rflex.zones: Determine zones for flexibly shaped spatial scan test

Description

rflex.zones determines the unique zones to consider for the flexibly shaped spatial scan test of Tango and Takahashi (2012). The algorithm uses a breadth-first search to find all subgraphs connected to each vertex (region) in the data set of size $k$ or less with the constraint that the middle p-value of each region must be less than alpha1.

Usage

rflex.zones(
  nn,
  w,
  cases,
  ex,
  alpha1 = 0.2,
  type = "poisson",
  pop = NULL,
  cl = NULL,
  loop = FALSE,
  verbose = FALSE,
  pfreq = 1
)

Value

Returns a list of zones to consider for clustering. Each element of the list contains a vector with the location ids of the regions in that zone.

Arguments

nn: An n by k matrix providing the k nearest neighbors of each region, presumably produced by the knn function.
w: A binary spatial adjacency matrix for the regions.
cases: The number of cases observed in each region.
ex: The expected number of cases for each region. The default is calculated under the constant risk hypothesis.
alpha1: The middle p-value threshold.
type: The type of scan statistic to compute. The default is "poisson". The other choice is "binomial".
pop: The population size associated with each region. The default is NULL since this argument is only needed for type = "binomial".
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). It can also be "future" to use a future backend (see Details), NULL (default) refers to sequential evaluation.
loop: A logical value indicating whether a loop should be used to implement the function instead of pbapply. The default is FALSE. If TRUE, then memory-saving steps are also taken.
verbose: A logical value indicating whether progress messages should be provided. The default is FALSE. If both loop and verbose are TRUE, informative messages are displayed that can be useful for diagnosing where the sequences of connected subgraphs are slowing down or having problems.
pfreq: The frequency that messages are reported from the loop (if verbose = TRUE). The default is pfreq = 1, meaning a message is returned for each index of the loop.

Author

Joshua French

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>

Examples

Run this code

data(nydf)
data(nyw)
coords <- cbind(nydf$x, nydf$y)
nn <- knn(coords, k = 5)
cases <- floor(nydf$cases)
pop <- nydf$pop
ex <- pop * sum(cases) / sum(pop)
# zones for poisson model
pzones <- rflex.zones(nn, w = nyw, cases = cases, ex = ex)
if (FALSE) {
pzones <- rflex.zones(nn,
  w = nyw, cases = cases,
  ex = ex, verbose = TRUE
)
# zones for binomial model
bzones <- rflex.zones(nn,
  w = nyw, cases = cases, ex = ex,
  type = "binomial", pop = pop
)
}

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