Hello everybody
When one is working with complex matrices, "transpose" very nearly
always means
*Hermitian* transpose, that is, A[i,j] <- Conj(A[j,i]).
One often writes A^* for the Hermitian transpose.
I have only once seen a "real-life" case
where transposition does not occur simultaneously
Hello Peter
thanks for this.
On 07/30/2010 11:01 AM, peter dalgaard wrote:
What's wrong with
t.complex<- function(x) t.default(Conj(x))
M<- matrix(rnorm(4)+1i*rnorm(4),2)
M
It's not going to help with the cross products though.
As a general matter, in my book, transpose is tran
Hello.
I am trying to write an S4 method for rbind(). I have a class of objects
called 'mdm', and I want to be able to rbind() them to one another.
I do not want the method for rbind() to coerce anything to an mdm object.
I want rbind(x1,x2,x1,x2) to work as expected [ie rbind() should take any
n
49, Martin Morgan wrote:
> On 10/26/2010 03:53 AM, Robin Hankin wrote:
>
>> Hello.
>>
>> I am trying to write an S4 method for rbind(). I have a class of objects
>> called 'mdm', and I want to be able to rbind() them to one another.
>>
>> I do not w
Hello everyone. R-2.12.0, suse linux 11.3.
I am debugging a package that uses S4 methods
and R CMD check gives the following warning:
> Warning in methods::findMethods(g, env) :
> non-generic function 'mdm' given to findMethods()
> See the information on DESCRIPTION files in the chapter 'Creat
e such a command
as
options(NA_string = "-")
available?
best wishes
Robin Hankin
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into producing jpg files instead of PDF?
Can anyone advise?
thanks
Robin
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>
> <>=
> null <- dev.off()
> @
>
> \begin{figure}
> \begin{center}
> \includegraphics{xyPlot.png}
> \end{center}
> \end{figure}
>
> Original message ----
>>Date: Sun, 13 Feb 2011 10:54:37 +1300
>>From: r-devel-boun...@r-proj
uot;foo", for signature "Oarray"
Three questions:
Why does the first call to setMethod() give an error message?
Why does (a) not find the method defined for arrays, even though 'a'
is an array?
How can I make "foo(a)" behave as desired when 'a' is
code2LazyLoadDB(package, lib.loc = lib.loc, keep.source =
keep.source, :
name space must not be loaded.
ERROR: lazy loading failed for package ‘MM’
This error seems to be system-dependent. All of the depencies are
packages which
are on CRAN and AFAICS pass R CMD check.
Can anyone advise?
--
Robin
could examine for Best Practice?
thanks
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ley", which
is poor form.
The issue does not arise on my Mac, and I expect that it is down
to some latex setting or style file.
Does anyone recognize this problem?
Can anyone advise?
--
Robin Hankin
Uncertainty Analyst
hankin.ro...@gmail.com
_
package?
>
> Thanks for the advice,
> Mohit Dayal
> Applied Statistics & Computing Lab
> ISB
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.e
citly or via an existing function
Error : unable to load R code in package 'Brobdingnag'
ERROR: lazy loading failed for package ‘Brobdingnag’
* removing ‘/Users/rksh/packages/Brobdingnag.Rcheck/Brobdingnag’
wt118:~/packages%
AFAICS, all the setGeneric() calls are pretty much like this:
setGe
"
> eigen(crossprod(matrix(1:2000, 50)) + (0+0i), T, T)
*** caught segfault ***
address 0x1038000a8, cause 'memory not mapped'
Traceback:
1: .Call("La_rs_cmplx", x, only.values, PACKAGE = "base")
2: eigen(crossprod(matrix(1:2000, 50)) + (0 + (0+0i)), T, T)
Possi
2:3] == dim(M1)) and all(dim(a)[5:7] ==
dim(M2)) for consistency.
Can any R-devel subscribers advise?
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4 7 10 11 14 17 20 21 24 27 30
This is not doing what I would want a[,M] to do.
