date:20090507

Am Mittwoch, den 06.05.2009, 16:08 +0200 schrieb baptiste auguie:
 I think the pgfSweave project on R-forge is working on this (as far as  
 i know it currently relies on eps2pgf)
Right, but eps2pgf fails me on more complex / stacked plots. Otherwise,
I would be content using eps2pgf.

Lasse
 
 http://r-forge.r-project.org/R/?group_id=331
 
 HTH,
 
 
 Baptiste
 
 On 6 May 2009, at 15:37, Lasse Bombien wrote:
 
  Hi all,
  I saw a thread from 2007 about the possible implementation of a PGF
  (http://sourceforge.net/projects/pgf/) graphics device. Does anyone  
  know
  if something came of it?
  I would very much like if that was the case.
 
  Regards,
  Lasse
 
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  PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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 _
 
 Baptiste Auguié
 
 School of Physics
 University of Exeter
 Stocker Road,
 Exeter, Devon,
 EX4 4QL, UK
 
 Phone: +44 1392 264187
 
 http://newton.ex.ac.uk/research/emag
 __

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[R] I need your help about plsr

2009-05-07 Thread yongkook Kwon

Hi, I need your help, so I send letter to you.

I have a problem about plsr in pls package. I want to show how classfied or
related each ohter samples, so I tried to use plsr and biplot.

But, I failed. Because, I had to change data type of my sample.
Unfortunately, I didn't know how change data type.

I want you to help me about that.

please, help me.

I show you my sample data , my scripts and error message.

sample data
 asdf
  sp mw.1 mw.2 mw.3
1  a125
2  a236
3  b347
4  c458
5  c569

My script
p1=plsr(sp~ .,data=asdf,varidation='CV')

error message

Warning message:
In model.response(mf, numeric) :
  using type=numeric with a factor response will be ignored

I use korean version R. so I can show origin error message directly.

The error message mean that colMeans(Y) : 'x' is must numerical value.

[[alternative HTML version deleted]]

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Re: [R] I need your help about plsr

2009-05-07 Thread Andris Jankevics

Hi,
plsr funtion in pls package are intented for calculation of regression
models. You must define your Y matrix as bianary identification matrix
or You can just use plsda function from R's caret package.

http://caret.r-forge.r-project.org/Classification_and_Regression_Training.html

Best regards,

Andris

On Thu, May 7, 2009 at 11:34 AM, yongkook Kwon yongkookk...@gmail.com wrote:
 Hi, I need your help, so I send letter to you.

 I have a problem about plsr in pls package. I want to show how classfied or
 related each ohter samples, so I tried to use plsr and biplot.

 But, I failed. Because, I had to change data type of my sample.
 Unfortunately, I didn't know how change data type.

 I want you to help me about that.

 please, help me.

 I show you my sample data , my scripts and error message.

 sample data
 asdf
  sp mw.1 mw.2 mw.3
 1  a    1    2    5
 2  a    2    3    6
 3  b    3    4    7
 4  c    4    5    8
 5  c    5    6    9

 My script
 p1=plsr(sp~ .,data=asdf,varidation='CV')

 error message

 Warning message:
 In model.response(mf, numeric) :
  using type=numeric with a factor response will be ignored

 I use korean version R. so I can show origin error message directly.

 The error message mean that colMeans(Y) : 'x' is must numerical value.

        [[alternative HTML version deleted]]

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Re: [R] Bumps chart in R

2009-05-07 Thread Andreas Christoffersen

On Thu, May 7, 2009 at 2:15 AM, Mike Lawrence mike.lawre...@dal.ca wrote:
 (cross posting to the ggplot2 group for posterity)

 Here's how I'd approach it:

 library(ggplot2)
 text = letters[1:20]
 tal1 = rnorm (20,5,2)
 tal2 = rnorm (20,6,3)
 dif = tal2-tal1
 df0 = data.frame(text,tal1,tal2)
 df = melt(
        data = df0
        , id.vars = 'text'
        , variable_name = 'tal'
 )
 df$dif = dif
 df$col = ifelse(dif0,'red',ifelse(dif0,'blue','black'))
 df$size = abs(dif)

 # draw the plot

 Unfortunately it's not perfect:
 (1) col isn't being interpreted literally, so instead of truly red  blue.
 (2) the lines ends are square whereas usually they're rounded.
 (3) attempting to remove the legend via opts(legend.position=none)
 seems to fail.


Thank you

with your melted data I was able to come very close to what I want.
legen.posistion=none works for me... Annonying that colours don't
work like expected... It seams to be a frequent concern.

My code:
qplot(tal,value,data=df,group=text,geom=line,size=size,colour=col,xlab=Change
from time to time, ylab = Points)+
geom_text(aes(label=text),subset(df,tal==tal1),size=3,hjust=2,vjust=0)+
theme_bw()+ opts(legend.position=none)+ opts(title=As time went
by) +opts(plot.title=theme_text(vjust=0,size=20))

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Re: [R] Create Pie chart from .csv file

2009-05-07 Thread Richard . Cotton

 Ive found out a way around my problem. I was trying to plaot a histogram 
of
 strings, but I had to change it into integers. I ran an sql query on the
 original DB that I got the CSV file from and used COUNT to get the 
number of
 each unique item in a given column. I then used these numbers to create 
a
 histogram in R. It's a round about way of doing it, but it will have to
 suffice.

Glad you found a solution to your problem.  For future reference, an 
easier way to convert strings to numbers is to use as.numeric or 
as.integer.

as.numeric(1.23)  # 1.23
as.integer(4) # 4

If the process of reading in your data from the CSV file converts the 
strings to factors, then see the FAQ on R (
http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-do-I-convert-factors-to-numeric_003f).

Regards,
Richie.

Mathematical Sciences Unit
HSL



ATTENTION:

This message contains privileged and confidential inform...{{dropped:20}}

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Re: [R] When was the package relaimpo first introduced in R?

2009-05-07 Thread Uwe Ligges




Dimitri Liakhovitski wrote:

Hello!
I am wondering when the package relaimpo was first introduced in R?
Or maybe there is a way to look it up? I am not seeing it in the help file.





The first archived version in
your_CRAN_Mirror/src/contrib/Archive/relaimpo/
is dated 01-Dec-2005, obviously.

Uwe Ligges

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Re: [R] Bumps chart in R

2009-05-07 Thread ONKELINX, Thierry

Dear Andreas and Mike,

You need to use scale_colour_manual() if you want to set the colours yourself. 
Ggplot2 interpretes the col variable in the dataset as an ordinairy factor. 

library(ggplot2)
df0 - data.frame(text = letters[1:21], tal1 = c(rnorm (20,5,2), 5), tal2 = 
c(rnorm (20,6,3), 5))
df0$dif - df0$tal2 - df0$tal1
df - melt(data = df0, id.vars = c('text', 'dif'), variable_name = 'tal')
df$Change - factor(ifelse(df$dif0,'Up',ifelse(df$dif0,'Down','Stable')), 
levels = c(Up, Stable, Down))
df$size - abs(df$dif)
ggplot(df, aes(x = tal, y = value, label = text, group = text, size = size, col 
= Change)) + geom_line() + geom_text(data = subset(df, tal==tal1), size=3, 
hjust=2, vjust=0) + scale_x_discrete(Change from time to time) + 
scale_y_continuous(Points) + theme_bw()+ opts(legend.position=none)+ 
opts(title=As time went by\n) +opts(plot.title=theme_text(vjust=0,size=20)) + 
scale_colour_manual(values = c(red, black, blue))

HTH,

Thierry


ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and 
Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology 
and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
thierry.onkel...@inbo.be 
www.inbo.be 

To call in the statistician after the experiment is done may be no more than 
asking him to perform a post-mortem examination: he may be able to say what the 
experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure 
that a reasonable answer can be extracted from a given body of data.
~ John Tukey

-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens 
Andreas Christoffersen
Verzonden: donderdag 7 mei 2009 12:22
Aan: Mike Lawrence; r-help@r-project.org; ggpl...@googlegroups.com
Onderwerp: Re: [R] Bumps chart in R

On Thu, May 7, 2009 at 2:15 AM, Mike Lawrence mike.lawre...@dal.ca wrote:
 (cross posting to the ggplot2 group for posterity)

 Here's how I'd approach it:

 library(ggplot2)
 text = letters[1:20]
 tal1 = rnorm (20,5,2)
 tal2 = rnorm (20,6,3)
 dif = tal2-tal1
 df0 = data.frame(text,tal1,tal2)
 df = melt(
        data = df0
        , id.vars = 'text'
        , variable_name = 'tal'
 )
 df$dif = dif
 df$col = ifelse(dif0,'red',ifelse(dif0,'blue','black'))
 df$size = abs(dif)

 # draw the plot

 Unfortunately it's not perfect:
 (1) col isn't being interpreted literally, so instead of truly red  blue.
 (2) the lines ends are square whereas usually they're rounded.
 (3) attempting to remove the legend via opts(legend.position=none)
 seems to fail.


Thank you

with your melted data I was able to come very close to what I want.
legen.posistion=none works for me... Annonying that colours don't
work like expected... It seams to be a frequent concern.

My code:
qplot(tal,value,data=df,group=text,geom=line,size=size,colour=col,xlab=Change
from time to time, ylab = Points)+
geom_text(aes(label=text),subset(df,tal==tal1),size=3,hjust=2,vjust=0)+
theme_bw()+ opts(legend.position=none)+ opts(title=As time went
by) +opts(plot.title=theme_text(vjust=0,size=20))

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Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer 
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in  this message 
and any annex are purely those of the writer and may not be regarded as stating 
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Re: [R] Matching multiple columns in a data frame

2009-05-07 Thread jim holtman

?merge

 merge(A,B)
  C1  C2
1  A 200


On Thu, May 7, 2009 at 2:19 AM, Raghavan, Nandini [PRDUS] 
nragh...@its.jnj.com wrote:

 Hello,



 I am trying to extract a subset of a dataframe A (2 columns) by
 extracting all entries in A (several repeated entries) that match
 dataframe B in both columns.  For example, part of A and B are shown
 below.

 The following does not seem to work correctly. This only seems to select
 on the first component and all instances of the second.

 ind - A$C1 %in% B[,1]  A$C2 %in% B[,2]

 Any suggestions as to how to do this in general (even for matches in
 multiple columns) would be appreciated.



 Regards,

 Nandini





 A:

   C1   C2

 1   F 1500

 2   P  120

 4   F  250

 5   I  200

 6   D 2010

 7   F 1000

 8   V0

 9   F 2100

 10  F  500

 11  E 1800

 12  A  500

 13  V0

 14  I  125

 15  I   30

 16  M  300

 17  D   75

 18  V  500

 19  A  200

 20  M 1000

 21  P  225



 B:

  C1   C2

 1   A  200

 2   A  600

 3   A 1500

 4   B  100

 5   B 1000

 6   C 5000

 7   C  225

 8   C  150

 9   C  150

 10  C  200














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-- 
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Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

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[R] error using lapply with oneway_test (coin package)

2009-05-07 Thread Matthieu Dubois

Dear expeRts,

I would like to use a oneway_test (from package coin) to test whether  
two groups differ on various variables. The variables are encoded  
within a data frame. Unfortunately, I obtained an error, that I don't  
understand. Could you please help me ?

Example:
library(coin)
y - as.data.frame(matrix(rnorm(200), ncol=2))
group - as.factor(unif(100))

lapply(y, function(var) oneway_test(var ~ group))

Error message is:
(in French, my locale) Erreur dans eval(expr, envir, enclos) : objet  
'var' introuvable
(my personal translation in English) Error in eval(expr, envir,  
enclos) : object 'var' not found

Thank you,

Matthieu

Matthieu Dubois
Post-doctoral fellow

Psychology and NeuroCognition Lab (CNRS UMR 5105)
Université Pierre Mendès-France
BP47 --- 38040 Grenoble Cedex 9 --- France

Email: matthieu.dub...@upmf-grenoble.fr
Gmail: matth...@gmail.com
http://web.upmf-grenoble.fr/LPNC/membre_matthieu_dubois





[[alternative HTML version deleted]]

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[R] Show name of dataset in graph

2009-05-07 Thread O. Günther

Hi,

Ive written a script to run several multivariate statistical analysis
automatically.
As one result a biplot and screeplot is produced.
Now Id like to display the name of the inputdatset as part of the title of
these graphics and I do not want to enter it each time I run the script.
How can I extract the name of a dataset?
An (shortened) extraction from the script:

Test1 - function(pri, sec, Pca, Ca, Dca){
#pri  - primary Parameters (biological Dataset (abundances))
#sec  secondary Parameters 
#Pca, Ca, Dca  Default=F, If set to TRUE these Methods are active
several mathematical Operations
biplot(pri, pc.biplot=T, main=paste(PCA - , ???).

Instead of the ??? I d like to have a variable.
For example if 
Test1(dataset.typ5, sec.typ5, Pca=TRUE)
then the title of the plots should be 
PCA  dataset.typ5

Does anyone know a way?

Regards,
oli

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[R] Generating plots with two lines, each line plotted with a different color

2009-05-07 Thread John Sorkin

R 2.9.0
windows xp

I would like to have the two lines generated by my plot have different colors, 
in addition to the two different line types specified by the plot command 
below. I would appreciate advice on how I can specify line colors.

plot(survfit(Surv(Age,Died) ~ Rx, data = GVHDdata),lty=c(1,2),lwd=2)

Thanks,
John

John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC,
University of Maryland School of Medicine Claude D. Pepper OAIC,
University of Maryland Clinical Nutrition Research Unit, and
Baltimore VA Center Stroke of Excellence

University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524

(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
jsor...@grecc.umaryland.edu
Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}

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Re: [R] Generating plots with two lines, each line plotted with a different color

2009-05-07 Thread Zeljko Vrba

On Thu, May 07, 2009 at 08:00:59AM -0400, John Sorkin wrote:
 I would like to have the two lines generated by my plot have different 
 colors, in addition to the two different line types specified by the plot 
 command below. I would appreciate advice on how I can specify line colors.
 
 plot(survfit(Surv(Age,Died) ~ Rx, data = GVHDdata),lty=c(1,2),lwd=2)
 

Try adding col=c(red,blue) as additional parameter.

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Re: [R] error using lapply with oneway_test (coin package)


On 07/05/2009 6:11 AM, Matthieu Dubois wrote:

Dear expeRts,

I would like to use a oneway_test (from package coin) to test whether  
two groups differ on various variables. The variables are encoded  
within a data frame. Unfortunately, I obtained an error, that I don't  
understand. Could you please help me ?


Example:
library(coin)
y - as.data.frame(matrix(rnorm(200), ncol=2))
group - as.factor(unif(100))

lapply(y, function(var) oneway_test(var ~ group))

Error message is:
(in French, my locale) Erreur dans eval(expr, envir, enclos) : objet  
'var' introuvable
(my personal translation in English) Error in eval(expr, envir,  
enclos) : object 'var' not found


That's a scoping problem, I think a bug in oneway_test.  Because the 
formula var ~ group is created with the anonymous function within 
lapply, its environment should be the evaluation frame of that function 
call and var should be visible.  If I replace oneway_test() with lm() it 
works.


I think a workaround is to construct the data argument explicitly, i.e.

lapply(y, function(var) oneway_test(var ~ group, data.frame(var=var, 
group=group)))


I've cc'd Torsten Hothorn, the maintainer of coin.

Duncan Murdoch



Thank you,

Matthieu

Matthieu Dubois
Post-doctoral fellow

Psychology and NeuroCognition Lab (CNRS UMR 5105)
Université Pierre Mendès-France
BP47 --- 38040 Grenoble Cedex 9 --- France

Email: matthieu.dub...@upmf-grenoble.fr
Gmail: matth...@gmail.com
http://web.upmf-grenoble.fr/LPNC/membre_matthieu_dubois





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Re: [R] convert large integers to hex

2009-05-07 Thread Gabor Grothendieck

There is an interface between R and bc -- not on CRAN but available
from its home page here:
http://r-bc.googlecode.com

 source(http://r-bc.googlecode.com/svn/trunk/R/bc.R;)
 bc(obase = 16; 123456789123456789, retclass = character)
[1] 1B69B4BACD05F15


On Wed, May 6, 2009 at 9:59 PM, jim holtman jholt...@gmail.com wrote:
 You can use the 'bc' command (use Cygwin if on Windows);

 /cygdrive/c: bc
 bc 1.06
 Copyright 1991-1994, 1997, 1998, 2000 Free Software Foundation, Inc.
 This is free software with ABSOLUTELY NO WARRANTY.
 For details type `warranty'.
 x=6595137340052185552
 obase=16
 x
 5B86A277DEB9A1D0

 You can call this from R.

