{"id":348864,"name":"BeeBDC","description":"Bee Biodiversity Data Cleaning.","url":"https://github.com/jbdorey/beebdc","last_synced_at":"2026-04-17T14:00:48.239Z","repository":{"id":192987819,"uuid":"620088662","full_name":"jbdorey/BeeBDC","owner":"jbdorey","description":"Repo for the BeeBDC package","archived":false,"fork":false,"pushed_at":"2026-04-10T21:40:11.000Z","size":73498,"stargazers_count":4,"open_issues_count":0,"forks_count":3,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-04-14T13:02:43.539Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://jbdorey.github.io/BeeBDC/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jbdorey.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-03-28T02:16:07.000Z","updated_at":"2026-04-10T21:33:44.000Z","dependencies_parsed_at":"2024-01-04T17:48:21.202Z","dependency_job_id":"9d470c8b-36c8-4ac2-a143-7171e16cd1b9","html_url":"https://github.com/jbdorey/BeeBDC","commit_stats":null,"previous_names":["jbdorey/beebdc"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/jbdorey/BeeBDC","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jbdorey","download_url":"https://codeload.github.com/jbdorey/BeeBDC/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31931958,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-17T12:37:54.787Z","status":"ssl_error","status_checked_at":"2026-04-17T12:37:25.095Z","response_time":62,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"owner":{"login":"jbdorey","name":"James B Dorey","uuid":"69567713","kind":"user","description":"Mostly a bee researcher looking at evolution, ecology, phylogenetics, and conservation","email":"","website":null,"location":"Adelaide, South Australia","twitter":"JamesBeeDorey","company":null,"icon_url":"https://avatars.githubusercontent.com/u/69567713?u=74fba1d984e6182083a9f1f40b8ffde947656680\u0026v=4","repositories_count":1,"last_synced_at":"2023-09-06T08:35:38.219Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/jbdorey","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-09-06T08:35:38.283Z","updated_at":"2023-09-06T08:35:38.283Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jbdorey","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jbdorey/repositories"},"packages":[{"id":8283965,"name":"BeeBDC","ecosystem":"cran","description":"Occurrence Data Cleaning","homepage":"https://jbdorey.github.io/BeeBDC/\nhttps://github.com/jbdorey/BeeBDC","licenses":"GPL (≥ 3)","normalized_licenses":["CNRI-Python-GPL-Compatible"],"repository_url":"https://github.com/jbdorey/BeeBDC","keywords_array":[],"namespace":null,"versions_count":13,"first_release_published_at":"2023-09-15T00:00:00.000Z","latest_release_published_at":"2026-02-06T00:00:00.000Z","latest_release_number":"1.3.3","last_synced_at":"2026-04-14T13:01:05.064Z","created_at":"2023-09-15T19:33:05.366Z","updated_at":"2026-04-14T13:01:05.065Z","registry_url":"https://cran.r-project.org/package=BeeBDC","install_command":null,"documentation_url":"http://cran.r-project.org/web/packages/BeeBDC/BeeBDC.pdf","metadata":{},"repo_metadata":{"id":192987819,"uuid":"620088662","full_name":"jbdorey/BeeBDC","owner":"jbdorey","description":"Repo for the BeeBDC package","archived":false,"fork":false,"pushed_at":"2024-06-20T01:42:55.000Z","size":61522,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-08-21T04:59:44.104Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://jbdorey.github.io/BeeBDC/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jbdorey.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-03-28T02:16:07.000Z","updated_at":"2024-07-02T18:48:26.000Z","dependencies_parsed_at":"2024-01-04T17:48:21.202Z","dependency_job_id":"9d470c8b-36c8-4ac2-a143-7171e16cd1b9","html_url":"https://github.com/jbdorey/BeeBDC","commit_stats":null,"previous_names":["jbdorey/beebdc"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jbdorey","download_url":"https://codeload.github.com/jbdorey/BeeBDC/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":219864766,"owners_count":16554093,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"},"owner_record":{"login":"jbdorey","name":"James B Dorey","uuid":"69567713","kind":"user","description":"Mostly a bee researcher looking at evolution, ecology, phylogenetics, and conservation","email":"","website":null,"location":"Adelaide, South Australia","twitter":"JamesBeeDorey","company":null,"icon_url":"https://avatars.githubusercontent.com/u/69567713?u=74fba1d984e6182083a9f1f40b8ffde947656680\u0026v=4","repositories_count":1,"last_synced_at":"2023-09-06T08:35:38.219Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/jbdorey","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-09-06T08:35:38.283Z","updated_at":"2023-09-06T08:35:38.283Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jbdorey","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jbdorey/repositories"},"tags":[]},"repo_metadata_updated_at":"2024-09-21T10:42:20.591Z","dependent_packages_count":0,"downloads":567,"downloads_period":"last-month","dependent_repos_count":0,"rankings":{"downloads":85.90160969433894,"dependent_repos_count":36.6267239430251,"dependent_packages_count":27.997829625610414,"stargazers_count":34.8589001447178,"forks_count":28.053357449694776,"docker_downloads_count":null,"average":42.68768417147741},"purl":"pkg:cran/BeeBDC","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/cran/BeeBDC","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/cran/BeeBDC","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/cran/BeeBDC/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":null,"versions_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages/BeeBDC/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages/BeeBDC/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages/BeeBDC/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages/BeeBDC/related_packages","codemeta_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages/BeeBDC/codemeta","maintainers":[{"uuid":"jbdorey@me.com","login":null,"name":"James