[R] Recall() and sapply()

2005-03-30 Thread Robin Hankin
Hi.
I'm having difficulty following the advice given in help(Recall).  
Consider the two
following toy functions:

f1 - function(n){
  if(length(n)1){return(sapply(n,f1))}
  matrix(n,n,n)
}
f2 - function(n){
  if(length(n)1){return(sapply(n,Recall))}
  matrix(n,n,n)
}
f1() works as desired (that is, f(1:3), say, gives me a three element 
list whose i-th element
is an i-by-i matrix whose elements are all i).

But f2() doesn't.
How do I modify either function to use Recall()?  What exactly is 
Recall() calling here?


--
Robin Hankin
Uncertainty Analyst
Southampton Oceanography Centre
European Way, Southampton SO14 3ZH, UK
 tel  023-8059-7743
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Re: [R] From FAQ 7.21 to a command like apply(sapply(list(f1,f2,f3),is.na),2,sum)

2005-03-30 Thread Heinz Tuechler
At 16:13 29.03.2005 -0800, Thomas Lumley wrote:
On Wed, 30 Mar 2005, Heinz Tuechler wrote:

 Dear all,

 Last December there was a thread regarding the famous FAQ 7.21 How can I
 turn a string into a variable? and asking what people want to do with
 these strings.
 My, certainly trivial application would be as follows:
 Assume I have a data.frame containing besides others also the columns f1,
 f2, ..., fn and I want to create a command like:
 apply(sapply(list(f1,f2,f3),is.na),2,sum)
 or
 summary(cbind(f1,f2,f3))

 Can I start from paste('f',1:3,sep='') to arrive at the abovementioned
 command?

No parse,as.name or other complications needed. It's all just indexing. 
Suppose your data frame is called dd

fs-paste('f',1:3,sep='')
apply(sapply(dd[,fs],is.na),2,sum)
summary(dd[,fs])

   -thomas


Thank you, Thomas, for your answer. I was curious if there was a simple way
to do this without referring to the data.frame, so that the resulting
command would correspond in its effect exactly to the abovementioned examples.
It's not urgent, but I will try further.

Many thanks

Heinz

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Re: [R] From FAQ 7.21 to a command likeapply(sapply(list(f1,f2,f3),is.na),2,sum)

2005-03-30 Thread Heinz Tuechler
At 09:32 30.03.2005 +0200, Heinz Tuechler wrote:
At 16:13 29.03.2005 -0800, Thomas Lumley wrote:
On Wed, 30 Mar 2005, Heinz Tuechler wrote:

 Dear all,

 Last December there was a thread regarding the famous FAQ 7.21 How can I
 turn a string into a variable? and asking what people want to do with
 these strings.
 My, certainly trivial application would be as follows:
 Assume I have a data.frame containing besides others also the columns f1,
 f2, ..., fn and I want to create a command like:
 apply(sapply(list(f1,f2,f3),is.na),2,sum)
 or
 summary(cbind(f1,f2,f3))

 Can I start from paste('f',1:3,sep='') to arrive at the abovementioned
 command?

No parse,as.name or other complications needed. It's all just indexing. 
Suppose your data frame is called dd

fs-paste('f',1:3,sep='')
apply(sapply(dd[,fs],is.na),2,sum)
summary(dd[,fs])

  -thomas


Thank you, Thomas, for your answer. I was curious if there was a simple way
to do this without referring to the data.frame, so that the resulting
command would correspond in its effect exactly to the abovementioned
examples.
It's not urgent, but I will try further.

Many thanks

Heinz

Continuation:
Maybe not an elegant solution, but it seems to work:
apply(sapply(eval(parse(text=paste('list(',paste('f',1:3,sep='',
collapse=','),')'))) ,is.na),2,sum)
What I missed in my earlier attempts was collapse=','.

Heinz

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[R] locfit

2005-03-30 Thread . .
Hallo all,
can somebody tell me if is possible use the locfit function like a 
semiparametric model. I need to  use two explicative variables and one of them 
is a dummy variable.
Thanks Michele


-

 Giochi, Rubrica… Scaricalo ora! 
[[alternative HTML version deleted]]

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[R] Habituation model

2005-03-30 Thread Laurent Fanchon
Dear all, 

I am looking at habituation of dogs trotting on a treadmill. 
I record the ground reaction force and I analyze it with several discrete variables (maximum, minimum,...)
For each variable, I get between 40 and 50 data per sample. 

I record data at time 1 min, 2 min, and 4 min a day, and I have 4 days of measurement (one day a week). 
That means I have 12 samples : Day1_Min1, Day1_Min2, Day1_Min4, Day2_Min1,...

Furthermore, I have 28 dogs to analyze. 

My questions is : when can I consider the data stabilized?
The problem is I am studying habituation with several sessions. 
It seems logical that values from each first minute could be very dissimilar to others. 
It is not a fully linear training system. 
I have already done some ANOVAs with Day and Min factors. I found a significant effect.
It is quite logical because the dog is learning. The question is then when does it stop learning? or more precisely when is it trained enough to be analyzed?

I could do comparisons among all samples with Student test, but it is surely a simple approach. 

I can presuppose the maximal allowed variability for each variable : in the region of 5%. 

I am really new to both R and stats so if these questions are very simple and I am just missing something, suggestions about good texts or examples on R would be great. 
I am generating data with Scilab, I have a single matrix corresponding to each dog. But I can change it if needed. 

Any help would be greatly appreciated
Thanks
Laurent Fanchon
DVM, MS
Ecole Nationale Veterinaire d'Alfort
France
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Re: [R] about memory

2005-03-30 Thread jon butchar
How much memory is free when R fails (e.g., what does top show while trying 
to run your clustering)?  If there's still a sizeable amount of free memory you 
may have to look into the system limits, maximum data segment size in 
particular.  Many Linux distros have it set to unlimited but default Debian 
may not.  If this turns out to be the problem, please do not, _do not_ raise it 
to unlimited, but only to enough for R to work.

hth,

jon b



On Wed, 30 Mar 2005 18:36:37 +0800
ronggui [EMAIL PROTECTED] wrote:

 here is my system memory:
 [EMAIL PROTECTED] free
  total   used   free sharedbuffers cached
 Mem:256728  79440 177288  0   2296  36136
 -/+ buffers/cache:  41008 215720
 Swap:   481908  60524 421384
 
 and i want to cluster my data using hclust.my data has 3 variables and 1 
 cases.but it fails and saying have not enough memory for the vector size.  I 
 read the help doc and use $R --max-vsize=800M to start the R 2.1.0beta under 
 debian linux.but it still can not get the solution.so is my pc'memory not 
 enough to carry this analysis or my mistake on setting the memory?
 
 thank you.
 
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[R] error messages on R CMD check

2005-03-30 Thread Johannes Hüsing
Dear all,
I am trying to wrap up a package. On entering
R CMD check, I get the following error messages:

[...]
* checking S3 generic/method consistency ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
package/namespace load failed for 'resper'
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
package/namespace load failed for 'resper'
Execution halted
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
package/namespace load failed for 'resper'
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... ERROR
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :

I am not getting these messages, nor their relation to
section 'Generic functions and methods' of the 'Writing
R Extensions' manual, as I did not write any generic methods
in my package.

There has been some discussion of the error message around
Christmas 2003: http://maths.newcastle.edu.au/~rking/R/devel/03b/1438.html,
but I can't see how the circumstances described there apply to
my situation (export a class name).

Could somebody give me a clue on how to give my search a
direction?

Greetings


Johannes

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Re: [R] Habituation model

2005-03-30 Thread Dimitris Rizopoulos
since you measure the same dog several times its measurements are 
correlated and you should take this into account in your analysis 
(i.e., aov() is not appropriate in this case). Probably you could 
find functions lme() and gls() in the nlme package very useful 
for your problem and for which a very good reference is:

@Book{pinheiro.bates:00,
 author= {J. Pinheiro and D. Bates},
 title = {Mixed-Effects Models in S and S-PLUS},
 year  = {2000},
 address   = {New York},
 publisher = {Springer-Verlag}
}
I hope it helps.
Best,
Dimitris

Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm

- Original Message - 
From: Laurent Fanchon [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Wednesday, March 30, 2005 2:06 PM
Subject: [R] Habituation model


Dear all,
I am looking at habituation of dogs trotting on a treadmill. I 
record the ground reaction force and I analyze it with several 
discrete variables (maximum, minimum,...)
For each variable, I get between 40 and 50 data per sample.
I record data at time 1 min, 2 min, and 4 min a day, and I have 4 
days of measurement (one day a week). That means I have 12 samples : 
Day1_Min1, Day1_Min2, Day1_Min4, Day2_Min1,...

Furthermore, I have 28 dogs to analyze.
My questions is : when can I consider the data stabilized?
The problem is I am studying habituation with several sessions. It 
seems logical that values from each first minute could be very 
dissimilar to others. It is not a fully linear training system. I 
have already done some ANOVAs with Day and Min factors. I found 
a significant effect.
It is quite logical because the dog is learning. The question is 
then when does it stop learning? or more precisely when is it 
trained enough to be analyzed?

I could do comparisons among all samples with Student test, but it 
is surely a simple approach.
I can presuppose the maximal allowed variability for each variable : 
in the region of 5%.
I am really new to both R and stats so if these questions are very 
simple and I am just missing something, suggestions about good texts 
or examples on R would be great. I am generating data with Scilab, I 
have a single matrix corresponding to each dog. But I can change it 
if needed.
Any help would be greatly appreciated

Thanks
Laurent Fanchon
DVM, MS
Ecole Nationale Veterinaire d'Alfort
France
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[R] fastbw question

2005-03-30 Thread Peter Flom
Hello

I am running R 2.0.1 on Windows, I am attempting to use Frank Harrell's
'fastbw' function (from the Design library), but I get an error that the
fit was not created with a Design library fitting function; yet when I
go to the help for fastbw (and also look in Frank's book Regression
Modeling Strategies) it appears that fastbw should work with a model
created with lm.

Relevant code

model.borrow.logols- lm(logborrow~age + sex + racgp + yrseduc + 
 needlchg + gallery  + totni + inject + poly(year.of.int,3)  + druginj
+ inj.years  + HTLV3)

fastbw(model.borrow.logols)


Thanks in advance


Peter

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

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[R] discriminant function analysis in R

2005-03-30 Thread Graham Jones
In message [EMAIL PROTECTED], r-help-
[EMAIL PROTECTED] writes
Dear R Users,

I'm very very interested in learning how to use R to carry out a 
classification of data using discriminant function analysis.  I've 
found the MASS package and the lda function, but the examples in the 
help system are a bit over my head.  I'm not exactly sure how to 
interpret the output, for example, of if the inputs I've chosen are 
best suited to my needs.
[...]

I would recommend writing your own simple version of lda in R. For
example, stick to two class problems, and don't worry too much about
efficiency or dealing with bad input. Then think about how you might
make your routines of more general use (but don't bother to implement
this). This is a good way of learning R, and having got this far on your
own, you will find the documentation and examples for lda make sense.
Well, it worked for me.

Here's some useful functions:
?%*%
?t
?determinant
?solve
?mean
?cov
?cat
?scan

-- 
Graham Jones, author of SharpEye Music Reader
http://www.visiv.co.uk
21e Balnakeil, Durness, Lairg, Sutherland, IV27 4PT, Scotland, UK

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Re: [R] Finding the height of a line of text for axis

2005-03-30 Thread Marc Schwartz
On Wed, 2005-03-30 at 11:06 +0100, Steven J. Murdoch wrote:
 I would like to draw only the ticks of an axis, but not the axis
 itself. I don't think this can be done using axis(), so I am trying to
 write a cut-down version in R, which only draws ticks.
 
 The point at which I am stuck is that the length of a tick is set by
 par(tcl) as a fraction of the height of a line of text. So I would
 like to draw a line whose length is also this length. However I cannot
 find out how to convert the into units I can pass into lines(). I
 thought par(cxy), but it is too large, as is shown in the code
 below. Here the red tick marks are longer than the black ones created
 by axis. I have found the relevant function in plot.c:
  GConvertYUnits(Rf_gpptr(dd)-tcl, LINES, NFC, dd);
 but can't find the corresponding R function.
 
 Can anyone suggest how to find this out, or solve the problem in a
 different way?
 
 # Inward pointing ticks
 par(tcl=1)
 
 drawticks - function(at) {
  # Start of the ticks
  base-par(usr)[1]
  # Length of the ticks
  l-par(cxy)[2]*par(tcl)
  for (i in at) {
   lines(c(base,base+l),rep(i,2),col=red)
  }
 }
 
 # Test plot
 plot(c(1,2,3), axes=FALSE)
 # Draw ticks in red
 drawticks(axTicks(2))
 # Overprint with normal axis
 axis(2, axTicks(2))

Steven,

Are you trying to do something like this:

 plot(1:5, axes = FALSE)
 axis(1, col.axis = white, tcl = 1)
 axis(2, col.axis = white, tcl = 1)

or perhaps something like this:

 plot(1:5, axes = FALSE)
 axis(1, col.axis = white, col = red, tcl = 1)
 axis(1, col.axis = white, col = black, tcl = 0)
 axis(2, col.axis = white, col = red, tcl = 1)
 axis(2, col.axis = white, col = black, tcl = 0)

or even something like this:

 plot(1:5, axes = FALSE)
 axis(1, col.axis = white, col = red, tcl = 1)
 axis(1, col.axis = white, col = white, tcl = 0)
 axis(2, col.axis = white, col = red, tcl = 1)
 axis(2, col.axis = white, col = white, tcl = 0)

If you do not want the axis labels, use:

 plot(1:5, axes = FALSE, ann = FALSE)


HTH,

Marc Schwartz

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RE: [R] Recall() and sapply()

2005-03-30 Thread McGehee, Robert
I doubt it's possible to use Recall inside a sapply like this. sapply
(and lapply) make a copy of the function (FUN - match.fun(FUN)) before
passing it inside an internal function (rval - .Internal(lapply(X,
FUN)). So, while I'm not precisely sure how Recall is coded up, I bet
that once it is copied inside of sapply (and lapply), it loses the
context from which it was called.