 On Wed, May 6, 2009 at 3:26 PM, Sundar Dorai-Raj sdorai...@gmail.comwrote:

 Hi,

 I'm wondering if someone has solved the problem of converting very
 large integers to hex. I know about format.hexmode and as.hexmode, but
 these rely on integers. The numbers I'm working with are overflowing
 and losing precision. Here's an example:

 x - 6595137340052185552 # stored as character
 as.integer(x) # warning about inaccurate conversion
 format.hexmode(as.numeric(x)) # warnings about loss of precision
 as.hexmode(x) # more warnings and does not do what I expected

 I'm planning on writing a function that will do this, but would like
 to know if anybody already has a solution. Basically, I would like the
 functionality of format.hexmode on arbitrarily large integers.

 Thanks,

 --sundar

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 R-help@r-project.org mailing list
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 --
 Jim Holtman
 Cincinnati, OH
 +1 513 646 9390

 What is the problem that you are trying to solve?

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Re: [R] Show name of dataset in graph

2009-05-07 Thread Richard . Cotton

 I?ve written a script to run several multivariate statistical analysis
 automatically.
 As one result a biplot and screeplot is produced.
 Now I?d like to display the name of the inputdatset as part of the title 
of
 these graphics and I do not want to enter it each time I run the script.
 How can I extract the name of a dataset?
 An (shortened) extraction from the script:
 
 Test1 - function(pri, sec, Pca, Ca, Dca){
 #pri  - primary Parameters (biological Dataset (abundances))
 #sec ? secondary Parameters 
 #Pca, Ca, Dca ? Default=F, If set to TRUE these Methods are active
 ?several mathematical Operations?
 biplot(pri, pc.biplot=T, main=paste(?PCA - ?, ???)?.
 
 Instead of the ??? I? d like to have a variable.
 For example if 
 Test1(dataset.typ5, sec.typ5, Pca=TRUE)
 then the title of the plots should be 
 ?PCA ? dataset.typ5?

This demonstrates the basic idea:

dfr1 - data.frame(x=1:10, y=runif(10))
dfr2 - data.frame(x=11:20, y=runif(10))

library(lattice)
myplot - function(dfr)
{
   xyplot(y~x, 
   data=dfr, 
   main=as.character(substitute(dfr))) 
}

myplot(dfr1)
myplot(dfr2)

Regards,
Richie.

Mathematical Sciences Unit
HSL


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Re: [R] PGF Device

Lasse Bombien lasse at phonetik.uni-muenchen.de writes:

 
 Am Mittwoch, den 06.05.2009, 16:08 +0200 schrieb baptiste auguie:
  I think the pgfSweave project on R-forge is working on this (as far as  
  i know it currently relies on eps2pgf)
 Right, but eps2pgf fails me on more complex / stacked plots. Otherwise,
 I would be content using eps2pgf.

Same for me; pgf/tikz is my method of choice for graphics in latex 
because it gets around the eps-detour that can cause strange problems.

Dieter

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Re: [R] When was the package relaimpo first introduced in R?

2009-05-07 Thread Dimitri Liakhovitski

Thanks a lot, Uwe.
Do you think you could expain how one looks this type of information up?
What's obvious to some of us might not be obvious to others.
Dimitri, der, obviously, deutsch spricht.

2009/5/7 Uwe Ligges lig...@statistik.tu-dortmund.de:


 Dimitri Liakhovitski wrote:

 Hello!
 I am wondering when the package relaimpo was first introduced in R?
 Or maybe there is a way to look it up? I am not seeing it in the help
 file.




 The first archived version in
 your_CRAN_Mirror/src/contrib/Archive/relaimpo/
 is dated 01-Dec-2005, obviously.

 Uwe Ligges




-- 
Dimitri Liakhovitski
MarketTools, Inc.
dimitri.liakhovit...@markettools.com

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Re: [R] convert large integers to hex

2009-05-07 Thread Sundar Dorai-Raj

Thanks for both answers. In the end I decided to use Gabor's bc package.

Thanks,

--sundar

On Thu, May 7, 2009 at 5:10 AM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
 There is an interface between R and bc -- not on CRAN but available
 from its home page here:
 http://r-bc.googlecode.com

 source(http://r-bc.googlecode.com/svn/trunk/R/bc.R;)
 bc(obase = 16; 123456789123456789, retclass = character)
 [1] 1B69B4BACD05F15


 On Wed, May 6, 2009 at 9:59 PM, jim holtman jholt...@gmail.com wrote:
 You can use the 'bc' command (use Cygwin if on Windows);

 /cygdrive/c: bc
 bc 1.06
 Copyright 1991-1994, 1997, 1998, 2000 Free Software Foundation, Inc.
 This is free software with ABSOLUTELY NO WARRANTY.
 For details type `warranty'.
 x=6595137340052185552
 obase=16
 x
 5B86A277DEB9A1D0

 You can call this from R.

 On Wed, May 6, 2009 at 3:26 PM, Sundar Dorai-Raj sdorai...@gmail.comwrote:

 Hi,

 I'm wondering if someone has solved the problem of converting very
 large integers to hex. I know about format.hexmode and as.hexmode, but
 these rely on integers. The numbers I'm working with are overflowing
 and losing precision. Here's an example:

 x - 6595137340052185552 # stored as character
 as.integer(x) # warning about inaccurate conversion
 format.hexmode(as.numeric(x)) # warnings about loss of precision
 as.hexmode(x) # more warnings and does not do what I expected

 I'm planning on writing a function that will do this, but would like
 to know if anybody already has a solution. Basically, I would like the
 functionality of format.hexmode on arbitrarily large integers.

 Thanks,

 --sundar

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 --
 Jim Holtman
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 +1 513 646 9390

 What is the problem that you are trying to solve?

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Re: [R] When was the package relaimpo first introduced in R?

2009-05-07 Thread Uwe Ligges




Dimitri Liakhovitski wrote:

Thanks a lot, Uwe.
Do you think you could expain how one looks this type of information up?
What's obvious to some of us might not be obvious to others.
Dimitri, der, obviously, deutsch spricht.



Dimitri,

on CRAN there is a package page and the link to the archives, or, on the 
package's page, there is a link to the particular package's archive. 
There you will find all CRAN versions including the dates.


Beste Gruesse,
Uwe




2009/5/7 Uwe Ligges lig...@statistik.tu-dortmund.de:


Dimitri Liakhovitski wrote:

Hello!
I am wondering when the package relaimpo was first introduced in R?
Or maybe there is a way to look it up? I am not seeing it in the help
file.




The first archived version in
your_CRAN_Mirror/src/contrib/Archive/relaimpo/
is dated 01-Dec-2005, obviously.

Uwe Ligges







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Re: [R] PGF Device

2009-05-07 Thread baptiste auguie

If one was to implement a Tikz output for R graphics, I'm not sure  
what route to take:


1) focus exclusively on Grid graphics and implement a conversion at  
the R level à la gridSVG (see Paul Murrell's webpage)


2) create a new device ( I have no idea where to find guidelines for  
this, and I'm not even clear on what exactly a Device is).


In any case, given that pdf is often the preferred output for R  
graphics (e.g. through the Sweave route), it seems that the pgf format  
would be an excellent addition if only for its perfect handling of  
LaTeX formulas.


Best wishes,

baptiste





On 7 May 2009, at 14:39, Dieter Menne wrote:


Lasse Bombien lasse at phonetik.uni-muenchen.de writes:



Am Mittwoch, den 06.05.2009, 16:08 +0200 schrieb baptiste auguie:
I think the pgfSweave project on R-forge is working on this (as  
far as

i know it currently relies on eps2pgf)
Right, but eps2pgf fails me on more complex / stacked plots.  
Otherwise,

I would be content using eps2pgf.


Same for me; pgf/tikz is my method of choice for graphics in latex
because it gets around the eps-detour that can cause strange problems.

Dieter

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_

Baptiste Auguié

School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK

Phone: +44 1392 264187

http://newton.ex.ac.uk/research/emag

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[R] Bubble Plot Over a Map

2009-05-07 Thread Rodrigo Aluizio

Hi everybody,

Well here is another doubt! Im elaborating some maps, and I pretend to plot
over it the abundance of species. I could do that using points(), but Id
like to use bubble() from sp package.

When trying to use bubble() I face the fallowing issue: When I call the
bubble function it overwrite everything I previously plotted. It doesnt
happen with points (obviously), only with bubble(). I tried to specify
panel.smooth as panel function to bubble, I tried to use add=T as argument,
but it didnt accept such thing.

The only thing that I thought right now, so I still have to try, is saving
the bubble() as an object and try to manipulate its properties over my map.

I already searched the list posts but wasnt able to find a similar doubt
with its possible solutions.

 

Bellow is the map code using points, Im trying to substitute the points()
functions with one bubble() function.

 

for (i in 1:length(colnames(Spp10ml))) {

png(paste(colnames(Spp10ml),'.png',sep='')[i],width=5.2,height=3.6,pointsize
=5,units='in',bg=NA,restoreConsole=T,res=1200)

par(mar=c(5,0,0,0))

map('worldHires','brazil',ylim=c(-5.15,-4.55),xlim=c(-37,-36.1),type='n')

rect(-37.1,-5.25,-36,-4.9,density=NULL,angle=45,col='#dbf4ff',border=F)

plot(Batimetria,ylab='',xlab='',border=F,col=Cor$Cor,add=T)

plot(Municipios,ylab='',xlab='',col=rgb(245,232,140,max=255,alpha=255),add=T
,lwd=0.2)

axis(1,xaxp=c(-37,-36.1,5),cex.axis=1.5)

axis(2,yaxp=c(-5.15,-4.55,5),cex.axis=1.5)

text(Prof$Long,Prof$Lat,rownames(Prof),col='black',cex=1.2,srt=-24,family='A
R',font=2)

text(c(-36.96,-36.96,-36.865,-36.54,-36.37,-36.2),c(-4.96,-5.05,-5.11,-5.14,
-5.14,-5.14),c('Areia

Branca','Serra

do Mel','Porto do
Mangue','Macau','Guamaré','Galinhos'),col='Black',cex=1.3,font=2)

rect(-36.20,-4.56,-36.155,-4.565,density=NULL,angle=45,col='black',border='b
lack',lwd=0.1)

rect(-36.155,-4.56,-36.111,-4.565,density=NULL,angle=45,col='white',border='
black',lwd=0.1)

shadowtext(c(-36.20,-36.155,-36.111,-36.215),c(-4.573,-4.573,-4.573,-4.562),
c('0','5','10','km'),col='white',cex=1)

Norte(-36.155,-4.60,0.02)

box(which='plot',lty='solid')

points(Pontos$long[Spp10ml[,i]0  Spp10ml[,i]=50],Pontos$lat[Spp10ml[,i]0
 Spp10ml[,i]=50],pch=21,bg=rgb(70,70,70,max=255,alpha=255),col=
'black',cex=1.5)

points(Pontos$long[Spp10ml[,i]=51 
Spp10ml[,i]=200],Pontos$lat[Spp10ml[,i]=51 
Spp10ml[,i]=200],pch=23,bg='yellow',col='black',cex=1.5)

points(Pontos$long[Spp10ml[,i]=201 
Spp10ml[,i]=400],Pontos$lat[Spp10ml[,i]=201 
Spp10ml[,i]=400],pch=22,bg='orange',col='black',cex=1.5)

points(Pontos$long[Spp10ml[,i]=401],Pontos$lat[Spp10ml[,i]=401],pch=24,bg=
'red',col='black',cex=1.5)

dev.off()}

 

Thanks in advance.

 

-

MSc.  mailto:r.alui...@gmail.com Rodrigo Aluizio

Centro de Estudos do Mar/UFPR
Laboratório de Micropaleontologia
Avenida Beira Mar s/n - CEP 83255-000
Pontal do Paraná - PR - Brasil




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Re: [R] When was the package relaimpo first introduced in R?

2009-05-07 Thread Dimitri Liakhovitski

Vielen Dank, Uwe!
Dimitri

2009/5/7 Uwe Ligges lig...@statistik.tu-dortmund.de:


 Dimitri Liakhovitski wrote:

 Thanks a lot, Uwe.
 Do you think you could expain how one looks this type of information up?
 What's obvious to some of us might not be obvious to others.
 Dimitri, der, obviously, deutsch spricht.


 Dimitri,

 on CRAN there is a package page and the link to the archives, or, on the
 package's page, there is a link to the particular package's archive. There
 you will find all CRAN versions including the dates.

 Beste Gruesse,
 Uwe



 2009/5/7 Uwe Ligges lig...@statistik.tu-dortmund.de:

 Dimitri Liakhovitski wrote:

 Hello!
 I am wondering when the package relaimpo was first introduced in R?
 Or maybe there is a way to look it up? I am not seeing it in the help
 file.



 The first archived version in
 your_CRAN_Mirror/src/contrib/Archive/relaimpo/
 is dated 01-Dec-2005, obviously.

 Uwe Ligges








-- 
Dimitri Liakhovitski
MarketTools, Inc.
dimitri.liakhovit...@markettools.com

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[R] RSPerl and Statistics::R

2009-05-07 Thread Daniel Klein

Greetings!
 
Being a Perl hacker for some time, and wanting to leverage what R provides, 
I've been trying to work with Statistics::R and RSPerl.
 
The former has a race condition that breeds some unreliability and the latter 
seems to have issues all around, and neither has been updated in some time.
 
Are these projects are abandoned, or is there some effort currently being 
undertaken to either refresh or reinvent the glue binding Perl and R together?
 
If not, then I'm probably going to give it a go myself, but I'm sort of hoping 
that there's a jewel of a library out there that doesn't come up as quickly in 
Google as the aforementioned libraries.
 
 
Thanks,
 
Daniel M. Klein
 


This email (including attachments and files, if any) is confidential, may be 
privileged and is intended for the above-named recipient(s) only. If you have 
received this message in error, please notify me by return email and delete 
this message from your system. Any unauthorized use or disclosure of this 
message is strictly prohibited. Copyright in this email and any document 
created by Genesis Genomics will be and remain vested in us and will not be 
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[R] extending strsplit to handle missing text that doesn't have the target on which to split

2009-05-07 Thread Chris Evans

I am sure there is an obvious answer to this that I'm missing but I
can't find it.  I'm parsing headers of Emails and most have a date like
this:
   Wed, 16 Nov 2005 05:28:00 -0800
and I can parse that using:

tmp.dat.data - matrix(unlist(strsplit(headers$Date.line,,)),
ncol = 2, byrow = TRUE)
before going on to look at the day and date/time data.

However, a very few headers I want to parse are missing the initial day
of the week and look like this:
   15 Nov 2005 09:10:00 +0100

That means that my use of strsplit() results in that date/time part
being all of the item in the list for those entries so the effect of
matrix(unlist()) is to pull the next list entry up in the matrix.
Because I happened to have only two errant entries I didn't see what was
happening for a moment. (An odd number gives a warning message about
dimensions not fitting but an odd number has silently moved things
up/left so doesn't: no quarrel with that from me, my stupidity that I
was slow to see what was happening!)

I'm sure I should be able to find a simple way to get around this but at
the moment I can't.

