: 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, either.
Ben Bolker
) a bug? Should I report it as such?
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Associate professor, Biology Dep't, Univ. of Florida
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GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc
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{alternative}. A confidence interval for the
underlying proportion with confidence level as specified by
--
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GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc
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Felix Andrews felix at 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 =
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
item to have it suppressed by default?
Ben Bolker
On 25/05/10 23:25 PM, Ben Bolker bolker at 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-library' )?
Bump.
From
Michael Dewey wrote:
At 13:40 01/06/2010, Ben Bolker wrote:
On 25/05/10 23:25 PM, Ben Bolker bolker at 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
Martin Maechler wrote:
BB == Ben Bolker bol...@ufl.edu
on Wed, 02 Jun 2010 13:45:18 -0400 writes:
BB Michael Dewey wrote:
At 13:40 01/06/2010, Ben Bolker wrote:
On 25/05/10 23:25 PM, Ben Bolker bolker at ufl.edu wrote:
Just curious: is there a particular
LC_MESSAGES=fr_FR.utf8
[7] LC_PAPER=fr_FR.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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Ben Bolker
Associate
Laurent lgautier at gmail.com writes:
Dear R-developpers,
The file NEWS disappeared in r5243, and the authoritative source of
information for what has changed in R is in ./doc/NEWS.Rd.
A quick glance at NEWS was extremely helpful for knowing what has
changed, and whether building a
of the time ...
cheers
Ben Bolker
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Ben Bolker
bbol...@gmail.com , bol...@mcmaster.ca
http://www.math.mcmaster.ca/~bolker
GPG key: http://www.math.mcmaster.ca/~bolker/benbolker-publickey.asc
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Paul Johnson pauljohn32 at gmail.com writes:
[snip: lots more snippage to try get gmane to let me post]
What do you think of this: The priority is to put the most important
thing at the top. The second priority is brevity.
I really like this.
Some suggestions:
in the results ...
This is in nlme 3.1-96, from a fresh tools/rsync-recommended. Sending it
to r-devel for comment because r-core is listed as the maintainer.
sincerely
Ben Bolker
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Janko Thyson janko.thyson at ku-eichstaett.de writes:
Dear List,
I'd like to set up a package repository so I can use install.packages() on
it for home-grown packages. I set up an AMPP infrastructure on a windows box
already, but I'm pretty lost with respect to what to do next as I didn't
anyone have a status report on r-forge ... ?
From here (Hamilton, ON) I can't ping ...
PING r-forge.wu-wien.ac.at (137.208.57.38) 56(84) bytes of data.
cheers
Ben Bolker
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in the documentation would
explain this, or one might have to dig through source code in R or C.)
Problems with unescaped/unrecognized quote characters are very
common.
Otherwise, this will likely be dismissed as a (doctor, it hurts
when I do this; well then, don't do that!) sort of situation.
Ben
Ben Bolker bbolker at gmail.com writes:
jgarcia at ija.csic.es writes:
Thanks. Yes, quote= solves the problem.
I would never say, however, from the documentations, that this was causing
the duplicate records. Rather, I would have expected some kind of
warning/error message
Ben Bolker bbolker at gmail.com writes:
Can simplify this still farther:
a b'c
d e'f
g h'i
One of the first things that happens in read.table is that
the first few lines are read with readTableHead:
lines - .Internal(readTableHead(file, nlines, comment.char
Ben Bolker bbolker at gmail.com writes:
Ben Bolker bbolker at gmail.com writes:
Can simplify this still farther:
a b'c
d e'f
g h'i
This example file leads to duplicate lines.
Arguably it should have behavior analogous to:
scan(what=)
1: a b'c
3: d e'f
5: g h'i
7: Read 6
Index: system.Rd
===
--- system.Rd (revision 53611)
+++ system.Rd (working copy)
@@ -181,7 +181,7 @@
\item The most important difference is that on a Unix-alike
\code{system} launches a shell which then runs
.)
If that doesn't work, please try your question again on R-help.
Ben Bolker
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Ravi Varadhan rvaradhan at jhmi.edu writes:
The decision about whether it belongs in a package or in base R is
about who should maintain the code.
Ok. I understand it now.
Thanks,
Ravi.