B. Dorey","email":"jbdorey@me.com","url":null,"packages_count":1,"html_url":null,"role":null,"created_at":"2023-09-18T22:59:38.640Z","updated_at":"2023-09-18T22:59:38.640Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/maintainers/jbdorey@me.com/packages"}],"registry":{"name":"cran.r-project.org","url":"https://cran.r-project.org","ecosystem":"cran","default":true,"packages_count":28010,"maintainers_count":15530,"namespaces_count":0,"keywords_count":0,"github":"r-project-org","metadata":{"icon_url":"https://cran.r-project.org/CRANlogo.png","funded_packages_count":546},"icon_url":"https://cran.r-project.org/CRANlogo.png","created_at":"2022-04-06T16:32:25.637Z","updated_at":"2026-04-03T06:40:33.945Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages","maintainers_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/maintainers","namespaces_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/namespaces"}}],"commits":{"id":11004854,"full_name":"jbdorey/beebdc","default_branch":"master","total_commits":636,"total_committers":4,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":159.0,"dds":0.04088050314465408,"past_year_total_commits":113,"past_year_total_committers":2,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":56.5,"past_year_dds":0.017699115044247815,"last_synced_at":"2026-04-16T05:31:17.243Z","last_synced_commit":"864d831ba349a3c191dc030d795569d3245ee793","created_at":"2025-09-08T15:09:15.550Z","updated_at":"2026-04-16T05:31:03.788Z","committers":[{"name":"jbdorey","email":"69567713+jbdorey","login":"jbdorey","count":610},{"name":"Erica Fischer","email":"54035657+efishy","login":"efishy","count":23},{"name":"Webb","email":"mdw2685@eid.utexas.edu","login":"mitchwebb","count":2},{"name":"olivroy","email":"52606734+olivroy","login":"olivroy","count":1}],"past_year_committers":[{"name":"jbdorey","email":"jbdorey@me.com","login":"jbdorey","count":111},{"name":"Webb","email":"mdw2685@eid.utexas.edu","login":"mitchwebb","count":2}],"commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2Fbeebdc/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2026-04-17T00:00:13.716Z","repositories_count":6214338,"commits_count":900600350,"contributors_count":34925129,"owners_count":1144748,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues_stats":{"full_name":"jbdorey/BeeBDC","html_url":"https://github.com/jbdorey/BeeBDC","last_synced_at":"2026-04-02T07:00:39.206Z","status":"error","issues_count":5,"pull_requests_count":8,"avg_time_to_close_issue":2143078.6,"avg_time_to_close_pull_request":2214030.5714285714,"issues_closed_count":5,"pull_requests_closed_count":7,"pull_request_authors_count":3,"issue_authors_count":4,"avg_comments_per_issue":3.4,"avg_comments_per_pull_request":0.125,"merged_pull_requests_count":6,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":2,"past_year_pull_requests_count":2,"past_year_avg_time_to_close_issue":3414029.0,"past_year_avg_time_to_close_pull_request":6201040.0,"past_year_issues_closed_count":2,"past_year_pull_requests_closed_count":1,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":2,"past_year_avg_comments_per_issue":4.0,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":1,"created_at":"2025-08-29T14:58:49.988Z","updated_at":"2026-04-02T07:00:39.206Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbdorey%2FBeeBDC/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":5},"pull_request_author_associations_count":{"OWNER":6,"CONTRIBUTOR":1,"COLLABORATOR":1},"issue_authors":{"teunbrand":2,"edzer":1,"PMassicotte":1,"clauswilke":1},"pull_request_authors":{"jbdorey":6,"efishy":1,"olivroy":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2026-04-04T00:00:10.542Z","repositories_count":14073722,"issues_count":34477241,"pull_requests_count":112559469,"authors_count":11221850,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"NONE":2},"past_year_pull_request_author_associations_count":{"OWNER":2},"past_year_issue_authors":{"clauswilke":1,"teunbrand":1},"past_year_pull_request_authors":{"jbdorey":2},"maintainers":[{"login":"jbdorey","count":6,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jbdorey"},{"login":"efishy","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/efishy"}],"active_maintainers":[{"login":"jbdorey","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jbdorey"}]},"events":{"total":{"PullRequestEvent":4,"ForkEvent":2,"IssuesEvent":3,"WatchEvent":1,"IssueCommentEvent":5,"PushEvent":124},"last_year":{"PullRequestEvent":4,"ForkEvent":1,"IssuesEvent":3,"WatchEvent":1,"IssueCommentEvent":5,"PushEvent":105}},"keywords":[],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/R-CMD-check.yaml","sha":null,"kind":"manifest","created_at":"2024-01-04T17:48:00.089Z","updated_at":"2024-01-04T17:48:00.089Z","repository_link":"https://github.com/jbdorey/BeeBDC/blob/main/.github/workflows/R-CMD-check.yaml","dependencies":[{"id":15431217523,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":15431217524,"package_name":"r-lib/actions/setup-pandoc","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431217525,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431217526,"package_name":"r-lib/actions/setup-r-dependencies","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431217527,"package_name":"r-lib/actions/check-r-package","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/pkgdown.yaml","sha":null,"kind":"manifest","created_at":"2024-01-04T17:48:00.316Z","updated_at":"2024-01-04T17:48:00.316Z","repository_link":"https://github.com/jbdorey/BeeBDC/blob/main/.github/workflows/pkgdown.yaml","dependencies":[{"id":15431218054,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":15431218057