I'll checkout afill() right now
best wishes
Robin
On Wed, Sep 28, 2011 at 10:39 AM, Simon Knapp wrote:
> a[M] gives the same as your `cobbled together' code.
>
> On Wed, Sep 28, 2011
of the above [for the very last part only!!], we would aim for
> the following. These *all* give an error in current R-devel,
> with the exception of 'm1 + NULL' which "only" gives a "bad
> warning" :
>
>
>
> m1 <- matrix(
s compatible, but is it
>>>> ever what the author actually intended? I have trouble thinking of a
>>>> case
>>>> where that less-than didn't carry an implicit assumption that y was
>>>> non-NULL. I can say that in my own code, I&
.16, so it is difficult for me to
investigate users' reports.
Can anyone advise?
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Neutral theorist
hankin.ro...@gmail.com
[[alternative HTML version deleted]]
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ent of Statistics / Rice University
> http://had.co.nz/
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel
--
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___
and adiag() and apad()
and aplus() etc etc that are not specific to magic hypercubes.
Does the List have any comments?
rksh
> Hadley
>
> --
> Assistant Professor / Dobelman Family Junior Chair
> Department of Statistics / Rice University
> http:/
stent with the special meaning of '.'
described under ?formula.
Is this the intended behaviour?
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nty.bib as R CMD INSTALL does not copy it to the system:
> system.file("doc","uncertainty.bib",package="emulator")
[1] ""
>
So I can't retrieve uncertainty.bib and this means that several other
packages can't bibtex correctly. Can anyone advise
n'
[1] 3 1
> C <- matrix(c(2,1i,1i,2),2,2)# 'C' is symmetric
> eigen(C,F,T)$values
[1] 2-1i 2+1i
> eigen(C,T,T)$values # answers disagree because 'C' is not Hermitian
[1] 3 1
>
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ger D. Peng wrote:
> The 'gmp' package may be of use here, but I'm not sure.
>
> -roger
>
> Robin Hankin wrote:
>> Hi
>>
>> Can I get R to handle really big numbers?I am not interested
>> in more than (say) 10 sig figs, but I would like to deal w
,101,12)
maybe adding a track object to a scalar would shift the values of the
x slot.
The algorithm itself is no problem...but what is the S4 equivalent to
the S3 technique of writing an Ops.track() function that tells
R what "+" means?
--
Robin Hankin
Uncertainty Analy
rogramming
with me. Most of my questions about S4 methods can be answered
by reading chapters 4 and 5 over and over and over again, with
occasional
reference to the Green Book.
?SetMethod does not reference Venables & Ripley. Could this be added?
>
> On Fri, 25 Aug 2006, Ro
when extracting the first
three elements, it seems to be lost.
What is the appropriate setClass() call to do what I want? Or indeed
is making "thing"
a vector class as sensible idea here?
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Wa
f a four-row matrix? What advantage does the
setClass() method above have over the single-column-of-a-four-row-matrix
method?
best wishes
Robin
On 29 Aug 2006, at 11:11, Martin Maechler wrote:
>>>>>> "Robin" == Robin Hankin <[EMAIL PROTECTED]>
>>
cos=,
cosh =,
cumsum =,
exp=,
floor =,
gamma =,
lgamma =,
sin=,
sinh =,
tan=,
od("j", quaternion)
S3method("k", quaternion)
what do I have to do to make onion work under R-devel?
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National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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ms to imply that there is no "Logic" group.
So, what is the correct way to specify that logical operations are
not allowed for "brob" objects?
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;)
}
setMethod("Logic",signature(e1="brob"), .logicBrob)
setMethod("Logic",signature(e2="brob"), .logicBrob)
but this does not work as desired (setMethod() gives an error). I want,
for example,
!new("brob", x=1:10,positive=rep(T,10))
to call .log
ignature)' formal arguments of the
function.
which seems to tell me (in conjunction with the advice from
Extremes.Rd quote above)
to use unnamed arguments to signature()
]
What is the correct way to make sum(x) call .Brob.max() if x is a
"brob" object?
