aving directory `/usr/local/src/R/r-devel/R/src/library'
make: [docs] Error 2 (ignored)
any ideas?
Ben Bolker
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witkovsky wrote:
>
> Full_Name: Viktor Witkovsky
> Version: 2.9.2
> OS: Windows XP
> Submission from: (NULL) (78.98.89.227)
>
>
> Hello,
>
> I have found strange behavior of the function qchisq (the non-central
> qchisq is
> based on inversion of pchisq, which is further based on pgamma). T
as numeric (and very ugly)
! ## I don't know how to safely convert the breakpoints
! ## back to a character format (e.g.
! ## levels(res) = [1970-01-01 00:00:00,1970-01-01 12:00:00)
! ## instead of [18000,61200)
! }
! }
res
}
--
Ben Bolker
As
to speak) if
length(breaks)!=length(levels(res))-1
I could keep working on a patch if requested, but probably won't otherwise.
Ben Bolker
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S
Ben Bolker wrote:
>
>
> [snip]
>
> It appears that glmmPQL looks in the global workspace, not
> within the data frame specified by the "data" argument, for
> the variables specified in the "form" argument of spatial
> correlation struc
Ben Bolker ufl.edu> writes:
> > [snip example and patches]
> The basic issue is that glmmPQL throws out data that are
> not involved in the fixed or random model terms, or in the offset
> term. It doesn't save variables that are only found in the
> correlation formu
Marc Schwartz me.com> writes:
>
[snip]
> See ?pdf and read through the "Note" section.
>
While I was reading this I noticed two minor typos
in pdf.Rd.
These patches are against the latest SVN devel version.
*** pdf.Rd.orig 2009-11-05 14:37:44.0 -0500
--- pdf.Rd 2009-11-0
xs4all.nl> writes:
>
> Full_Name: Ludo Pagie
> Version: 2.10.0
> OS: linux, ubuntu, 8.04
> Submission from: (NULL) (83.163.218.221)
>
> when I make a polygon with 100,000 vertices my X-server is being
> killed. This occurs in R-2.9.0 and a freshly installed R-2.10.0
> I'm running Ubuntu with a
Steve Kalke uni-rostock.de> writes:
> I would like to know if there is an R-package available for
> computing the density, distribution function,
> quantiles and random
> numbers of the p-generalized normal distribution or
> if somebody is already working on it.
I haven't been able to find
1. footnote 5, p. 52: "there is only a fine distinction between \dots
and \dots"
I should hope so :-) (from context, I think one of these should be
\ldots instead)
2. under "\keyword{key}", p. 45: "are not part of the packages' API."
Should that be "package's" ?
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Descripti
Ken Knoblauch inserm.fr> writes:
>
> Hi,
>
> I would have thought that these two constructions would
> produce the same result but they do not.
>
> Resp <- rbinom(10, 1, 0.5)
> Stim <- rep(0:1, 5)
> mm <- model.matrix(~ Stim)
> Xb <- mm %*% c(0, 1)
> ifelse(Resp, log(pnorm(Xb)), log(1 - pnorm(
live somewhere on the
same SVN server, which might not be true ...) Any ideas (including
pointing out the obvious, or the obvious-in-hindsight)?
thanks
Ben Bolker
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. And
https://svn.r-project.org/R/trunk/src/library/Recommended/ shows that
only Makefile.in and Makefile.win live here.
Does your src/library/Recommended have up-to-date source code for all
the packages ... ?
cheers
Ben
Kasper Daniel Hansen wrote:
> The obvious: the recommended packages
thanks!
Prof Brian Ripley wrote:
> On Tue, 15 Dec 2009, Ben Bolker wrote:
>
>> I followed the suggestions at
>> http://developer.r-project.org/SVNtips.html to check out an anonymous
>> copy of the development branch of R, but so far I have been unable to
>>
Does anyone have an address for a maintainer, or know what's going on?
cheers
Ben Bolker
b...@bolker-lap2:~$ ping wiki.r-project.org
PING econum.umh.ac.be (193.190.194.5) 56(84) bytes of data.