Here's a simple, reproducible example:

dat - c(Tue, 15 Nov 2005 09:44:50 EST,
 15 Nov 2005 09:10:00 +0100,
 Tue, 15 Nov 2005 09:44:50 EST,
 Tue, 15 Nov 2005 16:29:57 +,
 Wed, 16 Nov 2005 07:00:45 EST,
 Wed, 16 Nov 2005 05:28:00 -0800,
 Wed, 16 Nov 2005 14:06:21 +,
 15 Nov 2005 09:10:00 +0100)
tmp.dat.data - matrix(unlist(strsplit(dat,,)),ncol = 2, byrow = TRUE)


tmp.dat.data comes out as a 7x2 matrix contents:

 [,1]  [,2]
[1,] Tue  15 Nov 2005 09:44:50 EST
[2,] 15 Nov 2005 09:10:00 +0100  Tue
[3,]  15 Nov 2005 09:44:50 EST   Tue
[4,]  15 Nov 2005 16:29:57 + Wed
[5,]  16 Nov 2005 07:00:45 EST   Wed
[6,]  16 Nov 2005 05:28:00 -0800 Wed
[7,]  16 Nov 2005 14:06:21 + 15 Nov 2005 09:10:00 +0100

I'd like an 8x2 matrix with tmp.dat.data[2,1] ==  and
tmp.dat.data[8,1] == 

I'm sure there must be a simple way to achieve this by rolling a
slightly different variant of strsplit that pads things and then
applying that to the input vector but I'm failing to see how to do this
at the moment.

TIA,

Chris

--
Applied researcher, neither statistician nor programmer!

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[R] How to call time series functions from C ?

2009-05-07 Thread goon83

Hi everyone,
  I meet the problem to call R from C. 
 
  Can someone tell me is it possible to call time series functions(such as ar 
and arima)from  C program on linux platform, and then compile the C program to 
a standalone executable file?

  I know we can call some function defined in Rmath.h , but I have not found 
the entry point for time series function. 
 
  I would very much appreciate receiving your response ! ^_^


bin, dong
goo...@126.com
Buaa, Beijing PR China

  

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Re: [R] Show name of dataset in graph

2009-05-07 Thread S Ellison

The usual way of doing this in R functions is via deparse, as in the
examples in ?deparse:

fd-function(x) plot(x, main=deparse(substitute(x)))
q-1:10
fd(q)

as.character works for simple cases but is probably not the best
option. Compare 

fd(log(q)) 

with

fc-function(x) plot(x, main=as.character(substitute(x)))
fc(log(q))

In the case of an expression, substitute returns a 'call' object, and
applying as.character to that returns the individual elements of the
call (log and q in this case) and that is plotted as a multi-line
string. deparse() returns a the character string log(q) which is what
you normally want.

Steve E


 richard.cot...@hsl.gov.uk 07/05/2009 13:26:46 
 I?ve written a script to run several multivariate statistical
analysis
 automatically.
 As one result a biplot and screeplot is produced.
 Now I?d like to display the name of the inputdatset as part of the
title 
of
 these graphics and I do not want to enter it each time I run the
script.
 How can I extract the name of a dataset?
 An (shortened) extraction from the script:
 
 Test1 - function(pri, sec, Pca, Ca, Dca){
 #pri  - primary Parameters (biological Dataset (abundances))
 #sec ? secondary Parameters 
 #Pca, Ca, Dca ? Default=F, If set to TRUE these Methods are active
 ?several mathematical Operations?
 biplot(pri, pc.biplot=T, main=paste(?PCA - ?, ???)?.
 
 Instead of the ??? I? d like to have a variable.
 For example if 
 Test1(dataset.typ5, sec.typ5, Pca=TRUE)
 then the title of the plots should be 
 ?PCA ? dataset.typ5?

This demonstrates the basic idea:

dfr1 - data.frame(x=1:10, y=runif(10))
dfr2 - data.frame(x=11:20, y=runif(10))

library(lattice)
myplot - function(dfr)
{
   xyplot(y~x, 
   data=dfr, 
   main=as.character(substitute(dfr))) 
}

myplot(dfr1)
myplot(dfr2)

Regards,
Richie.

Mathematical Sciences Unit
HSL


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[R] Step and stepAIC

2009-05-07 Thread Peter-Heinz Fox

Hi all,
Â 
Iâm using step and stepAIC for stepwise regression. After each step, I 
would like to make an additional calculation based on the independent variables 
that have been selected until this step and their corresponding weights. Where 
do I have to add this calculation?
Â 
And a second question: Is it possible, to define a certain limit of factors for 
the regression, e.g. 20 variables are available but I want step to stop after 
the 10th factor has been selected?!
Â 
Thanks in advance
Â 
Peter-Heinz 


  
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Re: [R] Print to File Formatting

2009-05-07 Thread Luc Villandre



Brigid Mooney wrote:

Hello,

I am writing out to a file and have two quick questions that I can't
seem to track down the correct answers for.  Luckily, I *think* they
are both simple enough that someone might be able to point me in the
right direction on them without too much trouble.

Both questions relate to the process below where CompleteFrame is a
data frame containing what I want printed to a file.

filename - C:\\MyDocuments\\TestOut_050609.txt

output -file(filename, open=wt)
write.csv(CompleteFrame, output, row.names = FALSE, col.names=FALSE)
close(output)

Question #1:
Every time I run this process, I get the warning:
Warning message:
In write.csv(CompleteFrame, output, row.names = FALSE, col.names = FALSE) :
  attempt to set 'col.names' ignored

And it still prints the column names as the first row in my file,
which I do not want...

Question #2:
This process puts quotes around all data of class = character.
I can't have these quotes in my file - is it possible to get R to omit
them even if my data frame contains character strings?


Any help or hints on this are greatly appreciated!

Thanks,
Brigid

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Hi Brigid,

Re. Question 1: This is simply due to a convention about csv files. In 
order to ensure conformity of the output file, write.csv() doesn't allow 
users to change col.names.


Re. Question 2: The quote argument is what you should be modifying.

If you really want no column names, use write.table() instead (with 
sep=, and a filename with a .csv extension). After all, write.csv() is 
merely a wrapper for write.table().


Cheers,

--
*Luc Villandré*
/Biostatistician
McGill University Health Center -
Montreal Children's Hospital Research Institute/

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Re: [R] How to call time series functions from C ?


On 5/7/2009 9:24 AM, goon83 wrote:

Hi everyone,
  I meet the problem to call R from C. 
 
  Can someone tell me is it possible to call time series functions(such as ar and arima)from  C program on linux platform, and then compile the C program to a standalone executable file?


  I know we can call some function defined in Rmath.h , but I have not found the entry point for time series function. 


There are none, but you can write a front end for R, and it can evaluate 
R expressions, etc.  The procedure is described in the Writing R 
Extensions manual.


Remember that if you distribute the program you do need to follow the 
GPL, and distribute all of R as well as all of your own program in 
source code form.


Duncan Murdoch

 
  I would very much appreciate receiving your response ! ^_^



bin, dong
goo...@126.com
Buaa, Beijing PR China

  


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[R] Plotting counts vs. intervals for a shingle

2009-05-07 Thread Walcerz, Douglas (APG)

Hello!

Suppose I have a set of values:

a - c(1:10, 5:10)

Suppose I also have a set of intervals:

b - cbind(c(0,2.5,4.5,6.5), c(5.5,7.5,9.5,11))

I can create a shingle that counts how many values are in each interval:

c - shingle(a, b)

I can display the shingle to see the counts:

summary(c, showValues=FALSE)

The display looks like this:

Intervals:
  min  max count
1 0.0  5.5 6
2 2.5  7.5 8
3 4.5  9.510
4 6.5 11.0 8

Overlap between adjacent intervals:
[1] 4 6 6

I would like to plot the count vs. the Intervals

I can create a vector representing the intervals:

labels - as.character(levels(c))

But I can't seem to create a vector of counts, which would permit me to plot 
counts vs. intervals.

Thanks for any insights you can provide.

p.s.  My real data contains 25,094 values and 5,809 intervals.  Many of the 
intervals will not contain any of the values.

-Douglas

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Re: [R] data transformation using gamma

2009-05-07 Thread Patrizio Frederic

Roslina,
this code performs what you need:

dt  = matrix((1:(58*12))/58/12,58) # some numbers
# if dt is a data.frame use dt = as.matrix(dt)
a   = (1:12)/12 # some a coef
b   = (12:1)/12 # some b coef
dtgam   = matrix(pgamma(dt,a,b),58)
# dtgam is the transformation you're looking for

no loop needed no transform function involved
cheers,

Patrizio


2009/5/7 Roslina Zakaria zrosl...@yahoo.com:
 Hi R-users,

 I have this code to uniformise the data using gamma:

 length(dp1)
 [1] 696
 dim(dp1)
 [1] 58 12
 dim(ahall)
 [1]  1 12
 dim(bhall)
 [1]  1 12

 trans_dt - function(dt,a,b)
 + { n1 - ncol(dt)
 +   n2 - length(dt)
 +   trans  - vector(mode='numeric', length=n2)
 +   dim(trans) - dim(dt)
 +   for (i in 1:n1)
 +   {  dt[,i] - as.vector(dt[,i])
 +  trans[,i] - transform(dti,newdt=pgamma(dti,shape= 
 a[1,i],scale=b[1,i])) }
 +   trans
 + }

 trans_dt(dp1,ahall,bhall)
 Error in transform(dti, newdt = pgamma(dti, shape = a[1, i], scale = b[1,  :
   object dti not found

 and also try
 trans_dt - function(dt,a,b)
 { n1 - ncol(dt)
   n2 - length(dt)
   trans  - vector(mode='numeric', length=n2)
   dim(trans) - dim(dt)
   for (i in 1:n1)
   {  dti - dt[,i]
  ai  - a[1,i]
  bi  - b[1,i]
  trans[,i] - transform(dti,newdt=pgamma(dti,shape= ai,scale=bi)) }
   trans
 }

 trans_dt(dp1,ahall,bhall)
 Error in pgamma(dti, shape = ai, scale = bi) : object dti not found


 Thank you for any help given.



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-- 
+-
| Patrizio Frederic, PhD
| Assistant Professor,
| Department of Economics,
| University of Modena and Reggio Emilia,
| Via Berengario 51,
| 41100 Modena, Italy
|
| tel:  +39 059 205 6727
| fax:  +39 059 205 6947
| mail: patrizio.frede...@unimore.it
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Re: [R] Generating plots with two lines, each line plotted with a different color

2009-05-07 Thread Thomas Lumley


On Thu, 7 May 2009, John Sorkin wrote:


R 2.9.0
windows xp

I would like to have the two lines generated by my plot have different colors, 
in addition to the two different line types specified by the plot command 
below. I would appreciate advice on how I can specify line colors.

plot(survfit(Surv(Age,Died) ~ Rx, data = GVHDdata),lty=c(1,2),lwd=2)



 ,col=c(tomato,goldenrod)

-thomas

Thomas Lumley   Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle

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Re: [R] Step and stepAIC

Peter-Heinz Fox peterheinzfox at yahoo.de writes:

 Iâm using step and stepAIC for stepwise regression. After each step, 
 I would like to make an additional calculation based on the independent
 variables that have been selected until this step and
 their corresponding weights. Where do I have to add this calculation?

dropTerm is the toolbox function stepAIC uses; you could use it to build 
your own stepAIC version.

But also make sure you have read

http://markmail.org/thread/gk7ysg6tclz4vtdi

and consider some lasso variant method instead (this partly 
answers your second question).

Dieter

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Re: [R] error using lapply with oneway_test (coin package)

2009-05-07 Thread Torsten Hothorn



That's a scoping problem, I think a bug in oneway_test.  Because the formula 
var ~ group is created with the anonymous function within lapply, its 
environment should be the evaluation frame of that function call and var 
should be visible.  If I replace oneway_test() with lm() it works.


I think a workaround is to construct the data argument explicitly, i.e.

lapply(y, function(var) oneway_test(var ~ group, data.frame(var=var, 
group=group)))




yes, that would be the fix:

R lapply(y, function(var) oneway_test(var ~ group,
  data = data.frame(var = var, group = group)))
$V1

Asymptotic 2-Sample Permutation Test

data:  var by group (1, 2)
Z = -1.2054, p-value = 0.2280
alternative hypothesis: true mu is not equal to 0


$V2

Asymptotic 2-Sample Permutation Test

data:  var by group (1, 2)
Z = 0.5672, p-value = 0.5706
alternative hypothesis: true mu is not equal to 0

Thanks, Duncan.

Torsten



I've cc'd Torsten Hothorn, the maintainer of coin.

Duncan Murdoch



Thank you,

Matthieu

Matthieu Dubois
Post-doctoral fellow

Psychology and NeuroCognition Lab (CNRS UMR 5105)
Université Pierre Mendès-France
BP47 --- 38040 Grenoble Cedex 9 --- France

Email: matthieu.dub...@upmf-grenoble.fr
Gmail: matth...@gmail.com
http://web.upmf-grenoble.fr/LPNC/membre_matthieu_dubois





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Re: [R] Bubble Plot Over a Map

2009-05-07 Thread Olivier ETERRADOSSI


Hi Rodrigo,
did you consider having a look at package ggplot2 (thanks to Hadley
Wickham).
I guess you'll find something very close to your need (functions ggplot,
geom_point,...)
Hope this helps. regards. Olivier


Rodrigo Aluizio wrote:
 
 Hi everybody,
 
 Well here is another doubt! Im elaborating some maps, and I pretend to
 plot
 over it the abundance of species. I could do that using points(), but Id
 like to use bubble() from sp package.
 
 When trying to use bubble() I face the fallowing issue: When I call the
 bubble function it overwrite everything I previously plotted. It doesnt
 happen with points (obviously), only with bubble(). I tried to specify
 panel.smooth as panel function to bubble, I tried to use add=T as
 argument,
 but it didnt accept such thing.
 
 The only thing that I thought right now, so I still have to try, is saving
 the bubble() as an object and try to manipulate its properties over my
 map.
 
 I already searched the list posts but wasnt able to find a similar doubt
 with its possible solutions.
 
  
 
 Bellow is the map code using points, Im trying to substitute the points()
 functions with one bubble() function.
 
  
 
 for (i in 1:length(colnames(Spp10ml))) {
 
 png(paste(colnames(Spp10ml),'.png',sep='')[i],width=5.2,height=3.6,pointsize
 =5,units='in',bg=NA,restoreConsole=T,res=1200)
 
 par(mar=c(5,0,0,0))
 
 map('worldHires','brazil',ylim=c(-5.15,-4.55),xlim=c(-37,-36.1),type='n')
 
 rect(-37.1,-5.25,-36,-4.9,density=NULL,angle=45,col='#dbf4ff',border=F)
 
 plot(Batimetria,ylab='',xlab='',border=F,col=Cor$Cor,add=T)
 
 plot(Municipios,ylab='',xlab='',col=rgb(245,232,140,max=255,alpha=255),add=T
 ,lwd=0.2)
 
 axis(1,xaxp=c(-37,-36.1,5),cex.axis=1.5)
 
 axis(2,yaxp=c(-5.15,-4.55,5),cex.axis=1.5)
 
 text(Prof$Long,Prof$Lat,rownames(Prof),col='black',cex=1.2,srt=-24,family='A
 R',font=2)
 
 text(c(-36.96,-36.96,-36.865,-36.54,-36.37,-36.2),c(-4.96,-5.05,-5.11,-5.14,
 -5.14,-5.14),c('Areia
 
 Branca','Serra
 
 do Mel','Porto do
 Mangue','Macau','Guamaré','Galinhos'),col='Black',cex=1.3,font=2)
 
 rect(-36.20,-4.56,-36.155,-4.565,density=NULL,angle=45,col='black',border='b
 lack',lwd=0.1)
 
 rect(-36.155,-4.56,-36.111,-4.565,density=NULL,angle=45,col='white',border='
 black',lwd=0.1)
 
 shadowtext(c(-36.20,-36.155,-36.111,-36.215),c(-4.573,-4.573,-4.573,-4.562),
 c('0','5','10','km'),col='white',cex=1)
 
 Norte(-36.155,-4.60,0.02)
 
 box(which='plot',lty='solid')
 
 points(Pontos$long[Spp10ml[,i]0 
 Spp10ml[,i]=50],Pontos$lat[Spp10ml[,i]0
  Spp10ml[,i]=50],pch=21,bg=rgb(70,70,70,max=255,alpha=255),col=
 'black',cex=1.5)
 
 points(Pontos$long[Spp10ml[,i]=51 
 Spp10ml[,i]=200],Pontos$lat[Spp10ml[,i]=51 
 Spp10ml[,i]=200],pch=23,bg='yellow',col='black',cex=1.5)
 
 points(Pontos$long[Spp10ml[,i]=201 
 Spp10ml[,i]=400],Pontos$lat[Spp10ml[,i]=201 
 Spp10ml[,i]=400],pch=22,bg='orange',col='black',cex=1.5)
 
 points(Pontos$long[Spp10ml[,i]=401],Pontos$lat[Spp10ml[,i]=401],pch=24,bg=
 'red',col='black',cex=1.5)
 
 dev.off()}
 
  
 
 Thanks in advance.
 