A point that may not have been made (sorry if it was and I missed it):
A better question
Jari Oksanen jari.oksanen at oulu.fi writes:
Hello R Developers,
Dear R-developers,
I ran some standard tests with currently (today morning) compiled R release
candidate in Linux R 2.12.1 RC (2010-12-13 r53843). Some of these tests used
plot.TukeyHSD function. This worked OK on the
On 10-12-14 01:16 PM, Peter Ehlers wrote:
On 2010-12-14 09:27, Ben Bolker wrote:
Jari Oksanenjari.oksanenat oulu.fi writes:
Hello R Developers,
Dear R-developers,
I ran some standard tests with currently (today morning) compiled R
release
candidate in Linux R 2.12.1 RC (2010-12-13
. \code{pch=.} with
\code{cex = 1} corresponds to a square of side 1/72 inch, which is
also the \sQuote{pixel} size assumed for graphics parameters such as
\code{cra}.
Paul
On 15/12/2010 7:20 a.m., Ben Bolker wrote:
On 10-12-14 01:16 PM, Peter Ehlers wrote:
On 2010-12-14 09:27, Ben Bolker
on line 1714 of R-lang.texi (current SVN of R-devel, 53919)
@code{x$aa} will match @code{x$aabb} if @code{x} does not a component
should probably have contain or have inserted after not
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Karthi Subramanian karthi_subramanian at yahoo.ca writes:
I currently have a program that automates 2-way ANOVA on a series of
endpoints, but before the ANOVA is carried out I want the code to
test the assumptions of normality and equal variance and report along
with each anova result in
Uwe Ligges ligges at statistik.tu-dortmund.de writes:
On 28.01.2011 13:49, peter dalgaard wrote:
On Jan 28, 2011, at 09:47 , Andreas Mayr wrote:
Hi,
is it possible, that the current development version for Windows (
in the logarithmic axis case: it took me
quite a bit of digging in documentation and source code to figure out
how to do this for myself, so I think it would be useful to others ...
Ben Bolker
Index: axTicks.Rd
===
--- axTicks.Rd (revision
'maxcols'
parameter, although those would only help in the case where the user
already knows there is a problem.
cheers
Ben Bolker
===
writeLines(c(A,B,C,D,
1,a,b,c,
2,f,g,c,
3,a,i,j,
4,a,b,c,
5,d,e,f
(and the original
bug reporter) must be misunderstanding something.
Thoughts/references?
cheers
Ben Bolker
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:49 PM, Ben Bolker wrote:
Has anyone yet tried incorporating rasterImage into the base image()
function? It seems to make a *huge* difference, with
a very small number of added/changed lines of code. (Of course I have
barely tested it at all.)
Is there any reason this *shouldn't* go
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On 11-02-09 03:09 PM, Henrik Bengtsson wrote:
On Wed, Feb 9, 2011 at 11:53 AM, Simon Urbanek
simon.urba...@r-project.org wrote:
On Feb 9, 2011, at 2:36 PM, Henrik Bengtsson wrote:
On Wed, Feb 9, 2011 at 11:25 AM, Simon Urbanek
Bump.
It's been a week since I posted this to r-devel. Any
thoughts/discussion? Would R-core be irritated if I submitted a bug report?
cheers
Ben
Original Message
Subject: read.csv trap
Date: Fri, 04 Feb 2011 11:16:36 -0500
From: Ben Bolker bbol...@gmail.com
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On 02/11/2011 03:37 PM, Laurent Gatto wrote:
On 11 February 2011 19:39, Ben Bolker bbol...@gmail.com wrote:
[snip]
What is dangerous/confusing is that R silently **wraps** longer lines if
fill=TRUE (which is the default for read.csv). I
On 02/14/2011 02:59 PM, Simon Urbanek wrote:
On Feb 14, 2011, at 2:28 PM, Paul Murrell wrote:
Hi
On 15/02/2011 8:11 a.m., Simon Urbanek wrote:
On Feb 14, 2011, at 12:26 PM, Ben Bolker wrote:
Paul Murrellp.murrellat auckland.ac.nz writes:
Hi
On 12/02/2011 7:22 p.m., Michael
then?