^C
--- econum.umh.ac.be ping statistics ---
8 packets transmitted, 0 received, 100% p
who wants to write rgl code to do these?
http://tinyurl.com/yzojfn2
http://tinyurl.com/ylrz2p8
:-)
Ben Bolker
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gests that they
*don't* want it redistributed ... ? Would it be helpful if I did this,
or is this the sort of thing the package maintainer should do?
Mike Meyer: mi...@andrew.cmu.edu
Alan Genz: g...@gauss.math.wsu.edu
cheers
Ben Bolker
--
Ben Bolker
Associate professor, Biology Dep't, U
R" where the Bray Curtis distance formula is
actually the Canberra
> distance (Eq. 10.2 p. 289). There seems to be a certain slipperiness of
definition in this field.
Actually, the author is M. H. Henry (Hank) Stevens, not "Henry & Stevens" ...
Ben Bolker
_
Saptarshi Guha gmail.com> writes:
>
> Hello,
> Is it possible to extend the R lexer/parser to include multiline comments like
> /*
> acomment
>
> */
> ?
> This way I can integrate emacs org-mode with my R code, so that I can
> have a table of contents,
> section folding, html-output of source e
...
This does seem like a funny choice, but it is probably stuck
that way without an extremely compelling argument to the contrary.
If you want to scale columns by sd() instead you can say
scale(x,center=FALSE,scale=apply(x,2,sd))
Would you like to submit a patch for the documentation that
wo
[cc'ing back to r-devel]
Maria Rizzo wrote:
> Ben,
>
> I receive the digest version of r-devel - so I do not have the
> individual messages to reply to. In reply to yours:
>
> I think this is a bug for the following reasons. While it is true
> that one can define
e your homework' by searching
in various places on the web, or in books, for the answer to
your question, before posting to the list.
cheers
Ben Bolker
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Ben Bolker ufl.edu> writes:
[re: behavior of scale() when center=FALSE and scale=TRUE]
> Again, I agree with you that the behavior is not optimal, but it is
> very hard to make changes in R when the behavior is sub-optimal rather
> than actually wrong (by some definition). R-
ted) ... I went to bugzilla, and bug 14219 doesn't
seem to exist any more -- either as open or as closed -- don't know if
it got lost, or thrown away, when the bug system migrated?
cheers
Ben Bolker
[re: behavior of scale() when center=FALSE and scale=TRUE]
> Again, I
Thanks Simon!
How irritating/wrong would it be if I opened a new bug to submit my
suggested documentation patch? As detailed below, I think the
documentation is somewhat confusing (it depends on a highly non-standard
definition of "standard deviation" ...)
cheers
Ben Bolk
estion 2: For this type of model (GAM), is there a simple way
* of constructing an equation for the model
* (e.g., to come up with predicted values).
You probably want to use the predict() functions provided with
mgcv/GAM. It wouldn't hurt to read Simon Wood's book
sunsite.utk.edu/CRAN";
rather than
contrib.url(getOption("repos"))
[1] "http://mira.sunsite.utk.edu/CRAN/src/contrib";
Is this (as it seems to me) a bug? Should I report it as such?
--
Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bol...@ufl.edu /
{alternative}. A confidence interval for the
underlying proportion with confidence level as specified by
--
Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bol...@ufl.edu / people.biology.ufl.edu/bolker
GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc
signatur
Felix Andrews nfrac.org> writes:
>
> x <- seq(as.POSIXct("2000-01-01"), by = "days", length = 20)
>
> cut(x, breaks = 3)
> # Error in `levels<-.factor`(`*tmp*`, value = character(0)) :
> # number of levels differs
>
> cut(as.Date(x), breaks = 3)
> # Error in `levels<-.factor`(`*tmp*`, value
(" If missing,
defaults to the first element of ‘.libPaths()’.") It's one of the most
common questions I have to answer for students during introductory R
sessions ...
