0.2.4.tar.gz
works like a charm. Some other Unix systems will omit the ‘='
John Maindonald email:
john.maindon...@anu.edu.au<mailto:john.maindon...@anu.edu.au>
On 21/10/2021, at 02:31, Dirk Eddelbuettel
mailto:e...@debian.org>> wrote:
On 20 October 2021 at 09:31,
on what I am missing will be welcome.
John Maindonald email: john.maindon...@anu.edu.au
__
R-devel@r-project.org mailing list
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inst/doc/.install_extras
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual."
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Appl
gnore’ so that ‘.install_extras’ is not installed.
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National U
Sorry. This, and the description in the �Writing R Extensions� manual,
leaves me completely mystified. Is it that I have to remove the PDFs
that are created when I run �R CMD build�, and somehow ensure that
they are rebuilt when the package is installed? Do I need a Makefile?
John Maindonald
? Can I ignore the "The following files should probably not
be installed” message?
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
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transpose of a row vector
from the data matrix.
cf page 322 of “Modern Applied Statistics with S”, 4th edn.
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathe
he syntax checker happy. Another possibility
might be:
FARS <- NULL
data('FARS', package='gamclass', envir=environment())
I do not know whether this passes.
An FAQ that offers preferred solutions to such chestnuts,
or a web page, or a blog, would seem to me us
functions above, or family=NBII (linear; var = mu(1 + sigma)). Also note
the somewhat special purpose function glmnb.fit() in the stat mod package,
which requires preliminary setup steps.
John Maindonald email:
john.maindon...@anu.edu.au<mailto:john.maindon...@anu.edu.au>
phone
In Section 1.4.2 of "Writing R Extensions"
%\VignetteEngine{knitr::knitr}
should be
%\VignetteEngine{knitr::knit}
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Is this sort of thing best reported here, or is a huge report in
compress.
I take it then that the "Writing R Extensions manual [2.14.1 (2011-12-22)] is
anticipating what is in R-devel:
"
The --compact-vignettes option will run tools::compactPDF over the PDF files in
inst/doc (and its subdirectories) to losslessly compress them. This is not
enabled by
RAN upload site:
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
‘gs’ made some significant size reductions:
compacted ‘rockArt.pdf’ from 680Kb to 58Kb
consider running tools::compactPDF(gs_quality = "ebook") on these files
John Maindonald email: john.ma
IME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Application
op short of actually saying that Cp should be modified in the same
way as AIC when sigma^2 has to be estimated.
Better still, perhaps, give the AIC statistic. This would make the
output consistent with dropterm(), drop1() and add1(). Or if Cp
is to stay, allow AIC as a a further "test"
quot;, with partial matching allowed,
or NULL for no test."
test="Cp" is, following the help page, intended to work? Setting
the scale parameter does not help.
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre
Thanks. That seems to work.
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra
in marray-notes.pdf (also in the
inst/doc subdirectory)?
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian Natio
calls for
quasi links (or a glmm with observation level random effects) is in my
experience the rule rather than the exception!
At the very least, why not a function dispersion() or pearsonchisquare()
that gives this information.
Apologies that I misattributed this.
John Maindonald
r suss out how to calculate the Pearson
chi square from the glm model object, to discover that the information in the
model object is inconsistent with simple binomial or poisson assumptions.
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +
ernSmooth)
>> library(SMIR); data(bronchit); library(KernSmooth)
>> library(SMIR); data(bronchit); library(KernSmooth)
> \end{Sinput}
> \end{Schunk}
(I have omitted three blank lines at the start)
With keep.source=FALSE, the commands are split onto
separate lines, and ther
d{Schunk}
(I have omitted three blank lines at the start)
With keep.source=FALSE, the commands are split onto
separate lines, and there is no repetition.
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & I
Thanks. It is useful to have a list of items that are outstanding.
I will experiment a bit more, but may revert to using R-2.11.1 for
running Sweave(). Did any of these issues arise for R-2.11.1?
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax
ode between the comment line and the
named code chunk. The comment line does now appear in the output.
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical
/www.maths.anu.edu.au/~johnm/r/packages/testpkg
demonstrates the point.
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Austra
Full_Name: John Maindonald
Version: R-2.8.1
OS: MacOS X 10.5.6
Submission from: (NULL) (203.173.3.75)
The following code demonstrates an annoyance with plot.lm():
library(DAAGxtras)
x11(width=3.75, height=4)
nihills.lm <- lm(log(time) ~ log(dist) + log(climb), data = nihills)
plot(nihills
apply to lines as well as text?
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canber
Dear John -
The title above the graph is also redundant for the first of the
plots; do we want to be totally consistent? I am not sure.
It occurs to me that the text "Cook's distance", as well as the
contours, might be in red.
Regards
John.
