cmp.rel {relsurv}

Compute crude probability of death

Description

Estimates the crude probability of death due to disease and due to population reasons

Usage

cmp.rel(
  formula = formula(data),
  data = parent.frame(),
  ratetable = relsurv::slopop,
  na.action,
  tau,
  conf.int = 0.95,
  precision = 1,
  add.times,
  rmap
)

Arguments

formula

a formula object, with the response as a Surv object on the left of a ~ operator, and, if desired, terms separated by the + operator on the right. If no strata are used, ~1 should be specified.

NOTE: The follow-up time must be in days.

data

a data.frame in which to interpret the variables named in the formula.

ratetable

a table of event rates, organized as a ratetable object, such as slopop.

na.action

a missing-data filter function, applied to the model.frame, after any subset argument has been used. Default is options()$na.action.

tau

the maximum follow-up time of interest, all times larger than tau shall be censored. Equals maximum observed time by default

conf.int

the level for a two-sided confidence interval on the survival curve(s). Default is 0.95.

precision

the level of precision used in the numerical integration of variance. Default is 1, which means that daily intervals are taken, the value may be decreased to get a higher precision or increased to achieve a faster calculation. The calculation intervals always include at least all times of event and censoring as border points.

add.times

specific times at which the value of estimator and its variance should be evaluated. Default is all the event and censoring times.

rmap

an optional list to be used if the variables are not organized and named in the same way as in the ratetable object. See details below.

Details

NOTE: The follow-up time must be specified in days. The ratetable being used may have different variable names and formats than the user's data set, this is dealt with by the rmap argument. For example, if age is in years in the data set but in days in the ratetable object, age=age*365.241 should be used. The calendar year can be in any date format (date, Date and POSIXt are allowed), the date formats in the ratetable and in the data may differ.

Note that numerical integration is required to calculate the variance estimator. The integration precision is set with argument precision, which defaults to daily intervals, a default that should give enough precision for any practical purpose.

The area under the curve is calculated on the interval [0,tau].

Function summary may be used to get the output at specific points in time.

Value

An object of class cmp.rel. Objects of this class have methods for the functions print and plot. The summary function can be used for printing output at required time points. An object of class cmp.rel is composed of several lists, each pertaining the cumulative hazard function for one risk and one strata. Each of the lists contains the following objects:

time

the time-points at which the curves are estimated

est

the estimate

var

the variance of the estimate

lower

the lower limit of the confidence interval

upper

the upper limit of the confidence interval

area

the area under the curve calculated on the interval [0,tau]

index

indicator of event and censoring times among all the times in the output. The times added via paramater add.times are also included

add.times

the times added via parameter add.times

References

Package: Pohar Perme, M., Pavlic, K. (2018) "Nonparametric Relative Survival Analysis with the R Package relsurv". Journal of Statistical Software. 87(8), 1-27, doi: "10.18637/jss.v087.i08"

See Also

rs.surv, summary.cmp.rel

Examples

data(slopop)
data(rdata)
#calculate the crude probability of death
#note that the variable year must be given in a date format and that 
#age must be multiplied by 365.241 in order to be expressed in days.
fit <- cmp.rel(Surv(time,cens)~sex,rmap=list(age=age*365.241),
		ratetable=slopop,data=rdata,tau=3652.41)
fit
plot(fit,col=c(1,1,2,2),xscale=365.241,xlab="Time (years)")
#if no strata are desired:
fit <- cmp.rel(Surv(time,cens)~1,rmap=list(age=age*365.241),
		ratetable=slopop,data=rdata,tau=3652.41)