R: Ancillary arguments for controlling coxph fits

coxph.control {survival}

R Documentation

Ancillary arguments for controlling coxph fits

Description

This is used to set various numeric parameters controlling a Cox model fit. Typically it would only be used in a call to coxph.

Usage

coxph.control(eps = 1e-09, toler.chol = .Machine$double.eps^0.75,
iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix=TRUE)

Arguments

`eps`	Iteration continues until the relative change in the log partial likelihood is less than eps, or the absolute change is less than sqrt(eps). Must be positive.
`toler.chol`	Tolerance for detection of singularity during a Cholesky decomposition of the variance matrix, i.e., for detecting a redundant predictor variable.
`iter.max`	Maximum number of iterations to attempt for convergence.
`toler.inf`	Tolerance criteria for the warning message about a possible infinite coefficient value.
`outer.max`	For a penalized coxph model, e.g. with pspline terms, there is an outer loop of iteration to determine the penalty parameters; maximum number of iterations for this outer loop.
`timefix`	Resolve any near ties in the time variables.

Details

The convergence tolerances are a balance. Users think they want THE maximum point of the likelihood surface, and for well behaved data sets where this is quadratic near the max a high accuracy is fairly inexpensive: the number of correct digits approximately doubles with each iteration. Conversely, a drop of .0001 from the maximum in any given direction will be correspond to only about 1/20 of a standard error change in the coefficient. Statistically, more precision than this is straining at a gnat. Based on this the author originally had set the tolerance to 1e-5, but relented in the face of multiple "why is the answer different than package X" queries.

Asking for results that are too close to machine precision (double.eps) is a fool's errand; a reasonable critera is often the square root of that precision. The Cholesky decompostion needs to be held to a higher standard than the overall convergence criterion, however. The tolerance.inf value controls a warning message; if it is too small incorrect warnings can appear, if too large some actual cases of an infinite coefficient will not be detected.

The most difficult cases are data sets where the MLE coefficient is infinite; an example is a data set where at each death time, it was the subject with the largest covariate value who perished. In that situation the coefficient increases at each iteration while the log-likelihood asymptotes to a maximum. As iteration proceeds there is a race condition condition for three endpoint: exp(coef) overflows, the Hessian matrix become singular, or the change in loglik is small enough to satisfy the convergence criterion. The first two are difficult to anticipate and lead to numeric diffculties, which is another argument for moderation in the choice of eps.

See the vignette "Roundoff error and tied times" for a more detailed explanation of the timefix option. In short, when time intervals are created via subtraction then two time intervals that are actually identical can appear to be different due to floating point round off error, which in turn can make coxph and survfit results dependent on things such as the order in which operations were done or the particular computer that they were run on. Such cases are unfortunatedly not rare in practice. The timefix=TRUE option adds logic similar to all.equal to ensure reliable results. In analysis of simulated data sets, however, where often by defintion there can be no duplicates, the option will often need to be set to FALSE to avoid spurious merging of close numeric values.

Value