Re: [R] R logo
If we knew an elegant one, we'd have an R function to do it ... The R Logo was done "manually" (using software) in several phases IIRC. But yes, indeed, an 'Rfont' package on CRAN would be neat... Martin Maechler, ETH Zurich and R Core Team. I am not sur of what would be neat : a police with nice letter that have a border ? I do not know how to change a drawing in a police, but making the drawing of the police is not that hard (well I know that I am the one who ask, but it was only to avoid to work on Gimp again, because I did not for a long time and I thaught that I forget almost every thing... I was wrong) With Gimp (which is the free version of photoshop) : http://christophe.genolini.free.fr/kml/images/alphaRouge.jpg http://christophe.genolini.free.fr/kml/images/alphaBleu.jpg http://christophe.genolini.free.fr/kml/images/alphaVert.jpg http://christophe.genolini.free.fr/kml/images/alphaBlanc.jpg Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] probleme with R CMD check
Hi the list,
Back on an old problem. I thaught that was ok, but it is still not
working on my computer.
I write a toy package called packClassic. R CMD build packClassic works
fine.
When I run R CMD CHECK packClassic, I get
--- 8< ---
* checking for unstated dependencies in R code ... WARNING
Erreur dans .find.package(package, lib.loc) :
aucun package nommé 'packClassic' n'existe
--- 8< ---
I gess that my configuration is correct since on an other package (a
real one), I get no problem.
The program is called "progClassic.R". Obviouly, is in a directorie
called \packClassic\R\
The doc are in man, a data base is in data and some test are in tests
Here are the codes, the DESCRIPTION and NAMESPACE, then the file
00install.out and 00check.log :
I also put the package (since R CMD build works fine) on
http:\\christophe.genolini.free.fr/packClassic_1.0.tar.gz
http:\\christophe.genolini.free.fr/packClassic_1.0.zip
Does someone know what is wrong ?
Christophe
8< - packClassic.R
##
### ProgClassic.R ###
##
userA <- function(x){x+1}
privateA <- function(x){x+2}
.userB <- function(x){x+10}
.privateB <- function(x){x+20}
userC <- function(x){userA(privateA(x))}
privateC <- function(x){.userB(.privateB(x))}
--- 8< -- testsPackClassic.R
##
### Nom du programme : testClassique.R ###
##
load("../data/dn.Rda")
source("../R/progClassic.R")
userA(1)
privsateA(2)
.userB(3)
.privateB(4)
userC(5)
privateC(6)
--- 8< dn.Rda --
dn <- data.frame(age=c(1,2,4,8,12))
save(dn,file=dn.Rda")
--- 8< --- DESCRIPTION -
Package:packClassic
Type: Package
Title: A (Not So) Short Introduction To S4
Version: 1.0
Date: 2008-07-16
Author: Christophe Genolini
Maintainer: <[EMAIL PROTECTED]>
Description: This package is a toy example used to illustrate the
tutorial A (Not So) Short Introduction to S4.
License: GPL (>=2)
LazyLoad: ys
--- 8< --- NAMESPACE --
export("userA",
".userB",
"userC"
)
--- 8< man
dn.Rd
packClassic-internal.Rd
packClassic-package.Rd
userAC.Rd
--- 8< - 00install.out --
installing R.css in
C:/DOCUME~1/CHRIST~1/MESDOC~1/DOCSAR~1/R/TUTORI~1/PACKCL~1.RCH
-- Making package packClassic
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
installing R files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'packClassic'
Formats: text html latex example chm
dntexthtmllatex example
packClassic-internal texthtmllatex
packClassic-package texthtmllatex example
userACtexthtmllatex example
adding MD5 sums
* DONE (packClassic)
--- 8< - 00check.log --
* using log directory 'C:/Documents and Settings/Christophe/Mes
documents/Docs articles polys résumés/R/tutorial S4/packClassic.Rcheck'
* using R version 2.7.1 (2008-06-23)
* using session charset: ISO8859-1
* checking for file 'packClassic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'packClassic' version '1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'packClassic' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'data' contains no data sets.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies
... OK
* checking for unstated dependencies in R code ... WARNING
Erreur dans .find.package(package, lib.loc) :
aucun package nommé 'packClassic' n'existe
Calls: -> .find.package
Exécution arrêtée
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
*
[R] Sweave add code \201
Hi the list, I do not understand what change in my configuration, but Sweave add the code \201 before each special characters é è à ç ... Does someone know when it come from ? Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave add code \201
Peter Dalgaard a écrit : Christophe Genolini wrote: Hi the list, I do not understand what change in my configuration, but Sweave add the code \201 before each special characters é è à ç ... Does someone know when it come from ? MULE (multilingal environment) in Emacs used to be prone to do this, but I haven't seen it for a while, so I'm afraid I have forgotten the details (if I ever understood them). Thanks ! I thaught I had a it was Sweave and thanks to you I start to search in emacs. Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] path and R CMD check
Hi the list,
When I developpe my code, I put the file that define all the functions
in ./MyPack/R/prog.R and the tests in ./MyPack/tests/testsProg.R
The test files start by
load("../data/myData.rda")
source("../R/prog.R")
#test function number one...
But "R CMD check MyPack" does not find the file myData.rda.
Does someone knows what is wrong ?
Christophe
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Re: [R] path and R CMD check
Uwe Ligges-3 wrote:
>
>
>
> Christophe Genolini wrote:
>> Hi the list,
>>
>> When I developpe my code, I put the file that define all the functions
>> in ./MyPack/R/prog.R and the tests in ./MyPack/tests/testsProg.R
>> The test files start by
>>
>> load("../data/myData.rda")
>> source("../R/prog.R")
>> #test function number one...
>>
>> But "R CMD check MyPack" does not find the file myData.rda.
>> Does someone knows what is wrong ?
>
>
> Read Writing R Extensions, learn how a package works (and yes, it works
> without sourcing files separately since the package mechanism does the
> job for you) and just say:
>
> library("packagename")
> data("myData")
>
> Best wishes,
> Uwe Ligges
>
>
I try but I find it very hard. Do you have more precision about the part
that explain it ? I read it several time, but I did not find that much on
tests.
So I do it on my own way. But I would love to know more about the way used
by real programmer.
So far :
- I am writing my code in several files /myPack/R/progA.R and
/myPack/R/progB.R
- I am writing tests in /myPack/tests/testsProgA.R and
/myPack/tests/testsProgB.R
- I am writing a main program in /myPack/main.R. This main program is
calling the tests.
- Since the progB.R is an extension of progA.R, the testsB.R use some data
define in testsA.R
Before today, I was starting by
> load("../data/myData.rda")
> source("../R/prog.R")
But you tell me to do :
> library("myPack")
> data("myData")
Using this system is problematic during the development phase, since the
package is not ready and library(myPack) will not work
Any advice for a better way of working ?
Christophe
--
View this message in context:
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[R] [R-pkgs] KmL 1.1.1
‘kml’ is an implementation of k-means for longitudinal data (or trajectories). This algorithm is able to deal with missing value and provides an easy way to re roll the algorithm several times, varying the starting conditions and/or the number of clusters looked for. KmL 1.1.1 addition: - 7 imputations methods for longitudinal data - Calculus of three qualities criterion (Calinski&Harabatz, Ray&Turi, Davies&Bouldin) - Implementation of the Frechet distance between two trajectories - Calculus of the Frechet path - Optimization of the function 'dist' for trajectories - Possibility to use three different ways to define the starting conditions - Correction of minor bugs Christophe Genolini ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Dealing with an argument missing in ...
Hi the list
I define a S3 function that can have a various number of argument using
'...'
When some arguments are missing, I would like to give them some default
value:
func.numeric <- function(x,...){
if(missing(y)){y<-3}
}
But it does not works...
I precise that I can not put 'y' explicitly in the argument list since
func is an S3 function, I cannot change its arguments.
Any suggestions?
Thanks
Christophe
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[R] aggregate without removing empty subset
Hi the list,
As it is say in its doc, the aggregate function remove empty subsets. Is
it possible to NOT remove empty subset ?
--- 8< ---
m <- matrix(1:12,4)
part <- factor(c("A","B","A","B"),levels=c("A","B","C"))
aggregate(m,list(part),mean)
### I get:
# Group.1 V1 V2 V3
# 1 A 2 6 10
# 2 B 3 7 11
#
### I would like:
# Group.1 V1 V2 V3
# 1 A 2 6 10
# 2 B 3 7 11
# 3 C NA NA NA
--- 8< --
Thanks
Christophe
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Re: [R] aggregate without removing empty subset
As I told you in private, thanks, it works perfectly.
More precisely, I am working with 3D array. Your code works well (both
on matrix or on array).
But when part is a factor with only one value, the result has not a
correct dimension (vector if m is a matrix, a matrix if m is an array).
Any way to fix that ?
m1 <- matrix(1:12,4)
m2 <- array(1:24,dim=c(4,3,2))
part1 <- factor(c("A","B","A","B"),levels=c("A","B","C"))
part2 <- factor(c("A","A","A","A"),levels=c("A"))
apply(m1, 2, tapply, part1, mean) ##Perfect (dim=c(3,3))
apply(m1, 2, tapply, part2, mean) ## dim=NULL...
apply(m2, c(2,3), tapply, part1, mean) ## Perfect (dim=c(3,3,2))
apply(m2, c(2,3), tapply, part2, mean) ## dim=c(3,2)
Christophe
> Try this:
>
> apply(m, 2, tapply, part, mean)
>
> On Mon, Mar 15, 2010 at 2:10 PM, Christophe Genolini
> wrote:
>
>> Hi the list,
>>
>> As it is say in its doc, the aggregate function remove empty subsets. Is it
>> possible to NOT remove empty subset ?
>> --- 8< ---
>> m <- matrix(1:12,4)
>> part <- factor(c("A","B","A","B"),levels=c("A","B","C"))
>> aggregate(m,list(part),mean)
>>
>> ### I get:
>> # Group.1 V1 V2 V3
>> # 1 A 2 6 10
>> # 2 B 3 7 11
>> #
>> ### I would like:
>> # Group.1 V1 V2 V3
>> # 1 A 2 6 10
>> # 2 B 3 7 11
>> # 3 C NA NA NA
>> --- 8< --
>>
>>
>> Thanks
>> Christophe
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
>
>
>
[[alternative HTML version deleted]]
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[R] S4: Multiple inheritance
Hi all, Working with S4 object, I definine two class foo1 and foo2. I define '[' (resp. '[<-') for the two classes. Then I define a third class foo3 that inherit from both foo1 and foo2. Is there a way to make '[' (resp. '[<-') for foo3 inherit from '[' (resp. '[<-') for foo1 and foo2? Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Drawing a line with misc3d
Hi the list, I would like to draw some lines with misc3d. I find a lot of tools to draw surfaces, but nothing for simple line... Is it possible? Note that I know that it is possible to draw lines with rgl (using lines3d), but I need to do it with misc3d to export the drawing in .asy format. Any solution? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Exporting an rgl graph
Thanks a lot Both Asymptote and MeshLab work fine. Thanks for this article, Luke. On my particular case, I need to export lines (1D object in a 3D space) and not surfaces (2D objects). Is it possible to draw lines with misc3d ? Christophe Genolini Luke Tierney a écrit : The current issue of JCGS (Vol 18 No 1, http://pubs.amstat.org/toc/jcgs/19/1) has an editorial on including animations, 3D visualizations, and movies in on-line PDF files supporting JCGS articles. The online supplements to the editorial include examples. The 3D examples related to the misc3d packages are also available in http://www.stat.uiowa.edu/~luke/R/misc3d/misc3d-pdf/ <http://www.stat.uiowa.edu/%7Eluke/R/misc3d/misc3d-pdf/>. At some point the code there will be added to misc3d. It should be possible to adapt these ideas to other objects rendered with rgl. luke __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] savePlot for Mac and / or Linux?
