ing
plot.new(). So you'll want to catch that as well.
In RKWard we use this technique at a number of places to insert "hooks" where
there are none, regularly.
Regards
Thomas
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cution of
make failed (translated output)
However, if i take the commands from the makefile, they all work out fine.
Any hints?
Best Whishes,
Thomas
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PDF are titled foo-methods instead of just foo.
I'd appreciate guidance on the issues above and maybe some pointers to some
well-documented S4 packages.
thanks,
--
[*Thomas Themel*] Oh, well. Size isn't everything, I hear; uptime may
also
[extended contact] be imp
s_1.41
loaded via a namespace (and not attached):
[1] tools_2.13.0
Best Whishes
Thomas Roth
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invoked, and not the version that came
bundled with Rtools (4.2) ? Or is this something I should better stay
away from ?
If not likely to work, what would you suggest to do instead ?
thanks and best,
Thomas
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https
On 04.04.2011 11:04, Prof Brian Ripley wrote:
On Sun, 3 Apr 2011, Thomas Mang wrote:
Hi,
I have R version 2.8.1 and Rtools 28 installed (as you might guess,
set up years ago). In Rtools the MinGW GCC 4.2 compiler toolset is
included.
For my regular C/C++ programs I have also installed
in the dependency
tree.
-thomas
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at can come in handy in GUI development
as well, and personally, I would appreciate, if there was some slightly more
official support for this.
Regards
Thomas
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will give the same answer a year later if I keep the old
versions. This isn't so much because of changes in R as because of
changes in packages.
-thomas
--
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University of Auckland
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Hi,
There's a possibility to put images into documentation files. Have a look at
the package visualizationTools to see how it works. The original idea is/was
by Romain Francois as far as i remember.
For instance have a look at the documentation for the function CLT
HTH
Thomas
2011/5/11 H
tion going on in the
background...
2011/5/11 Simon Urbanek
>
> On May 11, 2011, at 4:00 PM, Thomas Roth wrote:
>
> Hi,
>
> There's a possibility to put images into documentation files. Have a look
> at
> the package visualizationTools to see how it works. The origin
i got the original idea from
http://romainfrancois.blog.free.fr/index.php?post/2010/04/03/embed-images-in-Rd-documents
i really won't mind if this is removed. i can put a "clean" package online.
Didn't mean to do any harm.
Thomas
2011/5/11 Simon Urbanek
>
> O
; On May 11, 2011, at 4:43 PM, Thomas Roth wrote:
>
> > i got the original idea from
> >
> >
> http://romainfrancois.blog.free.fr/index.php?post/2010/04/03/embed-images-in-Rd-documents
> >
> > i really won't mind if this is removed. i can put a &qu
think the five numbers come from four memory allocations before
example() is called. Looking at the code in src/main/memory.c, it
prints newline only when the call stack is not empty.
I don't see why this is done, and I may well be the person who did it
(I don't have svn on this computer to check), but it is clearly
deliberate.
-thomas
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University of Auckland
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e, and so clearly
deliberate not to, that I suspect there may have been a good reason.
If I can't work it out (after my grant deadline this week) I will just
assume it's wrong.
-thomas
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t will still interact badly with the compiler?
Regards
Thomas
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that. And of course not any more than you trust the rest
of any other person's work, in the first place.
Of course, if what I am doing is "illegal" because it steps on the compiler's
turf, then my assumptions do not hold, indeed. That's what I'm
phics::plot.new(). Of course, even better, I
> > would like to have a hook that is called every time before a new page /
> > frame is started on a device.
>
> For all of the above: all of them are already available a device callbacks
> (newPage, close, activate and newPage agai
ase package?
Regards
Thomas
P.S.: Just to let you know, why I do not feel too much ashamed or scared of
changing things in other people's packages, here's (slighlty simplified) the
pattern that I'm following:
backup <- original
replacement <- function() {
call.my
e of my comments are specific to RKWard, since it is not even
> available for OS X so I don't know anything about it)
Well, I can't blame you for not trying it, since compilation on the Mac does
take ages, and we don't promise the result is any useful, ATM. We simply don'
ily trump the ability
to sub-class GUIs.
