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       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

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)
    #> Birds
    #>   --Birds of prey and owls
    #>       --Owls
    #>       --Birds of prey
    #>   --Waterbirds
    #> Mammals
    #>   --Small mammals
    #>   --Bats
    #> ...150 more groups

You 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 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", "geographic_coverage", "count"
      )
    )

Click to show/hide output.

    #>         collection_name        taxonomic_coverage     geographic_coverage count
    #> HR.1227 Priv. coll. Mikko Hei… Biota                  Finland                  48
    #> HR.1349 JYV - Fungal collecti… <NA>                   Finland               14486
    #> HR.1350 JYV - Lichen collecti… <NA>                   Finland                 825
    #> HR.1351 JYV - Bryophyte colle… <NA>                   Finland               11214
    #> HR.1467 Per-Eric Grankvist´s … Lepidoptera            Finland                   5
    #> HR.1487 JYV - Fish collections <NA>                   Finland                1371
    #> HR.1507 Lingonblad Birger och… Lepidoptera            Finland                2799
    #> HR.157  Point counts of breed… Birds, landbirds       Finland              425914
    #> 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              549592
    #> HR.1916 Wildlife triangle      Siberian flying squir… Finland               18560
    #> HR.200  Finnish Insect Databa… Insecta                Finland             3725313
    #> HR.2009 Fish observation data… invasive alien fish s… Finland               35854
    #> HR.2029 LajiGIS: Miscellaneou… Biota                  Finland               44432
    #> HR.2049 Invasive alien specie… Invasive species       Finland                3908
    #> HR.206  The Finnish Nature As… biota                  Finland              141107
    #> HR.2089 Håkan Lindberg collec… Hymenoptera            Finland                2435
    #> HR.209  Atlas of Finnish Macr… Macrolepidoptera       Finland             1218546
    #> HR.2129 The Atlas of Finnish … fungi                  Finland              181432
    #> HR.2209 KUO Arachnida collect… Arachnida              Finland                   3
    #> HR.2289 Specimens that lack c… <NA>                   Finland                 109
    #> HR.2691 Luomus line transect … Aves                   Finland              580918
    #> HR.2692 Censuses of breeding … Aves                   Finland               14996
    #> HR.3051 Finvasive LIFE projec… <NA>                   Finland                2604
    #> HR.3071 Biodiversity observat… <NA>                   Finland                 529
    #> HR.3211 iNaturalist Suomi Fin… biota                  Finland             1670979
    #> HR.3431 Butterflies in Finnis… Papilionoidea, Others  Finland              732007
    #> HR.3491 LajiGIS: Species surv… Biota                  Finland              759186
    #> HR.3553 LajiGIS: Species moni… Biota                  Finland              797208
    #> HR.3691 eBird                  Aves                   Finland             2417556
    #> HR.3791 Finnish invasive spec… Biota                  Finland                8099
    #> HR.39   Winter Bird Census     Aves, Mammalia         Finland             1608783
    #> HR.3911 Bumblebee census       Bumblebees             Finland               52893
    #> HR.3991 Waterbird counts, Luo… Aves                   Finland               54931
    #> HR.3992 Waterbird counts, Luk… Aves                   Finland               54782
    #> HR.4011 Salmonidae in streams  Salmonoidei            Finland               25263
    #> HR.4051 LajiGIS: Species moni… Aquila chrysaetos; Ha… Finland                9812
    #> HR.4091 Retkikasvio            <NA>                   Finland                 220
    #> HR.4191 Porvoo Museum / Colle… Lepidoptera            Finland               10417
    #> HR.4251 LajiGIS: Species mapp… Biota                  Finland              638169
    #> HR.435  Löydös Open Invasive … Biota                  Finland               27935
    #> 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                 522
    #> HR.4412 Tiira.fi: The Fourth … Aves                   Finland              819404
    #> HR.4471 Fourth Finnish Bird A… Aves                   Finland              365368
    #> HR.4511 Finnish National Moth… Bombycoidea, Noctuoid… Finland             1224173
    #> HR.4611 Observations by FCG F… <NA>                   Finland                1591
    #> HR.4612 Pollinator monitoring… Insecta                Finland               16692
    #> HR.4672 Observations from pub… Biota                  Finland                 127
    #> HR.4711 Flying squirrel monit… Pteromys volans        Finland                2509
    #> HR.49   Finnish birds of prey… Accipitridae, Falconi… Finland              193879
    #> HR.4991 Bird atlas observatio… Aves                   Finland               15757
    #> HR.50   White-tailed Sea Eagl… Haliaeetus albicilla   Finland               32090
    #> HR.5095 Dragonfly - complete … Odonata                Finland                1066
    #> HR.5155 Observations from ele… Biota                  Finland                1423
    #> HR.5196 Pollinator monitoring… Insecta                Finland               16571
    #> HR.5235 Finnish butterflies -… Lepidoptera, Papilino… Finland                 751
    #> HR.5236 Charismatic flowering… Tracheophyta           Finland               16849
    #> HR.5255 Diurnal moths - compl… Lepidoptera            Finland                  36
    #> HR.5256 Bumblebees - complete… Hymenoptera            Finland                 461
    #> HR.5257 Amphibia and reptilia… Chordata               Finland                  91
    #> HR.5258 Subarctic plants - co… Tracheophyta           Finland                  66
    #> HR.5259 Macrolichens - comple… <NA>                   Finland                 286
    #> HR.5260 Bracket fungi, redlis… <NA>                   Finland                  33
    #> HR.5535 Observations of invas… <NA>                   Finland                6656
    #> 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.5895 Oma riista -observati… Aves                   Finland               35965
    #> HR.5938 Willow grouse countin… Lagopus lagopus        Finland                1067
    #> HR.60   Monitoring scheme of … Aves, Mammalia         Finland              956964
    #> HR.6058 Coll. Lilja Insects    <NA>                   Finland                 111
    #> HR.627  Alien mammal species … Invasive alien mammal… Finland                4255
    #> HR.64   Finnish bird nest rec… Aves                   Finland              973502
    #> HR.6678 Finnish Hemiptera Wor… Hemiptera              Finland              142664
    #> HR.6778 Line transect censuse… Aves                   Finland             1188179
    #> HR.7080 LajiGIS: Species surv… Biota                  Finland              140389
    #> HR.808  E. Sjöholm's butterfl… Lepidoptera            Finland                4946
    #> HR.847  Atlas of amphibians a… Amphibia, Reptilia     Finland                7747
    #> HR.95   Osprey monitoring      Pandion haliaetus      Finland              102550

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
    #> 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>           679165
    #> HR.160  1700 to present   MX.secureLe…      632
    #> HR.173  1950-             <NA>          5898405
    #> HR.1849 2000-             <NA>                1
    #> HR.203  2013-             <NA>            71709
    #> HR.2169 <NA>              <NA>                0
    #> HR.435  2015-             <NA>            27935
    #> HR.447  <NA>              <NA>          2011828
    #> HR.48   1913-             <NA>         15792308
    #> HR.7443 <NA>              <NA>                0