ajfit {flexsurv}

Aalen-Johansen nonparametric estimates comparable to a fitted flexsurvmix model

Description

Given a fitted flexsurvmix model, return the Aalen-Johansen estimates of the probability of occupying each state at a series of times covering the observed data. State 1 represents not having experienced any of the competing events, while state 2 and any further states correspond to having experienced each of the competing events respectively. These estimates can be compared with the fitted probabilities returned by p_flexsurvmix to check the fit of a flexsurvmix model.

Usage

ajfit(x, newdata = NULL, tidy = TRUE)

Arguments

x

Fitted model returned by flexsurvmix.

newdata

Data frame of alternative covariate values to check fit for. Only factor covariates are supported.

tidy

If TRUE then a single tidy data frame is returned. Otherwise the function returns the object returned by survfit, or a list of these objects if we are computing subset-specific estimates.

Details

This is only supported for models with no covariates or models containing only factor covariates.

For models with factor covariates, the Aalen-Johansen estimates are computed for the subsets of the data defined in newdata. If newdata is not supplied, then this function returns state occupancy probabilities for all possible combinations of the factor levels.

The Aalen-Johansen estimates are computed using survfit from the survival package (Therneau 2020).

References

Therneau T (2020). _A Package for Survival Analysis in R_. R package version 3.2-3, <URL: https://CRAN.R-project.org/package=survival>.