,"package_name":"r-lib/actions/setup-pandoc","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431218060,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431218063,"package_name":"r-lib/actions/setup-r-dependencies","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431218065,"package_name":"JamesIves/github-pages-deploy-action","ecosystem":"actions","requirements":"v4.4.1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/pr-commands.yaml","sha":null,"kind":"manifest","created_at":"2024-01-04T17:48:00.431Z","updated_at":"2024-01-04T17:48:00.431Z","repository_link":"https://github.com/jbdorey/BeeBDC/blob/main/.github/workflows/pr-commands.yaml","dependencies":[{"id":15431218837,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":15431218838,"package_name":"r-lib/actions/pr-fetch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431218848,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431218849,"package_name":"r-lib/actions/setup-r-dependencies","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431218850,"package_name":"r-lib/actions/pr-push","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/test-coverage.yaml","sha":null,"kind":"manifest","created_at":"2024-01-04T17:48:02.624Z","updated_at":"2024-01-04T17:48:02.624Z","repository_link":"https://github.com/jbdorey/BeeBDC/blob/main/.github/workflows/test-coverage.yaml","dependencies":[{"id":15431218981,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":15431218982,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431218983,"package_name":"r-lib/actions/setup-r-dependencies","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15431218984,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cran","filepath":"DESCRIPTION","sha":null,"kind":"manifest","created_at":"2024-01-04T17:48:03.254Z","updated_at":"2024-01-04T17:48:03.254Z","repository_link":"https://github.com/jbdorey/BeeBDC/blob/main/DESCRIPTION","dependencies":[{"id":15431219084,"package_name":"R","ecosystem":"cran","requirements":"\u003e= 2.10","direct":true,"kind":"depends","optional":false},{"id":15431219085,"package_name":"circlize","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219127,"package_name":"CoordinateCleaner","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219128,"package_name":"cowplot","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219172,"package_name":"dplyr","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219173,"package_name":"forcats","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219226,"package_name":"ggplot2","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219227,"package_name":"ggspatial","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219312,"package_name":"here","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219313,"package_name":"igraph","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219350,"package_name":"lubridate","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219351,"package_name":"mgsub","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219454,"package_name":"openxlsx","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219488,"package_name":"paletteer","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219516,"package_name":"readr","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431219739,"package_name":"rnaturalearth","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431220058,"package_name":"sf","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431220129,"package_name":"stringr","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431220130,"package_name":"tidyselect","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":15431220157,"package_name":"bdc","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431220186,"package_name":"BiocManager","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431220263,"package_name":"classInt","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431220451,"package_name":"ComplexHeatmap","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431220464,"package_name":"countrycode","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431220644,"package_name":"devtools","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431220645,"package_name":"emld","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431220652,"package_name":"formatR","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431220720,"package_name":"galah","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431220779,"package_name":"hexbin","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431221412,"package_name":"htmltools","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222421,"package_name":"htmlwidgets","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222720,"package_name":"httr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222736,"package_name":"janitor","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222748,"package_name":"knitr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222749,"package_name":"leaflet","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222780,"package_name":"magrittr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222781,"package_name":"pkgdown","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222782,"package_name":"plotly","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222783,"package_name":"prettydoc","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222823,"package_name":"purrr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222841,"package_name":"R.utils","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431222842,"package_name":"renv","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223372,"package_name":"rgnparser","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223398,"package_name":"rlang","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223399,"