Hi,
The Rd file sceleton created using function _promptMethdos_ contains
*only* the
following fields:
name
docType
alias
title
description
section{Methods}
keyword
while _promptClass_ creates in addition fields like:
author
references
seealso
examples
and even is invalid due to:
~Make other
define my class differently for subsetting using dimnames
to work? Even if they are not really being checked, I would like to be
able to use subsetting in this way as it makes code more readable when
using arrays with many dimensions.
_____
nction in one of the
Rd files.
Yours
Eryk
--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-30-83875219 __("<_
http://www.molgen.mpg.de/~wolski \__/'v'
http://r4proteomics.sourceforge.net||/ \
m
ion of the method the
old method stored months ago in the .Rdata file was called again and again.
Is not there a better way to avoid such problems than deleting the
.Rdata file?
Eryk
--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-3
ass(),
I see that R
recognises "matrix" as a subclass of "array" (and vice-versa).
So is this
new behaviour correct?
You conclude incorrectly, as noted above.
[this is a re-posting to R-devel of a question earlier posted to R-help,
which attract
Hi,
The following code generates a invalid (?) pdf file.
pdf("test.pdf")
x <- pixmapIndexed(rep(1:8, 9), nrow=6, col=terrain.colors(8))
plot(x)
dev.off()
This pdf can be viewed but not printed
Trying to print causes to crash gv as well as acrobat windows XP
Yours
/E.
--please do not edit
Hi,
This are the project which I have extracted from all your mails.
1. http://sourceforge.net/projects/rpgsql/ R PostgreSQL Interface
2. http://sourceforge.net/projects/r-spatial/ R package for spatial
data classes
3. http://sourceforge.net/projects/rpy/ RPy (R from Python)
4. ht
rge is 967697.
https://sourceforge.net/tracker/?func=detail&atid=350001&aid=967697&group_id=1
--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-30-83875219 __("<_
http://www.molgen.mpg.de/~wolski \__/
ut it.
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--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-30-83875219 __("<_
http://www.molgen.mpg.de/~wolski \__
ration.
Therefore why not use it to specify colors to borders of boxes?
Yours
/E
Dipl. bio-chem. Eryk Witold Wolski @MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin'v'
tel: 0049-30-83875219
.
I am using Windows XP and R 2.0.1beta .
Thanks.
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--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-30-83875219
ile.remove("hres.rda")
dFile <- paste(getwd(),"/hres.rda",sep="")
if(!file.exists(dFile))
download.file(url ="http://www.molgen.mpg.de/~wolski/hres.rda";, dest=
dFile,mode="wb")
load(dFile)
hresd
plot(hresd)
In one think you are right,
ile.remove("hres.rda")
dFile <- paste(getwd(),"/hres.rda",sep="")
if(!file.exists(dFile))
download.file(url ="http://www.molgen.mpg.de/~wolski/hres.rda";, dest=
dFile,mode="wb")
load(dFile)
hresd
plot(hresd)
In one think you are right, the X axis. B
drawn.
#The interested reader can download the
save(hresd,file="hres.rda")
#from the following loacation
www.molgen.mpg.de/~wolski/hres.rda
Yours
/E
--please do not edit the information below--
Version:
platform = i386-pc-mingw32
arch = i386
os = mingw32
system = i386, mingw
(), y = numeric(), model = NULL)
{
if(is.null(model))
model <- lm(y ~ x)
callNextMethod(.Object, x=x, y=y, model=model)
}
)
(unfortunately, lm() does not allow fitting vectors of length 0, so if
this were a real example there are a few b
nown to me. In this case sorry.
/E
--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin _
tel: 0049-30-83875219 __("< 'v'
http://www.molgen.mpg.de/~wolski \
;)
,def=function(object)
{
print(length(object))
}
)
xx<-as.list(1:4)
names(xx)<-letters[1:4]
mvca<-new("MVCa")
[EMAIL PROTECTED]<-xx
printlength(mvca)
Any suggestions?
/E
--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Mo
s foo")
if (!is.null([EMAIL PROTECTED])) cat(" does have a lm object in slot y!")
