--- title: "Occurrence records from FinBIF" author: "William K. Morris" output: rmarkdown::html_vignette: toc: true vignette: > %\VignetteIndexEntry{2. Occurrence records from FinBIF} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- The core purpose of `{finbif}` is accessing occurrence data stored in the FinBIF database. Occurrence data can be retrieved from FinBIF with the function `finbif_occurrence()`. Without any arguments specified `finbif_occurrence()` will retrieve the latest 10 occurrence records from FinBIF. ``` r finbif_occurrence() ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 60179988 #> A data.frame [10 x 12] #> 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 7 more variables: #> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification, #> requiresIdentification, occurrenceReliability, identificationVerificationStatus ```

The print method for the resulting `finbif_occ` object will display the number of records downloaded, the total number of records available, a data summary including up to 10 rows of some core record variables (when available), the number of remaining records and variables, as well as the names of additional variables. ## Darwin Core Variables You can switch from the default [Darwin Core ](http://rs.tdwg.org/dwc/) style variable names by setting `dwc = FALSE`. ``` r colnames(finbif_occurrence(dwc = FALSE)) #> [1] "record_id" "scientific_name" "abundance" #> [4] "lat_wgs84" "lon_wgs84" "date_time" #> [7] "coordinates_uncertainty" "any_issues" "requires_verification" #> [10] "requires_identification" "record_reliability" "record_quality" ``` The functions `to_dwc()` and `to_native()` can be used to translate variable names to and from Darwin Core style and `{finbif}`'s native variable names style. ## Choosing taxa You can limit the records to certain taxa by specifying them as an argument. ``` r finbif_occurrence("Cygnus cygnus") ```
Click to show/hide output. ```r #> 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 …5552470 Cygnus cygnus (Linn… 4 69.063377 27.11982 #> 9 …5552474 Cygnus cygnus (Linn… 1 68.713901 22.787894 #> 10 …5559118 Cygnus cygnus (Linn… 3 NA NA #> ...with 0 more records and 7 more variables: #> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification, #> requiresIdentification, occurrenceReliability, identificationVerificationStatus ```

Multiple taxa can be requested at once. ``` r finbif_occurrence("Cygnus cygnus", "Cygnus olor") ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 203083 #> 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 …0745953 Cygnus olor (J.F. G… NA 60.1741 24.9439 #> 8 …0745957 Cygnus olor (J.F. G… NA NA NA #> 9 …0745961 Cygnus olor (J.F. G… NA NA NA #> 10 …5552466 Cygnus cygnus (Linn… 1 67.773235 25.050461 #> ...with 0 more records and 7 more variables: #> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification, #> requiresIdentification, occurrenceReliability, identificationVerificationStatus ```

You can also chose higher taxonomic groups and use common names (in English, Finnish and Swedish). ``` r birds <- finbif_occurrence("Birds") linnut <- finbif_occurrence("Linnut") faglar <- finbif_occurrence("Fåglar") lapply(list(birds, linnut, faglar), nrow) #> [[1]] #> [1] 10 #> #> [[2]] #> [1] 10 #> #> [[3]] #> [1] 10 ``` ## Request size You can increase the number of records returned by using the `n` argument. ``` r finbif_occurrence(n = 1001) ```
Click to show/hide output. ```r #> Records downloaded: 1001 #> Records available: 60182673 #> A data.frame [1001 x 12] #> 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 991 more records and 7 more variables: #> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification, #> requiresIdentification, occurrenceReliability, identificationVerificationStatus ```

You can see how many records are available for a given request, without retrieving any records, by setting `count_only = TRUE`. ``` r finbif_occurrence(count_only = TRUE) #> [1] 60182646 ``` ## Checking taxa When you request occurrence records for specific taxa, by default, the taxon names are first checked against the FinBIF database. If any of the requested taxa are not found in the database you will receive a warning but the data will still be retrieved for the remaining taxa. ``` r finbif_occurrence("Vulpes vulpes", "Moomin") ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 8107 #> A data.frame [10 x 12] #> occurrenceID scientificName individualCount decimalLatitude decimalLongitude #> 1 …223360 Vulpes vulpes var. … NA 56 160 #> 2 …223410 Vulpes vulpes (Linn… NA 42.87 76.72 #> 3 …227292 Vulpes vulpes subsp… NA NA NA #> 4 …227296 Vulpes vulpes (Linn… NA 58.7 13.83 #> 5 …579385 Vulpes vulpes (Linn… NA 61.13 25.77 #> 6 …580318 Vulpes vulpes (Linn… NA 59.931 23.706 #> 7 …580322 Vulpes vulpes (Linn… NA NA NA #> 8 …580326 Vulpes vulpes (Linn… NA NA NA #> 9 …580330 Vulpes vulpes (Linn… NA NA NA #> 10 …580334 Vulpes vulpes (Linn… NA 69 27.5 #> ...with 0 more records and 7 more variables: #> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification, #> requiresIdentification, occurrenceReliability, identificationVerificationStatus ```

