---
title: "Metadata"
author: "William K. Morris"
output:
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%\VignetteIndexEntry{4. Metadata}
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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()
```
Click to show/hide output.
```r
#> 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.
``` r
finbif_metadata("red_list")
```
Click to show/hide output.
```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
```
## 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)
#> 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.
``` r
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.
``` r
finbif_collections(
filter = geographic_coverage == "Finland",
select = c(
"collection_name", "taxonomic_coverage", "geographic_coverage", "count"
)
)
```
Click to show/hide output.
```r
#> collection_name taxonomic_coverage geographic_coverage count
#> HR.1227 Priv. coll. Mikko Hei… Biota Finland 48
#> HR.1349 JYV - Fungal collecti… Finland 14486
#> HR.1350 JYV - Lichen collecti… Finland 825
#> HR.1351 JYV - Bryophyte colle… Finland 11214
#> HR.1467 Per-Eric Grankvist´s … Lepidoptera Finland 5
#> HR.1487 JYV - Fish collections 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… 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… Finland 109
#> HR.2691 Luomus line transect … Aves Finland 580918
#> HR.2692 Censuses of breeding … Aves Finland 14996
#> HR.3051 Finvasive LIFE projec… Finland 2604
#> HR.3071 Biodiversity observat… 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 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 Finland 992
#> HR.4374 Porvoo Museum / Pisces Finland 1
#> HR.4379 Porvoo Museum / Amphi… Finland 5
#> HR.4386 Porvoo Museum / Oology 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… 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… Finland 286
#> HR.5260 Bracket fungi, redlis… Finland 33
#> HR.5535 Observations of invas… Finland 6656
#> HR.5555 Observations by the f… 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 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.
``` 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"]
```
Click to show/hide output.
```r
#> 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.
``` r
finbif_collections(is_part_of == "HR.128", supercollections = TRUE)
```
Click to show/hide output.
```r
#> collection_name abbreviation description online_url has_children is_part_of
#> HR.129 Collections of… Herbarium … TRUE HR.128
#> HR.160 Zoological col… The collec… http://ww… TRUE HR.128
#> HR.173 Luomus monitor… Monitoring… TRUE HR.128
#> HR.1849 Genomic resour… Genomic re… TRUE HR.128
#> HR.203 Löydös Open Fi… A service … https://l… FALSE HR.128
#> HR.2169 Geological col… All the ge… TRUE HR.128
#> HR.435 Löydös Open In… A service … https://l… FALSE HR.128
#> HR.447 Hatikka.fi obs… Hatikka.fi… http://ha… FALSE HR.128
#> HR.48 Bird ringing a… TIPU Dataset co… FALSE HR.128
#> HR.7443 Luomus Botanic… Living col… TRUE HR.128
#> data_quality methods collection_type taxonomic_coverage geographic_coverage
#> HR.129 MY.dataQual… MY.collectionT…
#> HR.160 MY.dataQual… MY.collectionT… Animalia World
#> HR.173 MY.dataQual… MY.collectionT… Finland
#> HR.1849 MY.dataQual… Sampling… MY.collectionT… Biota World
#> HR.203 MY.collectionT… biota world
#> HR.2169 MY.dataQual… MY.collectionT…
#> HR.435 MY.dataQual… MY.collectionT… Biota Finland
#> HR.447 MY.dataQual… MY.collectionT… Biota World
#> HR.48 MY.dataQual… MY.collectionT… Aves Ringing data: Finl…
#> HR.7443 MY.collectionT…
#> temporal_coverage secure_level count
#> HR.129 679165
#> HR.160 1700 to present MX.secureLe… 632
#> HR.173 1950- 5898405
#> HR.1849 2000- 1
#> HR.203 2013- 71709
#> HR.2169 0
#> HR.435 2015- 27935
#> HR.447 2011828
#> HR.48 1913- 15792308
#> HR.7443 0
```