Re: [R] lme4: Extract fixed effects Val, SE, t, p

[Dieter Menne]

Zev Ross  zevross.com> writes:

> Using glmmPQL you can extract the full table of estimates, SE, p-values 
> etc using as an example:
> 
> mymodel<-glmmPQL(mymodel here)
> 
> summary(mymodel)[[18]]
> 
> How can I pull this table out of a lmer object in lme4?


Looks like it is not so easy, the code that produces the table is rather hidden 
in Matrix\r\lmer.R, about line 400


setMethod("show", "summary.lmer",
  function(object) {
  fcoef <- [EMAIL PROTECTED]
  useScale <- [EMAIL PROTECTED]


You might be able to write your own code using the outline given there, but you 
could run into trouble with method getFixDF.

Dieter

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[R] Help with data.frame and lapply

[Juan Daniel López Serna]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello:
I'm having problems with this line of code:

X.lm <- lapply(names(d), function(x) lm(d["cls"] ~ d[x], data=d))

d[x] is what is giving trouble here, but I don't know exactly how to
solve it. What I'm trying to do is to create a linear model from each
column of the data frame 'd' to apply ANOVA later.
Thanks very much in advance. Regards:


Juan Daniel López Serna

- 
Instituto de Ingeniería del Conocimiento
(http://www.iic.uam.es)
Universidad Autónoma de Madrid
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Re: [R] Help with data.frame and lapply

[Dimitris Rizopoulos]

you could use something like:

d <- data.frame(x1 = rnorm(100), x2 = rnorm(100), x3 = rnorm(100), cls 
= rnorm(100))
lapply(d[-match("cls", names(d))], function(x, y) lm(y ~ x), y = 
d$cls)


I hope it helps.

Best,
Dimitris


Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://www.med.kuleuven.be/biostat/
 http://www.student.kuleuven.be/~m0390867/dimitris.htm



- Original Message - 
From: "Juan Daniel López Serna" <[EMAIL PROTECTED]>
To: 
Sent: Friday, December 16, 2005 9:33 AM
Subject: [R] Help with data.frame and lapply


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello:
I'm having problems with this line of code:

X.lm <- lapply(names(d), function(x) lm(d["cls"] ~ d[x], data=d))

d[x] is what is giving trouble here, but I don't know exactly how to
solve it. What I'm trying to do is to create a linear model from each
column of the data frame 'd' to apply ANOVA later.
Thanks very much in advance. Regards:


Juan Daniel López Serna

- 
Instituto de Ingeniería del Conocimiento
(http://www.iic.uam.es)
Universidad Autónoma de Madrid
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.2.6 (GNU/Linux)
Comment: Using GnuPG with Fedora - http://enigmail.mozdev.org

iD8DBQFDonvRXHsVbn2qIYMRAqi8AJ0X6zOAevAGzMczQ+ahHlVJnUK4ZQCeIDi6
PPB3baK8JNOa3eoIgbmVCdM=
=WKlt
-END PGP SIGNATURE-

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Re: [R] Help with data.frame and lapply

[TEMPL Matthias]

> Hello:
>   I'm having problems with this line of code:
> 
> X.lm <- lapply(names(d), function(x) lm(d["cls"] ~ d[x], data=d))
> 
>   d[x] is what is giving trouble here, but I don't know 
> exactly how to solve it. 

How does d look like?
Probably d[,"cls"] and d[,x] instead of d["cls"] and d[x] solves your problem.
PLEASE do read 
the posting guide! http://www.R-project.org/posting-guide.html
and *give a reproducible example*.

Best,
Matthias

> What I'm trying to do is to create a 
> linear model from each column of the data frame 'd' to apply 
> ANOVA later.
>   Thanks very much in advance. Regards:
> 
> 
> Juan Daniel López Serna
> 
> - 
> Instituto de Ingeniería del Conocimiento
> (http://www.iic.uam.es)
> Universidad Autónoma de Madrid
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.2.6 (GNU/Linux)
> Comment: Using GnuPG with Fedora - http://enigmail.mozdev.org
> 
> iD8DBQFDonvRXHsVbn2qIYMRAqi8AJ0X6zOAevAGzMczQ+ahHlVJnUK4ZQCeIDi6
> PPB3baK8JNOa3eoIgbmVCdM=
> =WKlt
> -END PGP SIGNATURE-
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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>

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Re: [R] Help with data.frame and lapply

[Jacques VESLOT]

d <- data.frame(x1 = rnorm(100), x2 = rnorm(100), x3 = rnorm(100), cls = 
rnorm(100))
dd <- subset(d, sel=-cls)
lapply(paste("lm(cls ~", names(dd), ",data=d)"), function(x) 
eval(parse(text=x)))


Juan Daniel López Serna a écrit :

>-BEGIN PGP SIGNED MESSAGE-
>Hash: SHA1
>
>Hello:
>   I'm having problems with this line of code:
>
>X.lm <- lapply(names(d), function(x) lm(d["cls"] ~ d[x], data=d))
>
>   d[x] is what is giving trouble here, but I don't know exactly how to
>solve it. What I'm trying to do is to create a linear model from each
>column of the data frame 'd' to apply ANOVA later.
>   Thanks very much in advance. Regards:
>
>
>Juan Daniel López Serna
>
>- 
>Instituto de Ingeniería del Conocimiento
>(http://www.iic.uam.es)
>Universidad Autónoma de Madrid
>-BEGIN PGP SIGNATURE-
>Version: GnuPG v1.2.6 (GNU/Linux)
>Comment: Using GnuPG with Fedora - http://enigmail.mozdev.org
>
>iD8DBQFDonvRXHsVbn2qIYMRAqi8AJ0X6zOAevAGzMczQ+ahHlVJnUK4ZQCeIDi6
>PPB3baK8JNOa3eoIgbmVCdM=
>=WKlt
>-END PGP SIGNATURE-
>
>__
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>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>  
>

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[R] autocorrelation test

[Poizot Emmanuel]

Hi all,

I would like to test the relevance of a vector field (i.e. if the 
vectors are organized or not).
To do so, I would like to use an autocorrelation test, so that I have 
two questions:

- is the Watson test applicable to that perpuse ?
- is the kuiper test applicable to that purpuse ?

Regards


Emmanuel Poizot
Cnam/Intechmer
B.P. 324
50103 Cherbourg Cedex

Phone (Direct) : (00 33)(0)233887342
Fax : (00 33)(0)233887339


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Re: [R] The fastest way to select and execute a few selected functions inside a function

[Ales Ziberna]

- Original Message - 
From: "Ales Ziberna" <[EMAIL PROTECTED]>
To: "R-help" 
Sent: Wednesday, December 14, 2005 6:05 PM
Subject: The fastest way to select and execute a few selected functions 
inside a function


Dear useRs?



I have the following problem! I have a function that calls one or more
functions, depending on the input parameters. I am searching for the fastest
way to select and execute the selected functions and return their results in
a list. The number of possible functions is 10, however usually only 2 are
selected (although sometimes more, even all).



For examples, if I have function "myf" and the possible functions that I
want to call are "mean", "max" and "sum". I have thought of one way (myf) to
do that and am interested if there maybe exists a faster way (the speed is
very important, since this can be repeated millions of times in my
function).





myf<-function(FUN, x){

f<-list(mean=mean, max=max, sum=sum)

res<- vector( mode="list")

for(i in FUN){

res[[i]]<-f[[i]](x)

}

return(res)

}

myf(FUN=c("mean","max"),x=1:10)





In this case, it would be faster if I would compute all functions, even if I
need only one:

myf.all<-function(x){

list(mean=mean(x), max=max(x), sum=sum(x))

}



> gc();system.time(for(i in 1:1)myf.all(1:20))

 used (Mb) gc trigger (Mb) max used (Mb)

Ncells 165659  4.5 35  9.4   35  9.4

Vcells  61135  0.5 786432  6.0   283043  2.2

[1] 0.90 0.00 1.08   NA   NA

> gc();system.time(for(i in 1:1)myf(FUN="mean",1:20))

 used (Mb) gc trigger (Mb) max used (Mb)

Ncells 165659  4.5 35  9.4   35  9.4

Vcells  61135  0.5 786432  6.0   283043  2.2

[1] 1.14 0.00 1.40   NA   NA



This does (usually) not happen in my case, since most of functions I
consider are more complex.



Thanks in advance for any suggestions!


