Brian,
I used termplot(..., plot=FALSE) recently in R-devel: works like a charm. Thanks much
for the update.
Our in-house "gamterms" function, which this obviates, would also return the "constant"
attribute from the underlying predict(..., type="terms") call. I have occasionally found
t
I'm working on registering all the routines in the survival package, per a request from
R-core. Two questions:
1. In the coxph routine I have this type of structure:
if (survival has 2 columns) routines <- c("coxfit5_a", "coxfit5_b",
"coxfit5_c")
else routines
That was the correct direction: I changed the earler line to "routines <- list(Ccoxfit5a,
..." and the the later to .C(routnines[[1]]) and now it works as desired.
Terry T.
On 02/23/2013 03:09 AM, Duncan Murdoch wrote:
On 13-02-22 2:59 PM, Terry Therneau wrote:
I'm work
I think it would be a good idea. Several versions of the survival package had a duplicate
line in the S3methods, and were missing a line that should have been there, due to a
cut/paste error.
Terry T.
On 03/13/2013 06:00 AM, r-devel-requ...@r-project.org wrote:
Circa 80 CRAN and core-R pac
nique time points. At the very
end the numeric component "time" of the result is created using
as.numeric(levels(ftime)). It's this last line that breaks.
I could set the OutDec option within survfit and reset when I leave using on.exit. Any
other simple solutions? Any other
Thanks Martin. I had already changed the second argument to getOption.
By the way, per an off list comment from Brian R the bug I was addressing won't affect
anyone using R as shipped; the default decimal separator is "." whatever the region. It
only bit those who set the OutDec option themse
trates on providing you with power and on not getting in
your way."
Preface to "The C Book", M Banahan et al
Terry Therneau
On 03/21/2013 06:00 AM, r-devel-requ...@r-project.org wrote:
> Allowing partial matching on $-extraction has always been a source of
> accidents.
As a follow-up to my previous, let me make a concrete suggestion:
Add this as one of the options
df-partial-match = allowed, warn, fail
Set the default to warn for the current R-dev, and migrate it to fail at a
later date of
your choosing.
I expect that this is very little more work fo
Note: My apolgies for the "Subject" in the original post
On 03/21/2013 08:59 AM, Milan Bouchet-Valat wrote:
Le jeudi 21 mars 2013 à 08:51 -0500, Terry Therneau a écrit :
I am not in favor of the change, which is a choice of rigor over usability.
When I am developing code or functio
On 03/21/2013 10:00 AM, Simon Urbanek wrote:
I would think that the ability to hit the Tab key to trigger name
>> completion in your R GUI makes partial matching almost useless. The
>> avantage of interactive completion in the GUI is that you immediately
>> see the result of the partial matc
The thread is strange to me as well, since completion is logically impossible for my
Sweave files.
- an emacs buffer is open working on an .Rnw file
- there is no copy of R running anywhere on the machine
- the code chunk in the .Rnw file refers to a R data object saved somewhere
els
Assume a C program invoked by .Call, that returns a list.
Near the top of the program we allocate space for all the list elements. (It is my habit
to use "xyz2" for the name of the R object and "xyz" for the pointer to its contents.)
PROTECT(means2 = allocVector(REALSXP, nvar));
means
On 04/01/2013 12:44 PM, Simon Urbanek wrote:
On Apr 1, 2013, at 1:10 PM, Terry Therneau wrote:
Assume a C program invoked by .Call, that returns a list.
Near the top of the program we allocate space for all the list elements. (It is my habit to use
"xyz2" for the name of the R
Minimizing and then restoring a window that contains identified points
leads to an error on my linux box.
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: i686-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=C
[5] LC_MON
I'll be the "anybody" to argue that
} else {
is an ugly kludge which you will never find in my source code. Yes, it's necessary at the
command line because the parser needs help in guessing when an expression is finished, but
is only needed in that case. Since I can hardly imagine using
I have a debugging environment for the survival package, perhaps unique to me, but I find
it works very well.
To wit, a separate directory with copies of the source code but none of the package
accuements of DESCRIPTION, NAMESPACE, etc. This separate space does NOT contain a copy of
src/init.c
Martin,
Your suggestion below did the trick. The issue was obvious once this pointed
me to the correct bit of code.
Thanks much.
Terry T.
begin included text ---
trace(loadNamespace, quote(if (package == "survival") recover()))
will break into ?recover when survival is being loaded
Martin,
1. I'd vote for replacement.
2. The "Sig" argument was completely opaque to me. I'd vote for something
like this
bracket = "fixed" the old behavior, treat the upper and lower as fixed
values
= "search" expand the limits if needed
= "usearch" only the
When I run R CMD check on the survival package I get one error message that I
have not been able to figure out:
survfitCI: no visible binding for global variable 'n.nevent'
I've examined the code and can't see the problem -- the variable in question
appears several times. Is there as way t
I'm working on the next release of coxme (ready to start some testing), and
have written major chunks of it using noweb -- very similar to Sweave except
I'm
generating code and documentation for the code rather than vingetes.
