I have downloaded occurrence data using the rgbif
package successfully. However, the attributes that are available seem restricted. Specifically, I would like: Habitat, Identification remarks and Occurrence remarks. Is there a way to obtain that information via R?
library(rgbif)
# Request data
occ_download(pred_and(pred("phylumKey", 35), pred("gadm","ETH")),
format = "SIMPLE_CSV")
# Check download status using occurrence number,
# see result in console from previous step
occ_download_wait("download occurrence number")
# Load data
df <- occ_download_get("download occurrence number") %>%
occ_download_import()
Explore data : no attributes for habitat, etc
names(df)
[1] "gbifID" "datasetKey" "occurrenceID" "kingdom"
[5] "phylum" "class" "order" "family"
[9] "genus" "species" "infraspecificEpithet" "taxonRank"
[13] "scientificName" "verbatimScientificName" "verbatimScientificNameAuthorship" "countryCode"
[17] "locality" "stateProvince" "occurrenceStatus" "individualCount"
[21] "publishingOrgKey" "decimalLatitude" "decimalLongitude" "coordinateUncertaintyInMeters"
[25] "coordinatePrecision" "elevation" "elevationAccuracy" "depth"
[29] "depthAccuracy" "eventDate" "day" "month"
[33] "year" "taxonKey" "speciesKey" "basisOfRecord"
[37] "institutionCode" "collectionCode" "catalogNumber" "recordNumber"
[41] "identifiedBy" "dateIdentified" "license" "rightsHolder"
[45] "recordedBy" "typeStatus" "establishmentMeans" "lastInterpreted"
[49] "mediaType" "issue"
Thanks to the comment by @Grzegorz Sapijaszko I was able to resolve the issue. I had requested SIMPLE_CSV
as the file format for download (as in many of the tutorials I had followed). However, the number of attributes available from a SIMPLE_CSV
is limited. To get all available data, use DWCA
as a method of download. This downloads data into multiple separate text files into a folder.
Here is the updated code (also a simple tweak to make it more easily reproducible by saving the download number into a res
object and changed the phylum to one with fewer species to speed up the example).
library(rgbif)
# Request data
res<-occ_download(pred_and(pred("phylumKey", 13), pred("gadm","ETH")),
format = "DWCA")#!!!! change SIMPLE_CSV to DWCA
# Check download status using occurrence number,
# see result in console from previous step
occ_download_wait(res)
# Load data
df <- occ_download_get(res) %>%
occ_download_import()