getStdRate {diseasemapping} | R Documentation |
A function to calculate the standard rate according to the Canadian standard population data set from year 1991.
getStdRate(relativeRate, model, referencePopulation, scale = 1e+05)
relativeRate |
the relateve cancer rate calculated by glmmBUGS of different sex and age group of people from ontario . |
model |
the estimated cancer rate calculated by glm model of different sex and age group of people from ontario. |
referencePopulation |
the standard Canadian population from year 1991. |
scale |
the unit of the population. |
Lutong Zhou
data(referencepop) data(casedata) data(popdata) # get the age sex group rate: model = getRates(casedata, popdata, ~age*sex, S=c("M","F")) # calculate the relative rate using glmmBUGS: ontario = getSMR(popdata, model, casedata) ## Not run: library(spdep) popDataAdjMat <- poly2nb(popdata, popdata[["CSDUID"]]) library(glmmBUGS) forBugs = glmmBUGS(formula = observed + logExpected ~ 1, effects= "CSDUID", family="poisson", spatial =popDataAdjMat, data=ontario@data) startingValues=forBugs$startingValues source("getInits.R") library(R2WinBUGS) ontarioResult = bugs(forBugs$ragged, getInits, parameters.to.save=names(getInits()), model.file="model.bug", n.chain=3, n.iter=1000, n.burnin=100, n.thin=10, program="winbugs") ontarioParams=restoreParams(ontarioResult, forBugs$ragged) ontarioSummary = summaryChain(ontarioParams) ontario = mergeBugsData(ontario, ontarioSummary) ontario@data = ontario@data[!is.na(ontario$SMR),] relativeRate = ontario@data[,grep("Fitted", names(ontario), value=TRUE)] newpop <- getStdRate(relativeRate, model, referencepop, scale=100000) ## End(Not run)