diff --git a/docs/articles/v05_filtering.html b/docs/articles/v05_filtering.html index 60d9dd79..1a13541e 100644 --- a/docs/articles/v05_filtering.html +++ b/docs/articles/v05_filtering.html @@ -155,36 +155,25 @@

Time data from FinBIF. The date filters can be a single year, month or date,

-finbif_occurrence(filter = list(date_range_ym = c("2019-12")))
+finbif_occurrence(filter = list(date_range_ym = c("2020-12")))
Click to show/hide output. 
 
 #> Records downloaded: 10
-#> Records available: 20150
+#> Records available: 23847
 #> A data.frame [10 x 12]
-#>                     record_id      scientific_name abundance lat_wgs84 lon_wgs84
-#> 1  …KE.921/LGE.627772/1470480 Pteromys volans (Li…        NA  61.81362  25.75756
-#> 2             …JX.1054648#107 Pica pica (Linnaeus…  3         65.30543  25.70355
-#> 3              …JX.1054648#85 Poecile montanus (C…  1         65.30543  25.70355
-#> 4             …JX.1054648#103 Garrulus glandarius…  3         65.30543  25.70355
-#> 5             …JX.1054648#123 Passer montanus (Li…  3         65.30543  25.70355
-#> 6             …JX.1054648#149 Pyrrhula pyrrhula (…  1         65.30543  25.70355
-#> 7              …JX.1054648#93 Cyanistes caeruleus…  9         65.30543  25.70355
-#> 8              …JX.1054648#95 Parus major Linnaeu…  35        65.30543  25.70355
-#> 9             …JX.1054648#137 Carduelis flammea (…  2         65.30543  25.70355
-#> 10            …JX.1056695#107 Pica pica (Linnaeus…  6         62.7154   23.0893 
-#>              date_time
-#> 1  2019-12-31 12:00:00
-#> 2  2019-12-31 10:20:00
-#> 3  2019-12-31 10:20:00
-#> 4  2019-12-31 10:20:00
-#> 5  2019-12-31 10:20:00
-#> 6  2019-12-31 10:20:00
-#> 7  2019-12-31 10:20:00
-#> 8  2019-12-31 10:20:00
-#> 9  2019-12-31 10:20:00
-#> 10 2019-12-31 10:15:00
+#>    record_id      scientific_name abundance lat_wgs84 lon_wgs84           date_time
+#> 1       …107 Pica pica (Linnaeus…  31        65.0027   25.49381 2020-12-31 10:20:00
+#> 2        …45 Larus argentatus Po…  1         65.0027   25.49381 2020-12-31 10:20:00
+#> 3       …153 Emberiza citrinella…  2         65.0027   25.49381 2020-12-31 10:20:00
+#> 4        …49 Columba livia domes…  33        65.0027   25.49381 2020-12-31 10:20:00
+#> 5       …117 Corvus corax Linnae…  1         65.0027   25.49381 2020-12-31 10:20:00
+#> 6       …111 Corvus monedula Lin…  7         65.0027   25.49381 2020-12-31 10:20:00
+#> 7       …161 Sciurus vulgaris Li…  1         65.0027   25.49381 2020-12-31 10:20:00
+#> 8       …123 Passer montanus (Li…  28        65.0027   25.49381 2020-12-31 10:20:00
+#> 9       …149 Pyrrhula pyrrhula (…  1         65.0027   25.49381 2020-12-31 10:20:00
+#> 10       …77 Turdus pilaris Linn…  1         65.0027   25.49381 2020-12-31 10:20:00
 #> ...with 0 more record and 6 more variables:
 #> coordinates_uncertainty, any_issues, requires_verification, requires_identification,
 #> record_reliability, record_quality
@@ -269,19 +258,19 @@

Data Quality= "expert_verified" ) permissive <- list( - quality_issues = "both", - record_reliability = c("reliable", "unassessed", "unreliable"), + wild_status = c("wild", "non_wild", "wild_unknown"), record_quality = c( "expert_verified", "community_verified", "unassessed", "uncertain", "erroneous" - ) + ), + abundance_min = 0 ) c( strict = finbif_occurrence(filter = strict, count_only = TRUE), permissive = finbif_occurrence(filter = permissive, count_only = TRUE) ) -#> Error: 1 error occurred: -#> - Invalid name in record reliability: unassessed +#> strict permissive +#> 52654 51733557

Collection diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index aedc138f..6e8d3c49 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -7,5 +7,5 @@ articles: v03_selecting_variables: v03_selecting_variables.html v04_metadata: v04_metadata.html v05_filtering: v05_filtering.html -last_built: 2024-01-25T08:09Z +last_built: 2024-02-29T07:54Z diff --git a/docs/search.json b/docs/search.json index 10ba3070..7ab7375a 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":[]},{"path":"/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement helpdesk@laji.fi. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":[]},{"path":"/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing","text":"Small typos grammatical errors documentation may edited long changes made source file. YES: edit roxygen comment .R file R/. : edit .Rd file man/.","code":""},{"path":"/CONTRIBUTING.html","id":"prerequisites","dir":"","previous_headings":"","what":"Prerequisites","title":"Contributing","text":"make substantial pull request, always file issue make sure someone team agrees ’s problem. ’ve found bug, create associated issue illustrate bug minimal reprex.","code":""},{"path":"/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"","what":"Pull request process","title":"Contributing","text":"recommend create Git branch pull request (PR). Look build status making changes. README contains badges continuous integration services used package. New code follow style used project. use roxygen2, Markdown syntax, documentation. use testthat. Contributions test cases included easier accept. user-facing changes, add section top inst/NEWS.Rd current development version header describing changes made followed username, links relevant issue(s)/PR(s).","code":""},{"path":"/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing","text":"Please note project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2019-2024 LUOMUS - Finnish Museum Natural History Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"/articles/finbif.html","id":"installing-the-finbif-package","dir":"Articles","previous_headings":"","what":"Installing the finbif package","title":"Introduction to the finbif package","text":"can install current stable version finbif CRAN, can also install latest development version finbif GitHub,","code":"install.packages(\"finbif\") remotes::install_github(\"luomus/finbif@dev\")"},{"path":"/articles/finbif.html","id":"loading-the-finbif-package","dir":"Articles","previous_headings":"","what":"Loading the finbif package","title":"Introduction to the finbif package","text":"","code":"library(finbif)"},{"path":"/articles/finbif.html","id":"getting-a-finbif-access-token","dir":"Articles","previous_headings":"","what":"Getting a FinBIF access token","title":"Introduction to the finbif package","text":"use FinBIF API must first request set personal access token. can request API token sent email address function finbif_get_token(). Copy access token sent email set environment variable FINBIF_ACCESS_TOKEN either current session, , adding Renviron startup file (see details).","code":"finbif_request_token(\"your@email.com\") Sys.setenv( FINBIF_ACCESS_TOKEN = \"xtmSOIxjPwq0pOMB1WvcZgFLU9QBklauOlonWl8K5oaLIx8RniJLrv\" ) # Note: the above is not a real access token. Do not try using it."},{"path":"/articles/finbif.html","id":"working-with-taxa","dir":"Articles","previous_headings":"","what":"Working with taxa","title":"Introduction to the finbif package","text":"can check see taxon exists FinBIF database. taxon FinBIF database unique ID returned. taxon FinBIF database reported “found” taxa list element NA. can also specify taxonomic rank searching FinBIF search limited specified rank. function finbif_taxa() can used general search taxa FinBIF database. Searches can exact, partial likely (fuzzy matching). Information single taxon returned using exact fuzzy matching, multiple taxa, limit, n, may returned using partial matching.","code":"finbif_check_taxa(\"Ursus arctos\") #> [Ursus arctos] ID: MX.47348 (taxa <- finbif_check_taxa(c(\"Ursus arctos\", \"Moomin\"))) #> [Ursus arctos] ID: MX.47348 #> [Moomin ] Not found taxa[[1]] #> Ursus arctos #> \"MX.47348\" taxa[[2]] #> Moomin #> NA finbif_check_taxa(list(species = c(\"Ursus arctos\", \"Ursus\"), genus = \"Ursus\")) #> [species: Ursus arctos] ID: MX.47348 #> [species: Ursus ] Not found #> [genus: Ursus ] ID: MX.51311 birch_search <- finbif_taxa(\"Betula pendula\", 2, \"partial\") birch_search$content #> [[1]] #> [[1]]$matchingName #> [1] \"Betula pendula var. pendula\" #> #> [[1]]$nameType #> [1] \"MX.scientificName\" #> #> [[1]]$id #> [1] \"MX.37994\" #> #> [[1]]$scientificName #> [1] \"Betula pendula var. pendula\" #> #> [[1]]$taxonRank #> [1] \"MX.variety\" #> #> [[1]]$cursiveName #> [1] TRUE #> #> [[1]]$finnish #> [1] TRUE #> #> [[1]]$species #> [1] TRUE #> #> [[1]]$vernacularName #> [[1]]$vernacularName$sv #> [1] \"vanlig vårtbjörk\" #> #> [[1]]$vernacularName$fi #> [1] \"vihtakoivu\" #> #> #> [[1]]$informalGroups #> [[1]]$informalGroups[[1]] #> [[1]]$informalGroups[[1]]$id #> [1] \"MVL.343\" #> #> [[1]]$informalGroups[[1]]$name #> [[1]]$informalGroups[[1]]$name$fi #> [1] \"Putkilokasvit\" #> #> [[1]]$informalGroups[[1]]$name$en #> [1] \"Vascular plants\" #> #> [[1]]$informalGroups[[1]]$name$sv #> [1] \"Kärlväxter\" #> #> #> #> #> [[1]]$kingdomScientificName #> [1] \"Plantae\" #> #> [[1]]$type #> [1] \"partialMatches\" #> #> #> [[2]] #> [[2]]$matchingName #> [1] \"Betula nana × pendula\" #> #> [[2]]$nameType #> [1] \"MX.scientificName\" #> #> [[2]]$id #> [1] \"MX.38005\" #> #> [[2]]$scientificName #> [1] \"Betula nana × pendula\" #> #> [[2]]$taxonRank #> [1] \"MX.infragenericHybrid\" #> #> [[2]]$cursiveName #> [1] TRUE #> #> [[2]]$finnish #> [1] TRUE #> #> [[2]]$species #> [1] TRUE #> #> [[2]]$vernacularName #> named list() #> #> [[2]]$informalGroups #> [[2]]$informalGroups[[1]] #> [[2]]$informalGroups[[1]]$id #> [1] \"MVL.343\" #> #> [[2]]$informalGroups[[1]]$name #> [[2]]$informalGroups[[1]]$name$fi #> [1] \"Putkilokasvit\" #> #> [[2]]$informalGroups[[1]]$name$en #> [1] \"Vascular plants\" #> #> [[2]]$informalGroups[[1]]$name$sv #> [1] \"Kärlväxter\" #> #> #> #> #> [[2]]$kingdomScientificName #> [1] \"Plantae\" #> #> [[2]]$type #> [1] \"partialMatches\" #> #>"},{"path":"/articles/finbif.html","id":"getting-occurrence-data","dir":"Articles","previous_headings":"","what":"Getting occurrence data","title":"Introduction to the finbif package","text":"can download occurrence data FinBIF database data.frame finbif_occurrence() function. can search multiple taxa filter records filter argument. See ?filters vignette(\"v05_filtering\") details filtering FinBIF records.","code":"finbif_occurrence(\"Cygnus cygnus\", n = 100) #> Records downloaded: 100 #> Records available: 95730 #> A data.frame [100 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …JX.1594164#13 Cygnus cygnus (Linn… NA 64.94473 26.67958 2023-06-13 14:33:00 #> 2 …HR.4412/6489172c9ddda_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> 3 …HR.4412/64891730060a4_U Cygnus cygnus (Linn… NA 61.38348 22.97288 2023-06-13 12:00:00 #> 4 …HR.4412/648917378a3b6_U Cygnus cygnus (Linn… NA 62.76028 24.15774 2023-06-13 12:00:00 #> 5 …HR.4412/6489175adc05f_U Cygnus cygnus (Linn… NA 60.78752 21.39263 2023-06-13 12:00:00 #> 6 …HR.4412/6489173a1db9b_U Cygnus cygnus (Linn… NA 64.31374 26.68643 2023-06-13 12:00:00 #> 7 …HR.4412/648917456a396_U Cygnus cygnus (Linn… NA 61.87986 25.19067 2023-06-13 12:00:00 #> 8 …HR.4412/648917454912b_U Cygnus cygnus (Linn… NA 60.42215 24.00099 2023-06-13 12:00:00 #> 9 …HR.4412/64891750e74e7_U Cygnus cygnus (Linn… NA 63.86383 27.70835 2023-06-13 12:00:00 #> 10 …HR.4412/64891741330f8_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> ...with 90 more records and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( \"Cygnus cygnus\", \"Cygnus olor\", filter = list(coordinates_uncertainty_max = 100) ) #> Records downloaded: 10 #> Records available: 47293 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …HR.3211/167194019-U Cygnus olor (J.F. G… NA 60.12778 24.69528 2023-06-13 12:00:00 #> 2 …JX.1593978#37 Cygnus olor (J.F. G… 10 60.428 22.20038 2023-06-13 12:00:00 #> 3 …JX.1594262#19 Cygnus olor (J.F. G… 5 61.60789 21.51679 2023-06-13 12:00:00 #> 4 …JX.1594262#17 Cygnus cygnus (Linn… 5 61.60789 21.51679 2023-06-13 12:00:00 #> 5 …JX.1594053#296 Cygnus cygnus (Linn… 1 63.62644 23.70806 2023-06-13 03:10:00 #> 6 …JX.1594054#93 Cygnus cygnus (Linn… 1 63.63403 24.21195 2023-06-13 03:08:00 #> 7 …JX.1593931#255 Cygnus cygnus (Linn… 2 64.5582 27.78468 2023-06-13 05:03:00 #> 8 …JX.1593916#3 Cygnus cygnus (Linn… 2 66.11897 25.93173 2023-06-13 12:00:00 #> 9 …JX.1593873#63 Cygnus cygnus (Linn… 2 65.72167 27.94208 2023-06-13 09:27:00 #> 10 …HR.3211/167071964-U Cygnus olor (J.F. G… NA 60.18156 24.93153 2023-06-12 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/finbif.html","id":"random-sampling","dir":"Articles","previous_headings":"Getting occurrence data","what":"Random sampling","title":"Introduction to the finbif package","text":"possible request random sample records instead last n records (records ordered variable).","code":"finbif_occurrence(\"Birds\", sample = TRUE) #> Records downloaded: 10 #> Records available: 21748016 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3691/OBS1143679721_Unit Aythya marila (Linn… 11 59.9815 24.39929 #> 2 …KE.67/1662813#Unit Fringilla coelebs L… 1 59.83333 19.93333 #> 3 …KE.8_1165614#90 Poecile montanus (C… 6 62.44825 29.92951 #> 4 …KE.67/12308933#Unit Prunella modularis … 1 61.67291 22.25931 #> 5 …KE.67/9586054#Unit Larus argentatus Po… 1 50.85 6.833333 #> 6 …KE.67/8576210#Unit Periparus ater (Lin… 1 60.2 19.33333 #> 7 …KE.67/9862495#Unit Prunella modularis … 1 61.13488 24.39512 #> 8 …KE.67/4669401#Unit Larus argentatus Po… 1 60.01667 24.61667 #> 9 …JX.1031300#61 Motacilla alba Linn… NA 62.12915 30.16957 #> 10 …KE.67/11492752#Unit Bombycilla garrulus… 1 62.67061 30.93362 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/finbif.html","id":"caching","dir":"Articles","previous_headings":"","what":"Caching","title":"Introduction to the finbif package","text":"default finbif uses local caching repeated API requests. can turned per request session basis. See ?caching details.","code":""},{"path":"/articles/v02_occurrence_data.html","id":"darwin-core-variables","dir":"Articles","previous_headings":"","what":"Darwin Core Variables","title":"Occurrence records from FinBIF","text":"can switch default variable names Darwin Core style names setting dwc = TRUE. functions to_dwc() to_native() can used translate variable names Darwin Core style finbif’s native variable names style.","code":"colnames(finbif_occurrence(dwc = TRUE)) #> [1] \"occurrenceID\" \"scientificName\" \"individualCount\" #> [4] \"decimalLatitude\" \"decimalLongitude\" \"eventDateTime\" #> [7] \"coordinateUncertaintyInMeters\" \"hasIssues\" \"requiresVerification\" #> [10] \"requiresIdentification\" \"occurrenceReliability\" \"occurrenceQuality\""},{"path":"/articles/v02_occurrence_data.html","id":"choosing-taxa","dir":"Articles","previous_headings":"","what":"Choosing taxa","title":"Occurrence records from FinBIF","text":"can limit records certain taxa specifying argument. Multiple taxa can requested . can also chose higher taxonomic groups use common names (English, Finnish Swedish).","code":"finbif_occurrence(\"Cygnus cygnus\") #> Records downloaded: 10 #> Records available: 95730 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …JX.1594164#13 Cygnus cygnus (Linn… NA 64.94473 26.67958 2023-06-13 14:33:00 #> 2 …HR.4412/6489172c9ddda_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> 3 …HR.4412/64891730060a4_U Cygnus cygnus (Linn… NA 61.38348 22.97288 2023-06-13 12:00:00 #> 4 …HR.4412/648917378a3b6_U Cygnus cygnus (Linn… NA 62.76028 24.15774 2023-06-13 12:00:00 #> 5 …HR.4412/6489175adc05f_U Cygnus cygnus (Linn… NA 60.78752 21.39263 2023-06-13 12:00:00 #> 6 …HR.4412/6489173a1db9b_U Cygnus cygnus (Linn… NA 64.31374 26.68643 2023-06-13 12:00:00 #> 7 …HR.4412/648917456a396_U Cygnus cygnus (Linn… NA 61.87986 25.19067 2023-06-13 12:00:00 #> 8 …HR.4412/648917454912b_U Cygnus cygnus (Linn… NA 60.42215 24.00099 2023-06-13 12:00:00 #> 9 …HR.4412/64891750e74e7_U Cygnus cygnus (Linn… NA 63.86383 27.70835 2023-06-13 12:00:00 #> 10 …HR.4412/64891741330f8_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence(\"Cygnus cygnus\", \"Cygnus olor\") #> Records downloaded: 10 #> Records available: 138681 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …JX.1594164#13 Cygnus cygnus (Linn… NA 64.94473 26.67958 2023-06-13 14:33:00 #> 2 …HR.4412/6489172c9ddda_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> 3 …HR.4412/64891730060a4_U Cygnus cygnus (Linn… NA 61.38348 22.97288 2023-06-13 12:00:00 #> 4 …HR.4412/648917378a3b6_U Cygnus cygnus (Linn… NA 62.76028 24.15774 2023-06-13 12:00:00 #> 5 …HR.4412/64891759be4c7_U Cygnus olor (J.F. G… NA 63.40045 21.48901 2023-06-13 12:00:00 #> 6 …HR.4412/6489175adc05f_U Cygnus cygnus (Linn… NA 60.78752 21.39263 2023-06-13 12:00:00 #> 7 …HR.4412/6489173a1db9b_U Cygnus cygnus (Linn… NA 64.31374 26.68643 2023-06-13 12:00:00 #> 8 …HR.4412/648917456a396_U Cygnus cygnus (Linn… NA 61.87986 25.19067 2023-06-13 12:00:00 #> 9 …HR.4412/648917454912b_U Cygnus cygnus (Linn… NA 60.42215 24.00099 2023-06-13 12:00:00 #> 10 …HR.4412/64891750e74e7_U Cygnus cygnus (Linn… NA 63.86383 27.70835 2023-06-13 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality birds <- finbif_occurrence(\"Birds\") linnut <- finbif_occurrence(\"Linnut\") faglar <- finbif_occurrence(\"Fåglar\") sapply(list(birds, linnut, faglar), nrow) #> [1] 10 10 10"},{"path":"/articles/v02_occurrence_data.html","id":"request-size","dir":"Articles","previous_headings":"","what":"Request size","title":"Occurrence records from FinBIF","text":"can increase number records returned using n argument. can see many records available given request, without retrieving records, setting count_only = TRUE.","code":"finbif_occurrence(n = 1001) #> Records downloaded: 1001 #> Records available: 47159747 #> A data.frame [1001 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 991 more records and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence(count_only = TRUE) #> [1] 47159747"},{"path":"/articles/v02_occurrence_data.html","id":"checking-taxa","dir":"Articles","previous_headings":"","what":"Checking taxa","title":"Occurrence records from FinBIF","text":"request occurrence records specific taxa, default, taxon names first checked FinBIF database. requested taxa found database receive warning data still retrieved remaining taxa. can turn taxon name pre-checking setting value check_taxa argument FALSE. setting argument, on_check_fail \"error\" (default \"warn\"), can elevate warnings errors request fail taxa found FinBIF database. can useful strategy using finbif non-interactively (script), want proceed taxon names wrong misspelled.","code":"finbif_occurrence(\"Vulpes vulpes\", \"Moomin\") #> Records downloaded: 10 #> Records available: 5303 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3211/167313561-U Vulpes vulpes (Linn… NA 60.18049 25.04838 #> 2 …HR.3211/167310567-U Vulpes vulpes (Linn… NA 60.2241 24.89373 #> 3 …KE.176/64894ccdd5de884fa20e2972#Unit1 Vulpes vulpes (Linn… 1 60.21118 24.90744 #> 4 …KE.176/6489506dd5de884fa20e2976#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 5 …KE.176/648802d6d5de884fa20e290d#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 6 …KE.176/648802c7d5de884fa20e290c#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 7 …HR.3211/167167234-U Vulpes vulpes (Linn… NA 60.20261 24.86879 #> 8 …HR.3211/166968734-U Vulpes vulpes (Linn… NA 60.5 21.9 #> 9 …HR.3211/166944731-U Vulpes vulpes (Linn… NA 60.17493 24.74123 #> 10 …KE.176/64869a52d5de884fa20e28ae#Unit1 Vulpes vulpes (Linn… 1 60.23885 25.12012 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence(\"Vulpes vulpes\", \"Moomin\", check_taxa = FALSE) #> Records downloaded: 10 #> Records available: 5303 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3211/167313561-U Vulpes vulpes (Linn… NA 60.18049 25.04838 #> 2 …HR.3211/167310567-U Vulpes vulpes (Linn… NA 60.2241 24.89373 #> 3 …KE.176/64894ccdd5de884fa20e2972#Unit1 Vulpes vulpes (Linn… 1 60.21118 24.90744 #> 4 …KE.176/6489506dd5de884fa20e2976#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 5 …KE.176/648802d6d5de884fa20e290d#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 6 …KE.176/648802c7d5de884fa20e290c#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 7 …HR.3211/167167234-U Vulpes vulpes (Linn… NA 60.20261 24.86879 #> 8 …HR.3211/166968734-U Vulpes vulpes (Linn… NA 60.5 21.9 #> 9 …HR.3211/166944731-U Vulpes vulpes (Linn… NA 60.17493 24.74123 #> 10 …KE.176/64869a52d5de884fa20e28ae#Unit1 Vulpes vulpes (Linn… 1 60.23885 25.12012 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence(\"Vulpes vulpes\", \"Moomin\", on_check_fail = \"error\") #> Error: Cannot find the following taxa in the FinBIF taxonomy. #> Please check you are using accepted names and not synonyms or #> other names for the taxa you are selecting: #> #> Moomin"},{"path":"/articles/v02_occurrence_data.html","id":"aggregating-records","dir":"Articles","previous_headings":"","what":"Aggregating records","title":"Occurrence records from FinBIF","text":"can request records aggregate using aggregate argument finbif_occurrence. Aggregated requests return counts combination variables specify select argument. can request counts \"records\", \"species\" \"taxa\" using corresponding string value aggregate argument. Aggregating \"species\" count number unique species identifiers set records grouped combination selected variables. Note count include records taxa species identifiers, including records higher taxa (e.g., genus records), records non-species children aggregate complex taxa, hybrid taxa. Therefore, contexts results returned underestimate species richness. Likewise, aggregating \"taxa\", returns count number unique taxon identifiers, represent overestimate number taxa records higher taxa contribute count true identify may duplicate records. illustrate, can count number moths butterflies municipality following:","code":"finbif_occurrence(\"Lepidoptera\", select = \"municipality\", aggregate = \"species\") #> Records downloaded: 10 #> Records available: 309 #> A data.frame [10 x 2] #> municipality n_species #> 1 Raasepori 2038 #> 2 Virolahti 1978 #> 3 Kouvola 1508 #> 4 Rääkkylä 1367 #> 5 Kemiönsaari 2008 #> 6 Hanko 1945 #> 7 Parainen 1858 #> 8 Helsinki 1980 #> 9 Kuopio 1345 #> 10 Kotka 1719"},{"path":"/articles/v02_occurrence_data.html","id":"time-duration","dir":"Articles","previous_headings":"","what":"Time & duration","title":"Occurrence records from FinBIF","text":"default behaviour finbif_occurrence consolidate date time data occurrence recording events date_time variable. can turned (can speed data processing time) deselecting date_time variable.","code":"finbif_occurrence(select = \"-date_time\") #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 11] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":[]},{"path":"/articles/v02_occurrence_data.html","id":"timezone-input","dir":"Articles","previous_headings":"Time & duration > Timezone","what":"Timezone input","title":"Occurrence records from FinBIF","text":"FinBIF database doesn’t currently store timezone information, finbif makes assumptions appropriate timezone based time location occurrence recording events calculate date_time duration. default, fast heuristic used determine timezones. require greater accuracy (e.g., using data Finnish/Swedish border daytime/nighttime hours important), can switch accurate, though slower, timezone calculation method.","code":"finbif_occurrence(date_time_method = \"accurate\") #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v02_occurrence_data.html","id":"timezone-output","dir":"Articles","previous_headings":"Time & duration > Timezone","what":"Timezone output","title":"Occurrence records from FinBIF","text":"timezone calculated date_time variable determined timezone operating system. can override setting tzone argument different value. set global timezone option set timezone current session. may advisable reproducibility working multiple systems.","code":"Sys.timezone() finbif_occurrence(tzone = \"Etc/UTC\") #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality options(finbif_tz = \"Etc/UTC\")"},{"path":[]},{"path":"/articles/v03_selecting_variables.html","id":"limiting-variables","dir":"Articles","previous_headings":"Selecting variables","what":"Limiting variables","title":"Selecting and ordering variables","text":"retrieve limited set variables FinBIF simply specify desired variables select argument.","code":"finbif_occurrence( genus = \"Falco\", select = c(\"scientific_name\", \"life_stage\", \"sex\") ) #> Records downloaded: 10 #> Records available: 342668 #> A data.frame [10 x 3] #> scientific_name life_stage sex #> 1 Falco columbarius L… NA NA #> 2 Falco tinnunculus L… NA NA #> 3 Falco tinnunculus L… NA NA #> 4 Falco subbuteo Linn… NA NA #> 5 Falco tinnunculus L… NA NA #> 6 Falco subbuteo Linn… NA NA #> 7 Falco tinnunculus L… NA NA #> 8 Falco tinnunculus L… NA NA #> 9 Falco tinnunculus L… NA NA #> 10 Falco subbuteo Linn… NA NA"},{"path":"/articles/v03_selecting_variables.html","id":"extra-variables","dir":"Articles","previous_headings":"Selecting variables","what":"Extra variables","title":"Selecting and ordering variables","text":"get extra variables well default set, specify extra variables addition keyword \"default_vars\".","code":"finbif_occurrence(select = c(\"default_vars\", \"life_stage\")) #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 13] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1594385#3 Sciurus vulgaris Li… 1 60.23584 25.05693 #> 2 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 3 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 4 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 5 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 6 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 7 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 8 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 9 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 10 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> ...with 0 more record and 8 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality, life_stage"},{"path":"/articles/v03_selecting_variables.html","id":"ordering","dir":"Articles","previous_headings":"","what":"Ordering","title":"Selecting and ordering variables","text":"can change order occurrence records fetched server using order_by argument. default ordering date_start descending, load_date descending, reported_name.","code":""},{"path":"/articles/v03_selecting_variables.html","id":"ascending-order","dir":"Articles","previous_headings":"Ordering","what":"Ascending order","title":"Selecting and ordering variables","text":"default occurrence records ordered variables ascending order.","code":"finbif_occurrence(\"Cygnus cygnus\", order_by = \"abundance\") #> Records downloaded: 10 #> Records available: 95730 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.67/9403350#Unit Cygnus cygnus (Linn… 1 60.41667 16 #> 2 …HR.3691/OBS810893905_Unit Cygnus cygnus (Linn… NA 61.56563 29.56771 #> 3 …JX.1026351#259 Cygnus cygnus (Linn… 1 65.89416 28.90961 #> 4 …JX.1025175#3 Cygnus cygnus (Linn… 1 61.83248 23.40816 #> 5 …KE.67/9069501#Unit Cygnus cygnus (Linn… 1 52.71667 1.55 #> 6 …JX.1252188#3 Cygnus cygnus (Linn… NA 60.17258 24.27095 #> 7 …KE.67/9465507#Unit Cygnus cygnus (Linn… 1 61.8 22.76667 #> 8 …KE.67/9607357#Unit Cygnus cygnus (Linn… 1 63.13333 22.43333 #> 9 …MHU.10961285 Cygnus cygnus (Linn… NA 64.97813 24.74932 #> 10 …HR.3691/OBS886590077_Unit Cygnus cygnus (Linn… NA 61.27566 22.557 #> date_time #> 1 1997-04-01 13:00:00 #> 2 2007-05-18 12:00:00 #> 3 2013-06-24 03:12:00 #> 4 2014-06-08 03:45:00 #> 5 1997-01-03 14:00:00 #> 6 2021-05-23 06:15:00 #> 7 2000-03-22 12:00:00 #> 8 2003-06-07 12:00:00 #> 9 2008-07-12 12:00:00 #> 10 2020-03-31 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v03_selecting_variables.html","id":"descending-order","dir":"Articles","previous_headings":"Ordering","what":"Descending order","title":"Selecting and ordering variables","text":"can switch descending order prefixing variable dash.","code":"finbif_occurrence(\"Cygnus cygnus\", order_by = \"-abundance\") #> Records downloaded: 10 #> Records available: 95730 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …MHU.2981587 Cygnus cygnus (Linn… 6000 64.4 -14.54 #> 2 …HR.3691/OBS1101526155_Unit Cygnus cygnus (Linn… 1760 62.16389 21.45786 #> 3 …HR.3691/OBS604642304_Unit Cygnus cygnus (Linn… 1753 64.50736 24.27894 #> 4 …HR.3691/OBS663568887_Unit Cygnus cygnus (Linn… 1600 65.98787 24.06341 #> 5 …MHU.28815250 Cygnus cygnus (Linn… 1500 NA NA #> 6 …HR.3691/OBS671353848_Unit Cygnus cygnus (Linn… 1361 64.71656 24.53188 #> 7 …JX.1357345#5 Cygnus cygnus (Linn… 1300 64.8465 25.2883 #> 8 …JX.1398409#3 Cygnus cygnus (Linn… 1280 64.8448 25.2816 #> 9 …MHU.28815110 Cygnus cygnus (Linn… 1200 NA NA #> 10 …HR.3691/OBS1119137190_Unit Cygnus cygnus (Linn… 1163 64.71656 24.53188 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v03_selecting_variables.html","id":"multiple-variables","dir":"Articles","previous_headings":"Ordering","what":"Multiple variables","title":"Selecting and ordering variables","text":"can specify multiple variables order . Sorting primacy left right.","code":"finbif_occurrence(\"Cygnus olor\", order_by = c(\"municipality_id\", \"-abundance\")) #> Records downloaded: 10 #> Records available: 42951 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …12015253 Cygnus olor (J.F. G… 2500 NA NA 2008-08-17 12:00:00 #> 2 …13633876 Cygnus olor (J.F. G… 1500 NA NA 2008-10-03 12:00:00 #> 3 …781416 Cygnus olor (J.F. G… 1300 NA NA 2006-02-14 12:00:00 #> 4 …780984 Cygnus olor (J.F. G… 1300 NA NA 2006-02-14 12:00:00 #> 5 …2062563 Cygnus olor (J.F. G… 1200 NA NA 2006-12-19 12:00:00 #> 6 …10352894 Cygnus olor (J.F. G… 1100 NA NA 2008-06-28 12:00:00 #> 7 …927797 Cygnus olor (J.F. G… 1050 NA NA 2006-04-05 12:00:00 #> 8 …3110953 Cygnus olor (J.F. G… 960 NA NA 2007-10-06 12:00:00 #> 9 …26309317 Cygnus olor (J.F. G… 900 NA NA 2009-07-08 12:00:00 #> 10 …1260385 Cygnus olor (J.F. G… 800 58.66 23.57 2006-04-26 18:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v03_selecting_variables.html","id":"random-sample","dir":"Articles","previous_headings":"Ordering","what":"Random sample","title":"Selecting and ordering variables","text":"can also request random sample (random order) occurrence records setting sample argument TRUE.","code":"finbif_occurrence(sample = TRUE) #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.67/5632630#Unit Ficedula hypoleuca … 1 61.74637 22.77479 #> 2 …MHU.40397 Prunus padus L. NA 60.28016 20.25637 #> 3 …JX.775148#3 Yezognophos vittari… 1 60.44245 27.006 #> 4 …KE.67/11580538#Unit Cyanistes caeruleus… 1 60.32754 24.64944 #> 5 …JX.328070#23 Pechipogo strigilat… NA 61.54883 21.64192 #> 6 …HR.3691/OBS889952298_Unit Parus major Linnaeu… 5 66.6165 24.68816 #> 7 …JX.1025818#50 Garrulus glandarius… 1 63.43302 27.74526 #> 8 …HR.3691/OBS1104249688_Unit Alauda arvensis Lin… NA 60.05577 24.06798 #> 9 …KE.67/8616657#Unit Cyanistes caeruleus… 1 61.5 24.83333 #> 10 …JX.101375#9 Poecile montanus (C… 7 63.09517 23.1341 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v04_metadata.html","id":"general-metadata","dir":"Articles","previous_headings":"","what":"General metadata","title":"Metadata","text":"can see metadata available finbif calling finbif_metadata function without arguments. Calling finbif_metadata() specifying one metadata categories display data.frame requested metadata.","code":"finbif_metadata() #> metadata_name #> 1 regulatory_status #> 2 red_list #> 3 country #> 4 region #> 5 bio_province #> 6 municipality #> 7 bird_assoc_area #> 8 finnish_occurrence_status #> 9 habitat_type #> 10 habitat_qualifier #> 11 life_stage #> 12 record_basis #> 13 restriction_level #> 14 restriction_reason #> 15 sex_category #> 16 source #> 17 taxon_rank finbif_metadata(\"red_list\") #> code name #> MX.iucnCR CR Critically Endangered #> MX.iucnDD DD Data Deficient #> MX.iucnEN EN Endangered #> MX.iucnEX EX Extinct #> MX.iucnEW EW Extinct in the Wild #> MX.iucnLC LC Least Concern #> MX.iucnNT NT Near Threatened #> MX.iucnNA NA Not Applicable #> MX.iucnNE NE Not Evaluated #> MX.iucnRE RE Regionally Extinct #> MX.iucnVU VU Vulnerable"},{"path":"/articles/v04_metadata.html","id":"special-cases","dir":"Articles","previous_headings":"","what":"Special cases","title":"Metadata","text":"complex metadata accessed finbif functions","code":""},{"path":"/articles/v04_metadata.html","id":"informal-groups","dir":"Articles","previous_headings":"Special cases","what":"Informal groups","title":"Metadata","text":"Informal taxonomic groups relationships can displayed finbif_informal_groups() can select subgroup specifying parent informal group function argument.","code":"finbif_informal_groups(limit = 2) #> Algae #> --Macro algae #> --Brown algae and yellow green algae #> --Green algae #> --Red algae #> --Stoneworts #> Birds #> --Birds of prey and owls #> --Birds of prey #> --Owls #> --Waterbirds #> ...137 more groups finbif_informal_groups(\"Crustaceans\") #> Crustaceans #> --Macrocrustaceans #> --Amphipods, isopods, opossum shrimps #> --Crabs, shrimps and crayfishes #> --Other macrocrustaceans #> --Woodlice #> --Microcrustaceans #> --Branchiopoda #> --Copepods #> --Seed shrimps"},{"path":"/articles/v04_metadata.html","id":"collections","dir":"Articles","previous_headings":"","what":"Collections","title":"Metadata","text":"Another special case metadata finbif_collections(). Collections highest level