If there's not, would anyone get annoyed if I submitted a wishlist
ite
> On 25/05/10 23:25 PM, "Ben Bolker" ufl.edu> wrote:
> Just curious: is there a particular reason why install.packages()
> gives a warning in normal use when 'lib' is not specified (e.g. argument
> 'lib' is missing: using '/usr/local/lib/R/site
Michael Dewey wrote:
> At 13:40 01/06/2010, Ben Bolker wrote:
>
>>> On 25/05/10 23:25 PM, "Ben Bolker" ufl.edu> wrote:
>>> Just curious: is there a particular reason why install.packages()
>>> gives a warning in normal use when 'lib' is
Martin Maechler wrote:
>>>>>> "BB" == Ben Bolker
>>>>>> on Wed, 02 Jun 2010 13:45:18 -0400 writes:
>
> BB> Michael Dewey wrote:
> >> At 13:40 01/06/2010, Ben Bolker wrote:
> >>
> >>>>
propto \beta
$$
\end{document}
(7514 bytes)
and try to figure out how the fonts are being treated differently ...
Yvonnick Noel wrote:
> Hello Ben,
>> Does the workaround pointed out later in the thread you're
>> responding to (from the last paragraph of a very long 'Note&#
yone who has read this far: right now I am calling my
extended function mle(), but that seems to be asking for trouble
[i.e. confused questions from users who don't know they're using
bbmle::mle and not stats4::mle]. Any recommendations for what to
call it? mle2? mlex ("extended mle&q
ssian = TRUE, ...)
10: function (par)
11: fn(par, ...)
12: do.call("minuslogl", args, envir = environment(minuslogl))
13: minuslogl(ltheta = 2.30970721353114, lmu = -2.18543734742826)
14: lapply(arglist1, eval, envir = data, enclos = sys.frame(sys.nframe()))
15: is.vector(X)
h those
changes?
Thanks
-Ben
--
Ben Walton
Systems Programmer
Office of Planning & IT
Faculty of Arts & Science
University of Toronto
Cell: 416.407.5610
GPG Key Id: 8E89F6D2; Keyserver: pgp.mit.edu
Contact me to arrange for a CAcert assurance meeting.
Please Note: This e-mail is intended
for this reason. I prefer fewer surprises in
production machines when possible.
I'll discuss the required(1) changes with Martyn and submit them if he's
agreeable.
Thanks
-Ben
(1) assuming that they are required and I'm not missing the obvious.
--
Ben Walton
Systems Programmer
Office of P
ines/workstations, etc). FC has it's (very important)
place and I do suggest that home users work with it (or Ubuntu/Debian).
The other issue with FC in production is the legacy support one. I
can't be bothered to upgrade machines as often as the fc support cycle
would have me do (I miss
Wiki)
Ben Bolker
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Tony Plate wrote:
> I've wondered about this sort of thing too. Are there any successful
> models like this for other program languages/systems?
>
> -- Tony Plate
>
> Ben Bolker wrote:
>> Has anyone considered a bounty system for R?
>> (i.e., some kind of s
d I think Peter Dalgaard in particular)
in writing the original code. If I add "R Development Core
Team" to the author list I feel I am suggesting that they
might be responsible for my changes. Neither seems entirely
appropriate.
Suggestions?
Ben Bolker
PS this is my current DESCRIPT
specify it explicitly instead.
Does anyone have clever (or elegant) solutions to these two problems?
Ben Bolker
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udec.cl> writes:
>
> Full_Name: bernardo moises lagos alvarez
> Version: 2.4.0
> OS: Windows XP professional
> Submission from: (NULL) (152.74.219.16)
>
> > nlm(fllwfuncHnew,p=c(1,20),x=xdat)
>
> Erro en log(b) : el argumento "b" está ausente, sin default
>
> __
The current NEWS file on the R site states that there is
a new relink (sic) function, which should probably be
relist ...
Ben Bolker
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I have some binaries I would like to distribute with a package
(I am not the original author; I have the source code but can't distribute
it because it contains _Numerical Recipes_ code. The long-term
solution is to replace the code with new code written in R, or
in clean C, but in the meantim
fastmail.fm> writes:
> The problem is that fn is not the model to be fitted.
> The model is y = p1*x/(p2
> + x).
