R/bdsummary.R

In bdvis: Biodiversity Data Visualizations

#' Provides summary of biodiversity data
#'
#' Calculates some general indicators of the volume, spatial, temporal and
#' taxonomic aspects of the provided data set.
#'
#' The function returns information on the volume of the data set (number of
#' records), temporal coverage (minimum and maximum dates), taxonomic coverage
#' (brief breakdown of the records by taxonomic levels) and spatial coverage
#' (coordinates of the edges of the bounding box containing all records and
#' division of covered area in degree cells) of the records.
#'
#' To update spatial grid data to dataset, please use \link{format_bdvis} or 
#' \link{getcellid} function before using bdsummary.
#'
#' @import sqldf
#' @param indf input data frame containing biodiversity data set
#'
#' @return No return value, just displays the summary in console
#'
#' @export
#' @family Data preparation functions
#' @examples \dontrun{
#'  if (requireNamespace("rinat", quietly=TRUE)) {
#'   inat <- get_inat_obs_project("reptileindia") 
#'   inat <- format_bdvis(inat, source="rinat")
#'   bdsummary(inat)
#'  }
#'}
bdsummary <- function(indf){
  if(is.emptydf(indf)){
    cat("No data in dataset \n")
    return()
  }
  cellcover <- length(unique(indf$Cell_id))
  names(indf) <- gsub("\\.","_",names(indf))
  cat(paste("\n Total no of records =",dim(indf)[1],"\n"))
  cat(paste("\n Temporal coverage... \n"))
  if("Date_collected" %in% colnames(indf)){
    cat(paste(" Date range of the records from ",
              range(as.Date(indf$Date_collected),na.rm=T)[1]," to ",
              range(as.Date(indf$Date_collected),na.rm=T)[2],"\n"))
  }
  cat(paste("\n Taxonomic coverage... \n"))
  cat(paste(" No of Families : ",length(unique(indf$Family)),"\n"))
  cat(paste(" No of Genus : ",length(unique(indf$Genus)),"\n"))
  cat(paste(" No of Species : ",length(unique(indf$Scientific_name)),"\n"))
  cat(paste("\n Spatial coverage ... \n"))
  cat(paste(" Bounding box of records ",min(indf$Latitude,na.rm=T),",",
            min(indf$Longitude,na.rm=T),
            " - ",max(indf$Latitude,na.rm=T),",",max(indf$Longitude,na.rm=T),
            "\n"))
  if (!("cell_id" %in% colnames(indf))){
    indf <- getcellid(indf)
  }
  cat(paste(" Degree celles covered : ",cellcover,"\n"))
  latrng <- ceiling(max(indf$Latitude,na.rm=T))-ceiling(min(indf$Latitude,
                                                            na.rm=T))
  longrng <- ceiling(max(indf$Longitude,na.rm=T))-ceiling(min(indf$Longitude,
                                                              na.rm=T))
  cat(paste(" % degree cells covered : ",(cellcover/(latrng * longrng))*100,
            "\n"))
}