Much of the information in the FinBIF database consists of metadata that helps provide context for occurrence records and other information in FinBIF.
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 admin_status
#> 2 red_list
#> 3 countries
#> 4 provinces
#> 5 municipalities
#> 6 bird_assoc_areas
#> 7 finnish_occurrence_status
#> 8 habitat_types
#> 9 habitat_qualifiers
#> 10 life_stages
#> 11 record_basis
#> 12 restriction_levels
#> 13 restriction_reasons
#> 14 sex_categories
#> 15 sources
#> 16 taxon_ranks Calling finbif_metadata() and specifying one of the metadata categories will display a data.frame with the requested metadata.
Click to show/hide output.
Some more complex metadata is accessed with other {finbif} functions
Informal taxonomic groups and their relationships can be displayed with finbif_informal_groups()
Click to show/hide output.
#> [1] "Algae"
#> [2] "Macro algae"
#> [3] "Brown algae and yellow green algae"
#> [4] "Green algae"
#> [5] "Red algae"
#> [6] "Stoneworts"
#> [7] "Birds"
#> [8] "Crustaceans"
#> [9] "Macrocrustaceans"
#> [10] "Amphipods, isopods, opossum shrimps"
#> [11] "Crabs, shrimps and crayfishes"
#> [12] "Other macrocrustaceans"
#> [13] "Woodlice"
#> [14] "Microcrustaceans"
#> [15] "Branchiopoda"
#> [16] "Copepods"
#> [17] "Seed shrimps"
#> [18] "Fishes"
#> [19] "Fungi and lichens"
#> [20] "Ascomycota"
#> [21] "Erysiphales"
#> [22] "Non-lichenized Ascomycota"
#> [23] "Lichenized and lichenicolous fungi"
#> [24] "Lichenicolous fungi"
#> [25] "Lichenized fungi"
#> [26] "Macrofungi"
#> [27] "Agaricoid fungi"
#> [28] "Aphyllophoroid fungi"
#> [29] "Cantharelloid fungi"
#> [30] "Clavarioid fungi"
#> [31] "Corticioid fungi"
#> [32] "Hydnoid fungi"
#> [33] "Jelly fungi, tremelloid fungi"
#> [34] "Polypores"
#> [35] "Ramarioid fungi"
#> [36] "Boletoid fungi"
#> [37] "Cyphelloid fungi"
#> [38] "Gastroid fungi, puffballs"
#> [39] "Parasitic microfungi"
#> [40] "Exobasibium"
#> [41] "Rust fungi"
#> [42] "Smut fungi"
#> [43] "Insects and arachnids"
#> [44] "Aquatic insects"
#> [45] "Caddisflies"
#> [46] "Mayflies"
#> [47] "Stoneflies"
#> [48] "Archaeognatha and Zygentoma"
#> [49] "Beetles"
#> [50] "Booklice"
#> [51] "Cockroaches"
#> [52] "Dragonflies"
#> [53] "Earwigs"
#> [54] "Fleas"
#> [55] "Harvestmen"
#> [56] "Katydids, crickets, grasshopper"
#> [57] "Lice"
#> [58] "Mites and ticks"
#> [59] "Moths and butterflies"
#> [60] "Butterflies"
#> [61] "Geometer moths"
#> [62] "Macrolepidoptera"
#> [63] "Microlepidoptera"
#> [64] "Owlet moths"
#> [65] "Sphinx moths"
#> [66] "Net-winged insects, megalopterans, snakeflies, mecopterans"
#> [67] "Pseudoscorpions"
#> [68] "Sawflies, wasps, ants and bees"
#> [69] "Spiders"
#> [70] "Thrips"
#> [71] "True bugs"
#> [72] "Auchenorrhynchans"
#> [73] "Bladloppor"
#> [74] "Bladlöss"
#> [75] "Heteropterans"
#> [76] "Soft scales"
#> [77] "Whiteflies"
#> [78] "True flies"
#> [79] "Brachyceran flies"
#> [80] "Nematoceran flies"
#> [81] "Twisted-wing parasites"
#> [82] "Mammals"
#> [83] "Bats"
#> [84] "Molluscs"
#> [85] "Aquatic snails"
#> [86] "Bivalves"
#> [87] "Landsnails and slugs"
#> [88] "Mosses"
