R/check_assertions.R

In bioatlas/r-functionality: Swedish Biodiversity Data Infrastructure Data and Resources in R

#' Check assertions in occurrences object
#'
#' This provides a data.frame detailing the assertions that are found in a dataset returned from \code{\link{occurrences}}.
#'
#' @references \url{https://api.bioatlas.se/}, \samp{http://records.bioatlas.se/ws/assertions/codes}
#'  
#' @param x list: an object returned from \code{\link{occurrences}}
#' 
#' @return A dataframe of assertions column names, descriptions and categories/error codes. If no assertions are in the dataset, NULL is returned.
#'
#' @examples
#' #download species data with all possible assertions
#' \dontrun{
#'  x <- occurrences(taxon="golden plover",download_reason_id=10,qa=sbdi_fields("assertions")$name)
#'  asserts <- check_assertions(x) #data.frame of assertions, their description and column names
#'  asserts$description # List out descriptions of all (current) assertions
#'
#'  tmp <- x$data[,names(x$data) %in% asserts$name] ## assertion columns from data
#'  which(colSums(tmp)>0) ## discard those not seen in the data
#' }
#' @export
check_assertions <- function(x) {
  # ALA4R::check_assertions(x)
  
    if (! inherits(x, "occurrences")) {
      stop("check_assertions must have an object of class occurrences from e.g., ", getOption("ALA4R_server_config")$occurrences_function, "() in the ", getOption("ALA4R_server_config")$brand, " package")
    }
    ass <- sbdi_fields("assertions", as_is=TRUE) ## get all assertion fields
    ass$occurColnames <- NA
    temp_description <- rename_variables(ass$description, type="assertions")
    for (coi in colnames(x$data)) {
      ## match on either name or description
      tt <- which(coi==ass$name | coi==temp_description)
      if (length(tt)>0)
        ass$occurColnames[tt[1]] <- coi #place the colname
    }
    ass <- na.omit(ass)
    if (nrow(ass)<1) {
      if (sbdi_config()$warn_on_empty) {
        warning("no assertions in data")
      }
      NULL
    } else {
      ass
    }
  
}