lookup GBIF occurrence counts for species name

gistfile1.txt

#install.packages('rgbif')

fresh <- read.csv('Fresh.species.csv')

#fresh <- data.frame(predator.taxon.name = c('Arius felis', 'Ariopsis felis', 'Gadus morhua'))

# appends columns gbifSpeciesKey, gbifOccCount when gbif knows about species and has occurrences
appendOccCount <- function(df) { 
  names <- df$predator.taxon.name 

  message('resolving gbif species keys')
  df$gbifSpeciesKeys <- unlist(lapply(names, function(name) { 
    message('.', appendLF=FALSE); 
    taxon <- rgbif::name_backbone(name=name, rank='species')
    if (taxon$matchType == 'NONE') {
      NA
    } else {
      taxon$speciesKey    
    }
  }))
  
  message('retrieving occurrence counts for gbif species keys')
  df$gbifOccCount <- unlist(lapply(df$gbifSpeciesKeys, function(key) {
    message('.', appendLF=FALSE); 
    if (is.na(key)) {
      NA
    } else {
      rgbif::occ_count(taxonKey=key)
    }
  }))

  df
}

fresh.with.occ <- appendOccCount(fresh)