R/check_assertions.R

In jjvanderwal/ALA4R: Atlas of Living Australia (ALA) 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}}.
#'
#' @author Atlas of Living Australia \email{support@@ala.org.au}
#' @references \url{http://api.ala.org.au/}
#' @references \url{http://biocache.ala.org.au/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
#' x=occurrences(taxon="golden bowerbird",download_reason_id=10,qa=ala_fields('assertions')$name)
#' asserts = check_assertions(x) #data.frame of assertions, their description and column names
#' asserts[0:86,5] # List out descriptions of all (current) assertions
#' 
#' @export
check_assertions = function(x) {
    if (any(class(x)=='occurrences')) {
        cois = colnames(x$data) #get the column names
        ass = ala_fields('assertions') #get the assertions
        ass$occurColnames = NA
        temp_description=rename_variables(ass$description,type="assertions")
        for(coi in cois) {
            tt=which(coi==ass$name | coi==temp_description)
            if (length(tt)==0) {
                next
            } else {
                ass$occurColnames[tt[1]] = coi #place the colname
            }
        }
        ass = na.omit(ass)
        if (nrow(ass)==0) {
            if (ala_config()$warn_on_empty) {
                warning('no assertions in data');
            }
            return(NULL)
        } else {
            return(ass)
        }
    } else {
        stop('check_assertions must have an object of class occurrences from e.g., occurrences() in the ALA4R package')
    }
}