I can think of a couple ways around this. First, you could construct a
for loop instead of a sapply and use Recall. Second, you could replace
Recall by just asking R what the name of the calling function is and
pass that in to sapply. Something like this should work:

sapply(n, match.fun(sys.call()[[1]]))

HTH,
Robert

-Original Message-
From: Robin Hankin [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, March 30, 2005 3:28 AM
To: R-help@stat.math.ethz.ch
Subject: [R] Recall() and sapply()


Hi.

I'm having difficulty following the advice given in help(Recall).  
Consider the two
following toy functions:


f1 - function(n){
   if(length(n)1){return(sapply(n,f1))}
   matrix(n,n,n)
}

f2 - function(n){
   if(length(n)1){return(sapply(n,Recall))}
   matrix(n,n,n)
}


f1() works as desired (that is, f(1:3), say, gives me a three element 
list whose i-th element
is an i-by-i matrix whose elements are all i).

But f2() doesn't.

How do I modify either function to use Recall()?  What exactly is 
Recall() calling here?




--
Robin Hankin
Uncertainty Analyst
Southampton Oceanography Centre
European Way, Southampton SO14 3ZH, UK
  tel  023-8059-7743

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Re: [R] Recall() and sapply()

2005-03-30 Thread Gabor Grothendieck
I believe that the function that Recall executes is the
function in which Recall, itself, is evaluated -- not the
function in which Recall appears.  In normal cases these are
the same but if you pass Recall to another function then
they are not the same.  Here Recall is being passed to
sapply (which in turn is likely passing it to other
functions).  Because of lazy evaluation Recall does not get
evaluated until it is found within sapply (or a function
called by it or called by one called by it, etc.) and at
that point its recalling the wrong function.  AFAICS one
cannot pass Recall to another function.

You could rewrite the expression that uses sapply to use 
iteration instead or you could do it as shown below.  
In this example, the use of f2 within supply refers to 
the inner f2 which does not change even if the name of 
the outer f2 does.

  f2 - function(n) {
 f2 - function(n) if(length(n)1) sapply(n,f2) else matrix(n,n,n)
 f2(n)
   }
   f3 - f2
   f2(1:3)
   f3(1:3)  # gives same result



On Wed, 30 Mar 2005 09:28:08 +0100, Robin Hankin
[EMAIL PROTECTED] wrote:
 Hi.
 
 I'm having difficulty following the advice given in help(Recall).
 Consider the two
 following toy functions:
 
 f1 - function(n){
   if(length(n)1){return(sapply(n,f1))}
   matrix(n,n,n)
 }
 
 f2 - function(n){
   if(length(n)1){return(sapply(n,Recall))}
   matrix(n,n,n)
 }
 
 f1() works as desired (that is, f(1:3), say, gives me a three element
 list whose i-th element
 is an i-by-i matrix whose elements are all i).
 
 But f2() doesn't.
 
 How do I modify either function to use Recall()?  What exactly is
 Recall() calling here?
 
 --
 Robin Hankin
 Uncertainty Analyst
 Southampton Oceanography Centre
 European Way, Southampton SO14 3ZH, UK
  tel  023-8059-7743
 
 __
 R-help@stat.math.ethz.ch mailing list
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Re: [R] about memory

2005-03-30 Thread ronggui
[EMAIL PROTECTED] ulimit -a
core file size(blocks, -c) 0
data seg size (kbytes, -d) unlimited
file size (blocks, -f) unlimited
max locked memory (kbytes, -l) unlimited
max memory size   (kbytes, -m) unlimited
open files(-n) 1024
pipe size  (512 bytes, -p) 8
stack size(kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes(-u) unlimited
virtual memory(kbytes, -v) unlimited

so it seems the data segment size is not limited.
and it is still free mem(1000k or so),and swap(10k or so),and the error 
is(i translate it from chinese into english,maybe not exactly ,but i think the 
meanings are right):
error:can not allocate the vector size of 390585kb.
(: 390585 Kb)



On Wed, 30 Mar 2005 07:34:13 -0500
jon butchar [EMAIL PROTECTED] wrote:

 How much memory is free when R fails (e.g., what does top show while trying 
 to run your clustering)?  If there's still a sizeable amount of free memory 
 you may have to look into the system limits, maximum data segment size in 
 particular.  Many Linux distros have it set to unlimited but default Debian 
 may not.  If this turns out to be the problem, please do not, _do not_ raise 
 it to unlimited, but only to enough for R to work.
 
 hth,
 
 jon b
 
 
 
 On Wed, 30 Mar 2005 18:36:37 +0800
 ronggui [EMAIL PROTECTED] wrote:
 
  here is my system memory:
  [EMAIL PROTECTED] free
   total   used   free sharedbuffers cached
  Mem:256728  79440 177288  0   2296  36136
  -/+ buffers/cache:  41008 215720
  Swap:   481908  60524 421384
  
  and i want to cluster my data using hclust.my data has 3 variables and 
  1 cases.but it fails and saying have not enough memory for the vector 
  size.  I read the help doc and use $R --max-vsize=800M to start the R 
  2.1.0beta under debian linux.but it still can not get the solution.so is my 
  pc'memory not enough to carry this analysis or my mistake on setting the 
  memory?
  
  thank you.
  
  __
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[R] A question about multiple comparison of analysis of covariance using SPSS

2005-03-30 Thread xiaoyun wu
Hi, all,
I have a question about multiple comparison of analysis of covariance using 
SPSS 10.
The way I used was in the menu 'Analyze-General Linear Model-Mutivariate'. 
When I only chosed 'Dependent Variables' and 'Fixed Factor(s)', the button of 
'Post Hoc' can be pressed and I can chose some ways to do multiple comparison. 
However, after I chosed 'Covariate(s)', the button of 'Post Hoc' became grey 
and could not be pressed. How can I do multiple comparison? 
By the way, I am not in the mail-list. Pls mail back to me. Thanks!



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Re: [R] error messages on R CMD check

2005-03-30 Thread David Firth
Dear Johannes
I have noticed the same complaint, and you are right that it can be 
unconnected with faulty S3 methods, etc., in your package.

For example, in my relimp package (current version 0.9-1, new on CRAN 
today) the DESCRIPTION file has
  Suggests: tcltk
and that works fine (ie it passes R CMD check).

But if I change that to
  Depends: tcltk
I get the same kind of errors that you got:
david% R CMD check relimp
[...]
* checking S3 generic/method consistency ... WARNING
Error in .try_quietly({ : Error: package 'tcltk' could not be loaded
Execution halted
See section 'Generic functions and methods' of the 'Writing R 
Extensions'
manual.
* checking replacement functions ... WARNING
Error in .try_quietly({ : Error: package 'tcltk' could not be loaded
Execution halted
In R, the argument of a replacement function which corresponds to the 
right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error in .try_quietly({ : Error: package 'tcltk' could not be loaded
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... ERROR
Error in .try_quietly({ : Error: package 'tcltk' could not be loaded

In this case it is because the calling environment for R CMD check did 
not have the DISPLAY variable set, so tcltk could not be loaded.  If 
instead I do

david% setenv DISPLAY :0
david% R CMD check relimp
then all checks are passed.  This is with
david% R --version
R 2.0.1 (2004-11-15).
This is not really an explanation of what you got, just a confirmation 
that something here probably needs fixing (even if it's only the error 
message).  Perhaps one of us should file a bug report (having checked 
first that a fix is not already made in the latest development 
version)?

David
On 30 Mar, 2005, at 13:34, Johannes Hüsing wrote:
Dear all,
I am trying to wrap up a package. On entering
R CMD check, I get the following error messages:
[...]
* checking S3 generic/method consistency ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
	package/namespace load failed for 'resper'
Execution halted
See section 'Generic functions and methods' of the 'Writing R 
Extensions'
manual.
* checking replacement functions ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
	package/namespace load failed for 'resper'
Execution halted
In R, the argument of a replacement function which corresponds to the 
right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
	package/namespace load failed for 'resper'
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... ERROR
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :

I am not getting these messages, nor their relation to
section 'Generic functions and methods' of the 'Writing
R Extensions' manual, as I did not write any generic methods
in my package.
There has been some discussion of the error message around
Christmas 2003: 
http://maths.newcastle.edu.au/~rking/R/devel/03b/1438.html,
but I can't see how the circumstances described there apply to
my situation (export a class name).

Could somebody give me a clue on how to give my search a
direction?
Greetings
Johannes
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[R] Re:Plotting to A4 and replacing x-axis with actual years.

2005-03-30 Thread Marshall Mdoka
Hie,

I have written before and probably missed the reply.

1.) I have my figures in a 3X3 array and want to fit them onto a A4 size
page. I have written commands to try a represent them in eps format but
still their cutting out information.

2.) I have an odd number of years and wanted to represent them say 1980 1985
1990 1995 2000 instead of 1 5 10 etc. However, the years are not
overwritting in the year I want since the first year in my x-axis is 1979
which is year 1 and year 5 being 1984.

Could you please help especially on the first problem.

Thanking you in advance,

Marshall Mdoka

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[R] Re:Plotting to A4 and replacing x-axis with actual years.

2005-03-30 Thread Marshall Mdoka
Hie,

I have written before and probably missed the reply.

1.) I have my figures in a 3X3 array and want to fit them onto a A4 size
page. I have written commands to try a represent them in eps format but
still their cutting out information.

2.) I have an odd number of years and wanted to represent them say 1980 1985
1990 1995 2000 instead of 1 5 10 etc. However, the years are not
overwritting in the year I want since the first year in my x-axis is 1979
which is year 1 and year 5 being 1984.

Could you please help especially on the first problem.

Thanking you in advance,

Marshall Mdoka

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RE: [R] about memory

2005-03-30 Thread Huntsinger, Reid
hclust creates a distance matrix. In your case it is 10,000 x 10,000. For
various reasons several copies are created, so you probably need at least 

100M x 8 bytes per entry x 3 copies = 2.4 GB

just for the distance matrix. If you don't have that much RAM the
computation will probably take longer than you're willing to wait.

Reid Huntsinger

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of ronggui
Sent: Wednesday, March 30, 2005 5:37 AM
To: r-help@stat.math.ethz.ch
Subject: [R] about memory


here is my system memory:
[EMAIL PROTECTED] free
 total   used   free sharedbuffers cached
Mem:256728  79440 177288  0   2296  36136
-/+ buffers/cache:  41008 215720
Swap:   481908  60524 421384

and i want to cluster my data using hclust.my data has 3 variables and 1
cases.but it fails and saying have not enough memory for the vector size.  I
read the help doc and use $R --max-vsize=800M to start the R 2.1.0beta under
debian linux.but it still can not get the solution.so is my pc'memory not
enough to carry this analysis or my mistake on setting the memory?

thank you.

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Re: [R] fastbw question

2005-03-30 Thread Frank E Harrell Jr
Peter Flom wrote:
Hello
I am running R 2.0.1 on Windows, I am attempting to use Frank Harrell's
'fastbw' function (from the Design library), but I get an error that the
fit was not created with a Design library fitting function; yet when I
go to the help for fastbw (and also look in Frank's book Regression
Modeling Strategies) it appears that fastbw should work with a model
created with lm.
Relevant code

model.borrow.logols- lm(logborrow~age + sex + racgp + yrseduc + 
 needlchg + gallery  + totni + inject + poly(year.of.int,3)  + druginj
+ inj.years  + HTLV3)

fastbw(model.borrow.logols)
The error message was exactly correct.  lm is not a Design fitting 
function.  Try ols.  -Frank


Thanks in advance
Peter
Peter L. Flom, PhD
Assistant Director, Statistics and Data Analysis Core
Center for Drug Use and HIV Research
National Development and Research Institutes
71 W. 23rd St
www.peterflom.com
New York, NY 10010
(212) 845-4485 (voice)
(917) 438-0894 (fax)
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--
Frank E Harrell Jr   Professor and Chair   School of Medicine
 Department of Biostatistics   Vanderbilt University
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[R] R --max-vsize=4000M --max-nsize=4000M

2005-03-30 Thread Pavel Khomski
hello!
what's wrong???
i use 32 bit machine.
every time i 'm connecting the server  to do my work with R on it , 
after having done

 
 R --max-vsize=4000M --max-nsize=4000M
i become  wrong limits specification  for Ncells:
 .
 gc()
   used(Mb)   gc trigger   (Mb)   limit 
(Mb)
Ncells   698799 18.7  1644099   44   112000
Vcells 65744346501.6  189257063   1444   4000

is there anything wrong?
thanks a lot
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Re: [R] Recall() and sapply()

2005-03-30 Thread Thomas Lumley
On Wed, 30 Mar 2005, Robin Hankin wrote:
Hi.
I'm having difficulty following the advice given in help(Recall).  Consider 
the two
following toy functions:

f1 - function(n){
 if(length(n)1){return(sapply(n,f1))}
 matrix(n,n,n)
}
f2 - function(n){
 if(length(n)1){return(sapply(n,Recall))}
 matrix(n,n,n)
}
f1() works as desired (that is, f(1:3), say, gives me a three element list 
whose i-th element
is an i-by-i matrix whose elements are all i).