The question: I have directory with .Rnw objects and a Makefile th
The package coxme depends heavily on bdsmatrix, to the point of needing
access to some of its C calls. The kinship package (in progress) uses
the R level functions in bdsmatrix, but not the C calls. That is, I
don't want to always export the symbols.
For testing I can use an explicit dyn.load('s
://www.nabble.com/Dynamic-linking-to-binary-code-from-other-packages---td20167535.html#a20474561
>
> Take a look at 'xts' on cran, or R-forge. Specifically:
>
> http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/inst/api_example/README?rev=386&root=xts&view=m
R version 2.9.0 running on Centos (Red Hat linux).
I have a pair of packages coxme and bdsmatrix. The latter is installed
in my local library (I don't have permission for global install at
work.) That is, it is in the location pointed to in R_LIBS_USER. In R,
the command library(bdsmatrix) works
> Looks like a spelling error somewhere. The name is bdsmatrix (see
above).
That is so very obvious -- but only after someone else pointed it out.
The eye sometimes sees what it expects to see.
Thanks for the quick response.
Terry T.
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reate the .R files there, delete the config
and cleanup scripts, and submit that? Any ideas are appreciated.
Terry Therneau
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I'm currently packaging up some of the kinship matrix routines more
formally, these are used in coxme when dealing with family correlation
structures. One of my test programs exercises error conditions, i.e.,
it purposely feeds particular types of invalid pedigree data in to see
if the right erro
Kudos to Peter for actually answering the question of why the
inconsistency was there. It might be well to add a bit to the
documentation.
As to the larger discussion of global defaults let me offer two
opinions:
1. They are the salvation of those of us who do not agree with certain
global de
I get a warning about "1 warning message" using R CMD check on the
survival library. It comes from the code snippet:
if (library(cmprsk, logical.return=TRUE)) {
# further test of competing risks from survfit
.
.
}
This is a very useful additional test when I'm c
The suppressWarnings construct looks like a good idea; I was not aware
of it's existence.
Thanks for the feedback.
Terry T.
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is has a simple solution which I have missed.
Terry Therneau
tmt935% R --vanilla
R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under cer
Brian & Uwe,
Thanks for responding. Let me see if I can refine the query and move
towards a solution.
>From Uwe:
> Of course, after loading lme4, you can still use the ranef from coxme:
> coxme::ranef(fit)
Of course, but I'm interested in other users (as well as myself) and
prefer to avoid th
Doug wrote:
> I think a simpler solution, which I have implemented in lme4 but not
> yet released is to have
> importFrom(nlme, ranef, fixef)
> in the NAMESPACE file of packages that implement methods for those
> generics (and, of course, add nlme to the Imports: specification in
> the DESCRIPTIO
only) guess is memory corruption.
Questions:
Is this a rational guess? Any others?
Can you give any further insight on the error message?
Terry Therneau
sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
te replacement for kinship, at which point we will depreciate
it. (Pedigrees and plotting were finished last weekend!) But I can't
quite do that yet. The error does not arise with these newer libraries.
There have been no changes to kinship for some time.
Terry Therneau
> sessionInfo()
Peter,
There was no particular reason for an older kinship; just hadn't
downloaded it in a while. I grabbed a private copy just now and the
error went away, R 2.10.0. I remain curious as to what the message was
about, but not enough for either of us to do any work to find out.
I've sent off
e labeled with a tag, and
then referred to by that name in the future. This problem and solution
is discussed in a tutorial on Mecurial (http://hginit.com/, section on
"repository architecture"), precisely for matching the archive state to
a software release. I can't speak to any ot
the format is certainly not ambiguous. (Not standard, but not ambiguous).
Not important to fix, not something that date does any better.
> as.Date('09Sep2007')
Error in fromchar(x) : character string is not in a standard unambiguous format
Terry Therneau
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idea.
Not many (any?) people currently set na.action=na.fail because it is
a "better design".
--
Historically, languages designed for other people to use have been bad: Cobol,
PL/I, Pascal, Ada, C++. The good languages have been those that were designed
for their own creators: C, Perl, Smalltalk, Lisp. (Paul Graham)
Terry Therneau
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hes.) Is there another document that I should look at first?
Why "isNewList"? I would have guessed "isList". What's the difference?
Thanks for any help,
Terry Therneau
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All,
Thank you for the prompt and useful answers to my questions.
I had missed references in 5.7.6 which would have answered some of the
points.
