#' Get the taxonomical heirarchy for a given taxon
#'
#' Given the Taxon Version Key (a 16-character string), this function get details
#' of the taxonomical heirarchy above the given TVK. This gives the rank, name and
#' preferred Taxon Version Key for each level of the taxonomy
#'
#' @export
#' @param tvks A Taxon Version Key (TVK) which is a 16-character string ID
#' @param ... Further named parameters passed on to \code{\link[httr]{GET}}
#' @return A dataframe containing the JSON object returned by the NBN Gateway.
#' @author Tom August, CEH \email{tom.august@@ceh.ac.uk}
#' @seealso \code{\link{getFeature}}, \code{\link{getOccurrences}}
#' @examples \dontrun{
#' t <- getTaxonomy("NHMSYS0000528028") # Myotis daubentonii (Daubenton's Bat)
#' }
getTaxonomy <- function(tvks=NULL, ...) {
## return a JSON object (list of lists)
json <- runnbnurl(service = "ancestry",
tvks = tvks,
... = ...)
if (length(json) > 0) {
## find the unique names that are used in occ
n <- unique(unlist(c(sapply(json, names))))
## dimension a matrix for the required number of rows and cols
d <- matrix(nrow=length(json), ncol=length(n),
dimnames=list(seq(1:length(json)),n))
## now we can go through the list and insert
## the values into the correct cells of the matrix
## This should be quick because the matrix is pre-allocated
for (i in 1:length(json)) {
for (j in 1:length(json[[i]])) {
k <- grep(names(json[[i]][j]),n)
d[i,k] <- json[[i]][[j]]
}
}
## cooerce the matrix to a data.frame
d <- as.data.frame(d)
## we are only interested in presences (not absences)
if ("absence" %in% colnames(d)) {
d <- d[which(d$absence == FALSE),]
}
return(d[c('rank','name','ptaxonVersionKey')])
} else {
return(NULL)
}
}
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