Actually, I would say the model is
y_i ~ Normal(p1*x_i/(p2+x_i),sigma^2) ...
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I did some trawling on the ISI web of science,
selecting all papers citing all papers
with "R DEV COR TEAM" in the author field
(which is how ISI seems to be tagging things).
The results are interesting -- about 2400 references.
Enjoy these summaries ...
urlpref = "http://www.zoo.ufl.edu/bolke
themselves with ... (of course this won't prevent
you from sweeping the wrong margin of a square matrix,
but nothing will).
cheers
Ben Bolker
sweep <- function (x, MARGIN, STATS, FUN = "-", check.margin=TRUE, ...)
{
FUN <- match.fun(FUN)
dims <- dim(x)
Ben Bolker zoo.ufl.edu> writes:
> What would R-core think of the following 'enhanced'
> sweep?
(now posted at
http://wiki.r-project.org/rwiki/doku.php?id=rdoc:base:sweep
)
It always warns if dim(x)[MARGIN] is
> not a multiple of length(STATS) {it's very hard in
"New Scottland Yard" should be "New Scotland Yard"
cheers
Ben Bolker
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riate signs of df and deviance, and how to fix it ...
Ben Bolker
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h(start)==0 and then setting
oout <- list(par=start, value=f(start),
hessian = matrix(numeric(0),0,0)
or something along those lines.
Or one could change L-BFGS-B to behave the same
as the other methods.
cheers
Ben Bolker
-
library(stats4)
## usi
something along those lines.
Or one could change L-BFGS-B to behave the same
as the other methods.
cheers
Ben Bolker
-
library(stats4)
## using example from ?mle
x <- 0:10
y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8)
ll <- function(ymax=15, xhalf=6)
-sum(st
x = readLines("http://developer.r-project.org/R.svnlog.2007";)
rx = x[grep("^r",x)]
who = gsub(" ","",sapply(strsplit(rx,"\\|"),"[",2))
twho = table(who)
twho["ripley"]/sum(twho)
74% of all commits!
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R will always be arcane to those who do not make a serious effort
to learn it. It is ***not*** meant to be intuitive and easy for casual users
to just plunge into.
-- Bert Gunter, R-help, 06/08/2007
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hat its other implications are.
Or one could change L-BFGS-B to behave the same as the other methods.
If I don't hear anything in a few days would it be appropriate
to submit this as a bug report?
cheers
Ben Bolker
-
library(stats4)
## using example from ?mle
x <
ne
and above the diff/patch. Sorry if I wasn't clear about that.
cheers
Ben Bolker
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kage at some point ... ???
Ben Bolker
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Prof Brian Ripley wrote:
> On Tue, 14 Aug 2007, Peter Dalgaard wrote:
>
>> Ben Bolker wrote:
>>> Petr Savicky cs.cas.cz> writes:
>>>
>>>
>>>
>>>> Could you also include a script, which reproduces the problem? Just
>>>>
If one calls data.entry() with a matrix:
A = matrix(0,2,2)
data.entry(A)
everything works fine except that it triggers a warning:
Warning message:
the condition has length > 1 and only the first element will be used in:
if (dim(x) == dim(args[[i]])) rn <- dimnames(args[[i]])[[1]] else rn
the first line of dist() says
if (!is.na(pmatch(method, "euclidian")))
shouldn't that be "euclidean" ?
-
R version 2.5.1 (2007-06-27)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSA
were (fixable) problems compiling under R-devel.
cheers
Ben Bolker
Package: GeneR
Title: R for genes and sequences analysis
Description: Package manipulating nucleotidic sequences (Embl, Fasta,
GenBank)
Version: 2.6.0
Date: 2006-03-17
bioc
oops. sorry. should have figured something
this obvious would have been on purpose.
