#' Function for downloading data from GBIF
#'
#' library(rgbif) #
#' options(gbif_user="myusername",
#' gbif_pwd="mypassword", gbif_email="myemailaddress")
#' download.mg("Canis lupus")
#'@sp=character vector indicating column containing species names
#'
downloadgbif<- function(sp) {
results <- NULL
for (i in 1:length(sp)) {
# get species key
key <- name_backbone(name = sp[i])$speciesKey
if(is.null(key)){
next
} else {
count<-occ_count(taxonKey=key)
}
if(count < 2){
next
} else {
key1 <- paste("taxonKey = ", key)
did <- occ_download(key1, "hasCoordinate = TRUE", "hasGeospatialIssue = FALSE")
id = did[1]
res <- try(suppressMessages(occ_download_get(id, overwrite = TRUE)), silent = T)
while (class(res) == "try-error") {
res <- try(suppressMessages(occ_download_get(id, overwrite = TRUE)), silent = T)
}
options(warn = -1)
res1 <- suppressMessages(occ_download_import(x = res))
options(warn = -0)
if(dim(res1)[1]==0){
next
} else {
spdat <- data.frame(species = sp[i], lat = res1$decimalLatitude, lon = res1$decimalLongitude,year=res1$year)
results <- rbind(spdat, results)
toremove <- list.files(pattern = ".zip")
file.remove(toremove)
}
}
}
return(results)
}
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