparam_curve.Rd | 24 +-- man/srvf_to_f.Rd | 31 +--- man/vertFPCA.Rd | 6 56 files changed, 849 insertions(+), 656 deletions(-)
Title: Statistical Tools for Ranks
Description: Account for uncertainty when working with ranks.
Estimate standard errors consistently in linear regression with ranked variables.
Construct confidence sets of various kinds for positions of populations in a ranking
based on values of a certain feature and their estimation errors.
Theory based on Mogstad, Romano, Shaikh, and Wilhelm (2023)<doi:10.1093/restud/rdad006> and
Chetverikov and Wilhelm (2023) <arXiv:2310.15512>.
Author: Daniel Wilhelm [aut, cre],
Pawel Morgen [aut]
Maintainer: Daniel Wilhelm <d.wilhelm@lmu.de>
Diff between csranks versions 1.2.1 dated 2023-12-16 and 1.2.2 dated 2024-01-24
csranks-1.2.1/csranks/LICENSE |only csranks-1.2.2/csranks/DESCRIPTION | 8 ++++---- csranks-1.2.2/csranks/MD5 | 7 +++---- csranks-1.2.2/csranks/NEWS.md | 3 +++ csranks-1.2.2/csranks/inst/doc/Inference-for-Ranks.html | 4 ++-- 5 files changed, 12 insertions(+), 10 deletions(-)
Title: Load Census TIGER/Line Shapefiles
Description: Download TIGER/Line shapefiles from the United States Census Bureau
(<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>)
and load into R as 'sf' objects.
Author: Kyle Walker [aut, cre],
Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tigris versions 2.0.4 dated 2023-09-22 and 2.1 dated 2024-01-24
DESCRIPTION | 8 +- MD5 | 102 ++++++++++++++--------------- R/enumeration_units.R | 14 +-- R/helpers.R | 4 - R/landmarks.R | 4 - R/legislative.R | 40 +++++++---- R/metro_areas.R | 10 +- R/national.R | 6 - R/native.R | 10 +- R/places.R | 2 R/pumas.R | 2 R/tigris-package.R | 2 R/transportation.R | 10 +- R/water.R | 4 - man/address_ranges.Rd | 2 man/alaska_native_regional_corporations.Rd | 2 man/area_water.Rd | 2 man/block_groups.Rd | 2 man/blocks.Rd | 2 man/coastline.Rd | 2 man/combined_statistical_areas.Rd | 2 man/congressional_districts.Rd | 8 +- man/core_based_statistical_areas.Rd | 2 man/counties.Rd | 2 man/county_subdivisions.Rd | 2 man/divisions.Rd | 2 man/landmarks.Rd | 2 man/linear_water.Rd | 2 man/load_tiger_doc_template.Rd | 2 man/metro_divisions.Rd | 2 man/military.Rd | 2 man/nation.Rd | 2 man/native_areas.Rd | 2 man/new_england.Rd | 2 man/places.Rd | 2 man/primary_roads.Rd | 2 man/primary_secondary_roads.Rd | 2 man/pumas.Rd | 2 man/rails.Rd | 2 man/regions.Rd | 2 man/roads.Rd | 2 man/school_districts.Rd | 2 man/state_legislative_districts.Rd | 2 man/states.Rd | 2 man/tigris.Rd | 2 man/tracts.Rd | 2 man/tribal_block_groups.Rd | 2 man/tribal_census_tracts.Rd | 2 man/tribal_subdivisions_national.Rd | 2 man/urban_areas.Rd | 2 man/voting_districts.Rd | 2 man/zctas.Rd | 2 52 files changed, 158 insertions(+), 142 deletions(-)
Title: Repeatable Analysis in R
Description: Set of utilities to facilitate the reproduction of analysis in R.
It allow to make_structure(), clean_structure(), and run and log programs in a
predefined order to allow secondary files, analysis and reports be constructed in
an ordered and reproducible form.
Author: John J. Aponte [aut, cre]
Maintainer: John J. Aponte <john.j.aponte@gmail.com>
Diff between repana versions 1.23.2 dated 2021-09-20 and 2.0.0 dated 2024-01-24
repana-1.23.2/repana/R/master_spin.R |only repana-1.23.2/repana/R/repana.R |only repana-1.23.2/repana/inst/doc/using_repana.R |only repana-1.23.2/repana/inst/doc/using_repana.Rmd |only repana-1.23.2/repana/inst/doc/using_repana.html |only repana-1.23.2/repana/man/master_spin.Rd |only repana-1.23.2/repana/man/repana.Rd |only repana-1.23.2/repana/tests/testthat/test_master_spin.R |only repana-1.23.2/repana/vignettes/using_repana.Rmd |only repana-2.0.0/repana/DESCRIPTION | 19 - repana-2.0.0/repana/MD5 | 72 +++--- repana-2.0.0/repana/NAMESPACE | 5 repana-2.0.0/repana/NEWS.md | 170 ++++++++++---- repana-2.0.0/repana/R/master.R | 202 +++++++++++------ repana-2.0.0/repana/R/master_txt.R |only repana-2.0.0/repana/R/repana-package.R |only repana-2.0.0/repana/R/structure.R | 49 ++-- repana-2.0.0/repana/R/template.R | 8 repana-2.0.0/repana/README.md | 194 +++------------- repana-2.0.0/repana/build/vignette.rds |binary repana-2.0.0/repana/inst/WORDLIST | 13 + repana-2.0.0/repana/inst/doc/database.R |only repana-2.0.0/repana/inst/doc/database.Rmd |only repana-2.0.0/repana/inst/doc/database.html |only repana-2.0.0/repana/inst/doc/reports.R |only repana-2.0.0/repana/inst/doc/reports.Rmd |only repana-2.0.0/repana/inst/doc/reports.html |only repana-2.0.0/repana/inst/doc/structure.R |only repana-2.0.0/repana/inst/doc/structure.Rmd |only repana-2.0.0/repana/inst/doc/structure.html |only repana-2.0.0/repana/inst/doc/template.R |only repana-2.0.0/repana/inst/doc/template.Rmd |only repana-2.0.0/repana/inst/doc/template.html |only repana-2.0.0/repana/inst/rstudio/addins.dcf | 4 repana-2.0.0/repana/inst/templates/template_spin.txt | 44 --- repana-2.0.0/repana/man/make_structure.Rd | 10 repana-2.0.0/repana/man/master.Rd | 32 +- repana-2.0.0/repana/man/master_txt.Rd |only repana-2.0.0/repana/man/render_report.Rd | 2 repana-2.0.0/repana/man/repana-package.Rd |only repana-2.0.0/repana/tests/testthat/02_prog_a.R | 10 repana-2.0.0/repana/tests/testthat/03_prog_b.R | 10 repana-2.0.0/repana/tests/testthat/04_prog_c.R | 10 repana-2.0.0/repana/tests/testthat/05_prog_d.R | 12 - repana-2.0.0/repana/tests/testthat/test_get_con.R | 6 repana-2.0.0/repana/tests/testthat/test_master.R | 70 ++++- repana-2.0.0/repana/tests/testthat/test_master_txt.R |only repana-2.0.0/repana/tests/testthat/test_structure.R | 7 repana-2.0.0/repana/vignettes/database.Rmd |only repana-2.0.0/repana/vignettes/reports.Rmd |only repana-2.0.0/repana/vignettes/structure.Rmd |only repana-2.0.0/repana/vignettes/template.Rmd |only 52 files changed, 517 insertions(+), 432 deletions(-)
Title: Mixed Models for Repeated Measures
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see Cnaan, Laird and Slasor (1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>
for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso
(2008) <doi:10.1177/009286150804200402> for a review. This package
implements MMRM based on the marginal linear model without random
effects using Template Model Builder ('TMB') which enables fast and
robust model fitting. Users can specify a variety of covariance
matrices, weight observations, fit models with restricted or standard
maximum likelihood inference, perform hypothesis testing with
Satterthwaite or Kenward-Roger adjustment, and extract least square
means estimates by using 'emmeans'.
Author: Daniel Sabanes Bove [aut, cre],
Julia Dedic [aut],
Doug Kelkhoff [aut],
Kevin Kunzmann [aut],
Brian Matthew Lang [aut],
Liming Li [aut],
Christian Stock [aut],
Ya Wang [aut],
Craig Gower-Page [ctb],
Dan James [aut],
Jonathan Sidi [aut],
Daniel Leibov [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@roche.com>
Diff between mmrm versions 0.3.7 dated 2023-12-08 and 0.3.8 dated 2024-01-24
DESCRIPTION | 40 MD5 | 127 NAMESPACE | 3 NEWS.md | 19 R/fit.R | 23 R/interop-car.R |only R/mmrm-methods.R | 34 R/skipping.R |only R/testing.R | 10 R/tmb.R | 26 R/utils.R | 138 R/zzz.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 11 inst/WORDLIST | 1 inst/doc/algorithm.Rmd | 2 inst/doc/algorithm.html | 317 + inst/doc/between_within.html | 415 +- inst/doc/coef_vcov.Rmd | 2 inst/doc/coef_vcov.html | 139 inst/doc/covariance.html | 310 + inst/doc/empirical_wls.html | 232 - inst/doc/hypothesis_testing.R |only inst/doc/hypothesis_testing.Rmd |only inst/doc/hypothesis_testing.html |only inst/doc/introduction.R | 59 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 3970 +++++++++++--------- inst/doc/kenward.html | 379 + inst/doc/methodological_introduction.html | 281 + inst/doc/mmrm_review_methods.Rmd | 12 inst/doc/mmrm_review_methods.html | 339 + inst/doc/package_structure.Rmd | 2 inst/doc/package_structure.html | 283 - inst/doc/predict.Rmd | 2 inst/doc/predict.html | 284 + inst/doc/satterthwaite.html | 262 + man/Anova.mmrm.Rd |only man/car_add_mmrm.Rd |only man/emp_start.Rd |only man/h_get_contrast.Rd |only man/h_get_theta_from_cov.Rd |only man/h_register_s3.Rd |only man/mmrm-package.Rd | 1 man/mmrm_control.Rd | 11 man/mmrm_methods.Rd | 11 man/std_start.Rd |only src/utils.h | 6 tests/testthat/_snaps/car.md |only tests/testthat/_snaps/kenwardroger.md | 1167 ++--- tests/testthat/helper-examples.R | 19 tests/testthat/helper-skipping.R |only tests/testthat/test-between-within.R | 4 tests/testthat/test-car.R |only tests/testthat/test-emmeans.R | 3 tests/testthat/test-fit.R | 124 tests/testthat/test-mmrm-methods.R | 77 tests/testthat/test-satterthwaite.R | 4 tests/testthat/test-skipping.R |only tests/testthat/test-testing.R | 9 tests/testthat/test-tmb-methods.R | 92 tests/testthat/test-tmb.R | 2 tests/testthat/test-utils.R | 95 vignettes/algorithm.Rmd | 2 vignettes/coef_vcov.Rmd | 2 vignettes/hypothesis_testing.Rmd |only vignettes/introduction.Rmd | 2 vignettes/mmrm_review_methods.Rmd | 12 vignettes/package_structure.Rmd | 2 vignettes/predict.Rmd | 2 vignettes/subsections/_intro-customizations.Rmd | 79 vignettes/subsections/_intro-hypothesis_testing.Rmd | 30 73 files changed, 6073 insertions(+), 3412 deletions(-)
Title: Read Data from 'LimeSurvey'
Description: Read data from 'LimeSurvey'
(<https://www.limesurvey.org/>)
in a comfortable way.
Heavily inspired by 'limer'
(<https://github.com/cloudyr/limer/>),
which lacked a few comfort features for me.
Author: Maximilian Hagspiel [aut, cre, cph]
Maintainer: Maximilian Hagspiel <maxhag@mailbox.org>
Diff between ipanema versions 0.6.5 dated 2023-12-20 and 0.6.6 dated 2024-01-24
DESCRIPTION | 6 +++--- MD5 | 5 +++-- R/connect_to_limesurvey.R | 12 +++++------- README.md |only 4 files changed, 11 insertions(+), 12 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting absences under specified criteria, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially described in Barbosa (2015) <doi:10.1111/2041-210X.1237 [...truncated...]
