#' Create a list of datasets.
#'
#' @usage dataset(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, hasextensions = 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 hasextensions which extensions need to be present (e.g. MeasurementOrFact, DNADerivedData, default = \code{NULL}).
#' @param exclude quality flags to be excluded from the results.
#' @param verbose logical. Optional parameter to enable verbose logging (default = \code{FALSE}).
#' @return The datasets.
#' @examples
#' datasets <- dataset(scientificname = "Tellinidae")
#' datasets <- dataset(geometry = "POLYGON ((2.3 51.8, 2.3 51.6, 2.6 51.6, 2.6 51.8, 2.3 51.8))")
#' datasets <- dataset(areaid = 10181)
#' @export
dataset <- 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,
hasextensions = NULL,
exclude = NULL,
verbose = FALSE
) {
skip <- 0
result_list <- list()
last_page <- FALSE
i <- 1
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),
hasextensions = handle_vector(hasextensions),
exclude = handle_vector(exclude),
skip = skip,
size = page_size()
)
result <- http_request("GET", "dataset", query, verbose)
if (is.null(result)) return(invisible(NULL))
text <- content(result, "text", encoding = "UTF-8")
res <- fromJSON(text, simplifyVector = TRUE)
total <- res$total
skip <- skip + page_size()
if (!is.null(res$results) && is.data.frame(res$results) && nrow(res$results) > 0) {
res$results$node_id <- sapply(res$results$nodes, function(x) { return(paste0(x$id, collapse = ",")) })
res$results$node_name <- sapply(res$results$nodes, function(x) { return(paste0(x$name, collapse = ",")) })
res$results <- res$results[,!(names(res$results) %in% c("node", "feed", "institutes"))]
result_list[[i]] <- res$results
fetched <- fetched + nrow(res$results)
log_progress(fetched, total)
i <- i + 1
} else {
last_page <- TRUE
}
}
data <- bind_rows(result_list)
return(as_tibble(data))
}
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