Best regards,

Ales Ziberna

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Re: [R] lme4: Extract fixed effects Val, SE, t, p

[Doran, Harold]

There are certain functions which can easily extracts the various
components, however. For instance, you can grab the fixed effects using
fixef(), the variance components using VarCorr, and the standard errors
of the fixed effects using vcov() 

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Dieter Menne
Sent: Friday, December 16, 2005 3:28 AM
To: r-help@stat.math.ethz.ch
Subject: Re: [R] lme4: Extract fixed effects Val, SE, t, p

Zev Ross  zevross.com> writes:

> Using glmmPQL you can extract the full table of estimates, SE, 
> p-values etc using as an example:
> 
> mymodel<-glmmPQL(mymodel here)
> 
> summary(mymodel)[[18]]
> 
> How can I pull this table out of a lmer object in lme4?


Looks like it is not so easy, the code that produces the table is rather
hidden in Matrix\r\lmer.R, about line 400


setMethod("show", "summary.lmer",
  function(object) {
  fcoef <- [EMAIL PROTECTED]
  useScale <- [EMAIL PROTECTED]


You might be able to write your own code using the outline given there,
but you 
could run into trouble with method getFixDF.

Dieter

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[R] Vector of matrix

[Vieilledent Ghislain]

Dear statisticians,

I would like to save results for a "for loop" in a vector previously created.
My result would be of class "matrix".

I tried the following script:

Script:
#Creation of a previous vector
n.Tree<-2
VectorX<-rep(1,n.Tree)

#loop
for (i in 1:2) {
Ti<-MatOccurTree[Tree[i],1] #number of observation for Tree i
Xi<-matrix(data=1,nrow=Ti,ncol=2)
Xi[,2]<-treedata2$lnE[IdentTree==Tree[i]]
VectorX[i]<-Xi
}

Console:
> VectorX[i]<-Xi
Warning message:
le nombre d'objets à remplacer n'est pas multiple de la taille du remplacement 
"number of object to replace isn't a multiple of the length of the replacement"

Would you have any solution to create a vector of matrix "VectorX" ?

Thanks for your help.

Ghislain Vieilledent.

[[alternative HTML version deleted]]

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Re: [R] Vector of matrix

[Jacques VESLOT]

It seems that Xi is a matrix; so it can't be included in a vector.

You need to create a list for the result of your "for" loop.

res <- list()

for ( i in ...) {

res[[i]] <-  Xi }


 

Vieilledent Ghislain a écrit :

>Dear statisticians,
>
>I would like to save results for a "for loop" in a vector previously created.
>My result would be of class "matrix".
>
>I tried the following script:
>
>Script:
>#Creation of a previous vector
>n.Tree<-2
>VectorX<-rep(1,n.Tree)
>
>#loop
>for (i in 1:2) {
>   Ti<-MatOccurTree[Tree[i],1] #number of observation for Tree i
>   Xi<-matrix(data=1,nrow=Ti,ncol=2)
>   Xi[,2]<-treedata2$lnE[IdentTree==Tree[i]]
>   VectorX[i]<-Xi
>}
>
>Console:
>  
>
>>VectorX[i]<-Xi
>>
>>
>Warning message:
>le nombre d'objets à remplacer n'est pas multiple de la taille du remplacement 
>"number of object to replace isn't a multiple of the length of the replacement"
>
>Would you have any solution to create a vector of matrix "VectorX" ?
>
>Thanks for your help.
>
>Ghislain Vieilledent.
>
>   [[alternative HTML version deleted]]
>
>  
>
>
>
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>

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Re: [R] Hmisc latex function

[Marc Schwartz]

Paul,

I believe that the bug has been fixed in the CVS version of latex(), but
it has not yet made its way to an updated version of Hmisc on CRAN from
what I can see.

You can get the updated version of latex() from:

http://biostat.mc.vanderbilt.edu/cgi-bin/cvsweb.cgi/Hmisc/R/latex.s

Click on the 'download' link for version 1.14 at the top of the page.
You can save the updated code to a text file and then source() it into a
R session for the time being.

HTH,

Marc Schwartz

On Thu, 2005-12-15 at 15:53 -0600, Paul Johnson wrote:
> Does anybody suggest a work-around this problem?
> 
> pj
> 
> Marc Schwartz (via MN) wrote:
> > On Wed, 2005-10-12 at 08:33 -0500, Charles Dupont wrote:
> > 
> >>Marc Schwartz (via MN) wrote:
> >>
> >>>On Tue, 2005-10-11 at 10:01 -0400, Rick Bilonick wrote:
> >>>
> >>>
> I'm using R 2.2.0 on an up-to-date version of Fedora Core 4 with the
> latest version of Hmisc. When I run an example from the latex function I
> get the following:
> 
> 
> 
> >x <- matrix(1:6, nrow=2, dimnames=list(c('a','b'),c('c','d','enLine
> 
> 2')))
> 
> 
> >x
> 
>  c d enLine 2
> a 1 35
> b 2 46
> 
> 
> >latex(x)   # creates x.tex in working directory
> 
> sh: line 0: cd: “/tmp/Rtmpl10983”: No such file or directory
> This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
> entering extended mode
> ! I can't find file `“/tmp/Rtmpl10983/file643c9869”'.
> <*> “/tmp/Rtmpl10983/file643c9869”
> 
> Please type another input file name: q
> (/usr/share/texmf/tex/latex/tools/q.tex
> LaTeX2e <2003/12/01>
> Babel  and hyphenation patterns for american, french, german,
> ngerman, b
> ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch,
> esperanto, e
> stonian, finnish, greek, icelandic, irish, italian, latin, magyar,
> norsk, polis
> h, portuges, romanian, russian, serbian, slovak, slovene, spanish,
> swedish, tur
> kish, ukrainian, nohyphenation, loaded.
> File ignored
> xdvi-motif.bin: Fatal error: /tmp/Rtmpl10983/file643c9869.dvi: No such
> file.
> 
> 
> How can I fix this?
> 
> Rick B.
> >>>
> >>>
> >>>I get the same results, also on FC4 with R 2.2.0.
> >>>
> >>>I am cc:ing Frank here for his input, but a quick review of the code and
> >>>created files suggests that there may be conflict between the locations
> >>>of some of the resultant files during the latex system call. Some files
> >>>appear in a temporary R directory, while others appear in the current R
> >>>working directory.
> >>>
> >>>For example, if I enter the full filename:
> >>> 
> >>>  /tmp/RtmpC12100/file643c9869.tex
> >>>
> >>>at the latex prompt, I get:
> >>>
> >>>
> >>>
> latex(x)
> >>>
> >>>sh: line 0: cd: “/tmp/RtmpC12100”: No such file or directory
> >>>This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
> >>>entering extended mode
> >>>! I can't find file `“/tmp/RtmpC12100/file643c9869”'.
> >>><*> “/tmp/RtmpC12100/file643c9869”
> >>>
> >>>Please type another input file name: *** loading the extensions
> >>>datasource
> >>>/tmp/RtmpC12100/file643c9869.tex
> >>>(/tmp/RtmpC12100/file643c9869.tex
> >>>LaTeX2e <2003/12/01>
> >>>Babel  and hyphenation patterns for american, french, german,
> >>>ngerman, b
> >>>ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch,
> >>>esperanto, e
> >>>stonian, finnish, greek, icelandic, irish, italian, latin, magyar,
> >>>norsk, polis
> >>>h, portuges, romanian, russian, serbian, slovak, slovene, spanish,
> >>>swedish, tur
> >>>kish, ukrainian, nohyphenation, loaded.
> >>>(/usr/share/texmf/tex/latex/base/report.cls
> >>>Document Class: report 2004/02/16 v1.4f Standard LaTeX document class
> >>>(/usr/share/texmf/tex/latex/base/size10.clo))
> >>>(/usr/share/texmf/tex/latex/geometry/geometry.sty
> >>>(/usr/share/texmf/tex/latex/graphics/keyval.sty)
> >>>(/usr/share/texmf/tex/latex/geometry/geometry.cfg))
> >>>No file file643c9869.aux.
> >>>[1] (./file643c9869.aux) )
> >>>Output written on file643c9869.dvi (1 page, 368 bytes).
> >>>Transcript written on file643c9869.log.
> >>>xdvi-motif.bin: Fatal error: /tmp/RtmpC12100/file643c9869.dvi
> >>
> >>
> >>H,  It works for me.  Interesting.
> >>
> >>It almost looks like the temp dir is not being created, but thats not 
> >>possible because R does that.  It might be a Unicode issue with you 
> >>system shell.  Can you run this statement in R
> >>
> >>sys(paste('cd',dQuote(tempdir()),";",
> >>"echo Hello BOB > test.test",
> >>";","cat test.test"))
> >>
> >>
> >>What version of Hmisc are you using?  What local are you using?
> >>
> >>Charles
> > 
> > 
> > Hmisc version 3.0-7, Dated 2005-09-15, which is the latest according to
> > CRAN.
> > 
> > 
> >>sys(paste('cd',dQuote(tempdir()),";",
> > 
> > + "echo Hello BOB > test.test",
> > + ";","cat test.test"))
> > sh: line 0: cd: “/tmp/RtmpGY5553”: No such file or directory
> > [1] "Hello

[R] DUPLEX

[Dietrich Trenkler]

Hi all,

not to invent the wheel a second time I wonder if  someone out
there has programmend Snee's CADEX algorithm (Validation
of regression models: Methods and examples, Technometrics 19,
415-428).

