Re: [R] Make check fails on d-p-q-r-tests.R...

[Prof Brian Ripley]

You will have to show us the error!   It will be shown in 
d-p-q-r-tests.Rout.fail (unless this was a segfault or similar).

It is not OK to skip the test, but note that this test is random and does 
fail about 1 in 50 times, so you could just try rerunning it.

On Mon, 26 Sep 2005, Jeff Ross wrote:

> Hi,
>
> R-2.1.1
> OS:  OpenBSD-current (3.8) on i386
> Compiler:gcc version 3.3.5 (propolice)
> Thread model: single
>
> configure \
>  --with-readline \
>  --with-tcltk \
>  --with-tcl-config=/usr/local/lib/tcl8.4/tclConfig.sh \
>  --with-tk-config=/usr/local/lib/tk8.4/tkConfig.sh \
>  --with-libpng \
>  --with-jpeglib \
>  --with-zlib \
>  --with-bzlib \
>  --with-pcre \
>  --with-libiconv-prefix=/usr/local/

Please do NOT use unrecommended flags like --with-zlib, especially not on 
your first build.  None of those flags should have been needed.

>
> I'm brand new to R so I don't know how critical this error is.
>
> Here's the last bit what make check FORCE=FORCE outputs:
>
> running code in 'grDevices-Ex.R' ... OK
> comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.prev' ... OK
> running code in 'graphics-Ex.R' ... OK
> comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.prev' ... OK
> running code in 'stats-Ex.R' ... OK
> comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.prev' ... OK
> running code in 'datasets-Ex.R' ... OK
> comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.prev' ... OK
> running code in 'methods-Ex.R' ... OK
> comparing 'methods-Ex.Rout' to 'methods-Ex.Rout.prev' ... OK
> running code in 'grid-Ex.R' ... OK
> comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.prev' ... OK
> running code in 'splines-Ex.R' ... OK
> comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.prev' ... OK
> running code in 'stats4-Ex.R' ... OK
> comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.prev' ... OK
> running code in 'tcltk-Ex.R' ... OK
> comparing 'tcltk-Ex.Rout' to 'tcltk-Ex.Rout.prev' ... OK
> updating test dependencies
> `Makedeps' is up to date.
> running strict specific tests
> running code in 'eval-etc.R' ... OK
> comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK
> running code in 'simple-true.R' ... OK
> comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK
> running code in 'arith-true.R' ... OK
> comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK
> running code in 'arith.R' ... OK
> comparing 'arith.Rout' to './arith.Rout.save' ... OK
> running code in 'lm-tests.R' ... OK
> comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK
> running code in 'primitive-funs.R' ... OK
> comparing 'primitive-funs.Rout' to './primitive-funs.Rout.save' ... OK
> running code in 'ok-errors.R' ... OK
> comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK
> running code in 'method-dispatch.R' ... OK
> comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
> running code in 'd-p-q-r-tests.R' ...*** Error code 1
> Stop in /usr/local/src/R-2.1.1/tests.
> *** Error code 1
>
> Stop in /usr/local/src/R-2.1.1/tests (line 206 of Makefile).
> *** Error code 1
>
> Stop in /usr/local/src/R-2.1.1/tests (line 191 of Makefile).
>
>
> Tried finding this error in the archives to no avail.  If it is okay to
> ignore this error, how can I skip this test?
>
> Thanks for any input!
>
> Jeff Ross
>
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>

-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [R] create trend variable in a regression using R

[Vito Ricci]

Dear Giacomo,

what you mean precisely saying "to create a Trend
variable in a regression"? If it concerns about time
series analysis you could give a look to my
contribute:

http://cran.r-project.org/doc/contrib/Ricci-ts-italian.pdf

Best Regards

Vito 


Hi,
my name is Giacomo. 
I would like to know how to create a Trend variable in
a regression using R.
Thank you for your help.
My best regards,   
Giacomo


Diventare costruttori di soluzioni
Became solutions' constructors

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the scientific learning process."  
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the ability to read and write"
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Top 10 reasons to become a Statistician

 1. Deviation is considered normal
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10. No one wants our jobs


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Re: [R] calculating distances using Gower's coefficient on mixed variables.

[Martin Maechler]

> "nikonia" == nikonia  <[EMAIL PROTECTED]>
> on Mon, 26 Sep 2005 12:15:55 +0200 writes:

nikonia> I want to compute the distances in a mixed variable
nikonia> matrix using the Gower coefficient. I understand it
nikonia> is possible to calculate distances in a matrix with
nikonia> mixed variables using the dudi.pco command. How
nikonia> would this work?

No need for esoteric functions.  The recommended(*) package
'cluster' has  daisy() for computing dissimilarities.
One of its major features has always been the ability to work with
mixed variables (continuous, nominal, ordinal, .. (a)symmetric binary,...)
implementing a slight generalization of Gower's proposal.

Even though the help for daisy starts its 'Details' section with

 >> 'daisy' is fully described in chapter 1 of Kaufman and Rousseeuw (1990).

I think I should add some more details to the help page when I
get time..

Martin Maechler, ETH Zurich

(*) recommended packages are always available by library() 
in a normal R installation.

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Re: [R] hist(x, ...) with normal distribution curve

[Peter Wolf]

Knut Krueger wrote:
>.
>I am looking for a histogram or box plot with the adding  normal 
>distribution  curve
>I think that must be possible, but I am not able to find out how to do.
>
>
>
>Regards Knut
>
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>  
*There are a lot of answers to add a histogram.
Here is a simple way to add a tiny boxplot to a plot / histogram

x<-rexp(100)
hist(x)
boxplot(x,axes=F,add=T,horizontal=T,
 at=par()$usr[3]+diff(par()$usr[3:4])*.017,
 boxwex=0.02*diff(par()$usr[3:4]),pch=8)

Peter Wolf


*

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Re: [R] questions about boxplots

[Peter Wolf]

concerning question 1:  -- labeling of outliers --

you can get the outliers by boxplot(...)$out

try:

set.seed(17)
x<-rexp(99)
names(x)<-paste("x",1:99)
out<-boxplot(x)$out
text(rep(1.1,length(out)), out, names(out))

Peter Wolf

Stephen D. Weigand wrote:
>Dear Yulei,
>
>On Sep 26, 2005, at 6:56 PM, Yulei He wrote:
>
>  
>>Hi, there.
>>
>>I have two questions about using R to create boxplots.
>>
>>1. The function boxplot() plots the outliers. How can I label the exact
>>values arount these outlier points? Does R have an option allow me to
>>do that?
>>
>
>You can use identify(). Here's a toy example
>
>set.seed(1)
>y <- rt(30, 3)
>boxplot(y)
>identify(x = rep(1,30), y = y, label = format(y, digits = 2))
>### now click on the outlier in the plot and you should see "-7.398"
>### beside the outlier
>
>  
>>2. How can I put two boxplots in one x-y axis?
>>
>
>x <- rnorm(10)
>y <- rnorm(20, 3, 5)
>z <- runif(30)
>
>boxplot(x, y, z, labels = c("x", "y", "z"))
>### - or -
>boxplot(list(x = x, y = y, z = z))
>
>
>  
>>Thanks.
>>
>>Yulei
>>
>>
>
>Stephen Weigand
>Rochester, Minnesota, USA
>
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Re: [R] hist(x, ...) with normal distribution curve

[Romain Francois]

Le 27.09.2005 10:32, Peter Wolf a écrit :

>Knut Krueger wrote:
>  
>
>>I am looking for a histogram or box plot with the adding  normal 
>>distribution  curve
>>I think that must be possible, but I am not able to find out how to do.
>>
>>Regards Knut
>> 
>>
>>
>*There are a lot of answers to add a histogram.
>Here is a simple way to add a tiny boxplot to a plot / histogram
>
>x<-rexp(100)
>hist(x)
>boxplot(x,axes=F,add=T,horizontal=T,
> at=par()$usr[3]+diff(par()$usr[3:4])*.017,
> boxwex=0.02*diff(par()$usr[3:4]),pch=8)
>
>Peter Wolf
>
>  
>
The tufte axes, described there : 
http://www.cl.cam.ac.uk/users/sjm217/projects/graphics/
may be of interrest here.

What about making it a possibility for all plots ? For example using :
R> par(xaxt='tufte')
R> plot(rnorm(200), rnorm(200))
would produce a scatterplot with the tufte axes

Romain.

-- 
visit the R Graph Gallery : http://addictedtor.free.fr/graphiques
 ~ 
~~  Romain FRANCOIS - http://addictedtor.free.fr ~~
Etudiant  ISUP - CS3 - Industrie et Services   
~~http://www.isup.cicrp.jussieu.fr/  ~~
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~~   http://www.inria.fr/recherche/equipes/select.fr.html~~
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[R] Wrong signature

[Knut Krueger]

I've got a comlaint about the signature in the last post.
I answered form another computer and there is the automatic signature of 
our second business.
On this place is also a part  of the equine resarch program in progress.
I did not realize that there was the siganture below.
Sorry for that.

Regards Knut

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Re: [R] regression methods for circular(?) data.

[Ted Harding]

I retract the siggestion I proposed last night -- it was based
on a bad hunch! Sorry for wasting time.

Best wishes,
Ted.


E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
Fax-to-email: +44 (0)870 094 0861
Date: 27-Sep-05   Time: 09:59:29
-- XFMail --

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[R] About Coda Package

[Juan Pablo Sanchez Serrano]

Dear R users:
I am using the package coda (the last verison in CRAN) to analyse the output 
from a  MCMC Bayesian analysis. And I get unconsitented results. I have export 
the chain using the read.table function and after I have transformed this data 
frame to an mcmc object using the mcmc function. I am interested in three 
variables, when I use the function effectiveSize I have these figures:  
403.37301854.4534 369.8643. But when I run the function codamenu to 
perform same convergence test I get this warning mensage:

Checking effective sample size ...
***
WARNING !!!  
Some variables in your chain have an 
effective sample size of less than 200   
This is too small, and may cause errors  
in the diagnostic tests  
HINT:
Look at plots first to identify variables
with slow mixing.  (Choose menu Output   
Analysis then Plots) 
Re-run your chain with a larger sample   
size and thinning interval. If possible, 
reparameterize your model to improve mixing
***
Some thing is wrong. Could someone explain to me what is happening?
Thanks, 
Juan Pablo.

===
Juan Pablo Sánchez Serrano
Dep. Ciencia Animal, UPV.
C/ Camino de Vera s/n 46022
Valencia (Spain)
Telf. 963877007 Ext.74382

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Re: [R] plotting multiple plots on a single graph

[Petr Pikal]

Hi

***PLEASE do read the posting guide!***

see
?par
?points
?lines
?split.screen
?layout
?matplot
?lattice


HTH
Petr




On 26 Sep 2005 at 18:08, C Tate wrote:

> 
> __
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> http://www.R-project.org/posting-guide.html

Petr Pikal
[EMAIL PROTECTED]

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Re: [R] About Coda Package

[Martyn Plummer]

Dear Juan Pablo,

It is best to send package-specific queries the package maintainer (me
in this case) which you can find out by typeing "library(help=coda)"

The inconsistency comes from two different ways of estimating the
spectral density at frequency 0: spectrum0() adapted from Heidelberger &
Welch, fits a generalized linear model to the periodogram. This function
is called by the effectiveSize() function.  Unfortunately it crashes
when there is very high autocorrelation.  The alternative function
spectrum0.ar does the same thing by fitting an autoregressive model to
the data, and won't crash even on highly autocorrelated data. The latter
function is called by codamenu().

The two functions are giving different results here, but to be honest,
an effective sample size of 370 isn't sufficient for serious inference
from an MCMC sample either.   I can only reiterate the advice given by
the warning message.

Martyn

On Tue, 2005-09-27 at 11:11 +0200, Juan Pablo Sanchez Serrano wrote:
> Dear R users:
> I am using the package coda (the last verison in CRAN) to analyse the
> output from a  MCMC Bayesian analysis. And I get unconsitented
> results. I have export the chain using the read.table function and
> after I have transformed this data frame to an mcmc object using the
> mcmc function. I am interested in three variables, when I use the
> function effectiveSize I have these figures:  403.37301854.4534
> 369.8643. But when I run the function codamenu to perform same
> convergence test I get this warning mensage:
> 
> Checking effective sample size ...
> ***
> WARNING !!!  
> Some variables in your chain have an 
> effective sample size of less than 200   
> This is too small, and may cause errors  
> in the diagnostic tests  
> HINT:
> Look at plots first to identify variables
> with slow mixing.  (Choose menu Output   
> Analysis then Plots) 
> Re-run your chain with a larger sample   
> size and thinning interval. If possible, 
> reparameterize your model to improve mixing
> ***
> Some thing is wrong. Could someone explain to me what is happening?
> Thanks, 
> Juan Pablo.