> Quartz is fairly nice in that you can provide additional back-ends fairly
> quickly - see R_ext/QuartzDevice.h - so you could embed it directly into
> your GUI. (But then I suppose the Mac support is too far away from reality
> for this to be
need not be a model frame in the fitted object. (it's optional)
2) More importantly, if you have y~sin(x), the model frame will
contain sin(x), not x. For what termplot() does, it has to be able to
reconstruct 'x', which isn't possible without the original data.
It's q
this affect the structure of the hsearch class?
Currently, our implementation for showing an item from the result list is to
simply call help(help_type="html"), appropriately. What are the implications
of vignettes for the behavior of help(), if any (with or without specification
of help_
arning! I have added (untested) support for the new
result types in RKWard.
Regards
Thomas
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eplacement length
I note that in the matches of that query, several vignettes are listed twice.
This probably indicates a problem in my installation, but may still be worth
fixing.
Regards
Thomas
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uldn't happen for a base package.
It appears, the cause of the problem was failure to "make clean" every once in
a while, and this resulted in installing both displaylist.Rnw and
displaylist.Snw (into a single library location).
Regards
Thomas
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u are telling the
compiler you're passing ints to Rprintf(), but you are actually
passing doubles.
When I fix these problems the code works for me.
-thomas
Thomas Lumley
Professor of Biostatistics
University of Auckland
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e that options(mc.cores=1) will effectively disable forking in
mclapply(). However, this would make it look like (local) parallelization is
not worth while at all, while actually, parallelization with
makePSOCKCluster() works just fine. So, I'm looking for a way to selectively
disable the u
of the problem, though. And thus, I think it would be a good idea, if
they had a standard way of informing library(parallel), and any third party
using library(parallel), if there is a problem with forking.
Regards
Thomas
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Hi Folks,
If you need to send data from Java to R you may consider using the
JDataFrame API -- which is used to convert data into JSON which then
can be converted into a data frame in R.
Here's the project page:
https://coherentlogic.com/middleware-development/jdataframe/
and here's a partial e
ually. Interestingly, the JSON encoding is using all 16 cores, so
> the 2.7s real time add up to over 20s CPU time so on smaller machines you may
> see more overhead.
>
> If you need process separation, it may be a different story - in principle it
> is faster to use more native ser
"def numbers = numberList.toArray()",
"def result = [strings, numbers]",
"return (Object[]) result",
sep="\n")
result <- Evaluate (groovyScript=groovyScript)
temp <- lapply(result, .jevalArray)
On Fri, Jan 15, 2016 at 1:58 PM, Simon Ur
Many thanks for clarification,
Thomas
Am 28.08.2016 um 23:48 schrieb Roger Koenker:
Hi Kurt,
I have started to look into this, and I need some guidance about how to
prioritize my repairs. There are basically 4 categories of warnings from
gfortran’s pedantic critique of my packages:
Am 02.09.2016 um 16:02 schrieb Dirk Eddelbuettel:
On 2 September 2016 at 14:54, Thomas Petzoldt wrote:
| Hi,
|
| I have the same problem and, at a first look, the issues reported by the
| CRAN checks seemed easy to fix. However, after checking it again locally
| and on http://win-builder.r
stop("'prob' and 'mu' both specified")
.Call(C_rnbinom_mu, n, size, mu)
}
else .Call(C_rnbinom, n, size, prob)
}
--
Thomas Roh
thms...@gmail.com
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The attached patch corrects a dead link in the treering documentation.
The URL in the manual [1] refers to a personal home page belonging to
Christine Hallman (user "hallman") on the website of the University of
Arizona Laboratory of Tree-Ring Research (LTRR). It seems that the LTRR
personal homep
This dead link is still present in the svn HEAD.