Thank you in advance.

D. Trenkler



-- 
Dietrich Trenkler c/o Universitaet Osnabrueck 
Rolandstr. 8; D-49069 Osnabrueck, Germany
email: [EMAIL PROTECTED]

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Re: [R] notification (PR#8400)

[Ken Termiso]

I don't care what you guys say -- that email was for me!! That money is 
MINE, baby!!

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[R] multiple plots per page

[Bill Hunsicker]

R-help,

I would like to place nine (3X3) plots per page.  I am not properly
implement mfrow(3,3) in the script below:

jpeg("xyplot.jpg") #names output file
my_args <- commandArgs() #sets up to take args from dos batch command
mfcol(3,3) #set page for 3X3
TEMPS <- c(-15,25,85)#list of temps
VBATS <- c(3,3.6,4.7)#list of Bats
BOARDS <- c("YZ0DC","ZD0DC","0E0DC","2E0DC","3E0DC")#list of boards
#load the xtal data into "all" with formatting for memory saving
all <- read.csv(my_args[3], colClasses=c('factor',
rep('integer',3),'numeric', 'numeric',
'numeric', 'integer', 'integer', 'integer', 'numeric', 'factor',
'factor',
rep('integer', 5), 'numeric', 'integer', 'numeric'))
#get data by board and temp and voltage
for( T in TEMPS)
   for(V in  VBATS)
  for(B in BOARDS)
   {
board <- subset(all,(Temperature==T && BoardNumber == B &&
PS13==V))
   plot((board$FineTuneDACStep * board$ArrayID),board$OutpFreq)
   }

Can you help me?  

Regards,
Bill

Bill Hunsicker
RF Micro Devices
7625 Thorndike Road
Greensboro, NC  27409
336-678-5260
610-597-9985(m)

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Re: [R] millions of comparisons, speed wanted

[Martin Maechler]

I have not taken the time to look into this example,
but
daisy()
from the (recommended, hence part of R) package 'cluster'
is more flexible than dist(), particularly in the case of NAs
and for (a mixture of continuous and) categorical variables.

It uses a version of Gower's formula in order to deal with NAs
and asymmetric binary variables.  The example below look like
very well matching to this problem.

Regards,
Martin Maechler, ETH Zurich


> "Adrian" == Adrian DUSA <[EMAIL PROTECTED]>
> on Thu, 15 Dec 2005 22:04:01 +0200 writes:

Adrian> Dear Andy,
Adrian> On Thursday 15 December 2005 20:57, Liaw, Andy wrote:
>> Just some untested idea:
>> If the data are all 0/1, you could use dist(input, method="manhattan"), 
and
>> then check which entry equals 1.  This should be much faster than 
creating
>> all pairs of rows and check position-by-position.

Adrian> Thanks for the idea, I played a little with it. At the beginning 
yes, the data 
Adrian> are all 0/1, but during the minimizing iterations there are also 
"x" values; 
Adrian> for example comparing:
Adrian> 0 1 0 1 1
Adrian> 0 0 0 1 1
Adrian> should return
Adrian> 0 "x" 0 1 1

Adrian> whereas
Adrian> 0 "x" 0 1 1
Adrian> 0 0 0 1 1
Adrian> shouldn't even be compared (they have different number of figures).

Adrian> Replacing "x" with NA in dist is not yielding results either, as 
with
Adrian> NA 0 0 1 1
Adrian> 0 0 0 1 1
Adrian> dist returns 0.

Adrian> I even wanted to see if I could tweak the dist code, but it calls a 
C program 
Adrian> and I gave up.

Adrian> Nice idea anyhow, maybe I'll find a way to use it further.
Adrian> Best,
Adrian> Adrian

Adrian> -- 
Adrian> Adrian DUSA
Adrian> Romanian Social Data Archive
Adrian> 1, Schitu Magureanu Bd
Adrian> 050025 Bucharest sector 5
Adrian> Romania
Adrian> Tel./Fax: +40 21 3126618 \
Adrian> +40 21 3120210 / int.101

Adrian> __
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Adrian> https://stat.ethz.ch/mailman/listinfo/r-help
Adrian> PLEASE do read the posting guide! 
http://www.R-project.org/posting-guide.html

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[R] column name of a table

[[EMAIL PROTECTED]]

hy all,

I wish to switch in a part in my code that use "read.table" to "scan", actually 
i use this:

tab<-scan("data.dat",what=integer(),skip=1)
dim(tab)<-c(75,length(tab)/75)
tab<-t(tab)

It gives me a new tab with 75 columns, but i when i was using read.table with 
headers then attach i could use the columns names to access the data values, 
now how can i attach the columns names that are on the first line of the file 
data.dat?

Any help would be great!

thks all
guillaume.

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Re: [R] multiple plots per page

[Earl F. Glynn]

"Bill Hunsicker" <[EMAIL PROTECTED]> wrote in message
news:[EMAIL PROTECTED]
> R-help,
>
> I would like to place nine (3X3) plots per page.  I am not properly
> implement mfrow(3,3) in the script below:

Does this help?

jpeg("3x3.jpg")
oldpar <- par( mfcol=c(3,3) )
plot(1)
plot(2)
plot(3)
plot(4)
plot(5)
plot(6)
plot(7)
plot(8)
plot(9)
par(oldpar)
dev.off()

efg

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Re: [R] Need help for a statistical problem ("See the posting guide")

[Brett Magill]

In response to a thread where a statistical question
unrelated to R was asked, Uwe Ligges wrote:

> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 
> Please ask a local statistical consultant for help.
> 
> Uwe Ligges

Perhaps Uwe's admonition to "do read the posting
guide" was just a knee jerk reaction to an
unrecognized poster's name.  Of course, if the poster
did read the posting guide, they would have learned
that : 

"Questions about statistics: The R mailing lists are
primarily intended for questions and discussion about
the R software. However, questions about statistical
methodology are sometimes posted. If the question is
well-asked and of interest to someone on the list, it
may elicit an informative up-to-date answer. See also
the Usenet groups sci.stat.consult (applied statistics
and consulting) and sci.stat.math (mathematical stat
and probability)."

The language here is so equivocal!  OK, it is really
for R, but statistical questions are asked and you
might get an "informative and up-to-date answer" if
you do it well.  Sounds good to me!  I might start
using r-help for my statistical questions.  Thanks for
referring me to the posting guide Uwe (though I am not
sure why it was relevant the the original post).

My point: If r-help does not want statistical
questions, and people who ask statistical questions
are referred to the posting guide, shouldn't the
posting guide *actually* say no statistical questions!

Brett

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[R] tapply question

[Frank Johannes]

HI,
Suppose I have the following data structure.
   LRT  tp
1   1.50654010 522
2   0.51793929 522
3   0.90340299 522
4   1.20293325 522
5   1.05578774 523
6   0.01617942 523
7   0.68183543 523
8   0.43820244 523
9   1.14123995 524
10  0.05809550 524
11  0.93061597 524
12  1.39739700 524
13  1.05220953 525
14  0.03471461 525
15  0.63168798 525
16  1.40592603 525
17  1.41884492 526
18  0.23388479 526
19  0.21881064 526
20  0.99710830 526
21  2.02054187 527
22  1.99872887 527
23  1.04187450 527
24  1.31556807 527
25  2.5190 528
26  2.94778561 528
27  1.88800177 528
28  2.08249941 528


I have succesfully used a command line such as the one below to get
maxima for each "tp-category'

data.out<-data[tapply(LRT,tp, function(x) which(LRT==max(x))),]

However, when I try it on the above data, it gives me the following
error message:
>Error in "[.data.frame"(data, tapply(LRT, tp, function(x) which(LRT ==  : 
invalid subscript type

I don't know what to do.
Thanks for your help

--

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Re: [R] Looking for a sort of tapply() to data frames

[January Weiner]

Hi,

On 12/15/05, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> You don't get them as a column but you get them as the
> component labels.
>
>by(df, df$Day, function(x) colMeans(x[,-1]))
>
> If you convert it to a data frame you get them as the rownames:
>
>   do.call("rbind", by(df, df$Day, function(x) colMeans(x[,-1])))

Thanks! that helps a lot.  But I still run into problems with this. 
Sorry for bothering you with newbie questions, if my problems are
trivial, point me to a suitable guide (I did read the introductory
materials on R).