Hi all,
In the package rtlu, I use the function savePlot. It is convenient since
it let the user decide in which graphic format he wants his graph to be
export.
But when I run R CMD check, I get the following message :
rtlu(V1,fileOutput="First.tex",textBefore="\\section{Variable 1 to
3}",graphName="V1")
Error in savePlot(filename = nomBarplot, type = type) : can only copy
from 'windows' devices
Calls: rtlu ... r2lUniv -> r2lUniv.factor -> r2lBarplot -> savePlot
Execution halted
I guess this is a compatibility problem with Linux/Mac? Is there
something close to savePlot for Mac / Linux?
Christophe
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[R] "time series", "longitudinal data" or "trajectories"
Hi the list Strictly speaking, this is not a "R" question, but I need the information for the creation of a package. My question is about vocabulary: What is the difference between "time series", "longitudinal data" and "trajectories"? Sincerely Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] "time series", "longitudinal data" or "trajectories"
Thanks for yours answers. So if I understand: - Trajectories are continuous, the other are discrete. - The difference between time series and longitudinal is that time series are made at regular time whereas longitudinal are not ? - Repeated measures are over a short period of time. So if I measure the weight of my patient daily during one week, it will be repeated measure ; if I measure it once a week during one year, it will time series ; if I measure it once a week during one year but with some "missing week", it will longitudinal data ? Well I guess it is not as simple at that, but is it the idea ? Christophe At 04:02 PM 6/5/2009, Christophe Genolini wrote: Hi the list Strictly speaking, this is not a "R" question, but I need the information for the creation of a package. My question is about vocabulary: What is the difference between "time series", "longitudinal data" and "trajectories"? Sincerely Christophe "Longitudinal" data are measurements over long periods of time, often at irregular periods, but consistent across subjects. "Repeated measures" data are replicates at the same point in time, or over a short period of time (e.g., laboratory experiments). "Time series" typically have constant increments of time and typically a stochastic character, although this term might be considered all-encompassing for all measurements at different times. "Trajectory" implies a continuous curve in time, as opposed to discrete times. "Trajectory" also implies an underlying causal model, as it is a term from kinematics. I hope this helps. Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: r...@lcfltd.com Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 "Vere scire est per causas scire" __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] "R CMD check" does not find a mistake
Hi the list, I build a package. They was a mistake in it, but R CMD check did not find it. Is that normal ? Here is what Kurt gets (which is right, I did this mistake): --- 8< * checking for code/documentation mismatches ... WARNING S4 class codoc mismatches from documentation object 'LongData-class': Slots for class 'LongData' Code: id other time traj varName Docs: id time traj varName --- 8< But here is what I get : --- 8< R CMD check longitudinalData * checking for working pdflatex ... OK * using log directory 'C:/Documents and Settings/Christophe/Mes documents/Recher che/Trajectoires/kmeal/longitudinalData.Rcheck' * using R version 2.9.0 beta (2009-04-04 r48290) * using session charset: ISO8859-1 * checking for file 'longitudinalData/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'longitudinalData' version '0.5' * package encoding: latin1 * checking package dependencies ... OK * checking if this is a source package ... OK * checking for .dll and .exe files ... OK * checking whether package 'longitudinalData' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd files against version 2 parser ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking examples ... OK * checking PDF version of manual ... OK R CMD build longitudinalData * checking for file 'longitudinalData/DESCRIPTION' ... OK * preparing 'longitudinalData': * checking DESCRIPTION meta-information ... OK * removing junk files * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'longitudinalData_0.5.tar.gz' --- 8< Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sending a function as an argument to C code.
Hi the list,
I am writing a function (myFunc) that is using an other function (let
say distance).
+++
dist1 <- function(x,y)dist(rbind(x,y))
dist2 <- function(x,y)y2
myFunc <- function(x,distance){
cat("...\n")
cat(distance(1,x))
}
myFunc(x=3,distance=dist1)
myFunc(x=3,distance=dist2)
In order to optimize the code, I would like to write myFunc in C. Is it
possible, in the C code, to call a function define in R (dist1 or dist2)
that will be send to myFunc as an argument ?
Christophe
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[R] Crash caused by a call to a C function
Hi the list I write a function MyFunc. To optimize it, I write a C function MyFuncC then a function MyFunc2 that call .C(“MyFuncC”,….) The two functions MyFunc and MyFunc2 seem to behave exactly the same way (they give the same results). But when I test MyFunc2 several times (around 20), R crash. This is not link to a specific example since if I test MyFunc2 on the same example several time, I still get a crash. Any idea of what can cause this kind of error (or even how can I diagnose the problem)? And how I can correct it? Sincerely Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sweave: Changing the background color, adding a border
Hi all, I am using Sweave to produce a document. Unfortunately, I have to print several copies and I can't print them in color. So I would like to change the way of printing the code. I would like to print the code in a box with a black borderline and a grey background (quite classic). Is it possible to do it by changing some Schunk options? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave: Changing the background color, adding a border
Duncan Murdoch a écrit :
On 19/04/2009 6:03 AM, Christophe Genolini wrote:
Hi all,
I am using Sweave to produce a document. Unfortunately, I have to
print several copies and I can't print them in color. So I would like
to change the way of printing the code. I would like to print the
code in a box with a black borderline and a grey background (quite
classic). Is it possible to do it by changing some Schunk options?
It should be, if you know how to print things like that, but I don't
Here's some code I wrote a while ago to modify the Sweave formats in a
much simpler way:
% This removes the extra spacing after code and output chunks in Sweave,
% but keeps the spacing around the whole block.
\fvset{listparameters={\setlength{\topsep}{0pt}}}
\renewenvironment{Schunk}{\vspace{\topsep}}{\vspace{\topsep}}
% We want to avoid having examples switch us to an italic font shape.
\DefineVerbatimEnvironment{Soutput}{Verbatim}{fontshape=n}
Hi Duncan, hi Romain
Thanks for your answer. I finally succeed.
I used the listings package to define an environment that put code in a
grey box. The command is \lstnewenvironment{Sinput}[1][]{
Then I change the Schunk, Sinput and Soutput environment.
- For the Schunk, I use \renewenvironment as Duncan suggest.
- For Sinput, I would like to use something like \lstREnewenvironment
but it does not exist.
So I comment the line \usepackage{Sweave}, I copy the contain of file of
Sweave.sty in the .Rwn file and I remove the definition of Sinput and
Soutput.
Note: The line %\usepackage{Sweave} is necessary, otherwise the R
command 'Sweave()' add the line \package{Sweave}in the LaTeX file.
--- 8< --
The final file is :
%\usepackage{Sweave}
\RequirePackage[T1]{fontenc}
\RequirePackage{graphicx,ae,fancyvrb}
\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
\setkeys{Gin}{width=0.8\textwidth}
%\DefineVerbatimEnvironment{Sinput}{}{}
%\DefineVerbatimEnvironment{Soutput}{}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
\newenvironment{Schunk}{}{}
\usepackage{listings}
\definecolor{gris90}{gray}{0.90}
\lstloadlanguages{R}
\lstnewenvironment{Sinput}[1][]{
\lstset{%
language={R},
basicstyle=\small,% print whole listing small
keywordstyle=\color{black}\bfseries, % style for keyword
emph={in},% define a list of word to
emphasis
emphstyle=\color{black}\bfseries, % define the way to emphase
% emph={[2]out},% define a second list
of word to emphasis
% emphstyle=[2]\color{red}\bfseries,% define the way to
emphase the list 2
frame=single, % box arround the code
backgroundcolor=\color{gris90}, % background color
% commentstyle=\color{gris10}, % define the style of
the comments
showspaces=false, % show the space in code,
or not
stringstyle=\ttfamily,% style of the string
(like "hello word")
showstringspaces=false, % show the space in
string, on not
#1
}
}{}
\lstnewenvironment{Soutput}[1][]{
\lstset{%
language={R},
basicstyle=\small,% print whole listing small
keywordstyle=\color{black}\bfseries, % style for keyword
emph={in},% define a list of word to
emphasis
emphstyle=\color{black}\bfseries, % define the way to emphase
% emph={[2]out},% define a second list
of word to emphasis
% emphstyle=[2]\color{red}\bfseries,% define the way to
emphase the list 2
frame=single, % box arround the code
backgroundcolor=\color{gris90}, % background color
% commentstyle=\color{gris10}, % define the style of
the comments
showspaces=false, % show the space in code,
or not
stringstyle=\ttfamily,% style of the string
(like "hello word")
showstringspaces=false, % show the space in
string, on not
#1
}
}{}
--- 8< --
Christophe
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[R] Bug: more information on a crash
Hi the list, In the package KmL (new version, not release yet), the main function seems to work correctly but once in a while, R crash (full crash, anything link with R is closed and windows ask if it can send a crash report). More precisely, when I run it in a loop on 1000 data sets, the crash is certain... Is there a way to get more information on what cause this? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Number of download.
Hi the list Is there a way to know how many times an R package (on CRAN) has been download ? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Optimizing C code
Hi the list,
I need to write some efficient distances function, so I read the code
for the Euclidean distance.
I do not understand the purpose of the line 11 : if x[i] and y[i] are
not NA (line 9), can dev be NA ?
Christophe
#define both_FINITE(a,b) (R_FINITE(a) && R_FINITE(b))
#define both_non_NA(a,b) (!ISNAN(a) && !ISNAN(b))
1. static double R_euclidean2(double *x, double *y, int taille)
2. {
3.double dev, dist;
4.int count, i;
5.
6.count= 0;
7.dist = 0;
8.for(i = 0 ; i < taille ; i++) {
9.if(both_non_NA(x[i], y[i])) {
10.dev = (x[i] - y[i]);
11.if(!ISNAN(dev)) {
12.dist += dev * dev;
13.count++;
14.}
15.}
16.}
17.if(count == 0)return NA_REAL;
18.if(count != taille) dist /= ((double)count/taille);
19.return sqrt(dist);
20.}
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Re: [R] Optimizing C code
Thanks both of you.
> Inf - Inf
[1] NaN
So isn't the line 9 useless ? If either x[i] or y[i] are NA, then dev
will be NA and !ISNAN(dev) will detect it...
Sothe loop cool be
8.for(i = 0 ; i < taille ; i++) {
10.dev = (x[i] - y[i]);
11.if(!ISNAN(dev)) {
12. dist += dev * dev;
13. count++;
15. }
16. }
No ?
