Re: [R] problem in installing R packages on linux

[Uwe Ligges]

man4ish wrote:
> I am facing problem in installing the R package on linux .
> When i put the command install.packages("BART")

The screenshot is not there, but I suspect you want to install package 
"BARD" rather than "BART".

Uwe Ligges


> Then it asks for selecting the mirror , i have selected the mirrror , but it
> is showing no package in repository .I have selected different different
> repository still i am getting the same error what can i do , please help me
> out.i am sending the screenshot of unix terminal .
> I will be thankful to you.Please help me out .  
> http://www.nabble.com/file/p16760370/manish.png manish.png

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Re: [R] multivariate time series

[Pfaff, Bernhard Dr.]

Hello Erin,

have you considered the package bundle "dse" on CRAN?


Best,
Bernhard

>
>Dear R People:
>
>I was looking to see if there are any functions for Vector 
>ARMA modeling.
>
>I found Vector AR(p) but no Vector ARMAs.
>
>Thanks,
>Erin
>
>
>-- 
>Erin Hodgess
>Associate Professor
>Department of Computer and Mathematical Sciences
>University of Houston - Downtown
>mailto: [EMAIL PROTECTED]
>
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>
*
Confidentiality Note: The information contained in this ...{{dropped:10}}

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Re: [R] spatialpixelsdataframe

[Paul Hiemstra]

Dave Depew wrote:
> I have a spatialpixelsdataframe containing bathymetry data. Is it 
> possible to save this as  something similar to the meuse.grid so it can 
> be loaded without having to run the spatial interpolation each time the 
> script is called?
> I don't see a straightforward method in the sp documentation.
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>   
Hi Dave,

You can save the SpatialPixelsDataFrame to a file using:

save(SPDF_object, file ="test.rda")

And reload it with:

load(test.rda)

This is not specific to the sp-package. These kinds of questions are 
better to post to the r-sig-geo mailing list.

Paul

-- 
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
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Re: [R] vector in filename

[[Ricardo Rodriguez] Your XEN ICT Team]

Hi,

Simon Blomberg wrote:
> How about this:
>
> x <- 1
> y <- 1
> mmax <- 10
>
> my.files <- paste("foo", x:mmax, ".png", sep="")
>
> for (i in my.files) {
>   png(filename=i, pointsize=20, width=600, height=600, units="px",
>   bg="#eaedd5")
>   plot(x, y)
>   dev.off()
>   x <- x+1
>   y <- y+1
> }
>   

It does the trick! Thanks.
> Normally I would avoid for loops, but I think this application is a
> legitimate use.

Please, why do you avoid looping normally? Thanks again.

Greetings,

Ricardo

-- 
Ricardo Rodríguez
Your XEN ICT Team

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[R] Overall p-value from a factor in a coxph fit

[Kåre Edvardsen]

Hi all.

If I run the simple regression when x is a categorical variable ( x <-
factor(x) ):

> MyFit <-coxph( Surv(start, stop, event) ~ x )

How can I get the overall p-value on x other than for each dummy
variable?

> anova(MyFit)

does NOT provide that information as previously suggested on the list.

All the best,
Kare

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[R] validation of logistic regression model with weighted presences and absences

[Eva Mosner]

Hello everyone!

I want to validate logistic regression models of species distrubution
data where presences and absences are weighted differently.
I used lrm from Design package but unfortunately, validate.lrm ignores
weights in the validation process.
Has anyone an idea (package, code) how I can do the validation including
weights?

Thanks a lot!

Eva

[EMAIL PROTECTED]

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Re: [R] EM algorithm for multiple-locus haplotypes frequencies

[David Duffy]

From: "Marcin Kozak" <[EMAIL PROTECTED]>
Subject: [R] EM algorithm for multiple-locus haplotypes frequencies
> Hi all,
> 
> I've been looking in R for an EM algorithm adjusted for multiple-locus
> haplotypes frequencies, but failed in 100%. Has anyone heard of
> anything of this kind in R?
>

Look at all the libraries whose name starts haplo eg haplo.stats.


-- 
| David Duffy (MBBS PhD) ,-_|\
| email: [EMAIL PROTECTED]  ph: INT+61+7+3362-0217 fax: -0101  / *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v

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[R] how to find the multiregression on the

[man4ish]

I am trying to calculate the multi regression for the follwing data

0 1 2 3 7 5 0 4 4 3
0 3 4 5 4 0 5 4 5 4
0 1 1 0 1 0 1 1 1 0
1 0 4 5 6 1 2  3 2 1

keeping Ist column as dependent variable and other as independent
varialbles,how can i do this using lm  funciotn in stats please send me the
code for this , i will really thankful to you manish gupta 
http://www.nabble.com/file/p16760374/inp.txt inp.txt 
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[R] space between plots

[Agustin Lobo]

I've set

layout(matrix(c(1,3,2,4),ncol=2))
and

par(mar=c(0, 4, 4, 0) + 0.0) and
par(mar=c(0, 0, 4, 3) + 0.0)

for the upper-left and upper-right plots, but
still get an space between both plots,

is there any way to completely eliminate that space?

Thanks

Agus
-- 
Dr. Agustin Lobo
Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
LLuis Sole Sabaris s/n
08028 Barcelona
Spain
Tel. 34 934095410
Fax. 34 934110012
email: [EMAIL PROTECTED]
http://www.ija.csic.es/gt/obster

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Re: [R] Help with using 'get' function and variable scope

[Peter Waltman]

Hi Duncan -

Thanks for the reply.  Yeah, I understand what I'm doing is a bit weird, but
I'm actually calling a few functions w/in the for-loop that need the value
of the "i" var, and because I was a bit confused by the concept of
environments, I was hoping to avoid having to pass it in as an arg to each
function.

Thanks,

Peter

On Thu, Apr 17, 2008 at 7:25 PM, Duncan Murdoch <[EMAIL PROTECTED]>
wrote:

> On 17/04/2008 5:37 PM, Peter Waltman wrote:
>
> > Hi -
> >
> > I'm having a really hard time w/understanding R's get function, and
> > would
> > appreciate any help with this.
> >
> > Specifically, I'm using a for loop to call a function.  I'd like the
> > function to have access to the variable being incremented in the
> > for-loop,
> > i.e.
> >
> > t.fn <- function() return( get( "i" ) )
> >
> > t.fn2 <- function() {
> > for ( i in 1:5 )
> > cat( t.fn(), "\n" )
> >
> > }
> >
> > However, I keep getting err msg's from the 'get' function about how it
> > can't
> > find the 'i' variable.
> >
> > I've tried various combinations w/in the get fn, i.e. passing inherits=T
> > (should be the default val according to R's help) and envir=sys.frame().
> >
> > As I understand it, 'get' should search the enclosing environments,
> > which I
> > assume would be the call-stack of the functions.  If not, could someone
> > clarify?
> >
>
> The R Language manual describes this; R uses lexical scope.  get() will
> search the calling environment, and its parent -- which in your case is
> where t.fn was defined -- and the parent of that environment, etc.  The call
> stack is not searched.
>
> There are ways to look up the stack; passing envir=parent.frame() to get
> will work for your needs.  But it's not a natural thing to do in R; it means
> your t.fn wouldn't work if it was called from anywhere but t.fn2.  So why
> not define it there, and then i would be visible to it without this
> trickery?  I.e.
>
> t.fn2 <- function() {
>  t.fn <- function() return( i )
>  for ( i in 1:5 )
> cat( t.fn(), "\n" )
> }
>
> Duncan Murdoch
>
>
> > Thanks,
> >
> > Peter
> >
> > p.s.  when I define t.fn to be:
> >
> >  t.fn<- function() {
> >for ( j in sys.nframe():0 ) cat( j,":",ls( sys.frame( j ) ), "\n" )
> > }
> > and call that in t.fn2(), I do eventually see the 'i' variable, i.e.
> >
> > > t.fn2()
> > >
> > 2 : j
> > 1 : i
> > 0 : test t.fn t.fn2 t.fn3
> >
> >[[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>

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[R] Permanent change to the working directory

[francogrex]

Dear helpers,
I've looked in the help files (maybe not very thoroughly but I looked) and I
couldn't find a straightforward way to permanently set the working directory
(where I save and read files). Each time I startup R the working dir is
automatically "C:/R/bin" [using:getwd()], and I know I can change it using
setwd [for example setwd("C:/R/DATA"), but it's only a transient change for
the session, when I close and start a new R session it's in "C:/R/bin"
again. How can I set it definitively to "C:/R/DATA" without having to redo
it every session? Thanks
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Re: [R] Permanent change to the working directory

[Eik Vettorazzi]

On windows machines you could change the `Start in' field of the desktop 
shortcut for R to the desired working directory - you will find this in 
the properties of the shortcut. You could easily create several 
shortcuts for different projects this way.

You may also consider changing your .Rprofile, see ?.Rprofile

hth.


francogrex schrieb:
> Dear helpers,
> I've looked in the help files (maybe not very thoroughly but I looked) and I
> couldn't find a straightforward way to permanently set the working directory
> (where I save and read files). Each time I startup R the working dir is
> automatically "C:/R/bin" [using:getwd()], and I know I can change it using
> setwd [for example setwd("C:/R/DATA"), but it's only a transient change for
> the session, when I close and start a new R session it's in "C:/R/bin"
> again. How can I set it definitively to "C:/R/DATA" without having to redo
> it every session? Thanks
>   

-- 
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

T ++49/40/42803-8243
F ++49/40/42803-7790

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Re: [R] problem in installing R packages on linux

[man4ish]

Uwe Ligges-3 wrote:
> 
> 
> 
> man4ish wrote:
>> I am facing problem in installing the R package on linux .
>> When i put the command install.packages("BART")
> 
> The screenshot is not there, but I suspect you want to install package 
> "BARD" rather than "BART".
> 
> Uwe Ligges
> 
> 
>> Then it asks for selecting the mirror , i have selected the mirrror , but
>> it
>> is showing no package in repository .I have selected different different
>> repository still i am getting the same error what can i do , please help
>> me
>> out.i am sending the screenshot of unix terminal .
>> I will be thankful to you.Please help me out .  
>> http://www.nabble.com/file/p16760370/manish.png manish.png
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 
No i am trying to install  BART which is valid name , i have 30-40 times for
other packages still facing the same pblm .How can i rectify this.Please
help me out.
- Show quoted text -
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Re: [R] Permanent change to the working directory

[Chuck Cleland]

On 4/18/2008 3:15 AM, francogrex wrote:
> Dear helpers,
> I've looked in the help files (maybe not very thoroughly but I looked) and I
> couldn't find a straightforward way to permanently set the working directory
> (where I save and read files). Each time I startup R the working dir is
> automatically "C:/R/bin" [using:getwd()], and I know I can change it using
> setwd [for example setwd("C:/R/DATA"), but it's only a transient change for
> the session, when I close and start a new R session it's in "C:/R/bin"
> again. How can I set it definitively to "C:/R/DATA" without having to redo
> it every session? Thanks

?Startup

-- 
Chuck Cleland, Ph.D.
NDRI, Inc. (www.ndri.org)
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894

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[R] Is there any function to skip a loop in a for loop ?

[Ng Stanley]

Hi,

Is there any function to skip a loop in a for loop ?

Thanks
Stanley

[[alternative HTML version deleted]]

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Re: [R] Is there any function to skip a loop in a for loop ?

[Gabor Csardi]

next
break

Another 'Introduction to R', or even ?"for" question

G.

On Fri, Apr 18, 2008 at 04:55:01PM +0800, Ng Stanley wrote:
> Hi,
> 
> Is there any function to skip a loop in a for loop ?
> 
> Thanks
> Stanley
> 
>   [[alternative HTML version deleted]]
> 
> __
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-- 
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Re: [R] Permanent change to the working directory

[Udo]

If you have an R-icon on the desktop, use the right mouse button and
go to "properties". At the "execute in" line insert
your data directory "C:/R/DATA".

Hope it helps
Udo


Zitat von francogrex <[EMAIL PROTECTED]>:

>
> Dear helpers,
> I've looked in the help files (maybe not very thoroughly but I looked) and I
> couldn't find a straightforward way to permanently set the working directory
> (where I save and read files). Each time I startup R the working dir is
> automatically "C:/R/bin" [using:getwd()], and I know I can change it using
> setwd [for example setwd("C:/R/DATA"), but it's only a transient change for
> the session, when I close and start a new R session it's in "C:/R/bin"
> again. How can I set it definitively to "C:/R/DATA" without having to redo
> it every session? Thanks
> --
> View this message in context:
>
http://www.nabble.com/Permanent-change-to-the-working-directory-tp16761149p16761149.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>




Udo KN G
  Ö I

Clinic for Child an Adolescent Psychiatry
Philipps University of Marburg / Germany

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Re: [R] Is there any function to skip a loop in a for loop ?

[Eik Vettorazzi]

see ?next
hth.


Ng Stanley schrieb:
> Hi,
>
> Is there any function to skip a loop in a for loop ?
>
> Thanks
> Stanley
>
>   [[alternative HTML version deleted]]
>
> __
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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
> and provide commented, minimal, self-contained, reproducible code.
>   

-- 
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

T ++49/40/42803-8243
F ++49/40/42803-7790

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Re: [R] Permanent change to the working directory

[Prof Brian Ripley]

This is answered in rw-FAQ Q2.5 !

On Fri, 18 Apr 2008, Eik Vettorazzi wrote:


On windows machines you could change the `Start in' field of the desktop
shortcut for R to the desired working directory - you will find this in
the properties of the shortcut. You could easily create several
shortcuts for different projects this way.

You may also consider changing your .Rprofile, see ?.Rprofile

hth.


francogrex schrieb:

Dear helpers,
I've looked in the help files (maybe not very thoroughly but I looked) and I
couldn't find a straightforward way to permanently set the working directory
(where I save and read files). Each time I startup R the working dir is
automatically "C:/R/bin" [using:getwd()], and I know I can change it using
setwd [for example setwd("C:/R/DATA"), but it's only a transient change for
the session, when I close and start a new R session it's in "C:/R/bin"
again. How can I set it definitively to "C:/R/DATA" without having to redo
it every session? Thanks



--
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

T ++49/40/42803-8243
F ++49/40/42803-7790

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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)
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Re: [R] space between plots

[jim holtman]

When I try this:

layout(matrix(c(1,3,2,4),ncol=2))


par(mar=c(0, 4, 4, 0) + 0.0)
plot(1)
par(mar=c(0, 0, 4, 3) + 0.0)
plot(2)
plot(3)
plot(4)

the upper left and right are butted together.  Exactly what 'space'
are you talking about?

