---
title: "Metadata"
author: "William K. Morris"
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---
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.
```r
finbif_metadata()
```
<details closed>
<summary> Click to show/hide output. </summary>
```r
#> 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
```
</details>
<br>
Calling `finbif_metadata()` and specifying one of the metadata categories will
display a `data.frame` with the requested metadata.
```r
finbif_metadata("red_list")
```
<details closed>
<summary> Click to show/hide output. </summary>
```r
#> 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
```
</details>
<br>
## 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()`
```r
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.
```r
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.
```r
finbif_collections(
filter = geographic_coverage == "Finland",
select = c("collection_name", "taxonomic_coverage", "count")
)
```
<details closed>
<summary> Click to show/hide output. </summary>
```r
#> 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 HÃ¥kan 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
```
</details>
<br>
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.
``` r
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.
```r
finbif_collections(supercollections = TRUE)["HR.128", "collection_name"]
```
<details closed>
<summary> Click to show/hide output. </summary>
```r
#> Collections of the Finnish Museum of Natural History Luomus
```
</details>
<br>
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.
```r
finbif_collections(is_part_of == "HR.128", supercollections = TRUE)
```
<details closed>
<summary> Click to show/hide output. </summary>
```r
#> 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
```
</details>
<br>