But f2() doesn't.
How do I modify either function to use Recall()?  What exactly is Recall() 
calling here?

You can't use Recall here. I thought this was explicitly documented, but 
it turns out that it isn't, an omission I will fix.

You don't need Recall, because R can easily have recursive functions 
without it (unlike S)
- as you show in f1, the function can call itself
- the problem with f1 is that it stops working if you change the name, but
  ?local shows how to get around this. This is probably the best way to
  implement recursion.
- You can even implement Y, the appplicative-order fixed point operator
  to create anonymous recursive functions a la lambda calculus.

-thomas
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Re: [R] Solved - gnuclient problems witrh R/ESS in linux

2005-03-30 Thread Fredrik Lundgren
Finally,
I found a way to make fix() and edit() work with gnuclient
in ESS-5.2.6/R-2.0.1/Xemacs-21.4.15-r3 on gentoo-linux.
When invoking R/ESS the following is induced by ESS
options(STERM='iESS', editor='gnuclient -q')
It appears as if the problem is with 'gnuclient -q'
(whatever does -q signify?? From the man page it appears to disconnect 
the association between the opened buffer and gnuclient - which was teh 
very problem)
and when i changed a row in ess-5.2.6/lisp/gnu-cust.el
things worked in the expected way.
Change row

if (featurep 'xemacs) gnuclient -q emacsclient))) ;; unix
to
if (featurep 'xemacs) gnuclient emacsclient))) ;; unix
and all things work OK.
The only thing needed in init.el for gnuclient to work in this setup
is
(gnuserv-start)
and possibly
(setq gnuserv-frame (selected-frame))
if you whant the gnuclient frame to open within Xemacs
and no fuss with PATH
Many thanks to Richard M. Heiberger for all help!
Fredrik
PS A peculiar thing though - In the latest manual for ESS it's said:
4.9 Using emacsclient
When starting R or S under Unix, ESS sets options(editor=emacsclient).
(Under
Microsoft Windows, it will use gnuclient.exe rather than emacsclient,
but the same principle
applies.)
but I got options(editor=gnuclient -q)
now changed to options(editor=gnuclient )
DS
- Original Message - 
From: Fredrik Lundgren [EMAIL PROTECTED]
To: R-help r-help@stat.math.ethz.ch
Sent: Monday, March 28, 2005 7:37 PM
Subject: [R] gnuclient problems witrh R/ESS in linux


Dear list,
Not strictly R ...
In R on Xemacs with ESS (R-2.0.1, Xemacs-21.4.15-r3, ESS-5.2.6)
on gentoo-linux
when I use k-edit(k) or fix(k)
to change a small vector k - c(1,2,3,4,5,6)
the opened window (called '6b8b4567') appears not to be connected to 
the
gnuclient
and I'm able to edit the file but has no instructions in the
minibuffer
and
C-x # gives
'6b8b4567 does not belong to gnuserv client'

in init.el I have
(require 'gnuserv)
(gnuserv-start)
(setq gnuserv-frame (selected-frame))
Any help please?
Fredrik
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[R] Stratified Bootstrap question

2005-03-30 Thread Tim Hesterberg
Dear Qian,

You might try the S+Resample library, which has built-in support
for both sampling by subject and stratified sampling.

If you are a student, there is a free student version of S+.

See
www.insightful.com/downloads/libraries  (S+Resample)
www.insightful.com/Hesterberg/bootstrap (has link to the student version)

For the missing values, consider the S+Missing library,
which offers multiple imputation.  With S+, do
library(missing)

Tim Hesterberg

P.S.  The combination of sampling by subject and stratified sampling
was terribly messy to program.  If I'd known in advance how messy, I
never would have done it :-(  But it is done now.

Dear R users,

I have a question regarding stratified bootstrap question and how to implement
it using boot() in R's boot package.

My dataset is a longitudinal dataset (3 measurements per person at year
1, 4 and 7) composed of multiple clinic centers and multiple participants
within each clinic. It has missing values.

I want to do a bootstrap to find the standard errors and confidence
intervals for my variance components. My model is a mixed model with
random clinic and random participant within clinic.

I thought two methods to do bootstrap:
(1) bootstrap data; however, I have problem specifying the second
parameter for my statistic function, shall I use indices, weight or
frequency and how shall I relate to my dataset.
(2) bootstrap residuals; however, the dataset has multiple measurements
and missing values. I am wondering how to construct a new data frame
containing the residuals and fitted values.

Any ideas will be highly appreciated!
Sincerely yours,
Qian


| Tim Hesterberg   Research Scientist  |
| [EMAIL PROTECTED]  Insightful Corp.|
| (206)802-23191700 Westlake Ave. N, Suite 500 |
| (206)283-8691 (fax)  Seattle, WA 98109-3044, U.S.A.  |
|  www.insightful.com/Hesterberg   |

Download the S+Resample library from www.insightful.com/downloads/libraries

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[R] Installing GO 1.7.0

2005-03-30 Thread Tom 'spot' Callaway
I'm in the process of packaging R (and R modules) for future inclusion
in Fedora Extras, and I've managed to get several hundred modules
installed without issue, however, the GO metadata package is refusing to
comply.

Since I'm packaging this in rpm format, I can't use any of the automated
functions for build, I've got to do it locally through R.

The following steps work for other metadata packages (directory names
changing, obviously), but not for GO:

With the GO tarball unpacked into R-GO-1.7.0/GO...

cd R-GO-1.7.0/
rm -rf /var/tmp/R-GO-1.7.0-1-root-root
mkdir -p /var/tmp/R-GO-1.7.0-1-root-root/usr/lib/R/library
export R_LIBS=/var/tmp/R-GO-1.7.0-1-root-root/usr/lib/R/library
/usr/bin/R CMD INSTALL \
-l /var/tmp/R-GO-1.7.0-1-root-root/usr/lib/R/library GO

I get the following output:
* Installing *source* package 'GO' ...
** R
** data
** preparing package for lazy loading

** help
  Building/Updating help pages for package 'GO'
 Formats: text html latex example
  GOtexthtmllatex
  GOALLLOCUSID  texthtmllatex   example
  GOBPANCESTOR  texthtmllatex   example
  GOBPCHILDREN  texthtmllatex   example
  GOBPOFFSPRING texthtmllatex   example
  GOBPPARENTS   texthtmllatex   example
  GOCCANCESTOR  texthtmllatex   example
  GOCCCHILDREN  texthtmllatex   example
  GOCCOFFSPRING texthtmllatex   example
  GOCCPARENTS   texthtmllatex   example
  GOLOCUSID texthtmllatex   example
  GOLOCUSID2ALLGO   texthtmllatex   example
  GOLOCUSID2GO  texthtmllatex   example
  GOMFANCESTOR  texthtmllatex   example
  GOMFCHILDREN  texthtmllatex   example
  GOMFOFFSPRING texthtmllatex   example
  GOMFPARENTS   texthtmllatex   example
  GOQC  texthtmllatex
  GOTERMtexthtmllatex   example

But I never get the * DONE (GO) that I'm expecting. Instead, all of
the memory on the machine allocates (512MB), it starts to swap out, and
never completes.

When I look at the output from ps, I see:
 8290 pts/5S+ 0:00 /bin/sh /usr/lib/R/bin/INSTALL
-l /var/tmp/R-GO-1.7.0-1-root-root/us 8364 ?S  0:00 
 8421 pts/5D+ 1:11 /usr/lib/R/bin/exec/R --vanilla

When I kill the 8421 process, I get:

/usr/lib/R/bin/INSTALL: line 381:  8088 Doneecho
invisible(.libPaths(c(\${lib}\, .libPaths(;
tools:::.install_package_indices(\.\, \${R_PACKAGE_DIR}\)
  8089 Killed  | R_DEFAULT_PACKAGES=NULL LANG=C
${R_EXE} --vanilla /dev/null
ERROR: installing package indices failed

I let this run for over 6 hours, and it didn't seem to complete (or make
any changes).

Unfortunately, lots of Bioconductor seems to depend on GO... so any help
on getting this to install is appreciated.

Thanks,

~spot
-- 
Tom spot Callaway: Red Hat Sales Engineer || GPG Fingerprint: 93054260
Fedora Extras Steering Committee Member (RPM Standards and Practices)
Aurora Linux Project Leader: http://auroralinux.org
Lemurs, llamas, and sparcs, oh my!

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Re: [R] how i can get input from user input

2005-03-30 Thread Greg Snow
Also look at ?readline

Greg Snow, Ph.D.
Statistical Data Center
[EMAIL PROTECTED]
(801) 408-8111

 Uwe Ligges [EMAIL PROTECTED] 03/29/05 11:43PM 
Cuichang Zhao wrote:

 Hello, 
 Could you please tell me how i can get an input from the user in R?

Depends on the kind of input.

See, e.g., ?scan or ?menu

Uwe Ligges


 C-Ming 
  
 Mar 29, 2005
 
   
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Re: [R] about memory

2005-03-30 Thread jon butchar
Yes, you may need more memory unless you can somehow free a good amount of RAM 
or find a more memory-efficient method for clustering.  If I'm reading it 
correctly, R wanted to allocate about 382 MB memory on top of what it had 
already taken but your computer had only about 98 MB swap plus about 1 MB RAM 
left to give.


On Wed, 30 Mar 2005 22:02:04 +0800
ronggui [EMAIL PROTECTED] wrote:

 [EMAIL PROTECTED] ulimit -a
 core file size(blocks, -c) 0
 data seg size (kbytes, -d) unlimited
 file size (blocks, -f) unlimited
 max locked memory (kbytes, -l) unlimited
 max memory size   (kbytes, -m) unlimited
 open files(-n) 1024
 pipe size  (512 bytes, -p) 8
 stack size(kbytes, -s) 8192
 cpu time (seconds, -t) unlimited
 max user processes(-u) unlimited
 virtual memory(kbytes, -v) unlimited
 
 so it seems the data segment size is not limited.
 and it is still free mem(1000k or so),and swap(10k or so),and the error 
 is(i translate it from chinese into english,maybe not exactly ,but i think 
 the meanings are right):
 error:can not allocate the vector size of 390585kb.
 (´íÎó: ÎÞ·¨·ÖÅä´óСΪ390585 KbµÄÏòÁ¿)

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Re: [R] Installing GO 1.7.0

2005-03-30 Thread Seth Falcon
Hi Tom,

I'm cc'ing to Bioconductor as that is probably a better place for the
discussion.


Tom 'spot' Callaway [EMAIL PROTECTED] writes:

 I'm in the process of packaging R (and R modules) for future inclusion
 in Fedora Extras, and I've managed to get several hundred modules
 installed without issue, however, the GO metadata package is refusing to
 comply.

 ERROR: installing package indices failed

 I let this run for over 6 hours, and it didn't seem to complete (or make
 any changes).

We have a solution for this and will send or make available an updated
GO package shortly.  With the updated GO package you should be able to
R CMD INSTALL without it taking much time.

Best,

+ seth

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Re: [BioC] Follow-up to: [R] Annotation metadata kills help.search

2005-03-30 Thread Seth Falcon
Gerard Tromp [EMAIL PROTECTED] writes:

 Greetings,

 this is a follow-up to the mailing below. Seth Falcon replied and indicated
 that he and several others were unable to replicate the problem.
 Specifically he requested:

 
 We are not able to reproduce this issue.  If you reinstall the
 annotation packages does the error reappear?

 If so, an exact transcript of the commands entered, their output, and
 the output of traceback() right after the error would be helpful ---
 and it would be best to move the discussion to the bioconductor list.
 ===

 The answers are: Yes, the problem is reproducible. I did a complete
 reinstall of R and bioconductor end everything worked fine until I installed
 an annotation package.

With the added information from Gerard, we were able to reproduce the
problem and are currently working on a fix.  

Thanks,

+ seth

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RE: [R] how i can get input from user input

2005-03-30 Thread Berton Gunter
If you are on Windows and want to go GUI, see ?choose.files, ?winMenuAdd,
?winDialog, ?select.list

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
 
The business of the statistician is to catalyze the scientific learning
process.  - George E. P. Box
 
 

 -Original Message-
 From: [EMAIL PROTECTED] 
 [mailto:[EMAIL PROTECTED] On Behalf Of Greg Snow
 Sent: Wednesday, March 30, 2005 9:45 AM
 To: [EMAIL PROTECTED]; [EMAIL PROTECTED]
 Cc: r-help@stat.math.ethz.ch
 Subject: Re: [R] how i can get input from user input
 
 Also look at ?readline
 
 Greg Snow, Ph.D.
 Statistical Data Center
 [EMAIL PROTECTED]
 (801) 408-8111
 
  Uwe Ligges [EMAIL PROTECTED] 03/29/05 11:43PM 
 Cuichang Zhao wrote:
 
  Hello, 
  Could you please tell me how i can get an input from the user in R?
 