package_name":"rmarkdown","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223400,"package_name":"rmdformats","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223437,"package_name":"rnaturalearthdata","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223438,"package_name":"rvest","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223439,"package_name":"terra","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223497,"package_name":"testthat","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223498,"package_name":"tidyr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223499,"package_name":"utils","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":15431223500,"package_name":"xml2","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false}]}],"score":9.114710140960932,"created_at":"2026-03-19T00:13:10.856Z","updated_at":"2026-04-17T14:00:48.257Z","avatar_url":"https://github.com/jbdorey.png","language":"R","category":"Biosphere","sub_category":"Biodiversity Data Cleaning and Standardization","monthly_downloads":567,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"---\noutput: \n   rmarkdown::github_document:\n     html_preview: true\npkgdown:\n  as_is: true\nurlcolor: blue\neditor_options: \n  markdown: \n    wrap: 80\n\nvignette: \u003e\n  %\\VignetteIndexEntry{BeeBDC}\n  %\\VignetteEngine{knitr::rmarkdown}\n  %\\VignetteEncoding{UTF-8}\n---\n\n```{r setup, include=FALSE}\nlibrary(BeeBDC)\n```\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# \u003ca href='https://github.com/jbdorey/BeeBDC'\u003e\u003cimg src=\"https://photos.smugmug.com/photos/i-MpLFKTT/0/741daa6d/X4/i-MpLFKTT-X4.png\" alt=\"BeeBDC logo of a cuckoo bee sweeping up occurrence records in South America\" align=\"right\" width=\"155\"/\u003e\u003c/a\u003e\n\n# **BeeBDC: an occurrence data cleaning package**\n\n\u003c!-- badges: start --\u003e\n\n[![CRANstatus](https://www.r-pkg.org/badges/version/BeeBDC)](https://CRAN.R-project.org/package=BeeBDC)\n[![downloads](https://cranlogs.r-pkg.org/badges/grand-total/BeeBDC)](https://cranlogs.r-pkg.org:443/badges/grand-total/BeeBDC)\n[![R-CMD-check](https://github.com/jbdorey/BeeBDC/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jbdorey/BeeBDC/actions/workflows/R-CMD-check.yaml)\n[![License](https://img.shields.io/badge/license-GPL%20(%3E=%203)-lightgrey.svg?style=flat)](http://www.gnu.org/licenses/gpl-3.0.html)\n\n\u003c!-- badges: end --\u003e\n\n## **Overview**\n\nThe reliable implementation of biodiversity data continues to be a challenge for\nresearchers. We present the **BeeBDC** package which provides novel and updated\nfunctions for flagging, cleaning, visualising, and analysing occurrence\ndatasets. Our package is general and can be applied to any taxon; however, we\nalso provide some functions and data that are specific for use with bee\noccurrence data; specifically due to their input data. We add new functionality\nand keep conventions in other fantastic R packages, especially\n[bdc](https://brunobrr.github.io/bdc/) and\n[CoordinateCleaner](https://ropensci.github.io/CoordinateCleaner/articles/Cleaning_GBIF_data_with_CoordinateCleaner.html),\nwhile also removing many dependencies on sp-related packages. Hence, our package\nname is **Bee** **B**iodiversity **D**ata **C**leaning (**BeeBDC**).\n\nWe provide a full workflow that uses BeeBDC, bdc, and CoordinateCleaner to clean\noccurrence data in our Articles page and encourage users to read and also cite\nthis primary [publication](https://doi.org/10.1101/2023.06.30.547152). For our\nparallelised implementation of iChao and iNEXT species richness estimations,\ncite this [primary publication](https://doi.org/10.21203/rs.3.rs-6372769/v1).\n\n### **The *BeeBDC* vignettes**\n\nThe **BeeBDC** vignettes are split into several, depending on waht you're hoping\nto do with the package. So far, it is broadly split into the (1) data cleaning\nworkflow and (2) species richness estimation.\n\n1.  Data cleaning is broken into\n    -   1.1 The [full cleaning\n        workflow](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html)\n    -   1.2 A [more basic\n        workflow](https://jbdorey.github.io/BeeBDC/articles/basic_workflow.html)\n    -   1.3 A [bee-data specific\n        workflow](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_data_preparation.html)\n        to prepare those bee datasets\n2.  A short, but complete, vignette to [estimate species\n    richness](https://jbdorey.github.io/BeeBDC/articles/Species_richness_estimation.html)\n\n### ***BeeBDC*****'s structure**\n\nThe **BeeBDC** toolkit is intentionally organized using conventions in **bdc**\nand **CoordinateCleaner**.\n\n\u003e Like in the **bdc** package, we provide a suggested workflow here. While our\n\u003e functions can mostly be run out of order, there are a few exceptions mentioned\n\u003e throughout the documentation. Additionally, many functions require the\n\u003e database_id column that is generated early on in the **BeeBDC** or **bdc**\n\u003e workflows. When running very large datasets (e.g., the global bee occurrence\n\u003e dataset) you may require a machine that has a minimum amount of RAM (\\~32 GB).\n\u003e However, we do try to provide work-arounds, especially by alowing some\n\u003e functions to be broken into consumable chunks. Paper DOI -\n\u003e \u003chttps://doi.org/10.1101/2023.06.30.547152\u003e; Package GitHub -\n\u003e \u003chttps://github.com/jbdorey/BeeBDC/\u003e\n\n#### ![Workflow figure from Dorey et al. 2023](https://photos.smugmug.com/photos/i-V37Vg2w/4/X4/i-V37Vg2w-X4.jpg)\n\n## **Installation**\n\n### **Install *BeeBDC***\n\nYou can install *BeeBDC* from CRAN or GitHub.