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

View source: R/probtrans_mstate.R

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
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"), ...)
``` |

`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). |

`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.

An object of class `probtrans`

. See the ‘value’ section in the
the help page of `probtrans`

for details.

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

package.

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.

`mstate::probtrans`

; `mstate::msfit`

; `msfit_generic`

.

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