})
Eric
--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin _
tel: 0049-30-8387
Hi,
But "any" rises some other problems well known from S3. One has "any"
for "free" in S3. You don't need S4. . But I know how "if" polluted
functions look like in S3. They are hard to understand and to
maintain. Hence I am quite happy to use S4.
Type-checking is usefull if you program with d
;)
and
new("Ctest",test="bla",bla="brum")
within one initialization function? Using match.call? missing is not
enough I think.
/E
setClass("Ctest"
,representation(
test="character"
,bla="character"
,mod="lm"
)
)
J
e both S3 classes. (of course except that lm
is in in THE stats package)
Is it intended to keep two different "models" of treating S3 classes?
One for S3 class from the recomended, "base" packages and a different
one for S3 classes from contributed packages? I assume not.
If,
een book has no index
entry for 'unique'. In S-plus the implementation of unique.default(x)
uses
x[!duplicated(x)].
So what is the "Blue book", the "Green book", and MASS 4th Ed?
efg
______
[EMAIL PROTECTED]
Hi!
Consider this code.
setClass("Ctest"
,representation(
test="character"
,bla="character"
,mod="lm"
)
)
new("Ctest",test="bla") #This produces an error.
#Error in validObject(.Object)
evidence is pretty strong that unique(x) will always
return elements in the same order as they first appear in x. But it
would be nice if the documentation for 'unique' explicitly stated that
this is the behavior for all methods. (It does state this for the
array method for 'u
in x)
{
if(!i%in%res)
{
count<-count+1
res[count]<-i
}
}
res
}
/E
--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin _
tel: 0049-30-83875219 'v'
http://www.
Some addtitional info about Npatrick1
> is(Npatrick1)
[1] "Massvectorlist" "Mlist" "List" "list"
[5] "vector"
/E
Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Gene
or any extendion (that is: we can add methods).
>>>
>>>Now, I try to add a method for length to handle "Collection" classes.
>>>
>>> > getMethod("length")
>>>.Primitive("length")
>>>
>>>
>>>*** Q
Hi,
Is it intended to support assignment of a derived instance (S3) to a parent container
(S4)?
setClass("any")
setClass("myclass",representation(x="any",y="any")) # I define parent containers x,y
#I have an S3 object.
xx<-3
class(x)
#instantiate a new object of class myclass
tt<-new("myclass"
Hi,
Is it possible to have a slot to which any arbitrary class can be assigned?
/E
Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin'v'
tel: 0049-30-83875219/ \
ma
Hi!
Due to package maintenance I have removed some functions but forgot to update the
coresponding Rd files.
If R CMD check is checking for missing documentation entries why it does not check for
documentation entries which tell the user about nonexisting funcitons?
In my opinion checking for
Hi!
Due to package maintenance I have removed some functions but forgot to update the
coresponding Rd files.
If R CMD check is checking for missing documentation entries why it does not check for
documentation entries which tell the user about nonexisting funcitons?
In my opinion checking for
eg something working like R CMD makeRd (perl script)... which
genreates Rd files out of it..
Has nobody a perl-script that parseres the R files to generate Rd files? Would someone
be interested in something similar. If so let me know please.
/E
*** REPLY SEPARATOR ***
Hi!
I have renamed some functions and deleted others. I have noticed that R CMD check
complains only about newly added functions, but documented non-anymore-existing
functions seem not to matter.
I knew about prompt and promptMethods promptClass. They are extremely useful if you
are starting t
Hi!
To specify a prototype in the setClass declaration is a great feature.
But prototype seems no to work for slots of the "super" class.
eg. The following code is declaring first the super class "List". This class has a
slot "content".
The class "AtomList" inherits from it and I would like to
Hi!
Forgot to ask: Can you restore the behaviour from version 1.9.1? Please.
I have 2 packages on Bioconductor and one almost ready which rely on it. And as I just
tested the rewrite which changes the inheritance to a contains relation would have
more consequences then I thought and not be as ea
Hi!
I am open to any arbitrary way of extending a list. It does not matter to me how
complicated it gets. I do it once for my class.
What matters to me is what I can do with objects extending from list. Because this is
what I am doing often.
