Get plant species occurrence records from the AVH hub of ALA (ala.org.au)

getAVH.R

getAVH <- function(species, sleepInterval=0, progress=TRUE, verbose=FALSE, outpath=NULL) {
  require(httr)
  require(plyr)
  avh <- handle('http://biocache.ala.org.au')
  .getAVH <- function(x) {
    sp <- gsub('\\s+', '+', x)
    cfg <- c(accept_json())
    if (isTRUE(verbose)) cfg <- c(cfg, verbose())
    tt1 <- GET(handle=avh, path='ws/occurrences/search', 
               config=cfg,
               query=list(q=sprintf('raw_name:%s', sp),
                          pageSize=0,
                          qc='data_hub_uid:dh2',
                          fq='geospatial_kosher:true',
                          facet='off',
                          fl='year'))
    .count <- content(tt1)$totalRecords
    
    if (.count > 1) {
      
      tt2 <- GET(handle=avh, path='ws/occurrences/search', 
                 config=cfg,
                 query=list(q=sprintf('raw_name:%s', sp),
                            pageSize=.count,
                            qc='data_hub_uid:dh2',
                            fq='geospatial_kosher:true',
                            facet='off'))
      res <- content(tt2)
      res$requestTime <- Sys.time()
      if (length(res$occurrences) != .count) {
        warning('Not all occurrences were downloaded for species ', x, 
                call.=FALSE)
        res <- 'Error'
      }
    } else {
      warning('No records for ', x, call.=FALSE)
      res <- 'No records'
    }
    if (!is.null(outpath)) {
      save(res, file=paste0(outpath, '/', gsub('\\s+', '_', x), '.rda'))
    }
    Sys.sleep(sleepInterval)
    res
  }
  
  RES <- llply(species, function(x) tryCatch(.getAVH(x), error=function(e) {
    warning(x, ' failed.', call.=FALSE)
    return('Error')
  }), 
               .progress=if (isTRUE(progress)) {
                 create_progress_bar(name = "text") 
               } else 'none')
  names(RES) <- species
  RES
}


# Examples
# out1 <- getAVH('banksia ornata', 'callitris rhomboidea', 'Ballota nigra subsp. foetida')
# str(out1$'banksia ornata', max=1)