On Fri, Apr 18, 2008 at 4:19 AM, Agustin Lobo <[EMAIL PROTECTED]> wrote:
> I've set
>
> layout(matrix(c(1,3,2,4),ncol=2))
> and
>
> par(mar=c(0, 4, 4, 0) + 0.0) and
> par(mar=c(0, 0, 4, 3) + 0.0)
>
> for the upper-left and upper-right plots, but
> still get an space between both plots,
>
> is there any way to completely eliminate that space?
>
> Thanks
>
> Agus
> --
> Dr. Agustin Lobo
> Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
> LLuis Sole Sabaris s/n
> 08028 Barcelona
> Spain
> Tel. 34 934095410
> Fax. 34 934110012
> email: [EMAIL PROTECTED]
> http://www.ija.csic.es/gt/obster
>
> __
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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[R] spdep question - Moran's I

[Haenlein.Michael]

Dear all,

I would like to calculate a Moran's I statistic using the moran function in the 
spdep package. The problem I'm having deals with how to create the listw object.

My data stems from the area of social network analysis. I have list of poeple 
and for each pair of them I have a measure of their relationship strength. So 
my dataset looks like: Jim; Bob; 0.5

This measure of relationship strength can be interpreted like a distance 
measure in a spatial model.

I assume that I need to work with the nb2listw function, but I am lost what to 
do in detail.

Thanks very much for your help in advance!

Michael Haenlein
Assistant Professor of Marketing
ESCP-EAP European School of Management
Paris, France

[[alternative HTML version deleted]]

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[R] Vertical bars with barchart

[G. Draisma]

Hallo,
What is the right way to get vertical bars in
a barchart?

For instance
   barchart(VADeaths,
   key=simpleKey(colnames(VADeaths),points=F,rectangles=T))
gives what I need,
only I would like the bars to be vertical.
But
   barchart(VADeaths,horizontal=F,
   key=simpleKey(colnames(VADeaths),points=F,rectangles=T))
does not give what I need,
and I do not understand how to change the dimensions
accordingly.

Thanks,
Gerrit.




-- 
Gerrit Draisma
Department of Public Health
Erasmus MC, University Medical Center Rotterdam
Room AE-103
P.O. Box 2040 3000 CA  Rotterdam The Netherlands
Phone: +31 10 7043124 Fax: +31 10 010-7038474
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Re: [R] problem in installing R packages on linux

[Neil Shephard]

man4ish wrote:
> 
> 
> No i am trying to install  BART which is valid name , i have 30-40 times
> for other packages still facing the same pblm .How can i rectify
> this.Please help me out.
> 

Rather than sending a screenshot of a terminal (and note the posting
guidelines with regards to attachments), if you copy and paste the text that
shows the commands you are typing and the errors you are getting it will be
more informative to those who you are seeking help from.

Otherwise its people are just left to guess what the cause is.

Neil
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Re: [R] problem in installing R packages on linux

[Stefan Grosse]

On Fri, 18 Apr 2008 01:47:43 -0700 (PDT) man4ish wrote:
M> > The screenshot is not there, but I suspect you want to install
M> > package "BARD" rather than "BART".
M> > 
M> > Uwe Ligges
M> No i am trying to install  BART which is valid name , i have 30-40
M> times for other packages still facing the same pblm .How can i
M> rectify this.Please help me out.

You are wrong. There is no BART package on CRAN. Probably you mean BART
models which are in the BayesTree package:

http://cran.r-project.org/web/packages/BayesTree/index.html

hth
Stefan

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Re: [R] Matched pairs with two data frames

[Patrick Connolly]

On Wed, 16-Apr-2008 at 11:58AM +0200, Udo wrote:


|> I only "need" line 1, 6 and 9. To show this,
|> I added "needed" by hand.
|> 
|>age school out1 out2   needed
|> 11 10  9.5  1.1  yes
|> 21 10  9.5  2.0   no
|> 31 10  9.5  3.5   no
|> 41 10  9.5  4.9   no
|> 51 10  2.3  1.1   no
|> 61 10  2.3  2.0   yes
|> 71 10  2.3  3.5   no
|> 81 10  2.3  4.9   no
|> 92 20  3.3  6.5   yes
|> 10   2 20  4.1  6.5   no
|> 11   2 20  5.9  6.5   no
|> 12   3 33   NA  5.2   no
|> 13   4 11  4.6   NA   no
|> 
|> >Whatever it is, can't you subset them out?
|> Yes, that´s the problem. To describe what I mean, I added the
|> variable needed by hand. I don´t know how to compute such a
|> variable to subset.
|> 
|> 
|> My final data frame should look like this:
|> age school out1 out2 nedded
|> 11 10  9.5  1.1  yes
|> 61 10  2.3  2.0  yes
|> 92 20  3.3  6.5  yes


Now that I know what you want, I can see what can work.  Undoubtedly,
there are far more elegant ways of doing it, but this will work.  

  xx <- merge(treat, control)
  out <- xx[1, ] # set up the out dataframe
  for(i in 2:nrow(xx)){
x.i <- xx[i, ]
kk <- logical(4)
for(j in 1:4)
  kk[j] <- x.i[, j]%in%out[, j]
if(!kk[4]){ # don't add to output if last column value exists
  if(!all(kk[1:3])) # a different combination of first 3 cols
out <- rbind(out, x.i)
}   
  }
  out


  age school out1 out2
1   1 10  9.5  1.1
6   1 10  2.3  2.0
9   2 20  3.3  6.5

If you have very large dataframes, you might like to improve on it.


HTH


-- 
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   ___Patrick Connolly   
 {~._.~} Great minds discuss ideas
 _( Y )_Middle minds discuss events 
(:_~*~_:)Small minds discuss people  
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~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

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Re: [R] Vertical bars with barchart

[Stefan Grosse]

On Fri, 18 Apr 2008 12:00:13 +0200 G. Draisma wrote:
GD>barchart(VADeaths,horizontal=F,
GD>key=simpleKey(colnames(VADeaths),points=F,rectangles=T))
GD> does not give what I need,

Works for me. Do you have the current R (2.6.2) and lattice?

btw. it also works with
barchart(VADeaths, horizontal=F,auto.key=T)

Stefan

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[R] Working with graphs.

[hoogeebear]

Hi,

Im created some pie charts using R. I have two segments, I am just wondering
how can I add a number to each segment that represents each each segment?
Also is there a way to change the colors of each segment?

Sorry if this frustrates anyone because of its simplicity, but I am new to
R. 

Thanks in advance.

BR,

Jack. 
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Re: [R] Working with graphs.

[jim holtman]

?pie

Look at the example which I think addresses most of your questions

On Fri, Apr 18, 2008 at 6:31 AM, hoogeebear <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
> Im created some pie charts using R. I have two segments, I am just wondering
> how can I add a number to each segment that represents each each segment?
> Also is there a way to change the colors of each segment?
>
> Sorry if this frustrates anyone because of its simplicity, but I am new to
> R.
>
> Thanks in advance.
>
> BR,
>
> Jack.
> --
> View this message in context: 
> http://www.nabble.com/Working-with-graphs.-tp16763349p16763349.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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Re: [R] Help with using 'get' function and variable scope

[Gabor Grothendieck]

If you define your functions in the loop you can it directly
since then the scoping rules work in your favor:

for(i in 1:4) {
  f <- function() i*i
  print(f())
}

or via lapply:

F <- function(i) { f <- function() i*i; print(f()) }
lapply(1:4, F)

Often the sort of situation you discuss is really an attempt
to use object oriented programming without realizing it.

The body of the loop is an object whose methods are the
functions.  The proto package
http://r-proto.googlecode.com
can deal with such situations as can direct manipulation of
R environments or the use of function bodies as wrappers,
e.g.
demo(scoping)



On Fri, Apr 18, 2008 at 2:00 AM, Peter Waltman <[EMAIL PROTECTED]> wrote:
> Hi Duncan -
>
> Thanks for the reply.  Yeah, I understand what I'm doing is a bit weird, but
> I'm actually calling a few functions w/in the for-loop that need the value
> of the "i" var, and because I was a bit confused by the concept of
> environments, I was hoping to avoid having to pass it in as an arg to each
> function.
>
> Thanks,
>
> Peter
>
> On Thu, Apr 17, 2008 at 7:25 PM, Duncan Murdoch <[EMAIL PROTECTED]>
> wrote:
>
>
> > On 17/04/2008 5:37 PM, Peter Waltman wrote:
> >
> > > Hi -
> > >
> > > I'm having a really hard time w/understanding R's get function, and
> > > would
> > > appreciate any help with this.
> > >
> > > Specifically, I'm using a for loop to call a function.  I'd like the
> > > function to have access to the variable being incremented in the
> > > for-loop,
> > > i.e.
> > >
> > > t.fn <- function() return( get( "i" ) )
> > >
> > > t.fn2 <- function() {
> > > for ( i in 1:5 )
> > > cat( t.fn(), "\n" )
> > >
> > > }
> > >
> > > However, I keep getting err msg's from the 'get' function about how it
> > > can't
> > > find the 'i' variable.
> > >
> > > I've tried various combinations w/in the get fn, i.e. passing inherits=T
> > > (should be the default val according to R's help) and envir=sys.frame().
> > >
> > > As I understand it, 'get' should search the enclosing environments,
> > > which I
> > > assume would be the call-stack of the functions.  If not, could someone
> > > clarify?
> > >
> >
> > The R Language manual describes this; R uses lexical scope.  get() will
> > search the calling environment, and its parent -- which in your case is
> > where t.fn was defined -- and the parent of that environment, etc.  The call
> > stack is not searched.
> >
> > There are ways to look up the stack; passing envir=parent.frame() to get
> > will work for your needs.  But it's not a natural thing to do in R; it means
> > your t.fn wouldn't work if it was called from anywhere but t.fn2.  So why
> > not define it there, and then i would be visible to it without this
> > trickery?  I.e.
> >
> > t.fn2 <- function() {
> >  t.fn <- function() return( i )
> >  for ( i in 1:5 )
> > cat( t.fn(), "\n" )
> > }
> >
> > Duncan Murdoch
> >
> >
> > > Thanks,
> > >
> > > Peter
> > >
> > > p.s.  when I define t.fn to be:
> > >
> > >  t.fn<- function() {
> > >for ( j in sys.nframe():0 ) cat( j,":",ls( sys.frame( j ) ), "\n" )
> > > }
> > > and call that in t.fn2(), I do eventually see the 'i' variable, i.e.
> > >
> > > > t.fn2()
> > > >
> > > 2 : j
> > > 1 : i
> > > 0 : test t.fn t.fn2 t.fn3
> > >
> > >[[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> >
>
>[[alternative HTML version deleted]]
>
> __
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>

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[R] problem in installing R packages on linux

[Niels Steen Krogh]

install.packages("BayesTree") 

Is my guess for using function BART

/Niels

Niels Steen Krogh
Konsulent
ZiteLab ApS 

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[R] [R-pkgs] RExcelInstaller

[Erich Neuwirth]

RExcelInstaller_2.0-15

installs RExcel, an add-in for Excel, which connects R and Excel.

RExcel allows to transfer data between R and Excel,
writing VBA macros using R as a library for Excel,
and calling R functions as worksheet function in Excel.
RExcel integrates nicely with R Commander (Rcmdr),
turning R Commander's menus into Excel menus.
It comes with a comprehensive set of example worksheet
illustrating different usage scenarios.

This R package installs the Excel add-in for Excel versions
from 2000 to 2007. It only works on MS Windows (XP and Vista)

-- 
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Faculty of Computer Science
Computer Supported Didactics Working Group
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Re: [R] Problem with links in R website

[Friedrich . Leisch]

> On Thu, 17 Apr 2008 11:36:30 +0100,
> Robin Taylor (RT) wrote:

  > Not sure who to send this to...
  > On the books page http://www.r-project.org/doc/bib/R-books.html the entries
  > from [54] down have three forward slashes in the hyperlinks to publisher
  > info and so they don't work

Thanks a lot for the bug report, fixed in the SVN archive, will go
live later today.

Best,
Fritz

-- 
---
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Institut für Statistik  Tel: (+49 89) 2180 3165
Ludwig-Maximilians-Universität  Fax: (+49 89) 2180 5308
Ludwigstraße 33
D-80539 München http://www.statistik.lmu.de/~leisch
---
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  Münchner R Kurse --- http://www.statistik.lmu.de/R

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Re: [R] Help with using 'get' function and variable scope

[Duncan Murdoch]

On 18/04/2008 7:27 AM, Gabor Grothendieck wrote:
> If you define your functions in the loop you can it directly
> since then the scoping rules work in your favor:
> 
> for(i in 1:4) {
>   f <- function() i*i
>   print(f())
> }

f doesn't need to be in the loop, it just needs to be defined in the 
same environment as i was defined in.  Loops in R don't create new local 
frames.

Duncan Murdoch

> or via lapply:
> 
> F <- function(i) { f <- function() i*i; print(f()) }
> lapply(1:4, F)
> 
> Often the sort of situation you discuss is really an attempt
> to use object oriented programming without realizing it.
> 
> The body of the loop is an object whose methods are the
> functions.  The proto package
> http://r-proto.googlecode.com
> can deal with such situations as can direct manipulation of
> R environments or the use of function bodies as wrappers,
> e.g.
> demo(scoping)
> 
> 
> 
> On Fri, Apr 18, 2008 at 2:00 AM, Peter Waltman <[EMAIL PROTECTED]> wrote:
>> Hi Duncan -
>>
>> Thanks for the reply.  Yeah, I understand what I'm doing is a bit weird, but
>> I'm actually calling a few functions w/in the for-loop that need the value
>> of the "i" var, and because I was a bit confused by the concept of
>> environments, I was hoping to avoid having to pass it in as an arg to each
>> function.
>>
>> Thanks,
>>
>> Peter
>>
>> On Thu, Apr 17, 2008 at 7:25 PM, Duncan Murdoch <[EMAIL PROTECTED]>
>> wrote:
>>
>>
>>> On 17/04/2008 5:37 PM, Peter Waltman wrote:
>>>
 Hi -

 I'm having a really hard time w/understanding R's get function, and
 would
 appreciate any help with this.

