get.cross.PCF {IDSpatialStats}

Cross type Pair Correlation Function using homotypic and heterotypic case types

Description

A wrapper function of the pcf function from the spatstat.explore package (Baddeley et al. 2016) that takes epidemiological data used by IDSpatialStats functions and calculates the cross type Pair Correlation Function based on user defined case type homology

Usage

get.cross.PCF(epi.data, type, hom, het = NULL, r = NULL, correction = "none")

Arguments

epi.data

a three-column numerical matrix that contains coordinates (x and y) for each case and information on case type (e.g. genotype or serotype). First two columns must be x and y

type

an integer giving the column that contains information on case type. Must be an integer or a character

hom

a scalar or vector giving the homotypic case type(s). Equivalent to the 'j' point type used in the cross K function. Must be an integer or character

het

a scalar or vector giving the heterotypic case type(s). Equivalent to the 'i' point type used in the cross K function. The default is NULL, which uses any case type not defined in the hom argument as heterotypic. Must be an integer or a character

r

a numeric vector giving the spatial distances

correction

type of edge correction to be applied (default set to 'none'). See the pcf function in the spatstat.explore package for more details

Value

a data frame with two columns giving the radius r, the theoretical value of the Pair Correlation Function for a Poisson process (theo), and value of the Pair Correlation Function pcf

Author(s)

John Giles

References

Baddeley A, Rubak E, and Turner R. (2016). "Spatial Point Patterns: Methodology and Applications with R". CRC Press.

Examples

data(DengueSimR01)

g <- get.cross.PCF(epi.data=DengueSimR01, type=5, hom=2, het=NULL, r=NULL, correction='none')

plot(g$pcf, type='l', xlab='r', ylab='cross PCF')
abline(h=1, col='red', lty=2)