Ben,
Looking at your notes, it appears that your solution is to write your own
terms() function
for lme. It is easy to verify that the "varnames.fixed" attribute is not
returned by the
ususal terms function.
Then I also need to write my own terms function for the survival and coxme
pacakges?
Because of the need to treat strata() terms in a special way I manipulate the
formula/terms in nearly every routine.
Extrapolating: every R package that tries to examine formulas and partition
them into bits
needs its own terms function? This does not look like a good solution to me.
On 03/07/2018 07:39 AM, Ben Bolker wrote:
I knew I had seen this before but couldn't previously remember where.
https://github.com/lme4/lme4/issues/441 ... I initially fixed with
gsub(), but (pushed by Martin Maechler to do better) I eventually
fixed it by storing the original names of the model frame (without
backticks) as an attribute for later retrieval:
https://github.com/lme4/lme4/commit/56416fc8b3b5153df7df5547082835c5d5725e89.
On Wed, Mar 7, 2018 at 8:22 AM, Therneau, Terry M., Ph.D. via R-devel
<r-devel@r-project.org> wrote:
Thanks to Bill Dunlap for the clarification. On follow-up it turns out that
this will be an issue for many if not most of the routines in the survival
package: a lot of them look at the terms structure and make use of the
dimnames of attr(terms, 'factors'), which also keeps the unneeded
backquotes. Others use the term.labels attribute. To dodge this I will
need to create a fixterms() routine which I call at the top of every single
routine in the library.
Is there a chance for a fix at a higher level?
Terry T.
On 03/05/2018 03:55 PM, William Dunlap wrote:
I believe this has to do terms() making "term.labels" (hence the dimnames
of "factors")
with deparse(), so that the backquotes are included for non-syntactic
names. The backquotes
are not in the column names of the input data.frame (nor model frame) so
you get a mismatch
when subscripting the data.frame or model.frame with elements of
terms()$term.labels.
I think you can avoid the problem by adding right after
ll <- attr(Terms, "term.labels")
the line
ll <- gsub("^`|`$", "", ll)
E.g.,
> d <- data.frame(check.names=FALSE, y=1/(1:5), `b$a$d`=sin(1:5)+2, `x y
z`=cos(1:5)+2)
> Terms <- terms( y ~ log(`b$a$d`) + `x y z` )
> m <- model.frame(Terms, data=d)
> colnames(m)
[1] "y" "log(`b$a$d`)" "x y z"
> attr(Terms, "term.labels")
[1] "log(`b$a$d`)" "`x y z`"
> ll <- attr(Terms, "term.labels")
> gsub("^`|`$", "", ll)
[1] "log(`b$a$d`)" "x y z"
It is a bit of a mess.
Bill Dunlap
TIBCO Software
wdunlap tibco.com <http://tibco.com>
On Mon, Mar 5, 2018 at 12:55 PM, Therneau, Terry M., Ph.D. via R-devel
<r-devel@r-project.org <mailto:r-devel@r-project.org>> wrote:
A user reported a problem with the survdiff function and the use of
variables that
contain a space. Here is a simple example. The same issue occurs in
survfit for the
same reason.
lung2 <- lung
names(lung2)[1] <- "in st" # old name is inst
survdiff(Surv(time, status) ~ `in st`, data=lung2)
Error in `[.data.frame`(m, ll) : undefined columns selected
In the body of the code the program want to send all of the right-hand
side variables
forward to the strata() function. The code looks more or less like
this, where m is
the model frame
Terms <- terms(m)
index <- attr(Terms, "term.labels")
if (length(index) ==0) X <- rep(1L, n) # no coariates
else X <- strata(m[index])
For the variable with a space in the name the term.label is "`in st`",
and the
subscript fails.
Is this intended behaviour or a bug? The issue is that the name of
this column in the
model frame does not have the backtics, while the terms structure does
have them.
Terry T.
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