Or is is it bette
ALSE)
> {
> base::max(x, ..., na.rm = na.rm)
> },
> group = "Summary")
>
> i don't have bleeding edge devel version installed, so i am not sure
> whether recent changes to S4 have mooted the above.
>
> (also, i thought i s
> x <- new("brob",x=pi,positive=T)
> c(x,x)
but c(1,x) isn't dispatched to my function. How to
deal cleanly with this case? Perhaps if any argument
to c() is a brob object, I would like to coerce them all to brobs.
Is this possible?
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l way to ensure dispatch on _any_ applicable argument
>> is to
>> turn the computation into a pair-wise one and define the methods
>> (NOT S3
>> methods) for the two arguments of the pairwise function.
>>
>> I won't try to reproduce the details off the top of my head
t;ANY"), as
> well as the method ("brob", "brob"), equivalent to the function
> cPairOfBrobs(), and a default method that just uses c().
>
> Something like:
> -
> cWithMethods <- function(x, ...) {
>if(nargs()<3)
> cPa
NULL, "?") : syntax error at
2: structure(function(x){standardGeneric("getX")}
3: , generic = structure("getX", package = ".GlobalEnv"), package =
".GlobalEnv", group = list(), valueClass = character(0), signature =
"x", default = &
te("binary operator \"", .Generic, "\" not defined for
Glub numbers"))
}
setMethod("Arith",signature(e1 = "brob", e2="brob"), .ArithBrob)
setMethod("Arith",signature(e1 = "brob&quo
darwin8.7.0
system powerpc, darwin8.7.0
status alpha
major 2
minor 4.0
year 2006
month 09
day15
svn rev39323
language R
version.string R version 2.4.0 alpha (2006-09-15 r39323)
--
Robin Hankin
Uncertainty
he backslashes and ampersands are
being escaped somehow, and TeX isn't interpreting
them as desired.
How do I write an Rd file so that the output of R CMD Rd2dvi
includes a nicely typeset matrix?
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southam
0+ 3.1416e+01i
[4] 1e+100+ 3.1416e+40i 1e+100+3.1416e+100i
>
rksh
On 21 Sep 2006, at 14:11, Prof Brian Ripley wrote:
> On Thu, 21 Sep 2006, Martin Maechler wrote:
>
>>>>>>> "Robin" == Robin Hankin <[EMAIL PROTECTED]>
>>>>>>>
ument string to "["
> argstr <- paste(indvecstr,sep="",collapse=",")
> argstr <- paste("x[",argstr,"]",sep="")
>
> #Finally, return the subsetted array
> return(eval(parse(text=argstr)))
> }
>
&
ll(indlist[[i]])) {
>> indvecstr[i] <- "";
>> } else{
>> indvecstr[i] <-
>> paste("c(",paste(indlist[[i]],sep="",collapse=","),")",sep="")
>>}
>> }
>>
>> #Then build up
jj.pos))
} else {
x[i] <- as.brob(value)
return(x)
}
} )
setReplaceMethod("[",signature("ANY","brob"),
function(x,i,j,value){
x <- as.brob(x)
x[i] <- as.brob(value)
return(x)
}
)
--
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Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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arately.
How best to do this
in the context of an S3 method for plot()?
What is Best Practice here?
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Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
__
R-devel@
s:~/scratch% rm BACCO.dvi
octopus:~/scratch% R CMD Rd2dvi ./BACCO
Hmm ... looks like a package bundle
[snip].
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
__
R-deve
Hello everyone
I am trying to get one of my packages through R's QC.
The package is clean for me under R-2.4.1, R-2.5.0, and
R-devel, but Kurt gets
>
> * checking R code for possible problems ... WARNING
> hypercube: no visible binding for global variable ‘f’
Function hypercube() [cut-&-p
this eventuality gracefully? The
functions that do use pari/gp have "pure" R equivalents (but much
slower and less accurate) so I want users to be able to install the
package without pari/gp.