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Martin Maechler writes:
> There may be one small problem: IIUC, the wayback machine is a
> +- private endeavor and really great and phantastic but it does
> need (US? tax deductible) donations, https://archive.org/donate/,
> to continue thriving.
> This makes me hesitate a bit to link to it within
> If the R project cannot use or reference any site that uses non-open
> code, including minified javascript - which appears to be the
> principle issue for GitHub - I suspect that you will be obliged to
> discontinue links to almost every journal, university, charity,
> government and research est
stat.ethz.ch/pipermail/r-devel/2011-February/059947.html).
Is it relevant/possible to expose the drop argument explicitly?
Thanks,
Thomas
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_2hr",
"conc_3hr",
"conc_4hr",
"conc_5hr",
"conc_6hr",
"conc_8hr")))
Thanks,
Thomas
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in
my previous message).
____
De : SOEIRO Thomas
Envoyé : vendredi 12 mars 2021 23:59
À : r-devel@r-project.org
Objet : Potential improvements of ave?
Dear all,
I have two questions/suggestions about ave, but I am not sure if it's relevant
for bug reports.
1) I
Hi Abby,
Thank you for your positive feedback.
I agree for your general comment about sorting.
For ave specifically, ordering may not help because the output must maintain
the order of the input (as ave returns only x and not the entiere data.frame).
Thanks,
Thomas
k about it? (i.e is it relevant for a patch?)
Thanks,
Thomas
>
> De : Abby Spurdle
> Envoyé : lundi 15 mars 2021 10:22
> À : SOEIRO Thomas
> Cc : r-devel@r-project.org
> Objet : Re: [Rd] Potential improvements of ave?
>
> H
nette
also seems an excellent idea.
These changes will probably helps numerous users.
Best,
Thomas
On Wed, Mar 17, 2021 at 7:55 PM Michael Dewey
wrote:
>
> Comments in line
>
> On 13/03/2021 09:50, SOEIRO Thomas wrote:
> > Dear list,
> >
> > I have some questio
ust match the type of FUN(x) and warn for
coercion?
- Could ave be more flexible (i.e. allow different type of x and FUN(x)) if
using another approach than x[i] <- value[[j]] in split<-.default for
recycling?
This has already been discussed on r-help and stackoverflow (e.g.
https://stat.ethz.ch/pipermail/r-help/2016-November/442855.html)
Best,
Thomas
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t;
write.table(sep = ";", row.names = FALSE, col.names = FALSE)
ftable(formula = wool + tension ~ breaks, data = warpbreaks) |>
write.ftable2(sep = ";")
Best regards,
Thomas
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Dear Martin,
Thank you very much for your prompt feedback!
Best regards,
Thomas
-Message d'origine-
De : Martin Maechler [mailto:maech...@stat.math.ethz.ch]
Envoyé : jeudi 2 septembre 2021 11:30
À : SOEIRO Thomas
Cc : r-devel@r-project.org
Objet : Re: [Rd] sep hard cod
There is a small typo in the NEWS file: write.table -> write.ftable
-Message d'origine-
De : SOEIRO Thomas
Envoyé : jeudi 2 septembre 2021 13:10
À : 'Martin Maechler'
Cc : r-devel@r-project.org
Objet : RE: [Rd] sep hard coded in write.ftable
Dear Martin,
Thank you
DateTimeClasses:
It may be useful to add in the documentation of DateTimeClasses that
manipulating elements of POSIXlt objects may results in "invalid" entries
(e.g., mon = 12 or mday = 0), but that the object is nevertheless correctly
printed/coerced.
Is this behavi
c.Date manage
fractional days with round(x - 0.499).)