As Bill pointed out a newer version of acrobat would help, but the Sun system
here is still running 5.0. (An oversubscribed sysadmin). Then I
n begin to participate as well. (Retirement in 10 years -- I don't
expect to maintain this forever!)
Terry Therneau
[EMAIL PROTECTED]
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his means.
Thanks much,
Terry Therneau
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iscussess a good setup for this middle
ground between concieving of a library and packaging it for delivery; the
"build, test, make sure it acually works" part of development.
Terry Therneau
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Thanks to all for the replys. I've learned several things
First -- I didn't miss anything obvious in the documentation. This is good in
one sense at least: I wasn't being blind. I had one misunderstanding pointed
out, which is that I need not worry about my test suite being run with each
INS
The following code works in Splus but not in R
coxph <- function(formula, data, weights, subset, na.action,
init, control, method= c("efron", "breslow", "exact"),
singular.ok =TRUE, robust=FALSE,
model=FALSE, x=FALSE, y=TRUE, ...) {
method <- match.arg(method)
Ca
In a few of my test scripts for the survival code I expect warning messages
(I actually try to trigger a couple). Using R BATCH infile outfile these
messages don't end up in outfile, where I can compare them to what was
expected. I don't see an option to change this.
R < infile >& outfile wor
pendix of my book, for which I know ALL the
answers.
There has been a change to the C code. Is this possibly due to a messed up
calling chain? I've converted from "Chambers" style callback to Rinternals
style (much cleaner and less mysterious), and the result works well in Splus.
I thought I'd made it through the hard part
Hints appreciated, after which I can give more details.
Terry Therneau
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Brian,
Thank you. This explains why it works in Splus: PROTECT is a null macro
there, so I wouldn't have caught the miscount.
Terry
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27;t bother
him hint".
If this addition followed on some discussion, please point me to it.
The reaction of other experienced users in our group has been the same, when
I
pointed this out. So I am not alone in the "why?"
Terry Therneau
PS. Here are tw
Thanks for the replies:
Duncan:
> and got a warning in all R versions I tried back to 2.4.1. In 2.3.1
> this was an error.
It seems I have egg on my face wrt this point. A more true synopsis of what
I
saw should have been that 1. I've never noticed this in R before and 2. Until
recently
ct except a matrix. Any suggestions to work around
this?
Terry Therneau
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d also looks out for dates. So the result is like ns() in the
eyes
of model.frame, and it works. But having to write gender twice on the rhs is
confusing to users.
Thanks in advance for any comments.
Terry Therneau
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I am getting an error that I don't understand from R CMD check on my current
instance of the survival code. R2.7.1 on Linux. Here is the last of the
log
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating survival-Ex.R ... OK
* checking exampl
There are some warnings earlier in the log about my .Rd files (missing a
description of weights and subset in a couple). The only message that I
don't completely understand is
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Error in firstlib(which.lib.lo
> ... you need library(survival) in R code in tests/. It doesn't happen
> automatically like it does for examples.
Thanks Thomas, that is exactly the hint I needed. I had read the "check"
part
of the manual 3 times in vain; once you pointed it out I was able to fine the
answer in the ma
R core team -
It took far, far longer than I anticipated, but I have finally finished the
next release of the survival code. Primary changes
1. The source has been migrated to Rforge. This will now be the primary
source. I've used SCCS -> rcs -> cvs and now svn. Further changes will be
so
?
I'll be out of town for the next few days (son's wedding) so instant response
is not necessary.
Terry Therneau
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this? It makes reading
the document to look for errors rather challenging. (That is, when I'm
looking at a particular Rd file, and want to see what it turned out to be.)
Terry Therneau
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You've answered my question 2 about why the manual was in odd order
> R CMD check was more of a check of the latex version of the files, not
> the final manual.
I was looking at the result of R CMD check, and it was in random order
(perhaps file date?), not just a different collation choice. Very
E file exports diag, along with several other methods that
do work. Any help would be appreciated.
Terry Therneau
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> 2. R CMD check gives dozens of warnings ...
Yes, I see a lot of warnings too, but I think that they can and should be
ignored.
1. There is a set where the generic function has "..." and my realization of
the generic has a named argument. But this is exactly what the ... is for in a
generi
Duncan,
When
The generic solve method has "(a, b, ...)"
I have "solve.gchol(a, b, full=TRUE, ...)"
I was assuming that I would still get an error from CMD check. These are the
ones that I argued as "unavoidable".
But... I just checked, and none of those were the squawkers, only t
rary is already loaded.
I looked at the manual page for dyn.load, but don't see anything. What
are we missing?
Please reply via email, as I don't read this list. (But I likely will start
to later this summer, when I port the newest mixed-effects Cox model code
over from S).
Te
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