Title: Tools to Handle Taxonomic Lists
Description: Some tools to work with taxonomic name lists.
Author: Vijay Barve [aut, cre] (<https://orcid.org/0000-0002-4852-2567>)
Maintainer: Vijay Barve <vijay.barve@gmail.com>
Diff between taxotools versions 0.0.29 dated 2019-05-13 and 0.0.30 dated 2019-06-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 3 ++- R/melt_cs_field.R | 15 ++++++++------- R/taxotools.R | 2 +- man/melt_cs_field.Rd | 11 ++++++----- man/taxotools.Rd | 2 +- 7 files changed, 28 insertions(+), 25 deletions(-)
More information about SemNetDictionaries at CRAN
Permanent link
Title: Analyze Forest Diversity and Dynamics
Description: To help you access, transform, analyze, and
visualize ForestGEO data, we developed a collection of R packages
(<https://forestgeo.github.io/fgeo/>). This package, in particular,
helps you to install and load the entire package-collection with a
single R command, and provides convenient ways to find relevant
documentation. Most commonly, you should not worry about the
individual packages that make up the package-collection as you can
access all features via this package. To learn more about ForestGEO
visit <http://www.forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] (<https://orcid.org/0000-0002-1986-7988>),
Gabriel Arellano [aut, rev],
Richard Condit [aut],
Stuart Davies [aut, rev],
Matteo Detto [aut],
Erika Gonzalez-Akre [aut, rev]
(<https://orcid.org/0000-0001-8305-6672>),
Pamela Hall [aut],
Kyle Harms [aut],
Valentine Herrmann [aut, rev] (<https://orcid.org/0000-0002-4519-481X>),
Aaron Hogan [rev] (<https://orcid.org/0000-0001-9806-3074>),
Bier Kraichak [rev],
David Kenfack [aut, rev],
Lauren Krizel [rev],
Suzanne Lao [aut, rev],
Sean McMahon [aut, rev],
Haley Overstreet [rev],
Sabrina Russo [aut, rev],
Cara Scalpone [rev] (<https://orcid.org/0000-0001-8448-2147>),
Kristina Anderson-Teixeira [aut, rev],
Graham Zemunik [aut, rev],
Daniel Zuleta [aut, rev],
CTFS-ForestGEO [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between fgeo versions 1.1.3 dated 2019-05-24 and 1.1.4 dated 2019-06-19
fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-10-1.png |only fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-11-1.png |only fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-12-1.png |only fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-13-1.png |only fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-14-1.png |only fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-15-1.png |only fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-16-1.png |only fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-5-1.png |only fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-7-1.png |only fgeo-1.1.3/fgeo/man/figures/README-unnamed-chunk-8-1.png |only fgeo-1.1.4/fgeo/DESCRIPTION | 10 fgeo-1.1.4/fgeo/MD5 | 65 fgeo-1.1.4/fgeo/NAMESPACE | 46 fgeo-1.1.4/fgeo/NEWS.md | 5 fgeo-1.1.4/fgeo/R/attach.R | 100 - fgeo-1.1.4/fgeo/R/conflicts.R | 146 +- fgeo-1.1.4/fgeo/R/fgeo-package.R | 20 fgeo-1.1.4/fgeo/R/fgeo_browse.R | 48 fgeo-1.1.4/fgeo/R/fgeo_help.R | 78 - fgeo-1.1.4/fgeo/R/imports.R | 12 fgeo-1.1.4/fgeo/R/utils-pipe.R | 22 fgeo-1.1.4/fgeo/R/utils.R | 74 - fgeo-1.1.4/fgeo/R/zzz.R | 40 fgeo-1.1.4/fgeo/README.md | 932 +++++++------- fgeo-1.1.4/fgeo/inst/WORDLIST | 76 - fgeo-1.1.4/fgeo/inst/extdata/template-foreign.txt | 6 fgeo-1.1.4/fgeo/inst/extdata/template-native.txt | 8 fgeo-1.1.4/fgeo/man/fgeo-package.Rd | 122 - fgeo-1.1.4/fgeo/man/fgeo_browse.Rd | 50 fgeo-1.1.4/fgeo/man/fgeo_help.Rd | 100 - fgeo-1.1.4/fgeo/man/fgeo_packages.Rd | 52 fgeo-1.1.4/fgeo/man/figures/README-autoplot-sp-1.png |only fgeo-1.1.4/fgeo/man/figures/README-autoplot-sp-elev-1.png |only fgeo-1.1.4/fgeo/man/figures/README-fgeo-downloads-1.png |only fgeo-1.1.4/fgeo/man/pipe.Rd | 24 fgeo-1.1.4/fgeo/tests/spelling.R | 12 fgeo-1.1.4/fgeo/tests/testthat.R | 8 fgeo-1.1.4/fgeo/tests/testthat/test-fgeo_help.R | 34 fgeo-1.1.4/fgeo/tests/testthat/test-fgeo_packages.R | 108 - fgeo-1.1.4/fgeo/tests/testthat/test-zzz.R | 12 40 files changed, 1110 insertions(+), 1100 deletions(-)
Title: Visualising Statistical Models using Dynamic Nomograms
Description: Demonstrate the results of a statistical model object as a dynamic nomogram in an RStudio panel or web browser. The package provides two generics functions: DynNom, which display statistical model objects as a dynamic nomogram; DNbuilder, which builds required scripts to publish a dynamic nomogram on a web server such as the <https://www.shinyapps.io/>. Current version of 'DynNom' supports stats::lm, stats::glm, survival::coxph, rms::ols, rms::Glm, rms::lrm, rms::cph, mgcv::gam and gam::gam model objects.
Author: Amirhossein Jalali, Davood Roshan, Alberto Alvarez-Iglesias, John Newell
Maintainer: Amirhossein Jalali <amir.jalali@ucd.ie>
Diff between DynNom versions 4.1.1 dated 2017-04-19 and 5.0 dated 2019-06-19
DynNom-4.1.1/DynNom/R/DNbuilder-coxph.R |only DynNom-4.1.1/DynNom/R/DNbuilder-glm.R |only DynNom-4.1.1/DynNom/R/DNbuilder-lm.R |only DynNom-4.1.1/DynNom/R/DynNom_coxph.R |only DynNom-4.1.1/DynNom/R/DynNom_glm.R |only DynNom-4.1.1/DynNom/R/DynNom_lm.R |only DynNom-4.1.1/DynNom/R/DynNom_rmsGlm.R |only DynNom-4.1.1/DynNom/R/DynNom_rmscph.R |only DynNom-4.1.1/DynNom/R/DynNom_rmslrm.R |only DynNom-4.1.1/DynNom/R/DynNom_rmsols.R |only DynNom-4.1.1/DynNom/man/DNbuilder.coxph.Rd |only DynNom-4.1.1/DynNom/man/DNbuilder.glm.Rd |only DynNom-4.1.1/DynNom/man/DNbuilder.lm.Rd |only DynNom-4.1.1/DynNom/man/DynNom.coxph.Rd |only DynNom-4.1.1/DynNom/man/DynNom.glm.Rd |only DynNom-4.1.1/DynNom/man/DynNom.lm.Rd |only DynNom-4.1.1/DynNom/man/DynNom.rms.Glm.Rd |only DynNom-4.1.1/DynNom/man/DynNom.rms.cph.Rd |only DynNom-4.1.1/DynNom/man/DynNom.rms.lrm.Rd |only DynNom-4.1.1/DynNom/man/DynNom.rms.ols.Rd |only DynNom-5.0/DynNom/DESCRIPTION | 18 +-- DynNom-5.0/DynNom/MD5 | 42 +++----- DynNom-5.0/DynNom/NAMESPACE | 29 ++--- DynNom-5.0/DynNom/R/DNbuilder-core.R |only DynNom-5.0/DynNom/R/DNbuilder-surv.R |only DynNom-5.0/DynNom/R/DNbuilder.R | 116 ++++++++++++---------- DynNom-5.0/DynNom/R/DynNom-core.R |only DynNom-5.0/DynNom/R/DynNom-surv.R |only DynNom-5.0/DynNom/R/DynNom.R | 152 ++++++++++------------------- DynNom-5.0/DynNom/R/getclass-DN.R |only DynNom-5.0/DynNom/R/getdata-DN.R |only DynNom-5.0/DynNom/R/getpred-DN.R |only DynNom-5.0/DynNom/man/DNbuilder.Rd | 128 ++++++++++++++++++------ DynNom-5.0/DynNom/man/DynNom.Rd | 131 ++++++++++++++++-------- DynNom-5.0/DynNom/man/getclass.DN.Rd |only DynNom-5.0/DynNom/man/getdata.DN.Rd |only DynNom-5.0/DynNom/man/getpred.DN.Rd |only 37 files changed, 337 insertions(+), 279 deletions(-)
Title: R Client for the 'Civis data science API'
Description: A convenient interface for making
requests directly to the 'Civis data science API' <https://www.civisanalytics.com/platform/>.
