--- 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: 47159747 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality ```

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 variable names to [Darwin Core ](http://rs.tdwg.org/dwc/) style names by setting `dwc = TRUE`. ```r colnames(finbif_occurrence(dwc = TRUE)) #> [1] "occurrenceID" "scientificName" "individualCount" #> [4] "decimalLatitude" "decimalLongitude" "eventDateTime" #> [7] "coordinateUncertaintyInMeters" "hasIssues" "requiresVerification" #> [10] "requiresIdentification" "occurrenceReliability" "occurrenceQuality" ``` 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: 95730 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …JX.1594164#13 Cygnus cygnus (Linn… NA 64.94473 26.67958 2023-06-13 14:33:00 #> 2 …HR.4412/6489172c9ddda_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> 3 …HR.4412/64891730060a4_U Cygnus cygnus (Linn… NA 61.38348 22.97288 2023-06-13 12:00:00 #> 4 …HR.4412/648917378a3b6_U Cygnus cygnus (Linn… NA 62.76028 24.15774 2023-06-13 12:00:00 #> 5 …HR.4412/6489175adc05f_U Cygnus cygnus (Linn… NA 60.78752 21.39263 2023-06-13 12:00:00 #> 6 …HR.4412/6489173a1db9b_U Cygnus cygnus (Linn… NA 64.31374 26.68643 2023-06-13 12:00:00 #> 7 …HR.4412/648917456a396_U Cygnus cygnus (Linn… NA 61.87986 25.19067 2023-06-13 12:00:00 #> 8 …HR.4412/648917454912b_U Cygnus cygnus (Linn… NA 60.42215 24.00099 2023-06-13 12:00:00 #> 9 …HR.4412/64891750e74e7_U Cygnus cygnus (Linn… NA 63.86383 27.70835 2023-06-13 12:00:00 #> 10 …HR.4412/64891741330f8_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality ```

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: 138681 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time #> 1 …JX.1594164#13 Cygnus cygnus (Linn… NA 64.94473 26.67958 2023-06-13 14:33:00 #> 2 …HR.4412/6489172c9ddda_U Cygnus cygnus (Linn… NA 61.74701 23.11493 2023-06-13 12:00:00 #> 3 …HR.4412/64891730060a4_U Cygnus cygnus (Linn… NA 61.38348 22.97288 2023-06-13 12:00:00 #> 4 …HR.4412/648917378a3b6_U Cygnus cygnus (Linn… NA 62.76028 24.15774 2023-06-13 12:00:00 #> 5 …HR.4412/64891759be4c7_U Cygnus olor (J.F. G… NA 63.40045 21.48901 2023-06-13 12:00:00 #> 6 …HR.4412/6489175adc05f_U Cygnus cygnus (Linn… NA 60.78752 21.39263 2023-06-13 12:00:00 #> 7 …HR.4412/6489173a1db9b_U Cygnus cygnus (Linn… NA 64.31374 26.68643 2023-06-13 12:00:00 #> 8 …HR.4412/648917456a396_U Cygnus cygnus (Linn… NA 61.87986 25.19067 2023-06-13 12:00:00 #> 9 …HR.4412/648917454912b_U Cygnus cygnus (Linn… NA 60.42215 24.00099 2023-06-13 12:00:00 #> 10 …HR.4412/64891750e74e7_U Cygnus cygnus (Linn… NA 63.86383 27.70835 2023-06-13 12:00:00 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality ```

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") sapply(list(birds, linnut, faglar), nrow) #> [1] 10 10 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: 47159747 #> A data.frame [1001 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 991 more records and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality ```

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] 47159747 ``` ## 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: 5303 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3211/167313561-U Vulpes vulpes (Linn… NA 60.18049 25.04838 #> 2 …HR.3211/167310567-U Vulpes vulpes (Linn… NA 60.2241 24.89373 #> 3 …KE.176/64894ccdd5de884fa20e2972#Unit1 Vulpes vulpes (Linn… 1 60.21118 24.90744 #> 4 …KE.176/6489506dd5de884fa20e2976#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 5 …KE.176/648802d6d5de884fa20e290d#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 6 …KE.176/648802c7d5de884fa20e290c#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 7 …HR.3211/167167234-U Vulpes vulpes (Linn… NA 60.20261 24.86879 #> 8 …HR.3211/166968734-U Vulpes vulpes (Linn… NA 60.5 21.9 #> 9 …HR.3211/166944731-U Vulpes vulpes (Linn… NA 60.17493 24.74123 #> 10 …KE.176/64869a52d5de884fa20e28ae#Unit1 Vulpes vulpes (Linn… 1 60.23885 25.12012 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality ```

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: 5303 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …HR.3211/167313561-U Vulpes vulpes (Linn… NA 60.18049 25.04838 #> 2 …HR.3211/167310567-U Vulpes vulpes (Linn… NA 60.2241 24.89373 #> 3 …KE.176/64894ccdd5de884fa20e2972#Unit1 Vulpes vulpes (Linn… 1 60.21118 24.90744 #> 4 …KE.176/6489506dd5de884fa20e2976#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 5 …KE.176/648802d6d5de884fa20e290d#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 6 …KE.176/648802c7d5de884fa20e290c#Unit1 Vulpes vulpes (Linn… 1 60.11016 25.01864 #> 7 …HR.3211/167167234-U Vulpes vulpes (Linn… NA 60.20261 24.86879 #> 8 …HR.3211/166968734-U Vulpes vulpes (Linn… NA 60.5 21.9 #> 9 …HR.3211/166944731-U Vulpes vulpes (Linn… NA 60.17493 24.74123 #> 10 …KE.176/64869a52d5de884fa20e28ae#Unit1 Vulpes vulpes (Linn… 1 60.23885 25.12012 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality ```

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 = "municipality", aggregate = "species") ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 309 #> A data.frame [10 x 2] #> municipality n_species #> 1 Raasepori 2038 #> 2 Virolahti 1978 #> 3 Kouvola 1508 #> 4 Rääkkylä 1367 #> 5 Kemiönsaari 2008 #> 6 Hanko 1945 #> 7 Parainen 1858 #> 8 Helsinki 1980 #> 9 Kuopio 1345 #> 10 Kotka 1719 ```

## 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 = "-date_time") ```
Click to show/hide output. ```r #> Records downloaded: 10 #> Records available: 47159747 #> A data.frame [10 x 11] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 6 more variables: #> coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality ```

### 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: 47159747 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality ```

#### 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: 47159747 #> A data.frame [10 x 12] #> record_id scientific_name abundance lat_wgs84 lon_wgs84 #> 1 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983 #> 2 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111 #> 3 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111 #> 4 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111 #> 5 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111 #> 6 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111 #> 7 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111 #> 8 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111 #> 9 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111 #> 10 …JX.1594382#29 Dendrocopos major (… NA 64.12716 23.99111 #> ...with 0 more record and 7 more variables: #> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification, #> record_reliability, record_quality ```

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.