Hence, further proposals even more complicated are we
#NAIVE inheritance from list.
#define cass
setClass("Mlist"
,representation(info="character") #uniq names have to be unique?
,contains="listNamed"
)
Hi!
First of all thanks a lot to John Chambers. I think S4 makes some tasks really
easier.
This mail tries to summarise the mail exchange concerning contains="list" in S4.
I do not know all the R "internals" so instead of talking I try to use and to play
around with S4. People like I learn by
s P.
>>>
>>>__
>>>[EMAIL PROTECTED] mailing list
>>>https://stat.ethz.ch/mailman/listinfo/r-help
>>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
al with. But the
>>>spirit of that class is NOT equivalent to lists with a names attribute.)
>>>
>>>As for extending basic datatypes by S4 classes, that's generally OK,
>>>provided you understand the consequences (pages 314-316 of the green
>>>boo
Thank you very much.
Sincerely yours
Eryk.
Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin'v'
tel: 0049-30-83875219/ \
mail: [EMAIL PROTECTED]---W-W--
exisiting as. functions, as.vector in
>>>this case.
>>>
>>>The result is indeed the same as coercing mmm to "matrix" first and then
>>>to vector
>>>
>>>R> as(as(mmm, "matrix"), "vector")
>>> [1] 1 2 3 4
Hello!
as(object,"list") and as(object,"matrix") behave quite differently if it comes to
their attributes.
I define two classes. One of them "contains" a "list" the other a "matrix"
setClass("myclass"
,representation(info="character")
,contains="matrix"
)
setClass("mylist"
,representation(info="c
I had a typo in the previous mail
"Massvector" extends "matrix" not "Matrix"
/E
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Hi!
Concerning different behaviour between 1.9.1 patched and:
R : Copyright 2004, The R Foundation for Statistical Computing
Version 2.0.0 Under development (unstable) (2004-09-06), ISBN 3-900051-07-0
Subtitle:
as(x,"vector"); x is of class "Massvector"; never enters setAs("Massvector","vector"..
Hi!
In the R directory of the package I have several files. This is because i defined
several classes and I like to store each class in separate file.
There is a inheritance defined between those classes.
eg calibrestat (defined in file calibrestat.R) extends (contains) calibstat (defined
in fil
er ti
>>>zip each data file individually and use the functions to read from
>>>zipped files, or are there some other solution?
>>>Did'nt find anything in "Writing R extensions".
>>>
>>>Kjetil
>>>
>>>
How can I tell R CMD check to check for this? I would find it usefully if R CMD
check behaves with this respect similar on all platforms.
Eryk.
Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin 'v'
t
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
>~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
>
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Dipl. bio-chem. E
hods
in package lattice) and I would like to to provide intensive and extensive explanation
with examples.
But in case if my method "foo" which is so simple (it just prints "foo") I would like
to use promptClass.
Yours
Eryk.
*** REPLY SEPARATOR ***
On 8
Hi!
Have written some functions with signature "numeric".
eg.
setGeneric("foo",
function(object,...)
standardGeneric("foo"))
setMethod("foo",signature(object="numeric"),def =
To generate the Rd file sceleton i use
> promtClass("numeric")
A shell of class documentation has
Hi!
Pinned the problem with plot down a bit. I can reproduce it with only 2 lines of R on
my Windows XP machine.
(today reinstalled R1.9.0) and Bioconductor packages updated.
Can anyone reproduce this behaviour?
(I am surely reproducing this error only if library(ROC) is loaded at the beginning
Getting a crash with R1.8.1 on windows 2000 an linux with the strsplit.
Version:
platform = i386-pc-mingw32
arch = i386
os = mingw32
system = i386, mingw32
status =
major = 1
minor = 8.1
year = 2003
month = 11
day = 21
language = R
Version:
platform = i386-pc-mingw32
arch = i386
os
Hi!
I wondering about the behavior of the 'as' function.
After reading the following sentences:
?as:
Returns the version of this object coerced to be the given Class.
and page 285 of programming with data:
"When a class extends another class, a call to as on the ...
Specially page 292
"If t
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