  
 
 -
 
 MSc.  mailto:r.alui...@gmail.com Rodrigo Aluizio
 
 Centro de Estudos do Mar/UFPR
 Laboratório de Micropaleontologia
 Avenida Beira Mar s/n - CEP 83255-000
 Pontal do Paraná - PR - Brasil
 
 
 
 
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 and provide commented, minimal, self-contained, reproducible code.
 
 

-- 
View this message in context: 
http://www.nabble.com/Bubble-Plot-Over-a-Map-tp23426635p23428390.html
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[R] A potential bug for paste() ?

Hi, everyone,

Try the following command to see if you get TRUE or FALSE. I get FALSE on a
unix platform but TRUE on Windows. Any comment?

all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))

-- 
Jun Shen PhD
PK/PD Scientist
BioPharma Services
Millipore Corporation
15 Research Park Dr.
St Charles, MO 63304
Direct: 636-720-1589

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Re: [R] How to call time series functions from C ?

2009-05-07 Thread goon83

hi Duncan,
 
tks for you response, it's depressed to know that i can not use time series of 
R to finish my study.
 
I really think R is powerfull, i used it to finish all my statistic homework 
last year^_^.
 
but i still wonder can i use the function of time series in the embedded way of 
C code.
 
 
Can you give me some suggestion about how to use time series of R in C code?
 
 
 
tks 
 

bin dong 
goo...@126.com
Buaa, Beijing PR China
 
 


 


ÔÚ2009-05-07?21:51:13£¬Duncan?Murdoch?murd...@stats.uwo.ca?Ð´µÀ£º
On?5/7/2009?9:24?AM,?goon83?wrote:
?Hi?everyone,
???I?meet?the?problem?to?call?R?from?C.?
??
???Can?someone?tell?me?is?it?possible?to?call?time?series?functions(such?as?ar?and?arima)from??C?program?on?linux?platform,?and?then?compile?the?C?program?to?a?standalone?executable?file?
?
???I?know?we?can?call?some?function?defined?in?Rmath.h?,?but?I?have?not?found?the?entry?point?for?time?series?function.?

There?are?none,?but?you?can?write?a?front?end?for?R,?and?it?can?evaluate?
R?expressions,?etc.??The?procedure?is?described?in?the?Writing?R?
Extensions?manual.

Remember?that?if?you?distribute?the?program?you?do?need?to?follow?the?
GPL,?and?distribute?all?of?R?as?well?as?all?of?your?own?program?in?
source?code?form.

Duncan?Murdoch

??
???I?would?very?much?appreciate?receiving?your?response?!?^_^
?
?
?bin,?dong
?goo...@126.com
?Buaa,?Beijing?PR?China
?
???
?
? [[alternative?HTML?version?deleted]]
?
?__
?r-h...@r-project.org?mailing?list
?https://stat.ethz.ch/mailman/listinfo/r-help
?PLEASE?do?read?the?posting?guide?http://www.R-project.org/posting-guide.html
?and?provide?commented,?minimal,?self-contained,?reproducible?code.


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Re: [R] A potential bug for paste() ?

2009-05-07 Thread Sarah Goslee

It probably has less to do with paste() than with Theoph, but since
we have no idea what that might be, it's hard to tell.

See the bit about reproducible example, please.

Sarah

On Thu, May 7, 2009 at 10:38 AM, Jun Shen jun.shen...@gmail.com wrote:
 Hi, everyone,

 Try the following command to see if you get TRUE or FALSE. I get FALSE on a
 unix platform but TRUE on Windows. Any comment?

 all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))


-- 
Sarah Goslee
http://www.functionaldiversity.org

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Re: [R] PGF Device

I can only second Dieter and Baptiste.


Am Donnerstag, den 07.05.2009, 14:57 +0200 schrieb baptiste auguie:
 If one was to implement a Tikz output for R graphics, I'm not sure  
 what route to take:
 
 1) focus exclusively on Grid graphics and implement a conversion at  
 the R level à la gridSVG (see Paul Murrell's webpage)
 
 2) create a new device ( I have no idea where to find guidelines for  
 this, and I'm not even clear on what exactly a Device is).
 
 In any case, given that pdf is often the preferred output for R  
 graphics (e.g. through the Sweave route), it seems that the pgf format  
 would be an excellent addition if only for its perfect handling of  
 LaTeX formulas.
 
 Best wishes,
 
 baptiste
 
 
 
 
 
 On 7 May 2009, at 14:39, Dieter Menne wrote:
 
  Lasse Bombien lasse at phonetik.uni-muenchen.de writes:
 
 
  Am Mittwoch, den 06.05.2009, 16:08 +0200 schrieb baptiste auguie:
  I think the pgfSweave project on R-forge is working on this (as  
  far as
  i know it currently relies on eps2pgf)
  Right, but eps2pgf fails me on more complex / stacked plots.  
  Otherwise,
  I would be content using eps2pgf.
 
  Same for me; pgf/tikz is my method of choice for graphics in latex
  because it gets around the eps-detour that can cause strange problems.
 
  Dieter
 
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  PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
  and provide commented, minimal, self-contained, reproducible code.
 
 _
 
 Baptiste Auguié
 
 School of Physics
 University of Exeter
 Stocker Road,
 Exeter, Devon,
 EX4 4QL, UK
 
 Phone: +44 1392 264187
 
 http://newton.ex.ac.uk/research/emag
 
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-- 
Lasse Bombien
Institut für Phonetik und Sprachverarbeitung
Schellingstraße 3/II
D-80799 München

email: la...@phonetik.uni-muenchen.de
web: http://www.phonetik.uni-muenchen.de/~lasse
phone: +49 (0) 89 2180 2812

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Re: [R] How to call time series functions from C ?


On 5/7/2009 10:55 AM, goon83 wrote:

hi Duncan,
 
tks for you response, it's depressed to know that i can not use time series of R to finish my study.
 
I really think R is powerfull, i used it to finish all my statistic homework last year^_^.
 
but i still wonder can i use the function of time series in the embedded way of C code.
 
 
Can you give me some suggestion about how to use time series of R in C code?


I did, in the previous message.

Duncan Murdoch

 
 
 
tks 
 

bin dong 
goo...@126.com

Buaa, Beijing PR China
 
 



 



??2009-05-07?21:51:13??Duncan?Murdoch?murd...@stats.uwo.ca???

On?5/7/2009?9:24?AM,?goon83?wrote:

?Hi?everyone,
???I?meet?the?problem?to?call?R?from?C.?
??
???Can?someone?tell?me?is?it?possible?to?call?time?series?functions(such?as?ar?and?arima)from??C?program?on?linux?platform,?and?then?compile?the?C?program?to?a?standalone?executable?file?
?
???I?know?we?can?call?some?function?defined?in?Rmath.h?,?but?I?have?not?found?the?entry?point?for?time?series?function.?


There?are?none,?but?you?can?write?a?front?end?for?R,?and?it?can?evaluate?
R?expressions,?etc.??The?procedure?is?described?in?the?Writing?R?
Extensions?manual.

Remember?that?if?you?distribute?the?program?you?do?need?to?follow?the?
GPL,?and?distribute?all?of?R?as?well?as?all?of?your?own?program?in?
source?code?form.

Duncan?Murdoch


??
???I?would?very?much?appreciate?receiving?your?response?!?^_^
?
?
?bin,?dong
?goo...@126.com
?Buaa,?Beijing?PR?China
?
???
?
?   [[alternative?HTML?version?deleted]]
?
?__
?r-h...@r-project.org?mailing?list
?https://stat.ethz.ch/mailman/listinfo/r-help
?PLEASE?do?read?the?posting?guide?http://www.R-project.org/posting-guide.html
?and?provide?commented,?minimal,?self-contained,?reproducible?code.






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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Linear least squares fit with errors in both x and y values.

2009-05-07 Thread James Allsopp

Hi,
I'd like to perform a weighted linear least squares fit with R on data
with varying errors on both vectors. I can do this with one axis using
lm, but have no idea where to go from here. I've tried googling, but no
idea. Any suggestions?

I'm also trying to plot these errors on a graph. Again I can see how to
do it for one set of data but not the other.

Thanks,
James

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Re: [R] Step and stepAIC

I also wonder if stepAIC can work with an lme model. I tried. it doesn't for
now. Appreciate any comment.

Jun

On Thu, May 7, 2009 at 9:15 AM, Dieter Menne
dieter.me...@menne-biomed.dewrote:

 Peter-Heinz Fox peterheinzfox at yahoo.de writes:

  Iâm using step and stepAIC for stepwise regression. After each
 step,
  I would like to make an additional calculation based on the independent
  variables that have been selected until this step and
  their corresponding weights. Where do I have to add this calculation?

 dropTerm is the toolbox function stepAIC uses; you could use it to build
 your own stepAIC version.

 But also make sure you have read

 http://markmail.org/thread/gk7ysg6tclz4vtdi

 and consider some lasso variant method instead (this partly
 answers your second question).

 Dieter

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




-- 
Jun Shen PhD
PK/PD Scientist
BioPharma Services
Millipore Corporation
15 Research Park Dr.
St Charles, MO 63304
Direct: 636-720-1589

[[alternative HTML version deleted]]

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Re: [R] How to call time series functions from C ?

2009-05-07 Thread goon83

Hi Duncan,

Sorry, i miss the informatin in the previous message,  you said  that i can 
write a front end  to call , does the front end can be implemented by c, and 
i can compile the c code to a standalone program. i will appreiciate for more 
detail information


tks? 
? 

?bin?dong?
?goo...@126.com
?Buaa,?Beijing?PR?China


ÔÚ2009-05-07?23:05:47£¬Duncan?Murdoch?murd...@stats.uwo.ca?Ð´µÀ£º
On?5/7/2009?10:55?AM,?goon83?wrote:
?hi?Duncan,
??
?tks?for?you?response,?it's?depressed?to?know?that?i?can?not?use?time?series?of?R?to?finish?my?study.
??
?I?really?think?R?is?powerfull,?i?used?it?to?finish?all?my?statistic?homework?last?year^_^.
??
?but?i?still?wonder?can?i?use?the?function?of?time?series?in?the?embedded?way?of?C?code.
??
??
?Can?you?give?me?some?suggestion?about?how?to?use?time?series?of?R?in?C?code?

I?did,?in?the?previous?message.

Duncan?Murdoch

??
??
??
?tks?
??
?
?bin?dong?
?goo...@126.com
?Buaa,?Beijing?PR?China
??
??
?
?
??
?
?
?ÔÚ2009-05-07?21:51:13£¬Duncan?Murdoch?murd...@stats.uwo.ca?Ð´µÀ£º
On?5/7/2009?9:24?AM,?goon83?wrote:
?Hi?everyone,
???I?meet?the?problem?to?call?R?from?C.?
??
???Can?someone?tell?me?is?it?possible?to?call?time?series?functions(such?as?ar?and?arima)from??C?program?on?linux?platform,?and?then?compile?the?C?program?to?a?standalone?executable?file?
?
???I?know?we?can?call?some?function?defined?in?Rmath.h?,?but?I?have?not?found?the?entry?point?for?time?series?function.?

There?are?none,?but?you?can?write?a?front?end?for?R,?and?it?can?evaluate?
R?expressions,?etc.??The?procedure?is?described?in?the?Writing?R?
Extensions?manual.

Remember?that?if?you?distribute?the?program?you?do?need?to?follow?the?
GPL,?and?distribute?all?of?R?as?well?as?all?of?your?own?program?in?
source?code?form.

Duncan?Murdoch

??
???I?would?very?much?appreciate?receiving?your?response?!?^_^
?
?
?bin,?dong
?goo...@126.com
?Buaa,?Beijing?PR?China
?
???
?
?   [[alternative?HTML?version?deleted]]
?
?__
?r-h...@r-project.org?mailing?list
?https://stat.ethz.ch/mailman/listinfo/r-help
?PLEASE?do?read?the?posting?guide?http://www.R-project.org/posting-guide.html
?and?provide?commented,?minimal,?self-contained,?reproducible?code.

?


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Re: [R] Bumps chart in R

2009-05-07 Thread Andreas Christoffersen

Thank you Thierry! That was very helpfull

I have added geom_point which makes the lineending look more round.
Also - since the chart becomes verye clustered I also added text to
the right.

like so:
ggplot(df, aes(x = tal, y = value, label = text, group = text, size =
size, col = Change))+
 geom_line()+
 geom_text(data = subset(df, tal==tal1),size=3, hjust=1, vjust=0)+
 geom_text(data = subset(df, tal==tal2),hjust=-1, size=3)+
 geom_point() + scale_x_discrete(Change from time to time) +
 scale_y_continuous(Points) +
 theme_bw()+
 opts(legend.position=none)+
 opts(title=As time went by)+
 opts(plot.title=theme_text(vjust=0,size=20))+
 scale_colour_manual(values = c(red, black, blue))

Thanks for all your help!

On Thu, May 7, 2009 at 1:17 PM, ONKELINX, Thierry
thierry.onkel...@inbo.be wrote:
 Dear Andreas and Mike,

 You need to use scale_colour_manual() if you want to set the colours 
 yourself. Ggplot2 interpretes the col variable in the dataset as an 
 ordinairy factor.

 library(ggplot2)
 df0 - data.frame(text = letters[1:21], tal1 = c(rnorm (20,5,2), 5), tal2 = 
 c(rnorm (20,6,3), 5))
 df0$dif - df0$tal2 - df0$tal1
 df - melt(data = df0, id.vars = c('text', 'dif'), variable_name = 'tal')
 df$Change - factor(ifelse(df$dif0,'Up',ifelse(df$dif0,'Down','Stable')), 
 levels = c(Up, Stable, Down))
 df$size - abs(df$dif)
 ggplot(df, aes(x = tal, y = value, label = text, group = text, size = size, 
 col = Change)) + geom_line() + geom_text(data = subset(df, tal==tal1), 
 size=3, hjust=2, vjust=0) + scale_x_discrete(Change from time to time) + 
 scale_y_continuous(Points) + theme_bw()+ opts(legend.position=none)+ 
 opts(title=As time went by\n) +opts(plot.title=theme_text(vjust=0,size=20)) 
 + scale_colour_manual(values = c(red, black, blue))

 HTH,

 Thierry

 
 ir. Thierry Onkelinx
 Instituut voor natuur- en bosonderzoek / Research Institute for Nature and 
 Forest
 Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, 
 methodology and quality assurance
 Gaverstraat 4
 9500 Geraardsbergen
 Belgium
 tel. + 32 54/436 185
 thierry.onkel...@inbo.be
 www.inbo.be

 To call in the statistician after the experiment is done may be no more than 
 asking him to perform a post-mortem examination: he may be able to say what 
 the experiment died of.
 ~ Sir Ronald Aylmer Fisher

 The plural of anecdote is not data.
 ~ Roger Brinner

 The combination of some data and an aching desire for an answer does not 
 ensure that a reasonable answer can be extracted from a given body of data.
 ~ John Tukey

 -Oorspronkelijk bericht-
 Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] 
 Namens Andreas Christoffersen
 Verzonden: donderdag 7 mei 2009 12:22
 Aan: Mike Lawrence; r-help@r-project.org; ggpl...@googlegroups.com
 Onderwerp: Re: [R] Bumps chart in R

 On Thu, May 7, 2009 at 2:15 AM, Mike Lawrence mike.lawre...@dal.ca wrote:
 (cross posting to the ggplot2 group for posterity)

 Here's how I'd approach it:

 library(ggplot2)
 text = letters[1:20]
 tal1 = rnorm (20,5,2)
 tal2 = rnorm (20,6,3)
 dif = tal2-tal1
 df0 = data.frame(text,tal1,tal2)
 df = melt(
        data = df0
        , id.vars = 'text'
        , variable_name = 'tal'
 )
 df$dif = dif
 df$col = ifelse(dif0,'red',ifelse(dif0,'blue','black'))
 df$size = abs(dif)

 # draw the plot

 Unfortunately it's not perfect:
 (1) col isn't being interpreted literally, so instead of truly red  blue.
 (2) the lines ends are square whereas usually they're rounded.
 (3) attempting to remove the legend via opts(legend.position=none)
 seems to fail.