record aggregation FinBIF database. can subset collection metadata using filter select arguments. default, finbif_collections() displays lowest level collections. Higher level, “supercollections” can viewed setting supercollections = TRUE can limit output collections minimum number records nmin argument. finbif_collections() function returns data.frame row names ID number collection. can see child collections supercollection specifying ID filter. Note children supercollections may also supercollections.","code":"finbif_collections( filter = geographic_coverage == \"Finland\", select = c(\"collection_name\", \"taxonomic_coverage\", \"count\") ) #> collection_name taxonomic_coverage count #> HR.1227 Priv. coll. Mikko Heikkinen Biota 62 #> HR.1349 JYV - Fungal collections 13477 #> HR.1350 JYV - Lichen collections 608 #> HR.1351 JYV - Bryophyte collections 8367 #> HR.1467 Per-Eric Grankvist´s butterly co… Lepidoptera 5 #> HR.1487 JYV - Fish collections 1371 #> HR.1507 Lingonblad Birger och Hjördis bu… Lepidoptera 2796 #> HR.157 Point counts of breeding terrest… Birds, landbirds 393361 #> HR.1592 Herbarium of The Ark Nature Cent… 7871 #> HR.1687 Papilionoidea of Coll. Lauro Papilionoidea 550 #> HR.1688 Noctuidae I of Coll. Lauro Noctuidae 614 #> HR.1689 Noctuidae II of Coll. Lauro Noctuidae 839 #> HR.1690 Noctuidae III, Bombycoidea, Sphi… Noctuidae, Bombycoidea, Geometri… 521 #> HR.1691 Drepanidae & Geometridae of Coll… Drepanidae, Geometridae 1408 #> HR.175 National Finnish butterfly monit… Lepidoptera 450525 #> HR.1916 Wildlife triangle Siberian flying squirrel (Pterom… 18560 #> HR.200 Finnish Insect Database Insecta 3725381 #> HR.2009 Fish observation data from the n… invasive alien fish species - mu… 35582 #> HR.2049 Invasive alien species control Invasive species 1502 #> HR.206 The Finnish Nature League's Spri… biota 119323 #> HR.2089 Håkan Lindberg collection Hymenoptera 2435 #> HR.209 Atlas of Finnish Macrolepidoptera Macrolepidoptera 1218555 #> HR.2129 Fungal atlas fungi 116519 #> HR.2209 KUO Arachnida collection Arachnida 3 #> HR.2289 Specimens that lack collecting i… 109 #> HR.2691 Luomus line transect censuses of… Aves 628987 #> HR.2692 Censuses of breeding birds - Are… Aves 14963 #> HR.3051 VieKas LIFE project invasive spe… 1545 #> HR.3071 Observing species on milk farms 529 #> HR.3211 iNaturalist Suomi Finland biota 691050 #> HR.3491 LajiGIS: Aquatic species survey Biota 643837 #> HR.3553 LajiGIS: Species monitoring sites Biota 731965 #> HR.3671 Bird of prey nests for protection Aves 13323 #> HR.3691 eBird Aves 1100308 #> HR.3791 Invasive species observations Biota 3268 #> HR.39 Winter Bird Census Aves, Mammalia 1483842 #> HR.3911 Bumblebee census Bumblebees 29949 #> HR.3991 Waterbird counts, Luomus dataset Aves 39236 #> HR.3992 Waterbird counts, Luke dataset 2… Aves 30145 #> HR.4011 Salmonidae in streams Salmonidae 12630 #> HR.4051 LajiGIS: Species monitoring site… Aquila chrysaetos; Haliaeetus al… 8669 #> HR.4091 Retkikasvio 84 #> HR.4131 Butterflies in Finnish agricultu… Papilionoidea, Others 356987 #> HR.4191 Porvoo Museum / Butterfly Collec… Lepidoptera 10417 #> HR.4251 LajiGIS: Species mapping and sur… Biota 490816 #> HR.435 Löydös Open Invasive Species Obs… Biota 19232 #> HR.4352 NFI rare tree species 995 #> HR.4412 Tiira.fi: The Fourth Breeding Bi… Aves 329445 #> HR.4471 4th Finnish Bird Atlas 2022–2025… Aves 165551 #> HR.4511 Finnish National Moth Monitoring Bombycoidea, Noctuoidea, Sphingi… 1156373 #> HR.4611 Observations by FCG Finnish Cons… 462 #> HR.4612 Pollinator monitoring, line tran… Insecta 7885 #> HR.4672 Observations from publications Biota 127 #> HR.4711 Flying squirrel monitoring Pteromys volans 2509 #> HR.4991 Bird atlas observations manually… Aves 6620 #> HR.5095 Dragonfly complete lists Odonata 29 #> HR.5155 Observations from electronic sou… Biota 1372 #> HR.5196 Pollinator monitoring, pan traps Insecta 5688 #> HR.5235 Finnish butterflies - complete l… Lepidoptera, Papilinoidea 21 #> HR.5236 Charismatic flowering plants - c… Tracheophyta 277 #> HR.60 Monitoring scheme of birds and m… Aves, Mammalia 874130 #> HR.627 Alien mammal species observation… Invasive alien mammal species – … 3094 #> HR.808 E. Sjöholm´s butterfly collection Lepidoptera 4951 #> HR.847 Atlas of amphibians and reptiles… Amphibia, Reptilia 6690 collections <- finbif_collections(supercollections = TRUE, nmin = 10000) finbif_collections(supercollections = TRUE)[\"HR.128\", \"collection_name\"] #> Collections of the Finnish Museum of Natural History Luomus finbif_collections(is_part_of == \"HR.128\", supercollections = TRUE) #> collection_name abbreviation description online_url has_children is_part_of data_quality #> HR.129 Collections of… H Herbarium … TRUE HR.128 MY.dataQual… #> HR.160 Zoological col… MZH The collec… http://ww… TRUE HR.128 MY.dataQual… #> HR.173 Zoological mon… Monitoring… TRUE HR.128 MY.dataQual… #> HR.1849 Genomic resour… Genomic re… TRUE HR.128 MY.dataQual… #> HR.203 Löydös Open Fi… A service … https://l… FALSE HR.128 #> HR.435 Löydös Open In… A service … https://l… FALSE HR.128 MY.dataQual… #> HR.447 Hatikka.fi obs… Hatikka.fi… http://ha… FALSE HR.128 MY.dataQual… #> HR.48 Ringing and re… TIPU Dataset co… TRUE HR.128 MY.dataQual… #> methods collection_type taxonomic_coverage geographic_coverage temporal_coverage #> HR.129 MY.collectionT… #> HR.160 MY.collectionT… Animalia World 1700 to present #> HR.173 MY.collectionT… Finland 1950- #> HR.1849 Sampling… MY.collectionT… Biota World 2000- #> HR.203 MY.collectionT… biota world 2013- #> HR.435 MY.collectionT… Biota Finland 2015- #> HR.447 MY.collectionT… Biota World #> HR.48 MY.collectionT… Aves Ringing data: Finl… 1913- #> secure_level count #> HR.129 2 #> HR.160 MX.secureLe… 742 #> HR.173 5160221 #> HR.1849 1 #> HR.203 39375 #> HR.435 19232 #> HR.447 2010032 #> HR.48 12910437"},{"path":"/articles/v05_filtering.html","id":"location","dir":"Articles","previous_headings":"","what":"Location","title":"Filtering occurrence records","text":"Records can filtered name location. set coordinates. See ?filters section “Location” details","code":"finbif_occurrence(filter = c(country = \"Finland\")) #> Records downloaded: 10 #> Records available: 44691386 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1594385#3 Sciurus vulgaris Li… 1 60.23584 25.05693 #> 2 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 3 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 4 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 5 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 6 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 7 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 8 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 9 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 10 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( filter = list(coordinates = list(c(60, 68), c(20, 30), \"wgs84\")) ) #> Records downloaded: 10 #> Records available: 37318868 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1594385#3 Sciurus vulgaris Li… 1 60.23584 25.05693 #> 2 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 3 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 4 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 5 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 6 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 7 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 8 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 9 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 10 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"time","dir":"Articles","previous_headings":"","what":"Time","title":"Filtering occurrence records","text":"event import date records can used filter occurrence data FinBIF. date filters can single year, month date, , record events, range character vector. Records specific season time-span across years can also requested.","code":"finbif_occurrence(filter = list(date_range_ym = c(\"2019-12\"))) #> Records downloaded: 10 #> Records available: 20150 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.921/LGE.627772/1470480 Pteromys volans (Li… NA 61.81362 25.75756 #> 2 …JX.1054648#107 Pica pica (Linnaeus… 3 65.30543 25.70355 #> 3 …JX.1054648#85 Poecile montanus (C… 1 65.30543 25.70355 #> 4 …JX.1054648#103 Garrulus glandarius… 3 65.30543 25.70355 #> 5 …JX.1054648#123 Passer montanus (Li… 3 65.30543 25.70355 #> 6 …JX.1054648#149 Pyrrhula pyrrhula (… 1 65.30543 25.70355 #> 7 …JX.1054648#93 Cyanistes caeruleus… 9 65.30543 25.70355 #> 8 …JX.1054648#95 Parus major Linnaeu… 35 65.30543 25.70355 #> 9 …JX.1054648#137 Carduelis flammea (… 2 65.30543 25.70355 #> 10 …JX.1056695#107 Pica pica (Linnaeus… 6 62.7154 23.0893 #> date_time #> 1 2019-12-31 12:00:00 #> 2 2019-12-31 10:20:00 #> 3 2019-12-31 10:20:00 #> 4 2019-12-31 10:20:00 #> 5 2019-12-31 10:20:00 #> 6 2019-12-31 10:20:00 #> 7 2019-12-31 10:20:00 #> 8 2019-12-31 10:20:00 #> 9 2019-12-31 10:20:00 #> 10 2019-12-31 10:15:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( filter = list(date_range_ymd = c(\"2019-06-01\", \"2019-12-31\")) ) #> Records downloaded: 10 #> Records available: 911735 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.921/LGE.627772/1470480 Pteromys volans (Li… NA 61.81362 25.75756 #> 2 …JX.1054648#107 Pica pica (Linnaeus… 3 65.30543 25.70355 #> 3 …JX.1054648#85 Poecile montanus (C… 1 65.30543 25.70355 #> 4 …JX.1054648#103 Garrulus glandarius… 3 65.30543 25.70355 #> 5 …JX.1054648#123 Passer montanus (Li… 3 65.30543 25.70355 #> 6 …JX.1054648#149 Pyrrhula pyrrhula (… 1 65.30543 25.70355 #> 7 …JX.1054648#93 Cyanistes caeruleus… 9 65.30543 25.70355 #> 8 …JX.1054648#95 Parus major Linnaeu… 35 65.30543 25.70355 #> 9 …JX.1054648#137 Carduelis flammea (… 2 65.30543 25.70355 #> 10 …JX.1056695#107 Pica pica (Linnaeus… 6 62.7154 23.0893 #> date_time #> 1 2019-12-31 12:00:00 #> 2 2019-12-31 10:20:00 #> 3 2019-12-31 10:20:00 #> 4 2019-12-31 10:20:00 #> 5 2019-12-31 10:20:00 #> 6 2019-12-31 10:20:00 #> 7 2019-12-31 10:20:00 #> 8 2019-12-31 10:20:00 #> 9 2019-12-31 10:20:00 #> 10 2019-12-31 10:15:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( filter = list( date_range_md = c(begin = \"12-21\", end = \"12-31\"), date_range_md = c(begin = \"01-01\", end = \"02-20\") ) ) #> Records downloaded: 10 #> Records available: 1486845 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …433443#318 Accipiter nisus (Li… 1 64.8162 25.32106 2023-02-20 15:00:00 #> 2 …531663#107 Pica pica (Linnaeus… 10 62.9199 27.71032 2023-02-20 07:40:00 #> 3 …530610#107 Pica pica (Linnaeus… 21 65.78623 24.49119 2023-02-20 09:15:00 #> 4 …530449#107 Pica pica (Linnaeus… 4 65.74652 24.62216 2023-02-20 08:20:00 #> 5 …531663#153 Emberiza citrinella… 12 62.9199 27.71032 2023-02-20 07:40:00 #> 6 …531663#49 Columba livia domes… 10 62.9199 27.71032 2023-02-20 07:40:00 #> 7 …530610#49 Columba livia domes… 2 65.78623 24.49119 2023-02-20 09:15:00 #> 8 …530610#117 Corvus corax Linnae… 1 65.78623 24.49119 2023-02-20 09:15:00 #> 9 …531663#61 Dendrocopos major (… 6 62.9199 27.71032 2023-02-20 07:40:00 #> 10 …531663#111 Corvus monedula Lin… 7 62.9199 27.71032 2023-02-20 07:40:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"data-quality","dir":"Articles","previous_headings":"","what":"Data Quality","title":"Filtering occurrence records","text":"can filter occurrence records indicators data quality. See ?filters section “Quality” details.","code":"strict <- c( collection_quality = \"professional\", coordinates_uncertainty_max = 1, record_quality = \"expert_verified\" ) permissive <- list( quality_issues = \"both\", record_reliability = c(\"reliable\", \"unassessed\", \"unreliable\"), record_quality = c( \"expert_verified\", \"community_verified\", \"unassessed\", \"uncertain\", \"erroneous\" ) ) c( strict = finbif_occurrence(filter = strict, count_only = TRUE), permissive = finbif_occurrence(filter = permissive, count_only = TRUE) ) #> Error: 1 error occurred: #> - Invalid name in record reliability: unassessed"},{"path":"/articles/v05_filtering.html","id":"collection","dir":"Articles","previous_headings":"","what":"Collection","title":"Filtering occurrence records","text":"FinBIF database consists number constituent collections. can filter collection either collection not_collection filters. Use finbif_collections() see metadata FinBIF collections.","code":"finbif_occurrence( filter = c(collection = \"iNaturalist Suomi Finland\"), count_only = TRUE ) #> [1] 691076 finbif_occurrence( filter = c(collection = \"Notebook, general observations\"), count_only = TRUE ) #> [1] 2110409"},{"path":"/articles/v05_filtering.html","id":"informal-taxonomic-groups","dir":"Articles","previous_headings":"","what":"Informal taxonomic groups","title":"Filtering occurrence records","text":"can filter occurrence records based informal taxonomic groups Birds Mammals. See finbif_informal_groups() full list groups can filter . can use function see subgroups make higher level informal group:","code":"finbif_occurrence(filter = list(informal_groups = c(\"Birds\", \"Mammals\"))) #> Records downloaded: 10 #> Records available: 22116048 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …5#3 Sciurus vulgaris Li… 1 60.23584 25.05693 2023-06-14 08:56:00 #> 2 …2#9 Hirundo rustica Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 3 …2#37 Pica pica (Linnaeus… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 4 …2#49 Muscicapa striata (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 5 …2#39 Larus canus Linnaeu… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 6 …2#5 Emberiza citrinella… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 7 …2#31 Ficedula hypoleuca … NA 64.12716 23.99111 2023-06-14 08:48:00 #> 8 …2#41 Alauda arvensis Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 9 …2#21 Numenius arquata (L… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 10 …2#29 Dendrocopos major (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_informal_groups(\"macrofungi\") #> Error in finbif_informal_groups(\"macrofungi\"): Group not found"},{"path":"/articles/v05_filtering.html","id":"regulatory","dir":"Articles","previous_headings":"","what":"Regulatory","title":"Filtering occurrence records","text":"Many records FinBIF database include taxa one another regulatory statuses. See finbif_metadata(\"regulatory_status\") list regulatory statuses short-codes.","code":"# Search for birds on the EU invasive species list finbif_occurrence( filter = list(informal_groups = \"Birds\", regulatory_status = \"EU_INVSV\") ) #> Records downloaded: 10 #> Records available: 471 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1580858#3 Oxyura jamaicensis … 1 60.28687 25.0271 #> 2 …JX.1580860#3 Oxyura jamaicensis … 1 60.28671 25.02713 #> 3 …KE.176/62b1ad90d5deb0fafdc6212b#Unit1 Oxyura jamaicensis … 7 61.66207 23.57706 #> 4 …JX.1045316#34 Alopochen aegyptiac… 3 52.16081 4.485534 #> 5 …JX.138840#123 Alopochen aegyptiac… 4 53.36759 6.191796 #> 6 …JX.139978#214 Alopochen aegyptiac… 6 53.37574 6.207861 #> 7 …JX.139710#17 Alopochen aegyptiac… 30 52.3399 5.069133 #> 8 …JX.139645#57 Alopochen aegyptiac… 36 51.74641 4.535283 #> 9 …JX.139645#10 Alopochen aegyptiac… 3 51.74641 4.535283 #> 10 …JX.139442#16 Alopochen aegyptiac… 2 51.90871 4.53258 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"iucn-red-list","dir":"Articles","previous_headings":"","what":"IUCN red list","title":"Filtering occurrence records","text":"Filtering can done IUCN red list category. See finbif_metadata(\"red_list\") IUCN red list categories short-codes.","code":"# Search for near threatened mammals finbif_occurrence( filter = list(informal_groups = \"Mammals\", red_list_status = \"NT\") ) #> Records downloaded: 10 #> Records available: 42510 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1594024#23 Rangifer tarandus f… 15 63.31266 24.43298 #> 2 …JX.1588853#1075 Rangifer tarandus f… 1 63.84551 29.8366 #> 3 …JX.1593780#3 Pusa hispida botnic… 1 65.02313 25.40505 #> 4 …HR.3211/166639315-U Rangifer tarandus f… NA 63.7 24.7 #> 5 …HR.3211/166049302-U Rangifer tarandus f… NA 64.1 26.5 #> 6 …HR.3211/165761924-U Rangifer tarandus f… NA 63.9 24.9 #> 7 …JX.1589779#105 Rangifer tarandus f… 3 63.7261 23.40827 #> 8 …KE.176/647ad84dd5de884fa20e25e6#Unit1 Rangifer tarandus f… 1 64.12869 24.73877 #> 9 …HR.3211/165005253-U Pusa hispida botnic… NA 64.2865 23.87402 #> 10 …JX.1588052#18 Rangifer tarandus f… 2 64.13286 26.26767 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"habitat-type","dir":"Articles","previous_headings":"","what":"Habitat type","title":"Filtering occurrence records","text":"Many taxa associated one primary secondary habitat types (e.g., forest) subtypes (e.g., herb-rich alpine birch forests). Use finbif_metadata(\"habitat_type\") see habitat types FinBIF. can filter occurrence records based primary (primary/secondary) habitat type subtype codes. Note filtering based habitat taxa location (.e., filtering records primary_habitat = \"M\" return records taxa considered primarily inhabit forests, yet locations records may encompass habitats forests). may refine habitat based searching using specific habitat type qualifier “sun-exposed” “shady”. Use finbif_metadata(\"habitat_qualifier\") see qualifiers available. specify qualifiers use named list character vectors names habitat types subtypes elements character vectors qualifier codes.","code":"head(finbif_metadata(\"habitat_type\")) #> code name #> MKV.habitatMt Mt alpine birch forests (excluding herb-rich alpine … #> MKV.habitatTlk Tlk alpine calcareous rock outcrops and boulder fields #> MKV.habitatTlr Tlr alpine gorges and canyons #> MKV.habitatT T Alpine habitats #> MKV.habitatTp Tp alpine heath scrubs #> MKV.habitatTk Tk alpine heaths # Search records of taxa for which forests are their primary or secondary # habitat type finbif_occurrence(filter = c(primary_secondary_habitat = \"M\")) #> Records downloaded: 10 #> Records available: 26362337 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …5#3 Sciurus vulgaris Li… 1 60.23584 25.05693 2023-06-14 08:56:00 #> 2 …2#37 Pica pica (Linnaeus… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 3 …2#49 Muscicapa striata (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 4 …2#5 Emberiza citrinella… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 5 …2#31 Ficedula hypoleuca … NA 64.12716 23.99111 2023-06-14 08:48:00 #> 6 …2#29 Dendrocopos major (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 7 …2#15 Sylvia borin (Bodda… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 8 …2#11 Anthus trivialis (L… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 9 …2#45 Corvus monedula Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 10 …2#3 Phylloscopus trochi… NA 64.12716 23.99111 2023-06-14 08:48:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_metadata(\"habitat_qualifier\")[4:6, ] #> code name #> MKV.habitatSpecificTypeCA CA calcareous effect #> MKV.habitatSpecificTypeH H esker forests, also semi-open forests #> MKV.habitatSpecificTypeKE KE intermediate-basic rock outcrops and boulder fiel… # Search records of taxa for which forests with sun-exposure and broadleaved # deciduous trees are their primary habitat type finbif_occurrence(filter = list(primary_habitat = list(M = c(\"PAK\", \"J\")))) #> Records downloaded: 10 #> Records available: 178 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …502812#393 Pammene fasciana (L… NA 60.45845 22.17811 2022-08-14 12:00:00 #> 2 …435062#6 Pammene fasciana (L… 1 60.20642 24.66127 2022-08-04 #> 3 …435050#9 Pammene fasciana (L… 1 60.20642 24.66127 2022-07-25 #> 4 …501598#39 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-21 12:00:00 #> 5 …501387#162 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-20 12:00:00 #> 6 …448030#159 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-18 12:00:00 #> 7 …447556#78 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-14 12:00:00 #> 8 …446841#408 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-12 12:00:00 #> 9 …443339#36 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-10 12:00:00 #> 10 …440849#159 Pammene fasciana (L… 2 60.08841 22.48629 2022-07-08 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"status-of-taxa-in-finland","dir":"Articles","previous_headings":"","what":"Status of taxa in Finland","title":"Filtering occurrence records","text":"can restrict occurrence records status taxa Finland. example can request records rare species. , using negation occurrence status, can request records birds excluding considered vagrants. See finbif_metadata(\"finnish_occurrence_status\") full list statuses descriptions.","code":"finbif_occurrence(filter = c(finnish_occurrence_status = \"rare\")) #> Records downloaded: 10 #> Records available: 406005 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3211/167313706-U Pygaera timon (Hübn… NA 62.1281 27.45272 #> 2 …JX.1594282#21 Carterocephalus pal… 1 64.65322 24.58941 #> 3 …HR.3211/167197097-U Carterocephalus pal… NA 65.07819 25.55236 #> 4 …HR.3211/167183358-U Glaucopsyche alexis… NA 60.46226 22.76647 #> 5 …JX.1594291#3 Glaucopsyche alexis… 1 60.42692 22.20411 #> 6 …KE.176/6488c111d5de884fa20e295f#Unit1 Panemeria tenebrata… 1 61.16924 25.56036 #> 7 …JX.1593930#3 Hemaris tityus (Lin… 1 60.63969 27.29052 #> 8 …KE.176/64889455d5de884fa20e294f#Unit1 Pseudopanthera macu… 2 62.054 30.352 #> 9 …JX.1594170#199 Glaucopsyche alexis… 1 61.10098 28.68453 #> 10 …JX.1594112#3 Hemaris tityus (Lin… 1 61.25511 28.89127 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( filter = list( informal_groups = \"birds\", finnish_occurrence_status_neg = sprintf(\"vagrant_%sregular\", c(\"\", \"ir\")) ) ) #> Records downloaded: 10 #> Records available: 21725426 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …9 Hirundo rustica Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 2 …37 Pica pica (Linnaeus… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 3 …49 Muscicapa striata (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 4 …39 Larus canus Linnaeu… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 5 …5 Emberiza citrinella… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 6 …31 Ficedula hypoleuca … NA 64.12716 23.99111 2023-06-14 08:48:00 #> 7 …41 Alauda arvensis Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 8 …21 Numenius arquata (L… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 9 …29 Dendrocopos major (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 10 …15 Sylvia borin (Bodda… NA 64.12716 23.99111 2023-06-14 08:48:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Finnish Museum Natural History - Luomus. Copyright holder. William K. Morris. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Morris, William K. (2024). Introduction finbif package. R package version 0.9.4.9000, https://doi.org/10.5281/zenodo.3612814","code":"@Manual{, title = {Introduction to the finbif package}, author = {William K. Morris}, year = {2024}, note = {R package version 0.9.4.9000}, url = {https://luomus.github.io/finbif/articles/finbif.html}, doi = {10.5281/zenodo.3612814}, }"},{"path":"/index.html","id":"finbif-r-package-","dir":"","previous_headings":"","what":"FinBIF R package","title":"FinBIF R package","text":"finbif R package programmatic interface Finnish Biodiversity Information Facility (FinBIF) API. FinBIF aggregates Finnish biodiversity data multiple sources single open access portal researchers, citizen scientists, industry government. FinBIF allows users biodiversity information find, access, combine visualise data Finnish plants, animals microorganisms. finbif R package makes publicly available data FinBIF easily accessible programmers. Biodiversity information available taxonomy taxon occurrence. Occurrence data can filtered taxon, time, location variables. data accessed conveniently preformatted subsequent analyses.","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"FinBIF R package","text":"can install current stable version finbif CRAN, can also install latest development version finbif GitHub,","code":"install.packages(\"finbif\") remotes::install_github(\"luomus/finbif@dev\")"},{"path":"/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"FinBIF R package","text":"Read online documentation current stable version finbif , latest development version finbif .","code":""},{"path":"/index.html","id":"getting-a-finbif-access-token","dir":"","previous_headings":"","what":"Getting a FinBIF access token","title":"FinBIF R package","text":"First load finbif R package. use FinBIF API must first request set personal access token. can request API token sent email address function finbif_get_token. Copy access token sent email set environment variable FINBIF_ACCESS_TOKEN either current session, , adding Renviron startup file (see details).","code":"library(finbif) finbif_request_token(\"your@email.com\") Sys.setenv( FINBIF_ACCESS_TOKEN = \"xtmSOIxjPwq0pOMB1WvcZgFLU9QBklauOlonWl8K5oaLIx8RniJLrvcJU4v9H7Et\" ) # Note: the above is not a real access token. Do not try using it."},{"path":"/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"FinBIF R package","text":"Download occurrence data FinBIF.","code":"finbif_occurrence(\"Cygnus cygnus\", n = 100)"},{"path":"/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"FinBIF R package","text":"Data FinBIF comes many sources. information citing FinBIF contributed datasets please visit link: https://laji.fi/en//2986 cite finbif R package publications please use: Morris, William K. (2024). Introduction finbif package. R package version 0.9.4.9000, https://doi.org/10.5281/zenodo.3612814","code":""},{"path":"/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"FinBIF R package","text":"Development community effort, encourage participation. Please read contribution guide details. Please note ‘finbif’ project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"/reference/caching.html","id":null,"dir":"Reference","previous_headings":"","what":"Caching FinBIF downloads — caching","title":"Caching FinBIF downloads — caching","text":"Working cached data FinBIF.","code":""},{"path":"/reference/caching.html","id":"turning-caching-off","dir":"Reference","previous_headings":"","what":"Turning caching off","title":"Caching FinBIF downloads — caching","text":"default, local caching FinBIF API requests turned . request made using arguments request data FinBIF first instance subsequent requests use local cache exists. increase speed repeated requests save bandwidth computation FinBIF server. Caching can turned temporarily setting cache = FALSE requesting function. Setting options(finbif_use_cache = FALSE) turn caching current session.","code":""},{"path":"/reference/caching.html","id":"using-filesystem-caching","dir":"Reference","previous_headings":"","what":"Using filesystem caching","title":"Caching FinBIF downloads — caching","text":"default cached requests stored memory. can changed setting file path current session options(finbif_cache_path = \"path//cache\").","code":""},{"path":"/reference/caching.html","id":"using-database-caching","dir":"Reference","previous_headings":"","what":"Using database caching","title":"Caching FinBIF downloads — caching","text":"Caching can also done using database. Using database caching requires packages DBI, blob database backend package RSQLite installed. use database caching simply pass connection objected created DBI::dbConnect finbif_cache_path option (e.g., db <- DBI::dbConnect(RSQLite::SQLite(), \"-db.sqlite\"); options(finbif_cache_path = db) ).","code":""},{"path":"/reference/caching.html","id":"clearing-the-cache","dir":"Reference","previous_headings":"","what":"Clearing the cache","title":"Caching FinBIF downloads — caching","text":"cache files can deleted finbif_clear_cache().","code":""},{"path":"/reference/filters.html","id":null,"dir":"Reference","previous_headings":"","what":"Filtering FinBIF records — filters","title":"Filtering FinBIF records — filters","text":"Filters available FinBIF records occurrence data.","code":""},{"path":"/reference/filters.html","id":"taxa","dir":"Reference","previous_headings":"","what":"Taxa","title":"Filtering FinBIF records — filters","text":"Filters related taxa include: taxon_id Character vector. FinBIF taxon IDs. functions finbif_check_taxa() finbif_taxa() can used search taxon IDs. taxon_name Character vector. Filter based taxon names (scientific common) rather IDs. specified taxa found FinBIF taxonomy matches attempted occurrence record names originally supplied verbatim. quality_controlled_det Logical. TRUE (default) use quality controlled taxonomic determinations. , FALSE use originally recorded taxonomic determinations. subtaxa Logical. TRUE (default) return records taxa belonging specified taxa. , FALSE return records exact matches specified taxa (e.g., genus specified, return records species belonging genus, return records individuals identified genus identified lower taxonomic level). invalid_taxa Logical. TRUE (default) return records taxa found FinBIF taxonomic database well taxa FinBIF database. , FALSE limit records taxa found FinBIF database. informal_groups Character vector. Filter informal taxonomic groups. including informal groups linked recorded taxa FinBIF database. Use function finbif_informal_groups() see informal taxonomic groups available FinBIF. informal_groups_reported Character vector. Filter informal taxonomic groups including groups reported directly record linked recorded taxa FinBIF database. Use function finbif_informal_groups() see informal taxonomic groups available FinBIF. regulatory_status Character vector. Filter regulatory status code. Use function finbif_metadata() see regulatory statuses codes. red_list_status Character vector. Filter IUCN red list status code. Use function finbif_metadata() see red list statuses codes. primary_habitat Character vector named list character vectors. Filter primary habitat code. Use function finbif_metadata() see habitat (sub)types codes taxa FinBIF database. Habitat type/subtypes can refined indicating habitat qualifiers named list character vectors names habitat (sub)type codes elements character vector habitat qualifier codes. Use function finbif_metadata() see habitat qualifiers codes. records returned taxa whose primary habitat considered (sub)habitat/habitat qualifier combination supplied. primary_secondary_habitat Character named list character vectors. , except records returned taxa whose primary secondary habitat considered combination supplied. finnish_occurrence_status Character vector. Filter Finnish occurrence status taxa. Use finbif_metadata() see possible occurrence statuses taxa. finnish_occurrence_status_neg Character vector. Negation . Selecting status filter rather include records selected status. finnish Logical. TRUE, limit records taxa thought occur Finland. FALSE limit taxa thought occur Finland. unspecified (default) return records taxa. invasive Logical. TRUE, limit records invasive taxa. FALSE limit non-invasive taxa. unspecified (default) return records invasive non-invasive taxa. taxon_rank Character vector. Filter taxonomic rank. Use finbif_metadata() see taxonomic ranks available. Records returned limited specified ranks include records lower taxonomic levels.","code":""},{"path":"/reference/filters.html","id":"location","dir":"Reference","previous_headings":"","what":"Location","title":"Filtering FinBIF records — filters","text":"Filters related location record include: locality Character vector. Filter name locality. first try match strings countries, bio-provinces, municipalities (see ) FinBIF, none locality types match exactly return records verbatim locality matches original records. country Character vector. Filter country. Use finbif_metadata() see country names ISO codes (2 3 character) used FinBIF. region Character vector. Filter region. Use finbif_metadata() see region names codes. bio_province Character vector. Filter bio-province. Use finbif_metadata() see bio-province names codes. municipality Character vector. Filter municipality. Use finbif_metadata() see municipality names. location_tag Character vector Filter tags associated location (e.g., \"farmland\"). bird_assoc_area Character vector. Filter BirdLife Finland association area. Use finbif_metadata() see association names codes. coordinates Coordinates. character vector list coordinate data. Must length 3 4 (e.g., list(lat = c(60.4, 61), lon = c(22, 22.5), system = \"wgs84\", ratio = 1). first element minimum maximum latitude second minimum maximum longitude (can minimums ). third element coordinate system; either one \"wgs84\", \"euref\" \"ykj\". optional fourth element positive value less 1. 