---
This message and its attachments are strictly confidential. ...{{dropped}}

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Re: [R] dates are shown as X15.Feb.03

[roger bos]

This is a good example of where you did not give us enough information to
answer your question. as.Date has a lot of formatting options for working
with dates. If you are still having problems, please provide a short example
(i.e. reproducable code).
 Thanks,
 Roger

 On 9/26/05, Chris Buddenhagen <[EMAIL PROTECTED]> wrote:
>
> Why is R recognizing dates like this?
>
>
>
> Chris Buddenhagen, Botany Department, Charles Darwin Research Station,
> Santa
> Cruz,Galapagos. Mail: Charles Darwin Foundation, Casilla 17-01-3891
> Avenida
> 6 de Diciembre N36-109 y Pasaje California Quito, ECUADOR
>
>
>
>
>
>
>
> __
> EL CONTENIDO DE ESTE MENSAJE ES DE ABSOLUTA RESPONSABILIDAD DEL AUTOR.
> FUNDACION CHARLES DARWIN
> WWW.DARWINFOUNDATION.ORG 
> [[alternative HTML version deleted]]
>
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[R] Producing empirical bayes estimates in disease mapping for lognormal model

[Oarabile Molaodi]

I'm trying to produce empirical bayes estimates based on the lognormal 
model  in disease mapping
Is there a way this can be done in R?

thanks
Oarabile

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[R] regsubsets selection criterion

[Samuel Bertrand]

Hello,

I am using the 'regsubsets' function
(from leaps package)
to get the best linear models
to explain 1 variable
from 1 to 5 explanatory variables
(exhaustive search).

Is there anyone who can tell me
on which criterion is based
the 'regsubsets' function ?

Thank you.

samuel





Samuel BERTRAND
Doctorant
Laboratoire de Biomecanique
LBM - ENSAM - CNRS UMR 8005
http://bio-web.paris.ensam.fr
151, bd de l'Hopital
75013 PARIS
Tel. +33 (0) 1 44 24 64 53
Fax +33 (0) 1 44 24 63 66

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Re: [R] regsubsets selection criterion

[Ingmar Visser]

> Is there anyone who can tell me
> on which criterion is based
> the 'regsubsets' function ?

the leaps help page says:

cp or adjr2 or r2 is the value of the chosen model selection statistic for
each model

so each of these can be chosen as the selection statistic using the method
argument

hth, ingmar

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Re: [R] getting variable length numerical gradient

[Antonio, Fabio Di Narzo]

2005/9/26, Dimitris Rizopoulos <[EMAIL PROTECTED]>:
> AFAIK the deriv() is for symbolic derivatives, so I don't know if it
> will work in your case.

numericDeriv surely computes numerical gradient. The problem here is
its interface, which requires the vector of symbols involved in the
expression to differenziate.


>
> Best,
> Dimitris
>
>
> - Original Message -
> From: "Antonio, Fabio Di Narzo" <[EMAIL PROTECTED]>
> To: "Dimitris Rizopoulos" <[EMAIL PROTECTED]>
> Cc: 
> Sent: Monday, September 26, 2005 10:58 AM
> Subject: Re: getting variable length numerical gradient
>
>
> Tnx very much Dimitris,
> your code does what I need. I've just adapted it to my needs (e.g., I
> don't deal with scalar functions), and so solved my problem.
>
> Given this, is there a way to use the deriv function in the base
> package, within this context (variable length vector of indipendent
> variables)?
>
> Best,
> Antonio, Fabio Di Narzo.
>
> On 9/25/05, Dimitris Rizopoulos <[EMAIL PROTECTED]>
> wrote:
> > maybe you can find the following function useful (any comments are
> > greatly appreciated):
> >
> > fd <- function(x, f, scalar = TRUE, ..., eps =
> > sqrt(.Machine$double.neg.eps)){
> > f <- match.fun(f)
> > out <- if(scalar){
> > if(length(f0 <- f(x, ...)) != length(x))
> > stop("'f' must be vectorized")
> > x. <- x + eps * pmax(abs(x), 1)
> > c(f(x., ...) - f0) / (x. - x)
> > } else{
> > n <- length(x)
> > res <- array(0, c(n, n))
> > f0 <- f(x, ...)
> > ex <- pmax(abs(x), 1)
> > for(i in 1:n){
> > x. <- x
> > x.[i] <- x[i] + eps * ex[i]
> > res[, i] <- c(f(x., ...) - f0) / (x.[i] - x[i])
> > }
> > res
> > }
> > out
> > }
> >
> >
> > ## Examples
> >
> > x <- seq(-3.3, 3.3, 0.1)
> > all.equal(fd(x, pnorm, mean = 0.5), dnorm(x, mean = 0.5))
> >
> >
> > # Approximate the Hessian matrix for a logistic regression
> >
> > # the score vector function
> > gn <- function(b, y, X){
> > p <- as.vector(plogis(X %*% b))
> > -colSums(X * (y - p))
> > }
> >
> > # We simulate some data and fit the logistic regression
> > n <- 800
> > x1 <- runif(n,-3, 3); x2 <- runif(n, -3, 3)
> > pr <- plogis(0.8 + 0.4 * x1 - 0.3 * x2)
> > y <- rbinom(n, 1, pr)
> > fm <- glm(y ~ x1 + x2, binomial)
> >
> > ## The Hessian using forward difference approximation
> > fd(fm$coef, gn, scalar = FALSE, y = y, X = cbind(1, x1, x2))
> >
> > ## The true Hessian
> > solve(summary(fm)$cov.unscaled)
> >
> >
> > I hope it helps.
> >
> > Best,
> > Dimitris
> >
> > 
> > Dimitris Rizopoulos
> > Ph.D. Student
> > Biostatistical Centre
> > School of Public Health
> > Catholic University of Leuven
> >
> > Address: Kapucijnenvoer 35, Leuven, Belgium
> > Tel: +32/(0)16/336899
> > Fax: +32/(0)16/337015
> > Web: http://www.med.kuleuven.be/biostat/
> >  http://www.student.kuleuven.be/~m0390867/dimitris.htm
> >
> >
> > - Original Message -
> > From: "Antonio, Fabio Di Narzo" <[EMAIL PROTECTED]>
> > To: 
> > Sent: Sunday, September 25, 2005 11:37 AM
> > Subject: [R] getting variable length numerical gradient
> >
> >
> > > Hi all.
> > > I have a numerical function f(x), with x being a vector of generic
> > > size (say k=4), and I wanna take the numerically computed
> > > gradient,
> > > using deriv or numericDeriv (or something else).
> > >
> > > My difficulties here are that in deriv and numericDeric the
> > > function
> > > is passed as an expression, and one have to pass the list of
> > > variables
> > > involved as a char vector... So, it's a pure R programming
> > > question.
> > >
> > >
> > > Have a nice sunday,
> > > Antonio, Fabio Di Narzo.
> > >
> > > __
> > > R-help@stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide!
> > > http://www.R-project.org/posting-guide.html
> > >
> >
> >
> > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
> >
> >
>
>
> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
>
>

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[R] graphics guide?

[Karin Lagesen]

I am trying to create some graphs with R and it seems to be able to do
what I need. However, I have so far not been able to find any sort of
explanation of how the graphics system works. I am for instance trying
to create a multiple figure, and I seem to have to call plot.new()
before every new plot command, I have however not found any
explanation of what this actually does. ?plot.new does give an
explanation, but it is explained in R, so to speak. Where do I find
out what for instance a graphics frame is?

Thanks,

Karin
-- 
Karin Lagesen, PhD student
[EMAIL PROTECTED]
http://www.cmbn.no/rognes/

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Re: [R] graphics guide?

[Ko-Kang Kevin Wang]

Hi,

Karin Lagesen wrote:
> I am trying to create some graphs with R and it seems to be able to do
> what I need. However, I have so far not been able to find any sort of
> explanation of how the graphics system works. I am for instance trying
> to create a multiple figure, and I seem to have to call plot.new()
> before every new plot command, I have however not found any

Do you mean several graphs in the same window?

If so, you want something like, e.g.:
   par(mfrow = c(2, 2))

Take a look at ?par and the "mfrow" or "mfcol" options.

Cheers and HTH,

Kev

-- 
Ko-Kang Kevin Wang
PhD Student
Centre for Bioinformation Science
Building 27, Room 1004
Mathematical Sciences Institute (MSI)
Australian National University
Canberra, ACT 2601
Australia

Homepage: http://wwwmaths.anu.edu.au/~wangk/
Ph (W): +61-2-6125-2431
Ph (H): +61-2-6125-7488
Ph (M): +61-40-451-8301

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Re: [R] graphics guide?

[Peter Flom]

>>> Karin Lagesen <[EMAIL PROTECTED]> 9/27/2005 9:27:29 AM
>>>
<<<
I am trying to create some graphs with R and it seems to be able to do
what I need. However, I have so far not been able to find any sort of
explanation of how the graphics system works. I am for instance trying
to create a multiple figure, and I seem to have to call plot.new()
before every new plot command, I have however not found any
explanation of what this actually does. ?plot.new does give an
explanation, but it is explained in R, so to speak. Where do I find
out what for instance a graphics frame is?
>>>
If you'd like a more comprehensive reference in book form, I recommend
Paul Murrell's book R Graphics.

HTH

Peter

Peter L. Flom, PhD
Assistant Director, Statistics and Data Analysis Core
Center for Drug Use and HIV Research
National Development and Research Institutes
71 W. 23rd St
http://cduhr.ndri.org
www.peterflom.com
New York, NY 10010
(212) 845-4485 (voice)
(917) 438-0894 (fax)

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Re: [R] hist(x, ...) with normal distribution curve

[Rau, Roland]

 
> > >Knut Krueger wrote:
> >  
> >
> >>I am looking for a histogram or box plot with the adding  normal 
> >>distribution  curve
> >>I think that must be possible, but I am not able to find 
> out how to do.
> >>
Since there are various solutions, here is mine:

hist(rnorm(1), freq=FALSE)
xvals <- seq(-5,5,length=100)
lines(x=xvals, y=dnorm(xvals))


Is this what you are looking for?
Best,
Roland

+
This mail has been sent through the MPI for Demographic Rese...{{dropped}}

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Re: [R] graphics guide?

[Gichangi, Anthony]

you may want to look at some introduction notes of R graphics
at http://lib.stat.cmu.edu/R/CRAN/other-docs.html

Regards
Anthony

- Original Message - 
From: "Karin Lagesen" <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
Sent: Tuesday, September 27, 2005 3:27 PM
Subject: [R] graphics guide?


>
> I am trying to create some graphs with R and it seems to be able to do
> what I need. However, I have so far not been able to find any sort of
> explanation of how the graphics system works. I am for instance trying
> to create a multiple figure, and I seem to have to call plot.new()
> before every new plot command, I have however not found any
> explanation of what this actually does. ?plot.new does give an
> explanation, but it is explained in R, so to speak. Where do I find
> out what for instance a graphics frame is?
>
> Thanks,
>
> Karin
> -- 
> Karin Lagesen, PhD student
> [EMAIL PROTECTED]
> http://www.cmbn.no/rognes/
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html

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Re: [R] graphics guide?

[Tuszynski, Jaroslaw W.]

If you like to learn from examples than you will find plenty of them in the
following 3 web-sites

http://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html
http://www.stat.ucl.ac.be/ISpersonnel/lecoutre/R/svGraphGallery/dock/svGalle
ry.html
http://addictedtor.free.fr/graphiques/ 

 Jarek 
\ 
 Jarek Tuszynski, PhD.   o / \ 
 Science Applications International Corporation  <\__,|  
 (703) 676-4192   ">  \ 
 [EMAIL PROTECTED] `   \ 



-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] 
Sent: Tuesday, September 27, 2005 9:27 AM
To: [EMAIL PROTECTED]
Subject: [R] graphics guide?


I am trying to create some graphs with R and it seems to be able to do what
I need. However, I have so far not been able to find any sort of explanation
of how the graphics system works. I am for instance trying to create a
multiple figure, and I seem to have to call plot.new() before every new plot
command, I have however not found any explanation of what this actually
does. ?plot.new does give an explanation, but it is explained in R, so to
speak. Where do I find out what for instance a graphics frame is?

Thanks,

Karin
--
Karin Lagesen, PhD student
[EMAIL PROTECTED]
http://www.cmbn.no/rognes/

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Re: [R] regsubsets selection criterion

[Samuel Bertrand]

> > Is there anyone who can tell me
> > on which criterion is based
> > the 'regsubsets' function ?
> > Samuel


>the leaps help page says:
>
>cp or adjr2 or r2 is the value of the chosen model selection statistic for
>each model
>
>so each of these can be chosen as the selection statistic using the method
>argument
>
>hth, ingmar

In fact, 'regsubsets'
does not enable to choose
among cp, adrjr2 or r2
as 'leaps' function does.

Do you know the default criterion?
Or do you think it means that
the result would be the same
for the three criteria ?