-Message d'origine-
De : SOEIRO Thomas
Envoyé : mercredi 29 septembre 2021 17:00
À : 'r-devel@r-project.org'
Objet : trunc.Date and round.Date + documentation of DateTimeClasses
Dear All,
1) trunc.Date and round.Dat
voyé : jeudi 30 septembre 2021 15:27
À : SOEIRO Thomas
Cc : r-devel@r-project.org; Dirk Eddelbuettel
Objet : Re: [Rd] trunc.Date and round.Date + documentation of DateTimeClasses
EMAIL EXTERNE - TRAITER AVEC PRÉCAUTION LIENS ET FICHIERS
Excuse the exceptional top-reply:
Note that a very related issue
e même longueur que le vecteur [1]
Best regards,
Thomas
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arpbreaks[2], dnn = letters[1]) # as documented
> # a
> # A B
> # 27 27
>
> table(zzz = warpbreaks[2], dnn = letters[1]) # as documented
> # a
> # A B
> # 27 27
>
> table(zzz = warpbreaks$wool, dnn = letters[1]) # as documented
> # a
> # A B
>
# Warning messages:
# 1: In xtfrm.data.frame(x) : cannot xtfrm data frames
# 2: In xtfrm.data.frame(x) : cannot xtfrm data frames
Best regards,
Thomas
> -Message d'origine-
> De : Martin Maechler [mailto:maech...@stat.math.ethz.ch]
> Envoyé : jeudi 14 octobre 2021 11:4
s should be an error?
>
> table(warpbreaks[2], warpbreaks[3])
> #
> # 1:3
> # 1:2 0
> # Warning messages:
> # 1: In xtfrm.data.frame(x) : cannot xtfrm data frames
> # 2: In xtfrm.data.frame(x) : cannot xtfrm data frames
>
> Best regards,
>
> Thomas
>
#x27;t think we expose it at the R level, though it is part
> > of the official C API. I don't know of any plans for this to change, but I
> > suppose it could. Plus for functions in R itself, we could even use it
> > without exposing it more widely. A number of func
Dear Martin,
Should I finally report a bug for this (these?) remaining issue as initially
agreed?
Best regards,
Thomas
> > Dear Martin,
> >
> > Thank you for the perfect fix. It fixes both issues in the 1-dim case (i.e.
> > automatic dnn *and* disregard dnn/names
") since `apply` recently
gained a `simplify` argument.
Best,
Thomas
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for similar
functions), I suspect that I am missing something...
Best,
Thomas
dfs <- list(x = warpbreaks)
dfs$x$id <- seq_along(dfs$x$breaks)
dfs$y <- dfs$x[1:15, ]
dfs$z <- dfs$x[20:35, ]
identical(
Reduce(function(...) merge(..., by = "id", all = TRUE), dfs),
Reduc
. Of course this is minor, but imho one of
the strengths of R is also its documentation!
Best,
Thomas
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:59
À : SOEIRO Thomas; R Development List
Objet : RE: Documentation of addmargins
EMAIL EXTERNE - TRAITER AVEC PRÉCAUTION LIENS ET FICHIERS
Thomas SOEIRO wrote:
> Dear list,
> There is a minor typo in addmargins (section Details):
> - If the functions used to form margins are not commutat
atural to retry
until the requested data are available?
-thomas
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Professor of Biostatistics
University of Auckland
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e?
Thanks a lot for developing this great software!
Thomas
Example:
set.seed(357)
z1 <- matrix(runif(100, -1e-180, 1e-180), nrow = 10)
contour(z1)# ok
z2 <- matrix(c(runif(50, -1, 1), runif(50, -1e-180, 1e-180)), nrow = 10)
contour(z2) # Error in contour.default(z) : k !=
On 13.09.2013 16:44, Prof Brian Ripley wrote:
On 13/09/2013 15:14, Duncan Murdoch wrote:
On 13/09/2013 10:01 AM, Thomas Petzoldt wrote:
Dear R developers,
I found a small issue while plotting contours of data containing both
"usual" and "very small" numbers. It appeared w
ons that way, you need to make potentially
unsafe assumptions. For example, that you can't get an error halfway up a
chain of nested complex assignments when it's too late to back out of the
expression.