Christophe
Duncan Murdoch
Christophe
#define both_FINITE(a,b) (R_FINITE(a) && R_FINITE(b))
#define both_non_NA(a,b) (!ISNAN(a) && !ISNAN(b))
1. static double R_euclidean2(double *x, double *y, int taille)
2. {
3.double dev, dist;
4.int count, i;
5.
6.count= 0;
7.dist = 0;
8.for(i = 0 ; i < taille ; i++) {
9.if(both_non_NA(x[i], y[i])) {
10.dev = (x[i] - y[i]);
11.if(!ISNAN(dev)) {
12.dist += dev * dev;
13.count++;
14.}
15.}
16.}
17.if(count == 0)return NA_REAL;
18.if(count != taille) dist /= ((double)count/taille);
19.return sqrt(dist);
20.}
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Re: [R] Optimizing C code
Duncan Murdoch a écrit :
On 22/01/2010 12:52 PM, Christophe Genolini wrote:
Thanks both of you.
>
> > Inf - Inf
> [1] NaN
So isn't the line 9 useless ? If either x[i] or y[i] are NA, then dev
will be NA and !ISNAN(dev) will detect it...
Sothe loop cool be
8.for(i = 0 ; i < taille ; i++) {
10.dev = (x[i] - y[i]);
11.if(!ISNAN(dev)) {
12. dist += dev * dev;
13. count++;
15. }
16. }
No ?
That would presumably give the same answer, but there are lots of
reasons it might not be useless:
- the author might find it clearer, or easier to generalize to integer
data (where your version wouldn't work).
- it might be faster, because it can abort sooner.
- it might be essentially equivalent in all important respects.
Duncan Murdoch
That's 3 good reasons to keep the other code. Thanks.
Christophe
> Duncan Murdoch
>> Christophe
>>
>>
>> #define both_FINITE(a,b) (R_FINITE(a) && R_FINITE(b))
>> #define both_non_NA(a,b) (!ISNAN(a) && !ISNAN(b))
>>
>> 1. static double R_euclidean2(double *x, double *y, int taille)
>> 2. {
>> 3.double dev, dist;
>> 4.int count, i;
>> 5.
>> 6.count= 0;
>> 7.dist = 0;
>> 8.for(i = 0 ; i < taille ; i++) {
>> 9.if(both_non_NA(x[i], y[i])) {
>> 10.dev = (x[i] - y[i]);
>> 11.if(!ISNAN(dev)) {
>> 12.dist += dev * dev;
>> 13.count++;
>> 14.}
>> 15.}
>> 16.}
>> 17.if(count == 0)return NA_REAL;
>> 18.if(count != taille) dist /= ((double)count/taille);
>> 19.return sqrt(dist);
>> 20.}
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide >>
http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>> >
>
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[R] matrix to a C function
Hi the list,
Is there a way to give a matrix to a C function, and then to use it as a
matrix ?
I write a function to print a matrix, but I use it as a vector :
1. void printMatrix(double *mTraj,int *nbCol, int *nbLigne){
2. int i=0,j=0;
3. for(i=0 ; i < *nbLigne ; i++){
4. for(j=0 ; j < *nbCol ; j++){
5. Rprintf(" %f",mTraj[i * *nbCol + j]);
6. }
7. Rprintf("\n");
8.}
9. }
I would like to use it as a matrix (line 5 changes) :
1. void printMatrix(double *mTraj,int *nbCol, int *nbLigne){
2. int i=0,j=0;
3. for(i=0 ; i < *nbLigne ; i++){
4. for(j=0 ; j < *nbCol ; j++){
5. Rprintf(" %f",mTraj[i,j]);
6. }
7. Rprintf("\n");
8.}
9. }
It does not work, but is there an solution close to this ?
Thanks.
Christophe
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[R] microbenchmark
Hi the list,
I am using the function microbenchmark to measure the performance of some code. But I notice that
the first execution of the code takes much longueur than the next executions.
I compare it to several executions of the code :
--- 8< --
A <- matrix(1:9,3)
nbReroll <- 1000
temps <- matrix(NA,1000,2)
temps[,1] <- microbenchmark(colMeans(A),times=nbReroll)$time
for(j in 1:nbReroll){
temps[j,2] <- microbenchmark(colMeans(A),times=1)$time
}
--- 8< ---
Here is a plot of the result I get.
- In red, temps[,1], that is microbenchmarck(...,times=1000)
- In blue temps[,2], that is for(i in 1:1000)microbenchmark(...times=1)
So why is there such a bid difference? What is the correct execution time for
my instruction?
Christophe
--
Christophe Genolini
Maître de conférences en bio-statistique
Vice président Communication interne et animation du campus
Université Paris Ouest Nanterre La Défense
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Re: [R] Add axes to a 3D scene (afer makeTriangles)
Hi David,
Thanks for your answer.
Here is my (simplified) code :
8< -
library(misc3d)
#
### Fonction that draw a point A=(x,y,z), with radius r
misc3dPoint <- function(A,r,color="black",alpha=1){
t1 <- c(A[1]+r,A[2],A[3],A[1],A[2]+r,A[3],A[1],A[2],A[3]+r)
t2 <- c(A[1]+r,A[2],A[3],A[1],A[2]+r,A[3],A[1],A[2],A[3]-r)
t3 <- c(A[1]+r,A[2],A[3],A[1],A[2]-r,A[3],A[1],A[2],A[3]+r)
t4 <- c(A[1]+r,A[2],A[3],A[1],A[2]-r,A[3],A[1],A[2],A[3]-r)
t5 <- c(A[1]-r,A[2],A[3],A[1],A[2]+r,A[3],A[1],A[2],A[3]+r)
t6 <- c(A[1]-r,A[2],A[3],A[1],A[2]+r,A[3],A[1],A[2],A[3]-r)
t7 <- c(A[1]-r,A[2],A[3],A[1],A[2]-r,A[3],A[1],A[2],A[3]+r)
t8 <- c(A[1]-r,A[2],A[3],A[1],A[2]-r,A[3],A[1],A[2],A[3]-r)
return(data.frame(rbind(t1,t2,t3,t4,t5,t6,t7,t8),color=color,alpha=alpha))
}
#
### Fonction that draw several points MA=(A,B,C,D,...)
misc3dPoints <- function(MA,r,color="black",alpha=1){
dataV <- data.frame()
if(length(r)==1){r <- rep(r,ncol(MA))}else{}
if(length(color)==1){color <- rep(color,ncol(MA))}else{}
if(length(alpha)==1){alpha <- rep(alpha,ncol(MA))}else{}
for(i in 1:ncol(MA)){
dataV <-
rbind(dataV,misc3dPoint(MA[,i],r[i],color=color[i],alpha=alpha[i]))
}
return(dataV)
}
### Some points (points are in colomn)
MA <-
cbind(c(3.5,3.5,3.5),c(3,2,1),c(1.5,1,0.5),c(0.3,0.3,0.3),c(0,0,0),c(4,4,4))[3:1,]
### The radius of the points
r = 0.3
### Building the list of triangle3d from the points
listOfTriangles <- misc3dPoints(MA,r,color=c(1:4,1,1),alpha=c(1,1,1,1,0,0))
### Making the scene
myScene <- makeTriangles(
v1=as.matrix(listOfTriangles[,1:3]),
v2=as.matrix(listOfTriangles[,4:6]),
v3=as.matrix(listOfTriangles[,7:9]),
color=listOfTriangles$color,alpha=listOfTriangles$alpha
)
### Drawing the scene
drawScene.rgl(myScene,xlim=c(0,4),ylim=c(0,4),zlim=c(0,4))
### Then, I export the triangles into an asy file (with is the final pupose of
all this)
library(longitudinalData)
saveTrianglessASY(myScene)
8< -
So I rewrite my question: is it possible to add some axes to the "myScene"
object?
Christophe
On Jan 30, 2013, at 3:09 AM, cgenolin wrote:
Hi all,
I am drawing some 3D surfaces using the Triangle tools (package misc3) and
drawScene.rgl. Do you know if it is possible to add axes and graduation on
the scene?
You offer no code or data, so a specific answer is not called for. Certainly the specific answer
to the possibility of labels in rgl graph is is "yes". You might learn something by looking at the
work that Ben Bolker and I put into a question requesting labels on the scatter3d function in
package "car";
http://stackoverflow.com/questions/8204972/carscatter3d-in-r-labeling-axis-better/8206320#8206320
--
Christophe Genolini
Maître de conférences en bio-statistique
Vice président Communication interne et animation du campus
Université Paris Ouest Nanterre La Défense
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Re: [R] Problem with a submission to jss
Le 14/10/2012 00:00, Duncan Murdoch a écrit : On 12-10-13 3:20 PM, Christophe Genolini wrote: Hi the list, I am about to submit an article describing an R package to the Journal of Statistical Software but I encounter a strange behavior of LaTeX: the numbering of the figure is correct (1. 2. 3. ...), but when I make a reference to a figure, the section (or the subsection) number appears instead of the figure number. I check if this behavior occurs with the file example provide in the jss package style: it does (I joint the example to this mail). So does someone know what is wrong? Sincerely Christophe This body part will be downloaded on demand. I would guess you put the \label in the wrong place. Put it in the \caption and it should be fine. Duncan Murdoch It works, thanks. But it looks surprising for me. I use LaTeX for quite a long time and I always put the \label after the \caption (and I find several website that advice to do so). Is it something specific to the jss style? Christophe -- Christophe Genolini Maître de conférences en bio-statistique Vice président Communication interne et animation du campus Université Paris Ouest Nanterre La Défense __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] exporting 3D dynamic graph
Hi the list, Using misc3d, we can export 3d dynamic graph in pdf format. Is it also possible to export these graph into a format that we can publish on the web? Christophe -- Christophe Genolini Maître de conférences en bio-statistique Vice président Communication interne et animation du campus Université Paris Ouest Nanterre La Défense [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] exporting 3D dynamic graph
Perfect, thanks a lot ! > On 11/5/2012 8:23 AM, Christophe Genolini wrote: >> Hi the list, >> >> Using misc3d, we can export 3d dynamic graph in pdf format. >> >> Is it also possible to export these graph into a format that we can publish >> on the web? >> >> Christophe > You don't provide enough information to know exactly what your needs are, > but writeWebGL() in the > rgl function may be of some use in doing what you want. I don't think that > it can handle the > "dynamic" part on its own yet, but perhaps with some creative JavaScript > additions you can get there. > > Rob >> >> >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > -- > __ > Robert W. Baer, Ph.D. > Professor of Physiology > Kirksille College of Osteopathic Medicine > A. T. Still University of Health Sciences > Kirksville, MO 63501 USA -- Christophe Genolini Maître de conférences en bio-statistique Vice président Communication interne et animation du campus Université Paris Ouest Nanterre La Défense [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] r-help or r-devel ?
Hi the list, I have some basic questions about "writing a package". On which list shall I post them? Theoretically, I am supposed to post them on r-devel, but all the questions on this list are very advance questions, not basic ones... So I don't know what to do. Christophe -- Christophe Genolini Maître de conférences en bio-statistique Vice président Communication interne et animation du campus Université Paris Ouest Nanterre La Défense [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Is it possible to be sponsored by R?