Ben
Peter Dalgaard wrote:
> Ben Bolker wrote:
>> the first line of dist() says
>>
>> if (!is.na(pmatch(method, "euclidian")))
>>
>> shouldn't that be
my geostats books to check this, but found at least
one paper that cites the "correct" (1/(1+(d/r)^2) formula -- see below
cheers
Ben Bolker
@ARTICLE{Ekstrom+2005,
author = {Ekstr{\o}m, Claus T. and Bak, S{\o}ren and Rudemo, Mats},
title = {Pixel-level Signal Modelling with Spati
I'm resending this after a decent interval of 20 days -- any
opinions? Should I file it as a bug report? Is it my mistake?
cheers
Ben Bolker
Original Message
Subject:buglet (?) in de.restore()
Date: Tue, 21 Aug 2007 13:29:33 -0400
From: Ben B
"if more than one object are provided, "
could be
"if more than one object is provided"
or
"if multiple objects are provided"
cheers
Ben Bolker
> sessionInfo()
R version 2.5.1 (2007-06-27)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8
under factor.levels: specicifying
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question to r-help
* hint: the third argument to aggregate needs to be a function, further
optional
arguments can be specified. sd(x) is not a function. sd is.
sincerely
Ben Bolker
--
View this message in context:
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e, check out
ttm (TeX-to-MathML) as well.
The SGML approach does seem like the wave of
the future, but in the meanwhile TeX/tth works well
for me.
Ben Bolker
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7;t blame Petr for these comments, I'm just using his ideas as
an example)
cheers
Ben Bolker
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Sent from the R devel mailing list archive at Nabble.com.
_
tly more detail: in the "eureka" function, in stats/src/eureka.f, the
last
element of "vars" in the return list is bogus and varies among calls; if it
comes out to NaN or NA it triggers the bug.
Haven't spent any more time yet tracking this down, but hope that
will
e.r-project.org";)
works.
Ben Bolker
--
View this message in context:
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Sent from the R devel mailing list archive at Nabble.com.
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>
>
At this point I'd just like to advertise the "bbmle" package
(on CRAN) for those who respectfully disagree, as I do, with Peter over
this issue. I have added a data= argument to my version
be used more creatively and flexibly by
those who know how. ***
>>> It is not at all an unlikely design to have mle() as a generic function
>>> which works on many kinds of objects, the default method being
>>> function(object,...) mle(minuslogl(obj)
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Luke Tierney wrote:
> On Fri, 7 Dec 2007, Duncan Murdoch wrote:
>
>
>
> For working at the general likelihood I think is is better to
> encourage the approach of definign likelihood constructor functions.
> The problem with using f, data is that you
range(pu, f = -1/27)
ll <- if (par("xlog"))
10^pu
else pu
ll
})
i.e., extend pu, not ll ...
cheers
Ben Bolker
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Comment: Using GnuPG with M
i.edu.au/limma/Rdocs.html exist
anywhere, any more?
Ben Bolker
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.6 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
iD8DBQFHW4GNc5UpGjwzenMRAhVbAJoCtN0kyUmiSVSwW3cjQYQmgQd0qACdGigo
LMMGnNdlodrCETGuIWunTd4=
=JF
d a
new generic, "display", which does a similar thing but
has an intermediate level of detail (between "print/show"
and "summary")
Ben Bolker
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Agreed. It turns out a similar hack is done in the lme4
package for printMer ...
Martin Morgan wrote:
> Ben --
>
> My vote would be against overriding the generic for show. If for some
> reason your version proves inadequate, you force the user to
> (conditional on loadi
m having trouble sorting out what the limitations
are ...)
hoping for enlightenment (it would be lovely to be
shown how to make this work, but a definitive statement
that it is impossible would be useful too).
cheers
Ben Bolker
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.6 (GNU
being restricted to atomic vectors + Date/factor).
cheers
Ben
Martin Morgan wrote:
>
> Ben, Oleg --
>
> Some solutions, which you've probably already thought of, are (a) move
> the data.frame into its own slot, instead of extending it, (b) manage
> the data.frame attribut
. It would
have been helpful to have it in the R-ints manual section as well ...