\n\n```{r eval=FALSE}\n  # Install BeeBDC from CRAN\ninstall.packages(\"BeeBDC\")\n\n  # Or using the development version from GitHub (keeping in mind this may not be as stable)\nremotes::install_github(\"https://github.com/jbdorey/BeeBDC.git\", \n                          # To use the development version use \"devel\"; otherwise choose \"main\"\n                        ref = \"devel\", force = TRUE)\n```\n\n### **Install *sf* and *terra***\n\n\u003e ### First time using the *sf* or *terra* packages?\n\u003e\n\u003e The first time that you use **terra** or **sf** on a new computer you may need\n\u003e to install some dependencies. Try to install the **terra** and **sf** packages\n\u003e first but then come back here if that doesn't work.\n\u003e\n\u003e ##### Windows:\n\u003e\n\u003e On **Windows**, you need to first install\n\u003e [Rtools](https://cran.r-project.org/bin/windows/Rtools/) to get a C++ compiler\n\u003e that **R** can use. You need a recent version of **Rtools42**\n\u003e (rtools42-5355-5357).\n\u003e\n\u003e ##### MacOS:\n\u003e\n\u003e On **macOS**, you can use [MacPorts](https://www.macports.org/) or\n\u003e [Homebrew](https://brew.sh/).\n\u003e\n\u003e With **MacPorts** you can do\n\u003e\n\u003e `sudo port install R-terra`\n\u003e\n\u003e With **Homebrew**, you need to first install GDAL:\n\u003e\n\u003e `brew install pkg-config`\n\u003e\n\u003e `brew install gdal`\n\u003e\n\u003e Followed by (note the additional configuration argument needed for Homebrew)\n\u003e\n\u003e ```{r, eval = FALSE}\n\u003e   # Install terra\n\u003e install.packages(\"terra\", type = \"source\", configure.args = \"--with-proj-lib=$(brew --prefix)/lib/\")\n\u003e   # install sf\n\u003e install.packages(\"sf\", type = \"source\", configure.args = \"--with-proj-lib=$(brew --prefix)/lib/\")\n\u003e \u003e\n\u003e library(terra)\n\u003e library(sf)\n\u003e ```\n\nLoad the package with:\n\n```{r, message=FALSE, warning=FALSE,echo=TRUE,eval=FALSE}\nlibrary(BeeBDC)\n```\n\n### **Optional packages**\n\nBecause **BeeBDC** provides broad functionality that might not be required by\nall users, some dependencies are optional (but required for some functions).\nOptional packages can be downloaded prior to starting your workflow, if desired.\n*However, you will be prompted to download these packages if they aren't already\ninstalled when you run those functions*. The packages BiocManager and devtools\nmay also be required to download some extra packages.\n\n1.  The package, **rnaturalearthhires**, is a data package that allows the usage\n    of higher-resolution country maps and is very useful for multiple **BeeBDC**\n    functions.\n\n```{r eval=FALSE}\n  # rnaturalearthhires can be installed using devtools from their github page\nif (!require(\"devtools\", quietly = TRUE))\n    install.packages(\"devtools\")\n  # Install rnaturalearthhires\ndevtools::install_github(\"ropensci/rnaturalearthhires\")\n```\n\n2.  The package, **ComplexHeatmap**, is only used for one **BeeBDC** function\n    (`BeeBDC::chordDiagramR()`) and is less critical.\n\n```{r eval=FALSE}\n  # ComplexHeatmap can be installed using BiocManager\nif (!require(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n  # Install ComplexHeatmap\nBiocManager::install(\"ComplexHeatmap\")\n```\n\n3.  The package **taxadb** is used by `BeeBDC::taxadbToBeeBDC()` to download and\n    transform taxonomy files for **any taxon** and from multiple providers\n    (e.g., GBIF and ITIS) to work with **BeeBDC**.\n\n```{r eval=FALSE}\n  # taxadb can be installed using install.packages\n    install.packages(\"taxadb\")\n```\n\n4.  The packages **iNEXT** and **SpadeR** can be downloaded in order to estimate\n    species richness using occurrence data (see the [species richness\n    estimation](https://jbdorey.github.io/BeeBDC/articles/Species_richness_estimation.html)\n    vignette). Implemented in the functions `BeeBDC::iNEXTwrapper()`,\n    `BeeBDC::ChaoWrapper()`, `BeeBDC::ggRichnessWrapper()`, and\n    `BeeBDC::richnessEstimateR()`.\n\n```{r eval=FALSE}\n  # iNEXT and SpadeR can be installed using install.packages\n    install.packages(\"iNEXT\")\n    install.packages(\"SpadeR\")\n```\n\n## **BeeBDC workflow components**\n\n#### 1. [**Data merge**](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html#data-merge)\n\nIntegrate and merge different datasets from major the data repositories - GBIF,\nSCAN, iDigBio, the USGS, and ALA.\n\n-   `atlasDownloader()` Downloads ALA data and creates a new file in the path to\n    put those data. This function can also request downloads from other atlases\n    ([see here](https://galah.ala.org.au/R/articles/choosing_an_atlas.html)).\n    However, it will only send the download to your email and you must do the\n    rest yourself at this point.\n-   `repoMerge()` Locates data from GBIF, ALA, iDigBio, and SCAN within a\n    directory and reads it in along with its eml metadata.\n-   `repoFinder()` Find GBIF, ALA, iDigBio, and SCAN files in a directory.\n-   `importOccurrences()` Looks for and imports the most-recent version of the\n    occurrence data created by the `BeeBDC::repoMerge()` function.\n-   `USGS_formatter()` The function finds, imports, formats, and creates\n    metadata for the USGS dataset.\n-   `formattedCombiner()` Merges the Darwin Core version of the USGS dataset\n    that was created using `BeeBDC::USGS_formatter()` with the main dataset.\n-   `dataSaver()` Used at the end of 1.x in the example workflow in order to\n    save the occurrence dataset and its associated eml metadata.\n\n#### 2. [**Data preperation**](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html#data-preparation)\n\nThe reading in and formatting of the major and minor [bee] occurrence\nrepositories as well as some data modifications. This section is mostly, but not\nentirely, related to bee occurrence data.\n\n-   `fileFinder()` A function which can be used to find files within a\n    user-defined directory based on a user-provided character string.