| 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)