First: it works for colMeans, but it does not work for a function like this:

do.call("rbind", by(df, df$Day, function(x) cor(df$val1, df$val2))

it says "Error in do.call() : second argument must be a list". I
do not understand this, as the second argument is "b" of the class
"by", as it was in the case of colMeans, so it did not change...?

Second: in case of colMeans (where it works) it returns a matrix, and
I have troubles getting it back to the data.frame, so I can access
blah$Day.  Instead, I have smth like that:

> do.call("rbind",b)
V2 V3 V4 V5   V7
Tue 19 15  2  0 1.538462
Wed  5  3  6  1 1.285714

...and I do not know how to acces, for example, values for "Tue",
except with [1,] -- which is somewhat problematic.  For example, I
would like to display the 3 days for which V7 is highest.  How can I
do that?

> I think you want class(df) which shows its a data frame.

Ops. Sorry, I didn't guess it from the manual :-)

>aggregate(df[,-1], df[,1,drop = FALSE], mean)

But why is df[,1,drop=FALSE] a list?  I don't get it...

>aggregate(df[,-1], list(Day = df$Day), mean)

Yeah, I figured out that one.

> Another alternative is to use summaryBy from the doBy package found
> at http://genetics.agrsci.dk/~sorenh/misc/ :
>
>library(doBy)
>summaryBy(cbind(var1, var2) ~ Day, data = df)

I think I am not confident enough with the basic data types in R, I
need to understand them before I go over to specialized packages :-)

Again, thanks a lot,
January

--
 January Weiner 3  -+---
Division of Bioinformatics, University of Muenster  |  Schloßplatz 4
(+49)(251)8321634   |  D48149 Münster
http://www.uni-muenster.de/Biologie.Botanik/ebb/|  Germany

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Re: [R] column name of a table

[Florence Combes]

I am not sure to understand what you want, but maybe
colnames() is what you want.
for example

> mat
 [,1] [,2] [,3]
[1,]135
[2,]246
> colnames(mat)<-c("col1","col2","col3")
> mat
 col1 col2 col3
[1,]135
[2,]246


was it what you were looking for ?

florence.



On 12/16/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>
> hy all,
>
> I wish to switch in a part in my code that use "read.table" to "scan",
> actually i use this:
>
> tab<-scan("data.dat",what=integer(),skip=1)
> dim(tab)<-c(75,length(tab)/75)
> tab<-t(tab)
>
> It gives me a new tab with 75 columns, but i when i was using read.tablewith 
> headers then attach i could use the columns names to access the data
> values, now how can i attach the columns names that are on the first line of
> the file data.dat?
>
> Any help would be great!
>
> thks all
> guillaume.
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>

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Re: [R] tapply question

[Uwe Ligges]

Frank Johannes wrote:

> HI,
> Suppose I have the following data structure.
>LRT  tp
> 1   1.50654010 522
> 2   0.51793929 522
> 3   0.90340299 522
> 4   1.20293325 522
> 5   1.05578774 523
> 6   0.01617942 523
> 7   0.68183543 523
> 8   0.43820244 523
> 9   1.14123995 524
> 10  0.05809550 524
> 11  0.93061597 524
> 12  1.39739700 524
> 13  1.05220953 525
> 14  0.03471461 525
> 15  0.63168798 525
> 16  1.40592603 525
> 17  1.41884492 526
> 18  0.23388479 526
> 19  0.21881064 526
> 20  0.99710830 526
> 21  2.02054187 527
> 22  1.99872887 527
> 23  1.04187450 527
> 24  1.31556807 527
> 25  2.5190 528
> 26  2.94778561 528
> 27  1.88800177 528
> 28  2.08249941 528
> 
> 
> I have succesfully used a command line such as the one below to get
> maxima for each "tp-category'
> 
> data.out<-data[tapply(LRT,tp, function(x) which(LRT==max(x))),]
> 
> However, when I try it on the above data, it gives me the following
> error message:
> 
>>Error in "[.data.frame"(data, tapply(LRT, tp, function(x) which(LRT ==  : 
> 
> invalid subscript type


Works for me. Look at your data structures and check whether your data 
frame is OK.

Or much better easier:

   tapply(LRT, tp, max)

Uwe Ligges




> I don't know what to do.
> Thanks for your help
> 
> --
> 
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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[R] Butterworth low-pass filter

[Andy Bunn]

Has anybody implemented code to extract coefficients for a Butterworth
low-pass filter? I know Matlab has it implemented in the signal toolbox. I
want to make use of a 10 point Butterworth low-pass filter for smoothing.

In Matlab the code would look like this:
% Determine the filter coefficients
[b,a]=butter(10,0.1)
% Apply the filter to the input
outdata = filter (b,a,indata);

The archives contain similar questions but if somebody responded, they did
it off-list.

Thanks in advance,
Andy

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[R] dendrogram branches with different lty

[Patrick Kuss]

Dear r-list,

I am trying to visually seperate the two main clusters of a dendrogram.
The idea is to use:

'edgePar=list(lty=3)' for 'dend1[[1]]' and
'edgePar=list(lty=1)' for 'dend1[[2]]'

I have not found a way to solve this. Any suggestions?

Patrick

hc <- hclust(dist(USArrests), "ave")
(dend1 <- as.dendrogram(hc))
par(mfrow=c(2,2))
plot(dend1)
plot(dend1[[1]],edgePar=list(lty=3))
plot(dend1[[2]],edgePar=list(lty=1))


--
Patrick Kuss
PhD-student
Institute of Botany
University of Basel
Schönbeinstr. 6
CH-4056 Basel
+41 61 267 2976

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Re: [R] Looking for a sort of tapply() to data frames

[Gabor Grothendieck]

On 12/16/05, January Weiner <[EMAIL PROTECTED]> wrote:
> Hi,
>
> On 12/15/05, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> > You don't get them as a column but you get them as the
> > component labels.
> >
> >by(df, df$Day, function(x) colMeans(x[,-1]))
> >
> > If you convert it to a data frame you get them as the rownames:
> >
> >   do.call("rbind", by(df, df$Day, function(x) colMeans(x[,-1])))
>
> Thanks! that helps a lot.  But I still run into problems with this.
> Sorry for bothering you with newbie questions, if my problems are
> trivial, point me to a suitable guide (I did read the introductory
> materials on R).
>
> First: it works for colMeans, but it does not work for a function like this:
>
> do.call("rbind", by(df, df$Day, function(x) cor(df$val1, df$val2))

There are a number of problems:

1. the function does not depend on x and therefore will return the
same result for each day group.

2. although ?by says it returns a list, it apparently simplifies the result,
contrary to the documentation, in certain cases.  Try this:

do.call("rbind", as.list(by(df, df$Day, function(x) cor(x$val1, x$val2

or this:

do.call("rbind", by(df, df$Day, function(x) list(cor = cor(x$val1, x$val2


3. In your sample data val1 is constant for Wed so you won't be able
to get a correlation.  That's the source of the warning that you get
when running the line in #2.

>
> it says "Error in do.call() : second argument must be a list". I
> do not understand this, as the second argument is "b" of the class
> "by", as it was in the case of colMeans, so it did not change...?
>
> Second: in case of colMeans (where it works) it returns a matrix, and
> I have troubles getting it back to the data.frame, so I can access
> blah$Day.  Instead, I have smth like that:

Try blah[,"Day"] which works with both matrices and data frames.

>
> > do.call("rbind",b)
>V2 V3 V4 V5   V7
> Tue 19 15  2  0 1.538462
> Wed  5  3  6  1 1.285714


Another possibility is to coerce it to a data frame:

as.data.frame(do.call("rbind", b))

or change your function to return a list.