Samuel BERTRAND
Doctorant
LBM - ENSAM - CNRS UMR 8005
http://bio-web.paris.ensam.fr

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Re: [R] regsubsets selection criterion

[Thomas Lumley]

On Tue, 27 Sep 2005, Samuel Bertrand wrote:

> Hello,
>
> I am using the 'regsubsets' function
> (from leaps package)
> to get the best linear models
> to explain 1 variable
> from 1 to 5 explanatory variables
> (exhaustive search).
>
> Is there anyone who can tell me
> on which criterion is based
> the 'regsubsets' function ?
>

As you get a best model for each size, all the commonly used criteria are 
equivalent. RSS, AIC, BIC, Mallows Cp, adjusted R^2, etc, all give the 
same ordering for models with the same number of predictors.


-thomas

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[R] outer function and boolean operators

[Jarrod Hadfield]

Hi,

Could anyone tell me the name (if there is one) of the class of 
matrices (z) formed by:

a)  z<-outer(x,y, "==")

and

b) z<-outer(x,y, "!=")

Thanks in advance,

Jarrod.

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Re: [R] outer function and boolean operators

[Uwe Ligges]

Jarrod Hadfield wrote:

> Hi,
> 
> Could anyone tell me the name (if there is one) of the class of 
> matrices (z) formed by:
> 
> a)  z<-outer(x,y, "==")
> 
> and
> 
> b) z<-outer(x,y, "!=")

Yes, it is "matrix":

class(outer(x,y, "=="))
[1] "matrix"

in this case of "logical" values:

 > mode(outer(x,y, "=="))
[1] "logical"


Uwe Ligges


> Thanks in advance,
> 
> Jarrod.
> 
> __
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[R] multiple plots on same x axis

[IAIN GALLAGHER]

Hi.

I have two vectors of gene expression for each of
several days. I want to plot both vectors on the same
plot for a visual representation of up versus down
regulation. I've tried using add=T but that doesn't
work. 

eg

>plot(Day, gene1)
>plot(Day, gene2, add=T)

Any help would be appreciated.

Iain

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Re: [R] Make check fails on d-p-q-r-tests.R...

[Jeff Ross]

On 1:03:39 am 09/27/05 Prof Brian Ripley <[EMAIL PROTECTED]> wrote:

> You will have to show us the error!   It will be shown in
> d-p-q-r-tests.Rout.fail (unless this was a segfault or similar).
>
> It is not OK to skip the test, but note that this test is random and
> does fail about 1 in 50 times, so you could just try rerunning it.

I am so sorry.  I didn't even think to look for a .fail file.

Here is the last bit of it:

>> ## for PR#7902:
> ex <- -c(rev(1/x), ex)
> All.eq(-x, qcauchy(pcauchy(-x)))
[1] TRUE
> All.eq(+x, qcauchy(pcauchy(+x, log=TRUE), log=TRUE))
[1] TRUE
> All.eq(1/x, pcauchy(qcauchy(1/x)))
[1] TRUE
> All.eq(ex,  pcauchy(qcauchy(ex, log=TRUE), log=TRUE))
[1] "`is.NA' value mismatches: 1 in current, 0  in target"
Warning message:
NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p)
> II <- c(-Inf,Inf)
> stopifnot(pcauchy(II) == 0:1, ## qcauchy(0:1) == II,
+   pcauchy(II, log=TRUE) == c(-Inf,0),
+   qcauchy(c(-Inf,0), log=TRUE) == II)
Error in if (!(is.logical(r <- eval(ll[[i]])) && all(r)))
stop(paste(deparse(mc[[i +  :
  missing value where TRUE/FALSE needed
In addition: Warning message:
NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p)
Execution halted

This is from the latest R-patched source tar ball, and it is the identical
error as R-2.1.1.  I've consistently gotten the same error, even with
configuration file tweaks and making clean between runs.

Thanks!

Jeff Ross

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[R] quick "points" question

[Richard Nixon]

Hi
Just one of those niggles...

I've just been trying to plot a filled circle.
I thought that this would do it

plot(1,1,type="n")
points(1,1,pch=1,bg="blue",cex=5)
#bg: background ("fill") color for open plot symbols

But I need to do this instead
points(1.2,1,pch=19,col="blue",cex=5)

Am I misunderstanding the "bg" option in the points function?

Richard

-- 
Dr. Richard Nixon, MRC Biostatistics Unit, Cambridge, UK
http://www.mrc-bsu.cam.ac.uk/personal/richard

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Re: [R] quick "points" question

[Uwe Ligges]

Richard Nixon wrote:

> Hi
> Just one of those niggles...
> 
> I've just been trying to plot a filled circle.
> I thought that this would do it
> 
> plot(1,1,type="n")
> points(1,1,pch=1,bg="blue",cex=5)
> #bg: background ("fill") color for open plot symbols
> 
> But I need to do this instead
> points(1.2,1,pch=19,col="blue",cex=5)
> 
> Am I misunderstanding the "bg" option in the points function?
> 
> Richard
> 

Please read ?points and it's paragraph on te argument "pch" with quite 
some information regarding filled symbols...

Uwe Ligges

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Re: [R] quick "points" question

[Peter Dalgaard]

Richard Nixon <[EMAIL PROTECTED]> writes:

> Hi
> Just one of those niggles...
> 
> I've just been trying to plot a filled circle.
> I thought that this would do it
> 
> plot(1,1,type="n")
> points(1,1,pch=1,bg="blue",cex=5)
> #bg: background ("fill") color for open plot symbols
> 
> But I need to do this instead
> points(1.2,1,pch=19,col="blue",cex=5)
> 
> Am I misunderstanding the "bg" option in the points function?

Sort of. The quick answer is: example(points). I think you'll get the
point.
 

-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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[R] negative binomial in GEE

[Simon.Bond]

Dear R-help,


I was recently wanting to use GEE with the negative binomial "family". It
seems that this is lacking in the otherwise excellent implementations of
the GEE methodology ( packages: gee, yags, geepack).

I would have thought it a simple step to allow the creation of a family,
i.e providing the link function (log mu) and the variance function (mu +
mu^2/theta) , assuming theta is specified; and then to let the gee code
do the business in a similar fashion to glm.

However the gee codes all seem to rely a set of C routines with either the
normal, poisson, or binomial, hardwired in.

Does anyone have any suggestions for a way round this problem for the
future (I had to resort to using Stata), or maybe more realistically, how
much work it would take to build an extendible version of the gee
"algorithm"?


thanks Simon Bond.

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[R] time series: smooth and aggregate?

[jfontain]

I am working on automatic optimization of ARIMA parameters.
That takes a lot of computing power, which I would like to reduce by aggregating
and smoothing.

Any thoughts on the subject?
Suggested algorithms?
What is the best order? aggregate then smooth or smooth then aggregate?

Many thanks in advance,

--
Jean-Luc

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[R] Error in "make check-all"

[Fernando Mayer]

Dear R-users,

i'm a very newbie in linux, but decided to build R from source. 
Following the "R Installation and Administration" manual, i did this:

./configure --enable-R-shlib # this option is here because i intend to 
build the GNOME console after...
make
make check

no problems in make check, but:

make check-devel #and also
make check-all

indicated some WARNINGs in the log file:

/usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck

Right below is the content of this log file (I translated some words):

[start log file]

* using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck'
* using R version 2.1.1, 2005-06-20
* looks like 'tcltk' is a base package
* skipping installation test
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking S3 generic/method consistency ... WARNING
Erro: .First.lib failed for 'tcltk'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = 
FALSE)
Interrupted execution
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Error: .First.lib failed for 'tcltk'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = 
FALSE)
Interrupted execution
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error: .First.lib failed for 'tcltk'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = 
FALSE)
Interrupted execution
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... WARNING
Error: .First.lib failed for 'tcltk'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = 
FALSE)
Interrupted execution
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Error: .First.lib failed for 'tcltk'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = 
FALSE)
Interrupted execution
Error: .First.lib failed for 'tcltk'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = 
FALSE)
Interrupted execution
Error: .First.lib failed for 'tcltk'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = 
FALSE)
Interrupted execution
* checking Rd \usage sections ... OK
* checking DVI version of manual ... OK

[end log file]

The problem is in the tcltk package. I have searched in the archives, 
but didin't find anything similar to this problem (maybe there is, but i 
was not able to identify it). I really don't know what all the warnings 
means. What i need to know is what am i missing, and if there is 
something i can fix it. Also, are there any problems if i continue the 
installation without fix something?

P.S.: actually R is running already from where it was buit, but i want 
to install it. So i want to avoid future problems, if this warnings 
really make some.

Any help is appreciated. Thanks!

Fernando Mayer.

version
 _
platform i686-pc-linux-gnu
arch i686
os   linux-gnu [SuSE 9.3]
system   i686, linux-gnu
status
major2
minor1.1
year 2005
month06
day  20
language R


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Re: [R] Error in "make check-all"

[Prof Brian Ripley]

This is what happens if you don't have a usable X11 display.  Did you 
perhaps use a root account on a console owned by a normal user?

On Tue, 27 Sep 2005, Fernando Mayer wrote:

> Dear R-users,
>
> i'm a very newbie in linux, but decided to build R from source.
> Following the "R Installation and Administration" manual, i did this:
>
> ./configure --enable-R-shlib # this option is here because i intend to
> build the GNOME console after...
> make
> make check
>
> no problems in make check, but:
>
> make check-devel #and also
> make check-all
>
> indicated some WARNINGs in the log file:
>
> /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck
>
> Right below is the content of this log file (I translated some words):
>
> [start log file]
>
> * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck'
> * using R version 2.1.1, 2005-06-20
> * looks like 'tcltk' is a base package
> * skipping installation test
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking package dependencies ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking S3 generic/method consistency ... WARNING
> Erro: .First.lib failed for 'tcltk'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>   domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Interrupted execution
> See section 'Generic functions and methods' of the 'Writing R Extensions'
> manual.
> * checking replacement functions ... WARNING
> Error: .First.lib failed for 'tcltk'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>   domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Interrupted execution
> In R, the argument of a replacement function which corresponds to the right
> hand side must be named 'value'.
> * checking foreign function calls ... WARNING
> Error: .First.lib failed for 'tcltk'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>   domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Interrupted execution
> See section 'System and foreign language interfaces' of the 'Writing R
> Extensions' manual.
> * checking Rd files ... OK
> * checking for missing documentation entries ... WARNING
> Error: .First.lib failed for 'tcltk'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>   domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Interrupted execution
> All user-level objects in a package should have documentation entries.
> See chapter 'Writing R documentation files' in manual 'Writing R
> Extensions'.
> * checking for code/documentation mismatches ... WARNING
> Error: .First.lib failed for 'tcltk'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>   domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Interrupted execution
> Error: .First.lib failed for 'tcltk'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>   domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Interrupted execution
> Error: .First.lib failed for 'tcltk'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>   domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Interrupted execution
> * checking Rd \usage sections ... OK
> * checking DVI version of manual ... OK
>
> [end log file]
>
> The problem is in the tcltk package. I have searched in the archives,
> but didin't find anything similar to this problem (maybe there is, but i
> was not able to identify it). I really don't know what all the warnings
> means. What i need to know is what am i missing, and if there is
> something i can fix it. Also, are there any problems if i continue the
> installation without fix something?
>
> P.S.: actually R is running already from where it was buit, but i want
> to install it. So i want to avoid future problems, if this warnings
> really make some.
>
> Any help is appreciated. Thanks!
>
> Fernando Mayer.
>
> version
> _
> platform i686-pc-linux-gnu
> arch i686
> os   linux-gnu [SuSE 9.3]
> system   i686, linux-gnu
> status
> major2
> minor1.1
> year 2005
> month06
> day  20
> language R
>
>
>   [[alternative HTML version deleted]]
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-gui

Re: [R] Error in "make check-all"

[Peter Dalgaard]

Fernando Mayer <[EMAIL PROTECTED]> writes:

> Dear R-users,
..
> Erro: .First.lib failed for 'tcltk'
...
> The problem is in the tcltk package. I have searched in the archives, 
> but didin't find anything similar to this problem (maybe there is, but i 
> was not able to identify it). I really don't know what all the warnings 
> means. What i need to know is what am i missing, and if there is 
> something i can fix it. Also, are there any problems if i continue the 
> installation without fix something?

Well, tcl/tk isn't working...
 
> P.S.: actually R is running already from where it was buit, but i want 
> to install it. So i want to avoid future problems, if this warnings 
> really make some.
> 
> Any help is appreciated. Thanks!
> 
> Fernando Mayer.
> 
> version
>  _
> platform i686-pc-linux-gnu
> arch i686
> os   linux-gnu [SuSE 9.3]

Installing the tk-devel and tcl-devel packages should help.

> system   i686, linux-gnu
> status
> major2
> minor1.1
> year 2005
> month06
> day  20
> language R
> 
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
> 

-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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Re: [R] quick "points" question

[Prof Brian Ripley]

On Tue, 27 Sep 2005, Richard Nixon wrote:

> Hi
> Just one of those niggles...
>
> I've just been trying to plot a filled circle.
> I thought that this would do it
>
> plot(1,1,type="n")
> points(1,1,pch=1,bg="blue",cex=5)
> #bg: background ("fill") color for open plot symbols
>
> But I need to do this instead
> points(1.2,1,pch=19,col="blue",cex=5)
>
> Am I misunderstanding the "bg" option in the points function?

