From ccberry @ending from uc@d@edu  Tue May  1 18:43:18 2018
From: ccberry @ending from uc@d@edu (Berry, Charles)
Date: Tue, 1 May 2018 16:43:18 +0000
Subject: [Rd] issue with model.frame()
In-Reply-To: <bb6fa2$9b935h@ironport10.mayo.edu>
References: <bb6fa2$9b935h@ironport10.mayo.edu>
Message-ID: <EF41437C-933A-44C7-86C0-992953B39E9E@ucsd.edu>



> On May 1, 2018, at 6:11 AM, Therneau, Terry M., Ph.D. via R-devel <r-devel at r-project.org> 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



[Rd] issue with model.frame()
Berry, Charles