#' Create a checklist.
#'
#' @usage checklist(scientificname = NULL, taxonid = NULL, datasetid = NULL,
#' nodeid = NULL, instituteid = NULL, areaid = NULL, startdate = NULL, enddate = NULL,
#' startdepth = NULL, enddepth = NULL, geometry = NULL, redlist = NULL,
#' hab = NULL, wrims = NULL, dropped = NULL, flags = NULL, exclude = NULL,
#' verbose = FALSE)
#' @param scientificname the scientific name.
#' @param taxonid the taxon identifier (WoRMS AphiaID).
#' @param datasetid the dataset identifier.
#' @param nodeid the OBIS node identifier.
#' @param instituteid the OBIS institute identifier.
#' @param areaid the OBIS area identifier.
#' @param startdate the earliest date on which occurrence took place.
#' @param enddate the latest date on which the occurrence took place.
#' @param startdepth the minimum depth below the sea surface.
#' @param enddepth the maximum depth below the sea surface.
#' @param geometry a WKT geometry string.
#' @param redlist include only IUCN Red List species.
#' @param hab include only IOC-UNESCO HAB species.
#' @param wrims include only WRiMS species.
#' @param dropped only include dropped records (\code{TRUE}), exclude dropped records (\code{NULL}) or include dropped records (\code{include}).
#' @param flags quality flags which need to be set.
#' @param exclude quality flags to be excluded from the results.
#' @param verbose logical. Optional parameter to enable verbose logging (default = \code{FALSE}).
#' @return The checklist.
#' @examples
#' taxa <- checklist(scientificname = "Tellinidae")
#' taxa <- checklist(geometry = "POLYGON ((2.3 51.8, 2.3 51.6, 2.6 51.6, 2.6 51.8, 2.3 51.8))")
#' taxa <- checklist(areaid = 10181)
#' @export
checklist <- function(
scientificname = NULL,
taxonid = NULL,
datasetid = NULL,
nodeid = NULL,
instituteid = NULL,
areaid = NULL,
startdate = NULL,
enddate = NULL,
startdepth = NULL,
enddepth = NULL,
geometry = NULL,
redlist = NULL,
hab = NULL,
wrims = NULL,
dropped = NULL,
flags = NULL,
exclude = NULL,
verbose = FALSE
) {
result_list <- list()
last_page <- FALSE
partition <- 0
fetched <- 0
while (!last_page) {
query <- list(
scientificname = handle_vector(scientificname),
taxonid = handle_vector(taxonid),
datasetid = handle_vector(datasetid),
nodeid = handle_vector(nodeid),
instituteid = handle_vector(instituteid),
areaid = handle_vector(areaid),
startdate = handle_date(startdate),
enddate = handle_date(enddate),
startdepth = startdepth,
enddepth = enddepth,
geometry = geometry,
redlist = handle_logical(redlist),
hab = handle_logical(hab),
wrims = handle_logical(wrims),
dropped = dropped,
flags = handle_vector(flags),
exclude = handle_vector(exclude),
partition = partition
)
result <- http_request("GET", "checklist", query, verbose)
if (is.null(result)) return(invisible(NULL))
text <- content(result, "text", encoding = "UTF-8")
res <- fromJSON(text, simplifyVector = TRUE)
total <- res$total
partition = partition + 1
if (!("partitions" %in% names(res)) || partition >= res$partitions) {
last_page <- TRUE
}
if (is.data.frame(res$results)) {
result_list[[partition + 1]] <- res$results
fetched <- fetched + nrow(res$results)
}
log_progress(fetched, total)
}
if (length(result_list) > 0) {
data <- bind_rows(result_list)
data <- data[order(data$records, decreasing = TRUE),]
return(as_tibble(data %>% arrange(desc(.data$records))))
} else {
return(tibble())
}
}
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