 Depends on the kind of input.
 
 See, e.g., ?scan or ?menu
 
 Uwe Ligges
 
 
  C-Ming 
   
  Mar 29, 2005
  
  
  -
  
  
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[R] Step error

2005-03-30 Thread vasilis pappas
Could anyone tell me what am I doing wrong?

 pro-function(indep,dep){
+  d-data.frame(indep)
+  form-formula(lm(dep~.,data=d))
+ 
forward-step(lm(dep~X1,data=d),scope=form,trace=0,direction='f')
+  return(forward) 
+ }
 pro(m,q)
Error in inherits(x, data.frame) : Object d not
found

Where q is a vector with the dependent variable's
values
and m is a matrix containing the values of the
independent variables.

While writing the above without a function form has no
problem, that is :

 d-data.frame(m)
 form-formula(lm(q~.,data=d))

forward-step(lm(q~X1,data=d),scope=form,trace=0,direction='f')
 forward

Call:
lm(formula = q ~ X1 + X2 + X5, data = d)

Coefficients:
(Intercept)   X1   X2   X5  
-15.7988.7656.774   -4.245  


Thank you in advance!
Vasilis

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[R] compute adjusted mean

2005-03-30 Thread Steven Lu
Dear Sir/Madam:
I have a question about computing adjusted mean using R. I am really new to 
this area.
 
Suppose I have a response Y, and covariate: treat (binary), sex (binary) race 
(catogorical ) and age (continuous).
the model: Y~treat+sex+race+age;
I am asked to compute the adjusted mean of Y for treat=1.
 
would you please tell me (in detail) how I can do this? I searched the R 
homepage and got some information, but not quite helpful.
 
thanks a lot,
 
Steven L. Lu
 
 
 



-


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[R] PDF and PS output

2005-03-30 Thread Hans Halvorson
I'm using R 2.0 on Redhat Linux 9.  When I try to produce PDF or PS
output, the files are corrupted -- they won't open in Acroread, xpdf,
ggv, and on attempting to convert to PNG, I get message This file has
corrupted %%EOF marker.  Perhaps I am just doing something wrong.  I
did:

 pdf()
 hist(unlist(foo.bar))

I have no trouble viewing the output in Xwindows.

Thanks,
Hans

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Re: [R] Stratified Bootstrap question

2005-03-30 Thread Qian An
Dear Tim,

Thank you very much for your information. I will try to play with S+ as
you suggested. At the same time, I would like to share our idea with you
about the stratified bootstrapping for my scenario. I am not sure if it is
correct. I am playing with it now.

We created a new dataset containing clinic and patient id within clinic,
then stratified boot() function was used to bootstrap
the newly-created dataset. Based on the indices of the bootstrap result,
since patient id is unique, we found the patient ids from the new dataset,
then found the corresponding dataset to fit a mixed model from the
original dataset using patient ids.

I am trying to run the program now, but it takes longer than what I
expected. 500 times takes more than 3 hours and it is still running. I
will see if this is working properly.

Thank you very much for your input,
Qian



On 30 Mar 2005, Tim Hesterberg wrote:

 Dear Qian,

 You might try the S+Resample library, which has built-in support
 for both sampling by subject and stratified sampling.

 If you are a student, there is a free student version of S+.

 See
 www.insightful.com/downloads/libraries(S+Resample)
 www.insightful.com/Hesterberg/bootstrap   (has link to the student 
 version)

 For the missing values, consider the S+Missing library,
 which offers multiple imputation.  With S+, do
   library(missing)

 Tim Hesterberg

 P.S.  The combination of sampling by subject and stratified sampling
 was terribly messy to program.  If I'd known in advance how messy, I
 never would have done it :-(  But it is done now.

 Dear R users,
 
 I have a question regarding stratified bootstrap question and how to 
 implement
 it using boot() in R's boot package.
 
 My dataset is a longitudinal dataset (3 measurements per person at year
 1, 4 and 7) composed of multiple clinic centers and multiple participants
 within each clinic. It has missing values.
 
 I want to do a bootstrap to find the standard errors and confidence
 intervals for my variance components. My model is a mixed model with
 random clinic and random participant within clinic.
 
 I thought two methods to do bootstrap:
 (1) bootstrap data; however, I have problem specifying the second
 parameter for my statistic function, shall I use indices, weight or
 frequency and how shall I relate to my dataset.
 (2) bootstrap residuals; however, the dataset has multiple measurements
 and missing values. I am wondering how to construct a new data frame
 containing the residuals and fitted values.
 
 Any ideas will be highly appreciated!
 Sincerely yours,
 Qian

 
 | Tim Hesterberg   Research Scientist  |
 | [EMAIL PROTECTED]  Insightful Corp.|
 | (206)802-23191700 Westlake Ave. N, Suite 500 |
 | (206)283-8691 (fax)  Seattle, WA 98109-3044, U.S.A.  |
 |  www.insightful.com/Hesterberg   |
 
 Download the S+Resample library from www.insightful.com/downloads/libraries



***
Qian An
Division of Biostatistics
University of Minnesota
(phone) 612-626-2263
(fax) 612-626-8892
Email: [EMAIL PROTECTED]

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Re: [R] PDF and PS output

2005-03-30 Thread Hans Halvorson
Ach -- such a simple mistake.  Thank you for pointing out my error,
and I apologize for wasting your time.

Best wishes,
Hans



Peter Dalgaard [EMAIL PROTECTED] writes:

 Hans Halvorson [EMAIL PROTECTED] writes:

 I'm using R 2.0 on Redhat Linux 9.  When I try to produce PDF or PS
 output, the files are corrupted -- they won't open in Acroread, xpdf,
 ggv, and on attempting to convert to PNG, I get message This file has
 corrupted %%EOF marker.  Perhaps I am just doing something wrong.  I
 did:
 
  pdf()
  hist(unlist(foo.bar))
 
 I have no trouble viewing the output in Xwindows.

 Did you terminate the device properly (dev.off() or exit from R)?

 -- 
O__   Peter Dalgaard Blegdamsvej 3  
   c/ /'_ --- Dept. of Biostatistics 2200 Cph. N   
  (*) \(*) -- University of Copenhagen   Denmark  Ph: (+45) 35327918
 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907

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Re: [R] PDF and PS output

2005-03-30 Thread Ulises M. Alvarez
Hi:
dev.off()
Check your file now...
That's it!
Hans Halvorson wrote:
I'm using R 2.0 on Redhat Linux 9.  When I try to produce PDF or PS
output, the files are corrupted -- they won't open in Acroread, xpdf,
ggv, and on attempting to convert to PNG, I get message This file has
corrupted %%EOF marker.  Perhaps I am just doing something wrong.  I
did:

pdf()
hist(unlist(foo.bar))

I have no trouble viewing the output in Xwindows.
Thanks,
Hans
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http://sophie.fata.unam.mx/
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Re: [R] Stratified Bootstrap question

2005-03-30 Thread Qian An
Dear Tim,

Thank you so much for your help. My random mixed model is as follows:

b.lme - lme(sbp ~ age + gender, data=bdat, random=~1/clinic/id,
 na.action=na.omit)

When doing bootstrap with stratum clinic, a patient's data may appear
multiple times in the boostrap dataset and all of them share the same id.
I am wondering if the data from the same patient will cause problems in
lme fitting or not. Do you happen to know this or not?

I am really sorry for coming up more questions. Thank you so much for your
help.

Sincerely yours,
Qian








On 30 Mar 2005, Tim Hesterberg wrote:

 Dear Tim,
 
 Thank you very much for your information. I will try to play with S+ as
 you suggested. At the same time, I would like to share our idea with you
 about the stratified bootstrapping for my scenario. I am not sure if it is
 correct. I am playing with it now.
 
 We created a new dataset containing clinic and patient id within clinic,
 then stratified boot() function was used to bootstrap
 the newly-created dataset. Based on the indices of the bootstrap result,
 since patient id is unique, we found the patient ids from the new dataset,
 then found the corresponding dataset to fit a mixed model from the
 original dataset using patient ids.

 That sounds reasonable.  That is what the S+Resample library does
 internally.

 I am trying to run the program now, but it takes longer than what I
 expected. 500 times takes more than 3 hours and it is still running. I
 will see if this is working properly.

 This may be normal.  Fitting mixed models is iterative, unlike
 simple linear regression for which there is a closed-form solution.
 So running many replications can take a while.

 It might help if you specify starting values for the fixed-effects
 coefficients.  Run the model for the original data, and extract
 the fixed-effects coefficients.  Then specify those as starting
 values; this could make the bootstrap replicates run faster.

 
 Thank you very much for your input,
 Qian
 
 
 
 On 30 Mar 2005, Tim Hesterberg wrote:
 
  Dear Qian,
 
  You might try the S+Resample library, which has built-in support
  for both sampling by subject and stratified sampling.
 
  If you are a student, there is a free student version of S+.
 
  See
  www.insightful.com/downloads/libraries (S+Resample)
  www.insightful.com/Hesterberg/bootstrap(has link to the student 
  version)
 
  For the missing values, consider the S+Missing library,
  which offers multiple imputation.  With S+, do
 library(missing)
 
  Tim Hesterberg
 
  P.S.  The combination of sampling by subject and stratified sampling
  was terribly messy to program.  If I'd known in advance how messy, I
  never would have done it :-(  But it is done now.
 
  Dear R users,
  
  I have a question regarding stratified bootstrap question and how to 
  implement
  it using boot() in R's boot package.
  
  My dataset is a longitudinal dataset (3 measurements per person at year
  1, 4 and 7) composed of multiple clinic centers and multiple participants
  within each clinic. It has missing values.
  
  I want to do a bootstrap to find the standard errors and confidence
  intervals for my variance components. My model is a mixed model with
  random clinic and random participant within clinic.
  
  I thought two methods to do bootstrap:
  (1) bootstrap data; however, I have problem specifying the second
  parameter for my statistic function, shall I use indices, weight or
  frequency and how shall I relate to my dataset.
  (2) bootstrap residuals; however, the dataset has multiple measurements
  and missing values. I am wondering how to construct a new data frame
  containing the residuals and fitted values.
  
  Any ideas will be highly appreciated!
  Sincerely yours,
  Qian
 
  
  | Tim Hesterberg   Research Scientist  |
  | [EMAIL PROTECTED]  Insightful Corp.|
  | (206)802-23191700 Westlake Ave. N, Suite 500 |
  | (206)283-8691 (fax)  Seattle, WA 98109-3044, U.S.A.  |
  |  www.insightful.com/Hesterberg   |
  
  Download the S+Resample library from www.insightful.com/downloads/libraries
 
 
 
 ***
 Qian An
 Division of Biostatistics
 University of Minnesota
 (phone) 612-626-2263
 (fax) 612-626-8892
 Email: [EMAIL PROTECTED]
 ***
 



***
Qian An
Division of Biostatistics
University of Minnesota
(phone) 612-626-2263
(fax) 612-626-8892
Email: [EMAIL PROTECTED]

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[R] French Curve

2005-03-30 Thread dream home
Dear R experts,

Did someone implemented French Curve yet?  Or can anyone point me some
papers that I can follow to implement it?

thanks in advance for your help.

Paul

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Re: [R] Base and lattice graphics on the same graphics page

2005-03-30 Thread Paul Murrell
Hi
Deepayan Sarkar wrote:
On Tuesday 29 March 2005 22:32, John Maindonald wrote:
Although base graphics does not mix with lattice in the one graph,
I've found that print.trellis(position=..., ) and the use of
par(fig=...)
to put regular and trellis graphics on the one graphics page works
like a treat, at least in version 2.0.1 of R.  [Base graphics
functions that are themselves inconsistent with par(fig=...) are
obviously disallowed.]
I am wondering whether there are caveats of which I and others
should be aware, or whether there is a risk that the ongoing
development of R's graphics abilities will render such a cohabitation
unworkably fractious.

Paul would know better, but I think that's unlikely. In fact, the 
gridBase package allows you to do use grid (and hence lattice) 
functions to add to a base plot, as well as (I didn't realize this 
before) the other way round. The only caveat is that resizing the 
device may mess things up. 

Yep, sounds like you're doing exactly the sort of thing that gridBase 
does.  See R News 3(2) for a discussion.

Paul

You may have to be careful with new devices. Your example pasted on a 
fresh session (tested only on r-devel) starts a new page for the 
boxplot since it thinks that new=TRUE doesn't make sense (because 
there's no 'old' plot yet).

Deepayan
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--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
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Re: [BioC] Follow-up to: [R] Annotation metadata kills help.search

2005-03-30 Thread Seth Falcon
Hello Gerard, all,

The annotation packages breaking help.search was due to improperly
built annotation packages.

We have posted updated annotation packages to the Bioconductor meta
data repository.

Reinstalling the annotation data packages should resolve the issue and
allow help.search to function normally.

Please let us know (on [EMAIL PROTECTED]) if you find
otherwise.

Thanks,

+ seth

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RE: [R] NA's?

