getBrassHazardFromTable: Compute expected hazards with respect to a corrected...

In flexrsurv: Flexible Relative Survival Analysis

Compute expected hazards with respect to a corrected reference life table

Description

returns the cumulative hazard and the hazard rate of subjects in a reference life table

Usage

getBrassPseudoHazardFromTable(Y, startdate, startage, matchdata = NULL, 
        ratetable = survival::survexp.us, 
		age = 1, year = 2, rmap, 
		agemin = 16, scale = 365.25, 
		ratename = "rateend", 
		cumrateendname = "cumrateend", 
		cumrateentername = "cumrateenter", 
		idname = "Id_byperiod",
		origin = "01/01/1970", format="%d/%m/%Y",
		left.open = FALSE, 
		SplineBrass=R2bBSplineBasis(knots=c(-2.5,0,2.5), degree=3)*c(1, 0, 1),
		verbose=FALSE)

Arguments

Y	An object with interval data. It can be an object of class Surv with arguments time, time2 and event or a two-column matrix with starting time in the first column and ending time in the second column.
startdate	a numeric vector such that as.Date(startadate) is interpreted as the date of the start (when Y[,]==0).
startage	a numeric vector of age in days the start (when Y[,]==0).
matchdata	an optional data.frame in which to interpret the additional variables to be mapped to the ratetable variables.
ratetable	an object of class ratetable, ie a table of event rates.
age, year	character values of the names of the age and period variables in the rate table.
rmap	an optional list that maps data set names to the ratetable names. See survexp an example bellow.
agemin	numeric value of the age at which the cumulative hazard starts.
scale	numeric value to scale agemin.
ratename, cumrateendname, cumrateentername, idname	names of the returned variables
origin, format	passed to as.Date
left.open	logical, passed to findInterval
SplineBrass	Spline basis used to transform the rates
verbose	logical, if true the progression of the computation is output.

Details

The cumulative rates are computed using survexp.

Value

A data.frame with 3 columns with the rate at the ending time, the cumulative rate from agemin up to the starting time and upt to the ending time.

See Also

getHazardFromTable for the cumulative hazard and the hazard rate of subjects in a reference life table. survexp

Examples

if (requireNamespace("relsurv", quietly = TRUE) & requireNamespace("date", quietly = TRUE)) {

	library(date)
	# data from package relsurv
	data(rdata, package="relsurv")
	
	# rate table from package relsurv
	data(slopop, package="relsurv")
	
	tmpsurv <- Surv(rep(0, length(rdata$time)), rdata$time, rdata$cens)
	
	HH <- getPseudoHazardFromTable(tmpsurv, startdate=rdata$year,
	               startage=rdata$age*365.24 , matchdata=rdata, ratetable=slopop,
	               age="age", year="year",
	               rmap=list(sex=sex),
	               agemin=18, scale=365.24,
	               ratename = "poprate", 
	               cumrateendname ="cumrateend", 
	               cumrateentername ="cumrateenter", 
	               idname="Id_byperiod"
	               ) 
	summary(HH)
}	
					

flexrsurv documentation built on June 7, 2023, 5:09 p.m.