Author: Barbosa A.M.
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.10.5 dated 2023-10-09 and 4.10.7 dated 2024-01-24
DESCRIPTION | 13 +++++-------- MD5 | 30 +++++++++++++++--------------- NEWS | 45 ++++++++++++++++++++++++++++++++++++++++++--- R/corSelect.R | 6 ++++-- R/distPres.R | 4 ++-- R/selectAbsences.R | 8 ++++---- data/rotif.env.rda |binary data/rotifers.rda |binary man/appendData.Rd | 4 +++- man/corSelect.Rd | 4 ++-- man/distPres.Rd | 18 +++++++++--------- man/fuzSim.Rd | 5 +++++ man/fuzzySim-package.Rd | 4 ++-- man/multTSA.Rd | 8 ++++---- man/selectAbsences.Rd | 6 ++++-- man/sharedFav.Rd | 6 +++--- 16 files changed, 104 insertions(+), 57 deletions(-)
Title: Extracts the Backbone from Graphs
Description: An implementation of methods for extracting an unweighted unipartite
graph (i.e. a backbone) from an unweighted unipartite graph, a weighted unipartite
graph, the projection of an unweighted bipartite graph, or the projection
of a weighted bipartite graph (Neal, 2022 <doi:10.1371/journal.pone.0269137>).
Author: Zachary Neal [aut, cre] ,
Rachel Domagalski [aut],
Bruce Sagan [ctb],
Karl Godard [ctb]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between backbone versions 2.1.2 dated 2023-02-13 and 2.1.3 dated 2024-01-24
DESCRIPTION | 11 - MD5 | 75 +++++---- NAMESPACE | 3 NEWS.md | 8 + R/backbone.R | 1 R/backbone.extract.R | 23 +- R/disparity.R | 36 ++-- R/fastball.R | 10 + R/fdsm.R | 52 +++--- R/fixedcol.R | 20 +- R/fixedfill.R | 20 +- R/fixedrow.R | 22 +- R/global.R | 32 ++-- R/lans.R |only R/logit.R |only R/mlf.R |only R/osdsm.R | 44 ++--- R/sdsm.R | 70 ++++++-- R/sparsify.R | 184 +++++++++++------------ R/utils.R | 40 ++++- R/write.narrative.R | 36 +++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/backbone.R | 8 - inst/doc/backbone.html | 329 +++++++++++++++++++++--------------------- inst/tinytest/test_backbone.R | 47 ++++-- man/backbone.Rd | 1 man/backbone.extract.Rd | 15 - man/disparity.Rd | 19 +- man/fdsm.Rd | 25 +-- man/fixedcol.Rd | 14 + man/fixedfill.Rd | 14 + man/fixedrow.Rd | 14 + man/global.Rd | 26 +-- man/lans.Rd |only man/logit.Rd |only man/mlf.Rd |only man/osdsm.Rd | 30 ++- man/sdsm.Rd | 27 ++- man/sparsify.Rd | 19 +- man/trials.needed.Rd |only man/write.narrative.Rd | 48 +++--- 42 files changed, 747 insertions(+), 576 deletions(-)
Title: Statistical Tools for Topological Data Analysis
Description: Tools for the statistical analysis of persistent homology and for
density clustering. For that, this package provides an R interface for the
efficient algorithms of the C++ libraries 'GUDHI' <https://project.inria.fr/gudhi/software/>, 'Dionysus' <https://www.mrzv.org/software/dionysus/>, and 'PHAT' <https://bitbucket.org/phat-code/phat/>. This package also implements the methods in Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2014) <doi:10.1145/2582112.2582128> for analyzing the statistical significance of persistent homology features.
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria,
David L. Millman, Vincent Rouvreau.
Maintainer: Jisu Kim <jkim82133@snu.ac.kr>
Diff between TDA versions 1.9 dated 2023-02-04 and 1.9.1 dated 2024-01-24
DESCRIPTION | 10 - MD5 | 22 ++-- NEWS | 4 README.md | 2 inst/doc/article.pdf |binary man/TDA-package.Rd | 4 man/silhouette.Rd | 4 src/boost/container/detail/copy_move_algo.hpp | 85 +++++++--------- src/boost/container/detail/flat_tree.hpp | 60 ++++++----- src/boost/container/flat_map.hpp | 2 src/boost/container/vector.hpp | 138 +++++++++++++++++++------- src/topology/static-persistence.h | 14 ++ 12 files changed, 215 insertions(+), 130 deletions(-)
Title: R API for 'Date' and 'Datetime'
Description: Access to the C-level R date and 'datetime' code is provided for
C-level API use by other packages via registration of native functions.
Client packages simply include a single header 'RApiDatetime.h' provided
by this package, and also 'import' it. The R Core group is the original
author of the code made available with slight modifications by this package.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RApiDatetime versions 0.0.8 dated 2023-01-14 and 0.0.9 dated 2024-01-24
ChangeLog | 10 ++++++++++ DESCRIPTION | 9 +++++---- MD5 | 15 ++++++++------- README.md | 2 +- build |only inst/NEWS.Rd | 7 +++++++ man/RApiDatetime-package.Rd | 35 ++++++----------------------------- src/Makevars.win | 1 - src/datetime.c | 6 +----- 9 files changed, 38 insertions(+), 47 deletions(-)
Title: Metric Halfspace Depth
Description: Metric halfspace depth for object data, generalizing Tukey's depth for Euclidean data. Implementing the method described in Dai and Lopez-Pintado (2022) <doi:10.1080/01621459.2021.2011298>.
Author: Xiongtao Dai [aut, cre]
Maintainer: Xiongtao Dai <xiongtao.dai@hotmail.com>
Diff between MHD versions 0.1.1 dated 2023-04-24 and 0.1.2 dated 2024-01-24
MHD-0.1.1/MHD/R/pkgname.R |only MHD-0.1.1/MHD/man/Rpackage-package.Rd |only MHD-0.1.2/MHD/DESCRIPTION | 14 +++++++------- MHD-0.1.2/MHD/MD5 | 8 ++++---- MHD-0.1.2/MHD/R/MHD-package.R |only MHD-0.1.2/MHD/build |only MHD-0.1.2/MHD/man/MHD.Rd | 12 ++++++++++-- 7 files changed, 21 insertions(+), 13 deletions(-)
Title: Manage Spatial Metadata for Known Locations
Description: Utility functions for discovering and managing metadata
associated with spatially unique "known locations". Applications include
all fields of environmental monitoring (e.g. air and water quality) where
data are collected at stationary sites.
Author: Jonathan Callahan [aut, cre],
Eli Grosman [ctb],
Oliver Fogelin [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaLocationUtils versions 0.4.1 dated 2023-10-30 and 0.4.3 dated 2024-01-24
DESCRIPTION | 8 MD5 | 26 +-- NEWS.md | 10 + R/location_createID.R | 16 + R/location_getSingleElevation_USGS.R | 48 +---- R/table_addClustering.R | 1 R/table_getNearestLocation.R | 10 - R/table_save.R | 78 +++++---- R/utils.R | 6 inst/doc/Developer_Style_Guide.html | 14 - inst/doc/MazamaLocationUtils.html | 275 +++++++++++++++----------------- man/location_createID.Rd | 2 man/location_getSingleElevation_USGS.Rd | 8 man/table_save.Rd | 10 - 14 files changed, 267 insertions(+), 245 deletions(-)
More information about MazamaLocationUtils at CRAN
Permanent link
Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where
G is a weighted sum of genetic variants (genetic score) and E is a weighted
sum of environments (environmental score) using the alternating optimization algorithm
by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. This approach has greatly
enhanced predictive power over traditional GxE models which include only a single
genetic variant and a single environmental exposure. Although this approach was
originally made for GxE modelling, it is flexible and does not require the use of
genetic and environmental variables. It can also handle more than 2 latent variables
(rather than just G and E) and 3-way interactions or more. The LEGIT model produces
highly interpretable results and is very parameter-efficient thus it can even be
used with small sample sizes (n < 250). Tools to determine the type of interaction
(vantage sensitivity, diathesis-stress or differential susceptibility), with any
number of genetic vari [...truncated...]
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Diff between LEGIT versions 1.4.0 dated 2022-01-11 and 1.4.1 dated 2024-01-24
DESCRIPTION | 12 MD5 | 94 +++--- NAMESPACE | 4 R/LEGIT.R | 68 ++-- build/vignette.rds |binary inst/doc/ElasticNet.html | 271 ++++++++++------- inst/doc/GxE_testing.R | 4 inst/doc/GxE_testing.Rmd | 2 inst/doc/GxE_testing.html | 295 +++++++++++-------- inst/doc/LEGIT.html | 481 ++++++++++++++++++------------- man/GxE_interaction_RoS.Rd | 124 +++---- man/GxE_interaction_test.Rd | 284 +++++++++--------- man/IMLEGIT.Rd | 120 +++---- man/IMLEGIT_cv.Rd | 176 +++++------ man/IMLEGIT_net.Rd | 164 +++++----- man/IMLEGIT_to_LEGIT.Rd | 110 +++---- man/LEGIT.Rd | 168 +++++----- man/LEGIT_cv.Rd | 212 ++++++------- man/LEGIT_to_IMLEGIT.Rd | 110 +++---- man/backward_step.Rd | 75 +++- man/backward_step_IM.Rd | 72 ++-- man/best_model.Rd | 38 +- man/best_model.elastic_net_var_select.Rd | 110 +++---- man/bootstrap_var_select.Rd | 222 +++++++------- man/elastic_net_var_select.Rd | 238 +++++++-------- man/example_2way.Rd | 76 ++-- man/example_3way.Rd | 78 ++--- man/example_3way_3latent.Rd | 82 ++--- man/example_with_crossover.Rd | 130 ++++---- man/forward_step.Rd | 76 +++- man/forward_step_IM.Rd | 73 +++- man/genetic_var_select.Rd | 202 ++++++------- man/longitudinal_folds.Rd | 86 ++--- man/nes_var_select.Rd | 192 ++++++------ man/plot.LEGIT.Rd | 168 +++++----- man/plot.elastic_net_var_select.Rd | 114 +++---- man/predict.IMLEGIT.Rd | 64 ++-- man/predict.LEGIT.Rd | 66 ++-- man/r1nes_var_select.Rd | 192 ++++++------ man/rGE.IMLEGIT.Rd | 82 ++--- man/rGE.LEGIT.Rd | 60 +-- man/rGE.Rd | 32 +- man/stepwise_search.Rd | 252 ++++++++-------- man/stepwise_search_IM.Rd | 220 +++++++------- man/summary.IMLEGIT.Rd | 48 +-- man/summary.LEGIT.Rd | 48 +-- man/summary.elastic_net_var_select.Rd | 106 +++--- vignettes/GxE_testing.Rmd | 2 48 files changed, 3109 insertions(+), 2794 deletions(-)
Title: Korea Investment & Securities (KIS) Open Trading API
Description: API Wrapper to use Korea Investment & Securities (KIS) trading
system that provides various financial services like stock price
check, orders and balance check
<https://apiportal.koreainvestment.com/>.
Author: Seokhoon Joo [aut, cre]
Maintainer: Seokhoon Joo <seokhoonj@gmail.com>
Diff between kisopenapi versions 0.0.1 dated 2024-01-24 and 0.0.2 dated 2024-01-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 10 ++++++++-- R/env.R | 2 +- R/revise.R | 4 +++- 5 files changed, 19 insertions(+), 11 deletions(-)
Title: Analyze and Create Elegant Directed Acyclic Graphs
Description: Tidy, analyze, and plot directed acyclic graphs (DAGs).
'ggdag' is built on top of 'dagitty', an R package that uses the
'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing
DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using
'ggplot2' and 'ggraph', as well as common analytic and graphical
functions, such as determining adjustment sets and node relationships.