Yes. See the examples.   pch=1 is not an `open plot symbol': 21-25 are.
So in your case

points(1.3, 1, pch=21, col="blue", bg="red", cex=5)

may be illuminating.

-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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[R] make check in ~/fem outputs only 1 test, huh ?

[Courtney Thomas]

fem-4.0.1 [and all the other modules, except post] compiles OK, AFAIK,
but when I do a 

make check 

only 1 test is reported, as follows:


making checksrc
making checkview3d
making checkviewaxis
making checktests

make check-TESTS
$ELMER_HOME undefined, setting it to ../src
CC: no input files specified
test: unexpected operator
Tests completed, passed: 0 out of total 0 tests 
PASS: runtests
===
All 1 tests passed
===
 

As I understand it, about 50 tests should have been run. What's wrong
and how do I fix it, please ?

Gratefully,
Courtney

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Re: [R] Error in "make check-all"

[Peter Dalgaard]

Prof Brian Ripley <[EMAIL PROTECTED]> writes:

> This is what happens if you don't have a usable X11 display.  Did you 
> perhaps use a root account on a console owned by a normal user?

More likely on SUSE is to get done in by a lack of -devel packages.
I've already mentioned tcl-devel and tk-devel but you also need 
xorg-x11-devel, readline-devel, and libjpeg-devel. The latter two are
not going to cause that particular error though. 
 
> On Tue, 27 Sep 2005, Fernando Mayer wrote:
> 
> > Dear R-users,
> >
> > i'm a very newbie in linux, but decided to build R from source.
> > Following the "R Installation and Administration" manual, i did this:
> >
> > ./configure --enable-R-shlib # this option is here because i intend to
> > build the GNOME console after...
> > make
> > make check
> >
> > no problems in make check, but:
> >
> > make check-devel #and also
> > make check-all
> >
> > indicated some WARNINGs in the log file:
> >
> > /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck
> >
> > Right below is the content of this log file (I translated some words):
> >
> > [start log file]
> >
> > * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck'
> > * using R version 2.1.1, 2005-06-20
> > * looks like 'tcltk' is a base package
> > * skipping installation test
> > * checking package directory ... OK
> > * checking for portable file names ... OK
> > * checking for sufficient/correct file permissions ... OK
> > * checking DESCRIPTION meta-information ... OK
> > * checking package dependencies ... OK
> > * checking index information ... OK
> > * checking package subdirectories ... OK
> > * checking S3 generic/method consistency ... WARNING
> > Erro: .First.lib failed for 'tcltk'
> > Call sequence:
> > 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >   domain = NA)
> > 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> > FALSE)
> > Interrupted execution
> > See section 'Generic functions and methods' of the 'Writing R Extensions'
> > manual.
> > * checking replacement functions ... WARNING
> > Error: .First.lib failed for 'tcltk'
> > Call sequence:
> > 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >   domain = NA)
> > 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> > FALSE)
> > Interrupted execution
> > In R, the argument of a replacement function which corresponds to the right
> > hand side must be named 'value'.
> > * checking foreign function calls ... WARNING
> > Error: .First.lib failed for 'tcltk'
> > Call sequence:
> > 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >   domain = NA)
> > 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> > FALSE)
> > Interrupted execution
> > See section 'System and foreign language interfaces' of the 'Writing R
> > Extensions' manual.
> > * checking Rd files ... OK
> > * checking for missing documentation entries ... WARNING
> > Error: .First.lib failed for 'tcltk'
> > Call sequence:
> > 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >   domain = NA)
> > 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> > FALSE)
> > Interrupted execution
> > All user-level objects in a package should have documentation entries.
> > See chapter 'Writing R documentation files' in manual 'Writing R
> > Extensions'.
> > * checking for code/documentation mismatches ... WARNING
> > Error: .First.lib failed for 'tcltk'
> > Call sequence:
> > 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >   domain = NA)
> > 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> > FALSE)
> > Interrupted execution
> > Error: .First.lib failed for 'tcltk'
> > Call sequence:
> > 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >   domain = NA)
> > 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> > FALSE)
> > Interrupted execution
> > Error: .First.lib failed for 'tcltk'
> > Call sequence:
> > 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >   domain = NA)
> > 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> > FALSE)
> > Interrupted execution
> > * checking Rd \usage sections ... OK
> > * checking DVI version of manual ... OK
> >
> > [end log file]
> >
> > The problem is in the tcltk package. I have searched in the archives,
> > but didin't find anything similar to this problem (maybe there is, but i
> > was not able to identify it). I really don't know what all the warnings
> > means. What i need to know is what am i missing, and if there is
> > something i can fix it. Also, are there any problems if i continue the
> > installation without fix something?
> >
> > P.S.: actually R is running already from where it was buit, but i want
> > to install it. So i want to avoid future problems, if this warnings
> > really make some.
> 

Re: [R] Error in "make check-all"

[Fernando Mayer]

Dear Prof. Ripley, that was exactly what i did. Should i login on the 
system as root, instead of login as user and became root via console? 
What should i do to have X11 usable?

Thanks,
Fernando Mayer.


Prof Brian Ripley escreveu:

>This is what happens if you don't have a usable X11 display.  Did you 
>perhaps use a root account on a console owned by a normal user?
>
>On Tue, 27 Sep 2005, Fernando Mayer wrote:
>
>  
>
>>Dear R-users,
>>
>>i'm a very newbie in linux, but decided to build R from source.
>>Following the "R Installation and Administration" manual, i did this:
>>
>>./configure --enable-R-shlib # this option is here because i intend to
>>build the GNOME console after...
>>make
>>make check
>>
>>no problems in make check, but:
>>
>>make check-devel #and also
>>make check-all
>>
>>indicated some WARNINGs in the log file:
>>
>>/usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck
>>
>>Right below is the content of this log file (I translated some words):
>>
>>[start log file]
>>
>>* using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck'
>>* using R version 2.1.1, 2005-06-20
>>* looks like 'tcltk' is a base package
>>* skipping installation test
>>* checking package directory ... OK
>>* checking for portable file names ... OK
>>* checking for sufficient/correct file permissions ... OK
>>* checking DESCRIPTION meta-information ... OK
>>* checking package dependencies ... OK
>>* checking index information ... OK
>>* checking package subdirectories ... OK
>>* checking S3 generic/method consistency ... WARNING
>>Erro: .First.lib failed for 'tcltk'
>>Call sequence:
>>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>  domain = NA)
>>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>FALSE)
>>Interrupted execution
>>See section 'Generic functions and methods' of the 'Writing R Extensions'
>>manual.
>>* checking replacement functions ... WARNING
>>Error: .First.lib failed for 'tcltk'
>>Call sequence:
>>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>  domain = NA)
>>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>FALSE)
>>Interrupted execution
>>In R, the argument of a replacement function which corresponds to the right
>>hand side must be named 'value'.
>>* checking foreign function calls ... WARNING
>>Error: .First.lib failed for 'tcltk'
>>Call sequence:
>>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>  domain = NA)
>>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>FALSE)
>>Interrupted execution
>>See section 'System and foreign language interfaces' of the 'Writing R
>>Extensions' manual.
>>* checking Rd files ... OK
>>* checking for missing documentation entries ... WARNING
>>Error: .First.lib failed for 'tcltk'
>>Call sequence:
>>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>  domain = NA)
>>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>FALSE)
>>Interrupted execution
>>All user-level objects in a package should have documentation entries.
>>See chapter 'Writing R documentation files' in manual 'Writing R
>>Extensions'.
>>* checking for code/documentation mismatches ... WARNING
>>Error: .First.lib failed for 'tcltk'
>>Call sequence:
>>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>  domain = NA)
>>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>FALSE)
>>Interrupted execution
>>Error: .First.lib failed for 'tcltk'
>>Call sequence:
>>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>  domain = NA)
>>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>FALSE)
>>Interrupted execution
>>Error: .First.lib failed for 'tcltk'
>>Call sequence:
>>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>  domain = NA)
>>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>FALSE)
>>Interrupted execution
>>* checking Rd \usage sections ... OK
>>* checking DVI version of manual ... OK
>>
>>[end log file]
>>
>>The problem is in the tcltk package. I have searched in the archives,
>>but didin't find anything similar to this problem (maybe there is, but i
>>was not able to identify it). I really don't know what all the warnings
>>means. What i need to know is what am i missing, and if there is
>>something i can fix it. Also, are there any problems if i continue the
>>installation without fix something?
>>
>>P.S.: actually R is running already from where it was buit, but i want
>>to install it. So i want to avoid future problems, if this warnings
>>really make some.
>>
>>Any help is appreciated. Thanks!
>>
>>Fernando Mayer.
>>
>>version
>>_
>>platform i686-pc-linux-gnu
>>arch i686
>>os   linux-gnu [SuSE 9.3]
>>system   i686, linux-gnu
>>status
>>major2
>>minor1.1
>>year 2005
>>month06
>>day  20
>>language 

Re: [R] Error in "make check-all"

[Prof Brian Ripley]

On Tue, 27 Sep 2005, Fernando Mayer wrote:

> Dear Prof. Ripley, that was exactly what i did. Should i login on the system 
> as root, instead of login as user and became root via console? What should i 
> do to have X11 usable?

Well, I don't worry about this, but it you want to do a complete test you 
need the console running the user that is going to be running R.

(I see this when running tests remotely, as then I have no X11 display set 
to save bandwidth.  I just ignore it.)

>
> Thanks,
> Fernando Mayer.
>
>
> Prof Brian Ripley escreveu:
>
>> This is what happens if you don't have a usable X11 display.  Did you 
>> perhaps use a root account on a console owned by a normal user?
>> 
>> On Tue, 27 Sep 2005, Fernando Mayer wrote:
>> 
>> 
>>> Dear R-users,
>>> 
>>> i'm a very newbie in linux, but decided to build R from source.
>>> Following the "R Installation and Administration" manual, i did this:
>>> 
>>> ./configure --enable-R-shlib # this option is here because i intend to
>>> build the GNOME console after...
>>> make
>>> make check
>>> 
>>> no problems in make check, but:
>>> 
>>> make check-devel #and also
>>> make check-all
>>> 
>>> indicated some WARNINGs in the log file:
>>> 
>>> /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck
>>> 
>>> Right below is the content of this log file (I translated some words):
>>> 
>>> [start log file]
>>> 
>>> * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck'
>>> * using R version 2.1.1, 2005-06-20
>>> * looks like 'tcltk' is a base package
>>> * skipping installation test
>>> * checking package directory ... OK
>>> * checking for portable file names ... OK
>>> * checking for sufficient/correct file permissions ... OK
>>> * checking DESCRIPTION meta-information ... OK
>>> * checking package dependencies ... OK
>>> * checking index information ... OK
>>> * checking package subdirectories ... OK
>>> * checking S3 generic/method consistency ... WARNING
>>> Erro: .First.lib failed for 'tcltk'
>>> Call sequence:
>>> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>>  domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>> FALSE)
>>> Interrupted execution
>>> See section 'Generic functions and methods' of the 'Writing R Extensions'
>>> manual.
>>> * checking replacement functions ... WARNING
>>> Error: .First.lib failed for 'tcltk'
>>> Call sequence:
>>> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>>  domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>> FALSE)
>>> Interrupted execution
>>> In R, the argument of a replacement function which corresponds to the 
>>> right
>>> hand side must be named 'value'.
>>> * checking foreign function calls ... WARNING
>>> Error: .First.lib failed for 'tcltk'
>>> Call sequence:
>>> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>>  domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>> FALSE)
>>> Interrupted execution
>>> See section 'System and foreign language interfaces' of the 'Writing R
>>> Extensions' manual.
>>> * checking Rd files ... OK
>>> * checking for missing documentation entries ... WARNING
>>> Error: .First.lib failed for 'tcltk'
>>> Call sequence:
>>> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>>  domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>> FALSE)
>>> Interrupted execution
>>> All user-level objects in a package should have documentation entries.
>>> See chapter 'Writing R documentation files' in manual 'Writing R
>>> Extensions'.
>>> * checking for code/documentation mismatches ... WARNING
>>> Error: .First.lib failed for 'tcltk'
>>> Call sequence:
>>> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>>  domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>> FALSE)
>>> Interrupted execution
>>> Error: .First.lib failed for 'tcltk'
>>> Call sequence:
>>> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>>  domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>> FALSE)
>>> Interrupted execution
>>> Error: .First.lib failed for 'tcltk'
>>> Call sequence:
>>> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
>>>  domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>> FALSE)
>>> Interrupted execution
>>> * checking Rd \usage sections ... OK
>>> * checking DVI version of manual ... OK
>>> 
>>> [end log file]
>>> 
>>> The problem is in the tcltk package. I have searched in the archives,
>>> but didin't find anything similar to this problem (maybe there is, but i
>>> was not able to identify it). I really don't know what all the warnings
>>> means. What i need to know is what am i missing, and if there is
>>> something i can

[R] Weighting factor

[Ferran Carrascosa]

Hi everyone,

I would like some package of R or any help to solve the next problem
with a weighting fatcors:

Giving a data matrix with dichotomous (2 or more) variables in columns
and individuals in rows, and also a theorical distribution of the
dichotomous variables I would like a row weight (one per individual)
that transform the real distribution of variables to the theorical
distribution.