 Thank you

 with your melted data I was able to come very close to what I want.
 legen.posistion=none works for me... Annonying that colours don't
 work like expected... It seams to be a frequent concern.

 My code:
 qplot(tal,value,data=df,group=text,geom=line,size=size,colour=col,xlab=Change
 from time to time, ylab = Points)+
 geom_text(aes(label=text),subset(df,tal==tal1),size=3,hjust=2,vjust=0)+
 theme_bw()+ opts(legend.position=none)+ opts(title=As time went
 by) +opts(plot.title=theme_text(vjust=0,size=20))

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

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 is
 door een geldig ondertekend document. The views expressed in  this message
 and any annex are purely those of the writer and may not be regarded as 
 stating
 an official position of INBO, as long as the message is not confirmed by a 
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Re: [R] How to call time series functions from C ?

2009-05-07 Thread Whit Armstrong

you have a couple of options.

If you require specific R functions to do what you want, then you will
need to call R from C.

I believe that Dirk has been working on an RInside package that does this.

Alternatively, you can use my tslib package, which is a general time
series library written in c++.

It's public interface in R, is the fts package, which just wraps the
c++ library to R functions.

sources are available here:
http://github.com/armstrtw/tslib/tree/master
http://github.com/armstrtw/fts/tree/master

If you want to try out tslib, feel free to contact me off list for help.

-Whit

2009/5/7 Duncan Murdoch murd...@stats.uwo.ca:
 On 5/7/2009 10:55 AM, goon83 wrote:

 hi Duncan,
  tks for you response, it's depressed to know that i can not use time
 series of R to finish my study.
  I really think R is powerfull, i used it to finish all my statistic
 homework last year^_^.
  but i still wonder can i use the function of time series in the embedded
 way of C code.
   Can you give me some suggestion about how to use time series of R in C
 code?

 I did, in the previous message.

 Duncan Murdoch

    tks  
 bin dong goo...@126.com
 Buaa, Beijing PR China




 在2009-05-07?21:51:13，Duncan?Murdoch?murd...@stats.uwo.ca?写道：

 On?5/7/2009?9:24?AM,?goon83?wrote:

 ?Hi?everyone,
 ???I?meet?the?problem?to?call?R?from?C.?
 ??

 ???Can?someone?tell?me?is?it?possible?to?call?time?series?functions(such?as?ar?and?arima)from??C?program?on?linux?platform,?and?then?compile?the?C?program?to?a?standalone?executable?file?
 ?

 ???I?know?we?can?call?some?function?defined?in?Rmath.h?,?but?I?have?not?found?the?entry?point?for?time?series?function.?

 There?are?none,?but?you?can?write?a?front?end?for?R,?and?it?can?evaluate?
 R?expressions,?etc.??The?procedure?is?described?in?the?Writing?R?
 Extensions?manual.

 Remember?that?if?you?distribute?the?program?you?do?need?to?follow?the?
 GPL,?and?distribute?all?of?R?as?well?as?all?of?your?own?program?in?
 source?code?form.

 Duncan?Murdoch

 ??
 ???I?would?very?much?appreciate?receiving?your?response?!?^_^
 ?
 ?
 ?bin,?dong
 ?goo...@126.com
 ?Buaa,?Beijing?PR?China
 ?
 ???
 ?
 ?       [[alternative?HTML?version?deleted]]
 ?
 ?__
 ?r-h...@r-project.org?mailing?list
 ?https://stat.ethz.ch/mailman/listinfo/r-help

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




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[R] Draw a random number about the fitting of a glm model using family=quasi

2009-05-07 Thread jpl


Hi,

I desire to draw a random number about the fitting of a glm model using a
quasi linear error distribution.

For example, if my family is poisson, then this is what I want:
model1 = glm(amount~days,family=poisson(link=log),data=dataset1)
mean1 = predict(model1,newdata =data.frame(days=time),type=response)
rpois(length(mean1),mean1)

But I wish to change my model to:
model2 = glm(amount~days,family=quasi(link=log,
variance=mu),data=dataset2)
mean2 = predict(model2,newdata =data.frame(days=time),type=response)

Is there a way to draw a random number about the mean when I have a
quasi-linear error distribution?

Thanks.
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[R] Linear least squares fit with errors in both x and y values.

2009-05-07 Thread James Allsopp

HI,
I'd like to perform a weighted linear least squares fit with R on data 
with varying errors on both vectors. I can do this with one axis using
lm, but have no idea where to go from here. I've tried googling, but no
idea. Any suggestions?

Thanks,
James

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[R] How to save independent R sessions in BATCH mode???

2009-05-07 Thread mcnda839


Hi guys,

I already have put this question some time ago however replies were  
not straight to the problem. Even so thanks a lot for the answers!


I reformulate the problem.

I have a script file with the following commands:

for (i in 1:300)
- open session -- load(X_i.rdata)
- perform some calcules -- ()
- save session -- save.image(Y_i.rdata)
end for

The problem here is that, I cannot save.image and begin a new clean  
session. An hypothesis could be to delete all R objects after the  
save.image, but this does not seem too efficient to perform.
What should I do to begin a R clean session in the same batch  
processing? Are there any other suggestion on this?


Thanks in advance,

Diogo André Alagador

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Re: [R] Help with lme4 model specification

2009-05-07 Thread boeinguy2


Thanks! I made this correction


ONKELINX, Thierry wrote:
 
 
 Please note that the case of characters is important in R. Hence True
 differs from TRUE. You need to use REML = TRUE instead of REML = True!
 The only valid logical values are TRUE, FALSE, T and F. But I recommend
 to use only TRUE and FALSE. Because you can overwrite T and F. You could
 do something like T - FALSE, which is ofcourse not a good idea. TRUE
 and FALSE can not be overwritten.
 
 HTH,
 
 Thierry
 
 
 
 
 ir. Thierry Onkelinx
 Instituut voor natuur- en bosonderzoek / Research Institute for Nature
 and Forest
 Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
 methodology and quality assurance
 Gaverstraat 4
 9500 Geraardsbergen
 Belgium 
 tel. + 32 54/436 185
 thierry.onkel...@inbo.be 
 www.inbo.be 
 
 To call in the statistician after the experiment is done may be no more
 than asking him to perform a post-mortem examination: he may be able to
 say what the experiment died of.
 ~ Sir Ronald Aylmer Fisher
 
 The plural of anecdote is not data.
 ~ Roger Brinner
 
 The combination of some data and an aching desire for an answer does not
 ensure that a reasonable answer can be extracted from a given body of
 data.
 ~ John Tukey
 
 -Oorspronkelijk bericht-
 Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 Namens boeinguy2
 Verzonden: donderdag 7 mei 2009 0:21
 Aan: r-help@r-project.org
 Onderwerp: [R] Help with lme4 model specification
 
 
 I am new to R and am trying to specify a model for mixed model analysis.
 
 When I run the following model I get an error:
 
 AAT- lmer(Y ~ S + A + (1|S:A/H), data=AT, REML=True)
 
 The error looks like this:
 
 Error in Spar_loc:`:` : NA/NaN argument
 In addition: Warning messages:
 1: In model.matrix.default(mt, mf, contrasts) :
   variable 'Spar_loc' converted to a factor
 2: In Spar_loc:`:` :
   numerical expression has 720 elements: only the first used
 
 I am having trouble specifying th random component.  It should reflect
 the
 random term as H nested within the interaction of S  A.  What am I
 doing
 wrong?
 :confused:
 -- 
 View this message in context:
 http://www.nabble.com/Help-with-lme4-model-specification-tp23415908p2341
 5908.html
 Sent from the R help mailing list archive at Nabble.com.
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver
 weer 
 en binden het INBO onder geen enkel beding, zolang dit bericht niet
 bevestigd is
 door een geldig ondertekend document. The views expressed in  this message 
 and any annex are purely those of the writer and may not be regarded as
 stating 
 an official position of INBO, as long as the message is not confirmed by a
 duly 
 signed document.
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 

-- 
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[R] compiling 64 bit JRI.dll with 64bit XP

2009-05-07 Thread gatechatl


Hi all,
I was able to run my Java-R program using a 32-bit jdk on my 64-bit machine;
however I wish to use the 64-bit jdk so my Java program can take advantage
of the larger memory capabilities etc.  I'm currently trying to compile
JRI_0.4-1 on a 64-bit XP I got to a point that I was able to generate a
32-bit dll, but I don't know exactly how to modify it so that it's able to
generate a 64-bit dll.  I tried modifying the makefile adding -m64 to some
of the gcc command with no success.  I am not very experienced with creating
dll's, but I was wondering if anybody attempted to compile a 64-bit JRI.dll? 
And if so what type of modifications or resources should I use?  Thanks!

Tim
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Re: [R] How to call time series functions from C ?

2009-05-07 Thread Gabor Grothendieck

Do you have to use the entire xxxGB at once?  If not store it in a database
and fetch the portions for the current analysis as you need them.

On Thu, May 7, 2009 at 10:55 AM, goon83 goo...@126.com wrote:
 hi Duncan,

 tks for you response, it's depressed to know that i can not use time series 
 of R to finish my study.

 I really think R is powerfull, i used it to finish all my statistic homework 
 last year^_^.

 but i still wonder can i use the function of time series in the embedded way 
 of C code.


 Can you give me some suggestion about how to use time series of R in C code?



 tks

 
 bin dong
 goo...@126.com
 Buaa, Beijing PR China







 在2009-05-07?21:51:13，Duncan?Murdoch?murd...@stats.uwo.ca?写道：
On?5/7/2009?9:24?AM,?goon83?wrote:
?Hi?everyone,
???I?meet?the?problem?to?call?R?from?C.?
??
???Can?someone?tell?me?is?it?possible?to?call?time?series?functions(such?as?ar?and?arima)from??C?program?on?linux?platform,?and?then?compile?the?C?program?to?a?standalone?executable?file?
?
???I?know?we?can?call?some?function?defined?in?Rmath.h?,?but?I?have?not?found?the?entry?point?for?time?series?function.?

There?are?none,?but?you?can?write?a?front?end?for?R,?and?it?can?evaluate?
R?expressions,?etc.??The?procedure?is?described?in?the?Writing?R?
Extensions?manual.

Remember?that?if?you?distribute?the?program?you?do?need?to?follow?the?
GPL,?and?distribute?all?of?R?as?well?as?all?of?your?own?program?in?
source?code?form.

Duncan?Murdoch

??
???I?would?very?much?appreciate?receiving?your?response?!?^_^
?
?
?bin,?dong
?goo...@126.com
?Buaa,?Beijing?PR?China
?
???
?
? [[alternative?HTML?version?deleted]]
?
?__
?r-h...@r-project.org?mailing?list
?https://stat.ethz.ch/mailman/listinfo/r-help
?PLEASE?do?read?the?posting?guide?http://www.R-project.org/posting-guide.html
?and?provide?commented,?minimal,?self-contained,?reproducible?code.


[[alternative HTML version deleted]]


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Re: [R] Step and stepAIC

Jun Shen jun.shen.ut at gmail.com writes:

 
 I also wonder if stepAIC can work with an lme model. I tried. it doesn't for
 now. Appreciate any comment.
 

It can, and it displays a nice error message telling you exactly why it
did not work if you try out of the box. Check parameter method in your
lme call. 

Dieter

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[R] visualization of sub-parts in 3D arrays

2009-05-07 Thread jgarcia

Hello all;

Let's say we have a block of 3D data belonging to cubic cells,
 and increasing indexes are ordered
 x: from west to east
 y: from north to south
 z: from top to bottom

---
nx - 25
ny - 12
nz - 4
my.array - array(NA,dim=c(nx,ny,nz))

for(z in 1:nz){
 my.array[,,z] - runif(nx*ny,z-1,z)
}
---
Is there a way to relatively easy plot sub-blocks of this 3d array in R?
This would include simultaneous plots of several layers one over the
other, and keeping the gaps between them if they are
non-contiguous. Also this would include transversal cuts of thickness 1 or
1, and from a selected point of view.

I mean as a render in which lateral planes (xz and yz planes) are treated
similarly to xy planes.

Thanks and best regards,
Javier
---

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Re: [R] Step and stepAIC

Jun Shen jun.shen.ut at gmail.com writes:

 
 I also wonder if stepAIC can work with an lme model. I tried. it doesn't for
 now. Appreciate any comment.
 

It can do it, and it displays a nice error message, as I remember, why
it won't do it in the default setting. Check parameter method of your 
lme call.

Dieter

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[R] lasso based selection for mixed model

Dear useRs (called Frank Harrell, most likely),

after having preached for years to my medical colleagues to be cautious 
with stepwise selection procedures, they chanted back asking for an 
alternative when using mixed models.
There is a half dozen laXXX packages around for all types of linear models, 
but as far I see there is none for mixed models such as lme. Even 
boot.stepAIC (which I considered valid, but Frank objects) is not for 
lme.

I found one SPSS macro around that comes close.

Any ideas?

Dieter

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Re: [R] A potential bug for paste() ?

2009-05-07 Thread Gavin Simpson

On Thu, 2009-05-07 at 09:38 -0500, Jun Shen wrote:
 Hi, everyone,
 
 Try the following command to see if you get TRUE or FALSE. I get FALSE on a
 unix platform but TRUE on Windows. Any comment?
 
 all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))

And what is Theoph? Please do read the posting guide and provide a
reproducible example.

Is Theoph a list?

 a - list(A = rnorm(10), B = rnorm(10))
 paste(a[1], a[2])
[1] c(0.511810414967963, 0.165995305876871, 1.22637694512945,
-0.496453787173788, 0.325876407556065, 1.97392856823209,
-0.228962880984580, -0.172306887133861, -0.881280038259407,
-0.216958955239245) c(-0.281058662811336, 0.918418337792562,
-1.44005513590710, 0.22857441100305, 0.840138552938062,
0.0555436312146647, -0.602645008995437, -0.158866265592772,
0.959478898002479, -0.892389972305427)
 paste(a[[1]], a[[2]])
 [1] 0.511810414967963 -0.281058662811336 
 [2] 0.165995305876871 0.918418337792562  
 [3] 1.22637694512945 -1.44005513590710   
 [4] -0.496453787173788 0.22857441100305  
 [5] 0.325876407556065 0.840138552938062  
 [6] 1.97392856823209 0.0555436312146647  
 [7] -0.228962880984580 -0.602645008995437
 [8] -0.172306887133861 -0.158866265592772
 [9] -0.881280038259407 0.959478898002479 
[10] -0.216958955239245 -0.892389972305427
 typeof(a[[1]])
[1] double
 typeof(a[1])
[1] list

If it is, note that [ and [[ do not return the same thing for a list and
as such it is not surprising that they are not equal, pasted or
otherwise.

G
-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,  [f] +44 (0)20 7679 0565
 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London  [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

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Re: [R] I updated/reinstalled ggplot2 and the trouble started...

2009-05-07 Thread Tena Sakai

Hi,

 What device are you using to plot the graph?

I am not explicitly specifying any.  I am on
redhat linux and as I understand it R uses
DISPLAY environment variable, which is set
for an X11 server (X Darwin, v1.4.0, X11 6.8.2).

Other qplot()'s I have used (straight out of the
book) work fine.  I am coming to believe that
before the current incarnation, it simply ignored
the alpha parameter and gave the plot, whereas
with the latest it doens't want to ignore and not
going further.  I'd be curious if this problem is
reproducible with anybody else.

Regards,

Tena Sakaki
tsa...@gallo.ucsf.edu


-Original Message-
From: ONKELINX, Thierry [mailto:thierry.onkel...@inbo.be]
Sent: Thu 5/7/2009 1:01 AM
To: Tena Sakai; Ian Fellows; r-help@r-project.org
Subject: RE: [R] I updated/reinstalled ggplot2 and the trouble started...
 