Author: Malcolm Barrett [aut, cre]
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Diff between ggdag versions 0.2.10 dated 2023-05-28 and 0.2.11 dated 2024-01-24
DESCRIPTION | 10 MD5 | 144 ++-- NAMESPACE | 16 NEWS.md | 7 R/StatsandGeoms.R | 69 -- R/adjustment_sets.R | 25 R/as_tbl_graph.R | 5 R/canonical.R | 4 R/colliders.R | 38 - R/dag_labels.R | 19 R/dagify.R | 28 R/dplyr_methods.R | 46 - R/drelationship.R | 100 +- R/equivalence.R | 36 - R/exogenous.R | 11 R/geom_dag.R | 77 ++ R/ggdag.R | 4 R/instrumental.R | 45 - R/layouts.R | 84 ++ R/paths.R | 14 R/pull.R |only R/quick_plots.R | 2 R/relations.R | 124 ++- R/simulate_data.R | 2 R/status.R | 28 R/tidy_dag.R | 216 ++++-- R/utils.R | 19 README.md | 2 build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/bias-structures.R | 4 inst/doc/bias-structures.Rmd | 2 inst/doc/bias-structures.html | 342 +++++----- inst/doc/intro-to-dags.R | 10 inst/doc/intro-to-dags.Rmd | 2 inst/doc/intro-to-dags.html | 160 ++-- inst/doc/intro-to-ggdag.html | 300 ++++---- man/adjustment_sets.Rd | 2 man/as_tidy_dagitty.Rd |only man/canonicalize.Rd | 2 man/colliders.Rd | 2 man/control_for.Rd | 2 man/d_relationship.Rd | 2 man/dag.Rd | 2 man/equivalent.Rd | 6 man/exogenous.Rd | 2 man/figures/ggdag_geoms-1.png |binary man/figures/logo.png |only man/geom_dag_label.Rd |only man/ggdag-package.Rd | 6 man/ggdag.Rd | 2 man/instrumental.Rd | 2 man/paths.Rd | 2 man/pull_dag.Rd |only man/quick_plot.Rd | 2 man/status.Rd | 2 man/tidy_dagitty.Rd | 4 man/time_ordered_coords.Rd | 31 man/variable_family.Rd | 2 tests/testthat/_snaps/StatsandGeoms.md |only tests/testthat/_snaps/colliders/ggdag-collider-highlights-m.svg | 10 tests/testthat/_snaps/equivalence/ggdag-equivalent-class-plots-all-reversible-edges.svg | 68 + tests/testthat/_snaps/equivalence/ggdag-equivalent-class-plots-labels.svg | 314 ++++----- tests/testthat/_snaps/equivalence/ggdag-equivalent-dags-plots-6-equivalent-dags.svg | 342 +++++----- tests/testthat/_snaps/geom_dag/geom-dag-label-labels.svg |only tests/testthat/test-StatsandGeoms.R | 10 tests/testthat/test-as_tbl_graph.R | 2 tests/testthat/test-dag_labels.R | 8 tests/testthat/test-dplyr_methods.R | 2 tests/testthat/test-equivalence.R | 2 tests/testthat/test-exogenous.R | 5 tests/testthat/test-geom_dag.R | 18 tests/testthat/test-layouts.R | 33 tests/testthat/test-pull.R |only tests/testthat/test-tidy_dag.R | 99 ++ vignettes/bias-structures.Rmd | 2 vignettes/intro-to-dags.Rmd | 2 77 files changed, 1793 insertions(+), 1194 deletions(-)
Title: Fast Change Point Detection via Sequential Gradient Descent
Description: Implements fast change point detection algorithm based on the
paper "Sequential Gradient Descent and Quasi-Newton's Method for
Change-Point Analysis" by Xianyang Zhang, Trisha Dawn
<https://proceedings.mlr.press/v206/zhang23b.html>. The algorithm is
based on dynamic programming with pruning and sequential gradient
descent. It is able to detect change points a magnitude faster than
the vanilla Pruned Exact Linear Time(PELT). The package includes
examples of linear regression, logistic regression, Poisson
regression, penalized linear regression data, and whole lot more
examples with custom cost function in case the user wants to use their
own cost function.
Author: Xingchi Li [aut, cre, cph] ,
Xianyang Zhang [aut, cph],
Trisha Dawn [aut, cph]
Maintainer: Xingchi Li <anthony.li@stat.tamu.edu>
Diff between fastcpd versions 0.10.1 dated 2024-01-09 and 0.10.3 dated 2024-01-24
DESCRIPTION | 8 MD5 | 124 ++-- NEWS.md | 18 README.md | 22 inst/doc/comparison-packages.R | 18 inst/doc/comparison-packages.Rmd | 24 inst/doc/comparison-packages.html | 533 ++++++++++---------- inst/doc/examples-advanced.R | 7 inst/doc/examples-advanced.Rmd | 8 inst/doc/examples-advanced.html | 517 +++++++++---------- man/fastcpd.Rd | 8 man/fastcpd_ar.Rd | 4 man/fastcpd_arima.Rd | 4 man/fastcpd_arma.Rd | 4 man/fastcpd_binomial.Rd | 4 man/fastcpd_garch.Rd | 4 man/fastcpd_lasso.Rd | 6 man/fastcpd_lm.Rd | 6 man/fastcpd_ma.Rd | 4 man/fastcpd_mean.Rd | 4 man/fastcpd_meanvariance.Rd | 4 man/fastcpd_poisson.Rd | 6 man/fastcpd_ts.Rd | 4 man/fastcpd_variance.Rd | 4 man/transcriptome.Rd | 6 man/uk_seatbelts.Rd | 6 man/well_log.Rd | 4 tests/testthat/examples/data-transcriptome.txt | 6 tests/testthat/examples/data-uk_seatbelts.R | 6 tests/testthat/examples/data-well_log.R | 4 tests/testthat/examples/fastcpd.txt | 8 tests/testthat/examples/fastcpd_ar.R | 4 tests/testthat/examples/fastcpd_arima.txt | 4 tests/testthat/examples/fastcpd_arma.txt | 4 tests/testthat/examples/fastcpd_binomial.R | 4 tests/testthat/examples/fastcpd_garch.txt | 4 tests/testthat/examples/fastcpd_lasso.txt | 6 tests/testthat/examples/fastcpd_lm.R | 6 tests/testthat/examples/fastcpd_ma.txt | 4 tests/testthat/examples/fastcpd_mean.R | 4 tests/testthat/examples/fastcpd_meanvariance.R | 4 tests/testthat/examples/fastcpd_poisson.txt | 6 tests/testthat/examples/fastcpd_ts.txt | 4 tests/testthat/examples/fastcpd_variance.R | 4 tests/testthat/test-examples-data-bitcoin.R | 2 tests/testthat/test-examples-data-transcriptome.R | 3 tests/testthat/test-examples-data-uk_seatbelts.R | 4 tests/testthat/test-examples-data-well_log.R | 2 tests/testthat/test-examples-fastcpd_ar.R | 2 tests/testthat/test-examples-fastcpd_arima.R | 2 tests/testthat/test-examples-fastcpd_arma.R | 2 tests/testthat/test-examples-fastcpd_binomial.R | 2 tests/testthat/test-examples-fastcpd_garch.R | 2 tests/testthat/test-examples-fastcpd_lasso.R | 1 tests/testthat/test-examples-fastcpd_lm.R | 3 tests/testthat/test-examples-fastcpd_ma.R | 2 tests/testthat/test-examples-fastcpd_mean.R | 2 tests/testthat/test-examples-fastcpd_meanvariance.R | 2 tests/testthat/test-examples-fastcpd_poisson.R | 1 tests/testthat/test-examples-fastcpd_ts.R | 2 tests/testthat/test-examples-fastcpd_variance.R | 2 vignettes/comparison-packages.Rmd | 24 vignettes/examples-advanced.Rmd | 8 63 files changed, 903 insertions(+), 608 deletions(-)
Title: Core Functions to Read and Fit 13c Time Series from Breath Tests
Description: Reads several formats of 13C data (IRIS/Wagner,
BreathID) and CSV. Creates artificial sample data for testing. Fits
Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'.
Methods to fit breath test curves with Bayesian Stan methods are
refactored to package 'breathteststan'. For a Shiny GUI, see package
'dmenne/breathtestshiny' on github.
Author: Dieter Menne [aut, cre],
Menne Biomed Consulting Tuebingen [cph],
Benjamin Misselwitz [fnd],
Mark Fox [fnd],
Andreas Steingoetter [dtc],
University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between breathtestcore versions 0.8.6 dated 2023-02-13 and 0.8.7 dated 2024-01-24
DESCRIPTION | 8 - MD5 | 22 +-- NAMESPACE | 2 R/breathtest_parameters.R | 4 R/coef_by_group.R | 3 build/vignette.rds |binary inst/doc/data_formats.R | 30 ++-- inst/doc/data_formats.html | 200 +++++++++++++++---------------- inst/doc/methods_and_concepts.R | 20 +-- inst/doc/methods_and_concepts.html | 138 +++++++++++---------- man/t50_bluck_coward.Rd | 4 tests/testthat/test_plot_breathtestfit.R | 8 - 12 files changed, 223 insertions(+), 216 deletions(-)
More information about breathtestcore at CRAN
Permanent link
Title: Computation of Bayes Factors for Common Designs
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre, cph],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb, cph],
Simon Urbanek [ctb, cph],
Karl Forner [ctb, cph],
Alexander Ly [ctb, cph]
Maintainer: Richard D. Morey <richarddmorey@gmail.com>
Diff between BayesFactor versions 0.9.12-4.6 dated 2023-12-01 and 0.9.12-4.7 dated 2024-01-24
DESCRIPTION | 8 MD5 | 256 - NAMESPACE | 216 - NEWS | 401 +- R/BayesFactorPCL-package.R | 262 - R/RcppExports.R | 182 - R/aaClasses.R | 396 +- R/aaGenerics.R | 408 +- R/anovaBF-utility.R | 128 R/anovaBF.R | 468 +-- R/base64.R | 342 +- R/checkCallback.R | 14 R/checking.R | 164 - R/common.R | 986 +++--- R/contingency-utility.R | 872 ++--- R/contingency.R | 254 - R/correlation-JASP.R | 264 - R/correlation-utility.R | 294 - R/correlationBF.R | 206 - R/gaussApproxAOV.R | 172 - R/generalTest-utility.R | 378 +- R/generalTestBF.R | 290 - R/linearReg_R2stat.R | 180 - R/lmBF.R | 176 - R/logMean.R | 116 R/manual.R | 32 R/meta-ttest-utility.R | 472 +-- R/meta.ttestBF.R | 226 - R/methods-BFBayesFactor.R | 774 ++--- R/methods-BFBayesFactorList.R | 256 - R/methods-BFBayesFactorTop.R | 212 - R/methods-BFlinearModel-compare.R | 230 - R/methods-BFmodel.R | 920 +++--- R/methods-BFmodelSample.R | 452 +- R/methods-BFodds.R | 758 ++-- R/methods-BFprobability.R | 580 +-- R/model.matrix.R | 152 - R/nWayAOV-utility.R | 948 +++--- R/nWayAOV.R | 462 +-- R/newPriorOdds.R | 40 R/onAttach.R | 62 R/oneWayAOV-utility.R | 18 R/oneWayAOV_Fstat.R | 132 R/plot-BFBayesFactor.R | 242 - R/plot-BFBayesFactorTop.R | 244 - R/proportion-utility.R | 296 - R/proportionBF.R | 200 - R/regressionBF-utility.R | 186 - R/regressionBF.R | 236 - R/ttest-informed-JASP.R | 746 ++-- R/ttest-utility.R | 370 +- R/ttestBF.R | 278 - R/ttest_tstat.R | 180 - R/version.R | 44 build/vignette.rds |binary inst/doc/compare_lme4.R | 406 +- inst/doc/compare_lme4.Rmd | 556 +-- inst/doc/compare_lme4.html | 992 +++--- inst/doc/index.R | 8 inst/doc/index.Rmd | 48 inst/doc/index.html | 206 - inst/doc/manual.R | 1066 +++---- inst/doc/manual.Rmd | 2108 ++++++------- inst/doc/manual.html | 5013 ++++++++++++++++----------------- inst/doc/odds_probs.R | 88 inst/doc/odds_probs.Rmd | 248 - inst/doc/odds_probs.html | 620 ++-- inst/doc/priors.R | 154 - inst/doc/priors.Rmd | 262 - inst/doc/priors.html | 662 ++-- inst/tests/test-anovaBF.R | 24 inst/tests/test-contingencyBF.R | 24 inst/tests/test-correlationBF.R | 20 inst/tests/test-generalTestBF.R | 20 inst/tests/test-proportionBF.R | 60 inst/tests/test-regressionBF.R | 46 inst/tests/test-specialchars.R | 110 inst/tests/test-ttest.R | 54 man/BFBayesFactor-class.Rd | 168 - man/BFBayesFactorList-class.Rd | 148 man/BFInfo.Rd | 52 man/BFManual.Rd | 46 man/BFodds-class.Rd | 100 man/BFprobability-class.Rd | 102 man/BayesFactor-package.Rd | 134 man/anovaBF.Rd | 384 +- man/as.BFBayesFactor.Rd | 66 man/as.BFprobability.Rd | 64 man/compare-methods.Rd | 114 man/contingencyTableBF.Rd | 216 - man/correlationBF.Rd | 172 - man/enumerateGeneralModels.Rd | 66 man/extractBF-methods.Rd | 66 man/extractOdds-methods.Rd | 50 man/extractProbabilities-methods.Rd | 50 man/filterBF.Rd | 50 man/generalTestBF.Rd | 240 - man/grapes-same-grapes.Rd | 42 man/grapes-termin-grapes.Rd | 40 man/linearReg.R2stat.Rd | 156 - man/lmBF.Rd | 192 - man/logMeanExpLogs.Rd | 134 man/meta.ttestBF.Rd | 218 - man/model-classes.Rd | 58 man/model.matrix-methods.Rd | 84 man/nWayAOV.Rd | 312 +- man/newPriorOdds.Rd | 62 man/oneWayAOV.Fstat.Rd | 144 man/options-BayesFactor.Rd | 56 man/plot.BFBayesFactor.Rd | 120 man/plot.BFBayesFactorTop.Rd | 110 man/posterior-methods.Rd | 200 - man/priorLogodds-method.Rd | 40 man/priorOdds-method.Rd | 40 man/proportionBF.Rd | 166 - man/puzzles.Rd | 84 man/raceDolls.Rd | 70 man/recompute-methods.Rd | 176 - man/regressionBF.Rd | 224 - man/ttest.tstat.Rd | 180 - man/ttestBF.Rd | 256 - tests/run-all.R | 6 vignettes/compare_lme4.Rmd | 556 +-- vignettes/extra/manual.css | 280 - vignettes/extra/socialmedia/readme.txt | 60 vignettes/index.Rmd | 48 vignettes/manual.Rmd | 2108 ++++++------- vignettes/odds_probs.Rmd | 248 - vignettes/priors.Rmd | 262 - 129 files changed, 19500 insertions(+), 19496 deletions(-)
Title: Functions and Data Sets for "That's Weird: Anomaly Detection
Using R" by Rob J Hyndman
Description: All functions and data sets required for the examples in the book
Hyndman (2024) "That's Weird: Anomaly Detection Using R" <https://OTexts.com/weird/>.