Hi the list, I am a member of the organizing comity of the French Statistics Association (SFdS)'s conference. We are looking for sponsors. Some software (SAS, RITME, ...) are represented. Do you know if there is any possibility to be sponsored by R (or by an association close to R)? Do you think I can ask to the R fondation? Sincerely Christophe -- Christophe Genolini Maître de conférences en bio-statistique Vice président Communication interne et animation du campus Université Paris Ouest Nanterre La Défense [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How fast is the JSS reviewing process?
Hi all, I thought I read somewhere that the reviewing process of the Journal of Statistical Software was quite fast (arround 3 month). Is that correct? -- Christophe Genolini Maître de conférences en bio-statistique Vice président Communication interne et animation du campus Université Paris Ouest Nanterre La Défense __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Petit traité de programmation orienté obje t sous R
Bonjour (English below) J'ai le plaisir de vous annoncer la naissance de : "Petit traité de programmation orienté objet sous R", aux éditions De Boeck. J'y raconte comment faire de la programmation orienté objet S4, mais aussi comment construire un package. Le style est volontairement léger, l'ouvrage se veut pédagogique et simple à comprendre... A vous de me dire si j'ai réussi... Vous cherchiez une bonne résolution pour la rentrée 2010 ? Mettez-vous à l'objet... Christophe --- 8< -- Hi the list, I am pleased to announce the release of : "Petit traité de programmation orienté objet sous R", published by De Boeck. It is about object-oriented programming (S4), but also how to build a package. The style is intentionally light, the book is educational and easy to understand ... To you tell me if I succeeded ... You were looking for a good resolution for the 2010 academic year? Try S4 ! Christophe -- - Christophe Genolini Maitre de conférences INSERM U669, Equipe Biostatistiques UFR STAPS, Université de Paris Ouest-Nanterre-La Défense Web: http:\\christophe.genolini.free.fr - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] package under unix
Generally, I like to use a pdf device which can have any number of pages. I am proposing a graphical way a selecting a clusterization based a quality criterion. In order to avoid local maximum, you can build something like 10 000 clusterization. Exporting all of them has no sence. So I open two graph, on the left you can see all the quality criterion. On the rigth, you can see the clusterization that you are curently selecting on the left graph. The idea is not to export all the clusterization but to chose one. So you can change the selected clusterization by using the arrow. This is possible only on a screen. But an X11 device will also work for single plots and there's no need to specifically set it in the package. Thanks a lot. Is there a way to set the position at which the x11 windows shall open ? I do not want to be very precise, I just want the two windows to not open one on the top of the other... Why not let users set the device they wish to use? The function that is calling windows(5,5,xpos=0) is called "choice()". So users that do not like the output that I propose are free to not call "choice()", others are free to use it... Requests to the maintainer gets no response. Lol ! I am so proud when someone is using one of my two package that I answer very fast... ;-) May be it will change when I will have ten to maintain ? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A (not so) Short Introduction to S4
Hi the list, After months of keen work (!), thousands of questions on the R-help (and on the French R forum GuR), I am pleased to announce the birth of new a tutorial on S4: *** A (Not So) short Introduction to S4 *** http://christophe.genolini.free.fr/webTutorial/index.html It probably remains English faults. Moreover, my English translator was not a programmer at all. So all comments / corrections / suggestion of improvement are welcomes. Christophe PS : Am I allow to put the R logo on my web site or is it only for officials R core team tutorial / website? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R logo
Hi the list, I like the R logo (grey C and blue R) very much, specialy the drawing of the letter with border and shadow. I would like to make something closed with some other letters. Does anyone know how to get a similar result ? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] S4 : package creation
Hi the list, Using S4, how can we create a package? In "S4 Classes in 15 pages, more or less", they put all the classes definition in a function that will be called at the opening of the library and they add "by hand" a Rd file. Is it the only way ? Is there something like "S4.package.skeleton"? Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sweave and printing error
Hi the list. I am writing a tutorial for my student using LaTeX and sweave. I include some example that work (obiously) but I would also like to include some example that do NOT work (for pedagogie)... Is it possible ? At this point, I find that : - if there is a error in the code, Sweave stop - if I put the error in try(), Sweave compile but does not print the error as output. Any solution ? Thanks a lot Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] S4 : the list of all the object
Hi the list, Is it possible to get the list of all the S4 user define classes? I would like to set up a "package.skeleton.S4" but for that, I need the list of the classes... Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Journal for R
Hi the list I made up a new statistical procedure. I will publish it in a medical journal, but there will be only the way of using it, no calculation or algorithme detail. So is there a journal (I mean scientific journal) with selection commity to submit an article describing the detail of a package? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] tests Rin Rout
Hi the list,
Some rumour (!) say that is it possible to prepare some tests for
checking our code using .Rin and .Rout. It seems to be a very good
practice, but I did not manage to find information on it.
So does someone know how it works ? What are we suppose to write in Rin ?
More precisely :
- I have a package myPack.r in directories ~/myR/myPack/R/
- I create the directory ~/myR/myPack/tests
myPack.r is :
`f1` <- function(x){cat("\nXXX F1 = ",x,"XXX\n")}
`f2` <- function(x){cat("\nXXX F2 = ",f1(x^2),"XXX\n")}
What am I suppose to do to test it? Create myPack.Rin, but what in it?
Thanks for your help.
Christophe
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Re: [R] tests Rin Rout
> > See the paragraph in Writing R Extensions which explains this Well, I saw it again and again (before asking on the r-help) but I do not understand. Same for the Kurt Hornik slides on the web. > > Create tests/myPack.R with those lines in it plus lines to actually > run the code. Does it mean that each time I change the code, I will have to change it twice, once in R/ and once in tests/ > If the code generates errors, your test will fail. If you want to > see reports of changes to the output, also include > tests/myPack.Rout.save with the known correct versions of the output. > What should the Rout.save looks like ? I mean, what is the syntax of this file ? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] findGlobals on apply
Hi the list,
Considere the following:
f <- function(x){apply(x,2,mean)}
findGlobals(f)
findGlobals consideres mean as a global variable, which it is not.
Is there a way to tell to findGlobals that mean is a function ?
Thanks
Christophe
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Re: [R] findGlobals on apply
> > f <- function(x){apply(x,2,mean)}
> > findGlobals(f)
> mean is a global variable, so findGlobals gets it right.
That sound strange to me: a "variable" is something that vary... mean
does not vary. maen will ge an argument that is a line of x and will
make some calculous on it, that is the comportement of a function.
Of course, mean is an argument of an other function, but I do not think
this is a reason good enouth to say that mean is a variable.
Furthemore, I use findGlobals to detect some typo. In
f <- function(myObject){return(mObject^2)}
findGlobals will detect that mObject is a global so I know there is a
typo somewhere.
Considering mean as a globals do not let us use findGlobals this way.
Christophe
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Re: [R] findGlobals on apply
Hi Luke
Thanks for all these explanation, things are clearer.
Let me go back on my initial problem, that was, as a programmer, I would
like to have a tool to detect typo by detecting globals variables:
I get that findGlobals is not design for that.
I did not realy understand the use of checkUsage (sorry for that, I am
not a high level programmer).
But I find an example on which checkUsage does not detect the typo either:
mObjBis <- 3
f <- function(myOb){
myObBis <- myOb^2
plot(myObBis)
return(mObjBis)
}
checkUsage(f,all=TRUE)
So, my question is a more general question : is there a function that
can detect global variable with exclusion of the function and the
reserved word?
For example:
g <- function(x)return(x+pi)
we don't want pi to be considere as a global variable since it is a
constant...
Is there a function that can deal with that ?
Christophe
> On Tue, 8 Apr 2008, Christophe Genolini wrote:
>
>>
>>>> f <- function(x){apply(x,2,mean)}
>>>> findGlobals(f)
>>> mean is a global variable, so findGlobals gets it right.
>> That sound strange to me: a "variable" is something that vary... mean
>> does not vary. maen will ge an argument that is a line of x and will
>> make some calculous on it, that is the comportement of a function.
>> Of course, mean is an argument of an other function, but I do not think
>> this is a reason good enouth to say that mean is a variable.
>
> You are missing some points about R and findGlobals.
>
> In R, functions are first class values: they can be assigned to
> variables, passed as arguments, and returned as results, just like
> vectors. In contrast to many other languages there is not special
> mechanism for defining functions and associating them with a name --
> the way you define a function is
>
> foo <- function(...) ...
>
> which creates a function value and assigns it to a variable.
>
> findGlobals just looks at the function body and arguments and
> determines which of the variables used would have their definitions
> looked up in the global environment if this code is run. It does not
> try to detect which of these have values or not, never mind what the
> types of those falues are.
>
> The result returned by findGlobals with merge=FALSE separates into
> variables that are explicitly used as funcitons, i.e foo in foo(x) and
> ones that are not. One could argue that findGlobals should know
> enough about apply() to realize that the FUN argument is implicitly
> used as a function; if this change were made then
>
> apply(x, 2, pi)
>
> pi would be listed as a function because it is _used_ that way.
>
>> Furthemore, I use findGlobals to detect some typo. In
>>
>> f <- function(myObject){return(mObject^2)}
>>
>> findGlobals will detect that mObject is a global so I know there is a
>> typo somewhere.
>> Considering mean as a globals do not let us use findGlobals this way.
>
> You need to do some extra work to get this -- checking which globals
> have values, and maybe whether those that are used as functions have
> values that are functions. checkUsage does this, among other things.
> For this example checkUsage produces
>
> > checkUsage(f)
> : no visible binding for global variable ‘mObject’
>
> luke
>
>> Christophe
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
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[R] cls.attrib and integer
Hi the list, Is it a bug? The function cls.attrib seems to not work with integer : values <- round(runif(50,1,10)) dim(values) <- c(10,5) valuesBis <- as.integer(values) dim(valuesBis) <- c(10,5) cluster <- rep(1:2,5) library(clv) cls.attrib(values,cluster) cls.attrib(valuesBis,cluster) Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Clean programming with R
Hi all
Is there any compiler for R ? By compiler, I mean something that check
the cleanliness of the code : if we declare all the variables we use, if
we don't use external variable from a function and so on...
For exemple, something that will ring a bell on the following code
(saying "line 4 : 'pp' undefine in function 'power' ")
1. pp <- 3
2. power <- function(x){
3.p <- 2
4.return(2^pp)
5. }
thanks
Christophe
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[R] Oriented object programming
Hi all Two questions: - I would like to learn more on oriented object programming with R. Is there any tutorial for that? - Without waking up a troll, I am not very familiar with diffusion list, I am more use to forum. On a diffusion list, how can I check if someone already asks a question? I mean, I went on CRAN-R website, I find the R mailing list archive. But is there a way to search some key word like "object programming"? Thanks for your help Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rerolling k-means
Hi all I am working on k-means algorithm (in R: kmeans( ) ). The R-help advice us to try several random start in order to avoid local minimum. Does one know if there is a procedure that automaticly run this rerolling and select the best partition ? Or any studies that gives clues on the number of rerolling ? Thanks for helping. Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R to LaTeX Univariate Analysis
Hi all
Well, first: happy new year...