See
http://developer.r-project.org/Raster/raster-RFC.html
(near the bottom of the page, where it explains that the
Windows device supports alpha but not per-pixel alpha ...)
cheers
Ben Bolker
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https
pixel as well, but on Windows that's still no avail.
So basically, on Windows I can forget about alpha?
Cheers
Jors
On Tue, Feb 15, 2011 at 2:20 PM, Ben Bolker bbol...@gmail.com wrote:
Joris Meys jorismeys at gmail.com writes:
I believed the standard plotting device on R in 2.12.1 would
? Should I submit to the bug database as enhancement
request? Are there any hidden downsides to this?
Ben Bolker
Index: add.R
===
--- add.R (revision 54562)
+++ add.R (working copy)
@@ -330,7 +330,7 @@
drop1.default
On 11-02-23 03:20 PM, Martin Maechler wrote:
Ben Bolker bbol...@gmail.com
on Wed, 23 Feb 2011 09:14:37 -0500 writes:
By changing three lines in drop1 from access based on $
to access based on standard accessor methods (terms() and
residuals()), it becomes *much* easier
will probably occur elsewhere
already.
Thanks Prof. Ripley.
(I will say that, while I understand why residuals(x) and x$residuals
could be different, I am happy that a more transparent form of coding is
being introduced ...)
On Wed, 23 Feb 2011, Martin Maechler wrote:
Ben Bolker bbol
Ben Bolker bbolker at gmail.com writes:
On 02/11/2011 03:37 PM, Laurent Gatto wrote:
On 11 February 2011 19:39, Ben Bolker bbolker at gmail.com wrote:
[snip]
Bump. Is there any opinion about this from R-core??
Will I be scolded if I submit this as a bug ... ??
What is dangerous
simplify: logical or character string; should the result be simplified
to a vector, matrix or higher dimensional array if possible?
The default, ‘TRUE’, returns a vector or matrix if
appropriate, whereas ‘signify = array’, rather recommended
typically,
Ben Bolker
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Ben Bolker bbolker at gmail.com writes:
I have been struggling all day to import a particular function/method
combination (ranef(), which extracts the random effects from a mixed
model fit) from the nlme package into another package ... so far without
success.
Answered my own
Prof Brian Ripley ripley at stats.ox.ac.uk writes:
On Thu, 24 Mar 2011, Ben Bolker wrote:
Ben Bolker bbolker at gmail.com writes:
I have been struggling all day to import a particular function/method
combination (ranef(), which extracts the random effects from a mixed
model
On 03/24/2011 03:03 PM, Hadley Wickham wrote:
On Wed, Mar 23, 2011 at 7:20 PM, Ben Bolker bbol...@gmail.com wrote:
Ben Bolker bbolker at gmail.com writes:
I have been struggling all day to import a particular function/method
combination (ranef(), which extracts the random effects from
of lme4,
changing the order of the directive, ...).
Help ... ?
sincerely
Ben Bolker
=
test.R
=
library(coefsumtest)
library(lme4)
gm1 - glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
family = binomial, data = cbpp)
coef(summary(gm1)) ## works
f
On 11-03-26 02:52 PM, Martin Morgan wrote:
On 03/26/2011 11:14 AM, Ben Bolker wrote:
Dear list,
I have another (again possibly boneheaded) puzzle about importing,
again encapsulated in a nearly trivial package. (The package is posted
athttp://www.math.mcmaster.ca/bolker/misc
probably not looking for http://en.wikipedia.org/wiki/PD
good luck -- if you give more context you might get a more
useful answer.
Ben Bolker
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Joris Meys jorismeys at gmail.com writes:
The behaviour of hist.POSIXt when using the col argument is different
from the default hist, in the respect that it colors the axes as well.
I think this is due to the ... argument, which is passed to the
axis.POSIXct() function. In the default
would it be possible / make sense to copy some of the information in
?news into the R-exts manual, where package writers are most likely (?)
to look for it? The information therein seems more appropriate for the
extensions manual ...
cheers
Ben Bolker
*either* r-help *or* Stack Overflow to post your question:
don't cross-post.
(http://stackoverflow.com/questions/5895356/whats-r-save-terminal-flag)
As always, reproducible examples are helpful: please see the R-help
posting guide.
cheers
Ben Bolker
an
informative warning message. If there were any enthusiasm for it, I
would try to come up with a test and warning to incorporate into the
current version of bs() ...