Thanks in advance and best regards,

--
Ferran Carrascosa

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Re: [R] negative binomial in GEE

[Thomas Lumley]

On Tue, 27 Sep 2005, Simon.Bond wrote:

>
> Does anyone have any suggestions for a way round this problem for the
> future (I had to resort to using Stata), or maybe more realistically, how
> much work it would take to build an extendible version of the gee
> "algorithm"?
>

I don't think it would take that much work [and I've done it a couple of 
times, once in XLISP-Stat and once in SPIDA].  An entirely interpreted 
implementation will be relatively slow, though it might be possible to 
improve that quite a bit with sparse matrix techniques.

-thomas

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Re: [R] dates are shown as X15.Feb.03

[Duncan Murdoch]

On 9/27/2005 12:13 PM, Chris Buddenhagen wrote:
> Dear Duncan Murdoch
> 
> Thanks for responding. I will provide more complete info with future
> questions. The data for a small pilot study are below. 
> 
> The values for each month are the percentage cover of an invasive plant here
> in the Galapagos (TT=treatment) type = immediately herbicide applied or
> applied to regrowth later. I called the data glyphosate.txt.
> 
> 
> The code is
> 
> glyp<-read.delim("C:\\Chris\\active projects\\Aristolochia\\glyphosate.txt",
> header=T)
> list(names(glyp))
> 
> This is the output that mystified me:
> 
> [1] "TT" "type"   "CUADRANTES" "X15dec02"   "X15jan03"  
>  [6] "X15feb03"   "X15apr03"   "X15jun03"   "X15aug03"   "X15oct03"

It looks as though you have column headings like "15dec02".  That's not 
a legal R variable name, so it prepends the X to make it into one.  That 
way you can do things like glyp$X15dec02 to extract that column. 
glyp$15dec02 would give a syntax error.


> 
> While I have an expert on hand I have another question, how do I produce a
> graph of time against percentage cover with error bars. I wanted to only
> present months on the x axis. I start by reorganizing the data using this:

Various functions implement error bars, but I haven't used them in a 
long  time, so I'll leave this question for someone else to answer.

Duncan Murdoch

> 
> glyp2<-reshape(glyp, direction="long", idvar=c("TT", "type",
> "CUADRANTES"),varying=list(names(glyp)[4:10]),v.names="cover") but couldn't
> get month names to appear in the column time.
> 
> 
> 
> TTtypeCUADRANTES  "15dec02"   "15jan03"   "15feb03"
> "15apr03" "15jun03"   "15aug03"   "15oct03"
> T1immediate   1   63  59  60  55  4.5 1
> 2
> T1immediate   2   75  75  75  75  6.5 1
> 2
> T1immediate   22  72  70  70  65  35  2
> 3.5
> T1immediate   26  90  80  80  75  17.52
> 4
> T1immediate   33  75  80  85  85  40  1
> 2
> T2immediate   18  85  80  80  22.52.5 2
> 5
> T2immediate   21  90  85  85  60  16.50
> 1
> T2immediate   23  85  80  80  75  17.51
> 2
> T2immediate   28  90  85  85  27.527.50
> 1
> T2immediate   31  90  85  85  9   12.51
> 2
> T3immediate   3   50  58  60  65  35  1
> 2
> T3immediate   10  63  60  60  15  2.5 0
> 10
> T3immediate   12  90  85  85  17.515  0
> 5
> T3immediate   16  85  82  80  78  9   1
> 1.5
> T3immediate   34  75  80  85  85  35  1.5
> 2.5
> T4wait4   75  75  75  7.5 2.5 0   0
> T4wait11  63  60  60  12.52.5 1   2
> T4wait24  90  85  80  3.5 5.5 1   2
> T4wait29  85  80  80  1.5 4.5 1   2
> T4wait32  85  80  80  3.5 4.5 2   3.5
> T5wait6   50  50  50  1   1   0.5 2
> T5wait14  80  75  75  15  5.5 1   2
> T5wait15  90  80  80  1   5.5 1   3
> T5wait20  85  80  80  22.58.5 0   0
> T5wait25  85  80  80  22.58.5 1   1.5
> T6wait8   75  75  75  1.5 4.5 0   1.5
> T6wait9   90  85  85  1.5 3.5 1   2
> T6wait13  80  75  75  1   3.5 1   1.5
> T6wait19  90  85  80  1   2.5 1   2
> T6wait27  85  80  75  1   3.5 1   2
> Tccontrol 5   50  45  45  40  23  20  25
> Tccontrol 7   50  53  54  55  55  50  55
> Tccontrol 17  90  80  70  22.59   15  20
> Tccontrol 30  75  75  70  75  45  60  70
> Tccontrol 35  90  85  80  85  65  60  70
> 
> Chris Buddenhagen, Botany Department, Charles Darwin Research Station, Santa
> Cruz,Galapagos. Mail: Charles Darwin Foundation, Casilla 17-01-3891 Avenida
> 6 de Diciembre N36-109 y Pasaje California Quito, ECUADOR
>  
> 
> 
> 
> 
> 
> __
> EL CONTENIDO DE ESTE MENSAJE ES DE ABSOLUTA RESPONSABILIDAD DEL AUTOR.
> FUNDACION CHARLES DARWIN
> WWW.DARWINFOUNDATION.ORG

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[R] Using unsplit - unsplit does not seem to reverse the effect of split

[Søren Højsgaard]

In data OME in MASS I would like to extract the first 5 observations per 
subject (=ID). So I do
 
library(MASS)
OMEsub <- split(OME, OME$ID)
OMEsub <- lapply(OMEsub,function(x)x[1:5,])
unsplit(OMEsub, OME$ID)

- which results in 
 
[[1]]
[1] 1 1 1 1 1
[[2]]
[1] 30 30 30 30 30
[[3]]
[1] low low low low low
Levels: N/A high low
[[4]]
[1] 35 35 40 40 45
[[5]]
[1] coherent   incoherent coherent   incoherent coherent  
Levels: coherent incoherent
[[6]]
[1] 1 4 0 1 2


 
[[1094]]
[1] 4 5 5 5 2
[[1095]]
[1] 100 100 100 100 100
[[1096]]
[1] 18 18 18 18 18
[[1097]]
[1] N/A N/A N/A N/A N/A
Levels: N/A high low
There were 50 or more warnings (use warnings() to see the first 50)

warnings()
Warning messages:
1: number of items to replace is not a multiple of replacement length
2: number of items to replace is not a multiple of replacement length
3: number of items to replace is not a multiple of replacement length

 
According to documentation unsplit is the reverse of split, but I must be 
missing a point somewhere... Can anyone help? Thanks in advance. Søren

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Re: [R] multiple plots on same x axis

[Charles Annis, P.E.]

Try 

plot(Day, gene1)
lines(Day, gene2)


see 

?lines
 
for more details.


Charles Annis, P.E.

[EMAIL PROTECTED]
phone: 561-352-9699
eFax:  614-455-3265
http://www.StatisticalEngineering.com
 

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of IAIN GALLAGHER
Sent: Tuesday, September 27, 2005 10:35 AM
To: r-help@stat.math.ethz.ch
Subject: [R] multiple plots on same x axis

Hi.

I have two vectors of gene expression for each of
several days. I want to plot both vectors on the same
plot for a visual representation of up versus down
regulation. I've tried using add=T but that doesn't
work. 

eg

>plot(Day, gene1)
>plot(Day, gene2, add=T)

Any help would be appreciated.

Iain

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Re: [R] Using unsplit - unsplit does not seem to reverse the effect of split

[Peter Dalgaard]

Søren Højsgaard <[EMAIL PROTECTED]> writes:

> In data OME in MASS I would like to extract the first 5 observations per 
> subject (=ID). So I do
>  
> library(MASS)
> OMEsub <- split(OME, OME$ID)
> OMEsub <- lapply(OMEsub,function(x)x[1:5,])
> unsplit(OMEsub, OME$ID)
> 
> - which results in 
>  
> [[1]]
> [1] 1 1 1 1 1
> [[2]]
> [1] 30 30 30 30 30
> [[3]]
> [1] low low low low low
> Levels: N/A high low
> [[4]]
> [1] 35 35 40 40 45
> [[5]]
> [1] coherent   incoherent coherent   incoherent coherent  
> Levels: coherent incoherent
> [[6]]
> [1] 1 4 0 1 2
> 
> 
>  
> [[1094]]
> [1] 4 5 5 5 2
> [[1095]]
> [1] 100 100 100 100 100
> [[1096]]
> [1] 18 18 18 18 18
> [[1097]]
> [1] N/A N/A N/A N/A N/A
> Levels: N/A high low
> There were 50 or more warnings (use warnings() to see the first 50)
> 
> warnings()
> Warning messages:
> 1: number of items to replace is not a multiple of replacement length
> 2: number of items to replace is not a multiple of replacement length
> 3: number of items to replace is not a multiple of replacement length
> 
>  
> According to documentation unsplit is the reverse of split, but I must be 
> missing a point somewhere... Can anyone help? Thanks in advance. Søren

It only works if the first argument is or could have resulted from a
split on the second argument. That is clearly not the case when you
are creating subvectors. 

I have on occasion wanted an unsplit that worked without the 2nd
argument as in

unsplit(l, rep(seq(along=l), sapply(l,length)) )

but if you think about it, it's not really doing anything that
do.call("c",l) or do.call("rbind",l) won't do.

-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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Re: [R] Using unsplit - unsplit does not seem to reverse the effect of split

[Marc Schwartz (via MN)]

On Tue, 2005-09-27 at 19:12 +0200, Søren Højsgaard wrote:
> In data OME in MASS I would like to extract the first 5 observations
> per subject (=ID). So I do
>  
> library(MASS)
> OMEsub <- split(OME, OME$ID)
> OMEsub <- lapply(OMEsub,function(x)x[1:5,])
> unsplit(OMEsub, OME$ID)
> 
> - which results in 
>  
> [[1]]
> [1] 1 1 1 1 1
> [[2]]
> [1] 30 30 30 30 30
> [[3]]
> [1] low low low low low
> Levels: N/A high low
> [[4]]
> [1] 35 35 40 40 45
> [[5]]
> [1] coherent   incoherent coherent   incoherent coherent  
> Levels: coherent incoherent
> [[6]]
> [1] 1 4 0 1 2
> 
> 
>  
> [[1094]]
> [1] 4 5 5 5 2
> [[1095]]
> [1] 100 100 100 100 100
> [[1096]]
> [1] 18 18 18 18 18
> [[1097]]
> [1] N/A N/A N/A N/A N/A
> Levels: N/A high low
> There were 50 or more warnings (use warnings() to see the first 50)
> 
> warnings()
> Warning messages:
> 1: number of items to replace is not a multiple of replacement length
> 2: number of items to replace is not a multiple of replacement length
> 3: number of items to replace is not a multiple of replacement length
> 
>  
> According to documentation unsplit is the reverse of split, but I must
> be missing a point somewhere... Can anyone help? Thanks in advance.
> Søren


If you read the documentation for split/unsplit, you will also note that
in the Details section it says:

 'unsplit' works only with lists of vectors

as opposed to lists of data frames, which is the result of your split()
operation.

Also note that in the Value section, it indicates:

'unsplit' returns a vector for which 'split(x, f)' equals 'value'

as opposed to unsplit returning a data frame.


Thus, use:

  OME1 <- do.call("rbind", OMEsub)

where OME1 will be the result of rbind()'ing the data frames in the
OMEsub list.

See ?do.call for more information.

HTH,

Marc Schwartz

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Re: [R] Weighting factor

[Thomas Lumley]

On Tue, 27 Sep 2005, Ferran Carrascosa wrote:

> Hi everyone,
>
> I would like some package of R or any help to solve the next problem
> with a weighting fatcors:
>
> Giving a data matrix with dichotomous (2 or more) variables in columns
> and individuals in rows, and also a theorical distribution of the
> dichotomous variables I would like a row weight (one per individual)
> that transform the real distribution of variables to the theorical
> distribution.
>

You should be able to do this with postStratify() in the survey package 
(if you have joint distributions for the variables) or calibrate() if you 
have only marginal distributions.

You would need to create a survey design object, use postStratify() or 
calibrate() on it, then use weights() to extract the weights.

-thomas

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[R] missing handling

[Weiwei Shi]

Hi,
I have the following codes to replace missing using median, assuming missing
only occurs on continuous variables:

trn1<-read.table('trn1.fv', header=F, na.string='.', sep='|')

# median
m.trn1<-sapply(1:ncol(trn1), function(i) median(trn1[,i], na.rm=T))

#replace
trn2<-trn1
for (each in 1:nrow(trn1)){
index.missing=which(is.na(trn1[each,]))
trn2[each,]<-replace(trn1[each,], index.missing, m.trn1[index.missing])
}


Anyone can suggest some ways to improve it since replacing 10 takes 1.5 sec:
> system.time(for (each in 1:10){index.missing=which(is.na(trn1[each,]));
trn2[each,]<-replace(trn1[each,], index.missing, m.trn1[index.missing]);})
[1] 1.53 0.00 1.53 0.00 0.00


Another general question is
are there some packages in R doing missing handling?