2005-03-30 Thread Bill.Venables
Your message doesn't help us very much.  You haven't said what kind of
calculation it is you want to do, and that certainly matters.  For
example, for some kinds of computations the solution you started below
would work fine:

 M - matrix(1:16, 4, 4)
 is.na(diag(M)) - TRUE
 M
 [,1] [,2] [,3] [,4]
[1,]   NA59   13
[2,]2   NA   10   14
[3,]37   NA   15
[4,]48   12   NA
 rowSums(M, na.rm = TRUE)
[1] 27 26 25 24
 colSums(M, na.rm = TRUE)
[1]  9 20 31 42

You can also use apply( ) with functions that will accept missing values
(and ignore them) for computations on either the rows or the columns.

Hoping for a general mechanism that would somehow signal the diagonal
values as values to be ignored in a general way is not a possibility.
Just as a curiosity, what were you hoping that na.omit(M) would do?

V.

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Asha Jayanthi
Sent: Thursday, 31 March 2005 11:22 AM
To: r-help@stat.math.ethz.ch
Subject: [R] NA's?


I have a large matrix of data .

The size of the matrix ranges from 100 x 100 to 1000 x 1000

Now i have to do computations on that. And should not consider the
diagonal 
elements.

I tried setting diag(M) = NA  and M = na.omit(M).

But this omits all the rows. I only want to omit that diagonal elements
only 
but consider the whole row.

diag(M) = 0 seems like a good option but this will affect my result.

How to proceed with this. How to just ignore some specific values. what
if i 
want to consider only the upper / lower triangular matrix

Asha


http://adfarm.mediaplex.com/ad/ck/4686-26272-10936-31?ck=RegSell Start
your 
business.

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RE: [R] 2d plotting and colours

2005-03-30 Thread Mulholland, Tom
Since I was only concentrating on colour issues and not on your specific 
problem I was just showing the possibilities.

Does this code help

n - 5
par(mfrow = c(2,2))
palette(default)
barplot(1:25,col = 1:25)
palette(rainbow(n))
barplot(1:25,col = 1:25)
palette(rgb((0:15)/15, g=0,b=0, names=paste(red,0:15,sep=.)))
barplot(1:25,col = 1:25)


require(cluster)
x - runif(100) * 8 + 2
cl - kmeans(x, n)
palette(rainbow(n))
plot(x, col = cl$cluster)
abline(h = cl$centers, lty = 2,col = grey )
palette(palette()[order(cl$centers)])
points(x,col = cl$cluster,pch = 20,cex = 0.4)

However you may wish to choose your colours in a way that is different from 
cl$cluster which is why I changed the palette before plotting the points. You 
should see that they now are ordered from bottom to top of the last plot.

You could also choose to create a vector with your colours and then use the 
value in cl$cluster to select the colours

mycols - rainbow(n)
plot(x,col = mycols[cl$cluster])

Tom

 -Original Message-
 From: Asha Jayanthi [mailto:[EMAIL PROTECTED]
 Sent: Thursday, 31 March 2005 9:17 AM
 To: r-help@stat.math.ethz.ch
 Subject: RE: [R] 2d plotting and colours
 
 
 Thank you very much.
 
 the code
 plot(x, col = s)
 points(cl$centers, col = s, pch = 8, cex=2)
 
 does not plot the points according to the group colors. The 
 plots are used 
 to identify the groups by colors
 
 That could be done by
 
 plot(x, col = cl$cluster)
 
 This means that we need to set the default colours , say col 
 = cl$cluster = 
 a set of group numbers say 1...10 should produce 10 distinct 
 colours points 
 grouped by colour.
 
 how to do this when you have more than 8 group colours to plot
 
 From: Mulholland, Tom [EMAIL PROTECTED]
 To: r-help@stat.math.ethz.ch,Asha Jayanthi 
 [EMAIL PROTECTED]
 Subject: RE: [R] 2d plotting and colours
 Date: Wed, 30 Mar 2005 15:59:46 +0800
 
 And getting back to your question about the palette
 
 there are a lot of ways to do this
 
 assuming you have just started a session
 
 palette()
 # will give
 #[1] black   red green3  bluecyan
 #[6] magenta yellow  gray
 
 palette(rainbow(24))  # There's also 'heat.colors'  'topo.colors'
 palette()
 
 # [1] red #FF4000 #FF8000
 # [4] #FFBF00 yellow  #BFFF00
 # [7] #80FF00 #40FF00 green
 #[10] #00FF40 #00FF80 #00FFBF
 #[13] cyandeepskyblue #0080FF
 #[16] #0040FF blue#4000FF
 #[19] #8000FF #BF00FF magenta
 #[22] #FF00BF #FF0080 #FF0040
 
 palette(rgb((0:15)/15, g=0,b=0, names=paste(red,0:15,sep=.)))
 palette()
 # [1] black   #11 #22 #33 #44
 # [6] #55 #66 #77 #88 #99
 #[11] #AA #BB #CC #DD red2
 #[16] red
 
 If you are looking to use colours that take account of 
 colour blindness
 you could try the package dichromat. (I think 2.1 will have 
 some of this 
 inbuilt)
 
 Once you look through the help files associated with some of 
 these options 
 you
 will find the way that best suits your method of working.
 
 Tom
 
 
 
 
 
 
   -Original Message-
   From: Uwe Ligges [mailto:[EMAIL PROTECTED]
   Sent: Wednesday, 30 March 2005 3:18 PM
   To: TEMPL Matthias
   Cc: r-help@stat.math.ethz.ch; Asha Jayanthi
   Subject: Re: [R] 2d plotting and colours
  
  
   TEMPL Matthias wrote:
  
Hi!
   
There are more than 8 colors.
  
   Yes, e.g. for rgb space there are 16777216, see ?rgb.
  
   Uwe Ligges
  
  
  
x - rbind(matrix(rnorm(100, sd = 0.3), ncol = 2),
matrix(rnorm(100, mean = 1, sd = 0.3), 
 ncol = 2))
   
(cl - kmeans(x, i, 20))
   
s - c(tomato4, turquoise, slateblue, wheat,
   snow, skyblue,
peru, pink)
# see at:
colors()
   
plot(x, col = s)
   
points(cl$centers, col = s, pch = 8, cex=2)
   
   
Best,
Matthias
   
   
   
   
   
   Hi!
   
   I am new to R just 3 days in it and i apologize if my
   questions seem very
   trivial and consumed your valuable time.
   
   I am coding in perl and i stumbled upon R regarding 
 plotting good
   statistical graphs.
   
   I tried the kmean clustering for a large matrix ,say  150 *
   150 . I tried
   the example code given in the tutorial to perform 2d plot
   
   # i ranges from 2 to 10
   cl - kmeans(x, i, 20)
   plot(x, col = cl$cluster)
   points(cl$centers, col = 1:i )
   
   I see that there are only 8 colours defined , namely
   black,red,green,blue,cyan,magenta,yello,gray.
   
   How should i set my colour preferences to obtain my palette
   of colours? I
   checked in the totorial which talks about R.colors and
   palatte , but i
   failed to understand how to set it.
   
   Thank You
   
   Asha
   
   
   MSN Messenger!
   
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[R] Using kmeans given cluster centroids and data with NAs

2005-03-30 Thread Sophie.Bestley
Hello,

I have used the functions agnes and cutree to cluster my data (4977
objects x 22 variables) into 8 clusters. I would like to refine the
solution using a k-means or similar algorithm, setting the initial
cluster centres as the group means from agnes. However my data matrix
has NA's in it and the function kmeans does not appear to accept this?

 dim(centres)
[1]  8 22

 dim(data)
[1] 4977   22

 x - kmeans(data,centres)
Error in kmeans(data, centres) : NA/NaN/Inf in foreign function call
(arg 1)

I have looked extensively through the mail archives but cannot find
if/where someone has provided the answer.

Thanks in advance,
SB

Sophie Bestley
Pelagic Fisheries and Ecosystems
CSIRO Marine Research
GPO Box 1538 
Hobart, Tasmania 7001
AUSTRALIA 

Phone: +61 3 6232 5048  
Fax: +61 3 6232 5053
Email: [EMAIL PROTECTED]
Website: http://www.marine.csiro.au





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RE: [R] NA's?

2005-03-30 Thread Mulholland, Tom
See upper.tri and lower.tri.

I think that you might also look for specific packages that function using 
matrices, from what I have seen these often have the capacity to ignore the 
diagonal or use just the upper or lower triangle. This is not an area that I 
use very much, but I have seen various posts about different types of matrices 
and there appears to be quite a lot of code that deals with the range of types 
and uses. Obvious candidates include the Matrix package, but a search for 
matrix in all of the CRAN packages brings up a bewildering variety of matrix 
related functions. You may find it useful to search for the specific type of 
manipulation that you are attempting.

Tom

 -Original Message-
 From: Asha Jayanthi [mailto:[EMAIL PROTECTED]
 Sent: Thursday, 31 March 2005 9:22 AM
 To: r-help@stat.math.ethz.ch
 Subject: [R] NA's?
 
 
 I have a large matrix of data .
 
 The size of the matrix ranges from 100 x 100 to 1000 x 1000
 
 Now i have to do computations on that. And should not 
 consider the diagonal 
 elements.
 
 I tried setting diag(M) = NA  and M = na.omit(M).
 
 But this omits all the rows. I only want to omit that 
 diagonal elements only 
 but consider the whole row.
 
 diag(M) = 0 seems like a good option but this will affect my result.
 
 How to proceed with this. How to just ignore some specific 
 values. what if i 
 want to consider only the upper / lower triangular matrix
 
 Asha
 
 
 http://adfarm.mediaplex.com/ad/ck/4686-26272-10936-31?ck=RegSe
ll Start your 
business.

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RE: [R] Using kmeans given cluster centroids and data with NAs

2005-03-30 Thread Mulholland, Tom
Does ?na.omit help

x - kmeans(na.omit(data),centres)

of course if you have too many NAs you need to be sure that their removal does 
not unduly influence the results.

Although I am a bit confused as I thought that agnes did not allow NAs. I 
assume that you are running an alternative clustering method using the results 
of the first process as the starting point for the partitioning process and are 
thus using the same initial data.

Tom

 -Original Message-
 From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
 Sent: Thursday, 31 March 2005 11:33 AM
 To: r-help@stat.math.ethz.ch
 Subject: [R] Using kmeans given cluster centroids and data with NAs
 
 
 Hello,
 
 I have used the functions agnes and cutree to cluster my data (4977
 objects x 22 variables) into 8 clusters. I would like to refine the
 solution using a k-means or similar algorithm, setting the initial
 cluster centres as the group means from agnes. However my data matrix
 has NA's in it and the function kmeans does not appear to accept this?
 
  dim(centres)
 [1]  8 22
 
  dim(data)
 [1] 4977   22
 
  x - kmeans(data,centres)
 Error in kmeans(data, centres) : NA/NaN/Inf in foreign function call
 (arg 1)
 
 I have looked extensively through the mail archives but cannot find
 if/where someone has provided the answer.
 
 Thanks in advance,
 SB
 
 Sophie Bestley
 Pelagic Fisheries and Ecosystems
 CSIRO Marine Research
 GPO Box 1538 
 Hobart, Tasmania 7001
 AUSTRALIA 
 
 Phone: +61 3 6232 5048
 Fax: +61 3 6232 5053  
 Email: [EMAIL PROTECTED]
 Website: http://www.marine.csiro.au
 
 
 
 
 
   [[alternative HTML version deleted]]
 
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RE: [R] NA's?

2005-03-30 Thread Asha Jayanthi
I am sorry about that.
I like to do column mean, sd, var
as well as kmeans on the matrix
does this  na.rm = TRUE work for such fuctions and only the diagonal is 
ignored?

From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED],r-help@stat.math.ethz.ch
Subject: RE: [R] NA's?
Date: Thu, 31 Mar 2005 11:42:05 +1000
Your message doesn't help us very much.  You haven't said what kind of
calculation it is you want to do, and that certainly matters.  For
example, for some kinds of computations the solution you started below
would work fine:
 M - matrix(1:16, 4, 4)
 is.na(diag(M)) - TRUE
 M
 [,1] [,2] [,3] [,4]
[1,]   NA59   13
[2,]2   NA   10   14
[3,]37   NA   15
[4,]48   12   NA
 rowSums(M, na.rm = TRUE)
[1] 27 26 25 24
 colSums(M, na.rm = TRUE)
[1]  9 20 31 42
You can also use apply( ) with functions that will accept missing values
(and ignore them) for computations on either the rows or the columns.
Hoping for a general mechanism that would somehow signal the diagonal
values as values to be ignored in a general way is not a possibility.
Just as a curiosity, what were you hoping that na.omit(M) would do?
V.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Asha Jayanthi
Sent: Thursday, 31 March 2005 11:22 AM
To: r-help@stat.math.ethz.ch
Subject: [R] NA's?
I have a large matrix of data .
The size of the matrix ranges from 100 x 100 to 1000 x 1000
Now i have to do computations on that. And should not consider the
diagonal
elements.
I tried setting diag(M) = NA  and M = na.omit(M).
But this omits all the rows. I only want to omit that diagonal elements
only
but consider the whole row.
diag(M) = 0 seems like a good option but this will affect my result.
How to proceed with this. How to just ignore some specific values. what
if i
want to consider only the upper / lower triangular matrix
Asha
http://adfarm.mediaplex.com/ad/ck/4686-26272-10936-31?ck=RegSell Start
your
business.
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide!
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RE: [R] NA's?