Ben Bolker
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those packages). It would
be best if you could provide a reproducible question -- although I
recognize that could be difficult in this case.
You might also try stackoverflow.com or stackexchange.com
good luck
Ben Bolker
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skimmed through the relevant section
(1.3.1) in the R Extensions manual, and it doesn't say anything about
running on tarballs being preferred.
Add my vote to the wishlist that the src directory should get cleaned
after R CMD check.
Ben Bolker
So, it'd be something like:
R CMD build pkg
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On 06/02/2011 09:12 AM, Duncan Murdoch wrote:
On 11-06-02 9:06 AM, Ben Bolker wrote:
On 06/02/2011 06:47 AM, Benilton Carvalho wrote:
'R CMD check' should be applied on the .tar.gz, not on the source
directory.
Why?
Because that is what
Paul Johnson pauljohn32 at gmail.com writes:
I'd like to learn the process of revising R functions packages and
then submitting proposed patches to the R Core team. Would someone be
willing to mentor me through one example?
I don't know about mentoring, but I'll give my two cents (some
Dr. D. P. Kreil (Boku David.Kreil at boku.ac.at writes:
Dear John,
I suggest that you look at the abilities of the mgcv package.
There are notes of mine at
http://www.maths.anu.edu.au/%7Ejohnm/r-book/xtras/autosmooth.pdf
that may help you get started.
Thank you very much for
lost?
cheers
Ben Bolker
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Index
Prof Brian Ripley ripley at stats.ox.ac.uk writes:
It depends what you mean by 'vignette': the R docs have been unclear
(but R = 2.13.0 are more consistent). In most cases a 'vignette' is
an Sweave document, the vignette source being the .Rnw file, and the
vignette PDF the processed
:
methods(class=function)
[1] as.list.function head.function* print.function tail.function*
I find the same S3method syntax, so I guess the quotation marks aren't
the problem ...
Any ideas?
Ben Bolker
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i486-pc-linux-gnu (32-bit
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On 07/25/2011 12:55 PM, Uwe Ligges wrote:
On 25.07.2011 17:45, Ben Bolker wrote:
I recently suggested to someone (
http://stackoverflow.com/questions/6789055/r-inconsistency-why-add-t-sometimes-works-and-sometimes-not-in-the-plot-functi
was using R-devel and that worked as you
expected.
Best,
Uwe Ligges
On 25.07.2011 19:01, Ben Bolker wrote:
On 07/25/2011 12:55 PM, Uwe Ligges wrote:
On 25.07.2011 17:45, Ben Bolker wrote:
I recently suggested to someone (
http://stackoverflow.com/questions/6789055/r-inconsistency-why
the attached should probably read regarded by some OSes as separate
... Patch attached from latest SVN.
Ben Bolker
Index: R-admin.texi
===
--- R-admin.texi(revision 56743)
+++ R-admin.texi(working copy
Scott ncbi2r at googlemail.com writes:
It does look like you've got a memory issue. perhaps using
as.is=TRUE, and/or stringsAsFactors=FALSE will help as optional arguments
to read.table
if you don't specify these sorts of things, R can have to look through the
file and figure out
what is done with the splines package,
and no glaring differences leap out at me -- so I'm stumped.
If I do ./configure --without-parallel; make , it works.
If I'm being an idiot please be gentle ...
Ben Bolker
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On 11-09-20 09:29 PM, peter dalgaard wrote:
On Sep 20, 2011, at 20:57 , Ben Bolker wrote:
From SVN revision 57032, with configuration
R is now configured for i686-pc-linux-gnu
Source directory: . Installation directory:/usr/local
C compiler:gcc -std
is of length zero
I would guess that error messages with the word magic in them would
be disturbing to new users, who are probably worried already that R is
magic ...
Ben Bolker
Index: load.R
===
--- load.R (revision 56743
Just to save someone else a few seconds of googling: when you try to R
CMD check with recent versions of R-devel and you get
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: File
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On 09/23/2011 06:25 PM, Dirk Eddelbuettel wrote:
On 23 September 2011 at 18:03, Ben Bolker wrote:
| Just to save someone else a few seconds of googling: when you try to R
| CMD check with recent versions of R-devel and you get
|
| * checking
Mehmet Suzen msuzen at mango-solutions.com writes:
This might be obvious but I was wondering if anyone knows quick and easy
way of writing out a CSV file with varying row lengths, ideally an
initial data read from a CSV file which has the same format. See example
below.
refers to gammaCody(), which is now defunct. Perhaps
remove the sentence?