\n-   `PaigeIntegrater()` Replaces publicly available data with data that has been\n    manually cleaned and error-corrected for use in the paper Chesshire, P. R.,\n    Fischer, E. E., Dowdy, N. J., Griswold, T., Hughes, A. C., Orr, M. J., . . .\n    McCabe, L. M. (In Press). Completeness analysis for over 3000 United States\n    bee species identifies persistent data gaps. Ecography.\n-   `readr_BeeBDC()` Read in a variety of data files that are specific to\n    certain smaller data providers. There is an internal readr function for each\n    dataset and each one of these functions is called by readr_BeeBDC. While\n    these functions are internal, they are displayed in the documentation of\n    readr_BeeBDC for clarity.\n-   `idMatchR()` This function attempts to match database_ids from a prior bdc\n    or BeeBDC run in order to keep this column somewhat consistent between\n    iterations. However, not all records contain sufficient information for this\n    to work flawlessly.\n\n#### 3. [**Initial flags**](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html#initial-flags)\n\nFlagging and carpentry of several, mostly general, data issues. See bdc's\n[pre-filter](https://brunobrr.github.io/bdc/articles/prefilter.html) for more\nrelated functions.\n\n-   `countryNameCleanR()` This is a basic function for a user to manually fix\n    some country name inconsistencies.\n-   `jbd_CfC_chunker()` Because the `BeeBDC::jbd_country_from_coordinates()`\n    function is very RAM-intensive, this wrapper allows a user to specify\n    chunk-sizes and only analyse a small portion of the occurrence data at a\n    time. The prefix jbd\\_ is used to highlight the difference between this\n    function and the original `bdc::bdc_country_from_coordinates()`.\n-   `jbd_Ctrans_chunker()` Because the `BeeBDC::jbd_coordinates_transposed()`\n    function is very RAM-intensive, this wrapper allows a user to specify\n    chunk-sizes and only analyse a small portion of the occurrence data at a\n    time. The prefix jbd\\_ is used to highlight the difference between this\n    function and the original bdc::bdc_coordinates_transposed(). These functions\n    will preferably use the countryCode column generated by\n    `bdc::bdc_country_standardized()`.\n-   `jbd_coordCountryInconsistent()` Compares stated country name in an\n    occurrence record with record's coordinates using rnaturalearth data. The\n    prefix, jbd\\_ is meant to distinguish this function from the original\n    `bdc::bdc_coordinates_country_inconsistent()`. This functions will\n    preferably use the countryCode and country_suggested columns generated by\n    `bdc::bdc_country_standardized()`; please run it on your dataset prior to\n    running this function.\n-   `flagAbsent()` Flags occurrences that are \"ABSENT\" for the occurrenceStatus\n    (or some other user-specified) column.\n-   `GBIFissues()` This function will flag records which are subject to a\n    user-specified vector of GBIF issues.\n-   `flagRecorder()` This function is used to save the flag data for your\n    occurrence data as you run the BeeBDC script. It will read and append\n    existing files, if asked to. Your flags should also be saved in the\n    occurrence file itself automatically.\n\n#### 4. [**Taxonomy**](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html#taxonomy)\n\nHarmonisation of scientific names against a taxonomy downloaded from **taxadb**,\nfrom the provided [Discover Life](https://www.discoverlife.org) website's\ntaxonomic reference, or a custom taxonomy.\n\n-   `taxadbToBeeBDC()` Uses the **taxadb** to download a species taxonomy from\n    any of their sources and transforms it into the BeeBDC format that can then\n    be exported as a .csv or into the R enviornment to be be fed directly into\n    `BeeBDC::harmoniseR()`. This means that the taxonomy from ANY taxon can be\n    used. See also `BeeBDC::beesTaxonomy()` for the best global bee taxonomy.\n-   `harmoniseR()` Uses the Discover Life taxonomy to harmonise bee occurrences\n    and flag those that do not match the checklist. This function could be\n    hijacked to service other taxa if a user matched the format of the\n    beesTaxonomy file. `BeeBDC::harmoniseR()` prefers to use the names_clean\n    columns that is generated by `bdc::bdc_clean_names()`. While this is not\n    required, you may find better results by running that function on your\n    dataset first.\n\n#### 5. [**Space**](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html#space)\n\nFlagging of erroneous, suspicious, and low-precision geographic coordinates.\n\n-   `jbd_coordinates_precision()` This function flags occurrences where BOTH\n    latitude and longitude values are rounded. This contrasts with the original\n    function, `bdc::bdc_coordinates_precision()` that will flag occurrences\n    where only one of latitude OR longitude are rounded. The BeeBDC approach\n    saves occurrences that may have had terminal zeros rounded in one coordinate\n    column.\n-   `diagonAlley()` A simple function that looks for potential latitude and\n    longitude fill-down errors by identifying consecutive occurrences with\n    coordinates at regular intervals. This is accomplished by using a sliding\n    window with the length determined by minRepeats.\n-   `coordUncerFlagR()` To use this function, the user must choose a column,\n    probably \"coordinateUncertaintyInMeters\" and a threshold above which\n    occurrences will be flagged for geographic uncertainty.\n-   `countryOutlieRs()` This function flags country-level outliers using the\n    checklist provided with this package. For additional context and column\n    names, see `beesChecklist`.