 Specifically, I'm using a for loop to call a function.  I'd like the
 function to have access to the variable being incremented in the
 for-loop,
 i.e.

 t.fn <- function() return( get( "i" ) )

 t.fn2 <- function() {
 for ( i in 1:5 )
 cat( t.fn(), "\n" )

 }

 However, I keep getting err msg's from the 'get' function about how it
 can't
 find the 'i' variable.

 I've tried various combinations w/in the get fn, i.e. passing inherits=T
 (should be the default val according to R's help) and envir=sys.frame().

 As I understand it, 'get' should search the enclosing environments,
 which I
 assume would be the call-stack of the functions.  If not, could someone
 clarify?

>>> The R Language manual describes this; R uses lexical scope.  get() will
>>> search the calling environment, and its parent -- which in your case is
>>> where t.fn was defined -- and the parent of that environment, etc.  The call
>>> stack is not searched.
>>>
>>> There are ways to look up the stack; passing envir=parent.frame() to get
>>> will work for your needs.  But it's not a natural thing to do in R; it means
>>> your t.fn wouldn't work if it was called from anywhere but t.fn2.  So why
>>> not define it there, and then i would be visible to it without this
>>> trickery?  I.e.
>>>
>>> t.fn2 <- function() {
>>>  t.fn <- function() return( i )
>>>  for ( i in 1:5 )
>>> cat( t.fn(), "\n" )
>>> }
>>>
>>> Duncan Murdoch
>>>
>>>
 Thanks,

 Peter

 p.s.  when I define t.fn to be:

  t.fn<- function() {
for ( j in sys.nframe():0 ) cat( j,":",ls( sys.frame( j ) ), "\n" )
 }
 and call that in t.fn2(), I do eventually see the 'i' variable, i.e.

> t.fn2()
>
 2 : j
 1 : i
 0 : test t.fn t.fn2 t.fn3

[[alternative HTML version deleted]]

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 http://www.R-project.org/posting-guide.html
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>>>
>>[[alternative HTML version deleted]]
>>
>> __
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>

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[R] ts.plot() labeling x-axis

[Pologruto, Thomas]

Hello,

I have tried a few variants of a solution from the previous posts, but
perhaps my syntax is wrong.  I am using ts.plot(data_as_columns) and
would like the label the x axis using some labels (in my case minutes
after 9am).

Any ideas how to use the plot params and the Axis function to accomplish
this?

Any help is very appreciated.

Regards,
Tom  


==
Please access the attached hyperlink for an important electronic communications 
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Re: [R] Meaning of /, :, and %in% in lmer

[Douglas Bates]

On 4/16/08, Claus Wilke <[EMAIL PROTECTED]> wrote:
> Hello,

>  I asked this question a little while ago (
>  https://stat.ethz.ch/pipermail/r-help/2008-April/158761.html ) but got no
>  response. Can anybody explain to me the difference between /, :, and %in% in
>  the definition of random effects in lmer, such as:
>  (1|A/B), (1|A:B), (1|B %in% A)?

The first two, (1|A/B) and (1|A:B), are forms that lmer recognizes.
I'm not sure what the effect of the third form, (1|B %in% A), would be
and would not advise using it.

Most uses of the %in% operator in R at present are as a logical operator.

>  My understanding is that (1|A/B) is the same as (1|A) + (1|A:B), but I have
>  not seen this stated explicitly anywhere. And I don't understand why (1|A/B)
>  seems to be different from (1|A) + (1|B %in% A), isn't that what %in% means?

The short answer is that (1|A/B) is expanded to (1|A) + (1|A:B) so you
can choose whatever form makes sense to you.

There are different circumstances where a notation like (1|A/B) would
be used.  Some are reasonable choices and some are artifacts of
artificial ways of assigning labels to factor levels.  Rather than my
trying to guess what kind of application you have in mind, could you
describe a situation where you would want to fit an lmer model with
terms like that?

I am cc:ing the R-SIG-Mixed-Models list on this reply and I suggest we
move the discussion to that list.

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[R] Function redefinition - not urgent, but I am curious

[Alberto Monteiro]

This is just my curiousity working.

Suppose I write:

f1 <- function(x) x + 1
f2 <- function(x) 2 * f1(x)
f2(10)
# 22
f1 <- function(x) x - 1
f2(10)
# 18

This is quite obvious. But is there any way to define f2
in such a way that we "freeze" the definition of f1?

f1 <- function(x) x + 1
f2 <- function(x) 
# put something here
2 * f1(x)
# probably put something else here too

f2(10)
# 22
f1 <- function(x) x - 1
f2(10)
# 22 - f1 inside f2 does not change

Alberto Monteiro

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Re: [R] validation of logistic regression model with weighted presences and absences

[Frank E Harrell Jr]

Eva Mosner wrote:
> Hello everyone!
> 
> I want to validate logistic regression models of species distrubution
> data where presences and absences are weighted differently.
> I used lrm from Design package but unfortunately, validate.lrm ignores
> weights in the validation process.
> Has anyone an idea (package, code) how I can do the validation including
> weights?
> 
> Thanks a lot!
> 
> Eva
> 
> [EMAIL PROTECTED]

Code contributions to the predab.resample function in Design are welcomed.

Frank

-- 
Frank E Harrell Jr   Professor and Chair   School of Medicine
  Department of Biostatistics   Vanderbilt University

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Re: [R] Function redefinition - not urgent, but I am curious

[Gabor Grothendieck]

Try

f2 <- local({f1 <- f1; function(x) 2 * f1(x) })


On Fri, Apr 18, 2008 at 8:22 AM, Alberto Monteiro
<[EMAIL PROTECTED]> wrote:
> This is just my curiousity working.
>
> Suppose I write:
>
> f1 <- function(x) x + 1
> f2 <- function(x) 2 * f1(x)
> f2(10)
> # 22
> f1 <- function(x) x - 1
> f2(10)
> # 18
>
> This is quite obvious. But is there any way to define f2
> in such a way that we "freeze" the definition of f1?
>
> f1 <- function(x) x + 1
> f2 <- function(x)
> # put something here
> 2 * f1(x)
> # probably put something else here too
>
> f2(10)
> # 22
> f1 <- function(x) x - 1
> f2(10)
> # 22 - f1 inside f2 does not change
>
> Alberto Monteiro
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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Re: [R] Constrained Nelder-Mead

[Ben Bolker]

  ipc.com.co> writes:

> 
> Dear Mr,
> 
> I saw by the web your request about the code in Language C of the method
Nelder-Mead with constraints,
> I would like if you got the program, it's posible you can help us to get the
code in C,
> 


  This doesn't make much sense.
  I can imagine that you're looking for an implementation of
a constrained Nelder-Mead algorithm in C.  If there were one
in R (which there isn't, you could pull it out of the code).
You might search for COBYLA in http://www.jeannot.org/~js/code/index.en.html ...

  Ben Bolker

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[R] Labels in cluster nodes

[Ramon Hidalgo]

Hello all,

I am novice in R,
I've  started to work with cluster, and in the cluster i obtain:

$merge
  [,1] [,2]
 [1,]  -1  -2
 [2,]  -3   1

$height
 [1]   2.291288   3.834058

$order
 [1]  1 2 3


When i use plot, obtain (in 'chargraphics'):

|
   ---
   |  |
   |  |
   |  |
---   |
| |   |
| |   |
A B   C

and i like put in each node the cluster stage index


|
   -2-
   |  |
   |  |
   |  |
---1---  |
|  |  |
|  |  |
AB C

How do I have  this dendrogram?

Thank's
Ramón Hidalgo

[[alternative HTML version deleted]]

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Re: [R] Function redefinition - not urgent, but I am curious

[Dimitris Rizopoulos]

you could define 'f1' inside 'f2' or assign 'f1' to a new environemnt 
(or use local()):

# 1st
f2 <- function(x){
f1 <- function(x) x + 1
2 * f1(x)
}

f2(10)
f1 <- function(x) x - 1
f2(10)

# 2nd
myenv <- new.env()
assign("f1", function(x) x + 1, myenv)
f2 <- function(x){
f1 <- get("f1", envir = myenv)
2 * f1(x)
}
f1 <- function(x) x - 1
f2(10)


I hope it helps.

Best,
Dimitris


Dimitris Rizopoulos
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://med.kuleuven.be/biostat/
 http://www.student.kuleuven.be/~m0390867/dimitris.htm


- Original Message - 
From: "Alberto Monteiro" <[EMAIL PROTECTED]>
To: 
Sent: Friday, April 18, 2008 2:22 PM
Subject: [R] Function redefinition - not urgent, but I am curious


> This is just my curiousity working.
>
> Suppose I write:
>
> f1 <- function(x) x + 1
> f2 <- function(x) 2 * f1(x)
> f2(10)
> # 22
> f1 <- function(x) x - 1
> f2(10)
> # 18
>
> This is quite obvious. But is there any way to define f2
> in such a way that we "freeze" the definition of f1?
>
> f1 <- function(x) x + 1
> f2 <- function(x)
> # put something here
> 2 * f1(x)
> # probably put something else here too
>
> f2(10)
> # 22
> f1 <- function(x) x - 1
> f2(10)
> # 22 - f1 inside f2 does not change
>
> Alberto Monteiro
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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Re: [R] 3-D-Plot

[Uwe Ligges]

Edwin Sendjaja wrote:
> Hi Uwe,
> 
> I decided to use scatterplot3d, because it looks better.
> I have some questions:
> 
> Is it possible to get 1 axis( for example: z-axis) not as numeric, but as 
> character.
> 
> Because I have date set like this:
> 
> x=relative Time: 0,3 ms; 0,5ms, etc
> y=Delay:10 ms, 20 ms, etc
> z= Host: cnn.com, heise.de,etc


See ?scatterplot3d. You can use arguments x.ticklabs, y.ticklabs, 
z.ticklabs in order top specify character strings.


> If no, can you tell me little how to modify the code to get this. Thank you.
> 
> another question:
> 
> How can I change the width line of the axis (x,y,z). The default line is for 
> me too thin.

par(lwd=2) or more, for example.


First example from ?scatterplot3d  but with some other labels on x axis 
and thick lines:

   z <- seq(-10, 10, 0.01)
   x <- cos(z)
   y <- sin(z)
   par(lwd=3)
   scatterplot3d(x, y, z, highlight.3d=TRUE, col.axis="blue",
   col.grid="lightblue", main="scatterplot3d - 1", pch=20,
   x.ticklabs=paste(seq(0.3, 1.1, by=0.2), "ms"),
   xlab="relative Time")

Best wishes,
Uwe


> 
> Thank you in advance,
> 
> 
> Edwin Sendjaja 
> 
> Am Donnerstag, 17. April 2008 14:43:39 schrieb Uwe Ligges:
>> Edwin Sendjaja wrote:
>>> Hi Uwe,
>>>
>>> Thanks for your answer.
>>>
>>> What is the different between rgl and scatterplot3d? I dont need a
>>> graphik like vulcano. I just need 3D-"dot"-plot.
>> Sure, rgl can do it as well.
>> Difference is that scatterplot3d is based on R's standard devices while
>> rgl is based on an OpenGL device. Hence rgl is much more flexible and
>> can rotate things and easily draws nice transparent forms, but
>> scatterplot3d is nice for printing to 2D in different formats at the end.
>>
>> Uwe
>>
>>> Am Donnerstag, 17. April 2008 09:03:17 schrieb Uwe Ligges:
 Edwin Sendjaja wrote:
> Hello,
>
> I've got some problems. I hope someone can help me.
>
> First question:
> I am trying to get grid on scatterplot3d (from scatterplot3d package).
> It seems that scatterplot3d draw on grip on X and Z side. Is it
> possible to get Grid on the whole Box?
 At least there is no build in function to do it.

> Second question:
> Is it possible to use the standard package drawing 3d-plot(without
> scatterplot3d) ?because now I have already 2d-plot. I just want to add
> the z-axis.
 See, for example, ?cloud in package "lattice", ?plot3d in package "rgl",

> Third question:
> What is the best 3d-plot? it seems that scatterplot3 doesn't support
> anything( like turning the box vertically. I think, angle parameter
> just turn the box horisontally. I might wrong with this.
 You are right.

 Best wishes,
 Uwe

> Thank a lot in advance
>
> Edwin
>
> __
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> PLEASE do read the posting guide
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> minimal, self-contained, reproducible code.
 __
 R-help@r-project.org mailing list
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 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html and provide commented,
 minimal, self-contained, reproducible code.
>>> __
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html and provide commented,
>>> minimal, self-contained, reproducible code.
>> __
>> R-help@r-project.org mailing list
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>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html and provide commented, minimal,
>> self-contained, reproducible code.

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Re: [R] space between plots

[Agustin Lobo]

ok, I see: I was confused because the box
goes a bit beyond the axes:
layout(matrix(c(1,3,2,4),ncol=2))
par(mar=c(0, 4, 4, 0) + 0.0)
plot(1,yaxt="n")
par(mar=c(0, 0, 4, 3) + 0.0)
plot(2,bty="n",yaxt="n")

...and I'm not
plotting the box in my graphic.

