smerc_cluster: Prepare 'smerc_cluster'

Description Usage Arguments Value

View source: R/smerc_cluster.R

Description

smerc_cluster prepares a smerc_cluster.

Usage

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smerc_cluster(
  tobs,
  zones,
  pvalue,
  coords,
  cases,
  pop,
  ex,
  longlat,
  method,
  rel_param,
  alpha,
  w = NULL,
  d = NULL,
  a = NULL,
  shape_all = NULL,
  angle_all = NULL
)

Arguments

tobs

The vector of observed test statistics for each zone

zones

A list of zones

pvalue

The p-value associated with each test statistic

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.

ex

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

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.

method

A character string indicating the method used to construct the smerc_cluster.

rel_param

A names list with the relevant parameters associated with method.

alpha

The significance level of the test.

w

A binary spatial adjacency matrix for the regions.

d

A precomputed distance matrix based on coords

a

A single value >= 0 indicating the penalty to use for elliptic.test.

shape_all

A vector of shape parameters associated with zones.

angle_all

A vector of angle parameter associated with zones.

Value

A smerc_cluster object. The object generally has the following components:

clusters

A list containing information about the significant clusters. See further details below.

coords

The matrix of centroid coordinates.

number_of_regions

The number of regions considered.

total_population

The total population in the regions.

total_cases

The total number of cases in the regions.

cases_per_100k

The rate of cases per 100,000 persons.

method

The name of the method applied.

rel_param

A list of relevant method parameters.

alpha

The significance level.

longlat

A logical value indicating which type of distance was used.

Each element of the clusters component has:

locids

The ids of the regions in the cluster.

centroid

The cluster centroid.

r

The radius of the region (from the starting region to last region of the cluster).

max_dist

The maximum intercentroid distance between all the regions in the cluster.

population

The total population in the cluster.

cases

The number of cases in the cluster.

expected

The expected number of cases in the cluster.

smr

Standardized mortality ratio (cases/expected) in the cluster.

rr

Relative risk in the cluster window. This is (cases/pop)/((total_cases - cases)/ (total_population - population)).

loglikrat

The log of the likelihood ratio test statistic for the cluster. Only valid for the scan-type tests.

test_statistic

The test statistic for the cluster.

pvalue

The p-value of the test statistic associated with the cluster.

w

The adjacency information for the cluster.

For elliptic.test, clusters additionally has:

semiminor_axis

The semi-minor axis length for the ellipse.

semimajor_axis

The semi-major axis length for the ellipse.

angle

The rotation angle of the ellipse.

shape

The shape of the ellipse.


smerc documentation built on Oct. 1, 2021, 5:07 p.m.