-thomas
--
Thomas Lumley
Professor of Biostatistics
University of Auckland
ot printing information to
stdout for R CMD Sweave is intended or not, but I thought I'll report it
along with confirming R CMD Sweave no works again for me.
Best wishes
Thomas
> sessionInfo()
R Under development (unstable) (2014-04-22 r65449)
Platform: x86_64-unknown-linux-gnu
y instead.
>
As a follow-up to this, note that with traditional Unix symbol
resolution it was forbidden to have two different routines with the
same name linked into an object. That just isn't an option for R
because of the package system. This isn't theoretical: the PACKAG
rsity of Sydney
> Camperdown NSW 2050
> Australia
Dario,
When you use the constructor, the environment of the function is the
environment inside the constructor; when you use new() it is
R_GlobalEnv
The way functions print is that they print their environment when it
isn't
functions worked as expected. See example below.
The symptom is that super assignments (<<-) of unmodified variables lead
to "references" instead of copies.
Thomas Petzoldt and Karline Soetaert
## --
## Unexpected behavior:
#
hi,
Am a software developer having 4 yr experience in c++.I want to
integrate R environment in my c++ application,please help me to do so.
thanks®ards
blesson
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http
27;[' allows multiple columns and
> handles rownames. Sure enough, '[[,]]', which allows only one column, and
> does not handle rownames, is almost 3x faster:
That's part of it, but if you look at [.data.frame you see there is
also quite a bit of copying that could be avoided
atistics unit
> IRB Barcelona
> Tel (+34) 93 402 0553
> Fax (+34) 93 402 0257
>
> evarist.pla...@irbbarcelona.org
> http://www.irbbarcelona.org/bioinformatics
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r
general it's not
clear what (if anything) it means to have the same contrasts on
factors with different numbers of levels.
-thomas
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If .Call and .C re-enabled the GC on return from compiled code (and
threw some sort of error) that would help contain the potential
damage.
You'd might also want to re-enable GC if malloc() returned NULL,
rather than giving an out-of-memory error.
-thomas
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appened independently in R. I ported the 'survival'
version of rowsum() to R, added it to base R in version 0.63.1, and
later it made it faster using hashing.
So perhaps it isn't entirely StatSci's fault, although it's likely
that R would eventually have added a rowsum(
?
>
tracemem() isn't likely to give false positives. Since you're on
Linux, you could check by running under gdb and setting a breakpoint
on memtrace_report, which is the function that prints the message.
That would show where the duplicates are happening.
- thomas
--
Thomas Luml
ch")) {
myarg <- match.arg(myarg)
}
## test
plain("Zürich") ## works
plain("Z\u00BCrich") ## fails
escaped(&
On Thursday 19 January 2012, peter dalgaard wrote:
> On Jan 18, 2012, at 23:54 , Thomas Zumbrunn wrote:
> > plain("Zürich") ## works
> > plain("Z\u00BCrich") ## fails
> > escaped("Zürich") ## fails
> > escaped("Z\u00BCrich&q
On Friday 20 January 2012, Simon Urbanek wrote:
> On Jan 19, 2012, at 6:39 PM, Thomas Zumbrunn wrote:
> > On Thursday 19 January 2012, peter dalgaard wrote:
> >> On Jan 18, 2012, at 23:54 , Thomas Zumbrunn wrote:
> >>> plain("Zürich") ## works
> >>
and lose
data, I would prefer to make the user decide what to do.
-thomas
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inputs into numbers
that are indistinguishable from uniform random except that the same
input always gives the same output.
What's harder is to prove that you *have* a good quality hash
function, but for these (non-adversarial) purposes even something like
MD4 would be fine, and certainly the SHA family.
-thomas
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because the use is guarded
by an if(), but CMD check can't tell this. So, it's a good idea to
remove all Notes that can be removed without introducing other code
problems, which is nearly all of them, but occasionally there may be a
good reason for code that produces a Note.
