get.cross.PCF: Cross type Pair Correlation Function using homotypic and...
In IDSpatialStats: Estimate Global Clustering in Infectious Disease

Description Usage Arguments Value Author(s) References Examples

A wrapper function of the pcf function from the spatstat.core 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

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

`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.core package for more details

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

John Giles

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

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)