probtrans_mstate: Compute subject-specific or overall transition probabilities

Description Usage Arguments Details Value Author(s) References See Also

View source: R/probtrans_mstate.R

Description

This function is a wrapper for mstate::probtrans. Its purpose is to preclude the computation of (co-)variances of the transition probability estimator when the fitted Cox model is empirical Bayes. This help page is an adaptation of the mstate::probtrans help page.

Usage

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probtrans_mstate(object, ...)

## Default S3 method:
probtrans_mstate(
  object,
  predt,
  direction = c("forward", "fixedhorizon"),
  method = c("aalen", "greenwood"),
  variance = TRUE,
  covariance = FALSE,
  ...
)

## S3 method for class 'coxrfx'
probtrans_mstate(object, predt, direction = c("forward", "fixedhorizon"), ...)

Arguments

object

An msfit object containing estimated cumulative hazards for each of the transitions in the multi-state model and, if standard errors are requested, (co)variances of these cumulative hazards for each pair of transitions.

...

other arguments.

predt

A positive number indicating the prediction time. This is either the time at which the prediction is made (if direction= "forward") or the time for which the prediction is to be made (if direction="fixedhorizon").

direction

One of "forward" (default) or "fixedhorizon", indicating whether prediction is forward or for a fixed horizon.

method

A character string specifying the type of variances to be computed (so only needed if either variance or covariance is TRUE). Possible values are "aalen" or "greenwood".

variance

Logical value indicating whether standard errors are to be calculated (default is TRUE).

covariance

Logical value indicating whether covariances of transition probabilities for different states are to be calculated (default is FALSE).

Details

probtrans_mstate computes estimates of transition probabilities for an object generated by msfit_generic. It calls the method probtrans_mstate.coxrfx, if the msfit object was generated by msfit_generic.coxrfx, or the method probtrans_mstate.default otherwise. Both methods are identical to the function mstate::probtrans. The only reserve is that probtrans_mstate.coxrfx does not allow the computation of the (co-)variances of the transition probability estimator. In fact, this computation relies on asymptotic results for the fixed effects Cox model (see de Wreede et al, 2010, section 2.3.2), and msfit_generic.coxrfx produces estimates of cumulative hazards under a random effects/empirical Bayes Cox model.

probtrans_mstate should only be used for Markov models, as it relies on product limit calculations.

Value

An object of class probtrans. See the ‘value’ section in the the help page of probtrans for details.

Author(s)

Rui Costa, adapting the work of L. de Wreede, M. Fiocco and H. Putter in the mstate package.

References

de Wreede LC, Fiocco M, and Putter H (2010). The mstate package for estimation and prediction in non- and semi-parametric multi-state and competing risks models. Computer Methods and Programs in Biomedicine 99, 261–274.

See Also

mstate::probtrans; mstate::msfit; msfit_generic.


ebmstate documentation built on Jan. 6, 2021, 1:09 a.m.