\n-   `continentOutlieRs()` This function flags continent-level outliers using the\n    checklist provided with this package. This function works much the same as\n    `countryOutlieRs()`, but at a lower resolution. For additional context and\n    column names, see `beesChecklist`.\n-   `jbd_create_figures()` Creates figures (i.e., bar plots, maps, and\n    histograms) reporting the results of data quality tests implemented the bdc\n    and BeeBDC packages. Works like `bdc::bdc_create_figures()`, but it allows\n    the user to specify a save path.\n\n#### 6. [**Time**](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html#time)\n\nFlagging and, whenever possible, correction of inconsistent collection date.\n\n-   `dateFindR()` A function made to search other columns for dates and add them\n    to the eventDate column. The function searches the columns locality,\n    fieldNotes, locationRemarks, and verbatimEventDate for the relevant\n    information.\n\n#### 7. [**De-duplication**](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html#de-duplication)\n\n-   `dupeSummary()` This function uses user-specified inputs and columns to\n    identify duplicate occurrence records. Duplicates are identified iteratively\n    and will be tallied up, duplicate pairs clustered, and sorted at the end of\n    the function. The function is designed to work with Darwin Core data with a\n    database_id column, but it is also modifiable to work with other columns.\n\n#### 8. [**Filtering**](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html#data-filtering)\n\n-   `manualOutlierFindeR()` Uses expert-identified outliers with source\n    spreadsheets that may be edited by users. The function will also use the\n    duplicates file made using `BeeBDC::dupeSummary()` to identify duplicates of\n    the expert-identified outliers and flag those as well. The function will add\n    a flagging column called .expertOutlier where records that are FALSE are the\n    expert outliers.\n-   `summaryFun()` Using all flag columns (column names starting with \".\"), this\n    function either creates or updates the .summary flag column which is FALSE\n    when ANY of the flag columns are FALSE. Columns can be excluded and removed\n    after creating the .summary column. Additionally, the occurrence dataset can\n    be filtered to only those where .summary = TRUE at the end of the function.\n\n#### 9. [**Figures and tables**](https://jbdorey.github.io/BeeBDC/articles/BeeBDC_main.html#figures-and-tables)\n\n-   `chordDiagramR()` This function outputs a figure which shows the relative\n    size and direction of occurrence points duplicated between data providers,\n    such as, SCAN, GBIF, ALA, etc. This function requires the outputs generated\n    by `BeeBDC::dupeSummary()`.\n-   `dupePlotR()` Creates a plot with two bar graphs. One shows the absolute\n    number of duplicate records for each data source while the other shows the\n    proportion of records that are duplicated within each data source. This\n    function requires a dataset that has been run through\n    `BeeBDC::dupeSummary()`.\n-   `plotFlagSummary()` Creates a compound bar plot that shows the proportion of\n    records that pass or fail each flag (rows) and for each data source\n    (columns). The function can also optionally return a point map for a\n    user-specified species when plotMap = TRUE. This function requires that your\n    dataset has been run through some filtering functions - so that is can\n    display logical columns starting with \".\".\n-   `summaryMaps()` Builds an output figure that shows the number of species and\n    the number of occurrences per country. Breaks the data into classes for\n    visualisation. Users may filter data to their taxa of interest to produce\n    figures of interest.\n-   `interactiveMapR()` Uses the occurrence data (preferably uncleaned) and\n    outputs interactive .html maps that can be opened in your browser to a\n    specific directory. The maps can highlight if an occurrence has passed all\n    filtering (.summary == TRUE) or failed at least one filter (.summary ==\n    FALSE). This can be modified by first running `BeeBDC::summaryFun()` to set\n    the columns that you want to be highlighted. It can also highlight\n    occurrences flagged as expert-identified or country outliers.\n-   `dataProvTables()` This function will attempt to find and build a table of\n    data providers that have contributed to the input data, especially using the\n    'institutionCode' column. It will also look for a variety of other columns\n    to find data providers using a an internally set sequence of if-else\n    statements. Hence, this function is quite specific for bee data, but should\n    work for other taxa in similar institutions.\n-   `flagSummaryTable()` Takes a flagged dataset and returns the total number of\n    fails (FALSE) per flag (columns starting with \".\") and per species. Users\n    may define the column to group the summary by. While it is intended to work\n    with the scientificName column, users may select any grouping column (e.g.,\n    country).\n\n#### 10. [Species richness estimation](https://jbdorey.github.io/BeeBDC/articles/speciesRichness_example.html)\n\n-   `diversityPrepR()` Takes your occurrence dataset along with a taxonomy and\n    checklist in order to produce a file that's ready to be passed into the\n    `BeeBDC::richnessEstimateR()` function in order to estimate species richness\n    using iChao (non-parametric species richness; `BeeBDC::ChaoWrapper()`) and\n    iNEXT (hill numbers; `BeeBDC::iNEXTwrapper()`) for countries, continents, or\n    the entire globe.\n-   `richnessEstimateR()` Takes an output dataset from\n    `BeeBDC::diversityPrepR()` to estimate species richness using iChao\n    (non-parametric species richness; `BeeBDC::ChaoWrapper()`) and iNEXT (hill\n    numbers; `BeeBDC::iNEXTwrapper()`) for countries, continents, and/or the\n    entire globe. Has parallel functionality.