Second: I write a function in R that might interest some other people.
On the other hand, I am closer to beginners than experts; I don't know
how valuable my code is. I don't know how long it will take to me to
create a library and I don't know if it's worth to. So before starting
this long process, I would like some advices, both on the interest it
present, on the way of using it and on the inner R code...
My function is called "r2lUniv" for "R to LaTeX, Univariate analysis".
Given a variable, it performs some basic analysis in R and generates
LaTeX code to include in a document that print the analysis in a clean
LaTeX way. The basic analysis depends of the variable type. 4 types are
considered:
- Nominal: modality, size, barplot
- Ordinal: modality, size, quartile, barplot
- Discrete: modality, size, mean, var, quartile, boxplot, barplot
- Continuous: mean, var, quartile, boxplot, barplot
A generalization of r2lUniv deals with data.frame by runnig the basic
analysis on every column. So to use it:
> dataFrame <- read.csv("myData.csv")
> r2lUniv(dataFrame,"fileOut.tex")
It performs the basic analysis and creates all graphs. Then I add
\input{fileOut.tex} in my main.tex file.
My source file is available at:
http://christophe.genolini.free.fr/r2lUniv/mySource/
It is definitely NOT a code ready for a library, there is probably bugs
in it, all comments and all variables used for testing are in. But
still, any advices will be welcome...
Christophe
PS: Does the manual "Writing R Extensions" exists in French? Or
anything equivalent?
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[R] bug in mmlcr ?
Hi the list.
Is there a bug in mmlcr package ?
The following code does not compile:
mmlcrTest <- function(dataW){
dataL <-
reshape(dataW,idvar="id",timevar="T",varying=list(paste("T",0:10,sep="")),direction="long",v.names="score")
resultR <- mmlcr(outer= ~ 1 | id,
components = list(list(formula = formul,class=
"normlong")),
n.groups=3,
data=dataL,
max.iter=500
)
plot(resultR)
}
mmlcrTest(dataW)
The error is (translate from french):
"Error in inherits(x, "data.frame") : objet "dataL" not find"
It seems that mmlcr does not look for the data at the right place since
it did find dataL if we set it a a global variable but it does not find
it if we define it in a function.
Christophe
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[R] [R-pkgs] New package: R to LaTeX Univariate Analyses
Hi the list
*** New package ***
R to LaTeX : Univariate analyses
r2lUniv
*URL:*http://www.r-project.org, http://christophe.genolini.free.fr/r2lUniv
*** Description ***
r2lUniv performs some basic analyses, then generates a code to be
included in a LaTeX document
to print the analyses in a (so nice!) LaTeX way.
r2lUniv performs the analyses automatically according to the classical
statistics
type definition that are nominal, ordinal, discrete and continuous. The
analysis performed are:
- Nominal : modality, size, barplot
- Ordinal: modality, size, quartile, barplot
- Discrete: modality, size, mean, var, quartile, boxplot, barplot
- Continuous: mean, var, quartile, boxplot, barplot
*** I am a Rookie... ***
Well, I know that. This is my first package and I am almost a beginner in R.
So any comment on any subject (programming style, way of writing the
man, use of S3) are welcome
("You did a nice job, but classical usage is to..." or "Hmmm, that would
be more practical if...").
*** Other project ***
Well, Univariate Analysis is the first step, the second is Bivariate
analysis.
Also, before posting here, I submit this package on a French forum.
The first suggestion is to extend this package to HTML. I will not have
time to do it alone.
So if some people are interested, two other project are almost open :
- R to LaTeX Bivaraite Analysis
- R to HTML Univariate Analysis
Thanks
Christophe Genolini
Junior statistician
"PSIGIAM: Paris Sud Innovation Group in Adolescent Mental Health"
INSERM U669 / Maison de Solenn / Paris
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[R] package manual in pdf
Hi all, I am trying to write a pdf manual for my package. I create a file inst\doc\myDoc.tex. I taught that R CMD build will call latex on this file (like it is said in Writing R extension), but it does not happen. I also notice that a pdf manual is produce automatically but with a not so good presentation (very long lines that step outside the page for example). Where can I find the source code of this .pdf ? Is there a way to modify it? Sorry to ask these questions, but writing R extension is not that clear on the topic... Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Contributed Documentation
Hi the list, I wrote a tutorial about S4. Is it possible to have a link to it in the page "Contributed Documentation" or "R Documentation" on the CRAN web site ? Who shall I contact ? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A (Not So) Short Introduction to S4 (ex Contributed Documentation)
Here is the link : http://christophe.genolini.free.fr/webTutorial/index.php Any comments are welcome. Christophe On Tue, Jan 6, 2009 at 8:17 PM, Ben Bolker wrote: > Christophe Genolini u-paris10.fr> writes: > >> >> Hi the list, >> >> I wrote a tutorial about S4. Is it possible to have a link to it in the >> page "Contributed Documentation" or "R Documentation" on the CRAN web >> site ? Who shall I contact ? >> >> Christophe > > Try c...@r-project.org . Posting to the development list > (r-de...@r-project.org) might also be appropriate. > I would be curious to see the tutorial myself. > > Ben Bolker > > _ I would too. On Tue, Jan 6, 2009 at 8:17 PM, Ben Bolker wrote: > Christophe Genolini u-paris10.fr> writes: > >> >> Hi the list, >> >> I wrote a tutorial about S4. Is it possible to have a link to it in the >> page "Contributed Documentation" or "R Documentation" on the CRAN web >> site ? Who shall I contact ? >> >> Christophe > > Try c...@r-project.org . Posting to the development list > (r-de...@r-project.org) might also be appropriate. > I would be curious to see the tutorial myself. > > Ben Bolker > > _ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-help Digest, Vol 71, Issue 7
Thanks for your answer Here it is : http://christophe.genolini.free.fr/webTutorial/index.php Any comments are welcome... Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Strange behavior of savePlot
Hi all, I am using savePlot in a loop for saving several graph but I get some graph in 553x552, some other in 1920x1119. How comes ? My data are almost all the same (same label, same xlim / ylim, almost same data. Only the color changes). I save them in bmp. Thanks for your help. Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Strange behavior of savePlot
Uwe Ligges a écrit : Christophe Genolini wrote: Hi all, I am using savePlot in a loop for saving several graph but I get some graph in 553x552, some other in 1920x1119. How comes ? My data are almost all the same (same label, same xlim / ylim, almost same data. Only the color changes). I save them in bmp. Thanks for your help. Rather than using a Windows Device and copying the contents, just use the bmp() device directly if you really want bitmaps. Uwe Ligges I do not want a bitmaps. I use savePlot in a library, so I let the user decide whith export he wants. Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Strange behavior of savePlot
Uwe Ligges a écrit : Christophe Genolini wrote: Uwe Ligges a écrit : Christophe Genolini wrote: Hi all, I am using savePlot in a loop for saving several graph but I get some graph in 553x552, some other in 1920x1119. How comes ? My data are almost all the same (same label, same xlim / ylim, almost same data. Only the color changes). I save them in bmp. Thanks for your help. Rather than using a Windows Device and copying the contents, just use the bmp() device directly if you really want bitmaps. Uwe Ligges I do not want a bitmaps. I use savePlot in a library, so I let the user decide whith export he wants. Then, why not let the user choose a proper device? Because I program a graphical interface that let the user to chose the graph he want to export (that can be one but also 50). Then he sets dynamicaly the parameters for all the graphics he wants to export. Then all the graphs are exported at once. Anyway, the resulting bitmap is copied from the screen device, that means the size is also copied. That means if you have some 1600x1200 screen and your windows device is resized to fullscreen, than you will almost get 1600x1200 pixels in your bitmap... Ok, the "strange behevior" was occuring because I change the size of the windows during the export... Thanks a lot Christophe Uwe Ligges Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] probleme with savePlot (to eps)
Hi the list,
I used savePlot to export some eps graph but it seems that the graph
file hold a bug. I include the graph.eps in a LaTeX file. Running latex
is ok. But the dvi file contain some mistake, the graph overprint on
some text and hide it. Then, when I try to convert it to another format,
I get :
Ignoring remaining special text following unkown PS operator: "SDict"
Remainder of line unparsed
Current input buffer is --> begin /product where{pop
product(Distiller)search{...<--
Any idea to correct that ?
Christophe
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Re: [R] probleme with savePlot (to eps)
Thanks for your answer. Use the postscript device to save .ps or .eps files. Unfortunatly, I can't. I am using savePlot in a package. Several graphs (up to 100) are exported at the same time and I would like the user to chose the extension. It is why I need savePlot. Beside, I did not find any warning again postscript in the help page for savePlot. Where did you get this information ? I am using R 2.8.1 Christophe The help page for savePlot does not suggest that it would be of any value in saving plots as postscript files. ?postscript ?Devices __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] probleme with savePlot (to eps)
I am using windows XP pack3 and R 2.8.1 so I guess this is savePlot for
Windows.
As Gabor say, savePlot offer to export graph also in eps.
If you want to copy a screen device to postscript portably, use
dev.copy2eps().
I am exporting graph in a package, so I don't want to copy screen device
to postscript, I want to copy screen device to postscript OR to any
other type that the user may want...
It is why I can not use a specific function (postscrip(), dev.copy2eps()
) but I need a generic one.
Christophe
On Sun, 1 Mar 2009, David Winsemius wrote:
Unfortunately your burning desire to use savePlot for this purpose is
not going to reconfigure the capabilities of that function. Just read
the help page of savePlot:
savePlot {grDevices}
R Documentation
Save Cairo X11 Plot to FileDescription
Save the current page of a cairo X11() device to a file.
Usage
savePlot(filename = paste("Rplot", type, sep="."), type = c("png",
"jpeg", "tiff", "bmp"), device = dev.cur())
Do you see "ps" or "eps" in the supported types? I do not. Why would
you expect be a warning not to use a type of device that was not
documented as possible.
Have you looked at dev.copy or dev.print as a method of getting the
user choice of screen displayed graphics to an output file?
--
David Winsemius
On Mar 1, 2009, at 6:02 PM, Christophe Genolini wrote:
Thanks for your answer.
Use the postscript device to save .ps or .eps files.
Unfortunatly, I can't. I am using savePlot in a package. Several
graphs (up to 100) are exported at the same time and I would like
the user to chose the extension. It is why I need savePlot.
Beside, I did not find any warning again postscript in the help page
for savePlot. Where did you get this information ? I am using R 2.8.1
Christophe
The help page for savePlot does not suggest that it would be of any
value in saving plots as postscript files.
?postscript
?Devices
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[R] Redefining [ using next method
Hi all,
I would like to use an object and to add some definition to the [
function, but I do not manage...
My objet is a "trajectories", a matrix whose columne name does contain
information :
-
trajectories <- function(traj,varName,time){
colnames(traj) <- paste(varName,time,sep="")
class(traj) <- c("trajectories","matrix")
return(traj)
}
x <- trajectories(traj=matrix(1:12,4),varName="T",time=c(1,2,4))
--
Then I would like to define the [ operator in the following way :
---
> x["varName"]
[1] "T"
> x["time"]
[1] 1 2 4
> x[1,]
1 5 9
> x[,1]
1 2 3 4
For that, I write:
"[.trajectories" <- function(traj,slot,...){
if(slot=="varName"){return(gsub("(\\d+)$","",colnames(traj)[1],perl=T))}else{}
if(slot=="time"){return(as.numeric(gsub("(^.+\\D)(\\d+$)","\\2",colnames(traj),perl=T)))}else{}
NextMethod()
}
The ["varName"],["time"] and [1,] work fine, but not [,1]
Any idea of what is wrong and how to correct?
