R: Survival Curve Object

survfit.object {survival}

R Documentation

Survival Curve Object

Description

This class of objects is returned by the survfit class of functions to represent a fitted survival curve. For a multi-state model the object has class c('survfitms', 'survfit').

Objects of this class have methods for the functions print, summary, plot, points and lines. The print.survfit method does more computation than is typical for a print method and is documented on a separate page.

Arguments

`n`	total number of observations in each curve.
`time`	the time points at which the curve has a step.
`n.risk`	the number of subjects at risk at t.
`n.event`	the number of events that occur at time t.
`n.enter`	for counting process data only, and only if there was an `id` argument, the number of subjects that enter the risk set during the current interval. If there are event/censoring times at 1, 3, 5 for instance, someone who enters at time 1 is counted in the (1, 3] interval, i.e., appears in the row for time 3.
`n.censor`	for counting process data only, the number of subjects who exit the risk set, without an event, at time t. (For right censored data, this number can be computed from the successive values of the number at risk).
`surv`	the estimate of survival at time t+0. This may be a vector or a matrix. The latter occurs when a set of survival curves is created from a single Cox model, in which case there is one column for each covariate set.
`pstate`	a multi-state survival will have the `pstate` component instead of `surv`. It will be a matrix containing the estimated probability of each state at each time, one column per state.
`std.err`	for a survival curve this contains standard error of the cumulative hazard or -log(survival), for a multi-state curve it contains the standard error of prev. This difference is a reflection of the fact that each is the natural calculation for that case.
`cumhaz`	optional. Contains the cumulative hazard for each possible transition.
`counts`	optional. If weights were used, the `n.risk` etc elements contain weighted sums; the `counts` matrix will contain unweighted values. Weighted values are normally more useful for further computation, unweighted may be preferred for labeling or printout.
`strata`	if there are multiple curves, this component gives the number of elements of the `time` vector corresponding to the first curve, the second curve, and so on. The names of the elements are labels for the curves.
`upper`	optional upper confidence limit for the survival curve or pstate
`lower`	options lower confidence limit for the survival curve or pstate
`t0`	optional, the starting time for the curve
`p0`, `sp0`	for a multistate object, the distribution of starting states. If the curve has a strata dimension, this will be a matrix one row per stratum. The `sp0` element has the standard error of p0, if p0 was estimated.
`newdata`	for survival curves from a fitted model, this contains the covariate values for the curves
`n.id`	the total number of unique id values that contributed to the curve. This is only available if the original call used the id option.
`conf.type`	the approximation used to compute the confidence limits.
`conf.int`	the level of the confidence limits, e.g. 90 or 95%.
`transitions`	for multi-state data, the total number of transitions of each type.
`na.action`	the returned value from the na.action function, if any. It will be used in the printout of the curve, e.g., the number of observations deleted due to missing values.
`call`	an image of the call that produced the object.
`type`	type of survival censoring.
`influence.p`, `influence.c`	optional influence matrices for the `pstate` (or `surv`) and for the `cumhaz` estimates. A list with one element per stratum, each element of the list is an array indexed by subject, time, state.
`version`	the version of the object. Will be missing, 2, or 3

Structure

The following components must be included in a legitimate survfit or survfitms object.

Subscripts

Survfit objects can be subscripted. This is often used to plot a subset of the curves, for instance. From the user's point of view the survfit object appears to be a vector, matrix, or array of curves. The first dimension is always the underlying number of curves or “strata”; for multi-state models the state is always the last dimension. Predicted curves from a Cox model can have a second dimension which is the number of different covariate prediction vectors.

Details

The survfit object has evolved over time: when first created there was no thought of multi-state models for instance. This evolution has almost entirely been accomplished by the addition of new elements.

For both plots of the curves and computation of the restricted mean time in state (RMTS) we need the concept of a starting point t0 and starting prevalence of the states p0 for each curve. (Sojourn time, area under the curve and restricted mean survival time are other labels for the RMTS). Time 0 is not, by default, included as part of the standard tableau of results, i.e., time, number at risk, number of events, etc. For simple survival with a 0/1 status variable, the starting state p0 is the obvious default of "everyone alive", and t0 is formally not discernable from the data and so was left out. (A design decision made in 1986, and now far too late to change.) However, for plots t0 is assumed to be the minimum of 0 and all observed times. Negative survival times are unusual but not invalid. Multi-state survival curves include t0 and p0 as a part of the returned object. The first is a single value for all curves, the second is per curve.