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Selecting and ordering variables

William K. Morris

When requesting data using {finbif} you can select from among (or order by) many variables (properties of the occurrence records). The default set of variables returned is a small subset of those available. Note that not all variables are available for all records. See ?variables for details.

Selecting variables

Limiting variables

To retrieve a limited set of variables from FinBIF simply specify the desired variables in the select argument.

finbif_occurrence(
  genus  = "Falco",
  select = c("scientificName", "lifeStage", "sex")
)
Click to show/hide output. 

#> Records downloaded: 10
#> Records available: 473067
#> A data.frame [10 x 3]
#>          scientificName lifeStage    sex
#> 1  Falco rusticolus Li…      <NA> Female
#> 2  Falco peregrinus Tu…      <NA>   <NA>
#> 3  Falco subbuteo Linn…      <NA>   <NA>
#> 4  Falco columbarius L…      <NA>   <NA>
#> 5  Falco columbarius L…      <NA>   <NA>
#> 6  Falco tinnunculus L…      <NA>   <NA>
#> 7  Falco columbarius L…      <NA> Female
#> 8  Falco tinnunculus L…      <NA> Female
#> 9  Falco tinnunculus L…      <NA> Female
#> 10 Falco vespertinus L…  juvenile   <NA>


Extra variables

To get extra variables as well as the default set, specify the extra variables in addition to the keyword "default_vars".

finbif_occurrence(select = c("default_vars", "lifeStage"))
Click to show/hide output. 

#> Records downloaded: 10
#> Records available: 60179991
#> A data.frame [10 x 13]
#>    occurrenceID       scientificName individualCount decimalLatitude decimalLongitude
#> 1           …21 Polytrichum juniper…              NA  60.17967        24.914629      
#> 2           …25 Polytrichum juniper…              NA  60.373472       24.993816      
#> 3           …29 Polytrichum juniper…              NA  61.612783       21.44191       
#> 4           …33 Polytrichum juniper…              NA  61.322069       23.513515      
#> 5           …37 Polytrichum juniper…              NA  61.249458       25.040691      
#> 6           …41 Polytrichum juniper…              NA  62.605448       25.925676      
#> 7           …45 Polytrichum juniper…              NA  62.22789        30.629365      
#> 8           …49 Polytrichum juniper…              NA  66.004079       28.202282      
#> 9           …53 Polytrichum juniper…              NA  69.049179       20.812003      
#> 10          …57 Polytrichum pilifer…              NA  60.373472       24.993816      
#> ...with 0 more records and 8 more variables:
#> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification,
#> requiresIdentification, occurrenceReliability, identificationVerificationStatus,
#> lifeStage


Ordering

You can change the order of occurrence records before they are fetched from the server by using the order_by argument. The default ordering is date_start descending, then load_date descending, then reported_name.

Ascending order

By default occurrence records are ordered by variables in ascending order.

finbif_occurrence("Cygnus cygnus", order_by = "individualCount")
Click to show/hide output. 

#> Records downloaded: 10
#> Records available: 139837
#> A data.frame [10 x 12]
#>    occurrenceID       scientificName individualCount decimalLatitude decimalLongitude
#> 1      …0745928 Cygnus cygnus (Linn…              NA  66              29.25          
#> 2      …0745932 Cygnus cygnus (Linn…              NA              NA               NA
#> 3      …0745937 Cygnus cygnus (Linn…              NA              NA               NA
#> 4      …0745941 Cygnus cygnus (Linn…              NA  60.17           25             
#> 5      …0745945 Cygnus cygnus (Linn…              NA  60.17           25             
#> 6      …0745949 Cygnus cygnus (Linn…              NA  60.17           25             
#> 7      …5552466 Cygnus cygnus (Linn…  1               67.773235       25.050461      
#> 8      …5552474 Cygnus cygnus (Linn…  1               68.713901       22.787894      
#> 9      …6082839 Cygnus cygnus (Linn…  1                           NA               NA
#> 10     …7079647 Cygnus cygnus (Linn…              NA  61.85           23.5           
#> ...with 0 more records and 7 more variables:
#> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification,
#> requiresIdentification, occurrenceReliability, identificationVerificationStatus


Descending order

You can switch to descending order by prefixing the variable with a dash.

finbif_occurrence("Cygnus cygnus", order_by = "-individualCount")
Click to show/hide output. 