You can turn off taxon name pre-checking by setting the value of the `check_taxa` argument to `FALSE`. ``` r finbif_occurrence("Vulpes vulpes", "Moomin", check_taxa = FALSE) ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 8107 #> A data.frame [10 x 12] #> occurrenceID scientificName individualCount decimalLatitude decimalLongitude #> 1 …223360 Vulpes vulpes var. … NA 56 160 #> 2 …223410 Vulpes vulpes (Linn… NA 42.87 76.72 #> 3 …227292 Vulpes vulpes subsp… NA NA NA #> 4 …227296 Vulpes vulpes (Linn… NA 58.7 13.83 #> 5 …579385 Vulpes vulpes (Linn… NA 61.13 25.77 #> 6 …580318 Vulpes vulpes (Linn… NA 59.931 23.706 #> 7 …580322 Vulpes vulpes (Linn… NA NA NA #> 8 …580326 Vulpes vulpes (Linn… NA NA NA #> 9 …580330 Vulpes vulpes (Linn… NA NA NA #> 10 …580334 Vulpes vulpes (Linn… NA 69 27.5 #> ...with 0 more records and 7 more variables: #> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification, #> requiresIdentification, occurrenceReliability, identificationVerificationStatus ```

By setting the argument, `on_check_fail` to `"error"` (the default is `"warn"`), you can elevate the warnings to errors and the request will fail if any of the taxa are not found in the FinBIF database. ``` r finbif_occurrence("Vulpes vulpes", "Moomin", on_check_fail = "error") #> Error: #> ! Cannot find the following taxa in the FinBIF taxonomy. #> Please check you are using accepted names and not synonyms or #> other names for the taxa you are selecting: #> #> Moomin ``` This can be a useful strategy if you are using `{finbif}` non-interactively (in a script), and you do not want to proceed if any of your taxon names are wrong or misspelled. ## Aggregating records You can request records in aggregate using the `aggregate` argument to `finbif_occurrence`. Aggregated requests will return counts for the combination of the `variables` you specify with the `select` argument. You can request counts of `"records"`, `"species"` or `"taxa"` by using the corresponding string as the value for the `aggregate` argument. Aggregating by `"species"` will count the number of unique species identifiers for a set of records grouped by the combination of selected variables. Note that this count will not include records of taxa that do not have species identifiers, including records of higher taxa (e.g., genus only records), records of the non-species children of aggregate or complex taxa, and hybrid taxa. Therefore, in some contexts the results returned will be an underestimate of species richness. Likewise, aggregating by `"taxa"`, which returns a count the number of unique taxon identifiers, could represent an overestimate of the number of taxa as records of higher taxa will contribute to the count while their true identify may be a duplicate of other records. To illustrate, you can count the number of moths and butterflies by municipality with the following: ``` r finbif_occurrence( "Lepidoptera", select = "finnishCounty", aggregate = "species" ) ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 309 #> A data.frame [10 x 2] #> finnishCounty n_species #> 1 Raasepori 2078 #> 2 Virolahti 2037 #> 3 Rääkkylä 1396 #> 4 Kouvola 1578 #> 5 Kemiönsaari 2042 #> 6 Hanko 1994 #> 7 Parainen 1922 #> 8 Helsinki 2069 #> 9 Kuopio 1445 #> 10 Turku 1827 ```

## Time & duration The default behaviour of `finbif_occurrence` is to consolidate date and time data for occurrence recording events into a `date_time` variable. This can be turned off (which can speed up data processing time) by deselecting the `date_time` variable. ``` r finbif_occurrence(select = "-eventDateTime") ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 60179991 #> A data.frame [10 x 11] #> 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 6 more variables: #> coordinateUncertaintyInMeters, hasIssues, requiresVerification, requiresIdentification, #> occurrenceReliability, identificationVerificationStatus ```

### Timezone #### Timezone input The FinBIF database doesn't currently store timezone information, so `{finbif}` makes assumptions about the appropriate timezone based on the time and location of the occurrence recording events to calculate `date_time` and `duration`. By default, a fast heuristic is used to determine the timezones. If you require greater accuracy (e.g., you are using data on the Finnish/Swedish border and daytime/nighttime hours are important), you can switch to more accurate, though slower, timezone calculation method. ``` r finbif_occurrence(date_time_method = "accurate") ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 60179988 #> A data.frame [10 x 12] #> 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 7 more variables: #> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification, #> requiresIdentification, occurrenceReliability, identificationVerificationStatus ```

#### Timezone output The timezone of the calculated `date_time` variable is determined by the timezone of your operating system. ``` r Sys.timezone() ``` You can override this by setting the `tzone` argument to a different value. ``` r finbif_occurrence(tzone = "Etc/UTC") ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 60179988 #> A data.frame [10 x 12] #> 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 7 more variables: #> eventDateTime, coordinateUncertaintyInMeters, hasIssues, requiresVerification, #> requiresIdentification, occurrenceReliability, identificationVerificationStatus ```

Or set the global timezone option to set the timezone for the current session. ``` r options(finbif_tz = "Etc/UTC") ``` This may be advisable for reproducibility or when working with multiple systems.