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Metadata

William K. Morris

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.

finbif_metadata()
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_rank


Calling 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 groups

You 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 shrimps

Collections

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                   6690


By 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 Luomus


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.

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


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