thanks
Ben Bolker
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Bjørn-Helge Mevik wrote:
>
> Ben Bolker wrote:
>
>> http://cran.r-project.org/doc/manuals/R-ints.html#R-coding-standards
>>
>> gives detailed advice on how to set the indentation level for
>> C code to 4, but it took me a bit of poking around in the archiv
Martin Maechler stat.math.ethz.ch> writes:
>
> >>>>> "BB" == Ben Bolker ufl.edu>
> >>>>> on Sun, 23 Dec 2007 15:31:23 -0800 (PST) writes:
>
> BB> Bjørn-Helge Mevik wrote:
> >>
> >> Ben Bol
)
are posted at http://www.zoo.ufl.edu/bolker/R-ints_diff.txt ...
cheers
Ben Bolker
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Version: GnuPG v1.4.6 (GNU/Linux)
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iD4DBQFHb/LGc5UpGjwzenMRAv82AJdSx8PcYXi0dFTo4XatJzZ5WO4HAJ47acGW
bA/phOy/h/BwLS7RK1b
gmx.net> writes:
>
> Peter Dalgaard reminded me to be more specific about my computing platform;
it's Debian 4.1.1-19 on a
> 32-bit Pentium 4 machine (Dell Optiplex GX620).
>
> The problem I described (nls not returning) also occurs with different
> data at
> other values of the scal paramete
and the .bzrignore file, it seems to be necessary to specify
[.]bzr$
[.]bzrignore
in the .Rbuildignore file before calling R CMD build.
This is certainly sufficient in my case, but since the patch is just one
line, perhaps it should be considered for inclu
Full_Name: Ben Hansen
Version: 2.6.1
OS: Windows
Submission from: (NULL) (66.93.3.101)
Hi,
In R 2.6.0 or 2.6.1 on Windows, I get the following upon opening the GUI (no
previous commands or special settings):
> signif(digits=4, x=1/3)
[1] 4
It seems to be taking 4 to be the "x"
hits=-2.6 tests=BAYES_00,SPF_HELO_PASS,SPF_PASS
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From: Bert Gunter gene.com>
Subject: Re: Maximum number of variables allowed in a multiple
linearregression model
Newsgroups: gmane.comp.lang.r.general
Date: 2008-02-05 18:00:40 GMT
I can repeatably crash R (segfault)
by doing
n <- 10
z <- data.frame(a=1:n,b=1:n)
View(z)
and then hitting the "End" key on my keyboard.
I haven't got debugging going yet, but running under
gdb (without debugging symbols) does give this:
0xb7b63583 in strlen () from /lib/tls/i686/cm
be an integer -- so
I don't think this is a bug.
Should the function either (a) test for k == (or close to ==) an integer
or (b) be rewritten to work more generally?
Ben
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The warning in "identify" when no point is close enough
to the clicked point is
./src/main/plot.c:3190: REprintf(_("warning: no point with
%.2f inches\n"), tol);
that should probably be "within" ...
Ben Bolker
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Despite the spirited arguments of various R-core folks
who feel that mle() doesn't need a "data" argument, and
that users would be better off learning to deal with function
closures, I am *still* trying to make such things work
in a reasonably smooth fashion ...
Is there a standard idiom for
there are overlapping values -- and this would
be a reason that pch=1 gives an open circle ...]
cheers
Ben Bolker
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rs */", so I think it's intended
as a way to get the desired answer when a little bit of numeric fuzz is present
-- but I agree it seems like overkill. I don't know whether R-core members have
on the top of their heads the standard ways of dealing with this situation ...
Ben Bolker
get started in relaxing the assumptions of mixed
models (e.g. allowing for non-normal random effects distributions).
Ben Bolker
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models (e.g. allowing for non-normal random effects distributions).
>
> That sounds interesting. However, I currenlty don't have enough
> know-how to work at something like it now.
Do you think so? I don't think it would be too hard,
if you were interested ...
Ben
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quite different from those listed for R, so this
shouldn't mean any competition.)
sincerely
Ben Bolker
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optim ignores misspelled control parameters, so that trying
to set (e.g.) "maxint=1000" in the control argument silently
does nothing. The patch below (watch out for line breaks! also
posted at http://www.zoo.ufl.edu/bolker/optim_patch.R , and
http://www.zoo.ufl.edu/bolker/optim_new.R) adds
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