\n-   `iNEXTwrapper()` A wrapper for `iNEXT::iNEXT()` to interpolate and\n    extrapolate Hill numbers with order q (rarify species richness). The wrapper\n    has the ability to estimate species richness for multiple sites (or\n    countries) at once and to do this using multiple cores.\n-   `ChaoWrapper()` A wrapper for `SpadeR::ChaoSpecies()` to non-parametrically\n    estimate species richness. The wrapper has the ability to estimate species\n    richness for multiple sites (or countries) at once and to do this using\n    multiple cores at once.\n\n#### 11. **Datasets**\n\nWe provide two full datasets that are downloadable using the below two functions\n\n-   `beesTaxonomy()` Downloads the taxonomic information for the bees of the\n    world. Source of taxonomy is listed under \"source\" but are mostly derived\n    from the Discover Life website. The data will be sourced from the BeeBDC\n    article's Figshare. Please see also `BeeBDC::taxadbToBeeBDC()` for the\n    download of any other taxonomy (for any taxa or for bees).\n-   `beesChecklist()` Download the table contains taxonomic and country\n    information for the bees of the world based on data collated on Discover\n    Life. The data will be sourced from the BeeBDC article's Figshare.\n\nWe further provide five test datasets that are available with BeeBDC\n\n-   `BeeBDC::bees3sp` This test dataset includes 105 random occurrence records\n    from three bee species. The included species are: \"*Agapostemon tyleri*\n    Cockerell, 1917\", \"*Centris rhodopus* Cockerell, 1897\", and \"*Perdita\n    octomaculata* (Say, 1824)\".\n-   `BeeBDC::beesRaw` A small bee occurrence dataset with flags generated by\n    BeeBDC used to run example script and test functions. For data types, see\n    `ColTypeR()`.\n-   `BeeBDC::beesFlagged` A small bee occurrence dataset with flags generated by\n    BeeBDC used to run example script and test functions. For data types, see\n    `ColTypeR()`.\n-   `BeeBDC::beesCountrySubset` A very small bee occurrence dataset with the\n    columns \"scientificName\" and \"country_suggested\" and data for four\n    countries, Fiji, Uganda, Vietnam, and Zambia. This is the test dataset for\n    the species richness functions.\n-   There are also two small test datasets of the beesTaxonomy and beesChecklist\n    in the system files of the package that are filtered to include *only* those\n    species that occur in bees3sp, beesRaw, and beesFlagged. These are\n    accessible as follows but are only used internally for tests.\n\n```{r testData, eval = FALSE}\n  # Access the test taxonomy file\nsystem.file(\"extdata\", \"testTaxonomy.rda\", package=\"BeeBDC\") |\u003e load()\n  # View the file\nView(testTaxonomy)\n  # Access the test checklist file\nsystem.file(\"extdata\", \"testChecklist.rda\", package=\"BeeBDC\") |\u003e load()\n  # View the file\nView(testChecklist)\n```\n\n## Package info\n\n#### **Package website**\n\nSee *BeeBDC* package website\n(\u003chttps://jbdorey.github.io/BeeBDC/reference/index.html\u003e) for detailed\nexplanation on each module.\n\n#### **Getting help**\n\n\u003e This package is maintained by Dr James B Dorey, Lecturer in Biological\n\u003e Sciences at the University of Wollongong, Australia.\n\n\u003e If you encounter a clear bug, please file an issue\n\u003e [**here**](https://github.com/jbdorey/BeeBDC/issues). For questions or\n\u003e suggestion, flick us an email (jdorey\\@uow.edu.au).\n\n#### **Citations**\n\n-   **Original paper, dataset, and package citation:** Dorey, J.B., Fischer,\n    E.E., Chesshire, P.R., Nava-Bolaños, A., O’Reilly, R.L., Bossert, S.,\n    Collins, S.M., Lichtenberg, E.M., Tucker, E., Smith-Pardo, A.,\n    Falcon-Brindis, A., Guevara, D.A., Ribeiro, B.R., de Pedro, D., Hung,\n    J.K.-L., Parys, K.A., McCabe, L.M., Rogan, M.S., Minckley, R.L., Velzco,\n    S.J.E., Griswold, T., Zarrillo, T.A., Jetz, W., Sica, Y.V., Orr, M.C.,\n    Guzman, L.M., Ascher, J., Hughes, A.C. \u0026 Cobb, N.S. (2023) A globally\n    synthesised and flagged bee occurrence dataset and cleaning workflow.\n    Scientific Data, 10, 1–17. \u003chttps://www.doi.org/10.1038/S41597-023-02626-W\u003e\n    -   **Figshare live data link:**\n        \u003chttps://doi.org/10.25451/flinders.21709757\u003e\n-   **Species richness estimation citation:** Dorey J. B., Gilpin, A.-M.,\n    Johnson, N., Esquerre, D., Hughes, A. C., Ascher, J. S., \u0026 Orr, M. C.\n    (Accepted). Estimating global bee species richness and taxonomic gaps.\n    Nature Communications. \u003chttps://doi.org/10.21203/rs.3.rs-6372769/v1\u003e\n-   **BeeBDC package citation:** Dorey, J. B., O'Reilly, R. L., Bossert, S. \u0026\n    Fischer, E. (2023). BeeBDC: an occurrence data cleaning package. R package\n    version 1.3.3. url: \u003chttps://github.com/jbdorey/BeeBDC\u003e\n-   **Discover Life citation (for use of bee taxonomy and checklist):** Ascher,\n    J.S. \u0026 Pickering, J. (2026) Discover Life bee species guide and world\n    checklist (Hymenoptera: Apoidea: Anthophila).\n    \u003chttps://www.discoverlife.org/mp/20q?guide=Apoidea_species\u003e\n\nThis package and its data sets were created with the support, and as a part, of\nthe iDigBees project\n\n\u003ca href='https://idigbees.org'\u003e\u003cimg src=\"https://photos.smugmug.com/photos/i-rcd8CCs/0/b291edd1/O/i-rcd8CCs.png\" alt=\"The iDigBees logo with a colourful bee and the iDigBees text on the right\" align=\"left\" width=\"300\"/\u003e\u003c/a\u003e\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1101/2023.06.30.547152","https://doi.org/10.21203/rs.3.rs-6372769/v1","https://www.doi.org/10.1038/S41597-023-02626-W","https://doi.org/10.25451/flinders.21709757"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/348864","html_url":"https://ost.ecosyste.ms/projects/348864"}