[Rd] indexing by character with identical names
Hi all, I've been using R for a while, but was puzzled when I just barely noticed this behavior: x - 1:10 names(x) - c(a,b,a,letters[1:7]) x a b a a b c d e f g 1 2 3 4 5 6 7 8 9 10 x[a] a 1 ... that is, if a vector has identical (and therefore ambiguous) names, it only returns the first match when the vector is indexed by a non-unique name. From my perspective, a more sensible behavior would be to return *all* elements which carry the non-unique name (e.g. x[names(x)==a] ), since it's ambiguous as to which element the user actually wanted to extract. It just seems safer than quietly returning only the first matched element with no warning or other indication as to what's actually happening. I couldn't find that this behavior is explicitly documented in the help file for '[' or 'names'. I also couldn't find any prior discussion of this behavior. Is this something that could be addressed in an upcoming release of R? Thanks, jake R version 2.7.2 (2008-08-25) x86_64-unknown-linux-gnu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] indexing by character with identical names
2008/9/19 Jake Michaelson [EMAIL PROTECTED] ... that is, if a vector has identical (and therefore ambiguous) names, it only returns the first match when the vector is indexed by a non-unique name. From my perspective, a more sensible behavior would be to return *all* elements which carry the non-unique name (e.g. x[names(x)==a] ), since it's ambiguous as to which element the user actually wanted to extract. It just seems safer than quietly returning only the first matched element with no warning or other indication as to what's actually happening. Some people may think it sensible that indexing a vector with an index of length N returns a vector of length N: x[c(a,b,a)] a b a 1 2 1 I also couldn't find any prior discussion of this behavior. Is this something that could be addressed in an upcoming release of R? Changing this would probably (no, definitely!) break stuff. Breaking stuff is a bad thing. Perhaps the upcoming R version Aleph-null release would be the right place for it... R is not like other programming languages, so your perspective of sensibility of minimal use here. You will get bitten by these gotchas. I bet everyone on this mailing list has done a X[1,] and got bitten by not having drop=FALSE Ouch. Writing tests on edge cases is a good thing, since it catches these problems (if you write your tests well!). Barry __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] family=mono does not work (PR#12931)
Full_Name: Jaan Vajakas
Version: 2.7.2
OS: Windows XP
Submission from: (NULL) (193.40.5.245)
When I execute the following code in the R GUI, the text mono is printed in
monotype font in the first plot, but in normal (sans-serif) font in the
remaining three plots:
op=par(mfrow=c(2,2))
for (i in 1:4) {
hist(1:10,xlab=)
mtext(normal,side=1,line=2)
mtext(mono,side=1,line=3,family=mono)
}
par(op)
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[Rd] R spec file change for building on CentOS 5.2 (PR#12939)
--GZVR6ND4mMseVXL/
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
I built R 2.7.2 on CentOS 5.2 today. I used the R.spec file posted
on the web site, but I had to change one line to get it to work.
I have attached the diffs from my spec file to the original.
(Otherwise, the build went fine.)
--
Aram J. Agajanian
Computer Science/UNIX Support
Academic Computing
State University of New York at New Paltz
Support the Free Software Foundation - www.fsf.org
--GZVR6ND4mMseVXL/
Content-Type: text/plain; charset=us-ascii
Content-Disposition: attachment; filename=specfile.diffs
49c49
%if %(rpmquery centos-release | grep -v 'not installed$' | grep -c -e
'-[0-9]-[0-9].el[0-9]')
---
%if %(rpmquery centos-release | grep -v 'not installed$' | grep -c -e
'-[0-9]-[0-9].[0-9]')
128c128
Version: 2.7.2
---
Version: 2.7.1
131c131
Source0: R-%{version}.tar.gz
---
Source0: ftp://cran.r-project.org/pub/R/src/base/R-2/R-%{version}.tar.gz
--GZVR6ND4mMseVXL/--
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Re: [Rd] Extract method for a new class
Coster, Albart [EMAIL PROTECTED] writes:
Dear list,
I am trying to write a package for simulating meioses in R. We defined
a class 'haplotype' which contains the basic units of our simulation:
setClass(haplotype,representation(snp = numeric,qtl = list, hID
= numeric,phID0 = numeric,phID1 = numeric), prototype = list(hID
= 0,phID0 = NaN,phID1 = NaN))
In addition, we define a class 'haploList', which is just a list of
haplotypes:
setClass(haploList,contains = list,representation(genDist =
numeric,roundDec = integer))
Most things work fine, but when subsetting a haploList object an
object of class list is returned. I realize that I need to write a
function for subsetting this new object, and tried to find the code
for '[.listof' or something similar could not find it, probably due to
a suboptimal understanding of how it is organized.