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Uncertainty Analyst
National Oceanography Centr
t; Business School
> Dublin City University
> Dublin 9, Ireland
> Tel +353 (0)1 700 7496
>
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setClass("onion",
representation = "VIRTUAL"
)
setClass("octonion",
representation = representation(x="matrix"),
prototype = list(x=matrix(numeric(),0,8)),
contains = "onion"
)
jj
n.arith" <- function(o1,o2){stop("OO not implemented")}
".onion.real.arith" <- function(o,r){stop("OR not implemented")}
".real.onion.arith" <- function(r,o){stop("RO not implemented")}
setMethod("Arith", signature
(o1="onion&
x27;
>>>> sweep?
>>>>
>>>
>>> (now posted at
>>> http://wiki.r-project.org/rwiki/doku.php?id=rdoc:base:sweep
>>> )
>>>
>>> It always warns if dim(x)[MARGIN] is
>>>
>
> ___
on(x){unlist(sapply(x,function(i){seq_len
(i)}))}
is much faster.
Neither sequence0() nor mySequence() accepts vectors with any
element <0
although as Brian Ripley points out, sequence() itself does (which I
think is
undesirable).
Robin Ha
03
svn rev43063
language R
version.string R version 2.6.0 (2007-10-03)
>
>
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On 5 Oct 2007, at 15:47, Robin Hankin wrote:
> Hello
>
>
> One of my packages, untb_1.3-2, passes R CMD check under
> MacOSX (and apparently the systems used in the package check
> summary page on CRAN) but fails with the following message on
> R-2.6.0.tgz compiled last nig
package?
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European Way, Southampton SO14 3ZH, UK
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Hi
I have a bundle comprising three packages.
Each package has a vignette. Currently each
vignette has a separate .bib file.
How do I arrange the bundle so that each
vignette accesses a single, common, .bib file?
thanks
Robin
--
Robin K. S. Hankin
Uncertainty Analyst
University of Cambridg
utput?
best wishes and thanks again
Robin
Romain Francois wrote:
Hi Robin,
Something like:
<>=
bib <- system.file( "bib", "mybib.bib", package = "yada" )
cat( "\\bibliography{",bib,"}\n")
@
It would also be nice to be able to
etting about Sweave's
'result' code chunk option).
But I still don't understand why your first suggestion worked.
How does TeX 'know' that this is not to be included verbatim?
best wishes and thanks again
Robin
Robin Hankin wrote:
Hello Romain
this is brilliant
Hi
[R-2.9.0]
I am having difficulty including a LaTeX formula in an Rd
file.
The example given in section 2.7 in 'Parsing Rd files' is:
\deqn{ f(x) = \left\{
\begin{array}{ll}
0 & x<0 \\
1 & x\ge 0
\end{array}
\right. }{non latex}
For me, this gives:
\deqn{ f(x)
Hi
I read that bundles are to be deprecated in 2.10.
The BACCO bundle contains three packages
(emulator, calibrator, approximator) which I
am happy to unbundle.
But the 'BACCO' moniker has some considerable
cachet for me in terms of recognizability (eg
with grant-giving bodies), as it has becom
Hi
[R-2.10.0; suse linux]
I am having difficulty creating S4 objects in the data directory of a
package. I want
to create a bunch of simple S4 objects for use in the examples section
of the Rd files.
It says in R-exts that:
" R code should be “self-sufficient” and not make use of extra
fun
Hi
I am having difficulty defining an S4 method for head() and tail().
I can't quite provide minimal self-contained code
because the problem appears to require the whole corpus
of my package; and there also appears to be a difference
between sourcing the lines directly, and having them
installed
Hi Martin
I think you're absolutely right about this;
One thing I need again and again is
a multinomial function, and usually define:
> lmultinomial
function (x)
{
lfactorial(sum(x)) - sum(lfactorial(x))
}
> multinomial
function (x)
{
exp(lmultinomial(x))
}
It would be nice to have this
Martin Becker wrote:
Robin Hankin wrote:
...