What device are you using to plot the graph? According to the warning,
the device is causing the problem.

HTH,

Thierry




ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
thierry.onkel...@inbo.be 
www.inbo.be 

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
Namens Tena Sakai
Verzonden: donderdag 7 mei 2009 6:22
Aan: Ian Fellows; r-help@r-project.org
Onderwerp: Re: [R] I updated/reinstalled ggplot2 and the trouble
started...

Hi Ian,

Per your suggestion, I reinstalled R 2.9.0, then
I reinstalled ggplot2 on top.  The problem persists.

Here's the what happens after the installation:

   qplot (carat, price, data = diamonds, alpha = I(1/10))
  Warning message:
  In grid.Call.graphics(L_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only
once per page

The entire record of installing ggplot2 package, ending
up with the line above is in the attached file.  I would
think this should be reproducible with anybody else.

If you have any other suggestion, I am all ears.

Regards,

Tena Sakai
tsa...@gallo.ucsf.edu


-Original Message-
From: Ian Fellows [mailto:ifell...@gmail.com]
Sent: Tue 5/5/2009 11:43 PM
To: Tena Sakai
Subject: Re: I updated/reinstalled ggplot2 and the trouble started...

Tena,

May I suggest that you do a full clean install of R 2.9.0, then install
ggplot2 from cran. See if the problem persists after that.


Ian


On Tue, May 5, 2009 at 11:13 PM, tena tsa...@gallo.ucsf.edu wrote:


 Hi Hadley,

 Many thanks for your reply.

 I followed your instruction and got past the point where I
 was stuck at.  Namely, I was able to generate a few plots.
 But as I came to the second half of section 2.4, where I
 wanted to see the behavior of alpha paramter, which I
 had apparently misspelled, I encountered another hindrance:
qplot (carat, price, data = diamonds, alpha = I(1/10))
   Warning message:
  In grid.Call.graphics(L_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only
 once per page

 A plot was generated, but there are tic marks and labels on
 each direction, but no plot at all.

 I wonder if this is yet another (hidden) package to be updated...
 The warning message suggests grid, but I am hesitant to do
 something without knowing what is what.  I would appreciate
 your instruction.

 Regards,

 Tena Sakai


 On May 5, 5:24 pm, hadley wickham h.wick...@gmail.com wrote:
  Hi Tena,
 
  R isn't very good at detecting when package dependencies also need
to
  be updated, so you probably need to do:
 
  install.packages(c(reshape,plyr))
 
  And you want
 
  qplot (carat, price, data=diamonds, alpha = I(1/10))
 
  not
 
  qplot (carat, price, data=diamonds, slpha = i(1/10))
 
  Hadley
 
  On Tue, May 5, 2009 at 6:27 PM, tena tsa...@gallo.ucsf.edu wrote:
 
   Hi Folks,
 
   I am pretty new to R and I am even newer to ggplot.
 
   I am using R 2.7.1, 2.8.1, and 2.9.0 on linux host and
   what I am experiencing holds for all three.
 
   I was just typing a few examples from the chapter 2 of
   the book, ggplot2 --Elegant graphics for data analysis.
 
   I typed 3 qplot lines on page 13:
 qplot (carat, price, data=diamonds, slpha = i(1/10))
 qplot (carat, price, data=diamonds, slpha = i(1/100))
 qplot (carat, price, data=diamonds, slpha = i(1/200))
 
   To me, the plot looked identical.  I went

Re: [R] Step and stepAIC

Thanks a lot, Dieter,

I changed the method to ML for my lme call. Now I get a different error
when running the stepAIC

Error in terms.formula(formula, data = data) :
  'data' argument is of the wrong type

What does that mean?
The same dataset was used for an lm call and everything is fine to run
stepAIC.

Jun

On Thu, May 7, 2009 at 10:44 AM, Dieter Menne
dieter.me...@menne-biomed.dewrote:

 Jun Shen jun.shen.ut at gmail.com writes:

 
  I also wonder if stepAIC can work with an lme model. I tried. it doesn't
 for
  now. Appreciate any comment.
 

 It can do it, and it displays a nice error message, as I remember, why
 it won't do it in the default setting. Check parameter method of your
 lme call.

 Dieter

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




-- 
Jun Shen PhD
PK/PD Scientist
BioPharma Services
Millipore Corporation
15 Research Park Dr.
St Charles, MO 63304
Direct: 636-720-1589

[[alternative HTML version deleted]]

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Re: [R] Linear least squares fit with errors in both x and y values.

2009-05-07 Thread Gerard M. Keogh

James,

look up errors in variables models or instrumental variable models in
econometrics.

The statistics alternative is a random effects or mixed effects model
which plugs the variation in the x's into a randomly varying parameter -
these are available in R (?lmer or glmm - I think).
Someone on the list much more knowledgeable than I about these will be able
to give you some help if you ask a good question.

Gerard



   
 James Allsopp 
 jamesaalls...@go 
 oglemail.com  To 
 Sent by:  r-help@r-project.org
 r-help-boun...@r-  cc 
 project.org   
   Subject 
   [R] Linear least squares fit with   
 07/05/2009 15:19  errors in both x and y values.  
   
   
   
   
   
   




HI,
I'd like to perform a weighted linear least squares fit with R on data
with varying errors on both vectors. I can do this with one axis using
lm, but have no idea where to go from here. I've tried googling, but no
idea. Any suggestions?

Thanks,
James

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Re: [R] How to call time series functions from C ?


On 5/7/2009 11:17 AM, goon83 wrote:

Hi Duncan,

Sorry, i miss the informatin in the previous message,  you said  that i can write a 
front end  to call , does the front end can be implemented by c, and i can 
compile the c code to a standalone program. i will appreiciate for more detail information


See the Writing R Extensions manual, as I said in the original reply.

Duncan Murdoch




tks? 
? 


?bin?dong?
?goo...@126.com
?Buaa,?Beijing?PR?China


??2009-05-07?23:05:47??Duncan?Murdoch?murd...@stats.uwo.ca???

On?5/7/2009?10:55?AM,?goon83?wrote:

?hi?Duncan,
??
?tks?for?you?response,?it's?depressed?to?know?that?i?can?not?use?time?series?of?R?to?finish?my?study.
??
?I?really?think?R?is?powerfull,?i?used?it?to?finish?all?my?statistic?homework?last?year^_^.
??
?but?i?still?wonder?can?i?use?the?function?of?time?series?in?the?embedded?way?of?C?code.
??
??
?Can?you?give?me?some?suggestion?about?how?to?use?time?series?of?R?in?C?code?


I?did,?in?the?previous?message.

Duncan?Murdoch


??
??
??
?tks?
??
?
?bin?dong?
?goo...@126.com
?Buaa,?Beijing?PR?China
??
??
?
?
??
?
?
???2009-05-07?21:51:13??Duncan?Murdoch?murd...@stats.uwo.ca???

On?5/7/2009?9:24?AM,?goon83?wrote:

?Hi?everyone,
???I?meet?the?problem?to?call?R?from?C.?
??
???Can?someone?tell?me?is?it?possible?to?call?time?series?functions(such?as?ar?and?arima)from??C?program?on?linux?platform,?and?then?compile?the?C?program?to?a?standalone?executable?file?
?
???I?know?we?can?call?some?function?defined?in?Rmath.h?,?but?I?have?not?found?the?entry?point?for?time?series?function.?


There?are?none,?but?you?can?write?a?front?end?for?R,?and?it?can?evaluate?
R?expressions,?etc.??The?procedure?is?described?in?the?Writing?R?
Extensions?manual.

Remember?that?if?you?distribute?the?program?you?do?need?to?follow?the?
GPL,?and?distribute?all?of?R?as?well?as?all?of?your?own?program?in?
source?code?form.

Duncan?Murdoch


??
???I?would?very?much?appreciate?receiving?your?response?!?^_^
?
?
?bin,?dong
?goo...@126.com
?Buaa,?Beijing?PR?China
?
???
?
?   [[alternative?HTML?version?deleted]]
?
?__
?r-h...@r-project.org?mailing?list
?https://stat.ethz.ch/mailman/listinfo/r-help
?PLEASE?do?read?the?posting?guide?http://www.R-project.org/posting-guide.html
?and?provide?commented,?minimal,?self-contained,?reproducible?code.



?






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Re: [R] A potential bug for paste() ?

2009-05-07 Thread Douglas Bates

On Thu, May 7, 2009 at 9:56 AM, Sarah Goslee sarah.gos...@gmail.com wrote:
 It probably has less to do with paste() than with Theoph, but since
 we have no idea what that might be, it's hard to tell.

 See the bit about reproducible example, please.

Well, actually Theoph is one of the datasets in the (required)
datasets package.  It happens to be data from a pharmacokinetics
experiment so it is natural that PK/PD scientist would think of it.

 find(Theoph)
[1] package:datasets
 str(Theoph)
Classes ‘nfnGroupedData’, ‘nfGroupedData’, ‘groupedData’ and
'data.frame':   132 obs. of  5 variables:
 $ Subject: Ord.factor w/ 12 levels 67811..: 11 11 11 11
11 11 11 11 11 11 ...
 $ Wt : num  79.6 79.6 79.6 79.6 79.6 79.6 79.6 79.6 79.6 79.6 ...
 $ Dose   : num  4.02 4.02 4.02 4.02 4.02 4.02 4.02 4.02 4.02 4.02 ...
 $ Time   : num  0 0.25 0.57 1.12 2.02 ...
 $ conc   : num  0.74 2.84 6.57 10.5 9.66 8.58 8.36 7.47 6.89 5.94 ...
 - attr(*, formula)=Class 'formula' length 3 conc ~ Time | Subject
  .. ..- attr(*, .Environment)=environment: R_EmptyEnv
 - attr(*, labels)=List of 2
  ..$ x: chr Time since drug administration
  ..$ y: chr Theophylline concentration in serum
 - attr(*, units)=List of 2
  ..$ x: chr (hr)
  ..$ y: chr (mg/l)

 On Thu, May 7, 2009 at 10:38 AM, Jun Shen jun.shen...@gmail.com wrote:
 Hi, everyone,

 Try the following command to see if you get TRUE or FALSE. I get FALSE on a
 unix platform but TRUE on Windows. Any comment?

 all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))

There is a difference between Theoph[1] and Theoph[[1]].  The Theoph
object is a data frame.  Whenever you use the single bracket extractor
you will get another data frame.

 str(Theoph[1])
Classes ‘nfnGroupedData’, ‘nfGroupedData’, ‘groupedData’ and
'data.frame':   132 obs. of  1 variable:
 $ Subject: Ord.factor w/ 12 levels 67811..: 11 11 11 11
11 11 11 11 11 11 ...

A data frame is a special type of a list and, in general, this applies
to any list - single bracket extraction applied to a list always
produces a list, even if it is a list of one element.

The double bracket extractor returns the element of the list, not a sublist.

 str(Theoph[[1]])
 Ord.factor w/ 12 levels 67811..: 11 11 11 11 11 11 11 11 11 11 ...

I think of the distinction as being like the difference between an
element of a set (the [[ operator) and a subset of size one (the [
operator).

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Re: [R] dotplot: labeling coordinates for each point

2009-05-07 Thread Deepayan Sarkar

On Thu, May 7, 2009 at 7:42 AM, Qifei Zhu zhu_qi...@yahoo.com.sg wrote:
 Hi Deepayan,



 I guess I’m quite confusing when asking the question. I was actually looking
 for labels beside the dot in the graph (shown below), rather than the labels
 on the x-axis. Is that possible? Thanks a lot!

In that case

dotplot(y ~ x, xlab=Store, ylab=Revenue, main=test,
scales=list(x = list(draw = FALSE)),
panel = function(x, y, ...) {
panel.dotplot(x, y, ...)
id - y  90
panel.text(as.numeric(x[id]), y[id],
   labels = sprintf((%s,%g), as.character(x[id]), y[id]),
   pos = 4)
})

-Deepayan






 Best,

 Tony





 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
 Behalf Of Deepayan Sarkar
 Sent: Thursday, May 07, 2009 1:44 AM
 To: Qifei Zhu
 Cc: r-help@r-project.org
 Subject: Re: [R] dotplot: labeling coordinates for each point



 On Wed, May 6, 2009 at 6:54 PM, Qifei Zhu zhu_qi...@yahoo.com.sg wrote:

 Hi Deepayan,



 Thanks for the reply. here is a very simple example of what I'm looking
 for:



 y=c(100,0,-20)

 x=c(Atlanta, Baltimore, Berkeley CA)

 dotplot(y~x, xlab=Store, ylab=Revenue,main=test,
 scale=list(rot=60))



 Basically it produces a graph of city on the x-axis and its associated
 revenue

 on the y-axis. In the real data set, the x-axis will be filled of tens or
 even hundreds

 of cities, so I wanna label the dots in the graph whenever the revenue (y
 value) is

 greater than a threshold, let's say 90 in this case. The labels should be
 in (x,y)

 format, which is (Atlanta, 100) in this case. Appreciate a lot for your
 help!



 dotplot(y~x, xlab=Store, ylab=Revenue,main=test,

     xlim = ifelse(y  90, sprintf((%s,%g), x, y), ),

     scales=list(rot=60))



 -Deepayan







 Best,

 Tony



 -Original Message-

 From: Deepayan Sarkar [mailto:deepayan.sar...@gmail.com]

 Sent: Wednesday, May 06, 2009 8:40 PM

 To: Qifei Zhu

 Cc: David Winsemius; r-help@r-project.org

 Subject: Re: [R] dotplot: labeling coordinates for each point



 On Tue, May 5, 2009 at 7:04 PM, Qifei Zhu zhu_qi...@yahoo.com.sg wrote:

 Hi Deepayan,



 Thanks for the hint. I spent some time on the research but haven't got
 any luck in writing the custom panel function for the conditional labeling
 of points in a graph. Could you please provide some more thoughts and
 probably some pseudo code? Thank you so much for your time!





 I'll be happy to try if you provide a reproducible example.



 -Deepayan







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 https://stat.ethz.ch/mailman/listinfo/r-help

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Re: [R] A potential bug for paste() ?

2009-05-07 Thread Phil Spector

Theoph is in the datasets package, so it should be 
available in all versions of R:



class(Theoph)

[1] nfnGroupedData nfGroupedData  groupedDatadata.frame

The key to what's happening is that there are some methods
for groupedData objects in the nlme library, which I suspect
the original poster had loaded in Windows, but not Unix.

Here's what I see on a Linux system:


all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))

[1] FALSE

library(nlme)
all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))

[1] TRUE

So if nlme is loaded, the following methods are available for 
groupedData objects:



methods(class='groupedData')

 [1] as.data.frame.groupedData* asTable.groupedData*
 [3] collapse.groupedData*  formula.groupedData*
 [5] [.groupedData* isBalanced.groupedData*
 [7] lme.groupedData*   lmList.groupedData*
 [9] print.groupedData* update.groupedData*

Thus subscripting for these objects is performed differently when
the nlme package is loaded.
   - Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 spec...@stat.berkeley.edu


On Thu, 7 May 2009, Gavin Simpson wrote:


On Thu, 2009-05-07 at 09:38 -0500, Jun Shen wrote:

Hi, everyone,

Try the following command to see if you get TRUE or FALSE. I get FALSE on a
unix platform but TRUE on Windows. Any comment?

all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))


And what is Theoph? Please do read the posting guide and provide a
reproducible example.

Is Theoph a list?


a - list(A = rnorm(10), B = rnorm(10))
paste(a[1], a[2])

[1] c(0.511810414967963, 0.165995305876871, 1.22637694512945,
-0.496453787173788, 0.325876407556065, 1.97392856823209,
-0.228962880984580, -0.172306887133861, -0.881280038259407,
-0.216958955239245) c(-0.281058662811336, 0.918418337792562,
-1.44005513590710, 0.22857441100305, 0.840138552938062,
0.0555436312146647, -0.602645008995437, -0.158866265592772,
0.959478898002479, -0.892389972305427)

paste(a[[1]], a[[2]])

[1] 0.511810414967963 -0.281058662811336
[2] 0.165995305876871 0.918418337792562
[3] 1.22637694512945 -1.44005513590710
[4] -0.496453787173788 0.22857441100305
[5] 0.325876407556065 0.840138552938062
[6] 1.97392856823209 0.0555436312146647
[7] -0.228962880984580 -0.602645008995437
[8] -0.172306887133861 -0.158866265592772
[9] -0.881280038259407 0.959478898002479
[10] -0.216958955239245 -0.892389972305427

typeof(a[[1]])

[1] double

typeof(a[1])

[1] list

If it is, note that [ and [[ do not return the same thing for a list and
as such it is not surprising that they are not equal, pasted or
otherwise.

