predict.flexrsurv: Predictions for a relative survival model

In flexrsurv: Flexible Relative Survival Analysis

Predictions for a relative survival model

Description

Predict linear predictors, hazard and cumulative hazard for a model fitted by flexrsuv

Usage

  ## S3 method for class 'flexrsurv'
predict(object, newdata= NULL,
   type = c("lp", "link", "risk", "hazard", "hazardrate",
             "rate", "loghazard", "log", "lograte",
             "cumulative.rate", "cumulative.hazard", "cumulative", "cum",
             "survival", "surv", "netsurv"),
   se.fit=FALSE, na.action=na.pass, ...)

Arguments

object	the results of a flexrsurv fit.
newdata	Optional new data at which to do predictions. If absent predictions are for the data frame used in the original fit.
type	the type of predicted value. Choices are the linear predictor ("lp", "log", "loghazard", "lograte"), the hazard ("rate", "hazard", "hazardrate", "risk") or the cumulative hazard ("cum", "cumulative.hazard", "cumulative").
se.fit	if TRUE, pointwise standard errors are produced for the predictions (not available for cumulative hazard).
na.action	function determining what should be done with missing values in newdata. The default is to predict NA.
...	For future methods

Details

For cumulative hazard, the cumulative hazard is computed from 0 until the given end time. The cumulative hazard is computed using the same numerical integration method as the one used to fit the model.

Value

a vector or a list containing the predictions (element "fit") and their standard errors (element "se.fit") if the se.fit option is TRUE.

Note

To work correctly, arguments Boundary.knots and Boundary.knots.t must be included in the call to NPH(), NLL() and NPHNLL() in the formula of flexrsurv

See Also

predict, flexrsurv, flexrsurvclt

Examples

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

	# data from package relsurv
	data(rdata, package="relsurv")
	
	# rate table from package relsurv
	data(slopop, package="relsurv")
	
	
	# get the death rate at event (or end of followup) from slopop for rdata
	rdata$iage <- findInterval(rdata$age*365.24+rdata$time, attr(slopop, "cutpoints")[[1]])
	rdata$iyear <- findInterval(rdata$year+rdata$time, attr(slopop, "cutpoints")[[2]])
	therate <- rep(-1, dim(rdata)[1])
	for( i in 1:dim(rdata)[1]){
	  therate[i] <- slopop[rdata$iage[i], rdata$iyear[i], rdata$sex[i]]
	}
	
	rdata$slorate <- therate
	
	# change sex coding
	rdata$sex01 <- rdata$sex -1
	# centering age
	rdata$agec <- rdata$age- 60
	
	# fit a relative survival model with a non linear effect of age
	fit <- flexrsurv(Surv(time,cens)~sex01+NLL(age, Knots=60, Degree=3,
	                                           Boundary.knots = c(24, 95)), 
	                 rate=slorate, data=rdata,
	                 knots.Bh=1850,  # one interior knot at 5 years
	                 degree.Bh=3,
	                 Spline = "b-spline",
	                 initbyglm=TRUE, 
	                 int_meth= "BOOLE",
	                 step=50
	                 )
	summary(fit, correlation=TRUE)
	
	
	
	newrdata <- rdata
	newrdata$age <- rep(60, length(rdata$age))
	newrdata$sex <- factor(newrdata$sex, labels=c("m", "f"))
	
	
	
	linpred <- predict(fit, newdata=newrdata, type="lp", se.fit=TRUE )
	predhazard <- predict(fit, newdata=newrdata, type="hazard" , se.fit=TRUE )
	predcumhazard <- predict(fit, newdata=newrdata, type="cum", se.fit=TRUE)
	
	
	require(ggplot2)
	tmp <- cbind(newrdata, linpred)
	glp <- ggplot(tmp, aes(time, colour=sex))
	glp + geom_ribbon(aes(ymin = fit-2*se.fit, ymax = fit + 2*se.fit, fill=sex)) +
	   geom_line(aes(y=fit)) +
	   scale_fill_manual(values = alpha(c("blue", "red"), .3))
	
	
	tmp <- cbind(newrdata, predhazard)
	glp <- ggplot(tmp, aes(time, colour=sex))
	glp + geom_ribbon(aes(ymin = fit-2*se.fit, ymax = fit + 2*se.fit, fill=sex)) +
	   geom_line(aes(y=fit))  +
	   scale_fill_manual(values = alpha(c("blue", "red"), .3))
	
	
	tmp <- cbind(newrdata, predcumhazard)
	glp <- ggplot(tmp, aes(time, colour=sex))
	glp + geom_ribbon(aes(ymin = fit-2*se.fit, ymax = fit + 2*se.fit, fill=sex)) +
	   geom_line(aes(y=fit)) +
	   scale_fill_manual(values = alpha(c("blue", "red"), .3))
}

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