Is this the place to discuss having complex
arguments for gamma()?
...
If this discussion starts I would second the wish for the
functionality of gsl's lngamma_complex in base R.
Do you mean gsl or GSL? ;-)
[the GNU scientific library is
ns but
(IIRC) the patch I supplied only tested for the imaginary part being
>0; would it be
possible to include information about signed zero in these or other
functions?
> Duncan Murdoch
>
> __
> R-devel@r-project.org mailing
above.
+
}
\section{S4 methods}{
Both are S4 generic and members of the
245-10:~/scratch/R-devel/src/library/base/man%
--
Robin Hankin
Uncertainty Analyst and Neutral Theorist,
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059
.
My impression is that S3 is perfectly adequate for this task, although
I've not yet finalized the coding.
S4 seems to be "overkill" for such a simple system.
Can anyone give me some motivation for persisting with S4?
Or indeed reassure me that S3 is a good design decision?
(ax)
a <- 4
f(x) # should still give tr(ax) even though "a" has been
reassigned.
[my real example is very much more complicated than this but
I need this toy one too and I can't see how to modify
as.function.polynomial()
to do what I want]
--
Robin Hankin
Function",
which outlives short-lived polynomial "p".
Unfortunately, I don't see a way to modify as.function.polynomial()
to do what I want.
best wishes
rksh
On 14 Jan 2008, at 08:45, Antonio, Fabio Di Narzo wrote:
> 2008/1/14, Robin Hankin <[EMAIL PROTECT
e(text = jj )[[1]]
f
}
If f <- as.function.foo(x), somehow the "f" object has to include
within itself
the entirety of "x". In my case, "x" is [of course] an arbitrary-
dimensional
array of possibly complex elements.
So I can't use Bill/Kurt's
On 14 Jan 2008, at 11:50, Duncan Murdoch wrote:
> Robin Hankin wrote:
>> Hi
>>
[snip]
>> a <- crossprod(matrix(rnorm(12),ncol=3))
>> class(a) <- "foo"
>>
>> f <- as.function(a) # need help to write as.function.foo()
>> x &l
r of unary operators "+" and "-".
If trim is TRUE, then "a" is one thing, but "+a" returns
"trim(a)", which might be different.
Also "1*a" would be different from "a" and "a+0"
Does the List consider this to be
On 10 Mar 2008, at 11:03, Prof Brian Ripley wrote:
> On Mon, 10 Mar 2008, Martin Maechler wrote:
>
>> {Diverted from an R-help thread}
>>
>>>>>>> "Robin" == Robin Hankin <[EMAIL PROTECTED]>
>>>>>>>on Mon, 10 Mar 200
esentation=representation(x="numeric"),prototype=list(x=NaN))
[1] "foo"
>
But this is not the correct sense: to me "NaN" means "not a number"
and I want
the sense to be "not available".
Any advice?
--
Robin Hankin
Uncertainty
isher's Exact Test for Count Data
data: matrix(c(0, 20, 219, 1159), 2, 2)
p-value = 0.05867
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
0.00 1.082225
sample estimates:
odds ratio
0
>
*just* shy of the magic 5% . . .
ot;:
[1] 1 2 3 1 5 6 7 8 910
Slot "NC":
[1] 10051
# Desired behaviour: NC recalculated
>
> a[4] <- 1
Error in .local(x, i, j, ..., value) :
argument "value" is missing, with no default
>
# Undesired behaviour
t;> STAT-IMA-FSB-EPFL, Station 8
>> CH-1015 Lausanne Switzerland
>> http://stat.epfl.ch/
>> Tel: + 41 (0)21 693 7907
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r
ly that the conditions are
automatically met.
But OTOH, I want the check to be performed "by default" to
stop anyone (me) from being too clever and defining
a non-standard foo object that doesn't meet .checkfoo().
What is best practice here?