John Maindonald emai
distance",
lty = 2, col = 2, bty = "n", y.intersp=0.5)
If this second change is not made, then one wants fracht <- (1.5*par()
$cin[2])/par()$pin[2]
I prefer the "Cook's distance" text to be a bit closer to the x-axis,
as it separates it more c
Actually, this may be a useful feature! It allows calculation of a
basis for the orthogonal complement of the space spanned by
model.matrix(lm(y ~ poly(x,12)). However, the default ought surely to
be to disallow df > k-1 in poly(x,df), where k = length(unique(x)).
John Maindon
2)12 0 0 1
John Maindonald email: [EMAIL PROTECTED]
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra
Yes, I noticed after I had sent it that x was said to be numeric.
Incidentally, this does not happen, in my experience, with Date objects.
John Maindonald email: [EMAIL PROTECTED]
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room
.string = R version 2.6.0 (2007-10-03)
Locale:
C
Search Path:
.GlobalEnv, package:stats, package:graphics, package:grDevices,
package:utils, package:datasets, package:methods, Autoloads,
package:base
John Maindonald email: [EMAIL PROTECTED]
phone : +61 2 (6125)3473fax : +61 2(6125)
system = i386, darwin8.10.1
status = beta
major = 2
minor = 6.0
year = 2007
month = 09
day = 22
svn rev = 42941
language = R
version.string = R version 2.6.0 beta (2007-09-22 r42941)
Locale:
C
Search Path:
.GlobalEnv, package:testpkg, package:stats, package:graphics,
package:grDevices, pa
<- bquote(""< .(x), list(x=1.5))
> arg2 <- bquote("">= .(x), list(x=1.5))
> axis(1, at=1:2, labels=do.call(expression, list(arg1, arg2)))
For a unified approach to use of do.call(expression, ...), maybe
one should use bquote() and .()?
John Maindonald
While termplot is under discussion, here's another proposal. I'd like to
change the default for partial.resid to TRUE, and for smooth to
panel.smooth. I'd be surprised if those changes were to break existing code.
John Maindonald email: [EMAIL PROTECTED]
phone : +
While termplot is under discussion, here's another proposal. I'd like to
change the default for partial.resid to TRUE, and for smooth to
panel.smooth. I'd be surprised if those changes were to break existing
code.
John Maindonald email: [EMAIL PROTECTED]
phone : +
levance to glm's computations with
the doselin term. It has treated it as numeric. In my view, either
predict()
should maintain the stance (pretence?) that it is numeric, or else
the call
to .checkMFClasses() that follows on the use of glm() should report at
least a warni
meric.
> ###
>
> ## Note the following
> mframe <- model.frame(cbind(deaths, (20-deaths)) ~ sex+ doselin,
+ data=worms)
> class(mframe$doselin)
[1] "integer"
> attributes(mframe$doselin)
$levels
[1] "1"
For the earlier 2001 discussion, see
http://tolstoy.newcastle.edu.au/R/devel/01b/0089.html
John Maindonald email: [EMAIL PROTECTED]
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (B
(1) read.table(), with sep="\t", identifies 13 our of 1400 records,
in a file with 1400 records of 3 fields each, as having only 2 fields.
This happens under version 2.3.1 for Windows as well as with
R 2.3.1 for Mac OS X, and with R-devel under Mac OS X.
[R version 2.4.0 Under development (unstable
files that reflect what they want to appear in any citation,
with
citation("lattice") as maybe a suitable model?
John.
John Maindonald email: [EMAIL PROTECTED]
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Mathematical Sciences Institute, Room 1194,
John Dedman M
On 5 Feb 2006, at 2:27 AM, [EMAIL PROTECTED] wrote:
>>>>>> On Mon, 30 Jan 2006 10:06:52 +1100 (EST),
>>>>>> John Maindonald (JM) wrote:
>
>> The bibtex citations provided by citation() do not
>> work all that well in cases where there is no pri
other person who is wrestling with
this, and others on this list must be wrestling with it.
John Maindonald email: [EMAIL PROTECTED]
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Mathematical Sciences Institute, Room 1194,
John Dedman Mathematical Sciences Building (Building 27
667 1.216667 3.741667 5.57
> diff(dummy.coef(bdes.aov)$trt)
b c d
-3.125 2.525 1.825
> diff(model.tables(bdes.aov, type="means")[["table"]][["trt"]])/
+ diff(dummy.coef(bdes.aov)$trt)
trt
b c d
0.
appear replete with
the new plots!
For 2.2.0, I have nothing more to add to the comments
others have made, I hope we can in due course agree,
as a minimum, to put some version of John Fox's vif(),
and something akin to Werner Stahl's smooths for up to
20 simulated data sets, into 2.3.0
John
]
(9) How about a help(Diagnostics) entry?
(10) Maybe it would be useful to form a (small?) group to look at
what should go into:
(a) stats
(b) a specialist diagnostics package
Even if this idea is taken up, some preliminary wider canvassing
of the opinions of members of this list seems desi
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