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 finnish_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
#> 18 licenseCalling 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)
#> Birds
#> --Birds of prey and owls
#> --Owls
#> --Birds of prey
#> --Waterbirds
#> Mammals
#> --Small mammals
#> --Bats
#> ...150 more groupsYou can select a subgroup by specifying a parent informal group as a function argument.
finbif_informal_groups("Crustaceans")
#> Crustaceans
#> --Macrocrustaceans
#> --Crabs, shrimps and crayfishes
#> --Amphipods, isopods, opossum shrimps
#> --Woodlice
#> --Other macrocrustaceans
#> --Microcrustaceans
#> --Copepods
#> --Branchiopoda
#> --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", "geographic_coverage", "count"
)
)Click to show/hide output.
#> collection_name taxonomic_coverage geographic_coverage count
#> HR.1132 KUO Trichoptera colle… Trichoptera Finland 1246
#> HR.122 Veikko Salkio's Natur… Animalia Finland 1088
#> HR.1227 Priv. coll. Mikko Hei… Biota Finland 48
#> HR.1349 JYV - Fungal collecti… <NA> Finland 14490
#> HR.1350 JYV - Lichen collecti… <NA> Finland 847
#> HR.1351 JYV - Bryophyte colle… <NA> Finland 11412
#> HR.1467 Per-Eric Grankvist´s … Lepidoptera Finland 5
#> HR.1487 JYV - Fish collections <NA> Finland 1371
#> HR.1507 Birger and Hjördis Li… Lepidoptera Finland 2799
#> HR.155 Fungi indet. (by host) <NA> Finland 122
#> HR.157 Point counts of breed… Birds, landbirds Finland 429205
#> HR.1592 Main herbarium of The… <NA> Finland 7832
#> HR.1687 Papilionoidea of Coll… Papilionoidea Finland 550
#> HR.1688 Noctuidae I of Coll. … Noctuidae Finland 614
#> HR.1689 Noctuidae II of Coll.… Noctuidae Finland 839
#> HR.1690 Noctuidae III, Bombyc… Noctuidae, Bombycoide… Finland 521
#> HR.1691 Drepanidae & Geometri… Drepanidae, Geometrid… Finland 1408
#> HR.175 National Butterfly Re… Lepidoptera Finland 572003
#> HR.1789 Viruses (H) <NA> Finland 3
#> HR.1830 ZMUO Coll. Saalas Coleoptera Finland 16288
#> HR.1870 ZMUO Common vertebrat… <NA> Finland 34787
#> HR.1916 Wildlife triangle Siberian flying squir… Finland 18560
#> HR.200 Finnish Insect Databa… Insecta Finland 3725222
#> HR.2009 Fish observation data… invasive alien fish s… Finland 35854
#> HR.2029 LajiGIS: Miscellaneou… Biota Finland 46532
#> HR.2049 Invasive alien specie… Invasive species Finland 4103
#> HR.206 The Finnish Nature As… biota Finland 141160
#> HR.2089 Håkan Lindberg collec… Hymenoptera Finland 2435
#> HR.209 Atlas of Finnish Macr… Macrolepidoptera Finland 1218544
#> HR.2129 The Atlas of Finnish … fungi Finland 195336
#> HR.2190 Fossils of Finland <NA> Finland 2105
#> HR.2209 KUO Arachnida collect… Arachnida Finland 3
#> HR.2289 Specimens that lack c… <NA> Finland 109
#> HR.2592 KUO Ordines minores (… Apterygota, Dermapter… Finland 4
#> HR.2671 KUO Invertebrata varia Bryozoa, Annelida, Br… Finland 1
#> HR.2691 Luomus line transect … Aves Finland 590276
#> HR.2692 Censuses of breeding … Aves Finland 14996
#> HR.3051 Finvasive LIFE projec… <NA> Finland 2888
#> HR.3071 Biodiversity observat… <NA> Finland 529