All packages needed to run the examples are also loaded.
Author: Rob Hyndman [aut, cre, cph] ,
RStudio [cph]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between weird versions 1.0.0 dated 2024-01-12 and 1.0.2 dated 2024-01-24
weird-1.0.0/weird/data/wine_reviews.rda |only weird-1.0.0/weird/man/wine_reviews.Rd |only weird-1.0.2/weird/DESCRIPTION | 16 ++++++------ weird-1.0.2/weird/MD5 | 37 ++++++++++++++-------------- weird-1.0.2/weird/NAMESPACE | 1 weird-1.0.2/weird/NEWS.md | 5 +++ weird-1.0.2/weird/R/datasets.R | 24 ------------------ weird-1.0.2/weird/R/density.R | 7 +---- weird-1.0.2/weird/R/grubbs.R | 1 weird-1.0.2/weird/R/hdr.R | 6 ++-- weird-1.0.2/weird/R/log_scores.R | 28 ++++++++++----------- weird-1.0.2/weird/R/lookout.R | 8 +++--- weird-1.0.2/weird/R/peirce.R | 4 +-- weird-1.0.2/weird/R/wine_reviews.R |only weird-1.0.2/weird/inst |only weird-1.0.2/weird/man/density_scores.Rd | 28 ++++++++++----------- weird-1.0.2/weird/man/fetch_wine_reviews.Rd |only weird-1.0.2/weird/man/grubbs_anomalies.Rd | 1 weird-1.0.2/weird/man/hdr_table.Rd | 2 - weird-1.0.2/weird/man/hdrplot.Rd | 4 +-- weird-1.0.2/weird/man/lookout.Rd | 8 +++--- weird-1.0.2/weird/man/peirce_anomalies.Rd | 4 +-- 22 files changed, 81 insertions(+), 103 deletions(-)
Title: Modeling Species Distributions in Three Dimensions
Description: Facilitates modeling species' ecological niches and
geographic distributions based on occurrences and environments that
have a vertical as well as horizontal component, and projecting models
into three-dimensional geographic space. Working in three dimensions is
useful in an aquatic context when the organisms one wishes to model can
be found across a wide range of depths in the water column. The package
also contains functions to automatically generate marine training
model training regions using machine learning, and interpolate and smooth
patchily sampled environmental rasters using thin plate splines.
Davis Rabosky AR, Cox CL, Rabosky DL, Title PO, Holmes IA, Feldman A, McGuire JA (2016) <doi:10.1038/ncomms11484>.
Nychka D, Furrer R, Paige J, Sain S (2021) <doi:10.5065/D6W957CT>.
Pateiro-Lopez B, Rodriguez-Casal A (2022) <https://CRAN.R-project.org/package=alphahull>.
Author: Hannah L. Owens [aut, cre] ,
Carsten Rahbek [aut]
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between voluModel versions 0.2.0 dated 2023-04-11 and 0.2.1 dated 2024-01-24
DESCRIPTION | 8 MD5 | 40 +- NEWS.md | 8 R/inputProcessingUtilties.R | 7 R/visualizations.R | 70 +++- build/vignette.rds |binary inst/doc/a_Introduction.html | 378 +++++++++++++------------- inst/doc/b_RasterProcessing.html | 190 ++++++------- inst/doc/c_DataSampling.html | 294 ++++++++++---------- inst/doc/d_Visualization.html | 228 +++++++-------- inst/doc/e_GLMWorkflow.Rmd | 2 inst/doc/e_GLMWorkflow.html | 385 +++++++++++++-------------- inst/extdata/woa18_all_A00mn01_cropped.zip |binary inst/extdata/woa18_decav_t00mn01_cropped.zip |binary man/blendColor.Rd | 6 man/centerPointRasterTemplate.Rd | 5 man/figures/logo.png |binary man/figures/vmHex.ai | 371 ++++++++++++++------------ tests/testthat/test-marineBackground.R | 3 tests/testthat/test-visualizations.R | 30 ++ vignettes/e_GLMWorkflow.Rmd | 2 21 files changed, 1057 insertions(+), 970 deletions(-)
Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a
variable, each row is an observation, and each cell contains a single
value. 'tidyr' contains tools for changing the shape (pivoting) and
hierarchy (nesting and 'unnesting') of a dataset, turning deeply
nested lists into rectangular data frames ('rectangling'), and
extracting values out of string columns. It also includes tools for
working with missing values (both implicit and explicit).
Author: Hadley Wickham [aut, cre],
Davis Vaughan [aut],
Maximilian Girlich [aut],
Kevin Ushey [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between tidyr versions 1.3.0 dated 2023-01-24 and 1.3.1 dated 2024-01-24
DESCRIPTION | 17 LICENSE | 2 MD5 | 78 - NEWS.md | 14 R/data.R | 2 R/dep-lazyeval.R | 1 R/pivot-wide.R | 5 R/separate-wider.R | 5 R/utils.R | 2 README.md | 21 build/vignette.rds |binary inst/doc/in-packages.R | 12 inst/doc/in-packages.html | 354 +++--- inst/doc/nest.R | 2 inst/doc/nest.html | 164 +- inst/doc/pivot.R | 8 inst/doc/pivot.Rmd | 2 inst/doc/pivot.html | 1872 ++++++++++++++++---------------- inst/doc/programming.Rmd | 2 inst/doc/programming.html | 111 - inst/doc/rectangle.R | 4 inst/doc/rectangle.html | 763 ++++++------- inst/doc/tidy-data.R | 4 inst/doc/tidy-data.Rmd | 6 inst/doc/tidy-data.html | 602 +++++----- man/deprecated-se.Rd | 2 man/figures/logo.png |binary man/tidyr-package.Rd | 2 man/tidyr_legacy.Rd | 4 man/world_bank_pop.Rd | 2 tests/testthat/_snaps/append.md | 2 tests/testthat/_snaps/hoist.md | 2 tests/testthat/_snaps/pivot-long.md | 2 tests/testthat/_snaps/pivot-wide.md | 20 tests/testthat/_snaps/separate-wider.md | 8 tests/testthat/_snaps/unnest-helper.md | 2 tests/testthat/test-pivot-wide.R | 1 vignettes/pivot.Rmd | 2 vignettes/programming.Rmd | 2 vignettes/tidy-data.Rmd | 6 40 files changed, 2056 insertions(+), 2054 deletions(-)
Title: Measuring Cell Type Similarity with Gene Ontology in Single-Cell
RNA-Seq
Description: Traditional methods for analyzing single cell RNA-seq datasets focus solely on gene expression, but this package introduces a novel approach that goes beyond this limitation. Using Gene Ontology terms as features, the package allows for the functional profile of cell populations, and comparison within and between datasets from the same or different species. Our approach enables the discovery of previously unrecognized functional similarities and differences between cell types and has demonstrated success in identifying cell types' functional correspondence even between evolutionarily distant species.
Author: Yuyao Song [aut, cre, ctb],
Irene Papatheodorou [aut, ths]
Maintainer: Yuyao Song <ysong@ebi.ac.uk>
Diff between scGOclust versions 0.2.0 dated 2023-11-30 and 0.2.1 dated 2024-01-24
DESCRIPTION | 6 ++-- MD5 | 8 +++--- R/function.R | 20 +++++++++++---- README.md | 6 ++-- inst/doc/scGOclust_vignette.html | 52 +++++++++++++++++++-------------------- 5 files changed, 51 insertions(+), 41 deletions(-)
Title: Bayesian Inference from the Conditional Genetic Stock
Identification Model
Description: Implements Bayesian inference for the conditional genetic
stock identification model. It allows inference of mixed fisheries and also
simulation of mixtures to predict accuracy. A full description of the underlying
methods is available in a recently published article in the
Canadian Journal of Fisheries and Aquatic Sciences: <doi:10.1139/cjfas-2018-0016>.
Author: Eric C. Anderson [aut, cre],
Ben Moran [aut]
Maintainer: Eric C. Anderson <eric.anderson@noaa.gov>
Diff between rubias versions 0.3.3 dated 2022-02-09 and 0.3.4 dated 2024-01-24
DESCRIPTION | 8 MD5 | 22 NEWS.md | 8 R/eca-internal-funcs.R | 1 build/vignette.rds |binary inst/CITATION | 14 inst/doc/rubias-fully-bayesian.html | 615 +++++-- inst/doc/rubias-overview.html | 1934 +++++++++++++++--------- inst/doc/rubias-underlying-data-structures.html | 514 +++++- man/tidy_pi_traces.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 12 files changed, 2150 insertions(+), 972 deletions(-)
Title: Managing and Building of Quarterly Life Tables
Description: Manages, builds and computes statistics and datasets for the
construction of quarterly (sub-annual) life tables by exploiting micro-data from
either a general or an insured population.