Author: Patrick Miller [cre, aut],
Keith Ingersoll [aut],
Bill Lattner [ctb],
Anh Le [ctb],
Michelangelo D'Agostino [ctb],
Sam Weiss [ctb],
Stephen Hoover [ctb],
Danning Chen [ctb],
Elizabeth Sander [ctb],
Madison Hobbs [ctb],
Anna Bladey [ctb]
Maintainer: Patrick Miller <pmiller@civisanalytics.com>
Diff between civis versions 1.6.1 dated 2019-02-12 and 2.0.0 dated 2019-06-19
civis-1.6.1/civis/R/dbi-connection.R |only civis-1.6.1/civis/R/dbi-driver.R |only civis-1.6.1/civis/R/dbi-result.R |only civis-1.6.1/civis/R/dplyr.R |only civis-1.6.1/civis/R/sysdata.rda |only civis-1.6.1/civis/man/DBI.Rd |only civis-1.6.1/civis/man/dbIsReadOnly.Rd |only civis-1.6.1/civis/man/db_query_fields.CivisConnection.Rd |only civis-1.6.1/civis/man/dbi_driver.Rd |only civis-1.6.1/civis/man/enhancements_delete_civis_data_match_projects.Rd |only civis-1.6.1/civis/man/enhancements_delete_civis_data_match_shares_groups.Rd |only civis-1.6.1/civis/man/enhancements_delete_civis_data_match_shares_users.Rd |only civis-1.6.1/civis/man/enhancements_delete_data_unification_projects.Rd |only civis-1.6.1/civis/man/enhancements_delete_data_unification_shares_groups.Rd |only civis-1.6.1/civis/man/enhancements_delete_data_unification_shares_users.Rd |only civis-1.6.1/civis/man/enhancements_delete_person_matching_projects.Rd |only civis-1.6.1/civis/man/enhancements_delete_person_matching_shares_groups.Rd |only civis-1.6.1/civis/man/enhancements_delete_person_matching_shares_users.Rd |only civis-1.6.1/civis/man/enhancements_delete_table_deduplication_projects.Rd |only civis-1.6.1/civis/man/enhancements_delete_table_deduplication_shares_groups.Rd |only civis-1.6.1/civis/man/enhancements_delete_table_deduplication_shares_users.Rd |only civis-1.6.1/civis/man/enhancements_list_civis_data_match_projects.Rd |only civis-1.6.1/civis/man/enhancements_list_civis_data_match_shares.Rd |only civis-1.6.1/civis/man/enhancements_list_data_unification_projects.Rd |only civis-1.6.1/civis/man/enhancements_list_data_unification_shares.Rd |only civis-1.6.1/civis/man/enhancements_list_person_matching_projects.Rd |only civis-1.6.1/civis/man/enhancements_list_person_matching_shares.Rd |only civis-1.6.1/civis/man/enhancements_list_table_deduplication_projects.Rd |only civis-1.6.1/civis/man/enhancements_list_table_deduplication_shares.Rd |only civis-1.6.1/civis/man/enhancements_put_civis_data_match_archive.Rd |only civis-1.6.1/civis/man/enhancements_put_civis_data_match_projects.Rd |only civis-1.6.1/civis/man/enhancements_put_civis_data_match_shares_groups.Rd |only civis-1.6.1/civis/man/enhancements_put_civis_data_match_shares_users.Rd |only civis-1.6.1/civis/man/enhancements_put_data_unification_archive.Rd |only civis-1.6.1/civis/man/enhancements_put_data_unification_projects.Rd |only civis-1.6.1/civis/man/enhancements_put_data_unification_shares_groups.Rd |only civis-1.6.1/civis/man/enhancements_put_data_unification_shares_users.Rd |only civis-1.6.1/civis/man/enhancements_put_person_matching_archive.Rd |only civis-1.6.1/civis/man/enhancements_put_person_matching_projects.Rd |only civis-1.6.1/civis/man/enhancements_put_person_matching_shares_groups.Rd |only civis-1.6.1/civis/man/enhancements_put_person_matching_shares_users.Rd |only civis-1.6.1/civis/man/enhancements_put_table_deduplication_archive.Rd |only civis-1.6.1/civis/man/enhancements_put_table_deduplication_projects.Rd |only civis-1.6.1/civis/man/enhancements_put_table_deduplication_shares_groups.Rd |only civis-1.6.1/civis/man/enhancements_put_table_deduplication_shares_users.Rd |only civis-1.6.1/civis/man/reexports.Rd |only civis-1.6.1/civis/man/sql_escape_ident.CivisConnection.Rd |only civis-1.6.1/civis/man/sql_translate_env.CivisConnection.Rd |only civis-1.6.1/civis/man/tables_post.Rd |only civis-2.0.0/civis/DESCRIPTION | 21 civis-2.0.0/civis/MD5 | 852 - civis-2.0.0/civis/NAMESPACE | 158 civis-2.0.0/civis/R/await.R | 72 civis-2.0.0/civis/R/civis_future.R | 32 civis-2.0.0/civis/R/civis_ml.R | 6 civis-2.0.0/civis/R/civis_ml_plot.R | 7 civis-2.0.0/civis/R/civis_ml_utils.R | 2 civis-2.0.0/civis/R/civis_ml_workflows.R | 8 civis-2.0.0/civis/R/generate_client.R | 74 civis-2.0.0/civis/R/generated_client.R | 5971 +++++----- civis-2.0.0/civis/R/io.R | 109 civis-2.0.0/civis/R/logs.R | 9 civis-2.0.0/civis/R/pagination_helpers.R | 8 civis-2.0.0/civis/R/reports.R | 6 civis-2.0.0/civis/R/scripts.R |only civis-2.0.0/civis/R/tables.R | 34 civis-2.0.0/civis/R/utils.R | 26 civis-2.0.0/civis/README.md | 17 civis-2.0.0/civis/build/vignette.rds |binary civis-2.0.0/civis/inst/doc/civis_ml.R | 6 civis-2.0.0/civis/inst/doc/civis_ml.Rmd | 6 civis-2.0.0/civis/inst/doc/civis_ml.html | 98 civis-2.0.0/civis/inst/doc/civis_scripts.R |only civis-2.0.0/civis/inst/doc/civis_scripts.Rmd |only civis-2.0.0/civis/inst/doc/civis_scripts.html |only civis-2.0.0/civis/inst/doc/concurrency.Rmd | 4 civis-2.0.0/civis/inst/doc/concurrency.html | 9 civis-2.0.0/civis/inst/doc/data_import_and_export.R | 11 civis-2.0.0/civis/inst/doc/data_import_and_export.Rmd | 37 civis-2.0.0/civis/inst/doc/data_import_and_export.html | 39 civis-2.0.0/civis/inst/doc/quick_start.html | 5 civis-2.0.0/civis/man/CivisFuture.Rd | 34 civis-2.0.0/civis/man/aliases_delete.Rd |only civis-2.0.0/civis/man/aliases_delete_shares_groups.Rd |only civis-2.0.0/civis/man/aliases_delete_shares_users.Rd |only civis-2.0.0/civis/man/aliases_get.Rd |only civis-2.0.0/civis/man/aliases_get_object_type.Rd |only civis-2.0.0/civis/man/aliases_list.Rd |only civis-2.0.0/civis/man/aliases_list_shares.Rd |only civis-2.0.0/civis/man/aliases_patch.Rd |only civis-2.0.0/civis/man/aliases_post.Rd |only civis-2.0.0/civis/man/aliases_put.Rd |only civis-2.0.0/civis/man/aliases_put_shares_groups.Rd |only civis-2.0.0/civis/man/aliases_put_shares_users.Rd |only civis-2.0.0/civis/man/apps_delete_instances_projects.Rd | 4 civis-2.0.0/civis/man/apps_delete_instances_shares_groups.Rd | 8 civis-2.0.0/civis/man/apps_delete_instances_shares_users.Rd | 8 civis-2.0.0/civis/man/apps_list_instances_projects.Rd | 4 civis-2.0.0/civis/man/apps_list_instances_shares.Rd | 6 civis-2.0.0/civis/man/apps_put_instances_projects.Rd | 4 civis-2.0.0/civis/man/apps_put_instances_shares_groups.Rd | 10 civis-2.0.0/civis/man/apps_put_instances_shares_users.Rd | 10 civis-2.0.0/civis/man/await.Rd | 7 civis-2.0.0/civis/man/civis_ml_extra_trees_classifier.Rd | 2 civis-2.0.0/civis/man/civis_ml_gradient_boosting_classifier.Rd | 2 civis-2.0.0/civis/man/civis_ml_random_forest_classifier.Rd | 2 civis-2.0.0/civis/man/civis_ml_sparse_logistic.Rd | 2 civis-2.0.0/civis/man/civis_script.Rd |only civis-2.0.0/civis/man/clusters_get_kubernetes.Rd | 1 civis-2.0.0/civis/man/clusters_get_kubernetes_partitions.Rd | 7 civis-2.0.0/civis/man/clusters_list_kubernetes.Rd | 1 civis-2.0.0/civis/man/clusters_list_kubernetes_deployment_stats.Rd |only civis-2.0.0/civis/man/clusters_list_kubernetes_deployments.Rd |only civis-2.0.0/civis/man/clusters_list_kubernetes_partitions.Rd | 7 civis-2.0.0/civis/man/clusters_patch_kubernetes_partitions.Rd | 9 civis-2.0.0/civis/man/clusters_post_kubernetes_partitions.Rd | 9 civis-2.0.0/civis/man/credentials_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/credentials_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/credentials_list.Rd | 6 civis-2.0.0/civis/man/credentials_list_shares.Rd | 2 civis-2.0.0/civis/man/credentials_post_authenticate.Rd | 2 civis-2.0.0/civis/man/credentials_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/credentials_put_shares_users.Rd | 6 civis-2.0.0/civis/man/databases_get.Rd |only civis-2.0.0/civis/man/databases_list.Rd | 1 civis-2.0.0/civis/man/databases_post_schemas_scan.Rd |only civis-2.0.0/civis/man/download_civis.Rd | 2 civis-2.0.0/civis/man/enhancements_delete_cass_ncoa_projects.Rd | 4 civis-2.0.0/civis/man/enhancements_delete_cass_ncoa_shares_groups.Rd | 4 civis-2.0.0/civis/man/enhancements_delete_cass_ncoa_shares_users.Rd | 4 civis-2.0.0/civis/man/enhancements_delete_geocode_projects.Rd |only civis-2.0.0/civis/man/enhancements_delete_geocode_runs.Rd |only civis-2.0.0/civis/man/enhancements_delete_geocode_shares_groups.Rd |only civis-2.0.0/civis/man/enhancements_delete_geocode_shares_users.Rd |only civis-2.0.0/civis/man/enhancements_get_cass_ncoa.Rd | 2 civis-2.0.0/civis/man/enhancements_get_civis_data_match.Rd | 6 civis-2.0.0/civis/man/enhancements_get_data_unification.Rd | 9 civis-2.0.0/civis/man/enhancements_get_geocode.Rd |only civis-2.0.0/civis/man/enhancements_get_geocode_runs.Rd |only civis-2.0.0/civis/man/enhancements_get_table_deduplication.Rd | 4 civis-2.0.0/civis/man/enhancements_list_cass_ncoa_projects.Rd | 4 civis-2.0.0/civis/man/enhancements_list_cass_ncoa_shares.Rd | 2 civis-2.0.0/civis/man/enhancements_list_geocode_projects.Rd |only civis-2.0.0/civis/man/enhancements_list_geocode_runs.Rd |only civis-2.0.0/civis/man/enhancements_list_geocode_runs_logs.Rd |only civis-2.0.0/civis/man/enhancements_list_geocode_runs_outputs.Rd |only civis-2.0.0/civis/man/enhancements_list_geocode_shares.Rd |only civis-2.0.0/civis/man/enhancements_patch_cass_ncoa.Rd | 4 civis-2.0.0/civis/man/enhancements_patch_civis_data_match.Rd | 19 civis-2.0.0/civis/man/enhancements_patch_data_unification.Rd | 26 civis-2.0.0/civis/man/enhancements_patch_geocode.Rd |only civis-2.0.0/civis/man/enhancements_patch_table_deduplication.Rd | 13 civis-2.0.0/civis/man/enhancements_post_cass_ncoa.Rd | 4 civis-2.0.0/civis/man/enhancements_post_civis_data_match.Rd | 19 civis-2.0.0/civis/man/enhancements_post_data_unification.Rd | 26 civis-2.0.0/civis/man/enhancements_post_geocode.Rd |only civis-2.0.0/civis/man/enhancements_post_geocode_cancel.Rd |only civis-2.0.0/civis/man/enhancements_post_geocode_runs.Rd |only civis-2.0.0/civis/man/enhancements_post_table_deduplication.Rd | 14 civis-2.0.0/civis/man/enhancements_put_cass_ncoa.Rd | 4 civis-2.0.0/civis/man/enhancements_put_cass_ncoa_archive.Rd | 2 civis-2.0.0/civis/man/enhancements_put_cass_ncoa_projects.Rd | 4 civis-2.0.0/civis/man/enhancements_put_cass_ncoa_shares_groups.Rd | 6 civis-2.0.0/civis/man/enhancements_put_cass_ncoa_shares_users.Rd | 6 civis-2.0.0/civis/man/enhancements_put_civis_data_match.Rd | 19 civis-2.0.0/civis/man/enhancements_put_data_unification.Rd | 26 civis-2.0.0/civis/man/enhancements_put_geocode.Rd |only civis-2.0.0/civis/man/enhancements_put_geocode_archive.Rd |only civis-2.0.0/civis/man/enhancements_put_geocode_projects.Rd |only civis-2.0.0/civis/man/enhancements_put_geocode_shares_groups.Rd |only civis-2.0.0/civis/man/enhancements_put_geocode_shares_users.Rd |only civis-2.0.0/civis/man/enhancements_put_table_deduplication.Rd | 14 civis-2.0.0/civis/man/fetch_and_generate_client.Rd | 2 civis-2.0.0/civis/man/fetch_output_file_ids.Rd |only civis-2.0.0/civis/man/fetch_until.Rd | 2 civis-2.0.0/civis/man/files_delete_projects.Rd | 4 civis-2.0.0/civis/man/files_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/files_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/files_list_projects.Rd | 4 civis-2.0.0/civis/man/files_list_shares.Rd | 2 civis-2.0.0/civis/man/files_put_projects.Rd | 4 civis-2.0.0/civis/man/files_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/files_put_shares_users.Rd | 6 civis-2.0.0/civis/man/get_script_fun.Rd |only civis-2.0.0/civis/man/groups_list.Rd | 2 civis-2.0.0/civis/man/imports_delete_files_csv.Rd |only civis-2.0.0/civis/man/imports_delete_projects.Rd | 4 civis-2.0.0/civis/man/imports_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/imports_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/imports_get_files_csv.Rd |only civis-2.0.0/civis/man/imports_list.Rd | 6 civis-2.0.0/civis/man/imports_list_projects.Rd | 4 civis-2.0.0/civis/man/imports_list_shares.Rd | 2 civis-2.0.0/civis/man/imports_patch_files_csv.Rd |only civis-2.0.0/civis/man/imports_post_batches.Rd | 4 civis-2.0.0/civis/man/imports_post_files.Rd | 4 civis-2.0.0/civis/man/imports_post_files_csv.Rd |only civis-2.0.0/civis/man/imports_post_syncs.Rd | 2 civis-2.0.0/civis/man/imports_put_files_csv.Rd |only civis-2.0.0/civis/man/imports_put_files_csv_archive.Rd |only civis-2.0.0/civis/man/imports_put_projects.Rd | 4 civis-2.0.0/civis/man/imports_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/imports_put_shares_users.Rd | 6 civis-2.0.0/civis/man/imports_put_syncs.Rd | 2 civis-2.0.0/civis/man/imports_put_syncs_archive.Rd | 1 civis-2.0.0/civis/man/jobs_delete_projects.Rd | 4 civis-2.0.0/civis/man/jobs_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/jobs_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/jobs_list_projects.Rd | 4 civis-2.0.0/civis/man/jobs_list_runs.Rd |only civis-2.0.0/civis/man/jobs_list_runs_logs.Rd |only civis-2.0.0/civis/man/jobs_list_shares.Rd | 2 civis-2.0.0/civis/man/jobs_put_projects.Rd | 4 civis-2.0.0/civis/man/jobs_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/jobs_put_shares_users.Rd | 6 civis-2.0.0/civis/man/json_values_delete_shares_groups.Rd |only civis-2.0.0/civis/man/json_values_delete_shares_users.Rd |only civis-2.0.0/civis/man/json_values_get.Rd |only civis-2.0.0/civis/man/json_values_list_shares.Rd |only civis-2.0.0/civis/man/json_values_patch.Rd |only civis-2.0.0/civis/man/json_values_post.Rd |only civis-2.0.0/civis/man/json_values_put_shares_groups.Rd |only civis-2.0.0/civis/man/json_values_put_shares_users.Rd |only civis-2.0.0/civis/man/match_targets_get.Rd | 1 civis-2.0.0/civis/man/match_targets_list.Rd | 1 civis-2.0.0/civis/man/match_targets_patch.Rd | 5 civis-2.0.0/civis/man/match_targets_post.Rd | 11 civis-2.0.0/civis/man/media_delete_optimizations_shares_groups.Rd | 4 civis-2.0.0/civis/man/media_delete_optimizations_shares_users.Rd | 4 civis-2.0.0/civis/man/media_delete_ratecards_shares_groups.Rd | 4 civis-2.0.0/civis/man/media_delete_ratecards_shares_users.Rd | 4 civis-2.0.0/civis/man/media_delete_spot_orders_shares_groups.Rd | 4 civis-2.0.0/civis/man/media_delete_spot_orders_shares_users.Rd | 4 civis-2.0.0/civis/man/media_list_optimizations_shares.Rd | 2 civis-2.0.0/civis/man/media_list_ratecards_shares.Rd | 2 civis-2.0.0/civis/man/media_list_spot_orders_shares.Rd | 2 civis-2.0.0/civis/man/media_put_optimizations_shares_groups.Rd | 6 civis-2.0.0/civis/man/media_put_optimizations_shares_users.Rd | 6 civis-2.0.0/civis/man/media_put_ratecards_shares_groups.Rd | 6 civis-2.0.0/civis/man/media_put_ratecards_shares_users.Rd | 6 civis-2.0.0/civis/man/media_put_spot_orders_shares_groups.Rd | 6 civis-2.0.0/civis/man/media_put_spot_orders_shares_users.Rd | 6 civis-2.0.0/civis/man/models_delete_projects.Rd | 4 civis-2.0.0/civis/man/models_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/models_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/models_list_projects.Rd | 4 civis-2.0.0/civis/man/models_list_shares.Rd | 2 civis-2.0.0/civis/man/models_put_projects.Rd | 4 civis-2.0.0/civis/man/models_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/models_put_shares_users.Rd | 6 civis-2.0.0/civis/man/notebooks_delete_projects.Rd | 4 civis-2.0.0/civis/man/notebooks_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/notebooks_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/notebooks_list_deployments_logs.Rd | 4 civis-2.0.0/civis/man/notebooks_list_git.Rd | 4 civis-2.0.0/civis/man/notebooks_list_git_commits.Rd | 4 civis-2.0.0/civis/man/notebooks_list_projects.Rd | 4 civis-2.0.0/civis/man/notebooks_list_shares.Rd | 2 civis-2.0.0/civis/man/notebooks_put_git.Rd | 4 civis-2.0.0/civis/man/notebooks_put_projects.Rd | 4 civis-2.0.0/civis/man/notebooks_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/notebooks_put_shares_users.Rd | 6 civis-2.0.0/civis/man/projects_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/projects_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/projects_list_shares.Rd | 2 civis-2.0.0/civis/man/projects_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/projects_put_shares_users.Rd | 6 civis-2.0.0/civis/man/read_civis.Rd | 37 civis-2.0.0/civis/man/refresh_table.Rd | 2 civis-2.0.0/civis/man/remote_hosts_list.Rd | 4 civis-2.0.0/civis/man/remote_hosts_post.Rd | 4 civis-2.0.0/civis/man/reports_delete_projects.Rd | 4 civis-2.0.0/civis/man/reports_delete_services_projects.Rd |only civis-2.0.0/civis/man/reports_delete_services_shares_groups.Rd | 4 civis-2.0.0/civis/man/reports_delete_services_shares_users.Rd | 4 civis-2.0.0/civis/man/reports_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/reports_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/reports_list_git.Rd | 4 civis-2.0.0/civis/man/reports_list_git_commits.Rd | 4 civis-2.0.0/civis/man/reports_list_projects.Rd | 4 civis-2.0.0/civis/man/reports_list_services_projects.Rd |only civis-2.0.0/civis/man/reports_list_services_shares.Rd | 2 civis-2.0.0/civis/man/reports_list_shares.Rd | 2 civis-2.0.0/civis/man/reports_put_git.Rd | 4 civis-2.0.0/civis/man/reports_put_projects.Rd | 4 civis-2.0.0/civis/man/reports_put_services_projects.Rd |only civis-2.0.0/civis/man/reports_put_services_shares_groups.Rd | 6 civis-2.0.0/civis/man/reports_put_services_shares_users.Rd | 6 civis-2.0.0/civis/man/reports_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/reports_put_shares_users.Rd | 6 civis-2.0.0/civis/man/results_delete_projects.Rd | 4 civis-2.0.0/civis/man/results_delete_services_projects.Rd |only civis-2.0.0/civis/man/results_delete_services_shares_groups.Rd | 4 civis-2.0.0/civis/man/results_delete_services_shares_users.Rd | 4 civis-2.0.0/civis/man/results_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/results_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/results_list_git.Rd | 4 civis-2.0.0/civis/man/results_list_git_commits.Rd | 4 civis-2.0.0/civis/man/results_list_projects.Rd | 4 civis-2.0.0/civis/man/results_list_services_projects.Rd |only civis-2.0.0/civis/man/results_list_services_shares.Rd | 2 civis-2.0.0/civis/man/results_list_shares.Rd | 2 civis-2.0.0/civis/man/results_put_git.Rd | 4 civis-2.0.0/civis/man/results_put_projects.Rd | 4 civis-2.0.0/civis/man/results_put_services_projects.Rd |only civis-2.0.0/civis/man/results_put_services_shares_groups.Rd | 6 civis-2.0.0/civis/man/results_put_services_shares_users.Rd | 6 civis-2.0.0/civis/man/results_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/results_put_shares_users.Rd | 6 civis-2.0.0/civis/man/run_civis.Rd |only civis-2.0.0/civis/man/run_template.Rd |only civis-2.0.0/civis/man/scripts_delete_containers_projects.Rd | 4 civis-2.0.0/civis/man/scripts_delete_containers_shares_groups.Rd | 4 civis-2.0.0/civis/man/scripts_delete_containers_shares_users.Rd | 4 civis-2.0.0/civis/man/scripts_delete_custom_projects.Rd | 4 civis-2.0.0/civis/man/scripts_delete_custom_shares_groups.Rd | 4 civis-2.0.0/civis/man/scripts_delete_custom_shares_users.Rd | 4 civis-2.0.0/civis/man/scripts_delete_javascript_projects.Rd | 4 civis-2.0.0/civis/man/scripts_delete_javascript_shares_groups.Rd | 4 civis-2.0.0/civis/man/scripts_delete_javascript_shares_users.Rd | 4 civis-2.0.0/civis/man/scripts_delete_python3_projects.Rd | 4 civis-2.0.0/civis/man/scripts_delete_python3_shares_groups.Rd | 4 civis-2.0.0/civis/man/scripts_delete_python3_shares_users.Rd | 4 civis-2.0.0/civis/man/scripts_delete_r_projects.Rd | 4 civis-2.0.0/civis/man/scripts_delete_r_shares_groups.Rd | 4 civis-2.0.0/civis/man/scripts_delete_r_shares_users.Rd | 4 civis-2.0.0/civis/man/scripts_delete_sql_projects.Rd | 4 civis-2.0.0/civis/man/scripts_delete_sql_shares_groups.Rd | 4 civis-2.0.0/civis/man/scripts_delete_sql_shares_users.Rd | 4 civis-2.0.0/civis/man/scripts_get.Rd | 2 civis-2.0.0/civis/man/scripts_get_containers.Rd | 6 civis-2.0.0/civis/man/scripts_get_custom.Rd | 2 civis-2.0.0/civis/man/scripts_get_javascript.Rd | 2 civis-2.0.0/civis/man/scripts_get_python3.Rd | 3 civis-2.0.0/civis/man/scripts_get_r.Rd | 3 civis-2.0.0/civis/man/scripts_get_sql.Rd | 2 civis-2.0.0/civis/man/scripts_list_containers_projects.Rd | 4 civis-2.0.0/civis/man/scripts_list_containers_shares.Rd | 2 civis-2.0.0/civis/man/scripts_list_custom_projects.Rd | 4 civis-2.0.0/civis/man/scripts_list_custom_shares.Rd | 2 civis-2.0.0/civis/man/scripts_list_javascript_git.Rd | 4 civis-2.0.0/civis/man/scripts_list_javascript_git_commits.Rd | 4 civis-2.0.0/civis/man/scripts_list_javascript_projects.Rd | 4 civis-2.0.0/civis/man/scripts_list_javascript_shares.Rd | 2 civis-2.0.0/civis/man/scripts_list_python3_git.Rd | 4 civis-2.0.0/civis/man/scripts_list_python3_git_commits.Rd | 4 civis-2.0.0/civis/man/scripts_list_python3_projects.Rd | 4 civis-2.0.0/civis/man/scripts_list_python3_shares.Rd | 2 civis-2.0.0/civis/man/scripts_list_r_git.Rd | 4 civis-2.0.0/civis/man/scripts_list_r_git_commits.Rd | 4 civis-2.0.0/civis/man/scripts_list_r_projects.Rd | 4 civis-2.0.0/civis/man/scripts_list_r_shares.Rd | 2 civis-2.0.0/civis/man/scripts_list_sql_git.Rd | 4 civis-2.0.0/civis/man/scripts_list_sql_git_commits.Rd | 4 civis-2.0.0/civis/man/scripts_list_sql_projects.Rd | 4 civis-2.0.0/civis/man/scripts_list_sql_shares.Rd | 2 civis-2.0.0/civis/man/scripts_patch.Rd | 4 civis-2.0.0/civis/man/scripts_patch_containers.Rd | 12 civis-2.0.0/civis/man/scripts_patch_custom.Rd | 2 civis-2.0.0/civis/man/scripts_patch_javascript.Rd | 4 civis-2.0.0/civis/man/scripts_patch_python3.Rd | 9 civis-2.0.0/civis/man/scripts_patch_r.Rd | 9 civis-2.0.0/civis/man/scripts_patch_sql.Rd | 4 civis-2.0.0/civis/man/scripts_post.Rd | 4 civis-2.0.0/civis/man/scripts_post_containers.Rd | 26 civis-2.0.0/civis/man/scripts_post_containers_clone.Rd | 6 civis-2.0.0/civis/man/scripts_post_containers_runs_logs.Rd | 2 civis-2.0.0/civis/man/scripts_post_custom.Rd | 2 civis-2.0.0/civis/man/scripts_post_custom_clone.Rd | 2 civis-2.0.0/civis/man/scripts_post_javascript.Rd | 4 civis-2.0.0/civis/man/scripts_post_javascript_clone.Rd | 2 civis-2.0.0/civis/man/scripts_post_python3.Rd | 9 civis-2.0.0/civis/man/scripts_post_python3_clone.Rd | 3 civis-2.0.0/civis/man/scripts_post_r.Rd | 10 civis-2.0.0/civis/man/scripts_post_r_clone.Rd | 3 civis-2.0.0/civis/man/scripts_post_sql.Rd | 4 civis-2.0.0/civis/man/scripts_post_sql_clone.Rd | 2 civis-2.0.0/civis/man/scripts_put_containers.Rd | 26 civis-2.0.0/civis/man/scripts_put_containers_archive.Rd | 6 civis-2.0.0/civis/man/scripts_put_containers_projects.Rd | 4 civis-2.0.0/civis/man/scripts_put_containers_shares_groups.Rd | 6 civis-2.0.0/civis/man/scripts_put_containers_shares_users.Rd | 6 civis-2.0.0/civis/man/scripts_put_custom.Rd | 2 civis-2.0.0/civis/man/scripts_put_custom_archive.Rd | 2 civis-2.0.0/civis/man/scripts_put_custom_projects.Rd | 4 civis-2.0.0/civis/man/scripts_put_custom_shares_groups.Rd | 6 civis-2.0.0/civis/man/scripts_put_custom_shares_users.Rd | 6 civis-2.0.0/civis/man/scripts_put_javascript.Rd | 4 civis-2.0.0/civis/man/scripts_put_javascript_archive.Rd | 2 civis-2.0.0/civis/man/scripts_put_javascript_git.Rd | 4 civis-2.0.0/civis/man/scripts_put_javascript_projects.Rd | 4 civis-2.0.0/civis/man/scripts_put_javascript_shares_groups.Rd | 6 civis-2.0.0/civis/man/scripts_put_javascript_shares_users.Rd | 6 civis-2.0.0/civis/man/scripts_put_python3.Rd | 9 civis-2.0.0/civis/man/scripts_put_python3_archive.Rd | 3 civis-2.0.0/civis/man/scripts_put_python3_git.Rd | 4 civis-2.0.0/civis/man/scripts_put_python3_projects.Rd | 4 civis-2.0.0/civis/man/scripts_put_python3_shares_groups.Rd | 6 civis-2.0.0/civis/man/scripts_put_python3_shares_users.Rd | 6 civis-2.0.0/civis/man/scripts_put_r.Rd | 10 civis-2.0.0/civis/man/scripts_put_r_archive.Rd | 3 civis-2.0.0/civis/man/scripts_put_r_git.Rd | 4 civis-2.0.0/civis/man/scripts_put_r_projects.Rd | 4 civis-2.0.0/civis/man/scripts_put_r_shares_groups.Rd | 6 civis-2.0.0/civis/man/scripts_put_r_shares_users.Rd | 6 civis-2.0.0/civis/man/scripts_put_sql.Rd | 4 civis-2.0.0/civis/man/scripts_put_sql_archive.Rd | 2 civis-2.0.0/civis/man/scripts_put_sql_git.Rd | 4 civis-2.0.0/civis/man/scripts_put_sql_projects.Rd | 4 civis-2.0.0/civis/man/scripts_put_sql_shares_groups.Rd | 6 civis-2.0.0/civis/man/scripts_put_sql_shares_users.Rd | 6 civis-2.0.0/civis/man/search_list.Rd | 3 civis-2.0.0/civis/man/services_delete_projects.Rd | 4 civis-2.0.0/civis/man/services_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/services_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/services_delete_tokens.Rd | 2 civis-2.0.0/civis/man/services_get.Rd | 1 civis-2.0.0/civis/man/services_list_deployments_logs.Rd | 4 civis-2.0.0/civis/man/services_list_projects.Rd | 4 civis-2.0.0/civis/man/services_list_shares.Rd | 2 civis-2.0.0/civis/man/services_list_tokens.Rd | 15 civis-2.0.0/civis/man/services_patch.Rd | 8 civis-2.0.0/civis/man/services_post.Rd | 8 civis-2.0.0/civis/man/services_post_clone.Rd | 1 civis-2.0.0/civis/man/services_post_tokens.Rd | 23 civis-2.0.0/civis/man/services_put.Rd | 8 civis-2.0.0/civis/man/services_put_archive.Rd | 1 civis-2.0.0/civis/man/services_put_projects.Rd | 4 civis-2.0.0/civis/man/services_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/services_put_shares_users.Rd | 6 civis-2.0.0/civis/man/sql.Rd |only civis-2.0.0/civis/man/tables_delete_projects.Rd |only civis-2.0.0/civis/man/tables_get.Rd | 5 civis-2.0.0/civis/man/tables_list_columns.Rd | 3 civis-2.0.0/civis/man/tables_list_projects.Rd |only civis-2.0.0/civis/man/tables_patch.Rd | 9 civis-2.0.0/civis/man/tables_post_refresh.Rd | 5 civis-2.0.0/civis/man/tables_post_scan.Rd |only civis-2.0.0/civis/man/tables_put_projects.Rd |only civis-2.0.0/civis/man/templates_delete_reports_shares_groups.Rd | 4 civis-2.0.0/civis/man/templates_delete_reports_shares_users.Rd | 4 civis-2.0.0/civis/man/templates_delete_scripts_projects.Rd | 4 civis-2.0.0/civis/man/templates_delete_scripts_shares_groups.Rd | 4 civis-2.0.0/civis/man/templates_delete_scripts_shares_users.Rd | 4 civis-2.0.0/civis/man/templates_get_scripts.Rd | 1 civis-2.0.0/civis/man/templates_list_reports_shares.Rd | 2 civis-2.0.0/civis/man/templates_list_scripts_projects.Rd | 4 civis-2.0.0/civis/man/templates_list_scripts_shares.Rd | 2 civis-2.0.0/civis/man/templates_patch_scripts.Rd | 1 civis-2.0.0/civis/man/templates_post_scripts.Rd | 1 civis-2.0.0/civis/man/templates_put_reports_shares_groups.Rd | 6 civis-2.0.0/civis/man/templates_put_reports_shares_users.Rd | 6 civis-2.0.0/civis/man/templates_put_scripts.Rd | 1 civis-2.0.0/civis/man/templates_put_scripts_projects.Rd | 4 civis-2.0.0/civis/man/templates_put_scripts_shares_groups.Rd | 6 civis-2.0.0/civis/man/templates_put_scripts_shares_users.Rd | 6 civis-2.0.0/civis/man/transfer_table.Rd | 12 civis-2.0.0/civis/man/users_get.Rd | 5 civis-2.0.0/civis/man/users_list_me.Rd | 4 civis-2.0.0/civis/man/users_patch_me.Rd | 4 civis-2.0.0/civis/man/users_post_api_keys.Rd | 6 civis-2.0.0/civis/man/workflows_delete_projects.Rd | 4 civis-2.0.0/civis/man/workflows_delete_shares_groups.Rd | 4 civis-2.0.0/civis/man/workflows_delete_shares_users.Rd | 4 civis-2.0.0/civis/man/workflows_list_git.Rd | 4 civis-2.0.0/civis/man/workflows_list_git_commits.Rd | 4 civis-2.0.0/civis/man/workflows_list_projects.Rd | 4 civis-2.0.0/civis/man/workflows_list_shares.Rd | 2 civis-2.0.0/civis/man/workflows_put_git.Rd | 4 civis-2.0.0/civis/man/workflows_put_projects.Rd | 4 civis-2.0.0/civis/man/workflows_put_shares_groups.Rd | 6 civis-2.0.0/civis/man/workflows_put_shares_users.Rd | 6 civis-2.0.0/civis/man/write_civis_file.Rd | 29 civis-2.0.0/civis/man/write_job_output.Rd |only civis-2.0.0/civis/tests/testthat/test_autogen.R | 96 civis-2.0.0/civis/tests/testthat/test_await.R | 72 civis-2.0.0/civis/tests/testthat/test_civis_future.R | 24 civis-2.0.0/civis/tests/testthat/test_civis_ml_plot.R | 6 civis-2.0.0/civis/tests/testthat/test_civis_ml_utils.R | 31 civis-2.0.0/civis/tests/testthat/test_client_base.R | 8 civis-2.0.0/civis/tests/testthat/test_io.R | 50 civis-2.0.0/civis/tests/testthat/test_pagination.R | 2 civis-2.0.0/civis/tests/testthat/test_scripts.R |only civis-2.0.0/civis/tools/generate_default_client.R | 4 civis-2.0.0/civis/tools/integration_tests/smoke_test.R | 7 civis-2.0.0/civis/vignettes/civis_ml.Rmd | 6 civis-2.0.0/civis/vignettes/civis_scripts.Rmd |only civis-2.0.0/civis/vignettes/concurrency.Rmd | 4 civis-2.0.0/civis/vignettes/data_import_and_export.Rmd | 37 489 files changed, 5510 insertions(+), 4143 deletions(-)
Title: Genotype Quality Control with 'PLINK'
Description: Genotyping arrays enable the direct measurement of an individuals
genotype at thousands of markers. 'plinkQC' facilitates genotype quality
control for genetic association studies as described by Anderson and
colleagues (2010) <doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic
statistics (e.g. missing genotyping rates per individual, allele frequencies
per genetic marker) and relationship functions accessible from 'R' and
generates a per-individual and per-marker quality control report.
Individuals and markers that fail the quality control can subsequently be
removed to generate a new, clean dataset. Removal of individuals based on
relationship status is optimised to retain as many individuals as possible
in the study.
Author: Hannah Meyer [aut, cre] (<https://orcid.org/0000-0003-4564-0899>)
Maintainer: Hannah Meyer <hannah.v.meyer@gmail.com>
Diff between plinkQC versions 0.2.1 dated 2019-03-01 and 0.2.2 dated 2019-06-19
DESCRIPTION | 8 +++---- MD5 | 34 +++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 5 ++++ R/individualQC.R | 49 ++++++++++++++++++++++++++++++++++---------- R/plinkQC.R | 2 - README.md | 4 +-- build/vignette.rds |binary inst/doc/AncestryCheck.R | 2 - inst/doc/AncestryCheck.Rmd | 2 - inst/doc/AncestryCheck.pdf |binary inst/doc/Genomes1000.pdf |binary inst/doc/HapMap.pdf |binary inst/doc/plinkQC.R | 30 +++++++++++++++----------- inst/doc/plinkQC.Rmd | 42 +++++++++++++++++++++++-------------- inst/doc/plinkQC.pdf |binary vignettes/AncestryCheck.Rmd | 2 - vignettes/plinkQC.Rmd | 42 +++++++++++++++++++++++-------------- 18 files changed, 140 insertions(+), 83 deletions(-)
Title: Visualisation Toolbox for 'easystats' and Extra Geoms, Themes
and Color Palettes for 'ggplot2'
Description: Provides plotting utilities supporting easystats-packages (<https://github.com/easystats/easystats>)
and some extra themes, geoms, and scales for 'ggplot2'. Color scales are
based on <https://www.materialui.co/colors>.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, inv] (<https://orcid.org/0000-0001-5375-9967>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between see versions 0.1.0 dated 2019-05-24 and 0.2.0 dated 2019-06-19
DESCRIPTION | 16 ++++---- MD5 | 58 +++++++++++++++++------------ NAMESPACE | 22 +++++++++++ NEWS.md |only R/data_plot.R | 76 +++++++++++++++++++++++--------------- R/geom_point2.R | 8 ++-- R/geom_poolpoint.R |only R/plot.bayesfactor_models.R | 19 ++++++++- R/plot.check_collinearity.R |only R/plot.check_distribution.R |only R/plot.check_heteroscedasticity.R |only R/plot.check_homogeneity.R |only R/plot.check_normality.R |only R/plot.check_outliers.R |only R/plot.ci.R | 17 +++++++- R/plot.equivalence_test.R | 9 ++++ R/plot.hdi.R | 19 ++++++++- R/plot.p_direction.R | 10 ++++- R/plot.rope.R | 9 ++++ R/print.check_model.R |only R/scale_color_flat.R | 4 +- R/theme_abyss.R | 6 ++- R/theme_blackboard.R | 51 ++++++++++++++++++++----- R/theme_lucid.R |only R/theme_modern.R | 7 ++- R/utils.R | 20 ++++++++-- man/add_plot_attributes.Rd | 3 + man/data_plot.Rd | 66 ++++++++++++++++++++++----------- man/geom_point2.Rd | 10 ++--- man/geom_poolpoint.Rd |only man/geom_violindot.Rd | 3 + man/geom_violinhalf.Rd | 3 + man/theme_abyss.Rd | 17 +++++--- man/theme_blackboard.Rd | 7 +++ man/theme_lucid.Rd |only man/theme_modern.Rd | 17 +++++--- 36 files changed, 342 insertions(+), 135 deletions(-)
Title: Statistical Process Control -- Calculation of ARL and Other
Control Chart Performance Measures
Description: Evaluation of control charts by means of
the zero-state, steady-state ARL (Average Run Length) and RL quantiles.