Thanks,

--
Weiwei Shi, Ph.D

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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[R] dynamic lists (data frames?)

[tom wright]

Can someone please show me what I need to get something like this to
work

for(a in c(1:5)){
data$a<-c(a:10)
}

so that i end up with a structure
data$1<-[1,2,3,4,5,6,7,8,9,10]
data$2<-[2,3,4,5,67,8,9,10]
data$3<-[3,4,5,67,8,9,10]
data$4<-[4,5,67,8,9,10]
data$5<-[5,67,8,9,10]

thanks loads
Tom

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[R] Listing object sizes without RODBC objects: contributed function

[Leif Kirschenbaum]

I include my workaround for object.size failing on RODBC objects.
Code adapted from Petr Pikal's code 
(http://tolstoy.newcastle.edu.au/R/help/04/06/1228.html).

ls.objects<-function (pos = 1, order.by,...)
{
napply <- function(names, fn) sapply(names, function(x) fn(get(x,pos=pos)))
names <- ls(pos = pos,...)
obj.class <- napply(names, function(x) as.character(class(x))[1])
obj.drop <- match("RODBC",obj.class)
obj.class <- obj.class[-obj.drop]
names <- names[-obj.drop]
obj.mode <- napply(names, mode)
obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
obj.size <- napply(names, object.size)
obj.dim <- t(napply(names, function(x) as.numeric(dim(x))[1:2]))
vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
obj.dim[vec, 1] <- napply(names, length)[vec]
out <- data.frame(obj.type, obj.size, obj.dim)
names(out) <- c("Type", "Size", "Rows", "Columns")
if (!missing(order.by)) out <- out[order(out[[order.by]]), ]
out
} 


Leif S. Kirschenbaum, Ph.D.
Senior Yield Engineer
Reflectivity, Inc.

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Re: [R] dynamic lists (data frames?)

[Vincent Goulet]

Le 27 Septembre 2005 10:39, tom wright a écrit :
> Can someone please show me what I need to get something like this to
> work
>
> for(a in c(1:5)){
>   data$a<-c(a:10)
> }
>
> so that i end up with a structure
> data$1<-[1,2,3,4,5,6,7,8,9,10]
> data$2<-[2,3,4,5,67,8,9,10]
> data$3<-[3,4,5,67,8,9,10]
> data$4<-[4,5,67,8,9,10]
> data$5<-[5,67,8,9,10]
>
> thanks loads
> Tom

That's an exercise I give to my students! This will create the sequences:

> data <- lapply(1:5, seq, 10)

You can then assign the names with

> names(data) <- as.character(1:5)

but 'data$1' will not work. You will need either 'data$"1"' or 'data[["1"]]'. 
I'd use different names...

HTH.

-- 
  Vincent Goulet, Associate Professor
  École d'actuariat
  Université Laval, Québec 
  [EMAIL PROTECTED]   http://vgoulet.act.ulaval.ca

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Re: [R] missing handling

[jim holtman]

Use 'which(...arr.ind=T)'
 > x.1
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 10 3 4 10 7 9 8 4 10
[2,] 8 7 4 7 4 8 3 NA 3 4
[3,] 7 7 10 10 3 5 3 2 2 2
[4,] 3 4 5 10 10 2 6 9 4 5
[5,] 3 5 9 5 6 NA 3 NA 6 7
[6,] 9 6 10 5 10 4 2 10 NA 5
[7,] 5 2 5 10 3 7 6 4 6 8
[8,] 2 6 1 8 9 2 7 8 3 8
[9,] 9 1 4 9 8 10 2 NA 1 7
[10,] 2 4 8 7 NA 4 3 NA 5 5
> x.4
[1] 5.5 5.5 5.0 7.5 8.0 5.0 3.0 8.0 4.0 6.0
> Med <- apply(x.1, 2, median, na.rm=T) # get median
> Ind <- which(is.na(x.1), arr.ind=T) # determine which are NA
> x.1[Ind] <- Med[Ind[,'col']] # replace with median
> x.1
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 10 3 4 10 7 9 8 4 10
[2,] 8 7 4 7 4 8 3 8 3 4
[3,] 7 7 10 10 3 5 3 2 2 2
[4,] 3 4 5 10 10 2 6 9 4 5
[5,] 3 5 9 5 6 5 3 8 6 7
[6,] 9 6 10 5 10 4 2 10 4 5
[7,] 5 2 5 10 3 7 6 4 6 8
[8,] 2 6 1 8 9 2 7 8 3 8
[9,] 9 1 4 9 8 10 2 8 1 7
[10,] 2 4 8 7 8 4 3 8 5 5
>


 On 9/27/05, Weiwei Shi <[EMAIL PROTECTED]> wrote:
>
> Hi,
> I have the following codes to replace missing using median, assuming
> missing
> only occurs on continuous variables:
>
> trn1<-read.table('trn1.fv', header=F, na.string='.', sep='|')
>
> # median
> m.trn1<-sapply(1:ncol(trn1), function(i) median(trn1[,i], na.rm=T))
>
> #replace
> trn2<-trn1
> for (each in 1:nrow(trn1)){
> index.missing=which(is.na(trn1[each,]))
> trn2[each,]<-replace(trn1[each,], index.missing, m.trn1[index.missing])
> }
>
>
> Anyone can suggest some ways to improve it since replacing 10 takes 1.5sec:
> > system.time(for (each in 1:10){index.missing=which(is.na(trn1[each,]));
> trn2[each,]<-replace(trn1[each,], index.missing, m.trn1[index.missing]);})
> [1] 1.53 0.00 1.53 0.00 0.00
>
>
> Another general question is
> are there some packages in R doing missing handling?
>
> Thanks,
>
> --
> Weiwei Shi, Ph.D
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>
> [[alternative HTML version deleted]]
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>



--
Jim Holtman
Cincinnati, OH
+1 513 247 0281

What the problem you are trying to solve?

[[alternative HTML version deleted]]

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Re: [R] dynamic lists (data frames?)

[Gabor Grothendieck]

When sapply is used on a character vector it will use those
as the names so:

data <- sapply(as.character(1:5), function(x) seq(as.numeric(x),10))

will give data with the required names.

On 9/27/05, tom wright <[EMAIL PROTECTED]> wrote:
> Can someone please show me what I need to get something like this to
> work
>
> for(a in c(1:5)){
>data$a<-c(a:10)
> }
>
> so that i end up with a structure
> data$1<-[1,2,3,4,5,6,7,8,9,10]
> data$2<-[2,3,4,5,67,8,9,10]
> data$3<-[3,4,5,67,8,9,10]
> data$4<-[4,5,67,8,9,10]
> data$5<-[5,67,8,9,10]
>
> thanks loads
> Tom
>
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[R] Binding dataframe with different length in rows and columns

[Jérôme Lemaître]

Dear all,

I'm trying to combine in R the two following datasets. 
I'm would be very grateful if someone could help me with this problem.

Dataset 1:
X   Y   Z
1   27  48
2   25  50
3   27  40
4   28  56

Where X is a unique number and Y and Z some variables 

Dataset 2:
X   I   J
1   10  12
1   12  12
1   23  30
1   40  46
2   7   8
2   8   9
2   9   8
3   2   0
4   98  87
4   78  89
Where X IS NOT this time a unique number. I and J are some variables.

Thank you by advance


Jérôme Lemaître
Étudiant au doctorat
Université Laval
Québec, QC

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Re: [R] Binding dataframe with different length in rows and columns

[Nolwenn LeMeur]

Hi Jerome,

look at the merge() function

Nolwenn

On Tue, 27 Sep 2005, Jérôme Lemaître wrote:

> Dear all,
> 
> I'm trying to combine in R the two following datasets. 
> I'm would be very grateful if someone could help me with this problem.
> 
> Dataset 1:
> X Y   Z
> 1 27  48
> 2 25  50
> 3 27  40
> 4 28  56
> 
> Where X is a unique number and Y and Z some variables 
> 
> Dataset 2:
> X I   J
> 1 10  12
> 1 12  12
> 1 23  30
> 1 40  46
> 2 7   8
> 2 8   9
> 2 9   8
> 3 2   0
> 4 98  87
> 4 78  89
> Where X IS NOT this time a unique number. I and J are some variables.
> 
> Thank you by advance
> 
> 
> Jérôme Lemaître
> Étudiant au doctorat
> Université Laval
> Québec, QC
> 
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Re: [R] dynamic lists (data frames?)

[tom wright]

Hmm my bad,
Thanks for your replies but I think my example was a little to simple
the actual code I'm using is:


f_haardisolve<-function(v_dataset){
#pad data to make length a power of 2
v_dataset<-f_paddata(v_dataset)

l_cooef<-list() #holder for cooefficents
i_count<-1  #identity counter

while(length(v_dataset)>0){
#seperate odd and even points
v_dataset<-f_splitpoints(v_dataset)

v_dataset<-f_haarpredict(v_dataset)
v_dataset<-f_haaruplift(v_dataset)

str_idx<-paste('c',i_count,sep='')
l_cooef
$str_idx<-v_dataset[c((length(v_dataset)/2)+1:(length(v_dataset)/2))]
#should be no wrap on the previous line 

   v_dataset<-v_dataset[c(1:length(v_dataset)/2)]

i_count<-i_count+1
}
l_cooef
}

In this particular case I could probably calculate the number of
iterations and use l_cooef<-names() but more is there a more generic
method for adding another column of data?



On Tue, 2005-27-09 at 10:39 -0400, tom wright wrote:
> Can someone please show me what I need to get something like this to
> work
> 
> for(a in c(1:5)){
>   data$a<-c(a:10)
> }
> 
> so that i end up with a structure
> data$1<-[1,2,3,4,5,6,7,8,9,10]
> data$2<-[2,3,4,5,67,8,9,10]
> data$3<-[3,4,5,67,8,9,10]
> data$4<-[4,5,67,8,9,10]
> data$5<-[5,67,8,9,10]
> 
> thanks loads
> Tom
> 
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Re: [R] [ESS] Indentation in R code

[Göran Broström]

On Mon, Sep 26, 2005 at 07:05:33PM +0200, Göran Broström wrote:
> On Mon, Sep 26, 2005 at 09:27:56AM +0200, Martin Maechler wrote:
> > I'm crossposting to the ESS-help mailing list which is slightly
> > more appropriate here.  [This may be a rare case where
> > crossposting seems to make much sense.]
> > 
> > > "PD" == Peter Dalgaard <[EMAIL PROTECTED]>
> > > on 25 Sep 2005 19:40:45 +0200 writes:
> > 
> > PD> Seth Falcon <[EMAIL PROTECTED]> writes:
> > 
> > >> On 24 Sep 2005, [EMAIL PROTECTED] wrote:
> > >> 
> > >> > I am using emacs-21.3 when writing R functions on Linux debian, and
> > >> > I am trying to follow the advice i R-exts.pdf (2.1.1) regarding
> > >> > indentation. That is, I set 'c-default-style' to "bsd" and
> > >> > 'c-basic-offset' to 4. However, while this gives me the intended
> > >> > indentation in C code, it doesn't change the behavior in R code; I
> > >> > still get an indentation of size 2. This is my .emacs file after
> > >> > customization:
> > >> >
> > >> > (require 'ess-site)
> > >> > (custom-set-variables
> > >> >  ;; custom-set-variables was added by Custom -- don't edit or
> > >> >  ;; cut/paste it!  Your init file should contain only one such
> > >> >  ;; instance.
> > >> >  '(c-basic-offset 4)
> > >> >  '(c-default-style "bsd"))
> > >> >  (custom-set-faces
> > >> >  ;; custom-set-faces was added by Custom -- don't edit or 
> > cut/paste it!
> > >> >  ;; Your init file should contain only one such instance.
> > >> > )
> > >> 
> > >> Not sure if this is the best way, but I have the following after
> > >> loading ess-site:
> > >> 
> > >> (setq ess-indent-level 4)
> > 
> > 
> > 
> > PD> I have (I believe it stems from Martin M. originally):
> > 
> > yes, most probably  {IIRC, Kurt Hornik was involved too}.
> > 
> > PD>  (add-hook 'c-mode-hook '(lambda()
> > PD>(c-set-style "stroustrup")))
> > 
> > the above is not quite what I have or did recommend, 
> > which is rather  "bsd" + "offset 4"  as Göran has above
> > 
> > In fact, Göran mentions the "R-exts" manual and that has
> > the following  *before* giving the emacs-lisp statements:
> > 
> > >> (For GNU Emacs 20: for GNU Emacs 21 use
> > >> customization to set the `c-default-style' to `"bsd"' and
> > >> `c-basic-offset' to `4'.)
> > 
> > and indeed, that's what Göran did and you should do with a
> > current emacs, either customize via GUI or,
> > in your ~/.emacs file, find the section '(custom-set-variables ...)' and 
> > add 
> >  '(c-basic-offset 4)
> >  '(c-default-style "bsd")
> > 
> > to the lines already there, or if there's no such section, add
> > 
> > (custom-set-variables
> >   ;; custom-set-variables was added by Custom -- don't edit or cut/paste it!
> >   ;; Your init file should contain only one such instance.
> >  '(c-basic-offset 4)
> >  '(c-default-style "bsd")


> > to the end of your ~/.emacs file
> [...]
> 
> but this is not sufficient to get correct (4) indentation (ess) in R 
> functions. We need some reference to ess as well, right? Maybe another
> reference to the ESS manual is in order in 'R-exts'?

