Much of the information in the FinBIF database consists of metadata that helps provide context for occurrence records and other information in FinBIF.
General metadata
You can see some of the metadata available in finbif
by calling the finbif_metadata function without any
arguments.
Click to show/hide output.
#> 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_rankCalling finbif_metadata() and specifying one of the
metadata categories will display a data.frame with the
requested metadata.
finbif_metadata("red_list")Click to show/hide output.
#> 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 Special cases
Some more complex metadata is accessed with other finbif functions
Informal groups
Informal taxonomic groups and their relationships can be displayed
with finbif_informal_groups()
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 groupsYou can select a subgroup by specifying a parent informal group as a function argument.
finbif_informal_groups("Crustaceans")
#> Crustaceans
#> --Macrocrustaceans
#> --Amphipods, isopods, opossum shrimps
#> --Crabs, shrimps and crayfishes
#> --Other macrocrustaceans
#> --Woodlice
#> --Microcrustaceans
#> --Branchiopoda
#> --Copepods
#> --Seed shrimpsCollections
Another special case of metadata is
finbif_collections(). Collections are the highest level of
record aggregation in the FinBIF database.
You can subset collection metadata by using the filter
and select arguments.
finbif_collections(
filter = geographic_coverage == "Finland",
select = c("collection_name", "taxonomic_coverage", "count")
)Click to show/hide output.
#> collection_name taxonomic_coverage count
#> HR.1227 Priv. coll. Mikko Heikkinen Biota 62
#> HR.1349 JYV - Fungal collections <NA> 13477
#> HR.1350 JYV - Lichen collections <NA> 608
#> HR.1351 JYV - Bryophyte collections <NA> 8367
#> HR.1467 Per-Eric Grankvist´s butterly co… Lepidoptera 5
#> HR.1487 JYV - Fish collections <NA> 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… <NA> 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… <NA> 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… <NA> 1545
#> HR.3071 Observing species on milk farms <NA> 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 <NA> 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 <NA> 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… <NA> 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 6690By default, finbif_collections() only displays the
lowest level collections. Higher level, “supercollections” can be viewed
by setting supercollections = TRUE and you can limit the
output to collections with a minimum number of records in them with the
nmin argument.
collections <- finbif_collections(supercollections = TRUE, nmin = 10000)The finbif_collections() function returns a
data.frame where the row names are the ID number of the
collection.
finbif_collections(supercollections = TRUE)["HR.128", "collection_name"]Click to show/hide output.
#> Collections of the Finnish Museum of Natural History LuomusYou can see the child collections of a supercollection by specifying the ID as a filter. Note that the children of supercollections may also be supercollections.
finbif_collections(is_part_of == "HR.128", supercollections = TRUE)Click to show/hide output.
#> collection_name abbreviation description online_url has_children is_part_of data_quality
#> HR.129 Collections of… H Herbarium … <NA> TRUE HR.128 MY.dataQual…
#> HR.160 Zoological col… MZH The collec… http://ww… TRUE HR.128 MY.dataQual…
#> HR.173 Zoological mon… <NA> Monitoring… <NA> TRUE HR.128 MY.dataQual…
#> HR.1849 Genomic resour… <NA> Genomic re… <NA> TRUE HR.128 MY.dataQual…
#> HR.203 Löydös Open Fi… <NA> A service … https://l… FALSE HR.128 <NA>
#> HR.435 Löydös Open In… <NA> A service … https://l… FALSE HR.128 MY.dataQual…
#> HR.447 Hatikka.fi obs… <NA> Hatikka.fi… http://ha… FALSE HR.128 MY.dataQual…
#> HR.48 Ringing and re… TIPU Dataset co… <NA> TRUE HR.128 MY.dataQual…
#> methods collection_type taxonomic_coverage geographic_coverage temporal_coverage
#> HR.129 <NA> MY.collectionT… <NA> <NA> <NA>
#> HR.160 <NA> MY.collectionT… Animalia World 1700 to present
#> HR.173 <NA> MY.collectionT… <NA> Finland 1950-
#> HR.1849 Sampling… MY.collectionT… Biota World 2000-
#> HR.203 <NA> MY.collectionT… biota world 2013-
#> HR.435 <NA> MY.collectionT… Biota Finland 2015-
#> HR.447 <NA> MY.collectionT… Biota World <NA>
#> HR.48 <NA> MY.collectionT… Aves Ringing data: Finl… 1913-
#> secure_level count
#> HR.129 <NA> 2
#> HR.160 MX.secureLe… 742
#> HR.173 <NA> 5160221
#> HR.1849 <NA> 1
#> HR.203 <NA> 39375
#> HR.435 <NA> 19232
#> HR.447 <NA> 2010032
#> HR.48 <NA> 12910437