References:
PavÃa and Lledó (2022) <doi:10.1111/rssa.12769>.
PavÃa and Lledó (2023) <doi:10.1017/asb.2023.16>.
Acknowledgements:
The authors wish to thank ConsellerÃa de Educación, Universidades y Empleo, Generalitat Valenciana (grant AICO/2021/257), Ministerio de EconomÃa e Innovación (grant PID2021-128228NB-I00) and Fundación Mapfre (grant 'Modelización espacial e intra-anual de la mortalidad en España. Una herramienta automática para el cálculo de productos de vida') for supporting this research.
Author: Jose M. Pavia [aut, cre] ,
Josep Lledo [aut]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between qlifetable versions 0.0.1-15 dated 2023-04-19 and 0.0.2-4 dated 2024-01-24
DESCRIPTION | 25 ++++++++++++++++--------- MD5 | 41 ++++++++++++++++++++++++++++------------- NAMESPACE | 10 ++++++++++ NEWS.md |only R/SAI_shortcut_1.R |only R/annual2quarterly.R |only R/compute_SAI.R |only R/coord_age.R | 2 +- R/coord_time.R | 2 +- R/count_events_quarter.R | 5 +++-- R/crude_mx.R |only R/crude_mx_sh2.R |only R/crude_mx_sh3.R |only R/plot.R | 9 ++++++--- R/plot.SAI.R |only R/time_exposed_stock.R | 2 +- build/partial.rdb |binary man/SAI_shortcut_1.Rd |only man/annual2quarterly.Rd |only man/compute_SAI.Rd |only man/coord_age.Rd | 2 +- man/coord_time.Rd | 5 +++-- man/count_events_quarter.Rd | 4 ++-- man/crude_mx.Rd |only man/crude_mx_sh2.Rd |only man/crude_mx_sh3.Rd |only man/plot.SAI.Rd |only man/plot.qlifetable.Rd | 2 +- man/time_exposed_stock.Rd | 2 +- 29 files changed, 74 insertions(+), 37 deletions(-)
Title: Assessing Normality of Stationary Process
Description: Despite that several tests for normality in stationary processes have been proposed in the literature, consistent implementations of these tests in programming languages are limited. Seven normality test are implemented. The asymptotic Lobato & Velasco's, asymptotic Epps, Psaradakis and Vávra, Lobato & Velasco's and Epps sieve bootstrap approximations, El bouch et al., and the random projections tests for univariate stationary process. Some other diagnostics such as, unit root test for stationarity, seasonal tests for seasonality, and arch effect test for volatility; are also performed. Additionally, the El bouch test performs normality tests for bivariate time series. The package also offers residual diagnostic for linear time series models developed in several packages.
Author: Asael Alonzo Matamoros [aut, cre],
Alicia Nieto-Reyes [aut],
Rob Hyndman [ctb],
Mitchell O'Hara-Wild [ctb],
Trapletti A. [ctb]
Maintainer: Asael Alonzo Matamoros <asael.alonzo@gmail.com>
Diff between nortsTest versions 1.1.0 dated 2024-01-16 and 1.1.1 dated 2024-01-24
DESCRIPTION | 12 ++-- MD5 | 22 +++---- NAMESPACE | 2 NEWS.md | 13 ++++ R/autoplot.R | 12 +--- R/rejection_rates.R | 99 +++++++++++++++++++++++---------- R/rp_test.R | 44 ++++++++------ man/rp.sample.Rd | 13 ++-- man/rp.test.Rd | 11 ++- tests/testthat/test-basics.R | 112 +++++++++++++++++++------------------- tests/testthat/test-performance.R | 36 ++++++------ tests/testthat/test-statistics.R | 11 ++- 12 files changed, 221 insertions(+), 166 deletions(-)
Title: Visualizing Class Specific Heterogeneous Tendencies in
Categorical Data
Description: Performing multiple-class cluster correspondence analysis(MCCCA). The main functions are create.MCCCAdata() to create a list to be applied to MCCCA, MCCCA() to apply MCCCA, and plot.mccca() for visualizing MCCCA result. Methods used in the
package refers to Mariko Takagishi and Michel van de Velden (2022)<doi:10.1080/10618600.2022.2035737>.
Author: Mariko Takagishi [aut, cre]
Maintainer: Mariko Takagishi <m.takagishi0728@gmail.com>
Diff between mccca versions 1.1.0 dated 2022-11-28 and 1.1.0.1 dated 2024-01-24
mccca-1.1.0.1/mccca/DESCRIPTION | 6 +++--- mccca-1.1.0.1/mccca/MD5 | 5 ++--- mccca-1.1.0.1/mccca/src/Makevars | 2 +- mccca-1.1.0/mccca/man/mccca-package.Rd |only 4 files changed, 6 insertions(+), 7 deletions(-)
Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr'
and the piping syntax from 'magrittr'. Function 'kable()' is a light weight
table generator coming from 'knitr'. This package simplifies the way to
manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows
users to construct complex tables and customize styles using a readable
syntax.
Author: Hao Zhu [aut, cre] ,
Thomas Travison [ctb],
Timothy Tsai [ctb],
Will Beasley [ctb],
Yihui Xie [ctb],
GuangChuang Yu [ctb],
Stephane Laurent [ctb],
Rob Shepherd [ctb],
Yoni Sidi [ctb],
Brian Salzer [ctb],
George Gui [ctb],
Yeliang Fan [ctb],
Duncan Mu [...truncated...]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Diff between kableExtra versions 1.3.4 dated 2021-02-20 and 1.4.0 dated 2024-01-24
DESCRIPTION | 22 MD5 | 163 - NAMESPACE | 5 R/add_footnote.R | 24 R/add_header_above.R | 24 R/add_indent.R | 45 R/as_image.R | 10 R/cell_spec.R | 4 R/collapse_rows.R | 53 R/column_spec.R | 20 R/footnote.R | 31 R/footnote_marker.R | 41 R/graphics_helpers.R | 10 R/group_rows.R | 16 R/header_separate.R | 47 R/kableExtra-package.R | 9 R/kable_styling.R | 84 R/kable_xml.R | 2 R/kbl.R | 120 - R/landscape.R | 6 R/linebreak.R | 8 R/magic_mirror.R | 10 R/mini_plots.R | 22 R/print.R | 14 R/remove_column.R | 10 R/row_spec.R | 38 R/save_kable.R | 43 R/scroll_box.R | 14 R/spec_tools.R | 48 R/util.R | 181 + R/zzz.R | 34 README.md | 6 build/vignette.rds |binary inst/NEWS.md | 76 inst/WORDLIST |only inst/doc/awesome_table_in_html.R | 16 inst/doc/awesome_table_in_html.Rmd | 38 inst/doc/awesome_table_in_html.html | 1540 ++++++++++------- inst/doc/awesome_table_in_pdf.R | 24 inst/doc/awesome_table_in_pdf.Rmd | 36 inst/doc/awesome_table_in_pdf.pdf |binary inst/doc/best_practice_for_newline_in_latex_table.R | 2 inst/doc/best_practice_for_newline_in_latex_table.Rmd | 6 inst/doc/best_practice_for_newline_in_latex_table.pdf |binary inst/doc/legacy_features.R | 2 inst/doc/legacy_features.html | 188 -- inst/doc/use_kable_in_shiny.R | 4 inst/doc/use_kable_in_shiny.html | 160 - inst/rmarkdown |only man/add_footnote.Rd | 5 man/add_header_above.Rd | 4 man/add_indent.Rd | 10 man/as_image.Rd | 10 man/cell_spec.Rd | 4 man/collapse_rows.Rd | 13 man/column_spec.Rd | 4 man/footnote.Rd | 16 man/footnote_marker_number.Rd | 11 man/graphics_helpers.Rd | 10 man/group_rows.Rd | 6 man/header_separate.Rd | 4 man/html_dependency_kePrint.Rd | 4 man/kableExtra-package.Rd | 4 man/kableExtra_latex_packages.Rd | 2 man/kable_styling.Rd | 12 man/kbl.Rd | 41 man/landscape.Rd | 2 man/linebreak.Rd | 6 man/listify_args.Rd | 2 man/make_inline_plot.Rd | 6 man/rmd_format.Rd | 4 man/row_spec.Rd | 4 man/save_kable.Rd | 4 man/scroll_box.Rd | 4 man/spec_boxplot.Rd | 2 man/spec_color.Rd | 30 man/spec_font_size.Rd | 2 man/spec_plot.Rd | 8 man/spec_pointrange.Rd | 7 man/use_latex_packages.Rd |only vignettes/awesome_table_in_html.Rmd | 38 vignettes/awesome_table_in_pdf.Rmd | 36 vignettes/best_practice_for_newline_in_latex_table.Rmd | 6 83 files changed, 2217 insertions(+), 1360 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
Medical Research Council UK [cph, fnd],
Accelting [cph, fnd]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 0.3.2 dated 2023-12-05 and 0.3.3 dated 2024-01-24
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/readGENEActiv.R | 16 ++++++++-------- inst/NEWS.Rd | 9 +++++++-- man/GGIRread-package.Rd | 4 ++-- 5 files changed, 26 insertions(+), 21 deletions(-)
Title: Climate Services' Indicators Based on Sub-Seasonal to Decadal
Predictions
Description: Set of generalised tools for the flexible computation of climate
related indicators defined by the user. Each method represents a specific
mathematical approach which is combined with the possibility to select an
arbitrary time period to define the indicator. This enables a wide range of
possibilities to tailor the most suitable indicator for each particular climate
service application (agriculture, food security, energy, water management, ...).
This package is intended for sub-seasonal, seasonal and decadal climate
predictions, but its methods are also applicable to other time-scales,
provided the dimensional structure of the input is maintained. Additionally,
the outputs of the functions in this package are compatible with 'CSTools'.
This package is described in 'Pérez-Zanón et al. (2023)
<doi:10.1016/j.cliser.2023.100393>' and it was developed in the context of
'H2020 MED-GOLD' (776467) and 'S2S4E' (776787) projects. See 'Lledó et al. (2019)
<doi:10.1016/j.renene.2019.04.13 [...truncated...]
Author: Victoria Agudetse [cre],
Eva Rifa [ctb],
Nuria Perez-Zanon [aut] ,
Chou Chihchung [aut],
Llorenc Lledo [aut],
Gonzalez-Reviriego Nube [ctb],
Marcos Rauel [ctb],
Palma Lluis [ctb],
An-Chi Ho [ctb],
BSC-CNS [cph]
Maintainer: Victoria Agudetse <victoria.agudetse@bsc.es>
Diff between CSIndicators versions 1.1.0 dated 2023-11-20 and 1.1.1 dated 2024-01-24
DESCRIPTION | 18 ++++---- MD5 | 15 +++---- NAMESPACE | 1 NEWS.md | 8 +++ R/SelectPeriodOnData.R | 6 +- R/SelectPeriodOnDates.R | 17 +++++--- README.md | 97 +++++++++++++++++++++++++++--------------------- build/partial.rdb |binary inst/CITATION |only 9 files changed, 98 insertions(+), 64 deletions(-)
Title: Convolute Probabilistic Distributions
Description: Convolute probabilistic distributions using the random generator
function of each distribution. A new random number generator function is created that
perform the mathematical operation on the individual random samples from the
random generator function of each distribution. See the documentation for examples.
