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  admin_status             
#> 2  red_list                 
#> 3  countries                
#> 4  provinces                
#> 5  municipalities           
#> 6  bird_assoc_areas         
#> 7  finnish_occurrence_status
#> 8  habitat_types            
#> 9  habitat_qualifiers       
#> 10 life_stages              
#> 11 record_basis             
#> 12 restriction_levels       
#> 13 restriction_reasons      
#> 14 sex_categories           
#> 15 sources                  
#> 16 taxon_ranks              


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.


#>    status_name           status_code
#> 1  Critically Endangered CR         
#> 2  Data Deficient        DD         
#> 3  Endangered            EN         
#> 4  Extinct               EX         
#> 5  Extinct in the Wild   EW         
#> 6  Least Concern         LC         
#> 7  Near Threatened       NT         
#> 8  Not Applicable        NA         
#> 9  Not Evaluated         NE         
#> 10 Regionally Extinct    RE         
#> 11 Vulnerable            VU         


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 = 6)

Click to show/hide output.


#>   [1] "Algae"                                                     
#>   [2] "Macro algae"                                               
#>   [3] "Brown algae and yellow green algae"                        
#>   [4] "Green algae"                                               
#>   [5] "Red algae"                                                 
#>   [6] "Stoneworts"                                                
#>   [7] "Birds"                                                     
#>   [8] "Crustaceans"                                               
#>   [9] "Macrocrustaceans"                                          
#>  [10] "Amphipods, isopods, opossum shrimps"                       
#>  [11] "Crabs, shrimps and crayfishes"                             
#>  [12] "Other macrocrustaceans"                                    
#>  [13] "Woodlice"                                                  
#>  [14] "Microcrustaceans"                                          
#>  [15] "Branchiopoda"                                              
#>  [16] "Copepods"                                                  
#>  [17] "Seed shrimps"                                              
#>  [18] "Fishes"                                                    
#>  [19] "Fungi and lichens"                                         
#>  [20] "Ascomycota"                                                
#>  [21] "Erysiphales"                                               
#>  [22] "Non-lichenized Ascomycota"                                 
#>  [23] "Lichenized and lichenicolous fungi"                        
#>  [24] "Lichenicolous fungi"                                       
#>  [25] "Lichenized fungi"                                          
#>  [26] "Macrofungi"                                                
#>  [27] "Agaricoid fungi"                                           
#>  [28] "Aphyllophoroid fungi"                                      
#>  [29] "Cantharelloid fungi"                                       
#>  [30] "Clavarioid fungi"                                          
#>  [31] "Corticioid fungi"                                          
#>  [32] "Hydnoid fungi"                                             
#>  [33] "Jelly fungi, tremelloid fungi"                             
#>  [34] "Polypores"                                                 
#>  [35] "Ramarioid fungi"                                           
#>  [36] "Boletoid fungi"                                            
#>  [37] "Cyphelloid fungi"                                          
#>  [38] "Gastroid fungi, puffballs"                                 
#>  [39] "Parasitic microfungi"                                      
#>  [40] "Exobasibium"                                               
#>  [41] "Rust fungi"                                                
#>  [42] "Smut fungi"                                                
#>  [43] "Insects and arachnids"                                     
#>  [44] "Aquatic insects"                                           
#>  [45] "Caddisflies"                                               
#>  [46] "Mayflies"                                                  
#>  [47] "Stoneflies"                                                
#>  [48] "Archaeognatha and Zygentoma"                               
#>  [49] "Beetles"                                                   
#>  [50] "Booklice"                                                  
#>  [51] "Cockroaches"                                               
#>  [52] "Dragonflies"                                               
#>  [53] "Earwigs"                                                   
#>  [54] "Fleas"                                                     
#>  [55] "Harvestmen"                                                
#>  [56] "Katydids, crickets, grasshopper"                           
#>  [57] "Lice"                                                      
#>  [58] "Mites and ticks"                                           
#>  [59] "Moths and butterflies"                                     
#>  [60] "Butterflies"                                               
#>  [61] "Geometer moths"                                            
#>  [62] "Macrolepidoptera"                                          
#>  [63] "Microlepidoptera"                                          
#>  [64] "Owlet moths"                                               
#>  [65] "Sphinx moths"                                              
#>  [66] "Net-winged insects, megalopterans, snakeflies, mecopterans"
#>  [67] "Pseudoscorpions"                                           
#>  [68] "Sawflies, wasps, ants and bees"                            
#>  [69] "Spiders"                                                   
#>  [70] "Thrips"                                                    
#>  [71] "True bugs"                                                 
#>  [72] "Auchenorrhynchans"                                         
#>  [73] "Bladloppor"                                                
#>  [74] "Bladlöss"                                                  
#>  [75] "Heteropterans"                                             
#>  [76] "Soft scales"                                               
#>  [77] "Whiteflies"                                                
#>  [78] "True flies"                                                
#>  [79] "Brachyceran flies"                                         
#>  [80] "Nematoceran flies"                                         
#>  [81] "Twisted-wing parasites"                                    
#>  [82] "Mammals"                                                   
#>  [83] "Bats"                                                      
#>  [84] "Molluscs"                                                  
#>  [85] "Aquatic snails"                                            
#>  [86] "Bivalves"                                                  
#>  [87] "Landsnails and slugs"                                      
#>  [88] "Mosses"                                                    
#>  [89] "Hornworts"                                                 
#>  [90] "Liverworts"                                                
#>  [91] "Mosses"                                                    
#>  [92] "Myriapods"                                                 
#>  [93] "Chilopods, centipedes"                                     
#>  [94] "Millipedes"                                                
#>  [95] "Pauropods"                                                 
#>  [96] "Symphylans"                                                
#>  [97] "Other organisms"                                           
#>  [98] "Bacteria"                                                  
#>  [99] "Entognatha"                                                
#> [100] "Slime molds"                                               
#> [101] "Sponges, bryozoans and cnidarians"                         
#> [102] "Viruses and viroids"                                       
#> [103] "Reptiles and amphibians"                                   
#> [104] "Amphibians"                                                
#> [105] "Reptiles"                                                  
#> [106] "Vascular plants"                                           
#> [107] "Worms"                                                     
#> [108] "Annelids"                                                  
#> [109] "Earthworms, oligochaetes"                                  
#> [110] "Leeches"                                                   
#> [111] "Polychaetes"                                               
#> [112] "Parasitic worms"                                           
#> [113] "Monogeneans"                                               
#> [114] "Tapeworms"                                                 
#> [115] "Priapulid worms"                                           
#> [116] "Ribbon worms"                                              
#> [117] "Turbellarians"                                             
#> attr(,"class")
#> [1] "translation"