G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography,  [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London  [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

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Re: [R] A potential bug for paste() ?

Thanks for everyone's attention on this issue!

On Thu, May 7, 2009 at 11:20 AM, Phil Spector spec...@stat.berkeley.eduwrote:

 Theoph is in the datasets package, so it should be available in all
 versions of R:

  class(Theoph)

 [1] nfnGroupedData nfGroupedData  groupedDatadata.frame

 The key to what's happening is that there are some methods
 for groupedData objects in the nlme library, which I suspect
 the original poster had loaded in Windows, but not Unix.

 Here's what I see on a Linux system:

  all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))

 [1] FALSE

 library(nlme)
 all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))

 [1] TRUE

 So if nlme is loaded, the following methods are available for groupedData
 objects:

  methods(class='groupedData')

  [1] as.data.frame.groupedData* asTable.groupedData*
  [3] collapse.groupedData*  formula.groupedData*
  [5] [.groupedData* isBalanced.groupedData*
  [7] lme.groupedData*   lmList.groupedData*
  [9] print.groupedData* update.groupedData*

 Thus subscripting for these objects is performed differently when
 the nlme package is loaded.
   - Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 spec...@stat.berkeley.edu



 On Thu, 7 May 2009, Gavin Simpson wrote:

  On Thu, 2009-05-07 at 09:38 -0500, Jun Shen wrote:

 Hi, everyone,

 Try the following command to see if you get TRUE or FALSE. I get FALSE on
 a
 unix platform but TRUE on Windows. Any comment?

 all(paste(Theoph[1],Theoph[2])==paste(Theoph[[1]],Theoph[[2]]))


 And what is Theoph? Please do read the posting guide and provide a
 reproducible example.

 Is Theoph a list?

  a - list(A = rnorm(10), B = rnorm(10))
 paste(a[1], a[2])

 [1] c(0.511810414967963, 0.165995305876871, 1.22637694512945,
 -0.496453787173788, 0.325876407556065, 1.97392856823209,
 -0.228962880984580, -0.172306887133861, -0.881280038259407,
 -0.216958955239245) c(-0.281058662811336, 0.918418337792562,
 -1.44005513590710, 0.22857441100305, 0.840138552938062,
 0.0555436312146647, -0.602645008995437, -0.158866265592772,
 0.959478898002479, -0.892389972305427)

 paste(a[[1]], a[[2]])

 [1] 0.511810414967963 -0.281058662811336
 [2] 0.165995305876871 0.918418337792562
 [3] 1.22637694512945 -1.44005513590710
 [4] -0.496453787173788 0.22857441100305
 [5] 0.325876407556065 0.840138552938062
 [6] 1.97392856823209 0.0555436312146647
 [7] -0.228962880984580 -0.602645008995437
 [8] -0.172306887133861 -0.158866265592772
 [9] -0.881280038259407 0.959478898002479
 [10] -0.216958955239245 -0.892389972305427

 typeof(a[[1]])

 [1] double

 typeof(a[1])

 [1] list

 If it is, note that [ and [[ do not return the same thing for a list and
 as such it is not surprising that they are not equal, pasted or
 otherwise.

 G
 --
 %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,  [f] +44 (0)20 7679 0565
 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London  [w] 
 http://www.ucl.ac.uk/~ucfagls/http://www.ucl.ac.uk/%7Eucfagls/
 UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
 %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

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




-- 
Jun Shen PhD
PK/PD Scientist
BioPharma Services
Millipore Corporation
15 Research Park Dr.
St Charles, MO 63304
Direct: 636-720-1589

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Re: [R] Step and stepAIC

Jun Shen jun.shen.ut at gmail.com writes:

 I changed the method to ML for my lme call. Now I get a different error
 when running the stepAIC
 
 Error in terms.formula(formula, data = data) :
   'data' argument is of the wrong type
 
 What does that mean?
 The same dataset was used for an lm call and everything is fine to run
 stepAIC.

Show sessionInfo() (do you have the recent version?)

Show str(yourdataset)

Show lme( your formula)

Dieter

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[R] 64 bit R double precision

2009-05-07 Thread Paul Emberson


Hi,

If R is compiled for a 64 bit platform, does the double data type make 
use of the additional precision or is it set at a fixed length?


Thanks,

Paul

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Re: [R] Step and stepAIC

Hi, Dieter,

 sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32

 str(cov)
'data.frame':   40 obs. of  13 variables:
 $ ID   : int  2 3 4 5 6 7 8 9 10 11 ...
 $ AMT  : num  50 50 50 50 50 50 50 50 25 25 ...
 $ Cmax : num [1:40(1d)] 8901 5574 10496 10882 8130 ...
  ..- attr(*, dimnames)=List of 1
  .. ..$ ID: chr  2 3 4 5 ...
 $ biomarker: num  3817 2542 5127 4478 3362 ...
 $ CRCL : num  29.2 44.5 65.5 57.1 63.3 ...
 $ SEX  : chr  male male male male ...
 $ WT   : num  79.7 86.4 80.5 55.2 83.8 ...
 $ AGE  : int  48 21 20 61 67 24 60 36 23 22 ...
 $ AGE2 : num  0 0 0 1 1 0 1 0 0 0 ...
 $ SEX2 : num  1 1 1 1 1 0 1 0 0 0 ...
 $ AGE3 : num  1 0 0 1 1 0 1 1 0 0 ...
 $ CRCL2: num  0 1 1 1 1 1 1 1 1 1 ...
 $ WT2  : num  0 0 0 0 0 0 0 1 0 1 ...

lme(biomarker~Cmax+AGE,data=cov,method='ML',random=~1+AGE|ID,keep.data=T)-mod.lme2
Warning message:
In lme.formula(biomarker ~ Cmax + AGE, data = cov, method = ML,  :
  Fewer observations than random effects in all level 1 groups

 stepAIC(mod.lme2,scope=list(upper=~Cmax+AGE+SEX2+WT+CRCL,lower=~1+Cmax))
Start:  AIC=637.53
biomarker ~ Cmax + AGE

Error in terms.formula(formula, data = data) :
  'data' argument is of the wrong type

I also wonder if stepAIC tests random effect to each covariate (e.g. AGE,
WT, CRCL...)

Thanks.

Jun

On Thu, May 7, 2009 at 11:37 AM, Dieter Menne
dieter.me...@menne-biomed.dewrote:

 Jun Shen jun.shen.ut at gmail.com writes:

  I changed the method to ML for my lme call. Now I get a different error
  when running the stepAIC
 
  Error in terms.formula(formula, data = data) :
'data' argument is of the wrong type
 
  What does that mean?
  The same dataset was used for an lm call and everything is fine to run
  stepAIC.

 Show sessionInfo() (do you have the recent version?)

 Show str(yourdataset)

 Show lme( your formula)

 Dieter

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 http://www.R-project.org/posting-guide.html
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Re: [R] RSPerl and Statistics::R

2009-05-07 Thread Duncan Temple Lang

RSPerl is not abandonded, but I haven't had much time to work on it.

If you can send me an example to reproduce the race condition, we can
probably think about a solution.

Daniel Klein wrote:

Greetings!

Being a Perl hacker for some time, and wanting to leverage what R provides, I've been trying to work with Statistics::R and RSPerl.

The former has a race condition that breeds some unreliability and the latter seems to have issues all around, and neither has been updated in some time.

Are these projects are abandoned, or is there some effort currently being undertaken to either refresh or reinvent the glue binding Perl and R together?

If not, then I'm probably going to give it a go myself, but I'm sort of hoping that there's a jewel of a library out there that doesn't come up as quickly in Google as the aforementioned libraries.

Thanks,

Daniel M. Klein

This email (including attachments and files, if any) is confidential, may be
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received this message in error, please notify me by return email and delete
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[R] .First and loading a package in a workspace

2009-05-07 Thread Seth Schommer


Hi,
I'm writing a package called rNMR and I'd like to be able to save a
workspace with rNMR loaded, exit R, and then load the workspace, loading
rNMR at the same time. This is no problem on Windows but on Linux and Macs I
can't get it to work.  Here's the deal.  rNMR has includes a .onLoad
function:

.onLoad = function(lib,pkg){
   print(rNMR version 1.0)
}

and also calls a different function which writes a .First to the global
environment:

.First - function(){
   require(rNMR)
}

Actually these have been simplified from there original versions in order to
easier diagnose the problem.  I've tested both versions and neither work.  I
open R and load rNMR.  I know .onLoad runs because I see

[1] rNMR version 1.0

in R.  Then I create the .First function as above (normally this is done
internally by rNMR, but I'm doing this manually here to ensure it gets done
correctly).  Just to make sure I check that .First is in the right place:

 getAnywhere(.First)
2 differing objects matching ‘.First’ were found
in the following places
 .GlobalEnv
 namespace:rNMR
Use [] to view one of them

 .First
function(){
require(rNMR)
}

Both versions of .First are identical.  So, you'd expect that if I saved
this workspace and exited, when I reopen R and load the workspace, .First
should run, loading the rNMR package, and calling .onLoad.  Here's what I
get when I load the workspace:

 load(/home/undergrad/Desktop/test.RData)
[1] rNMR version 1.0

but if I check for rNMR:

 search()
[1] .GlobalEnvpackage:stats package:graphics
[4] package:grDevices package:utils package:datasets
[7] package:methods   Autoloads package:base

it's clearly not attached.  I can't access any rNMR functions without
loading rNMR again.  .First still exists in the workspace, but somehow rNMR
hasn't loaded.  If this is the case, why is .onLoad running (indicated by
the printed rNMR version info)?  Odder still, the original version of .First
was designed to open a tk toplevel containing rNMR menus, which it does. 
Commands from these menus work but commands typed in the console don't and
everything else seems to indicate that rNMR is not attached.  Any thoughts?  
Thanks in advance,

Seth
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Re: [R] 64 bit R double precision


On 5/7/2009 12:56 PM, Paul Emberson wrote:

Hi,

If R is compiled for a 64 bit platform, does the double data type make 
use of the additional precision or is it set at a fixed length?


It is still a 64 bit floating point value.  R may use long double 
internally for some calculations, but the numeric type that is saved 
doesn't change.


Duncan Murdoch

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Re: [R] Step and stepAIC

Jun Shen jun.shen.ut at gmail.com writes:

 
lme(biomarker~Cmax+AGE,data=cov,method='ML',random=~1+AGE|ID,keep.data=T)
 Warning message:
 In lme.formula(biomarker ~ Cmax + AGE, data = cov, method = ML,  :
   Fewer observations than random effects in all level 1 groups

That's why the posting guide says: tell the whole story. After
that warning, expect everything. You want too much from your data.


Dieter

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Re: [R] 64 bit R double precision

2009-05-07 Thread Peter Dalgaard


Paul Emberson wrote:

Hi,

If R is compiled for a 64 bit platform, does the double data type make 
use of the additional precision or is it set at a fixed length?


No. Double is double, 64 bits, although sometimes 80 bits when things 
are kept in registers. However, even though the FPU is identical between 
64 and 32 bit machines, you do not in general get the same results, due 
to tricks played by optimizing compilers.


--
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk)  FAX: (+45) 35327907

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Re: [R] How to do Naive Bayes in R?

2009-05-07 Thread Dylan Beaudette

On Wednesday 06 May 2009, spencerg wrote:
   help.search('bayes') only searches installed packages.

   To go beyond that, you might try the following:

Thanks for the clarification. 

Dylan

-- 
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Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341

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[R] help~ how can I drow colorful text in biplot.

2009-05-07 Thread yongkook Kwon

Hi.

I want to show easily classified samples in the  one biplot.

My samples have 14 types and each type have 21 samples

So, I cannot understand distribution of samples after plsda. I want to give
a color each types text in graph.

How can I do that?

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Re: [R] Help with lme4 model specification

2009-05-07 Thread boeinguy2



Thanks for your response.

This is suspicious : Spar_loc doesn't appear in your statement...

Yes Spar_loc should look suspicious.  I posted the real error messages but
hid the variable names in the model.  Spar_loc is the original form of S.

The precedence of modelling operators is not very clear (and does not
seem to be formally defined in the standard documentation...). In
doubt, use parentheses.

So try ...+(1|(S:A)/H), just in case..

This did not work.  However I did discover something that does:

AAT- lmer(Y ~ S + A + (1|H %in% S:A), data=AT, REML=TRUE) 

Not sure why this worked.  I read that it is an alternate way of specifying
nesting.

This runs without error.


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[R] Weighted multinomial logistic regression using the mlogit package

2009-05-07 Thread Freiman, Michael

I have been trying to use the mlogit package to do a multinomial logistic 
regression, including both alternative-specific and individual-specific 
variables. I used the mlogit.data function to turn my dataframe into the 
correct format for the mlogit function, and have been able to run the 
regression. However, I would like to weight the different cases differently. 
(Just to clarify, it's not the alternatives I want to weight differently; it's 
the individual instances in which a choice has to be made.) I have used the 
following line of code:

ML2-mlogit(choice~var1+var2+var3+var5,data=M,weights=weights)

Here, M is the dataframe in the appropriate format; var1, var2, var3 and var5 
are predictors (alternative-specific) that are columns of M; and weights is 
another column of M. This line works too, but it gives me the same answer as 
when the weights were omitted, which seems to indicate that the weights aren't 
properly being taken into account. Any suggestions?

Michael Freiman

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[R] increasing memory for R bg job

2009-05-07 Thread carol white

Hi,
Is the following command used to increase the memory or any other command when 
a background R job is run?

R --min-vsize=vl --max-vsize=vu --min-nsize=nl --max-nsize=nu --max-ppsize=N

source:
http://stat.ethz.ch/R-manual/R-patched/library/base/html/Memory.html

Thx

Carol





  
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[R] CHM error

2009-05-07 Thread tognox


Hi,
I would need some help in solving a problem with my R.
Whenever I try to type  ?paste  or in general any command for the html
help in R, I receive this error message. The strange thing is that I have
never had this kind of problem in the past with R, and now I really don't
understand why it says that. Also I have selected every single element in
the installation process.
The message is this one: 

Error in
print.help_files_with_topic(D:/Programmi/R/R-2.9.0/library/base/chm/print)
: 
CHM file could not be displayed

I would really appreciate some suggestion. Thanks very much.
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[R] for loop vectorization

2009-05-07 Thread miraceti

Hi, I am still not familiar with vectorization.
Could you help with making this for loop more efficient?
The code is trying to make a Q matrix for a multidimensional state space
with specific conditions.

thanks
Mira


tmp = 0:(maxvals[1])
for(i in 2:nchars) {
  tmp - outer(tmp, 0:(maxvals[i]), FUN=paste, sep=.)
}
states = tmp
stateidx = array(1:length(states), dim=dim(states))
transition - matrix(data=0, nrow=length(states), ncol=length(states))

findstatedim - function(x) which(stateidx==x, arr.ind = TRUE)
manhattandistance - function(x,y) sum(abs(findstatedim(x)-findstatedim(y)))

for(i in 1:length(states)) {
  for (j in 1:length(states)) {
if (manhattandistance(i, j)==1) {
  if (sum(findstatedim(i)-findstatedim(j))  0) {
transition[i,j] = gain
if (findstatedim(i)[findstatedim(i)-findstatedim(j) == -1] == 1)
{
  transition[i,j] = firstgain
}
  }
  else {
transition[i,j] = loss
  }
}
  }
}
transition

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[R] GAM ordered probit

2009-05-07 Thread Mehdi Shadmehr

Dear All,

Anyone know if there is a package that fits Generalized Linear Models(GAM)
to data with ordered dependent variable(response) ?

