Download species sighting data using the BIONET API (https://data.bionet.nsw.gov.au/)

get_bionet.R

get_bionet <- function(x, username, password, outdir, prefix='bionet_',
                       filetype='csv', matchtype='startswith',
                       return_data=FALSE, quiet=FALSE, verbose=FALSE) {
  # x: a vector of species names
  # username, password (optional): credentials for BIONET service
  # outdir: output directory  (must exist)
  # prefix: csv/rds files will be saved in outdir following the pattern
  #         outdir/prefix_Genus_species_yyyymmddHHMMSS.csv/rds
  # filetype: must be one of csv or rds
  # matchtype: must be one of 'startswith', 'contains', or 'equals'.
  #            Records will be returned where scientificName starts with,
  #            contains, or equals the search string, respectively. Using
  #            starts with can be useful when subspecies are desired, but
  #            may also return unwanted taxa (e.g. hybrids).
  # return_data: should occurrence data be returned to R? Consider memory requirements
  # quiet: should progress messages be suppressed?
  # verbose: should GET request messages be shown?
  #
  # Returns a list of tibbles containing all fields and records returned by the
  # query.
  require(httr)
  require(dplyr)
  x <- setdiff(unique(x), NA)
  stopifnot(dir.exists(outdir))
  filetype <- match.arg(filetype, c('csv', 'rds'))
  matchtype <- match.arg(matchtype, c('startswith', 'contains', 'equals'))
  auth <- !missing(username) & !missing(password)
  if(!auth & !quiet) {
    message('No credentials supplied - retrieving public data')
  } else {
    message('Using supplied credentials')
  }
  url <- 'https://data.bionet.nsw.gov.au'
  service <- 'biosvcapp/odata/SpeciesSightings_CoreData/'
  occ <- lapply(x, function(species, username, password) {
    if(!quiet) message('  - ', species)
    s <- switch(matchtype,
                startswith="startswith(toupper(scientificName), '%s')",
                contains="contains(toupper(scientificName), '%s')",
                equals="toupper(scientificName) eq '%s'")
    q <- list("$filter"=sprintf(s, toupper(species)))
    if(auth) {
      r <- GET(url, path=service, query=q, config=list(
        authenticate(username, password, "basic"),
        if(verbose) verbose() else NULL))
    } else {
      r <- GET(url, path=service, query=q,
               config=if(verbose) list(verbose()) else NULL)
    }
    stop_for_status(r)
    value <- content(r)$value
    dat <- lapply(value, function(x) {
      Filter(Negate(is.null), x)
    }) %>% bind_rows
    f <- sprintf('%s/%s%s_%s.%s', outdir, prefix, gsub(' +', '_', species),
                 format(Sys.time(), '%Y%m%d%H%M%S'), filetype)
    if(filetype=='csv') write.csv(dat, f, row.names=FALSE)
    if(filetype=='rds') saveRDS(dat, f)
    if(isTRUE(return_data)) dat else NULL
  }, username=username, password=password)
  if(isTRUE(return_data)) {
    occ <- setNames(occ, x)
    return(occ)
  } else {
    return(invisible(NULL))
  }
}
        

Example

library(sp)
library(httr)
library(dplyr)
occ <- get_bionet('Ninox strenua', outdir=tempdir(), return_data=TRUE)
coordinates(occ$`Ninox strenua`) <- ~decimalLongitude+decimalLatitude
plot(subset(countries110, name=='Australia'))
points(occ$`Ninox strenua`, pch='.', col=2)