Ben Bolker
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installed
version (2.9.0) doesn't have debugging symbols, and I'm having trouble
building the latest SVN version (./configure gives checking for
recommended packages... ls: cannot access
./src/library/Recommended/boot_*.tar.gz: No such file or directory)
Can anyone confirm?
cheers
Ben Bolker
R
: generic error
Cannot find new threads: generic error
??
cheers
Ben Bolker
Kjetil Halvorsen wrote:
I can reproduce this too.
Run from within emacs:
v - data.frame(1:3,2:4)
sessionInfo()
R version 2.9.0 (2009-04-17)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C
This patch fixes the problem for me with latest R-devel. Thanks!
(This kind of X-hacking would take me hours if not days to figure out ...)
cheers
Ben Bolker
Ei-ji Nakama wrote:
Hi
2009/5/13 Dirk Eddelbuettel e...@debian.org:
snip
#0 0xb70e685e in XmbLookupString () from /usr
not sure if yacas runs on Windows or not).
Ben Bolker
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Prof Brian Ripley wrote:
Thank you, included in R-patched and R-devel now.
[snip]
thanks!
I do wonder sometimes if people who only work with data in ASCII or in
a Western European language covered by Latin-1 realize the extent of
the overhead that using a UTF-8 locale implies,
expect the title to be at the top ...
Ben Bolker
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... to every call to the function
in Reduce() -- patch is included below my signature ...
It's not a big deal -- I could also do
Reduce(function(x,y) { merge(x,y,by=state,all=TRUE) }, z)
but there doesn't seem to be a good reason not to allow it ...
cheers
Ben Bolker
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Ben Bolker
that conservatism would
rule, or the opinion of the original author of the functions (I don't
know who contributed Reduce et al.), but perhaps Kurt doesn't have
strong feelings about this ...
cheers
Ben
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Associate professor, Biology Dep't, Univ. of Florida
bol...@ufl.edu
as you've shown the point is pretty
general.
Ben Bolker
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the variables in the formula
in the environment of z (i.e., ignoring the first argument of with ...)
Any advice on how to solve this without making a bigger mess?
sincerely
Ben Bolker
## set up a data frame for prediction
set.seed(1001)
f = factor(rep(letters[1:4],each=20))
x = runif(80
someone else can comment ...)
Ben Bolker
Adam D. I. Kramer-2 wrote:
This message is in MIME format. The first part should be readable text,
while the remaining parts are likely unreadable without MIME-aware
tools.
--1660387551-150661043-1249684349=:2997
Content-Type: TEXT/PLAIN
that seems to work, thank you.
would anyone care to explain *why* it works ... ? or where
I could go to read more about why it works ... ?
cheers
Ben Bolker
Felix Andrews wrote:
how about...
nrow(with(cc, model.matrix(params, data=environment(
cheers
-Felix
2009/8/10
probability distribution.
}
--
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Associate professor, Biology Dep't, Univ. of Florida
bol...@ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
signature.asc
Description: OpenPGP digital signature
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: [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). The
.
! ## levels(res) = [1970-01-01 00:00:00,1970-01-01 12:00:00)
! ## instead of [18000,61200)
! }
! }
res
}
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Associate professor, Biology Dep't, Univ. of Florida
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GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
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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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 structures provided to the correlation argument.
[snip example
Ben Bolker bolker at 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 formula argument. It's hard
Marc Schwartz marc_schwartz at 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
Steve Kalke steve.kalke at 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
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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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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are inside
src/library
Kasper
On Dec 15, 2009, at 10:57 AM, 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
figure out an analogous way to track
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
figure out an analogous way to track
who wants to write rgl code to do these?
http://tinyurl.com/yzojfn2
http://tinyurl.com/ylrz2p8
:-)
Ben Bolker
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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, Univ. of Florida
bol...@ufl.edu / people.biology.ufl.edu
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