Setting up control charts for given in-control ARL. The control charts
under consideration are one- and two-sided EWMA, CUSUM, and
Shiryaev-Roberts schemes for monitoring the mean or variance of normally
distributed independent data. ARL calculation of the same set of schemes under drift (in the mean) are added.
Eventually, all ARL measures for the multivariate EWMA (MEWMA) are provided.
Author: Sven Knoth
Maintainer: Sven Knoth <Sven.Knoth@gmx.de>
Diff between spc versions 0.6.0 dated 2018-04-12 and 0.6.1 dated 2019-06-19
DESCRIPTION | 8 MD5 | 56 - NAMESPACE | 3 R/euklid.ewma.arl.R |only R/p.ewma.arl.R | 35 R/pois.ewma.arl.R |only R/pois.ewma.crit.R |only R/tewma.arl.R |only R/xewma.arl.R | 11 man/euklid.ewma.arl.Rd |only man/lns2ewma.crit.Rd | 8 man/mewma.psi.Rd | 7 man/p.ewma.arl.Rd | 7 man/pois.ewma.arl.Rd |only man/pois.ewma.crit.Rd |only man/quadrature.nodes.weights.Rd | 3 man/sewma.arl.prerun.Rd | 2 man/sewma.crit.prerun.Rd | 4 man/sewma.q.Rd | 2 man/sewma.q.prerun.Rd | 2 man/sewma.sf.Rd | 2 man/sewma.sf.prerun.Rd | 2 man/tewma.arl.Rd |only man/xewma.arl.Rd | 8 man/xsewma.q.Rd | 2 man/xsewma.sf.Rd | 2 src/allspc.c | 2212 +++++++++++++++++++++++++++++++++++++++- src/cewma_arl_be.c |only src/cewma_crit_be.c |only src/euklid_ewma_arl.c |only src/ewma_p_arl_be.c | 15 src/spc_init.c | 16 src/tewma_arl_wowR.c |only src/xewma_ad.c | 2 src/xewma_arl.c | 20 35 files changed, 2342 insertions(+), 87 deletions(-)
Title: Ordinal Data Clustering, Co-Clustering and Classification
Description: Ordinal data classification, clustering and co-clustering using model-based approach with the Bos distribution for ordinal data (Christophe Biernacki and Julien Jacques (2016) <doi:10.1007/s11222-015-9585-2>).
Author: Margot Selosse, Julien Jacques, Christophe Biernacki
Maintainer: Margot Selosse <margot.selosse@gmail.com>
Diff between ordinalClust versions 1.3.1 dated 2018-08-06 and 1.3.3 dated 2019-06-19
ordinalClust-1.3.1/ordinalClust/man/plot-methods.Rd |only ordinalClust-1.3.1/ordinalClust/man/predict-methods.Rd |only ordinalClust-1.3.3/ordinalClust/DESCRIPTION | 11 ordinalClust-1.3.3/ordinalClust/MD5 | 91 - ordinalClust-1.3.3/ordinalClust/NAMESPACE | 3 ordinalClust-1.3.3/ordinalClust/R/RcppExports.R | 24 ordinalClust-1.3.3/ordinalClust/R/bosclassif.R | 9 ordinalClust-1.3.3/ordinalClust/R/bosclust.R | 8 ordinalClust-1.3.3/ordinalClust/R/boscoclust.R | 9 ordinalClust-1.3.3/ordinalClust/R/bosplot.R | 8 ordinalClust-1.3.3/ordinalClust/R/bossummary.R |only ordinalClust-1.3.3/ordinalClust/R/check-params-module.R | 2 ordinalClust-1.3.3/ordinalClust/R/get_seed.R |only ordinalClust-1.3.3/ordinalClust/R/methodsDef.R | 43 ordinalClust-1.3.3/ordinalClust/R/predictions.R | 3 ordinalClust-1.3.3/ordinalClust/R/testSeedR.R |only ordinalClust-1.3.3/ordinalClust/build/vignette.rds |binary ordinalClust-1.3.3/ordinalClust/data/Msimulated.RData |binary ordinalClust-1.3.3/ordinalClust/data/dataqol.RData |binary ordinalClust-1.3.3/ordinalClust/data/dataqol.classif.RData |binary ordinalClust-1.3.3/ordinalClust/inst/doc/ordinalClust.R | 90 - ordinalClust-1.3.3/ordinalClust/inst/doc/ordinalClust.Rmd | 93 - ordinalClust-1.3.3/ordinalClust/inst/doc/ordinalClust.html | 680 ++++++---- ordinalClust-1.3.3/ordinalClust/man/bosclassif.Rd | 10 ordinalClust-1.3.3/ordinalClust/man/bosclust.Rd | 10 ordinalClust-1.3.3/ordinalClust/man/boscoclust.Rd | 10 ordinalClust-1.3.3/ordinalClust/man/plot.Rd | 99 - ordinalClust-1.3.3/ordinalClust/man/predict.Rd |only ordinalClust-1.3.3/ordinalClust/man/summary.Rd |only ordinalClust-1.3.3/ordinalClust/src/Bos.cpp | 35 ordinalClust-1.3.3/ordinalClust/src/Bos.h | 7 ordinalClust-1.3.3/ordinalClust/src/BosPredict.cpp | 18 ordinalClust-1.3.3/ordinalClust/src/BosPredict.h | 8 ordinalClust-1.3.3/ordinalClust/src/ClassificationContext.cpp | 134 + ordinalClust-1.3.3/ordinalClust/src/ClassificationContext.h | 12 ordinalClust-1.3.3/ordinalClust/src/ClassificationMContext.cpp | 7 ordinalClust-1.3.3/ordinalClust/src/ClassificationMContext.h | 5 ordinalClust-1.3.3/ordinalClust/src/ClusteringContext.cpp | 158 +- ordinalClust-1.3.3/ordinalClust/src/ClusteringContext.h | 18 ordinalClust-1.3.3/ordinalClust/src/CoClusteringContext.cpp | 214 ++- ordinalClust-1.3.3/ordinalClust/src/CoClusteringContext.h | 17 ordinalClust-1.3.3/ordinalClust/src/Distribution.cpp | 25 ordinalClust-1.3.3/ordinalClust/src/Distribution.h | 4 ordinalClust-1.3.3/ordinalClust/src/Makevars | 3 ordinalClust-1.3.3/ordinalClust/src/RcppExports.cpp | 59 ordinalClust-1.3.3/ordinalClust/src/ordinalClust.cpp | 199 +- ordinalClust-1.3.3/ordinalClust/vignettes/figures/clust.pdf |only ordinalClust-1.3.3/ordinalClust/vignettes/figures/clust.png |binary ordinalClust-1.3.3/ordinalClust/vignettes/figures/coclust.pdf |only ordinalClust-1.3.3/ordinalClust/vignettes/figures/coclust.png |binary ordinalClust-1.3.3/ordinalClust/vignettes/ordinalClust.Rmd | 93 - 51 files changed, 1342 insertions(+), 877 deletions(-)
Title: Power Calculations for Assessing Correlates of Risk in Clinical
Efficacy Trials
Description: Calculates power for assessment of intermediate biomarker responses as correlates of risk in the active treatment group in clinical efficacy trials, as described in Gilbert, Janes, and Huang, Power/Sample Size Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials (2016, Statistics in Medicine). The methods differ from past approaches by accounting for the level of clinical treatment efficacy overall and in biomarker response subgroups, which enables the correlates of risk results to be interpreted in terms of potential correlates of efficacy/protection. The methods also account for inter-individual variability of the observed biomarker response that is not biologically relevant (e.g., due to technical measurement error of the laboratory assay used to measure the biomarker response), which is important because power to detect a specified correlate of risk effect size is heavily affected by the biomarker's measurement error. The methods can be used for a general binary clinical endpoint model with a univariate dichotomous, trichotomous, or continuous biomarker response measured in active treatment recipients at a fixed timepoint after randomization, with either case-cohort Bernoulli sampling or case-control without-replacement sampling of the biomarker (a baseline biomarker is handled as a trivial special case). In a specified two-group trial design, the computeN() function can initially be used for calculating additional requisite design parameters pertaining to the target population of active treatment recipients observed to be at risk at the biomarker sampling timepoint. Subsequently, the power calculation employs an inverse probability weighted logistic regression model fitted by the tps() function in the 'osDesign' package. Power results as well as the relationship between the correlate of risk effect size and treatment efficacy can be visualized using various plotting functions. To link power calculations for detecting a correlate of risk and a correlate of treatment efficacy, a baseline immunogenicity predictor (BIP) can be simulated according to a specified classification rule (for dichotomous or trichotomous BIPs) or correlation with the biomarker response (for continuous BIPs), then outputted along with biomarker response data under assignment to treatment, and clinical endpoint data for both treatment and placebo groups.
Author: Stephanie Wu [aut],
Michal Juraska [aut, cre],
Peter Gilbert [aut],
Yunda Huang [aut]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between CoRpower versions 1.0.1 dated 2019-04-25 and 1.0.2 dated 2019-06-19
DESCRIPTION | 6 +- MD5 | 24 ++++---- R/computePower.R | 145 ++++++++++++++++++++++++++++--------------------- R/plotPowerCont.R | 44 +++++++++++++- R/plotPowerTri.R | 56 ++++++++++++++++-- R/plotROCcurveTri.R | 2 R/plotRRgradVE.R | 59 ++++++++++++++++++- R/plotVElatCont.R | 22 ++----- man/computePower.Rd | 7 +- man/plotPowerCont.Rd | 14 ++++ man/plotPowerTri.Rd | 17 ++++- man/plotROCcurveTri.Rd | 2 man/plotRRgradVE.Rd | 14 ++++ 13 files changed, 297 insertions(+), 115 deletions(-)
Title: A Convenient API for Accessing United States Census Bureau's
Quarterly Workforce Indicator
Description: The purpose of this package is to access the
United States Census Bureau's Quarterly Workforce Indicator data. Additionally,
the data will be retrieved in a tidy format for further manipulation with full variable
descriptions added if desired. Information about the United States Census Bureau's
Quarterly Workforce Indicator is available at
<https://www.census.gov/data/developers/data-sets/qwi.html>.
Author: Michael DeWitt [aut, cre] (<https://orcid.org/0000-0001-8940-1967>),
Mona Ahmadiani [aut] (<https://orcid.org/0000-0002-1269-5685>),
Adam S. Hyde [aut] (<https://orcid.org/0000-0003-1205-0032>)
Maintainer: Michael DeWitt <me.dewitt.jr@gmail.com>
Diff between tidyqwi versions 0.1.0 dated 2019-03-06 and 0.1.1 dated 2019-06-19
DESCRIPTION | 15 +++--- MD5 | 30 +++++++------ NEWS.md | 7 +++ R/check_census_api_call.R | 20 ++++++-- R/check_fips.R | 3 - README.md | 33 +++++++++++--- build/vignette.rds |binary inst/CITATION |only inst/doc/multi_state_year.R | 4 - inst/doc/multi_state_year.Rmd | 6 +- inst/doc/multi_state_year.html | 13 +++-- inst/paper.bib | 70 ++++++++++++++++++++++++++++--- inst/paper.md | 24 ++++++++-- man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |only tests/testthat/test.R | 3 - vignettes/multi_state_year.Rmd | 6 +- 17 files changed, 174 insertions(+), 60 deletions(-)
Title: Adapt Numerical Records to Fit (in)Equality Restrictions
Description: Minimally adjust the values of numerical records in a data.frame, such
that each record satisfies a predefined set of equality and/or inequality
constraints. The constraints can be defined using the 'validate' package.