Author: Aponte John [aut, cre]
Maintainer: Aponte John <john.j.aponte@gmail.com>
Diff between convdistr versions 1.5.3 dated 2021-04-20 and 1.6.1 dated 2024-01-24
convdistr-1.5.3/convdistr/R/convdistr.R |only convdistr-1.5.3/convdistr/man/cinqnum.DIRAC.Rd |only convdistr-1.5.3/convdistr/man/cinqnum.DISTRIBUTION.Rd |only convdistr-1.5.3/convdistr/man/cinqnum.NA.Rd |only convdistr-1.5.3/convdistr/man/convdistr.Rd |only convdistr-1.6.1/convdistr/DESCRIPTION | 13 convdistr-1.6.1/convdistr/MD5 | 48 convdistr-1.6.1/convdistr/NAMESPACE | 7 convdistr-1.6.1/convdistr/NEWS.md | 113 - convdistr-1.6.1/convdistr/R/convdistr-package.R |only convdistr-1.6.1/convdistr/R/distributions.R | 88 + convdistr-1.6.1/convdistr/R/methods.R | 36 convdistr-1.6.1/convdistr/build/vignette.rds |binary convdistr-1.6.1/convdistr/inst/WORDLIST | 10 convdistr-1.6.1/convdistr/inst/doc/sample_size.R | 2 convdistr-1.6.1/convdistr/inst/doc/sample_size.html | 812 ++++++---- convdistr-1.6.1/convdistr/inst/doc/using-convdistr.R | 12 convdistr-1.6.1/convdistr/inst/doc/using-convdistr.html | 781 ++++++--- convdistr-1.6.1/convdistr/man/BETA.Rd | 6 convdistr-1.6.1/convdistr/man/BETABINOMIAL.Rd |only convdistr-1.6.1/convdistr/man/CONVOLUTION.Rd | 10 convdistr-1.6.1/convdistr/man/CONVOLUTION_assoc.Rd | 10 convdistr-1.6.1/convdistr/man/CONVOLUTION_comb.Rd | 10 convdistr-1.6.1/convdistr/man/cinqnum.Rd | 22 convdistr-1.6.1/convdistr/man/convdistr-package.Rd |only convdistr-1.6.1/convdistr/man/fitbeta.Rd | 6 convdistr-1.6.1/convdistr/man/metadata.Rd | 6 convdistr-1.6.1/convdistr/man/set_seed.Rd | 2 convdistr-1.6.1/convdistr/tests/testthat/test_distributions.R | 8 29 files changed, 1381 insertions(+), 621 deletions(-)
Title: Estimation Methods for Causal Inference Based on Inverse
Probability Weighting
Description: Various estimators of causal effects based on inverse probability weighting, doubly robust estimation, and double machine learning. Specifically, the package includes methods for estimating average treatment effects, direct and indirect effects in causal mediation analysis, and dynamic treatment effects. The models refer to studies of Froelich (2007) <doi:10.1016/j.jeconom.2006.06.004>, Huber (2012) <doi:10.3102/1076998611411917>, Huber (2014) <doi:10.1080/07474938.2013.806197>, Huber (2014) <doi:10.1002/jae.2341>, Froelich and Huber (2017) <doi:10.1111/rssb.12232>, Hsu, Huber, Lee, and Lettry (2020) <doi:10.1002/jae.2765>, and others.
Author: Hugo Bodory [aut, cre] ,
Martin Huber [aut] ,
Jannis Kueck [aut]
Maintainer: Hugo Bodory <hugo.bodory@unisg.ch>
Diff between causalweight versions 1.0.4 dated 2023-05-04 and 1.1.0 dated 2024-01-24
DESCRIPTION | 8 MD5 | 14 R/dyntreatDML.R | 6 R/functions.R | 3647 ++++++++++++++++++++++++++--------------------------- R/india.R |only R/rkd.R |only data/india.RData |only data/rkd.RData |only man/dyntreatDML.Rd | 6 man/india.Rd |only man/rkd.Rd |only 11 files changed, 1844 insertions(+), 1837 deletions(-)
Title: Map Layers and Spatial Utilities for British Columbia
Description: Various layers of B.C., including administrative boundaries,
natural resource management boundaries, census boundaries etc. All
layers are available in BC Albers
(<https://spatialreference.org/ref/epsg/3005/>) equal-area
projection, which is the B.C. government standard. The layers are
sourced from the British Columbia and Canadian government under open
licenses, including B.C. Data Catalogue (<https://data.gov.bc.ca>),
the Government of Canada Open Data Portal
(<https://open.canada.ca/en/using-open-data>), and Statistics Canada
(<https://www.statcan.gc.ca/en/reference/licence>).
Author: Andy Teucher [aut, cre] ,
Sam Albers [aut, ctb] ,
Stephanie Hazlitt [aut, ctb] ,
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gmail.com>
Diff between bcmaps versions 2.1.0 dated 2023-10-17 and 2.2.0 dated 2024-01-24
DESCRIPTION | 10 +++--- MD5 | 43 +++++++++++++++-------------- NAMESPACE | 8 +++++ NEWS.md | 5 +++ R/cded.R | 3 -- R/sysdata.rda |binary R/utils.R | 8 +++++ R/utm-convert.R |only README.md | 4 +- inst/doc/add_points.Rmd | 2 - inst/doc/add_points.html | 8 ++--- inst/doc/bcmaps.Rmd | 4 +- inst/doc/bcmaps.html | 14 ++++----- man/bcmaps-package.Rd | 2 - man/utm_convert.Rd |only tests/testthat/test-utm-convert.R |only vignettes/add_points.Rmd | 2 - vignettes/bcmaps.Rmd | 4 +- vignettes/bcmaps.Rmd.orig | 2 - vignettes/vignette-fig-bc_neighbours-1.png |binary vignettes/vignette-fig-bec-1.png |binary vignettes/vignette-fig-cded-1.png |binary vignettes/vignette-fig-convert-1.png |binary vignettes/vignette-fig-overlay-1.png |binary 24 files changed, 71 insertions(+), 48 deletions(-)
Title: Bayesian Additive Regression Trees for Confounder Selection
Description: Fit Bayesian Regression Additive Trees (BART) models to
select true confounders from a large set of potential confounders and
to estimate average treatment effect. For more information, see Kim et
al. (2023) <doi:10.1111/biom.13833>.
Author: Yeonghoon Yoo [aut, cre]
Maintainer: Yeonghoon Yoo <yooyh.stat@gmail.com>
Diff between bartcs versions 1.2.0 dated 2023-05-27 and 1.2.1 dated 2024-01-24
DESCRIPTION | 6 MD5 | 21 NAMESPACE | 24 - NEWS.md | 79 +-- R/RcppExports.R | 56 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/bartcs.R | 168 +++---- inst/doc/bartcs.html | 1121 ++++++++++++++++++++++++-------------------------- man/bartcs-package.Rd | 80 +-- vignettes/article.pdf |binary 12 files changed, 780 insertions(+), 775 deletions(-)
Title: Adversarial Random Forests
Description: Adversarial random forests (ARFs) recursively partition data into
fully factorized leaves, where features are jointly independent. The
procedure is iterative, with alternating rounds of generation and
discrimination. Data becomes increasingly realistic at each round, until
original and synthetic samples can no longer be reliably distinguished.
This is useful for several unsupervised learning tasks, such as density
estimation and data synthesis. Methods for both are implemented in this
package. ARFs naturally handle unstructured data with mixed continuous and
categorical covariates. They inherit many of the benefits of random forests,
including speed, flexibility, and solid performance with default parameters.
For details, see Watson et al. (2022) <arXiv:2205.09435>.
Author: Marvin N. Wright [aut, cre] ,
David S. Watson [aut] ,
Kristin Blesch [aut] ,
Jan Kapar [aut]
Maintainer: Marvin N. Wright <cran@wrig.de>
Diff between arf versions 0.1.3 dated 2023-02-06 and 0.2.0 dated 2024-01-24
DESCRIPTION | 30 - MD5 | 45 +- NAMESPACE | 4 NEWS.md | 9 R/adversarial_rf.R | 172 +++----- R/expct.R |only R/forde.R | 284 +++++++------- R/forge.R | 176 +++++--- R/lik.R | 344 +++++++++++------ R/utils.R | 311 +++++++++++++++ README.md | 12 build/vignette.rds |binary inst/doc/vignette.R | 148 +++---- inst/doc/vignette.Rmd | 190 +++++---- inst/doc/vignette.html | 743 +++++++++++++++++++------------------ man/adversarial_rf.Rd | 31 - man/expct.Rd |only man/forde.Rd | 21 - man/forge.Rd | 48 +- man/leaf_posterior.Rd |only man/lik.Rd | 79 +++ man/post_x.Rd |only man/prep_evi.Rd |only man/prep_x.Rd |only tests/testthat/test-arguments.R |only tests/testthat/test-return_types.R | 51 +- vignettes/vignette.Rmd | 190 +++++---- 27 files changed, 1799 insertions(+), 1089 deletions(-)
Title: Causal Analysis of Observational Time-to-Event Data
Description: Implements target trial emulation methods to apply randomized
clinical trial design and analysis in an observational setting. Using
marginal structural models, it can estimate intention-to-treat and
per-protocol effects in emulated trials using electronic health
records. A description and application of the method can be found in
Danaei et al (2013) <doi:10.1177/0962280211403603>.
