On 29/01/2014 9:20 AM, Therneau, Terry M., Ph.D. wrote:
An example of this is found in the coxph function in the survival library.
Look at it for
guideance.
Within a coxph formula the expression "tt(x)" means to use a time transform on
variable x.
The tt function is a fake, defined as tt <- function(x) x, whose only
purpose is to
allow the user to mark a variable for special treatment while staying inside
the syntax
rules of formulas.
tt is not exported, because no one would ever want to use it. It is
documented within
the coxph manual pages. I did export it at one time, for exactly the reasons
and error
message detailed by Axel. I recieved a request to cease doing so because of
package
issues --- someone had a package with a real and useful tt function, which
would be masked
if "require(survival)" ever occured, placing my library with its worthless
function before
his on the search path. Enough things depend on the survival package that this
was making
his package's results unpredictable.
I'm not familiar with how coxph handles formulas. Can a user put f(x)
into a formula, where f is a user-defined function? If a user defines a
tt function, will coxph use theirs, or yours?
I'd say the answers for situations like this should be "yes" and
"theirs", but that's not true of my tables package, where answers to the
corresponding questions would be "yes" and "mine".
Duncan Murdoch
The root issue is that formulas are often counterintuitive. R treats them
as though
they were a function, but with a special evaluation context. Thus even though
a formula
is evaluated within the coxph function, components of the formula are not "in"
the
survival namespace and so can't see non-exported functions in that namespace.
If you
found this confusing be assured that you are not alone.
Terry Therneau
On 01/29/2014 05:00 AM, r-devel-requ...@r-project.org wrote:
>> Hi,
>> >
>> >I've tried to put together a simpler example where I'm having the issue.
>> >
>> >I've built a foo package by only including a single .R file with the two
>> >functions listed below: trt and cmt. The second function calls the
>> >first. In the namespace file, if I only export(cmt), I get the following
>> >error message when running this
>> >
>> >library(foo)
>> >set.seed(1)
>> >dd <- data.frame(y = rbinom(100, 1, 0.5), treat = rbinom(100, 1, 0.5), x
>> >= rnorm(100),
>> >f = gl(4, 250, labels = c("A", "B", "C", "D")))
>> >dd2 <- cmt(y ~ x + f + trt(treat), data =dd)
>> > > Error could not find function "trt"
>> >
>> >The problem is solved by doing export(cmt, trt) in the namespace.
>> >However, I'd like to avoid exporting trt and should not be required.
>> >Sorry I can't seem to figure this out by myself, and so I'd appreciate
>> >your help.
> You are asking for non-standard evaluation of the formula argument. You
> want some parts of it to be evaluated in the global environment (f),
> some parts in the dd dataframe (x), and some parts evaluated in the
> package namespace (trt). R is flexible so this is possible, but it's
> not the way that the terms function works, so you'll need to do more
> work yourself, including specifying what the evaluation rules should be
> in case a variable occurs in more than one of those locations.
>
> Duncan Murdoch
>
>> >
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