>
> ...and I do not know how to acces, for example, values for "Tue",
> except with [1,] -- which is somewhat problematic.  For example, I
> would like to display the 3 days for which V7 is highest.  How can I
> do that?
>
> > I think you want class(df) which shows its a data frame.
>
> Ops. Sorry, I didn't guess it from the manual :-)
>
> >aggregate(df[,-1], df[,1,drop = FALSE], mean)
>
> But why is df[,1,drop=FALSE] a list?  I don't get it...

Because df is a one column data frame and data frames are lists.
Had we not specified drop, it would have automatically dropped it
since it has only one dimension simplifying it to a non-list.
We do not want that simplification here.

>
> >aggregate(df[,-1], list(Day = df$Day), mean)
>
> Yeah, I figured out that one.
>
> > Another alternative is to use summaryBy from the doBy package found
> > at http://genetics.agrsci.dk/~sorenh/misc/ :
> >
> >library(doBy)
> >summaryBy(cbind(var1, var2) ~ Day, data = df)
>
> I think I am not confident enough with the basic data types in R, I
> need to understand them before I go over to specialized packages :-)
> Again, thanks a lot,
> January
>
> --
>  January Weiner 3  -+---
> Division of Bioinformatics, University of Muenster  |  Schloßplatz 4
> (+49)(251)8321634   |  D48149 Münster
> http://www.uni-muenster.de/Biologie.Botanik/ebb/|  Germany
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

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[R] Wilcoxon Mann-Whitney Rank Sum Test

[Tuszynski, Jaroslaw W.]

Does anybody know what is relation between 'T' value calculated by
'wilcox_test' function (coin package) and more common 'W' value?

Jarek Tuszynski


>library(coin)
> ### Tritiated Water Diffusion Across Human Chorioamnion
> ### Hollander & Wolfe (1999), Table 4.1, page 110
> water_transfer <- data.frame(
+ pd = c(0.80, 0.83, 1.89, 1.04, 1.45, 1.38, 1.91, 1.64, 0.73, 1.46,
+1.15, 0.88, 0.90, 0.74, 1.21),
+ age = factor(c(rep("At term", 10), rep("12-26 Weeks", 5
> 
> ### Wilcoxon-Mann-Whitney test, cf. Hollander & Wolfe (1999), page 111
> ### exact p-value and confidence interval for the difference in location
> ### (At term - 12-26 Weeks)
> wt <- wilcox_test(pd ~ age, data = water_transfer, distribution = "exact",
conf.int = TRUE)
> print(wt)

Exact Wilcoxon Mann-Whitney Rank Sum Test

data:  pd by groups 12-26 Weeks, At term 
T = -1.2247, p-value = 0.2544
alternative hypothesis: true mu is not equal to 0 
95 percent confidence interval:
 -0.76  0.15 
sample estimates:
difference in location 
-0.305 

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Re: [R] Looking for a sort of tapply() to data frames

[Frank E Harrell Jr]

Gabor Grothendieck wrote:
> On 12/16/05, January Weiner <[EMAIL PROTECTED]> wrote:
> 
>>Hi,
>>
>>On 12/15/05, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
>>
>>>You don't get them as a column but you get them as the
>>>component labels.
>>>
>>>   by(df, df$Day, function(x) colMeans(x[,-1]))
>>>
>>>If you convert it to a data frame you get them as the rownames:
>>>
>>>  do.call("rbind", by(df, df$Day, function(x) colMeans(x[,-1])))
>>
>>Thanks! that helps a lot.  But I still run into problems with this.
>>Sorry for bothering you with newbie questions, if my problems are
>>trivial, point me to a suitable guide (I did read the introductory
>>materials on R).
>>
>>First: it works for colMeans, but it does not work for a function like this:
>>
>>do.call("rbind", by(df, df$Day, function(x) cor(df$val1, df$val2))
> 
> 
> There are a number of problems:
> 
> 1. the function does not depend on x and therefore will return the
> same result for each day group.
> 
> 2. although ?by says it returns a list, it apparently simplifies the result,
> contrary to the documentation, in certain cases.  Try this:
> 
> do.call("rbind", as.list(by(df, df$Day, function(x) cor(x$val1, x$val2
> 
> or this:
> 
> do.call("rbind", by(df, df$Day, function(x) list(cor = cor(x$val1, x$val2
> 
> 
> 3. In your sample data val1 is constant for Wed so you won't be able
> to get a correlation.  That's the source of the warning that you get
> when running the line in #2.
> 
> 
>>it says "Error in do.call() : second argument must be a list". I
>>do not understand this, as the second argument is "b" of the class
>>"by", as it was in the case of colMeans, so it did not change...?
>>
>>Second: in case of colMeans (where it works) it returns a matrix, and
>>I have troubles getting it back to the data.frame, so I can access
>>blah$Day.  Instead, I have smth like that:
> 
> 
> Try blah[,"Day"] which works with both matrices and data frames.
> 
> 
>>>do.call("rbind",b)
>>
>>   V2 V3 V4 V5   V7
>>Tue 19 15  2  0 1.538462
>>Wed  5  3  6  1 1.285714
> 
> 
> 
> Another possibility is to coerce it to a data frame:
> 
> as.data.frame(do.call("rbind", b))
> 
> or change your function to return a list.
> 
> 
>>...and I do not know how to acces, for example, values for "Tue",
>>except with [1,] -- which is somewhat problematic.  For example, I
>>would like to display the 3 days for which V7 is highest.  How can I
>>do that?
>>
>>
>>>I think you want class(df) which shows its a data frame.
>>
>>Ops. Sorry, I didn't guess it from the manual :-)
>>
>>
>>>   aggregate(df[,-1], df[,1,drop = FALSE], mean)
>>
>>But why is df[,1,drop=FALSE] a list?  I don't get it...
> 
> 
> Because df is a one column data frame and data frames are lists.
> Had we not specified drop, it would have automatically dropped it
> since it has only one dimension simplifying it to a non-list.
> We do not want that simplification here.
> 
> 
>>>   aggregate(df[,-1], list(Day = df$Day), mean)
>>
>>Yeah, I figured out that one.
>>
>>
>>>Another alternative is to use summaryBy from the doBy package found
>>>at http://genetics.agrsci.dk/~sorenh/misc/ :
>>>
>>>   library(doBy)
>>>   summaryBy(cbind(var1, var2) ~ Day, data = df)
>>
>>I think I am not confident enough with the basic data types in R, I
>>need to understand them before I go over to specialized packages :-)
>>Again, thanks a lot,
>>January

You might want to look at the summarize function in the Hmisc package.

Frank

>>
>>--
>> January Weiner 3  -+---
>>Division of Bioinformatics, University of Muenster  |  Schloßplatz 4
>>(+49)(251)8321634   |  D48149 Münster
>>http://www.uni-muenster.de/Biologie.Botanik/ebb/|  Germany
>>
>>__
>>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
>>
> 
> 
> __
> R-help@stat.math.ethz.ch mailing list
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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 Reference Card (especially useful for Newbies)

[Berton Gunter]

 
Newbies (and others!) may find useful the R Reference Card made available by
Tom Short and Rpad at http://www.rpad.org/Rpad/Rpad-refcard.pdf  or through
the "Contributed" link on CRAN (where some other reference cards are also
linked). It categorizes and organizes a bunch of R's basic, most used
functions so that they can be easily found. For example, paste() is under
the "Strings" heading and expand.grid() is under "Data Creation." For
newbies struggling to find the right R function as well as veterans who
can't quite remember the function name, it's very handy.
 
