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 
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 

I think you can avoid the problem by adding right after
     ll <- attr(Terms, "term.labels")
the line
     ll <- gsub("^`|`$", "", ll)


 > d <- data.frame(check.names=FALSE, y=1/(1:5), `b$a$d`=sin(1:5)+2, `x y 
 > 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 <>

On Mon, Mar 5, 2018 at 12:55 PM, Therneau, Terry M., Ph.D. via R-devel < <>> 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 
    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 
    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 

    Terry T.

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