Thanks

Agus
jim holtman escribió:
> When I try this:
> 
> layout(matrix(c(1,3,2,4),ncol=2))
> 
> 
> par(mar=c(0, 4, 4, 0) + 0.0)
> plot(1)
> par(mar=c(0, 0, 4, 3) + 0.0)
> plot(2)
> plot(3)
> plot(4)
> 
> the upper left and right are butted together.  Exactly what 'space'
> are you talking about?
> 
> On Fri, Apr 18, 2008 at 4:19 AM, Agustin Lobo <[EMAIL PROTECTED]> wrote:
>> I've set
>>
>> layout(matrix(c(1,3,2,4),ncol=2))
>> and
>>
>> par(mar=c(0, 4, 4, 0) + 0.0) and
>> par(mar=c(0, 0, 4, 3) + 0.0)
>>
>> for the upper-left and upper-right plots, but
>> still get an space between both plots,
>>
>> is there any way to completely eliminate that space?
>>
>> Thanks
>>
>> Agus
>> --
>> Dr. Agustin Lobo
>> Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
>> LLuis Sole Sabaris s/n
>> 08028 Barcelona
>> Spain
>> Tel. 34 934095410
>> Fax. 34 934110012
>> email: [EMAIL PROTECTED]
>> http://www.ija.csic.es/gt/obster
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
> 
> 
> 

-- 
Dr. Agustin Lobo
Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
LLuis Sole Sabaris s/n
08028 Barcelona
Spain
Tel. 34 934095410
Fax. 34 934110012
email: [EMAIL PROTECTED]
http://www.ija.csic.es/gt/obster

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Re: [R] spatialpixelsdataframe

[Dave Depew]

Thanks Paul,
Will keep that in mind for my next query :-)

Paul Hiemstra wrote:
> Dave Depew wrote:
>> I have a spatialpixelsdataframe containing bathymetry data. Is it 
>> possible to save this as  something similar to the meuse.grid so it 
>> can be loaded without having to run the spatial interpolation each 
>> time the script is called?
>> I don't see a straightforward method in the sp documentation.
>>
>> __
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>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>   
> Hi Dave,
>
> You can save the SpatialPixelsDataFrame to a file using:
>
> save(SPDF_object, file ="test.rda")
>
> And reload it with:
>
> load(test.rda)
>
> This is not specific to the sp-package. These kinds of questions are 
> better to post to the r-sig-geo mailing list.
>
> Paul
>

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Re: [R] survreg with frailty

[Terry Therneau]

  The combination of survreg + gamma frailty = invalid model, i.e., the example
that you quote.
  
  I did not realize that this had been added to the survreg help file until 
very 
recently.  I will try to fix the oversight.  Other, more detailed documentation 
states that Gaussian frailty + AIC is the only valid random effects choice for 
survreg.  
  
  Details: frailty(x) with no optional arguments defaults to "mle" as the 
method 
of choosing the variance of the random effect, via a calculation that is 
specific to the Cox model.  
  
Terry Therneau

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Re: [R] Help with using 'get' function and variable scope

[Gabor Grothendieck]

On Fri, Apr 18, 2008 at 7:49 AM, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> On 18/04/2008 7:27 AM, Gabor Grothendieck wrote:
> > If you define your functions in the loop you can it directly
> > since then the scoping rules work in your favor:
> >
> > for(i in 1:4) {
> >  f <- function() i*i
> >  print(f())
> > }
> >
>
> f doesn't need to be in the loop, it just needs to be defined in the same
> environment as i was defined in.  Loops in R don't create new local frames.
>

That's a good point. Do you know if R will optimize out constant expressions
from a loop?

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Re: [R] vector in filename

[hadley wickham]

On Thu, Apr 17, 2008 at 8:05 PM, [Ricardo Rodriguez] Your XEN ICT Team
<[EMAIL PROTECTED]> wrote:
> Hi,
>
>  I am trying to generate a group of graphics with an iteration. Some
>  thing like this...
>
>  x=1
>  y=1
>  max=10
>  myfiles <- paste("foo", x:max, ".png", sep="")
>  while (x =< max)
> {
> png(file=myfiles, pointsize = 20, width = 600, height = 600,
>  units = "px", bg="#eaedd5")
> plot(x,y)
> dev.off()
> x=x+1
> y=y+1
> }
>
>  I am getting only one *.png file with the name of the first position in
>  myfiles and the content of the last graphic in the iteration. Please,
>  could you tell me if it is possible to iterate file= in any other way?

Have you looked at ?png :

filename: the name of the output file. The page number is substituted
  if a C integer format is included in the character string, as
  in the default.  (The result must be less than 'PATH_MAX'
  characters long, and may be truncated if not. See
  'postscript' for further details.)  Tilde expansion is
  performed where supported by the platform.

so the default filename ("Rplot%03d.jpeg") already does what you want.

Hadley

-- 
http://had.co.nz/

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Re: [R] Help with using 'get' function and variable scope

[Duncan Murdoch]

On 4/18/2008 9:19 AM, Gabor Grothendieck wrote:
> On Fri, Apr 18, 2008 at 7:49 AM, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>> On 18/04/2008 7:27 AM, Gabor Grothendieck wrote:
>> > If you define your functions in the loop you can it directly
>> > since then the scoping rules work in your favor:
>> >
>> > for(i in 1:4) {
>> >  f <- function() i*i
>> >  print(f())
>> > }
>> >
>>
>> f doesn't need to be in the loop, it just needs to be defined in the same
>> environment as i was defined in.  Loops in R don't create new local frames.
>>
> 
> That's a good point. Do you know if R will optimize out constant expressions
> from a loop?

It doesn't.  Luke Tierney's experimental byte code compiler might do 
optimizations like that, but the regular evaluator does very little 
inspection of what  it is evaluating.

Duncan Murdoch

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Re: [R] Matched pairs with two data frames

[David Winsemius]

Udo <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]: 

> Daniel,
> thank you!
> 
> I want to perfrom the simplest way of matching:
> a one-to-one exact match (by age and school):
> for every case in "treat" find ONE case (if there is one) in
> "control" . The cases in "control" that could be matched, should be
> tagged as not available or taken away (deleted) from the control
> pool (thus, the used ones are not replaced).
> 
> #treatment group
> treat <- data.frame(age=c(1,1,2,2,2,4),
> school=c(10,10,20,20,20,11),
> out1=c(9.5,2.3,3.3,4.1,5.9,4.6))
> 
> #control group
> control <- data.frame(age=c(1,1,1,1,3,2),
>   school=c(10,10,10,10,33,20),
>   out2=c(1.1,2,3.5,4.9,5.2,6.5))
> 
> #one-to-one exat matching-alorithmus 
> 
> matched.data.frame <- ?
> 
> In my example I matched the cases "by hand" to make things clear.
> Case 1 from "treat" was matched with case 1 from "control",
> 2 with 2 and 3 with 6. Case 4, 5 and 6 could not be matched,
> because there is no "partner" in "control" .
> Thus my matched example data frame has 3 cases.

Is it really the case that SPSS would give the output that you describe 
without any warnings about non-uniqueness? How could they live with 
themselves after such arbitrary behavior? This link is evidence that 
SPSS may not behave as you allege.


If you really want to persist in what cannot possibly be called "one-
to-one exact matching", but instead "arbitrary convenience matching", 
then you need to construct a function that sequentially marches through 
"treat", grabs the first match (perhaps with something like):

> matched.first <- merge(treat[1,],control, by= c("age","school"))[1,]
> matched.first
  age school out1 out2
1   1 10  9.5  1.1

... except that the "1"'s would be replaced with an index variable, 
then mark that control as "taken" perhaps by using all of the variables 
as identifiers, and then attempt match/marking for each successive case 
among ("taken" == FALSE") controls.

-- 
David Winsemius

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[R] R CMD check Error

[Johannes Graumann]

Hi,

Can anyone give me a hint on what's wrong if "R CMD check " gives
me this error:

Rd files with unknown encoding:
  .Rd

I have checked that file over and over and can't find any weired characters
or some such.
How can I fix this?

Thanks for your time, Joh

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[R] [R-pkgs] new candisc package on CRAN

[Michael Friendly]

I'm happy to announce the candisc package, v 0.5-9, now on CRAN.

Generalized Canonical Discriminant Analysis

Description
This package includes functions for computing and visualizing 
generalized canonical discriminant analyses for a multivariate linear 
model. They are designed to provide low-rank visualizations of terms in 
a mlm via the plot method and the heplots package.

The methods are described in

Friendly, M. (2007). HE plots for Multivariate General Linear Models. 
Journal of Computational and Graphical Statistics, 16 (2), 421-444. 
http://www.math.yorku.ca/SCS/Papers/heplots.pdf

Friendly, M. (2006). Data Ellipses, HE Plots and Reduced-Rank Displays 
for Multivariate Linear Models: SAS Software and Examples. Journal of 
Statistical Software, 17(6), 1-42. http://www.jstatsoft.org/v17/i06/


-Michael


-- 
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University  Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA

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Re: [R] vector in filename

[[Ricardo Rodriguez] Your XEN ICT Team]

Thanks Hadley,

hadley wickham wrote:
> Have you looked at ?png :
>
> filename: the name of the output file. The page number is substituted
>   if a C integer format is included in the character string, as
>   in the default.  (The result must be less than 'PATH_MAX'
>   characters long, and may be truncated if not. See
>   'postscript' for further details.)  Tilde expansion is
>   performed where supported by the platform.
>
> so the default filename ("Rplot%03d.jpeg") already does what you want.
>
> Hadley
>
>   

Yes, I've read this help page. But as far as I understand, this only 
allows to generated a "paged" file name, but not to include the value of 
a variable in the file name. Foo is a dummy name. It is only the 
numerical part of the name what variates in the samples above. I guess 
it won't be difficult to get Foo from values in a vector once I 
understand how the whole thing does work.

Cheers,

Ricardo


-- 
Ricardo Rodríguez
Your XEN ICT Team

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Re: [R] vector in filename

[[Ricardo Rodriguez] Your XEN ICT Team]

Hi Richard, thanks for your input!

Richard Rowe wrote:
> which figures if you look at what you are doing line by line ... try it
>
>
> try something like:
>
> max=10
>
> for (i in 1:max){
> myfiles <- paste("foo", i, ".png", sep="") # generates names 
> foo1.png, foo2.png, etc
> png(file=myfiles, pointsize = 20, width = 600, height = 600, units = 
> "px", bg="#eaedd5")
>plot(x[i,],y[i,])# 
> you will need to change what you are plotting to something like 
> this
>dev.off()  }
>

There are at least two things I don't understand in your proposal:

1. How x and y variate? I mean, there is not x= or y= commands prior to 
enter for().
2. Whatever I set or not x and y, the code claims:

Error in x[i, ] : incorrect number of dimensions

Please, why to you use plot(x[i,],y[i,]) instead of plot(x,y)?

Thanks for your help,

Ricardo

-- 
Ricardo Rodríguez
Your XEN ICT Team

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Re: [R] R CMD check Error

[Prof Brian Ripley]

On Fri, 18 Apr 2008, Johannes Graumann wrote:

> Hi,
>
> Can anyone give me a hint on what's wrong if "R CMD check " gives
> me this error:
>
>Rd files with unknown encoding:
>  .Rd
>
> I have checked that file over and over and can't find any weired characters
> or some such.
> How can I fix this?

Remove the non-ASCII characters, or declare an encoding.

You didn't tell us your OS -- one good way I find on Linux to spot such 
characters is to use 'less 'in the C locale.  Another is something like 
(in R)

foo <- readLines("foo.Rd")
foo2 <- iconv(foo, "", "ASCII", sub="byte")
foo2[foo2 != foo]

which should show the line(s) concerned with non-ASCII characters 
highlighted as .

-- 
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] rzinb (VGAM) and dnbinom in optim

[Tim Howard]

Dear R-help gurus (and T.Yee, the VGAM maintainer) - 
I've been banging my head against the keyboard for too long now, hopefully 
someone can pick up on the errors of my ways...

I am trying to use optim to fit a zero-inflated negative binomial distribution. 
 No matter what I try I can't get optim to recognize my initial parameters. I 
think the problem is that dnbinom allows either 'prob' or 'mu' and I am trying 
to pass it 'mu'.  I've tried a wrapper function but it still hangs.  An example:

#set up dummy data,load VGAM, which is where I am getting the zero-inflated neg 
binom
#I get the same problem without VGAM, using dnbinom in the wrapper instead.
library(VGAM)
phi <- 0.09
size <- 0.7
munb <- 72
x <- rzinb(200, phi=phi, size=size, munb=munb)

#VGAM can fit using vglm... but I'd like to try optim
> fit <- vglm(x~1, zinegbinomial,trace=TRUE)
VGLMlinear loop  1 :  loglikelihood = -964.1915
VGLMlinear loop  2 :  loglikelihood = -964.1392
VGLMlinear loop  3 :  loglikelihood = -964.1392
> Coef(fit)
   phi   munb  k 
 0.1200317 62.8882874  0.8179183 

> #build my wrapper function for dzinb
> fncZiNB <- function(phi, size, munb){
+ -sum(dzinb(x=x,phi=phi, size=size, munb=munb,log=TRUE))}
> 
> #test the wrapper, seems to work.
> fncZiNB(phi=0.09, size=0.7, munb=72)
[1] 969.1435

#try it in optim
> solut <- optim(fn=fncZiNB,par=c(phi=0.09, munb=72, size=0.7),method = 
> "L-BFGS-B", hessian=TRUE)
Error in dnbinom(x = x, size = size, prob = prob, log = log.arg) : 
  argument "size" is missing, with no default

I have the same problem with dnbinom.
I'm sure I'm doing something obvious any suggestions?
Session info below. Thanks in advance.
Tim Howard
New York Natural Heritage Program

> sessionInfo()
R version 2.6.2 (2008-02-08) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats4splines   stats graphics  grDevices utils datasets  
methods  
[9] base 

other attached packages:
[1] VGAM_0.7-6  randomForest_4.5-23

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Re: [R] vector in filename

[[Ricardo Rodriguez] Your XEN ICT Team]

Mark,

Mark Leeds wrote:
> Oh, I'm sorry that didn't work. If you have time, can you resend it to me if
> you still have it ( I don't ) cause I'd like to see why. Thanks.

My fault! It does work! I've tried it this morning quickly, before 
leaving my SOHO, and it seems I was making any mistake. It does 
perfectly works as here...

x=1
y=1
max=10
myfiles <- paste("foo", x:max, ".png", sep="")
while (x =< max)
{
png(file=myfiles[x], pointsize = 20, width = 600, height = 600, 
units = "px", bg="#eaedd5")
plot(x,y)
dev.off()  
x=x+1
y=y+1
}

Thank you so much for your help and sorry for the noise!

Cheers,

Ricardo

-- 
Ricardo Rodríguez
Your XEN ICT Team

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[R] help me to debug this part of code?