#> Records downloaded: 10
#> Records available: 139837
#> A data.frame [10 x 12]
#>                   occurrenceID       scientificName individualCount decimalLatitude
#> 1                 …MHU.2981587 Cygnus cygnus (Linn…  6000            64.4          
#> 2  …HR.3691/OBS2052501157_Unit Cygnus cygnus (Linn…  2065            64.50736      
#> 3  …HR.3691/OBS2052518008_Unit Cygnus cygnus (Linn…  2065            64.50736      
#> 4  …HR.3691/OBS1101526155_Unit Cygnus cygnus (Linn…  1760            62.16389      
#> 5   …HR.3691/OBS604642304_Unit Cygnus cygnus (Linn…  1753            64.50736      
#> 6   …HR.3691/OBS663568887_Unit Cygnus cygnus (Linn…  1600            65.98787      
#> 7  …HR.3691/OBS1399623409_Unit Cygnus cygnus (Linn…  1580            64.50736      
#> 8                …MHU.28815250 Cygnus cygnus (Linn…  1500                        NA
#> 9   …HR.3691/OBS671353848_Unit Cygnus cygnus (Linn…  1361            64.71656      
#> 10 …HR.3691/OBS1686954463_Unit Cygnus cygnus (Linn…  1333            64.50734      
#> ...with 0 more records and 8 more variables:
#> decimalLongitude, eventDateTime, coordinateUncertaintyInMeters, hasIssues,
#> requiresVerification, requiresIdentification, occurrenceReliability,
#> identificationVerificationStatus


Multiple variables

You can specify multiple variables to order by. Sorting primacy is from left to right.

finbif_occurrence(
  "Cygnus olor", order_by = c("finnishCountyID", "-individualCount")
)
Click to show/hide output. 

#> Records downloaded: 10
#> Records available: 63246
#> A data.frame [10 x 12]
#>    occurrenceID       scientificName individualCount decimalLatitude decimalLongitude
#> 1     …12015253 Cygnus olor (J.F. G…  2500                        NA               NA
#> 2     …13633876 Cygnus olor (J.F. G…  1500                        NA               NA
#> 3       …780984 Cygnus olor (J.F. G…  1300                        NA               NA
#> 4       …781416 Cygnus olor (J.F. G…  1300                        NA               NA
#> 5      …2062563 Cygnus olor (J.F. G…  1200                        NA               NA
#> 6     …10352894 Cygnus olor (J.F. G…  1100                        NA               NA
#> 7       …927797 Cygnus olor (J.F. G…  1050                        NA               NA
#> 8      …3110953 Cygnus olor (J.F. G…  960                         NA               NA
#> 9     …26309317 Cygnus olor (J.F. G…  900                         NA               NA
#> 10     …1260385 Cygnus olor (J.F. G…  800             58.66           23.57          
#> ...with 0 more records and 7 more variables:
#> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification,
#> requiresIdentification, occurrenceReliability, identificationVerificationStatus


Random sample

You can also request a random sample (random order) of occurrence records by setting the sample argument to TRUE.

finbif_occurrence(sample = TRUE)
Click to show/hide output. 

#> Records downloaded: 10
#> Records available: 60182673
#> A data.frame [10 x 12]
#>                                         occurrenceID       scientificName individualCount
#> 1  …KE.881/ff60ea35-ef67-4380-b3d7-d65bd80068db_Unit Empetrum nigrum ste…  1             
#> 2                                       …MKC.3874933 Gymnocarpium dryopt…              NA
#> 3                         …KE.921/LGE.557997/1295765 Chara baltica A.Bru…              NA
#> 4                                     …JX.1417206#64 Micracanthia margin…  2             
#> 5                                      …MHU.29367059 Mareca penelope (Li…              NA
#> 6                                      …MKC.31354972 Ranunculus acris su…              NA
#> 7                                 …KE.67/120384#Unit Circus cyaneus (Lin…  1             
#> 8                                      …MHU.14434664 Columba palumbus Li…              NA
#> 9                               …KE.67/11306334#Unit Erithacus rubecula …  1             
#> 10                                    …JX.1350290#11 Rhyncolus elongatus…  4             
#> ...with 0 more records and 9 more variables:
#> decimalLatitude, decimalLongitude, eventDateTime, coordinateUncertaintyInMeters,
#> hasIssues, requiresVerification, requiresIdentification, occurrenceReliability,
#> identificationVerificationStatus


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