如何从 rgbif 中的搜索中保存出现数据

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)

Answer 2

To transform the object with class "gbif" to a data.frame you can do OS.df <- do.call(rbind.data.frame, OS) .

For occ_download you need to set a username, email and password. As by gbif website (http://www.gbif.org/developer/occurrence#download) Occurrence downloads are created asynchronously - the user requests a download and, once complete, is sent and email with a link to the resulting file.

OD <- occ_download(user = "name", pwd = "pass", email = "e@mail.com", "scientificName = Lupinus", "hasCoordinate = TRUE", "continent = africa,europe,asia","basisOfRecord = PRESERVED_SPECIMEN","decimalLatitude >= -1.50750278","decimalLatitude <= 47.62390556","decimalLongitude >= -18.75250000","decimalLongitude <= 52.85138889")

returns an object of class gbif download and you should receive a download link per mail or visit http://www.gbif.org/user/download to download directly. This can be done through the download option at gbif.org as well.

<<gbif download>> Username: philipprobeck E-mail: phill@gmx.li Download key: 0078579-160910150852091