#> HR.3211 iNaturalist Suomi Fin… biota Finland 1891538
#> HR.3431 Butterflies in Finnis… Papilionoidea, Others Finland 745157
#> HR.3491 LajiGIS: Species surv… Biota Finland 776645
#> HR.3553 LajiGIS: Species moni… Biota Finland 801392
#> HR.3671 Bird of prey nests fo… Aves Finland 10552
#> HR.3691 eBird Aves Finland 2417556
#> HR.3791 Finnish invasive spec… Biota Finland 8928
#> HR.3834 Tampere TMPM mammal c… <NA> Finland 4
#> HR.3835 Tampere TMPM fish col… <NA> Finland 7
#> HR.39 Winter Bird Census Aves, Mammalia Finland 1609602
#> HR.3911 Bumblebee census Bumblebees Finland 59284
#> HR.3991 Waterbird counts, Luo… Aves Finland 55949
#> HR.3992 Waterbird counts, Luk… Aves Finland 56879
#> HR.4011 Salmonidae in streams Salmonoidei Finland 25263
#> HR.4051 LajiGIS: Species moni… Aquila chrysaetos; Ha… Finland 10115
#> HR.4091 Retkikasvio <NA> Finland 238
#> HR.4191 Porvoo Museum / Colle… Lepidoptera Finland 10417
#> HR.4251 LajiGIS: Species mapp… Biota Finland 703366
#> HR.4271 Tampere TMPM bone and… <NA> Finland 20
#> HR.435 Löydös Open Invasive … Biota Finland 30045
#> HR.4352 NFI rare tree species <NA> Finland 992
#> HR.4374 Porvoo Museum / Pisces <NA> Finland 1
#> HR.4379 Porvoo Museum / Amphi… <NA> Finland 5
#> HR.4386 Porvoo Museum / Oology <NA> Finland 523
#> HR.4412 Tiira.fi: The Fourth … Aves Finland 819404
#> HR.4451 Vascular Plant Herbar… <NA> Finland 1505
#> HR.4471 Fourth Finnish Bird A… Aves Finland 365461
#> HR.4511 Finnish National Moth… Bombycoidea, Noctuoid… Finland 1254256
#> HR.4611 Observations by FCG F… <NA> Finland 1591
#> HR.4612 Pollinator monitoring… Insecta Finland 20298
#> HR.4672 Observations from pub… Biota Finland 127
#> HR.4711 Flying squirrel monit… Pteromys volans Finland 2509
#> HR.4874 ZMUT Collembola main … <NA> Finland 1217
#> HR.49 Finnish birds of prey… Accipitridae, Falconi… Finland 198731
#> HR.4931 Algae collection of I… <NA> Finland 1
#> HR.4991 Bird atlas observatio… Aves Finland 15760
#> HR.50 White-tailed Sea Eagl… Haliaeetus albicilla Finland 33609
#> HR.5016 KUO Mammal Collection… Mammalia Finland 42735
#> HR.5095 Dragonfly - complete … Odonata Finland 1240
#> HR.5155 Observations from ele… Biota Finland 1423
#> HR.5196 Pollinator monitoring… Insecta Finland 16571
#> HR.5235 Finnish butterflies -… Lepidoptera, Papilino… Finland 896
#> HR.5236 Charismatic flowering… Tracheophyta Finland 18406
#> HR.5255 Diurnal moths - compl… Lepidoptera Finland 36
#> HR.5256 Bumblebees - complete… Hymenoptera Finland 468
#> HR.5257 Amphibia and reptilia… Chordata Finland 106
#> HR.5258 Subarctic plants - co… Tracheophyta Finland 66
#> HR.5259 Macrolichens - comple… <NA> Finland 286
#> HR.5260 Bracket fungi, redlis… <NA> Finland 33
#> HR.5275 Porvoo Museum / Galls… <NA> Finland 15
#> HR.5555 Observations by the f… <NA> Finland 3729
#> HR.5575 Noteworthy macrofungi… Fungi Finland 816
#> HR.5795 Dataset from Luke to … Aves Finland 22536
#> HR.5835 Crowdsorsa mapping an… Plantae Finland 41425
#> HR.5875 Mines and galls (ZMUO) <NA> Finland 3026
#> HR.5895 Oma riista -observati… Aves Finland 35965
#> HR.5938 Willow grouse countin… Lagopus lagopus Finland 1067
