> On May 1, 2018, at 6:11 AM, Therneau, Terry M., Ph.D. via R-devel
> <[email protected]> wrote:
>
> A user sent me an example where coxph fails, and the root of the failure is a
> case where names(mf) is not equal to the term.labels attribute of the formula
> -- the latter has an extraneous newline. Here is an example that does not use
> the survival library.
>
> # first create a data set with many long names
> n <- 30 # number of rows for the dummy data set
> vname <- vector("character", 26)
> for (i in 1:26) vname[i] <- paste(rep(letters[1:i],2), collapse='') # long
> variable names
>
> tdata <- data.frame(y=1:n, matrix(runif(n*26), nrow=n))
> names(tdata) <- c('y', vname)
>
> # Use it in a formula
> myform <- paste("y ~ cbind(", paste(vname, collapse=", "), ")")
> mf <- model.frame(formula(myform), data=tdata)
>
> match(attr(terms(mf), "term.labels"), names(mf)) # gives NA
>
> ----
>
> In the user's case the function is ridge(x1, x2, ....) rather than cbind, but
> the effect is the same.
> Any ideas for a work around?
Maybe add a `yourclass' class to mf and dispatch to a model.frame.yourclass
method where the width cutoff arg here (around lines 57-58 of
model.frame.default) is made larger:
varnames <- sapply(vars, function(x) paste(deparse(x, width.cutoff = 500),
collapse = " "))[-1L]
??
>
> Aside: the ridge() function is very simple, it was added as an example to
> show how a user can add their own penalization to coxph. I never expected
> serious use of it. For this particular user the best answer is to use glmnet
> instead. He/she is trying to apply an L2 penalty to a large number of SNP *
> covariate interactions.
>
> Terry T.
>
HTH,
Chuck
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