Martin, I realize that it was stupid of me to cut here; I only refer to C
indentation, and forget that the lines of lisp code referring to ESS of 
course is necessary to get indentation working in R functions.

Once again, thanks for your good help.

Göran

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Re: [R] dynamic lists (data frames?)

[tom wright]

Got it thanks
the trick was to create a variable with the new name
str_idx<-paste('c',i,sep='')
then use double square brackets
l_cooef[str_idx]]<-whatever()


f_haardisolve<-function(v_dataset){
#pad data to make length a power of 2
v_dataset<-f_paddata(v_dataset)

l_cooef<-list() #holder for cooefficents
i_count<-1  #identity counter

while(length(v_dataset)>0){
#seperate odd and even points
v_dataset<-f_splitpoints(v_dataset)

v_dataset<-f_haarpredict(v_dataset)
v_dataset<-f_haaruplift(v_dataset)

str_idx<-paste('c',i_count,sep='')
l_cooef[[str_idx]]<-list()

l_cooef[[str_idx]]<-v_dataset[c((length(v_dataset)/2)+1:(length(v_dataset)/2))]
v_dataset<-v_dataset[c(1:length(v_dataset)/2)]

i_count<-i_count+1
}
l_cooef
}


On Tue, 2005-27-09 at 10:39 -0400, tom wright wrote:
> Can someone please show me what I need to get something like this to
> work
> 
> for(a in c(1:5)){
>   data$a<-c(a:10)
> }
> 
> so that i end up with a structure
> data$1<-[1,2,3,4,5,6,7,8,9,10]
> data$2<-[2,3,4,5,67,8,9,10]
> data$3<-[3,4,5,67,8,9,10]
> data$4<-[4,5,67,8,9,10]
> data$5<-[5,67,8,9,10]
> 
> thanks loads
> Tom
> 
> __
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Re: [R] Binding dataframe with different length in rows and columns

[venomousanimal]

Hello ,
How about cbind or rbind?
You could create a new data frame and push yours into it.
Greetz

Jérôme Lemaître schrieb:

>Dear all,
>
>I'm trying to combine in R the two following datasets. 
>I'm would be very grateful if someone could help me with this problem.
>
>Dataset 1:
>X  Y   Z
>1  27  48
>2  25  50
>3  27  40
>4  28  56
>
>Where X is a unique number and Y and Z some variables 
>
>Dataset 2:
>X  I   J
>1  10  12
>1  12  12
>1  23  30
>1  40  46
>2  7   8
>2  8   9
>2  9   8
>3  2   0
>4  98  87
>4  78  89
>Where X IS NOT this time a unique number. I and J are some variables.
>
>Thank you by advance
>
>
>Jérôme Lemaître
>Étudiant au doctorat
>Université Laval
>Québec, QC
>
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>  
>

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Re: [R] suggest some books or materials for matrices basics , its partitions, iterations, clusturing

[Spencer Graves]

  Your question seems almost too broad, but I will attempt a brief 
response.

  Have you reviewed the material on matrices in "An Introduction to R", 
avaliable via, e.g., "help.start()"?  Also, have you reviewed LAPACK 
(http://www.netlib.org/lapack/)?

  If the answer to both is "yes", submit another post (after reading 
the posting guide, www.R-project.org/posting-guide.html, which should 
increase the chances that you will get a quick, useful reply).

  spencer graves

booop booop wrote:

> Dear sir,
> Could anybody kindly suggest me some good
> e-books(which are available in the internet),or other
> materials in the web
> sites to refer examples ...
> in the following area
> 
> matrices & its basics
> partitioning of matrices...
> iterations of matrices
> Clusturing in matrices...
> 
> thank you sir..
> 
> with kind regards,
> boopathy.
> 
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-- 
Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA

[EMAIL PROTECTED]
www.pdf.com 
Tel:  408-938-4420
Fax: 408-280-7915

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[R] Dummy quesion about environment

[Ron Ophir]

Hi,
I'm trying to understand environment object in R.
I used the example:
  f <- function(x) {
 y <- 10
 g <- function(x) x + y
 return(g)
 }
 h <- f()
 h(3)
then i saw that f return an environment
> h
function(x) x + y

but I coudn't access to x and y object in that environment:
I tried 
get("x",env=h)
I tried
h$y
can I access y and x?
how can I see an environment tree? oes search does it?
Thanks,
Ron

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Re: [R] Dummy quesion about environment

[Roger D. Peng]

Try 'get("x", env = environment(h))'

-roger

Ron Ophir wrote:
> Hi,
> I'm trying to understand environment object in R.
> I used the example:
>   f <- function(x) {
>  y <- 10
>  g <- function(x) x + y
>  return(g)
>  }
>  h <- f()
>  h(3)
> then i saw that f return an environment
> 
>>h
> 
> function(x) x + y
> 
> but I coudn't access to x and y object in that environment:
> I tried 
> get("x",env=h)
> I tried
> h$y
> can I access y and x?
> how can I see an environment tree? oes search does it?
> Thanks,
> Ron
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
> 

-- 
Roger D. Peng
http://www.biostat.jhsph.edu/~rpeng/

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Re: [R] Dummy quesion about environment

[Peter Dalgaard]

"Ron Ophir" <[EMAIL PROTECTED]> writes:

> Hi,
> I'm trying to understand environment object in R.
> I used the example:
>   f <- function(x) {
>  y <- 10
>  g <- function(x) x + y
>  return(g)
>  }
>  h <- f()
>  h(3)
> then i saw that f return an environment
> > h
> function(x) x + y
> 
> but I coudn't access to x and y object in that environment:
> I tried 
> get("x",env=h)
> I tried
> h$y
> can I access y and x?

Well, there are special issues with x above, but the basic thing is to
take environment(h). Notice that h _is_ a function that _has_ an
associated environment. 

> get("y",env=environment(h))
[1] 10

As I said, x is stranger, which is because you used f() in the call:

> get("x",env=environment(h))

> str(get("x",env=environment(h)))
 symbol
> a <- get("x",env=environment(h))
> missing(a)
[1] TRUE
> evalq(x,environment(h))
Error in eval(expr, envir, enclos) : argument "x" is missing, with no
 default
> evalq(missing(x),environment(h))
[1] TRUE

You'll get the point if you look long and hard enough...

> how can I see an environment tree? 

You can't. You can see the parent of an environment, the grandparent,
etc., but there is no way to see which children a given environment
has. 

> oes search does it?

Huh?

> Thanks,
> Ron
> 
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> 

-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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Re: [R] Dummy quesion about environment

[venomousanimal]

Hej,

but in your function you add x and y to 10 and 3, so your values are 
merged to one value available in g variable.
And now you want to see what was your y and your x?
I guess I do not get the idea of your question.
Well, then you could return y and x as well as g.

Greetz n god luck.


Roger D. Peng schrieb:

>Try 'get("x", env = environment(h))'
>
>-roger
>
>Ron Ophir wrote:
>  
>
>>Hi,
>>I'm trying to understand environment object in R.
>>I used the example:
>>  f <- function(x) {
>> y <- 10
>> g <- function(x) x + y
>> return(g)
>> }
>> h <- f()
>> h(3)
>>then i saw that f return an environment
>>
>>
>>
>>>h
>>>  
>>>
>>function(x) x + y
>>
>>but I coudn't access to x and y object in that environment:
>>I tried 
>>get("x",env=h)
>>I tried
>>h$y
>>can I access y and x?
>>how can I see an environment tree? oes search does it?
>>Thanks,
>>Ron
>>
>>__
>>R-help@stat.math.ethz.ch mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>
>>
>>
>
>  
>

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Re: [R] Weighting factor

[Ferran Carrascosa]

Uau!
This package is very interesting, very thank you Thomas.

Thanks to all!

2005/9/27, Thomas Lumley <[EMAIL PROTECTED]>:
> On Tue, 27 Sep 2005, Ferran Carrascosa wrote:
>
> > Hi everyone,
> >
> > I would like some package of R or any help to solve the next problem
> > with a weighting fatcors:
> >
> > Giving a data matrix with dichotomous (2 or more) variables in columns
> > and individuals in rows, and also a theorical distribution of the
> > dichotomous variables I would like a row weight (one per individual)
> > that transform the real distribution of variables to the theorical
> > distribution.
> >
>
> You should be able to do this with postStratify() in the survey package
> (if you have joint distributions for the variables) or calibrate() if you
> have only marginal distributions.
>
> You would need to create a survey design object, use postStratify() or
> calibrate() on it, then use weights() to extract the weights.
>
>-thomas
>


--
Ferran Carrascosa

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Re: [R] Make check fails on d-p-q-r-tests.R...

[Prof Brian Ripley]

I am afraid this does look like a real problem, if a minor one. We have 
for the first problem

x <- 10^(ex <- c(1,2,5*(1:5),50,100,200,300,Inf))
ex <- -c(rev(1/x), ex)
qcauchy(ex, log=TRUE)

The first entry of the result should be Inf and the last -Inf.  From the 
output you have shown us I would guess the last is NaN.

If this is what is going on, it is a problem but a somewhat esoteric one 
that probably reflects a lack of IEC60559 (aka IEEE754) conformance.  It 
needs more hands-on debugging than we can provide on a help list.


On Tue, 27 Sep 2005, Jeff Ross wrote:

> On 1:03:39 am 09/27/05 Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
>
>> You will have to show us the error!   It will be shown in
>> d-p-q-r-tests.Rout.fail (unless this was a segfault or similar).
>>
>> It is not OK to skip the test, but note that this test is random and
>> does fail about 1 in 50 times, so you could just try rerunning it.
>
> I am so sorry.  I didn't even think to look for a .fail file.
>
> Here is the last bit of it:
>
>>> ## for PR#7902:
>> ex <- -c(rev(1/x), ex)
>> All.eq(-x, qcauchy(pcauchy(-x)))
> [1] TRUE
>> All.eq(+x, qcauchy(pcauchy(+x, log=TRUE), log=TRUE))
> [1] TRUE
>> All.eq(1/x, pcauchy(qcauchy(1/x)))
> [1] TRUE
>> All.eq(ex,  pcauchy(qcauchy(ex, log=TRUE), log=TRUE))
> [1] "`is.NA' value mismatches: 1 in current, 0  in target"
> Warning message:
> NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p)
>> II <- c(-Inf,Inf)
>> stopifnot(pcauchy(II) == 0:1, ## qcauchy(0:1) == II,
> +   pcauchy(II, log=TRUE) == c(-Inf,0),
> +   qcauchy(c(-Inf,0), log=TRUE) == II)
> Error in if (!(is.logical(r <- eval(ll[[i]])) && all(r)))
> stop(paste(deparse(mc[[i +  :
>  missing value where TRUE/FALSE needed
> In addition: Warning message:
> NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p)
> Execution halted
>
> This is from the latest R-patched source tar ball, and it is the identical
> error as R-2.1.1.  I've consistently gotten the same error, even with
> configuration file tweaks and making clean between runs.
>
> Thanks!
>
> Jeff Ross

-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [R] Simulate phi-coefficient (correlation between dichotomous vars)

[David Duffy]

On Tue, 27 Sep 2005, Bliese, Paul D LTC USAMH wrote:
> My situation is a bit more complicated and I'm not sure it is easily
> solved.  The problem is that I must assume one of the vectors is
> constant and generate one or more vectors that covary with the constant
> vector.
>
>> One way is to sample from the 2x2 table with the specified means and
>> pearson correlation (phi):
>>
>> for a fourfold table, a b
>>   c d
>> with marginal proportions p1 and p2
>> cov <- phi * sqrt(p1*(1-p1)*p2*(1-p2))
>> a <- p1*p2 + cov
>> b <- p1*(1-p2) - cov
>> c <- (1-p1)*p2 - cov
>> d <- (1-p1)*(1-p2) + cov
>

Calculate the conditional probabilities from the above

P(X2=1|X1=1)= a/(a+b) = p2 + cov/p1
P(X2=1|X1=0)= c/(c+d) = p2 - cov/(1-p1)


condsim <- function(X, phi, p2, p1=NULL) {
  if (!all(X %in% c(0,1))) stop("expecting 1's and 0's")
  if (is.null(p1)) p1 <- mean(X)
  covar <- phi  * sqrt(p1*(1-p1)*p2*(1-p2))
  if (covar>0 && covar>(min(p1,p2)-p1*p2)) {
warning("Specified correlation too large for given marginal proportions")
covar <- min(p1,p2)-p1*p2
  }else if (covar<0 && covar < -min(p1*p2,(1-p1)*(1-p2))) {
warning("Specified correlation too small for given marginal proportions")
covar <- -min(p1*p2,(1-p1)*(1-p2))
  }
  Y <- X
  i1 <- X==1
  i0 <- X==0
  Y[i1] <- rbinom(sum(i1),1, p2 + covar/p1)
  Y[i0] <- rbinom(sum(i0),1, p2 - covar/(1-p1))
  data.frame(X,Y)
}

David Duffy.