-- 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

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[R] R compile on AIX 5.3

[Matthew Beason]

I'm trying to compile R on AIX 5.3. I've gotten "configure" to work but
"make" generates the following errors:


Target "R" is up to date.
Target "R" is up to date.
Target "R" is up to date.
Target "R" is up to date.
Target "Makedeps" is up to date.
Target "libbz2.a" is up to date.
Target "Makedeps" is up to date.
Target "libpcre.a" is up to date.
Target "Makedeps" is up to date.
Target "libz.a" is up to date.
Target "R" is up to date.
Target "Makedeps" is up to date.
Target "libappl.a" is up to date.
Target "Makedeps" is up to date.
Target "libnmath.a" is up to date.
Target "Makedeps" is up to date.
Target "libunix.a" is up to date.
Target "Makedeps" is up to date.
gcc -I../../src/extra/zlib -I../../src/extra/bzip2
-I../../src/extra/pcre   -I. -I../../src/include -I../../src/include
-I/usr/local/include -DHAVE_CONFIG_H -mno-fp-in-toc  -g -O2 -c
platform.c -o platform.o
In file included from /usr/include/netdb.h:47,
 from platform.c:1365:
/usr/include/netinet/in.h:793: error: parse error before
"inet6_rth_space"
/usr/include/netinet/in.h:794: error: parse error before "socklen_t"
/usr/include/netinet/in.h:800: error: parse error before "socklen_t"
/usr/include/netinet/in.h:801: error: parse error before "socklen_t"
/usr/include/netinet/in.h:803: error: parse error before "socklen_t"
/usr/include/netinet/in.h:804: error: parse error before "socklen_t"
/usr/include/netinet/in.h:805: error: parse error before "socklen_t"
/usr/include/netinet/in.h:807: error: parse error before "socklen_t"
/usr/include/netinet/in.h:809: error: parse error before "socklen_t"
In file included from platform.c:1366:
/usr/include/sys/socket.h:374: error: parse error before "socklen_t"
/usr/include/sys/socket.h:378: error: parse error before
"msg_controllen"
/usr/include/sys/socket.h:380: error: parse error before '}' token
/usr/include/sys/socket.h:404: error: parse error before "socklen_t"
/usr/include/sys/socket.h:408: error: parse error before '}' token
/usr/include/sys/socket.h:475: error: parse error before "socklen_t"
/usr/include/sys/socket.h:476: error: parse error before "socklen_t"
/usr/include/sys/socket.h:477: error: parse error before "socklen_t"
/usr/include/sys/socket.h:478: error: parse error before "socklen_t"
/usr/include/sys/socket.h:484: error: parse error before "socklen_t"
/usr/include/sys/socket.h:485: error: parse error before "socklen_t"
/usr/include/sys/socket.h:486: error: parse error before "socklen_t"
/usr/include/sys/socket.h:490: error: parse error before "socklen_t"
/usr/include/sys/socket.h:491: error: parse error before "socklen_t"
make: 1254-004 The error code from the last command is 1.

Stop.
make: 1254-004 The error code from the last command is 2.

Stop.
make: 1254-004 The error code from the last command is 1.

Stop.
make: 1254-004 The error code from the last command is 1.

Any ideas on what may be preventing make from completing successfully? I
can provide an additional information required. 

Thanks!

Matt

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Re: [R] Looking for a sort of tapply() to data frames

[Gabor Grothendieck]

One other point.  The cor example could be done using tapply like
this:

tapply(rownames(df), df$Day, function(r) cor(df[r,"val1"], df[r, "val2"]))


On 12/16/05, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> On 12/16/05, January Weiner <[EMAIL PROTECTED]> wrote:
> > Hi,
> >
> > On 12/15/05, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> > > You don't get them as a column but you get them as the
> > > component labels.
> > >
> > >by(df, df$Day, function(x) colMeans(x[,-1]))
> > >
> > > If you convert it to a data frame you get them as the rownames:
> > >
> > >   do.call("rbind", by(df, df$Day, function(x) colMeans(x[,-1])))
> >
> > Thanks! that helps a lot.  But I still run into problems with this.
> > Sorry for bothering you with newbie questions, if my problems are
> > trivial, point me to a suitable guide (I did read the introductory
> > materials on R).
> >
> > First: it works for colMeans, but it does not work for a function like this:
> >
> > do.call("rbind", by(df, df$Day, function(x) cor(df$val1, df$val2))
>
> There are a number of problems:
>
> 1. the function does not depend on x and therefore will return the
> same result for each day group.
>
> 2. although ?by says it returns a list, it apparently simplifies the result,
> contrary to the documentation, in certain cases.  Try this:
>
> do.call("rbind", as.list(by(df, df$Day, function(x) cor(x$val1, x$val2
>
> or this:
>
> do.call("rbind", by(df, df$Day, function(x) list(cor = cor(x$val1, x$val2
>
>
> 3. In your sample data val1 is constant for Wed so you won't be able
> to get a correlation.  That's the source of the warning that you get
> when running the line in #2.
>
> >
> > it says "Error in do.call() : second argument must be a list". I
> > do not understand this, as the second argument is "b" of the class
> > "by", as it was in the case of colMeans, so it did not change...?
> >
> > Second: in case of colMeans (where it works) it returns a matrix, and
> > I have troubles getting it back to the data.frame, so I can access
> > blah$Day.  Instead, I have smth like that:
>
> Try blah[,"Day"] which works with both matrices and data frames.
>
> >
> > > do.call("rbind",b)
> >V2 V3 V4 V5   V7
> > Tue 19 15  2  0 1.538462
> > Wed  5  3  6  1 1.285714
>
>
> Another possibility is to coerce it to a data frame:
>
> as.data.frame(do.call("rbind", b))
>
> or change your function to return a list.
>
> >
> > ...and I do not know how to acces, for example, values for "Tue",
> > except with [1,] -- which is somewhat problematic.  For example, I
> > would like to display the 3 days for which V7 is highest.  How can I
> > do that?
> >
> > > I think you want class(df) which shows its a data frame.
> >
> > Ops. Sorry, I didn't guess it from the manual :-)
> >
> > >aggregate(df[,-1], df[,1,drop = FALSE], mean)
> >
> > But why is df[,1,drop=FALSE] a list?  I don't get it...
>
> Because df is a one column data frame and data frames are lists.
> Had we not specified drop, it would have automatically dropped it
> since it has only one dimension simplifying it to a non-list.
> We do not want that simplification here.
>
> >
> > >aggregate(df[,-1], list(Day = df$Day), mean)
> >
> > Yeah, I figured out that one.
> >
> > > Another alternative is to use summaryBy from the doBy package found
> > > at http://genetics.agrsci.dk/~sorenh/misc/ :
> > >
> > >library(doBy)
> > >summaryBy(cbind(var1, var2) ~ Day, data = df)
> >
> > I think I am not confident enough with the basic data types in R, I
> > need to understand them before I go over to specialized packages :-)
> > Again, thanks a lot,
> > January
> >
> > --
> >  January Weiner 3  -+---
> > Division of Bioinformatics, University of Muenster  |  Schloßplatz 4
> > (+49)(251)8321634   |  D48149 Münster
> > http://www.uni-muenster.de/Biologie.Botanik/ebb/|  Germany
> >
> > __
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide! 
> > http://www.R-project.org/posting-guide.html
> >
>

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Re: [R] R compile on AIX 5.3

[Prof Brian Ripley]

1) What version of R is this?  If not 2.2.1 beta, please do try that as 
there have been some recent AIX-related patches.

2) What is on lines 793 & 794 of /usr/include/netinet/in.h?
It looks like some other header file needs to be included first.

We only have reports of recent successful builds of R on AIX 5.2, no 
reports from 5.3.

On Fri, 16 Dec 2005, Matthew Beason wrote:

>
> I'm trying to compile R on AIX 5.3. I've gotten "configure" to work but
> "make" generates the following errors:
>
>
> Target "R" is up to date.
> Target "R" is up to date.
> Target "R" is up to date.
> Target "R" is up to date.
> Target "Makedeps" is up to date.
> Target "libbz2.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libpcre.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libz.a" is up to date.
> Target "R" is up to date.
> Target "Makedeps" is up to date.
> Target "libappl.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libnmath.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libunix.a" is up to date.
> Target "Makedeps" is up to date.
>gcc -I../../src/extra/zlib -I../../src/extra/bzip2
> -I../../src/extra/pcre   -I. -I../../src/include -I../../src/include
> -I/usr/local/include -DHAVE_CONFIG_H -mno-fp-in-toc  -g -O2 -c
> platform.c -o platform.o
> In file included from /usr/include/netdb.h:47,
> from platform.c:1365:
> /usr/include/netinet/in.h:793: error: parse error before
> "inet6_rth_space"
> /usr/include/netinet/in.h:794: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:800: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:801: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:803: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:804: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:805: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:807: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:809: error: parse error before "socklen_t"
> In file included from platform.c:1366:
> /usr/include/sys/socket.h:374: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:378: error: parse error before
> "msg_controllen"
> /usr/include/sys/socket.h:380: error: parse error before '}' token
> /usr/include/sys/socket.h:404: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:408: error: parse error before '}' token
> /usr/include/sys/socket.h:475: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:476: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:477: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:478: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:484: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:485: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:486: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:490: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:491: error: parse error before "socklen_t"
> make: 1254-004 The error code from the last command is 1.
>
> Stop.
> make: 1254-004 The error code from the last command is 2.
>
> Stop.
> make: 1254-004 The error code from the last command is 1.
>
> Stop.
> make: 1254-004 The error code from the last command is 1.
>
> Any ideas on what may be preventing make from completing successfully? I
> can provide an additional information required.
>
> Thanks!
>
> Matt
>
>   [[alternative HTML version deleted]]
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

