FinBIF aggregates Finnish
biodiversity data from multiple sources in a single open access portal
for researchers, citizen scientists, industry and government. FinBIF
allows users of biodiversity information to find, access, combine and
visualise data on Finnish plants, animals and microorganisms. The
{finbif} R package makes the publicly available data in
FinBIF easily accessible to programmers. Biodiversity information is
available on taxonomy and taxon occurrence. Occurrence data can be
filtered by taxon, time, location and other variables. The data accessed
are conveniently preformatted for subsequent analyses.
You can install the current stable version of {finbif}
from CRAN,
You can also install the latest development version of
{finbif} from GitHub,
To use the FinBIF API you must first request and set a personal
access token. You can request an API token to be sent to your email
address with the function finbif_get_token().
finbif_request_token("[email protected]")Copy the access token that was sent to your email and set it as the
environment variable FINBIF_ACCESS_TOKEN either for the
current session,
Sys.setenv(
FINBIF_ACCESS_TOKEN = "xtmSOIxjPwq0pOMB1WvcZgFLU9QBklauOlonWl8K5oaLIx8RniJLrv"
)
# Note: the above is not a real access token. Do not try using it., or by adding it to a Renviron startup file (see here
for details).
You can check to see if a taxon exists in the FinBIF database.
If the taxon is in the FinBIF database its unique ID is returned.
When a taxon is not in the FinBIF database it is reported as “not found”
and for that taxa the list element is NA.
(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
#> NAYou can also specify the taxonomic rank when searching FinBIF and the search will be limited to the specified rank.
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.51311The function finbif_taxa() can be used for a more
general search for taxa in the FinBIF database. Searches can be
exact, partial or likely (fuzzy
matching). Information for a single taxon is returned when using exact
or fuzzy matching, but multiple taxa, up to a limit, n, may
be returned when using partial matching.
#> [[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"
#>
#> You can download occurrence data from the FinBIF database as a
data.frame with the finbif_occurrence()
function.
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_qualityYou can search for multiple taxa at once and filter the records with
the filter argument.
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_qualitySee ?filters and vignette("v05_filtering")
for more details on filtering FinBIF records.
It is possible to request a random sample of records instead of the
last n records (or records ordered by some other
variable).
#> 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_qualityBy default {finbif} uses local caching for repeated API
requests. This can be turned on or off on a per request or session
basis. See ?caching for details.