[jinjin]

I am trying to solve the integration equation, for different values of K from
4 to 25, the integration is with respect to u,

Here is the equation:gamma(k/2) / ( sqrt(k-1)*gamma((k-1)/2) ) *
integrate(f= (1+u^2/k-1)^(-k/2), lower=0, upper= sqrt(a^2*k/(k+1-a^2)) ) = 
the similar expression as te left hand except k becomes k+1


my code is below, I don't know why R keep telling me the syntax wrong but I
am not clear, thanks.


f<-function(u,k){(1+u^2/(k-1))^(-k/2)}
g<-function(u,k){(1+u^2/k)^(-(k+1)/2)}

for(k in 4:25){
out<-uniroot(function(a){
m<-exp(lgamma(k/2)-lgamma((k-1)/2))*1/sqrt(k-1)
n<-exp(lgamma((k+1)/2)-lgamma(k/2)*1/sqrt(k)
m*integrate(f,lower=0,upper=sqrt(a^2*(k-1)/(k-a^2)),rel.tol=.Machine$double.eps^0.25)
-n*integrate(g,lower=0,upper=sqrt(a^2*k/(k+1-a^2)),rel.tol=.Machine$double.eps^0.25)
}
lower=1.4, upper=2)
print(unlist(out))}


-- 
View this message in context: 
http://www.nabble.com/help-me-to-debug-this-part-of-code--tp16763482p16763482.html
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] Overall p-value from a factor in a coxph fit

[Paul Johnson]

On Fri, Apr 18, 2008 at 3:06 AM, Kåre Edvardsen <[EMAIL PROTECTED]> wrote:
> Hi all.
>
>  If I run the simple regression when x is a categorical variable ( x <-
>  factor(x) ):
>
>  > MyFit <-coxph( Surv(start, stop, event) ~ x )
>
>  How can I get the overall p-value on x other than for each dummy
>  variable?
>
>  > anova(MyFit)
>
>  does NOT provide that information as previously suggested on the list.
>

It "should" work...  Here's a self contained example showing that
anova does give the desired significance test for an lm model.

> y <- rnorm(100)
> x <- gl(5,20)
> mod <- lm(y~x)
> anova(mod)
Analysis of Variance Table

Response: y
  Df  Sum Sq Mean Sq F value Pr(>F)
x  4   6.575   1.644  1.5125 0.2047
Residuals 95 103.237   1.087

If you provide a similar self contained example leading up to a coxph,
I would be glad to investigate your question.  You don't give enough
information for me to tell which version of coxph you are running, and
from what  package.

Suppose I "guess" that you are using the coxph from the package
"survival". If so, it appears to me there is a bug in that package at
the moment.  The methods anova.coxph and drop1.coxph did exist at one
time, until very recently.  There is a thread in r-help (which I found
by typing "RSiteSearch("anova.coxph")" ) discussing recent troubles
with anova.coxph.

http://finzi.psych.upenn.edu/R/Rhelp02a/archive/118481.html

As you see from the discussion in that thread, there used to be an
anova method for coxph, and in the version of survival I have now,
there is no such method.  The version I have is  2.34-1, Date:
 2008-03-31.

Here's what I see after I run "example(coxph)" in order to create some
coxph objects, on which I can test the diagnostics:

> drop1(test2)
Error in terms.default(terms1) : no terms component
> anova(test2)
Error in UseMethod("anova") : no applicable method for "anova"
>

In that survival package, I do find anova.survreg, but not
anova.coxph. If you are using the survival package, I'd suggest you
contact Thomas Lumley directly, since he maintains it.

I think if you had reported the exact error you saw, it would have
been easier for me to diagnose the trouble.

HTH
pj

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

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Re: [R] Problems with R2WinBUGS

[isabella]

   Hello,

   Further to my previous e-mail, I think I know why I am having problems with
   the initialization of model parameters in R2WinBUGS.   My model.bug file
   contains a portion of code which defines some pairwise odds ratios (e.g.,
   or[1,2], or[1,3], or[1,4], or[2,3], or[2,4], or[3,4])  as seen below:


   for (c in 1:(NT-1)) {

for (k in (c+1):NT) {

   or[c,k] <- log(d[k] - d[c])

}

   }


   Apparently, R2WinBUGS can't recognize these values because they form an
   incomplete  matrix.   In  trying to solve this issue, I arrived at the
   conclusion that R2WinBUGS may not be able to recognize WinBUGS parameters
   specified as a matrix (be it complete or incomplete).  Is my understanding
   correct?

   Any  thoughts  on  how  to  overcome this predicament would be greatly
   appreciated.  (Thank you very much to Peter Alspach for helping me to narrow
   down this problem.)

   Many thanks!

   Isabella

   Isabella R. Ghement, Ph.D.
   Ghement Statistical Consulting Company
   301-7031 Blundell Road, Richmond, B.C., Canada, V6Y 1J5
   Tel: 604-767-1250
   Fax: 604-270-3922
   E-mail: [EMAIL PROTECTED]
   Web: [2]www.ghement.ca

References

   1. mailto:[EMAIL PROTECTED]
   2. http://www.ghement.ca/
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[R] Legend Clipping

[Beck, Kenneth (STP)]

I am having trouble with legends clipping, not sure how to control that.
Here is my latest code to demo. I want the legend to show up in the
center of the window, in fairly large font. Right now, font is too
small, but if I increase it, the legend clips even more. In this
simplified example, the plots are dummy (I took them from an example),
my actual plots only have two bars, corresponding to the legend.

windows();
nf1 <- layout(matrix(1), widths=lcm(6), heights=lcm(6))
nf <- layout(matrix(c(1,2,5,0,3,4),3,2,byrow=TRUE), c(2.2,2.2),
c(2.2,1,2.2), TRUE)
layout.show(nf);
# par(mfrow=c(3,2));

par(font.axis=2);
par(font.lab=2);
# pmn=t(pmn);
tN <- table(Ni <- stats::rpois(100, lambda=5))
barplot(tN, col=rainbow(20))

# par (mfg=c(1,2));
par(font.axis=2);
par(font.lab=2);
tN <- table(Ni <- stats::rpois(100, lambda=5))
barplot(tN, col=rainbow(20))

# par (mfg=c(2,1));
par(font.axis=2);
par(font.lab=2);
tN <- table(Ni <- stats::rpois(100, lambda=5))
barplot(tN, col=rainbow(20))

# par (mfg=c(2,2));
par(font.axis=2);
par(font.lab=2);
tN <- table(Ni <- stats::rpois(100, lambda=5))
barplot(tN, col=rainbow(20))

# par (mfg=c(3,1));
plot(1, type="n", axes=FALSE, xlab="", ylab="",ylim=c(0,2),xlim=c(0,2));
# legend(1,0.8, legend = c("CPX","Home"), bty="n",
fill=c("blue","red"),lwd=1, cex=1, xjust=0.5, yjust=0.4);
# ltest=legend("center", legend = c("CPX","Home"), bty="n",
fill=c("blue","red"),lwd=1, cex=1, xjust=0.5,
yjust=0.4,trace=TRUE,plot=FALSE);
legend(0.5,0.5, legend = c("CPX","Home"), bty="n",
fill=c("blue","red"),lwd=1, cex=1, xjust=0.5, yjust=0.4);


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Re: [R] rzinb (VGAM) and dnbinom in optim

[Katharine Mullen]

I'm not going to look into what's happening in-depth but it looks like the
bounds for your parameters need to be set with care; the below (with
slight re-def. of your residual function) gives results that seem to match
vglm approximately, with 1e-10 standing in for a bound of 0 and 1-e-10
standing in for a bound of 1.

library(VGAM)
phi <- 0.09
size <- 0.7
munb <- 72
x <- rzinb(200, phi=phi, size=size, munb=munb)

fit <- vglm(x~1, zinegbinomial,trace=TRUE)

fncZiNB <- function(xx, x){
   phi <- xx[1]
   size <- xx[2]
   munb <- xx[3]
   -sum(dzinb(x=x,phi=phi, size=size, munb=munb,log=TRUE))
}

 solut <- optim(fn=fncZiNB,par=c(0.09, 72, 0.7),x=x,method =
"L-BFGS-B",  lower=c(1e-10,1e-10,1e-10),upper=c(1-1e-10,Inf,Inf),
control=list(trace=TRUE),hessian=TRUE)

##optim
solut$par
##vglm
Coef(fit)

On Fri, 18 Apr 2008, Tim Howard wrote:

> Dear R-help gurus (and T.Yee, the VGAM maintainer) -
> I've been banging my head against the keyboard for too long now, hopefully 
> someone can pick up on the errors of my ways...
>
> I am trying to use optim to fit a zero-inflated negative binomial 
> distribution.  No matter what I try I can't get optim to recognize my initial 
> parameters. I think the problem is that dnbinom allows either 'prob' or 'mu' 
> and I am trying to pass it 'mu'.  I've tried a wrapper function but it still 
> hangs.  An example:
>
> #set up dummy data,load VGAM, which is where I am getting the zero-inflated 
> neg binom
> #I get the same problem without VGAM, using dnbinom in the wrapper instead.
> library(VGAM)
> phi <- 0.09
> size <- 0.7
> munb <- 72
> x <- rzinb(200, phi=phi, size=size, munb=munb)
>
> #VGAM can fit using vglm... but I'd like to try optim
> > fit <- vglm(x~1, zinegbinomial,trace=TRUE)
> VGLMlinear loop  1 :  loglikelihood = -964.1915
> VGLMlinear loop  2 :  loglikelihood = -964.1392
> VGLMlinear loop  3 :  loglikelihood = -964.1392
> > Coef(fit)
>phi   munb  k
>  0.1200317 62.8882874  0.8179183
>
> > #build my wrapper function for dzinb
> > fncZiNB <- function(phi, size, munb){
> + -sum(dzinb(x=x,phi=phi, size=size, munb=munb,log=TRUE))}
> >
> > #test the wrapper, seems to work.
> > fncZiNB(phi=0.09, size=0.7, munb=72)
> [1] 969.1435
>
> #try it in optim
> > solut <- optim(fn=fncZiNB,par=c(phi=0.09, munb=72, size=0.7),method = 
> > "L-BFGS-B", hessian=TRUE)
> Error in dnbinom(x = x, size = size, prob = prob, log = log.arg) :
>   argument "size" is missing, with no default
>
> I have the same problem with dnbinom.
> I'm sure I'm doing something obvious any suggestions?
> Session info below. Thanks in advance.
> Tim Howard
> New York Natural Heritage Program
>
> > sessionInfo()
> R version 2.6.2 (2008-02-08)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
> States.1252;LC_MONETARY=English_United 
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats4splines   stats graphics  grDevices utils datasets  
> methods
> [9] base
>
> other attached packages:
> [1] VGAM_0.7-6  randomForest_4.5-23
>
> __
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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Re: [R] Overall p-value from a factor in a coxph fit

[Frank E Harrell Jr]

Paul Johnson wrote:
> On Fri, Apr 18, 2008 at 3:06 AM, Kåre Edvardsen <[EMAIL PROTECTED]> wrote:
>> Hi all.
>>
>>  If I run the simple regression when x is a categorical variable ( x <-
>>  factor(x) ):
>>
>>  > MyFit <-coxph( Surv(start, stop, event) ~ x )
>>
>>  How can I get the overall p-value on x other than for each dummy
>>  variable?
>>
>>  > anova(MyFit)
>>
>>  does NOT provide that information as previously suggested on the list.
>>
> 
> It "should" work...  Here's a self contained example showing that
> anova does give the desired significance test for an lm model.
> 
>> y <- rnorm(100)
>> x <- gl(5,20)
>> mod <- lm(y~x)
>> anova(mod)
> Analysis of Variance Table
> 
> Response: y
>   Df  Sum Sq Mean Sq F value Pr(>F)
> x  4   6.575   1.644  1.5125 0.2047
> Residuals 95 103.237   1.087
> 
> If you provide a similar self contained example leading up to a coxph,
> I would be glad to investigate your question.  You don't give enough
> information for me to tell which version of coxph you are running, and
> from what  package.
> 
> Suppose I "guess" that you are using the coxph from the package
> "survival". If so, it appears to me there is a bug in that package at
> the moment.  The methods anova.coxph and drop1.coxph did exist at one
> time, until very recently.  There is a thread in r-help (which I found
> by typing "RSiteSearch("anova.coxph")" ) discussing recent troubles
> with anova.coxph.
> 
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/118481.html
> 
> As you see from the discussion in that thread, there used to be an
> anova method for coxph, and in the version of survival I have now,
> there is no such method.  The version I have is  2.34-1, Date:
>  2008-03-31.
> 
> Here's what I see after I run "example(coxph)" in order to create some
> coxph objects, on which I can test the diagnostics:
> 
>> drop1(test2)
> Error in terms.default(terms1) : no terms component
>> anova(test2)
> Error in UseMethod("anova") : no applicable method for "anova"
> 
> In that survival package, I do find anova.survreg, but not
> anova.coxph. If you are using the survival package, I'd suggest you
> contact Thomas Lumley directly, since he maintains it.
> 
> I think if you had reported the exact error you saw, it would have
> been easier for me to diagnose the trouble.
> 
> HTH
> pj
> 

In the meantime you can do

library(Design)
f <- cph( . . . )
anova(f)  # multiple d.f. Wald statistics including tests of 
nonlinearity

cph uses coxph but anova.Design is separate from the survival package.

Frank

-- 
Frank E Harrell Jr   Professor and Chair   School of Medicine
  Department of Biostatistics   Vanderbilt University

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Re: [R] Response to R across the university

[Peter Dalgaard]

Antony Unwin wrote:
>  ...
>
> The course itself went very well.  We encouraged people to bring their  
> laptops and work in groups.  Using JGR as the interface to R helped a  
> lot, as it was easier for people to load their own data and use the  
> help.  Of course, JGR is compulsory in Augsburg. 
>   
Speaking of JGR... What are the appropriate channels to complain and/or 
contribute? I had looked into it at an earlier point (on Fedora Linux) 
and got stuck on some fairly simple usability issues, like font choice 
and color scheme. Things like

- if you select a bigger font, the window size remains the same. Changes 
to window size do not survive to subsequent invokations.

- output is quite unreadable in proportional fonts, so why make them 
available?

- some fonts have poor contrast, but there seems to be no way to select 
boldface versions.

- the latest version has turned to a blue-on-gray scheme, which doesn't 
help with the contrast either
 
This is all pretty trivial stuff, but the bottom line is that all the 
really exciting stuff isn't really of much use if students cannot read 
it in the back rows.

A couple other maybe not all that trivial things to do is to improve the 
data import (it is losing out on most of the things that I tried) and to 
get the wires connected between the DataTable and the edit() command.

best
-pd

-- 
   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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and provide commented, minimal, self-contained, reproducible code.

