smerc (version 1.3)

rflex.test: Restricted Flexibly-shaped Spatial Scan Test

Description

rflex.test performs the restricted flexibly shaped spatial scan test of Tango and Takahashi (2012).

Usage

rflex.test(
  coords,
  cases,
  pop,
  w,
  k = 50,
  ex = sum(cases)/sum(pop) * pop,
  type = "poisson",
  nsim = 499,
  alpha = 0.1,
  longlat = FALSE,
  alpha1 = 0.2,
  cl = NULL
)

Arguments

coords

An \(n \times 2\) matrix of centroid coordinates for the regions.

cases

The number of cases observed in each region.

pop

The population size associated with each region.

w

A binary spatial adjacency matrix for the regions.

k

An integer indicating the maximum number of regions to inclue in a potential cluster. Default is 10

ex

The expected number of cases for each region. The default is calculated under the constant risk hypothesis.

type

The type of scan statistic to compute. The default is "poisson". The other choice is "binomial".

nsim

The number of simulations from which to compute the p-value.

alpha

The significance level to determine whether a cluster is signficant. Default is 0.10.

longlat

The default is FALSE, which specifies that Euclidean distance should be used. If longlat is TRUE, then the great circle distance is used to calculate the intercentroid distance.

alpha1

The middle p-value threshold.

cl

A cluster object created by makeCluster, or an integer to indicate number of child-processes (integer values are ignored on Windows) for parallel evaluations (see Details on performance).

Value

Returns a list of length two of class scan. The first element (clusters) is a list containing the significant, non-ovlappering clusters, and has the the following components:

coords

The centroid of the significant clusters.

r

The radius of the window of the clusters.

pop

The total population in the cluster window.

cases

The observed number of cases in the cluster window.

expected

The expected number of cases in the cluster window.

smr

Standarized mortaility ratio (observed/expected) in the cluster window.

rr

Relative risk in the cluster window.

loglikrat

The loglikelihood ratio for the cluster window (i.e., the log of the test statistic).

pvalue

The pvalue of the test statistic associated with the cluster window.

The second element of the list is the centroid coordinates. This is needed for plotting purposes.

Details

The test is performed using the spatial scan test based on the Poisson test statistic and a fixed number of cases. The first cluster is the most likely to be a cluster. If no significant clusters are found, then the most likely cluster is returned (along with a warning).

References

Tango, T. and Takahashi, K. (2012), A flexible spatial scan statistic with a restricted likelihood ratio for detecting disease clusters. Statist. Med., 31: 4207-4218. <doi:10.1002/sim.5478>

See Also

print.smerc_cluster, summary.smerc_cluster, plot.smerc_cluster, scan.stat, scan.test

Examples

# NOT RUN {
data(nydf)
data(nyw)
coords = with(nydf, cbind(longitude, latitude))
out = rflex.test(coords = coords, cases = floor(nydf$cases),
                 w = nyw, k = 10,
                 pop = nydf$pop, nsim = 49,
                 alpha = 0.05, longlat = TRUE)

data(nypoly)
library(sp)
plot(nypoly, col = color.clusters(out))
# }