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

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Re: [R] dendrogram branches with different lty

[Romain Francois]

Hi Patrick,

You may want to try out my (highly experimental, so not on CRAN) package 
A2R.
http://addictedtor.free.fr/packages/A2R/A2R_0.0-3.tar.gz
2 dendro's are displayed on RGG, check 
http://addictedtor.free.fr/graphiques/search.php?q=dendrogram

You might also be interrested in Appendix B of Paul Murrel's book :
http://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html

Romain

Le 16.12.2005 17:40, Patrick Kuss a écrit :

>Dear r-list,
>
>I am trying to visually seperate the two main clusters of a dendrogram.
>The idea is to use:
>
>'edgePar=list(lty=3)' for 'dend1[[1]]' and
>'edgePar=list(lty=1)' for 'dend1[[2]]'
>
>I have not found a way to solve this. Any suggestions?
>
>Patrick
>
>hc <- hclust(dist(USArrests), "ave")
>(dend1 <- as.dendrogram(hc))
>par(mfrow=c(2,2))
>plot(dend1)
>plot(dend1[[1]],edgePar=list(lty=3))
>plot(dend1[[2]],edgePar=list(lty=1))
>
>
>--
>Patrick Kuss
>PhD-student
>Institute of Botany
>University of Basel
>Schönbeinstr. 6
>CH-4056 Basel
>+41 61 267 2976
>
-- 
visit the R Graph Gallery : http://addictedtor.free.fr/graphiques
mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php
+---+
| Romain FRANCOIS - http://francoisromain.free.fr   |
| Doctorant INRIA Futurs / EDF  |
+---+

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Re: [R] R compile on AIX 5.3

[Matthew Beason]

Professor,

It is version 2.2.0 of R. I'll download 2.2.1 straight away and
see if that makes a difference.

On lines 793 & 794 of /usr/include/netinet/in.h, I found the
following:

socklen_t   inet6_rth_space(int, int);
void*inet6_rth_init(void *, socklen_t, int, int);

I have one other question for you if you don't mind. Do I need a
library such as ATLAS to get the most use out of R? Is there a
difference with R if you don't use something like ATLAS?

I'm glad to be blazing new trails as far as compiling R on AIX
5.3. I think this is a useful exercise.

Thanks again!


Matthew Beason
Unix Systems Engineer - Unix Engineering
Harrah's Entertainment, Inc.
One Harrah's Court, Las Vegas, NV 89119-4312
Office: 702-494-4097
Mobile: 702-622-6902
[EMAIL PROTECTED]
The information contained in this email may be legally privileged and
confidential. It is intended to be read only by the person to whom it is
addressed. If you have received this in error or are not the intended
recipient, please immediately notify the sender and delete all copies of
this message. Thank you.


-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] 
Sent: Friday, December 16, 2005 11:14 AM
To: Matthew Beason
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R compile on AIX 5.3

1) What version of R is this?  If not 2.2.1 beta, please do try that as
there have been some recent AIX-related patches.

2) What is on lines 793 & 794 of /usr/include/netinet/in.h?
It looks like some other header file needs to be included first.

We only have reports of recent successful builds of R on AIX 5.2, no
reports from 5.3.

On Fri, 16 Dec 2005, Matthew Beason wrote:

>
> I'm trying to compile R on AIX 5.3. I've gotten "configure" to work 
> but "make" generates the following errors:
>
>
> Target "R" is up to date.
> Target "R" is up to date.
> Target "R" is up to date.
> Target "R" is up to date.
> Target "Makedeps" is up to date.
> Target "libbz2.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libpcre.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libz.a" is up to date.
> Target "R" is up to date.
> Target "Makedeps" is up to date.
> Target "libappl.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libnmath.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libunix.a" is up to date.
> Target "Makedeps" is up to date.
>gcc -I../../src/extra/zlib -I../../src/extra/bzip2
> -I../../src/extra/pcre   -I. -I../../src/include -I../../src/include
> -I/usr/local/include -DHAVE_CONFIG_H -mno-fp-in-toc  -g -O2 -c 
> platform.c -o platform.o In file included from 
> /usr/include/netdb.h:47,
> from platform.c:1365:
> /usr/include/netinet/in.h:793: error: parse error before 
> "inet6_rth_space"
> /usr/include/netinet/in.h:794: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:800: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:801: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:803: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:804: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:805: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:807: error: parse error before "socklen_t"
> /usr/include/netinet/in.h:809: error: parse error before "socklen_t"
> In file included from platform.c:1366:
> /usr/include/sys/socket.h:374: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:378: error: parse error before 
> "msg_controllen"
> /usr/include/sys/socket.h:380: error: parse error before '}' token
> /usr/include/sys/socket.h:404: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:408: error: parse error before '}' token
> /usr/include/sys/socket.h:475: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:476: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:477: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:478: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:484: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:485: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:486: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:490: error: parse error before "socklen_t"
> /usr/include/sys/socket.h:491: error: parse error before "socklen_t"
> make: 1254-004 The error code from the last command is 1.
>
> Stop.
> make: 1254-004 The error code from the last command is 2.
>
> Stop.
> make: 1254-004 The error code from the last command is 1.
>
> Stop.
> make: 1254-004 The error code from the last command is 1.
>
> Any ideas on what may be preventing make from completing successfully?

> I can provide an additional information required.
>
> Thanks!
>
> Matt
>
>   [[alternative HTML version deleted]]
>
> __
> R-help@stat.math.eth

[R] Multiple plots per page

[Bill Hunsicker]

R-help,
 
I am trying to run a number of plots and want to generate 45 plots with
9 pages per plot.
 
I sent an email about four hours ago, but my email has been funky, I
apologize in advance if this message is duplicate.
 
Regards,
Bill
 



Bill Hunsicker
RF Micro Devices
7625 Thorndike Road
Greensboro, NC 27409-9421
[EMAIL PROTECTED]
336-678-5260(w)
610-597-9985(m)
336-678-5088(lab)


 

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[R] partially linear models

[Elizabeth Lawson]

Hey,
   
   I am estiamting a partially linear model y=X\beta+f(\theta) where the 
f(\theta) is estiamted using wavelets.
   
  Has anyone heard of methods to test if the betas are significant or to 
address model fit?
   
  Thanks for any thoughts or comments.
   
  Elizabeth Lawson

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[R] basis and penalty matrices for natural cubic splines

[Wei Zhang]

Hi,
I am trying to get the basis matrix and penalty matrix
for natural cubic splines. I found R function "ns" can
generate the B-spline basis matrix for a natural cubic
spline; and  "bsplinepen"  
can compute the penalty matrix for functions expressed
in terms of a B-spline basis. However, these two
functions seem not compatible. I could not get the
penalty matrix by "bsplinepen" using the basis matrix
generated from "ns".
Anyone knows any compatible functions to give the
basis
matrix and penalty matrix for natural cubic splines? 
Thanks a lot!
Wei

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[R] selecting matrix cels by two factors

[Dimitri Joe]

Hi,

I have a (numeric) matrix X of the type

 > X <- matrix(c(1:9),ncol=3,nrow=3)
 > colnames(X) <- c("A","B","C")
 > rownames(X) <- c("D","E","F")

Also, a have a data frame Y like

 > Y <- as.data.frame(cbind(c("D","E","F","D","E","F"),
+   c("A","C","A","B","B","C") ) )

I want a matrix like

1 4  X["D","A"] X["D","B"]
8 5  or, equivalentely,  X["E","C"] X["E","B"]
3 9  X["F","A"] X["F","C"]


Any suggestions?
Thanks in advanced,

Dimitri

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Re: [R] selecting matrix cels by two factors

[Berton Gunter]

You can subscript any arbitrary array (of any dim) with an appropriately
dimensioned matrix of integer indices. So all you have to do is convert the
dimnames into indices. One simple way to do this is:

X[cbind(match(c("D","E","F","D","E","F"),rownames(X)),
match(c("A","C","A","B","B","C"),colnames(X)))]

This gives a vector, which you can dimension however you like.

