getSMR {diseasemapping}R Documentation

Calculate the standardized mortality/morbility ratios

Description

The getSMR function calculates the rate of observe value over expected value. It will also merge back the observed value, expected value and the ratio back to the population data set.

Usage

getSMR(popdata, model, casedata, regionCode = "CSDUID", regionCodeCases = "CSD2006", area = FALSE, area.scale = 1,  ...)
## S3 method for class 'data.frame':
getSMR(popdata, model, casedata=NULL, regionCode = "CSDUID", regionCodeCases = "CSD2006", area = FALSE, area.scale = 1, ...)
## S3 method for class 'list':
getSMR(popdata, model, casedata = NULL, regionCode = "CSDUID", regionCodeCases = "CSD2006", area = FALSE, area.scale = 1, years = NULL, personYears= TRUE, year.range = NULL, ...)
## S3 method for class 'SpatialPolygonsDataFrame':
getSMR(popdata, ...)

Arguments

popdata the name of population data set
model rates, either fitted model (usually a glm object), or a vector of rates.
... additional arguments
casedata the name of case data set
regionCode the name of district area column in population data set
regionCodeCases the name of district area column in case data set
area if TRUE, calculate the expected number of cases per area in each region
area.scale control the unit of area. e.g $10^6$: per square kilometers
years the vector of years
personYears a logic variable. If TRUE, it compute offset adding person years
year.range the range of the year vector

Details

If model is numeric, it's assumed to be a vector of rates, with the names of the elements corresponding to columns of the population data set. Names do not need to match exactly (can have M in one set of names, male in another for instance).

Otherwise, model is passed to the predict function.

Value

Returns a new population data set contains expected number of cases, observed number of cases and SMR. It has the same format as the population data set which put into the function.

Examples

data(casedata)
data(popdata)
therates = getRates(casedata, popdata, ~age*sex,breaks=c(seq(0, 80, by=10), Inf) )
thesmr = getSMR(popdata, therates, casedata)
head(thesmr@data)

[Package diseasemapping version 0.5.3 Index]