The core algorithms have recently been moved to the 'lintools' package,
refer to 'lintools' for a more basic interface and access to a version
of the algorithm that works with sparse matrices.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between rspa versions 0.2.4 dated 2019-05-17 and 0.2.5 dated 2019-06-19
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ R/adjust.R | 6 +++--- man/adjust.Rd | 6 +++--- 5 files changed, 16 insertions(+), 13 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev <selesnow@gmail.com>
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 1.9.0 dated 2019-05-21 and 1.9.1 dated 2019-06-19
DESCRIPTION | 14 MD5 | 14 NEWS.md | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rfacebookstat-get-statistics.Rmd | 2 inst/doc/rfacebookstat-get-statistics.html | 738 ++++++++++++++++------------- vignettes/rfacebookstat-get-statistics.Rmd | 2 8 files changed, 437 insertions(+), 345 deletions(-)
Title: 'ggplot2' Extension for Seasonal and Trading Day Adjustment with
'RJDemetra'
Description: Provides 'ggplot2' functions to return the results of seasonal and trading day adjustment
made by 'RJDemetra'. 'RJDemetra' is an 'R' interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>),
the seasonal adjustment software officially recommended to the members of the European Statistical System and
the European System of Central Banks.
Author: Alain Quartier-la-Tente [aut, cre]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between ggdemetra versions 0.1.0 dated 2019-04-24 and 0.2.0 dated 2019-06-19
DESCRIPTION | 6 +- MD5 | 43 ++++++++------ NEWS.md |only R/geom_arima.R | 7 +- R/geom_diagnostics.R | 11 ++- R/geom_outliers.R | 7 +- R/geom_sa.R | 16 +++-- R/seasonal_adjustment.R | 93 ++++++++++++++++++++++++++----- README.md | 55 ++++++++++++------ inst/doc/ggdemetra.R | 30 ++++------ inst/doc/ggdemetra.Rmd | 32 +++++----- inst/doc/ggdemetra.html | 91 +++++++++++++++--------------- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |only man/figures/ggdemetra.png |only man/figures/logo.png |only man/figures/logo.svg |only man/geom_arima.Rd | 2 man/geom_diagnostics.Rd | 6 +- man/geom_outlier.Rd | 2 man/geom_sa.Rd | 2 vignettes/ggdemetra.Rmd | 32 +++++----- 25 files changed, 266 insertions(+), 169 deletions(-)
Title: Partitioning Uncertainty Components of an Incomplete Ensemble of
Climate Projections
Description: These functions use data augmentation and Bayesian techniques for the assessment of single-member and incomplete ensembles of climate projections. It provides unbiased estimates of climate change responses of all simulation chains and of all uncertainty variables. It additionally propagates uncertainty due to missing information in the estimates.
- Evin, G., B. Hingray, J. Blanchet, N. Eckert, S. Morin, and D. Verfaillie. (2019) <doi:10.1175/JCLI-D-18-0606.1>.
Author: Guillaume Evin [aut, cre]
Maintainer: Guillaume Evin <guillaume.evin@irstea.fr>
Diff between QUALYPSO versions 1.0.1 dated 2019-05-24 and 1.1 dated 2019-06-19
DESCRIPTION | 8 - MD5 | 12 +- R/QUALYPSO.r | 111 ++++++++++++++++---------- man/QUALYPSO.Rd | 8 - man/plotQUALYPSOTotalVarianceDecomposition.Rd | 10 +- man/plotQUALYPSOeffect.Rd | 12 -- man/plotQUALYPSOgrandmean.Rd | 12 -- 7 files changed, 99 insertions(+), 74 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Author: Sacha Epskamp [aut, cre],
Giulio Costantini [aut],
Jonas Haslbeck [aut],
Adela Isvoranu [aut],
Angelique O. J. Cramer [ctb],
Lourens J. Waldorp [ctb],
Verena D. Schmittmann [ctb],
Denny Borsboom [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.6.2 dated 2019-05-09 and 1.6.3 dated 2019-06-19
DESCRIPTION | 8 ++-- MD5 | 20 +++++----- NEWS | 7 +++ R/PLOT.R | 4 +- R/clusteringTable.R | 21 +++++++++-- R/drawNode.R | 12 ++++-- R/ggmFit.R | 15 +++++--- R/glasso_methods.R | 4 +- R/qgraph.R | 96 +++++++++++++++++++++++++++++++++++++++++++++++++++- man/ggmFit.Rd | 6 ++- man/qgraph.Rd | 15 ++++++++ 11 files changed, 177 insertions(+), 31 deletions(-)
Title: Feature Selection (Including Multiple Solutions) and Bayesian
Networks
Description: Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. References: a) Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets. Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>. b) Tsagris, M., Lagani, V. and Tsamardinos, I. (2018). Feature selection for high-dimensional temporal data. BMC Bioinformatics, 19:17. <doi:10.1186/s12859-018-2023-7>. c) Tsagris, M., Borboudakis, G., Lagani, V. and Tsamardinos, I. (2018). Constraint-based causal discovery with mixed data. International Journal of Data Science and Analytics, 6(1): 19-30. <doi:10.1007/s41060-018-0097-y>. d) Tsagris, M., Papadovasilakis, Z., Lakiotaki, K. and Tsamardinos, I. (2018). Efficient feature selection on gene expression data: Which algorithm to use? BioRxiv. <doi:10.1101/431734>. e) Tsagris, M. (2019). Bayesian Network Learning with the PC Algorithm: An Improved and Correct Variation. Applied Artificial Intelligence, 33(2):101-123. <doi:10.1080/08839514.2018.1526760>. f) Borboudakis, G. and Tsamardinos, I. (2019). Forward-Backward Selection with Early Dropping. Journal of Machine Learning Research 20: 1-39.
Author: Michail Tsagris [aut, cre],
Ioannis Tsamardinos [aut, cph],
Vincenzo Lagani [aut, cph],
Giorgos Athineou [aut],
Giorgos Borboudakis [ctb],
Anna Roumpelaki [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MXM versions 1.4.3 dated 2019-05-27 and 1.4.4 dated 2019-06-19
DESCRIPTION | 12 MD5 | 213 ++++++++--------- R/MMPC.R | 4 R/MMPC.timeclass.R | 4 R/SES.timeclass.R | 3 R/beta.mod.R | 6 R/beta.reg.R | 4 R/beta.regs.R | 43 +-- R/betamle.wei.R | 4 R/bic.betafsreg.R | 4 R/bic.clogit.fsreg.R | 8 R/big.gomp.R | 16 - R/bs.reg.R | 5 R/censIndCR.R | 42 +-- R/censIndLLR.R | 2 R/censIndWR.R | 2 R/clogit.fsreg.R | 26 +- R/clogit.fsreg_2.R | 5 R/cond.regs.R | 266 ++++++++++----------- R/corgraph.R | 6 R/ebic.bsreg.R | 39 +-- R/ebic.model.R | 4 R/ebic.regs.R | 160 +++++++----- R/ebic.spml.bsreg.R |only R/ebic.univregs.R | 147 ++++++----- R/fbed.ebic.R | 16 - R/fbed.lr.R | 16 - R/fbed.reg.R | 6 R/fbedreg.bic.R | 8 R/gee.condregs.R | 3 R/generatefolds.R | 3 R/glmm.condregs.R | 6 R/kfbed.reg.R | 10 R/lm.fsreg_2.R | 6 R/mmhc.skel.R | 4 R/mmpc.or.R | 8 R/ordinal.reg.R | 3 R/perm.betaregs.R | 40 +-- R/perm.mmpc.R | 3 R/perm.univregs.R | 484 +++++++++++++++++++-------------------- R/perm.zipregs.R | 36 +- R/permCR.R | 22 - R/permFisher.R | 3 R/permMultinom.R | 1 R/permPois.R | 4 R/permReg.R | 3 R/permTobit.R | 1 R/permWR.R | 1 R/ridgereg.cv.R | 11 R/testIndBeta.R | 4 R/testIndGEEGamma.R | 8 R/testIndGEELogistic.R | 29 +- R/testIndGEENormLog.R | 15 - R/testIndGEEPois.R | 11 R/testIndGEEReg.R | 10 R/testIndGLMMCR.R | 10 R/testIndGLMMGamma.R | 70 ++--- R/testIndGLMMLogistic.R | 66 ++--- R/testIndGLMMNormLog.R | 54 ++-- R/testIndGLMMOrdinal.R | 45 +-- R/testIndGLMMPois.R | 44 +-- R/testIndGLMMReg.R | 41 +-- R/testIndLMM.R | 29 +- R/testIndLogistic.R | 1 R/testIndMVreg.R | 1 R/testIndMultinom.R | 7 R/testIndNB.R | 1 R/testIndNormLog.R | 15 - R/testIndPois.R | 1 R/testIndQBinom.R | 1 R/testIndRQ.R | 74 ++--- R/testIndReg.R | 12 R/testIndSPML.R | 1 R/testIndSpearman.R | 100 ++++---- R/testIndTimeLogistic.R | 9 R/testIndTimeMultinom.R | 1 R/testIndTobit.R | 20 - R/univregs.R | 275 +++++++++++----------- R/wald.betaregs.R | 35 +- R/wald.mmpc.R | 8 R/wald.univregs.R | 232 +++++++++--------- R/waldBeta.R | 38 +-- R/waldCR.R | 46 +-- R/waldZIP.R | 1 R/zip.reg.R | 6 R/zip.regs.R | 36 +- inst/doc/FBED_KVerrou_2_5.html | 39 +-- inst/doc/FS_guide.pdf |binary inst/doc/MMPC_tutorial.html | 14 - inst/doc/Networks_KVerrou.html | 8 inst/doc/SES_KMVerrou_11_12.html | 42 +-- inst/doc/article.pdf |binary inst/doc/guide.pdf |binary man/MXM-internal.Rd | 4 man/MXM-package.Rd | 7 man/bbc.Rd | 2 man/beta.mod.Rd | 2 man/big.gomp.Rd | 2 man/cv.gomp.Rd | 4 man/ebic.regs.Rd | 3 man/fbed.reg.Rd | 4 man/gomp.Rd | 2 man/logiquant.regs.Rd | 2 man/pc.sel.Rd | 2 man/sp.logiregs.Rd | 2 man/testIndTobit.Rd | 2 man/univregs.Rd | 34 +- man/wald.logisticregs.Rd | 2 108 files changed, 1639 insertions(+), 1618 deletions(-)
Title: Assessing Skill of Climate Forecasts on Seasonal-to-Decadal
Timescales
Description: Exploits dynamical seasonal forecasts in order to provide
information relevant to stakeholders at the seasonal timescale. The package
contains process-based methods for forecast calibration, bias correction,
statistical and stochastic downscaling, optimal forecast combination and
multivariate verification, as well as basic and advanced tools to obtain
tailored products. This package was developed in the context of the
ERA4CS project MEDSCOPE.
Doblas-Reyes et al. (2005) <doi:10.1111/j.1600-0870.2005.00104.x>.
Mishra et al. (2018) <doi:10.1007/s00382-018-4404-z>.
Terzago et al. (2018) <doi:10.5194/nhess-18-2825-2018>.
Torralba et al. (2017) <doi:10.1175/JAMC-D-16-0204.1>.
D'Onofrio et al. (2014) <doi:10.1175/JHM-D-13-096.1>.