2005-03-30 Thread Asha Jayanthi
i have not answered your query in the last mail.
I hoped na.omit(M) will just ingnore the diagonal elements. i learnt by 
practice that it removes the whole row which has atleast one NA!! (that is 
not the case in Perl)

Since I am bit new to R, i did not knew how to just ignore those elements in 
R


From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED],r-help@stat.math.ethz.ch
Subject: RE: [R] NA's?
Date: Thu, 31 Mar 2005 11:42:05 +1000
Your message doesn't help us very much.  You haven't said what kind of
calculation it is you want to do, and that certainly matters.  For
example, for some kinds of computations the solution you started below
would work fine:
 M - matrix(1:16, 4, 4)
 is.na(diag(M)) - TRUE
 M
 [,1] [,2] [,3] [,4]
[1,]   NA59   13
[2,]2   NA   10   14
[3,]37   NA   15
[4,]48   12   NA
 rowSums(M, na.rm = TRUE)
[1] 27 26 25 24
 colSums(M, na.rm = TRUE)
[1]  9 20 31 42
You can also use apply( ) with functions that will accept missing values
(and ignore them) for computations on either the rows or the columns.
Hoping for a general mechanism that would somehow signal the diagonal
values as values to be ignored in a general way is not a possibility.
Just as a curiosity, what were you hoping that na.omit(M) would do?
V.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Asha Jayanthi
Sent: Thursday, 31 March 2005 11:22 AM
To: r-help@stat.math.ethz.ch
Subject: [R] NA's?
I have a large matrix of data .
The size of the matrix ranges from 100 x 100 to 1000 x 1000
Now i have to do computations on that. And should not consider the
diagonal
elements.
I tried setting diag(M) = NA  and M = na.omit(M).
But this omits all the rows. I only want to omit that diagonal elements
only
but consider the whole row.
diag(M) = 0 seems like a good option but this will affect my result.
How to proceed with this. How to just ignore some specific values. what
if i
want to consider only the upper / lower triangular matrix
Asha
http://adfarm.mediaplex.com/ad/ck/4686-26272-10936-31?ck=RegSell Start
your
business.
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide!
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[R] Can I extract result row of table()?

2005-03-30 Thread Terry Mu
 x - c(5, 5, 8, 8, 8, 27)
 table(x)
x
 5  8 27 
 2  3  1 

I want a way to use only 2, 3, 1, nomatter table or what other function used.
Thanks.

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Re: [R] Can I extract result row of table()?

2005-03-30 Thread Uwe Ligges
Terry Mu wrote:
x - c(5, 5, 8, 8, 8, 27)
table(x)
x
 5  8 27 
 2  3  1 

I want a way to use only 2, 3, 1, nomatter table or what other function used.

as.vector() removes the attributes, if that is your question.
Uwe Ligges

Thanks.
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RE: [R] 2d plotting and colours

2005-03-30 Thread Asha Jayanthi
Thank you.
mycols - c(brown,orange,tomato)
plot(x,col = mycols[cl$cluster])
this works. I can define distinct colours and check the graph.
the rest of the examples does not give a wide palette to choose from
Asha
From: Mulholland, Tom [EMAIL PROTECTED]
To: Asha Jayanthi [EMAIL PROTECTED],r-help@stat.math.ethz.ch
Subject: RE: [R] 2d plotting and colours
Date: Thu, 31 Mar 2005 10:14:13 +0800
Since I was only concentrating on colour issues and not on your specific 
problem I was just showing the possibilities.

Does this code help
n - 5
par(mfrow = c(2,2))
palette(default)
barplot(1:25,col = 1:25)
palette(rainbow(n))
barplot(1:25,col = 1:25)
palette(rgb((0:15)/15, g=0,b=0, names=paste(red,0:15,sep=.)))
barplot(1:25,col = 1:25)
require(cluster)
x - runif(100) * 8 + 2
cl - kmeans(x, n)
palette(rainbow(n))
plot(x, col = cl$cluster)
abline(h = cl$centers, lty = 2,col = grey )
palette(palette()[order(cl$centers)])
points(x,col = cl$cluster,pch = 20,cex = 0.4)
However you may wish to choose your colours in a way that is different from 
cl$cluster which is why I changed the palette before plotting the points. 
You should see that they now are ordered from bottom to top of the last 
plot.

You could also choose to create a vector with your colours and then use the 
value in cl$cluster to select the colours

mycols - rainbow(n)
plot(x,col = mycols[cl$cluster])
Tom
 -Original Message-
 From: Asha Jayanthi [mailto:[EMAIL PROTECTED]
 Sent: Thursday, 31 March 2005 9:17 AM
 To: r-help@stat.math.ethz.ch
 Subject: RE: [R] 2d plotting and colours


 Thank you very much.

 the code
 plot(x, col = s)
 points(cl$centers, col = s, pch = 8, cex=2)

 does not plot the points according to the group colors. The
 plots are used
 to identify the groups by colors

 That could be done by

 plot(x, col = cl$cluster)

 This means that we need to set the default colours , say col
 = cl$cluster =
 a set of group numbers say 1...10 should produce 10 distinct
 colours points
 grouped by colour.

 how to do this when you have more than 8 group colours to plot

 From: Mulholland, Tom [EMAIL PROTECTED]
 To: r-help@stat.math.ethz.ch,Asha Jayanthi
 [EMAIL PROTECTED]
 Subject: RE: [R] 2d plotting and colours
 Date: Wed, 30 Mar 2005 15:59:46 +0800
 
 And getting back to your question about the palette
 
 there are a lot of ways to do this
 
 assuming you have just started a session
 
 palette()
 # will give
 #[1] black   red green3  bluecyan
 #[6] magenta yellow  gray
 
 palette(rainbow(24))  # There's also 'heat.colors'  'topo.colors'
 palette()
 
 # [1] red #FF4000 #FF8000
 # [4] #FFBF00 yellow  #BFFF00
 # [7] #80FF00 #40FF00 green
 #[10] #00FF40 #00FF80 #00FFBF
 #[13] cyandeepskyblue #0080FF
 #[16] #0040FF blue#4000FF
 #[19] #8000FF #BF00FF magenta
 #[22] #FF00BF #FF0080 #FF0040
 
 palette(rgb((0:15)/15, g=0,b=0, names=paste(red,0:15,sep=.)))
 palette()
 # [1] black   #11 #22 #33 #44
 # [6] #55 #66 #77 #88 #99
 #[11] #AA #BB #CC #DD red2
 #[16] red
 
 If you are looking to use colours that take account of
 colour blindness
 you could try the package dichromat. (I think 2.1 will have
 some of this
 inbuilt)
 
 Once you look through the help files associated with some of
 these options
 you
 will find the way that best suits your method of working.
 
 Tom
 
 
 
 
 
 
   -Original Message-
   From: Uwe Ligges [mailto:[EMAIL PROTECTED]
   Sent: Wednesday, 30 March 2005 3:18 PM
   To: TEMPL Matthias
   Cc: r-help@stat.math.ethz.ch; Asha Jayanthi
   Subject: Re: [R] 2d plotting and colours
  
  
   TEMPL Matthias wrote:
  
Hi!
   
There are more than 8 colors.
  
   Yes, e.g. for rgb space there are 16777216, see ?rgb.
  
   Uwe Ligges
  
  
  
x - rbind(matrix(rnorm(100, sd = 0.3), ncol = 2),
matrix(rnorm(100, mean = 1, sd = 0.3),
 ncol = 2))
   
(cl - kmeans(x, i, 20))
   
s - c(tomato4, turquoise, slateblue, wheat,
   snow, skyblue,
peru, pink)
# see at:
colors()
   
plot(x, col = s)
   
points(cl$centers, col = s, pch = 8, cex=2)
   
   
Best,
Matthias
   
   
   
   
   
   Hi!
   
   I am new to R just 3 days in it and i apologize if my
   questions seem very
   trivial and consumed your valuable time.
   
   I am coding in perl and i stumbled upon R regarding
 plotting good
   statistical graphs.
   
   I tried the kmean clustering for a large matrix ,say  150 *
   150 . I tried
   the example code given in the tutorial to perform 2d plot
   
   # i ranges from 2 to 10
   cl - kmeans(x, i, 20)
   plot(x, col = cl$cluster)
   points(cl$centers, col = 1:i )
   
   I see that there are only 8 colours defined , namely
   black,red,green,blue,cyan,magenta,yello,gray.
   
   How should i set my colour preferences to obtain my palette
   of colours? I
   checked in the totorial which talks about R.colors and
   palatte , but i
   failed to 

RE: [R] 2d plotting and colours

2005-03-30 Thread Mulholland, Tom
I'm not sure that I understand you comment about the other examples not giving 
a wide palette. Are you using wide to refer to the difference in colours rather 
than the number of choices in the palette? If this is your issue you should 
look at the dichromat package that I referred to, in particular the colorRamp 
function. You might also want to have a look at the RColorBrewer package and 
run the ColorBrewer example. This package specifically deals with the ability 
to distinguish one colour from another.As the ColorBrewer website notes the 
tool is designed to help people select good color schemes for maps and other 
graphics.

By the way if the mycols code works then

palette(c(brown,orange,tomato))
plot(x,col = cl$cluster)

should produce exactly the same result.

Tom

 -Original Message-
 From: Asha Jayanthi [mailto:[EMAIL PROTECTED]
 Sent: Thursday, 31 March 2005 2:36 PM
 To: Mulholland, Tom; r-help@stat.math.ethz.ch
 Subject: RE: [R] 2d plotting and colours
 
 
 Thank you.
 
 mycols - c(brown,orange,tomato)
 plot(x,col = mycols[cl$cluster])
 
 this works. I can define distinct colours and check the graph.
 
 the rest of the examples does not give a wide palette to choose from
 
 Asha
 From: Mulholland, Tom [EMAIL PROTECTED]
 To: Asha Jayanthi 
 [EMAIL PROTECTED],r-help@stat.math.ethz.ch
 Subject: RE: [R] 2d plotting and colours
 Date: Thu, 31 Mar 2005 10:14:13 +0800
 
 Since I was only concentrating on colour issues and not on 
 your specific 
 problem I was just showing the possibilities.
 
 Does this code help
 
 n - 5
 par(mfrow = c(2,2))
 palette(default)
 barplot(1:25,col = 1:25)
 palette(rainbow(n))
 barplot(1:25,col = 1:25)
 palette(rgb((0:15)/15, g=0,b=0, names=paste(red,0:15,sep=.)))
 barplot(1:25,col = 1:25)
 
 
 require(cluster)
 x - runif(100) * 8 + 2
 cl - kmeans(x, n)
 palette(rainbow(n))
 plot(x, col = cl$cluster)
 abline(h = cl$centers, lty = 2,col = grey )
 palette(palette()[order(cl$centers)])
 points(x,col = cl$cluster,pch = 20,cex = 0.4)
 
 However you may wish to choose your colours in a way that is 
 different from 
 cl$cluster which is why I changed the palette before 
 plotting the points. 
 You should see that they now are ordered from bottom to top 
 of the last 
 plot.
 
 You could also choose to create a vector with your colours 
 and then use the 
 value in cl$cluster to select the colours
 
 mycols - rainbow(n)
 plot(x,col = mycols[cl$cluster])
 
 Tom
 
   -Original Message-
   From: Asha Jayanthi [mailto:[EMAIL PROTECTED]
   Sent: Thursday, 31 March 2005 9:17 AM
   To: r-help@stat.math.ethz.ch
   Subject: RE: [R] 2d plotting and colours
  
  
   Thank you very much.
  
   the code
   plot(x, col = s)
   points(cl$centers, col = s, pch = 8, cex=2)
  
   does not plot the points according to the group colors. The
   plots are used
   to identify the groups by colors
  
   That could be done by
  
   plot(x, col = cl$cluster)
  
   This means that we need to set the default colours , say col
   = cl$cluster =
   a set of group numbers say 1...10 should produce 10 distinct
   colours points
   grouped by colour.
  
   how to do this when you have more than 8 group colours to plot
  
   From: Mulholland, Tom [EMAIL PROTECTED]
   To: r-help@stat.math.ethz.ch,Asha Jayanthi
   [EMAIL PROTECTED]
   Subject: RE: [R] 2d plotting and colours
   Date: Wed, 30 Mar 2005 15:59:46 +0800
   
   And getting back to your question about the palette
   
   there are a lot of ways to do this
   
   assuming you have just started a session
   
   palette()
   # will give
   #[1] black   red green3  bluecyan
   #[6] magenta yellow  gray
   
   palette(rainbow(24))  # There's also 'heat.colors'  
 'topo.colors'
   palette()
   
   # [1] red #FF4000 #FF8000
   # [4] #FFBF00 yellow  #BFFF00
   # [7] #80FF00 #40FF00 green
   #[10] #00FF40 #00FF80 #00FFBF
   #[13] cyandeepskyblue #0080FF
   #[16] #0040FF blue#4000FF
   #[19] #8000FF #BF00FF magenta
   #[22] #FF00BF #FF0080 #FF0040
   
   palette(rgb((0:15)/15, g=0,b=0, names=paste(red,0:15,sep=.)))
   palette()
   # [1] black   #11 #22 #33 #44
   # [6] #55 #66 #77 #88 #99
   #[11] #AA #BB #CC #DD red2
   #[16] red
   
   If you are looking to use colours that take account of
   colour blindness
   you could try the package dichromat. (I think 2.1 will have
   some of this
   inbuilt)
   
   Once you look through the help files associated with some of
   these options
   you
   will find the way that best suits your method of working.
   