1, coverage area returned records completely within box bound coordinates values. Values less 1 requires returned record's coverage overlap bounding box proportion. using system \"ykj\" coordinates coerced integers units inferred number integer digits (7 digits equals km's, 6 equals 10km's, etc.,). coordinate maximums specified assumed one unit minimums (e.g., c(666, 333, \"ykj\") equivalent list(c(6660000, 6670000), c(3330000, 3340000), \"ykj\")). coordinates_center Coordinates. character vector list coordinate data. Must length 3. first two elements latitude longitude third coordinate system (currently \"wgs84\" implemented). Records returned center point exactly matches specified. coordinates_cell_{1k|10k|50k|100k} Coordinates. vector coordinate data (lat, lon). Filter grid cell scale *. * 1, 10, 50 100. coordinates specify southeast corner cell. Coordinates system \"ykj\". coordinates_cell_{1k|10k|50k|100k}_center Coordinates. , except coordinates indicate center grid cell. coordinates_source Character. Filter source coordinates. Currently accepted values \"reported_value\" (coordinates recorded time observation) \"finnish_municipality\" (coordinates derived observer recorded municipality). coordinates_uncertainty_max Integer. Filter maximum uncertainty coordinates (.e., coordinates_uncertainty_max = 100 return records accurate 100m).","code":""},{"path":"/reference/filters.html","id":"time","dir":"Reference","previous_headings":"","what":"Time","title":"Filtering FinBIF records — filters","text":"Filters related time record include: date_range_ymd Dates. vector one two Date objects (begin end dates) objects coercible Date. supplying dates strings, day month--day can omitted (e.g., \"2001-04\" \"2001\"). Note however, omitting day, \"-\" allowed separate year month, months must two-digit/leading zero form. begin end dates partial date strings interpreted first last day month year (e.g., c(2001, 2003) equivalent c(\"2001-01-01\", \"2003-12-12\")). single date supplied partial date string records fall within month year returned (e.g., c(\"2001-01\") equivalent c(\"2001-01-01\", \"2001-01-31\")). Use empty strings begin end date specify open-ended date ranges (e.g., c(\"2000-01-01\", \"\") dates turn century). date_range_ym Dates. , days (supplied) ignored. date_range_d Integer vector. Filter day year (e.g., 1 366). begin end date omitted interpreted first last day year. date_range_md Character vector. Filter month day year (e.g., \"01-01\" \"12-31\"). begin end date omitted interpreted first last day year. {first|last}_import_date_{min|max} Date. Filter date record imported/modified. Either Date object object coercible Date class, number seconds since 1970-01-01 00:00.00 UTC (-called UNIX epoch). Note means specifying year, 2019, without month day interpreted 2019 seconds midnight Jan 1, 1970 year 2019.","code":""},{"path":"/reference/filters.html","id":"quality","dir":"Reference","previous_headings":"","what":"Quality","title":"Filtering FinBIF records — filters","text":"Filters related quality record: quality_issues. Character. Filter presence record quality issues. One \"without_issues\", \"with_issues\" \"\". Issues include quality issues record, event, document. default \"without_issues\" unless filtering record, event document ID record annotation status. requires_verification Logical. Show records requiring verification (TRUE) requiring verification (FALSE). collection_quality Character vector. Filter one collection quality types. Must one \"professional\", \"hobbyist\" \"amateur\". record_reliability Character vector. Filter reliability record. Must one \"reliable\", \"unassessed \"unreliable\". Default c(\"reliable\", \"unassessed\"). record_quality Character vector. Filter quality record. Must one \"expert_verified\", \"community_verified\", \"unassessed\", \"uncertain\", \"erroneous\".","code":""},{"path":"/reference/filters.html","id":"misc","dir":"Reference","previous_headings":"","what":"Misc","title":"Filtering FinBIF records — filters","text":"filters: keywords Character vector. Filter keywords. collection Character vector finbif_collections() data.frame. Filter collection. character vector can refer collection ID, collection name (English) abbreviated name. Use finbif_collections() see list collections metadata. Can also use results call finbif_collections() directly filter records. subcollections Logical. TRUE (default) include subcollections collections specified. FALSE include subcollections. not_collection Character vector finbif_collections() data.frame. collection, result negation specified collections. source Character vector. Filter information system data source. Use finbif_metadata() see data source IDs names descriptions. record_basis Character vector. Filter basis record. Use finbif_metadata() see list record bases. superrecord_basis Character vector. Filter superset record basis. One \"human_observation\", \"machine_observation\", \"specimen\". life_stage Character vector. Filter organism life stage. Use finbif_metadata() see list organism life stages. sex Character vector. Filter organism sex sex-related category name code. Use finbif_metadata() see list organism sexes sex-related categories codes. \"male\" \"female\" specified records returned sex specified male female respectively records corresponding {male|female}_abundance > 1. event_id Character. Filter event (list records, etc.) ID. document_id Character. Filter document (collection events) ID occurrences. record_id Character. individual_id Character. Filter individual (individual organism) ID. abundance_min Integer. Filter minimum number individual organisms record. abundance_max Integer. Filter maximum number individual organisms record. type_specimen Logical. Filter whether record type specimen. wild_status Character. Filter \"wildness\" status records. One \"wild\", \"non_wild\" \"unknown\". Default c(\"wild\", \"unknown\"). is_breeding_location Logical. Filter whether occurrence recorded known breeding location. has_document_media Logical. Filter whether media (images, video, audio, etc.) associated records' document. has_event_media Logical. Filter whether media (images, video, audio, etc.) associated records' event. has_record_media Logical. Filter whether media (images, video, audio, etc.) associated record. has_media Logical. Filter whether media (images, video, audio, etc.) associated record, document event. event_observer_name Character. Filter observer name. event_observer_id Integer. Filter observer ID. restriction_reason Character vector. Filter reason data security restrictions. See finbif_metadata() list reasons data may security restrictions. restriction_level Character vector. Filter data restriction level. See finbif_metadata() list levels data restrictions. restricted Logical. Filter records whether data restrictions place (TRUE) (FALSE). annotated Logical. Filter records (TRUE) (FALSE) annotations. unidentified Logical. Filter whether record identified species level linked FinBIF taxon database (FALSE) identified species level reliably linked taxon database (TRUE). taxon_census Character vector. Return records belonging surveys censuses given taxon taxonomic group. Specify taxonomic group FinBIF taxon ID. Use finbif_check_taxa() find taxon IDs. {record|event|document}_fact Character vector. Filter record, event document facts. Facts key-value pairs form \"=\". Value can omitted case records value recorded specified fact returned. has_sample Logical. Record includes sample samples (e.g., DNA sample preparation). complete_list_type Filter complete list type. Records made monitoring produces taxon lists given group taxa (e.g., birds) can include species observed breeding status recorded observed species (all_species_and_breeding), species observed without breeding status recorded species observed, species observed without breeding status recorded observed species (all_species), species observed (incomplete). complete_list_taxon_id Filter taxon ID target group (e.g., birds) complete list.","code":""},{"path":"/reference/finbif-package.html","id":null,"dir":"Reference","previous_headings":"","what":"finbif: Interface for the 'Finnish Biodiversity Information Facility' API — finbif-package","title":"finbif: Interface for the 'Finnish Biodiversity Information Facility' API — finbif-package","text":"programmatic interface 'Finnish Biodiversity Information Facility' ('FinBIF') API (https://api.laji.fi). 'FinBIF' aggregates Finnish biodiversity data multiple sources single open access portal researchers, citizen scientists, industry government. 'FinBIF' allows users biodiversity information find, access, combine visualise data Finnish plants, animals microorganisms. 'finbif' package makes publicly available data 'FinBIF' easily accessible programmers. Biodiversity information available taxonomy taxon occurrence. Occurrence data can filtered taxon, time, location variables. data accessed conveniently preformatted subsequent analyses.","code":""},{"path":"/reference/finbif-package.html","id":"package-options","dir":"Reference","previous_headings":"","what":"Package options","title":"finbif: Interface for the 'Finnish Biodiversity Information Facility' API — finbif-package","text":"finbif_api_url Character. base url API query. Default: \"https://api.laji.fi\" finbif_api_version Character. API version use. Default: \"v0\" finbif_allow_query Logical. remote API queries allowed. Default: TRUE finbif_use_cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated value. Default: TRUE finbif_cache_path Character. path directory store cached API queries. unset (default) memory caching used. finbif_tz Character. timezone used finbif functions compute dates times. Default: Sys.timezone() finbif_locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. default, system settings used set option set one supported languages, otherwise English used. finbif_hide_progress Logical. Global option suppress progress indicators downloading, importing processing FinBIF records. Default: FALSE","code":""},{"path":[]},{"path":"/reference/finbif-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"finbif: Interface for the 'Finnish Biodiversity Information Facility' API — finbif-package","text":"Maintainer: William K. Morris willi@mmorris.email (ORCID) contributors: Finnish Museum Natural History - Luomus [copyright holder]","code":""},{"path":"/reference/finbif_check_taxa.html","id":null,"dir":"Reference","previous_headings":"","what":"Check FinBIF taxa — finbif_check_taxa","title":"Check FinBIF taxa — finbif_check_taxa","text":"Check taxa FinBIF database.","code":""},{"path":"/reference/finbif_check_taxa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check FinBIF taxa — finbif_check_taxa","text":"","code":"finbif_check_taxa(taxa, cache = getOption(\"finbif_use_cache\"))"},{"path":"/reference/finbif_check_taxa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check FinBIF taxa — finbif_check_taxa","text":"taxa Character (list named character) vector(s). list vector can name taxonomic rank (genus, species, etc.,). elements vectors taxa check. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument.","code":""},{"path":"/reference/finbif_check_taxa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check FinBIF taxa — finbif_check_taxa","text":"object class finbif_taxa. list form taxa.","code":""},{"path":"/reference/finbif_check_taxa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check FinBIF taxa — finbif_check_taxa","text":"","code":"if (FALSE) { # Check a scientific name finbif_check_taxa(\"Cygnus cygnus\") # Check a common name finbif_check_taxa(\"Whooper swan\") # Check a genus finbif_check_taxa(\"Cygnus\") # Check a list of taxa finbif_check_taxa( list( species = c(\"Cygnus cygnus\", \"Ursus arctos\"), genus = \"Betula\" ) ) }"},{"path":"/reference/finbif_clear_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Clear cache — finbif_clear_cache","title":"Clear cache — finbif_clear_cache","text":"Remove cached API requests FinBIF.","code":""},{"path":"/reference/finbif_clear_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clear cache — finbif_clear_cache","text":"","code":"finbif_clear_cache()"},{"path":"/reference/finbif_clear_cache.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clear cache — finbif_clear_cache","text":"","code":"if (FALSE) { finbif_clear_cache() }"},{"path":"/reference/finbif_collections.html","id":null,"dir":"Reference","previous_headings":"","what":"FinBIF collections — finbif_collections","title":"FinBIF collections — finbif_collections","text":"Get information collections FinBIF database.","code":""},{"path":"/reference/finbif_collections.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FinBIF collections — finbif_collections","text":"","code":"finbif_collections( filter, select, subcollections = TRUE, supercollections = FALSE, locale = getOption(\"finbif_locale\"), nmin = 0, cache = getOption(\"finbif_use_cache\") )"},{"path":"/reference/finbif_collections.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FinBIF collections — finbif_collections","text":"filter Logical. Expression indicating elements rows keep: missing values taken false. select Expression. Indicates columns select data frame. subcollections Logical. Return subcollection metadata higher level collections. supercollections Logical. Return lowest level collection metadata. locale Character. Language data returned. One \"en\", \"fi\", \"sv\". nmin Integer. Filter collections number records. return information collections greater value specified. NA return information collections. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument.","code":""},{"path":"/reference/finbif_collections.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"FinBIF collections — finbif_collections","text":"data.frame.","code":""},{"path":"/reference/finbif_collections.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FinBIF collections — finbif_collections","text":"","code":"if (FALSE) { # Get collection metadata collections <- finbif_collections() }"},{"path":"/reference/finbif_informal_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"FinBIF informal groups — finbif_informal_groups","title":"FinBIF informal groups — finbif_informal_groups","text":"Display informal taxonomic groups used FinBIF database.","code":""},{"path":"/reference/finbif_informal_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FinBIF informal groups — finbif_informal_groups","text":"","code":"finbif_informal_groups( group, limit = 5, quiet = FALSE, locale = getOption(\"finbif_locale\") )"},{"path":"/reference/finbif_informal_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FinBIF informal groups — finbif_informal_groups","text":"group Character. Optional, supplied display top-level group subgroups. limit Integer. maximum number top-level informal groups (sub-groups) display. quiet Logical. Return informal group names without displaying . locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated .","code":""},{"path":"/reference/finbif_informal_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"FinBIF informal groups — finbif_informal_groups","text":"character vector (invisibly).","code":""},{"path":"/reference/finbif_informal_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FinBIF informal groups — finbif_informal_groups","text":"","code":"if (FALSE) { # Display the informal taxonomic groups used by FinBIF finbif_informal_groups() }"},{"path":"/reference/finbif_last_mod.html","id":null,"dir":"Reference","previous_headings":"","what":"Get last modified date for FinBIF occurrence records — finbif_last_mod","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"Get last modified date filtered occurrence data FinBIF.","code":""},{"path":"/reference/finbif_last_mod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"","code":"finbif_last_mod(..., filter)"},{"path":"/reference/finbif_last_mod.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"... Character vectors list character vectors. Taxa records download. filter List named character vectors. Filters apply records.","code":""},{"path":"/reference/finbif_last_mod.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"Date object","code":""},{"path":"/reference/finbif_last_mod.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"","code":"if (FALSE) { # Get last modified date for Whooper Swan occurrence records from Finland finbif_last_mod(\"Cygnus cygnus\", filter = c(country = \"Finland\")) }"},{"path":"/reference/finbif_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"FinBIF metadata — finbif_metadata","title":"FinBIF metadata — finbif_metadata","text":"Display metadata FinBIF database.","code":""},{"path":"/reference/finbif_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FinBIF metadata — finbif_metadata","text":"","code":"finbif_metadata(which, locale = getOption(\"finbif_locale\"))"},{"path":"/reference/finbif_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FinBIF metadata — finbif_metadata","text":"Character. category metadata display. unspecified, function returns categories metadata available. locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated .","code":""},{"path":"/reference/finbif_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"FinBIF metadata — finbif_metadata","text":"data.frame.","code":""},{"path":"/reference/finbif_metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FinBIF metadata — finbif_metadata","text":"","code":"if (FALSE) { finbif_metadata(\"red_list\") }"},{"path":"/reference/finbif_occurrence.html","id":null,"dir":"Reference","previous_headings":"","what":"Download FinBIF occurrence records — finbif_occurrence","title":"Download FinBIF occurrence records — finbif_occurrence","text":"Download filtered occurrence data FinBIF data.frame.","code":""},{"path":"/reference/finbif_occurrence.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download FinBIF occurrence records — finbif_occurrence","text":"","code":"finbif_occurrence( ..., filter = NULL, select = NULL, order_by = NULL, aggregate = \"none\", sample = FALSE, n = 10, page = 1, count_only = FALSE, quiet = getOption(\"finbif_hide_progress\"), cache = getOption(\"finbif_use_cache\"), dwc = FALSE, date_time_method = NULL, check_taxa = TRUE, on_check_fail = c(\"warn\", \"error\"), tzone = getOption(\"finbif_tz\"), locale = getOption(\"finbif_locale\"), seed = NULL, drop_na = FALSE, aggregate_counts = TRUE, exclude_na = FALSE, unlist = FALSE, facts = NULL, duplicates = FALSE, filter_col = NULL, restricted_api = NULL )"},{"path":"/reference/finbif_occurrence.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download FinBIF occurrence records — finbif_occurrence","text":"... Character vectors list character vectors. Taxa records download. filter List named character vectors. Filters apply records. select Character vector. Variables return. specified, default set commonly used variables used. Use \"default_vars\" shortcut set. Variables can deselected prepending - variable name. deselects specified default set variables without deselection returned. order_by Character vector. Variables order records returned. , though , variables can used order records returned. Ordering ascending default. return descending order append - front variable (e.g., \"-date_start\"). Default order \"-date_start\" > \"-load_data\" > \"reported_name\". aggregate Character. \"none\" (default), returns full records. one \"records\", \"species\", \"taxa\", \"individuals\", \"pairs\", \"events\" \"documents\"; aggregates combinations selected variables counting records, species, taxa, individuals events documents. Aggregation events documents done combination aggregation types. sample Logical. TRUE randomly sample records FinBIF database. n Integer. many records download/import. page Integer. page records start downloading . count_only Logical. return number records available. quiet Logical. Suppress progress indicator multipage downloads. Defaults value option finbif_hide_progress. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument. dwc Logical. Use Darwin Core (Darwin Core style) variable names. date_time_method Character. Passed lutz::tz_lookup_coords() date_time /duration variables selected. Default \"fast\" less 100,000 records requested \"none\" . Using method \"none\" assumes records timezone \"Europe/Helsinki\", Use date_time_method = \"accurate\" (requires package sf) greater accuracy cost slower computation. check_taxa Logical. Check first taxa FinBIF database. true records match known taxa (valid taxon ID) returned. on_check_fail Character. taxon found valid. One \"warn\" (default) \"error\". tzone Character. date_time selected timezone outputted date-time. Defaults system timezone. locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated . seed Integer. Set seed randomly sampling records. drop_na Logical. vector indicating columns check missing data. Values recycled number columns. Defaults columns. aggregate_counts Logical. count variables returned using aggregation. exclude_na Logical. records selected variables non-NA values returned. unlist Logical. variables contain non atomic data concatenated string separated \";\"? facts Character vector. Extra variables extracted record, event document \"facts\". duplicates Logical. TRUE, allow duplicate records/aggregated records making multi-filter set requests. FALSE (default) duplicate records removed. filter_col Character. name column, values derived names filter sets used using multiple filters, include using multiple filter sets. NULL (default), column included. restricted_api Character. using restricted data API token addition personal access token, string indicating name environment variable storing restricted data API token.","code":""},{"path":"/reference/finbif_occurrence.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download FinBIF occurrence records — finbif_occurrence","text":"data.frame. count_only = TRUE integer.","code":""},{"path":"/reference/finbif_occurrence.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download FinBIF occurrence records — finbif_occurrence","text":"","code":"if (FALSE) { # Get recent occurrence data for taxon finbif_occurrence(\"Cygnus cygnus\") # Specify the number of records finbif_occurrence(\"Cygnus cygnus\", n = 100) # Get multiple taxa finbif_occurrence(\"Cygnus cygnus\", \"Ursus arctos\") # Filter the records finbif_occurrence( species = \"Cygnus cygnus\", filter = list(coordinate_accuracy_max = 100) ) }"},{"path":"/reference/finbif_occurrence_load.html","id":null,"dir":"Reference","previous_headings":"","what":"Load FinBIF occurrence records from a file — finbif_occurrence_load","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"Load occurrence data file data.frame.","code":""},{"path":"/reference/finbif_occurrence_load.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"","code":"finbif_occurrence_load( file, select = NULL, n = -1, count_only = FALSE, quiet = getOption(\"finbif_hide_progress\"), cache = getOption(\"finbif_use_cache\"), dwc = FALSE, date_time_method = NULL, tzone = getOption(\"finbif_tz\"), write_file = tempfile(), dt = NA, keep_tsv = FALSE, facts = list(), type_convert_facts = TRUE, drop_na = FALSE, drop_facts_na = drop_na, locale = getOption(\"finbif_locale\"), skip = 0 )"},{"path":"/reference/finbif_occurrence_load.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"file Character Integer. Either path Zip archive tabular data file downloaded \"laji.fi\", URI linking data file (e.g., https://tun.fi/HBF.49381) integer representing URI (.e., 49381). select Character vector. Variables return. specified, default set commonly used variables used. Use \"default_vars\" shortcut set. Variables can deselected prepending - variable name. deselects specified default set variables without deselection returned. Use \"\" select available variables file. n Integer. many records import. Negative invalid values ignored causing records imported. count_only Logical. return number records available. quiet Logical. Suppress progress indicator multipage downloads. Defaults value option finbif_hide_progress. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument. dwc Logical. Use Darwin Core (Darwin Core style) variable names. date_time_method Character. Passed lutz::tz_lookup_coords() date_time /duration variables selected. Default \"fast\" less 100,000 records requested \"none\" . Using method \"none\" assumes records timezone \"Europe/Helsinki\", Use date_time_method = \"accurate\" (requires package sf) greater accuracy cost slower computation. tzone Character. date_time selected timezone outputted date-time. Defaults system timezone. write_file Character. Path write downloaded zip file file refers URI. ignored getOption(\"finbif_cache_path\") NULL use cache path instead. dt Logical. package, data.table, available return data.table object rather data.frame. keep_tsv Logical. Whether keep TSV file file ZIP archive represents URI. ignored file already TSV. TRUE tsv file kept directory ZIP archive. facts List. named list \"facts\" extract supplementary \"fact\" files local online FinBIF data archive. Names can include one \"record\", \"event\" \"document\". Elements list character vectors \"facts\" extracted joined return value. type_convert_facts Logical. facts converted character numeric integer data applicable? drop_na Logical. vector indicating columns check missing data. Values recycled number columns. Defaults columns. drop_facts_na Logical. missing \"NA\" facts dropped? value length one logical vector value TRUE interpreted FALSE. Argument ignored drop_na TRUE variables explicitly via recycling. drop missing/NA-data facts use drop_na argument. locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated . skip Integer. number lines data file skip beginning read data (including header).","code":""},{"path":"/reference/finbif_occurrence_load.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"data.frame, count_only = TRUE integer.","code":""},{"path":"/reference/finbif_occurrence_load.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"","code":"if (FALSE) { # Get occurrence data finbif_occurrence_load(49381) }"},{"path":"/reference/finbif_request_token.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a FinBIF personal access token — finbif_request_token","title":"Get a FinBIF personal access token — finbif_request_token","text":"personal access token use FinBIF API sent specified email address.","code":""},{"path":"/reference/finbif_request_token.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a FinBIF personal access token — finbif_request_token","text":"","code":"finbif_request_token(email, quiet = FALSE)"},{"path":"/reference/finbif_request_token.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a FinBIF personal access token — finbif_request_token","text":"email Character. email address send API access token. quiet Logical. Suppress messages.","code":""},{"path":"/reference/finbif_request_token.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a FinBIF personal access token — finbif_request_token","text":"access token already set NULL (invisibly) , invisibly, finbif_api object containing response FinBIF server.","code":""},{"path":"/reference/finbif_request_token.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a FinBIF personal access token — finbif_request_token","text":"","code":"if (FALSE) { # Request a token for example@email.com finbif_request_token(\"example@email.com\") }"},{"path":"/reference/finbif_taxa.html","id":null,"dir":"Reference","previous_headings":"","what":"Search the FinBIF taxa — finbif_taxa","title":"Search the FinBIF taxa — finbif_taxa","text":"Search FinBIF database taxon.","code":""},{"path":"/reference/finbif_taxa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search the FinBIF taxa — finbif_taxa","text":"","code":"finbif_taxa( name, n = 1, type = c(\"exact\", \"partial\", \"likely\"), cache = getOption(\"finbif_use_cache\") ) common_name(name, locale = getOption(\"finbif_locale\")) scientific_name(name) taxon_id(name)"},{"path":"/reference/finbif_taxa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search the FinBIF taxa — finbif_taxa","text":"name Character. name ID taxon. , functions finbif_taxa finbif_taxa object. n Integer. Maximum number matches return. types \"exact\" \"likely\" one taxon returned. type Character. Type match make. Must one exact, partial likely. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument. locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated .","code":""},{"path":"/reference/finbif_taxa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search the FinBIF taxa — finbif_taxa","text":"finbif_taxa finbif_taxa object. Otherwise, character vector.","code":""},{"path":"/reference/finbif_taxa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search the FinBIF taxa — finbif_taxa","text":"","code":"if (FALSE) { # Search for a taxon finbif_taxa(\"Ursus arctos\") # Use partial matching finbif_taxa(\"Ursus\", n = 10, \"partial\") # Get Sámi (Northern) name of Eurasian Eagle-owl common_name(\"Bubo bubo\", \"se\") # Get scientific name of \"Otter\" scientific_name(\"Otter\") # Get taxon identifier of \"Otter\" taxon_id(\"Otter\") }"},{"path":"/reference/finbif_update_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Update cache — finbif_update_cache","title":"Update cache — finbif_update_cache","text":"Update cached API requests FinBIF.","code":""},{"path":"/reference/finbif_update_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update cache — finbif_update_cache","text":"","code":"finbif_update_cache()"},{"path":"/reference/finbif_update_cache.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update cache — finbif_update_cache","text":"","code":"if (FALSE) { finbif_update_cache() }"},{"path":"/reference/to_dwc.