R/dc.zones.R

In jfrench/smerc: Statistical Methods for Regional Counts

#' Determine zones for the Double Connected scan test
#'
#' \code{dc.zones} determines the zones for the Double
#' Connected scan test (\code{\link{dc.test}}).  The
#' function returns the zones, as well as the associated
#' test statistic, cases in each zone, the expected number
#' of cases in each zone, and the population in each zone.
#'
#' Every zone considered must have a total population less
#' than \code{ubpop * sum(pop)}.  Additionally, the maximum
#' intercentroid distance for the regions within a zone must
#' be no more than \code{ubd * the maximum intercentroid
#' distance across all regions}.
#' @inheritParams dmst.test
#' @inheritParams mst.all
#' @inheritParams flex.zones
#' @return Returns a list with elements: \item{zones}{A list
#'   contained the location ids of each potential cluster.}
#'   \item{loglikrat}{The loglikelihood ratio for each zone
#'   (i.e., the log of the test statistic).}
#'   \item{cases}{The observed number of cases in each
#'   zone.} \item{expected}{The expected number of cases
#'   each zone.} \item{pop}{The total population in each
#'   zone.}
#' @author Joshua French
#' @references Costa, M.A. and Assuncao, R.M. and Kulldorff,
#'   M. (2012) Constrained spanning tree algorithms for
#'   irregularly-shaped spatial clustering, Computational
#'   Statistics & Data Analysis, 56(6), 1771-1783.
#'   <doi:10.1016/j.csda.2011.11.001>
#' @export
#' @examples
#' data(nydf)
#' data(nyw)
#' coords <- as.matrix(nydf[, c("longitude", "latitude")])
#' # find zone with max statistic starting from each individual region
#' all_zones <- dc.zones(coords,
#'   cases = floor(nydf$cases),
#'   nydf$pop, w = nyw, ubpop = 0.25,
#'   ubd = .25, longlat = TRUE
#' )
dc.zones <- function(coords, cases, pop, w,
                     ex = sum(cases) / sum(pop) * pop,
                     ubpop = 0.5, ubd = 1, longlat = FALSE,
                     cl = NULL, progress = TRUE) {
  # sanity checking
  arg_check_dmst_zones(
    coords = coords, cases = cases,
    pop = pop, w = w, ex = ex,
    ubpop = ubpop, ubd = ubd,
    longlat = longlat, type = "all",
    progress = progress
  )
  # setup various arguments and such
  ty <- sum(cases) # total number of cases
  # intercentroid distances
  d <- gedist(as.matrix(coords), longlat = longlat)
  # upperbound for population in zone
  max_pop <- ubpop * sum(pop)
  # find all neighbors from each starting zone within distance upperbound
  nn <- nndist(d, ubd)

  out <- mst.all(
    neighbors = nn, cases = cases, pop = pop,
    w = w, ex = ex, ty = ty, max_pop = max_pop,
    type = "all", nlinks = "two", early = TRUE,
    cl = cl, progress = progress
  )
  # return results in a list
  prep.mst(out)
}