Re: [R] help me to debug this part of code?

[Charles C. Berry]

On Fri, 18 Apr 2008, jinjin wrote:

>
> I am trying to solve the integration equation, for different values of K from
> 4 to 25, the integration is with respect to u,
>
> Here is the equation:gamma(k/2) / ( sqrt(k-1)*gamma((k-1)/2) ) *
> integrate(f= (1+u^2/k-1)^(-k/2), lower=0, upper= sqrt(a^2*k/(k+1-a^2)) ) =
> the similar expression as te left hand except k becomes k+1
>
>
> my code is below, I don't know why R keep telling me the syntax wrong but I
> am not clear, thanks.

First, you should format your code so that it is more readable. Use spaces 
and indentation.

Second, it is recommended that use an editor that features syntax 
highlighting to prepare your code. It will show you which parentheses and 
braces match. And if it features automatic indentation, this will give you 
clues when the nesting of an expression or arglist has gone awry.

Third, read the error messages that R provides and try to understand why R 
is telling you "unexpected symbol", etc. Often, an error immediately 
preceeded the point at which R got confused.

If all this fails, break apart your code into single expressions (or 
pieces you ***think*** are valid expressions) and try to evaluate them. 
For example,

 m<-exp(lgamma(k/2)-lgamma((k-1)/2))*1/sqrt(k-1)

is correctly parsed. It only fails for me because I tried to evaluate it 
without providing a value for 'k'.

HTH,

Chuck

>
>
> f<-function(u,k){(1+u^2/(k-1))^(-k/2)}
> g<-function(u,k){(1+u^2/k)^(-(k+1)/2)}
>
> for(k in 4:25){
> out<-uniroot(function(a){
> m<-exp(lgamma(k/2)-lgamma((k-1)/2))*1/sqrt(k-1)
> n<-exp(lgamma((k+1)/2)-lgamma(k/2)*1/sqrt(k)
> m*integrate(f,lower=0,upper=sqrt(a^2*(k-1)/(k-a^2)),rel.tol=.Machine$double.eps^0.25)
> -n*integrate(g,lower=0,upper=sqrt(a^2*k/(k+1-a^2)),rel.tol=.Machine$double.eps^0.25)
> }
> lower=1.4, upper=2)
> print(unlist(out))}
>
>
> -- 
> View this message in context: 
> http://www.nabble.com/help-me-to-debug-this-part-of-code--tp16763482p16763482.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Charles C. Berry(858) 534-2098
 Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED]  UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

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Re: [R] problem in installing R packages on linux

[Liviu Andronic]

On Fri, Apr 18, 2008 at 1:28 PM, Niels Steen Krogh
<[EMAIL PROTECTED]> wrote:
> install.packages("BayesTree")
>

What is the error message?
Liviu

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[R] Legend Clipping

[Beck, Kenneth (STP)]

I am having trouble with legends clipping, not sure how to control that.
Here is my latest code to demo. I want the legend to show up in the
center of the window, in fairly large font. Right now, font is too
small, but if I increase it, the legend clips even more. In this
simplified example, the plots are dummy (I took them from an example),
my actual plots only have two bars, corresponding to the legend.

windows();
nf1 <- layout(matrix(1), widths=lcm(6), heights=lcm(6)) nf <-
layout(matrix(c(1,2,5,0,3,4),3,2,byrow=TRUE), c(2.2,2.2), c(2.2,1,2.2),
TRUE) layout.show(nf); # par(mfrow=c(3,2));

par(font.axis=2);
par(font.lab=2);
# pmn=t(pmn);
tN <- table(Ni <- stats::rpois(100, lambda=5)) barplot(tN,
col=rainbow(20))

# par (mfg=c(1,2));
par(font.axis=2);
par(font.lab=2);
tN <- table(Ni <- stats::rpois(100, lambda=5)) barplot(tN,
col=rainbow(20))

# par (mfg=c(2,1));
par(font.axis=2);
par(font.lab=2);
tN <- table(Ni <- stats::rpois(100, lambda=5)) barplot(tN,
col=rainbow(20))

# par (mfg=c(2,2));
par(font.axis=2);
par(font.lab=2);
tN <- table(Ni <- stats::rpois(100, lambda=5)) barplot(tN,
col=rainbow(20))

# par (mfg=c(3,1));
plot(1, type="n", axes=FALSE, xlab="", ylab="",ylim=c(0,2),xlim=c(0,2));
# legend(1,0.8, legend = c("CPX","Home"), bty="n",
fill=c("blue","red"),lwd=1, cex=1, xjust=0.5, yjust=0.4); #
ltest=legend("center", legend = c("CPX","Home"), bty="n",
fill=c("blue","red"),lwd=1, cex=1, xjust=0.5,
yjust=0.4,trace=TRUE,plot=FALSE); legend(0.5,0.5, legend =
c("CPX","Home"), bty="n", fill=c("blue","red"),lwd=1, cex=1, xjust=0.5,
yjust=0.4);

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Re: [R] efficiently replacing values in a matrix

[Nnamdi]

Still it is pretty slow when entering values into a large matrix. Case in
point:

> a <- matrix(nrow=1,ncol=1)
> system.time(a[1,1] <- 1903908.80385)
   user  system elapsed
 30.840   6.226  41.416
> is.matrix(a)
[1] TRUE

Is there a better way to enter values into large matrices? If I have to
spend 41 secs each time I enter into a cell and I have 1x1 cells to
enter that is impractical! 

--Nnamdi

Rolf Turner-3 wrote:
> 
> 
> On 17/04/2008, at 9:33 AM, Charles C. Berry wrote:
> 
>   
> 
>> I'll lay odds that Matthew's 'matrix' is actually a data.frame, and  
>> I'll not be surprised if the columns are factors.
> 
>   
> 
> I suspect that you're right.
> 
> ***Why*** can't people distinguish between data frames and matrices?
> If they were the same  thing, there wouldn't be two
> different terms for them, would there?
> 
>   cheers,
> 
>   Rolf Turner
> 
> ##
> Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 

-- 
View this message in context: 
http://www.nabble.com/efficiently-replacing-values-in-a-matrix-tp16732795p16763578.html
Sent from the R help mailing list archive at Nabble.com.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Legend Clipping

[Beck, Kenneth (STP)]

Here is a better example. I am also trying to put gaps between the bars
on the graphs, and this work-around is the only way I can make it work
satisfactorily. Any suggestions about that?

windows();
nf <- layout(matrix(c(1,2,5,0,3,4),3,2,byrow=TRUE), c(2.2,2.2),
c(2.2,1,2.2), TRUE)
layout.show(nf);

par(font.axis=2);
par(font.lab=2);
ylimit=c(0,1.2);
pmn <- matrix(c(1:5), nrow=5, ncol=1)
pmn[,1]=c(0,0.8,0,0.75,0);
barplot(pmn,ylab="Slopes",beside=TRUE,ylim=ylimit,xlim=c(1,6.0),
col = c(NA,"blue", NA, "red",NA));

par(font.axis=2);
par(font.lab=2);
ylimit=c(0,1.2);
pmn <- matrix(c(1:5), nrow=5, ncol=1)
pstd=pmn;
pmn[,1]=c(0,0.8,0,0.75,0);
barplot(pmn,ylab="Slopes",beside=TRUE,ylim=ylimit,xlim=c(1,6.0),
col = c(NA,"blue", NA, "red",NA));

par(font.axis=2);
par(font.lab=2);
ylimit=c(0,1.2);
pmn <- matrix(c(1:5), nrow=5, ncol=1)
pstd=pmn;
pmn[,1]=c(0,0.8,0,0.75,0);
barplot(pmn,ylab="Slopes",beside=TRUE,ylim=ylimit,xlim=c(1,6.0),
col = c(NA,"blue", NA, "red",NA));

par(font.axis=2);
par(font.lab=2);
ylimit=c(0,1.2);
pmn <- matrix(c(1:5), nrow=5, ncol=1)
pstd=pmn;
pmn[,1]=c(0,0.8,0,0.75,0);
barplot(pmn,ylab="Slopes",beside=TRUE,ylim=ylimit,xlim=c(1,6.0),
col = c(NA,"blue", NA, "red",NA));

plot(1, type="n", axes=FALSE, xlab="", ylab="",ylim=c(0,2),xlim=c(0,2));
legend(0.5,0.5, legend = c("CPX","Home"), bty="n",
fill=c("blue","red"),lwd=1, cex=1, xjust=0.5, yjust=0.4);



-Original Message-
To: r-help@r-project.org
Subject: [R] Legend Clipping

I am having trouble with legends clipping, not sure how to control that.
Here is my latest code to demo. I want the legend to show up in the
center of the window, in fairly large font. Right now, font is too
small, but if I increase it, the legend clips even more. In this
simplified example, the plots are dummy (I took them from an example),
my actual plots only have two bars, corresponding to the legend.

windows();
nf1 <- layout(matrix(1), widths=lcm(6), heights=lcm(6)) nf <-
layout(matrix(c(1,2,5,0,3,4),3,2,byrow=TRUE), c(2.2,2.2), c(2.2,1,2.2),
TRUE) layout.show(nf); # par(mfrow=c(3,2));

par(font.axis=2);
par(font.lab=2);
# pmn=t(pmn);
tN <- table(Ni <- stats::rpois(100, lambda=5)) barplot(tN,
col=rainbow(20))

# par (mfg=c(1,2));
par(font.axis=2);
par(font.lab=2);
tN <- table(Ni <- stats::rpois(100, lambda=5)) barplot(tN,
col=rainbow(20))

# par (mfg=c(2,1));
par(font.axis=2);
par(font.lab=2);
tN <- table(Ni <- stats::rpois(100, lambda=5)) barplot(tN,
col=rainbow(20))

# par (mfg=c(2,2));
par(font.axis=2);
par(font.lab=2);
tN <- table(Ni <- stats::rpois(100, lambda=5)) barplot(tN,
col=rainbow(20))

# par (mfg=c(3,1));
plot(1, type="n", axes=FALSE, xlab="", ylab="",ylim=c(0,2),xlim=c(0,2));
# legend(1,0.8, legend = c("CPX","Home"), bty="n",
fill=c("blue","red"),lwd=1, cex=1, xjust=0.5, yjust=0.4); #
ltest=legend("center", legend = c("CPX","Home"), bty="n",
fill=c("blue","red"),lwd=1, cex=1, xjust=0.5,
yjust=0.4,trace=TRUE,plot=FALSE); legend(0.5,0.5, legend =
c("CPX","Home"), bty="n", fill=c("blue","red"),lwd=1, cex=1, xjust=0.5,
yjust=0.4);

__
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.

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and provide commented, minimal, self-contained, reproducible code.

[R] Fw: efficiently replacing values in a matrix

[Nnamdi]

- Forwarded Message 
From: Nnamdi <[EMAIL PROTECTED]>
To: roger koenker <[EMAIL PROTECTED]>
Sent: Friday, April 18, 2008 1:08:58 PM
Subject: Re: [R] efficiently replacing values in a matrix


I tried the sparse matrix implementation, still there are issues:

a <- matrix(nrow=1,ncol=1)
> a.csr <- as.matrix.csr(a)
Error in if (nnz == 0) { : missing value where TRUE/FALSE needed

I'm guessing this error here is because 'a' matrix is initialized with'NA's. 
Yet when I try initializing 'a' matrix with 0s I get:
> a<-matrix(nrow=1,ncol=1,rep(0,1*1))
Error: cannot allocate vector of size 762.9 Mb

Either way I cannot achieve my goal of being able to efficiently enter values 
into this matrix.

To answer your previous question, this matrix is somewhat dense. It is a 
symmetrical matrix thus only the upper triangle is filled.

Any other ideas? Thanks again

--Nnamdi


- Original Message 
From: roger koenker <[EMAIL PROTECTED]>
To: Nnamdi <[EMAIL PROTECTED]>
Sent: Friday, April 18, 2008 12:25:54 PM
Subject: Re: [R] efficiently replacing values in a matrix

is this really a dense matrix?  if not, then sparse representations
would be much more efficient...

url:www.econ.uiuc.edu/~rogerRoger Koenker
email[EMAIL PROTECTED]Department of Economics
vox: 217-333-4558University of Illinois
fax:   217-244-6678Champaign, IL 61820


On Apr 18, 2008, at 12:11 PM, Nnamdi wrote:

>
> Still it is pretty slow when entering values into a large matrix.  
> Case in
> point:
>
>> a <- matrix(nrow=1,ncol=1)
>> system.time(a[1,1] <- 1903908.80385)
>   user  system elapsed
> 30.840   6.226  41.416
>> is.matrix(a)
> [1] TRUE
>
> Is there a better way to enter values into large matrices? If I have  
> to
> spend 41 secs each time I enter into a cell and I have 1x1  
> cells to
> enter that is impractical!
>
> --Nnamdi
>
> Rolf Turner-3 wrote:
>>
>>
>> On 17/04/2008, at 9:33 AM, Charles C. Berry wrote:
>>
>> 
>>
>>> I'll lay odds that Matthew's 'matrix' is actually a data.frame, and
>>> I'll not be surprised if the columns are factors.
>>
>> 
>>
>> I suspect that you're right.
>>
>> ***Why*** can't people distinguish between data frames and matrices?
>> If they were the same  thing, there wouldn't be  
>> two
>> different terms for them, would there?
>>
>> cheers,
>>
>> Rolf Turner
>>
>> ##
>> Attention:\ This e-mail message is privileged and confid... 
>> {{dropped:9}}
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
> -- 
> View this message in context: 
> http://www.nabble.com/efficiently-replacing-values-in-a-matrix-tp16732795p16763578.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.






  

Be a better friend, newshound, and 






  

Be a better friend, newshound, and

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Re: [R] efficiently replacing values in a matrix

[Matthew Keller]

Nanmdi,

I think this is simply because a lot of time is taken transforming the
matrix from logical (default when you create it) to numeric (when you
add the number to [1,1]. If you do the same thing again to [1,2], it
is done instantaneously:
> a <- matrix(nrow=1,ncol=1)
> system.time(a[1,1] <- 1903908.80385)
   user  system elapsed
 10.000   0.781  10.755
>
> system.time(a[1,2] <- 1903908.80385)
   user  system elapsed
  0   0   0

By the way Rolf - I didn't see your full response last time through. I
do know the difference between a matrix and a data.frame, thank you
very much.


