getRates {diseasemapping}

Calculate the estimated coefficients of age and sex group from the glm model

Description

The getRates function calculates the estimated coefficient of the age and sex group from the case and population data set. It fits a glm model with Poisson distribution by default.

Usage

getRates(casedata, popdata, formula, family = 'poisson', minimumAge = 0, 
    maximumAge = 100, S = c("M", "F"), years = NULL, year.range = NULL, 
    case.years = grep("^year$", names(casedata), ignore.case = TRUE, 
        value = TRUE), fit.numeric=NULL, breaks = NULL) 

Arguments

casedata

A data frame of case data, with columns corresponding to variables in formula. Assumed to be one row per case, unless a column called y or cases or count is included, in which case this column gives the number of cases per row.

popdata

population data set

formula

the glm model you want to fit. ie. ~age*sex

family

the distribution to fit the model

minimumAge

the lower boundary of the age, default is 0

maximumAge

the higher boundary of the age, default is 100

S

vector of sexes to include in the analysis. Defaults to both "M" and "F"

years

a vector of census years

year.range

study period: a vector of two elements, starting dates and ending dates

case.years

variable name in the case data which contains time

fit.numeric

the variables which needed to be changed from factor to numeric

breaks

the age breaks

Details

It fits a glm model with Poisson or binomial distribution over case and population data sets. If there is no data set in some age and sex group, an NA will show there.

Value

A summary of the glm model contains set of estimated coefficients for different age and sex groups.

Author(s)

Patrick Brown

Examples

data('casedata')
data('popdata')
popdata = terra::unwrap(popdata)
therates = getRates(casedata, popdata, ~sex*age,
	breaks=c(seq(0, 80, by=10), Inf))
therates