#> [89] "Hornworts"
#> [90] "Liverworts"
#> [91] "Mosses"
#> [92] "Myriapods"
#> [93] "Chilopods, centipedes"
#> [94] "Millipedes"
#> [95] "Pauropods"
#> [96] "Symphylans"
#> [97] "Other organisms"
#> [98] "Bacteria"
#> [99] "Entognatha"
#> [100] "Slime molds"
#> [101] "Sponges, bryozoans and cnidarians"
#> [102] "Viruses and viroids"
#> [103] "Reptiles and amphibians"
#> [104] "Amphibians"
#> [105] "Reptiles"
#> [106] "Vascular plants"
#> [107] "Worms"
#> [108] "Annelids"
#> [109] "Earthworms, oligochaetes"
#> [110] "Leeches"
#> [111] "Polychaetes"
#> [112] "Parasitic worms"
#> [113] "Monogeneans"
#> [114] "Tapeworms"
#> [115] "Priapulid worms"
#> [116] "Ribbon worms"
#> [117] "Turbellarians"
#> attr(,"class")
#> [1] "translation"You can select a subgroup by specifying a parent informal group as a function argument.
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 Coll Mikko Heikkinen Biota 62
#> HR.1349 JYV - Fungal collections <NA> 13397
#> HR.1350 JYV - Lichen collections <NA> 398
#> HR.1351 JYV - Bryophyte collections <NA> 3227
#> 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 2797
#> HR.1592 Herbarium of The Ark Nature Cent… <NA> 1669
#> HR.1687 Papilionoidea of Coll. Lauro Papilionoidea 525
#> 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 349862
#> HR.1953 Drainage basin data <NA> 1
#> HR.200 Finnish Insect Database Insecta 3729202
#> HR.2049 Invasive alien species control Invasive species 93
#> HR.206 The Finnish Nature League's Spri… biota 86806
#> HR.2089 Håkan Lindberg collection Hymenoptera 2295
#> HR.209 Atlas of Finnish Macrolepidoptera Macrolepidoptera 1217381
#> HR.2209 KUO Arachnida collection Arachnida 3
#> HR.2289 Specimens that lack collecting i… <NA> 109
#> HR.2691 Line transect censuses of breedi… Aves 588124
#> HR.2692 Censuses of breeding birds - Are… Aves 14963
#> HR.3051 Viekas project invasive species … <NA> 662
#> HR.3071 Observing species on milk farms <NA> 160
#> HR.3211 iNaturalist <NA> 20463
#> HR.39 Winter Bird Census Aves 1365558
#> HR.435 Löydös Open Invasive Species Obs… Biota 11742
#> HR.60 Monitoring scheme of birds and m… Aves, Mammalia 771270
#> HR.627 Invasive mammal species of Finla… Mammalia 228
#> HR.808 E. Sjöholm´s butterfly collection Lepidoptera 4951
#> HR.847 Atlas of amphibians and reptiles… Amphibia, Reptilia 5142By 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.
The finbif_collections() function returns a data.frame where the row names are the ID number of the collection.
Click to show/hide output.
You 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
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.203 Löydös Open Fi… <NA> A service … http://ws… TRUE 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 Database o… <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.203 NA MY.collectionT… biota world 2013-
#> HR.447 NA MY.collectionT… Biota World <NA>
#> HR.48 NA MY.collectionT… <NA> Ringing data: Finl… 1913-
#> secure_level count
#> HR.129 <NA> 1512
#> HR.160 MX.secureLe… 953
#> HR.173 <NA> 4143322
#> HR.203 <NA> 14572
#> HR.447 <NA> 2012066
#> HR.48 <NA> 11944694