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert variable names — to_dwc","title":"Convert variable names — to_dwc","text":"Convert variable names Darwin Core FinBIF R package native style.","code":""},{"path":"/reference/to_dwc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert variable names — to_dwc","text":"","code":"to_dwc(...) to_native(...) from_schema( ..., to = c(\"native\", \"dwc\", \"short\"), file = c(\"none\", \"citable\", \"lite\") )"},{"path":"/reference/to_dwc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert variable names — to_dwc","text":"... Character. Variable names convert. to_dwc to_native names must opposite format. from_schema names must FinBIF schema (e.g., names returned https://api.laji.fi) FinBIF download file (citable lite). Character. Type variable names convert . file Character. variable names derived FinBIF download file type file.","code":""},{"path":"/reference/to_dwc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert variable names — to_dwc","text":"Character vector.","code":""},{"path":"/reference/to_dwc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert variable names — to_dwc","text":"","code":"to_dwc(\"record_id\", \"date_time\", \"scientific_name\") #> [1] \"occurrenceID\" \"eventDateTime\" \"scientificName\""},{"path":"/reference/variables.html","id":null,"dir":"Reference","previous_headings":"","what":"FinBIF record variables — variables","title":"FinBIF record variables — variables","text":"FinBIF record variables can selected finbif occurrence search.","code":""},{"path":"/reference/variables.html","id":"identifiers","dir":"Reference","previous_headings":"","what":"Identifiers","title":"FinBIF record variables — variables","text":"identifiers returned form URI. Identifiers include: record_id Character. ID record organism's occurrence time place. individual_id Character. ID individual organism (e.g., ringed bird captured multiple times single individual_id multiple record_ids corresponding capture). event_id Character. Event ID. event can contain one records (e.g., survey plants particular location time.) document_id Character. Document ID. set events share common metadata. form_id Character. Form ID. form used create document, event, record data. collection_id Character. Collection ID. documents, events, records belong collection (e.g., museum collection, datasets collected specific institution). Collections can part larger (super)collection (e.g., collections specific museum). lowest level collection ID record returned. Use finbif_collections() explore hierarchy collections. source_id Character. Source ID. source collection's data.","code":""},{"path":"/reference/variables.html","id":"taxa","dir":"Reference","previous_headings":"","what":"Taxa","title":"FinBIF record variables — variables","text":"Variables related taxonomy records include: taxon_id Character. taxon ID form URI. orig_taxon_id Character. taxon ID () annotation. annotated_taxon_id Character. new taxon ID record taxonomy annotated. reported_taxon_id Character. taxon ID originally reported record creator. scientific_name Character. Scientific name taxon. orig_scientific_name Character. scientific name () annotation. scientific_display_name Character. Scientific name taxon formatted display (e.g., taxa genus formatted Genus sp.). orig_scientific_display_name Character. Scientific display name () annotation. common_name Character. Common (vernacular) name taxon. orig_common_name Character. Common name () annotation. reported_name Character. name taxon originally reported record creator. scientific_name_italicised Logical. scientific name normally italicised (.e., taxonomic rank genus .) orig_scientific_name_italicised Logical. original scientific name normally italicised. scientific_name_author Character. authority taxon scientific name. orig_scientific_name_author Character. authority taxon scientific name () annotation. reported_author Character. authority taxon originally reported record creator. taxon_rank Character. taxonomic rank taxon. orig_taxon_rank Character. taxonomic rank taxon () annotation. informal_groups List. informal taxonomic groups taxon belongs (e.g., birds) form URIs. orig_informal_groups List. informal taxonomic groups taxon belonged () annotation. reported_informal_groups List. informal taxonomic groups taxon belongs reported record creator. taxon_checklist Character. checklist (URI) taxon found . orig_taxon_checklist Character. checklist (URI) taxon found () annotation. taxon_finnish Logical. taxon considered Finnish. definition Finnish taxon differs taxonomic group? orig_taxon_finnish Logical. taxon considered Finnish () annotation?","code":""},{"path":"/reference/variables.html","id":"abundance-sex-amp-life-history","dir":"Reference","previous_headings":"","what":"Abundance, sex & life history","title":"FinBIF record variables — variables","text":"Variables related abundance, sex life history include: abundance Integer. Number individuals recorded. abundance_interpreted Integer. Number individuals recorded inferred record. Note many records abundance_interpreted == 1L indicate record one individual may necessarily imply abundance specified place time (e.g., preserved museum specimen consisting single individual). {female|male}_abundance Integer. Number female male individuals recorded. pair_abundance Integer. Number mating pairs recorded. abundance_verbatim Character. abundance reported record creator. life_stage Character. Life stage individual(s) recorded. sex Character. Sex individual(s) recorded.","code":""},{"path":"/reference/variables.html","id":"location","dir":"Reference","previous_headings":"","what":"Location","title":"FinBIF record variables — variables","text":"Variables related location records include: {lat|lon}_{euref|wgs84} Numeric. Coordinates (EUREF WGS84 coordinate system) central point bounding box encompassing record's geographic coverage. {lat|lon}_{min|max}_{euref|ykj|wgs84}. Numeric. Vertices bounding box encompassing record's geographic coverage. Coordinates available EUREF, YKJ, WGS84. coordinates_uncertainty Integer. horizontal distance (meters) record's given coordinates describing smallest circle containing whole record's location. coordinates_source Character. Source coordinates. footprint_{euref|ykj|wgs84} Character. Well-Known Text (WKT) representation geographic shape defining location record either EUREF, YKJ WGS84 coordinate systems. country Character. country record's location. region Character. administrative area directly level country. bio_province Character. data Finland FinBIF uses concept Biogeographical Province. See link details. municipality. Character. Administrative level region higher_geography Character. Geographic place name higher level country. line_length_m Integer. length linear locations (e.g., line transect surveys). area_m2 Integer. size record's location meters squared. is_breeding_location Logical. Whether occurrence recorded known breeding location. location_id Character. location ID form URI. section Integer. numeric identifier sub-location location (e.g., specific part transect undergoes repeated surveys.)","code":""},{"path":"/reference/variables.html","id":"time","dir":"Reference","previous_headings":"","what":"Time","title":"FinBIF record variables — variables","text":"Variables related time record include: date_time POSIXct. date time recording event. variable computed records downloaded FinBIF. timezone accuracy can controlled see finbif_occurrence() details. duration Duration. duration recording event. variable computed records downloaded FinBIF. date_start Character. date recording event began. date_end Character. date recording event ended. hour_start Integer. hour (24 hour time) day recording event began. hour_end Integer. hour (24 hour time) day recording event ended. minute_start Integer. minute hour recording event began. minute_end Integer. minute hour recording event started. ordinal_day_start Integer. ordinal day year recording event began. ordinal_day_end Integer. ordinal day year recording event ended season_start Integer. day year recording event began. four digit number indicating day year MMDD (%m%d) format. season_end Integer. day year recording event ended. four digit number indicating day year MMDD (%m%d) format. century Integer. century recording event occurred (NA event spans multiple centuries). decade Integer. decade recording event occurred (NA event spans multiple decades). year Integer. year recording event occurred (NA event spans multiple years). month Integer. month year recording event occurred (NA event spans multiple months). day Integer. day month recording event occurred (NA event spans multiple days). formatted_date_time Character. Date time recording event formatted display. date_created Character. date original data created. first_load_date Character. date record first loaded FinBIF database. modified_date Character. recent date original data modified. load_date Character. recent date record loaded FinBIF database.","code":""},{"path":"/reference/variables.html","id":"data-restrictions","dir":"Reference","previous_headings":"","what":"Data restrictions","title":"FinBIF record variables — variables","text":"Variables related restricted records include: restriction Logical. record restricted way (e.g., geospatially aggregated). restriction_level Character. level restriction applied record. restriction_reason List. List reasons restriction applied.","code":""},{"path":"/reference/variables.html","id":"data-quality","dir":"Reference","previous_headings":"","what":"Data quality","title":"FinBIF record variables — variables","text":"Variables related quality records include: any_issues Logical. data quality issues associated record, event document. reported_taxon_confidence Reliability record's taxonomic identification reported original data author. {document|time|location|event|record}_issue Character. Issues record associated document, time, location, event, record . {document|time|location|event|record}_issue_message Character. Details issue. {document|time|location|event|record}_issue_source Character. Source determining issue. requires_verification Logical. record flagged expert verification? requires_identification Logical. record flagged expert identification? record_reliability Character. Indication record's reliability. record_quality Character. Indication record's quality.","code":""},{"path":"/reference/variables.html","id":"misc","dir":"Reference","previous_headings":"","what":"Misc","title":"FinBIF record variables — variables","text":"variables: collection Character. Collection name. documents, events, records belong collection (e.g., museum collection, datasets collected specific institution). Collections can part larger (super)collection (e.g., collections specific museum). lowest level collection name record returned. Use finbif_collections() explore hierarchy collections. observers_ids List. List observer identifiers record. determiner Character. Person determined taxonomic identification record. record_basis Character. type method used obtain record. superrecord_basis Character. Higher level type method used obtain record. type_specimen Logical. Whether record type specimen. is_wild Logical. Whether record \"wild\" organism. license Character. license data associated record. {document|event|record}_notes Character. Notes associated document, event record . {document|record}_keywords List. List keywords associated document record. record_annotation_count Integer. many annotations associated record. sample_count Integer. many material samples (DNA extractions, etc., ...) associated record. {document|event|record}_media_count Integer. many media items (images, audio, video, etc., ...) associated record's document, event record .","code":""},{"path":"/news/index.html","id":"finbif-094","dir":"Changelog","previous_headings":"","what":"finbif 0.9.4","title":"finbif 0.9.4","text":"CRAN release: 2024-01-12","code":""},{"path":"/news/index.html","id":"new-features-0-9-4","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.9.4","text":"New undocumented variable “source” can selected finbif_occurrence.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-9-4","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.9.4","text":"Record pagination now often require less queries FinBIF server faster. FinBIF collections field names sanitised. filtering records “collection_id” full URL ID can used QName.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-4","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.9.4","text":"Reading zero observation data downloads now produce zero row data.frame instead triggering error.","code":""},{"path":"/news/index.html","id":"finbif-093","dir":"Changelog","previous_headings":"","what":"finbif 0.9.3","title":"finbif 0.9.3","text":"CRAN release: 2023-09-28","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-3","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.9.3","text":"Fix bug resulting incorrect region assigned occurrences records.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-9-3","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.9.3","text":"New undocumented variables institution_code collection_code can selected using functions finbif_collections finbif_occurrence.","code":""},{"path":"/news/index.html","id":"finbif-092","dir":"Changelog","previous_headings":"","what":"finbif 0.9.2","title":"finbif 0.9.2","text":"CRAN release: 2023-08-28","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-2","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.9.2","text":"Fixed bug triggered localising variables multiple pages data requested.","code":""},{"path":"/news/index.html","id":"finbif-091","dir":"Changelog","previous_headings":"","what":"finbif 0.9.1","title":"finbif 0.9.1","text":"CRAN release: 2023-06-29","code":""},{"path":"/news/index.html","id":"new-features-0-9-1","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.9.1","text":"New option finbif_use_cache_metadata set caching metadata . ignored finbif_use_cache TRUE.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-1","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.9.1","text":"Fixed bug triggered trying compute variable identifier data returned contained zero records.","code":""},{"path":"/news/index.html","id":"finbif-090","dir":"Changelog","previous_headings":"","what":"finbif 0.9.0","title":"finbif 0.9.0","text":"CRAN release: 2023-05-23","code":""},{"path":"/news/index.html","id":"new-features-0-9-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.9.0","text":"New function finbif_update_cache can used update cached objects reached expiration longer valid. restricted data API token can explicitly declared via restricted_api argument finbif_occurrence. Cached data can use database backend passing DBI database connection object package option finbif_cache_path. Cached data can assigned timeout using number (hours) instead logical value cache argument finbif_ functions package option finbif_use_cache. Record aggregations finbif_occurrence can now combined multi-filter requests. Removing duplicate records aggregate record combinations can controlled duplicates argument adding column indicating filter sets can added filter_col argument.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-0","dir":"Changelog","previous_headings":"","what":"finbif 0.9.0","title":"finbif 0.9.0","text":"Fixed bug causing infinite recursion determining page size record download pagination. Fix bug triggered using aggregation selected variables.","code":""},{"path":"/news/index.html","id":"defunct-0-9-0","dir":"Changelog","previous_headings":"","what":"DEFUNCT","title":"finbif 0.9.0","text":"Mapping utilities finland_map, breaks_xy, hist_xy plot method finbif_occ objects now defunct. User access finbif_records classes methods now defunct.","code":""},{"path":"/news/index.html","id":"finbif-080","dir":"Changelog","previous_headings":"","what":"finbif 0.8.0","title":"finbif 0.8.0","text":"CRAN release: 2023-03-29","code":""},{"path":"/news/index.html","id":"deprecation-0-8-0","dir":"Changelog","previous_headings":"","what":"DEPRECATION","title":"finbif 0.8.0","text":"Mapping utilities finland_map, breaks_xy, hist_xy plot method finbif_occ objects deprecated --scope. User access finbif_records classes methods deprecated favour finbif_occurrence.","code":""},{"path":"/news/index.html","id":"new-features-0-8-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.8.0","text":"Record aggregations finbif_occurrence can now include “individual” “pair” sums.","code":""},{"path":"/news/index.html","id":"finbif-072","dir":"Changelog","previous_headings":"","what":"finbif 0.7.2","title":"finbif 0.7.2","text":"CRAN release: 2023-02-06","code":""},{"path":"/news/index.html","id":"minor-improvements-0-7-2","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.7.2","text":"Updated deprecated use tidy::pivot_wider. Added new filters variables upstream API.","code":""},{"path":"/news/index.html","id":"finbif-071","dir":"Changelog","previous_headings":"","what":"finbif 0.7.1","title":"finbif 0.7.1","text":"CRAN release: 2022-11-24","code":""},{"path":"/news/index.html","id":"new-features-0-7-1","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.7.1","text":"New function finbif_mod_date get last modified date FinBIF occurrence data. Region now selectable variable finbif_occurrence can also used filter records.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-7-1","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.7.1","text":"sake clarity “province” now referred “bio-province”. Many variables, including sex, life_stage record_quality now localised. variable restriction_reasons now referred singular restriction_reason. consistency, lang argument finbif_collections changed locale.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-7-1","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.7.1","text":"Fixed bug caused locale set incorrectly multipage requests.","code":""},{"path":"/news/index.html","id":"finbif-070","dir":"Changelog","previous_headings":"","what":"finbif 0.7.0","title":"finbif 0.7.0","text":"CRAN release: 2022-09-13","code":""},{"path":"/news/index.html","id":"new-features-0-7-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.7.0","text":"New function taxon_id returns FinBIF taxon identifiers given scientific name, vernacular name taxon identifier. New filters complete_list_taxon_id complete_list_type now available. New global option finbif_hide_progress suppress progress bars downloading, importing processing FinBIF records. sake clarity consistency term “administrative status” now referred “regulatory status” throughout. Regulatory status, informal taxonomic group habitat data now localised. Option unlist added finbif_occurrence casts list columns strings. cell multiple values values cast string separated semi-colons. New argument facts added finbif_occurrence can used automatically extract facts downloading occurrence records.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-7-0","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.7.0","text":"Fixed bug triggered incorrect data type applied taxonomic_order. Fixed bug preventing locale switching vernacular name data.","code":""},{"path":"/news/index.html","id":"finbif-066","dir":"Changelog","previous_headings":"","what":"finbif 0.6.6","title":"finbif 0.6.6","text":"CRAN release: 2022-08-08","code":""},{"path":"/news/index.html","id":"new-features-0-6-6","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.6.6","text":"New option exclude records NA values selected variables added finbif_occurrence.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-6","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.6","text":"warning/error message returned invalid taxon requested finbif_occurrence made detailed, warning user may using synonyms invalid taxon names.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-6","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.6","text":"Fix applied print method error triggered clashing class names. Fixed issue ordering variables.","code":""},{"path":"/news/index.html","id":"finbif-065","dir":"Changelog","previous_headings":"","what":"finbif 0.6.5","title":"finbif 0.6.5","text":"CRAN release: 2022-05-20","code":""},{"path":"/news/index.html","id":"new-features-0-6-5","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.6.5","text":"New variables filters (currently undocumented) added forthcoming Finnish atlas breeding birds. Skip rows argument added finbif_occurrence_load files can read chunks.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-5","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.5","text":"clarity, KKJ coordinate reference system now referred YKJ. selecting available variables download file imports using finbif_occurrence_load “extra” variables longer automatically added.","code":""},{"path":"/news/index.html","id":"finbif-064","dir":"Changelog","previous_headings":"","what":"finbif 0.6.4","title":"finbif 0.6.4","text":"CRAN release: 2022-03-10","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-4","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.4","text":"New administrative statuses added. number (interval ) api request retries can configured (currently undocumented). museum collections scientific names added non-Finnish species. New fields added citable download imports. New argument aggregate_counts (defaulting TRUE) added finbif_occurrence toggle inclusion aggregation count fields . New bird association area, occurrence types location tag metadata added. New filters variables (currently undocumented) added upstream API.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-4","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.4","text":"Fix bug triggered printing occurrence records records coordinate uncertainty.","code":""},{"path":"/news/index.html","id":"finbif-063","dir":"Changelog","previous_headings":"","what":"finbif 0.6.3","title":"finbif 0.6.3","text":"CRAN release: 2022-01-03","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-3","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.3","text":"Argument drop_na_facts changed drop_facts_na function finbif_occurrence_load avoid problems due partial matching argument drop_na. Data quality description appended description field data.frame returned finbif_collections(). Occurrence record filtering can now done using open-ended date ranges. New administrative statuses added.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-3","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.3","text":"Fix bug importing file downloads triggered string quotation errors.","code":""},{"path":"/news/index.html","id":"finbif-062","dir":"Changelog","previous_headings":"","what":"finbif 0.6.2","title":"finbif 0.6.2","text":"CRAN release: 2021-09-03","code":""},{"path":"/news/index.html","id":"new-features-0-6-2","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.6.2","text":"New package option, finbif_allow_query, default value, TRUE. set FALSE remote API queries trigger error meaning cached requests run cache found. Records can now aggregated document.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-2","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.2","text":"client-side error triggered attempt made filter taxon aggregate data event finbif_occurrence.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-2","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.2","text":"Fix bug preventing loading FinBIF archives triggered variables selected select = \"\". Fix bug preventing finbif_occ objects printing one columns contain missing data .","code":""},{"path":"/news/index.html","id":"finbif-061","dir":"Changelog","previous_headings":"","what":"finbif 0.6.1","title":"finbif 0.6.1","text":"CRAN release: 2021-07-26","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-1","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.1","text":"Fixed regression last release prevented collection names converted URIs.","code":""},{"path":"/news/index.html","id":"finbif-060","dir":"Changelog","previous_headings":"","what":"finbif 0.6.0","title":"finbif 0.6.0","text":"CRAN release: 2021-07-22","code":""},{"path":"/news/index.html","id":"new-features-0-6-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.6.0","text":"New variables lat_euref lon_euref available occurrence record downloads. new variables represent central point bounding box encompassing record’s geographic coverage EUREF (ETRS89/ETRS-TM35FIN) coordinate system. Option now available retain TSV data file loading FinBIF occurrence data finbif_occurrence_load ZIP archive online reference. Option now available extract “facts” using finbif_occurrence_load import records ZIP archive. user must supply named list, names refer one fact types: “record”, “event” /“document”, list elements character vectors indicating “facts” extract. “Lite” download files (occurrence record datasets less 10,000 records downloaded directly laji.fi) can now imported using finbif_occurrence_load. New filters (currently undocumented) ely_center_id region_id available finbif_occurrence. New function, from_schema, convert variable names FinBIF schema styles. New computed variable date_time_ISO8601 (currently undocumented) can selected creating finbif_occ objects. New computed variable epsg (currently undocumented). selected, column EPSG code first column contains geographic data.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-0","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.0","text":"Can now select available variables importing FinBIF download request file using finbif_occurrence_load select = \"\". New option, drop_na, drop columns contain missing data added finbif_occurrence finbif_occurrence_load. User can now select columns multiple times rename fly using named character vector value ‘select’ argument. variable taxon_rank now converted string fly via taxon_rank_id. Variables computed identifiers now localised multiple languages available.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-0","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.0","text":"Fixed bug prevented occurrence record counting caching use. Fixed bug triggered error selected variable computed ID using DWC style variable names.","code":""},{"path":"/news/index.html","id":"finbif-050","dir":"Changelog","previous_headings":"","what":"finbif 0.5.0","title":"finbif 0.5.0","text":"CRAN release: 2021-03-27","code":""},{"path":"/news/index.html","id":"new-features-0-5-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.5.0","text":"Getting records FinBIF can now speed (~1.5x) asynchronous processing. future package available asynchronous strategy (e.g., plan(multisession, workers = 2)) selected downloading records processing occur simultaneously separate threads, often leading significant speed sequential processing. Occurrence records can now requested using multiple sets filters time. list filters (unnamed elements) supplied record request made set filters results requests combined duplicate records removed. Occurrence records can now read directly FinBIF download request files. function finbif_occurrence_load can load data local file remotely using persistent identifier URI (e.g., http://tun.fi/HBF.49381). Aggregation records can now performed recording “event” level well “record” level.","code":""},{"path":"/news/index.html","id":"finbif-041","dir":"Changelog","previous_headings":"","what":"finbif 0.4.1","title":"finbif 0.4.1","text":"CRAN release: 2021-01-27","code":""},{"path":"/news/index.html","id":"new-features-0-4-1","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.4.1","text":"New functions scientific_name common_name now available get scientific common names taxa (given taxon name FinBIF ID code) extract names finbif_taxa- class object. Add ability extract complex record variables associated record media (currently undocumented).","code":""},{"path":"/news/index.html","id":"minor-improvements-0-4-1","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.4.1","text":"Collection name can selected variable occurrence records. Previously manually translated collection ID. Variables restriction_reasons_conservation, restriction_reason_embargo restriction_reason_custom longer use upstream can longer selected.","code":""},{"path":"/news/index.html","id":"finbif-040","dir":"Changelog","previous_headings":"","what":"finbif 0.4.0","title":"finbif 0.4.0","text":"CRAN release: 2020-12-17","code":""},{"path":"/news/index.html","id":"new-features-0-4-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.4.0","text":"Occurrence record requests can now made aggregation, aggregate = c(\"records\", \"species\", \"taxa\"). returns number records, /species taxa combination selected variables instead occurrence records .","code":""},{"path":"/news/index.html","id":"minor-improvements-0-4-0","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.4.0","text":"Error triggered attempting request less one record. New content requesting aggregated occurrence records added vignette: 2. Occurrence records FinBIF.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-4-0","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.4.0","text":"Fixed two bugs print method FinBIF occurrence records triggered attempting print one row data. Fixed bug triggering error attempting print occurrence record objects zero rows. Fixed bug triggered trying print occurrence record data NA values. Fixed bug causing incorrect subsetting occurrence records using logical vectors subset rows. Fixed bug printed occurrence records multi-element data incorrectly single element. Fixed bug triggered system locales (#1).","code":""},{"path":"/news/index.html","id":"finbif-031","dir":"Changelog","previous_headings":"","what":"finbif 0.3.1","title":"finbif 0.3.1","text":"CRAN release: 2020-11-24","code":""},{"path":"/news/index.html","id":"new-features-0-3-1","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.3.1","text":"Occurrence records can ordered total number records total number Finnish records taxon (variables: n_total_records & n_total_finnish_records, currently undocumented). New Finnish occurrence status, records_only, added. New administrative statuses added filters.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-3-1","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.3.1","text":"Filtering vignette updated reflect changes data quality filters.","code":""},{"path":"/news/index.html","id":"finbif-030","dir":"Changelog","previous_headings":"","what":"finbif 0.3.0","title":"finbif 0.3.0","text":"CRAN release: 2020-04-23","code":""},{"path":"/news/index.html","id":"new-features-0-3-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.3.0","text":"user facing functions finbif_ prefix can now also used alternative shorter prefix fb_. Crop Wild Relative, CWR, added admin statuses. two new utility functions, to_dwc to_native converting variable names Darwin Core style. Users can select order variables Darwin Core style using finbif_occurrence. changes variables filters flowed upstream changes “api.laji.fi”. variables is_unidentifiable, record_reliable, collection_reliability, taxon_reliability, taxon_reliability_message taxon_reliability_source deprecated replaced requires_verification, requires_identification, record_reliability record_quality. filters collection_reliability taxon_reliability deprecated replaced requires_verification, collection_quality, record_reliability, record_quality, expert_verified. Vernacular names now localised. Users can select language use taxon vernacular names. Missing names fallback gracefully languages. package-wide locale can set default set system locale (set can’t determined default English). New vignettes getting occurrence records, selecting ordering variables, metadata plotting added.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-3-0","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.3.0","text":"Caching defaults memory caching instead relying temporary directory. Front matter vignettes now visible using R help browser. Retired “quiet” option “on_check_fail” argument function finbif_occurrence(). Improved error messages taxa fail checking finbif_occurrence(). Global option set timezone, “finbif_tz”, default value “tzone” argument finbif_occurrence(). Avoids set system environment variable TZ specify “tzone” every time finbif_occurrence() run. Now record time information start time assumed midday. Previous behaviour assume start time midnight, making errors potentially biased. Package options now documented package level man page. News file now accessible via R internal help system. number default variables selected accessing occurrence records reduced speed downloads improve display finbif_occ objects. print method occurrence record objects updated. now aware console width truncating variable values considerate context. Variables can now “deselected” using select argument finbif_occurrence prepending variable name “-”. failures, API requests now automatically retried three times.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-3-0","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.3.0","text":"Ordering descending variables work ordering ascending descending variables. Fixed bug handling duplicates result infinite recursion. Fixed bug (“on_check_fail” = “warn”) taxa failed checks ‘finbif_occurrence()’ proceed taxa selected. Fixed bug print method finbif_occ objects caused error trying display single column objects list-col .","code":""},{"path":"/news/index.html","id":"finbif-020","dir":"Changelog","previous_headings":"","what":"finbif 0.2.0","title":"finbif 0.2.0","text":"CRAN release: 2020-01-16","code":""},{"path":"/news/index.html","id":"new-features-0-2-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.2.0","text":"Add capacity request random sample FinBIF records.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-2-0","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.2.0","text":"Add content vignettes.","code":""},{"path":"/news/index.html","id":"finbif-010","dir":"Changelog","previous_headings":"","what":"finbif 0.1.0","title":"finbif 0.1.0","text":"CRAN release: 2019-11-19 Initial release.","code":""}] +[{"path":[]},{"path":"/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement helpdesk@laji.fi. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":[]},{"path":"/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing","text":"Small typos grammatical errors documentation may edited long changes made source file. YES: edit roxygen comment .R file R/. : edit .Rd file man/.","code":""},{"path":"/CONTRIBUTING.html","id":"prerequisites","dir":"","previous_headings":"","what":"Prerequisites","title":"Contributing","text":"make substantial pull request, always file issue make sure someone team agrees ’s problem. ’ve found bug, create associated issue illustrate bug minimal reprex.","code":""},{"path":"/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"","what":"Pull request process","title":"Contributing","text":"recommend create Git branch pull request (PR). Look build status making changes. README contains badges continuous integration services used package. New code follow style used project. use roxygen2, Markdown syntax, documentation. use testthat. Contributions test cases included easier accept. user-facing changes, add section top inst/NEWS.Rd current development version header describing changes made followed username, links relevant issue(s)/PR(s).","code":""},{"path":"/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing","text":"Please note project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2019-2024 LUOMUS - Finnish Museum Natural History Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"/articles/finbif.html","id":"installing-the-finbif-package","dir":"Articles","previous_headings":"","what":"Installing the finbif package","title":"Introduction to the finbif package","text":"can install current stable version finbif CRAN, can also install latest development version finbif GitHub,","code":"install.packages(\"finbif\") remotes::install_github(\"luomus/finbif@dev\")"},{"path":"/articles/finbif.html","id":"loading-the-finbif-package","dir":"Articles","previous_headings":"","what":"Loading the finbif package","title":"Introduction to the finbif package","text":"","code":"library(finbif)"},{"path":"/articles/finbif.html","id":"getting-a-finbif-access-token","dir":"Articles","previous_headings":"","what":"Getting a FinBIF access token","title":"Introduction to the finbif package","text":"use FinBIF API must first request set personal access token. can request API token sent email address function finbif_get_token(). Copy access token sent email set environment variable FINBIF_ACCESS_TOKEN either current session, , adding Renviron startup file (see details).","code":"finbif_request_token(\"your@email.com\") Sys.setenv( FINBIF_ACCESS_TOKEN = \"xtmSOIxjPwq0pOMB1WvcZgFLU9QBklauOlonWl8K5oaLIx8RniJLrv\" ) # Note: the above is not a real access token. Do not try using it."