diseasemapping-package: Disease Mapping

In diseasemapping: Modelling Spatial Variation in Disease Risk for Areal Data

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

}

diseasemapping documentation built on Sept. 22, 2023, 1:07 a.m.