#> HR.60 Monitoring scheme of … Aves, Mammalia Finland 957039
#> HR.6058 Coll. Lilja Insects <NA> Finland 112
#> HR.6118 ZMUO Egg collections Aves Finland 3127
#> HR.6138 Porvoo museum / Osteo… vertebrates Finland 139
#> HR.627 Alien mammal species … Invasive alien mammal… Finland 4255
#> HR.64 Finnish bird nest rec… Aves Finland 975746
#> HR.6678 Finnish Hemiptera Wor… Hemiptera Finland 142664
#> HR.6778 Line transect censuse… Aves Finland 1224326
#> HR.6882 Porvoo Museum / Colle… Arachnida and Myriapo… Finland 11
#> HR.7000 ZMUT DNA barcoded Col… <NA> Finland 475
#> HR.7080 LajiGIS: Species surv… Biota Finland 140392
#> HR.7120 Teaching collection (… Insecta Finland 46
#> HR.7121 Teaching collection (… <NA> Finland 1054
#> HR.7203 Porvoo Museum / Main … <NA> Finland 3342
#> HR.7300 Old-growth forest pol… <NA> Finland 2
#> HR.7301 Indicator lichens, co… <NA> Finland 16
#> HR.7380 KUO Odonata collectio… Odonata Finland 2
#> HR.7420 Line transect censuse… Aves Finland 7311
#> HR.7480 Coll. Kanerva Herbari… <NA> Finland 128
#> HR.7540 Bird collection, Ostr… Birds Finland 15
#> HR.7562 Coll. Rydman Herbarium <NA> Finland 98
#> HR.7580 Coll. Anttila Herbari… <NA> Finland 80
#> HR.808 E. Sjöholm's butterfl… Lepidoptera Finland 4946
#> HR.829 KUO Lichen collections <NA> Finland 1957
#> HR.847 Atlas of amphibians a… Amphibia, Reptilia Finland 7956
#> HR.95 Osprey monitoring Pandion haliaetus Finland 106252By 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
#> HR.129 Collections of… <NA> Herbarium … <NA> TRUE HR.128
#> HR.160 Zoological col… <NA> The collec… http://ww… TRUE HR.128
#> HR.173 Luomus monitor… <NA> Monitoring… <NA> TRUE HR.128
#> HR.1849 Genomic resour… <NA> Genomic re… <NA> TRUE HR.128
#> HR.203 Löydös Open Fi… <NA> A service … https://l… FALSE HR.128
#> HR.2169 Geological col… <NA> All the ge… <NA> TRUE HR.128
#> HR.435 Löydös Open In… <NA> A service … https://l… FALSE HR.128
#> HR.447 Hatikka.fi obs… <NA> Hatikka.fi… http://ha… FALSE HR.128
#> HR.48 Bird ringing a… TIPU Dataset co… <NA> FALSE HR.128
#> HR.7443 Luomus Botanic… <NA> Living col… <NA> TRUE HR.128
#> data_quality methods collection_type taxonomic_coverage geographic_coverage
#> HR.129 MY.dataQual… <NA> MY.collectionT… <NA> <NA>
#> HR.160 MY.dataQual… <NA> MY.collectionT… Animalia World
#> HR.173 MY.dataQual… <NA> MY.collectionT… <NA> Finland
#> HR.1849 MY.dataQual… Sampling… MY.collectionT… Biota World
#> HR.203 <NA> <NA> MY.collectionT… biota world
#> HR.2169 MY.dataQual… <NA> MY.collectionT… <NA> <NA>
#> HR.435 MY.dataQual… <NA> MY.collectionT… Biota Finland
#> HR.447 MY.dataQual… <NA> MY.collectionT… Biota World
#> HR.48 MY.dataQual… <NA> MY.collectionT… Aves Ringing data: Finl…
#> HR.7443 <NA> <NA> MY.collectionT… <NA> <NA>
#> temporal_coverage secure_level count
#> HR.129 <NA> <NA> 157045
#> HR.160 1700 to present MX.secureLe… 14866
#> HR.173 1950- <NA> 5915207
#> HR.1849 2000- <NA> 1
#> HR.203 2013- <NA> 76763
#> HR.2169 <NA> <NA> 0
#> HR.435 2015- <NA> 30045
#> HR.447 <NA> <NA> 2011842
#> HR.48 1913- <NA> 15974888
#> HR.7443 <NA> <NA> 0