Thanks
Christophe
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[R] Integer vs numeric
Hi the list. I do not understand the philosophy behind numeric and integer. - 1 is numeric (which I find surprising) - 2 is numeric. - 1:2 is integer. Why is that ? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Integer vs numeric
> Further to the above: The help > > ?":" > > says: > > Value: > For numeric arguments [as opposed to factors], > a numeric vector. This will be of type 'integer' > if 'from' and 'to' are both integers and > representable in the integer type, otherwise of > type 'numeric' ??? This is very surprising since with a "to" numeric, the result is integer : > str(1:4.5) int [1:4] 1 2 3 4 Anyway, if I understand, 'integer' in R is not realy the math type integer. I am a bit confuse... Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Integer vs numeric
x[c(2,4)] work as well
Henrik Bengtsson a écrit :
> x[1:n]
>
> /H
>
> On Jan 29, 2008 5:07 AM, <[EMAIL PROTECTED]> wrote:
>
>> Seems strange to me to define an operator relatively to a very special case.
>> I have to admit that I do not use 1:1e7 every day :-)
>>
>> Wouldn't it be more appropriate to define a a:b operator numeric (that
>> is preserving the initial class of a and b) and in specific case that
>> need optimization, changing the type?
>>
>> for i in as.integer(1:1e7)
>>
>> That might appears as a minor point, but when using S4, for what I
>> know, if you define a class that can take either 1:3 or c(1,3,4), one
>> is integer, the other numeric, one of those will not be accepted by the
>> class...
>>
>> Christophe
>>
>>
>>
>>
>>> On 28-Jan-08 22:40:02, Peter Dalgaard wrote:
>>>
[...]
AFAIR, space is/was more of an issue. If you do something like
for i in 1:1e7
some.silly.simulation()
then you have 40 MB sitting there doing nothing, and 80 MB if
it had been floating point.
>>> Hmmm ... there's something to be said for good old
>>>
>>> for(i=1,i<=1e7,i++){}
>>>
>>> As pointed out in ?"for", when you do
>>>
>>> for(i in X){...} #(e.g. X=(1:1e7))
>>>
>>> the object X is created (or is already there) in full
>>> at the start and sits there, as you say doing nothing,
>>> until you end the loop. Whereas the C code just keeps
>>> track of i and of the condition.
>>>
>>> At least on a couple of my machines (64MB and 184MB RAM)
>>> knocking out 40MB would inflict severe trauma! Let alone 80MB.
>>> Mind you, the little one is no longer allowed to play with
>>> big boys like R, though the other one is still used for
>>> moderate-sized games.
>>>
>>> Would there be much of a time penalty in implementing
>>> a 'for' loop, C-style, as
>>>
>>> i<-1
>>> while(i<=1e7){
>>>...
>>>i<-i+1
>>> }
>>>
>>> ??
>>>
>>> It looks as though there might be:
>>>
>>> system.time(for(i in (1:1e7)) x<-cos(3) )
>>> #[1] 13.521 0.132 13.355 0.000 0.000
>>> system.time({i<-1;while(i<=1e7){x<-cos(3);i<-i+1}})
>>> #[1] 38.270 0.076 37.629 0.000 0.000
>>>
>>> which suggests that the latter is about 3 times as slow.
>>> (And no, this wasn't done on either of my puny babes).
>>>
>>> (And this isn't the first time I've wished for an R
>>> implementation of "++" as a CPU-level incrementation,
>>> as opposed to the R-arithmetic implementation which
>>> treats "adding 1 to a variable" as a full-dress
>>> arithmetic parade!
>>>
>>> Best wishes,
>>> Ted.
>>>
>>>
>>> E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
>>> Fax-to-email: +44 (0)870 094 0861
>>> Date: 28-Jan-08 Time: 23:34:52
>>> -- XFMail --
>>>
>>>
>>
>>
>> Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
>>
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
>
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Re: [R] learning S4
Robin Hankin a écrit :
> Christophe
>
> you might find the Brobdingnag package on CRAN helpful here.
>
Yep, I read it and I find it very usefull. A question anyway:
Is there a way to change a slot without using the <- ?
Instead of
> new("obj")
> [EMAIL PROTECTED] <- 3
I would like to have
> new("obj")
> setSlotA(obj,3)
In your vignette, 'Section 8 : Get and Set methods', you define 4 Gets,
but no Set...
Christophe
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[R] Hiding a function
Hi the list
Is it possible to 'hide' a function from the user ? I cut a big
fonction in sub
function and I would like to hide the sub function, just like if I
declare them
in the big function :
--
a <- function(x){
b <- function(y){y^2}
d <- function(y){y^3}
b(x)+d(x)+2
}
a(2)
# [1] 14
b(2)
# Error :
I would like the same, but with external declaration (for readability) :
b <- function(y){y^2}
d <- function(y){y^3}
a <- function(x){
b(x)+d(x)+2
}
a(2)
# [1] 14
b(2)
# Error
Is it possible ?
Thanks
Christophe
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Re: [R] Hiding a function
Duncan Murdoch a écrit :
> On 23/02/2008 5:15 AM, Christophe Genolini wrote:
>> Hi the list
>>
>> Is it possible to 'hide' a function from the user ? I cut a big
>> fonction in sub
>> function and I would like to hide the sub function, just like if I
>> declare them
>> in the big function :
>>
>> --
>> a <- function(x){
>> b <- function(y){y^2}
>> d <- function(y){y^3}
>> b(x)+d(x)+2
>> }
>> a(2)
>> # [1] 14
>> b(2)
>> # Error :
>>
>>
>> I would like the same, but with external declaration (for readability) :
>>
>>
>> b <- function(y){y^2}
>> d <- function(y){y^3}
>> a <- function(x){
>> b(x)+d(x)+2
>> }
>> a(2)
>> # [1] 14
>> b(2)
>> # Error
>>
>>
>> Is it possible ?
>
> Yes, as long as you're using a package with a NAMESPACE, just don't
> export b and d. There are other ways too, but they don't improve
> readability.
>
> Duncan Murdoch
If I understand, it is possible only in a package, not in a programme
(unless the "other ways"), is that it ?
Ok, thanks.
Christophe
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[R] Set without argument
Hi the list,
I am defining S4 objet. Is it possbile to define a method that change
the slot of an object without using <- ?
My object contain a numeric and a matrix. At some point, I would like to
impute the missing value in the matrix. So I would like to use something
like :
-
setClass("MyObj",representation(time="numeric",traj="matrix"))
a <- new("MyObj",time=3,traj=matrix(c(1:6,NA,8:12),ncol=3))
imputeMyObj(a)
-
I find 'setTime<-' to change le slot time, but it can not work in the
case of imputeMyObs since this mehod does not need a value...
Any solution ?
Thanks
Christophe
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Re: [R] Hiding a function
Gabor Csardi a écrit : > It depends what you mean by 'hiding', Well, the main idea was the to limit the existance of a function. a( ) need b( ) but no other function will need b(). So I would have like to let b( ) exists localy only when a( ) is called, not elsewhere. Christophe > you can start the function > names with a dot and then they are not listed by ls(), so this > is kind of hiding. > > >> .a <- function() TRUE >> ls() >> > character(0) > >> .a >> > function() TRUE > > Personally i would not do this though. > > G. > > On Sat, Feb 23, 2008 at 11:58:57AM +0100, Christophe Genolini wrote: > [...] > >> If I understand, it is possible only in a package, not in a programme >> (unless the "other ways"), is that it ? >> Ok, thanks. >> >> > [...] > > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Hiding a function
Ok, I saw FUNx
So, I reformulate my question : is there a way, without nesting b( ) in
a( ), to make b( ) available only in a( ) ?
> Just to clarify, what Duncan was referring to as the
> alternative was nesting the definition of one function
> in another, e.g. look at FUNx in by.data.frame --
> FUNx is available to by.data.frame but is not
> visible outside of by.data.frame .
>
> On Sat, Feb 23, 2008 at 6:09 AM, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
>> On 23/02/2008 5:58 AM, Christophe Genolini wrote:
>>
>>> Duncan Murdoch a écrit :
>>>
>>>> On 23/02/2008 5:15 AM, Christophe Genolini wrote:
>>>>
>>>>> Hi the list
>>>>>
>>>>> Is it possible to 'hide' a function from the user ? I cut a big
>>>>> fonction in sub
>>>>> function and I would like to hide the sub function, just like if I
>>>>> declare them
>>>>> in the big function :
>>>>>
>>>>> --
>>>>> a <- function(x){
>>>>> b <- function(y){y^2}
>>>>> d <- function(y){y^3}
>>>>> b(x)+d(x)+2
>>>>> }
>>>>> a(2)
>>>>> # [1] 14
>>>>> b(2)
>>>>> # Error :
>>>>>
>>>>>
>>>>> I would like the same, but with external declaration (for readability) :
>>>>>
>>>>>
>>>>> b <- function(y){y^2}
>>>>> d <- function(y){y^3}
>>>>> a <- function(x){
>>>>> b(x)+d(x)+2
>>>>> }
>>>>> a(2)
>>>>> # [1] 14
>>>>> b(2)
>>>>> # Error
>>>>>
>>>>>
>>>>> Is it possible ?
>>>>>
>>>> Yes, as long as you're using a package with a NAMESPACE, just don't
>>>> export b and d. There are other ways too, but they don't improve
>>>> readability.
>>>>
>>>> Duncan Murdoch
>>>>
>>> If I understand, it is possible only in a package, not in a programme
>>> (unless the "other ways"), is that it ?
>>>
>> Yes, that's right. Here's one of the other ways:
>>
>> a <- local( {
>> b <- function(y){y^2}
>> d <- function(y){y^3}
>> function(x){
>> b(x)+d(x)+2
>> }
>> })
>>
>> I don't find that more readable than if b and d had been defined locally
>> within a.