Author: Roonak Rezvani [aut] ,
Isaac Gravestock [aut, cre] ,
Li Su [aut],
Medical Research Council [fnd],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between TrialEmulation versions 0.0.3.2 dated 2023-08-25 and 0.0.3.8 dated 2024-01-24
TrialEmulation-0.0.3.2/TrialEmulation/man/data_extension.Rd |only TrialEmulation-0.0.3.2/TrialEmulation/man/extract_baseline.Rd |only TrialEmulation-0.0.3.2/TrialEmulation/man/weight_func.Rd |only TrialEmulation-0.0.3.2/TrialEmulation/man/weights_TE.Rd |only TrialEmulation-0.0.3.8/TrialEmulation/DESCRIPTION | 8 TrialEmulation-0.0.3.8/TrialEmulation/MD5 | 139 TrialEmulation-0.0.3.8/TrialEmulation/NAMESPACE | 80 TrialEmulation-0.0.3.8/TrialEmulation/NEWS.md | 50 TrialEmulation-0.0.3.8/TrialEmulation/R/RcppExports.R | 30 TrialEmulation-0.0.3.8/TrialEmulation/R/data.R | 14 TrialEmulation-0.0.3.8/TrialEmulation/R/data_extension.R | 431 +- TrialEmulation-0.0.3.8/TrialEmulation/R/data_manipulation.R | 167 TrialEmulation-0.0.3.8/TrialEmulation/R/data_preparation.R | 491 +- TrialEmulation-0.0.3.8/TrialEmulation/R/data_simulation.R | 308 - TrialEmulation-0.0.3.8/TrialEmulation/R/data_utils.R | 655 +-- TrialEmulation-0.0.3.8/TrialEmulation/R/generics.R | 243 - TrialEmulation-0.0.3.8/TrialEmulation/R/initiators.R | 350 - TrialEmulation-0.0.3.8/TrialEmulation/R/lr_utils.R | 140 TrialEmulation-0.0.3.8/TrialEmulation/R/modelling.R | 333 - TrialEmulation-0.0.3.8/TrialEmulation/R/package.R | 28 TrialEmulation-0.0.3.8/TrialEmulation/R/predict.R | 437 +- TrialEmulation-0.0.3.8/TrialEmulation/R/robust.R | 64 TrialEmulation-0.0.3.8/TrialEmulation/R/sampling.R | 19 TrialEmulation-0.0.3.8/TrialEmulation/R/utils.R | 272 - TrialEmulation-0.0.3.8/TrialEmulation/R/weighting.R |only TrialEmulation-0.0.3.8/TrialEmulation/README.md | 49 TrialEmulation-0.0.3.8/TrialEmulation/build/vignette.rds |binary TrialEmulation-0.0.3.8/TrialEmulation/data/te_data_ex.rda |binary TrialEmulation-0.0.3.8/TrialEmulation/data/te_model_ex.rda |binary TrialEmulation-0.0.3.8/TrialEmulation/inst/WORDLIST | 39 TrialEmulation-0.0.3.8/TrialEmulation/inst/doc/Getting-Started.R | 264 - TrialEmulation-0.0.3.8/TrialEmulation/inst/doc/Getting-Started.Rmd | 477 +- TrialEmulation-0.0.3.8/TrialEmulation/inst/doc/Getting-Started.html | 1924 ++++------ TrialEmulation-0.0.3.8/TrialEmulation/man/TrialEmulation-package.Rd | 74 TrialEmulation-0.0.3.8/TrialEmulation/man/calculate_predictions.Rd | 72 TrialEmulation-0.0.3.8/TrialEmulation/man/case_control_sampling_trials.Rd | 77 TrialEmulation-0.0.3.8/TrialEmulation/man/censor_func.Rd | 24 TrialEmulation-0.0.3.8/TrialEmulation/man/check_newdata.Rd | 44 TrialEmulation-0.0.3.8/TrialEmulation/man/data_manipulation.Rd | 34 TrialEmulation-0.0.3.8/TrialEmulation/man/data_preparation.Rd | 296 - TrialEmulation-0.0.3.8/TrialEmulation/man/expand.Rd | 74 TrialEmulation-0.0.3.8/TrialEmulation/man/expand_until_switch.Rd | 42 TrialEmulation-0.0.3.8/TrialEmulation/man/initiators.Rd | 321 - TrialEmulation-0.0.3.8/TrialEmulation/man/predict.TE_msm.Rd | 151 TrialEmulation-0.0.3.8/TrialEmulation/man/print_TE.Rd | 42 TrialEmulation-0.0.3.8/TrialEmulation/man/robust_calculation.Rd | 44 TrialEmulation-0.0.3.8/TrialEmulation/man/select_data_cols.Rd | 72 TrialEmulation-0.0.3.8/TrialEmulation/man/summary_TE.Rd | 62 TrialEmulation-0.0.3.8/TrialEmulation/man/te_data_ex.Rd | 62 TrialEmulation-0.0.3.8/TrialEmulation/man/te_model_ex.Rd | 4 TrialEmulation-0.0.3.8/TrialEmulation/man/trial_example.Rd | 60 TrialEmulation-0.0.3.8/TrialEmulation/man/trial_msm.Rd | 191 TrialEmulation-0.0.3.8/TrialEmulation/man/vignette_switch_data.Rd | 62 TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat.R | 10 TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/_snaps/data_utils.md | 697 +-- TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/_snaps/generics.md | 608 +-- TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/_snaps/modelling.md | 600 +-- TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/_snaps/predict.md | 1064 ++--- TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/_snaps/sampling.md | 1170 +++--- TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/data/prep_data_object.rds |binary TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/data/raw_data.rds |binary TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-data_extension.R | 476 +- TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-data_manipulation.R | 122 TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-data_preparation.R | 290 - TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-data_utils.R | 464 +- TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-generics.R | 193 - TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-lr_utils.R | 89 TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-modelling.R | 72 TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-predict.R | 249 - TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-robust.R | 84 TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-sampling.R | 423 +- TrialEmulation-0.0.3.8/TrialEmulation/tests/testthat/test-utils.R | 182 TrialEmulation-0.0.3.8/TrialEmulation/vignettes/Getting-Started.Rmd | 477 +- 73 files changed, 8116 insertions(+), 7974 deletions(-)
More information about TrialEmulation at CRAN
Permanent link
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.9 dated 2023-11-29 and 0.0.10 dated 2024-01-24
ChangeLog | 24 ++++++++ DESCRIPTION | 8 +- MD5 | 42 +++++++------- build/partial.rdb |binary inst/NEWS.Rd | 9 ++- src/ql/patterns/observable.cpp | 27 +++++---- src/ql/patterns/observable.hpp | 12 +++- src/ql/time/calendars/brazil.cpp | 2 src/ql/time/calendars/brazil.hpp | 1 src/ql/time/calendars/chile.cpp | 2 src/ql/time/calendars/chile.hpp | 1 src/ql/time/calendars/china.cpp | 24 ++++++-- src/ql/time/calendars/mexico.cpp | 3 + src/ql/time/calendars/mexico.hpp | 2 src/ql/time/calendars/southafrica.cpp | 2 src/ql/time/calendars/taiwan.cpp | 20 ++++++ src/ql/time/calendars/taiwan.hpp | 3 - src/ql/time/calendars/thailand.cpp | 97 ++++++++++++++++++++++++++------- src/ql/time/calendars/thailand.hpp | 7 +- src/ql/time/calendars/unitedstates.cpp | 11 ++- src/ql/time/calendars/unitedstates.hpp | 23 +++++++ src/ql/time/date.hpp | 4 - 22 files changed, 248 insertions(+), 76 deletions(-)
Title: Bayesian Network Meta-Analysis of Individual and Aggregate Data
Description: Network meta-analysis and network meta-regression models for
aggregate data, individual patient data, and mixtures of both individual
and aggregate data using multilevel network meta-regression as described by
Phillippo et al. (2020) <doi:10.1111/rssa.12579>. Models are estimated in a
Bayesian framework using 'Stan'.
Author: David M. Phillippo [aut, cre]
Maintainer: David M. Phillippo <david.phillippo@bristol.ac.uk>
Diff between multinma versions 0.5.1 dated 2023-05-24 and 0.6.0 dated 2024-01-24
DESCRIPTION | 24 MD5 | 202 NAMESPACE | 19 NEWS.md | 77 R/data.R | 57 R/doc-examples.R | 23 R/geom_km.R |only R/integration.R | 16 R/mcmc_array-class.R | 11 R/mspline.R |only R/multinma-package.R | 8 R/nma.R | 1266 ++ R/nma_data-class.R | 42 R/nma_data.R | 344 R/nma_dic-class.R | 9 R/nma_dic.R | 90 R/nma_prior-class.R | 2 R/nma_summary-class.R | 90 R/predict.R | 1751 +++ R/priors.R | 11 R/relative_effects.R | 40 R/stan_nma-class.R | 138 R/stanmodels.R | 4 README.md | 18 build/partial.rdb |binary build/vignette.rds |binary data/ndmm_agd.rda |only data/ndmm_agd_covs.rda |only data/ndmm_ipd.rda |only inst/REFERENCES.bib | 80 inst/doc/example_atrial_fibrillation.html | 1209 +- inst/doc/example_bcg_vaccine.html | 102 inst/doc/example_blocker.html | 58 inst/doc/example_diabetes.html | 402 inst/doc/example_dietary_fat.html | 86 inst/doc/example_hta_psoriasis.html | 312 inst/doc/example_ndmm.html |only inst/doc/example_ndmm.html.asis |only inst/doc/example_parkinsons.html | 482 - inst/doc/example_plaque_psoriasis.html | 2493 +++-- inst/doc/example_smoking.html | 234 inst/doc/example_statins.html | 60 inst/doc/example_thrombolytics.html | 450 inst/doc/example_transfusion.html | 124 inst/doc/vignette_overview.Rmd | 1 inst/doc/vignette_overview.html | 19 inst/stan/binomial_1par.stan | 43 inst/stan/binomial_2par.stan | 46 inst/stan/include/data_common.stan | 32 inst/stan/include/generated_quantities_common.stan | 8 inst/stan/include/transformed_data_common.stan | 26 inst/stan/include/transformed_parameters_common.stan | 31 inst/stan/include/transformed_parameters_theta.stan | 2 inst/stan/include/vector_functions.stan |only inst/stan/normal.stan | 33 inst/stan/ordered_multinomial.stan | 118 inst/stan/poisson.stan | 22 inst/stan/survival_mspline.stan |only inst/stan/survival_param.stan |only man/aa_example_ndmm.Rd |only man/aa_example_pso_mlnmr.Rd | 238 man/add_integration.Rd | 444 man/as.array.stan_nma.Rd | 6 man/dic.Rd | 6 man/geom_km.Rd |only man/make_knots.Rd |only man/mcmc_array-class.Rd | 6 man/mspline.Rd |only man/multi.Rd | 179 man/ndmm.Rd |only man/nma.Rd | 161 man/nma_data-class.Rd | 9 man/nma_dic-class.Rd | 2 man/plot.nma_summary.Rd | 29 man/plot_integration_error.Rd | 99 man/predict.stan_nma.Rd | 203 man/print.nma_data.Rd | 3 man/reexports.Rd |only man/set_agd_surv.Rd |only man/set_ipd.Rd | 5 man/stan_nma-class.Rd | 2 src/Makevars | 6 src/Makevars.win | 2 src/RcppExports.cpp | 4 src/stanExports_binomial_1par.h | 6794 +++++++++------ src/stanExports_binomial_2par.h | 7353 +++++++++------- src/stanExports_normal.h | 6624 ++++++++------ src/stanExports_ordered_multinomial.h | 8557 +++++++++++-------- src/stanExports_poisson.h | 6374 ++++++++------ src/stanExports_predict_delta_new.h | 798 + src/stanExports_survival_mspline.cc |only src/stanExports_survival_mspline.h |only src/stanExports_survival_param.cc |only src/stanExports_survival_param.h |only tests/testthat/test-add_integration.R | 2 tests/testthat/test-data_combine.R | 18 tests/testthat/test-data_set.R | 259 tests/testthat/test-example_atrial_fibrillation.R | 27 tests/testthat/test-example_bcg_vaccine.R | 92 tests/testthat/test-example_blocker.R | 13 tests/testthat/test-example_diabetes.R | 15 tests/testthat/test-example_dietary_fat.R | 24 tests/testthat/test-example_hta_psoriasis.R | 17 tests/testthat/test-example_parkinsons.R | 47 tests/testthat/test-example_plaque_psoriasis.R | 119 tests/testthat/test-example_smoking.R | 13 tests/testthat/test-example_statins.R | 17 tests/testthat/test-example_thrombolytics.R | 19 tests/testthat/test-example_transfusion.R | 30 tests/testthat/test-nma.R | 48 tests/testthat/test-predict.R | 2751 ++++++ vignettes/example_ndmm.html.asis |only vignettes/vignette_overview.Rmd | 1 113 files changed, 33465 insertions(+), 18666 deletions(-)
Title: End-to-End Automated Machine Learning and Model Evaluation
Description: Single unified interface for end-to-end modelling of regression,
categorical and time-to-event (survival) outcomes. Models created using
familiar are self-containing, and their use does not require additional
information such as baseline survival, feature clustering, or feature
transformation and normalisation parameters. Model performance,
calibration, risk group stratification, (permutation) variable importance,
individual conditional expectation, partial dependence, and more, are
assessed automatically as part of the evaluation process and exported in
tabular format and plotted, and may also be computed manually using export
and plot functions. Where possible, metrics and values obtained during the
evaluation process come with confidence intervals.
Author: Alex Zwanenburg [aut, cre] ,
Steffen Loeck [aut],
Stefan Leger [ctb],
Iram Shahzadi [ctb],
Asier Rabasco Meneghetti [ctb],
Sebastian Starke [ctb],
Technische Universitaet Dresden [cph],
German Cancer Research Center [cph]
Maintainer: Alex Zwanenburg <alexander.zwanenburg@nct-dresden.de>
Diff between familiar versions 1.4.1 dated 2022-12-17 and 1.4.6 dated 2024-01-24
DESCRIPTION | 6 MD5 | 44 NEWS.md | 34 R/FamiliarDataComputationCalibrationData.R | 17 R/FamiliarDataComputationDecisionCurveAnalysis.R | 6 R/FamiliarDataComputationVimp.R | 4 R/FamiliarModel.R | 7 R/Imputation.R | 1324 ++++++++++--------- R/Iterations.R | 2 R/LearnerMain.R | 4 R/ParseData.R | 2 R/TestDataCreators.R | 111 + build/vignette.rds |binary inst/CITATION | 37 inst/doc/evaluation_and_explanation_precompiled.Rmd | 4 inst/doc/evaluation_and_explanation_precompiled.html | 366 ++--- inst/doc/introduction_precompiled.html | 202 +- inst/doc/prospective_use_precompiled.html | 486 +++--- man/dot-get_default_sign_size.Rd | 5 man/dot-get_iteration_data.Rd | 4 man/extract_model_vimp.Rd | 5 tests/testthat/test-imputation.R | 1014 ++++++++------ vignettes/evaluation_and_explanation_precompiled.Rmd | 4 23 files changed, 2024 insertions(+), 1664 deletions(-)
Title: Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Description: Compute the median ranking according to the Kemeny's axiomatic approach.
