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.
finbif_metadata()
#> metadata_name
#> 1 admin_status
#> 2 red_list
#> 3 country
#> 4 province
#> 5 municipality
#> 6 bird_assoc_area
#> 7 finnish_occurrence_status
#> 8 habitat_type
#> 9 habitat_qualifier
#> 10 life_stage
#> 11 record_basis
#> 12 restriction_level
#> 13 restriction_reason
#> 14 sex_category
#> 15 source
#> 16 taxon_rank Calling finbif_metadata() and specifying one of the
metadata categories will display a data.frame with the
requested metadata.
finbif_metadata("red_list")
#> status_name status_code
#> 1 Critically Endangered CR
#> 2 Data Deficient DD
#> 3 Endangered EN
#> 4 Extinct EX
#> 5 Extinct in the Wild EW
#> 6 Least Concern LC
#> 7 Near Threatened NT
#> 8 Not Applicable NA
#> 9 Not Evaluated NE
#> 10 Regionally Extinct RE
#> 11 Vulnerable VU Some more complex metadata is accessed with other
{finbif} functions
Informal taxonomic groups and their relationships can be displayed
with finbif_informal_groups()
finbif_informal_groups(limit = 6)
#> Algae
#> °--Macro algae
#> ¦--Brown algae and yellow green algae
#> ¦--Green algae
#> ¦--Red algae
#> °--Stoneworts
#> ...142 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 shrimpsAnother 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")
)
#> collection_name taxonomic_coverage count
#> HR.1227 Coll Mikko Heikkinen Biota 67
#> HR.1349 JYV - Fungal collections <NA> 13399
#> HR.1350 JYV - Lichen collections <NA> 398
#> HR.1351 JYV - Bryophyte collections <NA> 4369
#> 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 376833
#> HR.1592 Herbarium of The Ark Nature Cent… <NA> 7806
#> 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 408864
#> HR.200 Finnish Insect Database Insecta 3725818
#> HR.2049 Invasive alien species control Invasive species 471
#> HR.206 The Finnish Nature League's Spri… biota 107275
#> HR.2089 Håkan Lindberg collection Hymenoptera 2400
#> HR.209 Atlas of Finnish Macrolepidoptera Macrolepidoptera 1218544
#> HR.2209 KUO Arachnida collection Arachnida 3
#> HR.2289 Specimens that lack collecting i… <NA> 109
#> HR.2691 Line transect censuses of breedi… Aves 603950
#> HR.2692 Censuses of breeding birds - Are… Aves 14963
#> HR.3051 VieKas LIFE project invasive spe… <NA> 1349
#> HR.3071 Observing species on milk farms <NA> 529
#> HR.3211 iNaturalist Suomi Finland biota 417052
#> HR.3491 LajiGIS: Aquatic species survey Biota 518824
#> HR.3553 LajiGIS: Species monitoring sites Biota 657410
#> HR.3671 Bird of prey nests for protection Aves 10246
#> HR.3691 eBird Aves 528002
#> HR.3791 Invasive species observations Biota 1385
#> HR.39 Winter Bird Census Aves 1404097
#> HR.3911 Bumblebee census Bumblebees 4154
#> HR.3991 Waterbird counts, Luomus dataset Aves 2424
#> HR.3992 Waterbird counts, Luke dataset Aves 15012
#> HR.4011 Salmonidae in streams Salmonidae 12630
#> HR.4051 LajiGIS: Species monitoring site… Aquila chrysaetos; Haliaeetus al… 7780
#> HR.4091 Retkikasvio <NA> 1227
#> HR.4131 Butterflies in Finnish agricultu… Papilionoidea, Others 356560
#> HR.435 Löydös Open Invasive Species Obs… Biota 17157
#> HR.60 Monitoring scheme of birds and m… Aves, Mammalia 826341
#> 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 6233By 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"]
#> 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)
#> 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 … 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.1849 Sampling… MY.collectionT… Biota World 2000-
#> 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> 1513
#> HR.160 MX.secureLe… 940
#> HR.173 <NA> 4765423
#> HR.1849 <NA> 1
#> HR.203 <NA> 26650
#> HR.447 <NA> 2010389
#> HR.48 <NA> 12456603