diseasemapping-package {diseasemapping}

Disease Mapping

Description

Functions for calculating observed and expected counts by region, and manipulating posterior samples from Bayesian models produced by glmmBUGS.

Author(s)

Patrick Brown

Examples

# creating SMR's
data('kentucky')
kentucky = terra::unwrap(kentucky)


kentucky2 = getSMR(kentucky, larynxRates, larynx, 
		regionCode="County")

if(require('mapmisc', quietly=TRUE)) {
	mycol = colourScale(kentucky2$SMR, breaks=9, 
	dec=-log10(0.5), style='equal', transform='sqrt')
	plot(kentucky2, col=mycol$plot)
	legendBreaks('topleft', mycol)
}

if(require("INLA", quietly=TRUE)) {

if(requireNamespace('INLA')) {
  INLA::inla.setOption(num.threads=2)
  # not all versions of INLA support blas.num.threads
  try(INLA::inla.setOption(blas.num.threads=2), silent=TRUE)
}

kBYM = bym(observed ~ offset(logExpected) + poverty, 
	data= kentucky2, 
	prior = list(sd=c(0.1, 0.5), propSpatial=c(0.5, 0.5))
)

kBYM$par$summary

}