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 Coll Mikko Heikkinen              Biota                                  62
#> HR.1349 JYV - Fungal collections          <NA>                                13397
#> HR.1350 JYV - Lichen collections          <NA>                                  398
#> HR.1351 JYV - Bryophyte collections       <NA>                                 3227
#> 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                          2797
#> HR.1592 Herbarium of The Ark Nature Cent… <NA>                                 1669
#> HR.1687 Papilionoidea of Coll. Lauro      Papilionoidea                         525
#> 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                        349862
#> HR.1953 Drainage basin data               <NA>                                    1
#> HR.200  Finnish Insect Database           Insecta                           3729202
#> HR.2049 Invasive alien species control    Invasive species                       93
#> HR.206  The Finnish Nature League's Spri… biota                               86806
#> HR.2089 Håkan Lindberg collection         Hymenoptera                          2295
#> HR.209  Atlas of Finnish Macrolepidoptera Macrolepidoptera                  1217381
#> HR.2209 KUO Arachnida collection          Arachnida                               3
#> HR.2289 Specimens that lack collecting i… <NA>                                  109
#> HR.2691 Line transect censuses of breedi… Aves                               588124
#> HR.2692 Censuses of breeding birds - Are… Aves                                14963
#> HR.3051 Viekas project invasive species … <NA>                                  662
#> HR.3071 Observing species on milk farms   <NA>                                  160
#> HR.3211 iNaturalist                       <NA>                                20463
#> HR.39   Winter Bird Census                Aves                              1365558
#> HR.435  Löydös Open Invasive Species Obs… Biota                               11742
#> HR.60   Monitoring scheme of birds and m… Aves, Mammalia                     771270
#> HR.627  Invasive mammal species of Finla… Mammalia                              228
#> HR.808  E. Sjöholm´s butterfly collection Lepidoptera                          4951
#> HR.847  Atlas of amphibians and reptiles… Amphibia, Reptilia                   5142


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.203 Löydös Open Fi… <NA>         A service … http://ws…  TRUE        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         Database o… <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.203 NA      MY.collectionT… biota              world               2013-            
#> HR.447 NA      MY.collectionT… Biota              World               <NA>             
#> HR.48  NA      MY.collectionT… <NA>               Ringing data: Finl… 1913-            
#>        secure_level count   
#> HR.129 <NA>             1512
#> HR.160 MX.secureLe…      953
#> HR.173 <NA>          4143322
#> HR.203 <NA>            14572
#> HR.447 <NA>          2012066
#> HR.48  <NA>         11944694