On Fri, Apr 18, 2008 at 11:11 AM, Nnamdi <[EMAIL PROTECTED]> wrote:
>
>  Still it is pretty slow when entering values into a large matrix. Case in
>  point:
>
>  > a <- matrix(nrow=1,ncol=1)
>  > system.time(a[1,1] <- 1903908.80385)
>user  system elapsed
>   30.840   6.226  41.416
>  > is.matrix(a)
>  [1] TRUE
>
>  Is there a better way to enter values into large matrices? If I have to
>  spend 41 secs each time I enter into a cell and I have 1x1 cells to
>  enter that is impractical!
>
>  --Nnamdi
>
>
>  Rolf Turner-3 wrote:
>  >
>  >
>  > On 17/04/2008, at 9:33 AM, Charles C. Berry wrote:
>  >
>  >   
>  >
>  >> I'll lay odds that Matthew's 'matrix' is actually a data.frame, and
>  >> I'll not be surprised if the columns are factors.
>  >
>  >   
>  >
>  > I suspect that you're right.
>  >
>  > ***Why*** can't people distinguish between data frames and matrices?
>  > If they were the same  thing, there wouldn't be two
>  > different terms for them, would there?
>  >
>  >   cheers,
>  >
>  >   Rolf Turner
>  >
>  > ##
>
> > Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
>  >
>  > __
>  > R-help@r-project.org mailing list
>  > https://stat.ethz.ch/mailman/listinfo/r-help
>  > PLEASE do read the posting guide
>  > http://www.R-project.org/posting-guide.html
>  > and provide commented, minimal, self-contained, reproducible code.
>  >
>  >
>
>  --
>  View this message in context: 
> http://www.nabble.com/efficiently-replacing-values-in-a-matrix-tp16732795p16763578.html
>  Sent from the R help mailing list archive at Nabble.com.
>
>
>
>  __
>  R-help@r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>



-- 
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
www.matthewckeller.com

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[R] RPy

[Doran, Harold]

I'm curious if there are users of RPy on this list. I've recently
created a gui front end using Tkinter for some python scripts I've
written for some of our internal operations and I am quite pleased with
how this program works. 

I wonder if it is possible to also get this gui to run R functions
through the use of RPy. Going even a step further, I wonder if it is
possible to get this program to run R functions withouth even having R
installed on the machine.

Currently, I can use py2exe to create a executable that allows for this
gui to appear and for all python scripts to run even if the user doesn't
have python on their machine. So (maybe) in theory if I can link Rpy to
my gui to run R, I can then use py2exe to compile it and that would
allow the user to run the functions even if R isn't on the machine.

I realize this is a broad question and has no minimal commented code.
But, if anyone has some experience using Rpy, Tkinter and R I can come
up with a small example to see if we could work out a possible way to
use Tkinter to run R.

[[alternative HTML version deleted]]

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[R] Correspondence and detrended correspondence analysis

[Monica Pisica]

Hi,

I hope someone knows the answer to this or has a real good reference about it 
(I am using Legendre & Legendre, Numerical Ecology, 1998) My data is a 
data.frame with locations as rows and vegetation assemblages / species as 
columns. I've done a PCA, a correspondance analysis (CA) using ca in ca package 
and a detrended correspondance analysis (DCA) using decorana from vegan 
package. As far as i understand what i've done  the relationships between 
vegetation categories and locations should be similar in all 3 analysis, 
although the 'arch' in locations / sites seen in the CA plot should be flatten 
out by the DCA - which it is!.

My problem is that the locations / sites are flipped in the DCA plot versus PCA 
or CA plots (locations with positive coordinates now have negative coordinates 
in DCA versus CA or PCA), although the vegetation categories keep same 
relationships between them in all three plots - which is expected. If some code 
is required i can provide it but i didn't want to clutter the message too much. 
But i am providing the resulting plots in case they will make my problem 
clearer.

PCA plot: ftp://stpfiles.er.usgs.gov/Monica/R_Data/pca_veg_lidarclass_phase2.pdf
CA plot: ftp://stpfiles.er.usgs.gov/Monica/R_Data/corresp_anal_phase2.pdf
DCA plot: 
ftp://stpfiles.er.usgs.gov/Monica/R_Data/detrend_corresp_anal_phase2.pdf
DCA how i would expect it: 
ftp://stpfiles.er.usgs.gov/Monica/R_Data/detrend_corresp_anal_phase2_a.pdf

Any thoughts on this will be very much appreciated,

Monica


_


esh_getintouch_042008
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[R] Embedding fonts in pdfs

[hadley wickham]

Hi all,

I'm having problems embedding fonts in my graphics - and I've tried
embedFonts to no avail.  I have a pdf file and pdffonts tells me:

name type  emb sub uni object ID
 - --- --- --- -
ZapfDingbats Type 1no  no  no   5  0
HelveticaType 1no  no  no  10  0

(both before and after running the gs script).  From reading the
documentation, I suspect that these aren't being embedded because they
are standard PS fonts, but my publisher (lulu.com) wants them
embedded.  Does anyone have any hints?

Thanks,

Hadley

-- 
http://had.co.nz/

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Re: [R] Embedding fonts in pdfs

[Jeffrey Horner]

hadley wickham wrote on 04/18/2008 02:40 PM:
> Hi all,
> 
> I'm having problems embedding fonts in my graphics - and I've tried
> embedFonts to no avail.  I have a pdf file and pdffonts tells me:
> 
> name type  emb sub uni object ID
>  - --- --- --- -
> ZapfDingbats Type 1no  no  no   5  0
> HelveticaType 1no  no  no  10  0
> 
> (both before and after running the gs script).  From reading the
> documentation, I suspect that these aren't being embedded because they
> are standard PS fonts, but my publisher (lulu.com) wants them
> embedded.  Does anyone have any hints?

Have you tried using the Cairo package? For instance, I just helped one 
of our users here at Vanderbilt to embed 'Gill Sans MT' (because 
apparently it's required by some journal) into her PDF graphic, like so:

CairoFonts(
 regular="Gill Sans MT",
 bold="Gill Sans MT:style=Bold",
 italic="Gill Sans MT:style=Italic",
 bolditalic="Gill Sans MT:style=Bold Italic"
)
CairoPDF(file="file.pdf")
...
dev.off()

Also, Preview or even Acrobat reader (or xpdf) should reveal in the 
"Properties" of the pdf file whether or not your desired fonts are embedded.

Best,

Jeff
-- 
http://biostat.mc.vanderbilt.edu/JeffreyHorner

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[R] using rbind() on multiple objects at once

[Andrew Yee]

Is there an efficient way to use rbind() with the five dataframes described
in the following example:

a <- c(1:5)
list.foo <- lapply(a, function(x) data.frame(beta=a*rnorm(10),
deta=a*rnorm(10)))
big.data.frame <- rbind(list.foo[[1]], list.foo[[2]], list.foo[[3]],
list.foo[[4]], list.foo[[5]]) #is there an easier method?

For example, I naively thought you could do something like

rbind(list.foo[[1:5]]) #gives an error message

but that results in an error message.

Thanks,
Andrew

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Re: [R] using rbind() on multiple objects at once

[Katharine Mullen]

 do.call(rbind, list.foo)

On Fri, 18 Apr 2008, Andrew Yee wrote:

> Is there an efficient way to use rbind() with the five dataframes described
> in the following example:
>
> a <- c(1:5)
> list.foo <- lapply(a, function(x) data.frame(beta=a*rnorm(10),
> deta=a*rnorm(10)))
> big.data.frame <- rbind(list.foo[[1]], list.foo[[2]], list.foo[[3]],
> list.foo[[4]], list.foo[[5]]) #is there an easier method?
>
> For example, I naively thought you could do something like
>
> rbind(list.foo[[1:5]]) #gives an error message
>
> but that results in an error message.
>
> Thanks,
> Andrew
>
>   [[alternative HTML version deleted]]
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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[R] Bug in Merge?

[Edwin Sendjaja]

Hello,


I find strange number in my merge data set.

My first coloumn consist row numbers.

---
my.data:


AbsTime   RelTime PE_IDEvent  Delay

4238   1208514343.812086107.153637  4   EKA  51620

##
Host.data:


 ID   Host

4   4vicky.planetlab.ntua.gr



data<-read.table("my.data")
mapping<-read.table("Host.data")

mergeXY <- merge(data,mapping, by.x="PE_ID", by.y="ID")


If I merge these data then i get:

"PE_ID" "AbsTime" "RelTime" "Ereignis"  "Delay" "Host"
"2" 4 1208514343.81209 107.153637 "EndpointKeepAlive" " 
51620 "vicky.planetlab.ntua.gr"


---

The first problem:

Why is the row number "2" now? Where does this nummber come from?

I think, there is a conflict between my row number from data and mapping (4238 
and 4).

The second problem:

Why is my AbsTime: 1208514343.81209? It was 1208514343.812086. It is 1 digit 
less. how can I avoid this?



I hope someone could answer this.



Thank you in advance,



Edwin

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Re: [R] Response to R across the university

[Antony Unwin]

On 18 Apr 2008, at 6:42 pm, Peter Dalgaard wrote:

> Antony Unwin wrote:
>> ...
>>
>> The course itself went very well.  We encouraged people to bring  
>> their  laptops and work in groups.  Using JGR as the interface to R  
>> helped a  lot, as it was easier for people to load their own data  
>> and use the  help.  Of course, JGR is compulsory in Augsburg.
> Speaking of JGR... What are the appropriate channels to complain and/ 
> or contribute?

This will do fine, though [EMAIL PROTECTED]  
would be the "official" route and Markus Helbig ([EMAIL PROTECTED])  
is the key person.

> I had looked into it at an earlier point (on Fedora Linux) and got  
> stuck on some fairly simple usability issues, like font choice and  
> color scheme. Things like
>
> - if you select a bigger font, the window size remains the same.  
> Changes to window size do not survive to subsequent invokations.
>
> - output is quite unreadable in proportional fonts, so why make them  
> available?
>
> - some fonts have poor contrast, but there seems to be no way to  
> select boldface versions.
>
> - the latest version has turned to a blue-on-gray scheme, which  
> doesn't help with the contrast either
> This is all pretty trivial stuff, but the bottom line is that all  
> the really exciting stuff isn't really of much use if students  
> cannot read it in the back rows.

Your points should certainly be looked into.  Having the font big  
enough for students to read in the back row has not been a problem for  
me.

> A couple other maybe not all that trivial things to do is to improve  
> the data import (it is losing out on most of the things that I tried)

Now what would Brian say to a comment like that?  Please insert your  
favourite put-down here:

 

And then perhaps you would be kind enough to let us know in a little  
more detail what hasn't worked for you.

> and to get the wires connected between the DataTable and the edit()  
> command.

Thanks for your comments.

Antony




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Re: [R] R CMD check Error

[Johannes Graumann]

On Friday 18 April 2008 16:35:12 Prof Brian Ripley wrote:
> On Fri, 18 Apr 2008, Johannes Graumann wrote:
> > Hi,
> >
> > Can anyone give me a hint on what's wrong if "R CMD check "
> > gives me this error:
> >
> >Rd files with unknown encoding:
> >  .Rd
> >
> > I have checked that file over and over and can't find any weired
> > characters or some such.
> > How can I fix this?
>
> Remove the non-ASCII characters, or declare an encoding.
>
> You didn't tell us your OS -- one good way I find on Linux to spot such
> characters is to use 'less 'in the C locale.  Another is something like
> (in R)
>
> foo <- readLines("foo.Rd")
> foo2 <- iconv(foo, "", "ASCII", sub="byte")
> foo2[foo2 != foo]
>
> which should show the line(s) concerned with non-ASCII characters
> highlighted as .
Perfekt - found the offending quote characters! Thanks!

Joh



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[R] Line-wrap problem

[Matthew Fero]

I'm wondering if someone can tell me how R determines where to wrap  
lines in its output.

I'd like to understand this because occasionally often after running  
a script the output of R no longer wraps at the correct location.   
For example, the statement, '1:40' would ordinarily return something  
like this...

   [1]1   2   34   5   6   78   9 10 11 12 13 14 15 16 17  
18 19 20
[21] 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40

and is instead returning longer lines like this...

   [1]1   2   34   5   6   78   9 10 11 12 13 14 15 16 17  
18 19 20
  21 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40

As you can imagine this makes it hard to read output because the  
results no longer line up in nice columns.  This seems to happen  
without my having resized the window but resizing the window can  
occasionally make it better.

Thanks,

Matthew


Other details:
System: Mac OS X v.10.4.11
Running R from command line (Terminal.app) or from R.app

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[R] 2.2e-16 a magic number? ks.test help

[Ashton, Gail]

Hello,
I'm trying to test my data for normality.
I enter the data (95ish species counts) 
run >ks.test (data,pnorm) 
and get a p- value <2.2e-16
But this seems to be the p-value no matter what the data I enter. (I
have multiple datasets and am testing them all for normality).
[Actually, I just entered a vector of 1's and the p-value changed.]
When I use the >Shapiro.test command, I get different p-values
(different from each other as well as from the ks.test results), and in
fact one variable that was significantly different from normal using the
ks.test (p<2.2e-16), is not significantly different from normal using
the Shapiro.test (p=0.2389).
I am happy to believe that all my data are not normally distributed, but
am just suspicious when the p-value remains the same regardless of the
data (including log and sqrt transformed data). 
Is 2.2e-16 simply the lowest the p-values can go + my data are just
really not normal?
Any help much appreciated.
Thanks,
Gail

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Re: [R] Response to R across the university

[Peter Dalgaard]

Antony Unwin wrote:
>
>> A couple other maybe not all that trivial things to do is to improve 
>> the data import (it is losing out on most of the things that I tried)
>
> Now what would Brian say to a comment like that?  Please insert your 
> favourite put-down here:
>
>  
He'd usually say something about reproducible examples, just like you...

Don't get me wrong. I realize that the Open dialog in DataTable is 
designed to read one, simple data format, not all of them. I just 
couldn't easily figure out which one that was.

