R/cepp.test.R

In jfrench/smerc: Statistical Methods for Regional Counts

#' Cluster Evalation Permutation Procedure Test
#'
#' \code{cepp.test} implements the Cluster Evaluation
#' Permutation Procedure test of Turnbull et al. (1990)
#' for finding disease clusters.
#'
#' @inheritParams scan.test
#' @inheritParams casewin
#' @inheritParams bn.test
#' @param nstar The size of the at-risk population
#' in each window.
#' @param simdist A character string indicating whether the
#' simulated data should come from a \code{"multinomial"}
#' or \code{"poisson"} distribution.  The default is
#' \code{"multinomial"}, which fixes the total number of
#' cases observed in each simulated data set.
#'
#' @return Returns a \code{smerc_cluster} object.
#' @author Joshua French
#' @seealso \code{\link{print.smerc_cluster}},
#' \code{\link{summary.smerc_cluster}},
#' \code{\link{plot.smerc_cluster}},
#' \code{\link{scan.test}}
#' @export
#' @references Bruce W. Turnbull, Eric J. Iwano, William S. Burnett,
#'   Holly L. Howe, Larry C. Clark (1990).  Monitoring for Clusters of Disease:
#'   Application to Leukemia Incidence in Upstate New York,
#'   American Journal of Epidemiology, 132(supp1):136-143.
#'   <doi:10.1093/oxfordjournals.aje.a115775>
#' @examples
#' data(nydf)
#' data(nyw)
#' coords <- with(nydf, cbind(x, y))
#' cases <- nydf$cases
#' pop <- nydf$pop
#' out <- cepp.test(
#'   coords = coords, cases = cases, pop = pop,
#'   nstar = 1000, alpha = 0.99
#' )
#' plot(out)
#' summary(out)
#'
#' # better plotting
#' if (require("sf", quietly = TRUE)) {
#'    data(nysf)
#'    plot(st_geometry(nysf), col = color.clusters(out))
#' }
cepp.test <- function(coords, cases, pop, nstar,
                      ex = sum(cases) / sum(pop) * pop,
                      nsim = 499, alpha = 0.10,
                      longlat = FALSE,
                      simdist = "multinomial") {
  # sanity checking
  arg_check_cepp_test(
    coords = coords, cases = cases,
    pop = pop, nstar = nstar, ex = ex,
    nsim = nsim, alpha = alpha,
    longlat = longlat, simdist = simdist
  )

  coords <- as.matrix(coords)

  # intercentroid distances
  d <- gedist(coords, longlat = longlat)

  # find smallest windows with at least n* pop
  nn <- casewin(d, pop, nstar)

  # determine nn weights
  wts <- cepp.weights(nn, pop, nstar)

  # observed number of cases in each window
  cstar <- sapply(seq_along(nn), function(i) {
    sum(cases[nn[[i]]] * wts[[i]])
  }, USE.NAMES = FALSE)

  csim <- cepp.sim(
    nsim = nsim, nn = nn, ty = sum(cases),
    ex = ex, wts = wts, simdist = simdist
  )

  pvalue <- mc.pvalue(cstar, csim)

  op <- order(cstar, decreasing = TRUE)

  # for the unique, non-overlapping clusters in order of
  # significance, find the associated test statistic,
  # p-value, centroid, window radius, cases in window,
  # expected cases in window, population in window,
  # standarized mortality ratio, relative risk
  sig_regions <- nn[op]
  sig_tstat <- cstar[op]
  sig_p <- pvalue[op]
  sig_wts <- wts[op]

  # significant, ordered, non-overlapping clusters and
  # information
  pruned <- sig_noc_mod(
    tobs = cstar, zones = nn, pvalue = pvalue,
    alpha = alpha, order_by = "tobs"
  )

  smerc_cluster(
    tobs = pruned$tobs, zones = pruned$zones,
    pvalue = pruned$pvalue, coords = coords,
    cases = cases, pop = pop, ex = ex,
    longlat = longlat, method = "CEPP",
    rel_param = list(
      nstar = nstar,
      simdist = simdist,
      nsim = nsim
    ),
    alpha = alpha, w = NULL, d = d,
    weights = sig_wts[pruned$sig]
  )
}

#' Argument checking for cepp.test
#'
#' Check the arguments of the cepp.test function
#'
#' @param coords A matrix of coordinates
#' @param cases A vector of case counts
#' @param pop A vector of population values
#' @param nstar Window radius (in terms of population)
#' @param ex A vector of expected counts
#' @param nsim Number of simulations to perform
#' @param longlat Logical. TRUE = great circle distance
#' @param alpha Significance level
#' @param simdist Simulation distribution
#'
#' @return NULL
#' @noRd
arg_check_cepp_test <- function(coords, cases, pop, nstar,
                                ex, nsim, longlat, alpha,
                                simdist) {
  arg_check_coords(coords)
  N <- nrow(coords)
  arg_check_cases(cases, N)
  arg_check_pop(pop, N)
  arg_check_nstar(nstar, pop)
  arg_check_ex(ex, N)
  arg_check_alpha(alpha)
  arg_check_nsim(nsim)
  arg_check_longlat(longlat)
  arg_check_simdist(simdist)
}