How to save occurrence data from a search in rgbif

Question

I am a new R user and I am interested in downloading a particular set of data using rgbif. I did:

occ_search(scientificName = "Lupinus", hasCoordinate = TRUE, continent = c('africa', 'europe', 'asia'),
       basisOfRecord = "PRESERVED_SPECIMEN", decimalLatitude = '-1.50750278, 47.62390556',
       decimalLongitude = '-18.75250000, 52.85138889',
       fields = c('scientificName', 'decimalLatitude', 'decimalLongitude', 'country'), return = 'data')

Which works fine to do the search. However, what I would like to do is save the search as an object to create an .csv file of it. If I go:

OS <- occ_search(scientificName = "Lupinus", hasCoordinate = TRUE, continent = c('africa', 'europe', 'asia'),
       basisOfRecord = "PRESERVED_SPECIMEN", decimalLatitude = '-1.50750278, 47.62390556',
       decimalLongitude = '-18.75250000, 52.85138889',
       fields = c('scientificName', 'decimalLatitude', 'decimalLongitude', 'country'), return = 'data')

Then

OS1 <- as.data.frame(OS)

I get the following error:

Error in as.data.frame.default(occ) : cannot coerce class ""gbif"" to a data.frame

I also tried using occ_download this way:

OD <- occ_download("scientificName = Lupinus",
                       "hasCoordinate = TRUE",
                       "continent = africa,europe,asia",
                       "basisOfRecord = PRESERVED_SPECIMEN",
                       "decimalLatitude >= -1.50750278", 
                       "decimalLatitude <= 47.62390556",
                       "decimalLongitude >= -18.75250000",
                       "decimalLongitude <= 52.85138889")                        

And all I get is a file with 0 observations and 235 columns.

Any help will be highly appreciated!

Answer 1

The reason your occ_search output is not compatible with as.data.frame is in the continent = c('africa', 'europe', 'asia') argument. If you look at the length(OS) and str(OS), you will see that it actually has three data.frames in it. You can access the individual elements like this:

OS$europe
# or
OS['europe']
# or
OS[[1]]

You can combine these like this

OC1 <- rbind(OS$africa, OS$europe, OS$asia)

Or, if you are not going to know all the different names, like this:

do.call(rbind, OS)