Simon Wood's mgcv has probit, logit,... other links, however, I could not
find a way to do GAM *ordered *probit. Yee's VGAM claims to fit ordinal
proportional odds model(cumulative logit model) (see:
http://www.stat.auckland.ac.nz/~yee/VGAM/) but I could not find how to do so
in the package's help.

Best,
Mehdi Shadmehr
PhD Candidate in Economics
UIUC

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Re: [R] for loop vectorization

2009-05-07 Thread miraceti

uhoh, missed two lines on the top.Sorry about that.
the whole code looks like this.


nchars = 4
maxvals = c(2,2,2,2)
tmp = 0:(maxvals[1])
for(i in 2:nchars) {
  tmp - outer(tmp, 0:(maxvals[i]), FUN=paste, sep=.)
}
states = tmp
stateidx = array(1:length(states), dim=dim(states))
transition - matrix(data=0, nrow=length(states), ncol=length(states))

findstatedim - function(x) which(stateidx==x, arr.ind = TRUE)
manhattandistance - function(x,y) sum(abs(findstatedim(x)-findstatedim(y)))

for(i in 1:length(states)) {
  for (j in 1:length(states)) {
if (manhattandistance(i, j)==1) {
  if (sum(findstatedim(i)-findstatedim(j))  0) {
transition[i,j] = gain
if (findstatedim(i)[findstatedim(i)-findstatedim(j) == -1] == 1)
{
  transition[i,j] = firstgain
}
  }
  else {
transition[i,j] = loss
  }
}
  }
}
transition



On Thu, May 7, 2009 at 2:54 PM, miraceti mirac...@gmail.com wrote:

 Hi, I am still not familiar with vectorization.
 Could you help with making this for loop more efficient?
 The code is trying to make a Q matrix for a multidimensional state space
 with specific conditions.

 thanks
 Mira


 tmp = 0:(maxvals[1])
 for(i in 2:nchars) {
   tmp - outer(tmp, 0:(maxvals[i]), FUN=paste, sep=.)
 }
 states = tmp
 stateidx = array(1:length(states), dim=dim(states))
 transition - matrix(data=0, nrow=length(states), ncol=length(states))

 findstatedim - function(x) which(stateidx==x, arr.ind = TRUE)
 manhattandistance - function(x,y)
 sum(abs(findstatedim(x)-findstatedim(y)))

 for(i in 1:length(states)) {
   for (j in 1:length(states)) {
 if (manhattandistance(i, j)==1) {
   if (sum(findstatedim(i)-findstatedim(j))  0) {
 transition[i,j] = gain
 if (findstatedim(i)[findstatedim(i)-findstatedim(j) == -1] ==
 1) {
   transition[i,j] = firstgain
 }
   }
   else {
 transition[i,j] = loss
   }
 }
   }
 }
 transition



[[alternative HTML version deleted]]

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Re: [R] dependency ‘Matrix’ is not availabl e when installing Rcmdr

2009-05-07 Thread Uwe Ligges




Uwe Ligges wrote:
Argh, it disappeared. Probably a bug in my scripts that removed the old 
version of Matrix from the Windows binary repository for R-2.8.x (new 
versions of Matrix won't pass checks under the outdated version of R).

I will compile an old version tomorrow and make it available again.


It's now waiting to be synced by CRAN (i.e. available from CRAN master 
within a couple of hours).


Uwe Ligges



Sorry for the inconvenience and thanks for the report.

If you upgrade to R-2.9.0 you won't see this problem and you can also 
get a newer version of Matrix.


Uwe Ligges


John Sorkin wrote:

R 2.8.1
Windows XP
Any suggestions for addressing the problem listed below, obtained when
installing Rcmdr
The downloaded packages are in
C:\Documents and Settings\jsorkin\Local
Settings\Temp\RtmpaxlG6g\downloaded_packages
updating HTML package descriptions
Warning message:
dependency ‘Matrix’ is not available

Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)

Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}

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Re: [R] levelplot question

2009-05-07 Thread Greg Snow

From the help for panel.levelplot in the section on 'col.regions':

 the exact number being one
  more than the length of 'at'

was what I based my assumption on (also the not longer than at phrase in the 
last sentence on recycling).

The second part was somewhat speculation on my part, automatically adding -Inf 
and Inf would mean that you would not need to make sure to span the range of 
the data, but on the other hand, it would make it hard to exclude values 
outside the region as in your example, arguments could be made for either 
direction, the current behavior is probably best overall.

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111


 -Original Message-
 From: Deepayan Sarkar [mailto:deepayan.sar...@gmail.com]
 Sent: Wednesday, May 06, 2009 6:35 PM
 To: Greg Snow
 Cc: Antje; r-h...@stat.math.ethz.ch
 Subject: Re: [R] levelplot question
 
 On Tue, May 5, 2009 at 8:58 AM, Greg Snow greg.s...@imail.org wrote:
  The function that is doing the color assignments is level.colors in
 the lattice package.
  Looking at the code confirms that the number of colors should be 1
 less than the length
  of the at variable (the documentation implies that it should be 1
 more, looks like a documentation bug to me).
 
 Could you point to the place where this is implied? I couldn't see
 anything obviously wrong in ?levelplot or ?level.colors.
 
  It is possible that at one time the author intended to prepend -Inf
 and append Inf to the at
  vector so that it did not need to span the entire range of the data,
 but that was not implemented.
  I think I would prefer that fix to changing the documentation.
 
 That is a slightly different issue though: e.g.,
 
  level.colors(c(1, 2, 3), at = c(1.5, 2.5, 3.5), colors = FALSE)
 [1] NA  1  2
 
 The first value doesn't fall in any interval, so gets a NA.
 
 level.colors() is mainly a helper function for levelplot(), and it is
 important there that the first and last intervals not be open-ended.
 levelplot() has no 'zlim' argument, and you need 'at' to restrict the
 values shown, e.g.,
 
 levelplot(volcano, at = do.breaks(c(120, 200), 10))
 
 -Deepayan
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Re: [R] levelplot question

2009-05-07 Thread Deepayan Sarkar

On Thu, May 7, 2009 at 12:02 PM, Greg Snow greg.s...@imail.org wrote:
 From the help for panel.levelplot in the section on 'col.regions':

  the exact number being one
          more than the length of 'at'

 was what I based my assumption on (also the not longer than at phrase in 
 the last sentence on recycling).

Thanks, that's definitely a documentation bug. I've reorganized the
documentation for levelplot colors (hopefully for the better). Should
show up in the next update.

-Deepayan


 The second part was somewhat speculation on my part, automatically adding 
 -Inf and Inf would mean that you would not need to make sure to span the 
 range of the data, but on the other hand, it would make it hard to exclude 
 values outside the region as in your example, arguments could be made for 
 either direction, the current behavior is probably best overall.

 --
 Gregory (Greg) L. Snow Ph.D.
 Statistical Data Center
 Intermountain Healthcare
 greg.s...@imail.org
 801.408.8111


 -Original Message-
 From: Deepayan Sarkar [mailto:deepayan.sar...@gmail.com]
 Sent: Wednesday, May 06, 2009 6:35 PM
 To: Greg Snow
 Cc: Antje; r-h...@stat.math.ethz.ch
 Subject: Re: [R] levelplot question

 On Tue, May 5, 2009 at 8:58 AM, Greg Snow greg.s...@imail.org wrote:
  The function that is doing the color assignments is level.colors in
 the lattice package.
  Looking at the code confirms that the number of colors should be 1
 less than the length
  of the at variable (the documentation implies that it should be 1
 more, looks like a documentation bug to me).

 Could you point to the place where this is implied? I couldn't see
 anything obviously wrong in ?levelplot or ?level.colors.

  It is possible that at one time the author intended to prepend -Inf
 and append Inf to the at
  vector so that it did not need to span the entire range of the data,
 but that was not implemented.
  I think I would prefer that fix to changing the documentation.

 That is a slightly different issue though: e.g.,

  level.colors(c(1, 2, 3), at = c(1.5, 2.5, 3.5), colors = FALSE)
 [1] NA  1  2

 The first value doesn't fall in any interval, so gets a NA.

 level.colors() is mainly a helper function for levelplot(), and it is
 important there that the first and last intervals not be open-ended.
 levelplot() has no 'zlim' argument, and you need 'at' to restrict the
 values shown, e.g.,

 levelplot(volcano, at = do.breaks(c(120, 200), 10))

 -Deepayan


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Re: [R] PGF Device

2009-05-07 Thread Greg Snow

Have you contacted the author of eps2pgf?

A while back I had a plot generated by R that produced an error in eps2pgf, I 
sent a copy of it to the author of eps2pgf and within a couple of days he sent 
me a new version that worked with my plot.  But he cannot fix problems that he 
does not know about.

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
 project.org] On Behalf Of Lasse Bombien
 Sent: Thursday, May 07, 2009 3:02 AM
 To: r-help@r-project.org
 Subject: Re: [R] PGF Device
 
 Am Mittwoch, den 06.05.2009, 16:08 +0200 schrieb baptiste auguie:
  I think the pgfSweave project on R-forge is working on this (as far
 as
  i know it currently relies on eps2pgf)
 Right, but eps2pgf fails me on more complex / stacked plots. Otherwise,
 I would be content using eps2pgf.
 
 Lasse
 
  http://r-forge.r-project.org/R/?group_id=331
 
  HTH,
 
 
  Baptiste
 
  On 6 May 2009, at 15:37, Lasse Bombien wrote:
 
   Hi all,
   I saw a thread from 2007 about the possible implementation of a PGF
   (http://sourceforge.net/projects/pgf/) graphics device. Does anyone
   know
   if something came of it?
   I would very much like if that was the case.
  
   Regards,
   Lasse
  
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   PLEASE do read the posting guide http://www.R-project.org/posting-
 guide.html
   and provide commented, minimal, self-contained, reproducible code.
 
  _
 
  Baptiste Auguié
 
  School of Physics
  University of Exeter
  Stocker Road,
  Exeter, Devon,
  EX4 4QL, UK
 
  Phone: +44 1392 264187
 
  http://newton.ex.ac.uk/research/emag
  __
 
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 PLEASE do read the posting guide http://www.R-project.org/posting-
 guide.html
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Re: [R] by-group processing

2009-05-07 Thread William Dunlap

Max,

Since the dataset is sorted by ID, with ties broken by N, the following
should do it and do it quickly.  It grabs the rows just before ID
changes.

 with(data, data[ c(ID[-1] != ID[-length(ID)], TRUE),, drop=FALSE])
  ID Type N
7  45900I 7
10 49270E 3
24 46550I 7

Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com  

 -Original Message-
 From: r-help-boun...@r-project.org 
 [mailto:r-help-boun...@r-project.org] On Behalf Of Max Webber
 Sent: Wednesday, May 06, 2009 3:09 PM
 To: r-help@r-project.org
 Subject: [R] by-group processing
 
 Given a dataframe like
 
data
 ID Type N
   1  45900A 1
   2  45900B 2
   3  45900C 3
   4  45900D 4
   5  45900E 5
   6  45900F 6
   7  45900I 7
   8  49270A 1
   9  49270B 2
   10 49270E 3
   18 46550A 1
   19 46550B 2
   20 46550C 3
   21 46550D 4
   22 46550E 5
   23 46550F 6
   24 46550I 7
   
 
 containing an identifier (ID), a variable type code (Type), and
 a running count of the number of records per ID (N), how can I
 return a dataframe of only those records with the maximum value
 of N for each ID? For instance,
 
data
 ID Type N
   7  45900I 7
   10 49270E 3
   24 46550I 7
 
 I know that I can use
 
 tapply ( data $ N , data $ ID , max )
45900 46550 49270
7 7 3

 
 to get the values of the maximum N for each ID, but how is it
 that I can find the index of these values to subsequently use to
 subscript data?
 
 
 --
 maxine-webber
 
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Re: [R] for loop vectorization

2009-05-07 Thread miraceti

this 'ifelse' usage looks promising.
thank you very much.

On Thu, May 7, 2009 at 3:12 PM, Patrick Burns pbu...@pburns.seanet.comwrote:

 If you haven't seen it yet,
 'The R Inferno' may be of use
 to you.


 Patrick Burns
 patr...@burns-stat.com
 +44 (0)20 8525 0696
 http://www.burns-stat.com
 (home of The R Inferno and A Guide for the Unwilling S User)

 miraceti wrote:

 Hi, I am still not familiar with vectorization.
 Could you help with making this for loop more efficient?
 The code is trying to make a Q matrix for a multidimensional state space
 with specific conditions.

 thanks
 Mira


 tmp = 0:(maxvals[1])
 for(i in 2:nchars) {
  tmp - outer(tmp, 0:(maxvals[i]), FUN=paste, sep=.)
 }
 states = tmp
 stateidx = array(1:length(states), dim=dim(states))
 transition - matrix(data=0, nrow=length(states), ncol=length(states))

 findstatedim - function(x) which(stateidx==x, arr.ind = TRUE)
 manhattandistance - function(x,y)
 sum(abs(findstatedim(x)-findstatedim(y)))

for(i in 1:length(states)) {
  for (j in 1:length(states)) {
if (manhattandistance(i, j)==1) {
  if (sum(findstatedim(i)-findstatedim(j))  0) {
transition[i,j] = gain
if (findstatedim(i)[findstatedim(i)-findstatedim(j) == -1] ==
 1)
 {
  transition[i,j] = firstgain
}
  }
  else {
transition[i,j] = loss
  }
}
  }
}
 transition

[[alternative HTML version deleted]]

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[[alternative HTML version deleted]]

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Re: [R] Do you use R for data manipulation?

2009-05-07 Thread Martin Waller



+1. I worked with Matthew for a while and saw in practice just how 
powerful that package is.

I'm surprised it isn't more widely used.

Martin
Tom Short wrote:

Another tool I find useful is Matthew Dowle's data.table package. It
has very fast indexing, can have much lower memory requirements than a
data frame, and has some built-in data manipulation capability.
Especially with a 64-bit OS, you can use this to keep things in memory
where you otherwise would have to use a database.

See here: http://article.gmane.org/gmane.comp.lang.r.packages/282

- Tom

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[R] Using lme() for split plot

2009-05-07 Thread Joshua Stults

Hi,

I'm trying to figure out how to use lme() for analyzing a split-plot
experiment.  I've been looking at the examples from the 'R Book',
those are nested but with only one factor at the whole-plot level, my
test is 2^2 at the whole-plot level, with a single many level factor
at the sub-plot level.  My question is about properly specifying the
random effects part of the model,

lme( y ~ block + a*b*poly(c, n), random=~ ? )

Where 'a' and 'b' are my two level whole-plot factors and 'c' is the
many level sub-plot factor.  I'm not sure what to use to get the right
error terms.  Do I use two error terms:

random = ~ 1 | block/a + 1 | block/b

or one:

random = ~ 1 | block/a*b

or something else entirely?  I haven't been able to find any relevant
examples on Google. Thanks for any suggestions/pointers.

-- 
Joshua Stults
Website: http://j-stults.blogspot.com

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[R] making an Affybatch object for expresso

2009-05-07 Thread George Chen

Hi All,

I have microarray data that does not come in a CEL file.  Currently it is in 
the form of columns = individual samples and rows = individual probes.  There 
are about 79 columns and it is in a tab delimited text file.  Is there a way to 
convert this file into an AffyBatch so that I can run expresso with it?

Thanks,

George

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Re: [R] PGF Device

No I haven't done that, and of course, you're right. I'll do that. But I
still wish there was a way to generate PGF code directly.

Lasse
Am Donnerstag, den 07.05.2009, 13:28 -0600 schrieb Greg Snow:
 Have you contacted the author of eps2pgf?
 
 A while back I had a plot generated by R that produced an error in eps2pgf, I 
 sent a copy of it to the author of eps2pgf and within a couple of days he 
 sent me a new version that worked with my plot.  But he cannot fix problems 
 that he does not know about.
 
-- 
Lasse Bombien
Institut für Phonetik und Sprachverarbeitung
Schellingstraße 3/II
D-80799 München

email: la...@phonetik.uni-muenchen.de
web: http://www.phonetik.uni-muenchen.de/~lasse
phone: +49 (0) 89 2180 2812

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Re: [R] PGF Device