>>
>> Duncan Murdoch
>>
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
>
[[alternative HTML version deleted]]
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[R] Standard method for S4 object
Hi the list, I am defining a new class MyClass. Shortly, I will submit a package with it. Before, I would like to know if there is a kind of "non official list" of what method a new S4 object have. More precisely, personnaly, I use 'print', 'summary' and 'plot' a lot. So for my new class, I define these 3 methods. Is there some other method that a R user can raisonnably expect ? Some "minimum basic tools"... Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Set without argument
Thanks a lot > The 'usual' way to write the above code is > > >> a <- imputeMyObj(a) >> :-( I was hopping something like the use of the superassignator <<- inside imputeMyObj (I was hoping even if I did not find it myself)... To bad. But thanks for teaching me 'usual' pratice. It is something that is not so easy to find in toturial, and as medium level programmer, it is not always clear to pick the good way when we hesitate between two... Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Hiding a function
After some private email with some high level programmer (Gabor), I have
the solution and I can answer to my own question :-)
The problem was 1° to define a function B( ) available only in a
function A( ) (for code safeness) and 2° to define B( ) elsewhere than
in A( ) (for code readability)
The solution is the following
# Definition of an environment that will be use in A() (a list will work as
well)
envA <- new.env()
# Definition of B(), in environment envA :
envA$b <- function(x) x2
# Definition of A :
A <- function(x) with(envA, {
B(3)
})
Thanks
Christophe
> On 23/02/2008 5:15 AM, Christophe Genolini wrote:
>> Hi the list
>>
>> Is it possible to 'hide' a function from the user ? I cut a big
>> fonction in sub
>> function and I would like to hide the sub function, just like if I
>> declare them
>> in the big function :
>>
>> --
>> a <- function(x){
>> b <- function(y){y^2}
>> d <- function(y){y^3}
>> b(x)+d(x)+2
>> }
>> a(2)
>> # [1] 14
>> b(2)
>> # Error :
>>
>>
>> I would like the same, but with external declaration (for readability) :
>>
>>
>> b <- function(y){y^2}
>> d <- function(y){y^3}
>> a <- function(x){
>> b(x)+d(x)+2
>> }
>> a(2)
>> # [1] 14
>> b(2)
>> # Error
>>
>>
>> Is it possible ?
>
> Yes, as long as you're using a package with a NAMESPACE, just don't
> export b and d. There are other ways too, but they don't improve
> readability.
>
> Duncan Murdoch
>
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Re: [R] Standard method for S4 object
> /I think your question should be more relevant on Rdev./
ok, I will
> Personnally I would find stuff like "names", "$", "$<-", or "["
> useful as these are usual operation with S3 objects.
Is it possible in S4 to define "$<-" ? If there is a slot name 'a' in
object 'B', I find (in "S4 in 15 pages more or less")
setGeneric("a<-", function(x, value) standardGeneric("a<-"))
setReplaceMethod("a", .
Then we can use
obj <- new("B")
a(obj)<- 3
But I did not find how to define
obj$a <- 3
Is it possible ? Is it the 'usual' way ?
Christophe
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[R] S4 : Signature
Hi the list
Is it possible to define a method with a signature that will have more
argument than the generic method?
For exemple, print has only one argument, plot has two, can I do
something like :
setMethod("print",signature=c(x="numeric",y="character"),function(x,y,...)
..
setMethod("plot",signature=c(x="numeric",y="character",z="numeric"),function(x,y,z,...)
..
Thanks
Christophe
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Re: [R] Set without argument
Hi Martin
What do you think of the following code ?
A <- 1
imputeMyObj <- function(x){
xImp <- 3 #Calcul for Imputation of x
nam<-deparse(substitute(x))
assign(nam,xImp,envir=parent.frame())
}
imputeMyObj(A)
A
I guess it is not usual, but do you think it is 'bad' programming or
will have side effect that I do not see ?
Christophe
> Christophe Genolini <[EMAIL PROTECTED]> writes:
>
>
>> Hi the list,
>>
>> I am defining S4 objet. Is it possbile to define a method that change
>> the slot of an object without using <- ?
>> My object contain a numeric and a matrix. At some point, I would like to
>> impute the missing value in the matrix. So I would like to use something
>> like :
>>
>> -
>> setClass("MyObj",representation(time="numeric",traj="matrix"))
>> a <- new("MyObj",time=3,traj=matrix(c(1:6,NA,8:12),ncol=3))
>> imputeMyObj(a)
>> -
>>
>
> Hi Christophe --
>
> The 'usual' way to write the above code is
>
>
>> a <- imputeMyObj(a)
>>
>
> with imputeMyObj designed to take a 'MyObj' as it's argument, and
> return a modified 'MyObj' (that the user can assign to 'a', if they
> like). Inside imputeMyObj, the developer would, in the end, write
> something like
>
> impuateMyObj <- function(obj) {
># calculate imputed values 'imp'
>slot(obj, "traj") <- imp
>obj
> }
>
> A better design would have a 'setter' method, minimally
>
>
>> setGeneric("traj<-",
>>
> +function(object, ..., value) standardGeneric("traj<-"))
> [1] "traj<-"
>
>> setReplaceMethod("traj",
>>
> + signature=signature(
> +object="MyObj",
> +value="matrix"),
> + function(object, ..., value) {
> + slot(object, "traj") <- value
> + object
> + })
> [1] "traj<-"
>
> and then the impute code would have
>
> impuateMyObj <- function(obj) {
># calculate imputed values 'imp'
>traj(obj) <- imp
>obj
> }
>
> It's possible to design 'MyObj' so that it can be modified in-place
> (e.g., storing data in a slot of class 'environment', which has
> reference-like behavior) but this will probably surprise both you and
> the user.
>
> Martin
>
>
>> I find 'setTime<-' to change le slot time, but it can not work in the
>> case of imputeMyObs since this mehod does not need a value...
>>
>> Any solution ?
>>
>> Thanks
>>
>> Christophe
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
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[R] tutorial on codetools
Hi the list Is there any tutorial to learn codetools ? It seems to be a very interesting pacakge, but the help gives not that much detail, and there is not that much examples provided... Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] inheritence in S4
Thanks Martin
Well it works except that "as" seems to not like the "initialize" method
: the following code (that is the same than yours with some initialize
for A B and C) does not compile. It seems that as(c,"A") does not work
if we definie a initialize for A...
--- 8< --
setClass("A", representation(x="numeric"))
setMethod("initialize","A",function(.Object,value)[EMAIL PROTECTED] <-
value;return(.Object)})
a <- new("A",4)
setClass("B", representation(y="numeric"))
setMethod("initialize","B",function(.Object,value)[EMAIL PROTECTED] <-
value;return(.Object)})
b <- new("B",5)
setClass("C", contains=c("A", "B"))
setMethod("initialize","C",function(.Object,valueA, valueB){
[EMAIL PROTECTED] <- valueA
[EMAIL PROTECTED] <- valueB
return(.Object)
})
c <- new("C",valueA=10,valueB=12)
setMethod("show", "A", function(object) cat("A\n"))
setMethod("show", "B", function(object) cat("B\n"))
setMethod("show", "C", function(object) {
callGeneric(as(object, "A"))
callGeneric(as(object, "B"))
cat("C\n")
})
c
--- 8<
Is there something wrong with the use of 'as' between class and father
class?
Christophe
> Hi Christophe --
>
> I don't know whether there's a particularly elegant way. This works
>
> setClass("A", representation(x="numeric"))
> setClass("B", representation(y="numeric"))
> setClass("C", contains=c("A", "B"))
>
> setMethod("show", "A", function(object) cat("A\n"))
> setMethod("show", "B", function(object) cat("B\n"))
> setMethod("show", "C", function(object) {
> callGeneric(as(object, "A"))
> callGeneric(as(object, "B"))
> cat("C\n")
> })
>
>
>> new("C")
>>
> A
> B
> C
>
> but obviously involves the developer in making explicit decisions
> about method dispatch when there is multiple inheritance.
>
> Martin
>
> [EMAIL PROTECTED] writes:
>
>
>> Hi the list
>>
>> I define a class A (slot a and b), a class C (slot c and d) and a class
>> E that inherit from A and B.
>> I define print(A) and print(B). For print(C), I would like to use both
>> of them, but I do not see how...
>>
>> Thanks for your help...
>>
>> Christophe
>>
>>
>> Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
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Re: [R] inheritence in S4
Hi Martin
I was not that much speaking about what we can do, but more about what
we can't. We can't decide that object will be 'never empty', we have to
allow empty oject, otherwise new("A") will not work and that will be
problematic.
So, at this point, I see :
- it is necessary to allow the creation of empty object (otherwise, we
are in trouble with 'as')
- so 'new' will have to create object either empty or valid.
- 'initialize' can check if an object is valid but has first to check
if the object is non empty
- I create an object Ccc containing an object Aaa : If Ccc is calling
the constructor of Aaa, then initialize of Aaa ic called. If Ccc is
setting the Aaa slot one bu one, the initialize of Aaa is not caller.
- In addition, I did not speak about the setteur, but the 'setSlotX
<-' does not call the initialize. So we have to check the validity of
the object after any 'setSlot' again.
In consequence, to program as safe as possible:
- for checking if an object is valid or not, I am thinking of setting
a method checkCoherance
- 'initialize' will just set slot to either empty or some value, then
call checkCoherance
- 'setSlotX<-' will change slot X, then call checkCoherance
- If I create a C object, its checkCoherance method will call
checkCoherance(as(object,"A"))
Here is an example (still the same stupid example with a single slot.
Obviously, it has no interest on so small object, it is just to simplify)
--- 8< --
setGeneric("checkCoherance",function(object){standardGeneric("checkCoherance")})
setClass("A", representation(x="numeric"))
setMethod("checkCoherance","A",
function(object){
cat("*** checkCoherance A ***\n")
if(length([EMAIL PROTECTED])>0){
if([EMAIL PROTECTED]<0){stop("Object incoherance : x should be
positive")}else{}
}else{}
return(TRUE)
}
)
setMethod("initialize","A",
function(.Object,value=numeric(0)){
cat("*** initialize A ***\n")
[EMAIL PROTECTED] <- value
checkCoherance(.Object)
return(.Object)
}
)
setGeneric("setX<-",function(object,value){standardGeneric("setX<-")})
setReplaceMethod("setX","A",
function(object,value){
[EMAIL PROTECTED] <- value
checkCoherance(object)
return(object)
}
)
a1 <- new("A")
a2 <- new("A",value=4)
try(a3 <- new("A",value=-4))
A <- function(val=numeric(0)){
new("A",value=val)
}
A()
A(val=4)
A(val=-4)
setClass("C", representation(y="numeric"),contains="A")
setMethod("checkCoherance","C",
function(object){
cat("*** checkCoherance C ***\n")
if(length([EMAIL PROTECTED])>0){
if([EMAIL PROTECTED]>0){stop("Object incoherance : y should be
négative")}else{}
}else{}
checkCoherance(as(object,"A"))
return(TRUE)
}
)
setMethod("initialize","C",
function(.Object,valueX=numeric(0), valueY=numeric(0)){
cat("*** initialize C ***\n")
[EMAIL PROTECTED] <- valueX
[EMAIL PROTECTED] <- valueY
checkCoherance(.Object)
return(.Object)
}
)
c <- new("C",valueX=10,valueY=12)
new("C")
C <- function(valX=numeric(0),valY=numeric(0)){
new("C",valueX=valX,valueY=valY)
}
C()
C(valX=5)
try(C(valX=-5))
C(valY=-3)
c1 <- C(valX=4,valY=-6)
as(c1,"A")
--- 8< --
> You're partly misunderstanding...
>
>
Lol. I guess so, and unfortunatly, it is not over ...
> setClass("A", representation(x="numeric"),
> prototype=prototype(x=0))
>
>
I do not understand the difference with
setClass("A", representation(x="numeric"),
prototype(x=0)
)
> If you have an initialize
> method on "A" then it will be called.