Rankings can or cannot contain ties, rankings can be both complete or incomplete.
The package contains both branch-and-bound algorithms and heuristic solutions recently proposed.
The searching space of the solution can either be restricted to the universe of the permutations or unrestricted to all possible ties.
The package also provide some useful utilities for deal with preference rankings, including both element-weight Kemeny distance and correlation coefficient.
This release declare as deprecated some functions that are still in the package for compatibility. Next release will not contains these functions.
Please type '?ConsRank-deprecated'
Essential references:
Emond, E.J., and Mason, D.W. (2002) <doi:10.1002/mcda.313>;
D'Ambrosio, A., Amodio, S., and Iorio, C. (2015) <doi:10.1285/i20705948v8n2p198>;
Amodio, S., D'Ambrosio, A., and Siciliano R. (2016) <doi:10.1016/j.ejor.2015.08.048>;
D'Ambr [...truncated...]
Author: Antonio D'Ambrosio [aut, cre],
Sonia Amodio [ctb],
Giulio Mazzeo [ctb],
Alessandro Albano [ctb],
Antonella Plaia [ctb]
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRank versions 2.1.3 dated 2023-03-23 and 2.1.4 dated 2024-01-24
DESCRIPTION | 10 ++--- MD5 | 8 ++-- R/consrank.R | 92 ++++++++++++++++++++++++++++++++++++++++--------------- R/kemenydesign.R | 47 +++++++++++++++++++++++----- R/univranks.R | 1 5 files changed, 116 insertions(+), 42 deletions(-)
Title: Functions for the Logitnormal Distribution
Description: Density, distribution, quantile and random generation function for the logitnormal distribution. Estimation of the mode and the first two moments. Estimation of distribution parameters.
Author: Thomas Wutzler
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between logitnorm versions 0.8.38 dated 2021-01-07 and 0.8.39 dated 2024-01-24
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Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters) first started as an open source project with support of Haag-Streit in 2010. It specifies basic functions that allow many visual field tests to be constructed. As of February 2022 it is fully implemented on the Haag-Streit Octopus 900 with partial implementations on the Centervue Compass, Kowa AP 7000, Android phones and the CrewT IMO. It also has a cousin: the R package 'visualFields', which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin [cre, aut, cph],
David Lawson [ctb, cph],
Matthias Muller [ctb],
Jonathan Dennis [ctb, cph],
Astrid Zeman [ctb],
Ivan Marin-Franch [ctb]
Maintainer: Andrew Turpin <andrew.turpin@lei.org.au>
Diff between OPI versions 2.11.1 dated 2023-11-06 and 2.11.2 dated 2024-01-24
DESCRIPTION | 12 +++---- MD5 | 10 ++--- NAMESPACE | 1 NEWS.md | 3 + R/compassClient.r | 86 ++++++++++++++++++++++++++------------------------- man/opiInitialize.Rd | 3 + 6 files changed, 60 insertions(+), 55 deletions(-)
Title: 'MicroRNA' Set Enrichment Analysis
Description: The tools for 'MicroRNA Set Enrichment Analysis' can identify risk pathways(or prior gene sets) regulated by microRNA set in the context of microRNA expression data. (1) This package constructs a correlation profile of microRNA and pathways by the hypergeometric statistic test. The gene sets of pathways derived from the three public databases (Kyoto Encyclopedia of Genes and Genomes ('KEGG'); 'Reactome'; 'Biocarta') and the target gene sets of microRNA are provided by four databases('TarBaseV6.0'; 'mir2Disease'; 'miRecords'; 'miRTarBase';). (2) This package can quantify the change of correlation between microRNA for each pathway(or prior gene set) based on a microRNA expression data with cases and controls. (3) This package uses the weighted Kolmogorov-Smirnov statistic to calculate an enrichment score (ES) of a microRNA set that co-regulate to a pathway , which reflects the degree to which a given pathway is associated with the specific phenotype. (4) This package can provide the visu [...truncated...]
Author: Junwei Han, Siyao Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between MiRSEA versions 1.1 dated 2015-07-01 and 1.1.1 dated 2024-01-24
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- build |only data/envData.rda |binary inst/doc/MiRSEA.R |only inst/doc/MiRSEA.pdf |binary 6 files changed, 8 insertions(+), 6 deletions(-)
Title: Knot Diagrams using Bezier Curves
Description: Makes visually pleasing diagrams of knot projections using optimized Bezier curves.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
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Title: Spatial Analysis and Data Mining for Field Ecologists
Description: Set of tools for reading, writing and transforming spatial and seasonal data, model selection and specific statistical tests for ecologists. It includes functions to interpolate regular positions of points between landmarks, to discretize polylines into regular point positions, link distant observations to points and convert a bounding box in a spatial object. It also provides miscellaneous functions for field ecologists such as spatial statistics and inference on diversity indexes, writing data.frame with Chinese characters.
Author: Patrick Giraudoux [aut, cre] ,
Jean-Philippe Antonietti [ctb],
Colin Beale [ctb],
Ulrike Groemping [ctb],
Renaud Lancelot [ctb],
David Pleydell [ctb],
Mike Treglia [ctb]
Maintainer: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Diff between pgirmess versions 2.0.2 dated 2023-04-07 and 2.0.3 dated 2024-01-24
DESCRIPTION | 11 +++++------ MD5 | 16 ++++++++-------- data/preybiom.rda |binary data/siegelp179.rda |binary man/dirProj.rd | 2 +- man/dirSeg.rd | 2 +- man/mergeTrackObs.rd | 9 +++++---- man/pave.rd | 2 +- man/selMod.rd | 29 ++++++++++++++--------------- 9 files changed, 35 insertions(+), 36 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-06-25 0.91
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-19 1.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-06 1.0.5
2023-09-22 1.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-22 1.0.4
2022-11-21 1.0.3
2022-05-02 1.0.1
2020-11-18 0.9
2020-04-04 0.8.2
2020-03-31 0.8.1
2019-08-05 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-30 1.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-31 0.16.2
2022-08-24 0.16.1
2022-07-01 0.15.1
2022-03-11 0.13.1
2021-10-09 0.12.0
2021-07-08 0.11.0
2021-02-24 0.10.4
2019-01-07 0.9.1
2018-12-17 0.8.3
2018-06-12 0.6.37
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-26 0.8.0
2021-10-11 0.7.0
2021-07-18 0.6.0
2021-03-05 0.5.0
2020-11-20 0.4.0
2019-04-11 0.3.0
2018-10-12 0.2.0
2018-06-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-08 0.5.6
2023-09-20 0.5.5
2023-09-13 0.5.4
2023-08-18 0.5.3
2023-08-11 0.5.2
2023-06-08 0.5
2023-06-08 0.5.1
2023-05-31 0.4.8
2023-05-19 0.4.7
2023-03-30 0.4.6
2023-02-27 0.4.5
2022-12-14 0.4.4
2022-09-07 0.4.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-14 0.6.0
2020-05-07 0.5.1
Title: Methods for Accessing Huge Amounts of Data [deprecated]
Description: DEPRECATED. Do not start building new projects based on this package. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix (Bioconductor). The main usage of it was inside the aroma.affymetrix package. (The package currently provides a class representing a matrix where the actual data is stored in a binary format on the local file system. This way the size limit of the data is set by the file system and not the memory.)
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.huge versions 0.10.0 dated 2023-06-24 and 0.10.1 dated 2024-01-24
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 135 +++++++++++++------------- R/AbstractFileArray.R | 10 - man/dimnames.AbstractFileArray.Rd | 4 man/length.AbstractFileArray.Rd | 4 man/readContiguousValues.AbstractFileArray.Rd | 2 7 files changed, 81 insertions(+), 92 deletions(-)
Title: R Object-Oriented Programming with or without References
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.oo versions 1.25.0 dated 2022-06-11 and 1.26.0 dated 2024-01-24
DESCRIPTION | 8 +- MD5 | 20 +++---- NEWS.md | 19 ++++++ R/060.Class.R | 4 - R/hashCode.R | 12 ++-- inst/CITATION | 57 +++++++++----------- man/DOLLAR.Class.Rd | 1 man/DOLLARLT_-.Class.Rd | 1 man/getMethods.Class.Rd | 2 man/hashCode.Rd | 2 tests/hashCode.R | 134 ++++++++++++++++++++++++++++++++++++++++++++---- 11 files changed, 193 insertions(+), 67 deletions(-)
Title: Task Tracking and Project Management with GitHub
Description: Provides programmatic access to 'GitHub' API with a
focus on project management. Key functionality includes
setting up issues and milestones from R objects or 'YAML' configurations,
querying outstanding or completed tasks, and generating progress updates
in tables, charts, and RMarkdown reports. Useful for those using 'GitHub' in personal,
professional, or academic settings with an emphasis on streamlining
the workflow of data analysis projects.
Author: Emily Riederer [cre, aut]
Maintainer: Emily Riederer <emilyriederer@gmail.com>
Diff between projmgr versions 0.1.0 dated 2019-08-05 and 0.1.1 dated 2024-01-24
DESCRIPTION | 9 +- MD5 | 119 +++++++++++++++++++-------------------- NAMESPACE | 2 NEWS.md | 15 ++++ R/api-engine.R | 15 ++-- R/browse.R | 18 ++--- R/check.R | 4 - R/get.R | 30 ++++++++- R/help.R | 16 ++++- R/listcol.R | 18 ++--- R/parse.R | 87 ++++++++++++++-------------- R/plan-todo.R | 24 +++---- R/post.R | 42 +++++++++++++ R/projmgr.R | 5 - R/repo-ref.R | 10 +-- R/report-taskboard.R | 4 - R/report.R | 30 ++++----- R/taskboard-helpers.R | 10 +-- R/utils.R | 2 R/viz-gantt.R | 20 +++--- R/viz-taskboard.R | 12 +-- R/viz-waterfall.R | 18 ++--- man/browse_docs.Rd | 6 + man/check_credentials.Rd | 2 man/check_internet.Rd | 3 man/check_rate_limit.Rd | 3 man/create_repo_ref.Rd | 9 ++ man/get_issue_comments.Rd | 24 ++++--- man/get_issue_events.Rd | 35 ++++++++--- man/get_issues.Rd | 19 +++--- man/get_milestones.Rd | 5 - man/get_repo_labels.Rd | 3 man/help.Rd | 3 man/listcol_extract.Rd | 5 - man/listcol_pivot.Rd | 11 ++- man/parse_issue_comments.Rd | 23 ++++--- man/parse_issue_events.Rd | 31 +++++----- man/parse_issues.Rd | 21 +++--- man/parse_milestones.Rd | 5 - man/parse_repo_labels.Rd | 3 man/pipe.Rd | 2 man/post_issue.Rd | 21 +++--- man/post_issue_update.Rd |only man/post_milestone.Rd | 5 - man/post_plan.Rd | 11 ++- man/post_todo.Rd | 11 ++- man/projmgr.Rd | 2 man/read_plan.Rd | 11 ++- man/read_todo.Rd | 11 ++- man/report_discussion.Rd | 27 +++++--- man/report_plan.Rd | 15 ++-- man/report_progress.Rd | 31 ++++++---- man/report_taskboard.Rd | 15 +++- man/report_todo.Rd | 15 ++-- man/taskboard_helpers.Rd | 18 ++--- man/template_yaml.Rd | 11 ++- man/validate_inputs.Rd | 2 man/viz_gantt.Rd | 3 man/viz_taskboard.Rd | 9 +- man/viz_waterfall.Rd | 35 +++++++---- tests/testthat/test-tb-helpers.R | 1 61 files changed, 586 insertions(+), 391 deletions(-)