   Tom
   
   
   
   
   
   
 -Original Message-
 From: Uwe Ligges [mailto:[EMAIL PROTECTED]
 Sent: Wednesday, 30 March 2005 3:18 PM
 To: TEMPL Matthias
 Cc: r-help@stat.math.ethz.ch; Asha Jayanthi
 Subject: Re: [R] 2d plotting and colours


 TEMPL Matthias wrote:

  Hi!
 
  There are more than 8 colors.
  

RE: [R] NA's?

2005-03-30 Thread Bill.Venables
is.na(diag(M)) - TRUE

cmeans - colMeans(M, na.rm = TRUE)
csd - apply(M, 2, sd, na.rm = TRUE)
cvar - csd ^2

(or

cvar - apply(M, 2, var, na.rm = TRUE)

)

Using 'kmeans' on a matrix but 'ignoring the diagonal entries' just
doesn't make sense as it stands, so I can't help you there.

V.

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Asha Jayanthi
Sent: Thursday, 31 March 2005 3:48 PM
To: r-help@stat.math.ethz.ch
Subject: RE: [R] NA's?


I am sorry about that.


I like to do column mean, sd, var

as well as kmeans on the matrix

does this  na.rm = TRUE work for such fuctions and only the diagonal is 
ignored?

From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED],r-help@stat.math.ethz.ch
Subject: RE: [R] NA's?
Date: Thu, 31 Mar 2005 11:42:05 +1000

Your message doesn't help us very much.  You haven't said what kind of
calculation it is you want to do, and that certainly matters.  For
example, for some kinds of computations the solution you started below
would work fine:

  M - matrix(1:16, 4, 4)
  is.na(diag(M)) - TRUE
  M
  [,1] [,2] [,3] [,4]
[1,]   NA59   13
[2,]2   NA   10   14
[3,]37   NA   15
[4,]48   12   NA
  rowSums(M, na.rm = TRUE)
[1] 27 26 25 24
  colSums(M, na.rm = TRUE)
[1]  9 20 31 42

You can also use apply( ) with functions that will accept missing
values
(and ignore them) for computations on either the rows or the columns.

Hoping for a general mechanism that would somehow signal the diagonal
values as values to be ignored in a general way is not a possibility.
Just as a curiosity, what were you hoping that na.omit(M) would do?

V.

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Asha Jayanthi
Sent: Thursday, 31 March 2005 11:22 AM
To: r-help@stat.math.ethz.ch
Subject: [R] NA's?


I have a large matrix of data .

The size of the matrix ranges from 100 x 100 to 1000 x 1000

Now i have to do computations on that. And should not consider the
diagonal
elements.

I tried setting diag(M) = NA  and M = na.omit(M).

But this omits all the rows. I only want to omit that diagonal elements
only
but consider the whole row.

diag(M) = 0 seems like a good option but this will affect my result.

How to proceed with this. How to just ignore some specific values. what
if i
want to consider only the upper / lower triangular matrix

Asha


http://adfarm.mediaplex.com/ad/ck/4686-26272-10936-31?ck=RegSell Start
your
business.

__
R-help@stat.math.ethz.ch mailing list
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argetID=9763Targets=9763Values=414,868,1093,2385Redirect=http:%2F%2Fw
ww.icicibanknripromotions.com%2Fm2i_feb%2Fnri_M2I_feb.jsp%3Fadid%3D44925
%26siteid%3D1093%26flightid%3D17307 
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RE: [R] how i can get input from user input

2005-03-30 Thread Martin Maechler
 BertG == Berton Gunter [EMAIL PROTECTED]
 on Wed, 30 Mar 2005 10:09:38 -0800 writes:

BertG If you are on Windows and want to go GUI, see
BertG ?choose.files, ?winMenuAdd, ?winDialog, ?select.list

with the big drawback that it will only work on Windows.

As Uwe says below, it depends on your context;
for relative simple things, however please consider a portable
solution, using
  menu(), readline(), ..

BTW, menu() has been improved in R 2.1.0 (alpha -- please test!),
and is now connected with select.list() which should work on all
platforms (and uses tcltk on Linux when available).


Martin Maechler, ETH Zurich


BertG -- Bert Gunter
BertG Genentech Non-Clinical Statistics
BertG South San Francisco, CA
 
BertG The business of the statistician is to catalyze the scientific 
learning
BertG process.  - George E. P. Box
 
 

 -Original Message-
 From: [EMAIL PROTECTED] 
 [mailto:[EMAIL PROTECTED] On Behalf Of Greg Snow
 Sent: Wednesday, March 30, 2005 9:45 AM
 To: [EMAIL PROTECTED]; [EMAIL PROTECTED]
 Cc: r-help@stat.math.ethz.ch
 Subject: Re: [R] how i can get input from user input
 
 Also look at ?readline
 
 Greg Snow, Ph.D.
 Statistical Data Center
 [EMAIL PROTECTED]
 (801) 408-8111
 
  Uwe Ligges [EMAIL PROTECTED] 03/29/05 11:43PM 
 Cuichang Zhao wrote:
 
  Hello, 
  Could you please tell me how i can get an input from the user in R?
 
 Depends on the kind of input.
 
 See, e.g., ?scan or ?menu
 
 Uwe Ligges
 
 
  C-Ming 
   
  Mar 29, 2005
  
 
  -
  
  
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Re: [R] Problems with lpSolve/Memory ? R crashes

2005-03-30 Thread Arne Henningsen
Unfortunately, I can't tell you how to solve this problem. However, I can 
confirm that this crash happens also on my machines (R 2.0.1 on Debian Sarge, 
AMD Athlon, 750 MHz, 256 MB RAM and R 2.0.0 on SuSE 9.0, Intel P4, 2.6 GHz, 
512 MB RAM):
R aaa(1000)
alloc of 8 bytes failed
alloc of 4 bytes failed
Speicherzugriffsfehler

We had a model, which consists of 1000+ linear programs with each about 550 
rows and 1100 columns (http://www.unipr.it/arpa/dipseq/EAAE/PR/Parallel/ 
42b4_henningsen.pdf). On MS-Windows 2000/XP this model always crashed after 
some hundreds linear programs, but using Linux on the same machines it 
_never_ crashed. I really can't see the reason why our much larger programs 
worked, but these small programs let R crash. 
I hope that this information may help to solve this problem.

Arne

On Wednesday 30 March 2005 12:16, TEMPL Matthias wrote:
 Hello!

 I have a curious problem, which I cannot solve.
 With my code I solve thousands of small linear programs with the package
 lpSolve automatically. But R crashes sometimes (~always, but always on
 different linear programs) in a strange way. For illustration, I tried to
 prepare a simple example, which shows the nature of the problem. The
 function aaa (see below) declares some constants (only in this special
 example) and in the end it solves the linear program.

 aaa(1)
   [,1] [,2]
  [1,]00
  [2,]00
  [3,]00
  [4,]00
  [5,]   520
  [6,]22
  [7,]00
  [8,]20
  [9,]00
 [10,]00
 [11,]00
 [12,]00
 [13,]   540

 Works fine.
 Now I make the *same* calculation, say 1000 times:
 aaa(1000)
 R (I have tried it with R2.0.1, 2.0.0, 1.9.1, 2.1.0dev) crashes completly -
 without warning and error message under Windows XP, Intel Pentium 3 with
 256 MB RAM Under Linux SuSe 8.2 R (2.0.1) it crashes again, but in this
 case I get the following message: Calloc of 40004 bytes failed on line 114
 of file lpkit.c
 ...
 Calloc of 80008 bytes failed on line 113 of file lpkit.c
 Error: cannot allocate vector of size 3 Kb

 Now I´m completly lost. Solving the linear program one time makes no
 problem. Solving it twice in the same way makes no problem either. Running
 the same calculation, say 1000 times, causes a crash. Why should there be a
 problem with memory?

 For any hint, I would be really happy.
 Thank you,
 Matthias


 ### -- function aaa 

 aaa - function(amount=1){
 f.obj - rep(0,33)

 w - c(3,4,5,6,11,13,17,22,25,26,27,28,33)

 m -
 matrix(c(0,0,1,1,1,1,0,0,0,0,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
,

  
 0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,-1,0,0,0,0,0,0,0,0,0,0,0,

  
 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,-1,-1,-1,0,0,0,0,1,

  
 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

  
 0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

  
 0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,0,

  
 0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,

  
 0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,

  
 0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,

  
 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

  
 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

  
 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

  
 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

  
 0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,0,0,0,1

   ),ncol=33,byrow=TRUE)

 f.dir - c(=,=,=,=,=,=,=,=,=,=,=,
 =,=,=,=,=,=,=,=,=,=,=,=,
 =,=,=,=,=,=,=,=,=,=)

 f.rhs - c(-52,0,54,0,2,0,0,0,0,0,0,0,0,0)

 lp.out - matrix( ncol = 2, nrow = 13 )

 for(ii in 1:amount){ # - simple iterate the same

 for( i in 1:13 ){

   f.obj[ w[i] ] - 1

   lp.out[ i, 1 ] - lp(min, f.obj, m, f.dir, f.rhs)$objval

   lp.out[ i, 2 ] - lp(max, f.obj, m, f.dir, f.rhs)$objval

   f.obj - rep( 0, 33 )

 }

 }
 lp.out

 }

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-- 
Arne Henningsen
Department of Agricultural Economics
University of Kiel
Olshausenstr. 40
D-24098 Kiel (Germany)
Tel: +49-431-880 4445
Fax: +49-431-880 1397
[EMAIL PROTECTED]
http://www.uni-kiel.de/agrarpol/ahenningsen/

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Re: [R] Finding the height of a line of text for axis

2005-03-30 Thread Steven J. Murdoch
Thanks for your reply.

On Wed, Mar 30, 2005 at 08:03:10AM -0600, Marc Schwartz wrote:
 or even something like this:
 
  plot(1:5, axes = FALSE)
  axis(1, col.axis = white, col = red, tcl = 1)
  axis(1, col.axis = white, col = white, tcl = 0)
  axis(2, col.axis = white, col = red, tcl = 1)
  axis(2, col.axis = white, col = white, tcl = 0)

This is the effect I am trying to achieve. I did try the route of
overdrawing in white, but decided against it. The reason I haven't
used that, is that firstly I wasn't sure if there would be some
rounding error in a printer which would cause the background to
appear. Secondly, the end of the ticks look weird due to the different
line end types:
 http://www.cl.cam.ac.uk/users/sjm217/volatile/r-lineend.png

Changing to square caps might help, but I was hoping there would be a
nice solution that would let me keep round caps. Any suggestions?

Thank you,
Steven Murdoch.
-- 
w: http://www.cl.cam.ac.uk/users/sjm217/

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[R] Cox model qustion in R

2005-03-30 Thread Chao Zhu
Dear all,

I have a beginner's R question for coxph() and survfit().
I have a data set with survival time (no censoring) and treatment 
indicator(0/1). I did something like

fit-coxph( Surv(t)~treat, method=breslow,data=data)
 fit
Call:
coxph(formula = Surv(t) ~ treat, data = data, method = breslow)


   coef exp(coef) se(coef) z   p
treat -1.96 0.1400.243 -8.07 6.7e-16

Likelihood ratio test=80.3  on 1 df, p=0  n= 144 

 plot(survfit(fit))

But it only gives me the curve with combined treatment. How do I get a plot 
with two curves for different treatments.
I don't want to do 
new-data.frame(treat=c(0,1))
and plot(survfit(fit,newdata=new)) cause it gives you predicted curves for two 
treatments.

Thanks you so much for your help.

Jimmy Chu
[[alternative HTML version deleted]]

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Re: [R] Finding the height of a line of text for axis

2005-03-30 Thread Paul Murrell
Hi
Steven J. Murdoch wrote:
Thanks for your reply.
On Wed, Mar 30, 2005 at 08:03:10AM -0600, Marc Schwartz wrote:
or even something like this:
plot(1:5, axes = FALSE)
axis(1, col.axis = white, col = red, tcl = 1)
axis(1, col.axis = white, col = white, tcl = 0)
axis(2, col.axis = white, col = red, tcl = 1)
axis(2, col.axis = white, col = white, tcl = 0)

This is the effect I am trying to achieve. I did try the route of
overdrawing in white, but decided against it. The reason I haven't
used that, is that firstly I wasn't sure if there would be some
rounding error in a printer which would cause the background to
appear. Secondly, the end of the ticks look weird due to the different
line end types:
 http://www.cl.cam.ac.uk/users/sjm217/volatile/r-lineend.png
Changing to square caps might help, but I was hoping there would be a
nice solution that would let me keep round caps. Any suggestions?

The function GConvertYUnits() (and the functions it calls) are in the 
file graphics.c (same directory as plot.c), but I'd book a week off 
before trying to trace the calculations performed therein.