Are there any examples I could copy?
oked in several packages but could not found any.
Thanks for your help!
Matthias
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Uncertainty Analyst and
Hi.
I have been pondering array indexing via matrices.
> a <- array(1:27,rep(3,3))
> index <- matrix(c(1,1,1,1,2,3),2,3,byrow=TRUE)
> a[index]
[1] 1 22
as expected and documented. But what was the thinking
behind the decision to access the array by rows rather
than columns?
The 'index' mat
Prof Brian Ripley wrote:
I think you meant \describe
On Mon, 5 Jan 2009, Robin Hankin wrote:
Hi
The aylmer package generates a warning (under R-2.9.0) for an Rd file
which I think is OK.
The package is clean under R-2.8.1.
Did you actually look at the help under 2.8.1: it is I am
Hi
I make a point of going through my packages every so often and perusing
the check results on CRAN.
The aylmer package generates a warning (under R-2.9.0) for an Rd file
which I think is OK.
The package is clean under R-2.8.1.
Specifically, the warning is:
* checking Rd files ... OK
Dear All
I am preparing a number of vignettes that require a very long time to
process with Sweave. The longest one takes 10 hours. I love the weaver
package!
Is a package that includes such a computationally intensive vignette
acceptable on CRAN? Are there any guidelines here?
--
Robin
thanks for this clarification Uwe
Could I include the r_env_cache/ directory in the package
and then assume that the CRAN checks use
Sweave( , driver=weaver())
in which case the process takes about 10 seconds?
rksh
Uwe Ligges wrote:
Robin Hankin wrote:
Dear All
I am preparing a
(or how it should be done).
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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https://stat.ethz.ch/mailman/listinfo/r-devel
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--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
;t help me:
find ~/downloads/R-2.1.1/ -name "*.h " | xargs
egrep "z_cos"
returned empty.
How do I access z_sin() from my c code?
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO1
t; best approach. I didn't see documentation for their API (the
>>> exports of
>>> their DLL), but I didn't spend long looking.
>>>
>>> Duncan Murdoch
>>>
>>> __
>>> R-devel@r-project.or
, and APL
> used to be my first `beloved' computer language (in high school!)
> -- but does J really provide computer algebra in the sense of
> Maxima , Maple or yacas... ??
>
> (and no, please refrain from flame wars about APL vs .. vs ..,
> it's hard to refrain for me, too...)
>
gt; Martin Maechler, ETH Zurich
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>
> --
> Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat.
> Centre for Res
e same way that (eg) complex matrices do.
Perhaps we could define "*" and "/" appropriately for vectors of class
"octonion" (if such a thing makes sense): or is there a better
way? Also, Mod(), Re(), and perhaps
Conj() would have to be generalized to work with
...)
just like rep.default(), but R CMD check complains about it, pointing
out that rep() and rep.octonion() have different arguments.
What do I have to do to my rep.octonion() function to make my package
pass R CMD check without warning?
--
Robin Hankin
Uncertainty Analyst
National Ocea
ons and methods' of the 'Writing R
Extensions'
manual.
I can suppress the warning by commenting out the first line. Is this a
sensible thing to do?
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 02
uot;An" as well.
There is a small number of functions and datasets that are specific
to octonions.
What is Best Practice in this situation? I don't want to edit two
separate
packages in tandem. Is there a mechanism for doing what I want
in the context of a bundle?
--
Robin
="")
> expr <- parse(text=code)
> y <- eval(expr)
>
> ndim <- length(dim(x))
> args <- rep(",", ndim)
> args[1] <- "i"
> args <- paste(args, collapse="")
> code <- paste("x[", args, "]", sep="&q
(), arev()
enjoy!
]
On 29 Nov 2005, at 15:17, Gabor Grothendieck wrote:
> I couldn't find it:
>
>> library(magic)
>> apltake
> Error: object "apltake" not found
>
> On 11/29/05, Robin Hankin <[EMAIL PROTECTED]> wrote:
>> Hi everyone
>>
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