},{"path":"/articles/finbif.html","id":"working-with-taxa","dir":"Articles","previous_headings":"","what":"Working with taxa","title":"Introduction to the finbif package","text":"can check see taxon exists FinBIF database. taxon FinBIF database unique ID returned. taxon FinBIF database reported “found” taxa list element NA. can also specify taxonomic rank searching FinBIF search limited specified rank. function finbif_taxa() can used general search taxa FinBIF database. Searches can exact, partial likely (fuzzy matching). Information single taxon returned using exact fuzzy matching, multiple taxa, limit, n, may returned using partial matching.","code":"finbif_check_taxa(\"Ursus arctos\") #> [Ursus arctos] ID: MX.47348 (taxa <- finbif_check_taxa(c(\"Ursus arctos\", \"Moomin\"))) #> [Ursus arctos] ID: MX.47348 #> [Moomin ] Not found taxa[[1]] #> Ursus arctos #> \"MX.47348\" taxa[[2]] #> Moomin #> NA finbif_check_taxa(list(species = c(\"Ursus arctos\", \"Ursus\"), genus = \"Ursus\")) #> [species: Ursus arctos] ID: MX.47348 #> [species: Ursus ] Not found #> [genus: Ursus ] ID: MX.51311 birch_search <- finbif_taxa(\"Betula pendula\", 2, \"partial\") birch_search$content #> [[1]] #> [[1]]$matchingName #> [1] \"Betula pendula var. pendula\" #> #> [[1]]$nameType #> [1] \"MX.scientificName\" #> #> [[1]]$id #> [1] \"MX.37994\" #> #> [[1]]$scientificName #> [1] \"Betula pendula var. pendula\" #> #> [[1]]$taxonRank #> [1] \"MX.variety\" #> #> [[1]]$cursiveName #> [1] TRUE #> #> [[1]]$finnish #> [1] TRUE #> #> [[1]]$species #> [1] TRUE #> #> [[1]]$vernacularName #> [[1]]$vernacularName$sv #> [1] \"vanlig vårtbjörk\" #> #> [[1]]$vernacularName$fi #> [1] \"vihtakoivu\" #> #> #> [[1]]$informalGroups #> [[1]]$informalGroups[[1]] #> [[1]]$informalGroups[[1]]$id #> [1] \"MVL.343\" #> #> [[1]]$informalGroups[[1]]$name #> [[1]]$informalGroups[[1]]$name$fi #> [1] \"Putkilokasvit\" #> #> [[1]]$informalGroups[[1]]$name$en #> [1] \"Vascular plants\" #> #> [[1]]$informalGroups[[1]]$name$sv #> [1] \"Kärlväxter\" #> #> #> #> #> [[1]]$kingdomScientificName #> [1] \"Plantae\" #> #> [[1]]$type #> [1] \"partialMatches\" #> #> #> [[2]] #> [[2]]$matchingName #> [1] \"Betula nana × pendula\" #> #> [[2]]$nameType #> [1] \"MX.scientificName\" #> #> [[2]]$id #> [1] \"MX.38005\" #> #> [[2]]$scientificName #> [1] \"Betula nana × pendula\" #> #> [[2]]$taxonRank #> [1] \"MX.infragenericHybrid\" #> #> [[2]]$cursiveName #> [1] TRUE #> #> [[2]]$finnish #> [1] TRUE #> #> [[2]]$species #> [1] TRUE #> #> [[2]]$vernacularName #> named list() #> #> [[2]]$informalGroups #> [[2]]$informalGroups[[1]] #> [[2]]$informalGroups[[1]]$id #> [1] \"MVL.343\" #> #> [[2]]$informalGroups[[1]]$name #> [[2]]$informalGroups[[1]]$name$fi #> [1] \"Putkilokasvit\" #> #> [[2]]$informalGroups[[1]]$name$en #> [1] \"Vascular plants\" #> #> [[2]]$informalGroups[[1]]$name$sv #> [1] \"Kärlväxter\" #> #> #> #> #> [[2]]$kingdomScientificName #> [1] \"Plantae\" #> #> [[2]]$type #> [1] \"partialMatches\" #> #>"},{"path":"/articles/finbif.html","id":"getting-occurrence-data","dir":"Articles","previous_headings":"","what":"Getting occurrence data","title":"Introduction to the finbif package","text":"can download occurrence data FinBIF database data.frame finbif_occurrence() function. can search multiple taxa filter records filter argument. See ?filters vignette(\"v05_filtering\") details filtering FinBIF records.","code":"finbif_occurrence(\"Cygnus cygnus\", n = 100) #> Records downloaded: 100 #> Records available: 95730 #> A data.frame [100 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …JX.1594164#13 Cygnus cygnus (Linn… NA 64.94473 26.67958 2023-06-13 14:33:00 #> 2 …HR.4412/6489172c9ddda_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> 3 …HR.4412/64891730060a4_U Cygnus cygnus (Linn… NA 61.38348 22.97288 2023-06-13 12:00:00 #> 4 …HR.4412/648917378a3b6_U Cygnus cygnus (Linn… NA 62.76028 24.15774 2023-06-13 12:00:00 #> 5 …HR.4412/6489175adc05f_U Cygnus cygnus (Linn… NA 60.78752 21.39263 2023-06-13 12:00:00 #> 6 …HR.4412/6489173a1db9b_U Cygnus cygnus (Linn… NA 64.31374 26.68643 2023-06-13 12:00:00 #> 7 …HR.4412/648917456a396_U Cygnus cygnus (Linn… NA 61.87986 25.19067 2023-06-13 12:00:00 #> 8 …HR.4412/648917454912b_U Cygnus cygnus (Linn… NA 60.42215 24.00099 2023-06-13 12:00:00 #> 9 …HR.4412/64891750e74e7_U Cygnus cygnus (Linn… NA 63.86383 27.70835 2023-06-13 12:00:00 #> 10 …HR.4412/64891741330f8_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> ...with 90 more records and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( \"Cygnus cygnus\", \"Cygnus olor\", filter = list(coordinates_uncertainty_max = 100) ) #> Records downloaded: 10 #> Records available: 47293 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …HR.3211/167194019-U Cygnus olor (J.F. G… NA 60.12778 24.69528 2023-06-13 12:00:00 #> 2 …JX.1593978#37 Cygnus olor (J.F. G… 10 60.428 22.20038 2023-06-13 12:00:00 #> 3 …JX.1594262#19 Cygnus olor (J.F. G… 5 61.60789 21.51679 2023-06-13 12:00:00 #> 4 …JX.1594262#17 Cygnus cygnus (Linn… 5 61.60789 21.51679 2023-06-13 12:00:00 #> 5 …JX.1594053#296 Cygnus cygnus (Linn… 1 63.62644 23.70806 2023-06-13 03:10:00 #> 6 …JX.1594054#93 Cygnus cygnus (Linn… 1 63.63403 24.21195 2023-06-13 03:08:00 #> 7 …JX.1593931#255 Cygnus cygnus (Linn… 2 64.5582 27.78468 2023-06-13 05:03:00 #> 8 …JX.1593916#3 Cygnus cygnus (Linn… 2 66.11897 25.93173 2023-06-13 12:00:00 #> 9 …JX.1593873#63 Cygnus cygnus (Linn… 2 65.72167 27.94208 2023-06-13 09:27:00 #> 10 …HR.3211/167071964-U Cygnus olor (J.F. G… NA 60.18156 24.93153 2023-06-12 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/finbif.html","id":"random-sampling","dir":"Articles","previous_headings":"Getting occurrence data","what":"Random sampling","title":"Introduction to the finbif package","text":"possible request random sample records instead last n records (records ordered variable).","code":"finbif_occurrence(\"Birds\", sample = TRUE) #> Records downloaded: 10 #> Records available: 21748016 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3691/OBS1143679721_Unit Aythya marila (Linn… 11 59.9815 24.39929 #> 2 …KE.67/1662813#Unit Fringilla coelebs L… 1 59.83333 19.93333 #> 3 …KE.8_1165614#90 Poecile montanus (C… 6 62.44825 29.92951 #> 4 …KE.67/12308933#Unit Prunella modularis … 1 61.67291 22.25931 #> 5 …KE.67/9586054#Unit Larus argentatus Po… 1 50.85 6.833333 #> 6 …KE.67/8576210#Unit Periparus ater (Lin… 1 60.2 19.33333 #> 7 …KE.67/9862495#Unit Prunella modularis … 1 61.13488 24.39512 #> 8 …KE.67/4669401#Unit Larus argentatus Po… 1 60.01667 24.61667 #> 9 …JX.1031300#61 Motacilla alba Linn… NA 62.12915 30.16957 #> 10 …KE.67/11492752#Unit Bombycilla garrulus… 1 62.67061 30.93362 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/finbif.html","id":"caching","dir":"Articles","previous_headings":"","what":"Caching","title":"Introduction to the finbif package","text":"default finbif uses local caching repeated API requests. can turned per request session basis. See ?caching details.","code":""},{"path":"/articles/v02_occurrence_data.html","id":"darwin-core-variables","dir":"Articles","previous_headings":"","what":"Darwin Core Variables","title":"Occurrence records from FinBIF","text":"can switch default variable names Darwin Core style names setting dwc = TRUE. functions to_dwc() to_native() can used translate variable names Darwin Core style finbif’s native variable names style.","code":"colnames(finbif_occurrence(dwc = TRUE)) #> [1] \"occurrenceID\" \"scientificName\" \"individualCount\" #> [4] \"decimalLatitude\" \"decimalLongitude\" \"eventDateTime\" #> [7] \"coordinateUncertaintyInMeters\" \"hasIssues\" \"requiresVerification\" #> [10] \"requiresIdentification\" \"occurrenceReliability\" \"occurrenceQuality\""},{"path":"/articles/v02_occurrence_data.html","id":"choosing-taxa","dir":"Articles","previous_headings":"","what":"Choosing taxa","title":"Occurrence records from FinBIF","text":"can limit records certain taxa specifying argument. Multiple taxa can requested . can also chose higher taxonomic groups use common names (English, Finnish Swedish).","code":"finbif_occurrence(\"Cygnus cygnus\") #> Records downloaded: 10 #> Records available: 95730 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …JX.1594164#13 Cygnus cygnus (Linn… NA 64.94473 26.67958 2023-06-13 14:33:00 #> 2 …HR.4412/6489172c9ddda_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> 3 …HR.4412/64891730060a4_U Cygnus cygnus (Linn… NA 61.38348 22.97288 2023-06-13 12:00:00 #> 4 …HR.4412/648917378a3b6_U Cygnus cygnus (Linn… NA 62.76028 24.15774 2023-06-13 12:00:00 #> 5 …HR.4412/6489175adc05f_U Cygnus cygnus (Linn… NA 60.78752 21.39263 2023-06-13 12:00:00 #> 6 …HR.4412/6489173a1db9b_U Cygnus cygnus (Linn… NA 64.31374 26.68643 2023-06-13 12:00:00 #> 7 …HR.4412/648917456a396_U Cygnus cygnus (Linn… NA 61.87986 25.19067 2023-06-13 12:00:00 #> 8 …HR.4412/648917454912b_U Cygnus cygnus (Linn… NA 60.42215 24.00099 2023-06-13 12:00:00 #> 9 …HR.4412/64891750e74e7_U Cygnus cygnus (Linn… NA 63.86383 27.70835 2023-06-13 12:00:00 #> 10 …HR.4412/64891741330f8_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence(\"Cygnus cygnus\", \"Cygnus olor\") #> Records downloaded: 10 #> Records available: 138681 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …JX.1594164#13 Cygnus cygnus (Linn… NA 64.94473 26.67958 2023-06-13 14:33:00 #> 2 …HR.4412/6489172c9ddda_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> 3 …HR.4412/64891730060a4_U Cygnus cygnus (Linn… NA 61.38348 22.97288 2023-06-13 12:00:00 #> 4 …HR.4412/648917378a3b6_U Cygnus cygnus (Linn… NA 62.76028 24.15774 2023-06-13 12:00:00 #> 5 …HR.4412/64891759be4c7_U Cygnus olor (J.F. G… NA 63.40045 21.48901 2023-06-13 12:00:00 #> 6 …HR.4412/6489175adc05f_U Cygnus cygnus (Linn… NA 60.78752 21.39263 2023-06-13 12:00:00 #> 7 …HR.4412/6489173a1db9b_U Cygnus cygnus (Linn… NA 64.31374 26.68643 2023-06-13 12:00:00 #> 8 …HR.4412/648917456a396_U Cygnus cygnus (Linn… NA 61.87986 25.19067 2023-06-13 12:00:00 #> 9 …HR.4412/648917454912b_U Cygnus cygnus (Linn… NA 60.42215 24.00099 2023-06-13 12:00:00 #> 10 …HR.4412/64891750e74e7_U Cygnus cygnus (Linn… NA 63.86383 27.70835 2023-06-13 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality birds <- finbif_occurrence(\"Birds\") linnut <- finbif_occurrence(\"Linnut\") faglar <- finbif_occurrence(\"Fåglar\") sapply(list(birds, linnut, faglar), nrow) #> [1] 10 10 10"},{"path":"/articles/v02_occurrence_data.html","id":"request-size","dir":"Articles","previous_headings":"","what":"Request size","title":"Occurrence records from FinBIF","text":"can increase number records returned using n argument. can see many records available given request, without retrieving records, setting count_only = TRUE.","code":"finbif_occurrence(n = 1001) #> Records downloaded: 1001 #> Records available: 47159747 #> A data.frame [1001 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 991 more records and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence(count_only = TRUE) #> [1] 47159747"},{"path":"/articles/v02_occurrence_data.html","id":"checking-taxa","dir":"Articles","previous_headings":"","what":"Checking taxa","title":"Occurrence records from FinBIF","text":"request occurrence records specific taxa, default, taxon names first checked FinBIF database. requested taxa found database receive warning data still retrieved remaining taxa. can turn taxon name pre-checking setting value check_taxa argument FALSE. setting argument, on_check_fail \"error\" (default \"warn\"), can elevate warnings errors request fail taxa found FinBIF database. can useful strategy using finbif non-interactively (script), want proceed taxon names wrong misspelled.","code":"finbif_occurrence(\"Vulpes vulpes\", \"Moomin\") #> Records downloaded: 10 #> Records available: 5303 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3211/167313561-U Vulpes vulpes (Linn… NA 60.18049 25.04838 #> 2 …HR.3211/167310567-U Vulpes vulpes (Linn… NA 60.2241 24.89373 #> 3 …KE.176/64894ccdd5de884fa20e2972#Unit1 Vulpes vulpes (Linn… 1 60.21118 24.90744 #> 4 …KE.176/6489506dd5de884fa20e2976#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 5 …KE.176/648802d6d5de884fa20e290d#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 6 …KE.176/648802c7d5de884fa20e290c#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 7 …HR.3211/167167234-U Vulpes vulpes (Linn… NA 60.20261 24.86879 #> 8 …HR.3211/166968734-U Vulpes vulpes (Linn… NA 60.5 21.9 #> 9 …HR.3211/166944731-U Vulpes vulpes (Linn… NA 60.17493 24.74123 #> 10 …KE.176/64869a52d5de884fa20e28ae#Unit1 Vulpes vulpes (Linn… 1 60.23885 25.12012 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence(\"Vulpes vulpes\", \"Moomin\", check_taxa = FALSE) #> Records downloaded: 10 #> Records available: 5303 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3211/167313561-U Vulpes vulpes (Linn… NA 60.18049 25.04838 #> 2 …HR.3211/167310567-U Vulpes vulpes (Linn… NA 60.2241 24.89373 #> 3 …KE.176/64894ccdd5de884fa20e2972#Unit1 Vulpes vulpes (Linn… 1 60.21118 24.90744 #> 4 …KE.176/6489506dd5de884fa20e2976#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 5 …KE.176/648802d6d5de884fa20e290d#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 6 …KE.176/648802c7d5de884fa20e290c#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 7 …HR.3211/167167234-U Vulpes vulpes (Linn… NA 60.20261 24.86879 #> 8 …HR.3211/166968734-U Vulpes vulpes (Linn… NA 60.5 21.9 #> 9 …HR.3211/166944731-U Vulpes vulpes (Linn… NA 60.17493 24.74123 #> 10 …KE.176/64869a52d5de884fa20e28ae#Unit1 Vulpes vulpes (Linn… 1 60.23885 25.12012 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence(\"Vulpes vulpes\", \"Moomin\", on_check_fail = \"error\") #> Error: Cannot find the following taxa in the FinBIF taxonomy. #> Please check you are using accepted names and not synonyms or #> other names for the taxa you are selecting: #> #> Moomin"},{"path":"/articles/v02_occurrence_data.html","id":"aggregating-records","dir":"Articles","previous_headings":"","what":"Aggregating records","title":"Occurrence records from FinBIF","text":"can request records aggregate using aggregate argument finbif_occurrence. Aggregated requests return counts combination variables specify select argument. can request counts \"records\", \"species\" \"taxa\" using corresponding string value aggregate argument. Aggregating \"species\" count number unique species identifiers set records grouped combination selected variables. Note count include records taxa species identifiers, including records higher taxa (e.g., genus records), records non-species children aggregate complex taxa, hybrid taxa. Therefore, contexts results returned underestimate species richness. Likewise, aggregating \"taxa\", returns count number unique taxon identifiers, represent overestimate number taxa records higher taxa contribute count true identify may duplicate records. illustrate, can count number moths butterflies municipality following:","code":"finbif_occurrence(\"Lepidoptera\", select = \"municipality\", aggregate = \"species\") #> Records downloaded: 10 #> Records available: 309 #> A data.frame [10 x 2] #> municipality n_species #> 1 Raasepori 2038 #> 2 Virolahti 1978 #> 3 Kouvola 1508 #> 4 Rääkkylä 1367 #> 5 Kemiönsaari 2008 #> 6 Hanko 1945 #> 7 Parainen 1858 #> 8 Helsinki 1980 #> 9 Kuopio 1345 #> 10 Kotka 1719"},{"path":"/articles/v02_occurrence_data.html","id":"time-duration","dir":"Articles","previous_headings":"","what":"Time & duration","title":"Occurrence records from FinBIF","text":"default behaviour finbif_occurrence consolidate date time data occurrence recording events date_time variable. can turned (can speed data processing time) deselecting date_time variable.","code":"finbif_occurrence(select = \"-date_time\") #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 11] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":[]},{"path":"/articles/v02_occurrence_data.html","id":"timezone-input","dir":"Articles","previous_headings":"Time & duration > Timezone","what":"Timezone input","title":"Occurrence records from FinBIF","text":"FinBIF database doesn’t currently store timezone information, finbif makes assumptions appropriate timezone based time location occurrence recording events calculate date_time duration. default, fast heuristic used determine timezones. require greater accuracy (e.g., using data Finnish/Swedish border daytime/nighttime hours important), can switch accurate, though slower, timezone calculation method.","code":"finbif_occurrence(date_time_method = \"accurate\") #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v02_occurrence_data.html","id":"timezone-output","dir":"Articles","previous_headings":"Time & duration > Timezone","what":"Timezone output","title":"Occurrence records from FinBIF","text":"timezone calculated date_time variable determined timezone operating system. can override setting tzone argument different value. set global timezone option set timezone current session. may advisable reproducibility working multiple systems.","code":"Sys.timezone() finbif_occurrence(tzone = \"Etc/UTC\") #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality options(finbif_tz = \"Etc/UTC\")"},{"path":[]},{"path":"/articles/v03_selecting_variables.html","id":"limiting-variables","dir":"Articles","previous_headings":"Selecting variables","what":"Limiting variables","title":"Selecting and ordering variables","text":"retrieve limited set variables FinBIF simply specify desired variables select argument.","code":"finbif_occurrence( genus = \"Falco\", select = c(\"scientific_name\", \"life_stage\", \"sex\") ) #> Records downloaded: 10 #> Records available: 342668 #> A data.frame [10 x 3] #> scientific_name life_stage sex #> 1 Falco columbarius L… NA NA #> 2 Falco tinnunculus L… NA NA #> 3 Falco tinnunculus L… NA NA #> 4 Falco subbuteo Linn… NA NA #> 5 Falco tinnunculus L… NA NA #> 6 Falco subbuteo Linn… NA NA #> 7 Falco tinnunculus L… NA NA #> 8 Falco tinnunculus L… NA NA #> 9 Falco tinnunculus L… NA NA #> 10 Falco subbuteo Linn… NA NA"},{"path":"/articles/v03_selecting_variables.html","id":"extra-variables","dir":"Articles","previous_headings":"Selecting variables","what":"Extra variables","title":"Selecting and ordering variables","text":"get extra variables well default set, specify extra variables addition keyword \"default_vars\".","code":"finbif_occurrence(select = c(\"default_vars\", \"life_stage\")) #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 13] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1594385#3 Sciurus vulgaris Li… 1 60.23584 25.05693 #> 2 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 3 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 4 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 5 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 6 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 7 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 8 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 9 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 10 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> ...with 0 more record and 8 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality, life_stage"},{"path":"/articles/v03_selecting_variables.html","id":"ordering","dir":"Articles","previous_headings":"","what":"Ordering","title":"Selecting and ordering variables","text":"can change order occurrence records fetched server using order_by argument. default ordering date_start descending, load_date descending, reported_name.","code":""},{"path":"/articles/v03_selecting_variables.html","id":"ascending-order","dir":"Articles","previous_headings":"Ordering","what":"Ascending order","title":"Selecting and ordering variables","text":"default occurrence records ordered variables ascending order.","code":"finbif_occurrence(\"Cygnus cygnus\", order_by = \"abundance\") #> Records downloaded: 10 #> Records available: 95730 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.67/9403350#Unit Cygnus cygnus (Linn… 1 60.41667 16 #> 2 …HR.3691/OBS810893905_Unit Cygnus cygnus (Linn… NA 61.56563 29.56771 #> 3 …JX.1026351#259 Cygnus cygnus (Linn… 1 65.89416 28.90961 #> 4 …JX.1025175#3 Cygnus cygnus (Linn… 1 61.83248 23.40816 #> 5 …KE.67/9069501#Unit Cygnus cygnus (Linn… 1 52.71667 1.55 #> 6 …JX.1252188#3 Cygnus cygnus (Linn… NA 60.17258 24.27095 #> 7 …KE.67/9465507#Unit Cygnus cygnus (Linn… 1 61.8 22.76667 #> 8 …KE.67/9607357#Unit Cygnus cygnus (Linn… 1 63.13333 22.43333 #> 9 …MHU.10961285 Cygnus cygnus (Linn… NA 64.97813 24.74932 #> 10 …HR.3691/OBS886590077_Unit Cygnus cygnus (Linn… NA 61.27566 22.557 #> date_time #> 1 1997-04-01 13:00:00 #> 2 2007-05-18 12:00:00 #> 3 2013-06-24 03:12:00 #> 4 2014-06-08 03:45:00 #> 5 1997-01-03 14:00:00 #> 6 2021-05-23 06:15:00 #> 7 2000-03-22 12:00:00 #> 8 2003-06-07 12:00:00 #> 9 2008-07-12 12:00:00 #> 10 2020-03-31 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v03_selecting_variables.html","id":"descending-order","dir":"Articles","previous_headings":"Ordering","what":"Descending order","title":"Selecting and ordering variables","text":"can switch descending order prefixing variable dash.","code":"finbif_occurrence(\"Cygnus cygnus\", order_by = \"-abundance\") #> Records downloaded: 10 #> Records available: 95730 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …MHU.2981587 Cygnus cygnus (Linn… 6000 64.4 -14.54 #> 2 …HR.3691/OBS1101526155_Unit Cygnus cygnus (Linn… 1760 62.16389 21.45786 #> 3 …HR.3691/OBS604642304_Unit Cygnus cygnus (Linn… 1753 64.50736 24.27894 #> 4 …HR.3691/OBS663568887_Unit Cygnus cygnus (Linn… 1600 65.98787 24.06341 #> 5 …MHU.28815250 Cygnus cygnus (Linn… 1500 NA NA #> 6 …HR.3691/OBS671353848_Unit Cygnus cygnus (Linn… 1361 64.71656 24.53188 #> 7 …JX.1357345#5 Cygnus cygnus (Linn… 1300 64.8465 25.2883 #> 8 …JX.1398409#3 Cygnus cygnus (Linn… 1280 64.8448 25.2816 #> 9 …MHU.28815110 Cygnus cygnus (Linn… 1200 NA NA #> 10 …HR.3691/OBS1119137190_Unit Cygnus cygnus (Linn… 1163 64.71656 24.53188 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v03_selecting_variables.html","id":"multiple-variables","dir":"Articles","previous_headings":"Ordering","what":"Multiple variables","title":"Selecting and ordering variables","text":"can specify multiple variables order . Sorting primacy left right.","code":"finbif_occurrence(\"Cygnus olor\", order_by = c(\"municipality_id\", \"-abundance\")) #> Records downloaded: 10 #> Records available: 42951 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …12015253 Cygnus olor (J.F. G… 2500 NA NA 2008-08-17 12:00:00 #> 2 …13633876 Cygnus olor (J.F. G… 1500 NA NA 2008-10-03 12:00:00 #> 3 …781416 Cygnus olor (J.F. G… 1300 NA NA 2006-02-14 12:00:00 #> 4 …780984 Cygnus olor (J.F. G… 1300 NA NA 2006-02-14 12:00:00 #> 5 …2062563 Cygnus olor (J.F. G… 1200 NA NA 2006-12-19 12:00:00 #> 6 …10352894 Cygnus olor (J.F. G… 1100 NA NA 2008-06-28 12:00:00 #> 7 …927797 Cygnus olor (J.F. G… 1050 NA NA 2006-04-05 12:00:00 #> 8 …3110953 Cygnus olor (J.F. G… 960 NA NA 2007-10-06 12:00:00 #> 9 …26309317 Cygnus olor (J.F. G… 900 NA NA 2009-07-08 12:00:00 #> 10 …1260385 Cygnus olor (J.F. G… 800 58.66 23.57 2006-04-26 18:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v03_selecting_variables.html","id":"random-sample","dir":"Articles","previous_headings":"Ordering","what":"Random sample","title":"Selecting and ordering variables","text":"can also request random sample (random order) occurrence records setting sample argument TRUE.","code":"finbif_occurrence(sample = TRUE) #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.67/5632630#Unit Ficedula hypoleuca … 1 61.74637 22.77479 #> 2 …MHU.40397 Prunus padus L. NA 60.28016 20.25637 #> 3 …JX.775148#3 Yezognophos vittari… 1 60.44245 27.006 #> 4 …KE.67/11580538#Unit Cyanistes caeruleus… 1 60.32754 24.64944 #> 5 …JX.328070#23 Pechipogo strigilat… NA 61.54883 21.64192 #> 6 …HR.3691/OBS889952298_Unit Parus major Linnaeu… 5 66.6165 24.68816 #> 7 …JX.1025818#50 Garrulus glandarius… 1 63.43302 27.74526 #> 8 …HR.3691/OBS1104249688_Unit Alauda arvensis Lin… NA 60.05577 24.06798 #> 9 …KE.67/8616657#Unit Cyanistes caeruleus… 1 61.5 24.83333 #> 10 …JX.101375#9 Poecile montanus (C… 7 63.09517 23.1341 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v04_metadata.html","id":"general-metadata","dir":"Articles","previous_headings":"","what":"General metadata","title":"Metadata","text":"can see metadata available finbif calling finbif_metadata function without arguments. Calling finbif_metadata() specifying one metadata categories display data.frame requested metadata.","code":"finbif_metadata() #> metadata_name #> 1 regulatory_status #> 2 red_list #> 3 country #> 4 region #> 5 bio_province #> 6 municipality #> 7 bird_assoc_area #> 8 finnish_occurrence_status #> 9 habitat_type #> 10 habitat_qualifier #> 11 life_stage #> 12 record_basis #> 13 restriction_level #> 14 restriction_reason #> 15 sex_category #> 16 source #> 17 taxon_rank finbif_metadata(\"red_list\") #> code name #> MX.iucnCR CR Critically Endangered #> MX.iucnDD DD Data Deficient #> MX.iucnEN EN Endangered #> MX.iucnEX EX Extinct #> MX.iucnEW EW Extinct in the Wild #> MX.iucnLC LC Least Concern #> MX.iucnNT NT Near Threatened #> MX.iucnNA NA Not Applicable #> MX.iucnNE NE Not Evaluated #> MX.iucnRE RE Regionally Extinct #> MX.iucnVU VU Vulnerable"},{"path":"/articles/v04_metadata.html","id":"special-cases","dir":"Articles","previous_headings":"","what":"Special cases","title":"Metadata","text":"complex metadata accessed finbif functions","code":""},{"path":"/articles/v04_metadata.html","id":"informal-groups","dir":"Articles","previous_headings":"Special cases","what":"Informal groups","title":"Metadata","text":"Informal taxonomic groups relationships can displayed finbif_informal_groups() can select subgroup specifying parent informal group function argument.","code":"finbif_informal_groups(limit = 2) #> Algae #> --Macro algae #> --Brown algae and yellow green algae #> --Green algae #> --Red algae #> --Stoneworts #> Birds #> --Birds of prey and owls #> --Birds of prey #> --Owls #> --Waterbirds #> ...137 more groups finbif_informal_groups(\"Crustaceans\") #> Crustaceans #> --Macrocrustaceans #> --Amphipods, isopods, opossum shrimps #> --Crabs, shrimps and crayfishes #> --Other macrocrustaceans #> --Woodlice #> --Microcrustaceans #> --Branchiopoda #> --Copepods #> --Seed shrimps"},{"path":"/articles/v04_metadata.html","id":"collections","dir":"Articles","previous_headings":"","what":"Collections","title":"Metadata","text":"Another special case metadata finbif_collections(). Collections highest level record aggregation FinBIF database. can subset collection metadata using filter select arguments. default, finbif_collections() displays lowest level collections. Higher level, “supercollections” can viewed setting supercollections = TRUE can limit output collections minimum number records nmin argument. finbif_collections() function returns data.frame row names ID number collection. can see child collections supercollection specifying ID filter. Note children supercollections may also supercollections.","code":"finbif_collections( filter = geographic_coverage == \"Finland\", select = c(\"collection_name\", \"taxonomic_coverage\", \"count\") ) #> collection_name taxonomic_coverage count #> HR.1227 Priv. coll. Mikko Heikkinen Biota 62 #> HR.1349 JYV - Fungal collections 13477 #> HR.1350 JYV - Lichen collections 608 #> HR.1351 JYV - Bryophyte collections 8367 #> HR.1467 Per-Eric Grankvist´s butterly co… Lepidoptera 5 #> HR.1487 JYV - Fish collections 1371 #> HR.1507 Lingonblad Birger och Hjördis bu… Lepidoptera 2796 #> HR.157 Point counts of breeding terrest… Birds, landbirds 393361 #> HR.1592 Herbarium of The Ark Nature Cent… 7871 #> HR.1687 Papilionoidea of Coll. Lauro Papilionoidea 550 #> HR.1688 Noctuidae I of Coll. Lauro Noctuidae 614 #> HR.1689 Noctuidae II of Coll. Lauro Noctuidae 839 #> HR.1690 Noctuidae III, Bombycoidea, Sphi… Noctuidae, Bombycoidea, Geometri… 521 #> HR.1691 Drepanidae & Geometridae of Coll… Drepanidae, Geometridae 1408 #> HR.175 National Finnish butterfly monit… Lepidoptera 450525 #> HR.1916 Wildlife triangle Siberian flying squirrel (Pterom… 18560 #> HR.200 Finnish Insect Database Insecta 3725381 #> HR.2009 Fish observation data from the n… invasive alien fish species - mu… 35582 #> HR.2049 Invasive alien species control Invasive species 1502 #> HR.206 The Finnish Nature League's Spri… biota 119323 #> HR.2089 Håkan Lindberg collection Hymenoptera 2435 #> HR.209 Atlas of Finnish Macrolepidoptera Macrolepidoptera 1218555 #> HR.2129 Fungal atlas fungi 116519 #> HR.2209 KUO Arachnida collection Arachnida 3 #> HR.2289 Specimens that lack collecting i… 109 #> HR.2691 Luomus line transect censuses of… Aves 628987 #> HR.2692 Censuses of breeding birds - Are… Aves 14963 #> HR.3051 VieKas LIFE project invasive spe… 1545 #> HR.3071 Observing species on milk farms 529 #> HR.3211 iNaturalist Suomi Finland biota 691050 #> HR.3491 LajiGIS: Aquatic species survey Biota 643837 #> HR.3553 LajiGIS: Species monitoring sites Biota 731965 #> HR.3671 Bird of prey nests for protection Aves 13323 #> HR.3691 eBird Aves 1100308 #> HR.3791 Invasive species observations Biota 3268 #> HR.39 Winter Bird Census Aves, Mammalia 1483842 #> HR.3911 Bumblebee census Bumblebees 29949 #> HR.3991 Waterbird counts, Luomus dataset Aves 39236 #> HR.3992 Waterbird counts, Luke dataset 2… Aves 30145 #> HR.4011 Salmonidae in streams Salmonidae 12630 #> HR.4051 LajiGIS: Species monitoring site… Aquila chrysaetos; Haliaeetus al… 8669 #> HR.4091 Retkikasvio 84 #> HR.4131 Butterflies in Finnish agricultu… Papilionoidea, Others 356987 #> HR.4191 Porvoo Museum / Butterfly Collec… Lepidoptera 10417 #> HR.4251 LajiGIS: Species mapping and sur… Biota 490816 #> HR.435 Löydös Open Invasive Species Obs… Biota 19232 #> HR.4352 NFI rare tree species 995 #> HR.4412 Tiira.fi: The Fourth Breeding Bi… Aves 329445 #> HR.4471 4th Finnish Bird Atlas 2022–2025… Aves 165551 #> HR.4511 Finnish National Moth Monitoring Bombycoidea, Noctuoidea, Sphingi… 1156373 #> HR.4611 Observations by FCG Finnish Cons… 462 #> HR.4612 Pollinator monitoring, line tran… Insecta 7885 #> HR.4672 Observations from publications Biota 127 #> HR.4711 Flying squirrel monitoring Pteromys volans 2509 #> HR.4991 Bird atlas observations manually… Aves 6620 #> HR.5095 Dragonfly complete lists Odonata 29 #> HR.5155 Observations from electronic sou… Biota 1372 #> HR.5196 Pollinator monitoring, pan traps Insecta 5688 #> HR.5235 Finnish butterflies - complete l… Lepidoptera, Papilinoidea 21 #> HR.5236 Charismatic flowering plants - c… Tracheophyta 277 #> HR.60 Monitoring scheme of birds and m… Aves, Mammalia 874130 #> HR.627 Alien mammal species observation… Invasive alien mammal species – … 3094 #> HR.808 E. Sjöholm´s butterfly collection Lepidoptera 4951 #> HR.847 Atlas of amphibians and reptiles… Amphibia, Reptilia 6690 collections <- finbif_collections(supercollections = TRUE, nmin = 10000) finbif_collections(supercollections = TRUE)[\"HR.128\", \"collection_name\"] #> Collections of the Finnish Museum of Natural History Luomus finbif_collections(is_part_of == \"HR.128\", supercollections = TRUE) #> collection_name abbreviation description online_url has_children is_part_of data_quality #> HR.129 Collections of… H Herbarium … TRUE HR.128 MY.dataQual… #> HR.160 Zoological col… MZH The collec… http://ww… TRUE HR.128 MY.dataQual… #> HR.173 Zoological mon… Monitoring… TRUE HR.128 MY.dataQual… #> HR.1849 Genomic resour… Genomic re… TRUE HR.128 MY.dataQual… #> HR.203 Löydös Open Fi… A service … https://l… FALSE HR.128 #> HR.435 Löydös Open In… A service … https://l… FALSE HR.128 MY.dataQual… #> HR.447 Hatikka.fi obs… Hatikka.fi… http://ha… FALSE HR.128 MY.dataQual… #> HR.48 Ringing and re… TIPU Dataset co… TRUE HR.128 MY.dataQual… #> methods collection_type taxonomic_coverage geographic_coverage temporal_coverage #> HR.129 MY.collectionT… #> HR.160 MY.collectionT… Animalia World 1700 to present #> HR.173 MY.collectionT… Finland 1950- #> HR.1849 Sampling… MY.collectionT… Biota World 2000- #> HR.203 MY.collectionT… biota world 2013- #> HR.435 MY.collectionT… Biota Finland 2015- #> HR.447 MY.collectionT… Biota World #> HR.48 MY.collectionT… Aves Ringing data: Finl… 1913- #> secure_level count #> HR.129 2 #> HR.160 MX.secureLe… 742 #> HR.173 5160221 #> HR.1849 1 #> HR.203 39375 #> HR.435 19232 #> HR.447 2010032 #> HR.48 12910437"},{"path":"/articles/v05_filtering.html","id":"location","dir":"Articles","previous_headings":"","what":"Location","title":"Filtering occurrence records","text":"Records can filtered name location. set coordinates. See ?filters section “Location” details","code":"finbif_occurrence(filter = c(country = \"Finland\")) #> Records downloaded: 10 #> Records available: 44691386 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1594385#3 Sciurus vulgaris Li… 1 60.23584 25.05693 #> 2 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 3 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 4 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 5 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 6 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 7 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 8 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 9 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 10 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( filter = list(coordinates = list(c(60, 68), c(20, 30), \"wgs84\")) ) #> Records downloaded: 10 #> Records available: 37318868 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1594385#3 Sciurus vulgaris Li… 1 60.23584 25.05693 #> 2 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 3 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 4 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 5 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 6 