R/density_data.R

In Hackout2/mapData: Tools to help with mapping outbreak data

#' Density data
#'
#' Process a SpatialPointsDataFrame to give numbers of cases at each unique (x,y) location. Weighting by 1/(local population density) gives corrected numbers which can be used to calculate estimated prevalence.
#' @param points SpatialPointsDataFrame containing the line list of patients. Should include: 1) a slot \code{@@coords} with an n x 2 vector giving the x and y coordinates of each case. (More than one case can have the same co-ordinates.) 2) a slot \code{@@bbox} giving the maximum and minimum x and y co-ordinates.
#' @param weights If required, the local population density at each (x, y) coordinate.
#' @return A data frame containing x and y co-ordinates, and (weighted) counts. For use by other functions including \code{estimate_density}.
#'
#' @export
#'
#' @examples
#' if(require(sp)){
#' # simulate a line list of patient locations
#' my.linelist <- data.frame(	longitude = round(runif(100, 0, 10), 0.01),
#'								latitude = round(runif(100, 0, 10), 0.01)
#'							)
#' #transform patients dataframe into spatialpointsdataframe
#' pointspatients <- SpatialPointsDataFrame(my.linelist, data=data.frame(id=1:100))
#'
#' my.density.data <- density_data(pointspatients)
#' print(head( my.density.data ))
#' }

density_data <- function(pointspatients, weights=NULL){

                                        # x co-ordinates
    xs <- pointspatients@coords[which(!duplicated(paste(pointspatients@coords[,1], pointspatients@coords[,2]))),1]

                                        # y co-ordinates
    ys <- pointspatients@coords[which(!duplicated(paste(pointspatients@coords[,1], pointspatients@coords[,2]))),2]

                                        # number of cases at each point
    ns <- tapply(
        pointspatients@data[,1],
        paste(pointspatients@coords[,1], pointspatients@coords[, 2], sep=","),
        length)

    if(!is.null(weights))
        ns <- ns*weights

    return(data.frame(	x = xs,
                      y = ys,
                      count = ns,
                      row.names = 1:length(xs)
                      ))

}