But if you
th a bound on the degree of freedom difference, but my copy
of Claeskens & Hjort's book on model selection and model averaging is
currently with a student so I can't be definitive.
-thomas
--
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Professor of Biostatistics
University of Auckland
___
orced to do that, but I thought it was supposed to be a last resort and
> that I was *supposed* to be able to fix my problems by proper use of
> imports.
'Imports' won't be enough -- the whole point of a generic is that it's
visible to the user, which doesn't happen with imports.
-thomas
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es on CRAN or
Bioconductor using it, and I can't think of any situation where it
would be used deliberately.
-thomas
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isn't a ... formal argument in
scope.
-thomas
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stitute(expr)
eval.parent(expr)
}
-thomas
On Sat, Oct 20, 2012 at 10:35 AM, Charles Geyer wrote:
> is it possible to set an option inside a function ((I want to set
> na.action = na.fail) and have the previous state restored if there is
> an error so that the fu
re should be
a warning, such as gcc's "control reaches end of a non-void function"
Also .C() doesn't pass SEXPs, so the declaration of the function is still
wrong for .C(), though this one the compiler won't notice.
--thomas
--
Thomas Lumley
P
more precisely a table of contents for the package.
The INDEX is part of what is displayed by help(package="pkgname"). It was
more important before package help pages and vignettes, especially for
non-GUI systems when it could be quite hard to work out which function help
pages to look at in
I agree that it's cleaner to remove the extra attributes -- that's the
point of as.matrix.Surv(), to produce a matrix that doesn't include any
extra details of how Surv objects are implemented.
-thomas
On Fri, Dec 7, 2012 at 3:48 AM, Terry Therneau wrote:
> 1. A Surv
ty of the matrices are actually invertible.
You can probably do slightly better by replacing the chol2inv() with
backsolve(): solving just the systems of linear equations you need is
usually preferable to constructing a matrix inverse.
Note that this approach will give wrong answers without warnin
that it appears to be unavailable.
Any suggestions for how to fix this? I've tried uploading a new version of
RMonetDB, but the situation didn't change: it built successfully, but the
Linux check of sqlsurvey still couldn't find it.
-thomas
--
Thomas Lumley
Professor of Biosta
hough - from a naive POV - it would
seem easy enough to make it functional across platforms(*).
Regards
Thomas
(*) E.g. changing the selectlist stub to:
--
SEXP selectlist(SEXP call, SEXP op, SEXP args, SEXP env)
{
if(ptr_do_selectlist) return ptr_do_selectlist(call, op, CDR(args), env);
#if
object is out of scope" it seems harmless to be able to prevent finalizers
from running during a particular code block, but I can't see any way to do
it.
Suggestions?
-thomas
--
Thomas Lumley
Professor of Biostatistics
University of Auckland
[[alternative
of running an R code block and knowing that no
other R code block would run during it (user interrupts are another issue,
but they can be caught, and in any case I'm happy to fail when the user
presses CTRL-C).
-thomas
On Fri, Feb 15, 2013 at 12:53 AM, wrote:
> It might help if
asible on
commodity desktops and laptops, and even on computers with enough memory,
the database (MonetDB) is faster.
-thomas
--
Thomas Lumley
Professor of Biostatistics
University of Auckland
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ith analysis in memory even
if you ignore the data loading time.
For example, using a data set already in memory, with 18000 records and 96
variables:
> system.time(svymean(~BPXSAR+BPXDAR,subset(dhanes,RIAGENDR==2)))
user system elapsed
0.090.010.10
Using MonetDB
...)
but it seems that could have different lazy-evaluation behaviour.
-thomas
--
Thomas Lumley
Professor of Biostatistics
University of Auckland
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he log(n) term is kept and various terms of
order 1 are discarded. What we're arguing about is one of the O(1) terms.
If it makes an important difference then presumably we should also worry
about the other O(1) terms that got discarded.
-thomas
--
Thomas Lumley
Professor of Biost
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