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 7 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 8 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 9 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 10 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"time","dir":"Articles","previous_headings":"","what":"Time","title":"Filtering occurrence records","text":"event import date records can used filter occurrence data FinBIF. date filters can single year, month date, , record events, range character vector. Records specific season time-span across years can also requested.","code":"finbif_occurrence(filter = list(date_range_ym = c(\"2020-12\"))) #> Records downloaded: 10 #> Records available: 23847 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …107 Pica pica (Linnaeus… 31 65.0027 25.49381 2020-12-31 10:20:00 #> 2 …45 Larus argentatus Po… 1 65.0027 25.49381 2020-12-31 10:20:00 #> 3 …153 Emberiza citrinella… 2 65.0027 25.49381 2020-12-31 10:20:00 #> 4 …49 Columba livia domes… 33 65.0027 25.49381 2020-12-31 10:20:00 #> 5 …117 Corvus corax Linnae… 1 65.0027 25.49381 2020-12-31 10:20:00 #> 6 …111 Corvus monedula Lin… 7 65.0027 25.49381 2020-12-31 10:20:00 #> 7 …161 Sciurus vulgaris Li… 1 65.0027 25.49381 2020-12-31 10:20:00 #> 8 …123 Passer montanus (Li… 28 65.0027 25.49381 2020-12-31 10:20:00 #> 9 …149 Pyrrhula pyrrhula (… 1 65.0027 25.49381 2020-12-31 10:20:00 #> 10 …77 Turdus pilaris Linn… 1 65.0027 25.49381 2020-12-31 10:20:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( filter = list(date_range_ymd = c(\"2019-06-01\", \"2019-12-31\")) ) #> Records downloaded: 10 #> Records available: 911735 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.921/LGE.627772/1470480 Pteromys volans (Li… NA 61.81362 25.75756 #> 2 …JX.1054648#107 Pica pica (Linnaeus… 3 65.30543 25.70355 #> 3 …JX.1054648#85 Poecile montanus (C… 1 65.30543 25.70355 #> 4 …JX.1054648#103 Garrulus glandarius… 3 65.30543 25.70355 #> 5 …JX.1054648#123 Passer montanus (Li… 3 65.30543 25.70355 #> 6 …JX.1054648#149 Pyrrhula pyrrhula (… 1 65.30543 25.70355 #> 7 …JX.1054648#93 Cyanistes caeruleus… 9 65.30543 25.70355 #> 8 …JX.1054648#95 Parus major Linnaeu… 35 65.30543 25.70355 #> 9 …JX.1054648#137 Carduelis flammea (… 2 65.30543 25.70355 #> 10 …JX.1056695#107 Pica pica (Linnaeus… 6 62.7154 23.0893 #> date_time #> 1 2019-12-31 12:00:00 #> 2 2019-12-31 10:20:00 #> 3 2019-12-31 10:20:00 #> 4 2019-12-31 10:20:00 #> 5 2019-12-31 10:20:00 #> 6 2019-12-31 10:20:00 #> 7 2019-12-31 10:20:00 #> 8 2019-12-31 10:20:00 #> 9 2019-12-31 10:20:00 #> 10 2019-12-31 10:15:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( filter = list( date_range_md = c(begin = \"12-21\", end = \"12-31\"), date_range_md = c(begin = \"01-01\", end = \"02-20\") ) ) #> Records downloaded: 10 #> Records available: 1486845 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …433443#318 Accipiter nisus (Li… 1 64.8162 25.32106 2023-02-20 15:00:00 #> 2 …531663#107 Pica pica (Linnaeus… 10 62.9199 27.71032 2023-02-20 07:40:00 #> 3 …530610#107 Pica pica (Linnaeus… 21 65.78623 24.49119 2023-02-20 09:15:00 #> 4 …530449#107 Pica pica (Linnaeus… 4 65.74652 24.62216 2023-02-20 08:20:00 #> 5 …531663#153 Emberiza citrinella… 12 62.9199 27.71032 2023-02-20 07:40:00 #> 6 …531663#49 Columba livia domes… 10 62.9199 27.71032 2023-02-20 07:40:00 #> 7 …530610#49 Columba livia domes… 2 65.78623 24.49119 2023-02-20 09:15:00 #> 8 …530610#117 Corvus corax Linnae… 1 65.78623 24.49119 2023-02-20 09:15:00 #> 9 …531663#61 Dendrocopos major (… 6 62.9199 27.71032 2023-02-20 07:40:00 #> 10 …531663#111 Corvus monedula Lin… 7 62.9199 27.71032 2023-02-20 07:40:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"data-quality","dir":"Articles","previous_headings":"","what":"Data Quality","title":"Filtering occurrence records","text":"can filter occurrence records indicators data quality. See ?filters section “Quality” details.","code":"strict <- c( collection_quality = \"professional\", coordinates_uncertainty_max = 1, record_quality = \"expert_verified\" ) permissive <- list( wild_status = c(\"wild\", \"non_wild\", \"wild_unknown\"), record_quality = c( \"expert_verified\", \"community_verified\", \"unassessed\", \"uncertain\", \"erroneous\" ), abundance_min = 0 ) c( strict = finbif_occurrence(filter = strict, count_only = TRUE), permissive = finbif_occurrence(filter = permissive, count_only = TRUE) ) #> strict permissive #> 52654 51733557"},{"path":"/articles/v05_filtering.html","id":"collection","dir":"Articles","previous_headings":"","what":"Collection","title":"Filtering occurrence records","text":"FinBIF database consists number constituent collections. can filter collection either collection not_collection filters. Use finbif_collections() see metadata FinBIF collections.","code":"finbif_occurrence( filter = c(collection = \"iNaturalist Suomi Finland\"), count_only = TRUE ) #> [1] 691076 finbif_occurrence( filter = c(collection = \"Notebook, general observations\"), count_only = TRUE ) #> [1] 2110409"},{"path":"/articles/v05_filtering.html","id":"informal-taxonomic-groups","dir":"Articles","previous_headings":"","what":"Informal taxonomic groups","title":"Filtering occurrence records","text":"can filter occurrence records based informal taxonomic groups Birds Mammals. See finbif_informal_groups() full list groups can filter . can use function see subgroups make higher level informal group:","code":"finbif_occurrence(filter = list(informal_groups = c(\"Birds\", \"Mammals\"))) #> Records downloaded: 10 #> Records available: 22116048 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …5#3 Sciurus vulgaris Li… 1 60.23584 25.05693 2023-06-14 08:56:00 #> 2 …2#9 Hirundo rustica Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 3 …2#37 Pica pica (Linnaeus… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 4 …2#49 Muscicapa striata (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 5 …2#39 Larus canus Linnaeu… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 6 …2#5 Emberiza citrinella… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 7 …2#31 Ficedula hypoleuca … NA 64.12716 23.99111 2023-06-14 08:48:00 #> 8 …2#41 Alauda arvensis Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 9 …2#21 Numenius arquata (L… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 10 …2#29 Dendrocopos major (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_informal_groups(\"macrofungi\") #> Error in finbif_informal_groups(\"macrofungi\"): Group not found"},{"path":"/articles/v05_filtering.html","id":"regulatory","dir":"Articles","previous_headings":"","what":"Regulatory","title":"Filtering occurrence records","text":"Many records FinBIF database include taxa one another regulatory statuses. See finbif_metadata(\"regulatory_status\") list regulatory statuses short-codes.","code":"# Search for birds on the EU invasive species list finbif_occurrence( filter = list(informal_groups = \"Birds\", regulatory_status = \"EU_INVSV\") ) #> Records downloaded: 10 #> Records available: 471 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1580858#3 Oxyura jamaicensis … 1 60.28687 25.0271 #> 2 …JX.1580860#3 Oxyura jamaicensis … 1 60.28671 25.02713 #> 3 …KE.176/62b1ad90d5deb0fafdc6212b#Unit1 Oxyura jamaicensis … 7 61.66207 23.57706 #> 4 …JX.1045316#34 Alopochen aegyptiac… 3 52.16081 4.485534 #> 5 …JX.138840#123 Alopochen aegyptiac… 4 53.36759 6.191796 #> 6 …JX.139978#214 Alopochen aegyptiac… 6 53.37574 6.207861 #> 7 …JX.139710#17 Alopochen aegyptiac… 30 52.3399 5.069133 #> 8 …JX.139645#57 Alopochen aegyptiac… 36 51.74641 4.535283 #> 9 …JX.139645#10 Alopochen aegyptiac… 3 51.74641 4.535283 #> 10 …JX.139442#16 Alopochen aegyptiac… 2 51.90871 4.53258 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"iucn-red-list","dir":"Articles","previous_headings":"","what":"IUCN red list","title":"Filtering occurrence records","text":"Filtering can done IUCN red list category. See finbif_metadata(\"red_list\") IUCN red list categories short-codes.","code":"# Search for near threatened mammals finbif_occurrence( filter = list(informal_groups = \"Mammals\", red_list_status = \"NT\") ) #> Records downloaded: 10 #> Records available: 42510 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …JX.1594024#23 Rangifer tarandus f… 15 63.31266 24.43298 #> 2 …JX.1588853#1075 Rangifer tarandus f… 1 63.84551 29.8366 #> 3 …JX.1593780#3 Pusa hispida botnic… 1 65.02313 25.40505 #> 4 …HR.3211/166639315-U Rangifer tarandus f… NA 63.7 24.7 #> 5 …HR.3211/166049302-U Rangifer tarandus f… NA 64.1 26.5 #> 6 …HR.3211/165761924-U Rangifer tarandus f… NA 63.9 24.9 #> 7 …JX.1589779#105 Rangifer tarandus f… 3 63.7261 23.40827 #> 8 …KE.176/647ad84dd5de884fa20e25e6#Unit1 Rangifer tarandus f… 1 64.12869 24.73877 #> 9 …HR.3211/165005253-U Pusa hispida botnic… NA 64.2865 23.87402 #> 10 …JX.1588052#18 Rangifer tarandus f… 2 64.13286 26.26767 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"habitat-type","dir":"Articles","previous_headings":"","what":"Habitat type","title":"Filtering occurrence records","text":"Many taxa associated one primary secondary habitat types (e.g., forest) subtypes (e.g., herb-rich alpine birch forests). Use finbif_metadata(\"habitat_type\") see habitat types FinBIF. can filter occurrence records based primary (primary/secondary) habitat type subtype codes. Note filtering based habitat taxa location (.e., filtering records primary_habitat = \"M\" return records taxa considered primarily inhabit forests, yet locations records may encompass habitats forests). may refine habitat based searching using specific habitat type qualifier “sun-exposed” “shady”. Use finbif_metadata(\"habitat_qualifier\") see qualifiers available. specify qualifiers use named list character vectors names habitat types subtypes elements character vectors qualifier codes.","code":"head(finbif_metadata(\"habitat_type\")) #> code name #> MKV.habitatMt Mt alpine birch forests (excluding herb-rich alpine … #> MKV.habitatTlk Tlk alpine calcareous rock outcrops and boulder fields #> MKV.habitatTlr Tlr alpine gorges and canyons #> MKV.habitatT T Alpine habitats #> MKV.habitatTp Tp alpine heath scrubs #> MKV.habitatTk Tk alpine heaths # Search records of taxa for which forests are their primary or secondary # habitat type finbif_occurrence(filter = c(primary_secondary_habitat = \"M\")) #> Records downloaded: 10 #> Records available: 26362337 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …5#3 Sciurus vulgaris Li… 1 60.23584 25.05693 2023-06-14 08:56:00 #> 2 …2#37 Pica pica (Linnaeus… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 3 …2#49 Muscicapa striata (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 4 …2#5 Emberiza citrinella… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 5 …2#31 Ficedula hypoleuca … NA 64.12716 23.99111 2023-06-14 08:48:00 #> 6 …2#29 Dendrocopos major (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 7 …2#15 Sylvia borin (Bodda… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 8 …2#11 Anthus trivialis (L… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 9 …2#45 Corvus monedula Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 10 …2#3 Phylloscopus trochi… NA 64.12716 23.99111 2023-06-14 08:48:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_metadata(\"habitat_qualifier\")[4:6, ] #> code name #> MKV.habitatSpecificTypeCA CA calcareous effect #> MKV.habitatSpecificTypeH H esker forests, also semi-open forests #> MKV.habitatSpecificTypeKE KE intermediate-basic rock outcrops and boulder fiel… # Search records of taxa for which forests with sun-exposure and broadleaved # deciduous trees are their primary habitat type finbif_occurrence(filter = list(primary_habitat = list(M = c(\"PAK\", \"J\")))) #> Records downloaded: 10 #> Records available: 178 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …502812#393 Pammene fasciana (L… NA 60.45845 22.17811 2022-08-14 12:00:00 #> 2 …435062#6 Pammene fasciana (L… 1 60.20642 24.66127 2022-08-04 #> 3 …435050#9 Pammene fasciana (L… 1 60.20642 24.66127 2022-07-25 #> 4 …501598#39 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-21 12:00:00 #> 5 …501387#162 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-20 12:00:00 #> 6 …448030#159 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-18 12:00:00 #> 7 …447556#78 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-14 12:00:00 #> 8 …446841#408 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-12 12:00:00 #> 9 …443339#36 Pammene fasciana (L… 1 60.08841 22.48629 2022-07-10 12:00:00 #> 10 …440849#159 Pammene fasciana (L… 2 60.08841 22.48629 2022-07-08 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/articles/v05_filtering.html","id":"status-of-taxa-in-finland","dir":"Articles","previous_headings":"","what":"Status of taxa in Finland","title":"Filtering occurrence records","text":"can restrict occurrence records status taxa Finland. example can request records rare species. , using negation occurrence status, can request records birds excluding considered vagrants. See finbif_metadata(\"finnish_occurrence_status\") full list statuses descriptions.","code":"finbif_occurrence(filter = c(finnish_occurrence_status = \"rare\")) #> Records downloaded: 10 #> Records available: 406005 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3211/167313706-U Pygaera timon (Hübn… NA 62.1281 27.45272 #> 2 …JX.1594282#21 Carterocephalus pal… 1 64.65322 24.58941 #> 3 …HR.3211/167197097-U Carterocephalus pal… NA 65.07819 25.55236 #> 4 …HR.3211/167183358-U Glaucopsyche alexis… NA 60.46226 22.76647 #> 5 …JX.1594291#3 Glaucopsyche alexis… 1 60.42692 22.20411 #> 6 …KE.176/6488c111d5de884fa20e295f#Unit1 Panemeria tenebrata… 1 61.16924 25.56036 #> 7 …JX.1593930#3 Hemaris tityus (Lin… 1 60.63969 27.29052 #> 8 …KE.176/64889455d5de884fa20e294f#Unit1 Pseudopanthera macu… 2 62.054 30.352 #> 9 …JX.1594170#199 Glaucopsyche alexis… 1 61.10098 28.68453 #> 10 …JX.1594112#3 Hemaris tityus (Lin… 1 61.25511 28.89127 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality finbif_occurrence( filter = list( informal_groups = \"birds\", finnish_occurrence_status_neg = sprintf(\"vagrant_%sregular\", c(\"\", \"ir\")) ) ) #> Records downloaded: 10 #> Records available: 21725426 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …9 Hirundo rustica Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 2 …37 Pica pica (Linnaeus… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 3 …49 Muscicapa striata (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 4 …39 Larus canus Linnaeu… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 5 …5 Emberiza citrinella… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 6 …31 Ficedula hypoleuca … NA 64.12716 23.99111 2023-06-14 08:48:00 #> 7 …41 Alauda arvensis Lin… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 8 …21 Numenius arquata (L… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 9 …29 Dendrocopos major (… NA 64.12716 23.99111 2023-06-14 08:48:00 #> 10 …15 Sylvia borin (Bodda… NA 64.12716 23.99111 2023-06-14 08:48:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Finnish Museum Natural History - Luomus. Copyright holder. William K. Morris. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Morris, William K. (2024). Introduction finbif package. R package version 0.9.4.9000, https://doi.org/10.5281/zenodo.3612814","code":"@Manual{, title = {Introduction to the finbif package}, author = {William K. Morris}, year = {2024}, note = {R package version 0.9.4.9000}, url = {https://luomus.github.io/finbif/articles/finbif.html}, doi = {10.5281/zenodo.3612814}, }"},{"path":"/index.html","id":"finbif-r-package-","dir":"","previous_headings":"","what":"FinBIF R package","title":"FinBIF R package","text":"finbif R package programmatic interface Finnish Biodiversity Information Facility (FinBIF) API. FinBIF aggregates Finnish biodiversity data multiple sources single open access portal researchers, citizen scientists, industry government. FinBIF allows users biodiversity information find, access, combine visualise data Finnish plants, animals microorganisms. finbif R package makes publicly available data FinBIF easily accessible programmers. Biodiversity information available taxonomy taxon occurrence. Occurrence data can filtered taxon, time, location variables. data accessed conveniently preformatted subsequent analyses.","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"FinBIF R package","text":"can install current stable version finbif CRAN, can also install latest development version finbif GitHub,","code":"install.packages(\"finbif\") remotes::install_github(\"luomus/finbif@dev\")"},{"path":"/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"FinBIF R package","text":"Read online documentation current stable version finbif , latest development version finbif .","code":""},{"path":"/index.html","id":"getting-a-finbif-access-token","dir":"","previous_headings":"","what":"Getting a FinBIF access token","title":"FinBIF R package","text":"First load finbif R package. use FinBIF API must first request set personal access token. can request API token sent email address function finbif_get_token. Copy access token sent email set environment variable FINBIF_ACCESS_TOKEN either current session, , adding Renviron startup file (see details).","code":"library(finbif) finbif_request_token(\"your@email.com\") Sys.setenv( FINBIF_ACCESS_TOKEN = \"xtmSOIxjPwq0pOMB1WvcZgFLU9QBklauOlonWl8K5oaLIx8RniJLrvcJU4v9H7Et\" ) # Note: the above is not a real access token. Do not try using it."},{"path":"/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"FinBIF R package","text":"Download occurrence data FinBIF.","code":"finbif_occurrence(\"Cygnus cygnus\", n = 100)"},{"path":"/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"FinBIF R package","text":"Data FinBIF comes many sources. information citing FinBIF contributed datasets please visit link: https://laji.fi/en//2986 cite finbif R package publications please use: Morris, William K. (2024). Introduction finbif package. R package version 0.9.4.9000, https://doi.org/10.5281/zenodo.3612814","code":""},{"path":"/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"FinBIF R package","text":"Development community effort, encourage participation. Please read contribution guide details. Please note ‘finbif’ project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"/reference/caching.html","id":null,"dir":"Reference","previous_headings":"","what":"Caching FinBIF downloads — caching","title":"Caching FinBIF downloads — caching","text":"Working cached data FinBIF.","code":""},{"path":"/reference/caching.html","id":"turning-caching-off","dir":"Reference","previous_headings":"","what":"Turning caching off","title":"Caching FinBIF downloads — caching","text":"default, local caching FinBIF API requests turned . request made using arguments request data FinBIF first instance subsequent requests use local cache exists. increase speed repeated requests save bandwidth computation FinBIF server. Caching can turned temporarily setting cache = FALSE requesting function. Setting options(finbif_use_cache = FALSE) turn caching current session.","code":""},{"path":"/reference/caching.html","id":"using-filesystem-caching","dir":"Reference","previous_headings":"","what":"Using filesystem caching","title":"Caching FinBIF downloads — caching","text":"default cached requests stored memory. can changed setting file path current session options(finbif_cache_path = \"path//cache\").","code":""},{"path":"/reference/caching.html","id":"using-database-caching","dir":"Reference","previous_headings":"","what":"Using database caching","title":"Caching FinBIF downloads — caching","text":"Caching can also done using database. Using database caching requires packages DBI, blob database backend package RSQLite installed. use database caching simply pass connection objected created DBI::dbConnect finbif_cache_path option (e.g., db <- DBI::dbConnect(RSQLite::SQLite(), \"-db.sqlite\"); options(finbif_cache_path = db) ).","code":""},{"path":"/reference/caching.html","id":"clearing-the-cache","dir":"Reference","previous_headings":"","what":"Clearing the cache","title":"Caching FinBIF downloads — caching","text":"cache files can deleted finbif_clear_cache().","code":""},{"path":"/reference/filters.html","id":null,"dir":"Reference","previous_headings":"","what":"Filtering FinBIF records — filters","title":"Filtering FinBIF records — filters","text":"Filters available FinBIF records occurrence data.","code":""},{"path":"/reference/filters.html","id":"taxa","dir":"Reference","previous_headings":"","what":"Taxa","title":"Filtering FinBIF records — filters","text":"Filters related taxa include: taxon_id Character vector. FinBIF taxon IDs. functions finbif_check_taxa() finbif_taxa() can used search taxon IDs. taxon_name Character vector. Filter based taxon names (scientific common) rather IDs. specified taxa found FinBIF taxonomy matches attempted occurrence record names originally supplied verbatim. quality_controlled_det Logical. TRUE (default) use quality controlled taxonomic determinations. , FALSE use originally recorded taxonomic determinations. subtaxa Logical. TRUE (default) return records taxa belonging specified taxa. , FALSE return records exact matches specified taxa (e.g., genus specified, return records species belonging genus, return records individuals identified genus identified lower taxonomic level). invalid_taxa Logical. TRUE (default) return records taxa found FinBIF taxonomic database well taxa FinBIF database. , FALSE limit records taxa found FinBIF database. informal_groups Character vector. Filter informal taxonomic groups. including informal groups linked recorded taxa FinBIF database. Use function finbif_informal_groups() see informal taxonomic groups available FinBIF. informal_groups_reported Character vector. Filter informal taxonomic groups including groups reported directly record linked recorded taxa FinBIF database. Use function finbif_informal_groups() see informal taxonomic groups available FinBIF. regulatory_status Character vector. Filter regulatory status code. Use function finbif_metadata() see regulatory statuses codes. red_list_status Character vector. Filter IUCN red list status code. Use function finbif_metadata() see red list statuses codes. primary_habitat Character vector named list character vectors. Filter primary habitat code. Use function finbif_metadata() see habitat (sub)types codes taxa FinBIF database. Habitat type/subtypes can refined indicating habitat qualifiers named list character vectors names habitat (sub)type codes elements character vector habitat qualifier codes. Use function finbif_metadata() see habitat qualifiers codes. records returned taxa whose primary habitat considered (sub)habitat/habitat qualifier combination supplied. primary_secondary_habitat Character named list character vectors. , except records returned taxa whose primary secondary habitat considered combination supplied. finnish_occurrence_status Character vector. Filter Finnish occurrence status taxa. Use finbif_metadata() see possible occurrence statuses taxa. finnish_occurrence_status_neg Character vector. Negation . Selecting status filter rather include records selected status. finnish Logical. TRUE, limit records taxa thought occur Finland. FALSE limit taxa thought occur Finland. unspecified (default) return records taxa. invasive Logical. TRUE, limit records invasive taxa. FALSE limit non-invasive taxa. unspecified (default) return records invasive non-invasive taxa. taxon_rank Character vector. Filter taxonomic rank. Use finbif_metadata() see taxonomic ranks available. Records returned limited specified ranks include records lower taxonomic levels.","code":""},{"path":"/reference/filters.html","id":"location","dir":"Reference","previous_headings":"","what":"Location","title":"Filtering FinBIF records — filters","text":"Filters related location record include: locality Character vector. Filter name locality. first try match strings countries, bio-provinces, municipalities (see ) FinBIF, none locality types match exactly return records verbatim locality matches original records. country Character vector. Filter country. Use finbif_metadata() see country names ISO codes (2 3 character) used FinBIF. region Character vector. Filter region. Use finbif_metadata() see region names codes. bio_province Character vector. Filter bio-province. Use finbif_metadata() see bio-province names codes. municipality Character vector. Filter municipality. Use finbif_metadata() see municipality names. location_tag Character vector Filter tags associated location (e.g., \"farmland\"). bird_assoc_area Character vector. Filter BirdLife Finland association area. Use finbif_metadata() see association names codes. coordinates Coordinates. character vector list coordinate data. Must length 3 4 (e.g., list(lat = c(60.4, 61), lon = c(22, 22.5), system = \"wgs84\", ratio = 1). first element minimum maximum latitude second minimum maximum longitude (can minimums ). third element coordinate system; either one \"wgs84\", \"euref\" \"ykj\". optional fourth element positive value less 1. 1, coverage area returned records completely within box bound coordinates values. Values less 1 requires returned record's coverage overlap bounding box proportion. using system \"ykj\" coordinates coerced integers units inferred number integer digits (7 digits equals km's, 6 equals 10km's, etc.,). coordinate maximums specified assumed one unit minimums (e.g., c(666, 333, \"ykj\") equivalent list(c(6660000, 6670000), c(3330000, 3340000), \"ykj\")). coordinates_center Coordinates. character vector list coordinate data. Must length 3. first two elements latitude longitude third coordinate system (currently \"wgs84\" implemented). Records returned center point exactly matches specified. coordinates_cell_{1k|10k|50k|100k} Coordinates. vector coordinate data (lat, lon). Filter grid cell scale *. * 1, 10, 50 100. coordinates specify southeast corner cell. Coordinates system \"ykj\". coordinates_cell_{1k|10k|50k|100k}_center Coordinates. , except coordinates indicate center grid cell. coordinates_source Character. Filter source coordinates. Currently accepted values \"reported_value\" (coordinates recorded time observation) \"finnish_municipality\" (coordinates derived observer recorded municipality). coordinates_uncertainty_max Integer. Filter maximum uncertainty coordinates (.e., coordinates_uncertainty_max = 100 return records accurate 100m).","code":""},{"path":"/reference/filters.html","id":"time","dir":"Reference","previous_headings":"","what":"Time","title":"Filtering FinBIF records — filters","text":"Filters related time record include: date_range_ymd Dates. vector one two Date objects (begin end dates) objects coercible Date. supplying dates strings, day month--day can omitted (e.g., \"2001-04\" \"2001\"). Note however, omitting day, \"-\" allowed separate year month, months must two-digit/leading zero form. begin end dates partial date strings interpreted first last day month year (e.g., c(2001, 2003) equivalent c(\"2001-01-01\", \"2003-12-12\")). single date supplied partial date string records fall within month year returned (e.g., c(\"2001-01\") equivalent c(\"2001-01-01\", \"2001-01-31\")). Use empty strings begin end date specify open-ended date ranges (e.g., c(\"2000-01-01\", \"\") dates turn century). date_range_ym Dates. , days (supplied) ignored. date_range_d Integer vector. Filter day year (e.g., 1 366). begin end date omitted interpreted first last day year. date_range_md Character vector. Filter month day year (e.g., \"01-01\" \"12-31\"). begin end date omitted interpreted first last day year. {first|last}_import_date_{min|max} Date. Filter date record imported/modified. Either Date object object coercible Date class, number seconds since 1970-01-01 00:00.00 UTC (-called UNIX epoch). Note means specifying year, 2019, without month day interpreted 2019 seconds midnight Jan 1, 1970 year 2019.","code":""},{"path":"/reference/filters.html","id":"quality","dir":"Reference","previous_headings":"","what":"Quality","title":"Filtering FinBIF records — filters","text":"Filters related quality record: quality_issues. Character. Filter presence record quality issues. One \"without_issues\", \"with_issues\" \"\". Issues include quality issues record, event, document. default \"without_issues\" unless filtering record, event document ID record annotation status. requires_verification Logical. Show records requiring verification (TRUE) requiring verification (FALSE). collection_quality Character vector. Filter one collection quality types. Must one \"professional\", \"hobbyist\" \"amateur\". record_reliability Character vector. Filter reliability record. Must one \"reliable\", \"unassessed \"unreliable\". Default c(\"reliable\", \"unassessed\"). record_quality Character vector. Filter quality record. Must one \"expert_verified\", \"community_verified\", \"unassessed\", \"uncertain\", \"erroneous\".","code":""},{"path":"/reference/filters.html","id":"misc","dir":"Reference","previous_headings":"","what":"Misc","title":"Filtering FinBIF records — filters","text":"filters: keywords Character vector. Filter keywords. collection Character vector finbif_collections() data.frame. Filter collection. character vector can refer collection ID, collection name (English) abbreviated name. Use finbif_collections() see list collections metadata. Can also use results call finbif_collections() directly filter records. subcollections Logical. TRUE (default) include subcollections collections specified. FALSE include subcollections. not_collection Character vector finbif_collections() data.frame. collection, result negation specified collections. source Character vector. Filter information system data source. Use finbif_metadata() see data source IDs names descriptions. record_basis Character vector. Filter basis record. Use finbif_metadata() see list record bases. superrecord_basis Character vector. Filter superset record basis. One \"human_observation\", \"machine_observation\", \"specimen\". life_stage Character vector. Filter organism life stage. Use finbif_metadata() see list organism life stages. sex Character vector. Filter organism sex sex-related category name code. Use finbif_metadata() see list organism sexes sex-related categories codes. \"male\" \"female\" specified records returned sex specified male female respectively records corresponding {male|female}_abundance > 1. event_id Character. Filter event (list records, etc.) ID. document_id Character. Filter document (collection events) ID occurrences. record_id Character. individual_id Character. Filter individual (individual organism) ID. abundance_min Integer. Filter minimum number individual organisms record. abundance_max Integer. Filter maximum number individual organisms record. type_specimen Logical. Filter whether record type specimen. wild_status Character. Filter \"wildness\" status records. One \"wild\", \"non_wild\" \"unknown\". Default c(\"wild\", \"unknown\"). is_breeding_location Logical. Filter whether occurrence recorded known breeding location. has_document_media Logical. Filter whether media (images, video, audio, etc.) associated records' document. has_event_media Logical. Filter whether media (images, video, audio, etc.) associated records' event. has_record_media Logical. Filter whether media (images, video, audio, etc.) associated record. has_media Logical. Filter whether media (images, video, audio, etc.) associated record, document event. event_observer_name Character. Filter observer name. event_observer_id Integer. Filter observer ID. restriction_reason Character vector. Filter reason data security restrictions. See finbif_metadata() list reasons data may security restrictions. restriction_level Character vector. Filter data restriction level. See finbif_metadata() list levels data restrictions. restricted Logical. Filter records whether data restrictions place (TRUE) (FALSE). annotated Logical. Filter records (TRUE) (FALSE) annotations. unidentified Logical. Filter whether record identified species level linked FinBIF taxon database (FALSE) identified species level reliably linked taxon database (TRUE). taxon_census Character vector. Return records belonging surveys censuses given taxon taxonomic group. Specify taxonomic group FinBIF taxon ID. Use finbif_check_taxa() find taxon IDs. {record|event|document}_fact Character vector. Filter record, event document facts. Facts key-value pairs form \"=\". Value can omitted case records value recorded specified fact returned. has_sample Logical. Record includes sample samples (e.g., DNA sample preparation). complete_list_type Filter complete list type. Records made monitoring produces taxon lists given group taxa (e.g., birds) can include species observed breeding status recorded observed species (all_species_and_breeding), species observed without breeding status recorded species observed, species observed without breeding status recorded observed species (all_species), species observed (incomplete). complete_list_taxon_id Filter taxon ID target group (e.g., birds) complete list.","code":""},{"path":"/reference/finbif-package.html","id":null,"dir":"Reference","previous_headings":"","what":"finbif: Interface for the 'Finnish Biodiversity Information Facility' API — finbif-package","title":"finbif: Interface for the 'Finnish Biodiversity Information Facility' API — finbif-package","text":"programmatic interface 'Finnish Biodiversity Information Facility' ('FinBIF') API (https://api.laji.fi). 