My question is, how could I define a extraction function for my new
class that uses all the existing functionality of the Extract function
for list?
You can find out what the generic looks like
getGeneric([)
standardGeneric for [ defined from package base
function (x, i, j, ..., drop = TRUE)
standardGeneric([, .Primitive([))
environment: 0xfc17a8
Methods may be defined for arguments: x, i, j, drop
Use showMethods([) for currently available ones.
and then write method(s) for your class:
setMethod([,
signature=signature(x=haploList, i=ANY, j=missing),
function(x, i, j, ..., drop=TRUE) {
## update and return x
[EMAIL PROTECTED] - [EMAIL PROTECTED], drop=drop]
x
})
Note though that extending 'list' has hazards, e.g.,
hlst - new(haploList, list(a=1,b=2))
names(hlst)
[1] a b
names(hlst[2])
[1] a
where the names have been confused! You'll want to manage the names
yourself (as a separate slot) or make sure that they're removed
entirely when you create / update your object.
(Here's a variant that I like
setMethod([,
signature=signature(x=haploList, i=ANY, j=missing),
function(x, i, j, ..., drop=TRUE) {
## feed updated values to 'initialize'
initialize(x, [EMAIL PROTECTED])
})
because the initialize call will [provided any initialize methods
defined on contained classes don't interfer] minimize copying. You'll
also likely want methods for $ and [[, and assignment methods [-
etc.)
Hope that helps,
Martin
Thanks in advance,
Albart Coster __
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Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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[Rd] readRegistry function (PR#12937)
Full_Name: Zivan Karaman Version: 2.7.2 OS: Windows XP Submission from: (NULL) (195.6.68.214) I'm puzzled by the readRegistry function. Shouldn't the hive argument be something like c(HLM, HCR, HCU, HU, HCC, HPD) rather than c(HLM, HCR, HCU, HU, HCC, HPD). For example, readRegistry(Test, HCC, HPD) Error in readRegistry(Test, HCC, HPD) : invalid 'hive' value Please note also that only the first character of the 'key' argument value is printed in case of error (key not found). readRegistry(SOFTWARE\\DummyTest, HLM) Error in readRegistry(SOFTWARE\\DummyTest, HLM) : Registry key 'S' not found sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] readRegistry function (PR#12937)
On 9/19/2008 1:25 PM, [EMAIL PROTECTED] wrote: Full_Name: Zivan Karaman Version: 2.7.2 OS: Windows XP Submission from: (NULL) (195.6.68.214) I'm puzzled by the readRegistry function. Shouldn't the hive argument be something like c(HLM, HCR, HCU, HU, HCC, HPD) rather than c(HLM, HCR, HCU, HU, HCC, HPD). Yes, that's a typo. I'll fix it. For example, readRegistry(Test, HCC, HPD) Error in readRegistry(Test, HCC, HPD) : invalid 'hive' value Please note also that only the first character of the 'key' argument value is printed in case of error (key not found). readRegistry(SOFTWARE\\DummyTest, HLM) Error in readRegistry(SOFTWARE\\DummyTest, HLM) : Registry key 'S' not found I'll also fix that. Thanks for the report! Duncan Murdoch sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
