On Tue, Jan 31, 2012 at 7:18 AM, Terry Therneau wrote:
> Three thinngs -
> My original questions to R-help was "who do I talk to". That was
> answered by Brian R, and the discussion of how to change Sweave moved
> offline. FYI, I have a recode in hand that allows arbitrary reordering
> of chun
Three thinngs -
My original questions to R-help was "who do I talk to". That was
answered by Brian R, and the discussion of how to change Sweave moved
offline. FYI, I have a recode in hand that allows arbitrary reordering
of chunks; but changes to code used by hundreds need to be approached
ca
OK, I did not realize the overhead problem is so overwhelming in your
situation. Therefore I re-implemented the chunk reference in the knitr
package in another way. In Sweave we use
<>=
# code in chunk a
@
<>=
# use code in a
<>
@
And in knitr, we can use real R code:
<>=
# code in chunk a
@
<
I prefer the code chunks myself.
Function calls have overhead. In a bioinformatics world with large
datasets and an R default that uses call-by-value rather than
call-by-reference, the function calls may have a _lot_ of overhead.
Writing the functions to make sure they use call-by-reference f
Maybe this is a my personal taste: I do not like pseudo R code in the
form <> inside a chunk, and I'm curious about why you do
not use real R functions to do the job.
coxme <- function(formula, data, subset, blah blah ){
coxme_check_arguments(...)
coxme_build(...)
coxme_compute(...)
coxme
Almost all of the coxme package and an increasing amount of the survival
package are now written in noweb, i.e., .Rnw files. It would be nice to
process these using the Sweave function + a special driver, which I can
do using a modified version of Sweave. The primary change is to allow
the follow