> And then perhaps you would be kind enough to let us know in a little 
> more detail what hasn't worked for you.
Anything in the data directory of the ISwR package, for instance 
(whitespace separated and comma separated files, mostly). I suspect that 
the format it _will_ read is TAB separated, but it would be nice if it 
said so somewhere. (Curiously, thuesen.txt does have tabs, but not 
equally many in the header as in the data lines, so it can't be read at 
all, the others just get all fields and headers jammed into one.)

-- 
   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] help me to debug this part of code?

[francogrex]

There are a lot of syntax errors such as unclosed parentheses, missing commas
etc; Example: exp@(@lgamma((k+1)/2)-lgamma(k/2)*1/sqrt(k), where the
parenthesis between the @s is not closed. I suggest you get an editor such
as "Tinn" that can highlight those for you. In addition I notice that you
use two functions: f and g, in a loop but you didn't pass any arguments to
them.


jinjin wrote:
> 
> I am trying to solve the integration equation, for different values of K
> from 4 to 25, the integration is with respect to u,
> Here is the equation:gamma(k/2) / ( sqrt(k-1)*gamma((k-1)/2) ) *
> integrate(f= (1+u^2/k-1)^(-k/2), lower=0, upper= sqrt(a^2*k/(k+1-a^2)) ) = 
> the similar expression as te left hand except k becomes k+1
> my code is below, I don't know why R keep telling me the syntax wrong but
> I am not clear, thanks.
> f<-function(u,k){(1+u^2/(k-1))^(-k/2)}
> g<-function(u,k){(1+u^2/k)^(-(k+1)/2)}
> for(k in 4:25){
> out<-uniroot(function(a){
> m<-exp(lgamma(k/2)-lgamma((k-1)/2))*1/sqrt(k-1)
> n<-exp(lgamma((k+1)/2)-lgamma(k/2)*1/sqrt(k)
> m*integrate(f,lower=0,upper=sqrt(a^2*(k-1)/(k-a^2)),rel.tol=.Machine$double.eps^0.25)
> -n*integrate(g,lower=0,upper=sqrt(a^2*k/(k+1-a^2)),rel.tol=.Machine$double.eps^0.25)
> }
> lower=1.4, upper=2)
> print(unlist(out))}
> 

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Re: [R] Bug in Merge?

[Peter Dalgaard]

Edwin Sendjaja wrote:
> Hello,
>
>
> I find strange number in my merge data set.
>
> My first coloumn consist row numbers.
>
> ---
> my.data:
>
>
> AbsTime   RelTime PE_IDEvent  Delay
>
> 4238   1208514343.812086107.153637  4   EKA  51620
>
> ##
> Host.data:
>
>
>  ID   Host
>
> 4   4vicky.planetlab.ntua.gr
>
> 
>
> data<-read.table("my.data")
> mapping<-read.table("Host.data")
>
> mergeXY <- merge(data,mapping, by.x="PE_ID", by.y="ID")
>
>
> If I merge these data then i get:
>
> "PE_ID" "AbsTime" "RelTime" "Ereignis"  "Delay" "Host"
> "2" 4 1208514343.81209 107.153637 "EndpointKeepAlive" " 
> 51620 "vicky.planetlab.ntua.gr"
>
>
> ---
>
> The first problem:
>
> Why is the row number "2" now? Where does this nummber come from?
>
>   
I don't know. Where did "Ereignis" and "EndpointKeepAlive" come from

That is, you are paraphrasing your results instead of giving us a 
reproducible example to go on!

(And I can't reproduce it. I get a rowname of 1, whatever I try.)

 
> I think, there is a conflict between my row number from data and mapping 
> (4238 
> and 4).
>
> The second problem:
>
> Why is my AbsTime: 1208514343.81209? It was 1208514343.812086. It is 1 digit 
> less. how can I avoid this?
>
>   
You're running out of floating point precision (the rel. error is about 
1e-16). Either user fewer digits (e.g. move the origin of time 
120850 units forward) or don't represent as floating point. Using 
colClasses, you can read it as a character variable and take it from 
there. One idea is to represent the integer and fractional parts separately.

-- 
   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 rbind() on multiple objects at once

[Andrew Yee]

Thanks!



On 4/18/08, Katharine Mullen <[EMAIL PROTECTED]> wrote:
>  do.call(rbind, list.foo)
>
> On Fri, 18 Apr 2008, Andrew Yee wrote:
>
> > Is there an efficient way to use rbind() with the five dataframes
> described
> > in the following example:
> >
> > a <- c(1:5)
> > list.foo <- lapply(a, function(x) data.frame(beta=a*rnorm(10),
> > deta=a*rnorm(10)))
> > big.data.frame <- rbind(list.foo[[1]], list.foo[[2]], list.foo[[3]],
> > list.foo[[4]], list.foo[[5]]) #is there an easier method?
> >
> > For example, I naively thought you could do something like
> >
> > rbind(list.foo[[1:5]]) #gives an error message
> >
> > but that results in an error message.
> >
> > Thanks,
> > Andrew
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list
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> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>

-- 
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[R] Distribution Graph Idea/Help

[Derek Ogle]

For pedagogical reasons (i.e., moving a way from tables of distributions) I 
want to plot a probability density or distribution function with a shaded area 
corresponding to the calculated value or user input.  For example, I want a 
plot to visually demonstrate the result of 

pnorm(1.3)

I have seen the interactive examples in TeachingDemos and rPanel but am 
interested in using the function from the "command line" rather than from a 
"GUI".  I have generated code to construct this type of graph, but my question 
is now how best to implement it.  My initial solution was to add a plot=TRUE 
argument to pnorm() but that requires altering a base function and I now think 
that this is not a good idea (although it worked nicely from the student's 
perspective).  Thus, I have considered three new options ...

1) making a new function called something like pnorm1() which would return what 
pnorm() returns but also would construct the graphic.  This implementation 
would be simple given the function that I have already made but it feels clumsy 
and inelegant.
2) creating a generic plot() function that would take, for example, an object 
returned from pnorm().  However, this does not seem immediately possible as, it 
appears to me, that pnorm() just returns a numeric.
3) creating a general function that would take the name of a distribution, type 
of calculation ("p" or "q" type), value of interest (x value or probability), 
and distribution parameters as arguments and then call the specific 
distribution functions and my graphing function to produce the results.  I 
would likely implement this just for distributions that I use regularly in my 
classes.

Has anybody already implemented a solution to this idea?  Does anyone have a 
suggestion on which of my three options above is best for this code?  Better 
ideas?

Thanks in advance for any help.

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[R] Problem with JGR_1.5-18

[Michael Kubovy]

R version 2.7.0 Under development (unstable) (2008-03-04 r44677)
i386-apple-darwin8.10.1

locale:
C

attached base packages:
[1] grid  grDevices datasets  graphics  stats utils  
methods   base

other attached packages:
[1] lattice_0.17-6 MASS_7.2-41JGR_1.5-18 iplots_1.1-2
JavaGD_0.5-1   rJava_0.5-1

The following opens a JavaGD window and freezes JGR:
super.sym <- trellis.par.get("superpose.symbol")
(from splom help page).
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
 McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/





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[R] How to insert a vector or matrix into an existing matrix

[Ng Stanley]

Hi,

Is there any functions to insert a vector or matrix into an existing matrix
say between row 5 and 6 or column 8 and 9, without creating a temporary
matrix ?

Thanks
Stanley

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Re: [R] eval and parent.frame [was: Error in Design package: dataset not found for options(datadist)]

[Gad Abraham]

Charles C. Berry wrote:
> On Fri, 18 Apr 2008, Gad Abraham wrote:
> 
>> Frank E Harrell Jr wrote:
>>> Gad Abraham wrote:
 Hi,

 Design isn't strictly an R base package, but maybe someone can explain
 the following.

 When lrm is called within a function, it can't find the dataset dd:

 > library(Design)
 > age <- rnorm(30, 50, 10)
 > cholesterol <- rnorm(30, 200, 25)
 > ch <- cut2(cholesterol, g=5, levels.mean=TRUE)
 > fit <- function(ch, age)
 + {
 +d <- data.frame(ch, age)
 +dd <- datadist(d)
 +options(datadist="dd")
 +lrm(ch ~ age, data=d, x=TRUE, y=TRUE)
 + }
 > fit(ch, age)
 Error in Design(eval(m, sys.parent())) :
dataset dd not found for options(datadist=)

 It works outside a function:
 > d <- data.frame(ch, age)
 > dd <- datadist(d)
 > options(datadist="dd")
 > l <- lrm(ch ~ age, data=d, x=TRUE, y=TRUE)


 Thanks,
 Gad
>>>
>>> My guess is that you'll need to put dd in the global environment, not in
>>> fit's environment.  At any rate it is inefficient to call datadist every
>>> time.  Why not call it once for the whole data frame containing all the
>>> predictors, at the top of the program?
>>
>> This is just sample code, in practice the datadist will be different for
>> each invocation of the function.
>>
>> I think it boils down to this behaviour, which I don't understand ---
>> although ls can see x in the parent of f2, eval cannot:
> 
> 
> That is because (from ?eval):
> 
> "Objects to be evaluated can be of types call or expression or name 
> (when the name is looked up in the current scope and its binding is 
> evaluated)..."
> 
> And 'x' is of type name (aka 'symbol').
> 
> So eval never gets around to looking in 'p', because it never succeeded 
> in looking up 'x' and evaluating its binding in the current scope.
> 
> What you probably want is
> 
> b <- evalq( x, envir=p)
> 

Thanks, that solves the problem with this sample code, but not with the 
Design::lrm function, because there are several more layers of 
evaluation there.

I can get around that with the ugly hack of setting a global NULL 
datadist and assigning to it with "<<-" within the fit function every 
time, so it's always visible to Design. But it's still an ugly hack :)

-- 
Gad Abraham
Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: [EMAIL PROTECTED]
web: http://www.csse.unimelb.edu.au/~gabraham

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Re: [R] 2.2e-16 a magic number? ks.test help

[Prof Brian Ripley]

It says 'less than 2.2e-16'.  The print() method does not report smaller 
values, because they may not be computed as accurately as they appear.

Note that the tests do different things, and you have not shown us how you 
used them.  The Shapiro-Wilk test tests normality (any normal, with 
variable mean and variance).  The Kolmogorov test is for a sample from a 
completely specified distibution -- have you perchance tested for a
N(0, 1) distribution by  ks.test(x, "pnorm")?  Note the comment in the 
help:

  If a single-sample test is used, the parameters specified in '...'
  must be pre-specified and not estimated from the data. There is
  some more refined distribution theory for the KS test with
  estimated parameters (see Durbin, 1973), but that is not
  implemented in 'ks.test'.


On Fri, 18 Apr 2008, Ashton, Gail wrote:

> Hello,
> I'm trying to test my data for normality.
> I enter the data (95ish species counts)
> run >ks.test (data,pnorm)
> and get a p- value <2.2e-16
> But this seems to be the p-value no matter what the data I enter. (I
> have multiple datasets and am testing them all for normality).
> [Actually, I just entered a vector of 1's and the p-value changed.]
> When I use the >Shapiro.test command, I get different p-values
> (different from each other as well as from the ks.test results), and in
> fact one variable that was significantly different from normal using the
> ks.test (p<2.2e-16), is not significantly different from normal using
> the Shapiro.test (p=0.2389).
> I am happy to believe that all my data are not normally distributed, but
> am just suspicious when the p-value remains the same regardless of the
> data (including log and sqrt transformed data).
> Is 2.2e-16 simply the lowest the p-values can go + my data are just
> really not normal?

Well, if they are counts they are from a discrete distribution, so there 
is a sure-fire test here -- the probability of integer observations from a 
normal distribution is 0 in real numbers, and very small in computer 
arithmetic unless the variance is extremely small.

I'm not suggesting that test, but trying to point out the futility of just 
testing normality -- the question needs to be 'is the normal distribution 
an adequate approximation for the analysis I have in nind'.

> Any help much appreciated.
> Thanks,
> Gail
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
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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and provide commented, minimal, self-contained, reproducible code.

[R] multiple separators in sep argument for read.table?

[Johan Jackson]

Hello,

Is there any way to add multiple separators in the sep= argument in
read.table? I would like to be able to create different columns if I see a
white space OR a "/".

Thanks in advance,

JJ

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Re: [R] R CMD check Error

[Prof Brian Ripley]

One thing I should add for the archives -- R 2.7.0 and later have

 o  New function showNonASCII() in package tools to aid detection
of non-ASCII characters in .R and .Rd files.


On Fri, 18 Apr 2008, Prof Brian Ripley wrote:

> On Fri, 18 Apr 2008, Johannes Graumann wrote:
>
>> Hi,
>>
>> Can anyone give me a hint on what's wrong if "R CMD check " gives
>> me this error:
>>
>>Rd files with unknown encoding:
>>  .Rd
>>
>> I have checked that file over and over and can't find any weired characters
>> or some such.
>> How can I fix this?
>
> Remove the non-ASCII characters, or declare an encoding.
>
> You didn't tell us your OS -- one good way I find on Linux to spot such
> characters is to use 'less 'in the C locale.  Another is something like
> (in R)
>
> foo <- readLines("foo.Rd")
> foo2 <- iconv(foo, "", "ASCII", sub="byte")
> foo2[foo2 != foo]
>
> which should show the line(s) concerned with non-ASCII characters
> highlighted as .
>
> -- 
> 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
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Mantel-Haenszel for 2x2

[Dr. Jeff Miller]

Hi all,

 

Does anyone know if an R function for the Mantel-Haenszel chi-square for a
2x2 table exists?  I’ve also seen it called the randomization Q statistic.

Note that I’m not looking for the Cochran-Mantel-Haenszel…I did see that out
there as cmh.test.

 

Thanks in advance,

Jeff


Internal Virus Database is out-of-date.
Checked by AVG Free Edition. 

11:27 AM
 

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Re: [R] multiple separators in sep argument for read.table?

[Prof Brian Ripley]

On Sat, 19 Apr 2008, Johan Jackson wrote:

> Hello,
>
> Is there any way to add multiple separators in the sep= argument in
> read.table? I would like to be able to create different columns if I see a
> white space OR a "/".

No.  read.table() uses scan(), and that requires 'sep' to be a single 
character (if specified).

You can read your dataset by readLines, change "/" to, say, "\t" by gsub() 
and then use read.table() on a textConnection() from the resulting 
character vector.

-- 
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

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.