-- 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 Dimitri Joe
> Sent: Friday, December 16, 2005 3:02 PM
> To: R-Help
> Subject: [R] selecting matrix cels by two factors
> 
> Hi,
> 
> I have a (numeric) matrix X of the type
> 
>  > X <- matrix(c(1:9),ncol=3,nrow=3)
>  > colnames(X) <- c("A","B","C")
>  > rownames(X) <- c("D","E","F")
> 
> Also, a have a data frame Y like
> 
>  > Y <- as.data.frame(cbind(  c("D","E","F","D","E","F"),
> + c("A","C","A","B","B","C") ) )
> 
> I want a matrix like
> 
> 1 4X["D","A"] X["D","B"]
> 8 5  or, equivalentely,  X["E","C"] X["E","B"]
> 3 9X["F","A"] X["F","C"]
> 
> 
> Any suggestions?
> Thanks in advanced,
> 
> Dimitri
> 
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> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>

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Re: [R] help with multivariate analysis

[Spencer Graves]

Dear Dr. Vidali:

  1.  I would first plot the data a number of different ways.  Maybe 
you've already done plenty of this, but I have had a tendancy to rush to 
the model I thought was the "best" without adequate data integrity 
checks.  I typically want to start with normal probability (using 
"qqnorm").  Outliers, the need for transformations, mixtures, etc., will 
jump off the page when I do this.  Sometimes, I find that I didn't get 
the data read properly.  Also, I may consider log(heart.frequency) and 
1/heart.frequency as well as heart.frequency.  In most cases, I will 
base the subsequent analysis on whichever looks most nearly normally 
distributed.

  2.  I will also want to make scatterplots of the two variables as 
well as plotting each vs. time (with one line for each patient and 
separate plots for the two groups, but on the same scale).  This can 
tell me how much correlation to expect as well as what kinds of effects 
I want to model.

  3.  Have you consulted Pinheiro and Bates (2000) Mixed-Effects Models 
in S and S-Plus (Springer)?  The first half of that book describes how 
to analyze data sets like you describe when effects are linear and 
additive.  The latter half describes what to do with nonlinear effects.

  4.  If you still would like further assistance from this group, 
please submit another post, but PLEASE do read the posting guide! 
"www.R-project.org/posting-guide.html".  Anecdotal evidence suggests 
that posts more consistent with that guide tend to get more useful 
replies quicker.

  hope this helps.
  spencer graves

Matteo Vidali wrote:

> dear R users,
> I need some help for multivariate analysis.
> I have 2  anaesthetic treatment groups (20 patients/group) where I 
> register heart frequency and pressure for 60 min (repeated measures 
> every 5 minutes). I would like to perform a test to check if treatments 
> are different in controlling freq and pressures during the anaesthesia, 
> but i would like to have also an overall measure and not only multiple p 
> for different time intervals. I also think I should choose a test in 
> which time is meaningful since the measures are not simple repeated 
> measurements but measurements taken at specific time points.
> 1 million dollar question how to do in R?
> thanks in advance
> 
> Dr Matteo Vidali
> Dep. of Medical Sciences
> University of East Piedmont "A. Avogadro"
> ITALY
> 
> 
> --
> 
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-- 
Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA

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

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Re: [R] what does this warnings mean? and what should I do?

[Spencer Graves]

  You actually received two different warning messages.  The first 8
warnings read, "optim or nlminb returned message false convergence (8)",
and the other 3 say, "... returned message singular convergence".  The
function "lmer" uses a nonlinear optimizer (either "optim" or "nlminb")
to minimize an objective function.  The first message says that the
nonlinear optimizer was still reducing the objective function when it
reached an iteration limit.  If this were the  only problem, you might
consider increasing the iteration limits, maxIter, msMaxIter, niterEM
and PQLmaxIt.  However, the "singular convergence" message says that the
estimated variance-covariance matrix of the observations became singular.

  Looking now at your output, I notice that "Corr" between
"(Intercept)" and "trust.cz1" for the "Random Effects" "commid" is
1.000.  This says that the structure of your data are not adequate to
allow you to distinguish between random effects for "(Intercept)" and
"trust.cz1" for "commid", while simultaneously estimating all the fixed
effects you have in the model.

  If I were you, I'd start be deleting all the terms from the model
that don't have a "Signif. code" beside it in the table of "Fixed
effects" and then refit the smaller model, preferably also using
'method="AGQ"'.  If I still get the same message from trying to fit the
reduced model, I would conclude that the data are not adequate to
distinguish between "(Intercept)" and "trust.cz1" for "commid".  I would
then delete "trust.cz1" from the model and go from there.

  hope this helps.
  spencer graves

ronggui wrote:

> I use lmer to fit a mixed effect model.It give some warnings.what does this 
> warnings mean? and what should I do?
> 
> 
>>(fm2.mlm <- lmer(qd ~ edu + jiankang + peixun +hunyin + cadcj + 
age + age2 + sex + dangyuan + Comp.1 + Comp.2+trust.cz1 +
(trust.cz1|commid), data = individual,na.action =
"na.exclude",family="quasibinomial"))
> 
> Generalized linear mixed model fit using PQL 
> Formula: qd ~ edu + jiankang + peixun + hunyin + cadcj + age + age2 +  
> sex + dangyuan + Comp.1 + Comp.2 + trust.cz1 + (trust.cz1 |  commid) 
>Data: individual 
>  Family: quasibinomial(logit link)
>   AIC  BIClogLik deviance
>  736.7059 821.8267 -349.3529 698.7059
> Random effects:
>  Groups   NameVariance Std.Dev. Corr  
>  commid   (Intercept) 1.56413  1.25065
>   trust.cz1   0.17922  0.42334  1.000 
>  Residual 0.89728  0.94725
> # of obs: 652, groups: commid, 39
> 
> Fixed effects:
>   Estimate  Std. Error  DF t value Pr(>|t|)  
> (Intercept)-1.6115e-01  6.7997e-01 637 -0.2370  0.81274  
> edu-5.2585e-02  4.1048e-02 637 -1.2810  0.20064  
> jiankang   -9.8243e-01  4.4645e-01 637 -2.2005  0.02813 *
> peixun -4.6307e-01  2.6397e-01 637 -1.7542  0.07988 .
> hunyin -1.2255e-02  2.8151e-01 637 -0.0435  0.96529  
> hunyin -2.7726e-01  1.3846e+00 637 -0.2002  0.84136  
> hunyin -2.9759e-01  8.7180e-01 637 -0.3414  0.73295  
> cadcj   2.2366e-01  7.6467e-01 637  0.2925  0.77000  
> age 9.3626e-02  4.0390e-02 637  2.3180  0.02076 *
> age2   -1.3095e-03  5.5104e-04 637 -2.3763  0.01778 *
> sex 3.9188e-01  1.9759e-01 637  1.9833  0.04776 *
> dangyuan   -5.2558e-01  5.9091e-01 637 -0.8894  0.37410  
> Comp.1  5.2463e-02  1.0309e-01 637  0.5089  0.61100  
> Comp.2 -1.5048e-01  1.1435e-01 637 -1.3160  0.18863  
> trust.cz1  -8.0709e-01  4.4632e-01 637 -1.8083  0.07103 .
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
> There were 11 warnings (use warnings() to see them)
> 
>>warnings()
> 
> Warning messages:
> 1: optim or nlminb returned message false convergence (8) 
>  in: LMEopt(x = mer, value = cv) 
> 2: optim or nlminb returned message false convergence (8) 
>  in: LMEopt(x = mer, value = cv) 
> 3: optim or nlminb returned message false convergence (8) 
>  in: LMEopt(x = mer, value = cv) 
> 4: optim or nlminb returned message false convergence (8) 
>  in: LMEopt(x = mer, value = cv) 
> 5: optim or nlminb returned message false convergence (8) 
>  in: LMEopt(x = mer, value = cv) 
> 6: optim or nlminb returned message false convergence (8) 
>  in: LMEopt(x = mer, value = cv) 
> 7: optim or nlminb returned message false convergence (8) 
>  in: LMEopt(x = mer, value = cv) 
> 8: optim or nlminb returned message false convergence (8) 
>  in: LMEopt(x = mer, value = cv) 
> 9: optim or nlminb returned message singular convergence (7) 
>  in: LMEopt(x = mer, value = cv) 
> 10: optim or nlminb returned message singular convergence (7) 
>  in: LMEopt(x = mer, value = cv) 
> 11: optim or nlminb returned message singular convergence (7) 
>  in: LMEopt(x = mer, value = cv) 
> 
> 
>>version
> 
>  _  
> platform i386-pc-mingw32
> arch i386   
> os   mingw32
> system