Only if you call the A constructor, right ? Not if you set the slot that
C has heritate from A one by one, right ?
Christophe
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[R] Sweave and extra line
Hi the list, I am using Sweave. Between the Sinput and the Soutput, there is always an extra line: > 2+2 [1] 4 Is it possible to remove it ? > 2+2 [1] 4 Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sweave and the prompt
Hi the list I would also like to remove the prompt, in order to let the reader cut-and-paste from pdf to R. So I set the prompt to " " with options(prompt=" ",continue=" ") But it add an extrat space at the start of each line. I also try some code options(prompt="\a",continue="\a") After a big figth in my office (my college did not like my new prompt :-) ), I gave up since it does not let the user cut-and-paste either... Is there any possibility to completly remove the prompt ? Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sealed for setGeneric
Hi the list When two setGeneric occurs on the same function, the second erage the first and erase all the function previously define. Is it possible to prevent that ? Is it possible to declare a setGeneric that can not be erased later ? Something like the |sealed for setMethod...| || |Thanks| || Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sealed for setGeneric
> an unusual strategy would be to use lockBinding to make the symbol > associated with the generic unchangeable. > This sounds nice, thanks. Why is it unusual ? Any side effect or just the practice? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] alias for a class
Hi the list Is it possible to give two names for a class ? One long name for using in programmation, and one short name for the "quick and durty" uses ? With function, we can do mcf <- myCoolFunction <- function(x) With class, I define "clusterizedLongData", I want to use it with the full name when I am writing my code, but I would like something like cld when I make a demo, or when I try things on console... Is it possible ? Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] changing the quote
Hi the list,
I am using R2.6.2. I don't now why, the quote used in the output of
'new' seams not compatible with Sweave. Is there a way to change them ?
Is it something link with R, or link with my computer configuration ?
> setClass("E",list(e="factor"))
[1] "E"
> new("E")
An object of class “E”
Thanks
Christophe
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[R] empty array
Hi the list Is it possible to create an empty matrix ? I do not mean an matrix with a single value that is NA (which is not empty) but a real empty one, with length=0. I do not understand why we have length(numeric()), length(factor()) and length(character()) to zero, and length(array()) to one... Any rason for that ? Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] empty array
John Kane a écrit : > Will > mymatrix <- NULL do what you want? > Well, in your code, 'mymatrix' is not a matrix : a<-array(dim=c(0,0)) # Solution of Gabor Csardi <0 x 0 matrix> class(a) [1] "matrix" b<-NULL class(b) [1] "NULL" Your definition will probably works in most case, but in S4, the uses of type is an important point, so I need to use matrix where I shall use matrix, even if it is an empty one. Christophe > --- Christophe Genolini <[EMAIL PROTECTED]> wrote: > > >> Hi the list >> >> Is it possible to create an empty matrix ? I do not >> mean an matrix with >> a single value that is NA (which is not empty) but a >> real empty one, >> with length=0. >> >> I do not understand why we have length(numeric()), >> length(factor()) and >> length(character()) to zero, and length(array()) to >> one... Any rason for >> that ? >> >> Thanks >> >> Christophe >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, >> reproducible code. >> >> > > > > Be smarter than spam. See how smart SpamGuard is at giving junk email > the boot with the All-new Yahoo! Mail. Click on Options in Mail and switch > to New Mail today or register for free at http://mail.yahoo.ca > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] length of S4
Hi the list,
With basic type, length gives the length of the vector
Wtih list, length gives the number of item
With S4 object, length gives...one. Even with an objet with empty slot.
setClass("E",representation(e="numeric"))
[1] "E"
length(new("E"))
[1] 1
setClass("E",representation(e="matrix"))
[1] "E"
length(new("E"))
[1] 1
Is there a way to get the real length of an S4 objet ? Furthermore, is
there a simple way to detect that an object is has all its slot to
object of size zero ?
Thanks
Christophe
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[R] setAs vs setIs
Hi the list
I am fighting with the twins setAs and setIs...
Here are some questions and comments (comments to myself but that migth
be wrong, it is why I am posting them)
1. Very surprising : using setIs define 'is', 'as<-' but not 'as' ???
2. Using setAs define 'as', 'as<-' but not 'is'...
What surprise me is that as<- can be define by both. I would have thing
that setis is for 'is', setAs is for 'as' and 'as<-'...
Since it is not the case, is there a possibility to set with only one
function 'as', 'is' and 'as<-'
Last point, I get a warning using setAs. I did not manage to find the
name of the variable it want me to use...
### Data
setClass("B",representation(b="numeric"))
setClass("C",representation(c="numeric"))
setClass("D",representation(d="numeric"))
b <- new("B",b=3)
c <- new("C",c=4)
d <- new("D",d=5)
### using setIs
setIs("C","B",
test=function(object){return([EMAIL PROTECTED]>0)},
replace=function(from,values){
[EMAIL PROTECTED] <- [EMAIL PROTECTED]
return(from)
}
)
is(c,"B") #Ok
as(c,"B") #not ok
as(c,"B") <- b#ok (!)
### using setAs
setAs("D","B",
function(from,to){to<-new("B",[EMAIL PROTECTED]);return(to)},
replace=function(from,values){
[EMAIL PROTECTED]<[EMAIL PROTECTED];
return(from)
}
)
is(d,"B") # not ok
as(d,"B") # ok
as(d,"B")<-b # ok
Thanks
Christophe
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Re: [R] setAs vs setIs
I works, great !
So using your code, we can define 'as','as<-' and 'is' with setIt. Is
there still any interest using setAs ?
Christophe
>
> It seems to me your problem here is simply that you did not define a
> coerce cal in setIs, so it does not know how to turn a C object into a
> B object, which is what you ask it to do here. It knows how to test if
> C object is also a B object, because of the test function you
> provided, and it can do the replacement you ask it in as(c,"B") <-b
> because of the replace command you provided, but the third part is
> missing. Perhaps something like this:
> setIs("C","B",
> test=function(object){return([EMAIL PROTECTED]>0)},
> replace=function(from,values){
> [EMAIL PROTECTED] <- [EMAIL PROTECTED]
> return(from)
> },
> coerce=function(from) {
> new("B",[EMAIL PROTECTED](1/3))
> }
> )
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[R] S4 : dumpMethod
Hi the list,
I almost finished the green book (chapter 7 and 8 on S4), this is
probably one of my last question :-)
I hope you will not miss them to much !
Here is my today nighmare: I do not manage to use dumpMethod :
setClass("A",representation(a="numeric"))
setMethod("plot","A",function(x,y,...){cat("A\n")})
dumpMethod("plot","A",file="")
#setMethod("plot", "A",
#NULL
#)
#[1] ""
Anything wrong in my code?
Christophe
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[R] legend at fixed distance form the bottom
Hi the list
I would like to add a legend under a graph but at a fixed distance from
the graphe. Is it possible ?
More precisely, here is my code :
--- 8<
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),,5),matrix(rnorm(20,2),,5))
listSymboles <- rep(symboles,each=2)
matplot(t(dn),pch=listSymboles,type="b")
legend("bottom", pch = unique(listSymboles), legend = c("ane", "cheval",
"poney", "mule"), inset = c(0,-0.175), horiz = TRUE, xpd = NA)
--- 8<
But when I change the size of the graph, the legend is misplaced.
Instead, I try to put some text in xlab, but I do not know how to get
the +, x , V and other symbol.
Does anyone got a solution ?
Thanks a lot.
Christophe
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Re: [R] legend at fixed distance form the bottom
Thanks for your answer.
Unfortunatly, I can not create the graphice with the final size since I
am writing a package in wich the user will have to chose between several
graphics, and then he will have to export one. And they might be one
graph, or 2x2, or 3x3...
I check the grconvertY but I did not understand what you suggest. To me,
the use of legend can not work since every length in the legend box
(xlength, ylength, distance to axes) will change when resizing the
graph. I was more expecting something like introduce the symbols used in
the graph *in* the xlab. Is it possible ?
Christophe
It is best to create the graphics device at the final size desired, then do the
plotting and add the legend. For getting a fixed distance, look at the
function grconvertY for one possibility.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Christophe Genolini
Sent: Friday, December 05, 2008 6:40 AM
To: r-help@r-project.org
Subject: [R] legend at fixed distance form the bottom
Hi the list
I would like to add a legend under a graph but at a fixed distance from
the graphe. Is it possible ?
More precisely, here is my code :
--- 8<
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),,5),matrix(rnorm(20,2),,5))
listSymboles <- rep(symboles,each=2)
matplot(t(dn),pch=listSymboles,type="b")
legend("bottom", pch = unique(listSymboles), legend = c("ane",
"cheval",
"poney", "mule"), inset = c(0,-0.175), horiz = TRUE, xpd = NA)
--- 8<
But when I change the size of the graph, the legend is misplaced.
Instead, I try to put some text in xlab, but I do not know how to get
the +, x , V and other symbol.
Does anyone got a solution ?
Thanks a lot.
Christophe
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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Re: [R] legend at fixed distance form the bottom
Thanks to answering me Gabor
I am not sur I understand : I had your line to my graph. Then I resize
my graph but the legend is still moving. In "inset = c(0,1.1)",
1.1 means "110% of the y length of the plot region". So when the plot
region change, the distance between the legend and the top axe is sitll
110%, that means that the distance between the legend and the bottom axe
is 10%...
Christophe
inset= is measured from the margin so the trick is to inset it relative to the
top even if you want it at the bottom:
legend("top", pch = unique(listSymboles), legend = c("ane", "cheval",
"poney", "mule"),
inset = c(0,1.1), horiz = TRUE, xpd = NA)
On Fri, Dec 5, 2008 at 8:39 AM, Christophe Genolini
<[EMAIL PROTECTED]> wrote:
Hi the list
I would like to add a legend under a graph but at a fixed distance from the
graphe. Is it possible ?
More precisely, here is my code :
--- 8<
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),,5),matrix(rnorm(20,2),,5))
listSymboles <- rep(symboles,each=2)
matplot(t(dn),pch=listSymboles,type="b")
legend("bottom", pch = unique(listSymboles), legend = c("ane", "cheval",
"poney", "mule"), inset = c(0,-0.175), horiz = TRUE, xpd = NA)
--- 8<
But when I change the size of the graph, the legend is misplaced.
Instead, I try to put some text in xlab, but I do not know how to get the +,
x , V and other symbol.
Does anyone got a solution ?
Thanks a lot.
Christophe
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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Re: [R] legend at fixed distance form the bottom
Lol.
To me, a "fixed amount" that depends on the size of the graph is not
much fixed...
--- 8< ---
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),,5),matrix(rnorm(20,2),,5))
listSymboles <- rep(symboles,each=2)
layout(matrix(c(1,1,1,2,2,3),3))
for(i in 1:3){
plot(dn)
legend("top", pch = unique(listSymboles), legend = c("a", "b","c","d"),inset =
c(0,1.1), horiz = TRUE, xpd = NA)
}
--- 8< ---
On this example, it is easy to see that index is at a fixed distance
from the bottom but that Legend is at a distance "porportional"
I would like to add a legend under a graph but at a fixed distance from the
graphe"
The top of the legend is always a fixed amount below the graph (which is
what you asked for).
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