Author: William K. Morris

# 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