'FinBIF' aggregates Finnish biodiversity data multiple sources single open access portal researchers, citizen scientists, industry government. 'FinBIF' allows users biodiversity information find, access, combine visualise data Finnish plants, animals microorganisms. 'finbif' package makes publicly available data 'FinBIF' easily accessible programmers. Biodiversity information available taxonomy taxon occurrence. Occurrence data can filtered taxon, time, location variables. data accessed conveniently preformatted subsequent analyses.","code":""},{"path":"/reference/finbif-package.html","id":"package-options","dir":"Reference","previous_headings":"","what":"Package options","title":"finbif: Interface for the 'Finnish Biodiversity Information Facility' API — finbif-package","text":"finbif_api_url Character. base url API query. Default: \"https://api.laji.fi\" finbif_api_version Character. API version use. Default: \"v0\" finbif_allow_query Logical. remote API queries allowed. Default: TRUE finbif_use_cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated value. Default: TRUE finbif_cache_path Character. path directory store cached API queries. unset (default) memory caching used. finbif_tz Character. timezone used finbif functions compute dates times. Default: Sys.timezone() finbif_locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. default, system settings used set option set one supported languages, otherwise English used. finbif_hide_progress Logical. Global option suppress progress indicators downloading, importing processing FinBIF records. Default: FALSE","code":""},{"path":[]},{"path":"/reference/finbif-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"finbif: Interface for the 'Finnish Biodiversity Information Facility' API — finbif-package","text":"Maintainer: William K. Morris willi@mmorris.email (ORCID) contributors: Finnish Museum Natural History - Luomus [copyright holder]","code":""},{"path":"/reference/finbif_check_taxa.html","id":null,"dir":"Reference","previous_headings":"","what":"Check FinBIF taxa — finbif_check_taxa","title":"Check FinBIF taxa — finbif_check_taxa","text":"Check taxa FinBIF database.","code":""},{"path":"/reference/finbif_check_taxa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check FinBIF taxa — finbif_check_taxa","text":"","code":"finbif_check_taxa(taxa, cache = getOption(\"finbif_use_cache\"))"},{"path":"/reference/finbif_check_taxa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check FinBIF taxa — finbif_check_taxa","text":"taxa Character (list named character) vector(s). list vector can name taxonomic rank (genus, species, etc.,). elements vectors taxa check. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument.","code":""},{"path":"/reference/finbif_check_taxa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check FinBIF taxa — finbif_check_taxa","text":"object class finbif_taxa. list form taxa.","code":""},{"path":"/reference/finbif_check_taxa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check FinBIF taxa — finbif_check_taxa","text":"","code":"if (FALSE) { # Check a scientific name finbif_check_taxa(\"Cygnus cygnus\") # Check a common name finbif_check_taxa(\"Whooper swan\") # Check a genus finbif_check_taxa(\"Cygnus\") # Check a list of taxa finbif_check_taxa( list( species = c(\"Cygnus cygnus\", \"Ursus arctos\"), genus = \"Betula\" ) ) }"},{"path":"/reference/finbif_clear_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Clear cache — finbif_clear_cache","title":"Clear cache — finbif_clear_cache","text":"Remove cached API requests FinBIF.","code":""},{"path":"/reference/finbif_clear_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clear cache — finbif_clear_cache","text":"","code":"finbif_clear_cache()"},{"path":"/reference/finbif_clear_cache.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clear cache — finbif_clear_cache","text":"","code":"if (FALSE) { finbif_clear_cache() }"},{"path":"/reference/finbif_collections.html","id":null,"dir":"Reference","previous_headings":"","what":"FinBIF collections — finbif_collections","title":"FinBIF collections — finbif_collections","text":"Get information collections FinBIF database.","code":""},{"path":"/reference/finbif_collections.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FinBIF collections — finbif_collections","text":"","code":"finbif_collections( filter, select, subcollections = TRUE, supercollections = FALSE, locale = getOption(\"finbif_locale\"), nmin = 0, cache = getOption(\"finbif_use_cache\") )"},{"path":"/reference/finbif_collections.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FinBIF collections — finbif_collections","text":"filter Logical. Expression indicating elements rows keep: missing values taken false. select Expression. Indicates columns select data frame. subcollections Logical. Return subcollection metadata higher level collections. supercollections Logical. Return lowest level collection metadata. locale Character. Language data returned. One \"en\", \"fi\", \"sv\". nmin Integer. Filter collections number records. return information collections greater value specified. NA return information collections. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument.","code":""},{"path":"/reference/finbif_collections.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"FinBIF collections — finbif_collections","text":"data.frame.","code":""},{"path":"/reference/finbif_collections.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FinBIF collections — finbif_collections","text":"","code":"if (FALSE) { # Get collection metadata collections <- finbif_collections() }"},{"path":"/reference/finbif_informal_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"FinBIF informal groups — finbif_informal_groups","title":"FinBIF informal groups — finbif_informal_groups","text":"Display informal taxonomic groups used FinBIF database.","code":""},{"path":"/reference/finbif_informal_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FinBIF informal groups — finbif_informal_groups","text":"","code":"finbif_informal_groups( group, limit = 5, quiet = FALSE, locale = getOption(\"finbif_locale\") )"},{"path":"/reference/finbif_informal_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FinBIF informal groups — finbif_informal_groups","text":"group Character. Optional, supplied display top-level group subgroups. limit Integer. maximum number top-level informal groups (sub-groups) display. quiet Logical. Return informal group names without displaying . locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated .","code":""},{"path":"/reference/finbif_informal_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"FinBIF informal groups — finbif_informal_groups","text":"character vector (invisibly).","code":""},{"path":"/reference/finbif_informal_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FinBIF informal groups — finbif_informal_groups","text":"","code":"if (FALSE) { # Display the informal taxonomic groups used by FinBIF finbif_informal_groups() }"},{"path":"/reference/finbif_last_mod.html","id":null,"dir":"Reference","previous_headings":"","what":"Get last modified date for FinBIF occurrence records — finbif_last_mod","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"Get last modified date filtered occurrence data FinBIF.","code":""},{"path":"/reference/finbif_last_mod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"","code":"finbif_last_mod(..., filter)"},{"path":"/reference/finbif_last_mod.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"... Character vectors list character vectors. Taxa records download. filter List named character vectors. Filters apply records.","code":""},{"path":"/reference/finbif_last_mod.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"Date object","code":""},{"path":"/reference/finbif_last_mod.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get last modified date for FinBIF occurrence records — finbif_last_mod","text":"","code":"if (FALSE) { # Get last modified date for Whooper Swan occurrence records from Finland finbif_last_mod(\"Cygnus cygnus\", filter = c(country = \"Finland\")) }"},{"path":"/reference/finbif_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"FinBIF metadata — finbif_metadata","title":"FinBIF metadata — finbif_metadata","text":"Display metadata FinBIF database.","code":""},{"path":"/reference/finbif_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FinBIF metadata — finbif_metadata","text":"","code":"finbif_metadata(which, locale = getOption(\"finbif_locale\"))"},{"path":"/reference/finbif_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FinBIF metadata — finbif_metadata","text":"Character. category metadata display. unspecified, function returns categories metadata available. locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated .","code":""},{"path":"/reference/finbif_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"FinBIF metadata — finbif_metadata","text":"data.frame.","code":""},{"path":"/reference/finbif_metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FinBIF metadata — finbif_metadata","text":"","code":"if (FALSE) { finbif_metadata(\"red_list\") }"},{"path":"/reference/finbif_occurrence.html","id":null,"dir":"Reference","previous_headings":"","what":"Download FinBIF occurrence records — finbif_occurrence","title":"Download FinBIF occurrence records — finbif_occurrence","text":"Download filtered occurrence data FinBIF data.frame.","code":""},{"path":"/reference/finbif_occurrence.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download FinBIF occurrence records — finbif_occurrence","text":"","code":"finbif_occurrence( ..., filter = NULL, select = NULL, order_by = NULL, aggregate = \"none\", sample = FALSE, n = 10, page = 1, count_only = FALSE, quiet = getOption(\"finbif_hide_progress\"), cache = getOption(\"finbif_use_cache\"), dwc = FALSE, date_time_method = NULL, check_taxa = TRUE, on_check_fail = c(\"warn\", \"error\"), tzone = getOption(\"finbif_tz\"), locale = getOption(\"finbif_locale\"), seed = NULL, drop_na = FALSE, aggregate_counts = TRUE, exclude_na = FALSE, unlist = FALSE, facts = NULL, duplicates = FALSE, filter_col = NULL, restricted_api = NULL )"},{"path":"/reference/finbif_occurrence.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download FinBIF occurrence records — finbif_occurrence","text":"... Character vectors list character vectors. Taxa records download. filter List named character vectors. Filters apply records. select Character vector. Variables return. specified, default set commonly used variables used. Use \"default_vars\" shortcut set. Variables can deselected prepending - variable name. deselects specified default set variables without deselection returned. order_by Character vector. Variables order records returned. , though , variables can used order records returned. Ordering ascending default. return descending order append - front variable (e.g., \"-date_start\"). Default order \"-date_start\" > \"-load_data\" > \"reported_name\". aggregate Character. \"none\" (default), returns full records. one \"records\", \"species\", \"taxa\", \"individuals\", \"pairs\", \"events\" \"documents\"; aggregates combinations selected variables counting records, species, taxa, individuals events documents. Aggregation events documents done combination aggregation types. sample Logical. TRUE randomly sample records FinBIF database. n Integer. many records download/import. page Integer. page records start downloading . count_only Logical. return number records available. quiet Logical. Suppress progress indicator multipage downloads. Defaults value option finbif_hide_progress. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument. dwc Logical. Use Darwin Core (Darwin Core style) variable names. date_time_method Character. Passed lutz::tz_lookup_coords() date_time /duration variables selected. Default \"fast\" less 100,000 records requested \"none\" . Using method \"none\" assumes records timezone \"Europe/Helsinki\", Use date_time_method = \"accurate\" (requires package sf) greater accuracy cost slower computation. check_taxa Logical. Check first taxa FinBIF database. true records match known taxa (valid taxon ID) returned. on_check_fail Character. taxon found valid. One \"warn\" (default) \"error\". tzone Character. date_time selected timezone outputted date-time. Defaults system timezone. locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated . seed Integer. Set seed randomly sampling records. drop_na Logical. vector indicating columns check missing data. Values recycled number columns. Defaults columns. aggregate_counts Logical. count variables returned using aggregation. exclude_na Logical. records selected variables non-NA values returned. unlist Logical. variables contain non atomic data concatenated string separated \";\"? facts Character vector. Extra variables extracted record, event document \"facts\". duplicates Logical. TRUE, allow duplicate records/aggregated records making multi-filter set requests. FALSE (default) duplicate records removed. filter_col Character. name column, values derived names filter sets used using multiple filters, include using multiple filter sets. NULL (default), column included. restricted_api Character. using restricted data API token addition personal access token, string indicating name environment variable storing restricted data API token.","code":""},{"path":"/reference/finbif_occurrence.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download FinBIF occurrence records — finbif_occurrence","text":"data.frame. count_only = TRUE integer.","code":""},{"path":"/reference/finbif_occurrence.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download FinBIF occurrence records — finbif_occurrence","text":"","code":"if (FALSE) { # Get recent occurrence data for taxon finbif_occurrence(\"Cygnus cygnus\") # Specify the number of records finbif_occurrence(\"Cygnus cygnus\", n = 100) # Get multiple taxa finbif_occurrence(\"Cygnus cygnus\", \"Ursus arctos\") # Filter the records finbif_occurrence( species = \"Cygnus cygnus\", filter = list(coordinate_accuracy_max = 100) ) }"},{"path":"/reference/finbif_occurrence_load.html","id":null,"dir":"Reference","previous_headings":"","what":"Load FinBIF occurrence records from a file — finbif_occurrence_load","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"Load occurrence data file data.frame.","code":""},{"path":"/reference/finbif_occurrence_load.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"","code":"finbif_occurrence_load( file, select = NULL, n = -1, count_only = FALSE, quiet = getOption(\"finbif_hide_progress\"), cache = getOption(\"finbif_use_cache\"), dwc = FALSE, date_time_method = NULL, tzone = getOption(\"finbif_tz\"), write_file = tempfile(), dt = NA, keep_tsv = FALSE, facts = list(), type_convert_facts = TRUE, drop_na = FALSE, drop_facts_na = drop_na, locale = getOption(\"finbif_locale\"), skip = 0 )"},{"path":"/reference/finbif_occurrence_load.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"file Character Integer. Either path Zip archive tabular data file downloaded \"laji.fi\", URI linking data file (e.g., https://tun.fi/HBF.49381) integer representing URI (.e., 49381). select Character vector. Variables return. specified, default set commonly used variables used. Use \"default_vars\" shortcut set. Variables can deselected prepending - variable name. deselects specified default set variables without deselection returned. Use \"\" select available variables file. n Integer. many records import. Negative invalid values ignored causing records imported. count_only Logical. return number records available. quiet Logical. Suppress progress indicator multipage downloads. Defaults value option finbif_hide_progress. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument. dwc Logical. Use Darwin Core (Darwin Core style) variable names. date_time_method Character. Passed lutz::tz_lookup_coords() date_time /duration variables selected. Default \"fast\" less 100,000 records requested \"none\" . Using method \"none\" assumes records timezone \"Europe/Helsinki\", Use date_time_method = \"accurate\" (requires package sf) greater accuracy cost slower computation. tzone Character. date_time selected timezone outputted date-time. Defaults system timezone. write_file Character. Path write downloaded zip file file refers URI. ignored getOption(\"finbif_cache_path\") NULL use cache path instead. dt Logical. package, data.table, available return data.table object rather data.frame. keep_tsv Logical. Whether keep TSV file file ZIP archive represents URI. ignored file already TSV. TRUE tsv file kept directory ZIP archive. facts List. named list \"facts\" extract supplementary \"fact\" files local online FinBIF data archive. Names can include one \"record\", \"event\" \"document\". Elements list character vectors \"facts\" extracted joined return value. type_convert_facts Logical. facts converted character numeric integer data applicable? drop_na Logical. vector indicating columns check missing data. Values recycled number columns. Defaults columns. drop_facts_na Logical. missing \"NA\" facts dropped? value length one logical vector value TRUE interpreted FALSE. Argument ignored drop_na TRUE variables explicitly via recycling. drop missing/NA-data facts use drop_na argument. locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated . skip Integer. number lines data file skip beginning read data (including header).","code":""},{"path":"/reference/finbif_occurrence_load.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"data.frame, count_only = TRUE integer.","code":""},{"path":"/reference/finbif_occurrence_load.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load FinBIF occurrence records from a file — finbif_occurrence_load","text":"","code":"if (FALSE) { # Get occurrence data finbif_occurrence_load(49381) }"},{"path":"/reference/finbif_request_token.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a FinBIF personal access token — finbif_request_token","title":"Get a FinBIF personal access token — finbif_request_token","text":"personal access token use FinBIF API sent specified email address.","code":""},{"path":"/reference/finbif_request_token.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a FinBIF personal access token — finbif_request_token","text":"","code":"finbif_request_token(email, quiet = FALSE)"},{"path":"/reference/finbif_request_token.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a FinBIF personal access token — finbif_request_token","text":"email Character. email address send API access token. quiet Logical. Suppress messages.","code":""},{"path":"/reference/finbif_request_token.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a FinBIF personal access token — finbif_request_token","text":"access token already set NULL (invisibly) , invisibly, finbif_api object containing response FinBIF server.","code":""},{"path":"/reference/finbif_request_token.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a FinBIF personal access token — finbif_request_token","text":"","code":"if (FALSE) { # Request a token for example@email.com finbif_request_token(\"example@email.com\") }"},{"path":"/reference/finbif_taxa.html","id":null,"dir":"Reference","previous_headings":"","what":"Search the FinBIF taxa — finbif_taxa","title":"Search the FinBIF taxa — finbif_taxa","text":"Search FinBIF database taxon.","code":""},{"path":"/reference/finbif_taxa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search the FinBIF taxa — finbif_taxa","text":"","code":"finbif_taxa( name, n = 1, type = c(\"exact\", \"partial\", \"likely\"), cache = getOption(\"finbif_use_cache\") ) common_name(name, locale = getOption(\"finbif_locale\")) scientific_name(name) taxon_id(name)"},{"path":"/reference/finbif_taxa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search the FinBIF taxa — finbif_taxa","text":"name Character. name ID taxon. , functions finbif_taxa finbif_taxa object. n Integer. Maximum number matches return. types \"exact\" \"likely\" one taxon returned. type Character. Type match make. Must one exact, partial likely. cache Logical Integer. TRUE number greater zero, data-caching used. logical cache invalidated number hours indicated argument. locale Character. One supported two-letter ISO 639-1 language codes. Current supported languages English, Finnish Swedish. data one language available language denoted locale preferred falling back languages order indicated .","code":""},{"path":"/reference/finbif_taxa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search the FinBIF taxa — finbif_taxa","text":"finbif_taxa finbif_taxa object. Otherwise, character vector.","code":""},{"path":"/reference/finbif_taxa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search the FinBIF taxa — finbif_taxa","text":"","code":"if (FALSE) { # Search for a taxon finbif_taxa(\"Ursus arctos\") # Use partial matching finbif_taxa(\"Ursus\", n = 10, \"partial\") # Get Sámi (Northern) name of Eurasian Eagle-owl common_name(\"Bubo bubo\", \"se\") # Get scientific name of \"Otter\" scientific_name(\"Otter\") # Get taxon identifier of \"Otter\" taxon_id(\"Otter\") }"},{"path":"/reference/finbif_update_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Update cache — finbif_update_cache","title":"Update cache — finbif_update_cache","text":"Update cached API requests FinBIF.","code":""},{"path":"/reference/finbif_update_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update cache — finbif_update_cache","text":"","code":"finbif_update_cache()"},{"path":"/reference/finbif_update_cache.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update cache — finbif_update_cache","text":"","code":"if (FALSE) { finbif_update_cache() }"},{"path":"/reference/to_dwc.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert variable names — to_dwc","title":"Convert variable names — to_dwc","text":"Convert variable names Darwin Core FinBIF R package native style.","code":""},{"path":"/reference/to_dwc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert variable names — to_dwc","text":"","code":"to_dwc(...) to_native(...) from_schema( ..., to = c(\"native\", \"dwc\", \"short\"), file = c(\"none\", \"citable\", \"lite\") )"},{"path":"/reference/to_dwc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert variable names — to_dwc","text":"... Character. Variable names convert. to_dwc to_native names must opposite format. from_schema names must FinBIF schema (e.g., names returned https://api.laji.fi) FinBIF download file (citable lite). Character. Type variable names convert . file Character. variable names derived FinBIF download file type file.","code":""},{"path":"/reference/to_dwc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert variable names — to_dwc","text":"Character vector.","code":""},{"path":"/reference/to_dwc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert variable names — to_dwc","text":"","code":"to_dwc(\"record_id\", \"date_time\", \"scientific_name\") #> [1] \"occurrenceID\" \"eventDateTime\" \"scientificName\""},{"path":"/reference/variables.html","id":null,"dir":"Reference","previous_headings":"","what":"FinBIF record variables — variables","title":"FinBIF record variables — variables","text":"FinBIF record variables can selected finbif occurrence search.","code":""},{"path":"/reference/variables.html","id":"identifiers","dir":"Reference","previous_headings":"","what":"Identifiers","title":"FinBIF record variables — variables","text":"identifiers returned form URI. Identifiers include: record_id Character. ID record organism's occurrence time place. individual_id Character. ID individual organism (e.g., ringed bird captured multiple times single individual_id multiple record_ids corresponding capture). event_id Character. Event ID. event can contain one records (e.g., survey plants particular location time.) document_id Character. Document ID. set events share common metadata. form_id Character. Form ID. form used create document, event, record data. collection_id Character. Collection ID. documents, events, records belong collection (e.g., museum collection, datasets collected specific institution). Collections can part larger (super)collection (e.g., collections specific museum). lowest level collection ID record returned. Use finbif_collections() explore hierarchy collections. source_id Character. Source ID. source collection's data.","code":""},{"path":"/reference/variables.html","id":"taxa","dir":"Reference","previous_headings":"","what":"Taxa","title":"FinBIF record variables — variables","text":"Variables related taxonomy records include: taxon_id Character. taxon ID form URI. orig_taxon_id Character. taxon ID () annotation. annotated_taxon_id Character. new taxon ID record taxonomy annotated. reported_taxon_id Character. taxon ID originally reported record creator. scientific_name Character. Scientific name taxon. orig_scientific_name Character. scientific name () annotation. scientific_display_name Character. Scientific name taxon formatted display (e.g., taxa genus formatted Genus sp.). orig_scientific_display_name Character. Scientific display name () annotation. common_name Character. Common (vernacular) name taxon. orig_common_name Character. Common name () annotation. reported_name Character. name taxon originally reported record creator. scientific_name_italicised Logical. scientific name normally italicised (.e., taxonomic rank genus .) orig_scientific_name_italicised Logical. original scientific name normally italicised. scientific_name_author Character. authority taxon scientific name. orig_scientific_name_author Character. authority taxon scientific name () annotation. reported_author Character. authority taxon originally reported record creator. taxon_rank Character. taxonomic rank taxon. orig_taxon_rank Character. taxonomic rank taxon () annotation. informal_groups List. informal taxonomic groups taxon belongs (e.g., birds) form URIs. orig_informal_groups List. informal taxonomic groups taxon belonged () annotation. reported_informal_groups List. informal taxonomic groups taxon belongs reported record creator. taxon_checklist Character. checklist (URI) taxon found . orig_taxon_checklist Character. checklist (URI) taxon found () annotation. taxon_finnish Logical. taxon considered Finnish. definition Finnish taxon differs taxonomic group? orig_taxon_finnish Logical. taxon considered Finnish () annotation?","code":""},{"path":"/reference/variables.html","id":"abundance-sex-amp-life-history","dir":"Reference","previous_headings":"","what":"Abundance, sex & life history","title":"FinBIF record variables — variables","text":"Variables related abundance, sex life history include: abundance Integer. Number individuals recorded. abundance_interpreted Integer. Number individuals recorded inferred record. Note many records abundance_interpreted == 1L indicate record one individual may necessarily imply abundance specified place time (e.g., preserved museum specimen consisting single individual). {female|male}_abundance Integer. Number female male individuals recorded. pair_abundance Integer. Number mating pairs recorded. abundance_verbatim Character. abundance reported record creator. life_stage Character. Life stage individual(s) recorded. sex Character. Sex individual(s) recorded.","code":""},{"path":"/reference/variables.html","id":"location","dir":"Reference","previous_headings":"","what":"Location","title":"FinBIF record variables — variables","text":"Variables related location records include: {lat|lon}_{euref|wgs84} Numeric. Coordinates (EUREF WGS84 coordinate system) central point bounding box encompassing record's geographic coverage. {lat|lon}_{min|max}_{euref|ykj|wgs84}. Numeric. Vertices bounding box encompassing record's geographic coverage. Coordinates available EUREF, YKJ, WGS84. coordinates_uncertainty Integer. horizontal distance (meters) record's given coordinates describing smallest circle containing whole record's location. coordinates_source Character. Source coordinates. footprint_{euref|ykj|wgs84} Character. Well-Known Text (WKT) representation geographic shape defining location record either EUREF, YKJ WGS84 coordinate systems. country Character. country record's location. region Character. administrative area directly level country. bio_province Character. data Finland FinBIF uses concept Biogeographical Province. See link details. municipality. Character. Administrative level region higher_geography Character. Geographic place name higher level country. line_length_m Integer. length linear locations (e.g., line transect surveys). area_m2 Integer. size record's location meters squared. is_breeding_location Logical. Whether occurrence recorded known breeding location. location_id Character. location ID form URI. section Integer. numeric identifier sub-location location (e.g., specific part transect undergoes repeated surveys.)","code":""},{"path":"/reference/variables.html","id":"time","dir":"Reference","previous_headings":"","what":"Time","title":"FinBIF record variables — variables","text":"Variables related time record include: date_time POSIXct. date time recording event. variable computed records downloaded FinBIF. timezone accuracy can controlled see finbif_occurrence() details. duration Duration. duration recording event. variable computed records downloaded FinBIF. date_start Character. date recording event began. date_end Character. date recording event ended. hour_start Integer. hour (24 hour time) day recording event began. hour_end Integer. hour (24 hour time) day recording event ended. minute_start Integer. minute hour recording event began. minute_end Integer. minute hour recording event started. ordinal_day_start Integer. ordinal day year recording event began. ordinal_day_end Integer. ordinal day year recording event ended season_start Integer. day year recording event began. four digit number indicating day year MMDD (%m%d) format. season_end Integer. day year recording event ended. four digit number indicating day year MMDD (%m%d) format. century Integer. century recording event occurred (NA event spans multiple centuries). decade Integer. decade recording event occurred (NA event spans multiple decades). year Integer. year recording event occurred (NA event spans multiple years). month Integer. month year recording event occurred (NA event spans multiple months). day Integer. day month recording event occurred (NA event spans multiple days). formatted_date_time Character. Date time recording event formatted display. date_created Character. date original data created. first_load_date Character. date record first loaded FinBIF database. modified_date Character. recent date original data modified. load_date Character. recent date record loaded FinBIF database.","code":""},{"path":"/reference/variables.html","id":"data-restrictions","dir":"Reference","previous_headings":"","what":"Data restrictions","title":"FinBIF record variables — variables","text":"Variables related restricted records include: restriction Logical. record restricted way (e.g., geospatially aggregated). restriction_level Character. level restriction applied record. restriction_reason List. List reasons restriction applied.","code":""},{"path":"/reference/variables.html","id":"data-quality","dir":"Reference","previous_headings":"","what":"Data quality","title":"FinBIF record variables — variables","text":"Variables related quality records include: any_issues Logical. data quality issues associated record, event document. reported_taxon_confidence Reliability record's taxonomic identification reported original data author. {document|time|location|event|record}_issue Character. Issues record associated document, time, location, event, record . {document|time|location|event|record}_issue_message Character. Details issue. {document|time|location|event|record}_issue_source Character. Source determining issue. requires_verification Logical. record flagged expert verification? requires_identification Logical. record flagged expert identification? record_reliability Character. Indication record's reliability. record_quality Character. Indication record's quality.","code":""},{"path":"/reference/variables.html","id":"misc","dir":"Reference","previous_headings":"","what":"Misc","title":"FinBIF record variables — variables","text":"variables: collection Character. Collection name. documents, events, records belong collection (e.g., museum collection, datasets collected specific institution). Collections can part larger (super)collection (e.g., collections specific museum). lowest level collection name record returned. Use finbif_collections() explore hierarchy collections. observers_ids List. List observer identifiers record. determiner Character. Person determined taxonomic identification record. record_basis Character. type method used obtain record. superrecord_basis Character. Higher level type method used obtain record. type_specimen Logical. Whether record type specimen. is_wild Logical. Whether record \"wild\" organism. license Character. license data associated record. {document|event|record}_notes Character. Notes associated document, event record . {document|record}_keywords List. List keywords associated document record. record_annotation_count Integer. many annotations associated record. sample_count Integer. many material samples (DNA extractions, etc., ...) associated record. {document|event|record}_media_count Integer. many media items (images, audio, video, etc., ...) associated record's document, event record .","code":""},{"path":"/news/index.html","id":"finbif-094","dir":"Changelog","previous_headings":"","what":"finbif 0.9.4","title":"finbif 0.9.4","text":"CRAN release: 2024-01-12","code":""},{"path":"/news/index.html","id":"new-features-0-9-4","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.9.4","text":"New undocumented variable “source” can selected finbif_occurrence.