Author: BSC-CNS [cph],
Louis-Philippe Caron [aut] (<https://orcid.org/0000-0001-5221-0147>),
Jost von Hardenberg [aut] (<https://orcid.org/0000-0002-5312-8070>),
Nuria Perez-Zanon [aut, cre] (<https://orcid.org/0000-0001-8568-3071>),
Llorenç LLedo [aut],
Nicolau Manubens [aut],
Niti Mishra [ctb],
Veronica Torralba [aut],
Deborah Verfaillie [aut],
Lauriane Batte [ctb],
Jesus Peña [ctb],
Bert van Schaeybroeck [ctb]
Maintainer: Nuria Perez-Zanon <nuria.perez@bsc.es>
Diff between CSTools versions 1.0.0 dated 2019-04-24 and 1.0.1 dated 2019-06-19
DESCRIPTION | 13 - MD5 | 30 +- NAMESPACE | 1 R/CST_Calibration.R | 2 R/CST_MultiMetric.R | 2 R/CST_RFWeights.R | 4 R/CST_RainFARM.R | 10 R/PlotCombinedMap.R |only R/PlotMostLikelyQuantileMap.R | 414 --------------------------------- inst/doc/MultiModelSkill_vignette.Rmd | 4 inst/doc/MultiModelSkill_vignette.html | 6 man/CST_BiasCorrection.Rd | 1 man/CST_RFWeights.Rd | 4 man/PlotCombinedMap.Rd |only man/RainFARM.Rd | 2 tests/testthat/test-PlotForecastPDF.R | 17 - vignettes/MultiModelSkill_vignette.Rmd | 4 17 files changed, 42 insertions(+), 472 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] (<https://orcid.org/0000-0002-6294-8185>),
Martin Maechler [ctb],
Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.0-10 dated 2019-03-04 and 1.0-11 dated 2019-06-19
DESCRIPTION | 12 ++-- MD5 | 20 +++--- R/mvt.R | 4 - R/noisy-root.R | 3 + build/vignette.rds |binary inst/NEWS | 5 + inst/doc/MVT_Rnews.pdf |binary man/pmvnorm.Rd | 2 src/mvt.f | 123 +++++++++++++++++++++---------------------- tests/bugfix-tests.R | 25 ++++++++ tests/bugfix-tests.Rout.save | 33 ++++++++++- 11 files changed, 145 insertions(+), 82 deletions(-)
Title: Metaheuristic for Optimization
Description: An implementation of metaheuristic algorithms for continuous optimization. Currently, the package contains the implementations of 21 algorithms, as follows: particle swarm optimization (Kennedy and Eberhart, 1995), ant lion optimizer (Mirjalili, 2015 <doi:10.1016/j.advengsoft.2015.01.010>), grey wolf optimizer (Mirjalili et al., 2014 <doi:10.1016/j.advengsoft.2013.12.007>), dragonfly algorithm (Mirjalili, 2015 <doi:10.1007/s00521-015-1920-1>), firefly algorithm (Yang, 2009 <doi:10.1007/978-3-642-04944-6_14>), genetic algorithm (Holland, 1992, ISBN:978-0262581110), grasshopper optimisation algorithm (Saremi et al., 2017 <doi:10.1016/j.advengsoft.2017.01.004>), harmony search algorithm (Mahdavi et al., 2007 <doi:10.1016/j.amc.2006.11.033>), moth flame optimizer (Mirjalili, 2015 <doi:10.1016/j.knosys.2015.07.006>, sine cosine algorithm (Mirjalili, 2016 <doi:10.1016/j.knosys.2015.12.022>), whale optimization algorithm (Mirjalili and Lewis, 2016 <doi:10.1016/j.advengsoft.2016.01.008>), clonal selection algorithm (Castro, 2002 <doi:10.1109/TEVC.2002.1011539>), differential evolution (Das & Suganthan, 2011), shuffled frog leaping (Eusuff, Landsey & Pasha, 2006), cat swarm optimization (Chu et al., 2006), artificial bee colony algorithm (Karaboga & Akay, 2009), krill-herd algorithm (Gandomi & Alavi, 2012), cuckoo search (Yang & Deb, 2009), bat algorithm (Yang, 2012), gravitational based search (Rashedi et al., 2009) and black hole optimization (Hatamlou, 2013).
Author: Lala Septem Riza [aut, cre],
Iip [aut],
Eddy Prasetyo Nugroho [aut],
Muhammad Bima Adi Prabowo [aut],
Enjun Junaeti [aut],
Ade Gafar Abdullah [aut]
Maintainer: Lala Septem Riza <lala.s.riza@upi.edu>
Diff between metaheuristicOpt versions 1.0.0 dated 2017-10-16 and 2.0.0 dated 2019-06-19
DESCRIPTION | 28 +- MD5 | 72 ++++-- NAMESPACE | 14 + R/ABC.Algorithm.R |only R/ALO.Algorithm.R | 99 ++++---- R/BA.Algorithm.R |only R/BHO.Algorithm.R |only R/CLONALG.Algorithm.R |only R/CS.Algorithm.R |only R/CSO.Algorithm.R |only R/DA.Algorithm.R | 122 +++++----- R/DE.Algorithm.R |only R/FFA.Algorithm.R | 108 ++++----- R/GA.Algorithm.R | 99 ++++---- R/GBS.Algorithm.R |only R/GOA.Algorithm.R | 92 ++++---- R/GWO.Algorithm.R | 124 +++++----- R/IHS.Algorithm.R | 113 +++++---- R/KH.Algorithm.R |only R/MFO.Algorithm.R | 107 ++++----- R/PSO.Algorithm.R | 94 ++++---- R/SCA.Algorithm.R | 106 ++++----- R/SFL.Algorithm.R |only R/WOA.Algorithm.R | 97 ++++---- R/metaheuristic.mainFunction.R | 468 ++++++++++++++++++++++++++++++++++------- man/ABC.Rd |only man/ALO.Rd | 63 ++--- man/BA.Rd |only man/BHO.Rd |only man/CLONALG.Rd |only man/CS.Rd |only man/CSO.Rd |only man/DA.Rd | 74 +++--- man/DE.Rd |only man/FFA.Rd | 80 +++---- man/GA.Rd | 65 ++--- man/GBS.Rd |only man/GOA.Rd | 64 +++-- man/GWO.Rd | 72 +++--- man/HS.Rd | 73 +++--- man/KH.Rd |only man/MFO.Rd | 67 ++--- man/PSO.Rd | 71 +++--- man/SCA.Rd | 66 ++--- man/SFL.Rd |only man/WOA.Rd | 57 ++-- man/metaOpt.Rd | 243 +++++++++++++++++---- 47 files changed, 1660 insertions(+), 1078 deletions(-)
More information about metaheuristicOpt at CRAN
Permanent link
More information about portfolioBacktest at CRAN
Permanent link
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are included.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>) and substantive model
compatible imputation (Bartlett et al., 2015,
<doi:10.1177/0962280214521348>).
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut],
Thorsten Henke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.3-33 dated 2019-05-11 and 3.4-17 dated 2019-06-19
DESCRIPTION | 8 MD5 | 50 - R/MIwaldtest.R | 8 R/NMIcombine.R | 19 R/NMIcombine_include_dimnames.R | 2 R/NMIwaldtest_compute_statistic.R | 9 R/RcppExports.R | 2 R/datlist2nested.datlist.R | 2 R/mice.impute.2l.groupmean.R | 4 R/mice.impute.2l.pls2.R | 649 +++++++++------------ R/mice.impute.ml.lmer.R | 32 - R/mice_imputation_pls_do_impute.R | 4 R/mice_ml_lmer_aggregate_data_higher_level.R | 7 R/mice_ml_lmer_arrange_cluster_identifiers.R | 5 R/mice_ml_lmer_draw_random_effects.R | 3 R/mice_ml_lmer_interactions_pls.R | 4 R/mice_multilevel_imputation_draw_random_effects.R | 10 R/miceadds_matrix2.R | 2 R/nested.datlist2datlist.R | 2 R/plausible.value.draw.R | 42 - build/partial.rdb |binary inst/NEWS | 19 man/NMIwaldtest.Rd | 14 man/filename_split.Rd | 4 man/mice.impute.pls.Rd | 4 src/RcppExports.cpp | 2 26 files changed, 439 insertions(+), 468 deletions(-)
Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Peter Rousseeuw [aut] (Fortran original,
<https://orcid.org/0000-0002-3807-5353>),
Anja Struyf [aut] (S original),
Mia Hubert [aut] (S original, <https://orcid.org/0000-0001-6398-4850>),
Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000),
<https://orcid.org/0000-0003-4198-9911>),
Matthias Studer [ctb],
Pierre Roudier [ctb],
Juan Gonzalez [ctb],
Kamil Kozlowski [ctb],
Erich Schubert [ctb] (fastpam options for pam(),
<https://orcid.org/0000-0001-9143-4880>),
Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.0.9 dated 2019-05-01 and 2.1.0 dated 2019-06-19
ChangeLog | 2 - DESCRIPTION | 12 ++++++---- MD5 | 48 +++++++++++++++++++++--------------------- R/ellipsoidhull.R | 23 ++++++++++++++++---- R/plotpart.q | 4 +-- build/partial.rdb |binary inst/NEWS.Rd | 32 ++++++++++++++++++++++++++-- man/animals.Rd | 2 - man/clara.Rd | 5 ++-- man/clusplot.default.Rd | 2 - man/ellipsoidhull.Rd | 12 +++++----- man/partition.object.Rd | 2 - man/plot.agnes.Rd | 4 +-- man/plot.diana.Rd | 2 - man/predict.ellipsoid.Rd | 4 +-- man/print.agnes.Rd | 2 - man/summary.agnes.Rd | 2 - man/summary.clara.Rd | 4 +-- man/summary.diana.Rd | 2 - man/summary.mona.Rd | 2 - man/volume.ellipsoid.Rd | 26 +++++++++++++++++----- src/cluster.h | 3 +- src/daisy.f | 14 ++++++------ tests/ellipsoid-ex.R | 9 +++++++ tests/ellipsoid-ex.Rout.save | 49 ++++++++++++++++++++++++++++--------------- 25 files changed, 174 insertions(+), 93 deletions(-)
Title: Efficient and Publishing-Oriented Workflow for Psychological
Science
Description: The main goal of the psycho package is to provide tools for psychologists, neuropsychologists and neuroscientists,
to facilitate and speed up the time spent on data analysis. It aims at supporting best practices and tools to format the output
of statistical methods to directly paste them into a manuscript, ensuring statistical reporting standardization and conformity.