A more accurate calculation than ...
  l-par(cxy)[2]*par(tcl)
... is ...
  l-par(cin)[2]/par(pin)[1]*diff(par(usr)[1:2])*par(tcl)
... but that still needs par(cex) and a par(mex) multipliers to be 
(possibly) fully par() compliant.  This general 
replicate-par()-in-R-code route is likely to be a recipe for unhappiness.

Some sort of overplotting trick is probably a better choice if you can 
cope with the compromise.  The following variation on Marc's suggestion 
might provide a slight improvement:

 plot(1:5, axes = FALSE)
 axis(1, col.axis = white, col = red, tcl = 1)
 axis(2, col.axis = white, col = red, tcl = 1)
 box(col=white)
Something like box(col=white, lwd=1.1) could be used to allay fears of 
axes peeking through from behind.

Paul
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
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RE: [R] Re:Plotting to A4 and replacing x-axis with actual years.

2005-03-30 Thread Mulholland, Tom
I think you need to read the posting guide (see the bottom of each post made) 
and once you have done this take some time to compose your message.

The issue is that I have too little information about what you have done. It 
looks to me as if you are using postscript, but I am not sure if you have 
plotted your 3 x 3 array to the device and used the command parameter or if 
your reference to written commands is actually the 'postscript' command.

Specifically the posting guide notes that a small reproducible example of the 
issue that you are facing will make it much easier for people to help you. It 
also talks about the need to identify the hardware that you are using as for 
certain processes the answer is quite different in Windows than it is in some 
flavour of Unix.

The same is true of your second inquiry. Dummy code would make it easier to see 
what you are doing.

Tom



 -Original Message-
 From: Marshall Mdoka [mailto:[EMAIL PROTECTED]
 Sent: Wednesday, 30 March 2005 10:47 PM
 To: r-help@stat.math.ethz.ch
 Subject: [R] Re:Plotting to A4 and replacing x-axis with actual years.
 
 
 Hie,
 
 I have written before and probably missed the reply.
 
 1.) I have my figures in a 3X3 array and want to fit them 
 onto a A4 size
 page. I have written commands to try a represent them in eps 
 format but
 still their cutting out information.
 
 2.) I have an odd number of years and wanted to represent 
 them say 1980 1985
 1990 1995 2000 instead of 1 5 10 etc. However, the years are not
 overwritting in the year I want since the first year in my 
 x-axis is 1979
 which is year 1 and year 5 being 1984.
 
 Could you please help especially on the first problem.
 
 Thanking you in advance,
 
 Marshall Mdoka
 
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RE: [R] 2d plotting and colours

2005-03-30 Thread Asha Jayanthi
Thank you very much.
the code
plot(x, col = s)
points(cl$centers, col = s, pch = 8, cex=2)
does not plot the points according to the group colors. The plots are used 
to identify the groups by colors

That could be done by
plot(x, col = cl$cluster)
This means that we need to set the default colours , say col = cl$cluster = 
a set of group numbers say 1...10 should produce 10 distinct colours points 
grouped by colour.

how to do this when you have more than 8 group colours to plot
From: Mulholland, Tom [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch,Asha Jayanthi [EMAIL PROTECTED]
Subject: RE: [R] 2d plotting and colours
Date: Wed, 30 Mar 2005 15:59:46 +0800
And getting back to your question about the palette
there are a lot of ways to do this
assuming you have just started a session
palette()
# will give
#[1] black   red green3  bluecyan
#[6] magenta yellow  gray
palette(rainbow(24))  # There's also 'heat.colors'  'topo.colors'
palette()
# [1] red #FF4000 #FF8000
# [4] #FFBF00 yellow  #BFFF00
# [7] #80FF00 #40FF00 green
#[10] #00FF40 #00FF80 #00FFBF
#[13] cyandeepskyblue #0080FF
#[16] #0040FF blue#4000FF
#[19] #8000FF #BF00FF magenta
#[22] #FF00BF #FF0080 #FF0040
palette(rgb((0:15)/15, g=0,b=0, names=paste(red,0:15,sep=.)))
palette()
# [1] black   #11 #22 #33 #44
# [6] #55 #66 #77 #88 #99
#[11] #AA #BB #CC #DD red2
#[16] red
If you are looking to use colours that take account of colour blindness
you could try the package dichromat. (I think 2.1 will have some of this 
inbuilt)

Once you look through the help files associated with some of these options 
you
will find the way that best suits your method of working.

Tom


 -Original Message-
 From: Uwe Ligges [mailto:[EMAIL PROTECTED]
 Sent: Wednesday, 30 March 2005 3:18 PM
 To: TEMPL Matthias
 Cc: r-help@stat.math.ethz.ch; Asha Jayanthi
 Subject: Re: [R] 2d plotting and colours


 TEMPL Matthias wrote:

  Hi!
 
  There are more than 8 colors.

 Yes, e.g. for rgb space there are 16777216, see ?rgb.

 Uwe Ligges



  x - rbind(matrix(rnorm(100, sd = 0.3), ncol = 2),
  matrix(rnorm(100, mean = 1, sd = 0.3), ncol = 2))
 
  (cl - kmeans(x, i, 20))
 
  s - c(tomato4, turquoise, slateblue, wheat,
 snow, skyblue,
  peru, pink)
  # see at:
  colors()
 
  plot(x, col = s)
 
  points(cl$centers, col = s, pch = 8, cex=2)
 
 
  Best,
  Matthias
 
 
 
 
 
 Hi!
 
 I am new to R just 3 days in it and i apologize if my
 questions seem very
 trivial and consumed your valuable time.
 
 I am coding in perl and i stumbled upon R regarding plotting good
 statistical graphs.
 
 I tried the kmean clustering for a large matrix ,say  150 *
 150 . I tried
 the example code given in the tutorial to perform 2d plot
 
 # i ranges from 2 to 10
 cl - kmeans(x, i, 20)
 plot(x, col = cl$cluster)
 points(cl$centers, col = 1:i )
 
 I see that there are only 8 colours defined , namely
 black,red,green,blue,cyan,magenta,yello,gray.
 
 How should i set my colour preferences to obtain my palette
 of colours? I
 checked in the totorial which talks about R.colors and
 palatte , but i
 failed to understand how to set it.
 
 Thank You
 
 Asha
 
 
 MSN Messenger!
 
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[R] NA's?

2005-03-30 Thread Asha Jayanthi
I have a large matrix of data .
The size of the matrix ranges from 100 x 100 to 1000 x 1000
Now i have to do computations on that. And should not consider the diagonal 
elements.

I tried setting diag(M) = NA  and M = na.omit(M).
But this omits all the rows. I only want to omit that diagonal elements only 
but consider the whole row.

diag(M) = 0 seems like a good option but this will affect my result.
How to proceed with this. How to just ignore some specific values. what if i 
want to consider only the upper / lower triangular matrix

Asha
http://adfarm.mediaplex.com/ad/ck/4686-26272-10936-31?ck=RegSell Start your 
business.

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[R] Contingency table: logistic regression

2005-03-30 Thread Suresh Krishna
Hi,
I am analyzing a data set with greater than 1000 independent cases 
(collected in an unrestricted manner), where each case has 3 variables 
associated with it: one, a factor variable with 0/1 levels (called XX), 
another factor variable with 8 levels (X) and a third response variable 
with two levels (Y: 0/1). I am trying to see if X1 has an effect on the 
relationship between X2 and the proportion of 1-s in Y.

I have three questions:
a) I have never used glm-s for this or any other sort of analysis before 
today, so am I interpreting the output correctly ?

After setting options(contrasts=c(contr.treatment,contr.poly))
I did:
~~Begin R output~~
Call:
glm(formula = Y ~ X * Fac, family = binomial, data = mat, subset = 
sactype  3  numstim == 16)

Deviance Residuals:
   Min  1Q  Median  3Q Max
-2.232  -0.901   0.416   0.985   1.656
Coefficients:
Estimate Std. Error z value Pr(|z|)
(Intercept)2.405  0.209   11.52   2e-16 ***
X2-2.511  0.293   -8.57   2e-16 ***
X3-3.283  0.286  -11.47   2e-16 ***
X4-2.009  0.302   -6.653e-11 ***
X5-3.098  0.276  -11.22   2e-16 ***
X6-2.580  0.288   -8.97   2e-16 ***
X7-3.484  0.288  -12.09   2e-16 ***
X8-2.811  0.328   -8.56   2e-16 ***
Fac   -1.558  0.721   -2.16  0.03071 *
X2:Fac 2.133  0.9422.26  0.02351 *
X3:Fac 1.848  0.9321.98  0.04748 *
X4:Fac 2.836  0.9822.89  0.00386 **
X5:Fac 3.263  0.9453.45  0.00056 ***
X6:Fac 3.630  0.9713.74  0.00018 ***
X7:Fac 3.256  0.8833.69  0.00023 ***
X8:Fac 3.350  1.0003.35  0.00081 ***
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1619.4  on 1178  degrees of freedom
Residual deviance: 1271.2  on 1163  degrees of freedom
AIC: 1303
Number of Fisher Scoring iterations: 5
End R output~~~
I am reading this like this: each of the X2X8 terms tell me whether 
the proportions associated with those factors at level 0 of Fac, are 
different from the proportion associated with factor X1 for level 0 of 
Fac. And each of the terms associated with Fac (X2:Fac,...X8:Fac) is 
telling me whether the difference between X2...X8 and X1 is different 
for Fac=0 and Fac=1; and this is the same thing as whether the 
proportion associated with X2..X8 are different for the two levels 
of Fac. So these X2...X8:Fac terms are like performing a simple 2x2 
analysis of the effect of Fac on Y, given X2 (X8).

How much of this is incorrect ?
My other two questions are:
b) Is this the right way to approach this analysis in R ? Or am I better 
off reading about multi-way contingency table analyses and using them ?

and
c) How do I incorporate a correction for multiple-testing into the above 
analysis ? The effect of Fac on the relationship between X and Y was 
planned.

I would greatly, and respectfully appreciate all pointers, tips and 
admonitions.

Thank you 
Suresh
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[R] Re: Contingency table: logistic regression

2005-03-30 Thread Suresh Krishna
Oops, I corrected some errors in the first paragraph; sorry for the 
repeated posting.

Suresh
~~
Hi,
I am analyzing a data set with greater than 1000 independent cases
(collected in an unrestricted manner), where each case has 3 variables
associated with it: one, a factor variable with 0/1 levels (called Fac),
another factor variable with 8 levels (X) and a third response variable
with two levels (Y: 0/1). I am trying to see if Fac has an effect on the
relationship between X and the proportion of 1-s in Y.
I have three questions:
a) I have never used glm-s for this or any other sort of analysis before
today, so am I interpreting the output correctly ?
After setting options(contrasts=c(contr.treatment,contr.poly))
I did:
~~Begin R output~~
Call:
glm(formula = Y ~ X * Fac, family = binomial, data = mat, subset =
sactype  3  numstim == 16)
Deviance Residuals:
   Min  1Q  Median  3Q Max
-2.232  -0.901   0.416   0.985   1.656
Coefficients:
Estimate Std. Error z value Pr(|z|)
(Intercept)2.405  0.209   11.52   2e-16 ***
X2-2.511  0.293   -8.57   2e-16 ***
X3-3.283  0.286  -11.47   2e-16 ***
X4-2.009  0.302   -6.653e-11 ***
X5-3.098  0.276  -11.22   2e-16 ***
X6-2.580  0.288   -8.97   2e-16 ***
X7-3.484  0.288  -12.09   2e-16 ***
X8-2.811  0.328   -8.56   2e-16 ***
Fac   -1.558  0.721   -2.16  0.03071 *
X2:Fac 2.133  0.9422.26  0.02351 *
X3:Fac 1.848  0.9321.98  0.04748 *
X4:Fac 2.836  0.9822.89  0.00386 **
X5:Fac 3.263  0.9453.45  0.00056 ***
X6:Fac 3.630  0.9713.74  0.00018 ***
X7:Fac 3.256  0.8833.69  0.00023 ***
X8:Fac 3.350  1.0003.35  0.00081 ***
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1619.4  on 1178  degrees of freedom
Residual deviance: 1271.2  on 1163  degrees of freedom
AIC: 1303
Number of Fisher Scoring iterations: 5
End R output~~~
I am reading this like this: each of the X2X8 terms tell me whether
the proportions associated with those factors at level 0 of Fac, are
different from the proportion associated with factor X1 for level 0 of
Fac. And each of the terms associated with Fac (X2:Fac,...X8:Fac) is
telling me whether the difference between X2...X8 and X1 is different
for Fac=0 and Fac=1; and this is the same thing as whether the
proportion associated with X2..X8 are different for the two levels
of Fac. So these X2...X8:Fac terms are like performing a simple 2x2
analysis of the effect of Fac on Y, given X2 (X8).
How much of this is incorrect ?
My other two questions are:
b) Is this the right way to approach this analysis in R ? Or am I better
off reading about multi-way contingency table analyses and using them ?
and
c) How do I incorporate a correction for multiple-testing into the above
analysis ? The effect of Fac on the relationship between X and Y was
planned.
I would greatly, and respectfully appreciate all pointers, tips and
admonitions.
Thank you 
Suresh
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html