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-9-4","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.9.4","text":"Record pagination now often require less queries FinBIF server faster. FinBIF collections field names sanitised. filtering records “collection_id” full URL ID can used QName.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-4","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.9.4","text":"Reading zero observation data downloads now produce zero row data.frame instead triggering error.","code":""},{"path":"/news/index.html","id":"finbif-093","dir":"Changelog","previous_headings":"","what":"finbif 0.9.3","title":"finbif 0.9.3","text":"CRAN release: 2023-09-28","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-3","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.9.3","text":"Fix bug resulting incorrect region assigned occurrences records.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-9-3","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.9.3","text":"New undocumented variables institution_code collection_code can selected using functions finbif_collections finbif_occurrence.","code":""},{"path":"/news/index.html","id":"finbif-092","dir":"Changelog","previous_headings":"","what":"finbif 0.9.2","title":"finbif 0.9.2","text":"CRAN release: 2023-08-28","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-2","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.9.2","text":"Fixed bug triggered localising variables multiple pages data requested.","code":""},{"path":"/news/index.html","id":"finbif-091","dir":"Changelog","previous_headings":"","what":"finbif 0.9.1","title":"finbif 0.9.1","text":"CRAN release: 2023-06-29","code":""},{"path":"/news/index.html","id":"new-features-0-9-1","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.9.1","text":"New option finbif_use_cache_metadata set caching metadata . ignored finbif_use_cache TRUE.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-1","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.9.1","text":"Fixed bug triggered trying compute variable identifier data returned contained zero records.","code":""},{"path":"/news/index.html","id":"finbif-090","dir":"Changelog","previous_headings":"","what":"finbif 0.9.0","title":"finbif 0.9.0","text":"CRAN release: 2023-05-23","code":""},{"path":"/news/index.html","id":"new-features-0-9-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.9.0","text":"New function finbif_update_cache can used update cached objects reached expiration longer valid. restricted data API token can explicitly declared via restricted_api argument finbif_occurrence. Cached data can use database backend passing DBI database connection object package option finbif_cache_path. Cached data can assigned timeout using number (hours) instead logical value cache argument finbif_ functions package option finbif_use_cache. Record aggregations finbif_occurrence can now combined multi-filter requests. Removing duplicate records aggregate record combinations can controlled duplicates argument adding column indicating filter sets can added filter_col argument.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-9-0","dir":"Changelog","previous_headings":"","what":"finbif 0.9.0","title":"finbif 0.9.0","text":"Fixed bug causing infinite recursion determining page size record download pagination. Fix bug triggered using aggregation selected variables.","code":""},{"path":"/news/index.html","id":"defunct-0-9-0","dir":"Changelog","previous_headings":"","what":"DEFUNCT","title":"finbif 0.9.0","text":"Mapping utilities finland_map, breaks_xy, hist_xy plot method finbif_occ objects now defunct. User access finbif_records classes methods now defunct.","code":""},{"path":"/news/index.html","id":"finbif-080","dir":"Changelog","previous_headings":"","what":"finbif 0.8.0","title":"finbif 0.8.0","text":"CRAN release: 2023-03-29","code":""},{"path":"/news/index.html","id":"deprecation-0-8-0","dir":"Changelog","previous_headings":"","what":"DEPRECATION","title":"finbif 0.8.0","text":"Mapping utilities finland_map, breaks_xy, hist_xy plot method finbif_occ objects deprecated --scope. User access finbif_records classes methods deprecated favour finbif_occurrence.","code":""},{"path":"/news/index.html","id":"new-features-0-8-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.8.0","text":"Record aggregations finbif_occurrence can now include “individual” “pair” sums.","code":""},{"path":"/news/index.html","id":"finbif-072","dir":"Changelog","previous_headings":"","what":"finbif 0.7.2","title":"finbif 0.7.2","text":"CRAN release: 2023-02-06","code":""},{"path":"/news/index.html","id":"minor-improvements-0-7-2","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.7.2","text":"Updated deprecated use tidy::pivot_wider. Added new filters variables upstream API.","code":""},{"path":"/news/index.html","id":"finbif-071","dir":"Changelog","previous_headings":"","what":"finbif 0.7.1","title":"finbif 0.7.1","text":"CRAN release: 2022-11-24","code":""},{"path":"/news/index.html","id":"new-features-0-7-1","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.7.1","text":"New function finbif_mod_date get last modified date FinBIF occurrence data. Region now selectable variable finbif_occurrence can also used filter records.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-7-1","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.7.1","text":"sake clarity “province” now referred “bio-province”. Many variables, including sex, life_stage record_quality now localised. variable restriction_reasons now referred singular restriction_reason. consistency, lang argument finbif_collections changed locale.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-7-1","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.7.1","text":"Fixed bug caused locale set incorrectly multipage requests.","code":""},{"path":"/news/index.html","id":"finbif-070","dir":"Changelog","previous_headings":"","what":"finbif 0.7.0","title":"finbif 0.7.0","text":"CRAN release: 2022-09-13","code":""},{"path":"/news/index.html","id":"new-features-0-7-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.7.0","text":"New function taxon_id returns FinBIF taxon identifiers given scientific name, vernacular name taxon identifier. New filters complete_list_taxon_id complete_list_type now available. New global option finbif_hide_progress suppress progress bars downloading, importing processing FinBIF records. sake clarity consistency term “administrative status” now referred “regulatory status” throughout. Regulatory status, informal taxonomic group habitat data now localised. Option unlist added finbif_occurrence casts list columns strings. cell multiple values values cast string separated semi-colons. New argument facts added finbif_occurrence can used automatically extract facts downloading occurrence records.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-7-0","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.7.0","text":"Fixed bug triggered incorrect data type applied taxonomic_order. Fixed bug preventing locale switching vernacular name data.","code":""},{"path":"/news/index.html","id":"finbif-066","dir":"Changelog","previous_headings":"","what":"finbif 0.6.6","title":"finbif 0.6.6","text":"CRAN release: 2022-08-08","code":""},{"path":"/news/index.html","id":"new-features-0-6-6","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.6.6","text":"New option exclude records NA values selected variables added finbif_occurrence.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-6","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.6","text":"warning/error message returned invalid taxon requested finbif_occurrence made detailed, warning user may using synonyms invalid taxon names.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-6","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.6","text":"Fix applied print method error triggered clashing class names. Fixed issue ordering variables.","code":""},{"path":"/news/index.html","id":"finbif-065","dir":"Changelog","previous_headings":"","what":"finbif 0.6.5","title":"finbif 0.6.5","text":"CRAN release: 2022-05-20","code":""},{"path":"/news/index.html","id":"new-features-0-6-5","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.6.5","text":"New variables filters (currently undocumented) added forthcoming Finnish atlas breeding birds. Skip rows argument added finbif_occurrence_load files can read chunks.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-5","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.5","text":"clarity, KKJ coordinate reference system now referred YKJ. selecting available variables download file imports using finbif_occurrence_load “extra” variables longer automatically added.","code":""},{"path":"/news/index.html","id":"finbif-064","dir":"Changelog","previous_headings":"","what":"finbif 0.6.4","title":"finbif 0.6.4","text":"CRAN release: 2022-03-10","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-4","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.4","text":"New administrative statuses added. number (interval ) api request retries can configured (currently undocumented). museum collections scientific names added non-Finnish species. New fields added citable download imports. New argument aggregate_counts (defaulting TRUE) added finbif_occurrence toggle inclusion aggregation count fields . New bird association area, occurrence types location tag metadata added. New filters variables (currently undocumented) added upstream API.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-4","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.4","text":"Fix bug triggered printing occurrence records records coordinate uncertainty.","code":""},{"path":"/news/index.html","id":"finbif-063","dir":"Changelog","previous_headings":"","what":"finbif 0.6.3","title":"finbif 0.6.3","text":"CRAN release: 2022-01-03","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-3","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.3","text":"Argument drop_na_facts changed drop_facts_na function finbif_occurrence_load avoid problems due partial matching argument drop_na. Data quality description appended description field data.frame returned finbif_collections(). Occurrence record filtering can now done using open-ended date ranges. New administrative statuses added.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-3","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.3","text":"Fix bug importing file downloads triggered string quotation errors.","code":""},{"path":"/news/index.html","id":"finbif-062","dir":"Changelog","previous_headings":"","what":"finbif 0.6.2","title":"finbif 0.6.2","text":"CRAN release: 2021-09-03","code":""},{"path":"/news/index.html","id":"new-features-0-6-2","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.6.2","text":"New package option, finbif_allow_query, default value, TRUE. set FALSE remote API queries trigger error meaning cached requests run cache found. Records can now aggregated document.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-2","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.2","text":"client-side error triggered attempt made filter taxon aggregate data event finbif_occurrence.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-2","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.2","text":"Fix bug preventing loading FinBIF archives triggered variables selected select = \"\". Fix bug preventing finbif_occ objects printing one columns contain missing data .","code":""},{"path":"/news/index.html","id":"finbif-061","dir":"Changelog","previous_headings":"","what":"finbif 0.6.1","title":"finbif 0.6.1","text":"CRAN release: 2021-07-26","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-1","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.1","text":"Fixed regression last release prevented collection names converted URIs.","code":""},{"path":"/news/index.html","id":"finbif-060","dir":"Changelog","previous_headings":"","what":"finbif 0.6.0","title":"finbif 0.6.0","text":"CRAN release: 2021-07-22","code":""},{"path":"/news/index.html","id":"new-features-0-6-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.6.0","text":"New variables lat_euref lon_euref available occurrence record downloads. new variables represent central point bounding box encompassing record’s geographic coverage EUREF (ETRS89/ETRS-TM35FIN) coordinate system. Option now available retain TSV data file loading FinBIF occurrence data finbif_occurrence_load ZIP archive online reference. Option now available extract “facts” using finbif_occurrence_load import records ZIP archive. user must supply named list, names refer one fact types: “record”, “event” /“document”, list elements character vectors indicating “facts” extract. “Lite” download files (occurrence record datasets less 10,000 records downloaded directly laji.fi) can now imported using finbif_occurrence_load. New filters (currently undocumented) ely_center_id region_id available finbif_occurrence. New function, from_schema, convert variable names FinBIF schema styles. New computed variable date_time_ISO8601 (currently undocumented) can selected creating finbif_occ objects. New computed variable epsg (currently undocumented). selected, column EPSG code first column contains geographic data.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-6-0","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.6.0","text":"Can now select available variables importing FinBIF download request file using finbif_occurrence_load select = \"\". New option, drop_na, drop columns contain missing data added finbif_occurrence finbif_occurrence_load. User can now select columns multiple times rename fly using named character vector value ‘select’ argument. variable taxon_rank now converted string fly via taxon_rank_id. Variables computed identifiers now localised multiple languages available.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-6-0","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.6.0","text":"Fixed bug prevented occurrence record counting caching use. Fixed bug triggered error selected variable computed ID using DWC style variable names.","code":""},{"path":"/news/index.html","id":"finbif-050","dir":"Changelog","previous_headings":"","what":"finbif 0.5.0","title":"finbif 0.5.0","text":"CRAN release: 2021-03-27","code":""},{"path":"/news/index.html","id":"new-features-0-5-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.5.0","text":"Getting records FinBIF can now speed (~1.5x) asynchronous processing. future package available asynchronous strategy (e.g., plan(multisession, workers = 2)) selected downloading records processing occur simultaneously separate threads, often leading significant speed sequential processing. Occurrence records can now requested using multiple sets filters time. list filters (unnamed elements) supplied record request made set filters results requests combined duplicate records removed. Occurrence records can now read directly FinBIF download request files. function finbif_occurrence_load can load data local file remotely using persistent identifier URI (e.g., http://tun.fi/HBF.49381). Aggregation records can now performed recording “event” level well “record” level.","code":""},{"path":"/news/index.html","id":"finbif-041","dir":"Changelog","previous_headings":"","what":"finbif 0.4.1","title":"finbif 0.4.1","text":"CRAN release: 2021-01-27","code":""},{"path":"/news/index.html","id":"new-features-0-4-1","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.4.1","text":"New functions scientific_name common_name now available get scientific common names taxa (given taxon name FinBIF ID code) extract names finbif_taxa- class object. Add ability extract complex record variables associated record media (currently undocumented).","code":""},{"path":"/news/index.html","id":"minor-improvements-0-4-1","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.4.1","text":"Collection name can selected variable occurrence records. Previously manually translated collection ID. Variables restriction_reasons_conservation, restriction_reason_embargo restriction_reason_custom longer use upstream can longer selected.","code":""},{"path":"/news/index.html","id":"finbif-040","dir":"Changelog","previous_headings":"","what":"finbif 0.4.0","title":"finbif 0.4.0","text":"CRAN release: 2020-12-17","code":""},{"path":"/news/index.html","id":"new-features-0-4-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.4.0","text":"Occurrence record requests can now made aggregation, aggregate = c(\"records\", \"species\", \"taxa\"). returns number records, /species taxa combination selected variables instead occurrence records .","code":""},{"path":"/news/index.html","id":"minor-improvements-0-4-0","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.4.0","text":"Error triggered attempting request less one record. New content requesting aggregated occurrence records added vignette: 2. Occurrence records FinBIF.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-4-0","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.4.0","text":"Fixed two bugs print method FinBIF occurrence records triggered attempting print one row data. Fixed bug triggering error attempting print occurrence record objects zero rows. Fixed bug triggered trying print occurrence record data NA values. Fixed bug causing incorrect subsetting occurrence records using logical vectors subset rows. Fixed bug printed occurrence records multi-element data incorrectly single element. Fixed bug triggered system locales (#1).","code":""},{"path":"/news/index.html","id":"finbif-031","dir":"Changelog","previous_headings":"","what":"finbif 0.3.1","title":"finbif 0.3.1","text":"CRAN release: 2020-11-24","code":""},{"path":"/news/index.html","id":"new-features-0-3-1","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.3.1","text":"Occurrence records can ordered total number records total number Finnish records taxon (variables: n_total_records & n_total_finnish_records, currently undocumented). New Finnish occurrence status, records_only, added. New administrative statuses added filters.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-3-1","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.3.1","text":"Filtering vignette updated reflect changes data quality filters.","code":""},{"path":"/news/index.html","id":"finbif-030","dir":"Changelog","previous_headings":"","what":"finbif 0.3.0","title":"finbif 0.3.0","text":"CRAN release: 2020-04-23","code":""},{"path":"/news/index.html","id":"new-features-0-3-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.3.0","text":"user facing functions finbif_ prefix can now also used alternative shorter prefix fb_. Crop Wild Relative, CWR, added admin statuses. two new utility functions, to_dwc to_native converting variable names Darwin Core style. Users can select order variables Darwin Core style using finbif_occurrence. changes variables filters flowed upstream changes “api.laji.fi”. variables is_unidentifiable, record_reliable, collection_reliability, taxon_reliability, taxon_reliability_message taxon_reliability_source deprecated replaced requires_verification, requires_identification, record_reliability record_quality. filters collection_reliability taxon_reliability deprecated replaced requires_verification, collection_quality, record_reliability, record_quality, expert_verified. Vernacular names now localised. Users can select language use taxon vernacular names. Missing names fallback gracefully languages. package-wide locale can set default set system locale (set can’t determined default English). New vignettes getting occurrence records, selecting ordering variables, metadata plotting added.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-3-0","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.3.0","text":"Caching defaults memory caching instead relying temporary directory. Front matter vignettes now visible using R help browser. Retired “quiet” option “on_check_fail” argument function finbif_occurrence(). Improved error messages taxa fail checking finbif_occurrence(). Global option set timezone, “finbif_tz”, default value “tzone” argument finbif_occurrence(). Avoids set system environment variable TZ specify “tzone” every time finbif_occurrence() run. Now record time information start time assumed midday. Previous behaviour assume start time midnight, making errors potentially biased. Package options now documented package level man page. News file now accessible via R internal help system. number default variables selected accessing occurrence records reduced speed downloads improve display finbif_occ objects. print method occurrence record objects updated. now aware console width truncating variable values considerate context. Variables can now “deselected” using select argument finbif_occurrence prepending variable name “-”. failures, API requests now automatically retried three times.","code":""},{"path":"/news/index.html","id":"bug-fixes-0-3-0","dir":"Changelog","previous_headings":"","what":"BUG FIXES","title":"finbif 0.3.0","text":"Ordering descending variables work ordering ascending descending variables. Fixed bug handling duplicates result infinite recursion. Fixed bug (“on_check_fail” = “warn”) taxa failed checks ‘finbif_occurrence()’ proceed taxa selected. Fixed bug print method finbif_occ objects caused error trying display single column objects list-col .","code":""},{"path":"/news/index.html","id":"finbif-020","dir":"Changelog","previous_headings":"","what":"finbif 0.2.0","title":"finbif 0.2.0","text":"CRAN release: 2020-01-16","code":""},{"path":"/news/index.html","id":"new-features-0-2-0","dir":"Changelog","previous_headings":"","what":"NEW FEATURES","title":"finbif 0.2.0","text":"Add capacity request random sample FinBIF records.","code":""},{"path":"/news/index.html","id":"minor-improvements-0-2-0","dir":"Changelog","previous_headings":"","what":"MINOR IMPROVEMENTS","title":"finbif 0.2.0","text":"Add content vignettes.","code":""},{"path":"/news/index.html","id":"finbif-010","dir":"Changelog","previous_headings":"","what":"finbif 0.1.0","title":"finbif 0.1.0","text":"CRAN release: 2019-11-19 Initial release.","code":""}] diff --git a/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.RData b/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.RData new file mode 100644 index 00000000..0508de04 Binary files /dev/null and b/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.RData differ diff --git a/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.rdb b/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.rdb similarity index 100% rename from inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.rdb rename to inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.rdb diff --git a/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.rdx b/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.rdx new file mode 100644 index 00000000..5940e359 Binary files /dev/null and b/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.rdx differ diff --git a/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.RData b/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.RData deleted file mode 100644 index f4873b3d..00000000 Binary files a/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.RData and /dev/null differ diff --git a/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.rdx b/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.rdx deleted file mode 100644 index 6fb2189c..00000000 Binary files a/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.rdx and /dev/null differ diff --git a/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.RData b/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.RData new file mode 100644 index 00000000..7a50c359 Binary files /dev/null and b/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.RData differ diff --git a/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdb b/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdb new file mode 100644 index 00000000..118dca5c Binary files /dev/null and b/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdb differ diff --git a/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdx b/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdx new file mode 100644 index 00000000..2295c22d Binary files /dev/null and b/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdx differ diff --git a/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.RData b/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.RData deleted file mode 100644 index 1074e3ce..00000000 Binary files a/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.RData and /dev/null differ diff --git a/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdb b/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdb deleted file mode 100644 index fae578f7..00000000 Binary files a/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdb and /dev/null differ diff --git a/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdx b/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdx deleted file mode 100644 index 8ea10877..00000000 Binary files a/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdx and /dev/null differ diff --git a/inst/vign/v05_filtering.Rmd b/inst/vign/v05_filtering.Rmd index c204f94e..aa6c69f7 100644 --- a/inst/vign/v05_filtering.Rmd +++ b/inst/vign/v05_filtering.Rmd @@ -51,7 +51,7 @@ See `?filters` section "Location" for more details The event or import date of records can be used to filter occurrence data from FinBIF. The date filters can be a single year, month or date, ```{details date-filter} -finbif_occurrence(filter = list(date_range_ym = c("2019-12"))) +finbif_occurrence(filter = list(date_range_ym = c("2020-12"))) ``` , or for record events, a range as a character vector. ```{details date-range-filter} @@ -80,12 +80,12 @@ strict <- c( record_quality = "expert_verified" ) permissive <- list( - quality_issues = "both", - record_reliability = c("reliable", "unassessed", "unreliable"), + wild_status = c("wild", "non_wild", "wild_unknown"), record_quality = c( "expert_verified", "community_verified", "unassessed", "uncertain", "erroneous" - ) + ), + abundance_min = 0 ) c( strict = finbif_occurrence(filter = strict, count_only = TRUE), diff --git a/inst/vign/v05_filtering.md b/inst/vign/v05_filtering.md index bd3f24fc..a5a4c600 100644 --- a/inst/vign/v05_filtering.md +++ b/inst/vign/v05_filtering.md @@ -71,7 +71,7 @@ The event or import date of records can be used to filter occurrence data from FinBIF. The date filters can be a single year, month or date, ```r -finbif_occurrence(filter = list(date_range_ym = c("2019-12"))) +finbif_occurrence(filter = list(date_range_ym = c("2020-12"))) ``` @@ -81,30 +81,19 @@ finbif_occurrence(filter = list(date_range_ym = c("2019-12"))) ```r #> Records downloaded: 10 -#> Records available: 20150 +#> Records available: 23847 #> A data.frame [10 x 12] -#> record_id scientific_name abundance lat_wgs84 lon_wgs84 -#> 1 …KE.921/LGE.627772/1470480 Pteromys volans (Li… NA 61.81362 25.75756 -#> 2 …JX.1054648#107 Pica pica (Linnaeus… 3 65.30543 25.70355 -#> 3 …JX.1054648#85 Poecile montanus (C… 1 65.30543 25.70355 -#> 4 …JX.1054648#103 Garrulus glandarius… 3 65.30543 25.70355 -#> 5 …JX.1054648#123 Passer montanus (Li… 3 65.30543 25.70355 -#> 6 …JX.1054648#149 Pyrrhula pyrrhula (… 1 65.30543 25.70355 -#> 7 …JX.1054648#93 Cyanistes caeruleus… 9 65.30543 25.70355 -#> 8 …JX.1054648#95 Parus major Linnaeu… 35 65.30543 25.70355 -#> 9 …JX.1054648#137 Carduelis flammea (… 2 65.30543 25.70355 -#> 10 …JX.1056695#107 Pica pica (Linnaeus… 6 62.7154 23.0893 -#> date_time -#> 1 2019-12-31 12:00:00 -#> 2 2019-12-31 10:20:00 -#> 3 2019-12-31 10:20:00 -#> 4 2019-12-31 10:20:00 -#> 5 2019-12-31 10:20:00 -#> 6 2019-12-31 10:20:00 -#> 7 2019-12-31 10:20:00 -#> 8 2019-12-31 10:20:00 -#> 9 2019-12-31 10:20:00 -#> 10 2019-12-31 10:15:00 +#> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time +#> 1 …107 Pica pica (Linnaeus… 31 65.0027 25.49381 2020-12-31 10:20:00 +#> 2 …45 Larus argentatus Po… 1 65.0027 25.49381 2020-12-31 10:20:00 +#> 3 …153 Emberiza citrinella… 2 65.0027 25.49381 2020-12-31 10:20:00 +#> 4 …49 Columba livia domes… 33 65.0027 25.49381 2020-12-31 10:20:00 +#> 5 …117 Corvus corax Linnae… 1 65.0027 25.49381 2020-12-31 10:20:00 +#> 6 …111 Corvus monedula Lin… 7 65.0027 25.49381 2020-12-31 10:20:00 +#> 7 …161 Sciurus vulgaris Li… 1 65.0027 25.49381 2020-12-31 10:20:00 +#> 8 …123 Passer montanus (Li… 28 65.0027 25.49381 2020-12-31 10:20:00 +#> 9 …149 Pyrrhula pyrrhula (… 1 65.0027 25.49381 2020-12-31 10:20:00 +#> 10 …77 Turdus pilaris Linn… 1 65.0027 25.49381 2020-12-31 10:20:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality @@ -212,19 +201,19 @@ strict <- c( record_quality = "expert_verified" ) permissive <- list( - quality_issues = "both", - record_reliability = c("reliable", "unassessed", "unreliable"), + wild_status = c("wild", "non_wild", "wild_unknown"), record_quality = c( "expert_verified", "community_verified", "unassessed", "uncertain", "erroneous" - ) + ), + abundance_min = 0 ) c( strict = finbif_occurrence(filter = strict, count_only = TRUE), permissive = finbif_occurrence(filter = permissive, count_only = TRUE) ) -#> Error: 1 error occurred: -#> - Invalid name in record reliability: unassessed +#> strict permissive +#> 52654 51733557 ``` ## Collection diff --git a/vignettes/v05_filtering.Rmd b/vignettes/v05_filtering.Rmd index bd3f24fc..a5a4c600 100644 --- a/vignettes/v05_filtering.Rmd +++ b/vignettes/v05_filtering.Rmd @@ -71,7 +71,7 @@ The event or import date of records can be used to filter occurrence data from FinBIF. The date filters can be a single year, month or date, ```r -finbif_occurrence(filter = list(date_range_ym = c("2019-12"))) +finbif_occurrence(filter = list(date_range_ym = c("2020-12"))) ``` @@ -81,30 +81,19 @@ finbif_occurrence(filter = list(date_range_ym = c("2019-12"))) ```r #> Records downloaded: 10 -#> Records available: 20150 +#> Records available: 23847 #> A data.frame [10 x 12] -#> record_id scientific_name abundance lat_wgs84 lon_wgs84 -#> 1 …KE.921/LGE.627772/1470480 Pteromys volans (Li… NA 61.81362 25.75756 -#> 2 …JX.1054648#107 Pica pica (Linnaeus… 3 65.30543 25.70355 -#> 3 …JX.1054648#85 Poecile montanus (C… 1 65.30543 25.70355 -#> 4 …JX.1054648#103 Garrulus glandarius… 3 65.30543 25.70355 -#> 5 …JX.1054648#123 Passer montanus (Li… 3 65.30543 25.70355 -#> 6 …JX.1054648#149 Pyrrhula pyrrhula (… 1 65.30543 25.70355 -#> 7 …JX.1054648#93 Cyanistes caeruleus… 9 65.30543 25.70355 -#> 8 …JX.1054648#95 Parus major Linnaeu… 35 65.30543 25.70355 -#> 9 …JX.1054648#137 Carduelis flammea (… 2 65.30543 25.70355 -#> 10 …JX.1056695#107 Pica pica (Linnaeus… 6 62.7154 23.0893 -#> date_time -#> 1 2019-12-31 12:00:00 -#> 2 2019-12-31 10:20:00 -#> 3 2019-12-31 10:20:00 -#> 4 2019-12-31 10:20:00 -#> 5 2019-12-31 10:20:00 -#> 6 2019-12-31 10:20:00 -#> 7 2019-12-31 10:20:00 -#> 8 2019-12-31 10:20:00 -#> 9 2019-12-31 10:20:00 -#> 10 2019-12-31 10:15:00 +#> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time +#> 1 …107 Pica pica (Linnaeus… 31 65.0027 25.49381 2020-12-31 10:20:00 +#> 2 …45 Larus argentatus Po… 1 65.0027 25.49381 2020-12-31 10:20:00 +#> 3 …153 Emberiza citrinella… 2 65.0027 25.49381 2020-12-31 10:20:00 +#> 4 …49 Columba livia domes… 33 65.0027 25.49381 2020-12-31 10:20:00 +#> 5 …117 Corvus corax Linnae… 1 65.0027 25.49381 2020-12-31 10:20:00 +#> 6 …111 Corvus monedula Lin… 7 65.0027 25.49381 2020-12-31 10:20:00 +#> 7 …161 Sciurus vulgaris Li… 1 65.0027 25.49381 2020-12-31 10:20:00 +#> 8 …123 Passer montanus (Li… 28 65.0027 25.49381 2020-12-31 10:20:00 +#> 9 …149 Pyrrhula pyrrhula (… 1 65.0027 25.49381 2020-12-31 10:20:00 +#> 10 …77 Turdus pilaris Linn… 1 65.0027 25.49381 2020-12-31 10:20:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality @@ -212,19 +201,19 @@ strict <- c( record_quality = "expert_verified" ) permissive <- list( - quality_issues = "both", - record_reliability = c("reliable", "unassessed", "unreliable"), + wild_status = c("wild", "non_wild", "wild_unknown"), record_quality = c( "expert_verified", "community_verified", "unassessed", "uncertain", "erroneous" - ) + ), + abundance_min = 0 ) c( strict = finbif_occurrence(filter = strict, count_only = TRUE), permissive = finbif_occurrence(filter = permissive, count_only = TRUE) ) -#> Error: 1 error occurred: -#> - Invalid name in record reliability: unassessed +#> strict permissive +#> 52654 51733557 ``` ## Collection