Author: Dominique Makowski [aut, cre, cph]
(<https://orcid.org/0000-0001-5375-9967>),
Hugo Najberg [ctb],
Viliam Simko [ctb],
Sasha Epskamp [rev] (Sasha reviewed the package for JOSS, see
https://github.com/openjournals/joss-reviews/issues/470)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between psycho versions 0.4.9 dated 2019-03-31 and 0.4.91 dated 2019-06-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/deprecated.R | 6 ++++++ build/vignette.rds |binary inst/doc/bayesian.html | 11 +++++++---- inst/doc/overview.html | 18 ++++++++++++++---- tests/testthat/test-deprecated.R | 12 ++++++------ 7 files changed, 42 insertions(+), 23 deletions(-)
Title: Virtual Machines in 'Azure'
Description: Functionality for working with virtual machines (VMs) in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/services/virtual-machines/>. Includes facilities to deploy, startup, shutdown, and cleanly delete VMs and VM clusters. Deployment configurations can be highly customised, and can make use of existing resources as well as creating new ones. A selection of predefined configurations is provided to allow easy deployment of commonly used Linux and Windows images, including Data Science Virtual Machines. With a running VM, execute scripts and install optional extensions. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureVM versions 1.0.0 dated 2018-12-25 and 2.0.0 dated 2019-06-19
AzureVM-1.0.0/AzureVM/R/params.R |only AzureVM-1.0.0/AzureVM/inst/CITATION |only AzureVM-1.0.0/AzureVM/inst/doc/intro.R |only AzureVM-1.0.0/AzureVM/inst/templates |only AzureVM-1.0.0/AzureVM/man/is_vm_template.Rd |only AzureVM-1.0.0/AzureVM/tests/testthat/test01_vm.R |only AzureVM-2.0.0/AzureVM/DESCRIPTION | 22 AzureVM-2.0.0/AzureVM/MD5 | 109 ++- AzureVM-2.0.0/AzureVM/NAMESPACE | 81 ++ AzureVM-2.0.0/AzureVM/NEWS.md | 17 AzureVM-2.0.0/AzureVM/R/AzureVM.R | 27 AzureVM-2.0.0/AzureVM/R/add_methods.R | 540 ++++++++------- AzureVM-2.0.0/AzureVM/R/autoscaler_config.R |only AzureVM-2.0.0/AzureVM/R/az_vm_resource.R | 136 ++- AzureVM-2.0.0/AzureVM/R/az_vm_template.R | 382 +++-------- AzureVM-2.0.0/AzureVM/R/az_vmss_resource.R |only AzureVM-2.0.0/AzureVM/R/az_vmss_template.R |only AzureVM-2.0.0/AzureVM/R/build_json.R |only AzureVM-2.0.0/AzureVM/R/get_paged_list.R |only AzureVM-2.0.0/AzureVM/R/ip_config.R |only AzureVM-2.0.0/AzureVM/R/is_vm.R |only AzureVM-2.0.0/AzureVM/R/lb_config.R |only AzureVM-2.0.0/AzureVM/R/load_tpls.R |only AzureVM-2.0.0/AzureVM/R/nic_config.R |only AzureVM-2.0.0/AzureVM/R/nsg_config.R |only AzureVM-2.0.0/AzureVM/R/pool.R |only AzureVM-2.0.0/AzureVM/R/vm_config.R |only AzureVM-2.0.0/AzureVM/R/vm_resource_config.R |only AzureVM-2.0.0/AzureVM/R/vm_template_builders.R |only AzureVM-2.0.0/AzureVM/R/vmss_config.R |only AzureVM-2.0.0/AzureVM/R/vmss_template_builders.R |only AzureVM-2.0.0/AzureVM/R/vnet_config.R |only AzureVM-2.0.0/AzureVM/README.md | 214 ++++-- AzureVM-2.0.0/AzureVM/build/vignette.rds |binary AzureVM-2.0.0/AzureVM/inst/doc/intro.html | 551 +++++++++++----- AzureVM-2.0.0/AzureVM/inst/doc/intro.rmd | 294 ++++---- AzureVM-2.0.0/AzureVM/inst/tpl |only AzureVM-2.0.0/AzureVM/man/autoscaler_config.Rd |only AzureVM-2.0.0/AzureVM/man/az_vm_resource.Rd | 12 AzureVM-2.0.0/AzureVM/man/az_vm_template.Rd | 81 +- AzureVM-2.0.0/AzureVM/man/az_vmss_resource.Rd |only AzureVM-2.0.0/AzureVM/man/az_vmss_template.Rd |only AzureVM-2.0.0/AzureVM/man/build_template.Rd |only AzureVM-2.0.0/AzureVM/man/create_vm.Rd | 184 +++-- AzureVM-2.0.0/AzureVM/man/defunct.Rd |only AzureVM-2.0.0/AzureVM/man/delete_vm.Rd | 21 AzureVM-2.0.0/AzureVM/man/get_vm.Rd | 43 - AzureVM-2.0.0/AzureVM/man/ip_config.Rd |only AzureVM-2.0.0/AzureVM/man/is_vm.Rd |only AzureVM-2.0.0/AzureVM/man/lb_config.Rd |only AzureVM-2.0.0/AzureVM/man/lb_rules.Rd |only AzureVM-2.0.0/AzureVM/man/list_vm_sizes.Rd | 3 AzureVM-2.0.0/AzureVM/man/nic_config.Rd |only AzureVM-2.0.0/AzureVM/man/nsg_config.Rd |only AzureVM-2.0.0/AzureVM/man/nsg_rules.Rd |only AzureVM-2.0.0/AzureVM/man/pool.Rd |only AzureVM-2.0.0/AzureVM/man/reexports.Rd |only AzureVM-2.0.0/AzureVM/man/scaleset_options.Rd |only AzureVM-2.0.0/AzureVM/man/vm_config.Rd |only AzureVM-2.0.0/AzureVM/man/vm_resource_config.Rd |only AzureVM-2.0.0/AzureVM/man/vmss_config.Rd |only AzureVM-2.0.0/AzureVM/man/vnet_config.Rd |only AzureVM-2.0.0/AzureVM/tests/resources |only AzureVM-2.0.0/AzureVM/tests/testthat/test00_resconfig.R |only AzureVM-2.0.0/AzureVM/tests/testthat/test01_vmconfig.R |only AzureVM-2.0.0/AzureVM/tests/testthat/test10_vm.R |only AzureVM-2.0.0/AzureVM/tests/testthat/test11_vmss.R |only AzureVM-2.0.0/AzureVM/tests/testthat/test12_del.R |only AzureVM-2.0.0/AzureVM/tests/testthat/test13_custom.R |only AzureVM-2.0.0/AzureVM/tests/testthat/test14_par.R |only AzureVM-2.0.0/AzureVM/vignettes/intro.rmd | 294 ++++---- 71 files changed, 1751 insertions(+), 1260 deletions(-)
Title: Integrated Stratigraphy
Description: Includes bases for litholog generation: graphical functions
based on R base graphics, interval management functions and svg importation
functions among others. Also include stereographic projection functions,
and other functions made to deal with large datasets while keeping options
to get into the details of the data.
When using for publication please cite Wouters, S., Da Silva, A.C. Crucifix,
M., Sinnesael, M., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2019,
Litholog generation with the StratigrapheR package and signal decomposition
for cyclostratigraphic purposes. Geophysical Research Abstracts Vol. 21,
EGU2019-5520, 2019, EGU General Assembly 2019.
<http://hdl.handle.net/2268/234402>
The palaeomagnetism functions are based on:
Tauxe, L., 2010. Essentials of Paleomagnetism. University of California
Press. <https://earthref.org/MagIC/books/Tauxe/Essentials/>;
Allmendinger, R. W., Cardozo, N. C., and Fisher, D., 2013, Structural
Geology Algorithms: Vectors & Tensors: Cambridge, England, Cambridge
University Press, 289 pp.;
Cardozo, N., and Allmendinger, R. W., 2013, Spherical projections
with OSXStereonet: Computers & Geosciences, v. 51, no. 0, p. 193 - 205,
<doi: 10.1016/j.cageo.2012.07.021>.
Author: Sebastien Wouters [aut, cre], Adam D. Smith [ctb]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>
Diff between StratigrapheR versions 0.0.5 dated 2019-04-26 and 0.0.6 dated 2019-06-19
DESCRIPTION | 8 ++++---- MD5 | 48 ++++++++++++++++++++++++------------------------ R/StratigrapheR.R | 4 ++-- R/fastPairs.R | 1 - R/folder.R | 5 ++++- R/weld.R | 4 ++-- R/weldlog.R | 4 ++-- man/StratigrapheR.Rd | 2 +- man/bedtext.Rd | 4 ++-- man/blackSet.Rd | 5 +++-- man/convertAxis.Rd | 6 +++--- man/earplanes.Rd | 4 ++-- man/earpoints.Rd | 8 ++++---- man/encircle.Rd | 4 ++-- man/fastPairs.Rd | 1 - man/folder.Rd | 5 ++++- man/greySet.Rd | 6 +++--- man/minorAxis.Rd | 10 +++++----- man/multigons.Rd | 6 +++--- man/neatPick.Rd | 3 ++- man/neatPicked.Rd | 9 +++++---- man/nlegend.Rd | 4 ++-- man/pdfDisplay.Rd | 4 ++-- man/ylink.Rd | 4 ++-- man/zijderveld.Rd | 13 +++++++------ 25 files changed, 90 insertions(+), 82 deletions(-)
More information about StratifiedMedicine at CRAN
Permanent link
Title: Geospatial Kriging with Metropolis Sampling
Description: Estimates kriging models for geographical point-referenced data. Method is described in Monogan and Gill (2016) <doi:10.1017/psrm.2015.5>.
Author: Jason S. Byers [aut, cre], Jeff Gill [aut], James E. Monogan III [aut]
Maintainer: Jason S. Byers <jaybyers55@gmail.com>
Diff between krige versions 0.1-1 dated 2018-08-24 and 0.2-1 dated 2019-06-19
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++++++---- R/krige.posterior.R | 4 +--- R/metropolis.krige.R | 11 +++++------ data/congCombined.rda |only data/lowerCombined.rda |only data/stateCombined.rda |only data/upperCombined.rda |only man/congCombined.Rd |only man/lowerCombined.Rd |only man/metropolis.krige.Rd | 14 +++++++++++--- man/stateCombined.Rd |only man/upperCombined.Rd |only 13 files changed, 34 insertions(+), 21 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 0.8.2 dated 2019-06-07 and 0.8.3 dated 2019-06-19
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NAMESPACE | 1 NEWS.md | 4 ++ R/gee.R | 75 +++++++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/jstable.html | 42 ++++++++++++++-------------- man/geeglm.display.Rd | 4 ++ 8 files changed, 82 insertions(+), 66 deletions(-)
Title: Phylogenetic Reconstruction and Analysis
Description: Package contains methods for estimation of phylogenetic trees and
networks using Maximum Likelihood, Maximum Parsimony, distance methods and
Hadamard conjugation. Allows to compare trees, models selection and offers
visualizations for trees and split networks.
Author: Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>),
Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>),
Leonardo de Oliveira Martins [aut]
(<https://orcid.org/0000-0001-5247-1320>),
Alastair Potts [aut],
Tim W. White [aut],
Cyrill Stachniss [ctb],
Michelle Kendall [ctb],
Keren Halabi [ctb],
Richel Bilderbeek [ctb],
Kristin Winchell [ctb]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.5.3 dated 2019-03-23 and 2.5.5 dated 2019-06-19
DESCRIPTION | 12 MD5 | 87 - NAMESPACE | 7 NEWS | 19 R/ancestral_pml.R | 120 +- R/bootstrap.R | 8 R/codonTest.R | 1 R/discrete.gamma.R |only R/dist.p.R | 2 R/distSeq.R | 66 + R/distTree.R | 36 R/mast.R | 4 R/neighborNet.R | 252 ---- R/networx.R | 36 R/parsimony.R | 83 - R/phyDat.R | 1497 ++++++++++++++--------------- R/phylo.R | 20 R/splits.R | 15 README.md | 12 build/vignette.rds |binary inst/doc/Ancestral.pdf |binary inst/doc/IntertwiningTreesAndNetworks.html | 596 +++++++---- inst/doc/Networx.html | 368 +++++-- inst/doc/Trees.pdf |binary inst/doc/phangorn-specials.pdf |binary inst/phangorn_sticker.png |only man/as.splits.Rd | 3 man/discrete.gamma.Rd |only man/dist.p.Rd | 1 man/mast.Rd | 3 man/maxCladeCred.Rd | 3 man/parsimony.Rd | 10 man/pml.fit.Rd | 11 man/writeDist.Rd | 5 src/init.c | 3 src/ml.c | 310 ------ src/phangorn.c | 71 - src/sankoff.c | 3 tests/testthat/test_distances.R | 23 tests/testthat/test_hadamard.R | 4 tests/testthat/test_parsimony.R | 16 tests/testthat/test_phyDat.R | 52 - tests/testthat/test_splits.R | 75 - tests/testthat/test_treeManipulation.R | 9 tests/testthat/test_treeRearrangement.R | 2 vignettes/phangorn.bib | 376 +++---- 46 files changed, 2052 insertions(+), 2169 deletions(-)
Title: Containerize R Markdown Documents for Continuous Reproducibility
Description: Persistent reproducible reporting by containerization of R Markdown documents.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>),
Miao-Zhu Li [ctb],
Teng-Fei Yin [ctb]
Maintainer: Nan Xiao <me@nanx.me>
Diff between liftr versions 0.9 dated 2018-05-14 and 0.9.2 dated 2019-06-19
liftr-0.9.2/liftr/DESCRIPTION | 17 liftr-0.9.2/liftr/MD5 | 45 - liftr-0.9.2/liftr/NEWS.md | 26 liftr-0.9.2/liftr/R/lift.R | 2 liftr-0.9.2/liftr/R/liftr-package.R | 18 liftr-0.9.2/liftr/R/parsers.R | 7 liftr-0.9.2/liftr/README.md | 17 liftr-0.9.2/liftr/build/vignette.rds |binary liftr-0.9.2/liftr/inst/doc/liftr-addins.Rmd | 7 liftr-0.9.2/liftr/inst/doc/liftr-addins.html | 653 +++++++++++++------ liftr-0.9.2/liftr/inst/doc/liftr-intro.Rmd | 17 liftr-0.9.2/liftr/inst/doc/liftr-intro.html | 773 ++++++++++++++--------- liftr-0.9.2/liftr/inst/doc/liftr-tidyverse.Rmd | 7 liftr-0.9.2/liftr/inst/doc/liftr-tidyverse.html | 761 ++++++++++++++-------- liftr-0.9.2/liftr/inst/examples/bioc-rnaseq.Rmd | 2 liftr-0.9.2/liftr/inst/templates/pkg-bioc.Rmd | 2 liftr-0.9.2/liftr/inst/templates/pkg-cran.Rmd | 2 liftr-0.9.2/liftr/inst/templates/pkg-remotes.Rmd | 2 liftr-0.9.2/liftr/man/liftr-package.Rd | 29 liftr-0.9.2/liftr/vignettes/custom.css |only liftr-0.9.2/liftr/vignettes/liftr-addins.Rmd | 7 liftr-0.9.2/liftr/vignettes/liftr-intro.Rmd | 17 liftr-0.9.2/liftr/vignettes/liftr-tidyverse.Rmd | 7 liftr-0.9/liftr/TODO |only liftr-0.9/liftr/vignettes/liftr.css |only 25 files changed, 1586 insertions(+), 832 deletions(-)