#' Get occdat via occ command
#'
#' @param species a string containing all species name and country (if any) in the end, separate by ','.
#' @return a list of occdat, exist species names, all species names, exist speices number, all species number, country name and the indicater of specific country
#' @examples
#' data <- Getoccdat('Pinus contorta,Danaus plexippus,Canada')
#' @import rgbif
#' @import spocc
#' @import countrycode
#' @export
Getoccdat <- function(species){
##Read the names
#species_c <- strsplit(species, ",")
#species_c <- species_c[[1]]
#species_n <- length(species_c)
##Check if user want see the occurrence data in specific country
#countryname <- species_c[species_n]
#country_code <- countrycode(countryname, 'country.name', 'iso2c')
#checkcountry <- !is.na(country_code)
#if(checkcountry == TRUE){
#}
namelist <- Readname(species)
#namelist contains the name "namelist[[1]]" the species number"namelist[[2]]"
#the indicater of the country "namelist[[3]]" and the countrycode "namelist[[4]]"
species_c <- namelist[[1]]
species_n <- namelist[[2]]
checkcountry <- namelist[[3]]
country_code <- namelist[[4]]
countryname <- namelist[[5]]
#Searching for the occurrence data
if(checkcountry == TRUE){
species_c <- species_c[1:species_n]
dat <- occ(query = species_c, from = 'gbif', limit = 300, has_coords = TRUE, gbifopts = list(country = country_code))
#Checking if some species are missing in this area
s_exist <- logical(length = species_n)
for(i in seq_along(species_c)){
s_exist[i] <- if(length(dat$gbif$data[i][[1]]) == 0){FALSE}else{TRUE}
}
species_ce <- species_c[s_exist]
species_ne <- length(species_ce)
}else{
dat <- occ(query = species_c, from = 'gbif', limit = 300, has_coords = TRUE)
#Checking if some species are missing in this area
s_exist <- logical(length = species_n)
for(i in seq_along(species_c)){
s_exist[i] <- if(length(dat$gbif$data[i][[1]]) == 0){FALSE}else{TRUE}
}
species_ce <- species_c[s_exist]
species_ne <- length(species_ce)
}
#If no specie is in that area, programme will return the species occurrance data in whole world
if(species_ne == 0){
dat <- occ(query = species_ce, from = 'gbif', limit = 300, has_coords = TRUE)
}
list(dat, species_ce, species_c, species_ne, species_n, countryname, checkcountry)
}
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