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Re: [R] R CMD build produces tar error under FreeBSD 5.4

[Eric van Gyzen]

On Sun, Sep 25, 2005 at 12:07:02PM +0100, Prof Brian Ripley wrote:
> On Sun, 25 Sep 2005, Andrew Robinson wrote:
> 
> > Hi R-helpers,
> >
> > I am trying to build a package under FreeBSD 5.4-RELEASE #0 using R
> > Version 2.1.1.
> >
> > I have constructed a package using package.skeleton(), when I try
> >
> > $ R CMD build foo
> > * checking for file 'foo/DESCRIPTION' ... OK
> > * preparing 'foo':
> > * checking DESCRIPTION meta-information ... OK
> > * cleaning src
> > * removing junk files
> > tar: Option -L is not permitted in mode -x
> > Error: cannot open file 'foo/DESCRIPTION' for reading
> >
> > foo/DESCRIPTION exists and the permissions are correct. The same
> > command works under Linux Fedora 2.  The man pages on each OS imply
> > that tar differs across the two platforms.  Does anyone have any
> > thoughts on a work-around?
> 
> No, because R does not use tar -L (which is to do with tape lengths on GNU
> tar).
> 
> It does use tar chf and tar xhf.  The h modifier would appear to be
> applicable only to dumps, so at a wild guess the error message means -h is
> not permitted.  Try replacing xhf by xf.

FreeBSD >= 5.3 uses bsdtar.  Previous versions used GNU tar.

In bsdtar, -h is a synonym for -L, and -L means:

 -L  (c and r mode only) All symbolic links will be followed.  Nor-
 mally, symbolic links are archived as such.  With this option,
 the target of the link will be archived instead.

The man page for bsdtar doesn't indicate an option to dereference
symlinks during extraction.  :(

Eric

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[R] different models

[Stephen Choularton]

Hi 
 
I have a largish dataset (26 columns 35000 rows) which I have been
subjecting to logistic regression and support vector machine analysis.
I have noticed that R easily copes with using the data in either
technique.  Now I have to try and see what the best modeling technique
to use is. 
 
I only have limited time (who doesn’t) so I thought it would be best to
try the data with any other techniques on R that can handle that data
set and then use predict()  and so on.  I have identified the following
techniques (you may know of more) and think the packages indicated will
support them:
 
Neural networks -> AMORE
Genetic/evolutionary   -> ?
Bayes   -> deal
Decision trees   -> knnTree
Gaussian processes  -> predict
 
Are these the right packages where I can go model = etc,
predict(model,etc using my dataset?
 
Have I missed some techniques?
 
Does anyone know the package I couldn’t find for genetic.
 
All help/comments welcome.
 
Thanks
 
Stephen
 
 

-- 



27/09/2005
 

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Re: [R] Help: x11 position in the Unix environment

[Brahm, David]

Shengzhe Wu <[EMAIL PROTECTED]> wrote:

> In the Unix environment, I open a window by x11(). May I specify the
> position of this window by specifying the position of the top left of
> the window as in Windows environment?

I use "xwit" (version 3.4), a system command which manipulates existing
X windows.  My R code for initiating a graphics window contains:

  system(paste("xwit -move 2045 0 -names 'R Graphics: Device ",
   dev.cur(), "'", sep=""), ignore.stderr=TRUE)

See, e.g, .
(I'm pretty sure I got the idea from another kind soul on R-help.)

-- David Brahm ([EMAIL PROTECTED])

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Re: [R] Make check fails on d-p-q-r-tests.R...

[Jeff Ross]

On Tue, 27 Sep 2005, Prof Brian Ripley wrote:

> I am afraid this does look like a real problem, if a minor one. We have for 
> the first problem
>
> x <- 10^(ex <- c(1,2,5*(1:5),50,100,200,300,Inf))
> ex <- -c(rev(1/x), ex)
> qcauchy(ex, log=TRUE)
>
> The first entry of the result should be Inf and the last -Inf.  From the 
> output you have shown us I would guess the last is NaN.
>
> If this is what is going on, it is a problem but a somewhat esoteric one that 
> probably reflects a lack of IEC60559 (aka IEEE754) conformance.  It needs 
> more hands-on debugging than we can provide on a help list.
>

Thanks for the analysis.  I'll move this over to r-devel.

Jeff

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[R] Plot Data Points in boxplots

[Aric Gregson]

Hello,

I would like to plot my data in a fashion similar to a boxplot, but 
plot the true data points without a box, just overlay lines of the 
summary generated by the boxplot. I have less than 10 observations 
within each group, so I think showing the actual data would be more 
effective than the box of the boxplot. I have been unable to find a way 
to do this.

Here is example data:
> d168teni
  d168dh10i d168hb10i d168icc10i d168rcs10i d168t410i d168tb410i
17252 29 8039 68
27647 28 6849 21
3   12385 87 71   164137
45847 50 7018  1

> boxplot(d168teni)

works to describe the data (each column a column in the plot). However, 
instead of the boxes, I want the data plotted (in a column) with the 5 
summary lines drawn over the points.

I have tried using functions from Design and have been unable to find a 
solution. I think I am missing the point.

Any suggestions on where to look or how to approach this differently?

thanks,

aric

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Re: [R] Plot Data Points in boxplots

[Gabor Grothendieck]

Try this:

boxplot(Sepal.Length ~ Species, iris)
with(iris, stripchart(Sepal.Length ~ Species, vertical = TRUE, add = TRUE))

On 9/27/05, Aric Gregson <[EMAIL PROTECTED]> wrote:
> Hello,
>
> I would like to plot my data in a fashion similar to a boxplot, but
> plot the true data points without a box, just overlay lines of the
> summary generated by the boxplot. I have less than 10 observations
> within each group, so I think showing the actual data would be more
> effective than the box of the boxplot. I have been unable to find a way
> to do this.
>
> Here is example data:
> > d168teni
>  d168dh10i d168hb10i d168icc10i d168rcs10i d168t410i d168tb410i
> 17252 29 8039 68
> 27647 28 6849 21
> 3   12385 87 71   164137
> 45847 50 7018  1
>
> > boxplot(d168teni)
>
> works to describe the data (each column a column in the plot). However,
> instead of the boxes, I want the data plotted (in a column) with the 5
> summary lines drawn over the points.
>
> I have tried using functions from Design and have been unable to find a
> solution. I think I am missing the point.
>
> Any suggestions on where to look or how to approach this differently?
>
> thanks,
>
> aric
>
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>

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[R] scatterplot3d + density() + polygon(color)

[klebyn]

Hi R Users,

How to use the function polygon()
together with the package scatterplot3d?

I am trying to color below of the curves
defined for the function density().

I tried to use the site: R GRAPH GALLERY
as tutorial.

I tried to adapt the example of this page:
[figure]:
http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=30

[code]:
http://addictedtor.free.fr/graphiques/sources/source_30.R

to my case but I do not obtain success.

Somebody could give a tip to me, please?

I am thankful anticipatedly.

Cleber Borges



#My code test
##
library(scatterplot3d)
x=c(0.4, -1.2, .8, -.7, 0)

d1 = density(x[1],bw=1.2, from=-3.0,  to=3.0  )
d2 = density(x[2],bw=0.8, from=-3.0,  to=3.0  )
d3 = density(x[3],bw=0.6, from=-2.5,  to=2.5  )
d4 = density(x[4],bw=0.5, from=-2.0,  to=2.0  )
d5 = density(x[5],bw=0.3, from=-1.5,  to=1.5  )

sx = c(d1$x,d2$x,d3$x,d4$x,d5$x)
sy = c(d1$y,d2$y,d3$y,d4$y,d5$y)
sz = c(rep(0.1,512),rep(0.2,512),rep(0.3,512),rep(0.4,512),rep(0.5,512))

scatterplot3d(x=sx,y=sz,z=sy,type='l')
##

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[R] need suggestion about building formual

[Simple]

hi,
I'm an newbie for R,I want do some fitting in R.

I wander if it is possible to write a few of equations but only one formual 
when fitting 

Currently,My problem is,in R, is there methods combination a few equations 
into one formual?
For example, 
y=f1(k);
k=f2(t);
t=f3(x);
although it is certain that the can be equations turn into one formual as 
y~f(x),but write such a complexity string make me painful.

I have searched the web and found out there were only examples with one 
formual.any suggestion? 

I hope that I have omit something.

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[R] gfortran Makefile for cygwin

[Joel Bremson]

Hi all,

I'm porting a package that I've worked on for OS X to Cygwin/Windows.

This package requires a Makefile. My question is, how can I find out
(or what is), the link command?

Here is the OS X Makefile:


RLIB_LOC=${R_HOME}

F90_FILES=\
class_data_frame.f90 \
class_old_dbest.f90 \
class_cm_data.f90 \
class_cm.f90 \
class_bgw.f90 \
class_cm_mle.f90 \
cme.f90


FORTRAN_FILES=\
dgletc.f \
dglfgb.f\
dglfg.f\
dmdc.f\
mecdf.f


%.o: %.f90
gfortran -c -g $<

%.o: %.f
gfortran -c -g $<

bpkg.so: $(F90_FILES:%.f90=%.o) $(FORTRAN_FILES:%.f=%.o)
gcc -Wall -bundle -flat_namespace -undefined suppress -L/sw/lib
-L/usr/local/lib -o $@ $^ \
-L$(RLIB_LOC)/lib -lR

###EOF

The -L lib dirs are not correct. On a *nix platform I would do something
like this

sh -x R CMD SHLIB ...

to get at the R internal link information but I can't get that to work on
Cygwin.

Regards,

Joel


--
Joel Bremson
Graduate Student
Institute for Transportation Studies - UC Davis
http://etrans.blogspot.com

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Re: [R] scatterplot3d + density() + polygon(color)

[Uwe Ligges]

klebyn wrote:
> Hi R Users,
> 
> How to use the function polygon()
> together with the package scatterplot3d?
> 
> I am trying to color below of the curves
> defined for the function density().
> 
> I tried to use the site: R GRAPH GALLERY
> as tutorial.
> 
> I tried to adapt the example of this page:
> [figure]:
> http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=30
> 
> [code]:
> http://addictedtor.free.fr/graphiques/sources/source_30.R
> 
> to my case but I do not obtain success.
> 
> Somebody could give a tip to me, please?
> 
> I am thankful anticipatedly.
> 
> Cleber Borges
> 
> 
> 
> #My code test
> ##
> library(scatterplot3d)
> x=c(0.4, -1.2, .8, -.7, 0)
> 
> d1 = density(x[1],bw=1.2, from=-3.0,  to=3.0  )
> d2 = density(x[2],bw=0.8, from=-3.0,  to=3.0  )
> d3 = density(x[3],bw=0.6, from=-2.5,  to=2.5  )
> d4 = density(x[4],bw=0.5, from=-2.0,  to=2.0  )
> d5 = density(x[5],bw=0.3, from=-1.5,  to=1.5  )
> 
> sx = c(d1$x,d2$x,d3$x,d4$x,d5$x)
> sy = c(d1$y,d2$y,d3$y,d4$y,d5$y)
> sz = c(rep(0.1,512),rep(0.2,512),rep(0.3,512),rep(0.4,512),rep(0.5,512))
> 
> scatterplot3d(x=sx,y=sz,z=sy,type='l')
> ##
> 
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Example:

 library(scatterplot3d)

 x <- c(0.4, -1.2, .8, -.7, 0)
 d <- vector(length = length(x), mode = "list")
 d[[1]] <- density(x[1], bw = 1.2, from = -3.0, to = 3.0)
 d[[2]] <- density(x[2], bw = 0.8, from = -3.0, to = 3.0)
 d[[3]] <- density(x[3], bw = 0.6, from = -2.5, to = 2.5)
 d[[4]] <- density(x[4], bw = 0.5, from = -2.0, to = 2.0)
 d[[5]] <- density(x[5], bw = 0.3, from = -1.5, to = 1.5)

 x <- lapply(d, "[[", "x")
 y <- lapply(d, "[[", "y")
 z <- lapply(seq(0.1, 0.5, 0.1), rep, each = 512)

 sx <- unlist(x)
 sy <- unlist(y)
 sz <- unlist(z)

 s3d <- scatterplot3d(x = sx, y = sz, z = sy, type = "n")
 for(i in rev(seq(along=d))){
 s3d_coords <- s3d$xyz.convert(x[[i]], z[[i]], y[[i]])
 polygon(s3d_coords, col = i, border = "black")
 }


Uwe Ligges

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